Modified sequence Experiment N duplicates Sequence Length Missed cleavages Proteins Leading proteins Gene names Protein names Phospho (STY) All Phospho (STY) Probabilities Max Score Min PEP Intensity Reporter intensity corrected 1 Reporter intensity corrected 2 Reporter intensity corrected 3 Reporter intensity corrected 4 Reporter intensity corrected 5 Reporter intensity corrected 6 Reporter intensity corrected 7 Reporter intensity corrected 8 Reporter intensity corrected 9 Reporter intensity corrected 10 Phosphoproteome Fullproteome TMT Channel Normal 1 TMT Channel Normal 2 TMT Channel Normal 3 TMT Channel Normal 4 TMT Channel Normal 5 TMT Channel Normal 6 TMT Channel Normal 7 TMT Channel Normal 8 TMT Channel Normal 9 TMT Channel Normal 10 TMT Channel Ratio 1 TMT Channel Ratio 2 TMT Channel Ratio 3 TMT Channel Ratio 4 TMT Channel Ratio 5 TMT Channel Ratio 6 TMT Channel Ratio 7 TMT Channel Ratio 8 TMT Channel Ratio 9 TMT Channel Ratio 10 Curve signal Log EC50 Curve slope Curve top Curve bottom R2 Curve RMSE Log EC50 error Curve slope error Curve top error Curve bottom error EC50 pEC50 Curve effect size Regulation AHVFECNLESSVESIIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHVFECNLESSVESIISPK 19 0 O60216;E5RFV8;E5RIN7;E5RJW1;E5RJK5 O60216 RAD21 Double-strand-break repair protein rad21 homolog 1 AHVFECNLESSVESIIS(1)PK 132.26 9.01E-06 68050000 51405 44523 51105 46413 50746 54299 53749 49644 75139 70156 TRUE FALSE 49396.03577 43253.24763 60340.81032 48808.38049 52378.29118 55396.96298 54406.79634 48618.83405 66609.53573 65404.27163 0.755241738 0.661321448 0.922582101 0.74625677 0.800838995 0.846993042 0.831853868 0.743358696 1.018427911 1 15.99709724 -5 0.084721521 1.706728379 0.611434929 0.440252783 0.082842834 221.792768 1.319814164 28.16293513 2.30224097 1.00E-05 5 -1.09529345 AIGSASEGAQSSLQEVYHK ddPTM_BT-474_Pertuzumab_2h_R1 3 AIGSASEGAQSSLQEVYHK 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;; 340.9 8.63E-76 1788670000 987460 1017830 847300 958230 970060 1013010 1010970 985240 1140460 1187390 FALSE TRUE 948868.9715 988802.485 1000425.958 1007684.365 1001262.861 1033493.756 1023342.553 964894.4497 1010999.762 1106967.018 0.857179082 0.893253791 0.903754079 0.910311101 0.904510112 0.933626513 0.924456228 0.871656006 0.913306129 1 20.07818081 -5 0.351896882 2.149397123 0.898176811 0.661006469 0.021371617 284.4513909 2.318185637 246.9305986 0.0170339 1.00E-05 5 -1.251220312 APS(ph)PPVEHPR ddPTM_BT-474_Pertuzumab_2h_R1 3 APSPPVEHPR 10 0 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR 98.902 0.0032597 822940000 531390 522530 505022 477867 521920 522420 549091 588490 621300 663509 TRUE FALSE 510622.6913 507627.956 596290.7096 502529.7731 538708.0308 532983.6903 555810.9399 576337.4758 550772.6287 618568.9444 0.825490345 0.820648952 0.963984233 0.812407053 0.870894078 0.861639911 0.898543234 0.931727144 0.890398126 1 19.23857488 -5 0.089480825 1.425015296 0.76947087 0.511319878 0.041645318 170.6068954 1.062472494 13.66035153 0.974840498 1.00E-05 5 -0.655544426 DEAAYGELR ddPTM_BT-474_Pertuzumab_2h_R1 4 DEAAYGELR 9 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 118.06 0.0024447 4577790000 3498350 3419410 3288480 3369510 3500790 3260040 3755580 3628400 3882480 4138280 FALSE TRUE 3361630.614 3321891.775 3882781.488 3543410.815 3613396.09 3325960.242 3801541.911 3553472.272 3441757.147 3857990.61 0.871342353 0.861041954 1.006425852 0.918460197 0.93660054 0.862096511 0.985368368 0.92106815 0.892111333 1 21.8794182 -5 0.216479844 1.383505416 0.909804731 0.211645246 0.047065521 248.8366099 2.487496993 41.7838952 0.092203681 1.00E-05 5 -0.473700685 DGALHMIGSLAEILLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGALHMIGSLAEILLK 16 0 O95373 O95373 IPO7 Importin-7 0 110.77 0.00065866 80359000 83173 89050 79636 81656 91729 92050 88098 100230 117310 140500 FALSE TRUE 79922.50721 86510.38119 94027.99669 85870.27595 94679.54659 93911.31407 89176.16968 98160.21547 103993.4606 130983.8099 0.610170885 0.660466216 0.717859687 0.655579312 0.722833965 0.716968869 0.680818261 0.74940724 0.793941333 1 16.99902897 -5 0.152182217 2.124775458 0.606395405 0.921503475 0.028692498 33.2871203 0.298875564 11.2089302 0.139287382 1.00E-05 5 -1.518380053 DGVADVSIEDSVISLSGDHCIIGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGVADVSIEDSVISLSGDHCIIGR 24 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 352.47 5.66E-102 1778540000 453080 482722 494527 601537 522769 483574 551600 549298 579704 727520 FALSE TRUE 435373.1327 468955.2412 583899.0296 632582.3967 539584.3397 493352.1976 558350.6458 537954.8043 513898.4322 678244.4224 0.641911851 0.691425135 0.86089765 0.93267615 0.795560305 0.727395879 0.823229248 0.793157727 0.757689139 1 19.37144575 -5 0.328763308 3.13101332 0.777530134 0.407924147 0.079109879 391.5853188 3.396092093 583.2515542 0.071611325 1.00E-05 5 -2.353483186 DKNTVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKNTVVR 7 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 101.54 0.0081925 310540000 546310 590020 479770 561520 539710 611510 602600 580710 655860 724270 FALSE TRUE 524959.6012 573193.2073 566475.1114 590500.1145 557070.2623 623875.1512 609974.7991 568718.1356 581409.5224 675214.5478 0.77747081 0.848905299 0.838955726 0.874537014 0.825027044 0.923965802 0.903379231 0.842277669 0.86107375 1 19.36498646 -5 0.12110891 1.44356885 0.790357858 0.644288534 0.034667228 103.8922383 0.813827553 11.42424918 0.334576255 1.00E-05 5 -0.653210991 DLAFTLEER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLAFTLEER 9 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 ; 95.608 0.018449 335660000 344470 401900 334490 409130 386000 382590 397540 410050 449480 506140 FALSE TRUE 331007.7316 390438.2055 394939.7837 430245.2483 398416.0406 390326.2319 402405.2134 401582.3242 398456.9148 471858.687 0.70149759 0.827447319 0.836987417 0.911809532 0.844354574 0.827210016 0.852808742 0.851064811 0.844441198 1 18.84799534 -5 0.125415708 1.50770674 0.766571484 0.58078617 0.045618626 117.2719527 0.940335499 15.23461275 0.395798279 1.00E-05 5 -0.741135256 DVDWTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVDWTAR 7 0 K7ESF4;Q9BRP1 K7ESF4;Q9BRP1 PDCD2L Programmed cell death protein 2-like 0 ; 195.85 5.45E-05 0 335260 359400 301070 360380 332230 356380 380470 358500 390900 447720 FALSE TRUE 322157.6686 349150.2639 355480.0463 378979.255 342916.4797 363586.2478 385126.3057 351096.8497 346526.6708 417395.5256 0.771828275 0.836497381 0.851662331 0.907961949 0.821562424 0.871083242 0.922689109 0.841161029 0.830211752 1 18.67105561 -5 0.200044613 1.642432405 0.830450255 0.556283658 0.0403925 111.1756222 1.100313755 28.71158713 0.098017363 1.00E-05 5 -0.81198215 EADLLQESLEHIEMYEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EADLLQESLEHIEMYEK 17 0 Q6N069;Q6N069-5;Q6N069-4;Q6N069-3;Q6N069-2 Q6N069 NAA16 "N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 ;; 122.17 5.78E-05 59720400 62406 63065.3 56912.3 61360.9 67009 67518 66597 61218.6 78386 82183 FALSE TRUE 59967.10453 61266.73939 67197.61862 64527.7434 69164.40534 68883.26022 67412.03401 59954.41452 69487.9499 76616.67221 0.782690018 0.799652838 0.877062612 0.842215428 0.902733091 0.899063588 0.879861159 0.782524388 0.906955991 1 16.22537074 -5 0.210959778 1.708532938 0.829093923 0.527957915 0.044127074 132.6960785 1.323549768 39.91957238 0.10195282 1.00E-05 5 -0.879439015 ECELS(ph)PGVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ECELSPGVNR 10 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ECELS(1)PGVNR 80.17 0.026025 72915000 70190 56381 62343 74820 66701 77310 68014 69949 80075 92930 TRUE FALSE 67446.8972 54773.06908 73609.76691 78681.46917 68846.49824 78873.26117 68846.37568 68504.52871 70985.2217 86635.76833 0.778510983 0.63222235 0.84964638 0.908186892 0.794665986 0.910400666 0.794664571 0.790718776 0.819352365 1 16.40267516 -5 0.151696302 1.645543393 0.752148198 0.398549527 0.072642689 151.75244 1.360340474 29.94557455 0.377094938 1.00E-05 5 -0.893395195 EFKDEDWNMGDIVYTLTNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFKDEDWNMGDIVYTLTNR 19 1 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 119.38 3.63E-05 0 121110 130750 92143 99521 100050 117340 106160 110450 132660 101800 FALSE TRUE 116376.8873 127021.138 108795.2898 104657.2907 103268.1991 119712.6952 107459.2178 108169.1689 117600.993 94904.99533 1.226246173 1.33840308 1.146359993 1.102758505 1.08812185 1.261395091 1.132281999 1.139762649 1.239144394 1 16.53419641 -5 0.093045701 0.501357948 1.306562777 0.34180065 0.075938813 252.0423972 1.620461921 25.75820962 1.660879103 1.00E-05 5 0.805204829 EIAEAYDVLSDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIAEAYDVLSDPR 13 0 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;; 201.48 2.36E-07 199782000 429930 484983 454861 613249 472619 497136 521173 565154 631679 729460 FALSE TRUE 413127.8603 471151.7597 537064.501 644898.8544 487821.2194 507188.4305 527551.2711 553483.3724 559973.4481 680053.0245 0.6074936 0.692816211 0.789739155 0.948306722 0.717328211 0.745807183 0.775750202 0.813882672 0.823426156 1 19.37528771 -5 0.068245099 1.743001276 0.492573324 0.519738932 0.076236669 299.9985887 1.478692367 35.99485962 4.729042614 1.00E-05 5 -1.250427952 ELGENLDQILR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELGENLDQILR 11 0 Q96P70 Q96P70 IPO9 Importin-9 0 ; 190.96 4.75E-06 151089000 172192 180842 172769 194349 190831 183118 204865 190291 222070 253800 FALSE TRUE 165462.5463 175684.5632 203992.2015 204379.3752 196969.2524 186820.7714 207372.1992 186361.4244 196861.5446 236609.8999 0.699305254 0.742507238 0.862145673 0.863782011 0.832464121 0.789572928 0.87643078 0.787631559 0.832008909 1 17.85215091 -5 0.15512619 1.660212894 0.758117496 0.592861726 0.049992589 104.8608795 0.950490601 21.49438744 0.24645917 1.00E-05 5 -0.902095398 ESLCDS(ph)PHQNLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESLCDSPHQNLSR 13 0 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1;U3KPT1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 ESLCDS(1)PHQNLSR;ESLCDS(1)PHQNLSR 307.07 6.48E-42 707200000 510710 586750 552240 633900 536720 562420 677230 604460 627800 805310 TRUE FALSE 490750.8886 570016.4645 652042.0525 666615.655 553984.0862 573792.5177 685518.1433 591977.6898 556534.776 750765.6364 0.653667223 0.759246877 0.868502794 0.887914447 0.737892172 0.76427648 0.913092062 0.788498649 0.741289624 1 19.51800309 -5 0.334560534 3.0928592 0.789706215 0.404177722 0.075507751 399.2657796 3.411943122 595.9634784 0.063293471 1.00E-05 5 -2.303152985 ESSIIAPAPAEDVDT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ESSIIAPAPAEDVDTPPR 18 0 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 ESSIIAPAPAEDVDT(1)PPR;ESSIIAPAPAEDVDT(1)PPR;ESSIIAPAPAEDVDT(1)PPR 191.62 2.41E-13 1722070000 1313346 1211949 1107486 1356564 1267406 1265969 1317717 1351680 1481439 1611255 TRUE FALSE 1262018.986 1177385.401 1307633.356 1426576.431 1308173.265 1291567.761 1333843.615 1323767.336 1313272.255 1502123.264 0.840156741 0.783814105 0.870523337 0.949706635 0.870882768 0.859828079 0.887972144 0.88126412 0.874277289 1 20.51857177 -5 0.134476661 1.424471967 0.819930833 0.550646204 0.037167247 118.3285158 0.991622143 13.61887765 0.275288517 1.00E-05 5 -0.604541134 EVDIGIPDATGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVDIGIPDATGR 12 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 107.55 0.0041907 1305000000 446220 471440 396510 502950 432480 502950 501720 487470 530700 608210 FALSE TRUE 428781.2291 457994.9928 468168.1773 528907.3098 446391.112 513119.9936 507860.1994 477403.5742 470457.1609 567015.395 0.756207385 0.807729379 0.825671016 0.932791798 0.787264536 0.904948963 0.895672682 0.841958752 0.829707915 1 19.11302838 -5 0.090694615 1.43904968 0.731206245 0.504096622 0.049483139 189.1289356 1.190915947 16.56776753 1.142152033 1.00E-05 5 -0.707843435 FLDELDAVQMD ddPTM_BT-474_Pertuzumab_2h_R1 4 FLDELDAVQMD 11 0 O15160;A0A2R8YEY5;E7EQB9 O15160 POLR1C DNA-directed RNA polymerases I and III subunit RPAC1 0 ;;; 105.4 0.0057493 62912600 233037 252848 213145 250195 258591 250594 250272 258550 284492 317916 FALSE TRUE 223929.6564 245637.0226 251665.0429 263107.5939 266908.8144 255661.1824 253334.9036 253210.8521 252197.6608 296383.2661 0.755540822 0.828781685 0.849120283 0.887727561 0.900552915 0.862603296 0.854754409 0.854335859 0.850917341 1 18.17710447 -5 0.172891555 1.56043594 0.818994454 0.642394426 0.03485396 94.64497315 0.898920034 18.3501345 0.129858807 1.00E-05 5 -0.741441487 GAASTLVPGVSETSASPGS(ph)PSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAASTLVPGVSETSASPGSPSVR 23 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 GAASTLVPGVSETSAS(0.057)PGS(0.943)PSVR;GAASTLVPGVSETSAS(0.004)PGS(0.996)PSVR 260.1 1.09E-43 582160000 591570 629010 539480 601580 609340 654040 669520 634010 667200 789570 TRUE FALSE 568450.7904 611071.2507 636976.0367 632627.6159 628939.9745 667265.1369 677713.786 620917.4719 591462.2531 736091.7206 0.772255379 0.830156397 0.865348731 0.859441287 0.854431529 0.906497272 0.920692037 0.843532748 0.803517057 1 19.48952602 -5 0.19588819 1.607915791 0.83098786 0.52472984 0.042072809 121.8003681 1.200414071 29.24938891 0.111567822 1.00E-05 5 -0.776927931 GFGEDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFGEDFK 7 0 H3BS10;H3BP20;P06865;H3BU85;H3BTD4;P06865-2 H3BS10 HEXA Beta-hexosaminidase;Beta-hexosaminidase subunit alpha 0 121.52 0.010306 145960000 263550 259220 237000 259990 252000 272000 265470 285910 282850 328730 FALSE TRUE 253250.1746 251827.2994 279831.172 273408.1151 260105.8089 277500.0264 268718.9013 280005.8586 250742.0538 306464.8243 0.826359682 0.821716815 0.913093934 0.892135388 0.848729734 0.905487365 0.876834403 0.913663939 0.81817564 1 18.22536197 -5 0.221033723 1.631987308 0.857131201 0.519616488 0.036990495 125.1214776 1.252050454 35.37110565 0.06920781 1.00E-05 5 -0.774856107 GS(ph)PVFLPR ddPTM_BT-474_Pertuzumab_2h_R1 6 GSPVFLPR 8 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR 122.44 0.0014583 3379480000 2051560 2251600 2173960 2618590 2193480 1787920 2809440 2469070 2491190 3017580 TRUE FALSE 1971382.767 2187386.573 2566842.931 2753735.744 2264035.276 1824072.967 2843822.767 2418082.842 2208400.555 2813196.619 0.700762525 0.777544861 0.912429268 0.978863591 0.804790984 0.648398678 1.010886601 0.859549889 0.785014649 1 21.42377896 -5 0.123409256 1.488788252 0.768568787 0.181334199 0.108335846 290.197191 2.302207804 35.9552557 0.987698681 1.00E-05 5 -0.720219465 HLFAILGGSEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLFAILGGSEGK 12 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 115.18 0.00097805 213610000 474130 492190 502690 479040 528810 537740 562150 453750 647590 653520 FALSE TRUE 455600.4754 478153.2231 593537.2653 503763.3118 545819.6539 548613.4712 569029.7599 444379.9039 574078.2981 609256.5083 0.74779747 0.784814305 0.974199302 0.826849291 0.895878249 0.900463867 0.933974036 0.729380643 0.942260428 1 19.21669023 -5 0.290886533 2.120801775 0.847461821 0.233999703 0.079431898 391.4186939 3.68207425 266.5586093 0.085232973 1.00E-05 5 -1.273339954 IADGYEQAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 IADGYEQAAR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 253.74 1.01E-16 1582920000 1081300 1171760 1011100 1179690 1117530 1064710 1229380 1210920 1225590 1397930 FALSE TRUE 1039041.601 1138342.552 1193828.262 1240573.942 1153476.367 1086239.166 1244425.52 1185914.079 1086466.161 1303246.956 0.797271458 0.873466496 0.916041473 0.951910102 0.885078889 0.833486824 0.954865472 0.909968808 0.833661001 1 20.31367906 -5 0.235013326 1.59083197 0.878244836 0.314267903 0.049802862 216.9636959 2.16839737 61.42086015 0.083217424 1.00E-05 5 -0.712587134 ILEVHVDK ddPTM_BT-474_Pertuzumab_2h_R1 6 ILEVHVDK 8 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;;;; 137.14 0.00076111 3852280000 8890850 8777290 7618360 8433900 8385470 9229760 9112210 9447500 10985200 11678400 FALSE TRUE 8543385.753 8526970.283 8995167.122 8869174.59 8655196.258 9416392.071 9223727.952 9252405.824 9738206.15 10887411.57 0.784703113 0.783195366 0.826198869 0.814626556 0.794972818 0.864888042 0.847191997 0.849826037 0.894446406 1 23.37615766 -5 0.108590765 1.592959564 0.720064981 0.927848263 0.016583914 39.46024547 0.286035144 5.133675995 0.213378367 1.00E-05 5 -0.872894583 IWDLNMENRPVETYQVHEYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IWDLNMENRPVETYQVHEYLR 21 1 P63151;P63151-2;A0A590UJY3;A0A590UJJ1;E5RFR9 P63151 PPP2R2A Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform 0 181.87 2.93E-17 347610000 179130 169680 183210 214150 171540 185450 232930 178670 219800 268530 FALSE TRUE 172129.4016 164840.8925 216320.1225 225202.3072 177057.7399 189199.9261 235780.667 174980.4021 194849.2255 250342.2239 0.687576386 0.658462204 0.86409763 0.8995778 0.707262791 0.755765141 0.941833396 0.698964798 0.778331447 1 17.93354212 -5 0.310582441 2.955650802 0.767783801 0.352902011 0.091024733 350.567711 3.172241557 449.0572141 0.087105271 1.00E-05 5 -2.187867002 KIEAYMEDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIEAYMEDDR 10 1 Q13572-2;Q13572;G3V588;G3V3C0 Q13572-2 ITPK1 Inositol-tetrakisphosphate 1-kinase 0 ; 136.38 0.0001913 623250000 1361730 1340210 1414980 1599870 1439260 1511510 1662520 1718200 2044750 2287400 FALSE TRUE 1308512.086 1301988.523 1670698.362 1682439.482 1485555.105 1542073.768 1682866.417 1682718.57 1812638.552 2132472.361 0.613612683 0.610553528 0.783456045 0.788961917 0.696635104 0.723138924 0.789162124 0.789092792 0.850017372 1 21.02409561 -5 0.040767203 2.298144925 8.05E-08 0.808002599 0.047542921 362.597317 1.103649649 56.58915046 16.64934555 1.00E-05 5 -2.298144844 LEQENDDLAHELVTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEQENDDLAHELVTSK 16 0 Q9Y3P9;A0A0U1RQV7;E9PS63;F5H8L0;B7ZAP0;Q5R372-7;Q5R372-8;Q5R372-6;Q5R372-5 Q9Y3P9 RABGAP1;RABGAP1L "Rab GTPase-activating protein 1;Rab GTPase-activating protein 1-like, isoform 10;Rab GTPase-activating protein 1-like" 0 132.79 3.72E-05 525870000 449640 418080 415630 397810 447950 471950 502710 461040 615780 695830 FALSE TRUE 432067.5717 406156.7677 490743.5866 418341.0218 462358.7186 481493.1524 508862.3154 451519.3629 545879.236 648700.8143 0.666050608 0.626107997 0.75650219 0.644890545 0.712745704 0.742242251 0.784432984 0.696036374 0.841496147 1 19.30719372 -5 0.137361512 2.023543668 0.603142667 0.819762819 0.044489509 53.34032651 0.45272963 14.79898777 0.276249626 1.00E-05 5 -1.420401 LGGLRPESPES(ph)LTSVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.264)PES(0.723)LT(0.009)S(0.003)VS(0.001)R 189.52 9.22E-10 3587200000 460640 498050 434530 608750 488950 571400 584360 582240 622940 805780 TRUE FALSE 442637.6795 483846.1016 513059.2371 640167.6605 504677.5208 582954.0995 591511.5725 570216.5405 552226.4628 751203.8029 0.589237804 0.644094319 0.682982747 0.852189057 0.671825035 0.776026555 0.787418235 0.759070359 0.735122028 1 19.51884484 -5 0.065721316 1.89928653 0.373180387 0.691737526 0.06157281 204.8995129 0.976249179 29.11325601 4.115688275 1.00E-05 5 -1.526106143 LKPGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKPGTR 6 1 A0A087X2I1;P62333;H0YJC0;H0YJS8;A6PVL3-2;A6PVL3 A0A087X2I1 PSMC6;KNCN 26S protease regulatory subunit 10B;Kinocilin 0 88.591 0.046631 657320000 646270 683630 578130 697500 667720 651500 740310 698420 776170 865670 FALSE TRUE 621013.0539 664133.5417 682610.9514 733498.0586 689197.8202 664673.7764 749370.1352 683997.3829 688062.4356 807037.3998 0.769497243 0.822927837 0.845823194 0.908877406 0.853984983 0.823597242 0.928544495 0.847541121 0.852578128 1 19.62227601 -5 0.122135409 1.456889965 0.78595948 0.601330189 0.038789028 111.130713 0.875514401 12.67402857 0.360718975 1.00E-05 5 -0.670930485 LKTEAEIALK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKTEAEIALK 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 93.959 0.0062704 0 399620 416820 319220 370380 403740 410720 417870 405770 477850 489550 FALSE TRUE 384002.4086 404932.7017 376910.155 389495.3562 416726.6638 419025.0398 422984.0181 397390.7077 423606.4713 456392.3425 0.841386616 0.887246923 0.825846799 0.853422198 0.913088641 0.918124606 0.926799113 0.870721681 0.928162968 1 18.79991506 -5 0.076069494 1.400817113 0.75454436 0.709902086 0.026392218 160.8082022 0.872521117 10.92734124 1.145082616 1.00E-05 5 -0.646272753 LSVEEFFMDLHNFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSVEEFFMDLHNFR 14 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 249.19 4.60E-18 1123260000 540170 531490 559730 619460 575430 500060 677250 577310 670510 784460 FALSE TRUE 519059.5592 516332.4256 660885.6621 651430.4048 593939.2285 510171.5558 685538.3881 565388.3468 594396.5158 731327.8255 0.709749501 0.706020484 0.903679088 0.890750197 0.812138152 0.69759626 0.93738863 0.773098366 0.812763435 1 19.48015873 -5 0.220224461 1.963983421 0.783079514 0.354615436 0.080514179 182.5047588 1.826031774 78.23100693 0.156371607 1.00E-05 5 -1.180903907 LVINGNPITIFQERDPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 283.83 1.59E-39 41501000000 8579100 9141500 6118700 6943600 7437100 7803400 7333000 8396200 8476700 7008300 FALSE TRUE 8243819.287 8880793.37 7224485.2 7301960.028 7676321.076 7961190.095 7422743.448 8222815.536 7514460.553 6533621.599 1.261753403 1.359245135 1.105739763 1.117597632 1.174895264 1.218495741 1.136084075 1.258538685 1.150121788 1 22.63945147 -5 0.206662415 0.078831411 1.229188025 0.418546472 0.072775973 155.5049103 1.547161096 59.48612724 0.170280737 1.00E-05 5 1.150356614 LVSDSLSEHEK ddPTM_BT-474_Pertuzumab_2h_R1 3 LVSDSLSEHEK 11 0 Q96KR1;H0Y8W1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ;; 186.81 3.86E-06 1214850000 1223480 1388070 1162420 1420440 1224940 1426840 1362390 1333630 1593120 1693790 FALSE TRUE 1175665.049 1348483.603 1372495.152 1493749.079 1264341.308 1455691.682 1379063.336 1306090.074 1412275.697 1579068.095 0.744530938 0.85397432 0.869180472 0.945968754 0.800688274 0.92186758 0.873340004 0.827127138 0.894372891 1 20.59064196 -5 0.194229977 1.603173252 0.835654339 0.415050494 0.053270383 145.7881248 1.434134709 34.18907769 0.136319409 1.00E-05 5 -0.767518913 NLAS(ph)PNCVKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLASPNCVKPK 11 1 Q8NG27-3;Q8NG27 Q8NG27-3 PJA1 E3 ubiquitin-protein ligase Praja-1 1 NLAS(1)PNCVKPK 61.657 0.052035 575360000 482650 440480 361060 398070 395910 377450 375210 433780 480830 358510 TRUE FALSE 463787.5044 427917.9417 426311.5737 418614.4404 408644.8047 385082.2976 379801.9322 424822.2914 426248.1942 334227.7984 1.38763893 1.280318225 1.275512018 1.252482416 1.222653552 1.152155205 1.136356503 1.271056128 1.275322389 1 18.3504722 -5 0.055330424 0.197726709 1.626029955 0.633675519 0.060906392 343.0196514 1.395233891 40.1520637 7.687665581 1.00E-05 5 1.428303245 PFVPNVHAAEFVPSFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 PFVPNVHAAEFVPSFLR 17 0 P15170-2;P15170-3;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 92.211 0.0033648 1230380000 608480 560960 623220 582330 624440 571460 678100 632140 823400 900250 FALSE TRUE 584699.9289 544961.97 735849.7175 612384.1211 644525.6797 583015.3127 686398.7906 619086.0881 729931.084 839275.2656 0.696672418 0.649324474 0.876768025 0.729658249 0.767955051 0.694665191 0.817847039 0.737643671 0.869715949 1 19.67878454 -5 0.168948566 1.977108105 0.696563084 0.605103494 0.063732595 88.33550087 0.831567776 28.697206 0.225952663 1.00E-05 5 -1.280545021 QQDLHLES(ph)PQRQPEYS(ph)PESPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 QQDLHLES(1)PQRQPEY(0.004)S(0.534)PES(0.462)PR 128.3 2.44E-05 461830000 170410 160050 120460 189960 161560 173890 195880 172260 175510 232090 TRUE FALSE 163750.1888 155485.5307 142229.8016 199763.8584 166756.7241 177406.1749 198277.238 168702.7708 155586.8406 216370.3376 0.756805164 0.718608347 0.65734427 0.923249742 0.770700485 0.819919112 0.916379021 0.77969454 0.719076572 1 17.72314321 -5 0.128343465 1.640145754 0.703660989 0.386852593 0.080393997 158.8544802 1.292983367 26.79087484 0.641717969 1.00E-05 5 -0.936484765 QYQDFLEDLEEDEAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 QYQDFLEDLEEDEAIR 16 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ; 173.68 9.63E-09 30293000 26480 29218 22377 31784 28066 27820 30103 31872 30324 38055 FALSE TRUE 25445.13232 28384.73125 26421.02167 33424.37605 28968.76838 28382.53946 30471.40952 31213.83206 26881.74665 35477.50095 0.717218847 0.800076964 0.744726121 0.942128818 0.816539147 0.800015184 0.85889391 0.879820484 0.75771252 1 15.11461677 -5 0.097596337 1.52015986 0.700720389 0.447723509 0.063037972 181.3450438 1.211293838 19.79113517 1.121605557 1.00E-05 5 -0.819439471 RNLDIERPTYTNLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 RNLDIERPTYTNLNR 15 2 P68363;F8VQQ4;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;; 234.29 6.70E-18 10843700000 4998610 5462960 4580400 5305890 5367340 5437660 5709560 5113860 6273990 6883390 FALSE TRUE 4803258.795 5307161.73 5408180.17 5579727.619 5539985.366 5547613.211 5779435.303 5008257.004 5561792.958 6417171.864 0.748500881 0.827025026 0.842766921 0.869499483 0.863306373 0.864495034 0.900620308 0.780446139 0.866704691 1 22.61350619 -5 0.284981646 2.193175541 0.83057436 0.574682405 0.04197591 182.1434695 1.730724433 129.0104442 0.047963935 1.00E-05 5 -1.362601182 RVES(ph)GGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVESGGAK 8 1 O15234 O15234 CASC3 Protein CASC3 1 RVES(1)GGAK 90.913 0.0078765 511010000 756240 675410 629080 796660 706510 654030 855490 823560 688360 976480 TRUE FALSE 726685.3047 656147.9681 742768.7498 837775.7181 729235.5358 667254.9347 865959.7425 806553.1982 610220.2586 910342.1398 0.798255154 0.720770729 0.815922627 0.92028665 0.801056552 0.7329716 0.951246465 0.885989084 0.670319687 1 19.79604934 -5 0.227489219 1.916486882 0.799579927 0.268308309 0.087137784 223.384425 2.235835693 94.73403113 0.156376252 1.00E-05 5 -1.116906955 S(ph)PETALEAFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPETALEAFK 10 0 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 S(0.994)PET(0.006)ALEAFK;S(1)PETALEAFK 137.62 9.06E-05 74337000 141824 143968 162436 167380 148490 152408 157907 168716 176111 210610 TRUE FALSE 136281.3613 139862.1736 191791.7986 176018.5019 153266.3157 155489.7942 159839.5131 165231.9556 156119.6176 196345.1971 0.694090629 0.712327959 0.976809219 0.896474701 0.780596205 0.791920538 0.814073965 0.841538057 0.795128274 1 17.58303278 -5 0.375354979 3.504733342 0.811772338 0.343157416 0.07802428 708.3137031 5.375145821 1442.009139 0.055764746 1.00E-05 5 -2.692961004 S(ph)PPSLHLLEAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPSLHLLEAFK 12 0 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 S(0.826)PPS(0.174)LHLLEAFK 61.11 0.056154 70196000 367490 366670 368870 384510 374700 323300 413710 414100 432050 487760 TRUE FALSE 353128.0845 356212.9306 435533.0145 404354.6072 386752.5658 329837.3475 418773.1067 405548.6903 383005.4953 454723.5807 0.776577463 0.783361465 0.957797292 0.889231666 0.850522344 0.725357913 0.920939939 0.89185762 0.842282018 1 18.79463029 -5 0.179320044 1.603166914 0.821771391 0.327218995 0.066620114 170.3463856 1.638788575 36.53116952 0.217341287 1.00E-05 5 -0.781395523 S(ph)PSPVQGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.896)PS(0.104)PVQGK 112.3 0.0032187 1541200000 1819200 1782000 1524200 1574700 1607800 1635200 1683700 1775100 1934800 1701400 TRUE FALSE 1748103.653 1731179.105 1799656.846 1655970.456 1659516.347 1668264.864 1704305.624 1738443.565 1715169.615 1586162.663 1.10209608 1.091425959 1.134597912 1.044010488 1.046246004 1.051761527 1.074483509 1.096005855 1.081332738 1 20.5971093 -5 0.271112052 0.455987189 1.08588496 0.452910691 0.026577274 217.2132085 2.106637641 66.34894252 0.035207874 1.00E-05 5 0.629897771 SLSNS(ph)PQLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLSNSPQLK 9 0 A0A1W2PRG7;B7ZM68;Q6ZNL6 A0A1W2PRG7 FGD5 "FYVE, RhoGEF and PH domain-containing protein 5" 1 SLSNS(1)PQLK;SLS(0.006)NS(0.994)PQLK;SLSNS(1)PQLK;SLSNS(1)PQLK 172.76 5.87E-05 869320000 1301050 1473670 1001700 1041840 1111470 1084690 1119830 1347450 1236380 1002710 TRUE FALSE 1250203.528 1431642.374 1182729.473 1095609.487 1147221.442 1106623.175 1133534.815 1319624.687 1096031.326 934795.5586 1.337408502 1.531503184 1.265227955 1.172031122 1.227243146 1.183813043 1.21260184 1.411671969 1.172482385 1 19.83429135 -5 0.087309022 0.190345555 1.509996224 0.440909709 0.104177968 251.3417504 1.533761532 39.56423313 3.003794668 1.00E-05 5 1.319650668 SSISSIS(ph)GRDDLMDYHRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSISSISGRDDLMDYHRR 18 2 E9PDY7;G5E9V3;A0A1W2PQ63;E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0 E9PDY7 PHLDB2 Pleckstrin homology-like domain family B member 2 1 SSIS(0.001)S(0.018)IS(0.981)GRDDLMDYHRR 56.017 0.081415 889360000 495790 550870 444300 538150 531920 554640 544080 528400 605390 660570 TRUE FALSE 476413.9787 535159.727 524594.8934 565923.986 549029.6899 565855.2008 550738.6138 517488.3553 536668.6652 615829.0055 0.773614062 0.869007017 0.851851551 0.918962863 0.891529442 0.918851168 0.89430444 0.84031176 0.871457272 1 19.23217029 -5 0.249338063 1.75493474 0.860168267 0.496680225 0.039852552 167.6788798 1.663168873 64.73128151 0.060340257 1.00E-05 5 -0.894766472 SVDCFLHDFASK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVDCFLHDFASK 12 0 O00186 O00186 STXBP3 Syntaxin-binding protein 3 0 113.77 0.0011302 213010000 227820 240360 199260 223300 232390 258730 273460 217300 354100 344330 FALSE TRUE 218916.5425 233505.1681 235270.7145 234824.5398 239865.0354 263961.6979 276806.6853 212812.6791 313904.0525 321008.2224 0.68196553 0.727411798 0.732911801 0.731521884 0.747223961 0.822289522 0.862304034 0.662950866 0.977869196 1 18.29225073 -5 0.100455009 1.823475436 0.59057028 0.595757053 0.071280166 132.8168776 0.907451839 22.46772409 1.174396386 1.00E-05 5 -1.232905156 SVRPTDSNVS(ph)PAISIHEIGAVGATK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVRPTDSNVSPAISIHEIGAVGATK 25 1 A6NIT2;A6NMN0;P46020-3;P46020-2;P46020 A6NIT2 PHKA1 "Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform" 1 S(0.05)VRPT(0.05)DS(0.026)NVS(0.873)PAISIHEIGAVGATK 149.14 1.20E-07 416910000 125870 164640 129710 176130 145720 175460 171770 144640 182550 216540 TRUE FALSE 120950.8612 159944.6284 153151.4824 185220.0904 150407.2161 179007.9214 173872.1726 141653.1335 161827.6893 201873.5529 0.599141688 0.792301052 0.758650552 0.917505477 0.745056566 0.886732902 0.861292478 0.701692378 0.801628975 1 17.62309239 -5 0.286848385 2.597155653 0.77433942 0.359216534 0.087497646 280.5990605 2.658014545 268.2936979 0.095100194 1.00E-05 5 -1.822816233 TAS(ph)PPALPK ddPTM_BT-474_Pertuzumab_2h_R1 4 TASPPALPK 9 0 Q13029-5;Q13029-3;Q13029-2;Q13029 Q13029-5 PRDM2 PR domain zinc finger protein 2 1 TAS(1)PPALPK;TAS(1)PPALPK;TAS(1)PPALPK;TAS(1)PPALPK 144.77 0.0001036 1052290000 2084100 1696080 1390040 1478800 1631620 1338690 1567040 1894050 1599540 1326830 TRUE FALSE 2002651.068 1647709.459 1641251.149 1555121.045 1684102.539 1365759.229 1586217.904 1854937.206 1417966.925 1236962.622 1.619006938 1.332060831 1.326839728 1.257209407 1.361482157 1.104123281 1.282349099 1.499590345 1.146329646 1 20.23837048 -5 0.104140654 0.042224943 1.525522433 0.430981443 0.130817707 206.7821083 1.452525776 43.70701292 2.058941783 1.00E-05 5 1.483297489 TGFLEIDEHMR ddPTM_BT-474_Pertuzumab_2h_R1 3 TGFLEIDEHMR 11 0 P35813;P35813-3;P35813-2;E9PL75;E9PJN3;E9PKB5 P35813 PPM1A Protein phosphatase 1A 0 ;; 150.46 3.39E-05 632740000 1281930 1274090 1227770 1383730 1320860 1155840 1373920 1393830 1489710 1581070 FALSE TRUE 1231830.758 1237754.201 1449655.351 1455144.471 1363346.661 1179211.877 1390734.444 1365046.923 1320604.366 1473982.721 0.835715874 0.839734539 0.983495485 0.987219491 0.924940735 0.800017436 0.943521538 0.926094251 0.895942909 1 20.49128818 -5 0.217954318 1.456855754 0.895503892 0.191033882 0.059447159 288.5315656 2.88548797 57.95529591 0.123000632 1.00E-05 5 -0.561351861 VVVLMGSTSDLGHCEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVVLMGSTSDLGHCEK 16 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 248.23 2.20E-20 2664400000 2693900 2989800 2271000 2799700 2781600 3060500 2779100 2736600 3426600 3420400 FALSE TRUE 2588619.41 2904533.831 2681420.218 2944192.853 2871072.69 3122385.407 2813111.457 2680088.254 3037626.733 3188733.261 0.811801803 0.910873878 0.840904522 0.923311112 0.900380325 0.979193037 0.882203441 0.840486812 0.952612365 1 21.60455199 -5 0.14819424 1.369220565 0.857651792 0.375168375 0.046534489 166.5726413 1.475244926 18.27734142 0.25331829 1.00E-05 5 -0.511568774 YEFTDALLCHDDELEGR ddPTM_BT-474_Pertuzumab_2h_R1 4 YEFTDALLCHDDELEGR 17 0 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ;;; 236.81 3.37E-20 728810000 651590 709070 651090 779280 703660 723760 800100 681980 920400 970900 FALSE TRUE 626125.1424 688848.0179 768756.4464 819498.7342 726293.8629 738394.9231 809891.8631 667896.8747 815920.0506 905140.0782 0.691743916 0.761040235 0.849323177 0.905383326 0.802410456 0.815779724 0.894769641 0.737893383 0.901429591 1 19.78778155 -5 0.149187796 1.635186717 0.759036156 0.477793424 0.063499033 133.8690801 1.189774994 25.36880731 0.342162724 1.00E-05 5 -0.876150561 YIEIYVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 YIEIYVQK 8 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 109.86 0.0082276 275040000 256440 248230 233820 270570 256240 273760 280540 265900 292600 344020 FALSE TRUE 246418.0413 241150.7234 276076.4753 284534.1501 264482.1923 279295.6148 283973.3324 260409.0721 259385.2747 320719.219 0.768329513 0.751906057 0.860804277 0.88717524 0.824653394 0.870841528 0.885426615 0.811953437 0.808761245 1 18.29095128 -5 0.227597419 1.863453745 0.812971371 0.570596071 0.044289196 128.9889371 1.29102891 51.48304223 0.08474095 1.00E-05 5 -1.050482374 YKDEDGDLITIFDSSDLSFAIQCSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YKDEDGDLITIFDSSDLSFAIQCSR 25 1 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 107.23 0.0033541 26826000 27333 28999 23428 32910 26433 27691 30127 35769 36021 44736 FALSE TRUE 26264.79614 28171.97691 27661.96075 34608.48904 27283.24145 28250.93099 30495.70324 35030.35765 31932.04709 41705.99087 0.629760751 0.675489931 0.663261085 0.829820568 0.654180392 0.677383043 0.731206779 0.839935868 0.765646528 1 15.34796701 -5 0.113307916 1.956603655 0.562402852 0.740052761 0.055719486 82.15616405 0.6142903 17.88689881 0.651340456 1.00E-05 5 -1.394200803 YLLHGLECVVAMHQAQLISK ddPTM_BT-474_Pertuzumab_2h_R1 2 YLLHGLECVVAMHQAQLISK 20 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 265.07 7.56E-37 314650000 401580 413550 390620 432280 468820 497000 464990 367910 583920 586400 FALSE TRUE 385885.8096 401755.9589 461213.7233 454590.0226 483900.0211 507049.6805 470680.6867 360312.5299 517635.8496 546682.6057 0.705868095 0.73489801 0.843659042 0.831542869 0.885157157 0.92750286 0.860976153 0.65908907 0.946867239 1 19.06034395 -5 0.159990783 1.647682564 0.766761019 0.328284579 0.085569287 192.4848475 1.770300294 40.08179655 0.402510094 1.00E-05 5 -0.880921545 YSMEELIQLGQDER ddPTM_BT-474_Pertuzumab_2h_R1 1 YSMEELIQLGQDER 14 0 E9PKG0 E9PKG0 PLEC 0 152.4 1.55E-05 41148000 51749 55131 53398 56667 65658 62158 68926 62761 60981 88598 FALSE TRUE 49726.59187 53558.71786 63048.20643 59591.59066 67769.9492 63414.87735 69769.53701 61464.96342 54058.69253 82597.17855 0.602037415 0.648432777 0.763321551 0.721472473 0.82048746 0.767760818 0.844696371 0.744153305 0.654485946 1 16.33380488 -5 0.093280703 1.717401845 0.556944646 0.559852991 0.07226935 166.1733146 1.070562961 24.53670022 1.571590757 1.00E-05 5 -1.160457199 YTCGEAPDYDR ddPTM_BT-474_Pertuzumab_2h_R1 4 YTCGEAPDYDR 11 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;; 207.83 5.03E-08 1733980000 1253410 1232790 1138560 1431360 1298870 1359300 1513690 1333240 1485100 1868400 FALSE TRUE 1204425.351 1197632.036 1344323.119 1505232.661 1340649.333 1386785.977 1532214.991 1305708.128 1316517.674 1741851.604 0.691462665 0.687562611 0.771778214 0.864156658 0.769669087 0.796156213 0.87964726 0.749609281 0.75581506 1 20.73219029 -5 0.157253489 1.775273291 0.716278451 0.592017251 0.057482076 103.0353353 0.940062385 25.22803991 0.272960655 1.00E-05 5 -1.05899484 ATNES(ph)EDEIPQLVPIGK ddPTM_BT-474_Pertuzumab_2h_R1 9 ATNESEDEIPQLVPIGK 17 0 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AT(0.032)NES(0.968)EDEIPQLVPIGK;AT(0.037)NES(0.963)EDEIPQLVPIGK;AT(0.001)NES(0.999)EDEIPQLVPIGK;AT(0.018)NES(0.982)EDEIPQLVPIGK;AT(0.11)NES(0.89)EDEIPQLVPIGK;AT(0.023)NES(0.977)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;AT(0.032)NES(0.968)EDEIPQLVPIGK 295.98 4.06E-46 9596730000 4502810 4281730 3531530 3506010 4008270 3803360 3654860 4615030 3996530 3763690 TRUE FALSE 4326835.207 4159619.253 4169756.029 3686955.596 4137199.645 3880266.545 3699589.27 4519728.018 3542860.669 3508771.924 1.233148036 1.185491489 1.18838047 1.050782347 1.179101901 1.105875967 1.054382944 1.288122487 1.009715292 1 21.74253474 -5 0.125728008 0.517666624 1.216578404 0.301239955 0.078630617 211.1068545 1.695506618 25.93728604 0.668036322 1.00E-05 5 0.69891178 AVEELHK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVEELHK 7 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;; 102.71 0.013871 282270000 793072 799490 640797 697427 768212 791352 780937 765410 916740 927570 FALSE TRUE 762077.8695 776689.328 756603.2724 733421.291 792922.2367 807353.6796 790494.3406 749604.016 812675.5185 864744.8577 0.881274821 0.898171664 0.874943939 0.848136054 0.91694357 0.933632241 0.914135925 0.866849926 0.939786471 1 19.721915 -5 0.190881308 1.462472039 0.875409483 0.629828599 0.025397922 95.4400667 0.934971957 16.72120017 0.07292189 1.00E-05 5 -0.587062556 RKEDEVEEWQHR ddPTM_BT-474_Pertuzumab_2h_R1 3 RKEDEVEEWQHR 12 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 204.48 6.78E-08 4026050000 3069080 2950990 2702870 3052570 2708580 2939520 3070920 3172680 3499640 3562430 FALSE TRUE 2949136.961 2866830.655 3191338.734 3210113.504 2795703.936 2998959.108 3108502.838 3107163.049 3102375.539 3321143.443 0.887988433 0.863205912 0.960915657 0.966568761 0.841789577 0.902989937 0.935973676 0.935570264 0.93412874 1 21.6632486 -5 0.135209007 1.303098341 0.880699557 0.369484244 0.036828537 162.5185054 1.366431875 13.1550413 0.260588895 1.00E-05 5 -0.422398784 S(ph)RTSPITR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.503)RT(0.306)S(0.191)PITR 72.652 0.027615 6287100000 95686 135650 138200 123870 169080 163690 142910 128340 196450 216500 TRUE FALSE 91946.48533 131781.3948 163175.8142 130262.9455 174518.6118 166999.924 144658.9753 125689.7342 174149.8196 201836.2622 0.455549882 0.652912383 0.808456382 0.645389209 0.864654398 0.827402976 0.716714498 0.622731182 0.862827213 1 17.62282587 -5 0.039812053 2.20215418 3.89E-13 0.480827816 0.107350567 915.6088232 2.723894748 135.198803 40.92128039 1.00E-05 5 -2.20215418 SGSSS(ph)PDSEITELKFPSINHD ddPTM_BT-474_Pertuzumab_2h_R1 3 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 S(0.002)GS(0.008)S(0.053)S(0.937)PDSEITELKFPSINHD;S(0.001)GS(0.012)S(0.099)S(0.888)PDSEITELKFPSINHD;S(0.006)GS(0.022)S(0.089)S(0.86)PDS(0.022)EITELKFPSINHD 236.02 4.91E-30 2518110000 1018840 1157270 950380 1092750 1026190 1180880 1194750 1103600 1259990 1453150 TRUE FALSE 979022.6064 1124265.793 1122134.807 1149146.958 1059198.333 1204758.203 1209371.708 1080810.274 1116961.218 1354726.856 0.722671586 0.829883742 0.828310742 0.848249928 0.781853795 0.889299712 0.892705199 0.797806783 0.824491825 1 20.36957057 -5 0.193675152 1.742520606 0.796231281 0.589165116 0.045440561 102.2933469 1.005613832 29.46206542 0.119227675 1.00E-05 5 -0.946289325 SPQLSLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQLSLSPR 9 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 SPQLSLS(1)PR;SPQLSLS(1)PR 118.77 0.0011362 178690000 401180 377810 464780 521240 433700 338580 502110 516380 471000 620350 TRUE FALSE 385501.4421 367035.2287 548776.085 548141.2589 447650.3544 345426.3196 508254.9724 505716.5725 417534.0546 578333.1419 0.666573319 0.634643257 0.94889268 0.947794998 0.774035451 0.597279136 0.878827332 0.874438167 0.72196114 1 19.14154125 -5 0.165771641 1.76779404 0.74107313 0.219431125 0.121324312 227.7684035 2.12758677 57.87605724 0.496693721 1.00E-05 5 -1.02672091 GHSLSDGLEEVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHSLSDGLEEVQK 13 0 C9JNK6;O75431-2;O75431;C9JAZ1 C9JNK6 MTX2 Metaxin-2 0 118.37 0.00043318 239880000 337310 357120 335980 455240 278290 424810 428120 321770 507200 504380 FALSE TRUE 324127.5523 346935.2873 396699.0598 478734.991 287241.4506 433399.9493 433359.4606 315125.3371 449624.7824 470217.8933 0.689313522 0.737818131 0.843649435 1.018113087 0.610868822 0.921700249 0.921614143 0.670168748 0.956205174 1 18.84296991 -5 0.138525316 1.622407144 0.745456365 0.201650667 0.125909581 253.5147904 2.162426164 43.87321087 0.793116507 1.00E-05 5 -0.876950779 KPGMFFNPEESELDLTYGNR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPGMFFNPEESELDLTYGNR 20 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 266.2 1.64E-36 2594900000 1937570 1973060 1664160 1962670 1767930 1961400 2144970 1964320 2239400 2706600 FALSE TRUE 1861847.622 1916790.261 1964910.731 2063963.634 1824797.074 2001060.852 2171220.784 1923756.106 1985192.7 2523279.571 0.737868147 0.759642444 0.77871305 0.81796867 0.723184658 0.793039691 0.860475712 0.762403076 0.78675099 1 21.26686863 -5 0.261979792 2.430162715 0.763582776 0.775528067 0.035901608 90.61814763 0.888518159 69.81629152 0.046889033 1.00E-05 5 -1.666579939 LDQVEQELNELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDQVEQELNELR 12 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 156.69 0.00017074 30355000 23509 27308 23112 26056 23846 28127 24960 28910 29229 32949 FALSE TRUE 22590.24229 26529.20258 27288.85252 27400.75328 24613.02825 28695.74721 25265.46795 28312.9984 25911.04646 30717.33488 0.735423251 0.86365574 0.888386073 0.892028992 0.801274861 0.9341874 0.822514975 0.921727048 0.843531724 1 14.90676543 -5 0.087938331 1.419710652 0.748133018 0.435218838 0.053325033 211.9398395 1.301055165 17.09534302 1.274816236 1.00E-05 5 -0.671577635 TFNVDMYEEIHR ddPTM_BT-474_Pertuzumab_2h_R1 4 TFNVDMYEEIHR 12 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3KSA5;J3KRJ4;J3QLT0;J3QS84;J3KRE8;J3QLE8;J3KTB0;J3QS88;J3QL53 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ;;; 164.81 5.63E-05 1296650000 884200 904890 830740 976300 921080 902950 956150 905740 1121130 1174020 FALSE TRUE 849644.4865 879083.4232 980873.1977 1026686.96 950707.3747 921208.2677 967851.6497 887036.1525 993864.0226 1094502.58 0.776283676 0.803180769 0.896181714 0.938039781 0.868620497 0.84166843 0.884284485 0.810446836 0.908050873 1 20.06184392 -5 0.279492628 2.035899865 0.848250486 0.462987846 0.047147689 224.278838 2.149582835 134.7636767 0.057662235 1.00E-05 5 -1.187649378 TTPPPGAQCEVPAS(ph)PQRPSRPGALPEQTRPLR ddPTM_BT-474_Pertuzumab_2h_R1 6 TTPPPGAQCEVPASPQRPSRPGALPEQTRPLR 32 3 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 TTPPPGAQCEVPAS(0.999)PQRPS(0.001)RPGALPEQTRPLR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR;TTPPPGAQCEVPAS(0.986)PQRPS(0.012)RPGALPEQT(0.002)RPLR;TTPPPGAQCEVPAS(0.999)PQRPS(0.001)RPGALPEQTRPLR;TTPPPGAQCEVPAS(0.925)PQRPS(0.027)RPGALPEQT(0.048)RPLR 221.85 4.15E-36 9494880000 332020 350479 307330 355519 427009 356398 352548 393961 403465 487609 TRUE FALSE 319044.2913 340483.6821 362871.3675 373867.3782 440744.1323 363604.6117 356862.5879 385825.5677 357665.3447 454582.8081 0.701839765 0.749002549 0.79825141 0.822440646 0.969557415 0.799864415 0.785033181 0.848746501 0.786799101 1 18.7941836 -5 0.024224079 2.079865699 1.33E-10 0.462113914 0.064534407 2284.288993 4.180855538 257.3068661 124.0266857 1.00E-05 5 -2.079865699 LKDLPFIVSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKDLPFIVSHR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 101.32 0.0020255 376810000 1082010 1113990 956350 1070090 1067450 1157140 1174910 1084590 1315910 1402540 FALSE TRUE 1039723.853 1082220.096 1129183.719 1125317.473 1101785.499 1180538.164 1189288.9 1062192.837 1166533.414 1307544.717 0.795172693 0.827673488 0.8635909 0.860634026 0.842636955 0.902866379 0.909558874 0.812356797 0.892155655 1 20.31842886 -5 0.167902119 1.547709022 0.820415961 0.671942363 0.032208695 86.8029814 0.81510422 15.88642333 0.128682636 1.00E-05 5 -0.727293062 ADEEEMLDNLPEAGDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADEEEMLDNLPEAGDSR 17 0 Q9NPD8 Q9NPD8 UBE2T Ubiquitin-conjugating enzyme E2 T 0 227.47 2.50E-18 0 69734 70521 62020 71462 66333 65405 74522 82902 75392 88269 FALSE TRUE 67008.71818 68509.81013 73228.39363 75150.16238 68466.66119 66727.53391 75434.02253 81190.04473 66833.81623 82290.46201 0.814295078 0.832536462 0.889877051 0.913230532 0.832012113 0.810878105 0.916680022 0.986627645 0.812169656 1 16.3284376 -5 0.059937512 1.47877936 0.673095399 0.364877324 0.054380303 436.6637855 1.912738041 30.5305825 5.108204596 1.00E-05 5 -0.805683961 DDPSKPVHLTAFLGYK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDPSKPVHLTAFLGYK 16 1 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 169.09 3.45E-09 4306000000 6136100 8082400 7643700 9271100 7610000 8322600 8742700 9321700 10439600 12556600 FALSE TRUE 5896294.428 7851897.865 9025086.623 9749582.582 7854782.561 8490888.674 8849695.778 9129203.637 9254540.374 11706130.3 0.503692875 0.670750937 0.770970969 0.832861273 0.670997363 0.725336935 0.755988149 0.779865199 0.790572131 1 23.48076091 -5 0.04000728 2.243369188 1.83E-11 0.666197942 0.069852797 563.0543819 1.682988754 84.91719712 25.55382079 1.00E-05 5 -2.243369188 NDIPSSYMALFPHLLQPVLWER ddPTM_BT-474_Pertuzumab_2h_R1 3 NDIPSSYMALFPHLLQPVLWER 22 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 146.64 8.39E-08 410254000 202368 176835 206079 248347 194983 186472 223613 217062 249457 276308 FALSE TRUE 194459.2348 171791.8389 243322.0595 261164.2184 201254.8053 190242.5916 226349.6428 212579.5938 221139.6872 257593.4131 0.754907637 0.666910838 0.944597366 1.013862177 0.781288632 0.738538262 0.87870897 0.825252445 0.85848347 1 17.97473618 -5 0.197624783 1.750165165 0.802329659 0.236497796 0.095469686 232.7328181 2.29794615 69.00652252 0.25128779 1.00E-05 5 -0.947835506 STVPGHAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 STVPGHAGR 9 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ; 117.89 0.0010783 599890000 930180 1043930 867050 1164960 974370 768540 1082670 1084530 1165520 1185370 FALSE TRUE 893827.5372 1014158.139 1023745.222 1225083.725 1005711.496 784080.4054 1095920.039 1062134.077 1033215.056 1105083.834 0.808832334 0.917720545 0.926395981 1.108588948 0.910077104 0.709521198 0.991707602 0.96113439 0.934965316 1 20.07572439 -5 0.010874883 2.052283812 4.45E-11 0.073937785 0.098774014 37076.00089 30.6239426 3401.718427 2450.018283 1.00E-05 5 -2.052283812 VFNVFCLYGNVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFNVFCLYGNVEK 13 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 208.72 1.02E-07 133434000 260770 277140 226590 251270 261230 263240 264480 269610 314000 301880 FALSE TRUE 250578.8201 269236.2385 267539.8535 264238.0748 269632.7002 268562.8932 267716.7854 264042.4593 278356.0364 281433.3987 0.890366322 0.95666058 0.95063292 0.938900912 0.958069303 0.954268024 0.951261601 0.938205844 0.989065398 1 18.10243402 -5 0.008160873 2.047664892 1.82E-12 0.567974001 0.018473166 15562.03033 9.652275845 1368.915764 1070.052805 1.00E-05 5 -2.047664892 ALINADELASDVAGAEALLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALINADELASDVAGAEALLDR 21 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 252.76 5.59E-36 255756000 121723 137914 140919 191336 134417 139722 156219 160571 187766 220613 FALSE TRUE 116965.9306 133980.8278 166386.198 201210.8739 138740.6449 142547.2746 158130.8549 157255.1527 166451.5909 205670.685 0.568704921 0.65143376 0.80899326 0.978315767 0.674576665 0.693085038 0.768854613 0.764596825 0.80931121 1 17.64997665 -5 0.141511255 1.84926099 0.662326561 0.40533525 0.100236717 159.6459932 1.378583291 38.38287327 0.639106891 1.00E-05 5 -1.186934429 FDLSQNHPLGMAIFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FDLSQNHPLGMAIFLK 16 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 222.57 9.52E-15 5801100000 4325800 4587900 4711700 4916800 4501800 3467700 5984300 4693700 5676600 6457300 FALSE TRUE 4156742.954 4457057.584 5563209.001 5170556.637 4646604.485 3537819.27 6057537.654 4596773.455 5032216.166 6019941.319 0.690495593 0.740382231 0.924130105 0.858904824 0.771868734 0.587683348 1.006245299 0.763591074 0.835924455 1 22.52131799 -5 0.198948541 1.912337713 0.767013369 0.248641799 0.110406588 208.8325006 2.064685158 75.50478842 0.265408706 1.00E-05 5 -1.145324345 GIHPTIISESFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GIHPTIISESFQK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 227.31 9.32E-12 3947100000 4060700 4911200 4039300 4445000 4242800 4235100 4870200 4684600 4933100 5624300 FALSE TRUE 3902003.355 4771137.385 4769291.364 4674406.983 4379273.515 4320736.624 4929802.964 4587861.373 4373115.169 5243361.151 0.744179781 0.90993873 0.909586661 0.891490563 0.835203487 0.824039485 0.94019901 0.874984812 0.834028983 1 22.32206049 -5 0.326985074 2.298931637 0.862948569 0.365618725 0.053737036 386.8917305 3.370228255 349.0189307 0.044805006 1.00E-05 5 -1.435983068 ITAHS(ph)SPPLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ITAHSSPPLTK 11 0 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 ITAHS(0.638)S(0.362)PPLTK 89.959 0.0076292 237430000 184740 201090 199580 180490 183530 206500 222680 199220 234900 260130 TRUE FALSE 177520.1566 195355.1101 235648.5456 189805.1105 189433.4091 210675.5715 225405.2245 195106.0374 208235.1368 242511.1634 0.732008185 0.805551 0.971701848 0.782665457 0.781132738 0.868725252 0.929463293 0.804523943 0.858662067 1 17.88769163 -5 0.182683791 1.660727417 0.806530766 0.372314447 0.066839911 155.8446753 1.508165246 37.45210776 0.203528941 1.00E-05 5 -0.85419665 VIY(ph)DFIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VIYDFIEK 8 0 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 VIY(1)DFIEK;VIY(1)DFIEK 143.01 0.0062692 93290000 68775 84873 69662 74341 75352 79349 73234 82550 93415 103083 TRUE FALSE 66087.19697 82452.50514 82251.47302 78177.74792 77775.76551 80953.49115 74130.2596 80845.31365 82810.92083 96101.09659 0.687684109 0.857976736 0.855884854 0.813494858 0.809311946 0.842378433 0.771377874 0.841252769 0.861706305 1 16.55226527 -5 0.22445435 1.96175609 0.795420154 0.601557065 0.047177344 106.8258943 1.069285315 46.43441872 0.083021318 1.00E-05 5 -1.166335936 MS(ph)PNQLCSVPLQPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MSPNQLCSVPLQPGR 15 0 Q86TB9-4 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR 271.82 2.19E-33 699640000 231770 264000 192430 256900 235430 222640 252460 252460 278050 282430 TRUE FALSE 222712.1722 256470.9785 227206.3816 270158.6398 243002.8198 227141.9333 255549.681 247246.6128 246486.9297 263300.7645 0.845847039 0.974060895 0.862915769 1.026045786 0.922909663 0.862670998 0.970561865 0.939027326 0.936142096 1 18.00635218 -5 0.094304918 1.216911328 0.877421154 0.180173428 0.052667407 371.7528895 2.416162542 16.23473764 1.010036761 1.00E-05 5 -0.339490174 LNNLSPAPHLASGSPPPGLPSGLPSGLQS(ph)GSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 34 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LNNLSPAPHLAS(0.002)GS(0.058)PPPGLPS(0.026)GLPS(0.018)GLQS(0.68)GS(0.215)PSR 219.92 2.08E-36 1164400000 171640 198440 173370 279440 172460 208090 223570 232540 240750 331810 TRUE FALSE 164932.119 192780.6855 204701.8156 293861.9319 178007.3325 212297.7224 226306.1165 227737.9677 213421.0693 309336.2132 0.533180766 0.623207621 0.661745398 0.94997585 0.575449381 0.686300903 0.731586238 0.736215024 0.689932379 1 18.23881621 -5 0.169144476 2.169934084 0.620236239 0.466556196 0.103874521 123.6408664 1.164459816 48.68299159 0.381285281 1.00E-05 5 -1.549697846 FDSSLDR ddPTM_BT-474_Pertuzumab_2h_R1 6 FDSSLDR 7 0 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;;;; 138.55 0.0064555 3583550000 1894390 1875970 2171250 2303660 1985770 1665900 2381190 2191920 2567300 2834880 FALSE TRUE 1820355.144 1822469.172 2563643.174 2422552.169 2049644.095 1699585.639 2410331.716 2146656.086 2275870.867 2642871.053 0.688779402 0.689579301 0.970022042 0.916636537 0.775536927 0.643083074 0.912012606 0.812243974 0.861135796 1 21.33367461 -5 0.157076846 1.706283183 0.755666263 0.275089439 0.101276492 198.9174363 1.813895391 43.65740881 0.474641848 1.00E-05 5 -0.95061692 VVS(ph)DADDSDS(ph)DAVSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVSDADDSDSDAVSDK 16 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 VVS(0.999)DADDS(0.117)DS(0.883)DAVSDK;VVS(1)DADDS(0.001)DS(0.999)DAVSDK 375.7 2.18E-104 246448000 323650 413960 420440 377740 413010 460030 537640 351960 618910 623880 TRUE FALSE 311001.4002 402154.2661 496422.8606 397235.2067 426294.8417 469332.1218 544219.7991 344691.903 548653.9315 581624.0519 0.534712069 0.691433349 0.853511575 0.682975894 0.732938812 0.806933827 0.935689983 0.592636948 0.943313692 1 19.1497274 -5 0.037701356 2.239973138 2.00E-19 0.433856859 0.111632271 1015.233658 2.865337274 148.2398696 47.7728242 1.00E-05 5 -2.239973138 ELLVSQHTVQLVGGLS(ph)PLSS(ph)PSDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLVSQHTVQLVGGLSPLSSPSDTK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 ELLVSQHTVQLVGGLS(0.997)PLS(0.042)S(0.948)PS(0.013)DT(0.001)K 140.21 2.10E-07 75258000 35152 44169 46655 46858 43112 46358 49150 44614 59790 67792 TRUE FALSE 33778.22098 42909.34337 55086.59633 49276.347 44498.73663 47295.39052 49751.5124 43692.70531 53002.88986 63200.38746 0.534462245 0.678941144 0.871618016 0.779684255 0.704089618 0.748340199 0.787202649 0.691336036 0.838648179 1 15.94764578 -5 0.157538478 1.959314541 0.663944116 0.530113483 0.081876667 117.6937033 1.074718749 35.33103059 0.379313724 1.00E-05 5 -1.295370425 SLLVS(ph)SPSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLVSSPSTK 10 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 SLLVS(0.479)S(0.479)PS(0.041)T(0.002)K 61.48 0.095785 43975000 201270 195250 208270 195610 183200 208210 222900 222890 234440 253420 TRUE FALSE 193404.1459 189681.6612 245909.0219 205705.4555 189092.7944 212420.1489 225627.9169 218287.2436 207827.3541 236255.6377 0.818622352 0.802866179 1.040859911 0.870690145 0.800373681 0.89911145 0.955016012 0.92394512 0.879671512 1 17.84998923 -5 0.016000805 2.088616997 1.28E-17 0.236438589 0.068073682 7847.092457 9.521353571 789.413457 487.180292 1.00E-05 5 -2.088616997 CTVFHGAQVEDAFR ddPTM_BT-474_Pertuzumab_2h_R1 8 CTVFHGAQVEDAFR 14 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 192.65 3.49E-07 56854460000 12895760 14168490 13245960 14778130 13870130 11852230 16829650 14596230 16616550 18257170 FALSE TRUE 12391779.44 13764418.54 15639799.63 15540831.06 14316275.33 12091890.21 17035616.29 14294812.75 14730308.91 17020595.61 0.72804617 0.808691943 0.91887499 0.913060354 0.841114827 0.710426972 1.0008825 0.83985385 0.865440272 1 24.02077819 -5 0.094122447 1.455535352 0.741594126 0.289007253 0.079488871 284.3910434 1.845490282 26.06750759 1.630202894 1.00E-05 5 -0.713941226 GISEETTTGVHNLYK ddPTM_BT-474_Pertuzumab_2h_R1 4 GISEETTTGVHNLYK 15 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 246.86 3.26E-18 3529050000 2633680 2818210 2351390 2671130 2570370 2606590 2879970 2977900 3198200 3434830 FALSE TRUE 2530752.874 2737837.41 2776338.479 2808987.339 2653048.285 2659297.036 2915215.934 2916405.324 2835153.744 3202185.905 0.790320409 0.854990151 0.867013522 0.877209326 0.828511637 0.830463038 0.910383101 0.910754532 0.885380746 1 21.61062564 -5 0.092626082 1.468291208 0.751684084 0.757610523 0.026986271 103.5213151 0.663141087 9.373405739 0.61164422 1.00E-05 5 -0.716607125 TIDQIHK ddPTM_BT-474_Pertuzumab_2h_R1 4 TIDQIHK 7 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 134.81 0.0031382 2855160000 3886620 4016740 3382270 3827930 3816690 4251960 4275100 4372130 5063030 5402600 FALSE TRUE 3734726.594 3902186.508 3993521.427 4025489.926 3939457.3 4337937.544 4327419.953 4281843.988 4488296.06 5036677.09 0.741506062 0.774754156 0.79288812 0.799235261 0.782154033 0.861269735 0.859181535 0.850132719 0.891122456 1 22.26404081 -5 0.051056423 1.817636392 0.423258147 0.947771822 0.016175033 106.5854979 0.402068568 11.53907641 2.504862052 1.00E-05 5 -1.394378245 LEPQELS(ph)PLSATVFPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEPQELSPLSATVFPK 16 0 Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2;Q9H869-7;Q9H869-5;Q9H869-6;Q9H869-4;Q9H869-3;Q9H869-2;Q9H869;Q9H869-8;Q9H869-9 Q3T8J9-3 GON4L;YY1AP1 GON-4-like protein;YY1-associated protein 1 1 LEPQELS(1)PLSATVFPK;LEPQELS(0.948)PLS(0.051)ATVFPK 158.45 9.94E-09 170433000 191482 194608 162368 198130 203888 197362 188675 209830 231983 253550 TRUE FALSE 183998.6717 189057.9704 191711.5095 208355.513 210446.2427 201352.7949 190984.0611 205496.9372 205649.2624 236376.8327 0.77841246 0.79981599 0.811041875 0.881454882 0.890299782 0.851829651 0.80796438 0.869361582 0.870005999 1 17.85072912 -5 0.133148344 1.530473261 0.777631994 0.738605642 0.030870408 81.8096926 0.681437588 11.58668812 0.242966712 1.00E-05 5 -0.752841268 LSEAVWQPEEHYSSS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSEAVWQPEEHYSSSPEK 18 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 LSEAVWQPEEHYSS(0.042)S(0.958)PEK;LSEAVWQPEEHYS(0.005)S(0.149)S(0.847)PEK;LSEAVWQPEEHYSS(0.01)S(0.99)PEK 253.13 1.09E-30 927560000 685880 777490 678030 764610 725110 827640 818370 829500 906100 1043720 TRUE FALSE 659075.0513 755316.7464 800565.1037 804071.6137 748433.8217 844375.4479 828385.4569 812370.5351 803243.3267 973027.9148 0.677344443 0.776253934 0.822756564 0.826360273 0.769180216 0.86778132 0.85134809 0.834889239 0.825509027 1 19.89212167 -5 0.027472694 2.150597791 4.97E-12 0.751059399 0.038823901 893.5707727 1.851345244 108.9175624 47.63005579 1.00E-05 5 -2.150597791 QLQPASELWSS(ph)DGAAGLVGSLQEVTIHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLQPASELWSSDGAAGLVGSLQEVTIHEK 29 0 Q9H1A4;F8WAS1 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 QLQPASELWS(0.178)S(0.822)DGAAGLVGSLQEVTIHEK;QLQPASELWS(0.032)S(0.968)DGAAGLVGSLQEVTIHEK 201.75 2.00E-25 181549000 159746 178387 144706 155155 165277 178030 176949 182817 182867 220930 TRUE FALSE 153502.9497 173299.5774 170857.5932 163162.5681 170593.2848 181629.8886 179114.5548 179041.7651 162108.7048 205966.2143 0.745282182 0.841398081 0.829541844 0.792181226 0.828258583 0.881843118 0.869630757 0.86927735 0.787064545 1 17.65204818 -5 0.145184196 1.569101519 0.777393352 0.643890681 0.039221262 86.04665393 0.753714249 14.24285289 0.214388736 1.00E-05 5 -0.791708167 VAASMPLS(ph)PGGQMEEVAGAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VAASMPLSPGGQMEEVAGAVK 21 0 A0A669KBI7;Q9UMN6 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 VAASMPLS(1)PGGQMEEVAGAVK 148.44 2.28E-09 0 42818 47868 39665 41076 42587 49715 43897 44171 55792 55234 TRUE FALSE 41144.62522 46502.85151 46833.34784 43195.93728 43956.84953 50720.27136 44434.22462 43258.85341 49458.72606 51492.95198 0.799034113 0.903091583 0.909509866 0.838870867 0.853647885 0.984994439 0.862918572 0.840092707 0.960495061 1 15.65208736 -5 0.177128894 1.487540899 0.854956599 0.371019298 0.05127689 156.2932302 1.497379673 26.69466342 0.168484191 1.00E-05 5 -0.6325843 AVEDIHGLFSLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEDIHGLFSLSK 13 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 178.15 1.48E-05 598730000 1928250 2170700 1907300 2102900 1991250 1798080 2377700 2189300 2564500 2788500 FALSE TRUE 1852891.858 2108793.761 2251991.538 2211430.921 2055300.365 1834438.41 2406799.004 2144090.19 2273388.711 2599632.411 0.712751484 0.81118921 0.866273065 0.850670622 0.790611917 0.705653 0.925822818 0.824766679 0.874503911 1 21.30987621 -5 0.147011385 1.665180636 0.758820294 0.503026316 0.060050425 117.2907401 1.034363774 22.57468978 0.323188639 1.00E-05 5 -0.906360342 LTPPVLEEMGHCDSVYLSEVGDTQVVVFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTPPVLEEMGHCDSVYLSEVGDTQVVVFK 29 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 176.68 2.94E-14 83291000 38783 40768 34221 34781 39509 44900 38531 40716 52798 51785 FALSE TRUE 37267.31748 39605.33656 40405.49594 36576.05158 40779.84287 45807.90876 39002.5539 39875.20037 46804.59239 48277.55582 0.771938779 0.820367475 0.836941623 0.757620202 0.84469568 0.94884482 0.807881701 0.825957315 0.969489685 1 15.55906502 -5 0.087458641 1.577796993 0.686786852 0.571082478 0.052353805 172.7112985 1.055436714 18.38629177 1.389977111 1.00E-05 5 -0.891010141 RQSS(ph)TPSAPELGQQPDVNISEWK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQSSTPSAPELGQQPDVNISEWK 23 1 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 RQS(0.118)S(0.829)T(0.04)PS(0.013)APELGQQPDVNISEWK;RQS(0.108)S(0.784)T(0.108)PS(0.001)APELGQQPDVNISEWK 254.16 1.00E-43 1169990000 1032380 1031450 596890 713300 828310 983270 776410 955350 887990 779720 TRUE FALSE 992033.4482 1002034.056 704761.3007 750113.4985 854953.3434 1003152.393 785911.9378 935621.6886 787189.098 726908.8699 1.36472877 1.378486489 0.969531849 1.031922335 1.176149279 1.380024972 1.081169828 1.287123775 1.082926802 1 19.47141498 -5 0.20484738 0.094973438 1.225721827 0.164501104 0.142371885 300.2882234 2.983852951 111.5555291 0.335117026 1.00E-05 5 1.130748389 DSLDWTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSLDWTR 7 0 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 108.7 0.016738 105000000 188100 184680 171180 199090 195210 167910 198990 208270 219240 235690 FALSE TRUE 180748.844 179413.1072 202116.0339 209365.0588 201489.1069 171305.2552 201425.2991 203969.1517 194352.7943 219726.5064 0.822608283 0.816529194 0.919852763 0.952843889 0.916999548 0.77962945 0.916709151 0.92828651 0.884521388 1 17.74534939 -5 0.090918446 1.3560447 0.794931779 0.3454901 0.052340254 265.2872708 1.67384341 18.46649132 1.264961411 1.00E-05 5 -0.561112921 ICDQWDALGSLTHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ICDQWDALGSLTHSR 15 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;; 190.18 2.27E-07 2570980000 1497121 1699630 1607450 2582800 1730760 1341970 2079660 1980130 2175340 2724440 FALSE TRUE 1438611.856 1651158.217 1897951.973 2716098.618 1786431.467 1369105.553 2105111.501 1939239.624 1928404.523 2539911.252 0.566402411 0.650085004 0.747251295 1.069367528 0.70334405 0.539036768 0.828813014 0.763506844 0.759240907 1 21.27634666 -5 0.190103212 2.09748292 0.694990957 0.257936088 0.138832618 213.0749387 2.085220479 88.69301396 0.394941704 1.00E-05 5 -1.402491964 TLDELGIHLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLDELGIHLTK 11 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 116.74 0.00094881 483410000 1533400 1833100 1675800 1873100 1725800 1566000 2055200 1940000 2268900 2425500 FALSE TRUE 1473473.033 1780821.783 1978654.338 1969770.915 1781311.924 1597665.593 2080352.152 1899938.322 2011343.984 2261218.725 0.651627822 0.787549547 0.875038897 0.871110297 0.787766307 0.706550665 0.920013677 0.840227573 0.889495546 1 21.10866912 -5 0.027948939 2.175162132 0.005178287 0.508966323 0.068271127 1510.336379 3.182523676 186.9898342 80.61418246 1.00E-05 5 -2.169983846 FQEYIDAHPETIVLDPLPAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 FQEYIDAHPETIVLDPLPAIR 21 0 Q13572-2;Q13572;G3V588;G3V5A3 Q13572-2 ITPK1 Inositol-tetrakisphosphate 1-kinase 0 ; 113.99 0.00018804 112134000 187994 211583 174903 194598 194712 220210 209132 198775 246540 260480 FALSE TRUE 180646.9866 205548.86 206511.8628 204641.2261 200975.0883 224662.7971 211691.42 194670.2268 218553.8128 242837.4576 0.743900832 0.846446269 0.850411896 0.84270865 0.827611565 0.925157096 0.871741214 0.801648266 0.900000416 1 17.88963145 -5 0.148672844 1.540667406 0.79589105 0.595087996 0.0422483 104.2078543 0.924482206 16.71417284 0.228635405 1.00E-05 5 -0.744776356 LFVPALDKPETDLLSHLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFVPALDKPETDLLSHLDR 19 1 V9GYV5;V9GY92;Q9UNI6 V9GYV5 DUSP12 Dual specificity protein phosphatase 12 0 ; 220.36 1.75E-19 461010000 828390 822320 694250 784990 786600 908870 858220 862220 1068330 1109040 FALSE TRUE 796015.603 798868.2387 819716.4185 825503.428 811901.7034 927247.9741 868723.1531 844414.8557 947057.6572 1033923.733 0.769897796 0.772656835 0.792820972 0.798418105 0.785262662 0.896824345 0.840219762 0.816709036 0.915984059 1 19.97969834 -5 0.088458762 1.635751246 0.653677441 0.826707649 0.029883581 87.21611318 0.538023874 10.3460914 0.760150232 1.00E-05 5 -0.982073806 LSVHDMKPLDS(ph)PGRR ddPTM_BT-474_Pertuzumab_2h_R1 10 LSVHDMKPLDSPGRR 15 2 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR 165.3 7.47E-07 5868689000 3416930 4306870 3240091 3970803 3515556 4121672 4085811 4016218 4183218 4696391 TRUE FALSE 3283392.598 4184042.284 3825647.519 4175736.619 3628637.051 4205015.032 4135814.377 3933281.695 3708356.63 4378300.254 0.749924036 0.955631647 0.873774592 0.95373464 0.828777571 0.960421805 0.944616435 0.898358145 0.846985454 1 22.06193946 -5 0.013069765 2.037250437 1.59E-15 0.226007486 0.06386974 12646.4841 12.54563163 1189.280861 801.6947554 1.00E-05 5 -2.037250437 KAPQHTAVGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPQHTAVGFK 11 1 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 79.286 0.017891 375770000 432230 452220 390850 452430 446600 480230 484590 452900 543630 608750 FALSE TRUE 415337.9737 439323.1284 461485.2894 475779.9665 460965.2946 489940.5796 490520.5574 443547.4567 481919.4015 567518.8203 0.731848811 0.774111999 0.81316297 0.838350993 0.81224671 0.863302788 0.864324741 0.781555502 0.849169022 1 19.11430871 -5 0.151587647 1.65021673 0.758394789 0.753180319 0.034149393 74.28886134 0.665698692 14.62050895 0.184659216 1.00E-05 5 -0.891821941 YESLELCR ddPTM_BT-474_Pertuzumab_2h_R1 3 YESLELCR 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 98.997 0.016579 355870000 396180 397280 482210 586330 471330 357279 613110 543400 588800 750600 FALSE TRUE 380696.8476 385949.9634 569356.0737 616590.5616 486490.7575 364503.4262 620613.4236 532178.6001 521961.8925 699761.1934 0.544038239 0.551545251 0.813643396 0.881144264 0.695223974 0.520896885 0.886893171 0.760514594 0.745914317 1 19.41650313 -5 0.041230607 2.246223176 3.30E-11 0.40474199 0.11925207 881.8966337 2.713628959 135.3539277 39.27937613 1.00E-05 5 -2.246223176 NADNDWFR ddPTM_BT-474_Pertuzumab_2h_R1 3 NADNDWFR 8 0 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ;; 112.41 0.0070868 2042620000 4112090 4348200 4101220 4321060 4412420 3859500 4634960 4761100 5272800 5424700 FALSE TRUE 3951384.977 4224193.593 4842401.685 4544070.424 4554349.497 3937541.734 4691684.027 4662781.621 4674253.849 5057280.237 0.781326087 0.835269828 0.957511045 0.89852059 0.90055312 0.778588797 0.927708928 0.921993918 0.924262376 1 22.26993029 -5 0.01807794 2.115030956 6.56E-16 0.413057809 0.052863959 4270.167879 5.849342231 448.2182373 259.8549721 1.00E-05 5 -2.115030956 ISTGMMMKETK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISTGMMMKETK 11 1 O75445;O75445-3 O75445 USH2A Usherin 0 50.04 0.04329 0 94444 110710 103570 105710 109400 113310 126530 117830 138660 170560 FALSE TRUE 90753.02407 107552.6592 122287.4029 111165.7058 112918.9504 115601.2058 128078.512 115396.7693 122919.8981 159007.8193 0.570745668 0.676398555 0.769065342 0.699121001 0.710147154 0.727015856 0.805485621 0.725730155 0.773043104 1 17.27873819 -5 0.122008442 1.919804753 0.586287889 0.804333351 0.046209331 66.70714041 0.525166527 15.10267631 0.431363457 1.00E-05 5 -1.333516864 VTGNEMLGLEEGDLEDDFDPAQHDQLMQK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTGNEMLGLEEGDLEDDFDPAQHDQLMQK 29 0 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 0 ; 180.35 1.11E-17 99182000 74420 69886 76560 74626 80252 83649 78338 71492 101689 111962 FALSE TRUE 71511.58412 67892.91971 90396.09507 78477.4568 82833.37846 85340.44009 79296.72388 70015.66522 90145.69104 104378.714 0.685116547 0.650447942 0.866039555 0.751853072 0.793584968 0.817603866 0.759702058 0.6707849 0.86364056 1 16.67146801 -5 0.295434882 2.964618789 0.743708935 0.524166223 0.06999775 215.7150828 2.012550459 261.7910236 0.07455264 1.00E-05 5 -2.220909854 TTVSMALEEYLVCHGIPCYTLDGDNIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTVSMALEEYLVCHGIPCYTLDGDNIR 27 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 140.31 2.24E-07 224310000 85790 85528 70563 88921 73846 84100 88989 86212 93242 102754 FALSE TRUE 82437.23195 83088.82518 83315.30377 93510.22347 76221.32366 85800.55962 90078.074 84431.69207 82657.55906 95794.38006 0.860564387 0.867366386 0.869730601 0.976155631 0.79567636 0.895674251 0.940327334 0.881384608 0.862864387 1 16.5476534 -5 0.35344547 2.350592623 0.881619382 0.36313136 0.046077758 489.8423475 3.974273796 502.1800651 0.033337257 1.00E-05 5 -1.468973241 LLPQLTYLDGYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPQLTYLDGYDR 13 0 Q92688;Q92688-2;P39687;H0YN26 Q92688;P39687 ANP32B;ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member B;Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 110.08 0.0025287 441260000 145142 184946 184170 165260 174646 185867 181774 204015 212429 254570 FALSE TRUE 139469.6902 179671.5212 217453.6158 173789.0884 180263.6472 189625.3581 183998.6046 199802.019 188314.9505 237327.7472 0.587667021 0.757060745 0.916258712 0.732274631 0.759555717 0.799002057 0.775293268 0.841882255 0.793480546 1 17.85652126 -5 0.113667803 1.700582306 0.66134575 0.511917072 0.072917244 141.5157669 1.060537941 23.04718613 0.830836272 1.00E-05 5 -1.039236556 ADLNQGIGEPQS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 ADLNQGIGEPQSPSR 15 0 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 ADLNQGIGEPQS(0.989)PS(0.011)R;ADLNQGIGEPQS(0.999)PS(0.001)R;ADLNQGIGEPQS(0.861)PS(0.139)R;ADLNQGIGEPQS(0.999)PS(0.001)R 260.58 5.38E-17 1648240000 1130990 1192677 1067443 1257297 1142243 1257290 1232495 1340855 1366996 1584533 TRUE FALSE 1086789.66 1158663.02 1260353.695 1322186.249 1178984.283 1282713.265 1247578.642 1313165.876 1211820.345 1477211.169 0.735703658 0.784358421 0.853198055 0.895055681 0.798114927 0.868334394 0.844549966 0.888949328 0.820343341 1 20.49444464 -5 0.054047313 1.582266549 0.559741531 0.634554623 0.041599735 322.8857011 1.28487736 26.62475201 5.293224693 1.00E-05 5 -1.022525018 YAETFLEPWFK ddPTM_BT-474_Pertuzumab_2h_R1 2 YAETFLEPWFK 11 0 Q9NXG2 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 0 ; 187.64 2.85E-05 79894000 369590 375640 299240 351160 377100 360010 358940 398550 400380 442630 FALSE TRUE 355146.0142 364927.115 353319.3246 369283.4097 389229.764 367289.6489 363332.8151 390319.8032 354930.5409 412650.2758 0.860646497 0.884349621 0.856219771 0.894906489 0.943243678 0.89007489 0.880486059 0.945885235 0.860124327 1 18.65456008 -5 0.14209328 1.357591485 0.857656068 0.544545759 0.029996384 103.6845729 0.897424326 10.55292983 0.172924724 1.00E-05 5 -0.499935417 SWHDIDKDNAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SWHDIDKDNAK 11 1 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ; 161.99 1.54E-05 426620000 798090 1015910 794230 824900 924410 1042520 990910 785020 1215400 1197460 FALSE TRUE 766899.7605 986937.2415 937765.0286 867473.1879 954144.4872 1063600.469 1003037.053 768809.0627 1077432.887 1116354.968 0.686967661 0.884071169 0.840024057 0.777058564 0.854696324 0.952743974 0.898492936 0.688677961 0.965134674 1 20.0903644 -5 0.184671254 1.68661521 0.800964828 0.277746669 0.088172996 203.123601 1.972086869 51.35009087 0.264536662 1.00E-05 5 -0.885650382 WDSNVIETFDIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 WDSNVIETFDIAR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 212.9 2.38E-08 719780000 470120 520440 460590 557700 516320 437610 581720 549090 590040 694760 FALSE TRUE 451747.1907 505597.5608 543828.8588 586482.9638 532927.9017 446458.774 588839.2634 537751.0996 523061.1328 647703.2864 0.697460087 0.78060058 0.839626524 0.905480914 0.822796353 0.689295212 0.909118845 0.830242969 0.807562882 1 19.30497354 -5 0.172741855 1.725834552 0.771421986 0.430103174 0.068059035 135.5889639 1.287382532 33.80101649 0.240170629 1.00E-05 5 -0.954412566 TAQEHDKR ddPTM_BT-474_Pertuzumab_2h_R1 4 TAQEHDKR 8 1 A0A087WY55;Q9NP79 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 ;;; 150.35 0.00031845 283898000 301258 287235 295008 302668 281643 251088 365193 322847 345539 414592 FALSE TRUE 289484.5043 279043.339 348322.508 318288.7318 290702.3029 256165.1714 369662.3412 316180.0966 306314.8613 386511.3146 0.748967736 0.721953869 0.901196148 0.823491369 0.752118481 0.662762413 0.956407555 0.818035811 0.792512017 1 18.56015112 -5 0.183665327 1.840290932 0.76093241 0.378227802 0.079758387 147.5641268 1.430353341 45.13222845 0.238876496 1.00E-05 5 -1.079358521 DYVFYLAVGNYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYVFYLAVGNYR 12 0 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 ; 125.48 0.0007084 249050000 356210 401010 327040 414120 356570 356940 417030 376000 449160 470290 FALSE TRUE 342288.9194 389573.5874 386143.403 435492.7828 368039.3979 364157.5714 422133.7379 368235.4686 398173.2398 438436.8394 0.780702917 0.888551217 0.880727549 0.993285107 0.839435387 0.8305816 0.962815393 0.839882591 0.908165565 1 18.7420095 -5 0.256086489 1.741228361 0.871732362 0.280096536 0.059377582 260.3508706 2.567898897 101.378603 0.079309584 1.00E-05 5 -0.869495999 KMTGT(ph)LET(ph)QFT(ph)CPFCNHEKSCDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KMTGTLETQFTCPFCNHEKSCDVK 24 2 K7EN05;K7EPC8;A0A024R7E8;K7EQ44;K7EMV4;P60002 K7EN05 ELOF1 Transcription elongation factor 1 homolog 3 KMT(0.668)GT(0.752)LET(0.756)QFT(0.702)CPFCNHEKS(0.121)CDVK 44.365 0.067217 301220000 37785 47024 42016 57786 41767 59301 63299 39070 65771 96902 TRUE FALSE 36308.32043 45682.92156 49609.22584 60768.34239 43110.47349 60500.10685 64073.6721 38263.19085 58304.95181 90338.74123 0.401913066 0.505684726 0.549146747 0.672672007 0.477209145 0.669702788 0.709260183 0.423552402 0.645403633 1 16.46305719 -5 0.262707899 3.876799581 0.524761002 0.645879776 0.099713229 128.9443054 1.263305889 200.5899407 0.132205633 1.00E-05 5 -3.352038579 S(ph)PHSPS(ph)PIATPPSQSSSCSDAPMLSTVHSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPHSPSPIATPPSQSSSCSDAPMLSTVHSAK 31 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 S(0.67)PHS(0.363)PS(0.922)PIAT(0.042)PPS(0.002)QSSSCSDAPMLSTVHSAK 203.58 4.30E-26 389030000 84918 103820 89226 104970 121170 121520 112510 100830 133890 155640 TRUE FALSE 81599.31068 100859.1553 105351.123 110387.5143 125067.5431 123977.2177 113886.931 98747.82526 118691.3685 145098.3642 0.562372368 0.695108838 0.726066924 0.760777111 0.861950056 0.854435668 0.784894659 0.680557812 0.818006248 1 17.14667173 -5 0.034516751 2.162859667 7.26E-14 0.596190537 0.072327678 986.9527136 2.556730672 133.2920544 47.22772118 1.00E-05 5 -2.162859667 YDVDTLDMVFLDHWK ddPTM_BT-474_Pertuzumab_2h_R1 5 YDVDTLDMVFLDHWK 15 0 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;;;; 290.34 6.80E-44 2030181000 2334889 2163455 2268660 2495681 2454418 2068799 2582125 2455452 3036645 3319006 FALSE TRUE 2243638.957 2101755.382 2678657.328 2624483.395 2533366.584 2110631.533 2613725.818 2404746.058 2691937.79 3094206.767 0.725109576 0.679254988 0.865700818 0.848192636 0.818745085 0.682123624 0.844715953 0.777176911 0.869992858 1 21.56113818 -5 0.175197952 1.860801895 0.740979124 0.527648638 0.064200878 111.1224474 1.060533604 33.1140555 0.220181262 1.00E-05 5 -1.119822771 DGLGFCALIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLGFCALIHR 11 0 P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4;G3V2X9 P12814-3 ACTN1 Alpha-actinin-1 0 ; 113.69 0.0013583 1026410000 1222880 1431660 1116280 1631600 1233510 992630 1616190 1423880 1496650 1648210 FALSE TRUE 1175088.498 1390830.459 1318016.628 1715807.072 1273186.969 1012701.659 1635969.417 1394476.38 1326756.566 1536575.269 0.764745159 0.90514958 0.857762489 1.116643686 0.828587441 0.65906414 1.064685506 0.907522338 0.863450424 1 20.55128701 -5 0.111812934 1.32962519 0.834079184 0.074877456 0.124889325 516.9789634 3.828623736 39.42295307 1.496955992 1.00E-05 5 -0.495546005 EEQTPQNK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEQTPQNK 8 0 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8;F5GXC7;F5H8H6;F5GXU1;F5GWW2 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 129.77 0.0025041 840820000 810160 793290 649380 745820 667000 754900 733900 751560 785310 671190 FALSE TRUE 778498.0515 770666.1459 766737.4114 784311.8596 688454.6608 770164.5952 742881.6877 736040.0234 696164.9011 625729.7035 1.244144312 1.231627876 1.225349232 1.253435557 1.100242896 1.230826331 1.187224585 1.176290688 1.112564894 1 19.25518007 -5 0.12257789 0.312657197 1.295015559 0.747981116 0.03889905 72.02040029 0.568776416 12.07642639 0.339504123 1.00E-05 5 0.982358362 VLEFNCR ddPTM_BT-474_Pertuzumab_2h_R1 3 VLEFNCR 7 0 P22102;P22102-2;F8WD69 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;; 140.98 0.0085261 411710000 349040 392410 330910 391590 349992 338337 373890 418060 408500 435840 FALSE TRUE 335399.1309 381218.851 390712.7981 411800.0068 361249.8105 345178.406 378465.7777 409426.9149 362128.7926 406320.1686 0.825455286 0.938222812 0.961588492 1.013486503 0.889076739 0.84952319 0.931447186 1.007646055 0.891240014 1 18.63225745 -5 0.009892557 2.045789807 2.05E-11 0.142794626 0.058221195 29318.16381 22.03340553 2643.004946 1960.791663 1.00E-05 5 -2.045789807 LLPEVHEDGS(ph)PNLAPIPVTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLPEVHEDGSPNLAPIPVTVK 21 0 O95644-6;O95644;F5H4S8 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 1 LLPEVHEDGS(1)PNLAPIPVTVK 74.222 0.002531 0 52458 47860 42981 49624 46984 54341 58405 47878 58583 67201 TRUE FALSE 50407.88336 46495.07966 50748.62281 52185.10059 48495.28303 55439.81225 59119.77786 46889.30257 51932.90344 62649.41641 0.8046026 0.742147051 0.810041429 0.832970259 0.774073979 0.884921447 0.943660472 0.748439575 0.828944728 1 15.93501345 -5 0.186458329 1.750897211 0.782871651 0.494681053 0.056377402 122.3519192 1.191176703 34.24760495 0.168162687 1.00E-05 5 -0.968025561 ELDQDMVTEDEDDPGSHKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDQDMVTEDEDDPGSHKR 19 1 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 51.611 0.08706 129710000 95408 92165 92356 100380 95510 110850 120690 101540 137780 153920 FALSE TRUE 91679.34988 89536.54444 109046.7836 105560.6238 98582.16589 113091.4629 122167.0403 99443.16352 122139.792 143494.8613 0.638903366 0.623970389 0.759935113 0.735640446 0.687008336 0.788122041 0.851368747 0.693008534 0.851178857 1 17.13063955 -5 0.077429028 1.905185697 0.447413975 0.750950457 0.054335666 136.6717568 0.753071917 21.27784144 2.144131463 1.00E-05 5 -1.457771722 PNS(ph)SPSPSPGQASETPHPRPS ddPTM_BT-474_Pertuzumab_2h_R1 1 PNSSPSPSPGQASETPHPRPS 21 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 PNS(0.43)S(0.254)PS(0.314)PS(0.003)PGQASETPHPRPS 189.12 1.38E-17 202550000 76514 62174 75657 78888 72973 68728 93220 93327 102290 127670 TRUE FALSE 73523.74829 60400.85839 89329.90288 82959.41913 75320.24282 70117.72725 94360.85425 91399.76484 90678.46803 119022.7972 0.617728284 0.50747302 0.750527672 0.697004449 0.632821985 0.589111741 0.792796477 0.767918138 0.761857982 1 16.8608784 -5 0.093329292 2.111009865 0.417554549 0.721078091 0.068633071 106.0440773 0.68347086 22.86183852 1.462294936 1.00E-05 5 -1.693455316 FKNELER ddPTM_BT-474_Pertuzumab_2h_R1 4 FKNELER 7 1 P41091;Q2VIR3;Q2VIR3-2;H7BZU1 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ;;; 131.06 0.0031944 2293930000 2769890 2557210 2351450 2475980 2703000 2500590 2782890 2826020 2908900 3231240 FALSE TRUE 2661639.637 2484280.875 2776409.323 2603765.625 2789944.45 2551153.643 2816947.84 2767661.699 2578693.867 3012385.237 0.88356549 0.824688969 0.921664762 0.864353467 0.926157922 0.846888244 0.935122044 0.918760876 0.856030575 1 21.52247485 -5 0.166079209 1.418319885 0.86130422 0.460165239 0.036481605 111.8172073 1.045295055 15.45171334 0.131504842 1.00E-05 5 -0.557015665 EEEMMIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEEMMIR 7 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 128.86 0.0086462 974630000 1345790 1392080 1124430 1320410 1361840 1226350 1416240 1383110 1510880 1571340 FALSE TRUE 1293195.039 1352379.241 1327639.514 1388556.518 1405644.82 1251147.637 1433572.369 1354548.295 1339371.237 1464911.742 0.882780171 0.923181378 0.906293175 0.947877253 0.959542326 0.854077144 0.978606647 0.92466205 0.914301659 1 20.48238232 -5 0.185799123 1.317824056 0.908501756 0.33166007 0.034027768 158.4151449 1.540731357 18.66072702 0.09326418 1.00E-05 5 -0.4093223 RDQALTEEHAR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDQALTEEHAR 11 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H0YJ11 P12814-3 ACTN1 Alpha-actinin-1 0 ;;; 199.15 3.33E-08 2997660000 1479258 1556888 1517327 2204008 1652744 1387361 1800136 1690321 2129385 2351491 FALSE TRUE 1421446.962 1512487.079 1791541.742 2317757.117 1705906.012 1415414.39 1822166.603 1655415.281 1887666.142 2192222.42 0.648404536 0.689933222 0.817226266 1.057263668 0.778162834 0.64565273 0.831196044 0.755131079 0.861074189 1 21.06396275 -5 0.241591318 2.224580606 0.766536427 0.258022846 0.112932031 270.0882532 2.691990682 162.5830535 0.185461681 1.00E-05 5 -1.458044179 SASNKS(ph)PLVLEANR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASNKSPLVLEANR 14 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.001)AS(0.005)NKS(0.995)PLVLEANR 108.75 0.00048889 587600000 250970 273840 246780 262600 259410 274660 275200 291200 311780 353690 TRUE FALSE 241161.8149 266030.3513 291378.6356 276152.8175 267754.1582 280213.8134 278567.9799 285186.6182 276388.0415 329734.2613 0.731382338 0.806802273 0.88367716 0.837501133 0.81203014 0.849817099 0.844825706 0.864898349 0.838214508 1 18.33094427 -5 0.143321024 1.576009138 0.776130894 0.709854477 0.034683792 77.99283343 0.678317679 12.83602363 0.203356401 1.00E-05 5 -0.799878245 NDLQDTEIS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDLQDTEISPR 11 0 Q9NS91 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 NDLQDTEIS(1)PR;NDLQDTEIS(1)PR 156.24 3.27E-05 1021060000 1921080 1862120 1590020 1853230 1880550 1751290 1928040 1993170 2072960 2237250 TRUE FALSE 1846002.07 1809014.161 1877371.984 1948875.422 1941039.599 1786702.284 1951635.93 1952010.343 1837646.271 2085719.065 0.885067458 0.867333569 0.900107793 0.934390185 0.930633292 0.856636118 0.935713713 0.935893225 0.881061262 1 20.99211342 -5 0.159860336 1.345251156 0.880076173 0.507372358 0.028601113 111.5052156 1.025141669 12.24812115 0.123435784 1.00E-05 5 -0.465174984 KLYGDADYLEER ddPTM_BT-474_Pertuzumab_2h_R1 4 KLYGDADYLEER 12 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;; 184.21 2.34E-05 1463180000 1472560 1537880 1230960 1332630 1429850 1459640 1522710 1522150 1702630 1847380 FALSE TRUE 1415010.727 1494021.168 1453421.855 1401407.194 1475842.424 1489154.921 1541345.38 1490717.071 1509354.58 1722255.307 0.821603348 0.867479497 0.843906155 0.813704674 0.8569243 0.864653989 0.894957544 0.865561026 0.876382598 1 20.71586759 -5 0.174553637 1.584374064 0.823854127 0.865847604 0.017935492 45.22365805 0.431035967 9.107993377 0.061623724 1.00E-05 5 -0.760519937 VHIEFTEGEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHIEFTEGEDK 11 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 143.24 3.73E-05 145390000 237510 207990 223560 249370 260850 236960 293380 224590 339020 374480 FALSE TRUE 228227.8466 202058.3288 263962.2651 262240.0156 269240.4771 241751.4936 296970.4722 219952.138 300535.8709 349116.136 0.653730444 0.578771096 0.756087267 0.751154096 0.771206053 0.692467258 0.850635194 0.6300257 0.860847838 1 18.41334751 -5 0.130675952 1.933787553 0.60557547 0.599965088 0.075234116 103.1043655 0.848861548 25.19333198 0.565689241 1.00E-05 5 -1.328212083 SPGETSKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGETSKPR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 111.06 0.0019936 149287000 191979 194880 164165 203440 189428 186263 207804 200662 226790 254250 FALSE TRUE 184476.2484 189322.2132 193833.2673 213939.5628 195521.1237 190029.3655 210347.1675 196518.2596 201045.75 237029.421 0.778284179 0.79872875 0.817760371 0.902586531 0.824881244 0.801712145 0.887430626 0.829088046 0.84818901 1 17.85470662 -5 0.194666476 1.733181929 0.804269836 0.698660355 0.034223524 79.68652637 0.784281333 22.68600931 0.089404568 1.00E-05 5 -0.928912094 AVDPDGDGHVSWDEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVDPDGDGHVSWDEYK 16 0 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;G3V1E2;Q9BRK5-4;Q9BRK5-3;H0Y3T6;Q9BRK5-2 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 ; 222.27 9.80E-15 713690000 985390 1313570 1124000 1375160 1182610 1130290 1478800 1382640 1590480 1844850 FALSE TRUE 946879.8694 1276108.27 1327131.803 1446132.172 1220649.725 1153145.238 1496897.997 1354088.001 1409935.378 1719896.666 0.550544627 0.741967988 0.771634616 0.840825034 0.709722711 0.670473559 0.870341821 0.787307765 0.819779122 1 20.71389046 -5 0.05028142 1.990108815 0.264851214 0.601558183 0.072757348 404.299101 1.503277264 53.62272539 11.90882329 1.00E-05 5 -1.725257601 QTEPVS(ph)PVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTEPVSPVLK 10 0 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 QTEPVS(1)PVLK 88.163 0.012298 0 159130 142570 137670 155370 160390 146690 141520 184340 175950 190710 TRUE FALSE 152911.0237 138504.0432 162550.0315 163388.6643 165549.09 149656.1723 143251.9641 180533.3146 155976.8936 177793.0418 0.860050664 0.779018356 0.914265428 0.918982333 0.931133684 0.841743697 0.805723118 1.015412711 0.877294702 1 17.43983934 -5 0.018169158 2.124434558 6.40E-10 0.293324702 0.06152506 4771.749422 6.569245195 503.7572846 291.2557118 1.00E-05 5 -2.124434558 VLTGVAGEDAECHAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLTGVAGEDAECHAAK 16 0 O95373 O95373 IPO7 Importin-7 0 ; 211.7 6.41E-12 1161780000 752620 683460 691220 713940 755130 819020 814480 757580 939180 1011060 FALSE TRUE 723206.7783 663968.39 816138.8301 750786.529 779419.4422 835581.1456 824447.8499 741935.7083 832568.2238 942580.0056 0.767263016 0.70441595 0.865856294 0.796522868 0.826900038 0.886482994 0.874671481 0.787132873 0.883286531 1 19.84625555 -5 0.061421855 1.62976078 0.555605166 0.648478892 0.045936702 261.009667 1.169290593 24.77737368 3.969833834 1.00E-05 5 -1.074155614 S(ph)RSPATAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.618)RS(0.382)PATAK;S(0.536)RS(0.464)PATAK 65.5 0.038825 1294850000 1269790 1182250 963460 1112510 1166540 1116790 1282520 1168820 1355400 1463140 TRUE FALSE 1220165.203 1148533.388 1137578.654 1169926.774 1204062.819 1139372.259 1298215.863 1144683.459 1201540.674 1364040.225 0.894522889 0.842008444 0.833977352 0.857692283 0.88271797 0.835292273 0.951743094 0.839185999 0.880868946 1 20.37945476 -5 0.254328841 1.830621549 0.85572947 0.577619888 0.034055003 126.6572764 1.251228797 54.76838246 0.044844455 1.00E-05 5 -0.974892079 SAVGHEYQSK ddPTM_BT-474_Pertuzumab_2h_R1 6 SAVGHEYQSK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 211.64 5.51E-08 6254220000 9276100 9946700 8069110 9536000 9059200 9061300 9700500 9947500 10668500 10934600 FALSE TRUE 8913579.757 9663029.855 9527377.673 10028154.1 9350597.395 9244525.694 9819217.621 9742080.649 9457456.606 10193989.8 0.874395593 0.947914413 0.934607338 0.983732012 0.91726572 0.906860402 0.963235967 0.95566906 0.92774829 1 23.28121548 -5 0.11636886 1.194609618 0.905902387 0.346063743 0.028528395 193.0773837 1.471271511 8.967861605 0.299765624 1.00E-05 5 -0.28870723 VGQGYPHDPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGQGYPHDPPK 11 0 P61081;M0QYI6 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 91.313 0.010834 562910000 1254500 1255700 1026900 1111900 1165900 1309300 1184300 1286400 1402800 1514100 FALSE TRUE 1205472.753 1219888.665 1212483.673 1169285.292 1203402.232 1335774.943 1198793.818 1259835.39 1243560.025 1411548.658 0.854007225 0.864220059 0.858974054 0.828370517 0.852540382 0.946318737 0.849275589 0.892519987 0.880989839 1 20.42884743 -5 0.182301358 1.54676173 0.843074951 0.674275081 0.028313953 78.07964982 0.755117518 15.41441622 0.084633982 1.00E-05 5 -0.703686779 QQETHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 QQETHLK 7 0 P40222 P40222 TXLNA Alpha-taxilin 0 ; 86.011 0.037808 434040000 259170 236582 205467 246560 234387 257670 249101 258780 279330 297600 FALSE TRUE 249041.3499 229834.913 242599.4575 259284.9911 241926.2707 262880.2639 252149.5726 253436.1026 247621.6294 277443.2869 0.897629756 0.828403223 0.874410984 0.934551324 0.87198459 0.94750991 0.908832848 0.91346994 0.8925126 1 18.08183337 -5 0.090911688 1.319161872 0.815877065 0.543897332 0.030094995 157.1434768 0.991444515 9.810614523 0.672159954 1.00E-05 5 -0.503284807 GDIFLVR ddPTM_BT-474_Pertuzumab_2h_R1 6 GDIFLVR 7 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 158.38 0.0033101 1354960000 1500790 1691290 1322700 1935900 1485730 1504170 1708170 1794340 1897460 2085620 FALSE TRUE 1442137.468 1643056.065 1561741.313 2035812.031 1533519.855 1534585.348 1729075.095 1757286.252 1682068.296 1944359.1 0.741703252 0.845037352 0.803216501 1.047035001 0.788701971 0.789249963 0.889277652 0.903786884 0.865101666 1 20.89086326 -5 0.074918096 1.459694695 0.703209397 0.28871222 0.077471319 389.8580746 2.087306007 30.60089056 3.314875452 1.00E-05 5 -0.756485298 SNSQSDS(ph)HDEEVS(ph)PTPPNPVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSQSDSHDEEVSPTPPNPVVK 22 0 P31321;C9JSK5;C9J4C2;C9IZL8;C9JR00 P31321 PRKAR1B cAMP-dependent protein kinase type I-beta regulatory subunit 2 S(0.216)NS(0.244)QS(0.245)DS(0.37)HDEEVS(0.837)PT(0.088)PPNPVVK 67.364 0.0033411 0 160030 181160 176440 165250 166620 192610 195730 184520 217420 253270 TRUE FALSE 153775.8507 175993.4942 208326.6329 173778.5723 171979.4836 196504.7062 198125.4023 180709.5975 192739.3931 236115.7973 0.65127303 0.745369417 0.882307051 0.735988758 0.728369239 0.832238708 0.839102697 0.765343105 0.816291817 1 17.84913504 -5 0.161077012 1.82389754 0.719860415 0.601768375 0.058228572 96.67058041 0.891813005 25.44923039 0.248122222 1.00E-05 5 -1.104037126 MDEISDHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 MDEISDHAK 9 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 166.07 6.10E-05 574700000 929670 1073410 956890 1127590 1039110 1020640 1171250 1110990 1355140 1521950 FALSE TRUE 893337.4686 1042797.398 1129821.309 1185785.055 1072533.917 1041278.04 1185584.108 1088047.668 1201310.188 1418866.971 0.629613267 0.734950788 0.79628417 0.835726731 0.755908721 0.733879963 0.835585106 0.766842622 0.846668654 1 20.4363079 -5 0.122254655 1.752817588 0.663026628 0.707457685 0.049864826 89.581518 0.706208703 16.61318028 0.471265356 1.00E-05 5 -1.08979096 EELGDEWLKPELFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EELGDEWLKPELFR 14 1 G3V158;E9PPM8;Q9Y315 G3V158 DERA Deoxyribose-phosphate aldolase 0 ; 167.88 3.26E-06 157790000 364520 347460 321790 339470 378140 372770 379510 377030 429490 467410 FALSE TRUE 350274.1554 337550.781 379944.6112 356990.0874 390303.2165 380307.6648 384154.5569 369244.1987 380736.0958 435751.9044 0.803838496 0.77463983 0.871928745 0.81925078 0.895700541 0.872761911 0.881590082 0.847372542 0.87374511 1 18.73314744 -5 0.092201228 1.464957899 0.733504652 0.738117715 0.029808167 110.5264422 0.705378783 10.1686234 0.671596497 1.00E-05 5 -0.731453247 EGGFLLLHTLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGGFLLLHTLLR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 227.81 1.21E-11 11066200000 3383200 3740400 3752500 4127200 3770700 2855800 4970200 3872000 4570600 5197700 FALSE TRUE 3250980.804 3633727.454 4430660.224 4340205.287 3891987.99 2913546.233 5031026.794 3792041.847 4051764.65 4845655.149 0.670906349 0.749893945 0.914357313 0.895690088 0.803191286 0.601269827 1.038255229 0.782565356 0.836164466 1 22.20826031 -5 0.116606039 1.586013559 0.720168485 0.226179382 0.114946971 258.9855775 1.97632549 36.15849976 1.200676614 1.00E-05 5 -0.865845073 GDDSRPGPWRPLVKPGGWR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDDSRPGPWRPLVKPGGWR 19 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 91.317 0.00091812 1196320000 831460 914250 924310 1043620 889240 877460 1047190 987340 1122340 1352930 FALSE TRUE 798965.624 888176.4851 1091353.378 1097481.353 917843.2122 895202.8424 1060005.824 966951.084 994936.6684 1261294.846 0.633448734 0.70417832 0.865264281 0.870122761 0.72769917 0.709749069 0.840410811 0.76663366 0.78882164 1 20.26647414 -5 0.217532823 2.14085049 0.740821228 0.508316905 0.07063162 136.3721691 1.363654051 68.13423314 0.146223146 1.00E-05 5 -1.400029262 STPSHGSVSSLNSTGSLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 STPSHGSVSSLNSTGSLSPK 20 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGS(0.003)LS(0.997)PK;STPSHGSVSSLNST(0.001)GS(0.018)LS(0.981)PK;STPSHGSVSSLNST(0.001)GS(0.005)LS(0.994)PK 402.82 3.43E-151 1967390000 632989 802630 677000 807080 635500 855230 772530 767170 892090 1065560 TRUE FALSE 608251.0901 779739.7783 799348.9598 848733.4955 655941.4346 872523.3366 781984.4532 751327.6714 790823.6831 993388.6721 0.612299201 0.784929203 0.80466889 0.854382096 0.66030694 0.878330266 0.787188817 0.756328004 0.796086875 1 19.92199877 -5 0.224880584 2.173226084 0.746132962 0.478714184 0.074245336 138.3754529 1.385096291 73.78943927 0.130457649 1.00E-05 5 -1.427093121 ALCELESGIPAAESQIVYAERPLTDNHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALCELESGIPAAESQIVYAERPLTDNHR 28 1 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 0 ; 133.62 9.42E-06 146490000 54839 76871 59151 75908 75347 69630 75546 66868 75607 90795 FALSE TRUE 52695.83125 74678.71434 69840.90151 79825.62098 77770.60468 71037.96631 76470.55455 65487.15243 67024.41033 84645.37378 0.622548273 0.882253938 0.825100043 0.943059466 0.918781514 0.83924216 0.903422729 0.773664874 0.791826031 1 16.3691436 -5 0.016387489 1.978028454 7.96E-09 0.220243286 0.088948989 10088.61311 12.53530236 966.5566434 589.6013857 1.00E-05 5 -1.978028446 KKQDPPVTHDLR ddPTM_BT-474_Pertuzumab_2h_R1 5 KKQDPPVTHDLR 12 2 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;;; 174.73 1.78E-05 5519660000 2778631 2652904 2108899 2091999 2469457 2554989 2348508 2630497 2680344 2339395 FALSE TRUE 2670039.029 2577245.775 2490023.962 2199967.319 2548889.327 2606652.628 2377249.743 2576176.318 2376082.586 2180945.693 1.224257457 1.181710202 1.141717545 1.008721733 1.168708297 1.195193735 1.090008683 1.181219838 1.089473522 1 21.05652242 -5 0.216340625 0.290193047 1.16191421 0.370715148 0.058767582 175.0035877 1.749349886 54.02929117 0.119664829 1.00E-05 5 0.871721163 IHNAENIQPGEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 IHNAENIQPGEQK 13 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;; 167.89 3.11E-05 1471580000 2137300 2042590 2113670 2174830 2187790 2272330 2604110 1797450 3402170 3245240 FALSE TRUE 2053771.953 1984337.333 2495657.187 2287073.237 2258162.252 2318278.069 2635979.877 1760332.029 3015969.925 3025437.004 0.67883481 0.655884532 0.824891473 0.755948061 0.746392091 0.766262218 0.871272439 0.581843888 0.996870839 1 21.52871211 -5 0.162297803 1.966569893 0.684976153 0.395286306 0.101976454 140.5750487 1.301208078 43.37973629 0.409126647 1.00E-05 5 -1.28159374 LSQYLDSSQVKPLFQFFVPDALNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSQYLDSSQVKPLFQFFVPDALNDR 25 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 184.59 1.69E-17 575730000 216567 252057 270912 260287 247999 275847 268680 278440 291860 341390 FALSE TRUE 208103.3222 244868.5811 319871.8248 273720.4433 255976.1131 281424.8153 271968.1862 272690.1167 258729.2764 318267.3512 0.653863242 0.769380146 1.005041276 0.860033058 0.80428015 0.884240291 0.854527444 0.856795759 0.812930624 1 18.27987964 -5 0.020738189 2.071207996 4.26E-19 0.303324874 0.081913071 4512.379691 7.082624785 481.8019947 257.8563845 1.00E-05 5 -2.071207996 CNDS(ph)LRHSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 CNDSLRHSPK 10 1 A6NHR9;A0A2R8YCU7;J3KTK7 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 1 CNDS(0.618)LRHS(0.382)PK 51.218 0.095714 130990000 57105 58331 46899 63179 53683 65441 58827 60762 70035 75640 TRUE FALSE 54873.27347 56667.45699 55374.69256 66439.67576 55409.76245 66764.26186 59546.94242 59507.24347 62084.92041 70516.83543 0.77815848 0.803601816 0.78526911 0.942181755 0.785766436 0.946784714 0.84443583 0.843872858 0.880426923 1 16.10568011 -5 0.066884898 1.504726213 0.651267889 0.499444053 0.052834704 289.8254599 1.402929507 23.3528441 3.191631971 1.00E-05 5 -0.853458325 REPFLLSGGDDGALK ddPTM_BT-474_Pertuzumab_2h_R1 1 REPFLLSGGDDGALK 15 1 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 125.98 0.00013974 765000000 382300 366780 309100 357870 358370 392950 375850 378070 435120 466790 FALSE TRUE 367359.2933 356319.7935 364961.2459 376339.7136 369897.2965 400895.7182 380449.7647 370262.7224 385727.0018 435173.8975 0.844166655 0.818798636 0.838656105 0.864803049 0.849998813 0.921231077 0.874247667 0.850838537 0.886374399 1 18.7312325 -5 0.16211961 1.525797025 0.822778197 0.79150679 0.022663325 62.70970184 0.580179713 10.60018957 0.100458937 1.00E-05 5 -0.703018828 VSILESLDKWER ddPTM_BT-474_Pertuzumab_2h_R1 2 VSILESLDKWER 12 1 P10644;P10644-2;K7EPB2;K7EM13 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ; 179.59 1.87E-05 1557530000 1085480 1134610 988310 1022180 1089390 923010 1190100 1177980 1194390 1313980 FALSE TRUE 1043058.242 1102252.034 1166919.602 1074934.832 1124431.219 941673.8946 1204664.8 1153654.301 1058807.854 1224982.964 0.851487957 0.899810092 0.952600678 0.877510026 0.917915801 0.768724074 0.983413513 0.94177171 0.864344963 1 20.22433026 -5 0.202791513 1.467141631 0.884215316 0.223302712 0.057671836 221.6394564 2.198839583 41.86504879 0.132836089 1.00E-05 5 -0.582926315 RPGHPAQPLPLPQTASS(ph)PQPQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPGHPAQPLPLPQTASSPQPQQK 23 1 O60346 O60346 PHLPP1 PH domain leucine-rich repeat-containing protein phosphatase 1 1 RPGHPAQPLPLPQTAS(0.254)S(0.746)PQPQQK 106.88 0.00065877 83410000 81934 75735 100850 88262 80030 98411 89324 94646 106850 124030 TRUE FALSE 78731.9287 73575.11195 119075.8384 92817.2124 82604.23763 100400.9378 90417.17383 92691.52703 94720.83595 115629.3376 0.680899245 0.636301422 1.029806456 0.802713345 0.714388228 0.868299862 0.781957033 0.801626377 0.819176499 1 16.81914796 -5 0.185160465 1.847212386 0.755062999 0.291481012 0.101240795 186.4509539 1.811611023 58.33189691 0.296580333 1.00E-05 5 -1.092149387 YLFLGDYVDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YLFLGDYVDR 10 0 P16298-3;P16298;P16298-4;G3V111;Q5F2F8;P48454-2;P48454;P16298-2;P48454-3;H0YB02;Q08209-3;Q08209-2;Q08209;E7ETC2;Q08209-5;E9PPC8;E9PK68 P16298-3;Q08209-3 PPP3CB;PPP3CC;PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform;Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform;Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 0 ;; 101.64 0.0074248 599125000 355440 416563 386415 412797 404559 347766 465796 435960 459495 536512 FALSE TRUE 341549.0118 404683.0311 456248.7863 434101.5026 417572.0076 354798.0668 471496.5508 426957.2737 407335.054 500173.5644 0.682860983 0.809085205 0.912180928 0.867901732 0.834854213 0.709349898 0.942665875 0.853618232 0.814387411 1 18.93206928 -5 0.130158917 1.544160571 0.762768508 0.354927359 0.074327309 174.7184734 1.434874676 24.99801041 0.569397235 1.00E-05 5 -0.781392063 SWPEGHFATITLTFIDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SWPEGHFATITLTFIDK 17 0 O95433;G3V438 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ; 226.75 1.97E-15 358510000 721110 730930 679990 727350 778970 663470 852280 761660 1025270 1032050 FALSE TRUE 692928.224 710084.5921 802879.3193 764888.6207 804026.2775 676885.818 862710.4576 745931.4548 908885.6479 962148.3342 0.720188561 0.738019874 0.834465218 0.794979935 0.835657298 0.703515034 0.89665016 0.77527698 0.944641918 1 19.87589981 -5 0.100990446 1.694727059 0.657426081 0.595597791 0.059299876 123.8333696 0.849572281 17.72239237 0.912450415 1.00E-05 5 -1.037300977 DDYPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DDYPSR 6 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 153.26 0.023621 2522250000 1355346 1200000 1077194 1192360 1169083 1066610 1184749 1340296 1274747 1129349 FALSE TRUE 1302377.58 1165777.175 1271866.918 1253897.842 1206687.616 1088177.585 1199248.313 1312618.419 1130043.065 1052857.186 1.23699358 1.107251002 1.208014662 1.190947698 1.146107594 1.033547189 1.13904177 1.246720292 1.073310872 1 20.00587833 -5 0.241744025 0.093234058 1.173120685 0.369063794 0.063781243 202.6825264 2.019991795 90.44324197 0.102759353 1.00E-05 5 1.079886627 RRES(ph)ASSSSSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRESASSSSSVK 12 2 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 RRES(0.999)AS(0.001)SSSSVK;RRES(0.724)AS(0.07)S(0.193)S(0.01)S(0.002)S(0.002)VK 112.5 0.00099785 247944000 82804 82672 72630 69803 74211 66536 70514 86691 72279 63090 TRUE FALSE 79567.92814 80314.2755 85755.85665 73405.5412 76598.06421 67881.40351 71376.97143 84900.80056 64074.19094 58816.85811 1.352808203 1.365497548 1.45801492 1.248035743 1.30231479 1.15411475 1.213546145 1.443477317 1.089384795 1 15.8439421 -5 0.115916994 1.44E-12 1.464484927 0.521580217 0.098926017 140.0123035 1.063990193 32.84375673 1.111807619 1.00E-05 5 1.464484927 AGLLVLAVLSDGAGDHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGLLVLAVLSDGAGDHIR 18 0 Q8TEX9;Q8TEX9-2;H0YN14 Q8TEX9 IPO4 Importin-4 0 ; 180.62 7.76E-14 272270000 213085 255910 237480 312340 273200 292710 292780 272310 331180 395030 FALSE TRUE 204757.4026 248611.6974 280397.9187 328459.9048 281987.7261 298628.7968 296363.1292 266686.7033 293585.8348 368274.2662 0.555991611 0.675072141 0.761383416 0.891889374 0.765700327 0.810886951 0.80473483 0.724152426 0.797193455 1 18.49042106 -5 0.033560936 2.159941646 3.00E-12 0.56880946 0.074182209 1050.924324 2.648971889 139.9089909 51.00526896 1.00E-05 5 -2.159941646 LDASESLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDASESLR 8 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 207.6 0.00014423 152300000 209470 242130 219900 233530 217220 196440 266440 229210 262270 272510 FALSE TRUE 201283.6808 235224.6895 259640.8216 245582.5113 224207.0786 200412.1514 269700.7724 224476.7334 232498.2091 254052.655 0.792291192 0.925889515 1.021996096 0.966659889 0.882522084 0.788860685 1.061593993 0.883583497 0.915157565 1 17.95476802 -5 0.31179899 1.718860198 0.915702381 0.085763527 0.082903022 860.0858628 7.762202982 406.6168564 0.076486553 1.00E-05 5 -0.803157818 HIPESK ddPTM_BT-474_Pertuzumab_2h_R1 1 HIPESK 6 0 O95202 O95202 LETM1 "LETM1 and EF-hand domain-containing protein 1, mitochondrial" 0 91.26 0.048095 1900700000 2050800 2031300 1835100 2024900 1781900 2138600 2095800 2077200 2429500 2451200 FALSE TRUE 1970652.469 1973369.313 2166743.392 2129405.332 1839216.432 2181843.957 2121449.027 2034305.094 2153713.345 2285178.041 0.862362772 0.86355167 0.948172682 0.931833447 0.804846012 0.95478073 0.928351747 0.89021733 0.942470699 1 21.12387514 -5 0.138040511 1.345633212 0.86475664 0.368430153 0.042969751 158.2747663 1.347278546 14.95590872 0.274001801 1.00E-05 5 -0.480876572 HSQAVEELAEQLEQTK ddPTM_BT-474_Pertuzumab_2h_R1 4 HSQAVEELAEQLEQTK 16 0 P35579 P35579 MYH9 Myosin-9 0 ;;; 155.22 2.80E-07 2538240000 1476830 1326080 1394240 1539250 1513100 1495970 1700590 1417110 2075140 2055750 FALSE TRUE 1419113.851 1288261.497 1646210.183 1618690.877 1561770.236 1526219.538 1721402.329 1387846.183 1839578.807 1916512.221 0.740466893 0.672190598 0.858961484 0.844602429 0.81490231 0.796352625 0.898195331 0.724152013 0.959857593 1 20.87005177 -5 0.07241272 1.662811049 0.577130526 0.506451774 0.069169798 262.4611411 1.363790978 28.71804577 3.344220165 1.00E-05 5 -1.085680523 DLPYDQSTWEEDEMNIPEYEEHK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLPYDQSTWEEDEMNIPEYEEHK 23 0 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 0 ;; 194.25 3.68E-18 240804000 168293 162751 146663 148780 170635 167284 160630 169628 199266 195684 FALSE TRUE 161715.9235 158109.5008 173168.2666 156458.5536 176123.6297 170666.5971 162595.838 166125.1225 176646.1591 182430.1484 0.886453938 0.866685152 0.949230531 0.857635402 0.965430502 0.935517504 0.891277234 0.910623184 0.968294773 1 17.47698464 -5 0.101623885 1.289599059 0.852690127 0.454210715 0.033502137 171.7416523 1.183966671 10.4203649 0.526989959 1.00E-05 5 -0.436908932 FLEGVR ddPTM_BT-474_Pertuzumab_2h_R1 6 FLEGVR 6 0 F8VWS0;P05388;F8VU65;F8VW21;Q8NHW5;F8VZS0 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;;;; 175.34 0.009844 4226670000 2938030 3299970 2895570 3310690 3016380 2429190 3441600 3546260 3196540 3617770 FALSE TRUE 2823208.539 3205858.087 3418863.911 3481555.108 3113404.602 2478309.886 3483719.33 3473028.492 2833682.18 3372735.216 0.837067946 0.950521723 1.013676939 1.032264582 0.923109703 0.734807131 1.032906264 1.029736481 0.840173331 1 21.68548763 -5 0.244777706 1.324548613 0.937975621 0.025412008 0.097370579 894.4992628 8.899619796 145.3947356 0.152623002 1.00E-05 5 -0.386572992 VDQDSALHNDLQILK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDQDSALHNDLQILK 15 0 Q7Z7E8;Q7Z7E8-2 Q7Z7E8 UBE2Q1 Ubiquitin-conjugating enzyme E2 Q1 0 162.37 1.60E-06 202140000 132080 124710 129290 137310 130870 132620 159190 140370 164030 184240 FALSE TRUE 126918.1676 121153.3929 152655.579 144396.5856 135079.5524 135301.6673 161138.2148 137471.3104 145410.0021 171761.2607 0.738921961 0.705359243 0.888766061 0.840681915 0.786437826 0.787730986 0.93815226 0.800362724 0.846582061 1 17.39004516 -5 0.07202928 1.60109647 0.604846867 0.53983086 0.057849152 242.725275 1.255331218 24.2618935 2.856782528 1.00E-05 5 -0.996249603 VVSISSEHLEPIT(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVSISSEHLEPITPTK 16 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 VVSISSEHLEPIT(1)PTK 185.85 5.87E-09 431210000 569140 641130 601030 666280 607540 672040 643920 674590 854450 870770 TRUE FALSE 546897.3796 622845.6001 709649.4908 700666.7906 627082.0759 685629.1093 651800.4856 660659.4808 757456.4181 811791.9723 0.673691535 0.767247794 0.874176532 0.863111258 0.772466466 0.8445872 0.802915658 0.813828546 0.933067145 1 19.63075055 -5 0.080097414 1.62098163 0.627292642 0.617682056 0.053639124 190.9153322 1.083160865 20.88438548 1.949122629 1.00E-05 5 -0.993688988 DRDPEAQFEMPYVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRDPEAQFEMPYVVR 15 1 O14744-2;O14744;O14744-4;O14744-3;O14744-5;H0YJD3;H7BZ44 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 ; 170.78 1.02E-06 418120000 110916 121135 143356 127248 140338 126139 118857 146794 164350 182126 FALSE TRUE 106581.2801 117680.3484 169263.6181 133815.2845 144852.0992 128689.617 120311.6075 143762.6526 145693.677 169790.4438 0.62772249 0.693091706 0.996897201 0.788120235 0.853122802 0.757932037 0.708588804 0.846706383 0.85807937 1 17.37339574 -5 0.161199283 1.769168845 0.739961317 0.335853926 0.095326422 171.8141461 1.585572377 42.20688767 0.410137374 1.00E-05 5 -1.029207528 LRDPDSHIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRDPDSHIVK 10 1 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 70.942 0.031527 114750000 172390 177460 162820 175490 174380 158750 218500 181580 236320 246350 FALSE TRUE 165652.8082 172399.0146 192245.1959 184547.0599 179989.0911 161960.0338 221174.0684 177830.3095 209493.9443 229664.4951 0.721281747 0.750655927 0.837069726 0.803550675 0.783704469 0.705202751 0.963031174 0.77430475 0.91217384 1 17.80916832 -5 0.095605701 1.683432813 0.648193422 0.537502134 0.065511006 149.5759679 0.982876782 20.19544566 1.210930143 1.00E-05 5 -1.035239392 IIQQVLQGLDYLHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 IIQQVLQGLDYLHTK 15 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 ; 171.46 1.08E-06 130343000 179067 164875 176939 174180 191613 190030 195773 196637 243297 262690 FALSE TRUE 172068.8637 160172.9264 208915.8133 183169.4507 197776.4062 193872.5368 198168.9285 192576.3772 215678.9445 244897.7723 0.702615063 0.654039949 0.853073555 0.747942494 0.807587608 0.791646796 0.809190409 0.78635414 0.880689696 1 17.90182013 -5 0.077769887 1.753837099 0.542962185 0.734740413 0.046953997 136.3575013 0.754206201 17.7022508 1.766418565 1.00E-05 5 -1.210874914 ESHTAVVYTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESHTAVVYTEK 11 0 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 0 ; 189.57 2.65E-06 773580000 1740010 1827170 1554000 1836380 1721440 1687630 1893490 1820440 2195530 2194820 FALSE TRUE 1672008.486 1775060.901 1834842.369 1931155.792 1776811.681 1721755.035 1916663.097 1782847.278 1946302.639 2046162.886 0.817143394 0.867507134 0.896723511 0.943793774 0.868362774 0.84145551 0.936710909 0.871312489 0.951196335 1 20.96448957 -5 0.12056929 1.38096911 0.831266873 0.530405887 0.036945093 129.6418238 1.012451752 11.93554122 0.354844379 1.00E-05 5 -0.549702237 FQDNFEFVQWFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FQDNFEFVQWFK 12 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 210.38 0.00023188 0 279880 295090 249300 291170 310080 247190 323040 327380 315720 386980 FALSE TRUE 268941.9802 286674.3221 294354.0556 306197.3186 320054.0048 252188.3512 326993.4602 320619.4886 279880.7892 360769.4999 0.745467619 0.794619063 0.815906155 0.848733939 0.887142635 0.699029023 0.906377785 0.888710073 0.775788389 1 18.46071785 -5 0.132350293 1.580329929 0.754212585 0.436980699 0.06282487 134.8632793 1.119189671 20.80958632 0.446102027 1.00E-05 5 -0.826117345 AGHFDK ddPTM_BT-474_Pertuzumab_2h_R1 4 AGHFDK 6 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ;;; 112.27 0.02714 2398760000 6280450 6053160 6253710 7125500 6275170 6541230 7675600 6507660 8857900 9234800 FALSE TRUE 6035003.071 5880529.803 7383894.51 7493247.909 6477016.542 6673498.152 7769536.289 6373274.547 7852388.327 8609318.77 0.700984971 0.683042406 0.85766304 0.870364788 0.752326254 0.775148224 0.90245657 0.740276289 0.9120801 1 23.03746766 -5 0.08375845 1.660618159 0.607951818 0.532225572 0.067533352 203.3295434 1.198341173 24.54981923 2.06294945 1.00E-05 5 -1.052666341 TEAS(ph)PESMLSPSHGSNPIEDPLEAETQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEASPESMLSPSHGSNPIEDPLEAETQHK 29 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;B5MCW3;Q9H0E9-3;Q9H0E9;H0YAH7 H7C128 BRD8 Bromodomain-containing protein 8 1 T(0.014)EAS(0.983)PES(0.002)MLSPSHGSNPIEDPLEAETQHK;T(0.163)EAS(0.668)PES(0.166)MLS(0.003)PS(0.001)HGSNPIEDPLEAETQHK 193.4 2.54E-18 217820000 85523 152678 134285 205262 136885 147477 164556 129260 171059 221170 TRUE FALSE 82180.66661 148323.7729 158553.2867 215855.5964 141288.0303 150459.086 166569.8856 126590.7358 151641.0995 206189.9589 0.398567743 0.719354976 0.768967061 1.046877343 0.685232351 0.729711024 0.807846737 0.613951991 0.735443667 1 17.65361455 -5 0.029366015 1.986530487 2.06E-09 0.220421673 0.153466038 3274.712966 7.243688757 378.5192728 156.4113955 1.00E-05 5 -1.986530485 EGEELVMDEEAYVLYHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGEELVMDEEAYVLYHR 17 0 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 ; 206.1 7.28E-12 68753000 112643 105358 102127 107071 106407 121495 123682 107079 140055 150208 FALSE TRUE 108240.787 102353.293 120583.6207 112596.9471 109829.6778 123951.7121 125195.6573 104867.7812 124156.5436 140034.2784 0.772959223 0.730915988 0.86110074 0.804067036 0.784305665 0.885152647 0.894035794 0.748872222 0.88661537 1 17.0954205 -5 0.149643932 1.654362117 0.757421869 0.57050331 0.051672013 105.3415557 0.93772385 20.51484917 0.27326038 1.00E-05 5 -0.896940248 AQPQDSATFAHT(ph)PPPAQATPAPGFK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQPQDSATFAHTPPPAQATPAPGFK 25 0 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 1 AQPQDS(0.002)AT(0.007)FAHT(0.992)PPPAQATPAPGFK;AQPQDSATFAHT(1)PPPAQATPAPGFK 245.31 2.96E-38 652600000 380460 403640 355830 394030 394140 419080 414060 432270 507910 561670 TRUE FALSE 365591.2026 392128.5824 420136.3964 414365.9355 406817.871 427554.0847 419127.3901 423343.4734 450254.1861 523627.5906 0.698189341 0.748869214 0.802357255 0.791337093 0.776922145 0.816523217 0.800430301 0.808481984 0.859874831 1 18.99818159 -5 0.12058898 1.71054441 0.684066837 0.906679511 0.022954538 45.15617795 0.352691258 7.764568006 0.230714416 1.00E-05 5 -1.026477573 SLS(ph)ESYELSSDLQDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSESYELSSDLQDK 15 0 A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 S(0.001)LS(0.999)ESYELSSDLQDK;S(0.007)LS(0.991)ES(0.002)YELSSDLQDK 260.08 7.25E-25 143310000 207023 198987 158724 177161 194549 187164 178001 206368 201609 193608 TRUE FALSE 198932.3123 193312.0856 187408.9576 186304.3004 200806.8453 190948.5843 180179.4295 202106.4287 178723.1915 180494.7577 1.102150084 1.071012189 1.038306929 1.032186767 1.112535609 1.057917619 0.998252978 1.119735727 0.990184944 1 17.46159741 -5 0.137491897 0.781358472 1.084688756 0.221747911 0.040578242 233.1205051 1.979735706 13.82807865 0.257199348 1.00E-05 5 0.303330284 HVATEYQENK ddPTM_BT-474_Pertuzumab_2h_R1 2 HVATEYQENK 10 0 O95239 O95239 KIF4A Chromosome-associated kinesin KIF4A 0 ; 160.53 0.0042666 0 327590 304930 307260 329150 327570 361190 374460 317170 449050 478300 FALSE TRUE 314787.4206 296233.695 362788.717 346137.4709 338106.5865 368493.5093 379042.7535 310620.3287 398075.7266 445904.315 0.705952847 0.664343638 0.813602167 0.776259523 0.758249192 0.826395926 0.850054016 0.696607586 0.892738001 1 18.76637463 -5 0.12419848 1.757831933 0.665341017 0.639447242 0.057658837 102.3896372 0.815735146 19.38592289 0.520976787 1.00E-05 5 -1.092490916 WDDPYYDIAR ddPTM_BT-474_Pertuzumab_2h_R1 6 WDDPYYDIAR 10 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;;;; 217.64 1.66E-08 5292130000 4624680 5162130 4249360 4749630 4841750 4049470 5260050 5202200 5154380 5614500 FALSE TRUE 4443942.393 5014911.107 5017313.879 4994758.973 4997489.286 4131353.058 5324424.065 5094772.752 4569276.391 5234224.914 0.849016323 0.958100041 0.958559092 0.954249971 0.954771598 0.789296052 1.017232571 0.973357629 0.872961416 1 22.31954449 -5 0.198677944 1.29920935 0.920943829 0.091204963 0.065167344 372.7187259 3.684022342 44.42429024 0.157288236 1.00E-05 5 -0.378265522 AYWQVHLDQVEVASGLTLCK ddPTM_BT-474_Pertuzumab_2h_R1 1 AYWQVHLDQVEVASGLTLCK 20 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 257.22 3.26E-36 335870000 361730 310500 290060 378120 337350 318860 372540 370410 385120 457320 FALSE TRUE 347593.1917 301644.844 342480.2943 397634.8185 348201.1691 325307.5677 377099.256 362760.9041 341402.7922 426345.3091 0.815285601 0.707512989 0.803293216 0.932659068 0.816711623 0.7630143 0.884492565 0.850861723 0.800765916 1 18.70166286 -5 0.160566615 1.655331716 0.773823657 0.470096758 0.058116328 121.2884367 1.117321043 25.39023969 0.251009097 1.00E-05 5 -0.881508059 TIDLGAAAHYTGDKAS(ph)PDQNASTHTPQSSVK ddPTM_BT-474_Pertuzumab_2h_R1 6 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 TIDLGAAAHYT(0.001)GDKAS(0.994)PDQNAS(0.002)T(0.003)HTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;T(0.003)IDLGAAAHY(0.001)T(0.052)GDKAS(0.939)PDQNAS(0.002)T(0.002)HT(0.001)PQSSVK;TIDLGAAAHYT(0.011)GDKAS(0.254)PDQNAS(0.254)T(0.254)HT(0.211)PQS(0.013)S(0.004)VK 323.74 1.47E-93 5116526000 1724387 1963204 1664503 1724655 1785740 2118268 1960432 1737415 2499789 2525750 TRUE FALSE 1656996.05 1907215.344 1965315.719 1813664.651 1843179.949 2161100.83 1984424.353 1701536.773 2216023.433 2354678.703 0.703703672 0.809968401 0.83464284 0.770238695 0.78277344 0.917790112 0.842758017 0.722619511 0.941114994 1 21.16709879 -5 0.155805735 1.710337738 0.753041325 0.495072818 0.064642191 123.5290642 1.122075684 27.02041059 0.304128904 1.00E-05 5 -0.957296414 SKCEELSGLHGQLQEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKCEELSGLHGQLQEAR 17 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 189.77 2.02E-10 664840000 1835570 2107880 1370270 1703950 1668570 1714050 1719600 1835830 1842820 1526610 FALSE TRUE 1763833.895 2047765.326 1617908.27 1791891.064 1722241.069 1748709.265 1740644.979 1797919.469 1633630.799 1423211.345 1.239333779 1.438834319 1.136801134 1.259047766 1.210109149 1.228706665 1.223040405 1.263283542 1.147848354 1 20.44071849 -5 0.158575318 0.084666608 1.311826797 0.53319189 0.072335817 101.0316285 0.925405159 28.97452568 0.302404141 1.00E-05 5 1.227160188 SLGGSSLTETEAAPSLTLPSVDYIPQDS(ph)PTPSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGGSSLTETEAAPSLTLPSVDYIPQDSPTPSVR 34 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SLGGSSLTETEAAPSLTLPSVDY(0.197)IPQDS(0.6)PT(0.16)PS(0.043)VR;SLGGSSLTETEAAPSLTLPSVDY(0.003)IPQDS(0.753)PT(0.193)PS(0.051)VR 145.59 1.43E-10 157362000 159991 160120 130998 161641 149473 163563 170128 178680 187466 211330 TRUE FALSE 153738.3748 155553.5344 154672.2526 169983.3114 154280.9348 166870.3559 172210.0774 174990.1956 166185.6456 197016.4309 0.780332758 0.789545997 0.785072859 0.862787487 0.78308664 0.846987001 0.874089925 0.888201024 0.843511604 1 17.58795643 -5 0.075583852 1.602939654 0.635402196 0.83004562 0.026634473 99.17350302 0.535101542 10.0328991 1.066168547 1.00E-05 5 -0.967537458 AQAVLQQYQHLPSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQAVLQQYQHLPSFR 15 0 Q9UID3;E9PKX7;Q9UID3-2;E9PRV0;E9PJ36 Q9UID3 VPS51 Vacuolar protein sorting-associated protein 51 homolog 0 108.66 0.0010615 348070000 313430 291990 254600 272770 304740 288890 334390 307840 332560 383490 FALSE TRUE 301180.8091 283662.7311 300611.8835 286847.6924 314542.2389 294731.5537 338482.3648 301482.9964 294809.183 357515.8807 0.84242638 0.79342694 0.84083505 0.802335526 0.879799348 0.824387306 0.946761761 0.843271621 0.824604441 1 18.4476478 -5 0.162258641 1.572975344 0.805117546 0.577990115 0.040440469 91.74800282 0.849158937 16.95782968 0.160104607 1.00E-05 5 -0.767857798 GLFS(ph)DEEDSEDLFSSQSASNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLFSDEEDSEDLFSSQSASNLK 22 0 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 GLFS(0.975)DEEDS(0.025)EDLFSSQSASNLK 177.5 4.10E-17 79408000 109560 93639 87849 106180 105990 101680 105720 106620 129330 136850 TRUE FALSE 105278.2741 90968.5074 103725.2685 111659.9625 109399.2646 103736.0393 107013.833 104418.2597 114649.0006 127581.0276 0.825187538 0.713025354 0.813014838 0.875208208 0.857488505 0.813099261 0.83879112 0.818446612 0.898636755 1 16.96105428 -5 0.138241712 1.614409513 0.758516216 0.664575057 0.04036024 87.5680844 0.746040873 14.75375697 0.268803069 1.00E-05 5 -0.855893297 GYYS(ph)PYSVS(ph)GSGSTAGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 GYY(0.074)S(0.925)PY(0.004)S(0.061)VS(0.93)GS(0.004)GS(0.001)T(0.001)AGS(0.001)R 91.475 0.0029721 0 93585 103140 91717 103870 83589 96560 106240 113500 111260 132330 TRUE FALSE 89927.59474 100198.5482 108292.3021 109230.7431 86277.7161 98512.50936 107540.1969 111156.1853 98630.23124 123367.1712 0.728942666 0.812197825 0.877804857 0.885411751 0.699357173 0.79853099 0.871708379 0.901019163 0.79948523 1 16.91259901 -5 0.153173498 1.647864739 0.772088056 0.450596571 0.062016115 131.2220306 1.182044814 25.69655867 0.310781827 1.00E-05 5 -0.875776683 DHGGALGPEEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHGGALGPEEFK 12 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ; 142.1 6.11E-05 435670000 670540 607470 779210 1018640 742620 641030 1035190 540640 1268120 1291120 FALSE TRUE 644334.5555 590145.5504 920030.5804 1071212.132 766507.0467 653992.0658 1047858.965 529475.5951 1124168.334 1203671.292 0.535307737 0.490287967 0.764353679 0.889954042 0.636807616 0.543331115 0.870552427 0.439883877 0.93394961 1 20.19901003 -5 0.207746317 2.597809569 0.616761702 0.294640025 0.163773312 194.1814955 1.933317144 128.8427876 0.358349025 1.00E-05 5 -1.981047868 VREYELR ddPTM_BT-474_Pertuzumab_2h_R1 5 VREYELR 7 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;;; 149.65 0.0018257 6901500000 5653600 6417870 4867660 5633250 5551320 5547680 5886990 6333540 6125120 6656540 FALSE TRUE 5432651.062 6234838.631 5747354.443 5923982.708 5729883.249 5659857.891 5959036.745 6202750.186 5429822.056 6205686.617 0.8754311 1.004697629 0.926143197 0.954605521 0.923327845 0.912043782 0.960254217 0.999526816 0.874975227 1 22.56515941 -5 0.298112271 1.459831582 0.940084526 0.137702243 0.043062945 546.1807321 5.069953034 157.0699218 0.041786784 1.00E-05 5 -0.519747055 EEGASEEGQHFLPTAQANDPGDCQFTSIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEGASEEGQHFLPTAQANDPGDCQFTSIQK 30 0 O15327;D6RJC3;E7EQN9;E9PG59;D6RE59;O15327-2;D6R9J5;D6RDJ7;Q9BS68 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 172.32 1.20E-12 120190000 98248 101090 99230 112880 99253 111920 112930 110720 142830 154070 FALSE TRUE 94408.35954 98207.01218 117163.0684 118705.7503 102445.5629 114183.0991 114312.0711 108433.5933 126616.5372 143634.7017 0.657280994 0.683727616 0.815701686 0.826442001 0.713236855 0.794954825 0.795852742 0.754926157 0.881517737 1 17.13204482 -5 0.113661115 1.770117541 0.638231384 0.713397143 0.050928344 95.41237192 0.715002924 16.92301372 0.61017821 1.00E-05 5 -1.131886157 LPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR 39 2 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 296.91 8.22E-93 1834180000 1145740 1273980 990580 965320 1105030 1179200 1066300 1152080 1290990 1080570 FALSE TRUE 1100963.214 1237647.338 1169599.841 1015140.281 1140574.294 1203044.232 1079349.698 1128289.145 1144442.227 1007382.031 1.092895426 1.228577937 1.161029088 1.007701397 1.132216238 1.1942284 1.071440292 1.120021114 1.136055828 1 19.94217947 -5 0.223827747 0.343864542 1.142552118 0.293155059 0.058960666 202.4816902 2.026713493 60.03695028 0.109127902 1.00E-05 5 0.798687577 S(ph)LEQNIQLPAALLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLEQNIQLPAALLSR 15 0 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 1 S(1)LEQNIQLPAALLSR 168.69 1.30E-06 49206000 28478 26847 25944 27397 27579 34362 32366 27245 39322 41902 TRUE FALSE 27365.04828 26081.34985 30632.65792 28810.96245 28466.10358 35056.82318 32762.10479 26682.38123 34858.33141 39063.94022 0.700519408 0.66765794 0.784167131 0.737533446 0.728705385 0.897421586 0.838678961 0.683043776 0.892340384 1 15.25354985 -5 0.101872612 1.755903674 0.60725864 0.599080455 0.066212188 138.9873539 0.959971731 22.22742657 1.116244498 1.00E-05 5 -1.148645034 YVLNFLEVHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 YVLNFLEVHDK 11 0 Q08AF3;B4E128;Q08AF3-2 Q08AF3 SLFN5 Schlafen family member 5 0 ; 138.94 4.72E-05 370940000 648900 655530 611560 637740 643050 654120 691340 654040 815990 824310 FALSE TRUE 623540.2706 636834.9262 722082.4961 670653.8378 663734.2873 667346.7546 699800.8257 640533.8454 723362.2361 768478.7495 0.811395593 0.828695558 0.939625847 0.872703166 0.863698948 0.868399751 0.91063133 0.833508859 0.941291137 1 19.55164584 -5 0.18046244 1.530511928 0.845658746 0.533266199 0.038715525 110.6134078 1.066339762 20.96709358 0.120962929 1.00E-05 5 -0.684853181 AEENTDQAS(ph)PQEDYAGFER ddPTM_BT-474_Pertuzumab_2h_R1 2 AEENTDQASPQEDYAGFER 19 0 Q9NU22 Q9NU22 MDN1 Midasin 1 AEENTDQAS(1)PQEDYAGFER;AEENTDQAS(1)PQEDYAGFER 368.83 6.62E-108 473510000 392010 398320 323310 427700 401580 418710 419220 428590 480190 532570 TRUE FALSE 376689.8158 386960.3036 381739.309 449773.6483 414497.1854 427176.6031 424350.5398 419739.4667 425680.8443 496498.5595 0.758692666 0.779378502 0.768862873 0.905891144 0.834840661 0.860378333 0.854686346 0.845399163 0.857365719 1 18.92143001 -5 0.050437647 1.648548458 0.506048646 0.739637681 0.03454984 297.1809246 1.10822861 26.15394746 5.78176109 1.00E-05 5 -1.142499813 DMFDPHGWSEDSYYEALAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DMFDPHGWSEDSYYEALAK 19 0 X6R3T8;J3QLH3;J3QQJ0;Q9UHR5-2;Q9UHR5;J3QLM2;J3KRR6 X6R3T8 SAP30BP SAP30-binding protein 0 ; 164.53 2.36E-11 167305000 407400 406220 350480 378420 390330 423240 411020 407100 490190 481950 FALSE TRUE 391478.3576 394635.0033 413819.5324 397950.3015 402885.3189 431798.2028 416050.1857 398693.2427 434545.6862 449307.0972 0.87129351 0.878319096 0.921017128 0.885697787 0.896681404 0.961031342 0.92598178 0.887351313 0.967146277 1 18.77734233 -5 0.075630745 1.317547494 0.805215165 0.644565592 0.024751377 188.9445852 1.020023413 10.12707008 1.074722003 1.00E-05 5 -0.512332329 GYYS(ph)PYSVSGSGSTAGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYS(0.675)PYS(0.325)VSGSGSTAGSR;GYYS(0.854)PYS(0.144)VS(0.002)GSGSTAGSR;GYYS(0.714)PYS(0.281)VS(0.005)GSGSTAGSR;GYYS(0.87)PYS(0.13)VSGSGSTAGSR 344.29 4.31E-76 3824340000 722340 823360 837250 945700 806170 949050 1101100 953530 1181770 1466680 TRUE FALSE 694110.1542 799878.579 988559.6995 994507.6903 832101.1902 968240.4412 1114575.591 933839.2723 1047620.424 1367340.457 0.507635206 0.584988599 0.722979924 0.727329968 0.608554501 0.7081195 0.815141237 0.682960317 0.766173793 1 20.38294108 -5 0.063948907 2.125350998 0.233578821 0.762388971 0.062865865 184.6976299 0.858446943 31.84299468 4.739721424 1.00E-05 5 -1.891772178 S(ph)PGETSKPRPFAGGGYR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PGETSKPRPFAGGGYR;S(1)PGETSKPRPFAGGGYR;S(0.988)PGET(0.009)S(0.002)KPRPFAGGGYR;S(0.989)PGET(0.011)SKPRPFAGGGYR;S(0.934)PGET(0.054)S(0.013)KPRPFAGGGYR 114.02 0.00020028 5027170000 1648360 1502170 1471150 1466730 1452890 1729070 1737870 1714260 1901190 2139120 TRUE FALSE 1583940.269 1459329.582 1737019.531 1542428.111 1499623.526 1764032.98 1759138.573 1678859.932 1685374.882 1994235.497 0.79425939 0.731773948 0.871020265 0.773443314 0.751979156 0.884566032 0.882111754 0.841856408 0.845123299 1 20.92740436 -5 0.102994187 1.601394134 0.698463504 0.646076775 0.044629318 110.3792145 0.768823162 14.03678568 0.682961211 1.00E-05 5 -0.90293063 DLEGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEGYR 6 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4;Q6N069;Q6N069-5;Q6N069-4;Q6N069-3;Q6N069-2 A0A0B4J1W3;Q6N069 NAA15;NAA16 "N-alpha-acetyltransferase 15, NatA auxiliary subunit;N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 ; 134.12 0.032967 898830000 763230 811010 684600 759940 788060 777830 785120 849130 936280 988860 FALSE TRUE 733402.1278 787880.7889 808322.4488 799160.5945 813408.6656 793558.2555 794728.5334 831595.1688 829997.4196 921883.6314 0.795547402 0.854642345 0.876816142 0.866877952 0.882333342 0.860800896 0.862070338 0.90206089 0.900327754 1 19.81422513 -5 0.115963793 1.439763943 0.797612807 0.842543594 0.019420399 60.88702364 0.462828301 6.265567853 0.211821167 1.00E-05 5 -0.642151136 AS(ph)PPHSK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASPPHSK 7 0 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 AS(1)PPHSK;AS(1)PPHSK;AS(1)PPHSK 123.86 0.002707 1472690000 1311330 1192970 1192250 1324160 1247710 1283750 1468830 1376820 1620750 1757250 TRUE FALSE 1260081.774 1158947.664 1407716.096 1392500.056 1287843.725 1309708.305 1486805.981 1348388.186 1436769.255 1638229.892 0.769172739 0.707438968 0.859290935 0.850002837 0.786119049 0.799465515 0.907568582 0.823076292 0.877025417 1 20.64370639 -5 0.07252722 1.631708621 0.602825873 0.673759 0.044016335 174.8430758 0.909782462 18.15443444 2.107103135 1.00E-05 5 -1.028882748 VYELPFLVALDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYELPFLVALDHR 13 0 E7ET49;Q8NCG7-2;Q8NCG7-4;Q8NCG7 E7ET49 DAGLB Sn1-specific diacylglycerol lipase beta 0 ; 123.02 0.00022828 121459000 118788 154579 121273 156854 131293 106696 169058 145362 155001 169508 FALSE TRUE 114145.6336 150170.5583 143189.7288 164949.2537 135516.1586 108853.4662 171126.9824 142360.2239 137405.9363 158027.0722 0.722316955 0.950283747 0.906108851 1.04380377 0.857550271 0.688827963 1.08289662 0.900859719 0.869508841 1 17.26981221 -5 0.01371196 2.057191852 1.74E-09 0.087810512 0.115223412 20594.8749 21.43171 1974.167184 1305.316061 1.00E-05 5 -2.05719185 VTLLEGDHVR ddPTM_BT-474_Pertuzumab_2h_R1 5 VTLLEGDHVR 10 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;;; 180.07 2.04E-06 2185300000 1669100 1712760 1640280 1907550 1763290 1469910 1961060 1875210 2034630 2285600 FALSE TRUE 1603869.727 1663913.762 1936715.084 2005998.884 1820007.824 1499632.587 1985060.039 1836486.258 1803667.332 2130794.276 0.752709797 0.780888977 0.908916973 0.941432454 0.854145257 0.703790415 0.931605675 0.861878727 0.846476524 1 21.02295988 -5 0.174483191 1.606589701 0.811921854 0.313536538 0.07228209 177.86559 1.695026241 37.41040388 0.253596998 1.00E-05 5 -0.794667847 SFSLASSSNS(ph)PISQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFSLASSSNSPISQR 15 0 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR 427.72 2.61E-153 7317900000 3279880 3780510 3361520 3778430 3344500 3891890 4041070 3993820 4726000 5220760 TRUE FALSE 3151698.664 3672693.556 3969021.441 3973435.225 3452078.88 3970586.682 4090525.823 3911346.221 4189524.293 4867153.275 0.647544568 0.75458761 0.815470813 0.816377665 0.709260359 0.815792406 0.840434971 0.803620926 0.860775089 1 22.21464678 -5 0.079563636 1.726935292 0.565036284 0.746943934 0.044776658 133.3087406 0.751997687 16.9486361 1.606234404 1.00E-05 5 -1.161899008 KIEMVR ddPTM_BT-474_Pertuzumab_2h_R1 6 KIEMVR 6 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;; 121.29 0.031612 5543510000 4208300 4636460 3985710 4611950 4255350 3518530 5010880 4691560 5022880 5407650 FALSE TRUE 4043834.983 4504232.7 4706016.459 4849973.292 4392227.197 3589677.087 5072204.648 4594677.647 4452703.72 5041385.049 0.802127777 0.893451434 0.933476894 0.962031911 0.871234225 0.71204184 1.00611332 0.911391929 0.883230239 1 22.26538872 -5 0.186571902 1.472014042 0.869314582 0.170050137 0.07749275 262.4629396 2.555686462 45.77799711 0.224095059 1.00E-05 5 -0.60269946 VATTPGS(ph)PSLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VATTPGSPSLGR 12 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 VAT(0.002)T(0.223)PGS(0.771)PS(0.004)LGR;VATTPGS(1)PSLGR;VAT(0.024)T(0.208)PGS(0.762)PS(0.006)LGR;VATT(0.009)PGS(0.989)PS(0.002)LGR 247.95 1.13E-16 2248660000 1838730 1936780 1739950 1819770 1823450 2038330 1994510 2052380 2315870 2573280 TRUE FALSE 1766870.399 1881544.931 2054397.67 1913688.548 1882102.925 2079546.429 2018919.41 2009997.636 2052982.147 2398989.454 0.736506114 0.784307296 0.856359609 0.797706111 0.784539891 0.866842672 0.841570773 0.837851802 0.855769559 1 21.19399538 -5 0.122463891 1.603562005 0.732480957 0.808674543 0.029463425 65.05559296 0.513450972 9.66251537 0.272504746 1.00E-05 5 -0.871081048 LNSLCMAWLVDHVYAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNSLCMAWLVDHVYAIR 17 0 P30153;B3KQV6;P30154-4;P30154;P30154-2;P30154-3;P30154-5 P30153 PPP2R1A;PPP2R1B Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform;Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform 0 169.28 1.99E-09 121850000 94461 95173 89480 91157 113770 94853 131520 103340 132540 161460 FALSE TRUE 90769.35969 92458.75922 105651.0265 95861.62369 117429.5154 96770.99265 133129.5811 101205.9929 117494.6149 150524.1704 0.603021823 0.614245267 0.701887452 0.636852031 0.78013727 0.64289338 0.884439893 0.672357088 0.780569755 1 17.19963564 -5 0.092683859 1.970800963 0.465026139 0.686993045 0.068907014 111.0202005 0.711537099 21.13572428 1.376909132 1.00E-05 5 -1.505774824 HSDLVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSDLVTK 7 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 99.375 0.010574 701750000 1300430 1302140 1347820 1210810 1354160 1484170 1546730 1184670 1861830 1864790 FALSE TRUE 1249607.758 1265004.242 1591401.056 1273300.049 1397717.786 1514180.934 1565659.344 1160206.151 1650482.864 1738486.112 0.718790762 0.727647022 0.915394748 0.732418879 0.803985592 0.870976721 0.900587778 0.667365786 0.949379378 1 20.72940011 -5 0.170030077 1.772203468 0.755453871 0.355626619 0.086672275 158.0954824 1.492023667 41.12184742 0.314433599 1.00E-05 5 -1.016749598 LKEEASKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEEASKR 8 2 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 50.607 0.086896 320030000 78400 80260 72274 65502 70464 70202 80750 72645 87329 71845 FALSE TRUE 75336.04132 77971.06338 85335.51953 68882.56607 72730.53855 71621.53254 81738.24266 71144.85536 77415.77803 66978.87416 1.124773181 1.164114273 1.274066198 1.028422274 1.085872814 1.069315265 1.220358564 1.062198436 1.155823818 1 16.03141851 -5 0.148112825 0.553869182 1.17079485 0.233449674 0.071611001 202.9855209 1.797210075 26.84137128 0.372842667 1.00E-05 5 0.616925669 EKDTAGVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKDTAGVTR 9 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ; 76.143 0.033075 214042000 390380 421920 335500 337180 371610 387100 375510 394380 433650 378130 FALSE TRUE 375123.518 409887.2547 396132.3132 354581.9002 383563.1731 394927.4272 380105.6037 386235.9152 384423.87 352518.9183 1.064123083 1.16273832 1.123719303 1.005852117 1.088064082 1.12030137 1.078255901 1.095645922 1.090505644 1 18.42734116 -5 0.334875086 0.030121716 1.096437482 0.333101984 0.039053012 445.1163892 3.800629644 307.9980081 0.032452839 1.00E-05 5 1.066315766 YAPSEAGLHEMDIR ddPTM_BT-474_Pertuzumab_2h_R1 4 YAPSEAGLHEMDIR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5F3 Q60FE5 FLNA Filamin-A 0 ;;; 124.62 7.28E-05 785740000 1332259 1400749 1127431 1618388 1277833 1448485 1400609 1526515 1666556 1831635 FALSE TRUE 1280192.845 1360801.01 1331182.861 1701913.199 1318935.659 1477774.359 1417750.072 1494991.932 1477375.55 1707576.73 0.749713218 0.796919392 0.779574257 0.996683293 0.772401987 0.865421936 0.830270199 0.875504981 0.865188383 1 20.70351898 -5 0.071672074 1.524333103 0.65357516 0.441911062 0.062180777 289.3766394 1.49002809 25.17598315 2.995184401 1.00E-05 5 -0.870757943 TNSMSSSGLGS(ph)PNR ddPTM_BT-474_Pertuzumab_2h_R1 8 TNSMSSSGLGSPNR 14 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSS(0.001)GLGS(0.998)PNR;TNSMSSSGLGS(1)PNR 282.46 2.30E-33 9391380000 3147820 3309500 2843860 3162040 3000240 2851240 3427440 3327870 3608030 3735390 TRUE FALSE 3024799.714 3215116.3 3357808.763 3325233.263 3096745.444 2908894.026 3469386.036 3259148.322 3198461.56 3482388.708 0.868599105 0.923250266 0.964225721 0.954871366 0.889258984 0.835315719 0.996266163 0.935894466 0.918467704 1 21.73164582 -5 0.189781889 1.336053585 0.909114922 0.232894999 0.044375475 220.1194839 2.153225808 27.82845469 0.1249891 1.00E-05 5 -0.426938663 FQNVADLHLYLYSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 FQNVADLHLYLYSAK 15 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 174.59 9.04E-07 1922820000 2967800 3100200 2645200 2920500 2935500 3136700 3349900 3004600 3729200 3863900 FALSE TRUE 2851815.095 3011785.331 3123246.482 3071227.355 3029923.023 3200126.223 3390897.078 2942553.96 3305876.85 3602194.611 0.791688235 0.83609734 0.867039907 0.852598953 0.841132518 0.88838238 0.941342 0.816878119 0.917739658 1 21.7804447 -5 0.102333487 1.445073342 0.7682993 0.653739742 0.035097692 120.2382295 0.833365908 11.38337317 0.564277658 1.00E-05 5 -0.676774042 WNGHTDMIDQDGLYEK ddPTM_BT-474_Pertuzumab_2h_R1 3 WNGHTDMIDQDGLYEK 16 0 Q9UHG3;Q9UHG3-2 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 ;; 216.93 1.47E-14 1327720000 1300870 1834210 1600860 1849220 1320780 1758890 1669020 1679580 1999320 2089110 FALSE TRUE 1250030.562 1781900.127 1890171.013 1944658.466 1363264.088 1794455.961 1689445.966 1644896.086 1772365.575 1947612.719 0.641827069 0.914915018 0.970506608 0.998483141 0.699966721 0.9213618 0.867444513 0.844570417 0.910019512 1 20.8932754 -5 0.253767177 1.82419923 0.855560439 0.142107583 0.10597746 408.0941176 4.033472203 174.7932767 0.145222761 1.00E-05 5 -0.968638791 LFPLIQAMHPTLAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFPLIQAMHPTLAGK 15 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;Q9H361;H0YB75;H0YAS6 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 154.72 2.43E-06 163360000 229000 257090 247570 321990 261020 246870 295670 299560 350960 392240 FALSE TRUE 220050.4268 249758.0449 292311.4062 338607.9425 269415.9454 251861.8805 299288.4979 293373.9813 311120.4921 365673.2354 0.601767932 0.68300882 0.799378729 0.925985032 0.736766925 0.688762141 0.818458856 0.802284534 0.850815597 1 18.48019551 -5 0.033645222 2.199257251 2.21E-09 0.548102687 0.075844846 1027.187592 2.595489356 139.398302 50.69167654 1.00E-05 5 -2.199257249 KVDIEVLSVLASLGASVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVDIEVLSVLASLGASVHK 19 1 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;A0A096LNY6;A0A096LP92;A0A096LPA2 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 181.26 2.07E-14 98277000 106000 135070 126160 129730 131940 147450 146390 139110 177780 204440 FALSE TRUE 101857.4028 131217.9358 148959.9184 136425.3808 136183.9699 150431.54 148181.5646 136237.3299 157599.1597 190593.0967 0.534423358 0.688471608 0.781559883 0.715793925 0.714527295 0.789281158 0.777476032 0.714807263 0.82688808 1 17.54013634 -5 0.078233676 1.880676249 0.450533625 0.744264311 0.056639838 144.9903023 0.806091999 22.3493676 2.200583964 1.00E-05 5 -1.430142624 DMAEAHK ddPTM_BT-474_Pertuzumab_2h_R1 4 DMAEAHK 7 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ;;; 92.925 0.015312 678930000 1300041 1249111 1044231 1227250 1234753 1310645 1337472 1290847 1582575 1578342 FALSE TRUE 1249233.96 1213487.577 1232946.77 1290588.52 1274469.952 1337147.14 1353840.382 1264190.558 1402927.721 1471439.49 0.848987654 0.824694175 0.837918772 0.877092485 0.8661382 0.908734031 0.920078869 0.859152256 0.953438949 1 20.48879679 -5 0.05571477 1.527125452 0.63861296 0.792795242 0.023968504 201.0635733 0.823119348 14.71149544 2.785160661 1.00E-05 5 -0.888512492 RLS(ph)APLPSSCGDPEK ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSAPLPSSCGDPEK 15 1 H0YKX0;Q96EP0-3;Q96EP0 H0YKX0 RNF31 E3 ubiquitin-protein ligase RNF31 1 RLS(0.999)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK 139.51 3.13E-06 2556910000 2438580 2419460 2103610 2325220 2474370 2327730 2354960 2651280 2755510 3059570 TRUE FALSE 2343277.598 2350459.37 2483779.122 2445224.883 2553960.358 2374798.295 2383780.705 2596530.141 2442716.057 2852342.599 0.821527399 0.82404525 0.870785691 0.857268998 0.895390462 0.83257821 0.835727344 0.910314961 0.856389432 1 21.44371585 -5 0.183790518 1.597332191 0.829774175 0.741276635 0.026210325 68.02328589 0.659491002 14.80830366 0.078114299 1.00E-05 5 -0.767558016 EVEEEPGIHSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVEEEPGIHSLK 12 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 174.42 3.04E-05 540460000 1198310 1261750 1123110 1300200 1172910 1370850 1415950 1302020 1669290 1749920 FALSE TRUE 1151478.72 1225766.125 1326080.96 1367303.478 1210637.715 1398569.526 1433278.82 1275132.832 1479799.197 1631396.36 0.70582401 0.751360096 0.812850263 0.838118505 0.742086807 0.857283712 0.87855953 0.781620496 0.907075211 1 20.63767591 -5 0.06097876 1.728017887 0.503998974 0.72571698 0.04379024 216.4204042 0.963120613 23.28424653 3.779145856 1.00E-05 5 -1.224018913 S(ph)PGVLFLQFGEETR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGVLFLQFGEETR 14 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 S(1)PGVLFLQFGEETR 165.02 4.23E-06 32357000 6391.3 6193.9 4998.7 6587.6 5839.3 5516.1 7307.7 7104.9 6528.6 9114.5 TRUE FALSE 6141.52093 6017.256036 5902.076285 6927.586825 6027.126388 5627.639321 7397.133819 6958.181332 5787.500698 8497.166797 0.722772787 0.708148514 0.694593436 0.815281963 0.709310119 0.662295969 0.870541205 0.818882517 0.681109461 1 13.05276617 -5 0.183111032 2.045437747 0.698125806 0.576005235 0.065874406 96.99189383 0.939294846 36.87966271 0.19812829 1.00E-05 5 -1.347311942 TVWDWELMNDIKPIWQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVWDWELMNDIKPIWQR 17 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 186.94 4.51E-10 542550000 310760 333830 315277 344080 338720 317440 369600 322346 413990 444460 FALSE TRUE 298615.1556 324309.4953 372254.5672 361838.01 349615.2364 323858.8543 374123.2754 315689.4425 366995.5908 414356.3283 0.720672366 0.782682617 0.898392378 0.873253249 0.84375503 0.781595048 0.902902284 0.761879139 0.88570046 1 18.66051243 -5 0.266588176 2.159519996 0.814214303 0.453834537 0.058637628 195.9189686 1.910936231 124.8481443 0.074441104 1.00E-05 5 -1.345305693 DPQALSEHLK ddPTM_BT-474_Pertuzumab_2h_R1 6 DPQALSEHLK 10 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;;; 153.95 1.54E-05 6955940000 4474725 4710570 5081745 5575540 5065189 4240105 5686143 5713951 6450380 7202100 FALSE TRUE 4299847.8 4576229.156 6000129.364 5863294.288 5228115.404 4325842.828 5755731.719 5595955.915 5718159.905 6714295.352 0.640401945 0.681565066 0.893635006 0.873255343 0.778654368 0.644273539 0.857235409 0.833439046 0.851639614 1 22.67880457 -5 0.074180877 1.72252383 0.54515822 0.458504083 0.082307189 290.3758522 1.54125294 35.17172942 3.891899182 1.00E-05 5 -1.177365609 RPWRPEEAVEDPDEEDEDNTS(ph)EAENGFSLEEVLR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.148)S(0.852)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.245)S(0.755)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.113)S(0.887)EAENGFSLEEVLR 275.94 4.44E-74 661670000 192375 187935 175001 222144 194752 197826 197763 213446 246555 254579 TRUE FALSE 184856.7723 182575.2778 206627.5736 233608.8785 201016.3749 201826.1773 200183.2828 209038.2655 218567.11 237336.1376 0.778881692 0.769268767 0.870611512 0.984295442 0.8469691 0.850381149 0.843458922 0.880768802 0.920917953 1 17.85657226 -5 0.020394938 2.113472979 1.60E-18 0.488762246 0.051824088 3097.988821 4.782856867 335.8866949 181.6272593 1.00E-05 5 -2.113472979 LHPTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHPTDK 6 0 G8JLM4 G8JLM4 USHBP1 0 ; 110.24 0.028873 2812390000 4149700 4158000 3743300 4126000 3819900 4155800 4491300 4272300 4929200 5205500 FALSE TRUE 3987525.136 4039417.911 4419797.579 4338943.354 3942770.553 4239833.123 4546265.873 4184075.512 4369657.881 4852926.848 0.821674272 0.83236736 0.910748857 0.894087937 0.812452088 0.873665162 0.936809067 0.862175681 0.90041701 1 22.21042368 -5 0.14328001 1.453214408 0.827182592 0.595155306 0.034606694 100.201062 0.871327862 12.90229952 0.20463701 1.00E-05 5 -0.626031816 SADESGQALLAAGHYASDEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SADESGQALLAAGHYASDEVR 21 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 257.37 1.77E-36 328960000 129610 112580 130820 167580 112220 132420 137480 156590 159030 210880 FALSE TRUE 124544.6979 109369.3286 154462.0841 176228.8239 115829.6582 135097.6231 139162.5214 153356.3618 140977.5811 196596.9098 0.633502826 0.556312552 0.785679105 0.896396714 0.589173341 0.687180807 0.707857115 0.780054793 0.717089507 1 17.58488112 -5 0.190656938 2.260276803 0.656275919 0.490104591 0.092474535 123.6319758 1.21079491 59.08778532 0.259237765 1.00E-05 5 -1.604000884 MFEELGQR ddPTM_BT-474_Pertuzumab_2h_R1 6 MFEELGQR 8 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;; 176.41 0.00060597 1286608000 1270135 1398589 1226399 1306845 1310779 1223760 1430845 1398410 1490839 1626842 FALSE TRUE 1220496.72 1358702.611 1448036.58 1374291.427 1352941.397 1248505.266 1448356.109 1369532.345 1321605.207 1516654.542 0.804729545 0.895855037 0.954757026 0.906133459 0.892056404 0.823196866 0.954967706 0.902995578 0.871395014 1 20.53246108 -5 0.280118862 1.773317203 0.886861391 0.339684458 0.045921766 275.6697648 2.639623949 124.0209818 0.05222062 1.00E-05 5 -0.886455813 FREDHPDLIQNAK ddPTM_BT-474_Pertuzumab_2h_R1 1 FREDHPDLIQNAK 13 1 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 145.17 2.50E-05 676070000 524160 559500 441950 524120 543630 553720 598650 532800 684410 703100 FALSE TRUE 503675.2477 543543.6078 521820.1961 551169.896 561116.3527 564916.5978 605976.4578 521797.4938 606718.6461 655478.4107 0.7684086 0.8292319 0.796090592 0.84086659 0.856040937 0.861838603 0.924479659 0.796055957 0.925611944 1 19.32218874 -5 0.079731038 1.529427036 0.680783623 0.697784253 0.037267618 148.6033156 0.839790658 13.82562147 1.303979963 1.00E-05 5 -0.848643413 KFDSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 KFDSSR 6 1 P62942;Q5W0X3;Q1JUQ5;Q5VVH2;A0A087WZM5;F8W6G9;P68106-2;P68106 P62942 FKBP1A;FKBP12-Exip2;FKBP1C;FKBP1B Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase FKBP1B 0 ;;;; 131.04 0.024858 1361980000 2127220 2567790 1864690 3115320 2275540 1911610 2849970 2857300 3259660 3506960 FALSE TRUE 2044085.891 2494559.143 2201680.963 3276102.039 2348734.811 1950264.064 2884848.785 2798295.756 2889637.062 3269430.476 0.62521161 0.762995012 0.673414217 1.002040589 0.718392646 0.596514922 0.882370433 0.855897006 0.883834993 1 21.64060791 -5 0.03550843 2.278359528 1.90E-13 0.380234569 0.109585983 1153.662452 3.072099263 166.3488133 57.22428278 1.00E-05 5 -2.278359528 HRDYETATLSDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 HRDYETATLSDIK 13 1 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ; 170.07 1.65E-05 1737110000 2178940 2072620 1883610 2657900 2119900 1938960 2542500 2157550 2840900 2905400 FALSE TRUE 2093784.616 2013510.907 2224020.228 2795074.538 2188088.509 1978167.1 2573615.876 2112995.839 2518412.942 2708614.67 0.773009405 0.743372961 0.821091406 1.031920328 0.807825688 0.730324295 0.950159469 0.780102043 0.929778964 1 21.36912374 -5 0.123632904 1.527876363 0.763752158 0.267871967 0.090007203 224.2716266 1.781352377 29.5428836 0.80651705 1.00E-05 5 -0.764124206 S(ph)PSPKPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPKPTK 8 1 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 S(0.993)PS(0.007)PKPTK 72.006 0.028629 224250000 206350 252540 239260 241480 266100 320100 311060 206590 427400 424840 TRUE FALSE 198285.6139 245337.8065 282499.6043 253942.8117 274659.3482 326572.6413 314866.8453 202323.8443 378883.3438 396065.2084 0.500638808 0.619437914 0.713265387 0.641164148 0.69347002 0.824542612 0.794987388 0.510834681 0.956618597 1 18.59537845 -5 0.079329013 2.040081488 0.36444469 0.517383142 0.111928604 237.8071939 1.338071742 43.48684773 4.149147206 1.00E-05 5 -1.675636797 KEDAENLAAAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEDAENLAAAQR 12 1 Q9Y6D6;E5RIF2;E5RHL7;E5RHZ1 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 ; 194.3 2.74E-06 196610000 453450 516770 409710 466480 474820 496800 556830 525440 585790 664770 FALSE TRUE 435728.6727 502032.2256 483753.7109 490555.0887 490093.0165 506845.6364 563644.6521 514589.4804 519293.575 619744.5358 0.703077877 0.810063174 0.780569546 0.791544032 0.790798447 0.81782994 0.909479018 0.830325159 0.837915536 1 19.24131412 -5 0.065661264 1.687827079 0.546020806 0.795453932 0.034239036 147.9832568 0.704487216 15.72015232 2.226210124 1.00E-05 5 -1.141806272 EEFEHQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEFEHQQK 8 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 119.27 0.0017256 2423600000 1470440 1421210 1734080 2094110 1711560 1592690 1907230 2123000 2652600 2932200 FALSE TRUE 1412973.579 1380678.482 2047466.83 2202187.268 1766613.882 1624895.283 1930571.251 2079159.308 2351487.969 2733599.482 0.516891223 0.505077094 0.749000299 0.805599826 0.646259225 0.594416005 0.706237788 0.760593979 0.860216716 1 21.38237045 -5 0.050741319 2.408199984 3.00E-12 0.676548014 0.083664969 351.8732015 1.319635463 65.52761975 14.35704174 1.00E-05 5 -2.408199984 VLSLNFSECHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSLNFSECHTK 12 0 Q9UN86-2;Q9UN86;D6RB17;D6RAC7;D6RE13;D6RBW8;D6RGJ4;D6RBM9;D6REX8;D6RBR0 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 150.14 6.79E-05 3120400000 1741160 1947940 1650520 1802550 1787410 1788920 2133400 2029960 2148980 2470100 FALSE TRUE 1673113.542 1892386.658 1948805.68 1895579.822 1844903.666 1825093.188 2159509.187 1988040.617 1905036.8 2302797.927 0.726556821 0.821777124 0.846277329 0.823163769 0.801157429 0.792554643 0.937776243 0.863315271 0.827270503 1 21.13495639 -5 0.083742323 1.557020132 0.672728702 0.636132247 0.043911008 154.1640246 0.908431729 15.63355076 1.314311206 1.00E-05 5 -0.88429143 QQDLHLES(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQDLHLESPQR 11 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 QQDLHLES(1)PQR;QQDLHLES(1)PQR 110.97 0.00052896 0 424830 420960 435550 647210 480980 531720 632820 502090 661860 813570 TRUE FALSE 408227.1739 408954.633 514263.5738 680612.5857 496451.1585 542471.7427 640564.6405 491721.666 586728.4275 758466.1792 0.538227261 0.539186379 0.678030989 0.897353902 0.654546204 0.715222059 0.844552675 0.648310603 0.773572301 1 19.53272533 -5 0.043764285 2.259896045 7.83E-13 0.550117579 0.095890933 607.5891268 1.97973816 97.00851154 26.11551746 1.00E-05 5 -2.259896045 LQFEDFIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQFEDFIDR 9 0 H3BTH1;H3BU04;Q9BVW5 H3BTH1 TIPIN TIMELESS-interacting protein 0 ; 126.31 0.0011097 46707000 87748 98351 100442 105100 102538 86980 115191 110033 109317 130706 FALSE TRUE 84318.71115 95546.12578 118594.1037 110524.2236 105836.2279 88738.79519 116600.7419 107760.7801 96907.79245 121853.1662 0.691969801 0.784108684 0.973254183 0.907027918 0.86855542 0.728243656 0.956895463 0.884349447 0.795283335 1 16.89478421 -5 0.0195357 2.072718727 2.37E-09 0.237217615 0.087435152 5669.432941 8.38727524 595.4896561 330.4302099 1.00E-05 5 -2.072718725 VLSSIEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLSSIEQK 8 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;; 160.78 0.00081746 1172360000 1442160 1494650 1308620 1406200 1435330 1250880 1596980 1589270 1625530 1733100 FALSE TRUE 1385798.793 1452024.045 1545116.744 1478774.151 1481498.693 1276173.651 1616524.319 1556451.019 1441006.649 1615715.593 0.857699708 0.898687895 0.956304903 0.915244092 0.916930368 0.789850427 1.000500537 0.963319922 0.891868999 1 20.62374184 -5 0.095571052 1.291238002 0.847984471 0.215494848 0.05471706 313.1761245 2.057311236 18.09808641 1.086236813 1.00E-05 5 -0.443253531 ELGMEERPYSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELGMEERPYSSR 12 1 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 ; 135.02 0.00012327 981790000 611950 658500 594210 667170 629360 641880 642720 723390 750590 845080 FALSE TRUE 588034.3175 639720.2247 701596.9651 701602.7237 649603.936 654859.2534 650585.7996 708451.7437 665386.1699 787841.9789 0.74638612 0.811990528 0.890530061 0.89053737 0.824535825 0.831206347 0.825782095 0.899230763 0.844568058 1 19.58754677 -5 0.154432994 1.565188471 0.798708035 0.60747898 0.040403342 97.74585071 0.884062693 16.92722044 0.197799196 1.00E-05 5 -0.766480436 YNMGLPVDFDQYNELHLPAVILK ddPTM_BT-474_Pertuzumab_2h_R1 2 YNMGLPVDFDQYNELHLPAVILK 23 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 251.02 1.52E-38 683560000 1015470 1111210 908220 1008420 992930 1107400 1097950 1109060 1266770 1340900 FALSE TRUE 975784.3097 1079519.379 1072355.557 1060464.677 1024868.495 1129792.387 1111387.041 1086157.523 1122971.58 1250079.649 0.78057771 0.863560478 0.857829786 0.848317688 0.819842557 0.903776322 0.889052983 0.868870655 0.898320024 1 20.25358859 -5 0.10638093 1.464039464 0.77129995 0.781052427 0.025751703 79.32297386 0.566237678 8.010152781 0.354275242 1.00E-05 5 -0.692739514 YQDDNSLAHPNLFIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 YQDDNSLAHPNLFIEK 16 0 Q96IZ7-2;Q96IZ7 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 0 ; 132.13 4.08E-05 186258000 225530 257010 221990 239550 247290 218430 264910 250650 299030 305900 FALSE TRUE 216716.0383 249680.3264 262108.5311 251913.2042 255244.3074 222846.8043 268152.0478 245473.9899 265085.368 285181.1205 0.759924212 0.875514922 0.919094962 0.883344605 0.895025263 0.781422009 0.940286816 0.86076522 0.92953337 1 18.12151895 -5 0.132170302 1.438851032 0.8199827 0.417357944 0.052094223 147.9802487 1.227007608 17.07749559 0.367922833 1.00E-05 5 -0.618868332 HLDVDLDRQS(ph)LSSIDKNPSER ddPTM_BT-474_Pertuzumab_2h_R1 5 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 HLDVDLDRQS(0.994)LS(0.005)S(0.001)IDKNPSER;HLDVDLDRQS(0.998)LS(0.002)SIDKNPSER;HLDVDLDRQS(0.994)LS(0.005)S(0.001)IDKNPSER;HLDVDLDRQS(0.998)LS(0.002)SIDKNPSER;HLDVDLDRQS(0.998)LS(0.001)SIDKNPSER 242.94 2.35E-30 8391150000 3877090 4202070 3611690 4015970 4298650 4768370 4960650 3533140 6218620 6097930 TRUE FALSE 3725569.036 4082231.078 4264402.725 4223234.693 4436919.981 4864789.708 5021359.919 3460179.424 5512708.328 5684911.77 0.655343335 0.718081695 0.750126457 0.742884826 0.780472971 0.855737064 0.883278426 0.608660181 0.969708687 1 22.43870653 -5 0.096008585 1.755925501 0.590585695 0.475678026 0.088415455 194.0488107 1.279394302 29.61842334 1.755766273 1.00E-05 5 -1.165339806 ALDEYYDK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDEYYDK 8 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 124.98 0.0029812 236720000 247280 245030 230050 268900 246170 232650 285240 281820 311860 359450 FALSE TRUE 237616.0242 238041.9843 271625.1524 282777.9612 254088.2816 237354.3424 288730.8524 276000.3185 276458.9602 335104.1313 0.709081154 0.710352282 0.810569393 0.843851015 0.758236792 0.708300257 0.861615317 0.823625532 0.824994187 1 18.35424995 -5 0.120640698 1.725570825 0.678291334 0.700542952 0.046823424 89.60236552 0.700041865 15.72699791 0.466635292 1.00E-05 5 -1.047279491 QSLS(ph)PMSQRPVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSLSPMSQRPVLK 13 1 Q9NSV4-1;Q9NSV4-7;Q9NSV4-6;Q9NSV4-5;Q9NSV4-4;Q9NSV4 Q9NSV4-1 DIAPH3 Protein diaphanous homolog 3 1 QSLS(0.997)PMS(0.002)QRPVLK 137.14 3.89E-05 210270000 207850 236580 202110 240350 212400 222480 251890 264990 249700 317720 TRUE FALSE 199726.9922 229832.97 238635.7729 252754.4923 219232.0389 226978.698 254972.7052 259517.8639 221355.1028 296200.5414 0.674296513 0.775937036 0.8056561 0.853322182 0.740147327 0.766300753 0.860811071 0.87615594 0.747314984 1 18.17621475 -5 0.110189061 1.640451481 0.681325587 0.579911577 0.056223572 122.8010005 0.899783156 17.83594329 0.708812893 1.00E-05 5 -0.959125894 KASS(ph)PNLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 KASSPNLHR 9 1 A0A087X030;P51956-2;P51956 A0A087X030 NEK3 Serine/threonine-protein kinase Nek3 1 KAS(0.433)S(0.567)PNLHR 131.32 0.00020603 95289000 153950 148570 120110 145060 140960 154830 156860 147370 177080 181550 TRUE FALSE 147933.4638 144332.9291 141816.5488 152546.564 145494.1064 157960.7687 158779.6996 144326.758 156978.6208 169253.4568 0.87403511 0.852762075 0.837894549 0.901290685 0.859622658 0.933279424 0.938117913 0.852725615 0.927476601 1 17.36882577 -5 0.116613422 1.380886514 0.823350676 0.617340068 0.030237246 110.0083877 0.839514054 9.890634768 0.328359963 1.00E-05 5 -0.557535838 NEEDDMVEMEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 NEEDDMVEMEEER 13 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 356.68 7.63E-76 916480000 493030 567450 485670 593800 550730 467340 604090 658230 688300 804930 FALSE TRUE 473761.8425 551266.8816 573441.3727 624446.0892 568444.7306 476789.935 611483.0341 644637.3205 610167.0696 750411.3741 0.63133617 0.734619571 0.764169351 0.832138359 0.757510814 0.635371413 0.81486376 0.859045242 0.813110103 1 19.51732217 -5 0.097971701 1.804322494 0.588552683 0.643629685 0.061268379 128.3615285 0.859991423 20.8660892 1.170026092 1.00E-05 5 -1.21576981 FGIDDQDYLVSLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 FGIDDQDYLVSLTR 14 0 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ;;; 274.8 1.11E-32 258749000 217992 253576 209374 268024 256831 181548 251413 273704 273412 292481 FALSE TRUE 209472.6316 246344.2608 247212.5393 281856.7508 265092.2024 185219.0249 254489.8675 268051.9168 242375.416 272671.0014 0.768224823 0.903448697 0.906633042 1.033688032 0.972205336 0.679276579 0.933322085 0.983059861 0.888893263 1 18.05680175 -5 0.013898959 2.071152457 2.76E-09 0.110372828 0.097513201 17451.59578 18.40738351 1688.8029 1110.361658 1.00E-05 5 -2.071152455 AS(ph)PTPLASPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPTPLASPGK 11 0 A0A1B0GTL5 A0A1B0GTL5 1 AS(0.886)PT(0.114)PLASPGK 93.614 0.0095645 203970000 163660 211660 184580 186980 203710 161820 239090 227010 244690 298500 TRUE FALSE 157263.9863 205623.664 217937.712 196630.0602 210262.5172 165092.1113 242016.0549 222322.1642 216913.817 278282.3291 0.565123868 0.738903058 0.783153255 0.706584787 0.755572651 0.593254023 0.869678128 0.798908665 0.779473917 1 18.08618978 -5 0.10403251 1.881543008 0.563633279 0.587151781 0.076336704 126.0129316 0.884468503 23.63916918 1.116987685 1.00E-05 5 -1.317909729 DFSHDDTLDVPTQVELLIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFSHDDTLDVPTQVELLIK 19 0 P42345;B1AKP8 P42345 MTOR Serine/threonine-protein kinase mTOR 0 ; 132.59 1.34E-05 82927000 96769 107799 94878 103717 103472 110516 114820 105774 137824 144215 FALSE TRUE 92987.1605 104724.6781 112024.5651 109069.8468 106800.2709 112750.7092 116225.2015 103589.7299 122178.7973 134447.1896 0.691625915 0.778927982 0.833223554 0.811246759 0.79436596 0.838624516 0.864467319 0.770486391 0.908749359 1 17.03668007 -5 0.100877859 1.617961414 0.678046027 0.720637312 0.04204744 106.4273928 0.729525532 13.78532671 0.712008392 1.00E-05 5 -0.939915387 KQVEVFR ddPTM_BT-474_Pertuzumab_2h_R1 4 KQVEVFR 7 1 A0A087X1Z3;Q9UL46;H0YLG1;H0YLD2 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 170.66 0.0015495 5216190000 4677850 4871290 4018120 4349290 4570120 4260810 4872900 4804200 5091860 5234000 FALSE TRUE 4495034.45 4732365.579 4744283.667 4573757.378 4717122.06 4346966.498 4932536.008 4704991.591 4513853.4 4879496.518 0.92120866 0.969847106 0.97228959 0.937342072 0.966723112 0.890863736 1.010869869 0.964237104 0.9250654 1 22.21830086 -5 0.296520071 1.3722131 0.951313215 0.161955058 0.032164192 493.8843454 4.5984162 114.1698193 0.031628053 1.00E-05 5 -0.420899885 FIKPLSNAYHELAQVYSTNNPSELR ddPTM_BT-474_Pertuzumab_2h_R1 1 FIKPLSNAYHELAQVYSTNNPSELR 25 1 Q9UNS2-2;Q9UNS2 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 132.84 3.99E-05 407540000 294780 341660 258100 319990 311000 342900 334380 303120 384840 414620 FALSE TRUE 283259.6717 331916.1913 304744.4114 336504.7222 321003.5974 349833.6729 338472.2425 296860.4661 341154.5766 386537.4181 0.732813069 0.858690972 0.78839563 0.87056183 0.83045931 0.905044781 0.875651946 0.767999299 0.882591337 1 18.56024855 -5 0.223882878 1.851825246 0.813538661 0.515838192 0.050353045 133.277356 1.334025906 51.38990813 0.093274895 1.00E-05 5 -1.038286585 KEVVEEAENGR ddPTM_BT-474_Pertuzumab_2h_R1 9 KEVVEEAENGR 11 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;; 201.04 7.18E-08 59047560000 30672310 30475820 24835890 26784440 27969050 28713850 27666230 30142880 31113350 28146380 FALSE TRUE 29473602.22 29606679.45 29324287.79 28166788.16 28868699.89 29294463.72 28004817.6 29520418.99 27581492.95 26240000.61 1.123231766 1.128303306 1.117541429 1.073429402 1.100179086 1.116404841 1.067256743 1.125015942 1.051123944 1 24.64526442 -5 0.161726689 0.606127408 1.130020854 0.699097362 0.021776333 73.62298273 0.680415017 9.245015608 0.088557053 1.00E-05 5 0.523893446 LDIFEFLNHVEDGLKDHYDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDIFEFLNHVEDGLKDHYDIK 21 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 281.96 3.01E-45 159785000 120936 90753 143841 103806 149382 118189 160216 82037 214768 208317 FALSE TRUE 116209.6874 88164.8133 169836.2684 109163.4401 154187.0077 120578.8626 162176.7713 80342.90728 190388.437 194207.504 0.598378976 0.453972228 0.8745093 0.562096921 0.793929197 0.620876434 0.835069541 0.413696204 0.980335121 1 17.56723942 -5 0.190554655 2.478212464 0.602365039 0.284803205 0.169655102 177.5004861 1.738123541 99.13900893 0.436149322 1.00E-05 5 -1.875847425 ATVMDVKPVDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATVMDVKPVDYR 12 1 P27694;I3L4R8 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 72.29 0.038569 206600000 491900 565060 447800 505440 499430 542800 511200 547650 585430 627230 FALSE TRUE 472676.0042 548945.0421 528727.4213 531525.819 515494.6195 553775.7879 517456.2185 536340.8361 518974.4407 584747.1534 0.808342548 0.938773346 0.904198367 0.908984021 0.881568412 0.947034602 0.884923023 0.917218379 0.887519397 1 19.15745341 -5 0.24197181 1.565465953 0.891126997 0.425207082 0.036055743 162.386623 1.618200438 45.30859269 0.05117341 1.00E-05 5 -0.674338956 IAESNHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IAESNHIK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 76.827 0.034795 405850000 287580 405250 394630 490490 348780 321830 442090 453690 507460 625770 FALSE TRUE 276341.0557 393692.6668 465948.4195 515804.2477 359998.8255 328337.6231 447500.4297 444321.143 449855.2682 583386.0405 0.473684724 0.674840739 0.798696553 0.884155965 0.617085087 0.562813644 0.767074285 0.761624571 0.771110786 1 19.15409134 -5 0.151270729 2.072039982 0.615723966 0.443599125 0.109342421 140.4414881 1.257150213 45.01582065 0.573506787 1.00E-05 5 -1.456316016 FNDIHVPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FNDIHVPVR 9 0 Q29RF7;Q29RF7-3 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 98.249 0.006142 202510000 149310 155220 138490 158860 149210 127660 173310 157250 171760 186140 FALSE TRUE 143474.8001 150793.2776 163518.2237 167058.7836 154009.4752 130241.3727 175431.0196 154002.7325 152262.5249 173532.572 0.826788876 0.868962385 0.942291247 0.962694102 0.887496067 0.750529835 1.010940007 0.887457212 0.877429079 1 17.40484696 -5 0.274204336 1.744659449 0.886687038 0.186142995 0.068404096 391.9086086 3.78510293 165.6537682 0.081183533 1.00E-05 5 -0.857972411 LLHDLQIGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLHDLQIGEK 10 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 ; 143.24 3.43E-05 1257610000 2334200 2493800 2038140 2243200 2377530 2352610 2370700 2517300 2784800 2795100 FALSE TRUE 2242976.883 2422679.266 2406477.236 2358971.821 2454005.412 2400181.386 2399713.336 2465316.875 2468681.179 2605785.387 0.860768079 0.929730928 0.923513213 0.905282466 0.941752695 0.921097109 0.920917489 0.946093599 0.947384689 1 21.31328684 -5 0.058794335 1.297042234 0.79538873 0.727251774 0.017482672 215.3505159 0.926709156 9.243771502 1.599150361 1.00E-05 5 -0.501653504 IAIVNHDK ddPTM_BT-474_Pertuzumab_2h_R1 1 IAIVNHDK 8 0 P61221;D6R9I9;D6RGF4 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 107.9 0.003915 207700000 267970 287570 261110 315520 289270 270930 309680 289690 362710 381310 FALSE TRUE 257497.4361 279368.7852 308298.3854 331804.025 298574.6323 276408.3902 313469.9565 283707.8003 321536.6814 355483.5341 0.724358265 0.785883897 0.867264882 0.933387888 0.839911286 0.7775561 0.881812873 0.79808985 0.904505133 1 18.43942321 -5 0.171396946 1.646638715 0.795659359 0.474132193 0.056942713 130.8304584 1.238539178 28.78268395 0.212089736 1.00E-05 5 -0.850979356 NFDVGHVPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFDVGHVPIR 10 0 F8VQZ7;P50579-3;P50579;F8VRR3;P50579-2 F8VQZ7 METAP2 Methionine aminopeptidase 2 0 ; 115.18 0.0012577 190159000 304940 296040 286360 327140 298200 332460 314070 342950 385320 446300 FALSE TRUE 293022.6077 287597.2291 338111.622 344023.7346 307791.8738 339182.569 317913.6826 335867.9627 341580.089 416071.7035 0.704259879 0.691220351 0.812628254 0.826837614 0.739756805 0.815202202 0.764083883 0.807235772 0.820964478 1 18.66647265 -5 0.149624921 1.80544437 0.705417937 0.774837388 0.038982154 65.11443227 0.579593923 15.5494906 0.207229023 1.00E-05 5 -1.100026433 QDPFQESGLHLS(ph)PTAAEAK ddPTM_BT-474_Pertuzumab_2h_R1 6 QDPFQESGLHLSPTAAEAK 19 0 H3BN50;Q15599-3;H3BQS0;Q15599 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 QDPFQESGLHLS(0.969)PT(0.031)AAEAK;QDPFQESGLHLS(0.994)PT(0.006)AAEAK;QDPFQESGLHLS(0.997)PT(0.003)AAEAK;QDPFQESGLHLS(0.953)PT(0.047)AAEAK;QDPFQESGLHLS(0.9)PT(0.1)AAEAK;QDPFQESGLHLS(0.932)PT(0.068)AAEAK 306.16 9.32E-51 1182636000 1800588 1724127 1736462 1748505 1710217 1777149 2129150 2032683 2252400 2578800 TRUE FALSE 1730219.03 1674956.586 2050279.311 1838745.553 1765227.683 1813084.17 2155207.175 1990707.386 1996716.995 2404135.579 0.719684466 0.696698057 0.852813514 0.764826064 0.734246312 0.754152214 0.89645825 0.828034576 0.830534273 1 21.19708683 -5 0.087075754 1.734182546 0.593416629 0.699401301 0.048420728 124.4549726 0.757772851 16.89186501 1.291032091 1.00E-05 5 -1.140765917 KAS(ph)GS(ph)ENEGDYNPGR ddPTM_BT-474_Pertuzumab_2h_R1 6 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGR;KAS(1)GS(1)ENEGDYNPGR;KAS(1)GS(1)ENEGDYNPGR;KAS(1)GS(1)ENEGDYNPGR;KAS(1)GS(1)ENEGDYNPGR;KAS(1)GS(0.999)ENEGDY(0.001)NPGR 142.94 3.01E-06 4567520000 4390970 3960060 3290330 3657910 3907330 3562910 3594900 4126450 4105380 3464320 TRUE FALSE 4219366.038 3847122.966 3884965.824 3846695.173 4033012.818 3634954.481 3638895.462 4041237.365 3639354.474 3229678.521 1.306435303 1.191178299 1.20289552 1.191045842 1.248735065 1.125484923 1.126705162 1.251281618 1.126847285 1 21.62295914 -5 0.149966706 0.293129518 1.260011819 0.631665232 0.049867466 91.94930519 0.819424653 19.35542653 0.25554877 1.00E-05 5 0.966882301 GNEFEDYCLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNEFEDYCLK 10 0 P26196;Q8IV96 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 152.62 4.12E-05 146820000 154800 149720 145380 158000 160290 127390 173710 170570 183880 197860 FALSE TRUE 148750.2449 145450.1322 171653.4 166154.3989 165445.8734 129965.9131 175835.9149 167047.6699 163006.7133 184458.766 0.806414616 0.788523828 0.930578707 0.900767161 0.896926056 0.70457976 0.953253233 0.90560982 0.88370272 1 17.49293883 -5 0.102438643 1.446187313 0.775322281 0.301766719 0.068996095 235.2339617 1.631684825 22.09981276 1.092250534 1.00E-05 5 -0.670865032 LEHCPQALR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEHCPQALR 9 0 Q6PJG6 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 93.111 0.0096207 179750000 82767 94958 96894 107800 98963 75493 107950 100460 131390 131230 FALSE TRUE 79532.37414 92249.89081 114404.9012 113363.5709 102146.2348 77019.52018 109271.1244 98385.46589 116475.158 122341.6752 0.65008407 0.754034883 0.935126162 0.926614506 0.834925912 0.62954443 0.893163545 0.804186028 0.952048089 1 16.90055641 -5 0.108678816 1.600071081 0.710299865 0.293394142 0.101760724 251.4438954 1.823733147 33.37400612 1.383744917 1.00E-05 5 -0.889771217 SNSQSDSHDEEVS(ph)PTPPNPVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSQSDSHDEEVSPTPPNPVVK 22 0 P31321;C9JSK5;C9J4C2;C9IZL8;C9JR00 P31321 PRKAR1B cAMP-dependent protein kinase type I-beta regulatory subunit 1 SNSQSDSHDEEVS(1)PTPPNPVVK;SNSQSDSHDEEVS(1)PTPPNPVVK 229.56 1.75E-26 852300000 634960 656900 626760 709530 595300 728430 823900 690780 932130 1101120 TRUE FALSE 610145.0612 638165.8552 740029.4742 746148.9283 614448.3651 743159.3537 833983.1347 676515.1516 826318.5102 1026540.162 0.594370375 0.62166672 0.720896758 0.726858 0.598562422 0.723945717 0.812421341 0.659024534 0.804954878 1 19.96935864 -5 0.138478114 2.081811534 0.577541101 0.750763847 0.058593038 69.74265328 0.594771272 20.6949784 0.374599916 1.00E-05 5 -1.504270433 EAFGFIER ddPTM_BT-474_Pertuzumab_2h_R1 4 EAFGFIER 8 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0;E9PNG3 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;; 121.05 0.0033731 981930000 843950 890270 794100 871230 856200 641090 1072810 920580 890620 1056580 FALSE TRUE 810967.501 864880.3713 937611.5347 916194.2847 883740.4506 654053.279 1085939.37 901569.7013 789520.5514 985016.8955 0.823303138 0.878036078 0.951873556 0.930130528 0.897183038 0.664002092 1.102457607 0.915283489 0.801529959 1 19.90978895 -5 0.23911679 1.593947619 0.882293043 0.081246828 0.107787026 479.0251031 4.780120407 138.7369587 0.168830778 1.00E-05 5 -0.711654576 LEDAADVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDAADVYR 9 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 169.09 0.00013663 539570000 858010 912600 784770 885010 826250 865510 937740 895910 1038860 1062870 FALSE TRUE 824478.0206 886573.5415 926595.3961 930685.4722 852827.0816 883011.2052 949216.3426 877409.1454 920932.9681 990880.8682 0.832065738 0.894732727 0.935122905 0.939250622 0.860675697 0.891137606 0.957952033 0.885483991 0.929408365 1 19.91835209 -5 0.156276844 1.352201926 0.876060949 0.461418124 0.034338022 130.0263444 1.1828081 14.20087308 0.15779705 1.00E-05 5 -0.476140977 S(ph)PSLLQSGAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSLLQSGAK 10 0 Q9BQG0;Q9BQG0-2;I3L1L3;I3L2H8 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 S(0.989)PS(0.011)LLQSGAK;S(0.999)PS(0.001)LLQSGAK;S(0.99)PS(0.01)LLQSGAK 114.93 0.0013528 745670000 730720 736730 814950 792720 683580 690360 855730 832970 892940 967250 TRUE FALSE 702162.6545 715719.1817 962229.5935 833632.3742 705567.9715 704319.5522 866202.6797 815768.8784 791577.1947 901737.296 0.778677623 0.793711411 1.067084169 0.924473655 0.782454019 0.781069559 0.960593161 0.904663567 0.877835705 1 19.78234767 -5 0.162288051 1.461099113 0.846537403 0.163649735 0.089138025 275.6456406 2.551397247 40.7860073 0.384766299 1.00E-05 5 -0.61456171 EFDKENEVFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFDKENEVFR 10 1 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 0 64.64 0.06508 315990000 438600 376560 439140 397240 396190 410350 460000 429320 518110 518220 FALSE TRUE 421459.0271 365820.8775 518502.3666 417741.604 408933.8112 418647.5582 465629.6176 420454.392 459296.3249 483120.4978 0.872368341 0.757204215 1.073236116 0.864673732 0.846442685 0.866548946 0.96379603 0.87028887 0.950686893 1 18.88202354 -5 0.126542652 1.363602448 0.846078951 0.171611504 0.078027897 270.764133 2.183836464 24.81989296 0.624961445 1.00E-05 5 -0.517523498 DADLWSSHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DADLWSSHDK 10 0 P34896-2;P34896;P34896-3;J3KRZ5;J3KRK5 P34896-2 SHMT1 "Serine hydroxymethyltransferase, cytosolic" 0 ; 154.24 1.48E-05 1727140000 1654580 1691590 1509200 1652340 1625000 1706790 1923920 1774440 2105550 2274320 FALSE TRUE 1589917.184 1643347.509 1781946.012 1737617.465 1677269.601 1741302.463 1947465.508 1737797.194 1866536.791 2120278.281 0.749862506 0.775062181 0.840430253 0.819523306 0.791061068 0.821261284 0.91849524 0.819608072 0.880326327 1 21.0158222 -5 0.084345523 1.595741444 0.657318833 0.780541636 0.032888177 107.2749129 0.63597115 11.62214479 0.960352147 1.00E-05 5 -0.938422611 FNQTYQLAHGTAEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FNQTYQLAHGTAEEK 15 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 162.29 1.60E-06 298310000 252340 262630 194900 249730 251940 245320 273130 275020 283370 329520 FALSE TRUE 242478.2738 255140.0495 230122.7655 262618.5952 260043.8789 250280.5385 276472.6466 269340.7409 251203.0256 307201.3169 0.789313914 0.830530455 0.749094333 0.854874575 0.846493373 0.814711802 0.899972205 0.876756466 0.817714677 1 18.22882487 -5 0.109495163 1.538209469 0.736816425 0.688803717 0.036255262 91.61917831 0.668200124 11.04220079 0.447454538 1.00E-05 5 -0.801393044 FYTAEIVSALEYLHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 FYTAEIVSALEYLHGK 16 0 E9PER6;O15530-5;O15530-2;O15530;O15530-3;Q6A1A2 E9PER6;Q6A1A2 PDPK1;PDPK2P 3-phosphoinositide-dependent protein kinase 1;Putative 3-phosphoinositide-dependent protein kinase 2 0 ; 184.31 1.84E-09 235820000 276773 305114 235993 251544 306880 313934 273530 304860 361250 383130 FALSE TRUE 265956.4052 296412.4475 278642.1847 264526.216 316751.0739 320281.9606 276877.542 298564.5345 320242.4145 357180.2638 0.744599946 0.829867934 0.780116409 0.740595836 0.886810124 0.896695571 0.775175927 0.835893146 0.896584853 1 18.44629284 -5 0.118286892 1.610955967 0.72527245 0.629596126 0.047564527 107.7200363 0.830265065 15.63475201 0.495365643 1.00E-05 5 -0.885683518 KFEEFQTDMAAHEER ddPTM_BT-474_Pertuzumab_2h_R1 2 KFEEFQTDMAAHEER 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 203.37 3.53E-09 604780000 581760 608750 633180 771270 623730 604120 756760 691590 864000 992720 FALSE TRUE 559024.176 591389.046 747609.711 811075.3371 643792.8419 616335.7203 766021.4553 677308.4248 765922.3422 925482.1902 0.604035585 0.639006404 0.807805616 0.876381356 0.695629639 0.66596173 0.827699834 0.731843824 0.827592741 1 19.8198457 -5 0.131100148 1.865829921 0.635763813 0.550257557 0.077847496 121.6945425 1.003954373 27.64482828 0.613488508 1.00E-05 5 -1.230066109 KTSYLTELIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSYLTELIDR 11 1 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;Q5JV98;Q9P289-2;Q5JV99;Q8NBY1;B4E0Y9;Q9P289-3;Q9P289 B4DR80;Q8NBY1 STK24;STK26 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit;Serine/threonine-protein kinase 26 0 131.35 0.00032889 1009400000 860150 958760 720880 819960 904580 916850 881560 901810 1044600 1089200 FALSE TRUE 826534.3871 931417.1035 851159.0519 862278.2339 933676.6372 935389.3352 892348.795 883187.3084 926021.3873 1015427.514 0.813976749 0.91726597 0.838227289 0.849177536 0.919491174 0.921177851 0.878791231 0.869768936 0.911952232 1 19.95365583 -5 0.170648872 1.46878197 0.851577948 0.583909475 0.032757631 98.79817123 0.933725345 15.67423203 0.117860243 1.00E-05 5 -0.617204022 IMVQSAS(ph)PDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 IMVQSASPDIR 11 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 IMVQS(0.001)AS(0.999)PDIR 118.52 0.0007445 197980000 133070 170550 149340 165120 140580 140270 176500 195580 150690 217180 TRUE FALSE 127869.4773 165686.081 176329.0601 173641.863 145101.8834 143106.3555 178660.0598 191541.2047 133584.3029 202470.2052 0.631547132 0.818323273 0.870888929 0.857616867 0.716657956 0.706802047 0.882401732 0.946021685 0.659772646 1 17.6273501 -5 0.141805911 1.661862692 0.735001242 0.263396084 0.101424808 198.2498907 1.713956577 37.31565368 0.616321288 1.00E-05 5 -0.926861451 VGGS(ph)DEEASGIPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGGSDEEASGIPSR 14 0 A8MV53;A0A0A6YYI3;A0A0B4J1V8;Q9NQ55-2;Q9NQ55;Q9NQ55-3;H7C446 A8MV53 PPAN;PPAN-P2RY11 Suppressor of SWI4 1 homolog 1 VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR;VGGS(0.997)DEEAS(0.003)GIPSR;VGGS(0.998)DEEAS(0.002)GIPSR 247.11 8.98E-18 4504250000 2030090 1798580 1719760 1520410 1822840 1794750 1696210 1884870 1820130 1661180 TRUE FALSE 1950751.838 1747286.259 2030558.888 1598878.542 1881473.304 1831041.075 1716968.725 1845946.776 1613516.473 1548666.799 1.259633021 1.128251901 1.311165765 1.032422561 1.214898715 1.182333783 1.108675363 1.191958643 1.041874517 1 20.56259535 -5 0.091563385 0.418089064 1.308627446 0.401446452 0.075456905 206.7745985 1.312203396 23.00298072 1.547065446 1.00E-05 5 0.890538382 LTPHEK ddPTM_BT-474_Pertuzumab_2h_R1 6 LTPHEK 6 0 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;;;; 117.7 0.022498 2438670000 6494920 6249050 5723520 6413380 5824770 6835330 6958350 6626580 8038800 8364280 FALSE TRUE 6241091.346 6070833.212 6757887.383 6744375.31 6012129.017 6973545.056 7043508.369 6489738.807 7126269.125 7797759.865 0.80036978 0.778535543 0.866644716 0.864911901 0.771007202 0.894301078 0.903273311 0.832256817 0.913886712 1 22.8946283 -5 0.092407282 1.520342996 0.719102657 0.661301833 0.038796312 126.9937033 0.811942945 12.8266644 0.842201889 1.00E-05 5 -0.801240339 FLAAGTHLGGTNLDFQMEQYIYK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLAAGTHLGGTNLDFQMEQYIYK 23 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 290.71 1.64E-61 2320200000 824500 712440 694840 709330 832690 761150 773680 884610 915540 994670 FALSE TRUE 792277.6285 692121.9088 820413.0446 745938.6063 859474.2301 776540.9745 783148.5273 866342.4944 811611.7375 927300.1149 0.854391815 0.746383935 0.884733035 0.804419836 0.926856598 0.837421415 0.844546997 0.934263331 0.875241709 1 19.82267681 -5 0.064335096 1.550193493 0.643344086 0.524416942 0.046790297 249.935546 1.168037283 20.75272394 3.054451134 1.00E-05 5 -0.906849407 EYIPGQPPLSQS(ph)SDS(ph)SPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLSQS(0.998)S(0.001)DS(0.506)S(0.492)PT(0.002)R 267.66 1.63E-31 796690000 389640 386270 318710 381250 364820 428050 403540 396450 452970 519030 TRUE FALSE 374412.438 375253.9578 376307.9867 400926.3582 376554.7666 436705.4643 408478.6432 388263.169 401550.7446 483875.6358 0.77377824 0.775517364 0.77769567 0.828573147 0.778205677 0.902515919 0.844181052 0.802402808 0.829863533 1 18.88427677 -5 0.162044406 1.697192788 0.762981956 0.746884242 0.0343643 69.23721238 0.640439669 15.5430472 0.147604417 1.00E-05 5 -0.934210832 KELIINEILVMK ddPTM_BT-474_Pertuzumab_2h_R1 2 KELIINEILVMK 12 1 Q13177;H7C1X3 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 ; 165.73 8.63E-05 487410000 1284560 1300560 1185970 1204920 1359670 1406280 1333260 1389920 1717270 1744400 FALSE TRUE 1234357.975 1263469.302 1400301.161 1267106.066 1403405.02 1434715.945 1349576.835 1361217.666 1522332.709 1626250.234 0.759020936 0.776921826 0.861061312 0.779158114 0.862969911 0.88222336 0.82987034 0.837028421 0.936099917 1 20.63311783 -5 0.065712114 1.623981964 0.595323537 0.757434614 0.03496207 173.7187146 0.827582538 16.63546224 2.352354083 1.00E-05 5 -1.028658427 HLNSSQPSGFGPANS(ph)LEDVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLNSSQPSGFGPANSLEDVVR 21 0 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 HLNSSQPSGFGPANS(1)LEDVVR 185.68 2.26E-17 349980000 610750 662530 667980 591920 822460 563430 837470 886890 820250 1230300 TRUE FALSE 586881.2148 643635.2931 788698.8451 622469.0621 848915.1728 574822.9406 847719.2084 868575.4116 727138.6588 1146970.685 0.51167935 0.561161067 0.687636446 0.542707037 0.740136765 0.501166201 0.73909405 0.757277778 0.633964467 1 20.12939709 -5 0.123115963 2.224191199 0.464737035 0.671270712 0.08296275 83.73489341 0.663234978 25.27514718 0.700001023 1.00E-05 5 -1.759454163 MLAEEDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLAEEDKR 8 1 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0 Q13439-5 GOLGA4 Golgin subfamily A member 4 0 95.909 0.0035785 0 124710 121820 145160 159090 140610 112960 142230 169410 163840 204710 FALSE TRUE 119836.1953 118345.8129 171393.6411 167300.654 145132.8483 115244.1286 143970.6533 165911.6243 145241.5701 190844.8094 0.627924834 0.62011544 0.89807861 0.876631932 0.760475744 0.60386305 0.754386005 0.869353612 0.76104543 1 17.54204042 -5 0.143403435 1.846663659 0.675646984 0.379169081 0.09988244 162.9645322 1.417785586 39.29311674 0.621098346 1.00E-05 5 -1.171016675 TEFLDLDNSPLSPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 TEFLDLDNSPLSPPSPR 17 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 TEFLDLDNSPLSPPS(1)PR;TEFLDLDNSPLSPPS(1)PR;TEFLDLDNSPLS(0.055)PPS(0.945)PR;TEFLDLDNSPLSPPS(1)PR 231.62 4.27E-16 667731000 502056 519497 447109 549429 516410 465004 538813 595632 609141 677037 TRUE FALSE 482435.0965 504681.4542 527911.5422 577785.0965 533020.7966 474406.6995 545407.1547 583331.9911 539993.8674 631180.6809 0.764337552 0.799583177 0.836387358 0.915403646 0.844482115 0.751617902 0.864106224 0.924191771 0.855529777 1 19.26769352 -5 0.087004267 1.530914902 0.701970362 0.561623746 0.047734023 178.0472712 1.083341201 17.54644291 1.343800897 1.00E-05 5 -0.828944541 KIGELVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KIGELVR 7 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 127.56 0.01679 0 1044600 1092500 920990 978670 1019200 1003100 1130600 1019300 1239300 1184400 FALSE TRUE 1003775.877 1061342.97 1087433.38 1029179.276 1051983.494 1023383.369 1144436.621 998251.0988 1098619.86 1104179.533 0.909069447 0.961205074 0.98483385 0.93207603 0.952728666 0.926826968 1.036458825 0.904065932 0.994964883 1 20.07454333 -5 0.116144736 1.148213753 0.930823212 0.159912971 0.03772608 323.8276904 2.464260278 11.30090803 0.380125152 1.00E-05 5 -0.217390541 TEEARPSPAPGPGT(ph)PTGTPTR ddPTM_BT-474_Pertuzumab_2h_R1 4 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 TEEARPSPAPGPGT(0.993)PT(0.007)GTPTR;TEEARPSPAPGPGT(0.992)PT(0.008)GTPTR;TEEARPS(0.001)PAPGPGT(0.959)PT(0.038)GT(0.003)PTR;TEEARPSPAPGPGT(0.926)PT(0.074)GTPTR 254.31 3.54E-36 3085470000 394698 408791 350572 438850 343286 404585 456478 431652 499090 537357 TRUE FALSE 379272.7658 397132.6809 413928.1588 461499.1011 354328.106 412765.9859 462064.5143 422738.2354 442435.3956 500961.3318 0.757089902 0.792741187 0.826267683 0.921226993 0.707296319 0.823947797 0.922355649 0.843854023 0.883172747 1 18.93433972 -5 0.09540497 1.573308376 0.699995801 0.519570198 0.056910761 162.3333196 1.064917228 18.45043077 1.112613111 1.00E-05 5 -0.873312576 RATS(ph)LPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 3 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.221)S(0.778)LPSIPNPFPELCS(0.002)PPS(0.237)QS(0.76)PILGGPSSAR;RAT(0.112)S(0.884)LPS(0.004)IPNPFPELCS(0.003)PPS(0.335)QS(0.661)PILGGPSSAR;RAT(0.182)S(0.817)LPSIPNPFPELCSPPS(0.041)QS(0.959)PILGGPSSAR 267.74 2.27E-59 1432970000 566320 604160 372418 400243 448432 535260 452059 563900 486659 442997 TRUE FALSE 544187.5883 586929.9483 439722.217 420899.5892 462856.2225 546083.3239 457591.4333 552255.2679 431415.5106 412992.4186 1.317669681 1.421163978 1.06472225 1.019146043 1.120737819 1.322259924 1.107989911 1.337204372 1.04460879 1 18.65575577 -5 0.027687479 7.94E-09 1.92137961 0.207201406 0.13220372 3499.490212 7.306132549 382.2303588 166.07917 1.00E-05 5 1.921379602 IFGPIWNR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFGPIWNR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 170.96 0.00067975 2131020000 628160 707420 641650 700710 647160 586380 760300 715970 820240 859570 FALSE TRUE 603610.8127 687245.0742 757610.4284 736873.7271 667976.4891 598237.0054 769604.7788 701184.9693 727129.7939 801350.5583 0.753241895 0.85760853 0.945416985 0.919539794 0.833563392 0.746535956 0.960384654 0.875004032 0.907380405 1 19.61207398 -5 0.14234374 1.470545023 0.822231844 0.310151043 0.066454513 186.5886495 1.616590041 24.68066351 0.401652207 1.00E-05 5 -0.648313179 ALPTSKPEGSLHS(ph)SPVGPSSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGSLHS(0.706)S(0.294)PVGPSSSK 118.01 6.79E-05 721720000 570470 596460 559410 543540 552880 644960 620670 638380 690480 854570 TRUE FALSE 548175.4017 579449.5448 660507.831 571592.1645 570663.8873 658001.5331 628265.9451 625197.2299 612099.6051 796689.2127 0.688066806 0.727321941 0.829065865 0.7174594 0.716294231 0.825919973 0.788596024 0.784744189 0.768304121 1 19.60365752 -5 0.200116245 2.079251795 0.724389275 0.756564719 0.041905253 68.54147862 0.678405362 29.55030386 0.100688231 1.00E-05 5 -1.35486252 VFHGADSDIEWLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFHGADSDIEWLQK 14 0 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 135.02 3.54E-05 300520000 274210 296160 247460 263080 283960 303920 279780 303280 348570 364010 FALSE TRUE 263493.57 287713.8068 292181.5267 276657.5903 293093.8313 310065.4706 283204.0313 297017.162 309001.7949 339355.2785 0.77645343 0.847824758 0.860990075 0.815244695 0.863678422 0.913689842 0.834535513 0.875239552 0.91055544 1 18.37243693 -5 0.100192288 1.478861824 0.753648444 0.757241724 0.02877178 92.51048159 0.630777634 9.180184982 0.483427027 1.00E-05 5 -0.72521338 KPVEGYDISFLITNFHTEQMYK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPVEGYDISFLITNFHTEQMYK 22 1 F8WCF6;P59998;P59998-3;R4GN08;P59998-4 F8WCF6 ARPC4-TTLL3;ARPC4 Actin-related protein 2/3 complex subunit 4 0 267.77 4.91E-38 618280000 624200 599540 604520 622090 694450 586180 752030 677520 871440 926040 FALSE TRUE 599805.5739 582441.7062 713770.2115 654196.1395 716787.6149 598032.9612 761233.5681 663528.9752 772517.7846 863318.486 0.694767439 0.674654505 0.826775081 0.757769178 0.830270203 0.692714185 0.881752888 0.768579598 0.894823634 1 19.71953336 -5 0.079322215 1.776652339 0.542240828 0.649783896 0.058681548 152.1877279 0.856252864 20.50025038 1.9563427 1.00E-05 5 -1.234411511 DVPLTIKDPAVGFLETISPGYSIHTYLWR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVPLTIKDPAVGFLETISPGYSIHTYLWR 29 1 P04062-4;P04062-5;P04062-2;P04062 P04062-4 GBA Glucosylceramidase 0 176.26 1.23E-13 339020000 194170 291100 228030 284790 237570 265000 275400 270490 301950 349370 FALSE TRUE 186581.6217 282798.113 269240.0935 299488.046 245211.6548 270358.4816 278770.4276 264904.287 267673.9019 325706.8587 0.572851375 0.868259619 0.826633171 0.91950181 0.752859967 0.830066897 0.855893636 0.813321181 0.821824579 1 18.31321457 -5 0.024249942 2.085432469 1.82E-13 0.375653788 0.083370525 2722.881455 4.988852327 307.6437273 148.1751316 1.00E-05 5 -2.085432469 DGNDLHMTYK ddPTM_BT-474_Pertuzumab_2h_R1 5 DGNDLHMTYK 10 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;;; 135.99 0.00012963 3161240000 7359500 8292590 7147190 8189310 7603920 8361830 8871500 8376500 10010330 10997650 FALSE TRUE 7071882.604 8056093.452 8438846.221 8611961.271 7848506.993 8530911.932 8980072.071 8203522.348 8873999.305 10252769.37 0.689753407 0.785748042 0.823079689 0.8399644 0.765501174 0.832059283 0.875867948 0.800127463 0.865522181 1 23.28951031 -4.999999999 0.096327344 1.605603272 0.670701549 0.739470667 0.039221725 105.243103 0.695717227 12.93056326 0.759623536 1.00E-05 4.999999999 -0.934901723 YFQS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 6 YFQSPSR 7 0 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 YFQS(0.997)PS(0.003)R;YFQS(0.862)PS(0.138)R;YFQS(0.541)PS(0.459)R;YFQS(0.972)PS(0.028)R;YFQS(1)PSR;YFQS(0.997)PS(0.003)R 137.05 0.003064 6318010000 3359450 4171290 3958890 4397740 3552600 1882460 6954110 3987610 4752680 6683190 TRUE FALSE 3228158.98 4052328.893 4674349.488 4624707.888 3666872.605 1920524.631 7039216.478 3905264.46 4213175.691 6230531.589 0.518119351 0.650398579 0.750232853 0.742265379 0.588532865 0.308244105 1.129793883 0.626794745 0.676214482 1 22.57092383 -4.999999999 0.163135122 2.261166301 0.585400092 0.226985733 0.193903067 204.4450658 1.896684126 83.04401736 0.765586693 1.00E-05 4.999999999 -1.675766209 QQQEMEEDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQQEMEEDQR 10 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 0 146.11 0.01223 0 53379 56243 43603 44632 49259 48741 48376 48349 58120 45318 FALSE TRUE 51292.88967 54639.00471 51483.03204 46935.46287 50843.46047 49726.57642 48968.03996 47350.57625 51522.46126 42248.57149 1.21407394 1.293274607 1.218574504 1.110936091 1.203436203 1.177000184 1.159046051 1.120761592 1.219507771 1 15.36661494 -4.999999999 0.089793268 0.416841387 1.337927571 0.614228793 0.0473109 140.1382265 0.875230621 15.81945709 1.118915383 1.00E-05 4.999999999 0.921086185 YS(ph)SSGS(ph)PANSFHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 Y(0.161)S(0.416)S(0.405)S(0.272)GS(0.747)PANSFHFK 61.648 0.044007 261530000 316570 332550 315820 338770 324910 348120 338810 322190 433230 428110 TRUE FALSE 304198.0944 323065.9996 372895.6994 356253.9603 335361.0252 355159.2249 342956.4581 315536.6639 384051.5466 399113.7284 0.762183991 0.809458499 0.934309378 0.892612644 0.840264319 0.889869728 0.859295067 0.790593361 0.962260928 1 18.60644038 -4.999999999 0.210623846 1.696796579 0.835882854 0.401328413 0.056265672 164.1052323 1.636553997 48.22270537 0.124260712 1.00E-05 4.999999999 -0.860913725 QDATVWIPS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QDATVWIPSPSR 12 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 QDATVWIPS(0.971)PS(0.029)R 127.32 0.00028509 104810000 127000 125690 122810 138990 115330 118130 142660 160390 139430 193830 TRUE FALSE 122036.6996 122105.4443 145004.4989 146163.2906 119039.6942 120518.6695 144405.9158 157077.8905 123602.4909 180701.7215 0.675348849 0.675729281 0.802452227 0.808864959 0.658763476 0.666948099 0.799139679 0.869266154 0.684013909 1 17.46325072 -4.999999999 0.168514948 1.99802337 0.683493583 0.548702238 0.071741532 105.895014 0.995845287 35.19618467 0.280398806 1.00E-05 4.999999999 -1.314529786 KVENTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVENTR 6 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 119.21 0.034002 748850000 873720 883570 744210 930530 940700 747400 1068000 981910 996890 1192180 FALSE TRUE 839574.0565 858371.4487 878705.3019 978554.7648 970958.4698 762512.9401 1081070.503 961633.2154 883727.2265 1111432.587 0.755398093 0.772310853 0.790606027 0.880444551 0.873609863 0.686063149 0.972682029 0.865219562 0.795124452 1 20.08398901 -4.999999999 0.064848918 1.596221455 0.591115878 0.381358063 0.073147214 367.2969736 1.728946145 34.01217108 4.931748579 1.00E-05 4.999999999 -1.005105578 DLKDYFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLKDYFSK 8 1 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RD83;D6RF44;Q14103-2;Q14103-4;D6RBQ9 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 101.82 0.0046745 10536500000 10080000 9763400 6661400 6652200 7981600 8678400 8254300 8718600 9536700 7402600 FALSE TRUE 9686062.456 9484957.391 7865263.162 6995520.839 8238335.413 8853883.194 8355318.593 8538557.863 8454133.797 6901215.308 1.403529961 1.374389433 1.139692476 1.013665061 1.193751397 1.28294551 1.210702495 1.237254234 1.225021017 1 22.71841901 -4.999999999 0.029481699 1.37E-08 1.938133937 0.319064068 0.103916744 2380.627991 5.286283886 268.898375 110.7296722 1.00E-05 4.999999999 1.938133923 ELDLYLAYFVHAADSSQSES(ph)PSQPSDADIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDLYLAYFVHAADSSQSESPSQPSDADIK 30 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;A0A590UK73;B1AKN7;S4R3K4 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 ELDLYLAYFVHAADS(0.013)S(0.013)QS(0.115)ES(0.686)PS(0.136)QPS(0.038)DADIK 78.921 0.0019836 27698000 24495 19482 18951 24306 22340 22010 22357 22617 29211 29150 TRUE FALSE 23537.70832 18926.39243 22375.86726 25560.43557 23058.58639 22455.05728 22630.61165 22149.95105 25895.08974 27175.64454 0.866132477 0.696446865 0.82337945 0.940564097 0.848501913 0.826293457 0.832753447 0.815066263 0.952878586 1 14.73002663 -4.999999999 0.142149762 1.586609812 0.779731674 0.415704629 0.062509639 140.266772 1.21432746 23.05261723 0.377163536 1.00E-05 4.999999999 -0.806878138 VASCS(ph)CELLTDAVDLPRPPETTAVGAVVTAPHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VASCSCELLTDAVDLPRPPETTAVGAVVTAPHSR 34 1 O14492;O14492-2 O14492 SH2B2 SH2B adapter protein 2 1 VAS(0.212)CS(0.609)CELLT(0.173)DAVDLPRPPET(0.003)T(0.002)AVGAVVTAPHSR 48.227 0.049153 39058000 45168 48949 39087 51436 49277 44061 43129 59173 52162 61967 TRUE FALSE 43402.78462 47553.02245 46150.89039 54090.61812 50862.03946 44951.94361 43656.8256 57951.05687 46240.78844 57769.9199 0.75130422 0.82314503 0.798874059 0.936311115 0.880424268 0.778120234 0.755701681 1.003135489 0.800430198 1 15.81803087 -4.999999999 0.087916964 1.507418301 0.710029544 0.314473243 0.075813038 273.7587516 1.680209863 26.21233737 1.955870305 1.00E-05 4.999999999 -0.797388757 SYS(ph)PYDYQPCLAGPNQDFHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSPYDYQPCLAGPNQDFHSK 21 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 S(0.213)YS(0.787)PYDYQPCLAGPNQDFHSK;S(0.124)YS(0.876)PYDYQPCLAGPNQDFHSK 167.72 7.56E-12 421730000 200864 187122 167389 195333 171390 211776 226864 211428 233951 290088 TRUE FALSE 193014.0128 181785.4638 197639.9158 205414.1595 176902.915 216058.2558 229640.4295 207061.9379 207393.8633 270440.0814 0.713703427 0.672183882 0.730808521 0.759555161 0.654129795 0.798913588 0.849136076 0.765648113 0.766875465 1 18.04494946 -4.999999999 0.130533488 1.868702909 0.638823029 0.764451383 0.045482634 68.00351309 0.559491043 15.36641514 0.346399904 1.00E-05 4.999999999 -1.229879879 KAGSALPGFANS(ph)PAGSTSVVLVPPAHGTLVPDGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAGSALPGFANSPAGSTSVVLVPPAHGTLVPDGNK 35 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 KAGS(0.005)ALPGFANS(0.976)PAGS(0.011)T(0.004)S(0.004)VVLVPPAHGTLVPDGNK 79.553 0.00093295 764470000 487510 546600 464460 478700 496480 549020 559960 568340 620280 750710 TRUE FALSE 468457.5702 531011.5032 548398.2539 503405.7644 512449.7301 560121.5606 566812.958 556603.5804 549868.4148 699863.743 0.669355392 0.758735552 0.783578603 0.719291104 0.73221357 0.800329444 0.809890445 0.79530278 0.785679242 1 19.41671454 -4.999999999 0.151780338 1.863905366 0.691035555 0.852903105 0.03170904 48.16434629 0.43187647 12.48626172 0.156874563 1.00E-05 4.999999999 -1.172869811 SLPGS(ph)PEFLHQEACPFVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPGSPEFLHQEACPFVGR 19 0 Q96S53-3;Q96S53-2;Q96S53 Q96S53-3 TESK2 Dual specificity testis-specific protein kinase 2 1 S(0.011)LPGS(0.989)PEFLHQEACPFVGR 185.96 2.26E-14 183220000 14211 6696.9 9682.5 12046 13787 8586.8 11278 12301 14125 16498 TRUE FALSE 13655.61841 6505.910969 11432.34314 12667.6955 14230.47138 8760.430979 11416.02354 12046.98005 12521.58922 15380.57577 0.887848324 0.422995281 0.743297475 0.823616469 0.92522358 0.569577571 0.742236423 0.783259368 0.814117066 1 13.90882189 -4.999999999 0.16474804 2.017559 0.671827086 0.242949987 0.139737549 184.3389763 1.717415643 60.90218041 0.53739062 1.00E-05 4.999999999 -1.345731915 GTGQSDDSDIWDDTALIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 0 228.19 5.96E-19 36320000 39658 32285 34203 41344 36774 38767 35477 44346 43808 51752 FALSE TRUE 38108.12152 31364.26341 40384.24294 43477.76879 37956.86911 39550.8953 35911.17814 43430.2396 38835.0995 48246.79094 0.78985816 0.650079783 0.837034799 0.901153589 0.786723186 0.819762196 0.744322626 0.900168462 0.804926063 1 15.55814537 -4.999999999 0.120311279 1.634194933 0.711231617 0.463244668 0.066516873 138.3818841 1.079128563 21.33875827 0.638979579 1.00E-05 4.999999999 -0.922963316 SS(ph)TPLPTISSSAENTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTPLPTISSSAENTR 16 0 P42166;P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 SS(0.98)T(0.02)PLPTISSSAENTR;S(0.017)S(0.982)T(0.002)PLPTISSSAENTR 241.33 7.04E-20 458680000 417030 454540 304290 464320 328210 313320 331390 522080 304990 326630 TRUE FALSE 400732.0065 441576.9642 359281.9719 488283.6108 338767.1727 319655.5451 335445.6499 511298.8656 270368.8138 304507.0592 1.316002354 1.450137036 1.179880601 1.603521482 1.11251008 1.049747569 1.101602212 1.679103489 0.887890135 1 18.21611615 -4.999999999 0.124092059 0.034084095 1.425204536 0.155950327 0.230899939 316.0047679 2.516168591 76.1095328 2.051425304 1.00E-05 4.999999999 1.391120441 KYPNKYESVIATLCENLDSLDEPEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYPNKYESVIATLCENLDSLDEPEAR 26 2 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 ; 171.79 3.12E-12 297780000 383520 378560 348500 383290 386330 390480 372090 399500 473240 476480 FALSE TRUE 368531.6144 367763.8394 411481.7023 403071.6428 398756.6553 398375.7731 376643.7487 391250.1854 419519.7792 444207.5852 0.829638274 0.82790986 0.926327501 0.907394777 0.897680878 0.896823437 0.847900309 0.880782315 0.944422818 1 18.7608745 -4.999999999 0.161101343 1.444640663 0.851025911 0.575164637 0.033106417 108.5880951 1.001823487 15.37333442 0.149786192 1.00E-05 4.999999999 -0.593614752 AAHVPENS(ph)DTEQDVLTVKPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAHVPENSDTEQDVLTVKPVR 21 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 AAHVPENS(0.999)DT(0.001)EQDVLTVKPVR;AAHVPENS(0.999)DT(0.001)EQDVLTVKPVR;AAHVPENS(0.999)DT(0.001)EQDVLTVKPVR;AAHVPENS(0.817)DT(0.183)EQDVLTVKPVR 226.56 1.44E-25 1843990000 1036060 1123380 916871 1082015 1088750 1113870 1152420 1162010 1216470 1365960 TRUE FALSE 995569.6298 1091342.302 1082569.985 1137857.924 1123770.633 1136393.215 1166523.661 1138014.087 1078381.425 1273442.313 0.781794055 0.857001759 0.850113095 0.893529226 0.882466855 0.892379029 0.916039658 0.893651857 0.846823931 1 20.28030218 -4.999999999 0.017914107 2.085364909 2.32E-18 0.666571962 0.030759183 2474.002791 3.35841588 255.4389031 148.8221308 1.00E-05 4.999999999 -2.085364909 ES(ph)PGAAATSSSGPQAQQHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESPGAAATSSSGPQAQQHR 19 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 ES(1)PGAAATSSSGPQAQQHR;ES(1)PGAAATSSSGPQAQQHR;ES(1)PGAAATSSSGPQAQQHR;ES(0.996)PGAAAT(0.002)SSS(0.002)GPQAQQHR 237.6 2.05E-24 5322675000 466782 485143 460532 543994 519231 488742 550831 525252 634864 676999 TRUE FALSE 448539.6434 471307.1966 543760.3769 572069.5955 535932.5367 498624.6981 557572.2346 514405.3626 562796.9003 631145.2547 0.710675776 0.746749172 0.861545536 0.906399266 0.849142939 0.790031604 0.883429338 0.815034826 0.89170741 1 19.26761255 -4.999999999 0.024434772 2.128428205 3.56E-13 0.59827858 0.050450087 1761.748565 3.252154598 203.6835556 97.56102717 1.00E-05 4.999999999 -2.128428205 RSS(ph)SEGLSK ddPTM_BT-474_Pertuzumab_2h_R1 3 RSSSEGLSK 9 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 RS(0.122)S(0.863)S(0.015)EGLSK;RS(0.116)S(0.825)S(0.059)EGLSK;RS(0.142)S(0.841)S(0.017)EGLSK 117.41 0.00086808 564700000 607790 629730 518390 624030 601470 674120 624950 662570 757460 799060 TRUE FALSE 584036.8949 611770.717 612074.6045 656236.2631 620816.8288 687751.1683 632598.325 648887.698 671476.3163 744938.9545 0.784006382 0.82123604 0.821643976 0.880926228 0.833379467 0.92323158 0.849194852 0.871061574 0.901384351 1 19.50676268 -4.999999999 0.053643494 1.572086508 0.585031227 0.791938517 0.026871388 218.5011173 0.863415043 17.30397522 3.481215145 1.00E-05 4.999999999 -0.987055282 HQDVFNQPTLNSFMGLGQAAWK ddPTM_BT-474_Pertuzumab_2h_R1 1 HQDVFNQPTLNSFMGLGQAAWK 22 0 P16930;H0YLC7 P16930 FAH Fumarylacetoacetase 0 201.31 1.54E-22 91053000 78875 85513 71888 92529 97238 97484 93383 81482 103090 119490 FALSE TRUE 75792.4778 83074.25297 84879.76074 97304.43278 100365.7486 99455.19327 94525.84909 79799.36823 91387.65539 111396.8359 0.680382681 0.745750562 0.761958453 0.873493686 0.90097486 0.892800882 0.848550575 0.716352198 0.820379274 1 16.76534873 -4.999999999 0.023496663 2.046578295 8.85E-09 0.433896145 0.070133179 3059.950572 5.434444478 335.7048633 165.3861679 1.00E-05 4.999999999 -2.046578286 VAEAVAHFEAQRDS(ph)PPTK ddPTM_BT-474_Pertuzumab_2h_R1 3 VAEAVAHFEAQRDSPPTK 18 1 Q6PJ61 Q6PJ61 FBXO46 F-box only protein 46 1 VAEAVAHFEAQRDS(1)PPTK;VAEAVAHFEAQRDS(0.995)PPT(0.005)K;VAEAVAHFEAQRDS(0.997)PPT(0.003)K 179.42 5.06E-14 914950000 1129290 996270 967040 965180 1030600 1090850 1087610 1068710 1251360 1287760 TRUE FALSE 1085156.098 967857.3551 1141805.64 1014993.055 1063750.185 1112907.734 1100920.497 1046640.765 1109310.859 1200538.868 0.90389085 0.806185773 0.951077612 0.845447892 0.886060596 0.927006833 0.917021952 0.871809146 0.924010782 1 20.19525068 -4.999999999 0.171690766 1.436445117 0.864376932 0.434817976 0.038977085 119.1135829 1.128355185 17.65591492 0.129070292 1.00E-05 4.999999999 -0.572068184 AIMTYVSSFYHAFSGAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIMTYVSSFYHAFSGAQK 18 0 O43707;P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 209.31 5.36E-16 204030000 392690 515620 392240 577670 445400 366120 624070 431840 580360 644580 FALSE TRUE 377343.2407 500915.0224 463126.4933 607483.6179 459726.6955 373523.1972 631707.5553 422922.3531 514479.9659 600922.0225 0.627940442 0.833577409 0.770693162 1.010919213 0.765035526 0.621583472 1.051230495 0.703789073 0.856150959 1 19.19681827 -4.999999999 0.19888248 1.857635074 0.775263862 0.175997617 0.13428954 259.9130875 2.569543695 88.76786087 0.31258038 1.00E-05 4.999999999 -1.082371211 LADHFGGK ddPTM_BT-474_Pertuzumab_2h_R1 5 LADHFGGK 8 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;;; 133.55 0.0009147 3355110000 9339030 9342760 7891850 8717740 8811670 9360100 9279410 9563230 10483330 10735120 FALSE TRUE 8974050.383 9076313.632 9318082.848 9167663.606 9095105.368 9549367.635 9392974.195 9365745.959 9293306.328 10008020.76 0.896685828 0.906903957 0.931061503 0.916031634 0.908781625 0.954171445 0.938544635 0.935823994 0.928585836 1 23.25465335 -4.999999999 0.106535872 1.239961624 0.878958331 0.790061358 0.01284192 77.79434183 0.555932686 4.100242775 0.180557941 1.00E-05 4.999999999 -0.361003293 IISPGS(ph)STPSSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 IISPGSSTPSSTR 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IISPGS(0.62)S(0.344)T(0.036)PSSTR 174.51 5.84E-07 0 437250 454820 423330 463610 363760 393310 391580 534240 411580 399500 TRUE FALSE 420161.7866 441848.9789 499835.1479 487536.9677 375460.6708 401262.9977 396372.2732 523207.7573 364859.1639 372441.5092 1.128128246 1.18635804 1.342050055 1.309029621 1.008106405 1.077385275 1.064253751 1.404805169 0.979641514 1 18.50665435 -4.999999999 0.194549838 0.188592538 1.214146256 0.143246337 0.13514561 292.7638662 2.88101749 91.94357857 0.363476497 1.00E-05 4.999999999 1.025553718 IINEPTAAAIAYGLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 IINEPTAAAIAYGLDK 16 0 Q53FA3;P34931;P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PI65;P11021;P54652 Q53FA3;P11142;P11021;P54652 HSPA1L;HSPA8;HSPA5;HSPA2 Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;78 kDa glucose-regulated protein;Heat shock-related 70 kDa protein 2 0 104.94 0.0030763 78146000 126740 132600 105680 155050 115840 128050 128590 151720 141850 171290 FALSE TRUE 121786.8607 128818.3778 124778.7268 163052.1491 119566.0988 130639.2587 130163.7229 148586.929 125747.7827 159688.3757 0.762653262 0.806686005 0.781388916 1.02106461 0.748746415 0.818088719 0.81511082 0.930480558 0.787457334 1 17.28489977 -4.999999999 0.160996116 1.604666562 0.792894529 0.292339856 0.079259546 170.6952593 1.574355797 33.0195422 0.32263968 1.00E-05 4.999999999 -0.811772033 GYPHLCSICDLPVHSNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GYPHLCSICDLPVHSNK 17 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 268.56 3.10E-28 1444700000 777690 776660 621610 828570 809110 708850 870610 818300 1020500 1049700 FALSE TRUE 747297.015 754510.4172 733948.7546 871332.597 835135.758 723183.4327 881264.7856 801401.819 904657.1183 978602.884 0.763636637 0.77100776 0.749996517 0.890384252 0.853395971 0.738995812 0.900533608 0.81892444 0.924437413 1 19.90036401 -4.999999999 0.076333124 1.646385416 0.615587508 0.620561608 0.050958501 176.6570066 0.961408121 19.20483 1.997260578 1.00E-05 4.999999999 -1.030797908 HEWQVNGLDDIKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEWQVNGLDDIKDR 14 1 Q9Y281;Q9Y281-3 Q9Y281 CFL2 Cofilin-2 0 147.68 4.79E-06 178230000 96562 96422 84755 94911 105630 99924 117430 87725 135440 137530 FALSE TRUE 92788.25029 93672.13897 100072.1139 99809.36808 109027.6849 101944.5317 118867.1435 85913.44809 120065.419 128214.9706 0.723692794 0.730586596 0.780502568 0.778453309 0.85035066 0.795106307 0.927092546 0.670073453 0.936438377 1 16.9682052 -4.999999999 0.117412862 1.673594171 0.686335623 0.491064494 0.072048031 141.6433268 1.086113315 22.7247057 0.737781696 1.00E-05 4.999999999 -0.987258548 SDTSGHFER ddPTM_BT-474_Pertuzumab_2h_R1 4 SDTSGHFER 9 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;; 160.75 6.51E-05 1914130000 1008760 1002510 353627 2329350 997310 910690 1366200 1087920 1823830 1915430 FALSE TRUE 969336.544 973919.3964 417535.2653 2449568.033 1029389.382 929104.7758 1382919.964 1065454.072 1616796.465 1785696.22 0.542833956 0.54540038 0.233822114 1.371771976 0.576463886 0.520303938 0.774443015 0.596660317 0.90541518 1 20.76805524 -4.999999999 0.050614107 2.35123079 3.77E-14 0.164188799 0.276199383 1076.945752 4.029332579 195.4919327 42.99275718 1.00E-05 4.999999999 -2.35123079 FSEAEHWLDYFPPLAIQDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSEAEHWLDYFPPLAIQDLK 20 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 141.97 1.85E-07 397260000 673030 642080 732120 722380 705930 770500 807270 768650 1004650 1088220 FALSE TRUE 646727.2435 623768.5071 864430.3699 759662.1184 728636.8796 786080.0379 817149.6117 752777.1089 890606.3438 1014513.89 0.637475001 0.614844718 0.852063612 0.748794202 0.718212818 0.77483418 0.805459264 0.742007691 0.877865106 1 19.95235719 -4.999999999 0.072715418 1.87125503 0.452206545 0.689942647 0.060381621 176.6787163 0.921440997 25.35733203 2.927154533 1.00E-05 4.999999999 -1.419048485 LKDEVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKDEVVR 7 1 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 111.74 0.0059383 548620000 734230 707650 616000 719610 717450 709360 716810 782750 853020 871820 FALSE TRUE 705535.4799 687468.5149 727324.9028 756749.1583 740527.4308 723703.7452 725582.5352 766585.939 756188.7458 812770.8549 0.868061983 0.845833128 0.894870797 0.931073197 0.911114647 0.890415473 0.892727059 0.943175969 0.930383688 1 19.63248914 -4.999999999 0.033549433 1.564208109 0.543496313 0.764708085 0.019907095 584.3039298 1.472310205 36.75410851 13.40367839 1.00E-05 4.999999999 -1.020711796 LAQMISDHNDADFEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAQMISDHNDADFEEK 16 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ; 197.75 4.25E-11 2838060000 409670 418120 381220 435270 401760 431530 443100 454350 562830 576510 FALSE TRUE 393659.6435 406195.627 450114.9342 457734.3369 414682.9753 440255.8323 448522.7903 444967.5137 498939.898 537462.4642 0.732441184 0.755765573 0.837481618 0.851658241 0.771557091 0.819137822 0.834519283 0.827904353 0.928325104 1 19.03580448 -4.999999999 0.090578117 1.643475596 0.655513215 0.785941392 0.035032638 99.82743727 0.627937092 12.19025567 0.843165521 1.00E-05 4.999999999 -0.987962382 QGSGRES(ph)PSLASR ddPTM_BT-474_Pertuzumab_2h_R1 6 QGSGRESPSLASR 13 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 QGSGRES(0.959)PS(0.04)LAS(0.001)R;QGSGRES(0.997)PS(0.003)LASR;QGSGRES(0.941)PS(0.059)LASR;QGSGRES(0.948)PS(0.052)LASR;QGS(0.001)GRES(0.992)PS(0.006)LASR;QGS(0.002)GRES(0.99)PS(0.007)LASR 220.32 5.52E-11 8302460000 3562700 3717150 2860500 3552140 3336870 3536070 3580830 3633420 4148630 4143180 TRUE FALSE 3423465.745 3611140.521 3377455.981 3735466.371 3444203.454 3607571.758 3624653.269 3558388.607 3677694.915 3862558.728 0.886320697 0.934908897 0.874408965 0.96709633 0.891689602 0.93398496 0.93840729 0.921251651 0.952139546 1 21.88112544 -4.999999999 0.126616289 1.268799786 0.886375235 0.526259541 0.025213728 109.7672379 0.88565813 7.440344612 0.186964389 1.00E-05 4.999999999 -0.382424551 DYRPTWK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYRPTWK 7 1 O00754;O00754-2 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 60.973 0.085988 406740000 154450 152500 141560 154850 159930 155380 176910 161180 197200 211840 FALSE TRUE 148413.9232 148150.8493 167143.041 162841.8271 165074.2937 158521.8901 179075.0775 157851.5767 174814.6827 197491.8881 0.751493769 0.750161694 0.84632864 0.824549447 0.835853539 0.802675449 0.906746496 0.799281318 0.885173991 1 17.59143387 -4.999999999 0.09323578 1.572941794 0.68310453 0.733772658 0.036972801 106.9869788 0.688989808 12.10762537 0.776490996 1.00E-05 4.999999999 -0.889837264 TPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPEKLDNTPASPPRSPAEPNDIPIAK 26 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 2 TPEKLDNT(0.022)PAS(0.978)PPRS(1)PAEPNDIPIAK 129.9 4.07E-05 264600000 401990 388840 265450 251200 321310 369900 320940 380690 380450 320410 TRUE FALSE 386279.7864 377750.6639 313422.7199 264164.4621 331645.228 377379.6314 324867.7597 372828.6185 337262.911 298708.3453 1.293167039 1.264613694 1.049260005 0.884355815 1.110264354 1.263371571 1.087575104 1.24813593 1.129070936 1 18.18837802 -4.999999999 0.011232547 6.55E-05 2.074946256 0.08687411 0.121756218 43193.27675 36.84507923 4027.510975 2869.563289 1.00E-05 4.999999999 2.074880787 ESMAGNKPANAVLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESMAGNKPANAVLHK 15 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y795 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 70.47 0.027994 706140000 1100200 1140700 842710 1121700 1121000 1067900 1086500 1227300 1228800 1361000 FALSE TRUE 1057202.968 1108168.353 995006.443 1179591.071 1157057.983 1089493.67 1099796.912 1201955.826 1089311.776 1268818.258 0.833218596 0.873386197 0.784199342 0.929676937 0.911917823 0.858668027 0.866788372 0.947303382 0.85852467 1 20.27505401 -4.999999999 0.081431247 1.403942413 0.757565265 0.479841107 0.042369187 207.6357719 1.194789871 14.99843636 1.347231434 1.00E-05 4.999999999 -0.646377148 IFEQKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IFEQKDR 7 1 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 83.614 0.020201 1108700000 520170 549840 596620 693810 510650 441230 653800 679030 656440 787710 FALSE TRUE 499841.1813 534159.1015 704442.5057 729617.6172 527075.521 450151.9729 661801.4 665007.7932 581923.6832 734357.7001 0.680650834 0.72738272 0.959263457 0.993545267 0.717736766 0.61298734 0.901197604 0.90556386 0.792425385 1 19.48612343 -4.999999999 0.159593819 1.68446379 0.768034618 0.192771391 0.119556305 251.667658 2.311983491 54.34415728 0.551665699 1.00E-05 4.999999999 -0.916429172 SLPSS(ph)PERR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.042)LPS(0.22)S(0.738)PERR 67.214 0.037689 280250000 30442 45851 42861 63125 48641 48783 50905 35396 58429 65383 TRUE FALSE 29252.29298 44543.37437 50606.93614 66382.88881 50205.58194 49769.42568 51527.99062 34665.06023 51796.38487 60954.55117 0.479903345 0.730763717 0.830240485 1.089055494 0.823656002 0.816500568 0.845350997 0.568703396 0.849754184 1 15.89544632 -4.999999999 0.021267114 1.942596239 1.84E-09 0.144678262 0.157621525 9089.385274 14.62704315 917.1158022 483.0969714 1.00E-05 4.999999999 -1.942596238 HLQEAEQTK ddPTM_BT-474_Pertuzumab_2h_R1 3 HLQEAEQTK 9 0 Q96P70 Q96P70 IPO9 Importin-9 0 ;; 167.67 5.98E-05 578360000 515372 489339 465144 502337 478471 542060 569115 468107 652092 664418 FALSE TRUE 495230.6925 475383.5308 549205.8679 528262.6728 493861.4543 553020.8246 576079.9996 458440.4269 578069.25 619416.3771 0.799511784 0.767470071 0.886650544 0.85283937 0.797301254 0.892809498 0.930036759 0.740116735 0.93324825 1 19.24055 -4.999999998 0.184840183 1.672494088 0.807856369 0.416059057 0.060282602 140.5672479 1.365105242 34.73515423 0.17813247 1.00E-05 4.999999998 -0.86463772 LEGFHTQISK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEGFHTQISK 10 0 Q06323;Q06323-3;Q06323-2;H0YKK6;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;; 166.86 5.42E-06 10501240000 11354380 11993920 10281820 11281630 11100930 10659470 12522460 12295130 13417320 13811860 FALSE TRUE 10910638.28 11651865.14 12139973.59 11863876.28 11458001.5 10875011.79 12675713.61 12041231.27 11894242.08 12876370.42 0.847338025 0.904902916 0.942810217 0.921368048 0.889847148 0.844571213 0.984416664 0.935141727 0.923726306 1 23.61822265 -4.999999998 0.081317629 1.304978649 0.823636405 0.415065404 0.037010623 257.2247755 1.478376219 13.81879056 1.245323096 1.00E-05 4.999999998 -0.481342244 WSHDGK ddPTM_BT-474_Pertuzumab_2h_R1 6 WSHDGK 6 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 137.83 0.012566 5428880000 13164780 12620750 10851490 12388140 12448730 14092280 14064770 12331540 16347020 16666440 FALSE TRUE 12650285.84 12260818.57 12812595.63 13027493.39 12849154.71 14377235.56 14236898.86 12076889.39 14491374.82 15537607.17 0.814172073 0.789105969 0.824618327 0.838449141 0.826971268 0.925318512 0.916286446 0.777268292 0.932664513 1 23.88926101 -4.999999998 0.102693345 1.497873563 0.743063878 0.574481999 0.04561164 144.5409037 1.004512702 15.31849114 0.751673102 1.00E-05 4.999999998 -0.754809685 YADLTEDQLPSCESLKDTIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 YADLTEDQLPSCESLKDTIAR 21 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;; 234.98 7.89E-30 7863800000 3846770 3628380 2738420 2995650 3357730 3358060 2988970 3441640 3453740 2942120 FALSE TRUE 3696433.976 3524902.155 3233313.41 3150255.855 3465734.435 3425962.274 3025549.909 3370568.931 3061685.914 2742847.592 1.347662913 1.285125052 1.178816285 1.14853478 1.263553413 1.249053095 1.103068912 1.228857535 1.116243543 1 21.38724303 -4.999999998 0.048470032 0.102851801 1.6704429 0.651851788 0.057574013 392.2531803 1.408734748 46.18379889 10.81913332 1.00E-05 4.999999998 1.567591099 KLDASILEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDASILEDR 10 1 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 0 ; 77.358 0.053295 362060000 381200 421900 355440 371440 390830 366050 395410 456300 432670 484000 FALSE TRUE 366302.2826 409867.8251 419675.9147 390610.0629 403401.4019 373451.7818 400249.1459 446877.2455 383555.1155 451218.2489 0.811807331 0.908358264 0.930095172 0.865678779 0.894027232 0.827652212 0.887041131 0.990379371 0.850043447 1 18.78346589 -4.999999998 0.13447648 1.383571585 0.847508948 0.341748296 0.048619721 166.3417621 1.393983765 16.97626704 0.343155665 1.00E-05 4.999999998 -0.536062638 VKDEPQR ddPTM_BT-474_Pertuzumab_2h_R1 7 VKDEPQR 7 1 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;;;; 118.32 0.0045891 12260990000 3924220 3545210 3233290 3196140 3647000 3024590 3422790 4023230 3515150 3209970 FALSE TRUE 3770857.144 3444104.082 3817617.427 3361093.168 3764309.067 3085749.282 3464679.128 3940148.895 3116124.909 2992555.873 1.260079111 1.150890486 1.275704645 1.12315135 1.257890989 1.031141744 1.157765895 1.316650068 1.04129214 1 21.51294675 -4.999999998 0.221244482 0.035830469 1.210750134 0.297824581 0.08995711 201.1913453 2.013317028 86.3547905 0.168027226 1.00E-05 4.999999998 1.174919664 DEVVS(ph)PLPSALQGPSGSLSAPPAASVISAPPSSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DEVVSPLPSALQGPSGSLSAPPAASVISAPPSSSSR 36 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 DEVVS(0.978)PLPS(0.022)ALQGPSGSLSAPPAASVISAPPSSSSR 147.76 2.20E-13 314450000 67943 77236 60285 68020 75569 70446 76939 67648 90779 94947 TRUE FALSE 65287.71245 75033.3049 71179.84053 71530.52035 77999.74552 71870.46639 77880.6025 66251.04516 80474.1485 88516.15512 0.737579624 0.847679215 0.804145192 0.808106952 0.881192201 0.811947449 0.879846197 0.748462753 0.909146453 1 16.43365317 -4.999999998 0.238079614 2.008202465 0.804025461 0.551440512 0.049941849 125.8622893 1.25651285 61.30831498 0.076658104 1.00E-05 4.999999998 -1.204177004 PWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_BT-474_Pertuzumab_2h_R1 6 PWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 38 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 PWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;PWLHPEQSPLPSLALSELS(0.002)VQHADS(0.997)LENIDESAVAESR;PWLHPEQS(0.001)PLPS(0.008)LALS(0.14)ELS(0.14)VQHADS(0.705)LENIDES(0.005)AVAES(0.001)R;PWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;PWLHPEQSPLPSLALSELS(0.012)VQHADS(0.988)LENIDESAVAESR;PWLHPEQSPLPSLALS(0.002)ELS(0.006)VQHADS(0.992)LENIDESAVAESR 470.58 6.77E-269 3242800000 281447 251486 282059.4 314641 293429 268799 341133 275669 404976 420566 TRUE FALSE 270447.7401 244313.8655 333033.808 330879.6597 302867.4103 274234.2999 345307.8877 269976.3388 359004.8223 392080.6902 0.689775719 0.623121392 0.849401198 0.843907053 0.772461939 0.699433323 0.880706182 0.688573412 0.915640151 1 18.58079107 -4.999999998 0.128209875 1.781630134 0.667283488 0.467965527 0.083433763 138.4592202 1.126225196 27.75211366 0.667209283 1.00E-05 4.999999998 -1.114346646 ADDGRPFPQVIK ddPTM_BT-474_Pertuzumab_2h_R1 8 ADDGRPFPQVIK 12 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;; 167.71 4.42E-05 74410160000 44779530 45283970 37021840 40979630 39734480 39305280 41484840 45883150 43156390 38333780 FALSE TRUE 43029496.46 43992515.51 43712510.03 43094593.62 41012575.64 40100059.69 41992543.88 44935646.92 38257457.53 35737398.94 1.204046678 1.230993772 1.223158689 1.205868219 1.147609419 1.122075498 1.175030784 1.257384372 1.070516005 1 25.0909313 -4.999999998 0.183823468 0.200215596 1.226406603 0.616466254 0.04710247 97.40967788 0.944444432 28.35770815 0.149455355 1.00E-05 4.999999998 1.026191008 MVEKDQDGGR ddPTM_BT-474_Pertuzumab_2h_R1 5 MVEKDQDGGR 10 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;;; 176.42 2.28E-06 4112843000 5466960 5939890 3417770 3711030 4600950 5869460 4570190 4595450 5067950 4322550 FALSE TRUE 5253305.159 5770490.153 4035437.067 3902556.703 4748943.735 5988144.503 4626121.352 4500552.352 4492657.563 4029779.838 1.303620885 1.431961642 1.001403855 0.968429259 1.178462329 1.485973116 1.147983646 1.116823383 1.114864271 1 21.94226959 -4.999999998 0.033339096 7.57E-08 1.836616994 0.158026727 0.156381756 2593.281987 6.494530335 292.6762312 107.406722 1.00E-05 4.999999998 1.836616918 EDLELIMTEMEISR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDLELIMTEMEISR 14 0 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 89.548 0.014204 4712200 7993.2 8198.5 7060.6 7101.8 8445.9 9287.7 6734.7 8491.4 9993.5 9781.8 FALSE TRUE 7680.816907 7964.686807 8336.607482 7468.324749 8717.570044 9475.503658 6817.121273 8316.049623 8859.079776 9119.269973 0.842262257 0.873390834 0.914174874 0.818960813 0.955950429 1.039063838 0.747551207 0.911920543 0.971468089 1 13.15470262 -4.999999998 0.118435246 1.348664837 0.84068162 0.189733611 0.075960408 292.1055807 2.25339528 24.35131615 0.768350443 1.00E-05 4.999999998 -0.507983217 QGDTGDWIGTFLGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 QGDTGDWIGTFLGHK 15 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 172.91 1.00E-06 3808200000 2610900 2803000 2317090 2703360 2557600 2721800 2902900 2807800 3266300 3376200 FALSE TRUE 2508863.141 2723061.184 2735839.706 2842880.734 2639867.527 2776836.661 2938426.559 2749817.949 2895523.317 3147526.967 0.797090277 0.865143083 0.869202944 0.903210922 0.838711647 0.882228076 0.933566762 0.873643968 0.919935984 1 21.58578731 -4.999999998 0.067622614 1.439653449 0.712442439 0.726494603 0.027514757 176.0953371 0.86086214 12.19700884 1.63165163 1.00E-05 4.999999998 -0.72721101 FLHCTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLHCTEK 7 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 72.138 0.0685 0 366160 395020 347990 397180 374740 428340 437110 445920 503700 573240 FALSE TRUE 351850.0624 383754.4164 410879.534 417678.5074 386793.8524 437001.3283 442459.4829 436711.5962 446522.0877 534413.9442 0.658384883 0.718084587 0.768841342 0.78156364 0.723772006 0.81772067 0.827934016 0.81717852 0.835535997 1 19.02759813 -4.999999998 0.047273423 2.002516579 0.256905062 0.901899382 0.027355058 176.4598543 0.618876502 22.78092001 5.528510513 1.00E-05 4.999999998 -1.745611517 KLS(ph)PIIEDSR ddPTM_BT-474_Pertuzumab_2h_R1 6 KLSPIIEDSR 10 1 O60566-3;O60566 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 1 KLS(1)PIIEDSR;KLS(1)PIIEDSR;KLS(1)PIIEDSR;KLS(1)PIIEDSR;KLS(0.999)PIIEDS(0.001)R;KLS(1)PIIEDSR 136.83 6.58E-05 5031650000 7041610 7129930 7063960 7136980 6986590 8471300 8164150 8247520 10087300 11477600 TRUE FALSE 6766416.096 6926591.377 8340574.709 7505320.393 7211320.012 8642595.49 8264065.31 8077205.83 8942231.993 10700211.93 0.632362811 0.647332167 0.779477525 0.70141792 0.673941793 0.807703207 0.772327255 0.754864098 0.835706064 1 23.35113604 -4.999999998 0.093327272 1.903212528 0.517259286 0.832888893 0.04208481 79.37461172 0.511572951 14.00463613 0.895819503 1.00E-05 4.999999998 -1.385953241 GHDLNEDGLVSWEEYK ddPTM_BT-474_Pertuzumab_2h_R1 6 GHDLNEDGLVSWEEYK 16 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ;;;;; 230.93 1.80E-15 7878780000 6139334 6566842 6193626 7338399 6882109 6695725 7793833 6648790 8911425 9218868 FALSE TRUE 5899402.04 6379562.096 7312951.995 7717134.652 7103478.286 6831117.147 7889216.26 6511490.163 7899837.394 8594465.859 0.686418695 0.742287211 0.850890807 0.897919054 0.826517715 0.794827423 0.917941428 0.757637562 0.919177238 1 23.03497655 -4.999999998 0.026024776 2.143362078 2.03E-08 0.533240665 0.062449654 1742.640699 3.42314503 207.4622955 94.74524078 1.00E-05 4.999999998 -2.143362058 YLDQMEDLYEDFHIVK ddPTM_BT-474_Pertuzumab_2h_R1 6 YLDQMEDLYEDFHIVK 16 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ;;;;; 219.95 1.19E-14 1344131000 1442145 1507439 1267769 1488419 1554852 1667688 1567082 1588795 1915093 2084220 FALSE TRUE 1385784.379 1464448.316 1496883.06 1565236.483 1604865.227 1701409.794 1586260.418 1555985.828 1697699.671 1943053.923 0.713199136 0.753683826 0.770376489 0.805554835 0.825949917 0.875636941 0.816374883 0.800793951 0.873727513 1 20.88989451 -4.999999998 0.060823432 1.707074572 0.505664004 0.852423551 0.029041429 166.4713904 0.739103965 17.54608034 2.860752774 1.00E-05 4.999999998 -1.201410568 GAAS(ph)PVLQEDHCDSLPSVLQVEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GAASPVLQEDHCDSLPSVLQVEEK 24 0 Q8N9B5-2;Q8N9B5 Q8N9B5-2 JMY Junction-mediating and -regulatory protein 1 GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK 346.75 5.47E-102 1714230000 1349220 1250730 1110400 1282510 1300800 1439060 1418870 1390180 1751830 1932520 TRUE FALSE 1296490.991 1215060.405 1311073.981 1348700.495 1342641.413 1468158.779 1436234.555 1361472.297 1552969.603 1801628.699 0.719621635 0.674423318 0.727715972 0.748600694 0.745237581 0.814906412 0.797186766 0.755689726 0.861980942 1 20.78087028 -4.999999998 0.109134795 1.821948363 0.60864514 0.89618943 0.028224829 50.63196872 0.368374217 9.205745962 0.376830177 1.00E-05 4.999999998 -1.213303222 FNHWELK ddPTM_BT-474_Pertuzumab_2h_R1 2 FNHWELK 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 125.25 0.0040673 3080500000 7185500 7026300 6340000 6998400 7207200 7253500 7679500 6747100 9130200 9303600 FALSE TRUE 6904682.716 6825916.803 7485779.033 7359588.263 7439026.133 7400170.74 7773484.018 6607770.027 8093777.973 8673458.885 0.796070265 0.786989008 0.863067334 0.848518262 0.857676993 0.853197189 0.896238066 0.761837937 0.93316612 1 23.04817601 -4.999999998 0.201841487 1.739880353 0.813998491 0.560070313 0.044745916 109.8866716 1.089297778 32.75697621 0.106599311 1.00E-05 4.999999998 -0.925881861 LLFGHSTEGDILELVDGHFDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLFGHSTEGDILELVDGHFDTK 22 0 Q9UHY7;A0A0C4DGY8;D6RA00;Q9UHY7-2 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 ; 348.17 3.46E-96 1183700000 410410 425170 372150 584940 457910 451170 599750 384840 739640 778620 FALSE TRUE 394370.7235 413044.5679 439405.7834 615128.8235 472639.091 460292.9665 607089.9199 376892.9195 655679.168 725883.3739 0.543297639 0.569023321 0.605339369 0.847421012 0.651122629 0.634114216 0.836346363 0.519219661 0.903284455 1 19.46937825 -4.999999998 0.124660237 2.103819826 0.5173217 0.489170659 0.115364991 135.1718923 1.079559314 37.32593852 0.990305108 1.00E-05 4.999999998 -1.586498127 TDLGAWLCDDNFPDDESR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDLGAWLCDDNFPDDESR 18 0 A0A087X2H1;Q9ULT8;H0YJD4 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 0 ; 202.89 2.89E-15 41504000 40193 40654 30835 39920 35789 38128 42227 44756 41998 50372 FALSE TRUE 38622.21312 39494.58772 36407.57042 41980.27598 36940.18569 38898.97428 42743.78666 43831.77296 37230.56311 46960.25957 0.822444626 0.841021495 0.775284693 0.893953235 0.786626523 0.828338145 0.910211891 0.933380125 0.792809994 1 15.51915276 -4.999999998 0.115288165 1.51034066 0.765264523 0.477132113 0.050348069 133.6791274 1.011963712 15.85690111 0.546297663 1.00E-05 4.999999998 -0.745076137 EFHAPLIIDENGVHELVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFHAPLIIDENGVHELVK 18 0 Q16222;Q16222-3;Q16222-2 Q16222 UAP1 UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 146.58 4.79E-08 63629000 65249 68408 63259 84540 67644 70146 70890 72961 91541 100590 FALSE TRUE 62698.99694 66457.07082 74691.30849 88903.11953 69819.83069 71564.40018 71757.57303 71454.32985 81149.64945 93776.9497 0.668597103 0.708671705 0.796478332 0.948027418 0.744530835 0.763134229 0.765194147 0.761960483 0.865347505 1 16.51694573 -4.999999997 0.205872511 2.041205071 0.745583336 0.497459602 0.070480793 133.7434294 1.329935347 57.32033382 0.167562519 1.00E-05 4.999999997 -1.295621735 S(ph)SPPVAFTEVLQAPAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPPVAFTEVLQAPAIR 17 0 A0A494C178;Q6ZSY5-2;Q6ZSY5 A0A494C178 PPP1R3F Protein phosphatase 1 regulatory subunit 3F 1 S(0.5)S(0.5)PPVAFTEVLQAPAIR 70.98 0.033028 19697000 15380 22582 18516 24674 17794 19665 20884 24425 27768 30354 TRUE FALSE 14778.9326 21937.98347 21862.25309 25947.4281 18366.36017 20062.63977 21139.58464 23920.61521 24615.89305 28298.09654 0.522258894 0.775245905 0.77256974 0.916931924 0.649031646 0.708974886 0.747032035 0.845308276 0.86987805 1 14.78841739 -4.999999997 0.067029131 1.884802581 0.429921592 0.486419301 0.093241276 314.2893781 1.524304242 43.24408363 5.885472403 1.00E-05 4.999999997 -1.454880989 DVHMPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVHMPK 6 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ; 91.584 0.047726 2877700000 6760800 6867800 6041400 6500900 6826300 6907700 7348900 6319800 8702800 8563700 FALSE TRUE 6496580.462 6671937.068 7133215.37 6836412.228 7045874.139 7047378.427 7438838.037 6189293.922 7714894.629 7983672.971 0.813733289 0.835697691 0.893475396 0.856299131 0.882535415 0.882723836 0.931756356 0.775243919 0.966333999 1 22.9286212 -4.999999997 0.194503074 1.59498035 0.84263887 0.431010717 0.049160416 138.0170081 1.358119756 31.78713818 0.125820312 1.00E-05 4.999999997 -0.75234148 YCRPESQEHPEADPGSAAPYLK ddPTM_BT-474_Pertuzumab_2h_R1 3 YCRPESQEHPEADPGSAAPYLK 22 1 P40763;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ;; 175.73 6.94E-13 849040000 303776 311467 254676 326111 314961 286604 308707 318100 377527 395722 FALSE TRUE 291904.0981 302584.2661 300701.6184 342941.6278 325092.0066 292399.3292 312485.0486 311531.1238 334671.7177 368919.3965 0.791240853 0.820190722 0.815087581 0.929584161 0.881200635 0.792583236 0.847027973 0.844442246 0.907167584 1 18.49294612 -4.999999997 0.192621832 1.680253881 0.818974808 0.593166211 0.04050123 103.7655826 1.018785402 27.00106948 0.112391531 1.00E-05 4.999999997 -0.861279073 SAALPIFSSFVSNWDEATKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAALPIFSSFVSNWDEATKR 20 1 O76021;J3QSV6;O76021-2;I3L3U9 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 213.93 4.14E-23 303150000 323640 306320 227220 211025 282810 273980 284440 306810 288570 271230 FALSE TRUE 310991.791 297584.0535 268283.7085 221916.0255 291906.8405 279520.0633 287921.0618 300474.2663 255812.7434 252859.3505 1.2299003 1.176875812 1.060999753 0.877626337 1.154423753 1.105436927 1.138660924 1.188305932 1.011679983 1 17.9479756 -4.999999997 0.010740108 3.39E-05 2.014474275 0.108679964 0.096059293 39533.90344 32.24793753 3553.086911 2569.387322 1.00E-05 4.999999997 2.014440361 DSGSDQDLDGAGVRAS(ph)DLEDEESAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSGSDQDLDGAGVRASDLEDEESAAR 26 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 DSGSDQDLDGAGVRAS(1)DLEDEESAAR 63.848 0.025406 294300000 66650 66313 62693 63156 69313 63784 78237 71819 84826 89139 TRUE FALSE 64045.24431 64421.81817 74023.0197 66415.48873 71542.51559 65073.75618 79194.48781 70335.91255 75196.9081 83101.53613 0.770686648 0.775218139 0.890753928 0.799208917 0.860904851 0.783063217 0.952984644 0.846385227 0.904879881 1 16.34258753 -4.999999997 0.046789668 1.719822181 0.470554956 0.609937864 0.046798172 397.5087363 1.380563216 36.49698746 8.984557478 1.00E-05 4.999999997 -1.249267226 SFLEDIR ddPTM_BT-474_Pertuzumab_2h_R1 5 SFLEDIR 7 0 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;; 132.09 0.0079152 1353020000 2582340 2925990 2834980 3219700 2925880 1900198 3398910 3178030 3216400 3856720 FALSE TRUE 2481419.298 2842543.63 3347323.95 3385869.103 3019993.587 1938621.305 3440506.877 3112402.57 2851287.756 3595500.919 0.690145644 0.79058348 0.93097569 0.941696075 0.839936814 0.539179755 0.956892226 0.865638096 0.793015444 1 21.77776135 -4.999999997 0.267498434 2.193036135 0.811079299 0.170240383 0.120800978 403.6657552 3.932904993 265.5011184 0.15463314 1.00E-05 4.999999997 -1.381956836 ASPS(ph)PQPSSQPLQIHR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 AS(0.135)PS(0.865)PQPSSQPLQIHR;AS(0.003)PS(0.997)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR;AS(0.18)PS(0.82)PQPSSQPLQIHR;AS(0.031)PS(0.969)PQPSSQPLQIHR 245.61 2.52E-20 5829350000 2141360 2421220 2018233 2373060 1983780 2612170 2445610 2477550 2851630 3193770 TRUE FALSE 2057673.284 2352169.176 2382972.598 2495533.911 2047590.085 2664989.867 2475540.107 2426387.727 2527924.917 2977453.113 0.691085033 0.789993692 0.800339252 0.838143815 0.687698515 0.895056871 0.831428746 0.814920549 0.849022578 1 21.50564736 -4.999999996 0.10888691 1.650987107 0.682040058 0.623614827 0.053049548 110.7875366 0.804684779 16.04656473 0.661442056 1.00E-05 4.999999996 -0.968947049 LSVHDMKPLDS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSVHDMKPLDSPGR 14 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR 217.91 3.37E-12 2560920000 2207910 2632220 2215320 2522930 2319060 2548610 2730010 2669160 2923050 3263960 TRUE FALSE 2121622.436 2557151.663 2615677.604 2653138.72 2393654.671 2600144.64 2763420.679 2614040.913 2591237.618 3042889.082 0.697239492 0.84036966 0.859603335 0.871914371 0.786638818 0.854498659 0.908156888 0.859065461 0.8515715 1 21.53701032 -4.999999996 0.022924489 2.122945994 1.98E-13 0.607519655 0.046002034 1780.917465 3.086757665 201.0422176 100.7589683 1.00E-05 4.999999996 -2.122945994 ELEHALEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEHALEK 8 0 F5H345;A0A3B3IRR1;A0A3F2YNY7;P08397-2;P08397;A0A3B3IU56;F5GY90;A0A1W2PNU5;F5H226;A0A3B3IU34;F5H0P4;P08397-4;P08397-3 F5H345 HMBS Porphobilinogen deaminase 0 81.594 0.025474 0 96244 88715 82278 117550 85114 87953 105440 104960 114150 133180 FALSE TRUE 92482.67808 86184.93506 97147.46486 123616.7696 87851.76911 89731.46992 106730.4063 102792.5393 101192.1706 124159.6 0.74486933 0.694146365 0.782440221 0.995627963 0.707571296 0.722710688 0.859622665 0.827906496 0.815016886 1 16.92183629 -4.999999996 0.152450547 1.740223665 0.734391392 0.384290701 0.082166573 148.4385006 1.333969035 33.18537175 0.409362658 1.00E-05 4.999999996 -1.005832274 SSFDWLTGSSTDPLVDHTS(ph)PSSDSLLFAHK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.02)S(0.927)PS(0.026)S(0.026)DS(0.001)LLFAHK;SSFDWLTGSSTDPLVDHT(0.432)S(0.55)PS(0.009)S(0.009)DSLLFAHK;SSFDWLTGSSTDPLVDHT(0.032)S(0.774)PS(0.171)S(0.022)DS(0.001)LLFAHK;SSFDWLTGSSTDPLVDHT(0.053)S(0.943)PS(0.004)S(0.001)DSLLFAHK 217.1 1.07E-34 1289197000 613273 629762 595153 645911 724315 737788 744333 471419 944155 838289 TRUE FALSE 589305.6132 611801.8044 702710.3862 679246.5441 747613.2498 752706.5789 753442.3699 461684.0329 836978.4826 781510.9394 0.754059327 0.782844838 0.89916897 0.86914528 0.956625445 0.963142729 0.964084227 0.590758247 1.07097475 1 19.57590654 -4.999999996 0.016704746 2.030508369 8.38E-14 0.129297744 0.125160447 13698.68827 17.348773 1353.445359 817.7665475 1.00E-05 4.999999996 -2.030508369 QHHHLLQSPVSHHEPESPQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QHHHLLQSPVSHHEPESPQLR 21 0 Q9Y6D6 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 ; 80.303 0.0022867 122593000 44063 46266 37106 43578 53264 46868 76847 41660.5 75325 106747 FALSE TRUE 42340.96925 44946.53898 43811.87962 45827.0658 54977.28493 47815.70307 77787.47657 40800.19612 66774.42179 99516.93061 0.425464984 0.451647159 0.440245487 0.460495169 0.552441525 0.480478073 0.781650681 0.409982461 0.670985544 1 16.60265437 -4.999999996 0.155627443 2.814206414 0.37064371 0.728327749 0.095751266 66.54749191 0.604150081 37.10205651 0.419639758 1.00E-05 4.999999996 -2.443562704 VECTYISIDQVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VECTYISIDQVPR 13 0 Q12765;Q12765-2;C9K052;B8ZZP4;C9J7U9 Q12765 SCRN1 Secernin-1 0 194.17 2.91E-06 192990000 74490 70992 60208 69841 73068 65862 71353 85822 72730 89835 FALSE TRUE 71578.84845 68967.37767 71088.92492 73445.50238 75418.29858 67193.77477 72226.23936 84049.74571 64473.99531 83750.39543 0.854668782 0.823487188 0.848818976 0.876957082 0.900512746 0.80230994 0.862398786 1.003574315 0.769835115 1 16.35380838 -4.999999996 0.127778402 1.439292317 0.810687626 0.28743547 0.061488884 178.736031 1.450687863 20.12892761 0.48975984 1.00E-05 4.999999996 -0.628604691 GDLLEGANAYHCEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GDLLEGANAYHCEK 14 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ;;; 190.11 6.41E-07 2051730000 1465000 1536540 1293040 1381300 1437590 1450970 1558680 1439830 1738130 1795440 FALSE TRUE 1407746.18 1492719.384 1526721.092 1452589.059 1483831.388 1480309.608 1577755.592 1410097.007 1540824.769 1673833.25 0.841031316 0.891796948 0.912110625 0.867821845 0.886486983 0.884382962 0.942600222 0.842435773 0.9205366 1 20.67472438 -4.999999995 0.300038286 1.943657554 0.880790507 0.574757652 0.02966309 189.0696587 1.748507354 112.1841837 0.028420646 1.00E-05 4.999999995 -1.062867047 SLS(ph)PNHNTLQTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.001)LS(0.999)PNHNTLQTLK;S(0.136)LS(0.864)PNHNTLQTLK 216.34 2.49E-07 180630000 273710 315270 260780 308870 273890 296480 335290 317540 369820 409270 TRUE FALSE 263013.1106 306278.8083 307908.747 324810.8177 282699.9206 302475.0287 339393.3793 310982.688 327839.584 381549.7784 0.689328432 0.802723067 0.806994957 0.851293425 0.740925396 0.792753779 0.889512715 0.815051418 0.859231489 1 18.54151176 -4.999999995 0.108797723 1.63835971 0.690559666 0.695471333 0.04417629 97.1915619 0.705505309 13.75782567 0.568522118 1.00E-05 4.999999995 -0.947800044 VLFDKDVNER ddPTM_BT-474_Pertuzumab_2h_R1 1 VLFDKDVNER 10 1 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 68.44 0.054692 329090000 698100 695340 541550 659170 744560 652260 696790 739290 844580 862850 FALSE TRUE 670817.4802 675509.584 639420.1317 693189.8427 768509.4486 665449.1441 705317.5245 724023.4032 748706.8192 804408.401 0.833926497 0.839759484 0.794894895 0.861738691 0.955372231 0.827252852 0.876815214 0.90006942 0.9307546 1 19.61756862 -4.999999995 0.06219284 1.527167198 0.656209924 0.634132279 0.036856512 243.090073 1.101519569 18.88791948 2.958950297 1.00E-05 4.999999995 -0.870957274 S(ph)GSTESLNPRPQTTISPADLHGMWYPTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSTESLNPRPQTTISPADLHGMWYPTVR 29 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.493)GS(0.493)T(0.011)ESLNPRPQT(0.001)T(0.001)ISPADLHGMWYPTVR;S(0.503)GS(0.419)T(0.078)ESLNPRPQTTISPADLHGMWYPTVR 191.02 1.98E-18 542830000 270700 264510 196654 205820 232450 254210 247690 231400 271340 216487 TRUE FALSE 260120.7447 256966.4338 232193.7523 216442.3949 239926.9654 259350.3004 250721.3043 226621.5091 240538.6208 201824.1427 1.288848506 1.273219499 1.150475604 1.072430642 1.188792194 1.285031102 1.242276078 1.122866205 1.191822829 1 17.62273924 -4.999999995 0.207350947 0.059638983 1.227157669 0.458911058 0.067316133 147.3014493 1.466201788 57.45029979 0.161472251 1.00E-05 4.999999995 1.167518687 EMVELPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EMVELPLR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 172.14 0.00066367 1727100000 2768480 2808120 2533600 3116840 2759920 2334240 3180550 3028890 3278810 3466000 FALSE TRUE 2660284.741 2728035.167 2991477.88 3277700.486 2848695.333 2381439.932 3219474.522 2966342.363 2906613.235 3231244.733 0.823300295 0.844267579 0.925797371 1.014377046 0.881609277 0.737003888 0.996357376 0.918018475 0.899533609 1 21.62365859 -4.999999995 0.090564025 1.324955494 0.814213145 0.175680501 0.075466711 413.9920883 2.603771572 26.13065521 1.808108202 1.00E-05 4.999999995 -0.51074235 S(ph)YELPDGQVITIGNER ddPTM_BT-474_Pertuzumab_2h_R1 4 SYELPDGQVITIGNER 16 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;Q9BYX7;P63261;P68133;P68032;P63267;P62736;Q6S8J3;A5A3E0 P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F" 1 S(1)YELPDGQVITIGNER;S(1)YELPDGQVITIGNER;S(1)YELPDGQVITIGNER;S(1)YELPDGQVITIGNER 223.34 9.24E-15 583680000 488461 475216 445608 480420 467023 463246 474767 541224 556594 573044 TRUE FALSE 469371.4041 461663.305 526139.2781 505214.5338 482045.2189 472613.1515 480577.3406 530047.5353 493411.7826 534231.2195 0.878592241 0.864163845 0.98485311 0.945685155 0.902315704 0.884660301 0.899568058 0.992168776 0.923592191 1 19.02710476 -4.999999995 0.063784364 1.296369338 0.805732148 0.328844355 0.039055314 454.1628889 2.105940078 20.26705838 3.031165951 1.00E-05 4.999999995 -0.49063719 RGPPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGPPEK 6 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 119.56 0.033528 371380000 395790 367620 374300 424650 387640 378960 439980 460780 547170 579690 FALSE TRUE 380322.0892 357135.8375 441944.3363 446566.2374 400108.7926 386622.8308 445364.6069 451264.732 485057.5555 540427.08 0.703743582 0.660840011 0.817768673 0.826320986 0.740356669 0.715402402 0.824097502 0.835015026 0.897544874 1 19.04374044 -4.999999994 0.069463611 1.858601617 0.474605439 0.736828567 0.049106592 167.4680997 0.83862833 22.56334781 2.86153108 1.00E-05 4.999999994 -1.383996178 GKMDMEEIIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKMDMEEIIQR 11 1 Q9H074;Q9H074-3;Q9H074-2;D6REB4 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ; 109 0.001813 554360000 1056650 1155190 916820 1128660 1026790 1099900 1163610 1144670 1344000 1385200 FALSE TRUE 1015354.95 1122245.112 1082509.769 1186910.278 1059817.633 1122140.732 1177850.607 1121032.164 1191434.755 1291379.17 0.786256255 0.869028352 0.838258657 0.919102852 0.820686641 0.868947523 0.912087352 0.868089087 0.922606452 1 20.30048123 -4.999999994 0.094126618 1.443423453 0.762841072 0.674957747 0.032852292 116.2814263 0.754608654 10.16088337 0.635363701 1.00E-05 4.999999994 -0.680582381 ASIHEAWTDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASIHEAWTDGK 11 0 O43707;O43707-2;P12814-3;P12814;P12814-2;P12814-4;H9KV75 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ;;; 161.19 2.66E-05 6083800000 5204120 5859200 6457200 10027700 5834600 5251000 8193500 8405800 9657000 11903400 FALSE TRUE 5000737.237 5692101.353 7624159.68 10545230.8 6022275.208 5357178.818 8293774.504 8232217.293 8560777.845 11097172.12 0.450631673 0.512932601 0.687036265 0.950262886 0.542685573 0.48275171 0.747377297 0.741830189 0.771437782 1 23.40368875 -4.999999994 0.072518474 2.189002819 0.250202395 0.453363875 0.134256925 300.4125852 1.563007066 58.77265412 6.823199768 1.00E-05 4.999999994 -1.938800425 CCWDEPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 CCWDEPVR 8 0 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 111.01 0.012205 0 304070 349630 258220 335920 255390 203610 380320 312080 304520 286430 FALSE TRUE 292186.6082 339658.8947 304886.0981 353256.8715 263604.8513 207727.1337 384974.4699 305635.4389 269952.1663 267029.841 1.094209573 1.271988529 1.14176789 1.32291159 0.987173757 0.777917303 1.441690818 1.144574096 1.010943815 1 18.02664145 -4.999999993 0.105843785 0.550875516 1.230002125 0.066490178 0.175636429 572.4301428 4.070693874 56.36235938 2.530769305 1.00E-05 4.999999993 0.679126609 WETFCTSSLGETNKR ddPTM_BT-474_Pertuzumab_2h_R1 1 WETFCTSSLGETNKR 15 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 179.79 1.05E-06 581600000 290930 308680 253950 279950 303860 308530 269220 318340 348280 398170 FALSE TRUE 279560.134 299876.7486 299844.4141 294398.253 313633.9329 314768.688 272514.7949 311766.1678 308744.7145 371201.5912 0.753122132 0.807854157 0.807767049 0.793095342 0.844915378 0.847972356 0.734142313 0.839883705 0.831744049 1 18.50184337 -4.999999993 0.274504626 2.368278541 0.794101905 0.743511737 0.034659515 107.1312933 1.03425606 83.20996539 0.040466075 1.00E-05 4.999999993 -1.574176636 LQLLSNLFHGMDK ddPTM_BT-474_Pertuzumab_2h_R1 4 LQLLSNLFHGMDK 13 0 Q7L2H7;J3KNJ2;E9PN86 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ;;; 218.68 2.37E-11 964230000 1635220 1669160 1563260 1551960 1692220 1586390 1858400 1683440 2019620 2060970 FALSE TRUE 1571313.795 1621557.191 1845775.857 1632056.842 1746651.793 1618467.893 1881143.655 1648676.376 1790361.205 1921378.666 0.817805372 0.843955031 0.960651791 0.849419675 0.909061719 0.842347176 0.979059302 0.858069471 0.931810702 1 20.87371044 -4.999999992 0.08966156 1.356825767 0.795930956 0.399535503 0.048114964 223.7567506 1.395783656 15.35932856 1.090454726 1.00E-05 4.999999992 -0.560894811 LHPESK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHPESK 6 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 119.7 0.020787 1031600000 918680 894000 839430 912630 830580 938960 1009300 936300 1117100 1144700 FALSE TRUE 882776.9699 868503.9953 991133.674 959730.9437 857296.36 957946.4145 1021652.115 916965.0778 990291.4913 1067168.449 0.82721427 0.813839648 0.928750915 0.899324698 0.80333743 0.897652489 0.957348501 0.859250551 0.92796174 1 20.02535649 -4.999999992 0.074227615 1.419389997 0.738813039 0.494261476 0.043781203 253.9763627 1.348797469 17.79211928 1.966118521 1.00E-05 4.999999992 -0.680576958 DQVTAQEIFQDNHEDGPTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQVTAQEIFQDNHEDGPTAK 20 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 351.02 4.11E-95 4141900000 2997700 2855900 2870100 3022300 2996400 2945300 3397700 3299000 4035900 4238300 FALSE TRUE 2880546.57 2774452.528 3388790.915 3178281.265 3092781.927 3004855.984 3439282.069 3230874.497 3577761.552 3951236.166 0.729024146 0.702173298 0.857653345 0.804376436 0.782737806 0.760485038 0.870431917 0.817687013 0.905479045 1 21.91387265 -4.999999991 0.07627773 1.721066446 0.572512425 0.738416192 0.043070634 137.8803436 0.749902497 16.69104638 1.738605461 1.00E-05 4.999999991 -1.148554021 KLPEEHAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KLPEEHAR 8 1 P41743;E9PBE1;Q05513-2;Q05513-3;Q05513 P41743;Q05513 PRKCI;PRKCZ Protein kinase C iota type;Protein kinase C zeta type 0 ;;; 138.98 0.00044292 160199000 682273 755050 658710 718640 693860 670790 795950 770190 832670 882750 FALSE TRUE 655609.0169 733516.7133 777753.5499 755729.0965 716178.637 684353.8334 805691.0742 754285.3074 738148.7924 822960.5562 0.79664695 0.891314544 0.945067833 0.918305368 0.870246613 0.831575497 0.97901542 0.916550984 0.8969431 1 19.65046376 -4.999999991 0.054226661 1.381909722 0.718668621 0.374359775 0.046800574 567.2718691 2.264385999 30.40934378 6.013911122 1.00E-05 4.999999991 -0.663241101 LREVIEIEDAS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LREVIEIEDASPTK 14 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 LREVIEIEDAS(0.987)PT(0.013)K 55.763 0.078802 117780000 101390 92154 94247 104060 102880 97171 112480 115720 134320 149220 TRUE FALSE 97427.56671 89525.85815 111279.5294 109430.5491 106189.2286 99135.8642 113856.5639 113330.3416 119072.5567 139113.1965 0.700347409 0.643546841 0.799920728 0.786629535 0.763329658 0.712627319 0.818445459 0.814662767 0.855940053 1 17.08589976 -4.99999999 0.082132155 1.827049651 0.527239543 0.802109188 0.041291293 104.0069334 0.602869029 15.2270253 1.340554855 1.00E-05 4.99999999 -1.299810108 EYELFEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EYELFEFR 8 0 A0A2R8YE10;Q9NRW7;B7Z7G7;A0A2R8YF01;A0A087WU65;A0A1B0GXI6;A0A2R8YD95;Q9NRW7-2 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;;; 145.63 0.0013173 422580000 568180 647110 558250 678320 536590 486495 735010 672690 682490 775860 FALSE TRUE 545974.8974 628655.0564 659138.1932 713328.1765 553849.9047 496332.2622 744005.2722 658798.7164 605016.5964 723310.3111 0.75482803 0.869136036 0.911279962 0.986199375 0.765715484 0.686195475 1.028611456 0.910810625 0.836455097 1 19.46425519 -4.99999999 0.136362611 1.461375863 0.816706549 0.158195285 0.099554794 286.0163254 2.417078159 35.69862451 0.684994662 1.00E-05 4.99999999 -0.644669314 IPIHNEDITYDELVLMMQR ddPTM_BT-474_Pertuzumab_2h_R1 4 IPIHNEDITYDELVLMMQR 19 0 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ;;; 209.66 2.13E-16 563663000 292123 284718 295991 371042 327729 285840 358424 331179 368470 428604 FALSE TRUE 280706.5102 276598.1214 349483.158 390191.5221 338270.7009 291619.8806 362810.5001 324340.0379 326642.8304 399574.2693 0.70251398 0.692232065 0.874638796 0.97651814 0.846577788 0.729826475 0.907992651 0.811714024 0.817477139 1 18.60810416 -4.99999999 0.023298349 2.08379202 2.77E-14 0.327214809 0.083697146 3376.22337 5.94614936 376.0844595 186.385148 1.00E-05 4.99999999 -2.08379202 LTPPESQS(ph)PLHWLADLAEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTPPESQSPLHWLADLAEQK 20 0 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 LTPPES(0.351)QS(0.649)PLHWLADLAEQK 201.35 8.17E-22 108190000 193460 174460 176560 189030 186250 194020 221960 203790 253990 267930 TRUE FALSE 185899.3693 169484.5716 208468.3196 198785.861 192240.9004 197943.2173 224676.4129 199581.6653 225158.12 249782.8625 0.74424389 0.678527622 0.834598169 0.795834666 0.769632066 0.792461162 0.899486901 0.799020651 0.901415405 1 17.93031497 -4.99999999 0.04816472 1.914718643 0.337507614 0.738799011 0.044440131 287.2415757 1.025435505 33.89362055 8.011844525 1.00E-05 4.99999999 -1.577211029 EQQEAIEHIDEVQNEIDRLNEQAS(ph)EEILK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 EQQEAIEHIDEVQNEIDRLNEQAS(1)EEILK 137.44 1.86E-06 117090000 34909 32633 36255 30900 33742 39576 33526 36429 47635 44163 TRUE FALSE 33544.71769 31702.33879 42807.08499 32494.7527 34827.34207 40376.25384 33936.30122 35676.72842 42227.6745 41171.80067 0.814749832 0.77000127 1.039718552 0.78924779 0.845902815 0.980677385 0.824260797 0.866533108 1.025645559 1 15.32936893 -4.99999999 0.0451879 1.59400255 0.566252377 0.248423535 0.085754752 1015.86265 3.412918668 75.14947493 19.3964684 1.00E-05 4.99999999 -1.027750172 MALNHPYFNDLDNQIK ddPTM_BT-474_Pertuzumab_2h_R1 1 MALNHPYFNDLDNQIK 16 0 P06493;A0A024QZP7;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 149.22 8.57E-07 514340000 625490 598000 572080 556200 605690 585410 673630 649200 723950 803100 FALSE TRUE 601045.1593 580945.6255 675467.5819 584905.5487 625172.5689 597247.3913 681874.0854 635793.7931 641770.231 748705.3217 0.802779334 0.775933613 0.902180821 0.781222641 0.835004842 0.797706887 0.910737597 0.849190963 0.857173326 1 19.51403848 -4.999999988 0.150748388 1.607932931 0.783213308 0.631067184 0.040452525 81.94316754 0.732211358 14.8094958 0.191390279 1.00E-05 4.999999988 -0.824719622 MHDYDGNNLLDGLELSTAITHVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 MHDYDGNNLLDGLELSTAITHVHK 24 0 Q8NI22-2;Q8NI22-3;Q8NI22;H7BZ18;A0A3B3IU18 Q8NI22-2 MCFD2 Multiple coagulation factor deficiency protein 2 0 144.76 7.75E-08 255170000 140690 153550 121560 168310 125140 146010 200390 119930 227240 203300 FALSE TRUE 135191.6793 149170.9043 143528.5961 176996.4993 129165.2417 148962.4222 202842.4328 117453.4036 201444.6679 189530.3099 0.713298466 0.787055666 0.757285714 0.933869096 0.68150177 0.785955673 1.070237435 0.619707759 1.062862547 1 17.53206906 -4.999999988 0.070857935 1.711142865 0.565520257 0.231701276 0.135605116 479.8164615 2.445697604 54.39924916 6.62608175 1.00E-05 4.999999988 -1.145622608 ADEASELACPTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADEASELACPTPK 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 174.42 4.65E-05 147766000 321510 355660 297260 359650 314930 382150 387720 367430 461750 493800 FALSE TRUE 308945.0338 345516.925 350981.4945 378211.5796 325060.0095 389877.3348 392465.0333 359842.4421 409334.0758 460354.4862 0.671102472 0.750545363 0.762415715 0.821565969 0.706108052 0.846906778 0.852527878 0.781663811 0.889171471 1 18.81238568 -4.999999987 0.06089998 1.827028489 0.443404848 0.769366374 0.043574867 184.2477412 0.818972222 22.38601008 3.641717188 1.00E-05 4.999999987 -1.383623641 DSDPVMAGIGEEIAHFQK ddPTM_BT-474_Pertuzumab_2h_R1 3 DSDPVMAGIGEEIAHFQK 18 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 ;; 300.01 1.66E-49 373223000 787231 774054 683825 731177 784406 813510 774379 804097 974497 945857 FALSE TRUE 756465.1422 751978.7378 807407.3891 768913.1326 809637.1314 829959.7296 783856.0818 787492.116 863876.186 881793.2629 0.857871311 0.852783492 0.915642502 0.871987987 0.918171147 0.941218043 0.888934079 0.893057533 0.979681091 1 19.75008093 -4.999999987 0.044287526 1.474805707 0.643974559 0.670970347 0.027001218 441.2380264 1.454152031 26.07810781 6.912548023 1.00E-05 4.999999987 -0.830831148 KGDVVHCWYTGTLQDGTVFDTNIQTSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGDVVHCWYTGTLQDGTVFDTNIQTSAK 28 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 329.83 4.79E-96 2370000000 1294490 1233040 1103430 1145770 1256700 1306610 1220950 1269260 1569410 1457380 FALSE TRUE 1243899.9 1197874.906 1302844.347 1204903.327 1297122.897 1333030.549 1235892.351 1243049.337 1391257.156 1358670.355 0.915527372 0.881652347 0.958911293 0.886825361 0.954700228 0.981128752 0.909633707 0.914901347 1.023984333 1 20.37376404 -4.999999986 0.028971289 1.480496121 0.609983179 0.370419929 0.03655719 1757.492876 3.836330875 88.53548343 37.01919823 1.00E-05 4.999999986 -0.870512942 DGVYFLYEALHGPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGVYFLYEALHGPPK 15 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 136.17 2.45E-05 929820000 1309450 1335510 1300700 1382090 1500770 1457470 1646940 1573960 1977010 2203900 FALSE TRUE 1258275.246 1297422.562 1535765.424 1453419.831 1549043.63 1486941.042 1667095.744 1541457.176 1752588.113 2054627.89 0.612410282 0.631463521 0.747466454 0.707388349 0.753929039 0.723703328 0.811385727 0.750236665 0.852995387 1 20.9704457 -4.999999985 0.048851685 2.179486245 0.139142187 0.891557519 0.034781884 172.036899 0.622461734 26.49415331 6.137146621 1.00E-05 4.999999985 -2.040344058 EFLEPDS(ph)WETLDQQQFFTEEELK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFLEPDSWETLDQQQFFTEEELK 23 0 P80303-2;P80303 P80303-2 NUCB2 Nucleobindin-2;Nesfatin-1 1 EFLEPDS(0.991)WET(0.009)LDQQQFFTEEELK 135.73 9.08E-06 9994300 4923.7 2902.1 3090.4 6322.5 5378.3 3307.2 5076.2 6205.4 7020.9 8979.2 TRUE FALSE 4731.276361 2819.334949 3648.904026 6648.804983 5551.297904 3374.07385 5138.324054 6077.256321 6223.916866 8371.030786 0.565196388 0.336796629 0.43589662 0.794263592 0.663155834 0.403065517 0.613822143 0.725986617 0.743506627 1 13.03118957 -4.999999983 0.08245458 2.489237991 0.158909001 0.57535307 0.124778578 177.3262844 1.031288747 46.71224278 4.074621446 1.00E-05 4.999999983 -2.330328991 FMLQDVLDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FMLQDVLDLR 10 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 121.5 0.0011942 370450000 542720 670650 560360 630890 649200 452190 697990 643840 703830 827390 FALSE TRUE 521509.9024 651523.7186 661629.5171 663450.3085 670082.1076 461333.5916 706532.2104 630544.479 623934.1691 771350.1383 0.676100096 0.844653661 0.857755103 0.860115628 0.868713279 0.598085835 0.915968216 0.817455586 0.808885794 1 19.55702636 -4.999999981 0.322217242 2.825635505 0.802604027 0.292461153 0.091171327 429.1004099 3.781387887 534.5228012 0.077341883 1.00E-05 4.999999981 -2.023031478 QLEAIDQLHLEYAK ddPTM_BT-474_Pertuzumab_2h_R1 4 QLEAIDQLHLEYAK 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 193.54 2.47E-07 2956100000 2551210 2599880 2683300 3791000 2753210 2289770 3561090 3357120 4185230 4749660 FALSE TRUE 2451505.893 2525733.968 3168232 3986653.964 2841769.5 2336070.718 3604671.685 3287794.299 3710140.236 4427961.298 0.553642123 0.570405611 0.715505802 0.900336226 0.641778306 0.527572524 0.814070278 0.742507461 0.837889039 1 22.07821118 -4.999999979 0.080591138 2.042368626 0.391237686 0.513330274 0.104949045 221.5772171 1.263760262 40.50023433 3.726664452 1.00E-05 4.999999979 -1.65113094 LS(ph)SGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 LS(0.994)S(0.006)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;LS(0.99)S(0.01)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 442.66 2.14E-231 833710000 175025 201322 188669 220486 184341 207417 246390 199364 259070 281630 TRUE FALSE 168184.8295 195580.4937 222765.6852 231865.3089 190270.4957 211611.1139 249405.3945 195247.0637 229661.4597 262554.9493 0.640570022 0.744912614 0.848453575 0.883111553 0.724688284 0.805968863 0.949916942 0.743642671 0.874717694 1 18.00225987 -4.999999979 0.028617113 2.160618751 2.48E-13 0.481892538 0.075487587 1556.369744 3.356518675 193.6451702 81.83064955 1.00E-05 4.999999979 -2.160618751 ALEAELDAQHLSETFDNIDNLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLSETFDNIDNLS(1)PK 199.3 1.07E-24 86835000 23712 32124 26675 29431 30340 31873 27001 33888 39574 41454 TRUE FALSE 22785.30882 31207.85497 31495.76588 30949.93744 31315.91365 32517.4939 27331.44631 33188.20096 35081.72543 38646.28366 0.589586027 0.807525382 0.814975281 0.800851583 0.810321477 0.841413218 0.707220559 0.858768239 0.907764528 1 15.23804207 -4.999999978 0.031314783 2.208263371 1.48E-12 0.59184603 0.066435029 1015.383546 2.3919547 134.0189876 52.24590951 1.00E-05 4.999999978 -2.208263371 RTNSS(ph)SSSPVVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTNSSSSSPVVLK 13 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 RTNS(0.063)S(0.612)S(0.063)S(0.198)S(0.064)PVVLK 211.17 2.55E-08 109670000 203420 204790 139250 163810 174810 184500 173090 194510 167400 168570 TRUE FALSE 195470.1215 198949.5897 164415.5726 172264.2537 180432.9224 188230.7164 175208.3272 190493.3005 148397.4538 157152.6038 1.243823626 1.265964324 1.046216026 1.096159081 1.148138294 1.197757542 1.114892932 1.212154912 0.944288865 1 17.26180665 -4.999999977 0.027806558 2.04E-06 1.836876623 0.356576117 0.081328857 2141.07865 4.488990604 223.9439913 96.95759666 1.00E-05 4.999999977 1.836874581 DSVVAGFQWATK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSVVAGFQWATK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 199.82 3.89E-07 301260000 250780 228030 225540 274460 281890 249430 282950 307220 364990 407500 FALSE TRUE 240979.2403 221526.8077 266300.0951 288624.9135 290957.2479 254473.6455 286412.8267 300875.7996 323557.8654 379899.662 0.634323387 0.583119254 0.700974814 0.759739853 0.765879196 0.669844359 0.753917035 0.791987542 0.851692954 1 18.5352589 -4.999999972 0.04763294 2.276715633 0.072451849 0.852945332 0.042876141 224.4320813 0.792809619 36.75752642 8.826210866 1.00E-05 4.999999972 -2.204263784 ASFNHFDK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASFNHFDK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 90.629 0.013061 259180000 523970 513580 627830 731060 524430 463940 747460 645210 786710 1058000 FALSE TRUE 503492.6731 498933.2012 741292.847 768790.0942 541298.7672 473321.1847 756607.6391 631886.188 697405.979 986340.7176 0.510465262 0.505842649 0.751558598 0.779436639 0.548794912 0.479875946 0.767085476 0.640636827 0.707063965 1 19.91172657 -4.99999997 0.196989479 2.65896985 0.571687965 0.550294228 0.104411091 112.9106092 1.114116694 73.40284723 0.271869338 1.00E-05 4.99999997 -2.087281885 YPDSHQLFVGNLPHDIDENELK ddPTM_BT-474_Pertuzumab_2h_R1 3 YPDSHQLFVGNLPHDIDENELK 22 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;; 276.3 1.06E-45 1970900000 1025657 947039 1035812 1155480 1146950 1010310 1316280 800356 1627750 1681530 FALSE TRUE 985573.1905 920030.375 1223006.27 1215114.461 1183842.688 1030739.16 1332389.028 783828.3689 1442974.644 1567638.475 0.628699286 0.586889381 0.780158365 0.775124163 0.755175831 0.657510757 0.849933865 0.500005825 0.92047667 1 20.58016146 -4.999999965 0.269615806 3.029752171 0.68446493 0.369945434 0.116462455 226.3018159 2.199033744 255.3937318 0.140847176 1.00E-05 4.999999965 -2.345287241 LEHQGIR ddPTM_BT-474_Pertuzumab_2h_R1 6 LEHQGIR 7 0 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ;;;;; 153.73 0.0017267 902430000 918745 995550 962499 1134147 915262 810844 1158817 1001447 1191357 1235570 FALSE TRUE 882839.4297 967157.8887 1136443.98 1192680.463 944702.2334 827239.8212 1172998.949 980766.7695 1056119.148 1151883.743 0.766431018 0.839631512 0.986596075 1.035417393 0.820136788 0.718162598 1.018331022 0.851445969 0.916862621 1 20.13556369 -4.999999963 0.232201601 1.622832033 0.873551582 0.117328678 0.099953919 407.3227066 4.073986773 119.2333748 0.173903999 1.00E-05 4.999999963 -0.749280451 VIEELRK ddPTM_BT-474_Pertuzumab_2h_R1 1 VIEELRK 7 1 P18074;E7EVE9;A8MX75;K7EIT8;P18074-2;K7ENL1;B4E0F6 P18074 ERCC2 TFIIH basal transcription factor complex helicase XPD subunit 0 91.065 0.046423 0 42989 46459 34179 43723 43843 52775 42215 48263 54468 59348 FALSE TRUE 41308.94235 45134.03481 40355.90561 45979.54927 45253.24991 53842.14666 42731.6398 47266.35218 48285.02099 55328.3071 0.74661497 0.815749427 0.72938985 0.831031197 0.817904112 0.973139239 0.772328705 0.854288784 0.872700133 1 15.75573016 -4.999999962 0.054768353 1.682896362 0.508079107 0.556884749 0.056198306 362.070102 1.458761253 34.6152211 6.737725481 1.00E-05 4.999999962 -1.174817255 SIPSLVDGFKPGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIPSLVDGFKPGQR 14 1 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 141.54 8.80E-06 474250000 618390 633420 463430 555810 546130 523300 559560 631510 547820 550440 FALSE TRUE 594222.6351 615355.4818 547182.1099 584495.4207 563696.7674 533881.4845 566408.0627 618469.0978 485633.7702 513158.2085 1.157971607 1.199153539 1.066302947 1.139016021 1.098485337 1.040383795 1.103768883 1.205221095 0.946362666 1 18.96904416 -4.999999961 0.038460615 0.420220522 1.457440882 0.320631063 0.065891964 1246.554894 3.586750199 85.14494049 26.8268737 1.00E-05 4.999999961 1.03722036 EKEEFR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKEEFR 6 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 0 ;; 91.041 0.04409 770540000 1081520 1176470 1007550 1229470 1081590 1000950 1232940 1257110 1376120 1482140 FALSE TRUE 1039253.003 1142918.227 1189636.698 1292923.094 1116380.325 1021189.895 1248029.089 1231150.239 1219908.627 1381753.338 0.752126284 0.827150691 0.860961697 0.935711938 0.807944728 0.739053684 0.903221331 0.891005801 0.882870042 1 20.39806867 -4.999999958 0.120974685 1.527010011 0.770381718 0.466297087 0.055990469 148.788788 1.164641384 18.92743408 0.556394639 1.00E-05 4.999999958 -0.756628293 EAKPEAPAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAKPEAPAAK 10 1 O75363;G3XAF7;O75363-2 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 89.301 0.010585 452020000 691130 678770 554980 662080 537940 530670 718470 683360 610740 588210 FALSE TRUE 664119.8755 659412.1442 655277.2315 696250.0281 555243.3286 541400.511 727262.8508 669248.3772 541411.3556 548370.0128 1.211079855 1.202494901 1.194954531 1.269671959 1.012534084 0.987290513 1.326226515 1.22043212 0.987310289 1 19.06479015 -4.999999951 0.13746937 0.417666388 1.229898475 0.210889985 0.109666858 255.4619098 2.169256627 40.56818005 0.755029608 1.00E-05 4.999999951 0.812232088 SPYQEFTDHLVK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPYQEFTDHLVK 12 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 ;;;;; 207.66 7.59E-08 6072340000 6422060 6150040 5875760 5767490 6265720 5976850 6607480 6725620 7427600 7504560 FALSE TRUE 6171078.795 5974646.881 6937640.538 6065150.85 6467262.574 6097706.002 6688344.317 6586733.597 6584449.987 6996269.467 0.88205276 0.853976095 0.991619973 0.866912128 0.92438729 0.871565344 0.955987237 0.94146368 0.941137276 1 22.73815443 -4.999999949 0.063087725 1.33881218 0.781190247 0.390693702 0.038739083 362.8874737 1.665950887 18.24992561 2.785415824 1.00E-05 4.999999949 -0.557621933 RQDLIDEWIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQDLIDEWIAK 11 1 O95251-4;O95251;O95251-2;E7EUP3;O95251-3;O95251-5 O95251-4 KAT7 Histone acetyltransferase KAT7;Histone acetyltransferase 0 123.64 0.0016339 0 415870 425080 350650 369470 431680 387580 397680 442670 454330 466480 FALSE TRUE 399617.3406 412957.1346 414020.2552 388538.391 445565.3792 395417.1332 402546.9268 433528.7098 402756.3631 434884.8941 0.918903705 0.949578015 0.952022617 0.893428115 1.024559338 0.9092455 0.925640169 0.99688151 0.926121759 1 18.73027407 -4.999999945 0.118844525 1.175606702 0.919923828 0.166181328 0.037927383 272.0758248 2.103893068 11.46108589 0.357522224 1.00E-05 4.999999945 -0.255682873 VLSTS(ph)PTISK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSTSPTISK 10 0 A0A087WX19;A0A087WX45;Q6IPM2-2;Q6IPM2-3;Q6IPM2-4;Q6IPM2;H7C427 A0A087WX19 IQCE IQ domain-containing protein E 1 VLST(0.016)S(0.983)PTISK;VLST(0.016)S(0.984)PT(0.001)ISK 208.17 1.24E-07 241920000 910720 897260 815370 861690 891910 917090 933210 1035310 1000050 1138820 TRUE FALSE 875128.0555 871671.0233 962725.4968 906161.9242 920599.0952 935634.1881 944630.9031 1013930.487 886528.5166 1061686.707 0.824280882 0.821024712 0.906788689 0.853511604 0.867109938 0.881271454 0.889745437 0.955018538 0.835018947 1 20.01792667 -4.999999934 0.051283978 1.500046088 0.631201311 0.571183587 0.035987507 360.4208548 1.365308018 24.38396555 5.257851071 1.00E-05 4.999999934 -0.868844778 QMVIDVLHPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 QMVIDVLHPGK 11 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 119.74 0.00054516 2230500000 2097180 2104930 2029420 1902160 1932310 2196760 2187960 2209240 2357700 2682600 FALSE TRUE 2015219.887 2044899.457 2396181.338 2000330.706 1994464.506 2241179.992 2214736.909 2163618.422 2090063.78 2500905.113 0.80579622 0.817663752 0.958125651 0.799842703 0.797497073 0.896147551 0.885574146 0.865134151 0.835722943 1 21.25401889 -4.999999919 0.261410048 1.949365476 0.84211402 0.457776555 0.048668047 183.6051051 1.801364046 93.69717988 0.063861537 1.00E-05 4.999999919 -1.107251456 IEVLEEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 IEVLEEELR 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 190.93 8.49E-05 626500000 234699 229922 186064 220588 209245 191774 229662 231796 219462 215849 FALSE TRUE 225526.7036 223364.8497 219689.9038 231972.5731 215975.5555 195651.8017 232472.6723 227009.3316 194549.5938 201229.355 1.120744554 1.11000132 1.091738846 1.152777005 1.073280563 0.972282606 1.155262224 1.128112405 0.966805235 1 17.61848125 -4.999999886 0.097038839 0.674000137 1.163879554 0.2583094 0.058885209 302.1201368 2.008886604 19.59643539 1.128243732 1.00E-05 4.999999886 0.489879416 TYGGDTGS(ph)PEISFTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TYGGDTGSPEISFTK 15 0 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 TYGGDT(0.162)GS(0.838)PEISFTK 138.39 1.14E-05 108480000 223310 244500 229730 211100 257130 275420 249140 304920 334450 380720 TRUE FALSE 214582.7983 237527.0994 271247.3213 221994.8963 265400.82 280989.1811 252189.0498 298623.2954 296484.6381 354933.4953 0.604571846 0.66921579 0.764220128 0.625454907 0.747748025 0.791667129 0.710524797 0.841349998 0.835324482 1 18.4371892 -4.999999877 0.050162435 2.217630833 0.140905822 0.821650991 0.047027327 207.3616379 0.769297495 33.05510206 7.366846096 1.00E-05 4.999999877 -2.076725011 T(ph)PESFLGPSASSLVNLDSLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPESFLGPSASSLVNLDSLVK 21 0 Q9H201 Q9H201 EPN3 Epsin-3 1 T(0.886)PES(0.114)FLGPSASSLVNLDSLVK;T(0.874)PES(0.122)FLGPS(0.003)ASSLVNLDSLVK 186.97 1.12E-16 174916000 106007 108826 112038 110435 105660 115255 122197 134447 139615 157946 TRUE FALSE 101864.1292 105722.389 132285.7589 116134.5636 109058.6499 117585.5351 123692.4834 131670.6225 123766.4905 147248.1767 0.691785335 0.717987763 0.898386396 0.788699501 0.740645163 0.79855342 0.840027267 0.894208848 0.840529868 1 17.16789024 -4.999999876 0.035514806 2.090354032 0.135388337 0.659810047 0.05198678 661.0226777 1.760552435 81.79218896 28.13134052 1.00E-05 4.999999876 -1.954965695 KEPLY(ph)AAFPGSHLTNGDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEPLYAAFPGSHLTNGDLR 19 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 KEPLY(1)AAFPGSHLTNGDLR 93.776 0.001056 70608000 51897 57634 43213 60990 54654 52948 64011 57976 74246 77578 TRUE FALSE 49868.80786 55990.33475 51022.55037 64137.70121 56411.99555 54018.64484 64794.38577 56778.77534 65817.90534 72323.57296 0.689523565 0.77416439 0.705476075 0.886815994 0.779994589 0.746902326 0.895895807 0.785065961 0.910047757 1 16.14217833 -4.999999867 0.057759164 1.821348008 0.438631563 0.647144399 0.056687284 261.7085995 1.107853047 30.56896541 5.450938539 1.00E-05 4.999999867 -1.382716445 HEDLVPPAGS(ph)PELS(ph)PPQPLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 HEDLVPPAGSPELSPPQPLFR 21 0 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 2 HEDLVPPAGS(1)PELS(1)PPQPLFR;HEDLVPPAGS(1)PELS(1)PPQPLFR 106.11 0.00019791 59337000 123268 131949 141536 187046 153693 147627 177805 114998 189605 204626 TRUE FALSE 118450.5503 128185.9437 167114.7037 196699.4665 158636.6749 150612.1191 179981.0308 112623.2511 168081.8353 190766.4988 0.620919035 0.67195207 0.87601704 1.031100679 0.831575124 0.789510318 0.943462463 0.590372271 0.881086755 1 17.54144831 -4.999999859 0.020778916 1.978868581 1.09E-11 0.165666334 0.133712241 8047.288194 12.65564597 821.407817 439.0744127 1.00E-05 4.999999859 -1.978868581 EECPAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EECPAVR 7 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 89.427 0.041599 138420000 224010 234780 208390 264790 249110 266180 265820 227350 281610 320430 FALSE TRUE 215255.4415 228084.3043 246050.7086 278455.8436 257122.8494 271562.342 269073.1847 222655.1431 249642.8134 298726.9907 0.720575804 0.763520912 0.823664136 0.932141562 0.860728549 0.909065302 0.900732753 0.745346587 0.835688844 1 18.18846807 -4.999999856 0.019564565 2.029012952 6.22E-12 0.374671203 0.066865147 4862.286596 7.203744114 500.1487424 277.2859442 1.00E-05 4.999999856 -2.029012952 ASPHAT(ph)PSTLHFPT(ph)SPIIQQPGPYFSHPAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPHATPSTLHFPTSPIIQQPGPYFSHPAIR 31 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;B1AKN6 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 2 AS(0.441)PHAT(0.498)PS(0.037)T(0.037)LHFPT(0.493)S(0.493)PIIQQPGPYFSHPAIR 79.9 0.0018287 240440000 48014 47526 58101 59516 58245 53560 53204 54916 57436 69649 TRUE FALSE 46137.5598 46170.60501 68601.14315 62587.62789 60118.50332 54643.0199 53855.12647 53781.96541 50916.10607 64931.61119 0.710556214 0.711065137 1.056513798 0.963900737 0.925874196 0.841547266 0.829413062 0.828286322 0.784149741 1 15.98663339 -4.999999845 0.011398652 1.916377097 2.54E-11 0.093880849 0.1066978 38747.41721 33.54116074 3345.181697 2371.53835 1.00E-05 4.999999845 -1.916377097 S(ph)QEALHEQSSYILSSAETPARPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQEALHEQSSYILSSAETPARPR 23 1 Q9NVE5;Q9NVE5-3 Q9NVE5 USP40 Ubiquitin carboxyl-terminal hydrolase 40 1 S(1)QEALHEQSSYILSSAETPARPR 66.383 0.017 139350000 30029 41985 41480 42693 37658 42594 31680 47287 48892 51623 TRUE FALSE 28855.43348 40787.62891 48976.35872 44896.39085 38869.30377 43455.27986 32067.70932 46310.50693 43341.98513 48126.52823 0.599574383 0.847508233 1.017658255 0.932882394 0.807648197 0.902938181 0.666320852 0.962265691 0.90058408 1 15.55454473 -4.999999837 0.020238501 2.097326135 1.84E-13 0.178171048 0.118825956 6819.686244 10.44860966 732.1135874 397.7484281 1.00E-05 4.999999837 -2.097326135 IYGADDIELLPEAQHK ddPTM_BT-474_Pertuzumab_2h_R1 5 IYGADDIELLPEAQHK 16 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;;; 223.96 8.24E-15 3044180000 4599180 4553140 3978901 4442040 4334340 4695641 5044080 4664040 5901150 6190160 FALSE TRUE 4419438.961 4423288.905 4697976.921 4671294.217 4473757.982 4790590.078 5105810.96 4567725.944 5231276.192 5770894.95 0.765815181 0.766482312 0.814081171 0.809457503 0.775227763 0.830129489 0.884752019 0.791510846 0.906493055 1 22.46036364 -4.999999836 0.119156978 1.64599294 0.715736552 0.807033051 0.031329887 63.70591079 0.493515162 9.792939714 0.302835318 1.00E-05 4.999999836 -0.930256388 IDST(ph)EVIYQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDSTEVIYQPR 11 0 K7EMR0;K7EQN8;K7EP59;Q15831-2;Q15831 K7EMR0 STK11 Serine/threonine-protein kinase STK11 1 IDS(0.332)T(0.668)EVIYQPR 202 4.64E-07 444430000 224520 205500 186750 196960 198250 186510 185570 235880 213340 190420 TRUE FALSE 215745.5102 199639.3412 220499.8792 207125.1292 204626.8913 190281.36 187841.0612 231008.9956 189122.5376 177522.6838 1.215312351 1.124584965 1.242094106 1.16675303 1.152680249 1.071870681 1.058124275 1.30129283 1.065342938 1 17.43764386 -4.999999819 0.254614489 6.41E-08 1.174991373 0.300475379 0.074687574 249.8886305 2.467992565 130.4382843 0.10601487 1.00E-05 4.999999819 1.174991308 DVPLVHLDEITLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVPLVHLDEITLFK 14 0 Q96ME1-4 Q96ME1-4 FBXL18 F-box/LRR-repeat protein 18 0 160.69 4.72E-06 146690000 302020 315940 272870 282480 309790 313790 308730 308720 380140 362780 FALSE TRUE 290216.7245 306929.7005 322183.679 297058.8267 319754.6767 320135.0488 312508.3301 302344.8241 336988.1009 338208.5875 0.85809981 0.907515988 0.952618268 0.878330231 0.945436303 0.946560971 0.92401063 0.893959631 0.99639132 1 18.36755377 -4.999999803 0.05671544 1.31029792 0.782149491 0.477938687 0.032321608 436.260123 1.815786657 19.21282563 3.53225016 1.00E-05 4.999999803 -0.528148429 ELEQHIQTS(ph)DPENFQSEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEQHIQTSDPENFQSEER 19 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 ELEQHIQT(0.026)S(0.974)DPENFQSEER 193.19 3.75E-15 367590000 127840 136330 123730 143050 136820 145230 155860 134730 162580 179650 TRUE FALSE 122843.8715 132442.0019 146090.7634 150432.8276 141220.9396 148166.6501 157767.4613 131947.7784 144124.6 167482.1455 0.733474432 0.790782811 0.872276641 0.898202177 0.843199967 0.884671316 0.941995703 0.787831909 0.860537101 1 17.35364778 -4.99999977 0.019927126 2.070518766 2.94E-08 0.481350556 0.053319946 3440.556908 5.190943665 363.0158098 199.075545 1.00E-05 4.99999977 -2.070518737 RQDEDYDEQVEESLQDEDDNDVYILTK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQDEDYDEQVEESLQDEDDNDVYILTK 27 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 267.43 2.28E-53 414520000 243500 277210 225260 234640 260070 292790 281670 289850 351810 385230 FALSE TRUE 233983.7508 269304.2422 265969.4929 246749.7985 268435.3877 298710.4144 285117.1617 283864.4962 311874.0037 359138.029 0.651514827 0.749862784 0.740577359 0.687061182 0.747443507 0.831742646 0.793892985 0.790405007 0.868395933 1 18.4541789 -4.999999762 0.079911685 1.858832327 0.50475193 0.872460087 0.033404286 84.54523732 0.478713824 12.57627833 1.180009739 1.00E-05 4.999999762 -1.354080397 LGFDKENVYDELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGFDKENVYDELR 13 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 101.2 0.0018701 538850000 535200 527440 413280 443010 472550 484000 489260 496570 482890 465510 FALSE TRUE 514283.7923 512397.9276 487968.8894 465873.7992 487749.9999 493786.8116 495247.7102 486315.656 428074.3516 433980.5931 1.185038687 1.180693183 1.124402559 1.073489936 1.123898183 1.137808509 1.141174786 1.120593095 0.98639054 1 18.727271 -4.999999756 0.047333828 0.402154796 1.426498961 0.601280664 0.0406917 462.189868 1.622951237 35.04158049 8.488794061 1.00E-05 4.999999756 1.024344165 EASIDILHSIVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EASIDILHSIVK 12 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 144.1 6.28E-05 568620000 1557950 1619560 1480820 1618200 1599510 1552650 1844630 1729530 2035300 2137480 FALSE TRUE 1497063.592 1573371.735 1748437.115 1701715.496 1650959.692 1584045.647 1867205.134 1693814.601 1804261.277 1992706.576 0.751271467 0.789565184 0.877418249 0.853971938 0.828501151 0.794921674 0.937019608 0.850007032 0.90543249 1 20.92629786 -4.99999973 0.038387374 1.799348963 0.37137665 0.682090587 0.039881843 537.5935755 1.543989817 50.50392489 15.94715718 1.00E-05 4.99999973 -1.427972313 YWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_BT-474_Pertuzumab_2h_R1 1 YWSQQIEESTTVVTTQSAEVGAAETTLTELR 31 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 136.34 1.43E-06 25910000 13653 14028 15804 20462 15239 17575 16642 17065 17486 23096 FALSE TRUE 13119.42567 13627.93517 18660.13436 21518.04627 15729.17627 17930.37854 16845.66977 16712.60179 15501.06259 21531.68735 0.609307829 0.632924627 0.866635952 0.999366465 0.730512942 0.832743772 0.782366449 0.776186349 0.719918617 1 14.39417376 -4.999999694 0.02568545 2.031508423 2.83E-06 0.269829498 0.108560643 3387.203409 6.568175337 380.3938144 175.4967527 1.00E-05 4.999999694 -2.031505591 APS(ph)PHVVQENLHSEVVEVCTSSTLK ddPTM_BT-474_Pertuzumab_2h_R1 3 APSPHVVQENLHSEVVEVCTSSTLK 25 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 APS(0.94)PHVVQENLHS(0.06)EVVEVCTSSTLK;APS(0.946)PHVVQENLHS(0.054)EVVEVCTSSTLK;APS(0.819)PHVVQENLHS(0.181)EVVEVCTSSTLK 119.02 0.0010125 547960000 158331 154932 155950 189949 181966 168403 221511 156979 222369 252664 TRUE FALSE 152143.2495 150513.4911 184133.6341 199752.2907 187819.1016 171808.224 224221.9179 153737.3288 197126.6034 235550.8422 0.645904078 0.638985153 0.781715032 0.848021976 0.797361198 0.729389131 0.951904547 0.652671531 0.836874967 1 17.84567896 -4.99999969 0.032098314 2.140860936 4.00E-07 0.452610649 0.088186606 1335.69731 3.223477261 172.7625602 65.79214361 1.00E-05 4.99999969 -2.140860536 LMHLTSEELNPNPDK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMHLTSEELNPNPDK 15 0 Q96RS6-2;Q96RS6;Q96RS6-3 Q96RS6-2 NUDCD1 NudC domain-containing protein 1 0 90.759 0.0058902 459800000 185940 191280 177640 208280 179140 201770 196230 202630 262040 246810 FALSE TRUE 178673.2592 185824.8817 209743.4996 219029.3558 184902.2008 205849.9276 198631.5214 198445.6197 232294.3178 230093.3389 0.776525127 0.807606524 0.911558329 0.951915239 0.803596496 0.894636623 0.863264979 0.862457039 1.009565592 1 17.81185969 -4.999999632 0.0207411 2.149214152 3.07E-09 0.471472203 0.055976216 2956.692185 4.641526163 327.6022528 175.3161223 1.00E-05 4.999999632 -2.149214149 WPSVSSLDS(ph)ALESSPSLHSPADPSHLS(ph)PPASSPRPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 WPSVSSLDSALESSPSLHSPADPSHLSPPASSPRPSR 37 1 O15211 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 2 WPS(0.247)VS(0.129)S(0.147)LDS(0.475)ALES(0.002)S(0.002)PS(0.011)LHS(0.009)PADPS(0.152)HLS(0.342)PPAS(0.228)S(0.198)PRPS(0.057)R 49.085 0.031921 32410000 3454 8394.8 3932.4 4615.4 4814.5 5705.3 4311.5 5757.1 5479.7 4502.3 TRUE FALSE 3319.013861 8155.388523 4643.072156 4853.601347 4969.362765 5820.665075 4364.265427 5638.213873 4857.667429 4197.355211 0.790739333 1.942982691 1.106189951 1.156347534 1.183927143 1.386745887 1.039765568 1.343277752 1.157316259 1 12.03526484 -4.999999628 0.163196874 0.027672225 1.318863671 0.054475582 0.28386694 365.0410438 3.387128657 114.3045086 1.052012254 1.00E-05 4.999999628 1.291191446 VNIVFNYDMPEDSDTYLHR ddPTM_BT-474_Pertuzumab_2h_R1 7 VNIVFNYDMPEDSDTYLHR 19 0 O00148 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;;;;; 190.71 1.12E-14 3936330000 1613486 1777788 1734294 1895286 1724520 2007651 1907135 1823948 2067106 2334974 FALSE TRUE 1550429.183 1727087.227 2047719.505 1993101.938 1779990.752 2048247.079 1930475.089 1786282.836 1832456.793 2176824.131 0.712243659 0.793397685 0.940691292 0.91560081 0.817700763 0.940933652 0.886830985 0.820591251 0.841802866 1 21.05379342 -4.999999583 0.017633467 2.040513846 4.12E-09 0.334687202 0.066228351 6136.960102 8.201404546 617.5246806 362.8330407 1.00E-05 4.999999583 -2.040513842 KPEDRPNTSEILR ddPTM_BT-474_Pertuzumab_2h_R1 3 KPEDRPNTSEILR 13 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 ;; 166.09 1.92E-05 1836570000 604044 734843 577295 641681 668201 631120 743113 703058 864466 867051 FALSE TRUE 580437.2927 713885.9971 681625.0484 674798.2333 689694.292 643881.6788 752207.4392 688539.6066 766335.4438 808324.8635 0.718074278 0.883167189 0.843256318 0.834810685 0.853238992 0.796563001 0.930575655 0.851810501 0.948053782 1 19.6245757 -4.999999563 0.054370999 1.642598786 0.558458281 0.603806528 0.047817186 321.5458914 1.286710783 28.22683234 5.558684263 1.00E-05 4.999999563 -1.084140505 EREELWK ddPTM_BT-474_Pertuzumab_2h_R1 1 EREELWK 7 1 Q16537-2;Q16537;Q16537-3 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 0 91.783 0.01473 271230000 383780 359440 327180 417250 385590 351960 408360 417270 423350 481960 FALSE TRUE 368781.4533 349189.1231 386308.7041 438784.3225 397992.8525 359076.8723 413357.6318 408653.2287 375293.0828 449316.4199 0.820761132 0.777156382 0.859769835 0.976559732 0.885774111 0.799162587 0.919970011 0.909499877 0.835253434 1 18.77737226 -4.999999379 0.017843664 2.076314277 9.66E-12 0.352258319 0.056470506 4830.979699 6.532536609 496.1374476 289.6736381 1.00E-05 4.999999379 -2.076314277 AFEDDDITHVEGSVDPIRDIEIIHEELQLK ddPTM_BT-474_Pertuzumab_2h_R1 6 AFEDDDITHVEGSVDPIRDIEIIHEELQLK 30 1 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;;; 291.07 4.44E-81 708626000 176936 169683 173398 194138 193065 191174 222348 166451 269497 257641 FALSE TRUE 170021.1455 164843.807 204734.8758 204157.4854 199275.1111 195039.6693 225069.1613 163013.7287 238904.8304 240190.7456 0.707858852 0.68630374 0.85238453 0.849980647 0.829653576 0.812019917 0.937043435 0.678684469 0.994646275 1 17.87382104 -4.99999935 0.028726919 2.17993717 6.31E-08 0.427445385 0.085245192 1705.922558 3.692911418 214.4767929 90.33649063 1.00E-05 4.99999935 -2.179937107 WGDEVEYMLVSFDHENK ddPTM_BT-474_Pertuzumab_2h_R1 1 WGDEVEYMLVSFDHENK 17 0 E1CEI4;P48506;A0A2R8YEL6;A0A0C4DGB2 E1CEI4 GCLC Glutamate--cysteine ligase catalytic subunit 0 116.43 0.00026647 12439000 21218 22816 20947 21476 26676 24471 24648 22718 29214 31437 FALSE TRUE 20388.7771 22165.31002 24732.58886 22584.37893 27534.05777 24965.82039 24949.6496 22248.86536 25897.7492 29307.74399 0.695678832 0.756295334 0.84389262 0.770594248 0.939480629 0.851850637 0.851298879 0.759146298 0.883648677 1 14.8389943 -4.999999295 0.024817046 2.104368246 1.68E-08 0.530337316 0.05999693 2010.212652 3.768093859 231.0204766 109.3939759 1.00E-05 4.999999295 -2.104368229 VPVPGPGS(ph)GGNGPER ddPTM_BT-474_Pertuzumab_2h_R1 6 VPVPGPGSGGNGPER 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER 201.72 6.58E-09 7754550000 837328 838268 858951 1052226 861764 914203 993607 997740 1025739 1230880 TRUE FALSE 804604.296 814361.4174 1014182.553 1106531.51 889483.4217 932688.811 1005767.06 977136.3203 909301.409 1147511.401 0.701173248 0.709676101 0.883810437 0.964288031 0.77514125 0.812792631 0.876476747 0.851526459 0.792411655 1 20.13007706 -4.99999929 0.023649983 2.098264048 9.85E-10 0.3841745 0.073528628 2789.67927 4.986359493 314.4614495 154.2091478 1.00E-05 4.99999929 -2.098264047 VMTFDDDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMTFDDDIR 9 0 F5GWV0;F5H4P3;Q6NXE6-2;Q6NXE6;B4E1N1 F5GWV0 ARMC6 Armadillo repeat-containing protein 6 0 92.439 0.016774 0 54911 55557 65571 79141 62870 70072 71590 81326 75857 104930 FALSE TRUE 52765.01741 53972.56876 77421.13832 83225.47649 64892.27065 71488.90385 72466.13983 79646.58968 67246.03138 97822.99764 0.539392767 0.551737015 0.791441074 0.850776183 0.66336416 0.73079854 0.740788379 0.814190851 0.687425585 1 16.57788605 -4.999999174 0.041353644 2.245578815 6.88E-10 0.553581912 0.087712978 643.4409727 1.985577932 98.88839249 28.59265541 1.00E-05 4.999999174 -2.245578815 S(ph)PRPTGSDLLPGAPILSLR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPRPTGSDLLPGAPILSLR 19 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 S(0.903)PRPT(0.068)GS(0.021)DLLPGAPILS(0.009)LR;S(0.998)PRPT(0.001)GS(0.001)DLLPGAPILSLR;S(0.999)PRPTGSDLLPGAPILSLR;S(0.994)PRPT(0.006)GSDLLPGAPILSLR;S(0.688)PRPT(0.261)GS(0.051)DLLPGAPILSLR 116.06 0.00033081 382904000 198583 221902 215349 252227 215424 234784 234662 232628 233954 285922 TRUE FALSE 190822.1568 215573.5722 254267.3547 265244.4657 222353.3086 239531.4933 237533.8638 227824.1505 207396.5227 266556.2483 0.715879512 0.808735768 0.95389756 0.995078778 0.834170311 0.898615189 0.891120975 0.854694467 0.77805913 1 18.02408047 -4.999999096 0.012834171 1.966296585 1.50E-06 0.16481373 0.080833391 19578.00235 19.07418219 1770.99208 1202.359164 1.00E-05 4.999999096 -1.966295088 SSFFIEPQKPVFPETR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSFFIEPQKPVFPETR 16 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 0 141.55 1.45E-06 304790000 241450 223750 180960 231780 209160 230130 212000 245530 249970 258570 FALSE TRUE 232013.8671 217368.8691 213663.4974 243742.1936 215887.8214 234783.3863 214594.5194 240459.7197 221594.4536 241056.8236 0.962486204 0.901732902 0.88636154 1.011139987 0.895588924 0.973975276 0.890223791 0.997522975 0.919262314 1 17.87901374 -4.999999027 0.136491881 1.216121432 0.914801558 0.1503486 0.043921533 240.3615736 2.032404308 14.03830188 0.268411141 1.00E-05 4.999999027 -0.301319875 SGDEGS(ph)EDEAPS(ph)GED ddPTM_BT-474_Pertuzumab_2h_R1 1 SGDEGSEDEAPSGED 15 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 SGDEGS(1)EDEAPS(1)GED 174.24 3.47E-11 0 196160 212110 182010 221170 195290 201410 217020 199080 250940 251470 TRUE FALSE 188493.8503 206060.8305 214903.2558 232584.6102 201571.6802 205482.6482 219675.9557 194968.9284 222454.3432 234437.7129 0.804025291 0.87895769 0.916675279 0.992095543 0.859809105 0.876491438 0.937033351 0.831644901 0.948884633 1 17.83884514 -4.999998966 0.353136456 2.265582847 0.889511019 0.274464845 0.053062107 620.6061537 5.039723617 595.3020044 0.039822941 1.00E-05 4.999998966 -1.376071828 LDNTLGGTSEVIHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDNTLGGTSEVIHR 14 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 106.19 0.0023369 0 358110 412710 344850 351170 379120 394560 399810 398310 484870 474060 FALSE TRUE 344114.6653 400939.9149 407172.0661 369293.9258 391314.7391 402538.2735 404702.9944 390084.7593 429829.5903 441951.494 0.778625415 0.907203438 0.921304876 0.83559832 0.885424632 0.910820031 0.915718127 0.882641567 0.972571869 1 18.75352851 -4.999998761 0.030063426 1.708465348 0.417894335 0.570386989 0.039063809 1128.564939 2.554505325 85.56804263 34.62865864 1.00E-05 4.999998761 -1.290571012 KGPGQPSS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 5 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.423)S(0.577)PQR;KGPGQPS(0.129)S(0.871)PQR;KGPGQPS(0.023)S(0.977)PQR;KGPGQPS(0.436)S(0.564)PQR;KGPGQPS(0.136)S(0.864)PQR 107.11 0.0013732 6450600000 3566750 3477570 3350950 3709440 3467600 3051140 4008430 4085520 4191400 4568200 TRUE FALSE 3427357.467 3378393.108 3956541.206 3900884.643 3579138.503 3112836.141 4057486.365 4001152.584 3715609.844 4258791.745 0.804772262 0.79327502 0.92902904 0.915960412 0.840411722 0.730920019 0.952731809 0.939504165 0.872456336 1 22.02201275 -4.999998745 0.068635066 1.496688885 0.688907128 0.336501657 0.065120136 390.0073227 1.932187966 30.36972368 3.945149791 1.00E-05 4.999998745 -0.807781757 TSAVSS(ph)PLLDQQR ddPTM_BT-474_Pertuzumab_2h_R1 6 TSAVSSPLLDQQR 13 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 TSAVS(0.007)S(0.993)PLLDQQR;TSAVSS(1)PLLDQQR;TSAVS(0.001)S(0.999)PLLDQQR;TSAVS(0.002)S(0.998)PLLDQQR;TSAVS(0.005)S(0.995)PLLDQQR;TSAVS(0.002)S(0.998)PLLDQQR 353.65 4.89E-76 4421730000 4046560 3954090 3573210 4092960 3813140 3578320 4423730 4459960 4480100 4841940 TRUE FALSE 3888415.961 3841323.225 4218968.533 4304198.156 3935793.111 3650676.082 4477868.931 4367860.267 3971537.83 4513991.091 0.861414186 0.85098157 0.934642636 0.953523848 0.871909809 0.808746851 0.991997733 0.967627135 0.87982846 1 22.10597214 -4.999998737 0.014911968 2.099888561 5.29E-07 0.271901342 0.053329075 7730.266259 8.744779356 769.6521123 490.8201414 1.00E-05 4.999998737 -2.099888031 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPS(0.001)S(0.001)DEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.392)QS(0.392)HLRNS(0.216)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.358)QS(0.358)HLRNS(0.284)PEDK 119.8 2.80E-07 1261010000 465510 417608 404199 414750 421823 512258 477750 439910 607810 579220 TRUE FALSE 447317.3546 405698.2287 477246.7507 436155.2972 435391.3199 522616.2077 483596.8474 430825.7048 538813.9569 539988.9135 0.828382479 0.751308441 0.883808424 0.807711578 0.806296776 0.967827662 0.895568104 0.797841759 0.99782411 1 19.04257026 -4.999998064 0.039194732 1.797972638 0.391655397 0.461890343 0.062453622 806.3263705 2.362864133 75.41083501 23.24728792 1.00E-05 4.999998064 -1.406317241 ENLLDFIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENLLDFIK 8 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 84.213 0.040972 129810000 375610 411540 365430 417970 482240 369260 455180 416280 452300 523400 FALSE TRUE 360930.7459 399803.2821 431471.3299 439541.4818 497751.6876 376726.6902 460750.629 407683.6725 400956.8002 487949.6518 0.7396885 0.819353556 0.884253792 0.900792695 1.020088211 0.772060578 0.944258547 0.835503563 0.821717566 1 18.89637277 -4.999998033 0.015691723 2.020251262 1.48E-07 0.216995612 0.078454759 9750.427794 11.60378409 944.5700714 588.3900685 1.00E-05 4.999998033 -2.020251114 DNLEFFLAGIGR ddPTM_BT-474_Pertuzumab_2h_R1 5 DNLEFFLAGIGR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 190.26 1.60E-05 4669175000 1946164 2158415 1917315 2302541 2218121 1918819 2556876 2306772 2717791 2971601 FALSE TRUE 1870105.759 2096859.118 2263816.471 2421375.417 2289468.876 1957618.835 2588167.813 2259136.352 2409278.76 2770331.817 0.675047569 0.756898182 0.817164376 0.874038049 0.826424063 0.706636953 0.934244698 0.815475005 0.869671548 1 21.40162736 -4.999997925 0.028717443 2.184577864 3.28E-11 0.565043173 0.061931599 1216.33756 2.632222565 153.2291674 64.55754435 1.00E-05 4.999997925 -2.184577864 TTYLVLDEADR ddPTM_BT-474_Pertuzumab_2h_R1 4 TTYLVLDEADR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 240.18 2.62E-15 1938890000 1702040 1753200 1494600 1720810 1691110 1592390 1670650 1818330 1915010 2027970 FALSE TRUE 1635522.395 1703200.453 1764707.467 1809621.21 1745506.089 1624589.217 1691095.914 1780780.85 1697626.093 1890613.786 0.865074828 0.900871699 0.933404527 0.957160698 0.923248366 0.859291955 0.89446926 0.941906202 0.89792326 1 20.85042325 -4.999995813 0.425699041 2.713994881 0.90941683 0.453033893 0.030120952 997.0872719 6.341979714 1600.830159 0.018208412 1.00E-05 4.999995813 -1.804578051 EQSIFGDHRDEEEETHMK ddPTM_BT-474_Pertuzumab_2h_R1 6 EQSIFGDHRDEEEETHMK 18 1 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 ;;;;; 160.97 2.53E-11 3350010000 3351830 3113610 3029890 3503130 3474190 3492360 3809900 2642000 4684940 4538980 FALSE TRUE 3220836.778 3024812.891 3577458.523 3683926.959 3585940.477 3562977.912 3856526.696 2587441.777 4153125.252 4231550.842 0.761148075 0.714823715 0.845424918 0.870585536 0.847429373 0.84200286 0.911374302 0.611464183 0.981466466 1 22.01275507 -4.999995674 0.350940299 3.21144225 0.804160385 0.24123048 0.097710298 635.3136075 5.191829575 1057.21155 0.074681148 1.00E-05 4.999995674 -2.407281865 AVSLDSPVSVGSS(ph)PPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 AVSLDSPVSVGS(0.226)S(0.774)PPVK;AVSLDSPVSVGSS(1)PPVK 420.48 2.18E-160 1349200000 595480 663920 616240 623290 555780 705660 742520 750200 830480 929610 TRUE FALSE 572207.9833 644985.6516 727608.2762 655458.0716 573657.1684 719928.9287 751607.1819 734708.1078 736207.3921 866646.6867 0.660255202 0.744231371 0.839567366 0.756315211 0.661927377 0.830706376 0.86725905 0.847759669 0.849489652 1 19.72508443 -4.999995461 0.048341411 1.995549846 0.287784939 0.691689587 0.05413197 348.8697069 1.249777648 44.67473451 10.50541845 1.00E-05 4.999995461 -1.707764907 EEHLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEHLDK 6 0 Q8N3L3;H7BY59 Q8N3L3 TXLNB Beta-taxilin 0 ; 93.593 0.045443 1439950000 2482170 2418670 2086450 2416770 2378860 2600810 2546830 2603400 3127300 3157400 FALSE TRUE 2385164.052 2349691.9 2463517.928 2541499.789 2455378.192 2653400.16 2577998.867 2549638.88 2772302.015 2943546.486 0.810302832 0.79825201 0.8369217 0.863414185 0.834156418 0.901429678 0.87581388 0.866179248 0.941823759 1 21.48912398 -4.999994729 0.044623416 1.696091124 0.485681069 0.872698309 0.020849897 221.8161451 0.736323609 19.18340954 5.034695648 1.00E-05 4.999994729 -1.210410055 RLHGLDEEAEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLHGLDEEAEQK 12 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 67.385 0.036032 289650000 182310 171610 129260 147060 158100 161100 165800 164730 183580 199650 FALSE TRUE 175185.1236 166715.8508 152620.1574 154649.7842 163185.4301 164357.5524 167829.11 161328.2679 162740.768 186127.5277 0.941210179 0.895707652 0.819976278 0.830880774 0.8767399 0.883037316 0.901688816 0.866761999 0.874350882 1 17.50593192 -4.999993161 0.538366617 6.185665676 0.874175723 0.561101896 0.032650932 3011.557155 11.85720272 18937.26305 0.014986038 1.00E-05 4.999993161 -5.311489954 HQIVEVAGDDKYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 HQIVEVAGDDKYGR 14 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;; 162.46 2.66E-06 3822100000 3456560 3438610 2987210 3263130 3442640 3493340 3878620 2858100 4460130 4332140 FALSE TRUE 3321473.814 3340544.21 3527065.297 3431540.53 3553375.642 3563977.728 3926087.712 2799079.236 3953834.741 4038720.299 0.822407487 0.827129378 0.873312593 0.849660357 0.879827118 0.882452229 0.972111813 0.693060927 0.978982066 1 21.94546681 -4.999992754 0.39013681 3.170766431 0.853450587 0.227728978 0.075936454 962.3124408 6.955217846 1773.416097 0.047760228 1.00E-05 4.999992754 -2.317315845 MVHNGIEYGDMQLICEAYHLMK ddPTM_BT-474_Pertuzumab_2h_R1 3 MVHNGIEYGDMQLICEAYHLMK 22 0 P52209-2;P52209;K7EM49;K7EPF6;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 270.47 1.54E-45 1079320000 460196 387094 467119 463479 544891 572040 556896 361073 644710 685932 FALSE TRUE 442211.0315 376054.4581 551537.7943 487399.2067 562417.9139 583607.0407 563711.4598 353616.7164 571525.2236 639473.2147 0.691523932 0.588069132 0.862487719 0.76218862 0.87950191 0.912637195 0.881524741 0.552981279 0.893743804 1 19.28652441 -4.999992261 0.027371822 2.041657395 0.006383018 0.254664622 0.121301585 3240.818467 6.690290204 373.3182148 163.7480468 1.00E-05 4.999992261 -2.035274377 NLSES(ph)PVITK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLSESPVITK 10 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 NLSES(1)PVITK 139.61 0.0046043 0 409630 380670 367530 410920 403610 463040 410110 450620 450720 530500 TRUE FALSE 393621.2067 369813.6643 433950.8467 432127.6304 416592.4822 472402.9861 415129.0489 441314.5395 399556.1552 494568.7625 0.795887724 0.747749742 0.877432785 0.873746308 0.842334805 0.955181608 0.839375796 0.892321903 0.807887973 1 18.91581159 -4.999992121 0.02038824 2.091362072 4.78E-11 0.457450244 0.052218681 2856.397266 4.408444118 306.4241997 165.7291869 1.00E-05 4.999992121 -2.091362071 LQPSS(ph)SPENSLDPFPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQPSSSPENSLDPFPPR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 LQPS(0.067)S(0.466)S(0.466)PENSLDPFPPR 153.95 1.64E-07 778950000 391040 460990 427600 426690 439000 512470 495580 472770 554440 622680 TRUE FALSE 375757.7245 447843.0166 504876.8319 448711.522 453120.8337 522832.4945 501645.0563 463007.1343 491502.2956 580505.329 0.647294186 0.771470983 0.869719547 0.772967102 0.780562746 0.900650637 0.864152371 0.797593254 0.846680075 1 19.14694979 -4.999991162 0.027993885 2.159881406 9.61E-10 0.617613882 0.055387999 1237.713085 2.612183691 152.6191378 65.7080041 1.00E-05 4.999991162 -2.159881405 QKEEEAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKEEEAQK 8 1 C9J6Y8;X6RET8;C9JP05;C9J3Q3;C9J6N5;C9JQ40;C9JW51;A0A1C7CYX8;Q9H098;Q9H098-2 C9J6Y8 FAM107B Protein FAM107B 0 71.349 0.044663 44804000 60896 70291 56677 70027 62999 61385 69132 66884 76062 90199 FALSE TRUE 58516.117 68286.3695 66919.79467 73641.10186 65025.42005 62626.24676 69978.0581 65502.82203 67427.76064 84089.74139 0.695877 0.8120654 0.795814014 0.875744183 0.773286003 0.744754898 0.832183058 0.778963295 0.801854775 1 16.35964219 -4.999989213 0.463444014 6.153668228 0.790112978 0.654767828 0.04580265 929.0330013 5.088124216 4929.696049 0.022727648 1.00E-05 4.999989213 -5.363555251 S(ph)PVGKSPPSTGSTYGSSQKEESAASGGAAYTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPVGKSPPSTGSTYGSSQKEESAASGGAAYTK 32 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.226)PVGKS(0.205)PPS(0.107)T(0.107)GS(0.107)T(0.107)Y(0.098)GS(0.033)S(0.01)QKEESAASGGAAYTK 47.871 0.04592 208790000 52861 49104 32539 27973 38579 42866 41163 45662 50136 35661 TRUE FALSE 50795.13368 47703.602 38419.52113 29416.68988 39819.92857 43732.77989 41666.76511 44719.06374 44444.77147 33245.64871 1.52787314 1.434882574 1.155625552 0.884828272 1.197748581 1.315443722 1.253299807 1.345110277 1.336859806 1 15.02087791 -4.99998832 0.023282035 5.57E-08 2.083680605 0.14664543 0.170218103 7124.518943 12.53890721 793.3898618 393.3918182 1.00E-05 4.99998832 2.083680549 S(ph)RSPLDKDTYPPSASVVGASVGGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPLDKDTYPPSASVVGASVGGHR 25 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 S(0.791)RS(0.209)PLDKDTYPPSASVVGASVGGHR 250.98 4.12E-40 464050000 183360 255630 234630 257530 238180 259070 243420 285230 261550 340410 TRUE FALSE 176194.0885 248339.6827 277032.8603 270821.1542 245841.276 264308.5729 246399.0468 279339.9008 231859.9405 317353.7275 0.555197791 0.782532742 0.872946609 0.853373163 0.774660118 0.832851642 0.776417686 0.880216228 0.730604119 1 18.27573226 -4.999985377 0.027695566 2.119659999 8.78E-10 0.399181512 0.085469693 1908.568203 3.985837019 230.0024888 99.91270427 1.00E-05 4.999985377 -2.119659998 MAPTPIPTRS(ph)PSDS(ph)STASTPVAEQIER ddPTM_BT-474_Pertuzumab_2h_R1 1 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 2 MAPT(0.001)PIPT(0.118)RS(0.672)PS(0.209)DS(0.27)S(0.25)T(0.232)AS(0.129)T(0.12)PVAEQIER 56.383 0.042062 110560000 28311 27854 29284 30694 28995 34420 28618 35400 34386 41000 TRUE FALSE 27204.57482 27059.63119 34576.27022 32278.12102 29927.65051 35115.99598 28968.23564 34668.97763 30482.64544 38223.03348 0.711732491 0.707940441 0.904592521 0.844467801 0.782974238 0.918712954 0.7578738 0.907017954 0.797494146 1 15.22215466 -4.999983912 0.025792331 2.137837438 1.61E-08 0.443737438 0.069054151 1831.823668 3.566678692 216.8115141 99.70724864 1.00E-05 4.999983912 -2.137837422 YSVGSLS(ph)PVSASVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSVGSLSPVSASVLK 15 0 Q9UBU7 Q9UBU7 DBF4 Protein DBF4 homolog A 1 YSVGSLS(1)PVSASVLK;YSVGSLS(1)PVSASVLK 268.61 1.21E-25 517860000 1165940 1083300 969870 1108820 1078120 885190 1184780 1230540 1156180 1372970 TRUE FALSE 1120373.776 1052405.345 1145147.084 1166046.333 1112798.709 903089.1483 1199279.692 1205128.919 1024935.294 1279977.519 0.875307386 0.822206116 0.894661872 0.910989698 0.869389261 0.705550789 0.936953715 0.941523504 0.800744762 1 20.28768704 -4.999983743 0.282552149 1.989967846 0.858920196 0.256035436 0.068249681 342.0207061 3.262633832 198.7039284 0.078613603 1.00E-05 4.999983743 -1.13104765 DWGEHNQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DWGEHNQR 8 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 97.431 0.0082369 161120000 49466 47299 47970 56892 55785 56637 47474 56926 51860 67129 FALSE TRUE 47532.81403 45950.07883 56639.24609 59828.20294 57579.37519 57782.23895 48055.00101 55750.45821 45973.07021 62582.29304 0.759524967 0.734234503 0.905036286 0.955992503 0.920058572 0.923300124 0.767868972 0.89083438 0.734601882 1 15.9334669 -4.999980568 0.014426805 1.963470985 2.09E-07 0.156818444 0.08688269 14771.8294 16.16917465 1365.538834 883.6417349 1.00E-05 4.999980568 -1.963470776 GMLDPLEVHLLDFPNIVIK ddPTM_BT-474_Pertuzumab_2h_R1 2 GMLDPLEVHLLDFPNIVIK 19 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 167.82 1.72E-11 111708000 276160 301080 273060 287730 299220 284260 300920 294260 346130 357370 FALSE TRUE 265367.3619 292493.4932 322408.0162 302579.7798 308844.683 290007.932 304602.749 288183.4282 306838.7735 333165.0116 0.796504293 0.877923801 0.96771271 0.908197948 0.927002153 0.87046335 0.914269921 0.864987073 0.920981384 1 18.34587737 -4.999979709 0.492315647 4.168037445 0.894336504 0.349636581 0.043497115 2562.946642 12.41810061 8934.518951 0.020794626 1.00E-05 4.999979709 -3.273700941 SRAEDLNTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRAEDLNTR 9 1 Q9Y3B3;A0A0A6YYA0;Q86XR7-2;Q9Y3B3-2 Q9Y3B3 TMED7;TMED7-TICAM2 Transmembrane emp24 domain-containing protein 7 0 68.626 0.052475 74008000 39201 44510 30551 47689 35724 37019 40832 43478 44490 53641 FALSE TRUE 37668.98158 43240.61838 36072.2453 50150.23501 36873.0949 37767.54954 41331.71423 42580.16411 39439.68172 50007.84729 0.75326141 0.86467666 0.721331696 1.002847307 0.737346175 0.75523246 0.826504568 0.851469648 0.788669856 1 15.60986688 -4.999976653 0.520640416 7.776397741 0.814120179 0.33861017 0.078861932 3512.494855 15.00354053 27836.92142 0.033315214 1.00E-05 4.999976653 -6.962277563 EGLHYTEVCGYDIASPNAGPLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGLHYTEVCGYDIASPNAGPLFR 23 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 219.34 2.10E-32 207208000 70615 93937 77781 91607 94809 86114 88086 84689 100290 110905 FALSE TRUE 67855.28773 91258.00873 91837.75693 96334.84825 97858.61759 87855.28408 89164.02282 82940.14255 88905.49965 103393.3056 0.656283184 0.882629762 0.888236975 0.93173197 0.946469571 0.84971927 0.862377137 0.802180974 0.859876751 1 16.65778325 -4.999966626 0.014606246 1.981718421 4.18E-07 0.2412663 0.076857661 12614.45281 13.97874132 1180.017106 759.4756497 1.00E-05 4.999966626 -1.981718004 LVEGESDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVEGESDNR 9 0 O94776 O94776 MTA2 Metastasis-associated protein MTA2 0 80.165 0.046331 0 88290 85706 80826 84441 87382 83051 93859 103070 102600 113690 FALSE TRUE 84839.52919 83261.74879 95433.05616 88799.01013 90192.72139 84730.34812 95007.67452 100941.5685 90953.27813 105989.675 0.800450885 0.785564714 0.900399554 0.837808118 0.850957618 0.799420775 0.896386129 0.952371714 0.85813338 1 16.69356421 -4.999965715 0.041077301 1.74114833 0.441464913 0.60932429 0.041346695 527.3226225 1.616793231 46.73398894 13.62399111 1.00E-05 4.999965715 -1.299683417 GGCGS(ph)PGLQCK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGCGSPGLQCK 11 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GGCGS(1)PGLQCK 87.214 0.014571 251060000 126990 149720 113700 126450 137560 134760 133700 153560 162000 169240 TRUE FALSE 122027.0904 145450.1322 134248.1192 132976.0997 141984.7423 137484.9395 135336.2606 150388.9323 143610.4392 157777.2241 0.773413851 0.92187027 0.850871348 0.842809223 0.899906455 0.871386478 0.857768042 0.953172635 0.910210203 1 17.26752943 -4.999960482 0.055796133 1.520390277 0.647634774 0.594530269 0.038372286 307.0192563 1.25860027 22.08823664 4.171792637 1.00E-05 4.999960482 -0.872755503 SQVDHVIWPDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQVDHVIWPDGK 12 0 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 ; 95.651 0.0059273 336170000 897450 944110 922440 1018730 995260 956730 1064670 1143040 1224630 1389220 FALSE TRUE 862376.6618 917184.9072 1089145.428 1071306.777 1027273.442 976075.7361 1077699.75 1119435.825 1085615.136 1295126.892 0.665862679 0.708181502 0.840956538 0.827182868 0.793183624 0.75365259 0.832119043 0.864344514 0.838230712 1 20.30466202 -4.999953855 0.031610617 2.21589544 8.33E-08 0.755832491 0.043116409 686.2525401 1.631558997 91.26064025 35.2641897 1.00E-05 4.999953855 -2.215895357 DLIEAIR ddPTM_BT-474_Pertuzumab_2h_R1 7 DLIEAIR 7 0 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;;;;; 183.89 0.0014796 4194300000 2743490 2992400 2719370 3275900 2876020 2661270 2979360 3344690 3316110 3654940 FALSE TRUE 2636271.378 2907059.682 3210820.651 3444969.592 2968529.795 2715082.703 3015822.299 3275620.983 2939679.095 3407387.658 0.773692823 0.853163765 0.942311522 1.011029544 0.871204011 0.796822368 0.885083413 0.961329121 0.862736909 1 21.70023466 -4.999950229 0.014668213 2.020611952 0.028795369 0.216015638 0.067970955 11148.00659 12.40579695 1049.091122 673.9497538 1.00E-05 4.999950229 -1.991816583 KTSFDQDS(ph)DVDIFPSDFPTEPPSLPR ddPTM_BT-474_Pertuzumab_2h_R1 9 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KT(0.026)S(0.017)FDQDS(0.957)DVDIFPSDFPTEPPSLPR;KT(0.053)S(0.04)FDQDS(0.907)DVDIFPSDFPTEPPSLPR;KT(0.069)S(0.069)FDQDS(0.862)DVDIFPSDFPTEPPSLPR;KT(0.046)S(0.032)FDQDS(0.922)DVDIFPSDFPTEPPSLPR;KT(0.069)S(0.05)FDQDS(0.881)DVDIFPSDFPTEPPSLPR;KT(0.061)S(0.041)FDQDS(0.898)DVDIFPSDFPTEPPSLPR;KT(0.018)S(0.018)FDQDS(0.965)DVDIFPSDFPTEPPSLPR;KT(0.003)S(0.003)FDQDS(0.994)DVDIFPSDFPTEPPSLPR;KT(0.009)S(0.009)FDQDS(0.982)DVDIFPSDFPTEPPSLPR 204.53 2.30E-25 26966100000 2146459 2031272 1548188 1757712 1888573 1855355 1731090 2069459 1942365 1819476 TRUE FALSE 2062573.009 1973342.111 1827980.011 1848427.727 1949320.666 1892871.549 1752275.597 2026723.948 1721875.868 1696241.27 1.215966765 1.163361691 1.077665096 1.089719817 1.149200117 1.115921174 1.033034409 1.194832353 1.01511259 1 20.69390996 -4.999931445 0.019632639 3.36E-06 1.90093332 0.420849706 0.054414015 3738.951415 5.558669249 360.6761565 199.5547519 1.00E-05 4.999931445 1.900929963 VEFATLQEALAHALTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEFATLQEALAHALTEK 17 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 173.87 1.42E-09 699850000 576970 572000 495700 509310 542690 568740 534700 564080 639180 583140 FALSE TRUE 554421.3745 555687.12 585284.0168 535595.5501 560146.1167 580240.3125 541243.8185 552431.5509 566622.9661 543643.4084 1.019825433 1.022153698 1.076595444 0.985196439 1.030355759 1.067317848 0.995586096 1.01616527 1.042269542 1 19.05230113 -4.99992721 0.179243481 0.887064037 1.03324845 0.082023622 0.027038858 347.4407025 3.342098205 13.93131708 0.083059782 1.00E-05 4.99992721 0.146184413 LQNDPQLEAEYQQLQEDHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQNDPQLEAEYQQLQEDHQR 20 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 328.16 9.43E-80 639070000 722590 741580 681440 837870 772500 803250 795170 796930 770270 807400 FALSE TRUE 694350.3839 720430.8645 804591.3666 881112.5711 797348.1641 819492.2653 804901.5283 780473.117 682832.1788 752714.0788 0.922462331 0.95711092 1.06892031 1.170580697 1.059297529 1.088716537 1.069332368 1.036878596 0.9071601 1 19.52174243 -4.999834982 0.002391825 0.647984118 1.408732331 0 0.077799492 5682370.15 1039.669957 171362.6018 159514.655 1.00E-05 4.999834982 0.760748213 LVIEEAER ddPTM_BT-474_Pertuzumab_2h_R1 2 LVIEEAER 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 167.9 0.00072108 958290000 531180 619640 514140 600950 615870 613310 598360 613830 685180 760900 FALSE TRUE 510420.8983 601968.4739 607056.535 631965.1015 635680.0179 625711.5484 605682.9087 601154.196 607401.2389 709363.5653 0.719547667 0.848603598 0.855776311 0.890890275 0.896127246 0.882074551 0.85383989 0.847455699 0.856262245 1 19.43616571 -4.999808832 0.018274218 2.045652261 0.002530744 0.545271021 0.043792769 3618.639425 5.010491436 367.96176 212.0751216 1.00E-05 4.999808832 -2.043121517 VLDNYLTSPLPEEVDETSAEDEGVSQR ddPTM_BT-474_Pertuzumab_2h_R1 5 VLDNYLTSPLPEEVDETSAEDEGVSQR 27 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;;;; 271.12 9.39E-61 1358769000 999799 1096579 933152 1107834 1139748 1098501 1116643 1120175 1115861 1124796 FALSE TRUE 960725.7497 1065305.641 1101793.324 1165009.446 1176409.03 1120713.443 1130308.811 1097042.995 989193.1374 1048612.565 0.916187524 1.015919202 1.050715356 1.111000845 1.121871956 1.068758358 1.077908895 1.046185246 0.943335194 1 20.00005031 -4.999751115 0.001298465 0.77468581 1.306401522 0 0.064365778 10266463.98 1077.022425 224329.7413 216767.9572 1.00E-05 4.999751115 0.531715712 RPAPAVS(ph)PGSWKPGPPGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPAPAVSPGSWKPGPPGSPR 20 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 RPAPAVS(1)PGS(0.001)WKPGPPGS(0.999)PR 66.886 0.012326 206910000 130270 121180 126300 142240 125240 106850 149280 150720 149290 166690 TRUE FALSE 125178.9044 117724.065 149125.2195 149581.0234 129268.4583 109010.5802 151106.9333 147607.5793 132343.2251 155399.9378 0.805527377 0.757555419 0.959622131 0.962555234 0.831843694 0.701484066 0.972374477 0.949856103 0.851629846 1 17.2456264 -4.999707847 0.020143129 2.101915289 0.022079016 0.204840293 0.087594123 5325.373777 8.121542989 566.181833 308.4941896 1.00E-05 4.999707847 -2.079836272 S(ph)PSTLLPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSTLLPK 8 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 S(0.828)PS(0.17)T(0.002)LLPK;S(0.981)PS(0.019)TLLPK;S(0.949)PS(0.038)T(0.012)LLPK 114.97 0.0026792 3552100000 1020970 919940 1016050 989800 948760 1042260 1159780 1203370 1266210 1438060 TRUE FALSE 981069.3637 893704.2119 1199672.837 1040883.697 979277.727 1063335.211 1173973.735 1178519.989 1122475.149 1340658.915 0.731781479 0.666615648 0.89483822 0.776397102 0.730445094 0.793143729 0.875669211 0.879060271 0.83725632 1 20.35451081 -4.99970396 0.031971614 2.241045928 2.53E-06 0.623600258 0.05716414 819.4852804 1.970152247 110.7647874 42.34363297 1.00E-05 4.99970396 -2.241043402 VVESLR ddPTM_BT-474_Pertuzumab_2h_R1 5 VVESLR 6 0 Q12905;B4DY09;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;;;; 126.04 0.041095 1761501000 1256550 1411480 1152960 1503870 1379740 1414230 1392070 1451460 1385660 1417630 FALSE TRUE 1207442.637 1371225.972 1361325.519 1581484.911 1424120.59 1442826.7 1409106.569 1421486.844 1228365.686 1321612.657 0.9136131 1.037539982 1.030048791 1.196632691 1.077562766 1.091716769 1.066202386 1.075569938 0.929444553 1 20.33386798 -4.999001442 0.00397645 0.606134457 1.467733008 0 0.078127182 1356327.889 410.0369504 47164.72443 41828.85847 1.00E-05 4.999001442 0.861598551 EGWPLDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGWPLDIR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 75.854 0.086804 101870000 124450 164340 112000 230780 117790 126600 204120 176500 153950 135700 FALSE TRUE 119586.3564 159653.1841 132240.8914 242690.5835 121578.8223 129159.9387 206618.0816 172855.2133 136474.2414 126508.9181 0.94528005 1.261991538 1.045308848 1.918367393 0.961029658 1.020955207 1.633229378 1.366348048 1.078771706 1 16.94887956 -4.996981445 0.002974304 0.951417441 1.547048934 0 0.311913837 16392919.63 3713.677862 388856.2848 355534.4436 1.01E-05 4.996981445 0.595631493 IEEPVSMEMDNHMSDKDESCYDNAEAAFS(ph)DDEEDLNSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEEPVSMEMDNHMSDKDESCYDNAEAAFSDDEEDLNSK 38 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK;IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK 363.75 2.04E-147 457110000 147049 173278 124281 154787 137201 168455 158722 148279 201095 179859 TRUE FALSE 141302.1625 168336.2811 146741.3413 162775.5756 141614.1948 171861.2755 160664.4873 145216.9868 178267.5387 167676.9897 0.842704552 1.003931913 0.875142985 0.970768714 0.844565465 1.024954442 0.958178505 0.866051967 1.063160419 1 17.3553252 -4.99282876 0.026988829 1.503257118 0.587269664 0.164488312 0.070421139 3730.127292 7.602941072 192.4822642 85.4782643 1.02E-05 4.99282876 -0.915987454 NLDIERPTYTNLNR ddPTM_BT-474_Pertuzumab_2h_R1 16 NLDIERPTYTNLNR 14 1 P68363;F8VQQ4;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;;;;;;;;;;;;;; 281.93 2.16E-33 2.8955E+11 61140137.6 63698559.3 58399040.5 64766423.3 59381199.7 59430871.2 63700048.9 67526059.9 75103802.9 73608195 FALSE TRUE 58750713.43 61881938.76 68953046.2 68109026.17 61291249.92 60632604.13 64479629.15 66131623.17 66578334.06 68622646.39 0.856141763 0.901771383 1.004814734 0.992515296 0.8931636 0.883565518 0.939626094 0.963699692 0.970209363 1 26.03218143 -4.990957401 0.010135029 2.063008592 6.42E-12 0.252774016 0.043994192 21263.32742 16.3916589 1941.999838 1430.791984 1.02E-05 4.990957401 -2.063008592 SLYEDLEDHPNVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLYEDLEDHPNVQK 14 0 P40337-3;P40337-2;P40337 P40337-3 VHL Von Hippel-Lindau disease tumor suppressor 0 151.74 6.86E-06 116550000 143450 148380 149530 145320 166840 162730 160030 167850 189970 211980 FALSE TRUE 137843.8154 144148.3477 176553.3973 152819.9826 172206.5601 166020.5121 161988.495 164383.8388 168405.402 197622.4058 0.697511068 0.729412979 0.893387552 0.773292795 0.871391882 0.84008952 0.819686889 0.8318077 0.852157433 1 17.592387 -4.987767997 0.026300053 2.133636555 5.22E-07 0.640847216 0.04876526 1286.84749 2.559020731 153.2717954 69.52504729 1.03E-05 4.987767997 -2.133636033 LSESSAS(ph)PQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSESSASPQPK 11 0 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2;A0A3B3IU80;A0A3B3IUB0;A0A3B3IS72;A0A3B3ISB4;A0A3B3IRI6;A0A3B3ITV8;A0A3B3IRT2;A0A3B3ITF8;A0A3B3IT49;Q8N5Y2-5;A0A3B3ITX5 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 1 LSESS(0.009)AS(0.991)PQPK;LSESSAS(1)PQPK 269.33 1.27E-21 1389220000 2436700 2255800 1752130 1812640 1837810 1861120 2067100 2343100 2246400 2255400 TRUE FALSE 2341471.07 2191466.793 2068778.867 1906190.568 1896924.828 1898753.122 2092397.788 2294714.166 1991398.09 2102639.749 1.11358642 1.042245489 0.983896013 0.906570214 0.902163496 0.90303302 0.995128999 1.09134918 0.947094285 1 21.00377026 -4.983113822 16.92591598 1.000000106 0.989846874 0 0.072466553 0 0 0 0.017680658 1.04E-05 4.983113822 -0.010153233 ILMAIDSELVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILMAIDSELVDR 12 0 O43592;F8WDU6 O43592 XPOT Exportin-T 0 ; 122.26 0.0008415 18515500 39266 50769 49923 64448 59649 64141 56504 52726 45592 61470 FALSE TRUE 37731.44131 49321.11783 58945.19663 67774.169 61567.66426 65437.97497 57195.51285 51637.18967 40416.5873 57306.58215 0.658413744 0.860653628 1.028593827 1.182659416 1.074355893 1.141892825 0.998061841 0.901069087 0.705269548 1 15.80641323 -4.97610917 15.42420134 0.922980399 0.965590609 0 0.165389992 0 0 0 0.038482691 1.06E-05 4.97610917 0.04261021 APS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPTK 6 0 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82;H3BTV0;P59025;Q96FF9;B5MBX0 Q15287;Q96FF9 RNPS1;RTP1;CDCA5 RNA-binding protein with serine-rich domain 1;Receptor-transporting protein 1;Sororin 1 APS(0.992)PT(0.008)K 98.009 0.042402 9540500000 6504400 5581800 4136000 4895300 4688000 5018200 5663800 5915700 5140000 5919000 TRUE FALSE 6250200.857 5422612.529 4883467.205 5147947.02 4838793.778 5119671.442 5733115.279 5793538.728 4556528.749 5518100.858 1.132672457 0.982695436 0.884990567 0.932920067 0.876894769 0.927795916 1.038965294 1.049915338 0.825742201 1 22.3957404 -4.952643481 16.87796789 0.999902487 0.967007702 0 0.088506273 0 0 0 0.01987734 1.12E-05 4.952643481 -0.032894786 ERFS(ph)PPRHELSPPQKR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERFSPPRHELSPPQKR 16 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR 189.11 7.64E-10 6452500000 1003930 1138710 663078 782370 877560 1029910 840520 916860 969520 826070 TRUE FALSE 964695.3057 1106235.106 782910.9447 822748.2095 905787.5144 1050735.486 850806.5352 897926.5206 859464.1542 770119.5431 1.25265657 1.436445959 1.016609631 1.068338308 1.176164821 1.364379719 1.104772035 1.165957323 1.116013951 1 19.55472288 -4.949508375 0.033320954 7.87E-10 1.835643178 0.23759395 0.118953596 1879.714704 4.742836598 212.8603766 78.7637095 1.12E-05 4.949508375 1.835643178 LTS(ph)PGALLFQ ddPTM_BT-474_Pertuzumab_2h_R1 2 LTSPGALLFQ 10 0 O60566-3;O60566;O60566-2 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 1 LT(0.017)S(0.983)PGALLFQ;LT(0.009)S(0.991)PGALLFQ 112.84 0.0016439 45820000 85712 95770 95221 104224 100180 112317 103501 100351 108007 136469 TRUE FALSE 82362.28028 93038.73337 112429.5529 109603.0131 103402.3807 114588.1267 104767.6762 98278.71678 95746.49816 127225.8331 0.647370729 0.731288066 0.883700662 0.861483949 0.812746737 0.900667136 0.823478013 0.772474539 0.752571202 1 16.95703211 -4.92568004 0.022029567 2.007721127 2.51E-06 0.374585054 0.074693364 3665.120926 6.178141284 389.3793004 201.9780981 1.19E-05 4.92568004 -2.007718615 AGGSPAS(ph)YHGSTSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGGSPASYHGSTSPR 15 0 I3L2B2;O95208-3;O95208-2;F6PQP6 I3L2B2 EPN2 Epsin-2 1 AGGS(0.135)PAS(0.808)YHGS(0.014)T(0.014)S(0.03)PR 148.24 3.74E-06 132680000 48052 97254 74877 141990 94714 116430 116480 74582 76934 117000 TRUE FALSE 46174.07472 94480.41114 88408.93953 149318.1209 97760.56183 118784.2944 117905.5171 73041.85564 68200.77485 109075.4858 0.423322201 0.866192898 0.810529872 1.368942983 0.896265198 1.089009996 1.080953399 0.669645018 0.625262169 1 16.73496737 -4.872367663 15.02835536 0.822053923 0.889917231 0 0.25707882 0 0 0 0.057548709 1.34E-05 4.872367663 0.067863308 RRS(ph)SPSARPPDVPGQQPQAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RRS(0.333)S(0.333)PS(0.333)ARPPDVPGQQPQAAK 55.763 0.066878 204410000 70150 71044 45757 48863 59271 65681 52805 67589 56617 49812 TRUE FALSE 67408.46045 69017.89468 54026.30776 51384.82529 61177.50554 67009.11482 53451.24339 66193.26353 50190.07552 46438.18887 1.451573846 1.486231405 1.163402559 1.106520873 1.317396458 1.442974337 1.151019122 1.425405795 1.08079313 1 15.50302409 -4.862094659 0.144082658 6.07E-16 1.401499059 0.341511471 0.139712232 168.0076672 1.520587981 48.36334989 0.821254401 1.37E-05 4.862094659 1.401499059 ELELAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELELAHR 7 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 ; 141.78 0.0025335 265670000 376590 435210 365630 495910 434170 415870 458100 431300 482560 558600 FALSE TRUE 361872.4465 422798.2369 431707.4744 521503.9745 448135.4724 424279.1763 463706.3648 422393.5043 427781.8119 520765.5245 0.694885566 0.811878316 0.828986279 1.001418009 0.860532142 0.81472209 0.890432149 0.811101128 0.821448026 1 18.99027442 -4.84007972 0.018013494 2.008698581 5.31E-07 0.30438324 0.072984598 6202.647238 8.679452574 629.1197317 370.3154935 1.45E-05 4.84007972 -2.00869805 AGNAIHAILLYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGNAIHAILLYR 12 0 P50416;P50416-2;H3BMD2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 121.08 0.00023066 0 141680 256290 167330 243030 134830 68137 279950 208380 192170 207870 FALSE TRUE 136142.989 248980.8601 197570.2532 255572.8074 139166.9294 69514.77682 283376.1118 204076.8802 170355.6672 193790.7797 0.702525627 1.284792086 1.019502855 1.31880788 0.718129777 0.358710445 1.462278609 1.053078379 0.879070033 1 17.56414041 -4.7537531 17.35668185 1.000345546 0.997828286 0 0.315059892 0 0 0 0.0690353 1.76E-05 4.7537531 -0.00251726 KGIEESLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGIEESLR 8 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PP40;A0A1W2PQ55 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 105.2 0.0071105 206960000 242880 343770 213180 378560 200260 118250 385430 306840 240030 242340 FALSE TRUE 233387.9811 333966.0162 251706.3682 398097.527 206701.5448 120641.096 390147.0076 300503.6468 212782.8007 225926.0959 1.033027991 1.478209123 1.114109316 1.762069695 0.914907788 0.533984777 1.726878898 1.330097108 0.941824802 1 17.7854914 -4.753091553 0.211116162 5.95E-06 1.263152414 0.031772553 0.361793086 566.4622387 6.21557943 239.2141474 0.771866014 1.77E-05 4.753091553 1.263146459 RDDDEPGPWTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDDDEPGPWTK 11 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2;A0A087WWG9 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 138.02 0.00010621 603670000 187130 186850 141680 173520 175500 170280 173900 190270 199200 231970 FALSE TRUE 179816.7527 181521.2209 167284.7277 182475.388 181145.1169 173723.1783 176028.2402 186340.858 176587.6511 216258.4653 0.831490007 0.839371632 0.773540714 0.843783792 0.837632491 0.803312731 0.813971559 0.861658099 0.816558329 1 17.72239708 -4.744723961 0.34076424 2.553887375 0.819604971 0.835701375 0.023322293 119.8938611 1.199539777 134.6113613 0.018260726 1.80E-05 4.744723961 -1.734282404 IQESHPELR ddPTM_BT-474_Pertuzumab_2h_R1 1 IQESHPELR 9 0 Q9H9B4 Q9H9B4 SFXN1 Sideroflexin-1 0 91.549 0.010678 279750000 98779 205610 163850 334820 150860 166970 289470 196660 152290 182680 FALSE TRUE 94918.60747 199746.2041 193461.3398 352100.1003 155712.5489 170346.2478 293012.6205 192598.9023 135002.6777 170306.9209 0.557338521 1.17286017 1.135957005 2.067444461 0.914305467 1.000230918 1.720497434 1.130892986 0.79270224 1 17.37777754 -4.7272249 16.90950753 1.027532724 1.18881949 0 0.419919205 0 0 0 0.090412446 1.87E-05 4.7272249 0.161286766 VKELVEFAQDDDRLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VKELVEFAQDDDRLR 15 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 149.57 1.88E-06 84521000 112010 124620 76576 80769 95883 123130 90472 96995 102270 82145 FALSE TRUE 107632.5254 121065.9596 90414.98662 84937.49777 98967.16377 125619.773 91579.2234 94992.01935 90660.73835 76581.24598 1.405468454 1.580882605 1.180641363 1.109116164 1.292315925 1.640346424 1.195843998 1.240408381 1.183850396 1 16.22470351 -4.708500632 0.100759619 4.17E-12 1.540505818 0.317572747 0.159236177 224.6486971 1.636350601 47.39629859 2.806627206 1.96E-05 4.708500632 1.540505818 (ac)S(ph)DSGEQNYGERES(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 S(0.913)DS(0.087)GEQNY(0.161)GERES(0.839)R 41.052 0.0038946 0 3274 3578.2 4062.5 3012.9 3989.6 7991 0 5600.6 2377.3 4617 TRUE FALSE 3146.04846 3476.153239 4796.68412 3168.39613 4117.929107 8152.583495 0 5484.945653 2107.43887 4304.286478 0.730910565 0.807602667 1.114397042 0.736102522 0.956704236 1.894061545 0 1.274298465 0.489613989 1 12.07155839 -4.693714392 9.781191776 1.285333846 0.91330756 0 0.472389606 0 0 0 0.09554217 2.02E-05 4.693714392 -0.372026287 WLPLGLGLNHLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 WLPLGLGLNHLGK 13 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 187.42 3.45E-07 0 399420 414330 410770 420780 400760 363140 476390 459840 466990 513350 FALSE TRUE 383810.2248 402513.7141 485005.2765 442496.5062 413650.8094 370482.9396 482220.2033 450344.1433 413979.253 478580.3473 0.801976569 0.841057758 1.013424975 0.924602334 0.864328867 0.774129029 1.007605528 0.941000076 0.865015154 1 18.86840163 -4.676289492 0.014702328 2.064147654 7.32E-07 0.176140182 0.074871973 10800.13959 12.6736223 1096.564732 719.3101294 2.11E-05 4.676289492 -2.064146922 DYNVTANSK ddPTM_BT-474_Pertuzumab_2h_R1 6 DYNVTANSK 9 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;; 250.62 4.75E-11 3132060000 2822650 2886420 2262220 2405890 2440590 2310170 2484020 2633740 2675940 2057660 FALSE TRUE 2712337.717 2804102.128 2671053.477 2530058.271 2519093.794 2356883.22 2514420.18 2579352.349 2372178.51 1918292.855 1.413933076 1.461769573 1.392411732 1.318911377 1.313195629 1.22863577 1.310759289 1.344608224 1.236609156 1 20.87139155 -4.670685465 0.109105154 3.96E-16 1.540885244 0.854362511 0.046645002 63.61887213 0.497753826 14.55913207 0.702130976 2.13E-05 4.670685465 1.540885244 S(ph)EPDDELLFDFLNSSQKEPTGR ddPTM_BT-474_Pertuzumab_2h_R1 3 SEPDDELLFDFLNSSQKEPTGR 22 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 S(1)EPDDELLFDFLNSSQKEPTGR;S(1)EPDDELLFDFLNSSQKEPTGR;S(1)EPDDELLFDFLNSSQKEPTGR 139 3.83E-07 206893000 97743 122571 82928.2 89347 89083.7 112030 77379.3 101960 112857 79936.6 TRUE FALSE 93923.0955 119075.3951 97915.17047 93958.20938 91949.15811 114295.3234 78326.29102 99854.49037 100045.9465 74522.42288 1.260333358 1.597846534 1.313902134 1.260804544 1.233845527 1.533703803 1.05104327 1.339925441 1.342494549 1 16.18538696 -4.650006464 0.144893433 2.16E-10 1.436956619 0.32279397 0.143941791 138.6394424 1.332997931 40.68305482 0.777218866 2.24E-05 4.650006464 1.436956619 ALVDHENVISCPHLGASTK ddPTM_BT-474_Pertuzumab_2h_R1 4 ALVDHENVISCPHLGASTK 19 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YF78 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ;;; 273.46 1.29E-39 10137100000 10277300 11103800 9610000 11374900 10566000 12186500 11568200 8518700 13198800 12739200 FALSE TRUE 9875651.754 10787130.5 11346740.77 11961959.95 10905864.99 12432919.38 11709775.09 8342785.868 11700527.56 11876362.64 0.831538414 0.908285712 0.955405381 1.007207368 0.918283259 1.046862559 0.985973185 0.702469782 0.985194534 1 23.50158972 -4.603809295 6.456960334 0.999156936 0.923548397 0 0.09714128 0 0 0 0.022903252 2.49E-05 4.603809295 -0.075608539 LEEVMQELR ddPTM_BT-474_Pertuzumab_2h_R1 8 LEEVMQELR 9 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;;;; 179.37 0.00011604 995349600 794163 855904 834505 1006661 866121 575204.6 1055412 1034802 961573 1135929 FALSE TRUE 763126.232 831494.4559 985318.617 1058614.895 893980.5686 586835.6311 1068328.448 1013432.977 852419.2643 1058991.517 0.720616001 0.785175747 0.930431076 0.999644358 0.844181048 0.554145734 1.008816814 0.956979315 0.804934932 1 20.0142596 -4.584049598 0.02182486 2.106459325 4.68E-06 0.12593996 0.131376194 5764.393828 10.16899376 665.2197847 359.2719728 2.61E-05 4.584049598 -2.106454649 MS(ph)ADMSEIEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSADMSEIEAR 11 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 MS(0.999)ADMS(0.001)EIEAR 86.262 0.010438 0 84594 95669 76196 89587 74033 86330 78528 86772 96017 71494 TRUE FALSE 81287.97296 92940.61379 89966.31217 94210.59581 76414.33868 88075.65175 79489.04915 84980.12788 85117.5527 66651.6477 1.21959435 1.394423349 1.349798771 1.413477372 1.146473363 1.321432474 1.192604413 1.274989153 1.27705099 1 16.02435292 -4.580237511 0.177672359 9.63E-10 1.35487753 0.556477476 0.078976557 79.89997597 0.877443702 28.34852679 0.24759635 2.63E-05 4.580237511 1.354877529 RVS(ph)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAKNGSEADIDEGLYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAKNGSEADIDEGLYSR 47 3 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(0.477)GPDPKPGS(0.173)NCS(0.173)PAQS(0.173)VLS(0.004)EVPSVPTNGMAKNGSEADIDEGLYSR 42.752 0.038976 91501000 96708 93827 75789 72480 92973 89043 74577 91753 98570 74231 TRUE FALSE 92928.54444 91151.14583 89485.75822 76220.70149 95963.56098 90843.51047 75489.69563 89858.26849 87380.74684 69203.26825 1.34283462 1.317150882 1.293085724 1.101403206 1.386691169 1.312705494 1.090840036 1.298468566 1.262667921 1 16.07855255 -4.536248308 0.208778773 6.85E-11 1.304943067 0.44986483 0.09057881 110.4856144 1.312817539 46.4716271 0.19559399 2.91E-05 4.536248308 1.304943067 LLGPSAAADILQLSSS(ph)LPLQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLGPSAAADILQLSSSLPLQSR 22 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LLGPSAAADILQLSS(0.031)S(0.969)LPLQSR;LLGPSAAADILQLSS(0.018)S(0.982)LPLQSR 269.85 1.34E-42 0 115452 105727 79981 83203 91301 98054 83989 109989 84872 76456 TRUE FALSE 110940.0082 102711.7695 94435.34587 87497.1168 94237.77958 100036.7191 85016.88251 107717.6887 75237.68637 71277.56702 1.556450547 1.441011159 1.324895754 1.227554762 1.322123966 1.403481113 1.192757919 1.511242502 1.055559126 1 16.12116047 -4.52427789 0.106947823 7.00E-14 1.565515006 0.497678017 0.124479322 142.3071888 1.132350101 32.30985051 1.77171521 2.99E-05 4.52427789 1.565515006 ECLIDPDLTQYAIIMLDEAHER ddPTM_BT-474_Pertuzumab_2h_R1 2 ECLIDPDLTQYAIIMLDEAHER 22 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 0 ; 183.86 4.11E-17 91853000 102774 120268 103171 124892 129361 135616 121889 110689 122436 133704 FALSE TRUE 98757.47846 116838.0744 121816.2947 131337.6911 133522.014 138358.2484 123380.714 108403.2335 108537.5786 124648.109 0.792290226 0.937343337 0.97728153 1.053667738 1.071191654 1.109990754 0.989832217 0.869674112 0.870751907 1 16.92750147 -4.515500409 15.56314236 0.984289165 0.96906755 0 0.095238123 0 0 0 0.022942419 3.05E-05 4.515500409 -0.015221615 S(ph)VILEAFS(ph)SPSEEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVILEAFSSPSEEVK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 2 S(1)VILEAFS(0.981)S(0.011)PS(0.008)EEVK 51.546 0.090025 467610000 134670 158190 157240 133770 183600 182980 324080 115060 352430 368560 TRUE FALSE 129406.9475 153678.5761 185656.7658 140673.8857 189505.6607 186679.981 328046.188 112683.9708 312423.6239 343597.1029 0.376624094 0.447263888 0.540332745 0.409415227 0.551534513 0.543310696 0.954740844 0.327953786 0.909273161 1 18.39035835 -4.512598644 0.075604559 2.544069271 2.55E-14 0.505867714 0.168385165 205.2168909 1.214453535 55.06131121 6.915313941 3.07E-05 4.512598644 -2.544069271 ALSTGEKGFGYK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALSTGEKGFGYK 12 1 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 116.01 0.00021034 590300000 1083610 1077140 766650 649250 973040 1118900 847090 933250 1072830 814020 FALSE TRUE 1041261.323 1046421.022 905200.709 682757.8703 1004338.715 1141524.925 857456.9408 913978.0614 951046.8361 758885.7003 1.372092428 1.378891474 1.192802432 0.899684722 1.323438714 1.504211931 1.129889442 1.204368538 1.253214859 1 19.53352308 -4.507743863 0.227692789 7.67E-14 1.274304664 0.19255108 0.155825642 232.028621 2.852270414 106.8070487 0.292600486 3.11E-05 4.507743863 1.274304664 KPS(ph)KYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 KPS(0.232)KY(0.046)PLCS(0.232)ADAAVS(0.151)T(0.151)T(0.151)PPGS(0.036)PPPPPPLPEPPVLK 63.116 0.0064485 258470000 190720 198780 157340 133150 159070 195820 169930 181200 188770 153220 TRUE FALSE 183266.4515 193110.989 185774.838 140021.8875 164186.631 199779.6146 172009.6542 177458.1567 167341.621 142842.2729 1.282998708 1.351917644 1.300559241 0.980255246 1.14942606 1.398602882 1.204192923 1.242336411 1.171513289 1 17.12406347 -4.50514497 0.238089942 2.34E-14 1.257345559 0.296950767 0.110068158 181.2814782 2.249043407 87.47872187 0.187367196 3.13E-05 4.50514497 1.257345559 LSVDYGK ddPTM_BT-474_Pertuzumab_2h_R1 6 LSVDYGK 7 0 P68363;F8VQQ4;C9JDS9;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;;;; 160.03 0.0031676 3008940000 4241710 4158430 4184350 4424450 4449380 3987750 4989880 5100120 5879570 6199900 FALSE TRUE 4075939.284 4039835.648 4940555.125 4652796.395 4592498.349 4068385.037 5050947.644 4994800.74 5212145.863 5779975.251 0.705182826 0.698936496 0.854770983 0.804985522 0.794553289 0.703875858 0.873870116 0.864156077 0.901759201 1 22.46263188 -4.4780752 0.033199548 2.215614647 7.60E-07 0.691868205 0.051877606 629.7976584 1.711260693 89.60268876 35.75197484 3.33E-05 4.4780752 -2.215613887 GEFGDVMLGDYR ddPTM_BT-474_Pertuzumab_2h_R1 4 GEFGDVMLGDYR 12 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 ;;; 172.27 8.42E-05 494608000 613549 718103 677760 712944 644113 617004 776200 730031 703041 817790 FALSE TRUE 589570.8268 697623.4055 800246.3087 749739.1253 664831.4796 629480.2436 785699.3678 714955.6047 623234.7331 762400.3549 0.773308699 0.91503552 1.049640525 0.983392938 0.872024095 0.825655759 1.030560076 0.937769244 0.817463855 1 19.54018927 -4.397132313 0.007465483 1.969202952 1.64E-07 0.049396076 0.088837205 95772.57936 59.81942756 8735.511801 7118.933894 4.01E-05 4.397132313 -1.969202787 KTS(ph)ATVGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSATVGPK 9 1 P16104 P16104 H2AFX Histone H2AX 1 KT(0.138)S(0.861)AT(0.001)VGPK 68.44 0.035564 328250000 726210 545800 462640 402310 459740 423140 467160 714800 598930 537960 TRUE FALSE 697828.9103 530234.3184 546249.3394 423073.2673 474527.9546 431696.1807 472877.2438 700039.1302 530941.9773 501523.49 1.391418197 1.057247226 1.089179969 0.843576175 0.946172939 0.860769614 0.942881546 1.395825209 1.058658244 1 18.93595775 -4.380139256 8.231762366 1.011202077 1.064684701 0 0.184563259 0 0 0 0.043611984 4.17E-05 4.380139256 0.053482623 EQSTPPKS(ph)PQ ddPTM_BT-474_Pertuzumab_2h_R1 5 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EQST(0.001)PPKS(0.999)PQ;EQST(0.002)PPKS(0.998)PQ;EQST(0.052)PPKS(0.948)PQ;EQSTPPKS(1)PQ;EQST(0.01)PPKS(0.99)PQ 130.4 0.00073032 3439468000 4635190 4744100 3722810 4237450 4289900 4120060 4246970 4627430 4622730 3733210 TRUE FALSE 4454041.65 4608802.913 4395604.58 4456145.302 4427888.529 4203370.436 4298945.689 4531871.953 4097977.07 3480356.362 1.279765974 1.324233048 1.262975432 1.28037041 1.272251479 1.207741392 1.235202733 1.302128714 1.177459043 1 21.7308036 -4.357661987 0.223313998 9.62E-12 1.299267279 0.855917492 0.033518275 40.77107107 0.530145079 18.34024395 0.065037475 4.39E-05 4.357661987 1.299267279 S(ph)RTASGSS(ph)VTSLDGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 S(0.499)RT(0.499)AS(0.004)GS(0.095)S(0.845)VT(0.058)S(0.001)LDGTR 184.66 2.14E-08 1093300000 1086700 1116200 691320 891130 1041000 926460 776130 1076100 953390 764400 TRUE FALSE 1044230.563 1084367.069 816256.9023 937121.3261 1074484.71 945193.656 785628.5111 1053878.159 845165.1641 712626.5071 1.46532658 1.521648519 1.145420349 1.315024514 1.507781004 1.326352088 1.102440764 1.478864662 1.185986145 1 19.44278662 -4.344696729 0.152448703 9.41E-10 1.454850644 0.402907751 0.137845456 114.7673668 1.240422208 35.56339557 0.690626467 4.52E-05 4.344696729 1.454850643 EYNEFAEVFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EYNEFAEVFLK 11 0 O95373 O95373 IPO7 Importin-7 0 170.52 3.63E-05 62647000 64638 78394 62530 70666 69660 67387 73269 73515 88087 84241 FALSE TRUE 62111.8755 76158.27988 73830.56197 74313.08073 71900.67716 68749.61131 74165.68794 71996.88956 78087.73305 78535.28204 0.79087862 0.969733321 0.940094185 0.946238159 0.91552071 0.875397777 0.944361388 0.916745795 0.9943013 1 16.26105331 -4.323248356 0.012259676 2.056230584 2.64E-07 0.322478875 0.047926441 10537.61435 10.93531946 1081.22987 775.939796 4.75E-05 4.323248356 -2.05623032 MYEEHLK ddPTM_BT-474_Pertuzumab_2h_R1 9 MYEEHLK 7 0 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;;;;;;; 125.01 0.0040911 15483160000 13222258 12571954 11771214 13199438 12837408 11815140 14323700 13281449 15974780 15572590 FALSE TRUE 12705517.54 12213414.18 13898534.22 13880662.58 13250334.89 12054050.23 14498997.73 13007182.44 14161389.95 14517844.61 0.875165555 0.841269108 0.957341437 0.956110425 0.912692982 0.830291999 0.998701813 0.895944459 0.975447136 1 23.79132394 -4.317133144 0.013660627 2.065672383 3.67E-07 0.306281873 0.049324391 7918.675799 9.163980269 832.1035537 575.1987289 4.82E-05 4.317133144 -2.065672015 LSQYLDSSQVKPLFQFFVPDALNDRHPDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSQYLDSSQVKPLFQFFVPDALNDRHPDVR 30 2 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 174.72 3.29E-13 140060000 97945 114210 79570 79735 97259 110090 95612 91910 117130 91630 FALSE TRUE 94117.20112 110952.8426 93950.06903 83850.13291 100387.4241 112316.0952 96782.12826 90012.02638 103833.8934 85423.81848 1.101767666 1.298851358 1.099811161 0.981577906 1.175169008 1.314810052 1.132964201 1.053711107 1.21551454 1 16.38235077 -4.297261185 0.35562792 3.53E-08 1.152827689 0.169729752 0.098953325 512.6947078 6.792354898 384.6819772 0.076237927 5.04E-05 4.297261185 1.152827654 RLS(ph)LPADIR ddPTM_BT-474_Pertuzumab_2h_R1 5 RLSLPADIR 9 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;H0YBX5;Q00537;Q00537-2;F5H6Z0;F8VQZ9;F8VZY6 E5RJM2;Q00537 CDK16;CDK17 Cyclin-dependent kinase 16;Cyclin-dependent kinase 17 1 RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR 104.17 0.002023 3543010000 3422490 3036580 2289320 2844630 2631770 2510610 2432450 3390760 2456150 2304310 TRUE FALSE 3288735.307 2949979.712 2703051.05 2991441.695 2716423.272 2561376.254 2462219.051 3320739.621 2177338.149 2148237.031 1.530899644 1.373209599 1.258264805 1.392510068 1.264489548 1.192315474 1.146157996 1.545797588 1.013546512 1 21.03472175 -4.255615406 0.062680476 7.37E-14 1.778713736 0.421251138 0.138192337 369.863762 1.933131357 60.79581251 11.6159172 5.55E-05 4.255615406 1.778713736 LKEHEDYCGAR ddPTM_BT-474_Pertuzumab_2h_R1 5 LKEHEDYCGAR 11 1 O14545;F8VNX8;F8VVF3;O14545-2 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 0 ;;;; 185.25 2.73E-06 1655400000 2307890 2109520 1912110 2146310 2032370 2210380 2286850 2334790 2603240 2813610 FALSE TRUE 2217695.107 2049358.555 2257670.812 2257081.316 2097743.027 2255075.398 2314837.154 2286575.771 2307731.109 2623041.689 0.845466969 0.781290882 0.860707179 0.860482441 0.799736823 0.859717712 0.882501092 0.871726813 0.879792006 1 21.32280931 -4.240248339 0.147936199 1.440618588 0.794219901 0.787271444 0.025473139 43.9036837 0.478824456 5.799040257 0.134824879 5.75E-05 4.240248339 -0.646398687 S(ph)PPVTLGPNLAPTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPVTLGPNLAPTSR 15 0 B4DF95;Q15735;C9K0M5 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 S(1)PPVTLGPNLAPTSR;S(1)PPVTLGPNLAPTSR 150.39 3.35E-06 511850000 61679 52950 55919 44894 57777 60977 42212 61094 64319 48925 TRUE FALSE 59268.51649 51439.91784 66024.80721 47210.98472 59635.44968 62209.99672 42728.60308 59832.38755 57017.77677 45611.26617 1.299427125 1.127789736 1.447554798 1.035072882 1.307471918 1.363917338 0.936799319 1.311789665 1.25008099 1 15.4771026 -4.234567628 0.277994037 1.69E-14 1.244434848 0.181249553 0.147477695 238.447215 3.415691114 136.3575468 0.160612758 5.83E-05 4.234567628 1.244434848 DNIPALVEEYLER ddPTM_BT-474_Pertuzumab_2h_R1 3 DNIPALVEEYLER 13 0 Q9H1I8;B1AH59 Q9H1I8 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 ;; 128.9 0.00037204 73605300 54708 57256 51689.3 56783 57141 58692 59382 62783 60856 72209 FALSE TRUE 52569.95088 55623.11494 61030.70633 59713.57743 58978.99216 59878.79245 60108.73468 61486.50911 53947.88201 67318.22011 0.780917125 0.826271325 0.906600119 0.887034407 0.876122275 0.889488646 0.892904396 0.913370986 0.801386043 1 16.03870941 -4.213886688 0.016592668 2.017141986 1.63E-06 0.445920093 0.04426284 4026.704765 5.757884405 435.2511932 280.1916698 6.11E-05 4.213886688 -2.017140352 EDYTGKDVLILGGGDGGILCEIVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDYTGKDVLILGGGDGGILCEIVK 24 1 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 ; 162.77 1.61E-11 327550000 638870 602460 405420 441590 553620 612960 520000 534500 630720 540870 FALSE TRUE 613902.2541 585278.4307 478688.4125 464380.5128 571427.6901 625354.4712 526363.9155 523462.3882 559123.3098 504236.3931 1.217488984 1.160722309 0.949333327 0.920957946 1.133253565 1.240200984 1.043883232 1.038128932 1.108851557 1 18.94374072 -4.201179672 0.010864344 5.64E-07 1.988120344 0.072817504 0.099399102 35204.0827 33.06672845 3490.74404 2617.364423 6.29E-05 4.201179672 1.98811978 EDTEEYNLR ddPTM_BT-474_Pertuzumab_2h_R1 5 EDTEEYNLR 9 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;; 268.28 1.88E-15 7013420000 3085650 2892610 2983730 3240570 2984660 2844460 3131350 3614000 3701470 3890560 FALSE TRUE 2965059.387 2810115.595 3522956.384 3407816.206 3080664.299 2901976.93 3169672.398 3539369.637 3281294.643 3627048.906 0.817485362 0.774766392 0.971301043 0.939556178 0.849358357 0.800093135 0.873898445 0.975826279 0.904673394 1 21.79036477 -4.19238063 0.019420607 2.097489596 9.25E-07 0.338909901 0.061532977 3680.764631 6.179083415 430.035072 257.359205 6.42E-05 4.19238063 -2.097488671 QLEESVDALSEELVQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLEESVDALSEELVQLR 17 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 60.474 0.077854 5516600 5537.3 4273 5138.1 5094.2 6559.1 5289.7 5563.7 4464 7097.8 5310.9 FALSE TRUE 5320.896194 4151.138224 6066.668966 5357.112272 6770.079408 5396.661358 5631.790225 4371.81684 6292.0875 4951.188013 1.0746706 0.838412561 1.225295616 1.081985224 1.367364639 1.089973022 1.137462405 0.882983403 1.270823787 1 12.27355902 -4.176609414 0.467560861 4.11E-05 1.096188607 0.034725856 0.153551102 3137.946779 38.00492674 3189.922374 0.078406501 6.66E-05 4.176609414 1.096147499 QEDEWDKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 QEDEWDKPR 9 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;; 132.25 0.00028303 2284400000 2621340 2753490 2151360 2575150 2397540 2291830 2250270 2507030 2763850 1958070 FALSE TRUE 2518895.135 2674963.161 2540158.609 2708053.8 2474659.051 2338172.373 2277809.477 2455258.954 2450109.335 1825448.175 1.379877648 1.46537338 1.391526006 1.483500785 1.35564465 1.28087579 1.247808351 1.345017069 1.342196053 1 20.79981928 -4.166234213 0.148140604 9.64E-12 1.493747225 0.806062298 0.056953626 43.97862324 0.490107094 13.38834466 0.325528513 6.82E-05 4.166234213 1.493747225 SWMEGLTLQDYSEHCK ddPTM_BT-474_Pertuzumab_2h_R1 1 SWMEGLTLQDYSEHCK 16 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 205.68 2.20E-11 74824000 66467 74822 55469 73474 73467 74965 67340 76627 77589 88263 FALSE TRUE 63869.39616 72688.14982 65493.4822 77266.00195 75830.13278 76480.84366 68164.12706 75044.62567 68781.422 82284.86839 0.776198558 0.883372013 0.795935917 0.939006204 0.921556226 0.929464252 0.828392004 0.912010035 0.83589393 1 16.32833953 -4.155337686 0.016166643 2.01468329 6.59E-07 0.354355332 0.054196805 5232.771674 7.365714357 566.3861255 370.3542353 6.99E-05 4.155337686 -2.014682631 EFLHNQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFLHNQGK 8 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 145.63 0.00056623 648260000 1100170 1214960 1033430 1142410 1174000 1194720 1216850 1182820 1492250 1458540 FALSE TRUE 1057174.14 1180310.53 1220193.79 1201369.917 1211762.776 1218878.057 1231742.174 1158394.354 1322856.036 1359751.787 0.777475824 0.868033815 0.897365094 0.883521484 0.891164688 0.896397467 0.905858103 0.851916037 0.972865819 1 20.37491189 -4.133080634 0.018178586 2.068306343 5.34E-07 0.639753276 0.034870039 2425.691492 3.85272979 277.2941866 172.3264107 7.36E-05 4.133080634 -2.068305809 TFS(ph)ATVR ddPTM_BT-474_Pertuzumab_2h_R1 12 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TFS(0.987)AT(0.013)VR;TFS(0.893)AT(0.107)VR;TFS(0.999)AT(0.001)VR;T(0.293)FS(0.518)AT(0.189)VR;TFS(0.955)AT(0.045)VR;TFS(0.997)AT(0.002)VR;TFS(0.917)AT(0.083)VR;T(0.004)FS(0.688)AT(0.308)VR;T(0.008)FS(0.983)AT(0.009)VR;T(0.227)FS(0.616)AT(0.158)VR;T(0.022)FS(0.747)AT(0.231)VR;TFS(0.639)AT(0.361)VR 186.54 0.00062667 1.93484E+11 37172983 35847009 29812082 32212729 34336197 31121300 31633735 35598046 33753380 30486101 TRUE FALSE 35720221.73 34824687.4 35199788.38 33875231.8 35440651.96 31750594.01 32020878.11 34862933.91 29921837.81 28421250.23 1.256813879 1.225304556 1.238502462 1.191898018 1.246977233 1.117142763 1.126652693 1.226650258 1.052798085 1 24.76046668 -4.106448577 0.080793763 0.392769533 1.408782894 0.714832973 0.045369347 110.6253066 0.754473446 12.63018911 1.604233745 7.83E-05 4.106448577 1.016013361 HSQDLAFLSMLNDIAAVPATAMPFR ddPTM_BT-474_Pertuzumab_2h_R1 6 HSQDLAFLSMLNDIAAVPATAMPFR 25 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 228.42 3.35E-34 4288440000 1942030 2081230 1975145 2196640 2244790 2314330 2281400 1733210 2507000 2627160 FALSE TRUE 1866133.321 2021875.358 2332097.638 2310008.854 2316995.709 2361127.338 2309320.456 1697418.608 2222415.87 2449220.113 0.761929608 0.825518028 0.952179686 0.943160985 0.94601367 0.964032316 0.942879916 0.693044532 0.907397362 1 21.22389101 -4.09751299 0.007807015 1.881726053 9.24E-07 0.079373631 0.090889014 93760.93477 64.47390001 8596.839655 7015.979649 7.99E-05 4.09751299 -1.881725129 RAS(ph)PNLFSEAQYQEAPVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RASPNLFSEAQYQEAPVEK 19 1 F6VUX8;Q9HC77-2;Q9HC77 F6VUX8 CENPJ Centromere protein J 1 RAS(0.999)PNLFS(0.001)EAQYQEAPVEK;RAS(1)PNLFSEAQYQEAPVEK 225.3 1.08E-19 401340000 424670 427330 374280 430050 401800 429490 429420 471800 507310 520330 TRUE FALSE 408073.4269 415142.9668 441920.7218 452244.932 414724.2619 438174.5821 434675.3704 462057.1651 449722.2956 485087.5856 0.841236591 0.85581033 0.911012227 0.932295415 0.854947177 0.903289622 0.896076056 0.952523171 0.927095042 1 18.88788573 -4.096822272 0.016827452 2.081230378 1.18E-10 0.697322162 0.025549718 2213.025419 3.275488283 251.531839 162.3820136 8.00E-05 4.096822272 -2.081230378 TSQTWHGGIATIFQSPGDEVWGVVWK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSQTWHGGIATIFQSPGDEVWGVVWK 26 0 O75223;B8ZZK2;H7BZK5;O75223-2;O75223-4 O75223 GGCT Gamma-glutamylcyclotransferase 0 ;; 249.79 7.25E-46 2522700000 1196399 1201366 1096051 1284468 1245007 1229759 1372900 1199757 1421371 1552561 FALSE TRUE 1149642.404 1167104.218 1294131.797 1350759.547 1285053.781 1254625.57 1389701.961 1174981.599 1260022.923 1447404.661 0.794278501 0.806342725 0.894105037 0.933228685 0.88783311 0.866810508 0.960133678 0.811785143 0.870539495 1 20.46503689 -3.98808018 0.015400919 1.987147801 2.33E-06 0.378134384 0.050827028 6068.445671 8.384008112 657.0442779 443.5773282 0.000102783 3.98808018 -1.987145467 RHS(ph)LENK ddPTM_BT-474_Pertuzumab_2h_R1 4 RHSLENK 7 1 O14578-4 O14578-4 CIT Citron Rho-interacting kinase 1 RHS(1)LENK;RHS(1)LENK;RHS(1)LENK;RHS(1)LENK 144.47 0.0014405 1222880000 995806 960824 964482 1013049 1070893 1194570 1177439 803516 1503870 1363831 TRUE FALSE 956888.8006 933422.2403 1138785.352 1065332.58 1105339.246 1218725.024 1191848.851 786923.1138 1333156.982 1271457.512 0.752592039 0.734135613 0.895653486 0.837882958 0.869348158 0.958525954 0.937387872 0.618914204 1.048526569 1 20.27805182 -3.849694454 0.021990054 2.025098351 2.75E-06 0.216057527 0.111260732 4392.739713 8.875937427 535.0359231 309.7893088 0.000141353 3.849694454 -2.025095602 RRDS(ph)DAPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRDSDAPGK 9 2 Q86YI8 Q86YI8 PHF13 PHD finger protein 13 1 RRDS(1)DAPGK;RRDS(1)DAPGK 74.392 0.032462 170514000 249290 216016 158328 176836 187483 171214 170057 244790 163432 145837 TRUE FALSE 239547.4712 209855.4352 186941.3916 185962.5272 193513.561 174676.0644 172138.2084 239735.001 144879.8845 135959.3301 1.761905351 1.543516249 1.374980235 1.367780549 1.423319465 1.284767028 1.26610074 1.763284659 1.065611933 1 17.05281563 -3.835120401 0.108151543 2.34E-20 1.714219329 0.413469066 0.18548305 150.772942 1.419487051 37.55675016 2.797618033 0.000146177 3.835120401 1.714219329 TLSFSHDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 TLSFSHDGK 9 0 Q96J01;D6REC9;Q96J01-2;H7C0C5 Q96J01 THOC3 THO complex subunit 3 0 ;;; 163.32 6.32E-05 962250000 3139620 3433120 2919780 3358450 3193170 3307280 3626180 3470120 3826940 4126240 FALSE TRUE 3016920.179 3335210.779 3447449.196 3531780.007 3295881.213 3374155.468 3670558.276 3398460.809 3392521.815 3846766.09 0.784274403 0.867016788 0.896194132 0.918116653 0.856792728 0.877140795 0.95419326 0.883459179 0.881915286 1 21.87521468 -3.834158451 0.016758327 2.03248413 3.70E-07 0.55939485 0.036414633 3047.344599 4.710787882 350.852859 231.5508334 0.000146501 3.834158451 -2.03248376 KEPVDEDLYPEHYR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEPVDEDLYPEHYR 14 1 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;;; 140.84 6.39E-06 1869320000 4164470 4081500 3742570 4106720 4217030 4334430 4462630 4457410 4873810 5339750 FALSE TRUE 4001717.908 3965099.616 4418935.652 4318668.311 4352674.6 4422075.144 4517245.001 4365362.926 4320555.521 4978083.976 0.803867096 0.796511195 0.887678005 0.867536251 0.874367452 0.888308668 0.907426436 0.876916289 0.867915355 1 22.24715914 -3.762457588 0.019591964 2.038983876 1.56E-06 0.749249818 0.026639948 1428.008634 2.614257644 172.3357277 106.7255361 0.000172799 3.762457588 -2.038982315 VENFEAAVHFYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VENFEAAVHFYGK 13 0 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 ; 130.47 0.00014171 1315720000 1990780 1948120 1829850 1812910 1942760 2037530 2006490 2108450 2392770 2386170 FALSE TRUE 1912978.117 1892561.525 2160544.6 1906474.502 2005250.64 2078730.253 2031046.025 2064909.771 2121152.781 2224552.581 0.859938368 0.850760527 0.971226582 0.857014808 0.901417506 0.934448694 0.91301327 0.928235992 0.953518833 1 21.08508377 -3.711657518 0.015431686 2.058699478 7.58E-10 0.561411122 0.03182605 3109.316678 4.529656504 363.5888088 250.1308766 0.000194242 3.711657518 -2.058699477 EMFPYEAST(ph)PTGISASCR ddPTM_BT-474_Pertuzumab_2h_R1 5 EMFPYEASTPTGISASCR 18 0 P42167;G5E972;H0YJH7;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 EMFPYEAS(0.195)T(0.774)PT(0.031)GISASCR;EMFPYEAS(0.014)T(0.915)PT(0.072)GISASCR;EMFPYEAS(0.023)T(0.489)PT(0.489)GISASCR;EMFPYEAS(0.041)T(0.957)PT(0.003)GISASCR;EMFPYEAS(0.262)T(0.736)PT(0.002)GISASCR 369.44 1.58E-106 1397510000 1235290 1611060 940885 1415385 1018274 1156248 1034427 1611035 1097565 971974 TRUE FALSE 1187013.501 1565114.146 1110923.849 1488433.189 1051027.708 1179628.127 1047086.627 1577766.564 972974.0226 906141.3352 1.309965074 1.727229611 1.22599401 1.642605995 1.15989379 1.301814718 1.15554449 1.741192574 1.073755257 1 19.78937657 -3.674057793 0.209177945 4.18E-15 1.460698101 0.217060022 0.229102237 121.2216938 1.989760002 52.35961831 0.495460036 0.000211808 3.674057793 1.460698101 MWDVSTGMCLMTLVGHDNWVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MWDVSTGMCLMTLVGHDNWVR 21 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 137.61 3.00E-06 60224000 51915 56038 47529 59232 57911 48608 63288 52203 60678 66911 FALSE TRUE 49886.1044 54439.85111 56118.54758 62288.97062 59773.75991 49590.88706 64062.53748 51124.98981 53790.08782 62379.05837 0.799725192 0.872726401 0.899637619 0.998555801 0.958234405 0.794992556 1.026987889 0.81958579 0.862310032 1 15.92877415 -3.641354437 0.009480882 1.933217215 1.02E-06 0.108227059 0.07834909 35779.53491 32.4740666 3705.880571 2953.670394 0.000228373 3.641354437 -1.933216191 S(ph)PPGGPDKDFAWLS ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPGGPDKDFAWLS 14 1 Q86UZ6 Q86UZ6 ZBTB46 Zinc finger and BTB domain-containing protein 46 1 S(1)PPGGPDKDFAWLS 80.632 0.041445 82475000 116960 124570 91784 108100 105470 89073 112570 127440 99669 86828 TRUE FALSE 112389.0739 121017.3856 108371.4105 113679.054 108862.5383 90874.11709 113947.6653 124808.3195 88354.99297 80947.06222 1.388426841 1.495018871 1.338793621 1.404362936 1.344860892 1.122636382 1.407681294 1.541851131 1.091515745 1 16.3046911 -3.636539648 0.23853695 4.58E-16 1.40886706 0.432487482 0.129047943 83.21321059 1.495609625 40.68638167 0.221560737 0.000230919 3.636539648 1.40886706 KYTELPHGAISEDQAVGPADIPCDSTGQTST(ph) ddPTM_BT-474_Pertuzumab_2h_R1 1 KYTELPHGAISEDQAVGPADIPCDSTGQTST 31 1 Q9H773;H3BPN2;H3BSA6 Q9H773 DCTPP1 dCTP pyrophosphatase 1 1 KYTELPHGAISEDQAVGPADIPCDS(0.013)T(0.013)GQT(0.14)S(0.14)T(0.695) 78.415 0.0013111 195680000 117450 142480 133760 187230 171910 163780 161580 134240 141620 171290 TRUE FALSE 112859.9242 138416.6099 157933.4075 196892.9627 177439.6413 167091.7438 163557.4644 131467.8971 125543.8913 159688.3757 0.706751031 0.866792021 0.989010044 1.232982437 1.111161914 1.046361346 1.024228994 0.823277815 0.786180527 1 17.28489977 -3.601729982 17.41617238 0.999459414 0.963186426 0 0.15274472 0 0 0 0.036726566 0.00025019 3.601729982 -0.036272988 VQEAVLDKWVNDPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQEAVLDKWVNDPHR 15 1 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ; 155.1 1.42E-06 785780000 1508420 1445550 1000360 1013780 1350790 1518120 1228980 1227540 1484260 1259250 FALSE TRUE 1449469.279 1404324.329 1181147.305 1066101.307 1394239.387 1548817.427 1244020.625 1202190.87 1315773.027 1173959.876 1.234683833 1.196228558 1.00612238 0.908124144 1.187638024 1.31931036 1.059678998 1.024047665 1.120798976 1 20.16295167 -3.59853352 0.016707043 4.64E-06 1.971461038 0.101686743 0.11464502 10213.50734 16.45875358 1181.183217 794.795404 0.000252038 3.59853352 1.971456399 QPSGS(ph)FSTPGSATYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPSGSFSTPGSATYVR 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 QPS(0.005)GS(0.972)FS(0.012)T(0.012)PGSATYVR;QPS(0.003)GS(0.995)FS(0.001)TPGSATYVR 140.3 1.80E-06 398440000 220990 232067 162519 190946 187843 182625 187297 235716 201427 165132 TRUE FALSE 212353.4665 225448.6764 191889.7985 200800.7459 193885.1407 186317.8026 189589.1967 230848.3822 178561.8514 153947.4626 1.379389195 1.464452045 1.246462886 1.304345928 1.259424075 1.210268747 1.231518815 1.499527036 1.15988824 1 17.23207856 -3.554013436 0.310948129 1.51E-15 1.333086158 0.460845485 0.102291523 104.6121428 2.195038658 67.60031014 0.101822964 0.000279246 3.554013436 1.333086158 QRT(ph)LEDEEEQERER ddPTM_BT-474_Pertuzumab_2h_R1 2 QRTLEDEEEQERER 14 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQERER;QRT(1)LEDEEEQERER 203.26 7.29E-07 741220000 316400 342740 186675 227181 298210 246770 237006 342690 223450 206558 TRUE FALSE 304034.7382 332965.3908 220411.3251 238905.8386 307802.1955 251759.8585 239906.5503 335613.3317 198084.8928 192567.6427 1.578846446 1.729082758 1.144591698 1.240633345 1.598410778 1.307384018 1.245830021 1.742833464 1.028650972 1 17.55500578 -3.544026917 0.202410112 4.37E-12 1.499427975 0.263482799 0.227600175 109.3284099 1.842191817 45.96822636 0.562811298 0.000285741 3.544026917 1.499427975 YSVLNNDDYFADVS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSVLNNDDYFADVSPLR 17 0 Q1ED39;H3BMC9 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR 178.72 1.00E-09 147471000 156125 143576 123779 133804 131632 148233 142465 155591 158783 178630 TRUE FALSE 150023.4624 139481.3531 146148.6187 140709.6405 135866.0628 151230.3728 144208.5293 152377.9915 140758.6195 166531.231 0.900872836 0.837568738 0.877604867 0.844944457 0.815859356 0.908120188 0.865954863 0.9150115 0.84523857 1 17.34543324 -3.540691631 0.26131948 1.360902077 0.856689854 0.609272472 0.031499682 53.68758614 1.054911846 10.42512166 0.040632877 0.000287944 3.540691631 -0.504212223 VFLQDGPARPAS(ph)PEAGNTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFLQDGPARPASPEAGNTLR 20 1 Q9UJX6-2;Q9UJX6 Q9UJX6-2 ANAPC2 Anaphase-promoting complex subunit 2 1 VFLQDGPARPAS(0.993)PEAGNT(0.007)LR;VFLQDGPARPAS(0.998)PEAGNT(0.002)LR 73.655 0.0088849 346310000 182338 192873 248544 260060 253127 239170 251854 265660 307410 373530 TRUE FALSE 175212.0294 187372.4509 293461.4296 273481.7278 261269.0598 244006.1813 254936.2646 260174.0282 272514.1056 348230.4804 0.503149607 0.538070219 0.842721836 0.785346899 0.750276253 0.700703112 0.732090609 0.747131692 0.782568215 1 18.40968296 -3.527501146 0.044305404 2.095504659 1.99E-17 0.598870376 0.085119936 422.1320831 1.818220676 70.82803029 25.29409205 0.000296824 3.527501146 -2.095504659 EWPQHWPDMLIELDTLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EWPQHWPDMLIELDTLSK 18 0 Q9HAV4 Q9HAV4 XPO5 Exportin-5 0 139.17 4.56E-07 122470000 130480 136270 136680 123830 147010 145380 130630 130840 165870 147120 FALSE TRUE 125380.6973 132383.713 161381.1164 130220.8811 151738.7102 148319.6832 132228.689 128138.1083 147041.133 137155.4314 0.914150436 0.96520941 1.176629426 0.949440207 1.106326659 1.08139854 0.964079131 0.934254714 1.072076633 1 17.06545223 -3.516294464 7.08016352 1.000045548 1.014511979 0 0.08272383 0 0 0 0.018335101 0.000304583 3.516294464 0.014466431 APKPDGPGGGPGGSHMGGNYGDDR ddPTM_BT-474_Pertuzumab_2h_R1 12 APKPDGPGGGPGGSHMGGNYGDDR 24 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ;;;;;;;;;;; 232 4.29E-34 38917720000 11263480 10637420 10881180 11736460 11051620 10850790 11598170 12201780 13628550 13925800 FALSE TRUE 10823290.75 10334051.2 12847651.28 12342180.11 11407105.39 11070200.41 11740111.87 11949808.98 12081494.14 12982593.16 0.83367711 0.79599284 0.989605937 0.950671407 0.878646142 0.852695626 0.90429637 0.920448544 0.930591754 1 23.63007524 -3.419420781 0.015354616 2.020989979 2.29E-07 0.343995757 0.050941697 5394.294688 8.277111479 648.166468 456.0641101 0.000380697 3.419420781 -2.02098975 TYDRDNSGMIDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TYDRDNSGMIDK 12 1 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 132.24 0.00016818 609860000 155648 177748 118492 145335 157217 167388 130013 150073 177569 134381 FALSE TRUE 149565.1041 172678.8011 139906.1402 152835.7568 162274.0276 170772.7 131604.138 146973.9401 157412.1115 125279.2552 1.193853714 1.378351115 1.116754247 1.219960612 1.29529847 1.363136297 1.050486274 1.173170609 1.256489842 1 16.93478801 -3.408923344 0.187121717 0.496655985 1.276405497 0.336005599 0.096728224 78.61138242 1.312169139 15.49042331 0.288737381 0.000390011 3.408923344 0.779749512 AAESLTAIPEPAS(ph)PQLLETPIHASQIQK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAESLTAIPEPASPQLLETPIHASQIQK 28 0 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AAESLTAIPEPAS(1)PQLLETPIHASQIQK;AAESLTAIPEPAS(1)PQLLETPIHASQIQK;AAESLTAIPEPAS(1)PQLLETPIHASQIQK;AAESLTAIPEPAS(1)PQLLETPIHASQIQK 337.17 2.48E-96 712100000 678860 1192290 977710 1486460 1079640 1395520 1194840 1022270 926560 1273270 TRUE FALSE 652329.4007 1158287.057 1154403.946 1563176.379 1114367.601 1423738.371 1209462.809 1001159.767 821380.7933 1187030.289 0.549547393 0.975785595 0.972514313 1.316879943 0.938786155 1.199411998 1.018898019 0.843415519 0.691962792 1 20.17892532 -3.384186898 7.859140284 0.995815952 0.962154447 0 0.210940678 0 0 0 0.046758035 0.00041287 3.384186898 -0.033661504 DWNDMER ddPTM_BT-474_Pertuzumab_2h_R1 1 DWNDMER 7 0 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 90.862 0.039147 1804100000 3895800 3438400 3416600 3884400 4027400 3933500 4282200 3335200 4864300 4798300 FALSE TRUE 3743547.829 3340340.199 4034055.622 4084874.35 4156944.979 4013038.065 4334606.845 3266326.954 4312125.057 4473306.867 0.836863631 0.746727264 0.901806145 0.913166584 0.929277848 0.897107707 0.96899385 0.730181732 0.963968086 1 22.0929103 -3.36520486 0.016310903 1.976555231 3.46E-06 0.232414638 0.075853382 6756.348153 11.13250429 809.584169 559.6011649 0.000431316 3.36520486 -1.976551771 VLSPT(ph)AAKPSPFEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLSPTAAKPSPFEGK 15 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 VLS(0.115)PT(0.885)AAKPSPFEGK 191.64 2.70E-07 4540300000 2379000 1857100 1505200 1474600 1779100 1547700 1425200 2301900 1479300 1247100 TRUE FALSE 2286026.05 1804137.326 1777223.123 1550704.283 1836326.367 1578995.554 1442642.024 2254364.961 1311376.066 1162632.806 1.966249393 1.55176881 1.528619452 1.333786794 1.579455145 1.358120591 1.24084063 1.939017159 1.127936575 1 20.14896409 -3.359220448 0.136748334 6.41E-28 1.746355523 0.361088924 0.241029534 108.4594189 1.418464999 34.20123728 1.793109319 0.0004373 3.359220448 1.746355523 VES(ph)PPLEEWPSPAPSFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VESPPLEEWPSPAPSFK 17 0 A0A0D9SFF0;Q08050-2;Q08050;Q08050-3 A0A0D9SFF0 FOXM1 Forkhead box protein M1 1 VES(1)PPLEEWPSPAPSFK;VES(1)PPLEEWPSPAPSFK 201.24 1.22E-11 90237000 156033 150176 132535 161692 145149 126554 176633 179371 169820 207377 TRUE FALSE 149935.0579 145893.1275 156487.0227 170036.9435 149817.8494 129113.0086 178794.6875 175666.9262 150542.7455 193331.1711 0.775534835 0.754628065 0.809424687 0.879511268 0.774928578 0.667833376 0.924810451 0.908632194 0.778678082 1 17.56071474 -3.358243283 0.137183924 1.413981929 0.728588356 0.408850719 0.071916891 83.71691992 1.098242989 10.39304953 0.540458484 0.000438285 3.358243283 -0.685393574 DIISDTSGDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIISDTSGDFR 11 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YN52 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 194.06 1.58E-06 705610000 760200 714730 421830 1309880 801470 577720 567090 948740 945330 1001670 FALSE TRUE 730490.5436 694346.6002 498064.0646 1377483.064 827250.0104 589401.8942 574030.2171 929148.1875 838020.1015 933825.9987 0.782255521 0.743550299 0.533358533 1.475096073 0.885871684 0.631168863 0.614707898 0.994990704 0.89740498 1 19.83279423 -3.35327731 0.021591879 1.998655149 1.08E-05 0.040208308 0.251093585 9335.642047 20.4002074 1200.188991 737.2482854 0.000443325 3.35327731 -1.998644328 DLIDFDDRQQIYAAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLIDFDDRQQIYAAEK 16 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 266.28 3.24E-27 667950000 1230000 1231180 625920 736590 1003090 1283330 879270 957220 1034310 728280 FALSE TRUE 1181930.24 1196067.952 739037.6675 774605.4982 1035355.301 1309279.812 890030.7693 937453.0725 916899.465 678952.9469 1.740813182 1.761635997 1.088496148 1.140882445 1.524929387 1.928380778 1.310887262 1.380733491 1.350460984 1 19.37295207 -3.327318165 0.194516297 7.30E-11 1.560575285 0.25884667 0.254149754 104.3427964 1.845189371 42.70526863 0.740581192 0.000470632 3.327318165 1.560575285 LPS(ph)AESLSR ddPTM_BT-474_Pertuzumab_2h_R1 5 LPSAESLSR 9 0 O43281-3;O43281-2;O43281 O43281-3 EFS Embryonal Fyn-associated substrate 1 LPS(1)AESLSR;LPS(1)AESLSR;LPS(1)AESLSR;LPS(1)AESLSR;LPS(1)AESLSR 178.54 5.33E-05 10616750000 1449920 1741350 1659950 1907320 1878650 1857280 1784620 1879640 1588290 1813340 TRUE FALSE 1393255.523 1691688.403 1959939.89 2005757.014 1939078.483 1894835.474 1806460.713 1840824.777 1407993.978 1690520.867 0.824157543 1.000690637 1.159370422 1.186472793 1.147030197 1.120858968 1.068582322 1.088909823 0.832875835 1 20.68903639 -3.320605519 9.747677778 1.00259789 1.058589913 0 0.123255625 0 0 0 0.027535369 0.000477963 3.320605519 0.055992022 AIVICPTDEDLKDR ddPTM_BT-474_Pertuzumab_2h_R1 3 AIVICPTDEDLKDR 14 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ;; 222.29 3.60E-12 2431560000 1480610 1588010 1307810 1382510 1044760 1427350 1303420 1477450 1594450 1793030 FALSE TRUE 1422746.124 1542721.51 1544160.359 1453861.507 1078365.654 1456211.995 1319371.644 1446940.141 1413454.72 1671586.481 0.851135218 0.922908582 0.923769351 0.8697495 0.645115085 0.871155643 0.789293081 0.865608904 0.845576784 1 20.67278657 -3.293621589 0.879281625 3.161077749 0.842537637 0.28079832 0.075525697 16679.0932 312.7401539 70969.58781 0.024822843 0.000508602 3.293621589 -2.318540112 LQDFKLDFGNSQGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQDFKLDFGNSQGK 14 1 O75223;B8ZZK2;O75223-2;O75223-4 O75223 GGCT Gamma-glutamylcyclotransferase 0 81.327 0.012599 889210000 2735000 2631500 1830600 1639500 2207200 2692300 2122700 2396900 2531500 1900800 FALSE TRUE 2628113.176 2556452.197 2161430.141 1724114.791 2278196.593 2746740.151 2148678.238 2347403.177 2244134.733 1772057.123 1.483086037 1.442646607 1.219729383 0.97294538 1.285622547 1.550029124 1.212533281 1.324676923 1.266400899 1 20.75699368 -3.291145733 0.394862882 2.36E-09 1.309939472 0.264620618 0.154241822 233.1148224 6.158077715 194.1447023 0.10320438 0.00051151 3.291145733 1.30993947 HLSPDGQYVPR ddPTM_BT-474_Pertuzumab_2h_R1 10 HLSPDGQYVPR 11 0 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;;;;;;;;; 226.4 4.76E-12 18586650000 4353982 7871208 6311859 9524660 6970730 8392250 8012880 6635020 6063777 8508630 FALSE TRUE 4183823.57 7646728.855 7452552.328 10016228.84 7194949.861 8561947.045 8110944.022 6498004.518 5375442.456 7932332.911 0.527439231 0.963994948 0.939515829 1.262709086 0.907040834 1.079373135 1.022516845 0.819179501 0.677662236 1 22.9193138 -3.284290415 9.688076629 0.999469633 0.929800771 0 0.196522618 0 0 0 0.043092128 0.000519648 3.284290415 -0.069668861 LQPFHS(ph)TELEDDAIYSVHVPAGLYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQPFHSTELEDDAIYSVHVPAGLYR 25 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 LQPFHS(0.912)T(0.088)ELEDDAIYSVHVPAGLYR;LQPFHS(0.928)T(0.072)ELEDDAIYSVHVPAGLYR 320.94 1.02E-74 264369000 68206 87388 44617 95801 92846 75988 71292 68657 75352 96458 TRUE FALSE 65540.43411 84895.7798 52680.2844 100745.3011 95832.47591 77524.52942 72164.49282 67239.20896 66798.35686 89924.81374 0.728835917 0.944075125 0.585825894 1.12032816 1.065695573 0.862103864 0.802498107 0.747726975 0.742824523 1 16.45643165 -3.278432188 10.04853173 0.99752169 0.853969195 0 0.160976518 0 0 0 0.035721138 0.000526705 3.278432188 -0.143552495 EQELDTLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQELDTLKR 9 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 67.726 0.096343 380700000 422240 371480 297700 320840 336410 318180 372430 378950 402380 384370 FALSE TRUE 405738.394 360885.7541 351501.0123 337398.5908 347230.9332 324613.8176 376987.9097 371124.5501 356703.5093 358336.2775 1.132283889 1.00711476 0.980924998 0.941569727 0.969008596 0.905891583 1.052050639 1.035687909 0.995443475 1 18.45095458 -3.268448741 9.997110783 1.000033386 1.000835058 0 0.05926359 0 0 0 0.013459921 0.000538953 3.268448741 0.000801672 HLQIEIEGLIDQMIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLQIEIEGLIDQMIDK 16 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 171.56 4.88E-09 123940000 205600 227900 205080 248170 227110 225790 257230 167200 305000 282240 FALSE TRUE 197564.9247 221400.5151 242142.518 260978.0834 234415.1994 230355.6285 260378.0577 163747.2616 270377.6787 263123.6334 0.750844469 0.841431506 0.92026138 0.991845849 0.890893746 0.875465368 0.989565454 0.622320616 1.027568961 1 18.00538131 -3.247035341 1.008503047 3.368313923 0.869164856 0.084804117 0.115515854 95356.7975 1600.559647 513562.339 0.035157536 0.000566193 3.247035341 -2.499149068 RIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIR 35 3 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 113.37 6.12E-06 98523000 99078 98212 75706 72428 95748 87277 89716 83235 95973 64954 FALSE TRUE 95205.92222 95411.08992 89387.75827 76166.01776 98827.82138 89041.80074 90813.97125 81516.16816 85078.54739 60554.60772 1.572232499 1.575620642 1.476151223 1.257807137 1.632044614 1.470438074 1.499703733 1.346159627 1.404988829 1 15.88594912 -3.24700853 0.208050682 1.36E-11 1.553435011 0.697490327 0.097254529 35.52556119 0.680608838 15.51531047 0.22458322 0.000566228 3.24700853 1.553435011 RFSEGTSADR ddPTM_BT-474_Pertuzumab_2h_R1 2 RFSEGTSADR 10 1 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ; 109.39 0.0032472 188624000 653960 816330 717830 1021050 869560 875360 888410 782890 767570 944100 FALSE TRUE 628402.5202 793049.0677 847557.849 1073746.513 897530.1871 893060.379 899282.6273 766723.0479 680438.6715 880155.2661 0.713967801 0.901033145 0.962964015 1.219951245 1.019740745 1.014662314 1.021731803 0.871122491 0.77308936 1 19.74739852 -3.244353494 11.43549209 0.999761658 0.955882753 0 0.136281573 0 0 0 0.031423915 0.0005697 3.244353494 -0.043878906 LQHSSALTASVEEGGVPGEDPSSRPAT(ph)PELAEPESAPTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQHSSALTASVEEGGVPGEDPSSRPATPELAEPESAPTLR 40 1 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 LQHSSALTASVEEGGVPGEDPS(0.015)S(0.054)RPAT(0.93)PELAEPESAPTLR 113.36 7.99E-06 112320000 15641 33656 32316 57370 27586 42094 46086 27557 28992 41392 TRUE FALSE 15029.73243 32696.16383 38156.22007 60330.87258 28473.32874 42945.16952 46650.01425 26987.93832 25700.9497 38588.48297 0.389487517 0.847303685 0.988798137 1.563442456 0.737871161 1.112901213 1.208910293 0.699378059 0.666026434 1 15.23588271 -3.243210714 9.643581543 0.999693659 0.93301274 0 0.313086737 0 0 0 0.069355865 0.000571201 3.243210714 -0.066680919 SIHEIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIHEIPR 7 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5;O75376;O75376-2;A0A088AWL3 C9J0Q5;Q9Y618;O75376 NCOR2;NCOR1 Nuclear receptor corepressor 2;Nuclear receptor corepressor 1 0 ; 137.18 0.002908 275420000 285030 359600 310070 421960 367340 376250 375330 329030 345530 402400 FALSE TRUE 273890.7125 349344.5601 366106.5465 443737.4062 379155.8247 383858.0328 379923.4008 322235.4155 306306.883 375145.0896 0.730092756 0.931225197 0.97590654 1.182842102 1.010691157 1.023225529 1.012737235 0.858962104 0.816502445 1 18.51708915 -3.238204452 9.859054069 0.999757991 0.958340968 0 0.120491129 0 0 0 0.027851469 0.000577824 3.238204452 -0.041417024 RAS(ph)CTSSTSGSK ddPTM_BT-474_Pertuzumab_2h_R1 5 RASCTSSTSGSK 12 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 RAS(0.83)CT(0.073)S(0.073)S(0.02)T(0.004)SGSK;RAS(0.932)CT(0.028)S(0.008)S(0.028)T(0.004)SGSK;RAS(0.997)CT(0.003)SSTSGSK;RAS(0.859)CT(0.121)S(0.016)S(0.003)T(0.001)SGSK;RAS(0.932)CT(0.057)S(0.005)S(0.005)TSGSK 187.77 1.07E-05 826122000 1648369 1487237 1138523 1239063 1317867 1171629 1302658 1669812 1306374 1096587 TRUE FALSE 1583948.917 1444822.457 1344279.432 1303011.19 1360257.389 1195320.141 1318600.318 1635329.799 1158079.9 1022314.186 1.549375856 1.413286128 1.314937669 1.274570194 1.330566873 1.169229732 1.289819056 1.599635241 1.132802338 1 19.96340721 -3.23050513 0.358298584 1.20E-17 1.364848941 0.370254128 0.137727858 131.4861539 3.505987867 99.04409924 0.106701441 0.000588159 3.23050513 1.364848941 VERLS(ph)SGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_BT-474_Pertuzumab_2h_R1 4 VERLSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 38 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 VERLS(0.969)S(0.031)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.808)S(0.192)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.96)S(0.04)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.824)S(0.176)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 365.77 1.85E-161 4695610000 624468 708440 595710 742610 642570 723080 741480 569950 815420 803900 TRUE FALSE 600063.1002 688235.9848 703368.0485 780936.1911 663238.8476 737701.173 750554.454 558180.3333 722856.9401 749451.137 0.800670078 0.918320022 0.938510883 1.042010816 0.884966097 0.984321908 1.001472167 0.744785491 0.964515102 1 19.51547489 -3.209768098 9.70624853 0.999184689 0.920295345 0 0.089727214 0 0 0 0.020125936 0.000616924 3.209768098 -0.078889344 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTR ddPTM_BT-474_Pertuzumab_2h_R1 8 APPQTHLPSGASSGTGSASATHGGGSPPGTR 31 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 APPQTHLPSGAS(0.001)S(0.001)GT(0.001)GSAS(0.003)AT(0.003)HGGGS(0.844)PPGT(0.148)R;APPQTHLPSGASSGTGSASAT(0.001)HGGGS(0.998)PPGT(0.001)R;APPQTHLPSGASSGTGSASATHGGGS(0.987)PPGT(0.013)R;APPQTHLPSGASSGTGSASATHGGGS(0.993)PPGT(0.007)R;APPQTHLPSGAS(0.064)S(0.064)GT(0.064)GS(0.064)AS(0.199)AT(0.199)HGGGS(0.341)PPGT(0.007)R;APPQTHLPSGASSGTGSASAT(0.003)HGGGS(0.989)PPGT(0.008)R;APPQTHLPSGASSGTGSASAT(0.001)HGGGS(0.951)PPGT(0.048)R;APPQTHLPSGASSGTGSASAT(0.004)HGGGS(0.867)PPGT(0.129)R 198.29 2.04E-25 38900160000 1079207 1492529 1461665 2062885 1672260 1987214 1589360 1205069 1656064 1979516 TRUE FALSE 1037030.397 1449963.534 1725820.38 2169350.742 1726049.762 2027396.829 1608811.063 1180183.904 1468074.558 1845441.618 0.56194159 0.78570003 0.935180156 1.175518489 0.935304452 1.09859711 0.871775648 0.639512999 0.795513953 1 20.81553467 -3.209048682 8.18207118 0.99761609 0.874575766 0 0.181933045 0 0 0 0.043509463 0.000617947 3.209048682 -0.123040324 VSEHVGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSEHVGSR 8 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ;;; 164.71 0.0003285 2050870000 1149010 1498150 1248610 1724190 1372710 1601670 1431390 1389440 1376570 1620920 FALSE TRUE 1104105.419 1455424.229 1474261.602 1813175.653 1416864.464 1634056.865 1448907.779 1360747.578 1220307.545 1511133.645 0.730647102 0.963134025 0.975599748 1.19987776 0.937616914 1.081345036 0.958821732 0.900481293 0.807544421 1 20.52719983 -3.207519736 9.930375882 0.9997693 0.960847721 0 0.124134129 0 0 0 0.02748219 0.000620126 3.207519736 -0.038921579 SGS(ph)S(ph)PGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.062)GS(0.947)S(0.991)PGLR;S(0.057)GS(0.945)S(0.998)PGLR 90.906 0.018 368860000 830940 770760 651140 768150 789610 763080 762800 764050 892360 837420 TRUE FALSE 798465.9461 748778.6795 768815.4825 807794.3136 815008.5228 778510.0004 772135.3746 748272.1005 791063.0339 780700.7975 1.022755387 0.959110945 0.984776095 1.034704097 1.043944781 0.997193807 0.989028546 0.958462068 1.013272993 1 19.57441022 -3.199696359 9.50606185 0.999991156 0.997609839 0 0.027675777 0 0 0 0.006621995 0.000631399 3.199696359 -0.002381317 S(ph)SPINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK 46 0 Q9NZB2;Q9NZB2-4;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 S(0.493)S(0.493)PINPAQS(0.007)GS(0.007)PNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK 196.54 5.17E-38 216240000 11651 22286 19360 26739 18103 25092 22872 17313 19015 25390 TRUE FALSE 11195.66604 21650.4251 22858.78266 28119.00299 18685.29944 25599.37743 23151.91438 16955.4805 16856.49692 23670.31268 0.472983445 0.914665784 0.965715281 1.187943876 0.789398082 1.081497223 0.97809922 0.7163184 0.712136639 1 14.53079114 -3.196388795 9.873220998 0.998593299 0.885621501 0 0.19923577 0 0 0 0.043881816 0.000636226 3.196388795 -0.112971798 STEDGAELEEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 STEDGAELEEQK 12 0 Q8IVF2;Q8IVF2-3;Q8IVF2-2 Q8IVF2 AHNAK2 Protein AHNAK2 0 ; 84.658 0.012113 1145860000 962660 1213990 1046940 1453370 1154330 1363850 1210080 1121150 1181670 1389860 FALSE TRUE 925038.1829 1179368.194 1236145.347 1528378.6 1191460.073 1391427.981 1224889.321 1097997.861 1047531.776 1295723.544 0.713916319 0.910200481 0.95401936 1.179556092 0.919532626 1.073861772 0.945332302 0.847401335 0.808453146 1 20.30532651 -3.191282653 10.00218009 0.99950989 0.937644537 0 0.125403971 0 0 0 0.028345869 0.00064375 3.191282653 -0.061865353 S(ph)ESPEPGYVVTSSGLLLPVLLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SESPEPGYVVTSSGLLLPVLLPR 23 0 Q96Q42 Q96Q42 ALS2 Alsin 1 S(0.48)ES(0.48)PEPGY(0.039)VVT(0.001)S(0.001)S(0.001)GLLLPVLLPR;S(0.47)ES(0.47)PEPGY(0.057)VVT(0.003)SSGLLLPVLLPR 90.972 0.0034458 34924000 40201 37396 36013 37972 40544 40686 45180 47890 48658 57436 TRUE FALSE 38629.90048 36329.50269 42521.3502 39931.73947 41848.13458 41508.6988 45732.92635 46901.05476 43134.54783 53545.80856 0.721436495 0.678475191 0.794111647 0.745749117 0.781538942 0.775199776 0.854089752 0.875905249 0.805563479 1 15.70848603 -3.188756133 0.03622975 2.095864634 3.69E-09 0.84068114 0.034217365 244.410997 0.925585634 39.28012932 17.86777902 0.000647506 3.188756133 -2.095864631 QILGVIDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 QILGVIDKK 9 1 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 120.09 0.0028915 0 1346670 1284320 1106170 1069140 1132490 1285800 1184940 1236140 1484800 1349870 FALSE TRUE 1294040.648 1247692.451 1306079.526 1124318.444 1168917.569 1311799.757 1199441.65 1210613.277 1316251.729 1258442.103 1.028287789 0.991457969 1.037854283 0.893420874 0.928860825 1.042399769 0.953116276 0.961993623 1.045937454 1 20.26320741 -3.172398332 9.857652112 0.999973532 0.98364842 0 0.050134608 0 0 0 0.010959633 0.00067236 3.172398332 -0.016325112 VEDLAWHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VEDLAWHR 8 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ;;; 117.72 0.0020241 730860000 1114260 1183390 1081480 1175590 1200010 1313940 1202820 1154370 1418180 1571330 FALSE TRUE 1070713.487 1149640.876 1276927.493 1236262.341 1238609.411 1340508.767 1217540.471 1130531.856 1257194.152 1464902.42 0.730911133 0.784790072 0.871680923 0.843921291 0.845523494 0.915084001 0.831141006 0.771745504 0.858210168 1 20.48237314 -3.164765407 1.270390503 6.200947328 0.827666095 0.511118385 0.05043146 339323.1194 4460.741331 5100240.026 0.014779756 0.000684281 3.164765407 -5.373281233 LGFTQSQIDEIDHDYER ddPTM_BT-474_Pertuzumab_2h_R1 2 LGFTQSQIDEIDHDYER 17 0 Q13546-2;Q13546 Q13546-2 RIPK1 Receptor-interacting serine/threonine-protein kinase 1 0 ; 254.05 4.99E-27 573460000 301380 332390 303120 437900 382970 348520 389700 281830 373230 435430 FALSE TRUE 289601.7364 322910.5626 357900.5269 460500.0715 395288.5779 355567.3132 394469.2652 276010.112 330862.4951 405937.9383 0.713413823 0.79546781 0.881663164 1.134410037 0.973766038 0.875915453 0.971747718 0.679931797 0.815056845 1 18.63089965 -3.163300915 9.767106421 0.998278433 0.877441876 0 0.132579142 0 0 0 0.031351644 0.000686593 3.163300915 -0.120836557 GPGASVHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPGASVHDR 9 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 150.35 8.54E-05 84385000 120650 175930 151710 204010 165990 184090 178370 161170 156930 194580 FALSE TRUE 115934.8646 170912.6487 179127.3718 214538.9805 171329.2191 187812.4259 180552.9454 157841.7832 139115.9643 181400.9233 0.639108459 0.942181801 0.987466704 1.182678548 0.944478209 1.035344377 0.995325394 0.87012668 0.766897774 1 17.46882227 -3.141354278 10.11904954 0.999609977 0.943457068 0 0.142364231 0 0 0 0.031666311 0.00072218 3.141354278 -0.056152909 DAESFLWAEHAVVGEIADGLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DAESFLWAEHAVVGEIADGLAR 22 0 I3L428;Q8IYR2 I3L428 SMYD4 SET and MYND domain-containing protein 4 0 112.32 0.00029643 11978000 13928 13989 12672 16340 16076 15284 15058 13214 13782 18934 FALSE TRUE 13383.67836 13590.04742 14962.11229 17183.30936 16593.09914 15593.05295 15242.28431 12941.12628 12217.52514 17651.58332 0.758214044 0.769905293 0.847635706 0.973471277 0.940034604 0.883379846 0.863508051 0.73314252 0.692148966 1 14.10750998 -3.140766408 10.07383197 0.997077743 0.840180782 0 0.100385766 0 0 0 0.023386704 0.000723159 3.140766408 -0.156896961 GLESDVAELR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLESDVAELR 10 0 Q03252 Q03252 LMNB2 Lamin-B2 0 78.516 0.069253 48228000 102600 120840 104230 140190 113650 124690 110530 129760 120630 118340 FALSE TRUE 98590.27857 117393.7615 123066.6796 147425.2227 117305.6555 127211.3172 111882.6992 127080.4107 106936.5881 110324.7264 0.893637191 1.064074803 1.11549499 1.336284508 1.063276197 1.153062612 1.014121701 1.151876055 0.969289402 1 16.75139664 -3.132249636 9.862035694 1.006000447 1.08990681 0 0.117242906 0 0 0 0.025297791 0.00073748 3.132249636 0.083906363 HNTEDFTLFTLDDVDAAFDK ddPTM_BT-474_Pertuzumab_2h_R1 3 HNTEDFTLFTLDDVDAAFDK 20 0 Q9P2I0 Q9P2I0 CPSF2 Cleavage and polyadenylation specificity factor subunit 2 0 ;; 160.77 2.36E-11 133309000 169609 164857 140091 178332 178114 177324 182152 115534 230801 207828 FALSE TRUE 162980.4928 160155.4398 165408.56 187535.7359 183843.1986 180909.6128 184381.2307 113148.1825 204601.4381 193751.6244 0.841182587 0.826601791 0.853714442 0.967918264 0.948860166 0.933719205 0.951637083 0.583985723 1.055998569 1 17.56384888 -3.123663634 9.929323258 0.998152155 0.87655303 0 0.12640601 0 0 0 0.028693781 0.000752205 3.123663634 -0.121599124 DMFCAGR ddPTM_BT-474_Pertuzumab_2h_R1 7 DMFCAGR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;;;; 175.93 0.0017928 2593350000 2284210 2530900 2243820 2550180 2425990 2272710 2609430 2548420 2716580 2943690 FALSE TRUE 2194940.548 2458721.21 2649328.188 2681795.095 2504024.172 2318665.753 2641364.985 2495794.236 2408205.227 2744311.254 0.799814724 0.8959338 0.965389106 0.977219727 0.912441753 0.84489897 0.962487393 0.909442846 0.877526273 1 21.38801269 -3.121301035 0.010010415 1.959035374 1.63E-06 0.20162555 0.053517993 19068.3323 20.29107529 2209.630261 1781.210507 0.000756308 3.121301035 -1.959033743 (ac)SCINLPTVLPGS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 6 SCINLPTVLPGSPSK 15 0 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 SCINLPT(0.001)VLPGS(0.873)PS(0.127)K;SCINLPT(0.001)VLPGS(0.834)PS(0.165)K;SCINLPTVLPGS(0.804)PS(0.196)K;SCINLPTVLPGS(0.879)PS(0.121)K;SCINLPT(0.004)VLPGS(0.877)PS(0.119)K;SCINLPTVLPGS(0.877)PS(0.123)K 77.562 5.22E-09 2098696000 6396230 5983960 4412850 5229660 5088560 4902950 5710410 6510320 5450100 5920860 TRUE FALSE 6146258.26 5813303.32 5210350.158 5499563.379 5252238.154 5002091.008 5780295.706 6375879.617 4831427.497 5519834.878 1.113485891 1.053166163 0.94393225 0.996327517 0.951520882 0.906203015 1.047186344 1.155085208 0.875284787 1 22.39619368 -3.110505782 10.32246786 1.000369394 1.011479435 0 0.084965768 0 0 0 0.019675574 0.000775344 3.110505782 0.011110042 HVAEDLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVAEDLGK 8 0 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 133.58 0.00091325 795970000 1039800 1537700 992160 2267600 1014900 1197500 2025900 1401400 1454200 1161800 FALSE TRUE 999163.4664 1493846.302 1171465.382 2384631.108 1047545.18 1221714.27 2050693.57 1372460.6 1289125.313 1083110.251 0.9224947 1.379219059 1.081575381 2.201651314 0.967163942 1.127968523 1.893337791 1.267147642 1.190206917 1 20.04674867 -3.110433095 9.128392822 1.071860728 1.338361403 0 0.402167141 0 0 0 0.083954125 0.000775473 3.110433095 0.266500675 AVEVAWETLQEEFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEVAWETLQEEFSR 15 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ; 142.91 1.05E-05 36897000 14051.5 17994 16004.9 21931 14833.9 17840.1 19942.4 18645.4 14914.8 18511.5 FALSE TRUE 13502.35185 17480.82874 18897.34146 23062.86154 15311.04587 18200.83905 20186.46106 18260.36597 13221.73443 17257.69962 0.782395809 1.01292925 1.095009293 1.336380981 0.887200856 1.054650356 1.169707522 1.058099653 0.76613539 1 14.07495255 -3.109789352 10.2361777 1.00076279 1.033513381 0 0.165110831 0 0 0 0.035780392 0.000776624 3.109789352 0.032750591 TLGDFAAEYAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLGDFAAEYAK 11 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 123.79 0.0021849 0 162920 154280 116960 141610 132370 122620 162690 163270 139580 154250 FALSE TRUE 156552.9063 149880.0855 138097.2738 148918.5091 136627.8013 125099.4604 164681.0489 159898.4174 123735.4636 143802.5101 1.08866602 1.042263347 0.960325892 1.035576562 0.950107207 0.869939338 1.145188973 1.111930642 0.860454129 1 17.13372933 -3.108077489 10.10543666 1.000426927 1.014452072 0 0.092303681 0 0 0 0.020915752 0.000779691 3.108077489 0.014025145 HPSKPDPSGECNPDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 HPSKPDPSGECNPDLR 16 1 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;;;;; 200.69 2.10E-11 6437451000 1871896 2362518 1932535 2827476 2192921 2312731 2427907 2033140 2344360 2746536 FALSE TRUE 1798740.235 2295141.3 2281787.064 2973402.375 2263458.296 2359496.005 2457620.452 1991154.949 2078238.081 2560510.67 0.702492771 0.896360764 0.891145305 1.161253655 0.883987058 0.921494307 0.959816524 0.777639778 0.811649842 1 21.28800014 -3.108040504 9.62908988 0.998737181 0.898831193 0 0.120189746 0 0 0 0.026830021 0.000779757 3.108040504 -0.099905988 KDEPDAFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEPDAFK 8 1 P13674;P13674-2 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 111.06 0.0053021 2270040000 2834100 2959700 2270420 2640130 2499020 2306880 2558020 2927700 2834500 2008900 FALSE TRUE 2723340.239 2875292.254 2680735.399 2776387.426 2579403.248 2353526.694 2589325.814 2867241.972 2512739.443 1872835.414 1.454126838 1.535261579 1.431377995 1.48245137 1.377271718 1.256664989 1.38256987 1.530963133 1.341676596 1 20.83679269 -3.105848117 0.319097229 1.55E-16 1.450935104 0.726424399 0.07873779 47.06070065 1.276623437 31.66688148 0.078741697 0.000783704 3.105848117 1.450935104 DSKPSS(ph)TPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.005)KPS(0.122)S(0.646)T(0.227)PR;DS(0.005)KPS(0.04)S(0.551)T(0.404)PR 69.721 0.032969 9683200000 22898000 17181800 17449000 16357500 15219900 17148200 17988000 22511200 18390700 20421400 TRUE FALSE 22003120.84 16691791.89 20602422.45 17201712.54 15709461.91 17494948.35 18208142.52 22046335.85 16303064.84 19038240.39 1.155732904 0.876750768 1.082160012 0.90353479 0.825153039 0.918937255 0.956398394 1.158002809 0.856332545 1 24.18239681 -3.090578171 10.98006309 0.999993824 0.977240737 0 0.115401203 0 0 0 0.025450671 0.000811749 3.090578171 -0.022753087 LGTAEIEDAIADHPAVPESAVIGYPHDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGTAEIEDAIADHPAVPESAVIGYPHDIK 29 0 Q9NUB1-2;Q9NUB1;Q9NUB1-3 Q9NUB1-2 ACSS1 "Acetyl-coenzyme A synthetase 2-like, mitochondrial" 0 ; 217.93 1.39E-34 235660000 117969 155353 127138 187363 125060 161853 192077 83502 209470 173504 FALSE TRUE 113358.6411 150922.4845 150114.6648 197032.8269 129082.6685 165125.7786 194427.6958 81777.65452 185691.8438 161752.4195 0.700815737 0.933046226 0.928052051 1.21811363 0.798026199 1.020855076 1.20200796 0.505572991 1.148000409 1 17.30342777 -3.063621964 10.2800188 0.999376772 0.929697697 0 0.216301828 0 0 0 0.046625852 0.00086373 3.063621964 -0.069679076 NDIDFFR ddPTM_BT-474_Pertuzumab_2h_R1 1 NDIDFFR 7 0 A0A0A0MTH9;O14981;O14981-2 A0A0A0MTH9 BTAF1 TATA-binding protein-associated factor 172 0 77.072 0.090824 57728000 138930 153800 128070 156550 154180 136910 148710 162310 174060 182610 FALSE TRUE 133500.462 149413.7746 151215.0979 164629.5643 159139.3397 139678.414 150529.9575 158958.2418 154301.4385 170241.662 0.784182088 0.877656931 0.888237909 0.967034522 0.934784928 0.820471395 0.884213392 0.933721158 0.906367082 1 17.37722462 -3.053419285 0.015764059 2.003395547 5.58E-07 0.398573831 0.047494007 4291.648711 7.293845588 546.7209572 391.3462608 0.000884261 3.053419285 -2.003394989 S(ph)PQREPQR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPQREPQR 8 1 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR 111.52 0.0019481 1136090000 237528 249399 197033 198898 215770 169887.2 283284 229618 243160 223030 TRUE FALSE 228245.1432 242286.3847 232641.2461 209163.1496 222710.438 173322.4356 286750.9143 224876.3081 215557.4962 207923.9794 1.097733622 1.165264273 1.11887646 1.005959727 1.071114734 0.833585602 1.379114208 1.081531378 1.036713018 1 17.66569663 -3.02970363 0.893941105 0.227482906 1.09272938 0.038857466 0.128990438 31069.71674 929.3082611 47705.37686 0.039973941 0.000933891 3.02970363 0.865246474 EHYLDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHYLDSK 7 0 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 ; 135.84 0.0030379 532590000 1231440 1254920 1119390 1152470 1326850 1328810 1335990 1042020 1599010 1562430 FALSE TRUE 1183313.963 1219130.91 1321688.674 1211949.115 1369529.335 1355679.449 1352340.245 1020501.923 1417497.088 1456605.224 0.812377948 0.836967278 0.907376035 0.832036776 0.94021998 0.930711648 0.928419192 0.700602954 0.973151177 1 20.47417849 -3.024418597 0.987776125 2.377354078 0.86600484 0.190701795 0.076807285 31438.90856 867.7515348 95675.34565 0.024063844 0.000945326 3.024418597 -1.511349238 SETAPAETATPAPVEKS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETAT(0.001)PAPVEKS(0.999)PAK 104.38 0.00067631 0 109510 88114 63058 82594 91239 66068 83622 81710 88857 58833 TRUE FALSE 105230.2281 85601.07499 74453.98332 86856.68624 94173.7853 67403.94023 84645.39105 80022.65995 78770.32588 54848.18851 1.918572536 1.560691015 1.357455649 1.583583498 1.716989893 1.228918257 1.543266849 1.458984556 1.436151822 1 15.74315635 -2.997336678 0.116938232 3.66E-15 1.841428958 0.561838964 0.15949458 69.82474815 0.873059253 20.03036667 1.900891234 0.001006151 2.997336678 1.841428958 GLS(ph)TSLPDLDSEPWIEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLSTSLPDLDSEPWIEVK 18 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;Q659C4-4 A0A3B3ISF0 LARP1B La-related protein 1B 1 GLS(0.333)T(0.333)S(0.333)LPDLDSEPWIEVK 128.9 2.34E-05 98021000 64642 52285 37274 47047 51395 41715 46992 58291 50543 37461 TRUE FALSE 62115.71917 50793.88299 44010.24096 49475.10131 53048.16685 42558.50588 47567.10215 57087.27048 44805.57053 34923.7331 1.778610522 1.454423066 1.26018146 1.416661305 1.518971832 1.218612734 1.362027994 1.634626811 1.282954786 1 15.09192016 -2.974495539 0.355399785 1.34E-16 1.456154897 0.406832603 0.162075271 95.81989198 2.977384969 72.29815382 0.123744795 0.001060485 2.974495539 1.456154897 YENGAFQER ddPTM_BT-474_Pertuzumab_2h_R1 2 YENGAFQER 9 0 P23919-2;P23919;H7C312;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 ; 91.085 0.020036 0 456900 461170 436360 455260 457030 484560 486430 480560 542360 571440 FALSE TRUE 439043.8429 448017.8831 515219.9588 478756.0232 471730.785 494358.1352 492383.0758 470636.2681 480793.5666 532735.8598 0.824130448 0.840975645 0.967120852 0.898674295 0.8854872 0.927961064 0.924253674 0.883432679 0.902498973 1 19.02306087 -2.965213654 0.013612183 1.977758113 2.16E-06 0.4563115 0.037096247 5137.386118 7.686262589 642.3814361 483.9299536 0.001083394 2.965213654 -1.977755957 VDHVQMIVLDEADK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDHVQMIVLDEADK 14 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 159.22 4.95E-06 365500000 699280 611300 745060 752820 717930 703670 883620 831830 1115690 1161340 FALSE TRUE 671951.3645 593866.3225 879708.9158 791673.1304 741022.8705 717898.6895 894434.0059 814652.4198 989041.5486 1082681.407 0.620636283 0.548514381 0.81252796 0.731215226 0.684432988 0.663074737 0.826128536 0.752439651 0.91351116 1 20.04617734 -2.964569714 0.048254259 2.122622199 1.50E-16 0.691066396 0.07208748 220.8763139 1.16866514 41.50915506 15.33374838 0.001085001 2.964569714 -2.122622199 IFDEVMGCFSDS(ph)PPQS(ph)PTFPEAGHTSLYDEDKVPR ddPTM_BT-474_Pertuzumab_2h_R1 4 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 2 IFDEVMGCFSDS(1)PPQS(0.85)PT(0.15)FPEAGHTSLYDEDKVPR;IFDEVMGCFS(0.007)DS(0.972)PPQS(0.532)PT(0.479)FPEAGHT(0.003)S(0.003)LY(0.004)DEDKVPR;IFDEVMGCFS(0.001)DS(0.999)PPQS(0.708)PT(0.291)FPEAGHTSLYDEDKVPR;IFDEVMGCFS(0.001)DS(0.999)PPQS(0.98)PT(0.02)FPEAGHTSLYDEDKVPR 193.15 2.96E-21 2877080000 249115 367102 284373 401775 406254 450252 389429 289839 330842 388794 TRUE FALSE 239379.3104 356632.6104 335765.5269 422510.6559 419321.5289 459356.4039 394194.9486 283853.7234 293286.2032 362460.6361 0.660428434 0.983920942 0.926350322 1.165673218 1.15687467 1.267327699 1.087552438 0.783129794 0.809153254 1 18.4674648 -2.944394045 2.102082852 2.046168719 0.989181484 0 0.182546969 12837768.94 5732969.298 70680214.34 0.04868183 0.001136596 2.944394045 -1.056987235 S(ph)EETQER ddPTM_BT-474_Pertuzumab_2h_R1 5 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(1)EETQER;S(1)EETQER;S(1)EETQER;S(1)EETQER;S(1)EETQER 123.75 0.0044197 154767000 77434.7 79068.1 74901.2 90103.4 79746.2 86452.2 83293.2 90093.7 82071.2 105211 TRUE FALSE 74408.46632 76813.1552 88437.51301 94753.64727 82311.30895 88200.32272 84312.5671 88233.23361 72754.82145 98084.96526 0.758612353 0.783128739 0.901641885 0.966036406 0.83918375 0.899223673 0.859587062 0.899559207 0.741753043 1 16.58174439 -2.918157824 0.015615349 1.921928196 4.64E-06 0.217966772 0.071869272 6468.347822 11.21683125 809.0682097 586.6420135 0.001207375 2.918157824 -1.921923551 LTHTGERPYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTHTGERPYR 10 1 A0A0C4DFM2;Q6ZN55;Q6ZN55-2 A0A0C4DFM2 ZNF574 Zinc finger protein 574 0 85.533 0.0085168 92779000 29164 32057 23940 32998 35364 38722 31943 29656 28305 34815 FALSE TRUE 28024.23864 31142.76575 28266.49054 34701.03073 36501.51518 39504.98537 32333.92799 29043.59324 25091.93506 32456.94904 0.863428001 0.959509956 0.870891793 1.069140254 1.124613257 1.217150303 0.996209716 0.89483436 0.773083602 1 14.98623977 -2.872209079 2.055013435 2.242249174 0.979980313 0.001887095 0.127020098 8438161.884 1523928.54 47900725.84 0.033435968 0.001342119 2.872209079 -1.262268861 AHVLAASVEQATENFLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHVLAASVEQATENFLEK 18 0 P35221-2;P35221;G3XAM7;E5RIB1;E5RJL0;E5RHV7;E5RG03;E5RIE0;E5RGY6;E5RFM3 P35221-2 CTNNA1 Catenin alpha-1 0 ; 214.28 1.01E-18 457520000 397060 471050 391780 519370 413960 526400 455940 353400 579390 574340 FALSE TRUE 381542.4562 457616.1152 462583.3611 546174.7479 427275.3993 537044.1687 461519.9301 346102.1665 513620.0762 535439.4402 0.71257817 0.854655225 0.863932177 1.020049527 0.79799015 1.002997031 0.861946087 0.646389004 0.959249614 1 19.03036389 -2.852075198 1.371172903 3.207056857 0.850217355 0.121793376 0.112975478 829244.6699 23368.20003 5677297.886 0.033246072 0.001405804 2.852075198 -2.356839503 RFS(ph)FSQR ddPTM_BT-474_Pertuzumab_2h_R1 7 RFSFSQR 7 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RFS(0.972)FS(0.028)QR;RFS(1)FSQR;RFS(0.999)FS(0.001)QR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(0.998)FS(0.002)QR 150.81 0.0011783 6380680000 1901445 1525953 1092262 1493353 1379514 1199561 1239165 2016839 1078934 1020854 TRUE FALSE 1827134.427 1482434.315 1289658.041 1570425.127 1423887.321 1223816.945 1254330.272 1975190.57 956457.9356 951710.6493 1.919842369 1.557652334 1.355094683 1.65010776 1.496134694 1.285912841 1.3179744 2.07541081 1.004988161 1 19.86016349 -2.851003627 0.272624766 6.15E-11 1.59494863 0.260964314 0.287301283 84.30329727 2.337391798 49.24171773 0.363359938 0.001409277 2.851003627 1.59494863 VLMAT(ph)HGFSGTSPFMNGGLGATSPLGVHPSAQSPMQHL ddPTM_BT-474_Pertuzumab_2h_R1 1 VLMATHGFSGTSPFMNGGLGATSPLGVHPSAQSPMQHL 38 0 E7ESP8 E7ESP8 ZEB2 1 VLMAT(0.249)HGFS(0.249)GT(0.249)S(0.249)PFMNGGLGAT(0.001)S(0.001)PLGVHPSAQSPMQHL 43.9 0.031356 213180000 74658 110990 80469 103420 124130 130180 132650 40063 122740 112100 TRUE FALSE 71740.28282 107824.6739 95011.53832 108757.5186 128122.7542 132812.3288 134273.4104 39235.68505 108807.0698 104507.3672 0.686461489 1.031742324 0.90913723 1.040668439 1.225968634 1.270841783 1.284822439 0.375434633 1.041142579 1 16.67324512 -2.847842531 1.917767622 2.243506651 0.970634435 0 0.265790033 7453939.364 751661.2456 40663392.64 0.06977106 0.001419572 2.847842531 -1.272872216 LGYEEHIPGQTR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGYEEHIPGQTR 12 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 69.864 0.04831 0 246660 271970 247210 281400 260250 274800 302470 246480 320530 346870 FALSE TRUE 237020.2545 264213.6819 291886.3462 295923.0877 268621.1776 280356.6443 306171.7183 241390.1019 284144.7782 323376.1859 0.732955192 0.817047431 0.902621649 0.915104762 0.830677054 0.866967502 0.946797358 0.746468393 0.878681828 1 18.30285391 -2.822570919 1.700665361 4.806736875 0.848076246 0.322442706 0.06584068 2104720.014 43437.61617 31065932.53 0.016589085 0.001504628 2.822570919 -3.958660629 LEEALR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEALR 6 0 A0A1B0GUG6;A0A1B0GTG4;Q86WH2;Q8WWW0-2;Q8WWW0;Q155Q3-2;Q155Q3 A0A1B0GUG6 RASSF3;RASSF5;DIXDC1 Ras association domain-containing protein 3;Ras association domain-containing protein 5;Dixin 0 134.12 0.032967 299600000 442770 445120 377160 597420 455710 373230 446720 469260 537230 572640 FALSE TRUE 425466.0589 432425.6134 445321.2019 628252.9178 470368.326 380776.9663 452187.093 459569.617 476245.9027 533854.5827 0.796969948 0.810006371 0.834161991 1.176824061 0.881079495 0.713259713 0.847022968 0.860851685 0.892089191 1 19.02608729 -2.774933805 0.959006696 1.726834972 0.868713173 0.107526084 0.114066438 21568.81677 987.6091276 33339.68088 0.036678061 0.00167906 2.774933805 -0.858121799 DDPYWSENKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDPYWSENKK 10 1 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 72.34 0.068565 0 575490 514200 503720 450800 541950 494130 573910 568800 586190 509350 FALSE TRUE 552999.2146 499535.5195 594753.4092 474065.842 559382.3139 504121.6472 580933.6823 557054.0812 519648.1687 474851.2708 1.164573517 1.051983116 1.252504617 0.998345948 1.17801583 1.061641146 1.223401343 1.173112752 1.094338798 1 18.85711619 -2.771570582 1.109495062 0.021941263 1.136235551 0.213420902 0.07645446 45177.23658 1938.249943 109520.272 0.020854359 0.001692113 2.771570582 1.114294287 HQTLEVSLS(ph)RDSPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HQTLEVSLSRDSPLK 15 1 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 HQTLEVSLS(0.648)RDS(0.352)PLK 184.8 2.71E-07 432850000 1541700 1485800 1439300 1359400 1504800 1533200 1656100 1283500 1873800 1863300 TRUE FALSE 1481448.66 1443426.439 1699413.527 1429558.797 1553203.259 1564202.354 1676367.847 1256995.276 1661094.08 1737097.031 0.852830114 0.830941745 0.978306621 0.822958517 0.894137305 0.900469189 0.965039843 0.723618344 0.956247147 1 20.72824691 -2.765688735 1.149253249 1.957299654 0.873800613 0.185753491 0.073878154 70429.49738 2988.260381 173380.5924 0.021049158 0.001715186 2.765688735 -1.08349904 AYGDFAWSNPLHPDIFPGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYGDFAWSNPLHPDIFPGLR 20 0 O95470;H0Y3V8;H7BXL7 O95470 SGPL1 Sphingosine-1-phosphate lyase 1 0 114.9 0.00011735 105610000 79197 125210 81780 124720 79847 75651 113450 115910 104920 95820 FALSE TRUE 76101.89368 121639.1334 96559.46519 131156.8141 82415.35127 77180.71505 114838.435 113516.418 93009.92146 89330.02605 0.851918409 1.361682502 1.080929554 1.468227649 0.922594058 0.863995215 1.285552463 1.270753217 1.041194384 1 16.44685756 -2.765102245 1.085985328 0.013100456 1.145656879 0.027181778 0.204059276 96861.68302 4268.80654 231626.0521 0.059047993 0.001717504 2.765102245 1.132556424 FSIDVFEETR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSIDVFEETR 10 0 Q93099;H7C4R8 Q93099 HGD "Homogentisate 1,2-dioxygenase" 0 ; 109.42 0.0047021 103965000 81022 88020 87266 90497 86454 90530 86629 84053 105893 112370 FALSE TRUE 77855.57067 85509.75578 103036.9074 95167.56102 89234.87143 92360.57863 87689.19162 82317.27618 93872.47058 104759.0798 0.743186851 0.816251498 0.983560638 0.908442124 0.851810379 0.881647479 0.837055764 0.785777007 0.896079564 1 16.67671577 -2.757018814 1.350667119 2.529063994 0.854808709 0.313190112 0.063962589 308794.4195 11620.80674 1437519.962 0.018789735 0.001749771 2.757018814 -1.674255285 MIASDSHRPEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 MIASDSHRPEVK 12 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;; 184.44 8.60E-06 1841640000 2016030 2141030 1829970 2105180 2091950 2195820 2056720 2126500 2409630 2656250 FALSE TRUE 1937241.319 2079969.921 2160686.286 2213828.592 2159239.472 2240220.985 2081890.755 2082587.032 2136098.904 2476339.822 0.782300273 0.839937194 0.872532222 0.893992243 0.871947966 0.904650067 0.840712868 0.84099404 0.862603301 1 21.23977787 -2.75059656 1.796905757 4.177800016 0.857656186 0.63701627 0.032459106 1274795.026 34562.39069 16576067.37 0.008590033 0.001775838 2.75059656 -3.32014383 HYLDQLNHILGILGSPSQEDLNCIINLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HYLDQLNHILGILGSPSQEDLNCIINLK 28 0 P28482 P28482 MAPK1 Mitogen-activated protein kinase 1 0 182.53 7.41E-18 138690000 64278 66319 55830 73116 71774 71223 79633 45147 91786 91145 FALSE TRUE 61765.9447 64427.64705 65919.72293 76889.52552 74082.67589 72663.17786 80607.57247 44214.69867 81366.83808 84971.66797 0.726900462 0.758225048 0.775784735 0.904884267 0.871851497 0.855145952 0.948640581 0.520346366 0.957576096 1 16.37469426 -2.733589387 1.166006301 2.424112183 0.8013178 0.165628377 0.123165762 82199.98334 3721.249073 305354.3117 0.03662069 0.001846761 2.733589387 -1.622794383 TDICQGALGDCWLLAAIASLTLNDTLLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDICQGALGDCWLLAAIASLTLNDTLLHR 29 0 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 190.48 3.68E-18 861764200 439508.9 475823 380616.3 474733.6 513575.5 507725.6 457658.9 431259.1 550738.3 599697.8 FALSE TRUE 422332.4063 462252.9939 449402.1322 499234.658 530095.1224 517992.1595 463259.8665 422353.4489 488220.7971 559079.7339 0.755406395 0.826810499 0.803824759 0.892957887 0.948156569 0.926508561 0.828611446 0.755444033 0.873257905 1 19.09269452 -2.733204592 1.748153549 3.995915662 0.843408799 0.355587387 0.062263392 2039653.887 56803.83344 24314139.09 0.017461503 0.001848398 2.733204592 -3.152506863 IHVWNGESGIK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHVWNGESGIK 11 0 Q6UXN9 Q6UXN9 WDR82 WD repeat-containing protein 82 0 ; 164.9 2.22E-05 942420000 944910 936120 829390 933910 985970 963840 1063870 773670 1156000 1171970 FALSE TRUE 907981.8725 909422.7742 979279.2227 982109.207 1017684.62 983329.5052 1076889.959 757693.4441 1024775.726 1092591.428 0.831035142 0.832353935 0.896290413 0.898880571 0.931441154 0.899997456 0.985629149 0.693482874 0.937931326 1 20.05932258 -2.720958852 1.683303551 3.093353828 0.872006563 0.181774986 0.076161436 3042651.111 97715.3312 24348837.87 0.019927695 0.001901258 2.720958852 -2.221347265 GFVEFAAKPPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFVEFAAKPPAR 12 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 158.42 6.70E-05 2549900000 2611900 2604600 2042790 2438100 2437100 2389300 2471800 2625200 2690900 2731100 FALSE TRUE 2509824.06 2530319.358 2411967.595 2563930.633 2515491.535 2437613.283 2502050.628 2570988.703 2385440.313 2546120.164 0.985744544 0.993794163 0.947310983 1.006995141 0.98797047 0.957383441 0.982691494 1.009767229 0.936892275 1 21.27986908 -2.704312226 2.236191399 1.712697743 0.9810433 0.062544638 0.023196815 5936861.828 1656418.806 20095820.33 0.005472124 0.001975549 2.704312226 -0.731654444 NEEPVRS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 NEEPVRSPER 10 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 NEEPVRS(1)PER;NEEPVRS(1)PER 137.4 5.58E-05 1377280000 756900 769630 723660 871250 761720 691900 887140 823630 858640 985980 TRUE FALSE 727319.5112 747680.9059 854441.4597 916215.3169 786221.4156 705890.6921 897997.0847 806621.7527 761170.7869 919198.6964 0.791253854 0.813405098 0.929550339 0.996754369 0.855333475 0.767941355 0.97693468 0.877527085 0.828080795 1 19.81001723 -2.701187801 2.085990943 4.601623082 0.875904099 0.217817195 0.072890664 4011424.538 146429.7463 69333260.38 0.018035748 0.001989813 2.701187801 -3.725718984 LCDLFITGEDFDDDV ddPTM_BT-474_Pertuzumab_2h_R1 2 LCDLFITGEDFDDDV 15 0 A0A087WZ47;E5RJC6;Q6NTE8-3;Q6NTE8 A0A087WZ47 C5orf45 UPF0544 protein C5orf45 0 ; 120.68 0.00027842 12572900 35921.7 48704 29862.3 32723.6 37885.2 36978.7 32357.8 35809.6 37844.4 28305.1 FALSE TRUE 34517.84025 47315.00961 35259.08189 34412.46892 39103.81186 37726.43465 32753.80444 35070.11925 33548.46237 26387.97037 1.308090004 1.793052249 1.336180138 1.304096846 1.48188024 1.429683076 1.241240004 1.329019199 1.271354405 1 14.68759277 -2.688799573 0.10248029 0.146684347 1.728525532 0.488009967 0.136710737 75.29631493 0.899963243 16.82747452 2.426217439 0.002047389 2.688799573 1.581841184 AHSEPLALCGETAPRDS(ph)PPASEAPASEPGYVNYTK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHSEPLALCGETAPRDSPPASEAPASEPGYVNYTK 35 1 K7ELE9;Q66K64 K7ELE9 DCAF15 DDB1- and CUL4-associated factor 15 1 AHSEPLALCGET(0.001)APRDS(0.84)PPAS(0.16)EAPASEPGYVNYTK;AHSEPLALCGETAPRDS(1)PPASEAPASEPGYVNYTK 306.79 1.77E-91 777390000 228193 219079 179559 222265 237207 245750 227199 170718 283850 296770 TRUE FALSE 219274.9653 212831.0814 212009.3056 233736.1233 244836.9786 250719.2334 229979.5293 167192.6136 251628.538 276669.5036 0.792551989 0.769261081 0.766290837 0.844820699 0.884943861 0.906204804 0.831242787 0.604304455 0.909491414 1 18.0778041 -2.67963626 1.313955143 2.551094769 0.801565909 0.294862426 0.085778068 192175.8989 9160.934694 879638.8892 0.026848777 0.002091047 2.67963626 -1.74952886 HAVSDPSILDSLDLNEDER ddPTM_BT-474_Pertuzumab_2h_R1 4 HAVSDPSILDSLDLNEDER 19 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;; 365.29 7.94E-108 2303620000 1315600 1206960 1347790 1918220 1426140 1365840 1598490 1003280 1872550 2003510 FALSE TRUE 1264184.898 1172538.683 1591365.634 2017219.564 1472013.088 1393458.221 1618052.799 982561.9174 1659985.974 1867810.483 0.676827178 0.627761057 0.851995237 1.079991564 0.788095528 0.746038334 0.866283177 0.526050114 0.888733621 1 20.83291665 -2.677487426 1.490411947 3.311441582 0.773992405 0.161520895 0.146520406 1328760.462 56715.33979 10335901.24 0.043044187 0.002101419 2.677487426 -2.537449177 EKEITNLEEQLEQFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEITNLEEQLEQFR 15 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A6I8PUA5;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 145.1 3.76E-06 21428000 46343 55254 51553 60600 46965 50798 65772 70466 70907 85535 FALSE TRUE 44531.86433 53678.21002 60869.77389 63727.57326 48475.67188 51825.17036 66576.93741 69010.85248 62857.93463 79741.63826 0.558451836 0.673151583 0.763337388 0.799175621 0.607909154 0.649913539 0.834908071 0.865430583 0.788269918 1 16.28304562 -2.644633778 0.046813672 2.074858909 9.76E-15 0.649984625 0.074772416 255.588826 1.414590821 48.26422424 19.6596039 0.002266555 2.644633778 -2.074858909 RLDSDAVNTIESQSVS(ph)PDHNKEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLDSDAVNTIESQSVSPDHNKEPK 24 2 Q3T7B4;Q9H3H1-6;Q9H3H1-3;Q9H3H1-2;Q9H3H1-5;Q9H3H1-4;Q9H3H1 Q3T7B4 TRIT1 "tRNA dimethylallyltransferase, mitochondrial" 1 RLDSDAVNTIESQSVS(1)PDHNKEPK 144.4 1.19E-07 136280000 29778 26308 29826 24398 32087 22404 23544 26324 45677 29035 TRUE FALSE 28614.24284 25557.7216 35216.22168 25657.1837 33119.1075 22857.02423 23832.13851 25780.4002 40491.93845 27068.43359 1.057107451 0.944189161 1.301007004 0.947863629 1.223532473 0.844416215 0.880440253 0.952415666 1.495909925 1 14.72432378 -2.620181709 2.05778688 0.001272688 1.052870907 0.003545697 0.198270936 6319110.786 974611.3753 28930421.08 0.046263454 0.002397829 2.620181709 1.051598219 NSLSSLPTYSTGGAEPT(ph)TSSPGGHLPSHGSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLSSLPTYSTGGAEPTTSSPGGHLPSHGSGR 32 0 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 1 NSLSSLPTYSTGGAEPT(0.255)T(0.187)S(0.187)S(0.187)PGGHLPS(0.052)HGS(0.133)GR 133.25 1.11E-07 538950000 17194 8063.5 17090 29968 20559 31658 15414 13149 17926 24334 TRUE FALSE 16522.03947 7833.536875 20178.54316 31514.65207 21220.29891 32298.14645 15602.64114 12877.46856 15891.11563 22685.83651 0.728297564 0.345305181 0.889477589 1.389177431 0.935398565 1.423714151 0.687770149 0.567643541 0.70048621 1 14.46950424 -2.603781003 2.029323479 3.597235323 0.845434711 0.01849948 0.320465809 10500333.27 428156.9234 126592330.9 0.085800652 0.002490113 2.603781003 -2.751800612 LPS(ph)SPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPS(0.5)S(0.5)PVYEDAASFK 85.42 0.0081226 5742500 10235 10600 11907 12968 11199 11033 14069 9472 13141 15160 TRUE FALSE 9835.004885 10297.69838 14058.85977 13637.28003 11559.22601 11256.09482 14241.18063 9276.39989 11649.28877 14133.1997 0.695879567 0.728617624 0.99474005 0.964911013 0.817877498 0.796429334 1.007640233 0.656355255 0.824249924 1 13.7868005 -2.592567078 2.112990915 4.020829428 0.83097293 0.156990675 0.116875373 2898868.255 288653.7672 41755464.61 0.029527066 0.002555247 2.592567078 -3.189856498 GFQFVSS(ph)SLPDICYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFQFVSSSLPDICYR 15 0 P62633-2;P62633;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 1 GFQFVS(0.063)S(0.537)S(0.4)LPDICYR 172.32 1.08E-06 24634000 73974 67925 54599 61012 60867 55495 50973 76280 46838 46815 TRUE FALSE 71083.0143 65987.84551 64466.25385 64160.83663 62824.84233 56617.14692 51596.82282 74704.79134 41521.1466 43644.17835 1.628694066 1.511950688 1.477087123 1.470089232 1.439478178 1.297243964 1.18221547 1.711678262 0.951355901 1 15.41350161 -2.584536763 0.085671843 1.72E-10 1.911464265 0.468996068 0.175910919 121.1904957 1.246243134 29.07600431 5.912411344 0.002602934 2.584536763 1.911464265 GKLPIVNEDDELVAIIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKLPIVNEDDELVAIIAR 18 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 188.1 3.61E-14 113368000 165721 173193 167728 175426 160629 196786 176822 174334 192052 227810 FALSE TRUE 159244.4401 168253.7052 198040.1807 184479.7569 165795.7777 200765.1477 178986.0005 170733.942 170251.0621 212380.2258 0.749808225 0.792228677 0.932479377 0.86862963 0.780655436 0.945309984 0.842762079 0.803906961 0.801633304 1 17.69628992 -2.581436451 2.194996034 4.072440119 0.837373739 0.397088582 0.060845254 3125643.146 330872.4797 47423841.72 0.015899538 0.002621583 2.581436451 -3.235066379 RPSGS(ph)QHSPSLQTFAPEADGTIFFPER ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RPS(0.222)GS(0.302)QHS(0.222)PS(0.222)LQT(0.032)FAPEADGTIFFPER 72.755 0.0088757 280110000 71348 93919 86934 139390 89562 106930 122020 93871 91032 95452 TRUE FALSE 68559.64128 91240.52208 102644.9076 146583.9346 92442.84307 109092.1979 123513.3173 91932.53105 80698.429 88986.95102 0.770446009 1.025324736 1.15348269 1.647252018 1.038835942 1.225934776 1.387993586 1.033101258 0.906856883 1 16.44130618 -2.579533745 16.46935486 1.011851963 1.14008572 0 0.239112106 0 0 0 0.053115451 0.002633093 2.579533745 0.128233757 LFIVDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFIVDAR 7 0 Q9UNZ2;Q9UNZ2-5;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 92.692 0.036019 332730000 735200 809230 699430 897610 801330 787760 753860 850630 904120 1029080 FALSE TRUE 706467.5712 786151.5527 825832.5597 943935.7597 827105.5072 803689.0469 763085.9642 833064.1932 801488.088 959379.495 0.736379686 0.819437519 0.860798635 0.983902371 0.86212548 0.837717557 0.795395324 0.868336459 0.835423409 1 19.87174208 -2.573726597 1.998780861 3.132031631 0.847957351 0.378806372 0.059623545 3148163.912 155171.3365 30478815.01 0.015034566 0.002668538 2.573726597 -2.284074281 ELPPAAAIGATSLVAAPHSSSS(ph)SPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELPPAAAIGATSLVAAPHSSSSSPSK 26 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 ELPPAAAIGATSLVAAPHS(0.025)S(0.02)S(0.02)S(0.466)S(0.466)PS(0.003)K;ELPPAAAIGATSLVAAPHS(0.034)S(0.028)S(0.094)S(0.368)S(0.368)PS(0.106)K 104.29 0.002215 178992000 84993 111139 112353 131669 114806 119180 125160 118251 117655 169409 TRUE FALSE 81671.3796 107969.4245 132657.6864 138464.4529 118498.8393 121589.9013 126691.7455 115809.0755 104299.2977 157934.7775 0.517120934 0.683632992 0.839952343 0.876719207 0.750302379 0.769874141 0.80217763 0.733271527 0.660394748 1 17.26896936 -2.565212183 2.249916797 5.748131353 0.746035113 0.396960669 0.096659292 2646663.718 316006.4797 64347934.62 0.02398388 0.002721371 2.565212183 -5.002096239 QVQPQVQPQAHSQGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QVQPQVQPQAHSQGPR 16 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 0 65.477 0.057246 77146000 98964 87571 91816 89218 97774 93519 86289 101070 113110 96750 FALSE TRUE 95096.37747 85073.56082 108409.1936 93822.55167 100918.9895 95410.01825 87345.03059 98982.86918 100270.227 90197.03632 1.054318205 0.943196853 1.201915252 1.040195504 1.118872566 1.05779549 0.968380272 1.097407112 1.111679841 1 16.46079241 -2.556769232 2.067937897 0.079185476 1.064981861 0.072729677 0.070590538 1466270.361 225997.4026 6357303.291 0.016472466 0.002774794 2.556769232 0.985796385 EFCENLSADCR ddPTM_BT-474_Pertuzumab_2h_R1 3 EFCENLSADCR 11 0 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;; 192.5 3.18E-06 1375740000 627790 640940 604330 683380 638280 520330 681960 671890 722140 734710 FALSE TRUE 603255.2727 622661.0187 713545.8742 718649.3237 658810.8559 530851.4291 690306.0305 658015.2367 640165.6947 684947.4373 0.880732214 0.909063944 1.041752747 1.04920361 0.961841479 0.775025061 1.007823364 0.960679902 0.934620176 1 19.38563375 -2.552427056 1.849128391 1.52200774 0.950348583 0.039510524 0.076945303 4698250.019 262995.9698 10273487.81 0.020529935 0.002802676 2.552427056 -0.571659157 HVSSETDESCKK ddPTM_BT-474_Pertuzumab_2h_R1 2 HVSSETDESCKK 12 1 Q96P16;A0A0C4DGQ6;Q96P16-3 Q96P16 RPRD1A Regulation of nuclear pre-mRNA domain-containing protein 1A 0 ; 272.97 6.09E-28 220500000 205310 258036 200574 254656 226919 266758 254501 212793 282043 312370 FALSE TRUE 197286.2582 250677.0659 236822.1835 267798.8267 234218.0557 272152.0295 257615.6594 208398.7502 250026.6611 291212.9017 0.677464003 0.860803434 0.813226963 0.919598085 0.804284612 0.934546608 0.884629966 0.715623343 0.85857 1 18.15171475 -2.549368891 1.900877492 2.890554239 0.829297307 0.299245018 0.078103699 2428204.953 131979.761 19784641.57 0.018856005 0.002822482 2.549368891 -2.061256932 IAVHCTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 IAVHCTVR 8 0 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 75.109 0.03924 234390000 88221 131770 109490 152550 151360 165410 132900 118180 101330 146020 FALSE TRUE 84773.22579 128012.0486 129277.2786 160423.1238 156228.6319 168754.7035 134526.47 115739.5417 89827.44321 136129.9353 0.622737575 0.940366631 0.949660912 1.178455888 1.147643474 1.23965903 0.988221067 0.850213742 0.659865466 1 17.05462483 -2.544335326 2.179661492 1.514686626 0.966503446 0.000905341 0.194810961 14385173.55 2808625.639 36747037.96 0.050086031 0.002855385 2.544335326 -0.54818318 HFVCEGCEQLLSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFVCEGCEQLLSGR 14 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ; 184.21 1.32E-06 692090000 179873 184776 158447 204701 174439 221353 209501 141181 237020 255780 FALSE TRUE 172843.3643 179506.3694 187081.8975 215265.6431 180049.9889 225828.9093 212064.9359 138265.563 210114.4833 238455.7928 0.724844477 0.752786784 0.784555893 0.902748642 0.755066534 0.947047277 0.889325998 0.5798373 0.881146483 1 17.8633623 -2.528896232 1.581579172 2.415019993 0.793829169 0.24688852 0.102911209 1112928.319 72154.53162 5610760.386 0.028595509 0.002958719 2.528896232 -1.621190824 SS(ph)S(ph)AS(ph)T(ph)AATWLWQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSASTAATWLWQAR 15 0 J3QKM6 J3QKM6 LLGL2 4 S(0.629)S(0.685)S(0.685)AS(0.725)T(0.725)AAT(0.551)WLWQAR 53.001 0.070884 455960000 0 10238 5866.4 6273.4 4286.9 5542.9 8845.4 4468 6247.8 8853.3 TRUE FALSE 0 9946.022264 6926.588977 6597.170926 4424.792032 5654.981236 8953.652651 4375.734239 5538.575937 8253.658105 0 1.205044132 0.839214429 0.799302666 0.536100717 0.685148472 1.084810218 0.530156954 0.671044992 1 13.01081796 -2.523397877 2.135468193 4.617707745 0.724163496 0.070864821 0.313362017 9768245.989 538668.5265 171961278.1 0.069961087 0.002996416 2.523397877 -3.893544248 QSVDHFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSVDHFAK 8 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 92.051 0.012052 859380000 572370 692420 586700 684280 603440 677050 720380 616150 740770 871660 FALSE TRUE 550001.1476 672672.8596 692729.7411 719595.7728 622850.1956 690740.4149 729196.2259 603426.2872 656680.8952 812621.6918 0.676823119 0.827781077 0.852462773 0.885523707 0.766470058 0.850014739 0.89733788 0.74256729 0.808101607 1 19.63222435 -2.519715206 2.126496398 3.369289609 0.814053445 0.435376159 0.064220926 2714794.306 155963.5399 31165520.91 0.015355082 0.003021933 2.519715206 -2.555236164 HGSEEARPQSCLVGSATGRPGGEGS(ph)PSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGSEEARPQSCLVGSATGRPGGEGSPSPK 29 2 Q9NQU5-2;Q9NQU5;H0YL16 Q9NQU5-2 PAK6 Serine/threonine-protein kinase PAK 6 1 HGSEEARPQSCLVGS(0.002)AT(0.002)GRPGGEGS(0.791)PS(0.205)PK 74.605 0.0031466 126870000 30137 51115 37015 49814 37984 47690 43003 38135 46769 56189 TRUE FALSE 28959.21272 49657.25025 43704.43389 52384.90651 39205.78986 48654.32447 43529.28358 37347.49892 41459.97919 52383.26898 0.552833248 0.947960126 0.834320476 1.000031261 0.748441069 0.928814208 0.830976845 0.712966175 0.79147369 1 15.67681847 -2.513797363 2.13680596 3.251509635 0.820330533 0.167798154 0.122369178 5591393.676 462862.6394 60845887.4 0.030338873 0.003063392 2.513797363 -2.431179102 DLYVNPNHQTSLGQER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLYVNPNHQTSLGQER 16 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 ; 109.48 0.00096926 611830000 190035 238130 192209 225590 217250 197941 225504 219960 240770 264970 FALSE TRUE 182608.2221 231338.7656 226945.442 237232.7269 224238.0436 201943.5026 228263.7854 215417.7491 213438.799 247023.3459 0.739234672 0.936505676 0.918720622 0.960365613 0.907760531 0.817507762 0.92405754 0.872054212 0.864043025 1 17.91428787 -2.512078334 2.055985554 2.277671221 0.886884192 0.244077774 0.061683199 3005689.756 248323.5486 17835713.43 0.014887201 0.003075542 2.512078334 -1.390787029 DGAGLGLSGGS(ph)PGASTPVLLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGAGLGLSGGSPGASTPVLLTR 22 0 Q8N612;Q8N612-2 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 DGAGLGLS(0.001)GGS(0.999)PGASTPVLLTR 189.51 2.21E-17 72173000 74005 78260 70243 90811 72373 106610 78769 74785 79476 108330 TRUE FALSE 71112.80278 76028.10142 82937.47265 95497.76659 74700.94327 108765.7272 79732.99858 73240.66362 70454.21767 100992.7126 0.704137961 0.752807796 0.821222349 0.945590668 0.739666668 1.076966094 0.789492593 0.725207411 0.697616846 1 16.62389167 -2.508750713 2.294265085 3.820935024 0.808101009 0.207562357 0.11372656 3530438.33 602634.8486 52510919.44 0.027704791 0.003099198 2.508750713 -3.012834015 EVAATEEDVTRLPSPTS(ph)PFSSLSQDQAATSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EVAATEEDVTRLPS(0.003)PT(0.024)S(0.965)PFS(0.006)S(0.002)LSQDQAATSK 235.31 6.02E-46 267150000 105260 92086 91436 109090 105200 108440 109950 97766 116140 138050 TRUE FALSE 101146.3228 89459.79744 107960.5192 114720.148 108583.8535 110632.7311 111295.601 95747.09794 102956.2741 128699.7505 0.785909238 0.695104669 0.838855699 0.891378169 0.843699021 0.859618846 0.864769361 0.743957137 0.7999726 1 16.97364973 -2.494543085 2.222670907 3.354425575 0.812652706 0.492475145 0.056729847 2049537.276 209412.6246 24510801.49 0.014917422 0.003202262 2.494543085 -2.541772868 SRWS(ph)GSQQVEQPTGSVLWMAPEVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRWSGSQQVEQPTGSVLWMAPEVIR 25 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.283)RWS(0.705)GS(0.012)QQVEQPTGSVLWMAPEVIR;S(0.195)RWS(0.485)GS(0.32)QQVEQPTGSVLWMAPEVIR 207.92 1.84E-25 402730000 77520 97186 74037 88105 83422 103920 95727 81618 104864 122584 TRUE FALSE 74490.4327 94414.35044 87417.13284 92652.10961 86105.34439 106021.3336 96898.53566 79932.55978 92960.27835 114281.2765 0.651816597 0.826157647 0.764929615 0.810737441 0.75345102 0.927722693 0.847895111 0.699437058 0.813434022 1 16.80222953 -2.493908431 1.870356939 2.773878417 0.788615988 0.428052749 0.073378415 2807632.819 190710.4085 21065334.12 0.017708941 0.003206945 2.493908431 -1.985262429 GDFNHER ddPTM_BT-474_Pertuzumab_2h_R1 1 GDFNHER 7 0 P05026-2;P05026;V9GYR2 P05026-2;V9GYR2 ATP1B1 Sodium/potassium-transporting ATPase subunit beta-1 0 69.825 0.05869 100440000 639580 586140 406090 604530 558930 400670 622010 487760 554290 353690 FALSE TRUE 614584.5065 569423.8611 479479.4964 635729.8657 576908.4911 408771.8219 629622.3444 477687.5855 491369.323 329734.2613 1.863878216 1.726917485 1.454139144 1.928006702 1.74961646 1.239700783 1.909484146 1.448704735 1.490197958 1 18.33094427 -2.47852767 0.185072933 7.91E-10 1.822440532 0.524220918 0.201566258 35.29695756 0.804995721 15.00414578 0.631311418 0.003322556 2.47852767 1.822440531 YCGDYDSFFESK ddPTM_BT-474_Pertuzumab_2h_R1 1 YCGDYDSFFESK 12 0 Q9UJC5 Q9UJC5 SH3BGRL2 SH3 domain-binding glutamic acid-rich-like protein 2 0 152.64 0.00016279 85226000 114850 120170 92383 133160 107050 118140 117990 135580 141600 151190 FALSE TRUE 110361.535 116742.8693 109078.6631 140032.4036 110493.3605 120528.8717 119433.9969 132780.2256 125526.1616 140949.7666 0.782984872 0.828258691 0.773883248 0.99349156 0.783920138 0.855119342 0.847351505 0.942039343 0.890573746 1 17.10482156 -2.477829409 0.024327987 2.022607047 6.38E-09 0.451773924 0.059445897 1165.278577 3.489262849 180.8727482 115.2230269 0.003327902 2.477829409 -2.022607041 IPLLSDLTHQISK ddPTM_BT-474_Pertuzumab_2h_R1 2 IPLLSDLTHQISK 13 0 Q13162;H7C3T4;A6NJJ0 Q13162;A6NJJ0 PRDX4 Peroxiredoxin-4 0 ; 145.17 4.17E-05 107109000 257570 288980 259120 263390 211252 108281 356150 217137 302130 344890 FALSE TRUE 247503.8796 280738.5733 305948.7481 276983.5895 218047.1124 110470.516 360508.6702 212653.0451 267833.469 321530.2931 0.769768463 0.873132577 0.951539418 0.861454101 0.678154181 0.343577319 1.121227698 0.661377947 0.832996065 1 18.29459514 -2.477413922 0.944657466 1.602648938 0.786681213 0.096458711 0.194524486 9881.82049 759.6679049 12451.41205 0.059261634 0.003331088 2.477413922 -0.815967725 DPMYNEYLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPMYNEYLDR 10 0 Q7L5D6;Q7L5D6-2 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 ; 140.78 9.00E-05 307690000 166143 183924 155000 197012 172381 153803 190793 190595 189404 220000 FALSE TRUE 159649.9479 178678.6676 183011.948 207179.8129 177925.7914 156913.002 193127.9818 186659.1466 167903.652 205099.204 0.778403547 0.871181672 0.892309401 1.010144403 0.867510882 0.765059049 0.94163204 0.910092009 0.818646044 1 17.64596237 -2.467409912 2.273855519 2.393683943 0.879411684 0.223441106 0.07017909 7442573.627 849820.4105 53274751.3 0.018103681 0.00340871 2.467409912 -1.514272259 EGHLSPDIVAEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGHLSPDIVAEQK 13 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;; 143.76 3.89E-05 6105100000 6673470 9419010 6942940 9399110 7925310 9456200 8754990 7676690 8633990 10503020 FALSE TRUE 6412663.414 9150389.057 8197683.703 9884199.193 8180234.794 9647410.843 8862136.187 7518163.669 7653895.652 9791641.1 0.654912016 0.934510259 0.837212436 1.009452766 0.835430416 0.985270063 0.905071591 0.767814465 0.781676491 1 23.22311925 -2.464863141 0.010224054 1.848744688 6.47E-06 0.089995606 0.105275048 31317.10255 39.5305919 3925.393616 3248.654199 0.003428758 2.464863141 -1.848738219 GHNCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHNCPK 6 0 P17844;J3KTA4;J3QRQ7;J3KRX8;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 71.995 0.086763 41516000 128960 131650 125800 140620 132530 124220 164780 111980 144440 187500 FALSE TRUE 123920.1006 127895.4709 148534.8584 147877.4151 136792.9478 126731.8135 166796.6269 109667.5739 128043.7767 174800.458 0.708923203 0.731665537 0.849739526 0.845978419 0.782566301 0.725008475 0.954211613 0.627387223 0.732513966 1 17.41534944 -2.456270034 2.243508872 3.402909473 0.772464625 0.381499312 0.086664512 3594291.391 265490.6739 44740034.99 0.02129445 0.003497276 2.456270034 -2.630444848 NSPSLQPPHPGSS(ph)TPTLASR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPSLQPPHPGSSTPTLASR 20 0 Q8TER5;Q8TER5-4;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 NSPSLQPPHPGS(0.124)S(0.437)T(0.437)PT(0.001)LASR 126.86 5.84E-06 0 60905 60473 51772 47741 53649 55352 52997 65471 63149 52873 TRUE FALSE 58524.76527 58748.36925 61128.35206 50204.91873 55374.66881 56471.25536 53645.59314 64119.00097 55980.59026 49291.86462 1.187310842 1.191847168 1.240130649 1.018523424 1.123403816 1.145650622 1.088325499 1.300802911 1.135696341 1 15.58906194 -2.44725194 1.756291102 4.45E-05 1.16386467 0.289109558 0.074494185 1470809.507 110930.305 5833968.157 0.019044159 0.003570656 2.44725194 1.163820185 ETPAATEAPSST(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETPAATEAPSSTPK 14 0 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 1 ETPAATEAPSST(1)PK 289.22 2.21E-42 427560000 736510 819030 631160 659680 675410 630310 673540 924070 731280 634420 TRUE FALSE 707726.3749 795672.0663 745224.6521 693726.1639 697135.176 643055.3001 681782.984 904987.6316 648268.1602 591450.1683 1.196595103 1.345290117 1.259995672 1.172924113 1.178687932 1.087251868 1.152731068 1.530116449 1.09606556 1 19.1738971 -2.443552309 1.381130464 0.014368536 1.240488911 0.214354171 0.125537397 185834.7132 16066.86203 566337.3566 0.037264924 0.003601204 2.443552309 1.226120376 WLDES(ph)DAEMELR ddPTM_BT-474_Pertuzumab_2h_R1 7 WLDESDAEMELR 12 0 H3BS72;Q9P035;H3BPZ1 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 1 WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR 293.13 3.69E-36 3718396000 2697566 4396123 2201091 4606002 2255552 1818009 3037507 4260301 3472598 2961978 TRUE FALSE 2592142.138 4270749.876 2598877.107 4843718.315 2328103.879 1854770.388 3074680.919 4172324.296 3078403.233 2761360.592 0.938719176 1.546610714 0.941158179 1.754105686 0.843100277 0.671687136 1.113465923 1.510966843 1.114813923 1 21.39694786 -2.438837795 1.692726975 0.00011351 1.180782381 0.017231362 0.327056045 4800273.758 407248.8533 18297184.46 0.082585907 0.00364051 2.438837795 1.180668871 EAEEES(ph)DHN ddPTM_BT-474_Pertuzumab_2h_R1 5 EAEEESDHN 9 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN 144.7 0.00010378 1048769000 1896110 1921060 1534660 1773680 1846400 1938250 1989870 1813780 1722540 2173050 TRUE FALSE 1822007.925 1866273.25 1812007.2 1865219.837 1905791.133 1977442.743 2014222.624 1776324.809 1527004.481 2025867.388 0.899371763 0.921221824 0.894435248 0.920701843 0.940728472 0.976096834 0.994251962 0.876821859 0.753753424 1 20.95010831 -2.420686024 2.374681616 1.867985364 0.913021295 0.159549303 0.062192668 2431553.567 1246633.977 11535489.92 0.016112603 0.003795893 2.420686024 -0.954964069 KQVEELFER ddPTM_BT-474_Pertuzumab_2h_R1 4 KQVEELFER 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 162.38 0.00010233 1348130000 1427090 1532960 1169260 1378120 1339990 1184840 1465970 1483620 1498840 1604110 FALSE TRUE 1371317.745 1489241.482 1380571.292 1449244.938 1383091.995 1208798.277 1483910.979 1452982.729 1328697.967 1495462.201 0.916985895 0.99584027 0.923173646 0.969094998 0.924859214 0.808310819 0.992275818 0.971594419 0.888486493 1 20.51216001 -2.419731157 2.945473885 2.09581457 0.936403984 0.122934335 0.053245407 2742025.963 24189833.71 5239847.732 0.012432178 0.003804248 2.419731157 -1.159410585 ALS(ph)IESLSPTDSSNGVNWR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALSIESLSPTDSSNGVNWR 19 0 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 ALS(0.99)IES(0.01)LSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR 366.58 7.70E-108 1697153000 714355 717138 620850 689592 664970 729596 720398 669217 782547 885364 TRUE FALSE 686437.2168 696685.9264 733051.4057 725181.9258 686359.364 744348.931 729214.4462 655397.4351 693715.5453 825397.5077 0.831644402 0.844061098 0.888119238 0.878585068 0.831550081 0.901806613 0.883470618 0.794038544 0.84046237 1 19.65472956 -2.41665585 2.278894909 2.301917813 0.853767735 0.658932093 0.031317432 2675443.963 348124.9275 17919597.04 0.008915235 0.003831282 2.41665585 -1.448150079 RPGHGS(ph)LTNISR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPGHGSLTNISR 12 1 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 RPGHGS(0.986)LT(0.014)NISR;RPGHGS(0.773)LT(0.227)NISR 121.62 0.00022849 541110000 158813 176607 128709 178855 167761 143671 179181 164311 184989 203807 TRUE FALSE 152606.4124 171570.3413 151969.5794 188085.728 173157.1849 146576.1261 181373.8707 160917.9204 163989.8243 190002.9704 0.803179088 0.902987679 0.799827388 0.989909408 0.911339357 0.771441235 0.954584396 0.846923183 0.863090845 1 17.53566245 -2.411765405 1.997916862 1.839515121 0.873737141 0.251792759 0.066362395 4025258.719 319573.8553 15295379.34 0.015079121 0.003874669 2.411765405 -0.965777981 LPHSSS(ph)SENIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPHSSSSENIK 11 0 F5H527;Q76I76;A0A3B3IS79;K7EKN7 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 LPHSSS(1)SENIK;LPHSS(0.002)S(0.997)S(0.001)ENIK 182.03 3.84E-06 266560000 307900 412050 320020 400660 363270 386370 345620 379080 395980 453210 TRUE FALSE 295866.9276 400298.7374 377854.7328 421338.1106 374954.9095 394182.6661 349849.8009 371251.8655 351030.0105 422513.683 0.700254073 0.94742195 0.894301766 0.99721767 0.887438501 0.93294651 0.82802005 0.878674184 0.830813355 1 18.68863854 -2.405066603 0.009212624 1.87908861 6.53E-07 0.118059441 0.079818249 30709.97068 35.44267435 3928.704822 3321.105822 0.003934897 2.405066603 -1.879087957 KGSSGAPQTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGSSGAPQTSR 11 1 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-8 Q5T5P2 KIAA1217 Sickle tail protein homolog 0 73.466 0.06972 11419000 12893 14364 11285 12561 10262 12722 12457 13119 12114 11259 FALSE TRUE 12389.12731 13954.35278 13324.45053 13209.27472 10592.08655 12979.24756 12609.45249 12848.08807 10738.86951 10496.4179 1.180319555 1.329439521 1.269428357 1.258455488 1.009114409 1.236540664 1.201310067 1.224045021 1.023098509 1 13.35760944 -2.402207311 0.10298771 0.578693854 1.379067237 0.415193395 0.086461478 87.79242633 1.141800066 10.0966295 1.647663619 0.003960889 2.402207311 0.800373382 YPHVEDYR ddPTM_BT-474_Pertuzumab_2h_R1 3 YPHVEDYR 8 0 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ;; 119.29 0.0017225 723790000 370354 383167 378480 438054 393053 281675 489071 377677 458108 491975 FALSE TRUE 355880.1562 372239.4523 446879.7552 460662.0194 405695.9067 287370.6615 495056.3972 369877.838 406105.5004 458653.095 0.775924462 0.811592588 0.974330622 1.004380052 0.884537597 0.626553412 1.079370013 0.806443567 0.885430633 1 18.80704385 -2.395378134 1.807134029 1.650457364 0.874506815 0.089776603 0.121988072 5172187.544 489578.4506 13709141.88 0.030480564 0.004023665 2.395378134 -0.775950549 NPS(ph)PTTRPVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 NPSPTTRPVSR 11 1 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4;A0A0U1RQR2 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 NPS(0.642)PT(0.337)T(0.021)RPVSR;NPS(0.997)PT(0.003)TRPVSR;NPS(0.975)PT(0.025)TRPVSR 122.33 0.00023806 3596350000 369588 441970 317869 441983 396225 415100 405146 434900 401431 512720 TRUE FALSE 355144.0924 429365.4483 375314.9993 464793.7956 408969.937 423493.6064 410104.2979 425919.163 355862.2358 477993.0177 0.742990126 0.898267197 0.785189292 0.972386161 0.85559814 0.88598283 0.857971315 0.89105729 0.74449254 1 18.86663002 -2.393003133 2.411620764 2.277637317 0.855939682 0.297582172 0.069047209 4753616.442 1152030.735 32938758.4 0.015685616 0.00404573 2.393003133 -1.421697635 S(ph)RT(ph)PLLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTPLLPR 8 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RT(1)PLLPR;S(1)RT(1)PLLPR 77.593 0.075188 1364300000 112310 91604 71334 81327 92209 87051 75357 101253 104114 79412 TRUE FALSE 107920.801 88991.54361 84225.64062 85524.29622 95174.98623 88811.23086 76279.24151 99162.09017 92295.4152 74033.35451 1.45773215 1.202046621 1.137671542 1.155213036 1.28556901 1.19961106 1.030336151 1.339424518 1.246673419 1 16.17588778 -2.38898976 1.674133825 6.97E-05 1.223250451 0.274895966 0.110944899 1245416.976 120347.7673 4692960.799 0.027862334 0.00408329 2.38898976 1.223180778 EGENNKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGENNKPR 8 1 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 160.11 0.00032402 778710000 1342700 1177600 907780 1191600 1062400 1093300 1210100 1295200 1238300 1449600 FALSE TRUE 1290225.8 1144016.001 1071836.039 1253098.619 1096573.061 1115407.275 1224909.566 1268453.667 1097733.375 1351417.301 0.954720499 0.846530528 0.793119963 0.927247726 0.811424465 0.825361104 0.906388845 0.938609907 0.812283056 1 20.3660418 -2.382825577 0.328031969 1.182202335 0.862796307 0.307805755 0.057197988 59.78896311 2.444317817 7.919690505 0.049934754 0.00414166 2.382825577 -0.319406029 QMDTVLSS(ph)SPDVLFDPINGLTPDEEALSNER ddPTM_BT-474_Pertuzumab_2h_R1 1 QMDTVLSSSPDVLFDPINGLTPDEEALSNER 31 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 QMDTVLS(0.011)S(0.495)S(0.495)PDVLFDPINGLTPDEEALSNER 157.1 4.56E-09 37043000 25821 24421 23397 30278 24607 24908 25160 27445 26317 33021 TRUE FALSE 24811.88677 23724.53699 27625.35836 31840.65121 25398.5065 25411.65683 25467.91561 26878.25116 23329.60449 30784.45826 0.805987442 0.770666055 0.897380039 1.034309291 0.825043153 0.825470327 0.827297833 0.873111066 0.757837097 1 14.90991456 -2.380149362 2.300396781 2.11793853 0.850775007 0.276023123 0.074343947 2460890.916 546478.93 14361724.47 0.019738104 0.00416726 2.380149362 -1.267163523 EAS(ph)PLPAESASAGATLRPLLLSGHGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EASPLPAESASAGATLRPLLLSGHGAR 27 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 EAS(1)PLPAESASAGATLRPLLLSGHGAR;EAS(1)PLPAESASAGATLRPLLLSGHGAR 162.61 7.30E-12 500170000 240820 260870 265150 312940 294070 315310 270530 285400 318020 412660 TRUE FALSE 231408.4882 253430.243 313068.5032 329090.8709 303529.0286 321685.7842 273840.8271 279506.3903 281919.7028 384710.1706 0.60151383 0.658756286 0.813777558 0.85542545 0.788981035 0.836176968 0.711810729 0.726537564 0.732810631 1 18.55341245 -2.377807667 2.146329842 2.615068264 0.750404091 0.502424402 0.075383734 5712619.462 500616.7138 44909204.05 0.01983201 0.004189791 2.377807667 -1.864664174 GEFGVEDDRPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEFGVEDDRPAR 12 1 Q96CN9 Q96CN9 GCC1 GRIP and coiled-coil domain-containing protein 1 0 95.417 0.0018997 0 106100 139370 103460 120350 114610 130640 118400 127360 124360 159370 FALSE TRUE 101953.4947 135395.3041 122157.5235 126561.2779 118296.5347 133281.6303 119849.0146 124729.9715 110243.1742 148575.7279 0.686205588 0.911288176 0.822190308 0.851830105 0.796203635 0.897061937 0.806652717 0.839504361 0.741999892 1 17.18083892 -2.37343599 2.432529262 2.429400275 0.823503453 0.422375437 0.063796492 2586478.607 1192112.767 21750843.97 0.014062512 0.004232179 2.37343599 -1.605896823 ISVSS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 6 ISVSSPGR 8 0 O75864;O75864-2 O75864 PPP1R37 Protein phosphatase 1 regulatory subunit 37 1 ISVS(0.015)S(0.985)PGR;IS(0.001)VS(0.047)S(0.952)PGR;ISVS(0.005)S(0.995)PGR;ISVS(0.021)S(0.978)PGR;ISVS(0.057)S(0.943)PGR;ISVS(0.022)S(0.978)PGR 151.22 0.00049994 7362950000 9537090 10359860 8971310 10376510 9917770 8902400 10369870 10570730 10743330 11769790 TRUE FALSE 9164369.979 10064406.94 10592625.28 10912042.92 10236784.08 9082412.628 10496779.57 10352440.73 9523792.218 10972611.64 0.835204077 0.917229851 0.965369561 0.994480009 0.932939615 0.827734812 0.956634566 0.9434801 0.867960385 1 23.38740361 -2.373134923 2.330610183 1.585504142 0.920958469 0.179171745 0.05307399 6209307.512 1864698.245 18656830.38 0.012897574 0.004235114 2.373134923 -0.664545673 IREEFPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IREEFPDR 8 1 P04350;M0QYM7;M0R042;K7ES63;K7ESM5;Q9BUF5 P04350;K7ESM5 TUBB4A;TUBB6 Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 107.79 0.0035894 517720000 349290 366890 295100 361050 349290 322470 348810 357820 393470 395320 FALSE TRUE 335639.3606 356426.6564 348431.1345 379683.8338 360525.2301 328990.5643 353078.8411 350430.892 348804.9352 368544.6243 0.91071566 0.967119401 0.945424547 1.030224859 0.978240371 0.892674978 0.958035521 0.95085064 0.946438809 1 18.49147979 -2.371241462 1.947769398 1.23972147 0.95463995 0.135933272 0.035175089 4440071.589 439404.4504 4684632.533 0.008652211 0.004253619 2.371241462 -0.28508152 WIDLTMEDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 WIDLTMEDIR 10 0 A0A0A0MSW4;P48739;P48739-3;P48739-2 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ; 140.5 9.11E-05 79515000 94147 103147 99332 106735 111263 81464 110963 106575 105979 129282 FALSE TRUE 90467.63115 100205.3486 117283.502 112243.6061 114841.8754 83111.2579 112320.9984 104374.189 93948.70822 120525.615 0.750609164 0.831402923 0.973100216 0.931284243 0.952842061 0.689573398 0.931926366 0.865991756 0.779491631 1 16.87898027 -2.367641311 2.172176402 1.863070386 0.862770476 0.184957041 0.089593123 6167144.512 648038.1841 26186661.7 0.021766393 0.004289026 2.367641311 -1.000299911 GIALIFNHER ddPTM_BT-474_Pertuzumab_2h_R1 2 GIALIFNHER 10 0 P55212;D6RBM3;D6RHU3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 ; 187.64 1.21E-06 814410000 637160 729590 652890 752250 741870 468070 844760 711190 704240 855730 FALSE TRUE 612259.0828 708782.8075 770881.7465 791073.7126 765732.9223 477534.6961 855098.4256 696503.678 624297.6276 797770.6449 0.767462537 0.88845436 0.966294951 0.991605442 0.959840936 0.598586447 1.071859978 0.873062556 0.78255277 1 19.60561451 -2.356345573 2.170744859 1.677333135 0.885955239 0.072175542 0.128499803 7011463.093 811571.5868 23350230.92 0.030129689 0.004402044 2.356345573 -0.791377896 EHASIDAQSGAGVPNPSTS(ph)ASPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHASIDAQSGAGVPNPSTSASPK 23 0 Q8IXJ6-5;Q8IXJ6-2;Q8IXJ6-3;Q8IXJ6 Q8IXJ6-5 SIRT2 NAD-dependent protein deacetylase sirtuin-2 1 EHASIDAQSGAGVPNPS(0.087)T(0.33)S(0.359)AS(0.224)PK 164.13 9.44E-12 538830000 173000 253990 179540 235250 195290 237940 243560 166320 241120 305950 TRUE FALSE 166238.9687 246746.4539 211986.8718 247391.2807 201571.6802 242751.3098 246540.7601 162885.4339 213749.0685 285227.734 0.582828908 0.86508577 0.743219703 0.867346514 0.70670435 0.851078913 0.864364614 0.571071514 0.749397913 1 18.12175474 -2.345212752 2.126387393 2.331098122 0.754470983 0.324287767 0.105790628 4488615.445 519879.5503 28717790.46 0.025470094 0.004516346 2.345212752 -1.57662714 IKWGDAGAEYVVESTGVFTTMEK ddPTM_BT-474_Pertuzumab_2h_R1 7 IKWGDAGAEYVVESTGVFTTMEK 23 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;; 232.07 1.34E-33 9586739000 6460211 6642024 4751363 4539782 5633247 6066355 5370018 6272308 6610120 5018778 FALSE TRUE 6207738.812 6452599.979 5610039.988 4774080.693 5814445.506 6189020.854 5435737.887 6142782.648 5859766.889 4678851.696 1.326765458 1.379099061 1.19902069 1.02035307 1.242707802 1.322764913 1.161767511 1.312882529 1.252394235 1 22.15772307 -2.334100961 1.825025267 3.28E-05 1.245613109 0.365452588 0.097405984 1311452.284 156016.2186 5391354.93 0.027412996 0.004633392 2.334100961 1.245580277 SRS(ph)PPPVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(0.246)RS(0.754)PPPVSK 85.554 0.0089245 396240000 434510 451060 371860 449340 404030 500460 468000 330050 553060 577880 TRUE FALSE 417528.8688 438196.2104 439063.374 472530.4912 417025.9919 510579.6441 473727.524 323234.3522 490278.9474 538739.6729 0.775010436 0.813372826 0.814982442 0.877103572 0.774077004 0.947729803 0.879325485 0.599982456 0.910047973 1 19.03922878 -2.331129134 1.47494882 1.579777481 0.811696348 0.248043009 0.091992544 255515.6092 29597.84508 490048.4679 0.026465231 0.004665206 2.331129134 -0.768081133 GKLEAIIT(ph)PPPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 GKLEAIITPPPAK 13 1 O75367-2;O75367-3;O75367;D6RCF2 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 1 GKLEAIIT(1)PPPAK;GKLEAIIT(1)PPPAK;GKLEAIIT(1)PPPAK 129.88 0.00024023 3680500000 6436640 6956440 7041280 8745260 5381570 7876990 7428590 7712200 7495650 9709950 TRUE FALSE 6185088.993 6758049.142 8313795.928 9196603.917 5554673.086 8036268.135 7519503.307 7552940.375 6644775.236 9052286.438 0.683262625 0.746557148 0.91841945 1.015942655 0.613621003 0.887761141 0.830674477 0.834368248 0.734043855 1 23.10985081 -2.330550138 2.290331055 2.062777748 0.814116268 0.207662612 0.112257645 4078125.98 626063.8602 22575734.87 0.026468742 0.00467143 2.330550138 -1.248661481 EATWVVDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EATWVVDVK 9 0 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 159.37 0.00015379 108530000 168550 185930 126150 164640 174300 177640 155960 206740 180720 209740 FALSE TRUE 161962.8797 180627.4584 148948.1112 173137.0901 179906.5178 181232.0025 157868.6851 202470.7468 160205.4232 195534.123 0.828310052 0.923764383 0.761749964 0.885457165 0.92007735 0.92685614 0.807371536 1.03547526 0.819322074 1 17.57706087 -2.321827426 0.024131095 1.803792909 0.202266494 0.222363903 0.073121376 1760.709687 5.438344516 222.7130607 144.878183 0.004766203 2.321827426 -1.601526415 AHFGLPSVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHFGLPSVEK 10 0 Q9Y6Q5;K7ERH5;K7EL08;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 98.943 0.0050328 368370000 354560 426860 338080 377780 380470 351980 478220 311300 435600 510390 FALSE TRUE 340703.4032 414686.3707 399178.5765 397277.2711 392708.1631 359097.2768 484072.5994 304871.5462 386152.5142 475820.8307 0.716032971 0.871517899 0.838926232 0.834930389 0.825327808 0.754690114 1.017342176 0.640727615 0.81155025 1 18.86005891 -2.321369507 2.109505718 1.901805005 0.810732249 0.262491731 0.094332901 4448811.793 564195.5108 19117993.19 0.023124289 0.004771232 2.321369507 -1.091072756 S(ph)FSKEVEER ddPTM_BT-474_Pertuzumab_2h_R1 4 SFSKEVEER 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(0.998)FS(0.002)KEVEER;S(0.994)FS(0.006)KEVEER;S(1)FSKEVEER;S(0.5)FS(0.5)KEVEER 142.83 6.26E-05 2966410000 4661230 4516620 2570280 2671970 3684890 4275280 3374280 4233020 4296000 3147440 TRUE FALSE 4479063.978 4387810.42 3034786.772 2809870.692 3803417.833 4361729.091 3415575.448 4145606.658 3808336.09 2934261.085 1.526470838 1.495371507 1.034259285 0.957607592 1.296209752 1.486482956 1.164032562 1.412828149 1.2978859 1 21.48456581 -2.316078499 1.684979443 6.18E-05 1.293375162 0.187387934 0.185292926 1271841.301 157899.8274 4819515.55 0.052066791 0.004829715 2.316078499 1.293313344 IALESEGRPEEQMESDNCS(ph)GGDDDWTHLSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 IALESEGRPEEQMESDNCSGGDDDWTHLSSK 31 1 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 1 IALESEGRPEEQMES(0.008)DNCS(0.992)GGDDDWTHLSSK 92.372 0.00029207 489290000 70707 75209 69268 78462 74929 79668 77489 72198 85108 105900 TRUE FALSE 67943.69227 73064.11296 81786.26846 82511.43322 77339.15933 81278.94154 78437.33356 70707.08607 75446.89664 98727.29867 0.688195597 0.740059881 0.828405816 0.835750946 0.783361445 0.823267147 0.794484754 0.716185766 0.764194885 1 16.59116143 -2.303051165 2.272842903 2.096982799 0.775409872 0.678048031 0.046536261 1902111.503 284471.776 10745729.3 0.012637 0.004976784 2.303051165 -1.321572926 VGHSELVGEIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGHSELVGEIIR 12 0 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;;; 210.91 3.80E-08 1598250000 937810 972570 885300 1081770 944370 871380 1083010 917950 1115290 1204460 FALSE TRUE 901159.3484 944833.2558 1045293.403 1137600.279 974746.5187 888999.9006 1096264.2 898994.0117 988686.9549 1122880.851 0.802542271 0.841436787 0.930903223 1.013108629 0.868076535 0.791713475 0.976296104 0.800613895 0.88049142 1 20.09877342 -2.296459053 2.156617646 1.529542681 0.878521235 0.206153108 0.071612665 6917943.744 938794.3075 17859311.36 0.01744925 0.005052903 2.296459053 -0.651021447 TASGSS(ph)VTS(ph)LDGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 TASGS(0.039)S(0.714)VT(0.375)S(0.871)LDGTR;T(0.002)AS(0.015)GS(0.131)S(0.518)VT(0.49)S(0.844)LDGTR 112.12 0.00089465 406910000 1237930 1254970 910890 962110 1135310 949650 871650 1267420 1034540 873800 TRUE FALSE 1189550.327 1219179.484 1075508.086 1011764.612 1171828.277 968852.5737 882317.5134 1241247.334 917103.3563 814616.7477 1.460257637 1.496629535 1.320262674 1.242013027 1.43850256 1.189335447 1.083107505 1.52371939 1.125809602 1 19.63576195 -2.292193373 0.050466105 8.84E-12 2.049831495 0.447364484 0.132051374 318.3351197 2.077129313 64.36368241 26.5445913 0.005102777 2.292193373 2.049831495 LSPFFTLDLS(ph)PTEDKSSKPSSFTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPFFTLDLSPTEDKSSKPSSFTEK 25 2 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 LSPFFTLDLS(0.984)PT(0.016)EDKSSKPSSFTEK 199.2 3.79E-25 206880000 279820 254550 158890 149490 218680 248980 184030 253380 270830 190660 TRUE FALSE 268884.325 247290.4832 187604.9575 157205.1968 225714.0408 254014.5462 186282.2142 248147.6145 240086.5138 177746.4284 1.512741086 1.391254302 1.055464007 0.884435194 1.269865408 1.429083827 1.048022263 1.396076516 1.350724828 1 17.43946105 -2.276424207 2.159386925 0.000203428 1.25292583 0.141858458 0.190991126 2901396.099 445346.6089 14193860.66 0.048195054 0.005291463 2.276424207 1.252722401 RGEVPAELR ddPTM_BT-474_Pertuzumab_2h_R1 6 RGEVPAELR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;;;; 163.66 0.00010077 1699513000 1345251 1400130 1348906 1568119 1436728 1131049 1543740 1513810 1578190 1836650 FALSE TRUE 1292677.104 1360199.663 1592683.32 1649049.81 1482941.661 1153919.586 1562632.752 1482549.294 1399040.488 1712252.06 0.754957249 0.79439219 0.930168728 0.963088232 0.866076728 0.673919228 0.91261841 0.865847576 0.817076247 1 20.70746366 -2.27373629 2.009214932 1.542682451 0.847100697 0.247692473 0.082170198 6934503.791 1047753.193 17051188.89 0.020543435 0.005324315 2.27373629 -0.695581754 KHEAFESDLAAHQDR ddPTM_BT-474_Pertuzumab_2h_R1 6 KHEAFESDLAAHQDR 15 1 O43707;O43707-2;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0;H7C5W8 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;;;; 178.14 2.95E-07 13060900000 3980120 4184920 4965300 7338930 4701990 3914420 6413860 1448090 7141640 7802850 FALSE TRUE 3824572.51 4065570.179 5862640.163 7717693.057 4853233.779 3993572.254 6492354.737 1418186.435 6330950.967 7274356.019 0.525760975 0.558890735 0.805932532 1.060945194 0.66717023 0.548993236 0.892498899 0.194956974 0.87031085 1 22.7943881 -2.269332897 1.507885164 1.860214185 0.662344332 0.142052571 0.231602731 368924.5364 50345.30992 1075026.522 0.065838813 0.005378573 2.269332897 -1.197869854 GKSETILS(ph)PPPEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKSETILSPPPEKR 14 2 Q9P0M6 Q9P0M6 H2AFY2 Core histone macro-H2A.2 1 GKSET(0.009)ILS(0.991)PPPEKR;GKSET(0.001)ILS(0.999)PPPEKR 113.54 0.00027627 308060000 781620 990600 1091380 1029160 609340 1404420 893300 825260 1222850 1416970 TRUE FALSE 751073.4263 962349.0579 1288616.644 1082275.071 628939.9745 1432818.335 904232.4726 808218.0926 1084037.195 1320997.36 0.568565426 0.728501878 0.975487675 0.819286324 0.476109941 1.084648901 0.684507403 0.611824154 0.820620258 1 20.33319615 -2.266284252 1.462455367 1.616363115 0.748582102 0.153383142 0.174491526 248128.1464 33719.15309 502270.921 0.047210751 0.005416463 2.266284252 -0.867781013 KDPDMVKDIINEEEVQFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDPDMVKDIINEEEVQFLK 19 2 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 154.43 2.02E-08 300790000 765370 712210 425150 332330 545210 764780 580040 553820 705670 474470 FALSE TRUE 735458.4942 691898.4681 501984.0624 349481.5911 562747.1748 780244.3756 587138.703 542383.4235 625565.3 442333.7243 1.662677869 1.564200128 1.134853697 0.790085793 1.272223084 1.763926946 1.327365902 1.226186008 1.414238313 1 18.75477571 -2.259174072 1.834067526 4.09E-05 1.334696685 0.133546566 0.265156305 2740229.21 417843.3538 11323041.35 0.072199596 0.00550587 2.259174072 1.33465579 LGGAPAAQGVSPS(ph)PSAILER ddPTM_BT-474_Pertuzumab_2h_R1 1 LGGAPAAQGVSPSPSAILER 20 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LGGAPAAQGVS(0.084)PS(0.74)PS(0.176)AILER 77.08 0.010977 290010000 35113 49151 39450 42688 40784 48645 37509 44171 44064 57929 TRUE FALSE 33740.74514 47749.2616 46579.49256 44891.1328 42095.8544 49628.63523 37968.04636 43258.85341 39062.03945 54005.41723 0.624765938 0.884156887 0.862496671 0.831233885 0.779474663 0.918956612 0.703041441 0.801009521 0.72329854 1 15.72081651 -2.256314384 2.322191254 1.796461105 0.797741866 0.348380063 0.085000291 2982812.967 774272.4447 12392774.76 0.019985494 0.005542244 2.256314384 -0.998719239 TSPDTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ; 119.57 0.011058 433380000 541250 523490 459170 515870 492590 491350 528190 552070 568060 624950 FALSE TRUE 520097.3516 508560.5778 542152.2332 542494.1125 508434.6047 501285.4337 534654.1472 540669.5616 503576.2103 582621.5799 0.892684668 0.872883181 0.930539225 0.931126019 0.872666963 0.860396269 0.91766966 0.927994397 0.864328112 1 19.15219961 -2.251359158 2.450345791 1.415856668 0.899304656 0.565332205 0.027087412 3182893.622 878386.1941 7336749.892 0.00706537 0.005605842 2.251359158 -0.516552012 ARPSAHS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ARPSAHSPGK 10 1 H9KVB4;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 ARPS(0.001)AHS(0.999)PGK 64.104 0.044845 37756000 37354 41183 42108 44449 37759 37298 48443 40302 47389 52620 TRUE FALSE 35894.16438 40008.50116 49717.85229 46743.01822 38973.55253 38052.19111 49035.85992 39469.74962 42009.59939 49056.00053 0.731697733 0.815567937 1.013491759 0.952850165 0.794470648 0.775688819 0.999589436 0.804585559 0.856360057 1 15.582142 -2.247616341 2.015928818 1.429991037 0.863772872 0.17062708 0.092023854 6957258.973 1131547.726 13609487.07 0.023460871 0.005654363 2.247616341 -0.566218165 DTIHCGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DTIHCGK 7 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 ; 73.616 0.048409 458560000 1130180 1041180 897740 1092010 1008710 1091220 1075480 1082430 1191330 1287360 FALSE TRUE 1086011.316 1011486.566 1059981.588 1148368.767 1041156.073 1113285.216 1088642.046 1060077.442 1056095.213 1200165.961 0.904884284 0.842788913 0.883195844 0.956841641 0.867510084 0.927609391 0.907076256 0.883275711 0.879957646 1 20.19480249 -2.232109156 2.364360679 1.37293318 0.894615801 0.522156229 0.030192645 3522502.634 417596.6223 7124158.413 0.007585136 0.005859909 2.232109156 -0.478317379 AGNNMLLVGVHGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGNNMLLVGVHGPR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 145.17 8.65E-06 1804540000 1141300 1383790 1081590 1278630 1263190 1027810 1387060 1264470 1414130 1462720 FALSE TRUE 1096696.734 1344325.664 1277057.373 1344620.248 1303821.654 1048593.022 1404035.255 1238358.253 1253603.891 1363648.672 0.804237013 0.985829922 0.936500287 0.986045948 0.956127249 0.768961276 1.029616561 0.908121189 0.919301223 1 20.37904057 -2.214991997 1.983610813 1.197817491 0.925900394 0.083605895 0.076670474 8581089.585 1534628.319 7603180.096 0.018106975 0.006095481 2.214991997 -0.271917097 EAARS(ph)PDKPGGSPSASR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(1)PDKPGGSPSASR;EAARS(1)PDKPGGSPSASR;EAARS(1)PDKPGGSPSASR;EAARS(1)PDKPGGSPSASR 171.39 9.03E-10 2962718000 4415120 4248380 3280962 4058700 3866890 4165760 4067010 4274560 4535260 4977260 TRUE FALSE 4242572.229 4127220.362 3873904.818 4268169.993 3991272.029 4249994.521 4116783.285 4186288.842 4020436.298 4640145.747 0.914318744 0.889459208 0.834867056 0.91983533 0.860160919 0.915918325 0.887209909 0.902189084 0.866446124 1 22.14573869 -2.186510801 2.445155118 1.319349009 0.888270625 0.626391114 0.025988262 3214284.981 913896.7522 5672217.744 0.006038143 0.006508624 2.186510801 -0.431078384 SLS(ph)LDPGQSLEPHPEGPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSLDPGQSLEPHPEGPQR 19 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 S(0.021)LS(0.979)LDPGQSLEPHPEGPQR 161.48 1.90E-11 432330000 557240 548110 296210 411700 603490 379960 332870 547680 341480 319900 TRUE FALSE 535462.4447 532478.4395 349741.7362 432947.8863 622901.8039 387643.0515 336943.7626 536370.2166 302716.622 298232.8881 1.79545069 1.785445069 1.172713507 1.451710739 2.088642228 1.299799811 1.129800824 1.798494526 1.015034338 1 18.18607984 -2.168048175 0.107564405 5.22E-09 1.958753687 0.294193382 0.309218648 105.5962875 1.537292176 31.0325161 5.257577264 0.006791283 2.168048175 1.958753682 ESDYFTPQGEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESDYFTPQGEFR 12 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 141.08 0.0001401 202270000 92067 153470 99469 146640 98525 68193 117640 163720 126640 92613 FALSE TRUE 88468.91985 149093.1859 117445.261 154208.108 101694.1461 69571.90918 119079.7135 160339.1248 112264.3581 86340.23902 1.024654563 1.726809974 1.360261013 1.786051437 1.177830259 0.805787776 1.379191381 1.857061396 1.300255355 1 16.39774547 -2.159598115 2.039000058 0.12874731 1.41171921 0.10523208 0.32024094 5419137.187 1192334.9 21784601.23 0.081763182 0.006924715 2.159598115 1.282971899 KPLSTHSTEYNLDSVPS(ph)PAEEFADFATFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPLSTHSTEYNLDSVPSPAEEFADFATFSK 30 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9 Q6ULP2-7 AFTPH Aftiphilin 1 KPLSTHSTEYNLDSVPS(1)PAEEFADFATFSK 186.59 1.99E-18 276130000 363680 461060 367290 486630 432700 514540 422880 386060 460950 479890 TRUE FALSE 349466.9835 447911.0202 433667.4733 511745.0326 446618.1885 524944.3513 428055.3319 378087.7261 408624.8885 447386.6229 0.781129711 1.001172135 0.969334913 1.143854122 0.998282393 1.173357281 0.956790637 0.845102886 0.913359648 1 18.77116259 -2.159180755 8.735244458 1.55900251 0.977252644 0.003959595 0.113012803 0.264470253 0.004819394 0.0235219 0.026948964 0.006931373 2.159180755 -0.581749865 KEDLVFIFWAPESAPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEDLVFIFWAPESAPLK 17 1 G3V1A4;E9PQB7;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ; 186.05 8.74E-10 18485500000 37470000 33869500 30756300 27323900 30528800 27548100 35680000 35519800 37147400 35733700 FALSE TRUE 36005630.97 32903575.02 36314647.58 28734089.75 31510786.58 28105141.46 36116662.51 34786303.72 32930582.89 33313424.67 1.080814456 0.987697163 1.090090495 0.862537852 0.945888539 0.843658127 1.084147393 1.044212778 0.988507883 1 24.98960034 -2.155432847 12.42416034 1.594286895 0.993035813 0.000684483 0.083462796 0.427328523 0.00534611 0.025135242 0.019387082 0.006991448 2.155432847 -0.601251083 KVTS(ph)PLQS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVTSPLQSPTK 11 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 2 KVT(0.149)S(0.851)PLQS(1)PTK 137.79 0.00024879 870030000 1245300 1064200 927550 795130 1003400 869030 1054500 1171900 1152000 1124100 TRUE FALSE 1196632.299 1033850.058 1095178.918 836166.7546 1035675.272 886602.382 1067405.286 1147699.855 1021229.79 1047963.706 1.141864258 0.986532312 1.045054244 0.797896673 0.988273989 0.846023939 1.018551769 1.095171378 0.974489655 1 19.99915732 -2.147219224 11.84539718 1.598952532 0.989197553 0.001212433 0.097896988 0.33962103 0.004220945 0.020789166 0.022658701 0.007124933 2.147219224 -0.609754979 ISHQSQDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISHQSQDKK 9 1 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ; 143.89 6.55E-05 1545660000 1751770 2300260 1809850 2166510 1755800 1902170 2161130 1962900 2338730 2912500 FALSE TRUE 1683308.892 2234658.837 2136930.155 2278323.841 1812276.902 1940633.181 2187578.555 1922365.429 2073247.175 2715233.781 0.619949893 0.823007894 0.787015162 0.839089384 0.667447832 0.714720476 0.805668584 0.707992602 0.763561204 1 21.37264499 -2.130943215 1.694714141 1.416941562 0.749864243 0.561974578 0.066821785 329876.3271 68131.39384 528155.3876 0.017327256 0.00739702 2.130943215 -0.667077319 QEIQHLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEIQHLFR 8 0 P04844-2;P04844;H0Y5M1 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 ; 186.16 0.00020897 443100000 242100 444660 224720 389520 229240 166335 324060 381070 306240 232330 FALSE TRUE 232638.4643 431978.7322 265331.9029 409623.1739 236613.7128 169698.4077 328025.9432 373200.7713 271476.9191 216594.0822 1.07407581 1.994416135 1.225019171 1.891202058 1.09242926 0.783485892 1.514473248 1.723042327 1.253390288 1 17.7246343 -2.125592918 1.326827877 0.379460818 1.422799623 0.089572972 0.367691759 71221.70768 12352.67457 132811.2634 0.103246336 0.007488711 2.125592918 1.043338805 SVIEDVINDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVIEDVINDVR 11 0 J3KNC0;P52655 J3KNC0 GTF2A1 Transcription initiation factor IIA subunit 1;Transcription initiation factor IIA alpha chain;Transcription initiation factor IIA beta chain 0 ; 117.52 0.0019627 45066000 71658 84257 65011 84464 76635 56054 95220 74834 84354 100035 FALSE TRUE 68857.52614 81854.07286 76759.93386 88823.19716 79100.03437 57187.45029 96385.33084 73288.65175 74778.48756 93259.54035 0.738342971 0.877701869 0.823078621 0.952430141 0.848170965 0.613207507 1.033517112 0.785856884 0.801832041 1 16.5089637 -2.11990683 2.453744514 1.325310814 0.834775592 0.179643393 0.108337293 11259107.38 3138921.688 20438979.1 0.024538918 0.007587403 2.11990683 -0.490535223 GDFFPPERPQQLPHGLGGIGMGLGPGGQPIDANHLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDFFPPERPQQLPHGLGGIGMGLGPGGQPIDANHLNK 37 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R019;M0R0N3 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 293.48 2.86E-92 2895800000 1190370 1236910 968900 1097010 1338580 1194220 1185210 1009050 1428510 1297990 FALSE TRUE 1143849.024 1201634.538 1144001.783 1153626.818 1381636.641 1218367.947 1199714.955 988212.7649 1266351.534 1210075.981 0.945270415 0.993024039 0.945396653 0.953350728 1.141776767 1.006852434 0.991437706 0.816653483 1.046505801 1 20.20666621 -2.118673307 9.076200536 1.301886735 0.974722082 0 0.078661745 0.165793265 0.002167784 0.026278656 0.019084537 0.007608984 2.118673307 -0.327164653 DIWDFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIWDFLR 7 0 Q8NFF5-2;Q8NFF5;Q8NFF5-3;Q5T190 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 0 ; 119.89 0.01089 139636000 340170 361620 367730 360450 360590 241260 426990 377790 379390 428310 FALSE TRUE 326875.7803 351306.9517 434186.9911 379052.8677 372188.7048 246138.4425 432215.6313 369988.5045 336323.2377 399300.1822 0.818621666 0.87980664 1.08736988 0.949293 0.932102517 0.616424568 1.082432843 0.926592376 0.842281704 1 18.6071142 -2.116788868 4.266039062 1.279079119 0.911386177 0.045524524 0.127947196 0.164260705 0.00449687 0.059919181 0.02854846 0.007642072 2.116788868 -0.367692941 EGMNIVEAMER ddPTM_BT-474_Pertuzumab_2h_R1 14 EGMNIVEAMER 11 0 P62937;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 ;;;;;;;;;;;;; 256.96 3.82E-20 21338315000 3908545 4166482 3659063 4562997 4136973 3304620 4386080 4347614 4428949 4976079 FALSE TRUE 3755794.74 4047658.013 4320337.08 4798493.822 4270042.494 3371441.681 4439758.159 4257834.252 3926193.277 4639044.737 0.8096052 0.87251972 0.931298861 1.034371103 0.920457279 0.726753431 0.957041462 0.91782565 0.846336584 1 22.14539633 -2.099183931 2.352842758 1.177636086 0.896226516 0.140042979 0.080213156 21760910.39 6341103.792 20685213.78 0.020936503 0.007958222 2.099183931 -0.28140957 APAPVVLGS(ph)PVVLGPPVGQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 APAPVVLGSPVVLGPPVGQAR 21 0 A0A0C4DFM2;Q6ZN55;Q6ZN55-2 A0A0C4DFM2 ZNF574 Zinc finger protein 574 1 APAPVVLGS(1)PVVLGPPVGQAR;APAPVVLGS(1)PVVLGPPVGQAR;APAPVVLGS(1)PVVLGPPVGQAR 110.26 0.00028988 145962000 87998 82782 75347 87188 79223 76020 87328 93408 83523 102534 TRUE FALSE 84558.94087 80421.13841 88963.87898 91687.78313 81771.27974 77557.17649 88396.74619 91479.09216 74041.8192 95589.28085 0.884606936 0.84131963 0.930688862 0.959184778 0.855444031 0.81135851 0.924755845 0.957001573 0.774582867 1 16.54456123 -2.092238526 2.664886859 1.195975574 0.888735073 0.256721297 0.059222049 6775785.269 4459018.164 8094816.568 0.014382639 0.008086516 2.092238526 -0.307240502 ITPEPAVS(ph)NTEEPSTTSTASNYPDVLTRPSLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 33 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IT(0.019)PEPAVS(0.471)NT(0.471)EEPS(0.005)T(0.016)T(0.016)S(0.002)TASNYPDVLTRPSLHR 128.11 5.11E-08 419770000 0 0 0 0 5931.7 0 0 0 0 6866.7 TRUE FALSE 0 0 0 0 6122.498518 0 0 0 0 6401.612293 0 0 0 0 0.956399456 0 0 0 0 1 12.64421959 -2.082309228 2.339668373 2.392503514 0.106266598 0.469260349 0.285143232 36465729.61 10932764.34 270671901.2 0.07271782 0.008273529 2.082309228 -2.286236916 DFLDEYIFLAVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFLDEYIFLAVGR 13 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ; 192.1 6.99E-06 411060000 360820 337840 327390 351520 375980 318500 359460 331760 413160 460120 FALSE TRUE 346718.7555 328205.134 386556.6558 369661.9893 388073.7382 324940.2882 363859.179 324909.0401 366259.8089 428955.6626 0.808285764 0.765126009 0.901157601 0.861772024 0.904694289 0.757514859 0.848244261 0.757442012 0.853840713 1 18.71046901 -2.078122488 1.679153329 1.235566052 0.825846082 0.48648854 0.052733655 292168.9028 68055.74278 263223.1335 0.014500651 0.008353674 2.078122488 -0.409719969 VFELMTSLHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFELMTSLHTK 11 0 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 192.3 1.45E-06 3990500000 3946300 5162700 4374800 5140500 4278000 4020900 5155800 4741800 5144900 5973200 FALSE TRUE 3792074.233 5015464.851 5165423.677 5405801.821 4415605.755 4102205.353 5218898.223 4643880.173 4560872.521 5568629.844 0.680970784 0.900664076 0.92759329 0.970759769 0.792942946 0.736663321 0.937196109 0.83393587 0.819029573 1 22.40889097 -2.074223022 2.140969178 1.215505599 0.850514562 0.218512415 0.087587988 7791772.279 2188168.607 8197837.966 0.020968454 0.008429018 2.074223022 -0.364991037 YLPDTLLLEECGLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLPDTLLLEECGLLR 15 0 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ; 214.04 1.56E-10 58406000 20155.3 20904.9 19305.2 18363.9 20630.7 14618.9 21867 21639.1 21178.1 24479 FALSE TRUE 19367.60859 20308.71272 22794.07908 19311.66308 21294.3052 14914.50417 22134.61489 21192.24502 18774.05087 22821.01553 0.848674266 0.889912752 0.998819665 0.846222775 0.933100684 0.653542528 0.969922432 0.928628483 0.822665006 1 14.47807537 -2.071022049 2.919084493 1.189276869 0.882569973 0.136655194 0.091861478 10563770.15 19741866.07 14050454.69 0.020834215 0.008491374 2.071022049 -0.306706896 ITPSYVAFTPEGER ddPTM_BT-474_Pertuzumab_2h_R1 4 ITPSYVAFTPEGER 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 194.43 3.35E-07 1037350000 414343 414746 320020 451100 337924 340658 406203 419413 417034 488523 FALSE TRUE 398150.0175 402917.8502 377854.7328 474381.3251 348793.6324 347546.3382 411174.2338 410751.975 369694.0487 455434.9021 0.874219379 0.884688126 0.829656952 1.041600727 0.765847393 0.763108705 0.902816697 0.901889541 0.81173851 1 18.79688533 -2.070597902 5.350408075 1.316813082 0.867237469 0.219646323 0.076705699 0.060032304 0.000792118 0.015380815 0.017147479 0.008499671 2.070597902 -0.449575613 LDDPSCPRPECYR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDDPSCPRPECYR 13 1 P41091;H7BZU1 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ;;; 143.86 3.56E-05 5592340000 5472500 5333200 5046300 5686600 5337200 4822800 5656200 5703800 6007600 6706200 FALSE TRUE 5258628.65 5181102.358 5958278.664 5980086.107 5508875.885 4920320.32 5725422.268 5586014.537 5325642.434 6251983.101 0.841113702 0.82871343 0.953022196 0.95651028 0.881140559 0.787001539 0.91577699 0.893478829 0.851832506 1 22.57588245 -2.070468388 2.102191386 1.166411308 0.881653345 0.333510877 0.051279579 4722236.296 1357955.192 3767594.848 0.01335884 0.008502206 2.070468388 -0.284757963 S(ph)SPQLDPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.722)S(0.278)PQLDPLR;S(0.69)S(0.31)PQLDPLR;S(0.721)S(0.279)PQLDPLR;S(0.732)S(0.268)PQLDPLR 128.81 0.0004268 5335610000 2995470 3034450 3173270 3345760 3035660 1880910 3472280 3323540 3413740 3860440 TRUE FALSE 2878403.721 2947910.457 3746750.478 3518435.075 3133304.761 1918943.289 3514774.801 3254907.738 3026226.547 3598968.96 0.799785648 0.819098606 1.041062182 0.977623067 0.870611777 0.533192509 0.976606034 0.904400058 0.840859307 1 21.77915223 -2.064219664 4.413698514 1.253033009 0.868255969 0.087142924 0.132286644 0.129889654 0.001889905 0.050510196 0.030671745 0.008625422 2.064219664 -0.38477704 EIRPVCR ddPTM_BT-474_Pertuzumab_2h_R1 6 EIRPVCR 7 1 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;;;; 156.4 0.00141 6641460000 2643450 2790720 2500030 2975240 2669970 2458230 2900330 2815210 3000100 3154270 FALSE TRUE 2540141.052 2711131.398 2951841.034 3128792.493 2755852.01 2507937.095 2935825.106 2757074.93 2659541.225 2940628.483 0.863808899 0.92195645 1.003812978 1.063987685 0.937164292 0.852857513 0.998366547 0.937580162 0.904412523 1 21.4876931 -2.050037789 0.003679602 1.907185772 0.028823914 0.03393638 0.0627446 352453.3328 177.8751604 46805.67365 44028.78351 0.008911734 2.050037789 -1.878361858 YEYHWADGTNIK ddPTM_BT-474_Pertuzumab_2h_R1 4 YEYHWADGTNIK 12 0 Q9H8S9;Q7L9L4;Q7L9L4-2;D6RCK3;Q9H8S9-2 Q9H8S9 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 0 ;;; 251.03 1.70E-17 2438240000 2652790 2596410 2517720 2381990 2463900 2314620 2721380 2472880 3106780 3140610 FALSE TRUE 2549116.034 2522362.929 2972728.01 2504924.789 2543153.581 2361423.202 2754685.062 2421814.164 2754111.359 2927893.687 0.87063135 0.861494029 1.015312825 0.855538164 0.868594919 0.806526279 0.940841901 0.827152357 0.940645957 1 21.48143174 -2.049865458 6.207557922 1.235299297 0.884633981 0.246738704 0.058833605 0.045590987 0.000366233 0.013555699 0.012783124 0.008915271 2.049865458 -0.350665316 QS(ph)PALQHRPMGQSQANHIPGDR ddPTM_BT-474_Pertuzumab_2h_R1 4 QSPALQHRPMGQSQANHIPGDR 22 1 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 QS(1)PALQHRPMGQSQANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR 217.48 7.60E-26 1434180000 408720 514340 476976 570040 517850 602660 623580 371493 559750 618980 TRUE FALSE 392746.7705 499671.5268 563176.1735 599459.8327 534507.1155 614846.1981 631211.5586 363821.5397 496209.5267 577055.9333 0.680604336 0.86589791 0.975947289 1.038824485 0.926265696 1.065488045 1.093848139 0.630478813 0.859898492 1 19.13835164 -2.034646976 8.110742901 1.185624485 0.902809786 0.037122525 0.146322393 0.117955035 0.000503873 0.034025533 0.035456568 0.009233217 2.034646976 -0.282814699 QLFHPEQLITGK ddPTM_BT-474_Pertuzumab_2h_R1 4 QLFHPEQLITGK 12 0 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;; 156.81 6.76E-05 30862360000 15764640 15909120 13787670 14938510 14324800 15359510 16124800 16194730 18017120 18748810 FALSE TRUE 15148540.44 15455407.47 16279408.67 15709488.29 14785570.2 15670089.82 16322140.13 15860303.17 15971892.07 17478936.4 0.866674041 0.884230432 0.931372957 0.898766832 0.84590789 0.896512777 0.933817697 0.90739521 0.913779403 1 24.05911406 -2.019636154 0.233652738 1.120791779 0.880304765 0.655766029 0.023509501 20.75222814 0.71660486 1.393587611 0.045836524 0.00955793 2.019636154 -0.240487013 LDMEIER ddPTM_BT-474_Pertuzumab_2h_R1 2 LDMEIER 7 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 143 0.005702 357250000 476140 568170 488040 506510 502170 396420 563630 524530 592380 618670 FALSE TRUE 457531.9224 551966.3479 576239.6844 532651.0418 518322.7541 404435.884 570527.8725 513698.2722 525135.5059 576766.9298 0.793270035 0.957000687 0.99908586 0.923511759 0.898669336 0.701211985 0.989182706 0.890651398 0.910481303 1 19.13762892 -2.017931039 4.103952834 1.119152972 0.899418816 0.11718345 0.085229418 0.088433897 0.000386387 0.078540894 0.019061926 0.00959553 2.017931039 -0.219734155 SGT(ph)PPRQGSIT(ph)SPQANEQS(ph)VTPQRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGTPPRQGSITSPQANEQSVTPQRR 25 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.45)GT(0.547)PPRQGS(0.101)IT(0.451)S(0.451)PQANEQS(0.596)VT(0.404)PQRR 86.081 0.092664 520750000 110020 111970 66094 60654 86002 104650 73565 102150 100810 62561 TRUE FALSE 105720.2968 108776.7252 78038.65605 63784.36021 88768.33244 106766.0947 74465.31048 100040.5668 89366.47143 58323.68775 1.812647671 1.865052253 1.338026779 1.093627009 1.521994508 1.830578601 1.276759295 1.715264769 1.532250015 1 15.83179432 -2.016946558 2.313055833 0.397651287 1.550310638 0.314008283 0.245606535 8681573.86 3197332.569 27775371.2 0.063856341 0.009617306 2.016946558 1.152659351 (ac)ATEGDVELELETETSGPERPPEKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATEGDVELELETETSGPERPPEKPR 25 2 J3QT56 J3QT56 HYPK 0 56.303 0.072249 86079000 54559 53246 43720 48155 50765 53878 51935 54610 61014 63202 FALSE TRUE 52426.77396 51727.47621 51621.17655 50640.28532 52397.90233 54967.45007 52570.59607 53482.28442 54087.94651 58921.27225 0.889776679 0.877908338 0.876104242 0.859456753 0.889286676 0.932896524 0.892217599 0.907690591 0.917969766 1 15.84650096 -2.013235828 0.198700765 1.135042914 0.865121871 0.832505464 0.015454329 13.41540795 0.390758304 0.876381347 0.045271652 0.009699831 2.013235828 -0.269921043 DTPLEHHLYVVSYEAAGEIVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTPLEHHLYVVSYEAAGEIVR 21 0 Q86TI2;Q86TI2-4;Q86TI2-2;M0R1L4 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 150.29 4.21E-08 100130000 21597 20963 20451 25559 30370 22691 25694 15909 31304 24125 FALSE TRUE 20752.96536 20365.15576 24146.95063 26878.10305 31346.87863 23149.82757 26008.45086 15580.47359 27750.50116 22490.99226 0.922723423 0.905480538 1.073627626 1.195060793 1.393752586 1.029293297 1.156394105 0.692742828 1.233849571 1 14.45705969 -2.01082208 7.352052128 0.937530318 1.052012149 0.005746152 0.186937099 0.211821436 0.000311797 0.200297883 0.045065976 0.009753892 2.01082208 0.114481831 EALAPNSLS(ph)PSPQGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EALAPNSLSPSPQGHR 16 0 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 EALAPNS(0.001)LS(0.987)PS(0.012)PQGHR 101.48 0.001096 223710000 28102 51332 39263 53972 55273 56355 45802 38891 45335 55293 TRUE FALSE 27003.74277 49868.06162 46358.6975 56757.50139 57050.90624 57494.53671 46362.53858 38087.88726 40188.76086 51547.95586 0.523856714 0.967411041 0.899331442 1.101062117 1.106753998 1.115360168 0.899405957 0.738882592 0.779638304 1 15.6536276 -2.006276582 8.197297101 1.100652241 0.910592811 0.024444589 0.177866805 0.159202574 0.0001219 0.08379928 0.042497394 0.009856516 2.006276582 -0.19005943 NVFYELEDVR ddPTM_BT-474_Pertuzumab_2h_R1 3 NVFYELEDVR 10 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 ;; 150.61 4.95E-05 318927000 477790 518520 438750 504330 454530 396410 467350 514530 538480 624110 FALSE TRUE 459117.4386 503732.3173 518041.8849 530358.5317 469150.3702 404425.6818 473069.5691 503904.7757 477354.0079 581838.4738 0.789080577 0.865759725 0.890353437 0.911521935 0.806324077 0.695082398 0.813059965 0.866056128 0.820423587 1 19.15025917 -2.003548337 6.861025257 1.178428146 0.831298815 0.438735418 0.058078204 0.039431918 2.04E-05 0.01398878 0.014230632 0.009918629 2.003548337 -0.347129331 STVDGLQVTQLNVDHTTENEDELFR ddPTM_BT-474_Pertuzumab_2h_R1 2 STVDGLQVTQLNVDHTTENEDELFR 25 0 Q15750;Q15750-2 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 0 ; 259.44 5.31E-45 467730000 83222 82243 79791 106956 89343 89958 91091 79702 101653 103004 FALSE TRUE 79969.59223 79897.51016 94211.00864 112476.012 92216.79873 91777.0124 92205.79891 78056.12585 90113.7776 96027.44733 0.832778486 0.832027846 0.981084172 1.171290241 0.960317089 0.955737291 0.960202541 0.812852242 0.938416881 1 16.55115921 -1.995358905 8.709425514 1.058033414 0.936305873 0.034254013 0.097767582 0.097627005 5.20E-05 0.083885448 0.024206265 0.010107438 1.995358905 -0.121727541 QALDYVELSPLTQAS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QALDYVELSPLTQASPQR 18 0 Q9H2D6-3;Q9H2D6-2;Q9H2D6;Q9H2D6-5;Q9H2D6-7;F6WYE2;F6TR96;H0Y5J9;Q9H2D6-6 Q9H2D6-3 TRIOBP TRIO and F-actin-binding protein 1 QALDYVELSPLTQAS(1)PQR;QALDYVELSPLTQAS(1)PQR 356.36 1.33E-90 853320000 597540 598230 560790 570820 540800 543960 609970 651070 609930 743500 TRUE FALSE 574187.4762 581169.0661 662137.2277 600280.0886 558195.3231 554959.2439 617434.9953 637625.177 540693.3034 693142.0828 0.828383517 0.838455896 0.95526912 0.866027476 0.805311547 0.800642837 0.890776957 0.919905446 0.780061285 1 19.40279159 -1.995055576 2.361164023 1.136344426 0.859892726 0.402843088 0.052919505 13438289.57 5926820.684 9972381.825 0.013140427 0.0101145 1.995055576 -0.2764517 NDS(ph)GEENVPLDLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 NDSGEENVPLDLTR 14 0 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 NDS(1)GEENVPLDLTR 189.59 7.35E-07 306960000 145480 141370 127170 145980 142170 126860 144770 156580 157440 143970 TRUE FALSE 139794.4808 137338.266 150152.4479 153514.0453 146743.0272 129425.1961 146541.7386 153346.5683 139568.0712 134218.7837 1.041541854 1.023241772 1.118714116 1.143759771 1.093312152 0.964285271 1.091812447 1.14251198 1.039854985 1 17.03422706 -1.994110838 3.578418849 0.925524795 1.078178187 0.135830617 0.054127966 0.048096829 7.92E-05 0.078378667 0.012938516 0.010136527 1.994110838 0.152653392 VLSEDEEDVDFDIIHNANDTFTVK ddPTM_BT-474_Pertuzumab_2h_R1 4 VLSEDEEDVDFDIIHNANDTFTVK 24 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ;;; 383.87 3.78E-137 1008650000 754850 712240 654760 655070 644170 747030 712380 656650 896260 874430 FALSE TRUE 725349.6275 691927.6126 773089.6971 688878.2412 664890.3131 762135.4584 721098.3195 643089.948 794520.3222 815204.0772 0.889776741 0.8487784 0.94833885 0.845037777 0.815612105 0.934901431 0.884561719 0.788869887 0.974627513 1 19.63680174 -1.993276431 4.39044785 1.117221956 0.874533309 0.279209792 0.056379589 0.050391315 7.72E-05 0.042522835 0.012378326 0.010156021 1.993276431 -0.242688647 ELPSQASGGLANPPPVNLEDS(ph)LDEDLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELPSQASGGLANPPPVNLEDSLDEDLIR 28 0 Q9NPG3;Q9NPG3-2;K7EJT1 Q9NPG3 UBN1 Ubinuclein-1 1 ELPSQASGGLANPPPVNLEDS(1)LDEDLIR;ELPSQASGGLANPPPVNLEDS(1)LDEDLIR 122.68 2.93E-05 64515000 33419 33892 38618 44532 40277 40007 37679 38847 45553 60994 TRUE FALSE 32112.94853 32925.43334 45597.13165 46830.30186 41572.54628 40815.96895 38140.12687 38044.79587 40382.01441 56862.82205 0.564744193 0.579032699 0.801879506 0.823566263 0.731102411 0.717797103 0.670739255 0.669062746 0.710165499 1 15.79519808 -1.992535056 1.90290608 1.292048401 0.698233581 0.573332506 0.078543838 918865.3015 294043.9267 1177307.392 0.022804762 0.010173372 1.992535056 -0.59381482 DEDLFR ddPTM_BT-474_Pertuzumab_2h_R1 5 DEDLFR 6 0 O75531;A0A0C4DFW4;Q5JUR7 O75531;A0A0C4DFW4 BANF1;TEX30 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed;Testis-expressed sequence 30 protein" 0 ;;;; 149.06 0.024861 3980390000 4913010 5464160 4108840 4916920 4871850 4797530 4884570 5225520 5506820 5701680 FALSE TRUE 4721004.138 5308327.507 4851398.789 5170682.83 5028557.48 4894539.344 4944348.829 5117611.186 4881708.88 5315500.135 0.888158032 0.99865062 0.912689054 0.972755658 0.94601775 0.920805045 0.930175657 0.96277134 0.918391263 1 22.34177401 -1.988858803 5.485596054 1.05057076 0.941787589 0.256895085 0.030815555 0.022591796 4.59E-05 0.035368103 0.006243759 0.010259854 1.988858803 -0.10878317 EDFATFDYILCMDESNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EDFATFDYILCMDESNLR 18 0 P24666;P24666-3;P24666-2 P24666;P24666-2 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ;;; 257.02 3.04E-30 189248000 189852 195384 153713 198915 193220 190903 183256 199972 210094 222460 FALSE TRUE 182432.3739 189811.8396 181492.3584 209181.027 199435.0968 194763.1895 185498.7417 195842.5083 186245.0099 207392.5861 0.87964752 0.915229629 0.875114978 1.008623456 0.961630792 0.939103915 0.89443285 0.944308145 0.898031185 1 17.6620048 -1.986297474 0.00822919 1.946030797 9.57E-07 0.213496153 0.040052564 19385.60239 22.31479555 2820.036162 2465.964213 0.010320542 1.986297474 -1.94602984 KKEIQNGNLHES(ph)DSESVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKEIQNGNLHESDSESVPR 19 2 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 KKEIQNGNLHES(0.963)DS(0.035)ES(0.002)VPR;KKEIQNGNLHES(1)DSESVPR 288.95 5.70E-42 466360000 317820 496420 172593 300880 227230 296070 284870 375040 333900 201696 TRUE FALSE 305399.243 482262.5876 203784.3944 316408.4529 234539.0593 302056.7383 288356.3243 367295.2929 295997.0718 188034.9503 1.624162118 2.564749728 1.083758068 1.68271086 1.247316305 1.606386142 1.533525144 1.953335231 1.574159864 1 17.52064132 -1.97578408 1.943617549 0.402404709 1.66607954 0.209725157 0.378972493 2187293.981 741671.5044 5874871.435 0.096093333 0.010573431 1.97578408 1.263674831 LPEEWSQWLGGSSWPGYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPEEWSQWLGGSSWPGYVR 19 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 291.51 3.46E-49 683420000 47586 51054 50587 50715 42621 46466 51256 51016 56873 64952 FALSE TRUE 45726.28651 49597.98991 59729.1962 53332.40723 43991.94317 47405.57436 51883.28626 49962.50177 50417.01547 60552.74319 0.755148059 0.819087415 0.98639951 0.880759556 0.726506197 0.782880706 0.856828007 0.825107157 0.832613236 1 15.8859047 -1.97176502 3.525282227 1.13386288 0.831656467 0.359830877 0.068177056 0.06180833 0.00049504 0.056882313 0.016199088 0.010671734 1.97176502 -0.302206413 SS(ph)PPLPPPAEER ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.05)S(0.95)PPLPPPAEER;S(0.058)S(0.942)PPLPPPAEER 141.37 6.34E-05 695590000 373080 356880 254264 305956 313713 347940 304241 311920 348590 296238 TRUE FALSE 358499.6211 346702.1318 300215.1609 321746.4258 323803.8636 354975.5852 307964.3924 305478.743 309019.5246 276173.5364 1.298095487 1.255377819 1.0870526 1.16501541 1.172465211 1.285335264 1.115111884 1.106111567 1.118932424 1 18.07521556 -1.969700745 0.029376227 1.76E-09 2.015267848 0.545251017 0.060909335 656.8642342 2.715625329 117.3311894 72.93826169 0.010722579 1.969700745 2.015267846 EIAQEFKTDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIAQEFKTDLR 11 1 Q5TEC6;A0A590UJL8 Q5TEC6 HIST2H3PS2 Histone H3 0 67.385 0.054828 143390000 422960 341660 274010 440230 232470 227890 413500 336970 452090 186950 FALSE TRUE 406430.2556 331916.1913 323529.7023 462950.3231 239947.6087 232498.0919 418560.5367 330011.4517 400770.6385 174287.71 2.331950174 1.904415356 1.856296708 2.65624193 1.37673281 1.33399017 2.40154935 1.893486648 2.299477333 1 17.41111131 -1.963305337 2.7319466 0.214428234 1.989614974 0.352727626 0.40829295 5254665.9 5605866.488 26233370.42 0.096420902 0.010881648 1.963305337 1.77518674 ESTLHLVLR ddPTM_BT-474_Pertuzumab_2h_R1 5 ESTLHLVLR 9 0 M0R2S1;P62987;P0CG48;Q96C32;Q5PY61;J3QKN0;F5GXK7;F5H747;F5H388;B4DV12;F5H265;F5H2Z3;F5GYU3;F5H6Q2;M0R1M6;J3QTR3;J3QS39;P0CG47;P62979;A0A2R8Y422 M0R2S1;P62979 UBA52;UBC;UBB;RPS27A Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40;Polyubiquitin-C;Ubiquitin;Polyubiquitin-B;Ubiquitin;Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;;; 193.1 3.40E-05 3285430000 2603290 3196360 2562380 3455400 2772840 2578090 3130610 2879440 3304600 3748980 FALSE TRUE 2501550.549 3105202.942 3025459.066 3633733.608 2862030.917 2630220.746 3168923.342 2819978.558 2929475.662 3495058.245 0.715739302 0.888455277 0.865639098 1.039677554 0.818879319 0.752554196 0.906686847 0.806847371 0.838176493 1 21.73688507 -1.963075566 2.151338105 1.123924076 0.851120007 0.224534476 0.084531989 6454979.964 2567031.353 3990799.185 0.021506792 0.010887406 1.963075566 -0.272804069 ILAAALTECHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILAAALTECHR 11 0 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 0 152.54 3.29E-05 509820000 194710 217810 171110 196620 197870 116610 221820 195070 218100 247040 FALSE TRUE 187100.5179 211598.2721 202033.3833 206767.5818 204234.6683 118967.9341 224534.6995 191041.7363 193342.2023 230307.7608 0.812393457 0.918763099 0.877232199 0.897788164 0.886790213 0.516560683 0.974933275 0.829506291 0.839494951 1 17.8132035 -1.957010489 8.192472335 1.070447034 0.841491305 0.144983047 0.116983182 0.075872903 0.000398138 0.057094367 0.025702587 0.01104052 1.957010489 -0.228955729 ESAAHDYTLR ddPTM_BT-474_Pertuzumab_2h_R1 3 ESAAHDYTLR 10 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ;; 162.36 6.79E-06 2005070000 1053490 1164610 1018640 1344170 1241900 1341850 1239340 1139960 1204600 1292620 FALSE TRUE 1012318.446 1131396.463 1202730.908 1413542.775 1281846.841 1368983.126 1254507.414 1116419.428 1067858.858 1205069.696 0.840049708 0.938863924 0.998059209 1.172996698 1.063711788 1.136019876 1.041024779 0.926435567 0.88613867 1 20.20068516 -1.946350841 5.138948629 0.997096939 1.005477173 0 0.10104798 0.005519959 5.76E-05 0.160690296 0.024701483 0.011314859 1.946350841 0.008380235 DTDSEEEIREAFRVFDKDGNGYISAAELR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTDSEEEIREAFRVFDKDGNGYISAAELR 29 3 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;; 260.46 1.79E-58 1149090000 443438.2 569816 596485 182518.1 451988 536978 437432.4 443486 424697 300347 FALSE TRUE 426108.1449 553565.4056 704283.1082 191937.881 466526.6045 547836.0631 442785.8286 434327.8591 376487.177 280004.2302 1.521791812 1.976989438 2.515258815 0.685482076 1.666141273 1.956527809 1.581354068 1.551147491 1.344576747 1 18.0950891 -1.945247032 0.137577036 2.55E-12 2.022870975 0.206752638 0.434294117 77.60078283 1.566561143 28.31709503 3.492461945 0.011343654 1.945247032 2.022870975 SRT(ph)ASGS(ph)SVTSLDGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 S(0.001)RT(0.998)AS(0.004)GS(0.604)S(0.344)VT(0.044)S(0.005)LDGTR 252.64 3.90E-25 1201100000 1058700 1081900 645180 823290 981200 855060 736560 954160 844060 678900 TRUE FALSE 1017324.834 1051045.271 761778.378 865780.0956 1012761.189 872349.899 745574.2416 934456.2626 748245.8474 632917.4983 1.60735773 1.660635508 1.203598226 1.367919354 1.600147242 1.378299544 1.177995937 1.476426651 1.182217034 1 19.27165793 -1.939430467 0.069147766 1.54E-11 2.058684512 0.527372836 0.144482917 128.8145122 1.275782003 31.58049399 10.58192925 0.011496603 1.939430467 2.058684512 ESENVVCHFYR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESENVVCHFYR 11 0 F8WCJ3;B8ZZX4;O14530-2;O14530 F8WCJ3 TXNDC9 Thioredoxin domain-containing protein 9 0 ; 115.14 0.0011637 695930000 619340 687220 577720 639560 578610 502850 693480 649650 697320 761890 FALSE TRUE 595135.5081 667621.1585 682126.8553 672567.7682 597221.5161 513017.9715 701967.0157 636234.5005 618163.157 710286.5117 0.837880909 0.939932193 0.960354511 0.946896439 0.840817763 0.722269061 0.988287127 0.895743464 0.870301135 1 19.43804156 -1.937273745 3.720078973 1.062660468 0.892764087 0.168091077 0.073580471 0.047822719 0.000806365 0.089098989 0.017011026 0.011553838 1.937273745 -0.169896381 IHNANPELTDGQIQAMLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IHNANPELTDGQIQAMLR 18 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 259.14 1.10E-30 762230000 165770 175200 161430 192950 177140 203930 203380 130570 212280 212040 FALSE TRUE 159291.5251 170203.4675 190603.992 202908.1726 182837.869 208053.6043 205869.0253 127873.6839 188182.8644 197678.3419 0.805811722 0.861012217 0.964212822 1.026456265 0.924926156 1.05248558 1.041434399 0.646877562 0.951965008 1 17.59279529 -1.919600709 10.03570305 1.013719783 0.912055104 0.037213948 0.117574827 0.040763277 0.000326568 0.12857551 0.028836373 0.012033703 1.919600709 -0.101664679 RKPYHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKPYHK 6 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 87.839 0.029238 268680000 192170 203870 120400 183060 153440 156680 178680 164860 212200 224600 FALSE TRUE 184659.7839 198055.8272 142158.9583 192507.7485 158375.537 159848.1769 180866.7393 161455.5834 188111.9456 209387.6419 0.881903928 0.945881167 0.678927166 0.919384481 0.756374805 0.763407885 0.863788988 0.771084587 0.898390869 1 17.67581677 -1.918533215 4.111020316 1.080614529 0.825688947 0.277262302 0.081441001 0.051884365 0.001028176 0.067992005 0.017293605 0.012063318 1.918533215 -0.254925582 EEEITLYPDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEITLYPDK 10 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 110.53 0.0043582 48375000 156000 163430 134080 144400 133560 118850 123530 164250 166670 195560 FALSE TRUE 149903.3475 158769.1364 158311.2386 151852.5013 137856.0787 121253.2284 125041.7971 160858.1801 147750.3203 182314.547 0.822223734 0.870852815 0.868341233 0.832914892 0.756144153 0.66507709 0.685857487 0.882311273 0.810414324 1 17.47607015 -1.912243046 9.181906323 1.031234301 0.800286267 0.413839892 0.071632163 0.040728467 0.000389266 0.061676202 0.018044446 0.012239311 1.912243046 -0.230948035 KGNEQHAFTR ddPTM_BT-474_Pertuzumab_2h_R1 3 KGNEQHAFTR 10 1 Q13045-3;Q13045;Q13045-2;K7EQZ7 Q13045-3 FLII Protein flightless-1 homolog 0 ;; 124.1 0.0002885 323561000 681620 751120 586220 649740 642010 623650 732450 656910 777030 843100 FALSE TRUE 654981.5368 729698.793 692162.9944 683273.1593 662660.8347 636260.6303 741413.9422 643344.5789 688824.812 785996.086 0.833313993 0.928374589 0.880618882 0.869308603 0.843084141 0.809495927 0.943279433 0.818508629 0.876371809 1 19.5841626 -1.91110376 5.251035757 1.045521773 0.866642802 0.480506262 0.041508507 0.021551513 0.000364851 0.039155964 0.008949382 0.01227146 1.91110376 -0.178878971 TQTPPVS(ph)PAPQPTEER ddPTM_BT-474_Pertuzumab_2h_R1 2 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVS(1)PAPQPTEER;TQTPPVS(1)PAPQPTEER 322.43 3.18E-58 849860000 246050 315170 285190 439750 372630 372640 366720 303900 324550 357030 TRUE FALSE 236434.094 306181.6602 336730.177 462445.5502 384615.9824 380175.0361 371208.0291 297624.3588 287708.4446 332848.0401 0.710336446 0.919884221 1.011663391 1.389359391 1.15553026 1.142187997 1.115247754 0.894174887 0.864383773 1 18.34450415 -1.906732369 2.814458463 0.982770974 1.031534402 0 0.180416616 0.031773505 0.001052933 0.284562075 0.043763092 0.012395602 1.906732369 0.048763428 FDYDWER ddPTM_BT-474_Pertuzumab_2h_R1 2 FDYDWER 7 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ; 84.227 0.050484 242790000 507460 661340 513680 597740 614130 525500 621880 581380 659680 758790 FALSE TRUE 487627.9022 642479.2307 606513.4027 628589.433 633884.0492 536125.97 629490.7535 569374.2998 584795.892 707396.4774 0.68932758 0.908230746 0.857388215 0.888595651 0.896080302 0.757886118 0.889869788 0.804887101 0.826687594 1 19.43215951 -1.905743111 2.545758898 1.09249426 0.839223965 0.356564583 0.066142297 24127167.83 12981185.96 13344356.45 0.015594425 0.01242387 1.905743111 -0.253270295 EEPVSS(ph)GPEEAVGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EEPVS(0.001)S(0.999)GPEEAVGK;EEPVS(0.001)S(0.999)GPEEAVGK;EEPVS(0.013)S(0.987)GPEEAVGK;EEPVS(0.014)S(0.986)GPEEAVGK 298.78 1.01E-43 2314530000 3909790 3495590 2948610 3120740 3196450 2989390 3337510 3992780 3697050 3227350 TRUE FALSE 3756991.084 3395899.196 3481489.418 3281801.765 3299266.717 3049837.514 3378355.446 3910327.698 3277376.383 3008758.71 1.248684739 1.128671164 1.157118185 1.090749403 1.096554106 1.013653074 1.122840271 1.299648152 1.089278569 1 21.52073698 -1.853640354 1.902596888 0.924499076 1.143381179 0.218554722 0.078137392 1010044.794 429566.5645 345047.2984 0.022364037 0.014007468 1.853640354 0.218882102 GPGQPSS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPGQPSSPQR 10 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GPGQPS(0.006)S(0.994)PQR;GPGQPS(0.002)S(0.998)PQR 115.04 0.0013385 266640000 431760 447760 416440 533100 455390 323180 528990 460480 480970 558580 TRUE FALSE 414886.3419 434990.3232 491699.9717 560613.3549 470038.0329 329714.921 535463.9379 450970.9271 426372.302 520746.8791 0.796714025 0.835320077 0.944220679 1.076556341 0.902622852 0.633157748 1.028261444 0.866007931 0.818770729 1 18.99022276 -1.850335858 2.408782126 1.05080515 0.883449587 0.086160617 0.118023097 22497244.06 12760805.65 6563494.558 0.029895386 0.014114456 1.850335858 -0.167355563 FGAVWTGDNTAEWDHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 FGAVWTGDNTAEWDHLK 17 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 269.91 1.22E-28 3966272000 2226406 2305496 2232562 2234460 2414606 2218477 2607328 2179734 2961760 2848000 FALSE TRUE 2139395.592 2239745.511 2636035.616 2349780.748 2492273.995 2263336.125 2639237.26 2134721.731 2625553.422 2655102.423 0.805767632 0.843562754 0.992818806 0.885005689 0.938673391 0.852447764 0.994024651 0.8040073 0.988870862 1 21.34033608 -1.847867329 0.013976531 1.947537771 4.02E-06 0.2278859 0.067784711 6202.520585 12.60875825 978.5814592 786.1486803 0.014194911 1.847867329 -1.947533748 GFDILGIKPVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFDILGIKPVQR 12 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 176.78 2.20E-05 927000000 2002660 2039420 1778890 1896220 1981290 1860750 2026360 2088980 2204680 2286430 FALSE TRUE 1924393.833 1981257.738 2100374.994 1994084.141 2045019.992 1898375.64 2051159.2 2045841.833 1954413.969 2131568.06 0.902806657 0.929483687 0.985366142 0.935501042 0.959396996 0.890600528 0.962277132 0.959782552 0.916890249 1 21.02348369 -1.844647797 2.771605583 1.021944551 0.940820429 0.301542887 0.028010566 10239734.14 9244466.107 1503224.336 0.006803417 0.014300532 1.844647797 -0.081124122 EFESWLER ddPTM_BT-474_Pertuzumab_2h_R1 2 EFESWLER 8 0 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5;E9PNZ4 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 ; 111.17 0.0076435 108908000 84896 85921 77543 101695 71590 73579 94504 92267 89922 117071 FALSE TRUE 81578.17046 83470.61721 91556.74503 106943.4911 73892.75737 75066.81779 95660.56822 90361.65421 79714.43154 109141.6769 0.747452053 0.764791412 0.838879772 0.979859337 0.677035203 0.687792417 0.876480653 0.827929869 0.730375726 1 16.73584259 -1.829551687 2.621284072 1.072200173 0.797908142 0.334177514 0.087634901 12700238.7 9094300.013 5791983.24 0.022239138 0.01480636 1.829551687 -0.274292031 KTQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 33 2 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 KTQQLHPVLQKPS(0.013)VFGNDS(0.672)DDDDET(0.156)S(0.156)VS(0.003)ESLQR 73.17 0.0014749 735270000 276690 283820 191130 194560 272440 286650 191930 268500 299760 238280 TRUE FALSE 265876.6489 275725.7315 225671.4427 204601.2649 281203.28 292446.2594 194278.8968 262955.3812 265732.5015 222141.0834 1.196881931 1.241218992 1.01589242 0.921041987 1.265876963 1.31648885 0.874574364 1.183731425 1.196233031 1 17.76111671 -1.821055558 2.255539438 0.948845884 1.129653592 0.074715806 0.14117853 14587330.02 8252904.341 4051240.91 0.036964108 0.01509887 1.821055558 0.180807709 ALADENEFVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALADENEFVR 10 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 86.898 0.030812 243530000 91643 126740 110310 157640 135010 142290 137790 109000 120740 159060 FALSE TRUE 88061.49024 123125.4993 130245.4708 165775.8193 139352.7193 145167.2013 139476.3152 106749.1119 107034.1014 148286.7245 0.593859569 0.830320446 0.878335342 1.117941069 0.93975182 0.978962896 0.940585313 0.719883134 0.721805015 1 17.17802992 -1.81778014 7.855578535 1.005019429 0.864450866 0.079937804 0.143060113 0.013656171 0.000316772 0.150411359 0.034467101 0.015213175 1.81778014 -0.140568563 VDS(ph)EGDFS(ph)ENDDAAGDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDSEGDFSENDDAAGDFR 18 0 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 2 VDS(1)EGDFS(1)ENDDAAGDFR;VDS(1)EGDFS(1)ENDDAAGDFR 319.18 2.56E-61 992790000 782230 677610 627820 670030 659410 557350 609760 788390 806520 744550 TRUE FALSE 751659.5868 658285.2262 741281.0398 704610.3286 680620.5215 568619.9989 617222.4253 772109.471 714967.2308 694120.9653 1.082894228 0.948372487 1.067942155 1.015111722 0.980550301 0.819194387 0.889214497 1.112355785 1.030032612 1 19.40482758 -1.815723459 8.16842133 1.000188424 0.993969077 0.000449584 0.085394103 0.000318873 7.19E-06 0.089976266 0.02056483 0.015285391 1.815723459 -0.006219346 EGHDAFELK ddPTM_BT-474_Pertuzumab_2h_R1 5 EGHDAFELK 9 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 0 ;;;; 128.86 0.00040557 654506000 1369892 1427122 1214567 1413895 1388642 1281670 1494025 1311719 1613420 1673040 FALSE TRUE 1316355.106 1386421.878 1434066.275 1486866.29 1433308.931 1307586.246 1512309.325 1284631.544 1430271.326 1559723.511 0.843966958 0.888889517 0.919436211 0.953288375 0.918950648 0.838344897 0.969600903 0.823627736 0.91700312 1 20.57285888 -1.795347539 1.934545228 1.041840936 0.895880656 0.306840773 0.046409384 687869.5019 330273.0358 134716.862 0.0118916 0.016019629 1.795347539 -0.145960281 AGEPNS(ph)PDAEEANSPDVTAGCDPAGVHPPR ddPTM_BT-474_Pertuzumab_2h_R1 7 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR 258.32 2.12E-58 9925570000 556283 610707 503514 567514 560545 582106 579457 571550 603168 740658 TRUE FALSE 534542.8454 593290.2343 594510.1804 596803.4656 578575.439 593876.5822 586548.5681 559747.2928 534698.8973 690492.574 0.774147131 0.859227538 0.860994315 0.864315545 0.837916961 0.860076711 0.849463977 0.810649258 0.774373132 1 19.39726637 -1.789877117 2.910924481 1.040368988 0.83491233 0.697666421 0.033069886 15950641.42 16669523 4636003.363 0.008052338 0.016222691 1.789877117 -0.205456658 VAPVINNGS(ph)PTILGK ddPTM_BT-474_Pertuzumab_2h_R1 4 VAPVINNGSPTILGK 15 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 VAPVINNGS(0.98)PT(0.02)ILGK;VAPVINNGS(0.988)PT(0.012)ILGK;VAPVINNGS(0.98)PT(0.02)ILGK;VAPVINNGS(0.984)PT(0.016)ILGK 252.38 1.27E-24 4251710000 3807390 3817820 2983890 3141290 2963610 3088720 3587220 3759870 3529180 4082780 TRUE FALSE 3658592.99 3708939.512 3523145.299 3303412.353 3058937.207 3151176.035 3631121.471 3682227.371 3128562.282 3806249.674 0.961206779 0.974434109 0.925621176 0.867891661 0.803661732 0.827895252 0.953989302 0.967416141 0.821954036 1 21.85993877 -1.776255956 7.347556979 1.00216834 0.904478856 0.183064795 0.062569392 0.00246402 7.50E-05 0.067167338 0.015500733 0.01673956 1.776255956 -0.097689484 TVDS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVDSPK 6 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 TVDS(1)PK;TVDS(1)PK 133.68 0.015063 1287710000 4514400 3575800 3005000 2975200 3295300 3413500 3911400 3974700 3603400 4247400 TRUE FALSE 4337972.257 3473821.685 3548070.346 3128750.429 3401296.317 3482523.309 3959268.883 3892621.056 3194357.139 3959719.815 1.095525052 0.87728977 0.896040758 0.790144398 0.858973987 0.879487305 0.99988612 0.98305467 0.806712921 1 21.91696692 -1.775057756 8.311495178 1.001192384 0.911687417 0.085939485 0.088150151 0.001989906 5.39E-05 0.087200988 0.020290125 0.016785808 1.775057756 -0.089504967 AKDEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 AKDEVR 6 1 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;F5H5B1;K7ELX1;K7EJ90;F5H7Q5;K7EPE6;Q9NY28 Q9NX02 NLRP2;GALNT8 "NACHT, LRR and PYD domains-containing protein 2;Probable polypeptide N-acetylgalactosaminyltransferase 8" 0 68.312 0.087981 100960000 469720 466390 372770 457170 397900 407190 488840 474670 441500 579550 FALSE TRUE 451362.8231 453089.0138 440137.8312 480764.5985 410698.8149 415423.6608 494822.5701 464867.8986 391382.7709 540296.5623 0.835398288 0.838593183 0.814622676 0.889816134 0.760135902 0.768880814 0.915835126 0.86039396 0.724385084 1 19.04339198 -1.76447345 2.900893507 1.035574872 0.828360272 0.467428742 0.056392383 10141054.94 11835862.5 2625578.883 0.013903744 0.017199925 1.76447345 -0.2072146 NGLPGSRPGS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 NGLPGSRPGSPER 13 1 Q92993-2;Q92993-4;Q92993;Q92993-3;H0YEP0;E9PRM3;E9PRL6 Q92993-2 KAT5 Histone acetyltransferase KAT5 1 NGLPGS(0.006)RPGS(0.994)PER 62.94 0.044106 624580000 308020 323650 289910 343810 348330 343550 357930 308280 423930 428670 TRUE FALSE 295982.2379 314419.8189 342303.186 361554.0753 359534.3508 350496.8164 362310.4544 301913.9103 375807.2437 399635.7991 0.74062994 0.786765899 0.856537845 0.904708928 0.899655015 0.877040588 0.906601599 0.755472635 0.940374322 1 18.6083263 -1.756344794 0.02133655 1.921642442 3.04E-06 0.456231896 0.058149728 1681.480703 5.363925789 283.1247929 204.5819227 0.017524886 1.756344794 -1.921639404 EAFEETHLTSLDPVK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAFEETHLTSLDPVK 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ;; 156.5 2.11E-06 506750000 370615 403294 324846 392525 375814 398379 428896 414063 495194 512182 FALSE TRUE 356130.9561 391792.45 383552.8984 412783.2623 387902.3986 406434.4963 434144.9575 405512.4544 438981.6531 477491.4569 0.745837336 0.820522429 0.803266515 0.864483032 0.812375579 0.851186949 0.909220367 0.849255936 0.919349753 1 18.8651154 -1.752879694 0.027436796 1.976130395 6.65E-12 0.839516054 0.027104252 308.7670014 1.269013372 55.95422969 36.87949934 0.017665271 1.752879694 -1.976130395 ELQGDGPPS(ph)SPTNDPTVK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELQGDGPPSSPTNDPTVK 18 0 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 ELQGDGPPS(0.803)S(0.185)PT(0.012)NDPTVK;ELQGDGPPS(0.784)S(0.215)PT(0.001)NDPTVK;ELQGDGPPS(0.674)S(0.326)PT(0.001)NDPTVK 211.29 3.34E-16 834675000 864760 803770 658886 772820 796640 782780 828080 821280 888710 793840 TRUE FALSE 830964.2232 780847.2666 777961.357 812705.3328 822264.6491 798608.3479 838214.2907 804320.281 787827.3666 740072.5097 1.122814606 1.055095624 1.051196129 1.098142847 1.111059576 1.079094734 1.132611034 1.086812806 1.064527268 1 19.4973071 -1.750914907 6.78968102 0.998181911 1.089294482 0.508482436 0.02626136 0.000734734 2.70E-05 0.025849295 0.005975925 0.017745371 1.750914907 0.091112571 YWCDAEYDAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 YWCDAEYDAYR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 125.48 0.00076173 593790000 336150 341620 323580 379600 339230 228870 438630 328570 380650 445690 FALSE TRUE 323012.8864 331877.3321 382058.104 399191.2015 350141.641 233497.9082 443998.0851 321784.9147 337440.2078 415503.0193 0.77740202 0.798736271 0.919507407 0.960741999 0.842693373 0.561964408 1.068579684 0.774446634 0.812124563 1 18.66449944 -1.746487014 2.654013754 1.034390169 0.838089406 0.131519405 0.126893945 38105254.61 31028301.97 8630367.141 0.031729355 0.017927222 1.746487014 -0.196300762 AYTNFDAERDALNIETAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AYTNFDAERDALNIETAIK 19 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YNB8;H0YKN4;H0YMD9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 122.94 2.94E-05 80988000 81007 120840 43670 81462 55840 68829 74553 86396 67149 44402 FALSE TRUE 77841.15688 117393.7615 51562.14043 85666.26358 57636.14431 70220.76954 75465.40192 84611.89241 59526.52703 41394.61299 1.880465869 2.835967123 1.245624411 2.069502706 1.392358574 1.696374588 1.823073015 2.044031489 1.438025935 1 15.33715541 -1.739244588 0.130732672 6.06E-22 2.30940563 0.31224436 0.409201551 62.62562137 1.28401435 25.38485167 3.882929878 0.018228688 1.739244588 2.30940563 DRELWVQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRELWVQR 8 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ;;; 143.03 0.00055443 2923160000 1765560 1999310 1652070 1836860 1656860 1322680 2076770 1924350 2008720 2259730 FALSE TRUE 1696559.963 1942291.636 1950635.799 1931660.565 1710154.407 1349425.496 2102186.132 1884611.5 1780698.527 2106676.474 0.805325347 0.921969586 0.925930404 0.916923214 0.811778376 0.640547095 0.997868519 0.894589902 0.845264353 1 21.00653734 -1.736946234 7.226063581 1.001664486 0.867528239 0.164402983 0.092481796 0.002537002 9.24E-05 0.09160586 0.021340064 0.018325413 1.736946234 -0.134136247 VTNGAFTGEIS(ph)PGMIK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTNGAFTGEISPGMIK 16 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK 252.66 1.63E-26 255930000 567440 561840 488160 526580 556480 524330 542230 598520 628210 524200 TRUE FALSE 545263.8175 545816.8733 576381.3711 553756.8569 574379.6846 534932.3118 548865.9729 586160.3528 556898.2345 488695.4671 1.115753786 1.116885484 1.179428519 1.133132788 1.17533254 1.094612796 1.123124747 1.199438899 1.139560876 1 18.8985762 -1.736848192 2.643284543 0.970808013 1.144846884 0.645924889 0.031455171 6949201.418 5489298.816 1331570.268 0.007819142 0.01832955 1.736848192 0.174038871 KLPEEEVESSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLPEEEVESSR 11 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 0 148.13 5.61E-05 289790000 188180 207340 181860 215900 213170 225360 211320 229840 270880 291210 FALSE TRUE 180825.7176 201426.8662 214726.1475 227042.6249 220026.8066 229916.9336 213906.1974 225093.7237 240130.838 271486.0873 0.666058874 0.741941763 0.790928734 0.836295617 0.810453342 0.846882932 0.787908506 0.829116976 0.884505134 1 18.05051874 -1.736011433 0.033422904 1.949530572 1.65E-17 0.82957115 0.034388015 254.8426145 1.283754853 47.75497791 28.83450322 0.0183649 1.736011433 -1.949530572 S(ph)SSPAPADIAQTVQEDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 S(0.333)S(0.333)S(0.333)PAPADIAQTVQEDLR;S(0.333)S(0.333)S(0.333)PAPADIAQTVQEDLR;S(0.57)S(0.256)S(0.173)PAPADIAQTVQEDLR 265.45 5.01E-31 687925000 342293 393312 335600 348619 330413 382053 390978 372606 400924 476019 TRUE FALSE 328915.8111 382095.1269 396250.3854 366611.2684 341041.0342 389778.3734 395762.9057 364911.5559 355412.7883 443777.8091 0.741172281 0.861005483 0.892902658 0.826114467 0.768495015 0.878318756 0.891804181 0.822284369 0.800880037 1 18.759478 -1.726862391 2.410143541 1.036180646 0.835255144 0.516855298 0.048765284 10889998.15 7731287.511 2362620.155 0.012057178 0.018755887 1.726862391 -0.200925501 AAEDDEDDDVDTK ddPTM_BT-474_Pertuzumab_2h_R1 25 AAEDDEDDDVDTK 13 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;;;;;;;;;;;;;;;;;; 383.67 1.43E-107 1.24193E+11 20744292.5 17772414.4 14913258.8 14328354.6 15785441.6 15832784.9 16195587.7 19289027.8 21826304.6 18030708.2 FALSE TRUE 19933582.62 17265562.54 17608416.41 15067842.7 16293194.67 16152934.66 16393794.15 18890702.64 19348674.01 16809472.27 1.18585416 1.027132932 1.0475294 0.896389991 0.969286507 0.960942402 0.975271197 1.123812951 1.15105779 1 24.0027711 -1.726786024 7.549879249 0.999714973 1.032932011 0.013800798 0.087776243 0.000445334 1.61E-05 0.089876127 0.021002705 0.018759185 1.726786024 0.033217038 SSS(ph)PATEQSWMENDFDELREEGFRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.077)S(0.398)S(0.524)PAT(0.001)EQSWMENDFDELREEGFRR 251.07 3.50E-40 344260000 48293 56650 26767 40748 53038 63579 40540 33674 58157 38550 TRUE FALSE 46405.65617 55034.39747 31604.39233 42851.00916 54744.01544 64864.61094 41036.14065 32978.62013 51555.26117 35938.97416 1.291234857 1.531329114 0.879390496 1.192326998 1.52324925 1.804854269 1.14182838 0.91762831 1.434522336 1 15.13326161 -1.723348298 7.056275376 0.996871535 1.280195986 0.095071418 0.2720872 0.014384769 0.000563976 0.282995968 0.066136735 0.018908266 1.723348298 0.283324451 FYLAEMVIAIDSVHQLHYVHR ddPTM_BT-474_Pertuzumab_2h_R1 1 FYLAEMVIAIDSVHQLHYVHR 21 0 Q5VT25-2;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 0 94.856 0.00052549 74189000 3276.7 2131.4 1656.7 1936.3 2143.8 2404.8 2943.1 1970.1 2995.1 1396.1 FALSE TRUE 3148.642941 2070.614559 1956.102543 2036.232675 2212.757274 2453.426704 2979.118538 1929.416747 2655.108804 1301.540903 2.41916557 1.590894726 1.502912846 1.564478434 1.700105827 1.88501698 2.288916568 1.482409613 2.039973386 1 10.34600494 -1.718050751 2.678270381 0.859516004 1.800123045 0.38325927 0.313919098 32517929.75 27952082.34 30743770.03 0.072946624 0.019140322 1.718050751 0.940607041 DLLPHQELR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLPHQELR 9 0 Q15650;H0YL91 Q15650 TRIP4 Activating signal cointegrator 1 0 ; 173.37 5.55E-05 259590000 203433 220147 173302 195681 200359 179996 216655 208364 223958 240771 FALSE TRUE 195482.6135 213868.6231 204621.5265 205780.1199 206803.7292 183635.6424 219306.4887 204061.2106 198535.2267 224463.3657 0.870888721 0.95279968 0.911603218 0.916764832 0.921325084 0.818109636 0.977025752 0.909106971 0.884488327 1 17.77612048 -1.714216531 2.727259555 1.015011185 0.909590143 0.311412295 0.041357806 14454109.51 11743040.1 1478944.74 0.009661809 0.019310053 1.714216531 -0.105421041 ANHEEVLAAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ANHEEVLAAGK 11 0 P00491 P00491 PNP Purine nucleoside phosphorylase 0 104.87 0.0025425 1281000000 2205500 2174200 1883300 2037300 1953400 1987000 2290800 2020600 2456500 2622500 FALSE TRUE 2119306.622 2112193.945 2223654.204 2142445.297 2016232.885 2027178.501 2318835.496 1978873.904 2177648.418 2444875.739 0.866836129 0.863926911 0.909516246 0.876300281 0.824677039 0.829154001 0.948447178 0.809396515 0.890699017 1 21.22132971 -1.705229659 3.700358496 1.010804024 0.866849902 0.497102455 0.039554506 0.003604734 0.000287153 0.039158694 0.008608535 0.0197138 1.705229659 -0.143954122 GAASTLVPGVSETSAS(ph)PGSPSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GAASTLVPGVSETSASPGSPSVR 23 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 GAASTLVPGVSETSAS(0.931)PGS(0.069)PSVR 306.06 1.70E-62 641780000 245490 274110 232880 261650 245590 287660 266460 270920 292840 320260 TRUE FALSE 235895.9794 266292.6512 274966.5964 275153.7879 253489.6254 293476.6823 269721.0172 265325.4073 259598.0309 298568.5049 0.790089964 0.891897996 0.920949771 0.921576735 0.849016628 0.982945882 0.903380674 0.888658391 0.869475603 1 18.18770246 -1.700269445 0.013268829 1.927817192 1.94E-06 0.336687442 0.047187688 4970.984535 10.01924027 802.8080808 658.0260917 0.019940248 1.700269445 -1.927815249 KAVVLPGGTATS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAVVLPGGTATSPK 14 1 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 KAVVLPGGTAT(0.248)S(0.752)PK;KAVVLPGGTAT(0.248)S(0.752)PK 131.45 3.44E-05 1913700000 2384900 1991530 1740140 1600720 1816450 1808030 1941870 2095500 2160600 2273700 TRUE FALSE 2291695.471 1934733.514 2054622.007 1683333.351 1874877.764 1844589.605 1965635.186 2052227.193 1915337.746 2119700.274 1.081141282 0.912739192 0.969298364 0.794137441 0.884501355 0.870212467 0.927317513 0.968168575 0.903588951 1 21.01542885 -1.69784239 8.474632393 1.000215749 0.921544498 0.093845202 0.071132526 0.000287764 1.03E-05 0.068351895 0.016066796 0.020051996 1.69784239 -0.078671251 LRENVFQEHQTLK ddPTM_BT-474_Pertuzumab_2h_R1 4 LRENVFQEHQTLK 13 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 144.8 2.35E-05 2663590000 2421397 2788914 2116092 2136658 2268365 2506179 2478526 2513753 2598622 2801283 FALSE TRUE 2326766.128 2709376.903 2498516.897 2246931.175 2341329.02 2556855.656 2508858.943 2461843.122 2303637.325 2611549.607 0.8909523 1.037459482 0.956718145 0.860382345 0.896528641 0.979056898 0.960678264 0.942675228 0.882095947 1 21.31647468 -1.69692889 9.208565809 1.000101275 0.937430354 0.129974774 0.050507465 0.000105483 3.47E-06 0.049120418 0.011559136 0.020094218 1.69692889 -0.062670921 ARNDEYENLFNMIVEIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARNDEYENLFNMIVEIPR 18 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;D6RGV9;D6RGI1;D6RAD3 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 61.648 0.052786 136360000 138000 131450 182790 102760 183930 186750 168360 150800 184070 93372 FALSE TRUE 132606.8074 127701.1747 215824.2191 108063.4559 189846.2755 190526.213 170420.44 147685.9273 163175.1453 87047.83127 1.523378647 1.467023047 2.479375028 1.241426172 2.180942049 2.188753128 1.957779275 1.696606626 1.874545786 1 16.40952073 -1.689225311 8.31575218 0.997788946 1.849033172 0.334524904 0.357740596 0.013901599 0.000519527 0.328358304 0.077332308 0.020453832 1.689225311 0.851244226 GKPLISR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKPLISR 7 1 Q9Y6Q5;K7EMG5;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 ; 109.86 0.0063228 1484350000 1380810 1526030 1341310 1361060 1378840 1008810 1616350 1588190 1492790 1724590 FALSE TRUE 1326846.419 1482509.119 1583714.554 1431304.47 1423191.641 1029208.829 1636131.375 1555393.321 1323334.737 1607781.983 0.825265137 0.922083426 0.985030664 0.89023542 0.885189445 0.640142034 1.017632609 0.967415569 0.82308096 1 20.61664036 -1.68585066 6.226342903 1.001187804 0.892663739 0.099214053 0.101889906 0.001712634 8.64E-05 0.100570543 0.023451993 0.020613386 1.68585066 -0.108524065 LSMWDRPDDLIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSMWDRPDDLIGR 13 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 217.2 2.39E-11 367320000 345320 399440 304440 390250 393210 379900 361660 371710 387370 403150 FALSE TRUE 331824.5126 388048.3623 359459.0802 410390.8493 405857.9568 387581.8383 366086.1033 364034.0586 343397.3816 375844.2914 0.882877618 1.032471082 0.956404257 1.091917208 1.079856648 1.031229813 0.97403662 0.968576793 0.913669276 1 18.51977557 -1.685541814 6.901528628 1.000024871 0.996319274 0 0.064189219 2.50E-05 1.14E-06 0.063360431 0.014833946 0.020628051 1.685541814 -0.003705597 LENGGFPYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LENGGFPYEK 10 0 Q9BRT3;J3KTI2 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ; 144.17 7.60E-05 454100000 285160 312060 265960 264310 268710 284510 289910 308510 288390 355520 FALSE TRUE 274015.6319 303160.3543 314024.8882 277951.0708 277353.3012 290262.9871 293458.0053 302139.1607 255653.1762 331440.3137 0.826742012 0.914675559 0.947455319 0.838615761 0.836812209 0.875762468 0.885402267 0.911594481 0.771340014 1 18.33838957 -1.679764853 6.277027397 1.001235955 0.8734892 0.392382445 0.048936202 0.000831913 4.24E-05 0.046569893 0.010873879 0.020904277 1.679764853 -0.127746756 DRWSEVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRWSEVTR 8 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 60.102 0.086109 123600000 55780 77222 74010 97349 88022 94248 77534 79802 61739 88111 FALSE TRUE 53600.05593 75019.70417 87385.25334 102373.1936 90853.30757 96153.75913 78482.88429 78154.06081 54730.64755 82143.16349 0.652519987 0.913279949 1.063816508 1.246277708 1.106036141 1.170563137 0.955440245 0.951437192 0.666283659 1 16.32585289 -1.672279415 8.556479642 1.000022297 0.985796955 0 0.185217818 8.13E-05 3.11E-06 0.185005548 0.043537882 0.021267703 1.672279415 -0.014225342 QLVAGNS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 QLVAGNSPK 9 0 Q96EU6-2;Q96EU6 Q96EU6-2 RRP36 Ribosomal RNA processing protein 36 homolog 1 QLVAGNS(1)PK;QLVAGNS(1)PK;QLVAGNS(1)PK 115.57 0.001525 664370000 2724990 2126660 1912970 1609680 1892610 1768710 2086750 2373230 2359660 2468290 TRUE FALSE 2618494.378 2066009.739 2258686.233 1692755.778 1953487.519 1804474.528 2112288.271 2324221.971 2091801.289 2301110.52 1.137926386 0.8978316 0.98156356 0.735625587 0.848932506 0.784175515 0.91794299 1.010043608 0.909039905 1 21.13389885 -1.669843609 13.23320852 1.000003777 0.911649923 0.053855598 0.108247586 1.22E-05 3.05E-07 0.106381015 0.025073174 0.021387321 1.669843609 -0.088353854 DLAILQCHGELDPMVPVR ddPTM_BT-474_Pertuzumab_2h_R1 3 DLAILQCHGELDPMVPVR 18 0 O95372;Q5QPQ1;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ;; 196.3 1.97E-15 1216250000 625740 651020 545820 696150 664780 668680 652120 624950 681190 722280 FALSE TRUE 601285.389 632453.547 644461.8157 732078.3849 686163.2524 682201.1677 660100.8396 612044.5641 603864.167 673359.3323 0.892963623 0.939251179 0.957084553 1.087203147 1.019014989 1.013130932 0.98030993 0.908941979 0.896793344 1 19.36101707 -1.668107569 6.934375761 1.000160589 0.967849602 0.028670963 0.058420536 0.000158879 7.60E-06 0.06196182 0.01453204 0.021472985 1.668107569 -0.032310987 RRAS(ph)PS(ph)PPPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRASPSPPPKR 11 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRAS(1)PS(1)PPPKR 69.431 0.078269 107060000 147230 139240 136050 121270 123920 142740 139230 134030 167070 126910 TRUE FALSE 141476.0888 135269.0115 160637.2614 127528.7592 127905.9993 145626.3006 140933.9384 131262.2337 148104.914 118314.2727 1.195765191 1.143302566 1.35771668 1.077881445 1.081069904 1.230843053 1.1911829 1.109437016 1.251792457 1 16.8522646 -1.666039317 2.681687385 0.977528641 1.176893172 0.308218001 0.081512004 17792008.72 15107696.67 2732186.887 0.019049904 0.021575491 1.666039317 0.199364531 EILSEVER ddPTM_BT-474_Pertuzumab_2h_R1 4 EILSEVER 8 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 164.77 0.00076339 2823650000 2681770 3076020 2413580 2769130 2762320 2864540 2838840 2793610 3083410 3151900 FALSE TRUE 2576963.464 2988294.921 2849767.596 2912045.131 2851172.531 2922462.961 2873582.573 2735920.977 2733394.224 2938419.006 0.876989789 1.016973725 0.969830235 0.991024468 0.970308362 0.994569854 0.977934926 0.931086061 0.930226158 1 21.4866087 -1.662701256 7.043847922 1.000150316 0.964282081 0.07913019 0.038136777 8.65E-05 4.14E-06 0.035476126 0.008326806 0.021741963 1.662701256 -0.035868235 LSTT(ph)PSPT(ph)SSLHEDGVEDFRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 2 LS(0.29)T(0.333)T(0.374)PS(0.188)PT(0.302)S(0.27)S(0.241)LHEDGVEDFRR 61.602 0.029544 209160000 49915 102590 103100 117810 100290 126030 105550 65837 111620 127020 TRUE FALSE 47964.26662 99664.23365 121732.4634 123890.1882 103515.9189 128578.4129 106841.7525 64477.44294 98949.36555 118416.8223 0.405046054 0.84163915 1.027999748 1.046221186 0.874165654 1.085812054 0.902251474 0.544495636 0.835602271 1 16.85351452 -1.661895693 7.423417625 1.000491125 0.841115383 0.051787216 0.204907531 0.001754079 7.99E-05 0.208947476 0.049101082 0.021782329 1.661895693 -0.159375743 NCPAVTLTS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 4 NCPAVTLTSPAK 12 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 NCPAVTLT(0.001)S(0.999)PAK;NCPAVTLT(0.007)S(0.993)PAK;NCPAVTLT(0.003)S(0.997)PAK;NCPAVTLTS(1)PAK 208.23 7.27E-08 914500000 4522940 3816490 3096110 3110410 3408860 3067270 3678210 4202050 4080200 4062570 TRUE FALSE 4346178.504 3707647.442 3655645.95 3270938.633 3518509.078 3129292.301 3723225.034 4115276.199 3617032.802 3787408.515 1.147533594 0.978940462 0.965210363 0.863635021 0.929001734 0.826235746 0.983053457 1.086567816 0.955015227 1 21.85277961 -1.643396087 7.216829073 1.000077152 0.971100092 0.009703282 0.089031474 0.000117005 5.78E-06 0.091263153 0.021453689 0.022730234 1.643396087 -0.02897706 GFDQTINLILDESHER ddPTM_BT-474_Pertuzumab_2h_R1 8 GFDQTINLILDESHER 16 0 F2Z2Y6;C9JIZ0;C9JNV3;O95777 F2Z2Y6 LSM8 U6 snRNA-associated Sm-like protein LSm8 0 ;;;;;;; 265.87 3.91E-27 4192169000 2821998 3251138 2590249 3331703 3185926 3143837 3157628 2938793 3210462 3409490 FALSE TRUE 2711711.198 3158418.727 3058364.614 3503652.591 3288404.203 3207407.538 3196271.996 2878105.898 2846023.813 3178562.205 0.8531251 0.993662708 0.962184918 1.102275924 1.034557133 1.009074962 1.005571636 0.905474146 0.895380876 1 21.59994289 -1.643265652 8.096043773 1.00003027 0.976603352 0.011127449 0.069604633 3.97E-05 1.75E-06 0.070407275 0.016573715 0.022737062 1.643265652 -0.023426918 SLS(ph)VPVDLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLSVPVDLSR 10 0 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 SLS(1)VPVDLSR;SLS(1)VPVDLSR;SLS(1)VPVDLSR;S(0.003)LS(0.997)VPVDLSR 243.91 8.79E-09 378280000 1591860 1242900 950310 1429400 1070740 927950 1180000 1673990 1364370 1450310 TRUE FALSE 1529648.351 1207453.709 1122052.157 1503171.505 1105181.325 946713.7848 1194441.193 1639421.522 1209492.438 1352079.212 1.131330426 0.893034741 0.829871613 1.111748108 0.817393918 0.700191066 0.883410663 1.212518843 0.894542588 1 20.36674824 -1.635915356 6.486408119 1.000225814 0.948077179 0.011425445 0.15260239 0.000524623 2.94E-05 0.155550299 0.036505192 0.023125155 1.635915356 -0.052148634 MLVTFDEELRPLPVSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLVTFDEELRPLPVSVR 17 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 215.45 5.12E-15 709610000 327670 369790 323790 339320 309260 350470 356560 368950 358570 420330 FALSE TRUE 314864.2941 359243.9513 382306.0557 356832.3459 319207.6288 357556.7435 360923.6879 361331.0536 317866.6368 391860.6747 0.803510825 0.916764489 0.975617306 0.910610247 0.8145947 0.912458857 0.921051055 0.922090623 0.811172586 1 18.57998127 -1.629704284 2.861453971 1.009229636 0.893901689 0.264365766 0.055371121 27297572.01 20787018.54 1826119.321 0.013341742 0.023458256 1.629704284 -0.115327947 VEADRPGK ddPTM_BT-474_Pertuzumab_2h_R1 4 VEADRPGK 8 1 P38159;P38159-2;H3BT71;H3BR27;P38159-3;H3BNC1;O75526;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL2;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2;RNA binding motif protein, X-linked-like-1" 0 ;;; 122.52 0.001265 1152250000 1715070 1720120 1382410 1554700 1590150 1745220 1643980 1815540 1923800 2086570 FALSE TRUE 1648043.168 1671063.862 1632242.239 1634938.253 1641298.619 1780509.544 1664099.519 1778048.465 1705418.289 1945244.755 0.847216353 0.859050696 0.839093504 0.840479456 0.843749155 0.91531389 0.855470508 0.914048713 0.876711419 1 20.89152026 -1.625277173 0.190333734 1.146684224 0.82544656 0.799827207 0.021676852 11.44278953 0.370024651 0.846133024 0.06763326 0.023698607 1.625277173 -0.321237664 VS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.489)S(0.489)S(0.011)S(0.011)ELDLPSGDHCEAGLLQLDVPLLR 225.53 9.81E-35 91084000 30951 32011 24404 32021 26974 29672 29667 33278 29093 36126 TRUE FALSE 29741.4007 31098.07762 28814.34566 33673.60765 27841.64321 30271.98817 30030.07362 32590.79767 25790.48461 33679.15384 0.883080402 0.923362795 0.855554323 0.999835323 0.826672883 0.898834582 0.891651666 0.967684575 0.765769969 1 15.03956827 -1.624716325 3.202216993 1.006441399 0.897174678 0.204846145 0.063559841 10413179.07 5840108.911 463449.3577 0.01364946 0.023729232 1.624716325 -0.109266721 ALSFLVNDCSLIHNNVCMAAVFVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALSFLVNDCSLIHNNVCMAAVFVDR 25 0 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PK59;Q96KG9-4;Q96KG9-5;Q96KG9-6 E9PS17 SCYL1 N-terminal kinase-like protein 0 213.47 3.42E-26 116390000 43794 46114 47942 39983 47825 41468 50244 50288 49462 65746 FALSE TRUE 42082.48206 44798.87387 56606.18586 42046.52742 49363.33456 42306.51137 50858.9011 49249.53523 43847.28112 61292.96486 0.686579319 0.730897485 0.923534797 0.685992716 0.805367054 0.690234376 0.829767351 0.803510408 0.715372167 1 15.90343387 -1.623823345 2.746384281 1.021341608 0.769533902 0.479219356 0.073727903 16218645.29 14708579.93 2461795.725 0.017777125 0.023778073 1.623823345 -0.251807707 DFTSEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFTSEPR 7 0 P41091;Q2VIR3;Q2VIR3-2 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ; 110.36 0.028538 321060000 1562120 1661180 1402260 1665810 1610340 1605860 1625870 1653710 1626260 1776630 FALSE TRUE 1501070.623 1613804.773 1655679.575 1751782.654 1662138.049 1638331.589 1645767.883 1619560.311 1441653.783 1656297.268 0.906280927 0.974344886 0.999627064 1.057649909 1.003526409 0.989153108 0.993642817 0.977819829 0.870407632 1 20.6595302 -1.616640496 7.391818394 1.000029465 0.979907581 0.013289656 0.049710299 2.42E-05 1.26E-06 0.048254055 0.011356937 0.024174612 1.616640496 -0.020121884 GANRTETVTSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GANRTETVTSFR 12 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 67.519 0.050292 106590000 115950 104140 81783 111720 95778 98725 111790 105160 116920 119830 FALSE TRUE 111418.5458 101170.0292 96563.00735 117485.8826 98858.78635 100721.2871 113158.1195 102988.4093 103647.7318 111713.8074 0.997356982 0.90561795 0.864378447 1.051668414 0.884928987 0.90160106 1.01292868 0.921895079 0.927796968 1 16.76944798 -1.615034224 2.734377027 1.005320246 0.939912313 0.086811637 0.057414715 9874374.689 10527920.67 379872.4179 0.013382098 0.024264189 1.615034224 -0.065407933 RDPTEEIEILLR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDPTEEIEILLR 12 1 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 0 ; 150.21 0.00010892 73716000 49589 53238 46727 55032 47962 53448 52508 55296 60182 62706 FALSE TRUE 47651.00706 51719.70437 55171.60834 57872.20812 49504.74129 54528.75518 53150.60861 54154.11828 53350.39166 58458.86677 0.815120266 0.884719585 0.94376801 0.989964591 0.846830327 0.932771335 0.909196698 0.926362779 0.912614195 1 15.83513424 -1.612292499 0.012748091 1.951541899 8.03E-07 0.334435247 0.044448187 5156.935084 10.25749924 860.4974481 714.516544 0.024417854 1.612292499 -1.951541096 FVIHCNSPVWGADK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVIHCNSPVWGADK 14 0 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 ; 204.28 1.39E-08 1925440000 2164500 2454700 2617600 2984500 1461930 1319250 2453400 2138900 2481500 3109700 FALSE TRUE 2079908.947 2384694.359 3090658.548 3138530.403 1508954.306 1345926.139 2483425.443 2094730.968 2199810.523 2899077.249 0.717438263 0.822570133 1.066083544 1.082596334 0.520494687 0.464260185 0.856626171 0.722550932 0.758796794 1 21.46716235 -1.609207147 6.546314386 1.000608252 0.780043683 0.10990045 0.188624354 0.001790836 0.000106906 0.195325719 0.045915616 0.024591944 1.609207147 -0.220564569 SGTT(ph)PKPVINSTPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGTTPKPVINSTPGR 15 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 1 S(0.054)GT(0.255)T(0.691)PKPVINSTPGR;S(0.031)GT(0.042)T(0.926)PKPVINSTPGR 117.07 0.00064501 1431110000 1844220 1605110 1368370 1406890 1470000 1509480 1461210 1805650 1829550 1706700 TRUE FALSE 1772145.844 1559333.834 1615664.898 1479499.762 1517283.885 1540002.72 1479092.725 1768362.697 1621867.154 1591103.689 1.113784008 0.98003282 1.015436586 0.92985754 0.953604655 0.967883319 0.92960172 1.111406321 1.01933467 1 20.60159643 -1.60840482 7.423076513 0.999997158 1.002293284 0.000123465 0.062753604 3.05E-06 1.61E-07 0.0627383 0.014769256 0.024637417 1.60840482 0.002296126 KDSPHS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSPHSR 7 1 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 KDS(0.264)PHS(0.736)R 55.549 0.077765 47631000 14736 15332 15617 13432 13549 15401 14742 15557 16394 20749 TRUE FALSE 14160.10083 14894.74637 18439.3393 14125.22713 13984.81589 15712.41877 14922.41701 15235.74251 14533.02185 19343.65175 0.732028317 0.770006954 0.953250169 0.730225467 0.722966691 0.812277794 0.771437431 0.787635278 0.751307046 1 14.23957256 -1.600116703 6.83227869 1.000401062 0.783566024 0.517089637 0.063386794 0.000381004 2.23E-05 0.060386097 0.01420738 0.025112115 1.600116703 -0.216835038 SSPCIHYFTGTPDPSR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSPCIHYFTGTPDPSR 16 0 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;;;; 179.39 2.63E-09 4777280000 2853930 3511840 2897850 3367000 3159970 3403010 3223440 3065860 3420260 3592110 FALSE TRUE 2742395.26 3411685.762 3421555.957 3540771.274 3261613.305 3471821.194 3262889.423 3002548.92 3032006.424 3348813.19 0.818915569 1.018774583 1.021721954 1.057321228 0.973960959 1.03673182 0.974342024 0.8966009 0.905397301 1 21.67521847 -1.591569633 7.073083669 1.000038647 0.970078468 0.017727633 0.070397734 4.40E-05 2.54E-06 0.069846738 0.016441803 0.025611226 1.591569633 -0.029960179 GPPQS(ph)PVFEGVYNNSR ddPTM_BT-474_Pertuzumab_2h_R1 6 GPPQSPVFEGVYNNSR 16 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR 300.25 7.41E-46 13957600000 4765470 4820130 4751750 5538560 5405160 5313050 5077370 4957440 5314070 5742050 TRUE FALSE 4579230.164 4682664.612 5610496.927 5824405.745 5579021.88 5420483.511 5139508.373 4855067.132 4710839.052 5353135.839 0.855429472 0.874751688 1.048076697 1.088036232 1.042196957 1.012580976 0.960093023 0.906957581 0.880014854 1 22.35195283 -1.590004614 6.889351144 1.000050852 0.966044124 0.018435546 0.078149812 6.73E-05 4.01E-06 0.08343292 0.019635932 0.025703685 1.590004614 -0.034006728 KEESSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEESSPSR 8 1 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 0 89.886 0.021787 101730000 81597 79605 66867 75043 69493 70292 84221 75701 86705 98413 FALSE TRUE 78408.09903 77334.74334 78951.35435 78915.97822 71728.30546 71713.3524 85251.72179 74137.7479 76862.6119 91747.39985 0.854608405 0.842909374 0.860529611 0.86014403 0.781802052 0.781639071 0.929200413 0.808063749 0.837763381 1 16.48537965 -1.586270701 2.682208253 1.012489524 0.839193454 0.579073647 0.041017342 9901370.649 9451100.06 876228.8067 0.010022114 0.025925629 1.586270701 -0.17329607 LKDNEK ddPTM_BT-474_Pertuzumab_2h_R1 4 LKDNEK 6 1 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0Y400;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;; 85.265 0.050079 2016170000 3365870 2885610 2603030 2447960 2400010 2703390 2888050 3056940 2986350 3361190 FALSE TRUE 3234328.079 2803315.228 3073455.425 2574299.509 2477208.501 2758054.398 2923394.82 2993813.121 2647352.068 3133533.607 1.032166392 0.894617891 0.980827337 0.82153244 0.790547928 0.880173869 0.932938716 0.955411205 0.844845596 1 21.57935904 -1.583320007 8.595962248 1.000025069 0.904300547 0.143953068 0.070455254 3.45E-05 1.67E-06 0.069467355 0.016369328 0.026102373 1.583320007 -0.095724523 VPVAS(ph)PSAHNISSSGGAPDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VPVASPSAHNISSSGGAPDR 20 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 VPVAS(0.907)PS(0.093)AHNISSSGGAPDR;VPVAS(0.953)PS(0.047)AHNISSSGGAPDR;VPVAS(0.851)PS(0.149)AHNISSSGGAPDR 203.33 6.91E-22 1798210000 407658 509503 448790 584673 509002 618042 532922 459998 471381 590063 TRUE FALSE 391726.2747 494972.4733 529896.3363 614848.0436 525374.5116 630539.2327 539444.0589 450498.8806 417871.8051 550097.5074 0.712103344 0.899790431 0.963277108 1.11770738 0.955057066 1.146231757 0.980633527 0.818943686 0.759632246 1 19.06932784 -1.582376714 8.44608023 1.000019299 0.935013969 0.023371326 0.132827864 5.06E-05 2.50E-06 0.134839932 0.031772645 0.026159129 1.582376714 -0.06500533 ELQNAGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELQNAGDR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 111.82 0.0073512 263470000 159760 175380 126070 145290 146270 146540 137190 179720 153840 186160 FALSE TRUE 153516.4026 170378.3341 148853.6534 152788.4343 150974.9074 149503.1392 138868.9723 176008.7192 136376.7281 173551.2174 0.884559641 0.981717885 0.857692937 0.880365097 0.869915577 0.861435267 0.800161326 1.014160095 0.785801046 1 17.40500196 -1.580077333 5.65975375 1.000467443 0.888727656 0.212663871 0.067057877 0.000380378 2.82E-05 0.06244153 0.014656581 0.026297997 1.580077333 -0.111739787 LEDS(ph)EVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEDSEVR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 LEDS(1)EVR 62.582 0.08873 109840000 101390 98536 104290 96766 98890 91037 96124 126060 95464 119850 TRUE FALSE 97427.56671 95725.84976 123137.5229 101760.1049 102070.8867 92877.83051 97300.39427 123456.8169 84627.32694 111732.4527 0.871971968 0.856741684 1.102074821 0.910747973 0.913529455 0.831252051 0.870833781 1.104932487 0.757410447 1 16.76968875 -1.578634307 2.714406502 1.00530124 0.92615033 0.045152231 0.105641192 29523939.66 27260077.93 1118565.059 0.025382091 0.026385522 1.578634307 -0.079150909 SLHDALCVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLHDALCVVK 10 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 96.171 0.0069221 1362330000 1590240 1884730 1686270 1777000 1624510 1151070 2001610 1648880 1904370 2277060 FALSE TRUE 1528091.663 1830979.346 1991016.5 1868711.183 1676763.839 1174345.424 2026106.302 1614830.052 1688193.901 2122832.698 0.719836125 0.862517026 0.937905517 0.880291313 0.789870931 0.55319735 0.954435224 0.760695863 0.795255275 1 21.01755925 -1.57702575 2.75281817 1.013085319 0.808866346 0.216962973 0.11044493 21295586.72 20881877.13 2032913.154 0.026155719 0.026483431 1.57702575 -0.204218973 IACKS(ph)PQPDPVDTPASTK ddPTM_BT-474_Pertuzumab_2h_R1 2 IACKSPQPDPVDTPASTK 18 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 IACKS(1)PQPDPVDTPASTK;IACKS(1)PQPDPVDTPASTK 140.87 7.51E-08 664740000 1100050 775140 668290 639880 959260 709910 756100 853860 617870 594060 TRUE FALSE 1057058.83 753033.7661 789064.869 672904.2835 990115.4691 724264.8666 765353.378 836227.4926 547731.9879 553823.7871 1.908655523 1.359699211 1.424757996 1.215015135 1.787780684 1.307753266 1.381943853 1.509916172 0.989000474 1 19.07906749 -1.575202286 0.076558219 1.30E-12 2.088368851 0.412730462 0.215946791 120.5643841 1.484739382 33.16595321 11.26397574 0.02659486 1.575202286 2.088368851 SEDFGVNEDLADSDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDFGVNEDLADSDAR 16 0 P04083 P04083 ANXA1 Annexin A1 0 180.84 3.97E-12 0 28698 33061 21668 31199 28355 29710 26721 32688 30918 36597 FALSE TRUE 27576.45043 32118.13265 25583.8896 32809.18413 29267.06433 30310.75656 27048.01959 32012.98138 27408.31826 34118.25259 0.808260926 0.941376835 0.749859317 0.961631433 0.857812523 0.888402959 0.792772711 0.93829487 0.803333001 1 15.05825614 -1.570161693 2.749802492 1.008827191 0.865533695 0.270758783 0.068328315 23076438.55 22186285.06 1486113.851 0.015113946 0.026905329 1.570161693 -0.143293496 LRQDLQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRQDLQDR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 143.04 0.00055437 1033410000 1030420 1433790 876190 1439680 1017820 814520 1161890 1439470 1350740 1112990 FALSE TRUE 990150.0472 1392899.713 1034537.024 1513982.057 1050559.105 830990.1525 1176109.557 1409744.441 1197409.658 1037606.196 0.954263815 1.342416534 0.997042064 1.459110463 1.012483454 0.800872388 1.133483553 1.358650755 1.154011669 1 19.98482757 -1.561443988 7.226594011 0.999899436 1.148493922 0.037186297 0.194554065 0.00031449 1.91E-05 0.187937437 0.044267424 0.027450864 1.561443988 0.148594486 SLHS(ph)AHSLASR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 S(0.001)LHS(0.998)AHS(0.001)LASR;S(0.001)LHS(0.999)AHSLASR 105.41 0.00097836 281460000 288730 506420 451700 670630 542960 572530 657020 216990 580190 643260 TRUE FALSE 277446.1124 491977.3974 533332.238 705241.2947 560424.8015 584106.9489 665060.8073 212509.0807 514329.2636 599691.4272 0.462648122 0.820384243 0.889344442 1.176006964 0.934521949 0.974012504 1.109005027 0.354364046 0.857656522 1 19.19386082 -1.557540655 8.467806613 1.000029481 0.835486645 0.035859955 0.243694802 0.000142735 7.46E-06 0.248315746 0.058518116 0.027698697 1.557540655 -0.164542836 LST(ph)TPSPT(ph)SSLHEDGVEDFRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 2 LS(0.116)T(0.717)T(0.167)PS(0.217)PT(0.641)S(0.125)S(0.018)LHEDGVEDFRR 120.27 2.42E-05 131010000 51914 84449 81534 114770 97086 106510 98545 57644 104680 102830 TRUE FALSE 49885.14349 82040.5972 96269.00751 120693.2935 100208.8594 108663.7052 99751.02319 56453.63126 92797.16525 95865.23251 0.520367418 0.855790938 1.004211902 1.258989211 1.04530972 1.133504841 1.040533889 0.588885353 0.967996038 1 16.54872007 -1.553488914 4.887908279 1.000442018 0.932710799 0.007878412 0.217162913 0.001126067 0.000102866 0.226352429 0.053004862 0.027958321 1.553488914 -0.067731219 S(ph)RSPQWR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.538)RS(0.462)PQWR 54.416 0.081022 658610000 29550 52967 41702 60869 56205 55836 52680 38104 52361 58333 TRUE FALSE 28395.15333 51456.43302 49238.47906 64010.45638 58012.88487 56965.04218 53324.7136 37317.13908 46417.1988 54382.05395 0.52214198 0.946202456 0.905417789 1.177051099 1.066765241 1.04749707 0.980557182 0.686203193 0.853538905 1 15.73084302 -1.55061738 5.0012273 1.000489367 0.913483393 0.021764041 0.180265122 0.001033042 9.28E-05 0.183312081 0.042965391 0.028143793 1.55061738 -0.087005974 EVVETPLLHPER ddPTM_BT-474_Pertuzumab_2h_R1 4 EVVETPLLHPER 12 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;;; 234.92 4.93E-16 3949730000 1368320 1424940 1319850 1646990 1497650 1368920 1615960 1558150 1642680 1896820 FALSE TRUE 1314844.542 1384302.106 1558376.255 1731991.351 1545823.272 1396600.5 1635736.602 1525973.658 1456209.853 1768346.692 0.743544548 0.782822799 0.881261724 0.979441056 0.874163013 0.78977754 0.925008998 0.862938057 0.823486627 1 20.75396972 -1.546648605 0.019453507 1.907084454 1.54E-06 0.329998404 0.065557704 2244.431752 6.958619482 390.6858722 295.9911915 0.028402162 1.546648605 -1.907082915 GIYPHEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIYPHEPK 8 0 B5MCF9;O00541-2;O00541 B5MCF9 PES1 Pescadillo homolog 0 75.854 0.037312 111140000 310920 318680 276540 245310 318740 252580 304740 311090 334530 383840 FALSE TRUE 298768.9027 309591.5584 326516.9296 257970.4785 328992.5616 257687.3407 308469.4993 304665.8828 296555.5569 357842.1749 0.834918083 0.865162298 0.912460723 0.720905742 0.919378946 0.720114505 0.862026672 0.851397359 0.828732826 1 18.44896391 -1.535793826 5.36735379 1.000528 0.836245752 0.372212717 0.064263703 0.000370144 3.20E-05 0.056723285 0.013327404 0.029120993 1.535793826 -0.164282248 EPRPNS(ph)SPSPSPGQASETPHPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EPRPNSSPSPSPGQASETPHPR 22 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNS(0.464)S(0.464)PS(0.072)PSPGQASETPHPR;EPRPNS(0.495)S(0.495)PS(0.01)PSPGQASETPHPR;EPRPNS(0.886)S(0.112)PS(0.002)PSPGQASETPHPR 236.02 1.06E-30 623390000 240833 304924 291397 331692 297225 236099 331060 280627 306369 411652 TRUE FALSE 231420.9801 296227.8661 344058.92 348810.6639 306785.5121 240873.0835 335111.6113 274831.9544 271591.2755 383770.4434 0.60301929 0.771888172 0.896522715 0.90890445 0.799398488 0.627648866 0.873208495 0.716136323 0.707692008 1 18.54988408 -1.530073991 3.194572933 1.007159787 0.772715907 0.322421821 0.100974054 50090413.04 62566520.57 3122086.613 0.024581362 0.029507065 1.530073991 -0.23444388 LSEEFLTAHPR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSEEFLTAHPR 11 0 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8Y6Q1 Q15813-2 TBCE Tubulin-specific chaperone E 0 ;; 176.95 8.20E-06 1317030000 410734 433729 371517 466312 421877 367141 443529 432824 465106 522650 FALSE TRUE 394682.0612 421359.4736 438658.3863 490378.4182 435447.0568 374564.8426 448957.0406 423886.0331 412309.1168 487250.45 0.810018875 0.864769799 0.900272922 1.006419631 0.893682206 0.76873165 0.921409186 0.869955139 0.846195456 1 18.89430399 -1.527778441 5.996692008 1.000178604 0.878756734 0.272097162 0.060800094 0.000147449 1.16E-05 0.059789309 0.014071831 0.029663443 1.527778441 -0.12142187 KDLQHPNEFIR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDLQHPNEFIR 11 1 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 ; 112.5 0.00098529 67809000 227350 247450 209950 208822 234130 161685 255030 228620 250990 269300 FALSE TRUE 218464.9107 240392.9683 247892.6353 219599.3284 241661.0041 164954.3815 258151.1334 223898.9171 222498.6674 251060.0711 0.870169875 0.957511751 0.987383753 0.874688386 0.962562478 0.657031525 1.028244485 0.891814123 0.886236774 1 17.93767307 -1.526019795 2.916348843 1.003961916 0.904389149 0.085591985 0.096000481 30094346.31 33416471.83 945152.0214 0.023307606 0.029783807 1.526019795 -0.099572767 KVVGCSCVVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVVGCSCVVVK 11 1 P25398 P25398 RPS12 40S ribosomal protein S12 0 90.412 0.01845 467550000 457690 519280 451950 414860 465920 418050 485930 508540 516010 576200 FALSE TRUE 439802.9688 504470.6428 533627.4186 436270.9743 480906.7399 426503.2574 491876.9567 498038.4713 457434.7081 537173.4608 0.818735475 0.939120563 0.993398702 0.812160328 0.895254094 0.793976785 0.915676206 0.927146458 0.851558652 1 19.0350285 -1.518107903 3.226325027 1.003121996 0.887954798 0.247492041 0.060652088 27504142.44 25721191.18 718736.3376 0.014406167 0.030331375 1.518107903 -0.115167198 T(ph)PPRDLPTIPGVT(ph)SPSSDEPPMEASQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(1)PPRDLPT(0.003)IPGVT(0.636)S(0.35)PS(0.01)S(0.002)DEPPMEASQSHLR 148.45 3.34E-08 287470000 42177 49261 57222 61058 51314 65034 59917 39854 49716 69184 TRUE FALSE 40528.67621 47856.12451 67563.2883 64209.2107 52964.56141 66349.03204 60650.28217 39031.00097 44072.44811 64498.10606 0.62837002 0.741977206 1.047523601 0.995520871 0.821180104 1.028697369 0.940342064 0.605149567 0.683313834 1 15.97696918 -1.517485237 6.70222631 1.000096699 0.834291946 0.092727481 0.157130835 0.000245398 1.77E-05 0.164443409 0.038737165 0.030374893 1.517485237 -0.165804752 MEKGEHSIVYLKPSYAFGSVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEKGEHSIVYLKPSYAFGSVGK 22 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 175.61 7.72E-13 909310000 1899900 1964100 1250000 1135500 1640300 2151700 1578200 1736700 1950400 1552500 FALSE TRUE 1825649.808 1908085.791 1475902.806 1194103.291 1693061.739 2195208.848 1597514.484 1700836.538 1728998.769 1447347.792 1.261376027 1.318332609 1.0197292 0.825028578 1.169768419 1.516711367 1.103753011 1.175140175 1.194597994 1 20.46498021 -1.516260166 2.615579656 0.990694203 1.172121176 0.085470334 0.172330283 47387674.61 46414837.96 3149408.18 0.04347124 0.030460697 1.516260166 0.181426973 VGSGS(ph)LDNLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGSGSLDNLGR 11 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 VGS(0.005)GS(0.995)LDNLGR;VGS(0.007)GS(0.993)LDNLGR 124.45 0.00096146 0 687500 669530 596880 638070 653610 662120 611470 710810 743940 752870 TRUE FALSE 660631.7399 650435.6599 704749.4935 671000.8692 674633.9592 675508.5201 618953.3528 696131.5251 659491.0501 701877.4443 0.941235176 0.92670831 1.004091953 0.956008595 0.96118484 0.962430871 0.881853887 0.991813501 0.939609978 1 19.42085962 -1.512955405 5.423668161 1.00010731 0.952987513 0.167790932 0.032174969 3.99E-05 3.58E-06 0.029746413 0.006995341 0.030693371 1.512955405 -0.047119796 MPLLELGGETTPPLS(ph)TERSPEAVGSECPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGETTPPLS(0.451)T(0.101)ERS(0.447)PEAVGSECPSR 159.03 7.25E-12 151240000 120360 134880 127540 134510 143350 154380 142360 130930 139400 149670 TRUE FALSE 115656.1981 131033.3545 150589.3151 141452.0772 147960.9829 157501.6694 144102.2443 128226.2497 123575.8964 139532.7176 0.828882287 0.939086952 1.079240179 1.013755624 1.060403506 1.128779487 1.032748783 0.918969056 0.885641006 1 17.09024392 -1.512817179 2.717960337 1.000352368 0.99250923 0 0.089010558 44724210.37 34086058.92 111615.6403 0.022842099 0.030703142 1.512817179 -0.007843139 KWDSNVIETFDIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KWDSNVIETFDIAR 14 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 233.78 5.45E-17 4579500000 2806300 2776900 2532250 2728200 2483940 2087580 3033000 2781300 2949800 3147400 FALSE TRUE 2696626.693 2697705.531 2989883.905 2869002.729 2563838.186 2129792.298 3070118.761 2723865.183 2614951.071 2934223.795 0.919025569 0.919393243 1.018969279 0.977772293 0.873770498 0.725845214 1.04631377 0.9283086 0.891190057 1 21.48454748 -1.511328262 2.920849466 1.002781046 0.925215507 0.071242832 0.083577144 73793981.34 84935353.09 1654075.561 0.020685386 0.030808584 1.511328262 -0.077565539 DGNLHEGDIILK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGNLHEGDIILK 12 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 119.01 0.00022863 0 696650 676980 643620 599680 672180 685990 718920 730030 821800 881960 FALSE TRUE 669424.1478 657673.1932 759936.4512 630629.5567 693801.2802 699861.1878 727718.358 714954.6254 728512.7093 822224.0636 0.814162681 0.799871011 0.924244965 0.766980176 0.843810478 0.851180619 0.885060886 0.869537462 0.886026986 1 19.64917207 -1.511283287 0.200946468 1.154468467 0.806120807 0.623566656 0.038641375 16.08735439 0.579822675 1.338795994 0.104956142 0.030811775 1.511283287 -0.34834766 NS(ph)PFTR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPFTR 6 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 NS(1)PFTR;NS(1)PFTR 92.439 0.049043 454850000 971040 856690 858590 872370 798270 737130 788050 1029730 1019310 933960 TRUE FALSE 933090.6833 832258.04 1013756.312 917393.1202 823947.0795 752035.2736 797694.3916 1008465.716 903602.2021 870702.0573 1.071653243 0.955847104 1.164297596 1.053624615 0.946301978 0.863711378 0.916150806 1.158221354 1.037785767 1 19.73181961 -1.511217078 2.914175134 0.999211963 1.02100955 0.002926796 0.094251763 1275196158 60769320.47 6713844.351 0.024264256 0.030816472 1.511217078 0.021797587 ITVGNDHFCVST(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 4 ITVGNDHFCVSTPER 15 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.123)T(0.877)PER;ITVGNDHFCVS(0.137)T(0.863)PER;ITVGNDHFCVS(0.103)T(0.897)PER;ITVGNDHFCVS(0.167)T(0.833)PER 150.69 1.15E-05 1097470000 1074710 1083230 1046370 1121470 906160 1056270 1077920 1138380 1199740 1367050 TRUE FALSE 1032709.145 1052337.341 1235472.335 1179349.201 935307.4594 1077628.503 1091111.907 1114872.055 1063550.545 1274458.486 0.81031211 0.825713315 0.969409635 0.925372787 0.733886172 0.845557949 0.856137661 0.874780989 0.834511721 1 20.28145295 -1.510132738 3.167618163 1.004055962 0.855504051 0.347396087 0.060405658 226164413.6 349680335.3 8291094.62 0.014921719 0.030893511 1.510132738 -0.148551911 GGYFDEFGIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 GGYFDEFGIIR 11 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 201.07 1.04E-07 534538000 873890 1044250 906450 1026110 930450 689670 1109970 957910 1017670 1297500 FALSE TRUE 839737.4127 1014469.012 1070265.679 1079067.66 960378.7693 703615.5999 1123554.145 938128.8238 902148.368 1209619.169 0.694216357 0.838668102 0.884795567 0.892072222 0.793951347 0.581683573 0.928849487 0.775557173 0.745811898 1 20.20612148 -1.508132037 5.83620668 1.000272007 0.798059865 0.285652851 0.097965114 0.000340453 2.87E-05 0.093139071 0.021923853 0.031036159 1.508132037 -0.202212141 LSETWLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSETWLR 7 0 Q9UJA5;Q9UJA5-4 Q9UJA5 TRMT6 tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 0 81.297 0.064172 34187000 33581 33849 29872 34415 33055 29191 35849 33185 37196 43416 FALSE TRUE 32268.61739 32883.65966 35270.5349 36191.16227 34118.24409 29781.26202 36287.73079 32499.71815 32973.66602 40475.39565 0.79724032 0.812435781 0.871406797 0.894152156 0.842937877 0.735786804 0.896538013 0.802949981 0.814659511 1 15.30475756 -1.506233388 5.215110703 1.000449819 0.830922864 0.546120831 0.046541095 0.000239668 2.27E-05 0.04437039 0.010430757 0.03117214 1.506233388 -0.169526954 EPELGLEELLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPELGLEELLR 11 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ; 99.973 0.01018 23019000 20447 22240.2 17246.9 23401 21970.5 20529.8 20970.6 20648.8 23602 29855 FALSE TRUE 19647.90863 21605.93127 20363.79849 24608.72841 22677.20109 20944.92662 21227.24448 20222.39506 20922.79991 27832.89426 0.705924021 0.77627325 0.73164502 0.884159879 0.814762593 0.752524205 0.762667521 0.726564578 0.751729221 1 14.76450332 -1.505885967 3.079953691 1.006968337 0.767736904 0.677640432 0.048135831 60532820.84 77189620.94 3611352.671 0.011913724 0.031197086 1.505885967 -0.239231434 KAPAPFRPASER ddPTM_BT-474_Pertuzumab_2h_R1 2 KAPAPFRPASER 12 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 131.79 0.00010821 2434960000 1192420 1351900 997780 1160730 1194620 878320 1227930 1299230 1248620 1375790 FALSE TRUE 1145818.908 1313345.136 1178101.041 1220635.414 1233046.037 896080.2322 1242957.775 1272400.446 1106881.892 1282606.518 0.893351852 1.023965743 0.918521016 0.951683464 0.96135956 0.698640011 0.969087368 0.99204271 0.862994127 1 20.29064721 -1.504906129 2.780802486 1.003140632 0.925079033 0.069645094 0.086256774 23838286.32 24476419.45 567882.6087 0.02056431 0.031267551 1.504906129 -0.078061599 SYLMWHQQTHTGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SYLMWHQQTHTGEK 14 0 Q5CZA5-2;Q5CZA5;O43296 Q5CZA5-2 ZNF805;ZNF264 Zinc finger protein 805;Zinc finger protein 264 0 51.211 0.096184 1158900000 734210 1046200 1034900 1840300 1169200 1200100 1281900 1076000 996500 1526100 FALSE TRUE 705516.2615 1016363.4 1221929.451 1935278.104 1206808.38 1224366.844 1297588.276 1053780.224 883381.4977 1422735.888 0.495887021 0.714372505 0.85885895 1.360251133 0.848230786 0.860572124 0.912037355 0.740671711 0.620903363 1 20.44023644 -1.498207328 7.941595792 1.000016971 0.836038213 0.053847086 0.216270563 6.71E-05 4.24E-06 0.216055422 0.050919486 0.031753578 1.498207328 -0.163978758 QETSLTSHDLFDIDPVVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QETSLTSHDLFDIDPVVAR 19 0 Q14669-3;Q14669;Q14669-2;Q14669-4;H7C2Y1 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 0 118.54 7.72E-05 65864000 62586 71875 55540 77454 83312 78445 69659 70603 70432 74286 FALSE TRUE 60140.06993 69825.19537 65577.31348 81451.41022 85991.80614 80031.21165 70511.50768 69145.02338 62436.85464 69254.54305 0.868391694 1.008239926 0.946902695 1.176116492 1.241677475 1.155609555 1.018149923 0.998418592 0.901556084 1 16.07962109 -1.49743037 4.442126783 0.999756532 1.041583467 0.005328199 0.115425444 0.000299232 3.39E-05 0.120159511 0.028157161 0.031810437 1.49743037 0.041826936 GQSQTS(ph)PDHRS(ph)DTSSPEVR ddPTM_BT-474_Pertuzumab_2h_R1 3 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GQS(0.322)QT(0.322)S(0.357)PDHRS(0.701)DT(0.091)S(0.099)S(0.108)PEVR;GQS(0.325)QT(0.325)S(0.356)PDHRS(0.916)DT(0.027)S(0.025)S(0.027)PEVR;GQS(0.317)QT(0.318)S(0.367)PDHRS(0.902)DT(0.03)S(0.033)S(0.033)PEVR 60.207 0.036705 333570000 166405 197150 173837 234692 220677 222642 225789 176876 203260 215358 TRUE FALSE 159901.7086 191527.475 205253.2129 246804.4822 227775.2761 227143.9738 228552.2733 173223.4488 180186.7769 200771.6108 0.79643585 0.953956958 1.022321891 1.229279783 1.13449942 1.13135504 1.138369475 0.862788559 0.897471391 1 17.61519576 -1.496981712 8.572952557 0.999998869 1.023204828 0.000610763 0.133257356 3.10E-06 1.82E-07 0.139118946 0.032789053 0.031843316 1.496981712 0.023205959 TSS(ph)IADEGTYTLDSILR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSSIADEGTYTLDSILR 17 0 A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3;E7ERV5 A0A087WY00 MYO5A Unconventional myosin-Va 1 T(0.14)S(0.14)S(0.72)IADEGTYTLDSILR;TSS(1)IADEGTYTLDSILR;T(0.003)S(0.196)S(0.801)IADEGTYTLDSILR;TS(0.001)S(0.999)IADEGTYTLDSILR 395.36 3.81E-122 415348000 368593 363828 309097 429281 485102 414334 374397 403298 373740 402210 TRUE FALSE 354187.9781 353451.9817 364957.7037 451436.2439 500705.7464 422712.1174 378978.9825 394969.7554 331314.602 374967.9584 0.944581984 0.942619159 0.973303706 1.203932853 1.33532942 1.127328637 1.010696978 1.053342683 0.883581102 1 18.51640779 -1.495844555 4.415223145 0.99964404 1.059890709 0.01193552 0.130098617 0.000494592 5.65E-05 0.136671524 0.03202385 0.031926804 1.495844555 0.060246668 (ac)ADDVDQQQTTNTVEEPLDLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADDVDQQQTTNTVEEPLDLIR 21 0 P62310 P62310 LSM3 U6 snRNA-associated Sm-like protein LSm3 0 ; 114.7 4.94E-36 306800000 9909.2 7850.6 9656.6 14014.3 0 11763.8 7559.1 13437 10320 5246.5 FALSE TRUE 9521.937509 7626.708575 11401.76243 14737.5797 0 12001.6721 7651.610527 13159.52125 9148.516865 4891.149882 1.946768702 1.559287439 2.331100601 3.013111448 0 2.453752673 1.564378666 2.690475976 1.870422515 1 12.25595796 -1.495798828 2.53305804 0.949123107 1.964386258 0.112180554 0.786959574 10151661.17 9634817.652 3585745.253 0.19341177 0.031930166 1.495798828 1.015263151 SASSASSLFS(ph)PSSTLFSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASSASSLFSPSSTLFSSSR 20 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 SASSASSLFS(0.981)PS(0.016)S(0.002)TLFSSSR 152.13 7.12E-08 177510000 81058 69985 70686 70466 69894 73808 81642 71206 80393 85648 TRUE FALSE 77890.16375 67989.09632 83460.5326 74102.7587 72142.20399 75300.44833 82641.15922 69735.57122 71267.12367 79846.98467 0.975492864 0.851492346 1.04525591 0.928059576 0.903505678 0.943059386 1.034994115 0.873365118 0.892546212 1 16.28495031 -1.495658664 3.458217396 1.001123005 0.937516402 0.082884531 0.061128264 9804856.258 4240969.932 82382.16286 0.013665922 0.031940473 1.495658664 -0.063606603 QPEDDSSQAFISTQNGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPEDDSSQAFISTQNGSPR 19 0 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 QPEDDSSQAFISTQNGS(1)PR 353.35 7.94E-91 291990000 70990 72416 64466 76309 66088 68756 73840 76425 74268 82654 TRUE FALSE 68215.63232 70350.76658 76116.44024 80247.31663 68213.78054 70146.29343 74743.67601 74846.79704 65837.408 77055.77096 0.885276099 0.912985046 0.987809729 1.041418646 0.885252067 0.910331472 0.969994526 0.971332791 0.854412423 1 16.23361539 -1.495363545 3.079323561 1.001635166 0.941043309 0.105293248 0.054291777 512726951 689384383.7 7303773.525 0.013176659 0.031962185 1.495363545 -0.060591856 PS(ph)DWWVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 PSDWWVVK 8 0 Q03188;H0Y8J2;Q03188-2 Q03188 CENPC Centromere protein C 1 PS(1)DWWVVK;PS(1)DWWVVK 69.954 0.055159 665000000 256720 423810 349690 526860 466200 502720 489370 380090 282340 497390 TRUE FALSE 246687.0986 411723.3538 412886.7618 554051.3077 481195.7464 512885.3428 495359.0564 372241.0087 250289.9469 463701.3323 0.531995665 0.887906342 0.890415302 1.194845193 1.037727763 1.106068297 1.068271799 0.802760274 0.539765425 1 18.82283635 -1.490832721 4.485307193 1.000447209 0.914042763 0.01460893 0.213184675 0.000981559 0.000111425 0.212518942 0.049832974 0.032297379 1.490832721 -0.086404446 IIFVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IIFVGR 6 0 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 B1ANR0 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ; 141.66 0.027043 331640000 348960 352560 285760 330600 314130 318210 333090 335750 372990 393860 FALSE TRUE 335322.2574 342505.334 337403.1887 347662.3056 324234.2767 324644.4242 337166.4551 328816.6452 330649.7389 367183.5114 0.913227983 0.932790617 0.918895261 0.946835288 0.883030601 0.884147611 0.918250533 0.895510378 0.900502688 1 18.48614175 -1.490103399 6.783332636 1.000031279 0.910039556 0.659758676 0.01931184 9.53E-06 7.16E-07 0.019505774 0.004595958 0.032351662 1.490103399 -0.089991723 VSS(ph)PVFGATSSIK ddPTM_BT-474_Pertuzumab_2h_R1 6 VSSPVFGATSSIK 13 0 F6Q6H0;I6L8A6;Q99708-3;Q99708;Q99708-2 F6Q6H0 RBBP8 DNA endonuclease RBBP8 1 VSS(1)PVFGATSSIK;VSS(1)PVFGATSSIK;VS(0.001)S(0.999)PVFGATSSIK;VS(0.012)S(0.988)PVFGATSSIK;VS(0.003)S(0.997)PVFGATSSIK;VSS(1)PVFGATSSIK 270.16 8.29E-26 3097790000 5007290 4976730 3801990 4107760 4219130 3899370 4801440 4942870 5051040 5481310 TRUE FALSE 4811599.571 4834798.533 4489094.168 4319761.986 4354842.148 3978217.933 4860201.459 4840798.007 4477667.115 5110055.991 0.941594295 0.94613416 0.878482384 0.845345333 0.852210261 0.778507699 0.951105324 0.947308213 0.876246194 1 22.28490767 -1.48915656 7.015995674 1.000027892 0.892955832 0.26913654 0.053891751 2.56E-05 1.86E-06 0.056768651 0.013377016 0.032422272 1.48915656 -0.107072061 S(ph)SGPYGGGGQYFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSGPYGGGGQYFAK 14 0 F8W6I7;P09651-2;P09651;P09651-3;Q32P51;H0YH80 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 1 S(0.701)S(0.299)GPYGGGGQYFAK 286.1 1.03E-33 306730000 444770 380470 432520 393740 384040 328700 392050 527690 409920 473150 TRUE FALSE 427387.8967 369619.3681 510685.9854 414060.9686 396392.9954 335346.5392 396848.0252 516793.0171 363387.6001 441103.1291 0.968906971 0.837943201 1.157747365 0.938694245 0.89864018 0.760245206 0.899671753 1.171592272 0.823815512 1 18.75075647 -1.479554908 5.731289861 1.000050759 0.951209128 0.012626554 0.127531066 8.48E-05 7.70E-06 0.126520956 0.029790296 0.033147066 1.479554908 -0.048841631 S(ph)RS(ph)PQAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPQAFR 8 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 2 S(1)RS(1)PQAFR 54.7 0.073176 238160000 40683 46868 48576 65237 47771 45865 36669 63647 62102 42613 TRUE FALSE 39093.06338 45531.37053 57354.76377 68603.88939 49307.5976 46792.42172 37117.76619 62332.66721 55052.44131 39726.78355 0.984048037 1.146112684 1.443730366 1.726892621 1.241167625 1.177855782 0.934325985 1.569033826 1.385776456 1 15.27782437 -1.472392997 5.828935701 0.999745783 1.302407299 0.11725652 0.236374275 0.000809196 7.32E-05 0.237160796 0.055853038 0.033698223 1.472392997 0.302661517 VGEAWQDRPGAPR ddPTM_BT-474_Pertuzumab_2h_R1 3 VGEAWQDRPGAPR 13 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;H7C1R1;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 ;; 107.14 0.0012026 1499550000 887400 906480 734210 850050 814380 848160 841470 893580 985930 998430 FALSE TRUE 852719.4269 880628.0779 866898.0794 893921.1824 840575.2723 865310.3763 851768.1616 875127.2607 874011.3598 930805.4468 0.916109193 0.946092528 0.931341864 0.96037382 0.903062262 0.929636133 0.915087212 0.940182789 0.938983934 1 19.82812013 -1.465462693 2.874582081 1.001988692 0.931561211 0.63036203 0.015801441 4388597.677 4530903.744 68839.92923 0.003591035 0.03424028 1.465462693 -0.070427482 ELHSWEPEPDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELHSWEPEPDVR 12 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 ;;; 155.99 6.44E-05 2163040000 1115200 1291170 1144940 1544570 1391970 1546660 1475190 1177900 1335740 1422460 FALSE TRUE 1071616.751 1254347.096 1351856.127 1624285.443 1436743.979 1577934.525 1493243.816 1153575.953 1184112.395 1326115.517 0.808087031 0.945880717 1.019410534 1.224844609 1.083422945 1.189892211 1.126028462 0.869891 0.892917985 1 20.33877502 -1.465011668 8.378654961 0.999999261 1.022454103 0.00052712 0.132409735 1.97E-06 1.26E-07 0.137864539 0.032493914 0.034275858 1.465011668 0.022454842 VLEGHVFDVNCCR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLEGHVFDVNCCR 13 0 F5H3E9;F5H5D4;F5H103;F5H3I1;F5H0C4;Q9BRP4-3;Q9BRP4-2;Q9BRP4 F5H3E9 PAAF1 Proteasomal ATPase-associated factor 1 0 ; 112.02 0.00093345 898760000 265695 306010 220731 308750 245940 220384 301140 277410 281350 338580 FALSE TRUE 255311.3457 297282.8944 260622.0018 324684.6245 253850.8835 224840.3155 304825.4414 271681.3866 249412.3275 315647.675 0.808849125 0.941818736 0.825673757 1.028629862 0.80422225 0.712314182 0.965714198 0.860710875 0.790160509 1 18.2679556 -1.462464714 2.986007891 1.003342836 0.864646882 0.179119423 0.089505816 21224609.14 24266343.47 590811.8609 0.020620443 0.034477462 1.462464714 -0.138695953 MDADGFLPITLIASFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDADGFLPITLIASFHR 17 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 103.61 0.00089073 101660000 92506 129960 111930 135310 124200 108890 120650 107160 130090 152880 FALSE TRUE 88890.76325 126253.668 132158.2409 142293.3653 128195.0058 111091.8304 122126.5508 104947.1086 115322.7286 142525.3014 0.623684092 0.88583337 0.927261613 0.998372667 0.899454374 0.779453397 0.856876285 0.736340197 0.80913864 1 17.12085853 -1.46018082 9.009773054 1.000002218 0.837938451 0.195061945 0.100315305 4.63E-06 2.77E-07 0.100542363 0.023697738 0.034659252 1.46018082 -0.162063767 RDPMYNEYLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDPMYNEYLDR 11 1 Q7L5D6;Q7L5D6-2 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 ;;; 186.58 6.36E-06 1072150000 575564 621046 540545 612806 573275 470855 669200 589078 604022 737198 FALSE TRUE 553070.3226 603334.3761 638233.5059 644432.9911 591714.911 480376.0107 677389.8698 576913.3334 535455.9548 687266.9228 0.804738747 0.877874893 0.928654479 0.93767497 0.860968121 0.698965707 0.985628505 0.839431252 0.77910916 1 19.390511 -1.460055487 2.939348545 1.003561601 0.861674904 0.22442798 0.079320615 18933769.28 21409891.35 553683.1013 0.019964146 0.034669255 1.460055487 -0.141886696 LDIPTGTT(ph)PQRK ddPTM_BT-474_Pertuzumab_2h_R1 3 LDIPTGTTPQRK 12 1 P52732 P52732 KIF11 Kinesin-like protein KIF11 1 LDIPT(0.003)GT(0.053)T(0.944)PQRK;LDIPT(0.004)GT(0.075)T(0.921)PQRK;LDIPT(0.041)GT(0.177)T(0.781)PQRK 113.52 0.00067794 2711110000 2950830 2637810 2796120 2592580 2703620 2574580 2899270 3105890 2853670 3219460 TRUE FALSE 2835508.301 2562582.241 3301441.083 2726383.364 2790584.393 2626639.772 2934752.134 3041752.286 2529733.345 3001403.107 0.944727583 0.853794759 1.099965905 0.908369608 0.929759947 0.875137287 0.977793395 1.013443439 0.842850245 1 21.51720566 -1.457053886 2.937255655 1.001406006 0.944579242 0.052951177 0.074117502 29015725.98 35543618.41 338852.743 0.017106887 0.0349097 1.457053886 -0.056826764 NYIVEDGDIIFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 NYIVEDGDIIFFK 13 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 168.94 6.83E-05 19770000 60914 58240 43174 56290 50671 54970 53863 56243 55821 71066 FALSE TRUE 58533.41354 56579.05222 50976.5022 59195.13365 52300.87873 56081.53106 54522.19151 55081.5624 49484.4341 66252.63652 0.883488063 0.853989444 0.769426016 0.893475894 0.78941581 0.846479989 0.822943725 0.831386723 0.74690513 1 16.01569025 -1.457004909 5.534610837 1.000170745 0.827172276 0.576805319 0.044607425 8.65E-05 8.49E-06 0.039771128 0.009364937 0.034913637 1.457004909 -0.172998468 REELITNWEQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 REELITNWEQIR 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 247.32 2.03E-16 719900000 236120 257860 234910 285400 237380 192207 273340 257060 255470 345520 FALSE TRUE 226892.1694 250506.0853 277363.4625 300129.5282 245015.5433 196093.5572 276685.2167 251751.6212 226470.1166 322117.6226 0.704376766 0.77768513 0.861062677 0.931738927 0.760639984 0.608763829 0.858957093 0.781551842 0.703066522 1 18.29722807 -1.45639012 5.555227763 1.000208414 0.781825947 0.366459669 0.087931542 0.000231401 2.26E-05 0.086800049 0.020439589 0.034963096 1.45639012 -0.218382467 ELVVNCCTEFIHLISSEANEICNK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELVVNCCTEFIHLISSEANEICNK 24 0 Q01658 Q01658 DR1 Protein Dr1 0 ; 249.51 2.84E-38 329480000 358800 378180 277386 320520 361520 363600 342080 336960 415440 356820 FALSE TRUE 344777.6993 367394.6767 327515.8206 337062.0756 373148.6191 370952.2411 346266.4774 330001.6582 368280.9929 332652.2636 1.036450784 1.104440633 0.984559122 1.013256522 1.121737802 1.115135178 1.040926262 0.992031904 1.107105026 1 18.34365533 -1.454551921 3.064242607 0.998860902 1.053542448 0.103395613 0.049518018 2604264.012 2542985.477 17321.97442 0.011996259 0.035111395 1.454551921 0.054681546 NPDILVGENDLTALSYLHEPAVLHNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NPDILVGENDLTALSYLHEPAVLHNLK 27 0 Q9ULV0 Q9ULV0 MYO5B Unconventional myosin-Vb 0 123.36 4.92E-05 100610000 101830 100720 94564 87246 87613 113380 108160 82042 117280 118940 FALSE TRUE 97850.37102 97847.56422 111653.8184 91748.77652 90431.15171 115672.6213 109483.6944 80347.80403 103966.8661 110884.0879 0.882456382 0.882431069 1.006941758 0.8274296 0.815546698 1.043185037 0.987370655 0.724610768 0.937617544 1 16.75869282 -1.454352155 2.237996792 1.006352901 0.894191236 0.090278362 0.092279837 1754926.26 1484250.399 69353.5952 0.024805217 0.035127549 1.454352155 -0.112161664 SSGQSAQLLSHEPGDPPCLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGQSAQLLSHEPGDPPCLR 20 0 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ; 91.725 0.0017538 369180000 243390 258150 245195 243409 266280 245719 271990 256410 290120 331950 FALSE TRUE 233878.0497 250787.8148 289507.1908 255971.3677 274845.138 250687.6065 275318.695 251115.0439 257186.7939 309466.7308 0.755745372 0.810386997 0.935503439 0.827136949 0.888124993 0.810063188 0.889655228 0.811444394 0.831064435 1 18.2394248 -1.45142187 3.046578473 1.003353435 0.841991233 0.49098473 0.048861481 21157473.48 23512409.55 599726.1816 0.011285713 0.035365364 1.45142187 -0.161362202 VSYGIGDEEHDQEGR ddPTM_BT-474_Pertuzumab_2h_R1 8 VSYGIGDEEHDQEGR 15 0 P27695;G3V3M6;G3V3C7;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;;;;; 297.72 3.92E-44 26895270000 7779490 8119418 7080033 8400060 8397572 8325566 7879416 7461761 8602738 8677050 FALSE TRUE 7475458.93 7887860.148 8359552.458 8833588.103 8667687.53 8493914.649 7975846.65 7307673.028 7626191.248 8089345.675 0.924111693 0.975092482 1.033402798 1.092002797 1.071494269 1.050012571 0.985969319 0.903370102 0.942745131 1 22.94759158 -1.451045116 6.320026866 1.000000999 0.997055212 7.76E-05 0.060277978 9.81E-07 8.52E-08 0.067437139 0.015889695 0.035396057 1.451045116 -0.002945787 NAEMHK ddPTM_BT-474_Pertuzumab_2h_R1 3 NAEMHK 6 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 70.912 0.089617 419930000 1212440 1137160 908780 1012120 1014620 947250 1095400 1089150 1199590 1310650 FALSE TRUE 1165056.504 1104729.31 1073016.762 1064355.634 1047256.174 966404.044 1108805.833 1066658.672 1063417.572 1221878.508 0.953496192 0.904123694 0.878169765 0.871081394 0.857086991 0.79091664 0.907459969 0.872966228 0.870313673 1 20.22066941 -1.442454267 2.601398105 1.004357155 0.876717431 0.462638424 0.039277563 6420686.792 6477308.637 204391.1338 0.009874416 0.036103203 1.442454267 -0.127639725 SQAIHQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQAIHQLK 8 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 80.239 0.025964 479810000 747280 748300 640020 698820 686220 641580 790710 722530 819010 897350 FALSE TRUE 718075.4714 726959.2167 755685.8512 734886.1839 708292.8895 654553.1872 800386.9455 707609.503 726039.4184 836571.6852 0.858354979 0.868974207 0.903312728 0.878449745 0.846661323 0.78242331 0.956746397 0.845844433 0.867874722 1 19.67412964 -1.440055832 2.486026197 1.005341989 0.8682077 0.472574126 0.041949329 2497398.506 2408635.652 92984.7123 0.010419089 0.036303138 1.440055832 -0.137134289 AFAHITGGGLLENIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFAHITGGGLLENIPR 16 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 179.79 2.57E-09 1085490000 718220 963110 755100 805640 823750 873080 854260 768910 854960 1063180 FALSE TRUE 690151.1684 935643.0458 891563.3671 847219.1769 850246.6669 890734.2758 864714.6894 753031.7398 757908.5251 991169.8716 0.696299583 0.943978497 0.899506122 0.854766878 0.857821339 0.898669644 0.872418255 0.759740345 0.764660576 1 19.91877281 -1.433391823 7.685974113 1.000006985 0.84184179 0.308863449 0.072266128 8.66E-06 6.39E-07 0.07009058 0.016519779 0.036864486 1.433391823 -0.158165195 RSS(ph)PVPPVPERR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSPVPPVPERR 12 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.386)S(0.614)PVPPVPERR 65.47 0.047777 660460000 143550 133650 108200 129290 132830 139600 139310 120230 142640 161540 TRUE FALSE 137939.9073 129838.4329 127754.1469 135962.6724 137102.5976 142422.8076 141014.9175 117747.2085 126448.1052 150598.7519 0.91594323 0.862148133 0.848308138 0.902814072 0.910383359 0.945710412 0.936361794 0.781860454 0.839635811 1 17.20035029 -1.430246915 3.147945186 1.001939721 0.879390393 0.350322339 0.047796805 19795118.67 21964029.1 333624.7993 0.012753718 0.037132406 1.430246915 -0.122549328 TLEDEEEQERER ddPTM_BT-474_Pertuzumab_2h_R1 2 TLEDEEEQERER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 0 ; 170.18 3.82E-05 351690000 390470 449580 356750 396880 411920 524020 402150 361340 496780 488540 FALSE TRUE 375210.0007 436758.4186 421222.6609 417363.0244 425169.7809 534616.0434 407071.632 353878.2027 440387.6171 455450.7507 0.823821237 0.95895861 0.924847879 0.916373557 0.933514283 1.17381746 0.893777497 0.776984564 0.966926976 1 18.79693553 -1.421599296 8.201298183 1.000001355 0.924936268 0.04108356 0.099042578 2.58E-06 1.82E-07 0.100956531 0.023795253 0.037879192 1.421599296 -0.075065087 S(ph)YSPAHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.581)Y(0.001)S(0.418)PAHNR;S(0.846)YS(0.154)PAHNR 94.692 0.0065568 1424380000 580740 711200 582870 784120 736500 712830 725520 573700 686250 741180 TRUE FALSE 558044.0388 690917.2723 688207.5749 824588.5272 760190.1914 727243.911 734399.1308 561852.8945 608349.777 690979.2184 0.807613346 0.99991035 0.995988818 1.193362268 1.10016361 1.052483044 1.062838232 0.813125604 0.880416894 1 19.3982828 -1.417123588 6.184247615 1.000002163 0.991296832 0.000507219 0.118076042 3.82E-06 3.60E-07 0.124058577 0.029233622 0.038271582 1.417123588 -0.008705331 LS(ph)NGSFSAPSLTNSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSNGSFSAPSLTNSR 15 0 O94806;O94806-2 O94806 PRKD3 Serine/threonine-protein kinase D3 1 LS(1)NGSFSAPSLTNSR;LS(0.999)NGS(0.001)FSAPSLTNSR 239.93 8.43E-18 368900000 342040 389310 282770 367960 350070 331360 366060 384390 340540 318420 TRUE FALSE 328672.6987 378207.26 333872.8292 386950.4597 361330.3195 338060.3262 370539.9518 376452.2122 301883.3269 296853.1298 1.107189602 1.274055154 1.124707122 1.303508102 1.217202324 1.138813414 1.248226529 1.268142978 1.01694507 1 18.1793898 -1.416860793 3.762223917 0.998720709 1.199926507 0.292109858 0.086593384 0.000864446 0.000133988 0.078002285 0.018270696 0.038294747 1.416860793 0.201205798 LKDLFNVDAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDLFNVDAFK 11 1 O14777 O14777 NDC80 Kinetochore protein NDC80 homolog 0 109.18 0.001791 52516000 159430 166230 147390 137310 160040 122320 172050 159140 174130 180210 FALSE TRUE 153199.2993 161489.2832 174026.6517 144396.5856 165187.8319 124793.3942 174155.5994 155853.7034 154363.4924 168004.2162 0.911877707 0.96122161 1.035846931 0.859481916 0.983236229 0.742799181 1.036614457 0.927677334 0.918807253 1 17.35813791 -1.414091615 2.978192598 1.001201689 0.933038576 0.059888328 0.081787697 130847330.2 148687538 1322509.275 0.01852529 0.038539705 1.414091615 -0.068163113 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR 31 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 137.88 3.35E-07 16751000 7905.4 6848.5 6183.9 6359.4 5976.9 6421.2 6080.7 7334.6 7572.1 8799.2 FALSE TRUE 7596.448228 6653.187485 7301.46829 6687.609396 6169.152417 6551.041064 6155.117426 7183.137947 6712.546953 8203.222346 0.926032223 0.811045612 0.890073191 0.815241757 0.752040132 0.798593624 0.75032922 0.87564833 0.818281728 1 13.00197502 -1.412286887 4.511021888 1.000391112 0.824818512 0.4836713 0.053798966 0.000210211 2.74E-05 0.051744416 0.012169309 0.038700191 1.412286887 -0.175572601 RVELLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVELLK 6 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 105.2 0.053201 2439100000 2666800 2801000 2209900 2443200 2443500 2499600 2512700 2766500 2841700 3231400 FALSE TRUE 2562578.508 2721118.222 2609278.089 2569293.845 2522097.397 2550143.625 2543451.174 2709370.808 2519122.129 3012534.4 0.850638754 0.903265444 0.866140513 0.852867886 0.837201194 0.846511039 0.844289504 0.899365932 0.836213565 1 21.52254628 -1.408778265 3.042998466 1.002188395 0.86195324 0.774163018 0.022716 7626179.16 9639722.231 145876.2573 0.005561495 0.039014113 1.408778265 -0.140235155 GIAPAS(ph)PMLGNASNPNK ddPTM_BT-474_Pertuzumab_2h_R1 8 GIAPASPMLGNASNPNK 17 0 H0YIY6;P27448-6;P27448-7;H0YKP9;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK;GIAPAS(0.998)PMLGNAS(0.002)NPNK;GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK 341.78 1.32E-72 2021584000 2040881 2053198 1889866 2076414 1884157 1753117 2058005 2292024 2133342 2275355 TRUE FALSE 1961121.114 1994642.803 2231406.826 2183577.975 1944762.621 1788566.227 2083191.481 2244692.903 1891173.96 2121243.179 0.924514989 0.94031784 1.05193353 1.029385974 0.916803241 0.843168876 0.982061605 1.058196875 0.891540385 1 21.01647859 -1.401813989 0.375493495 1.020247459 0.965046846 0.01503426 0.067822096 140.920831 11.5058559 2.867966144 0.05203962 0.03964478 1.401813989 -0.055200613 VASNPYTWFTMEALEETWR ddPTM_BT-474_Pertuzumab_2h_R1 1 VASNPYTWFTMEALEETWR 19 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 203.04 1.34E-21 0 14812 19141 14831 17574 18142 16735 17483 17118 14976 20115 FALSE TRUE 14233.13066 18595.11742 17511.29161 18480.99625 18725.55391 17073.39317 17696.96218 16764.50732 13275.98726 18752.59313 0.758995333 0.991602457 0.933806407 0.985516836 0.998558107 0.910455053 0.943707468 0.893983419 0.707954744 1 14.19480249 -1.401065744 6.81453809 1.000007267 0.912338835 0.081897916 0.092813743 9.90E-06 8.70E-07 0.086848045 0.020468584 0.039713143 1.401065744 -0.087668431 VDIAPHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDIAPHVR 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 99.139 0.0070255 727520000 800240 959260 800880 801660 773230 705460 941550 799330 1003820 1068110 FALSE TRUE 768965.7361 931902.844 945616.8315 843033.7687 798101.6452 719724.8845 953072.9705 782823.5562 889870.562 995765.9583 0.772235413 0.935865337 0.949637637 0.846618386 0.801495209 0.722785187 0.95712548 0.786152157 0.893654332 1 19.92544717 -1.399845743 4.298006686 1.000391061 0.851504938 0.250089266 0.07702418 0.000282946 3.95E-05 0.073109777 0.017187137 0.03982486 1.399845743 -0.148886123 GGLQEVAEQLELER ddPTM_BT-474_Pertuzumab_2h_R1 3 GGLQEVAEQLELER 14 0 Q9UIV1;Q9UIV1-2 Q9UIV1 CNOT7 CCR4-NOT transcription complex subunit 7 0 ;; 163.99 9.75E-06 48746800 75436 93942 81866 113036 97744 110276 97846 90528 91667 95548 FALSE TRUE 72487.87772 91262.86614 96661.0073 118869.8015 100888.0245 112505.8563 99043.46862 88658.56516 81261.34646 89076.44885 0.813771526 1.024545402 1.085146619 1.33446947 1.132600433 1.263025836 1.111892873 0.995308707 0.912265223 1 16.44275642 -1.395853594 8.625037238 0.999999484 1.083749364 0.01993875 0.145534451 1.50E-06 1.05E-07 0.146774236 0.034594806 0.040192628 1.395853594 0.08374988 GTYFPTWEGLFWEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GTYFPTWEGLFWEK 14 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 225.13 6.73E-12 169946000 163307 180268 148817 145671 160215 145135 162935 175535 176899 189254 FALSE TRUE 156924.7819 175126.9331 175711.5423 153189.0978 165368.461 148069.7291 164929.0473 171910.1409 156818.1671 176435.658 0.88941648 0.992582424 0.995895865 0.868243412 0.937273468 0.839227914 0.934782964 0.974350326 0.88881221 1 17.42878264 -1.395399602 2.88786983 1.001277874 0.928695237 0.162692722 0.050581452 9723028.687 11415323.85 103006.8729 0.012508653 0.040234666 1.395399602 -0.072582637 AALLELWELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALLELWELRR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 199.09 8.25E-08 990540000 394590 445560 379700 451750 390480 328370 411890 438250 460130 516690 FALSE TRUE 379168.9866 432853.065 448320.2364 475064.8716 403040.1438 335009.8664 416930.833 429199.9844 407897.9714 481694.1261 0.787157173 0.898605654 0.930715598 0.986237627 0.836713844 0.695482565 0.865551001 0.891021835 0.846798724 1 18.87775781 -1.393344356 2.737949304 1.002962857 0.863569121 0.236680258 0.07525668 10404433.27 11567048.42 243406.8899 0.020606266 0.040425523 1.393344356 -0.139393736 GSRPPLILQSQSLPCS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQS(0.002)QS(0.019)LPCS(0.49)S(0.49)PR 61.039 0.034986 575970000 140730 169110 129940 133290 112770 128360 157940 175560 148840 178440 TRUE FALSE 135230.116 164287.1484 153423.0485 140169.1129 116397.3495 130955.5271 159872.917 171934.6246 131944.3072 166354.0999 0.812905219 0.987574989 0.922267913 0.84259488 0.699696308 0.787209496 0.961039837 1.033546061 0.793153324 1 17.3438979 -1.388988825 7.784827377 1.000002051 0.882909238 0.121974109 0.099301168 3.89E-06 3.05E-07 0.105730795 0.024920551 0.040832989 1.388988825 -0.117092813 VCVEFDGESWR ddPTM_BT-474_Pertuzumab_2h_R1 1 VCVEFDGESWR 11 0 Q9Y4C1;F8WE62;C9JC73;C9J7Q7 Q9Y4C1 KDM3A Lysine-specific demethylase 3A 0 85.807 0.034758 40890000 140110 188540 137870 205600 193740 219450 172280 171310 156680 200700 FALSE TRUE 134634.3463 183163.0238 162786.1759 216211.0406 199971.8231 223887.4294 174388.4142 167772.3886 138894.3433 187106.4102 0.719560309 0.978924365 0.870019235 1.15555122 1.068759872 1.196578081 0.932028005 0.89666831 0.742328085 1 17.51349946 -1.385888872 4.068144606 1.000124266 0.9608555 0.005756725 0.149873695 0.00017306 2.61E-05 0.14866395 0.034929576 0.041125494 1.385888872 -0.039268766 AAVVT(ph)SPPPTTAPHK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAVVTSPPPTTAPHK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;P35611-5;A0A0A0MSR2;D6RJE2;D6RAH3;D6RF25 P35611 ADD1 Alpha-adducin 1 AAVVT(0.5)S(0.5)PPPTTAPHK;AAVVT(0.5)S(0.5)PPPTTAPHK;AAVVT(0.5)S(0.5)PPPTTAPHK;AAVVT(0.5)S(0.5)PPPTTAPHK 146.3 1.44E-05 6011700000 2767530 2897410 2802930 3129590 3648710 3472670 3077820 2901570 3207830 3276270 TRUE FALSE 2659371.868 2814778.704 3309481.802 3291108.515 3766074.071 3542889.767 3115487.282 2841651.566 2843690.587 3054365.315 0.870679043 0.921559281 1.083525204 1.077509785 1.233013632 1.159943033 1.020011348 0.930357463 0.931025039 1 21.54244119 -1.385021133 8.350801012 0.999999794 1.02817592 0.00415393 0.109573816 4.65E-07 3.44E-08 0.11752904 0.027701658 0.041207747 1.385021133 0.028176126 ERS(ph)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERSPAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 40 3 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 150.22 1.30E-13 2474250000 126547 142307 113742 144582 113086 134113 134214 140681 143377 160099 TRUE FALSE 121601.4033 138248.5437 134297.7096 152043.8943 116723.5139 136824.8567 135856.5511 137775.8882 127101.444 149255.3521 0.814720555 0.926255184 0.899784883 1.01868303 0.782039051 0.916716585 0.910229008 0.923088427 0.851570428 1 17.18742314 -1.38397262 3.420576321 1.000789619 0.898494577 0.203210511 0.062509222 23219124.12 35858742.78 183499.3738 0.014040211 0.041307354 1.38397262 -0.102295043 KRPETQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRPETQK 7 2 Q92466-4;Q92466;A0A087WTQ7;A0A087WV56;A0A087WW71;A0A087X0X5;Q92466-3;Q92466-2;Q92466-5 Q92466-4 DDB2 DNA damage-binding protein 2 0 51.787 0.084157 51814000 108190 91427 82613 95785 83473 80742 98636 95829 102000 117890 FALSE TRUE 103961.8152 88819.59148 97543.00682 100728.4753 86157.98485 82374.65856 99843.13687 93850.09766 90421.38762 109905.2053 0.945922579 0.808147269 0.887519445 0.916503227 0.783929975 0.749506435 0.908447754 0.853918587 0.822721612 1 16.74590019 -1.378268528 3.035884647 1.00189874 0.852025697 0.354931749 0.059457621 18086099.81 23435438.4 306619.6937 0.01386893 0.04185347 1.378268528 -0.149873044 LHAVDEELAS(ph)SPVCMDSFQPMDDSLIAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHAVDEELASSPVCMDSFQPMDDSLIAFR 29 0 A4PB68;Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2 A4PB68;Q3T8J9-3 GON4L GON-4-like protein 1 LHAVDEELAS(0.547)S(0.453)PVCMDSFQPMDDSLIAFR 223.27 9.97E-35 85980000 24511 30003 25727 31536 32621 35636 32872 24966 30535 33719 TRUE FALSE 23553.08302 29147.34382 30376.44119 33163.57674 33670.28409 36356.58434 33274.29737 24450.44338 27068.79481 31435.1821 0.749258679 0.927220454 0.966319874 1.05498281 1.071101926 1.156557141 1.058504998 0.77780505 0.861098712 1 14.9400925 -1.378067797 3.544846986 1.000231147 0.960472257 0.00957462 0.125787253 46.34760807 65178858.82 23021.84197 0.032289637 0.041872819 1.378067797 -0.039758889 AAFGISDSYVDGSSFDPQRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAFGISDSYVDGSSFDPQRR 20 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1;I3L1C0 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 63.337 0.056287 264390000 60286 63196 55987 53665 66814 74423 54616 65769 66010 57582 FALSE TRUE 57929.95647 61393.71196 66105.09632 56434.65708 68963.13299 75927.88405 55284.40695 64410.84717 58516.82154 53681.91985 1.07913347 1.143657159 1.231421985 1.051278666 1.284662195 1.41440329 1.029851524 1.199861096 1.090065737 1 15.71214865 -1.376862556 6.928974971 0.999991656 1.173412741 0.168403756 0.112589843 1.42E-05 1.27E-06 0.106386631 0.025074363 0.041989185 1.376862556 0.173421085 VHFTAER ddPTM_BT-474_Pertuzumab_2h_R1 6 VHFTAER 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 135.35 0.0030858 1611910000 418842 503898 458490 481809 419480 394451 567950 468721 508680 577627 FALSE TRUE 402473.1916 489527.3224 541349.3421 506675.2202 432972.9552 402427.0695 574900.742 459041.7476 450936.779 538503.8088 0.747391541 0.909050808 1.005284147 0.940894404 0.804029513 0.747305893 1.067588999 0.852439184 0.837388281 1 19.03859702 -1.372528958 3.661912461 1.00057 0.885365681 0.114216621 0.099663999 2623029556 449457294.4 13147312.76 0.023075065 0.04241027 1.372528958 -0.115204318 DSVLTWLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSVLTWLLR 9 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C0K6;A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;O60333-3 A0A3B3ITW6;A0A087WWA3;O60333-3 KIF1A;KIF1B;KIF1Bbeta Kinesin-like protein KIF1A;Kinesin-like protein;Kinesin-like protein KIF1B 0 ; 214.25 1.59E-06 262310000 266540 301240 258104 266460 264640 230986 295120 290530 291740 348510 FALSE TRUE 256123.3221 292648.9301 304749.1343 280212.0325 273152.3859 235656.6952 298731.7668 284530.454 258622.8983 324905.1073 0.788301927 0.900721237 0.937963508 0.862442683 0.84071435 0.725309298 0.919443124 0.875734015 0.795995177 1 18.3096589 -1.369695787 5.41363615 1.00005617 0.854875743 0.342725882 0.062091595 4.21E-05 4.91E-06 0.060189271 0.014181265 0.042687843 1.369695787 -0.145180427 KASTAPGAEER ddPTM_BT-474_Pertuzumab_2h_R1 1 KASTAPGAEER 11 1 F5GYV5;F8WCT1;Q66PJ3-2;A0A0C4DH18;Q66PJ3-5 F5GYV5 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 0 93.348 0.014939 99563000 86495 92812 75678 86137 77347 77408 89607 95805 96680 96487 FALSE TRUE 83114.67977 90165.09263 89354.69805 90582.54089 79834.9365 78973.2428 90703.63727 93826.59327 85705.29172 89951.84955 0.923990782 1.002370636 0.993361432 1.007011433 0.887529683 0.877950183 1.008357668 1.043075754 0.952790767 1 16.45686533 -1.358763768 3.382089909 1.000189014 0.971604563 0.027074279 0.052529268 261322.1697 25823745.15 7732.339583 0.013435894 0.043776016 1.358763768 -0.028584451 RVS(ph)PLNLSSVTP ddPTM_BT-474_Pertuzumab_2h_R1 3 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 1 RVS(1)PLNLSSVTP;RVS(1)PLNLSSVTP;RVS(1)PLNLSSVTP 99.991 0.0036916 2502700000 3464620 3813420 3352920 3633450 3546030 2922310 3946870 3630140 3868480 4337390 TRUE FALSE 3329218.82 3704664.995 3958867.229 3820972.79 3660091.275 2981401.11 3995172.976 3555176.34 3429346.368 4043614.712 0.823327408 0.916176555 0.979041652 0.944939877 0.905153319 0.737310877 0.98802019 0.87920749 0.848089299 1 21.94721411 -1.358510958 3.065536335 1.001110791 0.895179758 0.170168119 0.071572718 17958356.89 22616316.51 181191.1766 0.016984596 0.043801506 1.358510958 -0.105931033 KSQEKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSQEKPR 7 2 P14868;H7C278 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 57.177 0.065891 570250000 162610 157570 131680 123910 151920 117610 149440 164440 153530 215830 FALSE TRUE 156255.0214 153076.2579 155477.5052 130305.0099 156806.6448 119988.1548 151268.8914 161044.2565 136101.9181 201211.6419 0.776570481 0.760772371 0.772706309 0.647601743 0.779311989 0.596328094 0.751789956 0.800372459 0.676411746 1 17.61835425 -1.356823873 4.058086971 1.000656473 0.73252589 0.619948575 0.063581604 0.000369684 5.86E-05 0.060266483 0.014170712 0.043971991 1.356823873 -0.268130584 HEQILVLDPPTDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HEQILVLDPPTDLK 14 0 Q9P0L0-2;Q9P0L0;J3QKM9 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ; 120.7 0.00011884 794230000 559050 782490 465710 786720 485020 507550 696540 652670 862450 644250 FALSE TRUE 537201.7079 760174.1513 549874.1567 827322.7135 500621.1088 517813.0087 705064.4649 639192.1364 764548.2917 600614.3737 0.894420333 1.265660938 0.915519476 1.37746073 0.833515032 0.862138889 1.173905414 1.064230502 1.272943714 1 19.19607948 -1.35402957 4.870810302 0.999947355 1.073753181 0.014080739 0.183999466 9.78E-05 1.30E-05 0.165586 0.039001167 0.044255824 1.35402957 0.073805826 ALQDLENAASGDAAVHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALQDLENAASGDAAVHQR 18 0 Q96P16;A0A0C4DGQ6;Q96P16-3;K7EP82 Q96P16 RPRD1A Regulation of nuclear pre-mRNA domain-containing protein 1A 0 ; 237.39 7.55E-24 1160540000 804160 929260 651230 938060 870870 977140 859690 850720 846760 979510 FALSE TRUE 772732.5382 902758.4146 768921.7475 986473.389 898882.3245 996898.4403 870211.1434 833152.3347 750639.3547 913166.9152 0.846211711 0.988601755 0.842038553 1.08027719 0.984357087 1.09169356 0.952959562 0.912376829 0.822017686 1 19.80051906 -1.348422858 4.395678879 1.000066128 0.951637538 0.028360971 0.089482831 5.74E-05 8.51E-06 0.085736261 0.020180645 0.044830867 1.348422858 -0.04842859 TDLQGSAS(ph)PSKVEGVHT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 2 TDLQGSAS(0.991)PS(0.009)KVEGVHT(1)PR 163.31 3.96E-10 185700000 173910 136140 130440 97663 103540 126410 133350 151040 150390 158710 TRUE FALSE 167113.4049 132257.4205 154013.4096 102703.3991 106870.4581 128966.0968 134981.9772 147920.9712 133318.3577 147960.4303 1.1294466 0.893870207 1.040909446 0.69412747 0.722290804 0.871625586 0.912284297 0.999733313 0.901040619 1 17.17485188 -1.346582928 8.385895823 1.000000314 0.905182452 0.046771725 0.125288177 7.58E-07 5.91E-08 0.124951893 0.029451346 0.045021201 1.346582928 -0.094817863 GHEDDSYEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHEDDSYEAR 10 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 173.24 3.47E-06 40822000 17563 28873 22380 37314 26873 35356 27808 21400 25420 32025 FALSE TRUE 16876.61854 28049.57031 26424.56384 39239.78001 27737.39445 36070.92254 28148.32262 20958.08252 22534.42817 29855.91823 0.565268782 0.939497827 0.885069541 1.314304913 0.929041748 1.208166578 0.942805457 0.70197414 0.754772571 1 14.86572932 -1.34288127 8.459703317 1.000000217 0.921331356 0.013655857 0.210120956 8.88E-07 6.89E-08 0.209744054 0.049437011 0.045406574 1.34288127 -0.078668861 LGGAPAAQGVS(ph)PSPSAILER ddPTM_BT-474_Pertuzumab_2h_R1 4 LGGAPAAQGVSPSPSAILER 20 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LGGAPAAQGVS(0.995)PS(0.005)PSAILER;LGGAPAAQGVS(0.957)PS(0.043)PSAILER;LGGAPAAQGVS(0.999)PS(0.001)PSAILER;LGGAPAAQGVS(0.889)PS(0.11)PS(0.001)AILER 239.73 1.18E-29 1221910000 605480 650030 593950 728750 563770 644030 710920 657830 635020 769510 TRUE FALSE 581817.1722 631491.7808 701289.9773 766360.8748 581904.1741 657052.7279 719620.4516 644245.5806 562935.1918 717390.4023 0.811018896 0.880262377 0.977556955 1.068261957 0.811140172 0.915892833 1.003108558 0.898040423 0.784698527 1 19.45239892 -1.340316743 0.005567894 1.882542159 2.79E-06 0.033585296 0.089271328 118161.1676 112.0273384 19650.07526 18243.82853 0.045675494 1.340316743 -1.882539369 SDIDEIVLVGGSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDIDEIVLVGGSTR 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 219.92 1.12E-11 360405000 425819 522280 414795 589930 417928 399180 470900 497370 534970 586890 FALSE TRUE 409177.5227 507385.0858 489757.6836 620376.358 431371.0337 407251.6931 476663.0151 487099.1357 474242.4484 547139.4176 0.747848738 0.927341496 0.895124109 1.133854257 0.788411545 0.744328922 0.871191144 0.890265114 0.866767104 1 19.06154897 -1.339565348 2.74785472 1.001863014 0.878247417 0.112668579 0.105529325 16243426.28 18625444.91 244496.2259 0.025467082 0.045754588 1.339565348 -0.123615597 (ac)MENQVLTPHVYWAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 MENQVLTPHVYWAQR 15 0 H3BS72;Q9P035;Q9P035-2 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 0 45.829 0.00017076 0 25169 28261 28700 34105 25642 22454 27868 32168 36274 28632 FALSE TRUE 24185.36765 27455.02395 33886.72843 35865.16314 26466.79822 22908.03526 28209.05692 31503.71956 32156.32759 26692.72914 0.90606575 1.028558144 1.269511568 1.34363043 0.991535863 0.858212555 1.056806772 1.180235988 1.204684895 1 14.7041592 -1.339009891 3.873960012 0.999729192 1.098471516 0.033289962 0.148367016 0.000369902 6.31E-05 0.153128552 0.035993967 0.045813145 1.339009891 0.098742324 KAS(ph)SPNLHR ddPTM_BT-474_Pertuzumab_2h_R1 3 KASSPNLHR 9 1 A0A087X030;P51956-2;P51956 A0A087X030 NEK3 Serine/threonine-protein kinase Nek3 1 KAS(0.5)S(0.5)PNLHR;KAS(0.5)S(0.5)PNLHR;KAS(0.5)S(0.5)PNLHR 125.97 0.00022882 211330000 403570 413570 375710 425880 405290 416750 436020 413870 511910 503780 TRUE FALSE 387798.0382 401775.3885 443609.1546 447859.7178 418326.5209 425176.9705 441356.1432 405323.4399 453800.1229 469658.5319 0.825702105 0.85546277 0.944535497 0.953585823 0.890703548 0.90528957 0.93973837 0.863017304 0.966234172 1 18.84125269 -1.338785262 0.014004221 1.94324331 1.51E-06 0.444841429 0.039232674 3325.214695 7.936390001 603.5204534 500.8072473 0.045836847 1.338785262 -1.943241803 VKPPGGHS(ph)PQVNHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKPPGGHSPQVNHLK 15 1 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 VKPPGGHS(1)PQVNHLK;VKPPGGHS(1)PQVNHLK 179.46 4.04E-07 972330000 1583710 1410290 1262440 1226580 1291290 1460520 1481790 1037560 1943390 1897500 TRUE FALSE 1521816.862 1370069.91 1490590.991 1289883.941 1332825.516 1490052.715 1499924.589 1016134.023 1722784.515 1768980.635 0.860278983 0.774496839 0.842627082 0.729167926 0.753442683 0.842322796 0.84790334 0.574417833 0.973885457 1 20.75448682 -1.338724831 8.8368725 1.000000309 0.784599604 0.252453133 0.100292018 5.92E-07 4.44E-08 0.094361566 0.022241203 0.045843226 1.338724831 -0.215400705 SGSYS(ph)GRSPS(ph)PYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 SGS(0.001)YS(0.997)GRS(0.008)PS(0.994)PYGR 144.29 0.00010634 241490000 297760 310800 236970 272470 288890 294290 281160 299010 328780 289190 TRUE FALSE 286123.21 301936.2883 279795.7504 286532.2094 298182.4092 300240.7454 284600.9202 292835.339 291458.2728 269602.9037 1.061276441 1.11992966 1.037806888 1.062793484 1.106005926 1.113640622 1.055630026 1.086172793 1.081065036 1 18.04047651 -1.332191578 5.801262111 0.999989192 1.08088934 0.474205814 0.025420146 3.43E-06 3.95E-07 0.023769041 0.005601668 0.046538076 1.332191578 0.080900148 GNIPGSAVLVFDIHVIDFHNPSDSISITSHYKPPDCSVLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNIPGSAVLVFDIHVIDFHNPSDSISITSHYKPPDCSVLSK 41 1 O95302;O95302-3;O95302-2;C9J4P8 O95302 FKBP9 Peptidyl-prolyl cis-trans isomerase FKBP9;Peptidyl-prolyl cis-trans isomerase 0 91.223 7.40E-05 158620000 115990 131120 128160 139340 161700 151170 129140 120740 176650 124510 FALSE TRUE 111456.9826 127380.586 151321.3629 146531.3541 166901.2274 154226.761 130720.454 118246.6768 156597.4326 116076.8268 0.960200116 1.097381704 1.303631113 1.262365264 1.437851395 1.328661071 1.126154613 1.018693223 1.349084368 1 16.82472046 -1.331354186 3.219330373 0.998573549 1.20327567 0.153369935 0.146931221 16550730.62 24828578.21 229573.2151 0.039418217 0.046627895 1.331354186 0.204702121 S(ph)RS(ph)PLGFYVHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 2 S(0.974)RS(0.974)PLGFY(0.052)VHLK;S(0.998)RS(1)PLGFY(0.002)VHLK;S(1)RS(1)PLGFYVHLK;S(1)RS(1)PLGFYVHLK 111.22 0.0018653 1017300000 641690 584909 527893 509058 542993 466020 574460 590033 714783 606083 TRUE FALSE 616612.0454 568227.968 623295.008 535330.5444 560458.863 475443.2437 581490.4133 577848.6124 633643.8305 565032.4586 1.09128606 1.005655444 1.103113633 0.94743326 0.991905606 0.841444127 1.02912745 1.022682155 1.12142908 1 19.10797422 -1.328685556 3.610041775 0.999952627 1.01256053 0.001263655 0.077861117 2.97E-05 5.52E-06 0.075420808 0.017710055 0.046915294 1.328685556 0.012607903 CGGVEQASSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 CGGVEQASSSPR 12 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5;H7C1I7;Q5VZL5-3 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 CGGVEQASS(0.002)S(0.998)PR;CGGVEQASS(0.001)S(0.999)PR;CGGVEQAS(0.038)S(0.093)S(0.869)PR 145.79 6.73E-05 744270000 1235850 1279630 1000570 1169200 1164120 1219050 1155010 1224950 1427130 1228860 TRUE FALSE 1187551.616 1243136.205 1181395.257 1229542.552 1201564.977 1243700.026 1169145.358 1199654.354 1265128.185 1145628.218 1.036594244 1.085113116 1.031220459 1.07324744 1.048826276 1.085605266 1.020527724 1.047158525 1.104309553 1 20.1277075 -1.328210632 5.412236174 0.999986699 1.057514119 0.319243063 0.02582223 3.83E-06 4.76E-07 0.023121546 0.005448541 0.046966627 1.328210632 0.05752742 WNEEFYFR ddPTM_BT-474_Pertuzumab_2h_R1 2 WNEEFYFR 8 0 Q96PU5-7;Q96PU5;Q96PU5-2;Q96PU5-3;Q96PU5-5;Q96PU5-6 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 0 ; 123.72 0.0069492 98683000 140081 174859 135606 167337 142784 121835 170553 168818 162798 175105 FALSE TRUE 134606.4797 169872.1925 160113.0207 175973.2826 147376.777 124298.5872 172640.2786 165331.8493 144317.8535 163244.9824 0.824567332 1.040596716 0.980814347 1.077970545 0.902795142 0.761423631 1.057553354 1.012783651 0.884056903 1 17.31667912 -1.320636929 2.865909846 1.00046179 0.95859929 0.015068063 0.09985385 21912630.9 27103029.83 87415.25594 0.023868242 0.047792866 1.320636929 -0.0418625 LTPPS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTPPSPVR 8 0 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 LT(0.029)PPS(0.971)PVR;LTPPS(1)PVR 99.855 0.0068363 309660000 390790 437890 439400 485240 427580 436180 452550 474080 526100 565890 TRUE FALSE 375517.4948 425401.8059 518809.3544 510283.2946 441333.499 444999.8585 458088.4423 464290.0823 466379.3336 527561.7663 0.71179816 0.806354503 0.983409693 0.967248438 0.836553229 0.84350286 0.868312436 0.880067723 0.884027925 1 19.00898049 -1.316814276 0.017935671 1.907674129 4.15E-06 0.291991555 0.070277891 2908.955611 8.961735528 535.1838866 422.2435869 0.048215394 1.316814276 -1.907669974 WVGTIHGAAGTVYEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 WVGTIHGAAGTVYEDLR 17 0 O00762;O00762-2 O00762 UBE2C Ubiquitin-conjugating enzyme E2 C 0 142.32 5.91E-07 384760000 264970 263000 222720 251060 290560 173880 324120 267240 234490 312880 FALSE TRUE 254614.6795 255499.4975 262970.4584 264017.2367 299906.1263 177395.9727 328086.6775 261721.4006 207871.6783 291688.3589 0.872899695 0.875933131 0.901545949 0.905134636 1.028173107 0.608169532 1.124784955 0.897263784 0.712649895 1 18.15406828 -1.315006121 3.395090293 1.000491189 0.889693259 0.060999327 0.136364342 6937080.159 5410373.552 23809.80504 0.029638712 0.048416554 1.315006121 -0.11079793 ITPHTS(ph)PAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITPHTSPAPR 10 0 A0A0C4DFZ9;Q58A45-2;Q58A45-4;Q58A45-3;Q58A45 A0A0C4DFZ9 PAN3 PAB-dependent poly(A)-specific ribonuclease subunit PAN3 1 ITPHT(0.041)S(0.959)PAPR;ITPHT(0.013)S(0.987)PAPR 124.12 0.00028592 1300680000 321410 370680 363960 371930 346400 397330 358830 353740 377400 401570 TRUE FALSE 308848.9419 360108.5693 429735.6682 391125.3519 357542.2706 405364.2848 363221.4689 346435.1454 334559.1342 374371.3062 0.824980272 0.961902163 1.147886232 1.044752483 0.955047208 1.082786736 0.970217169 0.925378467 0.89365592 1 18.51411034 -1.312894919 6.72069156 1.000000415 0.98280463 0.003166751 0.088659749 5.67E-07 5.78E-08 0.088286563 0.020808841 0.048652491 1.312894919 -0.017195784 FPEHELTFDPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 FPEHELTFDPQR 12 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 191.79 4.92E-06 2095210000 1344530 1784710 1403260 1746640 1448760 1268750 1837260 1491550 1773890 1879760 FALSE TRUE 1291984.281 1733811.818 1656860.297 1836784.3 1495360.681 1294404.994 1859744.937 1460748.971 1572525.444 1752442.181 0.737247879 0.989368914 0.945457896 1.048128332 0.853301009 0.738629216 1.061230412 0.833550452 0.89733371 1 20.74093541 -1.307934338 3.455477623 1.000385128 0.904537516 0.069555452 0.108291022 11449091.18 8756397.178 29901.38778 0.024167552 0.049211393 1.307934338 -0.095847612 SSGGREDLESSGLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGGREDLESSGLQR 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 ; 165.57 2.76E-09 0 889960 930170 730610 770000 793320 941520 801290 879080 982340 800410 FALSE TRUE 855179.3793 903642.4623 862647.4793 809739.7923 818837.8583 960558.1795 811096.4267 860926.6908 870828.8815 746197.5178 1.146049617 1.210996339 1.156057825 1.085154765 1.097347336 1.287270671 1.086972829 1.153751748 1.167021949 1 19.50919804 -1.307452057 3.667414484 0.99956683 1.153431522 0.389255695 0.058048883 0.000203551 3.84E-05 0.054459062 0.012799381 0.049266073 1.307452057 0.153864692 RAS(ph)FAEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RASFAEK 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK 130.01 0.0022082 6917490000 7184120 6477610 4908670 5291370 5650540 5730230 5696710 6786490 6963140 6196220 TRUE FALSE 6903356.648 6292874.905 5795775.862 5564458.24 5832294.751 5846099.177 5766428.041 6646346.61 6172713.539 5776544.5 1.195066817 1.089383957 1.003329215 0.963284926 1.009651142 1.01204088 0.998248701 1.150574813 1.068582357 1 22.46177531 -1.304784173 5.663564227 0.999993835 1.053388573 0.052149607 0.069521231 5.76E-06 7.07E-07 0.071605853 0.016875712 0.049569647 1.304784173 0.053394738 MPLLELGGET(ph)TPPLSTERS(ph)PEAVGSECPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.498)T(0.498)PPLS(0.114)T(0.313)ERS(0.577)PEAVGSECPSR 70.473 0.014313 102220000 26646 30798 30463 32428 32055 34643 31963 25746 30311 37829 TRUE FALSE 25604.64486 29919.67119 35968.34175 34101.61297 33086.07819 35343.5052 32354.17276 25214.3361 26870.22235 35266.80814 0.726026715 0.848380468 1.019892178 0.966960572 0.938164805 1.002174766 0.917411426 0.714959403 0.761912511 1 15.10602339 -1.298826986 6.144508725 1.000005972 0.878520471 0.107218329 0.106151002 9.61E-06 1.10E-06 0.113750714 0.026809983 0.050254275 1.298826986 -0.121485501 ESVDHLTIPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESVDHLTIPSR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 169.65 1.66E-05 1110380000 1038170 1187650 1011100 1297330 1117330 1259160 1153500 1155180 1172280 1327530 FALSE TRUE 997597.1686 1153779.385 1193828.262 1364285.357 1153269.934 1284621.078 1167616.878 1131325.129 1039207.689 1237615.211 0.806064082 0.932260185 0.964619901 1.102350185 0.931848546 1.037981003 0.943440956 0.914117021 0.839685615 1 20.2391314 -1.29741795 5.386809605 1.000008726 0.946850452 0.041247233 0.081010393 8.54E-06 1.11E-06 0.078897965 0.018593376 0.050417586 1.29741795 -0.053158274 GANDFMCDEMER ddPTM_BT-474_Pertuzumab_2h_R1 4 GANDFMCDEMER 12 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 332.56 7.60E-58 3845670000 1918450 2215570 1828800 2179980 2332480 2441730 2198380 1976350 2274360 2390560 FALSE TRUE 1843474.853 2152384.113 2159304.841 2292489.029 2407506.338 2491103.454 2225284.432 1935537.682 2016184.188 2228645.242 0.827172857 0.965781396 0.968886748 1.028646904 1.080255526 1.11776581 0.998491994 0.868481733 0.904668069 1 21.08773555 -1.287373816 4.379321571 1.000018702 0.975298106 0.008201377 0.085538447 1.71E-05 2.79E-06 0.090831669 0.021393032 0.051597206 1.287373816 -0.024720596 IQALGLHLPDPPLESEDEDEEGAT(ph)ALNNHSSIPMDPEHVELVK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQALGLHLPDPPLESEDEDEEGATALNNHSSIPMDPEHVELVK 43 0 A0A2R8Y7W8;A0A2R8Y6W5;Q16626 A0A2R8Y7W8 MEA1 Male-enhanced antigen 1 1 IQALGLHLPDPPLES(0.442)EDEDEEGAT(0.551)ALNNHS(0.003)S(0.003)IPMDPEHVELVK 153.07 4.44E-14 1240300000 18634 30050 27806 33371 25374 36920 32865 16437 31974 37700 TRUE FALSE 17905.76268 29193.00342 32831.16274 35093.28131 26190.17775 37666.5477 33267.2117 16097.57021 28344.44557 35146.54542 0.509460104 0.830608046 0.934122041 0.998484514 0.745170754 1.071699857 0.946528636 0.458012872 0.806464625 1 15.10109527 -1.286612336 5.642889479 1.000018211 0.806849019 0.082062549 0.188964181 4.55E-05 5.76E-06 0.192405932 0.04534624 0.051687754 1.286612336 -0.193169192 KGS(ph)SGNASEVSVACLTER ddPTM_BT-474_Pertuzumab_2h_R1 4 KGSSGNASEVSVACLTER 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 KGS(0.974)S(0.026)GNASEVSVACLTER;KGS(0.952)S(0.048)GNASEVSVACLTER;KGS(0.921)S(0.078)GNASEVSVACLTER;KGS(0.951)S(0.049)GNASEVSVACLTER 286.85 4.47E-40 5588000000 2217570 2140840 1712030 1917080 2123350 2048580 2063440 2295470 2101000 2120750 TRUE FALSE 2130904.913 2079785.339 2021431.905 2016020.729 2191649.481 2090003.691 2088692.996 2248067.742 1862503.288 1977109.714 1.077787893 1.051932184 1.022417669 1.019680757 1.108511817 1.057100512 1.056437577 1.137047543 0.942033351 1 20.9149615 -1.281956619 8.510933894 0.999999956 1.058493502 0.07843745 0.050462781 4.16E-08 3.54E-09 0.047060588 0.011092278 0.052244837 1.281956619 0.058493546 GNYPGPSS(ph)PVVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNYPGPSSPVVVR 13 0 H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BV44;H3BP49;H3BU05 H3BRD5 MYO9A Unconventional myosin-IXa 1 GNYPGPS(0.194)S(0.806)PVVVR;GNYPGPS(0.263)S(0.737)PVVVR 162 4.32E-05 264650000 358660 431010 360230 492530 495680 480810 405980 478390 353180 425270 TRUE FALSE 344643.1707 418718.0168 425331.5743 517949.5323 511623.9974 490532.3076 410948.5047 468511.0793 313088.4871 396466.0841 0.869287903 1.05612569 1.07280696 1.306415739 1.290460945 1.237261716 1.036528775 1.181717928 0.789698034 1 18.59683793 -1.281667388 8.397361238 0.999999893 1.110918614 0.018925504 0.162168545 3.12E-07 2.69E-08 0.156930003 0.036988722 0.052279643 1.281667388 0.110918721 S(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPAPAPAPAAAAGPPTR 19 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 S(1)PS(1)PAPAPAPAAAAGPPTR 156.73 4.62E-10 0 77995 71530 62708 73377 62218 66399 69958 76875 81792 66034 TRUE FALSE 74946.86917 69490.03444 74040.73053 77163.99576 64219.29847 67741.63327 70814.16693 75287.50439 72507.31506 61561.45836 1.217431672 1.128791232 1.202712419 1.25344652 1.043173768 1.100390327 1.150300347 1.222964926 1.177803726 1 15.90973979 -1.281546989 3.6748042 0.999618188 1.166733942 0.408546601 0.060038779 7290648.271 15237555.03 30958.88701 0.01498569 0.052294138 1.281546989 0.167115754 AASEQQADTSGGDS(ph)PKDESKPPFSYAQLIVQAISSAQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AASEQQADTSGGDSPKDESKPPFSYAQLIVQAISSAQDR 39 2 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 AASEQQADT(0.005)S(0.004)GGDS(0.986)PKDES(0.005)KPPFSYAQLIVQAISSAQDR 167.49 1.74E-18 118790000 107300 79113 84559 67211 88052 79579 77078 96062 117730 86341 TRUE FALSE 103106.5974 76856.7747 99840.6923 70679.76776 90884.27255 81188.1419 78021.30362 94078.28613 104365.784 80493.04717 1.280937932 0.954825012 1.240364178 0.878085378 1.129094695 1.008635463 0.969292459 1.16877531 1.296581353 1 16.29657655 -1.279963309 5.680524943 0.999992402 1.093518251 0.043285324 0.138974122 1.24E-05 1.58E-06 0.125219392 0.029512096 0.05248518 1.279963309 0.093525849 LTDEDFS(ph)PFGSGGGLFSGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 LTDEDFSPFGSGGGLFSGGK 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 LTDEDFS(1)PFGSGGGLFSGGK;LTDEDFS(0.994)PFGS(0.006)GGGLFSGGK;LTDEDFS(1)PFGSGGGLFSGGK 336.94 4.78E-80 627980000 800600 809910 774410 865280 872070 905350 780140 772500 846760 934410 TRUE FALSE 769311.6669 786812.1598 914363.1137 909937.2045 900120.9235 923656.7973 789687.5867 756547.605 750639.3547 871121.5784 0.883127781 0.903217392 1.049638921 1.044558219 1.033289665 1.060307562 0.906518225 0.868475335 0.861692987 1 19.73251456 -1.27017411 6.163870946 1.000001362 0.957068214 0.027023555 0.077819947 1.64E-06 1.94E-07 0.084904028 0.020011437 0.053681654 1.27017411 -0.042933148 GFAFVTFDDHDSVDK ddPTM_BT-474_Pertuzumab_2h_R1 11 GFAFVTFDDHDSVDK 15 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;;;;;;;;; 306.05 6.61E-45 11923347000 8595998 9760577 9067507 11302771 12419521 11195138 11106216 9327815 9612315 11098234 FALSE TRUE 8260056.895 9482214.901 10706207.22 11886108.37 12819006.17 11421511.36 11242137.19 9135192.361 8521165.299 10346540.73 0.798339959 0.916462338 1.034762004 1.14880023 1.23896542 1.103896622 1.086559991 0.88292238 0.823576258 1 23.30264516 -1.269571254 8.339811168 0.999999991 1.010635782 0 0.138386457 2.40E-08 2.09E-09 0.146226098 0.034465794 0.053756223 1.269571254 0.010635791 LWEEQLAAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LWEEQLAAAK 10 0 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 166.19 1.31E-05 151985000 308880 306890 266930 280780 269480 214091 332240 313120 329220 363710 FALSE TRUE 296808.6281 298137.7977 315170.1888 295271.0894 278148.0689 218420.0667 336306.0525 306653.9626 291848.3258 339075.5977 0.875346472 0.879266452 0.929498292 0.870811971 0.820312847 0.644163332 0.991832072 0.904382281 0.860717574 1 18.37124744 -1.268190295 5.612198873 1.000010373 0.867270849 0.184727603 0.08544684 1.13E-05 1.48E-06 0.084445848 0.019902522 0.053927428 1.268190295 -0.132739524 VREEILAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VREEILAK 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 111.61 0.0029193 934140000 924160 947190 730100 800520 825630 707010 894800 913500 938840 1032130 FALSE TRUE 888042.8055 920177.0686 862045.311 841834.9331 852187.1388 721306.2266 905750.8301 894635.9058 832266.8191 962222.9158 0.922907562 0.956303424 0.8958894 0.874885559 0.885644194 0.749624868 0.941310808 0.929759509 0.864941798 1 19.87601163 -1.265949251 5.096532514 1.000019348 0.893403161 0.258978593 0.055077591 1.25E-05 1.79E-06 0.054870538 0.012930763 0.054206423 1.265949251 -0.106616187 QNPHDGVVTPAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_BT-474_Pertuzumab_2h_R1 3 QNPHDGVVTPAASPSLPQPGLQMPGQWGPVQGGPQPSGQHR 41 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QNPHDGVVTPAAS(0.995)PS(0.005)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVTPAAS(0.994)PS(0.006)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVTPAAS(0.993)PS(0.007)LPQPGLQMPGQWGPVQGGPQPSGQHR 238.2 3.06E-54 2225540000 41021.7 75441.1 80773.5 84148.5 67914.8 93424 97851.3 53171.5 71563.2 77483.1 TRUE FALSE 39418.52661 73289.59369 95371.06825 88491.41417 70099.34122 95313.09729 99048.83348 52073.48994 63439.64555 72235.10062 0.545697677 1.01459807 1.320287055 1.225047289 0.970433219 1.319484523 1.371200879 0.720889007 0.878238488 1 16.14041242 -1.259912314 8.379560972 0.999999968 1.050180628 0.000986007 0.260622391 1.56E-07 1.38E-08 0.258765624 0.060991604 0.054965184 1.259912314 0.05018066 EWLKDTCGANAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EWLKDTCGANAK 12 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 157.52 6.76E-05 338850000 533050 640090 327390 357560 494510 681470 435630 570090 594710 419670 FALSE TRUE 512217.8167 621835.2599 386556.6558 376013.7145 510416.3633 695249.7903 440961.3703 558317.4423 527201.014 391245.3771 1.309198387 1.589374077 0.988015906 0.961068773 1.304593979 1.777017266 1.127071133 1.427026298 1.347494552 1 18.57771418 -1.259352278 5.843333008 0.999985157 1.31585621 0.135086469 0.238747917 4.66E-05 5.90E-06 0.233192325 0.054961377 0.055036109 1.259352278 0.315871053 FDEHDGPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FDEHDGPVR 9 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 109.29 0.0024731 332950000 965460 1212400 1086000 1538100 1347100 1449200 1419100 1040000 1238600 1307600 FALSE TRUE 927728.7558 1177823.539 1282264.358 1617481.525 1390430.695 1478503.817 1436467.37 1018523.637 1097999.321 1219035.087 0.761035318 0.966193304 1.051868294 1.326853954 1.140599405 1.21284763 1.178364253 0.83551626 0.900711827 1 20.21730822 -1.256578117 8.413039907 0.999999974 1.046574176 0.00461543 0.169190958 8.98E-08 7.79E-09 0.176036756 0.041492238 0.055388791 1.256578117 0.046574202 SDSILLTHDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDSILLTHDGR 11 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;; 227.37 4.05E-12 1334620000 1354650 1497410 1188750 1444960 1362270 1105350 1548280 1444170 1468030 1563820 FALSE TRUE 1301708.78 1454705.333 1403583.569 1519534.559 1406088.652 1127700.934 1567228.314 1414347.385 1301385.389 1457901.078 0.892864955 0.997807982 0.962742664 1.042275488 0.964460945 0.773509912 1.074989474 0.970125755 0.892643135 1 20.4754614 -1.254982228 4.863516942 1.000009964 0.958134903 0.026054297 0.08071514 8.41E-06 1.29E-06 0.075401371 0.017768045 0.055592701 1.254982228 -0.041875061 LSS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 8 LSSPVK 6 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LSS(1)PVK;LS(0.019)S(0.981)PVK;LS(0.156)S(0.844)PVK;LS(0.001)S(0.999)PVK;LSS(1)PVK;LS(0.058)S(0.942)PVK;LSS(1)PVK;LSS(1)PVK 164.53 0.0079233 23906940000 26923400 22908800 22184800 21810000 21929400 18532000 24725500 26717100 26071500 28924700 TRUE FALSE 25871203.76 22255463.45 26194086.86 22935616.71 22634779.07 18906729.74 25028098.07 26165382.55 23111972.62 26965604.31 0.959414945 0.825327821 0.971388832 0.850550815 0.839394467 0.701142445 0.928148978 0.970324353 0.857090847 1 24.68461703 -1.253171909 5.509750312 1.000009139 0.880949701 0.17389429 0.079496068 9.20E-06 1.25E-06 0.079346017 0.0187006 0.055824918 1.253171909 -0.119059438 GDPFTDLCFLNS(ph)PIFK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDPFTDLCFLNSPIFK 16 0 Q5FBB7-6;Q5FBB7;Q5FBB7-5;Q5FBB7-4;Q5FBB7-3;Q5FBB7-2 Q5FBB7-6 SGOL1 Shugoshin-like 1 1 GDPFTDLCFLNS(1)PIFK;GDPFTDLCFLNS(1)PIFK 214.5 1.78E-14 225340000 491070 462950 438190 494440 436940 420480 479430 560000 445940 496640 TRUE FALSE 471878.4415 449747.1193 517380.6805 519958.1077 450994.5719 428982.3937 485297.4078 548435.8043 395318.7607 463002.1304 1.01917121 0.971371598 1.117447732 1.123014504 0.974065868 0.926523585 1.048153725 1.184521125 0.853816289 1 18.82065931 -1.24947186 4.046177891 0.999966815 1.036117044 0 0.094819975 32324.13534 25845698.08 1492.177582 0.022440317 0.05630256 1.24947186 0.036150229 GQTEHDEGMLEYLEDIIGCGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GQTEHDEGMLEYLEDIIGCGR 21 0 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9J578 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 ;;;;; 239.1 6.50E-30 697185000 360202 413010 353349.9 437441 422516 474500 424881 349726.6 438811 480728 FALSE TRUE 346124.9076 401231.3592 417208.0872 460017.3824 436106.6109 484094.7151 430080.8208 342504.6235 388999.0149 448167.8644 0.772310857 0.895270257 0.930919239 1.02643991 0.973087643 1.080163826 0.959642257 0.764232893 0.867976144 1 18.77367968 -1.243718888 4.184020884 1.000055828 0.918501544 0.061150878 0.095328289 25283951712 4570176651 14043378.25 0.024659941 0.057053345 1.243718888 -0.081554284 ESDTGLWLHNK ddPTM_BT-474_Pertuzumab_2h_R1 3 ESDTGLWLHNK 11 0 A0A0C4DFX9;Q9H3P2;F8W954;F8WF98;C9JHL4 A0A0C4DFX9 NELFA Negative elongation factor A 0 ;; 139.43 3.91E-05 831880000 1271670 1329460 1116190 1173790 1229300 1242080 1278950 1254730 1389840 1451070 FALSE TRUE 1221971.73 1291545.102 1317910.363 1234369.443 1268841.551 1267195.709 1294602.173 1228819.387 1232071.19 1352787.736 0.903298942 0.954728571 0.974218147 0.912463507 0.937945782 0.936729152 0.956988401 0.908360827 0.910764606 1 20.36750406 -1.237019181 5.320246299 1.000005795 0.933582323 0.438386751 0.022792719 1.56E-06 2.24E-07 0.022023784 0.005190603 0.057940311 1.237019181 -0.066423472 LSTTPS(ph)PTSSLHEDGVEDFRR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 1 LSTTPS(0.997)PT(0.001)S(0.001)SLHEDGVEDFRR;LST(0.001)T(0.023)PS(0.703)PT(0.22)S(0.042)S(0.01)LHEDGVEDFRR;LSTT(0.006)PS(0.67)PT(0.273)S(0.043)S(0.007)LHEDGVEDFRR;LSTTPS(0.951)PT(0.049)SSLHEDGVEDFRR 199.85 3.66E-22 4077410000 338024 734240 658904 840800 745420 834710 743300 373397 725150 864300 TRUE FALSE 324813.6484 713300.1941 777982.61 884193.7888 769397.1113 851588.4081 752396.7277 365686.2215 642834.0121 805760.1912 0.403114539 0.885251222 0.965526243 1.097341118 0.954871089 1.056875752 0.933772524 0.45384002 0.797798178 1 19.619991 -1.236173788 5.511946089 1.000010032 0.837230453 0.04514161 0.222447042 2.94E-05 4.08E-06 0.231147358 0.054478597 0.058053206 1.236173788 -0.162779579 NFSLLSFGEEAEEEEEEVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 NFSLLSFGEEAEEEEEEVNR 20 0 D6REK3;Q6UX04-2;Q6UX04 D6REK3 CWC27 Peptidyl-prolyl cis-trans isomerase CWC27 homolog 0 320.05 2.75E-66 18371000 20513 19609 17150 18411 13390 19947 14677 18157 20989 27081 FALSE TRUE 19711.32928 19049.77052 20249.3865 19361.19392 13820.70151 20350.34201 14856.62152 17782.0516 18606.41671 25246.77975 0.780746276 0.754542588 0.802058191 0.766877761 0.547424331 0.806056939 0.588456099 0.704329494 0.736981781 1 14.62381176 -1.231232902 9.312717754 1.00000002 0.716191335 0.503312312 0.083082943 3.32E-08 2.76E-09 0.078381093 0.018474599 0.058717438 1.231232902 -0.283808684 FS(ph)GGFGAR ddPTM_BT-474_Pertuzumab_2h_R1 5 FSGGFGAR 8 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 1 FS(1)GGFGAR;FS(1)GGFGAR;FS(1)GGFGAR;FS(1)GGFGAR;FS(1)GGFGAR 125.71 0.0013114 1932137000 1865660 1735840 1839970 1824620 1570540 1659560 1952650 2119180 1923800 2213290 TRUE FALSE 1792747.945 1686335.543 2172493.509 1918788.857 1621057.845 1693117.44 1976547.115 2075418.192 1705418.289 2063381.897 0.868839621 0.81726778 1.052879989 0.929924247 0.785631515 0.820554568 0.957916282 1.005833285 0.826516067 1 20.97657943 -1.229470926 3.844169605 1.000102793 0.904272383 0.112496519 0.084788076 7.827353588 45669308.66 8464.698232 0.020862946 0.058956144 1.229470926 -0.09583041 AEHDSILAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEHDSILAEK 10 0 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6;D6RBR8 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 152.04 1.87E-05 3247460000 5134000 8311600 6454800 9171700 6797500 8085300 7943900 7304400 7836100 10037600 FALSE TRUE 4933357.604 8074561.306 7621325.946 9645052.536 7016147.761 8248790.306 8041119.824 7153561.587 6946578.78 9357744.411 0.527195164 0.862874743 0.81444049 1.030702711 0.749769117 0.881493439 0.859301074 0.76445362 0.742334742 1 23.15772939 -1.228179306 0.021270791 1.815936495 4.48E-06 0.174645591 0.123122742 2865.229803 10.79912118 526.295657 400.8520901 0.059131745 1.228179306 -1.815932012 (ac)SDSGEQNYGERES(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 7 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R 109.83 8.76E-17 4154245000 12040.5 27171.4 20965.9 34884.6 35723.9 22566.1 13927.62 31410.6 32239.01 19627.5 TRUE FALSE 11569.94395 26396.49828 24754.90451 36684.99839 36872.99169 23022.402 14098.07038 30761.96013 28579.37274 18298.11194 0.63230261 1.442580434 1.352866601 2.004851566 2.015125484 1.258184564 0.77046585 1.681154877 1.5618755 1 14.15940717 -1.225170895 4.924480685 0.999933796 1.433067141 0.07466498 0.431420828 0.000319037 5.02E-05 0.424951976 0.100146887 0.05954278 1.225170895 0.433133345 HVDNIMFENHTVADR ddPTM_BT-474_Pertuzumab_2h_R1 4 HVDNIMFENHTVADR 15 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;; 191.44 1.01E-07 2582500000 1764710 1855170 1789140 2169460 2077810 2077110 2044680 1575430 2020920 2206260 FALSE TRUE 1695743.182 1802262.368 2112477.397 2281426.091 2144644.646 2119110.587 2069703.405 1542896.82 1791513.634 2056828.045 0.82444577 0.876233855 1.027055909 1.109196316 1.042695159 1.03028087 1.006259814 0.750134083 0.871007977 1 20.97198976 -1.22459731 7.462705613 1.000000087 0.946725453 0.019687058 0.108114978 1.78E-07 1.84E-08 0.118777629 0.02799611 0.059621471 1.22459731 -0.053274634 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGSAR ddPTM_BT-474_Pertuzumab_2h_R1 8 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGPDLPSLPSHALEDEGWAAAAPS(0.962)PGS(0.038)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.945)PGS(0.055)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.999)PGS(0.001)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR 351.32 3.67E-120 8375226000 1892672 2144441 1889538 2212561 2095901 2369066 2159012 2022195 2126669 2432637 TRUE FALSE 1818704.286 2083283.642 2231019.549 2326751.538 2163317.559 2416970.138 2185434.635 1980435.967 1885258.451 2267872.329 0.801942976 0.918607108 0.983750064 1.025962312 0.953897418 1.065743475 0.963649764 0.873257256 0.831289498 1 21.11290799 -1.224512141 3.912678233 1.000054631 0.939746605 0.055008274 0.078509086 12283814.1 3844345.084 5780.319986 0.019342126 0.059633165 1.224512141 -0.060308026 LLSVHDFDFEGDS(ph)DDSTQPQGHSLHLSSVPEAR ddPTM_BT-474_Pertuzumab_2h_R1 5 LLSVHDFDFEGDSDDSTQPQGHSLHLSSVPEAR 33 0 Q9BV36-2;Q9BV36-5;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(0.993)DDS(0.006)T(0.001)QPQGHSLHLSSVPEAR 367.8 7.10E-148 1487730000 101893.6 219433 159104.6 316836 254943 329600 262419 92829.6 171098.4 269848 TRUE FALSE 97911.48546 213174.9857 187858.3405 333187.9439 263143.4731 336264.7378 265630.5622 90912.63632 151676.0269 251570.9546 0.389200278 0.847375191 0.746740977 1.324429302 1.046001012 1.336659625 1.055887245 0.361379701 0.602915496 1 17.94060584 -1.224025632 3.994886798 1.00011171 0.858895909 0.017009059 0.326368994 28.43692982 137683558.9 27577.59535 0.085594609 0.059700005 1.224025632 -0.141215802 EAMECSDVIWQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAMECSDVIWQR 12 0 Q9NS86 Q9NS86 LANCL2 LanC-like protein 2 0 141.91 0.00014172 139260000 76225 81432 66315 83768 71642 66777 77256 83016 73908 99488 FALSE TRUE 73246.04273 79109.63909 78299.59567 88091.27652 73946.42999 68127.27669 78201.48204 81301.69059 65518.27369 92749.58915 0.789718245 0.852937892 0.844204232 0.949775383 0.797269623 0.734529148 0.843146398 0.876571976 0.706399611 1 16.50105327 -1.222591217 4.244447311 1.000086123 0.828292315 0.389441629 0.066535726 5.37E-05 9.83E-06 0.063744527 0.015017208 0.059897512 1.222591217 -0.171793808 DMEQFFDDLSDSFSGTEPEVHK ddPTM_BT-474_Pertuzumab_2h_R1 3 DMEQFFDDLSDSFSGTEPEVHK 22 0 F5GY68;F5H0F9;Q9UJX4-3;Q9UJX4;F5GZ05;F5H3S5 F5GY68 ANAPC5 Anaphase-promoting complex subunit 5 0 ;; 193.87 5.62E-18 88072000 145838 150167 155728 153438 158068 165021 188867 176218 221790 238748 FALSE TRUE 140138.4897 145884.3842 183871.5138 161356.9536 163152.4008 168357.8377 191178.4108 172579.0367 196613.329 222577.3853 0.629616929 0.655432195 0.826101508 0.724947655 0.733014275 0.756401363 0.858930078 0.775366448 0.883348184 1 17.76394749 -1.219374901 0.043516128 1.915133037 1.66E-09 0.784431559 0.048960156 130.7566569 1.01768886 29.07036719 16.7381524 0.06034275 1.219374901 -1.915133035 VPDEEENEES(ph)DNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VPDEEENEESDNEK 14 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 VPDEEENEES(1)DNEK 103.63 0.0011585 657670000 157720 218180 211370 341690 247210 250000 281090 220440 193340 274380 TRUE FALSE 151556.128 211957.72 249569.2609 359324.6618 255161.7342 255055.1713 284530.0635 215887.837 171392.8537 255795.9982 0.592488268 0.828620156 0.975657409 1.404731365 0.99752043 0.997103837 1.112331958 0.843984419 0.670037276 1 17.96463417 -1.212713043 6.463398488 1.000000393 0.951375487 0.003241664 0.216979613 1.28E-06 1.56E-07 0.216571937 0.051046079 0.061275513 1.212713043 -0.048624906 EKPLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKPLPR 6 1 Q15050;Q5BJH2-2;Q5BJH2 Q15050 RRS1;TMEM128 Ribosome biogenesis regulatory protein homolog;Transmembrane protein 128 0 72.234 0.078556 162120000 192930 208310 165600 192380 197540 189170 215520 216360 210700 240300 FALSE TRUE 185390.0823 202369.2028 195527.6038 202308.7549 203894.0535 192995.147 218157.5982 211892.0904 186782.2193 224024.267 0.827544644 0.903336078 0.872796534 0.903066251 0.91014271 0.861492148 0.973812352 0.945844364 0.833758868 1 17.77329549 -1.211415184 0.015225436 1.940193129 1.34E-06 0.366869947 0.043168061 2474.700741 6.709345627 470.1366406 387.2746816 0.061458905 1.211415184 -1.940191785 YKETDLLILFKDDYFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YKETDLLILFKDDYFAK 17 2 P05455 P05455 SSB Lupus La protein 0 ; 153.14 1.05E-07 739820000 1174960 1085520 726110 606530 934820 1195060 878880 1046020 1177560 836660 FALSE TRUE 1129041.264 1054562.032 857334.2292 637833.086 964889.3343 1219224.932 889635.9963 1024419.321 1043888.326 779992.273 1.44750314 1.352015999 1.099157336 0.817742827 1.237049863 1.563124372 1.140570269 1.313371115 1.338331624 1 19.57310031 -1.209557988 4.232276984 0.999887258 1.249721478 0.133706379 0.195206515 0.000215805 4.03E-05 0.196419457 0.046275675 0.061722287 1.209557988 0.249834221 CAPSAGSPAAAVGRES(ph)PGAAATSSSGPQAQQHR ddPTM_BT-474_Pertuzumab_2h_R1 3 CAPSAGSPAAAVGRESPGAAATSSSGPQAQQHR 33 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR 330.5 2.54E-117 3804120000 558942 623661 398303 559092 525695 574718 552897 540930 646561 561931 TRUE FALSE 537097.9287 605874.7989 470285.2123 587946.8051 542604.4571 586339.1917 559663.5189 529759.6065 573166.1059 523870.9129 1.025248617 1.156534528 0.897712014 1.122312369 1.035759848 1.119243648 1.068323331 1.011240734 1.094097977 1 18.99885184 -1.200310482 3.515427121 0.999922573 1.057043567 0.060001066 0.069624665 4550042.923 1555788.997 2991.70625 0.014857784 0.063050643 1.200310482 0.057120994 APASSLHTQEAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 APASSLHTQEAGR 13 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425;A0A0J9YWY6 O95425-2 SVIL Supervillin 0 134.68 9.27E-05 52482000 37380 47757 35924 52923 45971 51501 49050 43225 42405 46211 FALSE TRUE 35919.14827 46395.01712 42416.26593 55654.36237 47449.69896 52542.38551 49650.28857 42332.38864 37591.36218 43081.08781 0.833756762 1.076923065 0.984568127 1.291851371 1.101404384 1.219616035 1.152484561 0.982621164 0.872572261 1 15.39476706 -1.200083757 8.345952495 0.999999986 1.066862109 0.011197583 0.137308052 3.65E-08 3.46E-09 0.133746688 0.03152439 0.063083567 1.200083757 0.066862123 DREEALHQFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DREEALHQFR 10 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 204.56 1.11E-07 6131350000 2883270 2803520 2517930 2867050 2680440 2533080 3132160 2781570 3052500 3629790 FALSE TRUE 2770588.621 2723566.355 2972975.962 3015018.794 2766658.787 2584300.613 3170492.311 2724129.607 2705992.997 3383941.09 0.818746115 0.804850404 0.87855429 0.890978511 0.817584796 0.763695509 0.936923022 0.805016853 0.799657241 1 21.69027302 -1.19929327 3.754226697 1.000157795 0.8367114 0.503041025 0.049143354 23831938.6 52429419.84 48625.16844 0.011561181 0.063198494 1.19929327 -0.163446395 KFDGVEGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KFDGVEGPR 9 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YAN4 Q6PKG0 LARP1 La-related protein 1 0 77.744 0.050885 260200000 610660 660210 547640 587590 561070 370310 737450 570550 658070 784150 FALSE TRUE 586794.7321 641381.4572 646610.7302 617915.5903 579117.3261 377797.9219 746475.1337 558767.9431 583368.6525 731038.8221 0.802686142 0.877356219 0.884509428 0.845256875 0.792184093 0.516795977 1.021115584 0.764347838 0.797999552 1 19.4795885 -1.196515253 5.622147266 1.000005685 0.812927797 0.181348067 0.120197499 8.22E-06 1.18E-06 0.111724124 0.026332829 0.063604047 1.196515253 -0.187077888 RGNVAGDSK ddPTM_BT-474_Pertuzumab_2h_R1 10 RGNVAGDSK 9 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;;;;; 187.55 6.48E-05 28025800000 12310600 11313800 9542670 10021930 9822560 8696590 12541070 11741040 12115950 13698640 FALSE TRUE 11829488.14 10991141.5 11267242.74 10539163.01 10138511.56 8872441.008 12694551.37 11498583.42 10740598.15 12770818.91 0.926290493 0.860645005 0.882264702 0.8252535 0.793881084 0.694743311 0.994027983 0.90037949 0.84102658 1 23.6063477 -1.192443735 6.387709144 1.000000973 0.859842076 0.239725086 0.075978153 1.09E-06 1.38E-07 0.076150606 0.017948745 0.064203139 1.192443735 -0.140158897 KTDVEERPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTDVEERPR 9 2 A0A0C4DGA6;Q14527-2;Q14527 A0A0C4DGA6 HLTF Helicase-like transcription factor 0 98.04 0.0035339 136930000 422440 426020 362250 385820 416640 367560 421120 435040 442480 473700 FALSE TRUE 405930.5778 413870.3267 427716.6332 405732.2164 430041.604 374992.315 426273.7925 426056.272 392251.5254 441615.8771 0.919193804 0.937172661 0.968526395 0.918744632 0.973791085 0.849136851 0.96525921 0.964766654 0.888218802 1 18.75243252 -1.191554596 3.673858273 1.000068656 0.935044649 0.220323804 0.038095812 5630179386 17738746.85 3312461.826 0.008725021 0.064334718 1.191554596 -0.065024008 ETDKQILQNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETDKQILQNR 10 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4 Q9UM54-1 MYO6 Unconventional myosin-VI 0 90.685 0.009724 395410000 351650 393850 243480 300340 310980 369110 302290 354150 374830 312400 FALSE TRUE 337907.1292 382617.7836 287482.2522 315840.5834 320982.9541 376573.6571 305989.5154 346836.6787 332280.8698 291240.8697 1.160232523 1.313750312 0.987094471 1.084465184 1.102121946 1.292997296 1.050640714 1.190892882 1.140914289 1 18.1518533 -1.190468414 2.816249422 0.999242063 1.147304211 0.174459387 0.095937426 5692389.028 7234118.719 38968.33549 0.024519137 0.064495823 1.190468414 0.148062148 LDSEDKDKEGKPLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDSEDKDKEGKPLLK 15 3 P13639 P13639 EEF2 Elongation factor 2 0 ; 130.98 2.47E-05 2772500000 6234530 4727110 2575450 1521740 3077720 4165430 2852490 4033520 5031610 3127920 FALSE TRUE 5990877.675 4592297.451 3040891.106 1600277.184 3176717.659 4249657.849 2887399.626 3950226.402 4460442.727 2916063.192 2.054440278 1.574827824 1.042806999 0.548780009 1.08938574 1.457327077 0.990170458 1.354643621 1.529611134 1 21.47559055 -1.189299254 8.816699685 0.999999981 1.264193661 0.044367503 0.387735312 1.46E-07 1.38E-08 0.388817923 0.091645257 0.064669685 1.189299254 0.26419368 DPLELFR ddPTM_BT-474_Pertuzumab_2h_R1 7 DPLELFR 7 0 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;;;;; 127.31 0.0089977 1149480000 912303 952651 899521 1017198 966607 770383 1013341 1027380 1049226 1161793 FALSE TRUE 876649.1902 925482.3262 1062084.454 1069695.711 997698.792 785960.6721 1025742.57 1006164.244 930122.2632 1083103.725 0.809386183 0.85447248 0.980593483 0.987620747 0.921147965 0.725655959 0.947040017 0.928963885 0.858756407 1 20.04673998 -1.187289226 3.283896761 1.000213722 0.895926993 0.150436709 0.077134882 40151588.66 62628756.16 93857.55914 0.019058125 0.064969687 1.187289226 -0.104286729 LGPSDYFGEIALLMNRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGPSDYFGEIALLMNRPR 18 1 P10644 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ; 218.98 6.91E-19 695460000 278720 263560 227940 253180 236050 239410 272360 258090 286380 319220 FALSE TRUE 267827.3143 256043.5269 269133.8285 266246.6501 243642.7626 244251.0342 275693.2232 252760.3513 253871.343 297598.9451 0.899960563 0.860364363 0.904350748 0.894649173 0.818694981 0.820738911 0.926391803 0.849332148 0.853065332 1 18.18300989 -1.187218625 5.109254533 1.000009196 0.869287787 0.565548195 0.03425193 3.56E-06 5.66E-07 0.032907444 0.007755813 0.06498025 1.187218625 -0.13072141 KVFS(ph)PVIR ddPTM_BT-474_Pertuzumab_2h_R1 4 KVFSPVIR 8 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 KVFS(1)PVIR;KVFS(1)PVIR;KVFS(1)PVIR;KVFS(1)PVIR 89.403 0.0085323 1939770000 2057104 2110454 1775766 2043136 1951622 1709425 2172189 2105275 2102323 2316890 TRUE FALSE 1976710.101 2050265.918 2096686.418 2148582.494 2014397.694 1743990.745 2198772.899 2061800.336 1863676.107 2159964.977 0.915158404 0.949212575 0.970703896 0.994730247 0.932606647 0.807416214 1.017966922 0.95455267 0.862827003 1 21.04257649 -1.187090617 3.624392907 1.000065786 0.93843126 0.098307916 0.058625639 20049244.03 38454609.6 16469.12266 0.013995319 0.064999405 1.187090617 -0.061634526 DVIRPGMR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVIRPGMR 8 1 P25685;P25685-2 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 93.162 0.010273 797050000 1407500 1632700 1257100 1438200 1485500 1191500 1523900 1582700 1559400 1753600 FALSE TRUE 1352493.344 1586136.995 1484285.934 1512425.674 1533282.457 1215592.946 1542549.944 1550016.692 1382383.45 1634827.11 0.827300536 0.970216964 0.907916149 0.925128819 0.93788661 0.743560551 0.943555398 0.948122699 0.845583879 1 20.64070664 -1.186753424 3.82147536 1.000074522 0.900504549 0.180536004 0.066367097 85407.88111 32743364.25 4817.75507 0.015055339 0.065049891 1.186753424 -0.099569973 VTELNPDKNCIHTDDDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTELNPDKNCIHTDDDEK 18 1 Q9Y6N5;A0A1B0GXB4;H3BV36;H3BMS6;H3BNX3 Q9Y6N5 SQRDL "Sulfide:quinone oxidoreductase, mitochondrial" 0 63.447 0.026042 207470000 1032400 785410 803660 601390 838720 682080 732310 829890 1145600 920680 FALSE TRUE 992052.6666 763010.8758 948899.2393 632427.81 865698.1905 695872.1249 741272.2288 812752.4815 1015556.291 858321.5235 1.155805417 0.888956941 1.105528888 0.736819237 1.008594293 0.810735961 0.863630013 0.946909123 1.183188657 1 19.71115865 -1.186128811 5.11011306 1.000003248 0.953162743 0 0.141255647 4.88E-06 7.78E-07 0.127719689 0.030101732 0.065143515 1.186128811 -0.046840505 LSSPVLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 0 135.83 0.00081697 264130000 261100 330050 302520 335140 294980 262640 356350 314250 327720 407620 FALSE TRUE 250895.9233 320637.2972 357192.0935 352436.6156 304468.2996 267950.7607 360711.1179 307760.6277 290518.5995 380011.5343 0.660232389 0.84375675 0.939950663 0.927436627 0.801208048 0.705112178 0.949210972 0.809871806 0.764499425 1 18.53568368 -1.185943702 3.910084313 1.000104203 0.829716578 0.245276149 0.092675656 13313597.8 4038072.216 12545.6364 0.021528076 0.065171287 1.185943702 -0.170387625 SIVEGIIEEEEEDEEGSESISKR ddPTM_BT-474_Pertuzumab_2h_R1 3 SIVEGIIEEEEEDEEGSESISKR 23 1 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ;; 350.07 2.14E-101 894980000 337450 356808 250399 265929 317011 353776 288328 332671 372151 317116 FALSE TRUE 324262.0809 346632.1852 295651.6694 279653.6276 327207.9467 360929.5931 291856.6443 325801.2276 329905.9787 295637.4509 1.096823423 1.172490779 1.000048094 0.945934376 1.106787877 1.220852067 0.987211341 1.10202962 1.115914028 1 18.17346951 -1.177231185 3.545103365 0.999907749 1.08128553 0.088051731 0.080054901 13894855.95 19122593.01 14429.79686 0.019494565 0.066491911 1.177231185 0.081377781 SRTSPVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 81.163 0.021497 52157000 44980 57043 47610 64022 54710 60207 59404 47388 56850 60006 FALSE TRUE 43222.13187 55416.18949 56214.18608 67326.18309 56469.79684 61424.42679 60131.00392 46409.42124 50396.62633 55941.74017 0.77262759 0.990605393 1.004870172 1.203505341 1.009439404 1.09800708 1.074886189 0.829602746 0.900876987 1 15.77163751 -1.174098857 6.489876873 1.000000043 0.990167396 0.000458148 0.120824201 7.92E-08 9.97E-09 0.122354223 0.028839041 0.066973214 1.174098857 -0.009832647 KPSPSES(ph)PEPWKPFPAVS(ph)PEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 KPS(0.184)PS(0.146)ES(0.67)PEPWKPFPAVS(1)PEPR 110.59 0.00018892 263310000 292240 279760 222710 236880 249910 227490 278650 308940 282950 320330 TRUE FALSE 280818.9377 271781.5187 262958.6512 249105.4052 257948.5821 232090.0037 282060.2021 302560.281 250830.7022 298633.7638 0.940345573 0.910083024 0.880538918 0.834150171 0.863762285 0.777172684 0.94450205 1.01314827 0.839927472 1 18.18801776 -1.173694845 5.438198623 1.000003364 0.895172838 0.209221591 0.063651465 2.88E-06 4.37E-07 0.068261149 0.016088791 0.067035547 1.173694845 -0.104830526 VERPSTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VERPSTLR 8 1 Q9H425;Q9H425-3;Q9H425-2;E5RFY9 Q9H425 C1orf198 Uncharacterized protein C1orf198 0 ; 104.2 0.0042189 269420000 234350 267130 233180 274600 238770 194643 267860 274120 271430 292670 FALSE TRUE 225191.3429 259511.7139 275320.8131 288772.1389 246450.2539 198578.8148 271138.1508 268459.3262 240618.4043 272847.2002 0.825338661 0.951124709 1.009065927 1.058365776 0.903253739 0.727802282 0.99373624 0.9839182 0.88187969 1 18.05773371 -1.168221999 4.472013796 1.000012693 0.933429666 0.049352564 0.092392228 1.20E-05 2.24E-06 0.092009728 0.021682767 0.067885653 1.168221999 -0.066583027 LAAQES(ph)SETEDMSVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAAQESSETEDMSVPR 16 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 LAAQES(0.662)S(0.322)ET(0.016)EDMSVPR 75.574 0.0073553 0 92617 97055 84484 93227 93607 103920 88080 82222 118410 91037 TRUE FALSE 88997.42525 94287.08643 99752.13814 98038.45664 96617.95417 106021.3336 89157.94939 80524.08697 104968.5932 84870.9829 1.048620179 1.110946088 1.175338552 1.155146945 1.138409747 1.249205912 1.050511569 0.948782307 1.236801904 1 16.37298377 -1.162184597 4.188379413 0.999964578 1.114390555 0.147745341 0.086577483 3.08E-05 6.15E-06 0.09001409 0.021209959 0.068835965 1.162184597 0.114425977 MPLAQKPALAPKPTSQT(ph)PPAS(ph)PLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 MPLAQKPALAPKPTSQTPPASPLSK 25 2 F5H1N7;Q6ZU35 F5H1N7 KIAA1211 Uncharacterized protein KIAA1211 2 MPLAQKPALAPKPT(0.032)S(0.027)QT(0.941)PPAS(0.999)PLS(0.001)K 133.4 0.00011484 308950000 523170 467520 464280 417310 516580 541020 495890 510000 520600 470440 TRUE FALSE 502723.938 454186.7873 548185.7239 438847.4191 533196.2648 551959.7951 501958.8502 499468.3218 461503.6705 438576.6798 1.146262355 1.035592653 1.249919909 1.000617314 1.215742399 1.258525181 1.144517876 1.138839215 1.0522759 1 18.74246958 -1.161442006 7.765951028 0.999999957 1.140309742 0.196415966 0.083644647 5.92E-08 6.50E-09 0.076938891 0.018134665 0.068953767 1.161442006 0.140309785 KPPTHITVVHNYQFFELDVYHSDGTPLTADQIFVQLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPTHITVVHNYQFFELDVYHSDGTPLTADQIFVQLEK 38 1 P43155-2;P43155;P43155-3 P43155-2 CRAT Carnitine O-acetyltransferase 0 29.561 0.076781 212150000 49604 47213 40839 71872 39628 58143 58168 42359 61850 46328 FALSE TRUE 47665.42084 45866.53147 48219.51576 75581.32253 40902.67061 59318.6913 58879.87738 41484.27185 54829.0473 43190.1633 1.103617519 1.061967077 1.116446711 1.749966121 0.947036721 1.373430586 1.363270543 0.960502778 1.269479972 1 15.39841515 -1.158583849 4.966775068 0.999986149 1.20922678 0.074282394 0.227766544 3.37E-05 5.71E-06 0.21284991 0.050165885 0.069409058 1.158583849 0.209240631 DSFDDRGPSLNPVLDYDHGSR ddPTM_BT-474_Pertuzumab_2h_R1 5 DSFDDRGPSLNPVLDYDHGSR 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;; 234.64 5.30E-30 10661580000 6174510 9013380 6481440 8084020 7304800 8673960 7927720 7278420 7844270 9235850 FALSE TRUE 5933203.323 8756327.227 7652780.387 8501237.241 7539765.526 8849353.414 8024741.809 7128118.084 6953821.355 8610297.653 0.689082255 1.016959875 0.888793941 0.987333723 0.875668395 1.027763937 0.931993542 0.82785966 0.807616837 1 23.03763168 -1.154947526 4.088349391 1.000022151 0.900649329 0.089955611 0.098823841 2.98E-05 6.15E-06 0.090727016 0.021377065 0.069992656 1.154947526 -0.099372822 DNQVVQLHPSTVLDHKPEWVLYNEFVLTTK ddPTM_BT-474_Pertuzumab_2h_R1 1 DNQVVQLHPSTVLDHKPEWVLYNEFVLTTK 30 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 107.27 0.00018561 386500000 300900 340800 310510 405480 330220 423220 395620 146730 439090 482740 FALSE TRUE 289140.4953 331080.7177 366626.0643 426406.8714 340841.8262 431777.7984 400461.7159 143699.9742 389246.344 450043.5898 0.6424722 0.735663667 0.814645676 0.947479047 0.757352918 0.959413284 0.88982873 0.319302346 0.864908095 1 18.77970522 -1.154774326 6.764208538 1.000000476 0.753909762 0.12518852 0.177716325 1.37E-06 1.71E-07 0.18621695 0.043891672 0.070020575 1.154774326 -0.246090713 DFLLDIEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFLLDIEDR 9 0 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 ;;; 146.23 0.00022166 71991000 213828 223789 177943 220085 213803 174300 222927 228366 223233 251192 FALSE TRUE 205471.3654 217406.7568 210101.2584 231443.6132 220680.1677 177824.4654 225655.2473 223650.1623 197892.5257 234178.5421 0.877413291 0.92838035 0.897184074 0.988321181 0.94235862 0.759354225 0.963603434 0.955041227 0.845049781 1 17.83724936 -1.153622814 4.074740183 1.000029982 0.911631256 0.158173749 0.063790718 0.617795774 34174341.49 2094.124937 0.014728349 0.070206478 1.153622814 -0.088398726 SWHDIEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SWHDIEK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;; 124.08 0.0041813 1245250000 1229921 1627310 1506103 2019980 1668340 1570560 1905300 1092986 1799050 2147600 FALSE TRUE 1181854.328 1580900.712 1778289.315 2124231.41 1722003.671 1602317.799 1928617.631 1070415.457 1594829.386 2002141.139 0.590295212 0.789605029 0.888193784 1.060979852 0.860081059 0.800302121 0.96327756 0.534635364 0.796561918 1 20.93311225 -1.151536282 8.670660027 1.000000009 0.806457286 0.129238193 0.148311733 2.54E-08 2.47E-09 0.151238312 0.03564721 0.070544591 1.151536282 -0.193542723 EADLDHYSAIIMDEAHER ddPTM_BT-474_Pertuzumab_2h_R1 3 EADLDHYSAIIMDEAHER 18 0 Q92620 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 ;; 216.93 5.03E-19 210372000 147160 199919 165282 225593 185333 216978 208452 132676 195406 221484 FALSE TRUE 141408.8245 194217.5059 195152.1341 237235.8818 191294.4043 221365.4438 211003.0979 129936.1942 173224.3301 206482.6914 0.684845899 0.940599449 0.945125874 1.148938345 0.926442807 1.072077482 1.021892424 0.629283711 0.838929059 1 17.65566133 -1.151454592 5.407413588 1.000002319 0.910101028 0.02891696 0.152599013 4.58E-06 7.18E-07 0.158458988 0.037348178 0.070557861 1.151454592 -0.089901291 VHPEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHPEGK 6 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QLH6;J3QRW1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 77.906 0.071185 130340000 393880 347470 320800 339900 352900 373650 383770 338580 387430 449250 FALSE TRUE 378486.7341 337560.4958 378775.6962 357442.2797 364251.349 381205.459 388466.6921 331588.2047 343450.5706 418821.8973 0.903693758 0.805976235 0.904383698 0.853446971 0.869704644 0.91018512 0.927522402 0.791716495 0.82003967 1 18.67597735 -1.14860402 4.571396414 1.000017543 0.863174402 0.448535045 0.044795571 8.12E-06 1.51E-06 0.043952046 0.010358269 0.071022504 1.14860402 -0.13684314 DVLLPWYNAYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVLLPWYNAYR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 143.04 8.69E-05 967820000 1035210 1050170 873150 1069460 1046340 714450 1108180 1028070 1078480 1276850 FALSE TRUE 994752.8487 1020220.18 1030947.628 1124654.959 1079996.476 728896.6685 1121742.238 1006839.995 956055.4718 1190367.812 0.83566847 0.857062976 0.866074853 0.944796177 0.907279637 0.612328947 0.94234927 0.845822598 0.803159714 1 20.18297599 -1.146059556 3.584169215 1.000130122 0.848868081 0.210054422 0.089408944 19387280.33 31157325.92 28998.77475 0.021643011 0.071439835 1.146059556 -0.151262041 LSS(ph)SSSNDSGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSSSSNDSGNK 12 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LS(0.019)S(0.876)S(0.087)S(0.013)S(0.005)NDSGNK 110.14 0.001596 84113000 439520 490180 405200 566520 582650 499130 485970 559040 459700 482000 TRUE FALSE 422343.0725 476200.5463 478428.6536 595758.1651 601391.4664 509222.7506 491917.4462 547495.6286 407516.7832 449353.7107 0.93989003 1.059745441 1.064703912 1.325811162 1.338347614 1.133233661 1.094722119 1.218406827 0.906895333 1 18.77749199 -1.146058111 4.753568842 0.999988234 1.134866954 0.05586169 0.136751749 1.73E-05 3.12E-06 0.134706948 0.031747963 0.071440073 1.146058111 0.13487872 FNHPEIVQLVSELEAER ddPTM_BT-474_Pertuzumab_2h_R1 3 FNHPEIVQLVSELEAER 17 0 Q7Z4H3-2;Q7Z4H3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 ;; 179.46 9.15E-10 202808000 284536 301862 244896 310654 293140 321258 303151 253504 314727 338350 FALSE TRUE 273416.0185 293253.1913 289154.1549 326686.8902 302569.1143 327754.0569 306861.0526 248269.0538 279000.5104 315433.2531 0.866795165 0.929683819 0.916688878 1.035676762 0.959217557 1.039059939 0.972824043 0.787073181 0.88449936 1 18.26697523 -1.145898545 5.299420792 1.000002082 0.930050058 0.071961909 0.072400001 1.98E-06 3.20E-07 0.078060287 0.018398438 0.071466326 1.145898545 -0.069952025 YQDEDT(ph)PPQEHISPQITNEVIGPELVHVSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 YQDEDTPPQEHISPQITNEVIGPELVHVSEK 31 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UK02;E7EQD7;B4E2H8;C9JCP6;A8MUT6;A0A590UJ95;A0A590UJZ4;A0A590UJ86;C9JN61;A0A590UK13;A0A590UK52;C9IYP1;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UJ81;C9JUA9;A0A590UJ64;A0A590UK81;A0A590UJ29 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 1 YQDEDT(1)PPQEHISPQITNEVIGPELVHVSEK;Y(0.017)QDEDT(0.816)PPQEHIS(0.151)PQIT(0.016)NEVIGPELVHVSEK 217.83 1.43E-34 88672000 70988 153007 123842 213193 120072 166761 146699 108655 122598 189526 TRUE FALSE 68213.71048 148643.3902 146223.0043 224195.9163 123934.2249 170133.0217 148494.3462 106411.2363 108681.189 176689.2352 0.386066024 0.841270211 0.827571663 1.268871395 0.701424876 0.962894098 0.840426674 0.602250817 0.615097965 1 17.43085462 -1.144436392 8.574192526 1.00000001 0.791831124 0.076580949 0.224255882 4.25E-08 3.97E-09 0.217360589 0.05123238 0.071707339 1.144436392 -0.208168886 KPESPYGNLCDAPDS(ph)PRPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPESPYGNLCDAPDSPRPVK 20 2 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 KPESPYGNLCDAPDS(1)PRPVK;KPESPYGNLCDAPDS(1)PRPVK 162.47 1.10E-11 938840000 519110 497990 396350 522250 476410 556030 435130 469930 552960 557240 TRUE FALSE 498822.6073 483787.8128 467979.2618 549203.3851 491734.1603 567273.3076 440455.2511 460225.7813 490190.299 519497.6385 0.960201877 0.931260851 0.900830393 1.057181678 0.946557066 1.091965132 0.847848418 0.885905435 0.943585231 1 18.98675767 -1.144044776 10.61993859 0.999999998 0.947509433 0.03792004 0.070173481 0 0 0.069505962 0.016382712 0.071772029 1.144044776 -0.052490565 QYPWGVVQVENENHCDFVK ddPTM_BT-474_Pertuzumab_2h_R1 2 QYPWGVVQVENENHCDFVK 19 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;E7EW69;E7EX04;B5ME97;Q9P0V9;Q9P0V9-2;Q9P0V9-3;A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 D6RGI3;E7EW69;A0A087X142 SEPT11;SEPT10;SEPT8 Septin-11;Septin-10;Septin-8 0 ; 308.12 1.89E-61 765930000 665140 679660 530940 579190 604280 657200 589930 670620 700390 739380 FALSE TRUE 639145.5934 660276.7623 626892.6687 609082.0653 623717.215 670489.0343 597149.7398 656771.4626 620884.6635 689301.134 0.927237113 0.957893045 0.909461247 0.883622607 0.904854474 0.972708445 0.866311849 0.95280775 0.900745165 1 19.39477486 -1.142697455 4.028993912 1.000027047 0.92047089 0.361878081 0.03204032 0.23261083 16253944.93 896.9592321 0.007084612 0.071995035 1.142697455 -0.079556157 DLTEYLSR ddPTM_BT-474_Pertuzumab_2h_R1 8 DLTEYLSR 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;;;;;; 255.13 1.20E-12 6561733000 3345480 3531640 2953820 3275630 3269110 2795050 3564950 3495890 3589250 3905160 FALSE TRUE 3214734.943 3430921.085 3487640.981 3444685.657 3374263.892 2851567.826 3608578.924 3423698.65 3181813.387 3640660.035 0.883008826 0.942389856 0.95796942 0.946170646 0.926827515 0.783255728 0.991188106 0.94040603 0.873966082 1 21.7957686 -1.142187672 4.232610527 1.000018655 0.920276584 0.169013235 0.055104506 38268152024 7755674505 7243490.264 0.01271972 0.072079593 1.142187672 -0.079742071 DLTDYLMK ddPTM_BT-474_Pertuzumab_2h_R1 8 DLTDYLMK 8 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;P63261;I3L3I0;I3L1U9;I3L4N8;P68133;P68032;P63267;P62736 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ;;;;;;; 203.57 0.00021994 25820447000 14580360 14762690 13072720 12449510 12523660 10302780 15301710 15592310 15943990 15602040 FALSE TRUE 14010543.41 14341672.54 15435251.31 13092030.7 12926494.9 10511109.27 15488976.9 15270323.35 14134095.1 14545299.93 0.963235098 0.986000468 1.061184807 0.900086678 0.888705971 0.722646444 1.064878481 1.04984589 0.971729367 1 23.79404971 -1.138023627 7.535002373 1.000000012 0.96126379 0.015491819 0.097589873 2.18E-08 2.50E-09 0.101036573 0.023814541 0.072774021 1.138023627 -0.038736223 VIADNVKDWSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VIADNVKDWSK 11 1 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 ; 129.71 0.00021833 1246580000 1275000 1212080 816930 842710 1469720 1055670 1152400 1055220 1292040 932450 FALSE TRUE 1225171.59 1177512.665 964567.4235 886202.3641 1516994.879 1077016.371 1166503.416 1033429.338 1145373.036 869294.331 1.40938638 1.354561537 1.109598198 1.019450297 1.745087739 1.238954785 1.341896955 1.188814078 1.317589446 1 19.72948521 -1.137352504 5.691276103 0.999996364 1.29523754 0.191338268 0.186173434 8.39E-06 1.27E-06 0.17606511 0.041498434 0.072886567 1.137352504 0.295241176 TT(ph)PDQELAPASEPVWERPWSVEEIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPDQELAPASEPVWERPWSVEEIRR 26 2 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.462)T(0.538)PDQELAPASEPVWERPWSVEEIRR 157.75 2.43E-07 608040000 55096 58657 43452 62637 54729 70932 46488 47533 78330 54132 TRUE FALSE 52942.78741 56984.15979 51304.74298 65869.70308 56489.40799 72366.29364 47056.93405 46551.42694 69438.30679 50465.59142 1.049086832 1.129168572 1.016628192 1.305239892 1.119364826 1.433972963 0.932455812 0.922438946 1.375953493 1 15.62301244 -1.134173288 4.364738385 0.999986966 1.126724558 0.053062538 0.169134943 3.48E-05 6.91E-06 0.164440923 0.038752655 0.073422085 1.134173288 0.126737592 S(ph)PQEGPTWSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPQEGPTWSR 10 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(1)PQEGPTWSR 128.57 0.0034236 0 36480 42963 68609 48802 34458 50772 52995 61551 42233 62928 TRUE FALSE 35054.32127 41737.73731 81008.1725 51320.67707 35566.37286 51798.64463 53643.56866 60279.95034 37438.8869 58665.83051 0.597525356 0.711448844 1.380840803 0.874796736 0.606253633 0.882944027 0.914392044 1.027513798 0.63817194 1 15.84023284 -1.132389795 4.823963852 1.000008524 0.869397726 0.031676143 0.225916902 2.07E-05 3.72E-06 0.21851501 0.051501121 0.073724223 1.132389795 -0.130610797 EQLNRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQLNRPR 7 1 P82930;C9JJ19 P82930 MRPS34 "28S ribosomal protein S34, mitochondrial" 0 ; 81.119 0.042081 42127000 204661 243739 188025 299814 240647 255555 303226 228862 187671 240225 FALSE TRUE 196662.6219 236787.8024 222005.3001 315287.4365 248387.6293 260722.4972 306936.9705 224135.9197 166367.3749 223954.3468 0.878137106 1.057303891 0.991297125 1.407820125 1.10909939 1.164176989 1.37053366 1.000810759 0.742862897 1 17.77284514 -1.128508263 8.255258108 0.999999994 1.095934743 0.00953408 0.192637705 2.09E-08 2.35E-09 0.186035353 0.043848951 0.074386091 1.128508263 0.095934749 DINWDSSQWQPLIQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DINWDSSQWQPLIQDR 16 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 253.16 3.52E-26 293930000 232686 252500 218763 227890 230180 219490 245540 251600 251630 271450 FALSE TRUE 223592.3739 245298.9472 258298.3405 239651.4302 237583.9487 223928.2382 248544.992 246404.3721 223066.0173 253064.4497 0.883539249 0.969314131 1.020682047 0.946997615 0.938827832 0.884866438 0.98214108 0.973682287 0.881459318 1 17.94914533 -1.127054616 4.547202481 1.000005625 0.947573205 0.119775659 0.044916075 2.54E-06 4.87E-07 0.043054375 0.010146925 0.074635489 1.127054616 -0.052432419 VFDQQSS(ph)PMVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 VFDQQSSPMVTR 12 0 O15357;A0A0A0MTP6 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 1 VFDQQS(0.095)S(0.905)PMVT(0.001)R 75.102 0.016814 0 84025 97505 75635 105140 102420 93167 92685 95264 91135 97476 TRUE FALSE 80741.21011 94724.25287 89303.92699 110566.288 105714.4323 95050.90057 93819.30676 93296.76511 80789.73687 90873.8637 0.888497603 1.042370699 0.982724002 1.216700639 1.163309537 1.045965217 1.032412433 1.026662247 0.889031605 1 16.4715778 -1.12044518 6.908872136 0.999999967 1.03970462 0.0039579 0.097820273 5.13E-08 6.44E-09 0.096363313 0.022713032 0.075780038 1.12044518 0.039704653 EALAEAALES(ph)PRPALVR ddPTM_BT-474_Pertuzumab_2h_R1 11 EALAEAALESPRPALVR 17 1 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR 264.64 1.06E-27 96252480000 7807398 8297123 8222230 9271559 8927121 10348500 8159632 8019531 8922099 9991886 TRUE FALSE 7502276.255 8060497.176 9708169.864 9750065.271 9214269.954 10557753.76 8259492.017 7853924.882 7909299.726 9315126.661 0.805386392 0.865312676 1.04219408 1.046691647 0.989172803 1.133398841 0.886675224 0.843136671 0.849081286 1 23.15114396 -1.115850109 6.016558478 1.00000028 0.941604817 0.029408553 0.102887751 4.19E-07 6.16E-08 0.108129377 0.025486217 0.076586089 1.115850109 -0.058395462 LTGS(ph)TSSLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGS(0.94)T(0.056)S(0.003)SLNK;LTGS(0.941)T(0.056)S(0.003)SLNK 244.64 1.84E-12 1977030000 1916000 2166240 2091700 2151010 2095550 2322940 2490810 2324950 2869080 3092450 TRUE FALSE 1841120.602 2104460.956 2469716.72 2262023.884 2162955.269 2369911.438 2521293.278 2276938.97 2543394.067 2882995.607 0.638613738 0.729956352 0.856649491 0.784608856 0.750245773 0.822030888 0.87453941 0.789782324 0.882205322 1 21.45913721 -1.113924604 0.03574214 1.902964353 1.67E-13 0.720176759 0.049657452 236.9873535 1.569204313 51.45468686 33.22984041 0.076926398 1.113924604 -1.902964353 VWDISGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VWDISGLR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 169.97 0.00069305 343630000 1320830 1550010 1293930 1401760 1392530 1161620 1556110 1472640 1520550 1623040 FALSE TRUE 1269210.503 1505805.232 1527771.934 1474105.002 1437321.992 1185108.752 1575154.14 1442229.469 1347943.539 1513110.055 0.838809113 0.995172312 1.009689896 0.974221932 0.949912392 0.783227068 1.041004344 0.953155697 0.890843025 1 20.52908549 -1.113207972 4.450515283 1.00000639 0.94346463 0.053047515 0.07553334 4.64E-06 9.24E-07 0.070794585 0.016684557 0.077053439 1.113207972 -0.05654176 WIDLTMEDIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 WIDLTMEDIRR 11 1 A0A0A0MSW4;P48739;P48739-3;P48739-2 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 131.43 0.0003262 32448000 32627 39084 28450 31851 38696 32185 35853 33897 35531 40536 FALSE TRUE 31351.90077 37969.36259 33591.54787 33494.83393 39940.69198 32835.80275 36291.77974 33197.0151 31497.66984 37790.46061 0.829624732 1.004734051 0.888889612 0.886330396 1.056898787 0.868891308 0.96034235 0.878449602 0.83348203 1 15.20573448 -1.104233685 7.554714025 1.000000014 0.915703064 0.122239777 0.07013278 1.62E-08 1.87E-09 0.063331593 0.014927397 0.078662241 1.104233685 -0.084296951 LHQDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHQDEK 6 0 B1AMS2;Q14141-2;Q14141-4;Q14141 B1AMS2 6-Sep Septin-6 0 89.673 0.049899 84517000 176520 159990 137540 165860 145540 143600 172830 157460 157830 216930 FALSE TRUE 169621.4032 155427.2418 162396.5376 174420.0545 150221.4263 146503.6904 174945.1452 154208.396 139913.8001 202237.1379 0.838725296 0.768539564 0.803000573 0.862453139 0.742798419 0.724415367 0.865049551 0.762512749 0.6918304 1 17.62568843 -1.102218923 4.606469251 1.000015687 0.785639957 0.578039896 0.055260261 0.178087992 33005874.95 1070.325846 0.012582788 0.079028016 1.102218923 -0.214375731 IQEIIEQLDVTTSEYEKEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IQEIIEQLDVTTSEYEKEK 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 212.18 8.60E-17 1018290000 458365 599400 290259 419355 329819 430449 548350 472898 510269 300714 FALSE TRUE 440451.5891 582305.6989 342715.2581 440997.9618 340427.9277 439152.9737 555060.8713 463132.491 452345.4023 280346.3729 1.571097869 2.077093749 1.222470812 1.573046789 1.214311868 1.566465687 1.979911013 1.652001009 1.613523291 1 18.09685088 -1.100762099 3.496659584 0.999574953 1.615639562 0.331652161 0.258615942 25356521.42 41472749.2 128033.848 0.064584021 0.079293557 1.100762099 0.616064609 QYVETHWCAQSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QYVETHWCAQSEK 13 0 Q96P70 Q96P70 IPO9 Importin-9 0 153.09 4.55E-05 269080000 307950 312080 254760 236180 282410 235590 283300 297680 323920 341070 FALSE TRUE 295914.9735 303179.784 300800.7991 248369.2781 291493.9741 240353.7912 286767.1101 291532.804 287149.9596 317969.0251 0.930640881 0.953488422 0.946006609 0.78111155 0.916737012 0.755903161 0.901871212 0.916859131 0.903075259 1 18.27852671 -1.099500193 5.746493097 1.000000741 0.889313364 0.213753567 0.06356442 6.04E-07 9.46E-08 0.061638361 0.014528204 0.079524291 1.099500193 -0.110687377 FKPAYNPYTEPSMEVFSYHQGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKPAYNPYTEPSMEVFSYHQGLK 23 1 K7ER00;Q9Y285;Q9Y285-2;K7EPH2 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 246.16 8.68E-38 393480000 141800 164780 139090 171680 121150 139980 165410 150460 168310 202510 FALSE TRUE 136258.2992 160080.6357 164226.657 180540.4254 125046.8998 142810.4915 167434.3371 147352.9484 149204.1544 188793.8173 0.721730728 0.84791249 0.869873068 0.956283569 0.662346371 0.756436273 0.886863455 0.780496684 0.790302122 1 17.52645199 -1.097850643 5.013053116 1.000005679 0.810864526 0.333684441 0.081293926 5.11E-06 9.20E-07 0.077941824 0.018370512 0.079826917 1.097850643 -0.189141153 YLAADKDGNVTCER ddPTM_BT-474_Pertuzumab_2h_R1 4 YLAADKDGNVTCER 14 1 Q16658 Q16658 FSCN1 Fascin 0 ;;; 209.56 5.90E-09 2096290000 1427370 1566040 1105080 1231350 1396100 1409460 1258410 1499980 1605860 1293760 FALSE TRUE 1371586.802 1521378.073 1304792.538 1294900.121 1441006.824 1437960.247 1273810.798 1469004.889 1423569.505 1206132.483 1.137177567 1.261368958 1.081798689 1.073596922 1.194733452 1.192207545 1.056111842 1.217946544 1.180276234 1 20.20195695 -1.096922946 4.73931821 0.999992022 1.156066471 0.345418021 0.06400768 5.40E-06 1.03E-06 0.060440479 0.01424521 0.079997618 1.096922946 0.156074449 VQSGMGLILQGYES(ph)GS(ph)EEEGEIHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VQSGMGLILQGYESGSEEEGEIHEK 25 0 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 VQSGMGLILQGY(0.11)ES(0.945)GS(0.945)EEEGEIHEK 74.876 0.016895 50175000 91515 80919 71430 74893 72014 85426 80383 79888 91384 100700 TRUE FALSE 87938.49262 78611.26935 84338.98995 78758.23671 74330.39571 87153.37225 81366.7512 78238.28488 81010.47143 93879.49931 0.936716677 0.837363534 0.898374944 0.838929024 0.79176387 0.928353612 0.866714797 0.833390521 0.862919722 1 16.51852253 -1.095859325 3.980376869 1.000034548 0.862830933 0.469091358 0.042623877 12994207.86 21612239.86 5542.798692 0.009811634 0.080193778 1.095859325 -0.137203615 DILETHLR ddPTM_BT-474_Pertuzumab_2h_R1 8 DILETHLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;;;; 197.3 0.00014515 4433138000 4062741 4341980 3713492 4451399 4261307 3053987 4534111 4237121 4586111 4786070 FALSE TRUE 3903964.59 4218150.982 4384602.611 4681136.236 4398375.81 3115740.71 4589600.807 4149622.971 4065514.906 4461905.216 0.874954622 0.945369921 0.982674978 1.049133948 0.985761821 0.698298274 1.028619073 0.930011457 0.911161199 1 22.08922844 -1.094655429 3.983843294 1.000013364 0.937420891 0.041977458 0.09331185 27591.36229 48791864.79 1578.012533 0.021510757 0.08041639 1.094655429 -0.062592472 EEEADMSS(ph)PTQR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEEADMSSPTQR 12 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 EEEADMS(0.017)S(0.966)PT(0.017)QR;EEEADMS(0.013)S(0.987)PTQR;EEEADMS(0.041)S(0.959)PTQR 270.79 1.12E-27 362250000 443003 492088 540599 678100 609700 601460 527698 542836 536850 570590 TRUE FALSE 425689.953 478054.132 638297.2649 713096.8223 629311.5542 613621.9333 534156.126 531626.2469 475909.0387 531943.4311 0.800254178 0.898693553 1.199934481 1.340550105 1.183042251 1.153547346 1.004159643 0.999403726 0.894660994 1 19.02091331 -1.094435496 6.744420345 0.999999952 1.061201537 0.00733715 0.158103203 1.24E-07 1.65E-08 0.165507773 0.039010526 0.080457124 1.094435496 0.061201585 SASEPS(ph)LNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASEPSLNR 9 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0 P15056 BRAF Serine/threonine-protein kinase B-raf 1 SAS(0.115)EPS(0.885)LNR 94.801 0.0088912 656130000 734350 714880 566920 706200 588340 653090 686500 757940 746280 769690 TRUE FALSE 705650.7901 694492.3223 669375.0551 742647.0666 607264.4904 666295.9273 694901.5924 742288.2741 661565.4231 717558.2107 0.983405638 0.967855028 0.932851224 1.03496421 0.846292999 0.928560105 0.968425393 1.034464191 0.921967602 1 19.45273635 -1.087860461 5.498011915 1.000000374 0.961268925 0.050705729 0.052928875 2.45E-07 4.06E-08 0.051646138 0.012172994 0.081684478 1.087860461 -0.038731449 SIPLECPLSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIPLECPLSSPK 12 0 Q92667-2;Q92667;I3L2A2;I3L2N7 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 SIPLECPLS(0.186)S(0.814)PK;SIPLECPLS(0.159)S(0.841)PK 196.57 2.15E-07 465160000 510370 700210 518280 788480 498510 671210 649980 682170 624270 498220 TRUE FALSE 490424.1762 680240.6964 611944.7251 829173.5473 514545.0269 684782.3261 657934.6497 668082.9511 553405.4868 464475.1156 1.055867494 1.464536363 1.317497331 1.785184005 1.10779891 1.474314345 1.416512161 1.438361128 1.191464232 1 18.82524178 -1.087380329 7.741791575 0.999999967 1.378461387 0.221703008 0.200764879 1.02E-07 1.23E-08 0.177622508 0.041866023 0.081774834 1.087380329 0.378461419 LKVDSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKVDSFR 7 1 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;K7ENH2;B7Z8D3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ; 111.95 0.0058957 853820000 1806920 1903250 1630860 1536490 1523660 974630 2063950 1695060 1861670 2770100 FALSE TRUE 1736303.569 1848971.173 1925592.68 1615788.433 1572669.908 994337.6864 2089209.237 1660056.419 1650341.026 2582478.66 0.672339948 0.715967649 0.745637403 0.625673489 0.608976923 0.385032295 0.808993805 0.642815155 0.639053113 1 21.300325 -1.084917946 5.001958614 1.000009239 0.650980158 0.496997307 0.105806336 1.09E-05 1.99E-06 0.101973318 0.024034706 0.082239802 1.084917946 -0.349029081 EEAAEVASLDVANIISGSGRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEAAEVASLDVANIISGSGRPR 22 1 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 0 169.58 7.05E-18 0 48510 48616 40627 41570 47091 46041 48996 46813 46740 53305 FALSE TRUE 46614.17557 47229.51928 47969.20264 43715.43268 48605.72478 46971.98057 49595.6277 45846.29519 41434.27115 49694.60487 0.938012802 0.950395308 0.965279888 0.879681664 0.978088565 0.945212879 0.998008292 0.922560815 0.833778058 1 15.60080161 -1.083767766 4.563140082 1.000003437 0.937642433 0.154412199 0.045429676 1.84E-06 3.69E-07 0.042578424 0.010035169 0.082457893 1.083767766 -0.062361004 (ac)ASLEVSRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASLEVSRSPR 10 1 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 ASLEVSRS(1)PR;ASLEVS(0.001)RS(0.999)PR 94.791 1.04E-06 2561500000 53193 54461 35577 46243 59036 60746 40092 46001 55383 62490 TRUE FALSE 51114.15875 52907.8256 42006.55531 48629.60677 60934.94656 61974.32574 40582.65789 45051.06327 49096.15402 58257.49664 0.87738337 0.908171972 0.721049783 0.834735606 1.045958891 1.063800014 0.696608338 0.773309288 0.84274397 1 15.83015609 -1.083027646 4.54333681 1.000008228 0.856755158 0.111045914 0.115517175 1.23E-05 2.48E-06 0.120359325 0.02836703 0.082598537 1.083027646 -0.14325307 S(ph)SGSLGHRPSQEMDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGSLGHRPSQEMDK 15 1 Q5SW79;H0Y2V6;H0YB66 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.333)S(0.333)GS(0.333)LGHRPSQEMDK;S(0.333)S(0.333)GS(0.333)LGHRPSQEMDK 136.43 1.39E-05 490603000 880440 1228260 1002661 1237666 1254030 1277982 1125290 1155300 1071630 1314350 TRUE FALSE 846031.4314 1193231.227 1183864.147 1301542.091 1294367.014 1303823.672 1139061.636 1131442.651 949983.055 1225327.904 0.690453085 0.973805643 0.966161093 1.062199013 1.056343375 1.06406103 0.929597402 0.923379487 0.775288845 1 20.22473644 -1.081588981 4.756872003 1.000002199 0.948591164 0.017593069 0.116816265 2.73E-06 5.27E-07 0.113353111 0.026716441 0.08287261 1.081588981 -0.051411035 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR 37 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 254.41 2.79E-62 849590000 193753 244598 185004 258183 193221 232503 214031 235131 224623 262387 FALSE TRUE 186180.9186 237622.3045 218438.3382 271507.8556 199436.1289 237204.37 216650.3754 230275.4627 199124.7387 244615.2948 0.761117242 0.971412293 0.892987245 1.109938182 0.815305229 0.969703755 0.885677961 0.941378023 0.81403225 1 17.90015509 -1.081098233 0.006067291 1.887432388 2.85E-06 0.037197757 0.096759409 82998.6937 93.76495842 15127.93391 14051.98991 0.082966309 1.081098233 -1.887429536 DTELAEELLQWFLQEEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTELAEELLQWFLQEEKR 18 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 141.86 1.87E-07 508980000 200490 198450 167880 131040 167770 230620 191250 175410 227280 182740 FALSE TRUE 192654.6291 192790.4003 198219.6505 137802.9901 173166.4744 235283.2944 193590.5747 171787.7222 201480.1272 170362.857 1.130848781 1.131645733 1.163514477 0.808879309 1.016456741 1.381071546 1.136342616 1.008363708 1.182652902 1 17.3782513 -1.078060932 4.243092574 0.999987821 1.100175512 0.048540498 0.139013642 1.65E-05 3.58E-06 0.13757573 0.032422939 0.083548579 1.078060932 0.100187691 EETVLATVQALQTASHLSQQADLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EETVLATVQALQTASHLSQQADLR 24 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 95.319 0.0070491 86966000 52665 66186 56180 56821 58399 71965 58824 61196 67908 57801 FALSE TRUE 50606.79358 64298.44008 66332.97572 59753.53862 60277.45687 73420.18161 59543.90571 59932.28121 60199.36853 53886.08679 0.939143972 1.193228975 1.230985207 1.108886211 1.118608911 1.362507207 1.104995914 1.112203257 1.117159774 1 15.7176252 -1.076839107 7.167272228 0.999999964 1.147649356 0.147967071 0.102475384 5.70E-08 7.36E-09 0.095740591 0.022566268 0.083783962 1.076839107 0.147649391 ENLVRPGIDHLGR ddPTM_BT-474_Pertuzumab_2h_R1 3 ENLVRPGIDHLGR 13 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 ;; 176.87 9.57E-06 354989000 334905 364780 298537 332978 344338 362780 334017 363420 349034 379034 FALSE TRUE 321816.5423 354376.8316 352489.2768 350163.0345 355413.9445 370115.6602 338104.8 355915.25 309413.1236 353361.6896 0.910728446 1.002872813 0.997531105 0.990947929 1.005807803 1.047413093 0.956823589 1.007226478 0.875627247 1 18.43078611 -1.075935131 4.893458164 1.000000516 0.982855829 0.00769952 0.048319657 2.55E-07 4.81E-08 0.043848985 0.010334994 0.083958538 1.075935131 -0.017144687 YLYVDKNFINNPLAQADWAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 YLYVDKNFINNPLAQADWAAK 21 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 173.09 4.33E-12 87210000 160310 141510 82390 110200 124580 150190 114030 128910 153350 107280 FALSE TRUE 154044.908 137474.2734 97279.70576 115887.4352 128587.2288 153226.9447 115425.5333 126247.9635 135942.3509 100013.83 1.540236064 1.374552632 0.972662538 1.158714101 1.285694476 1.532057563 1.154095721 1.262305057 1.359235526 1 16.60983999 -1.072389135 4.306121846 0.99997207 1.281368016 0.218992927 0.16478108 4.57E-05 9.85E-06 0.161788757 0.038130117 0.084646862 1.072389135 0.281395945 VSIVNHLEFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSIVNHLEFLR 11 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 152.14 3.31E-05 227420000 157830 175670 179470 158980 153400 88596 191940 162260 182540 225220 FALSE TRUE 151661.8291 170660.0636 211904.2213 167184.9769 158334.2503 90387.47182 194289.0191 158909.2743 161818.8245 209965.6488 0.722317341 0.812799925 1.009232808 0.796249186 0.754095973 0.43048695 0.925337169 0.756834631 0.770691898 1 17.67979379 -1.067600346 18.73097494 1 0.778252634 0.183583736 0.142011359 0 0 0.13763629 0.032441185 0.085585394 1.067600346 -0.221747366 YISENES(ph)PRPSQK ddPTM_BT-474_Pertuzumab_2h_R1 3 YISENESPRPSQK 13 1 O94782 O94782 USP1 Ubiquitin carboxyl-terminal hydrolase 1 1 YISENES(0.998)PRPS(0.002)QK;YISENES(1)PRPSQK;YISENES(1)PRPSQK 144.73 2.51E-05 1558660000 656750 662310 558720 614070 547430 603930 655110 668770 670830 769310 TRUE FALSE 631083.4839 643421.5673 659693.1327 645762.2263 565038.5831 616141.8784 663127.4321 654959.6658 594680.1907 717203.9485 0.879921932 0.897124965 0.919812466 0.900388554 0.787835293 0.859088799 0.924600922 0.913212577 0.829164692 1 19.45202391 -1.058310058 5.467871734 1.000000834 0.882434264 0.434638307 0.041229322 4.38E-07 7.54E-08 0.041714498 0.009832132 0.087435932 1.058310058 -0.11756657 AIEVLSDEHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIEVLSDEHAR 11 0 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 ; 169.58 1.67E-05 524130000 415230 477050 354550 470970 461650 485120 447210 421050 480130 489430 FALSE TRUE 399002.3525 463445.0011 418625.0719 495276.8181 476499.3915 494929.4588 452683.0898 412355.1704 425627.6553 456280.4702 0.874467304 1.015702033 0.917473132 1.08546574 1.044312485 1.084704455 0.992115857 0.903731799 0.932820235 1 18.79956138 -1.055058071 4.739485229 1.00000051 0.984653896 0.004593469 0.071162779 4.01E-07 7.99E-08 0.071991324 0.016967954 0.088093107 1.055058071 -0.015346614 EHPVIESHPDNALEDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 EHPVIESHPDNALEDLR 17 0 Q13564-2;Q13564;Q13564-4;Q13564-3;H3BMR3;J3QRA5 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ;; 233.49 2.39E-20 694065000 417650 486270 476254 595068 543561 512991 590888 341797 553575 637380 FALSE TRUE 401327.7763 472402.0557 562323.692 625779.5308 561045.1332 523364.0295 598119.4641 334738.7725 490735.4868 594209.6849 0.675397568 0.795009014 0.94633882 1.053129134 0.944187124 0.880773307 1.006579797 0.563334427 0.825862485 1 19.18061259 -1.054084247 6.992324045 1.000000036 0.850263283 0.085846498 0.141819281 8.82E-08 1.17E-08 0.148605959 0.035026752 0.088290861 1.054084247 -0.149736753 IDKTDYMVGSYGPR ddPTM_BT-474_Pertuzumab_2h_R1 5 IDKTDYMVGSYGPR 14 1 P52565;J3KTF8;J3QQX2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;; 145.7 7.76E-06 12995200000 5175980 5317220 4091260 4825730 4423150 4143750 5406060 5470590 5409860 5619590 FALSE TRUE 4973696.979 5165578.092 4830641.692 5074786.504 4565424.637 4227539.464 5472220.979 5357620.405 4795755.373 5238970.164 0.949365395 0.985991126 0.922059401 0.968661081 0.87143551 0.806940931 1.044522265 1.022647627 0.915400398 1 22.32085182 -1.052988361 5.897229825 1.000000134 0.948321159 0.056846504 0.066547828 1.26E-07 2.03E-08 0.069276227 0.016328521 0.088513933 1.052988361 -0.051678976 S(ph)RERPSQPEGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRERPSQPEGLR 12 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(1)RERPSQPEGLR 108.14 0.0013691 3085700000 619390 817850 742200 604510 602880 801940 727910 766820 777620 981830 TRUE FALSE 595183.554 794525.7188 876332.0501 635708.8335 622272.1827 818155.7763 736818.3803 750984.899 689347.8376 915329.7796 0.650239474 0.868021271 0.957394886 0.69451344 0.679833866 0.893837166 0.804975864 0.82045282 0.753114181 1 19.80393209 -1.052821298 4.80725144 1.000005656 0.797759594 0.304723232 0.094095553 5.60E-06 1.10E-06 0.089353674 0.021060274 0.088547989 1.052821298 -0.202246063 VWQLGSSSPNFTLEGHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VWQLGSSSPNFTLEGHEK 18 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 200.45 1.51E-15 2957200000 2561700 2418400 2000900 1993000 2107540 2260000 2204740 2331300 2839700 2537800 FALSE TRUE 2461585.932 2349429.6 2362507.14 2095858.969 2175330.938 2305698.748 2231722.268 2283157.84 2517349.161 2365912.546 1.04043826 0.993033155 0.998560638 0.885856484 0.919446893 0.974549441 0.94328181 0.965022078 1.064007698 1 21.17396532 -1.046791242 7.46736106 1.000000002 0.970875386 0.010846065 0.050450302 1.76E-09 1.97E-10 0.049448634 0.011655154 0.089786028 1.046791242 -0.029124617 VAS(ph)FSIPGSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VASFSIPGSSSR 12 0 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 VAS(0.709)FS(0.291)IPGSSSR 66.393 0.061027 310450000 226720 370260 223440 434880 262290 178910 300990 409430 347040 280030 TRUE FALSE 217859.5317 359700.5473 263820.5784 457324.2089 270726.7961 182527.6828 304673.6057 400975.1274 307645.4741 261063.3187 0.834508398 1.377828755 1.010561651 1.751775053 1.037015837 0.699170162 1.167048696 1.535930553 1.178432404 1 17.99404024 -1.043240264 6.051562606 0.999999674 1.20121015 0.024828176 0.299643183 1.32E-06 2.09E-07 0.290426621 0.0684541 0.090523166 1.043240264 0.201210477 EPAHLMSLFGGKPMIIYK ddPTM_BT-474_Pertuzumab_2h_R1 6 EPAHLMSLFGGKPMIIYK 18 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;;;;; 261.98 4.91E-31 3750460000 5900730 6181900 5064380 5448470 5642140 5524030 6005160 6018130 6386810 6606210 FALSE TRUE 5670122.948 6005598.265 5979626.123 5729666.19 5823624.557 5635729.671 6078652.944 5893853.512 5661806.104 6158765.512 0.920659008 0.975130203 0.970913101 0.930327056 0.945583095 0.915074565 0.986992106 0.956986185 0.919308601 1 22.55420977 -1.03832745 4.368424864 1.000003195 0.949247317 0.29799526 0.024241879 7.33E-07 1.61E-07 0.022815031 0.005377216 0.091552994 1.03832745 -0.050755878 TKENILEEFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKENILEEFSK 11 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 166.48 1.86E-05 1614790000 3571000 3058700 2590500 2442550 2934300 2589600 2862200 3409900 3418900 3083400 FALSE TRUE 3431441.372 2971468.871 3058660.975 2568610.298 3028684.424 2641963.486 2897228.46 3339484.373 3030800.805 2874558.572 1.19372811 1.033713106 1.064045452 0.893566867 1.053617225 0.919084938 1.007886389 1.161738156 1.05435347 1 21.454909 -1.037302596 7.559917548 0.999999998 1.042372325 0.020725113 0.087466337 3.73E-09 5.12E-10 0.086575145 0.020405956 0.091769297 1.037302596 0.042372327 VVIEACDELGIILAHTNLR ddPTM_BT-474_Pertuzumab_2h_R1 3 VVIEACDELGIILAHTNLR 19 0 P31939-2;P31939 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;; 238.45 2.99E-24 1365251100 180609.4 221169.1 205698.4 215305.1 217952.1 240151.7 251001.9 181742 226043.6 246050.5 FALSE TRUE 173550.985 214861.5738 242872.6766 226417.022 224962.7272 245007.7319 254073.7363 177988.9642 200384.0782 229385.2805 0.756591638 0.936684226 1.058798002 0.987059944 0.980719978 1.068105728 1.107628771 0.775938909 0.873569907 1 17.80741329 -1.034565102 3.598131373 1.000015742 0.95188749 0.017415379 0.112571512 85724663126 1.19179E+11 15759946.75 0.028474428 0.092349574 1.034565102 -0.048128251 EGHGSSSFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGHGSSSFDR 10 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 93.096 0.0076601 0 37593 91451 49129 92006 70217 77863 71760 61744 61539 78248 FALSE TRUE 36123.824 88842.90702 58007.70317 96754.44069 72475.59357 79437.44321 72638.22035 60468.96482 54553.35071 72948.19326 0.495198337 1.217890438 0.795190403 1.326344579 0.993521434 1.088956966 0.99575078 0.82893026 0.7478369 1 16.15458463 -1.034510138 6.362052241 1.000000031 0.957130998 0.002227161 0.228987768 9.23E-08 1.45E-08 0.206733891 0.048727611 0.092361263 1.034510138 -0.042869033 VGEEFEEQTVDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGEEFEEQTVDGR 13 0 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 97.175 0.009071 171790000 151210 205760 187040 232990 213360 215190 209110 206700 156670 216200 FALSE TRUE 145300.546 199891.9263 220842.2887 245014.6418 220222.9182 219541.2892 211669.1507 202431.5728 138885.4784 201556.5814 0.720892094 0.991741003 1.095683838 1.215612212 1.092610902 1.089229077 1.05017236 1.00434117 0.689064467 1 17.62082537 -1.033923575 6.537209985 0.999999994 1.011639718 0 0.158671862 1.33E-08 2.10E-09 0.153857146 0.036264459 0.092486091 1.033923575 0.011639724 SQIHDIVLVGGSTR ddPTM_BT-474_Pertuzumab_2h_R1 8 SQIHDIVLVGGSTR 14 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;; 166.35 3.82E-06 25617860000 11171380 13265250 11110990 14193420 11728350 9292030 14032650 12506210 14088530 15805220 FALSE TRUE 10734790.12 12886938.06 13118993.06 14925944.11 12105603.03 9479921.213 14204385.77 12247952.39 12489259.14 14734718.37 0.728537177 0.874596835 0.890345694 1.012977902 0.821570031 0.643373085 0.964007958 0.831230844 0.847607591 1 23.81271615 -1.029426122 3.847824006 1.000024898 0.85026928 0.174133409 0.100213006 36796765334 68753629194 13232490.26 0.023916587 0.093448832 1.029426122 -0.149755618 YESQEPLAGQES(ph)PLPLATR ddPTM_BT-474_Pertuzumab_2h_R1 7 YESQEPLAGQESPLPLATR 19 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(0.995)PLPLAT(0.005)R 386.47 7.59E-127 16186125000 4072921 4613050 4218912 5080437 4821988 4821033 4579140 4735960 4535331 4748305 TRUE FALSE 3913746.744 4481490.331 4981363.248 5342638.962 4977091.623 4918517.59 4635180.885 4638160.771 4020499.239 4426698.073 0.884123263 1.012377681 1.125299979 1.20691289 1.12433501 1.111103018 1.047096687 1.047769849 0.908238866 1 22.07779955 -1.028885207 7.080361512 0.999999992 1.060329721 0.019662675 0.094443089 1.24E-08 1.80E-09 0.094817859 0.022348781 0.093565295 1.028885207 0.060329729 LVQAFQFTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVQAFQFTDK 10 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ; 185.6 3.33E-06 2874000000 1934150 1930000 1664480 1637830 1709780 1452650 2026010 2011890 1981660 2141900 FALSE TRUE 1858561.28 1874958.29 1965288.562 1722358.603 1764776.626 1482023.578 2050804.916 1970343.768 1756710.265 1996827.205 0.930757191 0.938968722 0.984205622 0.862547645 0.883790356 0.742189196 1.027031739 0.986737242 0.879750767 1 20.92927806 -1.025672142 4.895532 1.000001356 0.920195214 0.096756068 0.076402663 1.18E-06 2.34E-07 0.076959405 0.018139198 0.094260092 1.025672142 -0.079806142 TFEHVTSEIGAEEAEEVGVEHLLR ddPTM_BT-474_Pertuzumab_2h_R1 6 TFEHVTSEIGAEEAEEVGVEHLLR 24 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;;;;; 360.48 9.72E-103 1109144000 156482.3 184259.7 149792.8 178813.2 177718.7 195064.7 173923.2 144806.3 188970.1 200219.1 FALSE TRUE 150366.7987 179004.7938 176863.6911 188041.7707 183435.1834 199009.0419 176051.7241 141815.9993 167519.0065 186658.082 0.805573469 0.958998356 0.947527635 1.007412959 0.982733678 1.066168899 0.943177612 0.759763509 0.897464523 1 17.51003845 -1.02533098 5.131560773 1.000000724 0.927318851 0.055583324 0.086149117 7.95E-07 1.51E-07 0.093005929 0.021921489 0.094334167 1.02533098 -0.072681873 FKPNQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 FKPNQTR 7 1 Q9NZJ9;A0A024RBG1;Q9NZJ9-2 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ; 100.15 0.0091254 1516230000 627260 670010 519060 575740 587530 433800 706130 686930 657230 719400 FALSE TRUE 602745.9857 650901.9708 612865.6884 605454.0104 606428.436 442571.7332 714771.8302 672744.6554 582624.0057 670674.3972 0.89871626 0.970518591 0.913805106 0.902754023 0.904206927 0.659890604 1.065750882 1.003086831 0.868713653 1 19.355253 -1.023071841 5.562259937 1.000000305 0.91721798 0.062998439 0.100786378 3.88E-07 6.82E-08 0.099464486 0.023443918 0.094826159 1.023071841 -0.082782325 LLIDRDPEGAVAHAQDVISDLLCNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLIDRDPEGAVAHAQDVISDLLCNR 25 1 A0A087WYJ2;M0R2B7;P28340;M0QZR8;M0QXE6;M0QXQ2 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ; 227.44 3.24E-34 441550000 250260 263530 208899 269650 279530 264560 244280 255830 260300 277230 FALSE TRUE 240479.5625 256014.3824 246651.6962 283566.6688 288521.3363 269909.5845 247269.5717 250547.0211 230751.8353 258452.9652 0.930457743 0.990564694 0.954338814 1.097169338 1.116339819 1.044327676 0.956729483 0.969410511 0.892819454 1 17.97954223 -1.021429126 6.228229469 1.000000002 0.997717596 0 0.067879369 1.54E-09 3.37E-10 0.070348897 0.016581381 0.095185517 1.021429126 -0.002282406 IIPELVGS(ph)PTQSTSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 IIPELVGSPTQSTSSR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6;H7C409 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 IIPELVGS(0.875)PT(0.105)QS(0.005)T(0.005)S(0.005)S(0.005)R;IIPELVGS(0.989)PT(0.011)QSTSSR;IIPELVGS(0.992)PT(0.008)QSTSSR;IIPELVGS(0.992)PT(0.008)QSTSSR;IIPELVGS(0.998)PT(0.002)QSTSSR 194.32 2.43E-10 717388000 410179 487713 378271 417605 440593 469034 474483 429753 425327 501924 TRUE FALSE 394148.7512 473803.9028 446632.9843 439157.6441 454765.074 478518.1888 480289.8649 420878.4504 377045.6621 467928.2404 0.842327342 1.012556759 0.954490338 0.938514939 0.971869263 1.022631565 1.026417778 0.899450843 0.805776676 1 18.83592778 -1.018442326 4.14071025 1.000004211 0.947511754 0.051939754 0.070912182 9057904.975 2227867.806 368.0747118 0.016563573 0.095842398 1.018442326 -0.052492456 S(ph)PHQLLSPSSFSPSATPSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPHQLLSPSSFSPSATPSQK 20 0 A0A3B3ITS5;Q14181;E9PIQ6 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 1 S(1)PHQLLSPSSFSPSATPSQK;S(1)PHQLLSPSSFSPSATPSQK 183.24 2.86E-17 1028470000 825790 856420 727450 887330 835250 855120 876610 777220 845500 934160 TRUE FALSE 793517.2138 831995.7401 858916.397 933125.2076 862116.5748 872411.1123 887338.2154 761170.1354 749522.3846 870888.5111 0.911158206 0.955341274 0.986252989 1.071463449 0.989927601 1.001748331 1.018888416 0.874015589 0.860641029 1 19.73212852 -1.014934147 5.179238498 1.00000028 0.964622664 0.029934363 0.062299812 2.18E-07 4.16E-08 0.065393629 0.015413304 0.096619738 1.014934147 -0.035377616 QIQELVEAIVLPMNHK ddPTM_BT-474_Pertuzumab_2h_R1 2 QIQELVEAIVLPMNHK 16 0 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 171.91 4.76E-09 248240000 515120 485410 410380 484500 474320 473530 477530 468070 542480 586590 FALSE TRUE 494988.5409 471566.5821 484544.7949 509505.1031 489576.9336 483105.101 483374.155 458404.1909 480899.9447 546859.7368 0.905147166 0.862317246 0.886049497 0.931692478 0.895251379 0.883416841 0.883908839 0.838248202 0.879384442 1 19.06081132 -1.012733012 4.316705312 1.000005682 0.88267943 0.683721585 0.023405457 3311079.494 776805.3001 200.0134354 0.006057561 0.097110678 1.012733012 -0.117326252 EVLGEHIVPSDQQQIVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVLGEHIVPSDQQQIVR 17 0 Q8N9N8;E9PQD0;E9PS30;E9PLI6;E9PS76 Q8N9N8 EIF1AD Probable RNA-binding protein EIF1AD 0 ; 133.28 2.08E-05 795380000 402560 403370 394960 438040 400680 485450 431440 410650 425330 488260 FALSE TRUE 386827.5101 391866.2825 466338.0578 460647.2969 413568.2361 495266.1316 436720.0918 402169.934 377048.3215 455189.7153 0.849816015 0.860885625 1.02449164 1.011989686 0.908562347 1.088043326 0.959424339 0.883521575 0.828332251 1 18.79610844 -1.012322652 4.850103979 1.000000996 0.93853093 0.053296897 0.080958599 9.02E-07 1.84E-07 0.081057135 0.01910504 0.09720248 1.012322652 -0.061470066 LVEEEVNIPNRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEEEVNIPNRR 12 1 Q9NZL9;Q9NZL9-3;E5RJR3 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ; 149.23 0.00010758 488370000 273920 323580 244826 289330 296200 329970 263730 311000 310640 317540 FALSE TRUE 263214.9036 314351.8152 289071.5043 304262.356 305727.542 336642.2195 266957.6066 304577.7413 275377.4495 296032.733 0.889141214 1.061881948 0.976484936 1.027799706 1.032749112 1.137179041 0.901784083 1.028865079 0.930226353 1 18.17539718 -1.011278146 3.899450545 0.999999539 1.003313 0 0.072714615 1.01968E+12 2.59738E+11 4496577.461 0.015808009 0.09743654 1.011278146 0.003313461 RSAPGGGSK ddPTM_BT-474_Pertuzumab_2h_R1 5 RSAPGGGSK 9 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 ;;;; 158.94 0.00010652 795139000 821022 812749 601434 720571 639439 687678 764090 774930 780827 903400 FALSE TRUE 788935.5526 789570.1943 710126.5026 757759.7557 660007.1362 701583.3203 773441.162 758927.4247 692190.7925 842211.9133 0.936742333 0.937495875 0.843168437 0.899725762 0.783659226 0.833024693 0.918345074 0.901112194 0.821872478 1 19.68382376 -1.008196988 7.55237036 1.000000004 0.876466953 0.361020073 0.049849413 3.29E-09 4.40E-10 0.049507938 0.011669133 0.098130274 1.008196988 -0.123533051 DSDGRPDWEVAAEAWDNHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDGRPDWEVAAEAWDNHLR 20 1 K7EQL6;Q8NFA0;P35125-2;P35125;P35125-3 K7EQL6 USP32;USP6 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 32;Ubiquitin carboxyl-terminal hydrolase 6 0 ; 184.26 2.45E-17 193185000 167444 206880 169430 219358 203770 211430 214000 177977 213244 219920 FALSE TRUE 160900.1034 200979.985 200049.7699 230679.0927 210324.4471 215705.2595 216618.996 174301.7128 189037.4351 205024.6225 0.784784293 0.98027243 0.975735341 1.125128728 1.025849698 1.052094411 1.056551127 0.850150146 0.922023086 1 17.64543766 -1.007905699 4.302007269 1.000001094 0.977418068 0.005486629 0.096118228 1.17E-06 2.70E-07 0.096852192 0.022827049 0.098196114 1.007905699 -0.022583026 EAALPPVS(ph)PLKAALSEEELEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAALPPVSPLKAALSEEELEKK 22 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAALPPVS(1)PLKAALSEEELEKK 128.58 8.58E-06 740520000 1638600 1460800 827470 591740 1535600 1571700 914670 1081000 1029300 632880 TRUE FALSE 1574561.7 1419139.414 977012.236 622279.7723 1584993.969 1603480.851 925864.0051 1058676.972 912458.1792 590014.4739 2.668683177 2.405262035 1.655912319 1.054685605 2.686364553 2.717697483 1.569222529 1.794323731 1.546501348 1 19.17039082 -1.005307258 0.166236317 7.46E-10 2.46576208 0.324997866 0.51713328 32.42954667 1.156995118 17.07524989 2.844319188 0.098785395 1.005307258 2.465762079 EQFAWR ddPTM_BT-474_Pertuzumab_2h_R1 5 EQFAWR 6 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435;Q9NQ39 P46783 RPS10;RPS10-NUDT3;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ;;;; 148.07 0.025152 12043350000 4624070 4961600 4318580 4870840 4497790 3674210 5295990 4925990 4887650 5544130 FALSE TRUE 4443356.232 4820100.026 5099043.472 5122224.636 4642465.5 3748505.044 5360803.91 4824266.585 4332824.463 5168621.137 0.859679229 0.932569809 0.986538448 0.991023428 0.898201934 0.725242757 1.0371826 0.933375935 0.838294073 1 22.30134803 -1.004840806 4.237796509 1.000004999 0.91747541 0.085627894 0.084808275 10718346.12 2541469.344 494.2236253 0.01978518 0.098891552 1.004840806 -0.082529589 GPSYEDLYTQNVVINMDDQEDLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSYEDLYTQNVVINMDDQEDLHR 24 0 P29083;C9IYL4 P29083 GTF2E1 General transcription factor IIE subunit 1 0 ; 220.91 9.69E-33 237270000 136282 160328 131595 178524 157959 169096 155718 156094 162777 198277 FALSE TRUE 130955.9488 155755.6024 155377.1438 187737.645 163039.8947 172515.237 157623.7235 152870.6044 144299.2374 184847.5222 0.708453904 0.842616664 0.840569254 1.015635172 0.882023696 0.933284011 0.852722945 0.827009216 0.780639284 1 17.49597618 -1.00051994 0.013773187 1.838436259 2.97E-06 0.174839188 0.08128647 6660.860122 17.6354645 1274.395868 1083.732127 0.099880351 1.00051994 -1.838433287 LADS(ph)GDGAGPSPEEKDFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LADSGDGAGPSPEEKDFLK 19 1 Q92917 Q92917 GPKOW G patch domain and KOW motifs-containing protein 1 LADS(0.587)GDGAGPS(0.413)PEEKDFLK 53.496 0.071976 176320000 115950 136450 93791 126180 110340 131160 120800 125150 134230 117770 TRUE FALSE 111418.5458 132558.5796 110741.1201 132692.1649 113889.1863 133812.1451 122278.3865 122565.6088 118992.7731 109793.333 1.014802473 1.207346348 1.008632465 1.208563046 1.037305119 1.218763848 1.113714132 1.116330158 1.083788695 1 16.74443093 -1.000194219 8.125034823 0.999999999 1.115826285 0.165460841 0.075143325 9.39E-10 1.16E-10 0.063029996 0.014856312 0.099955289 1.000194219 0.115826286 AFSNLSALRKHEIIHT(ph)GQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AFSNLSALRKHEIIHTGQK 19 2 A0A0A0MS76;A8MXY4 A0A0A0MS76 ZNF99 Zinc finger protein 99 1 AFS(0.003)NLS(0.026)ALRKHEIIHT(0.97)GQK 65.716 0.028343 1522200000 1375300 1712800 1150100 1678700 1462500 1699900 1481900 1415500 1516900 1728800 TRUE FALSE 1321551.756 1663952.621 1357948.654 1765337.908 1509542.641 1734273.143 1500035.935 1386269.43 1344707.871 1611706.836 0.819970311 1.032416432 0.842553139 1.095321971 0.936611179 1.076047519 0.930712647 0.860125055 0.83433776 1 20.62015792 -0.994434201 4.785782203 1.000000935 0.939267219 0.037021508 0.096269407 9.31E-07 1.96E-07 0.090333348 0.021291446 0.10128982 0.994434201 -0.060733716 KHGTDLWLDSCVVPPLS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KHGTDLWLDSCVVPPLSPPPK 21 1 Q9NP61 Q9NP61 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 KHGTDLWLDSCVVPPLS(1)PPPK 65.071 0.011415 333840000 373480 375060 490770 633510 517240 497970 545230 358040 512260 547600 TRUE FALSE 358883.9887 364363.656 579463.0561 666205.527 533877.4943 508039.2946 551902.6878 350646.3489 454110.3924 510510.5642 0.702990327 0.713724028 1.135065749 1.304978924 1.045771688 0.995159219 1.081079857 0.686854246 0.889522028 1 18.96158129 -0.993271279 6.917530998 1.000000005 0.949969256 0.005768816 0.194524184 1.68E-08 2.43E-09 0.205184935 0.048362548 0.10156141 0.993271279 -0.05003075 LCDFGSASHVADNDITPY(ph)LVSR ddPTM_BT-474_Pertuzumab_2h_R1 10 LCDFGSASHVADNDITPYLVSR 22 0 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 LCDFGSASHVADNDIT(0.008)PY(0.978)LVS(0.015)R;LCDFGSASHVADNDITPY(0.999)LVSR;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDIT(0.007)PY(0.992)LVSR;LCDFGSASHVADNDIT(0.003)PY(0.997)LVSR;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDIT(0.021)PY(0.976)LVS(0.003)R;LCDFGSASHVADNDIT(0.006)PY(0.994)LVSR;LCDFGSASHVADNDIT(0.001)PY(0.999)LVSR;LCDFGSASHVADNDIT(0.001)PY(0.999)LVSR 310.25 2.07E-66 83210330000 15478706 17986145 15323660 19728546 16990118 18673665 18333574 16440258 16796484 20137769 TRUE FALSE 14873781.06 17473197.75 18092986.23 20746738.62 17536620.58 19051259.3 18557945.76 16100760.93 14889817.55 18773819.97 0.792261835 0.930721493 0.963734939 1.105088824 0.934099752 1.01477799 0.988501317 0.857617733 0.79311603 1 24.16221889 -0.993086485 7.188204864 1.000000004 0.936527196 0.044709475 0.09253288 5.51E-09 7.67E-10 0.092447482 0.021790079 0.101604634 0.993086485 -0.063472808 TECNHYNNIMALYLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TECNHYNNIMALYLK 15 0 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 130.9 6.96E-05 0 442280 410810 350050 336540 351500 262920 422740 422310 425930 463270 FALSE TRUE 424995.2086 399094.101 413311.8218 353908.8697 362806.3167 268236.4225 427913.6186 413589.1509 377580.212 431892.3103 0.984030506 0.924059289 0.956978886 0.819437766 0.840038843 0.621072467 0.990787769 0.957621011 0.874246202 1 18.7203121 -0.987187606 7.729491488 1.000000001 0.887406657 0.097518452 0.104454855 3.13E-09 4.05E-10 0.105023024 0.024754164 0.102994111 0.987187606 -0.112593344 VFAENK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFAENK 6 0 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 98.133 0.093712 59842000 211010 252690 207860 213280 194540 153890 257450 238340 259210 266990 FALSE TRUE 202763.4959 245483.5286 245424.9258 224287.4064 200797.5558 157001.7612 260600.7501 233418.1957 229785.5675 248906.5295 0.814617022 0.986247846 0.986012405 0.901090891 0.806718716 0.630765941 1.046982378 0.937774498 0.923180151 1 17.92524455 -0.986557568 6.080504149 1.00000007 0.897942088 0.074024384 0.112538285 1.10E-07 1.84E-08 0.112112183 0.026425077 0.103143635 0.986557568 -0.102057983 DMQGLS(ph)LDAASQPSK ddPTM_BT-474_Pertuzumab_2h_R1 3 DMQGLSLDAASQPSK 15 0 E9PLZ8;Q96EY5;M0QZK6;E9PQA6;Q96EY5-3;E9PLL0 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 DMQGLS(1)LDAASQPSK;DMQGLS(1)LDAASQPSK;DMQGLS(1)LDAASQPSK 231.86 1.44E-13 508280000 1084050 781090 324944 467320 678460 396600 532150 926330 745130 644540 TRUE FALSE 1041684.128 758814.078 383668.6091 491438.4412 700283.2821 404619.5237 538662.6109 907200.9618 660545.9662 600884.7317 1.733583951 1.262828023 0.638506171 0.817858094 1.16542033 0.673372949 0.896449156 1.509775359 1.099288984 1 19.19672874 -0.985287121 8.810277104 0.99999998 1.085231854 0.006202404 0.333928892 0 2.84E-10 0.335978444 0.079190878 0.103445804 0.985287121 0.085231874 YLEES(ph)DEDDLF ddPTM_BT-474_Pertuzumab_2h_R1 4 YLEESDEDDLF 11 0 P11388;P11388-2;P11388-3;P11388-4;J3QR57 P11388 TOP2A DNA topoisomerase 2-alpha 1 YLEES(1)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF 99.139 0.0052429 1768868000 1864156 1991551 1456451 2190656 2052026 1936896 1989057 1878242 1865327 2060598 TRUE FALSE 1791302.723 1934753.915 1719664.094 2303716.019 2118031.28 1976061.364 2013399.675 1839455.646 1653582.899 1921031.862 0.932469033 1.007143064 0.895177289 1.199207605 1.102548751 1.028645804 1.048082395 0.957535209 0.860778487 1 20.87345002 -0.984463259 5.547448012 0.999999981 1.008151307 0 0.094973992 2.30E-08 4.15E-09 0.093679901 0.022080513 0.103642228 0.984463259 0.008151326 ESALFSTELSVLHNFFSPSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESALFSTELSVLHNFFSPSPK 21 0 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 80.238 0.0066544 59200000 106680 115610 96608 70681 102090 127140 77789 116130 123920 71422 FALSE TRUE 102510.8277 112312.916 114067.2146 74328.85488 105373.8176 129710.8579 78741.00505 113731.8749 109853.1211 66584.52432 1.53955936 1.686772071 1.713119014 1.116308266 1.582557188 1.948063146 1.182572164 1.708082713 1.64982963 1 16.02289928 -0.98407513 4.791970086 0.999992299 1.568652093 0.342950277 0.236541507 1.86E-05 3.94E-06 0.218576941 0.051518382 0.103734895 0.98407513 0.568659795 GLEDNQGGQYESWNYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLEDNQGGQYESWNYYR 17 0 Q8IXB1-2;Q8IXB1;Q71S60;A0A087WXH7;E7EP04;A0A494C1G5;Q8IXB1-3 Q8IXB1-2 DNAJC10 DnaJ homolog subfamily C member 10 0 147.12 9.57E-07 170340000 56869 91730 53539 94115 62520 84467 78277 65493 65822 87315 FALSE TRUE 54646.49661 89113.95021 63214.68827 98972.28643 64531.01258 86174.98061 79234.97734 64140.54666 58350.16251 81401.07728 0.671323998 1.094751485 0.776582944 1.215859664 0.792753791 1.058646685 0.973389788 0.787956976 0.716822977 1 16.31276027 -0.983762893 5.064753397 1.000000667 0.906467684 0.028728531 0.171439364 1.20E-06 2.40E-07 0.153824979 0.036256637 0.103809502 0.983762893 -0.093532983 GPLTEAELALFDPFSKEEGAAPS(ph)PTHVAELATMEVESAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPLTEAELALFDPFSKEEGAAPSPTHVAELATMEVESAR 39 1 Q9NRS6 Q9NRS6 SNX15 Sorting nexin-15 1 GPLTEAELALFDPFS(0.025)KEEGAAPS(0.52)PT(0.454)HVAELAT(0.001)MEVESAR;GPLTEAELALFDPFSKEEGAAPS(0.846)PT(0.154)HVAELATMEVESAR 142.94 4.90E-13 116145000 64704 68641 52678 56727.2 68865 70552 59995 61084 74608 70425 TRUE FALSE 62175.29615 66683.42589 62198.08642 59654.89759 71080.10527 71978.60978 60729.23676 59822.59405 66138.81262 65655.05202 0.946999419 1.015663286 0.947346541 0.908610926 1.082629639 1.096314869 0.924974315 0.911165131 1.007368216 1 16.00261841 -0.982375557 0.003790292 1.038564261 0.923225396 0 0.064376637 2843827.816 2162.00522 33588.75571 32209.16279 0.104141647 0.982375557 -0.115338865 AVTNHSVYCSTK ddPTM_BT-474_Pertuzumab_2h_R1 5 AVTNHSVYCSTK 12 0 Q7Z4W1;J3KS22;J3QS36;J3QL34;J3QS45;J3KRZ4;J3KSZ5 Q7Z4W1 DCXR L-xylulose reductase 0 ;;;; 147.18 6.54E-05 3746050000 4326320 4900370 3766680 4499550 3985870 3347260 5163160 4700370 4960650 5178700 FALSE TRUE 4157242.631 4760616.246 4447402.865 4731772.315 4114079.128 3414943.891 5226348.297 4603305.717 4397537.809 4827942.036 0.861079648 0.986054971 0.921179839 0.980080597 0.852139296 0.707329099 1.082520929 0.95347162 0.91085141 1 22.20297692 -0.981683045 5.003632053 1.00000062 0.922732402 0.062057236 0.094394087 6.53E-07 1.33E-07 0.091373306 0.021536722 0.104307841 0.981683045 -0.077268218 YRVPDVLVADPPIAR ddPTM_BT-474_Pertuzumab_2h_R1 5 YRVPDVLVADPPIAR 15 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;; 89.866 0.005686 4625000000 4361300 5451940 4258950 5113370 4797430 5568180 5022870 4716530 5223190 5510240 FALSE TRUE 4190855.574 5296456.009 5028637.005 5377271.638 4951743.693 5680772.415 5084341.386 4619132.007 4630275.369 5137026.537 0.815813495 1.031035361 0.978900336 1.046767347 0.963931889 1.105848369 0.989744038 0.899183988 0.901353212 1 22.2925021 -0.981234601 4.055306388 1.000001912 0.973799818 0.010871166 0.078860832 3115.753481 42504580 193.112083 0.018406712 0.104415602 0.981234601 -0.026202095 GLEPGVFTLAEEDDEAEGAPGS(ph)PEREPPAILFR ddPTM_BT-474_Pertuzumab_2h_R1 3 GLEPGVFTLAEEDDEAEGAPGSPEREPPAILFR 33 1 Q9HCE9-2;Q9HCE9 Q9HCE9-2 ANO8 Anoctamin-8 1 GLEPGVFTLAEEDDEAEGAPGS(1)PEREPPAILFR;GLEPGVFTLAEEDDEAEGAPGS(1)PEREPPAILFR;GLEPGVFTLAEEDDEAEGAPGS(1)PEREPPAILFR 250.73 3.29E-48 100606000 26268.6 43253 30041.4 52051 32432.1 39228 42275 45782 32717.5 32811 TRUE FALSE 25241.99407 42019.46679 35470.54925 54737.35835 33475.30795 40021.21704 42792.3741 44836.5857 29003.54656 30588.68174 0.825206993 1.373693288 1.159597185 1.789464443 1.094369095 1.308366845 1.398961042 1.465790062 0.948179029 1 14.90071031 -0.979566763 11.73060231 0.999999995 1.293869209 0.071715712 0.262635302 0 0 0.237462381 0.05597042 0.104817365 0.979566763 0.293869214 CPEALFQPSFLGMESCGIHETTFNSIMK ddPTM_BT-474_Pertuzumab_2h_R1 7 CPEALFQPSFLGMESCGIHETTFNSIMK 28 0 P60709;A0A2R8Y793;P63261 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;; 202.14 2.95E-25 8557715000 3663295 4237728 3701060 4518050 4149421 4320618 4330913 3884308 4383399 4523610 FALSE TRUE 3520129.381 4116872.147 4369923.872 4751227.102 4282890.895 4407983.856 4383916.009 3804095.682 3885813.922 4217221.865 0.834703389 0.976204781 1.036209147 1.126624886 1.015571633 1.045234042 1.039527003 0.90203831 0.921415578 1 22.00786149 -0.977639722 7.220870895 0.9999748 0.991855089 0.000347077 0.079865479 6.08E-10 8.41E-11 0.081541116 0.019219425 0.105283491 0.977639722 -0.008119711 MQEHSDQVPVGNIPR ddPTM_BT-474_Pertuzumab_2h_R1 4 MQEHSDQVPVGNIPR 15 0 P33993;P33993-3;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 ;;; 189.37 2.61E-07 3859520000 2577970 2780390 2368410 2832600 2797610 2955310 2792810 2594380 2924570 3031930 FALSE TRUE 2477220.082 2701095.999 2796434.372 2978790.825 2887597.666 3015068.393 2826989.244 2540805.146 2592585.074 2826574.681 0.876403549 0.955607513 0.989336808 1.053851804 1.021589023 1.066686267 1.000146666 0.898898997 0.917217964 1 21.43062338 -0.974822583 4.711807442 1.000000339 0.977048741 0.013856987 0.060727448 2.37E-07 5.17E-08 0.064436044 0.015187497 0.105968654 0.974822583 -0.022951598 HQGGWTDGGSGGGGGYQDGGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQGGWTDGGSGGGGGYQDGGYR 22 0 Q8NCA5 Q8NCA5 FAM98A Protein FAM98A 0 ; 223.89 7.34E-26 747320000 133583 144150 132400 178269 156779 167243 152633 128743 141993 175133 FALSE TRUE 128362.4287 140038.9831 156327.6252 187469.4845 161821.9389 170624.768 154500.9683 126084.4121 125874.5499 163271.0859 0.786192043 0.857708408 0.957472809 1.148209944 0.991124289 1.045039709 0.946284931 0.772239686 0.770954326 1 17.3169098 -0.974341902 5.446332427 1.000000204 0.921535006 0.03956895 0.118632575 3.24E-07 6.10E-08 0.127121968 0.029962858 0.106086006 0.974341902 -0.078465198 CDNFTSSWR ddPTM_BT-474_Pertuzumab_2h_R1 3 CDNFTSSWR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ;; 167.12 0.0001401 1480200000 670570 649010 580853 603983 550517 515414 683910 628223 705510 728750 FALSE TRUE 644363.383 630500.8702 685826.0581 635154.635 568224.8793 525836.0242 692279.8952 615249.9755 625423.4625 679391.1134 0.948442466 0.928038147 1.009471635 0.934888053 0.836373729 0.77398131 1.018971078 0.905590261 0.920564679 1 19.37388282 -0.973333558 4.209369404 1.000003631 0.919559701 0.109305802 0.068859976 6205.848812 39654444.43 359.8227319 0.016544181 0.106332602 0.973333558 -0.08044393 GREDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_BT-474_Pertuzumab_2h_R1 3 GREDVSNFDDEFTSEAPILTPPREPR 26 2 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR 205.03 5.72E-25 8224200000 423552 503166 421792 546231 485118 506726 502222 450249 505879 520802 TRUE FALSE 406999.1196 488816.1983 498019.1971 574422.0474 500722.261 516972.3469 508368.3431 440951.2008 448453.7367 485527.6167 0.838261523 1.006773212 1.025727847 1.18308831 1.031295119 1.064764041 1.047043105 0.908189742 0.923642078 1 18.88919383 -0.972889983 7.193264699 0.999999886 1.006639639 0 0.090581155 6.83E-10 3.03E-18 0.091710898 0.021616465 0.106441263 0.972889983 0.006639754 DSGPPPSTVSEAEFEDIMKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSGPPPSTVSEAEFEDIMKR 20 1 Q8N684-2;Q8N684;Q8N684-3;F5H669 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 187.47 4.66E-17 93667000 47638 49635 40205 35511 48074 47207 47864 44737 49014 50473 FALSE TRUE 45776.25429 48219.4584 47470.93786 37343.72697 49620.34387 48161.55788 48449.77395 43813.16532 43450.1362 47054.41875 0.972836463 1.02475941 1.008851859 0.793628483 1.054531013 1.023528909 1.029654074 0.931116917 0.923401826 1 15.52204259 -0.969571229 0.002118105 0.492555316 1.449746061 0 0.073128589 2729057.295 1123.723076 257035.3263 250807.4993 0.107257772 0.969571229 0.957190745 IQEQST(ph)SPDTSLGSTTPSSHTLELVALDSEVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IQEQSTSPDTSLGSTTPSSHTLELVALDSEVLR 33 0 A0A494C0H4;H0Y9M2;Q17R98-2;Q17R98;A0A5F9ZGW8 A0A494C0H4 ZNF827 Zinc finger protein 827 1 IQEQS(0.081)T(0.44)S(0.44)PDT(0.019)S(0.019)LGS(0.001)T(0.001)TPSSHTLELVALDSEVLR 118.11 7.07E-06 230170000 34870 44993 40136 55586 43303 51850 41809 42660 40659 51053 TRUE FALSE 33507.24185 43709.84369 47389.46802 58454.80012 44695.88032 52898.44253 42320.67105 41779.05609 36043.56078 47595.13484 0.704005608 0.918367893 0.995678827 1.22816755 0.939085066 1.111425416 0.88918061 0.877800982 0.757295066 1 15.53852649 -0.969464297 7.078321413 1.000000003 0.944000533 0.014412679 0.145594617 6.44E-09 9.09E-10 0.143971802 0.033934478 0.107284184 0.969464297 -0.05599947 IHVSDQELQSANASVDDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 IHVSDQELQSANASVDDSR 19 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 303.86 3.55E-50 1995680000 360552 570100 533570 791540 589520 633410 600020 483010 564980 653310 FALSE TRUE 346461.2292 553841.3062 629997.9682 832391.4743 608482.4462 646217.9842 607363.2242 473035.6747 500845.839 609060.7318 0.568845127 0.90933675 1.03437627 1.36668058 0.999050529 1.061007467 0.997212909 0.776664214 0.822324955 1 19.21622657 -0.968781469 6.972205472 0.999999999 0.955956331 0.004784347 0.197856142 1.05E-08 1.29E-09 0.200923496 0.047358119 0.107452997 0.968781469 -0.044043669 IKVNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKVNGK 6 1 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4;K7EJT5 P35268 RPL22 60S ribosomal protein L22 0 ; 91.26 0.043863 3604400000 2758000 2609600 2551100 2306800 2414990 2356100 2401200 2844600 3072000 2747800 FALSE TRUE 2650214.311 2535176.763 3012140.519 2425854.224 2492670.347 2403741.956 2430586.604 2785858.016 2723279.439 2561689.059 1.034557376 0.989650463 1.175841583 0.946974504 0.973057342 0.938342594 0.94882187 1.087508262 1.063079623 1 21.28866394 -0.966277449 5.454421423 0.999999959 1.0177603 0.005384161 0.071448778 3.67E-08 6.83E-09 0.070445631 0.016604156 0.10807433 0.966277449 0.017760341 YRSPYS(ph)GPK ddPTM_BT-474_Pertuzumab_2h_R1 1 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.009)PYS(0.991)GPK 151.15 0.0002198 6521400000 927330 824530 683800 709690 702890 705280 770200 916350 910830 799220 TRUE FALSE 891088.9184 801015.2117 807377.871 746317.1859 725499.0952 719541.2448 779625.938 897427.0523 807436.3969 745088.1175 1.195951053 1.075061047 1.083600519 1.001649561 0.97370912 0.965712951 1.046354008 1.204457609 1.083679068 1 19.50705153 -0.964752511 7.674491499 1.000024345 1.071415592 0.068529802 0.077289326 1.24E-09 1.61E-10 0.082987775 0.019560406 0.108454478 0.964752511 0.071391247 TSSSTT(ph)PNRK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSSTTPNRK 10 1 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4;F6VD24 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 T(0.001)S(0.002)S(0.003)S(0.003)T(0.01)T(0.981)PNRK 61.235 0.054445 70334000 104270 96605 82959 105380 93697 100360 107680 92971 95619 114830 TRUE FALSE 100195.0131 93849.91999 97951.53671 110818.6744 96710.8491 102389.348 108997.8201 91051.11636 84764.73199 107052.4618 0.935943101 0.876672226 0.914986307 1.035181 0.903396778 0.956440854 1.018172008 0.850528001 0.791805537 1 16.70795845 -0.964158686 4.354041686 1.000002175 0.921934239 0.106041881 0.069243327 8926936.675 2050264.312 204.1088873 0.016503695 0.108602873 0.964158686 -0.078067935 DTEFILFKPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTEFILFKPVR 11 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 59.198 0.092571 148460000 104330 99822 106710 96806 107710 84853 103320 109310 114890 125950 FALSE TRUE 100252.6683 96975.1743 125994.8708 101802.1693 111174.59 86568.7858 104584.4611 107052.7103 101848.1689 117419.2943 0.853800637 0.825887899 1.073033793 0.866996943 0.946817051 0.737262017 0.890692298 0.911713113 0.867388698 1 16.84130997 -0.963006069 4.03777253 1.000006962 0.888502675 0.148278437 0.081794067 24714694.1 31276834.66 2166.545403 0.019795279 0.108891488 0.963006069 -0.111504288 ASESSKPWPDATYGTGS(ph)ASR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASESSKPWPDATYGTGSASR 20 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ASESSKPWPDATYGT(0.031)GS(0.967)AS(0.002)R;ASESSKPWPDATYGT(0.081)GS(0.686)AS(0.234)R 189.88 1.23E-17 614200000 595410 553760 510680 464980 515880 543640 474800 647150 595810 597280 TRUE FALSE 572140.7189 537967.307 602971.236 488977.6735 532473.7487 554632.7733 480610.7444 633786.1263 528176.1466 556825.6936 1.027504164 0.966132334 1.082872509 0.878152138 0.956266485 0.996061747 0.863126019 1.13821279 0.948548447 1 19.08686626 -0.96187583 4.979237172 1.000000077 0.988620448 0.000679592 0.079961863 6.63E-08 1.38E-08 0.074732977 0.017614612 0.109175244 0.96187583 -0.011379629 LRPKS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRPKSPPPK 9 2 Q9HCE5 Q9HCE5 METTL14 N6-adenosine-methyltransferase subunit METTL14 1 LRPKS(1)PPPK 70.488 0.041163 2961100000 2313300 2021000 1476600 1348900 1640800 1767500 1627000 2060200 2271700 1849700 TRUE FALSE 2222893.679 1963363.059 1743454.467 1418516.891 1693577.822 1803240.061 1646911.713 2017656.15 2013826.14 1724418.171 1.289068809 1.138565512 1.011039257 0.822606091 0.982115504 1.045709266 0.955053559 1.170050388 1.167829343 1 20.71767824 -0.961376861 6.988464328 1 1.058440421 0.021080091 0.125925901 5.75E-09 1.10E-09 0.128666993 0.030327099 0.109300749 0.961376861 0.058440421 EPPSS(ph)PLQPQK ddPTM_BT-474_Pertuzumab_2h_R1 3 EPPSSPLQPQK 11 0 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EPPS(0.015)S(0.985)PLQPQK;EPPS(0.156)S(0.844)PLQPQK;EPPS(0.008)S(0.992)PLQPQK 186.81 4.05E-06 1612960000 2200940 2302270 2451000 2896330 2827190 2546570 2562390 2559070 2464610 2663890 TRUE FALSE 2114924.832 2236611.514 2893950.222 3045809.938 2918129.134 2598063.39 2593749.295 2506224.31 2184837.805 2483462.358 0.851603337 0.90060214 1.165288539 1.226436926 1.175024508 1.046145669 1.04440854 1.009165411 0.87975475 1 21.24392145 -0.960293241 7.11373834 0.999999998 1.041619822 0.002288565 0.122687499 1.89E-09 5.32E-10 0.127040463 0.029943723 0.109573809 0.960293241 0.041619823 IYASSS(ph)PPDTGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 IYASSSPPDTGQR 13 0 A0A494C0H7;A0A494C094;F8WDA1;A0A494C188;A0A494C155;A0A494C1K7;Q9UGJ0-3;Q9UGJ0;E9PGP6 A0A494C0H7 PRKAG2 5-AMP-activated protein kinase subunit gamma-2 1 IYAS(0.001)S(0.202)S(0.796)PPDTGQR 195.94 1.53E-07 283150000 146390 201500 158890 194930 189810 187440 178190 202600 178530 171750 TRUE FALSE 140668.917 195753.4173 187604.9575 204990.3607 195915.411 191230.1652 180370.7425 198416.2392 158264.0229 160117.2195 0.878537095 1.222563181 1.171672591 1.280251813 1.223574901 1.194313552 1.126491848 1.239193634 0.988426 1 17.28876894 -0.959086423 7.183047018 0.999999995 1.16264366 0.110048034 0.11851343 9.61E-09 1.34E-09 0.107538426 0.025347049 0.109878716 0.959086423 0.162643665 AGAAAGDS(ph)DEESRADDK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGAAAGDSDEESRADDK 17 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(1)DEESRADDK 174.2 8.37E-10 462900000 242270 193630 213350 225500 166310 196710 236600 238700 243810 270150 TRUE FALSE 232801.8206 188107.862 251907.0909 237138.082 171659.5122 200687.611 239495.5816 233770.7616 216133.7109 251852.4999 0.924357791 0.746896942 1.000216758 0.941575256 0.681587486 0.796845817 0.950935892 0.928205047 0.858175762 1 17.94221953 -0.958587882 4.591513584 1.000001966 0.872234138 0.142826417 0.095481894 2.10E-06 4.76E-07 0.09394961 0.022143769 0.110004922 0.958587882 -0.127767828 SGDPMILSCLMEHLYTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGDPMILSCLMEHLYTEK 18 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ; 198.42 1.74E-15 196134000 241410 291620 237405 243975 232319 225420 256660 287290 337820 268616 FALSE TRUE 231975.4303 283303.2831 280309.3645 256566.579 239791.7516 229978.1468 259801.0819 281357.3611 299472.0899 250422.3991 0.926336586 1.131301689 1.119346215 1.024535265 0.957549135 0.918360928 1.037451453 1.12353113 1.195867826 1 17.93400408 -0.956209068 4.676343667 0.999999336 1.050526081 0.024944201 0.089496765 6.49E-07 1.45E-07 0.090765686 0.021393396 0.110609119 0.956209068 0.050526746 NPSPIRT(ph)MT(ph)DILSRGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 NPSPIRTMTDILSRGPK 17 2 D6RC56;D6RFY7;Q8N5Z0 D6RC56 AADAT "Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial" 2 NPS(0.533)PIRT(0.762)MT(0.704)DILS(0.001)RGPK 58.997 0.076169 846980000 378380 560450 370210 715480 453410 587030 507550 476580 452330 577970 TRUE FALSE 363592.4913 544466.5147 437115.1823 752406.0085 467994.3444 598900.1488 513761.5487 466738.4565 400983.3947 538823.5771 0.674789498 1.0104727 0.811239895 1.396386573 0.868548379 1.111495811 0.953487506 0.866217583 0.74418309 1 19.03945345 -0.954614483 7.316406179 1.000000001 0.947343936 0.006905058 0.194803208 4.02E-09 3.66E-10 0.179765019 0.04237102 0.111015985 0.954614483 -0.052656066 T(ph)VHRDSEEEDDYLFDDPLPIPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 TVHRDSEEEDDYLFDDPLPIPLR 23 1 B3KSJ7;Q96SD1-2;Q96SD1-3;Q96SD1 B3KSJ7 DCLRE1C Protein artemis 1 T(0.477)VHRDS(0.477)EEEDDY(0.045)LFDDPLPIPLR;T(0.474)VHRDS(0.474)EEEDDY(0.051)LFDDPLPIPLR;T(0.493)VHRDS(0.493)EEEDDY(0.013)LFDDPLPIPLR 119.01 0.0003334 260450000 115890 131204 110677 134117 128498 135955 135957 111141 133803 143605 TRUE FALSE 111360.8907 127462.1904 130678.7959 141038.7944 132631.2549 138704.1033 137620.8824 108845.8995 118614.2444 133878.5054 0.831805601 0.952073598 0.976099901 1.053483485 0.990683713 1.036044605 1.027953531 0.813019978 0.885984229 1 17.03056483 -0.953063607 5.116241503 1.00000021 0.952341985 0.031800182 0.079580418 2.07E-07 4.23E-08 0.083612903 0.019707664 0.111413135 0.953063607 -0.047658225 LMKPPS(ph)PEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR ddPTM_BT-474_Pertuzumab_2h_R1 8 LMKPPSPEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR 43 1 Q9Y6X9;Q9Y6X9-2;H7C1V1 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 LMKPPS(0.989)PEHQS(0.009)LDT(0.002)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.992)PEHQS(0.007)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.451)PEHQS(0.451)LDT(0.098)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.442)PEHQS(0.442)LDT(0.116)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.994)PEHQS(0.006)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.449)PEHQS(0.449)LDT(0.101)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.498)PEHQS(0.488)LDT(0.014)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.971)PEHQS(0.024)LDT(0.005)QQEGGEEEVGPVAQQAIAVAEPSTSECLR 298.96 5.44E-97 3541790000 988988 1038429 870062 1034661 1064438 1055696 1068963 941779 1127695 1145546 TRUE FALSE 950337.2556 1008814.022 1027301.558 1088059.978 1098676.615 1077042.896 1082045.289 922330.9345 999683.7913 1067957.149 0.889864595 0.944620318 0.96193144 1.018823629 1.028764699 1.008507595 1.013191671 0.863640395 0.93607107 1 20.02642233 -0.951275222 6.274913906 1.00000001 0.962160623 0.041944662 0.053216858 8.07E-09 1.42E-09 0.057011585 0.013437756 0.11187287 0.951275222 -0.037839387 EFWGDIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFWGDIAK 8 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 119.27 0.0040145 178201000 619250 587410 500440 506030 471640 363970 581980 622890 594760 634030 FALSE TRUE 595049.0254 570657.6419 590880.6402 532146.2689 486810.7289 371329.7228 589102.4453 610027.1038 527245.3382 591086.5834 1.006703658 0.965438327 0.999651585 0.900284804 0.823586159 0.628215448 0.996643236 1.032043563 0.891993412 1 19.17300995 -0.951130021 7.816392524 1 0.920164741 0.045456734 0.114005842 8.88E-10 1.14E-10 0.119182999 0.028091702 0.111910279 0.951130021 -0.07983526 TPILEDFELEGVCQLPDQS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPILEDFELEGVCQLPDQSPPR 22 0 Q7Z2Z1;Q7Z2Z1-2;H0YN97 Q7Z2Z1 TICRR Treslin 1 TPILEDFELEGVCQLPDQS(1)PPR;TPILEDFELEGVCQLPDQS(1)PPR 112.44 0.00018852 77298000 49867 47384 37415 57079 53751 51817 47134 48621 48433 51472 TRUE FALSE 47918.14251 46032.65471 44176.72279 60024.85403 55479.94973 52864.77524 47710.83999 47616.95936 42935.08889 47985.75559 0.998590976 0.95929832 0.920621594 1.250889004 1.156175391 1.101676416 0.994270891 0.992314464 0.894746542 1 15.55031859 -0.950688637 4.860959508 0.999999748 1.032405667 0.006774341 0.104330124 3.09E-07 6.65E-08 0.107374956 0.025308319 0.112024074 0.950688637 0.032405919 FSEAEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSEAEQR 7 0 P33993;P33993-3;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 90.777 0.039293 491650000 846840 931040 750980 913100 794210 789520 884840 878880 961870 1024640 FALSE TRUE 813744.5566 904487.6508 886698.7915 960225.2004 819756.4859 805484.6353 895668.9366 860730.8209 852682.5501 955240.2201 0.851874261 0.946869313 0.928246919 1.005218562 0.858167892 0.843227304 0.937637379 0.901062165 0.892636776 1 19.86550406 -0.949626131 4.261972787 1.000002915 0.909323977 0.25602923 0.047326584 2.12314E+11 36860234.63 6303738.126 0.011391018 0.112298478 0.949626131 -0.090678937 SSTFPQTDVLSSS(ph)LEAEHR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSTFPQTDVLSSSLEAEHR 19 0 D4PHA4;Q86WP2-3;Q86WP2;Q86WP2-2;Q86WP2-4 D4PHA4 GPBP1 Vasculin 1 SSTFPQTDVLSS(0.087)S(0.913)LEAEHR;SSTFPQTDVLSS(0.14)S(0.86)LEAEHR;SSTFPQTDVLSS(0.021)S(0.979)LEAEHR 176.27 6.14E-13 845780000 829370 858780 793600 916940 909960 950340 820780 848540 939280 965490 TRUE FALSE 796957.3035 834288.4352 937021.1735 964263.3833 939229.6898 969556.5259 830824.9512 831017.3525 832656.8722 900096.5023 0.885413177 0.926887765 1.041023014 1.07128889 1.043476658 1.07716953 0.923039862 0.923253618 0.925075111 1 19.77972016 -0.949440125 7.248035722 1 0.980622849 0.007734043 0.068399777 5.46E-10 7.53E-11 0.073239321 0.017262673 0.112346585 0.949440125 -0.019377151 VSSS(ph)PGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSSSPGVK 8 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 VSSS(1)PGVK;VSS(0.001)S(0.999)PGVK 155.57 0.00042675 1051340000 3413200 3155800 2734100 3009300 3027700 3163800 3311100 3527700 3614200 4116800 TRUE FALSE 3279808.371 3065799.674 3228212.69 3164610.334 3125088.72 3227774.204 3351622.232 3454851.762 3203931.168 3837965.469 0.854569536 0.798808561 0.841126038 0.824554144 0.814256602 0.841011789 0.873280976 0.900177917 0.834799373 1 21.8719103 -0.946614352 0.250817394 1.100350909 0.812234838 0.792044339 0.024908514 6.290895806 0.385369902 0.489346368 0.042535895 0.113079961 0.946614352 -0.288116072 SKQPPPASS(ph)PTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKQPPPASSPTKR 13 2 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 SKQPPPAS(0.194)S(0.805)PT(0.001)KR 95.662 0.0023968 491870000 392340 347520 317190 301520 305650 315870 335120 365950 411950 402360 TRUE FALSE 377006.919 337609.0699 374513.2889 317081.4833 315481.5098 322257.1078 339221.2988 358393.0046 365187.163 375107.7988 1.005062865 0.900032127 0.998415096 0.845307627 0.841042257 0.859105326 0.904330168 0.955440025 0.973552574 1 18.51694573 -0.946075986 6.296328336 1.000000019 0.917662832 0.143741986 0.058081017 1.60E-08 2.60E-09 0.057931705 0.01365463 0.113220225 0.946075986 -0.082337187 HFTILDAPGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 HFTILDAPGHK 11 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1;H3BSV8 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 199.68 2.86E-08 2222800000 1716530 2251500 2017130 2575000 2324900 2593500 2484400 1337340 2275500 2777800 FALSE TRUE 1649446.11 2187289.424 2381670.262 2707896.059 2399682.52 2645942.347 2514804.83 1309723.462 2017194.78 2589657.132 0.636936098 0.844625104 0.919685557 1.04565814 0.926641018 1.021734621 0.971095671 0.505751686 0.778942801 1 21.30432967 -0.945384057 4.612103441 1.000002112 0.845349424 0.070876174 0.161973678 1.01786E+12 2.32698E+11 24059953.03 0.042271352 0.113400754 0.945384057 -0.154652688 SS(ph)PSPQKR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPSPQKR 8 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 S(0.381)S(0.619)PSPQKR;S(0.077)S(0.923)PSPQKR;S(0.065)S(0.935)PSPQKR;S(0.134)S(0.866)PSPQKR 145.17 0.00035135 930775000 664895 609155 458776 499136 470188 509799 600283 614029 630744 698880 TRUE FALSE 638910.1683 591782.4958 541687.0286 524896.4688 485312.024 520107.4851 607629.4429 601349.0866 559144.5854 651544.2351 0.980609042 0.908276774 0.831389489 0.805619082 0.744864275 0.798268877 0.932598909 0.922959723 0.858183613 1 19.31350361 -0.944852182 7.866294537 1 0.865084042 0.260399723 0.068378044 1.09E-09 6.93E-11 0.073156258 0.017243095 0.11353972 0.944852182 -0.134915958 GKDSLYAQGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKDSLYAQGK 10 1 H0Y5B4;H7BZ11;J3KQN4;P83881;H7BY91;H0Y3V9 H0Y5B4 RPL36A;RPL36A-HNRNPH2 60S ribosomal protein L36a 0 100.72 0.0034837 639740000 348930 481590 287100 489300 346800 321160 402200 462320 429540 578700 FALSE TRUE 335293.4298 467855.5247 338985.3565 514552.8316 357955.137 327654.0752 407122.2439 452772.9304 380780.42 539504.1335 0.62148445 0.86719544 0.628327635 0.953751417 0.663489146 0.607324495 0.75462303 0.839239039 0.705797039 1 19.04127449 -0.944578277 0.50527273 1.076399936 0.738244671 0.329773627 0.111307841 21.06148407 3.438588349 2.528741215 0.05049987 0.113611351 0.944578277 -0.338155264 LKEEEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEEEKR 7 2 Q93034;I3L121;I3L3S9;J3KNW5;Q96AJ1-2;Q96AJ1 Q93034 CUL5;CLUAP1 Cullin-5;Clusterin-associated protein 1 0 71.223 0.030877 102970000 259320 209790 153290 157100 185690 187790 192010 199450 262670 206880 FALSE TRUE 249185.4877 203806.9946 180992.9129 165207.9498 191662.8875 191587.2425 194359.8758 195331.2878 232852.8028 192867.8333 1.292001281 1.056718433 0.938429752 0.856586332 0.993752479 0.993360267 1.007736088 1.01277276 1.207317979 1 17.55725302 -0.942285612 7.737228796 1.000000003 1.026622483 0 0.119753125 0 0 0.11612359 0.027370593 0.114212697 0.942285612 0.02662248 IDSIEDRYPR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDSIEDRYPR 10 1 Q13158 Q13158 FADD FAS-associated death domain protein 0 107.83 0.0020354 155080000 57367 56064 41402 42322 44103 53226 42193 49651 42466 35910 FALSE TRUE 55125.03422 54465.10961 48884.26238 44506.24349 45521.61305 54302.26619 42709.37056 48625.6895 37645.43771 33477.78371 1.6466154 1.626903085 1.460200078 1.329426221 1.359755874 1.622038862 1.275752628 1.452476362 1.12449014 1 15.0309164 -0.9413924 0.069345389 2.40E-10 2.212909933 0.672706572 0.117923777 64.7567347 0.903001854 20.50981795 9.378083112 0.11444784 0.9413924 2.212909933 LLDVTCSSLSVTQEEAEELLQALHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDVTCSSLSVTQEEAEELLQALHR 25 0 Q9P000;E9PJ95 Q9P000 COMMD9 COMM domain-containing protein 9 0 191.4 1.99E-28 0 61583 65075 61847 70337 68910 74587 68227 65822 71324 70314 FALSE TRUE 59176.26828 63219.12472 73024.12868 73967.101 71126.55273 76095.20024 69061.98243 64462.7527 63227.59853 65551.57015 0.90274372 0.964418161 1.113995111 1.128380309 1.085047278 1.160844814 1.053551918 0.98338991 0.96454743 1 16.00034272 -0.940893277 5.118139893 0.999999835 1.043395674 0.019851635 0.079797952 1.61E-07 3.34E-08 0.083049874 0.019574969 0.114579447 0.940893277 0.043395839 GGSGYHS(ph)RS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 3 GGSGYHSRSPAR 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GGS(0.001)GYHS(0.999)RS(1)PAR;GGS(0.002)GY(0.001)HS(0.998)RS(0.999)PAR;GGS(0.01)GY(0.01)HS(0.99)RS(0.99)PAR 78.501 0.014543 1724264000 540304 728221 588788 768057 691592 845170 702404 587839 735557 774071 TRUE FALSE 519188.3223 707452.8501 695195.0891 807696.5138 713837.6848 862259.9165 711000.2303 575699.9192 652059.6531 721642.4817 0.719453657 0.980337034 0.963351115 1.119247459 0.989184676 1.194857479 0.985252737 0.797763344 0.903577145 1 19.46092474 -0.939427427 4.211046239 1.000001163 0.963287199 0.007639284 0.130311356 3935.467071 76810670.45 235.5718694 0.032032511 0.114966834 0.939427427 -0.036713964 DHNS(ph)EDEDEDKYADDIDMPGQNFDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHNSEDEDEDKYADDIDMPGQNFDSK 26 1 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 DHNS(0.966)EDEDEDKY(0.034)ADDIDMPGQNFDSK;DHNS(1)EDEDEDKYADDIDMPGQNFDSK 120.91 8.93E-05 446830000 423500 299797 402710 306316 361240 340251 449240 234244 585620 436470 TRUE FALSE 406949.1518 291247.0831 475488.6552 322125.0055 372859.6127 347131.1083 454737.9335 229406.7795 519142.8727 406907.4981 1.000102366 0.715757474 1.168542377 0.791641852 0.916325244 0.853095875 1.117546213 0.563781156 1.27582528 1 18.63434134 -0.93435104 6.634261822 1.000000008 0.909416349 0 0.20664022 2.16E-08 3.26E-09 0.181278447 0.042727736 0.116318545 0.93435104 -0.090583659 GEFLHLCR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEFLHLCR 8 0 Q8NI27;F2Z2V2 Q8NI27 THOC2 THO complex subunit 2 0 94.114 0.010589 138800000 59099 69503 53992 55962 54427 35402 65028 79330 52312 74197 FALSE TRUE 56789.34574 67520.84249 63749.55545 58850.20553 56177.69388 36117.8527 65823.83212 77691.80778 46373.76107 69171.5711 0.820992567 0.976135736 0.92161497 0.850786018 0.812150035 0.522148798 0.951602386 1.123175411 0.670416478 1 16.0778916 -0.933810416 8.185900848 0.999999999 0.868479024 0.064000313 0.158463718 0 1.47E-10 0.161700562 0.038113188 0.116463432 0.933810416 -0.131520974 RGS(ph)SGSVVVDLLYWR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSSGSVVVDLLYWR 15 1 Q9NQC3-2;F8W914 Q9NQC3-2 RTN4 Reticulon-4;Reticulon 1 RGS(0.333)S(0.333)GS(0.333)VVVDLLYWR 91.207 0.0035019 84621000 44520 52584 36874 54479 41065 48194 54165 40696 58163 49075 TRUE FALSE 42780.10918 51084.35581 43537.95206 57290.66772 42385.89302 49168.5157 54827.88747 39855.61338 51560.58008 45751.10654 0.935061738 1.116570935 0.951626209 1.252224745 0.926445199 1.074695661 1.198394785 0.871139878 1.126979957 1 15.48151902 -0.933019578 4.69289099 0.999999547 1.046011721 0.014436662 0.120081836 5.22E-07 1.19E-07 0.106772285 0.025166221 0.116675702 0.933019578 0.046012173 HFGDEDQAMR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFGDEDQAMR 10 0 A0A0G2JM25;A0A0G2JNK1;K7ERG0;A0A0G2JMB6;A0A0G2JPH3;A0A0G2JNK3;Q8WX94;Q8WX94-2;Q8WX94-3;Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 A0A0G2JM25;Q9NX02 NLRP7;NLRP2 "NACHT, LRR and PYD domains-containing protein 7;NACHT, LRR and PYD domains-containing protein 2" 0 ; 166.97 5.38E-06 460450000 230850 222655 170534 246749 295109 220465 226691 201070 254399 248626 FALSE TRUE 221828.1268 216305.0974 201353.2873 259483.7455 304601.449 224922.9534 229465.3123 196917.8342 225520.692 231786.3396 0.957037102 0.933208997 0.868702132 1.11949542 1.314147545 0.970389169 0.98998635 0.849566176 0.972968004 1 17.82243602 -0.930916824 5.852910733 1.000000003 0.992815025 0 0.126871792 6.97E-09 1.36E-09 0.133674627 0.031507395 0.117241989 0.930916824 -0.007184978 AEHSVDIDVDIDWPIAEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEHSVDIDVDIDWPIAEQR 19 0 Q8NFW8;Q8NFW8-2 Q8NFW8 CMAS N-acylneuraminate cytidylyltransferase 0 ;;; 217.4 3.61E-19 391328000 223724 264984 215608 267110 260432 274698 258253 249392 257822 271167 FALSE TRUE 214980.6187 257426.9158 254573.1618 280895.5791 268809.0318 280252.5818 261413.5775 244241.968 228555.1274 252800.6176 0.85039594 1.018300186 1.007011629 1.111134861 1.063324269 1.108591365 1.03407017 0.966144665 0.904092441 1 17.94764046 -0.923675575 5.028532037 0.999999954 1.012889606 0 0.078926014 4.55E-08 9.75E-09 0.078304525 0.018456482 0.119213222 0.923675575 0.012889652 RLNNLSPAPHLASGS(ph)PPPGLPSGLPSGLQS(ph)GSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 35 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 RLNNLS(0.003)PAPHLAS(0.16)GS(0.837)PPPGLPS(0.13)GLPS(0.208)GLQS(0.422)GS(0.208)PS(0.033)R 128.66 3.60E-08 852330000 169590 173210 154140 194890 162620 208590 174570 170810 167570 216160 TRUE FALSE 162962.2353 168270.2204 181996.5268 204948.2963 167850.82 212807.8327 176706.4399 167282.7138 148548.1561 201519.2907 0.808668167 0.835008003 0.903122109 1.017015768 0.83292681 1.056017178 0.876871089 0.830107695 0.737141122 1 17.62055842 -0.922941842 4.831060993 1.000000743 0.881258321 0.139487108 0.090883732 7.33E-07 1.63E-07 0.088511594 0.020862252 0.119414801 0.922941842 -0.118742422 HPGGGDYEEL ddPTM_BT-474_Pertuzumab_2h_R1 2 HPGGGDYEEL 10 0 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 0 ; 106.14 0.008071 0 267970 313870 235330 341110 316960 307160 308940 216427 330170 329100 FALSE TRUE 257497.4361 304918.7349 277859.3659 358714.728 327155.3063 313370.9857 312720.9001 211957.7068 292690.4858 306809.7639 0.83927393 0.993836477 0.905640558 1.169176376 1.066313217 1.02138531 1.019266454 0.690844073 0.95398035 1 18.22698487 -0.920318854 5.736250011 1.000000029 0.955319779 0.005568757 0.124046529 5.02E-08 9.43E-09 0.132052904 0.031125148 0.120138207 0.920318854 -0.04468025 IEEACEIYAR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEEACEIYAR 10 0 P54920;M0R0Y2;M0R2M1 P54920 NAPA Alpha-soluble NSF attachment protein 0 131.5 0.00057785 268370000 208340 217710 179370 241620 221750 237260 221480 208580 227140 242960 FALSE TRUE 200197.8425 211501.124 211786.1491 254090.0372 228882.7901 242057.5598 224190.5385 204272.7501 201356.0194 226504.1028 0.883859674 0.933762883 0.935021249 1.121789999 1.010501741 1.06866744 0.989785773 0.90185011 0.888972946 1 17.78917766 -0.919865838 4.787106855 1.000000185 0.972546741 0.013144397 0.074840393 1.58E-07 3.58E-08 0.077526313 0.018273004 0.12026359 0.919865838 -0.027453444 VNLFPGLS(ph)PSALK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNLFPGLSPSALK 13 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VNLFPGLS(0.663)PS(0.337)ALK;VNLFPGLS(0.996)PS(0.004)ALK 193.77 1.66E-06 1343130000 3269700 3284400 3243000 2703700 2747800 3048800 3117300 3579100 3460600 3643200 TRUE FALSE 3141916.509 3190732.128 3829082.24 2843238.281 2836185.482 3110448.825 3155450.45 3505190.334 3067767.196 3396442.819 0.925060917 0.939433489 1.127380157 0.837122376 0.835045851 0.915796023 0.929045657 1.032018062 0.903229455 1 21.69559314 -0.915587855 7.762112384 0.999999999 0.943355209 0.045120484 0.082259969 0 7.83E-11 0.081610037 0.01923567 0.12145409 0.915587855 -0.05664479 SFPAAIEHTIQWAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFPAAIEHTIQWAR 14 0 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 188.4 8.38E-07 1626530000 1291710 1460770 1219130 1491590 1368920 1507250 1386320 1398540 1430070 1508810 FALSE TRUE 1241228.545 1419110.27 1439453.91 1568571.139 1412952.555 1537727.628 1403286.199 1369659.66 1267734.449 1406616.955 0.882421146 1.008881817 1.023344632 1.115137375 1.00450414 1.093209934 0.99763208 0.973726113 0.901264871 1 20.42379808 -0.913213477 6.067160672 0.999999999 1.004894656 0 0.068609484 9.96E-10 2.46E-10 0.066826734 0.015751208 0.122119923 0.913213477 0.004894658 VLVDVER ddPTM_BT-474_Pertuzumab_2h_R1 4 VLVDVER 7 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;; 163.34 0.0028812 1177880000 1266240 1397720 1162770 1419260 1372000 1370430 1304740 1404610 1351640 1417690 FALSE TRUE 1216753.941 1357858.394 1372908.405 1492508.179 1416131.626 1398141.034 1320707.798 1375604.313 1198207.494 1321668.594 0.920619546 1.027381902 1.038769031 1.129260532 1.071472556 1.057860526 0.999273044 1.040808807 0.906586946 1 20.33392904 -0.912876677 8.163806409 1 1.027827078 0.00075821 0.06355477 0 0 0.061150622 0.01441334 0.122214665 0.912876677 0.027827078 DYGNSPLHR ddPTM_BT-474_Pertuzumab_2h_R1 8 DYGNSPLHR 9 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;A0A087WUW5;K7ELW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;; 169.92 5.81E-05 22568929000 4213700 5444400 4380990 5941570 5161930 5397610 5198400 4897550 4883020 5561430 FALSE TRUE 4049023.946 5289131.043 5172732.348 6248215.14 5327968.166 5506753.372 5262019.574 4796413.881 4328720.041 5184749.392 0.780948825 1.020132439 0.997682232 1.205114205 1.027623085 1.062105987 1.014903359 0.925100428 0.834894749 1 22.30584283 -0.912289627 6.692434847 1 0.993146666 0 0.112604747 8.22E-10 6.89E-25 0.110355206 0.02601097 0.122379979 0.912289627 -0.006853334 RGLEVSK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGLEVSK 7 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;; 115.49 0.0090878 2648950000 3385730 3663480 2934030 2901470 3006740 1904270 3800000 3523150 3601290 3824810 FALSE TRUE 3253411.928 3559001.137 3464274.488 3051215.214 3103454.523 1942775.644 3846505.537 3450395.721 3192486.657 3565752.212 0.9124055 0.99810669 0.971541005 0.855700294 0.870350585 0.544843144 1.078736073 0.967648764 0.895319267 1 21.76577502 -0.910509761 7.841838413 0.999999999 0.904492269 0.04682489 0.13440588 9.85E-10 0 0.132143908 0.031146618 0.122882557 0.910509761 -0.09550773 LTWFVNEGLVDGWDDPRFPTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTWFVNEGLVDGWDDPRFPTVR 22 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 211.43 3.01E-23 752500000 55331 40823 33202 47802 44954 46079 41719 45714 44246 50672 FALSE TRUE 53168.60335 39658.76801 39202.33997 50269.06695 46399.98624 47010.74895 42229.5696 44769.98992 39223.37957 47239.94031 1.12550107 0.839517742 0.829855832 1.064122152 0.982219409 0.995148356 0.893937827 0.947714786 0.83030121 1 15.52771952 -0.910106584 4.594153997 1.000000421 0.942944788 0.028159706 0.095329814 11604987.72 2526033.725 65.35248069 0.021345314 0.122996688 0.910106584 -0.057055633 TWNHFSDNEAER ddPTM_BT-474_Pertuzumab_2h_R1 1 TWNHFSDNEAER 12 0 Q99543 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 77.204 0.029052 303070000 101650 136320 101370 143010 135990 128810 126210 118440 105200 149480 FALSE TRUE 97677.40562 132432.2871 119689.814 150390.7632 140364.2419 131414.6265 127754.5957 115994.1726 93258.13703 139355.5865 0.700922066 0.950319183 0.858880631 1.079187186 1.007237998 0.943016565 0.916752597 0.832361124 0.669209893 1 17.08841131 -0.910087727 6.563056744 1.000000007 0.893564861 0.071723843 0.120820824 1.32E-08 2.14E-09 0.118076878 0.027830985 0.123002028 0.910087727 -0.106435147 SSS(ph)KSEGSPSQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSKSEGSPSQR 12 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 S(0.031)S(0.031)S(0.882)KS(0.057)EGSPSQR;S(0.031)S(0.154)S(0.79)KS(0.024)EGSPSQR;S(0.001)S(0.036)S(0.927)KS(0.036)EGS(0.001)PSQR;S(0.002)S(0.034)S(0.816)KS(0.143)EGS(0.006)PSQR 145.92 0.00016917 315802000 611034 574802 410586 490921 426771 512836 509614 590894 598532 538210 TRUE FALSE 587154.1157 558409.2098 484788.0236 516257.4916 440498.4768 523205.8953 515850.8086 578691.8324 530589.1566 501756.5573 1.170197195 1.112908644 0.96618174 1.028900338 0.877912745 1.042748496 1.02808982 1.153331878 1.057463323 1 18.93662804 -0.909584796 8.129863676 1 1.049092192 0.030887481 0.081694889 0 0 0.083857255 0.019765345 0.123144552 0.909584796 0.049092191 RKS(ph)HEAEVLK ddPTM_BT-474_Pertuzumab_2h_R1 9 RKSHEAEVLK 10 2 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK 177.38 1.22E-06 51034060000 28961670 24640900 24031290 21021690 22337500 22326500 25769590 26720940 29186920 29505810 TRUE FALSE 27829815.92 23938165.66 28374278.68 22106621.94 23056005.97 22777957.13 26084965.95 26169143.25 25873743.2 27507355.21 1.011722709 0.870245993 1.03151606 0.803662212 0.838176037 0.828067873 0.948290585 0.951350759 0.940611811 1 24.7133141 -0.902366996 7.716927604 1.000000001 0.912317021 0.110288343 0.073402228 0 1.37E-10 0.070912166 0.016714158 0.125208267 0.902366996 -0.08768298 AQAVSEDAGGNEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 AQAVSEDAGGNEGR 14 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;; 169.58 7.70E-06 150712000 255368 271512 233836 300003 274876 296859 278336 261372 262212 297510 FALSE TRUE 245387.9362 263768.7436 276095.3669 315486.1908 283717.6362 302861.6924 281742.3592 255974.5769 232446.793 277359.3827 0.884729169 0.950999894 0.995442679 1.13746356 1.022924241 1.091946807 1.015802518 0.922898567 0.838070776 1 18.08139701 -0.901473238 4.680434215 1.000000078 0.989182278 0.000236563 0.086041153 7.42E-08 1.74E-08 0.088141326 0.02077496 0.125466205 0.901473238 -0.0108178 DKLYER ddPTM_BT-474_Pertuzumab_2h_R1 2 DKLYER 6 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ; 101.99 0.032763 1098120000 2082110 2041610 1668510 1675020 1822240 1816340 1909570 2003890 2146570 2169650 FALSE TRUE 2000738.839 1983385.282 1970046.873 1761467.983 1880854.005 1853067.639 1932939.889 1962508.971 1902900.373 2022697.673 0.989143789 0.980564376 0.97397001 0.870850848 0.929874014 0.916136734 0.955624716 0.970243352 0.940773502 1 20.94784927 -0.901236689 7.640855494 1.000001352 0.947555152 0.179862035 0.033654303 0 0 0.03450659 0.008133281 0.125534562 0.901236689 -0.052446199 IKDMDLWEQQEEER ddPTM_BT-474_Pertuzumab_2h_R1 5 IKDMDLWEQQEEER 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 257.54 2.17E-24 4954140000 3122296 3127145 2821437 3101300 3187248 3340954 3391514 3007672 4077486 3924068 FALSE TRUE 3000273.22 3037961.886 3331333.428 3261358.465 3289768.727 3408510.379 3433020.363 2945562.522 3614626.883 3658287.379 0.820130545 0.830432815 0.910626499 0.891498706 0.899264707 0.931722969 0.938422821 0.805175268 0.988065318 1 21.80273698 -0.901083534 0.017354194 1.921955356 3.12E-06 0.441658806 0.047617951 1815.262543 6.295268917 383.5985678 315.2689681 0.12557884 0.901083534 -1.921952238 IGLVRPGTALELLEAQAATGFIVDPVSNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGLVRPGTALELLEAQAATGFIVDPVSNLR 30 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 234.71 1.90E-45 880480000 406990 420500 349790 364270 369420 440130 431210 390250 424860 392100 FALSE TRUE 391084.3808 408507.7517 413004.834 383070.0184 381302.7298 449029.7302 436487.277 382191.2011 376631.674 365542.7178 1.069873265 1.117537655 1.129840136 1.047948707 1.043114009 1.228391945 1.194080078 1.045544563 1.030335596 1 18.47968049 -0.900650639 5.683521813 0.999999942 1.102550329 0.180878763 0.064210272 4.92E-08 9.51E-09 0.064794405 0.015272179 0.125704076 0.900650639 0.102550387 LESEVGHWR ddPTM_BT-474_Pertuzumab_2h_R1 1 LESEVGHWR 9 0 Q15643-2;Q15643;G3V4R7 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 111.46 0.002122 167850000 143490 157430 106770 147520 145600 146560 137600 140390 140820 160020 FALSE TRUE 137882.2522 152940.2505 126065.7141 155133.5249 150283.3562 149523.5436 139283.99 137490.8974 124834.704 149181.7029 0.924257127 1.025194428 0.845048097 1.039896461 1.007384641 1.002291439 0.933653305 0.921633785 0.836796347 1 17.18671107 -0.899944073 4.448538517 1.000000589 0.950912399 0.048987002 0.067350014 1.29348E+12 3.1978E+11 8815094.353 0.015516076 0.125908754 0.899944073 -0.04908819 VGYTPDWIFLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGYTPDWIFLLR 12 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 202.44 3.18E-07 4097700000 438680 415630 487920 489840 471140 317460 509570 462940 495620 575370 FALSE TRUE 421535.9006 403776.6393 576097.9977 515120.7011 486294.646 323879.2587 515806.2701 453380.1272 439359.2954 536399.6774 0.785861585 0.752753322 1.074008844 0.960329998 0.906590116 0.603802113 0.961608092 0.845228188 0.81908941 1 19.03294884 -0.898838425 3.978619424 1.000005622 0.860577278 0.107227694 0.123663579 29722369.41 65717182.93 2540.83132 0.02985237 0.126229707 0.898838425 -0.139428343 GFKDQIYEIFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFKDQIYEIFQK 12 1 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 140.82 5.47E-05 384090000 928130 866940 776700 745140 778210 740870 798480 891770 1002200 945150 FALSE TRUE 891857.6535 842215.72 917066.9676 783596.7647 803241.8314 755850.899 808252.0371 873354.6379 888434.4576 881134.1486 1.012170116 0.955831438 1.040780191 0.889304728 0.911599934 0.857815918 0.917286021 0.991171026 1.008285128 1 19.74900215 -0.897644141 5.757961833 1.000000022 0.951720064 0.055748315 0.056451567 1.66E-08 3.19E-09 0.057297755 0.013505204 0.126577309 0.897644141 -0.048279958 RDS(ph)FDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDSFDDR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDR;RDS(1)FDDR;RDS(1)FDDR;RDS(1)FDDR 122.94 0.0045465 2277470000 2422090 2510150 2562440 3194010 3260540 2622490 2597750 3009970 2475170 2894830 TRUE FALSE 2327432.045 2438562.98 3025529.909 3358853.239 3365418.23 2675518.545 2629542.042 2947813.068 2194199.078 2698760.586 0.86240775 0.903586258 1.121081257 1.244591038 1.247023633 0.991387883 0.974351729 1.092284022 0.813039545 1 21.36386557 -0.891333194 6.392617652 0.999999997 1.040254641 0 0.14227171 6.41E-09 1.34E-09 0.143354723 0.033789029 0.128430096 0.891333194 0.040254644 ILVTLLHTLER ddPTM_BT-474_Pertuzumab_2h_R1 2 ILVTLLHTLER 11 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 237.84 1.36E-15 2159560000 779840 743880 696260 821740 766340 549090 897900 746000 866550 939920 FALSE TRUE 749362.9906 722665.2707 822089.6702 864150.0999 790990.0221 560192.976 908888.7688 730594.8393 768182.8769 876258.3812 0.855184962 0.8247171 0.938181806 0.986181837 0.902690393 0.639301133 1.037238317 0.833766449 0.876662516 1 19.74099681 -0.890164579 4.885493603 1.000000461 0.878142206 0.11592821 0.101778796 4.89E-07 1.11E-07 0.094320546 0.022231482 0.128776145 0.890164579 -0.121858255 KLMEECKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLMEECKR 8 2 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 85.731 0.0092999 536440000 612540 946590 488900 708170 521980 362730 728330 859720 890390 616960 FALSE TRUE 588601.2596 919594.18 577255.1055 744718.7386 538769.9608 370064.6491 737243.5204 841966.4816 789316.66 575172.7497 1.023346916 1.598813888 1.003620401 1.294774029 0.936709816 0.643397396 1.281777554 1.463849743 1.372312337 1 19.1336358 -0.889437804 8.522777711 1.00000458 1.19209479 0.037092094 0.268444468 4.04E-09 0 0.271241897 0.063932328 0.128991828 0.889437804 0.19209021 FAPPLS(ph)PLSSDMLIMPK ddPTM_BT-474_Pertuzumab_2h_R1 2 FAPPLSPLSSDMLIMPK 17 0 Q5H9M0 Q5H9M0 MUM1L1 PWWP domain-containing protein MUM1L1 1 FAPPLS(0.917)PLS(0.034)S(0.049)DMLIMPK;FAPPLS(0.999)PLS(0.001)SDMLIMPK 254.56 5.08E-27 100011000 76851 75409 67048 71202 78402 69347 76943 82371 75894 72086 TRUE FALSE 73847.57796 73258.40915 79165.06507 74876.74375 80923.87153 70749.24385 77884.65145 80670.01006 67278.83129 67203.55101 1.098864224 1.090097295 1.177989316 1.114178382 1.204160648 1.052760498 1.158936548 1.200383147 1.001120183 1 16.03624985 -0.887703868 5.649644469 0.999999932 1.129833877 0.248216782 0.062416593 5.02E-08 9.94E-09 0.057083973 0.013454815 0.129507861 0.887703868 0.129833944 RAS(ph)PGLSMPS(ph)SSPPIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RASPGLSMPSSSPPIKK 17 2 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 2 RAS(0.994)PGLS(0.133)MPS(0.327)S(0.29)S(0.257)PPIKK 57.293 0.055653 151770000 145000 125240 99785 101840 122720 107780 121350 129920 134700 138300 TRUE FALSE 139333.2397 121668.2778 117818.3692 107095.9746 126667.4003 109959.3854 122835.1176 127237.1066 119409.4207 128932.8178 1.080665435 0.943656393 0.91379659 0.830633941 0.982429473 0.85284249 0.952706376 0.986848102 0.926136749 1 16.97626 -0.885721189 7.695437238 0.999995133 0.939685703 0.065400784 0.066633146 0 6.12E-11 0.063220572 0.014901232 0.130100454 0.885721189 -0.06030943 EVS(ph)SRPSTPGLSVVSGISATSEDIPNKIEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 EVS(0.551)S(0.449)RPSTPGLSVVSGISATSEDIPNKIEDLR 250.73 3.88E-48 324940000 59883 60546 43050 49115 47336 51785 51979 61734 62403 56064 TRUE FALSE 57542.70616 58819.28736 50830.09264 51649.83104 48858.60543 52832.12818 52615.13455 60459.17133 55319.27305 52266.73534 1.100943186 1.12536754 0.97251325 0.988196999 0.934793518 1.010817451 1.006665792 1.156742829 1.058403068 1 15.67360543 -0.88557038 8.110515236 1 1.041579872 0.029003098 0.067289284 0 0 0.07230472 0.017042386 0.130145639 0.88557038 0.041579872 IHNADVTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IHNADVTLR 9 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 99.815 0.0050817 302930000 84754 97336 65076 101740 91487 87279 92718 85524 117670 109940 FALSE TRUE 81441.71998 94560.07258 76836.68081 106990.8136 94429.76244 89043.84118 93852.71062 83757.89951 104312.5949 102493.6659 0.794602469 0.922594306 0.749672481 1.043877323 0.921322909 0.868774089 0.915692788 0.817200739 1.017746746 1 16.64517523 -0.885279822 0.016672032 1.923923482 4.26E-06 0.206848996 0.083092182 3268.214253 10.95545832 692.6255168 574.345235 0.13023274 0.885279822 -1.923919226 VITLWYRPPELLLGEER ddPTM_BT-474_Pertuzumab_2h_R1 2 VITLWYRPPELLLGEER 17 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61;A0A2R8YD28;Q9BVE2;A0A087X209;A0A2R8Y644;A0A2R8YEB7 Q9NYV4-3;Q9NYV4;Q9NYV4-2;A0A2R8Y4Z0 CDK12;CDK13 Cyclin-dependent kinase 12;Cyclin-dependent kinase 13 0 ; 144.5 4.65E-07 851530000 289590 336320 319800 347260 322370 368580 352990 345420 309240 369550 FALSE TRUE 278272.5026 326728.4829 377594.9739 365182.1302 332739.3238 376032.9401 357309.9972 338286.9563 274136.3716 344520.0493 0.80771062 0.9483584 1.096002902 1.059973522 0.965805399 1.091468961 1.037123958 0.981907895 0.795705133 1 18.39422842 -0.885245611 5.154818476 1.000000024 0.986784312 0 0.10064661 2.75E-08 5.89E-09 0.09706796 0.022879096 0.130242999 0.885245611 -0.013215712 AEISFEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEISFEDR 8 0 Q60FE5;P21333-2;P21333;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ;;; 155 0.00096795 1413150000 2089590 2285450 1850230 2096380 2095860 2309160 2030880 2176680 2275050 2351380 FALSE TRUE 2007926.513 2220271.204 2184607.719 2204574.423 2163275.24 2355852.797 2055734.517 2131730.797 2016795.862 2192118.938 0.915975168 1.01284249 0.996573535 1.005681938 0.986842093 1.074692051 0.937784206 0.97245216 0.920021184 1 21.06389465 -0.885085247 4.450000774 1.00000017 0.982862036 0.013888108 0.045408562 8.20E-08 2.05E-08 0.042635927 0.010049274 0.130291101 0.885085247 -0.017138134 YAVTTGDHGIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 YAVTTGDHGIIR 12 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 285.13 2.28E-28 2343330000 1360270 1437630 1318120 1481300 1302230 1126060 1654710 1339450 1537480 1721050 FALSE TRUE 1307109.145 1396630.2 1556333.605 1557750.071 1344117.411 1148829.705 1674960.836 1311789.889 1362951.716 1604481.751 0.814661272 0.870455647 0.969991466 0.970874284 0.83772683 0.716012946 1.043926386 0.817578566 0.84946539 1 20.61367595 -0.880519866 4.132996724 1.000002778 0.879082654 0.143901309 0.090027818 2.58771E+11 6.41681E+11 11754728.51 0.021265631 0.131667968 0.880519866 -0.120920124 KVVVSPT(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 3 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.215)PT(0.785)K;KVVVS(0.199)PT(0.801)K;KVVVS(0.19)PT(0.81)K 109.72 0.0020883 9789500000 19563700 16649400 14760000 13345300 13933400 12690000 16549900 18004400 17856000 18685500 TRUE FALSE 18799128.98 16174575.41 17427460.33 14034052.53 14381580.46 12946600.49 16752442.63 17632602.85 15829061.74 17419914.44 1.079174587 0.928510612 1.000433176 0.80563269 0.825582727 0.743206893 0.961683405 1.012209498 0.908676205 1 24.0542342 -0.880370047 7.941343833 0.999996914 0.918659807 0.059127131 0.097710471 0 0 0.100352797 0.023653381 0.131713398 0.880370047 -0.081337107 ELFSPLHALNFGIGGDGTQHVLWR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELFSPLHALNFGIGGDGTQHVLWR 24 0 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ; 293.07 4.20E-62 2302600000 759450 935700 848720 970690 888080 968740 981280 671380 871910 1102460 FALSE TRUE 729769.8544 909014.7521 1002102.584 1020787.427 916645.8997 988328.5865 993289.1982 657515.7684 772934.4321 1027789.402 0.710038314 0.884436783 0.975007702 0.993187345 0.891861599 0.961606127 0.966432614 0.639737836 0.752035807 1 19.97111325 -0.879362223 5.079689369 1.000000278 0.863281262 0.108757686 0.116945019 4.04E-07 8.93E-08 0.124461623 0.029335826 0.132019407 0.879362223 -0.136719015 NMDPLNDNVATLLHQSSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NMDPLNDNVATLLHQSSDR 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 131.59 1.53E-05 160130000 72992 94483 82477 103900 81612 105520 90176 74129 76032 111420 FALSE TRUE 70139.39194 91788.43735 97382.42859 109262.2915 84237.1241 107653.6867 91279.60086 72598.21025 67401.16611 103873.4242 0.675239047 0.883656605 0.937510527 1.051879173 0.810959346 1.036392971 0.878757985 0.69891034 0.648877869 1 16.66446706 -0.876964267 4.924390585 1.000000438 0.851454529 0.103774932 0.134372297 3.60753E+12 8.21553E+11 18857578.61 0.033127795 0.132750368 0.876964267 -0.148545909 DKQDEEQR ddPTM_BT-474_Pertuzumab_2h_R1 5 DKQDEEQR 8 1 P27797;K7EL50 P27797 CALR Calreticulin 0 ;;;; 140.45 0.00059228 5673440000 9545580 9022240 7241560 7978940 7754270 8104110 8998030 8538820 9343290 10187390 FALSE TRUE 9172528.18 8764934.549 8550270.98 8390734.05 8003693.137 8267980.657 9108150.583 8362490.383 8282678.889 9497389.001 0.965794723 0.922878335 0.900275958 0.88347798 0.842725631 0.870553018 0.959016271 0.880504145 0.872100626 1 23.17909952 -0.875985523 7.698781252 1.000000019 0.898657099 0.393768847 0.037313978 0 7.15E-11 0.036932242 0.008705013 0.133049877 0.875985523 -0.10134292 ASVSQTS(ph)PQSASSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQT(0.004)S(0.795)PQS(0.021)AS(0.027)S(0.154)PR;ASVSQT(0.001)S(0.548)PQS(0.36)AS(0.09)S(0.001)PR 307.89 4.67E-56 584830000 657730 722740 629050 821900 722750 825320 724950 686130 729080 778890 TRUE FALSE 632025.1844 702128.1628 742733.3281 864318.3575 745997.9101 842008.5359 733822.155 671961.1757 646317.895 726135.0865 0.870396151 0.966938764 1.022858339 1.190299675 1.027354171 1.15957561 1.010586279 0.92539417 0.890079418 1 19.46987844 -0.872601972 4.736342581 0.999999951 1.010745531 0 0.099133659 5.45E-08 1.29E-08 0.101561029 0.023938055 0.134090505 0.872601972 0.010745581 SSISSVLKDPDSNPYSLLDNTES(ph)DQTADTDASESHHSTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNR 40 1 B4DXZ6;P51114;P51114-3;H7C4S4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 1 SSISSVLKDPDSNPYSLLDNT(0.005)ES(0.838)DQT(0.074)ADT(0.015)DAS(0.015)ES(0.015)HHS(0.019)T(0.019)NR;SSISSVLKDPDSNPYSLLDNT(0.001)ES(0.999)DQTADTDASESHHSTNR 257.29 2.80E-63 178390000 34842 83515 60690 82877 66007 100721 75359 27047 75672 93593 TRUE FALSE 33480.33612 81133.23397 71658.03304 87154.2919 68130.1751 102757.6476 76281.26598 26488.47 67082.0318 87253.86275 0.383711793 0.929852632 0.821259149 0.998858837 0.780827037 1.177685943 0.874245146 0.303579339 0.768814465 1 16.41293138 -0.871239752 4.122290369 1.000004817 0.774869519 0.063468035 0.249733963 70795534.44 146042298.2 5256.332033 0.06401854 0.134511758 0.871239752 -0.225135298 DKNEFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKNEFHK 7 1 Q9GZL7 Q9GZL7 WDR12 Ribosome biogenesis protein WDR12 0 ; 90.657 0.010201 590750000 1019280 930280 764650 780000 809950 776860 846640 894320 1103360 1039150 FALSE TRUE 979445.4107 903749.3252 902839.2645 820255.8935 836002.7773 792568.6415 857001.4336 875851.9795 978111.1985 968767.4449 1.011022218 0.93288573 0.93194633 0.846700514 0.862955069 0.818120639 0.884630711 0.904088989 1.009644991 1 19.88579086 -0.870407097 5.449354421 1.000000066 0.905160066 0.154633521 0.060669066 4.99E-08 1.05E-08 0.060382203 0.014232212 0.134769899 0.870407097 -0.09484 VQESTKGPDEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 VQESTKGPDEAK 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 151.54 6.30E-05 841170000 1162570 913800 760900 651740 830860 861130 839620 1031010 1123900 912370 FALSE TRUE 1117135.479 887739.3187 898411.5561 685376.3795 857585.3665 878542.6386 849895.5207 1009719.283 996319.5838 850574.3672 1.313389543 1.043693947 1.056241042 0.805780665 1.008242665 1.03288163 0.999201896 1.187102883 1.171349175 1 19.69807785 -0.869451973 8.304775161 1.000000004 1.06297362 0.023473226 0.128216441 0 0 0.127550635 0.030063973 0.135066619 0.869451973 0.062973615 SLAGSSGPGASSGTSGDHGELVVR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLAGSSGPGASSGTSGDHGELVVR 24 0 P29692;P29692-2;E9PRY8;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;H0YCK7;E9PIZ1 P29692 EEF1D Elongation factor 1-delta 0 ;;;;; 346.07 8.83E-102 5989790000 577713 746070 552872 829414 697728 804409 690736 630609 730064 798866 FALSE TRUE 555135.3373 724792.8141 652788.269 872220.1559 720171.0548 820674.7011 699189.4338 617586.7038 647190.1954 744758.0943 0.745390136 0.973192262 0.876510472 1.171145588 0.966986543 1.101934584 0.938814145 0.829244702 0.868993839 1 19.50641237 -0.867710416 6.057116355 1.000000008 0.944103868 0.021055319 0.118636575 1.22E-08 2.30E-09 0.116774638 0.027524042 0.135609334 0.867710416 -0.05589614 VDINAPDVDVR ddPTM_BT-474_Pertuzumab_2h_R1 3 VDINAPDVDVR 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 129.89 0.0005481 586000000 423760 489960 431620 516020 414969 484190 457640 509660 480160 444260 FALSE TRUE 407198.9907 475986.8205 509623.3353 542651.854 428316.8548 493980.6535 463240.7352 499135.3429 425654.2498 414169.8745 0.983169023 1.149255052 1.230469348 1.310215657 1.034157434 1.19270059 1.118480034 1.205146423 1.027728659 1 18.65986309 -0.867226616 9.994021768 0.999998087 1.148926412 0.149450439 0.096955534 0 0 0.090008914 0.021215305 0.135760486 0.867226616 0.148928326 ESSSCGKDT(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 6 ESSSCGKDTPSK 12 1 O43148;O43148-2;K7EPP5 O43148 RNMT mRNA cap guanine-N7 methyltransferase 1 ESSSCGKDT(0.999)PS(0.001)K;ESSSCGKDT(0.996)PS(0.004)K;ESSS(0.008)CGKDT(0.992)PSK;ESSSCGKDT(1)PSK;ESSS(0.002)CGKDT(0.996)PS(0.002)K;ESSSCGKDT(0.999)PS(0.001)K 213.52 4.85E-08 6719760000 12108770 9055010 7811040 6998870 7667040 7249800 8643940 10413190 9951160 10483040 TRUE FALSE 11635545.88 8796769.981 9222668.684 7360082.519 7913657.305 7396395.923 8749727.123 10198153.99 8821546.035 9773014.363 1.190579022 0.90010816 0.943687213 0.753102599 0.809745797 0.75681828 0.895294614 1.043501381 0.90264331 1 23.22037218 -0.864973145 8.808692034 1 0.908377738 0.043746353 0.124989623 9.32E-10 0 0.12512243 0.029491639 0.136466752 0.864973145 -0.091622262 YPEPERPSS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 YPEPERPSSR 10 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 YPEPERPS(0.318)S(0.682)R;YPEPERPS(0.076)S(0.924)R 78.705 0.017685 3141300000 1781310 1832430 1188400 1502180 1515480 1310160 1230000 1790460 1145700 1039350 TRUE FALSE 1711694.436 1780170.891 1403170.316 1579707.69 1564226.791 1336652.333 1245053.108 1753486.375 1015644.939 968953.8987 1.766538571 1.837209069 1.448129078 1.630322858 1.614345938 1.379479802 1.284945661 1.80966956 1.048187061 1 19.8860685 -0.862650276 0.083792483 1.78E-12 2.304188466 0.548329336 0.193038599 58.50915978 1.028348217 21.0632144 8.494739242 0.137198614 0.862650276 2.304188466 ILDQMPATPSS(ph)PMYVD ddPTM_BT-474_Pertuzumab_2h_R1 1 ILDQMPATPSSPMYVD 16 0 P45985;P45985-2 P45985 MAP2K4 Dual specificity mitogen-activated protein kinase kinase 4 1 ILDQMPAT(0.001)PS(0.192)S(0.795)PMY(0.012)VD 111.63 0.00084106 153430000 267320 313150 268150 333660 343020 341750 309440 282740 335980 327560 TRUE FALSE 256872.8389 304219.2686 316610.67 350880.2326 354053.5498 348660.4192 313227.0193 276901.3202 297840.9589 305374.0694 0.841174365 0.996218406 1.036796184 1.149017771 1.159409345 1.141748609 1.025715837 0.906761077 0.975331532 1 18.22021804 -0.860246276 5.081315218 0.999999956 1.027366282 0.005833244 0.099146493 5.45E-08 1.23E-08 0.105961205 0.024975255 0.137960171 0.860246276 0.027366326 IDLEVR ddPTM_BT-474_Pertuzumab_2h_R1 3 IDLEVR 6 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 100.82 0.086601 298648000 495110 577930 513700 555090 634400 587800 610720 522780 599070 633770 FALSE TRUE 475760.5538 561448.0023 606537.0172 583738.2614 654806.0521 599685.7187 618194.174 511984.4103 531066.0851 590844.1934 0.80522168 0.950247135 1.026560003 0.987973256 1.108255035 1.014964225 1.046289666 0.866530324 0.898825936 1 19.17241821 -0.857065487 5.151848715 1.000000037 0.970510048 0.011643508 0.085918678 3.89E-08 8.80E-09 0.086961128 0.020496908 0.138974306 0.857065487 -0.029489989 LVGILDILDEENRLPQPSDQHFTSAVHQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVGILDILDEENRLPQPSDQHFTSAVHQK 29 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 264 1.69E-58 389010000 251870 335360 239880 382200 337440 370030 389440 207621 336570 356620 FALSE TRUE 242026.6419 325795.8612 283231.6521 401925.3878 348294.0641 377512.2601 394206.0832 203333.5538 298363.9846 332465.8098 0.727974531 0.979937941 0.851912118 1.20892247 1.047608668 1.135491979 1.185704129 0.611592374 0.897427573 1 18.34284646 -0.856805014 8.299483893 1 0.957531268 0.0037671 0.185117334 0 0 0.188760517 0.044491281 0.139057682 0.856805014 -0.042468732 S(ph)KDRDPNR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKDRDPNR 8 2 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR 75.566 0.029973 1425890000 3084400 2446070 2017270 2127180 2305720 2221640 2455370 2629570 2678060 2806160 TRUE FALSE 2963858.238 2376310.479 2381835.563 2236964.015 2379885.578 2266563.083 2485419.553 2575268.461 2374057.856 2616096.284 1.132931634 0.908342133 0.910454091 0.855077097 0.909708711 0.866391309 0.95004896 0.984393608 0.907481071 1 21.31898421 -0.856389164 7.777087858 1.000017186 0.933625462 0.06104964 0.074627115 0 0 0.070636936 0.016649285 0.139190898 0.856389164 -0.066391724 RFSDS(ph)EER ddPTM_BT-474_Pertuzumab_2h_R1 1 RFSDSEER 8 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RFS(0.334)DS(0.666)EER 125.17 0.0013489 515860000 674060 730590 565710 786300 768900 719200 666580 744090 695290 709840 TRUE FALSE 647716.99 709754.2885 667946.3812 826881.0372 793632.3668 733742.7168 674737.8054 728724.2815 616363.5941 661761.9045 0.978776484 1.072522132 1.009345471 1.249514412 1.199271764 1.108771466 1.019608111 1.10118802 0.931397818 1 19.33595272 -0.856211727 6.296112854 0.999999995 1.081472069 0.05061828 0.0924268 6.75E-09 1.07E-09 0.090615696 0.021358323 0.139247778 0.856211727 0.081472074 TAAGSSWEDPSLLEWDADDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAAGSSWEDPSLLEWDADDFR 21 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7EQ03 K7EP90 RBM42 RNA-binding protein 42 0 ; 233.97 2.13E-29 176150000 260567 276880 225720 271020 280360 277980 244782 268600 279130 297790 FALSE TRUE 250383.7536 268983.6535 266512.6251 285007.3747 289378.034 283600.9461 247777.7153 263053.3161 247444.3326 277620.4181 0.90189243 0.968890024 0.95998928 1.026608117 1.042351409 1.021542104 0.892505375 0.947528708 0.891304517 1 18.08275415 -0.856080013 7.258608889 0.999995896 0.963466562 0.044583244 0.052831987 0 5.56E-11 0.054206526 0.012776601 0.139290016 0.856080013 -0.036529334 GLNSSFETS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLNSSFETSPK 11 0 M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63;M0QZ79 M0QXD7 VRK3 Inactive serine/threonine-protein kinase VRK3 1 GLNSSFET(0.061)S(0.939)PK 77.22 0.018664 0 423050 349130 262610 286800 300420 301660 315940 385520 365560 367310 TRUE FALSE 406516.7383 339173.1542 310069.4687 301601.7824 310083.2821 307759.7719 319806.5682 377558.8773 324063.1614 342431.7665 1.18714669 0.990483908 0.905492711 0.880764613 0.90553305 0.898747727 0.933927864 1.102581344 0.946358349 1 18.38545702 -0.856036859 7.67536722 1 0.971985443 0.007725084 0.093978284 0 0 0.095102967 0.022415984 0.139303857 0.856036859 -0.028014557 LLIHQSLAGGIIGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLIHQSLAGGIIGVK 15 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 111.43 0.0019455 0 467360 733040 567720 842640 634960 716620 724090 584160 641350 780690 FALSE TRUE 449095.0545 712134.4169 670319.6329 886128.7514 655384.0651 731110.5474 732951.63 572096.8919 568546.6368 727813.1709 0.617047166 0.978457722 0.921005087 1.21752228 0.900483931 1.004530526 1.007060135 0.786049105 0.781171129 1 19.47320863 -0.854466219 7.304767709 0.999999957 0.920491493 0.026047604 0.153658064 0 1.51E-10 0.147699858 0.03481319 0.139808566 0.854466219 -0.079508464 ELGLAEHQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELGLAEHQLR 10 0 C9IYS7;A0A087WYI0;Q5TA45-2;Q5TA45-4;Q5TA45-3;Q5TA45;Q5TA45-5;J3QRY6;Q96HV7 C9IYS7 CPSF3L Integrator complex subunit 11 0 190.57 0.0036434 0 117670 139490 113450 151870 139660 141300 127180 129600 141630 146030 FALSE TRUE 113071.3263 135511.8818 133952.9387 159708.0289 144152.2907 144157.1828 128736.4669 126923.7147 125552.7562 136139.258 0.830556358 0.995391658 0.983940567 1.173122516 1.058859089 1.058895023 0.945623391 0.932307966 0.9222377 1 17.05472363 -0.853675933 7.356257695 0.999973463 0.992283836 0.000147257 0.088593314 0 0 0.090310222 0.021286323 0.140063207 0.853675933 -0.007689628 GSLTPHPAACDKDGQTDS(ph)AAEESSSQETSK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSLTPHPAACDKDGQTDSAAEESSSQETSK 30 1 A0A5F9ZH11;P55201-3;P55201;P55201-2;P55201-4 A0A5F9ZH11 BRPF1 Peregrin 1 GSLTPHPAACDKDGQTDS(1)AAEESSSQETSK;GSLTPHPAACDKDGQTDS(1)AAEESSSQETSK;GSLTPHPAACDKDGQT(0.001)DS(0.999)AAEESSSQETSK 382.38 1.13E-138 1374390000 649300 719400 555810 534430 631040 699820 614810 638610 723050 724020 TRUE FALSE 623924.6382 698883.4164 656257.2309 562011.9963 651337.9747 713970.8399 622334.2287 625422.4803 640972.3953 674981.4805 0.924358158 1.035411247 0.97225961 0.832633209 0.964971623 1.057763599 0.922001931 0.926577245 0.949614788 1 19.36448839 -0.846842315 7.882734423 0.99999767 0.953312765 0.051249732 0.059376599 0 0 0.0580988 0.013694019 0.14228453 0.846842315 -0.046684905 LISGGHDNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LISGGHDNR 9 0 Q15061;C9JEE7 Q15061 WDR43 WD repeat-containing protein 43 0 ; 127.76 0.00043624 184580000 155193 192310 159530 207463 169597 206107 182548 160209 192459 215181 FALSE TRUE 149127.886 186825.5071 188360.6197 218170.1903 175052.2415 210274.6248 184782.077 156900.6282 170611.8612 200606.5992 0.743384747 0.931302897 0.938955251 1.087552409 0.872614571 1.048193956 0.921116642 0.782130941 0.850479804 1 17.61400954 -0.845423218 7.341140491 0.999999921 0.90952264 0.06940081 0.100537614 7.49E-10 0 0.100512461 0.023691014 0.142750219 0.845423218 -0.09047728 GRPSKT(ph)PS(ph)PSQPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.436)KT(0.576)PS(0.564)PS(0.424)QPK;GRPS(0.345)KT(0.655)PS(0.999)PS(0.001)QPK;GRPS(0.044)KT(0.956)PS(0.796)PS(0.204)QPK;GRPS(0.299)KT(0.701)PS(0.935)PS(0.065)QPK 176.04 1.90E-05 1365350000 2916240 2236630 1846540 1595160 2091030 1956270 2035470 2593340 2886060 2320430 TRUE FALSE 2802270.117 2172843.502 2180250.854 1677486.399 2158289.879 1995827.12 2060380.691 2539786.623 2558446.568 2163265.209 1.295389074 1.004427702 1.007851855 0.775441861 0.997700083 0.92259937 0.952440173 1.174052359 1.182678184 1 21.04477912 -0.845320544 7.699147363 1.000000003 1.028043166 0.003416764 0.141149642 0 0 0.140956474 0.033223759 0.142783971 0.845320544 0.028043163 GPAGEAGAS(ph)PPVRR ddPTM_BT-474_Pertuzumab_2h_R1 5 GPAGEAGASPPVRR 14 1 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR 156 3.49E-06 5428160000 1457510 1642560 1218181 1766510 1448250 1638540 1520060 1591910 1571320 1579750 TRUE FALSE 1400548.898 1595715.797 1438333.405 1857679.793 1494834.277 1671672.401 1538662.949 1559036.502 1392950.341 1472752.125 0.950973944 1.083492442 0.976629658 1.261366228 1.0149938 1.135067044 1.044753508 1.058587168 0.945814518 1 20.4900832 -0.843069328 6.084311963 0.999999995 1.058338397 0.026025614 0.08981578 6.01E-09 1.19E-09 0.080702693 0.019021805 0.14352603 0.843069328 0.058338402 ADHQPLTEASYVNLPTIALCNTDSPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ADHQPLTEASYVNLPTIALCNTDSPLR 27 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 241.54 3.29E-45 1805780000 846350 950550 799760 956490 930730 971860 915570 825590 996610 1068910 FALSE TRUE 813273.7063 923441.2447 944294.4226 1005854.564 960667.7757 991511.6751 926775.0195 808541.278 883479.0109 996511.7736 0.816120519 0.926673692 0.947599865 1.009375494 0.964030532 0.994982399 0.930019137 0.811371526 0.886571573 1 19.92652732 -0.84218681 7.443465022 0.999997488 0.92017649 0.123322747 0.063373616 0 6.83E-11 0.068190297 0.016072607 0.143817982 0.84218681 -0.079820998 FVCYCEGEESGEGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVCYCEGEESGEGDR 15 0 Q9BUH6;Q9BUH6-2 Q9BUH6 C9orf142 Protein PAXX 0 176.78 1.82E-06 172320000 30467 38566 27403 36110 35458 35787 35605 28070 34293 41553 FALSE TRUE 29276.31596 37466.13544 32355.33168 37973.64143 36598.53877 36510.63766 36040.74464 27490.34469 30400.20241 38738.5783 0.755740588 0.967153083 0.835222486 0.980253873 0.94475689 0.942487806 0.930357959 0.709637418 0.784752661 1 15.24148339 -0.839111669 4.999849883 1.000000148 0.871960915 0.149889537 0.091259793 2.17E-07 5.05E-08 0.094079432 0.0221747 0.144839938 0.839111669 -0.128039233 LNQS(ph)PSLAPVKR ddPTM_BT-474_Pertuzumab_2h_R1 4 LNQSPSLAPVKR 12 1 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LNQS(0.936)PS(0.064)LAPVKR;LNQS(0.967)PS(0.033)LAPVKR;LNQS(0.798)PS(0.202)LAPVKR;LNQS(0.994)PS(0.006)LAPVKR 155.64 4.44E-05 2229840000 1712260 1810230 1464270 1533880 1440480 1625630 1757810 1762320 1765760 2117500 TRUE FALSE 1645342.986 1758604.013 1728896.162 1613043.731 1486814.347 1658501.352 1779322.605 1725927.476 1565318.327 1974079.839 0.833473375 0.890847461 0.8757985 0.817111699 0.753168295 0.840138945 0.901342777 0.874294667 0.792935674 1 20.91274891 -0.837744854 5.559611074 1.000000053 0.845893054 0.537211164 0.043834515 3.07E-08 6.49E-09 0.045283161 0.01067334 0.145296498 0.837744854 -0.154106999 SRPQGLTEAEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRPQGLTEAEQR 12 1 Q00653;Q00653-4;Q00653-3 Q00653 NFKB2 Nuclear factor NF-kappa-B p100 subunit;Nuclear factor NF-kappa-B p52 subunit 0 77.078 0.026805 122570000 81984 87204 72286 92097 91718 77806 82404 91376 87670 99107 FALSE TRUE 78779.97464 84717.0273 85349.68819 96850.13721 94668.19277 79379.29063 83412.4848 89489.05367 77718.06914 92394.39461 0.852648854 0.916906568 0.923753963 1.048225248 1.024609698 0.859135351 0.902787286 0.968555009 0.841155673 1 16.49551771 -0.837189892 0.0042828 1.904436432 8.86E-07 0.03354029 0.068831015 172168.4666 150.8837275 34344.14436 32758.26087 0.145482283 0.837189892 -1.904435547 EHQLASASELPLGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EHQLASASELPLGSR 15 0 O60232;H0YEB6;G3V1B8 O60232 SSSCA1 Sjoegren syndrome/scleroderma autoantigen 1 0 ; 162.59 1.59E-06 966160000 320880 387780 366870 417750 429180 432610 455170 269870 392030 490070 FALSE TRUE 308339.6548 376720.8941 433171.57 439310.1276 442984.9645 441357.6706 460740.5066 264297.0902 347528.3979 456877.1224 0.674885302 0.824556266 0.948113943 0.961549848 0.969593229 0.966031453 1.008456068 0.578486156 0.760660538 1 18.80144668 -0.83628389 4.221105588 1.00000172 0.852937296 0.091758472 0.137035283 40507925.33 88153190.89 1130.775219 0.036451619 0.145786097 0.83628389 -0.147064424 ILDAVVAQEPLHR ddPTM_BT-474_Pertuzumab_2h_R1 5 ILDAVVAQEPLHR 13 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;; 166.38 3.37E-05 1478517000 1597400 1755650 1477137 1804118 1751139 1717087 1708900 1646691 1791795 1829911 FALSE TRUE 1534971.842 1705580.581 1744088.515 1897228.746 1807465.976 1751807.676 1729814.029 1612686.255 1588397.943 1705969.498 0.899765115 0.999772026 1.022344489 1.112111763 1.059494896 1.026869283 1.013977115 0.945319513 0.931082265 1 20.70216042 -0.834387863 7.345541654 0.999996048 1.003807398 0 0.059464854 0 0 0.061914424 0.01459337 0.146423956 0.834387863 0.003811351 AELGSWS(ph)SQEHLEWEPACQTPQPSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AELGSWSSQEHLEWEPACQTPQPSAR 26 0 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AELGS(0.026)WS(0.532)S(0.442)QEHLEWEPACQTPQPSAR 150.55 8.65E-08 251470000 91312 114890 76519 109300 102650 102020 99196 89509 99174 113070 TRUE FALSE 87743.42609 111613.4497 90347.68546 114940.9861 105951.8305 104082.9143 100409.9903 87660.60787 87916.18329 105411.6682 0.832388175 1.058833919 0.857093783 1.090400978 1.005124312 0.987394622 0.952551004 0.83160251 0.834027056 1 16.68567504 -0.831322508 4.954072023 1.000000097 0.940414708 0.037940577 0.092103887 9.94E-08 2.33E-08 0.090141348 0.021246485 0.147461108 0.831322508 -0.059585389 FVEGVDSDYHDENMYYSQSSMFPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVEGVDSDYHDENMYYSQSSMFPHR 25 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VWH8;F8W145;F8VQF4;F8VVD4;F8VRS8;F8VRJ3 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 0 145.13 1.66E-07 157040000 36724 45591 43303 54657 52060 52026 49153 39311 44367 52786 FALSE TRUE 35288.78548 44290.78932 51128.81537 57477.85432 53734.55718 53078.00137 49754.54912 38499.21411 39330.64416 49210.7572 0.71709495 0.900022512 1.0389764 1.167993699 1.091927055 1.078585342 1.011050265 0.782333301 0.799228591 1 15.58668609 -0.83087494 4.454742644 1.000000238 0.958654167 0.00833184 0.142639156 7.48022E+12 1.97001E+12 20978568.6 0.036791079 0.147613154 0.83087494 -0.041346072 AAGDT(ph)PERK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGDTPERK 9 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4 I3L2J0 CIC Protein capicua homolog 1 AAGDT(1)PERK 69.451 0.03235 369140000 814450 691710 703990 574450 619890 645390 727520 757140 819930 830310 TRUE FALSE 782620.3936 671983.1081 831216.6532 604097.4333 639829.3248 658440.228 736423.6074 741504.7944 726854.9838 774072.3641 1.011042933 0.868114067 1.073822929 0.780414676 0.826575595 0.850618442 0.951362743 0.95792697 0.939001336 1 19.56210892 -0.830540595 7.42988515 1.000000783 0.9166124 0.07964367 0.083911714 0 0 0.080484 0.018970261 0.147726839 0.830540595 -0.083388383 SPS(ph)PPLPTHIPPEPPRT(ph)PPFPAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSPPLPTHIPPEPPRTPPFPAK 23 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 2 S(0.433)PS(0.566)PPLPTHIPPEPPRT(1)PPFPAK;S(0.403)PS(0.597)PPLPTHIPPEPPRT(1)PPFPAK;S(0.425)PS(0.574)PPLPTHIPPEPPRT(1)PPFPAK;S(0.44)PS(0.559)PPLPT(0.001)HIPPEPPRT(1)PPFPAK 174.53 3.93E-11 1063251000 718221 670372 463489 539199 499847 460558 501418 857590 596117 544990 TRUE FALSE 690152.1293 651253.6469 547251.7726 567027.125 515925.0327 469870.7983 507554.5035 839880.4668 528448.2973 508077.3419 1.358360376 1.281800217 1.077103282 1.116025216 1.015445859 0.924801717 0.998970947 1.653056331 1.040094202 1 18.9546886 -0.82993765 7.903179113 0.999997391 1.178979111 0.048223229 0.206126693 0 2.04E-10 0.216226828 0.050965152 0.147932075 0.82993765 0.17898172 QDEHGYISR ddPTM_BT-474_Pertuzumab_2h_R1 30 QDEHGYISR 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 152.64 8.00E-05 1.20758E+11 64947510.1 66724815.2 60142637.7 67525420.5 61875872.1 72494979.5 65846867.7 60523244.8 75662974.3 76432390 FALSE TRUE 62409289.6 64821888.8 71011750.2 71010415.54 63866165.72 73960877.66 66652721.36 59273418.64 67074030.66 71255556.15 0.875851554 0.909709955 0.996578429 0.996559698 0.896297344 1.037966464 0.935403847 0.831842762 0.941316499 1 26.08649918 -0.826452012 7.119670788 1.000000012 0.932900117 0.09541669 0.058794715 0 1.27E-10 0.060615098 0.014287116 0.149124152 0.826452012 -0.067099895 GPS(ph)PAPASS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.247)S(0.753)PKR;GPS(0.797)PAPAS(0.535)S(0.668)PKR;GPS(0.99)PAPAS(0.416)S(0.594)PKR 89.747 0.0061818 1360560000 4393920 4015420 3347370 3550640 3771180 3828880 3661020 4217500 4720900 3973270 TRUE FALSE 4222200.749 3900904.153 3952314.221 3733888.956 3892483.43 3906302.577 3705824.658 4130407.151 4185003.224 3704156.884 1.139854731 1.053115264 1.066994284 1.008026677 1.050841946 1.05457266 1.000450244 1.115073492 1.129812628 1 21.82071377 -0.82623294 6.816650154 0.999999999 1.066059325 0.172334063 0.044851877 0 9.54E-11 0.043636197 0.01028515 0.149199394 0.82623294 0.066059326 VGPCSS(ph)PPAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGPCSSPPAAR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 VGPCS(0.278)S(0.722)PPAAR 95.362 0.0081975 380260000 230860 231040 186760 251610 228080 227860 241110 210250 217010 264870 TRUE FALSE 221837.736 224450.9654 220511.6865 264595.6223 235416.4003 232467.4853 244060.7763 205908.264 192375.9346 246930.119 0.898382655 0.908965526 0.893012514 1.071540496 0.953372563 0.941430257 0.988379941 0.833872615 0.779070351 1 17.91374329 -0.825655107 5.277667699 1.00000005 0.920545932 0.092890247 0.076043122 4.70E-08 1.06E-08 0.076963262 0.018140403 0.149398038 0.825655107 -0.079454118 VDDS(ph)SEDKTEFTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDDSSEDKTEFTVK 14 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 1 VDDS(0.561)S(0.439)EDKTEFTVK 106.57 0.00056566 190080000 231780 194240 161950 136190 171330 163990 157660 211740 264680 194050 TRUE FALSE 222721.7814 188700.4654 191217.9676 143218.7822 176840.985 167305.9902 159589.4902 207367.495 234634.636 180906.8207 1.231140874 1.043080989 1.056997005 0.791671545 0.97752525 0.924818586 0.882164032 1.14626687 1.296991651 1 17.46488728 -0.825081804 6.542816964 0.999999999 1.028749361 0.001949901 0.147935326 1.10E-09 3.35E-10 0.147082573 0.034667694 0.149595385 0.825081804 0.028749362 LVSFHDDS(ph)DEDLLHI ddPTM_BT-474_Pertuzumab_2h_R1 11 LVSFHDDSDEDLLHI 15 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVS(0.013)FHDDS(0.987)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI 331.44 5.33E-69 5668714800 1046491.6 1618864.1 1119087.9 1838790 1282202.5 1422405.7 1628460 1166389.1 1607721 1550193.7 TRUE FALSE 1005593.551 1572695.681 1321331.978 1933690.172 1323445.708 1451167.718 1648389.581 1142302.757 1425219.252 1445197.7 0.695817293 1.088221827 0.914291503 1.338010829 0.915754092 1.004130935 1.140597982 0.790412798 0.986175976 1 20.46283543 -0.825035872 7.543940231 1 0.987990923 0.000480589 0.170635631 0 6.16E-18 0.156926391 0.036987905 0.149611207 0.825035872 -0.012009077 TSAADLVTETDHLVEDLIISELR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSAADLVTETDHLVEDLIISELR 23 0 O14732-2;O14732;Q6PIP6;K7EL65;K7ELF8 O14732-2 IMPA2 Inositol monophosphatase 2 0 191.66 1.15E-17 147510000 24850 28288 17032 28120 28526 26373 24929 17369 26667 31136 FALSE TRUE 23878.83453 27481.25394 20110.06127 29571.27657 29443.5647 26906.28013 25234.08856 17010.32408 23639.87396 29027.13099 0.822638467 0.946743719 0.692802237 1.018746103 1.014346361 0.926935567 0.869327684 0.586014653 0.814406149 1 14.82511436 -0.82444971 4.667012639 1.000000484 0.845680138 0.098110793 0.129646604 2257.299312 89418033.57 121.9212257 0.033646717 0.149813272 0.82444971 -0.154320346 VISGTTLGYLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 VISGTTLGYLSPK 13 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0;E5RJN7;E5RJ67 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 VISGTTLGYLS(1)PK;VISGTTLGYLS(1)PK 293.38 1.39E-40 687980000 611010 660000 725090 744130 802320 760280 726950 663610 741240 710850 TRUE FALSE 587131.0537 641177.4462 856129.8925 782534.6385 828127.3514 775653.3825 735846.6316 649906.2216 657097.5427 662703.4963 0.885963416 0.967517826 1.291874718 1.180821654 1.249619711 1.170438042 1.11037083 0.98068929 0.991540782 1 19.33800401 -0.823655197 5.501512582 0.999999968 1.096223895 0.044723925 0.1263945 5.49E-08 1.14E-08 0.131631099 0.031025737 0.150087596 0.823655197 0.096223927 KSKS(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSKSPPKVPIVIQDDSLPAGPPPQIR 26 3 Q7Z422-5;Q7Z422;Q7Z422-4 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 KS(0.169)KS(0.831)PPKVPIVIQDDSLPAGPPPQIR 129.03 0.00045761 797720000 289660 233100 160940 137640 191070 169560 213150 266190 253510 216880 TRUE FALSE 278339.767 226452.2162 190025.4381 144743.6169 197215.9401 172988.6194 215758.5935 260693.0835 224732.6076 202190.5244 1.376621223 1.119994208 0.939833549 0.71587735 0.975396551 0.855572336 1.067105365 1.289343723 1.111489316 1 17.62535586 -0.817850599 8.681643445 1.00000002 1.04956645 0.006599858 0.184413856 0 0 0.194887818 0.045935499 0.15210707 0.817850599 0.049566429 EALNSCNKR ddPTM_BT-474_Pertuzumab_2h_R1 7 EALNSCNKR 9 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;;; 185.29 6.90E-05 11741113000 5372412 5647723 4208486 4563381 4668411 4470874 5280370 5456002 5808442 5674800 FALSE TRUE 5162452.2 5486655.47 4969053.037 4798897.64 4818574.68 4561278.136 5344992.748 5343333.652 5149092.015 5290440.741 0.975807584 1.037088541 0.939251242 0.90708844 0.910807798 0.862173561 1.010311429 1.009997827 0.97328224 1 22.33495649 -0.816207784 6.740025267 1 0.960397147 0.05401481 0.051606864 0 6.09E-11 0.055089697 0.012984766 0.152683538 0.816207784 -0.039602854 HLAQVGDSMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLAQVGDSMDR 11 0 P55957;P55957-2 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ; 167.84 1.88E-05 1301180000 454050 529530 443270 540670 508250 572910 518360 400630 554040 574590 FALSE TRUE 436305.224 514428.3229 523378.7495 568574.0435 524598.3228 584494.6327 524703.8447 392356.8505 491147.7019 535672.5075 0.814499938 0.960341096 0.977049862 1.06142099 0.979326576 1.091141742 0.979523566 0.732456576 0.916880547 1 19.03099173 -0.814108473 4.694348357 1.000000158 0.941878604 0.023972052 0.100834049 1.85E-07 4.70E-08 0.108895195 0.025666774 0.153423373 0.814108473 -0.058121554 SNVSSPATPTASSSSSTT(ph)PTRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSSS(0.001)T(0.015)T(0.957)PT(0.027)RK 195.38 1.75E-19 607430000 193670 186140 156300 187530 177670 185480 182100 208380 211160 220920 TRUE FALSE 186101.1623 180831.4695 184546.8869 197208.4458 183384.9169 189230.5327 184328.5943 204076.8802 187190.0021 205956.8916 0.90359279 0.878006402 0.896046184 0.957522927 0.890404373 0.918787088 0.89498629 0.990871821 0.908879526 1 17.65198288 -0.811674176 0.110501068 1.117590574 0.840137565 0.469049962 0.029964887 34.59251348 0.839027394 1.702284351 0.538576725 0.154285753 0.811674176 -0.277453008 LAEAFAEELHER ddPTM_BT-474_Pertuzumab_2h_R1 4 LAEAFAEELHER 12 0 Q99707-2;Q99707;B1ANE3 Q99707-2 MTR Methionine synthase 0 ;;; 147.24 6.16E-05 240682000 369266 473521 446684 649074 537603 502054 608902 456907 440254 575711 FALSE TRUE 354834.6765 460016.6447 527409.7352 682572.7869 554895.4887 512205.8759 616353.9248 447471.7108 390278.2116 536717.5812 0.661119905 0.857092558 0.982657833 1.271754105 1.033868664 0.954330348 1.148376626 0.833719122 0.727157495 1 19.03380362 -0.81072768 6.248559667 1.000000002 0.95324434 0.005822133 0.175178504 5.22E-09 8.35E-10 0.175123399 0.041276979 0.154622368 0.81072768 -0.046755663 MFDYTDDPEGPVMPGSHSVER ddPTM_BT-474_Pertuzumab_2h_R1 2 MFDYTDDPEGPVMPGSHSVER 21 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ; 110.16 0.00027868 1143960000 1056600 1191080 1241220 1211980 1267780 1292550 1108880 1401170 1173820 1194490 FALSE TRUE 1015306.904 1157111.565 1465536.065 1274530.433 1308559.295 1318686.247 1122450.805 1372235.35 1040572.875 1113586.128 0.911745287 1.039085828 1.316050934 1.144527936 1.175085844 1.184179843 1.007960477 1.232266921 0.934434121 1 20.08678171 -0.808023175 8.280340824 1.000000007 1.11909861 0.049813123 0.124685275 0 0 0.116126769 0.027371342 0.15558826 0.808023175 0.119098603 AS(ph)PATHR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASPATHR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AS(0.988)PAT(0.012)HR;AS(0.999)PAT(0.001)HR;AS(1)PATHR 99.802 0.010763 95635000 78623 74048 71544 100678 78749 80613 89859 77463 75801 92354 TRUE FALSE 75550.32624 71936.22354 84473.59229 105874.0036 81282.0331 82243.05009 90958.72132 75863.36198 67196.38826 86098.78132 0.87748427 0.835508034 0.981124134 1.22968063 0.944055559 0.955217354 1.056446095 0.881120044 0.780456903 1 16.3937052 -0.807084077 7.441993734 1.000016461 0.954342612 0.014395542 0.119451509 0 0 0.119379597 0.028138041 0.155925061 0.807084077 -0.045673849 GGYIGSTYFER ddPTM_BT-474_Pertuzumab_2h_R1 4 GGYIGSTYFER 11 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;;; 192.26 3.42E-06 1704880000 669570 842760 708270 775190 751070 655190 777800 783200 835790 894900 FALSE TRUE 643402.4642 818725.3099 836270.1444 815197.6488 775228.8487 668438.3907 787318.9491 767026.6463 740914.6231 834287.6259 0.771199817 0.981346582 1.002376301 0.977118231 0.929210532 0.801208564 0.943702057 0.919379148 0.888080561 1 19.67018532 -0.806987002 4.657436191 1.000000225 0.917947959 0.113848668 0.071760702 9043664.495 1941768.662 20.88643527 0.016613906 0.155959918 0.806987002 -0.082052266 SFHPEQDAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFHPEQDAGK 10 0 U3KQC1;A0A0A0MQU0;Q9BV38;K7EIR0;K7EML4 U3KQC1 WDR18 WD repeat-containing protein 18 0 ; 100.72 0.0038198 579060000 793900 1016060 789780 937380 903430 1003580 918450 770640 950950 1083070 FALSE TRUE 762873.5103 987082.9636 932510.8146 985758.2941 932489.6464 1023873.075 929690.2658 754726.0147 843002.1427 1009712.704 0.75553522 0.977587941 0.923540737 0.976276014 0.923519772 1.014024159 0.920747319 0.747466098 0.834893073 1 19.94551343 -0.804745658 4.896846857 1.000000098 0.896819607 0.113231887 0.086415189 1.46E-07 3.57E-08 0.089669184 0.0211352 0.15676689 0.804745658 -0.10318049 S(ph)S(ph)PLAS(ph)LSKTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPLASLSKTR 11 1 X6RDY0;Q5T130;X6RIY5;Q5T124-7;Q5T124-6;Q5T124-3;Q5T124-2;Q5T124 X6RDY0 UBXN11 UBX domain-containing protein 11 3 S(1)S(1)PLAS(0.333)LS(0.333)KT(0.333)R 59.8 0.079652 160350000 36138 29886 24742 33380 32545 30960 28748 40454 25054 26746 TRUE FALSE 34725.68701 29033.68054 29213.42978 35102.7458 33591.83948 31586.03241 29099.82662 39618.61076 22209.97495 24934.4696 1.39267799 1.164399364 1.17160823 1.40779998 1.347204894 1.266761753 1.167052161 1.588909305 0.890733804 1 14.60585389 -0.803289526 7.788926298 1.000001687 1.285335237 0.159184647 0.178916354 0 0 0.16278628 0.038369094 0.157293391 0.803289526 0.28533355 QGQEHIGSSCSFAEQALR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGQEHIGSSCSFAEQALR 18 0 O75382;O75382-2;O75382-4;A0A1W2PPI7;E9PMK8 O75382 TRIM3 Tripartite motif-containing protein 3 0 165.16 2.89E-11 247740000 113430 118990 88397 128620 125730 116820 96226 137400 97090 115100 FALSE TRUE 108997.0302 115596.5217 104372.3043 135258.0936 129774.2196 119182.1804 97403.64257 134562.642 86068.75023 107304.1745 1.015776234 1.077278887 0.972677016 1.260511012 1.209405135 1.110694724 0.907733954 1.254029889 0.80210067 1 16.71134668 -0.802896089 6.252790521 0.999999997 1.082162916 0.011076831 0.142698801 5.82E-09 9.31E-10 0.130203001 0.030689141 0.157435951 0.802896089 0.082162919 AIS(ph)TGSLASSTLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 AISTGSLASSTLNK 14 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 AIS(0.988)T(0.011)GSLASSTLNK;AIS(0.959)T(0.04)GS(0.001)LASSTLNK 213.99 2.75E-10 170682000 363110 329950 264460 286590 254940 298410 282880 381870 337670 324320 TRUE FALSE 348919.2598 320540.1491 312253.8049 301380.9442 263140.3766 304444.0547 286341.9701 373984.2511 299339.1172 302353.5175 1.154010916 1.060150223 1.032744079 0.996783324 0.87030698 1.006914215 0.947043621 1.236910535 0.990030213 1 18.20587684 -0.801669192 7.917423213 0.999999527 1.037900636 0.007623454 0.097413126 0 0 0.099798347 0.023522696 0.157881342 0.801669192 0.037901109 LAQECCYHNNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAQECCYHNNR 11 0 Q9NVH2-4;Q9NVH2-3;Q9NVH2-2;Q9NVH2 Q9NVH2-4 INTS7 Integrator complex subunit 7 0 ; 155.97 3.13E-05 267600000 211770 208248 182795 225060 237329 199406 211436 215260 211177 230720 FALSE TRUE 203493.7943 202308.9709 215830.1228 236675.3736 244962.9028 203438.1259 214023.617 210814.8058 187205.0723 215093.1289 0.946072965 0.940564545 1.003426394 1.100339071 1.138869029 0.945814155 0.99502768 0.980109438 0.87034427 1 17.71460191 -0.800559627 7.466730435 0.999979937 0.995375885 0 0.074451246 0 0 0.075390361 0.017769679 0.158285223 0.800559627 -0.004604053 QIFDEYENETFLCHR ddPTM_BT-474_Pertuzumab_2h_R1 4 QIFDEYENETFLCHR 15 0 S4R3N1;Q9Y3A3-2;Q9Y3A3-3;Q9Y3A3;B4DM50 S4R3N1 HSPE1-MOB4;MOB4 MOB-like protein phocein 0 ;;; 278.2 1.32E-33 1305410000 1083804 1166994 973499 1142671 1211828 1198129 1143413 1124530 1164492 1261983 FALSE TRUE 1041447.741 1133712.474 1149431.925 1201644.387 1250807.548 1222355.989 1157406.43 1101308.063 1032303.75 1176507.767 0.885202606 0.96362515 0.976986261 1.021365452 1.063152818 1.038969757 0.983764377 0.936082271 0.877430459 1 20.16607941 -0.799446889 5.396573218 1.000000007 0.97554692 0.017382649 0.057753535 5.80E-09 1.40E-09 0.059847621 0.014106215 0.158691297 0.799446889 -0.024453087 NDQDTWDYTNPNLSGQGDPGSNPNKR ddPTM_BT-474_Pertuzumab_2h_R1 4 NDQDTWDYTNPNLSGQGDPGSNPNKR 26 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 276.03 1.98E-60 15667100000 2897900 2823160 2201250 2472740 2359740 2508280 2521370 2812900 3147250 2945510 FALSE TRUE 2784646.864 2742646.241 2599064.842 2600358.408 2435643.18 2558999.14 2552227.28 2754812.632 2789987.374 2746007.984 1.014070928 0.998775771 0.94648845 0.946959522 0.886976001 0.931897924 0.92943185 1.003206345 1.016015755 1 21.38890439 -0.796122953 5.475179376 1.00000001 0.962075804 0.064632126 0.040913812 5.12E-09 1.23E-09 0.042924557 0.010117412 0.159910524 0.796122953 -0.037924206 IYVLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 IYVLLR 6 0 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 147.63 0.025284 879890000 538670 602190 571700 593120 475660 342740 631100 716550 573510 704610 FALSE TRUE 517618.1809 585016.1308 675018.9074 623730.9943 490960.0359 349670.4376 638823.5906 701752.9921 508407.5492 656886.1371 0.787987676 0.890589857 1.02760413 0.949526804 0.74740508 0.532315142 0.972502774 1.068302332 0.77396602 1 19.32528379 -0.79576538 5.945310419 1.000000009 0.87576529 0.063472965 0.150879609 1.88E-08 3.75E-09 0.157407836 0.03710138 0.16004224 0.79576538 -0.124234718 KVEEDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEEDLK 7 1 P50502;Q3KNR6;Q8NFI4;F6VDH7 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 85.676 0.033089 1310500000 817570 874830 851270 811770 1019700 915080 922000 844770 944690 963460 FALSE TRUE 785618.4605 849880.7049 1005113.425 853665.547 1052499.577 933583.5446 933283.7118 827325.2043 837452.7517 898203.996 0.874654827 0.946200093 1.119025778 0.950413882 1.171782336 1.039389213 1.039055399 0.921088314 0.932363645 1 19.77668362 -0.795439909 4.753289639 0.999999996 1.001945435 0 0.088700061 3.89E-09 8.18E-10 0.086976003 0.020500402 0.160162224 0.795439909 0.001945438 IFVGGLSPDT(ph)PEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IFVGGLSPDTPEEK 14 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IFVGGLS(0.38)PDT(0.62)PEEK 211.51 4.18E-08 156240000 438630 428110 356770 344530 364550 393660 374070 449930 461820 414290 TRUE FALSE 421487.8547 415900.722 421246.2753 362311.2346 376276.0818 401620.0749 378647.9806 440638.7883 409396.1297 386229.7693 1.09128785 1.076822024 1.090662369 0.938071747 0.974228586 1.039847539 0.980369745 1.140872153 1.059980774 1 18.55909984 -0.793227842 8.097215793 1.000002176 1.044966546 0.04571508 0.059414782 0 0 0.061233547 0.014432886 0.160980087 0.793227842 0.04496437 EIEHLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIEHLSR 7 0 O95347-2;O95347;Q5T821 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ; 130.27 0.0035794 412070000 262980 429610 347450 508220 375250 465880 390850 332020 393810 495580 FALSE TRUE 252702.4509 417357.9434 410241.944 534449.2951 387320.257 475300.4128 395633.3392 325163.671 349106.3398 462013.9252 0.546958516 0.903344944 0.887942812 1.156781789 0.838330267 1.028757764 0.856323409 0.703796256 0.755618653 1 18.81757681 -0.792389201 7.306865838 1.00001122 0.85813046 0.070572881 0.158993845 0 3.19E-10 0.156459874 0.036877946 0.161291247 0.792389201 -0.14188076 VDCTQHYELCSGNQVR ddPTM_BT-474_Pertuzumab_2h_R1 4 VDCTQHYELCSGNQVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 273.88 3.24E-35 5688970000 1998860 2368740 1957550 2447710 2045330 2324670 2316250 2154450 2361860 2443030 FALSE TRUE 1920742.341 2301185.854 2311322.83 2574036.606 2111119.897 2371676.42 2344596.96 2109959.855 2093751.555 2277561.402 0.843332847 1.010372696 1.014823499 1.130172211 0.926921178 1.041322714 1.029433041 0.926411842 0.919295327 1 21.11905852 -0.792281821 8.114532576 1 0.986390209 0.002326162 0.07682984 0 0 0.073091842 0.017227912 0.161331131 0.792281821 -0.013609791 VEEAS(ph)PGRPSSVDTLLSPTALIDSILR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VEEAS(0.736)PGRPS(0.132)S(0.132)VDTLLSPTALIDSILR;VEEAS(0.956)PGRPS(0.022)S(0.022)VDTLLSPTALIDSILR 175.48 6.57E-13 594820000 51767 49624 38528 57785 45403 51603 50237 47686 46667 55824 TRUE FALSE 49743.88841 48208.77211 45490.86665 60767.29077 46863.42873 52646.44802 50851.81543 46701.26744 41369.5578 52042.99076 0.955823016 0.926325936 0.874101699 1.167636408 0.900475319 1.011595361 0.977111705 0.897359409 0.79491123 1 15.66741625 -0.790050795 4.993356059 1.000000026 0.947367252 0.029658241 0.093462847 4.85E-08 1.17E-08 0.087966402 0.020733861 0.162162042 0.790050795 -0.052632774 EVSQVDTICECLLEHEEQVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSQVDTICECLLEHEEQVLR 21 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 0 ; 303.23 2.71E-55 256630000 140233 161963 130529 156845 150383 159823 154395 131577 157931 171440 FALSE TRUE 134752.5393 157343.9738 154118.4939 164939.7892 155220.2058 163054.7306 156284.5322 128859.889 140003.335 159828.2161 0.843108574 0.984456798 0.964275881 1.031981669 0.971168981 1.02018739 0.977828171 0.806239925 0.875961319 1 17.2861626 -0.789874362 4.91488137 1.000000056 0.941112192 0.056326595 0.071565919 10110158.64 2057050.538 7.227955722 0.018489636 0.162227934 0.789874362 -0.058887864 MNDILNHK ddPTM_BT-474_Pertuzumab_2h_R1 2 MNDILNHK 8 0 Q13867;K7ESE8;J3KSD8;K7ES02 Q13867 BLMH Bleomycin hydrolase 0 ; 99.802 0.0065549 566070000 896420 804510 736470 737710 782420 351600 862520 739680 1112910 995900 FALSE TRUE 861386.9154 781566.1625 869566.5117 775783.3015 807587.2499 358709.5929 873075.7778 724405.3495 986577.1225 928446.8059 0.927771963 0.841799614 0.936581941 0.835571081 0.869826084 0.386354491 0.940361658 0.780233552 1.062610282 1 19.82445973 -0.789748388 6.301555954 1.000000004 0.832627544 0.069584009 0.169628703 9.44E-09 1.87E-09 0.158368567 0.037327828 0.162274998 0.789748388 -0.16737246 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_BT-474_Pertuzumab_2h_R1 6 RVGDPPQPLPEEPMEVQGAERASPEPQR 28 2 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR 161.68 7.11E-12 7382740000 1582573 1654562 1264664 1425719 1574890 1947948 1604693 1491913 1551314 1501305 TRUE FALSE 1520724.298 1607375.512 1493216.917 1499300.528 1625547.767 1987336.843 1624331.713 1461104.475 1375215.338 1399620.275 1.086526342 1.148436858 1.066872882 1.071219498 1.161420562 1.419911442 1.160551717 1.043929201 0.982563173 1 20.41660404 -0.789627763 7.638411793 1.000011413 1.128966399 0.103721852 0.111685147 0 2.24E-10 0.115022775 0.027111128 0.162320076 0.789627763 0.128954986 GVEFPMADLDALSPIHT(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVEFPMADLDALSPIHTPQR 20 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-5 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 GVEFPMADLDALS(0.001)PIHT(0.999)PQR 120.08 0.00015274 26937000 16670 19320 19271 23151 21465 18513 22170 20533 18910 20448 TRUE FALSE 16018.51797 18769.01252 22753.69838 24345.82588 22155.44122 18887.34554 22441.32309 20108.98637 16763.41608 19063.03875 0.840291948 0.984576109 1.193602903 1.277121985 1.162219807 0.990783568 1.177216465 1.054867833 0.879367466 1 14.21849049 -0.789311465 7.504135302 1.000011598 1.074762303 0.011253633 0.134890866 0 0 0.133864656 0.031552202 0.162438337 0.789311465 0.074750705 ELS(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSPEAR 7 0 Q9P0B6 Q9P0B6 CCDC167 Coiled-coil domain-containing protein 167 1 ELS(1)PEAR 80.438 0.031376 143210000 106370 131620 114310 148430 123880 138730 123390 126430 137720 131470 TRUE FALSE 102212.9428 127866.3265 134968.3598 156090.4901 127864.7127 141535.2157 124900.0837 123819.1763 122086.603 122565.4198 0.83394601 1.043249611 1.101194448 1.273527969 1.043236444 1.154772822 1.019048309 1.010229284 0.996093377 1 16.90319247 -0.78755449 7.591695422 1 1.058222827 0.01900295 0.107690174 0 0 0.105419977 0.024847727 0.163096826 0.78755449 0.058222827 VEWTSDTVDNEHMGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEWTSDTVDNEHMGR 15 0 O60927 O60927 PPP1R11 Protein phosphatase 1 regulatory subunit 11 0 ; 176.4 8.01E-07 396880000 174973 262800 216661 287940 231460 258440 259070 214340 229390 289340 FALSE TRUE 168134.8617 255305.2013 255816.4623 302800.6179 238905.1211 263665.8339 262240.5762 209913.8041 203350.6089 269742.7441 0.623315605 0.946476622 0.948371987 1.122553339 0.885677655 0.97747146 0.972187693 0.778200002 0.753868689 1 18.04122463 -0.784090736 7.381904714 0.999993035 0.897463938 0.055272832 0.13333554 0 0 0.129947697 0.030628966 0.164402821 0.784090736 -0.102529097 PVSSAASVYAGAGGS(ph)GSR ddPTM_BT-474_Pertuzumab_2h_R1 5 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSS(0.001)AAS(0.049)VYAGAGGS(0.948)GS(0.003)R;PVSSAASVYAGAGGS(0.994)GS(0.006)R;PVSSAASVYAGAGGS(0.977)GS(0.023)R;PVSSAASVYAGAGGS(0.947)GS(0.053)R;PVSSAASVYAGAGGS(0.983)GS(0.017)R 326.82 9.10E-75 4934960000 2103210 1648400 1491800 1397137 1590280 1565900 1642230 1855610 1988900 1929270 TRUE FALSE 2021014.228 1601389.246 1761401.445 1469243.408 1641432.8 1597563.571 1662328.102 1817291.005 1763128.41 1798598.824 1.123660374 0.890353771 0.97931869 0.816882224 0.912617521 0.88822674 0.924235065 1.010392635 0.980278863 1 20.778442 -0.782985744 7.320427245 0.999999203 0.943823077 0.036613835 0.079235913 0 0 0.074712476 0.017609899 0.16482165 0.782985744 -0.056176126 SDHTLTS(ph)PGGGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDHTLTSPGGGGK 13 0 C9J0Q5;Q9Y618;Q9Y618-4 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SDHT(0.004)LT(0.277)S(0.719)PGGGGK 197.25 1.42E-07 367910000 548380 622170 512790 633220 579640 655150 667550 435670 654010 707240 TRUE FALSE 526948.7033 604426.3208 605462.56 665900.5601 598284.647 668397.5819 675719.6766 426673.2623 579769.5266 659338.0049 0.799208751 0.916716944 0.91828858 1.009953249 0.907402034 1.013740414 1.024845635 0.64712372 0.879320656 1 19.33065872 -0.781539244 4.36064419 1.000000471 0.896416081 0.067541281 0.107726162 6438368.969 2952980.138 28.40416932 0.027369827 0.165371534 0.781539244 -0.10358439 LGVDLDAQTWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGVDLDAQTWR 11 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 145.99 8.37E-05 246730000 266090 357880 268630 413270 298410 346950 357080 297070 329270 376540 FALSE TRUE 255690.9086 347673.6128 317177.4166 434598.9142 308008.6287 353965.5667 361450.0519 290935.4007 291892.65 351036.6104 0.728388154 0.990419809 0.903545121 1.238044413 0.877425942 1.008343735 1.02966483 0.82878934 0.831516262 1 18.42126197 -0.781361998 7.461631815 0.999999968 0.942851734 0.017940999 0.133586355 0 0 0.12590029 0.029674983 0.16543904 0.781361998 -0.057148234 DVLSNAHIQNELER ddPTM_BT-474_Pertuzumab_2h_R1 2 DVLSNAHIQNELER 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 0 ; 220.6 4.58E-12 841860000 509460 606710 479660 608250 559240 575990 567950 548970 580200 628300 FALSE TRUE 489549.74 589407.2248 566345.232 639641.8554 577228.4625 587636.9124 574900.742 537633.5777 514338.1284 585744.6814 0.835773257 1.006252798 0.966880708 1.09201479 0.985460869 1.003230471 0.981486918 0.917863354 0.878092699 1 19.15991242 -0.779356172 7.509106416 0.999994252 0.967274889 0.02240211 0.068258797 0 0 0.066168394 0.01559604 0.166204902 0.779356172 -0.032719363 STAGDTHLGGEDFDNR ddPTM_BT-474_Pertuzumab_2h_R1 12 STAGDTHLGGEDFDNR 16 0 P11142;E9PKE3;P11142-2;E9PN89;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;;;;;;;;;; 197.88 4.22E-11 1.64311E+11 36900240 40835910 33883370 41621890 35878620 29832410 42821460 37397650 43262510 46379440 FALSE TRUE 35458137.83 39671309.83 40006848.69 43770000.73 37032688.4 30435641.77 43345521.84 36625375.46 38351531.24 43238119.22 0.820066609 0.917507758 0.925268014 1.012301218 0.856482406 0.703907624 1.00248398 0.847062178 0.886984261 1 25.36580043 -0.778196532 4.034760149 1.000001277 0.887584461 0.139940542 0.084839388 19498076.57 44311352.4 404.0136416 0.020456314 0.16664929 0.778196532 -0.112416816 GVVDSDDLPLNVSR ddPTM_BT-474_Pertuzumab_2h_R1 5 GVVDSDDLPLNVSR 14 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 290.61 4.26E-43 5424280000 4102210 4953040 4047580 5135330 4548180 4974820 4627200 4504740 4972650 4868570 FALSE TRUE 3941891.098 4811784.149 4779067.744 5400364.997 4694476.34 5075414.269 4683829.058 4411715.545 4408175.619 4538817.417 0.868484174 1.060140496 1.052932362 1.189817633 1.03429504 1.118223934 1.031949212 0.971996698 0.971216776 1 22.11388502 -0.77794501 7.041897752 0.999999686 1.036958167 0.012662753 0.082292361 0 0 0.080472549 0.018967562 0.166745833 0.77794501 0.036958481 DKTIIMWK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKTIIMWK 8 1 P63244;D6RHH4;D6RAC2;D6REE5;E9PD14;D6RAU2;D6RBD0;D6R909;D6RGK8 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 143.03 0.00055443 3151500000 3091500 2960900 2663400 2417900 2606000 2384100 3090900 3048800 3315300 3213500 FALSE TRUE 2970680.762 2876458.031 3144735.627 2542688.109 2689824.357 2432308.135 3128727.359 2985841.215 2938961.043 2995846.783 0.991599697 0.960148579 1.049698418 0.8487377 0.897851109 0.811893368 1.044354931 0.996660187 0.981011799 1 21.51453241 -0.775138943 7.867498999 1.000003537 0.954788317 0.033419813 0.074674216 0 0 0.075037433 0.017686492 0.167826701 0.775138943 -0.045215221 S(ph)RTPLISR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTPLISR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.923)RT(0.077)PLISR 93.839 0.0065309 169660000 54651 77400 59118 89496 88757 72492 85342 54498 72651 85947 TRUE FALSE 52515.1785 75192.62778 69801.93767 94114.89929 91611.94951 73957.83791 86386.44092 53372.59726 64403.96306 80125.73314 0.655409647 0.938432946 0.871155058 1.17459018 1.143352403 0.923022293 1.078136044 0.666110564 0.803786256 1 16.28997803 -0.774799005 4.246986938 1.000000465 0.919306099 0.020707126 0.170407153 40358950.02 102004590.9 343.1804334 0.04340147 0.167958116 0.774799005 -0.080694366 WTELAGCTADFR ddPTM_BT-474_Pertuzumab_2h_R1 3 WTELAGCTADFR 12 0 Q12907;D6RBV2;D6RDX1;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ;; 125.7 0.00069939 364140000 455490 569360 398520 564920 426560 307009 542200 585450 537390 537600 FALSE TRUE 437688.9472 553122.4103 470541.429 594075.5889 440280.6898 313216.9323 548835.6058 573360.2529 476387.7401 501187.8732 0.873303148 1.103622893 0.938852383 1.185335122 0.878474347 0.624949144 1.095069604 1.144002646 0.950517292 1 18.93499198 -0.769647346 5.274565171 1.000000003 0.989339574 0 0.157850087 7.03E-09 1.33E-09 0.157284331 0.03707226 0.169962321 0.769647346 -0.01066043 GHWDDVFLDSTQR ddPTM_BT-474_Pertuzumab_2h_R1 3 GHWDDVFLDSTQR 13 0 Q9H6T3;Q9H6T3-3 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 0 ;; 213.99 1.51E-09 648671000 835850 837960 757400 923250 891580 847210 877970 808090 902150 946670 FALSE TRUE 803184.0579 814062.2012 894279.0283 970899.0431 920258.4804 864341.1667 888714.8595 791402.6591 799741.7141 882551.1977 0.910070781 0.922396574 1.013288556 1.100105065 1.04272532 0.979366601 1.006983914 0.896721529 0.906170335 1 19.75132045 -0.768821361 7.492346732 1.000002297 0.97621244 0.013154228 0.063718431 0 0 0.068405636 0.016123363 0.170285881 0.768821361 -0.023789857 IPEVPLHDT(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 IPEVPLHDTPER 12 0 Q96AY2;Q96AY2-2 Q96AY2 EME1 Crossover junction endonuclease EME1 1 IPEVPLHDT(1)PER;IPEVPLHDT(1)PER 107.5 0.0066511 273720000 104416 113399 96164 135550 119606 128447 115605 96268 115505 126787 TRUE FALSE 100335.3073 110164.9715 113542.974 142545.7517 123453.2356 131044.2863 117019.8086 94280.03216 102393.3566 118199.6036 0.848863315 0.932024882 0.960603678 1.205974872 1.044447121 1.108669424 0.990018621 0.797634081 0.866274958 1 16.85086567 -0.768339664 4.634275368 1.000000041 0.972065722 0.004819397 0.117246321 16665172.41 3596068.833 9.1249781 0.03062872 0.170474857 0.768339664 -0.027934319 SMS(ph)PTSTPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SMSPTSTPK 9 0 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 SMS(0.929)PT(0.06)S(0.011)TPK;SMS(0.894)PT(0.077)S(0.028)T(0.001)PK;SMS(0.763)PT(0.231)S(0.006)TPK 147.19 9.76E-05 756900000 1209480 1152600 961280 1070800 1137480 1185720 1268500 1149840 1454070 1468830 TRUE FALSE 1162212.184 1119728.977 1135004.68 1126064.116 1174068.077 1209696.071 1284024.282 1126095.402 1289010.07 1369344.836 0.848735946 0.817711468 0.828866951 0.822337871 0.857394023 0.8834123 0.937692427 0.822360718 0.941333429 1 20.38505437 -0.767392399 0.169604683 1.127873954 0.791638386 0.681683767 0.033837951 11.95141872 0.486004592 0.88509931 0.170427976 0.170847096 0.767392399 -0.336235568 SKPELPPGLSPEATAPVT(ph)PSRPEGGEPGLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKPELPPGLSPEATAPVTPSRPEGGEPGLSK 31 2 Q9BRP8-2;Q9BRP8 Q9BRP8-2 WIBG Partner of Y14 and mago 1 SKPELPPGLSPEAT(0.025)APVT(0.918)PS(0.053)RPEGGEPGLS(0.003)K;SKPELPPGLSPEAT(0.007)APVT(0.842)PS(0.149)RPEGGEPGLS(0.002)K 123.4 0.00035729 237510000 316970 261280 249280 218950 242460 228100 233520 354800 287720 267680 TRUE FALSE 304582.462 253828.5502 294330.4412 230250.0357 250258.9461 232712.3383 236377.8876 347473.256 255059.2318 249549.7952 1.220527798 1.017145897 1.179445733 0.92266169 1.002841721 0.932528669 0.947217318 1.392400486 1.022077504 1 17.92896819 -0.767241223 4.749229204 0.999999891 1.079638649 0.018223109 0.143026603 1.85E-05 47750987.38 15.13287436 0.035313695 0.170906577 0.767241223 0.079638757 AENSHNAGQVDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 AENSHNAGQVDTR 13 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;E9PDP5;D6RHC4;Q8IWZ3-5;Q8IWZ3-3;Q8IWZ3-2 Q8IWZ3-6 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 0 ; 171.21 2.55E-05 367700000 285197 296652 267109 332567 316997 309942 294160 286777 320788 334978 FALSE TRUE 274051.1859 288191.7754 315381.5381 349730.8227 327193.4964 316209.2396 297760.0181 280854.9547 284373.4911 312289.6417 0.877554518 0.922834884 1.009900733 1.119892485 1.047724461 1.012551162 0.953473886 0.899341244 0.910608144 1 18.25252519 -0.766605116 8.282241881 1 0.973697561 0.01273373 0.071709023 0 0 0.077996076 0.018383851 0.171157086 0.766605116 -0.026302439 S(ph)SSRPCSPVHHHEGHAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSRPCSPVHHHEGHAK 17 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 1 S(0.265)S(0.265)S(0.265)RPCS(0.205)PVHHHEGHAK 59.469 0.030769 219630000 39826 57819 40734 59200 57784 60289 56755 7753.3 61204 22892 TRUE FALSE 38269.55589 56170.05873 48095.53992 62255.31909 59642.67484 61508.08489 57449.58467 7593.191646 54256.37851 21341.50445 1.793198599 2.631963406 2.253615252 2.917100771 2.794679962 2.882087579 2.69191822 0.355794582 2.54229399 1 14.38137426 -0.764468912 5.318686549 0.999999665 2.249854662 0.220970836 0.732443238 3.27E-06 7.54E-07 0.791733659 0.186613363 0.172001046 0.764468912 1.249854997 ERS(ph)PYKR ddPTM_BT-474_Pertuzumab_2h_R1 3 ERSPYKR 7 2 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 ERS(1)PYKR;ERS(1)PYKR;ERS(1)PYKR 91.087 0.0086937 4368780000 2938800 2823370 2103060 2224330 2371220 2467750 2464140 2836240 3132560 2770080 TRUE FALSE 2823948.447 2742850.252 2483129.724 2339127.938 2447492.445 2517649.596 2494296.882 2777670.653 2776964.922 2582460.014 1.093511006 1.06210754 0.961536562 0.905775085 0.947736821 0.974903612 0.965860795 1.075590963 1.075317684 1 21.30031458 -0.764362891 7.891262725 0.999991687 1.004912456 0.000173245 0.06203034 0 0 0.065936495 0.015541381 0.17204304 0.764362891 0.004920769 LHIIEVGTPPTGNQPFPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHIIEVGTPPTGNQPFPK 18 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 262.23 7.94E-31 1916360000 2369240 2431680 2034210 2234740 2241740 2492340 2515250 1857410 2842800 2991200 FALSE TRUE 2276647.481 2362330.867 2401836.998 2350075.199 2313847.603 2542736.822 2546032.382 1819053.834 2520097.262 2788603.36 0.816411367 0.847137639 0.861304635 0.842742727 0.829751422 0.911831657 0.913013453 0.652317164 0.903713055 1 21.41111131 -0.761864211 8.597342081 1 0.834104181 0.298421757 0.071747119 0 0 0.072609715 0.017114274 0.17303573 0.761864211 -0.165895819 YRDQFTDQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 YRDQFTDQQK 10 1 E9PDF6;O43795;O43795-2;H7C2Y7 E9PDF6 MYO1B Unconventional myosin-Ib 0 ; 197.73 2.82E-07 841080000 800750 910840 644550 753760 649500 542880 848940 918260 843540 844590 FALSE TRUE 769455.8047 884863.735 761034.5229 792661.6439 670391.7574 553857.4056 859329.5817 899297.6101 747784.8756 787385.167 0.977229235 1.123800361 0.966533985 1.006701265 0.851415274 0.703413563 1.091371311 1.142131764 0.949706582 1 19.58671001 -0.760098949 7.870169617 0.999996651 0.988365578 0 0.124491442 0 0 0.13116526 0.030915948 0.173740494 0.760098949 -0.011631074 LDKESYPVFYLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDKESYPVFYLFR 13 1 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 121.76 0.00022153 171290000 104130 109640 91986 86847 73952 72080 109110 106000 102200 122870 FALSE TRUE 100060.4845 106513.1745 108609.9164 91329.18408 76330.73324 73537.50699 110445.3208 103811.063 90598.68446 114547.9055 0.873525221 0.929857025 0.948161522 0.797301214 0.666365159 0.641980372 0.964184551 0.906267666 0.790923973 1 16.80559155 -0.759249609 8.004745449 0.999999999 0.840314205 0.174496672 0.106925089 0 0 0.113207097 0.026683169 0.174080606 0.759249609 -0.159685793 APAASEGNHTDGAEEAAGSCAQAPSHS(ph)PPNKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 APAASEGNHTDGAEEAAGSCAQAPSHSPPNKPK 33 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 APAASEGNHTDGAEEAAGSCAQAPS(0.022)HS(0.978)PPNKPK 164.58 2.07E-14 683590000 129060 130180 116430 105610 110680 122160 134520 108800 154560 151890 TRUE FALSE 124016.1925 126467.3939 137471.491 111060.5448 114240.1227 124630.1589 136166.296 106553.242 137014.9968 141602.355 0.875806003 0.893116459 0.970827717 0.784312837 0.80676711 0.880141851 0.961610391 0.752482132 0.967603941 1 17.11148573 -0.759040762 8.875230648 1 0.87046645 0.197397066 0.073383098 0 0 0.068978425 0.016258371 0.17416434 0.759040762 -0.12953355 HYFQNTQGLIFVVDSNDR ddPTM_BT-474_Pertuzumab_2h_R1 4 HYFQNTQGLIFVVDSNDR 18 0 P61204;F5H423;F5H0C7;P84077;P84085;C9J1Z8;P18085;C9JPM4;C9JAK5 P61204;P84077;P84085;P18085 ARF3;ARF1;ARF5;ARF4 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 ;;; 315.96 2.53E-61 9205070000 3413213 3610595 3546258 4656138 4171874 4114873 4333495 2864912 4427683 4656015 FALSE TRUE 3279820.862 3507624.366 4187145.707 4896441.84 4306066.116 4198078.551 4386529.608 2805750.566 3925070.988 4340658.957 0.755604367 0.808085685 0.964633653 1.128041131 0.992030509 0.967152359 1.01056767 0.646388162 0.904256941 1 22.04948264 -0.757000508 7.076332173 1.000000049 0.903390155 0.040092216 0.132137404 0 0 0.140784615 0.033183252 0.174984464 0.757000508 -0.096609894 IHIDLPNEQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 IHIDLPNEQAR 11 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;;; 185.99 4.22E-06 1370850000 1004870 1121660 973430 1270170 1181020 1195630 1215000 824670 1221400 1271240 FALSE TRUE 965598.5695 1089671.355 1149350.455 1335723.626 1219008.581 1219806.458 1229869.533 807640.2763 1082751.793 1185137.782 0.81475638 0.91944698 0.969803235 1.127061887 1.028579629 1.029252865 1.037743924 0.681473739 0.913608366 1 20.17662336 -0.755742422 6.050554887 1.000000002 0.941656274 0.015632309 0.120294486 2.90E-09 6.40E-10 0.129883894 0.030613927 0.175492103 0.755742422 -0.058343728 EEKDGELNVLDDILTEVPEQDDELYNPESEQDKNEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEKDGELNVLDDILTEVPEQDDELYNPESEQDKNEK 36 2 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ;; 157.74 5.55E-15 135159000 251667.2 168713.1 124067.5 88431.6 151299.3 143392.1 155280.4 200892.6 232194 168656 FALSE TRUE 241831.7676 163901.5676 146489.2571 92995.56547 156165.9794 146291.5865 157180.768 196744.0976 205836.3106 157232.7789 1.538049313 1.042413476 0.931671234 0.591451516 0.993215158 0.930414049 0.999669211 1.251291868 1.309118315 1 17.26254249 -0.754622854 8.525866895 0.999998821 1.052188371 0.003878158 0.242833177 0 0 0.244165501 0.057550361 0.175945087 0.754622854 0.052189549 ENAEQGEVDMESHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ENAEQGEVDMESHR 14 0 P14209-3;P14209 P14209-3 CD99 CD99 antigen 0 ;;; 249.73 3.57E-18 2379380000 1461790 1923620 1352470 2185940 1456530 1722930 1972510 1808440 1791470 1600700 FALSE TRUE 1404661.631 1868760.241 1596891.415 2298756.625 1503380.61 1757768.825 1996650.167 1771095.082 1588109.836 1492283.163 0.941283575 1.252282601 1.070099465 1.540429244 1.007436556 1.177905687 1.337983445 1.1868358 1.064214805 1 20.50908988 -0.753628327 7.464336863 0.99999591 1.187711993 0.087756095 0.165398828 0 1.65E-18 0.148001454 0.034884277 0.176348461 0.753628327 0.187716083 AIVEYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AIVEYR 6 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 99.511 0.090068 272180000 371030 438090 370020 450270 399960 435950 414810 429660 410550 439420 FALSE TRUE 356529.7374 425596.1021 436890.8451 473508.4887 412825.0766 444765.2077 419886.5689 420787.3709 363946.0852 409657.692 0.870311346 1.038906654 1.066477827 1.155863781 1.007731784 1.085699637 1.024969327 1.027168241 0.888415114 1 18.64405938 -0.752145036 7.635500853 1 1.026574595 0 0.081129549 0 0 0.076529505 0.018038177 0.176951792 0.752145036 0.026574595 LEEHQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEEHQAR 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 ; 142.64 0.0033029 170860000 501950 512650 432030 502130 533120 492690 499680 484090 539120 561020 FALSE TRUE 482333.2391 498029.7239 510107.4315 528044.9895 550268.289 502652.5294 505795.2333 474093.3723 477921.3578 523021.6157 0.922205172 0.952216331 0.975308508 1.009604524 1.052094737 0.961054982 0.967063728 0.90645082 0.913769801 1 18.99651105 -0.749548169 7.50003988 0.999993956 0.962397431 0.067803874 0.042045369 0 0 0.045397124 0.010700205 0.178013046 0.749548169 -0.037596525 VERPPS(ph)PFSMAPQASLPPVPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VERPPSPFSMAPQASLPPVPPR 22 1 P22681;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 VERPPS(0.997)PFS(0.003)MAPQASLPPVPPR;VERPPS(0.976)PFS(0.024)MAPQASLPPVPPR 148.9 4.07E-08 385380000 95907 82958 72610 89585 86510 91557 84795 81328 97011 97403 TRUE FALSE 92158.84841 80592.11906 85732.2422 94208.49259 89292.67272 93408.34527 85832.74658 79648.54838 85998.71798 90805.80805 1.014900372 0.887521633 0.944127298 1.037472102 0.98333658 1.028660471 0.945234104 0.87713055 0.947061866 1 16.47049696 -0.74387136 6.695537946 1.000000002 0.958003612 0.036669132 0.052124974 8.10E-10 0 0.054365554 0.012814084 0.180355188 0.74387136 -0.041996389 SEAHLTELLEEICDR ddPTM_BT-474_Pertuzumab_2h_R1 8 SEAHLTELLEEICDR 15 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;;;;;; 273.61 1.87E-33 2731534000 1049632 1441549 1086219 1467276 1226557 1494724 1233059 1149900 1338599 1513168 FALSE TRUE 1008611.221 1400437.434 1282522.936 1543002.29 1266010.32 1524948.343 1248149.545 1126154.163 1186646.853 1410679.784 0.714982403 0.992739423 0.909152418 1.093800527 0.897446986 1.081002479 0.884785874 0.79830602 0.841187963 1 20.42795911 -0.743380055 6.626155224 1 0.914924944 0.051432657 0.11220277 8.13E-10 1.23E-10 0.109097146 0.025714444 0.180559334 0.743380055 -0.085075057 AEASWDSAVHGCPQLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEASWDSAVHGCPQLSR 17 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 99.663 0.0015255 278830000 56688 68893 49215 64347 58108 61826 64319 67127 60569 54127 FALSE TRUE 54472.57029 66928.23909 58109.24528 67667.95638 59977.09659 63076.16408 65106.15516 65740.80399 53693.46105 50460.93008 1.079499926 1.326337802 1.151569049 1.34099701 1.188584842 1.250000029 1.290228996 1.30280603 1.064060075 1 15.62287918 -0.742428977 7.842897674 1.000011288 1.234224962 0.322502878 0.094754767 0 0 0.083314649 0.019637451 0.180955181 0.742428977 0.234213674 KELQAEATVSGS(ph)PEAPGTNVVSEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KELQAEATVSGSPEAPGTNVVSEPR 25 1 Q9BZV1-2;Q9BZV1;K7EJ02 Q9BZV1-2 UBXN6 UBX domain-containing protein 6 1 KELQAEATVS(0.059)GS(0.941)PEAPGTNVVSEPR;KELQAEATVS(0.015)GS(0.985)PEAPGTNVVSEPR 121.83 0.00010944 710610000 158523 148007 121108 147541 151069 156517 144073 143478 164603 165493 TRUE FALSE 152327.7459 143785.9853 142994.9096 155155.6087 155928.2716 159681.881 145836.2085 140515.1292 145917.9575 154284.0117 0.98732036 0.931956485 0.926829087 1.005649302 1.010657358 1.034986576 0.945245116 0.910756258 0.945774976 1 17.23522904 -0.740636553 5.66009693 1.000000003 0.963954547 0.057656653 0.039273259 1.27E-09 3.37E-10 0.042660663 0.010055214 0.181703564 0.740636553 -0.036045456 AVGS(ph)PLCVPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVGSPLCVPAR 11 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 AVGS(1)PLCVPAR 119.74 0.00057185 222470000 69725 76366 62925 73459 62452 63598 76214 79112 68299 84186 TRUE FALSE 67000.06991 74188.11645 74296.94726 77250.22779 64460.8253 64883.99513 77146.72973 77478.30955 60545.98385 78484.00723 0.853677995 0.945264125 0.946650788 0.984279862 0.821324338 0.826716135 0.982961146 0.987185954 0.771443584 1 16.26011108 -0.738775078 5.124261185 1.00000003 0.911809823 0.120360265 0.075392049 2.63E-08 6.51E-09 0.073403264 0.017301309 0.182484055 0.738775078 -0.088190207 AASDS(ph)NPAGPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AASDSNPAGPLR 12 0 Q9BUU2-2;Q9BUU2 Q9BUU2-2 METTL22 Methyltransferase-like protein 22 1 AAS(0.323)DS(0.677)NPAGPLR 74.733 0.037459 296980000 188060 222110 190780 234200 202810 198480 215850 220080 225750 249980 TRUE FALSE 180710.4073 215775.6403 225258.1899 246287.0901 209333.5678 202493.4016 218491.6369 215535.2711 200123.8064 233048.6319 0.775419301 0.925882458 0.966571604 1.05680556 0.898239848 0.868889038 0.937536664 0.924851046 0.858721224 1 17.83027152 -0.738089507 0.007015464 1.897953161 1.64E-06 0.079860567 0.071383214 38101.75247 56.96228123 7993.197606 7421.811311 0.182772349 0.738089507 -1.897951523 LVEAEVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEAEVHR 8 0 F8VZX1;H0YIC9;F8VYY9;P54619-2;P54619;P54619-3;H0YHF8 F8VZX1 PRKAG1 5-AMP-activated protein kinase subunit gamma-1 0 ; 166.68 0.00031706 452130000 419070 466410 409630 469200 474210 461420 465180 425110 480830 498110 FALSE TRUE 402692.2811 453108.4435 483659.2532 493415.4682 489463.3953 470750.2285 470873.012 416331.3299 426248.1942 464372.566 0.867175002 0.975743351 1.041532788 1.062542244 1.054031679 1.013733935 1.013998342 0.896545921 0.917901326 1 18.82492322 -0.736779962 6.008709828 0.999999999 0.984432224 0.00574608 0.064740709 5.09E-10 8.47E-11 0.068331682 0.016105932 0.183324301 0.736779962 -0.015567775 NPHPSSAFLNLIGFVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NPHPSSAFLNLIGFVSR 17 0 P53004;C9J1E1 P53004 BLVRA Biliverdin reductase A 0 ; 189.55 3.49E-10 724020000 730990 1094830 893880 1167440 1011200 1086570 978600 899430 929460 1226100 FALSE TRUE 702422.1026 1063606.52 1055424 1227691.718 1043726.166 1108541.19 990576.3995 880856.4562 823951.5974 1143055.155 0.614512869 0.930494487 0.923336023 1.074044164 0.913102191 0.969805512 0.866604201 0.770615882 0.720832756 1 20.12446359 -0.736237875 7.431319682 1.00001345 0.871868684 0.092175988 0.125529412 0 0 0.124654719 0.029381399 0.18355327 0.736237875 -0.128144766 NPHQALLHTANRPEDECVGEGLACHQLCAR ddPTM_BT-474_Pertuzumab_2h_R1 3 NPHQALLHTANRPEDECVGEGLACHQLCAR 30 1 P04626-5;P04626-4;P04626;B4DTR1;J3QLU9;P04626-6;F5H1T4 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ;; 319.31 4.75E-93 2622840000 304329 567610 232330 652940 286397 326679 656660 253887 547010 351540 FALSE TRUE 292435.4862 551422.3185 274317.1992 686638.3116 295609.2196 333284.6732 664696.4015 248644.1447 484915.7181 327729.8827 0.892306444 1.682551234 0.837022236 2.09513489 0.901990435 1.016949295 2.028183686 0.758686217 1.479620089 1 18.3221477 -0.735512841 8.202781123 1.00002936 1.293054798 0.034370297 0.474714793 0 0 0.414584888 0.097718595 0.183859959 0.735512841 0.293025438 SYELPDGQVITIGNER ddPTM_BT-474_Pertuzumab_2h_R1 14 SYELPDGQVITIGNER 16 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;Q9BYX7;P63261;P68133;P68032;P63267;P62736;Q6S8J3;A5A3E0 P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F" 0 ;;;;;;;;;;;;; 310.29 2.32E-45 57536240000 3381541 3689580 3051218 3714202 3453521 3747933 3592012 3716200 3580937 3821970 FALSE TRUE 3249386.639 3584356.791 3602640.967 3905892.41 3564606.639 3823718.773 3635972.117 3639459.171 3174444.044 3563104.568 0.911953769 1.005964524 1.011096054 1.096204823 1.000421563 1.073142452 1.020450579 1.021429235 0.89092082 1 21.76470339 -0.734939485 5.631132502 1.000000001 1.010161939 0 0.059648458 8.32E-10 4.29E-19 0.055829215 0.013159071 0.184102852 0.734939485 0.010161939 QLAPIWDK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLAPIWDK 8 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 124.23 0.0030562 1108710000 2159680 2419400 1993710 2018220 2014460 1813120 2290000 2233990 2558300 2421500 FALSE TRUE 2075277.318 2350401.081 2354017.747 2122380.576 2079256.935 1849782.529 2318025.705 2187857.326 2267892.509 2257489.648 0.919285419 1.04115697 1.042759044 0.940150746 0.92104827 0.819398011 1.026815652 0.969154976 1.004608155 1 21.10628794 -0.733484875 7.696230142 1 0.966132102 0.024748641 0.065654813 0 0 0.065195286 0.015366676 0.184720513 0.733484875 -0.033867897 DYPSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 DYPSSR 6 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;; 138.07 0.028989 837390000 577540 569480 496460 596320 614850 578930 550820 601430 579220 594270 FALSE TRUE 554969.0983 553238.988 586181.3657 627096.1467 634627.2086 590636.3613 557561.0999 589010.2603 513469.3739 554019.5636 1.001713901 0.998591069 1.058051744 1.131902532 1.145496026 1.066092969 1.006392439 1.063157872 0.926807296 1 19.0795774 -0.732697641 6.097127967 0.999999999 1.048950978 0.039220088 0.061869366 0 3.03E-10 0.062056131 0.01462677 0.185055654 0.732697641 0.048950979 VQEFEHINGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VQEFEHINGR 10 0 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 0 ;; 110.39 0.0018927 638550000 377980 421260 374110 444590 442390 420850 391120 416400 429560 445110 FALSE TRUE 363208.1237 409246.0773 441719.999 467535.3432 456619.8761 429359.8753 395906.6436 407801.1945 380798.1497 414962.3032 0.875279805 0.98622471 1.064482233 1.126693532 1.100388813 1.034696096 0.954078576 0.982742749 0.91766926 1 18.66262076 -0.731782564 7.51901147 1.00000018 1.009088099 0 0.075097311 0 0 0.077917725 0.018365384 0.185445985 0.731782564 0.00908792 S(ph)PEPEATLTFPFLDK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPEPEATLTFPFLDK 15 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(0.999)PEPEAT(0.001)LTFPFLDK;S(1)PEPEATLTFPFLDK;S(0.996)PEPEAT(0.004)LTFPFLDK;S(1)PEPEATLTFPFLDK 169.3 1.26E-06 2190170000 960046 916400 846092 918782 926936 800859 939246 1050630 980160 926255 TRUE FALSE 922526.3409 890265.1692 998999.6456 966200.4491 956751.7383 817052.9177 950740.7735 1028934.123 868896.346 863518.9238 1.06833367 1.030973549 1.15689375 1.118910568 1.107968467 0.946189939 1.101007456 1.191559438 1.006227336 1 19.71986827 -0.730261801 5.094932421 0.99999997 1.088209405 0.102304514 0.068889126 2.39E-08 5.99E-09 0.068310579 0.016100953 0.186096497 0.730261801 0.088209435 DGMEYPFIGEGEPHVDGEPGDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGMEYPFIGEGEPHVDGEPGDLR 23 0 Q9UBS4;H7C2Y5 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ;; 216.44 2.55E-32 580333000 299149 351562 288146 325702 305779 347825 338630 308181 358199 369267 FALSE TRUE 287457.9264 341535.796 340220.392 342511.5193 315614.6592 354858.2598 342774.2552 301816.9547 317537.7512 344256.2172 0.835011576 0.992097685 0.988276682 0.994931978 0.916801625 1.030796953 0.995695177 0.87672187 0.922387848 1 18.39312318 -0.729449395 5.439887098 1.000000006 0.951844904 0.060229599 0.058608511 4.22E-09 1.01E-09 0.056670399 0.013357339 0.186444941 0.729449395 -0.048155102 MLLVDELR ddPTM_BT-474_Pertuzumab_2h_R1 4 MLLVDELR 8 0 P18085;C9JPM4;C9JAK5;U3KQF2 P18085 ARF4 ADP-ribosylation factor 4 0 ;;; 135.77 0.001907 508460000 793460 1051920 871060 1197680 1111120 1042190 1067760 981990 944660 1107250 FALSE TRUE 762450.706 1021920.272 1028479.919 1259492.408 1146860.184 1063263.796 1080827.566 961711.5633 837426.1571 1032254.971 0.738626335 0.98998823 0.996342907 1.220136927 1.111024132 1.030039889 1.047054842 0.931660869 0.811259021 1 19.97736794 -0.729204644 5.014248013 1.000000001 0.996546277 0 0.131102298 1.94E-09 5.81E-10 0.130297063 0.030711299 0.186550044 0.729204644 -0.003453724 KGADSLEDFLYHEGYACTSIHGDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGADSLEDFLYHEGYACTSIHGDR 24 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 206.94 3.28E-25 2010980000 1083108 1418500 1126482 1404083 1271022 1515360 1379050 718700 1431794 1637690 FALSE TRUE 1040778.942 1378045.769 1330062.356 1476547.892 1311905.577 1546001.617 1395927.226 703858.5938 1269262.748 1526767.798 0.681687774 0.902590277 0.871162175 0.967107044 0.859269877 1.012597737 0.914302246 0.461012208 0.831339742 1 20.54204923 -0.728256917 5.08779629 0.999999815 0.823331062 0.096140988 0.150343777 1.13E-07 2.84E-08 0.161740443 0.038122575 0.186957582 0.728256917 -0.176668753 AHFNLDESGVLSLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHFNLDESGVLSLDR 15 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 206.95 3.64E-09 759490000 289620 337220 312090 366930 342870 366910 386490 233700 413700 441110 FALSE TRUE 278301.3302 327602.8158 368491.6054 385867.3013 353898.7249 374329.1716 391219.9802 228874.0133 366738.5104 411233.2268 0.676748162 0.796635083 0.896064767 0.938317422 0.860579111 0.910260035 0.951333586 0.556555255 0.891801748 1 18.64959731 -0.727780296 8.335135992 1 0.823753622 0.151197671 0.119097198 0 0 0.121883834 0.028728295 0.187162873 0.727780296 -0.176246378 LLSPLS(ph)SAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLSPLSSAR 9 0 A0A087WZ13;Q8IY67-2;E9PAU2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 LLS(0.461)PLS(0.539)SAR 134.59 0.00025657 244920000 421900 426330 367220 390980 372880 361260 423950 439240 450570 458120 TRUE FALSE 405411.6816 414171.4858 433584.8228 411158.5247 384874.0238 368564.9247 429138.4269 430169.5405 399423.1825 427091.1243 0.949239304 0.969749691 1.01520448 0.962695081 0.901152007 0.862965545 1.004793597 1.007207867 0.935217708 1 18.70418439 -0.726546735 6.005123263 1.000000001 0.960045908 0.070408093 0.04582201 7.18E-10 1.20E-10 0.048198101 0.011360401 0.187695243 0.726546735 -0.039954092 LTTTGQVTS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 5 LTTTGQVTSPVK 12 0 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.002)S(0.998)PVK;LTTTGQVT(0.002)S(0.998)PVK;LTTTGQVT(0.093)S(0.907)PVK;LTTTGQVTS(1)PVK;LTTTGQVT(0.018)S(0.982)PVK 250.78 2.53E-17 15315110000 10213300 9210600 8418550 9032400 8375500 6861180 9941800 10452100 9659100 11147600 TRUE FALSE 9814152.945 8947922.706 9939969.255 9498563.246 8644905.564 6999917.761 10063470.72 10236260.48 8562639.462 10392563.12 0.944343838 0.860992866 0.956450217 0.91397696 0.831835752 0.673550661 0.968333856 0.984960145 0.82391989 1 23.30904817 -0.723590472 5.539851436 1.000000009 0.889633338 0.130634099 0.088601431 1.07E-08 2.54E-09 0.08980255 0.021166662 0.188977252 0.723590472 -0.110366672 DKLSELQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKLSELQLR 9 1 Q9BVK6 Q9BVK6 TMED9 Transmembrane emp24 domain-containing protein 9 0 ; 164.64 5.66E-05 1758820000 1960470 2411100 1928960 2192500 1643400 1129110 2462900 2427300 2588900 2328700 FALSE TRUE 1883852.665 2342337.789 2277565.981 2305655.188 1696261.453 1151941.378 2493041.707 2377175.407 2295018.926 2170975.075 0.867744953 1.078933524 1.049098172 1.062036692 0.781336218 0.530610135 1.148351142 1.094980516 1.057137391 1 21.04991173 -0.722766609 8.102179967 0.999836722 0.971449772 0.001925461 0.179142902 0 0 0.184070569 0.043385849 0.189336084 0.722766609 -0.028386951 FVDHVFDEQVIDSLTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 FVDHVFDEQVIDSLTVK 17 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 188.06 4.32E-10 159340000 156250 251370 120570 222180 156450 138740 191660 226980 219730 164690 FALSE TRUE 150143.5773 244201.1737 142359.6811 233646.7364 161482.3563 141545.4179 194005.5924 222292.7837 194787.1716 153535.3996 0.977908532 1.590520325 0.927210802 1.521777629 1.051759768 0.921907379 1.263588677 1.447827564 1.268679224 1 17.2282118 -0.722551847 6.187810096 0.999999997 1.234490765 0.069618521 0.234131016 9.61E-09 1.81E-09 0.215017887 0.050680201 0.189429736 0.722551847 0.234490768 ESEIIDFFLGASLKDEVLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ESEIIDFFLGASLKDEVLK 19 1 P15880;E9PQD7;E9PPT0;E9PMM9;I3L404 P15880 RPS2 40S ribosomal protein S2 0 ;; 199.76 6.19E-16 715190000 301800 276628 242484 197873 259205 254827 254722 281942 317825 289318 FALSE TRUE 290005.3223 268738.8403 286306.2528 208085.2492 267542.5642 259979.7765 257839.364 276119.7992 281746.8384 269722.2342 1.075199912 0.99635405 1.061485545 0.771479778 0.991918835 0.963879664 0.955944047 1.023719087 1.044581435 1 18.04111493 -0.719505991 7.530869638 0.999999999 0.984222742 0.001052849 0.081319747 0 0 0.077265038 0.018211544 0.190762941 0.719505991 -0.015777257 SLDGALYDDEDDDDIER ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDGALYDDEDDDDIER 17 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 0 ; 265.77 3.24E-27 316920000 143272 165260 135235 157522 184123 163445 154471 159478 174586 163077 FALSE TRUE 137672.7718 160546.9466 159674.9728 165651.7293 190045.4835 166749.9699 156361.4623 156184.7236 154767.7292 152031.6495 0.905553365 1.056010029 1.050274553 1.089587134 1.25003895 1.096810897 1.02847968 1.027317167 1.017996777 1 17.21401217 -0.718864938 8.659659754 1 1.061664967 0.042066936 0.081375757 0 0 0.082021197 0.019332582 0.19104473 0.718864938 0.061664967 NKDEVK ddPTM_BT-474_Pertuzumab_2h_R1 3 NKDEVK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 91.626 0.043483 863550000 1968860 1656760 1361880 1171170 1385750 1326490 1621850 1744060 1719040 1745980 FALSE TRUE 1891914.775 1609510.827 1608002.011 1231614.224 1430323.907 1353312.537 1641698.685 1708044.552 1523901.786 1627723.219 1.162307419 0.988811124 0.987884176 0.756648433 0.878726733 0.831414408 1.008585898 1.049345817 0.936216777 1 20.63442397 -0.715486224 8.011846827 0.999997977 0.954987517 0.014852957 0.108517647 0 0 0.110844725 0.026126352 0.192536812 0.715486224 -0.04501046 ELTIPASANVFYAMDGASHDFLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELTIPASANVFYAMDGASHDFLLR 24 0 O15211 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 0 152.07 1.00E-07 99891000 71818 94816 58308 84896 82699 84556 75433 85374 70024 94181 FALSE TRUE 69011.27316 92111.94051 68845.55265 89277.49273 85359.08844 86265.78025 76356.17162 83610.99707 62075.16908 87802.03698 0.785987154 1.049086601 0.78409972 1.016804345 0.97217663 0.982503177 0.869640093 0.952267168 0.706990079 1 16.42196679 -0.713666168 5.124231212 1.000000021 0.912457318 0.061886114 0.107765478 12606294.18 2460134.222 3.218125195 0.022981258 0.193345394 0.713666168 -0.087542703 FVEKPQVFVSNK ddPTM_BT-474_Pertuzumab_2h_R1 1 FVEKPQVFVSNK 12 1 Q9Y5P6;Q9Y5P6-2 Q9Y5P6 GMPPB Mannose-1-phosphate guanyltransferase beta 0 136.99 9.14E-05 520950000 278030 265380 245120 243830 232360 232060 286820 245700 294380 320710 FALSE TRUE 267164.2802 257811.6222 289418.6367 256414.0955 239834.0704 236752.4122 290330.189 240626.2091 260963.2165 298988.026 0.893561805 0.86228076 0.967994072 0.85760657 0.80215276 0.791845798 0.971042863 0.80480216 0.872821631 1 18.18972818 -0.707506193 17.22706328 1 0.867299303 0.301035335 0.05965292 0 0 0.056729753 0.013371331 0.196107321 0.707506193 -0.132700697 GFHCESSAHWPIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFHCESSAHWPIFK 14 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 160.56 2.74E-06 843910000 1399600 1633700 1480400 1757300 1613200 1884300 1860600 779160 1805100 2055700 FALSE TRUE 1344902.085 1587108.476 1747941.211 1847994.464 1665090.043 1922401.837 1883370.579 763070.0737 1600192.616 1916465.608 0.701761659 0.828143468 0.912065003 0.964272177 0.868833772 1.003097488 0.982731217 0.398165284 0.834970692 1 20.87001668 -0.705745546 4.566399573 1.000000221 0.820223451 0.07737518 0.168477315 5442636.769 2085808.218 11.27841113 0.043846659 0.196903962 0.705745546 -0.179776771 HKSDFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 HKSDFGK 7 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 129.47 0.0021977 6349200000 10398900 18895700 12873500 18936400 13093500 18519500 16668400 12110900 15534000 18176000 FALSE TRUE 9992499.491 18356813.14 15200027.82 19913709.87 13514664.32 18893976.98 16872392.87 11860805.68 13770645.44 16944923.33 0.589704615 1.083322289 0.89702547 1.175202123 0.797564206 1.115022866 0.995719635 0.699962192 0.812670862 1 24.01434977 -0.70405392 4.989921479 1.000000002 0.911394577 0.023216346 0.178557284 22258863.84 4460764.762 7.396822085 0.040659098 0.19767242 0.70405392 -0.088605425 DVDWGEVDYLIVDTPPGTSDEHLSVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVDWGEVDYLIVDTPPGTSDEHLSVVR 27 0 I3L3A0;I3L531;P53384-2;P53384 I3L3A0 NUBP1 Cytosolic Fe-S cluster assembly factor NUBP1 0 89.297 0.0071129 60670000 25957 34559 29917 35347 31078 35152 31353 32361 31013 37809 FALSE TRUE 24942.57174 33573.41116 35323.6674 37171.26291 32077.65209 35862.79752 31736.70739 31692.73404 27492.53426 35248.16275 0.70762757 0.95248684 1.002142087 1.054558876 0.910051747 1.017437356 0.900379053 0.899131517 0.779970702 1 15.10526044 -0.703765472 7.621991434 1 0.922400876 0.056079766 0.100674897 0 0 0.096144718 0.022661527 0.197803753 0.703765472 -0.077599124 FLEETNR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLEETNR 7 0 A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 A0A669KAX4 CUL4B Cullin-4B 0 102.72 0.019862 125510000 138970 147430 124690 163290 148030 159940 143640 143850 135610 167850 FALSE TRUE 133538.8988 143225.4407 147224.2567 171717.4165 152791.5194 163174.0964 145397.9093 140879.4472 120216.1213 156481.37 0.853385286 0.915287492 0.940842074 1.09736652 0.976419873 1.042770116 0.929170733 0.900295334 0.768245583 1 17.25563138 -0.703607567 5.415967175 1.000000006 0.941348043 0.04313617 0.087219931 5.86E-09 1.44E-09 0.08742325 0.020605856 0.197875686 0.703607567 -0.058651963 SLDLLAALPT(ph)PPHNQTEDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLDLLAALPTPPHNQTEDVR 20 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(1)PPHNQTEDVR 210.88 1.20E-21 927786000 634388 675836 568714 697620 682009 734303 647577 668221 701980 732136 TRUE FALSE 609595.4156 656561.819 671493.2708 733624.2518 703946.4389 749151.1098 655502.241 654422.0028 622294.1733 682547.7766 0.893117576 0.961928002 0.983804056 1.074832088 1.031351157 1.09758047 0.960375615 0.95879296 0.911722512 1 19.38057051 -0.702427182 8.808073164 0.999991303 0.989098759 0.002280829 0.062139332 0 0 0.063411815 0.014946308 0.198414231 0.702427182 -0.010892544 VLDAPGGGSVLVMEHMDMR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLDAPGGGSVLVMEHMDMR 19 0 Q9HA64;I3L3W5;I3L139;I3L2G3 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;;; 233.49 3.52E-25 443020000 317162 370083 304737 367019 367184 354344 367337 338704 365993 361925 FALSE TRUE 304766.9584 359528.5952 359809.7547 385960.8946 378994.8068 361509.0785 371832.5801 331709.644 324447.009 337411.4974 0.903250069 1.065549331 1.066382614 1.143887797 1.123242124 1.071418968 1.102015145 0.983101188 0.961576625 1 18.36414961 -0.701821159 5.153340182 0.99999999 1.051181336 0.033320546 0.071948573 4777189.588 927008.6919 0.615386929 0.017410421 0.198691295 0.701821159 0.051181347 LIHEDGIIRPYDR ddPTM_BT-474_Pertuzumab_2h_R1 5 LIHEDGIIRPYDR 13 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ;;;; 204.13 4.82E-08 1629765000 191487 208988 152733.7 236255 207411.1 222633.3 199949 198813.7 208223.7 221834 FALSE TRUE 184003.4763 203027.8669 180336.0771 248448.1489 214082.6664 227135.0979 202396.0357 194708.1276 184587.0185 206808.9856 0.8897267 0.981716855 0.871993432 1.201341171 1.03517101 1.098284474 0.978661711 0.941487755 0.892548348 1 17.65793934 -0.698007692 8.703376982 1 0.991194786 0.000352858 0.097219939 0 0 0.095215791 0.022442577 0.200443653 0.698007692 -0.008805214 GLVAAYSGES(ph)DS(ph)EEEQER ddPTM_BT-474_Pertuzumab_2h_R1 2 GLVAAYSGESDSEEEQER 18 0 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 2 GLVAAYSGES(1)DS(1)EEEQER;GLVAAYSGES(1)DS(1)EEEQER 321.68 1.68E-61 451450000 391970 421840 346850 458170 422110 441590 427800 413870 431560 427800 TRUE FALSE 376651.3791 409809.5362 409533.5106 481816.2086 435687.5515 450519.2524 433035.5444 405323.4399 382571.118 398824.725 0.944403282 1.027542955 1.026850857 1.208090117 1.092428639 1.129617158 1.085779084 1.016294664 0.959246241 1 18.60539533 -0.696581295 9.348207745 0.999999824 1.059019076 0.042495165 0.074820369 0 0 0.075245163 0.017735455 0.201103072 0.696581295 0.059019252 KEAYVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEAYVHK 7 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 69.598 0.038498 515760000 630270 596130 582660 530540 518270 485470 639830 575310 682190 745950 FALSE TRUE 605638.3516 579128.9561 687959.6232 557921.233 534940.6252 495286.536 647660.4309 563429.6475 604750.6512 695426.1421 0.8708881 0.832768458 0.989263391 0.802272447 0.769227087 0.712205806 0.931314473 0.810193367 0.869611616 1 19.40753778 -0.695999927 7.812570762 0.999999965 0.841428509 0.282967955 0.074894709 0 0 0.072336536 0.017049885 0.201372459 0.695999927 -0.158571457 LLVLDVDYTLFDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLVLDVDYTLFDHR 14 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 ; 216.84 5.98E-12 236570000 378720 424280 397970 475230 495550 414210 431000 391800 448320 497660 FALSE TRUE 363919.2037 412179.9498 469892.0318 499756.6773 511489.8158 422585.61 436274.7069 383709.1931 397428.5931 463953.0449 0.784388006 0.888408761 1.012800836 1.07717081 1.102460306 0.910837022 0.940342372 0.827043162 0.856613826 1 18.82361928 -0.69144343 7.486242815 1 0.935277625 0.039048761 0.098784426 0 0 0.105350364 0.024831319 0.203496325 0.69144343 -0.064722375 AYPVSGCFDYLSEDLPDTIHIGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AYPVSGCFDYLSEDLPDTIHIGGR 24 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 ; 250.83 1.05E-38 263640000 142540 139033 135670 162029 153581 165807 143696 131475 153650 162287 FALSE TRUE 136969.3792 135067.915 160188.587 170391.3361 158521.0723 169159.7311 145454.5946 128759.9953 136208.2962 151295.1569 0.905312384 0.892744472 1.058781987 1.126218047 1.047760388 1.118077634 0.961396237 0.851051666 0.900281932 1 17.20700628 -0.689891049 4.777754336 1 0.983282786 0.002238896 0.093588158 1.07E-08 2.89E-09 0.102959753 0.024267833 0.204225022 0.689891049 -0.016717214 GQDIEYIEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQDIEYIEIR 10 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494BZX8;H7C0V2 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 116.52 0.0025118 190450000 259050 284820 233960 289560 296580 274490 264830 260570 287440 314920 FALSE TRUE 248926.0396 276697.2125 276241.7764 304504.2263 306119.765 280040.3759 268071.0688 255189.1384 254811.0162 293590.1879 0.84786907 0.942460695 0.94090943 1.037174398 1.042677098 0.953847872 0.913079114 0.869201864 0.867913938 1 18.16344423 -0.689286773 7.565250802 1 0.936252591 0.087696385 0.062766102 0 0 0.067460699 0.015900639 0.204509378 0.689286773 -0.063747409 SPTDWALFTYEGNSNDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPTDWALFTYEGNSNDIR 18 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;F8WC20;F8WBB2;F8WFE1;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 220.69 1.55E-18 65126000 39549 39805 41697 44221 43423 42414 44720 43060 40208 44266 FALSE TRUE 38003.38136 38669.80037 49232.57544 46503.25111 44819.74023 43271.64014 45267.29674 42170.79595 35643.75641 41267.82439 0.920896168 0.937044803 1.193001477 1.126864617 1.086069859 1.04855637 1.096915028 1.021880765 0.863717846 1 15.33272976 -0.689284021 6.356513075 0.999993897 1.041012566 0.003818585 0.096291249 7.09E-10 2.75E-18 0.095204501 0.022439916 0.204510674 0.689284021 0.041018669 VECVGDDIAWMR ddPTM_BT-474_Pertuzumab_2h_R1 1 VECVGDDIAWMR 12 0 Q16822;Q16822-3;H0YML5;H0YM31;Q16822-2 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 133.23 0.00038841 29361000 34533 53109 33762 74416 40364 45681 61068 53437 44996 38773 FALSE TRUE 33183.41218 51594.38332 39863.54443 78256.61868 41662.34472 46604.70112 61815.36845 52333.50728 39888.24272 36146.87017 0.918016194 1.427354099 1.102821468 2.164962507 1.152585121 1.289314978 1.710116758 1.447801899 1.103504744 1 15.14158311 -0.683901955 7.516352513 0.999999798 1.396420871 0.090019816 0.341241451 0 0 0.311986054 0.073535818 0.207060875 0.683901955 0.396421074 LYDEVQEVVYFPAVVHDNLGER ddPTM_BT-474_Pertuzumab_2h_R1 3 LYDEVQEVVYFPAVVHDNLGER 22 0 H9KVC8;F8WBX0;C9JNS3;F8W0M9;C9JID8;Q0VDG4-2;Q0VDG4 H9KVC8 SCRN3 Secernin-3 0 ;; 149.73 6.12E-08 137026000 161665 165532 153745 178464 182517 162987 173485 161169 182363 185861 FALSE TRUE 155346.9531 160811.1894 181530.1415 187674.5484 188387.8251 166282.7088 175608.1613 157840.8038 161661.9168 173272.4689 0.896547236 0.92808275 1.047657153 1.083118106 1.087234609 0.959660296 1.013479882 0.91093989 0.932992516 1 17.40268292 -0.68246831 7.604595605 1.000002612 0.985623883 0.004573342 0.066874094 0 0 0.070621749 0.016645706 0.207745531 0.68246831 -0.01437873 GIVEESVTGVHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GIVEESVTGVHR 12 0 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 210.35 4.45E-08 422640000 381130 430840 356350 378460 419550 394870 441330 342100 463170 469440 FALSE TRUE 366235.0182 418552.865 420750.372 397992.366 433045.2068 402854.5419 446731.1286 335035.5155 410592.8834 437644.4107 0.83683239 0.956376581 0.961397796 0.909396661 0.989491003 0.920506539 1.020762787 0.765542772 0.93818834 1 18.73939962 -0.68190157 6.244733584 1 0.918823731 0.09830371 0.070208635 5.08E-10 8.14E-11 0.068188425 0.016072166 0.208016809 0.68190157 -0.08117627 DFAVSTVPVSGPSHLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DFAVSTVPVSGPSHLR 16 0 O95865;A0A140T971;Q5SSV3;Q5SRR8;H0Y7N1 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ;; 110.38 0.00089875 2084890000 886750 1004480 812950 1018350 1002800 924890 1074770 867320 957550 1077540 FALSE TRUE 852094.8296 975833.2139 959868.149 1070907.166 1035055.973 943591.9095 1087923.357 849409.5389 848852.9384 1004557.256 0.848229232 0.971406267 0.955513629 1.066048908 1.030360357 0.939311228 1.082987904 0.845556123 0.845002048 1 19.93812836 -0.679978023 8.553688566 0.99999999 0.957062768 0.025239385 0.083944615 0 0 0.082823623 0.019521715 0.208940186 0.679978023 -0.042937222 LS(ph)SPVKRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSPVKRPR 9 2 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.571)S(0.429)PVKRPR 66.056 0.033817 260670000 197320 208770 158070 155760 139770 136740 195790 202120 199680 200660 TRUE FALSE 189608.5163 202816.084 186636.7652 163798.7923 144265.829 139504.9765 198186.1366 197946.1514 177013.1635 187069.1195 1.013574644 1.084177253 0.9976888 0.875605727 0.771189972 0.745740274 1.059427324 1.058144454 0.946244704 1 17.5132119 -0.676058053 8.117429054 1.000017113 0.954563426 0.015917021 0.112873285 0 0 0.122845917 0.02895506 0.21083463 0.676058053 -0.045453687 GGGTSSGGSSTNS(ph)LTGSRPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGGTSSGGSSTNSLTGSRPPK 21 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 GGGTSSGGSST(0.001)NS(0.998)LT(0.001)GSRPPK 155.39 1.51E-08 204600000 60448 59294 44390 52761 45769 53733 51517 65636 55719 56616 TRUE FALSE 58085.62533 57602.99317 52412.26045 55484.00153 47241.20145 54819.51808 52147.48046 64280.59366 49394.01271 52781.34789 1.100495301 1.09135131 0.993007237 1.051204711 0.895035905 1.038615349 0.987990693 1.217865709 0.935823254 1 15.68774057 -0.674471387 7.886235876 0.999998534 1.042500923 0.006812213 0.086683572 0 0 0.085062241 0.020049363 0.211606309 0.674471387 0.042502389 SAS(ph)PSVPGPTKPKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASPSVPGPTKPKPK 15 2 Q03164-2;Q03164;Q03164-3;A0A3B3ITZ6 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 S(0.153)AS(0.694)PS(0.153)VPGPTKPKPK;S(0.117)AS(0.87)PS(0.013)VPGPTKPKPK 117.26 0.0002004 2447400000 6744700 5539100 5109300 4756200 4860100 5850100 5134400 6082000 6594000 6450800 TRUE FALSE 6481109.667 5381130.291 6032664.166 5001668.052 5016429.53 5968393.03 5197236.323 5956404.575 5845476.764 6013881.57 1.077691603 0.894784879 1.003123207 0.831687155 0.834141722 0.992436077 0.86420663 0.990442613 0.971997319 1 22.51986503 -0.672434503 8.288149543 0.999995341 0.936392309 0.049239477 0.077529905 0 0 0.071654711 0.016889177 0.212601095 0.672434503 -0.063603032 RPDHPDFDASTLYVPEDFLNSCTPGMR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPDHPDFDASTLYVPEDFLNSCTPGMR 27 1 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 106.88 0.0012138 176180000 70186 71524 66111 87246 77601 76720 76747 65904 81345 88267 FALSE TRUE 67443.05353 69484.20555 78058.72833 91748.77652 80097.10664 78271.33097 77686.25274 64543.05937 72111.05663 82288.59747 0.819591725 0.844396523 0.948597141 1.114963426 0.973368232 0.951180763 0.944070687 0.784349975 0.876318941 1 16.32840491 -0.672309372 7.527298028 0.999992792 0.916111091 0.071664349 0.089045477 0 0 0.0959643 0.022619003 0.21266236 0.672309372 -0.083881701 AATFGLILDDVSLTHLTFGK ddPTM_BT-474_Pertuzumab_2h_R1 3 AATFGLILDDVSLTHLTFGK 20 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ;; 356.18 2.46E-95 535630000 972456 1187172 1081027 1402909 946942 1281946 1220514 1118953 1229724 1224746 FALSE TRUE 934451.3444 1153315.017 1276392.626 1475313.302 977401.2494 1307867.826 1235451.015 1095846.23 1090130.887 1141792.863 0.818407064 1.010091283 1.117884573 1.292102403 0.856023261 1.145451044 1.082027271 0.959759222 0.954753636 1 20.12286952 -0.67171741 7.657910419 0.999989999 1.032041411 0.001801766 0.133664897 0 0 0.126582929 0.029835882 0.212952425 0.67171741 0.032051412 AAGSPS(ph)PLPAPDPAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGSPSPLPAPDPAPK 16 0 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3KRF7 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 AAGSPS(1)PLPAPDPAPK 176.29 3.38E-09 374160000 259050 253060 212410 244820 283500 269090 231010 267310 272310 262630 TRUE FALSE 248926.0396 245842.9766 250797.212 257455.1895 292619.035 274531.1842 233837.1695 261789.9551 241398.5104 244841.8362 1.016680987 1.004088927 1.024323359 1.051516332 1.195134947 1.121259293 0.955053977 1.069220682 0.98593653 1 17.90149057 -0.669181536 5.525855938 0.999999998 1.049211129 0.042867717 0.065934258 1.97E-09 3.57E-10 0.066202679 0.01560412 0.214199506 0.669181536 0.049211131 VKT(ph)TPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VKTTPLR 7 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 VKT(0.77)T(0.23)PLR 90.629 0.02748 694960000 432120 412230 360150 385690 365480 329810 409110 476010 461540 421200 TRUE FALSE 415232.2727 400473.604 425237.1165 405595.5071 377235.9961 336478.9842 414116.8106 466180.2272 409147.9141 392671.7488 1.057453901 1.019868644 1.0829328 1.032912371 0.960690442 0.856896339 1.054613202 1.187200833 1.041959131 1 18.58296428 -0.668158245 7.665832414 1 1.038522373 0.010207769 0.080082432 0 0 0.08794485 0.0207288 0.214704801 0.668158245 0.038522373 IEDGEDLKHDFER ddPTM_BT-474_Pertuzumab_2h_R1 1 IEDGEDLKHDFER 13 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 0 124.3 0.0001282 147420000 64745 79548 72101 71933 78745 82619 78536 65917 86450 83271 FALSE TRUE 62214.69382 77279.36893 85131.25458 75645.47075 81277.90444 84289.61279 79497.14706 64555.79091 76636.55843 77630.981 0.801415788 0.995470725 1.096614438 0.974423739 1.046977681 1.085772867 1.024038934 0.831572525 0.98719039 1 16.2443449 -0.667040153 9.410005325 1.000000515 0.981795126 0.003108038 0.092413285 0 0 0.093552992 0.022050652 0.215258271 0.667040153 -0.018205389 VEELDRK ddPTM_BT-474_Pertuzumab_2h_R1 4 VEELDRK 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;;; 101.64 0.014284 1142640000 1537950 1872660 1492040 2050990 1835030 1921480 1884270 1801500 1709660 1940270 FALSE TRUE 1477845.214 1819253.57 1761684.818 2156841.84 1894055.406 1960333.642 1907330.26 1764298.395 1515586.564 1808853.785 0.817006452 1.005749379 0.973923284 1.192380422 1.047102548 1.083743561 1.054441368 0.975368164 0.83787124 1 20.78664436 -0.666901874 7.222624605 1 1.007937037 0 0.105385909 0 0 0.102108744 0.024067262 0.21532682 0.666901874 0.007937036 FVSEIIGIYYPSDESVQDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FVSEIIGIYYPSDESVQDDR 20 0 O15296-4;O15296;O15296-3 O15296-4 ALOX15B Arachidonate 15-lipoxygenase B 0 ;;; 274.09 4.18E-44 181946000 254667 262265 241229 294685 290117 259836 267412 300801 273362 248357 FALSE TRUE 244714.3321 254785.459 284824.4464 309893.7282 299448.8768 265090.0619 270684.668 294589.3542 242331.0918 231535.5592 1.056919002 1.100416108 1.230154225 1.338428228 1.293317009 1.144921596 1.16908465 1.272328774 1.046625808 1 17.82087425 -0.666817017 7.445914645 1.000000439 1.194396452 0.2443491 0.095152226 0 0 0.094606315 0.022298922 0.215368897 0.666817017 0.194396013 (ac)GS(ph)PEDDLIGIPFPDHSSELLSCLNEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSPEDDLIGIPFPDHSSELLSCLNEQR 27 0 O15156 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 1 GS(1)PEDDLIGIPFPDHSSELLSCLNEQR;GS(1)PEDDLIGIPFPDHSSELLSCLNEQR 53.259 0.004313 74469000 1641.5 2864.6 3556.2 3450.3 4539.5 3655.6 1320.8 3566.4 2906.5 4061.3 TRUE FALSE 1577.348365 2782.904413 4198.884447 3628.370396 4685.51714 3729.518737 1336.964345 3492.752594 2576.566305 3786.224534 0.416601908 0.73500776 1.108989816 0.9583083 1.237516977 0.985023129 0.3531128 0.922489557 0.680510699 1 11.88654425 -0.665827919 8.002540308 0.999999819 0.834817275 0.03602673 0.268989153 0 0 0.265054249 0.062473886 0.215859955 0.665827919 -0.165182544 DAIHFYNK ddPTM_BT-474_Pertuzumab_2h_R1 5 DAIHFYNK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 124.08 0.0013201 4833780000 7698130 8015310 7739540 7311030 6469200 4154350 8681180 7621440 8821030 9942800 FALSE TRUE 7397278.569 7786721.207 9138247.043 7688353.134 6677287.693 4238353.803 8787422.878 7464054.601 7819703.655 9269365.3 0.798035068 0.840049017 0.985854667 0.829436848 0.720360831 0.457243152 0.948006966 0.805239017 0.843607238 1 23.14403913 -0.665432712 8.171147895 1.000034457 0.804209748 0.158935788 0.135868019 0 0 0.134641455 0.031735295 0.216056476 0.665432712 -0.195824709 KYENILK ddPTM_BT-474_Pertuzumab_2h_R1 1 KYENILK 7 1 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 0 80.438 0.070895 0 552450 569430 435040 475790 447300 367200 581570 572110 640460 552440 FALSE TRUE 530859.6432 553190.4139 513661.4054 500345.5789 461687.8107 374625.0356 588687.4276 560295.7286 567757.6658 515022.7467 1.030749897 1.074108702 0.997356736 0.971501904 0.896441591 0.727395126 1.143031898 1.08790482 1.102393379 1 18.97427663 -0.664147116 7.629893453 0.999999999 1.005382392 0 0.114408305 0 0 0.118706685 0.027979434 0.216696993 0.664147116 0.005382393 ENDHLFLSLTEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 ENDHLFLSLTEQR 13 0 Q13137;Q13137-3;Q13137-4;Q13137-5;Q13137-2;D6REB0 Q13137 CALCOCO2 Calcium-binding and coiled-coil domain-containing protein 2 0 ;;; 209.11 4.05E-08 942250000 679094 700965 605616 684114 615552 667484 704693 640249 762616 865219 FALSE TRUE 652554.2557 680974.1645 715064.2831 719421.2055 635351.7891 680980.9838 713317.2437 627027.6344 676047.0288 806616.9465 0.809001421 0.844234884 0.886497967 0.891899443 0.787674734 0.844243339 0.884332082 0.777354898 0.838126488 1 19.62152419 -0.662600478 9.696096439 0.999999979 0.839292534 0.612642444 0.038069564 0 0 0.03768197 0.008881725 0.217470084 0.662600478 -0.160707445 MGAPESGLAEYLFDKHTLGDS(ph)DNES ddPTM_BT-474_Pertuzumab_2h_R1 2 MGAPESGLAEYLFDKHTLGDSDNES 25 1 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 MGAPESGLAEYLFDKHTLGDS(1)DNES;MGAPESGLAEYLFDKHTLGDS(0.999)DNES(0.001) 249.97 1.26E-39 304940000 306720 369260 260760 158982 332070 323740 257680 193135 316830 131808 TRUE FALSE 294733.0433 358729.0663 307885.1326 167187.0801 342751.3331 330286.2446 260833.5649 189146.6948 280864.7867 122880.5268 2.398533365 2.919332101 2.505564882 1.360566108 2.789305533 2.687864817 2.122659886 1.539273144 2.285673687 1 16.90689678 -0.661503616 0.182515548 3.32E-13 2.796256867 0.45463448 0.456117176 15.9489426 0.746765122 10.29694843 1.942784894 0.218020024 0.661503616 2.796256867 DSLLDGHFVLATLSDTDSHSQDLGS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 10 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLATLSDTDSHS(0.004)QDLGS(0.996)PER;DSLLDGHFVLATLSDTDSHS(0.001)QDLGS(0.999)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHS(0.002)QDLGS(0.998)PER 303.74 1.47E-71 5961996000 1758450 1956024 1698534 2104903 1972712 2082516 1993043 1456340 2157106 2167739 TRUE FALSE 1689727.83 1900240.111 2005496.877 2213537.296 2036166.073 2124625.9 2017434.456 1426266.07 1912240.37 2020916.107 0.83611973 0.940286489 0.992370178 1.095313798 1.007546066 1.051318208 0.998277192 0.70575224 0.946224519 1 20.946578 -0.660815894 5.095021823 1.000000003 0.946340457 0.014743639 0.10575615 15381105.78 3018849.686 1.419449147 0.028051564 0.218365541 0.660815894 -0.053659547 MCQGGDFTR ddPTM_BT-474_Pertuzumab_2h_R1 1 MCQGGDFTR 9 0 P62937-2 P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 123.16 0.001316 128590000 129340 124480 153680 149690 144580 102230 145030 149260 158330 194890 FALSE TRUE 124285.2498 120929.9523 181453.3946 157415.5188 149230.547 104297.1606 146804.9205 146177.7288 140357.0422 181689.9267 0.684051406 0.665584243 0.998698155 0.866396512 0.82134739 0.574039313 0.807997026 0.804545037 0.772508662 1 17.47111891 -0.655045372 1.097955004 1.007302673 0.781072531 0.265204945 0.111024394 111.6931095 66.82435471 3.571351027 0.033908463 0.221286351 0.655045372 -0.226230142 RAVS(ph)PSNPK ddPTM_BT-474_Pertuzumab_2h_R1 6 RAVSPSNPK 9 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 RAVS(0.985)PS(0.015)NPK;RAVS(1)PSNPK;RAVS(0.995)PS(0.005)NPK;RAVS(1)PSNPK;RAVS(0.998)PS(0.002)NPK;RAVS(0.999)PS(0.001)NPK 133.07 0.00017591 7498210000 5562980 5770860 5053680 4974050 4623310 5084120 5233290 5639880 6239330 6345320 TRUE FALSE 5345572.591 5606280.723 5966992.395 5230761.317 4772022.965 5186924.39 5297336.568 5523414.507 5531067.416 5915545.825 0.903648243 0.947719938 1.008696842 0.884239844 0.806691911 0.876829382 0.895494131 0.933711727 0.935005421 1 22.49607986 -0.654687792 7.836033973 1 0.910494743 0.224601712 0.050038751 0 0 0.052578176 0.012392795 0.221468624 0.654687792 -0.089505257 GEWKPR ddPTM_BT-474_Pertuzumab_2h_R1 6 GEWKPR 6 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;; 132.72 0.013476 19181160000 22887500 25809100 22483800 22859800 20745300 19506300 25621800 24062000 27506000 26872200 FALSE TRUE 21993031.2 25073049.74 26547122.81 24039597.02 21412591.41 19900730.75 25935367.25 23565111.29 24383634.19 25052121.96 0.877890952 1.00083537 1.059675618 0.959583266 0.854721666 0.794373059 1.035256307 0.940643325 0.973316122 1 24.57842947 -0.65412238 6.251766675 1 0.946182457 0.043670944 0.077989222 0 9.31E-11 0.078083321 0.018404415 0.221757144 0.65412238 -0.053817542 TDSEKPFRGS(ph)QS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDSEKPFRGSQSPKR 15 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 TDSEKPFRGS(1)QS(1)PKR 92.993 0.0024112 300410000 162710 134760 107950 93275 114650 116640 115050 135520 168070 129540 TRUE FALSE 156351.1133 130916.7767 127458.9663 98088.93393 118337.8214 118998.5407 116458.0163 132721.4646 148991.3982 120766.1404 1.294660182 1.084052006 1.055419722 0.812222148 0.979892385 0.98536345 0.964326722 1.098995664 1.233718306 1 16.88185649 -0.653114203 6.566077556 1 1.045468908 0.010287235 0.130724124 0 0 0.129384486 0.030496216 0.222272532 0.653114203 0.045468908 LLQTCFSS(ph)PADDSMDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQTCFS(0.115)S(0.885)PADDSMDR;LLQT(0.001)CFS(0.494)S(0.505)PADDSMDR;LLQTCFS(0.079)S(0.921)PADDSMDR 255.72 1.35E-26 335631000 295737 331490 266201 352510 326166 358859 335178 289518 341988 378330 TRUE FALSE 284179.2711 322036.2298 314309.4423 370703.0833 336657.4256 366115.3749 339280.0086 283539.3521 303166.956 352705.3721 0.805712908 0.913046002 0.891138801 1.051027607 0.954500419 1.03802041 0.961936039 0.803898592 0.859547316 1 18.42810402 -0.651737407 8.852837747 0.999999976 0.920468557 0.081458624 0.08070066 0 0 0.08399219 0.019797149 0.222978296 0.651737407 -0.079531419 GQDTPKPAGQHGSLS(ph)PAAAHTAS(ph)PEPPTQSGPLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 2 GQDTPKPAGQHGS(0.041)LS(0.959)PAAAHTAS(1)PEPPTQSGPLTR;GQDT(0.001)PKPAGQHGS(0.404)LS(0.595)PAAAHT(0.03)AS(0.859)PEPPT(0.097)QS(0.01)GPLT(0.003)R 259.81 7.77E-60 1412510000 266915 355805 286056 365460 288474 360246 359937 221544 356556 393421 TRUE FALSE 256483.6667 345657.7898 337752.6825 384321.4344 297753.0282 367530.4209 364342.0167 216969.039 316081.2577 366774.2452 0.699295739 0.942426559 0.920873499 1.047841934 0.81181553 1.002061692 0.993368595 0.591560181 0.861786949 1 18.48453281 -0.650787743 5.206795938 1.000000011 0.869640683 0.071064854 0.135008809 2.04E-08 5.29E-09 0.136875337 0.032261823 0.223466413 0.650787743 -0.130359328 HKGEMENALR ddPTM_BT-474_Pertuzumab_2h_R1 2 HKGEMENALR 10 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A087WX84;Q99996-4 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ; 134.57 0.00010051 186051000 130773 135278 116597 147731 152827 142069 148489 121328 152333 150743 FALSE TRUE 125662.2466 131420.0039 137668.6716 155355.4146 157742.8192 144941.7325 150306.2528 118822.5344 135040.7965 140533.0423 0.894182923 0.935153767 0.979617813 1.105472507 1.122460715 1.0313712 1.069543862 0.845513144 0.960918473 1 17.10054985 -0.650764525 7.170906101 1 0.992360503 0.000216974 0.085338191 0 0 0.091407037 0.021544845 0.223478359 0.650764525 -0.007639496 RDDMESLGYVLMYFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDDMESLGYVLMYFNR 16 1 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;H0Y9X2;U3KQK7 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 ; 201.4 5.30E-11 384680000 370390 410570 286500 315460 361870 278720 384730 356880 394750 404960 FALSE TRUE 355914.7493 398860.9456 338276.9232 331740.9284 373509.8772 284355.9094 389438.4408 349510.3033 349939.6349 377531.6985 0.942741366 1.056496573 0.896022571 0.878710131 0.989347063 0.753197441 1.031538391 0.925777371 0.926914578 1 18.52623826 -0.648509408 15.76100524 0.999999999 0.934382257 0.05774507 0.080604481 0 0 0.073612532 0.01735064 0.224641811 0.648509408 -0.065617742 AVGEPMRPLAEECCQLGLGLCDQVDDPDLRR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVGEPMRPLAEECCQLGLGLCDQVDDPDLRR 31 2 Q8TEX9;Q8TEX9-2;H0YN14;H0YMR4 Q8TEX9 IPO4 Importin-4 0 ;;; 176.78 2.35E-18 1090890000 157970 211927 151358 187116 180914 206427 178544 170370 195808 218361 FALSE TRUE 151796.3578 205883.0495 178711.7575 196773.0792 186733.2631 210601.0954 180729.0749 166851.8 173580.6967 203571.215 0.745667101 1.011356392 0.877883239 0.966605614 0.917287167 1.034532782 0.887792878 0.819623737 0.852678001 1 17.63517405 -0.647324096 6.047967056 1.000000001 0.90357485 0.112761567 0.082710344 5.85E-10 9.68E-11 0.078571407 0.018519458 0.22525576 0.647324096 -0.096425151 SSPS(ph)TENMHFPSSISSQTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPSTENMHFPSSISSQTR 19 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 S(0.131)S(0.131)PS(0.561)T(0.177)ENMHFPSSISSQTR;S(0.072)S(0.072)PS(0.799)T(0.057)ENMHFPSSISSQTR;S(0.047)S(0.047)PS(0.879)T(0.027)ENMHFPSSISSQTR 166.6 1.26E-11 643530000 367354 497516 425544 484499 471936 527548 463440 466608 448008 521903 TRUE FALSE 352997.3995 483327.3308 502449.267 509504.0515 487116.25 538215.382 469111.7174 456972.3817 397152.01 486554.0449 0.725505015 0.993368231 1.032668975 1.047168463 1.001155483 1.106178003 0.964151305 0.939201691 0.816254667 1 18.89224054 -0.639520744 8.794314513 0.999999998 0.968103496 0.006196394 0.106760622 0 0 0.102265546 0.02410422 0.229339708 0.639520744 -0.031896503 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 18 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 T(0.996)PPRDLPT(0.004)IPGVTSPSSDEPPMEASQSHLR;T(0.934)PPRDLPT(0.062)IPGVT(0.002)S(0.001)PS(0.001)SDEPPMEASQSHLR;T(0.96)PPRDLPT(0.039)IPGVT(0.001)SPSSDEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.863)PPRDLPT(0.089)IPGVT(0.03)S(0.005)PS(0.006)S(0.007)DEPPMEASQSHLR;T(0.982)PPRDLPT(0.018)IPGVTSPSSDEPPMEASQSHLR;T(0.974)PPRDLPT(0.026)IPGVTSPSSDEPPMEASQSHLR;T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.954)PPRDLPT(0.046)IPGVTSPSSDEPPMEASQSHLR;T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;T(0.989)PPRDLPT(0.011)IPGVTSPSSDEPPMEASQSHLR;T(0.991)PPRDLPT(0.009)IPGVTSPSSDEPPMEASQSHLR;T(0.993)PPRDLPT(0.007)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.904)PPRDLPT(0.096)IPGVTSPSSDEPPMEASQSHLR 162.1 5.79E-12 48704613000 977480.8 1062085 973763 1208615.8 1043297 1126379.1 1046817.6 1071414.3 1095239 1204158 TRUE FALSE 939279.7697 1031795.376 1149743.635 1270992.606 1076855.596 1149155.257 1059628.867 1049289.22 970912.0603 1122599.306 0.836700829 0.919112786 1.024179891 1.132187237 0.95925197 1.02365577 0.943906576 0.934696124 0.86487855 1 20.09841164 -0.637353952 8.485062212 1 0.964630473 0.01883735 0.080528356 0 0 0.081069552 0.019108277 0.230486794 0.637353952 -0.035369527 HTGPNSPDTANDGFVR ddPTM_BT-474_Pertuzumab_2h_R1 8 HTGPNSPDTANDGFVR 16 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;E5RGH4;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;;;; 322.17 3.23E-58 27240686000 8981491 10339996 8372909 10731938 9893867 10795729 10099183 7570869 10827715 11221546 FALSE TRUE 8630484.402 10045109.44 9886079.911 11285814.61 10212112.22 11014026.04 10222779.82 7414527.909 9598598.187 10461500.69 0.824975752 0.960197751 0.944996344 1.078794997 0.97616131 1.052815113 0.977181011 0.708744197 0.917516374 1 23.31858648 -0.635708585 4.72168487 1.000000004 0.93263184 0.030394628 0.101263951 6875096.796 2184104.433 1.627642675 0.026583941 0.231361673 0.635708585 -0.067368165 APVIRPGGTLGLSEAADSDAHLFQDSTEPR ddPTM_BT-474_Pertuzumab_2h_R1 3 APVIRPGGTLGLSEAADSDAHLFQDSTEPR 30 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 273.93 1.64E-71 1848540000 845865 1112130 861927 1079808 1112740 1080504 1037881 1007370 1087020 1079434 FALSE TRUE 812807.6606 1080413.141 1017696.382 1135537.02 1148532.293 1102352.531 1050582.898 986567.4575 963626.0468 1006322.974 0.807700591 1.073624641 1.011301947 1.128402163 1.141315783 1.09542618 1.043981828 0.980368612 0.957571348 1 19.94066197 -0.632469975 19.67993426 0.999997513 1.032945674 0.003234425 0.092836332 0 0 0.089836488 0.021174663 0.233093426 0.632469975 0.032948161 KDS(ph)SDRENPPHDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 KDSSDRENPPHDSR 14 2 Q92613 Q92613 JADE3 Protein Jade-3 1 KDS(0.911)S(0.089)DRENPPHDSR;KDS(0.955)S(0.045)DRENPPHDSR;KDS(0.782)S(0.218)DRENPPHDSR 105.79 0.00051111 290512900 200382 292177 241997 311996 251640 305615 255904.4 246374 275369 325371 TRUE FALSE 192550.8499 283844.398 285731.2411 328098.1509 259734.2291 311794.7447 259036.2346 241286.2908 244110.2656 303333.3324 0.634783024 0.935750766 0.941971128 1.081642259 0.856266692 1.027894766 0.853965611 0.795449313 0.80475912 1 18.21054451 -0.631667964 8.383430046 1.000000069 0.886404037 0.079558206 0.119946943 0 0 0.116202773 0.027389256 0.233524277 0.631667964 -0.113596032 VTSFSTPPT(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 4 VTSFSTPPTPER 12 0 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 VTSFSTPPT(1)PER;VTSFSTPPT(1)PER;VTSFSTPPT(1)PER;VTSFS(0.002)T(0.006)PPT(0.992)PER 189.99 8.07E-05 1071210000 1319400 1471300 1227520 1482450 1545190 1524560 1411460 1422940 1488190 1542910 TRUE FALSE 1267836.389 1429339.965 1449360.17 1558959.422 1594892.44 1555387.648 1428733.87 1393555.792 1319256.91 1438407.331 0.881416802 0.993696245 1.00761456 1.083809425 1.108790539 1.081326279 0.99327488 0.96881861 0.917165035 1 20.45604085 -0.631611143 7.313714822 0.999998239 1.008192584 0 0.068940432 0 0 0.071289044 0.016802989 0.233554832 0.631611143 0.008194345 EIDCLS(ph)PEAQK ddPTM_BT-474_Pertuzumab_2h_R1 3 EIDCLSPEAQK 11 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 EIDCLS(1)PEAQK;EIDCLS(1)PEAQK;EIDCLS(1)PEAQK 197.36 6.01E-08 729870000 1528650 1350610 1187590 1196420 1232210 1318570 1226900 1454020 1462430 1607740 TRUE FALSE 1468908.668 1312091.925 1402213.931 1258167.38 1271845.154 1345232.389 1241915.169 1423993.979 1296421.077 1498846.338 0.980026191 0.875401228 0.93552881 0.839423861 0.848549395 0.897511876 0.828580714 0.950060018 0.864945955 1 20.51542105 -0.630092331 5.558869604 1.000000003 0.890958901 0.319567099 0.047665 1.96E-09 3.52E-10 0.043743041 0.010310333 0.234373049 0.630092331 -0.109041102 AGPEMDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGPEMDKR 8 1 A5YKK6-3;A5YKK6-2;A5YKK6 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 72.485 0.073513 0 150470 149480 140210 148630 120920 99148 180030 142850 158160 174810 FALSE TRUE 144589.466 145216.9768 165549.066 156300.8121 124809.5016 101152.8405 182233.261 139900.0976 140206.3399 162969.963 0.887215432 0.8910659 1.015825634 0.959077423 0.765843591 0.620683951 1.118201524 0.858440997 0.860320131 1 17.31424656 -0.627959344 8.863151174 1 0.889053473 0.066468742 0.127458384 0 0 0.123186386 0.02903531 0.235526976 0.627959344 -0.110946527 SSSSGDQSSDSLNS(ph)PTLLAL ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSSGDQSSDSLNSPTLLAL 20 0 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 SSSSGDQS(0.001)S(0.001)DSLNS(0.877)PT(0.122)LLAL 94.384 0.0014431 19279000 42860 45218 40288 51629 40839 49244 45209 46408 50926 42657 TRUE FALSE 41184.98382 43928.42691 47568.9378 54293.57888 42152.62352 50239.74742 45762.28127 45449.65858 45145.09398 39767.8034 1.035636377 1.104622915 1.196167093 1.365264718 1.059968616 1.263327193 1.150736962 1.142875761 1.135217189 1 15.27931326 -0.627351674 6.004323548 1.000000007 1.164835996 0.218330717 0.09150271 1.29E-09 2.14E-10 0.086331563 0.020348544 0.235856759 0.627351674 0.164835989 MMLDDIVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 MMLDDIVSR 9 0 A0A087WTP3;Q92945;M0R0I5;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 97.431 0.015578 147085000 248920 284830 228780 285480 286080 286900 265210 284160 274520 284050 FALSE TRUE 239191.9312 276706.9273 270125.6352 300213.657 295282.023 292701.3146 268455.7193 278291.9967 243357.6405 264811.0405 0.903255131 1.044922171 1.020069385 1.133690108 1.115066889 1.105321417 1.013763319 1.050907833 0.918986006 1 18.01460375 -0.625993708 7.36138977 1.000000331 1.041248092 0.010510058 0.073075965 0 0 0.07047736 0.016611673 0.236595397 0.625993708 0.041247761 GSEEDS(ph)PKKESK ddPTM_BT-474_Pertuzumab_2h_R1 6 GSEEDSPKKESK 12 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GS(0.01)EEDS(0.979)PKKES(0.011)K;GSEEDS(1)PKKESK 211.12 2.80E-08 4949480000 5553180 3656110 3154650 2333974 3451210 3316540 3633590 4420440 5506110 3969240 TRUE FALSE 5336155.586 3551841.323 3724765.43 2454430.678 3562221.304 3383602.711 3678058.961 4329156.369 4881079.476 3700399.839 1.442048378 0.959853388 1.006584583 0.663287965 0.962658485 0.914388406 0.993962577 1.169915835 1.319068125 1 21.81924974 -0.625390353 7.509913608 1.000000061 1.033828042 0.000626923 0.207595816 0 0 0.203369962 0.04793476 0.236924323 0.625390353 0.033827981 GSNEEQVNGS(ph)PLER ddPTM_BT-474_Pertuzumab_2h_R1 2 GSNEEQVNGSPLER 14 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GSNEEQVNGS(1)PLER;GSNEEQVNGS(1)PLER 297.73 1.12E-43 782940000 488260 561690 497780 567150 573110 589820 555740 560520 524640 598520 TRUE FALSE 469178.2594 545671.1512 587739.9191 596420.6795 591544.6036 601746.5645 562541.3124 548945.0661 465085.0667 557981.7073 0.840848819 0.977937348 1.053331877 1.068889305 1.060150532 1.078434215 1.008171603 0.983804772 0.833513107 1 19.0898583 -0.624222638 4.144326527 0.999999971 0.997937706 0 0.084184097 3.08E-09 1.19E-09 0.082718806 0.019496971 0.237562213 0.624222638 -0.002062265 SWEEQMIEVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 SWEEQMIEVGR 11 0 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 ;; 181.53 1.44E-05 330140000 216741 314842 217033 488481 244668 273942 382541 331702 269211 249126 FALSE TRUE 208270.5221 305863.0144 256255.691 513691.5629 252537.9684 279481.2949 387222.6512 324852.2378 238651.2959 232252.4741 0.896741888 1.316941899 1.103349671 2.2117808 1.087342425 1.203351206 1.667248767 1.398703024 1.027551146 1 17.82533444 -0.622527086 7.235524163 0.999945041 1.351650811 0.062510244 0.361708745 0 0 0.335190185 0.079005084 0.238491505 0.622527086 0.35170577 SLS(ph)SPSGLHPAEEDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSPSGLHPAEEDGR 16 0 A0A1B0GW72;Q96PX9 A0A1B0GW72 PLEKHG4B Pleckstrin homology domain-containing family G member 4B 1 S(0.079)LS(0.458)S(0.458)PS(0.005)GLHPAEEDGR 115.26 0.00080957 0 114930 131200 105240 137510 122800 124570 126220 119340 129850 139160 TRUE FALSE 110438.4085 127458.3045 124259.2091 144606.9076 126749.9735 127088.8907 127764.7181 116875.5873 115109.9724 129734.5692 0.85126431 0.982454447 0.957795673 1.114636665 0.976994599 0.979606989 0.984816297 0.900882378 0.887272938 1 16.98520343 -0.621252515 7.677847936 1.000001433 0.96244699 0.029243455 0.068112438 0 0 0.067463419 0.01590128 0.23919246 0.621252515 -0.037554443 APVDEDRLS(ph)PLVAADSLLEHVR ddPTM_BT-474_Pertuzumab_2h_R1 6 APVDEDRLSPLVAADSLLEHVR 22 1 Q01094 Q01094 E2F1 Transcription factor E2F1 1 APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR 237.97 9.30E-31 371026000 162254 179910 130008 185419 175726 160380 176696 162555 156911 193368 TRUE FALSE 155912.9343 174779.143 153503.3376 194988.4968 181378.3864 163622.9935 178858.4585 159198.1824 139099.1211 180271.0131 0.864880779 0.969535478 0.851514256 1.081640877 1.006142825 0.907650047 0.992164272 0.883104719 0.771611135 1 17.45980791 -0.620411745 6.337329179 1.000000123 0.930478468 0.061872556 0.085116625 0 0 0.081385171 0.019182669 0.239655972 0.620411745 -0.069521655 RNS(ph)TTFPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSTTFPSR 9 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RNS(0.986)T(0.012)T(0.002)FPSR 135.26 0.00013827 1114200000 74052 80729 68206 54229 69000 70180 65650 87789 64657 86298 TRUE FALSE 71157.96597 78426.68796 80532.34143 57027.76519 71219.44766 71599.08768 66453.44434 85976.12647 57317.40842 80452.95959 0.884466729 0.974814206 1.000986686 0.708833652 0.885230923 0.889949705 0.825991296 1.068650885 0.712433809 1 16.29585787 -0.61983348 8.735007972 0.999999968 0.895125079 0.083472235 0.109893857 0 0 0.102867182 0.024246027 0.239975287 0.61983348 -0.104874889 LLHIEELR ddPTM_BT-474_Pertuzumab_2h_R1 8 LLHIEELR 8 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;;;;;;; 210.1 4.19E-05 4589783000 3040607 3453691 2744972 3459311 3461461 3349953 3311054 3033054 3442480 3559602 FALSE TRUE 2921776.717 3355195.114 3241049.502 3637846.455 3572802.037 3417691.345 3351575.669 2970420.375 3051704.102 3318506.986 0.880449169 1.011055613 0.976658936 1.096229862 1.076629355 1.029888248 1.009964928 0.895107465 0.91960153 1 21.66210288 -0.61973874 5.531403485 1 0.989720372 0.002220984 0.06881496 0 9.73E-11 0.072249597 0.017029393 0.240027643 0.61973874 -0.010279628 SQHSGNAQVTQTK ddPTM_BT-474_Pertuzumab_2h_R1 4 SQHSGNAQVTQTK 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 170.74 2.63E-05 332733000 520890 656840 522518 645080 573590 625970 617100 539681 654280 692290 FALSE TRUE 500533.0429 638107.5663 616948.626 678372.6561 592040.0433 638627.5423 624652.2544 528536.3988 580008.8774 645400.5817 0.775538568 0.988700017 0.95591582 1.051087767 0.917321831 0.989505681 0.967852016 0.818927676 0.898680438 1 19.29983535 -0.619275466 7.673669215 0.999999596 0.930339383 0.068473746 0.078163767 0 0 0.076720691 0.01808324 0.240283823 0.619275466 -0.069660213 S(ph)PTNSLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTNSLLK 8 0 Q14106-2;Q14106 Q14106-2 TOB2 Protein Tob2 1 S(1)PTNSLLK;S(0.999)PT(0.001)NSLLK 112.95 0.0030873 452120000 665190 665120 603340 572940 542830 503870 647260 641230 753460 743150 TRUE FALSE 639193.6394 646151.4288 712376.9592 602509.5021 560290.6199 514058.5966 655181.3615 627988.3764 667930.3796 692815.7886 0.922602588 0.932645358 1.028234303 0.86965325 0.808715144 0.741984529 0.945679028 0.906429078 0.964080771 1 19.40211228 -0.619262473 6.489891701 1.000002867 0.900719332 0.128042242 0.076454871 0 0 0.078601976 0.018526663 0.240291012 0.619262473 -0.099283534 EINYILR ddPTM_BT-474_Pertuzumab_2h_R1 1 EINYILR 7 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 92.491 0.036363 72648000 138730 136250 123400 118780 124180 106780 133490 143910 145720 143400 FALSE TRUE 133308.2782 132364.2834 145701.125 124910.25 128174.3625 108939.1648 135123.6906 140938.2082 129178.4765 133687.3903 0.99716419 0.990102979 1.089864382 0.934345788 0.958761797 0.814879882 1.010743723 1.054237112 0.966272707 1 17.02850387 -0.618404383 6.31731556 0.999999888 0.983021691 0.005460023 0.070011246 0 0 0.070975479 0.016729081 0.240766255 0.618404383 -0.016978197 FSEEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 FSEEQR 6 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;; 152.26 0.023917 3952230000 4802870 5245710 4515020 5321460 4989920 5129990 5022710 5083330 5444750 5406300 FALSE TRUE 4615168.531 5096107.487 5330984.55 5596101.188 5150425.309 5233721.913 5084179.427 4978357.459 4826684.806 5040126.486 0.915685061 1.011107063 1.057708485 1.110309673 1.021884138 1.038410827 1.008740444 0.987744548 0.957651523 1 22.26502851 -0.617777837 7.715412602 0.999999298 1.015267153 0.001743174 0.05046515 0 0 0.050808097 0.011975583 0.241113853 0.617777837 0.015267855 EKEAENER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEAENER 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 61.593 0.077504 260080000 237060 233310 187920 198330 192870 204540 226200 237780 241950 229780 FALSE TRUE 227795.4331 226656.2272 221881.3243 208565.8351 199073.8387 208675.9389 228968.3033 232869.7599 214484.8503 214216.7959 1.06338736 1.058069356 1.035779306 0.973620365 0.929310131 0.974134348 1.068862515 1.08707517 1.001251323 1 17.70871208 -0.617083763 7.936587177 0.999997807 1.02406569 0.014242446 0.048325545 0 0 0.053437116 0.012595249 0.2414995 0.617083763 0.024067883 TAAAAAEHSQR ddPTM_BT-474_Pertuzumab_2h_R1 6 TAAAAAEHSQR 11 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;;; 220.29 9.25E-12 2068370000 2053150 2122140 1819640 1993820 1950650 1907050 2141200 2084980 2344630 2419110 FALSE TRUE 1972910.628 2061618.645 2148489.426 2096721.289 2013394.429 1945611.858 2167404.646 2041924.434 2078477.432 2255261.525 0.874803479 0.914137284 0.952656444 0.929702062 0.892754302 0.862698998 0.961043596 0.905404722 0.921612597 1 21.10486331 -0.61607483 0.591568076 1.013396444 0.911612669 0.447729987 0.029297085 12.56002698 3.239830995 0.370004654 0.012020235 0.242061193 0.61607483 -0.101783775 QREEKS(ph)PDDLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 QREEKSPDDLKK 12 3 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 QREEKS(1)PDDLKK;QREEKS(1)PDDLKK 151.48 0.00038129 774220000 1648010 1010310 909390 805200 954520 889810 1059080 1395030 1529870 1166920 TRUE FALSE 1583603.947 981496.948 1073737.002 846756.4685 985223.0027 907802.5679 1072041.338 1366222.143 1356205.571 1087883.469 1.455674245 0.902207797 0.98699634 0.778352179 0.905632846 0.834466736 0.985437658 1.25585339 1.246645997 1 20.0530926 -0.613998675 7.687479949 0.999999977 1.029979095 0.001519917 0.204044172 0 0 0.204135777 0.048115264 0.243221143 0.613998675 0.029979118 TEELEEESFPER ddPTM_BT-474_Pertuzumab_2h_R1 1 TEELEEESFPER 12 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 154.05 0.00066074 0 38538 50272 41841 56611 40634 53800 50936 44674 49642 52575 FALSE TRUE 37031.89235 48838.29178 49402.59945 59532.70049 41941.02951 54887.87286 51559.37 43751.46629 44006.84828 49014.04842 0.755536291 0.996414158 1.00792734 1.214604841 0.855694048 1.11983961 1.05193045 0.892631148 0.897841531 1 15.58090769 -0.613131113 5.402287665 1.000000001 0.982811439 0.001040897 0.126989517 8.88E-10 1.64E-10 0.119235537 0.028104085 0.243707496 0.613131113 -0.017188562 QSS(ph)SEQCSDGEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSSSEQCSDGEGR 13 0 O60343-2;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 QS(0.198)S(0.77)S(0.025)EQCS(0.007)DGEGR;QS(0.006)S(0.99)S(0.004)EQCSDGEGR 128.06 0.00017797 21066000 31539 34138 29594 36757 30618 33207 37344 29417 35219 36962 TRUE FALSE 30306.42101 33164.41766 34942.29411 38654.03317 31602.85578 33878.46829 37801.02704 28809.52867 31221.08677 34458.53082 0.879504154 0.962444332 1.014039 1.121755114 0.917127197 0.983166359 1.097000544 0.836063755 0.906048111 1 15.07257357 -0.61020487 5.301459612 0.999999992 0.969045498 0.011792194 0.086212578 11364302.19 2143617.635 0.181544576 0.020667141 0.245355123 0.61020487 -0.030954494 LFEGNALLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFEGNALLR 9 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 80.455 0.055985 46777000 74940 80444 74168 65357 66186 64517 69276 85664 83080 86935 FALSE TRUE 72011.26195 78149.81588 87571.80746 68730.0826 68314.9328 65821.57794 70123.82041 83895.00846 73649.1067 81046.81502 0.888514397 0.964255238 1.080508931 0.848029409 0.842907063 0.812142685 0.865226109 1.035142571 0.908723022 1 16.30646787 -0.610132009 11.18826253 1 0.921385755 0.082114379 0.082442389 0 0 0.085599623 0.020176025 0.245396289 0.610132009 -0.078614245 QPPPAS(ph)SPTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPPPASSPTKR 11 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 QPPPAS(0.585)S(0.408)PT(0.007)KR 69.602 0.033109 121200000 71799 62883 59196 62560 51997 62806 68678 63823 69176 80634 TRUE FALSE 68993.0157 61089.63841 69894.03401 65788.7291 53669.53073 64075.98035 69518.50191 62505.03275 61323.43049 75172.58736 0.917794879 0.812658451 0.929780874 0.875169146 0.713950825 0.852384927 0.924785275 0.831487048 0.815768522 1 16.19791904 -0.60849816 7.537437904 0.999996503 0.851977211 0.336347104 0.062090729 0 0 0.059169839 0.013946465 0.246321228 0.60849816 -0.148019292 KVEDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVEDAK 6 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 91.906 0.075939 532370000 606070 625160 501690 402160 522950 436870 627890 580610 594140 654250 FALSE TRUE 582384.1144 607331.0489 592356.543 422915.5258 539771.1617 445703.8107 635574.3056 568620.2006 526695.718 609937.0648 0.954826568 0.995727402 0.971176499 0.693375678 0.884962061 0.730737377 1.0420326 0.932260447 0.863524695 1 19.21830086 -0.607875401 8.083033918 1.000000916 0.899320806 0.079149911 0.10550419 0 0 0.103499738 0.024395122 0.246674694 0.607875401 -0.10068011 SAAMLGNSEDHTALSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAAMLGNSEDHTALSR 16 0 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 0 201.75 3.22E-11 607150000 285370 376010 304410 377630 313450 366050 350390 321160 318620 395510 FALSE TRUE 274217.4249 365286.563 359423.6586 397119.5296 323532.4039 373451.7818 354678.1776 314527.9338 282451.5934 368721.7554 0.743697438 0.99068351 0.974782891 1.077016812 0.877443219 1.012828173 0.961912804 0.853022446 0.766029097 1 18.49217302 -0.606547215 5.404562493 1.000000001 0.924456364 0.051644562 0.102221365 2.92E-09 6.76E-10 0.098007353 0.023100554 0.247430245 0.606547215 -0.075543637 DSKPSST(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.001)KPS(0.041)S(0.041)T(0.916)PR;DSKPSS(0.096)T(0.904)PR 115.91 0.008908 9853200000 15085300 11767500 12165400 10947600 9881540 10938100 12947700 15032400 12257600 13588400 TRUE FALSE 14495749.8 11431902.42 14363958.4 11512606.95 10199388.71 11159275.88 13106157.83 14721975.69 10866168.64 12668045.56 1.144276733 0.902420374 1.133873282 0.908791091 0.805127252 0.880899569 1.034584045 1.162134728 0.857762042 1 23.59469063 -0.605315468 8.091319002 1.000000625 0.988275883 0 0.123976679 0 0 0.123541825 0.029119087 0.248133003 0.605315468 -0.011724741 LSSLS(ph)LSPANHENQPSEGER ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSLSLSPANHENQPSEGER 20 0 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 LS(0.022)S(0.02)LS(0.51)LS(0.448)PANHENQPSEGER 74.763 0.0085731 154030000 43492 50393 50630 59877 58663 51665 50419 50929 52943 60022 TRUE FALSE 41792.28456 48955.84098 59779.96726 62967.25915 60549.94867 52709.7017 51036.0428 49877.29835 46933.1326 55956.65648 0.746868866 0.874888602 1.068326291 1.125286304 1.082086609 0.941973753 0.912063837 0.891355944 0.838740832 1 15.77202214 -0.604558938 7.552588252 0.999999096 0.948161675 0.020852977 0.112328737 0 0 0.117789152 0.027763169 0.248565621 0.604558938 -0.051837421 QAGAPGGSSGSGGS(ph)PELSALR ddPTM_BT-474_Pertuzumab_2h_R1 2 QAGAPGGSSGSGGSPELSALR 21 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 QAGAPGGSSGS(0.006)GGS(0.994)PELSALR;QAGAPGGSSGSGGS(1)PELSALR 224.08 3.47E-25 174080000 142494 186191 155250 179269 181569 181526 177722 178180 173039 172795 TRUE FALSE 136925.1769 180881.015 183307.1285 188521.0946 187409.3318 185196.5801 179897.015 174500.5207 153396.3382 161091.4407 0.849984185 1.122846839 1.137907313 1.170273813 1.163372374 1.149636376 1.116738507 1.083238935 0.952231462 1 17.29752032 -0.603205627 9.087547674 0.999999971 1.093498089 0.050855296 0.098317146 0 0 0.093047688 0.02193155 0.249341388 0.603205627 0.093498119 S(ph)SPATADKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPATADKR 9 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.991)S(0.009)PATADKR 122.7 0.00035432 516040000 336270 298280 292840 292930 285980 243850 292340 393000 303530 345910 TRUE FALSE 323128.1966 289773.3464 345762.7022 308048.1524 295178.8064 248780.8141 295917.7444 384884.4127 269074.5469 322481.2076 1.002006284 0.898574365 1.072194888 0.955243733 0.915336458 0.771458331 0.917627872 1.193509586 0.834388301 1 18.29885557 -0.602673789 7.476296383 0.999999981 0.962612306 0.007467827 0.113255807 0 0 0.114875818 0.02707649 0.249646919 0.602673789 -0.037387675 GGCWPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGCWPR 6 0 Q9Y4W6 Q9Y4W6 AFG3L2 AFG3-like protein 2 0 ; 122.76 0.044387 838450000 831560 739180 726760 633910 676990 607040 734100 784550 892900 854370 FALSE TRUE 799061.7159 718099.3101 858101.6987 666626.1711 698765.9982 619314.7647 743084.1354 768348.7683 791541.7353 796502.7589 1.003212741 0.901565377 1.077336756 0.836941446 0.877292628 0.777542523 0.932933536 0.964652991 0.993771492 1 19.60331983 -0.599429314 6.441189887 0.999997848 0.927151666 0.061241711 0.082389435 0 0 0.080570475 0.018990643 0.251518935 0.599429314 -0.072846182 EES(ph)EES(ph)EAEPVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 EES(1)EES(1)EAEPVQR;EES(1)EES(1)EAEPVQR 328.38 3.44E-62 2099230000 1875660 1850710 1706700 1577230 1689600 1792850 1678410 1927220 2054200 1949200 TRUE FALSE 1802357.134 1797929.563 2015138.655 1658631.029 1743947.518 1829102.655 1698950.884 1887422.234 1821015.828 1817178.948 0.991843503 0.989406995 1.108937927 0.91275052 0.959700485 1.006561658 0.934938678 1.038655128 1.002111449 1 20.79326907 -0.59733591 6.234873152 1 0.994753402 0.001003081 0.051698235 0 0 0.048404151 0.011408968 0.252734244 0.59733591 -0.005246598 RGS(ph)LEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RGSLEK 6 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 RGS(1)LEK;RGS(1)LEK;RGS(1)LEK;RGS(1)LEK;RGS(1)LEK;RGS(1)LEK 105.1 0.020375 9049440000 4980460 4182160 3604070 3750010 3852230 3816450 4265720 4865240 4692120 4300600 TRUE FALSE 4785818.117 4062888.892 4255405.621 3943548.466 3976140.476 3893621.234 4317925.157 4764771.094 4159490.209 4009316.531 1.193674303 1.013361968 1.061379312 0.98359619 0.991725259 0.971143386 1.076972876 1.188424774 1.037456179 1 21.93492489 -0.595346846 7.969599806 0.999992893 1.060025836 0.049819951 0.07465299 0 0 0.077648975 0.018302039 0.253894419 0.595346846 0.060032943 IEYDCELVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 IEYDCELVPR 10 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 188.66 2.55E-06 962210000 459080 444970 367100 433250 463280 455150 425310 438160 444190 514570 FALSE TRUE 441138.6461 432279.8913 433443.1361 455610.0844 478181.8219 464353.4448 430515.071 429111.8429 393767.4134 479717.7156 0.919579644 0.901113045 0.903537897 0.949746215 0.996798339 0.967972267 0.897434172 0.89450906 0.820831503 1 18.87182619 -0.594078357 6.207408509 1 0.918226614 0.231268548 0.045423287 3.50E-10 0 0.046950451 0.011066327 0.254637079 0.594078357 -0.081773386 EQQAQVEKEDFSDMVAEHAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQQAQVEKEDFSDMVAEHAAK 21 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 154.65 1.91E-08 1733600000 1183280 1086210 826840 754260 967340 971480 968160 1026780 1277110 1113240 FALSE TRUE 1137036.109 1055232.354 976268.381 793187.449 998455.3696 991123.9912 980008.6317 1005576.634 1132137.827 1037839.263 1.095580163 1.016758945 0.940673971 0.764268107 0.96205203 0.954987951 0.944277853 0.968913655 1.09086047 1 19.98515159 -0.59300251 7.990465649 1.000006601 0.963678574 0.003708612 0.087844466 0 0 0.086824261 0.020464674 0.255268655 0.59300251 -0.036328027 AVVPSKR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVVPSKR 7 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;G3V2D6 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 143.56 0.0038702 10733100000 3734200 4585800 4005900 4280400 3278200 3756900 4622300 4106100 4483300 5035900 FALSE TRUE 3588263.336 4455017.474 4729855.241 4501311.957 3383646.28 3832867.092 4678869.09 4021307.6 3974374.58 4694814.007 0.764303619 0.948923103 1.007463817 0.958783873 0.720719985 0.816404459 0.996603717 0.856542473 0.846545693 1 22.16263657 -0.589810151 6.381539029 1.000002361 0.884373034 0.130628099 0.092452643 0 2.12E-10 0.090775431 0.021395974 0.257151966 0.589810151 -0.115629328 SLSYS(ph)PVER ddPTM_BT-474_Pertuzumab_2h_R1 5 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSYS(1)PVER;SLS(0.003)YS(0.997)PVER;SLSYS(1)PVER;SLSYS(1)PVER;SLS(0.01)YS(0.99)PVER 209.21 9.22E-06 3914770000 2313060 2476670 2099860 2587150 2457530 2479810 2397350 2472970 2520870 2448290 TRUE FALSE 2222663.058 2406037.797 2479351.413 2720673.122 2536578.684 2529953.457 2426689.486 2421902.305 2234711.406 2282465.138 0.973799346 1.054139998 1.086260365 1.191988906 1.111332937 1.108430274 1.063187974 1.061090601 0.979078002 1 21.12216139 -0.588626008 5.178029367 1 1.074655171 0.103342354 0.060358231 4027071.603 777723.0068 0.181452088 0.014671557 0.25785407 0.588626008 0.074655171 KS(ph)PENTEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPENTEGK 9 1 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 KS(0.998)PENT(0.002)EGK 62.869 0.048877 346470000 228900 156290 145070 136280 163410 152160 174070 199170 175480 171880 TRUE FALSE 219954.3349 151832.7622 171287.3761 143313.4271 168666.2311 155236.7795 176200.3207 195057.0699 155560.2461 160238.4145 1.372669192 0.947542839 1.068953263 0.894376218 1.052595481 0.968786292 1.099613481 1.21729281 0.970804951 1 17.28986053 -0.586860176 8.017632511 0.999999719 1.06674472 0.021151507 0.134261024 0 0 0.125529132 0.0295875 0.258904634 0.586860176 0.066745001 DKNQDLCQQEAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKNQDLCQQEAVK 13 1 Q14554;H7C4F9 Q14554 PDIA5 Protein disulfide-isomerase A5 0 145.1 3.80E-05 328600000 209570 214460 151240 186620 155440 162220 180300 197460 238130 212400 FALSE TRUE 201379.7727 208343.8108 178572.4323 196251.4806 160439.8688 165500.1995 182506.5653 193382.382 211098.4807 198013.9588 1.016997862 1.052167292 0.901817394 0.991099222 0.810245246 0.835800671 0.921685352 0.976609847 1.066078785 1 17.59524261 -0.586278742 6.498780223 1.000011295 0.948130208 0.027147198 0.081615045 0 0 0.082952803 0.019552163 0.259251488 0.586278742 -0.051881087 LSGWEEEEESWLYSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSGWEEEEESWLYSSPK 17 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 LSGWEEEEESWLYS(0.009)S(0.991)PK 176.32 1.17E-09 33190000 36367 31403 30791 24934 29042 29351 27788 34425 38765 33760 TRUE FALSE 34945.73743 30507.41719 36355.61864 26220.84673 29976.16231 29944.49733 28128.07786 33714.11172 34364.55972 31473.40513 1.110325918 0.969307803 1.155121872 0.833111213 0.952428318 0.951422231 0.893709395 1.07119365 1.091860241 1 14.94184565 -0.585751476 6.437378536 1.00000019 0.999038377 0 0.09722087 0 0 0.092162724 0.021722962 0.25956643 0.585751476 -0.000961813 LLDYTEKPLYENLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDYTEKPLYENLR 14 1 Q99986;H0YJ50;H0YJJ9 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 120.3 0.00012512 524140000 581260 596650 461610 458170 493000 460240 587030 573550 603970 590780 FALSE TRUE 558543.7166 579634.1262 545033.1955 481816.2086 508857.7927 469546.3681 594214.2487 561705.9921 535409.8576 550765.9444 1.014121738 1.052414609 0.989591316 0.874811185 0.923909326 0.852533409 1.078887057 1.019863334 0.972118671 1 19.07107983 -0.58522188 8.279939956 0.999992446 0.977666686 0.010228002 0.069457012 0 0 0.072238602 0.017026802 0.259883149 0.58522188 -0.02232576 LFDSTTLEHQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LFDSTTLEHQK 11 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;; 176.42 8.67E-06 1536080000 2294920 2466780 2093640 1946360 2055380 1343270 2412000 2241090 2649420 2815270 FALSE TRUE 2205231.989 2396429.85 2472007.321 2046811.873 2121493.164 1370431.84 2441518.778 2194810.708 2348668.949 2624589.255 0.84021985 0.913068529 0.941864452 0.779859884 0.808314352 0.522150975 0.930247951 0.836249216 0.894871052 1 21.32366023 -0.585082946 6.496824305 0.999992028 0.829216443 0.165617015 0.114704552 0 1.29E-10 0.112066966 0.026414437 0.2599663 0.585082946 -0.170775585 YQSHDYAFSSVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YQSHDYAFSSVEK 13 0 Q9UHG3;Q9UHG3-2;F8W8W4;C9JGT6;C9JM55;C9K055 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 148.57 4.33E-05 637440000 590480 881520 698000 826930 510750 644620 814140 718150 860350 859060 FALSE TRUE 567403.3888 856379.9127 824144.1269 869607.9564 527178.7376 657654.6581 824103.6889 703319.9515 762686.6749 800875.101 0.708479247 1.069305203 1.0290545 1.08582219 0.658253374 0.821170064 1.029004008 0.878189309 0.952316627 1 19.61121774 -0.583693024 9.605475332 1 0.919371338 0.03091016 0.141180266 0 0 0.134638168 0.031734521 0.260799633 0.583693024 -0.080628661 MIATDPDDTHAYNVADFESLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 MIATDPDDTHAYNVADFESLSR 22 0 H0Y4P7;A0A087X0A8;D6RGG3;Q99715-2;Q99715-4;Q99715 H0Y4P7 COL12A1 Collagen alpha-1(XII) chain 0 ; 180.63 5.25E-17 266740000 307400 330120 309640 385470 332330 410390 325060 283390 368020 456840 FALSE TRUE 295386.4682 320705.3008 365598.8359 405364.1529 343019.6963 418688.367 329038.1815 277537.8975 326243.9125 425897.8199 0.693561822 0.753009961 0.85841913 0.95178734 0.805403738 0.983072341 0.772575407 0.651653717 0.766014516 1 18.70014782 -0.582592301 8.420112452 1.00000286 0.801282884 0.261788155 0.098676997 0 0 0.105034467 0.024756861 0.26146147 0.582592301 -0.198719976 FADQDDIGNVSFDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FADQDDIGNVSFDR 14 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 341.74 1.13E-68 3325900000 2020850 2097860 1907490 2148840 2113940 2050070 2110200 2107890 2201110 2270290 FALSE TRUE 1941872.948 2038031.087 2252215.875 2259741.89 2181936.8 2091523.82 2136025.259 2064361.335 1951249.221 2116521.236 0.917483328 0.962915492 1.064112108 1.06766795 1.030907114 0.988189386 1.009215132 0.975355834 0.921913368 1 21.01326353 -0.580355507 7.731425125 1 0.996647177 0 0.049438753 0 0 0.050423361 0.0118849 0.262811578 0.580355507 -0.003352823 VECYDYDNDGSHDLIGTFQTTMTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VECYDYDNDGSHDLIGTFQTTMTK 24 0 O75131;H0YB26 O75131 CPNE3 Copine-3 0 ; 295.78 5.92E-62 551210000 488050 589200 344480 649090 398930 322350 524650 568770 582060 540510 FALSE TRUE 468976.4664 572396.5929 406735.1989 682589.6127 411761.9457 328868.1379 531070.8236 557024.7007 515986.989 503900.7763 0.93069209 1.135931159 0.807173194 1.354611155 0.817148862 0.652644634 1.053919439 1.105425367 1.023985303 1 18.94278015 -0.579714285 4.643302231 1 0.993237366 0 0.188071473 70.79539017 114813812.3 0.580963405 0.043423124 0.263199897 0.579714285 -0.006762634 EAVLDVIPTDIHQR ddPTM_BT-474_Pertuzumab_2h_R1 8 EAVLDVIPTDIHQR 14 0 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;;;; 160.27 4.78E-06 14025180000 7305150 7612980 6707610 7938610 6911420 4593820 7956760 7597020 8047480 8963670 FALSE TRUE 7019656.662 7395865.264 7919824.337 8348322.613 7133732.101 4686710.188 8054137.209 7440138.882 7133963.808 8356552.647 0.840018242 0.885037835 0.947738221 0.99901514 0.853669258 0.560842537 0.963810982 0.890335907 0.853696986 1 22.99447648 -0.578885669 0.984787947 1.005215514 0.868914272 0.110247819 0.113643619 100.9815802 55.32552167 2.141878756 0.035824657 0.263702551 0.578885669 -0.136301242 HPASLTSS(ph)GSSGSPSSSIK ddPTM_BT-474_Pertuzumab_2h_R1 1 HPASLTSSGSSGSPSSSIK 19 0 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 HPAS(0.001)LT(0.04)S(0.25)S(0.296)GS(0.188)S(0.188)GS(0.034)PS(0.001)S(0.001)SIK 58.83 0.038585 0 15639 20821 19072 22718 18671 23622 19784 16391 22208 25905 TRUE FALSE 15027.81059 20227.20547 22518.73465 23890.4787 19271.56967 24099.65302 20026.12251 16052.52012 19687.04094 24150.43128 0.622258477 0.837550487 0.932436129 0.98923611 0.797980353 0.997897418 0.829224219 0.664688756 0.815183825 1 14.55976133 -0.574932162 7.621382055 0.999999998 0.831111834 0.157823556 0.116533305 0 0 0.118893965 0.028023576 0.266114071 0.574932162 -0.168888164 MDATANDVPSPYEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDATANDVPSPYEVR 15 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 250.69 1.46E-18 599580000 371760 409350 341290 452620 401280 391040 399840 403320 431200 418230 FALSE TRUE 357231.2082 397675.7388 402968.695 475979.7724 414187.5356 398947.0967 404733.3615 394991.3011 382251.9837 389902.9096 0.916205546 1.019935294 1.033510356 1.220764864 1.062283777 1.023195998 1.038036269 1.013050407 0.980377356 1 18.5727554 -0.572061192 7.675973755 0.99999827 1.038095842 0.016766719 0.073035478 0 0 0.072710178 0.017137953 0.267879086 0.572061192 0.038097572 QLVHELDEAEYR ddPTM_BT-474_Pertuzumab_2h_R1 4 QLVHELDEAEYR 12 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;; 216.84 3.81E-11 11069270000 4168460 4487410 3922450 4364600 4369580 4490320 4476380 4103580 4827290 5005090 FALSE TRUE 4005551.975 4359433.46 4631323.969 4589857.529 4510131.509 4581117.347 4531163.277 4018839.639 4279316.277 4666090.796 0.858438498 0.934279604 0.992549046 0.983662284 0.966576028 0.981789156 0.971083392 0.861286206 0.917109517 1 22.15378295 -0.57155277 7.419275699 1 0.940806053 0.128185348 0.04635338 0 0 0.04882085 0.011507185 0.268192871 0.57155277 -0.059193947 HGGSPQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 6 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGSPQPLATTPLSQEPVNPPS(0.063)EAS(0.879)PT(0.058)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.989)PT(0.011)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.793)PT(0.207)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.747)PT(0.253)R;HGGSPQPLATTPLSQEPVNPPS(0.009)EAS(0.752)PT(0.239)R;HGGSPQPLATTPLSQEPVNPPS(0.084)EAS(0.667)PT(0.248)R 278.7 7.54E-62 11708720000 1447560 1503390 1487310 1857860 1624670 1594460 1684860 1383410 1776360 1832810 TRUE FALSE 1390987.755 1460514.789 1756100.002 1953744.377 1676928.986 1626701.074 1705479.821 1354842.1 1574715.06 1708672.146 0.814075279 0.854765961 1.027757142 1.14342847 0.981422322 0.952026448 0.998131692 0.792921043 0.921601645 1 20.70444417 -0.570950814 7.61333836 0.999997772 0.941591403 0.028536174 0.09967769 0 0 0.105402868 0.024843694 0.268564859 0.570950814 -0.058406369 YYETHNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 YYETHNVK 8 0 Q13823 Q13823 GNL2 Nucleolar GTP-binding protein 2 0 107.01 0.0040859 83683000 146350 161170 129020 138390 141230 114260 153860 164050 151060 155790 FALSE TRUE 140630.4802 156573.5894 152336.784 145532.3245 145772.7912 116570.4155 155742.9847 160662.3102 133912.3021 145238.2045 0.968274709 1.078046853 1.048875429 1.002025087 1.003680758 0.802615371 1.07232794 1.10619868 0.922018435 1 17.14806147 -0.570408149 6.339478007 1.000000624 1.008928385 0 0.084676122 0 0 0.084003454 0.019799804 0.268900649 0.570408149 0.008927761 TS(ph)SESIISVPASSTSGSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSESIISVPASSTSGSPSR 20 0 Q6H8Q1-7;Q6H8Q1-2;Q6H8Q1;D6RAL0;F5GYR0;Q6H8Q1-8;Q6H8Q1-3;Q6H8Q1-5;Q6H8Q1-9;Q6H8Q1-4;Q6H8Q1-6 Q6H8Q1-7 ABLIM2 Actin-binding LIM protein 2 1 T(0.25)S(0.749)S(0.001)ESIISVPASSTSGSPSR 178.76 6.37E-17 88877000 66035 62902 61821 54429 58426 56755 60217 74230 73232 66162 TRUE FALSE 63454.27919 61108.09655 72993.4299 57238.08721 60305.32535 57902.62499 60953.95366 72697.12456 64919.01037 61680.78881 1.028752719 0.990715225 1.183406232 0.927972685 0.977700294 0.938746506 0.988216183 1.178602381 1.052499678 1 15.91253359 -0.568662922 7.138880369 1.000000005 1.034644629 0.007853615 0.084327202 0 0 0.085917771 0.020251013 0.26998341 0.568662922 0.034644623 FESDPATHNEPGVR ddPTM_BT-474_Pertuzumab_2h_R1 4 FESDPATHNEPGVR 14 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;D6R9Y6;D6RDP1 D6RGI3 11-Sep Septin-11 0 ;;; 170.79 3.12E-06 4172010000 4775390 5548400 4574120 5746230 5306230 5699600 5522020 5215130 5504230 5774860 FALSE TRUE 4588762.479 5390165.064 5400765.235 6042793.619 5476909.707 5814849.817 5589600.133 5107435.743 4879412.886 5383723.588 0.85233991 1.001196472 1.003165401 1.122418995 1.01730886 1.080079562 1.038240549 0.948680901 0.906326784 1 22.36017291 -0.567316637 4.322839323 0.999999982 1.001736242 0 0.07517746 1.11E-09 2.56E-10 0.074174603 0.017483111 0.27082164 0.567316637 0.00173626 EKVELQHIS(ph)QK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKVELQHISQK 11 1 Q9UBU7 Q9UBU7 DBF4 Protein DBF4 homolog A 1 EKVELQHIS(1)QK;EKVELQHIS(1)QK 85.493 0.0091643 683710000 1578260 1190850 1114050 1031990 1142860 1046790 1191550 1307600 1423990 1537100 TRUE FALSE 1516579.854 1156888.124 1315383.617 1085251.128 1179621.13 1067956.811 1206132.545 1280597.603 1262344.625 1432990.848 1.058331849 0.807324154 0.917928833 0.757332909 0.823188181 0.745264223 0.841688938 0.893653721 0.880916041 1 20.45059796 -0.56661547 8.112892216 0.99999997 0.853460904 0.197061911 0.085222177 0 0 0.07905007 0.01863228 0.271259234 0.56661547 -0.146539066 LECVEPNCR ddPTM_BT-474_Pertuzumab_2h_R1 4 LECVEPNCR 9 0 H0Y5B4;H7BZ11;J3KQN4;P83881;Q969Q0 H0Y5B4;Q969Q0 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a;60S ribosomal protein L36a-like 0 ;;; 177.97 0.00011981 1630810000 1341200 1323160 1137950 1291050 1346230 1384020 1257300 1344130 1433270 1407730 FALSE TRUE 1288784.421 1285424.772 1343602.879 1357681.245 1389532.711 1412005.833 1272687.214 1316373.246 1270571.198 1312383.193 0.982018383 0.979458423 1.023788544 1.034515873 1.058785816 1.075909719 0.969752752 1.003040311 0.968140407 1 20.32375759 -0.56525505 7.618263921 1 1.011692193 0.007093012 0.035579521 0 0 0.036584518 0.008623054 0.272110281 0.56525505 0.011692193 NQDNLQGWNK ddPTM_BT-474_Pertuzumab_2h_R1 2 NQDNLQGWNK 10 0 P30085;P30085-3;A0A494BXC7;P30085-2;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ; 180.67 4.59E-06 110382000 268950 259720 210862 240773 219348 196706 255280 261360 268130 279470 FALSE TRUE 258439.1367 252313.0399 248969.454 253199.3234 226403.5276 200683.5301 258404.193 255962.8247 237693.0065 260541.248 0.991931752 0.968418789 0.955585559 0.97182049 0.868973836 0.770256271 0.991797633 0.982427261 0.912304705 1 17.99115227 -0.564715128 6.44118181 1 0.936649139 0.079920762 0.066073646 0 0 0.067802858 0.015981287 0.272448783 0.564715128 -0.063350861 FAMEPEEFDSDTLR ddPTM_BT-474_Pertuzumab_2h_R1 7 FAMEPEEFDSDTLR 14 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;;; 386.5 1.51E-113 3257690000 1640750 1986030 1611750 2036650 1985750 2025150 1895210 1842620 1960180 1980690 FALSE TRUE 1576627.676 1929390.369 1903029.078 2141761.751 2049623.452 2066099.921 1918404.147 1804569.253 1737668.584 1846536.102 0.853829868 1.044870104 1.030594027 1.159880789 1.109982875 1.118905782 1.038920466 0.977272663 0.941042302 1 20.81639004 -0.562179256 5.84049768 1 1.035880349 0.007969969 0.085702983 0 0 0.085954922 0.020259769 0.274044281 0.562179256 0.035880349 RQDFNPCEYDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQDFNPCEYDLK 12 1 Q9BZE9;Q9BZE9-2;J3QL04;C9JAL9;J3QR50;J3QRW3;J3KRG1 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 0 122.34 0.00035615 0 274780 266470 221130 198860 223390 215490 245910 300140 258130 271550 FALSE TRUE 264041.2938 258870.5365 261093.11 209123.1884 230575.5422 219847.3554 248919.5201 293942.0041 228828.1646 253157.6766 1.042991456 1.02256641 1.031345814 0.826059044 0.910798145 0.868420655 0.983258827 1.161102472 0.903895816 1 17.94967671 -0.561768118 8.091538994 1.000000001 0.980226537 0.00138908 0.093800549 0 0 0.099683092 0.02349553 0.274303837 0.561768118 -0.019773464 SRS(ph)PIIHS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPIIHSPK 10 1 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 2 S(0.397)RS(0.603)PIIHS(1)PK 92.575 0.012443 157730000 121350 118180 107700 94986 92808 110520 119070 113100 145810 126180 TRUE FALSE 116607.5078 114809.6221 127163.7858 99888.23884 95793.25361 112754.7901 120527.2143 110764.4455 129258.2601 117633.7162 0.991276239 0.975992477 1.081014779 0.849146334 0.814335011 0.958524424 1.024597523 0.941604576 1.09881983 1 16.8439421 -0.561638665 8.040198688 0.999999701 0.965995954 0.008068242 0.08505899 0 0 0.083595683 0.019703691 0.274385613 0.561638665 -0.034003747 YTVQDESHSEWVSCVR ddPTM_BT-474_Pertuzumab_2h_R1 5 YTVQDESHSEWVSCVR 16 0 P63244;J3KPE3;D6RHH4;H0YAF8;D6R9L0;H0Y8W2;D6R9Z1;D6RFX4;D6RFZ9;H0YAM7;D6RBD0 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;;; 276.18 2.75E-35 9247450000 2706226 2836866 2363667 3006564 2815414 2869228 3009978 2679137 2922018 3062419 FALSE TRUE 2600463.696 2755961.359 2790834.206 3161733.128 2905974.348 2927245.756 3046815.011 2623811.885 2590322.767 2854998.633 0.910845864 0.965310921 0.977525584 1.107437703 1.0178549 1.025305484 1.067186154 0.919023867 0.907293873 1 21.44505862 -0.560122408 7.559786267 1.000000001 0.991253499 0.001342414 0.063816071 0 0 0.06478247 0.015269375 0.275345252 0.560122408 -0.008746503 VFSWLQQEGHLSEEEMAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VFSWLQQEGHLSEEEMAR 18 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 248.13 1.84E-24 88895000 46896 64588 53064 71367 63242 71540 60896 56800 62806 70455 FALSE TRUE 45063.25247 62746.01348 62653.8452 75050.25942 65276.23636 72986.58782 61641.26346 55627.06015 55676.52618 65683.0201 0.686071566 0.955285147 0.953881918 1.142612799 0.993806866 1.111194152 0.938465731 0.846901681 0.847654784 1 16.00323284 -0.557498404 5.986527228 0.999980649 0.947482156 0.017413659 0.124749403 0 0 0.124518661 0.02934933 0.277013922 0.557498404 -0.052498493 GGAAPEGPNEAEVTSGKPEQEVPDAEEEKS(ph)VSGTDVQEECR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGAAPEGPNEAEVTSGKPEQEVPDAEEEKSVSGTDVQEECR 41 2 P49321;P49321-3;P49321-4;E9PPR5 P49321 NASP Nuclear autoantigenic sperm protein 1 GGAAPEGPNEAEVTSGKPEQEVPDAEEEKS(0.993)VS(0.006)GTDVQEECR;GGAAPEGPNEAEVTSGKPEQEVPDAEEEKS(0.639)VS(0.18)GT(0.18)DVQEECR 220.75 2.46E-44 650060000 188905 162388 119461 110719 144347 136676 134414 149837 188199 175215 TRUE FALSE 181522.3838 157756.8532 141050.2601 116433.2209 148990.0523 139439.6824 136058.9987 146742.8136 166835.4385 163347.532 1.11126493 0.96577433 0.863497957 0.712794491 0.912104704 0.853638134 0.83294187 0.898347296 1.021352674 1 17.31758513 -0.553855576 9.721500653 1 0.897728928 0.058635237 0.103552665 0 0 0.101633542 0.023955256 0.279347265 0.553855576 -0.102271071 LDINLLDNVVNCLYHGEGAQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDINLLDNVVNCLYHGEGAQQR 22 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;C9JF49 O14980 XPO1 Exportin-1 0 ; 278.98 1.44E-45 1973830000 384610 402200 339800 375580 400370 418920 357180 372510 449190 417960 FALSE TRUE 369579.016 390729.6498 401209.4188 394963.7288 413248.2647 427390.8494 361551.2757 364817.5383 398199.8344 389651.1969 0.948486798 1.002767739 1.029662996 1.013634071 1.060559464 1.096854964 0.927884422 0.936266952 1.021939205 1 18.57182372 -0.552968743 5.763584798 1 1.001395298 0 0.051410692 0 2.10E-18 0.054722202 0.012898147 0.279918277 0.552968743 0.001395298 CPNLTHLNLSGNK ddPTM_BT-474_Pertuzumab_2h_R1 2 CPNLTHLNLSGNK 13 0 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 199.31 1.19E-07 1621490000 2335600 2271900 1928910 1911380 1904630 1485660 2137700 2265900 2621500 2527100 FALSE TRUE 2244322.17 2207107.636 2277506.945 2010026.551 1965894.154 1515701.063 2163861.812 2219108.373 2323918.31 2355937.266 0.95262391 0.936827847 0.966709504 0.853174904 0.834442488 0.643353745 0.918471745 0.941921674 0.986409249 1 21.16786969 -0.55229465 6.633908269 1.000002075 0.890800708 0.10299209 0.094891903 0 0 0.097767385 0.023043993 0.280353092 0.55229465 -0.109201367 MPLLELGGET(ph)TPPLS(ph)TERSPEAVGSECPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.496)T(0.496)PPLS(0.355)T(0.355)ERS(0.298)PEAVGSECPSR 59.954 0.016602 86910000 63617 70963 57219 69664 63668 71296 66073 67402 65998 76431 TRUE FALSE 61130.77731 68939.20472 67559.74613 73259.36739 65715.93904 72737.65397 66881.62114 66010.12515 58506.18373 71254.26029 0.857924523 0.967509935 0.94815027 1.028140171 0.922273823 1.020818316 0.938633295 0.926402504 0.821090325 1 16.12068866 -0.551411158 5.412448263 0.999999999 0.941768839 0.084322703 0.060523828 7569960.937 1398620.564 0.077294373 0.013747545 0.280923999 0.551411158 -0.05823116 VDSSTNS(ph)SPSPQQSESLS(ph)PAHTSDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDSSTNSSPSPQQSESLSPAHTSDFR 26 0 F2Z3H6;Q9BQE9-2;Q9BQE9-3;Q9BQE9 F2Z3H6 BCL7B B-cell CLL/lymphoma 7 protein family member B 2 VDS(0.003)S(0.004)T(0.017)NS(0.509)S(0.436)PS(0.031)PQQS(0.01)ES(0.391)LS(0.598)PAHT(0.001)S(0.001)DFR 116.59 0.00050685 234210000 54152 95068 71987 112730 79050 103440 85104 82565 78840 99423 TRUE FALSE 52035.67997 92356.75372 84996.65224 118548.0088 81592.71504 105531.6277 86145.52821 80860.0039 69890.41372 92688.99165 0.561400864 0.996415562 0.917009137 1.278986929 0.880284849 1.138556217 0.929404093 0.872379799 0.754031439 1 16.50011038 -0.551408422 6.506272937 1.000000011 0.938103194 0.010235643 0.185405956 0 0 0.173003355 0.040777282 0.280925769 0.551408422 -0.061896817 KTKPYIQVDIGGGQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTKPYIQVDIGGGQTK 16 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 164.01 4.23E-09 1280670000 1912830 2118300 1557220 1660710 1523550 1626870 1790100 1824730 2363500 2165500 FALSE TRUE 1838074.489 2057888.158 1838644.294 1746419.442 1572556.369 1659766.426 1812007.779 1787048.688 2095205.389 2018828.756 0.910465775 1.019347556 0.910748021 0.865065666 0.778944903 0.822143246 0.897553977 0.885190823 1.03783215 1 20.94508711 -0.551064124 6.551846723 0.999999775 0.898262049 0.129009273 0.07466616 0 0 0.075607091 0.017820762 0.281148568 0.551064124 -0.101737726 IPCES(ph)PPLEVVDTTASTK ddPTM_BT-474_Pertuzumab_2h_R1 2 IPCESPPLEVVDTTASTK 18 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 IPCES(1)PPLEVVDTTASTK;IPCES(1)PPLEVVDTTASTK 192.55 1.42E-18 0 252930 160692 155810 154376 230190 141059 131791 202663 117084 97116 TRUE FALSE 243045.216 156109.2215 183968.333 162343.3639 237594.2704 143911.3096 133403.8977 198477.9382 103793.1152 90538.24682 2.684448004 1.724235083 2.031940527 1.793091534 2.624242005 1.589508464 1.473453511 2.192199929 1.146400762 1 16.46623975 -0.551017862 0.140603554 9.36E-10 2.575456581 0.462452597 0.393902278 22.96801056 0.826003964 12.26269732 3.449269985 0.281178518 0.551017862 2.57545658 EHIEDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHIEDFK 7 0 A0A669KBJ7;Q9H2P0;A0A2R8YCL6 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 128.57 0.0037452 847130000 2123300 2078000 1827520 1951310 2149200 2144800 2171800 1564650 2670400 2551500 FALSE TRUE 2040319.089 2018737.475 2157793.517 2052017.343 2218330.97 2188169.326 2198379.138 1532339.431 2367267.387 2378684.632 0.857750986 0.848678066 0.907137284 0.862668937 0.932587254 0.919907286 0.924199496 0.644196128 0.995200185 1 21.18173258 -0.54859095 8.557614443 1 0.865131813 0.135686832 0.088806343 0 0 0.089065087 0.020992842 0.282754191 0.54859095 -0.134868187 ILVLDDTNHER ddPTM_BT-474_Pertuzumab_2h_R1 1 ILVLDDTNHER 11 0 K7EN66;C9K0L8;K7ERZ0;K7ERC4;P09543-2;P09543 K7EN66 CNP "2,3-cyclic-nucleotide 3-phosphodiesterase" 0 208.72 1.86E-08 152560000 189160 250150 186970 275730 196990 221900 253200 253310 199760 217680 FALSE TRUE 181767.4181 243015.9669 220759.6381 289960.4583 203326.3623 226386.97 256298.7373 248079.06 177084.0823 202936.3397 0.895686886 1.197498522 1.087827042 1.428824718 1.001921896 1.115556585 1.262951415 1.222447691 0.872609029 1 17.63066771 -0.548557034 5.665992789 1.000000026 1.139948513 0.035731832 0.161924179 0 7.77E-10 0.147721321 0.034818249 0.282776273 0.548557034 0.139948487 EWNGVVSESDS(ph)PVKRPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 EWNGVVSESDSPVKRPGR 18 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 EWNGVVSESDS(1)PVKRPGR;EWNGVVSESDS(1)PVKRPGR;EWNGVVSESDS(1)PVKRPGR;EWNGVVSESDS(1)PVKRPGR 262.78 3.86E-31 14407300000 9253100 8492600 6722400 7508900 7459600 7311700 8402700 8733400 8499400 9269500 TRUE FALSE 8891478.622 8250399.363 7937287.219 7896435.229 7699544.809 7459547.584 8505534.756 8553052.238 7534583.744 8641668.509 1.028907625 0.954722963 0.918490129 0.913762802 0.890978959 0.863206865 0.984246821 0.989745468 0.871889929 1 23.04287846 -0.547120279 7.678648803 1 0.937215286 0.124098765 0.051447533 0 0 0.051666544 0.012177921 0.283713317 0.547120279 -0.062784713 NPISGLLEYAQFASQTCEFNMIEQSGPPHEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NPISGLLEYAQFASQTCEFNMIEQSGPPHEPR 32 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 256.05 3.61E-59 306380000 147381 171967 147994 172180 167724 171253 170147 150612 189140 172496 FALSE TRUE 141621.1876 167062.6695 174739.8079 181066.2304 173118.9948 174715.853 172229.3099 147501.8096 167669.6201 160812.6923 0.880659266 1.03886495 1.08660458 1.125944898 1.076525692 1.086455618 1.070993262 0.917227412 1.042639221 1 17.29502175 -0.543821574 6.988916333 0.999999994 1.035880524 0.021234722 0.073725221 0 0 0.075419038 0.017776438 0.28587648 0.543821574 0.03588053 YQEALHLGSQLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YQEALHLGSQLLR 13 0 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 172.85 2.27E-05 2613400000 2315800 3067500 2537100 3350900 2962400 2722400 3000800 2832000 2728400 3287100 FALSE TRUE 2225295.976 2980017.903 2995610.407 3523840.351 3057688.286 2777448.793 3037524.688 2773518.21 2418683.47 3064461.789 0.726162089 0.972444138 0.977532309 1.149905136 0.99778966 0.906341467 0.991209843 0.905058833 0.789268601 1 21.54720229 -0.541184211 7.684114493 0.999806855 0.944461411 0.02365586 0.11129164 0 0 0.107914855 0.025435775 0.287617819 0.541184211 -0.055345444 NYQQNYQNSES(ph)GEKNEGSESAPEGQAQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(0.143)ES(0.857)GEKNEGSESAPEGQAQQR 505.12 2.06E-301 1050400000 882430 744320 584840 502970 653610 580220 520440 831120 854900 737970 TRUE FALSE 847943.66 723092.7224 690533.5977 528928.342 674633.9592 591952.4459 526809.3004 813957.0816 757855.336 687986.6346 1.232500193 1.051027282 1.003702053 0.76880613 0.980591665 0.860412712 0.765726068 1.183100137 1.101555318 1 19.39202101 -0.539999771 6.714227181 1.000000025 0.989253999 0 0.151201329 0 0 0.151545874 0.035719705 0.288403302 0.539999771 -0.010746027 TLHPDLGTDKDK ddPTM_BT-474_Pertuzumab_2h_R1 5 TLHPDLGTDKDK 12 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;; 163.99 3.51E-05 5808650000 11110300 8983700 9189800 8648900 8437400 7569100 9093000 10593900 12212100 9227400 FALSE TRUE 10676097.19 8727493.672 10850601.29 9095270.765 8708796.634 7722152.388 9204282.854 10375132.26 10825833.61 8602419.979 1.241057426 1.014539361 1.261342891 1.057292109 1.012365899 0.897672098 1.069964368 1.206071348 1.258463738 1 23.03631114 -0.539761389 6.573877893 0.999961836 1.108879028 0.075309787 0.118125771 0 0 0.117797501 0.027765137 0.288561649 0.539761389 0.108917192 ERPLLLEEQPLLLQDLLDQER ddPTM_BT-474_Pertuzumab_2h_R1 3 ERPLLLEEQPLLLQDLLDQER 21 1 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 0 ;; 168.3 1.00E-11 62106000 42624 40163.2 36604.9 42483 41445 44922 38284.8 41696 41316 46516 FALSE TRUE 40958.20696 39017.78486 43220.2197 44675.55272 42778.11606 45830.35362 38753.34083 40834.96303 36625.98089 43365.42989 0.944489817 0.899743989 0.996651476 1.030211227 0.986456636 1.056840754 0.893645951 0.941647832 0.844589365 1 15.40425779 -0.539380574 5.271766015 0.999999998 0.956870104 0.045006201 0.061711921 3.497507307 44522792.55 0.139918546 0.014831332 0.288814788 0.539380574 -0.043129895 MTNNEDSLS(ph)PTSSTLSNLELDAAEKDR ddPTM_BT-474_Pertuzumab_2h_R1 4 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 MTNNEDS(0.007)LS(0.925)PT(0.067)S(0.001)STLSNLELDAAEKDR;MTNNEDS(0.192)LS(0.7)PT(0.102)S(0.004)S(0.001)TLSNLELDAAEKDR;MT(0.001)NNEDS(0.224)LS(0.589)PT(0.14)S(0.034)S(0.009)T(0.002)LSNLELDAAEKDR;MTNNEDS(0.341)LS(0.645)PT(0.011)S(0.002)S(0.001)TLSNLELDAAEKDR 181.13 1.05E-17 1574330000 660380 687660 615750 659040 707130 723750 628020 740300 720880 697160 TRUE FALSE 634571.6195 668048.6101 727029.7223 693053.1334 729875.4786 738384.7209 635705.8966 725012.5463 639048.7246 649940.7322 0.976353055 1.027860814 1.118609261 1.066332819 1.122987747 1.136080083 0.978098256 1.11550563 0.983241537 1 19.30994864 -0.538440028 6.061212899 1 1.063971939 0.069483835 0.060993239 0 0 0.056578966 0.01333579 0.289440948 0.538440028 0.063971939 SLQEEHVAVAQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLQEEHVAVAQLR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 156.24 4.71E-05 3212500000 1573250 1974000 1616770 2102200 1874910 1943090 2051460 1841990 1784340 1981050 FALSE TRUE 1511765.651 1917703.453 1908956.304 2210694.794 1935218.183 1982380.611 2076566.381 1803952.263 1581789.204 1846871.719 0.818554768 1.038352276 1.033616079 1.196994232 1.047835734 1.073372119 1.124369581 0.976760998 0.856469449 1 20.81665223 -0.537958293 5.921923588 1.000000137 1.02826675 0 0.107888257 0 0 0.10394478 0.02450002 0.289762185 0.537958293 0.028266613 ET(ph)ERQWLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETERQWLIR 9 1 Q9BZV3 Q9BZV3 IMPG2 Interphotoreceptor matrix proteoglycan 2 1 ET(1)ERQWLIR 68.735 0.092523 263560000 16175 16469 17673 15677 18424 23310 19366 14871 15493 13057 TRUE FALSE 15542.86312 15999.32024 20866.90423 16486.09185 19016.62469 23781.34417 19603.0069 14563.90865 13734.29959 12172.63776 1.276868944 1.314367564 1.71424671 1.354356564 1.562243539 1.953672215 1.610415695 1.196446402 1.128292804 1 13.57135421 -0.536899093 7.139098069 0.99990977 1.462176596 0.242101936 0.242280423 0 0 0.249283299 0.058756637 0.290469748 0.536899093 0.462266826 LLDSSTVTHLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDSSTVTHLFK 12 0 G3V5Z7;P60900;G3V3I1;G3V295;P60900-2;G3V3U4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 224.82 1.92E-11 3483300000 5278200 5818800 5119500 5256800 4843700 3969700 6124400 5640200 5821600 6452900 FALSE TRUE 5071922.109 5652853.521 6044707.533 5528104.078 4999502.009 4049970.054 6199352.239 5523727.899 5160756.374 6015839.335 0.843094675 0.939661651 1.004798698 0.91892482 0.831056438 0.673217789 1.030504954 0.918197377 0.857861403 1 22.52033461 -0.535328958 11.28502674 1 0.896135102 0.103255952 0.095377793 0 0 0.09414258 0.022189619 0.291521803 0.535328958 -0.103864898 LLEDFGDGGAFPEIHVAQYPLDMGR ddPTM_BT-474_Pertuzumab_2h_R1 5 LLEDFGDGGAFPEIHVAQYPLDMGR 25 0 Q13573;G3V3A4;G3V5R3 Q13573 SNW1 SNW domain-containing protein 1 0 ;;;; 197.12 8.27E-25 892380000 705798 704230 613243 726258 725851 770748 685346 697556 750266 788787 FALSE TRUE 678214.6339 684146.0499 724069.6516 763740.2624 749198.6566 786333.0526 693733.4694 683151.2248 665098.9491 735361.7539 0.922287065 0.930353049 0.984644153 1.038591222 1.018816457 1.06931459 0.94339074 0.929000211 0.904451374 1 19.48809462 -0.534011792 6.006265769 0.999999988 0.972273686 0.025883591 0.052627841 0 0 0.055997662 0.013198775 0.292407298 0.534011792 -0.027726302 GHSAQIAKPIRPGQHPAAS(ph)PTHPSAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHSAQIAKPIRPGQHPAASPTHPSAIR 27 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 1 GHSAQIAKPIRPGQHPAAS(0.953)PT(0.047)HPSAIR;GHSAQIAKPIRPGQHPAAS(0.994)PT(0.006)HPSAIR 178.89 1.25E-17 6386400000 1015040 1371740 1476950 1831720 1476340 1650710 1661140 758950 1507670 2024470 TRUE FALSE 975371.1146 1332619.318 1743867.72 1926255.289 1523827.817 1684088.487 1681469.528 743277.4173 1336525.622 1887350.844 0.516793747 0.706079277 0.923976443 1.020613255 0.807389798 0.892302824 0.890915186 0.393820481 0.708149005 1 20.8479312 -0.53294197 7.58024996 1.000001238 0.75698349 0.132772772 0.181860289 0 0 0.194196849 0.045772636 0.293128489 0.53294197 -0.243017748 LDS(ph)PPPS(ph)PITEASEAAEAAEAGNLAVSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 LDS(0.999)PPPS(0.994)PIT(0.007)EASEAAEAAEAGNLAVSSR;LDS(0.999)PPPS(0.986)PIT(0.015)EASEAAEAAEAGNLAVSSR;LDS(0.5)PPPS(0.5)PIT(0.5)EAS(0.5)EAAEAAEAGNLAVSSR;LDS(0.914)PPPS(0.844)PIT(0.237)EAS(0.005)EAAEAAEAGNLAVSSR;LDS(1)PPPS(0.986)PIT(0.014)EASEAAEAAEAGNLAVSSR 239.93 1.16E-45 709277000 127116.4 132965 122086.5 129221.3 134244.5 136915.9 129675.8 141896.9 144918.2 129917 TRUE FALSE 122148.5506 129172.9684 144150.2463 135890.4268 138562.5963 139684.4333 131262.8112 138966.6794 128467.6935 121117.6059 1.008511931 1.066508601 1.190167567 1.121970879 1.144033481 1.153295859 1.083763259 1.147369769 1.060685542 1 16.88604907 -0.531285223 7.61441235 1 1.113860177 0.280094338 0.051527552 0 0 0.049248087 0.011607885 0.294248852 0.531285223 0.113860177 DSLPLPVRSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSLPLPVRSR 10 1 A0A0A0MSK4;A0A0A0MRC4;Q86YR5-4;Q86YR5 A0A0A0MSK4 GPSM1 G-protein-signaling modulator 1 0 ; 61.78 0.081505 1161520000 120816 129897 100723 112318 131770 122364 126915 140107 101254 118124 FALSE TRUE 116094.3772 126192.4647 118925.8867 118114.7454 136008.5017 124838.2839 128468.2237 137213.7415 89760.07041 110123.3563 1.054221203 1.145919168 1.079933365 1.072567614 1.235055908 1.133622223 1.166584711 1.246000359 0.815086585 1 16.74876096 -0.530330411 8.090843501 1.000007107 1.12163749 0.054077334 0.115649837 0 0 0.105991686 0.02498248 0.29489648 0.530330411 0.121630383 VPGEDGTLPPTQGS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPGEDGTLPPTQGSPLR 17 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 VPGEDGTLPPT(0.101)QGS(0.899)PLR;VPGEDGT(0.001)LPPT(0.047)QGS(0.952)PLR 92.439 0.0034704 120710000 128506 129877 92836 89389 108567 109237 111664 124112 126328 126684 TRUE FALSE 123483.8434 126173.0351 109613.5303 94002.377 112059.1562 111445.847 113030.5774 121549.0438 111987.7751 118103.5798 1.045555466 1.068325239 0.928113529 0.795931649 0.948820995 0.943628018 0.957046159 1.029173239 0.948216601 1 16.84969317 -0.529122988 8.049914624 0.999979988 0.963548751 0.023230452 0.07228557 0 0 0.075295851 0.017747402 0.29571749 0.529122988 -0.036431237 T(ph)PVDRDT(ph)EDGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPVDRDTEDGLK 12 1 Q9NVR0 Q9NVR0 KLHL11 Kelch-like protein 11 2 T(1)PVDRDT(1)EDGLK 82.749 0.0456 725480000 419100 732660 564330 792820 641150 785080 665390 636820 564140 758650 TRUE FALSE 402721.1087 711765.2541 666316.9845 833737.5352 661773.172 800954.8555 673533.2419 623669.4445 500101.1923 707265.9598 0.569405473 1.006361531 0.942102437 1.178817563 0.935677962 1.132466287 0.952305469 0.881803282 0.707090714 1 19.4318933 -0.528007108 10.40080132 1 0.937402343 0.011662589 0.171140348 0 0 0.160990155 0.037945744 0.296478286 0.528007108 -0.062597657 SHPLDPIDTVDFER ddPTM_BT-474_Pertuzumab_2h_R1 7 SHPLDPIDTVDFER 14 0 P47897;A0A1B0GVU9;P47897-2;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 0 ;;;;;; 242.79 1.68E-17 4036244000 1985810 2170510 1808526 2334180 2178700 2308650 2287080 1891014 2364040 2433590 FALSE TRUE 1908202.35 2108609.18 2135366.879 2454647.31 2248779.864 2355332.485 2315069.969 1851963.9 2095684.09 2268760.782 0.841076929 0.929410098 0.941204069 1.081933066 0.991193026 1.038158145 1.020411666 0.816288749 0.923713116 1 21.11347307 -0.527464155 7.549493838 0.999999996 0.952872343 0.02976775 0.079152102 0 0 0.082873153 0.019533389 0.296849174 0.527464155 -0.047127653 ELFSPLHALNFGIGGDTTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELFSPLHALNFGIGGDTTR 19 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 260.53 4.11E-31 2124500000 1200390 1442190 1173780 1638150 1441810 1521930 1360980 1452390 1319790 1416190 FALSE TRUE 1153477.432 1401060.153 1385908.157 1722695.118 1488187.128 1552704.467 1377636.08 1422397.639 1169972.972 1320270.19 0.873667709 1.061191992 1.049715556 1.304804979 1.127183768 1.176050538 1.043450114 1.077353446 0.886161773 1 20.33240177 -0.527375949 6.090958943 1 1.077117923 0.020407045 0.12005415 0 0 0.11604651 0.027352425 0.296909471 0.527375949 0.077117924 ARLS(ph)YSDK ddPTM_BT-474_Pertuzumab_2h_R1 7 ARLSYSDK 8 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 ARLS(1)YSDK;ARLS(0.997)YS(0.003)DK;ARLS(0.999)YS(0.001)DK;ARLS(0.997)YS(0.003)DK;ARLS(0.997)YS(0.003)DK;ARLS(1)YSDK;ARLS(1)YSDK 174.77 0.00016353 12798800000 6638021 5667107 5054840 5288318 5287829 4747785 5216186 6892293 6522440 5921286 TRUE FALSE 6378599.801 5505486.657 5968362.032 5561248.726 5457916.822 4843788.466 5280023.245 6749964.741 5782039.955 5520232.025 1.155494873 0.99732885 1.08117956 1.007430249 0.988711488 0.877461028 0.956485746 1.222768302 1.047426979 1 22.39629748 -0.5241738 7.938112613 1 1.040183938 0.0130794 0.09349314 0 0 0.097323056 0.022939264 0.29910674 0.5241738 0.040183938 MAPALSGANLTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 MAPALSGANLTSPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MAPALSGANLT(0.054)S(0.946)PR;MAPALSGANLT(0.002)S(0.998)PR;MAPALSGANLTS(1)PR;MAPALSGANLT(0.001)S(0.999)PR;MAPALSGANLT(0.01)S(0.99)PR;MAPALSGANLT(0.011)S(0.989)PR 197.73 2.42E-08 6720360000 2618040 2756690 2498340 2855110 2651910 2863520 2723300 2810020 2641380 3003890 TRUE FALSE 2515724.102 2678071.9 2949845.613 3002462.569 2737211.094 2921422.336 2756628.56 2751992.105 2341541.616 2800433.855 0.898333699 0.956306072 1.053353075 1.072141934 0.977423941 1.043203478 0.984357676 0.982702055 0.836135305 1 21.41721892 -0.523925646 5.358716786 0.999999991 0.98465533 0.001168562 0.067949004 0 1.72E-18 0.065698534 0.015485293 0.299277697 0.523925646 -0.015344661 DYIAPWER ddPTM_BT-474_Pertuzumab_2h_R1 1 DYIAPWER 8 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 0 106.93 0.01462 0 207270 212920 189590 250100 215970 242970 217720 222530 209230 250820 FALSE TRUE 199169.6593 206847.7301 223853.1304 263007.691 222916.8712 247883.0199 220384.5225 217934.6777 185479.0876 233831.738 0.851764867 0.884600747 0.957325692 1.12477328 0.953321705 1.060091423 0.942491915 0.932014959 0.79321605 1 17.83511123 -0.523690732 6.351963926 1.00000001 0.950630279 0.028921941 0.090380236 0 0 0.089162536 0.021015811 0.299439624 0.523690732 -0.049369731 KAVVVCPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAVVVCPK 8 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 92.439 0.018883 2028670000 4829900 4226900 3912900 3312400 3735700 3612300 3971200 4737700 4520900 4561200 FALSE TRUE 4641142.168 4106352.951 4620048.072 3483353.361 3855862.183 3685343.181 4019800.734 4639864.839 4007706.385 4252265.861 1.091451551 0.965685845 1.086490879 0.819175817 0.906778247 0.866677508 0.945331469 1.091151163 0.942487256 1 22.01980037 -0.522630475 5.974011511 1.000000015 0.970454793 0.010419855 0.090453339 0 0 0.090497234 0.021330403 0.300171548 0.522630475 -0.029545222 S(ph)PFLKPDER ddPTM_BT-474_Pertuzumab_2h_R1 5 SPFLKPDER 9 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 S(1)PFLKPDER;S(1)PFLKPDER;S(1)PFLKPDER;S(1)PFLKPDER;S(1)PFLKPDER 105.17 0.0019024 2304670000 2607190 2447000 2160390 2172620 2138080 1987010 2288920 2649830 2634630 2592830 TRUE FALSE 2505298.132 2377213.956 2550820.531 2284749.179 2206853.285 2027188.704 2316932.488 2595110.085 2335557.848 2417215.315 1.03643979 0.983451471 1.055272369 0.945198868 0.9129734 0.83864631 0.958513076 1.073594921 0.966218373 1 21.20491456 -0.52169254 6.536412554 1 0.976895141 0.012054088 0.066134457 0 0 0.070149007 0.016534279 0.300820522 0.52169254 -0.023104859 GPQLFHMDPSGTFVQCDAR ddPTM_BT-474_Pertuzumab_2h_R1 8 GPQLFHMDPSGTFVQCDAR 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;;;;;; 221.85 2.57E-19 7331610000 3755900 3846880 3460770 4066770 3910090 3868870 4015100 3532800 4081240 4392120 FALSE TRUE 3609115.276 3737170.749 4086208.123 4276656.487 4035861.596 3947101.202 4064237.995 3459846.445 3617954.745 4094637.8 0.881424793 0.912698737 0.997941289 1.04445294 0.985645567 0.96396834 0.992575703 0.844970084 0.883583585 1 21.96530441 -0.521300362 6.887790264 1.000002727 0.945216076 0.070016302 0.059859466 0 0 0.0643602 0.015169845 0.301092292 0.521300362 -0.054786651 QSAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSAPSPTR 8 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 QS(0.002)APS(0.988)PT(0.01)R 63.212 0.078403 186180000 184310 234520 185720 226890 231990 225510 218770 215530 220690 225280 TRUE FALSE 177106.9614 227831.7192 219283.7353 238599.8201 239452.169 230069.9667 221447.3727 211079.2302 195638.1964 210021.5849 0.843279806 1.084801447 1.044100945 1.136072848 1.140131235 1.095458673 1.054402921 1.005035888 0.931514713 1 17.68017808 -0.520673704 6.338829714 1 1.044420963 0.010023967 0.087551395 0 0 0.084631133 0.019947749 0.301527062 0.520673704 0.044420963 TVAISDAAQLPHDYCTT(ph)PGGTLFSTTPGGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDY(0.001)CT(0.092)T(0.879)PGGT(0.026)LFS(0.002)TTPGGTR 109.27 0.00042173 436170000 36052 38218 28208 39523 38302 35364 35952 36196 37127 37874 TRUE FALSE 34643.04798 37128.06006 33305.81308 41562.78677 39534.01861 36079.08431 36391.99133 35448.53995 32912.49861 35308.76025 0.981145975 1.051525452 0.943273365 1.177123934 1.119666008 1.021816797 1.03067882 1.003958783 0.932134076 1 15.10773855 -0.519856643 5.665113662 1 1.032035844 0.013255813 0.071030244 0 0 0.069537719 0.016390197 0.302094875 0.519856643 0.032035844 NSQGSEMFGDDDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSQGSEMFGDDDKR 14 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 149.22 2.02E-06 0 150790 139090 117830 119840 116350 121610 131890 148910 170810 131170 FALSE TRUE 144896.9601 135123.2894 139124.5021 126024.9568 120092.5034 124069.0375 133504.1093 145834.9565 151420.3649 122285.7391 1.184904807 1.104979946 1.137700137 1.030577709 0.982064665 1.014583045 1.09173899 1.192575337 1.238250397 1 16.89989664 -0.519778072 7.457110587 1.000000359 1.10614104 0.145893676 0.078625616 0 0 0.083833952 0.019759852 0.302149534 0.519778072 0.106140681 TPAAAAAMNLAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 10 TPAAAAAMNLASPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR 208.59 8.21E-09 7561161000 1307236 1401801 1231047 1422827 1473049 1453423 1368760 1459961 1417161 1481663 TRUE FALSE 1256147.772 1361823.008 1453524.577 1496259.272 1520430.959 1482812.209 1385511.294 1429812.295 1256290.825 1381308.645 0.90938964 0.98589335 1.052280808 1.08321864 1.100717761 1.073483623 1.003042513 1.035114274 0.909493203 1 20.39760429 -0.518796566 6.025111734 0.999999337 1.02349565 0 0.06390733 0 0 0.063339528 0.01492927 0.302833164 0.518796566 0.023496314 KREENLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KREENLK 7 2 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 96.111 0.0072959 368660000 397700 387990 305646 297773 338264 248046 366185 367850 433380 422010 FALSE TRUE 382157.4443 376924.9051 360883.0313 313141.1002 349144.5688 253061.6601 370666.4816 360253.769 384184.5193 393426.8868 0.971355688 0.958055785 0.917281059 0.79593213 0.887444607 0.643224112 0.942148323 0.91568162 0.976508043 1 18.58573603 -0.518635039 8.25565694 0.999999999 0.886868287 0.104952805 0.096272683 0 0 0.094675713 0.02231528 0.302945818 0.518635039 -0.113131712 GSLVDNIQQHFLLSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSLVDNIQQHFLLSDR 16 0 O43427-2;O43427;E9PSD3 O43427-2 FIBP Acidic fibroblast growth factor intracellular-binding protein 0 78.441 0.021128 94967000 31164 41162 29722 40654 35934 34162 43180 36147 35409 39250 FALSE TRUE 29946.07643 39988.10006 35093.42656 42752.15781 37089.84974 34852.77905 43708.44976 35400.55182 31389.51877 36591.56254 0.818387474 1.09282297 0.959057885 1.168361088 1.013617544 0.9524813 1.194495308 0.96745122 0.857834883 1 15.1592234 -0.517997357 6.105333359 1.00000197 1.013062245 0 0.115783616 0 0 0.105051006 0.024760759 0.303390964 0.517997357 0.013060275 ELGPQDLLWMLDHQEDGGEALR ddPTM_BT-474_Pertuzumab_2h_R1 5 ELGPQDLLWMLDHQEDGGEALR 22 0 Q8N0W3-2;Q8N0W3 Q8N0W3-2 FUK L-fucose kinase 0 ;;;; 228.29 3.76E-26 273705000 98518.3 118689 97854.9 118267.3 111772.2 121049 118244.9 104254 122147.4 125881.1 FALSE TRUE 94668.09592 115304.1059 115539.4572 124371.0895 115367.4543 123496.6937 119692.0165 102101.1185 108281.7392 117355.061 0.806680983 0.982523506 0.984528969 1.059784627 0.983063307 1.05233377 1.019913547 0.870018878 0.92268487 1 16.84052053 -0.516084425 9.219410966 1 0.966993011 0.018666291 0.07521171 0 0 0.075034796 0.017685871 0.304730255 0.516084425 -0.033006989 GWDDLFNK ddPTM_BT-474_Pertuzumab_2h_R1 2 GWDDLFNK 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 174.27 0.00063491 1087340000 1192040 1350030 1127970 1180910 1291520 1292980 1341150 1404390 1578560 1642510 FALSE TRUE 1145453.759 1311528.466 1331819.271 1241856.907 1333062.914 1319124.941 1357563.395 1375388.856 1399368.487 1531261.335 0.748045897 0.856502046 0.869753085 0.811002589 0.870565255 0.861462973 0.88656545 0.898206482 0.913866533 1 20.54628909 -0.515333172 0.025193096 1.911330581 3.06E-10 0.803276905 0.027512652 266.650649 1.583539733 67.3772922 53.01499059 0.305257841 0.515333172 -1.91133058 SRT(ph)S(ph)PAPWK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.346)RT(0.725)S(0.929)PAPWK 80.522 0.054708 1537200000 2535100 2102400 1814400 1938100 1899700 1739100 2006900 2661900 2487500 2037600 TRUE FALSE 2436025.489 2042441.61 2142302.441 2038125.573 1960805.576 1774265.794 2031461.043 2606930.835 2205129.428 1899591.537 1.282394368 1.075200416 1.127770049 1.072928329 1.032224843 0.934024899 1.069419927 1.372363892 1.160843995 1 20.8572578 -0.513371162 7.491577509 1.000013922 1.129408342 0.090225146 0.118646294 0 0 0.127434367 0.030036568 0.306640023 0.513371162 0.129394419 S(ph)PSPGPNHTSNSSNASNATVVPQNSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPGPNHTSNSSNASNATVVPQNSSAR 28 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.934)PS(0.066)PGPNHTSNSSNASNATVVPQNSSAR 230.69 2.93E-35 276160000 11814 18292 14495 24729 15383 19324 21173 16745 12798 18620 TRUE FALSE 11352.29582 17770.33007 17114.56894 26005.26665 15877.80817 19714.74452 21432.12151 16399.2099 11345.22469 17358.85082 0.653977382 1.023704291 0.985927532 1.498098401 0.914680835 1.135717147 1.234650942 0.944717486 0.653570033 1 14.08338382 -0.512841978 6.699242246 1.000000536 1.025195291 0 0.23997218 0 0 0.226828789 0.053464058 0.307013888 0.512841978 0.025194756 SLVHDLFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLVHDLFQK 9 0 Q9NTJ3;E9PD53;Q9NTJ3-2 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 120.12 0.0007167 360310000 336850 410210 366200 370500 344860 329740 428600 370580 439170 498890 FALSE TRUE 323685.5296 398511.2124 432380.4861 389621.5494 355952.7351 336407.5687 433845.335 362927.3935 389317.2628 465099.7359 0.695948642 0.856829582 0.929651111 0.837716127 0.765325601 0.723301999 0.932800648 0.78032165 0.837061887 1 18.8271806 -0.5127706 0.921148032 1.007706272 0.819413079 0.349453652 0.074747649 31.23189301 16.40527871 0.94451078 0.02316845 0.307064351 0.5127706 -0.188293193 SEDES(ph)ET(ph)EDEEEKSQEDQEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDESETEDEEEKSQEDQEQK 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 SEDES(1)ET(1)EDEEEKSQEDQEQK 243.88 9.20E-30 696880000 1323400 982600 834090 667600 965340 767330 861480 1050800 1363500 1105000 TRUE FALSE 1271680.065 954577.2101 984828.6172 702054.916 996391.0378 782845.9383 872023.0499 1029100.613 1208721.196 1030157.366 1.234452237 0.926632417 0.955998229 0.681502593 0.967222165 0.759928497 0.846494991 0.998974183 1.173336459 1 19.97443331 -0.512614551 8.36896589 0.999999998 0.935891284 0.002601298 0.159573855 0 0 0.152306964 0.035899096 0.307174704 0.512614551 -0.064108714 SKDYDVYS(ph)DNDICSQESEDNFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKDYDVYSDNDICSQESEDNFAK 23 1 A0A0C4DGZ1;Q8N5P1 A0A0C4DGZ1 ZC3H8 Zinc finger CCCH domain-containing protein 8 1 S(0.047)KDYDVYS(0.953)DNDICSQESEDNFAK;S(0.01)KDYDVYS(0.99)DNDICSQESEDNFAK 271.13 7.95E-52 1063830000 876480 732700 608870 507260 629430 635110 576750 761870 888020 812830 TRUE FALSE 842226.1926 711804.1134 718906.3532 533439.7494 649676.1876 647952.3593 583808.439 746137.1183 787215.6925 757776.3001 1.111444357 0.939332773 0.948705249 0.703954121 0.857345614 0.855070763 0.770423196 0.984640346 1.038849714 1 19.53141249 -0.511164059 8.307862992 1 0.904192849 0.045530073 0.115486422 0 0 0.113911546 0.026849209 0.308202347 0.511164059 -0.09580715 TEESGEDRGDGPPDRDPTLS(ph)PSAFILR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEESGEDRGDGPPDRDPTLSPSAFILR 27 2 Q9H7N4;M0R3G4;M0R2L3;M0R232 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 TEESGEDRGDGPPDRDPTLS(1)PSAFILR;TEESGEDRGDGPPDRDPT(0.007)LS(0.992)PS(0.002)AFILR 264.58 1.48E-53 330250000 216220 207820 194376 246300 226500 207288 211440 236300 210430 233190 TRUE FALSE 207769.8834 201893.1771 229504.0671 259011.5725 233785.5782 211479.5054 214027.666 231420.3224 186542.8686 217395.8336 0.955721551 0.928689266 1.055696714 1.191428411 1.075391254 0.972785457 0.984506752 1.064511305 0.858079318 1 17.72996477 -0.510849868 7.744955276 1.000004078 1.017290544 0 0.088005196 0 0 0.087163572 0.020544651 0.308425396 0.510849868 0.017286466 LVNHFVEEFK ddPTM_BT-474_Pertuzumab_2h_R1 4 LVNHFVEEFK 10 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;; 157.38 9.28E-06 7487093000 6078020 6192640 5202650 5307310 4242340 3908810 5772290 5522990 7411780 7567910 FALSE TRUE 5840484.259 6016031.97 6142884.587 5581220.905 4378798.719 3987848.816 5842933.012 5408938.326 6570425.807 7055328.715 0.827811785 0.852693363 0.870673052 0.791064617 0.620637095 0.565225091 0.828158864 0.766645828 0.931271394 1 22.75028187 -0.508902237 6.550137653 1.000000003 0.77838026 0.270128829 0.106279868 0 0 0.108982574 0.025687439 0.309811663 0.508902237 -0.221619743 ITADGAHFELR ddPTM_BT-474_Pertuzumab_2h_R1 4 ITADGAHFELR 11 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ;;; 187.85 3.41E-06 1815600000 1681560 1782180 1555400 1788020 1822840 1684760 1823890 1676830 1845850 1878940 FALSE TRUE 1615842.776 1731353.971 1836495.38 1880299.926 1881473.304 1718827.002 1846211.311 1642202.875 1636316.846 1751677.72 0.922454375 0.988397552 1.048420813 1.073428008 1.074097868 0.98124614 1.053967457 0.937502861 0.934142638 1 20.74030594 -0.506614101 6.479899779 0.99998963 1.003646453 0 0.055589591 0 0 0.056831951 0.013395419 0.311448253 0.506614101 0.003656823 GSFAGIEDDADEALEISQAQLLFENR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSFAGIEDDADEALEISQAQLLFENR 26 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 ; 229.98 6.98E-35 56650000 43805 54574 47808 54591 54668 59300 50366 51793 51723 56853 FALSE TRUE 42093.05217 53017.60295 56447.96908 57408.44805 56426.44587 60499.08663 50982.39417 50723.45645 45851.62188 53002.29567 0.794174132 1.000288804 1.06500989 1.08313135 1.064603809 1.141442759 0.961890302 0.957004896 0.86508747 1 15.69376723 -0.505231651 6.693208245 0.99998302 0.999659032 0 0.099568374 0 0 0.098771518 0.02328067 0.312441237 0.505231651 -0.000323988 NGSSS(ph)DSSVGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NGSSSDSSVGEK 12 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 NGSS(0.07)S(0.929)DSSVGEK 127.03 0.00021246 0 263660 224740 198970 196970 201050 197020 219870 254900 268580 232170 TRUE FALSE 253355.8757 218330.6352 234928.3051 207135.6453 207516.9558 201003.8794 222560.8348 249636.2259 238091.9244 216444.9191 1.170532793 1.008712222 1.085395333 0.956990102 0.9587518 0.928660651 1.028256222 1.15334759 1.100011612 1 17.72364041 -0.504548529 7.877929245 0.999999995 1.042673289 0.026360117 0.079027984 0 0 0.082432411 0.019429506 0.312933077 0.504548529 0.042673294 YRQDDDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 YRQDDDQR 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 108.98 0.0033807 1923580000 1693740 1945420 1755950 1901730 1917100 1988150 1828600 1788910 1990350 2070980 FALSE TRUE 1627546.768 1889938.526 2073289.226 1999878.513 1978765.263 2028351.755 1850978.954 1751968.383 1764413.812 1930710.68 0.842978073 0.978882308 1.073847701 1.035825064 1.024889582 1.050572608 0.958703431 0.907421501 0.913867536 1 20.88070056 -0.503963487 6.294828835 0.999999624 0.978655266 0.009457058 0.069078093 0 0 0.071804704 0.016924531 0.313354917 0.503963487 -0.021344358 APDWVDAEECHR ddPTM_BT-474_Pertuzumab_2h_R1 4 APDWVDAEECHR 12 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 ;;; 190.46 6.62E-06 1934950000 1858520 2003090 1562540 1973000 1942740 1870330 1903320 1787920 1946590 2122660 FALSE TRUE 1785886.984 1945963.834 1844925.737 2074826.766 2005229.996 1908149.354 1926613.4 1750998.827 1725621.264 1978890.348 0.902468894 0.983361123 0.932303166 1.048479906 1.013310312 0.964252191 0.973582696 0.884838733 0.872014595 1 20.91626024 -0.502723789 5.595536328 0.999999998 0.953833679 0.065733165 0.05331265 0 7.35E-11 0.055235841 0.013019213 0.314250669 0.502723789 -0.046166319 S(ph)GAQASSTPLSPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(1)GAQASSTPLSPTR 194.01 2.02E-07 300610000 103670 102720 77241 86771 83741 85777 95818 99700 115220 93413 TRUE FALSE 99618.46179 99790.52617 91200.16692 91249.26171 86434.60532 87511.46971 96990.64935 97641.16016 102140.7086 87086.05431 1.143908317 1.145884114 1.047241922 1.047805673 0.99251948 1.004885 1.113733423 1.12120317 1.172871012 1 16.41015409 -0.501834394 7.558676245 1.000000749 1.085613905 0.165377172 0.05898088 0 0 0.062357409 0.014697782 0.314894885 0.501834394 0.085613156 ASPDSSSCGERS(ph)PPPPPPPPSDEALLHCVLEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPDSSSCGERSPPPPPPPPSDEALLHCVLEGK 33 1 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 1 AS(0.029)PDS(0.135)S(0.135)S(0.135)CGERS(0.566)PPPPPPPPSDEALLHCVLEGK 72.943 0.0019117 56077000 30681 27992 21959 31544 31627 29238 30033 25392 31270 33364 TRUE FALSE 29481.9526 27193.69557 25927.47978 33171.98962 32644.31118 29829.21239 30400.55284 24867.64633 27720.36069 31104.22656 0.947843938 0.87427654 0.833567738 1.066478524 1.049513677 0.959008331 0.97737691 0.799494123 0.891208809 1 14.92482301 -0.50181274 6.01428829 1 0.928998646 0.054198581 0.082049883 0 1.08E-10 0.086962073 0.020497157 0.314910586 0.50181274 -0.071001354 QQLVASHLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QQLVASHLEK 10 0 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18;F8VX93 Q13561 DCTN2 Dynactin subunit 2 0 ; 82.171 0.018813 150368000 357880 334380 303850 276350 278010 228246 330730 324810 370420 403720 FALSE TRUE 343893.6539 324843.8098 358762.4541 290612.4566 286952.4441 232861.2905 334777.5727 318102.56 328371.4745 376375.6848 0.91369785 0.863083942 0.953203059 0.772133983 0.762409623 0.618693768 0.889477153 0.845172982 0.872456664 1 18.5218139 -0.501137373 6.725141049 0.99999992 0.830213673 0.23699344 0.090226478 0 0 0.09094134 0.021435079 0.315400681 0.501137373 -0.169786246 GAVIVVSHDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GAVIVVSHDAR 11 0 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;;; 204.5 3.30E-08 1592895000 1333620 1329250 1266300 1456640 1401310 1305630 1397920 1388440 1418370 1469060 FALSE TRUE 1281500.656 1291341.091 1495148.579 1531817.365 1446384.409 1332030.733 1415028.163 1359768.229 1257362.584 1369559.258 0.935702963 0.942888075 1.091700538 1.118474689 1.056094799 0.972598101 1.033199663 0.992850964 0.918078263 1 20.38528026 -0.501092608 7.780853522 0.999997235 1.01106798 0 0.064297979 0 0 0.065533799 0.015446465 0.315433193 0.501092608 0.011070744 LLSVTS(ph)DEGSMNAFTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLSVTSDEGSMNAFTGR 17 0 A0A3B3ISD5;A0A3B3ISF5;A0A3B3IT63;A0A3B3IS73;A0A3B3IRI4;A0A3B3IU93;A0A3B3ITI0;A0A3B3ISI1;Q8WYB5-3;Q8WYB5-2;Q8WYB5 A0A3B3ISD5 KAT6B Histone acetyltransferase KAT6B 1 LLSVT(0.027)S(0.973)DEGSMNAFTGR 92.38 0.0034856 39023000 53864 61854 59069 85888 71042 56297 67295 68346 63523 67690 TRUE FALSE 51758.93533 60089.98448 69744.08228 90320.68997 73327.13045 57435.36391 68118.57634 66934.63122 56312.13535 63105.29601 0.820199549 0.952217774 1.105201729 1.431269571 1.161980612 0.910151248 1.0794431 1.060681677 0.892351972 1 15.94547347 -0.50042107 7.624776591 0.999999982 1.057560597 0.002533766 0.164250109 0 0 0.165870899 0.039096146 0.315921316 0.50042107 0.057560614 VADWTGATYQDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VADWTGATYQDKR 13 1 O15371-2;O15371;O15371-3;B0QYA5;B0QYA6;B0QYA8 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 140.53 6.32E-05 1026100000 403730 413010 307640 336565 363330 361650 369370 373210 432260 436750 FALSE TRUE 387951.7853 401231.3592 363237.3914 353935.16 375016.8394 368962.8108 373890.4606 365503.0831 383191.657 407168.5335 0.952803946 0.985418386 0.892105754 0.869259608 0.921035907 0.9061673 0.918269537 0.897670259 0.94111314 1 18.63526655 -0.499207461 7.605459507 1 0.917974956 0.363106452 0.031465233 0 0 0.031878375 0.007513805 0.316805373 0.499207461 -0.082025044 LIHPDEDISLEER ddPTM_BT-474_Pertuzumab_2h_R1 7 LIHPDEDISLEER 13 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;;;;;; 227.57 8.88E-12 11284478000 6055973 6372313 5418594 6296148 6581619 6572410 6375729 5858213 6630800 7141880 FALSE TRUE 5819298.88 6190580.872 6397854.472 6621092.953 6793322.752 6705308.633 6453757.079 5737238.854 5878099.383 6658154.106 0.874010843 0.929774345 0.960905135 0.994433719 1.020301219 1.007082222 0.969301247 0.861686101 0.882842195 1 22.66669083 -0.498083876 6.13200413 1 0.945046524 0.087530586 0.053747768 7892775.625 1287144.484 0.058668786 0.014229271 0.317626058 0.498083876 -0.054953477 GQSQTS(ph)PDHRSDT(ph)S(ph)SPEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GQS(0.286)QT(0.341)S(0.373)PDHRS(0.412)DT(0.588)S(0.574)S(0.426)PEVR 55.881 0.083312 228420000 96260 109320 88308 103140 104140 106090 101380 97974 108830 119750 TRUE FALSE 92498.05278 106202.3006 104267.22 108463.0678 107489.7577 108235.2125 102620.7188 95950.80266 96476.07465 111639.2258 0.828544377 0.95129915 0.93396581 0.971549802 0.96283145 0.969508805 0.919217399 0.859472125 0.864177209 1 16.7684845 -0.496510227 7.626796566 0.999999999 0.919398884 0.20662894 0.04821012 0 0 0.049733066 0.011722196 0.318779051 0.496510227 -0.080601115 IGQQVDREPGDVAT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 4 IGQQVDREPGDVATPPR 17 1 H3BT22;Q9Y5N6 H3BT22 ORC6 Origin recognition complex subunit 6 1 IGQQVDREPGDVAT(1)PPR;IGQQVDREPGDVAT(1)PPR;IGQQVDREPGDVAT(1)PPR;IGQQVDREPGDVAT(1)PPR 156.05 1.25E-07 2945740000 1566110 1588460 1274800 1573180 1564290 1483790 1627440 1569070 1531170 1721300 TRUE FALSE 1504904.69 1543158.676 1505184.718 1654372.008 1614606.809 1513793.25 1647357.098 1536668.156 1357358.001 1604714.818 0.937801953 0.961640448 0.937976456 1.030944558 1.006164329 0.943340981 1.02657312 0.957595792 0.845856214 1 20.6138855 -0.496141466 10.98374558 1 0.965488819 0.043512581 0.051062053 0 0 0.048352188 0.01139672 0.319049842 0.496141466 -0.034511181 VDSFHESTEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDSFHESTEGK 11 0 Q8WWY3-4;Q8WWY3;E7EVX8;Q8WWY3-3;Q8WWY3-2 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 110.84 0.0017407 280040000 317630 499080 402400 548050 487350 525920 486480 428320 446970 538380 FALSE TRUE 305216.6684 484846.7271 475122.6313 576334.9262 503026.0553 536554.4627 492433.6878 419475.0423 396231.8395 501915.0431 0.608104245 0.965993615 0.946619628 1.148271872 1.002213547 1.069014508 0.981109641 0.835749094 0.789440056 1 18.93708366 -0.494707925 9.006124109 0.999999985 0.937019416 0.018332663 0.14470547 0 0 0.141785471 0.033419156 0.320104717 0.494707925 -0.062980569 T(ph)SSPPRK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSSPPRK 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.375)S(0.375)S(0.25)PPRK;T(0.333)S(0.333)S(0.333)PPRK;T(0.333)S(0.333)S(0.333)PPRK 73.26 0.028934 13134600000 900780 789390 662370 713850 759230 726460 777800 808840 883040 887460 TRUE FALSE 865576.5217 766877.3701 782074.9933 750691.884 783651.3225 741149.5189 787318.9491 792137.1713 782801.0012 827351.5437 1.046201616 0.926906314 0.945275318 0.907343305 0.947180589 0.895809677 0.951613561 0.957437231 0.946152826 1 19.65814094 -0.494526842 6.436583828 1 0.944869165 0.144731918 0.038231599 0 0 0.034970839 0.008242706 0.320238216 0.494526842 -0.055130836 FEGGDRDLEHLSK ddPTM_BT-474_Pertuzumab_2h_R1 7 FEGGDRDLEHLSK 13 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;;; 219.35 1.36E-11 6907255000 3800652 5532762 4039631 5162670 4420790 5272740 5006288 4295001 5260421 5259109 FALSE TRUE 3652118.318 5374973.045 4769682.183 5429116.017 4562988.725 5379358.415 5067556.45 4206307.728 4663280.062 4902904.863 0.744888677 1.096283366 0.972827806 1.107326405 0.93067046 1.097177809 1.033582456 0.857921548 0.951125953 1 22.22520534 -0.492927421 5.779020241 1.000000486 0.97985769 0.003336382 0.109465404 0 0 0.100958866 0.023796233 0.321419765 0.492927421 -0.020142796 SEPVKEESSELEQPFAQDTSS(ph)VGPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDR 26 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 SEPVKEESSELEQPFAQDT(0.002)S(0.084)S(0.914)VGPDR 143.48 1.58E-07 786130000 280970 246880 181980 175190 202330 196250 181730 297060 265920 228220 TRUE FALSE 269989.3818 239839.2241 214867.8341 184231.5769 208838.1282 200218.3095 183954.0661 290925.6072 235733.8764 212762.4561 1.268970977 1.127262904 1.009895439 0.865902661 0.981555355 0.94104154 0.864598339 1.367372856 1.107967452 1 17.69888407 -0.492572449 7.652525953 1.000000539 1.062352503 0.012545812 0.15611477 0 0 0.162957566 0.038409467 0.321682586 0.492572449 0.062351964 GHNGWVTQIATTPQFPDMILSASR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHNGWVTQIATTPQFPDMILSASR 24 0 P63244;J3KPE3;D6RHH4;D6RAC2;D6REE5;E9PD14;D6RFZ9;D6RAU2;D6RBD0;D6R909;D6RGK8;D6RHJ5;D6RDI0 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 272.18 6.35E-52 3516700000 900900 980070 823980 1041880 962160 971780 1069430 778770 1031050 1089100 FALSE TRUE 865691.832 952119.3632 972891.5153 1095651.552 993108.7502 991430.0574 1082518.004 762688.1274 914009.5265 1015334.287 0.85261755 0.937739792 0.958198229 1.079104257 0.978110129 0.976456789 1.066169062 0.751169479 0.900205517 1 19.95352337 -0.488701118 5.056188268 0.999999998 0.941836081 0.031680103 0.091184947 17686610.86 65987302.03 0.688371108 0.023583207 0.324562905 0.488701118 -0.058163917 HGEVCPAGWKPGSETIIPDPAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGEVCPAGWKPGSETIIPDPAGK 23 1 Q13162 Q13162 PRDX4 Peroxiredoxin-4 0 93.322 0.0027663 589000000 852760 906380 923740 730140 693800 456960 1021800 678340 1197800 1209400 FALSE TRUE 819433.1964 880530.9298 1090680.366 767822.6129 716116.7071 466200.0443 1034305.094 664332.042 1061830.766 1127486.261 0.726778875 0.780968213 0.967355794 0.681003964 0.635144509 0.413486231 0.917354943 0.589215199 0.941768253 1 20.10467842 -0.484756761 7.465571219 0.999999798 0.730177171 0.182818229 0.164397056 0 0 0.154362862 0.036383676 0.327524083 0.484756761 -0.269822626 EIAATCSGTEWGQSSGAAS(ph)PGLFQAGHR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIAATCSGTEWGQSSGAASPGLFQAGHR 28 0 P49757-3;P49757;G3V3Z8 P49757-3 NUMB Protein numb homolog 1 EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR 291.64 2.28E-71 2261820000 394457 441388 350839 485625 465363 474179 402139 440291 443699 467870 TRUE FALSE 379041.1843 428800.0464 414243.4117 510688.1644 480331.8235 483767.2243 407060.4974 431198.837 393332.1497 436180.7482 0.869000262 0.9830788 0.949705858 1.170817755 1.101221972 1.109098066 0.933238111 0.988578333 0.901764123 1 18.73456657 -0.483655397 5.970767931 1.000000017 1.005687091 0 0.09260602 0 0 0.093227662 0.021973971 0.328355733 0.483655397 0.005687075 VEHTPDGVK ddPTM_BT-474_Pertuzumab_2h_R1 6 VEHTPDGVK 9 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;;; 135.71 0.00021314 5487610000 4421380 4349020 3585050 3764670 3678030 3277490 4242540 4248320 4843880 4632510 FALSE TRUE 4248587.582 4224990.208 4232948.284 3958965.07 3796337.175 3343763.093 4294461.474 4160590.707 4294023.05 4318745.971 0.983754916 0.978290975 0.980133657 0.916693201 0.879036924 0.774243986 0.994376956 0.963379355 0.99427544 1 22.04218103 -0.4803408 6.638773803 1.000000513 0.939471355 0.06861186 0.065713296 0 0 0.067417513 0.01589046 0.330871378 0.4803408 -0.060529158 GHPAGGEENMTETDAFYKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHPAGGEENMTETDAFYKR 19 1 P55212;D6RBM3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 211.29 8.83E-17 341600000 283370 337120 279410 237660 316770 332260 263850 316750 344130 313770 FALSE TRUE 272295.5871 327505.6677 329905.6024 249925.6611 326959.1947 338978.5248 267079.0752 310209.0018 305065.8051 292518.0784 0.93086755 1.119608297 1.127812695 0.854393897 1.117740129 1.158829316 0.913034424 1.060478051 1.04289556 1 18.15816626 -0.479811793 0.454048925 0.9920769 1.040713734 0.01004844 0.098580384 58.14553931 10.98353835 0.834683861 0.05293861 0.331274653 0.479811793 0.048636834 HREDIEDYISLFPLDDVQPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 HREDIEDYISLFPLDDVQPSK 21 1 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1;B9TX62 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 0 ; 133.26 6.12E-06 101083000 112834 124789 99507 118342 122840 120555 127213 85583 150787 149254 FALSE TRUE 108424.3225 121230.1399 117490.1284 124449.6448 126791.2602 122992.7047 128769.8707 83815.68114 133670.2919 139144.8936 0.779218839 0.871251087 0.844372548 0.894388874 0.911217486 0.883918206 0.925437272 0.602362609 0.960655389 1 17.08622844 -0.479469633 7.778911002 1.000004418 0.84215771 0.167380622 0.096193967 0 0 0.096455232 0.022734716 0.331535751 0.479469633 -0.157846708 NYYEQWGK ddPTM_BT-474_Pertuzumab_2h_R1 7 NYYEQWGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 202.45 0.0002409 47629880000 14063870 13394500 11320190 11896320 12193570 11795160 12864170 13758200 15428470 13322860 FALSE TRUE 13514238.41 13012501.97 13366000.15 12510290.5 12585787.25 12033666.22 13021605.56 13474088.36 13677094.77 12420490.83 1.088059933 1.04766407 1.076124957 1.007229962 1.013308365 0.968855932 1.048397019 1.084827367 1.101171843 1 23.56621885 -0.479213115 6.493938611 1.000002058 1.047354599 0.11780051 0.039645324 0 0 0.041378256 0.009752948 0.331731632 0.479213115 0.047352541 SVDIS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVDISPTR 8 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SVDIS(0.992)PT(0.008)R 115.23 0.002626 654140000 808940 972820 837270 1037200 928850 1024100 984670 914030 931230 1058600 TRUE FALSE 777325.7305 945076.1261 988583.314 1090730.016 958727.3038 1044808.004 996720.686 895154.9611 825520.6744 986900.0791 0.787643802 0.957620884 1.001705578 1.105208156 0.971453265 1.058676583 1.009950964 0.907037075 0.836478476 1 19.9125445 -0.479123163 6.25212705 0.999999848 0.966236332 0.012664052 0.091304869 0 0 0.090272921 0.021277532 0.331800348 0.479123163 -0.033763516 LNSVQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNSVQSSERPLFLVHPIEGSTTVFHSLASR 30 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 271.34 2.06E-71 27213000000 5947700 6912600 6022200 8290900 7031500 8101500 8450200 4214740 8163000 8173100 FALSE TRUE 5715257.308 6715459.416 7110545.503 8718794.343 7257674.583 8265317.881 8553616.075 4127704.146 7236370.462 7619528.657 0.750080164 0.881348403 0.933200179 1.144269513 0.952509651 1.084754485 1.122591234 0.541726967 0.949713662 1 22.86127032 -0.477871372 3.995413369 1.000000047 0.919857474 0.01279249 0.171487115 10753199.04 29013298.06 13.33319837 0.045138193 0.332758094 0.477871372 -0.080142573 KNS(ph)VHEQEAINSDPELSNCENFQK ddPTM_BT-474_Pertuzumab_2h_R1 3 KNSVHEQEAINSDPELSNCENFQK 24 1 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 KNS(1)VHEQEAINSDPELSNCENFQK;KNS(0.999)VHEQEAINS(0.001)DPELSNCENFQK;KNS(0.994)VHEQEAINS(0.006)DPELSNCENFQK 264.84 1.34E-44 1034550000 655740 563760 506310 484220 491050 567210 550050 519230 709880 682770 TRUE FALSE 630112.9558 547682.1168 597811.4798 509210.6522 506845.0692 578679.3748 556781.6764 508507.7191 629297.3985 636525.3798 0.989925894 0.860424634 0.93917933 0.799984837 0.796268437 0.909122233 0.874720308 0.798880509 0.98864463 1 19.27985851 -0.474781264 11.32893928 1 0.874603157 0.18601127 0.070217965 0 0 0.065406431 0.015416444 0.33513419 0.474781264 -0.125396843 QLSPEDSSS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLSPEDSSSPVK 12 0 Q96AY2;Q96AY2-2 Q96AY2 EME1 Crossover junction endonuclease EME1 1 QLSPEDSS(0.001)S(0.999)PVK;QLSPEDSS(0.001)S(0.999)PVK 236.12 4.80E-16 1006450000 2007850 1794650 1679660 1677660 1609720 1616090 1770140 1993110 1919820 2052480 TRUE FALSE 1929381.002 1743468.339 1983211.926 1764244.234 1661498.106 1648768.447 1791803.503 1951951.582 1701890.082 1913463.701 1.00831858 0.911158303 1.036451292 0.922016045 0.868319637 0.861666958 0.936418863 1.020114246 0.889428987 1 20.8677551 -0.474440965 13.40204055 1 0.942116802 0.083812876 0.059543609 0 0 0.059373771 0.013994532 0.335396893 0.474440965 -0.057883198 GRDS(ph)PYQSR ddPTM_BT-474_Pertuzumab_2h_R1 10 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GRDS(1)PYQSR;GRDS(0.999)PY(0.001)QSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(0.55)PYQS(0.45)R;GRDS(0.999)PYQS(0.001)R 144.51 6.02E-05 39072530000 1305614 1424091 1211939 1554105 1428301 1478153 1459937 1402618 1428631 1477644 TRUE FALSE 1254589.161 1383477.319 1430963.337 1634312.545 1474243.599 1508042.266 1477804.146 1373653.448 1266458.798 1377561.856 0.910731635 1.004294154 1.038765215 1.186380516 1.070183232 1.094718368 1.072767905 0.997162808 0.919348044 1 20.39368567 -0.473577166 6.081353743 0.999998673 1.038318132 0.011085809 0.077839203 0 0 0.078288202 0.018452706 0.336064651 0.473577166 0.038319458 RVEIMEEESEQ ddPTM_BT-474_Pertuzumab_2h_R1 3 RVEIMEEESEQ 11 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ;; 205.32 6.19E-07 1591710000 850410 905540 786230 948960 916910 962950 891210 895000 938870 946910 FALSE TRUE 817175.037 879714.8858 928319.2506 997935.9393 946403.2429 982421.5088 902116.8946 876517.9372 832293.4137 882774.9423 0.925688981 0.996533594 1.051592208 1.130453405 1.072077602 1.112878789 1.0219104 0.992912118 0.942814951 1 19.75168615 -0.471468183 5.882823176 1 1.031090768 0.013619446 0.063482822 0 0 0.065505696 0.015439841 0.337700588 0.471468183 0.031090768 VQEFEHVNGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQEFEHVNGR 10 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 159.94 7.53E-06 3407410000 2343580 2642560 2391000 3041770 3027080 2761240 2863540 2699320 2699120 2903400 FALSE TRUE 2251990.303 2567196.776 2823106.888 3198756.114 3124448.777 2817074.165 2898584.859 2643578.099 2392727.213 2706750.132 0.831990466 0.948442468 1.042987624 1.181770004 1.154317401 1.040758854 1.070872714 0.976661299 0.883985258 1 21.36813028 -0.468422731 5.962081777 0.999999983 1.022544359 0 0.104359006 0 0 0.107118223 0.025248007 0.340077006 0.468422731 0.022544376 S(ph)RT(ph)SPAPWK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.988)RT(0.752)S(0.261)PAPWK;S(0.996)RT(0.867)S(0.138)PAPWK 92.856 0.02244 7428900000 5553600 4893400 4451900 4489500 4612000 4153700 4355300 5958800 5372200 4828700 TRUE FALSE 5336559.172 4753845.023 5256457.362 4721203.633 4760349.169 4237690.66 4408601.464 5835748.698 4762370.378 4501647.848 1.185467934 1.056023302 1.167674047 1.048772315 1.057468138 0.941364319 0.979330595 1.296358332 1.057917131 1 22.10202177 -0.468073512 5.482943939 1 1.093120061 0.064364335 0.09860186 6705486.707 1222971.902 0.100389436 0.024334666 0.340350574 0.468073512 0.093120061 WTCVDVYER ddPTM_BT-474_Pertuzumab_2h_R1 1 WTCVDVYER 9 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 0 86.136 0.033367 129510000 86648 118280 79446 120500 101120 118350 95510 94524 115870 126510 FALSE TRUE 83261.70037 114906.7702 93803.65947 126719.0194 104372.6166 120743.1181 96678.87995 92572.04637 102716.9234 117941.365 0.705958426 0.97427031 0.795341477 1.074423884 0.88495344 1.023755474 0.819719866 0.784898889 0.870915165 1 16.84771027 -0.463282555 7.46075924 1 0.881868957 0.096931112 0.108431507 0 0 0.101843374 0.024004714 0.344125967 0.463282555 -0.118131043 LNLDSIIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNLDSIIGR 9 0 P62136;P62136-2;P62136-3;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 79.986 0.059073 108980000 325330 397930 341400 415910 410490 407610 370620 385300 351900 446190 FALSE TRUE 312615.7439 386581.426 403098.5744 437375.1649 423693.7836 415852.1535 375155.7584 377343.4204 311953.7873 415969.1539 0.75153588 0.929351185 0.969058813 1.051460573 1.018570199 0.999718728 0.901883601 0.907142794 0.74994452 1 18.66611702 -0.463275609 6.813314286 1 0.928467799 0.051430222 0.097112158 0 0 0.096127359 0.022657436 0.344131471 0.463275609 -0.071532201 LQEDGLLSNVSHVIVDEVHER ddPTM_BT-474_Pertuzumab_2h_R1 4 LQEDGLLSNVSHVIVDEVHER 21 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ;;; 237.01 4.39E-30 175477000 155326 172133 164814 207980 208626 201297 205645 124251 214565 226900 FALSE TRUE 149255.6882 167223.9354 194599.5561 218713.8727 215336.6448 205367.3633 208161.745 121685.1734 190208.4807 211531.8609 0.705594361 0.790537816 0.919953879 1.033952388 1.017986812 0.970857829 0.984068046 0.575256951 0.899195421 1 17.69051545 -0.461892134 7.444348327 0.999999857 0.870548435 0.062697336 0.139806208 0 0 0.149725377 0.03529061 0.345229474 0.461892134 -0.129451421 SLLNHT(ph)PPSGRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLNHTPPSGRPR 13 1 B3KRP1;Q9UKI8;Q9UKI8-2;F8W7X8 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 S(0.009)LLNHT(0.963)PPS(0.028)GRPR 65.943 0.092498 187600000 152110 152640 121600 163410 157970 167450 143310 137990 160220 186710 TRUE FALSE 146165.373 148286.8567 143575.825 171843.6097 163051.2485 170835.9537 145063.8706 135140.4583 142032.4973 174063.9654 0.839722183 0.851910137 0.824845192 0.987244024 0.936731782 0.981455026 0.833394036 0.776383888 0.815978752 1 17.40925804 -0.461559871 6.835395185 0.999999987 0.869895333 0.238712195 0.068505858 0 0 0.074653779 0.017596065 0.345493697 0.461559871 -0.130104653 YETSSTSAGDRYDSLLGR ddPTM_BT-474_Pertuzumab_2h_R1 3 YETSSTSAGDRYDSLLGR 18 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YIS3;H0YIM2 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ;; 271.82 5.25E-39 1979010000 433506 480884 385426 447820 441700 477138 415861 490605 467086 477860 FALSE TRUE 416564.1063 467169.6592 455081.052 470932.0439 455907.6816 486786.0573 420950.4313 480473.8353 414064.3555 445494.1166 0.935060848 1.048655059 1.02151978 1.057100479 1.023375314 1.09268796 0.944906825 1.078518924 0.929449661 1 18.76504685 -0.45982696 6.280874269 1.00000004 1.02085613 0 0.056623581 0 0 0.04910192 0.011573433 0.346875031 0.45982696 0.02085609 STPFIVPSS(ph)PTEQEGR ddPTM_BT-474_Pertuzumab_2h_R1 5 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.002)S(0.997)PTEQEGR;STPFIVPS(0.417)S(0.582)PT(0.001)EQEGR;STPFIVPS(0.202)S(0.69)PT(0.107)EQEGR;STPFIVPS(0.024)S(0.971)PT(0.005)EQEGR;STPFIVPS(0.145)S(0.797)PT(0.058)EQEGR 335.61 1.07E-71 12449800000 5987980 6520250 5261880 6688140 6543660 6956240 6329190 6500000 6589760 6498740 TRUE FALSE 5753963.122 6334298.854 6212818.766 7033315.707 6754142.767 7096899.939 6406648.52 6365772.729 5841718.071 6058574.551 0.949722261 1.045509765 1.025458829 1.16088622 1.114807239 1.171381136 1.057451463 1.050704695 0.964206683 1 22.53054697 -0.456118628 6.572003332 0.999999997 1.06531575 0.057848111 0.069766803 0 0 0.06941923 0.016362269 0.349849592 0.456118628 0.065315753 DLFDYS(ph)PPLHK ddPTM_BT-474_Pertuzumab_2h_R1 7 DLFDYSPPLHK 11 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 DLFDY(0.002)S(0.998)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK 153.7 2.08E-05 4009721000 1726892 1628198 1625748 1785887 1723835 1666196 1903479 1964329 2251342 2343127 TRUE FALSE 1659403.151 1581763.387 1919556.828 1878056.842 1779283.718 1699887.625 1926774.345 1923764.92 1995779.095 2184424.921 0.759652179 0.724109752 0.878746992 0.859748863 0.814531871 0.77818542 0.882051073 0.880673399 0.913640508 1 21.05882209 -0.455999976 0.030802494 1.894594547 1.02E-08 0.70441489 0.04206341 239.2044163 1.788675884 62.93466804 47.35973325 0.349945186 0.455999976 -1.894594537 SGQGFHGNSEVNAILS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 7 SGQGFHGNSEVNAILSPR 18 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 1 SGQGFHGNSEVNAILS(1)PR;SGQGFHGNSEVNAILS(1)PR;SGQGFHGNSEVNAILS(1)PR;SGQGFHGNS(0.001)EVNAILS(0.998)PR;SGQGFHGNSEVNAILS(1)PR;SGQGFHGNSEVNAILS(1)PR;SGQGFHGNSEVNAILS(1)PR 227.44 1.91E-19 4564080000 873896.8 972038.4 837909 1113281.7 1011773.1 1090771 977183.1 910748.9 1025978.3 1087391.3 TRUE FALSE 839743.9469 944316.8166 989337.7955 1170738.302 1044317.701 1112827.137 989142.1591 891941.6169 909513.5446 1013741.319 0.828361172 0.931516551 0.975927268 1.154868881 1.030161917 1.097742705 0.975734283 0.8798513 0.897185039 1 19.95125813 -0.455032755 10.79367578 1 0.976874843 0.005964597 0.094345295 0 0 0.098951467 0.023323084 0.350725421 0.455032755 -0.023125157 ES(ph)HTPVSIQEEIVGDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESHTPVSIQEEIVGDFK 17 0 Q12830-4;Q12830;E7ETD6;E9PE19;A0A2R8Y7Q1;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 ES(0.499)HT(0.499)PVS(0.002)IQEEIVGDFK;ES(0.435)HT(0.334)PVS(0.231)IQEEIVGDFK 129.11 2.24E-05 234850000 208593 207540 172662 214580 189757 217430 210710 163645 268790 231120 TRUE FALSE 200440.9549 201621.1624 203865.8642 225654.4995 195860.7062 221826.5836 213288.732 160265.6736 238278.0861 215466.0365 0.930267054 0.935744518 0.946162409 1.047285703 0.909009649 1.029519952 0.989894906 0.743809447 1.105873064 1 17.71710095 -0.454776269 7.852733725 1.000000757 0.947910786 0.002323759 0.093211163 0 0 0.090243133 0.02127051 0.350932614 0.454776269 -0.052089971 SFDWGYEER ddPTM_BT-474_Pertuzumab_2h_R1 4 SFDWGYEER 9 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;A0A0G2JI50 P18615 NELFE Negative elongation factor E 0 ;;; 148.14 0.00021104 839557000 1300350 1446500 1216520 1481050 1413910 1344400 1453980 1375510 1371220 1508360 FALSE TRUE 1249530.884 1405247.236 1436372.225 1557487.168 1459389.699 1371584.689 1471774.242 1347105.238 1215564.854 1406197.434 0.888588511 0.999324279 1.021458432 1.107587833 1.037827025 0.975385573 1.04663414 0.957977312 0.864433987 1 20.42336774 -0.453378586 7.018494648 1 0.994559136 0 0.069263168 0 0 0.068028778 0.016034537 0.352063834 0.453378586 -0.005440863 SLVPAAELLESR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLVPAAELLESR 12 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 106.4 0.004481 44719000 45384 53927 44688 52461 51044 49107 50858 52195 51151 51806 FALSE TRUE 43610.34311 52389.05476 52764.11568 55168.5185 52685.87662 50099.97719 51480.41542 51117.15501 45344.55292 48297.13348 0.902959243 1.084723895 1.092489593 1.142273144 1.09086964 1.037328172 1.06591037 1.058389004 0.93886634 1 15.55964994 -0.452030484 6.578473837 1.00000226 1.053720853 0.027590216 0.069314834 0 0 0.065376946 0.015409494 0.35315838 0.452030484 0.053718594 VWDPDNPLTDR ddPTM_BT-474_Pertuzumab_2h_R1 5 VWDPDNPLTDR 11 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 0 ;;;; 210.08 3.25E-08 896717000 1189965 1169132 1066174 1178921 1316214 1194050 1208295 1318492 1161162 1221327 FALSE TRUE 1143459.852 1135789.5 1258855.359 1239765.254 1358551.219 1218194.509 1223082.476 1291264.679 1029351.758 1138605.434 1.004263477 0.997526857 1.105611585 1.088845369 1.193171205 1.069900487 1.074193429 1.134075634 0.904046061 1 20.11883646 -0.449801041 6.093744225 1 1.072678782 0.046911462 0.076426042 0 0 0.072463237 0.017079749 0.354975974 0.449801041 0.072678781 LCAAAASILGKPADR ddPTM_BT-474_Pertuzumab_2h_R1 1 LCAAAASILGKPADR 15 1 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 131.72 4.73E-05 963310000 623320 584550 467530 616530 629140 595050 556820 597840 641520 649050 FALSE TRUE 598959.9653 567879.2063 552023.0711 648349.1872 649376.8595 607082.3187 563634.5297 585494.3951 568697.3391 605089.2654 0.98987042 0.938504844 0.912300222 1.071493454 1.073191836 1.003293817 0.931489884 0.967616563 0.93985693 1 19.20678847 -0.449536697 7.039523102 1.000000256 0.98049762 0.011569862 0.053022259 0 0 0.055160778 0.01300152 0.355192104 0.449536697 -0.019502636 APFDLFENKK ddPTM_BT-474_Pertuzumab_2h_R1 2 APFDLFENKK 10 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ; 85.813 0.022423 975000000 3029030 3647880 2438880 3172570 2532140 2864770 3468580 3365850 3335550 3188760 FALSE TRUE 2910652.159 3543846.034 2879639.869 3336306.718 2613588.583 2922697.612 3511029.52 3296344.021 2956912.348 2972782.445 0.979100292 1.192097336 0.968668216 1.122284183 0.879172503 0.983152204 1.181058347 1.108841324 0.994661534 1 21.50338246 -0.448601883 8.058563147 1.000001703 1.05322703 0.013680397 0.097348853 0 0 0.092716625 0.021853518 0.355957475 0.448601883 0.053225327 VGVEASEETPQTSSSSARPGT(ph)PSDHQSQEASQFER ddPTM_BT-474_Pertuzumab_2h_R1 4 VGVEASEETPQTSSSSARPGTPSDHQSQEASQFER 35 1 Q6Y7W6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 VGVEASEETPQTSSSSARPGT(0.992)PS(0.008)DHQSQEASQFER;VGVEASEETPQTSSS(0.005)S(0.008)ARPGT(0.855)PS(0.132)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.977)PS(0.023)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.947)PS(0.053)DHQSQEASQFER 340.68 5.66E-118 7371000000 1242060 1809520 1503030 2133380 1690350 2118650 1742200 1430870 1697950 2073380 TRUE FALSE 1193518.922 1757914.261 1774660.956 2243483.997 1744721.643 2161490.555 1763521.565 1401322.034 1505205.834 1932948.126 0.6174604 0.9094472 0.91811101 1.160654012 0.902622072 1.118235159 0.912348108 0.724966188 0.778709896 1 20.88237149 -0.448521983 7.078712909 1.000000138 0.897713034 0.039956289 0.155275489 0 0 0.156483144 0.036883431 0.356022968 0.448521983 -0.102287104 NSATCHSEDS(ph)DLEID ddPTM_BT-474_Pertuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 1 NSATCHSEDS(1)DLEID;NSATCHSEDS(1)DLEID 246.86 3.42E-18 1684900000 1264010 1284720 1114070 1331900 1259980 1319450 1197090 1247260 1419410 1412380 TRUE FALSE 1214611.092 1248081.043 1315407.231 1400639.519 1300508.401 1346130.183 1211740.346 1221503.645 1258284.527 1316718.245 0.922453301 0.947872522 0.999004333 1.06373518 0.987689209 1.022337306 0.920273073 0.927687947 0.9556217 1 20.32851524 -0.44649547 7.822559258 0.999988852 0.971119215 0.034408825 0.044579942 0 0 0.047660079 0.011233588 0.357688131 0.44649547 -0.028869637 IVEIGDENATLDGTDVLFTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 IVEIGDENATLDGTDVLFTGR 21 0 O95865;A0A140T971;Q5SSV3;Q5SRR8;H0Y7N1 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ;;; 384.32 1.24E-130 350909000 299456 305997 250592 313034 294498 305712 294491 320285 309319 312764 FALSE TRUE 287752.9285 297270.2652 295879.5488 329189.7223 303970.7956 311893.7061 298095.069 313671.0028 274206.4039 291580.2157 0.986873982 1.019514525 1.014744941 1.128985111 1.042494584 1.069666902 1.022343262 1.075762298 0.940414984 1 18.15353331 -0.445490279 6.284337537 1 1.038909124 0.029602752 0.049065236 3.39E-10 0 0.045499644 0.010724369 0.358516973 0.445490279 0.038909124 LFRPPS(ph)PAPAAPGAR ddPTM_BT-474_Pertuzumab_2h_R1 6 LFRPPSPAPAAPGAR 15 1 Q86U90 Q86U90 YRDC "YrdC domain-containing protein, mitochondrial" 1 LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR 134.29 2.18E-05 4541480000 3445940 3700090 3126720 3577400 3585890 3766350 3566800 3507070 3866170 3931930 TRUE FALSE 3311268.855 3594567.056 3691787.858 3762030.043 3701233.408 3842508.178 3610451.565 3434647.779 3427298.59 3665616.879 0.903331953 0.980617226 1.007139584 1.02630203 1.009716381 1.048256898 0.984950606 0.936990387 0.934985489 1 21.80562458 -0.444118942 6.268357545 0.999998995 0.983022379 0.015559746 0.042672513 0 0 0.044324312 0.010447341 0.359650823 0.444118942 -0.016976616 VMEIVDADEKVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMEIVDADEKVR 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 69.602 0.045175 136010000 114560 125770 94046 103150 107970 101030 119410 108730 132610 123040 FALSE TRUE 110082.8685 122183.1627 111042.2042 108473.5839 111442.9531 103072.8958 120871.3753 106484.6875 117556.6687 114706.3912 0.959692545 1.065181822 0.968055948 0.945662946 0.97154964 0.898580234 1.053745777 0.928323927 1.024848463 1 16.80758625 -0.443060337 11.30140739 1 0.977705083 0.013294725 0.05083134 0 0 0.045958371 0.010832492 0.360528551 0.443060337 -0.022294917 EPGDQRPLGTYPDEHFTEEAPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EPGDQRPLGTYPDEHFTEEAPR 22 1 O15296-4;O15296;I3L1D5;O15296-2 O15296-4 ALOX15B Arachidonate 15-lipoxygenase B 0 ;; 169.9 4.67E-12 2866330000 1209960 1299570 1096280 1460480 1462120 1294250 1338770 1324770 1327370 1322760 FALSE TRUE 1162673.426 1262507.536 1294402.183 1535855.548 1509150.418 1320420.622 1355154.268 1297413.037 1176692.522 1233168.287 0.942834354 1.023791764 1.04965575 1.24545495 1.223799244 1.070754605 1.09892079 1.052097309 0.954202711 1 20.23393826 -0.442472638 6.053670484 0.999981945 1.079905895 0.048585175 0.093799883 0 0 0.096065057 0.022642751 0.361016758 0.442472638 0.07992395 SINQQSGAHVELQR ddPTM_BT-474_Pertuzumab_2h_R1 3 SINQQSGAHVELQR 14 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;; 191.96 4.28E-07 546880000 312154 344187 284389 352001 340196 343671 329254 333900 356801 367443 FALSE TRUE 299954.6766 334371.1238 335784.4185 370167.8138 351138.7133 350620.2631 333283.5089 327004.8483 316298.4463 342555.7583 0.875637526 0.976107146 0.980232883 1.080606018 1.025055644 1.023542167 0.972932146 0.954603274 0.923348794 1 18.38597931 -0.440692247 7.143919882 1 0.98243464 0.010034885 0.053805693 0 0 0.054286977 0.012795563 0.362499785 0.440692247 -0.01756536 VSHS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 3 VSHSPPPK 8 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.283)HS(0.717)PPPK;VS(0.012)HS(0.988)PPPK;VS(0.185)HS(0.815)PPPK 65.627 0.041084 3634090000 1701900 1578990 1310900 1403810 1467050 1471810 1488170 1595470 1788910 1646250 TRUE FALSE 1635387.866 1533958.751 1547808.791 1476260.802 1514238.996 1501571.007 1506382.67 1562522.987 1585840.437 1534748.021 1.065574181 0.999485733 1.008510042 0.961891322 0.986636878 0.978382761 0.98151791 1.018097411 1.033290426 1 20.54957038 -0.440601532 6.514677216 1.000000441 1.001460753 0 0.028582913 0 0 0.02782511 0.006558441 0.362575511 0.440601532 0.001460312 LHLVDLAGSER ddPTM_BT-474_Pertuzumab_2h_R1 1 LHLVDLAGSER 11 0 O95239;O95239-2;Q2VIQ3;Q5JRK0;H0Y718;J3KPF9;A0A087X011;E9PES4;Q9Y496 O95239;J3KPF9 KIF4A;KIF4B;KIF6;KIF3A Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B;Kinesin-like protein;Kinesin-like protein KIF3A 0 80.979 0.016972 0 33839 37258 37677 50396 42709 37802 44497 31558 42362 51377 FALSE TRUE 32516.53447 36195.43832 44486.07202 52996.9436 44082.77377 38566.38234 45041.5676 30906.31627 37553.24336 47897.19003 0.678881881 0.755690225 0.928782503 1.106472918 0.920362421 0.805190917 0.940380168 0.645263663 0.784038549 1 15.5476534 -0.435898927 7.668933745 0.999999998 0.839872726 0.118130795 0.130674659 0 0 0.137017853 0.032295417 0.366522865 0.435898927 -0.160127272 RPASMGS(ph)EGLGGDADPMKR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPASMGSEGLGGDADPMKR 19 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 RPAS(0.432)MGS(0.568)EGLGGDADPMKR 70.315 0.017069 317940000 67824 63498 50555 37469 47929 59069 53260 67324 63992 60517 TRUE FALSE 65173.3631 61687.09921 59691.41309 39402.77958 49470.67981 60263.41565 53911.81181 65933.73587 56727.89644 56418.12969 1.155184751 1.093391425 1.05801829 0.698406342 0.876857848 1.06815692 0.95557602 1.168662206 1.005490553 1 15.78387122 -0.432964922 8.244197108 0.999999971 1.010807873 0.000206652 0.1329348 0 0 0.137125328 0.03232075 0.369007402 0.432964922 0.010807902 TALAEAELEYNPEHVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TALAEAELEYNPEHVSR 17 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ;; 197.14 1.54E-11 403360000 205115 288692 209848 415330 211069 253992 328351 283709 272568 240633 FALSE TRUE 197098.879 280458.7868 247772.2016 436765.2311 217858.2261 259127.8923 332369.4578 277850.31 241627.2233 224334.7126 0.87859287 1.250180071 1.104475535 1.946935568 0.971130253 1.155094944 1.48157837 1.238552459 1.077083527 1 17.77529335 -0.432334548 7.638811286 0.999999998 1.251595441 0.053706717 0.28561597 0 0 0.262971613 0.061983004 0.369543401 0.432334548 0.251595443 KFQSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFQSEK 6 1 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 ; 91.626 0.076449 1668130000 1280880 1368380 1150610 1272610 1087170 1096390 1331600 1359120 1471090 1419290 FALSE TRUE 1230821.794 1329355.142 1358550.822 1338289.555 1122139.81 1118559.757 1347896.519 1331053.697 1304098.031 1323160.224 0.930213719 1.004681911 1.026747024 1.011434239 0.848075532 0.845369848 1.01869486 1.005965621 0.985593435 1 20.33555634 -0.430820066 6.129019045 0.999999901 0.966933152 0.025373163 0.064642955 0 0 0.067633001 0.015941251 0.370834331 0.430820066 -0.03306675 DFDPAVTEYIQR ddPTM_BT-474_Pertuzumab_2h_R1 6 DFDPAVTEYIQR 12 0 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;; 277.7 1.54E-27 5896140000 2305690 2383210 2003050 2235060 1986040 1274080 2429460 2441680 2439080 2646520 FALSE TRUE 2215581.086 2315243.184 2365045.693 2350411.714 2049922.78 1299842.771 2459192.458 2391258.455 2162205.864 2467268.843 0.897989326 0.938383018 0.958568297 0.952637051 0.830846945 0.526834672 0.996726589 0.969192499 0.876356004 1 21.2344835 -0.430275183 17.9688956 1 0.887998453 0.068627454 0.128082814 0 0 0.129323287 0.030481791 0.371299887 0.430275183 -0.112001547 LIES(ph)PFER ddPTM_BT-474_Pertuzumab_2h_R1 1 LIESPFER 8 0 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3;H7BZH9 E9PDC2 PRUNE2 Protein prune homolog 2 1 LIES(1)PFER 91.658 0.012934 42171000 19123 20629 17222 19456 18998 21776 18056 20248 21150 21767 TRUE FALSE 18375.65202 20040.68112 20334.3985 20460.12649 19609.08792 22216.32564 18276.97473 19829.87172 18749.14067 20292.7017 0.905530091 0.987580728 1.002054768 1.008250493 0.966312333 1.09479388 0.900667393 0.977192294 0.923935164 1 14.30867333 -0.428492207 7.914301878 0.999999999 0.976442374 0.018496589 0.054248945 0 0 0.049931992 0.011769083 0.372827375 0.428492207 -0.023557625 ASSVST(ph)KESPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSVSTKESPAR 12 1 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVS(0.019)T(0.8)KES(0.181)PAR 202.92 8.35E-07 383870000 501630 451100 358450 380750 385000 383210 441190 472250 491140 505100 TRUE FALSE 482025.745 438235.0697 423229.8887 400400.5531 397383.8746 390958.7688 446589.4152 462497.8725 435387.8462 470889.1271 1.023650191 0.930654467 0.898788832 0.850307493 0.843901147 0.830256522 0.948396107 0.982179978 0.924607983 1 18.84502789 -0.427624858 6.296041366 1 0.914727243 0.159552371 0.058698001 0 0 0.06258139 0.014750575 0.373572709 0.427624858 -0.085272757 FLCADYAEQDELDYHR ddPTM_BT-474_Pertuzumab_2h_R1 4 FLCADYAEQDELDYHR 16 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;;; 243.04 5.60E-20 1891200000 1733730 1822970 1444050 1866840 1748960 1880010 1763540 1653690 1942760 1983720 FALSE TRUE 1665973.915 1770980.68 1705021.958 1963187.836 1805216.887 1918025.09 1785122.73 1619540.724 1722226.03 1849360.877 0.900837654 0.957617684 0.921951999 1.061549349 0.976130137 1.037128618 0.965264677 0.875729958 0.931254711 1 20.81859534 -0.424623024 6.476278352 1.000000001 0.957610946 0.049526887 0.054241779 0 0 0.05633724 0.013278815 0.37616378 0.424623024 -0.042389054 VLQNFHPDEAES(ph)DEDNDVVIEGTLEPARPPQTPGAPAGSLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLQNFHPDEAESDEDNDVVIEGTLEPARPPQTPGAPAGSLSR 42 1 Q9BYG4 Q9BYG4 PARD6G Partitioning defective 6 homolog gamma 1 VLQNFHPDEAES(0.999)DEDNDVVIEGTLEPARPPQTPGAPAGSLSR;VLQNFHPDEAES(1)DEDNDVVIEGTLEPARPPQTPGAPAGSLSR 283.14 2.50E-81 1634250000 240968 235324 206975 281803 246471 264506 252138 233816 248087 266590 TRUE FALSE 231550.7042 228612.7899 244379.9866 296346.8866 254398.9636 269854.4925 255223.7403 228987.6179 219925.2038 248533.6218 0.931667524 0.919846531 0.983287431 1.192381475 1.023599792 1.085786666 1.026918364 0.921354689 0.884891156 1 17.92308151 -0.424006253 5.789788556 1.000004603 0.99882964 0 0.087407873 0 0 0.090414391 0.021310876 0.376698375 0.424006253 -0.001174963 LEPVS(ph)PPS(ph)PPHTDPELELVPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEPVSPPSPPHTDPELELVPPR 22 0 C9J0Q5;C9JE98;C9J330;H7C1Y3;H0YGK8;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 LEPVS(1)PPS(0.996)PPHT(0.004)DPELELVPPR;LEPVS(1)PPS(0.996)PPHT(0.004)DPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR 162.71 8.41E-12 2433350000 1619720 1775000 1437590 1827450 1668070 1794250 1721620 1731640 1744230 1861300 TRUE FALSE 1556419.552 1724378.738 1697394.492 1921764.914 1721724.986 1830530.964 1742689.701 1695881.029 1546232.323 1735232.493 0.896951595 0.993745071 0.978194276 1.107497077 0.992215737 1.054919713 1.004297526 0.97732208 0.89108078 1 20.72669754 -0.423344816 6.27310857 1.000002454 0.993472081 0 0.060984237 0 0 0.058309557 0.013743694 0.377272529 0.423344816 -0.006530373 RS(ph)SLSLEEADSEVEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSLSLEEADSEVEGR 16 1 Q5JTZ5 Q5JTZ5 C9orf152 Uncharacterized protein C9orf152 1 RS(0.662)S(0.336)LS(0.001)LEEADSEVEGR;RS(0.637)S(0.362)LS(0.001)LEEADSEVEGR 228.29 2.60E-15 750410000 199116 194000 189475 217707 202567 212571 179091 218039 206404 222791 TRUE FALSE 191334.3266 188467.3099 223717.3473 228942.8844 209082.7515 216869.3313 181282.7692 213536.4185 182973.8832 207701.1671 0.921200055 0.90739649 1.077111652 1.102270572 1.006651789 1.04414113 0.872805732 1.028094456 0.880947786 1 17.6641498 -0.422108447 8.617714014 1 0.987190982 0.001070886 0.07856064 0 0 0.076067592 0.017929304 0.378348096 0.422108447 -0.012809017 AHTPT(ph)PGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.425)PT(0.481)PGIY(0.066)MGRPT(0.027)HSGGGGGGGGGGGGGGGGR 90.182 0.00059471 156460000 56179 50100 48162 36263 39565 37989 41642 73502 44947 49863 TRUE FALSE 53983.46257 48671.19705 56865.94476 38134.53778 40837.64416 38757.16361 42151.62725 71984.15801 39844.80499 46485.7346 1.161290943 1.047013616 1.22329883 0.820349256 0.878498415 0.833743168 0.906764787 1.548521469 0.857140483 1 15.50450043 -0.421051533 8.319973691 1.000005908 1.051783807 0 0.218684319 0 0 0.226251246 0.05332793 0.379269978 0.421051533 0.051777899 LVALHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVALHK 6 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 88.626 0.051089 279220000 237930 259810 217250 222980 231040 154340 254180 246560 265670 287100 FALSE TRUE 228631.4326 252400.4732 256511.9077 234488.0245 238471.6114 157460.8605 257290.7309 241468.4498 235512.2554 267654.4613 0.854203705 0.943008654 0.958369633 0.876084872 0.890968192 0.588299032 0.961279441 0.902164861 0.879911563 1 18.03001217 -0.42008033 3.518954193 0.999862578 0.875470321 0.123850033 0.101335796 402330.0596 995035.6082 2.360850036 0.02520094 0.38011908 0.42008033 -0.124392257 ESRPSEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ESRPSEER 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 62.463 0.072486 162110000 89328 77974 68500 71936 94766 127790 82602 56198 58128 73014 FALSE TRUE 85836.963 75750.25786 80879.47377 75648.62558 97814.23445 130374.0014 83612.90799 55037.49166 51529.55313 68068.69675 1.261034324 1.112850128 1.188203648 1.111357044 1.436992908 1.915329771 1.228360641 0.808558035 0.757022767 1 16.05470387 -0.419898051 7.030505637 0.999971895 1.196883259 0.037507349 0.306210645 0 0 0.326803009 0.077028208 0.380278655 0.419898051 0.196911364 GGAGTGGT(ph)GSPQASLEILAPEDSQVLQQATR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGAGTGGTGSPQASLEILAPEDSQVLQQATR 31 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3;D6RCL7;D6RJA4;D6RF61;D6RIC7;D6RBK2 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 GGAGT(0.196)GGT(0.423)GS(0.379)PQAS(0.002)LEILAPEDSQVLQQATR 89.086 0.0021606 52330000 33605 38009 29224 34884 35207 39747 31704 33848 38819 39522 TRUE FALSE 32291.67945 36925.02053 34505.42688 36684.36742 36339.46513 40550.71157 32092.00304 33149.02697 34412.42986 36845.13974 0.876416257 1.002168015 0.936498739 0.995636539 0.986275677 1.100571523 0.870996915 0.899685202 0.933974742 1 15.1691867 -0.419363982 10.93718057 1 0.955098047 0.039078589 0.06566587 0 0 0.06530394 0.015392286 0.380746586 0.419363982 -0.044901953 RGCS(ph)PPAPAGSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGCSPPAPAGSPR 13 1 Q9C073;D6RFX7 Q9C073 FAM117A Protein FAM117A 1 RGCS(1)PPAPAGSPR 67.902 0.03178 285800000 138660 157640 106490 132050 117810 126840 133550 153260 141400 159380 TRUE FALSE 133241.0139 153144.2615 125735.1119 138865.1163 121599.4656 129404.7917 135184.4248 150095.1274 125348.8648 148585.0506 0.896732298 1.030684183 0.846216435 0.934583363 0.818382907 0.870913939 0.909811749 1.010163047 0.843616934 1 17.18092945 -0.415853499 6.34566942 1 0.913172795 0.14470965 0.066368773 0 0 0.064224227 0.015137796 0.383836704 0.415853499 -0.086827205 DKLEEILR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKLEEILR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ;; 114.5 0.0024122 715260000 1496390 1442840 1245100 1206430 1252440 1073750 1424740 1431260 1636030 1546490 FALSE TRUE 1437909.424 1401691.616 1470117.267 1268693.997 1292725.87 1095461.961 1442176.394 1401703.981 1450314.733 1441744.855 0.99733973 0.972218913 1.019679219 0.879971233 0.896639836 0.759816799 1.000299318 0.97222749 1.005944102 1 20.45938444 -0.413316716 6.764735525 1.000002831 0.943659823 0.045178446 0.075792448 0 0 0.076370403 0.018000677 0.386085315 0.413316716 -0.056343008 QALAPGLS(ph)PSQRPGGSSSACSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QALAPGLSPSQRPGGSSSACSR 22 1 Q9BWK5-3;Q9BWK5-2;Q9BWK5 Q9BWK5-3 MRI Modulator of retrovirus infection homolog 1 QALAPGLS(0.851)PS(0.148)QRPGGSSSACSR 82.342 0.0014208 0 41405 41014 35815 42930 40823 41814 38016 45544 41977 47198 TRUE FALSE 39786.84682 39844.32088 42287.5672 45145.62244 42136.10887 42659.50773 38481.25118 44603.50048 37211.94694 44001.23742 0.904221089 0.905527281 0.961054045 1.026008019 0.957611907 0.969507001 0.874549295 1.013687412 0.845702283 1 15.42525648 -0.411635859 0.004135173 1.92489738 4.46E-07 0.029242261 0.056908051 114245.609 117.0961461 27761.90677 26747.68569 0.387582483 0.411635859 -1.924896934 RGSRS(ph)S(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGS(0.466)RS(0.681)S(0.854)PEPK 122.52 0.012772 314970000 1743500 1374100 1160400 1090500 1253300 1251900 1370000 1488600 1790000 1454100 TRUE FALSE 1675362.092 1334912.013 1370110.093 1146780.836 1293613.533 1277214.276 1386766.47 1457859.89 1586806.704 1355612.512 1.235870928 0.984729782 1.010694488 0.845950318 0.95426497 0.942167666 1.022981462 1.075425224 1.170545927 1 20.37051343 -0.410211781 7.975461663 1.000000005 1.019131521 0.000896306 0.106987659 0 0 0.105061006 0.024763117 0.388855475 0.410211781 0.019131516 GMWSEGNGSHTIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GMWSEGNGSHTIR 13 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 160.48 4.38E-05 2086620000 560040 619790 583050 599040 635590 617840 656160 569500 629200 716220 FALSE TRUE 538153.0176 602114.196 688420.1049 629956.5262 656034.3296 630333.1481 664190.2824 557739.626 557775.8538 667709.7815 0.80596845 0.901760335 1.031016954 0.943458586 0.982514182 0.944022636 0.994728999 0.835302464 0.835356721 1 19.34886165 -0.410150068 7.014609307 0.999999999 0.922375287 0.102211916 0.071202041 0 0 0.071613039 0.016879355 0.388910736 0.410150068 -0.077624712 AQS(ph)TDS(ph)LGTSGSLQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 2 AQS(0.999)T(0.001)DS(1)LGTSGSLQSK;AQS(0.995)T(0.005)DS(0.949)LGT(0.051)SGSLQSK 348.99 5.43E-87 625580000 1700330 1323530 1074110 1082590 1216860 1135140 1072070 1573370 1539720 1519690 TRUE FALSE 1633879.224 1285784.22 1268225.57 1138462.6 1256001.407 1158093.309 1085190.313 1540879.36 1364937.441 1416760.043 1.153250497 0.907552572 0.895159048 0.803567693 0.886530795 0.817423751 0.765966205 1.087607861 0.963421751 1 20.434164 -0.409050352 6.341663635 1.000014162 0.917212315 0.040617592 0.115824537 15441659.6 2434953.23 0.114587984 0.027791668 0.389896779 0.409050352 -0.082801847 FYRPENTHK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYRPENTHK 9 1 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 79.148 0.016681 647660000 246130 287130 228280 251050 266110 227220 276250 273870 299570 319090 FALSE TRUE 236510.9675 278941.3335 269535.2741 264006.7206 274669.6698 231814.5441 279630.8301 268214.4888 265564.0695 297477.7501 0.795054311 0.937688057 0.906068686 0.887483923 0.92332845 0.779266833 0.940005866 0.901628739 0.892719101 1 18.18242224 -0.407348418 0.486212865 1.019697839 0.882003627 0.313746611 0.051912072 9.463231458 2.087709556 0.369305897 0.024934099 0.391427724 0.407348418 -0.137694212 VEMEDAHTAVVGIPHGLEDWSFFAVYDGHAGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEMEDAHTAVVGIPHGLEDWSFFAVYDGHAGSR 33 0 O75688;B8ZZF0;C9JIR6;A0A3B3IS24;O75688-5;O75688-4;O75688-2 O75688 PPM1B Protein phosphatase 1B 0 137.64 4.55E-09 56645000 401730 347570 313950 236530 315040 291760 329120 320010 483900 350010 FALSE TRUE 386029.9475 337657.6439 370687.7488 248737.3416 325173.5477 297659.5871 333147.869 313401.6817 428969.7007 326303.5109 1.183039515 1.034796233 1.136021331 0.762288279 0.996537079 0.91221693 1.020975435 0.960460648 1.314634033 1 18.31585498 -0.405600572 6.84599793 0.999987665 1.020482863 0 0.144591096 0 0 0.134156548 0.031621002 0.393006224 0.405600572 0.020495199 DLDLLASVPS(ph)PSSSGSR ddPTM_BT-474_Pertuzumab_2h_R1 7 DLDLLASVPSPSSSGSR 17 0 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 DLDLLASVPS(0.848)PS(0.12)S(0.025)S(0.005)GS(0.001)R;DLDLLAS(0.002)VPS(0.855)PS(0.114)S(0.021)S(0.004)GS(0.004)R;DLDLLASVPS(0.78)PS(0.201)S(0.018)S(0.002)GSR;DLDLLASVPS(0.851)PS(0.074)S(0.074)S(0.001)GSR;DLDLLAS(0.005)VPS(0.978)PS(0.013)S(0.003)S(0.001)GS(0.001)R;DLDLLAS(0.001)VPS(0.941)PS(0.043)S(0.011)S(0.003)GS(0.001)R;DLDLLAS(0.083)VPS(0.916)PS(0.001)SSGSR 297.49 3.54E-46 3694266000 3044730 3327820 2794510 3273620 3315070 3257590 3197890 3402020 3174590 3434300 TRUE FALSE 2925738.585 3232913.832 3299540.121 3442571.921 3421702.237 3323460.702 3237026.734 3331767.098 2814223.852 3201691.802 0.913810187 1.009751729 1.030561442 1.075235261 1.068716931 1.038032674 1.011036332 1.040627051 0.878980247 1 21.61040301 -0.405308854 6.309740165 1.000000609 1.01501877 0 0.060605095 0 0 0.057345983 0.013516578 0.393270297 0.405308854 0.015018161 DEVLDNLLAFVCDIRPEIHENYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEVLDNLLAFVCDIRPEIHENYR 23 1 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 136.56 6.54E-06 693260000 267123 275790 286134 276877 282800 318060 341590 304657 392840 419340 FALSE TRUE 256683.5378 267924.7392 337844.7788 291166.6552 291896.5188 324491.3911 345770.4806 298365.7265 348246.4501 390937.7283 0.656584206 0.685338661 0.864190776 0.74479037 0.746657326 0.830033449 0.884464342 0.76320525 0.890797753 1 18.5765793 -0.405056354 0.038771942 1.844138725 2.62E-10 0.682885443 0.056573393 158.567845 1.534100262 42.90162149 30.29254847 0.393499011 0.405056354 -1.844138725 SFS(ph)SQRPGMER ddPTM_BT-474_Pertuzumab_2h_R1 2 SFSSQRPGMER 11 1 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.126)FS(0.794)S(0.08)QRPGMER;S(0.133)FS(0.835)S(0.032)QRPGMER 91.845 0.0063213 448130000 896970 428110 196099 170551 163539 119786 94636 670930 120603 83292 TRUE FALSE 861915.4207 415900.722 231538.4515 179353.1575 168799.3805 122208.155 95794.18368 657075.061 106912.653 77650.55865 11.09992556 5.35605576 2.981800202 2.309747163 2.173833433 1.573821967 1.233657366 8.461948922 1.376843321 1 16.24470868 -0.404963767 12.74252913 0.999797616 4.086204628 0.077987762 3.158707749 0 0 3.080853018 0.72616402 0.393582911 0.404963767 3.086407013 KREHSPS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 KREHSPSK 8 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.355)PS(0.645)K 69.672 0.041987 58418000 56431 48170 38745 40216 41481 34817 47116 47901 55779 56112 TRUE FALSE 54225.61413 46796.23876 45747.08338 42291.55258 42815.27404 35521.0236 47692.6197 46911.82761 49447.20176 52311.48426 1.036591007 0.894569126 0.874513198 0.808456368 0.818467964 0.679029167 0.911704578 0.896778753 0.945245627 1 15.67484008 -0.404233154 6.86642576 1.00001661 0.868905748 0.150444027 0.089160548 0 0 0.08858916 0.020880665 0.394245592 0.404233154 -0.131110862 RAELYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RAELYEK 7 1 Q99614;H0YB37 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ; 112.84 0.010043 1215520000 836770 883650 675920 698440 697400 562900 814700 825500 854170 956140 FALSE TRUE 804068.1033 858449.1672 798073.7798 734486.5721 719832.5044 574282.2237 824670.5423 808453.1365 757208.2026 891379.7862 0.902048841 0.963056579 0.895324072 0.823988364 0.807548607 0.644262112 0.925161817 0.906968218 0.849478768 1 19.76568072 -0.398576984 6.851609071 0.999999983 0.859523754 0.204833474 0.084125549 0 0 0.086630561 0.020419019 0.399413754 0.398576984 -0.140476229 REEDEENDNDNES(ph)DHDEADS ddPTM_BT-474_Pertuzumab_2h_R1 12 REEDEENDNDNESDHDEADS 20 1 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 REEDEENDNDNES(0.998)DHDEADS(0.002);REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(0.938)DHDEADS(0.062);REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS 383.01 6.40E-131 4459577000 2399587 2393488 2103782 2492885 2469646 2656385 2351538 2280463 2729912 2705594 TRUE FALSE 2305808.487 2325228.066 2483982.206 2621543.094 2549084.406 2710098.925 2380316.825 2233370.642 2420023.834 2522341.708 0.914153891 0.921852919 0.984792107 1.039329082 1.01060233 1.074437661 0.943693242 0.885435401 0.959435364 1 21.2663323 -0.39832228 6.274953892 0.999999999 0.968370513 0.023620199 0.055685653 0 0 0.060946948 0.014365334 0.39964807 0.39832228 -0.031629486 REGT(ph)PPPPPPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 REGTPPPPPPSR 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 REGT(1)PPPPPPSR 91.657 0.0047903 573770000 339290 349430 254680 353360 366890 340660 310320 348400 352680 353980 TRUE FALSE 326030.1717 339464.5985 300706.3413 371596.9519 378691.3501 347548.3786 314117.789 341205.4182 312645.245 330004.6193 0.987956388 1.028666202 0.911218582 1.126035607 1.147533483 1.053162163 0.951858764 1.03394134 0.947396572 1 18.33212669 -0.398146748 6.258956134 0.999999925 1.023404561 0.006411214 0.071905234 0 0 0.071239564 0.016791326 0.399809631 0.398146748 0.023404635 SGFEPPGDFPFEDYSQHIYR ddPTM_BT-474_Pertuzumab_2h_R1 3 SGFEPPGDFPFEDYSQHIYR 20 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ;; 217.91 1.03E-24 408940000 537410 619960 497250 601880 564520 588750 569950 572580 577330 640350 FALSE TRUE 516407.4231 602279.3478 587114.1363 632943.0989 582678.2985 600654.9284 576925.2186 560756.0229 511793.9188 596978.5241 0.865035177 1.008879421 0.983476143 1.060244336 0.976045661 1.006158353 0.966408665 0.939323611 0.857307086 1 19.18731951 -0.397849371 5.941079682 0.999999998 0.967260036 0.029017152 0.059625685 0 0 0.057280612 0.01350117 0.400083489 0.397849371 -0.032739962 TRQPDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TRQPDAK 7 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 82.241 0.022823 267110000 275830 234784 200947 206788 214196 226111 241140 236843 259648 282150 FALSE TRUE 265050.2587 228088.1902 237262.5929 217460.3535 221085.8089 230683.1193 244091.1435 231952.1093 230173.8476 263039.7292 1.007643444 0.867124487 0.902002879 0.826720565 0.840503484 0.876989647 0.927963028 0.881813975 0.875053545 1 18.00492119 -0.397401325 7.833163724 0.999999999 0.886868494 0.322618044 0.047879479 0 0 0.044941974 0.010592925 0.400496454 0.397401325 -0.113131506 FWEVISDEHGIDPAGGYVGDSALQLER ddPTM_BT-474_Pertuzumab_2h_R1 2 FWEVISDEHGIDPAGGYVGDSALQLER 27 0 K7ESM5;Q9BUF5;K7EL29;K7ESQ3;K7EQT3;K7EJ64;K7ERA8;K7EJZ4;K7EN98;K7EPE5 K7ESM5 TUBB6 Tubulin beta-6 chain 0 ; 220.05 2.87E-34 146330000 96620 115515 88512 111051 105135 112901 105252 103822 110449 119798 FALSE TRUE 92843.98358 112220.6253 104508.0873 116782.3554 108516.7628 115183.9356 106540.1055 101678.0394 97911.29256 111683.9748 0.831309808 1.004805081 0.935748281 1.045650065 0.971641303 1.031338075 0.953942638 0.910408495 0.876681662 1 16.76906267 -0.394995486 6.663614486 0.999999997 0.955019284 0.047184914 0.063715684 0 0 0.060749748 0.014318853 0.40272122 0.394995486 -0.044980713 TFEINPR ddPTM_BT-474_Pertuzumab_2h_R1 4 TFEINPR 7 0 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;; 189.62 0.0012852 2011680000 1824600 2264670 1725180 2094060 1894890 2140480 2058590 1999430 2265850 2185950 FALSE TRUE 1753292.615 2200083.829 2036958.402 2202134.688 1955840.858 2183761.972 2083783.64 1958141.072 2008640.207 2037893.659 0.860345488 1.07958716 0.999541067 1.080593522 0.959736465 1.071577981 1.022518339 0.960865187 0.985645251 1 20.95864734 -0.389986713 8.010034501 1 1.005228001 0 0.06430772 0 0 0.057221984 0.013487351 0.407392741 0.389986713 0.005228002 GTEDITSPHGIPLDLLDR ddPTM_BT-474_Pertuzumab_2h_R1 5 GTEDITSPHGIPLDLLDR 18 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;J3QLR1 Q9Y265 RUVBL1 RuvB-like 1 0 ;;;; 195.27 3.04E-15 1766221000 1216996 1493140 1223636 1497936 1397082 1535858 1404155 1378034 1465209 1560311 FALSE TRUE 1169434.451 1450557.109 1444774.245 1575244.656 1442020.411 1566914.101 1421339.469 1349577.116 1298884.617 1454629.746 0.803939596 0.997200224 0.993224735 1.082917946 0.991331585 1.077191021 0.977114261 0.927780502 0.892931428 1 20.47222055 -0.389967265 6.258417458 0.999996129 0.976607835 0.008008742 0.078445013 0 0 0.076283551 0.017980205 0.407410985 0.389967265 -0.023388294 AAGS(ph)PSPLPAPDPAPK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAGSPSPLPAPDPAPK 16 0 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3KRF7 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 AAGS(0.616)PS(0.384)PLPAPDPAPK;AAGS(0.762)PS(0.238)PLPAPDPAPK;AAGS(0.966)PS(0.034)PLPAPDPAPK;AAGS(0.841)PS(0.159)PLPAPDPAPK 154.65 3.51E-07 2857590000 4629480 4456160 3865270 4275000 4746610 4521970 4218550 4706660 4816990 4713100 TRUE FALSE 4448554.803 4329074.68 4563810.271 4495633.262 4899289.021 4613407.332 4270177.877 4609465.826 4270185.49 4393877.539 1.012443966 0.985251555 1.03867489 1.023158525 1.115026301 1.049962656 0.971847267 1.049065611 0.971848999 1 22.06706323 -0.389659304 6.376873195 0.999999356 1.026231866 0.027883432 0.04113141 2675639.953 419584.8845 0.039699654 0.00962858 0.407699985 0.389659304 0.02623251 SNMS(ph)PHGLPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SNMSPHGLPAR 11 0 E7ESY4;Q13330-3;Q13330;H0Y4T7 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 S(0.001)NMS(0.999)PHGLPAR;S(0.003)NMS(0.997)PHGLPAR;S(0.001)NMS(0.999)PHGLPAR 126.09 0.00020277 1576730000 958630 1053450 920790 1045860 1043470 1067810 1077260 902330 1079820 1190840 TRUE FALSE 921165.6798 1023406.637 1087197.236 1099836.96 1077034.16 1089401.85 1090443.83 883696.5702 957243.3606 1110183.346 0.829741937 0.921835696 0.979295213 0.990680471 0.970140801 0.981281023 0.982219589 0.795991557 0.862238984 1 20.08236653 -0.387479712 5.370154091 0.999999994 0.923522703 0.103441864 0.067374253 1899356.205 424424.9576 0.073570376 0.017510233 0.409751251 0.387479712 -0.076477291 HSGNITFDEIVNIAR ddPTM_BT-474_Pertuzumab_2h_R1 6 HSGNITFDEIVNIAR 15 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;; 275.83 1.60E-33 6166530000 2959150 3254510 2596360 3304740 3177930 3268200 3312470 2785060 3500190 3563350 FALSE TRUE 2843503.146 3161694.561 3065580.008 3475298.027 3280151.005 3334285.243 3353008.999 2727547.538 3102863.105 3322001.131 0.855960921 0.951743975 0.922811248 1.04614595 0.987402134 1.003697805 1.009334093 0.821055572 0.934034331 1 21.66362113 -0.386703546 6.302031884 0.999999998 0.946527757 0.052528382 0.065953724 0 0 0.068151592 0.016063484 0.410484208 0.386703546 -0.053472241 GEADRDTYR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEADRDTYR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ; 187.5 3.69E-05 7619500000 4479000 4945300 4657500 5114700 4645800 4905300 5089600 5019500 5011100 5079400 FALSE TRUE 4303955.728 4804264.886 5499213.856 5378670.28 4795236.376 5004488.527 5151888.047 4915845.571 4442260.936 4735367.714 0.908895779 1.014549487 1.161306616 1.135850604 1.012642875 1.056832083 1.087959449 1.038112744 0.938102636 1 22.17504503 -0.384282466 6.394929309 1.000002104 1.046421098 0.016637856 0.074767668 0 0 0.07326394 0.017268476 0.412778942 0.384282466 0.046418993 GQKPALDCSQVSPPRPATSPENNASLS(ph)DTSPMDSSPSGIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK 41 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 GQKPALDCS(0.042)QVS(0.133)PPRPAT(0.133)S(0.133)PENNAS(0.133)LS(0.149)DT(0.138)S(0.138)PMDS(0.001)S(0.001)PSGIPK 42.015 0.074714 71739000 26792 28829 22090 25364 22923 21820 25831 29192 29185 29045 TRUE FALSE 25744.93902 28006.82515 26082.15439 26673.03908 23660.33911 22261.21535 26147.1275 28589.175 25872.04115 27077.75628 0.95077815 1.034311147 0.963231743 0.985053518 0.873792454 0.82212186 0.965631245 1.055817724 0.955472118 1 14.72482058 -0.384194448 5.99224621 1 0.960698105 0.035493845 0.064785992 0 57559263.59 0.069551062 0.01686861 0.412862608 0.384194448 -0.039301895 FNVWDVGGQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 FNVWDVGGQDK 11 0 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 97.911 0.0066941 0 172650 145070 131750 116960 124650 125300 134000 174050 179200 143430 FALSE TRUE 165902.6471 140932.7456 155560.1558 122996.3196 128659.4805 127833.6518 135639.9321 170455.8067 158857.9673 133715.3583 1.240714972 1.053975754 1.163367901 0.919836892 0.962189251 0.956013232 1.014393064 1.274766106 1.188030823 1 17.02880566 -0.384125202 7.742346187 1.000010179 1.085659774 0.044708026 0.119144849 0 0 0.125260391 0.029524157 0.412928442 0.384125202 0.085649595 LS(ph)PERS(ph)SDSESNENEPHLPHGVSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPERSSDSESNENEPHLPHGVSQR 25 1 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-2;V9GYS7 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 2 LS(0.956)PERS(0.547)S(0.488)DS(0.005)ES(0.004)NENEPHLPHGVSQR 62.57 0.079886 569630000 417290 416790 389840 437620 375230 497020 402640 351280 509330 536950 TRUE FALSE 400981.8455 404903.5573 460292.7599 460205.6206 387299.6137 507070.0849 407567.6288 344025.9452 451512.9937 500581.8982 0.801031453 0.808865759 0.919515391 0.919341315 0.7736988 1.012961289 0.814187709 0.687252069 0.901976271 1 18.9332466 -0.383263081 7.872918733 1.00000853 0.84139679 0.206877909 0.087780232 0 0 0.088813999 0.02093366 0.413748964 0.383263081 -0.158611739 VSHYIINSSGPRPPVPPSPAQPPPGVS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSHYIINSSGPRPPVPPSPAQPPPGVSPSR 30 1 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 VSHYIINSSGPRPPVPPS(0.003)PAQPPPGVS(0.498)PS(0.498)R;VSHYIINSSGPRPPVPPSPAQPPPGVS(0.767)PS(0.233)R 123.02 1.01E-05 925420000 341883 339227 330921 401871 376182 411600 343909 359290 377023 410683 TRUE FALSE 328521.8344 329552.5781 390725.786 422611.6105 388282.2357 419922.834 348117.8612 351870.5359 334224.9296 382867.0746 0.858057159 0.86074933 1.020525952 1.103807662 1.01414371 1.096784921 0.909239484 0.919040992 0.872952917 1 18.54648407 -0.381538128 6.383665462 1.000000004 0.964538324 0.015723043 0.088377978 0 0 0.092183034 0.02172775 0.415395581 0.381538128 -0.03546168 DQREEELGEYYMK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQREEELGEYYMK 13 1 O00267;O00267-2;M0QYL9 O00267 SUPT5H Transcription elongation factor SPT5 0 ; 206.67 5.48E-08 436780000 333370 355090 263080 255880 297150 339180 297310 311300 358840 364540 FALSE TRUE 320341.5318 344963.1809 310624.4082 269085.9975 306708.0996 346038.452 300948.5687 304871.5462 318105.9876 339849.3811 0.942598544 1.015047253 0.914006102 0.79178016 0.902482443 1.018211217 0.885535138 0.897078421 0.9360205 1 18.37453597 -0.379530617 8.25931181 1.000003586 0.920022369 0.123479025 0.061597163 0 0 0.061829897 0.014573446 0.417320177 0.379530617 -0.079981218 SSSS(ph)TPTSPKPLLQSPKPSLAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSSTPTSPKPLLQSPKPSLAAR 23 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.04)S(0.04)S(0.036)S(0.228)T(0.228)PT(0.228)S(0.203)PKPLLQSPKPSLAAR 82.342 0.0046128 971590000 305390 307060 296100 347490 334630 328350 269790 346030 328060 348290 TRUE FALSE 293455.0212 298302.9494 349611.8567 365424.0005 345393.6779 334989.462 273091.7707 338884.3596 290820.0041 324700.0081 0.903772756 0.91870324 1.076722661 1.125420362 1.063731658 1.031689109 0.841058712 1.043684482 0.895657521 1 18.30874789 -0.378957902 7.813930683 0.999992522 0.994121886 0 0.089302827 0 0 0.088560912 0.020874007 0.41787087 0.378957902 -0.005870636 PAVEASTGGEATQETGKEEAGKEEPPPLT(ph)PPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 PAVEASTGGEATQETGKEEAGKEEPPPLTPPAR 33 2 Q9C0C2;E9PKK0;E9PKE7 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 PAVEASTGGEATQETGKEEAGKEEPPPLT(1)PPAR;PAVEASTGGEATQETGKEEAGKEEPPPLT(1)PPAR;PAVEASTGGEATQETGKEEAGKEEPPPLT(1)PPAR;PAVEASTGGEATQETGKEEAGKEEPPPLT(1)PPAR 222.31 1.94E-34 5731120000 2733370 2015850 2197390 1807890 2514390 2150550 2017250 2297220 2216220 1623460 TRUE FALSE 2626546.878 1958359.932 2594507.254 1901195.42 2595267.638 2194035.594 2041937.709 2249781.604 1964643.997 1513501.608 1.735410696 1.293926562 1.714241491 1.256156855 1.714743892 1.449642064 1.349148027 1.486474538 1.298078566 1 20.52945878 -0.378675283 0.308225358 0.822245545 1.557025775 0.487913565 0.162600877 6.406037503 0.715469038 1.345020899 0.164548273 0.418142891 0.378675283 0.73478023 RPVINAGDGVGEHPTQALLDIFTIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPVINAGDGVGEHPTQALLDIFTIR 25 1 F8VPD4;P27708;H7C2E4 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 130.6 5.80E-05 113680000 52451 66070 54263 66182 60893 64855 65600 59576 63301 68029 FALSE TRUE 50401.15693 64185.74829 64069.53117 69597.66095 62851.67865 66166.41254 66402.83242 58345.73478 56115.33586 63421.33524 0.794703498 1.012052932 1.010220471 1.097385615 0.991017903 1.043283184 1.047010949 0.919970142 0.884802183 1 15.95268063 -0.377158834 6.324511073 0.999999822 0.984048403 0.001312505 0.084642483 0 0 0.08161347 0.019236479 0.419605495 0.377158834 -0.015951419 SAGQGEVLVYVEDPAGHQEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAGQGEVLVYVEDPAGHQEEAK 22 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 207.55 7.95E-23 117430000 92546 109570 73216 104870 87488 83555 113450 104360 119350 155870 FALSE TRUE 88929.2 106445.1709 86447.75988 110282.3533 90302.13097 85244.53935 114838.435 102204.9295 105801.8884 145312.7861 0.611984688 0.732524465 0.594908144 0.75893083 0.621432796 0.586627933 0.790284449 0.703344367 0.728097583 1 17.14880213 -0.37643124 0.412325478 1.073289459 0.655235135 0.702036782 0.064508048 3.771650594 0.657256455 0.459257244 0.039456039 0.420309068 0.37643124 -0.418054324 YQAEIPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 YQAEIPDR 8 0 O94776 O94776 MTA2 Metastasis-associated protein MTA2 0 94.309 0.022087 0 290800 292310 275120 295920 306730 288980 306670 325110 300730 300650 FALSE TRUE 279435.2145 283973.605 324840.304 311192.4667 316596.249 294823.3736 310423.1192 318396.3649 266592.3912 280286.7077 0.996962064 1.013154021 1.158957222 1.110264804 1.129544286 1.051863558 1.107519945 1.135966695 0.951141755 1 18.0965438 -0.376358093 6.401746378 0.999999998 1.081419544 0.088198023 0.065158161 0 0 0.062192152 0.014658831 0.420379866 0.376358093 0.081419546 VREEAER ddPTM_BT-474_Pertuzumab_2h_R1 3 VREEAER 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;; 97.635 0.010809 330600000 186299 208208 189124 224168 216716 216590 209128 223977 204883 213596 FALSE TRUE 179018.2291 202270.1117 223302.9138 235737.3373 223686.867 220969.5982 211687.371 219351.7967 181625.5408 199128.9527 0.899006532 1.015774497 1.121398525 1.183842601 1.123326688 1.109680914 1.063066762 1.101556523 0.912100116 1 17.60334347 -0.376217954 6.280847346 1.000000272 1.069215942 0.026856325 0.088331206 0 0 0.086299522 0.020340992 0.420515537 0.376217954 0.06921567 LGS(ph)PKPER ddPTM_BT-474_Pertuzumab_2h_R1 8 LGSPKPER 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER 114.83 0.0015625 24330000000 22748600 16654350 14090240 12090160 15067560 14096850 15679270 19646100 22404100 16790300 TRUE FALSE 21859559.56 16179384.24 16636659.8 12714134.61 15552221.75 14381897.97 15871157.6 19240401.17 19860880.49 15653078.03 1.396502306 1.033623177 1.062836317 0.812245016 0.993556777 0.918790409 1.013932057 1.229176852 1.268816297 1 23.89994304 -0.372293455 7.802583477 1.000022348 1.072314709 0.018936354 0.164535826 0 0 0.164826773 0.038850043 0.424332744 0.372293455 0.072292362 YALQMEQLNGILLHLESELAQTR ddPTM_BT-474_Pertuzumab_2h_R1 4 YALQMEQLNGILLHLESELAQTR 23 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 334.15 1.19E-86 23502000000 5046030 5432820 4765200 5906120 5592550 6117460 5631550 4806340 5481370 6784740 FALSE TRUE 4848825.569 5277881.293 5626377.641 6210935.561 5772439.45 6241159.233 5700470.593 4707087.399 4859147.857 6325203.517 0.766588072 0.834420786 0.889517251 0.981934501 0.912609284 0.986712794 0.901231174 0.744179596 0.768220002 1 22.59268047 -0.371853603 7.82848212 0.999999829 0.86593696 0.195881547 0.082011694 0 0 0.088263976 0.020804019 0.424762723 0.371853603 -0.134062869 S(ph)SPQHSLSNPLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPQHSLSNPLPR 13 0 Q86UE8-2;Q86UE8 Q86UE8-2 TLK2 Serine/threonine-protein kinase tousled-like 2 1 S(0.5)S(0.5)PQHSLSNPLPR 174.87 1.24E-05 229410000 84985 95291 76204 106150 100290 83010 96777 83050 89157 115170 TRUE FALSE 81663.69224 92573.39398 89975.75795 111628.4142 103515.9189 84688.51907 97961.38588 81334.98848 79036.27114 107369.4333 0.760586041 0.86219505 0.83800161 1.039666605 0.964109763 0.788758182 0.912376855 0.757524614 0.736115193 1 16.71222381 -0.371697344 7.800696591 0.999980631 0.853697494 0.18708742 0.093004781 0 0 0.094203002 0.022203861 0.424915581 0.371697344 -0.146283137 ATVT(ph)PSPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.57)PS(0.43)PVK 130.23 0.0041026 10192000000 1273400 1023600 915550 973430 908770 635880 1089200 1529500 969660 1069500 TRUE FALSE 1223634.12 994407.9302 1081010.251 1023668.839 938001.4124 648737.9293 1102529.955 1497915.291 859588.2619 997061.8124 1.227239981 0.997338297 1.084195822 1.026685433 0.940765558 0.65064966 1.105778941 1.502329416 0.862121336 1 19.92732342 -0.37151311 8.284498314 0.999611514 1.064040002 0 0.212975159 0 0 0.224515798 0.052918881 0.425095874 0.37151311 0.064428488 VGSEIER ddPTM_BT-474_Pertuzumab_2h_R1 3 VGSEIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 127.12 0.0090405 4435350000 3155700 3206670 2743090 3358830 3327510 3469020 3063200 3095300 3567690 3422890 FALSE TRUE 3032371.755 3115218.911 3238827.383 3532179.619 3434542.381 3539165.961 3100688.358 3031380.973 3162700.788 3191054.612 0.950272598 0.97623491 1.014970841 1.106900398 1.076303229 1.10908975 0.971681383 0.94996211 0.991114592 1 21.60560187 -0.371327155 6.348928972 0.999980288 1.015430997 0.0068964 0.057808041 0 0 0.063034845 0.014857455 0.42527793 0.371327155 0.015450709 CVACQNPDKPS(ph)PSTSVPAPASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 CVACQNPDKPSPSTSVPAPASFK 23 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 CVACQNPDKPS(0.898)PS(0.045)T(0.045)S(0.012)VPAPASFK 69.444 0.014804 287600000 151200 131440 123750 113450 121700 128000 124560 141530 166920 135880 TRUE FALSE 145290.9368 127691.4599 146114.3778 119305.1681 125614.591 130588.2477 126084.4025 138607.356 147971.9414 126676.7266 1.146942621 1.008010416 1.153442955 0.941808107 0.991615385 1.030877978 0.995324129 1.0941817 1.168106766 1 16.95079197 -0.37111375 6.93084534 0.999996541 1.054031263 0.049613993 0.074653052 4765272.702 687545.6241 0.070444025 0.017085186 0.425486956 0.37111375 0.054034722 ALLSTLHTVLWDGESR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALLSTLHTVLWDGESR 16 0 O14976-2;O14976;A0A087X1U9;H0Y8H5 O14976-2 GAK Cyclin-G-associated kinase 0 ; 236.17 1.01E-19 448460000 296810 330680 292810 363450 328880 338020 350450 337370 323449 350280 FALSE TRUE 285210.3371 321249.3302 345727.2805 382207.6981 339458.7239 344854.996 354738.9119 330403.1916 286732.4255 326555.2236 0.873390828 0.983751926 1.058709999 1.170422858 1.039513991 1.056038829 1.08630604 1.011783514 0.878051872 1 18.31696746 -0.370203515 6.30926565 0.999999738 1.026146249 0 0.085928651 0 0 0.084478505 0.019911775 0.426379666 0.370203515 0.026146511 IQDLEHHLGLALNEVQAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQDLEHHLGLALNEVQAAK 19 0 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 84.581 0.0018353 264770000 351920 340230 300570 302150 378570 365870 375090 190850 486420 459630 FALSE TRUE 338166.5773 330526.9735 354889.6851 317743.9977 390747.0479 373268.1421 379680.4636 186908.8808 431203.6408 428498.8507 0.789188995 0.771360233 0.828216189 0.741528238 0.91189754 0.871106519 0.886071136 0.436194591 1.006312246 1 18.70893181 -0.370045981 8.055144876 1.000001142 0.785259138 0.129425519 0.144307649 0 0 0.142754081 0.033647459 0.426534357 0.370045981 -0.214742004 DIS(ph)ENKR ddPTM_BT-474_Pertuzumab_2h_R1 3 DISENKR 7 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 1 DIS(1)ENKR;DIS(1)ENKR;DIS(1)ENKR 138.66 0.0016931 2587990000 3481850 2779720 2209660 2109550 2458610 2357390 2270430 3150090 3336100 2701800 TRUE FALSE 3345775.453 2700445.107 2608994.716 2218424.128 2537693.424 2405058.041 2298216.202 3085039.541 2957399.914 2518804.679 1.328318738 1.072113741 1.035806681 0.880744802 1.00749909 0.954841025 0.912423349 1.224803005 1.174128323 1 21.26430782 -0.368921371 6.939329697 1.000004969 1.059824559 0.019395639 0.134408489 0 0 0.134990509 0.031817568 0.427640304 0.368921371 0.059819591 SAPAS(ph)PTHPGLMSPR ddPTM_BT-474_Pertuzumab_2h_R1 10 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 S(0.024)APAS(0.938)PT(0.038)HPGLMSPR;SAPAS(0.46)PT(0.46)HPGLMS(0.08)PR;S(0.004)APAS(0.994)PT(0.002)HPGLMSPR;S(0.042)APAS(0.932)PT(0.026)HPGLMSPR;SAPAS(0.98)PT(0.02)HPGLMSPR;SAPAS(0.977)PT(0.023)HPGLMSPR;S(0.002)APAS(0.768)PT(0.23)HPGLMSPR;S(0.001)APAS(0.971)PT(0.027)HPGLMSPR;SAPAS(0.978)PT(0.022)HPGLMSPR;S(0.003)APAS(0.973)PT(0.025)HPGLMSPR 211.29 9.36E-10 13245940000 2792330 4188452 3808267 4140020 4020160 4456233 4078858 3336933 4268032 4266707 TRUE FALSE 2683202.657 4069001.45 4496505.561 4353686.928 4149472.097 4546341.084 4128776.284 3268024.167 3783542.9 3977719.135 0.674558099 1.022948406 1.130423092 1.094518437 1.043178756 1.14295176 1.037975821 0.821582434 0.951184026 1 21.92350998 -0.367132394 6.158934969 1 0.994525077 0 0.137741398 0 0 0.138103094 0.032551211 0.429405503 0.367132394 -0.005474923 LFEAVEEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 LFEAVEEGR 9 0 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 ;; 117.4 0.0026939 324768000 346912 356216 333661 413360 402761 361590 385419 409816 332930 365378 FALSE TRUE 333354.2955 346057.0685 393960.9649 434693.5591 415716.1733 368901.5975 390135.873 401353.1564 295137.1822 340630.6226 0.978638658 1.015930587 1.156563558 1.276143512 1.220431006 1.082995988 1.145334116 1.178265046 0.86644348 1 18.37784861 -0.366547534 6.243153203 0.999999996 1.116054619 0.054005525 0.116274609 10759738.07 48961552.17 0.113372268 0.028343067 0.429984169 0.366547534 0.116054624 RQTIEER ddPTM_BT-474_Pertuzumab_2h_R1 4 RQTIEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 171.73 0.0014858 824100000 980160 1164480 988220 1207810 1103200 1176220 1093890 1045280 1137090 1193880 FALSE TRUE 941854.2636 1131270.171 1166813.337 1270145.219 1138685.43 1200003.974 1107277.353 1023694.603 1008012.31 1113017.444 0.846216983 1.016399317 1.048333378 1.141172787 1.02306162 1.078153789 0.994842766 0.919747132 0.905657243 1 20.08604477 -0.366381684 6.154827906 1 1.000541887 0 0.082597109 0 0 0.084376678 0.019887774 0.430148405 0.366381684 0.000541887 RAS(ph)PHSAK ddPTM_BT-474_Pertuzumab_2h_R1 3 RASPHSAK 8 1 A0A1B0GV68 A0A1B0GV68 1 RAS(0.995)PHS(0.005)AK;RAS(0.995)PHS(0.005)AK;RAS(0.849)PHS(0.151)AK 89.805 0.0083581 291807000 206119 398378 220952 478490 196116 281413 447300 290952 302877 314083 TRUE FALSE 198063.6416 387016.6495 260882.9415 503184.9262 202424.2492 287103.3637 452774.1912 284943.7395 268495.6727 292809.8787 0.676424042 1.321733581 0.890963593 1.718469775 0.691316325 0.980511194 1.546307772 0.973135677 0.916962481 1 18.1596047 -0.365877973 7.927512026 0.999999995 1.097299129 0.002625739 0.329232756 0 0 0.29372456 0.069231543 0.430647596 0.365877973 0.097299133 DDS(ph)HSAEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.956)HS(0.044)AEDS(1)EDEKEDHK 147.91 5.07E-07 1119000000 698110 458370 523420 384900 474820 351000 515310 523390 816840 563440 TRUE FALSE 670827.0894 445297.7364 618013.6374 404764.7351 490093.0165 358097.4605 521616.5179 512581.8136 724115.7477 525277.7069 1.277090348 0.84773774 1.176546481 0.770572841 0.933016974 0.681729789 0.993029994 0.975830131 1.378538891 1 19.00272083 -0.363509057 7.29216287 1.000000199 0.984472325 0 0.208974687 0 0 0.191733178 0.045191944 0.433003038 0.363509057 -0.015527874 RPAEATSSPT(ph)SPERPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEATSS(0.004)PT(0.969)S(0.027)PERPR;RPAEAT(0.001)S(0.008)S(0.062)PT(0.918)S(0.011)PERPR;RPAEAT(0.006)S(0.249)S(0.249)PT(0.494)S(0.001)PERPR 190.57 1.34E-09 8842400000 275036 300867 256884 305925 275015 308834 294246 289816 295732 323480 TRUE FALSE 264287.2891 292286.5677 303308.6532 321713.8259 283861.1072 315078.8351 297847.0706 283831.1983 262161.7432 301570.4115 0.876370091 0.969215005 1.005763966 1.066795062 0.941276387 1.044793597 0.987653494 0.941177209 0.869321834 1 18.20213536 -0.363430931 5.897011746 0.999999995 0.971371312 0.021222644 0.060996602 0 0 0.059077425 0.013924682 0.433080938 0.363430931 -0.028628683 ILEFFGLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILEFFGLKK 9 1 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 134.25 0.0021176 0 678520 804510 526770 578640 630350 626580 647160 669610 806170 746210 FALSE TRUE 652002.6883 781566.1625 621969.0569 608503.6797 650625.7802 639249.8769 655080.1377 655782.3195 714656.9613 695668.532 0.937231826 1.12347494 0.894059496 0.874703471 0.935252567 0.91890009 0.941655555 0.942664918 1.027295225 1 19.40804054 -0.362919975 6.670693052 0.999997086 0.952812513 0.03705825 0.067937391 0 0 0.065673889 0.015479484 0.433590767 0.362919975 -0.047184574 SQS(ph)PHYFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSPHYFR 8 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 SQS(1)PHYFR;SQS(1)PHYFR 148.28 0.00033738 2762100000 1061460 1207440 973580 1290840 1235800 1284370 1155830 1050630 1266350 1374730 TRUE FALSE 1019976.97 1173004.993 1149527.563 1357460.407 1275550.629 1310340.841 1169975.393 1028934.123 1122599.257 1281618.313 0.795850808 0.915252991 0.896934409 1.059176819 0.995265608 1.022411141 0.912889104 0.802839748 0.875923234 1 20.28953524 -0.361890718 6.492660649 0.999996395 0.919308488 0.079624868 0.081981762 0 0 0.087550161 0.020635771 0.434619574 0.361890718 -0.080687907 TVQSLEIDLDSMR ddPTM_BT-474_Pertuzumab_2h_R1 14 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;; 356.68 7.63E-76 7747611000 6528593 6556692 5734678 6671166 6566899 6579321 6663138 6711112 6831685 6908628 FALSE TRUE 6273448.368 6369701.564 6771061.882 7015465.677 6778129.27 6712359.378 6744683.476 6572525.192 6056180.76 6440700.472 0.974032001 0.988976524 1.051292777 1.089239549 1.052390078 1.042178472 1.047197196 1.020467451 0.940298464 1 22.61878617 -0.361595103 6.427623949 0.999999677 1.026784969 0.018782004 0.041883921 2829075.095 440143.1586 0.041960393 0.01017689 0.434915511 0.361595103 0.026785293 KLEEAKSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEEAKSR 8 2 F8W9W8;E7EU40;Q92959 F8W9W8 SLCO2A1 Solute carrier organic anion transporter family member 2A1 0 76.827 0.01957 631110000 437230 386660 381680 328730 371020 321600 417410 423580 513620 406990 FALSE TRUE 420142.5682 375632.8354 450658.0664 345695.7947 382954.1953 328102.9723 422518.3884 414832.925 455316.0109 379424.2048 1.107316199 0.990007571 1.187742007 0.91110633 1.009303546 0.864739171 1.113577845 1.093322249 1.200018357 1 18.53345219 -0.361208432 6.156337768 1.00000012 1.049943634 0.02182729 0.10466799 0 0 0.100045455 0.02358094 0.435302908 0.361208432 0.049943515 AELSYR ddPTM_BT-474_Pertuzumab_2h_R1 2 AELSYR 6 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 129.2 0.037913 842670000 853200 921670 717820 809170 727720 566310 882490 899950 875610 941090 FALSE TRUE 819856.0007 895384.874 847546.0418 850931.3607 751127.7747 577761.1762 893290.1766 881365.718 776214.4237 877349.1361 0.934469491 1.020557082 0.96603052 0.969889096 0.856133258 0.658530512 1.018169552 1.004578088 0.884726948 1 19.74279154 -0.360531927 6.876250943 0.999995427 0.929141275 0.045001218 0.102740535 0 0 0.104803895 0.024702515 0.435981512 0.360531927 -0.070854152 SLKEEGVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLKEEGVQR 9 1 P40222 P40222 TXLNA Alpha-taxilin 0 ; 97.456 0.0060909 683790000 777850 825890 688880 729640 671420 584770 851680 867270 767140 950120 FALSE TRUE 747450.762 802336.4258 813375.9401 767296.8078 693016.8341 596594.4501 862103.1146 849360.5714 680057.4833 885767.5261 0.843845298 0.905809258 0.918272477 0.866250777 0.782391331 0.673533893 0.973283722 0.958897844 0.767760686 1 19.75656858 -0.359176551 5.887319049 0.999999996 0.86315455 0.190516051 0.088381976 5879503.843 1498008.594 0.090670096 0.021990729 0.437344278 0.359176551 -0.136845446 YS(ph)PESQAQSVHHQRPGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSPESQAQSVHHQRPGSR 18 1 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 YS(0.999)PES(0.001)QAQSVHHQRPGSR;Y(0.002)S(0.992)PES(0.006)QAQSVHHQRPGSR 160.98 2.37E-11 458310000 130761 162545 172728 240360 187356 185113 207140 99058 183574 247790 TRUE FALSE 125650.7156 157909.3757 203943.7919 252765.0084 193382.4759 188856.1117 209675.0413 97012.41768 162735.4491 231006.9626 0.543926097 0.683569768 0.882846948 1.094187836 0.837128343 0.817534284 0.907656804 0.419954518 0.704461231 1 17.81757681 -0.357351174 7.840533779 1.000024382 0.761123227 0.13014484 0.181376838 0 0 0.192615531 0.045399916 0.439186342 0.357351174 -0.238901155 QGYVIYR ddPTM_BT-474_Pertuzumab_2h_R1 4 QGYVIYR 7 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;; 108.24 0.016978 1429217000 1992660 2018690 1667660 1777290 1744920 1688260 1778840 2015650 2075370 2235120 FALSE TRUE 1914784.644 1961118.938 1969043.259 1869016.15 1801046.936 1722397.774 1800609.976 1974026.123 1839782.698 2083733.332 0.918920197 0.941156389 0.944959333 0.896955537 0.864336578 0.826592226 0.864126877 0.947350649 0.882926174 1 20.99073923 -0.355389965 0.993070405 1.002322702 0.899366515 0.385277888 0.038250448 25.98698786 16.89207448 0.291415785 0.013050434 0.441174127 0.355389965 -0.102956186 ECELALWAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ECELALWAFR 10 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 0 ; 133.23 0.00047118 60066000 64123 62419 60031 70927 65433 42072 76307 67020 74135 89339 FALSE TRUE 61617.00227 60638.87123 70879.93708 74587.55097 67537.71187 42922.72467 77240.86789 65636.01358 65719.5056 83287.98996 0.739806571 0.728062609 0.851022304 0.895537892 0.810893766 0.51535311 0.927395029 0.788060963 0.789063413 1 16.34582085 -0.355340101 0.660429632 1.017851742 0.780418366 0.269729885 0.10740236 13.00790857 4.768775511 0.690772816 0.040122125 0.441224784 0.355340101 -0.237433376 EIWELIGIPEDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIWELIGIPEDQR 13 0 O43663-2;O43663-4;O43663;O43663-3;H0YLA0;H0YM42 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 ; 158.41 0.00010983 74606000 125481 134793 113969 154842 149696 136527 137434 139773 121225 149882 FALSE TRUE 120577.0638 130948.8356 134565.7335 162833.4142 154511.1078 139287.6695 139115.9584 136886.6387 107464.0462 139730.3586 0.862926747 0.937153793 0.963038633 1.165340272 1.105780514 0.996831833 0.995602958 0.979648518 0.769081589 1 17.09228598 -0.35401493 6.232238024 0.999999998 0.984357926 0 0.105628811 0 0 0.105142886 0.024782416 0.442573158 0.35401493 -0.015642071 RYS(ph)GNMEYVISR ddPTM_BT-474_Pertuzumab_2h_R1 1 RYSGNMEYVISR 12 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 RYS(1)GNMEYVISR 136.39 6.78E-05 159100000 164970 141120 134120 127430 103690 139960 154720 152070 162450 179280 TRUE FALSE 158522.79 137095.3958 158358.4675 134006.6776 107025.283 142790.0871 156613.5096 148929.7014 144009.357 167137.2059 0.948459017 0.820256597 0.947475857 0.801776462 0.640343857 0.854328552 0.937035586 0.891062529 0.861623576 1 17.3506734 -0.352873933 7.710644723 0.999993175 0.855681225 0.198652491 0.086874791 0 0 0.087536822 0.020632627 0.443737434 0.352873933 -0.14431195 AQGGQTQS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 8 AQGGQTQSPTK 11 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.006)QS(0.992)PT(0.001)K;AQGGQT(0.009)QS(0.989)PT(0.003)K;AQGGQT(0.007)QS(0.993)PTK;AQGGQT(0.001)QS(0.994)PT(0.004)K;AQGGQT(0.009)QS(0.99)PT(0.001)K;AQGGQT(0.01)QS(0.989)PT(0.001)K;AQGGQT(0.025)QS(0.83)PT(0.144)K;AQGGQT(0.08)QS(0.92)PTK 221.52 8.75E-12 3413834000 3330254 2751433 2860395 2661188 2638626 2730679 3496253 3067513 3568922 4413503 TRUE FALSE 3200103.992 2672964.825 3377332.006 2798532.232 2723499.802 2785895.2 3539041.19 3004167.785 3163792.937 4114572.511 0.777748839 0.649633666 0.82082209 0.680151395 0.661915617 0.677080108 0.860123666 0.730128774 0.76892385 1 21.97231112 -0.352119565 0.450408153 1.050760681 0.715963202 0.60598521 0.065110216 4.584792651 0.932151647 0.437676851 0.035669197 0.444508873 0.352119565 -0.334797479 EEQTDTS(ph)DGESVTHHIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 EEQTDT(0.005)S(0.984)DGES(0.005)VT(0.005)HHIR;EEQTDT(0.001)S(0.998)DGES(0.001)VTHHIR;EEQTDT(0.006)S(0.99)DGES(0.002)VT(0.002)HHIR;EEQTDT(0.041)S(0.912)DGES(0.023)VT(0.023)HHIR 132.14 4.11E-05 2771690000 556170 566190 521770 632050 564830 590280 644160 431957 728880 717950 TRUE FALSE 534434.2615 550042.8156 616065.4457 664670.1762 582998.2699 602215.866 652043.4228 423036.937 646140.5981 669322.607 0.798470358 0.821790284 0.920431253 0.993049046 0.87102731 0.899739318 0.974184072 0.632037425 0.96536497 1 19.35234222 -0.349261479 7.860812236 0.999999992 0.865991464 0.114146841 0.101538006 0 0 0.101576354 0.023941776 0.447443827 0.349261479 -0.134008527 NKFEEAER ddPTM_BT-474_Pertuzumab_2h_R1 7 NKFEEAER 8 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;;; 140.83 0.00058659 24506600000 15858710 17152150 13730560 13549020 13050280 10452980 16232640 15515970 17771150 18533690 FALSE TRUE 15238934.08 16662987.48 16211977.63 14248286.55 13470054.11 10664346.42 16431299.9 15195559.8 15753843.55 17278386.67 0.881965103 0.964383295 0.938280751 0.82463061 0.779589806 0.617207302 0.950974198 0.879454783 0.911765887 1 24.04246518 -0.348100674 6.989983878 0.999995829 0.860942923 0.154193772 0.097723202 0 0 0.099740244 0.023509001 0.448641378 0.348100674 -0.139052906 KCAADLGLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KCAADLGLNK 10 1 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 105.03 0.0064433 0 851330 698830 596960 532680 633920 414550 666130 708470 836550 774270 FALSE TRUE 818059.0824 678900.0526 704843.9513 560171.6786 654310.6125 422932.485 674282.2982 693839.8469 741588.3511 721828.0033 1.133315802 0.940528837 0.976470777 0.776045922 0.906463326 0.585918644 0.934131532 0.961226004 1.027375424 1 19.46129559 -0.344508389 7.068244065 0.999999715 0.908725517 0.029572764 0.139762121 0 0 0.136458431 0.032163561 0.452367724 0.344508389 -0.091274198 SRDEIVEMIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRDEIVEMIR 10 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 178.81 1.98E-06 730680000 151415 188609 154339 182852 164979 164422 187106 167839 177972 193463 FALSE TRUE 145497.5344 183230.056 182231.4906 192289.0136 170285.6994 167746.7255 189395.8592 164373.066 157769.3647 180359.5787 0.806708108 1.015915303 1.010378777 1.066142508 0.944145582 0.930068293 1.050101473 0.911363107 0.87474902 1 17.46051652 -0.343163315 7.934136825 0.999998994 0.962470193 0.022744942 0.077157788 0 0 0.072622869 0.017117374 0.453770945 0.343163315 -0.037528801 MPLDLS(ph)PLATPIIR ddPTM_BT-474_Pertuzumab_2h_R1 5 MPLDLSPLATPIIR 14 0 B8ZZU6;E9PBF9;P15336-5;P15336;E9PEK8;H7C2N6;P15336-3;P15336-7;P15336-4;C9JCI8 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR 186.69 1.08E-06 511441000 345248 368231 357291 437195 370265 373895 376035 383506 411007 398095 TRUE FALSE 331755.3265 357729.4124 421861.4316 459758.6863 382174.91 381455.4131 380637.0288 375586.4671 364351.2084 371131.6711 0.893901955 0.96388813 1.136689387 1.238802081 1.029755582 1.027816925 1.025611821 1.012003276 0.981730304 1 18.5015716 -0.342793141 7.848123572 1 1.038777123 0.011074486 0.089744074 0 0 0.092016529 0.021688504 0.454157886 0.342793141 0.038777123 LSEGFSIHTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSEGFSIHTR 10 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;; 232.88 6.69E-12 3208380000 1930020 2773110 2162890 3058660 2564900 2770320 2742650 2379170 2481850 2977890 FALSE TRUE 1854592.685 2694023.618 2553772.336 3216517.809 2647402.338 2826337.768 2776215.371 2330039.308 2200120.793 2776194.858 0.668034046 0.970401487 0.919882237 1.158606645 0.953608256 1.01806174 1.000007389 0.839292423 0.79249509 1 21.4046774 -0.339591647 6.491086804 0.999958072 0.932776957 0.026893386 0.12779494 23412725.9 110769157.4 0.123346577 0.030836646 0.457518176 0.339591647 -0.067181115 VWSEVNQAVLDYENR ddPTM_BT-474_Pertuzumab_2h_R1 2 VWSEVNQAVLDYENR 15 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 ; 211.77 2.82E-09 125901000 139789 176630 151008 170778 172617 162361 174528 165904 155402 185681 FALSE TRUE 134325.8913 171592.6853 178298.5048 179591.873 178169.3826 165644.0507 176663.9259 162478.0244 137761.4165 173104.6605 0.775980791 0.991265543 1.03000407 1.037475667 1.02925815 0.956901161 1.020561349 0.938611496 0.795827311 1 17.40128504 -0.338220115 7.113666827 1.00000008 0.96249811 0.01401178 0.090556203 0 0 0.086272992 0.020334739 0.458965335 0.338220115 -0.03750197 VQVNHEK ddPTM_BT-474_Pertuzumab_2h_R1 6 VQVNHEK 7 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;;;;; 106.36 0.0077204 3331841000 3472455 3605050 2824679 3498970 2903488 2958470 3631700 3517640 3752030 3575010 FALSE TRUE 3336747.62 3502237.504 3335161.33 3679552.261 2996881.328 3018292.29 3676145.831 3444999.505 3326115.284 3332871.388 1.001163031 1.050816877 1.000687078 1.104018677 0.899189011 0.90561319 1.102996606 1.033643097 0.997972888 1 21.66833422 -0.336763274 6.743173734 1.000002883 1.013534135 0.000674143 0.065777915 0 0 0.064325044 0.015161558 0.46050752 0.336763274 0.013531251 SVAAEGALLPQTPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVAAEGALLPQTPPSPR 17 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 SVAAEGALLPQT(0.001)PPS(0.999)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQT(0.002)PPS(0.998)PR;SVAAEGALLPQTPPS(1)PR 348.4 1.41E-87 1597290000 1207990 1294120 1073920 1304950 1214540 1291500 1268350 1264900 1259640 1385820 TRUE FALSE 1160780.415 1257212.965 1268001.233 1372298.626 1253606.782 1317615.015 1283872.447 1238779.373 1116650.948 1291957.177 0.898466633 0.973107303 0.981457633 1.062185845 0.970316048 1.019859666 0.993742261 0.958839345 0.864309567 1 20.30112682 -0.332010781 6.494104483 0.999999942 0.97393031 0.022474431 0.053198375 0 0 0.051194993 0.012066776 0.465574536 0.332010781 -0.026069632 SDVLELTDDNFESR ddPTM_BT-474_Pertuzumab_2h_R1 7 SDVLELTDDNFESR 14 0 H7BZJ3 H7BZJ3 PDIA3 0 ;;;;;; 340.93 1.39E-68 14311531000 5650483 6888759 5382189 6663552 6421324 6476412 6494168 6366035 6616920 6670836 FALSE TRUE 5429655.877 6692298.338 6354870.278 7007458.717 6627871.718 6607369.488 6573645.571 6234574.153 5865794.982 6219014.336 0.873073382 1.076102735 1.021845253 1.126779637 1.065743116 1.062446415 1.057023704 1.002501975 0.943203322 1 22.56825451 -0.331194251 8.01841081 1.000000091 1.031412952 0.005368361 0.069042937 0 0 0.064698369 0.015249552 0.4664507 0.331194251 0.031412861 EFFNGKEPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 EFFNGKEPSR 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 120.77 0.00048584 3368100000 6928600 8211300 6004200 6924900 5935100 5803600 7521100 7343900 8470500 8069900 FALSE TRUE 6657822.652 7977121.764 7089292.503 7282294.919 6126007.882 5920952.768 7613145.472 7192245.899 7508964.351 7523318.485 0.884958236 1.060319562 0.942309237 0.967963131 0.81426938 0.787013441 1.011939809 0.955993809 0.998092048 1 22.84293773 -0.330988386 6.884329749 1 0.937454026 0.052655537 0.081352184 0 0 0.081201971 0.019139488 0.46667186 0.330988386 -0.062545973 IIWCPFIPEESEDCCEESSPTVALLHEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IIWCPFIPEESEDCCEESSPTVALLHEDR 29 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ; 217.67 2.45E-34 316270000 174708 207333 153752 173544 213420 180167 179867 176617 205534 201589 FALSE TRUE 167880.2182 201420.0658 181538.4066 182500.6266 220284.8481 183810.1002 182068.2662 172969.7972 182202.642 187935.1975 0.893287795 1.071752756 0.965962784 0.971082741 1.172131943 0.978050427 0.968782158 0.920369359 0.969497169 1 17.51987576 -0.329990428 6.632757765 0.999999958 0.99016245 0.001571319 0.074837276 0 0 0.072541861 0.017098281 0.46774545 0.329990428 -0.009837508 DNSTMGYMAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DNSTMGYMAAK 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 122.7 0.00089646 403720000 350170 343350 270810 292780 283450 262470 330320 332760 371370 365410 FALSE TRUE 336484.9693 333557.9942 319751.3911 307890.4109 292567.4267 267777.3232 334362.555 325888.3897 329213.6345 340660.4552 0.987742968 0.979150908 0.93862198 0.903804378 0.858824152 0.786053442 0.981512676 0.956636982 0.966398152 1 18.37797496 -0.329733002 6.889423472 1.000000412 0.927959812 0.109854417 0.060808448 0 0 0.063431775 0.014951013 0.468022787 0.329733002 -0.0720406 DVDEAHYAYSFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVDEAHYAYSFK 12 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 135.6 0.00012484 442110000 815930 827940 653570 775540 761060 720600 876820 816930 943130 1054000 FALSE TRUE 784042.5535 804327.9618 771684.6376 815565.7123 785540.1861 735171.0257 887550.7854 800060.11 836069.8363 982611.6412 0.797917021 0.818561401 0.785340419 0.829998016 0.799441156 0.748180659 0.903256941 0.814218025 0.850864982 1 19.90626181 -0.329317252 0.401848841 1.042524215 0.798829443 0.721626587 0.035591502 3.393254919 0.586097618 0.239429544 0.022911267 0.46847104 0.329317252 -0.243694772 FAGYVTSIAATELEDDDDDYSSSTSLLGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 FAGYVTSIAATELEDDDDDYSSSTSLLGQK 30 0 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 234.45 2.12E-45 90151000 169288 172030 128727 164531 162260 177920 156250 171983 207380 198056 FALSE TRUE 162672.0378 167123.8728 151990.8324 173022.4646 167479.2403 181517.6643 158162.2342 168431.4909 183839.0918 184641.4907 0.881015622 0.905126319 0.823167273 0.937072507 0.907050954 0.983081666 0.856590973 0.912208249 0.995654287 1 17.49436725 -0.329143325 0.121107886 1.112738991 0.824326456 0.404497918 0.043489879 29.35174484 0.990586381 1.730123281 0.641175635 0.468658691 0.329143325 -0.288412535 EFGYDS(ph)PHDLDS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 2 EFGYDSPHDLDSD 13 0 Q96CW6 Q96CW6 SLC7A6OS Probable RNA polymerase II nuclear localization protein SLC7A6OS 2 EFGYDS(1)PHDLDS(1)D;EFGYDS(1)PHDLDS(1)D 183.96 1.45E-05 416730000 492810 529830 449390 488360 516460 544170 483240 500110 556700 566370 TRUE FALSE 473550.4404 514719.7672 530604.7696 513564.3181 533072.4049 555173.4902 489154.0357 489782.5537 493505.7499 528009.2554 0.896860113 0.974830956 1.00491566 0.972642644 1.00958913 1.051446513 0.926411859 0.927602213 0.934653597 1 19.01020369 -0.329117024 6.577640085 1.000000001 0.967191841 0.04859381 0.044320614 0 0 0.045583395 0.010744109 0.468687073 0.329117024 -0.03280816 CTGDFSPS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 CTGDFSPSPEK 11 0 A0A2R8YH03;Q5VWN6;Q5VWN6-2 A0A2R8YH03 FAM208B Protein FAM208B 1 CTGDFS(0.007)PS(0.993)PEK;CTGDFS(0.001)PS(0.999)PEK 142.39 3.95E-05 283020000 882130 794640 675090 712630 681590 717580 750610 820730 857690 1015780 TRUE FALSE 847655.3844 771977.6452 797093.7803 749408.9197 703513.9614 732089.9593 759796.1897 803781.6387 760328.6269 946980.3158 0.895114048 0.815199252 0.841721593 0.791366945 0.742902413 0.773078328 0.802335779 0.848783893 0.802898027 1 19.85297491 -0.328719975 0.856435975 1.007001828 0.809716106 0.6597783 0.040263409 8.726906414 4.74744891 0.253192177 0.0136894 0.469115762 0.328719975 -0.197285722 DYTYEELLNR ddPTM_BT-474_Pertuzumab_2h_R1 6 DYTYEELLNR 10 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;;; 291.74 9.12E-32 4443550000 2147780 2164660 2078280 2170680 2276420 2169170 2136430 2355070 2129130 2334750 FALSE TRUE 2063842.383 2102926.016 2453871.427 2282709.055 2349643.117 2213032.104 2162576.269 2306436.982 1887440.088 2176615.303 0.94818886 0.966145011 1.127379479 1.048742537 1.07949398 1.016730931 0.993550062 1.059643833 0.867144546 1 21.05365502 -0.328618577 6.06860696 0.999992991 1.019416236 0 0.070368877 4446952.024 732779.6478 0.066146369 0.016042851 0.469225303 0.328618577 0.019423245 MEGGGAEVHAQLPSLEGDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEGGGAEVHAQLPSLEGDLR 20 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 136.58 5.13E-06 440010000 356840 382950 377330 519480 397750 387830 409660 404930 432770 433940 FALSE TRUE 342894.2983 372028.6409 445521.9247 546290.4251 410543.99 395672.1883 414673.5416 396568.054 383643.7639 404548.8573 0.847596754 0.919613625 1.101280888 1.350369468 1.014819304 0.978057857 1.025027099 0.980272338 0.948324923 1 18.62595442 -0.327416346 7.807315275 1.00000482 1.02356804 0.00037107 0.128178299 0 0 0.130756333 0.030819563 0.47052603 0.327416346 0.023563221 AS(ph)SPPDRIDIFGR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR 192.96 1.37E-06 15868340000 1512820 1701890 1036610 1165810 1321810 1578340 1215710 1271710 1309590 1096310 TRUE FALSE 1453697.322 1653353.764 1223948.486 1225977.594 1364327.219 1610255.116 1230588.223 1245448.744 1160930.833 1022055.947 1.422326562 1.617674422 1.197535702 1.199521021 1.334885065 1.575505843 1.204032153 1.218571985 1.135877969 1 19.96304274 -0.327413208 0.052349871 1.45E-11 2.214384017 0.453206012 0.137444753 130.3369891 1.781684695 46.15051665 29.45842419 0.47052943 0.327413208 2.214384017 KRPQS(ph)PSPR ddPTM_BT-474_Pertuzumab_2h_R1 5 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 KRPQS(0.971)PS(0.029)PR;KRPQS(0.891)PS(0.109)PR;KRPQS(0.993)PS(0.007)PR;KRPQS(0.994)PS(0.006)PR;KRPQS(0.995)PS(0.005)PR 98.156 0.0033867 2843460000 1672519 1558875 1172389 1366543 1437525 1357168 1421123 1623841 1683718 1480438 TRUE FALSE 1607155.108 1514417.411 1384265.772 1437070.448 1483764.297 1384610.867 1438515.128 1590308.116 1492589.391 1380166.616 1.164464558 1.097271441 1.002970045 1.041229683 1.075061721 1.003220083 1.042276427 1.152258066 1.081455945 1 20.39641101 -0.32623118 6.731933294 0.999995851 1.073456575 0.151906977 0.051998204 0 0 0.053280677 0.012558376 0.471811824 0.32623118 0.073460724 NSQEDSEDSEDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 5 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;;; 201.57 5.79E-09 3607490000 2321988 1529749 1459745 1172617 1575808 1394707 1444135 1981421 2309965 1700513 FALSE TRUE 2231242.142 1486122.056 1723553.393 1233135.904 1626495.295 1422908.931 1461808.756 1940503.964 2047747.457 1585335.74 1.407425623 0.937417872 1.087185099 0.77783896 1.025962674 0.897544221 0.922081499 1.224033443 1.291680624 1 20.59635697 -0.325508367 6.768471537 0.999995856 1.052296243 0.007216879 0.185540837 12059963.21 1781785.227 0.178456432 0.043282042 0.472597732 0.325508367 0.052300387 QCEGIT(ph)SPEGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QCEGITSPEGSK 12 0 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 1 QCEGIT(0.612)S(0.388)PEGSK 197.47 0.00033578 0 375540 362850 311860 329610 361530 370730 322490 354690 440700 370080 TRUE FALSE 360863.4816 352501.8733 368220.0393 346621.2116 373158.9408 378226.4146 326436.7291 347365.5276 390673.5836 345014.152 1.045938202 1.02170265 1.067260682 1.004657953 1.081575752 1.096263479 0.946154606 1.006815302 1.13234075 1 18.39629601 -0.324753567 7.964518956 0.999999998 1.039329411 0.056354032 0.050747125 0 0 0.048826604 0.011508541 0.473419817 0.324753567 0.039329413 EIFMQVEDERR ddPTM_BT-474_Pertuzumab_2h_R1 3 EIFMQVEDERR 11 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;; 145.31 5.82E-05 476100000 336047 363704 295169 353448 365944 354145 344325 351533 363530 375458 FALSE TRUE 322913.9117 353331.518 348512.6043 371689.4936 377714.9211 361306.0545 348538.9523 344273.7207 322263.5984 350027.8952 0.922537649 1.00943817 0.995670942 1.061885349 1.079099484 1.032220744 0.995746216 0.983560812 0.92067976 1 18.41711038 -0.324721386 6.446370347 1.000000006 1.003704262 0 0.048918561 0 0 0.049260648 0.011610846 0.473454898 0.324721386 0.003704255 AGQATEGHCPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGQATEGHCPR 11 0 C9J8T0;P57772-2;P57772 C9J8T0 EEFSEC Selenocysteine-specific elongation factor 0 101.35 0.0033496 43411000 44130 45590 35503 40840 33553 40365 40925 42675 55422 43181 FALSE TRUE 42405.35081 44289.81784 41919.18186 42947.75729 34632.26272 41181.20796 41425.85239 41793.74634 49130.72691 40256.31241 1.053383886 1.100195601 1.041307049 1.066857711 0.860293967 1.022975168 1.029052338 1.038191127 1.220447775 1 15.2969274 -0.323384805 6.876978875 0.999999105 1.042466658 0.025207221 0.083360899 0 0 0.079970687 0.018849272 0.474914244 0.323384805 0.042467553 VEPSSQS(ph)PGRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEPSSQSPGRSPR 13 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 2 VEPS(0.107)S(0.172)QS(0.721)PGRS(1)PR 73.11 0.021464 157730000 156600 179140 137850 147150 143670 179710 165430 178010 201730 244680 TRUE FALSE 150479.8989 174031.1026 162762.5615 154744.4291 148291.276 183343.8593 167454.5818 174334.0313 178830.4561 228107.6057 0.659688214 0.762934239 0.713534128 0.67838347 0.650093519 0.803760395 0.734103457 0.764262247 0.783974106 1 17.79935502 -0.323201514 0.361004401 1.07518104 0.695254624 0.81739262 0.040877608 2.766337378 0.4062716 0.305182699 0.033232709 0.47511472 0.323201514 -0.379926416 KENPLQFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KENPLQFK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-3;A0A2R8Y5P0;E9PNV3;E9PQ82 P15311;A0A2R8Y5S7 EZR;RDX Ezrin;Radixin 0 ; 186.16 0.00033507 2539600000 4477200 4576900 3878800 3852000 3583500 2556040 4355900 4554900 4695700 5206300 FALSE TRUE 4302226.074 4446371.293 4579785.443 4050802.182 3698766.532 2607724.88 4409208.807 4460839.723 4162663.822 4853672.664 0.886385707 0.916083881 0.943571139 0.834584955 0.762055208 0.537268386 0.908427311 0.919064806 0.857631759 1 22.21064538 -0.322750032 7.032740573 1.000000866 0.843030167 0.151610824 0.113010985 15903719.93 2261382.789 0.117481714 0.028493501 0.475608895 0.322750032 -0.156970699 GTTVTPDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTTVTPDKR 9 1 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ; 91.867 0.016776 276000000 349030 353720 324380 314350 317130 193717 412080 356100 371330 426590 FALSE TRUE 335389.5217 343632.2519 383002.6818 330573.6412 327330.7745 197634.0905 417123.1583 348746.4106 329178.1751 397696.6793 0.843329953 0.864056126 0.96305225 0.831220521 0.823066401 0.496946796 1.048847476 0.876915571 0.827711651 1 18.60130899 -0.322230223 8.650261612 1.000000535 0.846370624 0.11099882 0.133822373 0 0 0.127996026 0.030168953 0.476178493 0.322230223 -0.153629911 FPVIQHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FPVIQHFK 8 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;Q68CR8;B7ZBQ0 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 103.92 0.0046803 443120000 946140 925340 871850 900220 788440 524810 1001900 982910 1088500 1114900 FALSE TRUE 909163.8028 898950.2092 1029412.689 946680.4621 813800.8886 535422.0178 1014161.552 962612.565 964938.0434 1039386.83 0.874711682 0.864885126 0.990403822 0.910806674 0.782962479 0.515132579 0.975730616 0.926135042 0.928372398 1 19.98730125 -0.321974532 10.60906082 1 0.865292929 0.091341184 0.129259798 0 0 0.130708943 0.030808393 0.476458926 0.321974532 -0.134707071 FEDMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 FEDMAK 6 0 P26583;D6R9A6;P09429;Q5T7C4;B2RPK0;P23497 P26583;P09429;P23497 HMGB2;HMGB1;HMGB1P1;SP100 High mobility group protein B2;High mobility group protein B1;Putative high mobility group protein B1-like 1;Nuclear autoantigen Sp-100 0 117.7 0.05234 468410000 930300 776020 849190 788450 749750 712020 854610 973650 952610 886650 FALSE TRUE 893942.8475 753888.6694 1002657.523 829141.999 773866.3897 726417.5322 865068.9728 953543.7873 844473.7065 826596.4058 1.081474395 0.912039617 1.212995261 1.003079608 0.936208268 0.878805578 1.046543352 1.153578434 1.021627605 1 19.65682356 -0.321167787 6.772304486 0.999998923 1.031554056 0.005239731 0.099067414 0 0 0.09900773 0.023336346 0.477344819 0.321167787 0.031555133 ELHQQYK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELHQQYK 7 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 92.47 0.015646 269300000 385620 424290 347410 362370 312570 236470 420820 379570 443480 466460 FALSE TRUE 370549.5441 412189.6646 410194.7151 381071.9591 322624.0979 241251.5854 425970.121 371731.7469 393138.0096 434866.2487 0.852100031 0.947853888 0.943266387 0.876296931 0.741892706 0.554771924 0.979542842 0.854818575 0.904043509 1 18.73021222 -0.318067509 7.015116949 1.000000614 0.850950081 0.127564796 0.117278054 0 0 0.117929481 0.027796246 0.48076461 0.318067509 -0.149050533 GNWDEQFDKENTEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GNWDEQFDKENTEER 15 1 A0A2R8YD12;A0A024QZX5;A0A087X1N8;P35237;A0A2R8Y6A7 A0A2R8YD12 SERPINB6 Serpin B6 0 ; 230.82 2.52E-13 2719400000 1509840 1566730 1275610 1338520 1340380 552500 1641390 1410610 1752760 1731940 FALSE TRUE 1450833.784 1522048.394 1506141.103 1407601.178 1383494.54 563671.9285 1661477.822 1381480.411 1553794.033 1614634.161 0.898552637 0.942658363 0.932806415 0.871777156 0.856847064 0.349101947 1.029011935 0.855599642 0.962319558 1 20.62277589 -0.317372646 7.07899267 0.999999926 0.853659225 0.056512871 0.177109124 0 0 0.169432329 0.039935583 0.48153444 0.317372646 -0.146340701 TAPS(ph)PLVEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 TAPSPLVEAK 10 0 Q8TEH3;Q8TEH3-7;Q8TEH3-6;A0A0A0MS48;Q8TEH3-4;Q8TEH3-3;Q8TEH3-5;Q8TEH3-2 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 T(0.001)APS(0.999)PLVEAK;TAPS(1)PLVEAK;T(0.001)APS(0.999)PLVEAK;T(0.001)APS(0.999)PLVEAK 155.99 1.23E-05 1201870000 2280620 2221730 1720690 1707630 1818400 1924150 1829440 2209940 2373240 2166820 TRUE FALSE 2191490.849 2158368.436 2031656.96 1795760.989 1876890.487 1963057.631 1851829.234 2164303.967 2103839.745 2020059.351 1.084864585 1.068467832 1.005741221 0.888964469 0.929126407 0.971782156 0.916720211 1.071406127 1.041474224 1 20.94596625 -0.317020677 6.878559366 1.000000036 0.995925539 0 0.066181621 0 0 0.069128174 0.016293667 0.481924852 0.317020677 -0.004074497 SQKPVMVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQKPVMVK 8 1 P46779 P46779 RPL28 60S ribosomal protein L28 0 ; 82.287 0.018845 846230000 1426930 1301640 1166450 1083550 1237350 1045110 1274170 1438230 1511670 1332440 FALSE TRUE 1371163.998 1264518.502 1377253.463 1139472.145 1277150.486 1066242.84 1289763.674 1408530.048 1340071.559 1242192.652 1.103825559 1.017972936 1.108727749 0.917307105 1.028142039 0.858355456 1.03829601 1.133906279 1.078795271 1 20.24445751 -0.315718798 6.874731051 0.999984599 1.032741672 0.013143929 0.081968182 0 0 0.082574676 0.019463038 0.48337168 0.315718798 0.032757073 YFLNHIDQTTTWQDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFLNHIDQTTTWQDPR 16 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8;P46937-4 P46937-6 YAP1 Transcriptional coactivator YAP1 0 ; 189.31 1.04E-09 2170650000 1741650 1836880 1396810 1830130 1789770 1835220 1727570 1651880 1861880 1957080 FALSE TRUE 1673584.393 1784493.981 1649244.639 1924583.229 1847339.577 1872329.406 1748712.518 1617768.101 1650527.188 1824525.228 0.917271171 0.978059362 0.903930849 1.054840568 1.012504266 1.026200886 0.958447979 0.886678943 0.904633799 1 20.79908967 -0.313728153 6.556797255 1 0.959933576 0.045328092 0.054656944 0 0 0.05736789 0.013521741 0.485592362 0.313728153 -0.040066424 WGQPPSPT(ph)PVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_BT-474_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 WGQPPS(0.137)PT(0.856)PVPRPPDADPNT(0.079)PS(0.928)PKPLEGRPER 106.97 9.43E-06 1636900000 209850 158280 145830 144240 168240 151250 154930 196260 187790 174640 TRUE FALSE 201648.83 153766.0094 172184.725 151684.2437 173651.5924 154308.3786 156826.0797 192207.1624 166472.8665 162811.4772 1.238541861 0.944442075 1.057571173 0.931655718 1.06658078 0.947773346 0.96323725 1.180550448 1.02248852 1 17.31284288 -0.313334326 6.807577667 0.999986787 1.038966072 0.014234853 0.097856082 0 0 0.090957886 0.021438979 0.486032906 0.313334326 0.038979285 SRS(ph)ESET(ph)STMAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 2 S(0.008)RS(0.922)ES(0.291)ET(0.454)S(0.323)T(0.001)MAAK 165.58 1.26E-05 0 688380 650490 514260 514770 548740 575610 543830 669570 679000 685430 TRUE FALSE 661477.3486 631938.6621 607198.2217 541337.3414 566390.7205 587249.2286 550485.5542 655743.1455 601922.7666 639005.2156 1.03516737 0.988941321 0.950224203 0.847156374 0.88636322 0.919005376 0.861472709 1.02619373 0.941968472 1 19.28546818 -0.312877704 6.867807314 1 0.939412839 0.08128505 0.060904012 0 0 0.062224352 0.01466642 0.486544196 0.312877704 -0.060587161 FEGAIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FEGAIYR 7 0 P22102;P22102-2 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 83.614 0.051531 279930000 424190 422230 389190 451530 346070 233940 513180 430660 461040 507200 FALSE TRUE 407612.1858 410188.4138 459525.2905 474833.5174 357201.6558 238670.4271 519460.4503 421766.7205 408704.672 472846.8922 0.862038416 0.86748675 0.971826818 1.004201413 0.755427733 0.504752027 1.098580659 0.891973126 0.86434886 1 18.85101359 -0.31241826 7.033093049 1.000000006 0.873427943 0.062809946 0.150968585 0 0 0.147751695 0.034825408 0.487059187 0.31241826 -0.126572063 VDVRPLPAS(ph)PARPCPSPGPAAASS(ph)PARPPGLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDVRPLPASPARPCPSPGPAAASSPARPPGLQR 33 3 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 2 VDVRPLPAS(1)PARPCPS(0.017)PGPAAAS(0.474)S(0.508)PARPPGLQR 91.835 0.00037022 218640000 55026 45857 44948 40750 35916 47113 47140 51369 51733 58310 TRUE FALSE 52875.52309 44549.20326 53071.10346 42853.11238 37071.27076 48065.65714 47716.91342 50308.2122 45860.48672 54360.61176 0.972680795 0.819512544 0.976278628 0.788311812 0.681950949 0.884200078 0.877784702 0.925453386 0.843634485 1 15.73027407 -0.311367849 8.023051542 0.999999997 0.863610752 0.193563276 0.083698014 0 0 0.081773608 0.019274224 0.488238644 0.311367849 -0.136389245 DDRGPPQRPK ddPTM_BT-474_Pertuzumab_2h_R1 6 DDRGPPQRPK 10 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 125.72 0.00022587 2722560000 2823720 2829940 2102140 2229830 2360430 2589930 2580480 2615460 3078360 2794030 FALSE TRUE 2713365.901 2749232.882 2482043.46 2344911.794 2436355.375 2642300.159 2612060.686 2561449.837 2728917.478 2604787.859 1.041684025 1.055453661 0.952877391 0.900231389 0.93533735 1.014401288 1.002792099 0.983362168 1.047654406 1 21.31273445 -0.310619215 8.110521386 1.000006807 0.989507666 0 0.048510493 0 0 0.050074748 0.011802731 0.489080992 0.310619215 -0.010499141 APPCEYKDWLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 APPCEYKDWLTK 12 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 124.3 0.00029678 1054700000 1281800 1244500 783380 916460 1010700 1008500 969890 1173300 1302400 1133100 FALSE TRUE 1231705.839 1209008.078 924954.1922 963758.6104 1043210.083 1028892.561 981759.8039 1149070.945 1154557.012 1056354.128 1.16599709 1.144510204 0.875609957 0.912344246 0.987557161 0.974003446 0.929385116 1.087770583 1.09296398 1 20.01066213 -0.308629504 6.900406106 0.999999798 1.014387625 0.001518947 0.095249615 0 0 0.097038058 0.02287209 0.491326847 0.308629504 0.014387827 NKESKDPADETEAD ddPTM_BT-474_Pertuzumab_2h_R1 3 NKESKDPADETEAD 14 2 P16949 P16949 STMN1 Stathmin 0 ;; 113.59 0.0020935 8106000000 6217200 5051800 3805350 3042290 3980100 4461100 4400500 5384400 6036100 4867100 FALSE TRUE 5974224.951 4907727.61 4493061.395 3199302.951 4108123.531 4551306.499 4454354.635 5273210.258 5350907.233 4537446.982 1.316648982 1.0816055 0.990217938 0.705088779 0.905382156 1.003054475 0.981687423 1.162153581 1.179277081 1 22.11344936 -0.308353288 8.286951462 1.000000005 1.028850324 0.002780318 0.158258427 0 0 0.163094172 0.038441665 0.491639436 0.308353288 0.02885032 DMDDEESWIKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DMDDEESWIKEK 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 174.68 2.71E-05 256930000 216840 205630 160780 150910 164350 177830 178280 197780 251540 197470 FALSE TRUE 208365.6531 199765.6337 189836.5225 158698.4832 169636.467 181425.8444 180461.844 193695.7739 222986.2337 184095.181 1.131836542 1.085121472 1.03118681 0.86204583 0.92146066 0.985500237 0.980263812 1.052150159 1.211255137 1 17.49009234 -0.307615368 7.495899562 1.000000003 1.021348558 0.002520003 0.09576671 0 0 0.097123176 0.022892152 0.492475503 0.307615368 0.021348555 DIPRT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIPRTPSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DIPRT(0.998)PS(0.002)R;DIPRT(0.996)PS(0.004)R 141.1 0.0010331 3694500000 621110 664320 539280 653860 634090 699240 571220 649460 655790 713190 TRUE FALSE 596836.3345 645374.244 636739.8922 687605.793 654486.0807 713379.1119 578210.7612 636048.424 581347.4685 664885.0061 0.897653473 0.970655434 0.957669201 1.034172506 0.984359814 1.07293608 0.869640248 0.956629219 0.874357916 1 19.34274532 -0.305383549 6.294351407 0.999999999 0.960279114 0.038924303 0.061951057 7963087.745 1265116.42 0.059113351 0.014337094 0.495012825 0.305383549 -0.039720885 S(ph)PAVKPAAAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPAVKPAAAPK 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 S(1)PAVKPAAAPK 85.909 0.0090021 183020000 789820 535670 636660 480540 506570 493180 567990 918440 614500 644580 TRUE FALSE 758952.9612 520393.2161 751718.6244 505340.727 522864.2841 503152.4375 574941.2315 899473.893 544744.5362 600922.0225 1.262980774 0.865991254 1.250942046 0.840942266 0.870103382 0.837300712 0.956765121 1.496822981 0.906514516 1 19.19681827 -0.305137477 8.347775505 0.999980194 1.04743261 0 0.216579687 0 0 0.219279865 0.05168476 0.495293379 0.305137477 0.047452416 SAS(ph)WGSADQLK ddPTM_BT-474_Pertuzumab_2h_R1 5 SASWGSADQLK 11 0 Q86VQ1;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 SAS(0.948)WGS(0.052)ADQLK;SAS(0.996)WGS(0.004)ADQLK;SAS(0.995)WGS(0.005)ADQLK;S(0.001)AS(0.985)WGS(0.014)ADQLK;SAS(0.998)WGS(0.002)ADQLK 200.05 5.05E-08 2231070000 3709040 3518130 3083760 2895950 2960660 2677220 3379670 3587570 3912290 3778420 TRUE FALSE 3564086.616 3417796.377 3641064.03 3045410.327 3055892.318 2731355.223 3421031.412 3513485.426 3468183.241 3522504.248 1.011804774 0.970274593 1.033657811 0.864558312 0.867534033 0.775401541 0.971192984 0.997439656 0.984578867 1 21.74817002 -0.304123011 6.970365161 0.999999991 0.941420628 0.048977732 0.076883495 0 0 0.080313354 0.018930039 0.496451685 0.304123011 -0.058579363 TDS(ph)SPNQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TDSSPNQAR 9 0 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 T(0.005)DS(0.513)S(0.482)PNQAR;TDS(0.559)S(0.441)PNQAR;TDS(0.5)S(0.5)PNQAR 192.14 3.68E-05 422259000 804479 736691 685122 754464 742789 786879 763942 744482 847451 839143 TRUE FALSE 773039.0713 715681.294 808938.7859 793401.9775 766681.4828 802790.2325 773291.3507 729108.1865 751251.9153 782307.0972 0.988152957 0.914834208 1.034042499 1.014182257 0.98002624 1.026182985 0.988475438 0.931997408 0.96030308 1 19.57737553 -0.303892028 6.373605329 1 0.980460169 0.019843451 0.036447424 0 0 0.036826041 0.008679981 0.496715797 0.303892028 -0.01953983 LQIT(ph)PDSNGEQFSSLIQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LQITPDSNGEQFSSLIQR 18 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;K7ERN1;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 LQIT(0.99)PDS(0.01)NGEQFSSLIQR;LQIT(0.989)PDS(0.011)NGEQFSSLIQR;LQIT(1)PDSNGEQFSSLIQR 183.39 7.11E-13 764900000 289990 375459 361057 447628 344431 419934 395203 392260 317964 384689 TRUE FALSE 278656.8702 364751.2769 426308.0316 470730.1347 355509.9359 428425.3532 400039.6125 384159.6939 281870.0597 358633.6714 0.776995838 1.01705809 1.18870052 1.312565362 0.991289899 1.194604376 1.115454695 1.071175756 0.78595537 1 18.45215142 -0.301639803 6.725766712 1 1.06713165 0 0.162823735 0 0 0.155927187 0.03675239 0.499298426 0.301639803 0.06713165 KGVCGDWK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGVCGDWK 8 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 80.688 0.039766 431090000 727910 740250 669940 500340 571720 231820 753950 632830 773020 884910 FALSE TRUE 699462.4725 719138.7948 791013.0607 526162.6074 590109.893 236507.5592 763177.0656 619761.8394 685270.0104 824974.2575 0.847859756 0.871710588 0.958833628 0.637792758 0.715307039 0.286684775 0.925091976 0.751249913 0.830656235 1 19.65398958 -0.301571495 12.51940745 1 0.755879127 0.136166206 0.182495959 0 0 0.177823282 0.041913349 0.499376965 0.301571495 -0.244120873 DQMEGSPNSSESFEHIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQMEGSPNSSESFEHIAR 18 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 80.236 0.0089382 198790000 119510 116280 111490 158120 153780 122350 140830 126690 118770 152360 FALSE TRUE 114839.4171 112963.8083 131638.7231 166280.5921 158726.4734 124824.0008 142553.5197 124073.8072 105287.7275 142040.5215 0.808497574 0.79529283 0.926768796 1.170656024 1.117473181 0.878791485 1.003611633 0.873509939 0.741251344 1 17.11594304 -0.300664766 6.918751998 1 0.931270362 0.026575145 0.131526074 18295531.17 2644339.764 0.135239146 0.032800311 0.500420663 0.300664766 -0.068729638 EVPWS(ph)PSAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVPWSPSAEK 10 0 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EVPWS(0.999)PS(0.001)AEK;EVPWS(0.994)PS(0.006)AEK 246.56 1.33E-12 1553770000 3487650 3450850 3036880 3376620 3765030 3533160 3284460 3527200 3695680 3670570 TRUE FALSE 3351348.782 3352435.137 3585711.771 3550887.763 3886135.609 3604602.916 3324656.204 3454362.087 3276161.9 3421959.024 0.97936555 0.979683016 1.047853509 1.03767688 1.135646447 1.053374073 0.971565171 1.009469156 0.957393667 1 21.70639105 -0.297893585 6.478605258 1.000003761 1.020870472 0.011782507 0.050249299 0 2.71E-18 0.051684937 0.012182257 0.503623997 0.297893585 0.020866711 IKWDEQTSNTKGDDDEES(ph)DEEAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKWDEQTSNTKGDDDEESDEEAVK 24 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 IKWDEQTSNTKGDDDEES(1)DEEAVK 217.67 6.42E-33 439630000 352160 246300 195060 133560 209670 188410 177430 293180 312320 232760 TRUE FALSE 338397.1979 239275.7652 230311.6811 140453.0476 216414.226 192219.7793 179601.4414 287125.7305 276866.743 216994.9579 1.559470327 1.102678917 1.061368814 0.647264107 0.997323754 0.885826017 0.827675644 1.323190794 1.275913255 1 17.72730199 -0.297478191 7.372785126 0.999984394 1.063502415 0.006081907 0.24997941 0 0 0.249090857 0.058711278 0.504105933 0.297478191 0.063518021 NKYNTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 NKYNTPK 7 1 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 94.302 0.013042 1136400000 1383700 1038700 846680 744430 954300 868780 969040 1057000 1326500 1111200 FALSE TRUE 1329623.474 1009077.293 999693.9103 782850.1215 984995.9262 886347.3268 980899.4014 1035172.581 1175921.281 1035937.434 1.283497854 0.974071657 0.965013791 0.755692473 0.95082569 0.855599284 0.946871277 0.99926168 1.135127704 1 19.98250544 -0.295850158 7.063949522 1.000000546 0.972709673 0 0.13626916 0 0 0.1306399 0.03079212 0.505999214 0.295850158 -0.027290873 NPFDTFFGQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NPFDTFFGQR 10 0 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 113.93 0.0033114 646170000 413303 369406 328879 393590 454245 387075 434065 275245 467318 527864 FALSE TRUE 397150.6618 358870.9026 388314.7512 413903.2271 468856.203 394901.9217 439377.2173 269561.0946 414270.0198 492111.3011 0.807034224 0.729247432 0.789079117 0.841076452 0.952744231 0.802464647 0.892841145 0.547764487 0.841821797 1 18.90862512 -0.29538057 8.105401098 0.999973971 0.78987515 0.248742506 0.10256472 0 0 0.105800028 0.024937306 0.50654663 0.29538057 -0.210098821 AAPDLGSHLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAPDLGSHLDR 11 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 0 113.22 0.0014204 348970000 101150 112020 90317 123870 116490 105550 100760 105870 117470 126510 FALSE TRUE 97196.94617 108825.2993 106639.291 130262.9455 120237.0066 107684.2933 101993.131 103683.7475 104135.2981 117941.365 0.824112441 0.922706798 0.904172094 1.104472087 1.019464262 0.913032449 0.864778282 0.879112663 0.882941265 1 16.84771027 -0.292912961 7.857486867 1.00000226 0.925088161 0.080545905 0.077069721 0 0 0.080598979 0.018997362 0.509432959 0.292912961 -0.074914099 RAS(ph)AILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RASAILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK 37 2 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 RAS(1)AILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK 199.78 1.73E-30 61145000 217780 176780 159520 124710 144130 144800 143410 234870 204740 169150 TRUE FALSE 209268.9168 171738.4075 188348.8125 131146.298 148766.0723 147727.9552 145165.0945 230019.8524 181498.7735 157693.3198 1.327062662 1.089065838 1.194399437 0.831654113 0.94338855 0.93680541 0.920553227 1.458653116 1.150960445 1 17.26676202 -0.291139911 7.944308251 0.999977465 1.099455677 0.022181244 0.18631655 0 0 0.194669117 0.045883951 0.51151702 0.291139911 0.099478212 SQS(ph)PINCIRPSVLGPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSPINCIRPSVLGPLK 17 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 SQS(1)PINCIRPSVLGPLK;SQS(1)PINCIRPSVLGPLK 179.5 5.53E-10 835770000 894020 890040 748320 698780 749060 487390 879340 856750 995650 963270 TRUE FALSE 859080.71 864656.9306 883558.0703 734844.1195 773154.1952 497245.3597 890101.626 839057.8131 882627.9861 898026.8649 0.956631414 0.962840829 0.983888239 0.818287457 0.860947735 0.55370878 0.991174831 0.934334869 0.982852541 1 19.77639908 -0.290642928 11.88273904 0.999999999 0.892674237 0.060118845 0.125833824 0 0 0.124745793 0.029402865 0.512102707 0.290642928 -0.107325762 DPIPAAHSFVDLLLCVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPIPAAHSFVDLLLCVAR 18 0 Q6PJG6;Q6PJG6-2 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 203.9 1.13E-15 38667000 46608 47788 36226 53284 47698 43701 50819 46224 46217 52824 FALSE TRUE 44786.50783 46425.13303 42772.84404 56033.99363 49232.24949 44584.66416 51440.93812 45269.45825 40970.63992 49246.18343 0.909441193 0.94271535 0.86855145 1.137834239 0.999717055 0.905342527 1.044567001 0.919248053 0.831955637 1 15.5877243 -0.288482957 7.15080655 1 0.955479133 0.026738706 0.084894216 0 0 0.08083846 0.019053808 0.514656003 0.288482957 -0.044520867 EGLLLWCQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGLLLWCQR 9 0 O43707;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;G3V2N5;A0A494C1A0;G3V2W4;Q08043;A0A494C166;A0A494C033;A0A087WSZ2;G3V2X9 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ; 151.27 0.0001937 883400000 714080 850570 648300 814450 644780 344690 1003890 709640 802690 926510 FALSE TRUE 686172.9641 826312.5764 765462.2314 856483.8621 665519.9343 351659.868 1016175.906 694985.686 711571.9964 863756.6525 0.794405418 0.956649739 0.886201257 0.991580047 0.770494713 0.407128405 1.176460874 0.804608201 0.823810728 1 19.72026539 -0.284798968 7.182338721 1 0.850619003 0.05749889 0.186454019 0 0 0.17456845 0.041146178 0.519040244 0.284798968 -0.149380997 DKVVALAEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKVVALAEGR 10 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3;F8VWB3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 ; 104.24 0.0040789 267710000 965010 955660 846820 810820 798260 535540 970710 948380 988220 1056160 FALSE TRUE 927296.3423 928405.5125 999859.2114 852666.5174 823936.7579 546368.9857 982589.8394 928795.6216 876041.4086 984625.3425 0.941775823 0.942902313 1.015471742 0.865980674 0.836802307 0.554900389 0.997932713 0.943298513 0.889720557 1 19.90921535 -0.284589465 7.077442868 0.999991382 0.889932164 0.069532538 0.123048228 16710349.03 2361071.582 0.123409526 0.029931207 0.519290689 0.284589465 -0.110059217 VKKDDEEEDPLDQLISR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKKDDEEEDPLDQLISR 17 2 Q9NYJ1;Q9NYJ1-2 Q9NYJ1 COA4 "Cytochrome c oxidase assembly factor 4 homolog, mitochondrial" 0 ; 164.59 1.45E-09 250930000 573760 475460 440160 355000 366570 440130 444600 550740 650150 492860 FALSE TRUE 551336.8249 461900.3463 519706.7033 373321.5925 378361.057 449029.7302 450041.1478 539367.0265 576347.6977 459478.1532 1.199919563 1.005271618 1.131080335 0.812490409 0.823458209 0.97726024 0.979461471 1.173868709 1.254352777 1 18.80963674 -0.283450491 7.791909558 0.999999908 1.034025411 0.005464994 0.143346928 0 0 0.147296191 0.034718045 0.52065436 0.283450491 0.034025502 IDLMPHDLITQLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDLMPHDLITQLLR 14 0 F2Z2B9;Q9BSJ2-3;Q9BSJ2;Q9BSJ2-4;B3KTU7 F2Z2B9 TUBGCP2 Gamma-tubulin complex component 2 0 95.264 0.003837 38973000 80624 88908 83785 96044 92338 88708 103920 105850 117920 134550 FALSE TRUE 77473.12495 86372.43089 98926.81329 101000.8423 95308.13563 90501.73654 105191.804 103664.1605 104534.216 125436.8087 0.617626722 0.688573249 0.788658563 0.805193017 0.759809953 0.721492658 0.838603957 0.826425366 0.833361571 1 16.93660123 -0.28014502 0.042484404 1.823127867 8.48E-12 0.810204527 0.042566348 90.1613606 1.018734498 25.75225992 18.02845079 0.524632245 0.28014502 -1.823127867 DRAEAEAR ddPTM_BT-474_Pertuzumab_2h_R1 5 DRAEAEAR 8 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3 P35579;P35580;P35749 MYH9;MYH10;MYH11 Myosin-9;Myosin-10;Myosin-11 0 ;;;; 186.78 0.00018757 2157992000 1797169 1947125 1573480 1854618 1821240 1680242 1899055 1844901 2050209 2128596 FALSE TRUE 1726933.649 1891594.901 1857842.838 1950335.057 1879821.839 1714217.644 1922296.203 1806803.15 1817477.869 1984424.297 0.870244157 0.953220994 0.936212503 0.982821597 0.94728826 0.863836251 0.968692132 0.910492354 0.915871607 1 20.9202891 -0.280074054 9.981895784 1.000007464 0.929408007 0.255243359 0.036973463 0 0 0.034177817 0.008055789 0.52471798 0.280074054 -0.070599457 NYGSPLISGS(ph)TPK ddPTM_BT-474_Pertuzumab_2h_R1 1 NYGSPLISGSTPK 13 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NYGS(0.004)PLIS(0.164)GS(0.504)T(0.329)PK 73.834 0.037502 89875000 310970 266810 232150 206230 208960 193840 197350 314620 316200 294950 TRUE FALSE 298816.9486 259200.84 274104.6691 216873.555 215681.3882 197759.5776 199765.2283 308122.9871 280306.3016 274972.7738 1.086714675 0.942641835 0.996842943 0.788709195 0.784373613 0.71919694 0.726490938 1.120558166 1.019396567 1 18.06892925 -0.279105924 12.00673621 1 0.907713082 0.036037412 0.140262718 0 0 0.147212298 0.034698271 0.525888987 0.279105924 -0.092286917 DLAEITTLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLAEITTLDR 10 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 120.27 0.0013532 112730000 50244 46876 38969 50090 51283 50673 38930 47899 50301 59605 FALSE TRUE 48280.40893 45539.14238 46011.56516 52675.1509 52932.56427 51697.64278 39406.43699 46909.86891 44591.04136 55567.90026 0.868854297 0.819522461 0.828024182 0.947942079 0.95257449 0.930350842 0.709158287 0.844190057 0.802460434 1 15.76196411 -0.277174831 8.646715684 1.000000016 0.854496047 0.271212466 0.070832581 0 0 0.072688434 0.017132828 0.528232562 0.277174831 -0.14550397 TAS(ph)GSSVTS(ph)LDGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 T(0.186)AS(0.814)GS(0.187)S(0.197)VT(0.218)S(0.399)LDGTR;T(0.026)AS(0.974)GS(0.07)S(0.039)VT(0.22)S(0.671)LDGTR 123.02 0.00015397 3066500000 2400000 2936800 2102500 2376300 2575900 2601900 2183500 2656900 2620600 1816650 TRUE FALSE 2306205.347 2853045.339 2482468.52 2498941.128 2658756.163 2654512.201 2210222.326 2602034.087 2323120.474 1693606.677 1.361712479 1.684597361 1.465788104 1.475514452 1.569878177 1.567372304 1.305038741 1.536386294 1.371700115 1 20.69166743 -0.274039661 0.469964563 0.919276611 1.523394075 0.679296623 0.102305847 3.353415312 0.769279332 0.558240794 0.050681699 0.532059667 0.274039661 0.604117464 DGQDAIAQS(ph)PEKESK ddPTM_BT-474_Pertuzumab_2h_R1 5 DGQDAIAQSPEKESK 15 1 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(0.997)PEKES(0.003)K;DGQDAIAQS(1)PEKESK 257.77 2.23E-24 12564920000 8060840 5561040 4569030 3664260 5197840 4967570 5332110 6571370 7317720 5573750 TRUE FALSE 7745813.461 5402444.584 5394755.359 3853372.898 5365033.244 5068017.669 5397365.957 6435668.913 6487043.104 5196234.948 1.490658821 1.039684433 1.038204664 0.741570182 1.032484731 0.975324965 1.038707066 1.23852539 1.2484122 1 22.30903523 -0.273581709 7.938842344 0.999987744 1.083676678 0.019373556 0.188194907 0 0 0.185676216 0.043764304 0.532621007 0.273581709 0.083688933 SLHLS(ph)PQEQSASYQDR ddPTM_BT-474_Pertuzumab_2h_R1 5 SLHLSPQEQSASYQDR 16 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 S(0.038)LHLS(0.962)PQEQSASYQDR;SLHLS(0.999)PQEQS(0.001)ASYQDR;S(0.027)LHLS(0.973)PQEQSASYQDR;SLHLS(0.997)PQEQS(0.003)ASYQDR;SLHLS(1)PQEQSASYQDR 227.46 5.26E-15 2012640000 532248 619249 583510 759187 670550 644348 675418 623338 625916 746439 TRUE FALSE 511447.1597 601588.6248 688963.2371 798368.7321 692118.8497 657377.158 683683.9675 610465.8525 554864.6397 695882.0217 0.734962456 0.864498013 0.990057532 1.147275985 0.994592227 0.944667541 0.982471089 0.877254813 0.797354469 1 19.40848321 -0.273413972 7.211750707 1.000000204 0.933537085 0.035206812 0.110016684 0 0 0.112099846 0.026422187 0.53282676 0.273413972 -0.066463119 WMGGAELSDDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 WMGGAELSDDGR 12 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;; 205.18 2.44E-07 1470120000 874710 950260 821540 1005540 918110 954200 986700 935490 950750 1022060 FALSE TRUE 840525.3662 923159.5152 970010.5531 1057436.04 947641.842 973494.5778 998775.5298 916171.8046 842824.8459 952834.9658 0.88213111 0.968855624 1.018025773 1.109778795 0.994549818 1.021682256 1.048214608 0.961522024 0.884544413 1 19.86186683 -0.273409674 6.54225026 1 0.993248125 0 0.066173911 0 0 0.06530438 0.01539239 0.532832033 0.273409674 -0.006751875 GADSLEDFLYHEGYACTSIHGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 GADSLEDFLYHEGYACTSIHGDR 23 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;;;; 279.15 4.19E-52 2576365000 601089 811806 805794 1165308 848043 976084 1053796 528691 977180 1165497 FALSE TRUE 577597.7773 788654.0877 951418.9006 1225449.686 875321.0733 995821.0872 1066692.671 517773.3461 866254.6231 1086556.85 0.531585418 0.725828646 0.875627355 1.127828411 0.805591602 0.916492393 0.981718233 0.476526696 0.797247399 1 20.05133223 -0.272769128 7.946643163 1.000013059 0.800850027 0.091340617 0.184917738 25706965.66 3234946.36 0.189083024 0.045859369 0.533618493 0.272769128 -0.199163032 VKAQT(ph)PPGPSLS(ph)GSKSPCPQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKAQTPPGPSLSGSKSPCPQEK 22 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKAQT(1)PPGPS(0.018)LS(0.451)GS(0.338)KS(0.193)PCPQEK 89.024 0.0049016 3377700000 2100400 1674000 1314300 983840 1355900 1404300 1497800 1788200 2160400 1523200 TRUE FALSE 2018314.046 1626259.159 1551823.246 1034616.1 1399513.755 1432695.908 1516130.524 1751273.045 1915160.449 1420032.307 1.421315582 1.145226873 1.092808409 0.728586311 0.985550644 1.008917826 1.067673261 1.233262818 1.348673857 1 20.43749232 -0.272512543 7.990916548 0.999992602 1.103938993 0.030397387 0.185587162 0 0 0.188974724 0.04454177 0.533933853 0.272512543 0.103946391 IAHLAQIEDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IAHLAQIEDDR 11 0 A6NHR9;A6NHR9-2;J3KTL8;A6NHR9-3;A0A2R8YCU7 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 0 ;;; 178.67 7.44E-06 1002900000 634600 654050 576020 687960 671500 674720 687540 635620 678490 755830 FALSE TRUE 609799.1304 635397.1344 680119.6275 723465.698 693099.4073 688363.3007 695954.3202 622494.2249 601470.6597 704636.9609 0.865408947 0.90173688 0.965205723 1.026721189 0.983626244 0.976904901 0.987677852 0.883425451 0.853589427 1 19.42652063 -0.272202069 9.709571609 1 0.941032351 0.096620723 0.05606395 0 0 0.058565307 0.013803975 0.534315695 0.272202069 -0.058967649 TLNAET(ph)PKS(ph)SPLPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 T(0.027)LNAET(0.973)PKS(0.819)S(0.181)PLPAK 134.06 8.59E-05 513030000 968180 696050 502380 463180 568320 498480 584580 864640 841680 656430 TRUE FALSE 930342.4552 676199.3355 593171.2414 487084.7753 586600.5289 508559.6071 591734.2649 846784.8818 746136.015 611969.4114 1.520243394 1.104956102 0.969282501 0.795929937 0.958545506 0.831021286 0.966934382 1.383704587 1.219237434 1 19.22310002 -0.269097216 8.074079976 1.000005088 1.078304549 0.012172184 0.221058203 0 0 0.229422633 0.054075433 0.538149306 0.269097216 0.078299461 VREEFK ddPTM_BT-474_Pertuzumab_2h_R1 6 VREEFK 6 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 104.45 0.030846 31229330000 21169650 18920130 16833770 16651090 18636150 15758690 19135590 21205220 20152990 20708450 FALSE TRUE 20342316.67 18380546.42 19876006.7 17510454.75 19235598.69 16077341.51 19369777.07 20767324.8 17865307.06 19305848.24 1.05368676 0.952071424 1.029532941 0.907002611 0.99636123 0.832770532 1.003311372 1.075701235 0.925383171 1 24.20253461 -0.26769741 7.079808135 1.000000016 0.978872853 0.008775988 0.069665679 0 0 0.067470453 0.015902938 0.539886652 0.26769741 -0.021127163 LGS(ph)LVDEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSLVDEFK 9 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 LGS(1)LVDEFK 86.014 0.015131 13439000 34961 25762 25335 19550 25512 24184 22521 32952 33376 27585 TRUE FALSE 33594.68547 25027.29298 29913.59807 20558.97784 26332.61665 24673.01705 22796.61873 32271.52968 29587.2964 25716.64338 1.306340216 0.973194387 1.163199941 0.799442507 1.02395232 0.959418252 0.886453897 1.254888875 1.150511595 1 14.65041473 -0.266916144 7.280477255 0.999999895 1.053842123 0.01202599 0.15314389 0 0 0.146718195 0.03458181 0.540858745 0.266916144 0.053842228 LIAQACVSIFPDSGHFNVDNIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIAQACVSIFPDSGHFNVDNIR 22 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 231.89 4.50E-26 2072750000 541860 631370 532660 617520 585500 671360 593030 566120 618100 723830 FALSE TRUE 520683.5121 613363.9458 628923.511 649390.2812 604333.1392 684935.3592 600287.6785 554429.4242 547935.8793 674804.3494 0.771606633 0.908950789 0.93200868 0.962338612 0.895567937 1.015013255 0.889572924 0.821615072 0.811992216 1 19.36410975 -0.265700839 8.125827926 0.999999804 0.892452075 0.18493873 0.069177736 0 0 0.069857177 0.016465494 0.542374373 0.265700839 -0.107547729 LTPLSHEVISR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTPLSHEVISR 11 0 P41091;Q2VIR3;Q2VIR3-2;H7BZU1 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ;;; 234.65 1.67E-15 2200050000 1191060 1388160 1149650 1443080 1358010 1393860 1320030 1359770 1289400 1490740 FALSE TRUE 1144512.058 1348571.036 1357417.329 1517557.532 1401691.625 1422044.804 1336184.922 1331690.274 1143032.718 1389770.852 0.823525732 0.970354957 0.976720246 1.091948021 1.00857751 1.023222499 0.961442615 0.958208522 0.822461283 1 20.4064156 -0.263048049 6.671142259 1.000000001 0.967163684 0.015110282 0.078875795 10324374.45 1547617.148 0.076435053 0.018538223 0.545697484 0.263048049 -0.032836317 YDDMAACMK ddPTM_BT-474_Pertuzumab_2h_R1 4 YDDMAACMK 9 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 139.19 0.00026889 3776450000 3757790 3864980 3030370 3061210 3237650 2737850 3819310 3509870 4020340 3918410 FALSE TRUE 3610931.412 3754754.555 3578025.269 3219199.415 3341791.953 2793211.203 3866051.858 3437389.958 3563967.858 3653012.601 0.988480415 1.02785152 0.979472468 0.881245089 0.914804387 0.764632239 1.058318785 0.940974022 0.975624299 1 21.8006553 -0.262017041 10.16301803 1 0.947281328 0.038295663 0.078213707 0 0 0.076165532 0.017952388 0.546994499 0.262017041 -0.052718672 SVPGALDKDS(ph)LEETEESIDALVSSQLSTNTHR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVPGALDKDSLEETEESIDALVSSQLSTNTHR 32 1 Q8TDW5;Q8TDW5-2 Q8TDW5 SYTL5 Synaptotagmin-like protein 5 1 SVPGALDKDS(1)LEETEESIDALVSSQLSTNTHR;SVPGALDKDS(1)LEETEESIDALVSSQLSTNTHR;SVPGALDKDS(1)LEETEESIDALVSSQLSTNTHR;SVPGALDKDS(1)LEETEESIDALVSSQLSTNTHR 384.76 2.74E-166 317232000 190462 163702.9 125407.4 144720 150644 151168.7 149201.2 170243.7 180532 173211.1 TRUE FALSE 183018.5345 159034.2536 148071.3069 152189.0165 155489.6011 154225.4347 151027.1689 166728.1081 160038.7642 161479.3579 1.133386563 0.9848581 0.916967399 0.942467313 0.962906981 0.955078325 0.93527229 1.032504156 0.991078775 1 17.30099023 -0.261663138 11.6426377 1 0.980833518 0.004423089 0.058885322 0 0 0.056902991 0.013412164 0.547440423 0.261663138 -0.019166482 ISLSKS(ph)PTKTDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISLSKSPTKTDPK 13 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 IS(0.024)LS(0.054)KS(0.838)PT(0.038)KT(0.046)DPK;IS(0.004)LS(0.023)KS(0.942)PT(0.026)KT(0.005)DPK 91.657 0.0033558 11410500000 19596600 15209400 10182700 8230200 12442000 12711300 12768800 16161100 17892100 13716200 TRUE FALSE 18830743.21 14775642.8 12022940.4 8654961.608 12842208.23 12968331.2 12925068.39 15827367.64 15861063.82 12787189.56 1.47262564 1.15550354 0.940233219 0.676846274 1.00430264 1.014165868 1.010782576 1.237751858 1.24038701 1 23.60819588 -0.260356588 8.019214889 1.000033205 1.073872248 0.013148772 0.20202122 0 0 0.206652597 0.048708484 0.549089845 0.260356588 0.073839043 QTDVGITHFR ddPTM_BT-474_Pertuzumab_2h_R1 4 QTDVGITHFR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 152.85 1.73E-05 1945540000 2156340 2243420 1693140 2236510 2182980 2017080 2175530 2137370 2152280 2339500 FALSE TRUE 2072067.849 2179439.858 1999128.062 2351936.549 2253197.534 2057866.74 2202154.787 2093232.563 1907962.197 2181043.581 0.950035051 0.999264699 0.916592442 1.078353761 1.033082307 0.943523897 1.009679406 0.959738989 0.874793248 1 21.05658717 -0.260058042 6.578846902 0.999999998 0.977218753 0.016186652 0.055888386 0 0 0.052905462 0.012469937 0.549467434 0.260058042 -0.022781245 NECDPALALLSDYVLHNSNTMR ddPTM_BT-474_Pertuzumab_2h_R1 1 NECDPALALLSDYVLHNSNTMR 22 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 180.83 5.18E-17 25735000 22505 38676 31846 47097 29702 37851 34828 32577 32137 44749 FALSE TRUE 21625.47972 37572.99835 37601.28061 49527.68181 30657.3918 38616.37315 35254.23548 31904.27357 28488.94249 41718.11037 0.518371506 0.900639986 0.901317923 1.18719859 0.734870097 0.925650103 0.845058301 0.764758357 0.682891489 1 15.34838619 -0.259652501 7.840918254 1.000001058 0.839206364 0.083108169 0.167342523 0 0 0.158580569 0.037377799 0.549980763 0.259652501 -0.160794694 EGT(ph)PPPPPPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGTPPPPPPSR 11 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 EGT(1)PPPPPPSR 112.73 0.016624 214530000 432140 332660 284120 291530 302000 305640 324590 386670 418530 344490 TRUE FALSE 415251.491 323172.8625 335466.8042 306575.8982 311714.1043 311820.2502 328562.4295 378685.1294 371020.229 321157.3855 1.292984405 1.006275668 1.044555783 0.954597067 0.970596095 0.970926606 1.023057368 1.17912633 1.155259838 1 18.29292095 -0.259533034 7.542759726 1.000008012 1.061708072 0.033451395 0.104357073 0 0 0.104217461 0.024564291 0.550132074 0.259533034 0.06170006 ISS(ph)KS(ph)PGHMVILDQTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISSKSPGHMVILDQTK 16 1 Q9NWH9;Q9NWH9-3 Q9NWH9 SLTM SAFB-like transcription modulator 2 IS(0.025)S(0.976)KS(0.999)PGHMVILDQTK 203.64 1.55E-11 531490000 1351900 933910 887170 703630 929940 743100 886980 1301200 1175000 866930 TRUE FALSE 1299066.253 907275.8012 1047501.354 739944.4286 959852.3646 758125.9911 897835.1266 1274329.765 1041618.926 808212.0589 1.607333421 1.122571473 1.296072414 0.915532527 1.187624404 0.938028557 1.110890535 1.576726988 1.288794091 1 19.62437435 -0.259496727 10.59358957 0.999983853 1.22774183 0.08780727 0.2195472 0 0 0.219874485 0.051824913 0.550178067 0.259496727 0.227757977 DRT(ph)PPLLYR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRTPPLLYR 9 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 DRT(1)PPLLYR;DRT(1)PPLLYR;DRT(1)PPLLYR;DRT(1)PPLLYR 126.83 0.00074762 7883050000 1079370 1084090 906240 890390 997770 858610 1055860 1107940 1078500 1105820 TRUE FALSE 1037187.027 1053172.815 1070017.727 936343.1346 1029864.178 875971.6825 1068781.931 1085060.652 956073.2014 1030921.826 1.00607728 1.021583584 1.037923245 0.908258134 0.998974075 0.849697484 1.036724515 1.052514967 0.927396411 1 19.97550351 -0.259033643 6.884037438 0.999989888 0.986673883 0.002553331 0.062959088 0 0 0.061364195 0.01446368 0.550765029 0.259033643 -0.013316004 IANDNSLNHEYLPILGLAEFR ddPTM_BT-474_Pertuzumab_2h_R1 3 IANDNSLNHEYLPILGLAEFR 21 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;; 235.35 8.45E-30 1064695000 1015127 1122099 928163 1082641 864378 553494 1325764 994023 1185374 1307142 FALSE TRUE 975454.7146 1090097.835 1095902.701 1138516.232 892181.5034 564686.0279 1341989.096 973496.0777 1050815.313 1218608.108 0.800466293 0.894543396 0.899306917 0.934275937 0.7321316 0.463386075 1.10124747 0.798859019 0.86230783 1 20.21680281 -0.257321099 7.043867734 1.000002536 0.834228786 0.095592211 0.155019011 0 0 0.147171871 0.034688743 0.552941137 0.257321099 -0.16577375 YIQWEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YIQWEK 6 0 Q12996;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 0 104.11 0.079355 146120000 263900 291650 216840 202420 239800 249630 254280 264670 283440 303770 FALSE TRUE 253586.4962 283332.4276 256027.8116 212866.9205 247513.3848 254677.6896 257391.9547 259204.472 251265.0795 283195.3873 0.895447128 1.000483907 0.904067732 0.751660973 0.874002176 0.899300275 0.9088847 0.915284936 0.887249901 1 18.11143824 -0.256994537 0.634833166 1.008337091 0.890631977 0.238129873 0.05734171 11.81010899 4.38499716 0.305453915 0.023724171 0.55335707 0.256994537 -0.117705114 KREDCSPADKPYIDEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KREDCSPADKPYIDEAR 17 3 Q96DG6 Q96DG6 CMBL Carboxymethylenebutenolidase homolog 0 ; 262.25 1.08E-27 2376200000 2959100 2851200 2162600 2251900 2222500 1944170 2697700 2555200 3219500 2979800 FALSE TRUE 2843455.101 2769886.568 2553429.927 2368120.829 2293988.731 1983482.449 2730715.26 2502434.227 2854035.857 2777975.492 1.023570981 0.997088195 0.91916935 0.852462823 0.825777167 0.714002861 0.982987527 0.900812205 1.027379783 1 21.40560244 -0.25672749 7.019919559 1 0.910132357 0.064063104 0.094107045 0 0 0.094534936 0.022282098 0.553697433 0.25672749 -0.089867643 KDEEGQKEEDKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEEGQKEEDKPR 13 3 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 115.12 0.00030196 541270000 346597 250258 239964 176648 219161 210658 237863 309229 335039 261855 FALSE TRUE 333051.6061 243120.8869 283330.8328 185764.8244 226210.5126 214917.6491 240774.0385 302843.3131 297006.7773 244119.3276 1.364298392 0.99591003 1.160624337 0.760959103 0.926639094 0.88037949 0.986296501 1.240554429 1.216645893 1 17.897227 -0.256342428 7.871345085 0.99999906 1.052840686 0.008943819 0.175848118 0 0 0.176029395 0.041490526 0.55418858 0.256342428 0.052841626 DGWGGYGSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGWGGYGSDK 10 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ; 101.97 0.0069992 191042000 224234 226645 201580 186833 233800 188630 223901 271340 239730 322550 FALSE TRUE 215470.6874 220181.3065 238009.9901 196475.4735 241320.3893 192444.2278 226641.1674 265736.7342 212516.8554 300703.4012 0.716555538 0.732220872 0.791510802 0.653386269 0.802519653 0.639980217 0.753703372 0.883717088 0.706732463 1 18.19798166 -0.256290685 0.380967384 1.058590528 0.720628198 0.56311747 0.068169449 4.52430109 0.754623256 0.440435247 0.050081317 0.554254611 0.256290685 -0.337962331 SLFDYHDTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLFDYHDTR 9 0 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3;C9J4G8;C9JV02 A0A087X142 8-Sep Septin-8 0 ;; 114.5 0.0016287 1031310000 833700 998820 826090 1040260 967760 958940 1029710 928070 984140 1036590 FALSE TRUE 801118.0823 970334.6315 975382.8393 1093947.943 998888.8793 978330.4238 1042311.899 908905.0302 872424.5531 966380.836 0.828987965 1.004091343 1.009315172 1.132005005 1.033638957 1.012365299 1.078572608 0.940524684 0.902775097 1 19.88223232 -0.253874395 6.524023085 0.999999921 0.999650411 0 0.081965126 0 0 0.07980492 0.0188102 0.55734692 0.253874395 -0.000349511 FNDEHIPESPYLVPVIAPSDDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 FNDEHIPESPYLVPVIAPSDDAR 23 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;; 150.06 8.82E-08 3549610000 3523590 3563570 3190200 3646570 3396610 3856290 3558970 3364670 4028920 3931560 FALSE TRUE 3385884.207 3461940.473 3766740.106 3834769.915 3505865.045 3934266.826 3602525.739 3295188.389 3571573.892 3665271.939 0.923774351 0.944524862 1.027683667 1.046244311 0.956508849 1.073390158 0.982880888 0.899029715 0.974436263 1 21.80548881 -0.253519704 6.612916621 1.000000011 0.979324074 0.011124486 0.051929195 0 0 0.053740063 0.012666654 0.557802294 0.253519704 -0.020675937 ARTEKEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 ARTEKEEK 8 2 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 0 ;;; 137.95 0.00040837 467191000 533384 462362 314159 314584 374088 422266 403879 467531 444315 475014 FALSE TRUE 512538.7636 449175.8885 370934.5197 330819.7179 386120.8803 430804.5078 408821.792 457876.3215 393878.2239 442840.8787 1.157388101 1.014305386 0.837624839 0.747039702 0.87191788 0.9728201 0.923179886 1.033952247 0.889435106 1 18.75642888 -0.253136565 9.056094234 0.999999995 0.937676336 0.027890272 0.108564991 0 0 0.110997898 0.026162456 0.55829461 0.253136565 -0.062323659 TIQAPTQVPVVVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 TIQAPTQVPVVVSPR 15 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 TIQAPTQVPVVVS(1)PR;TIQAPTQVPVVVS(1)PR 247.74 2.79E-18 585820000 346100 343690 338670 372260 350080 372800 353620 369390 327900 440050 TRUE FALSE 332574.0294 333888.2977 399875.2027 391472.3832 361340.6411 380338.2714 357947.7073 361761.9674 290678.1667 410245.0215 0.810671701 0.813875319 0.974722865 0.954240424 0.880792264 0.927100273 0.872521758 0.881819275 0.708547701 1 18.6461263 -0.252724173 7.603206492 0.999999998 0.87602602 0.214695003 0.07397201 0 0 0.071440809 0.01683876 0.558825 0.252724173 -0.123973978 MEELHNQEMQKR ddPTM_BT-474_Pertuzumab_2h_R1 4 MEELHNQEMQKR 12 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 158.42 4.58E-05 1805330000 1718180 1740660 1365580 1372050 1485430 1417870 1606780 1636960 1826010 1756340 FALSE TRUE 1651031.626 1691018.081 1612370.683 1442861.665 1533210.205 1446540.303 1626444.254 1603156.204 1618729 1637381.527 1.008336541 1.032757517 0.984725097 0.881200649 0.936379322 0.883447308 0.993320266 0.979097527 0.988608319 1 20.64295909 -0.252314543 6.92868725 1 0.964440326 0.044832106 0.047869298 0 0 0.049630363 0.011697989 0.559352338 0.252314543 -0.035559674 GVQYLNEIKDSVVAGFQWATK ddPTM_BT-474_Pertuzumab_2h_R1 2 GVQYLNEIKDSVVAGFQWATK 21 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 256.53 1.72E-36 1470090000 972870 950970 679660 665490 868760 1033330 881440 838170 1015700 882660 FALSE TRUE 934849.1648 923849.2667 802489.681 699836.0187 896704.4544 1054224.641 892227.3264 820861.4966 900401.9942 822876.652 1.13607448 1.122706866 0.975224755 0.850474998 1.08971916 1.281145404 1.084278335 0.997551084 1.094212592 1 19.65031666 -0.251158262 0.976984201 0.99877116 1.065384255 0.034235757 0.107543891 76.75718955 52.8334927 0.504698569 0.035557707 0.560843561 0.251158262 0.066613096 SRS(ph)DIDVNAAASAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSDIDVNAAASAK 14 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.004)RS(0.996)DIDVNAAASAK;S(0.358)RS(0.642)DIDVNAAASAK 224.41 1.91E-12 2311050000 2890910 2510430 2021390 2067030 2248000 2108090 2106660 3101590 2737060 2258820 TRUE FALSE 2777930.041 2438834.994 2386700.139 2173709.666 2320308.962 2150717.024 2132441.935 3037541.083 2426360.423 2105828.109 1.31916277 1.158135834 1.133378421 1.032235089 1.101851073 1.021316514 1.012638176 1.442444931 1.152212003 1 21.00595625 -0.249813175 7.016627442 1.000000317 1.158114193 0.11060711 0.128963278 0 0 0.134571847 0.031718888 0.562583285 0.249813175 0.158113876 S(ph)LPSHMEEAPNVFQLYQRPTSASR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPSHMEEAPNVFQLYQRPTSASR 24 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(1)LPSHMEEAPNVFQLYQRPTSASR;S(1)LPSHMEEAPNVFQLYQRPTSASR 253.69 5.23E-44 483540000 53782 50751 29259 42327 43259 46462 44080 50330 47305 43744 TRUE FALSE 51680.13998 49303.63117 34546.75216 44511.50154 44650.46502 47401.49347 44619.46423 49290.66791 41935.13472 40781.17992 1.267254652 1.208980007 0.84712488 1.091471645 1.094879185 1.16233747 1.094119011 1.208662133 1.028296258 1 15.3156159 -0.249503188 0.008898901 2.56E-06 2.150643989 0.077295775 0.111511125 20655.39514 49.13125811 6156.834071 5717.579868 0.562984984 0.249503188 2.150641433 (ac)ADEAALALQPGGS(ph)PSAAGADR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADEAALALQPGGSPSAAGADR 21 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 ADEAALALQPGGS(0.934)PS(0.066)AAGADR;ADEAALALQPGGS(0.892)PS(0.108)AAGADR 105.68 4.56E-46 517950000 9884.5 12668.5 7291.1 6624.7 6407.5 7233.4 11719 9341.6 7344.3 13387.3 TRUE FALSE 9498.202812 12307.20678 8608.76396 6966.601561 6613.603057 7379.664304 11862.42063 9148.692696 6510.605854 12480.56625 0.761039413 0.986109648 0.689773508 0.558195952 0.529912099 0.591292427 0.950471348 0.733035065 0.521659492 1 13.60739577 -0.248255385 9.787889337 0.999999989 0.710501255 0.245845401 0.155794241 0 0 0.158516429 0.037362681 0.564604864 0.248255385 -0.289498734 FSFWDK ddPTM_BT-474_Pertuzumab_2h_R1 1 FSFWDK 6 0 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 100.67 0.087001 1092100000 982850 847110 1004300 828420 774260 505290 957700 985730 1066400 1054800 FALSE TRUE 944439.1354 822951.2522 1185799.351 871174.8555 799164.7761 515507.31 969420.6191 965374.331 945346.7427 983357.4565 0.960423017 0.836879048 1.205868062 0.885918798 0.812690005 0.524231862 0.985827293 0.981712524 0.961345985 1 19.90735641 -0.247528618 10.36131747 1 0.907313859 0.02874342 0.163614941 0 0 0.1631466 0.038454022 0.565550488 0.247528618 -0.092686141 LVELLMHNDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVELLMHNDYK 11 0 C9JYI4;P52294;Q5TFJ7;O60684;O15131 C9JYI4;O60684;O15131 KPNA1;KPNA6;KPNA5 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed;Importin subunit alpha-7;Importin subunit alpha-6" 0 ; 187.58 3.53E-06 971820000 1743800 1823020 1627700 1693760 1703620 1553110 1933400 1789170 2061160 2285500 FALSE TRUE 1675650.368 1771029.255 1921861.598 1781175.157 1758418.484 1584514.948 1957061.528 1752223.014 1827185.758 2130701.049 0.786431475 0.831195561 0.901985569 0.835957328 0.82527696 0.74365897 0.91850592 0.822369245 0.857551442 1 21.02289676 -0.247119434 0.648823123 1.012192984 0.832025241 0.526530259 0.047260838 5.803289764 2.243728671 0.222779838 0.017594199 0.566083591 0.247119434 -0.180167742 ELMETMHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELMETMHR 8 0 E9PM90;Q9UK41;Q9UK41-2 E9PM90 VPS28 Vacuolar protein sorting-associated protein 28 homolog 0 ; 190.52 0.00018602 586650000 503800 596620 482500 582770 563590 542320 601870 511500 581770 667500 FALSE TRUE 484110.939 579604.9818 569698.4832 612846.8295 581718.3842 553286.082 609235.8651 500937.3463 515729.9086 622289.6305 0.777951159 0.931407103 0.915487669 0.984825714 0.934803274 0.889113453 0.979023007 0.80499067 0.828761855 1 19.24722668 -0.246647024 7.622089887 0.999999999 0.896548337 0.183430428 0.066880954 0 0 0.065526539 0.015444753 0.566699691 0.246647024 -0.103451662 EFAPS(ph)DEELDSYR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFAPSDEELDSYR 13 0 I3L0X5;O75391;I3L4C3 I3L0X5 SPAG7 Sperm-associated antigen 7 1 EFAPS(1)DEELDSYR;EFAPS(1)DEELDSYR 170.74 2.76E-05 120149000 159549 173227 141308 169226 177152 166885 155758 165130 184162 182644 TRUE FALSE 153313.6487 168286.7356 166845.499 177959.7741 182850.255 170259.529 157664.213 161720.0078 163256.7018 170273.3592 0.900397158 0.98833274 0.979868488 1.045141618 1.073862969 0.999918777 0.925947628 0.949766943 0.958791807 1 17.3774932 -0.246301327 7.552299026 1 0.981015216 0.014139204 0.049139751 0 0 0.051679961 0.012181084 0.567150962 0.246301327 -0.018984784 VRS(ph)PDEALPGGLSGCSSGSGHSPYALER ddPTM_BT-474_Pertuzumab_2h_R1 1 VRSPDEALPGGLSGCSSGSGHSPYALER 28 1 Q5JSZ5-5 Q5JSZ5-5 PRRC2B Protein PRRC2B 1 VRS(0.998)PDEALPGGLS(0.002)GCSSGSGHSPYALER 98.377 0.0010432 237750000 34996 52208 38008 42164 45774 46043 48446 45487 44155 38439 TRUE FALSE 33628.31763 50719.07896 44876.89108 44340.08909 47246.36228 46974.02101 49038.89664 44547.67755 39142.70951 35835.49229 0.938408139 1.415330883 1.252302905 1.237323286 1.318423698 1.310823935 1.368444899 1.243116104 1.092288874 1 15.12910155 -0.246267501 8.12691417 0.99999998 1.256223625 0.22669243 0.131599569 0 0 0.117499824 0.027694974 0.567195138 0.246267501 0.256223644 TNSSS(ph)SSPVVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TNSSSSSPVVLK 12 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 TNS(0.183)S(0.066)S(0.748)S(0.002)SPVVLK 233.59 5.58E-16 587430000 681560 566620 463820 474870 523890 477170 511980 664620 664890 546480 TRUE FALSE 654923.8817 550460.5524 547642.5916 499378.0976 540741.3976 486818.7043 518245.7644 650895.3647 589414.4746 509466.4228 1.285509412 1.080464831 1.074933631 0.980198253 1.061387706 0.9555462 1.017232424 1.277602086 1.156925066 1 18.95862754 -0.245188942 7.063092085 0.999999959 1.098382869 0.071765225 0.106657366 0 0 0.110323224 0.026003433 0.568605502 0.245188942 0.09838291 DS(ph)REHEEPTTSEMAEETYSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSREHEEPTTSEMAEETYSPK 21 1 P24593;C9JXX4 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 DS(0.996)REHEEPT(0.002)T(0.002)SEMAEETYSPK;DS(0.987)REHEEPT(0.011)T(0.002)SEMAEETYSPK 208.58 1.85E-22 1374960000 297720 276090 269700 297540 264900 313820 277330 267040 347370 261000 TRUE FALSE 286084.7733 268216.1835 318440.7894 312896.0751 273420.7491 320165.6554 280724.0475 261525.5307 307938.0139 243322.2375 1.175744462 1.102308553 1.308720455 1.285932919 1.123698154 1.315809269 1.153713078 1.074811465 1.265556396 1 17.89250865 -0.243418387 0.407405381 0.961601325 1.213302368 0.317434618 0.085432435 7.374381092 1.378590904 0.529305775 0.057564248 0.570928356 0.243418387 0.251701042 LAEEEDLFDSAHPEEGDLDLASESTAHAQSSK ddPTM_BT-474_Pertuzumab_2h_R1 3 LAEEEDLFDSAHPEEGDLDLASESTAHAQSSK 32 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;; 396.82 7.09E-167 1779560000 765617 886798 758566 900470 834201 881706 888607 673705 1017177 1075460 FALSE TRUE 735695.8412 861507.3893 895655.7504 946943.3646 861033.8328 899534.6994 899482.0383 659792.7563 901711.3313 1002618.136 0.733774719 0.859257735 0.893316925 0.944470612 0.858785416 0.897185745 0.897133221 0.65806984 0.899356693 1 19.93534081 -0.242744369 7.926136926 1.000000123 0.843553988 0.228191108 0.082738152 0 0 0.085325626 0.020111443 0.571815115 0.242744369 -0.156446135 SLEDVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLEDVVR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 110.63 0.015726 85723000 181210 191120 170450 192160 181740 173070 208660 189370 186440 211430 FALSE TRUE 174128.1129 185669.4447 201254.1066 202077.4006 187585.8322 176569.594 211213.6435 185459.4433 165276.1128 197109.6578 0.883407312 0.94196016 1.021026108 1.02520294 0.951682603 0.895793722 1.071554006 0.940894756 0.838498299 1 17.58863894 -0.242565696 7.656867733 0.999999997 0.958480365 0.035876499 0.067630744 0 0 0.064560689 0.0152171 0.572050414 0.242565696 -0.041519632 NCLALADDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NCLALADDKK 10 1 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 ; 119.74 0.0010452 1153840000 1360510 1182150 1086860 1007180 816180 917080 966980 1317990 1473130 1365960 FALSE TRUE 1307339.765 1148436.239 1283279.779 1059160.681 842433.1709 935623.9859 978814.1905 1290773.046 1305906.458 1273442.313 1.026618758 0.901836093 1.007725098 0.831730397 0.661540113 0.734720353 0.76863646 1.013609359 1.025493221 1 20.28030218 -0.240954014 7.273119509 1 0.88167388 0.067279605 0.12677596 0 134077050.7 0.133478738 0.03237335 0.574177257 0.240954014 -0.11832612 DDNGKPYVLPSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDNGKPYVLPSVR 13 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 167.61 2.88E-05 890430000 999920 1005010 841830 952700 763490 433960 1326800 1173880 809720 913910 FALSE TRUE 960842.0209 976348.0988 993967.4074 1001868.961 788048.3492 442734.9685 1343037.775 1149638.968 717803.9802 852010.0617 1.127735533 1.14593494 1.166614635 1.17588865 0.924928454 0.519635845 1.576316802 1.349325577 0.842482985 1 19.70051094 -0.239346581 8.346913303 1.000000751 1.115482831 0.003648805 0.272078055 0 0 0.272563563 0.064243848 0.576306368 0.239346581 0.11548208 FSSETWQNLGTLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSSETWQNLGTLHR 14 0 F8W9U3;Q96IU4;B4DQI4 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 218.16 5.49E-12 1138250000 1031470 1133900 885340 1217550 1120460 1064100 1118730 1037550 1178030 1243060 FALSE TRUE 991159.012 1101562.282 1045340.632 1280387.901 1156500.613 1085616.831 1132421.352 1016124.23 1044304.973 1158866.439 0.855283214 0.950551543 0.902037195 1.104862354 0.9979585 0.936792019 0.977180212 0.876826005 0.901143512 1 20.14428287 -0.238633648 7.578772741 1 0.946053906 0.056109103 0.067805091 0 0 0.067706721 0.015958627 0.577253204 0.238633648 -0.053946094 EKTPSPKEEDEEPES(ph)PPEKK ddPTM_BT-474_Pertuzumab_2h_R1 8 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK 203.33 7.65E-22 77671400000 18484170 11943870 9232610 6265450 11339850 10339930 11203350 14243310 16665860 11535600 TRUE FALSE 17761788.2 11603242.52 10901148.01 6588810.625 11704606.57 10549010.47 11340459.95 13949180.67 14774021.44 10754283.54 1.651601256 1.078941473 1.013656369 0.612668487 1.088366932 0.980912437 1.054506319 1.297081356 1.373780168 1 23.35840808 -0.237841072 8.116558051 1.000020499 1.112598693 0.018345483 0.259793986 0 0 0.256330806 0.06041775 0.578307638 0.237841072 0.112578194 TLS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLSPGR 6 0 Q13523 Q13523;REV__F5H6U2 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.016)LS(0.984)PGR 78.728 0.072399 1308900000 1448500 1807500 1525900 1889500 1720700 1784700 1720500 1698100 1802400 1945500 TRUE FALSE 1391891.019 1755951.87 1801664.073 1987017.321 1776047.878 1820787.857 1741555.994 1663033.642 1597799.108 1813729.552 0.767419275 0.968144268 0.993347697 1.095542232 0.979224205 1.003891597 0.9602071 0.916913792 0.880946725 1 20.79052792 -0.237741495 7.234479461 1 0.957490439 0.026246945 0.081684026 0 0 0.079871498 0.018825893 0.57844025 0.237741495 -0.042509561 QMVEHGGFYR ddPTM_BT-474_Pertuzumab_2h_R1 3 QMVEHGGFYR 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 155 1.35E-05 1340010000 853810 1002130 838760 880040 949240 968180 931550 889290 1016730 1072520 FALSE TRUE 820442.1613 973550.2336 990342.5901 925458.9699 979773.1667 987757.263 942950.5876 870925.8507 901315.0729 999877.2651 0.820542871 0.973669737 0.990464155 0.92557257 0.979893434 0.98787851 0.943066335 0.871032757 0.901425709 1 19.93139149 -0.236125947 8.384180191 0.99999809 0.934174945 0.12745054 0.052751608 0 0 0.052236842 0.012312342 0.580596018 0.236125947 -0.065823144 DLLWLPIEQYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLLWLPIEQYR 11 0 H7C3T2;Q2TAZ0-3;Q2TAZ0-4;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 0 102.52 0.0051191 0 134450 168450 142780 161950 140710 159900 157300 170710 153060 162370 FALSE TRUE 129195.5454 163645.9709 168583.5221 170308.2589 145236.0649 163133.2876 159225.0845 167184.7788 135685.2705 151372.5353 0.853493965 1.081080994 1.113699535 1.125093522 0.959461138 1.077694096 1.051875653 1.104459132 0.896366506 1 17.20774394 -0.235229242 6.708306904 0.999999998 1.04126845 0 0.090685508 0 0 0.083094149 0.019585479 0.581796036 0.235229242 0.041268453 RAAEDDEDDDVDTK ddPTM_BT-474_Pertuzumab_2h_R1 7 RAAEDDEDDDVDTK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;; 284.68 2.33E-33 18244400000 20179440 18242637 14416888 13919852 15148458 16907950 16533173 18444630 20629737 18078769 FALSE TRUE 19390805.18 17722374.85 17022340.36 14638257.23 15635721.91 17249840.33 16735510.92 18063741.94 18287935.74 16854277.87 1.150497537 1.051506032 1.009971504 0.868518802 0.927700494 1.023469559 0.992953305 1.071760065 1.085061958 1 24.00661148 -0.233008888 7.898993283 1.000000001 1.01650873 0.004266624 0.075739048 0 0 0.078223624 0.018437485 0.584778117 0.233008888 0.016508729 GYGFVHFETQEAAER ddPTM_BT-474_Pertuzumab_2h_R1 6 GYGFVHFETQEAAER 15 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YBN4;E5RGH3 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ;;;;; 265.03 3.57E-25 12986560000 5475460 5985760 5292320 6068270 5977460 5990220 6172180 5535290 6175890 6551220 FALSE TRUE 5261472.97 5815051.985 6248759.951 6381454.142 6169730.429 6111346.353 6247716.985 5420984.327 5474828.859 6107500.034 0.861477354 0.95211657 1.023128926 1.044855359 1.010189176 1.00062977 1.022958158 0.887594645 0.896410778 1 22.54215054 -0.232964295 6.786237585 1.000000008 0.968956274 0.024472662 0.061670715 8650818.872 1274758.852 0.063997783 0.015521742 0.584838164 0.232964295 -0.031043734 LHDINAQMVEDQGFLDSLR ddPTM_BT-474_Pertuzumab_2h_R1 6 LHDINAQMVEDQGFLDSLR 19 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 ;;;;; 263.92 2.68E-31 2567330000 1221639 1332092 1285554 1610730 1453223 1530935 1513046 900238 1585090 1537721 FALSE TRUE 1173895.997 1294102.04 1517882.205 1693859.968 1499967.238 1561891.555 1531563.11 881647.7707 1405157.228 1433569.787 0.818862122 0.90271297 1.058812915 1.181567848 1.046316162 1.089512048 1.068356158 0.61500164 0.980180554 1 20.45118071 -0.232599978 5.101503636 0.999999992 0.963970209 0 0.153828655 55258250.87 227029547.2 0.166660764 0.041665188 0.585328974 0.232599978 -0.036029783 SNSFFEGVDWEHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSFFEGVDWEHIR 14 0 Q15208 Q15208 STK38 Serine/threonine-protein kinase 38 0 ; 178.03 2.03E-06 211853000 222780 237310 207160 242010 240690 221670 247890 225340 253860 259310 FALSE TRUE 214073.5113 230542.1512 244598.4202 254500.1651 248432.0124 226152.3193 250923.752 220686.6503 225042.8771 241746.7027 0.885528154 0.953651688 1.011796304 1.052755476 1.027654192 0.93549288 1.037961425 0.912883807 0.930903605 1 17.88313669 -0.232334183 7.59961831 0.999999999 0.974066244 0.021781721 0.054698968 0 0 0.054504027 0.012846722 0.585687313 0.232334183 -0.025933755 RRS(ph)PS(ph)LSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(1)PS(0.98)LS(0.019)S(0.001)K;RRS(1)PS(0.922)LS(0.077)S(0.001)K 86.699 0.068672 2984400000 3922100 3436310 2502930 2752870 3059490 2903230 2742150 4066400 3498000 3159770 TRUE FALSE 3768819.996 3338309.803 2955265.128 2894945.951 3157901.274 2961935.3 2775709.252 3982427.419 3100921.705 2945755.963 1.279406727 1.133260815 1.00322809 0.982751452 1.072017273 1.005492422 0.942273999 1.351920345 1.052674337 1 21.49020649 -0.232161786 7.033525219 1.000000028 1.096084397 0.044830152 0.12499442 0 6.62E-18 0.126532359 0.029823963 0.585919853 0.232161786 0.096084369 TIELSDDDFLGECECTLGQIVSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TIELSDDDFLGECECTLGQIVSSK 24 0 O75131;A0A087WYQ3;H0YB26;E5RHZ0;A0A087WXR6;A0A087WUS8 O75131 CPNE3 Copine-3 0 154.79 5.45E-08 23930000 31984 40734 22413 39505 24823 19310 27349 41279 37983 33862 FALSE TRUE 30734.02992 39572.3062 26463.52767 41543.85778 25621.45434 19700.46143 27683.70524 40426.57422 33671.32908 31568.49658 0.973566475 1.253537878 0.838289134 1.315991013 0.811614651 0.624054471 0.876940882 1.280598654 1.06661174 1 14.94619793 -0.231444377 7.200688057 0.99999563 1.013444717 0 0.216018549 0 0 0.215776075 0.050858909 0.586888531 0.231444377 0.013449087 KS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_BT-474_Pertuzumab_2h_R1 6 KSPTMEQAVQTASAHLPAPAAVGR 24 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 KS(0.98)PT(0.02)MEQAVQTASAHLPAPAAVGR;KS(0.943)PT(0.056)MEQAVQTASAHLPAPAAVGR;KS(0.963)PT(0.037)MEQAVQTASAHLPAPAAVGR;KS(0.712)PT(0.288)MEQAVQTASAHLPAPAAVGR;KS(0.848)PT(0.149)MEQAVQT(0.002)ASAHLPAPAAVGR;KS(0.973)PT(0.026)MEQAVQT(0.001)ASAHLPAPAAVGR 208.82 3.65E-25 4394430000 836076 764741 788007 824111 802895 813413 899441 964904 1019346 1110356 TRUE FALSE 803401.2256 742931.3354 930417.394 866643.4675 828720.8468 829860.7682 910448.628 944978.3952 903634.1155 1035150.599 0.776120138 0.717703623 0.898823219 0.837214863 0.800579981 0.801681194 0.879532533 0.912889773 0.87294942 1 19.98140924 -0.230823788 0.030416231 1.880976741 1.02E-10 0.658886702 0.044532781 231.259482 1.908716475 66.36485006 51.71795383 0.58772777 0.230823788 -1.880976741 KS(ph)PPKADEKER ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPPKADEKER 11 3 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KS(1)PPKADEKER 96.993 0.0047089 452480000 399470 323410 246160 160550 270720 273980 265800 349810 408940 290230 TRUE FALSE 383858.2708 314186.6635 290646.5878 168836.0047 279427.9547 279520.0633 269052.9399 342586.3013 362518.8456 270572.4636 1.418689344 1.161192308 1.074191305 0.623995519 1.032728722 1.033069144 0.994384042 1.266153609 1.339821654 1 18.0456555 -0.229263 8.037364315 1.000009536 1.094855945 0.020101205 0.20941066 0 0 0.212006578 0.04997043 0.589843775 0.229263 0.094846409 KVCGDSDK ddPTM_BT-474_Pertuzumab_2h_R1 4 KVCGDSDK 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;; 116.52 0.0036174 1155530000 1258780 1049050 962030 993870 995590 984740 1148590 1123780 1112970 1332870 FALSE TRUE 1209585.486 1019132.121 1135890.221 1045163.75 1027614.057 1004652.117 1162646.788 1100573.55 986630.3116 1242593.528 0.973436171 0.820165322 0.914128551 0.841114754 0.826991316 0.808512273 0.935661391 0.885706811 0.794008893 1 20.24492301 -0.227837966 7.348732624 0.99999995 0.867440238 0.334528768 0.056419377 0 52396888.28 0.051626343 0.012521227 0.591782386 0.227837966 -0.132559712 NLFEEYR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLFEEYR 7 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ; 120.92 0.010442 328830000 523350 614240 476210 659770 496680 497820 598930 605870 651070 741800 FALSE TRUE 502896.9034 596722.4766 562271.7402 693820.8088 512656.1633 507886.2615 606259.8845 593358.5728 577163.2631 691557.2253 0.727194923 0.862867822 0.813051646 1.003273169 0.74130693 0.734409595 0.876659027 0.858003577 0.834584966 1 19.39948911 -0.226977262 0.610107391 1.014229057 0.825968099 0.305137258 0.078443583 8.599874794 3.072269195 0.365511431 0.031191566 0.592956369 0.226977262 -0.188260958 FPDEDEILEKDEALEDEDNKKDDGISFSNQTGPAWAGSER ddPTM_BT-474_Pertuzumab_2h_R1 1 FPDEDEILEKDEALEDEDNKKDDGISFSNQTGPAWAGSER 40 3 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 97.248 5.77E-05 405950000 149370 84446 82436 61277 85388 66314 96967 110980 136000 94582 FALSE TRUE 143532.4553 82037.68276 97334.01898 64439.51331 88134.58257 67654.91452 98153.71115 108688.2242 120561.8502 88175.8769 1.627797311 0.930386923 1.103862217 0.730806606 0.999531682 0.767272375 1.113158322 1.232629922 1.367288361 1 16.4280964 -0.225831933 8.109157334 1.00000761 1.080593701 0.009137075 0.256124365 0 0 0.24530858 0.057819787 0.594522188 0.225831933 0.080586091 EKELTELR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKELTELR 8 1 A6NHC7;A0A3B3ITB1;V9GXZ4;Q59H18-3;Q59H18;Q59H18-4;Q59H18-1 A6NHC7 FPGT-TNNI3K;TNNI3K Serine/threonine-protein kinase TNNI3K 0 60.436 0.084181 3791100 18542 18461 15731 16205 16332 16490 18297 18093 18280 21031 FALSE TRUE 17817.35814 17934.51036 18573.94163 17041.34199 16857.33361 16823.4391 18520.92416 17719.37323 16204.93104 19606.55164 0.908745121 0.914720278 0.947333421 0.86916569 0.859780645 0.858051911 0.944629352 0.903747561 0.826505922 1 14.2590482 -0.225142104 8.078949352 0.999999995 0.895094572 0.427824466 0.037181869 0 0 0.036471183 0.00859634 0.595467271 0.225142104 -0.104905422 KPSPSES(ph)PEPWKPFPAVSPEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPSPSES(1)PEPWKPFPAVSPEPR 189.12 1.17E-17 1542400000 881940 693630 510230 532480 590440 608540 556710 777800 857450 684880 TRUE FALSE 847472.8098 673848.3515 602439.911 559961.3566 609432.0388 620845.0957 563523.1835 761738.1582 760115.8707 638492.4676 1.327302753 1.055374003 0.943534876 0.877005423 0.954485871 0.972360877 0.882583918 1.193026068 1.190485259 1 19.28431007 -0.224305934 8.4077696 0.999999998 1.036046646 0.005773769 0.142059451 0 0 0.142633741 0.033619095 0.596614859 0.224305934 0.036046648 TVAS(ph)DLQK ddPTM_BT-474_Pertuzumab_2h_R1 6 TVASDLQK 8 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK 187.33 0.00021273 5830170000 7754690 6126450 5018580 4892730 5377980 5303930 5267780 7276000 7030870 5972080 TRUE FALSE 7451628.142 5951729.644 5925549.044 5145244.382 5550967.611 5411179.099 5332248.667 7125748.057 6232755.113 5567585.702 1.33839487 1.068996503 1.064294177 0.924142825 0.997015207 0.971907643 0.957730864 1.279863201 1.119471787 1 22.40862043 -0.224294868 7.1520528 1.000000019 1.078557275 0.03346951 0.129025032 0 64516747.88 0.130632148 0.031682949 0.596630062 0.224294868 0.078557256 CLSSLKDER ddPTM_BT-474_Pertuzumab_2h_R1 2 CLSSLKDER 9 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 95.642 0.007211 908060000 4472300 4532500 3722200 3608400 3673300 2578300 4520600 4400500 4760600 5090300 FALSE TRUE 4297517.572 4403237.538 4394884.34 3794629.956 3791455.031 2630434.993 4575924.455 4309628.137 4220196.646 4745529.447 0.905592857 0.92787066 0.926110435 0.799622044 0.798953009 0.554297476 0.964260049 0.908144852 0.889299433 1 22.17813762 -0.222688627 8.782793349 0.999999967 0.854077746 0.134602251 0.11201082 0 0 0.113029827 0.026641386 0.598840787 0.222688627 -0.145922221 RMS(ph)DEFVDSFKK ddPTM_BT-474_Pertuzumab_2h_R1 6 RMSDEFVDSFKK 12 2 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(0.518)DEFVDS(0.482)FKK;RMS(0.678)DEFVDS(0.322)FKK;RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK;RMS(0.999)DEFVDS(0.001)FKK;RMS(1)DEFVDSFKK 158.45 5.78E-05 4791000000 5560900 5120130 3521920 3517440 4313260 4637290 4096400 5122940 5428010 4788910 TRUE FALSE 5343573.88 4974108.906 4158409.289 3698975.5 4451999.925 4731059.181 4146532.969 5017149.499 4811845.061 4464552.86 1.196888926 1.114133724 0.931427943 0.828520933 0.997188311 1.059693844 0.928767807 1.12377424 1.077788798 1 22.09008426 -0.221526753 7.835577674 1.000000001 1.025225157 0.005792142 0.104219329 0 0 0.105981977 0.024980192 0.600445019 0.221526753 0.025225156 IETIEVMEDR ddPTM_BT-474_Pertuzumab_2h_R1 8 IETIEVMEDR 10 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;; 292.81 8.51E-32 11851930000 5173082 5256470 4407210 5283570 5454941 5260120 5005823 5297536 5472642 5488386 FALSE TRUE 4970912.236 5106560.622 5203690.885 5556255.681 5630404.131 5366483.23 5067085.759 5188140.03 4851410.623 5116652.728 0.971516439 0.998027596 1.017010761 1.085916121 1.100407714 1.048826941 0.990312618 1.013971498 0.948161011 1 22.28676889 -0.218146453 6.67672031 1.000000039 1.022028858 0.013036364 0.045412565 0 0 0.047037682 0.011086888 0.605136776 0.218146453 0.022028819 LVTDQNISENWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVTDQNISENWR 12 0 P24666;F2Z2Q9;G5E9R5;P24666-4 P24666 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ; 211.64 6.87E-08 351090000 202087 210226 189903 209996 214701 216012 203081 206782 223951 239851 FALSE TRUE 194189.2166 204230.5603 224222.6965 220833.9187 221607.0527 220379.9106 205566.366 202511.8794 198529.0214 223605.6781 0.868444926 0.913351405 1.002759404 0.987604253 0.99106183 0.985573857 0.91932534 0.905665192 0.88785322 1 17.7705973 -0.21799641 7.439696761 1 0.941900556 0.131620143 0.045903546 0 0 0.048488999 0.011428967 0.605345879 0.21799641 -0.058099443 VNEEKDGPIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNEEKDGPISPK 12 1 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 VNEEKDGPIS(1)PK 61.692 0.050299 367770000 590210 482890 398820 373120 359980 366540 389990 519530 597760 522960 TRUE FALSE 567143.9407 469118.45 470895.6457 392376.7679 371559.0836 373951.6899 394762.8143 508801.5239 529904.7908 487539.4534 1.163278042 0.962216384 0.965861619 0.804810288 0.762110802 0.767018315 0.809704346 1.043610974 1.086896224 1 18.89515945 -0.217619188 7.274811363 1.000016587 0.921725621 0.021396472 0.134052837 18813036.8 2586050.548 0.138792767 0.033662191 0.605871901 0.217619188 -0.078290967 VEGIVHPTTAEIDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEGIVHPTTAEIDLK 15 0 Q9P0M6;Q5SQT3 Q9P0M6 H2AFY2 Core histone macro-H2A.2;Histone H2A 0 ; 126.16 8.60E-05 424930000 342010 444950 449390 542520 391640 499690 425550 420180 457750 555720 FALSE TRUE 328643.8711 432260.4617 530604.7696 570519.5222 404237.4563 509794.0742 430758.0082 411503.1362 405788.139 518080.5894 0.634348937 0.834349849 1.024174193 1.101217714 0.780259798 0.984005355 0.831449811 0.794284026 0.783252929 1 18.98281701 -0.216245391 7.898167345 0.999999961 0.86830332 0.089293937 0.130246522 0 0 0.12901441 0.030408988 0.607791481 0.216245391 -0.131696641 PVLISTPTPTIVRPGSLPLHLGYDPLHPTLPS(ph)PTSVITQAPPSNR ddPTM_BT-474_Pertuzumab_2h_R1 1 PVLISTPTPTIVRPGSLPLHLGYDPLHPTLPSPTSVITQAPPSNR 45 1 P17544;K7ELQ4;P17544-2;P17544-1;P17544-3 P17544 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 PVLISTPTPTIVRPGSLPLHLGYDPLHPT(0.02)LPS(0.914)PT(0.025)S(0.041)VITQAPPSNR 201.7 1.59E-36 331300000 75629 53989 68037 78122 60834 73402 88860 42941 82695 92864 TRUE FALSE 72673.33507 52449.28658 80332.79937 82153.88578 62790.78086 74886.23873 89947.49526 42054.25334 73307.81029 86574.23857 0.839433719 0.605830181 0.927906508 0.948941477 0.725282508 0.864994483 1.038963747 0.485759437 0.846762403 1 16.40165017 -0.215084335 8.275436223 0.999996201 0.797150632 0.113083552 0.156906385 0 0 0.151986787 0.035823629 0.609418544 0.215084335 -0.202845569 LHPVILASIVDSYER ddPTM_BT-474_Pertuzumab_2h_R1 2 LHPVILASIVDSYER 15 0 O00303;E9PQV8;A0A1W2PP79 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 270.79 2.22E-33 1159640000 708600 784110 689340 777720 762690 767250 780380 704250 834380 885140 FALSE TRUE 680907.1286 761747.9505 813919.0723 817858.2224 787222.6165 782764.3207 789930.5239 689706.9914 739664.6804 825188.6794 0.82515326 0.92311973 0.986342994 0.991116629 0.953991052 0.948588293 0.957272614 0.835817321 0.89635825 1 19.6543645 -0.214178487 7.713303503 1 0.924496982 0.149943334 0.054142943 0 0 0.056756905 0.013377731 0.610690991 0.214178487 -0.075503018 KT(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK 31 2 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KT(0.611)PES(0.389)FLGPNAALVDLDSLVSRPGPTPPGAK 219.35 3.28E-33 792640000 222650 193470 140440 133030 149920 159390 187090 212940 194000 186340 TRUE FALSE 213948.5918 187952.425 165820.6321 139895.6942 154742.313 162612.975 189379.6634 208542.7146 171977.9333 173719.0258 1.231578354 1.08193345 0.954533513 0.805298634 0.890762035 0.936068886 1.090149237 1.200459844 0.989977537 1 17.40639624 -0.211641536 8.375742663 1.000030898 1.023534846 0.001584789 0.126974669 0 0 0.137824972 0.032485657 0.61426881 0.211641536 0.023503948 LIGDAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LIGDAAK 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65;P11021;P54652 A0A0G2JIW1;Q53FA3;P11142;P11021;P54652 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA5;HSPA2 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;78 kDa glucose-regulated protein;Heat shock-related 70 kDa protein 2 0 124.37 0.009661 300880000 686760 727990 633060 534440 503870 263780 705060 688540 779520 856750 FALSE TRUE 659920.6599 707228.438 747468.0243 562022.5124 520077.4362 269113.8123 713688.7352 674321.4084 691032.1576 798721.5594 0.826221168 0.885450542 0.935830535 0.703652613 0.651137346 0.336930698 0.893538839 0.844250916 0.865172787 1 19.60733313 -0.20550358 8.944000418 0.999981512 0.771958156 0.143905215 0.167298664 0 0 0.171773252 0.040487344 0.623012012 0.20550358 -0.228023356 TSS(ph)DSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.122)S(0.122)S(0.751)DS(0.004)ALHTSVMNPSPQDTYPGPTPPSILPSR 271.84 1.52E-73 116800000 20903 31191 30597 34959 29722 32981 29748 30433 27685 36973 TRUE FALSE 20086.08765 30301.46322 36126.55853 36763.23818 30678.03512 33647.89842 30112.06492 29804.54792 24542.31486 34468.78578 0.582732672 0.879098655 1.048094898 1.066566093 0.890023667 0.976184616 0.873603878 0.86468227 0.712015649 1 15.07300286 -0.204114313 7.524726644 0.999999992 0.889196852 0.0605348 0.138034613 0 0 0.134561608 0.031716475 0.62500816 0.204114313 -0.11080314 DWEQFHQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 DWEQFHQPR 9 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ;;; 186.78 4.13E-05 4578000000 2634410 2654610 2374820 2992300 2805330 2796020 2752890 2502000 2932340 3235470 FALSE TRUE 2531454.345 2578903.122 2804002.802 3146732.962 2895565.987 2852557.44 2786580.691 2450332.826 2599473.057 3016328.735 0.83925015 0.854980789 0.929607827 1.043232763 0.959963665 0.945705091 0.923831895 0.812356026 0.861800316 1 21.52436224 -0.203162397 7.408028605 1 0.907286489 0.15403073 0.064768719 0 0 0.070590096 0.016638245 0.626379597 0.203162397 -0.09271351 GESFYQDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GESFYQDR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 195.06 0.00037708 2573310000 1706660 1864710 1696890 2004620 1855400 1810140 1985030 1797480 1979480 2097910 FALSE TRUE 1639961.84 1811530.297 2003555.77 2108078.678 1915080.626 1846742.271 2009323.391 1760361.41 1754777.729 1955816.687 0.838504882 0.926227038 1.024408772 1.07785085 0.979171841 0.944230757 1.027357729 0.900064623 0.897209713 1 20.89933973 -0.199324544 7.647759334 0.999999998 0.96078239 0.031798511 0.068316717 0 0 0.068854416 0.016229142 0.631939433 0.199324544 -0.039217608 EAENQGLDISS(ph)PGMSGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAENQGLDISSPGMSGHR 18 0 Q15545 Q15545 TAF7 Transcription initiation factor TFIID subunit 7 1 EAENQGLDIS(0.007)S(0.993)PGMSGHR;EAENQGLDIS(0.009)S(0.991)PGMSGHR 161.2 2.49E-11 1087450000 309920 375490 346510 389780 403690 379780 371840 356580 371870 457210 TRUE FALSE 297807.9838 364781.3928 409132.0651 409896.5925 416675.0555 387459.4118 376390.6891 349216.4984 329656.8766 426242.7595 0.698681625 0.855806661 0.959856927 0.96165057 0.977553392 0.909011129 0.88304301 0.81929016 0.773401704 1 18.7013158 -0.197989439 7.271203305 0.999999988 0.876432131 0.170835325 0.084530237 0 0 0.086283007 0.0203371 0.633885126 0.197989439 -0.123567857 LTNEDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTNEDFR 7 0 Q13123;E7EQZ7;D6REL4;D6RAY9;D6RCQ4 Q13123 IK Protein Red 0 86.794 0.075003 0 442260 494670 388000 488440 468670 479790 444370 481830 477080 526750 FALSE TRUE 424975.9903 480562.4959 458120.231 513648.4469 483745.1962 489491.6825 449808.333 471880.0421 422923.8785 491072.7533 0.865403318 0.978597352 0.932896863 1.045972198 0.985078469 0.996780374 0.915970862 0.960916766 0.861224484 1 18.90557725 -0.19626006 7.291422665 0.999999999 0.954002653 0.065334725 0.055005676 0 0 0.051508595 0.012140692 0.636414315 0.19626006 -0.045997345 IHPMAYQLQLQAASNFKS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 IHPMAYQLQLQAASNFKSPVK 21 1 P67870;Q5SRQ6 P67870 CSNK2B Casein kinase II subunit beta 1 IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAAS(0.113)NFKS(0.887)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK 347.76 1.71E-95 16639870000 10369670 8414430 5541850 6589300 7185210 6301650 7788290 8148140 9839600 9084460 TRUE FALSE 9964411.832 8174458.695 6543385.573 6929374.563 7416328.805 6429073.681 7883605.423 7979878.062 8722649.859 8469161.433 1.176552355 0.965202843 0.77261316 0.818188981 0.87568632 0.759115732 0.930860214 0.942227649 1.029930759 1 23.0137877 -0.196027431 8.779202395 0.999999997 0.909826492 0.035307243 0.118840536 0 0 0.117200468 0.027624415 0.636755301 0.196027431 -0.090173505 GNAGQSNYGFANSAMER ddPTM_BT-474_Pertuzumab_2h_R1 4 GNAGQSNYGFANSAMER 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 423.72 3.98E-160 1356100000 378792 507300 435549 581392 482202 459724 543956 458528 463967 582529 FALSE TRUE 363988.3899 492832.3007 514262.393 611397.7108 497712.4653 469019.9343 550613.0962 449059.2366 411299.4113 543073.792 0.670237443 0.907486806 0.946947543 1.125809641 0.916472996 0.863639419 1.013882652 0.826884381 0.757354557 1 19.05078872 -0.195514493 7.646805893 1 0.900959379 0.062557963 0.121013362 0 0 0.117472724 0.027688587 0.637507806 0.195514493 -0.099040621 DVSEELSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVSEELSR 8 0 P40222 P40222 TXLNA Alpha-taxilin 0 102 0.017535 0 330280 377440 332100 370410 389070 383240 341680 370320 383960 411820 FALSE TRUE 317372.2925 366675.7808 392117.8575 389526.9045 401584.7899 390989.3754 345861.582 362672.7626 340374.4705 383927.0646 0.826647355 0.955066247 1.021334242 1.014585687 1.045992395 1.018394928 0.900852308 0.94463974 0.88656024 1 18.55047274 -0.195259923 7.263720722 0.999999999 0.961401965 0.032343961 0.066761956 9098029.763 1252530.18 0.067124321 0.016280039 0.637881604 0.195259923 -0.038598034 DRLEFWCTDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRLEFWCTDVK 11 1 Q9UNM6;J3KNQ3;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 92.295 0.0092129 198758000 315820 333120 293980 309840 320020 335690 349440 349810 384140 409060 FALSE TRUE 303477.4052 323619.7438 347108.7255 325830.8795 330313.7339 342477.8818 353716.5512 342586.3013 340534.0376 381354.0018 0.795789224 0.848607179 0.910200821 0.854405298 0.866160398 0.898057658 0.927528096 0.898341959 0.892960441 1 18.54077131 -0.193345943 0.020114657 1.898019163 8.26E-07 0.745577561 0.025954827 446.6297367 2.478444513 126.3778706 107.4982739 0.640699016 0.193345943 -1.898018336 KRET(ph)DDEGEDD ddPTM_BT-474_Pertuzumab_2h_R1 10 KRETDDEGEDD 11 2 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD 247.64 6.29E-16 76862620000 12899680 11567910 9824780 9745880 10366540 10202670 11262810 12574100 13247410 11386520 TRUE FALSE 12395546.24 11238004.53 11600336.3 10248866.03 10699989.17 10408974.98 11400647.64 12314440.44 11743619.55 10615300.86 1.167705599 1.058660954 1.092793926 0.965480505 1.007977948 0.980563351 1.073982527 1.160065137 1.10629173 1 23.33964192 -0.190274685 7.538212031 1.000000684 1.068254954 0.089822491 0.065099209 0 0 0.068952828 0.016252337 0.645245992 0.190274685 0.06825427 LS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSYSDKNLIDSMDQSAFAGFSFVNPK 26 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 LS(1)YSDKNLIDSMDQSAFAGFSFVNPK;LS(1)YSDKNLIDSMDQSAFAGFSFVNPK 399.85 4.49E-146 639170000 656100 586550 446090 392320 457620 480440 467100 635160 663880 557720 TRUE FALSE 630458.8866 569822.1683 526708.3862 412567.6822 472339.7629 490154.826 472816.5095 622043.724 588519.1256 519945.1276 1.212548889 1.095927509 1.013007639 0.79348312 0.90844156 0.942704912 0.909358477 1.196364176 1.13188699 1 18.98799985 -0.188103716 7.690832053 1.000003642 1.019991186 0.002357831 0.129801253 0 0 0.136733036 0.032228286 0.648479549 0.188103716 0.019987545 ELSNSVSTYRPFGLGSES(ph)PYKQPSDGMERPSSLMDSSQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSNSVSTYRPFGLGSESPYKQPSDGMERPSSLMDSSQEK 40 3 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ELSNSVSTYRPFGLGS(0.002)ES(0.787)PY(0.001)KQPS(0.174)DGMERPS(0.015)S(0.02)LMDS(0.001)S(0.001)QEK 119.94 2.87E-06 290880000 356590 280380 226080 211060 257260 252130 250270 306920 333330 278210 TRUE FALSE 342654.0686 272383.8369 266937.6851 221952.8319 265535.0015 257228.2413 253332.8791 300581.9947 295491.7758 259366.5889 1.321118769 1.050188608 1.029190715 0.855749512 1.023782603 0.991755501 0.97673675 1.158907923 1.139282346 1 17.98463312 -0.186801905 13.87771818 1.000005056 1.054255249 0.020539264 0.118444562 0 0 0.116363634 0.027427172 0.650426303 0.186801905 0.054250193 SFGTRPLS(ph)SGFSPEEAQQQDEEFEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SFGTRPLSSGFSPEEAQQQDEEFEKK 26 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(0.103)FGT(0.092)RPLS(0.717)S(0.073)GFS(0.015)PEEAQQQDEEFEKK 87.357 0.0064182 163920000 160270 128110 107700 93367 114170 124630 107370 149930 157480 127140 TRUE FALSE 154006.4712 124456.4282 127163.7858 98185.68206 117842.3817 127150.104 108684.0262 146833.8931 139603.5306 118528.6946 1.299318041 1.050010959 1.072852327 0.828370568 0.994209733 1.072736897 0.916942742 1.238804609 1.177803663 1 16.85487684 -0.186408627 7.700863652 0.999957674 1.067882076 0.024446889 0.134463223 0 0 0.132926273 0.031331023 0.651015566 0.186408627 0.067924402 S(ph)RSDIDVNAAAGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SRSDIDVNAAAGAK 14 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 S(0.5)RS(0.5)DIDVNAAAGAK;S(0.5)RS(0.5)DIDVNAAAGAK;S(0.5)RS(0.5)DIDVNAAAGAK;S(0.5)RS(0.5)DIDVNAAAGAK 194.19 1.05E-07 2671090000 7705950 6350330 4967850 4967650 5603560 5156470 4986340 8073050 6583280 6025510 TRUE FALSE 7404792.955 6169224.806 5865651.004 5224031.012 5783803.596 5260737.356 5047364.321 7906338.696 5835973.654 5617396.841 1.318189397 1.098235532 1.044193809 0.929973644 1.029623464 0.936508049 0.898523723 1.407473768 1.038910695 1 22.42147029 -0.186337468 7.215754751 1.000012476 1.083608354 0.020625125 0.156874226 0 0 0.159692461 0.037639874 0.651122244 0.186337468 0.083595878 TSQVGAASAPAKES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 TSQVGAASAPAKESPR 16 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR 237.18 5.71E-20 73772700000 13971480 11747540 10302020 10134520 9798070 10404060 11337860 12393030 13308960 13007550 TRUE FALSE 13425459.12 11412511.66 12163824.18 10657563.79 10113233.82 10614437.22 11476616.12 12137109.6 11798182.66 12126537.05 1.107114014 0.941118772 1.003074837 0.878862922 0.833975419 0.875306543 0.946405068 1.000871852 0.972922658 1 23.53166429 -0.185080887 10.31907051 0.999999985 0.948141166 0.036472246 0.074077814 0 0 0.074610202 0.017585793 0.653008918 0.185080887 -0.051858818 IEEVPELPLVVEDKVEGYKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEEVPELPLVVEDKVEGYKK 20 2 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 72.644 0.0089494 547470000 695540 719260 478300 387860 538950 578110 550250 675590 738390 593020 FALSE TRUE 668357.5278 698747.409 564739.4497 407877.5011 556285.8162 589799.7803 556984.1241 661638.8304 654571.0628 552854.2272 1.208921801 1.263890868 1.021497932 0.737766813 1.006207041 1.066826934 1.007470137 1.196769054 1.183984911 1 19.07653961 -0.182782288 7.845354816 0.999999385 1.074425664 0.024955446 0.143628862 0 0 0.150284805 0.035422468 0.656474275 0.182782288 0.074426278 GSLLTILGSPS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 GSLLTILGSPSPER 14 0 Q96A19 Q96A19 CCDC102A Coiled-coil domain-containing protein 102A 1 GSLLTILGSPS(1)PER;GSLLTILGSPS(1)PER 157.23 5.62E-06 36256000 70537 80388 70814 85490 81115 81821 77042 80492 75537 92099 TRUE FALSE 67780.33606 78095.41295 83611.66505 89902.14915 83724.13764 83475.47668 77984.86304 78829.81207 66962.35644 85861.0527 0.78941888 0.909555736 0.973802002 1.047065536 0.97511194 0.972215854 0.908268191 0.91810908 0.779892097 1 16.38971624 -0.181761582 7.246626091 0.999999997 0.926548445 0.079719863 0.078872009 10572200.12 1458913 0.078007449 0.018919585 0.658018976 0.181761582 -0.073451552 TPLYLQPDAYGS(ph)LDR ddPTM_BT-474_Pertuzumab_2h_R1 4 TPLYLQPDAYGSLDR 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR 184.01 5.06E-07 3102180000 2046180 1935890 1158500 1563770 1576040 1119390 1594110 2094280 1840110 1683620 TRUE FALSE 1966213.023 1880680.313 1367866.721 1644476.357 1626734.758 1142024.833 1613619.195 2051032.386 1631228.427 1569586.918 1.252694579 1.198200808 0.871481984 1.047712834 1.036409478 0.72759579 1.028053418 1.306733869 1.039272441 1 20.58195349 -0.180899719 7.23883731 0.999995595 1.061521702 0.009843898 0.162915723 0 0 0.168164579 0.039636771 0.65932612 0.180899719 0.061526108 S(ph)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 37 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 S(1)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 295.54 6.33E-92 6710700000 412310 399470 408410 425820 414630 434440 462240 375350 490980 458610 TRUE FALSE 396196.4694 388077.5067 482218.772 447796.6212 427966.9505 443224.6745 467897.0314 367598.8913 435246.0088 427547.9362 0.926671458 0.907681862 1.127870658 1.047360035 1.000980041 1.036666621 1.094373266 0.859784039 1.018005168 1 18.70572666 -0.178208927 6.716800041 0.999979944 0.999159963 0 0.079226853 0 0 0.079041564 0.018630275 0.663423838 0.178208927 -0.000819981 RVS(ph)VELTNSLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVSVELTNSLFK 12 1 P14923 P14923 JUP Junction plakoglobin 1 RVS(1)VELTNSLFK;RVS(1)VELTNSLFK 205.98 5.85E-08 2486400000 2929000 3122900 2524500 3815300 2003760 2181700 3274500 3609500 2935100 3373200 TRUE FALSE 2814531.442 3033837.95 2980733.307 4012208.09 2068212.76 2225815.469 3314574.311 3534962.564 2601919.753 3144730.159 0.894999348 0.96473713 0.947850263 1.275851309 0.657675748 0.707792197 1.054009134 1.124090903 0.827390466 1 21.5845048 -0.177962513 7.181638221 0.999999999 0.953009364 0.005240839 0.176170258 23652619.27 3293485.062 0.174581194 0.042342159 0.663800365 0.177962513 -0.046990635 KKEEPSQNDISPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKEEPSQNDISPK 13 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 114.74 0.0004044 388710000 714730 602510 521660 466230 537250 537460 545830 650300 732260 618750 FALSE TRUE 686797.5614 585327.0047 615935.5663 490292.1862 554531.1342 548327.8094 552510.0308 636871.0777 649136.9147 576841.5114 1.190617436 1.014710268 1.06777261 0.849959957 0.961323211 0.950569261 0.95781947 1.104065961 1.125329752 1 19.13781546 -0.177522251 7.150447028 0.999995378 1.019659241 0.00352921 0.095213112 0 0 0.094692674 0.022319277 0.664473628 0.177522251 0.019663863 QRPPLER ddPTM_BT-474_Pertuzumab_2h_R1 2 QRPPLER 7 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 ; 75.738 0.038902 213890000 340290 367530 280880 403110 376260 360300 344390 353680 364220 413600 FALSE TRUE 326991.0906 357048.4042 331641.2641 423914.5554 388362.7446 367585.5129 348604.7478 346376.3844 322875.2725 385586.5036 0.848035622 0.925987816 0.860095623 1.099401954 1.007200047 0.953315299 0.9040896 0.898310447 0.837361447 1 18.55669503 -0.177257234 7.242156868 0.999999998 0.929147356 0.078250931 0.075513997 7483573.989 1033335.018 0.07576006 0.018940015 0.664879229 0.177257234 -0.070852642 CAAPRPPSSSPEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 CAAPRPPSSSPEQR 14 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 120.53 0.0001133 122680000 76990 71933 62609 70474 61460 64417 79172 72387 72260 82160 FALSE TRUE 73981.14568 69881.54127 73923.83903 74111.17159 63436.91672 65719.55588 80140.93062 70892.18315 64057.34774 76595.23002 0.965871447 0.912348475 0.965123272 0.967569019 0.828209755 0.858011078 1.046291402 0.925543055 0.836309881 1 16.22496693 -0.17687016 7.571077333 0.999999999 0.925844125 0.112321139 0.064595625 8480379.528 1120102.08 0.062474788 0.015152362 0.665472082 0.17687016 -0.074155874 EAEGGRPPAAT(ph)SPAEVVWSSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAEGGRPPAATSPAEVVWSSEK 22 1 O75564;O75564-2 O75564 JRK Jerky protein homolog 1 EAEGGRPPAAT(0.664)S(0.336)PAEVVWSSEK 163.94 2.35E-11 179910000 136580 145770 115860 125020 135280 155380 150870 148350 183620 197330 TRUE FALSE 131242.3026 141612.7823 136798.4793 131472.2972 139631.4041 158521.8901 152716.3922 145286.5207 162776.2274 183964.6633 0.713410392 0.769782521 0.743612805 0.714660603 0.759012092 0.861697498 0.830139818 0.789752325 0.884823338 1 17.48906915 -0.176163622 0.181041648 1.150198786 0.677213414 0.841429612 0.033817474 5.068185655 0.303252334 0.590568474 0.164243023 0.666555594 0.176163622 -0.472985372 GVWDHGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVWDHGGR 8 0 Q9Y3S2;D6RBR7;D6R8Y9 Q9Y3S2 ZNF330 Zinc finger protein 330 0 157.58 0.00037464 139910000 328550 328780 300240 373190 346530 348110 343030 316910 356160 405910 FALSE TRUE 315709.9028 319403.5163 354500.0468 392450.3806 357676.4522 355149.0227 347228.1038 310365.6978 315730.2099 378417.3542 0.834290234 0.844050921 0.936796484 1.037083464 0.945190405 0.938511458 0.917579757 0.820167718 0.834343897 1 18.52961873 -0.16943424 7.453926741 0.999999999 0.901457352 0.173470403 0.064890643 0 0 0.070050916 0.016511159 0.67696429 0.16943424 -0.098542647 KS(ph)SPSKDR ddPTM_BT-474_Pertuzumab_2h_R1 3 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.492)S(0.492)PS(0.016)KDR;KS(0.756)S(0.191)PS(0.053)KDR;KS(0.941)S(0.053)PS(0.006)KDR 67.93 0.045536 1166430000 2477370 2096390 1656420 1473610 1795420 1858190 2148170 2257270 2115610 2106870 TRUE FALSE 2380551.642 2036603.01 1955771.941 1549663.189 1853171.315 1895763.875 2174459.947 2210656.586 1875454.822 1964169.818 1.211988709 1.036877255 0.995724465 0.788965992 0.943488337 0.965173101 1.10706311 1.125491577 0.954833337 1 20.90548824 -0.169235323 8.326819818 0.999999938 1.016482511 0.001201934 0.110762146 0 0 0.114888502 0.02707948 0.677274426 0.169235323 0.016482573 NENQLIIFADDTYPR ddPTM_BT-474_Pertuzumab_2h_R1 4 NENQLIIFADDTYPR 15 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;;; 180.85 1.42E-06 164618000 204311 233167 196160 222045 217650 219990 225853 197916 247751 252741 FALSE TRUE 196326.3002 226517.3055 231610.4756 233504.7691 224650.9099 224438.3485 228617.0566 193828.9654 219627.3451 235622.627 0.833223459 0.961356337 0.98297213 0.991011653 0.953435215 0.952533088 0.970267837 0.822624584 0.932114831 1 17.84611856 -0.167788696 8.514253752 1.000003571 0.931996918 0.114039922 0.05568456 0 0 0.057313176 0.013508845 0.679534177 0.167788696 -0.068006654 EVS(ph)PEVVR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVSPEVVR 8 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR 176.6 0.00027208 5005730000 3517370 3680420 3096740 3630760 3510730 3670580 3496590 3714410 3696540 3831890 TRUE FALSE 3379907.292 3575458.025 3656389.805 3818143.959 3623655.819 3744801.643 3539382.314 3637706.135 3276924.276 3572352.677 0.946129231 1.000869272 1.023524309 1.068803756 1.014361164 1.04827322 0.990770686 1.018294235 0.917301446 1 21.76844309 -0.166787148 6.26794514 0.999995084 1.007575146 0 0.042512234 0 0 0.040177656 0.009469964 0.681103092 0.166787148 0.007580061 EGTAPS(ph)ENGETKAEEAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGTAPSENGETKAEEAQK 18 1 Q15651 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 EGTAPS(0.998)ENGET(0.002)KAEEAQK 107.56 0.0002523 912550000 342920 274090 214480 185680 266770 195950 233090 325720 329380 267000 TRUE FALSE 329518.3073 266273.2216 253241.3071 195262.9671 275350.8993 199912.2433 235942.6251 318993.7682 291990.1633 248915.8522 1.32381407 1.069731876 1.017377177 0.784453723 1.106200738 0.803131827 0.947881073 1.281532556 1.173047681 1 17.92529859 -0.165791679 7.292768023 1.000003212 1.053557236 0.009523602 0.170272858 0 0 0.171630359 0.040453663 0.682666075 0.165791679 0.053554024 ENVDYIIQELR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENVDYIIQELR 11 0 A0A2R8YE10;Q9NRW7;B7Z7G7;A0A2R8YF01;A0A1B0GXI6;A0A2R8YD95;Q9NRW7-2 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ; 106.67 0.0053523 152335000 114248 154265 136006 161357 130511 161342 149489 143127 144038 160064 FALSE TRUE 109783.0619 149865.5132 160585.3096 169684.6541 134709.0048 164604.4458 151318.4911 140171.3774 127687.4101 149222.7227 0.735699362 1.004307591 1.076145152 1.137123429 0.902737883 1.10307896 1.014044566 0.939343385 0.855683423 1 17.18710771 -0.164867098 6.766853407 0.999999997 0.9832586 0 0.115768383 0 102589482.3 0.109772706 0.026623793 0.684120968 0.164867098 -0.016741398 ANS(ph)FVGTAQYVSPELLTEK ddPTM_BT-474_Pertuzumab_2h_R1 5 ANSFVGTAQYVSPELLTEK 19 0 E9PER6;O15530-5;O15530-2;O15530;O15530-4;Q6A1A2 E9PER6;Q6A1A2 PDPK1;PDPK2P 3-phosphoinositide-dependent protein kinase 1;Putative 3-phosphoinositide-dependent protein kinase 2 1 ANS(1)FVGTAQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK;ANS(0.64)FVGT(0.36)AQYVSPELLTEK;ANS(0.999)FVGT(0.001)AQYVSPELLTEK;ANS(0.998)FVGT(0.002)AQYVSPELLTEK 391.32 5.11E-127 2412821000 2440965 1868349 1424006 1481204 1569434 1484563 1553488 2314493 2055373 1765082 TRUE FALSE 2345569.389 1815065.516 1681355.561 1557649.116 1619916.27 1514581.881 1572500.051 2266697.911 1822055.674 1645531.424 1.425417561 1.103026955 1.021770558 0.946593358 0.984433507 0.920421123 0.955618366 1.377486858 1.107274919 1 20.65012215 -0.164407966 7.356449947 1.000001045 1.09387555 0.027488551 0.166939807 11619975.01 1579562.615 0.171382044 0.041566251 0.684844597 0.164407966 0.093874505 IGRPSETGIIGIIDPECR ddPTM_BT-474_Pertuzumab_2h_R1 6 IGRPSETGIIGIIDPECR 18 1 Q16531;F5GY55;F5H2L3;F5GWI0;F5GZY8 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;;; 150.29 5.11E-08 2809150000 2053040 2033418 1644179 2070294 2023761 1935224 1960715 2053247 2130374 2187090 FALSE TRUE 1972804.927 1975426.91 1941318.72 2177142.121 2088857.11 1974355.555 1984710.817 2010846.732 1888542.875 2038956.446 0.967556188 0.968842132 0.952113873 1.067772745 1.024473629 0.968316689 0.973395396 0.986213676 0.92623012 1 20.95939953 -0.16290776 7.734921133 0.999999997 0.983663603 0.018870394 0.037229542 0 0 0.036808899 0.008675941 0.687214382 0.16290776 -0.016336394 SREDLT(ph)AVVSVSTK ddPTM_BT-474_Pertuzumab_2h_R1 3 SREDLTAVVSVSTK 14 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(0.423)REDLT(0.576)AVVS(0.001)VSTK;S(0.196)REDLT(0.749)AVVS(0.055)VSTK;S(0.393)REDLT(0.607)AVVSVSTK 168.69 2.20E-05 2209130000 1689780 1487700 1153300 1218080 1225200 1229110 1285480 1690350 1592420 1527280 TRUE FALSE 1623741.529 1445272.253 1361726.965 1280945.255 1264609.671 1253963.446 1301212.089 1655443.682 1411655.158 1423835.965 1.140399294 1.015055307 0.956379104 0.89964384 0.8881709 0.880693758 0.913877807 1.162664606 0.991445077 1 20.44135152 -0.16281077 7.401243905 1.000047002 0.985062497 0.002465059 0.094910219 0 0 0.100887435 0.023779396 0.687367874 0.16281077 -0.014984505 SNVSSPATPTASSSSSTT(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNVSSPATPTASSSSSTTPTR 21 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSSST(0.001)T(0.999)PTR;SNVSSPATPTASSSSST(0.037)T(0.962)PT(0.001)R 402.38 2.06E-150 641910000 579770 591470 476190 594630 587090 559870 560550 590570 559910 670000 TRUE FALSE 557111.9474 574601.8547 562248.1258 625318.9256 605974.283 571190.955 567410.1786 578374.5231 496351.3641 624620.3032 0.891920971 0.919921834 0.900143852 1.001118475 0.970148232 0.914461077 0.908408157 0.925961773 0.794644941 1 19.25261994 -0.16252842 7.690940949 0.999999992 0.918430503 0.199060347 0.051036452 0 0 0.04887836 0.01152074 0.687814901 0.16252842 -0.081569488 LGLHQQGSEPSYLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGLHQQGSEPSYLDR 15 0 U3KQC1;A0A0A0MQU0;Q9BV38 U3KQC1 WDR18 WD repeat-containing protein 18 0 ; 165.89 9.11E-09 341920000 536970 655980 513970 650570 597680 595260 654230 595920 624420 656070 FALSE TRUE 515984.6187 637272.0927 606855.8122 684145.9957 616904.92 607296.565 662236.6624 583614.0438 553538.4594 611633.7945 0.843616921 1.041917727 0.992188165 1.118554929 1.008618107 0.992908781 1.082733931 0.954188681 0.905016146 1 19.2223086 -0.161640013 6.742858719 1.000000589 0.999527513 0 0.076396464 0 0 0.071183064 0.016778009 0.689223357 0.161640013 -0.000473075 TLNAET(ph)PKSS(ph)PLPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 T(0.382)LNAET(0.618)PKS(0.214)S(0.786)PLPAK;T(0.073)LNAET(0.927)PKS(0.422)S(0.578)PLPAK;T(0.016)LNAET(0.984)PKS(0.295)S(0.705)PLPAK 111.65 0.0018932 3350330000 4314400 3273520 2317680 2056370 2693670 2489950 2650300 4164920 3721250 2902100 TRUE FALSE 4145788.478 3180162.415 2736536.333 2162499.502 2780314.342 2540298.495 2682735.164 4078912.947 3298829.301 2705538.182 1.532334123 1.175426921 1.011457295 0.799286263 1.027638183 0.938925391 0.991571726 1.507616109 1.219287653 1 21.36748417 -0.161239801 7.98615982 1.000003674 1.133882303 0.030948073 0.224488651 0 0 0.235497582 0.055507312 0.689858785 0.161239801 0.133878629 EAATQEDPEQLPELEAHGVS(ph)ESEGEERPVAEEEILLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAATQEDPEQLPELEAHGVSESEGEERPVAEEEILLR 37 1 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;X6RJY0 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 EAATQEDPEQLPELEAHGVS(0.994)ES(0.006)EGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(0.928)ES(0.072)EGEERPVAEEEILLR 244.75 2.86E-50 163129000 71121 70550 69426 81334 73883 76885 68410 72202 85686 84413 TRUE FALSE 68341.51269 68537.98308 81972.82257 85531.65749 76259.51379 78439.66738 69247.22204 70711.00347 75959.28451 78695.63232 0.868428281 0.870924867 1.041643865 1.08686664 0.96904379 0.996747406 0.879937298 0.89853784 0.965228721 1 16.26399595 -0.16071945 8.756608862 0.999999997 0.951765368 0.037686357 0.070926995 0 0 0.074979268 0.017672783 0.690685835 0.16071945 -0.048234629 LADVAAPPGGPPPPHSPYSGPPS(ph)RGS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LADVAAPPGGPPPPHSPYSGPPSRGSPVR 29 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 LADVAAPPGGPPPPHS(0.049)PY(0.164)S(0.458)GPPS(0.576)RGS(0.753)PVR;LADVAAPPGGPPPPHS(0.272)PY(0.141)S(0.345)GPPS(0.648)RGS(0.594)PVR 73.371 0.0037439 987230000 382224 463011 351507 496720 356030 463900 424445 432680 421200 480130 TRUE FALSE 367286.2635 449806.3796 415032.1341 522355.7787 367482.0283 473280.3758 429639.4849 423745.0068 373387.1418 447610.3674 0.820549054 1.00490608 0.927217429 1.166987668 0.820986409 1.057349003 0.959851505 0.946682735 0.83417894 1 18.77188393 -0.159506389 7.376023559 0.999999998 0.955557143 0.017472654 0.104627548 0 94334783.5 0.0926036 0.022459672 0.69261774 0.159506389 -0.044442855 LTLDDIER ddPTM_BT-474_Pertuzumab_2h_R1 3 LTLDDIER 8 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 0 ;; 118.06 0.0045586 353648000 508410 545860 443330 529450 532330 528840 502800 546380 531690 587380 FALSE TRUE 488540.7751 530292.6073 523449.5928 556774.9779 549452.8779 539533.5071 508953.4168 535097.0621 471334.7802 547596.2294 0.892155112 0.968400765 0.955904304 1.016761891 1.003390543 0.985276154 0.929431923 0.977174482 0.860734159 1 19.06275299 -0.158408388 7.167220454 1.000001019 0.95929176 0.071663267 0.046313592 5909192.881 824474.8254 0.043619397 0.010579258 0.69437106 0.158408388 -0.04070926 TQQS(ph)PISNGSPELGIK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQQSPISNGSPELGIK 16 0 Q15723-2;Q15723-3;Q15723-1;Q15723 Q15723-2 ELF2 ETS-related transcription factor Elf-2 1 T(0.001)QQS(0.999)PISNGSPELGIK;TQQS(0.999)PISNGSPELGIK 226.44 6.24E-15 202092000 423280 403770 316290 357060 370290 363660 366520 427540 413080 403790 TRUE FALSE 406737.7496 392254.8749 373450.6388 375487.9094 382200.7141 371013.4544 371005.5814 418711.1496 366188.8902 376440.9436 1.080482228 1.042009063 0.992056377 0.997468303 1.015300595 0.985582096 0.985561182 1.112289077 0.972765838 1 18.52206403 -0.152702143 7.030314573 0.999999821 1.023389588 0.015478952 0.043187553 0 2.24E-18 0.042804063 0.010089014 0.703554682 0.152702143 0.023389767 ERGS(ph)PLLGDHAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERGSPLLGDHAVR 13 1 Q9C073;D6RJ87;D6RFX7 Q9C073 FAM117A Protein FAM117A 1 ERGS(1)PLLGDHAVR 95.094 0.0029395 404200000 127890 131230 126020 145650 120160 148670 131130 115080 165380 158840 TRUE FALSE 122891.9174 127487.4489 148794.6173 153167.014 124025.0555 151676.2093 132734.8082 112703.5578 146606.7557 148081.6253 0.829893089 0.860926861 1.004814858 1.034341794 0.837545207 1.024274341 0.896362448 0.761090767 0.990040158 1 17.17603311 -0.15208815 7.998360624 1.000000013 0.909084506 0.070072959 0.089693095 0 0 0.090080456 0.021232167 0.70455005 0.15208815 -0.090915507 FSDHVALLSVFQAWDDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 FSDHVALLSVFQAWDDAR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 220.64 6.68E-19 1316140000 605570 855750 654274 779241 738777 800013 774606 695623 803729 855853 FALSE TRUE 581903.6549 831344.8479 772515.866 819457.7214 762540.4331 816189.811 784085.8599 681258.142 712493.0534 797885.314 0.729307389 1.041935267 0.968204142 1.027036978 0.955701803 1.022941263 0.982704965 0.853829654 0.892976774 1 19.60582187 -0.151708477 8.318919476 0.999999993 0.945787937 0.034333478 0.090482684 0 0 0.085042625 0.020044739 0.705166258 0.151708477 -0.054212055 ALSTGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALSTGEK 7 0 P62937;F8WE65;C9J5S7;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37 P62937 PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D" 0 ; 92.47 0.036399 2545520000 1575960 1260300 1022470 1128740 1165850 1112330 1110500 1594270 1358550 1290220 FALSE TRUE 1514369.741 1224357.478 1207253.074 1186994.407 1203350.624 1134822.075 1124090.631 1561347.767 1204333.1 1202832.25 1.259003274 1.017895453 1.003675345 0.986832874 1.000430961 0.943458304 0.934536492 1.298059449 1.001247763 1 20.19800402 -0.150264792 7.549719006 1.000000522 1.053740723 0.014134358 0.119189657 0 0 0.119618489 0.028194348 0.707514278 0.150264792 0.053740202 RSYS(ph)PDGKES(ph)PSDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSYSPDGKESPSDKK 15 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 RS(0.325)Y(0.076)S(0.601)PDGKES(0.881)PS(0.117)DKK 63.998 0.098048 546980000 374760 234190 227740 138220 223010 207540 249060 296490 357350 243450 TRUE FALSE 360113.9649 227511.1305 268897.684 145353.5508 230183.3192 211736.601 252108.0708 290367.3779 316785.1261 226960.9147 1.586678329 1.002424276 1.184775292 0.640434284 1.014198059 0.932920989 1.110799501 1.279371729 1.395769517 1 17.79208434 -0.149665135 8.194347088 1.000000073 1.113374928 0.020450116 0.247952611 16389890.4 2000146.083 0.240882066 0.058422483 0.708491861 0.149665135 0.113374855 VTEHGT(ph)PKPFR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTEHGTPKPFR 11 1 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 VT(0.14)EHGT(0.86)PKPFR;VTEHGT(1)PKPFR;VTEHGT(1)PKPFR;VT(0.001)EHGT(0.999)PKPFR 139.86 5.70E-05 2465320000 2207440 2119630 1708090 2104490 1599780 1786480 1927830 2403730 2291470 2182620 TRUE FALSE 2121170.804 2059180.228 2016779.859 2213102.981 1651238.377 1822603.85 1951423.36 2354092.136 2031351.932 2034789.203 1.042452359 1.011987003 0.991149283 1.087632555 0.81150341 0.895721211 0.95902974 1.156921873 0.998310748 1 20.95644791 -0.148935672 6.666674759 0.99997965 0.999804645 0 0.090772936 0 0 0.094828527 0.022351298 0.709682879 0.148935672 -0.000175006 FKMPEMSIKPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKMPEMSIKPQK 12 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 76.262 0.017768 162520000 560870 679320 467650 587670 447250 554590 595370 574710 701750 618520 FALSE TRUE 538950.5803 659946.4587 552164.7578 617999.7191 461636.2024 565804.1898 602656.3162 562842.0377 622090.282 576627.0895 0.934660529 1.144494372 0.95757686 1.071749369 0.800580151 0.981230678 1.045140485 0.976093645 1.078843317 1 19.13727909 -0.147307714 5.503417321 1.000000001 0.99818568 0 0.090020139 5061328.317 919670.0327 0.082635809 0.020531032 0.712348126 0.147307714 -0.00181432 GLEISGTFTHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLEISGTFTHR 11 0 P63010;P63010-2;P63010-3;A0A087X253 P63010 AP2B1 AP-2 complex subunit beta 0 196.88 5.90E-08 491770000 280070 328580 263810 327670 306650 291230 313750 291710 317900 360820 FALSE TRUE 269124.5548 319209.2201 311486.3354 344581.088 316513.6757 297118.8701 317589.7664 285686.0866 281813.3247 336381.34 0.800057919 0.948950439 0.925991719 1.024376346 0.94093708 0.883279881 0.9441361 0.849292314 0.837779303 1 18.35973815 -0.146177521 10.39975934 1 0.909093714 0.169023251 0.06214762 0 0 0.061203711 0.014425853 0.714204329 0.146177521 -0.090906286 VFDDES(ph)DEKEDEEYADEKGLEAADKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFDDESDEKEDEEYADEKGLEAADKK 26 3 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VFDDES(0.999)DEKEDEEY(0.001)ADEKGLEAADKK 88.191 0.0084349 296250000 559830 317800 246340 143350 308100 241250 279240 447630 445190 317470 TRUE FALSE 537951.2247 308736.6552 290859.1178 150748.3107 318010.3163 246128.2403 282657.4227 438386.2841 394653.8976 295967.4741 1.817602513 1.043143866 0.982740143 0.509340802 1.074477245 0.831605706 0.955028668 1.481197504 1.333436719 1 18.17507911 -0.142144811 8.73044993 0.999986552 1.10173789 0.008729703 0.342622573 0 0 0.341197638 0.080421054 0.720867073 0.142144811 0.101751338 DNFWEMGDTGPCGPCSEIHYDR ddPTM_BT-474_Pertuzumab_2h_R1 11 DNFWEMGDTGPCGPCSEIHYDR 22 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;;;;;;;; 297.99 1.27E-55 14002730000 2688434 2974264 2321236 2862776 2659273 2901812 2745570 2629575 3110144 3126617 FALSE TRUE 2583367.027 2889440.903 2740734.981 3010524.212 2744810.931 2960488.627 2779171.107 2575273.357 2757093.492 2914848.446 0.886278335 0.991283409 0.940266718 1.032823582 0.941665058 1.015657823 0.953453038 0.883501631 0.945878849 1 21.47498944 -0.141160017 7.399372726 1 0.953695988 0.079828424 0.046229755 6171878.873 834108.3656 0.045504712 0.011036514 0.722503547 0.141160017 -0.046304012 LEKPAK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEKPAK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 81.297 0.056772 47567680000 19335100 19054550 16096840 15749470 16929940 15681400 18451890 19585570 21201120 18575740 FALSE TRUE 18579462.92 18511132.89 19005897.06 16562302.03 17474506.9 15998488.65 18677709.75 19181121.14 18794457.74 17317588.58 1.072866631 1.06892093 1.097490968 0.956386159 1.00906121 0.923828891 1.078539871 1.10760924 1.085281455 1 24.04573472 -0.139650283 7.941507068 0.999979105 1.045624365 0.048527547 0.058828322 0 0 0.061664072 0.014534361 0.725019549 0.139650283 0.04564526 ARFEELNADLFR ddPTM_BT-474_Pertuzumab_2h_R1 10 ARFEELNADLFR 12 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;;;;;;;; 231.74 2.47E-12 27582470000 11638520 13751520 10068698 11194070 9211572 6421412 13023380 11917052 12500550 14459350 FALSE TRUE 11183673.77 13359340.11 11888335.71 11771797.29 9507870.579 6551257.35 13182764.02 11670960.71 11081539.97 13480005.35 0.829649061 0.991048577 0.881923664 0.873278385 0.705331366 0.485998127 0.977949465 0.865797929 0.822072372 1 23.68431773 -0.139432027 16.90456927 1 0.829670722 0.126441604 0.136965483 0 0 0.138218702 0.03257846 0.725384002 0.139432027 -0.170329278 ERS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSPVK 6 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 ERS(1)PVK 56.378 0.091981 2065900000 2776200 2407200 1925600 2172100 2203500 2061900 2492000 2508400 2363300 2786400 TRUE FALSE 2667703.035 2338549.013 2273598.755 2284202.341 2274377.579 2103593.031 2522497.841 2456600.663 2095028.092 2597674.646 1.026958106 0.900247079 0.875243849 0.879325802 0.875543664 0.8097985 0.971059961 0.945692205 0.806501343 1 21.30878932 -0.138832613 7.449249083 1.000000535 0.900891314 0.179744229 0.064650402 8366099.514 1123079.165 0.061667737 0.014956623 0.72638587 0.138832613 -0.099109221 GFDQELNVDWR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFDQELNVDWR 11 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 ; 199.08 1.20E-07 345380000 413820 491750 420100 501940 487620 438770 494650 465730 476150 527420 FALSE TRUE 397647.4569 477725.7715 496021.4151 527845.1836 503304.7401 447642.23 500703.6747 456112.5127 422099.4482 491697.3736 0.80872398 0.971584957 1.008794111 1.073516378 1.023606729 0.910401914 1.018316756 0.927628532 0.858453738 1 18.90741112 -0.138814521 7.657145593 0.999999988 0.962153664 0.022735006 0.077305419 0 0 0.07505608 0.017690888 0.726416131 0.138814521 -0.037846324 QTELFAHFIQPAAQKT(ph)PTS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTELFAHFIQPAAQKTPTSPLK 22 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 2 QTELFAHFIQPAAQKT(0.961)PT(0.233)S(0.806)PLK 85.537 0.047654 312120000 206350 168670 136820 125220 136610 145760 133260 190900 191430 174820 TRUE FALSE 198285.6139 163859.6967 161546.4175 131682.6192 141004.1847 148707.3671 134890.8757 186957.8483 169699.6689 162979.2857 1.21663077 1.005401981 0.991208281 0.807971508 0.865166295 0.912431089 0.827656565 1.147126443 1.041234585 1 17.31432909 -0.135904411 7.203035989 1 0.975998963 0.001727524 0.126136147 0 0 0.127636219 0.030084145 0.731300026 0.135904411 -0.024001037 LPIGDVATQYFADR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPIGDVATQYFADR 14 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 150.06 1.70E-05 742990000 167433 184149 161981 175186 178265 161684 184336 179207 215698 164769 FALSE TRUE 160889.5333 178897.2508 191254.5699 184227.3705 183999.0556 164953.3613 186591.9591 175506.3128 191212.8673 153609.0489 1.047396195 1.164627033 1.24507359 1.199326288 1.197839951 1.07385185 1.214719839 1.142551914 1.244802105 1 17.22890368 -0.135759512 8.114073264 0.999989094 1.170826237 0.394451166 0.063190676 3978509.355 490322.0811 0.058489176 0.014185709 0.73154406 0.135759512 0.170837143 VADSSKGPDEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VADSSKGPDEAK 12 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 136.99 9.14E-05 206490000 491910 424670 300830 277110 351310 350160 375300 442380 514150 380020 FALSE TRUE 472685.6134 412558.8274 355196.6729 291411.6803 362610.2052 357240.4751 379893.0337 433244.6984 455785.8475 354280.9069 1.334211368 1.164496362 1.002584859 0.82254413 1.023510435 1.008353733 1.072293274 1.222884694 1.286509768 1 18.43453419 -0.135192627 8.014732022 0.999999969 1.097202973 0.042402265 0.145144644 0 0 0.151298414 0.035661378 0.732499569 0.135192627 0.097203004 NSQEDS(ph)EDSEDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 9 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NS(0.001)QEDS(0.965)EDS(0.034)EDKDVK;NSQEDS(0.944)EDS(0.056)EDKDVK;NS(0.075)QEDS(0.87)EDS(0.055)EDKDVK;NSQEDS(0.997)EDS(0.003)EDKDVK;NSQEDS(0.997)EDS(0.003)EDKDVK;NSQEDS(0.988)EDS(0.012)EDKDVK;NSQEDS(0.997)EDS(0.003)EDKDVK;NSQEDS(0.989)EDS(0.011)EDKDVK;NSQEDS(0.809)EDS(0.191)EDKDVK 205.68 2.59E-09 26877720000 9099850 6061635 5646623 4047140 5608980 4888338 6153352 7650550 9021720 6563980 TRUE FALSE 8744217.802 5888763.105 6667093.385 4256013.38 5789397.936 4987183.544 6228658.562 7492563.469 7997612.168 6119395.788 1.428934834 0.9623112 1.089501908 0.695495687 0.946073458 0.814979733 1.017855157 1.224395958 1.306928404 1 22.54495778 -0.130080735 8.1567234 1.000028943 1.043210101 0.003535379 0.210456553 0 0 0.208729035 0.049197905 0.741172445 0.130080735 0.043181158 SVPVTVDDDDDDNDPENRYDSICK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVPVTVDDDDDDNDPENRYDSICK 24 1 A0A096LP59 A0A096LP59 ATRX 0 ; 183.86 2.49E-17 315480000 196932 191215 134130 147588 163268 179937 162894 182906 189452 190439 FALSE TRUE 189235.6797 185761.7354 158370.2747 155205.0344 168519.6635 183575.4494 164887.5455 179128.9272 167946.2032 177540.3969 1.065873925 1.046306861 0.892023886 0.874195603 0.94919053 1.03399256 0.92873255 1.00894743 0.945960503 1 17.4377878 -0.126889135 10.98087771 0.999999959 0.970745788 0.01814959 0.062113996 0 0 0.062161202 0.014651536 0.746639334 0.126889135 -0.029254171 GPSPAPAS(ph)SPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GPSPAPAS(0.5)S(0.5)PKR 59.709 0.059483 82061000 43684 59795 40634 44687 42628 48647 45388 53096 53880 52910 TRUE FALSE 41976.78098 58089.70515 47977.4677 46993.30143 43999.16833 49630.67567 45943.47192 51999.54905 47763.76828 49326.35857 0.85100101 1.177660521 0.972653751 0.952701614 0.892001145 1.006169462 0.931418277 1.054193955 0.968321394 1 15.59007117 -0.126148994 7.069904944 1 0.984782283 0.000786461 0.085602642 7665585.661 1084255.737 0.077674268 0.019418567 0.747912868 0.126148994 -0.015217717 QLIVGVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLIVGVNK 8 0 A0A2U3TZH3;Q05639;A0A2R8Y488;P68104;Q5VTE0;A0A087WV01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 126.67 0.0028134 881060000 2244250 2127120 1874850 1879110 1966740 2084040 2216950 2254800 2449800 2780900 FALSE TRUE 2156542.229 2066456.62 2213677.101 1976091.092 2030001.978 2126180.717 2244081.697 2208237.592 2171708.974 2592547.166 0.83182372 0.797075805 0.853861843 0.76221992 0.783014483 0.820112646 0.865589536 0.85176371 0.837673853 1 21.30593881 -0.123919201 0.416592638 1.031310986 0.804942153 0.787026448 0.028519865 2.315625995 0.486973968 0.146492485 0.019041608 0.751762743 0.123919201 -0.226368832 TPTS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 7 TPTSPLK 7 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 TPT(0.022)S(0.978)PLK;TPT(0.026)S(0.973)PLK;TPT(0.003)S(0.997)PLK;T(0.007)PT(0.201)S(0.792)PLK;TPT(0.002)S(0.998)PLK;TPT(0.003)S(0.997)PLK;TPT(0.002)S(0.998)PLK 154.28 0.001772 35153750000 22179100 19716600 16554800 18510300 17395000 17633800 19405100 21672600 20794700 20721200 TRUE FALSE 21312316.25 19154301.87 19546620.62 19465618.8 17954525.97 17990367.52 19642585.42 21225053.24 18434172.83 19317734.67 1.103251319 0.991539754 1.011848488 1.007655356 0.929432269 0.931287639 1.016816193 1.09873407 0.954261623 1 24.20342259 -0.123635047 7.10844788 1.000000541 1.007730642 0 0.057096919 3936792.801 553818.8605 0.058138218 0.014100589 0.752254774 0.123635047 0.007730101 LEDLDTCMMT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 LEDLDTCMMTPK 12 0 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 LEDLDT(0.002)CMMT(0.998)PK;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK 291.75 4.31E-35 2056638000 2938987 2221127 1665973 1765176 1767511 1668456 1695728 2813934 2334387 2151272 TRUE FALSE 2824128.139 2157782.633 1967051.38 1856276.945 1824364.597 1702193.323 1716480.827 2755825.28 2069397.174 2005564.431 1.408146303 1.075897936 0.980796902 0.925563356 0.909651452 0.848735297 0.855859228 1.374089626 1.03182782 1 20.93557688 -0.122064583 7.449980072 0.999991979 1.046982267 0.005240995 0.18770113 0 1.00E-17 0.1915332 0.045144808 0.754979949 0.122064583 0.046990288 EKTPSPKEEDEEPES(ph)PPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKTPSPKEEDEEPESPPEK 19 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK 174.98 1.80E-12 2642000000 4299190 3134390 2397010 1793250 2812740 2870210 2823840 3448450 4050590 3023870 TRUE FALSE 4131172.902 3045000.266 2830203.028 1885799.847 2903214.337 2928247.613 2858398.999 3377238.302 3590784.005 2819060.592 1.465443103 1.080147151 1.003952535 0.668946192 1.029851698 1.038731704 1.013954438 1.198001317 1.273751978 1 21.42678306 -0.121660345 8.087822524 1.000001857 1.073775127 0.013652231 0.196052232 13245568.91 1637717.481 0.194745746 0.047232781 0.755683005 0.121660345 0.07377327 IFYPEIEEVQALDDTERGS(ph)GGFGSTGKN ddPTM_BT-474_Pertuzumab_2h_R1 3 IFYPEIEEVQALDDTERGSGGFGSTGKN 28 2 P33316-2;H0YNW5;P33316;A0A0C4DGL3 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 IFYPEIEEVQALDDT(0.04)ERGS(0.96)GGFGSTGKN;IFYPEIEEVQALDDT(0.001)ERGS(0.999)GGFGSTGKN;IFYPEIEEVQALDDT(0.07)ERGS(0.925)GGFGS(0.004)T(0.001)GKN 221.77 1.81E-34 281978000 207750 194097 167455 159662 196184 218463 167892 201044 200699 214150 TRUE FALSE 199630.9003 188561.5436 197717.8435 167902.175 202494.4365 222880.4715 169946.7125 196892.3711 177916.4909 199645.4298 0.999927224 0.944482144 0.990344952 0.841001846 1.014270333 1.116381536 0.851242689 0.98621026 0.891162353 1 17.60708052 -0.121367843 0.003083894 0.892028203 1.030494117 0 0.079428569 3420641.37 3333.983172 75631.94288 74059.27892 0.756192137 0.121367843 0.138465914 SSTVAS(ph)LDTDSTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTVASLDTDSTK 13 0 C9IZZ8;C9J6Y2;C9J0J6;C9JZ07;G3V1A3;C9J5T5;C9JBU8;A8MPU2;O14713-2;O14713 C9IZZ8 ITGB1BP1 Integrin beta-1-binding protein 1 1 SSTVAS(1)LDTDSTK;SSTVAS(1)LDTDSTK 248.99 1.85E-17 476520000 1071750 1030810 825470 804270 893530 899960 901430 1080510 1136720 1015480 TRUE FALSE 1029864.825 1001412.308 974650.7915 845778.4711 922271.2039 918157.8078 912461.97 1058197.091 1007684.311 946700.6351 1.087846344 1.057791947 1.029523754 0.893395905 0.974195189 0.969850208 0.963833694 1.11777372 1.064417065 1 19.85254876 -0.119732786 7.349656822 1.000000001 1.017800703 0.006701319 0.064343215 0 3.57E-18 0.068167304 0.016067188 0.759044459 0.119732786 0.017800703 EES(ph)EEEEDEDDEEEEEEEKEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EESEEEEDEDDEEEEEEEKEK 21 1 H0Y993;A0A494C028;P35659;B4DFG0;H0Y8X0;A0A494C198;D6R9L5 H0Y993 DEK Protein DEK 1 EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK 269.25 8.78E-38 2693130000 1953240 1243040 1131020 816730 1220000 1036880 1231760 1590910 1942210 1368800 TRUE FALSE 1876905.221 1207589.716 1335420.473 858881.5332 1259242.408 1057846.424 1246834.647 1558057.153 1721738.463 1276089.957 1.470825165 0.94632021 1.046493992 0.6730572 0.986797523 0.828974806 0.977074258 1.220961849 1.349229695 1 20.2832986 -0.117041022 7.551695299 0.999999975 1.041635106 0.002038191 0.225462746 14969369.4 1982252.646 0.220577532 0.05349791 0.763763638 0.117041022 0.041635132 EIEGEEIEIVLAKPPDKK ddPTM_BT-474_Pertuzumab_2h_R1 3 EIEGEEIEIVLAKPPDKK 18 2 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 194.92 2.69E-15 1267910000 1358860 1101090 980850 831480 995060 957220 1012350 1239380 1347290 1158290 FALSE TRUE 1305754.249 1069687.991 1158111.414 874392.7824 1027067.009 976575.6442 1024739.442 1213786.37 1194351.288 1079837.987 1.209213109 0.990600446 1.072486269 0.809744418 0.951130652 0.904372375 0.948975175 1.124044889 1.106046742 1 20.04238344 -0.114841149 7.295536793 1.000000001 1.00865976 0 0.111684636 0 5.81E-18 0.111078956 0.026181561 0.767642217 0.114841149 0.008659759 ASSQQEKEDKPAETK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSQQEKEDKPAETK 15 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 144.33 2.39E-06 454860000 1075040 881530 556170 442280 708600 805730 700740 845170 1029370 792200 FALSE TRUE 1033026.248 856389.6275 656682.2909 465106.1238 731392.7625 822022.4126 709315.8657 827716.9442 912520.2331 738543.5884 1.398734299 1.159565449 0.889158475 0.629761237 0.990317666 1.113031682 0.960425189 1.12074217 1.235567199 1 19.49432354 -0.114160296 8.302576392 1.000000009 1.042117716 0.003034597 0.198089365 0 0 0.200460102 0.047248899 0.76884661 0.114160296 0.042117708 S(ph)WASPVYTEADGTFSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SWASPVYTEADGTFSR 16 0 E9PMS6;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(1)WASPVYTEADGTFSR;S(1)WASPVYTEADGTFSR;S(0.996)WAS(0.004)PVYTEADGTFSR;S(0.999)WAS(0.001)PVYTEADGTFSR 333.66 1.28E-71 2788490000 871980 751500 595130 759830 624890 567604 667180 972160 716390 775190 TRUE FALSE 837902.0576 730067.9558 702683.2296 799044.9174 644990.1544 579081.3418 675345.1484 952084.5563 635068.4106 722685.6908 1.159428045 1.010215042 0.972322046 1.105660355 0.892490556 0.801290726 0.934493594 1.317425498 0.878761568 1 19.4630088 -0.113101962 7.154469865 1.000023219 1.019265143 0 0.144501571 0 7.71E-18 0.147396616 0.034741716 0.770722501 0.113101962 0.019241924 EIST(ph)PTHWSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.09)T(0.783)PT(0.09)HWS(0.037)K 103.21 0.031794 381920000 395800 508700 427770 541370 472330 500180 467810 456560 536930 547080 TRUE FALSE 380331.6984 494192.3741 505077.5547 569310.1706 487522.9234 510293.9823 473535.1987 447131.8765 475979.9574 510025.7843 0.745710727 0.968955667 0.990298079 1.116238018 0.955878974 1.000525852 0.928453449 0.876684847 0.933246852 1 18.96021066 -0.112833396 7.729034979 1 0.949007397 0.030691096 0.089443419 0 0 0.088130733 0.020772613 0.77119926 0.112833396 -0.050992603 SKAELMEISEDKTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKAELMEISEDKTK 14 2 P05455;E7ERC4;E9PGX9;E9PFL9 P05455 SSB Lupus La protein 0 180.49 9.83E-07 2019400000 1621200 1283300 1149800 904050 1246100 1182800 1275900 1454500 1498200 1275700 FALSE TRUE 1557841.712 1246701.54 1357594.437 950708.1288 1286181.938 1206717.026 1291514.846 1424464.067 1328130.617 1189295.703 1.309885933 1.048268767 1.141511261 0.799387509 1.081465219 1.014648437 1.085949308 1.197737504 1.116737086 1 20.18167604 -0.109574287 7.807850149 1 1.085981166 0.043008935 0.124627142 0 0 0.12014791 0.028319134 0.777008399 0.109574287 0.085981167 AQS(ph)PGSPLHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 AQS(0.755)PGS(0.245)PLHAR;AQS(0.977)PGS(0.023)PLHAR 152.55 0.00043734 284590000 228260 250220 192444 250610 215060 235660 271650 279590 293400 349690 TRUE FALSE 219339.3468 243083.9706 227222.9117 263544.0121 221977.6002 240425.2067 274974.534 273816.3688 260094.462 326005.1848 0.672809382 0.745644492 0.696991711 0.808404358 0.680902055 0.737488905 0.843466751 0.839914153 0.797823084 1 18.31453538 -0.109416379 0.18729566 1.153233796 0.65002768 0.783442152 0.043722669 5.067221989 0.329454122 0.644091485 0.182447723 0.777290967 0.109416379 -0.503206116 QYPDS(ph)PHPVPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 QYPDSPHPVPHR 12 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 QY(0.002)PDS(0.998)PHPVPHR 71.08 0.029341 240910000 1218300 864790 800860 555020 851060 806090 883390 989030 1234100 945380 TRUE FALSE 1170687.489 840127.0359 945593.217 583664.6487 878435.1178 822389.6921 894201.1911 968606.1849 1094010.142 881348.5705 1.32829113 0.953229022 1.072893573 0.662240421 0.996694324 0.933103791 1.014582903 1.099004659 1.241291106 1 19.74935319 -0.108856182 7.764887094 1.000000004 1.02198722 0 0.171224908 0 0 0.163328293 0.038496848 0.778294243 0.108856182 0.021987216 TASDTDSSYCIPTAGMS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TASDTDSSYCIPTAGMSPSR 20 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 TASDTDSSYCIPTAGMS(0.976)PS(0.024)R;TASDTDSSYCIPTAGMS(0.997)PS(0.003)R 325.35 2.13E-67 439060000 423700 411560 316109 419480 321441 435620 423570 424790 486300 549840 TRUE FALSE 407141.3356 399822.7118 373236.9281 441129.4131 331780.4417 444428.5349 428753.7764 416017.9381 431097.2627 512598.8471 0.794268926 0.779991438 0.728126741 0.860574337 0.647251635 0.867010407 0.83643141 0.811585786 0.841003184 1 18.96747071 -0.108333215 0.3495403 1.050413796 0.764605507 0.551220968 0.058963358 3.930519746 0.632122107 0.322524882 0.04938917 0.77923201 0.108333215 -0.285808289 SILS(ph)PGGSCGPIK ddPTM_BT-474_Pertuzumab_2h_R1 4 SILSPGGSCGPIK 13 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 1 SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;S(0.001)ILS(0.997)PGGS(0.001)CGPIK;SILS(1)PGGSCGPIK 187.63 7.13E-06 4314980000 5707530 5796040 4988240 5238550 5306880 4454920 5912910 5908210 6113410 6811480 TRUE FALSE 5484473.418 5630742.614 5889725.931 5508912.193 5477580.615 4545001.535 5985273.961 5786203.399 5419441.326 6350132.393 0.863678594 0.886712633 0.927496557 0.86752714 0.862593136 0.715733351 0.942543177 0.911194136 0.853437533 1 22.59835524 -0.101149598 0.653933203 1.007060565 0.868685284 0.296923729 0.059233812 7.405069164 3.237258071 0.200765677 0.023155539 0.792228391 0.101149598 -0.138375281 STQIENQHQGAQDTSDLMS(ph)PSKR ddPTM_BT-474_Pertuzumab_2h_R1 8 STQIENQHQGAQDTSDLMSPSKR 23 1 Q9NVR2;H0YBW3 Q9NVR2 INTS10 Integrator complex subunit 10 1 STQIENQHQGAQDT(0.001)S(0.001)DLMS(0.832)PS(0.166)KR;STQIENQHQGAQDT(0.002)S(0.003)DLMS(0.943)PS(0.052)KR;STQIENQHQGAQDT(0.004)S(0.01)DLMS(0.817)PS(0.169)KR;STQIENQHQGAQDT(0.002)S(0.002)DLMS(0.799)PS(0.197)KR;STQIENQHQGAQDTSDLMS(0.859)PS(0.141)KR;STQIENQHQGAQDTSDLMS(0.984)PS(0.016)KR;STQIENQHQGAQDTSDLMS(0.846)PS(0.154)KR;STQIENQHQGAQDT(0.003)S(0.003)DLMS(0.856)PS(0.138)KR 178.69 2.39E-17 6402600000 2251946 1977065 1586119 1735310 1922984 1749735 1958116 2025683 2140238 2090982 TRUE FALSE 2163937.461 1920681.042 1872765.986 1824869.557 1984838.527 1785115.841 1982080.009 1983851.938 1897287.155 1949357.927 1.110077032 0.985289061 0.960709145 0.936138783 1.018201173 0.915745547 1.016786082 1.017695063 0.973288245 1 20.89456758 -0.099482556 11.85105518 1 0.991313636 0.001226887 0.051210501 0 0 0.047868709 0.011282763 0.795275208 0.099482556 -0.008686364 NLEAQHK ddPTM_BT-474_Pertuzumab_2h_R1 6 NLEAQHK 7 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;;;; 120.62 0.0045174 4450880000 5599410 5414810 4374130 4554480 4509990 4546430 5132790 5379860 5864220 5545930 FALSE TRUE 5380578.867 5260384.92 5164632.593 4789537.259 4655057.924 4638361.93 5195606.619 5268764.011 5198538.33 5170299.221 1.040670692 1.017423692 0.998904004 0.926355914 0.900345942 0.89711673 1.004894765 1.019044312 1.005461794 1 22.30181635 -0.098846808 7.143322748 1 0.978493132 0.016129353 0.04930962 7251849.944 1015192.902 0.053537227 0.012984685 0.796440235 0.098846808 -0.021506869 LATNTS(ph)APDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LATNTSAPDLK 11 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 LATNT(0.028)S(0.972)APDLK;LATNT(0.007)S(0.993)APDLK 201.76 4.44E-08 700820000 5930200 2426900 1729230 1228120 1279080 984210 856060 5083400 1370480 964880 TRUE FALSE 5698441.228 2357687.188 2041740.328 1291503.42 1320222.77 1004111.401 866536.7184 4978426.014 1214908.856 899527.8182 6.33492496 2.621027544 2.269791202 1.435757065 1.467684204 1.116264978 0.96332398 5.534488109 1.35060732 1 19.77880837 -0.096472423 9.446346452 0.999977017 2.596481648 0.064771189 1.781771111 0 0 1.744759846 0.411243839 0.800806477 0.096472423 1.596504631 QAQEEAER ddPTM_BT-474_Pertuzumab_2h_R1 4 QAQEEAER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 150.17 0.0011479 151614000 324577 335601 278204 356403 311402 316033 333474 336003 348545 356029 FALSE TRUE 311892.172 326029.9881 328481.6514 374797.0015 321418.5281 322423.4038 337555.1546 329064.4206 308979.6328 331914.8387 0.939675289 0.982269998 0.989656421 1.129196281 0.968376495 0.971404005 1.016993262 0.991412201 0.93090033 1 18.3404536 -0.090612476 8.091746543 0.999999993 0.994571568 0 0.05206012 0 0 0.049853158 0.011750502 0.811685007 0.090612476 -0.005428424 YELDTWYHSPYPEEYAR ddPTM_BT-474_Pertuzumab_2h_R1 3 YELDTWYHSPYPEEYAR 17 0 O95251-4;O95251;O95251-2;E7EUP3;O95251-3;O95251-5 O95251-4 KAT7 Histone acetyltransferase KAT7;Histone acetyltransferase 0 ;; 226.67 2.00E-15 926980000 503320 588050 491747 572730 559640 537590 556650 558980 575170 612280 FALSE TRUE 483649.698 571279.3898 580616.6218 602288.6639 577641.3289 548460.4381 563462.4492 547436.8677 509879.1129 570809.7302 0.847304579 1.000822795 1.017180666 1.055147858 1.011968259 0.960846336 0.987128319 0.959053146 0.893255819 1 19.1226504 -0.089286271 7.756288647 0.999999999 0.975622627 0.01565724 0.058208648 0 0 0.056178564 0.013241415 0.814167437 0.089286271 -0.024377372 TEMDKS(ph)PFNSPS(ph)PQDSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 TEMDKSPFNSPSPQDSPR 18 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 2 TEMDKS(1)PFNS(0.002)PS(0.997)PQDSPR;TEMDKS(1)PFNSPS(0.999)PQDS(0.001)PR;TEMDKS(1)PFNS(0.003)PS(0.978)PQDS(0.019)PR;TEMDKS(1)PFNS(0.005)PS(0.685)PQDS(0.31)PR 203.7 6.57E-16 1848550000 2183630 1936800 1485670 1494320 1646870 1662520 1686720 2022430 2173090 1919560 TRUE FALSE 2098291.325 1881564.36 1754163.618 1571442.034 1699843.069 1696137.293 1707362.584 1980666.114 1926409.934 1789546.491 1.172526858 1.051419658 0.980228022 0.878123056 0.949873656 0.947802866 0.954075567 1.106797797 1.0764794 1 20.77116259 -0.089162855 7.18626945 1.000000001 1.009931548 0.00093391 0.084150328 0 0 0.087459596 0.020614425 0.814398838 0.089162855 0.009931547 KGNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAKEK 23 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 KGNAEGS(1)S(1)DEEGKLVIDEPAKEK 80.984 0.015049 1222400000 1022100 645480 507460 303870 613290 512620 567250 785660 948920 647190 TRUE FALSE 982155.202 627071.5424 599169.3104 319552.7671 633017.0298 522985.5276 574192.1752 769435.8464 841202.5798 603355.2448 1.627822432 1.039307353 0.993062239 0.529626236 1.049161394 0.866795362 0.951665176 1.275261719 1.394207786 1 19.20264816 -0.088145231 8.029775993 0.999918125 1.063175937 0.003773191 0.285437462 19107599.13 2379592.653 0.280994849 0.068151261 0.816309347 0.088145231 0.063257812 VVDDEIYYFR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVDDEIYYFR 10 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9 Q86U86-8 PBRM1 Protein polybromo-1 0 ;;; 186.76 3.03E-06 864500000 433336 470255 377860 460101 457134 448084 437774 471347 458451 482110 FALSE TRUE 416400.75 456843.7878 446147.7075 483846.8677 471838.1303 457144.5655 443131.6092 461613.5197 406409.5645 449456.2603 0.926454445 1.016436588 0.992638766 1.076516027 1.04979766 1.017105792 0.985928217 1.027048815 0.90422495 1 18.7778212 -0.087698679 6.873983731 0.999999992 1.005207305 0 0.049746413 0 2.44E-18 0.046633754 0.010991681 0.817149126 0.087698679 0.005207314 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEKNESR ddPTM_BT-474_Pertuzumab_2h_R1 4 KISENSYSLDDLEIGPGQLSSSTFDSEKNESR 32 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.91)ENS(0.088)YS(0.002)LDDLEIGPGQLSSSTFDSEKNESR;KIS(0.999)ENS(0.001)YSLDDLEIGPGQLSSSTFDSEKNESR;KIS(1)ENSYSLDDLEIGPGQLSSSTFDSEKNESR;KIS(0.954)ENS(0.046)YSLDDLEIGPGQLSSSTFDSEKNESR 352.27 5.81E-132 8692200000 2517780 2312600 1908170 1658400 1981890 2219950 1948020 2313910 2751200 2317590 TRUE FALSE 2419382.374 2246646.912 2253018.766 1743990.223 2045639.292 2264838.91 1971860.451 2266126.95 2438895.31 2160617.565 1.119764281 1.039817017 1.042766107 0.807172103 0.946784533 1.048236831 0.912637425 1.048832976 1.128795465 1 21.0430123 -0.086190154 7.555361522 0.999999658 1.004450983 0 0.092756983 0 0 0.090939439 0.021434631 0.819992436 0.086190154 0.004451325 S(ph)RSSSS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSSSSPPPK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.627)RS(0.203)S(0.225)S(0.301)S(0.644)PPPK 58.071 0.064573 91809000 83227 78791 66899 77197 79392 79433 77693 87391 94831 99492 TRUE FALSE 79974.39683 76543.95782 78989.13746 81181.14642 81945.71578 81039.18968 78643.83017 85586.34531 84066.18244 92753.31822 0.862226801 0.825242259 0.851604438 0.875237113 0.883480153 0.873706636 0.847881582 0.922730819 0.906341509 1 16.50111127 -0.083260214 0.246212351 1.056454718 0.834060604 0.842818298 0.018558313 2.774779263 0.267067446 0.170031344 0.037535877 0.825543165 0.083260214 -0.222394114 VYGVESDLSEVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYGVESDLSEVAR 13 0 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 0 ; 172.1 5.58E-05 474550000 246490 255810 244660 281680 249120 267580 252100 269050 264940 298170 FALSE TRUE 236856.8983 248514.5493 288875.5044 296217.5386 257133.171 272990.6509 255185.2752 263494.0235 234865.1219 277974.6803 0.852080837 0.894018653 1.039215169 1.065627769 0.925023713 0.982070204 0.918016256 0.947906562 0.844915521 1 18.08459395 -0.082977949 7.991012866 0.999999998 0.946093621 0.057787663 0.068758367 0 0 0.068072096 0.016044747 0.826079891 0.082977949 -0.053906377 VKEYQVETIVDTLCTNMLSDKEQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKEYQVETIVDTLCTNMLSDKEQLR 25 2 Q86VP6;Q86VP6-2 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 281.28 1.54E-53 638850000 702640 770180 480840 466330 592100 744070 609320 672770 718630 609750 FALSE TRUE 675180.052 748215.2205 567738.4842 490397.3472 611145.4342 759115.6052 616777.0404 658877.0644 637054.1351 568451.0894 1.187753994 1.316235001 0.998746409 0.862690487 1.075106453 1.335410591 1.085013385 1.159074328 1.120684166 1 19.1166767 -0.079795171 0.009253787 2.87E-05 2.175368878 0.047854918 0.134227791 20519.04052 55.63680084 6766.705827 6311.159024 0.832156153 0.079795171 2.175340201 ELMDEEDVLQECK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELMDEEDVLQECK 13 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PNN8;E9PKG4;E9PJD8 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 182.08 9.63E-07 0 50787 48643 39805 39942 59000 46620 40881 50703 52882 44666 FALSE TRUE 48802.18789 47255.74927 46998.64896 42003.41141 60897.78858 47562.68834 41381.31391 49655.96533 46879.05706 41640.73204 1.171981987 1.134844345 1.128670094 1.008709726 1.462457205 1.142215471 0.993770087 1.192485408 1.125798101 1 15.34570781 -0.079367516 0.538735119 0.985822504 1.160273542 0.130612088 0.12019968 10.45375571 3.430858214 0.439139248 0.054556377 0.832975991 0.079367516 0.174451038 DYGPGSYGGMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYGPGSYGGMDR 12 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-2 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 176.65 5.68E-05 322990000 84267 80113 79790 89666 86501 81336 84707 83519 89648 98075 FALSE TRUE 80973.75248 77828.25568 94209.82792 94293.67301 89283.38322 82980.66965 85743.6696 81794.30346 79471.53488 91432.29289 0.88561437 0.851211899 1.030378053 1.031295071 0.976497257 0.907564133 0.937783215 0.894588781 0.869184534 1 16.48041618 -0.079288392 8.129300201 0.999999999 0.933123476 0.103821205 0.060159892 0 0 0.062644469 0.014765443 0.833127765 0.079288392 -0.066876523 TDDVHAK ddPTM_BT-474_Pertuzumab_2h_R1 4 TDDVHAK 7 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 105.95 0.0078123 1057850000 4406770 3884380 3119940 3486190 3536680 3605340 4043790 3855600 3876930 4541590 FALSE TRUE 4234548.556 3773601.286 3683782.561 3666112.684 3650440.524 3678242.445 4093279.112 3775980.513 3436837.16 4233984.064 1.000133324 0.891264877 0.870051116 0.865877771 0.862176255 0.868742629 0.966767718 0.891826813 0.811726522 1 22.01358441 -0.078729363 7.999026717 0.999999999 0.892320343 0.284855949 0.051305433 6607347.965 826018.9219 0.048589285 0.011784633 0.834200867 0.078729363 -0.107679657 EISTPT(ph)HWSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.156)T(0.156)PT(0.368)HWS(0.319)K 130.44 0.0099802 0 449620 616860 448300 626850 538650 524090 548250 544700 555560 619080 TRUE FALSE 432048.3533 599267.7568 529317.7824 659201.8036 555976.1664 534687.4589 554959.6475 533451.7547 492495.1579 577149.1602 0.748590457 1.038323882 0.917124755 1.142168869 0.96331452 0.926428549 0.961553244 0.9242875 0.853323875 1 19.1385847 -0.078242138 7.966506644 0.999999999 0.949048782 0.025804364 0.098547462 0 0 0.090268253 0.021276431 0.835137263 0.078242138 -0.050951216 AFFSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFFSGR 6 0 P51659-3;P51659;P51659-2;A0A2R8Y7L2;E7ET17;E7EPL9 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 102.81 0.08195 356200000 171980 214110 170820 190790 173600 148880 214750 194030 217930 251640 FALSE TRUE 165258.8315 208003.7924 201690.9739 200636.6948 179184.0017 151890.4556 217378.1747 190023.2127 193191.5 234596.1987 0.704439511 0.886646048 0.859736752 0.855242736 0.763797549 0.647454888 0.926605699 0.810001244 0.823506524 1 17.83982011 -0.076278694 0.723913632 1.007612388 0.807138387 0.345463617 0.079608723 6.791152374 3.528772875 0.225509782 0.028039617 0.838921463 0.076278694 -0.200474001 DYYINIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYYINIR 7 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 153.15 0.0041078 3270500000 3416100 3544300 3289200 4012200 3810700 3329500 3822100 3612500 3817700 3956300 FALSE TRUE 3282595.035 3443220.034 3883631.608 4219270.123 3933274.626 3396824.771 3868876.003 3537900.613 3384330.701 3688336.277 0.889993425 0.93354287 1.052949437 1.143949414 1.066408898 0.920963957 1.048948825 0.959213138 0.917576502 1 21.81453877 -0.073256703 7.711754604 0.999999975 0.996941948 0 0.07825013 10774217.62 1397116.165 0.079324247 0.019238956 0.844779364 0.073256703 -0.003058028 RKPNAGGS(ph)PAPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 RKPNAGGSPAPVR 13 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR 121.13 0.0001306 2528990000 2595540 2464630 1896020 2148940 2106180 2150670 2276040 2533680 2590430 2449870 TRUE FALSE 2494103.427 2394341.166 2238672.991 2259847.051 2173927.192 2194158.021 2303894.858 2481358.623 2296375.246 2283938.123 1.092018826 1.048338894 0.980181104 0.989451959 0.951832789 0.960690659 1.008737862 1.086438638 1.005445473 1 21.12309213 -0.070823035 7.174745096 0.999999999 1.014697428 0.00749659 0.045908243 0 0 0.0490554 0.011562469 0.849526567 0.070823035 0.014697429 EKEYEIER ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEYEIER 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 105.98 0.0039075 2207900000 4005900 3664400 3296800 3044000 3270500 3301500 3642200 3814200 4204200 3850200 FALSE TRUE 3849344.999 3559894.9 3892605.097 3201101.205 3375698.603 3368258.592 3686774.333 3735435.437 3726956.841 3589422.525 1.072413452 0.991773712 1.084465557 0.891815099 0.940457296 0.938384536 1.027121858 1.040678664 1.038316558 1 21.77532033 -0.07040029 7.30465064 1 1.001820996 0 0.059403139 0 0 0.059449903 0.014012477 0.850353904 0.07040029 0.001820995 ISELGSQLSDEAVEDGLFHEFKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ISELGSQLSDEAVEDGLFHEFKR 23 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 173.09 2.76E-12 23847000 20419 16768 13019 13140 17162 20256 13950 15445 20508 15806 FALSE TRUE 19621.00291 16289.79306 15371.82291 13818.15697 17714.03132 20665.5902 14120.72427 15126.05535 18180.01782 14735.44554 1.331551384 1.105483578 1.043186842 0.937749519 1.202137476 1.402440811 0.958282818 1.026508178 1.233760986 1 13.84700306 -0.06966772 0.015510326 2.52E-09 2.1291293 0.065387117 0.14746256 4699.000939 21.49310367 1560.316705 1389.381288 0.851789496 0.06966772 2.129129298 VTYVVLDEADR ddPTM_BT-474_Pertuzumab_2h_R1 3 VTYVVLDEADR 11 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;; 159.4 6.68E-05 744955000 553970 549810 464170 571380 578490 482610 580300 552460 572430 610570 FALSE TRUE 532320.24 534129.9571 548055.8444 600868.9903 597097.6562 492368.7049 587401.885 541051.5079 507450.1462 569215.5501 0.935182182 0.9383615 0.96282655 1.055608882 1.048983388 0.864995176 1.031949821 0.950521306 0.891490308 1 19.11861555 -0.068517317 7.987078327 0.999999998 0.967632245 0.027464961 0.060870578 0 0 0.057973736 0.013664541 0.854048792 0.068517317 -0.032367753 TPSPKEEDEEPES(ph)PPEKK ddPTM_BT-474_Pertuzumab_2h_R1 9 TPSPKEEDEEPESPPEKK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK 209.41 4.14E-16 47452390000 11208540 7780010 6149540 4915000 7200410 6893660 7125690 9339390 10782770 7858560 TRUE FALSE 10770497.87 7558131.732 7260898.674 5168663.739 7432017.727 7033054.528 7212896.326 9146528.333 9558755.155 7326292.732 1.470115686 1.031644791 0.991074059 0.705495116 1.0144309 0.959974545 0.984521994 1.24845248 1.30471925 1 22.80465192 -0.066659809 9.395973726 0.999999973 1.067550557 0.010701884 0.202618666 0 0 0.20220714 0.04766068 0.857709443 0.066659809 0.067550584 SLEDQVEMLR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLEDQVEMLR 10 0 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 225.87 7.67E-09 2792380000 1488040 1942470 1654200 1990390 1792480 1920940 1857450 1777470 1884180 2016580 FALSE TRUE 1429885.752 1887072.657 1953150.737 2093114.266 1850136.747 1959782.723 1880182.029 1740764.623 1670295.786 1879995.24 0.760579453 1.003764593 1.038912597 1.113361471 0.984117782 1.042440258 1.000099356 0.925940974 0.888457454 1 20.84229758 -0.066475611 6.987744627 0.999999992 0.979739444 0.00294512 0.092496693 8841059.362 1265223.608 0.089626736 0.022406684 0.858073301 0.066475611 -0.020260547 SQET(ph)PEKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQETPEKPR 9 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 S(0.006)QET(0.994)PEKPR;S(0.007)QET(0.993)PEKPR 81.494 0.03415 767740000 1424180 1430760 1052480 1170350 1144180 1128400 1238240 1513040 1376080 1368510 TRUE FALSE 1368521.471 1389956.126 1242686.548 1230751.904 1180983.589 1151217.021 1253393.952 1481795.195 1219873.167 1275819.599 1.072660643 1.089461337 0.974029988 0.964675496 0.925666599 0.902335269 0.982422556 1.161445707 0.956148635 1 20.28299292 -0.064465223 7.265945192 1.000000001 1.008887652 0 0.076657553 5578434.275 767750.7582 0.082313282 0.019963903 0.862054606 0.064465223 0.008887652 AAEDDEDDDVDTKK ddPTM_BT-474_Pertuzumab_2h_R1 15 AAEDDEDDDVDTKK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;;;;;;;; 266.35 1.18E-24 90466554000 21762716 15871404 15365446.9 11424962.8 14431934.1 13655421.8 15844965.8 19413386 22563507 17250841 FALSE TRUE 20912205 15418767.1 18142324.96 12014606.5 14896150.37 13931543.78 16038881.23 19012492.79 20002192.28 16082426.17 1.300314068 0.958733896 1.128083833 0.747064303 0.926237758 0.866258836 0.99729239 1.182190584 1.243729775 1 23.93898173 -0.057266763 7.930033204 1.000015183 1.031319722 0.003066269 0.165866307 0 0 0.164742469 0.038830172 0.876462294 0.057266763 0.031304539 YLHDESGLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 YLHDESGLNR 10 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310 Q15019-2 2-Sep Septin-2 0 ;;; 251.56 1.08E-14 4390430000 1796370 2091330 1951890 2379010 2120670 1928410 2235840 1946460 2301130 2439940 FALSE TRUE 1726165.874 2031687.316 2304639.943 2501790.991 2188883.276 1967403.771 2263202.879 1906264.921 2039915.37 2274680.691 0.758860741 0.893174732 1.013170751 1.099842717 0.962281557 0.864914262 0.9949541 0.83803627 0.896791966 1 21.11723261 -0.055070292 8.091234364 1 0.927416309 0.055795319 0.092346219 0 0 0.093117132 0.021947919 0.880906283 0.055070292 -0.072583691 GIVDLIEER ddPTM_BT-474_Pertuzumab_2h_R1 1 GIVDLIEER 9 0 F8WAU4;C9IZ01;Q96RP9;Q96RP9-2 F8WAU4 GFM1 "Elongation factor G, mitochondrial" 0 103.56 0.0079146 10919000 12754 17478 12191 18185 13728 15634 16912 13121 18696 16043 FALSE TRUE 12255.55958 16979.54455 14394.18489 19123.53003 14169.57359 15950.13019 17118.97411 12850.04676 16573.70846 14956.39332 0.819419449 1.135269994 0.96241016 1.278619091 0.947392415 1.06644228 1.144592399 0.85916748 1.108135371 1 13.8684747 -0.054971066 7.442039105 1.000000008 1.033869087 0.006234293 0.133459636 8128051.325 1092180.542 0.119830214 0.029063095 0.881107573 0.054971066 0.033869079 YQQEVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YQQEVDR 7 0 P33176;O60282;O60282-2;Q12840;J3KNA1;A0A0G2JMZ6 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ; 160.52 0.0031254 762360000 1474520 1675360 1296850 1543840 1496990 1527450 1503200 1588170 1645610 1687340 FALSE TRUE 1416894.128 1627580.373 1531219.643 1623517.767 1545142.043 1558336.086 1521596.611 1555373.735 1458807.252 1573054.959 0.90072767 1.034662117 0.973405052 1.032079495 0.9822556 0.990643128 0.967287635 0.988759945 0.927372082 1 20.58513765 -0.054763277 7.861814348 0.999999999 0.981318191 0.020795705 0.039025615 4661591.801 592940.7536 0.034299108 0.008318756 0.881529241 0.054763277 -0.018681808 LTEYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTEYSR 6 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 144.9 0.026088 2097850000 2027860 2198230 1777920 2138470 2097800 2040830 2043550 2141510 2205460 2328690 FALSE TRUE 1948608.989 2135538.633 2099229.694 2248836.693 2165277.642 2082096.981 2068559.576 2097287.07 1955105.427 2170965.752 0.897577029 0.983681401 0.966956614 1.035869263 0.997379917 0.959064867 0.952829207 0.966061794 0.900569447 1 21.04990554 -0.050322685 7.861167354 0.999999999 0.965758861 0.07093532 0.039177176 0 0 0.037667853 0.008878398 0.890588976 0.050322685 -0.034241138 LPPVLSHPIFDNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPPVLSHPIFDNR 13 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4;E9PQS6;E9PI38 Q04206 RELA Transcription factor p65 0 ; 169.62 2.82E-05 1650900000 1083520 1127350 1058170 1158020 1128160 1079210 1170230 1168050 1170580 1245600 FALSE TRUE 1041174.841 1095199.082 1249404.858 1217785.551 1164448.291 1101032.366 1184551.625 1143929.359 1037700.666 1161234.403 0.896610399 0.943133513 1.075928215 1.048699167 1.002767648 0.948156861 1.020079686 0.985097717 0.893618604 1 20.14722779 -0.047062123 7.840407189 0.999999998 0.984828463 0.00340722 0.057557022 7702546.273 982416.6592 0.056678808 0.01374663 0.897300433 0.047062123 -0.015171535 MS(ph)VDAVEIETLR ddPTM_BT-474_Pertuzumab_2h_R1 2 MSVDAVEIETLR 12 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 1 MS(1)VDAVEIETLR;MS(1)VDAVEIETLR 244.58 2.18E-16 260810000 209258 210690 199313 254430 242240 205652 214180 231240 214021 257700 TRUE FALSE 201079.966 204681.3275 235333.2928 267561.1628 250031.8696 209810.4243 216801.1989 226464.8132 189726.2333 240245.7495 0.836976165 0.851966488 0.979552368 1.113697801 1.040733791 0.873315864 0.902414296 0.942638168 0.789717336 1 17.87415138 -0.045382574 7.760850714 0.999999997 0.932292223 0.049855248 0.093404492 12952781.51 1668989.89 0.095343846 0.023124279 0.900777286 0.045382574 -0.067707774 TKFENLCK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKFENLCK 8 1 P07900;P07900-2;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ; 128.86 0.0010174 3885400000 5774400 5944000 4265500 3715000 3731900 2027910 5374700 5177400 6046200 6269700 FALSE TRUE 5548730.064 5774482.94 5036370.736 3906731.595 3851939.953 2068915.73 5440477.186 5070484.881 5359860.724 5845047.635 0.949304507 0.987927439 0.861647509 0.668383192 0.659009164 0.353960457 0.930784063 0.867483928 0.916991795 1 22.47878335 -0.043327654 9.179831205 1 0.796730273 0.097840578 0.182475757 25723642.88 2802191.179 0.188466475 0.045709834 0.905049527 0.043327654 -0.203269727 IFYPEIEEVQALDDTER ddPTM_BT-474_Pertuzumab_2h_R1 6 IFYPEIEEVQALDDTER 17 0 P33316-2;H0YNW5;P33316;A0A0C4DGL3;H0YKC5 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;;;; 283.21 1.01E-35 2933600000 163312 142947 139202 169063 148440 155421 154988 153687 166252 174300 FALSE TRUE 156929.5865 138870.2915 164358.8979 177788.3617 153214.7074 158563.7191 156884.7895 150513.3097 147379.7699 162494.5057 0.965753185 0.854615305 1.011473571 1.094119219 0.942891618 0.975809726 0.965477502 0.92626707 0.906983096 1 17.31003141 -0.043262449 7.849365444 0.999999999 0.960360118 0.037470636 0.060246661 0 0 0.060169291 0.014182038 0.905185423 0.043262449 -0.039639881 TAAEAEEILENTNGDDLIEDDEMEGISHK ddPTM_BT-474_Pertuzumab_2h_R1 2 TAAEAEEILENTNGDDLIEDDEMEGISHK 29 0 Q7Z4Q2;Q7Z4Q2-2;Q7Z4Q2-3 Q7Z4Q2 HEATR3 HEAT repeat-containing protein 3 0 ; 174.86 7.92E-13 112862000 136415 138321 125246 143437 137470 145020 153982 160327 180965 194731 FALSE TRUE 131083.751 134376.2205 147880.7383 150839.8008 141891.8474 147952.4038 155866.4778 157016.1914 160422.6119 181541.6959 0.722058645 0.740194807 0.814582774 0.830882404 0.781593709 0.814977535 0.858571233 0.864904289 0.883668135 1 17.46994141 -0.038904545 0.034716326 1.848385596 8.89E-13 0.914908906 0.02189245 73.11020983 0.766319081 22.93871118 17.79832399 0.914314179 0.038904545 -1.848385596 NNRPAFFS(ph)PSLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 NNRPAFFSPSLKR 13 2 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 NNRPAFFS(0.5)PS(0.5)LKR;NNRPAFFS(0.998)PS(0.002)LKR 122.31 0.00012343 1006330000 1158740 1052550 864340 856350 867490 980630 908930 1152040 1186830 1082370 TRUE FALSE 1113455.16 1022532.305 1020545.465 900546.3261 895393.6037 1000459.01 920053.7572 1128249.971 1052106.034 1009060.116 1.103457705 1.013351225 1.011382225 0.89246053 0.887354073 0.991476122 0.911792809 1.118119678 1.042659419 1 19.9445807 -0.038568437 7.46530501 0.999999483 0.996532692 0.000127476 0.076684289 0 0 0.079075148 0.018638191 0.915022057 0.038568437 -0.003466791 LLEQYKEESKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEQYKEESKK 11 2 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 112.51 0.00085309 9539000000 13709300 10269800 9331810 6708700 9789000 9697500 10242500 11862100 12816300 11055800 FALSE TRUE 13173525.4 9976915.359 11018275.65 7054936.811 10103872.08 9893590.094 10367850.78 11617143.49 11361447.35 10306980.82 1.278116806 0.967976514 1.069010979 0.684481415 0.98029406 0.959892161 1.005905702 1.127114108 1.102306054 1 23.29711846 -0.036200302 8.202726806 0.999999999 1.014266454 0.000472155 0.144284807 0 0 0.140140649 0.033031468 0.920025147 0.036200302 0.014266455 SYSS(ph)PDITQAIQEEEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.292)S(0.705)PDIT(0.002)QAIQEEEKR 212.32 1.78E-12 151330000 187370 159100 129780 127850 131980 143770 123850 201110 170950 155120 TRUE FALSE 180047.3733 154562.6238 153234.1329 134448.3538 136225.2566 146677.1279 125365.7133 196957.0082 151544.4727 144613.5842 1.245023932 1.068797407 1.059610919 0.929707638 0.941994884 1.014269363 0.866901363 1.361953715 1.047926953 1 17.14184355 -0.035653287 9.032911288 0.999999999 1.06467153 0.014870185 0.140051751 0 0 0.141726474 0.03340525 0.921184694 0.035653287 0.06467153 LMDQNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMDQNLK 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 85.064 0.049054 103980000 284790 264160 261020 272680 287120 256150 293330 275230 293180 308550 FALSE TRUE 273660.0919 256626.4154 308192.1204 286753.0475 296355.4756 261329.5285 296919.8603 269546.4043 259899.4355 287651.6337 0.951359422 0.892143084 1.071407509 0.99687613 1.030258274 0.908493114 1.032220316 0.937058486 0.9035215 1 18.13396314 -0.033246314 7.879131828 0.999999998 0.971115786 0.023379435 0.058507359 7480197.284 949368.1829 0.055034025 0.013347712 0.926304314 0.033246314 -0.028884212 EYWDYEAHVPSWGNQDDYQLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EYWDYEAHVPSWGNQDDYQLVR 22 0 P19784;H3BNI9 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ; 210.38 4.56E-23 958640000 564190 686840 626340 730350 692660 648880 694320 622540 733060 780130 FALSE TRUE 542140.8311 667251.9957 739533.5709 768043.451 714940.038 662000.7982 702817.2959 609684.3314 649846.102 727291.1002 0.745424811 0.917448317 1.016832972 1.056033067 0.983017718 0.910228103 0.966349369 0.838294778 0.893515818 1 19.4721734 -0.028832935 7.835881003 0.999999999 0.928062668 0.06461523 0.084724023 5846819.583 746159.8237 0.086048661 0.020869866 0.935765578 0.028832935 -0.071937332 DVDFMYVELIQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVDFMYVELIQR 12 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 190.56 1.51E-05 383343000 264990 259373 205864 259511 269406 237519 239079 263973 272674 281048 FALSE TRUE 254633.8978 251975.936 243068.2042 272904.3938 278071.6887 242321.7969 242004.9203 258521.8653 241721.1907 262012.3686 0.971839227 0.961694814 0.927697442 1.041570653 1.061292221 0.924848694 0.923639298 0.986678097 0.922556412 1 17.99927539 -0.021022078 8.149863553 0.999999998 0.970408572 0.036884691 0.046950709 0 0 0.046627648 0.010990242 0.952747728 0.021022078 -0.029591426 RQS(ph)SSYDDPWK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQSSSYDDPWK 11 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCF0;H7C1V2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 RQS(0.68)S(0.188)S(0.131)Y(0.002)DDPWK;RQS(0.995)S(0.004)SYDDPWK 138.21 3.81E-05 519270000 1027940 1008240 941400 1219330 1088400 1019420 1101470 1302960 1453790 1545800 TRUE FALSE 987766.9684 979485.9824 1111531.921 1282259.767 1123409.374 1040033.371 1114950.119 1276053.421 1288761.854 1441101.589 0.685424939 0.67967865 0.771307123 0.889777499 0.77954905 0.721693306 0.773679058 0.88547083 0.894289385 1 20.45874061 -0.018883664 0.040721073 1.830191781 4.91E-10 0.69142326 0.055347304 118.6806322 1.480285625 38.0152597 28.35189899 0.957450513 0.018883664 -1.83019178 IDS(ph)TEVIYQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDSTEVIYQPR 11 0 K7EMR0;K7EQN8;K7EP59;Q15831-2;Q15831 K7EMR0 STK11 Serine/threonine-protein kinase STK11 1 IDS(0.839)T(0.161)EVIYQPR;IDS(0.622)T(0.378)EVIYQPR 174.9 1.10E-05 776380000 488030 429080 346580 380030 366570 367640 393170 495320 434290 421970 TRUE FALSE 468957.2481 416843.0585 409214.7156 399643.3938 378361.057 375073.9327 397981.7321 485091.4689 384991.2199 393389.596 1.192093672 1.059618919 1.040227601 1.015897212 0.961797314 0.953441414 1.011673252 1.233107011 0.97865125 1 18.58559928 -0.017974499 7.166703992 0.999999999 1.054743967 0.024438046 0.088864139 2069915.682 288823.9307 0.091676196 0.022234744 0.959456968 0.017974499 0.054743968 DAESIHQYLLQR ddPTM_BT-474_Pertuzumab_2h_R1 5 DAESIHQYLLQR 12 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;;; 234.63 5.01E-16 2551860000 2468230 3092730 2385690 3187130 2843440 2754470 2912760 2704680 3024180 3313220 FALSE TRUE 2371768.843 3004528.368 2816837.252 3351618.161 2934901.83 2810167.271 2948407.228 2648827.413 2680887.765 3088812.658 0.767857784 0.972713046 0.911948235 1.085083018 0.950171524 0.909788835 0.954543883 0.857555218 0.867934725 1 21.55862094 -0.015661377 7.853890633 0.999999998 0.923283259 0.083777769 0.078850471 9804174.257 2496641.105 0.075592129 0.018333784 0.964580821 0.015661377 -0.076716739 (ac)S(ph)DQDHSMDEMTAVVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SDQDHSMDEMTAVVK 15 0 P08047;H3BUU5;P08047-3 P08047 SP1 Transcription factor Sp1 1 S(1)DQDHSMDEMTAVVK;S(0.851)DQDHS(0.149)MDEMTAVVK;S(0.907)DQDHS(0.093)MDEMTAVVK 131.37 4.69E-18 221174000 182549 189524 157551 186279 189150 184522 171837 180237 189207 225237 TRUE FALSE 175414.7833 184118.9611 186023.9704 195892.8815 195234.1815 188253.1613 173939.9926 176515.043 167729.0146 209981.4974 0.835382095 0.876834213 0.885906486 0.932905442 0.929768499 0.896522616 0.828358664 0.840621889 0.798779972 1 17.67990268 -0.00910176 8.090463277 0.999999998 0.870590822 0.468189044 0.041724407 3031255.648 374670.2038 0.044567232 0.010809141 0.979260507 0.00910176 -0.129409176 ALINLSPPS(ph)MVVQKPDYLNDFTHEIPNIQTDSYESMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALINLSPPSMVVQKPDYLNDFTHEIPNIQTDSYESMAK 38 1 Q9H5V7 Q9H5V7 IKZF5 Zinc finger protein Pegasus 1 ALINLS(0.136)PPS(0.713)MVVQKPDY(0.124)LNDFT(0.027)HEIPNIQTDSYESMAK 92.846 0.00024159 94250000 50355 42773 41205 43119 38541 39741 49927 48115 50654 59711 TRUE FALSE 48387.07093 41553.15592 48651.6601 45344.37676 39780.70627 40544.59025 50538.02156 47121.40844 44903.97028 55666.72078 0.869227974 0.746463153 0.873981068 0.81456885 0.714622771 0.728345225 0.907867768 0.846491544 0.806657365 1 15.76452748 -0.005761306 0.526352181 1.016631396 0.800176896 0.454370974 0.061849314 3.927470092 1.312761514 0.205786422 0.029771476 0.986821706 0.005761306 -0.216454501 WGEPEPFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 WGEPEPFLR 9 0 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ; 134.81 0.00055468 225996000 354220 380360 289890 351320 361330 346920 335800 375760 369500 383190 FALSE TRUE 340376.6908 369512.5052 342279.5716 369451.6673 372952.5076 353934.9601 339909.6208 368000.4247 327555.9091 357236.2 0.952805709 1.034364673 0.958132383 1.034194371 1.043994163 0.990758944 0.951498255 1.030131954 0.9169169 1 18.44651876 0.004997697 7.970518761 0.999999998 0.994511496 0 0.042223586 0 0 0.037948225 0.008944483 1.01157409 -0.004997697 -0.005488502 EGEFVAQFK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGEFVAQFK 9 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 122.13 0.0013826 131440000 60729 63154 63065 60792 69192 60457 65909 64131 66898 75455 FALSE TRUE 58355.64354 61352.90975 74462.24837 63929.48241 71417.62352 61679.48196 66715.61406 62806.67244 59304.0195 70344.36564 0.829570969 0.872179445 1.058538913 0.908807434 1.015257197 0.876821923 0.948414467 0.892845815 0.843052872 1 16.10214725 0.006183163 7.901371863 0.999999997 0.920078007 0.113786251 0.069420336 2996558.603 252830.2067 0.065554589 0.015899323 1.014339092 -0.006183163 -0.07992199 FNDILGR ddPTM_BT-474_Pertuzumab_2h_R1 4 FNDILGR 7 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A087WY74 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ;;; 133.6 0.0075747 510475000 1488350 1558530 1301530 1476140 1408290 1296020 1549790 1597000 1642560 1749820 FALSE TRUE 1430183.637 1514082.25 1536745.423 1552323.762 1453588.927 1322226.412 1568756.794 1564021.392 1456103.475 1631303.133 0.87671237 0.928142796 0.942035476 0.951585105 0.891059974 0.810533852 0.961658665 0.958755832 0.892601409 1 20.63759346 0.008555159 0.534398794 1.006721657 0.910984994 0.246030764 0.04479582 6.455209095 2.235306169 0.147364628 0.021877222 1.019894286 -0.008555159 -0.095736662 FENYGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FENYGDK 7 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 116.37 0.012727 404500000 512230 501060 477950 491820 415660 500930 460210 547030 562230 665490 FALSE TRUE 492211.4853 486770.2594 564326.1969 517202.8891 429030.0814 511059.1478 465842.1876 535733.6393 498408.0075 620415.7695 0.79335747 0.784587181 0.909593574 0.833639173 0.691520271 0.823736554 0.750854847 0.86350745 0.803345163 1 19.24287583 0.011858904 0.873359363 1.003280758 0.804047842 0.515180819 0.05646223 4.866080108 3.561128806 0.105904137 0.018190908 1.027682365 -0.011858904 -0.199232916 KVVVS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 5 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.5)PT(0.5)K;KVVVS(0.547)PT(0.453)K;KVVVS(0.639)PT(0.361)K;KVVVS(0.632)PT(0.368)K;KVVVS(0.5)PT(0.5)K 96.64 0.0053885 50751590000 52354080 43685200 38324180 37210680 37062570 35477540 43716670 48958990 47326790 50086810 TRUE FALSE 50308024.67 42439340.87 45250211.84 39131127.65 38254721.22 36194920.17 44251687.68 47947969.75 41954451.21 46694385.75 1.077389152 0.908874594 0.969071787 0.838026393 0.819257403 0.775145011 0.947687543 1.026846568 0.898490269 1 25.47674576 0.012157617 17.30277104 1 0.918927475 0.072304325 0.088187001 0 0 0.091119243 0.021477012 1.028389459 -0.012157617 -0.081072525 GNAEGSS(ph)DEEGKLVIDEPAKEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.111)S(0.889)DEEGKLVIDEPAKEK;GNAEGS(0.096)S(0.904)DEEGKLVIDEPAKEK;GNAEGS(0.149)S(0.851)DEEGKLVIDEPAKEK 212.77 6.74E-26 2223460000 4433920 3177740 2612990 1841440 2864430 2905800 2758620 3599030 4415970 2993350 TRUE FALSE 4260637.504 3087113.967 3085215.419 1936476.939 2956566.992 2964557.267 2792380.817 3524708.773 3914687.599 2790607.738 1.526777643 1.106251489 1.105571154 0.6939266 1.059470649 1.062333923 1.000635374 1.263061348 1.402808265 1 21.41214792 0.020185571 9.349769485 0.999999985 1.120796377 0.030148637 0.216533913 0 137306864.3 0.212666798 0.051579276 1.047576073 -0.020185571 0.120796392 IVLLDSSLEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 IVLLDSSLEYK 11 0 P49368;P49368-2;B4DUR8;Q5SZX6 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 105.4 0.0057493 129858000 556080 515070 485780 483180 520820 531780 546340 552320 643730 662040 FALSE TRUE 534347.7788 500380.7079 573571.2521 508116.9777 537572.6483 542532.956 553026.2723 540914.399 570656.4691 617199.4411 0.865761929 0.81072774 0.929312656 0.823262213 0.870986933 0.879023732 0.896025232 0.87640131 0.924590061 1 19.23537723 0.025338632 0.334477231 1.031690736 0.851132627 0.644762897 0.030862846 2.87519141 0.472283241 0.149843979 0.028458717 1.060079979 -0.025338632 -0.180558109 NKEEAAEYAK ddPTM_BT-474_Pertuzumab_2h_R1 3 NKEEAAEYAK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;; 150.06 2.03E-05 9906350000 6106570 4776040 4860830 3677270 4695660 4405480 4999200 5789840 5948710 5262420 FALSE TRUE 5867918.493 4639832.015 5739290.11 3867054.345 4846700.168 4494561.824 5060381.705 5670277.781 5273437.38 4905991.606 1.196071858 0.945748054 1.169853226 0.788230934 0.987914484 0.916137284 1.031469703 1.155786278 1.074897351 1 22.22611333 0.027191695 8.612065336 1.000000001 1.028968937 0.00536524 0.120526774 0 0 0.115462004 0.027214655 1.064612827 -0.027191695 0.028968936 DDPDGKQEAKPQQAAGMLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 DDPDGKQEAKPQQAAGMLSPK 21 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DDPDGKQEAKPQQAAGMLS(1)PK;DDPDGKQEAKPQQAAGMLS(1)PK;DDPDGKQEAKPQQAAGMLS(1)PK 175.11 1.11E-12 2125106000 3068930 2052381 1724523 1144985 1820616 1721098 2027246 2547700 2765330 2059556 TRUE FALSE 2948992.823 1993849.103 2036182.668 1204077.813 1879177.767 1755899.781 2052056.043 2495089.105 2451421.332 1920060.438 1.535885415 1.038430387 1.060478425 0.627104121 0.978707613 0.914502349 1.068745547 1.29948467 1.276741754 1 20.87272029 0.032087887 9.963173329 0.999999009 1.079758159 0.011647308 0.232325568 0 0 0.234103874 0.055178812 1.076683076 -0.032087887 0.07975915 DLHVSTGEFTDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLHVSTGEFTDLK 13 0 O43264;O43264-2 O43264 ZW10 Centromere/kinetochore protein zw10 homolog 0 171.73 2.46E-05 212290000 200520 285180 228120 308100 239320 295240 273570 199980 285060 350660 FALSE TRUE 192683.4567 277046.9456 269346.3585 324001.0779 247017.9451 301209.9551 276918.0315 195850.3431 252701.1839 326909.4859 0.589409194 0.847472948 0.823917231 0.991103323 0.755615716 0.921386402 0.847078606 0.599096544 0.773000463 1 18.31853171 0.033506417 10.36638208 0.999999443 0.793113782 0.209876253 0.119757503 0 0 0.119580578 0.028185412 1.080205582 -0.033506417 -0.206885661 KFGVVLDEIKPSSAPELQAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KFGVVLDEIKPSSAPELQAVR 21 2 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 185.41 2.03E-17 471200000 307910 251890 213740 201850 251560 274350 239460 261900 303650 247620 FALSE TRUE 295876.5368 244706.3438 252367.5726 212267.5027 259651.6559 279897.545 242390.5831 256491.6735 269180.925 230848.4768 1.281691527 1.060030143 1.093217404 0.919510086 1.124770929 1.212472999 1.049998624 1.111082373 1.166050254 1 17.81658669 0.047016554 0.007793937 6.40E-06 2.150714831 0.074873293 0.094947273 21297.38197 52.36723824 7419.889775 7028.93995 1.114337008 -0.047016554 2.150708434 SES(ph)ELIDELSEDFDR ddPTM_BT-474_Pertuzumab_2h_R1 6 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 SES(1)ELIDELSEDFDR;S(0.001)ES(0.999)ELIDELSEDFDR;SES(1)ELIDELSEDFDR;S(0.014)ES(0.986)ELIDELSEDFDR;SES(1)ELIDELSEDFDR;SES(1)ELIDELSEDFDR 278.2 1.38E-33 342623000 312489 334944 318029 358151 334602 343675 324089 332026 378335 381839 TRUE FALSE 300276.5844 325391.7251 375503.9148 376635.216 345364.7772 350624.344 328055.2981 325169.5471 335387.9969 355976.7044 0.84352875 0.914081514 1.054855304 1.058033325 0.970189265 0.984964296 0.921563951 0.913457378 0.942162767 1 18.44142331 0.048113321 8.200529313 0.999999999 0.957128409 0.042849758 0.062315045 8476155.014 2067221.254 0.065023489 0.015770513 1.11715471 -0.048113321 -0.04287159 FS(ph)PTMGR ddPTM_BT-474_Pertuzumab_2h_R1 6 FSPTMGR 7 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 FS(0.99)PT(0.01)MGR;FS(0.999)PT(0.001)MGR;FS(0.994)PT(0.006)MGR;FS(0.994)PT(0.006)MGR;FS(0.993)PT(0.007)MGR;FS(0.993)PT(0.007)MGR 167.23 0.0011476 12180030000 9850870 10584250 11016360 12046190 10824650 10591740 13597410 13603090 15365530 17567950 TRUE FALSE 9465887.11 10282397.55 13007261.31 12667895.31 11172834.7 10805912.24 13763819.17 13322181.44 13621299.45 16378057.1 0.57796154 0.627815466 0.794188299 0.773467526 0.682183157 0.659779861 0.840381682 0.813416473 0.831679812 1 23.96526089 0.053894469 0.051443657 1.776550105 4.27E-11 0.739384823 0.060428108 62.21227686 1.029815996 20.76217873 14.60363195 1.132125231 -0.053894469 -1.776550104 YFPSSCLDLNSPT(ph)SPTPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 YFPSSCLDLNSPTSPTPTR 19 0 A0A096LNR9;A0A1B0GUM4;A0A669KBC2;O76039;O76039-1 A0A096LNR9 CDKL5 Cyclin-dependent kinase-like 5 1 YFPSSCLDLNS(0.021)PT(0.565)S(0.326)PT(0.044)PT(0.044)R 72.063 0.033046 0 36921 41195 35090 42988 35875 37733 42335 41840 38418 42858 TRUE FALSE 35478.0865 40020.15893 41431.54357 45206.61583 37028.95196 38495.98711 42853.10839 40975.98938 34056.9497 39955.18949 0.887946896 1.001626058 1.036950246 1.131432898 0.926762016 0.963479028 1.072529224 1.025548618 0.852378631 1 15.28609528 0.059289199 7.853511748 0.999999952 0.998024349 0 0.080768819 10562909.74 2.13E-07 0.076482468 0.018549723 1.146275998 -0.059289199 -0.001975603 DCGEYAHTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DCGEYAHTR 9 0 Q5T8A0;Q9Y399 Q5T8A0 MRPS2 "28S ribosomal protein S2, mitochondrial" 0 101.66 0.004764 0 79384 115850 78813 152870 76485 95672 142630 102640 95582 102540 FALSE TRUE 76281.58552 112546.0714 93056.26229 160759.639 78945.20949 97606.55339 144375.5486 100520.4481 84731.93207 95594.87447 0.797967317 1.177323283 0.973444055 1.681676344 0.825830987 1.021043795 1.510285456 1.0515255 0.886364803 1 16.54464565 0.062418746 20.54907428 0.999999992 1.120831779 0.008698072 0.27425133 0 0 0.250737694 0.059099441 1.154565951 -0.062418746 0.120831787 TFSATVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ; 130.04 0.0083798 573980000 416830 450000 366120 469050 479110 422040 420780 462580 433300 471060 FALSE TRUE 400539.8228 437166.4406 432286.0283 493257.7267 494521.0083 430573.938 425929.6315 453027.5613 384113.6005 439154.6866 0.912070018 0.995472561 0.984359365 1.123198139 1.12607476 0.98046076 0.969885201 1.03158995 0.874665835 1 18.74436967 0.069658691 8.713396239 0.999999407 1.006574945 0 0.075817546 0 0 0.074325581 0.017518707 1.173974574 -0.069658691 0.006575538 EVHELYK ddPTM_BT-474_Pertuzumab_2h_R1 4 EVHELYK 7 0 P10155-3;P10155-5;P10155-4;P10155;D6RE09;H0Y9N5 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;; 114.6 0.005868 1877000000 3266640 3160880 2756260 2937810 2983340 2850720 3072520 3206620 3494100 3571640 FALSE TRUE 3138976.097 3070734.797 3254377.495 3089430.726 3079301.841 2908363.512 3110122.419 3140402.176 3097464.416 3329729.642 0.942712002 0.922217455 0.97736989 0.927832304 0.92479035 0.87345335 0.93404653 0.943140289 0.93024502 1 21.66697361 0.078054843 1.087333254 1.000357427 0.930007614 0.423338045 0.024264456 7.271832514 7.569030077 0.03204018 0.007468684 1.196891667 -0.078054843 -0.070349813 EAILEYILHQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAILEYILHQK 11 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2;M0QX85 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 0 ; 164.65 2.25E-05 388250000 734010 699160 615580 642020 714080 725970 747800 755540 885410 928910 FALSE TRUE 705324.0777 679220.6413 726828.9995 675154.7291 737049.0317 740649.6108 756951.8001 739937.835 784901.9687 865994.0983 0.814467534 0.784324792 0.839300176 0.779629712 0.85110168 0.855259421 0.874084248 0.854437503 0.906359489 1 19.72399767 0.083611241 0.214214732 1.080688961 0.773709932 0.876642326 0.021248151 2.420839744 0.212589323 0.203400345 0.059825924 1.212303169 -0.083611241 -0.306979029 EKEQLSSLQEELESLLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEQLSSLQEELESLLEK 18 1 Q15545 Q15545 TAF7 Transcription initiation factor TFIID subunit 7 0 83.758 0.0035978 52184000 101180 91173 80590 68231 83881 92911 83599 94939 105360 93743 FALSE TRUE 97225.77374 88572.83531 95154.40571 71752.41009 86579.10854 94789.72408 84622.10957 92978.47647 93399.97451 87393.70311 1.112503193 1.013492187 1.088801622 0.821024943 0.990679024 1.084628763 0.968286119 1.063903613 1.068726592 1 16.41524171 0.085331264 8.238642035 1.000000013 1.020748691 0.006558718 0.080556638 0 43557046.38 0.076561617 0.01856892 1.217114017 -0.085331264 0.020748678 FISADVHGIWSR ddPTM_BT-474_Pertuzumab_2h_R1 2 FISADVHGIWSR 12 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 164.11 5.82E-05 800130000 697520 914160 790330 934520 891920 760810 913090 810210 896980 1022860 FALSE TRUE 670260.1473 888089.0519 933160.2118 982750.6892 920609.4168 776194.0995 924264.6686 793478.8804 795158.5908 953580.7811 0.702887643 0.931320208 0.978585381 1.030589866 0.965423627 0.813978338 0.969256813 0.832104522 0.833865999 1 19.86299563 0.08644057 8.180461159 0.999999994 0.900780032 0.097695938 0.094124692 9830532.902 103209263.7 0.091194056 0.022798515 1.22022683 -0.08644057 -0.099219962 SSFFSDR ddPTM_BT-474_Pertuzumab_2h_R1 7 SSFFSDR 7 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;;;;;; 123.69 0.0098156 4993010000 4522110 4796780 4423960 4565830 4291260 3389890 4872840 4784860 5120570 5462400 FALSE TRUE 4345380.942 4659980.531 5223467.982 4801473.033 4429292.275 3458435.898 4932475.274 4686050.969 4539304.361 5092426.783 0.853302586 0.915080517 1.025732564 0.942865404 0.869780257 0.679133161 0.968590317 0.920199969 0.891383333 1 22.2799219 0.087819896 0.980136979 1.000776189 0.897793037 0.112951371 0.086576909 14.42331465 13.21064703 0.124496924 0.027829628 1.224108449 -0.087819896 -0.102983152 ARS(ph)PTDDK ddPTM_BT-474_Pertuzumab_2h_R1 3 ARSPTDDK 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.998)PT(0.002)DDK;ARS(0.999)PT(0.001)DDK;ARS(0.999)PT(0.001)DDK 84.213 0.010666 2071230000 2011650 1595190 1622860 1839180 1684040 1639790 2082710 2119640 2057070 2526030 TRUE FALSE 1933032.494 1549696.743 1916146.902 1934100.3 1738208.676 1672947.677 2108198.828 2075868.693 1823560.038 2354939.738 0.820841596 0.658062165 0.81367131 0.821295029 0.738111744 0.710399358 0.895224109 0.881495462 0.774355287 1 21.16725871 0.093623018 0.255324585 1.074093708 0.733042325 0.490244171 0.067037016 5.119296699 0.582030501 0.497501795 0.127160561 1.240574979 -0.093623018 -0.341051383 (ac)ADHSFS(ph)DGVPSDSVEAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADHSFSDGVPSDSVEAAK 18 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;E9PKT8;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 ADHS(0.086)FS(0.911)DGVPS(0.002)DS(0.001)VEAAK 79.97 4.86E-20 263090000 317720 301650 233770 254080 296800 293080 306820 323250 333200 380650 TRUE FALSE 305303.1511 293047.2373 276017.4392 267193.0992 306346.8415 299006.2784 310574.9549 316574.7745 295376.5329 354868.2365 0.8603282 0.825791681 0.777802606 0.752936081 0.863269265 0.842583944 0.875183866 0.892091041 0.832355513 1 18.43692392 0.102648522 0.299584821 1.04314081 0.800960646 0.651496822 0.037673297 3.166957609 0.461507156 0.222863154 0.050603705 1.266626359 -0.102648522 -0.242180164 LRQEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRQEAK 6 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 88.029 0.047213 216120000 333180 346430 291420 283850 268660 303940 312260 326570 357120 381480 FALSE TRUE 320158.9573 336550.1556 344086.0766 298499.5325 277301.6929 310085.875 316081.5313 319826.2154 316581.2348 355642.0198 0.900228149 0.946317186 0.967506811 0.839325827 0.779721398 0.871904493 0.888763177 0.89929254 0.890168251 1 18.44006627 0.118170056 1.12063936 1.000451625 0.885657397 0.321317437 0.049316225 9.001457308 10.11428039 0.06318129 0.016082449 1.312713814 -0.118170056 -0.114794228 ETEAVIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETEAVIHK 8 0 Q86Y56;H0Y650;E9PGY2;Q86Y56-3 Q86Y56 DNAAF5 "Dynein assembly factor 5, axonemal" 0 72.547 0.047521 0 249790 258970 220770 224130 235230 255030 268830 277650 298300 341110 FALSE TRUE 240027.9306 251584.4292 260668.05 235697.3762 242796.3866 260186.8813 272120.022 271916.4305 264438.2346 318006.3159 0.754789822 0.791130291 0.819694569 0.741171997 0.763495486 0.81818149 0.855706344 0.855066132 0.83155026 1 18.27869589 0.12787166 0.290210004 1.056207472 0.758786348 0.845477664 0.027639531 1.971694138 0.278307421 0.170654047 0.040859321 1.342368216 -0.12787166 -0.297421124 EKDLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKDLFR 6 1 O60524-4;O60524-3;O60524;O60524-5;O60524-2 O60524-4 NEMF Nuclear export mediator factor NEMF 0 ; 83.843 0.051552 446820000 1260510 1369420 1174190 1144530 1218230 1037230 1274420 1295360 1417170 1523550 FALSE TRUE 1211247.876 1330365.482 1386392.253 1203599.33 1257415.474 1058203.501 1290016.733 1268610.363 1256298.803 1420358.601 0.852776105 0.936640565 0.976086075 0.847391165 0.88528029 0.745025587 0.908233126 0.893162024 0.8844941 1 20.43782379 0.130173742 1.228439236 1.000261089 0.881410029 0.275987151 0.057845017 11.06113445 14.12232364 0.063928378 0.017105436 1.349502651 -0.130173742 -0.118851061 S(ph)LSDLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSDLFR 7 0 O75410-3;E7ET87;E7EVI4;O75410-2;O75410;O75410-9;O75410-7;H0YAY0;O75410-6;O75410-4;O75410-5;O75410-10;B4E3H6;H0YBT8;O75410-8 O75410-3 TACC1 Transforming acidic coiled-coil-containing protein 1 1 S(0.97)LS(0.03)DLFR 82.279 0.026141 21602000 19206 16187 21430 13667 18208 17500 15333 18888 17366 13722 TRUE FALSE 18455.40829 15725.36261 25302.87771 14372.35551 18793.67686 17853.86199 15520.64984 18497.9562 15394.68448 12792.59672 1.442663182 1.229254932 1.97793132 1.12349008 1.469105708 1.39564018 1.213252492 1.445989161 1.203405753 1 13.64302152 0.148481345 0.284808164 0.880319289 1.495283726 0.277437626 0.217872071 6.697671559 0.931531203 1.200604133 0.29835596 1.407606765 -0.148481345 0.614964437 QEPLGSDS(ph)EGVNCLAYDEAIMAQQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEPLGSDSEGVNCLAYDEAIMAQQDR 26 0 J3KR44;Q96FW1;F5H6Q1;F5GYJ8;F5H3F0 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 1 QEPLGS(0.387)DS(0.613)EGVNCLAYDEAIMAQQDR 173.25 2.52E-12 105570000 24938 27203 21012 24609 25108 22895 18852 27028 22364 17484 TRUE FALSE 23963.39539 26427.19707 24809.33581 25879.07344 25915.62162 23357.95259 19082.71642 26469.86235 19825.33248 16299.79311 1.470165617 1.621321013 1.522064461 1.587693369 1.589935618 1.433021415 1.170733658 1.623938548 1.216293504 1 13.99256603 0.165243546 0.306448752 0.872754077 1.591453509 0.612830432 0.129347424 3.097018478 0.488206617 0.65253056 0.156862385 1.462997372 -0.165243546 0.718699432 IISVT(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 8 IISVTPVK 8 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 IIS(0.001)VT(0.999)PVK;IISVT(1)PVK;IISVT(1)PVK;IISVT(1)PVK;IISVT(1)PVK;IISVT(1)PVK;IISVT(1)PVK;IISVT(1)PVK 197.79 0.0015781 4235970000 8612860 8199810 7368010 8037470 7929100 7060670 8602150 9715440 8486460 10043640 TRUE FALSE 8276259.909 7965959.447 8699573.307 8452284.79 8184146.703 7203441.585 8707425.685 9514812.769 7523112.639 9363375.317 0.883897059 0.850757251 0.929106547 0.902696357 0.874059452 0.769321034 0.929945174 1.016173383 0.803461613 1 23.15859726 0.199971636 0.351392332 1.01760672 0.873548751 0.174321811 0.067288383 6.708606165 1.348691112 0.281920364 0.065099714 1.584789684 -0.199971636 -0.144057969 YGQHPPDAVDEPQMLTNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YGQHPPDAVDEPQMLTNEK 19 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 244.74 1.56E-24 237600000 205510 191390 176030 165970 192840 194710 196420 201280 229860 238870 FALSE TRUE 197478.442 185931.7446 207842.5368 174535.7316 199042.8737 198647.1696 198823.8467 197123.4977 203767.2565 222691.1221 0.886781835 0.834931105 0.93332206 0.783757026 0.893806955 0.892030036 0.892823409 0.885187949 0.915021912 1 17.76468452 0.204691007 0.442670237 1.01424691 0.864109579 0.516531366 0.037413047 2.431171513 0.717787439 0.098913404 0.021117675 1.602105114 -0.204691007 -0.150137331 LASDLLEWIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LASDLLEWIR 10 0 O43707;O43707-2;K7EJH8;P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2W4 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ; 130.66 0.00063011 812990000 996610 943820 897650 1015700 859030 672110 1038310 1022620 1049080 1151270 FALSE TRUE 957661.3794 916903.1777 1059875.323 1068120.399 886661.4801 685700.5247 1051017.148 1001502.54 929992.8365 1073293.457 0.892264248 0.854289357 0.987498168 0.995180201 0.826112816 0.638875156 0.979244904 0.933111567 0.866485144 1 20.03361316 0.209962385 0.815887647 1.001063314 0.885659425 0.100834388 0.099875206 8.757514127 6.908937645 0.139036536 0.035039137 1.621669637 -0.209962385 -0.115403888 RLEEESAQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLEEESAQLK 10 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 79.286 0.044029 295570000 157180 166180 141390 151070 145800 138700 167350 179020 180630 222380 FALSE TRUE 151037.2318 161440.7091 166942.3182 158866.7408 150489.7894 141504.609 169398.0794 175323.1744 160125.6397 207318.0045 0.728529257 0.77871051 0.805247564 0.766294954 0.725888664 0.682548577 0.817092947 0.845672689 0.772367263 1 17.66148589 0.210245269 0.534244173 1.014643228 0.754733128 0.724459561 0.043460992 1.663060976 0.673763467 0.103001392 0.022052795 1.622726277 -0.210245269 -0.2599101 QLAEAHAQAK ddPTM_BT-474_Pertuzumab_2h_R1 3 QLAEAHAQAK 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 121.9 0.00050283 813350000 2058790 2133290 1790500 1919830 1895180 1868060 2193360 2122280 2287330 2384200 FALSE TRUE 1978330.211 2072450.658 2114083.179 2018912.656 1956140.186 1905833.453 2220202.996 2078454.176 2027681.888 2222716.01 0.890050821 0.932395613 0.951126086 0.908308865 0.880067529 0.857434528 0.998869395 0.935096597 0.912254142 1 21.0838922 0.224023001 0.437481402 1.008010077 0.911350662 0.306746769 0.037368764 4.161344308 1.222552216 0.109868712 0.024200784 1.675031586 -0.224023001 -0.096659414 QLLCGAAIGTHEDDKYR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLLCGAAIGTHEDDKYR 17 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 193.9 6.28E-11 581640000 413303 350638 334118 350418 355431 310875 376523 397012 414147 464963 FALSE TRUE 397150.6618 340638.1476 394500.555 368503.115 366863.7609 317161.1055 381131.0011 388813.5635 367134.7688 433470.6419 0.916211211 0.785839027 0.910097517 0.850122429 0.846340503 0.7316784 0.879254474 0.896977848 0.846965707 1 18.72557476 0.234417832 0.752393492 1.002580687 0.845618969 0.401302426 0.054176601 2.943574799 2.100880367 0.073756551 0.018560452 1.715607088 -0.234417832 -0.156961718 LEIFHPFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEIFHPFFK 9 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 ; 127.3 0.00044929 136646000 479540 559260 443760 503150 488770 466830 541560 527690 605550 666130 FALSE TRUE 460799.0466 543310.4524 523957.3034 529117.6318 504491.7309 476269.6225 548187.7733 516793.0171 536810.5027 621012.4218 0.742012608 0.874878559 0.843714691 0.852024232 0.81236979 0.76692447 0.88273238 0.832178229 0.86441186 1 19.2442626 0.247884155 0.714268168 1.004267301 0.824002409 0.619885301 0.041199749 1.812484588 1.208076147 0.056698717 0.014220611 1.769636858 -0.247884155 -0.180264892 RAS(ph)DDGKLTDPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RASDDGKLTDPSK 13 2 P04049;P04049-2;A0A0B4J1W9 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 RAS(0.994)DDGKLT(0.006)DPSK;RAS(1)DDGKLTDPSK 91.475 0.0051308 847440000 2111500 1984370 1453660 1475670 2000630 2127900 1697740 1824210 2122800 1727690 TRUE FALSE 2028980.246 1927777.711 1716368.698 1551829.506 2064982.081 2170927.596 1718517.45 1786539.426 1881828.644 1610672.017 1.259710372 1.196877881 1.065622721 0.963467105 1.28206243 1.347839642 1.066956793 1.10918884 1.168349995 1 20.61923132 0.260113462 0.674073251 0.996211721 1.164702589 0.164159651 0.109696979 5.536570536 3.405300292 0.175884255 0.043833886 1.820176329 -0.260113462 0.168490868 VDS(ph)PSHGLVTSSLCIPS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDSPSHGLVTSSLCIPSPAR 20 0 Q9UER7-3;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 2 VDS(0.938)PS(0.062)HGLVTSSLCIPS(1)PAR;VDS(0.998)PS(0.002)HGLVTSSLCIPS(1)PAR 227.36 2.00E-25 258736000 138056 127766 106503 109155 109470 133518 129716 125094 151370 162751 TRUE FALSE 132660.6189 124122.2388 125750.4612 114788.5026 112991.202 136217.8254 131303.5032 122510.7652 134187.1122 151727.7298 0.87433338 0.818059025 0.828790238 0.756542675 0.74469711 0.89777805 0.865388966 0.807438201 0.884394121 1 17.21112525 0.281277678 0.600517956 1.007937842 0.814773959 0.57185905 0.046197468 1.939725003 1.008543627 0.081333959 0.020066859 1.911074768 -0.281277678 -0.193163883 DTQLKEYEELLASVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTQLKEYEELLASVR 15 1 Q8WVV4-1;Q8WVV4 Q8WVV4-1 POF1B Protein POF1B 0 141.13 4.39E-06 48498000 109330 100930 69499 77358 93003 120450 88824 96082 105900 73820 FALSE TRUE 105057.2627 98051.57522 82059.0153 81350.45565 95994.52596 122885.5815 89911.05468 94097.87312 93878.67597 68820.10565 1.526548989 1.424751885 1.192369795 1.182073972 1.394861648 1.785605825 1.306464933 1.367302073 1.364116999 1 16.07054249 0.282024459 1.25206626 0.999572253 1.394142549 0.346356894 0.162958428 5.672665434 8.705697137 0.167239893 0.049011526 1.914363738 -0.282024459 0.394570296 LLEDFLQEGEEPDEDDAYQVLSTLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEDFLQEGEEPDEDDAYQVLSTLKR 26 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 0 174.28 4.43E-12 78011000 41641 47649 33804 32459 36146 48051 36115 39737 48888 39774 FALSE TRUE 40013.62368 46290.09717 39913.13477 34134.21288 37308.66892 49022.62414 36556.98617 38916.41706 43338.4392 37080.07155 1.079113982 1.248382089 1.076403931 0.920554127 1.006164966 1.322074691 0.985893086 1.049523786 1.168779816 1 15.17835641 0.293591138 0.01003861 5.46E-06 2.113267555 0.034874707 0.116895855 10765.10473 39.93100337 4323.923319 4078.905453 1.966034514 -0.293591138 2.1132621 SDSKS(ph)SPQAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.202)KS(0.399)S(0.399)PQAGR 125.73 0.00019517 662700000 427910 430540 326300 408690 360730 392030 443340 412060 472170 484560 TRUE FALSE 411186.8041 418261.4207 385269.6685 429782.5399 372333.2081 399957.1152 448765.7275 403550.817 418571.2411 451740.3196 0.910228258 0.925889062 0.852856501 0.951392916 0.824219561 0.885369532 0.993415261 0.89332477 0.926574899 1 18.78513416 0.299148546 0.453233146 1.008438777 0.895357644 0.307914596 0.044339512 3.415156681 1.127748608 0.104778585 0.025634019 1.991354344 -0.299148546 -0.113081133 QNKPTGFALGSIEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QNKPTGFALGSIEGR 15 1 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 ; 158.45 1.66E-06 1812730000 1313490 1150290 963400 1108690 1104910 1113440 1187920 1205520 1319180 1340020 FALSE TRUE 1262157.359 1117484.855 1137507.811 1165909.624 1140450.434 1135954.52 1202458.12 1180625.591 1169432.217 1249259.252 1.010324604 0.894517974 0.910545837 0.93328076 0.912901331 0.909302467 0.962536894 0.945060514 0.936100505 1 20.25264147 0.310868645 0.577151341 1.002694739 0.928197281 0.273239213 0.031589833 3.021919809 1.50860423 0.051406196 0.01310838 2.045825769 -0.310868645 -0.074497458 LIDLHSPSEIVK ddPTM_BT-474_Pertuzumab_2h_R1 4 LIDLHSPSEIVK 12 0 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ;;; 168.02 4.77E-05 3935460000 4452260 4445300 4073750 3904470 4143430 3216630 4698020 4347520 4903660 5360910 FALSE TRUE 4278260.757 4318524.396 4809967.245 4105980.165 4276707.189 3281672.462 4755515.774 4257742.193 4347017.075 4997810.791 0.856026956 0.864083211 0.962414835 0.821555744 0.855716106 0.656621989 0.95151977 0.851921445 0.869784243 1 22.25286485 0.31483884 1.002864339 1.000523108 0.85128176 0.240435885 0.078298806 4.439639484 5.218911728 0.079191685 0.02360826 2.064613869 -0.31483884 -0.149241348 ATQPETTEEVTDLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATQPETTEEVTDLKR 15 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 153.23 4.31E-06 247780000 192330 217920 202900 221570 220280 172380 219430 223470 248180 285690 FALSE TRUE 184813.531 211705.135 239568.5435 233005.2543 227365.5063 175865.6417 222115.45 218855.2664 220007.6469 266339.9618 0.693900869 0.794868083 0.899484035 0.87484151 0.853666512 0.660305125 0.833954651 0.821713966 0.826040694 1 18.02290938 0.323706804 1.209418235 1.000231281 0.806818892 0.402825371 0.071154731 3.988457487 6.128557842 0.071060151 0.02109053 2.107205079 -0.323706804 -0.193412389 QAFPNTNR ddPTM_BT-474_Pertuzumab_2h_R1 3 QAFPNTNR 8 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 106.94 0.0095357 233570000 227842 264432 218181 228254 227774 209862 255595 247027 277630 294909 FALSE TRUE 218937.6827 256890.6583 257611.1601 240034.2163 235100.5576 214105.5534 258723.0481 241925.8061 246114.6063 274934.5508 0.796326552 0.934370226 0.936990856 0.873059481 0.855114633 0.778750989 0.941035048 0.879939627 0.895175254 1 18.06872869 0.324780721 0.860692629 1.001026763 0.874866033 0.341129188 0.052388807 3.079720647 2.92462961 0.057850179 0.017026255 2.112422189 -0.324780721 -0.12616073 LLLEFTDTSYEEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLLEFTDTSYEEKR 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 104.24 0.0017141 107902000 105517 94995 73090 98623 85277 102317 107056 107550 116873 136825 FALSE TRUE 101393.279 92285.83561 86298.98888 103712.9448 88020.01215 104385.9198 108366.1834 105329.0549 103606.067 127557.7209 0.794881551 0.723482945 0.676548533 0.813066776 0.690040646 0.818342623 0.849546249 0.825736413 0.812228898 1 16.9607907 0.341489768 0.277306669 1.059983657 0.714743622 0.700054548 0.04805335 2.310253767 0.353302371 0.240785331 0.075090323 2.195279226 -0.341489768 -0.345240034 EVIGGLCSLANIPLT(ph)PETQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVIGGLCSLANIPLTPETQR 20 0 Q01664 Q01664 TFAP4 Transcription factor AP-4 1 EVIGGLCSLANIPLT(0.996)PET(0.004)QR 166.6 1.67E-10 24866000 28666 30096 30346 32126 25232 33528 33030 39354 36767 43972 TRUE FALSE 27545.70103 29237.69155 35830.19724 33784.02671 26043.6102 34205.95913 33434.23102 38541.32615 32593.3643 40993.73727 0.671949006 0.713223372 0.874040759 0.824126536 0.635307048 0.834419143 0.815593631 0.940175956 0.795081553 1 15.3231159 0.343731516 0.039127627 1.805780212 4.45E-11 0.49863477 0.076634334 137.8192018 2.082261198 52.90887315 42.58763157 2.206640149 -0.343731516 -1.805780212 FYALSASFEPFSNK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYALSASFEPFSNK 14 0 P27797 P27797 CALR Calreticulin 0 224.58 7.20E-12 111230000 53877 72940 52936 60852 60333 50332 66637 63748 70197 72610 FALSE TRUE 51771.42728 70859.82262 62502.71275 63992.57901 62273.66574 51349.74753 67452.52354 62431.58152 62228.53085 67692.06003 0.764807974 1.046796664 0.923338908 0.945348376 0.919955246 0.758578591 0.99646138 0.922288101 0.919288478 1 16.046699 0.364452639 0.79853055 1.000619349 0.912270027 0.091927744 0.084764359 5.94591133 5.228644672 0.09079571 0.027220115 2.314475774 -0.364452639 -0.088349322 SAS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SASPPK 6 0 P52701;P52701-3;P52701-2;A0A087WWJ1;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 S(0.001)AS(0.999)PPK;SAS(1)PPK;SAS(1)PPK 98.629 0.041662 2698270000 9292600 7603900 7116400 7432800 7213000 7337400 8610900 8890300 8938200 10395600 TRUE FALSE 8929434.918 7387044.217 8402491.783 7816407.699 7445012.696 7485767.255 8716282.77 8706712.198 7923573.008 9691496.753 0.921367994 0.762219129 0.866996296 0.806522243 0.768200505 0.772405692 0.899374265 0.898386743 0.817579906 1 23.20828806 0.379503234 0.519800522 1.007621807 0.819202549 0.431212182 0.056439301 2.101020287 0.931286079 0.100997665 0.027792609 2.396090595 -0.379503234 -0.188419258 RSELIAK ddPTM_BT-474_Pertuzumab_2h_R1 6 RSELIAK 7 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;; 125.5 0.0064834 9269160000 11146670 10740730 9553130 10455810 10439800 9617890 11054770 11377920 12022550 12311590 FALSE TRUE 10711045.81 10434414.9 11279593.1 10995435.61 10775605.65 9812370.326 11190061.58 11142961.98 10657800.53 11477715.04 0.933203671 0.909102104 0.982738555 0.957981233 0.93882847 0.85490625 0.97493809 0.97083452 0.928564657 1 23.45233213 0.38165843 0.58524108 1.001630374 0.936259689 0.200399554 0.035806366 3.697410677 2.002654884 0.056541454 0.015954068 2.408010799 -0.38165843 -0.065370684 KPWTSLS(ph)SESVSCPQGSLS(ph)PATSLMQVSERPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPWTSLSSESVSCPQGSLSPATSLMQVSERPR 32 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 2 KPWTS(0.001)LS(0.986)S(0.013)ESVSCPQGS(0.134)LS(0.865)PAT(0.001)SLMQVSERPR 235.42 7.45E-47 1226700000 273150 242990 214700 249020 253540 269670 249550 286580 308480 324680 TRUE FALSE 262474.996 236060.1631 253501.066 261871.952 261695.3444 275122.9122 252604.0675 280662.0229 273462.6437 302689.1344 0.867143766 0.779876567 0.837496418 0.865151478 0.864568016 0.908928934 0.834532987 0.927228602 0.903443872 1 18.20747736 0.385683417 0.157130993 1.095770672 0.770711749 0.705070092 0.030972357 5.292930398 0.378543423 0.477582696 0.222816489 2.430431677 -0.385683417 -0.325058923 RPMSDPSWNR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPMSDPSWNR 10 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 78.683 0.04693 109680000 139100 146250 128760 136720 127870 98416 144960 137460 155810 172500 FALSE TRUE 133663.8182 142079.0932 152029.7963 143776.1356 131983.0547 100406.039 146734.0638 134621.403 138123.102 160816.4214 0.83115777 0.883486226 0.945362389 0.894038895 0.820706328 0.624351905 0.912432092 0.837112291 0.858886803 1 17.29505521 0.388046828 1.61626902 1.000016885 0.844402994 0.241995489 0.082490687 7.768015795 18.79005801 0.08196663 0.023325206 2.44369403 -0.388046828 -0.155613891 EKEAAYQER ddPTM_BT-474_Pertuzumab_2h_R1 4 EKEAAYQER 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ;;; 131.83 0.00029387 1831630000 2496610 2504360 2002500 2081690 2267670 2282470 2380680 2449130 2677040 2736640 FALSE TRUE 2399039.721 2432938.105 2364396.295 2189126.27 2340611.665 2328623.107 2409815.474 2398554.61 2373153.642 2551284.935 0.940326064 0.953612853 0.926747249 0.858048523 0.917424641 0.912725613 0.944549721 0.94013592 0.930179773 1 21.2827926 0.391516531 0.628440499 1.001875379 0.919417474 0.460859586 0.024863616 2.020636312 1.241432741 0.037028695 0.010765451 2.463295599 -0.391516531 -0.082457905 QLPAHDQDPSK ddPTM_BT-474_Pertuzumab_2h_R1 3 QLPAHDQDPSK 11 0 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ;; 117.98 0.00078252 1164720000 541223 582210 433617 517947 523558 541990 485197 563810 605510 633110 FALSE TRUE 520071.4068 565605.9408 511981.2377 544678.3067 540398.7186 552949.4091 491134.986 552167.1265 536775.0433 590228.8958 0.881135116 0.958282363 0.867428283 0.922825552 0.915574826 0.936838933 0.832109355 0.935513545 0.909435385 1 19.17091503 0.394975806 1.509273033 0.999980173 0.90626533 0.387395977 0.035317495 4.095320809 9.175665547 0.031196722 0.008988125 2.482994775 -0.394975806 -0.093714843 ELSPDIAHLASLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSPDIAHLASLK 13 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 145.17 4.17E-05 300230000 519190 592020 510860 551160 491830 504880 598740 564030 656420 711610 FALSE TRUE 498899.4808 575136.1692 603183.766 579605.4337 507650.1586 515089.0195 606067.5592 552382.5834 581905.9535 663412.0209 0.752020562 0.866936611 0.909214405 0.873673397 0.765210974 0.776424007 0.913561317 0.832638792 0.877141106 1 19.33954563 0.395048457 0.831239053 1.001550154 0.835537257 0.455897815 0.054047795 2.043145735 1.967125815 0.059472787 0.018344875 2.483410181 -0.395048457 -0.166012897 SSQQPST(ph)PQQAPPGQPQQGTFVAHK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSQQPSTPQQAPPGQPQQGTFVAHK 25 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 SSQQPS(0.001)T(0.999)PQQAPPGQPQQGTFVAHK;SSQQPS(0.006)T(0.994)PQQAPPGQPQQGTFVAHK;SSQQPS(0.003)T(0.997)PQQAPPGQPQQGTFVAHK;SSQQPS(0.005)T(0.995)PQQAPPGQPQQGTFVAHK 254.65 2.81E-44 3218970000 2223560 2092050 1975680 1873120 1809210 1996720 2051230 2110490 2364630 2576270 TRUE FALSE 2136660.817 2032386.782 2332729.325 1969791.948 1867404.883 2037095.046 2076333.566 2066907.644 2096207.116 2401776.938 0.889616676 0.846201306 0.971251446 0.820139421 0.777509707 0.848161632 0.864498919 0.860574357 0.872773438 1 21.19567074 0.407159142 1.561184872 1.000019508 0.858512962 0.442745099 0.04691053 4.053479631 9.640329595 0.046000451 0.01317658 2.553636878 -0.407159142 -0.141506546 FTYFSSLS(ph)PMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTYFSSLSPMAR 12 0 Q9H425 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 FTYFSSLS(1)PMAR;FTYFSSLS(1)PMAR 209.67 5.50E-08 301300000 439430 502930 470250 424130 422110 421190 482320 507990 534570 594010 TRUE FALSE 422256.5898 488586.9288 555234.6357 446019.4001 435687.5515 429706.7504 488222.7764 497499.829 473887.8547 553777.1736 0.762502699 0.88228073 1.002631856 0.805413118 0.786756068 0.775956054 0.88162315 0.898375471 0.855737429 1 19.07894606 0.408115173 0.765266446 1.001172343 0.846852077 0.308617765 0.068085733 2.723367657 2.332558254 0.08078205 0.024917215 2.559264501 -0.408115173 -0.154320266 RGAAGDWGER ddPTM_BT-474_Pertuzumab_2h_R1 2 RGAAGDWGER 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 ; 126.71 0.00060192 449980000 409770 464550 351150 417680 421400 386670 459360 425750 488930 478650 FALSE TRUE 393755.7354 451301.4888 414610.6163 439236.5149 434954.7137 394488.7323 464981.7851 416958.1137 433428.7162 446230.6092 0.882404137 1.01136381 0.929139794 0.984326278 0.974730789 0.884046778 1.042021268 0.934400521 0.971311038 1 18.76742995 0.409760368 0.006098505 1.953077555 6.49E-08 0.102325883 0.047638548 17659.42422 43.17832474 7024.280234 6801.495521 2.5689779 -0.409760368 -1.95307749 VFFPVSEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFFPVSEYK 9 0 Q9NU53 Q9NU53 GINM1 Glycoprotein integral membrane protein 1 0 ; 81.784 0.047234 1169090000 970870 885080 917730 860040 830900 412100 1038330 940630 1026740 1313900 FALSE TRUE 932927.327 859838.385 1083584.226 904426.7675 857626.6531 420432.9444 1051037.393 921205.6618 910188.7796 1224908.383 0.76163029 0.701961385 0.884624712 0.738362787 0.700155755 0.343236237 0.858053882 0.752060868 0.743066822 1 20.22424242 0.417023369 0.994343714 1.000298684 0.71240527 0.271851671 0.1383433 3.066409242 3.957888851 0.13903838 0.043142869 2.612301918 -0.417023369 -0.287893414 S(ph)TECLLLSLLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 STECLLLSLLHR 12 0 H0YES2;Q5TB30 H0YES2 DEPDC1 DEP domain-containing protein 1A 1 S(0.5)T(0.5)ECLLLSLLHR;S(0.5)T(0.5)ECLLLSLLHR 108.37 0.00095266 15291000 43633 35436 32944 33052.6 31924.5 27380 32574 42552 25722.2 26274.2 TRUE FALSE 41927.77412 34425.39998 38897.71364 34758.44865 32951.38054 27933.64236 32972.65036 41673.28633 22802.32369 24494.62503 1.711713246 1.405426698 1.588010169 1.419023504 1.345249437 1.140398856 1.346117784 1.70132371 0.930911319 1 14.58017759 0.42625192 0.054178546 3.97E-13 2.450430056 0.419755895 0.195705507 95.25848685 2.134960134 54.21362959 41.04748076 2.668406072 -0.42625192 2.450430056 ISHLNDLSIPVDEEDPSEDIFTVLTAEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISHLNDLSIPVDEEDPSEDIFTVLTAEEK 29 0 Q96PZ0;Q96PZ0-2;E7EUH7 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 177.73 1.31E-17 93316000 47176 47222 44218 45642 48974 50057 50324 49058 63399 61044 FALSE TRUE 45332.30976 45875.2748 52209.17622 47997.58909 50549.29319 51069.18684 50939.88017 48044.93516 56202.21131 56909.43551 0.79656931 0.806110171 0.917408085 0.843403008 0.888240987 0.897376443 0.895104295 0.844234963 0.987572813 1 15.79638025 0.428545723 0.023004877 1.869587016 1.10E-09 0.625291665 0.0398735 312.9550299 2.937797722 126.1747141 111.9957162 2.682537015 -0.428545723 -1.869587015 ASPDS(ph)RHSPATISSSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPDSRHSPATISSSTR 17 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 AS(0.1)PDS(0.449)RHS(0.449)PAT(0.001)ISSSTR 54.235 0.077711 45388000 122040 133840 112080 121230 111580 133380 119970 123380 145450 128600 TRUE FALSE 117270.5419 130023.0142 132335.3492 127486.6948 115169.072 136077.035 121438.2287 120832.1599 128939.1258 119889.8075 0.978152725 1.084521003 1.103808172 1.063365582 0.960624381 1.135017545 1.012915371 1.007860155 1.075480297 1 16.87134949 0.429994272 0.35282449 0.994628958 1.055136963 0.047420095 0.05375244 8.835963258 2.119344942 0.162389227 0.049867587 2.691499304 -0.429994272 0.060508004 QLHEQAMQFGQLLTHLDTTQQMIANSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLHEQAMQFGQLLTHLDTTQQMIANSLK 28 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 55.469 0.038218 173540000 39084 42804 27676 37493 32825 41074 38242 35023 41775 31602 FALSE TRUE 37556.55407 41583.27183 32677.66885 39428.01822 33880.84594 41904.54442 38710.01704 34299.76281 37032.87714 29461.56839 1.274764248 1.411441213 1.109162568 1.338286465 1.150001435 1.422346016 1.313915692 1.164220531 1.256989331 1 14.84654661 0.445956036 0.776640025 0.997742305 1.282998237 0.40614585 0.099780969 1.791168937 1.625861304 0.103226198 0.032753274 2.792261164 -0.445956036 0.285255932 IEFTFER ddPTM_BT-474_Pertuzumab_2h_R1 1 IEFTFER 7 0 O43747;O43747-2;B3KNW1 O43747 AP1G1 AP-1 complex subunit gamma-1 0 116.9 0.012449 356680000 145430 151510 131620 148980 142520 98082 154660 147330 164400 175070 FALSE TRUE 139746.4348 147189.0831 155406.6619 156668.8757 147104.2852 100065.2852 156552.7753 144287.584 145738.0012 163212.353 0.85622462 0.901825631 0.95217463 0.959908198 0.901306075 0.613098723 0.959196853 0.884048183 0.89293487 1 17.31639073 0.447051834 1.267597552 0.999954782 0.879108224 0.12677506 0.095171 5.702969919 10.82503792 0.092559327 0.027641323 2.799315401 -0.447051834 -0.120846558 ELNMIIMLPDETTDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELNMIIMLPDETTDLR 16 0 A0A2R8YD12;A0A024QZX5;A0A087X1N8;P35237 A0A2R8YD12 SERPINB6 Serpin B6 0 ; 140.1 4.03E-06 34750000 55052 60986 55413 64334 54187 25526 67705 57139 66422 77582 FALSE TRUE 52900.50698 59246.73899 65427.36176 67654.28545 55929.97407 26042.15321 68533.59404 55959.05968 58882.05302 72327.30204 0.7314044 0.819147643 0.904601166 0.935390697 0.773289926 0.36005979 0.94754805 0.773692065 0.814105481 1 16.14225272 0.448707092 1.25862109 1.000015098 0.782146812 0.147129758 0.157516064 5.159986831 9.716986812 0.153277687 0.045844904 2.810004993 -0.448707092 -0.217868285 TYGHTYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TYGHTYEK 8 0 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 ; 72.547 0.045871 207759000 108432 129671 112523 107777 113116 110076 126620 125540 141319 153962 FALSE TRUE 104194.3576 125972.91 132858.4092 113339.3839 116754.4789 112301.8121 128169.6134 122947.5551 125277.0596 143534.0166 0.725921005 0.877651953 0.925623154 0.789634308 0.813427239 0.782405557 0.892956363 0.856574337 0.87280397 1 17.13103316 0.44909815 0.625552137 1.004459622 0.827732364 0.473429334 0.054400322 1.720483345 1.101399024 0.071253437 0.022059908 2.812536388 -0.44909815 -0.176727258 EIYENMAPGENKR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIYENMAPGENKR 13 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 140.1 6.28E-05 2103990000 1768610 1706210 1825500 1850020 1847850 1690350 2132710 2215840 2317950 2627890 FALSE TRUE 1699490.766 1657550.561 2155408.458 1945499.754 1907287.773 1724530.035 2158810.743 2170082.13 2054826.034 2449900.67 0.693697825 0.67657868 0.879794224 0.794113728 0.778516369 0.703918349 0.881182968 0.88578372 0.838738509 1 21.22429183 0.454566189 0.039096847 1.795752291 1.64E-09 0.614543347 0.060934355 102.8673559 1.684300857 42.16972563 34.62949426 2.848171844 -0.454566189 -1.79575229 S(ph)PARTPPS(ph)EEDSAEAER ddPTM_BT-474_Pertuzumab_2h_R1 1 SPARTPPSEEDSAEAER 17 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 S(0.969)PART(0.134)PPS(0.636)EEDS(0.261)AEAER 108.71 0.0076785 110130000 105630 103770 94275 114180 102800 107100 99068 113550 125010 124900 TRUE FALSE 101501.8628 100810.5812 111312.5896 120072.8435 106106.6554 109265.6354 100280.4238 111205.1528 110819.3889 116440.4118 0.871706492 0.865769707 0.955961835 1.031195628 0.911252835 0.93838242 0.861216671 0.955039158 0.951726185 1 16.82923232 0.459886242 0.010092918 1.912347542 8.28E-07 0.207617339 0.048275483 4504.379568 18.9343471 1838.591149 1747.228408 2.883276164 -0.459886242 -1.912346715 QKPQAER ddPTM_BT-474_Pertuzumab_2h_R1 7 QKPQAER 7 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;;; 127.02 0.0035526 9137700000 2317970 2319680 1956050 2111320 1969810 1673984 2439000 2262520 2495720 2731800 FALSE TRUE 2227381.17 2253524.998 2309551.747 2220285.478 2033170.728 1707833.103 2468849.212 2215798.171 2212416.329 2546772.753 0.874589681 0.884855154 0.906854271 0.871803531 0.798332213 0.670587158 0.969403025 0.870041573 0.868713679 1 21.2802388 0.461691085 0.840724396 1.000241117 0.851378966 0.255476124 0.073856085 2.679828856 2.798313783 0.078952951 0.02525917 2.895283429 -0.461691085 -0.148862151 QKSPEIHR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKSPEIHR 8 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 59.931 0.087099 228100000 244130 213070 205020 217050 211760 195590 230300 229630 253780 256760 FALSE TRUE 234589.1297 206993.4522 242071.6746 228251.9765 218571.4527 199544.9638 233118.4803 224888.0603 224971.9583 239369.4165 0.980029668 0.864744775 1.01128907 0.953555303 0.913113529 0.833627649 0.973885819 0.939502061 0.939852558 1 17.86887931 0.470386596 1.005834143 0.99996938 0.931304121 0.13321162 0.050402957 3.889898869 5.405738535 0.048229465 0.01512366 2.953837478 -0.470386596 -0.068665258 IRS(ph)IEALLEAGQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 IRSIEALLEAGQAR 14 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 IRS(1)IEALLEAGQAR;IRS(1)IEALLEAGQAR;IRS(1)IEALLEAGQAR 169.39 2.02E-06 138908000 94641 105329 72464 83760 91430 92171 84848 93948 93965 73411 TRUE FALSE 90942.32509 102325.12 85559.85675 88082.86364 94370.92898 94034.76077 85886.3952 92007.94097 83298.48713 68438.80758 1.328812238 1.495133005 1.250165802 1.287030951 1.378909603 1.37399765 1.254937049 1.344382584 1.217123589 1 16.062527 0.474306224 0.699953737 0.992719322 1.352203827 0.702663627 0.067590543 0.94562391 0.744526713 0.076402653 0.024563489 2.980617343 -0.474306224 0.359484504 MQASIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 113.71 0.01412 359640000 620680 638000 546420 547270 616990 503710 615940 626600 690940 728270 FALSE TRUE 596423.1394 619804.8647 645170.249 575514.6703 636836.0437 513895.3613 623478.058 613660.491 612507.3879 678943.6242 0.87845753 0.91289592 0.950255995 0.847661941 0.937980741 0.756904319 0.91830608 0.903846018 0.902147639 1 19.37293226 0.475572318 1.126355739 0.999964138 0.887532023 0.293250924 0.051933297 2.547981518 4.220687165 0.048157623 0.014773245 2.98931938 -0.475572318 -0.112432115 AIAHYEQSADYYK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIAHYEQSADYYK 13 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R027;A0A087WZQ7;Q9H115-3;Q9H115-2;Q9H115 P54920 NAPA;NAPB Alpha-soluble NSF attachment protein;Beta-soluble NSF attachment protein 0 ; 211.38 2.24E-08 1082740000 1247530 1242480 1311680 1572160 1281300 1215640 1667240 1591750 1864290 2052680 FALSE TRUE 1198775.148 1207045.687 1548729.754 1653299.366 1322514.178 1240221.074 1687644.182 1558879.806 1652663.615 1913650.155 0.626433805 0.630755671 0.809306628 0.863950687 0.691095065 0.648091852 0.881897967 0.814610655 0.863618468 1 20.86789568 0.482440948 0.047024253 1.756584838 5.65E-11 0.589647723 0.077389608 77.07440093 1.557259106 32.06700972 25.47315662 3.036973122 -0.482440948 -1.756584838 EGPTDHLESACPLNLPLQNNHTAADMYLS(ph)PVRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 35 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 EGPTDHLESACPLNLPLQNNHTAADMY(0.127)LS(0.878)PVRS(0.995)PK 212.21 1.24E-28 346190000 171090 161040 137820 135930 156800 132320 158370 171070 173680 191780 TRUE FALSE 164403.6137 156447.2969 162727.1398 142945.3636 161843.6144 134995.6011 160308.1794 167537.3447 153964.5745 178790.5698 0.919531796 0.875031032 0.910155049 0.799512881 0.905213371 0.755048777 0.896625474 0.93705918 0.861144828 1 17.44791112 0.505857511 0.72703273 1.000125993 0.866681088 0.325896385 0.053938668 1.900309533 1.63695348 0.058504929 0.019249972 3.205217546 -0.505857511 -0.133444905 QLPALDGSLMGPES(ph)PPAQEEEAPVS(ph)PHK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLPALDGSLMGPESPPAQEEEAPVSPHK 28 0 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 2 QLPALDGSLMGPES(1)PPAQEEEAPVS(1)PHK 101.24 0.00066562 71718000 75869 75827 72269 80680 73760 64838 80781 87099 91056 107360 TRUE FALSE 72903.9556 73664.4882 85329.61592 84843.90447 76132.55739 66149.06878 81769.62204 85300.37521 80719.70462 100088.4116 0.72839557 0.735994178 0.852542413 0.847689589 0.760653069 0.66090637 0.816973921 0.852250264 0.806484021 1 16.61091542 0.508399259 0.694455989 1.00266189 0.772836213 0.569290776 0.057898784 1.29809202 1.039385207 0.070527322 0.023238902 3.224031373 -0.508399259 -0.229825677 STSMDSGSSES(ph)PASLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 STSMDSGSSESPASLKR 17 1 F8W7U0;Q15811-6;Q15811-12;Q15811-11;Q15811-3;Q15811-10;Q15811-7;Q15811-2;Q15811-4;Q15811-9;Q15811-8;Q15811;H0Y7J7 F8W7U0 ITSN1 Intersectin-1 1 STSMDSGSS(0.004)ES(0.986)PAS(0.009)LKR 89.557 0.0024622 207150000 72296 74520 61354 68925 57616 68486 70994 75443 80801 89419 TRUE FALSE 69470.59239 72394.76256 72442.03261 72482.22751 59469.27097 69870.83384 71862.84581 73885.07569 71628.80923 83362.57148 0.83335472 0.868432454 0.868999496 0.869481666 0.713380956 0.838155933 0.862051692 0.886309939 0.859244238 1 16.34711216 0.509003868 0.724078757 1.001253516 0.8353893 0.531315333 0.045008964 1.345622361 1.15465187 0.051834586 0.01708922 3.228522873 -0.509003868 -0.165864215 EELRHT(ph)PELPLAPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EELRHTPELPLAPR 14 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 EELRHT(1)PELPLAPR;EELRHT(1)PELPLAPR;EELRHT(1)PELPLAPR 107.98 0.0012496 401900000 285863 259262 274023 314320 288836 307949 330750 332360 392640 432880 TRUE FALSE 274691.1579 251868.1016 323545.0517 330542.0929 298126.6723 314175.9398 334797.8174 325496.6499 348069.1533 403560.652 0.680668833 0.624114617 0.801725961 0.819064225 0.738740684 0.778509843 0.829609665 0.806561909 0.862495269 1 18.62242599 0.514697067 0.04362043 1.758152867 6.64E-11 0.79044884 0.044438758 53.06767393 1.017851356 22.41343509 18.21502277 3.271124447 -0.514697067 -1.758152867 DVYVQLYLQHLTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVYVQLYLQHLTAR 14 0 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 ; 263.56 1.26E-24 940340000 467920 600930 433200 672700 524850 552510 569180 542050 632510 527670 FALSE TRUE 449633.1691 583792.0648 511488.8765 707418.1276 541732.2769 563682.1308 576145.7951 530856.4781 560710.1165 491930.4409 0.914017779 1.186737019 1.039758539 1.438045034 1.101237557 1.145857389 1.171193623 1.079129149 1.139815856 1 18.90809481 0.520877733 0.820283505 1.000087525 1.147357151 0.089867189 0.126042371 3.702421706 3.932530664 0.123067005 0.040437497 3.318010323 -0.520877733 0.147269626 KAS(ph)LTSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KASLTSK 7 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 KAS(0.986)LTS(0.014)K;KAS(0.93)LT(0.051)S(0.019)K 106.4 0.0047229 959210000 1347320 1141530 999520 984270 1144260 1184200 1100040 1191350 1330410 1492160 TRUE FALSE 1294665.245 1108974.682 1180155.498 1035068.293 1181066.162 1208145.335 1113502.619 1166748.206 1179387.434 1391094.674 0.930680901 0.797195693 0.848364615 0.744067469 0.849019254 0.868485343 0.800450637 0.838726672 0.847812486 1 20.40778918 0.533147149 1.951413794 0.999990579 0.831078833 0.528432234 0.046519199 2.55093988 9.807744895 0.041765054 0.01153943 3.413085351 -0.533147149 -0.168911746 STAPSAAASASASAAAS(ph)SPAGGGAEALELLEHCGVCR ddPTM_BT-474_Pertuzumab_2h_R1 7 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.002)T(0.002)APS(0.011)AAAS(0.01)AS(0.009)AS(0.008)AAAS(0.479)S(0.479)PAGGGAEALELLEHCGVCR;S(0.003)T(0.003)APS(0.014)AAAS(0.013)AS(0.012)AS(0.028)AAAS(0.463)S(0.463)PAGGGAEALELLEHCGVCR;STAPS(0.001)AAAS(0.004)AS(0.005)AS(0.014)AAAS(0.488)S(0.488)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.563)S(0.437)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.5)S(0.5)PAGGGAEALELLEHCGVCR;STAPSAAAS(0.001)AS(0.005)AS(0.014)AAAS(0.51)S(0.469)PAGGGAEALELLEHCGVCR;STAPSAAASAS(0.004)AS(0.004)AAAS(0.526)S(0.466)PAGGGAEALELLEHCGVCR 231.35 2.92E-40 297700000 45549.3 46276.2 41686.5 50801.7 47300.8 49636.8 41984.4 48144.8 54062.2 54842.9 TRUE FALSE 43769.183 44956.44809 49220.17786 53423.58183 48822.27319 50640.4901 42498.21765 47150.59306 47925.2857 51128.34153 0.856064986 0.879286258 0.962678944 1.044891741 0.954896477 0.990458297 0.831206653 0.922200714 0.937352636 1 15.64183561 0.5354001 0.005917158 1.896931423 8.11E-07 0.081360383 0.061170031 27405.82965 71.67054537 11645.56614 11326.47496 3.430837119 -0.5354001 -1.896930612 MSWFVDLAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 MSWFVDLAGK 10 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ; 100.45 0.0093162 943870000 964000 937910 799910 857180 859880 892680 904030 966790 1061460 1121800 FALSE TRUE 926325.8142 911161.7251 944471.5309 901419.1625 887538.8211 910730.6012 915093.7896 946825.4486 940967.5108 1045819.487 0.885741589 0.87124187 0.903092305 0.861926149 0.848653933 0.870829634 0.875001662 0.905343093 0.899741803 1 19.99620243 0.536128876 0.816013109 1.000646248 0.873182361 0.861512593 0.014892664 0.534298505 0.570837152 0.015875352 0.005249688 3.436599132 -0.536128876 -0.127463888 LEHEYIQNFK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEHEYIQNFK 10 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;; 172.27 3.77E-06 6866100000 10855870 11104030 9251620 10139430 10269350 10188770 11438150 11168210 12617220 12998530 FALSE TRUE 10431610.6 10787353.94 10923593.54 10662727.2 10599672.97 10394793.91 11578133.5 10937582.56 11184966.08 12118127.99 0.860826904 0.890183199 0.901425827 0.879898876 0.874695579 0.857788754 0.955439117 0.902580215 0.92299455 1 23.53066351 0.545840939 0.40545977 1.01073352 0.875968544 0.701778987 0.023077282 1.216021899 0.402000493 0.049796888 0.016968807 3.514317047 -0.545840939 -0.134764976 SAT(ph)PEPVTDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SATPEPVTDNR 11 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 SAT(1)PEPVTDNR 140.01 0.00043372 182800000 278820 249750 241560 227930 243260 230420 254140 289510 268610 260430 TRUE FALSE 267923.4061 242627.3745 285215.2655 239693.4946 251084.6788 235079.2503 257250.2413 283531.5173 238118.5189 242790.8441 1.103515279 0.999326706 1.174736496 0.987242725 1.03416041 0.968237707 1.059554953 1.167801522 0.98075576 1 17.88935449 0.553235901 0.004248538 1.23E-05 2.088974658 0.041411668 0.071323269 73781.1094 139.3447547 34592.60497 33915.24972 3.574669551 -0.553235901 2.088962361 ALSGTS(ph)PDDVQPGPSVGPPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALSGTSPDDVQPGPSVGPPSK 21 0 Q9Y314;M0R3B2;A0A075B797 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 1 ALS(0.006)GT(0.23)S(0.764)PDDVQPGPSVGPPSK 223.46 5.08E-33 0 60039 53399 42325 59704 64081 52827 47835 58507 64606 80787 TRUE FALSE 57692.6095 51876.1128 49974.06901 62785.33059 66142.22356 53895.19813 48420.41904 57298.81 57272.19773 75315.22453 0.766015236 0.688786539 0.663532099 0.833633983 0.878205223 0.715595 0.642903468 0.760786552 0.760433207 1 16.20065391 0.55689868 2.340440374 0.999985012 0.742029337 0.552795224 0.068812872 3.7458256 18.80470497 0.070146919 0.018875796 3.604945304 -0.55689868 -0.257955675 QWYESHYALPLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QWYESHYALPLGR 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 176.89 1.59E-05 5325000000 5465300 5517300 4555400 5567900 4886600 4013800 4959300 5419100 5975400 6786800 FALSE TRUE 5251710.034 5359952.006 5378662.114 5855259.986 5043781.927 4094961.786 5019993.397 5307193.691 5297097.643 6327123.991 0.830031155 0.847138765 0.850095892 0.925422039 0.797168182 0.64720745 0.793408412 0.83880033 0.837204653 1 22.59311844 0.559107006 1.653748237 0.999904069 0.815156739 0.406055746 0.066394852 2.454463046 7.93566261 0.068832621 0.019568965 3.623322627 -0.559107006 -0.184747329 SSS(ph)TEPPPPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSTEPPPPVR 11 0 Q8N684-2;Q8N684;Q8N684-3;F5H669;F5H6M0;F5H047;J3QT54;F5H5B7;F5H1W4;F5H2K8;F5H6P5;F5H6A8;F5GXA3;C9JM38;C9J286;C9J323 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 S(0.001)S(0.022)S(0.945)T(0.033)EPPPPVR;S(0.002)S(0.012)S(0.978)T(0.007)EPPPPVR 141.44 4.00E-05 917240000 604610 575130 529980 631220 546300 555360 566370 620610 679560 717830 TRUE FALSE 580981.1728 558727.8555 625759.1753 663797.3398 563872.2356 566589.7597 573301.4055 607794.1866 602419.1977 669210.7347 0.868158777 0.834905698 0.935070439 0.991910777 0.842592933 0.846653723 0.856682919 0.908225399 0.900193566 1 19.35210106 0.559318667 1.421682986 0.999888217 0.885207618 0.356043714 0.046091178 2.204481616 5.742346093 0.046576233 0.013637988 3.625088948 -0.559318667 -0.114680599 ATGEADVEFVTHEDAVAAMSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ATGEADVEFVTHEDAVAAMSK 21 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;; 243.93 3.99E-30 572030000 809323 803500 634789 711427 774084 799754 759755 802054 941420 947676 FALSE TRUE 777693.7624 780584.9667 749509.4931 748143.8327 798983.1149 815925.5738 769053.109 785491.3046 834553.9484 883489.0604 0.880252849 0.883525333 0.848351753 0.846805995 0.904349754 0.923526516 0.870472701 0.889078699 0.944611525 1 19.75285275 0.561372346 0.508000009 1.007504265 0.870906641 0.739485076 0.022656596 0.956260555 0.470983939 0.037076226 0.012665929 3.642271756 -0.561372346 -0.136597624 GSGGEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSGGEWK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 98.299 0.026439 261310000 148010 151890 124790 151400 126910 140600 150350 166650 157920 176850 FALSE TRUE 142225.6056 147558.2459 147342.3289 159213.7721 130992.1754 143443.0283 152190.0283 163208.6193 139993.5837 164871.792 0.862643657 0.894987821 0.893678216 0.965682305 0.79450932 0.870027714 0.923081059 0.989912327 0.849105732 1 17.33098506 0.56880977 0.36982049 1.009992102 0.879430777 0.246716871 0.054075048 3.376221912 0.972387834 0.137837305 0.049124077 3.705183915 -0.56880977 -0.130561324 FAKPVYPGQTLQTEMWK ddPTM_BT-474_Pertuzumab_2h_R1 2 FAKPVYPGQTLQTEMWK 17 1 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7EPL9 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ; 186.75 4.61E-10 476560000 689180 764310 609370 701330 645310 694230 803990 784300 876190 985190 FALSE TRUE 662246.0837 742512.6271 719496.7144 737525.7253 666066.9822 708267.8063 813829.4701 768103.9309 776728.5845 918462.2038 0.721037927 0.808430248 0.783371065 0.803000627 0.725198032 0.771145294 0.886078346 0.836293456 0.845683776 1 19.80886083 0.57223944 0.367812555 1.025682535 0.758158179 0.765844211 0.037664629 1.145062606 0.327646444 0.09598909 0.034388462 3.734559987 -0.57223944 -0.267524355 NFNIHGTNK ddPTM_BT-474_Pertuzumab_2h_R1 1 NFNIHGTNK 9 0 H7C3P4;F6S8M0;P15586-2;P15586;H0YFA9;F5H4C6 H7C3P4 GNS N-acetylglucosamine-6-sulfatase 0 79.974 0.022855 0 325250 385130 311500 370990 274080 321180 321170 380970 399760 462780 FALSE TRUE 312538.8704 374146.4695 367794.9793 390136.8384 282896.0321 327674.4797 325100.5745 373102.8364 354380.9207 431435.4984 0.724416214 0.867212992 0.852491231 0.904276166 0.655708752 0.759498189 0.753532279 0.864794014 0.821399542 1 18.71878536 0.575953875 1.086246161 0.999434883 0.796122729 0.417489429 0.072002743 1.475971226 2.596456494 0.070750449 0.022083943 3.766637923 -0.575953875 -0.203312154 ELISNSSDALDKIR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELISNSSDALDKIR 14 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 218.21 4.99E-12 4631580000 3444720 4152660 2249110 2025510 3201090 3876220 2686460 2686030 2954290 2272270 FALSE TRUE 3310096.534 4034230.203 2655574.208 2130046.814 3304055.967 3954599.824 2719337.701 2630562.542 2618931.385 2118367.129 1.562569816 1.90440559 1.25359489 1.005513532 1.559718295 1.866815138 1.283695193 1.24178784 1.236297216 1 21.01452121 0.586826705 0.060713242 2.58E-10 2.459120829 0.283170668 0.257634209 80.06501384 2.289865019 51.46514024 39.4288801 3.862128374 -0.586826705 2.459120829 QQSNEHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 QQSNEHLR 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 174.92 0.00026916 710748000 525938 532670 577963 893550 570452 366974 725597 619117 758506 925350 FALSE TRUE 505383.7615 517478.7731 682413.7708 939666.2226 588801.1067 374394.4657 734477.0731 606332.0176 672403.5788 862675.2203 0.585833173 0.599853527 0.791043668 1.089246799 0.682529291 0.433992373 0.851394657 0.702850857 0.779440006 1 19.71845799 0.590907004 1.484321005 1.000065567 0.72090048 0.206558921 0.165815367 2.905998185 8.460036917 0.16396874 0.047630093 3.898584964 -0.590907004 -0.279165088 VS(ph)PSFSAELK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSPSFSAELK 10 0 Q13416 Q13416 ORC2 Origin recognition complex subunit 2 1 VS(0.997)PS(0.002)FSAELK 63.408 0.082635 84883000 84040 80892 68316 70730 84283 87760 84452 83250 113100 116580 TRUE FALSE 80755.62389 78585.03936 80662.22088 74380.38378 86994.03924 89534.56733 85485.54884 81530.85841 100261.3622 108683.9328 0.743031852 0.723060321 0.742172452 0.684373319 0.800431462 0.823806841 0.786551854 0.750164779 0.922503995 1 16.72977915 0.591194573 0.392074002 1.029501464 0.723904114 0.774483721 0.043539542 1.045080167 0.337742398 0.099400509 0.035886868 3.901167282 -0.591194573 -0.30559735 GFGFILFK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFILFK 8 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 168.43 0.00071391 192589000 520330 589140 535100 523280 493340 332600 624180 563210 620000 694890 FALSE TRUE 499994.9283 572338.304 631804.4732 550286.5435 509208.7291 339325.3999 631818.9016 551579.5167 549620.1993 647824.4814 0.771806165 0.883477424 0.975271067 0.849437709 0.786028845 0.523792184 0.975293339 0.851433579 0.848409122 1 19.30524346 0.593161183 0.9522783 0.998953617 0.824925187 0.15765019 0.120197023 2.690790456 3.901768036 0.119972838 0.038851048 3.918872944 -0.593161183 -0.174028431 GVVIPTWNIS(ph)PIKK ddPTM_BT-474_Pertuzumab_2h_R1 2 GVVIPTWNISPIKK 14 1 A4PB68;Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2 A4PB68;Q3T8J9-3 GON4L GON-4-like protein 1 GVVIPTWNIS(1)PIKK;GVVIPTWNIS(1)PIKK 122.1 6.78E-05 465240000 564550 480980 355880 351440 452980 398720 418710 489240 508990 571730 TRUE FALSE 542486.7619 467262.9213 420195.4325 369577.8605 467550.5131 406782.3916 423834.2982 479137.023 451211.5891 533006.2179 1.017786929 0.876655667 0.788349964 0.69338377 0.877195232 0.763185077 0.795177024 0.898933271 0.846540948 1 19.02379284 0.599952302 1.003908025 0.999232166 0.82859046 0.2476812 0.083669516 1.859120105 2.957875995 0.081954567 0.026182124 3.980634496 -0.599952302 -0.170641706 EKENNPSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKENNPSGK 9 1 I3VM54;Q9Y2K7;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 ; 94.801 0.0077301 82832000 159883 138112 131059 128005 137427 143459 146823 157622 173148 192363 FALSE TRUE 153634.5956 134173.181 154744.2767 134611.3534 141847.4643 146359.8393 148619.8638 154367.0506 153492.9649 179334.0827 0.856694909 0.748174463 0.862882696 0.750617793 0.790967685 0.816129523 0.828731837 0.860779213 0.85590515 1 17.45229017 0.601343466 0.590552069 1.004705779 0.798810382 0.713251072 0.036525072 0.717393336 0.472285439 0.041241448 0.014591704 3.993405998 -0.601343466 -0.205895397 AASAPAKES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 9 AASAPAKESPR 11 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR 157.28 1.98E-05 12647110000 25601530 23362450 18671590 20349550 20442940 21990740 22314550 23524120 25348210 25839130 TRUE FALSE 24600993.9 22696175.8 22045961.66 21399792.71 21100505.73 22435407.83 22587642.14 23038338.7 22470787.47 24089022.71 1.021253299 0.942179186 0.915187051 0.888362844 0.875938637 0.931354007 0.937673662 0.956383286 0.932822711 1 24.52187253 0.603277887 0.783998047 0.999606647 0.927255258 0.215433882 0.037571924 2.06894572 2.200697983 0.040055117 0.013655894 4.011232972 -0.603277887 -0.072351388 IMEYYEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IMEYYEK 7 0 P36543;C9J8H1;P36543-3;P36543-2;Q96A05 P36543 ATP6V1E1;ATP6V1E2 V-type proton ATPase subunit E 1;V-type proton ATPase subunit E 2 0 94.662 0.032653 62960000 106760 102620 92562 104310 102560 89451 118060 116470 128960 149420 FALSE TRUE 102587.7012 99693.37808 109290.0124 109693.4516 105858.9355 91259.76051 119504.8536 114064.8538 114321.0014 139299.6503 0.736453401 0.715675724 0.784567744 0.787463941 0.759936836 0.655132732 0.857897729 0.818845227 0.820684052 1 17.08783211 0.608444623 0.501852665 1.011239453 0.741485168 0.711200738 0.047422214 0.897098931 0.44863811 0.071057954 0.025477136 4.059239 -0.608444623 -0.269754285 RKQEELQQLEQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 RKQEELQQLEQQR 13 2 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 235.25 6.23E-17 1607210000 1055170 1065250 769600 918580 964160 1057960 991390 967900 1112180 949630 FALSE TRUE 1013932.79 1034870.113 908683.8397 965988.0239 995173.082 1079352.676 1003522.927 947912.5268 985929.989 885310.7143 1.145284671 1.16893436 1.026401042 1.091128807 1.1240947 1.219179502 1.133526243 1.070711685 1.113654193 1 19.75582436 0.622982233 0.979089387 1.000777526 1.125218137 0.355373154 0.04974489 1.480657293 2.31578648 0.050770581 0.016375786 4.19741812 -0.622982233 0.124440611 FS(ph)PVLGR ddPTM_BT-474_Pertuzumab_2h_R1 9 FSPVLGR 7 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 FS(1)PVLGR;FS(1)PVLGR;FS(1)PVLGR;FS(1)PVLGR;FS(1)PVLGR;FS(1)PVLGR;FS(1)PVLGR;FS(1)PVLGR;FS(1)PVLGR 167.04 0.001155 3625133000 2868564 3072295 2568526 2803902 2668752 2521297 2936822 2965052 3239600 3207864 TRUE FALSE 2756457.348 2984676.155 3032715.785 2948611.718 2754594.832 2572279.353 2972763.706 2903822.64 2871854.19 2990592.514 0.921709439 0.998021677 1.014085259 0.985962382 0.921086647 0.860123651 0.994038369 0.970985725 0.960296054 1 21.51199992 0.623700259 1.057952612 0.999523857 0.958676469 0.074305038 0.043891264 4.017980348 7.142500316 0.04487165 0.014159456 4.204363519 -0.623700259 -0.040847388 FKLDLDFPNLPYLLDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKLDLDFPNLPYLLDGK 17 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 156.39 5.92E-08 452460000 1473670 1178940 1102300 1142670 1257810 1288770 1580200 1487050 1667960 2076120 FALSE TRUE 1416077.347 1145317.786 1301510.131 1201643.336 1298268.601 1314829.812 1599538.96 1456341.898 1478620.173 1935502.543 0.731632904 0.591741814 0.672440414 0.620843067 0.670765639 0.679322183 0.82642049 0.752436055 0.763946386 1 20.88427677 0.624195909 0.348045412 1.040351913 0.630150621 0.796436555 0.050295308 0.97202611 0.263849489 0.128110262 0.049333728 4.209164599 -0.624195909 -0.410201292 DRS(ph)PLRR ddPTM_BT-474_Pertuzumab_2h_R1 5 DRSPLRR 7 2 Q96PK6;Q9BWF3;E9PB51;Q9BQ04 Q96PK6;Q9BWF3 RBM14;RBM4;RBM4B RNA-binding protein 14;RNA-binding protein 4;RNA-binding protein 4B 1 DRS(1)PLRR;DRS(1)PLRR;DRS(1)PLRR;DRS(1)PLRR;DRS(1)PLRR 76.943 0.03102 54265900000 6216290 5879840 4555220 5654260 5538850 5882560 5598410 5791630 6407650 5756020 TRUE FALSE 5973350.514 5712152.72 5378449.584 5946077.036 5717012.141 6001509.394 5666925.016 5672030.817 5680280.435 5366159.638 1.113151847 1.064476852 1.002290268 1.108069353 1.06538242 1.118399339 1.056048533 1.057000015 1.058537356 1 22.35545854 0.628019392 0.908829958 1.000129618 1.074018625 0.323133643 0.032248554 1.494108918 2.076824073 0.030920969 0.010197867 4.246385248 -0.628019392 0.073889007 LKAEQEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKAEQEAR 8 1 Q8N5G2;Q8N5G2-2;Q8N5G2-3 Q8N5G2 TMEM57 Macoilin 0 ; 108.98 0.0033807 964870000 1167300 1191000 1109500 1235700 1111240 756490 1350010 1222230 1384200 1554870 FALSE TRUE 1121680.625 1157033.846 1310011.331 1299474.625 1146984.044 771786.7461 1366531.826 1196990.523 1227071.419 1449557.27 0.773809113 0.798198091 0.903732028 0.896463115 0.791265076 0.532429289 0.942723585 0.825762837 0.846514618 1 20.4671809 0.636552436 0.971324014 0.999208936 0.80477629 0.231009792 0.105943029 1.872092522 2.929608132 0.103903687 0.033643142 4.330643517 -0.636552436 -0.194432645 ELPSLSPAPDT(ph)GLSPSKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 ELPSLSPAPDT(0.915)GLS(0.061)PS(0.024)KR 85.224 0.0021524 1154400000 294860 340800 264400 315560 264770 270470 294490 309240 345950 366300 TRUE FALSE 283336.5452 331080.7177 312182.9615 331846.0894 273286.5675 275939.0887 298094.0567 302854.0859 306679.2063 341490.1747 0.829706288 0.96951755 0.914178459 0.971758821 0.800276517 0.808044006 0.872921328 0.886860321 0.898061581 1 18.38148454 0.637953898 2.198825845 0.999985028 0.883201051 0.281528191 0.056351378 3.233424114 17.87580431 0.056065361 0.01523418 4.344641012 -0.637953898 -0.116783977 KVEAPFIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEAPFIPK 9 1 P22694-2;P22694-4;A0A0A0MS54;P22694-9;P22694-6;P22694-7;P22694-5;P22694;P22694-3;P22694-10;A0A087WVC4;P22612;P17612-2;P17612 P22694-2;P17612-2 PRKACB;PRKACG;PRKACA cAMP-dependent protein kinase catalytic subunit beta;cAMP-dependent protein kinase catalytic subunit gamma;cAMP-dependent protein kinase catalytic subunit alpha 0 87.298 0.021869 0 1002100 1116400 875000 942220 1006700 846590 987190 1081600 1117100 1147400 FALSE TRUE 962936.8241 1084561.365 1033131.964 990848.0871 1039081.42 863708.6298 999271.5265 1059264.582 990291.4913 1069685.576 0.900205486 1.013906693 0.965827704 0.926298446 0.971389578 0.807441597 0.934173134 0.990257891 0.92577811 1 20.02875536 0.638598991 0.986998667 0.998711272 0.937739327 0.099917028 0.054247987 3.045905278 4.904773261 0.053258471 0.017167291 4.351099266 -0.638598991 -0.060971945 EKFEPTVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKFEPTVFR 9 1 E7ETZ4;Q9Y6E2;Q75MG1;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ; 93.843 0.0083219 1242210000 536580 566530 452360 516680 515230 468520 566960 551220 634020 677480 FALSE TRUE 515609.8604 550373.1191 534111.5147 543345.9167 531802.8409 477993.7954 573898.6261 539837.1144 562048.7076 631593.6762 0.816363241 0.871403784 0.845656844 0.860277639 0.842001529 0.75680586 0.908651634 0.854722165 0.889889701 1 19.2686372 0.640054436 0.853710649 1.00043777 0.840305835 0.633923628 0.036247907 0.749144292 0.949071109 0.034496104 0.01161168 4.365705506 -0.640054436 -0.160131936 EFNFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFNFEK 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 103.92 0.079739 721120000 593250 656100 566740 604110 646410 577710 613220 652710 719800 727740 FALSE TRUE 570065.1341 637388.6704 669162.5251 635288.1895 667202.3647 589391.692 620724.7698 639231.3104 638091.3216 678449.5216 0.84024694 0.939478399 0.986311441 0.936382397 0.983422264 0.8687333 0.914916659 0.942194356 0.940514071 1 19.37188195 0.644495454 1.525358602 0.999889679 0.92873785 0.209536813 0.042711928 2.261296717 7.464931608 0.040337462 0.01167092 4.410577463 -0.644495454 -0.07115183 IEVLDS(ph)PASK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEVLDSPASK 10 0 Q8N5I9 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 IEVLDS(1)PASK 147.96 2.72E-05 156450000 475440 426630 396990 432590 381590 410800 453610 494030 528000 624590 TRUE FALSE 456859.2792 414462.9301 468734.924 454916.0217 393864.1889 419106.6575 459161.4149 483828.1079 468063.6536 582285.963 0.784596072 0.711785886 0.804990939 0.781258781 0.676410242 0.719760881 0.788549689 0.830911508 0.80383812 1 19.15136831 0.646481349 0.705056312 1.001365396 0.747643813 0.761619001 0.040922451 0.611210991 0.56442074 0.044860163 0.015918047 4.430791859 -0.646481349 -0.253721584 VHAYFAPVT(ph)PPPSVGGSR ddPTM_BT-474_Pertuzumab_2h_R1 5 VHAYFAPVTPPPSVGGSR 18 0 J3KTA1;Q96IG2-2;Q96IG2 J3KTA1 FBXL20 F-box/LRR-repeat protein 20 1 VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(0.987)PPPS(0.011)VGGS(0.002)R;VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(1)PPPSVGGSR 173.56 2.95E-11 4926760000 1065010 1589690 1015920 1889880 1095600 1165860 1638850 1359740 1530420 1160280 TRUE FALSE 1023388.232 1544353.598 1199519.343 1987416.933 1130840.969 1189434.488 1658906.737 1331660.894 1356693.138 1081693.202 0.946098422 1.427718686 1.108927504 1.837320351 1.045435958 1.099604292 1.533620377 1.231089269 1.254230992 1 20.04485994 0.660306141 2.014254648 1.000212795 1.291998779 0.09766023 0.250702638 3.848407847 19.83956074 0.224177987 0.061758714 4.574105117 -0.660306141 0.291785984 VTSLEEELTDLRVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTSLEEELTDLRVEK 15 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 0 99.069 0.0024484 28481000 43106 41872 26070 33978 45219 42404 30234 40234 37792 26660 FALSE TRUE 41421.36986 40677.85156 30781.42892 35731.60865 46673.5102 43261.43793 30604.01274 39403.15384 33502.0106 24854.29445 1.666567922 1.636652838 1.238475266 1.43764325 1.877885139 1.740602133 1.231337015 1.585366018 1.347936497 1 14.60120753 0.660498588 0.852517033 0.997480879 1.565579488 0.434930809 0.194042942 1.152214567 1.483426419 0.196530538 0.06644646 4.576132465 -0.660498588 0.568098609 SS(ph)PQLDPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.201)S(0.799)PQLDPLR 93.162 0.010055 2766400000 921440 910020 987810 1029600 977670 585310 1092200 1064300 1129500 1314400 TRUE FALSE 885429.1061 884067.1206 1166329.241 1082737.779 1009117.643 597145.3692 1105566.67 1042321.833 1001283.895 1225374.517 0.722578358 0.721466872 0.951814506 0.883597434 0.823517732 0.487316621 0.902227568 0.850614909 0.81712479 1 20.22479132 0.6631814 0.889510411 0.998308944 0.787940859 0.205698364 0.123254761 1.930073411 2.675212926 0.12312124 0.041096749 4.604488577 -0.6631814 -0.210368084 SFKDEWTQLDMFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFKDEWTQLDMFYR 14 1 Q9NRN7;E9PLW6;E9PNF3 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 58.671 0.097583 143240000 199270 178940 150690 153350 211040 139220 195940 187430 206310 212660 FALSE TRUE 191482.3081 173836.8064 177923.0351 161264.4119 217828.2933 142035.1238 198337.9723 183559.505 182890.5537 198256.3488 0.96583191 0.876828447 0.897439281 0.813413608 1.098720392 0.716421566 1.000411707 0.925869492 0.922495319 1 17.59700754 0.663737954 0.58989649 1.001241844 0.902906232 0.069958645 0.097443841 3.623101503 2.498864301 0.106151157 0.039319609 4.610393072 -0.663737954 -0.098335613 AQSELAAHQK ddPTM_BT-474_Pertuzumab_2h_R1 6 AQSELAAHQK 10 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;;;; 180.19 2.02E-06 2762900000 3012280 3037770 2709020 2933070 2982530 2384350 3299990 3104510 3519360 3732140 FALSE TRUE 2894556.767 2951135.774 3198600.176 3084446.094 3078465.786 2432563.191 3340376.265 3040400.784 3119857.007 3479358.834 0.831922462 0.848183793 0.919307358 0.886498416 0.88477962 0.699141223 0.960055121 0.873839385 0.896675841 1 21.73039004 0.664550069 0.83419051 0.999794932 0.85898808 0.299334861 0.064169394 1.455663515 1.813325484 0.061918664 0.021093194 4.619022412 -0.664550069 -0.140806852 SVS(ph)SDS(ph)LGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSSDSLGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR 44 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 S(0.449)VS(0.516)S(0.039)DS(0.673)LGPPRPAPART(0.317)PT(0.006)QPPPEPGDLPTIEEALQIIHSAEPR 78.342 0.0010935 40508000 9186.8 9204.8 6633.2 6108.9 9708.7 10622 6765.9 8696.1 8874.5 6586.9 TRUE FALSE 8827.769699 8942.288116 7831.966795 6424.181061 10020.98915 10836.78412 6848.703108 8516.522496 7867.103965 6140.763396 1.437568773 1.456217662 1.275406051 1.046153491 1.63188003 1.764729142 1.115285294 1.386883348 1.281128006 1 12.5842023 0.666454521 0.944372239 1.00070212 1.397573558 0.255505101 0.202518137 1.647259431 2.532523157 0.200809657 0.06580839 4.639322049 -0.666454521 0.396871438 EMFFEDHIDDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 EMFFEDHIDDAK 12 0 Q9UIV1 Q9UIV1 CNOT7 CCR4-NOT transcription complex subunit 7 0 ;;; 158.4 6.11E-05 834890000 1077420 1052090 940590 969090 1092440 1137710 1145240 1074960 1427670 1366640 FALSE TRUE 1035313.235 1022085.423 1110575.536 1019104.851 1127579.325 1160715.276 1159255.79 1052761.7 1265606.887 1274076.256 0.812599113 0.802216837 0.871671167 0.799877438 0.885017141 0.911024965 0.90987944 0.826294106 0.993352542 1 20.2810202 0.672001503 0.025903584 1.853228394 3.12E-08 0.630703302 0.042574203 190.9960636 2.457480413 92.16097646 82.96061034 4.698957348 -0.672001503 -1.853228363 VKDILSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKDILSK 7 1 Q52LJ0;Q52LJ0-1;H0YNA1 Q52LJ0 FAM98B Protein FAM98B 0 67.563 0.08438 0 654670 611390 498550 540370 556270 584210 597830 639660 713160 785850 FALSE TRUE 629084.7726 593953.7558 588649.0752 568258.5605 574162.9297 596023.1265 605146.4224 626450.7975 632205.0666 732623.6795 0.858673819 0.810721483 0.803480821 0.77564864 0.783707851 0.813546085 0.825998994 0.855078555 0.862932887 1 19.48271281 0.676249543 0.743071306 1.001070859 0.804749375 0.871017853 0.021871703 0.390282668 0.403733145 0.023337402 0.008259121 4.745145598 -0.676249543 -0.196321485 DLLHPSLEEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLHPSLEEEK 11 0 H0YMV8;Q71UM5;C9JLI6 H0YMV8 RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ; 223.71 6.74E-12 540590000 1401100 1566710 1333390 1388580 1408790 1294080 1480110 1513650 1678060 1709670 FALSE TRUE 1346343.463 1522028.965 1574363.234 1460244.78 1454105.01 1320247.184 1498224.029 1482392.599 1487573.664 1593872.528 0.844699585 0.954925151 0.987759815 0.916161584 0.912309475 0.828326708 0.939989869 0.930057186 0.933307801 1 20.60410482 0.677203473 1.142340939 0.999653595 0.915098046 0.251368783 0.044801321 1.62454235 3.4813078 0.043590463 0.013513785 4.755579789 -0.677203473 -0.084555549 EGDIIPPLTGAT(ph)PPLIGHLK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGDIIPPLTGATPPLIGHLK 20 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7C3N7 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 EGDIIPPLT(0.003)GAT(0.997)PPLIGHLK;EGDIIPPLTGAT(1)PPLIGHLK;EGDIIPPLTGAT(1)PPLIGHLK 202.46 4.26E-21 382241000 620850 619560 533020 543570 568720 683050 638280 628990 804630 820880 TRUE FALSE 596586.4956 601890.7554 629348.571 571623.7128 587013.3953 696861.739 646091.4616 616001.1367 713291.7757 765281.0664 0.77956521 0.786496337 0.822375724 0.746946106 0.76705595 0.910595818 0.844253817 0.804934505 0.932065103 1 19.54563018 0.688496062 0.355116491 1.026117983 0.773831564 0.69513877 0.043162443 1.296772312 0.381720034 0.107080316 0.043957893 4.880856758 -0.688496062 -0.252286419 TRPWLQELSMGS(ph)PGPVTNK ddPTM_BT-474_Pertuzumab_2h_R1 1 TRPWLQELSMGSPGPVTNK 19 1 A0A1B0GV70;Q96N21-2;Q96N21 A0A1B0GV70 ENTHD2 AP-4 complex accessory subunit tepsin 1 TRPWLQELSMGS(1)PGPVTNK 158.67 2.11E-11 285730000 388080 357830 277500 306530 329940 349190 320660 374480 408390 452950 TRUE FALSE 372913.4046 347625.0388 327650.423 322350.05 340552.8197 356250.861 324584.333 366746.8571 362031.2793 422271.2931 0.883113322 0.823226784 0.775923981 0.763371925 0.806478739 0.84365399 0.768663033 0.868510039 0.857342863 1 18.68781065 0.697565808 0.926785811 0.999866074 0.807826569 0.696395171 0.036982081 0.564234401 0.865062613 0.035714743 0.011819924 4.983859697 -0.697565808 -0.192039505 RVNALK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVNALK 6 1 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6;F8VRJ2;F8VVB5 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 130.01 0.025572 1490790000 1520330 1573480 1344490 1414990 1416690 1462200 1565300 1592700 1791170 1870890 FALSE TRUE 1460913.823 1528605.891 1587469.251 1488017.803 1462259.12 1491766.686 1584456.61 1559810.188 1587843.891 1744172.954 0.837596879 0.87640729 0.910155869 0.853136611 0.838368189 0.855285987 0.908428609 0.894297888 0.910370664 1 20.73411168 0.697711386 0.643282458 1.001742654 0.863920133 0.763308827 0.022513617 0.605720342 0.49775816 0.025878497 0.00961015 4.985530599 -0.697711386 -0.137822521 VNLAELFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNLAELFK 8 0 P30044-2;P30044;P30044-3 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ; 132.9 0.0021927 497190000 763400 812200 733380 837780 803770 554090 882610 893720 877800 984860 FALSE TRUE 733565.484 789036.8512 865918.0799 881017.9262 829623.992 565294.0794 893411.6452 875264.3697 778155.824 918154.555 0.798956428 0.859372583 0.9431071 0.959552966 0.903577712 0.6156851 0.973051476 0.95328653 0.847521607 1 19.8083775 0.697906238 0.680017555 0.997622451 0.868617792 0.116616603 0.101626947 2.750508949 2.487363913 0.110627117 0.04048125 4.987767923 -0.697906238 -0.12900466 DLAKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLAKPR 6 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 88.734 0.046482 366920000 380920 405650 318490 380130 371020 381030 336580 357600 394650 289580 FALSE TRUE 366033.2253 394081.2592 376048.2278 399748.5549 382954.1953 388734.6877 340699.1667 350215.435 349850.9865 269966.4887 1.355846894 1.459741396 1.392944101 1.480733986 1.418524933 1.439936822 1.262005401 1.297255214 1.295905237 1 18.04242081 0.697958583 0.478416973 0.982134211 1.437419945 0.855782852 0.050780735 0.516062655 0.253855929 0.073800715 0.028948423 4.988369132 -0.697958583 0.455285734 LLVHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLVHLK 6 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 84.566 0.055705 1165420000 1303350 1339140 1171360 1288580 1294510 1113380 1432200 1411540 1541370 1664150 FALSE TRUE 1252413.641 1300949.038 1383050.809 1355083.768 1336149.09 1135893.306 1449727.692 1382391.206 1366400.14 1551435.638 0.807261101 0.838545284 0.891465153 0.873438598 0.86123398 0.732156255 0.934442691 0.891039997 0.880732726 1 20.56517242 0.699810402 0.600610021 1.00197883 0.843205849 0.455536951 0.050086593 1.176251985 0.859820537 0.057844843 0.021855249 5.009684799 -0.699810402 -0.15877298 FLRPHYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLRPHYGK 8 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 114.6 0.001577 1508460000 2618500 2772500 2419800 2650700 2541000 2029610 2772000 2677600 3100800 3338800 FALSE TRUE 2516166.125 2693431.015 2857111.688 2787502.945 2622733.573 2070650.105 2805924.565 2622306.624 2748810.184 3112660.102 0.808365206 0.865314852 0.917900315 0.89553721 0.842601982 0.665234891 0.901455499 0.842464817 0.883106441 1 21.56971661 0.707100662 1.535740854 0.99993091 0.842823958 0.333330659 0.067160395 1.265617981 4.666251997 0.065611234 0.018995841 5.094489387 -0.707100662 -0.157106952 SAS(ph)PSTQQEK ddPTM_BT-474_Pertuzumab_2h_R1 5 SASPSTQQEK 10 0 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 1 SAS(1)PSTQQEK;SAS(1)PSTQQEK;SAS(0.994)PS(0.006)TQQEK;SAS(1)PSTQQEK;S(0.015)AS(0.96)PS(0.022)T(0.003)QQEK 250.13 3.88E-13 1179869000 2010195 1893036 1607864 1829867 1744805 1780915 2059020 1886384 2292329 2330805 TRUE FALSE 1931634.357 1839048.467 1898440.792 1924306.655 1800928.237 1816926.322 2084218.903 1847429.511 2032113.422 2172937.501 0.88895072 0.84634209 0.873674825 0.885578464 0.828798912 0.836161335 0.959171123 0.850199101 0.935191841 1 21.05121525 0.709034517 0.692842671 1.00203912 0.863757951 0.561334231 0.035879543 0.815334995 0.767911221 0.03582592 0.013095758 5.117225048 -0.709034517 -0.138281169 LQHALEDQIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQHALEDQIYR 11 0 Q8ND04;Q8ND04-2;Q8ND04-3 Q8ND04 SMG8 Protein SMG8 0 ; 173.72 1.18E-05 2465200000 2754100 3114000 2526400 2749600 2643100 1991100 3041600 2805400 3213400 3279200 FALSE TRUE 2646466.727 3025191.769 2982976.679 2891507.186 2728117.712 2031361.406 3078824.011 2747467.51 2848628.304 3057096.863 0.86567971 0.989563597 0.975754715 0.945834337 0.892388378 0.664474008 1.007107118 0.898717847 0.931808324 1 21.54373083 0.710211691 1.325899309 0.999757771 0.905871103 0.089359548 0.091590268 2.701069027 7.772748452 0.088371636 0.026418894 5.131114323 -0.710211691 -0.093886668 (ac)SDEFSLADALPEHS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 5 SDEFSLADALPEHSPAK 17 0 Q8NDC0 Q8NDC0 MAPK1IP1L MAPK-interacting and spindle-stabilizing protein-like 1 SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(0.999)PAK 127.61 2.04E-88 5267375000 2385333 2169283 1834901 1786253 1907721 2050002 2170390 2140976 2373206 2358576 TRUE FALSE 2292111.549 2107417.173 2166508.428 1878441.731 1969084.579 2091454.445 2196951.882 2096764.097 2103809.604 2198827.547 1.042424429 0.958427675 0.985301658 0.854292432 0.895515695 0.95116802 0.999146971 0.953582786 0.956786996 1 21.06830303 0.710588808 0.733954252 0.999013632 0.949110799 0.065153054 0.049329208 3.273147755 3.407552277 0.052582723 0.018882398 5.135571827 -0.710588808 -0.049902833 EFLLIFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFLLIFHK 8 0 Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2;C9JTV4 Q9BUP0 EFHD1;PP1187 EF-hand domain-containing protein D1 0 ; 98.392 0.0075549 658670000 800060 887510 790620 904340 686950 446290 997850 819980 989740 1111580 FALSE TRUE 768792.7707 862199.0838 933502.6212 951013.0958 709046.3706 455314.2896 1010061.987 803047.1265 877388.8645 1036291.697 0.741869083 0.832004238 0.900810674 0.917707919 0.684215046 0.439368849 0.974688874 0.774923826 0.846662062 1 19.98299872 0.714675422 1.140408528 0.999270076 0.781554793 0.177689457 0.141632743 1.796091565 3.998808574 0.138761027 0.043133323 5.184124487 -0.714675422 -0.217715283 NSLS(ph)PVQATQKPLVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLSPVQATQKPLVSK 16 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NS(0.005)LS(0.995)PVQATQKPLVSK 166.27 4.08E-09 814340000 300680 299210 304650 300200 315570 324820 341190 368350 443100 465890 TRUE FALSE 288929.0932 290676.8238 359707.0319 315693.358 325720.5956 331388.083 345365.5853 360743.4438 392801.1456 434334.8553 0.665221982 0.669245906 0.828179059 0.72684325 0.749929672 0.762978331 0.795159728 0.830565264 0.904373989 1 18.72844821 0.715675267 0.150299018 1.170580597 0.579723145 0.831990936 0.040303018 3.392029632 0.297108868 0.642597017 0.380558434 5.196073277 -0.715675267 -0.590857452 KKPFVYTQGQAVLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KKPFVYTQGQAVLNR 15 2 Q9H4A4;A6NKB8;C9JMZ3;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 267.11 1.21E-25 1991300000 1786600 1737800 1509000 1682700 1507500 1613600 1743300 1931600 1990500 2275200 FALSE TRUE 1716777.697 1688239.645 1781709.868 1769544.349 1555990.107 1646228.098 1764635.027 1891711.785 1764546.785 2121098.677 0.809381343 0.795926971 0.839993861 0.834258381 0.733577425 0.776120468 0.831943863 0.891854681 0.831902261 1 21.01638031 0.718514729 0.65771834 1.000245483 0.799876843 0.711802743 0.03658229 0.654930062 0.567971577 0.041922278 0.015625795 5.230157038 -0.718514729 -0.200368641 VDDQIYSEFRK ddPTM_BT-474_Pertuzumab_2h_R1 3 VDDQIYSEFRK 11 1 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 ;; 196.38 9.73E-08 1235700000 1545770 1672870 1099160 1157470 1342160 1555520 1334480 1544280 1577550 1427160 FALSE TRUE 1485359.599 1625161.386 1297802.663 1217207.165 1385331.795 1586973.68 1350811.765 1512390.078 1398473.138 1330497.182 1.116394397 1.221469243 0.975426841 0.914851367 1.041213626 1.192767412 1.015268415 1.136710471 1.051090642 1 20.34353402 0.719533001 0.006345797 3.51E-06 2.112566532 0.045437146 0.090916849 24834.67101 81.11285152 13663.60069 13332.83826 5.242434352 -0.719533001 2.112563018 NDSWGSFDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 ;;; 133.12 0.00047799 926590000 978720 1006780 867300 899200 927480 859460 954840 972170 1089270 1119060 FALSE TRUE 940470.5404 978067.6201 1024040.403 945607.8198 957313.2365 876838.8701 966525.6175 952094.3498 965620.6362 1043265.069 0.901468445 0.937506343 0.981572596 0.906392678 0.917612661 0.840475633 0.926442997 0.912610206 0.925575546 1 19.99267433 0.719692393 3.173543992 0.999999013 0.916106327 0.36785592 0.033009192 3.011711562 32.78364856 0.032700728 0.008505056 5.244358754 -0.719692393 -0.083892686 FVS(ph)EGDGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 FVSEGDGGR 9 0 Q53EL6;Q53EL6-2 Q53EL6 PDCD4 Programmed cell death protein 4 1 FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR 169.21 6.15E-05 5309270000 4480190 4921740 3556990 4186080 4699830 3958680 3427430 4447060 3785790 2724420 TRUE FALSE 4305099.222 4781376.794 4199817.218 4402124.09 4851004.3 4038727.222 3469375.914 4355226.657 3356042.991 2539892.607 1.694992619 1.882511403 1.653541259 1.733193001 1.909924966 1.590117319 1.365953783 1.714728664 1.321332635 1 21.27633607 0.725260506 0.409183544 0.939165764 1.796979117 0.743986282 0.134765276 0.86772575 0.332711428 0.242373864 0.100210299 5.312029836 -0.725260506 0.857813353 KGDLLLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGDLLLNR 8 1 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 100.02 0.010266 1176110000 1215340 1333750 1188340 1076920 1043420 558070 1368900 1243000 1338260 1534990 FALSE TRUE 1167843.169 1295712.756 1403099.472 1132499.97 1076982.552 569354.5578 1385653.008 1217331.616 1186346.335 1431023.76 0.816089293 0.905444614 0.980486496 0.791391451 0.752595856 0.397865202 0.968294899 0.85067184 0.829019314 1 20.4486162 0.73405177 1.044706712 0.99684714 0.802668999 0.122679337 0.15424994 2.142211415 4.175405543 0.153519518 0.04904304 5.420655037 -0.73405177 -0.194178141 AVSVEAAERDWEEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVSVEAAERDWEEKR 15 2 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 ; 164.41 8.34E-07 283410000 350030 406760 201791 243380 306290 395040 271460 319300 339260 279560 FALSE TRUE 336350.4406 395159.6031 238259.1225 255940.871 316142.096 403027.9795 274782.2087 312706.3434 300748.6271 260625.1522 1.290552496 1.51619903 0.91418315 0.982026749 1.213014528 1.546389426 1.054319609 1.199831792 1.153950893 1 17.9916168 0.735260945 0.983683773 1.001040486 1.217701523 0.102992989 0.193915038 2.424534535 4.26100009 0.191593096 0.062413922 5.435768406 -0.735260945 0.216661037 LGNDFHTNK ddPTM_BT-474_Pertuzumab_2h_R1 4 LGNDFHTNK 9 0 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 111.06 0.0021866 2072150000 5702910 5243870 5258540 4949280 5121700 4426740 5596100 5659970 6299200 6770800 FALSE TRUE 5480033.972 5094319.962 6208875.154 5204712.934 5286444.132 4516251.716 5664586.746 5543089.642 5584141.224 6312207.685 0.868164396 0.807058357 0.983629732 0.824547162 0.837495278 0.715478948 0.897401833 0.878153875 0.884657398 1 22.58971324 0.736470943 1.056031541 0.999025197 0.847144191 0.33002234 0.064350081 1.084669779 2.159261649 0.06132801 0.01952961 5.450934238 -0.736470943 -0.151881006 FTFPDPPPLSPPVLGLHGVTFGYQGQKPLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTFPDPPPLSPPVLGLHGVTFGYQGQKPLFK 31 1 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 166.35 7.83E-13 217540000 209910 223600 178990 176190 211630 167600 207710 215100 230660 238280 FALSE TRUE 201706.4851 217223.1469 211337.4746 185283.187 218437.2711 170988.9868 210252.0171 210658.1098 204476.4438 222141.0834 0.90801072 0.977861203 0.951366003 0.834078885 0.983326757 0.769731489 0.94647966 0.948307745 0.920480087 1 17.76111671 0.738274883 0.982726859 0.998545246 0.912167683 0.142100123 0.062952503 1.834485691 3.227313113 0.058192898 0.018968647 5.47362302 -0.738274883 -0.086377563 DDGELGGNFLHSFQNDNYSPSMTMS(ph)V ddPTM_BT-474_Pertuzumab_2h_R1 2 DDGELGGNFLHSFQNDNYSPSMTMSV 26 0 Q9BWW4-2;Q9BWW4;Q9NW25;Q9BWW4-3 Q9BWW4-2 SSBP3 Single-stranded DNA-binding protein 3 1 DDGELGGNFLHSFQNDNYSPSMT(0.009)MS(0.991)V;DDGELGGNFLHSFQNDNYSPSMT(0.013)MS(0.987)V 190.77 4.33E-18 90036000 162616 174318 127483 150140 160351 168772 151596 158723 175917 150070 TRUE FALSE 156260.7869 169346.6213 150522.0139 157888.7434 165508.8355 172184.6855 153451.2772 155445.3146 155947.6397 139905.6252 1.116901387 1.210434684 1.075882501 1.128537492 1.183003437 1.230720246 1.096819924 1.111072656 1.114663112 1 17.09409445 0.740163323 0.809999677 1.000757735 1.152214657 0.477667858 0.046287335 0.869442357 1.097263102 0.045799187 0.015999371 5.497475754 -0.740163323 0.151456923 AHPPELK ddPTM_BT-474_Pertuzumab_2h_R1 3 AHPPELK 7 0 P62308;A8MWD9;C9JVQ0 P62308 SNRPG;SNRPGP15 Small nuclear ribonucleoprotein G;Putative small nuclear ribonucleoprotein G-like protein 15 0 ;; 84.244 0.021688 2421020000 2805550 2720970 2437190 2621520 2682720 2015500 2861780 2830550 3184800 3496990 FALSE TRUE 2695906.004 2643370.6 2877644.448 2756816.961 2769012.125 2056254.791 2896803.32 2772098.153 2823274.856 3260135.753 0.826930597 0.810816113 0.882676265 0.845614162 0.849354854 0.630726739 0.888552974 0.850301449 0.86599917 1 21.63650061 0.740502973 1.069726096 0.998975985 0.818751932 0.385710624 0.067983639 0.952125464 1.946124431 0.064742418 0.020541261 5.501776862 -0.740502973 -0.180224053 AVDWIFSHIDDLDAEAAMDISEGR ddPTM_BT-474_Pertuzumab_2h_R1 5 AVDWIFSHIDDLDAEAAMDISEGR 24 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;;; 227.19 4.61E-33 205778000 135758 126908.1 100872.3 122122 141681 140720 119912 121961 135402 144839 FALSE TRUE 130452.4273 123288.8052 119102.1685 128424.7311 146238.298 143565.4548 121379.5189 119442.4627 120031.7326 135028.9255 0.966107275 0.913054775 0.882049295 0.95109052 1.083014602 1.063220005 0.898914943 0.884569453 0.88893348 1 17.04290896 0.745684274 0.003631949 1.007009918 0.891027139 0 0.070661067 1758125.023 3656.250402 58735.24749 58012.67333 5.567808304 -0.745684274 -0.115982779 ERECSPSS(ph)PLPPLPEDEEGSEVTNSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERECSPSSPLPPLPEDEEGSEVTNSK 26 1 Q96GY3 Q96GY3 LIN37 Protein lin-37 homolog 1 ERECS(0.063)PS(0.399)S(0.538)PLPPLPEDEEGSEVTNSK 125.02 6.96E-05 230040000 62960 68680 55298 60072 59774 62759 67719 70408 74748 81210 TRUE FALSE 60499.45359 66721.31364 65291.5787 63172.32312 61696.685 64028.02998 68547.76538 68954.0502 66262.92041 75709.57437 0.799099111 0.881279735 0.862395268 0.834403358 0.814912586 0.84570585 0.905404184 0.910770544 0.875225108 1 16.20818814 0.749198014 0.41478909 1.009478376 0.834591002 0.729298065 0.02843171 0.903929952 0.360729241 0.051945872 0.021933727 5.613038414 -0.749198014 -0.174887374 DLGEELEALRGELEDTLDSTNAQQELR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGEELEALRGELEDTLDSTNAQQELR 27 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 191.62 4.23E-18 251679000 154181 166292 111276 126781 149514 166628 139942 152994 162911 141013 FALSE TRUE 148155.4361 161549.515 131386.0485 133324.1826 154323.2536 169997.3323 141654.6521 149834.6204 144418.0263 131462.0639 1.126982429 1.228867935 0.999421769 1.014164685 1.173899519 1.29312843 1.077532543 1.139755576 1.09855286 1 17.00428701 0.753085399 1.960343353 0.999977799 1.131758902 0.179321632 0.084665841 1.749643853 10.59232571 0.083625923 0.023196049 5.663506439 -0.753085399 0.131781103 AKPPADPAAAAS(ph)PCR ddPTM_BT-474_Pertuzumab_2h_R1 4 AKPPADPAAAASPCR 15 1 Q9GZT9-2;Q9GZT9 Q9GZT9-2 EGLN1 Egl nine homolog 1 1 AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR 140.95 2.94E-06 2120490000 2871380 2953690 2462980 2354160 2487800 2867850 2439850 2943490 3113880 2651940 TRUE FALSE 2759163.295 2869453.653 2908095.275 2475658.48 2567822.346 2925839.892 2469709.614 2882705.903 2760405.397 2472321.742 1.116021126 1.160631161 1.176260851 1.001349637 1.038627903 1.18343816 0.998943452 1.165991406 1.116523529 1 21.23743507 0.753770239 0.010065553 3.20E-07 2.155042827 0.143302489 0.068562278 4207.999402 22.54169559 2456.398441 2366.732508 5.67244428 -0.753770239 2.155042507 TDLQGSAS(ph)PSKVEGVHTPR ddPTM_BT-474_Pertuzumab_2h_R1 5 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 TDLQGSAS(0.967)PS(0.033)KVEGVHTPR;TDLQGSAS(1)PSKVEGVHTPR;TDLQGSAS(0.998)PS(0.001)KVEGVHTPR;TDLQGS(0.001)AS(0.997)PS(0.002)KVEGVHTPR;TDLQGS(0.001)AS(0.998)PS(0.001)KVEGVHTPR 241.82 1.34E-24 4052040000 3023740 2662980 2496790 2614460 2678850 2691260 2857730 2986140 3428200 3723740 TRUE FALSE 2905568.898 2587034.418 2948015.494 2749392.594 2765017.643 2745679.121 2892703.755 2924475.165 3039045.108 3471527.773 0.836971238 0.745214956 0.849198303 0.791983465 0.796484379 0.790913771 0.833265336 0.842417332 0.875420076 1 21.72713928 0.754353508 0.765598123 1.001178798 0.799912222 0.825241651 0.027235954 0.349217513 0.404262528 0.02461964 0.008811901 5.680067641 -0.754353508 -0.201266576 ETHADLWPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETHADLWPAK 10 0 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ; 110.38 0.0018935 827940000 750660 753780 681780 686910 699850 558460 866520 709820 880610 894390 FALSE TRUE 721323.3773 732282.9324 804992.8121 722361.5074 722361.3108 569752.4438 877124.731 695161.9689 780646.8446 833812.1687 0.865090969 0.878234883 0.965436632 0.86633601 0.866335774 0.683310301 1.051945227 0.833715308 0.936238249 1 19.6693629 0.761536169 0.998490685 1.000331249 0.874363102 0.156388631 0.088910318 1.653689234 3.053285397 0.081190446 0.026380759 5.774789641 -0.761536169 -0.125968146 AVS(ph)PSNPK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVSPSNPK 8 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AVS(0.92)PS(0.08)NPK;AVS(0.983)PS(0.017)NPK;AVS(0.996)PS(0.004)NPK 146.57 0.00057813 6517200000 2843350 2892110 2732200 2618410 2325770 2747060 2600220 3047010 3321540 3710940 TRUE FALSE 2732228.739 2809629.854 3225969.317 2753546.454 2400580.504 2802607.435 2632042.27 2984088.179 2944492.704 3459594.728 0.789753989 0.812126875 0.932470295 0.795915901 0.69389067 0.810097036 0.760794971 0.862554262 0.851109143 1 21.72217161 0.765181549 1.184759304 0.998902566 0.803149875 0.511456163 0.057514641 0.705029869 1.770091057 0.057049985 0.017598512 5.823466071 -0.765181549 -0.19575269 DRELALR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRELALR 7 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;; 152.63 0.0016423 1251940000 860520 961320 788980 912970 842970 691680 1025660 954890 989070 1061040 FALSE TRUE 826889.927 933904.0948 931566.2368 960088.4911 870084.8956 705666.2435 1038212.334 935171.1878 876794.9201 989174.8157 0.835939122 0.944124416 0.941760973 0.970595365 0.879606801 0.713388809 1.049574168 0.945405375 0.886390258 1 19.91586598 0.766072098 0.594353327 0.997585356 0.902943589 0.090336476 0.085230135 3.088302722 2.32332227 0.097344913 0.038294967 5.835419715 -0.766072098 -0.094641767 VAS(ph)CSCELLTDAVDLPRPPETTAVGAVVTAPHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VASCSCELLTDAVDLPRPPETTAVGAVVTAPHSR 34 1 O14492;O14492-2 O14492 SH2B2 SH2B adapter protein 2 1 VAS(0.571)CS(0.429)CELLTDAVDLPRPPETTAVGAVVTAPHSR 141.75 1.75E-10 63478000 34518 42757 27593 34417 30382 33014 32804 42514 30391 34623 TRUE FALSE 33168.9984 41537.61222 32579.6689 36193.26549 31359.26462 33681.5657 33205.46516 41636.07104 26941.14109 32277.95337 1.027605376 1.286872552 1.009347418 1.121299888 0.971538197 1.043485171 1.028735149 1.289922895 0.83466076 1 14.97826148 0.76957754 0.012745923 6.51E-07 2.101963281 0.056875202 0.128523337 3868.564136 26.61904921 2243.267062 2142.034673 5.88271136 -0.76957754 2.10196263 S(ph)ETPPVPPPPPYLASYPGFPENGAPGPPISR ddPTM_BT-474_Pertuzumab_2h_R1 1 SETPPVPPPPPYLASYPGFPENGAPGPPISR 31 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.5)ET(0.5)PPVPPPPPYLASYPGFPENGAPGPPISR 111.18 6.24E-05 163320000 194460 190080 155430 176500 193140 200730 195350 220400 245910 275290 TRUE FALSE 186860.2882 184659.1045 183519.6585 185609.1862 199352.5235 204788.8981 197740.7517 215848.663 217995.3277 256644.3631 0.728090366 0.71951358 0.715073794 0.723215519 0.776765642 0.797948163 0.770485466 0.841041901 0.849406257 1 17.96941105 0.769807794 0.301310502 1.044039023 0.69570349 0.961787935 0.016317802 0.426763778 0.102412556 0.050701727 0.023739038 5.885831079 -0.769807794 -0.348335534 VQVEYK ddPTM_BT-474_Pertuzumab_2h_R1 1 VQVEYK 6 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 119.89 0.047989 751820000 654690 648450 577650 651960 616620 494790 644900 737190 743780 877290 FALSE TRUE 629103.991 629956.8409 682044.2048 685607.7337 636454.1423 504794.9928 652792.4791 721966.7689 659349.2126 817870.3669 0.769197683 0.770240452 0.833927028 0.838284111 0.778184622 0.617206605 0.798161305 0.882739855 0.806178142 1 19.64151267 0.774870733 0.886107165 0.996780887 0.77619835 0.504660064 0.064635891 0.787816592 1.193496334 0.066711105 0.022654622 5.954848717 -0.774870733 -0.220582537 VTANNDKNR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTANNDKNR 9 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ;;; 143.5 9.28E-05 445053000 331103 337118 253896 307273 256788 211094 316864 298128 352807 384629 FALSE TRUE 318163.1287 327503.7247 299780.6551 323131.3964 265047.8192 215362.4653 320741.8764 291971.5526 312757.8284 358577.7352 0.887291924 0.913340937 0.836026963 0.901147407 0.739164184 0.600601889 0.894483524 0.814248973 0.872217647 1 18.45192639 0.776455264 1.796124738 0.99999562 0.820982736 0.260773609 0.08967191 1.165306322 6.348928955 0.089862054 0.025323353 5.976614778 -0.776455264 -0.179012884 EVDETRK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVDETRK 7 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 ; 79.469 0.052177 1003610000 1587050 1556530 1207910 1361480 1364990 1485970 1530170 1653370 1764120 1987140 FALSE TRUE 1525026.331 1512139.288 1426206.207 1431746.146 1408896.143 1516017.332 1548896.678 1619227.332 1563864.493 1852549.238 0.82320421 0.816247826 0.769861431 0.772851872 0.760517515 0.818341181 0.836089345 0.874053601 0.844168922 1 20.82108046 0.77689399 0.542051823 1.003590053 0.787089089 0.850876533 0.02536274 0.460279314 0.297055848 0.033123692 0.013478527 5.982655421 -0.77689399 -0.216500964 DKTYSYLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKTYSYLNK 9 1 G3V2V8;J3KMY5;H0YIZ1;G3V3E8;E7EMS2;G3V3D1;P61916-2;P61916 G3V2V8 NPC2 Epididymal secretory protein E1 0 ; 116.55 0.001929 725100000 1476390 1379200 1404940 1471670 1193300 1153540 1744950 1523570 1902310 2251600 FALSE TRUE 1418691.047 1339866.566 1658843.911 1547623.065 1231683.578 1176865.369 1766305.22 1492107.747 1686367.744 2099097.126 0.675857743 0.638306131 0.790265438 0.73728035 0.586768265 0.560653128 0.841459501 0.710833114 0.803377663 1 21.00133749 0.777769895 0.814348875 1.000238628 0.678855745 0.595715912 0.079184088 0.659695545 0.864765862 0.079125999 0.027779745 5.994733699 -0.777769895 -0.321382883 NDS(ph)PTQIPVSSDVCR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDSPTQIPVSSDVCR 15 0 Q8TC07-2;Q8TC07-3;Q8TC07 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 NDS(1)PTQIPVSSDVCR;NDS(0.691)PT(0.309)QIPVSSDVCR 335.46 5.17E-69 1602360000 756100 708370 561870 598880 687490 756150 732740 762970 868360 955570 TRUE FALSE 726550.7761 688167.9812 663412.4077 629788.2686 709603.7402 771439.8711 741707.4913 747214.4029 769787.4133 890848.3928 0.815571743 0.772486078 0.744697317 0.706953365 0.796548263 0.865960895 0.832585541 0.83876719 0.864105969 1 19.7648204 0.781772668 0.362341724 1.021007887 0.754331482 0.77930904 0.03580913 0.924004085 0.300783806 0.083177762 0.037411428 6.050240909 -0.781772668 -0.266676405 SALQHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SALQHEK 7 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 62.2 0.086891 113540000 135010 142950 137680 127380 128760 94627 158940 136720 169110 186010 FALSE TRUE 129733.6599 138873.206 162561.8387 133954.0971 132901.6823 96540.42277 160885.1553 133896.6842 149913.3418 173411.377 0.748126577 0.800830997 0.93743468 0.772464295 0.766395404 0.556713316 0.92776586 0.772133216 0.864495423 1 17.40383903 0.782561605 1.234288781 0.999981383 0.783506613 0.306635157 0.099146895 0.984870523 2.710824832 0.093653662 0.028601652 6.061241741 -0.782561605 -0.21647477 KKGDS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 KKGDSPER 8 2 Q9Y4E5-4 Q9Y4E5-4 ZNF451 Zinc finger protein 451 1 KKGDS(1)PER 67.153 0.04712 21784000 108910 100440 80219 67306 79220 83409 89740 96888 105220 115800 TRUE FALSE 104653.6768 97575.54954 94716.35776 70779.67073 81768.18325 85095.58713 90838.26496 94887.22894 93275.86672 107956.7629 0.969403621 0.903839157 0.877354556 0.655629799 0.757416035 0.788237669 0.841431908 0.87893733 0.864011334 1 16.7200941 0.784027852 0.998228387 0.998114566 0.823456424 0.275467329 0.081442007 1.175577939 2.211281856 0.084268157 0.027438749 6.081740029 -0.784027852 -0.174658143 LTEDFVSHLETELEQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTEDFVSHLETELEQSR 17 0 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 0 204.52 8.71E-12 18574000 20532 22036 18324 21227 19650 19121 21017 22371 23730 24269 FALSE TRUE 19729.58674 21407.55486 21635.55442 22322.52801 20282.0601 19507.63972 21274.21233 21909.03103 21036.26988 22625.23901 0.872016721 0.946180274 0.956257496 0.98662065 0.896435175 0.862207012 0.940286744 0.968344733 0.929770062 1 14.46564541 0.784986221 0.844066503 0.998447955 0.926397136 0.243551276 0.038288458 1.419015221 1.990376761 0.039234516 0.013596595 6.095175583 -0.784986221 -0.072050819 NAYAVLYDIILK ddPTM_BT-474_Pertuzumab_2h_R1 2 NAYAVLYDIILK 12 0 Q06323;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 186.72 2.65E-05 67019000 292710 272820 250230 236070 261390 242070 243560 282800 311430 334250 FALSE TRUE 281270.5696 265039.4407 295452.1273 248253.601 269797.8467 246964.8213 246540.7601 276960.0812 276077.772 311610.9498 0.90263378 0.85054598 0.948144241 0.796678041 0.865816323 0.792542179 0.791181312 0.888800863 0.885969419 1 18.2493864 0.785330859 1.631550042 0.999390944 0.851307233 0.451918789 0.048328185 0.678558119 3.146220733 0.045981 0.013194255 6.100014381 -0.785330859 -0.148083711 KFAEAFEAIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KFAEAFEAIPR 11 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 86.803 0.022765 523980000 772980 817440 638820 731080 751140 667140 770080 769080 875580 890370 FALSE TRUE 742771.087 794127.4116 754268.9845 768811.1264 775301.1003 680630.0279 779504.4694 753198.2292 776187.8291 830064.4468 0.894835443 0.956705729 0.908687256 0.926206549 0.934025187 0.81997251 0.939089094 0.90739729 0.935093452 1 19.66286383 0.785584364 2.054550008 1.000007201 0.911393905 0.371100029 0.034976088 0.850589265 5.992228046 0.032257933 0.008889086 6.103576096 -0.785584364 -0.088613297 NLTMS(ph)PLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLTMSPLHK 9 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 NLT(0.001)MS(0.999)PLHK 101.72 0.002443 105120000 91829 92443 76082 83988 86674 70634 87893 93363 100950 107470 TRUE FALSE 88240.22116 89806.61615 89831.70983 88322.63075 89461.94793 72062.26788 88968.66083 91435.02142 89490.57922 100190.9612 0.880720378 0.896354472 0.896604931 0.881542903 0.892914359 0.719249192 0.88799089 0.912607488 0.893200127 1 16.61239283 0.786098805 1.111518837 0.998364893 0.867104086 0.366255826 0.051518578 0.898554634 2.051471791 0.050647389 0.015933945 6.110810341 -0.786098805 -0.131260807 DLLEEEEAWEASHKNDLQDTEIS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLLEEEEAWEASHKNDLQDTEISPR 25 1 Q9NS91 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 DLLEEEEAWEASHKNDLQDTEIS(1)PR 304.42 9.28E-64 182970000 168020 162570 148910 157890 140900 152740 178890 174370 193090 210300 TRUE FALSE 161453.5926 157933.6628 175821.3495 166038.7218 145432.1765 155828.5075 181079.3093 170769.1986 171171.2327 196056.1937 0.823506718 0.80555304 0.896790589 0.846893529 0.741788228 0.79481553 0.923609226 0.871021697 0.873072304 1 17.58090769 0.78645772 0.591364367 1.001108162 0.823089879 0.546999648 0.046596674 0.912359736 0.689658763 0.05525065 0.022006994 6.115862599 -0.78645772 -0.178018283 DKSDSPAIQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKSDSPAIQLR 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 70.438 0.047211 624000000 689340 729840 638640 554840 655270 693780 689800 742960 797150 848090 FALSE TRUE 662399.8307 709025.6778 754056.4545 583475.3589 676347.3547 707808.7069 698241.9787 727617.6164 706660.8739 790648.1089 0.83779348 0.89676516 0.953719418 0.737970979 0.855434102 0.895225953 0.883126097 0.920279968 0.893774191 1 19.59267622 0.787325311 0.583665037 1.000931594 0.860805435 0.370512858 0.052734472 1.26393547 0.934357702 0.06014164 0.024072044 6.128092478 -0.787325311 -0.140126159 S(ph)RFTPELQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRFTPELQPK 10 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.5)RFT(0.5)PELQPK 87.498 0.0077729 486330000 246560 267830 240250 250540 240090 267010 230890 270890 298990 310490 TRUE FALSE 236924.1626 260191.7506 283668.5193 263470.3994 247812.7129 272409.1251 233715.7009 265296.0268 265049.9087 289460.2357 0.818503315 0.89888599 0.979991323 0.910212758 0.856120055 0.941093427 0.807419024 0.916519764 0.915669498 1 18.14300565 0.787704908 2.027290995 0.999743024 0.892348783 0.301804569 0.049892216 0.995388929 6.8823856 0.046658477 0.012886155 6.133451113 -0.787704908 -0.107394241 TPEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPEELR 6 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 98.133 0.093712 778910000 1117000 1153500 880760 1154700 997080 978880 958910 1122600 1250100 1340600 FALSE TRUE 1073346.405 1120603.309 1039932.924 1214294.205 1029151.984 998673.6243 970645.4274 1099417.918 1108193.889 1249799.968 0.858814556 0.896626131 0.832079494 0.971590844 0.823453361 0.799066771 0.776640624 0.879675105 0.886697005 1 20.25326578 0.789598047 2.019763908 0.999686587 0.853514655 0.417832861 0.0515905 0.785196953 5.415822965 0.050752132 0.014026209 6.16024588 -0.789598047 -0.146171931 KVVAEVYDQER ddPTM_BT-474_Pertuzumab_2h_R1 4 KVVAEVYDQER 11 1 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5 A0A0J9YVP6 PUF60 Poly(U)-binding-splicing factor PUF60 0 ;;; 134.68 0.0002176 3581080000 1848710 1778680 1667710 1964180 1781170 1479250 1944880 1987690 2189350 2396740 FALSE TRUE 1776460.369 1727953.788 1969102.295 2065551.565 1838462.951 1509161.449 1968682.023 1946643.507 1940824.167 2234406.665 0.795047919 0.773338987 0.881264063 0.924429558 0.822796933 0.675419328 0.881075972 0.871212719 0.868608296 1 21.09146035 0.791406337 0.927610444 0.998490127 0.822294221 0.396225368 0.065422731 0.925807113 1.539118545 0.065990354 0.02207317 6.185949032 -0.791406337 -0.176195905 ANKLDHVVTIIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ANKLDHVVTIIK 12 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;Q99873-5;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 163.99 3.51E-05 2653100000 3552960 3758400 3083590 3212310 3277470 3804700 3711700 3686200 4536700 4661600 FALSE TRUE 3414106.395 3651214.112 3640863.307 3378097.704 3382892.799 3881633.641 3757124.895 3610078.682 4021712.835 4345865.68 0.785598692 0.840158068 0.837776309 0.777312957 0.778416327 0.893178466 0.864528536 0.830692651 0.925411214 1 22.05121215 0.792459558 0.506522217 1.008206239 0.808419641 0.737750144 0.03447758 0.688191518 0.398772312 0.04602133 0.019289229 6.200968975 -0.792459558 -0.199786598 DIFLDDGVDEQVLMELK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIFLDDGVDEQVLMELK 17 0 J3KNC0;P52655 J3KNC0 GTF2A1 Transcription initiation factor IIA subunit 1;Transcription initiation factor IIA alpha chain;Transcription initiation factor IIA beta chain 0 192.51 4.24E-10 6841600 34503 30822 25987 28353 27546 23087 32174 33474 36148 42885 FALSE TRUE 33154.58461 29942.98674 30683.42898 29816.30173 28432.04211 23553.83496 32567.75504 32782.7502 32044.63058 39980.36075 0.829271772 0.748942385 0.767462534 0.745773704 0.711150214 0.589135128 0.814593826 0.819971346 0.801509291 1 15.28700387 0.793019285 0.89913441 0.997219295 0.739700622 0.585130937 0.063590435 0.617109761 0.97247126 0.063631832 0.021539733 6.208966042 -0.793019285 -0.257518673 SES(ph)EVEEAAAIIAQRPDNPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SESEVEEAAAIIAQRPDNPR 20 1 Q16643;Q16643-3;Q16643-2;D6R9W4;D6R9Q9 Q16643 DBN1 Drebrin 1 S(0.026)ES(0.974)EVEEAAAIIAQRPDNPR 104.77 0.00064689 0 35507 33223 24839 34987 30330 31810 32640 32522 34508 28335 TRUE FALSE 34119.34718 32275.51257 29327.95984 36792.68326 31305.592 32453.21999 33039.45808 31850.40933 30590.79651 26415.84521 1.291624285 1.221823959 1.110241206 1.392826274 1.185106581 1.228551263 1.250743931 1.205731222 1.158047235 1 14.68911595 0.795906987 1.280089563 1.000129525 1.238432909 0.530112878 0.068313115 0.556012704 1.659128265 0.061178527 0.018522956 6.250388132 -0.795906987 0.238303384 EVCFACVDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVCFACVDGK 10 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 123.88 0.0010475 314950000 256010 265430 192710 217060 250710 204040 255680 289350 272570 332840 FALSE TRUE 246004.8462 257860.1963 227536.9838 228262.4926 258774.3148 208165.8286 258809.0883 283374.8214 241628.9963 310296.4503 0.792805866 0.831012395 0.733289032 0.735627147 0.833958347 0.670861134 0.834070412 0.913239004 0.778703708 1 18.24328767 0.796657213 0.565277962 0.999857448 0.769096634 0.507465305 0.062908117 0.9344736 0.657250931 0.073460867 0.029872591 6.261194755 -0.796657213 -0.230760814 S(ph)PGSISYLPSFFTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGSISYLPSFFTK 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.977)PGS(0.023)ISYLPSFFTK;S(0.999)PGS(0.001)ISYLPSFFTK 238.88 2.55E-17 3883200000 5080400 4892700 4275400 4311200 4351900 4737300 4605900 4874400 5463300 5490400 TRUE FALSE 4881852.351 4753164.986 5048059.886 4533701.549 4491882.816 4833091.452 4662268.382 4773741.937 4843129.088 5118530.318 0.953760562 0.928619094 0.986232292 0.885742834 0.877572767 0.944234214 0.910860754 0.932639184 0.946195253 1 22.2872982 0.799641118 1.88437817 0.999917977 0.92610732 0.348340585 0.029923244 0.816710395 5.069840789 0.028885127 0.008079359 6.304361647 -0.799641118 -0.073810657 LEILQIHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEILQIHTK 9 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 115.57 0.0014539 6534900000 646880 742700 632060 539490 589090 339150 757330 671540 781480 925810 FALSE TRUE 621599.2144 721518.9232 746287.3021 567333.1436 608038.6148 346007.8454 766598.4311 657672.4643 692769.6666 863104.0641 0.720190346 0.835958204 0.864655067 0.657317196 0.704478915 0.400887749 0.88818772 0.761985132 0.802649061 1 19.71917499 0.803382799 1.05304873 0.997322032 0.721843753 0.29113949 0.129510356 1.04178212 2.190215493 0.125879972 0.040329304 6.358911773 -0.803382799 -0.275478279 KGEDVLGSVR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGEDVLGSVR 10 1 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 147.71 4.24E-05 1612700000 2513870 2667940 2347340 2468860 2322330 1962440 2885200 2644890 2991180 3225110 FALSE TRUE 2415625.181 2591852.963 2771556.554 2596278.16 2397029.854 2002121.881 2920509.941 2590272.097 2651633.786 3006670.427 0.803422004 0.862034276 0.921802579 0.863506069 0.797237313 0.665893363 0.971343555 0.861508489 0.881917008 1 21.51973531 0.80480362 0.840387901 0.997957592 0.837084547 0.289322243 0.075895629 1.1767985 1.661757375 0.075186211 0.026182314 6.379749398 -0.80480362 -0.160873045 ILQEHEQIK ddPTM_BT-474_Pertuzumab_2h_R1 3 ILQEHEQIK 9 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 166.19 6.09E-05 1342090000 1154530 1177770 1040380 1046200 1115360 855210 1230130 1157440 1374770 1500490 FALSE TRUE 1109409.691 1144181.153 1228399.809 1100194.507 1151236.567 872502.9322 1245184.699 1133538.46 1218711.873 1398860.476 0.793081019 0.817938009 0.878143196 0.786493383 0.822981696 0.623724058 0.89014217 0.810329893 0.871217605 1 20.41582064 0.80556607 1.193446983 0.999568295 0.799420963 0.444041245 0.067896015 0.678001443 1.793481029 0.062940831 0.019423358 6.39095957 -0.80556607 -0.200147332 NSVSNFLHSLER ddPTM_BT-474_Pertuzumab_2h_R1 2 NSVSNFLHSLER 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 203.74 1.22E-07 1040960000 825040 991170 887480 895650 764040 734340 950970 911220 1103510 1239290 FALSE TRUE 792796.5247 962902.8021 1047867.378 941874.6038 788616.0405 749188.8579 962608.2553 892402.9886 978244.1711 1155351.784 0.686194919 0.833428238 0.906968243 0.815227549 0.682576555 0.64845086 0.833173297 0.772408024 0.846706764 1 20.13990076 0.805755029 1.691334347 1.000022835 0.773860748 0.451829228 0.076399275 0.683606148 3.498718789 0.077265984 0.022039968 6.393740835 -0.805755029 -0.226162087 KGEITGEVR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGEITGEVR 9 1 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5F3 Q60FE5 FLNA Filamin-A 0 ;;; 100.69 0.0072019 3177150000 6786700 7480600 5368740 8182800 6258900 6583900 7030300 7438200 8685800 9659300 FALSE TRUE 6521468.261 7267260.612 6338990.745 8605115.289 6460223.203 6717030.969 7116338.914 7284598.571 7699824.398 9005067.007 0.724199859 0.807019049 0.703935988 0.955585925 0.717398682 0.745916823 0.790259407 0.808944405 0.855054648 1 23.10230558 0.808918079 1.258886551 0.999710538 0.779270336 0.498030259 0.067590455 0.575634308 1.686545708 0.06056554 0.018428976 6.440477678 -0.808918079 -0.220440201 VTLTSEEEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 254.15 9.81E-17 2339500000 465690 468170 391530 434480 415150 387300 402720 426490 392570 309690 FALSE TRUE 447490.32 454818.25 462288.1805 456903.5649 428503.6768 395131.4714 407648.6078 417682.8325 348007.0994 288714.4205 1.549941008 1.575322248 1.601195326 1.582545008 1.484178297 1.368589317 1.411944049 1.446698893 1.205367916 1 18.13928364 0.816364284 0.322909767 0.921649723 1.619229122 0.905593972 0.055832872 0.640419845 0.177331613 0.154056281 0.073995771 6.551855098 -0.816364284 0.697579399 WSCPHCEK ddPTM_BT-474_Pertuzumab_2h_R1 2 WSCPHCEK 8 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;F2Z2R5;Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5;H7C2H0 Q14839-2;Q12873-3;H7C2H0 CHD4;CHD5;CHD3 Chromodomain-helicase-DNA-binding protein 4;Chromodomain-helicase-DNA-binding protein 3 0 ; 83.168 0.023604 236840000 485040 516600 422280 531970 473300 465970 503820 529370 600950 635400 FALSE TRUE 466084.1006 501867.0738 498595.3896 559425.0355 488524.1243 475392.2327 509985.8999 518438.3245 532732.6754 592363.792 0.786820712 0.847227802 0.841704703 0.944394379 0.824702878 0.802534252 0.860933613 0.875202589 0.899333623 1 19.17612393 0.818690557 1.080406809 0.999613596 0.8455072 0.585435938 0.039803398 0.542427722 1.209319155 0.038436974 0.0122279 6.587043893 -0.818690557 -0.154106396 S(ph)RVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALR 34 2 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.428)RVPVRPPQQY(0.135)S(0.428)DDEDDY(0.009)EDDEEDDVQNTNSALR 85.359 0.00032942 270040000 13660 14656 11191 14345 12321 10567 14926 13496 15907 16160 TRUE FALSE 13126.1521 14238.02523 13213.46264 15085.34717 12717.31615 10780.67198 15108.66885 13217.30288 14101.30405 15065.46881 0.871274055 0.945076812 0.877069463 1.001319465 0.844136769 0.715588218 1.002867488 0.877324367 0.936001676 1 13.87895795 0.819588863 1.219376115 0.999897238 0.891050242 0.153452071 0.078433663 1.391977449 3.880469539 0.073612606 0.022602811 6.600682805 -0.819588863 -0.108846996 RVPVLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVPVLGK 7 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 120.65 0.0072397 698930000 1243530 1279160 1110990 1121670 1139780 810210 1244260 1313220 1336000 1487110 FALSE TRUE 1194931.473 1242679.609 1311770.607 1179559.523 1176442.059 826593.0013 1259487.626 1286101.548 1184342.881 1386386.715 0.861903436 0.896344141 0.946179441 0.850815656 0.848567031 0.596221092 0.908467755 0.927664362 0.85426589 1 20.4028983 0.8220963 0.997446601 0.995366823 0.848067443 0.181215384 0.092406623 1.409732752 2.728411927 0.09261738 0.030270876 6.638902649 -0.8220963 -0.14729938 VLGSEGEEEDEALS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLGSEGEEEDEALSPAK 17 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK 297.11 3.67E-46 3632210000 2835340 2263260 2069600 2124980 2183910 2233770 2495020 2654190 2786590 3162860 TRUE FALSE 2724531.778 2198714.041 2443622.758 2234650.472 2254157.449 2278938.36 2525554.801 2599380.049 2470267.986 2948636.675 0.923997114 0.745671401 0.82872969 0.757858875 0.764474466 0.772878659 0.856516105 0.881553184 0.837766147 1 21.49161664 0.822881967 0.661017364 0.998452282 0.796745652 0.527310592 0.053498056 0.722230055 0.678644599 0.053525495 0.020742815 6.650923723 -0.822881967 -0.20170663 EQAGGDATENFEDVGHSTDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 EQAGGDATENFEDVGHSTDAR 21 0 P00167-2;P00167;P00167-3 P00167-2 CYB5A Cytochrome b5 0 ;; 194.62 3.02E-18 711360000 307438 466530 269653 482030 278285 373733 373807 369932 373100 276792 FALSE TRUE 295422.9831 453225.0212 318385.2955 506907.6261 287236.2898 381290.1373 378381.7619 362292.7749 330747.2522 258044.6313 1.144852275 1.756382293 1.233838092 1.964418417 1.113126393 1.477613138 1.466342314 1.403992686 1.281744365 1 17.97726109 0.824523008 1.143730669 0.999103221 1.46641215 0.234273636 0.247893564 0.945691644 2.350930901 0.211530758 0.066158197 6.676102682 -0.824523008 0.467308929 RPDDVPLSLS(ph)PSKR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPDDVPLSLSPSKR 14 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 RPDDVPLSLS(0.968)PS(0.032)KR;RPDDVPLS(0.008)LS(0.979)PS(0.013)KR;RPDDVPLS(0.001)LS(0.995)PS(0.004)KR;RPDDVPLS(0.035)LS(0.963)PS(0.002)KR 187.75 4.76E-07 8368700000 3206120 3033940 2453500 2493920 2633850 2807300 2982990 3208340 3295580 3690650 TRUE FALSE 3080821.286 2947415.002 2896902.028 2622631.51 2718570.177 2864065.529 3019496.724 3142086.658 2921479.575 3440678.988 0.895410847 0.856637603 0.841956497 0.762242429 0.790126073 0.832412887 0.877587457 0.913217033 0.849099723 1 21.71426187 0.824895588 0.617985472 0.998111593 0.828744866 0.566883692 0.041422628 0.79419841 0.664296053 0.048340239 0.019286311 6.681832556 -0.824895588 -0.169366727 KLVEESR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLVEESR 7 1 Q15404 Q15404 RSU1 Ras suppressor protein 1 0 ; 135.83 0.004873 397360000 675550 701520 614820 661280 662600 527660 709480 719640 778470 825050 FALSE TRUE 649148.7591 681513.3365 725931.6506 695408.74 683913.1308 538329.6467 718162.8285 704779.1825 690101.3492 769168.6286 0.843961564 0.886038914 0.943787388 0.904104398 0.889158899 0.699885079 0.933687103 0.916286957 0.897204233 1 19.5529404 0.828139273 0.987024301 0.997564495 0.873400717 0.25075207 0.064834553 1.137912197 2.170895487 0.063488579 0.020839805 6.731925068 -0.828139273 -0.124163778 KELNQLEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KELNQLEDK 9 1 P35555 P35555 FBN1 Fibrillin-1 0 95.523 0.012807 544790000 657250 646860 635900 349010 588250 723910 669150 612740 665970 526780 FALSE TRUE 631563.9434 628412.1861 750821.2755 367022.4479 607171.5955 738547.9562 677339.2579 600086.7049 590371.8776 491100.7214 1.286017136 1.279599395 1.528853945 0.747346587 1.236348409 1.503862495 1.379226762 1.221921856 1.202140115 1 18.90565942 0.828297046 1.900007204 1.00097182 1.274720233 0.142939154 0.202444362 1.276499863 8.479537316 0.193902998 0.054225112 6.734371123 -0.828297046 0.273748413 LT(ph)QTSSTEQLNVLETETEVLNK ddPTM_BT-474_Pertuzumab_2h_R1 4 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.2)QT(0.2)S(0.2)S(0.2)T(0.2)EQLNVLETETEVLNK;LT(0.311)QT(0.206)S(0.206)S(0.138)T(0.138)EQLNVLETETEVLNK;LT(0.275)QT(0.112)S(0.112)S(0.251)T(0.251)EQLNVLETETEVLNK;LT(0.417)QT(0.249)S(0.15)S(0.092)T(0.092)EQLNVLETETEVLNK 282.58 3.41E-45 1174060000 335786 305940 293406 284762 300631 320556 302613 338833 371429 385350 TRUE FALSE 322663.1119 297214.8907 346430.991 299458.6009 310301.0691 327037.862 306316.4684 331835.9801 329265.9371 359249.9013 0.89815783 0.82732073 0.964317568 0.833566272 0.863747124 0.910335287 0.852655679 0.923691222 0.916537307 1 18.45462823 0.831228323 0.913141333 0.999593817 0.878275128 0.460916116 0.039075471 0.654652511 1.089746982 0.034501442 0.011663517 6.779978595 -0.831228323 -0.121318689 STLPDADRER ddPTM_BT-474_Pertuzumab_2h_R1 4 STLPDADRER 10 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 153.1 1.54E-05 7205310000 5724380 5980470 5569980 7517300 5492560 4784090 7189550 6814660 7775170 8850830 FALSE TRUE 5500664.901 5809912.851 6576599.29 7905268.754 5669233.181 4880827.578 7277537.864 6673934.89 6892565.298 8251355.401 0.666637738 0.704116181 0.797032605 0.958056994 0.687066901 0.591518283 0.8819809 0.808828921 0.835325224 1 22.97619969 0.831941713 0.733727646 0.999749127 0.749655826 0.365126486 0.099440186 1.057968631 1.1997583 0.103019752 0.038228868 6.791124815 -0.831941713 -0.250093301 TLPGACGS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLPGACGSPQK 11 0 Q9UBZ9-2;Q9UBZ9 Q9UBZ9-2 REV1 DNA repair protein REV1 1 TLPGACGS(1)PQK 100.73 0.004 53808000 118890 115110 87963 100430 105500 96926 109450 127680 120170 141350 TRUE FALSE 114243.6474 111827.1755 103859.8708 105613.2043 108893.5033 98885.91013 110789.4818 125043.3634 106528.8054 131776.2386 0.866951801 0.848614111 0.788153251 0.801458635 0.826351583 0.750407746 0.840739446 0.948906758 0.808406785 1 17.00773073 0.836858233 0.625404277 0.996681513 0.814836369 0.497356557 0.050634159 0.839098583 0.721841638 0.05583195 0.02227427 6.868441971 -0.836858233 -0.181845144 TDGFGIDTCR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDGFGIDTCR 10 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;K7EIV0;A0A075B7C0;U3KPR7;K7EM73 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ; 132.84 0.00049541 326470000 304340 329710 254110 287310 316910 234090 303200 338570 336650 369700 FALSE TRUE 292446.0563 320306.9936 300033.3296 302138.1035 327103.698 238823.4602 306910.6523 331578.4112 298434.9034 344659.8897 0.848506209 0.929342239 0.870520007 0.876626821 0.949062272 0.692925018 0.890473947 0.962045254 0.865882315 1 18.39481389 0.837082559 0.871315555 0.995660122 0.87087328 0.209929795 0.071111938 1.281756192 1.971648521 0.068527326 0.023623724 6.871990634 -0.837082559 -0.124786842 SPS(ph)TLLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSTLLPK 8 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 S(0.298)PS(0.702)TLLPK 135.86 0.00085549 1192500000 485060 437640 479470 480270 450890 508060 554820 629680 619510 761680 TRUE FALSE 466103.3189 425158.9357 566120.8948 505056.7923 465393.2863 518333.3213 561610.0531 616676.888 549185.822 710090.7352 0.656399663 0.598738886 0.797251487 0.711256699 0.655399744 0.729953646 0.790899001 0.868448013 0.77340232 1 19.43764386 0.839287131 0.182563097 1.130402698 0.56624635 0.746865481 0.055755619 2.665209527 0.331299647 0.523734323 0.312692932 6.90696303 -0.839287131 -0.564156347 LRDFVLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRDFVLVK 8 1 O14929;O14929-2 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 0 ; 115.71 0.0021985 240820000 209651 213554 179129 169879 182242 127407 216644 193627 235615 257419 FALSE TRUE 201457.6071 207463.649 211501.595 178646.4755 188103.9794 129983.2568 219295.3541 189628.5348 208868.973 239983.7818 0.839463424 0.864490289 0.881316201 0.744410619 0.783819548 0.541633505 0.913792392 0.790172291 0.870346202 1 17.87257739 0.839520166 1.345950855 0.999668468 0.790751492 0.294205129 0.097671684 0.83454456 2.856650765 0.093361795 0.027987938 6.910670174 -0.839520166 -0.208916976 EALEHLCTYEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EALEHLCTYEK 11 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ;; 179.6 7.03E-06 1497630000 4050470 4109550 3664850 3618180 3648880 3443910 4342980 4111490 4941620 5375440 FALSE TRUE 3892173.154 3992349.658 4327169.919 3804914.703 3766249.539 3513548.22 4396130.688 4026586.295 4380668.015 5011356.661 0.776670554 0.796660451 0.86347275 0.759258413 0.751542904 0.701117174 0.877233649 0.803492261 0.874148122 1 22.25676979 0.845088205 0.96247035 0.999711958 0.783929796 0.653999279 0.047678353 0.465239193 0.858554078 0.046063862 0.015285807 6.999841484 -0.845088205 -0.215782162 RIVAVTGAEAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RIVAVTGAEAQK 12 1 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 97.276 0.0080377 331180000 305440 288380 237930 233420 279340 228030 275170 299110 315630 343240 FALSE TRUE 293503.0671 280155.6848 280929.2437 245466.8342 288325.2248 232640.9228 278537.6128 292933.274 279801.0056 319992.0491 0.917219875 0.875508268 0.8779257 0.767102917 0.901038715 0.727020948 0.870451668 0.915439227 0.874399868 1 18.28767653 0.846348474 0.949575815 0.996990512 0.847622314 0.357845972 0.058467024 0.806952667 1.454898837 0.055033779 0.018357686 7.020183658 -0.846348474 -0.149368198 SGVTNMSS(ph)PHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGVTNMSSPHK 11 0 Q9NVG8 Q9NVG8 TBC1D13 TBC1 domain family member 13 1 SGVTNMS(0.01)S(0.989)PHK 68.168 0.037344 241140000 360840 313910 292400 273560 295960 263940 311110 306080 362580 424540 TRUE FALSE 346737.9739 304957.5942 345243.1844 287678.4644 305479.8222 269277.0476 314917.4572 299759.341 321421.4385 395785.5277 0.876075424 0.770512242 0.872298657 0.726854431 0.771831714 0.680361026 0.79567704 0.757378227 0.812110135 1 18.59435933 0.846412413 4.845818712 0.999996515 0.778457386 0.574199601 0.056104674 1.163694362 36.14468964 0.052378392 0.013255998 7.021217288 -0.846412413 -0.221539129 MATEVAADALGEEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 MATEVAADALGEEWK 15 0 P62753;A2A3R5;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 209.64 5.31E-09 63926000 47693 58447 44857 41402 49698 46821 46855 49703 58668 65824 FALSE TRUE 45829.10483 56780.14879 52963.65774 43538.76218 51296.5813 47767.7527 47428.42551 48676.61568 52008.2546 61365.68185 0.746819777 0.925275285 0.86308269 0.709496919 0.835916424 0.778411504 0.772881912 0.793222111 0.847513676 1 15.90514445 0.847002807 3.513438563 0.999961621 0.804592628 0.512184375 0.057617966 0.646635326 13.38020453 0.054909989 0.014167797 7.030768643 -0.847002807 -0.195368992 VKPFVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKPFVVR 7 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 112.75 0.005732 1128210000 979990 1227550 1001700 1176250 1025130 932270 1234990 1156090 1382990 1480480 FALSE TRUE 941690.9074 1192541.476 1182729.473 1236956.403 1058104.237 951121.1381 1250104.177 1132216.337 1225998.773 1380205.771 0.682282981 0.864031655 0.856922567 0.896211586 0.76662789 0.689115462 0.905737538 0.820324303 0.888272458 1 20.39645194 0.847627673 1.023892589 0.999699943 0.80842587 0.398462406 0.073412571 0.760877613 1.572230859 0.069427344 0.022537595 7.040891845 -0.847627673 -0.191274073 LAEAHAK ddPTM_BT-474_Pertuzumab_2h_R1 4 LAEAHAK 7 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ;;; 105.12 0.0079989 1365610000 4071980 4077820 3474110 3628560 3621820 3432270 4216530 3905200 4688230 4800170 FALSE TRUE 3912842.52 3961524.566 4101958.958 3815830.416 3738319.13 3501672.851 4268133.155 3824556.255 4156041.785 4475050.21 0.874368406 0.885246954 0.916628589 0.852689967 0.835369203 0.782487947 0.953762071 0.854639853 0.928714001 1 22.09347244 0.847974547 1.218351302 1.000472249 0.866936196 0.46307852 0.043842808 0.592718051 1.689307733 0.041415103 0.012742184 7.0465177 -0.847974547 -0.133536053 NFYQEHPDLAR ddPTM_BT-474_Pertuzumab_2h_R1 6 NFYQEHPDLAR 11 0 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;; 209.19 1.70E-08 14853920000 4415170 4333800 3678750 4140040 4045160 3641380 4002220 4244450 4876390 5121350 FALSE TRUE 4242620.275 4210204.267 4343581.958 4353707.961 4175276.245 3715011.199 4051200.366 4156800.624 4322842.651 4774476.403 0.888604303 0.881814866 0.90975043 0.911871291 0.874499294 0.778098138 0.848511967 0.87062963 0.905406643 1 22.1869111 0.85131381 2.630244316 0.999899044 0.869586543 0.544770291 0.035726721 0.481897917 6.271512299 0.03758618 0.010009163 7.100906763 -0.85131381 -0.130312501 IDYGTGHEAAFAAFLCCLCK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDYGTGHEAAFAAFLCCLCK 20 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;Q5T948;Q5T949;C9IZ76 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ; 184.22 4.08E-17 335690000 874330 825860 804000 734670 822780 613400 879060 814770 986260 1098800 FALSE TRUE 840160.217 802307.2814 949300.6849 772586.4067 849245.4659 625803.3683 889818.1992 797944.7148 874303.8995 1024377.297 0.820166768 0.783214626 0.92671 0.754201024 0.829035813 0.610911009 0.86864303 0.778955876 0.853497927 1 19.96631575 0.854841408 2.799388723 0.999993795 0.796444693 0.383822246 0.077857879 0.584860557 8.623271472 0.071100737 0.018785269 7.158819434 -0.854841408 -0.203549102 LGGSPTSLGTWGSWIGPDHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGGSPTSLGTWGSWIGPDHDK 21 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 317.58 8.99E-67 7049600000 1492370 1471720 1567410 1504010 1277940 1416940 1676500 1546480 1942600 2112900 FALSE TRUE 1434046.53 1429747.987 1850675.854 1581632.136 1319046.101 1445591.498 1697017.508 1514544.648 1722084.192 1969791.401 0.72801949 0.725837257 0.939528852 0.802943974 0.669637455 0.7338805 0.861521432 0.768885805 0.874246984 1 20.90961143 0.858760634 1.388808995 1.000753159 0.777338573 0.471435225 0.072955746 0.555156687 2.054498906 0.071273861 0.021232751 7.223715512 -0.858760634 -0.223414585 AGEPNSPDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 AGEPNSPDAEEANS(1)PDVTAGCDPAGVHPPR 274.5 1.69E-71 4219200000 94952 108790 83888 96477 95857 119000 77498 98807 118700 139380 TRUE FALSE 91241.17087 105687.4157 99048.42768 101456.1895 98940.32746 121406.2615 78446.44371 96766.60092 105225.6736 129939.6685 0.702181035 0.813357591 0.762264741 0.780794585 0.761432814 0.934327931 0.603714359 0.744704077 0.80980408 1 16.9874824 0.862753071 4.337353264 0.999973615 0.762467976 0.449629862 0.078508147 0.854603595 25.79510516 0.073259044 0.018636449 7.290428764 -0.862753071 -0.237505639 KLALDIEIATYR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLALDIEIATYR 12 1 K7EPI4 K7EPI4 GFAP 0 ; 140.1 9.52E-05 952490000 1126110 1276340 914420 1094540 1088060 1173320 1037570 1175070 1221300 1120180 FALSE TRUE 1082100.376 1239940.033 1079676.035 1151029.341 1123058.438 1197045.334 1050268.092 1150804.394 1082663.144 1044309.211 1.036187716 1.187330362 1.033866238 1.102192079 1.07540796 1.146255651 1.005706051 1.101976677 1.036726606 1 19.99411751 0.863925733 0.556572159 0.997491936 1.096229337 0.226416624 0.051430956 1.489509052 1.061855598 0.053184066 0.022577535 7.310140648 -0.863925733 0.098737401 RTS(ph)PQVLGSILK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSPQVLGSILK 12 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 RT(0.213)S(0.787)PQVLGSILK 183.88 9.20E-06 317960000 453320 466440 476140 452290 441720 410760 567380 496330 636800 702410 TRUE FALSE 435603.7532 453137.5879 562189.0897 475632.7411 455928.325 419065.8486 574323.7662 486080.6121 564513.1337 654835.1451 0.665211323 0.691987275 0.858520032 0.726339667 0.696249015 0.639956257 0.87705092 0.742294631 0.862069084 1 19.32077223 0.865685357 0.764781193 1.001605478 0.724297319 0.585573711 0.071224158 0.596907315 0.74281368 0.069198723 0.025384651 7.339819106 -0.865685357 -0.27730816 FYGDEEKDKGLQTSQDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 FYGDEEKDKGLQTSQDAR 18 2 P27797 P27797 CALR Calreticulin 0 ;; 105.79 0.00026312 2358530000 4295900 4594700 2616460 1815390 3582000 5562400 3857600 3662080 3701300 2309650 FALSE TRUE 4128011.479 4463663.655 3089312.525 1909082.495 3697218.283 5674875.539 3904810.463 3586456.768 3281143.941 2153215.348 1.917138238 2.073022403 1.434743871 0.886619398 1.717068516 2.635535523 1.813478836 1.665628462 1.52383455 1 21.03806118 0.865687224 1.813003195 1.002827506 1.769101232 0.23812563 0.420220169 0.857892751 5.487984034 0.430790505 0.12168358 7.33985066 -0.865687224 0.766273726 NKLDLETLTDILQHQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 NKLDLETLTDILQHQIR 17 1 P18440;F5H5R8 P18440 NAT1 Arylamine N-acetyltransferase 1 0 ; 262.5 1.44E-27 554150000 1620860 1450460 1407130 1393460 1330080 1458260 1404360 1560760 1841320 2065500 FALSE TRUE 1557514.999 1409094.301 1661429.692 1465376.638 1372863.231 1487747.016 1421546.978 1528529.761 1632301.073 1925601.845 0.808845818 0.731768254 0.862810605 0.760996694 0.712952802 0.772614038 0.738235156 0.793793257 0.847683584 1 20.876878 0.866153806 1.782920094 0.999565316 0.769374121 0.749653666 0.040204426 0.248460631 1.536250286 0.037353687 0.010583082 7.347740425 -0.866153806 -0.230191196 IFDEVMGCFSDS(ph)PPQSPTFPEAGHTSLYDEDKVPR ddPTM_BT-474_Pertuzumab_2h_R1 3 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 IFDEVMGCFS(0.054)DS(0.767)PPQS(0.169)PT(0.01)FPEAGHTSLYDEDKVPR;IFDEVMGCFS(0.064)DS(0.924)PPQS(0.01)PT(0.002)FPEAGHTSLYDEDKVPR;IFDEVMGCFS(0.001)DS(0.999)PPQSPTFPEAGHTSLYDEDKVPR 149.48 8.94E-11 361083000 65869 108727 82535 136246 90332 137519 166884 170189 235622 315962 TRUE FALSE 63294.76666 105626.2124 97450.91048 143277.6724 93237.61082 140299.7284 168926.3763 166674.5377 208875.1784 294561.6123 0.214877852 0.35858784 0.330833708 0.486409859 0.31653008 0.47630011 0.573484016 0.565839304 0.709105225 1 18.1682099 0.866404637 0.227487155 1.187587767 0.177827366 0.926324391 0.058699399 0.829532723 0.141630608 0.297569769 0.1677498 7.35198542 -0.866404637 -1.009760401 KDVGRPQPGR ddPTM_BT-474_Pertuzumab_2h_R1 6 KDVGRPQPGR 10 2 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;; 180.66 1.11E-06 4019430000 2447970 2866870 2002440 2598290 2113310 2174210 2291940 2732210 2890800 3196710 FALSE TRUE 2352300.626 2785109.675 2364325.452 2732388.058 2181286.535 2218174.016 2319989.447 2675788.909 2562648.503 2980193.984 0.789311246 0.934539728 0.793346159 0.916849062 0.731927702 0.744305246 0.778469274 0.897857295 0.859893187 1 21.50697481 0.870234745 1.20587649 0.997045585 0.818941841 0.400906652 0.066285191 0.650479985 1.848239246 0.063673503 0.01967555 7.41711043 -0.870234745 -0.178103744 KKYPDRVPVIVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKYPDRVPVIVEK 13 3 F5GZY7;H6UMI1;Q9H0R8;O95166;Q9H0R8-2 F5GZY7 GABARAPL1;GABARAP Gamma-aminobutyric acid receptor-associated protein-like 1;Gamma-aminobutyric acid receptor-associated protein 0 ; 127.36 7.79E-05 705570000 1810590 1738920 1399440 1204680 1338500 1523920 1445760 1678540 1802950 1925070 FALSE TRUE 1739830.141 1689327.704 1652349.938 1266853.679 1381554.068 1554734.707 1463453.643 1643877.562 1598286.675 1794683.294 0.969435748 0.94129572 0.920691658 0.705892612 0.769803827 0.866300317 0.815438383 0.915970839 0.890567533 1 20.77529785 0.873466539 1.173808786 0.997830597 0.854933411 0.228522871 0.076585632 1.008426574 2.728933115 0.078562699 0.024469198 7.47251059 -0.873466539 -0.142897185 WSGS(ph)HQFEQLSGSILWMAPEVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 WSGSHQFEQLSGSILWMAPEVIR 23 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 WS(0.459)GS(0.522)HQFEQLS(0.017)GS(0.002)ILWMAPEVIR 89.396 0.003768 243040000 192270 192370 161680 169620 183720 194120 162910 203130 228510 255070 TRUE FALSE 184755.8758 186883.7959 190899.1726 178374.1085 189629.5207 198045.2394 164903.7413 198935.2945 202570.5028 237793.8817 0.776958072 0.785906663 0.802792617 0.750120681 0.797453321 0.832844134 0.693473441 0.836587103 0.851874326 1 17.85935207 0.875824984 1.535677254 0.998856448 0.780858024 0.759103963 0.037394989 0.240868988 1.10621243 0.033375512 0.009736455 7.513200598 -0.875824984 -0.217998423 EEEEVGFDWSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEEVGFDWSDR 12 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 208.6 1.51E-07 143120000 140990 157020 168200 166450 139400 143710 173840 181500 197700 223510 FALSE TRUE 135479.9549 152541.9433 198597.4816 175040.5044 143883.9276 146615.9147 175967.5059 177751.9616 175257.9248 208371.4686 0.650184768 0.732067324 0.953093448 0.840040652 0.690516454 0.703627592 0.844489445 0.853053265 0.841084079 1 17.66879822 0.876063385 0.729171221 0.998773755 0.771942386 0.40177881 0.084262019 0.949164496 1.092640452 0.088972486 0.033461193 7.517326015 -0.876063385 -0.226831369 DSSLPGDLHVTSGPES(ph)PFNNIFNDVDKSEDLPSHQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSLPGDLHVTSGPESPFNNIFNDVDKSEDLPSHQK 36 1 Q8IWU2 Q8IWU2 LMTK2 Serine/threonine-protein kinase LMTK2 1 DSSLPGDLHVT(0.001)S(0.006)GPES(0.993)PFNNIFNDVDKSEDLPSHQK 134.61 3.53E-09 51933000 55796 65705 50765 69112 63648 68068 72236 61887 67198 49559 TRUE FALSE 53615.43063 63831.15773 59939.36476 72678.8786 65695.29572 69444.3816 73120.04578 60609.01182 59569.96476 46202.32479 1.160448763 1.381557271 1.297323566 1.573056744 1.421904548 1.503049509 1.582605337 1.311817362 1.289328297 1 15.49567783 0.877703263 1.673088775 1.002687937 1.417833614 0.505430286 0.121756591 0.421894205 2.315470583 0.116646391 0.033460256 7.545764778 -0.877703263 0.415145678 AGLGS(ph)PERPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 AGLGSPERPPK 11 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 AGLGS(1)PERPPK;AGLGS(1)PERPPK;AGLGS(1)PERPPK;AGLGS(1)PERPPK 145 2.21E-05 14918800000 14292400 15191200 11173500 15453600 12446200 14094300 16261100 16467400 17165200 19792600 TRUE FALSE 13733837.21 14757961.85 13192800 16251162.15 12846543.33 14379296.4 16460108.21 16127342.44 15216678.46 18452029.57 0.744299545 0.79980155 0.71497826 0.880724913 0.696213025 0.779279935 0.892048657 0.874014556 0.824661504 1 24.13727617 0.877887165 0.323593447 1.025986063 0.745452885 0.589459449 0.056719884 1.380224218 0.400440459 0.136262174 0.069475519 7.548960706 -0.877887165 -0.280533178 VKVGVNGFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKVGVNGFGR 10 1 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 169.41 4.23E-06 2861300000 1905780 1960250 1474840 1626050 1762960 1970040 1788010 1817450 1908140 1554240 FALSE TRUE 1831300.011 1904345.589 1741376.396 1709970.635 1819667.209 2009875.559 1809892.201 1779919.022 1691535.947 1448969.94 1.263863355 1.314275428 1.201802982 1.18012844 1.255835031 1.387106456 1.249088853 1.228403 1.167405824 1 20.46659624 0.87813379 1.474057291 1.000799104 1.264008803 0.689694888 0.053949064 0.328455909 1.390849494 0.054200795 0.015951049 7.55324879 -0.87813379 0.2632097 EVGKDVSDEKLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVGKDVSDEKLR 12 2 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 92.856 0.004218 646030000 764800 1011470 445030 674100 544180 767430 831700 791040 774650 488610 FALSE TRUE 734910.7705 982623.8659 525456.8206 708890.3818 561684.0439 782947.9604 841878.5934 774704.7476 686714.9796 455516.0095 1.613358818 2.157166478 1.153541939 1.556235932 1.233072015 1.718815462 1.848186619 1.700719034 1.507553994 1 18.79714223 0.878345493 5.143388423 1.000022083 1.626874328 0.322193512 0.269901753 1.371204023 56.81181511 0.258911207 0.065384911 7.556931628 -0.878345493 0.626852246 MVINHLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MVINHLEK 8 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 105.78 0.0043212 3521200000 5576000 5793100 5111500 5499500 5319100 5369400 6167700 5980400 6793600 6922800 FALSE TRUE 5358083.755 5627886.46 6035261.755 5783329.854 5490193.682 5477972.947 6243182.158 5856902.65 6022419.009 6453912.59 0.830207054 0.872011572 0.935132243 0.896096712 0.850676796 0.848783257 0.967348422 0.907496432 0.933142327 1 22.62174261 0.880534756 0.353001558 1.012978607 0.86593256 0.535046598 0.035746789 1.497671473 0.499792877 0.077170172 0.038496493 7.595122032 -0.880534756 -0.147046047 AIQWGEDGRPFHYLFYTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIQWGEDGRPFHYLFYTGK 19 1 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 ; 86.96 0.0016782 228040000 342400 375650 303460 466590 327570 371490 415080 400610 420190 350330 FALSE TRUE 329018.6295 364936.8298 358301.9724 490670.7658 338106.5865 379001.7823 420159.8732 392337.2635 372491.7928 326601.8371 1.007399813 1.117375313 1.097060493 1.502351518 1.035225612 1.160439836 1.286459002 1.201270841 1.140507341 1 18.31717338 0.884700288 4.440126793 1.000027884 1.182953098 0.133187492 0.133382223 1.389969498 50.20370303 0.124742271 0.031697972 7.668321062 -0.884700288 0.182925215 DGNLASTLGQHK ddPTM_BT-474_Pertuzumab_2h_R1 3 DGNLASTLGQHK 12 0 Q9BZK7;A0A0D9SF63;A0A1B0GVH3 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ;; 173.19 3.37E-05 1057020000 678550 671290 624080 618750 616970 591720 734580 701200 799980 848150 FALSE TRUE 652031.5158 652145.4665 736865.1386 650683.7617 636815.4004 603684.9838 743570.0098 686719.975 709169.6242 790704.045 0.82462145 0.824765562 0.931910167 0.822916951 0.805377694 0.763477799 0.940389789 0.868491794 0.896883769 1 19.59277828 0.885752057 0.731441421 0.99882887 0.837656112 0.485299794 0.049814903 0.739854278 0.860846624 0.050018844 0.018825234 7.686914612 -0.885752057 -0.161172758 FEELNADLFR ddPTM_BT-474_Pertuzumab_2h_R1 11 FEELNADLFR 10 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;;;;;;;;; 359.43 4.20E-66 11456423000 3848755 4007557 3970961 4502519 3653357 2087054 4967591 4519439 4773267 5737624 FALSE TRUE 3698341.4 3893265.398 4688601.986 4734894.545 3770870.546 2129255.662 5028385.865 4426111.005 4231425.741 5349009.616 0.691406758 0.727847897 0.876536466 0.885190883 0.704966118 0.398065402 0.940059231 0.827463647 0.79106714 1 22.35084037 0.886262789 0.859720849 0.992950321 0.74457056 0.216086678 0.142399001 1.235823055 1.912646712 0.141856102 0.049520322 7.69595978 -0.886262789 -0.248379761 WVTYFNKPDIDAWELRK ddPTM_BT-474_Pertuzumab_2h_R1 2 WVTYFNKPDIDAWELRK 17 2 H3BRI0;H3BNX8;P20674 H3BRI0 COX5A "Cytochrome c oxidase subunit 5A, mitochondrial" 0 ; 128.69 2.03E-05 449740000 303680 541960 242650 478930 215490 312790 501290 417230 399540 236690 FALSE TRUE 291811.8499 526503.8314 286502.2527 503647.6347 222421.4316 319114.8281 507424.937 408614.0547 354185.8942 220658.7755 1.322457488 2.386054352 1.298395009 2.282472717 1.007988153 1.446191421 2.299591013 1.851791545 1.605129429 1 17.7514576 0.886951578 5.223286932 1.000036497 1.759269578 0.191256704 0.45087457 1.579700743 71.3640036 0.40835296 0.103072723 7.708175214 -0.886951578 0.759233081 QDVHLLMTNCIK ddPTM_BT-474_Pertuzumab_2h_R1 1 QDVHLLMTNCIK 12 0 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9;H3BN71;B4DGE1;H3BRM7 O43747 AP1G1 AP-1 complex subunit gamma-1 0 115.8 0.00091006 253070000 338780 321970 269170 322540 343020 287720 330410 326160 373180 392480 FALSE TRUE 325540.1031 312787.7308 317815.0067 339186.3281 354053.5498 293537.8955 334453.6564 319424.682 330818.1709 365896.98 0.889704263 0.854851906 0.8685915 0.926999529 0.96763179 0.802241919 0.914065091 0.872990758 0.904129274 1 18.48107798 0.887082903 6.688197546 0.999999718 0.887299844 0.391932526 0.041945539 2.501701437 147.9821128 0.039240311 0.009847502 7.710506421 -0.887082903 -0.112699874 KEELTLEGIR ddPTM_BT-474_Pertuzumab_2h_R1 6 KEELTLEGIR 10 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;; 159.44 1.23E-05 16205790000 11488630 11904700 11053880 10214270 10487560 9407460 12542000 11871590 13604970 14404130 FALSE TRUE 11039641.64 11565189.61 13051562.01 10741429.7 10824901.89 9597685.287 12695492.75 11626437.52 12060590.84 13428525.45 0.822103788 0.861240473 0.971928159 0.79989644 0.806112476 0.714723692 0.945412272 0.865801503 0.898132181 1 23.67879756 0.887870383 0.943408498 0.997954406 0.842625321 0.324765089 0.06837714 0.875389479 1.60040467 0.066753298 0.0224255 7.724500092 -0.887870383 -0.155329085 SVS(ph)PESNDSISEELNHFKPIVCSPCT(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSPESNDSISEELNHFKPIVCSPCTPPK 29 1 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 2 S(0.131)VS(0.743)PES(0.095)NDS(0.011)IS(0.02)EELNHFKPIVCS(0.088)PCT(0.912)PPK 98.041 0.014417 131300000 54118 40862 36977 34398 39709 35533 41570 40105 50793 60226 TRUE FALSE 52003.00873 39696.65577 43659.56645 36173.2849 40986.27605 36251.50161 42078.74609 39276.81774 45027.19158 56146.83938 0.926196547 0.707014967 0.777596156 0.644262176 0.729983673 0.64565525 0.749441047 0.699537466 0.801954163 1 15.77691719 0.889791822 3.859362361 0.999937115 0.729087728 0.525374058 0.07564767 0.378046902 11.41936362 0.068448376 0.017541473 7.758751135 -0.889791822 -0.270849387 RNS(ph)PAFLSTDLGDEDVGLGPPAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RNSPAFLSTDLGDEDVGLGPPAPR 24 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 RNS(1)PAFLSTDLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR 261.79 2.72E-44 719905000 202142 233701 242185 206028 189049 251512 215200 224583 272531 307766 TRUE FALSE 194242.0672 227036.0763 285953.2169 216661.1298 195129.9328 256597.745 217833.682 219945.2826 241594.4234 286920.7347 0.676988602 0.79128501 0.996627926 0.755125383 0.680083065 0.894315795 0.75921206 0.766571586 0.842024971 1 18.1302927 0.891660451 4.647378548 0.999978703 0.79304741 0.329016933 0.090132751 0.825218343 33.41746718 0.085780165 0.021750528 7.792206467 -0.891660451 -0.206931293 AQQEQELAADAFK ddPTM_BT-474_Pertuzumab_2h_R1 4 AQQEQELAADAFK 13 0 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;; 237.87 2.16E-16 533649000 437677 539041 423605 457663 488187 505501 526600 590440 630610 710110 FALSE TRUE 420572.099 523668.0785 500159.8465 481283.0423 503889.9782 515722.5766 533044.6883 578247.2077 559025.7965 662013.6172 0.635292218 0.791023122 0.755512928 0.726998705 0.761147452 0.7790211 0.805186894 0.873467241 0.844432474 1 19.33650137 0.892299285 0.19916904 1.094534864 0.648713083 0.843014702 0.03626769 1.594294588 0.232195754 0.254862629 0.153647614 7.803677002 -0.892299285 -0.445821781 YFEITDESPYVHYLNTFSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 YFEITDESPYVHYLNTFSSK 20 0 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0 Q9ULV4 CORO1C Coronin-1C;Coronin 0 ; 345.16 3.15E-83 625420000 874630 952260 781750 878360 894320 830740 923530 927640 1061680 1061560 FALSE TRUE 840448.4926 925102.4772 923029.6149 923692.2649 923086.615 847538.132 934832.4364 908483.9098 941162.5373 989659.5957 0.849229873 0.93476836 0.93267384 0.933343413 0.932731435 0.856393588 0.944599982 0.917976154 0.950996223 1 19.91657285 0.893457447 1.249582267 1.000008338 0.912881165 0.433622159 0.031451403 0.553987311 1.710675773 0.028614756 0.008770499 7.824515359 -0.893457447 -0.087127174 IEHAPSPS(ph)SGGTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEHAPSPSSGGTLK 14 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 IEHAPS(0.259)PS(0.741)SGGTLK 195.95 1.64E-08 969070000 780910 717710 724570 756610 659770 681890 785750 864450 952630 1113900 TRUE FALSE 750391.1739 697241.6135 855515.917 795658.7328 680992.1012 695678.283 795366.2435 846598.8054 844491.4362 1038454.561 0.722603763 0.671422361 0.823835678 0.766195039 0.655774578 0.669916922 0.765913381 0.815248772 0.81321944 1 19.98600666 0.893956431 0.854170827 0.997599053 0.721577128 0.728967621 0.050681406 0.402043159 0.617698422 0.051707572 0.018122042 7.833510529 -0.893956431 -0.276021925 VLVPEHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLVPEHEK 8 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 105.14 0.004446 616250000 735760 761210 791250 729710 684970 662860 829030 829400 958510 1060670 FALSE TRUE 707005.6858 739501.0361 934246.4763 767370.4205 707002.6821 676263.4834 839175.9171 812272.6002 849703.9632 988829.8762 0.714992238 0.747854665 0.944800009 0.776038871 0.7149892 0.683902762 0.848655504 0.821448279 0.859302478 1 19.91536281 0.894760109 0.965156237 0.998274234 0.774305541 0.48831769 0.070553217 0.62244799 1.190167424 0.070281209 0.023420202 7.84802015 -0.894760109 -0.223968693 TADSSSS(ph)EDEEEYVVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TADSSSSEDEEEYVVEK 17 0 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 1 TADSSS(0.037)S(0.962)EDEEEYVVEK;TADSSS(0.024)S(0.976)EDEEEYVVEK 278.89 7.93E-36 323310000 650630 648550 445170 546110 550910 568920 602200 624530 684670 713840 TRUE FALSE 625202.6603 630053.989 525622.1218 574294.8025 568630.5205 580423.9522 609569.9037 611633.2373 606949.132 665490.981 0.939460756 0.946750605 0.789826063 0.862964066 0.854452632 0.872174032 0.915970195 0.919070663 0.912032093 1 19.34405959 0.895845366 0.718246806 0.998413971 0.876722051 0.399580487 0.043037556 0.873015304 0.989006149 0.04469784 0.017015062 7.867656063 -0.895845366 -0.12169192 LSHETVTIELK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSHETVTIELK 11 0 P62314;J3QLR7 P62314 SNRPD1 Small nuclear ribonucleoprotein Sm D1 0 ; 172.8 1.29E-05 1033850000 1874360 1805060 1595980 1605800 1653180 1169440 1773090 1680650 2047750 2249200 FALSE TRUE 1801107.939 1753581.456 1884409.088 1688675.53 1706356.036 1193086.878 1794789.606 1645943.99 1815298.005 2096859.681 0.85895492 0.836289368 0.898681541 0.805335496 0.813767393 0.568987467 0.855941684 0.784956669 0.865722214 1 20.99979889 0.89586647 2.986755246 0.999933502 0.801649527 0.334247092 0.084582198 0.492820185 9.461421614 0.082087605 0.021546769 7.868038388 -0.89586647 -0.198283975 APLDLDKYVEIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 APLDLDKYVEIAR 13 1 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 156.24 4.29E-05 2149700000 1679460 1794810 1313480 1486980 1631980 1655810 1652720 1623760 1856710 1700110 FALSE TRUE 1613824.846 1743623.776 1550855.054 1563723.216 1684474.119 1689291.613 1672946.482 1590228.789 1645944.065 1584960.035 1.018211696 1.100105831 0.978482119 0.986601038 1.062786494 1.065825999 1.055513353 1.003324218 1.038476698 1 20.59601503 0.899196872 1.076599861 1.001673212 1.036154331 0.069748078 0.036441466 1.876658604 4.3903083 0.035295605 0.011315636 7.928606647 -0.899196872 0.034481118 IPS(ph)PIGFTPGPQQLLGDPFQGMR ddPTM_BT-474_Pertuzumab_2h_R1 1 IPSPIGFTPGPQQLLGDPFQGMR 23 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7;H7C0J7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 IPS(0.999)PIGFT(0.001)PGPQQLLGDPFQGMR 107.85 0.00084208 264190000 148740 173520 138610 182840 185860 187150 178470 165130 190510 154280 TRUE FALSE 142927.0764 168571.3795 163659.9104 192276.3943 191838.3557 190934.3012 180654.1692 161720.0078 168884.1035 143830.4782 0.993718982 1.172014316 1.137866692 1.336826497 1.333780977 1.327495421 1.256021474 1.124379268 1.17418857 1 17.13400989 0.900042458 1.192668511 1.004752351 1.224699381 0.27358557 0.103521051 0.813786399 2.307289871 0.104527404 0.032470162 7.94405894 -0.900042458 0.21994703 GLLPGGTQVLDGTSGFS(ph)PAPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLPGGTQVLDGTSGFSPAPK 21 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK 261.88 1.21E-36 497270000 330610 306900 257060 247610 267370 276490 271220 322250 352730 394580 TRUE FALSE 317689.3957 298147.5125 303516.4603 260389.1818 275970.1989 282080.8172 274539.2715 315595.4249 312689.5692 367854.7451 0.863627287 0.810503375 0.825098668 0.7078587 0.750215139 0.766826637 0.746325214 0.857934902 0.850035437 1 18.48877668 0.90013786 1.156762038 0.997600222 0.781401404 0.671302743 0.045294243 0.362025528 0.968796064 0.044818988 0.014047927 7.945804209 -0.90013786 -0.216198818 FWIQDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FWIQDK 6 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 104.11 0.079355 1034930000 1428530 1334100 1143980 1274720 1289290 1159520 1225820 1377070 1572380 1679760 FALSE TRUE 1372701.468 1296052.774 1350722.634 1340508.452 1330761.184 1182966.289 1240821.952 1348633.023 1393890.014 1565988.359 0.876571949 0.827626059 0.862536829 0.856014315 0.849789959 0.75541193 0.792357073 0.861202458 0.890102411 1 20.57864206 0.900680628 1.810994559 0.999188207 0.831973627 0.685814823 0.034274693 0.275822728 1.828836636 0.034688682 0.009819487 7.955740851 -0.900680628 -0.16721458 AIAQGIQELSAELPPEESESSRVDFGS(ph)SER ddPTM_BT-474_Pertuzumab_2h_R1 2 AIAQGIQELSAELPPEESESSRVDFGSSER 30 1 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 1 AIAQGIQELSAELPPEES(0.016)ES(0.016)S(0.016)RVDFGS(0.764)S(0.189)ER;AIAQGIQELSAELPPEES(0.192)ES(0.158)S(0.158)RVDFGS(0.381)S(0.111)ER 88.634 0.00070581 97977000 21913 35016 22105.3 23503 29058 34067 27008 30035 28778 20321 TRUE FALSE 21056.61573 34017.37796 26100.21944 24715.99265 29992.67696 34755.85808 27338.53198 29414.76675 25511.24209 18944.64057 1.111481406 1.79562013 1.37770993 1.304642997 1.583174769 1.834601082 1.443074725 1.552669561 1.346620539 1 14.20950215 0.902559021 3.150278447 1.000264918 1.512088933 0.354307434 0.204482596 0.409074462 8.966381268 0.185590079 0.048435189 7.990225222 -0.902559021 0.511824014 (ac)MAAPEEHDS(ph)PTEAS(ph)QPIVEEEET(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 2 MAAPEEHDSPTEASQPIVEEEETK 24 0 Q9H0S4;Q9H0S4-2;F5H1N9 Q9H0S4 DDX47 Probable ATP-dependent RNA helicase DDX47 3 MAAPEEHDS(0.963)PT(0.21)EAS(0.828)QPIVEEEET(0.999)K;MAAPEEHDS(0.863)PT(0.31)EAS(0.827)QPIVEEEET(1)K 44.258 0.010803 4805090000 1622550 1684910 1208310 1725400 1298730 1594010 1637000 1586320 1698910 1466000 TRUE FALSE 1559138.952 1636858.016 1426678.496 1814448.101 1340504.83 1626241.974 1657034.096 1553561.938 1506056.859 1366706.514 1.140800118 1.197666068 1.043880658 1.327606243 0.980828595 1.189898458 1.212428622 1.136719494 1.101960694 1 20.38227204 0.903357199 2.175157393 1.000511396 1.155370099 0.218887631 0.089007966 0.600215196 5.94329772 0.077093046 0.0211629 8.004923738 -0.903357199 0.154858703 SLYGER ddPTM_BT-474_Pertuzumab_2h_R1 2 SLYGER 6 0 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 0 ; 123.1 0.044052 707230000 631720 744970 576120 867180 584190 464800 807100 786100 855640 1018650 FALSE TRUE 607031.684 723724.185 680237.6997 911935.2637 602981.0019 474198.5745 816977.5312 769866.7603 758511.3343 949655.9282 0.63921223 0.762090946 0.716299114 0.960279651 0.63494681 0.499337245 0.860287928 0.810679676 0.798722265 1 19.85704538 0.903452302 0.861946728 0.994999001 0.723368021 0.324516165 0.119456718 0.907845319 1.424506772 0.117290555 0.040998821 8.006676875 -0.903452302 -0.271630981 EGDVTSGMVKDPPDVLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGDVTSGMVKDPPDVLDR 18 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ; 163.79 2.94E-11 891450000 646310 559280 455200 472630 538890 578090 504430 556040 633770 640130 FALSE TRUE 621051.4907 543329.882 537464.7659 497022.4909 556223.8863 589779.3759 510603.3652 544557.5797 561827.0866 596773.4249 1.040682217 0.91044584 0.900617795 0.832849571 0.932052037 0.988280227 0.855606741 0.912503066 0.941441195 1 19.18682377 0.904128693 3.740038489 0.999940325 0.916983495 0.144965081 0.056387097 0.765421996 23.75374348 0.053192214 0.013665694 8.019156565 -0.904128693 -0.08295683 LLEDFLEEAEREQEEEPPQVWTGPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEDFLEEAEREQEEEPPQVWTGPPR 26 1 A0A0A0MRX4;Q3MIN7;Q3MIN7-2 A0A0A0MRX4 RGL3 Ral guanine nucleotide dissociation stimulator-like 3 0 100.93 0.0040862 7496800 4065 4437.4 3470.7 5279.8 5834.7 4241 4806.6 4660.9 4913 3988 FALSE TRUE 3906.135306 4310.849697 4097.932695 5552.291111 6022.378424 4326.755926 4865.424609 4564.650786 4355.296837 3717.889208 1.05063252 1.159488477 1.102220229 1.493398754 1.619838055 1.163766773 1.308652393 1.227753311 1.171443417 1 11.86026806 0.904315191 1.411101989 1.001024923 1.278446994 0.196491698 0.165705677 0.91665526 3.619818272 0.167137027 0.049746098 8.022600956 -0.904315191 0.277422071 VKPAPLEIKPLPEWEELQAPVRS(ph)PITR ddPTM_BT-474_Pertuzumab_2h_R1 1 VKPAPLEIKPLPEWEELQAPVRSPITR 27 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 VKPAPLEIKPLPEWEELQAPVRS(0.979)PIT(0.021)R 169.27 4.56E-12 1031800000 463770 430510 358090 396820 405810 453280 366080 447230 429380 379450 TRUE FALSE 445645.3557 418232.2763 422804.8287 417299.9278 418863.2472 462445.6322 370560.1965 437994.5442 380638.5825 353749.5135 1.259776589 1.182283679 1.19520964 1.179648061 1.184067345 1.307268602 1.047521431 1.238148824 1.076011607 1 18.43236864 0.905486846 1.009216792 0.997294979 1.203342878 0.488346416 0.06605148 0.528397048 1.101780182 0.057592425 0.018894934 8.044273837 -0.905486846 0.206047899 KANLQIDQINTDLNLER ddPTM_BT-474_Pertuzumab_2h_R1 1 KANLQIDQINTDLNLER 17 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 100.97 0.0019303 63447000 77603 76459 50219 55156 63952 81508 66070 72314 74975 61806 FALSE TRUE 74570.18897 74278.46418 59294.69042 58002.60777 66009.07416 83156.14761 66878.58442 70820.69063 66464.15232 57619.82457 1.294175911 1.289112987 1.029067528 1.006643255 1.145596583 1.443186407 1.160687054 1.229102851 1.153494528 1 15.81427765 0.90563992 5.85093061 1.000004237 1.196423025 0.195108675 0.121654277 1.743342323 106.4436927 0.122692762 0.030870738 8.047109672 -0.90563992 0.196418787 EKVS(ph)SIDLEIDSLSSLLDDMTK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKVSSIDLEIDSLSSLLDDMTK 22 1 Q15942;H7C3R3;C9IZ41 Q15942 ZYX Zyxin 1 EKVS(0.499)S(0.499)IDLEIDS(0.002)LSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK 123.79 3.60E-05 132643800 75129 67183 61230 49500 76905 74743 75635 67833 71660 54417 TRUE FALSE 72192.87562 65267.00662 72295.62305 52054.70093 79378.71917 76254.35467 76560.64375 66432.22485 63525.45722 50731.28812 1.423044403 1.286523742 1.42506973 1.026086718 1.564689605 1.503103065 1.509140544 1.309492175 1.25219484 1 15.63058817 0.906498056 1.850351851 1.002136943 1.383992456 0.399864352 0.143778214 0.461268214 3.220088482 0.136895481 0.038617781 8.063025917 -0.906498056 0.381855513 EEAPASPLRPLYPQIS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 EEAPASPLRPLYPQIS(1)PLK 92.147 0.0011888 212610000 603850 475610 609850 281740 491610 447560 682220 431740 713600 1153400 TRUE FALSE 580250.8744 462046.0685 720063.461 296280.6352 507423.0821 456609.9698 690569.2124 422824.4181 632595.1197 1075279.191 0.539628107 0.429698698 0.669652558 0.275538332 0.471898914 0.424643175 0.642223172 0.393222915 0.588307786 1 20.03627987 0.907088408 6.25403515 0.999993923 0.48048 0.666759323 0.109934215 0.636456165 42.48201858 0.097642502 0.024532602 8.073993738 -0.907088408 -0.519513923 ADEDEWQLLDGFVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADEDEWQLLDGFVR 14 0 O75140;O75140-9;O75140-4;O75140-1;A0A2R8Y7U0;O75140-8;H0Y770;A0A2R8Y6H3;A0A2R8Y5T1;A0A2R8Y721;A0A2R8Y5K9;A0A5F9UWT1;A0A2R8Y842;A0A2R8Y6V4;A0A2R8YEW8;H7C1T0;O75140-6;O75140-5 O75140 DEPDC5 DEP domain-containing protein 5 0 106.49 0.0046925 0 9158.6 10262 7684.7 10830 11532 10308 8660.4 10598 11067 9301.3 FALSE TRUE 8800.671787 9969.337808 9073.496235 11388.9376 11902.93725 10516.43482 8766.388566 10379.1476 9810.720557 8671.314666 1.014917821 1.14969162 1.046380691 1.313403796 1.372679658 1.212784362 1.010964185 1.196952019 1.13139944 1 13.08203502 0.908731197 6.152540225 1.000001883 1.167405836 0.15821904 0.113611417 2.092026803 139.5305969 0.114087536 0.028673773 8.104592758 -0.908731197 0.167403953 LLGHEVEDVIIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLGHEVEDVIIK 12 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 156.51 7.32E-05 179734000 222289 230957 196891 230192 198897 149523 297111 225978 293349 329933 FALSE TRUE 213601.7001 224370.3325 232473.5835 242072.2367 205294.7026 152546.4575 300747.1333 221311.4753 260049.2513 307586.344 0.69444468 0.729454792 0.75579943 0.7870058 0.667437637 0.495946782 0.977764908 0.719510081 0.845451225 1 18.23063193 0.911777605 0.758804769 0.998556434 0.712059313 0.383156151 0.110431561 0.828142678 1.04157134 0.105358116 0.039159664 8.161643209 -0.911777605 -0.286497121 DSDKEGT(ph)SNSTSEDGPGDGFTILSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSDKEGTSNSTSEDGPGDGFTILSSK 26 1 Q9P0M6;Q5SQT3 Q9P0M6 H2AFY2 Core histone macro-H2A.2;Histone H2A 1 DS(0.059)DKEGT(0.256)S(0.215)NS(0.153)T(0.215)S(0.103)EDGPGDGFTILSSK 68.708 0.053098 227280000 138530 150560 158270 171260 94610 187900 151690 154920 206270 251200 TRUE FALSE 133116.0944 146266.1762 186872.9097 180098.7491 97653.21657 191699.4667 153546.4276 151720.8479 182855.0944 234186.0003 0.568420377 0.624572673 0.797967895 0.769041484 0.416989984 0.818577825 0.655660148 0.647864722 0.780811381 1 17.83729531 0.913693077 2.98311938 0.999709756 0.665151029 0.460375253 0.11191337 0.315525657 6.374814476 0.103126946 0.027089408 8.197719939 -0.913693077 -0.334558727 DLNKDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLNKDGK 7 1 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ;; 87.639 0.017505 885190000 1300280 1235620 911020 931470 1010380 1124970 1132910 1174140 1320550 1360910 FALSE TRUE 1249463.62 1200381.327 1075661.58 979543.2783 1042879.79 1147717.664 1146774.891 1149893.599 1170646.7 1268734.354 0.984811057 0.946125029 0.847822538 0.772063337 0.821984356 0.904616211 0.90387313 0.906331255 0.922688581 1 20.2749586 0.914775267 0.878140171 0.998667996 0.876122074 0.279236232 0.057000313 1.001668664 1.63389842 0.060140076 0.020883799 8.218172768 -0.914775267 -0.122545922 IADLGNACWVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 IADLGNACWVHK 12 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;A8MPP7;A8MPY5;E7ETV6;Q9UPE1-2;Q9UPE1-3;Q9UPE1-4;Q9UPE1;P78362;P78362-2;H7C521 H3BLV9;P78362 SRPK1;SRPK3;SRPK2 SRSF protein kinase 1;SRSF protein kinase 3;SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 ; 151.78 6.93E-05 1083140000 1150130 1182510 992230 1082860 1080610 1033250 1183710 1117520 1324020 1416490 FALSE TRUE 1105181.648 1148785.973 1171548.033 1138746.534 1115368.802 1054143.023 1198196.597 1094442.821 1173722.8 1320549.871 0.836910194 0.869930018 0.887166823 0.86232755 0.844624521 0.798260669 0.907346723 0.828778107 0.888813688 1 20.33270736 0.915748042 6.202452448 0.999997424 0.855501917 0.694769828 0.028987151 0.489725677 35.58511688 0.026697463 0.006708848 8.236601252 -0.915748042 -0.144495507 TMLEDLGMDDEGDDDPVPLPNVNAAILKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TMLEDLGMDDEGDDDPVPLPNVNAAILKK 29 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3;E5RI56 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 86.519 0.0030935 186580000 165510 163430 131460 124790 136700 162940 130160 161590 184930 204030 FALSE TRUE 159041.6862 158769.1364 155217.7463 131230.4269 141097.0796 166234.7584 131752.937 158253.11 163937.5217 190210.8664 0.836133546 0.834700664 0.816029858 0.689920767 0.74179295 0.873949852 0.692667772 0.831987746 0.861872536 1 17.53724014 0.915764391 1.742897021 0.998841834 0.784859632 0.548851217 0.058903483 0.335123697 2.070249982 0.055586551 0.01585935 8.23691134 -0.915764391 -0.213982202 YNVYPTYDFACPIVDSIEGVTHALR ddPTM_BT-474_Pertuzumab_2h_R1 2 YNVYPTYDFACPIVDSIEGVTHALR 25 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 219.64 1.31E-33 856510000 335540 380370 277290 365470 369750 375280 352910 365920 386950 337230 FALSE TRUE 322426.7258 369522.22 327402.4713 384331.9505 381643.3445 382868.4187 357229.0181 358363.6241 343025.0582 314389.1117 1.025565816 1.175365832 1.041392526 1.222472205 1.213920363 1.217817044 1.136263963 1.139872886 1.091084409 1 18.26219173 0.915861384 1.693908264 1.000284896 1.152191109 0.325888814 0.064930506 0.52948762 3.077014717 0.061275618 0.017575527 8.238751135 -0.915861384 0.151906213 GHS(ph)PAQKPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHSPAQKPK 9 1 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4 Q14966 ZNF638 Zinc finger protein 638 1 GHS(1)PAQKPK;GHS(1)PAQKPK;GHS(1)PAQKPK;GHS(1)PAQKPK 147.91 5.51E-05 1518780000 2467380 2075950 2198620 2357920 2190900 2088490 2751790 2353460 3228680 3490900 TRUE FALSE 2370952.062 2016745.939 2595959.542 2479612.534 2261372.288 2130720.699 2785467.229 2304860.229 2862173.782 3254458.234 0.728524348 0.619687147 0.797662577 0.761912538 0.694853683 0.654708263 0.855892757 0.708216257 0.879462441 1 21.63398597 0.919225016 1.030697775 1.0027686 0.718445618 0.639945056 0.065775721 0.383711678 0.837252699 0.059980114 0.019556106 8.302808395 -0.919225016 -0.284322982 QLQEERPELSESELTR ddPTM_BT-474_Pertuzumab_2h_R1 3 QLQEERPELSESELTR 16 1 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 0 ;; 205.78 1.98E-11 1370990000 382494 431540 353613 477560 388560 442990 428000 437980 463637 406732 FALSE TRUE 367545.7116 419232.9017 417518.7352 502206.9288 401058.3853 451947.5613 433237.992 428935.5599 411006.8715 379183.6794 0.969307836 1.105619584 1.101098908 1.324442364 1.057688944 1.191896133 1.142554428 1.131207864 1.083925532 1 18.53253734 0.919584298 2.431303559 1.000213156 1.133551676 0.168426982 0.08632102 0.632333816 8.191457797 0.079797817 0.021552434 8.309679958 -0.919584298 0.13333852 HRPELIEYDK ddPTM_BT-474_Pertuzumab_2h_R1 2 HRPELIEYDK 10 1 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 114.83 0.00078292 1519470000 1600030 1499650 1589080 1991670 1420780 915250 2436000 1563820 2439700 2726500 FALSE TRUE 1537499.059 1456881.45 1876262.105 2094460.327 1466480.679 933756.9821 2465812.497 1531526.571 2162755.484 2541831.726 0.604878381 0.573162037 0.738153547 0.823996453 0.576938538 0.36735594 0.970092737 0.602528702 0.850864934 1 21.27743709 0.920164434 0.938231235 1.001811015 0.645556382 0.337894698 0.154775683 0.78403811 1.443448808 0.14426762 0.048754516 8.32078755 -0.920164434 -0.356254633 ELFASLTPWACGSHTPLLAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELFASLTPWACGSHTPLLAGR 21 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 0 205.62 4.65E-22 153400000 71173 98832 85621 88938 85159 111840 97974 89637 98641 77141 FALSE TRUE 68391.48047 96013.40813 101094.6193 93528.10084 87898.21657 114101.4814 99173.03512 87785.96463 87443.68722 71916.17136 0.950988897 1.335073966 1.405728606 1.300515573 1.222231591 1.586590043 1.379008827 1.220670719 1.215911325 1 16.1340286 0.920662937 1.514523228 1.003871208 1.317480551 0.26240971 0.15298656 0.6372963 2.934151943 0.14353866 0.042109246 8.330344027 -0.920662937 0.313609343 RGPEVTSQGVQTSS(ph)PACK ddPTM_BT-474_Pertuzumab_2h_R1 3 RGPEVTSQGVQTSSPACK 18 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 RGPEVTSQGVQT(0.001)S(0.018)S(0.981)PACK;RGPEVTSQGVQT(0.003)S(0.234)S(0.763)PACK;RGPEVTSQGVQT(0.001)S(0.185)S(0.814)PACK 189.51 1.98E-14 2716520000 1822360 1556370 1694830 1655300 1601970 1934570 1986410 2031160 2528500 2840450 TRUE FALSE 1751140.156 1511983.851 2001123.482 1740730.231 1653498.82 1973688.331 2010720.28 1989215.836 2241475.28 2648063.791 0.661290775 0.570977125 0.75569308 0.657359629 0.624418047 0.745332623 0.759317161 0.751196343 0.846458189 1 21.33650645 0.922784943 0.393439634 1.026963338 0.632847849 0.828310085 0.048068891 0.560218509 0.228902591 0.078426137 0.03940332 8.371146518 -0.922784943 -0.394115489 LDYHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDYHEK 6 0 O95478;A0A0A0MQZ6 O95478 NSA2 Ribosome biogenesis protein NSA2 homolog 0 99.171 0.093742 0 613430 567870 521450 533640 565540 575280 584640 573280 683010 722910 FALSE TRUE 589456.4774 551674.9036 615687.6146 561181.2244 583731.1077 586912.5558 591794.9992 561441.5677 605477.5682 673946.6618 0.874633722 0.818573538 0.913555404 0.832678988 0.866138436 0.870859059 0.878103614 0.833065285 0.898405768 1 19.36227489 0.9246095 5.656716321 0.999991674 0.860522813 0.722851696 0.025987926 0.263681416 18.97806381 0.02282496 0.005748011 8.406389329 -0.9246095 -0.13946886 IWGLDFGDCHK ddPTM_BT-474_Pertuzumab_2h_R1 2 IWGLDFGDCHK 11 0 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 0 ; 119.27 0.00074183 266940000 455480 462950 382250 415520 420190 427740 427060 431250 520920 557890 FALSE TRUE 437679.338 449747.1193 451331.0781 436965.037 433705.793 436389.1959 432286.488 422344.5368 461787.3455 520103.6134 0.841523356 0.864726004 0.867771472 0.840149973 0.833883445 0.839042807 0.831154556 0.812039228 0.887875672 1 18.98843954 0.925845169 5.042796113 0.999975676 0.840932344 0.910035351 0.015121244 0.128864667 7.958743711 0.01692735 0.004278306 8.430341525 -0.925845169 -0.159043333 VIRPLDQPSSFDATPYIK ddPTM_BT-474_Pertuzumab_2h_R1 2 VIRPLDQPSSFDATPYIK 18 1 Q86VP6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 212.83 1.35E-16 587890000 871840 886420 683570 741170 726730 854910 819560 825760 925700 956590 FALSE TRUE 837767.5289 861140.1695 807106.3049 779421.8725 750105.9304 872196.8659 829590.0204 808707.7674 820618.4169 891799.3073 0.939412626 0.965621034 0.905031321 0.873987977 0.841115175 0.978019223 0.930242952 0.906827086 0.920182837 1 19.76635955 0.927867372 18.8155616 1 0.916681234 0.29358523 0.038241153 2312.624625 603244.7864 0.038273508 0.009568377 8.469687214 -0.927867372 -0.083318766 NVHELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NVHELEK 7 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3;P13533 P35580;P35749;P13533 MYH10;MYH11;MYH6 Myosin-10;Myosin-11;Myosin-6 0 84.476 0.04011 0 399700 403890 312670 341060 326570 361840 335720 365210 435080 460390 FALSE TRUE 384079.2821 392371.4526 369176.4243 358662.1475 337074.4206 369156.6527 339828.6418 357668.2859 385691.5424 429207.3752 0.894857135 0.914176865 0.860135323 0.835638361 0.785341632 0.860089258 0.791758626 0.833322786 0.898613502 1 18.71131534 0.928980932 3.558400836 0.999832169 0.844705452 0.602462683 0.037951245 0.22251138 6.995583664 0.039534735 0.010202918 8.49143193 -0.928980932 -0.155126717 (ac)SVPAFIDISEEDQAAELR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVPAFIDISEEDQAAELR 18 0 Q7L2H7;E7ESM3;E9PRI2 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ; 89.959 1.82E-10 29671000 7877.6 6912.1 5926.9 7826.4 9615 7315.8 6684 7815.7 7230.9 5509 FALSE TRUE 7569.734683 6714.973676 6998.022673 8230.321442 9924.275207 7463.730488 6765.800791 7654.303064 6410.078546 5135.870523 1.473895155 1.30746553 1.362577706 1.602517315 1.932345288 1.453255189 1.317362025 1.490361377 1.248099717 1 12.32639312 0.930697265 1.077126927 0.99851119 1.510088337 0.461969777 0.170009168 0.588106667 1.399045448 0.174047342 0.055948758 8.525056489 -0.930697265 0.511577147 RPFGVSLLYIGWDK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPFGVSLLYIGWDK 14 1 P25789;H0YN18;P25789-2;H0YMZ1;H0YL69;H0YLC2;H0YMI6;H0YMA1;H0YKT8;H0YMV3;H0YKS0 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type;Proteasome subunit beta type 0 87.932 0.010818 107900000 170590 176300 171350 159600 179620 126530 187550 167590 215750 243530 FALSE TRUE 163923.1542 171272.0966 202316.7567 167836.9751 185397.6404 129088.5233 189845.293 164129.2079 191258.9645 227035.4962 0.72201553 0.754384664 0.891123899 0.739254337 0.816602001 0.568582999 0.836192121 0.722923114 0.842418775 1 17.79255835 0.932005946 3.889790947 0.999889519 0.758554047 0.457044156 0.081355368 0.260796948 10.16306922 0.074116106 0.018993457 8.550784202 -0.932005946 -0.241335472 NVVHELR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVVHELR 7 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 95.605 0.013343 967790000 1002600 1082810 1003220 942510 870170 743800 970480 1032320 1174010 1232790 FALSE TRUE 963417.2836 1051929.319 1184524.171 991153.0541 898159.8083 758840.1456 982357.0245 1011002.231 1040741.307 1149292.035 0.838270217 0.915284616 1.030655512 0.862403135 0.781489631 0.660267471 0.854749702 0.879673921 0.905549917 1 20.132314 0.93236083 1.695098819 0.998722358 0.851444422 0.210072721 0.088502357 0.789297556 4.635754191 0.093070804 0.026720121 8.557774335 -0.93236083 -0.147277936 AISGVHTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 AISGVHTVR 9 0 P41091;Q2VIR3;Q2VIR3-2;H7BZU1 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 79.974 0.025425 134270000 72617 93416 81267 102990 76364 92557 97464 89980 95879 79231 FALSE TRUE 69779.04736 90751.86714 95953.75467 108305.3262 78820.31741 94428.56596 98656.79359 88121.88156 84995.21788 73864.6138 0.944688448 1.228624405 1.299049027 1.466268091 1.067091715 1.278400591 1.335643531 1.193018917 1.150689261 1 16.17259576 0.932671915 1.955049394 1.001416817 1.238540718 0.205899793 0.135518116 0.603662769 4.848431535 0.126298076 0.035349972 8.563906455 -0.932671915 0.2371239 LASVLLYSDYGIGEVPVEPLDVPLPSTIRPASPVAGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 LASVLLYSDYGIGEVPVEPLDVPLPSTIRPASPVAGSPK 39 1 Q13057;Q13057-2;K7EN91 Q13057 COASY Bifunctional coenzyme A synthase;Phosphopantetheine adenylyltransferase;Dephospho-CoA kinase 1 LASVLLYSDYGIGEVPVEPLDVPLPS(0.01)T(0.055)IRPAS(0.298)PVAGS(0.637)PK 191.8 2.94E-24 236840000 138730 130840 131490 129530 124650 119350 126880 134800 162810 175660 TRUE FALSE 133308.2782 127108.5713 155253.168 136215.0588 128659.4805 121763.3388 128432.7954 132016.3329 144328.4914 163762.3917 0.814034754 0.776176813 0.948039207 0.831784742 0.785647297 0.743536642 0.784263066 0.806145608 0.881328673 1 17.32124455 0.932734277 2.907814958 0.999698276 0.810674189 0.560766436 0.051431636 0.246523642 4.902619364 0.051945275 0.013697928 8.565136269 -0.932734277 -0.189024087 LVSQKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVSQKPK 7 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 91.626 0.027393 0 1075800 1201400 1028500 853330 984970 617960 1261700 1036000 1277500 1353900 FALSE TRUE 1033756.547 1167137.248 1214372.829 897370.4636 1016652.455 630455.5746 1277141.062 1014606.238 1132483.556 1262199.147 0.819012237 0.924685499 0.962108738 0.710957907 0.805461212 0.49948978 1.011838001 0.80384006 0.897230487 1 20.26750812 0.93340247 1.159645418 0.998315044 0.81246091 0.152606617 0.1352617 1.121065653 3.064603943 0.127655846 0.040089995 8.578324496 -0.93340247 -0.185854134 AFYAELYHIISSNLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AFYAELYHIISSNLEK 16 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 311.64 1.12E-57 1700320000 1720860 1906000 1716290 1499110 1668920 1230590 1991090 1701980 2083620 2212450 FALSE TRUE 1653606.889 1851642.746 2026461.782 1576479.247 1722602.327 1255473.373 2015457.555 1666833.518 1847096.193 2062598.791 0.801710394 0.89772318 0.982479865 0.764316964 0.835161125 0.608685207 0.977144738 0.808122998 0.895518896 1 20.97603179 0.93395896 3.797667433 0.999975286 0.837358609 0.199034282 0.102020015 0.484171971 18.02512266 0.095224336 0.024446969 8.589323505 -0.93395896 -0.162616677 IEPELDGSAQVTSHDASTNGLINFIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEPELDGSAQVTSHDASTNGLINFIK 26 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48 P06744 GPI Glucose-6-phosphate isomerase 0 302.53 9.58E-71 107000000 83611 75577 75133 75232 89973 72445 80628 83395 87357 76392 FALSE TRUE 80343.38968 73421.61796 88711.20442 79114.73254 92867.06326 73909.88754 81614.74958 81672.86411 77440.59959 71217.9018 1.128134748 1.03094329 1.245630694 1.110882665 1.303984826 1.037799285 1.145986438 1.146802448 1.087375472 1 16.11995231 0.934721561 2.500907187 1.00013243 1.144717285 0.243567939 0.078366552 0.468501082 6.590531286 0.070370295 0.018943905 8.60441921 -0.934721561 0.144584854 LAHEDAECEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAHEDAECEK 10 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 93.258 0.0089085 124410000 86644 83647 69195 75036 66950 83892 88354 76272 97883 115080 FALSE TRUE 83257.85669 81261.46946 81700.07573 78908.61695 69103.50755 85588.35372 89435.30268 74696.95655 86771.7322 107285.5291 0.77603995 0.757431782 0.761519996 0.735501028 0.644108373 0.79776233 0.83361944 0.696244472 0.808792508 1 16.71109597 0.935031072 7.883517801 0.999999095 0.75002242 0.697113547 0.049450705 0.737420422 89.35010447 0.047757399 0.011961649 8.610553544 -0.935031072 -0.249976675 VYEHTS(ph)RFSPK ddPTM_BT-474_Pertuzumab_2h_R1 3 VYEHTSRFSPK 11 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LNN3;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 VYEHT(0.016)S(0.492)RFS(0.492)PK;VYEHT(0.022)S(0.489)RFS(0.489)PK;VYEHT(0.002)S(0.669)RFS(0.329)PK 136.24 6.24E-05 799354000 850242 1002676 739212 824121 786403 855526 855225 869145 1021689 1049315 TRUE FALSE 817013.6026 974080.6622 872804.0521 866653.9836 811698.3667 872825.3219 865691.4994 851196.852 905711.148 978243.9604 0.835183897 0.99574411 0.89221512 0.885928274 0.82975045 0.892236862 0.884944384 0.870127378 0.925854066 1 19.89983477 0.935252076 4.238178292 0.999944126 0.887329382 0.402538318 0.042614415 0.297218494 14.27227776 0.040031529 0.010201829 8.614936414 -0.935252076 -0.112614744 CTEYLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 CTEYLDR 7 0 O75351;K7EKZ3;K7EL71 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 ; 133.79 0.0075314 580640000 578700 613900 518700 572290 626520 532470 614780 613670 646020 566040 FALSE TRUE 556083.7642 596392.1731 612440.6284 601825.9555 646672.5848 543236.9082 622303.8615 600997.5 572686.5179 527701.6066 1.053784482 1.130169334 1.160581322 1.140466407 1.225451234 1.029439557 1.179272251 1.138896476 1.085246872 1 19.00936285 0.935683564 3.100283753 1.000234777 1.135362216 0.363602882 0.053533055 0.305182803 7.089575041 0.048335082 0.012650477 8.623499932 -0.935683564 0.135127439 VAQNS(ph)PSVENIQTSQAEQAKPLQEDILMQNIETVHPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VAQNSPSVENIQTSQAEQAKPLQEDILMQNIETVHPFR 38 1 Q92576-2;Q92576 Q92576-2 PHF3 PHD finger protein 3 1 VAQNS(0.841)PS(0.159)VENIQTSQAEQAKPLQEDILMQNIETVHPFR;VAQNS(0.846)PS(0.154)VENIQTSQAEQAKPLQEDILMQNIETVHPFR 279.87 8.23E-77 406900000 211851 180557 181790 164454 176732 198318 189421 199277 225045 224206 TRUE FALSE 203571.6287 175407.6911 214643.4969 172941.4906 182416.7453 202328.1258 191739.1909 195161.8603 199498.8351 209020.3279 0.973932204 0.839189628 1.026902498 0.827390773 0.87272251 0.967983008 0.917323175 0.933697991 0.954447049 1 17.67328373 0.9364459 0.779829332 1.000175153 0.912489039 0.162307043 0.058226592 1.287831032 1.719074589 0.052734584 0.019427934 8.638650433 -0.9364459 -0.087686113 SFLVASVLPGPDGNINS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFLVASVLPGPDGNINSPTR 20 0 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 SFLVASVLPGPDGNINS(0.994)PT(0.006)R 262.12 2.14E-36 177880000 182630 175930 134660 165640 162720 176100 177450 183380 186110 156090 TRUE FALSE 175492.6177 170912.6487 158996.0575 174188.7003 167954.0366 179660.8627 179621.6862 179593.1389 164983.573 145517.8853 1.205986586 1.174513005 1.092622101 1.197026056 1.1541814 1.234630797 1.234361576 1.234165399 1.133768352 1 17.15083696 0.938461622 5.890042333 1.000015255 1.191565538 0.660754225 0.041506423 0.286257792 25.92690154 0.043625232 0.010975246 8.678838802 -0.938461622 0.191550283 INAGMLAQFIDKPVCFVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 INAGMLAQFIDKPVCFVGR 19 1 P35244 P35244 RPA3 Replication protein A 14 kDa subunit 0 160.09 2.93E-11 353210000 298590 322010 260180 259340 292970 282210 307480 309250 333850 279880 FALSE TRUE 286920.7727 312826.5901 307200.3137 272724.5685 302393.6461 287916.4796 311243.0322 302863.8794 295952.7476 260923.4783 1.099635704 1.198920818 1.177357882 1.045228165 1.15893613 1.103451791 1.192851767 1.160738318 1.13425112 1 17.99326724 0.940014433 18.46722543 0.999999999 1.144724461 0.468064115 0.045180505 583.6157956 179674.4268 0.042476226 0.010619056 8.709925358 -0.940014433 0.144724462 IFHELTQTDK ddPTM_BT-474_Pertuzumab_2h_R1 4 IFHELTQTDK 10 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;; 190.86 8.55E-07 2854610000 5147740 4995230 4345910 4552060 4445210 4395480 5406430 5091510 5949580 6267210 FALSE TRUE 4946560.63 4852770.931 5131312.611 4786992.362 4588194.217 4484359.617 5472595.508 4986368.539 5274208.621 5842726.284 0.84661858 0.830566194 0.878239432 0.819307996 0.785283101 0.7675115 0.936651015 0.853431822 0.902696509 1 22.47821027 0.940254882 0.770428048 0.998671514 0.82837953 0.593182923 0.042534149 0.531385444 0.695442368 0.042126981 0.015626328 8.714748967 -0.940254882 -0.170291984 AQEQQQQMAELHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQEQQQQMAELHSK 14 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 202.82 1.59E-08 1190390000 606030 700250 546560 677630 623030 580030 704390 695630 698340 578380 FALSE TRUE 582345.6776 680279.5556 645335.5502 712602.5655 643070.3258 591758.604 713010.5355 681264.9974 619067.3709 539205.8074 1.080006316 1.261632472 1.196826038 1.321578061 1.192624999 1.097463336 1.322334674 1.263460052 1.148109613 1 19.04047651 0.940403944 4.837730788 1.000079416 1.223134657 0.4168408 0.077838718 0.27734785 18.33083809 0.073074246 0.018500522 8.717740626 -0.940403944 0.223055241 ANIVHLMLSSPEQIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ANIVHLMLSSPEQIQK 16 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 235.35 1.06E-19 949900000 1438100 1430790 1462470 1111270 1502680 1536170 1553510 1305240 1891830 2362600 FALSE TRUE 1381897.462 1389985.27 1726770.861 1168622.778 1551015.067 1567232.41 1572522.32 1278286.338 1677077.39 2202578.998 0.627399727 0.631071699 0.783976812 0.530570199 0.704181357 0.711544245 0.713945934 0.580358906 0.761415319 1 21.07076233 0.941395861 6.419593323 0.999986739 0.661319569 0.688927449 0.069216673 0.274563457 29.14800614 0.063417293 0.015926149 8.737674473 -0.941395861 -0.33866717 AYEDGCK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYEDGCK 7 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 108.09 0.017057 1352220000 2054400 1967400 1510240 1754800 1717440 1840460 1837360 1890130 2148000 2121600 FALSE TRUE 1974111.777 1911291.678 1783173.963 1845365.438 1772683.017 1877675.362 1859846.161 1851098.155 1904168.045 1977902.142 0.998083644 0.96632267 0.901548123 0.932991273 0.896244045 0.949326725 0.940312527 0.935889656 0.962721059 1 20.91553962 0.94185333 2.738661363 0.999927546 0.938141615 0.30601721 0.027670581 0.382821958 6.700093298 0.026951407 0.007165938 8.746883247 -0.94185333 -0.061785931 MLQEDELRDAVLLVFANK ddPTM_BT-474_Pertuzumab_2h_R1 2 MLQEDELRDAVLLVFANK 18 1 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 286.28 8.38E-40 506680000 722820 803730 403200 481970 730660 971460 574760 642890 694940 506490 FALSE TRUE 694571.3953 780808.4073 476067.2091 506844.5295 754162.3425 991103.5868 581794.0848 629614.0968 616053.3246 472184.9812 1.470973078 1.653607036 1.008221837 1.073402479 1.597175625 2.098973128 1.232131703 1.333405597 1.304686403 1 18.84899263 0.941955531 1.207160358 1.009281173 1.445404996 0.171314723 0.295466103 1.059830753 3.137750652 0.296296346 0.092023562 8.748941873 -0.941955531 0.436123824 DAVDWVHYK ddPTM_BT-474_Pertuzumab_2h_R1 4 DAVDWVHYK 9 0 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;; 120.12 0.0018813 828940000 2004660 2122710 1810040 1960010 1970500 1499920 2253810 1986540 2287460 2520250 FALSE TRUE 1926315.671 2062172.389 2137154.492 2061166.351 2033882.922 1530249.41 2281392.801 1945517.255 2027797.131 2349551.223 0.819865365 0.877687777 0.909601149 0.877259594 0.865647406 0.651294339 0.970990876 0.828037812 0.863057213 1 21.16395379 0.942000777 18.92757657 1.000000001 0.852125914 0.24702868 0.07800931 1147.574977 374504.8936 0.071900262 0.017975065 8.749853413 -0.942000777 -0.147874087 ETLEQQKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETLEQQKR 8 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 136.27 0.0012799 1850400000 769910 775930 587910 632610 664880 687840 767360 728540 883520 903140 FALSE TRUE 739821.066 753801.2361 694158.415 665259.0779 686266.469 701748.5961 776751.1812 713495.3944 783226.5136 841969.5234 0.878679151 0.895283279 0.824446011 0.790122516 0.815072814 0.833460804 0.922540733 0.847412376 0.93023143 1 19.68340849 0.942593023 0.84921039 1.000675548 0.841778548 0.627818174 0.037200119 0.476582883 0.741741493 0.037781784 0.013372423 8.761793693 -0.942593023 -0.158897 VPQIEVETHK ddPTM_BT-474_Pertuzumab_2h_R1 4 VPQIEVETHK 10 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 167.6 5.19E-06 2031690000 1242160 1365340 1073280 1118380 1214630 1129720 1328930 1275260 1477920 1487660 FALSE TRUE 1193615.014 1326401.84 1267245.571 1176099.726 1253699.677 1152563.712 1345193.843 1248925.435 1310152.718 1386899.463 0.860635573 0.95637923 0.913725619 0.848006476 0.903958586 0.831036238 0.96992888 0.900516201 0.944663079 1 20.40343178 0.942783093 0.843189553 0.999425125 0.893512521 0.392505809 0.040959526 0.720214633 1.106936537 0.037880669 0.013452226 8.765629158 -0.942783093 -0.105912604 GAPQHYPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GAPQHYPK 8 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 ; 103.92 0.0046803 572570000 1102240 1187500 1038500 1039390 1044160 892490 1181320 1085500 1340200 1434160 FALSE TRUE 1059163.242 1153633.663 1226180.051 1093033.042 1077746.355 910536.7593 1195777.348 1063084.046 1188066.115 1337023.066 0.792180232 0.862837517 0.917097156 0.81751248 0.806079104 0.681017989 0.894358054 0.795112719 0.88859059 1 20.35059292 0.943224135 3.841357002 0.999902914 0.822668906 0.446493623 0.061491839 0.248243216 9.853466397 0.059160213 0.015177558 8.774535491 -0.943224135 -0.177234008 EVLHELYK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLHELYK 8 0 P21283;E7EV59 P21283 ATP6V1C1 V-type proton ATPase subunit C 1 0 84.476 0.017425 71598000 201000 200920 186300 217010 160610 125050 213850 202600 265580 311270 FALSE TRUE 193144.6978 195189.9583 219968.5542 228209.9121 165776.1665 127578.5967 216467.1603 198416.2392 235432.4718 290187.4056 0.66558608 0.672634148 0.758022402 0.786422524 0.571272782 0.439642087 0.745956427 0.68375207 0.811311819 1 18.14662538 0.944973971 1.582303043 0.999548979 0.660606636 0.553237913 0.094545354 0.356256766 1.816042638 0.095160905 0.02771163 8.809960701 -0.944973971 -0.338942343 LADINYEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LADINYEGR 9 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 80.688 0.054446 98491000 210030 238360 146640 185790 186890 227070 184590 202620 216730 197440 FALSE TRUE 201821.7954 231562.2062 173141.11 195378.6442 192901.4866 231661.511 186849.0676 198435.8262 192127.719 184067.2129 1.096457061 1.258030708 0.940640689 1.061452722 1.047994825 1.258570211 1.015113255 1.078061774 1.043791102 1 17.48987314 0.947474091 0.012885254 2.62E-07 2.114137882 0.097690339 0.093345514 2263.40886 18.68808934 1558.975127 1503.699745 8.860823613 -0.947474091 2.11413762 LKLEDFFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKLEDFFAR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 145.99 8.74E-05 4451300000 4142700 4359200 3631100 3812500 3774900 3447400 4690100 4350400 5035700 5498300 FALSE TRUE 3980798.704 4234879.884 4287320.543 4009263.582 3896323.087 3517108.79 4747498.847 4260562.72 4464068.447 5125895.244 0.776605552 0.826173709 0.836404245 0.782158704 0.760125383 0.686145273 0.926179452 0.831184119 0.870885618 1 22.28937256 0.947985792 0.755636721 0.997494798 0.78946818 0.562508872 0.055573546 0.568268921 0.721045919 0.054860488 0.020584293 8.871269886 -0.947985792 -0.208026618 GLSAS(ph)LPDLDSENWIEVK ddPTM_BT-474_Pertuzumab_2h_R1 8 GLSASLPDLDSENWIEVK 18 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLSAS(1)LPDLDSENWIEVK;GLS(0.001)AS(0.999)LPDLDSENWIEVK;GLS(0.012)AS(0.988)LPDLDSENWIEVK;GLS(0.002)AS(0.998)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.013)AS(0.987)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.003)AS(0.997)LPDLDSENWIEVK 372.59 1.12E-107 6067028000 6282652 5407295 4384766 4471945 4984068 4777906 4514145 6626723 5954461 5256623 TRUE FALSE 6037119.014 5253084.241 5177190.755 4702742.617 5144385.074 4874518.533 4569390.457 6489878.854 5278535.55 4900587.242 1.231917465 1.071929543 1.056442932 0.959628384 1.049748697 0.994680493 0.932416919 1.32430636 1.077123065 1 22.22452321 0.948002449 23.35958053 1 1.08182812 0.039602461 0.113112855 36038.8849 16190264.07 0.115265131 0.028816282 8.871610157 -0.948002449 0.08182812 FKDPNAPK ddPTM_BT-474_Pertuzumab_2h_R1 3 FKDPNAPK 8 1 P09429;Q5T7C4;B2RPK0;P23497 P09429;P23497 HMGB1;HMGB1P1;SP100 High mobility group protein B1;Putative high mobility group protein B1-like 1;Nuclear autoantigen Sp-100 0 ;; 92.491 0.010707 15045510000 37200900 34627110 29642720 27694000 31360150 29708190 32324940 38780600 37706900 35012800 FALSE TRUE 35747047.7 33639578.73 34999818.9 29123290.66 32368877.71 30308909.96 32720542.29 37979767.06 33426570.79 32641351.87 1.095146054 1.030581664 1.072253963 0.892220726 0.991652485 0.928543342 1.002426076 1.163547613 1.024055956 1 24.96019747 0.949268873 21.91729701 0.999999996 1.025909725 0.005975499 0.074152191 27456.96061 11862209.11 0.078012178 0.019503045 8.897517953 -0.949268873 0.025909729 MAVTFIGNSTAIQELFK ddPTM_BT-474_Pertuzumab_2h_R1 2 MAVTFIGNSTAIQELFK 17 0 Q5JP53;P07437;Q5ST81 Q5JP53 TUBB Tubulin beta chain 0 ; 276.45 4.63E-27 146980000 434030 406520 384160 336571 351978 291269 466600 399080 479230 508410 FALSE TRUE 417067.6278 394926.4476 453586.2576 353941.4696 363299.692 297158.6587 472310.3904 390838.8585 424829.8195 473974.9379 0.879936036 0.833222215 0.956983632 0.746751445 0.766495574 0.626950151 0.996488111 0.824598153 0.896312833 1 18.85445125 0.949424853 0.964902393 0.997066216 0.81961093 0.227631084 0.098915817 0.9625637 1.888130812 0.094204818 0.031588505 8.900714136 -0.949424853 -0.177455286 FGHTFCK ddPTM_BT-474_Pertuzumab_2h_R1 1 FGHTFCK 7 0 Q00577 Q00577 PURA Transcriptional activator protein Pur-alpha 0 100.07 0.010067 309990000 358340 437060 347150 463800 443840 417510 402530 363390 469370 479100 FALSE TRUE 344335.6766 424595.4767 409887.7273 487736.7736 458116.5167 425952.3383 407456.2826 355885.8695 416089.0854 446650.1303 0.77092931 0.950622082 0.917693066 1.091988428 1.025671965 0.953659944 0.912249331 0.796788908 0.931577217 1 18.76878566 0.950223509 22.16677301 1.000000003 0.926187321 0.055359691 0.089361302 13209.33507 5882470.071 0.093502323 0.02337558 8.917097366 -0.950223509 -0.073812682 VYVGNLGNNGNKTELER ddPTM_BT-474_Pertuzumab_2h_R1 4 VYVGNLGNNGNKTELER 17 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 327.53 5.97E-72 3344510000 1160790 1306270 756110 778310 970310 1284300 975630 1049450 1133390 986080 FALSE TRUE 1115425.043 1269016.459 892755.8966 818478.6724 1001520.902 1310269.426 987570.0518 1027778.491 1004732.319 919291.9233 1.21335238 1.38042816 0.971134276 0.890335977 1.089448169 1.42530288 1.074272521 1.118011009 1.092941527 1 19.81016354 0.95125158 1.318934601 1.002220148 1.146458159 0.078589941 0.155524545 1.545296106 5.449451359 0.155386143 0.047159071 8.938231119 -0.95125158 0.144238011 REALEK ddPTM_BT-474_Pertuzumab_2h_R1 1 REALEK 6 1 O43707;O43707-2;F5GXS2;O43707-3;Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3;Q4VCS5;E7ERM3;Q4VCS5-2;A6NP16 O43707;Q9Y2J4;Q4VCS5 ACTN4;AMOTL2;AMOT Alpha-actinin-4;Angiomotin-like protein 2;Angiomotin 0 89.046 0.081152 305880000 563620 500970 465240 525100 490790 438370 574360 541160 646160 677680 FALSE TRUE 541593.1073 486682.8261 549319.2172 552200.4739 506576.7061 447234.1418 581389.1895 529984.8569 572810.6257 631780.13 0.857249352 0.770335759 0.869478464 0.874039001 0.801824372 0.707895232 0.920239751 0.838875475 0.90666135 1 19.26906304 0.952540804 1.011687699 0.999269603 0.822076508 0.485826658 0.055737949 0.512053851 1.095791602 0.052038801 0.017140864 8.964804109 -0.952540804 -0.177193096 KGEQCVHTASGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGEQCVHTASGPR 13 1 Q04721 Q04721 NOTCH2 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain 0 78.763 0.014505 48684000 64897 73537 53381 72983 61201 63123 70603 70122 75802 68422 FALSE TRUE 62360.75349 71439.79676 63028.13415 76749.66138 63169.58575 64399.39031 71467.06063 68673.9562 67197.27475 63787.717 0.977629494 1.11996165 0.98809202 1.203204394 0.990309557 1.009589202 1.120389065 1.076601569 1.053451635 1 15.96099102 0.955182418 15.24347688 0.999999994 1.064530368 0.062419609 0.068913615 108.7807082 37001.93213 0.060942738 0.015236184 9.019499072 -0.955182418 0.064530374 KKQEEEQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKQEEEQEK 9 2 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 0 ; 94.692 0.0048088 48668000 94591 74251 68424 57538 65392 65647 78861 79827 88696 96878 FALSE TRUE 90894.27914 72133.43418 80789.73888 60507.54308 67495.39307 66974.42732 79826.12451 78178.54455 78627.60192 90316.36677 1.006398756 0.79867511 0.894519363 0.669951031 0.747321836 0.741553604 0.883850041 0.865607723 0.870579771 1 16.46269983 0.955493626 0.942101718 0.995727935 0.810325018 0.264135439 0.089174411 0.842596617 1.586886193 0.085455765 0.028953856 9.025964603 -0.955493626 -0.185402918 ITEFCHR ddPTM_BT-474_Pertuzumab_2h_R1 5 ITEFCHR 7 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;; 186.43 0.00059898 11938240000 5890440 7350850 5866400 7785720 6206900 4705920 7602900 6488140 7669920 8256370 FALSE TRUE 5660235.093 7141210.955 6926588.977 8187541.942 6406550.575 4801076.927 7695946.564 6354157.642 6799262.837 7697158.706 0.735366816 0.927772341 0.899889068 1.063709643 0.832326683 0.623746646 0.999842521 0.825519894 0.883347102 1 22.87589456 0.955617456 19.97059537 1.000000005 0.868202235 0.104452766 0.118582286 1584.07497 712783.0488 0.112045635 0.028011409 9.028538536 -0.955617456 -0.13179777 YDNQIHIIDFDDENNIINK ddPTM_BT-474_Pertuzumab_2h_R1 1 YDNQIHIIDFDDENNIINK 19 0 A8MUM1;Q53HC9;F8WDS8;C9J0U9;D3YTH5 A8MUM1 TSSC1 Protein TSSC1 0 184.8 2.41E-14 245230000 106740 102640 73512 88903 99130 86453 96286 95191 116110 122580 FALSE TRUE 102568.4828 99712.8077 86797.25367 93491.29448 102318.6065 88201.13889 97464.37687 93225.27258 102929.6796 114277.5474 0.897538363 0.87254942 0.759530246 0.818107289 0.895351789 0.771815119 0.852874244 0.815779431 0.90069906 1 16.80218245 0.955739096 3.449452948 0.999802597 0.833678266 0.567645155 0.044440906 0.173804423 5.415775307 0.041523818 0.010754459 9.031067657 -0.955739096 -0.166124331 VVSIGVPVSELLDDPSGPAGSLTSVEFCGGTHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VVSIGVPVSELLDDPSGPAGSLTSVEFCGGTHLR 34 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 209.54 1.25E-27 143440000 71051 73638 78162 87197 65407 62466 84035 91250 91694 108090 FALSE TRUE 68274.24837 71537.91634 92287.6121 91697.24762 67510.87556 63729.10532 85063.44547 89365.65561 81285.28153 100768.968 0.677532476 0.709920105 0.915833653 0.909975059 0.669957 0.632427885 0.844143263 0.886837063 0.806649935 1 16.6206919 0.955928211 0.768832348 0.993825298 0.766419415 0.330212182 0.097821188 0.953154309 1.250854622 0.102777466 0.038279738 9.035001121 -0.955928211 -0.227405883 QRS(ph)DDESPSTSSGSSDADQRDPAAPEPEEQEER ddPTM_BT-474_Pertuzumab_2h_R1 2 QRSDDESPSTSSGSSDADQRDPAAPEPEEQEER 33 2 R4GN77;R4GND1;A0A1B0GX65;Q969T4;R4GMM6;R4GNG6 R4GN77 UBE2E3 Ubiquitin-conjugating enzyme E2 E3 1 QRS(0.972)DDES(0.026)PS(0.001)TSSGSSDADQRDPAAPEPEEQEER;QRS(0.805)DDES(0.053)PS(0.06)T(0.06)S(0.015)S(0.004)GS(0.001)S(0.001)DADQRDPAAPEPEEQEER 79.917 0.00069319 413390000 48159.7 44529 40031.7 39955.6 46051.5 50138.3 45337 45270.8 53064 60650 TRUE FALSE 46277.56568 43259.07652 47266.31869 42017.7133 47532.78832 51152.13078 45891.84777 44335.94216 47040.39718 56542.12148 0.818461785 0.765076997 0.835948802 0.743122334 0.840661565 0.904673002 0.811640005 0.784122368 0.83195317 1 15.78703839 0.955993605 21.05723607 1.000000001 0.812068296 0.63662077 0.042127483 771.0256468 368940.1783 0.041364485 0.010341121 9.036361675 -0.955993605 -0.187931704 QKYPEQQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKYPEQQGR 9 1 A0A0G2JKR7;P28702;P28702-3 A0A0G2JKR7 RXRB Retinoic acid receptor RXR-beta 0 ; 105.86 0.0027624 107686000 150363 152676 123749 139833 135305 129545 149871 156571 161537 169798 FALSE TRUE 144486.6477 148321.83 146113.1971 147049.7979 139657.2082 132164.4887 151705.1661 153337.7541 143199.997 158297.4302 0.912754222 0.936981919 0.923029495 0.92894621 0.88224558 0.834912408 0.958355205 0.968668625 0.904626163 1 17.27227831 0.956788671 0.72671985 0.995354173 0.910314688 0.310158036 0.036503672 0.988986044 1.175715604 0.038434466 0.014748977 9.052919769 -0.956788671 -0.085039484 S(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPQPPAEEDEDDFDDTLVAIDTYNCDLHFK 30 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 S(0.999)PQPPAEEDEDDFDDT(0.001)LVAIDTYNCDLHFK;S(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;S(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;S(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK 182.64 1.02E-17 220593000 123135 134396 112709 143504 90398.1 117371 130419 117976 144432 172159 TRUE FALSE 118322.7481 130563.1577 133078.0235 150910.2586 93305.83698 119744.322 132015.1067 115539.7544 128036.6849 160498.5176 0.737220193 0.813485131 0.829154222 0.940259517 0.581350148 0.746077433 0.822531627 0.719880508 0.797743722 1 17.29220045 0.957474645 21.81969843 1.000000001 0.773866033 0.372139744 0.087620497 1839.503067 943848.8931 0.083571214 0.020892803 9.067230273 -0.957474645 -0.226133968 RDPEEDGMMK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDPEEDGMMK 10 1 Q8N3U4;Q8N3U4-2;B1AMT4 Q8N3U4 STAG2 Cohesin subunit SA-2 0 98.898 0.0081182 171270000 252740 219300 199850 224860 254240 214290 232810 228520 278880 290810 FALSE TRUE 242862.6414 213045.7787 235967.3406 236465.0515 262417.8605 218623.0906 235659.1984 223800.9821 247222.7116 271113.1797 0.89579799 0.785818598 0.870364698 0.872200503 0.967927346 0.806390493 0.869228116 0.825489128 0.911880093 1 18.04853572 0.958054494 5.472892315 0.999966945 0.860380205 0.441788298 0.047795766 0.211687817 21.8806766 0.04467806 0.011262599 9.079344472 -0.958054494 -0.13958674 LKDLFDYSPPLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDLFDYSPPLHK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 93.823 0.003267 190670000 592920 613150 546700 588210 543470 628120 597250 597750 699270 776160 FALSE TRUE 569748.0309 595663.5623 645500.8513 618567.5886 560951.2061 640821.0168 604559.3242 585406.2536 619891.8012 723589.9919 0.787390701 0.823205916 0.892080955 0.854859237 0.775233506 0.885613433 0.835499842 0.809030335 0.856689297 1 19.46481293 0.958659088 19.3109877 1.000000001 0.833889661 0.659321218 0.035831156 208.8877672 97575.72384 0.033994322 0.00849858 9.091992912 -0.958659088 -0.166110339 VKELVEFAQDDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VKELVEFAQDDDR 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 79.837 0.017715 116690000 141010 172670 99204 132920 128970 169710 138760 141130 157590 138130 FALSE TRUE 135499.1733 167745.6207 117132.3696 139780.0171 133118.4372 173141.6525 140458.1864 138215.6162 139701.0439 128774.3321 1.052221907 1.302632427 0.909594076 1.085464897 1.033734247 1.344535434 1.090731236 1.073316506 1.084851629 1 16.97448553 0.959016354 1.324604544 1.003149015 1.116601605 0.075011703 0.1197277 1.366793233 4.872471287 0.110114043 0.033403021 9.099475378 -0.959016354 0.11345259 MNVPETMNEVLDMS(ph)DDEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MNVPETMNEVLDMSDDEVR 19 0 Q12955;Q12955-4;Q12955-5;H0Y8Z4 Q12955;Q12955-4 ANK3 Ankyrin-3 1 MNVPETMNEVLDMS(1)DDEVR 156.67 3.34E-10 0 35332 35680 37711 41266 28934 43252 36454 36177 43806 48338 TRUE FALSE 33951.18638 34662.44133 44526.21658 43395.74321 29864.68839 44126.58507 36900.13496 35429.93231 38833.32653 45064.0242 0.753398903 0.769182112 0.988065699 0.96297976 0.662716855 0.979197616 0.818837989 0.786213236 0.861736767 1 15.45968853 0.95982677 20.28768146 1.000000006 0.840571923 0.17987323 0.101838338 1009.760543 509937.2293 0.095945334 0.023986333 9.116471314 -0.95982677 -0.159428083 VT(ph)SPISTDGMAEELTMDGVAGEHSQIPNGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTSPISTDGMAEELTMDGVAGEHSQIPNGSR 31 0 F8VZQ2;Q9UKN5 F8VZQ2 PRDM4 PR domain zinc finger protein 4 1 VT(0.498)S(0.498)PIS(0.003)T(0.001)DGMAEELTMDGVAGEHSQIPNGSR;VT(0.54)S(0.459)PISTDGMAEELTMDGVAGEHSQIPNGSR 150.07 4.24E-08 185934000 26850.9 27466 19783.6 24759 22832 27628 25322 27665 28565 22871.7 TRUE FALSE 25801.53714 26682.69657 23358.9366 26036.81496 23566.41202 28186.65709 25631.89821 27093.70808 25322.42095 21322.57939 1.210057033 1.251382213 1.095502386 1.221091243 1.105232701 1.321915917 1.202101197 1.270658094 1.187587134 1 14.38009435 0.959983506 22.28347867 0.999999998 1.211656794 0.480679081 0.064974724 1544.874058 860276.3925 0.06024816 0.01506204 9.119762027 -0.959983506 0.211656796 AQELDALDNSHPIEVSVGHPSEVDEIFDAISYSK ddPTM_BT-474_Pertuzumab_2h_R1 4 AQELDALDNSHPIEVSVGHPSEVDEIFDAISYSK 34 0 E9PLK3;P55786;P55786-2;A6NEC2;A6NEC2-2;E9PJ74;E9PRQ5 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 ;;; 313.88 1.13E-104 690875000 535208 721842 591532 725066 624136 777958 716908 437796 754356 846945 FALSE TRUE 514291.4797 701255.7729 698434.991 762486.7432 644211.9013 793688.8438 725681.7346 428755.3596 668724.6694 789580.6608 0.651347614 0.888136967 0.88456446 0.965685687 0.815891185 1.005202993 0.919072326 0.543016541 0.846936485 1 19.59072713 0.961869942 23.96823259 1.000000003 0.828274162 0.1197461 0.133420557 10173.01929 6394682.038 0.138222467 0.034555617 9.159461516 -0.961869942 -0.171725841 EEASLLSHS(ph)PGTSNQSQPCSPKPIR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHS(0.996)PGT(0.003)S(0.001)NQSQPCSPKPIR;EEASLLSHS(1)PGTSNQSQPCSPKPIR;EEASLLS(0.004)HS(0.995)PGT(0.001)SNQSQPCSPKPIR 249.96 1.27E-39 4618450000 1335140 1471450 1058870 1385990 1268080 1506960 1315160 1197830 1526690 1555350 TRUE FALSE 1282961.253 1429485.687 1250231.363 1457521.11 1308868.945 1537431.764 1331255.321 1173094.392 1353386.552 1450004.759 0.88479796 0.985848962 0.862225697 1.005183673 0.902665275 1.060294288 0.918104105 0.80902796 0.933366972 1 20.4676262 0.961997144 23.07686242 1.000000003 0.924522208 0.084337587 0.069295029 6884.480985 4180540.487 0.068728391 0.017182098 9.162144647 -0.961997144 -0.075477795 YSDFVVHEIGK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSDFVVHEIGK 11 0 Q96PZ0;Q96PZ0-2;E7EUH7;H0Y863 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 ; 110.66 0.0017644 481100000 958200 933710 820150 871940 887070 901920 962550 975350 1143380 1172820 FALSE TRUE 920752.4847 907081.505 968369.3491 916940.9279 915603.4122 920157.4404 974329.9748 955208.6817 1013588.296 1093383.857 0.842112748 0.829609381 0.885662746 0.83862673 0.837403448 0.841568526 0.891114286 0.873626106 0.927019628 1 20.06036855 0.962043637 0.810682106 1.000827373 0.846152603 0.877630928 0.017724961 0.21757691 0.31429656 0.016682981 0.006056209 9.16312555 -0.962043637 -0.15467477 ILEFFGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILEFFGLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 138.9 0.0015953 243360000 472150 517230 496310 551430 463190 361130 618960 557110 621890 697690 FALSE TRUE 453697.856 502479.1068 586004.2574 579889.3684 478088.927 368432.296 626535.0176 545605.4838 551295.6544 650434.8349 0.69753007 0.772527976 0.900942302 0.89154107 0.735029708 0.566439982 0.963255632 0.838831893 0.847580149 1 19.311045 0.962521956 0.780432308 0.99490705 0.784080522 0.27082288 0.106124491 1.043474985 1.409612741 0.106256856 0.039321441 9.173223107 -0.962521956 -0.210826528 NVDVYDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVDVYDKR 8 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 ; 140.75 0.0010334 1687850000 2106900 2050240 1749960 1656560 1867510 1653310 2065210 1835600 2216590 2502430 FALSE TRUE 2024560.019 1991769.163 2066216.7 1742055.26 1927580.155 1686741.061 2090484.658 1797694.219 1964971.996 2332938.187 0.867815543 0.853759938 0.88567143 0.746721568 0.826245704 0.723011467 0.896073745 0.770570874 0.842273493 1 21.15371665 0.962610275 22.40070773 1.000000001 0.819348004 0.479539715 0.055498679 1342.543466 804338.5236 0.050928924 0.012732231 9.175088778 -0.962610275 -0.180651997 DVAEEIANYRPTLDTLHEQASALPQEHAESPDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVAEEIANYRPTLDTLHEQASALPQEHAESPDVR 34 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 143.06 1.72E-10 85875000 30354 33044 31493 47542 33822 31679 43758 30070 43599 58261 FALSE TRUE 29167.73212 32101.61747 37184.48566 49995.64832 34909.91535 32319.57108 44293.52349 29449.04399 38649.8243 54314.93058 0.537011312 0.591027497 0.684608914 0.920477073 0.642731473 0.595040272 0.815494433 0.542190585 0.711587475 1 15.72906121 0.963280523 22.33185858 1.000000005 0.667939281 0.431478919 0.114300361 1439.378116 875395.5273 0.110239512 0.027559878 9.18925965 -0.963280523 -0.332060724 LLECPHLNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLECPHLNVR 10 0 Q8TEX9;Q8TEX9-2;H0YN14;H0YMR4 Q8TEX9 IPO4 Importin-4 0 176.6 0.0030045 0 148360 173340 161780 159140 137250 107380 178470 146360 189890 239830 FALSE TRUE 142561.9272 168396.5129 191017.2448 167353.2345 141664.7709 109551.2972 180654.1692 143337.6149 168334.4833 223586.1005 0.637615339 0.753161814 0.854334166 0.748495699 0.633602762 0.489973647 0.807984794 0.641084641 0.752884383 1 17.77047098 0.963547778 18.01454723 1.000000004 0.698408629 0.461613386 0.09821056 109.562006 54146.40969 0.096698654 0.024174991 9.194916256 -0.963547778 -0.301591375 S(ph)PSDLHIS(ph)PLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSDLHISPLAK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 2 S(0.998)PS(0.002)DLHIS(1)PLAK;S(1)PSDLHIS(1)PLAK 188.47 4.84E-06 234070000 532280 465020 485370 431780 439920 524240 531800 470730 577630 662430 TRUE FALSE 511477.9091 451758.0849 573087.156 454064.2175 454070.4263 534840.492 538308.3275 461009.261 512059.864 617563.0261 0.828219773 0.731517377 0.92798165 0.735251624 0.735261677 0.866050054 0.871665409 0.74649751 0.829162114 1 19.23622685 0.963827271 22.86085567 1.000000001 0.803714751 0.442650387 0.06511915 1743.819278 1102080.809 0.060179029 0.015044757 9.2008356 -0.963827271 -0.19628525 EFALHK ddPTM_BT-474_Pertuzumab_2h_R1 3 EFALHK 6 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;F8WCE3 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;; 74.743 0.079523 954060000 1055090 1096450 983570 996380 979880 785180 1144220 1140110 1246660 1377080 FALSE TRUE 1013855.916 1065180.32 1161322.978 1047803.291 1011398.73 801056.8776 1158223.307 1116566.33 1105144.383 1283809.145 0.789724797 0.829703016 0.904591608 0.816167493 0.787810816 0.62396882 0.902177174 0.869729223 0.860832303 1 20.29199931 0.964966915 0.96050127 0.994712023 0.806463141 0.378694726 0.073743587 0.688774539 1.347893162 0.072940992 0.024548128 9.22501147 -0.964966915 -0.188248882 HAPVLELEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HAPVLELEGK 10 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 0 97.456 0.0059274 0 267070 300840 274180 298760 298050 281990 320960 243160 337500 370980 FALSE TRUE 256632.6091 292260.3378 323730.4251 314179.0394 307637.0489 287692.031 324888.0045 238138.661 299188.4149 345853.1942 0.742027581 0.845041603 0.936034221 0.908417342 0.889501829 0.8318328 0.939381246 0.688554176 0.865073447 1 18.39980026 0.964992223 23.98202503 1.000000003 0.845550918 0.260778271 0.07643869 4955.13623 3394513.277 0.076740112 0.019185028 9.22554907 -0.964992223 -0.154449085 HVDWVK ddPTM_BT-474_Pertuzumab_2h_R1 2 HVDWVK 6 0 P40123;E9PDI2;F8WDB9;Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2 P40123;Q01518-2 CAP2;CAP1 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein;Adenylyl cyclase-associated protein 1 0 ; 123.34 0.018832 1738990000 2266300 2324800 1995160 2354100 1880440 1891790 2212300 2007220 2840700 3269200 FALSE TRUE 2177730.49 2258498.98 2355729.794 2475595.383 1940926.06 1930043.29 2239374.789 1965770.206 2518235.645 3047774.172 0.714531447 0.741032259 0.772934496 0.812263391 0.636833949 0.633263221 0.734757453 0.644985519 0.826254015 1 21.53932458 0.965019486 4.911734701 0.999848312 0.711172123 0.717262278 0.056203181 0.108945948 9.084452713 0.057638675 0.014585551 9.226128226 -0.965019486 -0.288676189 AIT(ph)PPQQPYK ddPTM_BT-474_Pertuzumab_2h_R1 3 AITPPQQPYK 10 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 AIT(1)PPQQPYK;AIT(1)PPQQPYK;AIT(1)PPQQPYK 153.74 0.00017577 2906930000 2302190 2343630 1933760 2042080 2037610 1918810 2396590 2369000 2565170 2752870 TRUE FALSE 2212217.87 2276791.967 2283233.448 2147471.994 2103151.576 1957609.653 2425920.185 2320079.322 2273982.656 2566415.663 0.861987363 0.887148563 0.889658476 0.83675923 0.819489846 0.762779655 0.945256149 0.904015416 0.886053919 1 21.29132342 0.965059055 0.759359958 0.995614781 0.852226816 0.467040954 0.045595544 0.687689364 0.886050468 0.046877887 0.017604397 9.226968853 -0.965059055 -0.143387965 RDESLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDESLK 6 1 P12429;D6RA82;D6RFJ9 P12429 ANXA3 Annexin A3;Annexin 0 ; 140.98 0.018777 1043950000 1664880 1624800 1373170 1410100 1343920 1394550 1394750 1636730 1853170 2004460 FALSE TRUE 1599814.649 1578462.295 1621332.365 1482875.43 1387148.407 1422748.756 1411819.368 1602930.954 1642805.911 1868696.139 0.856112781 0.844686443 0.86762761 0.793534807 0.742308168 0.761359071 0.7555104 0.857780417 0.879118802 1 20.83360057 0.965300485 1.577181421 0.997893996 0.804328648 0.661620444 0.042484633 0.281475223 1.432285703 0.04490632 0.013104583 9.232099673 -0.965300485 -0.193565349 LYEQLSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYEQLSGK 8 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 122.13 0.0032649 836070000 541920 524680 456020 495190 499810 454490 475910 556970 622400 671450 FALSE TRUE 520741.1673 509716.6401 538432.9581 520746.8152 515886.8426 463680.0992 481734.3289 545468.3749 551747.7613 625972.0934 0.831891985 0.814280134 0.860154892 0.831901008 0.824137127 0.740736055 0.769577964 0.871394077 0.881425493 1 19.25573882 0.965326365 1.48393515 0.997563672 0.813138551 0.727890645 0.034797769 0.245890822 1.102717399 0.035625475 0.010529491 9.232649852 -0.965326365 -0.184425121 SSS(ph)PIPLT(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPIPLTPSK 11 0 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 2 S(0.008)S(0.011)S(0.981)PIPLT(0.999)PS(0.001)K;SS(0.002)S(0.998)PIPLT(0.999)PS(0.001)K 190.37 1.22E-05 489070000 718310 673320 590280 648810 646230 568970 606790 793130 721480 824200 TRUE FALSE 690237.6511 654117.5728 696956.7267 682295.1619 667016.5748 580474.9632 614216.0775 776751.5883 639580.6151 768376.1999 0.898306912 0.851298586 0.907051425 0.887970192 0.868085939 0.755456719 0.799368952 1.010900114 0.832379523 1 19.55145331 0.967503121 0.917893394 0.99052241 0.861139161 0.23585293 0.066515907 0.928264583 1.675877222 0.06558126 0.02249838 9.279041576 -0.967503121 -0.129383249 YHPGYFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 YHPGYFGK 8 0 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ; 140.53 0.00064813 6192500000 7537800 7646800 7082800 7820700 6817200 6723500 8140900 7264100 8665100 8900300 FALSE TRUE 7243214.443 7428720.751 8362819.516 8224327.264 7036481.429 6859453.777 8240530.769 7114093.797 7681474.175 8297474.753 0.872942028 0.895298988 1.007875259 0.991184367 0.848026856 0.826691732 0.993137191 0.85738059 0.925760476 1 22.9842409 0.967846944 22.69693328 1.000000003 0.911929591 0.15425063 0.061808428 2543.812459 1795688.437 0.060477722 0.01511943 9.286390532 -0.967846944 -0.088070412 GLVETAAHLGYSVVAINHIVDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLVETAAHLGYSVVAINHIVDFK 23 0 P78346;P78346-2 P78346 RPP30 Ribonuclease P protein subunit p30 0 ; 229.86 2.71E-33 188665000 271810 265470 201073 252300 255830 262170 273340 216456 290440 300480 FALSE TRUE 261187.3647 257899.0555 237411.3639 265321.2332 264059.0043 267471.257 276685.2167 211986.108 257470.4688 280128.222 0.932385045 0.920646459 0.847509624 0.947142103 0.942636206 0.954817245 0.987709181 0.756746701 0.919116493 1 18.09572781 0.967969682 23.78412034 1.000000005 0.905119903 0.14763276 0.062275329 4585.647445 3405077.746 0.063985394 0.015996349 9.289015379 -0.967969682 -0.094880102 S(ph)SPPLPPPAEER ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.625)S(0.375)PPLPPPAEER;S(0.604)S(0.396)PPLPPPAEER 132.99 0.00017959 752900000 413490 452980 313927 385590 390710 396330 382520 423020 435200 386480 TRUE FALSE 397330.3537 440061.4539 370660.5922 405490.3461 403277.542 404344.0641 387201.3942 414284.4892 385797.9205 360303.3654 1.102766146 1.221363707 1.028745851 1.125413707 1.119272204 1.122232272 1.074653837 1.149821314 1.070758582 1 18.4588526 0.968454371 5.390996409 1.000038811 1.118120307 0.380371748 0.046756901 0.183658243 20.40653091 0.041756855 0.010531449 9.299388068 -0.968454371 0.118081496 S(ph)PEAVGPELEAEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPEAVGPELEAEEK 14 0 Q96N64-3;Q96N64-2;Q96N64 Q96N64-3 PWWP2A PWWP domain-containing protein 2A 1 S(1)PEAVGPELEAEEK;S(1)PEAVGPELEAEEK;S(1)PEAVGPELEAEEK;S(1)PEAVGPELEAEEK 231.58 5.12E-13 1436090000 1220970 1027490 848950 853620 973610 886630 975550 1209940 1142140 1034320 TRUE FALSE 1173253.143 998186.9912 1002374.15 897675.4305 1004927.05 904558.2661 987489.0727 1184954.316 1012489.055 964264.5851 1.216733623 1.035179562 1.039521896 0.930943067 1.042169406 0.938080979 1.024085182 1.22886844 1.050011658 1 19.87906954 0.969010305 23.82441318 0.999999993 1.05914563 0.0315856 0.09338589 10612.90411 8159048.677 0.096182901 0.024045725 9.311299692 -0.969010305 0.059145637 VHDSQKPQDQDK ddPTM_BT-474_Pertuzumab_2h_R1 3 VHDSQKPQDQDK 12 1 Q8N1G2 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 ;; 266.85 5.41E-22 170665000 157544 223733 178898 233556 179911 215353 224290 148271 234102 266629 FALSE TRUE 151387.0063 217352.3539 211228.8482 245609.8531 185698.0007 219707.5852 227034.9281 145209.152 207527.7224 248569.9803 0.609031735 0.874411116 0.849776179 0.988091373 0.747065275 0.88388624 0.913364228 0.584178153 0.834886506 1 17.92329255 0.969519138 24.18625349 1.000000005 0.804647695 0.183283926 0.122000528 4649.544991 3689371.185 0.11925674 0.029814185 9.322215489 -0.969519138 -0.19535231 KPLFFGEGTVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPLFFGEGTVLR 12 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 96.591 0.0086551 374130000 152850 172930 145740 157430 165080 133050 170090 176370 191290 203450 FALSE TRUE 146876.453 167998.2057 172078.46 165554.9812 170389.9481 135740.3622 172171.6123 172727.8979 169575.5612 189670.1503 0.774378324 0.885738771 0.907251139 0.872857331 0.89834878 0.71566539 0.907742268 0.910675178 0.894055079 1 17.53313312 0.969906689 0.919338474 0.996444362 0.853652074 0.355275187 0.059830314 0.724428385 1.31267473 0.056738961 0.019457946 9.330538073 -0.969906689 -0.142792288 MLLS(ph)WDGGESR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLLSWDGGESR 11 0 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 MLLS(1)WDGGESR;MLLS(1)WDGGESR 149.41 3.61E-05 40465000 97056 102201 74440 84850 103397 89044 83042 110631 103850 80410 TRUE FALSE 93262.94422 99286.32755 87892.96391 89229.11867 106722.8584 90844.53069 84058.29284 108346.4312 92061.38337 74963.75908 1.244107091 1.324457695 1.172472739 1.190296748 1.423659375 1.211845988 1.121319073 1.445317478 1.228078534 1 16.19390568 0.97009608 23.9379901 0.999999995 1.271956229 0.388021977 0.099734635 2192.430529 1755035.609 0.09509843 0.023774608 9.334607903 -0.97009608 0.271956234 NGEFELMHVDEFIDELLHSER ddPTM_BT-474_Pertuzumab_2h_R1 6 NGEFELMHVDEFIDELLHSER 21 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 ;;;;; 296.49 3.92E-55 198679000 102202 95725.4 84185.3 100662 106632 103675 94509.6 77296.1 110778 112282 FALSE TRUE 98207.83285 92995.40532 99399.4564 105857.1779 110061.9151 105771.3795 95666.23676 75699.90852 98202.94586 104677.0401 0.938198412 0.888403084 0.949582222 1.011274084 1.051442752 1.010454436 0.913918053 0.72317586 0.938151726 1 16.67558551 0.970467072 24.05222766 1.000000007 0.926102124 0.038325947 0.085747432 8688.230914 7075883.294 0.098265615 0.024566404 9.342585299 -0.970467072 -0.073897883 EHQISPGDFPSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHQISPGDFPSLR 13 0 A0A024R571;Q9H4M9;C9JC03;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ;;; 159.22 4.59E-05 4038780000 2335270 2704340 2212250 2911030 2733080 2868010 2914960 1873350 3015110 3153410 FALSE TRUE 2244005.067 2627214.871 2612052.786 3061268.607 2820992 2926003.127 2950634.152 1834664.668 2672847.353 2939826.732 0.763312015 0.893663168 0.888505692 1.041309195 0.959577641 0.995297817 1.00367621 0.624072381 0.909185335 1 21.4872997 0.971907075 24.06928973 1.000000011 0.890043443 0.06280214 0.117696282 6397.178917 5480944.291 0.123833403 0.030958351 9.373614206 -0.971907075 -0.109956568 S(ph)SSPTSSLTQPIEMPTLSS(ph)SPTEERPTVGPGQQDNPLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPTSSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLK 39 1 Q7LBC6;Q7LBC6-2 Q7LBC6 KDM3B Lysine-specific demethylase 3B 2 S(0.159)S(0.159)S(0.159)PT(0.159)S(0.158)S(0.158)LT(0.049)QPIEMPT(0.046)LS(0.069)S(0.286)S(0.286)PT(0.286)EERPT(0.026)VGPGQQDNPLLK 67.871 0.005206 59083000 35293 38038 28053 30482 27769 37433 36436 34549 33745 33652 TRUE FALSE 33913.71054 36953.19348 33122.80114 32055.17967 28662.2151 38189.92091 36881.91467 33835.55108 29914.40907 31372.72007 1.08099363 1.17787662 1.05578353 1.021753281 0.913603125 1.217297092 1.175604621 1.07850231 0.95351659 1 14.937223 0.972163124 0.009246344 1.52E-06 2.113269447 0.072705015 0.091392439 6309.970828 38.28236201 4426.523073 4317.691483 9.379142285 -0.972163124 2.113267922 MVIQGPSS(ph)PQGEAMVTDVLEDQKEGR ddPTM_BT-474_Pertuzumab_2h_R1 11 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.208)S(0.791)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.162)S(0.838)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.094)S(0.906)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.132)S(0.868)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.242)S(0.758)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.01)S(0.99)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.151)S(0.849)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.23)S(0.77)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.101)S(0.899)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.011)S(0.989)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.178)S(0.822)PQGEAMVTDVLEDQKEGR 271.34 1.02E-60 6122210000 3743018 3618686 2542036 2556236 3229771 3761714 3047724 3482527 3618277 3097959 TRUE FALSE 3596736.718 3515484.618 3001438.452 2688163.646 3333659.517 3837778.434 3085022.958 3410611.6 3207545.364 2888131.478 1.245350756 1.217217653 1.039231931 0.930762213 1.154261689 1.328810154 1.068172617 1.180905934 1.110595341 1 21.46170499 0.972323373 19.72410393 0.999999992 1.142045378 0.143744874 0.106551255 351.2722618 250341.9586 0.106387992 0.026596998 9.382603696 -0.972323373 0.142045385 VTTHIPQTPVRPET(ph)PNRTPSATLSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTTHIPQTPVRPETPNRTPSATLSEK 26 2 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 1 VTTHIPQTPVRPET(0.925)PNRT(0.018)PS(0.022)AT(0.033)LS(0.002)EK 101.2 0.0043449 279150000 215300 211820 163270 181450 191990 214210 183890 205840 239250 245590 TRUE FALSE 206885.838 205779.101 192776.5209 190814.6562 198165.5327 218541.473 186140.5008 201589.3321 212091.343 228955.9706 0.903605342 0.8987715 0.841980755 0.833412013 0.865518083 0.954513099 0.812996929 0.880472047 0.926341176 1 17.80471066 0.972664659 2.652267123 0.999431402 0.871963206 0.516070601 0.038065055 0.221298164 3.63444441 0.036082043 0.009655349 9.389979816 -0.972664659 -0.127468196 EKEHQVVR ddPTM_BT-474_Pertuzumab_2h_R1 6 EKEHQVVR 8 1 Q9H307 Q9H307 PNN Pinin 0 ;;;;; 135.83 0.00049087 883396000 1239552 1316480 1141784 1198030 1199255 1177606 1308440 1264073 1493900 1507100 FALSE TRUE 1191108.937 1278935.279 1348129.768 1259860.472 1237830.126 1201418 1324453.08 1237969.451 1324318.735 1405022.775 0.847750627 0.910259465 0.959507413 0.89668331 0.881003603 0.855087919 0.942655951 0.881102764 0.942560333 1 20.42216209 0.972887117 3.941498979 0.999900156 0.898921342 0.488971445 0.033064649 0.173608539 7.798911391 0.031328495 0.00802673 9.394790874 -0.972887117 -0.100978814 EAIHSQLLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAIHSQLLEK 10 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ; 132.55 0.00022054 1109080000 1488520 1522540 1246810 1374140 1475340 1455420 1583880 1514350 1788160 1762580 FALSE TRUE 1430346.993 1479118.65 1472136.302 1445059.53 1522795.651 1484849.59 1603263.997 1483078.143 1585175.573 1643198.887 0.870464923 0.900145845 0.895896604 0.879418518 0.926726316 0.903633517 0.975696862 0.90255547 0.964688807 1 20.64807568 0.973006846 0.083413986 1.135516825 0.759632037 0.702266934 0.022600301 11.1361943 0.631623635 1.502093075 1.210364867 9.397381251 -0.973006846 -0.375884788 IEPADAHVLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEPADAHVLQK 11 0 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;B0AZT5 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 129.7 0.00023948 313790000 400140 399530 329530 388310 380800 410680 423160 427480 548590 575760 FALSE TRUE 384502.0864 388135.7956 389083.4014 408350.7256 393048.7778 418984.231 428338.7587 418652.3886 486316.3631 536763.2624 0.716334581 0.723104249 0.724869656 0.760765042 0.732257227 0.780575461 0.798003121 0.779957232 0.906016483 1 19.03392641 0.973416289 0.579408576 1.008399872 0.726959601 0.933913135 0.022425632 0.209264389 0.168606119 0.023866585 0.010454495 9.406245057 -0.973416289 -0.281440271 CPSIILHDR ddPTM_BT-474_Pertuzumab_2h_R1 4 CPSIILHDR 9 0 Q9UHG3;Q9UHG3-2 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 ;;; 125.75 0.00049291 1383730000 979900 1351050 1204140 1555360 960060 1135920 1351970 1176250 1448820 1497270 FALSE TRUE 941604.4247 1312519.377 1421754.884 1635632.316 990941.2018 1158889.081 1368515.813 1151960.026 1284356.028 1395858.569 0.674570079 0.940295389 1.018552248 1.171775101 0.70991519 0.830233883 0.980411514 0.825269875 0.920119026 1 20.41272134 0.973429216 22.01249396 1.000000012 0.899345672 0.048986488 0.1390497 2056.471175 1703684.589 0.133414206 0.033353552 9.40652504 -0.973429216 -0.100654339 FQLEELRK ddPTM_BT-474_Pertuzumab_2h_R1 1 FQLEELRK 8 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 0 71.379 0.078398 264620000 309090 346230 201200 297730 279730 251670 283600 307810 355600 378200 FALSE TRUE 297010.4211 336355.8594 237561.3157 313095.881 288727.7695 256758.9398 287070.7816 301453.6159 315233.7788 352584.1771 0.842381594 0.95397321 0.673771913 0.88800321 0.81889032 0.728220256 0.814190767 0.854983393 0.89406672 1 18.42760821 0.973800398 1.519888716 0.998588126 0.817360718 0.371661973 0.073002496 0.452126101 2.132791184 0.066754837 0.019641986 9.414568019 -0.973800398 -0.181227408 HIIEDPCTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIIEDPCTLR 10 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 143.5 3.39E-05 1146750000 697610 705880 566770 745400 742850 759070 696860 456590 785350 829550 FALSE TRUE 670346.63 685748.9935 669197.9467 783870.1833 766744.4449 774418.9155 705388.3811 447161.2569 696200.3605 773363.8396 0.866793346 0.886709409 0.865308038 1.013585253 0.991440775 1.001364268 0.912104168 0.578202954 0.900223575 1 19.56078778 0.973825984 24.20286577 1.000000014 0.877024126 0.065233566 0.117499372 5582.325162 5161931.424 0.131925888 0.032981472 9.415122686 -0.973825984 -0.122975888 AEPHFLSILQHLLLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEPHFLSILQHLLLVR 16 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 242.26 3.53E-20 260130000 158947 194693 185178 214050 211935 173944 239022 145319 225581 234515 FALSE TRUE 152735.1755 189140.5463 218643.7839 225097.1462 218752.0817 177461.2669 241947.2227 142318.1119 199973.9906 218631.0902 0.698597694 0.865112762 1.00005806 1.02957519 1.000553405 0.811692732 1.106646006 0.650950932 0.914664014 1 17.73813905 0.974278163 24.00237779 1.000000015 0.894075397 0.04862063 0.138225585 5606.837623 5232038.591 0.133677574 0.033419394 9.424930647 -0.974278163 -0.105924617 TSADAQEPASPVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSADAQEPASPVVSPQQSPPTSPHTWR 27 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;F2Z3L2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 TSADAQEPASPVVSPQQS(1)PPT(0.339)S(0.661)PHTWR;TSADAQEPASPVVSPQQS(0.996)PPT(0.08)S(0.924)PHT(0.001)WR 197.89 3.06E-25 1118690000 358190 380330 328780 388230 336490 346130 411710 348290 427520 437380 TRUE FALSE 344191.5388 369483.3608 388197.8597 408266.5968 347313.5064 353128.9858 416748.6301 341097.6898 378989.7219 407755.863 0.844111808 0.906138683 0.952035016 1.001252548 0.851768271 0.866030431 1.022054293 0.836524305 0.929452538 1 18.6373461 0.975297205 23.48805014 1.000000005 0.910906349 0.16163741 0.061429601 1936.003969 1840805.454 0.057512734 0.014378183 9.447071563 -0.975297205 -0.089093656 ALGEYLER ddPTM_BT-474_Pertuzumab_2h_R1 4 ALGEYLER 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 101.6 0.012282 1074105000 1357350 1497470 1364670 1441620 1352100 1273830 1474720 1436270 1701720 1714160 FALSE TRUE 1304303.261 1454763.622 1611296.226 1516022.181 1395591.524 1299587.715 1492768.064 1406610.523 1508547.88 1598058.416 0.816179964 0.910331942 1.008283683 0.948665058 0.873304449 0.813229167 0.934113578 0.88019969 0.943987945 1 20.60788872 0.976260432 4.420445078 0.99990822 0.90108899 0.247374572 0.055761139 0.280590815 17.60102013 0.05550342 0.014117562 9.468047592 -0.976260432 -0.09881923 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 491.95 2.07E-284 715450000 215343 336681 246877 349061 311647 366520 320714 218368 354913 382222 FALSE TRUE 206927.1575 327079.1875 291493.1656 367076.08 321671.4088 373931.2855 324638.9939 213858.6245 314624.7642 356333.7635 0.580711621 0.917901196 0.818034089 1.030146783 0.902725034 1.049384941 0.911053139 0.600163797 0.882949629 1 18.44286966 0.977293827 24.21841396 1.000000016 0.849955681 0.083035876 0.148081835 3709.064901 3956096.113 0.148757042 0.037189261 9.490603434 -0.977293827 -0.150044335 SGSS(ph)S(ph)PDSEITELKFPSINHD ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.308)GS(0.391)S(0.422)S(0.867)PDS(0.011)EIT(0.001)ELKFPSINHD 76.959 0.0059542 78486000 69657 73565 66711 70219 60708 72840 70397 65949 85846 99622 TRUE FALSE 66934.72743 71466.99823 78767.16168 73843.01101 62660.72795 74312.87471 71258.53954 64587.1301 76101.12198 92874.51321 0.720700708 0.769500649 0.84810309 0.795083694 0.67468163 0.800142818 0.76725613 0.695423619 0.819397264 1 16.50299512 0.9773929 21.06711023 1.000000002 0.759089058 0.689554488 0.048714672 127.8911099 119180.1462 0.048186116 0.012046529 9.492768725 -0.9773929 -0.240910944 QAEEECAHRGS(ph)PLPK ddPTM_BT-474_Pertuzumab_2h_R1 4 QAEEECAHRGSPLPK 15 1 H7C1J2;F2Z2A4;H7C1M5;Q9H147 H7C1J2;H7C1M5 DNTTIP1 Deoxynucleotidyltransferase terminal-interacting protein 1 1 QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK 173.36 5.90E-07 3094340000 1823950 1672190 1196427 1308154 1464731 1568206 1574690 1526320 1795470 1787380 TRUE FALSE 1752668.018 1624500.778 1412647.973 1375667.985 1511845.403 1599916.2 1593961.527 1494800.959 1591655.773 1666319.161 1.051820119 0.974903738 0.847765546 0.825572926 0.907296416 0.960149915 0.956576366 0.897067617 0.955192625 1 20.66823332 0.978163285 7.041447099 0.999994126 0.923810485 0.1142483 0.061492878 0.40885326 107.8892446 0.062352753 0.015636713 9.509622666 -0.978163285 -0.076183641 VYS(ph)SSEFLAVQPTPTFAER ddPTM_BT-474_Pertuzumab_2h_R1 1 VYSSSEFLAVQPTPTFAER 19 0 O60307;V9GYV0 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 VY(0.003)S(0.492)S(0.492)S(0.014)EFLAVQPTPTFAER 121.82 3.61E-05 36953000 35039 37046 30854 40498 41020 40571 35724 43995 39999 26501 TRUE FALSE 33669.63714 35989.48435 36430.00414 42588.10663 42339.44555 41391.37342 36161.201 43086.48788 35458.48121 24706.06367 1.362808645 1.456706533 1.474536965 1.723791665 1.713726886 1.675352819 1.463656918 1.743964092 1.435213707 1 14.59257755 0.97821917 21.31191401 0.999999995 1.584657673 0.649887082 0.127270386 148.2595682 145068.7756 0.12795509 0.03199031 9.510846438 -0.97821917 0.584657679 SPLELGEKLS(ph)PLPGGPGAGDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPLELGEKLSPLPGGPGAGDPR 22 1 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 SPLELGEKLS(1)PLPGGPGAGDPR;SPLELGEKLS(1)PLPGGPGAGDPR 99.34 0.00061936 306150000 588860 585310 489150 550190 616370 556550 511980 629170 640330 567240 TRUE FALSE 565846.7002 568617.5319 577550.2861 578585.3718 636196.1008 567803.8223 518245.7644 616177.4196 567642.4229 528820.3296 1.07001692 1.075256567 1.092148418 1.094105766 1.203047737 1.073717841 0.980003482 1.165192382 1.073412634 1 19.01241811 0.978293624 23.81497736 0.999999995 1.095739483 0.20270623 0.055960081 1511.989909 1658870.536 0.053530186 0.013382547 9.512477099 -0.978293624 0.095739488 ES(ph)SPSHGLLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ESSPSHGLLK 10 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 ES(0.498)S(0.498)PS(0.004)HGLLK;ES(0.497)S(0.497)PS(0.007)HGLLK;ES(0.49)S(0.49)PS(0.019)HGLLK 157.68 5.63E-06 934950000 1016040 1155570 992600 1061380 1021240 1080760 1321750 1228130 1548880 1720330 TRUE FALSE 976332.0335 1122614.275 1171984.9 1116157.949 1054089.112 1102613.708 1337925.972 1202768.686 1373057.636 1603810.517 0.60875772 0.6999669 0.730750228 0.695941283 0.657240429 0.687496245 0.834216984 0.749944382 0.856122105 1 20.61307227 0.978775328 0.469056301 1.013472871 0.667077296 0.836652201 0.044101821 0.434019167 0.244409536 0.056171582 0.027552988 9.523033854 -0.978775328 -0.346395575 HVLDTLIQLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVLDTLIQLAK 11 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 96.113 0.0072543 97700000 588230 582530 533800 584820 550410 586400 630570 543540 734170 798370 FALSE TRUE 565241.3213 565916.8148 630269.5343 615002.6303 568114.4375 598257.4098 638287.1043 532315.7091 650830.0995 744295.6888 0.759431137 0.760338698 0.846799926 0.826288046 0.763291318 0.803789971 0.857571949 0.715193863 0.874424116 1 19.50551635 0.979051135 8.85073644 0.999997972 0.792507799 0.705988403 0.041725997 0.175548823 72.17786849 0.039882199 0.009981161 9.529083555 -0.979051135 -0.207490172 SSSSASSFASVVEETEGVDGEDTGLESVS(ph)SSGTPHKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSSASSFASVVEETEGVDGEDTGLESVSSSGTPHKR 37 1 J3KPC5;P47736-3;P47736;P47736-4;X6R8W7;P47736-2 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 SSSSASSFASVVEETEGVDGEDT(0.007)GLES(0.031)VS(0.241)S(0.241)S(0.241)GT(0.241)PHKR 116.39 2.86E-06 60090000 39927 38034 36811 37146 37212 42000 37018 42217 42235 36905 TRUE FALSE 38366.6087 36949.30756 43463.56656 39063.10951 38408.95778 42849.26878 37471.03736 41345.2042 37440.65986 34405.39148 1.115133619 1.07393946 1.26327778 1.135377562 1.116364503 1.245423084 1.089103648 1.201707128 1.088220719 1 15.07034704 0.979741942 5.522546758 1.00006349 1.155704899 0.392239658 0.060408169 0.147491058 19.06632473 0.054414209 0.013714277 9.544252973 -0.979741942 0.155641409 DEDMLYS(ph)PELAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEDMLYSPELAQR 13 0 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 DEDMLY(0.026)S(0.974)PELAQR;DEDMLYS(1)PELAQR 181.58 1.25E-05 284149000 656432 639591 571610 604777 637999 652915 664531 616081 768175 840380 TRUE FALSE 630777.9117 621350.4909 674912.6424 635989.6134 658520.8173 666117.3886 672663.7292 603358.7121 680974.9945 783460.3141 0.805117886 0.793084831 0.861450963 0.811770044 0.840528621 0.8502248 0.858580476 0.770120325 0.869188882 1 19.57950067 0.980522633 23.64222346 1.000000001 0.823883919 0.780493174 0.028149671 303.1479779 367971.2118 0.027350203 0.006837551 9.561425224 -0.980522633 -0.176116082 NQLS(ph)QNR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQLSQNR 7 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 NQLS(1)QNR;NQLS(1)QNR 58.604 0.069922 474920000 0 8375.2 0 4742.5 0 4329.6 6343.6 0 4990 8981.2 TRUE FALSE 0 8136.347496 0 4987.260993 0 4417.147478 6421.234874 0 4423.55612 8372.895324 0 0.971748383 0 0.595643538 0 0.527553171 0.766907339 0 0.528318574 1 13.03151087 0.980859966 23.85859351 1.000000026 0.363505347 0.247325629 0.337940399 983.8129475 1226353.383 0.295616333 0.073904083 9.568854836 -0.980859966 -0.636494679 MEELHNQEVQKR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEELHNQEVQKR 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;; 144.28 4.01E-05 2389980000 3106380 3272840 2619170 2806700 2960160 3095940 3003060 3010300 3585670 3592100 FALSE TRUE 2984979.235 3179501.808 3092512.282 2951554.123 3055376.235 3158542.028 3039812.347 2948136.253 3178639.774 3348803.867 0.891356841 0.94944402 0.923467723 0.881375631 0.912378376 0.943185135 0.90773078 0.880355007 0.949186605 1 21.67521445 0.981220892 6.743561566 0.999988172 0.911352825 0.612540042 0.022106574 0.10422429 26.27367572 0.021975489 0.00551442 9.576810455 -0.981220892 -0.088635346 TASGSS(ph)VTSLDGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 TASGS(0.077)S(0.923)VTSLDGTR;TASGS(0.032)S(0.965)VT(0.002)SLDGTR 332.81 1.84E-68 1973090000 1134980 1308190 838930 1035390 1228420 1160810 1102650 1321910 1213330 884340 TRUE FALSE 1090623.727 1270881.702 990543.3129 1088826.602 1267933.245 1184282.374 1116144.561 1294612.097 1075597.865 824442.8641 1.322861504 1.541503672 1.201469933 1.320681698 1.537927369 1.436463853 1.353816752 1.570287224 1.30463603 1 19.65305999 0.98156108 23.63866071 0.999999993 1.416298891 0.555159513 0.1106876 442.1429035 566827.8452 0.105524286 0.026381072 9.584315025 -0.98156108 0.416298898 IDHYLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDHYLGK 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 94.407 0.014223 3472900000 2790600 2941900 2688400 2789700 2578400 2601300 3255900 2660900 3405200 3688300 FALSE TRUE 2681540.267 2857999.892 3174253.683 2933676.751 2661336.578 2653900.068 3295746.678 2605951.485 3018655.972 3438488.156 0.77986026 0.831179217 0.92315388 0.853187976 0.773984512 0.771821786 0.95848714 0.757877115 0.8779021 1 21.71334295 0.981733438 23.63192522 1.000000005 0.832714955 0.394241454 0.06322255 601.413854 778066.746 0.059011421 0.014752855 9.588119491 -0.981733438 -0.16728505 KEAESSPFVER ddPTM_BT-474_Pertuzumab_2h_R1 2 KEAESSPFVER 11 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 118.24 0.0011978 5197600000 727940 922220 711200 771000 791550 815460 771380 818160 1002830 1054840 FALSE TRUE 699491.3 895919.1885 839729.6606 810791.4024 817010.9246 831949.1599 780820.3792 801264.7101 888992.9426 983394.7472 0.71130266 0.91104736 0.853909036 0.824482137 0.83080668 0.845997157 0.794005033 0.81479458 0.90400416 1 19.90741112 0.981771539 3.345320218 0.99953712 0.826438017 0.574762317 0.047829207 0.152476017 4.385255018 0.042876678 0.011150314 9.588960718 -0.981771539 -0.173099103 GGHFAAFEEPELLAQDIR ddPTM_BT-474_Pertuzumab_2h_R1 3 GGHFAAFEEPELLAQDIR 18 0 P07099 P07099 EPHX1 Epoxide hydrolase 1 0 ;; 193.18 1.37E-14 302530000 141068 256926 171150 309847 170450 108641 277373 247154 240503 211882 FALSE TRUE 135554.9066 249598.722 202080.6122 325838.2408 175932.679 110837.7955 280767.5737 242050.1835 213202.1077 197531.0434 0.686246092 1.263592384 1.023032171 1.649554597 0.89065838 0.56111583 1.421384552 1.225377942 1.079334691 1 17.59171988 0.982785238 21.96834116 0.999999941 1.112520437 0.003319994 0.310217675 1595.485432 2036066.971 0.293664137 0.073416034 9.611368703 -0.982785238 0.112520496 LELEDEWQFR ddPTM_BT-474_Pertuzumab_2h_R1 4 LELEDEWQFR 10 0 Q4ZG55;Q4ZG55-4;Q9C091-3;Q9C091 Q4ZG55 GREB1;GREB1L Protein GREB1;GREB1-like protein 0 ;;; 182.65 4.08E-06 122562000 207230 196087 191705 205724 175727 241327 190387 175777 255447 308429 FALSE TRUE 199131.2225 190494.7907 226350.358 216341.4403 181379.4185 246206.7973 192717.0131 172147.1435 226449.7275 287538.8291 0.692536807 0.662501101 0.787199276 0.75239035 0.63079974 0.856255825 0.670229526 0.598691815 0.787544862 1 18.13339726 0.98292452 23.69001488 1.000000004 0.703840525 0.602745413 0.072037365 367.9999443 510553.598 0.070793245 0.017698311 9.614451665 -0.98292452 -0.296159479 DTGKTPVEPEVAIHR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTGKTPVEPEVAIHR 15 1 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;;; 192.4 8.15E-08 3437560000 5076739 5411249 3272619 3810643 4087681 5560981 4409075 4530741 4849233 4117309 FALSE TRUE 4878334.427 5256925.477 3864054.052 4007310.742 4219164.972 5673427.846 4463034.579 4437179.615 4298768.399 3838439.994 1.270915902 1.36954739 1.006673039 1.04399463 1.099187425 1.478055631 1.162720945 1.155985145 1.119925909 1 21.87208866 0.983615932 1.476436636 1.002660043 1.200298892 0.174673428 0.136004734 0.837840773 3.728067364 0.134301489 0.039793563 9.629770383 -0.983615932 0.197638849 LNVDFALIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNVDFALIHK 10 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 97.911 0.0057359 199300000 349540 337120 279090 291550 287240 245820 366910 342560 368750 409840 FALSE TRUE 335879.5904 327505.6677 329527.7713 306596.9304 296479.3355 250790.6488 371400.3543 335486.0163 326891.0459 382081.1718 0.879079147 0.85716254 0.86245488 0.802439254 0.77595903 0.656380548 0.972045685 0.878049067 0.855553924 1 18.54351964 0.983968763 0.792528449 0.992554107 0.820891554 0.302961172 0.076675445 0.890149178 1.244945166 0.076573527 0.028224844 9.637597023 -0.983968763 -0.171662553 EAVTEILGIEPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAVTEILGIEPDR 13 0 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 103.43 0.0037483 18944000 36448 35816 33562 35822 32497 32487 34813 32664 42576 47089 FALSE TRUE 35023.57186 34794.56275 39627.39998 37670.77771 33542.29552 33143.9094 35239.05191 31989.47699 37742.95097 43899.62009 0.797810364 0.79259371 0.902682071 0.858111702 0.764068014 0.75499308 0.802718835 0.728695987 0.859755754 1 15.42192083 0.984245015 23.01914767 1.000000003 0.798913039 0.621111738 0.047330435 227.7299445 332731.0092 0.049886131 0.012471533 9.643729385 -0.984245015 -0.201086964 QLSSGVSEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;; 187.41 2.87E-06 2967140000 1887394 1802896 1679828 1827389 1755782 1791011 1876578 1968148 2266290 2335540 FALSE TRUE 1813632.556 1751479.171 1983410.287 1921700.765 1812258.323 1827226.47 1899544.123 1927505.056 2009030.26 2177351.796 0.832953388 0.804407985 0.910927803 0.882586254 0.832322239 0.839196713 0.872410295 0.885252011 0.922694378 1 21.05414309 0.984297676 1.019744646 0.999817785 0.851689678 0.732107425 0.027924128 0.308238079 0.676447778 0.0276276 0.009104979 9.64489882 -0.984297676 -0.148128107 LMELHGEGS(ph)SSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMELHGEGSSSGK 13 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 1 LMELHGEGS(0.974)S(0.025)S(0.001)GK 132.84 7.35E-05 288610000 337560 305200 268270 270440 308750 316800 278550 342380 335670 287430 TRUE FALSE 324367.782 296495.9948 316752.3566 284397.4408 318681.2241 323205.9131 281958.9782 335309.7334 297566.1488 267962.1101 1.210498685 1.106484774 1.182078901 1.061334532 1.189277186 1.206162741 1.052234505 1.251332635 1.110478451 1 18.03166949 0.98465957 24.43732105 0.999999993 1.157079761 0.371867187 0.062070512 665.1326216 1059559.115 0.05535168 0.01383792 9.652939192 -0.98465957 0.157079767 GAGWTGHVAGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAGWTGHVAGTR 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ; 90.614 0.0087615 390890000 171814 181117 185527 186789 173404 120045 209736 169137 221930 234110 FALSE TRUE 165099.3189 175951.7205 219055.8559 196429.2027 178981.6971 122472.3921 212302.8119 165644.2618 196737.4368 218253.5212 0.756456611 0.806180443 1.003676159 0.900004736 0.820063274 0.561147383 0.972734876 0.758953445 0.901417011 1 17.7356454 0.984726781 7.561459845 0.999990669 0.825950812 0.183361177 0.117679537 0.266689845 102.5480425 0.111745098 0.027999876 9.65443319 -0.984726781 -0.174039857 LLEFYDATAHFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEFYDATAHFAK 13 0 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 0 200.44 1.10E-07 290940000 335980 384010 305270 336320 347500 333220 367660 320850 413350 434520 FALSE TRUE 322849.5302 373058.4108 360439.0797 353677.5155 358677.6531 339957.9367 372159.5331 314224.3354 366428.2409 405089.5734 0.796983066 0.920928198 0.889776246 0.873084717 0.885428006 0.839216704 0.918709237 0.775690998 0.904561028 1 18.62788143 0.985577935 24.77366266 1.000000005 0.862639345 0.462044925 0.045083972 616.652059 1059262.677 0.041972551 0.010493138 9.673373015 -0.985577935 -0.137360661 ITAEEMYDIFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ITAEEMYDIFGK 12 0 Q9Y3B4 Q9Y3B4 SF3B6 Splicing factor 3B subunit 6 0 171.62 0.00033277 0 60497 65838 47759 49251 58565 62789 55703 63351 64674 57137 FALSE TRUE 58132.71036 63960.3647 56390.11369 51792.85001 60448.79641 64058.6366 56384.70998 62042.77971 57332.47866 53267.0601 1.091344449 1.200748917 1.05863011 0.97232417 1.134825093 1.202593807 1.058528664 1.164749464 1.076321437 1 15.70095604 0.985599966 23.22255049 0.999999994 1.111657188 0.200152762 0.067099296 505.3670408 814995.0409 0.065089942 0.016272486 9.673863743 -0.985599966 0.111657194 VHAYFAPVT(ph)PPPSVGGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 VHAYFAPVTPPPSVGGSR 18 0 J3KTA1;Q96IG2-2;Q96IG2 J3KTA1 FBXL20 F-box/LRR-repeat protein 20 2 VHAYFAPVT(0.993)PPPS(0.048)VGGS(0.958)R 63.165 0.048261 0 34646 68440 32141 87579 47992 43414 66177 56555 48366 27746 TRUE FALSE 33291.99602 66488.15821 37949.59367 92098.96269 49535.70627 44291.86083 66986.89392 55387.11949 42875.69445 25866.73871 1.287058117 2.570411329 1.467119381 3.560516992 1.915034857 1.712309438 2.589692295 2.141248656 1.657560891 1 14.65881055 0.985766208 2.702351506 1.005056492 2.191084332 0.253393155 0.618683615 0.340725303 5.814941408 0.548940496 0.146647264 9.677567467 -0.985766208 1.18602784 LISWYDNEFGYSNRVVDLMAHMASKE ddPTM_BT-474_Pertuzumab_2h_R1 2 LISWYDNEFGYSNRVVDLMAHMASKE 26 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 147.39 1.08E-07 196081000 113213 87538 76099 86681 116059 121192 103618 103464 100112 76882 FALSE TRUE 108788.5108 85041.50195 89851.78211 91154.6168 119792.1431 123642.5853 104886.1081 101327.4322 88747.70546 71674.71366 1.517808795 1.186492385 1.253605038 1.271782085 1.671330613 1.725051681 1.463362778 1.413712411 1.238201047 1 16.12917662 0.986541759 2.32739329 1.001541369 1.438009348 0.415456952 0.164033174 0.331484494 3.994146942 0.17286295 0.047225738 9.694864853 -0.986541759 0.436467979 EVQVEHIK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVQVEHIK 8 0 Q96DG6 Q96DG6 CMBL Carboxymethylenebutenolidase homolog 0 ;; 131.11 0.0010193 1615540000 3012190 2917290 2573190 2941910 2563040 2189940 3213690 2747800 3305040 3341020 FALSE TRUE 2894470.285 2834091.746 3038222.673 3093742.328 2645482.509 2234222.087 3253020.1 2691056.97 2929865.715 3114729.74 0.929284569 0.909899729 0.975437013 0.993261883 0.849345764 0.71730849 1.044398831 0.863977679 0.940648454 1 21.57067556 0.986860223 22.5205214 1.00000001 0.910623101 0.093809139 0.085191536 462.065638 791948.9625 0.080949701 0.020237425 9.701976614 -0.986860223 -0.089376909 VKTT(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VKTTPLR 7 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 VKT(0.127)T(0.873)PLR 76.815 0.064243 724110000 248330 247380 190360 198710 229450 228300 204590 239390 282410 300500 TRUE FALSE 238624.9891 240324.9646 224762.2865 208965.4469 236830.4676 232916.3824 207093.8336 234446.5128 250352.0008 280146.8673 0.85178532 0.857853478 0.802301624 0.745913916 0.845379675 0.831408128 0.739233087 0.836870014 0.893645548 1 18.09582383 0.987485371 2.223445259 0.998813621 0.810593678 0.691207254 0.039085855 0.174645397 1.89395952 0.037856286 0.010417811 9.715952241 -0.987485371 -0.188219944 DFLRPFEHIMK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFLRPFEHIMK 11 1 Q9Y6D6;E5RIF2;E5RHL7;Q9Y6D5 Q9Y6D6;Q9Y6D5 ARFGEF1;ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 1;Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 ; 69.864 0.032048 934690000 1104600 1204340 1047710 1051810 1107040 1012910 1231610 1096430 1366970 1398040 FALSE TRUE 1061431.011 1169993.402 1237054.503 1106094.04 1142648.947 1033391.734 1246682.812 1073788.337 1211797.296 1303349.506 0.81438709 0.897682009 0.9491349 0.848654974 0.876701869 0.792873845 0.956522258 0.823868297 0.92975621 1 20.31379258 0.987572373 7.041316011 0.999985658 0.872477249 0.390659184 0.051224036 0.125172761 41.11953102 0.046101442 0.011561327 9.717898826 -0.987572373 -0.127508409 GAGGSSSS(ph)PPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GAGGSSSSPPEK 12 0 A0A087WXR4;Q8NG45;Q8NG42;P06401-5;P06401;Q8NG44 A0A087WXR4 PGR;PR Progesterone receptor 1 GAGGSSS(0.064)S(0.936)PPEK;GAGGSS(0.004)S(0.184)S(0.812)PPEK 168.76 4.79E-05 447560000 779650 604500 788930 747610 550340 722110 723850 629340 1071840 1317150 TRUE FALSE 749180.4161 587260.2519 931507.2007 786194.2417 568042.1859 736711.559 732708.6928 616343.9091 950169.2167 1227938.257 0.610112448 0.478249007 0.758594494 0.640255515 0.462598329 0.599958145 0.596698318 0.501933958 0.773792339 1 20.22780659 0.988034298 4.227113916 0.999316278 0.580157325 0.720006425 0.082414862 0.090446693 4.862803702 0.078772991 0.020092916 9.728240477 -0.988034298 -0.419158953 LPSFELLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSFELLHK 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 114.84 0.0015728 186840000 283360 325070 272760 303750 238870 179450 295720 279100 371560 414420 FALSE TRUE 272285.9779 315799.3219 322053.7995 319426.5739 246553.4705 183078.602 299339.1098 273336.4875 329382.0665 386350.9643 0.704763293 0.81738976 0.833578351 0.826778249 0.638159325 0.473866041 0.774785461 0.707482348 0.852546252 1 18.55955247 0.988053777 2.843965606 0.999552672 0.722713072 0.423866863 0.10239679 0.26562084 5.104807969 0.105311774 0.027940183 9.728676837 -0.988053777 -0.2768396 HVEDGNVTVQHAALSALR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVEDGNVTVQHAALSALR 18 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3;H0Y8M2 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ; 143.04 6.27E-08 208771000 386373 380228 367148 409608 368974 357559 447919 398251 515485 528625 FALSE TRUE 371273.116 369384.2697 433499.8108 430747.918 380842.3838 364789.088 453400.7667 390026.9777 456969.3039 492820.7579 0.753363388 0.749530664 0.879629772 0.874045809 0.772780727 0.740206418 0.920011504 0.791417511 0.927252549 1 18.9107035 0.988701933 1.232207491 1.002669698 0.807002644 0.518188316 0.060059297 0.411110412 1.283260416 0.056839661 0.017620714 9.743207083 -0.988701933 -0.195667053 TLS(ph)PGKNGVVK ddPTM_BT-474_Pertuzumab_2h_R1 4 TLSPGKNGVVK 11 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 TLS(1)PGKNGVVK;TLS(1)PGKNGVVK;T(0.047)LS(0.953)PGKNGVVK;T(0.476)LS(0.524)PGKNGVVK 159.66 1.72E-05 4700670000 6042070 10117670 4718984 8105960 6280360 6792440 8481240 9425600 6728290 4136138 TRUE FALSE 5805939.225 9829123.958 5571809.382 8524309.567 6482373.483 6929787.791 8585035.952 9230958.066 5964522.726 3855993.689 1.505692097 2.549050841 1.444973678 2.210664813 1.681116207 1.797147078 2.226413382 2.393924578 1.546818591 1 21.87867126 0.989136711 7.400902983 1.000091325 2.000310365 0.428272436 0.353244813 0.107583725 43.82338515 0.323483746 0.081073915 9.752966019 -0.989136711 1.000219039 ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK 38 0 P68363;P68363-2;F8VVB9;F8VS66;F8W0F6;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1C;TUBA1A Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ; 364.51 1.91E-161 3320300000 719230 896930 748500 1017570 823030 895740 936910 606550 1025600 1094800 FALSE TRUE 691121.6964 871350.4346 883770.6003 1070086.91 849503.5074 913852.4765 948376.1848 594024.5305 909178.1877 1020648.221 0.677139961 0.853722582 0.865891482 1.04843852 0.832317629 0.895364787 0.929190063 0.582007119 0.890785061 1 19.96105428 0.989229856 24.96810907 1.000000033 0.83198646 0.145075953 0.121822032 999.1734472 2316360.158 0.12385232 0.03096308 9.755057996 -0.989229856 -0.168013573 DLHILPPPLIPT(ph)PPPDDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLHILPPPLIPTPPPDDPR 19 0 Q9NRS6;E9PK26;E9PMW6;Q9NRS6-2 Q9NRS6 SNX15 Sorting nexin-15 1 DLHILPPPLIPT(1)PPPDDPR;DLHILPPPLIPT(1)PPPDDPR;DLHILPPPLIPT(1)PPPDDPR;DLHILPPPLIPT(1)PPPDDPR 127.28 8.73E-05 366054000 257296 260853 228672 274753 267425 293653 277810 206850 302833 298788 TRUE FALSE 247240.5879 253413.7278 269998.1172 288933.0353 276026.968 299590.8649 281209.9219 202578.4752 268456.6674 278550.8226 0.887595971 0.9097576 0.969295709 1.037272238 0.990939339 1.075533944 1.009546191 0.727258578 0.963761891 1 18.08758105 0.989274516 24.82879007 1.000000042 0.944136049 0.021166648 0.091900106 2242.984464 5192374.763 0.099809338 0.024952334 9.756061203 -0.989274516 -0.055863992 HLEVQILADQYGNAISLFGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLEVQILADQYGNAISLFGR 20 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 164.94 1.74E-11 604830000 214940 219510 208720 227540 231150 268600 270470 175210 304110 362190 FALSE TRUE 206539.9072 213249.7897 246440.347 239283.3667 238585.1497 274031.276 273780.0928 171591.8523 269588.7077 337658.5487 0.611682743 0.631554541 0.729850756 0.708654846 0.706587026 0.81156327 0.810819373 0.508181573 0.798406286 1 18.36520556 0.989302822 24.85706332 1.000000013 0.689117114 0.549309579 0.086138176 354.3126953 823319.5093 0.086838933 0.021709733 9.756697094 -0.989302822 -0.310882899 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_BT-474_Pertuzumab_2h_R1 28 CGSGPVHISGQHLVAVEEDAESEDEEEEDVK 31 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.022)GPVHIS(0.021)GQHLVAVEEDAES(0.957)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(0.999)EDEEEEDVK;CGSGPVHIS(0.001)GQHLVAVEEDAES(0.999)EDEEEEDVK;CGS(0.003)GPVHIS(0.003)GQHLVAVEEDAES(0.995)EDEEEEDVK;CGSGPVHIS(0.001)GQHLVAVEEDAES(0.999)EDEEEEDVK;CGS(0.006)GPVHIS(0.005)GQHLVAVEEDAES(0.989)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 279.56 1.31E-71 61715390000 4173137.8 5028010.6 4274604.4 5710496.2 5234811.8 5833887.8 5559159.8 3090849.3 5979388 6355230.6 TRUE FALSE 4010046.961 4884616.661 5047120.503 6005215.593 5403194.276 5951853.008 5627194.461 3027022.182 5300632.942 5924785.171 0.676825715 0.824437768 0.851865571 1.013575247 0.911964589 1.004568577 0.949771899 0.510908344 0.894654032 1 22.49833141 0.989726116 24.98289242 1.000000045 0.836316119 0.097189186 0.144925803 1197.272929 2911402.22 0.153397462 0.038349365 9.766211294 -0.989726116 -0.163683926 TAS(ph)GSSVT(ph)SLDGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 T(0.026)AS(0.973)GS(0.02)S(0.015)VT(0.645)S(0.321)LDGTR 116.58 0.0018752 204510000 266770 306820 255680 254920 280330 266380 254780 318190 291930 232420 TRUE FALSE 256344.3335 298069.794 301887.0636 268076.4517 289347.069 271766.3861 257898.0739 311619.2653 258791.3303 216677.9864 1.183065884 1.375634872 1.393252119 1.237211293 1.335378244 1.25424087 1.190236619 1.438167626 1.194359125 1 17.72519306 0.989980022 24.16262582 0.999999994 1.305659224 0.560663248 0.081664726 195.6244652 471739.4537 0.075847654 0.018961914 9.771922689 -0.989980022 0.30565923 HGLTSGSAS(ph)PPPPALPLYPDPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 HGLTSGSASPPPPALPLYPDPVR 23 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 HGLTSGS(0.011)AS(0.989)PPPPALPLYPDPVR;HGLT(0.001)S(0.001)GS(0.015)AS(0.983)PPPPALPLYPDPVR;HGLT(0.001)S(0.016)GS(0.128)AS(0.855)PPPPALPLYPDPVR;HGLTS(0.001)GS(0.03)AS(0.969)PPPPALPLYPDPVR 186.44 1.76E-17 3625260000 852260 961840 741381 930840 872140 949320 920260 689301 1078150 1160900 TRUE FALSE 818952.737 934409.2649 875365.0386 978880.764 900193.1752 968515.9008 931522.4172 675066.6935 955762.932 1082271.209 0.756698257 0.863378104 0.808822254 0.904469005 0.831763025 0.89489205 0.860710707 0.623750025 0.883108526 1 20.04563064 0.990897131 24.95938613 1.000000025 0.813833072 0.344410514 0.076928666 449.0904407 1231375.814 0.080377053 0.020094263 9.79258006 -0.990897131 -0.186166953 GDFVTSFYWPWQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDFVTSFYWPWQTK 14 0 G3V3Y1;Q8N8N7;Q8N8N7-2 G3V3Y1 PTGR2 Prostaglandin reductase 2 0 ; 213.73 1.45E-09 186999000 298090 307930 273220 301970 289250 272030 323980 319330 333610 304340 FALSE TRUE 286440.3132 299148.1379 322596.9317 317554.7079 298553.9889 277530.633 327944.9642 312735.7239 295739.9914 283726.7807 1.009563893 1.054352843 1.136998527 1.119227121 1.052258755 0.978161569 1.155847761 1.102242528 1.042340771 1 18.11414281 0.99133758 5.430639066 1.000071264 1.079605873 0.168088023 0.052706619 0.244936794 29.82342136 0.052131606 0.013146362 9.802516457 -0.99133758 0.079534609 AHEAQDAGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHEAQDAGYR 10 0 P16298-3;P16298;P16298-4;G3V111;Q5F2F8;P48454-2;P48454;P16298-2;P48454-3;Q08209-3;Q08209-2;Q08209;E7ETC2;Q08209-5;E5RJH4;H0YB04;H0YC26 P16298-3;Q08209-3 PPP3CB;PPP3CC;PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform;Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform;Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 0 ; 141.1 3.81E-05 947550000 409070 344700 300710 398160 367020 418010 351430 309710 424780 420110 FALSE TRUE 393083.0921 334869.4935 355054.9863 418709.0853 378825.5316 426462.4486 355730.9055 303314.3803 376560.7552 391655.5755 1.003644827 0.855010153 0.906549041 1.069074747 0.967241513 1.088871129 0.908274841 0.774441625 0.961458942 1 18.57922597 0.99179879 24.59481776 1.000000042 0.937236642 0.022936078 0.089849079 1116.926411 3349592.08 0.095154712 0.023788678 9.812932004 -0.99179879 -0.062763399 AS(ph)PPAESMSVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPPAESMSVYR 12 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 AS(1)PPAESMSVYR;AS(1)PPAESMSVYR 182.37 1.78E-05 335290000 46565 53521 45002 44138 48048 46509 49202 52861 52811 46884 TRUE FALSE 44745.18832 51994.63348 53134.86246 46415.96747 49593.50756 47449.44385 49804.14879 51769.40188 46816.11668 43708.50492 1.023718116 1.18957703 1.21566415 1.061943609 1.134642048 1.085588352 1.139461276 1.184423992 1.07109856 1 15.41562641 0.991917772 6.767789255 1.000026388 1.133522897 0.33976684 0.056570472 0.123833378 36.3647604 0.053007564 0.013300877 9.815620794 -0.991917772 0.133496509 HPALFK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPALFK 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 88.626 0.051089 4323700000 5081600 5029300 4773100 5544100 4527400 3840400 5730200 4771500 6302700 6631400 FALSE TRUE 4883005.454 4885869.288 5635705.347 5830231.665 4673027.933 3918055.519 5800327.902 4672966.858 5587243.919 6182249.371 0.789842849 0.790306084 0.911594633 0.943059931 0.755878266 0.633758893 0.938222895 0.755868387 0.903755831 1 22.55970042 0.992967765 5.71099863 0.999909261 0.816928584 0.296649186 0.090592851 0.168251763 24.59760716 0.087272127 0.021975944 9.839380716 -0.992967765 -0.182980678 GGS(ph)WIQEINVAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGSWIQEINVAEK 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 GGS(1)WIQEINVAEK;GGS(1)WIQEINVAEK 221.31 2.03E-11 112561000 128680 133855 90866 116902 117797 121307 121153 133820 130045 111835 TRUE FALSE 123651.0433 130037.5865 107287.5075 122935.3262 121586.0475 123759.9107 122635.7067 131056.5702 115282.8368 104260.3158 1.185983779 1.247239522 1.029034937 1.179119066 1.166177625 1.187027966 1.176245302 1.257012979 1.105721154 1 16.66983061 0.993100319 22.59667024 0.999999996 1.179551328 0.479047418 0.057900287 62.92240663 206075.7511 0.055992845 0.013998211 9.842384323 -0.993100319 0.179551333 DVFRPGDVFFNTGDLLVCDDQGFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVFRPGDVFFNTGDLLVCDDQGFLR 25 1 H0YDP0;H7BZH4;X6R3N0;Q5K4L6-2;Q5K4L6 H0YDP0 SLC27A3 Long-chain fatty acid transport protein 3 0 81.373 0.019985 63719000 18829 25093 16012 29709 17851 24073 20530 26477 22835 17612 FALSE TRUE 18093.14186 24377.37221 18905.72459 31242.28505 18425.19363 24559.77255 20781.25228 25930.2407 20242.86653 16419.12355 1.1019554 1.484693877 1.151445418 1.902798584 1.122178877 1.495802896 1.265673665 1.579270697 1.232883501 1 14.0030895 0.993289687 22.07077839 0.999999976 1.398469161 0.20867396 0.233849957 74.98292192 246629.8653 0.202216141 0.050554035 9.846676893 -0.993289687 0.398469184 ILEPDDFLDDLDDEDYEEDT(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILEPDDFLDDLDDEDYEEDTPKR 23 1 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 1 ILEPDDFLDDLDDEDY(0.052)EEDT(0.948)PKR 73.805 0.011233 24824000 18756 16160 17308 13132 15031 12686 15866 21014 18259 16485 TRUE FALSE 18022.99478 15699.13262 20435.94061 13809.74409 15514.48577 12942.51961 16060.17285 20580.05356 16186.31487 15368.45627 1.172726426 1.021516563 1.329732815 0.89857718 1.009501898 0.842148319 1.045008853 1.339110006 1.053216705 1 13.90768464 0.993330302 24.83417661 0.99999993 1.089557276 0.024448946 0.154138092 1071.940497 3991318.611 0.155990526 0.038997631 9.847597782 -0.993330302 0.089557346 AVPS(ph)PTTGEEGSVHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVPSPTTGEEGSVHSR 16 0 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 AVPS(0.991)PT(0.009)TGEEGSVHSR 145.17 8.02E-07 377690000 245430 249550 176740 236560 251070 228360 198680 266240 256730 230780 TRUE FALSE 235838.3243 242433.0783 208680.8496 248768.8899 259145.8946 232977.5957 201111.5053 260742.051 227587.0867 215149.065 1.096162441 1.126814464 0.969936121 1.156262938 1.204494635 1.082865945 0.934754261 1.211913475 1.057811182 1 17.71497705 0.994251858 24.87663079 0.999999976 1.099403328 0.114280543 0.084759756 418.6213448 1811705.507 0.080182961 0.02004574 9.868516197 -0.994251858 0.099403351 S(ph)PPSSSEIFTPAHEENVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPPSSSEIFTPAHEENVR 18 0 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 S(0.76)PPS(0.021)S(0.028)S(0.191)EIFTPAHEENVR;S(0.916)PPS(0.033)S(0.033)S(0.017)EIFTPAHEENVR;S(0.977)PPS(0.022)S(0.001)SEIFTPAHEENVR;S(0.867)PPS(0.128)S(0.003)S(0.002)EIFTPAHEENVR 215.06 6.26E-19 4964060000 352320 357703 353292 376258 371512 375035 378906 389439 401226 352026 TRUE FALSE 338550.9449 347501.6607 417139.7233 395676.7205 383462.0209 382618.4647 383543.165 381396.9486 355680.5066 328182.9655 1.031592071 1.058865624 1.271058425 1.205658922 1.168439746 1.165869362 1.168686999 1.162147304 1.083787228 1 18.32414083 0.994694862 2.895856654 1.000471762 1.158411043 0.361597663 0.064253783 0.273528664 5.447122418 0.064130381 0.016981562 9.878587749 -0.994694862 0.157939281 ELDGHVLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELDGHVLK 8 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;A0A0C4DG68;H0YC97;Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;H0YDK8 Q8TB72-3;Q5T1Z4 PUM2;PUM1 Pumilio homolog 2;Pumilio homolog 1 0 ;; 86.011 0.016336 1042160000 2178430 2323110 1965610 2093530 2143870 1946060 2344340 2370760 2577580 2699790 FALSE TRUE 2093294.547 2256857.177 2320839.452 2201577.334 2212829.526 1985410.667 2373030.734 2321802.978 2284983.924 2516930.819 0.831685373 0.896670326 0.922091078 0.874707131 0.879177731 0.788822105 0.942827159 0.922473896 0.907845344 1 21.26323413 0.994994563 0.744939489 0.997020182 0.873893465 0.455564102 0.041007329 0.676339014 0.851129206 0.040418523 0.015429993 9.885407181 -0.994994563 -0.123126717 DLVHTEGQLQNEEIVAHDGSATYLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLVHTEGQLQNEEIVAHDGSATYLR 25 0 Q9Y547 Q9Y547 HSPB11 Intraflagellar transport protein 25 homolog 0 ;;; 401.97 1.04E-158 1565140000 192505 229301 184341 264512 214330 224173 231424 166154 268200 283112 FALSE TRUE 184981.6918 222761.56 217655.5193 278163.496 221224.1191 228705.9317 234256.2361 162722.8618 237755.0604 263936.5721 0.700856612 0.843996564 0.824650853 1.053902814 0.838171525 0.866518535 0.887547468 0.616522601 0.900803775 1 18.00983174 0.995004031 24.98578543 1.000000044 0.826387435 0.195039699 0.108336282 289.205354 1446378.128 0.10983346 0.027458365 9.885622713 -0.995004031 -0.173612609 (ac)ADQLYLENIDEFVTDQNK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADQLYLENIDEFVTDQNK 18 0 Q15054 Q15054 POLD3 DNA polymerase delta subunit 3 0 105.65 3.71E-13 11458000 19406 20094 18380 17904 19688 18628 16213 21825 22281 23382 FALSE TRUE 18647.59207 19520.93879 21701.67486 18828.02759 20321.2824 19004.67092 16411.41954 21374.30612 19751.75429 21798.31631 0.855460201 0.895525072 0.995566563 0.8637377 0.932240918 0.871841231 0.752875557 0.980548489 0.906113757 1 14.41192909 0.995547129 1.498575526 0.994834545 0.890653465 0.201304452 0.064547342 0.69144837 3.17252518 0.060439768 0.01786773 9.897992704 -0.995547129 -0.10418108 TTSRS(ph)PVLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TTSRSPVLSR 10 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 T(0.102)T(0.102)S(0.102)RS(0.694)PVLSR;T(0.078)T(0.078)S(0.078)RS(0.767)PVLSR;T(0.011)T(0.031)S(0.011)RS(0.946)PVLS(0.002)R 90.412 0.0065699 1711690000 1214790 1305200 958230 1216570 1110250 1153970 1190430 1275530 1327610 1223610 TRUE FALSE 1167314.664 1267976.974 1131403.477 1279357.323 1145962.2 1177304.064 1204998.838 1249189.86 1176905.279 1140733.805 1.023301544 1.111545015 0.991820767 1.121521356 1.004583361 1.032058539 1.056336573 1.095075691 1.031708952 1 20.12153074 0.995679653 24.36362598 0.999999993 1.056592962 0.141760149 0.041625837 180.8804315 1020041.677 0.036850597 0.009212649 9.901013518 -0.995679653 0.056592969 HVTLPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 5 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HVTLPS(0.686)S(0.314)PR;HVTLPS(0.686)S(0.314)PR;HVTLPS(0.689)S(0.311)PR;HVTLPS(0.674)S(0.326)PR;HVTLPS(0.5)S(0.5)PR 138.45 8.78E-05 15376850000 2319470 2882090 2518450 3065900 2711050 2851850 3152570 2124370 3277010 3298170 TRUE FALSE 2228822.548 2799895.615 2973589.938 3224131.466 2798253.385 2909516.361 3191152.095 2080501.017 2905017.563 3074782.008 0.724871728 0.910599713 0.967089677 1.048572373 0.910065617 0.946251264 1.037846614 0.676633664 0.944788136 1 21.5520527 0.995883831 24.99344535 1.000000066 0.901220976 0.067297486 0.113335836 411.6063305 2499296.751 0.112970325 0.028242581 9.905669426 -0.995883831 -0.09877909 KALDSNSLENDDLSAPGREPGHFNPESR ddPTM_BT-474_Pertuzumab_2h_R1 1 KALDSNSLENDDLSAPGREPGHFNPESR 28 2 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 181.62 8.23E-18 378910000 42838 40761 29930 39271 39503 45416 37532 32168 47104 48538 FALSE TRUE 41163.8436 39598.53619 35339.01679 41297.78102 40773.64987 46334.34264 37991.32784 31503.71956 41756.9514 45250.47803 0.909688591 0.875096528 0.780964497 0.912648503 0.901065616 1.023952556 0.839578486 0.696207442 0.922795807 1 15.46564541 0.996459792 24.99769285 1.000000037 0.859824016 0.197823057 0.082187765 186.8072466 1319071.123 0.087571309 0.021892827 9.918815034 -0.996459792 -0.140176021 TGFSTSPESPYTHWK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGFSTSPESPYTHWK 15 0 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 210.34 1.93E-09 3710800000 1578760 1754810 1609430 1686730 1590120 1612410 1763500 1637700 2022220 2040360 FALSE TRUE 1517060.314 1704764.537 1900289.803 1773782.337 1641267.654 1645014.035 1785082.241 1603880.923 1792666.063 1902164.6 0.797544184 0.896223459 0.999014387 0.93250728 0.862842077 0.864811613 0.93844783 0.843187242 0.942434773 1 20.85921066 0.996471383 22.84763913 1.000000005 0.894623738 0.292694546 0.053126896 48.36414378 313163.5948 0.051743148 0.012935787 9.919079765 -0.996471383 -0.105376267 DALHSEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DALHSEK 7 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ;; 113.89 0.0060283 926310000 1732240 1673230 1628530 1734070 1580780 1772600 2084730 2003410 2210180 2475520 FALSE TRUE 1664542.146 1625511.119 1922841.597 1823565.561 1631627.224 1808443.187 2110243.549 1962038.883 1959289.632 2307850.825 0.721252053 0.70433977 0.833174127 0.790157466 0.7069899 0.783604888 0.914376062 0.850158451 0.848967191 1 21.13811854 0.996483451 0.149494712 1.133877804 0.621470187 0.71513159 0.048072283 3.713153542 0.413537677 0.715080271 0.507085207 9.919355396 -0.996483451 -0.512407617 HDADGQATLLNLLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HDADGQATLLNLLLR 15 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 171.21 1.10E-06 83717000 91362 87453 75721 92353 94084 84186 100992 64324 107869 112856 FALSE TRUE 87791.47203 84958.92607 89405.4691 97119.3494 97110.2973 85888.2986 102227.9703 62995.68692 95624.16334 105212.1626 0.834423225 0.807500996 0.849763629 0.923081011 0.922994974 0.816334314 0.971636432 0.598749093 0.908869859 1 16.68294197 0.996583433 24.99981176 1.000000059 0.83400951 0.211768081 0.095605573 164.8912281 1206556.703 0.095266319 0.02381658 9.921639266 -0.996583433 -0.165990549 GLFITIHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLFITIHDR 9 0 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 ; 148.52 8.98E-05 898090000 589530 607340 579450 669030 595510 582040 644460 568720 787580 834670 FALSE TRUE 566490.5158 590019.2578 684169.5048 703558.7185 614665.12 593809.2476 652347.0943 556975.7333 698177.2202 778137.0575 0.728008659 0.758245931 0.879240358 0.904157837 0.789918838 0.763116525 0.838344721 0.715781016 0.897241962 1 19.56966476 0.997536444 7.106345532 0.999966442 0.798861382 0.552120108 0.058352267 0.081533516 29.57943964 0.059011172 0.014797167 9.943435119 -0.997536444 -0.20110506 KLEHLITELVHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLEHLITELVHQR 13 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 202.13 3.92E-08 1752080000 1597450 1731720 1454240 1716090 1671960 1865890 1809470 1287430 2015770 2050230 FALSE TRUE 1535019.888 1682333.041 1717053.517 1804657.611 1725740.112 1903619.574 1831614.835 1260844.121 1786948.24 1911366.096 0.803100929 0.88017311 0.898338377 0.944171613 0.902883082 0.995947128 0.958275256 0.659656004 0.934906319 1 20.8661727 0.998380438 24.99922401 1.000000072 0.875606155 0.151040493 0.088989027 92.12632487 1422069.964 0.093524375 0.023381094 9.962777654 -0.998380438 -0.124393917 HLDQIIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLDQIIPR 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 123.16 0.0013597 488640000 162769 186918 161188 184793 180950 201497 186194 143350 214976 216971 FALSE TRUE 156407.8075 181587.2817 190318.2572 194330.1889 186770.4211 205571.4074 188472.6979 140389.7724 190572.8257 202275.3609 0.773242014 0.897723187 0.940886999 0.960721009 0.923347363 1.016294849 0.931763004 0.694052759 0.942145523 1 17.62596107 0.998505808 24.99920224 1.000000066 0.889058503 0.128048403 0.088614881 95.1459971 1591911.888 0.093768621 0.023442155 9.965654077 -0.998505808 -0.110941563 TRDDGDEEGLLTHS(ph)EEELEHSQDTDADDGALQ ddPTM_BT-474_Pertuzumab_2h_R1 6 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLT(0.001)HS(0.999)EEELEHSQDTDADDGALQ;TRDDGDEEGLLTHS(1)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.029)HS(0.965)EEELEHS(0.005)QDTDADDGALQ;TRDDGDEEGLLT(0.014)HS(0.986)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.127)HS(0.873)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.014)HS(0.986)EEELEHSQDTDADDGALQ 405.46 3.02E-186 19162170000 2093440 2670500 2685750 3283730 2242490 3133810 3217880 1771795 3346790 3479260 TRUE FALSE 2011626.05 2594339.955 3171124.769 3453203.699 2314621.727 3197177.785 3257261.378 1735206.814 2966876.43 3243606.621 0.620181879 0.799831872 0.977653933 1.064618526 0.71359508 0.985686046 1.004209745 0.534962163 0.914684417 1 21.62916743 0.998736343 24.99840588 1.000000108 0.835353177 0.087576125 0.166296381 93.82978685 1856238.586 0.164974059 0.041243515 9.970945513 -0.998736343 -0.164646932 LLDIDETEY(ph)HADGGKVPIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDIDETEYHADGGKVPIK 19 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 LLDIDETEY(1)HADGGKVPIK;LLDIDETEY(1)HADGGKVPIK 338.58 1.59E-75 484680000 1056560 2009870 521700 2575500 632050 546420 2129180 1555620 1168490 664910 TRUE FALSE 1015268.467 1952550.475 615982.7952 2708421.864 652380.4623 557468.9868 2155237.542 1523495.903 1035847.914 619875.0535 1.637859858 3.149909751 0.993720899 4.369302892 1.052438647 0.899324765 3.47689027 2.457746759 1.671059205 1 19.24161792 0.999383155 4.142936515 1.004353999 2.291650206 0.114429068 1.098963605 0.36445848 17.70020918 0.995146246 0.254229554 9.985806693 -0.999383155 1.287296206 LMS(ph)DVEDVSLENVHTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LMSDVEDVSLENVHTR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 LMS(1)DVEDVSLENVHTR;LMS(1)DVEDVSLENVHTR;LMS(1)DVEDVSLENVHTR;LMS(1)DVEDVSLENVHTR 225.86 4.18E-15 151093000 121597 137660 129299 99580 143048 162567 98762 149738 137962 118822 TRUE FALSE 116844.8548 133734.0716 152666.2055 104719.3357 147649.2688 165854.2161 99970.6789 146645.858 122301.1321 110774.0801 1.054803206 1.207268627 1.378176243 0.945341506 1.332886436 1.49722946 0.902473564 1.323828262 1.104059109 1 16.75726082 0.99989292 24.98920918 0.999999989 1.207478371 0.115937536 0.180945117 5.813193425 1356866.871 0.163195892 0.040798973 9.997534687 -0.99989292 0.207478382 YKQENTR ddPTM_BT-474_Pertuzumab_2h_R1 2 YKQENTR 7 1 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 68.735 0.056221 201056000 157268 167898 144563 149883 152567 132136 179177 169190 193384 206093 FALSE TRUE 151121.7927 163109.7134 170688.7499 157618.4796 157474.4561 134807.8805 181369.8217 165696.1674 171431.8591 192134.1375 0.786543165 0.848936662 0.888383252 0.820356453 0.819606855 0.701634193 0.943974996 0.862398372 0.89225091 1 17.55175435 0.999910368 0.802865449 0.996863157 0.823565992 0.459031447 0.057995701 0.621981917 0.894404469 0.05554886 0.020397346 9.997936365 -0.999910368 -0.173297166 RLS(ph)TSPDVIQGHQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSTSPDVIQGHQPR 15 1 Q9Y385 Q9Y385 UBE2J1 Ubiquitin-conjugating enzyme E2 J1 1 RLS(0.965)T(0.034)S(0.001)PDVIQGHQPR;RLS(0.967)T(0.031)S(0.002)PDVIQGHQPR 233.46 7.65E-18 4258700000 559790 1043690 450760 920440 487310 455060 643530 967720 651210 472700 TRUE FALSE 537912.7879 1013924.983 532222.3591 967944.0187 502984.7687 464261.625 651405.7126 947736.2438 577287.3709 440683.608 1.220632622 2.300800313 1.207719891 2.19646023 1.141373901 1.053503277 1.478170962 2.150604712 1.309981493 1 18.74938371 0.999954821 24.99997092 0.999999875 1.619158989 0.150701759 0.444586793 2.103172439 1164199.186 0.416631426 0.104157856 9.998959769 -0.999954821 0.619159114 AHTMTDDVTFWK ddPTM_BT-474_Pertuzumab_2h_R1 8 AHTMTDDVTFWK 12 0 A0A087WVQ6;Q00610-2;Q00610;J3KSQ2 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;; 204 1.19E-07 15871090000 22720970 23423510 21147750 23708240 25421540 25455280 26726920 16292680 28927730 29772810 FALSE TRUE 21833009.37 22755494.43 24969618.85 24931825.11 26239246.92 25970003.2 27054012.04 15956230.46 25643975.37 27756271.06 0.786597354 0.819832548 0.899602789 0.89824116 0.945344815 0.93564453 0.974699086 0.574869385 0.923898434 1 24.72631043 0.999991789 24.99999991 1.000000113 0.847831815 0.152017066 0.108433669 0.424710417 1285886.243 0.113389589 0.028347397 9.999810929 -0.999991789 -0.152168298 VHGPGIQSGTTNKPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHGPGIQSGTTNKPNK 16 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 188.59 6.94E-10 681980000 717110 723860 714780 767160 725120 744030 736680 665650 1002500 1110600 FALSE TRUE 689084.5484 703216.2215 843956.6462 806753.2195 748444.1433 759074.7964 745695.7102 651904.0949 888700.4028 1035378.073 0.665539059 0.679187864 0.815119296 0.779187082 0.722870382 0.733137794 0.720215861 0.629629033 0.858334193 1 19.98172624 1.000042886 5.481955042 0.999751091 0.719034402 0.760021183 0.050627689 0.06751616 8.026022894 0.053182778 0.013408137 10.00098753 -1.000042886 -0.280716689 NVIGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVIGAR 6 0 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 110.54 0.066582 472130000 465780 444120 404790 461310 436080 396850 438050 447120 525630 520630 FALSE TRUE 447576.8027 431454.1324 477944.5575 485118.2644 450106.9092 404874.5789 443410.9869 437886.8158 465962.686 485367.2664 0.922140477 0.888923012 0.984707026 0.999486982 0.927353244 0.834161277 0.913557666 0.902176241 0.96002083 1 18.88871729 1.000077869 4.745742984 0.999871184 0.921326683 0.244979328 0.043880353 0.237698017 17.25105421 0.045382092 0.011504918 10.00179317 -1.000077869 -0.078544502 S(ph)SSLESLQTAVAEVTLNGDIPFHRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSLESLQTAVAEVTLNGDIPFHRPR 26 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.461)S(0.461)S(0.074)LES(0.005)LQTAVAEVTLNGDIPFHRPR;S(0.317)S(0.317)S(0.317)LES(0.049)LQTAVAEVTLNGDIPFHRPR 166.03 7.24E-12 125002000 29097 25806 27527 28533 25848 26444 28307 31701 30699 27632 TRUE FALSE 27959.85707 25070.03815 32501.74123 30005.59155 26679.42439 26978.7158 28653.42953 31046.36327 27214.17822 25760.46003 1.085378795 0.973198387 1.261691026 1.164792535 1.035673445 1.047291693 1.112302711 1.205194443 1.056432152 1 14.65287074 1.000355741 24.99853305 0.999999979 1.114032019 0.162273507 0.079964271 16.81442506 1181472.44 0.079373101 0.019843275 10.00819459 -1.000355741 0.11403204 NTGS(ph)PDRKPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 NTGSPDRKPSK 11 2 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 NT(0.004)GS(0.544)PDRKPS(0.451)K;NT(0.039)GS(0.961)PDRKPSK 100.43 0.00318 1285480000 754760 622000 383550 592910 532920 448300 585480 710510 638230 583740 TRUE FALSE 725263.1448 604261.169 452866.017 623510.1562 550061.8558 457364.9332 592645.2794 695837.7202 565780.8061 544202.7699 1.332707559 1.110360333 0.832164116 1.145731317 1.010766366 0.840431101 1.089015551 1.278636859 1.039650728 1 19.05378477 1.000412337 24.99999553 0.999999911 1.080254668 0.027528676 0.152397881 53.00387484 3213362.373 0.152630675 0.038157669 10.00949891 -1.000412337 0.080254757 GPAVGIDLGTTYSCVGVFQHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPAVGIDLGTTYSCVGVFQHGK 22 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 332.13 8.62E-81 3456200000 3790100 4285500 3661200 3969800 3687600 2992100 4431400 3870300 4914200 5125000 FALSE TRUE 3641978.702 4163281.736 4322860.283 4174681.854 3806215.003 3052602.312 4485632.799 3790376.953 4356360.618 4777879.185 0.762258433 0.871366055 0.904765507 0.873752075 0.796632743 0.638903202 0.93883345 0.793317873 0.911777056 1 22.18793894 1.000558837 3.824167857 0.999764582 0.825902741 0.332543295 0.080273054 0.223029134 8.676009295 0.076244052 0.019595432 10.01287598 -1.000558837 -0.173861841 IKIIAPPER ddPTM_BT-474_Pertuzumab_2h_R1 2 IKIIAPPER 9 1 P60709;P63267-2;Q562R1;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ; 115.23 0.0013766 7366700000 4403500 4962700 2942020 3214300 3130600 4717200 3597600 3766600 3730400 3034920 FALSE TRUE 4231406.352 4821168.655 3473708.459 3380190.408 3231298.592 4812585.016 3641628.505 3688818.394 3306940.631 2829362.165 1.495533659 1.703977212 1.227735531 1.194682833 1.142059024 1.700943441 1.287084612 1.303763244 1.168793685 1 21.43204543 1.000638698 0.045889745 5.53E-12 2.462054122 0.338964088 0.182852685 85.65079844 2.681845417 74.98351296 66.76324589 10.01471738 -1.000638698 2.462054122 DIDISS(ph)PEFK ddPTM_BT-474_Pertuzumab_2h_R1 6 DIDISSPEFK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 DIDISS(1)PEFK;DIDIS(0.001)S(0.999)PEFK;DIDISS(1)PEFK;DIDIS(0.035)S(0.965)PEFK;DIDISS(1)PEFK;DIDISS(1)PEFK 322.77 1.69E-42 11574790000 20121000 18451400 17974700 17783800 17011000 17711400 17944400 20706400 20102500 18008700 TRUE FALSE 19334649.08 17925184.14 21223128.14 18701624.05 17558174.26 18069536.64 18164008.93 20278805.6 17820548.48 16788954.71 1.151629116 1.067677199 1.264112537 1.113924266 1.045817001 1.076275263 1.081902313 1.207865883 1.061444788 1 24.00100907 1.000980138 24.97192673 0.999999988 1.126452359 0.287286459 0.063897055 31.14776822 793558.8404 0.062274232 0.015568558 10.022594 -1.000980138 0.12645237 HVPVVYVDYPGPASLTQIYGTFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVPVVYVDYPGPASLTQIYGTFNR 24 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 263.02 3.80E-44 684920000 401840 454830 393570 435780 462920 488000 487700 338470 519880 513410 FALSE TRUE 386135.6485 441858.6937 464696.8539 458270.658 477810.2422 497867.6944 493668.6185 331480.4762 460865.4019 478636.2834 0.806741281 0.923161718 0.970876781 0.957450728 0.998274178 1.040179593 1.031406593 0.692551918 0.962871846 1 18.86857024 1.00109352 24.99962901 1.00000012 0.923330394 0.048729373 0.100611819 97.76868376 2235085.167 0.105173999 0.0262935 10.02521096 -1.00109352 -0.076669726 AGAHLQGGAKR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGAHLQGGAKR 11 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;; 129.85 0.00015345 824620000 1833160 2020890 1387590 1659010 1775510 1968260 1904190 1948660 1919080 1657320 FALSE TRUE 1761518.081 1963256.196 1638358.38 1744631.705 1832620.892 2008059.566 1927494.047 1908419.49 1701234.084 1545068.24 1.140090796 1.270659861 1.0603793 1.129161586 1.186110001 1.299657525 1.247513862 1.235168415 1.101073752 1 20.55923913 1.001682155 4.284019115 1.000486508 1.198703958 0.453407348 0.068400831 0.158124136 8.348260918 0.069080654 0.017610696 10.03880817 -1.001682155 0.19821745 MAPPVDDLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 MAPPVDDLSPK 11 0 Q92576-2;Q92576;E7EVH3;E7ER40 Q92576-2 PHF3 PHD finger protein 3 1 MAPPVDDLS(1)PK;MAPPVDDLS(1)PK;MAPPVDDLS(1)PK 184.96 4.90E-06 1242760000 1436880 1270870 1107120 997420 1196470 1061570 1175410 1500040 1386420 1299870 TRUE FALSE 1380725.141 1234626.032 1307201.212 1048896.966 1234955.544 1083035.673 1189795.019 1469063.65 1229039.414 1211828.647 1.139373247 1.018812383 1.078701362 0.865548911 1.019084296 0.893720144 0.981817868 1.212270112 1.014202311 1 20.20875429 1.001895385 24.99604925 0.999999874 1.03004282 0.005837461 0.097847615 394.6860949 5204978.069 0.100141376 0.025035344 10.04373822 -1.001895385 0.030042945 HMEMYADR ddPTM_BT-474_Pertuzumab_2h_R1 2 HMEMYADR 8 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 147.51 0.00053616 741420000 531530 533700 611560 542560 508400 407190 675280 474220 738560 807370 FALSE TRUE 510757.22 518479.3985 722082.4961 570561.5866 524753.1477 415423.6608 683544.2786 464427.1913 654721.7651 752686.1108 0.678579308 0.688838802 0.959340801 0.758033898 0.697173948 0.551921518 0.908139886 0.617026387 0.869847013 1 19.52168882 1.00205069 7.570288989 0.999968612 0.735244643 0.354071485 0.116208362 0.106387949 48.98900093 0.108320269 0.027141651 10.04733055 -1.00205069 -0.264723969 DLDIIDNYDYSHTVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLDIIDNYDYSHTVK 15 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ;;; 300.74 2.73E-44 2379800000 2680440 2468520 2251300 2410520 2136790 2243410 2389420 2552220 3151240 3409980 FALSE TRUE 2575685.441 2398120.227 2658159.99 2534927.226 2205521.791 2288773.287 2418662.437 2499515.765 2793524.446 3179019.017 0.810213914 0.754358566 0.83615731 0.79739291 0.693774331 0.719962125 0.760820374 0.786253794 0.878737885 1 21.60015022 1.002095231 2.027670743 0.999342708 0.76609589 0.77614215 0.039294041 0.155299595 1.358681786 0.03982407 0.011138815 10.04836103 -1.002095231 -0.233246818 GASIVEDKLVEDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 GASIVEDKLVEDLR 14 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;; 129.93 5.93E-05 283093000 1112319 1763230 683260 1356672 838468 1346089 1445134 1259215 1122346 755180 FALSE TRUE 1068848.344 1712944.407 806740.281 1426690.005 865438.0847 1373307.842 1462819.982 1233211.77 994941.9873 704030.986 1.518183667 2.43305258 1.145887464 2.026459109 1.229261356 1.950635511 2.077777841 1.751644167 1.413207667 1 19.4252794 1.002138114 2.859833068 1.004228398 1.779723127 0.297781833 0.371510232 0.281412754 5.389018934 0.326341413 0.086610866 10.04935329 -1.002138114 0.775494729 PRPS(ph)PSSTREPLLSSSENGNGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 PRPSPSSTREPLLSSSENGNGGR 23 2 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 1 PRPS(0.932)PS(0.055)S(0.012)T(0.001)REPLLSSSENGNGGR;PRPS(0.845)PS(0.067)S(0.067)T(0.019)REPLLS(0.001)S(0.001)S(0.001)ENGNGGR 157.96 6.28E-10 699330000 109403 110966 73363 91069 93585 88379 98002 109903 101700 88806 TRUE FALSE 105127.4098 107801.3583 86621.32605 95769.082 96595.24652 90166.08393 99201.37779 107633.4646 90155.44236 82791.09052 1.26979134 1.30208888 1.046263861 1.156755895 1.166734801 1.089079554 1.198213203 1.30006096 1.088951019 1 16.3371879 1.002382851 24.52307333 0.999999992 1.190715067 0.376271155 0.079745932 47.87866914 492732.9469 0.080975963 0.020243991 10.05501796 -1.002382851 0.190715075 HEVLLISAEQDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEVLLISAEQDKR 13 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4;C9JIZ1 Q00341 HDLBP Vigilin 0 98.531 0.0021271 293630000 175650 162560 144740 168150 163370 156520 182360 122630 213960 226860 FALSE TRUE 168785.4038 157923.948 170897.7377 176828.2417 168624.9444 159684.9416 184591.7762 120097.6476 189672.1578 211494.5701 0.798060223 0.746704503 0.808047874 0.836088801 0.79730153 0.755030928 0.872796763 0.567852156 0.896818096 1 17.6902611 1.003845359 24.99808699 1.000000062 0.768072508 0.47752566 0.077239807 69.46823063 451598.3142 0.075780737 0.018945184 10.08893581 -1.003845359 -0.231927555 AQPPEAGPQGLHDLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQPPEAGPQGLHDLGR 16 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 0 ; 147.17 1.51E-06 210400000 160876 245990 136452 263530 185723 193381 216676 242740 200925 156555 FALSE TRUE 154588.7881 238974.606 161111.9118 277130.8149 191696.949 197291.2963 219327.7457 237727.3342 178116.8363 145951.3904 1.059179961 1.637357516 1.103873771 1.898788454 1.313430098 1.351760307 1.502745161 1.628811713 1.220384649 1 17.15512843 1.003977714 6.36419626 1.00020793 1.452058991 0.252231824 0.239318724 0.14352554 29.12641421 0.210619952 0.052906689 10.09201098 -1.003977714 0.451851061 HSPESPS(ph)IAVVESELVAEYITTER ddPTM_BT-474_Pertuzumab_2h_R1 1 HSPESPSIAVVESELVAEYITTER 24 0 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 HS(0.003)PES(0.438)PS(0.559)IAVVESELVAEYITTER 211.03 2.26E-25 67583000 29780 25463 23217 31693 30851 29713 33375 15211 34384 35047 TRUE FALSE 28616.16468 24736.82017 27412.82836 33328.67953 31843.35043 30313.81722 33783.45323 14896.88753 30480.87247 32673.23547 0.875828924 0.757097355 0.838999504 1.02006058 0.974600463 0.927787431 1.033979425 0.455935487 0.93290034 1 14.9958217 1.004307625 24.99974674 1.000000282 0.846915348 0.069739301 0.158002279 249.3123669 1446899.128 0.164444874 0.041111219 10.09968026 -1.004307625 -0.153084934 VDCTANTNTCNK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDCTANTNTCNK 12 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 207.88 1.71E-07 112200000 48230 52767 43743 49019 45338 50520 51203 47781 58562 57449 FALSE TRUE 46345.11828 51262.13682 51648.33316 51548.87646 46796.33794 51541.54901 51829.63763 46794.30565 51914.28727 53557.92806 0.865326945 0.957134428 0.964345243 0.96248825 0.873751835 0.962351437 0.967730446 0.87371389 0.969310971 1 15.70881253 1.004488383 24.9797459 1.000000016 0.929582054 0.257504178 0.039933128 126.2882945 702842.0909 0.037515883 0.009378971 10.10388474 -1.004488383 -0.070417962 RMEELHNQEVQK ddPTM_BT-474_Pertuzumab_2h_R1 8 RMEELHNQEVQK 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;;;; 207.47 5.07E-08 7054700000 3791080 3727830 3378926 3340223 3571156 3514630 3856740 4005310 4294470 4500090 FALSE TRUE 3642920.402 3621515.938 3989573.092 3512612.309 3686025.476 3585698.227 3903939.938 3922598.949 3806979.769 4195294.896 0.868334764 0.863232747 0.950963685 0.837274231 0.878609387 0.854695156 0.930551972 0.934999576 0.907440326 1 22.00034079 1.004577696 0.560612574 0.99936774 0.875718497 0.541521017 0.032853513 0.701193693 0.539915787 0.035400797 0.016013759 10.10596281 -1.004577696 -0.123649242 NSPTPATS(ph)TESLSPLHNVALR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPTPATSTESLSPLHNVALR 21 0 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 NSPTPAT(0.171)S(0.805)T(0.024)ESLSPLHNVALR 157.68 2.17E-09 236860000 64427 69018 65051 85493 57101 64701 77498 88346 82471 96760 TRUE FALSE 61909.12161 67049.67422 76807.16275 89905.30398 58937.70552 66009.29855 78446.44371 86521.62423 73109.23783 90206.35902 0.686305514 0.743292102 0.851460624 0.996662596 0.653365308 0.731758817 0.86963319 0.959152161 0.810466564 1 16.46094152 1.004631189 0.034600963 1.77874379 8.51E-11 0.313033146 0.099731463 152.2142936 3.59188706 95.53434519 87.54269543 10.10720766 -1.004631189 -1.77874379 DWSHYFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DWSHYFK 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 125.25 0.0040673 1599470000 4172700 4017600 3405200 5388100 4029600 3837400 3865000 3906000 5234900 5448000 FALSE TRUE 4009626.271 3903021.982 4020595.388 5666180.487 4159215.744 3914994.857 3912301.026 3825339.735 4640656.098 5079002.107 0.789451586 0.768462367 0.791611286 1.115609005 0.818904118 0.770819695 0.770289309 0.753167582 0.913694462 1 22.27611364 1.00507403 6.254893018 0.999903108 0.821747877 0.244144068 0.100561131 0.178697549 33.20261813 0.101447556 0.025491899 10.11751903 -1.00507403 -0.178155231 EIDVDAVASDGVVAAIAISEHVENAGVHSGDATLVTPPQDITAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIDVDAVASDGVVAAIAISEHVENAGVHSGDATLVTPPQDITAK 44 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 234.67 4.41E-55 25716000 16496 18652 14956 17189 16851 21430 22037 8187.6 26457 30035 FALSE TRUE 15851.31808 18120.06322 17658.88189 18076.12635 17393.02772 21863.32928 22306.6954 8018.523199 23453.71228 28000.7027 0.566104296 0.647128875 0.630658526 0.64555974 0.621163972 0.780813593 0.7966477 0.286368642 0.83761156 1 14.77317541 1.005279298 24.99569596 1.000000114 0.61756367 0.471372848 0.131492266 92.59193245 438388.5926 0.13184403 0.032961007 10.12230218 -1.005279298 -0.382436444 DLVVLLFETALLSSGFSLEDPQTHSNR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLVVLLFETALLSSGFSLEDPQTHSNR 27 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;; 241.82 3.19E-45 29038600000 13157096.9 13472535 9759388.7 13464992.7 13294401.1 13529467.2 12934674.8 10321058.9 15027891.4 14800566.6 FALSE TRUE 12642903.01 13088311.49 11523127.33 14159922.59 13722027.59 13803042.3 13092973.22 10107925.43 13321988.17 13798111.04 0.916277813 0.948558209 0.83512354 1.026221817 0.994485951 1.000357386 0.948896061 0.732558638 0.965493619 1 23.71796744 1.005327946 24.99944824 1.000000147 0.918600582 0.075591729 0.082113207 291.5590356 1368025.213 0.087394337 0.021848584 10.1234361 -1.005327946 -0.081399564 NKDEMSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 NKDEMSTK 8 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 61.56 0.077698 283020000 167270 158860 132830 138960 147270 131600 165730 146540 181380 181150 FALSE TRUE 160732.9035 154329.4683 156835.3358 146131.7423 152007.0733 134261.0422 167758.2533 143513.8978 160790.5028 168880.5491 0.951754979 0.91383803 0.928676136 0.865296465 0.900086328 0.795005954 0.993354499 0.849795305 0.952096044 1 17.36564365 1.00551611 8.41002066 0.999994133 0.898843892 0.278026861 0.052117898 0.119566152 80.40686742 0.046494679 0.011639734 10.12782316 -1.00551611 -0.101150241 VGQTIER ddPTM_BT-474_Pertuzumab_2h_R1 2 VGQTIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 130 0.0083885 899190000 869080 1121940 692960 1067940 820330 1053080 995350 1006380 1014130 875810 FALSE TRUE 835115.3928 1089943.37 818193.2868 1123056.511 846716.6595 1074373.999 1007531.391 985597.9013 899010.214 816490.6086 1.022810776 1.334912316 1.002085362 1.375467764 1.037019472 1.31584367 1.23397793 1.207114804 1.101066203 1 19.63907677 1.00552907 3.266527734 1.00078027 1.197193523 0.184331937 0.126718454 0.316885362 8.221468822 0.106276935 0.027745891 10.12812541 -1.00552907 0.196413252 SHFTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHFTDK 6 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 94.163 0.044794 403390000 632860 628420 684850 800010 602770 628410 730290 428070 1012490 1152070 FALSE TRUE 608127.1315 610498.0769 808617.6294 841298.612 622158.6445 641116.8808 739227.5075 419230.2049 897556.3799 1074039.273 0.566205675 0.568413179 0.75287529 0.783303398 0.579269921 0.596921264 0.688268601 0.390330424 0.835683017 1 20.03461532 1.005571978 23.07590651 1.00000001 0.614748679 0.593380283 0.104564978 29.8982427 123818.8902 0.106863598 0.0267159 10.12912609 -1.005571978 -0.385251331 SGS(ph)VSNYR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSVSNYR 8 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.003)GS(0.952)VS(0.046)NYR;S(0.006)GS(0.964)VS(0.03)NYR;S(0.012)GS(0.942)VS(0.045)NYR;S(0.011)GS(0.947)VS(0.042)NYR 125.97 0.0012999 1755370000 1926420 1855600 1435280 1657230 1695790 1927850 1445870 1838470 1674640 1438310 TRUE FALSE 1851133.377 1802680.105 1694667.024 1742759.839 1750336.625 1966832.448 1463564.99 1800504.952 1484541.888 1340891.983 1.380523861 1.344388756 1.2638356 1.299701886 1.305352443 1.466809015 1.091486122 1.342766588 1.10713011 1 20.35476159 1.006286207 0.845911508 0.995800314 1.327340781 0.560903562 0.092362445 0.460403884 0.72740741 0.082403868 0.029509991 10.14579789 -1.006286207 0.331540467 EAGLAHLCEFIEDCEHTVLATK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAGLAHLCEFIEDCEHTVLATK 22 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ; 283.73 4.40E-46 95642000 170548 164376 133059 160741 164598 171731 164598 130679 190407 187631 FALSE TRUE 163882.7956 159688.1574 157105.7212 169036.8623 169892.4442 175203.5185 166612.3996 127980.433 168792.7956 174922.5852 0.936887569 0.9129076 0.89814429 0.966352413 0.971243616 1.001606043 0.952492209 0.731640416 0.964957129 1 17.41635705 1.006394449 24.99981654 1.000000151 0.9143198 0.111641035 0.070120209 273.0075911 1067348.273 0.076423436 0.019105859 10.14832692 -1.006394449 -0.085680351 RLEEQAAQHK ddPTM_BT-474_Pertuzumab_2h_R1 4 RLEEQAAQHK 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 151.07 1.33E-05 2207220000 1914400 1941130 1670630 1668610 1633540 1572900 2045720 1908160 2163200 2263590 FALSE TRUE 1839583.132 1885770.873 1972550.004 1754727.162 1686084.298 1604705.116 2070756.133 1868755.829 1917642.605 2110275.033 0.871726719 0.893613791 0.934735981 0.831515861 0.798987938 0.760424632 0.981273105 0.88555084 0.908716909 1 21.00899961 1.00676548 0.837131251 0.995705701 0.860563513 0.32892273 0.058805638 0.816477897 1.266527933 0.059132575 0.021286241 10.15700065 -1.00676548 -0.135142187 SHSESASPSALSSS(ph)PNNLS(ph)PTGWSQPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SHSESASPSALSSSPNNLSPTGWSQPK 27 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 2 SHSESASPSALS(0.059)S(0.423)S(0.518)PNNLS(0.876)PT(0.118)GWS(0.006)QPK;SHSESASPSALS(0.004)S(0.037)S(0.958)PNNLS(0.951)PT(0.049)GWSQPK;SHSESASPSALSS(0.007)S(0.993)PNNLS(0.965)PT(0.035)GWSQPK 221.23 1.38E-34 915470000 452300 522520 455920 495530 495690 555600 563050 300002 616270 627820 TRUE FALSE 434623.616 507618.2412 538314.8859 521104.3627 511634.319 566834.6127 569940.7743 293806.8539 546313.6132 585297.1922 0.742569111 0.867282891 0.919729145 0.890324385 0.874144496 0.96845606 0.973763042 0.501978922 0.93339524 1 19.15880983 1.006811224 24.99983632 1.000000281 0.834813786 0.135481779 0.130133959 260.9784105 957886.8625 0.135699522 0.033924881 10.15807053 -1.006811224 -0.165186495 DLVILLYETALLSSGFSLEDPQTHANR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLVILLYETALLSSGFSLEDPQTHANR 27 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 328.64 3.68E-95 21527200000 11074590 11609777 9195732 10948942 11477678 11834911 10840911 9580157 12753400 12337536 FALSE TRUE 10641782.78 11278677.53 10857605.33 11514018.21 11846867.94 12074221.01 10973585.31 9382323.41 11305687.5 11501903.7 0.925219256 0.980592241 0.943983328 1.001053261 1.029991926 1.049758486 0.954066875 0.815719176 0.982940546 1 23.45536933 1.006847572 24.98436589 1.000000151 0.957643297 0.033271703 0.06125665 511.3099562 1865578.174 0.068349724 0.017087431 10.15892074 -1.006847572 -0.042356854 EVWYFGLHYVDNK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVWYFGLHYVDNK 13 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 251.3 2.04E-18 3049300000 2551400 2349530 2169910 2172510 2274820 2218140 2412740 2307580 2774200 2727200 FALSE TRUE 2451688.467 2282523.705 2562061.006 2284633.501 2347991.651 2262992.311 2442267.834 2259927.667 2459284.446 2542484.315 0.964288532 0.897753308 1.007699828 0.898583125 0.923502905 0.890071297 0.960583245 0.888865923 0.967276153 1 21.27780744 1.007427436 11.13003369 0.999999691 0.927693605 0.2823595 0.036751022 0.228284489 317.9841656 0.032616157 0.008156408 10.17249386 -1.007427436 -0.072306086 RVEHNQSYSQAGITETEWTSGSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVEHNQSYSQAGITETEWTSGSSK 24 1 P42167 P42167 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 177.47 2.75E-17 203810000 55209 80654 44111 85581 43003 44346 57938 81067 60539 50795 FALSE TRUE 53051.37124 78353.82689 52082.83894 89997.84567 44386.23055 45242.7065 58647.06258 79392.93812 53666.86652 47354.60941 1.120300049 1.654618798 1.099847293 1.900508668 0.937315947 0.955402379 1.238465765 1.676561989 1.133297628 1 15.53121724 1.007433104 24.95341877 0.999999802 1.337622278 0.105408728 0.308568166 282.2082406 947386.6065 0.291179425 0.072794856 10.17262661 -1.007433104 0.337622476 DVQFEHGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVQFEHGYR 9 0 A0A0C4DFM1;Q92544 A0A0C4DFM1 TM9SF4 Transmembrane 9 superfamily member 4 0 99.34 0.005403 419450000 185850 245830 173850 226440 199630 186100 209470 236800 230540 212350 FALSE TRUE 178586.7765 238819.1691 205268.5623 238126.5955 206051.2802 189863.0695 212033.5565 231909.9972 204370.0657 197967.3454 0.902102194 1.206356375 1.036880915 1.202857952 1.040834689 0.959062562 1.071053189 1.171455812 1.032342305 1 17.59490295 1.007441834 24.93101951 0.999999945 1.081922508 0.056140803 0.094546491 342.0928164 1146044.949 0.086431168 0.021607792 10.1728311 -1.007441834 0.081922563 VEESGEHVILGTGELYLDCVMHDLR ddPTM_BT-474_Pertuzumab_2h_R1 10 VEESGEHVILGTGELYLDCVMHDLR 25 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;;;;;;; 266.4 1.10E-45 1316698500 477364 520715 441522 568787 519436 574107 544086 366593.1 610553 601828 FALSE TRUE 458708.0871 505864.718 521314.847 598142.1652 536144.1307 585715.8369 550744.6872 359022.8244 541245.5831 561065.6535 0.817565795 0.901614125 0.929151239 1.066082305 0.955581806 1.043934579 0.981604708 0.639894497 0.96467424 1 19.09781007 1.007591938 24.99962761 1.000000286 0.909984395 0.051133257 0.114649458 462.338462 1522434.431 0.122755747 0.030688937 10.17634772 -1.007591938 -0.090015891 HEDLKDMLEFPAQELR ddPTM_BT-474_Pertuzumab_2h_R1 2 HEDLKDMLEFPAQELR 16 1 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ; 119.23 0.00012637 167619000 214824 200102 173290 195178 225407 229445 215074 160195 248200 246496 FALSE TRUE 206428.4406 194395.2869 204607.3578 205251.16 232657.4209 234084.5351 217706.1399 156886.9173 220025.3765 229800.6064 0.898293716 0.845930261 0.890369095 0.893170663 1.01243171 1.018641938 0.947369737 0.682708892 0.957462123 1 17.81002308 1.007608554 24.99837715 1.000000191 0.891546498 0.11919027 0.089233545 301.305039 989951.1932 0.096387214 0.024096804 10.17673706 -1.007608554 -0.108453692 RPSVGS(ph)QSNQAGQGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSVGSQSNQAGQGK 15 1 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 RPS(0.301)VGS(0.699)QSNQAGQGK 145.48 2.48E-06 195800000 194420 168970 124780 156640 152230 132040 135970 209000 145480 115990 TRUE FALSE 186821.8515 164151.141 147330.5217 164724.2092 157126.6162 134709.9393 137634.0415 204684.077 128965.7203 108133.894 1.727690038 1.518035974 1.362482347 1.52333559 1.453074613 1.245769798 1.272811294 1.892876224 1.192648443 1 16.72245927 1.007997375 24.97531604 0.99999987 1.497793624 0.44718099 0.185592768 127.9874011 399694.934 0.184804226 0.046201057 10.1858523 -1.007997375 0.497793754 RGDTYELQVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDTYELQVR 10 1 A0A087WU53;Q9H0U3 A0A087WU53 MAGT1 Magnesium transporter protein 1 0 ; 101.39 0.0053907 426730000 88176 136903 81016 109503 73020 72107 105692 120268 97660 82726 FALSE TRUE 84729.98444 132998.6605 95657.39339 115154.463 75368.75462 73565.05294 106985.4903 117784.4238 86574.04622 77122.89434 1.098635952 1.724502972 1.240324215 1.493129426 0.977255266 0.953867896 1.387207926 1.527230335 1.122546644 1 16.23487157 1.008114044 23.38817939 0.999999906 1.312264067 0.151849216 0.233660287 117.203036 337825.8158 0.229134036 0.057283509 10.18858902 -1.008114044 0.312264162 HAQPTCPGAQLCTVYYASLNFR ddPTM_BT-474_Pertuzumab_2h_R1 2 HAQPTCPGAQLCTVYYASLNFR 22 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 214.49 1.50E-25 1273160000 518590 514890 522110 589220 552210 592180 584330 391800 684860 692640 FALSE TRUE 498322.9295 500205.8413 616466.8913 619629.7148 569972.3362 604154.2853 591481.2053 383709.1931 607117.564 645726.8759 0.771724003 0.77463996 0.954686748 0.959584831 0.88268331 0.935618925 0.915992856 0.594228315 0.940207984 1 19.30056455 1.00838299 24.98019304 1.000000227 0.843366437 0.181952224 0.106374636 254.89255 759541.9622 0.112752407 0.028188102 10.19490046 -1.00838299 -0.15663379 FNGS(ph)TEALDKLDADAVSPTVSQLSAVFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 FNGSTEALDKLDADAVSPTVSQLSAVFEK 29 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 FNGS(0.869)T(0.131)EALDKLDADAVSPTVSQLSAVFEK;FNGS(0.87)T(0.13)EALDKLDADAVSPTVSQLSAVFEK 207.62 9.91E-26 4254400000 3629600 2235710 1246480 1076440 1266270 982510 803229 3504290 1399390 953670 TRUE FALSE 3487751.219 2171949.74 1471746.664 1131995.197 1307000.725 1002377.025 813059.1568 3431925.187 1240537.114 889077.0815 3.922889581 2.442926249 1.655364529 1.273225034 1.470064578 1.127435457 0.914497937 3.860098588 1.395308843 1 19.76194898 1.009290993 24.99935623 0.999998221 2.07017125 0.115819102 1.008315371 356.8957134 960297.9339 1.015805229 0.253951307 10.2162378 -1.009290993 1.070173029 (ac)AAEVYFGDLELFEPFDHPEESIPKPVHTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAEVYFGDLELFEPFDHPEESIPKPVHTR 29 1 Q6NZY4 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 0 116.35 2.86E-33 83040000 59618 59844 55725 69645 57104 71193 67496 42691 74162 73175 FALSE TRUE 57288.06265 58137.30771 65795.7471 73239.3868 58940.80202 72632.57124 68322.03624 41809.41593 65743.44067 68218.79207 0.839769525 0.852218369 0.964481268 1.07359548 0.863996565 1.064700342 1.001513427 0.612872416 0.963714523 1 16.05788159 1.009483843 24.99811144 1.000000387 0.901076491 0.050625677 0.126974596 506.4144493 1334833.363 0.132232294 0.033058073 10.22077536 -1.009483843 -0.098923896 S(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_BT-474_Pertuzumab_2h_R1 18 SPQPPVEEEDEHFDDTVVCLDTYNCDLHFK 30 0 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK 324.12 7.72E-93 13929316900 925718 884674.4 846831.3 940095.5 881858.8 858944.6 981901.2 834398.6 1172342.9 1227115.3 TRUE FALSE 889539.9171 859444.3523 999872.5536 988613.9414 910224.5892 876313.0483 993918.0006 817167.9773 1039263.449 1144001.688 0.77756871 0.751261437 0.87401318 0.864171751 0.795649691 0.766006779 0.868808159 0.714306619 0.90844573 1 20.12565775 1.00958618 6.984050947 0.99994045 0.802165361 0.617263832 0.050727053 0.073614036 19.40190334 0.048826536 0.012246377 10.22318405 -1.00958618 -0.197775089 FDPETNSDDACTYHPGVPVFHDALK ddPTM_BT-474_Pertuzumab_2h_R1 1 FDPETNSDDACTYHPGVPVFHDALK 25 0 Q9UHD1-2;Q9UHD1;E9PPQ5;E9PIZ4;E9PSD5;E9PL00 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 0 192.18 3.24E-18 239630000 183160 172300 151750 170050 143270 196230 164150 111990 240690 259200 FALSE TRUE 176001.9047 167386.1727 179174.6007 178826.3009 147878.4097 200197.905 166158.9168 109677.3674 213367.8803 241644.1531 0.728351596 0.69269697 0.741481217 0.740039842 0.611967671 0.828482305 0.687618197 0.453879665 0.882983832 1 17.88252456 1.009749399 24.55328666 1.00000005 0.67992145 0.559341212 0.093677474 93.89200994 236460.1745 0.097180489 0.024295122 10.22702691 -1.009749399 -0.320078601 VSALNSVHCEHVEDEGESR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSALNSVHCEHVEDEGESR 19 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4;A0A087WWN5 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 254.26 3.90E-31 2481400000 1370830 1679990 1476570 1937180 1894680 1999780 1866180 668280 2129040 2177930 FALSE TRUE 1317256.448 1632078.33 1743419.045 2037158.092 1955624.103 2040216.922 1889018.869 654479.7845 1887360.305 2030416.861 0.648761579 0.803814409 0.858650792 1.003320122 0.963163841 1.004826625 0.930360117 0.322337643 0.929543258 1 20.95334452 1.009897986 24.98865211 1.000000616 0.805012051 0.087220734 0.194998314 416.0693757 1050412.446 0.210801714 0.052700429 10.23052652 -1.009897986 -0.194988565 YLSHSEFK ddPTM_BT-474_Pertuzumab_2h_R1 3 YLSHSEFK 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ;; 132.08 0.00097737 964510000 1690990 1734680 1515150 1527180 1642480 1490410 1843660 1714200 2098730 2134710 FALSE TRUE 1624904.241 1685208.625 1788971.309 1605997.943 1695311.861 1520547.111 1866223.263 1678801.171 1860490.969 1990124.19 0.81648384 0.846785659 0.898924458 0.806983781 0.851862346 0.764046344 0.937742113 0.843566034 0.934861743 1 20.92442703 1.01031826 0.972618165 1.000751194 0.839469209 0.559804214 0.045077253 0.411152677 0.833969201 0.040053209 0.013486822 10.24043157 -1.01031826 -0.161281985 (ac)S(ph)DAAVDTSSEITTK ddPTM_BT-474_Pertuzumab_2h_R1 3 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 S(0.99)DAAVDT(0.009)S(0.001)SEITTK;S(0.988)DAAVDT(0.009)S(0.002)S(0.001)EITTK;S(0.988)DAAVDT(0.008)S(0.003)SEITTK 76.533 5.75E-44 2434430000 1070080 1057860 852000 975490 1000630 925520 981950 1091650 1062830 941410 TRUE FALSE 1028260.091 1027690.869 1005975.353 1025835.156 1032816.173 944234.6485 993967.3978 1069107.046 942181.9941 877647.4622 1.171609484 1.170960907 1.146218039 1.16884649 1.176800728 1.075870084 1.132536059 1.2181509 1.073531269 1 19.74328202 1.010329899 6.070097298 1.000113277 1.15744109 0.684547807 0.034644424 0.072597961 11.00538923 0.034767133 0.008742079 10.24070602 -1.010329899 0.157327814 YSHSGSS(ph)S(ph)PDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHS(0.002)GS(0.516)S(0.844)S(0.633)PDT(0.006)K 141.82 8.89E-05 261090000 757210 756880 578620 668080 697760 723550 736280 644370 867970 861030 TRUE FALSE 727617.3961 735294.5235 683189.5053 702559.6889 720204.0841 738180.6767 745290.8149 631063.5343 769441.6844 802711.6712 0.906449255 0.916013246 0.851101996 0.875232931 0.897213919 0.91960875 0.928466399 0.786164643 0.958553005 1 19.61452235 1.010467736 24.99781882 1.000000038 0.882840827 0.488980972 0.039635141 134.4096044 320979.8998 0.039799665 0.009949916 10.24395675 -1.010467736 -0.117159212 QIS(ph)LPDLSQEEPQLK ddPTM_BT-474_Pertuzumab_2h_R1 5 QISLPDLSQEEPQLK 15 0 H0YBZ4;Q15390-2;Q15390 H0YBZ4 MTFR1 Mitochondrial fission regulator 1 1 QIS(1)LPDLSQEEPQLK;QIS(1)LPDLSQEEPQLK;QIS(1)LPDLSQEEPQLK;QIS(1)LPDLSQEEPQLK;QIS(0.987)LPDLS(0.013)QEEPQLK 318.09 2.10E-56 821078000 930972 812099 586064 718055 660658 650764 731631 953910 810639 740642 TRUE FALSE 894588.585 788938.7316 691978.8017 755113.9046 681908.6646 663922.894 740584.919 934211.4252 718618.6592 690477.6576 1.295608301 1.142598494 1.002174066 1.093610917 0.987589761 0.961541458 1.072568983 1.352992982 1.040755847 1 19.39723521 1.010667919 24.98591742 0.999999687 1.116048852 0.092047765 0.120343134 433.920204 1016303.957 0.126815154 0.031703789 10.24867965 -1.010667919 0.116049165 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR ddPTM_BT-474_Pertuzumab_2h_R1 3 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR 33 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 221.72 5.79E-36 3611810000 384984 382563 289992 338134 378688 381409 361707 373296 458694 434912 FALSE TRUE 369938.3997 371652.6778 342400.0052 355585.1363 390868.8434 389121.3513 366133.6785 365587.3071 406624.9801 405455.0229 0.91240305 0.916631086 0.844483324 0.877002667 0.96402516 0.959715207 0.90301922 0.901671669 1.002885541 1 18.62918236 1.010895425 0.336151829 1.012944191 0.889086257 0.432031352 0.037196907 1.841884377 0.617150264 0.083528014 0.04770748 10.25404986 -1.010895425 -0.123857934 DGLTVHLVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGLTVHLVIK 10 0 Q9NRR5;Q9NRR5-2;C9IYQ4;Q9H347 Q9NRR5 UBQLN4;UBQLN3 Ubiquilin-4;Ubiquilin-3 0 90.15 0.011262 0 374020 351800 345210 338060 346670 330710 336230 362180 431540 438990 FALSE TRUE 359402.8849 341767.0084 407597.1262 355507.3171 357820.9554 337397.1828 340344.8833 354700.8564 382553.3884 409256.8163 0.878184237 0.835091793 0.995944624 0.868665598 0.874318866 0.824414327 0.831616896 0.866695049 0.934751416 1 18.64264692 1.01099942 3.258795123 0.999381148 0.871060811 0.445014113 0.045575314 0.201833108 5.136320869 0.044595931 0.011650066 10.25650557 -1.01099942 -0.128320336 APQT(ph)S(ph)SSPPPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 APQT(0.809)S(0.413)S(0.392)S(0.385)PPPVR 95.98 0.030461 721500000 490700 485120 404970 435770 437290 446410 491630 498330 496600 441140 TRUE FALSE 471522.9015 471284.8526 478157.0875 458260.1419 451355.83 455436.7161 497646.715 488039.3114 440228.0499 411261.1949 1.146529036 1.14595021 1.162660357 1.114280043 1.0974919 1.107414757 1.210050258 1.186689426 1.070434204 1 18.64969543 1.011312439 4.942089569 1.000305709 1.147575698 0.669431696 0.033096342 0.096461205 7.24312209 0.036218805 0.009166526 10.26390064 -1.011312439 0.147269989 EHTALLK ddPTM_BT-474_Pertuzumab_2h_R1 5 EHTALLK 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;; 121.52 0.0044301 4103740000 7674230 7224600 6246000 6750930 7715020 7498450 7957810 5339910 8829310 8767490 FALSE TRUE 7374312.607 7018561.482 7374791.142 7099346.306 7963180.625 7650073.797 8055200.059 5229638.992 7827043.744 8173660.093 0.902204462 0.858680371 0.902263008 0.868563927 0.974249055 0.935942247 0.985507101 0.63981606 0.957593496 1 22.96255082 1.011413552 24.99999878 1.000000312 0.875787409 0.153365759 0.090982326 307.2138793 672911.9491 0.093377645 0.023344411 10.26629057 -1.011413552 -0.124212903 GHLENNPALEK ddPTM_BT-474_Pertuzumab_2h_R1 5 GHLENNPALEK 11 0 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;Q8NHW5;F8VWV4;F8VPE8;F8VZS0;F8VS58 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;;; 213.63 1.86E-09 15895750000 25041500 24106700 20685100 22564600 23347400 23231400 26340700 19526500 29593000 29586200 FALSE TRUE 24062850.5 23419200.52 24423357.71 23729161.71 24098390.32 23701154.83 26663065.37 19123270.95 26233726.7 27582300.32 0.872401874 0.849066258 0.885472112 0.860303943 0.873690375 0.859288549 0.966673013 0.693316755 0.951107283 1 24.71723944 1.011888448 24.99046604 1.000000138 0.854202008 0.367231673 0.06349183 171.1447088 359758.4602 0.06045302 0.015113255 10.27752278 -1.011888448 -0.145798129 HLQDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLQDIK 6 0 Q99733;Q99733-2;C9JZI7;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 138.07 0.012461 176440000 538950 519470 451230 466990 484650 421790 559970 457550 625270 641820 FALSE TRUE 517887.2382 504655.2242 532777.2986 491091.4099 500239.2074 430318.8828 566823.0804 448101.4326 554291.9709 598348.9597 0.865527097 0.843412888 0.890412342 0.820744153 0.836032551 0.719177122 0.947311884 0.748896485 0.926369073 1 19.19062759 1.012243488 8.281591548 0.99998427 0.833511442 0.438312976 0.061413894 0.104498969 47.14696461 0.054377043 0.013614557 10.28592819 -1.012243488 -0.166472828 KKEEMNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KKEEMNR 7 2 Q99543;Q99543-2;H7C3L7 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 91.318 0.0092758 163960000 168690 159350 154190 144470 168060 128780 191160 170580 220190 237760 FALSE TRUE 162097.4083 154805.494 182055.5629 151926.114 173465.8025 131384.0198 193499.4733 167057.4634 195194.9543 221656.3034 0.731300693 0.698403301 0.82134169 0.68541301 0.78258908 0.592737575 0.872970767 0.753677928 0.880619912 1 17.75796486 1.012354439 0.978354661 1.000382011 0.730124807 0.581093901 0.071659704 0.377821478 0.774856217 0.062119351 0.020872826 10.28855631 -1.012354439 -0.270257204 FSHDLK ddPTM_BT-474_Pertuzumab_2h_R1 4 FSHDLK 6 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ;;; 142.63 0.011502 1790860000 2573670 2467620 2313880 2504530 2501140 2527090 2678440 2528330 3221310 3341970 FALSE TRUE 2473088.131 2397245.894 2732049.588 2633789.093 2581591.44 2578189.491 2711219.55 2476119.102 2855640.394 3115615.395 0.793771958 0.769429339 0.876889231 0.845351162 0.8285976 0.827505698 0.870203541 0.79474479 0.916557415 1 21.57108572 1.01239789 4.092543588 0.999565927 0.827368205 0.752800068 0.032106444 0.084175934 3.697116194 0.031030921 0.00793693 10.28958572 -1.01239789 -0.172197722 AHQVVEDGYEFFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHQVVEDGYEFFAK 14 0 F8W0W8;P36873;P36873-2;F8VYE8;P62140;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 113.4 0.000538 431510000 129070 120990 112150 141140 125160 141600 132970 103290 154380 151190 FALSE TRUE 124025.8017 117539.4837 132417.9998 148424.2523 129185.8851 144463.249 134597.3266 101157.0254 136855.4296 140949.7666 0.879929103 0.833910452 0.93946945 1.053029429 0.916538481 1.024927195 0.954931178 0.717681397 0.9709518 1 17.10482156 1.012987206 24.99611739 1.000000322 0.909608161 0.091825479 0.089615241 443.8774602 854315.7225 0.094579338 0.023644834 10.30355766 -1.012987206 -0.090392161 ELFALKPMNCPGHCLMFDHRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELFALKPMNCPGHCLMFDHRPR 22 2 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 91.811 0.00069775 275970000 271750 264250 234520 319240 199140 182700 341330 199780 346870 354990 FALSE TRUE 261129.7096 256713.8487 276902.9809 335716.0147 205545.519 186394.3192 345507.2986 195654.4732 307494.7718 330946.2111 0.789039732 0.775696594 0.836700864 1.014412625 0.62108437 0.563216356 1.043998351 0.591197199 0.929138215 1 18.33623723 1.013161412 24.74705154 1.000000113 0.779125792 0.195623632 0.153575204 242.8596914 456640.562 0.142012588 0.035503147 10.30769151 -1.013161412 -0.220874321 FHSETLTEGDLVDLMK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHSETLTEGDLVDLMK 16 0 O75828 O75828 CBR3 Carbonyl reductase [NADPH] 3 0 ; 101.15 0.0018139 138892000 156676 157729 136987 162597 153789 168682 174696 105418 191680 189937 FALSE TRUE 150552.9287 153230.7234 161743.5982 170988.6507 158735.7629 172092.8656 176833.9819 103241.0815 169921.29 177072.3978 0.850233749 0.865356347 0.913432021 0.9656426 0.896445549 0.971878552 0.998653568 0.583044465 0.95961478 1 17.43397982 1.013371325 24.99998997 1.000000512 0.872412426 0.116950979 0.110026314 384.4304697 718756.0548 0.114693862 0.028673465 10.31267485 -1.013371325 -0.127588086 LGHAEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LGHAEQK 7 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;; 138.37 0.0027925 3812930000 5715900 5283920 4979270 5139360 5183940 4987250 5694300 5197620 6582200 6651800 FALSE TRUE 5492516.309 5133227.775 5879134.852 5404602.986 5350686.138 5088095.612 5763988.547 5090287.331 5835016.251 6201267.661 0.885708634 0.827770716 0.948053716 0.871531964 0.862837476 0.820492823 0.929485528 0.820846254 0.940939268 1 22.56413173 1.013572254 5.963315714 0.999893134 0.870759278 0.514687984 0.040741151 0.095675458 12.88184502 0.036559507 0.009196661 10.31744718 -1.013572254 -0.129133856 EDAS(ph)PLPHVCCCK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDASPLPHVCCCK 13 0 C9J7Z4;Q8NCE0-5;Q8NCE0-3;Q8NCE0-2;Q8NCE0 C9J7Z4 TSEN2 tRNA-splicing endonuclease subunit Sen2 1 EDAS(1)PLPHVCCCK 100.45 0.0015423 123240000 150830 137880 119230 103550 128640 134360 130620 136820 163530 168630 TRUE FALSE 144935.3968 133947.7974 140777.5133 108894.2279 132777.8224 137076.8513 132218.5666 133994.6192 144966.76 157208.5399 0.921930812 0.852038938 0.895482608 0.692673744 0.844596754 0.87194278 0.84103934 0.85233677 0.922130312 1 17.26232006 1.013790526 2.089492313 0.99982605 0.842465514 0.423992705 0.057061518 0.297088136 2.76032893 0.053971731 0.015038462 10.32263393 -1.013790526 -0.157360535 QKEQTFR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKEQTFR 7 1 A1L0T0;M0R026;M0QZX5 A1L0T0 ILVBL Acetolactate synthase-like protein 0 78.77 0.045364 0 188310 234120 159110 206050 172330 184380 186550 241930 207560 188610 FALSE TRUE 180950.637 227443.1268 187864.7164 216684.2652 177873.151 188108.2899 188833.0547 236934.061 183998.659 175835.2767 1.029091775 1.293501117 1.068413119 1.232313955 1.011589678 1.069798356 1.073920195 1.347477397 1.046426305 1 17.42386501 1.013848267 24.98462399 0.999999743 1.149409801 0.15961001 0.10905692 297.2174214 536228.7981 0.103759909 0.025939977 10.32400643 -1.013848267 0.149410058 SFKLS(ph)GFSFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFKLSGFSFK 10 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 SFKLS(1)GFSFK;SFKLS(1)GFSFK 125.28 0.00025029 1237540000 3383780 2476480 2013950 1818910 1843040 1670600 1866750 3961280 2513150 2286900 TRUE FALSE 3251538.137 2405853.215 2377915.565 1912784.163 1902323.055 1704380.677 1889595.845 3879478.184 2227867.748 2132006.226 1.525107243 1.12844568 1.115341755 0.897175693 0.892268996 0.79942575 0.886299403 1.819637361 1.044963059 1 21.02378022 1.013979065 24.99741846 0.999998403 1.145507832 0.020693038 0.302077477 946.7766622 1693023.323 0.31928967 0.079822417 10.32711624 -1.013979065 0.145509429 S(ph)PSMPSLNQTWPELNQSSEDTAIVHPVPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSMPSLNQTWPELNQSSEDTAIVHPVPIR 30 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2 E9PMG1 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.604)PS(0.396)MPSLNQTWPELNQSSEDTAIVHPVPIR 190.23 1.60E-18 157730000 15575 15698 12913 15453 14585 14288 13750 14684 15977 13227 TRUE FALSE 14966.31178 15250.30841 15246.66635 16250.53118 15054.13977 14576.91315 13918.27661 14380.77027 14163.35794 12331.12351 1.213702204 1.236733084 1.236437729 1.317846762 1.220824669 1.182123684 1.128711151 1.166217357 1.148586171 1 13.59001663 1.01448549 0.392787292 0.988301024 1.258679695 0.800173615 0.03580566 0.610557997 0.261410658 0.060715658 0.032977926 10.33916558 -1.01448549 0.27037867 DNDFSYRPNMICNFLHENEDEEVVASAPDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DNDFSYRPNMICNFLHENEDEEVVASAPDK 30 1 Q969F1 Q969F1 GTF3C6 General transcription factor 3C polypeptide 6 0 99.446 0.00032337 137800000 94293 91528 51061 63869 72105 96161 73039 72252 91616 88906 FALSE TRUE 90607.92531 88917.71106 60288.85855 67165.28674 74424.32281 98105.44131 73932.87313 70759.97095 81216.13577 82884.31743 1.093185395 1.072792946 0.727385595 0.81034976 0.897930092 1.18364299 0.892000748 0.853719656 0.979873374 1 16.33881153 1.014832502 24.46516339 1.000000156 0.933449896 0.019516302 0.132091347 673.6220631 1111086.595 0.132317568 0.033079392 10.34743013 -1.014832502 -0.066550261 QKT(ph)VDIDDAQILPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKTVDIDDAQILPR 14 1 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 QKT(1)VDIDDAQILPR 132.79 7.82E-05 255020000 302300 203860 98213 117300 115980 101840 85715 274050 110680 76530 TRUE FALSE 290485.7818 198046.1124 115962.2738 123353.8671 119710.602 103899.2746 86764.00581 268390.7717 98116.07041 71346.55493 4.07147594 2.775832871 1.625338097 1.72893936 1.677875016 1.456261969 1.216092436 3.761790208 1.375204038 1 16.12255615 1.01490726 24.96170082 0.999997982 2.259084872 0.189709883 0.925352104 314.6671622 526897.5296 0.923742689 0.230935672 10.34921145 -1.01490726 1.259086889 LYGAQFHPEVGLTENGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYGAQFHPEVGLTENGK 17 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 177.67 1.02E-09 347020000 356400 326850 310220 311380 339370 324550 343280 337930 399680 394180 FALSE TRUE 342471.494 317528.558 366283.6548 327450.3591 350286.1443 331112.6234 347481.1633 330951.6274 354310.002 367481.8375 0.93194128 0.864065991 0.996739478 0.891065423 0.953206685 0.901031261 0.945573707 0.900593155 0.964156499 1 18.48731342 1.015027001 4.962638658 0.999861423 0.922937296 0.332839808 0.035263416 0.154102402 11.28863339 0.030232663 0.007650495 10.35206525 -1.015027001 -0.076924127 HQAS(ph)DSENEELPKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQASDSENEELPKPR 15 1 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 1 HQAS(0.982)DS(0.018)ENEELPKPR;HQAS(0.996)DS(0.004)ENEELPKPR 92.563 0.0031457 973460000 73691 117949 118874 126578 132519 119398 155104 63533 180540 190524 TRUE FALSE 70811.07425 114585.21 140357.1761 133110.7057 136781.594 121812.3094 157002.2091 62221.02135 160045.8561 177619.6398 0.398666917 0.645115654 0.79021203 0.749414344 0.770081474 0.685804281 0.8839237 0.35030485 0.901059457 1 17.43843159 1.015248865 24.92826808 1.000000255 0.663644216 0.357613836 0.158888883 192.4760535 314651.3801 0.15292434 0.038231085 10.35735507 -1.015248865 -0.336356039 MYS(ph)FDDVLEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 MYSFDDVLEEGK 12 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK 241.52 3.12E-16 88998000 285030 148424 93215 116691 98501 47523 86509 429120 124217 92406 TRUE FALSE 273890.7125 144191.0928 110061.0241 122713.4365 101669.3741 48483.94762 87567.72302 420258.522 110116.4069 86147.25931 3.179331701 1.673774581 1.277591707 1.424461294 1.18018118 0.562803135 1.016488786 4.878373675 1.278234593 1 16.39451728 1.015609754 24.99986697 0.999992645 1.961668315 0.061201326 1.195417063 579.2478448 927693.5389 1.268547357 0.317136839 10.36596537 -1.015609754 0.96167567 SAS(ph)MKLPDNTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASMKLPDNTVK 12 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 S(0.004)AS(0.996)MKLPDNTVK 87.138 0.0064903 164060000 1215300 349560 96272 153540 196800 76022 129530 583520 176790 97538 TRUE FALSE 1167804.732 339590.8911 113670.492 161464.2178 203130.2507 77559.21693 131115.2269 571470.1081 156721.5404 90931.66438 12.84266312 3.734572477 1.25006501 1.775665483 2.233878068 0.852939594 1.441909458 6.284610669 1.723508983 1 16.47249514 1.016258628 24.73285064 0.999996265 3.5498218 0.074225283 3.402275571 494.8453891 752762.6622 3.248490658 0.812122666 10.38146461 -1.016258628 2.549825535 QAS(ph)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK ddPTM_BT-474_Pertuzumab_2h_R1 2 QASPQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK 37 0 F8VPD4;P27708;H7BZB3 F8VPD4;H7BZB3 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 QAS(1)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK;QAS(0.999)PQNLGT(0.001)PGLLHPQTSPLLHSLVGQHILSVQQFTK 329.56 8.55E-129 1157580000 344320 357710 361280 426400 426420 558170 445700 149573 542930 554060 TRUE FALSE 330863.5937 347508.461 426571.3326 448406.5551 440136.1866 569456.5798 451154.6099 146484.2653 481298.8625 516533.0227 0.640546837 0.672771044 0.825835549 0.868108205 0.852096898 1.102459194 0.873428397 0.283591288 0.931787207 1 18.97850106 1.016662169 24.99876779 1.000001094 0.753785052 0.140364558 0.20106785 385.4961642 578369.7955 0.215209377 0.053802344 10.39111542 -1.016662169 -0.246216043 GLIAEAAQLGPVGGVFNLAVVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLIAEAAQLGPVGGVFNLAVVLR 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 121.76 0.00015866 4141100 6910 8533.5 6797.1 7503.3 7047.3 8712.6 8257.2 5975 10065 10086 FALSE TRUE 6639.949561 8290.132935 8025.487171 7890.546212 7273.982805 8888.774741 8358.254084 5851.614162 8922.463396 9402.866236 0.706162291 0.881660201 0.853514978 0.839163933 0.773592075 0.945326087 0.888904923 0.622322387 0.948908893 1 13.19888488 1.016916843 24.99829104 1.000000215 0.813625572 0.34843598 0.089236784 208.5777143 308217.5104 0.088149746 0.022037437 10.39721065 -1.016916843 -0.186374643 QQNDQNRPSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQNDQNRPSEK 11 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 0 78.692 0.026618 55816000 81365 73061 64453 78447 73312 71123 76396 70941 92291 93035 FALSE TRUE 78185.16585 70977.37181 76101.09085 82495.65907 75670.14706 72561.15579 77330.9571 69476.04356 81814.5126 86733.65658 0.901439752 0.818337132 0.877411305 0.951137797 0.872442718 0.836597448 0.891591109 0.801027494 0.943284485 1 16.40430431 1.017012822 7.600739481 0.999969723 0.867162046 0.526553224 0.04080937 0.10004791 28.37053696 0.039826021 0.009978841 10.3995087 -1.017012822 -0.132807677 FHGVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FHGVLK 6 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 93.595 0.04544 285950000 471700 475020 512750 470510 583450 534350 561930 339190 641260 635080 FALSE TRUE 453265.4425 461472.8947 605415.3311 494793.0775 602217.1991 545154.9231 568807.0674 332185.608 568466.8532 592065.4659 0.765566426 0.779428832 1.022547954 0.835706701 1.017146302 0.92076798 0.960716509 0.561062293 0.960141886 1 19.17539718 1.017363143 24.96156532 1.000000763 0.852008811 0.125217468 0.130596689 389.8737961 560487.5494 0.133032172 0.033258043 10.40790078 -1.017363143 -0.147991952 NSLESYAFNMK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSLESYAFNMK 11 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 192.5 3.18E-06 1044710000 668100 652460 577520 649280 575550 658340 623610 678100 773990 780270 FALSE TRUE 641989.9134 633852.4796 681890.7109 682789.4186 594063.0885 671652.0859 631241.9257 664096.998 686129.9 727421.6179 0.88255545 0.871368769 0.937407817 0.938643287 0.816669554 0.923332589 0.867779992 0.91294647 0.943235509 1 19.47243228 1.017421349 1.779675508 0.999321401 0.892213312 0.487505255 0.034849578 0.296317456 1.936871465 0.032027521 0.009173064 10.40929579 -1.017421349 -0.107108089 GHPDLQGQPAEEIFESVGDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GHPDLQGQPAEEIFESVGDR 20 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 ;; 257.75 3.13E-36 1814920000 470620 701970 508490 717910 543090 438610 667330 664090 662180 620250 FALSE TRUE 452227.6501 681950.5029 600385.4543 754961.4211 560558.9831 447478.9947 675496.9842 650376.3094 587012.1025 578239.915 0.782076156 1.179355636 1.038298185 1.305619694 0.969422844 0.773863898 1.168195011 1.124751669 1.015170498 1 19.14130867 1.0174489 24.01896998 0.999999731 1.055019169 0.00338504 0.160338414 764.1351321 1051850.329 0.15094043 0.037735107 10.40995615 -1.0174489 0.055019438 FSEGTSADR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSEGTSADR 9 0 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 74.486 0.095278 438750000 1225600 1218000 1143100 1310400 1363900 1493000 1484500 770990 1588100 1563100 FALSE TRUE 1177702.197 1183263.833 1349683.598 1378029.901 1407771.082 1523189.483 1502667.755 755068.7871 1407825.546 1457229.845 0.808178752 0.811995333 0.926198158 0.945650342 0.966059738 1.045263716 1.031181018 0.518153529 0.966097113 1 20.47479702 1.017659584 24.99824944 1.000001093 0.872395959 0.073822567 0.143314174 523.1671985 740573.4693 0.151246629 0.037811657 10.41500744 -1.017659584 -0.127605134 HS(ph)PATISSSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSPATISSSTR 11 0 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 HS(1)PATISSSTR;HS(1)PATISSSTR 179.98 7.20E-06 285710000 360250 353840 338610 417640 386430 385120 396740 246580 486310 486880 TRUE FALSE 346171.0317 343748.8296 399804.3593 439194.4505 398859.8719 392907.3903 401595.4228 241488.0368 431106.1276 453903.1839 0.762653896 0.757317511 0.880814177 0.967594998 0.878733364 0.865619375 0.884760092 0.53202543 0.949775509 1 18.79202508 1.017759483 24.99983915 1.000000585 0.810165148 0.247410324 0.112039508 277.2231613 390242.7449 0.119222949 0.029805737 10.41740342 -1.017759483 -0.189835437 SVPNT(ph)PLRPNQQSVVNSSFSELFVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVPNTPLRPNQQSVVNSSFSELFVK 25 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 S(0.001)VPNT(0.999)PLRPNQQSVVNSSFSELFVK 187.29 2.26E-17 586150000 533740 285790 149500 196760 190910 125880 160830 471830 186070 140100 TRUE FALSE 512880.8507 277639.549 176517.9756 206914.8072 197050.7935 128425.3798 162798.2856 462086.5456 164948.1137 130610.9022 3.92678438 2.125699649 1.351479644 1.584207778 1.508685647 0.983266922 1.246437188 3.537886484 1.262896978 1 16.9949158 1.018141101 24.98747945 0.999996521 2.009528006 0.135016476 0.923338232 400.4342451 551554.6212 0.921452867 0.230363217 10.42656129 -1.018141101 1.009531485 IYNEIPDINLDVPHSYSVLER ddPTM_BT-474_Pertuzumab_2h_R1 2 IYNEIPDINLDVPHSYSVLER 21 0 Q53EL6;Q53EL6-2 Q53EL6 PDCD4 Programmed cell death protein 4 0 ; 181.61 4.97E-17 288450000 187255 216328 146238 237388 219508 173994 209841 211898 206286 172829 FALSE TRUE 179936.8676 210158.5372 172666.4596 249639.6231 226568.6742 177512.2779 212409.0969 207522.2323 182869.2781 161123.1379 1.116766157 1.304334933 1.071642856 1.549371657 1.406183352 1.101718103 1.318302881 1.287972882 1.134965968 1 17.29780416 1.018203504 3.213928751 1.001202514 1.275336592 0.277461711 0.138634927 0.275324592 6.660420971 0.129759985 0.03397073 10.42805958 -1.018203504 0.274134078 MTNHCVFSANEDHETIR ddPTM_BT-474_Pertuzumab_2h_R1 2 MTNHCVFSANEDHETIR 17 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ; 185.59 3.30E-10 916560000 403600 441990 377940 427090 421810 456520 418520 355190 502540 486780 FALSE TRUE 387826.8658 429384.878 446242.1652 449132.1661 435377.9017 465751.1472 423641.973 347855.2024 445493.766 453809.957 0.854601931 0.946177737 0.983323875 0.989692181 0.959383757 1.026313196 0.933522869 0.76652175 0.981674728 1 18.79172874 1.018381876 24.99940962 1.0000005 0.928875483 0.100756873 0.070202865 473.4996881 643959.0049 0.076267485 0.019066871 10.43234345 -1.018381876 -0.071125018 NSS(ph)PQRPAVSAPVGASEIAEETRPGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSPQRPAVSAPVGASEIAEETRPGQR 27 2 P0CG23 P0CG23 ZNF853 Zinc finger protein 853 1 NS(0.201)S(0.799)PQRPAVSAPVGASEIAEETRPGQR 185.83 6.07E-18 192490000 51208 37716 30273 38119 53290 32089 37202 41592 39491 33558 TRUE FALSE 49206.73475 36640.37661 35744.00452 40086.32616 55004.12125 32737.86157 37657.2892 40733.11067 35008.14724 31285.08677 1.572849553 1.171177081 1.142525344 1.281323797 1.758157861 1.046436655 1.203681789 1.301997689 1.11900432 1 14.93318748 1.018807612 0.634691906 0.996261786 1.331492577 0.225549537 0.197997539 1.345345506 1.288912963 0.200610242 0.084617083 10.44257521 -1.018807612 0.33523079 QPIDIFLSHDWPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPIDIFLSHDWPR 13 0 Q9UK59 Q9UK59 DBR1 Lariat debranching enzyme 0 ; 167.61 3.16E-05 718430000 974560 970560 826630 1035080 1019230 1040930 1063170 832750 1154950 1110450 FALSE TRUE 936473.1178 942880.5791 976020.4293 1088500.603 1052014.459 1061978.318 1076181.392 815553.4215 1023844.918 1035238.232 0.904596728 0.910786087 0.942797898 1.051449385 1.016205184 1.025829886 1.039549505 0.787792989 0.9889945 1 19.98153137 1.019102365 24.99996623 1.000000663 0.955938041 0.031110272 0.075993647 798.1360039 1044546.363 0.080097332 0.020024333 10.44966493 -1.019102365 -0.044062621 YLYPNIDKDHAFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 YLYPNIDKDHAFGK 14 1 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ; 187.16 5.89E-07 2011250000 1803520 1789660 1447190 1347450 1663890 1783040 1842780 1839220 2202800 2374410 FALSE TRUE 1733036.445 1738620.649 1708729.426 1416992.056 1717410.533 1819094.29 1865332.493 1801239.464 1952747.379 2213589.096 0.782907924 0.785430617 0.771927106 0.640133283 0.77584884 0.821784989 0.842673329 0.813718981 0.882163443 1 21.07795601 1.019301797 0.53341761 1.003822376 0.749453294 0.730230445 0.045073205 0.522760376 0.371643394 0.053494857 0.025085157 10.45446463 -1.019301797 -0.254369082 EVLDKNDMVELLGPRPFAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLDKNDMVELLGPRPFAEK 20 2 Q9Y4W6 Q9Y4W6 AFG3L2 AFG3-like protein 2 0 79.568 0.0041668 150680000 140540 231480 152220 245850 165620 178630 233400 235090 189620 149160 FALSE TRUE 135047.5414 224878.417 179729.5401 258538.348 170947.3177 182242.021 236256.419 230235.3093 168095.1326 139057.2603 0.97116498 1.617164156 1.292485841 1.859222218 1.229330402 1.3105538 1.698986579 1.65568708 1.208819533 1 17.08531955 1.019408157 5.899281355 1.000588165 1.475298385 0.2547249 0.250131617 0.169921549 19.98078633 0.230166224 0.057915757 10.45702527 -1.019408157 0.474710219 FLLHEPIVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLLHEPIVNK 10 0 B5MCF9;O00541-2;O00541 B5MCF9 PES1 Pescadillo homolog 0 113.22 0.0015171 161080000 295990 308780 279450 261620 302500 280580 277750 295270 350930 348960 FALSE TRUE 284422.3836 299973.8967 329952.8313 275122.2396 312230.1872 286253.5198 281149.1876 289172.5713 311093.8976 325324.6284 0.874272523 0.922075584 1.014226414 0.84568525 0.959749616 0.879901166 0.8642112 0.8888739 0.956256829 1 18.31152052 1.019530426 4.362795689 0.999654221 0.906477958 0.292748952 0.047183209 0.209577818 10.36014124 0.044410106 0.01131331 10.45996969 -1.019530426 -0.093176263 KAESGWFHVEEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAESGWFHVEEDR 13 1 O43719;Q5H919;Q5H918 O43719 HTATSF1 HIV Tat-specific factor 1 0 102.64 0.0010865 172570000 103240 105060 93731 124060 101410 100680 100700 103530 153720 175450 FALSE TRUE 99205.26666 102063.7917 110670.2767 130462.7515 104671.9447 102715.8186 101932.3967 101392.0693 136270.35 163566.6152 0.606512928 0.623989141 0.676606755 0.797612345 0.639934651 0.627975449 0.623185829 0.61988242 0.833118359 1 17.31951879 1.019774983 3.539663376 0.9985736 0.652853272 0.817835681 0.052825844 0.083833617 2.508077148 0.054584646 0.014140418 10.46586149 -1.019774983 -0.345720328 HKTFVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HKTFVEK 7 1 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 71.379 0.032731 394130000 532980 649680 491020 527360 505180 613950 640460 451840 684290 665470 FALSE TRUE 512150.5524 631151.7625 579758.2367 554577.1128 521429.5735 626364.4897 648298.1411 442509.3461 606612.268 620397.1242 0.825520513 1.017335087 0.934495365 0.893906647 0.840477096 1.009618622 1.044972834 0.713267887 0.977780593 1 19.24283247 1.019944605 24.99913334 1.00000068 0.907736027 0.100365828 0.095516639 439.9519675 551446.3976 0.092908843 0.023227211 10.46994994 -1.019944605 -0.092264654 KHNMCGETEEEK ddPTM_BT-474_Pertuzumab_2h_R1 7 KHNMCGETEEEK 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;; 193.85 1.48E-06 845374000 1188122 879873 874158 939119 1049247 1133314 1287685 498576.6 1550309 1599167 FALSE TRUE 1141688.879 854779.8835 1032137.796 987587.0441 1082996.983 1156230.386 1303444.074 488280.819 1374324.422 1490853.995 0.765795231 0.573349159 0.69231313 0.662430424 0.72642726 0.775549041 0.874293579 0.327517531 0.921837032 1 20.50770754 1.020539273 24.99576211 1.00000049 0.666916607 0.40945488 0.138829544 176.2087263 214440.7053 0.135163136 0.033790784 10.48429599 -1.020539273 -0.333083883 IKENSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKENSEK 7 1 P17980;E9PKD5;E9PLG2;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 88.177 0.017145 363830000 725350 638710 506850 599630 636550 672990 751670 730410 810650 931300 FALSE TRUE 697002.5201 620494.6162 598449.0698 630576.9762 657025.2088 686598.3189 760869.1623 715326.7783 718628.4105 868222.2215 0.802792768 0.714672581 0.689280987 0.72628523 0.756747746 0.790809429 0.876353016 0.823898261 0.827701011 1 19.72770482 1.020895167 0.343525097 1.01962848 0.711506364 0.78651887 0.039772326 0.725841671 0.252843027 0.082074849 0.046978326 10.49289113 -1.020895167 -0.308122116 LDALVAEEHLTVDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDALVAEEHLTVDAR 15 0 A6NFX8;Q9UKK9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ;;; 220.14 1.71E-12 1367020000 1696760 1680190 1455330 1669230 1617750 1216540 1670920 1608100 2032960 2115090 FALSE TRUE 1630448.743 1632272.626 1718340.505 1755379.16 1669786.398 1241139.272 1691369.219 1574892.173 1802186.904 1971833.07 0.82686956 0.827794528 0.871443192 0.890227062 0.846819349 0.629434251 0.857764911 0.798694472 0.913965249 1 20.91110599 1.021008507 3.437542385 0.999447959 0.818732412 0.421585864 0.068411331 0.200720856 5.596382198 0.066586503 0.017303357 10.49562988 -1.021008507 -0.180715547 ELAEAAKEPLPVEQDDDIEVIVDET(ph)SDHTEETSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVR 36 1 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5;C9J1B2;C9JAY7;C9JK97 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 ELAEAAKEPLPVEQDDDIEVIVDET(0.236)S(0.236)DHT(0.197)EET(0.165)S(0.165)PVR 100.18 0.00019453 24935000 33664 32607 27179 27807 30567 41474 30376 34428 34257 30135 TRUE FALSE 32348.37366 31677.08029 32090.84989 29242.1226 31550.21532 42312.6327 30747.75057 33717.04977 30368.28898 28093.92961 1.151436418 1.127541812 1.14226989 1.04086979 1.123026068 1.506113003 1.094462434 1.200154277 1.080955544 1 14.77797081 1.021074357 3.679101271 1.000423173 1.172972597 0.180996828 0.118955711 0.339057485 11.02001852 0.114279792 0.029496206 10.49722139 -1.021074357 0.172549425 GCHLLVATPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GCHLLVATPGR 11 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 119.22 0.00061494 1931180000 1810670 2148130 1689410 1883240 1830810 1843930 2300440 1639870 2488940 2450380 FALSE TRUE 1739907.015 2086867.436 1994723.968 1980434.242 1889699.666 1881215.528 2328593.473 1606006.111 2206405.966 2284413.58 0.761642738 0.913524352 0.873188631 0.866933317 0.827214338 0.823500414 1.019339709 0.703027738 0.965852237 1 21.12339244 1.021126161 24.99801437 1.000000201 0.850644267 0.314455139 0.080114481 207.8385274 245928.8697 0.071781066 0.017945266 10.49847361 -1.021126161 -0.149355934 SS(ph)MSLYTAASVIDTASK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSMSLYTAASVIDTASK 17 0 Q96PE2;A0A2R8Y4D7 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.006)S(0.994)MSLYTAASVIDTASK 497.45 1.10E-219 0 106570 116770 101550 100800 96051 93913 101190 140400 113240 104510 TRUE FALSE 102405.1266 113439.8339 119902.344 106002.3001 99140.56765 95811.9852 102428.3935 137500.6909 100385.4699 97431.44461 1.051048016 1.164304136 1.230632928 1.087968063 1.017541801 0.983378473 1.051286819 1.411255796 1.030319014 1 16.57209984 1.02162891 24.99953192 0.999998871 1.135631229 0.118163242 0.118102689 396.6521246 458464.3839 0.125070736 0.031267684 10.51063391 -1.02162891 0.135632357 GLKPSCTIIPLMK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLKPSCTIIPLMK 13 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 122.64 0.00021222 1020690000 1412030 1408480 1122720 1238330 1185840 1327110 1376270 1394050 1637160 1676920 FALSE TRUE 1356846.307 1368311.529 1325620.479 1302240.36 1223983.621 1353945.073 1393113.204 1365262.38 1451316.46 1563340.715 0.867914648 0.875248445 0.847940866 0.832985636 0.782928257 0.866058858 0.891112981 0.873298039 0.928343033 1 20.5762008 1.021805016 0.886355661 0.999962312 0.84521622 0.765194086 0.026457914 0.30650004 0.52806641 0.027018378 0.009486275 10.51489684 -1.021805016 -0.154746092 SSFDWLTGSSTDPLVDHT(ph)SPSSDSLLFAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.589)S(0.408)PS(0.001)S(0.001)DSLLFAHK 176.98 3.24E-17 330020000 219280 233060 196360 248550 251280 259740 252910 170290 295280 289390 TRUE FALSE 210710.2952 226413.357 231846.62 261377.6953 259362.6494 264992.1208 256005.1882 166773.452 261761.0523 269789.3575 0.781017817 0.839222715 0.859361622 0.968821371 0.961352411 0.982218584 0.948907661 0.618161715 0.970242321 1 18.04147391 1.021859173 24.99900491 1.000000965 0.865505198 0.164378945 0.104634762 354.2427954 405124.5408 0.111149817 0.027787454 10.51620814 -1.021859173 -0.134495768 HTNPSSS(ph)SPGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HTNPSSSSPGTR 12 0 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 1 HTNPS(0.099)S(0.099)S(0.492)S(0.308)PGT(0.002)R;HTNPS(0.069)S(0.069)S(0.431)S(0.431)PGTR 74.46 0.038229 29540000 41993 44786 45660 49205 48771 56559 49067 33795 58712 57250 TRUE FALSE 40351.86713 43508.74713 53911.7777 51744.47595 50339.76351 57702.66173 49667.49662 33097.12144 52047.2599 53372.40651 0.756043615 0.815191781 1.010105806 0.969498648 0.943179572 1.081132846 0.930583796 0.620116716 0.975171691 1 15.70380644 1.022247611 24.99453538 1.000001263 0.885823731 0.087202806 0.1258246 501.1423083 563016.7071 0.134310415 0.033577604 10.52561816 -1.022247611 -0.114177531 DGNVLLHEMQIQHPTASLIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGNVLLHEMQIQHPTASLIAK 21 0 P40227 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 283.48 2.12E-45 6639100000 2805200 3023600 2651600 2971800 2856000 3320400 3093200 2000050 3837500 3796300 FALSE TRUE 2695569.683 2937369.888 3130803.105 3125174.954 2947865.834 3387540.763 3131055.507 1958748.269 3401883.088 3539173.22 0.761638246 0.829959345 0.884614262 0.883024017 0.832924994 0.957155966 0.884685578 0.55344798 0.961208417 1 21.75498094 1.022671891 24.97881521 1.000000915 0.818290769 0.274334995 0.102947822 251.5020436 277092.0915 0.108627621 0.027156905 10.53590608 -1.022671891 -0.181710146 FQEMIETTLDMDQVENHEFLVKPSFDPNLSELR ddPTM_BT-474_Pertuzumab_2h_R1 1 FQEMIETTLDMDQVENHEFLVKPSFDPNLSELR 33 1 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 104.98 6.77E-06 194690000 20073 24909 17361 21367 24231 25524 20622 18413 26672 25836 FALSE TRUE 19288.52497 24198.61971 20498.51889 22469.75343 25010.41212 26040.11277 20874.3782 18032.76512 23644.30638 24086.10471 0.800815458 1.004671366 0.851051639 0.93289279 1.038375131 1.081125947 0.866656458 0.74867918 0.981657543 1 14.55591347 1.022984696 24.99992866 1.00000073 0.912772386 0.085343615 0.09917978 502.3639872 546407.8203 0.103667449 0.025916862 10.54349742 -1.022984696 -0.087228344 STPDGTEHGEFLALDLGGTNFR ddPTM_BT-474_Pertuzumab_2h_R1 2 STPDGTEHGEFLALDLGGTNFR 22 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 207.22 8.34E-23 358770000 288270 294270 261800 346120 289050 332030 326360 309180 322980 271120 FALSE TRUE 277004.0897 285877.7077 309113.0837 363983.2947 298347.5558 338743.8741 330354.0913 302795.325 286316.6644 252756.8009 1.095931301 1.131038637 1.222966435 1.440053416 1.180373999 1.340196873 1.307003769 1.197971029 1.132775314 1 17.94739039 1.023296552 1.911418146 1.002438651 1.248038692 0.3848956 0.095900914 0.352335697 2.676596178 0.093858314 0.026565176 10.55107117 -1.023296552 0.24560004 RTS(ph)MGGTQQQFVEGVR ddPTM_BT-474_Pertuzumab_2h_R1 3 RTSMGGTQQQFVEGVR 16 1 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0 A0A2R8Y804 CTNNB1 Catenin beta-1 1 RT(0.212)S(0.788)MGGTQQQFVEGVR;RT(0.193)S(0.807)MGGTQQQFVEGVR;RT(0.209)S(0.791)MGGTQQQFVEGVR 275.76 1.74E-35 2910120000 389915 631150 323726 744400 371225 405290 505330 661220 465350 412599 TRUE FALSE 374676.6907 613150.22 382230.4894 782818.5732 383165.7893 413485.2415 511514.3797 647565.5759 412525.4189 384653.3022 0.974063367 1.594033423 0.993701308 2.035127656 0.996132848 1.074955653 1.329806287 1.683504528 1.07246036 1 18.55319917 1.023818503 24.70189253 0.999999456 1.353348825 0.114041592 0.333259403 312.9817486 324588.4254 0.303047971 0.075761993 10.56375945 -1.023818503 0.353349368 ERDAAIMK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDAAIMK 8 1 A0A0D2X7Z3;Q49AN0-2;Q49AN0 A0A0D2X7Z3 CRY2 Cryptochrome-2 0 68.383 0.051665 579990000 383220 636000 366470 689750 302250 238440 749880 555110 470690 366890 FALSE TRUE 368243.3387 617861.9027 432699.2811 725348.0802 311972.1457 243261.4202 759057.2558 543646.7845 417259.2445 342040.2135 1.076608317 1.806401348 1.265053827 2.120651466 0.91209201 0.711207076 2.219204719 1.589423591 1.219912829 1 18.38380643 1.024074457 4.758570259 1.002061834 1.486568239 0.090032908 0.469128017 0.376038799 22.39453379 0.443390082 0.112428997 10.56998708 -1.024074457 0.484506405 HGGSDNASTDCER ddPTM_BT-474_Pertuzumab_2h_R1 1 HGGSDNASTDCER 13 0 O43847;O43847-2;F5H7V1;G3V1R5 O43847 NRD1 Nardilysin 0 86.756 0.0086804 44552000 25656 27027 24812 30271 28169 31797 27939 18802 34160 33280 FALSE TRUE 24653.33516 26256.21642 29296.08034 31833.28994 29075.08147 32439.95713 28280.92584 18413.73213 30282.30001 31025.91596 0.794604588 0.846267245 0.944245462 1.026022567 0.937122421 1.04557613 0.911525896 0.593495198 0.976032426 1 14.92118618 1.02409307 24.99980462 1.000001671 0.880084484 0.098199336 0.121502167 459.3075962 476591.8172 0.132431282 0.033107821 10.5704401 -1.02409307 -0.119917187 SLENYHFVDEHGK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLENYHFVDEHGK 13 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 190.86 2.35E-06 2222900000 1818090 1986510 1654330 2124840 1758630 1739290 2010080 891060 2745590 2785110 FALSE TRUE 1747037.033 1929856.68 1953304.231 2234503.247 1815197.931 1774459.635 2034679.96 872659.2996 2433922.134 2596472.019 0.672850322 0.743261112 0.752291655 0.860592077 0.699101673 0.683411807 0.783632539 0.336094244 0.937395865 1 21.30812125 1.024227796 24.99989473 1.000000853 0.684865973 0.422199832 0.130606883 178.4058531 184090.7026 0.13548538 0.033871345 10.57371976 -1.024227796 -0.31513488 VNEIVETNRPDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNEIVETNRPDSK 13 1 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 87.519 0.0075971 300170000 183850 168640 134580 157800 178690 148250 175560 184310 192570 203670 FALSE TRUE 176664.9387 163830.5523 158901.5997 165944.0769 184437.7261 151247.7166 177708.5558 180503.9341 170710.2609 189875.2495 0.930426368 0.862832585 0.836873685 0.873963707 0.971362653 0.796563623 0.935922698 0.950644882 0.899065367 1 17.53469233 1.024266278 0.492665893 1.000765215 0.875875846 0.307631603 0.050122793 1.200290078 0.747617611 0.058407601 0.028733569 10.57465672 -1.024266278 -0.124889369 HLVYESDQNK ddPTM_BT-474_Pertuzumab_2h_R1 5 HLVYESDQNK 10 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;; 204.34 1.89E-07 3565930000 5833380 5652110 5306790 5671150 5318260 4802680 6503370 5050520 7208770 7272540 FALSE TRUE 5605405.06 5490917.357 6265845.002 5963838.731 5489326.663 4899793.48 6582960.187 4946224.997 6390460.651 6779964.388 0.826760251 0.80987407 0.924170784 0.879626852 0.809639454 0.7226872 0.970943181 0.729535542 0.94255077 1 22.69284626 1.024391788 11.18098211 0.999998274 0.834917107 0.372267502 0.073145094 0.421083355 189.2916172 0.066593601 0.016653097 10.57771321 -1.024391788 -0.165081166 IHQETFGK ddPTM_BT-474_Pertuzumab_2h_R1 5 IHQETFGK 8 0 Q15393;Q15393-2;J3QL37 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;;;; 133.23 0.00092812 2983170000 3976130 4085330 3536590 3997520 4166890 4412800 4319470 3098080 5127130 5003350 FALSE TRUE 3820738.444 3968820.388 4175730.484 4203832.486 4300921.801 4502029.839 4372332.966 3034103.565 4545119.697 4664468.648 0.819115473 0.850862271 0.895221042 0.901245737 0.922060394 0.965175281 0.937369998 0.650471424 0.974413173 1 22.15328132 1.025445959 24.99944316 1.000001044 0.863699298 0.250029869 0.083158134 261.157925 256574.3495 0.087609784 0.021902446 10.60341987 -1.025445959 -0.136301747 LSGFS(ph)FK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSGFSFK 7 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FK;LSGFS(1)FK 119.68 0.0049587 613570000 4850800 1705020 645990 922670 1136450 455220 614660 3988900 920460 646820 TRUE FALSE 4661225.373 1656394.499 762734.763 970289.1093 1173004.946 464424.8603 622182.3929 3906527.821 815973.2397 603010.3053 7.729926557 2.74687594 1.264878488 1.609075501 1.94524859 0.770177319 1.031793964 6.47837655 1.353166327 1 19.20182313 1.025510438 24.99991501 0.999978868 2.887120862 0.092649799 2.223632941 471.6730859 462232.1774 2.193200938 0.548300235 10.60499427 -1.025510438 1.887141993 VHFEESSK ddPTM_BT-474_Pertuzumab_2h_R1 6 VHFEESSK 8 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;;; 156.01 0.00039986 7013800000 10293810 9480420 10293400 10944050 9741500 6514520 11669800 8711030 13048900 13422000 FALSE TRUE 9891516.525 9210047.704 12153646.36 11508873.73 10054844.19 6646248.058 11812618.5 8531144.186 11567643.58 12512915.98 0.79050451 0.736043278 0.971288097 0.919759531 0.803557237 0.531151018 0.94403403 0.681787059 0.924456265 1 23.5769147 1.025885274 8.659732712 0.999974662 0.798096564 0.230518135 0.124429352 0.271857959 78.38217144 0.11788583 0.029506811 10.61415131 -1.025885274 -0.201878098 LSGFS(ph)FKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSGFSFKK 8 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FKK;LSGFS(1)FKK 96.103 0.005622 2838700000 20076500 6597400 1984830 2541500 3352300 1399470 1796290 12613900 2898500 1952410 TRUE FALSE 19291888.18 6409248.612 2343532.933 2672667.12 3460129.774 1427768.242 1818273.534 12353418.56 2569474.432 1820171.532 10.59893963 3.521233301 1.28753411 1.468360027 1.900991041 0.784414116 0.998957243 6.786952956 1.411666091 1 20.79564298 1.026103642 24.99534276 0.999981223 3.261240228 0.08188963 2.941987155 506.1617049 484669.5607 2.857373366 0.714343341 10.61948955 -1.026103642 2.261259005 HLPDNECIEK ddPTM_BT-474_Pertuzumab_2h_R1 3 HLPDNECIEK 10 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 171.74 3.93E-06 2337640000 5509530 5417710 4383680 5188820 5304580 5436720 5565280 4275130 6921450 6793330 FALSE TRUE 5294211.476 5263202.215 5175908.49 5456615.622 5475206.633 5546654.203 5633389.561 4186847.072 6135756.013 6333211.708 0.835944181 0.831047888 0.817264404 0.861587434 0.864522913 0.875804325 0.889499644 0.661093812 0.968822186 1 22.59450588 1.026331677 24.9903784 1.000000272 0.82695075 0.51438006 0.060506546 142.5984831 135334.2252 0.062037596 0.015509399 10.62506698 -1.026331677 -0.173049523 VDLNSNGFICDYELHELFK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDLNSNGFICDYELHELFK 19 0 P13797;U3KQI3 P13797 PLS3 Plastin-3 0 249.06 5.76E-25 235190000 185360 160840 155170 145870 176690 178830 189230 182220 231930 239030 FALSE TRUE 178115.9263 156253.0007 183212.6707 153398.3682 182373.3943 182446.0651 191545.8533 178457.0933 205602.2787 222840.2852 0.799298592 0.7011883 0.82217033 0.688378082 0.818404061 0.818730172 0.859565644 0.800829586 0.92264412 1 17.76565054 1.026992561 0.393447581 1.017082493 0.745736581 0.702492614 0.047753263 0.700181324 0.302401937 0.070195932 0.038490008 10.64124791 -1.026992561 -0.271345912 DVHLELK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVHLELK 7 0 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;E5RHA5;A0A2R8YF29;Q8TE04-3;Q9H999;Q8TE04-2;Q8TE04-4;Q8TE04 V9GYZ0;Q8TE04 PANK2;PANK3;PANK1 "Pantothenate kinase 2, mitochondrial;Pantothenate kinase 1;Pantothenate kinase 3" 0 ; 111.01 0.0066756 636390000 847600 847480 764450 759940 838920 840390 887010 766700 1040880 1008660 FALSE TRUE 814474.8549 823310.7002 902603.1201 799160.5945 865904.6237 857383.2616 897865.4937 750867.3771 922723.6661 940342.5598 0.866146966 0.875543377 0.959866286 0.849861134 0.920839554 0.911777578 0.954828094 0.798504087 0.981263324 1 19.84282689 1.027678265 24.43378992 1.000000085 0.892345688 0.424890555 0.046078688 121.3615509 107134.9198 0.043240255 0.010810064 10.65806255 -1.027678265 -0.107654397 VALGHGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VALGHGLK 8 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 85.265 0.016865 719820000 1170600 1218400 1177800 1079800 1090000 923770 1198500 1254100 1367800 1428800 FALSE TRUE 1124851.658 1183652.425 1390654.66 1135528.607 1125060.84 942449.2623 1213167.602 1228202.397 1212533.078 1332026.103 0.844466677 0.888610532 1.04401457 0.852482248 0.844623718 0.707530626 0.910768639 0.922055802 0.91029228 1 20.34519092 1.027811275 1.230107569 0.995099601 0.872986591 0.192770464 0.078565816 0.86064927 2.690032261 0.078505478 0.024438986 10.66132727 -1.027811275 -0.12211301 KLLDIVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLLDIVAR 8 1 Q12931-2;Q12931 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 111.61 0.0088886 0 62665 104790 63039 125050 70235 45966 111790 97411 85800 72048 FALSE TRUE 60215.98252 101801.4918 74431.54959 131503.8455 72494.17256 46895.46401 113158.1195 95399.42881 76060.3437 67168.12479 0.896496407 1.515622062 1.108137972 1.957831128 1.079294275 0.698180337 1.684699697 1.420308057 1.132387482 1 16.03548913 1.028173293 5.513002193 1.000774711 1.314633421 0.066403948 0.354305503 0.397700703 33.45062055 0.330597071 0.083349008 10.67021801 -1.028173293 0.31385871 RVS(ph)VCAETYNPDEEEEDTDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVSVCAETYNPDEEEEDTDPR 21 1 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 1 RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR 201.08 4.36E-22 1028350000 1452110 606430 241620 622360 280570 155757 257660 922370 302020 227950 TRUE FALSE 1395359.936 589135.2102 285286.1088 654480.0742 289594.7889 158906.5133 260813.3202 903322.7372 267735.9558 212510.7435 6.566067734 2.77226083 1.342454994 3.079750527 1.36273011 0.747757552 1.227294752 4.250715622 1.259870214 1 17.69717625 1.028195463 24.81215735 0.999993988 2.561166627 0.120594632 1.649135334 359.6088348 316456.4219 1.587813854 0.396953464 10.67076273 -1.028195463 1.561172639 ECLQALEFLHANQVIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ECLQALEFLHANQVIHR 17 0 Q13177;H7C1X3 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 ; 242.42 1.21E-20 1924210000 760660 894910 848980 989080 986600 984610 993840 486110 1086930 1050380 FALSE TRUE 730932.5662 869388.043 1002409.571 1040126.537 1018334.885 1004519.489 1006002.911 476071.6586 963546.2632 979236.827 0.746430839 0.887822046 1.023664086 1.062180781 1.039927071 1.025818741 1.027333617 0.486166008 0.983976742 1 19.90129829 1.028282331 24.99981942 1.000004771 0.902289338 0.031752715 0.1696457 716.6938729 633510.3921 0.182633437 0.045661221 10.67289731 -1.028282331 -0.097715433 YSHSGSSS(ph)PDTK ddPTM_BT-474_Pertuzumab_2h_R1 5 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHSGS(0.001)S(0.034)S(0.965)PDTK;YSHSGSS(0.014)S(0.985)PDTK;YSHSGS(0.004)S(0.456)S(0.54)PDTK;YSHSGS(0.034)S(0.064)S(0.902)PDTK;YS(0.001)HS(0.004)GS(0.005)S(0.137)S(0.854)PDTK 222.73 2.53E-11 7254233000 10821640 10714251 9060824 9452130 9705409 10521202 10528296 9333127 12813200 12781530 TRUE FALSE 10398718.34 10408691.05 10698316.45 9939955.562 10017592.29 10733947.91 10657144.44 9140394.666 11358699.25 11915825.59 0.872681315 0.873518245 0.89782419 0.834181022 0.840696452 0.900814453 0.894368951 0.767080266 0.95324484 1 23.50637558 1.028360846 10.75980378 0.999997075 0.858867053 0.614284443 0.03782577 0.25306635 93.53945481 0.038094605 0.009527063 10.67482701 -1.028360846 -0.141130021 RVAIFIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVAIFIEK 8 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 111.46 0.0051792 1191040000 1626190 1700770 1369800 1379950 1408400 1231340 1417510 1641720 1834920 1962890 FALSE TRUE 1562636.697 1652265.705 1617353.331 1451169.385 1453702.465 1256238.538 1434857.911 1607817.908 1626627.574 1829941.712 0.853927033 0.902906193 0.883827786 0.793013994 0.794398234 0.686491012 0.784100336 0.878617006 0.888895839 1 20.80336627 1.028746508 1.553129071 0.996034434 0.816393321 0.47701432 0.05879266 0.38095537 1.871029905 0.062419667 0.018366967 10.68431067 -1.028746508 -0.179641113 KVEAPETNIDKT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEAPETNIDKTPK 14 2 O75152;E9PBY7;E9PQ61 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 KVEAPETNIDKT(1)PK 213.03 7.64E-08 446210000 1691600 777530 606750 371830 497750 354000 428320 1425500 578540 498990 TRUE FALSE 1625490.402 755355.6057 716403.2221 391020.1909 513760.5808 361158.1225 433561.9083 1396062.927 512866.5646 465192.9628 3.49422827 1.623746845 1.540013025 0.840554828 1.104403166 0.776361965 0.932004443 3.001040511 1.102481348 1 18.82746975 1.028885276 24.96592881 0.99998714 1.641918383 0.074569359 0.864479708 498.7772426 431098.2407 0.858865508 0.214716377 10.68772512 -1.028885276 0.641931243 ALRPPTS(ph)PGVFGALQNFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALRPPTSPGVFGALQNFK 18 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ALRPPT(0.409)S(0.591)PGVFGALQNFK 114.84 0.00012506 376040000 187490 195530 148360 211870 210390 154550 165820 194080 161990 132500 TRUE FALSE 180162.6835 189953.6758 175171.9523 222804.6361 217157.3854 157675.1069 167849.3548 190072.1802 143601.5743 123525.657 1.458504151 1.537766975 1.418101766 1.803711403 1.757994175 1.276456331 1.358821793 1.538726325 1.162524271 1 16.9144512 1.029247234 0.721123859 0.990443945 1.562504507 0.557012536 0.15703842 0.570721613 0.684810774 0.16030423 0.06279764 10.6966364 -1.029247234 0.572060563 MGANSLER ddPTM_BT-474_Pertuzumab_2h_R1 2 MGANSLER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 118.32 0.0044398 474990000 525970 497930 545170 583970 480550 459140 549790 572950 654190 676340 FALSE TRUE 505414.5109 483729.5239 643694.3462 614108.7617 496007.3272 468424.1254 556518.4945 561118.3823 579929.0938 630530.8894 0.801569787 0.767178154 1.020876783 0.973955078 0.786650322 0.742904326 0.882618923 0.889914185 0.919747317 1 19.26620752 1.030161408 1.394766803 0.997836022 0.855944754 0.226811626 0.083939467 0.719264818 2.855529089 0.085027899 0.025623207 10.71917617 -1.030161408 -0.141891268 HDAATCFVDAGNAFK ddPTM_BT-474_Pertuzumab_2h_R1 4 HDAATCFVDAGNAFK 15 0 P54920;M0R2M1;M0R058;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;; 200.16 7.06E-09 2012320000 1996550 1844010 1642450 1877070 1890620 2009290 1912260 1437650 2387820 2318830 FALSE TRUE 1918522.619 1791420.64 1939277.251 1973945.808 1951433.509 2049919.22 1935662.81 1407962.025 2116764.684 2161773.579 0.887476208 0.828680977 0.897076951 0.913114041 0.902700231 0.94825806 0.895404972 0.651299488 0.979179644 1 21.04378399 1.030423042 24.99998726 1.000001586 0.859188185 0.288760739 0.077737099 215.8961084 177410.903 0.083311875 0.020827992 10.72563571 -1.030423042 -0.1408134 EWSGLLEELAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EWSGLLEELAR 11 0 Q01813;Q01813-2;Q5VSR5;V9GYV7 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;; 172.88 2.99E-05 425114000 306776 325476 253606 326322 328762 308321 292005 317156 311094 264094 FALSE TRUE 294786.8548 316193.7432 299438.2456 343163.5175 339336.9283 314555.4619 295578.6445 310606.6178 275779.9133 246206.6781 1.197314618 1.284261441 1.216206838 1.393802638 1.378260455 1.277607351 1.200530574 1.261568614 1.120115488 1 17.90951037 1.031030644 1.089964186 0.998222419 1.290703597 0.674490423 0.063026224 0.311117457 0.778229047 0.061780241 0.019984119 10.74065197 -1.031030644 0.292481178 KHEDFDK ddPTM_BT-474_Pertuzumab_2h_R1 4 KHEDFDK 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 126.52 0.0025602 2255500000 4331130 3866140 3435920 3476620 3630130 3908110 4220800 2859390 5342210 5253700 FALSE TRUE 4161864.651 3755881.473 4056867.176 3656048.775 3746896.428 3987134.662 4272455.413 2800342.597 4735784.717 4897862.219 0.849730855 0.766840982 0.828293446 0.746458069 0.765006499 0.814056109 0.872310249 0.571747932 0.966908522 1 22.22372076 1.031220558 24.62306888 1.000000155 0.772609641 0.526446964 0.078630023 102.0993928 80523.50481 0.076536399 0.0191341 10.74534981 -1.031220558 -0.227390514 RDHALLEEQSK ddPTM_BT-474_Pertuzumab_2h_R1 3 RDHALLEEQSK 11 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 126.19 0.0002029 2423690000 1516740 1510430 1572250 1773660 1484390 999030 1876220 1516200 2275840 2552370 FALSE TRUE 1457464.124 1467354.015 1856390.55 1865198.805 1532136.752 1019231.071 1899181.742 1484889.94 2017496.184 2379495.706 0.612509667 0.616665965 0.780161336 0.783863068 0.643891371 0.428339109 0.798144639 0.624035562 0.847867125 1 21.18222442 1.031236199 3.339303436 0.999234657 0.663808861 0.52616628 0.104493686 0.165447577 4.183944041 0.100124904 0.026121757 10.7457368 -1.031236199 -0.335425797 HEELMLGDPCLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HEELMLGDPCLK 12 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 150.68 6.08E-05 1838550000 1928740 1992360 1756220 1941770 1940430 1978780 2059510 1279260 2572700 2514200 FALSE TRUE 1853362.708 1935539.844 2073608.021 2041984.982 2002845.693 2018792.287 2084714.899 1252842.834 2280657.882 2343910.995 0.790713774 0.82577361 0.884678653 0.871187083 0.8544888 0.861292213 0.889417262 0.53450956 0.973013859 1 21.16048636 1.031435998 24.99999116 1.000002207 0.808147526 0.329870994 0.098437793 191.6699935 152428.1267 0.103398916 0.025849729 10.75068156 -1.031435998 -0.191854681 VDEHLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDEHLAK 7 0 P12429;D6RA82;D6RFJ9 P12429 ANXA3 Annexin A3;Annexin 0 ; 102.72 0.0085375 1248100000 2214500 2274700 2113070 2160400 2032800 1871290 2037500 2099670 2742900 2841600 FALSE TRUE 2127954.892 2209827.783 2494948.754 2271898.503 2098186.858 1909128.766 2062435.534 2056311.081 2431537.491 2649135.901 0.80326377 0.834169279 0.941797192 0.857599832 0.792026886 0.720660939 0.77853142 0.776219551 0.917860609 1 21.33709043 1.032285279 4.318444064 0.99918013 0.812722535 0.547374578 0.055502396 0.14406168 6.326098423 0.060075904 0.015319299 10.77172552 -1.032285279 -0.186457595 SQS(ph)MDAMGLSNK ddPTM_BT-474_Pertuzumab_2h_R1 4 SQSMDAMGLSNK 12 0 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 SQS(1)MDAMGLSNK;SQS(1)MDAMGLSNK;S(0.001)QS(0.999)MDAMGLSNK;SQS(1)MDAMGLSNK 213.29 1.08E-08 1848880000 3074170 3258390 3037690 2874180 3645510 3099430 2743420 3652250 3145520 2661800 TRUE FALSE 2954028.038 3165463.907 3586668.156 3022516.774 3762771.14 3162102.598 2776994.795 3576829.761 2788453.757 2481513.915 1.19041365 1.275618036 1.445354843 1.218013228 1.51632079 1.274263497 1.119072828 1.441390169 1.123690558 1 21.24278911 1.032524433 5.923223827 1.000467319 1.312223928 0.430791034 0.118344524 0.130271152 12.42091532 0.108272729 0.027243266 10.77765885 -1.032524433 0.311756609 HELS(ph)PPQKR ddPTM_BT-474_Pertuzumab_2h_R1 9 HELSPPQKR 9 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR 128.85 0.00019085 19189420000 3123430 3020710 3000520 3303100 3194070 3165800 3459390 2176670 4124540 4009150 TRUE FALSE 3001362.902 2934562.308 3542780.71 3473573.387 3296810.162 3229814.645 3501727.05 2131721.004 3656339.511 3737606.7 0.803017317 0.785144758 0.947874133 0.929357652 0.882064494 0.864139784 0.93689019 0.570343852 0.978256891 1 21.83368333 1.032801087 24.99999378 1.000002858 0.83454496 0.247076935 0.104248766 222.6561817 169701.1104 0.107402229 0.026850557 10.78452663 -1.032801087 -0.165457898 ASPRPWT(ph)PEDPWSLYGPSPGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPRPWTPEDPWSLYGPSPGGR 22 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 ASPRPWT(1)PEDPWSLYGPSPGGR;ASPRPWT(1)PEDPWSLYGPSPGGR 132.28 1.75E-05 202180000 174027 178510 137717 165722 183419 178760 163460 174522 182552 161169 TRUE FALSE 167225.8324 173419.0696 162605.5254 174274.9323 189318.8387 182374.6497 165460.4724 170918.0597 161829.4623 150252.8801 1.112962576 1.154181334 1.08221237 1.159877482 1.260001396 1.213784718 1.101213316 1.137535997 1.077047323 1 17.19703312 1.033731934 1.225542973 1.00083728 1.159499695 0.502399228 0.049156824 0.418689067 1.299869627 0.049851742 0.015544778 10.80766648 -1.033731934 0.158662414 RIS(ph)LTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RISLTK 6 1 A0A0A0MRX4;Q3MIN7;Q3MIN7-2 A0A0A0MRX4 RGL3 Ral guanine nucleotide dissociation stimulator-like 3 1 RIS(1)LTK 93.162 0.028134 150630000 107220 106380 79444 92774 99892 91747 94795 118210 98451 91563 TRUE FALSE 103029.7239 103346.1466 93801.29802 97562.07726 103105.1169 93602.1872 95955.12957 115768.9222 87275.25522 85361.35645 1.206983208 1.210690069 1.098873096 1.142930259 1.20786643 1.096540532 1.124105023 1.356221679 1.022421138 1 16.38129548 1.034217525 24.90972283 0.99999957 1.182019613 0.472048598 0.071806468 127.1181955 92539.26788 0.072920782 0.018230196 10.81975746 -1.034217525 0.182020043 EGYGLSWNPNLSGHLLSASDDHTICLWDISAVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGYGLSWNPNLSGHLLSASDDHTICLWDISAVPK 34 0 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 124.82 4.51E-08 438590000 315400 370810 275570 343930 341550 368840 365740 212820 434840 421730 FALSE TRUE 303073.8193 360234.8619 325371.629 361680.2685 352536.2659 376298.1975 370216.0355 208425.1926 385478.7862 393165.8515 0.77085489 0.916241481 0.827568386 0.919917809 0.896660441 0.957097866 0.941628156 0.530120283 0.980448289 1 18.5847785 1.034402562 24.99981481 1.000004773 0.838704277 0.193015628 0.118544746 250.4899982 182026.4442 0.123178125 0.030794531 10.82436833 -1.034402562 -0.161300496 HERPAGPGT(ph)PPPDSGPLAK ddPTM_BT-474_Pertuzumab_2h_R1 4 HERPAGPGTPPPDSGPLAK 19 1 Q9P2K8-2;Q9P2K8;H0YME5 Q9P2K8-2 EIF2AK4 Eukaryotic translation initiation factor 2-alpha kinase 4 1 HERPAGPGT(1)PPPDSGPLAK;HERPAGPGT(1)PPPDSGPLAK;HERPAGPGT(1)PPPDSGPLAK;HERPAGPGT(1)PPPDSGPLAK 206.94 5.51E-16 1326260000 1112550 1176690 1118180 1159000 1157800 1287070 1242250 821030 1544520 1499260 TRUE FALSE 1069070.316 1143131.953 1320260 1218816.129 1195041.688 1313095.437 1257453.027 804075.4436 1369192.565 1397713.785 0.764870696 0.817858395 0.944585375 0.872006946 0.854997426 0.93945946 0.899649872 0.575279039 0.979594377 1 20.41463753 1.034660566 24.9999981 1.000003058 0.829479267 0.27786304 0.100824511 201.5139975 145347.5466 0.105514786 0.026378696 10.83080074 -1.034660566 -0.170523791 LSGLS(ph)FKR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSGLSFKR 8 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FKR;LSGLS(1)FKR 121.9 0.0008658 1921030000 9097400 2100100 366780 698820 823070 388430 526940 4327500 669380 428810 TRUE FALSE 8741863.55 2040207.204 433065.305 734886.1839 849544.794 396284.3207 533388.8493 4238135.613 593394.7887 399766.3168 21.86743401 5.103499516 1.083296133 1.838289403 2.125103488 0.991289921 1.334251604 10.60153253 1.484354143 1 18.60879739 1.035302843 24.97962666 0.999941782 5.175446129 0.071765744 6.144256544 444.6935445 314655.4243 5.860279374 1.46507023 10.84683022 -1.035302843 4.175504347 SYS(ph)EPEKMNEVGIVEEAEPAPLGPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYSEPEKMNEVGIVEEAEPAPLGPQR 26 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.018)YS(0.982)EPEKMNEVGIVEEAEPAPLGPQR 181.21 1.24E-17 229060000 525560 269600 103710 148960 124770 87283 116880 354720 150190 132390 TRUE FALSE 505020.5342 261911.272 122452.704 156647.8435 128783.3404 89047.92206 118310.4124 347394.908 133141.0608 123423.1074 4.091782689 2.122060265 0.992137588 1.269193806 1.043429736 0.721485012 0.958575869 2.814666681 1.078736905 1 16.913253 1.035830465 24.99719634 0.999982853 1.69828151 0.075010449 0.98831343 439.7231339 306772.4363 0.976820711 0.244205178 10.860016 -1.035830465 0.698298657 LRQEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRQEVK 6 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 110.63 0.026025 287690000 231720 261560 196340 181690 185930 215030 189740 215880 274430 287990 FALSE TRUE 222664.1262 254100.5649 231823.0056 191067.0427 191910.6073 219378.0539 192062.0949 211422.0026 243277.8569 268484.1808 0.829337973 0.94642658 0.863451265 0.711651026 0.714792979 0.817098621 0.715357211 0.787465399 0.906116167 1 18.03447756 1.036556646 3.434338069 0.99859098 0.795968306 0.463699613 0.070150152 0.196032224 5.16137894 0.073634404 0.019158164 10.87819016 -1.036556646 -0.202622674 AWVWNTHADFADECPKPELLAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AWVWNTHADFADECPKPELLAIR 23 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 252.31 1.10E-43 3319700000 1369580 1223540 1039760 1225430 1255350 1330920 1176030 1188440 1529720 1518430 FALSE TRUE 1316055.299 1188645.837 1227667.761 1288674.589 1295729.473 1357832.114 1190422.607 1163898.299 1356072.599 1415585.384 0.929689805 0.839685017 0.867250945 0.910347482 0.915331203 0.959201847 0.840940166 0.822202823 0.957958887 1 20.43296734 1.036567419 7.053006869 0.999901704 0.88269526 0.45909535 0.041705965 0.146593958 20.06762495 0.043372244 0.010877352 10.87845998 -1.036567419 -0.117206445 VNVCEHCLVANHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNVCEHCLVANHAK 14 0 O95159;E9PQ47;E9PNY1;E9PJX1;E9PJ47;E9PMQ3 O95159 ZFPL1 Zinc finger protein-like 1 0 ; 225.55 1.58E-12 315800000 250230 321320 243810 292410 306190 296720 305680 197330 353310 339840 FALSE TRUE 240450.735 312156.2682 287871.8905 307501.3151 316038.8794 302719.8817 309421.0033 193255.0665 313203.73 316822.3341 0.758945027 0.985272295 0.908622466 0.970579666 0.997527148 0.955487821 0.97663886 0.609979303 0.988578444 1 18.27331451 1.03728509 24.99996241 1.000007278 0.890739227 0.103395556 0.116104023 330.7912026 221797.3047 0.120013214 0.030003304 10.8964515 -1.03728509 -0.109268051 LVSDVSATK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVSDVSATK 9 0 Q9BVV2 Q9BVV2 C20orf195 Uncharacterized protein C20orf195 0 79.597 0.061631 398160000 458200 422660 397990 419990 386880 350100 450970 465410 495580 530990 FALSE TRUE 440293.0374 410606.1506 469915.6462 441665.7342 399324.3466 357179.2619 456489.1058 455799.1209 439323.836 495025.5743 0.889434931 0.82946452 0.949275493 0.892207912 0.806674175 0.721536988 0.92215257 0.920758733 0.887477049 1 18.91714354 1.037313668 0.969888371 0.993171526 0.857130239 0.302926622 0.062443266 0.739476885 1.500146171 0.062624827 0.021185452 10.89716854 -1.037313668 -0.136041287 ITNQVHGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ITNQVHGLK 9 0 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 82.645 0.017866 468020000 1022700 1000600 804040 932080 949810 851200 1025800 993680 1207900 1233000 FALSE TRUE 982731.7533 972063.8677 949347.9138 980184.7605 980361.5012 868411.8472 1038354.047 973160.1608 1070784.256 1149487.812 0.85493012 0.845649565 0.82588776 0.852714357 0.852868113 0.755477212 0.903318884 0.846603288 0.931531631 1 20.13255974 1.037801326 1.348128531 1.000834404 0.837347163 0.69015746 0.034637361 0.229736672 0.853667382 0.030708038 0.00933746 10.90941156 -1.037801326 -0.163487241 HPDADSLYVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 HPDADSLYVEK 11 0 P54577 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 ;; 157.38 3.06E-05 1076800000 2606280 2452200 2367540 2670760 2523060 2442430 2876280 2243460 3379250 3391090 FALSE TRUE 2504423.696 2382265.657 2795407.144 2808598.244 2604216.516 2491817.608 2911480.775 2197131.767 2995651.707 3161408.454 0.792186057 0.753545672 0.884228402 0.88840094 0.823751994 0.788198565 0.920944199 0.694985099 0.947568703 1 21.59213601 1.037858574 10.31255579 0.999990393 0.81882961 0.495323732 0.06388874 0.285184355 74.9070131 0.060536618 0.01514116 10.91084971 -1.037858574 -0.181160783 SHTPS(ph)PTSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHTPSPTSPK 10 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 SHTPS(1)PTSPK;SHTPS(0.977)PT(0.021)S(0.002)PK 135.26 9.59E-05 312156000 930590 883280 786170 740970 742880 886840 929030 395956 1353020 1335420 TRUE FALSE 894221.514 858089.7192 928248.4073 779211.5505 766775.4099 904772.5124 940399.747 387779.3702 1199430.842 1244970.814 0.71826705 0.689244848 0.745598529 0.625887404 0.615898302 0.726741946 0.75535887 0.311476676 0.963420852 1 20.24768049 1.037930937 24.86606564 1.000000457 0.642468695 0.544360925 0.122045883 96.96080162 63563.46569 0.124242178 0.031060544 10.91266785 -1.037930937 -0.357531762 PSVSFLQVHSESQS(ph)PLHDI ddPTM_BT-474_Pertuzumab_2h_R1 3 PSVSFLQVHSESQSPLHDI 19 0 Q68DY1-3 Q68DY1-3 1 PSVSFLQVHSES(0.018)QS(0.981)PLHDI;PSVSFLQVHSES(0.003)QS(0.997)PLHDI;PSVSFLQVHS(0.001)ES(0.085)QS(0.914)PLHDI 214.49 2.76E-19 174032000 156077 139390 132561 136768 154296 147576 155704 106326 184895 178232 TRUE FALSE 149977.3383 135414.7337 156517.7215 143826.6129 159259.071 150560.0878 157609.5521 104130.3309 163906.4947 166160.1879 0.902606937 0.814964977 0.941968852 0.865590095 0.958467085 0.906114092 0.948539804 0.626686406 0.986436624 1 17.34221523 1.038281815 24.99996873 1.000005083 0.863467114 0.219888357 0.091759271 199.6143413 130357.7011 0.093334504 0.023333626 10.92148805 -1.038281815 -0.136537969 HVTSEQEWDKYCHYVAGLVGIGLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 HVTSEQEWDKYCHYVAGLVGIGLSR 25 1 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2 E9PNM1 FDFT1 Squalene synthase 0 85.467 0.011221 315920000 274680 367760 338220 480930 360180 418170 438750 183990 492220 476090 FALSE TRUE 263945.2019 357271.8449 399343.8777 505750.8549 371765.5168 426625.6839 444119.5537 180190.5422 436345.2492 443844.0002 0.594680117 0.804949137 0.899739272 1.139478859 0.837604015 0.961206378 1.000620834 0.405977195 0.983104985 1 18.75969317 1.038737506 24.99995728 1.000012359 0.825727247 0.09763787 0.195705362 330.0038897 212973.0476 0.199810989 0.049952747 10.93295362 -1.038737506 -0.174285113 DFFQSYGNVVELR ddPTM_BT-474_Pertuzumab_2h_R1 5 DFFQSYGNVVELR 13 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;;; 253.16 2.08E-23 731197000 990335 1307251 788677 1271421 857259 656349 1023946 1357784 1105686 1043343 FALSE TRUE 951631.6133 1269969.481 931208.4779 1337039.19 884833.5143 669620.8265 1036477.357 1329745.286 980173.1607 972676.4493 0.978363991 1.30564432 0.957367148 1.374598091 0.90968946 0.688431212 1.065593146 1.367099293 1.007707302 1 19.89160046 1.041921365 24.99909301 0.99998716 1.094115675 0.018527429 0.20722931 567.7100654 338542.3909 0.206153015 0.051538254 11.01339879 -1.041921365 0.094128514 HGLEVIYMIEPIDEYCVQQLK ddPTM_BT-474_Pertuzumab_2h_R1 4 HGLEVIYMIEPIDEYCVQQLK 21 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 312.1 1.45E-66 5320857000 2294155 2108219 1843503 2069343 2102113 2253323 2360953 1596314 2700076 2594072 FALSE TRUE 2204496.886 2048094.658 2176665.001 2176142.04 2169729.374 2298886.735 2389847.049 1563349.558 2393574.692 2418373.193 0.91156191 0.846889415 0.900053394 0.899837149 0.897185505 0.950592217 0.988204408 0.646446778 0.989745792 1 21.20560546 1.042122538 24.99999619 1.000007717 0.873677621 0.217690297 0.086458977 177.8912108 105579.0086 0.087232452 0.021808113 11.01850157 -1.042122538 -0.126330096 KATGAAT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 KATGAATPK 9 1 P10412 P10412 HIST1H1E Histone H1.4 1 KATGAAT(1)PK;KATGAAT(1)PK;KAT(0.039)GAAT(0.961)PK;KAT(0.003)GAAT(0.997)PK;KAT(0.015)GAAT(0.985)PK;KAT(0.009)GAAT(0.991)PK 91.076 0.0064448 4377610000 25955920 9866150 6506450 4691600 5362620 2459847 3431644 15296380 2909032 2136334 TRUE FALSE 24941533.95 9584777.062 7682310.25 4933734.038 5535113.543 2509586.792 3473641.486 14980504.41 2578810.883 1991638.195 12.52312494 4.812509162 3.857282045 2.477224051 2.779176236 1.26006159 1.744112708 7.521699696 1.294818953 1 20.92552416 1.043372033 23.50094079 0.999991017 4.377271539 0.159464074 3.154628175 120.7507852 65427.53051 3.046663683 0.761665921 11.0502482 -1.043372033 3.377280522 WDEMNILATYHPADKDYGLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 WDEMNILATYHPADKDYGLMK 21 1 P41236;E7EMN6;E7EUI7 P41236 PPP1R2 Protein phosphatase inhibitor 2 0 216.82 3.63E-25 366280000 424470 388970 379720 366900 391430 405150 416730 362740 494870 473780 FALSE TRUE 407881.2431 377876.9564 448343.8508 385835.753 404020.7014 413342.4106 421830.0664 355249.2922 438694.4323 441690.4586 0.923454956 0.855524382 1.015063473 0.873543328 0.914714578 0.935819198 0.955035496 0.804294694 0.99321691 1 18.75267614 1.0440089 24.99815689 1.000001562 0.907750593 0.291030851 0.054254699 133.280481 75706.21947 0.050971459 0.012742865 11.06646463 -1.0440089 -0.092250969 IWEVIGDHFNK ddPTM_BT-474_Pertuzumab_2h_R1 1 IWEVIGDHFNK 11 0 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 169.58 1.67E-05 101660000 286050 262600 263300 248320 279400 272750 275550 259830 345770 347850 FALSE TRUE 274870.8498 255110.9051 310884.1671 261135.825 288387.1547 278265.1919 278922.2633 254464.4197 306519.6392 324289.8097 0.847608656 0.786675676 0.958661536 0.805254489 0.889288365 0.858075658 0.860101844 0.784682133 0.945202809 1 18.30692416 1.044197072 5.920673777 0.999644248 0.848352158 0.521333267 0.048832386 0.117065434 9.293348678 0.044744418 0.011259393 11.07126056 -1.044197072 -0.15129209 LDAFIEALHQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDAFIEALHQEK 12 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ; 232.6 6.75E-13 448940000 884940 1038370 874930 1142370 692400 909540 1090650 975810 1157570 1141230 FALSE TRUE 850355.5664 1008756.704 1033049.314 1201327.853 714671.6748 927931.522 1103997.701 955659.1825 1026167.507 1063933.476 0.799256331 0.94813889 0.970971717 1.129138128 0.671725903 0.872170623 1.037656702 0.898232084 0.964503449 1 20.02097652 1.044368881 0.892558446 0.998360957 0.915123745 0.052842387 0.118193286 2.301185737 4.031407194 0.112477083 0.039497888 11.07564128 -1.044368881 -0.083237212 LKNWEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKNWEIR 7 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 103.56 0.0076133 2100740000 3781400 3977900 3089800 3482400 3610400 3479700 3752900 3943400 4201600 4263800 FALSE TRUE 3633618.707 3864454.187 3648195.592 3662127.081 3726531.795 3550061.918 3798829.113 3861967.412 3724651.983 3975009.028 0.914115838 0.972187524 0.91778297 0.921287739 0.937490146 0.893095309 0.955678109 0.971561922 0.937017238 1 21.92252671 1.044803645 0.693644362 0.997200341 0.928990045 0.429483419 0.023361552 0.696591041 0.783796641 0.023003261 0.009255616 11.08673445 -1.044803645 -0.068210296 VAVAT(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VAVATPAK 8 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAK 110.53 0.01534 0 1740000 714200 502500 554570 542460 365500 475010 1589600 454000 400100 TRUE FALSE 1671998.876 693831.7153 593312.9281 583191.4242 559908.7185 372890.6604 480823.3145 1556774.205 402463.8233 373000.8706 4.482560251 1.860134305 1.590647569 1.563512233 1.501092256 0.999704531 1.289067539 4.173647643 1.078988965 1 18.50881947 1.045358151 24.99998624 0.999905418 2.157144255 0.140661258 1.129557701 222.5647715 122669.956 1.118827027 0.279706757 11.10089898 -1.045358151 1.157238837 AIIEEYLHLNDMK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIIEEYLHLNDMK 13 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 226.04 1.14E-11 720920000 1208300 1076600 942790 1043900 931060 1035400 1102000 1120300 1483200 1619200 FALSE TRUE 1161078.3 1045896.422 1113173.125 1097775.804 961008.3905 1056336.497 1115486.606 1097165.414 1314833.354 1509530.142 0.769165363 0.692862231 0.737430207 0.727230132 0.636627493 0.69977834 0.73896279 0.726825774 0.871021597 1 20.52566813 1.04593145 2.08347106 1.000108027 0.711225805 0.883500362 0.033527858 0.090534444 0.813497274 0.031606062 0.008840578 11.11556264 -1.04593145 -0.288882222 TSSGDPPS(ph)PLVK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSSGDPPSPLVK 12 0 Q99618;F5GX58;F8WDL1 Q99618 CDCA3 Cell division cycle-associated protein 3 1 TSSGDPPS(1)PLVK;TSSGDPPS(1)PLVK;TSS(0.001)GDPPS(0.999)PLVK 158.52 0.00024815 738690000 2914320 2824200 2587980 2756470 2600160 2371140 2551320 2976840 2388420 2299750 TRUE FALSE 2800425.152 2743656.581 3055685.555 2898731.747 2683796.508 2419086.075 2582543.817 2915367.214 2117296.575 2143985.884 1.306177048 1.279698995 1.425235855 1.352029306 1.251779001 1.128312501 1.204552622 1.359788437 0.987551546 1 21.03186398 1.04593773 0.346882928 0.963408004 1.352393572 0.543383884 0.09586547 1.349221967 0.48352871 0.193934038 0.113127203 11.11572336 -1.04593773 0.388985568 VDVSAPDVEAHGPEWNLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDVSAPDVEAHGPEWNLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 305.43 4.96E-50 2666980000 3276690 3484700 2880280 3381480 2962800 3260180 3274890 3472660 3679120 3492360 FALSE TRUE 3148633.332 3385319.768 3400810.667 3555998.588 3058101.153 3326103.073 3314969.083 3400948.357 3261481.722 3255819.347 0.967078636 1.039775064 1.044532975 1.092197757 0.93927237 1.021587109 1.018167389 1.044575265 1.001739155 1 21.63458922 1.046724986 23.23018037 0.999999883 1.022922203 0.036409812 0.040198497 177.0166444 88005.73142 0.037539951 0.009384988 11.13589137 -1.046724986 0.02292232 FFT(ph)TPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 FFTTPSK 7 0 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 FFT(0.867)T(0.133)PSK 128 0.042486 138200000 1725800 753000 490280 446500 398820 287720 331000 1614300 284460 235480 TRUE FALSE 1658353.828 731525.1773 578884.5022 469543.9185 411648.4075 293537.8955 335050.877 1580964.141 252169.2934 219530.7299 7.554085158 3.332222226 2.636917859 2.13885281 1.875128861 1.33711529 1.526214017 7.201561904 1.148674236 1 17.74406338 1.047151337 24.99991723 0.999807227 3.399072277 0.170227575 2.097098688 188.1182407 99740.73669 2.091076922 0.52276923 11.14682896 -1.047151337 2.39926505 GSNTIASAAADKIPGLLGVFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSNTIASAAADKIPGLLGVFQK 22 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 135.1 5.98E-06 66215000 117930 123850 117300 96000 103230 125450 116160 119560 147350 150870 FALSE TRUE 113321.1652 120317.9193 138498.7193 100954.5715 106550.4867 127986.685 117581.6008 117091.0442 130623.4457 140651.4405 0.805687911 0.855433253 0.984694638 0.71776422 0.757549914 0.909956446 0.835978646 0.832490899 0.92870322 1 17.1017648 1.047497748 3.075603508 0.99922763 0.838031295 0.364225679 0.070111069 0.245189881 4.99425782 0.0670739 0.017706212 11.15572367 -1.047497748 -0.161196335 RT(ph)SPQVLGSILK ddPTM_BT-474_Pertuzumab_2h_R1 3 RTSPQVLGSILK 12 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 RT(0.5)S(0.5)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK 173.03 2.00E-05 3550130000 4543380 4392280 4453980 4125210 4107910 3986220 5345890 4801930 5917790 6378020 TRUE FALSE 4365819.687 4267016.475 5258913.264 4338112.582 4240044.656 4066824.1 5411314.601 4702768.467 5246027.289 5946031.024 0.734240987 0.717624321 0.884440939 0.729581222 0.713088216 0.683956085 0.910071706 0.790908834 0.882273783 1 22.50349556 1.047691267 0.731628788 0.998901167 0.752008522 0.564535456 0.066963495 0.520148155 0.642676415 0.064850939 0.025295588 11.16069569 -1.047691267 -0.246892644 EAHEPLAVADAK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAHEPLAVADAK 12 0 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 0 ;;; 113.65 0.001143 1405510000 6718400 6369500 5142390 5607190 5825290 6011200 5886690 6214600 7175100 7062700 FALSE TRUE 6455837.5 6187848.096 6071734.265 5896577.748 6012665.743 6132750.583 5958733.073 6086266.338 6360612.728 6584337.038 0.980484058 0.939783012 0.922148157 0.89554616 0.913177091 0.931415046 0.904986036 0.924355224 0.966021741 1 22.65060676 1.04801166 3.094677877 0.999456151 0.924330826 0.540207741 0.021894848 0.168053386 3.461040028 0.021541766 0.005682312 11.16893234 -1.04801166 -0.075125326 VAAGVLCELAQDKEAADAIDAEGASAPLMELLHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VAAGVLCELAQDKEAADAIDAEGASAPLMELLHSR 35 1 P14923 P14923 JUP Junction plakoglobin 0 162.2 8.90E-15 100110000 98314 118970 82107 102840 88242 111150 107560 106820 107020 93400 FALSE TRUE 94471.78019 115577.0921 96945.56136 108147.5847 91080.38407 113397.5292 108876.3515 104614.1297 94871.53826 87073.93481 1.084960504 1.327344312 1.113370627 1.242020186 1.046012039 1.302313137 1.250389703 1.201440246 1.089551523 1 16.4099533 1.049156669 3.137329614 1.001490867 1.200605972 0.347444681 0.086967685 0.221874649 4.681197389 0.076279307 0.020087767 11.19841787 -1.049156669 0.199115105 IDFVAHDDIPYSSAGSDDVYK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDFVAHDDIPYSSAGSDDVYK 21 0 P49585;C9JEJ2;C9J050;H7C1T3;H7BZN1;Q9Y5K3-2;Q9Y5K3-4;Q9Y5K3-3;Q9Y5K3 P49585 PCYT1A;PCYT1B Choline-phosphate cytidylyltransferase A;Choline-phosphate cytidylyltransferase B 0 ; 267.7 3.57E-37 1168440000 991740 937420 742600 877530 925880 980600 935970 959300 1213610 1272240 FALSE TRUE 952981.7044 910685.6994 876804.339 922819.4285 955661.7711 1000428.404 947424.6808 939490.1198 1075846.081 1186070.052 0.803478431 0.767817801 0.739251731 0.778047997 0.80573805 0.843481717 0.798793191 0.792103399 0.907067908 1 20.17775779 1.049636366 2.57205214 0.999524477 0.789506184 0.873082046 0.025963115 0.089502242 1.256049261 0.027426967 0.00742913 11.21079383 -1.049636366 -0.210018293 T(ph)SPHWK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPHWK 6 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 T(0.897)S(0.103)PHWK;T(0.713)S(0.287)PHWK 138.24 0.04558 1326450000 1895040 1655580 1682720 1697010 1746300 1704500 1807990 1883400 2154700 2168400 TRUE FALSE 1820979.742 1608364.479 1986824.936 1784592.889 1802471.325 1738966.158 1830116.722 1844507.132 1910107.489 2021532.337 0.900791795 0.795616499 0.982831142 0.882792156 0.891636158 0.860221786 0.905311624 0.912430189 0.944880997 1 20.94701785 1.050412218 1.136376267 0.99959099 0.886308644 0.402324311 0.043263983 0.476803196 1.288757394 0.038840578 0.012416802 11.23083942 -1.050412218 -0.113282346 FSSDELQILTYQLCHTYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSSDELQILTYQLCHTYVR 19 0 Q9UKV8-2;Q9UKV8 Q9UKV8-2 AGO2 Protein argonaute-2 0 ; 138.3 2.19E-06 170598000 287169 290100 257884 277610 308080 287790 294230 302720 316700 288740 FALSE TRUE 275946.118 281826.632 304489.3754 291937.4854 317989.673 293609.311 297830.8748 296468.7262 280749.5437 269183.3826 1.025123153 1.046968908 1.13115963 1.084530117 1.181312419 1.090740848 1.106423702 1.101363403 1.04296759 1 18.03822983 1.051269606 3.134708135 1.000577709 1.098564246 0.372235289 0.040427312 0.231836775 4.855408467 0.039225971 0.010333597 11.25303336 -1.051269606 0.097986537 (ac)AS(ph)PGHSDLGEVAPEIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPGHSDLGEVAPEIK 16 0 F8WDN0;S4R325;Q8TCY9-2 F8WDN0 URGCP;URGCP-MRPS24 Up-regulator of cell proliferation 1 AS(0.94)PGHS(0.06)DLGEVAPEIK;AS(0.998)PGHS(0.002)DLGEVAPEIK 76.073 4.52E-12 230870000 463810 444740 384080 367200 457000 420740 435230 454770 527680 529220 TRUE FALSE 445683.7924 432056.4506 453491.7998 386151.236 471699.82 429247.6511 440556.4749 445378.8406 467779.9786 493375.458 0.903335959 0.875715327 0.919161649 0.782672161 0.956066647 0.870022301 0.892943635 0.902717866 0.948121701 1 18.91232643 1.051314384 1.411130356 1.000253306 0.883967998 0.437260162 0.041693804 0.360473553 1.458985076 0.036247294 0.010915074 11.25419366 -1.051314384 -0.116285307 GTDIMYTGTLDCWR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTDIMYTGTLDCWR 14 0 P05141 P05141 SLC25A5 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed" 0 ; 184.03 1.94E-07 181210000 94492 165470 96259 206647 104684 85892 194183 163297 130229 106500 FALSE TRUE 90799.14817 160750.9576 113655.1426 217312.0764 108051.2559 87628.79509 196559.4696 159924.8599 115445.9499 99286.66014 0.914515082 1.619058969 1.144717149 2.188733876 1.088275663 0.882583773 1.979716806 1.61073864 1.162753886 1 16.59931227 1.051725211 5.461503797 1.002141407 1.454655654 0.104347029 0.414243226 0.351217044 21.25954096 0.3859747 0.097363307 11.26484476 -1.051725211 0.452514247 TLTPIIQEYFEHGDTNEVAEMLR ddPTM_BT-474_Pertuzumab_2h_R1 3 TLTPIIQEYFEHGDTNEVAEMLR 23 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 0 ;; 251.02 1.52E-38 203808000 127141 151665 106803 141284 141536 132510 139653 136060 138827 116753 FALSE TRUE 122172.1892 147339.6627 126104.6779 148575.6842 146088.634 135189.443 141362.1152 133250.3135 123067.941 108845.2153 1.122439685 1.353662283 1.158568868 1.365018056 1.342168634 1.242033861 1.298744412 1.224218383 1.130669278 1 16.73191846 1.052258501 1.694944906 1.001177974 1.273844163 0.557037456 0.075901199 0.23948419 1.390807889 0.06630883 0.019224173 11.27868587 -1.052258501 0.272666189 KKFS(ph)FK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKFSFK 6 2 P49006 P49006 MARCKSL1 MARCKS-related protein 1 KKFS(1)FK 67.125 0.078439 655000000 4171200 2113600 1128300 715010 909830 433780 612200 2307700 1079900 999560 TRUE FALSE 4008184.892 2053322.197 1332208.909 751911.7518 939095.5082 442551.3288 619692.2867 2260045.189 957314.2793 931858.9109 4.301278708 2.203468973 1.429625122 0.806894416 1.007765765 0.474912375 0.665006558 2.42530834 1.027316762 1 19.82975201 1.052370378 24.99980823 0.999936724 1.586869359 0.051890881 1.072656521 321.4523384 153448.816 1.062790488 0.265697622 11.28159171 -1.052370378 0.586932635 VKS(ph)PGGPGSHVR ddPTM_BT-474_Pertuzumab_2h_R1 6 VKSPGGPGSHVR 12 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 VKS(1)PGGPGSHVR;VKS(1)PGGPGSHVR;VKS(0.992)PGGPGS(0.008)HVR;VKS(0.902)PGGPGS(0.098)HVR;VKS(1)PGGPGSHVR;VKS(0.999)PGGPGS(0.001)HVR 127.88 0.0001586 7549550000 1536810 1467930 1225820 1316690 1373750 1354970 1401650 1486680 1647960 1629810 TRUE FALSE 1476749.766 1426066.074 1447352.942 1384644.529 1417937.916 1382368.422 1418803.812 1455979.538 1460890.49 1519421.517 0.971915791 0.938558562 0.952568412 0.91129717 0.933209054 0.909799161 0.933778939 0.958245965 0.961478084 1 20.53509073 1.052684618 1.278306406 0.998575842 0.935100783 0.549682697 0.017616561 0.334249339 1.122074121 0.016886058 0.005213828 11.28975762 -1.052684618 -0.06347506 KAS(ph)VHSSGR ddPTM_BT-474_Pertuzumab_2h_R1 5 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.804)VHS(0.163)S(0.033)GR;KAS(0.659)VHS(0.113)S(0.229)GR;KAS(0.472)VHS(0.264)S(0.264)GR;KAS(0.597)VHS(0.367)S(0.036)GR;KAS(0.474)VHS(0.139)S(0.387)GR 151.7 5.04E-05 1570280000 2507890 1450340 604642 1141557 795967 547237 549455 2598200 377835 312370 TRUE FALSE 2409878.886 1408977.723 713914.2596 1200472.894 821570.0014 558302.5071 556179.3947 2544546.262 334944.7548 291212.9017 8.275316349 4.838308039 2.451520024 4.122320428 2.821200561 1.91716268 1.909872095 8.737752508 1.150171414 1 18.15171475 1.052960686 24.99990474 0.999702409 4.330303689 0.249095493 2.297368377 119.0968428 56218.70122 2.285826324 0.571456581 11.29693646 -1.052960686 3.33060128 LEFLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEFLHK 6 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 111.69 0.027635 2803000000 4280100 4123500 3625600 4051200 4049600 3958600 4219200 4448700 4932400 5007400 FALSE TRUE 4112828.96 4005901.817 4280826.571 4260282.917 4179859.062 4038645.604 4270835.832 4356832.79 4372494.63 4668244.338 0.881022642 0.858117426 0.917009964 0.91260924 0.895381381 0.865131581 0.914869815 0.933291506 0.936646481 1 22.15444864 1.053232176 0.700769895 0.999945182 0.887707865 0.765230297 0.018872278 0.354455821 0.406684253 0.019549997 0.007833687 11.30400072 -1.053232176 -0.112237317 VHIEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHIEVK 6 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 91.093 0.048284 129850000 502730 507620 447300 533130 463070 502190 573640 462720 698990 726590 FALSE TRUE 483082.7558 493143.1746 528137.0601 560644.9032 477965.0671 512344.6259 580660.3779 453164.6703 619643.5856 677377.4121 0.713166319 0.728018333 0.779679172 0.827669912 0.705611168 0.756365088 0.857218395 0.668998792 0.914768598 1 19.36960035 1.054495921 5.362011547 0.999048692 0.756740543 0.705084851 0.053783622 0.086134158 4.873745261 0.050053761 0.012634758 11.3369419 -1.054495921 -0.242308149 DGWPAMGIHGDK ddPTM_BT-474_Pertuzumab_2h_R1 7 DGWPAMGIHGDK 12 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;;; 121.28 0.00037907 6576580000 4608050 4579540 3920620 3950130 4102170 4036550 4727810 4614000 5567620 5787220 FALSE TRUE 4427962.312 4448936.003 4629163.248 4153996.683 4234120.024 4118171.807 4785670.353 4518719.288 4935607.119 5395246.435 0.820715488 0.824602927 0.858007749 0.769936412 0.784787141 0.763296331 0.887016082 0.837537144 0.914806613 1 22.36325743 1.054572668 0.993997986 0.999640377 0.808393932 0.752674732 0.034389876 0.266399837 0.565925924 0.032974726 0.011069913 11.33894551 -1.054572668 -0.191246445 AQLLHALS(ph)LDEGGPEPEPSLSDSSSGGSFGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AQLLHALSLDEGGPEPEPSLSDSSSGGSFGR 31 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 AQLLHALS(0.999)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR 180.2 2.19E-18 512991000 160000.3 172851.5 85698.8 161286.9 169045 151820 143171.2 173091 147552 127585.6 TRUE FALSE 153747.3114 167921.9445 101186.4795 169610.9362 174482.4859 154889.9044 144923.372 169516.6104 130802.5155 118944.1137 1.292601262 1.411771792 0.85070607 1.425971669 1.466928296 1.302207395 1.21841567 1.425178642 1.099697257 1 16.85992435 1.055051328 5.837543481 1.000977492 1.299441898 0.270702968 0.167552085 0.218136005 14.48085861 0.157973682 0.039770412 11.35144966 -1.055051328 0.298464406 SVGKPALER ddPTM_BT-474_Pertuzumab_2h_R1 2 SVGKPALER 9 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 89.9 0.010756 2856800000 4280500 4560000 3720600 3934400 4126100 2958500 4780100 4531200 4947000 5399500 FALSE TRUE 4113213.328 4429953.265 4392995.184 4137454.855 4258819.754 3018322.897 4838600.294 4437629.137 4385437.3 5033787.056 0.817121043 0.880043835 0.872701832 0.821936806 0.846046864 0.59961275 0.961224668 0.881568705 0.871200401 1 22.26321276 1.055079252 0.919604854 0.991868585 0.824481691 0.260261191 0.086884398 0.807602124 1.494011039 0.082210944 0.028525178 11.35217955 -1.055079252 -0.167386894 LDHLAEK ddPTM_BT-474_Pertuzumab_2h_R1 3 LDHLAEK 7 0 O43707;O43707-2;P12814-3;P12814;P12814-2;P12814-4;H9KV75 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ;; 145.34 0.0022931 1760150000 4265410 4061170 4301520 5837100 4159400 3383670 5611300 4760600 7008800 7756300 FALSE TRUE 4098713.062 3945349.408 5078900.351 6138353.431 4293190.878 3452090.126 5679972.768 4662291.946 6213190.407 7230958.892 0.566828428 0.545619117 0.702382689 0.848898953 0.593723591 0.477404197 0.785507545 0.644768144 0.859248476 1 22.78575554 1.055286066 1.687917807 1.003136442 0.642168587 0.549065748 0.106229349 0.280284434 1.611503862 0.102730346 0.02981547 11.35758683 -1.055286066 -0.360967855 TNQGS(ph)MENLCPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TNQGSMENLCPGK 13 0 B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;A0A2R8YGT1;F8W9A8;Q6PFW1;H7C398 B7WPL9 PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 1 TNQGS(1)MENLCPGK 116.96 0.00057114 127310000 165070 148040 118370 133410 157070 145690 149840 164270 187170 196670 TRUE FALSE 158618.8819 143818.0441 139762.0921 140295.3061 162122.2992 148635.9516 151673.7867 160877.7671 165923.2463 183349.3657 0.865118247 0.784393464 0.762272024 0.76518021 0.884226125 0.810670662 0.827239222 0.877438362 0.904956751 1 17.48423575 1.055290461 0.617178032 1.002809297 0.800214667 0.725621941 0.036628786 0.413082387 0.38060585 0.037641405 0.016347627 11.35770176 -1.055290461 -0.20259463 EFDLTKEEDLAALR ddPTM_BT-474_Pertuzumab_2h_R1 3 EFDLTKEEDLAALR 14 1 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YGE5;A0A2R8YD53;A0A2R8Y4Q3;A0A2R8YE54;A0A2R8Y4G4 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ;; 145.69 7.76E-06 628520000 531395 646370 471128 557080 404812 618550 566850 562060 597429 538869 FALSE TRUE 510627.4959 627936.1605 556271.3098 585830.9656 417833.1456 631057.5048 573787.2799 550453.2646 529611.3645 502370.9227 1.016435213 1.249945274 1.107292012 1.166132312 0.831722392 1.2561585 1.14215862 1.095710838 1.054223763 1 18.93839344 1.055336826 2.344668169 1.001267595 1.112420602 0.083610469 0.114674011 0.689796431 7.889474235 0.103805255 0.028537046 11.35891438 -1.055336826 0.111153007 HEDPCAK ddPTM_BT-474_Pertuzumab_2h_R1 3 HEDPCAK 7 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;; 102.72 0.0085375 971460000 1398240 1375600 1456490 1518290 1383340 1543270 1722510 1136400 2218520 2323090 FALSE TRUE 1343595.235 1336369.235 1719710.142 1596649.129 1427836.387 1574475.977 1743590.593 1112932.943 1966682.91 2165745.045 0.620384767 0.617048271 0.794050134 0.737228573 0.659281844 0.726990455 0.80507657 0.513879944 0.908086072 1 21.04643199 1.056352853 6.97426217 0.999472104 0.685969756 0.633677404 0.083476676 0.111803246 10.30515233 0.080911746 0.020296124 11.38551954 -1.056352853 -0.313502348 ENQQHYGDLLNHCAVLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENQQHYGDLLNHCAVLEK 18 0 Q14789;Q14789-2;Q14789-4;Q14789-3;H7C5I7 Q14789 GOLGB1 Golgin subfamily B member 1 0 107.89 0.00023546 278810000 155700 168390 119490 159820 136030 150140 157380 130250 196390 193730 FALSE TRUE 149615.0719 163587.6821 141084.501 168068.3294 140405.5285 153175.9337 159306.0635 127560.292 174096.6305 180608.4945 0.828394435 0.905758516 0.781162046 0.930567135 0.777402684 0.848110351 0.882051888 0.706280689 0.963944863 1 17.46250622 1.056748392 9.979004981 0.999970099 0.831463479 0.480780144 0.062700273 0.265338551 43.93896111 0.05848105 0.014628498 11.39589377 -1.056748392 -0.16850662 RLDLVHTAALMLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDLVHTAALMLDK 14 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 128.96 4.59E-05 238440000 448360 412350 386430 410020 431680 346240 442970 454260 506880 527000 FALSE TRUE 430837.5955 400590.1817 456266.4971 431181.1813 445565.3792 353241.21 448391.1994 444879.3723 449341.1074 491305.8206 0.876923451 0.815358103 0.928681237 0.877622783 0.906900266 0.718984378 0.912651918 0.905503972 0.914585353 1 18.90626181 1.057240533 1.107366688 0.996205799 0.861041201 0.352790341 0.056999162 0.551668842 1.423119232 0.052887432 0.017066809 11.40881487 -1.057240533 -0.135164598 RT(ph)SNERPGSGQGQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.803)S(0.197)NERPGSGQGQGR 114.55 0.00096003 53979000 15780 14866 12383 16935 14797 17198 13862 15637 16716 14638 TRUE FALSE 15163.30015 14442.03624 14620.88356 17809.01738 15272.95894 17545.75534 14031.6473 15314.09049 14818.46976 13646.55522 1.111144894 1.058291708 1.071397383 1.305019259 1.119180533 1.285727794 1.028218996 1.122194593 1.085876217 1 13.7362492 1.057794274 0.957960954 1.004440966 1.14672451 0.209216848 0.085259238 0.896679109 1.784175426 0.08041302 0.027420434 11.4233708 -1.057794274 0.142283544 QLLHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLLHEK 6 0 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 70.912 0.089617 89511000 269480 278450 234570 254430 246360 268650 250780 251030 340820 348330 FALSE TRUE 258948.4237 270508.8786 276962.017 267561.1628 254284.3931 274082.2871 253849.1207 245846.1428 302131.5424 324737.2988 0.797408935 0.833008341 0.852880214 0.823931109 0.783046463 0.844012339 0.781706079 0.757061612 0.930387558 1 18.30891357 1.057909272 4.838110245 0.998852304 0.808777478 0.830646628 0.02898043 0.070973698 3.205742123 0.03096119 0.007850099 11.42639602 -1.057909272 -0.190074826 NVVHQLS(ph)VTLEDLYNGATR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVVHQLSVTLEDLYNGATR 19 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 NVVHQLS(0.996)VT(0.004)LEDLYNGATR;NVVHQLS(0.965)VT(0.035)LEDLYNGATR 131.37 1.01E-05 49420000 37795 35149 38729 34663 35671 38613 34378 37643 46486 46834 TRUE FALSE 36317.92962 34146.58493 45728.19182 36451.96158 36818.39011 39393.78132 34798.72825 36865.6589 41209.10417 43661.89146 0.831799274 0.782068385 1.047325031 0.834869044 0.843261455 0.90224633 0.797004598 0.844344064 0.943823155 1 15.41408701 1.058315406 3.974208126 0.998787908 0.86031389 0.303676059 0.0699925 0.230141111 7.302022284 0.065594065 0.016850929 11.43708651 -1.058315406 -0.138474018 DFMIQGGDFTR ddPTM_BT-474_Pertuzumab_2h_R1 3 DFMIQGGDFTR 11 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;; 147.74 8.18E-05 885620000 523882 551374 512747 717100 459958 449714 692690 663281 778160 909480 FALSE TRUE 503408.1123 535649.3534 605411.7889 754109.6169 474752.9668 458807.5252 701167.3474 649584.0156 689826.5391 847880.1095 0.593725583 0.63175129 0.714029946 0.889405953 0.55992936 0.541123114 0.826965204 0.766127202 0.813589718 1 19.69350076 1.058333046 0.783873486 0.996081098 0.668207133 0.496949768 0.102523746 0.580503875 0.810809219 0.102337861 0.038471762 11.43755105 -1.058333046 -0.327873965 LKEEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEEEER 7 1 A0A087WUT6;O60841;Q9H2L5-3;Q9H2L5;Q9H2L5-2 A0A087WUT6 EIF5B;RASSF4 Eukaryotic translation initiation factor 5B;Ras association domain-containing protein 4 0 68.224 0.081416 0 466740 400680 388030 408160 426250 409080 452360 439520 541590 549690 FALSE TRUE 448499.2848 389252.9987 458155.6527 429225.1865 439960.7184 417351.8779 457896.117 430443.7584 480110.9737 512459.0067 0.87519056 0.759578803 0.89403376 0.837579554 0.858528609 0.81441027 0.893527309 0.839957446 0.936876838 1 18.96707708 1.060320609 2.536216265 1.000303464 0.845134619 0.639234031 0.037935186 0.146490121 1.961175962 0.033055303 0.008985725 11.49001536 -1.060320609 -0.155168846 QATVGDINTERPGMLDFTGK ddPTM_BT-474_Pertuzumab_2h_R1 4 QATVGDINTERPGMLDFTGK 20 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ;;; 287.37 1.81E-45 2502260000 2749280 2544870 2244510 2753320 2422900 2308310 2617270 2978210 3396670 3805660 FALSE TRUE 2641835.098 2472292.799 2650142.886 2895419.175 2500834.779 2354985.61 2649300.933 2916708.923 3011094.262 3547899.258 0.744619536 0.696832863 0.746961143 0.816093966 0.704877618 0.663769019 0.746723833 0.822094628 0.848697791 1 21.75853361 1.06048775 1.115015166 0.995915661 0.72983691 0.810875832 0.040260461 0.211593094 0.55272986 0.040304336 0.012981016 11.49443821 -1.06048775 -0.266078751 SMVS(ph)PVPS(ph)PTGTISVPNSCPAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMVSPVPSPTGTISVPNSCPASPR 24 0 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 3 S(0.323)MVS(0.665)PVPS(0.484)PT(0.262)GT(0.261)IS(0.024)VPNS(0.299)CPAS(0.682)PR 41.911 0.092955 58133000 146610 131270 143290 139790 146020 139150 144410 180580 185760 216280 TRUE FALSE 140880.3191 127526.3081 169185.6905 147004.5787 150716.8659 141963.7083 146177.3328 176850.9599 164673.3036 201631.163 0.698703102 0.632473206 0.83908503 0.729076679 0.747487956 0.704076226 0.724973911 0.877101324 0.816705618 1 17.62135911 1.060839376 0.675140775 0.999074133 0.717888345 0.687152462 0.056873195 0.41742345 0.44956822 0.056480882 0.023202253 11.50374843 -1.060839376 -0.281185788 S(ph)RS(ph)PLLNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPLLNDR 9 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PLLNDR;S(1)RS(1)PLLNDR 101.2 0.0023569 1705920000 500620 446930 415350 474980 459050 439810 470080 507130 550910 561080 TRUE FALSE 481055.2169 434183.994 490412.9844 499493.7747 473815.7601 448703.2595 475832.9797 496657.5883 488373.0064 523077.5518 0.91966328 0.830056638 0.937553108 0.954913421 0.905823158 0.857814024 0.909679603 0.949491307 0.933653155 1 18.99666533 1.060912234 0.923538679 0.997602586 0.901279602 0.405753036 0.035533479 0.588231718 1.097220397 0.034783753 0.012056515 11.50567848 -1.060912234 -0.096322984 QDPVVHLS(ph)PNK ddPTM_BT-474_Pertuzumab_2h_R1 1 QDPVVHLSPNK 11 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 QDPVVHLS(1)PNK 95.428 0.0050017 183920000 410020 432410 394400 381650 381480 369930 449060 461780 514360 564100 TRUE FALSE 393995.9651 420078.0902 465676.8534 401347.0022 393750.6507 377410.2381 454555.7306 452244.0816 455972.0092 525893.0046 0.749194155 0.798790032 0.885497334 0.763172354 0.748727683 0.717655939 0.864350213 0.859954549 0.867043306 1 19.00440978 1.061216239 0.839617738 0.995323667 0.784481931 0.645321251 0.04853534 0.407575522 0.642566435 0.048901588 0.017737809 11.51373525 -1.061216239 -0.210841736 ITVGNDHFCVS(ph)TPERR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITVGNDHFCVSTPERR 16 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.5)T(0.5)PERR;ITVGNDHFCVS(0.794)T(0.206)PERR 140.2 8.10E-07 278530000 340520 331840 282760 338460 327520 335640 286710 361420 347700 322060 TRUE FALSE 327212.1019 322376.2481 333861.022 355927.9612 338054.9782 342426.8708 290218.8427 353956.5507 308230.5537 300246.5893 1.08981122 1.073704946 1.111956085 1.185452138 1.125924458 1.140485464 0.96660163 1.178886166 1.026591357 1 18.19578833 1.061255003 8.059904072 1.000096344 1.108462814 0.307065995 0.058238114 0.250649793 27.58154365 0.054118727 0.013553229 11.514763 -1.061255003 0.10836647 EKALEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKALEHK 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 71.501 0.032533 218400000 334310 314940 240790 251390 268380 307710 287910 303000 382310 401090 FALSE TRUE 321244.7956 305958.2196 284306.1093 264364.268 277012.6864 313932.107 291433.5287 296742.9441 338911.7716 373923.817 0.859118304 0.818236779 0.760331641 0.707000346 0.740826537 0.839561677 0.779392795 0.793591985 0.906365832 1 18.51238484 1.061407315 2.428169586 0.999406483 0.783128361 0.724202438 0.042895706 0.142894786 1.744000928 0.043345528 0.011862493 11.51880206 -1.061407315 -0.216278122 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVK 36 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 247.08 2.46E-50 239280000 170140 134210 132400 123760 154610 155660 142650 197910 192880 241820 FALSE TRUE 163490.7407 130382.4622 156327.6252 130147.2684 159583.1711 158807.5519 144395.7934 193823.0893 170985.071 225441.316 0.725203098 0.578343245 0.69342935 0.577299985 0.707870118 0.70442967 0.640502797 0.859749636 0.75844603 1 17.78239241 1.061761864 0.563842758 1.001697292 0.640127921 0.725655757 0.063521104 0.40576777 0.320884947 0.062586769 0.028891703 11.52820961 -1.061761864 -0.361569371 GLSTS(ph)LPDLDSEPWIEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLSTSLPDLDSEPWIEVK 18 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;Q659C4-4 A0A3B3ISF0 LARP1B La-related protein 1B 1 GLS(0.004)T(0.028)S(0.968)LPDLDSEPWIEVK;GLS(0.073)T(0.073)S(0.855)LPDLDSEPWIEVK 172.91 1.01E-11 216060000 137867 137188 101007 115823 125732 119639 122592 136947 123846 107606 TRUE FALSE 132479.0052 133275.5326 119261.2118 121800.6389 129776.284 122058.1826 124092.3176 134118.9966 109787.5213 100317.7498 1.320593868 1.328533912 1.188834599 1.214148435 1.293652263 1.216715714 1.236992634 1.336941836 1.094397766 1 16.61421737 1.061970891 4.785714913 1.001628791 1.265339718 0.764728338 0.050029328 0.083489802 3.58229593 0.049898802 0.012660207 11.53375949 -1.061970891 0.263710927 LTISPDYAYGATGHPGIIPPHATLVFDVELLKLE ddPTM_BT-474_Pertuzumab_2h_R1 1 LTISPDYAYGATGHPGIIPPHATLVFDVELLKLE 34 1 P62942;Q5W0X3;Q1JUQ5;Q5VVH2 P62942 FKBP1A;FKBP12-Exip2;FKBP1C Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 122.09 5.56E-08 80345000 97349 109070 68727 89990 109590 101250 98799 89566 108500 87897 FALSE TRUE 93544.49345 105959.4304 81147.49772 94634.39468 113115.0619 103297.3444 100008.1317 87716.4308 96183.53487 81943.6579 1.141570878 1.293076647 0.990284054 1.154871495 1.380400446 1.260589862 1.220449932 1.070448074 1.173776438 1 16.32234467 1.062457509 1.0295827 1.011676313 1.203223152 0.234772316 0.104353688 0.79168849 1.79210801 0.101859917 0.033764292 11.54669007 -1.062457509 0.191546839 ERPPS(ph)HTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPPSHTLK 9 1 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 ERPPS(1)HTLK;ERPPS(0.999)HT(0.001)LK 87.831 0.0079911 436030000 219856 226280 178992 192829 196214 200841 191288 216086 243180 241260 TRUE FALSE 211263.7845 219826.716 211339.8361 202780.9278 202525.4015 204902.1426 193629.0398 211623.7486 215575.2259 224919.2453 0.939287272 0.97735841 0.939625401 0.901572151 0.900436071 0.911003157 0.860882489 0.940887687 0.958456114 1 17.77904759 1.062866138 2.309813226 0.998374014 0.919418847 0.423558961 0.029388671 0.285331089 3.129210296 0.03031093 0.008360351 11.5575595 -1.062866138 -0.078955167 CILPFDKETGFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 CILPFDKETGFHR 13 1 Q9GZT3-2;Q9GZT3;H0YJW7;A0A087WUN7;H0YJ40;G3V4X6;G3V2S9 Q9GZT3-2 SLIRP "SRA stem-loop-interacting RNA-binding protein, mitochondrial" 0 103.35 0.00097188 346860000 438410 616250 350250 558750 348400 450940 592900 509540 478600 400250 FALSE TRUE 421276.4525 598675.1534 413547.9663 587587.1545 359606.6024 460058.3158 600156.0876 499017.8209 424271.3345 373140.711 1.129001581 1.604421967 1.108289592 1.574706638 0.963729209 1.232935196 1.608390802 1.337344884 1.137027727 1 18.50936025 1.064075037 3.671215706 1.004121495 1.330027175 0.196479532 0.211273993 0.299809849 8.076471093 0.189954803 0.049189488 11.58977586 -1.064075037 0.32590568 GPFLVSAPLSTIINWER ddPTM_BT-474_Pertuzumab_2h_R1 1 GPFLVSAPLSTIINWER 17 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q14839-2;Q12873-3 CHD4;CHD3 Chromodomain-helicase-DNA-binding protein 4;Chromodomain-helicase-DNA-binding protein 3 0 68.44 0.066605 0 43876 44160 38478 34048 33621 50693 40283 45885 39785 33638 FALSE TRUE 42161.27741 42900.60004 45431.83054 35805.22136 34702.45 51718.04719 40775.9954 44937.45872 35268.77359 31359.6683 1.344442709 1.368018298 1.44873441 1.141760207 1.106594932 1.649189867 1.300268709 1.432969835 1.124653911 1 14.93662268 1.064814331 4.593045978 1.002335382 1.348888464 0.394660701 0.1457306 0.180998783 7.097233497 0.138905967 0.035327141 11.60952179 -1.064814331 0.346553081 AANVTLLTSLVEGEAVHLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AANVTLLTSLVEGEAVHLAR 20 0 A0A6E1XE14;P05549-5;P05549-6;P05549;Q92481;Q92481-2;Q6VUC0 A0A6E1XE14 TFAP2A;TFAP2B;TFAP2E Transcription factor AP-2-alpha;Transcription factor AP-2-beta;Transcription factor AP-2-epsilon 0 144.27 1.58E-07 109150000 148370 112770 97930 82605 126660 121410 113450 144620 108710 96646 FALSE TRUE 142571.5364 109553.91 115628.1294 86868.25395 130734.1339 123864.9934 114838.435 141633.5465 96369.69655 90100.08034 1.582368582 1.215913566 1.283329926 0.964130705 1.450987984 1.374748978 1.27456529 1.571958049 1.069585024 1 16.45924077 1.066015055 8.860042161 1.000223669 1.334532517 0.341968784 0.170439113 0.283649756 33.49306707 0.163942803 0.041030156 11.64166385 -1.066015055 0.334308848 RVS(ph)LVGADDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RVSLVGADDLR 11 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 RVS(1)LVGADDLR;RVS(1)LVGADDLR;RVS(1)LVGADDLR;RVS(1)LVGADDLR 137.61 4.58E-05 1506260000 1199010 1560020 970020 1567720 1188710 1039420 1258620 1499400 1075980 817390 TRUE FALSE 1152151.364 1515529.757 1145324.192 1648630.217 1226945.937 1060437.785 1274023.368 1468436.866 953839.2613 762027.4472 1.511955203 1.988812559 1.502995983 2.163478787 1.610107275 1.39160051 1.671886456 1.92701309 1.251712474 1 19.53948344 1.066027837 4.82664359 1.004856866 1.728146841 0.52974262 0.229778359 0.13053269 5.513635518 0.213073047 0.054043765 11.64200649 -1.066027837 0.723289974 EDHKPFGDDEVELFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EDHKPFGDDEVELFR 15 1 F6WE04;Q5SRH9-5;Q5SRH9-6;Q5SRH9-4;Q5SRH9;A0A0A0MRQ0;Q5SRH9-2;E9PHX9 F6WE04 TTC39A Tetratricopeptide repeat protein 39A 0 ;;; 236.81 6.12E-18 579210000 1205170 1063310 1104360 1040880 1092750 1207990 1258650 979150 1536550 1525700 FALSE TRUE 1158070.624 1032985.44 1303942.418 1094599.942 1127899.296 1232416.385 1274053.735 958930.2103 1362127.286 1422362.98 0.814187827 0.726246011 0.916743782 0.76956442 0.792975712 0.866457017 0.895730382 0.67418108 0.957650969 1 20.43985825 1.066505719 8.403892202 0.99982358 0.806269946 0.493943106 0.070204252 0.181531038 19.57524472 0.065979118 0.016518231 11.65482399 -1.066505719 -0.193553634 KSPHLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPHLEK 7 1 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 80.455 0.019388 676990000 3366800 3246900 2936200 2965000 3106100 3110200 3601900 3409700 4193900 4314300 FALSE TRUE 3235221.734 3154301.591 3466836.655 3118024.005 3206010.527 3173090.375 3645981.13 3339288.503 3717826.054 4022088.618 0.804363613 0.784244677 0.861949346 0.775225089 0.797100917 0.788916077 0.906489507 0.830237426 0.924352098 1 21.93951344 1.066509545 0.691644022 1.001635045 0.802142786 0.753237311 0.035198097 0.336513997 0.378309688 0.03303987 0.013389434 11.65492667 -1.066509545 -0.199492259 VDWQENDFSKR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDWQENDFSKR 11 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 77.912 0.05022 133320000 92943 115860 79202 86932 98585 97692 109030 89151 125780 123520 FALSE TRUE 89310.68481 112555.7862 93515.56324 91418.57094 101756.0761 99667.39917 110364.3418 87310.0007 111501.9817 115153.8804 0.775576859 0.977438067 0.812092158 0.79388181 0.883653036 0.865514899 0.958407493 0.758202854 0.968286795 1 16.8132035 1.066734665 8.329743 0.999859262 0.855814357 0.36810807 0.069217705 0.228481024 24.20070387 0.062565222 0.015664553 11.66096964 -1.066734665 -0.144044905 DSENT(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSENTPVK 8 0 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 DSENT(1)PVK;DSENT(1)PVK 144.17 0.0065916 534180000 1355540 1028500 1013330 1097020 1027730 966400 1339760 1415650 1347000 1725800 TRUE FALSE 1302563.998 999168.187 1196461.272 1153637.334 1060787.869 985941.2701 1356156.384 1386416.333 1194094.207 1608910.029 0.809594057 0.621021791 0.743647097 0.717030358 0.659320813 0.612800749 0.842903804 0.861711536 0.742175874 1 20.61765222 1.066736201 0.591039112 0.991771019 0.693672221 0.538762236 0.077677609 0.618255947 0.530302025 0.08123781 0.036433072 11.6610109 -1.066736201 -0.298098798 FLYQLHETEKEDLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLYQLHETEKEDLIR 15 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 256.26 5.70E-25 1192350000 1494320 1638160 1355540 1421290 1364560 1459800 1366070 1543110 1891640 1955930 FALSE TRUE 1435920.322 1591441.281 1600516.232 1494642.947 1408452.312 1489318.156 1382788.373 1511244.239 1676908.958 1823453.119 0.787473123 0.872762378 0.877739173 0.8196772 0.77240939 0.816757031 0.758335029 0.828781515 0.91963371 1 20.79824168 1.066847586 2.794799565 0.998262713 0.816127611 0.732040777 0.036319558 0.128173808 2.065706516 0.036930469 0.009905796 11.66400202 -1.066847586 -0.182135102 DSPTQEREELFIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSPTQEREELFIQK 14 1 E9PFR3;Q14738;H0Y8C4 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 0 ; 198.78 1.97E-08 372130000 184986 176677 132154 143720 158952 185399 157012 169725 174803 157512 FALSE TRUE 177756.5426 171638.3449 156037.1675 151137.4064 164064.8354 189147.8948 158933.5598 166220.1194 154960.0963 146843.5719 1.210516336 1.168851606 1.06260809 1.029240875 1.11727625 1.288091077 1.082332428 1.131953665 1.05527327 1 17.16392059 1.067191284 1.933013369 0.99959581 1.135586335 0.289810278 0.070625396 0.441149626 3.317772663 0.069467448 0.019716265 11.6732365 -1.067191284 0.135990525 S(ph)EEHHLYSNPIKEEMTESK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEEHHLYSNPIKEEMTESK 19 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(1)EEHHLYSNPIKEEMTESK 188.69 9.44E-15 295170000 110160 101880 104120 108800 96797 125190 158620 59757 200260 213540 TRUE FALSE 105854.8254 98974.48215 122936.8001 114415.181 99910.56341 127721.4276 160561.239 58522.99707 177527.3244 199076.7456 0.531728732 0.497167471 0.617534709 0.574729011 0.501869584 0.641568794 0.806529354 0.29397204 0.891753197 1 17.60296518 1.067413918 7.395274528 0.999176471 0.55932812 0.621285433 0.122498524 0.121844223 10.49179028 0.115527989 0.028957737 11.67922212 -1.067413918 -0.439848352 KSDIDEIVLVGGSTR ddPTM_BT-474_Pertuzumab_2h_R1 6 KSDIDEIVLVGGSTR 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;; 202.34 9.55E-09 11240870000 14028400 16341800 11764000 14515600 12442800 12150000 14524500 14376800 17382900 17510800 FALSE TRUE 13480154.62 15875747.86 13890016.49 15264751.86 12843033.96 12395681.32 14702255.18 14079914.06 15409666.07 16324777.92 0.825748116 0.972493956 0.850854851 0.935066433 0.786720287 0.759316996 0.900609812 0.862487326 0.943943381 1 23.96056003 1.06763459 2.345050356 1.000188241 0.861942897 0.362422678 0.060667563 0.307199341 3.454321574 0.058100619 0.015998967 11.68515802 -1.06763459 -0.138245345 VVTVHLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVTVHLEK 8 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 144.12 0.00059047 1499400000 2676300 2621600 2848200 2818500 2578200 2185700 2967300 2958700 3667700 3926800 FALSE TRUE 2571707.237 2546834.535 3362933.098 2963963.123 2661130.144 2229896.352 3003614.705 2897601.811 3251358.072 3660834.338 0.70249211 0.695697838 0.918624769 0.809641423 0.72691903 0.609122442 0.820472719 0.791514049 0.888146737 1 21.80374106 1.067976719 1.437031672 0.998932422 0.75422004 0.502317967 0.078699113 0.353998304 1.477443783 0.077549768 0.023293298 11.69436701 -1.067976719 -0.244712382 IIANALSSEPACLAEIEEDKAR ddPTM_BT-474_Pertuzumab_2h_R1 3 IIANALSSEPACLAEIEEDKAR 22 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 192.94 8.16E-18 226348000 281224 274729 194452 238543 274262 253927 238286 269802 306738 307186 FALSE TRUE 270233.4552 266893.9979 229593.802 250854.2328 283083.8863 259061.5779 241202.2153 264230.4944 271918.3882 286380.0186 0.943618401 0.931957471 0.80171027 0.875948797 0.988490355 0.904607728 0.842245267 0.92265688 0.949501957 1 18.12757131 1.0680847 2.209409276 0.998316502 0.898301451 0.289938858 0.049659759 0.372048681 3.691740789 0.048402149 0.013451216 11.69727501 -1.0680847 -0.100015051 DLLTPPADKPGQDNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLTPPADKPGQDNR 15 1 I3VM54;Q9Y2K7;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 ; 99.055 0.0024532 747300000 341053 315753 346402 281662 352720 329195 324315 310240 435700 438860 FALSE TRUE 327724.2717 306748.0336 409004.5471 296198.6096 364065.5591 335851.5484 328284.064 303833.4356 386241.1626 409135.6213 0.801016227 0.749746582 0.999679631 0.723961919 0.889840777 0.820880732 0.802384459 0.742622788 0.944041884 1 18.64221963 1.068942312 5.690697778 0.999003906 0.815837501 0.409630801 0.07615992 0.162522497 8.80428975 0.069406527 0.017489011 11.72039671 -1.068942312 -0.183166405 IEDTVFHVFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEDTVFHVFDK 11 0 Q9Y2L1;G3V1J5;Q9Y2L1-2 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 ; 107.85 0.0021423 33542000 140119 131146 115157 121845 125735 109677 140111 136437 168799 176981 FALSE TRUE 134642.9946 127405.8445 135968.4316 128133.4351 129779.3805 111894.7441 141825.7203 133619.5283 149637.6452 164993.9192 0.816048223 0.772185091 0.82408147 0.776594893 0.786570687 0.678174957 0.859581498 0.809845168 0.906928242 1 17.33205333 1.070222415 1.2840242 1.000006743 0.782132873 0.712720454 0.043862634 0.223840654 0.756280915 0.039732545 0.01227597 11.75499408 -1.070222415 -0.21787387 DSDKEGTSNS(ph)TSEDGPGDGFTILSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDKEGTSNSTSEDGPGDGFTILSSK 26 1 Q9P0M6;Q5SQT3 Q9P0M6 H2AFY2 Core histone macro-H2A.2;Histone H2A 1 DSDKEGT(0.011)S(0.046)NS(0.894)T(0.046)S(0.003)EDGPGDGFTILSSK;DS(0.002)DKEGT(0.175)S(0.121)NS(0.513)T(0.175)S(0.015)EDGPGDGFTILSSK 162 1.00E-11 391240000 525600 561910 618930 593340 372620 674070 499290 557540 830230 903510 TRUE FALSE 505058.9709 545884.877 730784.419 623962.3485 384605.6607 687700.1572 505400.4604 546026.6042 735985.771 842314.4629 0.59960857 0.648077293 0.867590967 0.740771263 0.45660579 0.816441113 0.600013988 0.648245552 0.873766038 1 19.68399941 1.072391257 3.683877466 0.996915089 0.673130867 0.493430609 0.110694403 0.165424484 4.351111981 0.103877162 0.026912981 11.81384469 -1.072391257 -0.323784221 IKAEYEGDGIPTVFVAVAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKAEYEGDGIPTVFVAVAGR 20 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 165.06 1.57E-11 2091270000 2395800 2614600 1830180 2036380 2278900 2520400 2186800 2438100 2526400 2360700 FALSE TRUE 2302169.487 2540034.168 2160934.238 2141477.816 2352202.888 2571364.215 2213562.713 2387752.383 2239613.664 2200807.686 1.046056637 1.154137267 0.981882357 0.973041774 1.068790746 1.168372971 1.005795611 1.084943677 1.017632607 1 21.06960165 1.072883421 5.66473294 1.000298755 1.060228207 0.103346538 0.061739226 0.427546006 22.14352191 0.05918049 0.014915286 11.8272403 -1.072883421 0.059929453 VVAIGECGLDFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVAIGECGLDFDR 13 0 E5RG17;Q6P1N9;H0YBX2;G5EA19;U3KQS5;Q6P1N9-2;E5RK70;A0A0D9SGD3;E5RG62;E5RGF2 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 ; 138.25 1.15E-05 225550000 101754 119179 85048 116239 104682 107891 111315 130340 105062 93643 FALSE TRUE 97777.34119 115780.1316 100418.0655 122238.1087 108049.1916 110072.6299 112677.3063 127648.4335 93135.80222 87300.4762 1.120009254 1.326225659 1.150257935 1.400199793 1.237670129 1.26084799 1.290683753 1.462173392 1.066841858 1 16.4137019 1.072885261 7.349835611 1.000696827 1.288596937 0.512084986 0.097486426 0.15035965 11.84979065 0.092928201 0.023295082 11.82729043 -1.072885261 0.28790011 HAGVQTSRPIS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 HAGVQTSRPISR 12 1 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 HAGVQTS(0.001)RPIS(0.999)R 80.507 0.012205 215560000 27524 29727 19774 31125 26194 26760 27383 30772 24220 19315 TRUE FALSE 26448.33165 28879.21507 23347.60167 32731.36498 27036.5538 27301.10553 27718.12135 30136.54745 21470.64714 18006.77785 1.468798687 1.603796932 1.296600751 1.817724707 1.501465394 1.516157181 1.539316005 1.673622438 1.192364749 1 14.13625243 1.07333796 4.476533201 1.004603827 1.555301126 0.676893445 0.129051015 0.097840896 3.498797116 0.116403071 0.029663857 11.83962534 -1.07333796 0.550697298 ELGIIPTIIRDEELK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELGIIPTIIRDEELK 15 1 Q8NDH3-3;Q8NDH3-2;Q8NDH3;Q8NDH3-5;Q8NDH3-4;H0YEP3 Q8NDH3-3 NPEPL1 Probable aminopeptidase NPEPL1 0 ;; 230.38 3.07E-13 320004000 440510 475630 300259 408336 422240 409238 427669 452369 423780 376041 FALSE TRUE 423294.3822 462065.4981 354522.4805 429410.2699 435821.7331 417513.0728 432902.9412 443027.4221 375674.271 350571.4081 1.207441258 1.31803532 1.011270378 1.224886742 1.24317535 1.190950155 1.234849537 1.263729476 1.071605563 1 18.41934881 1.073982203 4.693738242 1.00181526 1.212577788 0.477721021 0.075261976 0.151731079 5.816454127 0.0704185 0.017893613 11.85720158 -1.073982203 0.210762528 SS(ph)PRPTAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPRPTAEK 9 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.115)S(0.885)PRPTAEK 55.452 0.077758 212260000 236930 224100 210460 199780 200910 182460 221490 240840 254000 271010 TRUE FALSE 227670.5137 217708.8874 248494.8037 210090.6697 207372.4526 186149.4662 224200.6609 235866.5698 225166.9849 252654.2513 0.901114913 0.861687014 0.983536997 0.831534275 0.820775631 0.736775515 0.887381311 0.933554724 0.891206001 1 17.94680493 1.074403709 1.107713407 0.99212628 0.861013487 0.292511043 0.062431962 0.6612037 1.7070594 0.062634293 0.020251917 11.86871521 -1.074403709 -0.131112794 KEEMDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEEMDK 6 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 84.244 0.089907 609970000 171930 133520 124380 143860 128230 171080 164990 175980 199990 232250 FALSE TRUE 165210.7855 129712.1403 146858.2328 151284.6318 132354.6344 174539.3548 167009.197 172345.9515 177287.9736 216519.5006 0.763029589 0.599078328 0.678267927 0.698711347 0.611282744 0.806113788 0.771335591 0.795983507 0.818808343 1 17.72413744 1.075260228 0.422067323 1.012708529 0.656063973 0.755440155 0.054787372 0.532911982 0.262651257 0.072250578 0.039835431 11.89214589 -1.075260228 -0.356644555 ES(ph)PVSAPLEGLICR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESPVSAPLEGLICR 14 0 O75376;O75376-2;A0A088AWL3 O75376 NCOR1 Nuclear receptor corepressor 1 1 ES(1)PVSAPLEGLICR;ES(1)PVSAPLEGLICR 209.79 6.44E-09 214630000 82778 79654 76219 77625 75976 76431 83466 93189 108197 120466 TRUE FALSE 79542.94424 77382.34591 89993.46878 81631.23555 78419.83704 77976.48719 84487.48188 91264.61458 95914.93016 112306.7305 0.708265158 0.689026789 0.801318571 0.726859692 0.698264803 0.694317133 0.75229224 0.812637089 0.854044363 1 16.77708487 1.076808946 0.998294024 0.997311457 0.720343564 0.882186656 0.031838395 0.170463497 0.365505562 0.031373441 0.010545931 11.93462964 -1.076808946 -0.276967893 TNPS(ph)PTNPFSSDLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNPSPTNPFSSDLQK 15 0 P49757-3;P49757;G3V3Z8;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;P49757-9 P49757-3 NUMB Protein numb homolog 1 TNPS(0.937)PT(0.063)NPFSSDLQK;TNPS(0.996)PT(0.004)NPFSSDLQK 256.89 1.73E-16 104050000 149943 145420 115394 118300 146799 133031 121150 139509 165091 164571 TRUE FALSE 144083.0618 141272.764 136248.2627 124405.4772 151520.9232 135720.978 122632.6699 136628.0904 146350.5618 153424.4596 0.939114025 0.920796882 0.888047858 0.810858174 0.987593005 0.884611087 0.799303255 0.890523524 0.953893285 1 17.22716898 1.0770057 3.437003252 0.998293232 0.887190134 0.321363631 0.05244947 0.24494526 5.652003315 0.050292871 0.013140308 11.94003774 -1.0770057 -0.111103098 AYSGS(ph)DLPSSSSGGANGTAGGGGGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AYS(0.085)GS(0.913)DLPS(0.001)S(0.001)SSGGANGTAGGGGGAR;AYS(0.256)GS(0.744)DLPSSSSGGANGTAGGGGGAR 355.43 4.22E-110 2179260000 618925 620843 504825 625027 612883 580041 579681 660467 622250 563788 TRUE FALSE 594736.7267 603137.1655 596058.1073 657284.7184 632596.9383 591769.8264 586775.3095 646828.1256 551614.7887 525602.1366 1.131534074 1.147516579 1.134048106 1.250536618 1.203566147 1.125889309 1.116386842 1.230642116 1.049491146 1 19.00361161 1.077033199 5.466978241 1.001127071 1.16842543 0.633528965 0.044144749 0.11439553 5.414619276 0.043658262 0.01101725 11.94079379 -1.077033199 0.167298359 TFIGPGGNMPGYLRPETAQGIFLNFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFIGPGGNMPGYLRPETAQGIFLNFK 26 1 P41250 P41250 GARS Glycine--tRNA ligase 0 185.7 1.28E-17 462920000 163530 146770 109830 153440 153600 135590 161880 165400 197770 211880 FALSE TRUE 157139.0668 142584.2633 129678.7242 161359.0568 158540.6835 138331.7227 163861.1359 161984.4322 175319.9787 197529.1789 0.795523313 0.721838992 0.656504142 0.816887195 0.802619058 0.700310321 0.829554078 0.820053185 0.887564965 1 17.59170626 1.077119215 0.644460069 1.003367987 0.741913519 0.715931176 0.049368638 0.399053109 0.397758451 0.049165984 0.020900963 11.94315903 -1.077119215 -0.261454468 SMGSQEDDSGNKPSSYS(ph) ddPTM_BT-474_Pertuzumab_2h_R1 1 SMGSQEDDSGNKPSSYS 17 1 Q9UNS2-2;Q9UNS2;H7C3P9 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 1 SMGSQEDDSGNKPS(0.003)S(0.015)Y(0.005)S(0.977) 135.27 3.73E-05 374800000 380460 357970 351230 351280 373110 424670 389340 438340 558930 592760 TRUE FALSE 365591.2026 347761.0461 414705.0741 369409.6029 385111.422 433257.1184 394104.8594 429288.1258 495482.6096 552611.8372 0.661569619 0.629304374 0.750445514 0.668479352 0.696893183 0.784017079 0.713167603 0.776834836 0.896619609 1 19.07590694 1.077454803 0.549450324 1.011951693 0.673876401 0.866398679 0.039786908 0.297793062 0.226268386 0.042720865 0.020187759 11.9523913 -1.077454803 -0.338075292 YSTSPYLLEAASHLS(ph)PENFVEDEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSTSPYLLEAASHLSPENFVEDEAK 25 0 Q9BX63;Q9BX63-2 Q9BX63 BRIP1 Fanconi anemia group J protein 1 YSTSPYLLEAASHLS(1)PENFVEDEAK 174.72 1.77E-12 58410000 50449 42118 31340 38802 40630 35260 39722 40978 49075 48710 TRUE FALSE 48477.39731 40916.83588 37003.83515 40804.57587 41936.90085 35972.98136 40208.12972 40131.78998 43504.21174 45410.82831 1.067529466 0.901036986 0.814868095 0.898564888 0.92350002 0.792167478 0.885430441 0.883749349 0.958014054 1 15.47074873 1.077753294 3.468117818 0.99907353 0.890054953 0.193899722 0.069417927 0.320542907 7.495138058 0.064955464 0.016954782 11.96060902 -1.077753294 -0.109018577 HNVGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 HNVGVK 6 0 O75874;C9J4N6;C9JLU6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 74.832 0.079288 973180000 2587100 2590300 2272700 2529200 2541700 2724700 2783600 1868650 3308900 3147900 FALSE TRUE 2485993.272 2516427.18 2683427.446 2659732.315 2623456.089 2779795.301 2817666.529 1830061.724 2933287.544 2934689.929 0.84710594 0.85747634 0.914381932 0.90630778 0.893946602 0.947219423 0.960124101 0.623596281 0.999522135 1 21.48477665 1.078607202 24.99966571 1.000488471 0.863779412 0.255227765 0.08917961 39.65673656 12608.58024 0.092087686 0.023021922 11.98414905 -1.078607202 -0.136709059 FMDQHPEMDFSK ddPTM_BT-474_Pertuzumab_2h_R1 3 FMDQHPEMDFSK 12 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ;; 131.32 0.00020077 1071860000 1522070 1586170 1348610 1313540 1407210 1210010 1527810 1359310 1909260 1933790 FALSE TRUE 1462585.822 1540933.985 1592333.827 1381331.957 1452474.188 1234477.231 1546507.796 1331239.773 1692528.809 1802812.681 0.811279972 0.854738821 0.883249737 0.766209364 0.805671162 0.684750692 0.857830551 0.738423791 0.938826772 1 20.78181807 1.079239277 5.079026325 0.998443529 0.800323416 0.597759253 0.056475387 0.12144713 5.07419971 0.053875241 0.013637225 12.00160357 -1.079239277 -0.198120112 LQHYAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQHYAK 6 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 90.285 0.049203 2102300000 4769400 5071400 4464400 4765400 4635200 4832500 5232300 5007400 6316300 6400800 FALSE TRUE 4583006.575 4926768.637 5271216.39 5011342.865 4784295.418 4930216.461 5296334.453 4903995.44 5599300.104 5967268.115 0.768024243 0.825632189 0.883355044 0.839805212 0.801756403 0.826209979 0.887564351 0.821815837 0.9383356 1 22.50863917 1.079738201 3.183166633 0.999528881 0.833965722 0.73831513 0.033574582 0.110202238 2.208447074 0.031937679 0.008429779 12.0153991 -1.079738201 -0.16556316 QLSES(ph)ESSLEMDDERYFNEMSAQGLRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.356)ES(0.642)ES(0.002)SLEMDDERYFNEMSAQGLRPR;QLS(0.348)ES(0.429)ES(0.112)S(0.112)LEMDDERYFNEMSAQGLRPR 337.42 1.95E-96 314734000 37585 51289 37220 39061 47297 50883 42973 50864 41228 34649.1 TRUE FALSE 36116.13665 49826.28794 43946.48195 41076.94289 48818.35096 51911.88912 43498.91643 49813.64063 36547.97028 32302.28559 1.118067529 1.542500384 1.360475927 1.271641995 1.511297113 1.607065512 1.34662039 1.542108854 1.131436046 1 14.97934863 1.07997026 4.943841663 1.003530651 1.421687304 0.503046582 0.140267628 0.138065005 5.521406226 0.128150965 0.032481324 12.02182108 -1.07997026 0.418156652 RGFGFVYFQNHDAADK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGFGFVYFQNHDAADK 16 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 149.44 5.42E-07 469920000 576210 562870 458210 499040 505920 492820 553910 551110 683310 698380 FALSE TRUE 553691.0762 546817.4987 541018.7398 524795.5142 522193.3763 502785.1581 560688.9163 539729.3859 605743.5135 651078.1005 0.850421901 0.839864677 0.830958282 0.806040802 0.802044142 0.772234787 0.861169982 0.828977945 0.930369971 1 19.31247109 1.081041395 1.99568652 1.000809625 0.82069159 0.850215585 0.024545228 0.109672998 0.868795696 0.023796832 0.006730652 12.05150806 -1.081041395 -0.180118034 MLWGSDPYPHAEPQQAT(ph)TPK ddPTM_BT-474_Pertuzumab_2h_R1 1 MLWGSDPYPHAEPQQATTPK 20 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 MLWGSDPYPHAEPQQAT(0.614)T(0.386)PK 138.25 7.84E-06 133250000 149360 134090 128860 115990 130550 147040 118010 144720 160770 161030 TRUE FALSE 143522.8461 130265.8845 152147.8685 121976.2578 134749.2593 150013.2495 119454.2417 141731.4814 142520.0636 150123.2947 0.956033149 0.86772599 1.013486074 0.8125072 0.897590608 0.999266968 0.795707568 0.944100526 0.949353423 1 17.19578833 1.081971142 2.278378747 0.996936881 0.907103776 0.14804321 0.067999245 0.492834366 5.116539589 0.059682716 0.016541333 12.0773358 -1.081971142 -0.089833105 QDS(ph)LEPVLRDPCYLINEGICNR ddPTM_BT-474_Pertuzumab_2h_R1 1 QDSLEPVLRDPCYLINEGICNR 22 1 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;E7EWD5 D6RD37 TSC22D3 1 QDS(1)LEPVLRDPCYLINEGICNR 149.07 4.00E-08 194390000 51620 51719 33786 50660 67096 54498 47666 57236 45926 36993 TRUE FALSE 49602.63333 50244.02476 39891.88177 53274.56867 69254.20378 55599.9869 48249.35077 56054.0566 40712.67302 34487.43116 1.438281474 1.456879306 1.156707833 1.544753172 2.008099805 1.612181164 1.399041597 1.625347401 1.180507554 1 15.07378305 1.082195927 4.184793899 1.00446945 1.531831303 0.436658772 0.204287562 0.190431543 5.908212325 0.207838599 0.053261839 12.08358849 -1.082195927 0.527361853 KT(ph)GSYGALAEITASK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTGSYGALAEITASK 15 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 KT(0.5)GS(0.5)YGALAEITASK 154.84 1.41E-06 78792000 348020 195600 71608 102470 75203 74426 82617 313490 95940 92545 TRUE FALSE 334418.9936 190021.6795 84549.15851 107758.489 77621.97279 75930.94471 83628.09156 307016.3219 85049.29341 86276.84472 3.876115251 2.202464405 0.979975088 1.248985047 0.899684881 0.880084859 0.969299374 3.558501971 0.985771949 1 16.3966858 1.083523057 21.57522823 0.9867369 1.805658701 0.092459904 1.043344582 20.80956251 5364.236951 1.056124125 0.264031243 12.12057036 -1.083523057 0.818921801 DLEEAEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEEAEGR 8 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 ; 129.77 0.0025041 456670000 434960 645890 447640 939080 454230 526500 760270 670970 581060 485710 FALSE TRUE 417961.2823 627469.8496 528538.5057 987546.0313 468840.7205 537146.1907 769574.4117 657114.235 515100.5048 452812.4291 0.923034032 1.385716931 1.167234978 2.180916353 1.035397198 1.186244361 1.69954348 1.451184183 1.137558229 1 18.78855403 1.084286387 4.313021352 1.005498188 1.39807939 0.120229704 0.341054388 0.382835605 12.31670958 0.314822098 0.080500661 12.1418926 -1.084286387 0.392581202 HKEQNNDSQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HKEQNNDSQLK 11 1 O95347-2;O95347 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ; 190.15 1.44E-06 407460000 557710 516920 436410 471180 447690 488900 560260 400370 675220 649650 FALSE TRUE 535914.0766 502177.9477 515278.9949 495497.6563 462090.3554 498785.893 567116.6295 392102.2196 598571.8564 605648.6269 0.884859724 0.829157246 0.850788679 0.818127268 0.762967726 0.823556549 0.936378957 0.647408749 0.988315386 1 19.20812152 1.085070561 13.7402971 0.999989754 0.816261664 0.485636722 0.072042189 0.589762297 92.00591244 0.068132447 0.017034267 12.16383613 -1.085070561 -0.18372809 LFEHYYQELK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFEHYYQELK 10 0 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 106.29 0.0024361 1328060000 3558400 3516400 3076300 3011900 3105200 2470640 3726200 3316400 4144900 4159400 FALSE TRUE 3419333.794 3416115.715 3632255.842 3167344.52 3205081.578 2520598.034 3771802.35 3247915.181 3674388.329 3877680.133 0.881798827 0.880968929 0.936708474 0.816814284 0.826546148 0.650027322 0.972695586 0.837592341 0.947573859 1 21.88676237 1.08553362 1.482341384 1.001456997 0.846008711 0.270625246 0.081947936 0.528768059 2.32690353 0.076924391 0.022988272 12.17681253 -1.08553362 -0.155448286 EVSAYIK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSAYIK 7 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 81.784 0.061099 160000000 435350 475230 404330 415360 432300 350370 508790 491510 523820 580840 FALSE TRUE 418336.0407 461676.9057 477401.4253 436796.7794 446205.3221 357454.7215 515016.7242 481360.1467 464358.1496 541499.1894 0.772551555 0.852590206 0.881629067 0.806643459 0.824018449 0.660120511 0.951094174 0.888939736 0.857541726 1 19.04659965 1.086086869 0.740142612 0.992087835 0.814627741 0.366835137 0.071128899 0.740549895 0.939141662 0.069224099 0.027044231 12.1923345 -1.086086869 -0.177460094 FEVIEFDDGAGSVLR ddPTM_BT-474_Pertuzumab_2h_R1 3 FEVIEFDDGAGSVLR 15 0 P10586-2;P10586;A2A437 P10586-2 PTPRF Receptor-type tyrosine-protein phosphatase F 0 ;; 193.28 2.31E-07 64468000 90083 106396 91433 126625 90749 97328 101514 114780 110219 103360 FALSE TRUE 86562.45677 103361.6903 107956.977 133160.1314 93668.024 99296.03884 102756.3587 112409.7529 97707.4012 96359.33514 0.898329743 1.072669193 1.12035826 1.381912103 0.972070053 1.030476587 1.06638717 1.166568374 1.013989989 1 16.55613682 1.086313325 8.985498271 1.000133875 1.095346519 0.065808432 0.121406718 0.701386656 62.2804756 0.116627624 0.029186741 12.19869365 -1.086313325 0.095212644 LATEEPPPRS(ph)PPESESEPYTFSHPNNGDVSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LATEEPPPRSPPESESEPYTFSHPNNGDVSSK 32 1 Q9H5V8-2;Q9H5V8 Q9H5V8-2 CDCP1 CUB domain-containing protein 1 1 LAT(0.168)EEPPPRS(0.829)PPES(0.002)ES(0.001)EPYTFSHPNNGDVSSK 73.303 0.0016347 114050000 58352 109020 58560 145230 71448 74526 94341 88403 70713 46284 TRUE FALSE 56071.53933 105910.8563 69143.09466 152725.3377 73746.18981 76032.96678 95495.57338 86577.44716 62685.95669 43149.14345 1.299482095 2.454529751 1.602421024 3.539475537 1.709099739 1.762096781 2.213151079 2.006469659 1.452774069 1 15.3970443 1.086965624 2.307774813 1.004189881 2.111849335 0.270039761 0.58067939 0.343102801 3.631223396 0.519202446 0.143733575 12.21702955 -1.086965624 1.107659454 SPSPSPTS(ph)PGSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPSPTSPGSLR 13 0 O15075-2;O15075;Q5VZY9;O15075-3;O15075-4 O15075-2 DCLK1 Serine/threonine-protein kinase DCLK1 1 SPS(0.001)PS(0.005)PT(0.357)S(0.637)PGSLR 178.51 1.52E-05 341890000 145680 189950 134450 206560 184440 176370 166100 185030 168830 142870 TRUE FALSE 139986.6645 184532.812 158748.1058 217220.5864 190372.6801 179936.3222 168132.7815 181209.0658 149665.1262 133193.2876 1.051003898 1.385451288 1.191862658 1.630867367 1.429296352 1.350941368 1.262321732 1.360496982 1.123668684 1 17.02316185 1.088299617 3.171690624 1.001359832 1.342087415 0.372417448 0.14420873 0.225683354 4.409544079 0.134070657 0.035457096 12.25461345 -1.088299617 0.340727583 HAEVMK ddPTM_BT-474_Pertuzumab_2h_R1 1 HAEVMK 6 0 Q9NT62;Q9NT62-2 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 76.592 0.07465 66188000 274700 249420 230170 263280 227610 236370 261080 240080 316230 308680 FALSE TRUE 263964.4203 242306.7858 271766.8391 276867.9124 234931.2824 241149.5633 264275.1751 235122.2641 280332.8961 287772.8287 0.917266656 0.842007173 0.944379775 0.962105817 0.816377569 0.837985867 0.918346518 0.817041224 0.974146508 1 18.13457085 1.088714322 6.703703812 0.999326761 0.880609286 0.418251754 0.049988977 0.185704559 10.69847462 0.048309325 0.012127967 12.2663209 -1.088714322 -0.118717475 ALGALVDSCAPGLCPDWDSWDASKPVTNAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALGALVDSCAPGLCPDWDSWDASKPVTNAR 30 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ; 155.39 7.55E-09 1025210000 431120 443250 318003 407280 376290 381840 417250 448880 502850 535400 FALSE TRUE 414271.3538 430608.944 375473.216 428299.7696 388393.7096 389561.0664 422356.4303 439610.4711 445768.5761 499136.8811 0.829975443 0.862707126 0.752244986 0.858080791 0.778130658 0.780469409 0.846173557 0.880741311 0.893078819 1 18.92907598 1.09006393 0.936496736 0.996634043 0.811138329 0.731546645 0.034936028 0.273382515 0.523792908 0.032379135 0.011202759 12.30449885 -1.09006393 -0.185495714 ASYDVSDSGQLEHVQPWS(ph)V ddPTM_BT-474_Pertuzumab_2h_R1 1 ASYDVSDSGQLEHVQPWSV 19 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 ASYDVSDSGQLEHVQPWS(1)V 115.57 0.00014199 62640000 54661 69794 43865 64381 65895 49816 56839 64714 50770 40295 TRUE FALSE 52524.78769 67803.54346 51792.38127 67703.71113 68014.57252 50823.31365 57534.61268 63377.63329 45006.80245 37565.78376 1.398208221 1.804928226 1.378711585 1.802270693 1.810545814 1.352915035 1.531569607 1.687110635 1.198079687 1 15.19713158 1.092361543 4.067093278 1.006120868 1.601932272 0.583257586 0.171349758 0.129542221 3.730496362 0.155955674 0.040107438 12.36976768 -1.092361543 0.595811403 AFS(ph)WLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFSWLR 6 0 Q9P206-2 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 AFS(1)WLR 75.109 0.082403 9519200 57776 21206 7630.2 9043 11450 7760.6 8953.7 40377 7896.1 7900.6 TRUE FALSE 55518.05005 20601.22564 9009.146873 9509.710314 11818.29965 7917.524649 9063.278059 39543.20084 6999.767831 7365.485325 7.537595636 2.796995002 1.223157263 1.29111795 1.604551381 1.074949484 1.230506567 5.368716262 0.950347129 1 12.84656487 1.093180258 22.88278089 0.96940679 2.66447372 0.110222956 2.018650955 19.06840582 4656.148418 1.972816598 0.49320438 12.39310867 -1.093180258 1.695066931 IDAHLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDAHLNK 7 0 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 110.61 0.0067645 985080000 1788030 1856690 1550570 1659930 1593560 1586900 1850170 1666280 2181990 2146700 FALSE TRUE 1718151.811 1803739.019 1830792.491 1745599.186 1644818.305 1618988.205 1872812.934 1631870.736 1934299.643 2001302.097 0.858516969 0.901282731 0.914800666 0.872231728 0.821874072 0.808967426 0.935797218 0.8154045 0.96652057 1 20.93250753 1.093630534 5.654515519 0.9988021 0.86693037 0.576650073 0.040566476 0.132803077 5.915422342 0.038880687 0.009804201 12.40596451 -1.093630534 -0.13187173 VQISPDS(ph)GGLPER ddPTM_BT-474_Pertuzumab_2h_R1 1 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 VQIS(0.34)PDS(0.66)GGLPER 192.4 2.88E-06 1101900000 924490 937110 710290 916260 939900 922310 900530 958820 946890 858410 TRUE FALSE 888359.9087 910384.5403 838655.2033 963548.2884 970132.7371 940959.7401 911550.9555 939020.0319 839403.0169 800269.1261 1.110076448 1.137597979 1.04796646 1.204030316 1.212258108 1.175804126 1.139055507 1.173380306 1.048900913 1 19.61012573 1.094731337 4.134118485 1.001656416 1.15132851 0.561090508 0.045278837 0.148674116 4.355358999 0.045222742 0.011616298 12.43744969 -1.094731337 0.149672093 T(ph)PSPSQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSPSQPK 8 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.869)PS(0.131)PSQPK 116.37 0.012049 0 264500 241600 188500 220180 219590 213540 227540 235450 273870 268500 TRUE FALSE 254163.0476 234709.8046 222566.1432 231543.5162 226653.3118 217857.9251 230324.7026 230587.8752 242781.4258 250314.2558 1.015375839 0.937660557 0.889146894 0.925011304 0.905475044 0.870337666 0.92014217 0.921193539 0.969906508 1 17.93338093 1.09473974 2.896102858 0.999476671 0.919635582 0.330655757 0.036197818 0.266094028 4.351399419 0.034703511 0.00930658 12.43769033 -1.09473974 -0.079841089 ALFEEVPELLTEAEKK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALFEEVPELLTEAEKK 16 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;; 169.25 9.12E-09 247035000 341523 316712 250905 259834 293717 310546 286557 307655 357359 349811 FALSE TRUE 328175.9036 307679.6839 296249.1149 273244.0639 303164.6741 316825.4529 290063.9703 301301.8167 316793.1045 326117.9894 1.006310336 0.943461244 0.908410834 0.837868725 0.929616531 0.9715056 0.889444863 0.923904312 0.971406407 1 18.3150345 1.095230672 3.404280174 0.9989103 0.923101724 0.244661673 0.042848344 0.302237294 6.571374477 0.041781304 0.01096209 12.45175802 -1.095230672 -0.075808576 HLIPAANTGESK ddPTM_BT-474_Pertuzumab_2h_R1 6 HLIPAANTGESK 12 0 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;; 177.1 2.37E-05 6536690000 10031100 9371000 9034700 9802200 9125900 9447800 10396300 8192800 12993500 12620100 FALSE TRUE 9639073.522 9103748.255 10667471.27 10308092.72 9419442.861 9638840.989 10523533.03 8023615.817 11518532.35 11765329.39 0.819277829 0.773777593 0.906687005 0.876141447 0.800610213 0.819258065 0.894452903 0.681971201 0.979023364 1 23.48803838 1.095787953 9.333570921 0.999688007 0.820660041 0.545569488 0.061462672 0.199206739 16.62333265 0.059925434 0.014993967 12.4677462 -1.095787953 -0.179027966 FEGLS(ph)PLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 FEGLSPLQR 9 0 Q9Y3E2 Q9Y3E2 BOLA1 BolA-like protein 1 1 FEGLS(1)PLQR 75.566 0.039755 62722000 135460 137960 119810 122160 128020 134420 126250 147350 132090 119960 TRUE FALSE 130166.0734 134025.5159 141462.3322 128464.6922 132137.8796 137138.0645 127795.0853 144307.171 117095.697 111835.0024 1.163911751 1.198421899 1.264920009 1.148698436 1.181543138 1.226253513 1.142710981 1.290357831 1.047039786 1 16.77101227 1.096954987 5.986652171 1.001885857 1.203312408 0.713937463 0.045611422 0.094935981 4.47189475 0.042200944 0.010623385 12.50129453 -1.096954987 0.201426551 DNNLLGK ddPTM_BT-474_Pertuzumab_2h_R1 4 DNNLLGK 7 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PS65;E9PM13;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;; 109.86 0.016129 1281550000 1636100 1565420 1436600 1639840 1494160 1228150 1657670 1781280 2042750 2265690 FALSE TRUE 1572159.403 1520775.754 1696225.577 1724472.339 1542221.013 1252984.034 1677957.061 1744495.946 1810865.584 2112232.798 0.744311614 0.719984916 0.803048593 0.816421533 0.730137802 0.593203569 0.794399681 0.825901362 0.857322917 1 21.01033742 1.096959743 1.175824618 0.994007417 0.741672693 0.641360627 0.059912717 0.305840003 0.877748004 0.059906867 0.019048724 12.50143142 -1.096959743 -0.252334724 QLHLEGASLELS(ph)DDDTESK ddPTM_BT-474_Pertuzumab_2h_R1 3 QLHLEGASLELSDDDTESK 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK 333.71 1.49E-75 6961180000 3811860 3330130 3232360 2872100 2987780 3150360 3259180 3428010 3958960 3901120 TRUE FALSE 3662888.297 3235157.953 3816519.355 3020329.425 3083884.657 3214062.438 3299066.82 3357220.396 3509555.458 3636893.668 1.007147481 0.889538779 1.049389865 0.830469544 0.847944685 0.883738358 0.907111156 0.923101059 0.964987096 1 21.79427532 1.097409297 2.324164968 0.999399504 0.913339513 0.155614406 0.06320883 0.499267805 5.281588038 0.059315698 0.016431562 12.51437881 -1.097409297 -0.086059992 CTHWAEGGK ddPTM_BT-474_Pertuzumab_2h_R1 5 CTHWAEGGK 9 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;;; 103.7 0.0033798 2300880000 4537110 4203520 3625040 3925300 3918790 4058500 4497440 3647580 5480550 5351700 FALSE TRUE 4359794.725 4083639.725 4280165.367 4127885.203 4044841.439 4140565.651 4552481.016 3572256.198 4858420.94 4989224.592 0.873842146 0.818491862 0.857881879 0.827360069 0.810715446 0.829901636 0.912462635 0.715994266 0.973782769 1 22.25038418 1.097660081 7.919854939 0.999297622 0.829165516 0.629868151 0.048025409 0.132355693 8.812347502 0.044648689 0.011184259 12.52160735 -1.097660081 -0.170132106 IGSLEWYYEHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGSLEWYYEHVK 12 0 Q9BV36-2;Q9BV36-5;C9JKV5;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ; 147.71 6.58E-05 562010000 763700 824840 691490 682490 711920 488710 856600 752450 910280 926440 FALSE TRUE 733853.7597 801316.3708 816457.6251 717713.3907 734819.5533 498592.051 867083.327 736911.6446 806948.8306 863691.3936 0.849671266 0.927780891 0.945311753 0.830983608 0.850789482 0.577280328 1.003927252 0.853211749 0.934302271 1 19.72015639 1.099038866 1.275814465 0.997472379 0.850127131 0.166207685 0.106376329 0.814763882 2.707814295 0.100037767 0.03106367 12.56142372 -1.099038866 -0.147345248 EKPSEDMESNTFFDPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKPSEDMESNTFFDPR 16 1 O43395;O43395-3 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 ;; 100.45 0.0018699 833350000 1704950 1681770 1465180 1392080 1580960 1547320 1517140 1812650 1647330 1551320 FALSE TRUE 1638318.669 1633807.566 1729970.619 1463925.416 1631813.014 1578607.871 1535707.213 1775218.144 1460332.005 1446247.715 1.132806401 1.129687224 1.196178636 1.012223149 1.128308102 1.091519699 1.061856276 1.227464788 1.009738505 1 20.46388325 1.099084516 10.85390077 1.000101756 1.122840793 0.398845693 0.05782658 0.33464237 32.55749303 0.054771903 0.013697751 12.56274417 -1.099084516 0.122739037 LALDGETLGEEEQEDEQPPWASPS(ph)PTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LALDGETLGEEEQEDEQPPWASPSPTSR 28 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LALDGETLGEEEQEDEQPPWAS(0.005)PS(0.616)PT(0.189)S(0.189)R 69.045 0.0080375 45160000 9948.1 14141 9384.4 15311 13604 13217 10136 16830 9335.4 7629 TRUE FALSE 9559.317254 13737.71253 11080.36983 16101.20254 14041.58501 13484.2568 10260.0474 16482.45462 8275.684529 7112.281035 1.344057864 1.931548045 1.557920698 2.263859157 1.974273084 1.895911696 1.442581831 2.31746391 1.163576705 1 12.79609662 1.099375033 6.809479226 1.006207418 1.856224452 0.501802559 0.304092122 0.152561209 8.324629648 0.277891161 0.069752093 12.57115071 -1.099375033 0.850017034 LSSS(ph)PGLFGAFSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSSPGLFGAFSVR 14 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 LSS(0.087)S(0.913)PGLFGAFSVR;LSS(0.01)S(0.99)PGLFGAFSVR 309.98 1.13E-55 929630000 1142690 1301720 981300 897920 873790 929280 1160610 1177120 1283410 1396020 TRUE FALSE 1098032.411 1264596.22 1158642.739 944261.7588 901896.2489 948070.6783 1174813.892 1152812.061 1137722.677 1301466.322 0.843688686 0.971670337 0.890259486 0.725536837 0.6929847 0.728463474 0.90268482 0.885779402 0.874185262 1 20.31170655 1.099702138 1.006573746 0.990785121 0.818524527 0.290735913 0.083582889 0.756939066 1.647524795 0.089117022 0.029953579 12.58062269 -1.099702138 -0.172260594 HEANNPQLK ddPTM_BT-474_Pertuzumab_2h_R1 4 HEANNPQLK 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 140.75 0.00010835 2092430000 2182020 1879480 2136460 2375050 2112740 1977870 2394010 1930750 2998030 2979880 FALSE TRUE 2096744.246 1825879.071 2522565.847 2497626.615 2180698.201 2017863.887 2423308.611 1890879.338 2657706.203 2778050.073 0.754753943 0.657252037 0.908034694 0.89905745 0.784974404 0.726359797 0.872305591 0.68064984 0.956680453 1 21.40564117 1.100277958 6.488542441 0.998202483 0.786504095 0.471806809 0.082165007 0.173681252 8.892821982 0.079758677 0.02003908 12.59731409 -1.100277958 -0.211698388 SAVEDEGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAVEDEGLK 9 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 133.23 0.00065763 233690000 214230 187920 193030 211240 208180 179650 200960 202900 264590 266110 FALSE TRUE 205857.6548 182560.7056 227914.8149 222142.1217 214876.2988 183282.6461 203419.4086 198710.0441 234554.8525 248086.1327 0.829782997 0.735876301 0.91869228 0.895423373 0.866135872 0.738786341 0.819954773 0.800971993 0.945457329 1 17.92048157 1.101451801 4.197611597 0.997731712 0.825264861 0.530411594 0.056300839 0.158807829 4.680139986 0.055715887 0.014304815 12.6314091 -1.101451801 -0.17246685 GVLTGPEYEALDALPDAERR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVLTGPEYEALDALPDAERR 20 1 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;O60936-1;H3BQJ5 H3BM67 NOL3 Nucleolar protein 3 0 ;;; 265.37 1.98E-36 1546580000 329540 362791 281841 313638 387332 386350 309268 345682 336240 278219 FALSE TRUE 316661.2125 352444.5559 332775.9382 329824.8948 399790.8855 394162.2617 313052.9143 338543.5459 298071.4448 259374.9793 1.220862603 1.358822493 1.282991671 1.271614154 1.541362573 1.519661853 1.206951091 1.305228233 1.149191204 1 17.98467979 1.101671892 1.270644822 1.00168226 1.355666197 0.529015314 0.105585052 0.350855716 1.156925416 0.103375904 0.032146327 12.63781204 -1.101671892 0.353983937 SES(ph)PIPVAEQGTLMR ddPTM_BT-474_Pertuzumab_2h_R1 3 SESPIPVAEQGTLMR 15 0 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SES(1)PIPVAEQGTLMR;SES(1)PIPVAEQGTLMR;S(0.001)ES(0.999)PIPVAEQGTLMR 290.53 7.05E-44 1621280000 1081710 1140940 810510 1043850 956380 1093310 1024390 1073690 1116730 1027610 TRUE FALSE 1039435.577 1108401.508 956987.1867 1097723.224 987142.8313 1115417.477 1036926.791 1051517.926 989963.4921 958009.0594 1.084995561 1.15698437 0.998933337 1.145838041 1.030410748 1.164307859 1.082376812 1.097607498 1.033355042 1 19.86967977 1.101939204 3.089395653 1.000519031 1.095776511 0.293188161 0.049960083 0.261475606 4.751135511 0.042538593 0.011321933 12.64559311 -1.101939204 0.09525748 TPADTGFAFPDWAYKPESS(ph)PGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 TPADTGFAFPDWAYKPES(0.139)S(0.859)PGS(0.002)R;TPADTGFAFPDWAYKPES(0.141)S(0.76)PGS(0.099)R;TPADTGFAFPDWAYKPES(0.04)S(0.96)PGSR;TPADTGFAFPDWAYKPES(0.112)S(0.888)PGSR 233.08 2.98E-37 1208052000 815344 797627 782266 839876 847797 849624 887429 849923 824200 690525 TRUE FALSE 783479.4551 774879.4589 923638.8676 883222.101 875067.1605 866803.9794 898289.6216 832371.793 730640.2713 643755.1267 1.217045772 1.203686661 1.434767397 1.371984571 1.359316803 1.346480895 1.395390241 1.29299443 1.13496614 1 19.29615249 1.102029004 2.384232853 1.002922152 1.33564942 0.714299607 0.068792523 0.145942059 1.614171539 0.068517323 0.018925304 12.64820815 -1.102029004 0.332727268 S(ph)VDFDSLTVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVDFDSLTVR 10 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR 256.92 3.67E-17 1311790000 4390430 3095070 1246550 767360 1118210 341810 291580 3019140 363103 219881 TRUE FALSE 4218847.142 3006801.634 1471829.314 806963.5416 1154178.24 348721.6324 295148.4433 2956793.704 321885.0697 204988.264 20.58092039 14.66816478 7.180066241 3.936632887 5.630460093 1.701178524 1.439830932 14.42420969 1.570260967 1 17.64518179 1.102893037 10.56350878 1.008596626 8.297493329 0.200015292 5.890097865 0.581747425 52.74941873 5.976696456 1.494792458 12.67339692 -1.102893037 7.288896703 HLAGLGLTEAIDK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLAGLGLTEAIDK 13 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ; 203.61 8.45E-08 1827730000 3225400 3443500 3226800 3342400 3032700 3089300 3690600 2997800 4317100 4163900 FALSE TRUE 3099347.802 3345294.752 3809954.54 3514901.665 3130249.55 3151767.763 3735766.667 2935894.382 3827040.907 3881875.344 0.798415077 0.861772843 0.981472665 0.905464847 0.806375597 0.811918849 0.962361317 0.756308259 0.985874241 1 21.88832236 1.103499527 9.335339612 0.99966777 0.862498219 0.373936631 0.068611183 0.284459349 22.1576238 0.065663376 0.016429794 12.69110763 -1.103499527 -0.137169552 DGKDQGINVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGKDQGINVR 10 1 I3L2B2;O95208-3;O95208-2;F6PQP6;O95208;E9PBC1 I3L2B2 EPN2 Epsin-2 0 115 0.0025 0 167160 163850 116100 125540 139440 149810 145710 169830 147030 137290 FALSE TRUE 160627.2024 159177.1584 137081.8526 132019.1344 143925.2142 152839.2608 147493.2426 166322.9512 130339.7708 127991.226 1.254986044 1.243656799 1.071025389 1.031470192 1.124492817 1.19413858 1.152369949 1.299487132 1.018349264 1 16.96568539 1.103763419 9.119340126 1.000474552 1.170429546 0.407874842 0.078342251 0.280906071 21.24115519 0.082563934 0.020660939 12.69882151 -1.103763419 0.169954994 ALQHTES(ph)PSETNKPHSK ddPTM_BT-474_Pertuzumab_2h_R1 5 ALQHTESPSETNKPHSK 17 1 Q14669-3;Q14669;Q14669-2;G5E9G6;C9JLD7;C9JLJ5;C9JSX9 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 ALQHTES(0.991)PS(0.008)ET(0.001)NKPHSK;ALQHTES(0.864)PS(0.135)ETNKPHSK;ALQHTES(1)PSETNKPHSK;ALQHTES(0.942)PS(0.051)ET(0.006)NKPHSK;ALQHTES(1)PSETNKPHSK 280.47 3.85E-36 1669708000 1242618 1011871 928296 1002413 1114441 1133003 1144036 912355 1404480 1330700 TRUE FALSE 1194055.115 983013.4298 1096059.737 1054147.655 1150288.007 1155913.097 1158037.055 893514.5504 1245049.318 1240570.504 0.96250484 0.792388201 0.883512653 0.849728131 0.927225017 0.931759294 0.933471376 0.720244877 1.003610286 1 20.2425723 1.105147098 20.30929636 1.002267742 0.870326444 0.343637736 0.06978756 2.833831519 527.8192516 0.067752193 0.016938077 12.73934498 -1.105147098 -0.131941298 DCLHGIEAK ddPTM_BT-474_Pertuzumab_2h_R1 6 DCLHGIEAK 9 0 Q8N684-2;Q8N684;Q8N684-3;F5H669 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ;;;;; 162.88 6.34E-05 4333480000 10778830 10185660 8435380 8799110 9526430 9709650 10050840 10319860 11813400 11746770 FALSE TRUE 10357581.41 9895174.95 9959840.81 9253233.122 9832856.273 9905985.776 10173845.19 10106751.28 10472392.36 10951150.8 0.945798445 0.903573983 0.90947892 0.844955319 0.897883378 0.904561169 0.929020645 0.922893992 0.956282362 1 23.38457915 1.105215128 0.884232096 0.999699944 0.899204344 0.62800013 0.023771589 0.371473201 0.64366859 0.023042404 0.008207135 12.74134067 -1.105215128 -0.1004956 SASMVLAES(ph)PIALQLRY(ph)LQT(ph)LS(ph)T(ph)VATEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASMVLAESPIALQLRYLQTLSTVATEK 28 1 Q8TAV4-2;Q8TAV4 Q8TAV4-2 STOML3 Stomatin-like protein 3 5 S(0.026)AS(0.026)MVLAES(0.979)PIALQLRY(0.978)LQT(0.979)LS(0.671)T(0.671)VAT(0.671)EK 40.756 0.080167 21283000 16828 17076 13520 15700 14574 16000 15610 18059 22428 24548 TRUE FALSE 16170.34316 16589.0092 15963.36475 16510.27888 15042.78595 16323.53096 15801.03985 17686.07534 19882.06747 22885.34209 0.706580793 0.724874862 0.697536645 0.721434655 0.65731095 0.713274501 0.690443682 0.772812365 0.868768637 1 14.48213624 1.105258291 1.482813598 0.998516213 0.700878621 0.961217558 0.019337231 0.061888863 0.270357456 0.017540027 0.005252953 12.74260705 -1.105258291 -0.297637592 TVFPFSYQES(ph)PPRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVFPFSYQESPPRSPR 16 1 A0A494C0H7;A0A494C094;F8WDA1;A0A494C188;A0A494C155;A0A494C1K7;Q9UGJ0-3;Q9UGJ0;A0A494C1R6 A0A494C0H7 PRKAG2 5-AMP-activated protein kinase subunit gamma-2 2 TVFPFS(0.001)YQES(0.999)PPRS(1)PR 71.148 0.023585 66640000 77426 81485 72301 83982 84388 82742 64178 83154 82616 68028 TRUE FALSE 74400.10632 79161.12758 85367.39903 88316.32108 87102.41666 84415.09993 64963.42956 81436.84084 73237.77803 63420.40297 1.173125727 1.248196541 1.346055765 1.392553767 1.37341317 1.331040107 1.024330129 1.284079524 1.154798371 1 15.95265942 1.105439031 0.616037979 1.006269835 1.30795973 0.449085205 0.099009639 0.741600757 0.687165185 0.104125159 0.046014495 12.74791123 -1.105439031 0.301689895 FSS(ph)VSSPQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSSVSSPQPR 10 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 FS(0.015)S(0.705)VS(0.065)S(0.214)PQPR 138.22 7.40E-05 649540000 757940 1033400 845990 1191900 876510 910850 990930 1107200 938050 842210 TRUE FALSE 728318.8669 1003928.444 998879.2119 1253414.102 904703.7402 929268.0111 1003057.298 1084335.933 831566.4966 785166.3665 0.927598147 1.278618757 1.272187978 1.596367541 1.152244644 1.183530078 1.277509252 1.381026976 1.059095922 1 19.58263885 1.106144137 5.972273037 1.003302407 1.270607979 0.245934 0.160646819 0.26131182 11.86724559 0.151981663 0.038271554 12.76862514 -1.106144137 0.267305572 SSS(ph)PFLSK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSPFLSK 8 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 SSS(1)PFLSK;SS(0.002)S(0.998)PFLSK;S(0.001)S(0.104)S(0.894)PFLSK 192.21 0.00018581 1483010000 2980580 3162810 3409530 3836660 3835700 4110200 4865900 3605140 5555600 6293600 TRUE FALSE 2864095.638 3072609.756 4025707.916 4034670.482 3959078.774 4193311.06 4925450.34 3530692.599 4924951.579 5867328.866 0.488143021 0.523681189 0.686122767 0.687650305 0.674766809 0.71468826 0.839470644 0.601754679 0.839385637 1 22.48427243 1.106451488 0.068997576 1.569946347 1.23E-13 0.738144105 0.075101037 15.02391461 0.795525417 9.347825135 8.134221865 12.77766472 -1.106451488 -1.569946347 KVPELMEMFLPATK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVPELMEMFLPATK 14 1 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9 O43747 AP1G1 AP-1 complex subunit gamma-1 0 110.55 0.0011276 117070000 449380 433200 363020 371950 466210 375340 472240 477570 541920 587250 FALSE TRUE 431817.7328 420845.5601 428625.7893 391146.3841 481206.0681 382929.632 478019.4144 467708.0126 480403.5135 547475.0344 0.788744154 0.768702742 0.782913854 0.714455198 0.878955272 0.699446747 0.873134635 0.854300166 0.877489353 1 19.06243365 1.106452529 0.592458958 1.000946483 0.768699779 0.6442127 0.051204028 0.458466291 0.39766987 0.048256494 0.021912286 12.77769534 -1.106452529 -0.232246704 DHALLEEQSK ddPTM_BT-474_Pertuzumab_2h_R1 4 DHALLEEQSK 10 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 197.79 3.09E-07 3143800000 3358760 3214150 3378370 4362130 3258720 2684480 4267200 2426130 5619630 5624970 FALSE TRUE 3227495.946 3122485.589 3988916.61 4587260.052 3363539.688 2738762.025 4319423.27 2376029.568 4981713.162 5243985.772 0.61546619 0.595441278 0.760665033 0.874765923 0.641409004 0.522267249 0.823690883 0.453096113 0.949986018 1 22.32223234 1.107589739 7.57523653 0.997705545 0.662008161 0.511801191 0.123114374 0.174747181 10.4309295 0.118093557 0.029597714 12.81119786 -1.107589739 -0.335697384 SQEPLDLVLVPDDCRPGT(ph)PPSDLIEIQVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQEPLDLVLVPDDCRPGTPPSDLIEIQVVK 30 1 Q8NCA9 Q8NCA9 ZNF784 Zinc finger protein 784 1 SQEPLDLVLVPDDCRPGT(0.972)PPS(0.028)DLIEIQVVK;SQEPLDLVLVPDDCRPGT(0.997)PPS(0.003)DLIEIQVVK 181.05 1.11E-17 327950000 460210 485800 337580 412970 408980 470670 403770 455410 524580 520360 TRUE FALSE 442224.4844 471945.4596 398588.2154 434283.4312 422135.2131 480187.2699 408711.458 446005.6244 465031.8776 485115.5537 0.911585871 0.972851635 0.821635613 0.895216465 0.870174559 0.98984101 0.842503307 0.919380178 0.958600222 1 18.88796891 1.10760277 2.586918017 0.998185336 0.901061506 0.300758895 0.049028474 0.302606101 3.900366072 0.044203444 0.012080121 12.81158228 -1.10760277 -0.097123829 TELFVHAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TELFVHAFK 9 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 76.827 0.034331 505980000 710160 694610 601910 629070 572990 539920 722850 627080 840040 831200 FALSE TRUE 682406.1621 674800.4029 710688.5264 661536.3781 591420.7437 550837.5523 731696.4545 614130.5789 744682.1809 774902.0836 0.880635343 0.87082022 0.917133327 0.853703187 0.763219968 0.710847943 0.944243757 0.792526684 0.96100165 1 19.5636545 1.107867346 5.228826392 0.998072359 0.84153879 0.413222324 0.066790275 0.192532525 7.436069397 0.065061471 0.016469691 12.81938957 -1.107867346 -0.156533569 IKPVTENLVLSSHTGFCQSS(ph)GDEALSK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKPVTENLVLSSHTGFCQSSGDEALSK 27 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 1 IKPVTENLVLSSHTGFCQS(0.216)S(0.784)GDEALSK 118.77 0.00020363 1072700000 200590 240070 217730 197220 191980 220290 250850 209510 295940 294510 TRUE FALSE 192750.721 233223.4387 257078.6544 207398.5478 198155.2111 224744.4147 253919.9773 205183.5453 262346.1319 274562.5754 0.702028384 0.849436375 0.936320815 0.755378068 0.721712385 0.818554439 0.924816417 0.747310681 0.955505795 1 18.06677546 1.108023118 5.458005124 0.997675719 0.811491705 0.451175618 0.075814546 0.178836199 7.27082157 0.072218197 0.018246116 12.82398845 -1.108023118 -0.186184014 VS(ph)TTTDSPVSPAQAASPFIPLDELSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSTTTDSPVSPAQAASPFIPLDELSSK 27 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 VS(0.168)T(0.168)T(0.168)T(0.168)DS(0.168)PVS(0.157)PAQAAS(0.004)PFIPLDELSSK 48.984 0.075588 51290000 10562 13181 9279.6 10537 10979 10025 9068.7 12539 13947 15173 TRUE FALSE 10149.22536 12805.09079 10956.63014 11080.81583 11332.14951 10227.71237 9179.685463 12280.06527 12363.79503 14145.3192 0.71749709 0.905252869 0.774576381 0.783355658 0.801123633 0.723045711 0.648955696 0.868136314 0.87405557 1 13.78803711 1.108282341 1.789996395 0.992019278 0.773077909 0.534466606 0.067112495 0.259053702 1.612589796 0.063501016 0.018347586 12.83164514 -1.108282341 -0.218941369 SS(ph)PPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPPLR 6 0 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 S(0.423)S(0.577)PPLR 70.525 0.095076 209650000 129930 158350 127610 142180 132730 159610 122460 152170 135110 117240 TRUE FALSE 124852.192 153834.013 150671.9657 149517.9268 136999.381 162837.4236 123958.7021 149027.6363 119772.8792 109299.2304 1.142297082 1.407457422 1.378527233 1.367968707 1.253434087 1.489831383 1.134122369 1.363482943 1.095825458 1 16.73792372 1.108517882 3.79057227 1.001790232 1.320918508 0.507191446 0.107653478 0.153294142 3.857868827 0.094271062 0.024482265 12.83860634 -1.108517882 0.319128276 CYPDRVDYVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 CYPDRVDYVDK 11 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 135.6 0.00010641 2212700000 968430 868660 889090 759000 859300 899460 903820 936460 1124020 1125730 FALSE TRUE 930582.6849 843886.6673 1049768.341 798172.081 886940.1649 917647.6975 914881.2195 917121.7737 996425.9619 1049483.304 0.886705564 0.804097277 1.000271597 0.760538141 0.845120795 0.874380463 0.871744425 0.873879337 0.94944432 1 20.00124779 1.108643251 2.122537434 1.000262926 0.861826979 0.379393047 0.058254023 0.287604325 2.499972949 0.051323634 0.014435838 12.84231302 -1.108643251 -0.138435947 GLEVTAYSPLGSSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLEVTAYSPLGSSDR 15 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 105.03 0.0031337 129650000 53880 53640 44071 53383 52693 61138 46458 55528 56184 50688 FALSE TRUE 51774.31003 52110.23972 52035.61005 56138.10303 54387.9182 62374.25225 47026.5669 54381.3274 49806.22786 47254.85661 1.095639977 1.10274887 1.101169568 1.187985893 1.150948751 1.319954323 0.995168968 1.150809277 1.053991726 1 15.52817499 1.109146887 1.118871135 1.00111903 1.145563832 0.255295459 0.078108091 0.659903453 1.731328838 0.071734398 0.023218413 12.85721443 -1.109146887 0.144444802 VDGEIILHLYDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDGEIILHLYDK 12 0 P08243-2;P08243;P08243-3;F8WEJ5;C9J057;C9JT45;C9JM09 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ; 115.14 0.00022479 249540000 808130 762030 763230 708260 781220 745490 827720 779620 960120 930570 FALSE TRUE 776547.3862 740297.6505 901162.639 744813.3835 806348.6508 760564.3186 837849.885 763520.5746 851131.2028 867541.665 0.895112497 0.853328065 1.038754305 0.858533271 0.92946389 0.876689097 0.965774808 0.880096721 0.981083949 1 19.72657352 1.110417741 5.776775863 0.998910028 0.913255137 0.260779442 0.05307563 0.251999313 10.91800317 0.04674894 0.011786962 12.89489294 -1.110417741 -0.085654891 AGGDAEPRPAEPPAWAGGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGGDAEPRPAEPPAWAGGAR 20 1 Q96HS1;Q96HS1-2 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 132.67 1.11E-05 391200000 385230 453410 278140 474930 310100 431300 395270 424750 380870 332970 FALSE TRUE 370174.7857 440479.1907 328406.0852 499441.1942 320074.6481 440021.1815 400107.4325 415978.7641 337635.2343 310417.6453 1.192505617 1.418988892 1.057949154 1.608933003 1.03110971 1.417513431 1.288932632 1.340061592 1.087680547 1 18.24385104 1.110483584 4.258644525 1.004213393 1.298099522 0.278299143 0.163787531 0.229909334 6.815515893 0.137262684 0.035244194 12.89684807 -1.110483584 0.293886129 TPLALAGS(ph)PTPK ddPTM_BT-474_Pertuzumab_2h_R1 6 TPLALAGSPTPK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 TPLALAGS(0.998)PT(0.002)PK;TPLALAGS(0.999)PT(0.001)PK;TPLALAGS(0.999)PT(0.001)PK;TPLALAGS(0.995)PT(0.005)PK;TPLALAGS(1)PTPK;TPLALAGS(1)PTPK 191.84 5.09E-06 3234240000 5282140 4716520 4164730 4263450 4600150 4399600 4888120 5134510 5288270 5531180 TRUE FALSE 5075708.129 4582009.468 4917389.355 4483487.165 4748118.002 4488562.926 4947942.275 5028480.574 4687967.76 5156548.252 0.984322822 0.888580741 0.953620351 0.869474491 0.920793866 0.870458824 0.959545423 0.975164069 0.90912904 1 22.29797423 1.111064225 0.679825469 0.993568375 0.916173632 0.215582996 0.040265856 0.986085808 1.082059612 0.038354262 0.015892968 12.91410237 -1.111064225 -0.077394743 RRS(ph)S(ph)PSARPPDVPGQQPQAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 2 RRS(0.924)S(0.937)PS(0.139)ARPPDVPGQQPQAAK 114.9 0.00023897 185020000 163580 145720 133600 165660 148080 139820 160950 160020 155710 138730 TRUE FALSE 157187.1128 141564.2083 157744.4919 174209.7325 152843.1277 142647.2562 162919.7542 156715.5311 138034.4536 129333.6935 1.215360889 1.094565572 1.21967051 1.346978716 1.181773469 1.102939631 1.259685313 1.211714649 1.067273731 1 16.98073864 1.11140303 3.676327444 1.003073103 1.204925371 0.508003341 0.068513274 0.175088461 4.190066536 0.066899394 0.017446212 12.92418097 -1.11140303 0.201852268 IIIEELSLVAASPT(ph)LSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 IIIEELSLVAASPTLSPR 18 0 Q16513-3;Q16513-2;Q16513;Q16513-4;B1AL79;H0Y5V5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 IIIEELSLVAAS(0.004)PT(0.498)LS(0.498)PR 92.264 0.02646 449200000 24411 18489 21191 39033 32586 27536 15313 29387 24768 18708 TRUE FALSE 23456.99113 17961.71182 25020.68509 41047.49781 33634.15828 28092.79679 15500.40507 28780.14818 21956.44048 17440.8905 1.344942286 1.029862083 1.434599059 2.353520757 1.928465653 1.610743258 0.888739315 1.650153597 1.25890593 1 14.09018608 1.111884418 0.762286657 1.021303439 1.582830553 0.162110204 0.394031664 1.334226071 1.784643953 0.412209796 0.159140239 12.93851453 -1.111884418 0.561527114 QVVESAYEVIK ddPTM_BT-474_Pertuzumab_2h_R1 2 QVVESAYEVIK 11 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 156.51 7.22E-05 114499000 191714 202345 165257 177533 181652 160178 167073 179726 165454 135667 FALSE TRUE 184221.6049 196574.3187 195122.616 186695.4994 187495.0016 163416.9089 169117.6894 176014.5953 146672.3556 126478.1533 1.45654882 1.554215599 1.542737706 1.476108677 1.482429943 1.292056412 1.337129654 1.391660068 1.159665537 1 16.94852868 1.112066598 0.336955777 0.949106372 1.55888119 0.866084447 0.06166183 0.537845557 0.190711149 0.123195332 0.076863505 12.94394318 -1.112066598 0.609774818 LISQIVS(ph)SITASLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LISQIVSSITASLR 14 0 P68363;P68363-2;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 1 LIS(0.101)QIVS(0.596)S(0.202)IT(0.067)AS(0.035)LR 61.503 0.088604 273620000 156480 136930 109910 124910 142170 166990 129780 137880 130500 104910 TRUE FALSE 150364.5886 133024.8905 129773.1819 131356.6201 146743.0272 170366.6522 131368.2865 135032.7298 115686.1871 97804.35226 1.537401814 1.360112177 1.326865103 1.343054957 1.500373182 1.741912791 1.34317424 1.380641318 1.182832711 1 16.57761105 1.112584943 1.606381342 1.001797652 1.450439672 0.608408173 0.118527704 0.255379404 1.290302184 0.117421272 0.034619926 12.95940142 -1.112584943 0.44864202 QSPAS(ph)PPPLGGGAPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 QSPASPPPLGGGAPVR 16 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 QS(0.005)PAS(0.995)PPPLGGGAPVR;QS(0.005)PAS(0.995)PPPLGGGAPVR;QS(0.037)PAS(0.963)PPPLGGGAPVR;QS(0.256)PAS(0.744)PPPLGGGAPVR 190.8 8.38E-10 1602280000 1250860 1637430 1162650 1834800 1545080 1403950 1627110 1789810 1357800 1176770 TRUE FALSE 1201975.008 1590732.1 1372766.718 1929494.248 1594778.901 1432338.831 1647023.059 1752849.798 1203668.236 1097066.32 1.095626569 1.44998718 1.251306957 1.758776305 1.453675929 1.305608244 1.501297624 1.597761016 1.097169984 1 20.06521931 1.112867877 5.744526688 1.006716736 1.440000849 0.431563083 0.174380089 0.176103434 7.561746301 0.164731099 0.0415476 12.96784698 -1.112867877 0.433284113 NTGIICTIGPASR ddPTM_BT-474_Pertuzumab_2h_R1 2 NTGIICTIGPASR 13 0 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 158.01 9.08E-05 769490000 379930 330180 305730 303650 339040 303550 347930 367900 420030 438530 FALSE TRUE 365081.9156 320763.5897 360982.2119 319321.4129 349945.5295 309687.989 352188.0714 360302.7364 372349.9553 408827.9725 0.892996419 0.784593059 0.882968476 0.781065471 0.855972568 0.757501956 0.861457863 0.881306468 0.910774165 1 18.64113439 1.113151622 1.112003948 0.99698857 0.826426191 0.607561767 0.042801591 0.286630604 0.743560147 0.036726071 0.011918642 12.97632223 -1.113151622 -0.170562379 MDELQLFR ddPTM_BT-474_Pertuzumab_2h_R1 14 MDELQLFR 8 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;;;;;;; 215.09 1.99E-05 7915113000 3487776 3954373 2912457 4205090 3126739 2819781 4073909 3980344 4290801 4683435 FALSE TRUE 3351469.858 3841598.154 3438802.767 4422115.199 3227313.4 2876798.904 4123766.717 3898148.505 3803727.259 4366221.776 0.767590386 0.879844944 0.787592327 1.012801325 0.739154712 0.658876038 0.944470283 0.892796726 0.871171336 1 22.05795398 1.113281008 0.879342634 0.990875616 0.824417703 0.226830853 0.09644514 0.89476205 1.535585355 0.092118158 0.032943864 12.98018875 -1.113281008 -0.166457913 QMGYTEAIEVIQAAS(ph)SPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QMGYTEAIEVIQAASSPVK 19 0 P19838;P19838-2;P19838-3 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 1 QMGYTEAIEVIQAAS(0.5)S(0.5)PVK 96.666 0.0013007 27546000 30367 30185 29693 26366 32442 28954 30104 35382 38637 41976 TRUE FALSE 29180.22407 29324.15335 35059.18562 27726.75242 33485.52639 29539.46972 30472.42176 34651.34934 34251.08974 39132.92813 0.745669324 0.749347283 0.89589988 0.708527415 0.855686707 0.754849461 0.77869005 0.885478061 0.875249857 1 15.25609544 1.113289954 0.940544447 0.996545249 0.783616405 0.598454002 0.055033027 0.350561586 0.67696035 0.048794374 0.016910919 12.98045615 -1.113289954 -0.212928844 QLSESESSLEMDDERYFNEMS(ph)AQGLRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.165)ES(0.192)ES(0.192)S(0.165)LEMDDERY(0.025)FNEMS(0.26)AQGLRPR 55.702 0.051008 114610000 30584 31632 21978 32577 26271 29346 25902 29955 21803 15604 TRUE FALSE 29388.74347 30729.88633 25949.9135 34258.30287 27116.03057 29939.39623 26218.99642 29336.41878 19328.01485 14547.12718 2.020243798 2.112436768 1.783851421 2.354987514 1.864012752 2.058096822 1.802348745 2.01664689 1.328648234 1 13.82844665 1.113539436 2.950041931 1.002125429 2.004669607 0.821328226 0.159428339 0.083778656 1.374209523 0.138744171 0.037269355 12.98791496 -1.113539436 1.002544178 IINEAS(ph)QFKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IINEASQFKPK 11 1 Q8N3K9 Q8N3K9 CMYA5 Cardiomyopathy-associated protein 5 1 IINEAS(1)QFKPK 59.542 0.060152 36124000 50623 59316 45828 46678 59002 62423 52348 52717 52992 42305 TRUE FALSE 48644.59719 57624.36576 54110.13904 49087.05717 60899.85291 63685.23583 52988.65048 51628.37553 46976.57032 39439.64467 1.233393394 1.461077204 1.37197329 1.244612054 1.544127829 1.614751765 1.343537725 1.309047684 1.191100242 1 15.26735893 1.113681256 1.422384747 1.00586357 1.409615444 0.563614284 0.112746761 0.292032891 1.177905427 0.109083334 0.033009349 12.99215688 -1.113681256 0.403751874 ASLGSLEGEAEAEASS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEASS(1)PK;ASLGSLEGEAEAEAS(0.002)S(0.998)PK;ASLGSLEGEAEAEASS(1)PK;ASLGSLEGEAEAEAS(0.003)S(0.997)PK;ASLGSLEGEAEAEAS(0.02)S(0.98)PK 385.12 1.94E-126 3654190000 3970890 3696850 3902810 4293890 4259140 4088990 4134070 4424950 4204810 3799440 TRUE FALSE 3815703.229 3591419.458 4608134.585 4515498.177 4396139.106 4171672.179 4184663.985 4333573.236 3727497.597 3542100.545 1.07724306 1.013923634 1.300960977 1.274808019 1.241110762 1.177739628 1.181407454 1.223447269 1.052340991 1 21.75617373 1.11438284 4.54023177 1.002965399 1.190020225 0.383319803 0.082167269 0.215352324 6.928828359 0.083515161 0.021342816 13.01316212 -1.11438284 0.187054825 CLHMFLQDEIIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 CLHMFLQDEIIDK 13 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 96.464 0.0042253 503120000 218950 246910 175300 214210 205530 224540 210390 190230 295330 290770 FALSE TRUE 210393.1919 239868.3686 206980.6095 225265.4038 212141.0591 229080.3526 212964.8158 186301.684 261805.3765 271075.8889 0.776141297 0.884875337 0.763552267 0.831004944 0.782589185 0.845078305 0.785628027 0.687267631 0.965801044 1 18.04833727 1.115612771 6.858675166 0.997550221 0.793623406 0.693823716 0.050240201 0.119609755 6.292372579 0.050737397 0.012737023 13.05006788 -1.115612771 -0.203926815 GYIWNYGTLPQTWEDPHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GYIWNYGTLPQTWEDPHEK 19 0 Q9H2U2-2;Q9H2U2;H0Y9D8;D6RGV9;D6RGI1 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ; 252.12 7.64E-31 829790000 780850 806980 644380 903810 673330 680220 869680 804750 861560 803540 FALSE TRUE 750333.5187 783965.7205 760833.8002 950455.7424 694988.271 693974.5145 880323.404 788131.6313 763759.3208 749115.5201 1.001625916 1.046521797 1.015642821 1.268770593 0.927745124 0.926391853 1.175150401 1.052082903 1.019548121 1 19.51482869 1.115672921 4.10621251 1.001995641 1.055112335 0.028929647 0.098675918 0.873740799 24.51894539 0.092506297 0.023856766 13.05187545 -1.115672921 0.053116694 VDS(ph)PSHGLVTSSLCIPSPAR ddPTM_BT-474_Pertuzumab_2h_R1 7 VDSPSHGLVTSSLCIPSPAR 20 0 Q9UER7-3;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 VDS(0.961)PS(0.039)HGLVTSSLCIPSPAR;VDS(0.977)PS(0.023)HGLVTSSLCIPSPAR;VDS(0.972)PS(0.028)HGLVTSSLCIPSPAR;VDS(0.998)PS(0.002)HGLVTSSLCIPSPAR;VDS(0.689)PS(0.251)HGLVT(0.056)S(0.003)SLCIPSPAR;VDS(0.934)PS(0.066)HGLVTSSLCIPSPAR;VDS(0.899)PS(0.101)HGLVTSSLCIPSPAR 352.24 2.40E-95 3092162000 1793647 1633365 1474633 1644340 1592496 1802515 1815832 1796166 2373620 2383188 TRUE FALSE 1723549.292 1586783.029 1741131.986 1729204.584 1643720.08 1838963.088 1838054.695 1759074.544 2104176.609 2221772.554 0.775754156 0.714196881 0.78366797 0.778299552 0.73982374 0.827700876 0.827292016 0.791743755 0.947071114 1 21.0832797 1.116978155 0.760991359 1.007039949 0.76148587 0.830903917 0.034911047 0.245295208 0.327208025 0.03322075 0.012851997 13.09116074 -1.116978155 -0.245554079 GKGS(ph)PRPQAPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GKGSPRPQAPK 11 2 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GKGS(1)PRPQAPK;GKGS(1)PRPQAPK;GKGS(1)PRPQAPK;GKGS(1)PRPQAPK 72.496 0.024073 9871760000 7425510 7560850 6406900 6247830 5950420 7331540 7090060 7927220 8685760 9363820 TRUE FALSE 7135312.86 7345221.961 7564769.351 6570281.255 6141820.663 7479788.762 7176830.275 7763520.137 7699788.938 8729600.131 0.817369954 0.841415626 0.866565391 0.752644011 0.703562657 0.856830628 0.82212589 0.889332847 0.882032261 1 23.05748414 1.11750679 0.849873548 0.995320552 0.803242472 0.613525524 0.047250093 0.411280286 0.665010469 0.047672855 0.017355701 13.10710534 -1.11750679 -0.19207808 LCHDNNEDHQLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LCHDNNEDHQLDR 13 0 Q96PM5-2;Q96PM5;D6RAF6;H0YAI4;Q96PM5-5;Q96PM5-3;Q96PM5-4;Q96PM5-6 Q96PM5-2 RCHY1 RING finger and CHY zinc finger domain-containing protein 1 0 ; 173.68 1.23E-05 561600000 477820 526250 412960 465720 479300 504040 499610 490600 528000 476050 FALSE TRUE 459146.2661 511241.8653 487591.0582 489755.865 494717.1198 514232.0341 505724.3766 480468.9386 468063.6536 443806.7095 1.034563598 1.15194713 1.098656347 1.103534161 1.114713025 1.158684678 1.139514942 1.082608551 1.054656551 1 18.75957195 1.11751667 1.788740401 1.002338038 1.116008334 0.538169959 0.033431942 0.235641052 1.454014965 0.030136962 0.008719132 13.10740354 -1.11751667 0.113670295 RLQEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLQEAK 6 1 Q9BUZ4;F6SA91 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 0 94.006 0.072111 166720000 321310 368950 258280 255040 273840 302920 301560 307430 378580 374280 FALSE TRUE 308752.85 358427.9072 304956.9414 268202.645 282648.3123 309045.2499 305250.5815 301081.4631 335605.1855 348929.6822 0.884856937 1.027221029 0.873978217 0.768643823 0.810043762 0.885694928 0.874819762 0.862871456 0.961813232 1 18.4125768 1.117587529 3.870142225 0.998306485 0.872912317 0.326971463 0.062599977 0.265079509 6.81752101 0.064390113 0.016717001 13.10954229 -1.117587529 -0.125394168 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPKLPLPAFR ddPTM_BT-474_Pertuzumab_2h_R1 4 RADDFPVRDDPSDVTDEDEGPAEPPPPPKLPLPAFR 36 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 2 RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR 185.37 8.16E-23 463773000 206560 219305 140746 176064 174343 208886 183005 203512 196311 180785 TRUE FALSE 198487.4068 213050.6361 166181.9331 185150.6841 179950.9009 213109.818 185244.6699 199309.4061 174026.5983 168540.2709 1.177685343 1.264093353 0.986007274 1.098554566 1.067702692 1.264444497 1.099112212 1.182562512 1.032552026 1 17.36273382 1.118260534 5.319922142 1.002275508 1.141119803 0.279696371 0.081593697 0.259339167 10.16286699 0.076992943 0.019489994 13.12987325 -1.118260534 0.138844295 ATEVSKT(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATEVSKTPEAR 11 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 ATEVS(0.043)KT(0.957)PEAR 146.96 5.74E-05 1100600000 833700 754000 753620 749340 846170 761570 753760 859530 829150 767870 TRUE FALSE 801118.0823 732496.6582 889815.8982 788013.5272 873387.8265 776969.4672 762984.7404 841780.4051 735028.3681 715861.481 1.119096506 1.023237984 1.243000108 1.100790513 1.220051434 1.085362864 1.065827343 1.175898449 1.026774575 1 19.44932093 1.118760532 5.779025498 1.001969419 1.128978304 0.342819237 0.064478937 0.215541468 9.32134942 0.058649436 0.014794128 13.14499823 -1.118760532 0.127008885 QQS(ph)PQEPK ddPTM_BT-474_Pertuzumab_2h_R1 10 QQSPQEPK 8 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK 166.69 0.0003325 18243521000 14918240 13551320 11014690 12587409 13356971 12899270 13240440 13788830 13674060 12374840 TRUE FALSE 14335218.69 13164849.62 13005289.5 13237046.69 13786610.1 13160102.08 13402480.47 13504085.84 12121838.04 11536681.06 1.242577359 1.141129719 1.127299041 1.147387764 1.195023944 1.140718202 1.161727571 1.170534729 1.050721431 1 23.45972491 1.119287309 3.573462675 1.001866336 1.163780356 0.763889649 0.031748384 0.096826409 2.197592018 0.029108521 0.007632409 13.16095212 -1.119287309 0.16191402 EAILAIHK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAILAIHK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 98.392 0.0075549 1604290000 1863970 1765740 1902230 2267500 1639300 1023800 2398800 2159400 2534100 2946200 FALSE TRUE 1791123.992 1715382.824 2246005.276 2384525.947 1692029.573 1044501.937 2428157.232 2114807.635 2246439.592 2746651.25 0.65211191 0.624536087 0.817724957 0.868157523 0.616033642 0.380281966 0.884042789 0.769958558 0.817883083 1 21.38924231 1.12040679 1.018969911 0.988922822 0.684809769 0.329875117 0.137834267 0.633114587 1.406967858 0.135270321 0.045382791 13.19492088 -1.12040679 -0.304113052 LDEDEDEDDADLSKYNLDAS(ph)EEEDSNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDEDEDEDDADLSKYNLDASEEEDSNKK 28 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 LDEDEDEDDADLSKYNLDAS(0.826)EEEDS(0.174)NKK 77.439 0.0039407 189080000 105190 127390 107720 84285 110850 123030 98621 103360 109710 84822 TRUE FALSE 101079.0585 123756.9619 127187.4002 88634.95895 114415.5909 125517.7509 99827.9533 101225.5799 97256.18074 79076.93039 1.278237003 1.565019802 1.608400827 1.12087 1.446889635 1.587286586 1.262415635 1.2800899 1.229893223 1 16.27096925 1.120442549 0.742425423 1.0032295 1.436140351 0.442983653 0.146321687 0.598819594 0.765409587 0.140530954 0.055215184 13.19600736 -1.120442549 0.432910851 KFNGEDIDTIS(ph)PTLGFNIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFNGEDIDTISPTLGFNIK 19 1 V9GYD0;P36404-2;P36404 V9GYD0 ARL2-SNX15;ARL2 ADP-ribosylation factor-like protein 2 1 KFNGEDIDTIS(1)PTLGFNIK 153.1 3.01E-08 126160000 288520 308570 212810 201690 243270 304710 235570 268740 306790 247290 TRUE FALSE 277244.3194 299769.8857 251269.5009 212099.2451 251095.0005 310871.445 238452.9761 263190.4251 271964.4854 230540.828 1.202582301 1.300289794 1.08991324 0.920007301 1.089156323 1.348444211 1.034319943 1.141621757 1.179680353 1 17.81466274 1.121224033 0.014294872 1.36E-05 2.211171781 0.099771991 0.119266906 1811.052137 19.78343632 1549.601189 1505.870956 13.21977406 -1.121224033 2.211158198 AT(ph)SNVFAMFDQSQIQEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSNVFAMFDQSQIQEFK 18 0 J3QRS3;P19105;O14950;J3KTJ1;P24844-2;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 1 AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK 201.67 5.07E-15 286350000 1668410 273040 60339 100139 74615 70891 75557 531820 82847 68162 TRUE FALSE 1603206.693 265253.1665 71243.59953 105307.1858 77015.05924 72324.46459 76481.68917 520837.7312 73442.55588 63545.32703 25.2293405 4.174235604 1.121146162 1.657197952 1.21197046 1.138155518 1.203576923 8.196318369 1.155750695 1 15.95549842 1.121678827 11.63733909 1.006611192 4.84921749 0.053687214 7.009920249 1.49800355 143.3167077 6.565301834 1.641701109 13.23362508 -1.121678827 3.842606299 DVACGANHTLVLDSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVACGANHTLVLDSQK 16 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 206.95 1.87E-11 1121020000 1355710 1249250 1303150 1312360 1345070 1062410 1457660 1507850 1763900 1935220 FALSE TRUE 1302727.354 1213622.613 1538658.193 1380091.057 1388335.398 1083892.658 1475499.279 1476712.371 1563669.467 1804145.826 0.722074311 0.672685431 0.852845802 0.764955381 0.769525045 0.600778852 0.817838147 0.818510538 0.866709024 1 20.78288452 1.122072306 1.06780577 0.995236046 0.738953423 0.604390615 0.066185843 0.333805772 0.805419356 0.062576227 0.020628094 13.24562045 -1.122072306 -0.256282624 HGNQYIQVNEPWK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGNQYIQVNEPWK 13 0 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 180.18 1.31E-05 848930000 332050 323000 353260 365730 320890 293730 444940 335170 497350 499170 FALSE TRUE 319073.1189 313788.3563 417101.9402 384605.3691 331211.7183 299669.4219 450385.3088 328248.6224 440892.9131 465360.7713 0.68564679 0.67429052 0.896298025 0.826467104 0.711731067 0.643950759 0.967819672 0.705363758 0.947421743 1 18.82799007 1.12223273 5.108650399 0.996769914 0.768941448 0.41943618 0.099199807 0.192134291 7.186629251 0.092769193 0.023545053 13.25051413 -1.12223273 -0.227828466 KHPEVDVLINFASLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KHPEVDVLINFASLR 15 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 171.46 7.02E-07 1109800000 1652370 1827510 1602080 1675420 1681330 1282490 1973890 1771660 2085400 2121200 FALSE TRUE 1587793.554 1775391.204 1891611.494 1761888.627 1735411.506 1308422.827 1998047.056 1735074.602 1848674.135 1977529.235 0.802917866 0.897782532 0.956552986 0.890954529 0.877565538 0.661645251 1.010375483 0.877395171 0.934840357 1 20.91526759 1.122760053 1.054246061 0.995915618 0.86739482 0.18972177 0.086865764 0.867651739 2.046802069 0.08074633 0.026746981 13.26661275 -1.122760053 -0.128520799 HTQENCETWGVNGETGTLVDMK ddPTM_BT-474_Pertuzumab_2h_R1 4 HTQENCETWGVNGETGTLVDMK 22 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 308 4.06E-67 3160010000 2012860 1816560 1628280 1740550 1862160 1933390 2027800 1607690 2572630 2504070 FALSE TRUE 1934195.206 1764753.487 1922546.417 1830379.994 1922058.068 1972484.47 2052616.823 1574490.64 2280595.828 2334467.109 0.828538213 0.755955602 0.823548299 0.784067588 0.823339108 0.844939928 0.879265686 0.674453983 0.976923521 1 21.15466183 1.122770281 7.970077771 0.998101765 0.800362686 0.664463397 0.053147479 0.137954839 8.693164038 0.051347806 0.012863764 13.26692521 -1.122770281 -0.19773908 NADGTICYDSTHYK ddPTM_BT-474_Pertuzumab_2h_R1 4 NADGTICYDSTHYK 14 0 P14550;Q5T621 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 218.21 5.47E-12 3071530000 1510940 1590270 1391570 1451150 1406440 1371830 1519080 1546570 1816870 1780660 FALSE TRUE 1451890.794 1544917.057 1643057.654 1526044.025 1451679.42 1399569.343 1537670.955 1514632.789 1610626.535 1660054.312 0.874604393 0.930642477 0.989761384 0.919273553 0.874477063 0.843086478 0.926277498 0.912399539 0.970225205 1 20.66279901 1.123118519 2.59287685 0.999976862 0.90921503 0.407609353 0.037613866 0.279696503 3.538825224 0.038278362 0.010493934 13.27756752 -1.123118519 -0.090761832 RIVNAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RIVNAK 6 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 122.51 0.030768 561840000 1038400 1088600 925330 894910 932060 874930 1014600 1017800 1236700 1226600 FALSE TRUE 997818.18 1057554.194 1092557.715 941096.4123 962040.5564 892621.6841 1027016.978 996782.0743 1096315.001 1143521.289 0.872583824 0.924822479 0.955432771 0.822981103 0.841296586 0.78059035 0.898117934 0.871677758 0.958718487 1 20.12505179 1.123365746 2.780753624 0.999908891 0.870172128 0.468217628 0.04713949 0.231597695 3.352041527 0.04760207 0.012925452 13.28512809 -1.123365746 -0.129736762 FSSVSS(ph)PQPR ddPTM_BT-474_Pertuzumab_2h_R1 3 FSSVSSPQPR 10 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 FS(0.012)S(0.299)VS(0.184)S(0.505)PQPR;FSS(0.002)VS(0.031)S(0.967)PQPR;FSS(0.023)VS(0.19)S(0.786)PQPR 132.17 0.000242 1725510000 2250150 2964750 2221500 3115150 2628310 2502960 2871040 3170350 2663870 2467050 TRUE FALSE 2162211.65 2880198.233 2622974.467 3275923.265 2712851.978 2553571.566 2906176.646 3104881.165 2361478.645 2299954.506 0.940110617 1.252284871 1.140446239 1.424342636 1.179524191 1.110270468 1.263580057 1.349975035 1.026750155 1 21.13317389 1.1247485 7.750644037 1.00251215 1.218761609 0.271520541 0.126421655 0.287989595 17.69528235 0.119031707 0.029830399 13.32749413 -1.1247485 0.216249459 SIDGTADDEDEGVPTDQAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIDGTADDEDEGVPTDQAIR 20 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 235.22 1.31E-26 0 55429 55763 40496 58905 59158 51569 51871 56109 54166 48282 FALSE TRUE 53262.7734 54172.69384 47814.52803 61945.09411 61060.8708 52611.76051 52505.81281 54950.32954 48017.30276 45011.81713 1.183306447 1.203521592 1.062266113 1.376196254 1.356552005 1.168843292 1.166489517 1.220797849 1.066771035 1 15.45801619 1.125598003 2.867629955 0.999783551 1.21935442 0.425914273 0.086813269 0.239929331 3.670032747 0.085208184 0.023052913 13.35358892 -1.125598003 0.219570868 AVFVDLEPTVIDEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVFVDLEPTVIDEIR 15 0 P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2 P68366-2 TUBA4A Tubulin alpha-4A chain 0 ; 152.85 3.05E-08 13112000 35666 42535 36864 43904 40381 39358 40610 42310 44817 41794 FALSE TRUE 34272.13329 41321.94345 43526.14484 46169.8907 41679.89154 40153.84573 41106.99733 41436.28371 39729.56205 38963.25515 0.879601387 1.060536223 1.117107507 1.184959791 1.069723035 1.030556753 1.055019586 1.063470789 1.019667425 1 15.24982659 1.126230851 2.980381675 1.000174401 1.063680549 0.062805743 0.072587588 0.664464887 10.91525567 0.070014603 0.018845823 13.37306177 -1.126230851 0.063506149 EAVCIVLSDDTCSDEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAVCIVLSDDTCSDEK 16 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 298.82 1.96E-45 1071210000 1753460 1597260 1098180 1504440 1233640 1370090 1399980 1552620 2074950 2205130 FALSE TRUE 1684932.845 1551707.709 1296645.555 1582084.329 1273321.151 1397794.159 1417113.374 1520557.854 1839410.375 2055774.581 0.819609728 0.754804405 0.630733334 0.769580645 0.619387535 0.67993552 0.689333056 0.739652036 0.894752952 1 20.97125065 1.127072799 2.353675217 0.99844667 0.705340291 0.736652144 0.057997751 0.131278076 1.366891201 0.054042757 0.01502769 13.39901269 -1.127072799 -0.293106379 IGDQEFDHLPALLEFYK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGDQEFDHLPALLEFYK 17 0 P46109 P46109 CRKL Crk-like protein 0 ; 115.15 0.00032875 335100000 575350 551540 503810 526620 512220 518850 614150 536450 701730 683570 FALSE TRUE 552864.6859 535810.6192 594859.6742 553798.9213 528696.0215 529341.5025 621666.1514 525372.12 622072.5523 637271.195 0.867550095 0.840789013 0.933448238 0.869016089 0.829624853 0.830637736 0.975512711 0.824409018 0.976150432 1 19.28154793 1.127080308 5.97505543 0.997879442 0.872587728 0.506521227 0.046244948 0.159730549 7.293194536 0.042326534 0.010670082 13.39924438 -1.127080308 -0.125291714 (ac)AEPPS(ph)PVHCVAAAAPTATVSEKEPFGK ddPTM_BT-474_Pertuzumab_2h_R1 3 AEPPSPVHCVAAAAPTATVSEKEPFGK 27 1 Q6PCB5 Q6PCB5 RSBN1L Round spermatid basic protein 1-like protein 1 AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK 150.23 5.05E-34 2856690000 2721690 2622310 2020260 2121140 2235640 2587590 2399210 2710910 2993380 3146020 TRUE FALSE 2615323.346 2547524.286 2385365.922 2230612.29 2307551.391 2639912.843 2428572.25 2654928.761 2653584.052 2932937.263 0.891707906 0.868591469 0.813302743 0.760538699 0.78677148 0.900091821 0.828034162 0.905211576 0.90475309 1 21.48391478 1.128098399 0.808041363 0.997472007 0.828239512 0.597652706 0.042286435 0.431195136 0.638509732 0.042594456 0.015960606 13.43069228 -1.128098399 -0.169232496 GS(ph)PSGGSTAEASDTLSIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSPSGGSTAEASDTLSIR 18 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 GS(0.608)PS(0.392)GGSTAEASDTLSIR;GS(0.862)PS(0.138)GGSTAEASDTLSIR 304.24 4.39E-42 257140000 163143 195138 140013 243110 178250 184726 206362 208591 185878 166393 TRUE FALSE 156767.1912 189572.8553 165316.4637 255656.9362 183983.5731 188461.2863 208887.5199 204283.523 164777.9087 155123.0539 1.010598923 1.222080474 1.065711766 1.648091175 1.186049195 1.21491475 1.346592364 1.316912721 1.062239974 1 17.24305359 1.1284839 5.080263917 1.00589988 1.260978307 0.223900874 0.164624136 0.284718955 10.67578258 0.153024124 0.038885928 13.44261932 -1.1284839 0.255078427 EHIMQMLQNPDWK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHIMQMLQNPDWK 13 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 126.48 0.0001018 0 544360 577870 501240 492570 523060 541510 603540 379220 779880 732660 FALSE TRUE 523085.8094 561389.7134 591825.218 517991.5967 539884.6999 552459.7032 610926.3031 371388.9745 691351.2919 683036.2856 0.765824335 0.821903207 0.86646234 0.758366148 0.790418769 0.808829216 0.894427303 0.543732423 1.012173594 1 19.3816027 1.128523984 23.52747608 1.00618806 0.779643392 0.503178336 0.089353843 5.19732187 1096.824038 0.088143284 0.022035828 13.44386008 -1.128523984 -0.226544668 RLS(ph)AEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSAEK 6 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 RLS(1)AEK;RLS(1)AEK 81.163 0.038344 811700000 969950 1197610 916180 1498670 1192000 1050960 1352000 1211590 1112700 932910 TRUE FALSE 932043.2817 1163455.335 1081754.106 1576016.538 1230341.763 1072211.131 1368546.18 1186570.243 986390.9608 869723.1747 1.071655107 1.337730636 1.243791286 1.812089851 1.414636057 1.232818858 1.573542272 1.364307952 1.134143587 1 19.73019675 1.129787023 3.203767375 1.007452461 1.39556772 0.312847304 0.190778884 0.266491578 4.974816418 0.179485615 0.047893083 13.48301516 -1.129787023 0.388115259 LGEESIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGEESIR 7 0 Q02487-2;J3QRL9;Q14574-2;Q08554-2 Q02487-2 DSC2;DSC3 Desmocollin-2 0 118.69 0.029705 0 128090 198040 153660 311850 161250 163920 251950 207680 190390 162170 FALSE TRUE 123084.1012 192392.0931 181429.7801 327944.6159 166436.7527 167234.5747 255033.4395 203391.3354 168777.7254 151186.0815 0.814123231 1.272551621 1.200042877 2.16914555 1.100873514 1.1061506 1.686884381 1.34530463 1.116357563 1 17.2059658 1.130565234 3.802177709 1.010177825 1.359083407 0.093685452 0.349965948 0.4910336 12.24154871 0.326936768 0.085364226 13.507197 -1.130565234 0.348905582 ATISNPITGDLETVHYR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATISNPITGDLETVHYR 17 0 P13674 P13674 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;; 265.37 1.52E-27 964020000 689922 822790 594795 784290 719260 678060 757973 692920 668397 522429 FALSE TRUE 662959.0855 799324.8348 702287.6876 824767.3009 742395.6511 691770.8378 767249.3003 678610.9599 592523.3747 487044.4185 1.361188139 1.641174407 1.441937657 1.693412899 1.52428736 1.420344452 1.575316893 1.39332458 1.21656948 1 18.89369383 1.130642805 1.489833283 1.001388255 1.529754353 0.759437801 0.09569238 0.161391795 0.703326607 0.083018695 0.024913872 13.50960979 -1.130642805 0.528366098 EGAAHAFAQYNLDQFTPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGAAHAFAQYNLDQFTPVK 19 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 151.23 5.40E-10 0 161520 176140 152850 160950 143510 180630 179070 175830 213440 213490 FALSE TRUE 155207.6198 171116.6597 180473.3951 169256.6488 148126.1295 184282.4624 181261.5122 172199.0491 189211.186 199030.1321 0.77981971 0.85975253 0.906764183 0.850407157 0.744239718 0.925902326 0.910723971 0.865190849 0.950666032 1 17.60262734 1.131308268 0.50865374 1.004763455 0.835831147 0.500931323 0.051492581 0.83253266 0.562671828 0.058794093 0.029986055 13.53032622 -1.131308268 -0.168932307 LDLVHTAALMLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDLVHTAALMLDK 13 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 169.62 2.82E-05 58206000 172010 159690 168510 168390 168440 155920 212240 202350 230720 261000 FALSE TRUE 165287.659 155135.7976 198963.5055 177080.6281 173858.0256 159072.8092 214837.4566 198171.4018 204529.6329 243322.2375 0.679295328 0.637573446 0.817695528 0.727761794 0.714517618 0.653753684 0.882933918 0.814440159 0.840571067 1 17.89250865 1.131693918 0.394906836 1.017105991 0.684105233 0.683336606 0.061271298 0.718673569 0.325719942 0.091343927 0.054216181 13.54234638 -1.131693918 -0.333000758 ATENDIYNFFSPLNPMR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATENDIYNFFSPLNPMR 17 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 ; 229.48 2.19E-18 63885000 76415 90238 72044 81745 80621 77427 80108 80427 77746 65896 FALSE TRUE 73428.61732 87664.50059 85063.95341 85963.86925 83214.24768 78992.62699 81088.38567 78766.15434 68920.60002 61432.80523 1.195267204 1.426998169 1.384666598 1.399315381 1.354557185 1.285837863 1.319952513 1.282151353 1.121885933 1 15.90672164 1.132005979 1.314877285 0.996245741 1.349606203 0.769951307 0.061514216 0.180250304 0.627438168 0.055890373 0.017284935 13.55208069 -1.132005979 0.353360462 KSDYIK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSDYIK 6 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 102.77 0.056526 5006500000 5009600 5434700 4771600 4777400 4611600 4501000 5678400 5330100 6332500 6474400 FALSE TRUE 4813819.294 5279707.677 5633934.264 5023962.187 4759936.302 4592013.304 5747893.958 5220031.572 5613661.148 6035883.121 0.79753355 0.874719999 0.933406786 0.83234915 0.78860644 0.760785657 0.952287154 0.86483311 0.93004802 1 22.52513344 1.132072747 0.956593743 0.997360208 0.84254402 0.444427824 0.056001079 0.524943473 1.043486586 0.054670642 0.01886333 13.55416435 -1.132072747 -0.154816188 EMNPALGIDCLHK ddPTM_BT-474_Pertuzumab_2h_R1 6 EMNPALGIDCLHK 13 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 177.84 1.51E-05 3441260000 3017770 2774160 2342590 2855730 2708180 3081120 2927180 3029660 3593450 3597480 FALSE TRUE 2899832.212 2695043.673 2765948.124 3003114.568 2795291.069 3143422.357 2963003.704 2967096.462 3185536.621 3353819.475 0.864635748 0.80357446 0.824715863 0.895431191 0.833464976 0.937266415 0.883471435 0.884691762 0.94982352 1 21.6773736 1.132108797 0.18357506 1.057224883 0.783557851 0.699606637 0.031737497 2.180485306 0.348671228 0.23932851 0.177146775 13.55528949 -1.132108797 -0.273667032 ELSNS(ph)PLRENS(ph)FGSPLEFR ddPTM_BT-474_Pertuzumab_2h_R1 5 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.31)NS(0.69)PLRENS(0.955)FGS(0.045)PLEFR;ELS(0.002)NS(0.998)PLRENS(0.999)FGS(0.001)PLEFR;ELS(0.024)NS(0.979)PLRENS(0.996)FGS(0.001)PLEFR;ELS(0.001)NS(0.999)PLRENS(1)FGSPLEFR;ELS(0.457)NS(0.543)PLRENS(0.994)FGS(0.006)PLEFR 316.12 6.06E-62 588653000 1040394 1116762 890441 1066368 1069631 1155364 1011695 1131106 1135366 1054481 TRUE FALSE 999734.2523 1084913.041 1051363.496 1121403.38 1104036.653 1178726.252 1024076.426 1107748.266 1006484.012 983060.0626 1.016961517 1.103608093 1.069480428 1.140727228 1.12306124 1.199037878 1.041723151 1.126836811 1.023827587 1 19.90692004 1.132552186 4.837695566 1.001695552 1.104715091 0.356514142 0.049033346 0.211050165 7.486136799 0.045286271 0.011555484 13.56913572 -1.132552186 0.103019538 KFPVFK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFPVFK 6 1 P04080;A0A1W2PS52 P04080 CSTB Cystatin-B 0 103.71 0.05524 638600000 311620 342860 295180 402510 331980 326740 359510 408320 499440 554320 FALSE TRUE 299441.5459 333081.9685 348525.5922 423283.5893 342658.4382 333346.9067 363909.7909 399888.0493 442745.665 516775.4127 0.579442324 0.644539118 0.674423712 0.819086162 0.66307032 0.645051793 0.704193315 0.773814 0.856746769 1 18.97917791 1.13270624 1.111304368 0.998812188 0.674042746 0.77466393 0.056939355 0.226186898 0.584790995 0.056011548 0.018230652 13.57394985 -1.13270624 -0.324769443 NVVHQLSVTLEDLYNGATR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVVHQLSVTLEDLYNGATR 19 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 249.14 5.58E-25 1179740000 678310 705430 642340 705780 653170 655340 615560 710460 907240 922330 FALSE TRUE 651800.8953 685311.8271 758425.1268 742205.3904 674179.8062 668591.4238 623093.4074 695788.7527 804253.9187 859859.7676 0.758031623 0.797004178 0.882033508 0.863170273 0.784057856 0.777558678 0.724645379 0.809188636 0.935331491 1 19.71374187 1.133188566 3.355775549 0.996285716 0.798956484 0.713046569 0.043639999 0.12917076 2.610969146 0.045423736 0.012059927 13.58903339 -1.133188566 -0.197329231 KVDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVDEGAGDSAAVASGGAQTLALAGSPAPSGHPK 33 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 KVDEGAGDSAAVASGGAQTLALAGS(0.999)PAPS(0.001)GHPK;KVDEGAGDSAAVASGGAQTLALAGS(1)PAPSGHPK 359.3 1.51E-132 3801600000 2554800 2378800 2166790 2160290 2296650 2541200 2826800 2754300 3502200 3836700 TRUE FALSE 2454955.592 2310958.953 2558377.153 2271782.826 2370523.833 2592584.805 2861395.224 2697422.742 3104644.938 3576836.892 0.686348208 0.646090113 0.71526246 0.635137384 0.662743062 0.72482612 0.79997923 0.754136357 0.867986166 1 21.7702529 1.133826467 0.552171687 1.005787971 0.661560247 0.908563008 0.032627744 0.227110068 0.175726781 0.034348213 0.01655637 13.60900793 -1.133826467 -0.344227724 EES(ph)WESGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESWESGR 8 0 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 EES(1)WESGR;EES(1)WESGR 182.4 0.00023996 328310000 393250 416080 376130 373710 387700 444920 418750 463220 541840 566990 TRUE FALSE 377881.3552 404213.8058 444105.058 392997.2179 400170.7226 453916.5872 423874.7878 453654.3451 480332.5948 528587.2623 0.714889257 0.764705914 0.84017359 0.743485978 0.757057067 0.858735387 0.801901253 0.858239268 0.90871012 1 19.01178213 1.134265585 0.427713729 1.013317262 0.75372932 0.807451676 0.036093854 0.474239881 0.243276066 0.047903489 0.027309317 13.62277503 -1.134265585 -0.259587942 GS(ph)PSFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSPSFLK 7 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 GS(0.989)PS(0.011)FLK;GS(0.997)PS(0.003)FLK 93.649 0.015504 467160000 1316160 1234870 1337300 1291990 1239070 1311420 1389740 1558390 1678620 1839070 TRUE FALSE 1264723.012 1199652.717 1578979.858 1358669.759 1278925.812 1337937.811 1406748.054 1526208.702 1488070.095 1714508.151 0.737659376 0.699706628 0.920952086 0.792454535 0.745943267 0.780362467 0.820496568 0.890172905 0.867928271 1 20.70936333 1.135362597 0.618928089 1.000173691 0.774259407 0.592479132 0.056584431 0.546536786 0.511972348 0.058734889 0.026117879 13.65722916 -1.135362597 -0.225914284 QLS(ph)SGVSEIR ddPTM_BT-474_Pertuzumab_2h_R1 11 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.5)S(0.5)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.499)S(0.499)GVS(0.002)EIR;QLS(0.5)S(0.5)GVS(0.001)EIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.855)S(0.145)GVSEIR;QLS(0.5)S(0.5)GVS(0.001)EIR;QLS(0.499)S(0.499)GVS(0.003)EIR;QLS(0.8)S(0.2)GVSEIR 212.02 5.05E-08 1.73889E+11 20180970 18710940 11213750 18234490 20321780 16691490 17002550 22267940 16006240 14977770 TRUE FALSE 19392275.38 18177322.31 13240324.07 19175574.21 20975448.51 17029003.36 17210632.29 21808099.26 14189278.74 13963312.3 1.388801952 1.301791575 0.948222298 1.373282629 1.502182868 1.219553284 1.232560866 1.561814188 1.016182868 1 23.73513787 1.135423834 10.29811821 1.001917066 1.316173408 0.372733625 0.159828479 0.389390557 35.79345786 0.158139324 0.0395559 13.65915502 -1.135423834 0.314256342 DIHFMPCSGLTGANLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIHFMPCSGLTGANLK 16 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 150.59 7.25E-07 454780000 345820 334460 285660 319670 285670 345430 310950 266830 458230 447730 FALSE TRUE 332304.9721 324921.5283 337285.1165 336168.207 294858.835 352414.8313 314755.4991 261319.8673 406213.6515 417404.8483 0.796121496 0.778432569 0.808052704 0.805376862 0.706409703 0.844299803 0.754077248 0.626058534 0.973188628 1 18.67108783 1.136778218 7.818761823 0.996197794 0.761797431 0.69836147 0.058332789 0.141204124 9.402397694 0.060670901 0.015207052 13.70181875 -1.136778218 -0.234400363 AKHDELTYF ddPTM_BT-474_Pertuzumab_2h_R1 3 AKHDELTYF 9 1 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 ;; 120.12 0.00065364 1622180000 4301450 4614660 3617820 3990640 3774410 2334680 4345030 3911560 5151110 5105880 FALSE TRUE 4133344.578 4483054.415 4271640.552 4196597.409 3895817.325 2381888.829 4398205.777 3830784.919 4566377.588 4760054.2 0.868339814 0.941807431 0.897393259 0.881628072 0.818439699 0.500391115 0.923982289 0.804777584 0.959312099 1 22.18254657 1.137011097 4.315434549 0.997868832 0.829350056 0.207267795 0.118212351 0.340457031 10.36094765 0.115333751 0.029760561 13.70916794 -1.137011097 -0.168518777 ISSIQSIVPALEIANAHRK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISSIQSIVPALEIANAHRK 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 85.146 0.0020015 569210000 354590 534270 336060 497740 289430 413100 479890 406550 390430 313390 FALSE TRUE 340732.2308 519033.1427 396793.5176 523428.421 298739.7788 421453.165 485763.0374 398154.6004 346110.0232 292163.8162 1.166236926 1.776514113 1.358119985 1.791557996 1.022507793 1.442523481 1.662639281 1.362778614 1.184643697 1 18.15641799 1.137214221 2.37693649 1.009378854 1.465547189 0.290883064 0.23323435 0.31688153 3.319460971 0.204702077 0.056970955 13.71558136 -1.137214221 0.456168336 SHSESASPSALSSS(ph)PNNLSPTGWSQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSESASPSALSSSPNNLSPTGWSQPK 27 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 SHSESASPSALS(0.002)S(0.054)S(0.944)PNNLSPTGWSQPK;SHSESASPSALSS(0.018)S(0.982)PNNLSPTGWSQPK 226.28 9.50E-35 1125690000 606460 654960 500330 622060 552660 711490 830480 437270 1189850 1220380 TRUE FALSE 582758.8727 636281.1821 590750.7608 654164.5911 570436.8108 725876.8153 840643.6627 428240.2217 1054783.216 1137722.576 0.512215267 0.559258642 0.519239728 0.574977244 0.501384804 0.638008624 0.738882818 0.376401269 0.927100542 1 20.11771738 1.137316561 6.41017474 0.990611117 0.554622259 0.771885993 0.089594121 0.094324067 4.911673066 0.084520707 0.021275353 13.71881377 -1.137316561 -0.435988859 PS(ph)SPALYFTHDASLVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 PSSPALYFTHDASLVHK 17 0 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 PS(0.619)S(0.381)PALYFTHDASLVHK;PS(0.5)S(0.5)PALYFTHDASLVHK 264.69 2.88E-27 291290000 343130 297330 425690 436940 410660 389380 510080 180482 675140 635740 TRUE FALSE 329720.1002 288850.4395 502621.6524 459490.5258 423869.2519 397253.5304 516322.5116 176754.9836 598500.9376 592680.7635 0.556319895 0.487362603 0.848047859 0.77527491 0.715172953 0.670265605 0.871164619 0.298229662 1.009820083 1 19.17689571 1.137635382 24.99999941 1.004971872 0.653578995 0.425937189 0.1635401 13.15560289 3246.518462 0.159872407 0.039968107 13.72888863 -1.137635382 -0.351392877 NTEESS(ph)SPVRK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTEESSSPVRK 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 NTEES(0.049)S(0.476)S(0.476)PVRK 92.457 0.0061136 132150000 153790 141010 126560 148080 149610 136600 142630 145620 158550 142260 TRUE FALSE 147779.7168 136988.5329 149432.2073 155722.4265 154422.3415 139362.1456 144375.5486 142612.8961 140552.0687 132624.6035 1.114270753 1.032904373 1.126730662 1.174159413 1.164356669 1.0508016 1.088603056 1.075312516 1.059773715 1 17.01698891 1.13793134 0.712367148 1.001987556 1.114181733 0.423684549 0.040570772 0.709878213 0.845295554 0.042276936 0.017111672 13.73824762 -1.13793134 0.112194177 YSHSGS(ph)SSPDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHSGS(0.952)S(0.024)S(0.024)PDTK;YSHS(0.099)GS(0.52)S(0.061)S(0.319)PDTK 288.53 3.04E-29 545910000 1305570 1255190 1157330 1169420 1134750 1378600 1297630 1219150 1685700 1664120 TRUE FALSE 1254546.881 1219393.21 1366485.276 1229773.906 1171250.264 1406476.237 1313510.784 1193974.126 1494346.403 1551407.67 0.808650689 0.78599148 0.880803481 0.792682626 0.754959697 0.90658069 0.8466574 0.769606951 0.963219682 1 20.56514641 1.138256646 5.511520896 0.995772057 0.818478705 0.672536116 0.045800865 0.116713374 5.019502406 0.043567497 0.011037319 13.74854203 -1.138256646 -0.177293352 TPADTGFAFPDWAYKPES(ph)SPGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 TPADTGFAFPDWAYKPES(0.62)S(0.379)PGS(0.002)R;TPADTGFAFPDWAYKPES(0.494)S(0.494)PGS(0.012)R 152.5 3.71E-08 706427000 428171 385627 343721 388863 392418 411332 406679 421571 375583 328474 TRUE FALSE 411437.604 374629.2955 405839.0307 408932.266 405040.4814 419649.4149 411656.0593 412865.4115 332948.3924 306226.1634 1.343574303 1.223374552 1.325291824 1.335392971 1.322684113 1.370390466 1.344287682 1.348236894 1.08726305 1 18.22423802 1.138415271 4.034771982 1.005851094 1.327120397 0.899446763 0.038277009 0.060568069 1.665399564 0.038054225 0.009894828 13.75356459 -1.138415271 0.321269303 DYTEGWVEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYTEGWVEFR 10 0 Q9ULW3 Q9ULW3 ABT1 Activator of basal transcription 1 0 ; 144.66 7.40E-05 135905000 173461 173582 144831 160946 183931 185860 158939 175904 175021 156214 FALSE TRUE 166681.9523 168631.6113 171005.1834 169252.4423 189847.3077 189618.2165 160884.143 172271.5209 155153.3498 145633.4866 1.144530397 1.157917833 1.174216091 1.162180802 1.303596529 1.302023463 1.104719435 1.182911464 1.065368642 1 17.1519826 1.138960467 1.43243995 0.998642493 1.199536698 0.534753927 0.060769715 0.31581104 1.277824804 0.060086866 0.018210526 13.7708411 -1.138960467 0.200894204 DLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI ddPTM_BT-474_Pertuzumab_2h_R1 1 DLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 34 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 275.21 5.40E-74 848960000 99653 109250 74317 104960 88959 105510 117680 76685 139090 129700 FALSE TRUE 95758.45059 106134.297 87747.73507 110376.9982 91820.44703 107643.4845 119120.203 75101.42795 123301.0863 120915.3035 0.791946493 0.877757355 0.725695859 0.912845562 0.759378213 0.890238716 0.985154068 0.621107716 1.019731025 1 16.88363732 1.139126147 24.98533717 1.009893795 0.82080285 0.370956387 0.098627281 14.82949559 3714.916682 0.090876091 0.022719026 13.77609558 -1.139126147 -0.189090944 ELSPLISLPS(ph)PVPPLS(ph)PIHSNQQTLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSPLISLPSPVPPLSPIHSNQQTLPR 27 0 A0A669KBI3;F5GXF9;P51825;P51825-3;P51825-2;E7ETI4;E7EMC5 A0A669KBI3 AFF1 AF4/FMR2 family member 1 2 ELSPLIS(0.046)LPS(0.954)PVPPLS(1)PIHSNQQTLPR;ELSPLIS(0.001)LPS(0.999)PVPPLS(1)PIHSNQQTLPR 200.15 2.64E-25 377520000 100053 100033 91612 98491 99182 98866 89986 101941 93651 82904 TRUE FALSE 96142.81815 97180.15678 108168.3263 103574.1323 102372.2791 100865.1383 91087.27559 99835.88273 83020.1311 77288.83824 1.243941821 1.257363405 1.399533604 1.340091722 1.32454157 1.30504146 1.17853079 1.291724459 1.074154212 1 16.23797246 1.139376144 1.013808169 0.992548811 1.311149888 0.749506333 0.05894369 0.246551867 0.542233665 0.055753671 0.018796983 13.78402792 -1.139376144 0.318601077 LHTVQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHTVQPK 7 0 A2A3N6;Q5VWC4;P55036-2;P55036;A6PVX3 A2A3N6;Q5VWC4 PIPSL;PSMD4 Putative PIP5K1A and PSMD4-like protein;26S proteasome non-ATPase regulatory subunit 4 0 70.912 0.055741 220550000 696120 727310 614910 689510 693330 679670 756490 673200 958030 947200 FALSE TRUE 668914.8608 706567.8309 726037.9156 725095.6937 715631.5891 693413.3931 765748.1509 659298.1847 849278.4508 883045.3003 0.757509111 0.800149019 0.822197814 0.8211308 0.810413224 0.785252345 0.867167461 0.746618757 0.961760909 1 19.75212792 1.139626058 5.634744892 0.995479197 0.803114139 0.828127795 0.0328392 0.073544173 3.278543705 0.029736883 0.007526618 13.7919622 -1.139626058 -0.192365058 EHSNPNYDK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHSNPNYDK 9 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 147.73 9.17E-05 1767450000 2730110 2713420 2553300 2552260 2612280 2593600 3029060 2219150 3624240 3424000 FALSE TRUE 2623414.283 2636035.918 3014738.108 2683982.444 2696306.359 2646044.369 3066130.542 2173323.777 3212831.469 3192089.43 0.821848617 0.825802652 0.944440365 0.840823073 0.84468384 0.828938044 0.960540301 0.68084677 1.00649795 1 21.60606964 1.139687671 24.99951808 1.00327365 0.843435709 0.442890337 0.071671145 13.36387784 3369.502666 0.067176702 0.016794177 13.79391898 -1.139687671 -0.159837941 LAQTLSTQLFQMVHTQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAQTLSTQLFQMVHTQR 17 0 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 0 ; 179.09 9.35E-10 706530000 305860 325230 251275 276630 300780 331550 299440 330320 313450 290950 FALSE TRUE 293906.6531 315954.7588 296685.9821 290906.9075 310454.8619 338254.1682 303104.6363 323498.7766 277868.4701 271243.6973 1.083552008 1.164837236 1.093798621 1.072492782 1.144560647 1.247048951 1.117462412 1.19264993 1.024423693 1 18.04923009 1.139747206 6.206832671 1.003324994 1.141572467 0.506128852 0.05043057 0.171630116 8.69919981 0.049095 0.012374638 13.79581004 -1.139747206 0.138247474 YMVENHGEDYK ddPTM_BT-474_Pertuzumab_2h_R1 1 YMVENHGEDYK 11 0 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2 D6RIC3 NOP16 Nucleolar protein 16 0 142.1 0.0016351 0 413760 428370 351800 329440 373230 396920 383620 407630 485270 480950 FALSE TRUE 397589.8018 416153.307 415378.0857 346442.4379 385235.2819 404945.9944 388314.8563 399212.2981 430184.184 448374.8281 0.886735331 0.928137087 0.926408129 0.77266255 0.859181332 0.903141677 0.866049635 0.890353947 0.959429828 1 18.77434576 1.139817892 2.542405057 0.999259444 0.877264561 0.499446968 0.0414519 0.224525671 2.673141448 0.040711106 0.011237298 13.79805565 -1.139817892 -0.121994883 VFEHFLENLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFEHFLENLDK 11 0 A0A5F9ZHB6;P49642;A0A3B3ITS8 A0A5F9ZHB6 PRIM1 DNA primase small subunit 0 190.15 2.40E-06 143210000 374560 390240 338250 333960 352850 336700 403050 392880 473640 486380 FALSE TRUE 359921.7811 379110.7373 399379.2993 351195.7156 364199.7407 343508.3047 407982.6465 384766.8907 419874.3729 453437.0494 0.793763504 0.836082402 0.880782238 0.774519233 0.803198021 0.757565587 0.899755869 0.848556357 0.925981618 1 18.79054275 1.14081076 0.997559564 0.999161399 0.814186864 0.691081132 0.039865495 0.287825214 0.615282305 0.037322548 0.012668607 13.82963633 -1.14081076 -0.184974535 TLSSFFT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLSSFFTPR 9 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 TLS(0.001)S(0.004)FFT(0.995)PR;TLSSFFT(1)PR;TLSSFFT(1)PR;TLSSFFT(1)PR 147.74 0.0010247 259205000 1387600 572420 277190 299723 269007 160105 153928 772310 140029 125863 TRUE FALSE 1333371.058 556095.1421 327284.3991 315191.7399 277659.8545 163342.4328 155811.8169 756361.5286 124133.495 117338.1869 11.36348782 4.739251191 2.789240295 2.686182123 2.36632133 1.392065423 1.327886692 6.445996385 1.057912162 1 16.84031308 1.140820324 12.96954863 1.007553179 3.904901782 0.156841795 2.843187043 1.337084081 170.2404658 2.750566668 0.687719646 13.8299409 -1.140820324 2.897348603 IRTPS(ph)GEFLER ddPTM_BT-474_Pertuzumab_2h_R1 1 IRTPSGEFLER 11 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 1 IRT(0.001)PS(0.999)GEFLER 191.89 0.00089806 0 65687 80519 60969 73096 71973 81606 62719 73970 76690 66406 TRUE FALSE 63119.87942 78222.67696 71987.45455 76868.49332 74288.07691 83256.12923 63486.57388 72442.49365 67984.47271 61908.26247 1.019571167 1.26352564 1.162808512 1.241651603 1.19997031 1.344830656 1.025494358 1.170158728 1.098148615 1 15.91784435 1.141099863 0.880899614 1.005744826 1.197613388 0.276374162 0.093165163 0.683666378 1.176193 0.08296304 0.029788335 13.83884557 -1.141099863 0.191868562 KMYSEIDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KMYSEIDIK 9 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 72.096 0.076515 328180000 737830 738160 578790 621470 640860 666500 736760 728010 815520 838440 FALSE TRUE 708994.7879 717108.3995 683390.2281 653544.1412 661473.8439 679977.0867 745776.6893 712976.3391 722945.5885 781651.712 0.907046933 0.917427018 0.87428994 0.836106582 0.846251385 0.869923364 0.95410357 0.912140699 0.92489478 1 19.57616639 1.141132984 0.689105751 0.995934274 0.876458839 0.581850521 0.030609357 0.531426535 0.597793092 0.032896336 0.013615317 13.83990102 -1.141132984 -0.119475435 LFIGGLS(ph)FETTEESLR ddPTM_BT-474_Pertuzumab_2h_R1 6 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 LFIGGLS(1)FETTEESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(0.998)FET(0.002)TEESLR 290.27 1.73E-45 522106000 288410 270886 158275.7 309116 267995 178059.3 253404 398874 147288.1 135082 TRUE FALSE 277138.6183 263160.5965 186879.6398 325069.5138 276615.3026 181659.781 256505.234 390637.1125 130568.5724 125932.7758 2.200686966 2.089691066 1.483963477 2.581293962 2.196531449 1.442513912 2.036842532 3.101949512 1.036811676 1 16.94229429 1.141457998 11.60210326 1.005455536 2.152992928 0.495065684 0.453690408 0.422961949 47.69319444 0.460726774 0.115211063 13.85026228 -1.141457998 1.147537392 TPS(ph)PSQPK ddPTM_BT-474_Pertuzumab_2h_R1 5 TPSPSQPK 8 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.006)PS(0.992)PS(0.002)QPK;T(0.003)PS(0.997)PSQPK;T(0.384)PS(0.615)PS(0.002)QPK;T(0.33)PS(0.669)PS(0.001)QPK;T(0.006)PS(0.992)PS(0.001)QPK 133.83 0.00094668 12575630000 15352980 14883460 11470810 13064780 13481590 13146110 13577770 14231930 16439530 15936010 TRUE FALSE 14752968.57 14458998.29 13543840.53 13739054.86 13915237.59 13411933.35 13743938.81 13938035.67 14573383.47 14856649.85 0.993021221 0.973234103 0.911634902 0.924774764 0.93663361 0.90275624 0.925103503 0.938168148 0.980933361 1 23.82460549 1.142091282 3.347720016 0.999040206 0.935940498 0.406101973 0.025683851 0.228694922 4.582277587 0.025605256 0.006823068 13.87047333 -1.142091282 -0.063099708 KAPPPPISPTQLS(ph)DVSSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAPPPPISPTQLSDVSSPR 19 1 Q9P0K7-3;Q9P0K7;Q9P0K7-2 Q9P0K7-3 RAI14 Ankycorbin 1 KAPPPPISPT(0.001)QLS(0.999)DVSSPR;KAPPPPISPT(0.001)QLS(0.999)DVSSPR 197.28 4.87E-16 375580000 312620 373850 322120 380880 323080 363530 357870 377670 327460 285800 TRUE FALSE 300402.4648 363188.164 380334.2495 400537.2624 333472.1616 370880.8257 362249.7201 369870.9825 290288.1136 266442.5114 1.127456963 1.363101414 1.427453327 1.503278363 1.251572656 1.391973164 1.359579288 1.388183066 1.089496237 1 18.02346476 1.145110511 4.214909212 1.006992511 1.359619224 0.619671332 0.096884567 0.128128699 3.815349171 0.089791191 0.023296197 13.96723729 -1.145110511 0.352626713 LLILPQEEDYGFDIEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLILPQEEDYGFDIEEK 17 0 Q8TCU6;Q8TCU6-3 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 176.91 2.46E-09 27957000 64884 55486 58075 53802 52333 66766 58475 63647 82549 84956 FALSE TRUE 62348.26155 53903.59361 68570.44437 56578.72767 54016.33847 68116.05426 59190.63454 62332.66721 73178.38359 79201.85445 0.787207092 0.680584994 0.865768167 0.714361148 0.682008507 0.860031053 0.747338998 0.787010199 0.923947856 1 16.27324659 1.145328698 2.473458056 0.999248933 0.761553452 0.640011985 0.060501158 0.155533933 1.742906321 0.053879123 0.014946454 13.97425609 -1.145328698 -0.23769548 DSQDASAEQS(ph)DHDDEVASLASASGGFGTK ddPTM_BT-474_Pertuzumab_2h_R1 5 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 DSQDAS(0.004)AEQS(0.996)DHDDEVASLASASGGFGTK;DSQDAS(0.001)AEQS(0.999)DHDDEVASLASASGGFGTK;DSQDASAEQS(1)DHDDEVASLASASGGFGTK;DSQDAS(0.004)AEQS(0.996)DHDDEVASLASASGGFGTK;DSQDAS(0.009)AEQS(0.991)DHDDEVASLASASGGFGTK 315.94 2.10E-92 12576820000 4532410 4124610 3750910 3871760 3805620 4308840 4221490 4214330 5194050 5071630 TRUE FALSE 4355278.406 4006980.161 4428782.876 4071581.998 3928031.223 4395967.697 4273153.857 4127302.613 4604443.219 4728123.983 0.92114302 0.847477811 0.936689243 0.861141123 0.830780081 0.929748821 0.903773647 0.872926054 0.973841472 1 22.17283644 1.146318306 4.525197635 0.997698071 0.886905065 0.580677111 0.03385707 0.13613954 4.550404031 0.030723318 0.007917211 14.00613493 -1.146318306 -0.110793006 ITITNDK ddPTM_BT-474_Pertuzumab_2h_R1 1 ITITNDK 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13;P54652;P17066 A0A0G2JIW1;Q53FA3;P11142;P54652;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA2;HSPA6 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6 0 101.41 0.02112 356680000 1333300 1401900 1115100 1089900 1110600 1307700 1242700 1337200 1619600 1639600 FALSE TRUE 1281193.162 1361919.185 1316623.375 1146149.87 1146323.458 1334142.59 1257908.534 1309586.353 1435749.798 1528548.432 0.838176361 0.890988572 0.861355354 0.749828953 0.749942517 0.872816695 0.822943198 0.856751625 0.9392897 1 20.54373083 1.14687226 1.801684828 1.000308956 0.825537548 0.634009818 0.044080582 0.222973487 1.362382333 0.044708042 0.01297318 14.02401152 -1.14687226 -0.174771409 SRLT(ph)PVSPESSSTEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.203)RLT(0.797)PVSPESSSTEEK;S(0.006)RLT(0.994)PVSPESSSTEEK;S(0.032)RLT(0.968)PVSPESSSTEEK 217.82 2.25E-14 2186150000 1790320 1648260 1625750 1434670 1386480 1738230 1893780 1843800 2637080 2818780 TRUE FALSE 1720352.315 1601253.239 1919559.19 1508713.491 1431077.388 1773378.202 1916956.646 1805724.886 2337729.734 2627861.52 0.654658665 0.609336994 0.730464362 0.574122144 0.544578692 0.674837006 0.729473997 0.687146135 0.889593959 1 21.32545782 1.148055571 1.150640284 1.005844403 0.632449462 0.823610726 0.056022283 0.179631558 0.492474013 0.053227468 0.017160172 14.0622745 -1.148055571 -0.373394941 LGEVVNTHGPVEPDKDNIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGEVVNTHGPVEPDKDNIR 19 1 P30419;P30419-2;K7EN82 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 ; 245.78 7.94E-25 4458700000 2708700 2346170 1850680 2116870 2347300 2279970 2295380 2580400 2915900 3043300 FALSE TRUE 2602841.009 2279259.529 2185139.044 2226121.914 2422803.036 2326072.556 2323471.547 2527113.838 2584899.256 2837174.58 0.917406009 0.803355403 0.770181384 0.784626343 0.853949226 0.819855278 0.818938518 0.890714958 0.911082199 1 21.4360235 1.148787723 1.016418171 0.998105147 0.817966707 0.666322354 0.039453994 0.286778106 0.632916276 0.036989899 0.012476439 14.08600125 -1.148787723 -0.18013844 KRS(ph)PTESVNTPVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KRSPTESVNTPVGK 14 2 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 KRS(0.989)PT(0.01)ES(0.002)VNTPVGK;KRS(0.991)PT(0.009)ESVNTPVGK 135.28 2.66E-05 699990000 375160 380770 321280 343920 378100 401190 394050 387360 547520 559680 TRUE FALSE 360498.3324 369910.8124 379342.4428 361669.7524 390261.9299 409302.3367 398872.5018 379360.8806 485367.825 521772.3751 0.690911113 0.70895055 0.72702669 0.693156192 0.747954373 0.784446161 0.764456918 0.727062027 0.930229058 1 18.99306104 1.149432268 3.493037519 0.997607074 0.730950836 0.915632451 0.028801914 0.061118692 1.321915044 0.029553125 0.007857152 14.10692211 -1.149432268 -0.266656239 LS(ph)LQGHPTDLQTSNVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSLQGHPTDLQTSNVK 16 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 LS(1)LQGHPTDLQTSNVK;LS(1)LQGHPTDLQTSNVK 221.25 6.92E-15 1820940000 1633650 1564660 1414240 1302240 1435050 1355520 1632460 1760550 2029080 2272640 TRUE FALSE 1569805.152 1520037.429 1669824.628 1369448.762 1481209.687 1382929.543 1652438.534 1724194.027 1798747.345 2118712.069 0.740924251 0.717434639 0.788131928 0.64635907 0.699108533 0.652721794 0.779925955 0.813793461 0.848981498 1 21.01475611 1.149475648 0.961421965 0.994113491 0.709648033 0.812853641 0.043074578 0.212981883 0.426534135 0.041440286 0.014307642 14.10833126 -1.149475648 -0.284465458 QTDDLRGEIAVLEATVQNNQDER ddPTM_BT-474_Pertuzumab_2h_R1 2 QTDDLRGEIAVLEATVQNNQDER 23 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 210.32 6.23E-25 118651000 78146 90350 55299 76055 79372 93680 71879 80570 78597 69408 FALSE TRUE 75091.96793 87773.30646 65292.75942 79980.20766 81925.07246 95574.27379 72758.6767 78906.20134 69674.99807 64706.93434 1.160493364 1.356474501 1.009053513 1.236037659 1.266094172 1.477032945 1.124433995 1.21943965 1.076777918 1 15.98163271 1.149786074 1.652283819 0.998812147 1.23956123 0.302875174 0.119732205 0.428260108 2.228613483 0.110469807 0.032555185 14.11841925 -1.149786074 0.240749084 FEDENFHYK ddPTM_BT-474_Pertuzumab_2h_R1 3 FEDENFHYK 9 0 Q08752 Q08752 PPID Peptidyl-prolyl cis-trans isomerase D 0 ;; 102.06 0.0036456 1160630000 2067890 2054540 1986600 2136020 1894710 1865000 2025300 2219960 2881510 2997820 FALSE TRUE 1987074.573 1995946.531 2345622.812 2246260.248 1955655.068 1902711.578 2050086.227 2174117.05 2554413.065 2794774.981 0.710996265 0.714170745 0.839288611 0.803735636 0.699754034 0.680810294 0.7335425 0.777922038 0.913995968 1 21.4143007 1.149814164 2.284999785 0.998651332 0.741854495 0.787254238 0.045525075 0.132146875 1.262604696 0.046723231 0.013108552 14.11933243 -1.149814164 -0.256796837 KKYELR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKYELR 6 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 119.57 0.011756 16617100000 22859000 23379000 19025500 22074000 22859000 21129200 23140000 25523000 29722000 31676000 FALSE TRUE 21965645.01 22712253.81 22463831.07 23213241.79 23594280.5 21556446.9 23423194.24 24995941.13 26348083.16 29530556.31 0.743827674 0.769110259 0.760697863 0.78607533 0.798978531 0.729970905 0.793184998 0.846443286 0.892231182 1 24.8157052 1.150170754 1.040691854 0.998123524 0.765369172 0.932984599 0.020054027 0.111697447 0.256842456 0.019002586 0.006351671 14.13093028 -1.150170754 -0.232754352 LGESVQDLSSFDEYSSELK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGESVQDLSSFDEYSSELK 19 0 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 110.77 0.00053314 26341000 36884 35754 32022 32212 36430 37145 34466 41519 44441 47095 FALSE TRUE 35442.5325 34734.33093 37809.08773 33874.46518 37601.80403 37896.09735 34887.80522 40661.61814 39396.24399 43905.2137 0.80725111 0.791120871 0.861152572 0.771536278 0.856431409 0.863134333 0.794616454 0.92612277 0.897302181 1 15.42210465 1.150595138 0.561745808 1.003216005 0.809909197 0.725235693 0.0351306 0.401160775 0.319929219 0.034748561 0.016652558 14.14474552 -1.150595138 -0.193306808 KMECPFYHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KMECPFYHPK 10 1 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;G3V411;Q6PJT7-8;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6;Q6PJT7-6;H0YJ51 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 ; 93.821 0.0055338 666630000 899440 871760 762200 816600 767520 804900 798690 903730 1045610 1061630 FALSE TRUE 864288.8904 846898.2583 899946.495 858744.8239 792207.9778 821175.6295 808464.6071 885067.6597 926916.7364 989724.8545 0.873261782 0.855690604 0.909289578 0.867660158 0.800432539 0.829700927 0.816857941 0.894256273 0.936539819 1 19.91666798 1.15133873 1.881983936 0.996823462 0.851289362 0.721474614 0.029978989 0.176168072 1.162820505 0.030489967 0.008792482 14.16898464 -1.15133873 -0.1455341 DLDKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDKPR 6 1 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 ; 86.086 0.049227 852330000 595360 653010 497730 518450 569430 637400 587600 612200 742360 730960 FALSE TRUE 572092.673 634386.7942 587680.8829 545207.2666 587746.2331 650288.6647 594791.2246 599557.8561 658090.405 681451.4281 0.839520837 0.93093472 0.862395849 0.800067685 0.862491748 0.954270015 0.872829963 0.879824785 0.965718726 1 19.3782513 1.15163374 3.194929977 0.998931203 0.8755985 0.533784261 0.040813778 0.185179481 3.387201743 0.03930865 0.010579946 14.1786127 -1.15163374 -0.123332704 FEHQEWK ddPTM_BT-474_Pertuzumab_2h_R1 4 FEHQEWK 7 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;;; 150.17 0.0019672 1261270000 2581070 2565750 2244640 2397310 2409900 2232150 2733020 2473600 3187430 3105160 FALSE TRUE 2480198.931 2492577.322 2650296.38 2521035.456 2487416.622 2277285.602 2766467.516 2422519.296 2825606.309 2894844.747 0.856764057 0.861040069 0.915522804 0.870870695 0.859257349 0.786669338 0.955653155 0.836839108 0.976082158 1 21.46505455 1.151763083 5.523977056 0.996840896 0.869162232 0.563907413 0.042384725 0.142421721 6.628383446 0.038073451 0.009675313 14.18283608 -1.151763083 -0.127678664 QS(ph)PNSSSAAASVASR ddPTM_BT-474_Pertuzumab_2h_R1 3 QSPNSSSAAASVASR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 QS(0.864)PNS(0.059)S(0.038)S(0.038)AAASVASR;QS(0.998)PNS(0.002)SSAAASVASR;QS(0.861)PNS(0.115)S(0.018)S(0.007)AAASVASR 208.82 2.83E-09 1641220000 1272480 1232840 1127110 1364170 1311730 1270370 1302700 1385340 1362250 1270670 TRUE FALSE 1222750.075 1197680.61 1330803.849 1434574.977 1353922.987 1296057.752 1318642.832 1356732.245 1207613.091 1184606.389 1.03219946 1.011036764 1.123414378 1.211014047 1.142930681 1.094083034 1.113148506 1.14530215 1.019421389 1 20.17597634 1.152329167 6.088653965 1.003392365 1.11203579 0.353171567 0.053846345 0.250750215 13.55488558 0.056107029 0.014183996 14.20133482 -1.152329167 0.108643424 HVGDLGNVTADK ddPTM_BT-474_Pertuzumab_2h_R1 4 HVGDLGNVTADK 12 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 158.34 7.37E-05 2431020000 7351730 6851410 7153550 7292180 7292860 6723600 8221890 7488370 10168520 10139120 FALSE TRUE 7064416.264 6656014.495 8446355.615 7668530.284 7527441.465 6859555.799 8322511.949 7333732.543 9014232.24 9452388.371 0.747368388 0.70416219 0.893568407 0.811279645 0.796353384 0.72569551 0.880466568 0.775860265 0.953645987 1 23.17224748 1.152390005 4.048529639 0.997789124 0.793887147 0.62385676 0.057767655 0.134725297 3.804421275 0.053601167 0.014017119 14.20332437 -1.152390005 -0.203901978 APQTLPS(ph)PEADALAGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 APQTLPSPEADALAGSK 17 0 P31274 P31274 HOXC9 Homeobox protein Hox-C9 1 APQTLPS(1)PEADALAGSK;APQTLPS(1)PEADALAGSK 183.65 7.13E-10 192994000 245480 222190 176514 209166 237610 195947 219310 262270 205800 192779 TRUE FALSE 235886.3702 215853.3587 208414.0063 219961.0823 245252.9414 199909.1826 221993.9814 256854.0328 182438.4468 179721.9066 1.31250761 1.20104089 1.159647203 1.223896889 1.364624636 1.112325071 1.235208248 1.429174872 1.015115242 1 17.45540675 1.152432807 9.882967589 1.003623418 1.255314271 0.551814424 0.089142964 0.290709359 30.7489077 0.089131499 0.022302443 14.20472424 -1.152432807 0.251690853 DKDNPNQYHYVA ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDNPNQYHYVA 12 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 101.71 0.0022954 997130000 1779960 1753590 1534180 1436440 1519490 1247030 1716290 1587930 2120410 2094170 FALSE TRUE 1710397.195 1703579.33 1811440.454 1510574.841 1568365.776 1272245.801 1737294.47 1555138.691 1879709.946 1952330.001 0.876079963 0.872587795 0.927835178 0.773729257 0.803330265 0.6516551 0.889856976 0.796555239 0.962803392 1 20.8967655 1.152443446 4.749823302 0.996361839 0.822890513 0.425946035 0.073441752 0.198596664 7.331007592 0.071053981 0.018273658 14.20507222 -1.152443446 -0.173471326 GSAPQSGAKPSPQPATWVEGASS(ph)PRPPSSGAGPGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSAPQSGAKPSPQPATWVEGASSPRPPSSGAGPGSR 36 2 Q9P2Y4 Q9P2Y4 ZNF219 Zinc finger protein 219 1 GSAPQSGAKPS(0.001)PQPAT(0.007)WVEGAS(0.452)S(0.521)PRPPS(0.009)S(0.01)GAGPGS(0.001)R 52.465 0.030229 75122000 44343 41335 32262 41809 45457 40424 40659 43391 42102 38470 TRUE FALSE 42610.02654 40156.16627 38092.46106 43966.7675 46919.16569 41241.40098 41156.597 42494.96069 37322.75747 35864.39263 1.18808722 1.119666703 1.062124806 1.225916969 1.308238123 1.149926095 1.147561522 1.184878861 1.040663308 1 15.13026458 1.15272882 4.118912977 1.002861051 1.172935144 0.499657931 0.061681656 0.185351485 5.396842618 0.061966038 0.016175401 14.21440941 -1.15272882 0.170074093 EDNS(ph)EGEEILEEVGGDLEEEDDHHMEFCR ddPTM_BT-474_Pertuzumab_2h_R1 10 EDNSEGEEILEEVGGDLEEEDDHHMEFCR 29 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR 251.08 1.11E-46 1523528000 346375.8 345124.6 357445 766887 359507 322520.2 667213 235972.7 903888 903275 TRUE FALSE 332839.0508 335281.9843 422043.2628 806466.13 371070.8692 329041.7794 675378.5523 231099.7813 801282.4236 842095.3797 0.395251012 0.398152029 0.501182257 0.957689769 0.440651829 0.390741699 0.802021444 0.274434211 0.951534046 1 19.68362412 1.153806173 8.104220811 0.989004659 0.524868358 0.462627934 0.196520407 0.238527936 19.72664504 0.184584182 0.046280684 14.24971483 -1.153806173 -0.4641363 TDQDEEHCR ddPTM_BT-474_Pertuzumab_2h_R1 3 TDQDEEHCR 9 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ;; 221.68 4.11E-07 268530000 281790 272213 224400 256014 237772 243204 253401 245531 323117 311348 FALSE TRUE 270777.3353 264449.7518 264954.0718 269226.9132 245420.1523 248121.7515 256502.1972 240460.699 286438.1128 290260.1226 0.932878181 0.911078481 0.912815957 0.927536689 0.845517979 0.85482549 0.883697681 0.828431742 0.986832467 1 18.14698686 1.153923833 7.766088969 0.997022255 0.884804449 0.615399316 0.033605544 0.179814858 14.03370309 0.035322624 0.008863091 14.25357591 -1.153923833 -0.112217806 ERS(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_BT-474_Pertuzumab_2h_R1 5 ERSPSPLRGNVVPSPLPTR 19 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR 139.75 8.95E-07 6886610000 1450182 1551449 1188538 1658358 1613316 1679800 1618301 1531422 1616789 1406838 TRUE FALSE 1393507.284 1507203.194 1403333.255 1743946.055 1665209.774 1713766.707 1638106.252 1499797.601 1433257.891 1311551.609 1.062487572 1.149175666 1.069979439 1.32968161 1.269648684 1.306671194 1.248983449 1.143529229 1.092795648 1 20.32284315 1.154156775 1.855384632 1.005714539 1.207676818 0.361531995 0.086735706 0.367397404 2.356387413 0.087338209 0.025253257 14.26122313 -1.154156775 0.20196228 SMSPT(ph)STPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SMSPTSTPK 9 0 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 SMS(0.47)PT(0.481)S(0.049)T(0.001)PK 110.84 0.024839 362630000 628780 650320 509860 575300 602960 617650 640290 605640 803580 788200 TRUE FALSE 604206.5824 631773.5103 602003.0438 604991.3019 622354.756 630139.3062 648126.0606 593133.3224 712360.9673 734814.5119 0.822257281 0.859772773 0.819258512 0.823325196 0.846954906 0.857548804 0.882026756 0.807187818 0.969443248 1 19.48702059 1.154768048 5.393580314 0.995618083 0.840601951 0.874086199 0.022070953 0.064059487 2.932131067 0.020802371 0.005300256 14.28131007 -1.154768048 -0.155016132 GNSSESIEAIREYEEEFFQNSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNSSESIEAIREYEEEFFQNSK 22 1 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1;A0A2R8YGE5;A0A2R8YD53;A0A2R8Y4Q3 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 151.94 4.10E-08 60442000 27570 30328 19732 22514 29901 25806 28979 27771 23984 20594 FALSE TRUE 26492.53392 29463.07513 23298.01134 23675.95024 30862.79282 26327.815 29333.65367 27197.51915 21261.43687 19199.15004 1.379880561 1.534603098 1.21349181 1.233177 1.607508289 1.371301071 1.527862099 1.416600167 1.107415528 1 14.22875482 1.155249904 3.927150669 1.009417881 1.4144252 0.594980523 0.1191068 0.144499413 3.885704561 0.112553335 0.029583703 14.29716416 -1.155249904 0.405007319 S(ph)QDIPFVSTDIINTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQDIPFVSTDIINTLK 16 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 S(1)QDIPFVSTDIINTLK 172.66 4.71E-09 74150000 89176 74777 80454 72180 81287 92256 75911 95486 108780 115140 TRUE FALSE 85690.90333 72644.43317 94993.82749 75905.21845 83901.67018 94121.47953 76840.02153 93514.18073 96431.75044 107341.4652 0.798301972 0.676760216 0.884968612 0.707137901 0.78163336 0.876841762 0.715846587 0.871184127 0.898364395 1 16.71184796 1.155431723 1.174611013 0.999004891 0.776412969 0.540026978 0.065981018 0.317968601 0.902476099 0.05741703 0.018407528 14.30315098 -1.155431723 -0.222591921 EDAGDNDDTEGAIGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDAGDNDDTEGAIGVR 16 0 Q9H0S4;Q9H0S4-2 Q9H0S4 DDX47 Probable ATP-dependent RNA helicase DDX47 0 224.42 2.73E-13 0 53771 63106 53391 74936 69580 53858 57436 66757 68349 64768 FALSE TRUE 51669.56987 61306.27867 63039.94138 78803.45594 71818.10389 54947.04566 58138.91895 65378.44462 60590.30806 60381.20567 0.855722725 1.015320545 1.044032504 1.30509908 1.189411558 0.910002459 0.962864492 1.082761497 1.003463038 1 15.88181194 1.156945299 9.440386997 1.000897865 1.050850249 0.018561358 0.123218501 1.933118271 204.2920088 0.124676783 0.031210422 14.3530864 -1.156945299 0.049952384 SESAPTLHPYSPLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 SESAPTLHPYSPLS(1)PK;SESAPTLHPYSPLS(1)PK;SESAPTLHPYSPLS(1)PK;SESAPTLHPYSPLS(1)PK 314.2 9.70E-58 3394980000 2283410 2110480 1869260 2279400 2227720 1985670 2120760 2216080 2231490 2040060 TRUE FALSE 2194171.813 2050291.177 2207076.863 2397040.107 2299376.637 2025821.608 2146714.495 2170317.174 1978180.61 1901884.919 1.153682744 1.078031145 1.160468145 1.26034971 1.208998827 1.065165188 1.128729963 1.141140114 1.04011583 1 20.85899852 1.158050931 2.120805462 0.997604636 1.152192435 0.48933046 0.053633632 0.268620258 2.204892486 0.054164158 0.015372877 14.3896732 -1.158050931 0.154587799 KEAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK 33 1 Q3ZCM7;A0A075B736;Q5SQY0 Q3ZCM7 TUBB8 Tubulin beta-8 chain 0 ; 368.01 2.72E-148 5558300000 3834800 3844700 2770000 3445800 3144800 3980300 3470800 3685100 4515000 4457000 FALSE TRUE 3684931.776 3735052.92 3270600.618 3623638.151 3245955.348 4060784.393 3513276.689 3609001.397 4002476.128 4155123.42 0.886840511 0.898903003 0.787124782 0.872089174 0.781193486 0.977295734 0.845528841 0.868566594 0.963262874 1 21.9864599 1.158099343 3.358626998 0.998182807 0.862950861 0.447341654 0.052735196 0.197317564 3.96606164 0.047203958 0.012664924 14.39127734 -1.158099343 -0.135231946 QIATLHAQVADMK ddPTM_BT-474_Pertuzumab_2h_R1 2 QIATLHAQVADMK 13 0 P35579 P35579 MYH9 Myosin-9 0 ; 129.77 0.0001498 1297950000 1753050 1866460 1453670 1697820 1699350 1559950 1593530 1853930 2144610 2191950 FALSE TRUE 1684538.868 1813230.388 1716380.506 1785444.694 1754011.136 1591493.258 1613032.097 1815645.698 1901162.864 2043487.274 0.824345172 0.887321595 0.839927181 0.873724401 0.858342089 0.778812414 0.789352651 0.88850355 0.930352191 1 20.96260183 1.158165336 1.983796549 0.995491162 0.83889439 0.713007852 0.033479723 0.171711702 1.242803794 0.033360093 0.009556277 14.39346432 -1.158165336 -0.156596772 IDKDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDKDKR 6 2 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 81.381 0.034887 719230000 1498900 1336300 1212900 1165300 1324100 1350700 1430700 1465000 1781300 1828600 FALSE TRUE 1440321.331 1298190.032 1432098.011 1225441.273 1366690.879 1378012.079 1448209.335 1434747.238 1579094.292 1704747.293 0.844888469 0.761514646 0.840064693 0.718840427 0.801697052 0.808338036 0.84951555 0.841618722 0.9262923 1 20.70112646 1.158341697 0.869586577 1.001466454 0.791748865 0.770439347 0.036003737 0.239850675 0.403007411 0.031842798 0.011543552 14.39931052 -1.158341697 -0.209717589 ILIQHQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILIQHQK 7 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ; 128.82 0.0037209 878500000 1089470 1041380 1048030 1058270 984160 685700 1171900 1129500 1309790 1387210 FALSE TRUE 1046892.308 1011680.862 1237432.334 1112887.442 1015816.4 699565.3238 1186242.063 1106175.43 1161108.13 1293253.031 0.809503077 0.782276042 0.956836987 0.860533411 0.785473821 0.54093461 0.917254423 0.855343389 0.897819763 1 20.30257314 1.159811583 1.278328174 0.9919831 0.804945441 0.253454857 0.104361993 0.62166507 2.043433872 0.101461789 0.031739033 14.44812807 -1.159811583 -0.187037659 VSLDVNHFAPDELTVK ddPTM_BT-474_Pertuzumab_2h_R1 6 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 218.43 1.33E-14 35314350000 20019280 18754330 17670450 17942010 16981540 19738660 19331430 19560310 24832400 24569100 FALSE TRUE 19236904.41 18219474.87 20863893.39 18867999.29 17527766.66 20137789.23 19568013.82 19156382.76 22013530.06 22905012.97 0.839855643 0.79543613 0.910887648 0.823749775 0.765237142 0.879186982 0.854311405 0.836340184 0.961079135 1 24.44916004 1.160800492 3.594973073 0.99834551 0.837513925 0.691431411 0.038404573 0.119842431 2.749348058 0.035393142 0.009431839 14.48106462 -1.160800492 -0.160831585 GQFQGRPVSVWDVLFSSYLSEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQFQGRPVSVWDVLFSSYLSEAR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 241.29 2.49E-37 260460000 157720 153540 124830 148120 143050 157080 142590 163920 140600 127650 FALSE TRUE 151556.128 149161.1895 147389.5578 155764.491 147651.3332 160256.2652 144335.0591 160534.9947 124639.6774 119004.1518 1.273536475 1.253411644 1.238524502 1.308899636 1.240724218 1.346644321 1.212857341 1.348986504 1.047355706 1 16.86065238 1.161180918 5.982289885 1.009042452 1.277937704 0.843655306 0.043868234 0.069001921 3.925874511 0.038345763 0.009729258 14.49375506 -1.161180918 0.268895252 TFFGDDFIPNDILIGCEEEEQENGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TFFGDDFIPNDILIGCEEEEQENGK 25 0 P52701;P52701-3;A0A494C0M1;P52701-4;A0A087WYT6 P52701 MSH6 DNA mismatch repair protein Msh6 0 ; 196.1 8.76E-25 102556000 214340 205429 164235 162060 193874 206980 178994 199045 236080 230500 FALSE TRUE 205963.3558 199570.3661 193915.9179 170423.936 200110.1333 211165.2774 181184.5821 194934.6512 209281.1881 214888.0297 0.95846826 0.92871793 0.902404467 0.793082501 0.931229783 0.982675851 0.843158097 0.90714523 0.973908079 1 17.71322559 1.163278896 3.919393246 0.996981425 0.903000581 0.288194649 0.051568872 0.272162788 7.396604632 0.049086075 0.012966931 14.56394049 -1.163278896 -0.093980844 ENLPSHFK ddPTM_BT-474_Pertuzumab_2h_R1 4 ENLPSHFK 8 0 Q8TBX8;F8VNT5;Q8TBX8-2;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ;;; 122.28 0.0013971 819010000 1731490 1750930 1543950 1623550 1622340 1054770 1869330 1829540 2042230 2231660 FALSE TRUE 1663821.457 1700995.191 1822976.11 1707341.61 1674524.039 1076098.172 1892207.42 1791759.36 1810404.612 2080507.68 0.799718969 0.817586595 0.876216958 0.820637014 0.804863186 0.517228647 0.909493119 0.861212567 0.870174443 1 20.98850418 1.163663383 1.151353151 0.988165789 0.78939546 0.291254365 0.099436095 0.597385219 1.634759978 0.095230056 0.030766222 14.57683986 -1.163663383 -0.198770329 AFAAVPTSHPPEDAPAQPPTPGPAAS(ph)PEQLSFR ddPTM_BT-474_Pertuzumab_2h_R1 6 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 AFAAVPTSHPPEDAPAQPPT(0.245)PGPAAS(0.755)PEQLSFR;AFAAVPTSHPPEDAPAQPPT(0.187)PGPAAS(0.789)PEQLS(0.024)FR;AFAAVPTSHPPEDAPAQPPT(0.002)PGPAAS(0.998)PEQLSFR;AFAAVPTSHPPEDAPAQPPT(0.04)PGPAAS(0.96)PEQLSFR;AFAAVPTSHPPEDAPAQPPT(0.024)PGPAAS(0.976)PEQLSFR;AFAAVPTSHPPEDAPAQPPT(0.038)PGPAAS(0.962)PEQLSFR 255.66 1.75E-59 4334390000 1328430 1738215 1167177 2347745 1685422 1528523 1995783 1905171 1396242 1183104 TRUE FALSE 1276513.487 1688642.81 1378111.848 2468912.401 1739635.129 1559430.782 2020207.989 1865828.553 1237746.462 1102971.312 1.157340606 1.530994316 1.249453936 2.238419416 1.577226089 1.413845279 1.831605198 1.691638334 1.122192797 1 20.07296384 1.164915433 5.304773788 1.022104565 1.60492565 0.346653412 0.288701485 0.22035382 10.55502002 0.269748431 0.069149129 14.61892482 -1.164915433 0.582821085 HLLENAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLLENAK 7 0 Q96A70-3;Q96A70-4;Q96A70;Q96A70-2 Q96A70-3 AZIN2 Antizyme inhibitor 2 0 129.4 0.0036644 133920000 233990 212210 178870 192970 228890 217680 213250 184100 274960 255040 FALSE TRUE 224845.4121 206157.9786 211195.7879 202929.2048 236252.4547 222081.6387 215859.8173 180298.2707 243747.6935 237765.9136 0.945658731 0.867062799 0.888250905 0.853483166 0.993634668 0.934034805 0.90786696 0.758301591 1.025158274 1 17.85918238 1.165294181 24.99999967 1.012582721 0.890014827 0.387917173 0.05968192 51.05836468 17419.53539 0.061142019 0.015285507 14.63167956 -1.165294181 -0.122567894 ACDEGHCTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ACDEGHCTAK 10 0 A0A0A0MT83;P26440;A0A0S2Z4K7;P26440-2;H0YLC3 A0A0A0MT83 IVD "Isovaleryl-CoA dehydrogenase, mitochondrial" 0 76.143 0.036882 101300000 169230 240180 158930 323480 154630 182600 281980 223590 206180 177250 FALSE TRUE 162616.3045 233330.3016 187652.1864 340174.8416 159603.8144 186292.2971 285430.9556 218972.7884 182775.3108 165244.6996 0.984093922 1.412028961 1.135601849 2.058612726 0.965863442 1.1273723 1.727322911 1.325142585 1.106088796 1 17.33424447 1.165421226 3.871062487 1.014802119 1.35989632 0.117255674 0.320639645 0.437103219 11.64252753 0.287633931 0.076201329 14.63596041 -1.165421226 0.345094201 QLLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLLSPK 6 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 QLLS(1)PK 90.15 0.051773 630290000 1395100 1390000 1335100 1247600 1475300 1255100 1424700 1400500 1400800 1255700 TRUE FALSE 1340577.95 1350358.561 1576382.269 1311988.786 1522754.364 1280478.982 1442135.905 1371579.186 1241787.057 1170650.321 1.145156607 1.15351146 1.3465868 1.120734999 1.300776447 1.093818504 1.231910058 1.171638671 1.060766853 1 20.15887877 1.166019739 2.513471049 1.001423229 1.200362307 0.453276138 0.074496399 0.219635334 2.479404217 0.064273074 0.01789859 14.65614453 -1.166019739 0.198939078 MGIISIS(ph)T(ph)IQKM ddPTM_BT-474_Pertuzumab_2h_R1 1 MGIISISTIQKM 12 1 X6RDV4;Q8WWT9-4 X6RDV4 SLC13A3 2 MGIISIS(1)T(1)IQKM 82.749 0.031266 374400000 18775 12208 15335 9662 19201 9332.4 12916 14804 8998.7 8090.1 TRUE FALSE 18041.25224 11859.83979 18106.37563 10160.65698 19818.6176 9521.107522 13074.06987 14498.29223 7977.205302 7542.150321 2.392056837 1.572474598 2.400691428 1.347183037 2.627714479 1.262386338 1.733467157 1.92230221 1.057683149 1 12.88076019 1.166335403 0.491309065 0.94114378 2.031247003 0.366643777 0.443527484 1.025434421 0.658902644 0.465468117 0.247422194 14.66680112 -1.166335403 1.090103223 VLHAAFIPFGDITDIQIPLDYETEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLHAAFIPFGDITDIQIPLDYETEK 25 0 Q9UNP9-2;Q9UNP9;Q9UNP9-3;E9PK21 Q9UNP9-2 PPIE Peptidyl-prolyl cis-trans isomerase E 0 79.635 5.91E-05 0 66764 61527 53161 53428 64118 58451 63463 62823 76810 74907 FALSE TRUE 64154.78907 59772.3102 62768.37526 56185.42548 66180.4137 59632.91927 64239.67918 61525.6831 68090.85081 69833.48217 0.918682372 0.855926245 0.898829234 0.804562851 0.947688868 0.853930198 0.91989798 0.881034157 0.975045905 1 16.09163129 1.167013608 3.573803541 0.999573605 0.883850133 0.532822093 0.038589975 0.154896034 3.528692478 0.03276014 0.008769167 14.68972303 -1.167013608 -0.115723472 YYS(ph)DS(ph)DDELTVEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 YYSDSDDELTVEQR 14 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 2 YYS(0.999)DS(1)DDELTVEQR 151.8 4.31E-07 0 89722 97871 79540 93803 89766 96119 90841 94173 98160 89428 TRUE FALSE 86215.56505 95079.81491 93914.64736 98644.18407 92653.40491 98062.59204 91952.73933 92228.29464 87017.28832 83370.96191 1.034119831 1.14044282 1.12646712 1.183195945 1.111339042 1.176219991 1.10293485 1.106240021 1.043736168 1 16.34725736 1.167191343 1.560085454 0.999770347 1.129822554 0.533845741 0.039035514 0.260545233 1.211712565 0.034926661 0.010433191 14.69573607 -1.167191343 0.130052207 S(ph)SSPTLTPSQEGSPVFAGFEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 S(0.332)S(0.332)S(0.332)PT(0.002)LT(0.001)PSQEGSPVFAGFEGR 71.073 0.017609 112570000 44376 40637 34030 42642 42117 44807 41613 42835 41056 36588 TRUE FALSE 42641.73686 39478.07255 40179.97799 44842.75873 43471.73155 45713.02824 42122.27234 41950.44228 36395.495 34109.86217 1.250129263 1.157380008 1.177957794 1.314656697 1.274462246 1.340170418 1.234900104 1.229862556 1.067007976 1 15.0579013 1.167246698 2.724480953 1.000472555 1.250105377 0.737141958 0.051965811 0.136280123 1.801308581 0.052774405 0.014568828 14.6976093 -1.167246698 0.249632822 DVFLNGSYNDYVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVFLNGSYNDYVR 13 0 Q96MU7-2;Q96MU7;J3QR07;J3KRG5 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 117.98 0.00055349 0 42706 48371 35738 40854 52566 50555 43747 49965 41552 37215 FALSE TRUE 41037.00231 46991.50644 42196.65159 42962.47984 54256.83313 51577.25674 44282.38887 48933.20529 36835.19116 34694.3949 1.182813605 1.354440871 1.216238292 1.238311836 1.563850106 1.486616408 1.276355705 1.41040665 1.061704384 1 15.08241498 1.167690455 5.57481914 1.011339009 1.346014959 0.538265058 0.115139471 0.160253671 8.582064449 0.112663051 0.0288142 14.71263482 -1.167690455 0.33467595 AYIVEWR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYIVEWR 7 0 Q93034 Q93034 CUL5 Cullin-5 0 100.82 0.022129 29153000 44673 57831 52883 61466 55564 58390 56145 48674 66455 67561 FALSE TRUE 42927.12977 56181.7165 62440.13448 64638.26763 57351.26652 59570.68581 56832.1193 47668.86489 58911.307 62985.03329 0.681544925 0.891985184 0.991348757 1.02624805 0.910553881 0.94579113 0.902311491 0.756828446 0.935322313 1 15.94272143 1.167748296 0.008134813 1.822052689 1.17E-06 0.077896764 0.098796683 9817.604565 63.96240504 7211.703443 7107.540434 14.71459441 -1.167748296 -1.822051524 VDVECPDVNIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDVECPDVNIEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 238.47 2.00E-19 100540000 100870 106180 85440 99528 91449 92985 103790 113190 124970 134970 FALSE TRUE 96927.88888 103151.8504 100880.9086 104664.652 94390.54014 94865.22041 105060.2131 110852.5869 110783.9295 125828.3617 0.770318294 0.819782194 0.801734261 0.831804933 0.750153136 0.753925579 0.834948589 0.880982518 0.880436875 1 16.94109762 1.167772717 0.912721116 0.994235133 0.790553119 0.824905827 0.029777393 0.22043267 0.402512653 0.029764544 0.010555406 14.71542187 -1.167772717 -0.203682013 VGEVTYVELLMDAEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 VGEVTYVELLMDAEGK 16 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 252.99 3.55E-26 28602000 79231 71041 63406 63391 71029 70901 74199 78090 91559 93769 FALSE TRUE 76134.56493 69014.98024 74864.87466 66662.61711 73313.71229 72334.6668 75107.06956 76477.41421 81165.60617 87417.94211 0.870926072 0.789483012 0.856401705 0.762573626 0.838657494 0.8274579 0.859172245 0.874848027 0.928477658 1 16.4156418 1.168980139 0.882820237 1.000216795 0.820231639 0.785340638 0.02952703 0.218763228 0.376970356 0.025409106 0.009159739 14.75639049 -1.168980139 -0.179985155 HELQANCYEEVK ddPTM_BT-474_Pertuzumab_2h_R1 6 HELQANCYEEVK 12 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;; 199.31 1.73E-07 28097100000 19575200 16574800 19340300 21034500 19243400 15898600 21981200 17113800 29243900 28907400 FALSE TRUE 18810179.54 16102102.93 22835522.43 22120093.07 19862381.44 16220080.58 22250212.5 16760394.05 25924255.07 26949476.05 0.697979416 0.597492244 0.847345692 0.820798632 0.737022917 0.601869979 0.825626905 0.621919106 0.961957666 1 24.68375389 1.169032136 7.168014621 0.989675197 0.719780567 0.587098942 0.088016086 0.165874864 13.86497421 0.082945656 0.020922017 14.75815735 -1.169032136 -0.26989463 RAEPPKPEVVDSTESIPVS(ph)DEDS(ph)DAMVDDPNDEDFVPFRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RAEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 41 3 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 2 RAEPPKPEVVDSTESIPVS(1)DEDS(1)DAMVDDPNDEDFVPFRPR 126.88 4.56E-09 40955000 27731 28372 20823 19592 23422 27570 25198 24053 30708 23592 TRUE FALSE 26647.24186 27562.85834 24586.17931 20603.14547 24175.3899 28127.48429 25506.38066 23556.29714 27222.15658 21994.09283 1.211563581 1.25319369 1.117853757 0.936758139 1.099176497 1.278865399 1.159692326 1.071028359 1.237703087 1 14.42482848 1.170093217 0.012281368 4.68E-05 2.226972571 0.108219519 0.101205928 2318.034829 22.85174711 2092.019921 2046.851281 14.79425899 -1.170093217 2.226925736 LACDVDQVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LACDVDQVTR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 179.1 4.99E-06 235474000 161893 167858 128763 171282 177510 171118 164292 172245 168300 154222 FALSE TRUE 155566.0426 163070.8542 152033.3384 180121.8845 183219.7704 174578.1232 166302.6546 168688.0806 149195.2896 143776.4066 1.081999796 1.134197592 1.057428976 1.25279167 1.274338222 1.214233457 1.156675553 1.173266773 1.037689654 1 17.13346743 1.170279707 3.82478287 1.002308336 1.171429953 0.463302639 0.0646667 0.203400779 5.334034429 0.065156071 0.01734428 14.80061313 -1.170279707 0.169121617 RWS(ph)APESR ddPTM_BT-474_Pertuzumab_2h_R1 2 RWSAPESR 8 1 P54253 P54253 ATXN1 Ataxin-1 1 RWS(1)APESR;RWS(1)APESR 122.55 0.00084879 724090000 551550 604070 432270 588140 586700 545490 554020 615720 522550 473450 TRUE FALSE 529994.8162 586842.515 510390.8048 618493.9759 605571.7383 556520.1815 560800.2625 603005.1668 463232.3147 441382.8098 1.200759985 1.329554532 1.156344999 1.401264304 1.371987592 1.26085604 1.270553021 1.366172749 1.049502392 1 18.75167092 1.170741285 6.115571002 1.011320186 1.298172147 0.682688546 0.07369544 0.115066716 7.501206927 0.068015168 0.017312308 14.81635193 -1.170741285 0.286851961 IINQNSVAVLQT(ph)PPDIQSEHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IINQNSVAVLQTPPDIQSEHSR 22 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 IINQNSVAVLQT(1)PPDIQSEHSR;IINQNSVAVLQT(1)PPDIQSEHSR 177.85 2.30E-16 579620000 104104 131883 106564 128430 129973 156587 116353 133973 125580 114786 TRUE FALSE 100035.5006 128121.826 125822.4853 135058.2877 134153.6996 159753.2964 117776.9628 131206.4107 111324.6849 107011.442 0.934811257 1.197272213 1.175785346 1.262092027 1.253638836 1.492861824 1.100601587 1.226097026 1.040306371 1 16.70740554 1.171190933 3.842201419 1.000470733 1.213512252 0.238395729 0.132196898 0.30369685 8.050989741 0.122824089 0.032700459 14.83170001 -1.171190933 0.213041519 DNPEAAVHIFEGTHENPELIWNDNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNPEAAVHIFEGTHENPELIWNDNSR 26 0 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 147.41 1.10E-07 188500000 23051 24581 23718 28474 34723 29419 38219 63193 45909 85370 FALSE TRUE 22150.14144 23879.97395 28004.3702 29943.54655 35839.89683 30013.87234 38686.73555 61888.04247 40697.60279 79587.81386 0.278310716 0.300045607 0.351867564 0.376232806 0.4503189 0.377116431 0.486088682 0.777607016 0.511354701 1 16.28025993 1.173256174 0.289724491 1.087350985 0.219790586 0.851277849 0.083651836 0.646210965 0.190578718 0.215106082 0.148415424 14.90239856 -1.173256174 -0.8675604 RCSSS(ph)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RCSSSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 36 2 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RCS(0.282)S(0.282)S(0.436)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 259.74 2.11E-62 141310000 41291 41560 30673 38846 41064 37632 32716 40501 35644 31951 TRUE FALSE 39677.30207 40374.74949 36216.29342 40850.84672 42384.86085 38392.94482 33116.38819 39664.6402 31597.84255 29786.93031 1.332037295 1.35545184 1.215845105 1.371435267 1.422934838 1.288919148 1.111775797 1.331612213 1.060795531 1 14.86239183 1.174460205 0.721500508 0.99358344 1.332011523 0.618294293 0.084990763 0.440832466 0.5360909 0.08179194 0.033124143 14.94377106 -1.174460205 0.338428084 S(ph)RAPGPRDTDDDEEEPDPYGFIVQTAEIAEIAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRAPGPRDTDDDEEEPDPYGFIVQTAEIAEIAR 33 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.499)RAPGPRDT(0.499)DDDEEEPDPY(0.002)GFIVQTAEIAEIAR;S(0.494)RAPGPRDT(0.494)DDDEEEPDPY(0.011)GFIVQTAEIAEIAR;S(0.495)RAPGPRDT(0.495)DDDEEEPDPY(0.01)GFIVQTAEIAEIAR 126.05 5.20E-08 36263200 22965.9 27145.4 10705.3 20797.7 21254.7 23613.9 18746.2 20335.6 19506 16001.9 TRUE FALSE 22068.36724 26371.23977 12639.98585 21871.07179 21938.37673 24091.38924 18975.6216 19915.66275 17291.76066 14918.07706 1.479303743 1.7677372 0.84729324 1.466078483 1.47059012 1.614912508 1.271988442 1.335002003 1.159114582 1 13.86477396 1.175186131 1.248087698 1.002536863 1.424388721 0.274179931 0.226466181 0.573989044 1.802402986 0.208960488 0.065960804 14.96877055 -1.175186131 0.421851858 ADDLLPLGDQTQDGDFGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 ADDLLPLGDQTQDGDFGSR 19 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ;;; 313.31 3.15E-61 303108000 220076 213840 182498 216457 213432 217899 205524 228694 227101 213534 FALSE TRUE 211475.1866 207741.4926 215479.4482 227628.3717 220297.2341 222305.0671 208039.2642 223971.389 201321.4466 199071.152 1.062309554 1.043553978 1.082424279 1.143452326 1.106625606 1.116711612 1.045049783 1.125082096 1.011303971 1 17.60292465 1.175357026 7.773592041 1.003615912 1.091308532 0.532903842 0.031837068 0.212300662 22.13516531 0.031235955 0.007873071 14.97466192 -1.175357026 0.08769262 NPEDKS(ph)PQLSLSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPEDKSPQLSLSPR 14 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 NPEDKS(1)PQLSLSPR 104.76 0.00062913 406070000 263210 232910 201980 200800 227280 220840 198630 248500 268710 273280 TRUE FALSE 252923.4622 226267.6348 238482.279 211163.3121 234590.6676 225305.5361 201060.8934 243368.3882 238207.1673 254770.5022 0.992750181 0.888123362 0.936067076 0.828837366 0.920792107 0.884347027 0.789184351 0.955245549 0.934987235 1 17.95883872 1.176210934 1.950827636 0.991452864 0.892478006 0.247328996 0.055309308 0.410286945 2.834489193 0.049903827 0.014377705 15.00413399 -1.176210934 -0.098974858 RRAS(ph)QEANLLTLAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRASQEANLLTLAQK 15 2 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2;H7C1L3 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RRAS(1)QEANLLTLAQK 123.55 8.04E-05 536810000 268300 306960 181730 190470 256490 284490 200560 235790 204740 155140 TRUE FALSE 257814.5394 298205.8013 214572.6536 200300.1795 264740.2338 290242.5827 203014.5133 230920.8541 181498.7735 144632.2296 1.782552479 2.061821228 1.483574264 1.384893119 1.830437341 2.006762832 1.403660262 1.596607165 1.254898538 1 17.14202955 1.176401443 1.057016275 0.998916606 1.733752922 0.552041126 0.215722415 0.377637625 0.888709797 0.20890609 0.069704179 15.01071719 -1.176401443 0.734836316 RGS(ph)SDPTVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSSDPTVQR 10 1 H7BXG1;A0A2R8YDG4;H7BZJ9;H7BZI2;Q2KHT3;Q2KHT3-2 H7BXG1;Q2KHT3 CLEC16A Protein CLEC16A 1 RGS(0.984)S(0.016)DPTVQR 109.6 0.0012233 254080000 110640 121810 95812 118470 128840 109450 92999 124210 147640 150120 TRUE FALSE 106316.0665 118336.0981 113127.3597 124584.2509 132984.2556 111663.154 94137.14958 121645.0201 130880.5262 139952.2387 0.759659634 0.845546303 0.808328332 0.890191197 0.950211707 0.797866151 0.672637683 0.869189527 0.93517994 1 17.09457504 1.177162147 2.8937205 0.992172703 0.822583029 0.418276255 0.070644914 0.254018834 3.758294614 0.069262947 0.019076523 15.0370328 -1.177162147 -0.169589674 MVNHFIAEFK ddPTM_BT-474_Pertuzumab_2h_R1 4 MVNHFIAEFK 10 0 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 152.54 1.78E-05 24712600000 38118000 38899800 34389400 34548200 30929800 19022200 42436800 37808200 45119200 48744700 FALSE TRUE 36628306.42 37790415.79 40604329.57 36331236.74 31924685.11 19406841.92 42956154.25 37027447.46 39997457.57 45443178.05 0.806024314 0.831597116 0.893518704 0.799487146 0.70251876 0.427057322 0.94527179 0.814807613 0.880164181 1 25.4375604 1.177217433 1.238904492 0.98918471 0.765519378 0.233490037 0.131357933 0.667653193 2.06877707 0.128229295 0.040576768 15.03894716 -1.177217433 -0.223665331 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSK ddPTM_BT-474_Pertuzumab_2h_R1 7 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.997)PMAQT(0.989)PPCHLPNIPGVT(0.006)S(0.007)PGT(0.002)LIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK 228.62 4.01E-35 1749460000 640548 623635 711446 703471 657033 705791 780396 864226 1133514 1271780 TRUE FALSE 615514.676 605849.5404 840020.1182 739777.2226 678167.0631 720062.5776 789946.7197 846379.4311 1004842.243 1185641.208 0.519140759 0.510988937 0.708494368 0.623946956 0.571983378 0.607319122 0.666261188 0.713857974 0.847509547 1 20.17723606 1.177373132 0.896529906 1.002977244 0.587637521 0.867118961 0.052452343 0.189226231 0.334586235 0.051630662 0.018500375 15.04433972 -1.177373132 -0.415339723 LFSSSS(ph)SPPPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 LFSSSSSPPPAK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 LFSSS(0.015)S(0.492)S(0.492)PPPAK;LFS(0.004)S(0.012)S(0.009)S(0.555)S(0.42)PPPAK;LFSS(0.018)S(0.271)S(0.356)S(0.356)PPPAK 170 4.44E-05 796350000 2464040 2573520 1979450 2528470 2488860 2290810 2266610 2484990 2306210 2082780 TRUE FALSE 2367742.593 2500125.729 2337180.648 2658964.64 2568916.442 2337131.748 2294349.451 2433674.088 2044418.709 1941711.455 1.219410117 1.2875887 1.203670422 1.369392261 1.323016576 1.203645238 1.181611946 1.253365469 1.05289522 1 20.8888974 1.177886145 2.952421526 0.997463734 1.258102799 0.730082738 0.055915425 0.127893891 1.970599155 0.054256514 0.014918385 15.06212144 -1.177886145 0.260639065 LTWHAYPEDAENK ddPTM_BT-474_Pertuzumab_2h_R1 4 LTWHAYPEDAENK 13 0 P45973 P45973 CBX5 Chromobox protein homolog 5 0 ;;; 161.87 4.14E-05 2181470000 2112280 1913520 1790010 2377570 1995110 1924900 2320740 2487930 2850570 3119380 FALSE TRUE 2029729.762 1858948.283 2113504.626 2500276.673 2059284.525 1963822.797 2349141.91 2436553.376 2526985.244 2908101.614 0.69795696 0.639230856 0.726764366 0.859762486 0.708119866 0.675293734 0.807792238 0.837850151 0.86894668 1 21.47164625 1.178545743 0.521537295 1.008589259 0.703972095 0.71440537 0.056621459 0.498881362 0.353239975 0.065761799 0.033670416 15.08501488 -1.178545743 -0.304617164 QAQTQTS(ph)PEHLVLQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 QAQTQTSPEHLVLQQK 16 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 QAQT(0.049)QT(0.107)S(0.843)PEHLVLQQK 186.36 9.75E-10 1115400000 853950 855950 806000 773980 755900 910750 832170 842200 1160200 1145800 TRUE FALSE 820576.6899 831539.1441 951662.1294 813925.2006 780214.21 929165.989 842354.3454 824808.2757 1028498.96 1068193.945 0.768190733 0.77845334 0.890907624 0.761963877 0.730405011 0.869847646 0.788578094 0.772152173 0.962839159 1 20.02674218 1.178749271 5.295820528 0.992811601 0.795369856 0.717099615 0.046937658 0.103465525 5.537121383 0.043450887 0.011260319 15.09208598 -1.178749271 -0.197441745 S(ph)RERPSQPEGLRK ddPTM_BT-474_Pertuzumab_2h_R1 4 SRERPSQPEGLRK 13 3 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(0.998)RERPS(0.002)QPEGLRK;S(1)RERPSQPEGLRK;S(1)RERPSQPEGLRK;S(1)RERPSQPEGLRK 147.36 0.00023619 7171100000 1822130 1862610 1450010 1246170 1276700 1823860 1572470 1653860 2070940 2033850 TRUE FALSE 1750919.145 1809490.186 1712059.062 1310484.983 1317766.215 1860739.699 1591714.358 1619707.213 1835855.573 1896095.528 0.923434036 0.954324379 0.902939244 0.69114924 0.694989359 0.98135335 0.839469497 0.854232917 0.968229473 1 20.85460022 1.179064368 3.899246403 0.997323249 0.85220458 0.239147792 0.092552467 0.32969611 9.153063506 0.091475163 0.024470559 15.10303985 -1.179064368 -0.145118669 KLFIGGLS(ph)FETTEESLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLFIGGLSFETTEESLR 17 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 KLFIGGLS(0.98)FET(0.018)T(0.003)EESLR 75.945 0.012833 214670000 178650 167470 136060 152930 165500 154890 151780 168350 149020 134590 TRUE FALSE 171668.1605 162693.9196 160649.0686 160822.7356 170823.4578 158021.9819 153637.529 164873.5137 132103.8743 125474.0994 1.368156148 1.296633491 1.280336495 1.281720581 1.36142406 1.259399212 1.224456121 1.31400436 1.052837796 1 16.93703007 1.181251446 4.550138289 1.005832957 1.295826091 0.87200411 0.041770549 0.065049098 2.552888295 0.038777372 0.010229674 15.17928956 -1.181251446 0.289993135 EEEHDCFLEEIMTK ddPTM_BT-474_Pertuzumab_2h_R1 5 EEEHDCFLEEIMTK 14 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;;; 162.97 4.35E-06 229802000 266322 243584 265201 304943 265907 264757 319741 339923 439494 489696 FALSE TRUE 255913.8418 236637.2228 313128.7201 320681.1448 274460.1401 270110.5679 323654.086 332903.4713 389604.4836 456528.4537 0.560564932 0.518340578 0.685890918 0.702434081 0.60118956 0.591662066 0.708946142 0.729206402 0.853406793 1 18.80034526 1.182090028 0.83214786 1.002921922 0.607716711 0.848461675 0.053429298 0.22074155 0.342884031 0.054016265 0.020130974 15.20862768 -1.182090028 -0.395205212 LAHEIEALK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAHEIEALK 9 0 O43847;O43847-2;G3V1R5;H0Y5G9 O43847 NRD1 Nardilysin 0 ; 129.1 0.00039879 304230000 587010 606310 532920 530360 590910 602040 690610 619790 808250 815640 FALSE TRUE 564069.0002 589018.6324 629230.4987 557731.9432 609917.1568 614213.6613 699061.8918 606991.1199 716500.8485 760395.9763 0.741809554 0.774620922 0.82750372 0.733475663 0.802104661 0.807755012 0.919339283 0.798256617 0.94227333 1 19.53639137 1.182920893 0.363943651 1.018292228 0.753354943 0.729853283 0.044014747 0.685639134 0.279778376 0.069336075 0.044475321 15.23775174 -1.182920893 -0.264937285 LRNELQTDKPFIPLVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRNELQTDKPFIPLVEK 17 2 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ; 93.269 0.0017456 2488400000 1488810 1602920 1228250 1343550 1386560 1629740 1337870 1384700 1882660 1819280 FALSE TRUE 1430625.659 1557206.291 1450222.097 1412890.777 1431159.962 1662694.459 1354243.253 1356105.461 1668948.33 1696058.545 0.843500163 0.918132393 0.855054268 0.833043636 0.843815189 0.980328459 0.798464922 0.799562884 0.984015755 1 20.69375454 1.183086512 9.038554789 0.993669568 0.857650264 0.514503698 0.051680533 0.298519389 44.4471652 0.051063163 0.012847444 15.24356376 -1.183086512 -0.136019304 SLPEEDVAEIQHAEEFLIKPESK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 265.05 3.21E-44 232270000 428960 383290 348060 343220 392620 384760 395190 424650 545220 559970 FALSE TRUE 412195.769 372358.9445 410962.1846 360933.6253 405248.9789 392540.1108 400026.4534 415880.8291 483328.9113 522042.7331 0.789582428 0.71327292 0.787219433 0.691387127 0.776275491 0.751930993 0.766271472 0.796641353 0.925841661 1 18.99380838 1.183132652 1.810907047 1.001346454 0.750927506 0.89165867 0.02933863 0.084813242 0.509449466 0.024716714 0.00720912 15.24518336 -1.183132652 -0.250418948 NFEES(ph)PERK ddPTM_BT-474_Pertuzumab_2h_R1 1 NFEESPERK 9 1 Q6MZP7-3;Q6MZP7;Q6MZP7-4;Q6MZP7-2 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 NFEES(1)PERK 75.479 0.01207 0 292890 276780 234780 245810 269940 265390 281930 288310 346770 345560 TRUE FALSE 281443.535 268886.5054 277209.9687 258496.2836 278622.8653 270756.3676 285380.3437 282356.2977 307406.1234 322154.9134 0.873627945 0.834649711 0.860486546 0.802397458 0.864872313 0.840453944 0.88584818 0.876461249 0.95421833 1 18.29739507 1.183182452 1.116731058 1.002159571 0.845668551 0.850725614 0.021247409 0.148925491 0.385010584 0.018431565 0.00603501 15.24693162 -1.183182452 -0.156491019 RGPNYTSGYGTNSELSNPS(ph)ETESER ddPTM_BT-474_Pertuzumab_2h_R1 2 RGPNYTSGYGTNSELSNPSETESER 25 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 1 RGPNYTSGYGTNSELSNPS(0.992)ET(0.008)ESER;RGPNYTSGYGTNSELSNPS(0.997)ET(0.003)ESER 256.97 3.99E-45 1577340000 338500 344770 304740 315630 346270 332790 281160 396750 325380 309660 TRUE FALSE 325271.0458 334937.4972 359813.2969 331919.7021 357408.089 339519.2418 284600.9202 388556.9739 288444.2265 288686.4524 1.126727781 1.160212038 1.246380957 1.149758499 1.2380494 1.176083044 0.985847856 1.345948071 0.999160938 1 18.13914388 1.183230542 24.84898057 0.999577964 1.179850029 0.39923046 0.087844526 90.95144956 40844.08594 0.080029032 0.020007294 15.24862001 -1.183230542 0.180272066 LFDQAFGLPR ddPTM_BT-474_Pertuzumab_2h_R1 3 LFDQAFGLPR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;; 199.46 6.47E-07 3528700000 2438308 2481752 1736539 2654200 2609784 1730358 2781398 2643514 3070851 3288199 FALSE TRUE 2343016.228 2410974.863 2050370.226 2791183.58 2693730.073 1765347.024 2815437.581 2588924.512 2722260.869 3065486.353 0.764321206 0.786490163 0.66885642 0.910519004 0.87872845 0.575878285 0.918430962 0.844539565 0.888035553 1 21.54768455 1.184497255 0.821210094 0.99620336 0.775544752 0.333005989 0.098511763 0.676003653 1.026057897 0.091475806 0.034356372 15.29316079 -1.184497255 -0.220658608 QPPPASS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPPPASSPTK 10 0 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 QPPPAS(0.008)S(0.99)PT(0.002)K 120.57 0.0028257 0 154540 127010 117110 122070 120250 108240 130770 141920 149700 157190 TRUE FALSE 148500.4059 123387.7992 138274.3821 128370.0473 124117.9505 110428.687 132370.4024 138989.3024 132706.6836 146543.3813 1.013354576 0.841988209 0.943573029 0.875986661 0.846970702 0.753556292 0.903284756 0.948451586 0.905579511 1 17.16096828 1.184748022 1.198230721 0.988687327 0.879727474 0.194501913 0.066699067 0.688243016 2.009171367 0.062901833 0.020129507 15.30199381 -1.184748022 -0.108959853 S(ph)PQKPIVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPQKPIVR 8 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y467;A0A2R8YES9;H7C5K3 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(1)PQKPIVR 80.24 0.015723 1010400000 1893000 1947600 1735800 1967800 1890100 1672800 1936900 1897900 2299500 2201900 TRUE FALSE 1819019.467 1892056.355 2049497.673 2069358.394 1950896.783 1706625.162 1960604.362 1858707.702 2038470.4 2052763.352 0.886132084 0.921711874 0.99840913 1.008084245 0.950375883 0.831379399 0.955104913 0.905466137 0.993037214 1 20.96913589 1.185554105 9.489864843 0.997128688 0.933482045 0.215372587 0.049140356 0.694654719 115.8055539 0.04903143 0.012331977 15.33042184 -1.185554105 -0.063646643 TPSNTPSAEADWS(ph)PGLELHPDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPSNTPSAEADWSPGLELHPDYK 23 0 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 TPSNTPSAEADWS(1)PGLELHPDYK;TPSNTPSAEADWS(1)PGLELHPDYK 148.66 6.68E-08 369460000 307860 325440 281540 289670 330350 335600 361270 354810 484630 495760 TRUE FALSE 295828.4908 316158.7698 332420.5408 304619.9034 340976.0078 342386.0619 365691.3303 347483.0495 429616.8341 462181.7336 0.640069629 0.684057259 0.719242057 0.659091178 0.737753102 0.740803967 0.791228436 0.75183207 0.929540921 1 18.81810072 1.185819758 0.499593724 1.014547918 0.671952326 0.885371533 0.037081551 0.27955853 0.184899396 0.040531498 0.021492183 15.33980215 -1.185819758 -0.342595592 LEEHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEHFK 6 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 132.94 0.01468 326550000 758440 741990 669910 684610 743320 846420 823150 846910 1068600 1116200 FALSE TRUE 728799.3263 720829.1717 790977.6391 719942.8041 767229.5629 863535.1923 833223.9559 829421.0125 947297.0079 1040598.78 0.700365348 0.692706147 0.760117785 0.691854361 0.737296235 0.829844518 0.800715869 0.797061296 0.91033838 1 19.98898249 1.185874735 0.330567661 1.029992029 0.681582886 0.888851171 0.031820151 0.4701347 0.167346719 0.062362397 0.041706007 15.34174412 -1.185874735 -0.348409143 ETASQTTSSEISSVMVGETEASSSSQDKDKDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETASQTTSSEISSVMVGETEASSSSQDKDKDSR 33 2 Q9NY27-2;Q9NY27;Q9NY27-3;H7C559 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 0 46.048 0.05303 192180000 33898 34861 28360 27083 32957 33000 25495 32818 45154 45599 FALSE TRUE 32573.22868 33866.79841 33485.28286 28480.75688 34017.09184 33667.28261 25807.01544 32140.29683 40028.30722 42510.53911 0.766238899 0.796668288 0.787693677 0.669969317 0.800203727 0.791974962 0.607073351 0.756054793 0.941609023 1 15.37553293 1.186776083 4.154807601 0.991279516 0.743459132 0.698716555 0.059320805 0.113469453 3.704990467 0.055593562 0.014890469 15.37361789 -1.186776083 -0.247820384 S(ph)RLTPVSPESSSTEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.626)RLT(0.373)PVS(0.001)PESSSTEEK 128.05 3.81E-05 682090000 254520 235190 196650 194770 176040 204730 219620 250830 341200 370720 TRUE FALSE 244573.077 228482.6115 232189.0295 204822.103 181702.4865 208869.7809 222307.7753 245650.2728 302468.4064 345610.8042 0.707654605 0.661098 0.671822254 0.592638021 0.525743074 0.604349686 0.643231556 0.710771393 0.875170576 1 18.39878879 1.186966594 1.666621406 0.999238742 0.624797192 0.876573336 0.046796309 0.118066013 0.610643297 0.048335093 0.014303448 15.38036331 -1.186966594 -0.37444155 HIAEEADRK ddPTM_BT-474_Pertuzumab_2h_R1 4 HIAEEADRK 9 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;P67936;P67936-2 TPM3;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-4 chain 0 ;;; 127.76 0.00028319 5145700000 6322100 5834600 5158500 5477100 5620000 6021200 6103300 5144300 7543300 6782900 FALSE TRUE 6075025.343 5668202.921 6090755.7 5759773.787 5800772.404 6142952.789 6177994.011 5038068.407 6687016.208 6323488.141 0.960707952 0.896372824 0.96319556 0.910853892 0.917337437 0.971450037 0.976991476 0.796722994 1.057488535 1 22.59228916 1.186997974 24.99999932 1.028744773 0.921895457 0.394093847 0.051786267 118.4738817 57438.76003 0.050400208 0.012600097 15.38147466 -1.186997974 -0.106849316 ATDIPASAS(ph)PPPVAGVPFFK ddPTM_BT-474_Pertuzumab_2h_R1 3 ATDIPASASPPPVAGVPFFK 20 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 ATDIPAS(0.001)AS(0.999)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPAS(0.001)AS(0.999)PPPVAGVPFFK 280.54 1.07E-44 1153587000 1589980 1562295 1252103 1505009 1548577 1544404 1564433 1583472 1629941 1519995 TRUE FALSE 1527841.824 1517739.876 1478385.865 1582682.695 1598388.386 1575632.907 1583578.999 1550772.75 1444916.931 1417044.385 1.07818911 1.071060224 1.043288327 1.116889994 1.127973409 1.111915 1.117522511 1.094371331 1.019669494 1 20.43445352 1.188077183 4.161061447 1.002413385 1.096377209 0.665334967 0.024358673 0.134450499 4.423607901 0.025002709 0.006705692 15.41974468 -1.188077183 0.093963824 AGHGAGKPTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGHGAGKPTAK 11 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 121.08 0.00025184 1091600000 1511050 1569400 1234740 1388300 1384920 1522280 1495560 1344640 1832030 1718080 FALSE TRUE 1451996.495 1524642.249 1457884.985 1459950.329 1429467.21 1553061.545 1513863.111 1316872.714 1624065.635 1601712.911 0.906527309 0.951882349 0.910203679 0.911493139 0.892461564 0.969625414 0.945152593 0.822165261 1.013955512 1 20.61118415 1.188865855 24.99999866 1.006978512 0.912974138 0.48852178 0.038176591 109.9721571 55321.15429 0.038345518 0.009586435 15.44777214 -1.188865855 -0.094004374 LVEALR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVEALR 6 0 O75688;O75688-3 O75688 PPM1B Protein phosphatase 1B 0 121.68 0.045473 406110000 319540 346610 294730 310380 338510 295290 325740 364980 345220 331100 FALSE TRUE 307052.0235 336725.0222 347994.2672 326398.749 349398.4816 301260.9661 329726.5036 357443.0355 306032.0729 308674.3021 0.994744368 1.090874815 1.127383345 1.057421194 1.131932523 0.975983307 1.068201989 1.157994148 0.991440074 1 18.23572585 1.188976265 24.99977384 0.995719332 1.079265597 0.252532524 0.054652889 168.825208 85115.31123 0.052103253 0.013025897 15.45169991 -1.188976265 0.083546264 LEHALEK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEHALEK 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;; 125.25 0.0040673 1340880000 1884200 2041070 1696710 1693810 1807660 1627940 2090210 1876480 2401930 2325360 FALSE TRUE 1810563.381 1982860.682 2003343.24 1781227.737 1865805.026 1660858.062 2115790.615 1837730.032 2129272.976 2167861.296 0.835184144 0.914662154 0.924110433 0.821652077 0.860666238 0.766127457 0.975980622 0.847715689 0.982199821 1 21.04784102 1.189143134 6.208664476 0.995514616 0.870639492 0.435558879 0.055896496 0.18990192 16.07037887 0.050283789 0.013002666 15.45763805 -1.189143134 -0.124875125 LFSSSSS(ph)PPPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFSSSSSPPPAK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 LFSSS(0.01)S(0.149)S(0.841)PPPAK 167.3 5.20E-05 244030000 900450 932840 754490 946640 955660 895150 890880 966970 872170 797750 TRUE FALSE 865259.4185 906236.3165 890843.1265 995496.2038 986399.6718 913250.5463 901782.8559 947001.7316 773164.918 743717.6819 1.163424562 1.218521945 1.19782432 1.338540454 1.326309292 1.227953252 1.212533839 1.273334969 1.039594643 1 19.50439555 1.190112212 5.541935104 1.008768472 1.247453591 0.745610654 0.052628575 0.099142479 6.552617831 0.051475189 0.013468359 15.49216849 -1.190112212 0.238685119 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(ph)TGSPTEFLEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGS(0.001)DT(0.534)T(0.442)GS(0.022)PTEFLEEK 124.63 2.03E-09 279970000 135710 108270 107900 77348 107080 115370 127600 118220 175280 177080 TRUE FALSE 130406.3032 105182.2456 127399.9302 81339.93955 110524.3254 117702.8604 129161.607 115778.7157 155382.9492 165086.2139 0.789928487 0.637135247 0.77171756 0.492711885 0.66949458 0.712978132 0.782388813 0.701322739 0.941223047 1 17.33286012 1.190225401 2.556378524 1.006231283 0.687795358 0.639232028 0.083083454 0.161557439 1.841462917 0.076204906 0.021357002 15.4962067 -1.190225401 -0.318435925 NLFQQYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLFQQYDR 8 0 Q9UBV8 Q9UBV8 PEF1 Peflin 0 ; 101.54 0.012379 163562000 315690 331720 298880 311090 278840 234190 347390 346600 396130 427780 FALSE TRUE 303352.4858 322259.6704 352894.2645 327145.3922 287809.1418 238925.4823 351641.4627 339442.5889 351162.9831 398806.0796 0.760651608 0.808061078 0.884876843 0.820311948 0.721676917 0.599101906 0.881735462 0.851146977 0.880535682 1 18.60532788 1.190489777 1.151422074 0.990000585 0.779261974 0.441176523 0.077390468 0.451602599 1.229037325 0.077487421 0.025139136 15.50564288 -1.190489777 -0.210738611 ESEDDPES(ph)EPDDHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESEDDPESEPDDHEK 15 0 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 1 ESEDDPES(1)EPDDHEK 159.26 1.14E-06 194300000 597820 497710 412600 423890 443800 501520 479490 502930 639380 628440 TRUE FALSE 574456.5335 483515.7981 487165.9982 445767.0137 458075.23 511661.078 485358.1421 492544.3197 566800.2629 585875.199 0.980510072 0.825288046 0.831518383 0.760856603 0.781864859 0.873327765 0.828432647 0.840698361 0.967441981 1 19.16023385 1.190665116 3.768702025 0.99774844 0.834768481 0.515230869 0.055854505 0.167770917 4.404234754 0.051259859 0.013907482 15.51190427 -1.190665116 -0.162979959 ATDFVADR ddPTM_BT-474_Pertuzumab_2h_R1 3 ATDFVADR 8 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;; 145.65 0.0013167 1547150000 1808830 2422810 1703590 3113320 1770490 1728320 2782580 2505800 2142930 1968400 FALSE TRUE 1738138.924 2353713.831 2011466.609 3273998.818 1827439.419 1763267.815 2816634.046 2454054.354 1899673.57 1835078.515 0.947174145 1.282622957 1.096120189 1.784119204 0.995837183 0.960867778 1.53488476 1.337302102 1.035200159 1 20.80741036 1.19073814 8.577759239 1.014388076 1.257558675 0.109806812 0.253113616 0.681189783 108.7243606 0.234762923 0.059475252 15.51451272 -1.19073814 0.243170599 YFDLGLPNR ddPTM_BT-474_Pertuzumab_2h_R1 3 YFDLGLPNR 9 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;; 153.78 0.00017977 1042588000 512463 730786 540130 1054414 593005 586625 872977 768580 634874 561513 FALSE TRUE 492435.3794 709944.6988 637743.5061 1108832.433 612079.5444 598486.9594 883660.7537 752708.5544 562805.7651 523481.2244 0.940693489 1.356198973 1.218273887 2.1181895 1.169248324 1.14328257 1.688046701 1.437890261 1.075121206 1 18.99777827 1.190739978 5.747857366 1.020661149 1.403515002 0.164081346 0.311130585 0.340599289 24.70264126 0.283609697 0.074020873 15.51457837 -1.190739978 0.382853854 DQAAKGDEVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQAAKGDEVTR 11 1 Q9H074;Q9H074-3;Q9H074-2;D6REB4;D6RJ02;D6RJF2 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 93.649 0.0082922 232480000 367160 410500 283210 302760 361590 322510 338050 367550 465620 464350 FALSE TRUE 352810.9813 398792.9419 334392.347 318385.4799 373220.8707 329031.3732 342187.157 359959.9641 412764.7696 432899.1609 0.814995761 0.921214403 0.772448591 0.73547262 0.862142745 0.760064705 0.790454655 0.83150996 0.95348942 1 18.72367148 1.192194071 2.893522131 0.998421405 0.808393658 0.645258169 0.049981667 0.153921638 2.254104051 0.046816291 0.012990201 15.56661093 -1.192194071 -0.190027747 AAGGAPS(ph)PPPPVRR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAGGAPSPPPPVRR 14 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR 98.507 0.001562 2427670000 3210250 3778030 2564160 2759540 3134430 3446970 3001730 3702960 3220910 3062240 TRUE FALSE 3084789.881 3670284.283 3027560.751 2901960.19 3235251.788 3516670.095 3038466.07 3626492.582 2855285.8 2854831.757 1.080550499 1.285639434 1.060504089 1.016508305 1.133254798 1.231830943 1.06432404 1.27029993 1.000159044 1 21.4449743 1.192207177 24.07727206 1.000077807 1.145575284 0.29586832 0.088029219 120.021407 62338.42408 0.082994572 0.020749013 15.56708072 -1.192207177 0.145497478 WCPTTNKPVKS(ph)PTPTVNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 WCPTTNKPVKSPTPTVNPR 19 2 C9JA69;Q8WY36-2;Q8WY36;C9JYU6;C9JZA0;C9J8D0;Q8WY36-3 C9JA69;Q8WY36-3 BBX HMG box transcription factor BBX 1 WCPT(0.009)T(0.009)NKPVKS(0.802)PT(0.172)PT(0.009)VNPR;WCPT(0.025)T(0.025)NKPVKS(0.788)PT(0.104)PT(0.058)VNPR 76.417 0.0067869 1626930000 969380 879980 685620 824370 1039800 840580 840910 885910 785840 688140 TRUE FALSE 931495.5579 854883.832 809526.7855 866915.8345 1073246.111 857577.1035 851201.3081 867615.6489 696634.7377 641531.6649 1.451986876 1.332566853 1.261865672 1.351321972 1.672943317 1.336765043 1.326826647 1.352412821 1.08589299 1 19.29116095 1.192982016 2.334252871 0.994629467 1.390551811 0.631111052 0.10607427 0.184833264 1.760247171 0.102075615 0.028889651 15.59487925 -1.192982016 0.395922344 S(ph)PTLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPTLLR 6 0 P55197-1;P55197;Q5JT35;H0Y5P4 P55197-1 MLLT10 Protein AF-10 1 S(0.994)PT(0.006)LLR;S(0.998)PT(0.002)LLR;S(0.992)PT(0.008)LLR 113.5 0.027364 731894000 207091 208123 206290 293088 210317 226054 228117 241679 245066 229632 TRUE FALSE 198997.6548 202187.5358 243571.1919 308214.3068 217082.0373 230624.9668 230908.7641 236688.2442 217247.1351 214078.8201 0.929553212 0.94445371 1.13776408 1.439723494 1.014028558 1.077289975 1.078615642 1.105612615 1.014799759 1 17.70778254 1.193166064 5.596480617 1.003361265 1.096032676 0.058005792 0.133456955 0.633017284 44.27432862 0.128635235 0.033787326 15.60148954 -1.193166064 0.092671412 GDEELDSLIK ddPTM_BT-474_Pertuzumab_2h_R1 6 GDEELDSLIK 10 0 Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-4;Q71UI9-2;Q71UI9-3;C9J386 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z;Histone H2A 0 ;;;;; 243.03 5.03E-12 3193188000 5873490 5353500 4638330 4865800 5143990 4832260 5196310 6048680 5306440 5131030 FALSE TRUE 5643947.517 5200823.422 5476579.41 5116924.521 5309451.11 4929971.608 5259903.996 5923772.644 4704075.178 4783500.768 1.179878041 1.0872421 1.144889418 1.069702874 1.109950927 1.03062001 1.099593008 1.23837602 0.983395928 1 22.1896354 1.193304578 24.99999463 0.991697149 1.119691222 0.463783167 0.055195686 138.0932924 76281.30442 0.055749335 0.013937543 15.60646626 -1.193304578 0.127994073 EAYVHK ddPTM_BT-474_Pertuzumab_2h_R1 5 EAYVHK 6 0 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;;;; 76.805 0.074088 5624370000 6129660 6545920 5461800 5613530 5629310 5662200 5911870 6219970 7334980 7122880 FALSE TRUE 5890106.111 6359236.771 6448868.757 5903244.956 5810381.869 5776693.563 5984221.233 6091525.446 6502343.821 6640440.993 0.887005263 0.957652779 0.971150676 0.888983874 0.874999398 0.869926195 0.901178286 0.917337486 0.979203614 1 22.66284762 1.193408925 3.108436754 0.999185588 0.908209624 0.523007324 0.031391081 0.210987792 3.596261864 0.032083438 0.008857964 15.61021646 -1.193408925 -0.090975963 FREDHNCK ddPTM_BT-474_Pertuzumab_2h_R1 4 FREDHNCK 8 1 Q86SF2;H0YAK0;H0YAH3 Q86SF2 GALNT7 N-acetylgalactosaminyltransferase 7;Polypeptide N-acetylgalactosaminyltransferase 0 ;;; 99.136 0.0042226 399358000 466829 541000 439099 551690 459720 408041 549260 489403 611890 585380 FALSE TRUE 448584.8066 525571.2097 518453.957 580162.787 474507.3113 416291.8686 555982.0082 479296.657 542430.8125 545731.6912 0.821987826 0.963057888 0.950016217 1.063091619 0.869488283 0.762814173 1.018782704 0.878264291 0.993951462 1 19.0578323 1.193424014 12.84315776 0.997114481 0.919897078 0.126627361 0.08462087 2.886834675 811.3916803 0.07975293 0.01999165 15.61075882 -1.193424014 -0.077217403 SFGTEDRPTDRPIPPRDEVFEYIIFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFGTEDRPTDRPIPPRDEVFEYIIFR 26 3 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;I3L4Q1 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 264.08 2.45E-53 871906000 321005 361238 283958 299809 327279 323965 314362 349497 329351 306783 FALSE TRUE 308459.7697 350935.8459 335275.5272 315282.1784 337806.2263 330515.7943 318209.2562 342279.7648 291964.4552 286004.3142 1.078514395 1.227029903 1.17227437 1.102368611 1.181122835 1.155632198 1.112602994 1.196764342 1.02083934 1 18.12567738 1.194029659 8.110499766 1.008179068 1.155628739 0.637419308 0.043079212 0.159681451 24.90505629 0.037787222 0.009637463 15.63254399 -1.194029659 0.147449671 LEVDEDFEEDNAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEVDEDFEEDNAAK 14 0 Q92620 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 70.488 0.085431 0 68119 68910 53849 56645 50831 60299 60805 66280 81409 82742 FALSE TRUE 65456.83417 66944.75427 63580.71216 59568.45524 52466.02528 61518.28709 61549.14978 64911.29484 72167.79161 77137.81064 0.848570028 0.867859143 0.824248337 0.772234197 0.680159637 0.797511448 0.797911546 0.84149776 0.935569613 1 16.23515058 1.194063623 1.826093703 0.99936237 0.796126624 0.672191866 0.047708091 0.207611038 1.256920855 0.049509936 0.014450959 15.63376655 -1.194063623 -0.203235746 TGPFAEHSNQLWNISAVPSWSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGPFAEHSNQLWNISAVPSWSK 22 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;Q68CR8;B7ZBQ0;B4DDQ6;B7ZBP7;B7ZBP9 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 ; 163.68 1.48E-11 946860000 1197680 1131210 988720 986330 1001490 886830 1106270 1129020 1324550 1324960 FALSE TRUE 1150873.341 1098948.998 1167403.698 1037234.61 1033703.835 904762.3102 1119808.863 1105705.342 1174192.637 1235219.279 0.931715818 0.88967928 0.945098346 0.839716986 0.836858567 0.732471008 0.90656686 0.895149032 0.950594487 1 20.23633574 1.194650981 1.632685204 0.997664317 0.865713149 0.371065004 0.056601529 0.393668471 1.956323275 0.056020416 0.016660834 15.65492464 -1.194650981 -0.131951168 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 33 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 356.27 2.17E-132 1296847000 810313 846208 680656 758014 750443 824877 839228 642454 1091763 1012866 FALSE TRUE 778645.0721 822074.9764 803665.6803 797135.1934 774581.6806 841556.5781 849498.7233 629187.1004 967830.6413 944263.6837 0.824605548 0.870598955 0.851103028 0.844187071 0.82030231 0.891230482 0.899641422 0.666325637 1.024958026 1 19.84883026 1.194812184 24.99999604 1.012480054 0.8321985 0.573968167 0.061671323 115.1463251 65797.6452 0.062112998 0.015528589 15.66073656 -1.194812184 -0.180281554 ENTHQTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENTHQTLK 8 0 C9JRZ6;Q9NX63 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 0 ; 107.57 0.0039768 361590000 380270 541050 360700 564950 326910 401140 482050 492560 484650 486320 FALSE TRUE 365408.628 525619.7837 425886.5137 594107.1372 337425.357 409251.3256 487949.4721 482388.4639 429634.5638 453381.1132 0.805963498 1.159333215 0.93935654 1.310392339 0.7442422 0.902665139 1.076245697 1.06398006 0.947623426 1 18.79036477 1.195798569 24.99208489 0.973811861 1.008527259 0.002297211 0.158040338 1420.400785 830114.149 0.143249341 0.035813703 15.69634621 -1.195798569 0.034715398 KPASFMTSICDER ddPTM_BT-474_Pertuzumab_2h_R1 2 KPASFMTSICDER 13 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 160.47 7.02E-05 2219800000 3459200 3509000 3231100 3778900 3370700 2895300 4001400 3808500 4257400 4431500 FALSE TRUE 3324010.64 3408926.756 3815031.645 3973929.482 3479121.627 2953844.95 4050370.33 3729853.144 3774117.8 4131350.558 0.804582084 0.825136165 0.923434502 0.961895977 0.842126946 0.714982887 0.980398607 0.90281691 0.913531241 1 21.97818205 1.196601212 0.827280385 0.993672432 0.859305396 0.258720325 0.07285631 0.85781903 1.316683886 0.071583744 0.02684283 15.72538228 -1.196601212 -0.134367036 EALQQQHSVQVDQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EALQQQHSVQVDQLR 15 0 A0A087X0G7;A0A087WUW6;A0A087X1B1;Q9Y6K9;Q9Y6K9-2;A0A087WV30;C9JN51;C9J2V2 A0A087X0G7;C9J2V2 IKBKG NF-kappa-B essential modulator 0 176.33 8.05E-07 331470000 83187 95423 70172 75605 71992 86785 76176 95689 80842 77045 FALSE TRUE 79935.96007 92701.62947 82853.64137 79506.98311 74307.68806 88539.85216 77108.26467 93712.98871 71665.15508 71826.67353 1.112900767 1.29062958 1.153521906 1.106928376 1.034541688 1.232687633 1.073532448 1.304710132 0.997751275 1 16.13223208 1.197899023 24.87896196 0.998874657 1.166063455 0.377715377 0.084570338 167.5754822 102527.8624 0.079409094 0.019853193 15.77244506 -1.197899023 0.167188799 VQSHQQASEEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VQSHQQASEEKK 12 1 O60566-3;O60566;O60566-2 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 0 138.24 5.07E-05 79325000 173380 149410 127740 106990 133970 146020 162870 148890 211500 208510 FALSE TRUE 166604.1179 145148.9731 150825.4596 112511.7667 138279.2667 148972.6244 164863.2518 145815.3695 187491.4067 194387.432 0.857072477 0.74669937 0.775901292 0.578801652 0.71135909 0.766369631 0.848116826 0.750127557 0.964524325 1 17.56857542 1.198980792 3.607487488 1.002109273 0.750507635 0.609482352 0.073001773 0.152265715 3.639760467 0.069891359 0.019181816 15.81178104 -1.198980792 -0.251601638 LAASTEPQGPRPVLGR ddPTM_BT-474_Pertuzumab_2h_R1 6 LAASTEPQGPRPVLGR 16 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;F5GWK5;F5H3G8;F5H5A8;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;;;;; 176.23 2.96E-09 5968220000 3266570 3206170 2660040 2892700 2807920 3050740 3101730 3231000 3726750 3675290 FALSE TRUE 3138908.833 3114733.171 3140768.4 3041992.594 2898239.297 3112428.053 3139689.9 3164278.721 3303704.964 3426359.335 0.916106143 0.909050355 0.916648866 0.887820656 0.845865542 0.908377595 0.916334101 0.92351047 0.964202712 1 21.70824503 1.199011146 1.198229941 1.000001918 0.896939709 0.745247061 0.019663668 0.226763563 0.659734309 0.019741787 0.006332205 15.81288624 -1.199011146 -0.103062209 YGINTTDIFQTVDLWEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGINTTDIFQTVDLWEGK 18 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 246.18 6.70E-24 91136000 159470 171367 127181 156614 134694 143155 140014 163761 206334 209352 FALSE TRUE 153237.7361 166479.7809 150165.4358 164696.8673 139026.5548 146049.6922 141727.5332 160379.2781 182911.8293 195172.4026 0.785140389 0.852988326 0.76939892 0.843853256 0.712326912 0.748311187 0.726165848 0.821731331 0.937180805 1 17.57438954 1.199619747 2.592073985 0.996281397 0.778200205 0.762329479 0.042808114 0.125966955 1.464363367 0.040966672 0.011508891 15.83506123 -1.199619747 -0.218081193 ADPSHFELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADPSHFELLK 10 0 E9PGT3;Q15418-4;Q15418;Q15418-2;E9PAN7 E9PGT3 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 0 87.298 0.01475 0 148300 151020 124150 130580 142820 119950 160050 135250 173770 160820 FALSE TRUE 142504.272 146713.0575 146586.6667 137319.2494 147413.935 122375.4712 162008.7398 132457.0402 154044.3581 149927.5182 0.950487768 0.978559902 0.977716889 0.915904239 0.983234678 0.816230887 1.080580415 0.88347384 1.027458868 1 17.19390568 1.199665497 24.99999152 1.013729616 0.949259105 0.135777782 0.066017639 346.3211326 222591.716 0.056833327 0.014209308 15.83672943 -1.199665497 -0.06447051 VQAWYMDDAPGDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQAWYMDDAPGDPR 14 0 Q9BV57 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ; 89.805 0.013967 340220000 328710 358790 313680 335550 342240 424430 266620 371430 345480 309450 FALSE TRUE 315863.6498 348557.6605 370368.9538 352867.7757 353248.4604 433012.2654 269882.9753 363759.8407 306262.5588 288490.6759 1.094883392 1.208211182 1.283816029 1.223151406 1.224470979 1.500957575 0.93549982 1.260906751 1.061602972 1 18.13816517 1.199681113 0.975870476 1.002122194 1.234583353 0.228828523 0.135593657 0.728031201 1.48592242 0.120773314 0.041790548 15.83729889 -1.199681113 0.232461159 NVFEVGPGDS(ph)PTFPR ddPTM_BT-474_Pertuzumab_2h_R1 4 NVFEVGPGDSPTFPR 15 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 NVFEVGPGDS(0.998)PT(0.002)FPR;NVFEVGPGDS(0.992)PT(0.008)FPR;NVFEVGPGDS(1)PTFPR;NVFEVGPGDS(0.998)PT(0.002)FPR 270.95 2.30E-33 1171750000 894370 992220 823750 949570 872130 945720 901120 1047020 1132150 1167950 TRUE FALSE 859417.0316 963922.8571 972619.9492 998577.4215 900182.8535 964843.1064 912148.1761 1025398.671 1003633.078 1088843.706 0.78929329 0.885272011 0.893259468 0.917098952 0.826732844 0.886117173 0.837721861 0.941731734 0.921742095 1 20.05436545 1.199865225 1.080603902 0.995497056 0.865506759 0.55088751 0.038755572 0.347736865 0.846450739 0.035097536 0.011660296 15.84401428 -1.199865225 -0.129990297 SAVDQAGGAQIVIDHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAVDQAGGAQIVIDHLR 17 0 P52306-4;P52306;P52306-5;D6RHH8;D6REZ0 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 137.05 8.27E-06 129270000 45965 58960 47620 46179 48869 59179 50433 52728 54736 49743 FALSE TRUE 44168.63698 57278.51853 56225.9933 48562.30372 50440.91577 60375.63993 51050.21414 51639.14837 48522.59875 46373.8623 0.952446805 1.235146604 1.212450085 1.047191269 1.087701418 1.301932531 1.100840249 1.113539951 1.046335076 1 15.50102427 1.200396023 1.747304465 1.001412947 1.141491238 0.18335782 0.09413494 0.534654191 2.98311127 0.085140616 0.025052253 15.86339079 -1.200396023 0.14007829 EYHPDKNPNAGDK ddPTM_BT-474_Pertuzumab_2h_R1 3 EYHPDKNPNAGDK 13 1 O60884;I3L320 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;; 181.71 7.10E-06 1867510000 1770120 1669730 1914830 2013230 1851930 1702770 2207690 2373830 3016410 3422420 FALSE TRUE 1700941.753 1622110.935 2260882.376 2117133.042 1911499.01 1737201.176 2234708.371 2324809.581 2673999.783 3190616.445 0.533107562 0.508400481 0.708603624 0.663549843 0.599100219 0.544471956 0.700400192 0.728639628 0.838082492 1 21.60540376 1.20077397 0.907134023 0.999468687 0.595066308 0.825817426 0.060066476 0.219570752 0.394897075 0.059669212 0.021352789 15.87720201 -1.20077397 -0.404402379 QAS(ph)PLISPLLNDQACPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QASPLISPLLNDQACPR 17 0 C9JME2;Q9Y4F1;Q9Y4F1-2 C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 QAS(1)PLISPLLNDQACPR;QAS(1)PLISPLLNDQACPR 141.74 1.02E-05 0 83676 117993 66565 141419 78914 92913 108720 97365 86728 72527 TRUE FALSE 80405.84941 114627.9552 78594.77623 148717.6515 81452.34048 94791.76452 110050.5479 95354.37873 76883.00103 67614.68169 1.189177371 1.695311614 1.162392165 2.199487564 1.204654647 1.401940557 1.627613192 1.410261445 1.137075545 1 16.04504892 1.201238665 2.632185431 1.00722309 1.505395796 0.255887579 0.29207295 0.333571026 3.994210851 0.250121143 0.070227197 15.89419968 -1.201238665 0.498172706 ASELGHSLNENVLKPAQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASELGHSLNENVLKPAQEK 19 1 Q8N6T3;Q8N6T3-4;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 124.63 1.74E-05 36989000 74608 69219 63779 51754 62801 65035 69494 73240 85127 88465 FALSE TRUE 71692.23688 67244.94189 75305.28406 54425.03014 64821.0512 66350.05226 70344.48836 71727.56841 75463.73984 82473.18675 0.869279334 0.815355203 0.913088084 0.659911812 0.785965157 0.804504529 0.852937677 0.869707734 0.915009384 1 16.33163753 1.20162436 1.022519883 0.996744698 0.806648472 0.489409028 0.061865425 0.413368888 0.914304117 0.058345519 0.019806507 15.90832152 -1.20162436 -0.190096225 KDDPTLLSSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDDPTLLSSGR 11 1 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ; 142.12 6.06E-05 1838970000 1872180 2029760 1600050 1810870 1694710 1563920 1991740 2072200 2221700 2415400 FALSE TRUE 1799013.136 1971873.232 1889214.628 1904329.218 1749221.886 1595543.534 2016115.51 2029408.346 1969501.93 2251802.807 0.79892126 0.875686462 0.838978716 0.845690934 0.776809533 0.708562726 0.895333954 0.901237151 0.874633393 1 21.10264906 1.202132177 0.944415259 0.988712803 0.816684994 0.530495689 0.051519081 0.43019195 0.829303813 0.051459519 0.018075029 15.92693389 -1.202132177 -0.172027809 ELLHSQNTWLNTELK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLHSQNTWLNTELK 15 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 74.296 0.016413 0 193710 207870 141730 191780 198550 173840 214570 155890 263250 240560 FALSE TRUE 186139.599 201941.7511 167343.7638 201677.7888 204936.5411 177355.1639 217195.9718 152670.817 233366.9636 224266.6569 0.829992303 0.900453745 0.746182094 0.899276743 0.913807446 0.790822703 0.968471974 0.680755753 1.040578064 1 17.77485562 1.202134238 24.99483446 1.020289635 0.841052189 0.435093477 0.081616015 174.3137923 119605.7556 0.073852592 0.018465388 15.92700945 -1.202134238 -0.179237446 NALPPVLTTVNGQS(ph)PPEHSAPAK ddPTM_BT-474_Pertuzumab_2h_R1 6 NALPPVLTTVNGQSPPEHSAPAK 23 0 Q6PKG0;A0A0B4J210;H0YBM7 Q6PKG0 LARP1 La-related protein 1 1 NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK 259.72 6.92E-44 8496700000 4827170 4167070 4009910 3640310 3421090 3871400 3773640 4397470 5567560 5657290 TRUE FALSE 4638518.86 4048229.244 4734589.937 3828186.835 3531132.467 3949682.361 3819822.935 4306660.708 4935553.93 5274116.709 0.879487337 0.767565351 0.897702914 0.725844164 0.669521109 0.748880349 0.724258325 0.816565303 0.935806734 1 22.33049807 1.202459427 2.527924053 0.996577489 0.770954499 0.583768594 0.065719116 0.19082624 2.105502855 0.063152041 0.017798311 15.93893968 -1.202459427 -0.22562299 VNVEHMTEK ddPTM_BT-474_Pertuzumab_2h_R1 4 VNVEHMTEK 9 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;; 159.83 6.58E-05 1912310000 4322070 4838120 3876770 4195070 4158920 3541190 4670970 4503950 5091520 5045700 FALSE TRUE 4153158.726 4700141.555 4577388.577 4411578.065 4292695.439 3612795.288 4728134.728 4410941.859 4513551.995 4703950.245 0.882908728 0.999190321 0.973094599 0.937845393 0.912572458 0.768034333 1.005141314 0.937710143 0.959523753 1 22.16544137 1.202557253 1.250148611 0.994944549 0.924907535 0.120977705 0.063836588 0.9933269 3.105887559 0.060924791 0.01930571 15.94253038 -1.202557253 -0.070037014 S(ph)FDYNYR ddPTM_BT-474_Pertuzumab_2h_R1 10 SFDYNYR 7 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR 179.36 0.00073663 47931310000 7875328 7396960 7098171 7671950 7280925 6888709 7465837 8594300 7807350 8036280 TRUE FALSE 7567551.475 7186005.943 8380968.398 8067900.259 7515122.565 7028003.416 7557206.146 8416824.702 6921092.359 7491975.598 1.010087577 0.959160351 1.118659329 1.076872202 1.003089568 0.938070783 1.008706722 1.12344529 0.923800708 1 22.83691477 1.202829779 24.99997002 0.961900402 1.031511267 0.166509014 0.060630084 379.1844363 265297.511 0.06096308 0.015242816 15.95253769 -1.202829779 0.069610865 HNDLDDVGK ddPTM_BT-474_Pertuzumab_2h_R1 6 HNDLDDVGK 9 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;;; 126.39 0.00047492 10219810000 19481900 17426810 18225300 18588900 18518700 18679400 21932000 14230760 28483100 26667700 FALSE TRUE 18720525.81 16929814.44 21519017.13 19548275.36 19114370.8 19057110.27 22200410.38 13936889.83 25249817.9 24861472.93 0.752993431 0.680965866 0.865556807 0.786287901 0.768835011 0.766531827 0.892964405 0.560581824 1.015620353 1 24.56740844 1.203713577 24.99016453 1.007811121 0.758520234 0.565735403 0.087075008 146.3511068 104950.8079 0.082458582 0.020618308 15.98503446 -1.203713577 -0.249290887 SSTS(ph)PCGTSK ddPTM_BT-474_Pertuzumab_2h_R1 6 SSTSPCGTSK 10 0 H0Y459;O75376;O75376-2;A0A088AWL3;O75376-3 H0Y459;O75376 NCOR1 Nuclear receptor corepressor 1 1 SST(0.004)S(0.991)PCGT(0.006)SK;SST(0.005)S(0.994)PCGTSK;SST(0.002)S(0.998)PCGTSK;SST(0.002)S(0.998)PCGTSK;SST(0.002)S(0.998)PCGTSK;S(0.027)S(0.027)T(0.027)S(0.919)PCGTSK 212.2 4.71E-08 1536106000 4153190 3590480 3538340 3882390 3668510 3740470 4236310 4406430 4813740 5165870 TRUE FALSE 3990878.743 3488083.026 4177796.748 4082760.613 3786510.956 3816104.866 4288155.229 4315435.681 4267304.416 4815981.024 0.828674101 0.724272585 0.867486132 0.847752637 0.786238762 0.792383701 0.890401189 0.896065757 0.886071684 1 22.19939828 1.205036813 0.483575863 1.003432819 0.796569289 0.667015983 0.04140138 0.552206505 0.34753252 0.047798066 0.026205114 16.03381296 -1.205036813 -0.20686353 AMDSDWFAENYMGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AMDSDWFAENYMGR 14 0 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 244.27 3.26E-17 645380000 282810 442830 323250 741230 351610 353200 604470 511710 377520 333130 FALSE TRUE 271757.4725 430200.922 381668.4657 779484.9691 362919.855 360341.946 611867.6847 501143.0097 334665.5123 310566.8084 0.875037078 1.385212168 1.228941585 2.509878545 1.168572575 1.160271917 1.970164448 1.613639952 1.077595877 1 18.24454413 1.205321829 8.432972783 1.033429627 1.517566235 0.139254785 0.443252265 0.523434016 113.9271458 0.405760106 0.105290327 16.04433898 -1.205321829 0.484136609 WTETEIEMLR ddPTM_BT-474_Pertuzumab_2h_R1 4 WTETEIEMLR 10 0 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3 F8W038 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 0 ;;; 234.47 1.01E-11 431250000 507496 560016 429656 542749 574957 544736 517844 537921 558365 503815 FALSE TRUE 487662.4953 544044.892 507304.3968 570760.3409 593451.0141 555750.9351 524181.5298 526812.7434 494981.7461 469691.1613 1.038262023 1.158303449 1.080080782 1.215182205 1.263491977 1.1832263 1.116013187 1.121615195 1.053845137 1 18.84135292 1.206082587 1.382529793 1.000959754 1.157649052 0.408710731 0.060593236 0.397781244 1.476796788 0.059251496 0.01828934 16.07246864 -1.206082587 0.156689297 ELAEEEPHLVEQFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELAEEEPHLVEQFQK 15 0 Q5QNY5;P40855;E9PS71;P40855-5;B7Z8B3 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 0 ; 200.55 6.86E-09 530060000 933350 965620 876990 932460 934580 990660 900280 995820 1139190 1104410 FALSE TRUE 896873.6501 938081.463 1035481.602 980584.3723 964641.6145 1010691.824 911297.8959 975255.969 1009873.927 1029607.327 0.871083205 0.911106048 1.005705354 0.952386747 0.936902438 0.98162843 0.885092668 0.947211566 0.980834053 1 19.97366279 1.206534406 0.008497246 1.916564487 9.13E-07 0.2445943 0.038492326 2926.215948 20.67836049 2346.675004 2314.776961 16.08919835 -1.206534406 -1.916563574 WSNS(ph)QPADLAHMGR ddPTM_BT-474_Pertuzumab_2h_R1 4 WSNSQPADLAHMGR 14 0 Q9BRG2;Q9BRG2-2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 WS(0.011)NS(0.989)QPADLAHMGR;WS(0.016)NS(0.984)QPADLAHMGR;WS(0.017)NS(0.983)QPADLAHMGR;WS(0.032)NS(0.968)QPADLAHMGR 161.95 2.95E-06 757240000 681600 625060 491697 633430 634800 524000 564370 749220 541960 539060 TRUE FALSE 654962.3185 607233.9008 580557.5856 666121.3982 655218.9185 534595.639 571276.9289 733748.3452 480438.9729 502548.9861 1.303280549 1.208307882 1.155225862 1.325485508 1.303791146 1.063768217 1.136758694 1.460053379 0.956004263 1 18.9389047 1.206535007 24.9997198 0.978001376 1.244431619 0.498231089 0.107010492 191.3004099 149327.905 0.106132313 0.02654197 16.08922061 -1.206535007 0.266430243 AVSPS(ph)NPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVSPSNPK 8 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AVS(0.388)PS(0.612)NPK 72.365 0.048612 218360000 408050 403570 357850 369940 317940 386990 379400 429290 465040 486020 TRUE FALSE 392102.9549 392060.5787 422521.4553 389032.6477 328166.8288 394815.2029 384043.2107 420425.0115 412250.6088 453101.4325 0.865375668 0.865282144 0.932509644 0.858599465 0.724267913 0.87136163 0.847587721 0.927882768 0.909841769 1 18.78947453 1.207269927 1.105526799 0.992567161 0.851415123 0.44240356 0.050977751 0.445939736 1.127272394 0.0499772 0.016488362 16.1164701 -1.207269927 -0.141152038 TLS(ph)SSAQEDIIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 T(0.001)LS(0.985)S(0.014)SAQEDIIR;T(0.001)LS(0.492)S(0.492)S(0.014)AQEDIIR 157.23 7.75E-05 236920000 371560 282440 241140 265410 350840 274640 259610 413140 209647 212596 TRUE FALSE 357039.0244 274385.0877 284719.3621 279107.8419 362125.0872 280193.409 262787.1848 404608.5146 185848.7515 198196.6836 1.801437935 1.384408068 1.436549578 1.408236691 1.82709963 1.413713913 1.325890929 2.04144947 0.937698594 1 17.5965733 1.207393241 24.9977649 0.968847527 1.576168077 0.541513593 0.22486378 174.040394 139584.9558 0.215461725 0.053887541 16.12104688 -1.207393241 0.60732055 NVQRPESVSDHMYR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVQRPESVSDHMYR 14 1 Q7Z4H3-2;Q7Z4H3;V9GYS5;V9GZ04;Q7Z4H3-3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 ; 188.4 5.03E-07 442510000 490920 493940 460430 495770 461790 523080 485900 517950 664360 649220 FALSE TRUE 471734.3037 479853.3148 543639.9432 521356.7491 476643.8947 533657.036 491846.5895 507254.1515 588944.638 605247.7511 0.77940695 0.79282131 0.898210596 0.861393947 0.787518655 0.881716677 0.81263679 0.83809341 0.973063736 1 19.20716629 1.207413369 4.285751403 0.996797798 0.832110229 0.728851851 0.03799469 0.102783479 3.872243011 0.034230814 0.009410466 16.12179406 -1.207413369 -0.164687568 STS(ph)TPNVHMVSTTLPVDSR ddPTM_BT-474_Pertuzumab_2h_R1 5 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.06)T(0.175)S(0.761)T(0.005)PNVHMVSTTLPVDSR;S(0.045)T(0.159)S(0.795)T(0.001)PNVHMVSTTLPVDSR;S(0.043)T(0.153)S(0.773)T(0.031)PNVHMVSTTLPVDSR;S(0.042)T(0.151)S(0.805)T(0.003)PNVHMVSTTLPVDSR;S(0.058)T(0.058)S(0.866)T(0.019)PNVHMVSTTLPVDSR 247.64 5.79E-25 7569870000 1897770 1819129 1322279 1671520 1526777 1648146 1639182 2073270 1496673 1527189 TRUE FALSE 1823603.05 1767249.222 1561244.229 1757787.348 1575887.169 1681472.641 1659242.8 2030456.25 1326776.956 1423751.129 1.280843972 1.241262736 1.096571021 1.234617 1.106855782 1.181015844 1.165402272 1.426131442 0.931888255 1 20.44126556 1.20863216 24.99995561 0.965943586 1.217053905 0.551857385 0.090345577 183.9194589 153627.9979 0.091186257 0.022808578 16.1671013 -1.20863216 0.251110319 DLELER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLELER 6 0 A0A494BX66;A0A590UJT6;Q2TAC2-2;Q2TAC2 A0A494BX66 CCDC57 Coiled-coil domain-containing protein 57 0 ; 114.19 0.059325 550450000 839180 916940 783980 894900 820130 790520 738150 810140 746940 572520 FALSE TRUE 806383.9178 890789.769 925662.6255 941085.8962 846510.2263 806504.856 747183.7005 793410.3259 662150.5026 533742.7105 1.510810175 1.668949761 1.734286216 1.763182668 1.585989297 1.51103676 1.399894904 1.486503348 1.240579945 1 19.02578494 1.20901106 0.539981555 0.990045787 1.676986855 0.856281497 0.083648413 0.301925507 0.22640387 0.092829129 0.046894055 16.18121246 -1.20901106 0.686941068 HSGIDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSGIDFK 7 0 A0A0A0MTH3;Q13418;Q13418-3 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 104.37 0.0081676 234560000 330580 346350 265810 313170 334330 343590 328090 287070 440500 420740 FALSE TRUE 317660.5681 336472.4371 313847.7799 329332.7412 345084.0281 350537.6252 332105.2636 281141.9042 390496.2867 392242.905 0.80985676 0.857816503 0.800136283 0.839614272 0.879771243 0.893674865 0.846682653 0.716754594 0.9955471 1 18.58138783 1.209106749 24.71763092 0.997774139 0.829659095 0.672265288 0.04670339 132.5850077 111261.5489 0.0492957 0.012331796 16.18477809 -1.209106749 -0.168115045 HRPELIEYDKLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HRPELIEYDKLR 12 2 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 111.39 0.00083312 435370000 817050 780910 694540 874130 715460 572820 967730 675770 1072090 983800 FALSE TRUE 785118.7827 758639.2114 820058.828 919243.9541 738473.4207 584402.8129 979573.3692 661815.1133 950390.8378 917166.3497 0.85602659 0.827155523 0.894122237 1.002265243 0.805168464 0.637183007 1.068043294 0.72158678 1.036225149 1 19.8068239 1.209479058 24.91335493 1.018112955 0.852656005 0.243995982 0.117334858 320.3266892 274406.9816 0.10659453 0.026666379 16.19865881 -1.209479058 -0.16545695 HDGKDEIIK ddPTM_BT-474_Pertuzumab_2h_R1 2 HDGKDEIIK 9 1 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ; 99.568 0.0031538 649850000 1120540 1077210 900530 825980 928100 991960 1137830 698380 1535500 1243100 FALSE TRUE 1076748.058 1046489.025 1063275.803 868608.9268 957953.1794 1012018.111 1151755.104 683958.2089 1361196.477 1158903.73 0.929109149 0.9029991 0.91748415 0.74950913 0.826602896 0.873254684 0.993831562 0.590176899 1.174555265 1 20.1443293 1.20964389 24.99992705 1.087277787 0.843586273 0.416347908 0.113291261 229.8308266 198694.5318 0.10803233 0.027026647 16.20480801 -1.20964389 -0.243691515 YDGSTIVPGEQGAEYQHFIQQCTDDVR ddPTM_BT-474_Pertuzumab_2h_R1 3 YDGSTIVPGEQGAEYQHFIQQCTDDVR 27 0 Q14019 Q14019 COTL1 Coactosin-like protein 0 ;; 230.88 4.49E-35 2708430000 823382 825200 701623 850220 859860 887710 790420 867450 877750 826920 FALSE TRUE 791203.3211 801666.104 828421.8836 894099.9561 887518.1778 905660.1044 800093.3964 849536.8544 778111.4998 770911.9719 1.026321227 1.039893183 1.074599843 1.159795137 1.151257485 1.174790556 1.037853122 1.101989443 1.009338975 1 19.55620661 1.209990927 4.921206651 1.000413432 1.097488168 0.343835774 0.050290202 0.228765513 12.97568681 0.048746246 0.013383204 16.21776215 -1.209990927 0.097074736 AEEDVEPECIMEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEEDVEPECIMEK 13 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 206.11 1.21E-06 0 337080 360320 284320 333740 331060 324660 328690 364430 360990 354370 FALSE TRUE 323906.5409 350044.0264 335702.9487 350964.3614 341708.8456 331224.8476 332712.6065 356904.3931 320011.9286 330368.2043 0.980441025 1.059557251 1.016147875 1.062343037 1.034327278 1.002592996 1.007096331 1.080323071 0.968652323 1 18.33371532 1.210188857 24.9997234 0.984326123 1.032330778 0.273604165 0.029859934 301.0719158 265281.5322 0.027500354 0.006881002 16.22515508 -1.210188857 0.048004655 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPTPNDDTLDEGVGLVHSNIATEHIPSPAKK 31 2 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAKK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAKK 306.01 1.66E-82 3210620000 630720 472690 514450 532260 528290 596700 667630 411456 864140 739730 TRUE FALSE 606070.7651 459209.344 607422.5589 559730.0024 545282.9276 608765.6828 675800.6557 402959.2898 766046.45 689627.4282 0.878837964 0.665880337 0.880798144 0.811641155 0.790692054 0.882745752 0.979950373 0.584314477 1.110812039 1 19.39545763 1.21045861 24.99896897 1.055406373 0.806335406 0.44195346 0.110551179 217.5073579 193484.8245 0.102678741 0.025690471 16.23523615 -1.21045861 -0.249070967 RLS(ph)EQLAHTPTAFK ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSEQLAHTPTAFK 14 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(0.991)EQLAHT(0.008)PT(0.001)AFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK 171.79 1.81E-06 3349000000 2824280 2995620 2585990 2846360 2551970 2523340 2984980 3122840 3304550 3486410 TRUE FALSE 2713904.015 2910187.851 3053335.918 2993260.981 2634056.433 2574363.664 3021511.078 3058352.263 2929431.338 3250272.345 0.834977419 0.895367385 0.939409254 0.920926206 0.810410991 0.792045524 0.929617816 0.940952615 0.901287962 1 21.63212918 1.210500575 0.943026036 0.989655449 0.87414749 0.356210411 0.049691086 0.629912874 1.20941382 0.050742433 0.017863107 16.23680499 -1.210500575 -0.115507958 MVEPENAVTITPLRPEDDYS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 MVEPENAVTITPLRPEDDYSPR 22 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;A0A669KAX5;H0YDF9 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR 265.39 8.85E-38 3195370000 1752880 2550750 1671580 3209020 2202140 1851490 2282600 2368750 1678780 1460600 TRUE FALSE 1684375.512 2478005.107 1973671.69 3374637.907 2272973.833 1888928.396 2310535.142 2319834.485 1488211.932 1361672.261 1.236990398 1.819824916 1.449446939 2.47830407 1.669251771 1.387212217 1.696836462 1.703665817 1.092929609 1 20.37694807 1.210847819 5.090058865 1.01716349 1.696484865 0.391941282 0.315770894 0.181973916 11.49587345 0.276584853 0.075962157 16.24979246 -1.210847819 0.679321375 FFQGS(ph)QEFLASASASAER ddPTM_BT-474_Pertuzumab_2h_R1 11 FFQGSQEFLASASASAER 18 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(0.999)QEFLAS(0.001)ASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(0.996)QEFLAS(0.001)AS(0.001)AS(0.001)AER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER 205.21 1.36E-18 880250000 499389 493999 423129 500844 477728 442108 470590 595818 441554 490379 TRUE FALSE 479872.3258 479910.6322 499597.8228 526692.6189 493094.555 451047.7267 476349.2212 583514.1501 391430.6411 457165.1935 1.049669425 1.049753216 1.092816841 1.152083812 1.078591638 0.986618695 1.04196301 1.276374839 0.856212692 1 18.80235604 1.210899453 24.99999907 0.928106321 1.094405897 0.393079981 0.080866025 259.9225435 234910.1917 0.081092993 0.020291879 16.25172457 -1.210899453 0.166299576 S(ph)PIALPVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPIALPVK 8 0 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(1)PIALPVK;S(1)PIALPVK;S(1)PIALPVK;S(1)PIALPVK 120.12 0.0016396 517820000 1329710 1353560 1341380 1324040 1214420 1033850 1480440 1518370 1651770 1817650 TRUE FALSE 1277743.463 1314957.794 1583797.205 1392373.863 1253482.922 1054755.155 1498558.068 1487015.129 1464267.994 1694538.947 0.754036056 0.775997387 0.934647863 0.821683011 0.739719158 0.622443738 0.884345604 0.877533757 0.864109968 1 20.69246136 1.211590229 1.049204262 0.986374688 0.788094922 0.389858009 0.08047724 0.531060406 1.225600053 0.08025109 0.027015174 16.27759464 -1.211590229 -0.198279766 HLLTDLPLPPELPGGDLS(ph)PPDSPEPK ddPTM_BT-474_Pertuzumab_2h_R1 4 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HLLTDLPLPPELPGGDLS(0.999)PPDS(0.001)PEPK;HLLTDLPLPPELPGGDLS(0.997)PPDS(0.003)PEPK;HLLTDLPLPPELPGGDLS(0.997)PPDS(0.003)PEPK;HLLTDLPLPPELPGGDLS(0.968)PPDS(0.032)PEPK 247.76 9.91E-46 1524700000 1000060 811051 746132 728395 833551 839157 886414 644403 1244672 1098098 TRUE FALSE 960976.5496 787920.6196 880974.65 765987.5532 860362.9249 856125.3295 897262.1997 631095.8529 1103382.053 1023722.844 0.938707732 0.769662047 0.860559726 0.748237238 0.840425638 0.836286241 0.876469842 0.616471398 1.077813257 1 19.96539375 1.212302882 24.99999965 1.038906997 0.804845034 0.537471001 0.084476307 187.5546935 178566.1605 0.080086147 0.020046762 16.3043272 -1.212302882 -0.234061964 QSHSGSIS(ph)PYPK ddPTM_BT-474_Pertuzumab_2h_R1 8 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSGS(0.001)IS(0.999)PYPK;QSHSGSIS(1)PYPK;QSHSGS(0.003)IS(0.988)PY(0.009)PK;QSHSGSIS(1)PYPK;QSHSGS(0.011)IS(0.989)PYPK;QSHSGSIS(1)PYPK;QSHSGS(0.001)IS(0.999)PYPK;QSHSGSIS(1)PYPK 276.1 7.92E-28 25794900000 12140120 10963230 9605890 10232710 10217930 10438490 10926060 10363820 13358730 12568850 TRUE FALSE 11665670.69 10650569.41 11341888 10760821.39 10546599 10649563.42 11059776.39 10149803.5 11842302.97 11717550.59 0.995572462 0.90894162 0.967940178 0.918350751 0.900068569 0.908855766 0.943864189 0.86620522 1.010646626 1 23.48216769 1.212608186 24.98559983 1.005323485 0.923395537 0.454664365 0.034539877 216.100335 208044.1169 0.032326561 0.008092431 16.31579297 -1.212608186 -0.081927949 (ac)S(ph)DLEDDETPQLSAHALAALQEFYAEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 SDLEDDETPQLSAHALAALQEFYAEQK 27 0 Q8WVE0 Q8WVE0 N6AMT2 Protein-lysine N-methyltransferase N6AMT2 1 S(0.493)DLEDDET(0.493)PQLS(0.014)AHALAALQEFYAEQK;S(0.818)DLEDDET(0.181)PQLS(0.001)AHALAALQEFYAEQK;S(0.5)DLEDDET(0.5)PQLS(0.001)AHALAALQEFYAEQK 83.283 1.60E-25 138221000 80379 97248 74309 78715 87464 91284 78811 92509 92663 88841 TRUE FALSE 77237.69982 94474.58226 87738.28929 82777.49058 90277.35899 93129.82502 79775.51259 90598.65682 82144.28471 82823.71994 0.93255531 1.140670599 1.059337704 0.999441834 1.089994015 1.124434221 0.963196445 1.093873312 0.991796611 1 16.33775638 1.212660233 24.94580515 0.995898185 1.053437294 0.101790579 0.064312922 530.2277627 510671.6543 0.056575766 0.014163976 16.31774841 -1.212660233 0.057539109 SLETCMYDHK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLETCMYDHK 10 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 159.09 7.79E-06 2490280000 1666320 1879870 1798640 1535150 1639210 1735000 1902110 1781460 2320420 2247280 FALSE TRUE 1601198.372 1826257.948 2123694.259 1614379.275 1691936.678 1770082.889 1925388.591 1744672.228 2057015.65 2095069.724 0.76426973 0.87169316 1.013662808 0.770561121 0.807580129 0.844880182 0.919009315 0.832751392 0.981836369 1 20.99856683 1.212767601 9.049818421 0.991869152 0.856535802 0.387156018 0.069273494 0.311608003 96.27298906 0.062777995 0.016553951 16.32178304 -1.212767601 -0.13533335 RLS(ph)EDYGVLK ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 1 RLS(0.99)EDY(0.01)GVLK;RLS(1)EDYGVLK;RLS(1)EDYGVLK 135.81 8.22E-05 641440000 910735 831982 757606 808677 815506 651980 866004 995012 747569 750463 TRUE FALSE 875142.4693 808254.688 894522.2571 850412.9169 841737.4911 665163.4823 876602.416 974464.6545 662708.1012 699633.4726 1.25085849 1.155254458 1.278558405 1.215512051 1.203112092 0.950731359 1.252945221 1.39282166 0.947221834 1 19.41623979 1.212845278 24.99754291 0.973610477 1.214725018 0.446059428 0.106450578 250.0381225 243052.3584 0.108934479 0.027272395 16.32470259 -1.212845278 0.24111454 KEVEETDEMDQVELVDFDPNQER ddPTM_BT-474_Pertuzumab_2h_R1 3 KEVEETDEMDQVELVDFDPNQER 23 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;; 181.38 6.84E-17 390960000 551116 573628 496238 514311 537917 600391 585996 596702 730170 725107 FALSE TRUE 529577.7774 557268.6911 585919.2454 540854.6523 555219.5888 612531.3174 593167.5943 584379.8952 647284.1627 675994.857 0.783405039 0.824368241 0.86675104 0.800086934 0.821337001 0.90611831 0.877473531 0.864473877 0.957528236 1 19.36665274 1.212917481 0.308363587 1.02322154 0.795622743 0.786961081 0.030195889 0.768431697 0.251057339 0.067047593 0.046990906 16.32741685 -1.212917481 -0.227598797 YGEYFPGTGDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 YGEYFPGTGDLR 12 0 Q92769;Q92769-3;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ;;;;; 192.21 1.02E-05 4093663000 2893367 2901020 2443133 2844233 2751571 2732546 2750590 2980210 3104630 2967750 FALSE TRUE 2780291.019 2818285.75 2884661.48 2991024.206 2840077.78 2787799.952 2784252.543 2918667.622 2752205.418 2766741.649 1.00489723 1.018629893 1.042620471 1.081063787 1.026506317 1.007611229 1.006329067 1.054911514 0.994746083 1 21.3997565 1.212972936 24.99442691 0.997372975 1.031125036 0.248441723 0.022888254 377.9502196 369178.0242 0.023043671 0.005770246 16.32950186 -1.212972936 0.033752061 TLS(ph)FGSDLNYATR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLSFGSDLNYATR 13 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 T(0.01)LS(0.989)FGSDLNYATR;T(0.004)LS(0.996)FGSDLNYATR 97.223 0.0040668 123884000 112054 109859 82526 99870 96769 96287 94111 121306 91414 93059 TRUE FALSE 107674.8058 106725.9289 97440.28398 105024.3027 99881.66277 98233.98911 95262.75857 118800.9887 81037.06596 86756.03104 1.241121851 1.230184549 1.123152855 1.210570624 1.151293594 1.132301558 1.098053443 1.369368645 0.934079913 1 16.40467643 1.213059473 24.99970259 0.967039591 1.194274331 0.593992055 0.075223223 180.2924861 176742.6695 0.073663231 0.018443248 16.33275595 -1.213059473 0.227234739 AAPSTAPAEAT(ph)PPKPGEAEAPPKHPGVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAPSTAPAEATPPKPGEAEAPPKHPGVLK 29 2 O95817 O95817 BAG3 BAG family molecular chaperone regulator 3 1 AAPSTAPAEAT(0.999)PPKPGEAEAPPKHPGVLK 61.941 0.024521 107940000 30327 30909 36999 31319 25152 41944 36497 36393 55172 54986 TRUE FALSE 29141.78731 30027.50558 43685.54234 32935.37734 25961.03692 42792.13642 36943.6612 35641.47183 48909.10586 51261.74924 0.568489912 0.585768259 0.852205455 0.642494215 0.506440715 0.83477714 0.720686706 0.695283957 0.954105285 1 15.64559509 1.213590086 3.475280462 1.001710574 0.676883548 0.575212213 0.103972953 0.164405424 3.614040475 0.094804488 0.026449914 16.35272321 -1.213590086 -0.324827025 RLSQPESAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSQPESAEK 10 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;;; 85.288 0.022996 549590000 438837 430990 346439 322015 359692 377101 385060 388796 493020 476630 FALSE TRUE 421686.7649 418698.5872 409048.2338 338634.2327 371261.8198 384726.2406 389772.4795 380767.2267 437054.4365 444347.4256 0.949002381 0.942277513 0.920559477 0.762093383 0.835521483 0.865823044 0.877179561 0.856913318 0.983587192 1 18.7613286 1.213728532 8.36659289 0.992941193 0.873597533 0.441709221 0.051935888 0.231388229 63.52737806 0.050659046 0.013510042 16.35793704 -1.213728532 -0.11934366 INWAMEDKQEMVDIIETVYR ddPTM_BT-474_Pertuzumab_2h_R1 1 INWAMEDKQEMVDIIETVYR 20 1 K7ESL1;P83876 K7ESL1 TXNL4A Thioredoxin-like protein 4A 0 66.045 0.021903 64778000 63109 60447 70450 60704 61688 58119 63513 61121 81338 77803 FALSE TRUE 60642.63051 58723.11074 83181.88215 63836.94071 63672.25054 59294.206 64290.29109 59858.82999 72104.85124 72533.33351 0.836065676 0.809601709 1.146809034 0.880104879 0.877834334 0.817475265 0.886355114 0.825259603 0.994092616 1 16.14635653 1.214044378 22.79980684 0.997047097 0.885555155 0.191567673 0.09211382 167.1738946 155457.4126 0.088923503 0.022298648 16.36983787 -1.214044378 -0.111491942 ADSGPTQPPLSLS(ph)PAPETK ddPTM_BT-474_Pertuzumab_2h_R1 6 ADSGPTQPPLSLSPAPETK 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLS(0.07)LS(0.93)PAPETK;ADSGPTQPPLSLS(1)PAPETK 386.42 7.62E-127 16867980000 5951260 6009640 5102740 6023360 6660570 6286400 5900820 6432170 6171570 5759560 TRUE FALSE 5718678.18 5838250.951 6024918.628 6334226.331 6874813.283 6413515.315 5973036 6299343.442 5470999.247 5369459.871 1.065037884 1.087306934 1.122071637 1.179676631 1.280354719 1.19444329 1.112409096 1.173180095 1.018910538 1 22.35634554 1.214779683 8.187402172 1.007966953 1.154264932 0.488350444 0.05824468 0.200376637 54.28709199 0.057247374 0.015364141 16.39757714 -1.214779683 0.146297979 AQS(ph)PSYVISTGVSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQSPSYVISTGVSPSR 16 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AQS(0.975)PS(0.025)YVISTGVSPSR 250.1 3.80E-17 0 108140 118960 89054 117960 99413 110400 104750 105400 115180 99238 TRUE FALSE 103913.7692 115567.3773 105148.0388 124047.9297 102610.7094 112632.3636 106031.9618 103223.4532 102105.2493 92516.52187 1.123191481 1.249153934 1.136532553 1.34081921 1.109106864 1.217429724 1.146086771 1.115729938 1.103643406 1 16.49742341 1.21513691 0.699201412 1.002416274 1.203621229 0.468575283 0.064805182 0.520945327 0.598431069 0.057169871 0.0238785 16.41107046 -1.21513691 0.201204955 TAHETDKSEGGKR ddPTM_BT-474_Pertuzumab_2h_R1 4 TAHETDKSEGGKR 13 2 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;;; 152.4 2.65E-05 1413992000 1197934 1254434 769510 967021 895189 1117043 1098270 902419 1426677 1225937 FALSE TRUE 1151117.415 1218658.771 908577.5747 1016929.07 923983.5672 1139630.375 1111710.957 883783.7323 1264726.608 1142903.195 1.007187153 1.066283458 0.794973344 0.889777082 0.808453044 0.997136398 0.972707891 0.773279606 1.106591191 1 20.12427178 1.215685541 24.98381814 1.053295645 0.909531164 0.248661531 0.096824509 375.5448595 410153.7381 0.093961596 0.02355387 16.43181516 -1.215685541 -0.143764482 SRPALS(ph)PLGDIDFCPPNPGPDGPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRPALSPLGDIDFCPPNPGPDGPR 24 1 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 S(0.274)RPALS(0.726)PLGDIDFCPPNPGPDGPR;S(0.045)RPALS(0.955)PLGDIDFCPPNPGPDGPR;S(0.056)RPALS(0.944)PLGDIDFCPPNPGPDGPR 129.25 4.35E-05 1556300000 302432 278658 244637 274131 291085 290407 260139 315559 290481 291268 TRUE FALSE 290612.6231 270710.9467 288848.3478 288278.9338 300448.0134 296279.2285 263322.6589 309042.5964 257506.8147 271540.1589 1.070238098 0.996946263 1.063740807 1.061643828 1.106458855 1.091106486 0.969737441 1.138110096 0.948319452 1 18.05080605 1.215700812 24.99869616 0.974159666 1.06173793 0.352824536 0.047716838 288.1633232 315117.2772 0.043585027 0.010926521 16.43239297 -1.215700812 0.087578264 S(ph)YSPDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYSPDHR 7 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 S(0.645)Y(0.001)S(0.353)PDHR 98.523 0.011748 254360000 533290 602510 433450 535930 611820 525810 532270 557340 491400 445270 TRUE FALSE 512448.4372 585327.0047 511784.057 563589.4115 631499.7459 536442.2385 538784.0795 545830.7342 435618.3321 415111.4663 1.234483937 1.410047788 1.232883451 1.35768211 1.52127753 1.292284801 1.297926276 1.314901607 1.049400866 1 18.66313926 1.215941722 3.31943126 0.997733433 1.338832997 0.702208598 0.080558307 0.122973357 2.420320465 0.072346194 0.020251885 16.44151081 -1.215941722 0.341099564 GGAVERPLT(ph)PAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGAVERPLTPAPR 13 1 H9KVB4;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR 104.45 0.0024741 1221380000 785140 820750 567670 726780 744370 819080 752900 946590 608920 577390 TRUE FALSE 754455.8608 797343.0136 670260.5968 764289.2029 768313.3371 835642.3588 762114.2154 927042.5857 539797.9544 538282.861 1.401597404 1.481271412 1.245182868 1.419865387 1.42734126 1.552422377 1.415824784 1.722222 1.002814679 1 19.03800496 1.21641346 24.99759101 1.001406422 1.463447979 0.716318165 0.114951468 148.1292754 167189.7974 0.117097084 0.02936929 16.45937956 -1.21641346 0.462041557 EKEEYISR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEEYISR 8 1 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 0 ; 142.43 0.0005633 716660000 1047720 1015360 880120 969710 996250 873100 1149480 895640 1339180 1171820 FALSE TRUE 1006773.944 986402.9269 1039177.262 1019756.849 1028295.286 890754.6802 1163547.68 877144.721 1187161.901 1092451.588 0.921573052 0.902925986 0.951234154 0.933457245 0.941273094 0.815372224 1.065079399 0.802914043 1.086695204 1 20.05913792 1.216507703 24.99997126 1.043347659 0.917116862 0.33342011 0.071610759 285.0248025 323105.8612 0.061541108 0.015436256 16.46295167 -1.216507703 -0.126230797 YSHSGS(ph)SS(ph)PDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHS(0.015)GS(0.622)S(0.447)S(0.914)PDT(0.003)K 155.8 0.00010621 298330000 836150 819770 657660 754430 814280 800620 848160 729020 1078500 1034900 TRUE FALSE 803472.3336 796390.9622 776513.7916 793366.2227 840472.0557 816809.0849 858540.0358 713965.4822 956073.2014 964805.3012 0.83278184 0.82544215 0.804839889 0.822307072 0.871131258 0.846605096 0.889858332 0.740009908 0.990949366 1 19.87987831 1.216601592 24.89746038 0.995475046 0.828564213 0.754492159 0.037956228 123.2940859 139788.7965 0.03679421 0.009229993 16.46651113 -1.216601592 -0.166910833 HLLTDLPLPPELPGGDLSPPDS(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HLLTDLPLPPELPGGDLS(0.428)PPDS(0.572)PEPK 81.312 0.010983 142120000 44471 40721 37618 35784 41983 41545 40283 31251 60997 50855 TRUE FALSE 42733.02415 39559.67695 44416.40941 37630.81653 43333.42132 42385.06836 40775.9954 30605.65593 54072.87628 47410.54555 0.901340064 0.834406702 0.936846621 0.793722495 0.914003853 0.894000857 0.860061721 0.645545323 1.140524237 1 15.53292037 1.216643099 24.99999673 1.070262255 0.842849145 0.525575425 0.084569296 218.5409997 249270.1123 0.08470444 0.021247112 16.46808497 -1.216643099 -0.227413111 DIHEELPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DIHEELPK 8 0 Q9BVP2-2;Q9BVP2 Q9BVP2-2 GNL3 Guanine nucleotide-binding protein-like 3 0 ; 112.84 0.0029633 843770000 837830 781020 738740 709850 748910 828550 840980 728980 1041660 943850 FALSE TRUE 805086.6773 758746.0743 872246.7512 746485.4436 772999.3703 845303.8487 851272.1648 713926.3083 923415.1238 879922.1988 0.914952116 0.862287683 0.991277129 0.848353916 0.878486043 0.960657487 0.967440265 0.811351628 1.049428148 1 19.74701644 1.216725807 24.99995876 1.024714202 0.90355214 0.433628742 0.055017079 248.5881854 284615.7975 0.051384881 0.012891377 16.47122147 -1.216725807 -0.121162062 SS(ph)PVNRPSSATNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPVNRPSSATNK 13 1 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80;A0A0A0MR72 Q96L91-4 EP400 E1A-binding protein p400 1 S(0.421)S(0.508)PVNRPS(0.064)S(0.007)ATNK 135.72 0.00021238 54952000 97776 89987 76874 80581 82779 86877 94389 96277 111320 114920 TRUE FALSE 93954.80582 87420.65887 90766.84185 84739.79507 85441.66171 88633.71246 95544.16082 94288.84631 98683.42029 107136.366 0.876964651 0.815975584 0.847208518 0.790952673 0.797503825 0.827298104 0.891799529 0.880082551 0.92110106 1 16.70908874 1.217277745 0.802589006 0.997281243 0.823702198 0.803147158 0.026856873 0.244616982 0.355313856 0.025976536 0.00995219 16.49216782 -1.217277745 -0.173579045 LRS(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_BT-474_Pertuzumab_2h_R1 15 LRSYEDMIGEEVPSDQYYWAPLAQHER 27 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 LRS(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.996)Y(0.004)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.963)Y(0.037)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.981)Y(0.019)EDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(0.528)Y(0.472)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.916)Y(0.084)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.866)Y(0.134)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(0.522)Y(0.477)EDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER 296.41 6.94E-71 19500484000 3419461 3768951 2889537 3869472 3254784 3331852 3172421 3656560 3273255.6 3099956 TRUE FALSE 3285824.684 3661464.208 3411740.613 4069175.914 3359477.083 3399224.33 3211246.037 3581050.758 2901689.347 2889993.219 1.136966226 1.266945605 1.180535854 1.408022651 1.162451545 1.17620495 1.111160406 1.239120817 1.004047113 1 21.46263468 1.217346999 0.7646025 0.989530425 1.231993512 0.451763219 0.085072148 0.553805902 0.740350842 0.078908346 0.031119092 16.49479792 -1.217346999 0.242463087 KRDS(ph)DAGSSTPTTSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 KRDSDAGSSTPTTSTR 16 2 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KRDS(0.999)DAGS(0.001)STPTTSTR;KRDS(0.856)DAGS(0.14)S(0.003)TPTTSTR;KRDS(0.997)DAGS(0.003)STPTTSTR;KRDS(0.999)DAGS(0.001)STPTTSTR 196.11 3.68E-11 965246000 590210 585265 488295 554830 609757 552426 570658 635510 593751 574954 TRUE FALSE 567143.9407 568573.8152 576540.7686 583464.8428 629370.3877 563596.4322 577641.8833 622386.4964 526350.8757 536011.8535 1.058080968 1.060748585 1.075611975 1.088529739 1.174172518 1.051462628 1.077666249 1.161143158 0.981976186 1 19.03190538 1.217364463 24.99990737 0.990987936 1.095343346 0.512153191 0.039956383 222.4647865 262380.4451 0.039284279 0.009861406 16.4954612 -1.217364463 0.10435541 QFAPEYEK ddPTM_BT-474_Pertuzumab_2h_R1 4 QFAPEYEK 8 0 P13667;A0A499FI48;C9JMN9 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;; 105.78 0.010053 454060000 1150700 1221010 977780 1098840 1072190 1000380 1107030 1164050 1351980 1311300 FALSE TRUE 1105729.372 1186187.99 1154486.597 1155551.264 1106677.965 1020608.369 1120578.164 1140011.961 1198508.898 1222484.483 0.904493584 0.970309241 0.944377301 0.945248206 0.90526954 0.834864068 0.91663999 0.932536958 0.980387821 1 20.22138472 1.217675099 2.549899737 0.999312477 0.918155157 0.424295304 0.033834271 0.286287998 3.177262491 0.034140358 0.009675021 16.50726408 -1.217675099 -0.081157321 KKPKVT(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKPKVTPTK 9 3 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 KKPKVT(0.875)PT(0.125)K 56.729 0.063574 305020000 215160 151870 136230 115300 160030 175260 143700 179140 192290 197570 TRUE FALSE 206751.3093 147538.8163 160849.7914 121250.6468 165177.5103 178803.8773 145458.6436 175440.6964 170462.0453 184188.4079 1.122499031 0.801021182 0.873289439 0.65829684 0.896785591 0.970766181 0.78972746 0.952506721 0.925476512 1 17.49082274 1.217879141 1.133044044 0.996342729 0.865948267 0.09426197 0.116174582 0.993696223 2.614279846 0.105466256 0.034562312 16.51502139 -1.217879141 -0.130394461 SGS(ph)GSESTGAEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSGSESTGAEER 13 0 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 S(0.008)GS(0.987)GS(0.005)ESTGAEER 158.52 4.94E-05 61481000 61665 57401 39481 50709 57412 47112 56342 61390 51976 51761 TRUE FALSE 59255.06363 55763.97968 46616.09495 53326.09757 59258.70912 48064.63692 57031.53025 60122.27505 46075.90238 48255.18137 1.227952356 1.155606053 0.966032945 1.105085424 1.228027902 0.996051316 1.18187371 1.245923719 0.954838446 1 15.55839624 1.217921023 24.98821778 0.977419025 1.13788001 0.33586354 0.090501309 327.0850838 395989.3335 0.088836857 0.022312056 16.51661415 -1.217921023 0.160460985 NSLDASRPAGLS(ph)PTLTPGER ddPTM_BT-474_Pertuzumab_2h_R1 2 NSLDASRPAGLSPTLTPGER 20 1 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;E7ERW0;G5E9M9;E7EWF5;F8W708;E7EQU6;Q14135-5 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 NSLDASRPAGLS(0.987)PT(0.013)LTPGER;NSLDASRPAGLS(0.974)PT(0.026)LTPGER 228.64 1.76E-25 1373410000 735170 776290 577510 719750 745390 739260 725500 838530 701860 685410 TRUE FALSE 706438.7436 754150.9693 681878.9036 756896.3838 769366.1463 754208.3437 734378.886 821214.0625 622187.7952 638986.5702 1.105561175 1.180229765 1.067125563 1.184526278 1.204041184 1.180319554 1.149286887 1.285182038 0.973710285 1 19.28542608 1.21796735 24.999815 0.98685486 1.173023847 0.636377091 0.055184872 173.9844851 211208.1298 0.054537294 0.013697092 16.51837611 -1.21796735 0.186168986 ASCGPPS(ph)LPDPTFLPDAER ddPTM_BT-474_Pertuzumab_2h_R1 1 ASCGPPSLPDPTFLPDAER 19 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 ASCGPPS(0.999)LPDPT(0.001)FLPDAER 153.14 5.11E-08 58798000 73803 77802 58881 67755 68839 76205 56466 80742 65492 65236 TRUE FALSE 70918.69717 75583.16314 69522.1065 71251.84367 71053.26895 77745.91731 57157.0478 79074.64948 58057.62272 60817.50761 1.16609016 1.242786265 1.143126531 1.171567966 1.168302874 1.27834764 0.9398124 1.300195496 0.954620224 1 15.89219907 1.218547717 24.99955379 0.977309856 1.174838478 0.417234736 0.094046791 246.542998 307966.5131 0.081639234 0.020517489 16.5404651 -1.218547717 0.197528622 AFVSMVYSEEGAEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFVSMVYSEEGAEDR 15 0 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 226.73 1.92E-12 121650000 75953 74982 65409 68481 67086 66568 76229 78305 77085 76403 FALSE TRUE 72984.67279 72843.58678 77229.86132 72015.31262 69243.88212 67914.05057 77161.9133 76687.97439 68334.63397 71228.15676 1.024660417 1.022679655 1.084260282 1.01105119 0.972141991 0.953471965 1.083306333 1.076652519 0.9593767 1 16.12016004 1.218702563 24.95831875 0.979688343 1.030256773 0.170593373 0.042940838 517.7642615 650727.0696 0.04471951 0.011241705 16.54636359 -1.218702563 0.05056843 DVIKEIEDFDSLEALR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVIKEIEDFDSLEALR 16 1 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;; 207.13 1.66E-11 235744000 550443 557942 333321 329868 488244 599972 418314 466290 484740 417938 FALSE TRUE 528931.079 542030.0404 393559.5194 346892.527 503948.8117 612103.8449 423433.4519 456660.9486 429714.3474 389630.687 1.357519047 1.391137964 1.010083478 0.890311104 1.293401235 1.570984692 1.08675591 1.172035376 1.102876036 1 18.57174778 1.218755145 1.374148046 1.010115323 1.227441284 0.138303941 0.185922862 0.898323689 3.287872991 0.185530527 0.057477384 16.54836704 -1.218755145 0.217325961 LELSVHLQPITR ddPTM_BT-474_Pertuzumab_2h_R1 2 LELSVHLQPITR 12 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 172.33 3.60E-05 611680000 464320 593660 481420 645610 564330 574590 565680 530230 592120 680420 FALSE TRUE 446173.8611 576729.3981 568423.3031 678930.0095 582482.187 586208.6035 572602.9611 519280.5652 524905.02 634334.5473 0.703373106 0.909188062 0.896093876 1.070302748 0.918257076 0.924131605 0.902682919 0.818622551 0.827489252 1 19.27488439 1.218761677 0.007636354 1.813880384 9.74E-07 0.073057329 0.091579751 10162.51527 65.26229844 7793.503424 7701.452166 16.54861595 -1.218761677 -1.81387941 EPHLNYS(ph)PTCLEPPVLSIHPGAID ddPTM_BT-474_Pertuzumab_2h_R1 1 EPHLNYSPTCLEPPVLSIHPGAID 24 0 O75054;O75054-2 O75054 IGSF3 Immunoglobulin superfamily member 3 1 EPHLNYS(0.877)PT(0.123)CLEPPVLSIHPGAID 163.76 1.05E-11 148750000 38301 105540 37425 171340 51811 69926 97583 80408 61688 49327 TRUE FALSE 36804.15458 102530.1025 44188.53001 180182.8779 53477.54787 71339.95163 98777.24994 78747.5467 54685.43686 45986.03835 0.800333229 2.229591985 0.960911868 3.918208317 1.162908347 1.551339367 2.147983464 1.712422934 1.189174776 1 15.4889083 1.218925608 3.158484048 1.016927606 1.85688177 0.107269143 0.834903502 0.50831236 8.900814436 0.713756881 0.200536983 16.55486364 -1.218925608 0.839954164 SNAAT(ph)PTKGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNAATPTKGPEGK 13 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 SNAAT(0.955)PT(0.045)KGPEGK;S(0.001)NAAT(0.962)PT(0.038)KGPEGK 96.143 0.0070691 429290000 480410 430410 333730 337640 360260 350500 365860 400350 534470 522900 TRUE FALSE 461635.0461 418135.1282 394042.4348 355065.6409 371848.0901 357587.3501 370337.5041 392082.6326 473799.2063 487483.5172 0.946975702 0.857742084 0.808319504 0.728364403 0.762791104 0.733537315 0.759692361 0.804299261 0.971928669 1 18.89499391 1.219091772 4.496798064 0.996229685 0.794055492 0.59395506 0.061510334 0.137982378 6.172902139 0.058353825 0.016380702 16.56119884 -1.219091772 -0.202174193 DRKPGSHASS(ph)SAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRKPGSHASSSAR 13 2 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 DRKPGSHAS(0.066)S(0.467)S(0.467)AR 66.673 0.028817 20597000 24089 22994 21217 23989 17931 22403 18779 27248 17259 16547 TRUE FALSE 23147.57525 22338.23363 25051.38387 25227.07516 18507.7669 22856.00401 19008.82302 26685.31928 15299.83068 15426.25695 1.500530901 1.448065704 1.623944418 1.635333525 1.199757463 1.48162993 1.232238195 1.729863528 0.991804475 1 13.91310043 1.219215154 24.97293779 0.995901426 1.480811692 0.602660033 0.157691647 179.4766779 231679.1259 0.147173728 0.037018703 16.56590451 -1.219215154 0.484910266 DEESHEFVIEAGALMLADNGVCCIDEFDK ddPTM_BT-474_Pertuzumab_2h_R1 3 DEESHEFVIEAGALMLADNGVCCIDEFDK 29 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 302.16 3.87E-81 251968000 227966 188187 195629 196442 219006 194642 218365 218463 302302 294995 FALSE TRUE 219056.8367 182820.091 230983.512 206580.3952 226050.5269 198577.7946 221037.4162 213951.6627 267985.9443 275014.7259 0.796527662 0.664764734 0.839895068 0.751161213 0.821957901 0.722062406 0.803729384 0.777964387 0.974442163 1 18.06914935 1.219299551 4.240121249 0.999517841 0.770681854 0.761557756 0.048200888 0.085700874 3.218587069 0.039443347 0.011073631 16.5691241 -1.219299551 -0.228835987 SVEEEEQVWR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEEEEQVWR 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 167.12 1.24E-05 488540000 173220 235540 166160 245850 202700 198410 217840 243500 201580 201430 FALSE TRUE 166450.3709 228822.6298 196188.8082 258538.348 209220.0296 202421.9861 220505.9911 238471.6399 178697.4835 187786.9667 0.886378719 1.218522424 1.044741345 1.376764067 1.114134986 1.07793416 1.174234799 1.26990517 0.951596837 1 17.51873741 1.21950488 24.99645396 0.975798212 1.155817317 0.219890503 0.126496778 381.169672 499987.7782 0.11461563 0.028839764 16.57695964 -1.21950488 0.180019105 HGAEVIDTPVFELK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGAEVIDTPVFELK 14 0 B3KWE1;P12081-4;P12081;B4DDD8;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 178.58 1.97E-06 97170000 218710 213130 161640 190340 185700 195560 213040 174280 279730 257540 FALSE TRUE 210162.5714 207051.7411 190851.9437 200163.4702 191673.2091 199514.3572 215647.2472 170681.0571 247976.2231 240096.5864 0.875325112 0.862368533 0.794896531 0.833678951 0.798317094 0.830975401 0.898168735 0.71088498 1.032818612 1 17.87325537 1.21958396 24.99977312 1.016409563 0.82336447 0.702920798 0.049607676 145.6067086 191816.634 0.046830043 0.011785189 16.57997839 -1.21958396 -0.193045093 FYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQK 34 1 P04040 P04040 CAT Catalase 0 252 1.31E-59 85468000 48724 51061 30350 42386 34953 46072 43308 49366 40644 40441 FALSE TRUE 46819.81221 49604.79027 35834.92013 44573.54654 36077.29499 47003.60741 43838.01626 48346.57485 36030.26351 37701.89505 1.24184241 1.315710794 0.950480608 1.182262761 0.956909326 1.246717369 1.162753655 1.282338057 0.95566187 1 15.20234942 1.219678372 24.92003431 0.977830699 1.16677386 0.291620752 0.118164499 341.3550743 450494.5682 0.111556439 0.028080746 16.58358314 -1.219678372 0.188943161 RS(ph)ISSPNVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSISSPNVNR 10 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RS(0.503)IS(0.411)S(0.086)PNVNR 52.265 0.092634 971790000 103360 62839 64469 59500 104020 123130 64759 94460 73652 67145 TRUE FALSE 99320.57693 61046.89325 76119.98241 62570.80213 107365.8978 125619.773 65551.54001 92509.36799 65291.33373 62597.20934 1.586661418 0.975233463 1.216028369 0.999578141 1.71518665 2.0067951 1.047195885 1.477851313 1.043039049 1 15.93381072 1.220287244 18.97351674 1.021505905 1.367936462 0.167697959 0.31708441 32.27436901 33491.03166 0.303672321 0.077496256 16.60684926 -1.220287244 0.346430557 ALCSFVTEDEVEWMR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALCSFVTEDEVEWMR 15 0 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 163.99 9.09E-09 0 19500 23455 14499 24948 18033 18345 22043 25961 15170 15396 FALSE TRUE 18737.91844 22786.08636 17119.29183 26235.56927 18613.04782 18715.94847 22312.76883 25424.89628 13447.9652 14353.21521 1.305485786 1.587524888 1.192714774 1.827853125 1.29678595 1.303955121 1.554548476 1.771372888 0.936930507 1 13.80908633 1.220585544 24.99891852 0.968464551 1.491201214 0.508624152 0.200886452 216.7887626 301491.9899 0.188706504 0.047568106 16.61825979 -1.220585544 0.522736663 AAS(ph)ALLLR ddPTM_BT-474_Pertuzumab_2h_R1 8 AASALLLR 8 0 F5H672;F5H5N2;B4DNC9;B3KQ30;Q9H1K1 F5H672 ISCU "Iron-sulfur cluster assembly enzyme ISCU, mitochondrial" 1 AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR 147.75 0.00055828 2537848000 2107790 2248514 1963947 2038441 2297070 2270670 2076607 2412180 2253540 2205800 TRUE FALSE 2025415.237 2184388.582 2318875.911 2143645.184 2370957.343 2316584.503 2102021.138 2362367.64 1997727.587 2056399.201 0.984932904 1.06223956 1.127638986 1.042426579 1.152965505 1.126524705 1.02218535 1.148788445 0.971468762 1 20.97168893 1.220612772 24.99895198 0.985734274 1.086605069 0.344023919 0.053839962 294.0455912 409555.3281 0.04935528 0.012438308 16.61930171 -1.220612772 0.100870795 AKWDAWNELK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKWDAWNELK 10 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 132.32 0.00020674 4967800000 11319000 10779100 9523100 10225000 9425900 5806000 10934500 11754900 13938800 15525900 FALSE TRUE 10876640.97 10471690.62 11244136.01 10752713.48 9729092.634 5923401.298 11068319.68 11512157.21 12356525.86 14474316.96 0.751444161 0.723466997 0.776833618 0.742882272 0.672162469 0.40923529 0.764686839 0.795350636 0.853686284 1 23.78699193 1.220638092 1.424447567 0.986326514 0.688443432 0.489830163 0.100801738 0.342633671 1.332679539 0.099817414 0.030669213 16.62027066 -1.220638092 -0.297883082 HINMDGTINVDDFK ddPTM_BT-474_Pertuzumab_2h_R1 3 HINMDGTINVDDFK 14 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 204.82 1.31E-08 750620000 1944840 1814830 1575180 1538510 1758940 1814320 1809980 1703580 2271010 2148610 FALSE TRUE 1868833.503 1763072.825 1859850.066 1617912.685 1815517.903 1851006.793 1832131.077 1668400.478 2013214.466 2003082.731 0.93297869 0.880179734 0.928493884 0.807711364 0.906361916 0.924079053 0.91465572 0.83291641 1.005058071 1 20.93379058 1.22071908 24.99885191 1.002529203 0.889072329 0.561768554 0.039402676 194.6808466 272771.803 0.036815344 0.009283492 16.62337033 -1.22071908 -0.113456873 VEADIPGHGQEVLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 VEADIPGHGQEVLIR 15 0 B0QYF8;P02144;F2Z2F1;F2Z337 B0QYF8 MB Myoglobin 0 ;;; 162.46 1.59E-06 1370140000 1809720 1945660 1651830 2066430 1906240 1724680 1906520 2098780 1956670 1928950 FALSE TRUE 1738994.142 1890171.682 1950352.426 2173078.7 1967555.941 1759554.211 1929852.562 2055439.46 1734557.025 1798300.498 0.967020886 1.051087782 1.084553125 1.208406883 1.094119666 0.978453942 1.073153549 1.142989985 0.964553492 1 20.77820269 1.220721206 24.99377119 0.982276658 1.079381072 0.23113369 0.067243113 411.0026838 575816.7533 0.066637466 0.016805771 16.6234517 -1.220721206 0.097104414 NS(ph)EEEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSEEEEEEK 9 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 NS(1)EEEEEEK 155.66 7.63E-05 227440000 131420 88401 143630 139080 121900 109900 140390 162160 200980 229290 TRUE FALSE 126283.9611 85879.89003 169587.136 146257.9355 125821.0242 112122.2533 142108.1348 158811.3393 178165.593 213759.9841 0.590774563 0.401758498 0.793353053 0.684215692 0.588608877 0.524524053 0.664802327 0.742942324 0.833484311 1 17.70563228 1.220988961 1.122056032 0.994672407 0.599619843 0.644459794 0.096305133 0.288498737 0.745862638 0.092156603 0.030318963 16.63370371 -1.220988961 -0.395052564 KISSIQSIVPALEIANAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 KISSIQSIVPALEIANAHR 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 176.46 3.87E-13 1084740000 1435390 2197710 1094480 1985870 1094800 1582510 1913320 1545400 1317760 1069880 FALSE TRUE 1379293.372 2135033.463 1292276.883 2088360.989 1130015.236 1614509.436 1936735.782 1513486.95 1168173.409 997416.0746 1.382866596 2.140564522 1.29562468 2.093771137 1.132942676 1.618692016 1.941753128 1.517407818 1.171199702 1 19.92783593 1.221013866 2.916947086 1.018373791 1.66170936 0.34315252 0.315149816 0.25771929 3.774434046 0.264055318 0.074464566 16.6346576 -1.221013866 0.643335569 DLKPENLLLASK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLKPENLLLASK 12 1 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;Q5SWX3;Q13555-6;Q13555-11;Q13555-5;E9PBE8;E9PF82;E9PBG7;E7EQE4;A0A5F9ZH90;H7BXS4;A0A5F9ZHY2;A0A5K1VW76;A0A5F9ZHM9;A0A5F9ZH21;A0A5F9ZHR5;D6RFJ0;A0A5F9ZH50;Q9UQM7;Q9UQM7-2;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5 Q13555-8;E9PF82;Q13557 CAMK2G;CAMK2B;CAMK2D;CAMK2A Calcium/calmodulin-dependent protein kinase type II subunit gamma;Calcium/calmodulin-dependent protein kinase type II subunit alpha;Calcium/calmodulin-dependent protein kinase type II subunit delta 0 ; 167.89 4.38E-05 1636140000 2079660 1936580 1738990 1654530 1780650 1931530 2075420 2148010 2584800 2728300 FALSE TRUE 1998384.588 1881350.635 2053264.177 1739920.492 1837926.224 1970586.86 2100819.611 2103652.843 2291384.34 2543509.811 0.785679921 0.739667143 0.807256244 0.684062819 0.72259451 0.774751036 0.82595302 0.827066927 0.900874976 1 21.27838923 1.221021289 0.81793552 0.998800301 0.74795607 0.842718044 0.034365921 0.21104978 0.316485896 0.032959361 0.012501779 16.63494191 -1.221021289 -0.250844231 HIGYDDSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HIGYDDSSK 9 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 101.65 0.0047681 0 272480 223180 195750 213290 213640 226520 219810 210190 296400 273870 FALSE TRUE 261831.1804 216815.1249 231126.3794 224297.9225 220511.9246 231100.3896 222500.1005 205849.503 262753.9146 255320.541 1.025499865 0.849187943 0.905240051 0.878495407 0.863666996 0.905138258 0.871453976 0.806239491 1.029113888 1 17.96195008 1.221064341 24.99392379 1.014557095 0.882282336 0.463103866 0.054166796 226.4293043 323451.9439 0.049999061 0.012615273 16.63659106 -1.221064341 -0.132274759 INPYMSS(ph)PCHIEMILTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 INPYMSSPCHIEMILTEK 18 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 1 INPYMS(0.183)S(0.817)PCHIEMILTEK 243.52 2.76E-24 277360000 723950 722250 582310 599750 664320 727170 663620 654960 855520 799860 TRUE FALSE 695657.2336 701652.1372 687546.3704 630703.1694 685688.4561 741873.8756 671741.5801 641434.8471 758404.9562 745684.7698 0.93291061 0.940950071 0.922033543 0.845804011 0.919541989 0.994889403 0.900838541 0.86019572 1.017058397 1 19.50820635 1.221122067 24.99806755 1.008529313 0.913008189 0.474339478 0.039502782 251.1115989 359957.4326 0.039944953 0.010079226 16.63880252 -1.221122067 -0.095521124 SRQPS(ph)PLLLLPPPAGLTSDPGPSVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 1 S(0.011)RQPS(0.989)PLLLLPPPAGLTSDPGPSVR;S(0.017)RQPS(0.983)PLLLLPPPAGLTSDPGPSVR;S(0.046)RQPS(0.954)PLLLLPPPAGLTSDPGPSVR;S(0.065)RQPS(0.935)PLLLLPPPAGLTSDPGPSVR 113.41 0.001252 1418320000 595434 638123 440316 615580 612460 621965 544784 646511 597394 564416 TRUE FALSE 572163.781 619924.3568 519890.896 647350.1576 632160.3321 634541.5584 551451.2296 633160.3219 529580.3376 526187.6016 1.087376022 1.178143223 0.988033345 1.230264939 1.20139724 1.205922672 1.048012587 1.203297683 1.006447769 1 19.00521773 1.221442792 24.22028339 1.003223554 1.144002178 0.357438254 0.074845685 201.0497687 284457.0754 0.068026718 0.017202742 16.65109473 -1.221442792 0.140778623 (ac)MDVAESPERDPHS(ph)PEDEEQPQGLSDDDILR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDVAESPERDPHSPEDEEQPQGLSDDDILR 30 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 MDVAES(0.46)PERDPHS(0.54)PEDEEQPQGLSDDDILR 53.266 1.42E-17 155240000 5619.7 7509.1 5913.6 7067.8 2541.7 4502.1 9317.9 8661.5 2902 2793 TRUE FALSE 5400.075911 7294.94782 6982.319067 7432.570005 2623.456089 4593.135547 9431.935247 8482.636998 2572.577126 2603.827622 2.073899157 2.801624715 2.681559642 2.854478515 1.007538313 1.76399371 3.622334738 3.257756745 0.987998247 1 11.34641823 1.221478559 24.67471817 0.993996412 2.550590219 0.419785591 0.710513265 244.3191586 352903.2832 0.738443713 0.186579622 16.65246613 -1.221478559 1.556593807 DLKPSNLLLNTTCDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLKPSNLLLNTTCDLK 16 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 94.01 0.0038646 285350000 260850 260660 222330 192860 246860 244500 251030 249390 319680 308290 FALSE TRUE 250655.6936 253226.232 262509.9767 202813.5277 254800.4761 249443.9575 254102.1802 244240.0093 283391.2666 287409.2437 0.872121197 0.881065023 0.913366506 0.705661116 0.886542384 0.867905132 0.884112762 0.849798727 0.986020014 1 18.13274694 1.221537499 7.046262299 0.995102614 0.857299274 0.505179959 0.053623605 0.128603727 27.41386275 0.045645319 0.012786434 16.65472625 -1.221537499 -0.13780334 LRVQS(ph)PEPPAPER ddPTM_BT-474_Pertuzumab_2h_R1 2 LRVQSPEPPAPER 13 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LRVQS(1)PEPPAPER;LRVQS(1)PEPPAPER 115.8 0.00038487 1450100000 446710 582890 420460 588140 513890 487410 522470 593290 484210 456330 TRUE FALSE 429252.0793 566266.5479 496446.4751 618493.9759 530419.7386 497265.7642 528864.1441 581038.3542 429244.5108 425422.3626 1.009002152 1.331069068 1.166949645 1.45383513 1.246807373 1.16887547 1.243150785 1.365791752 1.008984361 1 18.69853635 1.221676044 24.69231078 1.004491727 1.257418571 0.413434492 0.115689402 213.8645287 312749.5407 0.104288445 0.026359995 16.66004018 -1.221676044 0.252926845 IPTPVIHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 IPTPVIHTK 9 0 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 137.95 0.0014834 0 370510 405240 302510 410560 331510 311380 377610 420560 353780 370340 FALSE TRUE 356030.0596 393682.952 357180.2863 431749.0508 342173.3202 317676.3169 382231.3041 411875.289 313620.3776 345256.5419 1.031204384 1.140262107 1.034535897 1.25051664 0.991069766 0.92011672 1.107093589 1.192954337 0.90836911 1 18.39730923 1.221685392 24.99993633 0.954184512 1.087182304 0.231661779 0.093984898 409.850043 607159.0598 0.090910172 0.022969616 16.66039876 -1.221685392 0.132997793 LDPITGR ddPTM_BT-474_Pertuzumab_2h_R1 6 LDPITGR 7 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RD83;D6RF44;Q14103-2;Q14103-4;D6RBQ9 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;;;; 164.89 0.0027471 2963100000 854480 954512 746027 946734 914197 904621 908527 1067164 829596 859719 FALSE TRUE 821085.9769 927290.2523 880850.6742 995595.0552 943602.9768 922913.0564 919645.8252 1045126.69 735423.74 801489.4664 1.024450116 1.156958751 1.099017156 1.242181085 1.177311763 1.151497425 1.147420975 1.303980569 0.917571311 1 19.61232403 1.221934295 24.9999735 0.958785486 1.169141321 0.552248046 0.073324581 200.6391771 301680.5738 0.070485836 0.017821997 16.6699499 -1.221934295 0.210355835 TAHETDKSEGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TAHETDKSEGGK 12 1 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 110.38 0.00089897 396310000 214630 201800 156530 193060 189570 205290 203800 185840 262500 249390 FALSE TRUE 206242.0223 196044.8616 184818.453 203023.8497 195667.6912 209441.1045 206294.1654 182002.3391 232702.1005 232498.5932 0.887067829 0.843208808 0.794922887 0.873226143 0.84158656 0.900827405 0.887292102 0.782810496 1.000875306 1 17.82686246 1.222055073 24.93238782 1.000437876 0.849742266 0.723808773 0.036822536 136.7599263 206576.4104 0.035544423 0.008990808 16.67458651 -1.222055073 -0.15069561 KGPAS(ph)PTRPAAPRPAEAPLLDL ddPTM_BT-474_Pertuzumab_2h_R1 1 KGPASPTRPAAPRPAEAPLLDL 22 3 A0A0D9SFE4 A0A0D9SFE4 DNM1 1 KGPAS(0.974)PT(0.026)RPAAPRPAEAPLLDL 98 0.0067781 74815000 130410 135670 97229 105350 121410 134550 111850 132630 124200 120370 TRUE FALSE 125313.433 131800.8244 114800.4431 110787.1261 125315.2629 137270.6932 113218.8538 129891.1442 110101.3367 112217.2327 1.116704004 1.174515012 1.023019731 0.98725591 1.11672031 1.223258584 1.008925733 1.157497303 0.981144643 1 16.77593472 1.22214265 24.98740301 0.990572196 1.099940433 0.273773338 0.071916726 370.7313777 564221.2488 0.068060073 0.017218591 16.67794933 -1.22214265 0.109368237 GTLGGLFSQILQGEDIVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTLGGLFSQILQGEDIVR 18 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;Q9BZZ5-3 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 185.62 1.21E-13 22046000 24721 30273 24897 17972 23517 23747 29120 26366 23003 21020 FALSE TRUE 23754.87599 29409.64368 29396.44173 18899.53707 24273.44566 24227.18061 29476.37927 25821.53289 20391.79588 19596.29668 1.21221251 1.500775589 1.500101892 0.964444323 1.238675147 1.236314239 1.504181109 1.317674115 1.040594364 1 14.25829342 1.222217825 6.407146003 1.013882745 1.315884242 0.347691002 0.158317352 0.180380426 27.6946705 0.140799274 0.039740683 16.68083649 -1.222217825 0.302001497 TEMDWVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEMDWVLK 8 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 141.47 0.0028122 526710000 797330 716660 610990 696650 684710 647840 649570 758140 850390 850380 FALSE TRUE 766169.4621 696221.5585 721409.4844 732604.19 706734.319 660939.7687 657519.632 742484.1441 753857.2923 792783.0052 0.96643023 0.878199399 0.909970925 0.924091694 0.891459976 0.833695683 0.829381593 0.936554062 0.950899915 1 19.59656651 1.222852253 2.16801963 0.99273502 0.890437508 0.434332296 0.039437173 0.279551617 2.266094056 0.037863364 0.010890187 16.70522205 -1.222852253 -0.102297512 S(ph)PSKPPGPNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSKPPGPNR 10 1 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6;C9JPJ6;C9JE09 Q92766 RREB1 Ras-responsive element-binding protein 1 1 S(0.976)PS(0.024)KPPGPNR 62.088 0.052908 170980000 162210 136210 131660 171620 150090 103130 168170 173910 138580 146480 TRUE FALSE 155870.6539 132325.4242 155453.8908 180477.3288 154917.7812 105215.3593 170228.1148 170318.6977 122848.9794 136558.7791 1.141418039 0.96899976 1.138366144 1.321609126 1.134440291 0.770476713 1.246555629 1.247218954 0.899605138 1 17.05916254 1.223177679 24.9829605 0.949802487 1.124431506 0.173109856 0.149644786 492.6180178 800023.267 0.1460696 0.037069545 16.71774431 -1.223177679 0.174629019 DLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_BT-474_Pertuzumab_2h_R1 6 DLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 34 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 423.68 3.46E-208 15755700000 1028697 1019415 917789 941593 941726 1036615 1024817 841787 1448000 1208076 TRUE FALSE 988494.384 990342.2823 1083653.888 990188.7276 972017.472 1057576.066 1037359.017 824403.8043 1283629.111 1126251.936 0.877684958 0.879325709 0.962177159 0.879189367 0.863055095 0.939022639 0.921071905 0.731988801 1.139735319 1 20.10309816 1.223332339 24.99998091 1.0698677 0.880090858 0.563427971 0.06624595 199.70596 327844.4303 0.064054402 0.016261583 16.72369886 -1.223332339 -0.189776842 RRT(ph)NS(ph)SSSSPVVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRTNSSSSSPVVLK 14 2 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 2 RRT(0.992)NS(0.978)S(0.022)S(0.004)S(0.004)S(0.001)PVVLK 97.579 0.003221 281740000 240300 259870 202600 258100 257330 241490 230400 270680 244150 231740 TRUE FALSE 230908.8103 252458.762 239214.3268 271420.5719 265607.2532 246373.0933 233219.7041 265090.3634 216435.1156 216044.0434 1.068804336 1.168552292 1.107247962 1.256320552 1.229412526 1.140383643 1.079500737 1.227020006 1.00181015 1 17.72096593 1.223518895 24.923193 1.000904849 1.162294504 0.52329818 0.060565132 201.5154864 333888.8706 0.057017863 0.014483473 16.73088427 -1.223518895 0.161389655 IRDSAGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 IRDSAGQK 8 1 P52209-2;P52209;K7EPF6;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 114.89 0.0023423 156150000 177220 170520 140720 154060 153160 141900 168120 198710 178830 214620 FALSE TRUE 170294.0465 165656.9366 166151.2343 162011.0551 158086.5305 144769.3152 170177.5029 194606.5691 158529.9681 200083.5962 0.851114483 0.82793862 0.830409076 0.809716829 0.790102405 0.723544148 0.850532008 0.972626306 0.792318666 1 17.61024337 1.223531136 0.759110885 0.980855405 0.809175266 0.398602736 0.06139215 0.609585384 0.804198557 0.061303345 0.024318991 16.73135586 -1.223531136 -0.171680138 DQRPS(ph)SPIR ddPTM_BT-474_Pertuzumab_2h_R1 4 DQRPSSPIR 9 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.907)S(0.093)PIR;DQRPS(0.624)S(0.376)PIR;DQRPS(0.54)S(0.46)PIR;DQRPS(0.5)S(0.5)PIR 107.85 0.0016395 2978270000 448252 393636 378827 441915 397012 367507 441034 460784 436887 447429 TRUE FALSE 430733.8163 382409.8867 447289.4659 464722.2861 409782.2515 374938.2433 446431.506 451268.6494 387293.4193 417124.2353 1.032627164 0.916776956 1.072317137 1.11411001 0.982398568 0.898864683 1.070260292 1.081856702 0.928484577 1 18.67011761 1.223639739 24.99937579 0.96424232 1.022508676 0.098277282 0.068854609 684.6871676 1147136.132 0.067513634 0.017151145 16.73554035 -1.223639739 0.058266356 EAPEEDPRLPDNFRPPGEDFRS(ph)PPDDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAPEEDPRLPDNFRPPGEDFRSPPDDFR 28 3 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 EAPEEDPRLPDNFRPPGEDFRS(1)PPDDFR 73.758 0.05367 107870000 19637 27272 25713 22329 26795 25870 28571 31193 20446 19659 TRUE FALSE 18869.56433 26494.22926 30359.91108 23481.40237 27656.88551 26393.10912 28920.66044 30548.85365 18125.0558 18327.47842 1.029577768 1.445601444 1.656524176 1.281212932 1.509039317 1.440084038 1.577994516 1.666833426 0.988955239 1 14.16172069 1.223661556 24.9856679 0.994477004 1.469384574 0.509879523 0.178241338 208.2073543 349153.0496 0.168669274 0.042867086 16.73638108 -1.223661556 0.47490757 HIDCAAIYGNEPEIGEALKEDVGPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 HIDCAAIYGNEPEIGEALKEDVGPGK 26 1 P14550;Q5T621;V9GYP9;V9GYG2 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ; 258.48 6.37E-53 508040000 922980 782960 778730 642950 762970 818820 824100 722850 1092690 965250 FALSE TRUE 886908.9212 760630.7474 919463.8338 676132.7266 787511.623 835377.1014 834185.5823 707922.8949 968652.4121 899872.7577 0.9855937 0.845264779 1.02177094 0.751364813 0.875136641 0.928328027 0.927003929 0.786692217 1.076432644 1 19.77936149 1.22373971 24.99996226 1.038216407 0.886121074 0.351422104 0.080314871 278.8737703 470392.0366 0.071905985 0.018280692 16.73939315 -1.22373971 -0.152095333 KKGGSSDEGPEPEAEES(ph)DLDSGSVHSASGRPDGPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KKGGSSDEGPEPEAEESDLDSGSVHSASGRPDGPVR 36 3 H7C2H0 H7C2H0 CHD3 1 KKGGSSDEGPEPEAEES(0.999)DLDSGSVHSASGRPDGPVR 99.525 0.00012224 87577000 61121 62240 56458 48409 46218 63780 55024 57151 69691 66333 TRUE FALSE 58732.32375 60464.97614 66661.2165 50907.39429 47704.64394 65069.6753 55697.40017 55970.81188 61779.96985 61840.20683 0.949743327 0.977761545 1.077959145 0.823208668 0.771417924 1.052222795 0.90066646 0.905087721 0.999025925 1 15.91625752 1.223748684 23.53827299 0.999513158 0.930793882 0.085208992 0.08804082 360.0888291 572198.145 0.084172498 0.021475796 16.73973907 -1.223748684 -0.068719276 LDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LDSSEMDHS(1)ENEDYTMSSPLPGK;LDS(0.016)S(0.013)EMDHS(0.971)ENEDYTMSSPLPGK;LDSSEMDHS(1)ENEDYTMSSPLPGK;LDS(0.001)S(0.004)EMDHS(0.996)ENEDYTMSSPLPGK 248.73 4.90E-38 3058940000 1718780 1600350 1435180 1573290 1538610 1508550 1733330 1581350 2070780 1992640 TRUE FALSE 1651608.177 1554709.585 1694548.951 1654487.685 1588100.788 1539053.915 1754543.011 1548694.57 1835713.736 1857676.718 0.889071904 0.836910734 0.912187215 0.890621963 0.854885445 0.82848318 0.944482425 0.83367281 0.988177177 1 20.82506803 1.224054301 24.13755326 0.99408886 0.873789644 0.650548097 0.035267644 100.0396659 166452.0507 0.030964775 0.00789735 16.75152311 -1.224054301 -0.120299216 RAS(ph)SASVPAVGASAEGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RASSASVPAVGASAEGTR 18 1 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 RAS(0.486)S(0.486)AS(0.027)VPAVGASAEGTR;RAS(0.478)S(0.478)AS(0.044)VPAVGASAEGTR 116.44 9.82E-05 611080000 203282 207946 167988 177433 217850 218270 170347 225440 178258 170694 TRUE FALSE 195337.5147 202015.5837 198347.1685 186590.3384 224857.3431 222683.5689 172431.7575 220784.5852 158022.8992 159132.7433 1.227513022 1.269478421 1.246425873 1.172545225 1.413017449 1.399357318 1.083571828 1.387423987 0.993025671 1 17.27987119 1.224227059 24.9789992 0.996512485 1.275166163 0.56004513 0.098702187 186.1746053 324435.9312 0.089526513 0.022801906 16.75818801 -1.224227059 0.278653678 GYNDDYYEESYFTTR ddPTM_BT-474_Pertuzumab_2h_R1 3 GYNDDYYEESYFTTR 15 0 P50402;Q5HY57 P50402 EMD Emerin 0 ;; 247.14 7.15E-18 449210000 260946 394460 239672 419530 299607 318399 329850 376540 289847 267505 FALSE TRUE 250747.9418 383210.387 282986.0619 441181.9936 309244.1313 324837.2459 333886.803 368764.3174 256944.7837 249386.6481 1.005458567 1.536611482 1.134728198 1.76906822 1.240018797 1.302544657 1.338831912 1.478685087 1.030306898 1 17.9280247 1.224248484 23.90913951 1.015152583 1.363346469 0.304718056 0.202052167 172.1863186 287631.4403 0.172601278 0.044084983 16.75901478 -1.224248484 0.348193886 HKLDVTSVEDYK ddPTM_BT-474_Pertuzumab_2h_R1 3 HKLDVTSVEDYK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 159.64 3.83E-05 2386160000 4202780 3794670 3483690 3305150 3646580 3907680 3890820 3432180 5554350 5342230 FALSE TRUE 4038530.711 3686449.727 4113270.277 3475729.188 3763875.557 3986695.967 3938437.019 3361304.284 4923843.474 4980396.004 0.810885461 0.74019209 0.825892213 0.697882093 0.755738209 0.800477706 0.790787925 0.674907032 0.988644973 1 22.24782903 1.22444263 24.99851071 0.9943228 0.75965666 0.803394906 0.045939475 106.3387445 188287.0181 0.042808235 0.010912661 16.76650838 -1.22444263 -0.23466614 LNHQEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNHQEFK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 130.04 0.003602 365290000 608010 674410 522910 584710 557690 476040 625030 578270 762600 736460 FALSE TRUE 584248.297 655176.4871 617411.4691 614886.9532 575628.6053 485665.855 632679.3041 566328.5224 676032.8451 686578.9082 0.85095579 0.954262473 0.899257844 0.895580895 0.838401236 0.707370776 0.921495398 0.824855695 0.984639693 1 19.38906601 1.22445077 22.22833253 0.992320644 0.862216899 0.40233208 0.063762582 72.69971259 114515.5406 0.060839477 0.01563146 16.76682261 -1.22445077 -0.130103744 KLFIGGLSFETTDESLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLFIGGLSFETTDESLR 17 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 262.59 3.81E-27 3488500000 1589530 1727300 1277680 1472580 1587930 1838010 1623230 1503580 1590740 1311650 FALSE TRUE 1527409.41 1678039.095 1508585.198 1548580.03 1639007.211 1875175.822 1643095.574 1472530.548 1410165.864 1222810.777 1.249097112 1.372280263 1.233702897 1.266410191 1.340360456 1.533496316 1.343703871 1.204217836 1.153216745 1 20.22176974 1.224638922 1.579388741 1.014842595 1.334582239 0.624951928 0.08282426 0.242458746 1.123540707 0.082124834 0.024707977 16.77408819 -1.224638922 0.319739644 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.018)PS(0.982)PGLPAEGAPEAPRPS(0.533)S(0.467)PPPEVLEPHSLDQPPATSPR;HT(0.134)PS(0.866)PGLPAEGAPEAPRPS(0.492)S(0.469)PPPEVLEPHS(0.013)LDQPPAT(0.013)S(0.014)PR 263.56 3.19E-63 794928000 66470 77741 56458.2 68697 74127 60855.4 65561 52709 109432 90517 TRUE FALSE 63872.27891 75523.9028 66661.45265 72242.4604 76511.36228 62085.93788 66363.35513 51620.54073 97009.73814 84386.20297 0.756904288 0.894979276 0.789956774 0.85609327 0.906680945 0.73573565 0.786424235 0.61171778 1.149592406 1 16.36471952 1.225234736 24.9998342 1.074796339 0.790504228 0.626769909 0.087185535 175.441448 329124.7882 0.086775762 0.022205885 16.79711655 -1.225234736 -0.284292111 SSS(ph)FSLPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSFSLPSR 9 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 SS(0.016)S(0.984)FSLPSR;SS(0.009)S(0.991)FSLPSR 210.64 6.77E-06 700920000 1284060 1299470 939250 1236040 1210000 1140880 1077700 1324660 1143180 1129940 TRUE FALSE 1233877.516 1262410.388 1108993.369 1299832.173 1248920.749 1163949.375 1090889.215 1297305.308 1013410.999 1053408.157 1.171319499 1.198405745 1.052767022 1.233930233 1.185600036 1.10493674 1.035580755 1.231531481 0.962030711 1 20.00663311 1.225243701 24.99197357 0.981015202 1.150578834 0.520036785 0.065605359 202.2723384 379595.0276 0.059979545 0.015341054 16.7974633 -1.225243701 0.169563632 HQLEETKK ddPTM_BT-474_Pertuzumab_2h_R1 3 HQLEETKK 8 1 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 ;; 172.23 0.00018486 770450000 1621170 1466990 1485970 1354540 1571560 1490720 1743290 1353990 2370270 2177160 FALSE TRUE 1557812.884 1425152.882 1754517.834 1424447.972 1622110.655 1520863.38 1764624.904 1326029.633 2101206.887 2029699.014 0.767509307 0.702149861 0.864422667 0.701802564 0.799187783 0.749304882 0.869402257 0.653313434 1.035230777 1 20.95283437 1.22536033 24.9999337 1.017615646 0.763194362 0.705226888 0.065745117 127.6004308 241654.3856 0.056747579 0.014526103 16.80197485 -1.22536033 -0.254421284 VAS(ph)GSDLHLTDIDSDSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VAS(0.559)GS(0.441)DLHLTDIDSDSNR;VAS(0.565)GS(0.435)DLHLTDIDSDSNR 176.46 5.23E-13 1498940000 566830 648040 483550 626660 553430 595860 617270 601020 625360 577350 TRUE FALSE 544677.6569 629558.5337 570938.2415 659001.9977 571231.5786 607908.6975 624824.3349 588608.727 554371.7545 538245.5702 1.011950097 1.169649261 1.060739322 1.224351921 1.06128431 1.12942629 1.16085365 1.093569106 1.029960645 1 19.03790502 1.225450073 2.828653324 1.002841125 1.119661295 0.326209705 0.058207595 0.264692362 3.618956051 0.048270213 0.013663041 16.80544716 -1.225450073 0.11682017 VFITDDFHDMMPK ddPTM_BT-474_Pertuzumab_2h_R1 3 VFITDDFHDMMPK 13 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 195.77 1.47E-07 5989710000 6618010 7600860 6491910 6790490 6556230 6809090 7608030 6812990 9090760 8325200 FALSE TRUE 6359370.853 7384090.915 7665142.549 7140948.003 6767117.092 6946774.465 7701139.347 6672299.376 8058815.036 7761326.789 0.81936646 0.95139544 0.987607243 0.920067947 0.871902096 0.895049861 0.992245212 0.859685407 1.038329561 1 22.88787187 1.225724258 24.99770849 1.01916485 0.915496171 0.395963301 0.052734174 262.431846 511048.3116 0.047822109 0.012271329 16.81606039 -1.225724258 -0.10366868 KLLELDPEHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLLELDPEHQR 11 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 102.66 0.0018426 321845000 616710 723740 508320 608120 613950 622330 537680 560830 590440 437520 FALSE TRUE 592608.2914 703099.6438 600184.7315 639505.1461 633698.2593 634913.939 544260.2887 549248.6645 523415.7265 407886.3807 1.452875897 1.723763472 1.471450776 1.567851187 1.553614657 1.556595094 1.334342882 1.346572699 1.283239037 1 18.63780781 1.225799807 0.552746802 0.997481197 1.583710573 0.826202647 0.079251683 0.286580323 0.223093624 0.07685319 0.038375925 16.81898591 -1.225799807 0.586229376 KAEGAQNQGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KAEGAQNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 150.09 3.56E-05 883572000 909670 1053910 731720 887060 774230 765930 999420 1012090 834370 848940 FALSE TRUE 874119.0907 1023853.519 863958.081 932841.2729 799133.8111 781417.6294 1011651.201 991189.9878 739655.8156 791440.5376 1.104465906 1.293658171 1.09162728 1.178662488 1.009720596 0.987335867 1.278240313 1.252387186 0.93456903 1 19.59412144 1.22594735 24.99552412 0.967284383 1.154538724 0.340869148 0.10116692 301.1811246 596827.9582 0.100120379 0.025718921 16.82470079 -1.22594735 0.18725434 KRT(ph)SESR ddPTM_BT-474_Pertuzumab_2h_R1 2 KRTSESR 7 2 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 KRT(0.499)S(0.499)ES(0.001)R;KRT(0.495)S(0.495)ES(0.01)R 85.355 0.033559 463840000 876070 942120 702180 678640 756580 806390 839160 937130 729450 750820 TRUE FALSE 841832.2159 915251.66 829079.5459 713664.6917 780916.0828 822695.7583 849429.8911 917777.938 646645.8941 699966.2926 1.202675364 1.307565335 1.184456387 1.019570084 1.115648126 1.175336251 1.213529709 1.311174477 0.923824334 1 19.41692592 1.226024843 24.99999471 0.961911999 1.193109367 0.556808625 0.081826864 206.9036257 412613.8262 0.084907979 0.021813244 16.82770318 -1.226024843 0.231197368 INISEGNCPER ddPTM_BT-474_Pertuzumab_2h_R1 5 INISEGNCPER 11 0 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;F8VXH9;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;Q15365 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15365 PCBP2;PCBP3;PCBP1 Poly(rC)-binding protein 3;Poly(rC)-binding protein 2;Poly(rC)-binding protein 1 0 ;;;; 248.11 8.01E-16 4012590000 1414728 1517813 1290006 1406831 1372914 1455993 1428330 1536461 1517168 1438110 FALSE TRUE 1359438.866 1474526.459 1523138.78 1479437.717 1417075.026 1485434.176 1445810.33 1504732.543 1344945.449 1340705.529 1.013972745 1.099813813 1.136072573 1.103477001 1.05696217 1.107949616 1.078395143 1.122343804 1.003162455 1 20.35456097 1.226065941 24.97417415 1.001581116 1.092573254 0.533889195 0.032921782 182.6365444 365039.8489 0.029999026 0.007706231 16.82929567 -1.226065941 0.090992138 IFFDT(ph)DDDDDMPHSTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFFDTDDDDDMPHSTSR 17 0 Q8NG27-3;Q8NG27 Q8NG27-3 PJA1 E3 ubiquitin-protein ligase Praja-1 1 IFFDT(1)DDDDDMPHSTSR;IFFDT(1)DDDDDMPHSTSR 245.03 5.51E-20 63682000 24868 30141 23357 29170 29825 26493 24776 31996 23450 23728 TRUE FALSE 23896.13107 29281.40819 27578.12947 30675.4672 30784.34821 27028.70661 25079.2161 31335.27142 20788.05431 22120.88143 1.080252211 1.323699885 1.246701203 1.386719932 1.391642025 1.221863907 1.133734937 1.416547145 0.939748011 1 14.43312125 1.226342086 24.99701934 0.969873729 1.281235432 0.570319074 0.105883221 172.5204949 352936.5771 0.096434047 0.024821697 16.83999994 -1.226342086 0.311361703 LASALAPSIYEHEDIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LASALAPSIYEHEDIKK 17 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 166.92 1.48E-09 1013700000 609850 540530 478670 470210 478760 521790 530240 486970 736900 687530 FALSE TRUE 586016.3878 525114.6136 565176.317 494477.5945 494159.7502 532340.9513 536729.2357 476913.8993 653250.2013 640962.9807 0.914274935 0.81925888 0.881761247 0.771460458 0.770964572 0.830533069 0.837379462 0.744058415 1.019169938 1 19.28988151 1.226593837 24.99794486 1.009585161 0.817350256 0.703009176 0.048923137 132.2754524 276307.4972 0.045946264 0.01184713 16.84976455 -1.226593837 -0.192234906 AADAEAEVASLNRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AADAEAEVASLNRR 14 1 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 J3KN67 TPM3 Tropomyosin alpha-3 chain 0 95.428 0.0060483 288760000 84186 90204 63628 70968 70615 91984 71397 88374 71895 70383 FALSE TRUE 80895.91805 87631.47024 75126.995 74630.66698 72886.39561 93843.9795 72270.77784 86549.04602 63733.78101 65615.89672 1.232870723 1.335521948 1.144951129 1.137386986 1.110803925 1.43020189 1.101421781 1.319025577 0.971316163 1 16.00175776 1.226710668 24.99777778 0.985657849 1.225815274 0.466814236 0.102965396 209.6764055 442304.1415 0.091368711 0.023581615 16.854298 -1.226710668 0.240157425 RQEIEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQEIEQK 7 1 Q9H307 Q9H307 PNN Pinin 0 101.72 0.014192 173100000 166830 152770 135510 143670 150140 143950 144160 157520 176640 170230 FALSE TRUE 160310.0992 148413.1492 159999.6714 151084.8259 154969.3895 146860.7676 145924.2732 154267.157 156588.5677 158700.1705 1.010144467 0.93517952 1.008188403 0.952014264 0.976491638 0.925397668 0.919496638 0.972066737 0.986694389 1 17.27594415 1.226784562 3.21162387 0.997209689 0.959840611 0.157604121 0.029528228 0.415717369 7.54250472 0.026141743 0.007391388 16.85716594 -1.226784562 -0.037369077 KVDWLTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVDWLTEK 8 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3QL52;Q14240;Q14240-2;E7EQG2;P38919;I3L3H2;J3KTN0 P60842;Q14240;P38919;J3KTN0 EIF4A1;EIF4A2;EIF4A3 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed;Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 160.36 0.00056729 7354800000 19935600 19263900 18947700 17393300 18160600 12623300 22271000 20467400 24230000 25755000 FALSE TRUE 19156494.71 18714512.43 22371970.88 18290970.3 18744752.19 12878551.77 22543559.16 20044741.04 21479511.98 24010590.91 0.797835205 0.7794274 0.931754281 0.761787595 0.780686834 0.536369631 0.938900639 0.834829143 0.894584896 1 24.51716757 1.22681912 1.151404845 0.989592927 0.782302414 0.304745071 0.102804035 0.560305384 1.512197663 0.096133093 0.031383261 16.85850737 -1.22681912 -0.207290514 S(ph)GSNIEQYIHDLDSNSFELDLQFSEDEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSNIEQYIHDLDSNSFELDLQFSEDEKR 29 1 E9PER6;O15530-5;O15530-2;O15530;O15530-3;O15530-4 E9PER6 PDPK1 3-phosphoinositide-dependent protein kinase 1 1 S(0.5)GS(0.5)NIEQYIHDLDSNSFELDLQFSEDEKR 252.18 3.53E-58 39027000 23513 24720 20228 19775 25193 22602 25153 20984 33602 29857 TRUE FALSE 22594.08597 24015.0098 23883.64957 20795.59012 26003.35572 23059.02793 25460.82994 20550.67307 29787.64183 27834.7588 0.811721996 0.862770537 0.85805125 0.747108688 0.934204457 0.828425642 0.914713511 0.738309723 1.070159869 1 14.76459996 1.226896811 24.99993805 1.035080065 0.837375399 0.625667161 0.061311493 148.5002554 318282.1169 0.053540094 0.013833344 16.86152345 -1.226896811 -0.197704666 FKEIAEAYDVLSDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FKEIAEAYDVLSDPR 15 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 117.18 0.00035622 1996510000 3672400 3897600 2979000 3483200 3294200 3957700 3399800 3913400 4518900 4505700 FALSE TRUE 3528878.548 3786444.264 3517371.567 3662968.369 3400160.935 4037727.406 3441407.769 3832586.922 4005933.417 4200524.926 0.84010418 0.901421687 0.837364765 0.872026338 0.809460959 0.96124353 0.819280407 0.912406661 0.953674478 1 22.0021382 1.226958186 1.838144506 0.997702986 0.865014871 0.543303467 0.042164641 0.227989933 1.371861559 0.035799101 0.010509251 16.86390651 -1.226958186 -0.132688115 LKPGGVGAPSSS(ph)SPSPSPSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPS(0.015)S(0.032)S(0.4)S(0.4)PS(0.133)PS(0.016)PS(0.004)AR 80.944 0.003533 145640000 50054 47405 45332 44919 39017 44843 48518 52598 58498 61896 TRUE FALSE 48097.83434 46053.05581 53524.5008 47237.27497 40272.01724 45749.75618 49111.7778 51511.83292 51857.55228 57703.72879 0.833530785 0.798094972 0.927574386 0.818617375 0.697910137 0.792838819 0.851102326 0.892695048 0.898686331 1 15.81637693 1.226997138 1.073780329 0.991817825 0.813317593 0.529329537 0.054475033 0.390533095 0.93483947 0.054516688 0.018242113 16.86541909 -1.226997138 -0.178500232 ELWTILLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELWTILLGR 9 0 Q5SRE5;Q5SRE5-2;H7C4K7 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 0 100.02 0.010523 0 52764 56840 51981 47967 55349 52794 54791 60205 54125 54435 FALSE TRUE 50701.92455 55218.97885 61375.12301 50442.58262 57129.35085 53861.53085 55461.54865 58961.74571 47980.95691 50748.06896 0.999090716 1.088100099 1.209408048 0.993980336 1.125744329 1.061351337 1.092879981 1.161852006 0.94547355 1 15.63106531 1.227118413 24.98706312 0.972736709 1.095559461 0.356086404 0.063727132 248.8802124 543477.9296 0.056684517 0.014665344 16.87012937 -1.227118413 0.122822752 GDQCCYSHSPPTPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDQCCYSHSPPTPR 14 0 Q9NXH9-2;Q9NXH9 Q9NXH9-2 TRMT1 tRNA (guanine(26)-N(2))-dimethyltransferase 0 105.14 0.0010172 54683000 27245 23599 20320 24060 22534 26926 23212 22744 31633 27596 FALSE TRUE 26180.23528 22925.97963 23992.27602 25301.73948 23258.82657 27470.46217 23496.0754 22274.32845 28042.15446 25726.89834 1.017621127 0.891128784 0.932575536 0.98347415 0.904066486 1.067772018 0.913288306 0.865799218 1.089993597 1 14.65098991 1.227221099 24.99955922 1.044996797 0.942963281 0.286442898 0.061631303 298.4514015 657957.0621 0.056272938 0.014568649 16.87411866 -1.227221099 -0.102033516 ERESSANNSVSPS(ph)ESLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERESSANNSVSPSESLR 17 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 ERESSANNS(0.015)VS(0.399)PS(0.421)ES(0.164)LR 296.75 9.51E-46 761290000 371580 440710 332870 471140 387400 418050 409250 445640 411740 387650 TRUE FALSE 357058.2428 428141.3823 393027.0137 495455.5919 399861.0728 426503.2574 414258.5239 436437.3783 365001.0014 361394.1202 0.988002358 1.184693824 1.087530183 1.370956427 1.10644045 1.180161031 1.146279092 1.207649361 1.009980464 1 18.46321351 1.227749762 24.7610834 1.004990025 1.164869147 0.304505996 0.092736974 236.7304971 542185.2161 0.080344345 0.020907158 16.8946719 -1.227749762 0.159879122 IQQQFSDLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQQQFSDLKR 10 1 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 97.452 0.0096995 587450000 799130 791870 699910 728560 767290 778490 796830 826130 943910 924030 FALSE TRUE 767899.1161 769286.6429 826399.3064 766161.0689 791970.5797 794231.6012 806581.8439 809070.1268 836761.294 861444.6251 0.891408564 0.893019262 0.959317967 0.889390968 0.919351699 0.921976385 0.93631305 0.93920155 0.971346584 1 19.71639854 1.227889626 0.594344345 1.002263868 0.908213081 0.699990779 0.019156383 0.414939012 0.363302274 0.018827763 0.008889613 16.90011369 -1.227889626 -0.094050788 SCSSSCAVHDLIFWR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCSSSCAVHDLIFWR 15 0 O95197-3;B7Z4M1;O95197-6;O95197-5 O95197-3 RTN3 Reticulon-3;Reticulon 0 ; 175.01 8.80E-07 1460720000 585520 743180 781840 769400 676570 800710 727430 802530 775180 739900 FALSE TRUE 562637.2311 721985.234 923135.8799 809108.8262 698332.4885 816900.9048 736332.5059 785957.4751 687184.8162 689785.914 0.815669354 1.046680165 1.338293319 1.172985429 1.012390184 1.184281801 1.067479766 1.139422333 0.996229123 1 19.39578914 1.227953873 24.50004082 0.998114422 1.10614347 0.08413842 0.127975488 449.0529611 1037202.918 0.117941045 0.030771788 16.90261398 -1.227953873 0.108029048 QADEEFQILANSWR ddPTM_BT-474_Pertuzumab_2h_R1 1 QADEEFQILANSWR 14 0 A0A087WU53;Q9H0U3;Q9H0U3-2 A0A087WU53 MAGT1 Magnesium transporter protein 1 0 131.36 4.88E-05 0 24986 40901 23425 44035 31704 31505 36523 38940 28622 27646 FALSE TRUE 24009.5195 39734.54353 27658.41859 46307.65163 32723.78795 32142.05269 36969.9794 38135.87539 25372.95055 25773.5118 0.931557938 1.541681391 1.073133487 1.79671486 1.269667409 1.247096358 1.434417618 1.479653828 0.984458414 1 14.65360151 1.227997486 24.82958019 0.992228803 1.36316154 0.272449827 0.2304814 253.6327227 596164.7579 0.195160754 0.050895303 16.90431147 -1.227997486 0.370932737 VVGSELVDTYTVYIIQVTDGSHEWTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVGSELVDTYTVYIIQVTDGSHEWTVK 27 0 Q9Y2I1;C9J715;Q9Y2I1-4;Q9Y2I1-3 Q9Y2I1 NISCH Nischarin 0 ; 286.42 1.36E-61 142733000 180117 186892 160429 158039 178115 176538 187388 172396 232749 213793 FALSE TRUE 173077.8285 181562.0231 189422.089 166195.4117 183844.2307 180107.7193 189681.3104 168835.9624 206328.3093 199312.6097 0.868373701 0.910940976 0.950376844 0.833842936 0.922391368 0.903644379 0.951677421 0.847091223 1.035199477 1 17.60467346 1.228002412 24.99999783 1.01759982 0.899511437 0.607809849 0.038247997 147.4014432 349009.3373 0.033288489 0.008670101 16.9045032 -1.228002412 -0.118088383 SLS(ph)PIIGK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLSPIIGK 8 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 S(0.037)LS(0.963)PIIGK;S(0.002)LS(0.998)PIIGK;S(0.001)LS(0.999)PIIGK;SLS(1)PIIGK 126.29 0.0012853 1033043000 2283140 2538710 2017020 2449160 1969220 2404160 2289490 2573410 2422760 2545100 TRUE FALSE 2193912.365 2466308.476 2381540.382 2575561.441 2032561.75 2452773.762 2317509.463 2520268.184 2147738.442 2372718.11 0.924640966 1.039444368 1.003718213 1.085489857 0.856638528 1.03374006 0.976731898 1.062186095 0.905180617 1 21.17810928 1.228177098 24.99803555 0.952590372 1.000786815 0.066203746 0.067219284 620.1367127 1492911.544 0.05763215 0.015051133 16.91130407 -1.228177098 0.048196443 NSNSLFTLDELIDQDDCISHSEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSNSLFTLDELIDQDDCISHSEPK 24 0 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 0 ; 202.17 1.34E-24 79577000 63990 60776 50528 55070 57414 58368 53919 56280 74900 69382 FALSE TRUE 61489.20006 59042.72799 59659.53359 57912.1693 59260.77345 59548.24095 54578.87685 55117.79833 66397.66601 64682.69534 0.95062829 0.912805623 0.92234149 0.895327089 0.916176624 0.920620896 0.843794102 0.852125875 1.026513593 1 15.98109218 1.228231541 24.99697617 1.013256884 0.898519113 0.669227178 0.03129872 145.80504 352844.8872 0.03239645 0.00845413 16.9134242 -1.228231541 -0.11473777 EFCPNEQNWR ddPTM_BT-474_Pertuzumab_2h_R1 3 EFCPNEQNWR 10 0 Q8WW22-3;Q8WW22;Q8WW22-2 Q8WW22-3 DNAJA4 DnaJ homolog subfamily A member 4 0 ;; 193.01 1.44E-06 556052000 447457 436123 373161 408059 454448 381558 419647 473665 429516 451226 FALSE TRUE 429969.8858 423685.199 440599.4936 429118.9739 469065.7326 389273.3642 424782.7655 463883.6522 380759.1444 420664.0611 1.022121749 1.00718183 1.047390387 1.020098966 1.115060154 0.92537823 1.009790959 1.102741344 0.905138279 1 18.68230904 1.2282329 24.99993212 0.952569169 1.032287468 0.251943479 0.054185267 315.7998847 764420.635 0.048471128 0.012658816 16.91347713 -1.2282329 0.079718299 SPS(ph)PLVSLQAVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSPLVSLQAVK 12 0 Q9UPZ3-2;Q9UPZ3 Q9UPZ3-2 HPS5 Hermansky-Pudlak syndrome 5 protein 1 S(0.005)PS(0.995)PLVSLQAVK;S(0.009)PS(0.991)PLVSLQAVK;S(0.027)PS(0.973)PLVSLQAVK 135.14 0.00013955 342270000 682473 656618 592158 536608 586636 533065 649618 599940 810240 766170 TRUE FALSE 655801.2006 637891.8975 699174.1231 564302.4032 605505.6797 543843.9395 657568.2194 587551.0293 718264.952 714276.6235 0.918133366 0.893060023 0.97885623 0.790033419 0.847718741 0.761391206 0.920607224 0.82258191 1.005583731 1 19.44612338 1.228242291 24.99118117 1.002792002 0.865093428 0.43770561 0.061751101 211.860524 513112.7319 0.056595328 0.014780736 16.91384284 -1.228242291 -0.137698574 MLDHEYTTK ddPTM_BT-474_Pertuzumab_2h_R1 2 MLDHEYTTK 9 0 P11387;E5RJ33;H0YBR3;H0YC03;E5RGE7;E5RGR4;E5RFE3;E5RGR2;E5RJ95;E5RFS0;E5RIC7;Q969P6-2;Q969P6 P11387;Q969P6-2 TOP1;TOP1MT "DNA topoisomerase 1;DNA topoisomerase I, mitochondrial" 0 ; 148.94 8.88E-05 495410000 1421450 1426040 892610 1593150 1347760 1241160 1334040 1552140 1141260 1195660 FALSE TRUE 1365898.163 1385370.735 1053924.483 1675372.662 1391111.924 1266257.106 1350366.381 1520087.767 1011708.949 1114676.883 1.225375876 1.24284513 0.945497748 1.503011938 1.247995671 1.135985795 1.211441989 1.363702603 0.907625308 1 20.08819414 1.228289041 24.96406831 0.953812469 1.236425734 0.402340343 0.136814793 219.9076057 534445.7367 0.122488121 0.032005449 16.91566366 -1.228289041 0.282613265 FYHDWNDKEIEVLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 FYHDWNDKEIEVLNK 15 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 277.41 8.48E-34 5315600000 7288400 6337400 5588900 5585500 6577800 6609600 7177300 6249300 8811600 8118800 FALSE TRUE 7003561.27 6156663.557 6598938.554 5873768.324 6789380.911 6743250.641 7265137.944 6120249.771 7811344.109 7568906.445 0.925306888 0.813415201 0.871848345 0.776039229 0.89700949 0.890914783 0.959866263 0.80860423 1.032030739 1 22.85165344 1.228531318 24.99905538 1.016015484 0.866592064 0.551058594 0.053474421 162.4951319 405021.7848 0.047539761 0.012452294 16.92510289 -1.228531318 -0.14942342 DIDFLKEEEHDCFLEEIMTK ddPTM_BT-474_Pertuzumab_2h_R1 3 DIDFLKEEEHDCFLEEIMTK 20 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;; 155.87 1.50E-08 448711000 947590 788455 619308 611252 744963 772974 763182 723482 1022620 955000 FALSE TRUE 910557.1352 765969.0354 731230.732 642798.789 768925.4115 788604.0639 772522.0496 708541.8439 906536.4648 890316.9994 1.022733628 0.860332933 0.821315029 0.721988673 0.863653521 0.885756494 0.867693249 0.795830973 1.01821763 1 19.76395958 1.228759862 24.99206059 1.009108955 0.848945202 0.420081411 0.072196577 208.9771339 532875.794 0.066772558 0.017517682 16.93401196 -1.228759862 -0.160163753 WLIS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 WLISPVK 7 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 WLIS(1)PVK;WLIS(1)PVK;WLIS(1)PVK;WLIS(1)PVK 117.89 0.0053807 1820422000 2854610 2896510 2320658 2503700 2747370 2228895 2836770 3055900 2448053 2601930 TRUE FALSE 2743048.685 2813904.371 2740052.523 2632916.257 2835741.651 2273964.784 2871487.24 2992794.597 2170160.287 2425698.964 1.130828156 1.160038576 1.129592981 1.085425808 1.169041045 0.937447234 1.183777246 1.233786485 0.89465359 1 21.20996909 1.228881222 24.99990574 0.947326731 1.131178248 0.464149289 0.077934739 198.6082461 512946.7399 0.072888433 0.01913318 16.93874469 -1.228881222 0.183851517 LDIDSPPITAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDIDSPPITAR 11 0 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 244.61 1.60E-15 5858300000 1498200 1531260 1161780 1515060 1366570 1483470 1372630 1548220 1483140 1440110 FALSE TRUE 1439648.688 1487589.964 1371739.49 1593252.428 1410526.965 1513466.78 1389428.657 1516248.716 1314780.165 1342570.067 1.072308048 1.108016632 1.021726555 1.186718271 1.050617022 1.127290722 1.034902156 1.129362819 0.979300967 1 20.35656595 1.229017483 24.99933159 0.989650406 1.091674792 0.425172085 0.047307646 188.3032317 493264.5753 0.038561866 0.01013944 16.9440601 -1.229017483 0.102024386 SRS(ph)SPSTDHYK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSSPSTDHYK 11 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.243)RS(0.713)S(0.039)PS(0.004)T(0.002)DHYK 124.96 0.00020479 197830000 225740 203260 190400 226240 194600 184540 222510 228180 220870 221320 TRUE FALSE 216917.8312 197463.2238 224809.5154 237916.2735 200859.4857 188271.5252 225233.1439 223468.0033 195797.7636 206329.7993 1.051316058 0.95702717 1.089563971 1.153087311 0.973487526 0.912478594 1.091617133 1.083062185 0.948955334 1 17.65459267 1.229081016 24.98598089 0.974477662 1.040080733 0.119866821 0.069832915 498.3390262 1313455.274 0.06644906 0.017496709 16.94653902 -1.229081016 0.065603071 LWLNGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LWLNGR 6 0 H0Y943 H0Y943 APBB2 0 109.94 0.067761 534770000 411930 412160 341340 459340 384540 301980 453770 391790 503980 450680 FALSE TRUE 395831.3202 400405.6003 403027.7311 483046.5924 396909.0783 308086.2425 459323.373 383699.3996 446770.3033 420155.0422 0.942107747 0.952994871 0.959235736 1.14968653 0.944672891 0.733267988 1.093223517 0.913232881 1.063346285 1 18.68056227 1.2292034 24.97889475 1.031673134 0.962962783 0.067429914 0.104859654 667.334787 1781373.058 0.093890301 0.024742201 16.95131521 -1.2292034 -0.068710351 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 44 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR;RNS(1)PMAQT(0.991)PPCHLPNIPGVT(0.008)S(0.001)PGT(0.001)LIEDSKVEVNNLNNLNNHDR 214.02 2.21E-36 186989000 51479 44658 40621 41734 45891 53743 41840 40860 69765 61347 TRUE FALSE 49467.14377 43384.39756 47962.11831 43887.89674 47367.12569 54829.72028 42352.05044 40016.22672 61845.56968 57191.91305 0.86493249 0.758575737 0.838617136 0.767379414 0.828213696 0.958697084 0.740525158 0.699683305 1.081369137 1 15.80352354 1.22927284 24.9999857 1.04068471 0.802552117 0.630188712 0.071514108 140.629002 378518.6501 0.068390527 0.018035052 16.95402582 -1.22927284 -0.238132593 DGLPRT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLPRTPSR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.99)PS(0.01)R;DGLPRT(0.992)PS(0.008)R 94.538 0.013991 961270000 449530 489580 379140 448700 458710 478760 450520 495390 461930 446610 TRUE FALSE 431961.8706 475617.6577 447659.0319 471857.4608 473464.8237 488440.8552 456033.5985 485160.0234 409493.643 416360.7069 1.037470307 1.142321189 1.075171179 1.133290085 1.137150591 1.173119478 1.095284908 1.165239696 0.983506936 1 18.6674744 1.229273653 24.99998839 0.991753358 1.122780679 0.628712272 0.03933459 126.9590778 341754.5181 0.03403517 0.008976075 16.95405755 -1.229273653 0.131027321 (ac)MNTAPSRPS(ph)PTRR ddPTM_BT-474_Pertuzumab_2h_R1 2 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNT(0.001)APS(0.139)RPS(0.43)PT(0.43)RR;MNT(0.001)APS(0.118)RPS(0.441)PT(0.441)RR 51.888 0.0048925 1949080000 90978 58082 71860 68842 85371 64614 72279 86602 66415 74404 TRUE FALSE 87422.47918 56425.55823 84846.70052 72394.94387 88117.03575 65920.53935 73163.57202 84813.63844 58875.84763 69364.55081 1.260333674 0.813463903 1.22319974 1.043687922 1.270346809 0.950349113 1.054768915 1.222723098 0.84878871 1 16.08191093 1.22928842 24.99890992 0.924394351 1.101059536 0.201497168 0.143540374 332.7704472 897155.239 0.120278 0.031730204 16.95463403 -1.22928842 0.176665185 ILHCLGLAEEIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILHCLGLAEEIQK 13 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 189.56 5.16E-06 1685690000 1457210 1425960 1135870 1213700 1313230 1278380 1369280 1351770 1612840 1535600 FALSE TRUE 1400260.622 1385293.017 1341146.976 1276339.202 1355471.236 1304229.719 1386037.658 1323855.477 1429757.165 1431592.444 0.978114007 0.967658793 0.936821776 0.891552067 0.946827598 0.91103423 0.968178942 0.924743269 0.998718015 1 20.4491894 1.22929957 24.94912423 0.999359069 0.939627182 0.45919827 0.025481471 186.1672684 501513.2071 0.023350153 0.006161073 16.95506934 -1.22929957 -0.059731887 LKTDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHK ddPTM_BT-474_Pertuzumab_2h_R1 3 LKTDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHK 37 1 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;; 207.85 9.38E-31 1131400000 356213 298353 342985 366897 345778 295826 385706 362900 542850 524840 FALSE TRUE 342291.8021 289844.2646 404970.0192 385832.5981 356900.2634 301807.8044 390426.3854 355405.9882 481227.9438 489292.1193 0.699565328 0.592374684 0.827665117 0.788552652 0.729421647 0.616825394 0.797941291 0.726367694 0.983518689 1 18.90033652 1.229302572 5.176992849 1.000283548 0.723249598 0.699491835 0.070645398 0.094829086 6.965985558 0.061117208 0.017684184 16.95518655 -1.229302572 -0.277033949 RFLT(ph)RMT(ph)RVSEFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFLTRMTRVSEFLK 14 3 E5RGY9;E9PDG8;O60641-3;O60641-4;O60641 E5RGY9 SNAP91 Clathrin coat assembly protein AP180 2 RFLT(0.988)RMT(0.989)RVS(0.023)EFLK 43.512 0.080262 0 95482 103400 84262 92044 86087 105930 97343 92730 126010 113200 TRUE FALSE 91750.45788 100451.1332 99490.0178 96794.40187 88856.06654 108071.9772 98534.31275 90815.09309 111705.8731 105532.8632 0.869401769 0.951846943 0.942739681 0.917196776 0.841975323 1.024059937 0.933683687 0.860538513 1.058493721 1 16.6873328 1.229322083 24.99946293 1.029246904 0.918546244 0.429806096 0.05139292 201.7231201 545842.5346 0.045930792 0.012121122 16.95594827 -1.229322083 -0.11070066 S(ph)PGAAGLTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGAAGLTSR 10 0 Q53T59;F6TR53 Q53T59 HS1BP3 HCLS1-binding protein 3 1 S(1)PGAAGLTSR 70.195 0.050491 0 65702 84965 61310 89002 72899 89809 71017 86713 70006 67783 TRUE FALSE 63134.2932 82541.88139 72390.08083 93595.40389 75243.86254 91624.99951 71886.12729 84922.34625 62059.21237 63191.99704 0.999086849 1.306207831 1.145557732 1.481127489 1.190718225 1.449946256 1.137582774 1.343878184 0.982073922 1 15.94745424 1.229347987 24.92244921 0.991036705 1.264314532 0.365136637 0.13987115 199.0918476 538572.3586 0.116046716 0.030631559 16.95695967 -1.229347987 0.273277827 DVS(ph)PDPSLSTPGSAGSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVSPDPSLSTPGSAGSAR 18 0 P23771;P23771-2 P23771 GATA3 Trans-acting T-cell-specific transcription factor GATA-3 1 DVS(0.432)PDPS(0.432)LS(0.093)T(0.025)PGS(0.008)AGS(0.008)AR 69.485 0.020689 0 114660 120550 91353 120020 103070 118630 109080 130360 103000 113220 TRUE FALSE 110178.9604 117112.032 107862.5192 126214.2466 106385.3402 121028.7799 110414.9537 127668.0204 91307.87181 105551.5086 1.043840699 1.109524948 1.021894625 1.19575976 1.00789976 1.146632403 1.04607651 1.209532883 0.86505511 1 16.68758767 1.229718551 24.99990818 0.932527541 1.100269077 0.450258124 0.072933564 171.9312682 486097.4216 0.060590439 0.016045717 16.97143444 -1.229718551 0.167741536 EPTPS(ph)IASDISLPIATQELR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 EPTPS(1)IASDISLPIATQELR;EPT(0.01)PS(0.99)IASDISLPIATQELR 162.77 2.16E-11 53658000 31186 47433 31957 49109 36602 38038 36275 44227 32907 31216 TRUE FALSE 29967.21664 46080.25728 37732.34078 51643.52138 37779.33657 38807.15442 36718.9443 43313.69699 29171.53532 29101.71252 1.02974066 1.583420813 1.296567711 1.774587023 1.298182592 1.333500714 1.261745139 1.488355607 1.002399268 1 14.82881643 1.229855871 24.7526832 1.001199207 1.394053462 0.39111146 0.190302983 170.0576652 483552.8336 0.160271989 0.042589169 16.9768015 -1.229855871 0.392854255 DSDLSHVQNK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSDLSHVQNK 10 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;; 164.97 6.00E-06 5178820000 7089260 7107820 6179710 6535370 6484040 6767140 7027500 7233750 8431120 8221620 FALSE TRUE 6812203.882 6905111.933 7296521.064 6872661.229 6692605.035 6903976.207 7113504.647 7084370.535 7474054.604 7664762.354 0.888769092 0.900890545 0.951956594 0.896656793 0.873165367 0.90074237 0.928078956 0.924277911 0.975118896 1 22.86980963 1.229984452 1.355466463 1.00120389 0.904025963 0.730510112 0.01999498 0.21245558 0.757230038 0.019481619 0.006068107 16.98182855 -1.229984452 -0.097177927 RFES(ph)IPDMLELDHLTVSGDVTFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFESIPDMLELDHLTVSGDVTFGK 24 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 1 RFES(0.995)IPDMLELDHLT(0.004)VS(0.001)GDVTFGK 84.641 0.0060173 74443000 112520 113750 87058 98126 97154 106630 100060 114040 96564 94783 TRUE FALSE 108122.594 110505.9614 102791.3172 103190.2946 100279.0466 108786.1317 101284.5642 111685.0341 85602.45955 88363.26299 1.223614773 1.250587152 1.163281139 1.167796334 1.134849973 1.231123976 1.146229335 1.263930624 0.968756208 1 16.43115907 1.230028521 24.99930133 0.984377938 1.197097453 0.800497137 0.042592633 83.96628186 246014.4174 0.038378965 0.010207262 16.98355182 -1.230028521 0.212719515 RDYS(ph)YER ddPTM_BT-474_Pertuzumab_2h_R1 1 RDYSYER 7 1 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 RDYS(1)YER 108.4 0.0044475 374440000 257290 238660 205410 239850 252180 227910 234480 248870 235110 221130 TRUE FALSE 247234.8224 231853.6505 242532.1563 252228.6872 260291.5987 232518.4964 237349.6364 243730.7475 208421.2985 206152.6681 1.199280245 1.124669657 1.176468675 1.223504355 1.262615716 1.127894674 1.151329442 1.18228277 1.011004613 1 17.65335361 1.230081404 6.739165892 1.002906406 1.180235326 0.757830466 0.039687333 0.069251826 14.47640508 0.034718123 0.010158679 16.98561999 -1.230081404 0.177328921 GWDLVDAVT(ph)PGPQPTLEQLEEGGPRPLER ddPTM_BT-474_Pertuzumab_2h_R1 1 GWDLVDAVTPGPQPTLEQLEEGGPRPLER 29 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 GWDLVDAVT(1)PGPQPTLEQLEEGGPRPLER 192.73 3.26E-18 56121000 49193 51092 43233 58032 51645 51260 39890 52703 35925 32268 TRUE FALSE 47270.48317 49634.90618 51046.16481 61027.03847 53306.20833 52296.51232 40378.18575 51614.66463 31846.94461 30082.45962 1.571363638 1.649961699 1.696874706 2.028658536 1.772002988 1.738438711 1.342250144 1.715772756 1.058654944 1 14.87663491 1.23027973 1.185579848 0.963520346 1.731447563 0.677596701 0.175922906 0.252237993 0.715174468 0.164372251 0.053185344 16.99337848 -1.23027973 0.767927217 QLLEELER ddPTM_BT-474_Pertuzumab_2h_R1 2 QLLEELER 8 0 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ; 154.28 0.00099468 175416000 197104 197634 171396 202574 201901 204351 197154 216859 201047 198727 FALSE TRUE 189400.9578 191997.6718 202371.0699 213028.8684 208395.329 208483.1172 199566.8296 212380.7859 178224.9874 185267.0433 1.022313275 1.036329335 1.092320935 1.149847618 1.124837561 1.125311407 1.077184728 1.146349519 0.9619897 1 17.49924674 1.230281837 24.99712912 0.98099478 1.099607231 0.553492282 0.041548677 153.5736093 463685.7275 0.040019237 0.010684191 16.99346092 -1.230281837 0.118612451 S(ph)IAEELELSILK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIAEELELSILK 12 0 Q9UBT7-3;Q9UBT7-2;Q9UBT7 Q9UBT7-3 CTNNAL1 Alpha-catulin 1 S(1)IAEELELSILK 201.95 1.49E-07 12352000 23948 23550 21842 24855 22359 23401 23941 27257 29799 31249 TRUE FALSE 23012.08568 22878.37706 25789.33527 26137.76953 23078.19754 23874.18425 24233.99712 26694.13342 26416.34245 29132.4774 0.789911732 0.785322056 0.885243466 0.897203804 0.792181085 0.819504086 0.831855005 0.916301524 0.906766084 1 14.83034077 1.230447635 1.000802592 0.994820757 0.828029364 0.66476244 0.038597835 0.311481985 0.659987881 0.038403412 0.013221915 16.99994963 -1.230447635 -0.166791393 LTPVS(ph)PESSSTEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 LTPVSPESSSTEEK 14 0 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 LTPVS(0.996)PES(0.003)SSTEEK;LTPVS(1)PESSSTEEK;LTPVS(0.999)PES(0.001)SSTEEK;LTPVS(1)PESSSTEEK;LTPVS(0.999)PES(0.001)SSTEEK 334.79 1.54E-68 4691690000 3258540 3032580 3048336 3036532 3030570 3395750 3661790 3686790 4326570 4663150 TRUE FALSE 3131192.654 2946093.788 3599238.125 3193247.78 3128051.036 3464414.392 3706604.081 3610656.498 3835435.912 4347310.697 0.72025969 0.677681903 0.82792291 0.734534061 0.719537032 0.796909776 0.852620008 0.830549448 0.882254842 1 22.05169178 1.230620108 0.329660188 1.025701223 0.701712821 0.819475562 0.038745591 0.5928405 0.213553654 0.07350456 0.051069216 17.00670224 -1.230620108 -0.323988401 AEITFDDHK ddPTM_BT-474_Pertuzumab_2h_R1 5 AEITFDDHK 9 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;; 202.36 2.00E-05 3374000000 3025422 2846805 2605066 2755395 2662428 2497068 2902686 2803562 3511245 3293624 FALSE TRUE 2907185.163 2765616.909 3075859.376 2897601.266 2748067.415 2547560.426 2938209.94 2745667.465 3112663.188 3070543.913 0.946798107 0.900692837 1.001731114 0.943676869 0.894977402 0.829677249 0.956902107 0.894195798 1.013717203 1 21.5500628 1.230639542 24.98650712 1.006858666 0.920417399 0.379633239 0.043853944 203.8902108 643132.4275 0.040021909 0.010722582 17.00746329 -1.230639542 -0.086441267 KLENEVEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLENEVEQR 9 1 P12270 P12270 TPR Nucleoprotein TPR 0 124.67 0.00083888 424540000 913770 914650 751580 790240 905990 873030 868310 913410 935270 882140 FALSE TRUE 878058.8582 888565.0775 887407.2248 831024.3811 935131.9911 890683.2648 878936.6375 894547.7643 829102.0706 822391.8721 1.067689125 1.080464323 1.079056415 1.010496832 1.137088076 1.083039966 1.068756474 1.087739063 1.008159369 1 19.64946648 1.230798652 22.82891868 1.004079447 1.077121244 0.502034219 0.028965058 50.61893121 148857.6165 0.024720093 0.006700426 17.01369536 -1.230798652 0.073041797 GLLS(ph)PPMGQSGLR ddPTM_BT-474_Pertuzumab_2h_R1 3 GLLSPPMGQSGLR 13 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR 185.27 9.23E-06 1579030000 407904 448282 358468 436895 427587 402745 454162 460236 419130 400326 TRUE FALSE 391962.6607 435497.4363 423251.1417 459443.2033 441340.7242 410888.7798 459720.1704 450731.9658 371552.1195 373211.5634 1.050242541 1.166891594 1.134078317 1.231052969 1.182548365 1.100954043 1.231795087 1.207711684 0.995553611 1 18.50963416 1.230900559 24.99988568 0.997776657 1.168456541 0.59695746 0.054217132 123.6983942 403694.0802 0.048644758 0.013074018 17.01768807 -1.230900559 0.170679883 IDLFER ddPTM_BT-474_Pertuzumab_2h_R1 3 IDLFER 6 0 Q9UHG3;F8W8W4 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 ;; 129.67 0.037443 956689000 335870 490323 418482 526229 310157 396958 470841 484034 441607 467694 FALSE TRUE 322743.8291 476339.4681 494111.0065 553387.7418 320133.4816 404984.7627 476603.293 474038.5288 391477.6247 436016.6688 0.740209841 1.092479949 1.1332388 1.269189417 0.734223034 0.928828624 1.093085029 1.087202767 0.897850135 1 18.73402376 1.230995422 24.98119878 0.948925116 1.020742623 0.018517304 0.162368542 864.5565255 2854751.935 0.145415488 0.03911318 17.02140567 -1.230995422 0.071817507 QSKLSPQMQVHQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSKLSPQMQVHQDK 14 1 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;J3KSK9 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 0 63.76 0.042915 292310000 392460 250120 256370 200840 287970 230210 303610 170890 504150 324080 FALSE TRUE 377122.2293 242986.8225 302701.7619 211205.3765 297232.8166 234865.0039 307325.67 167361.0618 446921.0056 302129.7729 1.248212732 0.804246533 1.00189319 0.699055159 0.983791878 0.777364646 1.017197567 0.553937668 1.479235235 1 18.20480883 1.231120571 24.99998498 1.239617467 0.871254757 0.305574085 0.212511077 202.158762 679263.6818 0.175122828 0.047240367 17.02631135 -1.231120571 -0.36836271 GKPELR ddPTM_BT-474_Pertuzumab_2h_R1 3 GKPELR 6 1 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32;B9ZVP7 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;; 100.82 0.033949 2504990000 8847300 8597400 7835600 7978000 8796000 8652800 8176200 9336600 8468400 8468000 FALSE TRUE 8501537.735 8352210.57 9251667.222 8389745.536 9078931.328 8827765.544 8276262.781 9143795.947 7507102.734 7894454.817 1.076899917 1.057984467 1.171919713 1.062739066 1.150039051 1.118223582 1.04836407 1.15825553 0.95093365 1 22.91240821 1.231195247 24.99997497 0.975466759 1.106378485 0.591203929 0.043264586 116.3702936 394974.2371 0.036052754 0.009728464 17.02923925 -1.231195247 0.130911726 RDSAS(ph)YR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSASYR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 RDS(0.054)AS(0.943)Y(0.003)R 76.815 0.042093 443030000 294080 313960 243460 293280 325790 266940 279090 330650 268770 284130 TRUE FALSE 282587.0285 305006.1682 287458.6377 308416.2159 336269.3312 272337.7097 282505.5869 323821.962 238260.3564 264885.622 1.066826604 1.151463661 1.085217973 1.164337323 1.269488803 1.028133228 1.066519144 1.222497316 0.899483915 1 18.01501001 1.231300544 24.9999495 0.949741895 1.134238059 0.490116623 0.074248436 147.1670429 506745.8159 0.065135126 0.017620196 17.03336858 -1.231300544 0.184496164 GYYSPYSVSGS(ph)GSTAGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYS(0.333)VS(0.049)GS(0.617)GSTAGSR 353.62 1.81E-90 570280000 327590 371040 276130 316370 336950 327490 308940 362980 324650 334270 TRUE FALSE 314787.4206 360458.3025 326032.8335 332697.8936 347788.3028 334112.0722 312720.9001 355484.3362 287797.093 311629.5952 1.010133266 1.156688287 1.046219096 1.06760686 1.116031045 1.072144871 1.00350193 1.140727138 0.923522982 1 18.24947273 1.231343698 24.99992134 0.961761464 1.078568478 0.449487619 0.050813883 147.7636555 511842.0359 0.041459163 0.011228115 17.03506121 -1.231343698 0.116807013 SQSGGYSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQSGGYSDR 9 0 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;Q14011-3;F6WMK9 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ;;; 179.37 0.00011604 1021564000 912083 982736 738503 989562 966699 920647 930547 963644 915796 859571 FALSE TRUE 876437.788 954709.3315 871966.92 1040633.413 997793.7513 939263.1131 941935.3125 943744.4146 811838.6774 801351.4905 1.093699579 1.191374001 1.088120419 1.298597963 1.245138698 1.172098791 1.175433407 1.177690971 1.013086875 1 19.61207565 1.231365856 5.129962491 1.000822993 1.183588914 0.583483449 0.058722652 0.118457278 8.464528614 0.050067093 0.014572784 17.03593034 -1.231365856 0.182765921 DRDFTAEDYEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DRDFTAEDYEK 11 1 A0A087WZV0;O43314-2;O43314 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 0 79.646 0.024238 129130000 222670 198320 162810 173650 187490 202990 179800 192750 242760 230770 FALSE TRUE 213967.8102 192664.1078 192233.3887 182612.0973 193520.7861 207094.5969 182000.4462 188769.6451 215202.9025 215139.7424 0.994552693 0.895530067 0.893528023 0.848806898 0.899512029 0.962605024 0.845963857 0.877428052 1.000293577 1 17.71491453 1.231448681 24.88818457 1.000146882 0.898089056 0.443525769 0.043668765 147.2671759 515337.2762 0.038636596 0.010469917 17.0391796 -1.231448681 -0.102057826 MVEINFLCVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 MVEINFLCVHK 11 0 P30419;P30419-2;Q5VUC6;O60551 P30419;O60551 NMT1;NMT2 Glycylpeptide N-tetradecanoyltransferase 1;Glycylpeptide N-tetradecanoyltransferase;Glycylpeptide N-tetradecanoyltransferase 2 0 ; 134.3 0.0013408 97081000 324140 286050 270890 286930 292670 279630 298300 284980 391690 352270 FALSE TRUE 311472.2504 277892.1341 319845.8489 301738.4917 302083.9963 285284.3102 301950.6846 279095.0634 347226.9933 328410.4391 0.94842372 0.846173267 0.973921078 0.918784715 0.919836766 0.868682223 0.919430836 0.849836151 1.057295847 1 18.32514046 1.231471342 24.9999068 1.028647976 0.903642648 0.59080437 0.040922768 113.6806685 400870.7732 0.034638341 0.00938381 17.04006873 -1.231471342 -0.125005328 RT(ph)GTPSDPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RTGTPSDPR 9 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 RT(0.499)GT(0.499)PS(0.001)DPR;RT(0.498)GT(0.498)PS(0.004)DPR;RT(0.499)GT(0.499)PS(0.002)DPR 67.153 0.036159 3517960000 2633056 3135385 2369590 2948387 2246102 2727792 2608651 3010679 2497630 2530232 TRUE FALSE 2530153.261 3045966.89 2797827.624 3100553.606 2318349.911 2782949.823 2640576.451 2948507.427 2214109.513 2358857.133 1.072618271 1.291289263 1.186094565 1.314430435 0.982827607 1.179787357 1.119430429 1.249972873 0.938636547 1 21.16965661 1.231606357 24.9999697 0.969318153 1.178058958 0.424570438 0.095504217 156.2520269 561687.8592 0.080544009 0.021870427 17.04536702 -1.231606357 0.208740805 LPDS(ph)DDDEDEETAIQR ddPTM_BT-474_Pertuzumab_2h_R1 6 LPDSDDDEDEETAIQR 16 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;H3BRM1;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR 495.38 9.57E-258 12588280000 533114 536291 436451 534015 501623 586928 506884 559524 553995 533384 TRUE FALSE 512279.3155 520996.5058 515327.4045 561575.5781 517758.1594 598796.0863 513087.398 547969.6339 491107.8101 497257.4266 1.030209481 1.047740019 1.036339282 1.129345784 1.041227605 1.204197372 1.03183456 1.101983811 0.987632932 1 18.92363339 1.231611033 24.96529394 0.993816404 1.079006606 0.289998984 0.052576519 208.4989908 748965.8638 0.044467391 0.012056999 17.04555055 -1.231611033 0.085190203 LGLALNYSVFYYEIQNAPEQACHLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGLALNYSVFYYEIQNAPEQACHLAK 26 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 321.7 2.91E-82 1447780000 525300 530840 436880 445830 532830 541860 497060 464620 714900 606200 FALSE TRUE 504770.6953 515700.9629 515833.9343 468839.3397 549968.9609 552816.7805 503143.169 455025.4346 633747.5491 565141.5341 0.893175718 0.912516479 0.912751768 0.829596325 0.973152613 0.97819174 0.890295862 0.805153059 1.121396165 1 19.1082527 1.231621472 24.99986687 1.060698105 0.897933842 0.555915755 0.057670838 132.1588546 476111.7008 0.053200498 0.014451624 17.04596027 -1.231621472 -0.162764263 MEREDS(ph)S(ph)EEEEEEIDDEEIER ddPTM_BT-474_Pertuzumab_2h_R1 3 MEREDSSEEEEEEIDDEEIER 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER 149.94 6.47E-09 974980000 250854 239694 184408 233613 229878 219397 217622 249092 231710 236671 TRUE FALSE 241050.3483 232858.1618 217734.6277 245669.7949 237272.2346 223833.3577 220285.3231 243948.1632 205407.2522 220641.0624 1.092499944 1.055370924 0.986827318 1.113436422 1.075376596 1.014468274 0.998387702 1.105633559 0.930956595 1 17.75134178 1.231751399 24.99949966 0.965478288 1.053984802 0.395469037 0.044374846 172.8078282 634422.1314 0.038409326 0.010462518 17.05106065 -1.231751399 0.088506514 FDEATQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDEATQLR 8 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 99.442 0.015844 281219000 335890 377110 313670 389410 373680 339130 372070 391870 369880 361150 FALSE TRUE 322763.0475 366355.192 370357.1466 409507.4968 385699.7566 345987.441 376623.504 383777.7476 327892.7731 336688.9888 0.95863856 1.088111593 1.099997799 1.216278258 1.145566886 1.027617334 1.118609507 1.139858327 0.973874359 1 18.36105701 1.231950931 24.99892359 0.986937105 1.10466589 0.315002027 0.06592475 196.7919493 744265.1908 0.059369115 0.016182327 17.05889637 -1.231950931 0.117728785 KPSPS(ph)ESPEPWKPFPAVSPEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.394)PS(0.603)ES(0.002)PEPWKPFPAVSPEPR 183.47 2.22E-17 3570800000 892990 810920 639160 593770 808030 760960 738040 763640 955950 910540 TRUE FALSE 858090.9635 787793.3556 754670.43 624414.5409 834021.0188 776347.1326 747072.3543 747870.5671 847434.5637 848868.3148 1.01086464 0.928051315 0.889031216 0.735584696 0.982509306 0.914567217 0.880080386 0.881020712 0.998310985 1 19.69518124 1.232006895 24.62506872 0.999155598 0.898641369 0.234737619 0.069341713 194.8323695 732025.0913 0.060932237 0.016663688 17.06109477 -1.232006895 -0.100514229 RLEIS(ph)PDS(ph)SPER ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEISPDSSPER 12 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 RLEIS(0.999)PDS(0.843)S(0.158)PER;RLEIS(1)PDS(0.732)S(0.268)PER 126.77 0.0001882 501750000 457220 563180 398430 560950 476480 495440 505570 549020 507790 512930 TRUE FALSE 439351.3369 547118.6578 470435.164 589900.6967 491806.4119 505458.1363 511757.3169 537682.5451 450147.808 478188.7942 0.918782168 1.144147802 0.983785421 1.233614639 1.028477492 1.057026309 1.070199308 1.124414774 0.94136001 1 18.8672208 1.232043294 24.99957821 0.970679972 1.075634893 0.183090694 0.083300171 245.7984022 942806.1075 0.066870951 0.018275134 17.06252474 -1.232043294 0.104954921 DEVQEVVFVPAGTHT(ph)PGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEVQEVVFVPAGTHTPGSR 19 0 J3KS57;J3KT79;J3QR84;J3QRJ1;J3QL71;Q96FV2-2;Q96FV2 J3KS57 SCRN2 Secernin-2 1 DEVQEVVFVPAGT(0.044)HT(0.956)PGSR;DEVQEVVFVPAGTHT(1)PGSR 167.51 6.56E-11 237680000 271800 267930 218500 249850 251460 254070 250250 286590 250320 267700 TRUE FALSE 261177.7555 260288.8987 257987.8105 262744.7884 259548.4393 259207.4695 253312.6344 280671.8163 221904.723 249568.4406 1.04651756 1.042955985 1.033735716 1.052796531 1.039989025 1.038622788 1.015002673 1.124628642 0.889153783 1 17.92907598 1.232163536 24.99999992 0.944576906 1.050009181 0.564999361 0.036744495 112.0255417 437779.0374 0.0310313 0.008499626 17.06724943 -1.232163536 0.105432275 KRQS(ph)PEPSPVTLGR ddPTM_BT-474_Pertuzumab_2h_R1 7 KRQSPEPSPVTLGR 14 2 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 KRQS(0.999)PEPS(0.001)PVTLGR;KRQS(0.926)PEPS(0.074)PVTLGR;KRQS(0.998)PEPS(0.002)PVTLGR;KRQS(0.95)PEPS(0.048)PVT(0.002)LGR;KRQS(1)PEPSPVTLGR;KRQS(0.998)PEPS(0.002)PVTLGR;KRQS(0.999)PEPSPVTLGR 144.3 7.00E-06 6015010000 2988960 2879320 2093590 2540380 2663630 2786850 2663270 2833840 2831870 2706850 TRUE FALSE 2872148.139 2797204.613 2471948.285 2671489.316 2749308.078 2843202.016 2695863.895 2775320.214 2510407.99 2523512.638 1.138154846 1.108456748 0.979566437 1.058639166 1.089476643 1.126684279 1.068298155 1.099784551 0.994806981 1 21.26700188 1.232178551 24.81701609 0.997403418 1.081941558 0.404737149 0.041789169 155.8535361 606013.5831 0.038022832 0.01044463 17.06783952 -1.232178551 0.08453814 QSQQEAEEEEREEEEEAQIIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSQQEAEEEEREEEEEAQIIQR 22 1 Q9NQZ2 Q9NQZ2 UTP3 Something about silencing protein 10 0 ; 256.76 3.67E-37 549810000 74196 92681 76784 90972 88600 99264 75273 95478 84219 84584 FALSE TRUE 71296.33829 90037.82862 90660.57685 95667.07582 91449.89946 101271.1861 76194.21349 93506.34593 74658.81219 78855.05034 0.904144224 1.141814357 1.149711736 1.213201633 1.159721528 1.284270134 0.966256608 1.185800345 0.946785423 1 16.26691554 1.232274357 24.99983824 0.97339263 1.130986456 0.243343697 0.107033925 214.4251456 852706.828 0.089958701 0.024693366 17.07160513 -1.232274357 0.157593826 YDAFGEDSSSAMGVENR ddPTM_BT-474_Pertuzumab_2h_R1 1 YDAFGEDSSSAMGVENR 17 0 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 0 126.1 0.00010406 62189000 80921 65393 69499 47820 69429 72985 65505 72756 64046 60070 FALSE TRUE 77758.51786 63528.05567 82059.0153 50287.99593 71662.24684 74460.80671 66306.66978 71253.56317 56775.76658 56001.4054 1.388510115 1.134401096 1.465302785 0.897977391 1.279650865 1.329623894 1.18401796 1.272353125 1.013827531 1 15.77317541 1.232293156 24.31269288 1.006913469 1.238969517 0.294527674 0.14659545 135.8791352 527065.386 0.118424151 0.03260137 17.07234413 -1.232293156 0.232056048 LSIAEVVHQLQEIAAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSIAEVVHQLQEIAAAR 17 0 O14976-2;O14976 O14976-2 GAK Cyclin-G-associated kinase 0 ; 227.22 1.82E-15 291570000 288290 316380 269526 289520 306012 302726 297365 317610 320790 307226 FALSE TRUE 277023.3081 307357.1522 318235.3438 304462.1619 315855.1539 308847.3271 301004.2418 311051.2425 284375.2641 286417.3094 0.967201698 1.073109558 1.111089775 1.063001962 1.102779558 1.078312368 1.050928949 1.086007138 0.992870384 1 18.12775916 1.232465581 24.99631327 0.996435139 1.06971845 0.355952992 0.037534729 159.2974856 653261.5573 0.031822045 0.008760067 17.07912357 -1.232465581 0.073283312 PCSEETPAISPSKR ddPTM_BT-474_Pertuzumab_2h_R1 1 PCSEETPAISPSKR 14 1 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 90.861 0.0090902 0 72060 55646 58011 64971 59408 58174 60490 56210 86902 71818 FALSE TRUE 69243.81553 54059.03056 68494.87815 68324.1611 61318.91227 59350.31814 61230.29471 55049.24386 77037.24928 66953.70289 1.034204421 0.807409123 1.023018522 1.020468744 0.915840493 0.886438174 0.914516928 0.822198646 1.150604761 1 16.03087623 1.232735246 24.99985928 1.075302368 0.922829173 0.335881647 0.082587725 163.94092 703524.5957 0.070846334 0.019584002 17.08973174 -1.232735246 -0.152473195 RPS(ph)TYGIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSTYGIPR 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 RPS(0.5)T(0.5)YGIPR;RPS(0.5)T(0.5)YGIPR 128.08 0.00026177 318580000 122117 138873 104966 155647 141306 141665 115500 151211 101101 103478 TRUE FALSE 117344.5326 134912.478 123935.6912 163679.9603 145851.2358 144529.5634 116913.5235 148088.44 89624.43833 96469.34289 1.216391955 1.398501057 1.284715822 1.696704418 1.511892084 1.498191643 1.211924121 1.535082914 0.929045805 1 16.55778292 1.232798864 24.99992118 0.964522596 1.424085247 0.610836035 0.145116541 95.72480793 415323.4137 0.125371536 0.034698571 17.09223534 -1.232798864 0.45956265 EGATVYATGTHAQVEDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGATVYATGTHAQVEDGR 18 0 J3QKT4;J3KQ22;E2QRB3;P32322-2;P32322;P32322-3;J3QR88;J3QLK9;J3QL23;J3QL32;J3QL24 J3QKT4 PYCR1 "Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 1, mitochondrial" 0 253.26 1.68E-30 1350800000 483180 747390 454470 966000 484790 620520 772910 712550 581810 541890 FALSE TRUE 464296.7914 726075.169 536602.8386 1015855.376 500383.7106 633067.3396 782369.1038 697835.5935 515765.3679 505187.3076 0.919058702 1.437239531 1.062185907 2.010848967 0.990491453 1.253133897 1.548671338 1.381340313 1.020938888 1 18.94645887 1.232980383 23.3162524 1.010468749 1.342432126 0.14945896 0.298271124 106.8302713 446319.095 0.240855777 0.067302415 17.09938075 -1.232980383 0.331963377 S(ph)TNTAVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 STNTAVSR 8 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 S(0.963)T(0.036)NT(0.001)AVSR;S(0.984)T(0.015)NT(0.001)AVSR 89.032 0.014888 933840000 385540 378300 359260 387670 419620 406700 383060 429970 333420 316530 TRUE FALSE 370472.6706 367511.2544 424186.2737 407677.6952 433117.4584 414923.7527 387748.0029 421090.9692 295571.5594 295091.1412 1.255451686 1.245416087 1.437475459 1.38153146 1.467741311 1.406086781 1.313994047 1.426986143 1.001628033 1 18.17080109 1.233122229 24.99223545 1.000813723 1.370430331 0.80897157 0.071128556 58.23456488 267604.025 0.064552806 0.017957072 17.10496656 -1.233122229 0.369616608 DLHEEMNYITAIIEEQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLHEEMNYITAIIEEQPK 18 0 P49354;P49354-2;E9PQP6;H0YCW1;E9PN85 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 104.45 0.00050625 17708000 21504 18046 17124 16771 20291 20335 20621 17553 28099 23189 FALSE TRUE 20663.59991 17531.34575 20218.68772 17636.55332 20943.67844 20746.18763 20873.36597 17190.52442 24909.31932 21618.38838 0.955834429 0.810946008 0.935254163 0.815812586 0.968789999 0.959654683 0.96553756 0.795180664 1.15222832 1 14.39997136 1.233192709 24.99999951 1.076114168 0.898517656 0.473530678 0.073876008 114.5753814 533584.1688 0.061288464 0.017089292 17.10774268 -1.233192709 -0.177596511 TIPGTALVEMGDEYAVER ddPTM_BT-474_Pertuzumab_2h_R1 1 TIPGTALVEMGDEYAVER 18 0 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;B7WPG3;Q8WVV9-5 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 0 121.45 8.89E-05 16659000 8899.8 10569 9889.5 9607.9 7338.2 10718 8617.5 10512 7823.6 7623 FALSE TRUE 8551.985977 10267.58247 11676.75264 10103.76487 7574.239867 10934.7253 8722.963543 10294.92353 6935.497727 7106.68742 1.203371623 1.444777554 1.643065461 1.421726365 1.06579049 1.538652913 1.22743031 1.448624784 0.975911464 1 12.79496153 1.233341608 24.99165452 0.987955448 1.378387944 0.480021226 0.160743378 112.0778291 536664.5803 0.135897494 0.03799224 17.11360911 -1.233341608 0.390432496 ILELT(ph)PEPDRPR ddPTM_BT-474_Pertuzumab_2h_R1 6 ILELTPEPDRPR 12 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR 202.25 2.25E-07 11988020000 3147410 3256720 2721370 3275250 3012020 3252290 3066350 3421460 3261270 3300790 TRUE FALSE 3024405.738 3163841.534 3213182.096 3444286.045 3108904.359 3318053.532 3103876.909 3350805.655 2891064.302 3077224.553 0.982835567 1.028147761 1.044181872 1.119283297 1.010294928 1.07826175 1.008661167 1.088905147 0.939503846 1 21.55319829 1.233347297 24.99999279 0.969751915 1.047132299 0.346035434 0.041339923 141.7481784 679701.5246 0.033894751 0.009452577 17.11383327 -1.233347297 0.077380384 GFENVIHDKLPLQES(ph)EEEEREER ddPTM_BT-474_Pertuzumab_2h_R1 2 GFENVIHDKLPLQESEEEEREER 23 2 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5;C9JBL0 P23497 SP100 Nuclear autoantigen Sp-100 1 GFENVIHDKLPLQES(1)EEEEREER;GFENVIHDKLPLQES(1)EEEEREER 211.87 2.13E-25 380850000 459450 438520 338260 357500 414410 434070 393420 392020 429690 366390 TRUE FALSE 441494.1861 426013.839 399391.1066 375950.6178 427739.874 442847.1928 398234.7916 383924.65 380913.3926 341574.079 1.292528366 1.247207751 1.169266438 1.100641533 1.252260931 1.296489459 1.165881184 1.12398649 1.115170665 1 18.38183897 1.233426128 0.99960341 1.007243906 1.219863283 0.594293494 0.057745113 0.369068116 0.779882154 0.058020337 0.019997247 17.11694 -1.233426128 0.212619377 RVEDVLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVEDVLGK 8 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 97.565 0.013054 1242510000 1821640 1819390 1649090 1607320 1702840 1754660 1745050 1800250 2149000 2047700 FALSE TRUE 1750448.295 1767502.779 1947117.247 1690273.978 1757613.395 1790140.427 1766406.444 1763074.208 1905054.529 1909007.455 0.916941571 0.925875262 1.019963145 0.885420313 0.920694883 0.937733597 0.925300967 0.923555434 0.997929329 1 20.86439131 1.233479836 24.87116679 0.998964722 0.932169602 0.407515336 0.032327802 120.8661368 591622.1422 0.027222754 0.007628683 17.11905694 -1.233479836 -0.06679512 SSS(ph)LESLQTAVAEVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSLESLQTAVAEVR 15 0 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 R4GN62 PARD3B Partitioning defective 3 homolog B 1 SSS(0.999)LES(0.001)LQTAVAEVR;SSS(1)LESLQTAVAEVR;SSS(1)LESLQTAVAEVR;SSS(1)LESLQTAVAEVR 364.38 2.31E-97 683620000 765850 796560 700060 851380 831770 795840 784980 884850 786970 811950 TRUE FALSE 735919.7353 773842.8887 826576.4148 895319.8238 858524.6374 811932.4301 794586.8201 866577.5383 697636.4648 756955.9033 0.97220952 1.022309074 1.091974329 1.182789935 1.134180517 1.07262844 1.049713486 1.14481905 0.921634222 1 19.52984973 1.233627518 24.99914745 0.960817081 1.087736069 0.395354151 0.060696301 133.1132083 674529.882 0.054835669 0.01540851 17.12487924 -1.233627518 0.126918988 NVDLLSDMVQEHDEPILK ddPTM_BT-474_Pertuzumab_2h_R1 8 NVDLLSDMVQEHDEPILK 18 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ;;;;;;; 338.58 3.12E-75 5320005000 9129025 8893049 7767372 7982116 8312590 9082080 9011625 9146700 11426440 11004040 FALSE TRUE 8772252.61 8639427.95 9171108.905 8394073.963 8579972.007 9265725.88 9121911.962 8957817.449 10129358.43 10258726.57 0.855101513 0.842154033 0.893981221 0.81823742 0.836358387 0.903204293 0.889185602 0.87319 0.987389455 1 23.29034832 1.233694396 3.372686466 1.00272352 0.862963569 0.805204201 0.025580589 0.099026912 2.014504183 0.023903938 0.006807963 17.12751654 -1.233694396 -0.139759951 GIFPVLCK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIFPVLCK 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 99.919 0.015056 189070000 186250 213030 203360 207500 200940 152000 218050 202350 253560 233270 FALSE TRUE 178971.1441 206954.593 240111.6757 218209.0999 207403.4176 155073.5441 220718.5611 198171.4018 224776.9318 217470.4151 0.822967777 0.951644815 1.104111911 1.003396714 0.953708657 0.713078807 1.014936036 0.911256833 1.03359775 1 17.73045962 1.233750754 24.94274585 1.016798903 0.938766713 0.09390439 0.101672304 332.9618201 1726551.603 0.088683347 0.02498316 17.12973934 -1.233750754 -0.07803219 GSSSS(ph)SPEHSASSDSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSSSSPEHSASSDSTK 17 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 GS(0.026)S(0.019)S(0.089)S(0.433)S(0.433)PEHSASSDSTK 149.12 2.17E-07 127300000 182160 208200 150920 172920 167840 206750 196550 184030 261840 243410 TRUE FALSE 175040.9858 202262.3398 178194.6012 181844.4219 173238.726 210930.6267 198955.4377 180229.7162 232117.0209 226923.6239 0.771365197 0.891323417 0.785262451 0.801346368 0.763423054 0.929522555 0.876750663 0.794230733 1.022886101 1 17.79184728 1.234168276 24.99727616 1.011443168 0.828656972 0.660809461 0.052941275 68.14337884 387786.7461 0.044724207 0.012687918 17.14621542 -1.234168276 -0.182786196 SSS(ph)MADGDNSYCLEAIIR ddPTM_BT-474_Pertuzumab_2h_R1 7 SSSMADGDNSYCLEAIIR 18 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2;Q9ULV0-3 Q9ULV0 MYO5B Unconventional myosin-Vb 1 S(0.034)S(0.034)S(0.931)MADGDNSYCLEAIIR;S(0.001)S(0.058)S(0.941)MADGDNSYCLEAIIR;S(0.112)S(0.112)S(0.775)MADGDNSYCLEAIIR;SS(0.003)S(0.997)MADGDNSYCLEAIIR;S(0.001)S(0.005)S(0.994)MADGDNSYCLEAIIR;S(0.142)S(0.142)S(0.715)MADGDNSYCLEAIIR;S(0.138)S(0.138)S(0.723)MADGDNSYCLEAIIR 338.14 3.48E-75 1478383000 1440610 1642470 1290170 1663980 1739650 1649800 1506950 1747550 1512850 1553940 TRUE FALSE 1384309.369 1595628.364 1523332.419 1749858.207 1795607.422 1683160.086 1525392.505 1711462.482 1341117.61 1448690.26 0.955559243 1.10142824 1.051523891 1.207889813 1.239469521 1.161849522 1.052945925 1.181386063 0.925744894 1 20.46631774 1.234183034 24.99974259 0.962872388 1.124056741 0.366589869 0.081878691 122.6838814 700584.7525 0.071110678 0.020187254 17.14679809 -1.234183034 0.161184353 VVVS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 4 VVVSPTK 7 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VVVS(1)PTK;VVVS(1)PTK;VVVS(0.972)PT(0.028)K;VVVS(1)PTK 148.69 0.0021681 15504800000 30056700 27420900 24018900 24644700 24461500 23978100 28724900 30560500 30477000 34039800 TRUE FALSE 28882050.93 26638882.78 28359649.53 25916615.92 25248326.36 24462953.61 29076443.92 29929415 27017378.73 31734254.03 0.910122258 0.839436237 0.893660507 0.816676387 0.795617453 0.77086903 0.91624791 0.943126471 0.851363284 1 24.91953759 1.234211863 0.798029857 0.984364734 0.842354957 0.386946967 0.053047933 0.608661009 0.872947779 0.053023106 0.020458076 17.14793634 -1.234211863 -0.142009777 EKESVNAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKESVNAK 8 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ; 87.913 0.013668 563170000 583320 572360 415120 610010 439950 531770 641110 586590 855270 856760 FALSE TRUE 560523.2095 556036.8532 490141.4183 641492.6892 454101.3913 542522.7537 648956.096 574476.7115 758183.3352 798730.8821 0.701767294 0.696150438 0.613650266 0.803139961 0.568528652 0.679230972 0.812484043 0.719236885 0.949235033 1 19.60734997 1.234266003 1.261283626 1.010929012 0.683008018 0.70510299 0.071103141 0.213833743 0.673313808 0.062607561 0.019897524 17.15007419 -1.234266003 -0.327920994 LDKPFPELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDKPFPELR 9 1 Q13564-2;Q13564;Q13564-4;Q13564-3;H3BMR3;J3QRA5 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 107.24 0.0025582 279230000 714820 687730 634180 707460 694570 612390 758260 711690 880670 829480 FALSE TRUE 686884.0441 668116.6138 748790.4333 743972.0954 716911.4748 624772.9454 767539.8127 696993.3528 780700.0337 773298.5808 0.888252043 0.863982723 0.968307006 0.962076116 0.927082362 0.807932357 0.992552982 0.901325012 1.009571274 1 19.56066604 1.234773373 24.99363974 1.004785693 0.91577279 0.334225935 0.051235392 116.3476987 767772.8899 0.042421399 0.012202428 17.17012169 -1.234773373 -0.089012904 YHPDKNPNEGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 YHPDKNPNEGEK 12 1 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;; 164.81 3.38E-05 1874690000 2950080 2628390 2558150 2966600 2379830 2603380 3243290 2905100 4956100 4761520 FALSE TRUE 2834787.612 2553430.891 3020464.611 3119706.582 2456379.393 2656022.127 3282982.353 2845108.67 4393504.306 4439018.009 0.638606919 0.575224269 0.680435313 0.702792053 0.553360988 0.598335515 0.739574011 0.640931995 0.989746898 1 22.08180913 1.234937997 7.301244087 0.998318783 0.64236741 0.873478571 0.053845687 0.040235896 12.83252012 0.04473837 0.013460324 17.17663145 -1.234937997 -0.355951373 NQDECVIALHDCNGDVNR ddPTM_BT-474_Pertuzumab_2h_R1 4 NQDECVIALHDCNGDVNR 18 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ;;; 286.6 8.12E-40 5066710000 2656100 2647460 2124880 2750770 2338870 2484720 2520080 2604670 3129580 2975090 FALSE TRUE 2552296.676 2571957.033 2508893.084 2892737.569 2414101.878 2534962.741 2550921.493 2550882.654 2774323.199 2773584.504 0.920215941 0.927304371 0.904567025 1.042959955 0.870390599 0.91396629 0.919720127 0.919706124 1.000266332 1 21.40332025 1.234949956 24.86938391 1.000133221 0.927338088 0.326577786 0.041804069 101.8424118 701410.6092 0.033747263 0.009739483 17.17710443 -1.234949956 -0.072795133 AAAS(ph)PPTPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAASPPTPIR 10 0 Q6PGN9-4;Q5T2Z1;Q6PGN9-2 Q6PGN9-4 PSRC1 1 AAAS(0.707)PPT(0.293)PIR;AAAS(0.993)PPT(0.007)PIR 97.749 0.0061326 282170000 457460 470810 466710 510540 542300 534270 514000 561960 461570 476190 TRUE FALSE 439581.9575 457382.9598 551054.8789 536889.0306 559743.572 545073.3055 520290.4858 550355.3296 409174.5087 443937.2272 0.990189447 1.030287464 1.241290086 1.209380511 1.260861982 1.227816169 1.171991115 1.239714302 0.921694518 1 18.75999617 1.234970041 24.99999016 0.960847166 1.178180866 0.473940519 0.0885211 85.08504899 592374.1572 0.07923622 0.022827729 17.17789885 -1.234970041 0.2173337 GYIWNYGAIPQTWEDPGHNDK ddPTM_BT-474_Pertuzumab_2h_R1 4 GYIWNYGAIPQTWEDPGHNDK 21 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 268.3 2.75E-37 11131770000 3161080 2995720 2359460 2540750 2642350 2812510 2752880 2803520 3498120 3246460 FALSE TRUE 3037541.499 2910284.999 2785866.908 2671878.412 2727343.587 2869380.879 2786570.569 2745626.332 3101028.083 3026574.373 1.00362361 0.961577229 0.920468677 0.882806131 0.901132188 0.94806224 0.920701171 0.907172927 1.024599994 1 21.52925437 1.235084147 24.99807888 1.012300037 0.927890314 0.493668329 0.032961171 77.97271525 560630.8453 0.029172802 0.008431926 17.18241273 -1.235084147 -0.084409723 AAGISLIVPGKS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGISLIVPGKSPTR 15 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 AAGISLIVPGKS(0.996)PT(0.004)R 138.66 5.58E-06 3057900000 1043700 1033800 931500 1012700 1137800 983260 1136900 1145900 1009100 1011800 TRUE FALSE 1002911.05 1004317.036 1099842.771 1064965.568 1174398.37 1003142.191 1150813.722 1122236.765 894551.1985 943269.8848 1.063228103 1.064718648 1.165989489 1.129014703 1.245029009 1.063473145 1.220025934 1.189730302 0.948351276 1 19.84731108 1.235168348 24.99999644 0.974175556 1.147077734 0.533610225 0.06289387 68.04798234 501453.3024 0.053133382 0.015369929 17.18574438 -1.235168348 0.172902178 LEVPDMNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEVPDMNIR 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 111.74 0.0048295 50106000 128620 137500 102960 155180 120990 126540 122180 146140 128250 141220 FALSE TRUE 123593.3882 133578.6346 121567.1623 163188.8584 124881.7532 129098.7255 123675.2754 143122.1579 113691.5977 131655.0436 0.938766832 1.014610842 0.923376416 1.239518471 0.948552747 0.980583212 0.939388815 1.087099696 0.86355672 1 17.00640327 1.235246763 24.99999583 0.931778407 1.011314546 0.095243328 0.094969864 204.9644622 1546142.694 0.075364988 0.021866539 17.18884767 -1.235246763 0.079536139 FKDHVEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKDHVEGK 8 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 124.23 0.00078932 582220000 2132300 2111300 1863500 1805500 1877800 2127900 2106900 2067700 2709300 2571900 FALSE TRUE 2048967.359 2051087.791 2200275.903 1898682.071 1938201.142 2170927.596 2132684.872 2025001.272 2401751.622 2397702.922 0.854554307 0.855438667 0.917659933 0.791875446 0.808357501 0.905419756 0.889470023 0.844558871 1.001688575 1 21.19322149 1.235265769 24.95013884 1.000844387 0.858806187 0.701120615 0.037196085 46.79967185 354359.7879 0.031681157 0.009189371 17.18959991 -1.235265769 -0.1420382 S(ph)LQENEEEEIGNLELAWDMLDLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLQENEEEEIGNLELAWDMLDLAK 24 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;E9PI86 P49321 NASP Nuclear autoantigenic sperm protein 1 S(1)LQENEEEEIGNLELAWDMLDLAK;S(1)LQENEEEEIGNLELAWDMLDLAK 111.58 0.0059017 385840000 80505 77987 66475 73513 71585 73889 65580 74235 95512 88960 TRUE FALSE 77358.7756 75762.88712 78488.51123 77307.01474 73887.59654 75383.08621 66382.58766 72702.02131 84669.87818 82934.65996 0.932767743 0.913525023 0.946389739 0.932143627 0.89091336 0.908945503 0.800420327 0.876618067 1.020922715 1 16.33968754 1.235424056 24.99960555 1.010461419 0.897270153 0.557900605 0.039185712 66.04482491 526358.2849 0.036295229 0.010553181 17.19586615 -1.235424056 -0.113191266 ARS(ph)PGREEVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ARSPGREEVAR 11 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 ARS(1)PGREEVAR;ARS(1)PGREEVAR 104.7 0.0020204 2316400000 1179040 1198230 884720 1211390 1169630 1288970 1096760 1248420 1060020 1045730 TRUE FALSE 1132961.813 1164057.654 1044608.584 1273909.983 1207252.211 1315033.857 1110182.477 1222639.691 939690.9736 974901.7757 1.162129192 1.194025575 1.071501366 1.306705983 1.238332149 1.348888564 1.138763417 1.25411577 0.963882718 1 19.89489734 1.23547502 24.99977621 0.981941226 1.21537996 0.595369548 0.076620696 54.7564403 443602.9173 0.062972861 0.018345042 17.19788418 -1.23547502 0.233438734 EKHNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKHNIR 6 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 72.234 0.078556 24433000 36141 35934 28934 30585 37133 32150 29446 33026 44824 41065 FALSE TRUE 34728.56976 34909.1975 34163.01743 32163.49552 38327.41667 32800.09503 29806.36896 32344.00156 39735.76744 38283.63097 0.907138871 0.911857016 0.892366178 0.840137017 1.001143718 0.856765521 0.778566928 0.844851983 1.037931002 1 15.22444005 1.235560547 24.99974762 1.01896557 0.876121231 0.501686228 0.055693062 67.77137173 564692.6744 0.049033358 0.01429759 17.20127133 -1.235560547 -0.142844339 DSPGRPVPVATETSSMHGANETPSGRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSPGRPVPVATETSSMHGANETPSGRPR 28 2 Q9Y6A5;A0A494BZT8;A0A494C117 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 0 168.26 3.06E-12 147170000 32574 32300 24269 33242 21996 28873 36262 30589 28593 26135 FALSE TRUE 31300.97207 31378.83563 28654.94816 34957.6236 22703.52132 29456.83184 36705.7852 29957.32646 25347.24251 24364.85317 1.284677229 1.287872962 1.176077194 1.434756178 0.931814411 1.208988687 1.506505496 1.229530351 1.040319937 1 14.57251391 1.235621238 4.948923162 1.010913731 1.261297576 0.302295554 0.145129403 0.216199111 13.66441311 0.121641178 0.035755744 17.20367533 -1.235621238 0.250383845 LS(ph)LCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSLCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR 34 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 LS(0.499)LCEDS(0.499)PMVT(0.001)LTVDNVHLEHGVVYEYVSTAGVR 97.138 0.00032742 106610000 22873 19321 10799 20551 13611 20029 21101 16609 34680 30496 TRUE FALSE 21979.09787 18769.984 12750.61952 21611.63957 14048.81018 20434.0001 21359.24035 16266.01835 30743.27179 28430.47876 0.773082228 0.660206399 0.448484165 0.760157427 0.494146099 0.718735702 0.751279658 0.572133114 1.081349071 1 14.79515077 1.235842066 24.99937191 1.040674742 0.64379759 0.679628395 0.108018111 38.32324854 352380.9968 0.084380472 0.024778316 17.21242521 -1.235842066 -0.396877151 GQVIIIS(ph)DS(ph)DDDDDER ddPTM_BT-474_Pertuzumab_2h_R1 2 GQVIIISDSDDDDDER 16 0 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 2 GQVIIIS(1)DS(1)DDDDDER;GQVIIIS(1)DS(1)DDDDDER 250.79 7.69E-21 262050000 296620 309190 241260 315320 343370 315650 290480 329000 292470 290940 TRUE FALSE 285027.7625 300372.2039 284861.0488 331593.703 354414.8079 322032.6593 294034.9811 322206.035 259270.0317 271234.3747 1.050854129 1.107426757 1.050239481 1.222535689 1.306673641 1.187285571 1.084062378 1.187924781 0.955889282 1 18.0491805 1.235847994 24.9987566 0.977944557 1.152285917 0.441405673 0.077205752 70.1593473 646505.8172 0.068091672 0.019992328 17.21266016 -1.235847994 0.17434136 GPPPTDPYGRPPPYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPPPTDPYGRPPPYDR 16 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 ; 93.716 0.0039556 1964100000 889470 876860 790130 909380 902520 913860 864680 948790 938070 924450 FALSE TRUE 854708.529 851852.8113 932924.0673 956313.2108 931550.3754 932338.8753 875262.2125 929197.1549 831584.2263 861836.1781 0.991729694 0.988416167 1.082484225 1.10962296 1.080890312 1.081805219 1.015578407 1.078159839 0.964898257 1 19.71705414 1.236028815 24.99998988 0.982449105 1.055308961 0.331515314 0.040346851 81.78264299 807471.1184 0.035310106 0.010382956 17.21982822 -1.236028815 0.072859856 SPSFGDPQLS(ph)PEARPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSFGDPQLSPEARPR 16 1 O95425-2;O95425-3 O95425-2 SVIL Supervillin 1 SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR 168.81 3.54E-09 2923810000 2638360 3060390 2280560 2936230 2366520 2914300 2789650 2893960 2953150 2845600 TRUE FALSE 2535249.974 2973110.674 2692707.923 3087769.182 2442641.265 2973229.143 2823790.571 2834198.715 2617920.793 2652864.977 0.955664912 1.120716923 1.015018837 1.163937558 0.92075597 1.12076158 1.064430567 1.068353926 0.986827756 1 21.33911982 1.236046267 24.98288881 0.993413846 1.057165265 0.101865831 0.071017247 134.7721645 1338978.74 0.052070534 0.015390196 17.22052023 -1.236046267 0.063751419 GKTEESGEDRGDGPPDRDPTLS(ph)PSAFILR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKTEESGEDRGDGPPDRDPTLSPSAFILR 29 3 Q9H7N4;M0R3G4;M0R2L3;M0R232 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GKTEESGEDRGDGPPDRDPT(0.183)LS(0.634)PS(0.183)AFILR;GKTEESGEDRGDGPPDRDPT(0.246)LS(0.71)PS(0.044)AFILR 144.36 3.68E-07 1033600000 696140 710140 510790 539660 625880 641740 615010 659450 581690 557280 TRUE FALSE 668934.0792 689887.5025 603101.1155 567511.9173 646011.9986 654716.4225 622536.6764 645832.1271 515658.9898 519534.9292 1.287563245 1.32789436 1.160848061 1.09234603 1.243442861 1.260197122 1.198257598 1.243096644 0.992539598 1 18.98686122 1.236310094 24.96692511 0.996269654 1.224615559 0.68598799 0.062349892 35.06225167 388929.813 0.054190937 0.016063876 17.23098458 -1.236310094 0.228345905 MNGVMFPGNS(ph)PSYTER ddPTM_BT-474_Pertuzumab_2h_R1 14 MNGVMFPGNSPSYTER 16 0 Q9NY27-2;Q9NY27;Q9NY27-3 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 MNGVMFPGNS(0.98)PS(0.02)YTER;MNGVMFPGNS(0.995)PS(0.005)YTER;MNGVMFPGNS(0.87)PS(0.13)YTER;MNGVMFPGNS(0.894)PS(0.105)YTER;MNGVMFPGNS(0.987)PS(0.011)Y(0.002)TER;MNGVMFPGNS(0.984)PS(0.016)YTER;MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(0.97)PS(0.03)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.707)PS(0.293)YTER 454.28 1.25E-182 9075470000 5382720 5825150 4709053 5604316 5500540 5633720 5419902 5948930 5466186 5499820 TRUE FALSE 5172357.351 5659022.425 5560083.629 5893555.42 5677469.865 5747637.678 5486232.382 5826082.517 4845687.481 5127312.293 1.008785316 1.103701531 1.084405106 1.149443428 1.107299408 1.120984514 1.070001605 1.136283921 0.945073599 1 22.28977134 1.236316177 24.99999196 0.972536754 1.100561777 0.620531263 0.039069403 35.56632821 396115.1095 0.030436615 0.009028181 17.23122593 -1.236316177 0.128025023 SFSERFPEDGPELEEILTQLATADAR ddPTM_BT-474_Pertuzumab_2h_R1 5 SFSERFPEDGPELEEILTQLATADAR 26 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;;;; 242.73 3.24E-45 825925000 338670 415880 281155 331696 362985 383012 351666 395027 349421 371366 FALSE TRUE 325434.402 404019.5096 331965.9628 348814.8703 374660.7422 390756.7651 355969.7937 386869.5544 309756.193 346213.05 0.939983059 1.166967882 0.958848786 1.007515084 1.082168168 1.128659838 1.028181328 1.117432039 0.894698201 1 18.40130058 1.236385297 24.99998779 0.947349101 1.057870261 0.250632668 0.073290812 73.34429786 842816.1713 0.055810282 0.016593028 17.23396857 -1.236385297 0.110521161 KIEIDNGDELTADFLYEEVHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIEIDNGDELTADFLYEEVHPK 22 1 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 217.17 8.33E-26 165420000 80333 77655 74505 69834 86111 82941 81996 82248 115140 110130 FALSE TRUE 77193.49755 75440.35543 87969.71085 73438.14111 88880.83852 84618.12385 82999.49158 80549.55006 102069.7899 102670.797 0.751854469 0.734779096 0.856813363 0.715277793 0.865687626 0.824169348 0.808404084 0.784541977 0.99414627 1 16.64766636 1.2364201 24.95949205 0.997073272 0.794085289 0.754079367 0.046681134 25.33784546 295415.8485 0.036690619 0.010902229 17.23534972 -1.2364201 -0.202987983 TS(ph)PTFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPTFR 6 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 T(0.209)S(0.79)PTFR;T(0.158)S(0.842)PTFR 128.57 0.017382 778120000 1479180 1367410 1217630 1239050 1304590 1328980 1355930 1457220 1590800 1592090 TRUE FALSE 1421372.01 1328412.806 1437682.827 1302997.519 1346553.322 1355852.886 1372524.277 1427127.898 1410219.053 1484256.326 0.957632442 0.895002286 0.96862166 0.87787904 0.907224243 0.913489713 0.924721864 0.961510403 0.95011827 1 20.50130883 1.23649966 0.993778998 0.995961733 0.918224821 0.455412885 0.026605132 0.411788361 0.860851109 0.023584387 0.008153459 17.23850742 -1.23649966 -0.077736912 VEGHVFPEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEGHVFPEFK 10 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 70.942 0.052472 86336000 178420 199480 164600 173320 166300 183470 173480 184520 235240 223520 FALSE TRUE 171447.1491 193791.0257 194346.8815 182265.066 171649.1905 187179.8891 175603.1001 180709.5975 208536.5414 208380.7913 0.822758893 0.929985074 0.932652575 0.874673068 0.823728471 0.898258846 0.842702914 0.867208519 1.00074743 1 17.66886277 1.236501598 24.9959472 1.000373795 0.87500219 0.656772235 0.036538045 33.2025 403019.7304 0.030253067 0.009014442 17.23858436 -1.236501598 -0.125371605 ETPQGELRPEVVEDEVPRS(ph)PVAEEPGGGGSSSSEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETPQGELRPEVVEDEVPRSPVAEEPGGGGSSSSEAK 36 2 Q7L8J4 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 ETPQGELRPEVVEDEVPRS(1)PVAEEPGGGGSSSSEAK;ETPQGELRPEVVEDEVPRS(1)PVAEEPGGGGSSSSEAK 281.62 1.08E-76 1057594000 490082 502638 436020 482715 499530 551395 470301 521036 469416 442929 TRUE FALSE 470929.0536 488303.2564 514818.5132 507627.979 515597.8361 562544.5847 476056.6843 510276.4245 416129.8636 412929.0243 1.140460045 1.182535563 1.246748189 1.229334702 1.248635494 1.362327547 1.15287775 1.235748505 1.007751548 1 18.6555343 1.236506156 24.92016597 1.00387562 1.226516395 0.695259341 0.058505665 28.45219535 345074.0587 0.047975967 0.014282004 17.23876525 -1.236506156 0.222640775 DIDPQNDLTFLR ddPTM_BT-474_Pertuzumab_2h_R1 5 DIDPQNDLTFLR 12 0 Q9NP97;B1AKR6;Q8TF09;H3BQI1 Q9NP97 DYNLRB1;DYNLRB2 Dynein light chain roadblock-type 1;Dynein light chain roadblock-type 2 0 ;;;; 319.29 2.95E-46 2371140000 1695810 1831590 1524270 1770630 1727660 1734860 1730430 1849310 1828270 1792730 FALSE TRUE 1629535.87 1779354.847 1799739.496 1862012.426 1783231.753 1769940.058 1751607.52 1811121.102 1620732.454 1671306.8 0.975007024 1.06464884 1.076845673 1.114105696 1.066968526 1.05901565 1.048046666 1.083655677 0.96973964 1 20.67254516 1.236513409 24.99998132 0.98486979 1.063875601 0.440196211 0.034237917 47.7736151 583326.8345 0.027612564 0.008218587 17.23905315 -1.236513409 0.079005811 KRS(ph)WGHES(ph)PEER ddPTM_BT-474_Pertuzumab_2h_R1 2 KRSWGHESPEER 12 2 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 2 KRS(1)WGHES(1)PEER;KRS(1)WGHES(1)PEER 126.01 0.00015827 849830000 490880 462920 387630 440520 442340 505220 439210 431130 618140 515960 TRUE FALSE 471695.8669 449717.9748 457683.3638 463255.29 456568.2678 515435.8946 444585.1834 422227.0148 547971.3387 481013.5696 0.980629023 0.934938229 0.951497822 0.963081541 0.9491796 1.071562066 0.924267446 0.877786078 1.139201414 1 18.87571807 1.236529344 24.99983062 1.069600687 0.954130157 0.393670023 0.056018828 54.14690218 666329.0694 0.04605921 0.013721852 17.23968572 -1.236529344 -0.115470531 SERPPTILMTEEPSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SERPPTILMTEEPSSPK 17 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SERPPTILMTEEPS(0.037)S(0.963)PK;SERPPTILMTEEPS(0.159)S(0.841)PK 117.38 0.00013338 809310000 502260 497310 494060 521710 558280 493240 512930 570320 519480 541580 TRUE FALSE 482631.1239 483127.2057 583347.6323 548635.5156 576237.5832 503213.6507 519207.3908 558542.6927 460510.8082 504898.3042 0.955897692 0.956880231 1.155376494 1.086625784 1.141294353 0.996663381 1.028340532 1.106247908 0.912086264 1 18.94563331 1.236700603 24.99964619 0.956043128 1.056896939 0.236533548 0.069751445 71.79292939 964807.7243 0.057896849 0.017292312 17.24648531 -1.236700603 0.100853811 S(ph)PPLGLISR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPPLGLISR 9 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 S(1)PPLGLISR;S(1)PPLGLISR;S(1)PPLGLISR;S(1)PPLGLISR 98.634 0.0061694 1240800000 58336 62017 65039 87455 80939 68446 68193 81346 60376 67940 TRUE FALSE 56056.16463 60248.33588 76792.99408 91968.56303 83542.47644 69830.02502 69027.56633 79666.17667 53522.3696 63338.36329 0.885027047 0.951213968 1.212424668 1.452019886 1.318986979 1.102491782 1.089822388 1.257787106 0.845022934 1 15.95079197 1.236780658 24.99948386 0.922511417 1.167746035 0.252075125 0.162155613 68.94913824 968251.4523 0.141573859 0.042419937 17.2496647 -1.236780658 0.245234619 QIYYSDKYDDEEFEYR ddPTM_BT-474_Pertuzumab_2h_R1 5 QIYYSDKYDDEEFEYR 16 1 P61024;Q5T179 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ;;;; 209.31 1.15E-11 5593600000 5294640 4764660 4264030 4169270 4536870 4241350 4463860 5349180 5688600 6083780 FALSE TRUE 5087719.615 4628776.562 5034635.074 4384446.524 4682802.544 4327113.003 4518490.054 5238717.564 5042853.977 5671720.162 0.897032905 0.816115117 0.887673392 0.773036469 0.825640619 0.762927803 0.796670133 0.92365586 0.889122494 1 22.43535492 1.23680116 1.305706691 0.987190022 0.822717274 0.559161268 0.047258213 0.290764423 0.970608572 0.043916866 0.013830362 17.25047903 -1.23680116 -0.164472748 KIEITVEPSQRPGTAINRS(ph)PS(ph)PISNQPSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KIEITVEPSQRPGTAINRSPSPISNQPSPR 30 3 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 2 KIEIT(0.001)VEPS(0.022)QRPGT(0.439)AINRS(0.539)PS(0.581)PIS(0.413)NQPS(0.007)PR 55.3 0.027455 115970000 86146 98633 69644 82243 96329 101890 86157 94459 90845 87381 TRUE FALSE 82779.31908 95820.08341 82230.22002 86487.57109 99427.50977 103950.2856 87211.41514 92508.38864 80532.65645 81462.60704 1.016163392 1.176246218 1.009422888 1.061684302 1.220529435 1.27604909 1.070569901 1.135593274 0.988584326 1 16.31385037 1.236839679 24.96806869 0.99429209 1.123498512 0.276480463 0.081753873 59.56898724 864121.8772 0.067582328 0.020268388 17.25200911 -1.236839679 0.129206422 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTT(ph)GSPTEFLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.028)T(0.959)GS(0.014)PTEFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.126)T(0.514)GS(0.357)PT(0.003)EFLEEK 182.05 3.15E-28 398610000 116423 97432 85007 63077 90725 92509 89498 92266 134837 127296 TRUE FALSE 111873.0604 94653.33476 100369.6559 66332.41153 93643.25202 94379.59536 90593.3033 90360.67486 119530.869 118674.1285 0.942691232 0.797590308 0.845758525 0.558945849 0.78907891 0.795283661 0.763378711 0.761418482 1.007219269 1 16.85664593 1.236861048 24.97125371 1.003609773 0.776134053 0.491632468 0.090088589 35.77445933 525544.1782 0.072226039 0.021664985 17.25285799 -1.236861048 -0.22747572 LEPVYSPPGS(ph)PPPGDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEPVYSPPGSPPPGDPR 17 0 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 LEPVYS(0.161)PPGS(0.839)PPPGDPR 115.8 0.00031166 854430000 73770 93179 83113 87469 110310 91521 86027 102590 62942 70416 TRUE FALSE 70886.98684 90521.62615 98133.36794 91983.28557 113858.2213 93371.61733 87079.82416 100471.4806 55797.08803 65646.6616 1.079826226 1.378922004 1.494872177 1.40118756 1.734409924 1.42233611 1.326492803 1.530488805 0.849960785 1 16.00243403 1.236948552 24.99999959 0.924980176 1.431962738 0.606019467 0.159803783 27.39688487 424806.5908 0.127961375 0.03846539 17.25633457 -1.236948552 0.506982562 HIISATSLST(ph)SPTELGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATSLS(0.025)T(0.66)S(0.314)PTELGSR;HIISATSLS(0.002)T(0.992)S(0.005)PTELGSR 288.57 5.55E-40 1864930000 765210 668110 704450 731440 725970 737500 809390 747970 1049480 962930 TRUE FALSE 735304.7472 649056.1569 831759.7854 769189.7061 749321.4844 752412.7553 819295.5569 732524.1581 930347.4302 897709.8934 0.819089499 0.72301326 0.926535166 0.856835501 0.834703382 0.83814689 0.912650694 0.815992074 1.036356441 1 19.77588977 1.236956739 24.99993363 1.018178305 0.842284297 0.638645726 0.053340169 26.15557602 407627.243 0.042602395 0.012801426 17.25665984 -1.236956739 -0.175894008 KITIGQAPTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KITIGQAPTEK 11 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 83.877 0.021556 0 655270 572530 444430 415680 537850 572130 508570 506060 773340 665180 FALSE TRUE 629661.324 556202.005 524748.3873 437133.2946 555150.4337 583698.8606 514794.0318 495609.6842 685553.6853 620126.7661 1.015375175 0.896916623 0.846195352 0.704909574 0.895220887 0.941257324 0.830143222 0.799207051 1.105505717 1 19.24220364 1.237132877 24.99999993 1.052752909 0.85988127 0.449820031 0.082313997 33.89205772 593352.9038 0.06778511 0.020461302 17.26366012 -1.237132877 -0.192871639 VCEEIAIIPSKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VCEEIAIIPSKK 12 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73 H3BNC9 RPS17 40S ribosomal protein S17 0 ; 119.39 0.0008389 2187500000 2680150 2760240 2254240 2353400 2372690 2305770 2456590 2685850 3108000 3076000 FALSE TRUE 2575406.775 2681520.658 2661631.313 2474859.256 2449009.729 2352394.249 2486654.483 2630386.259 2755192.87 2867659.78 0.898086584 0.935090235 0.928154494 0.863024015 0.85400986 0.820318458 0.867137204 0.917258831 0.960780944 1 21.45144244 1.237229583 2.035434401 0.996574415 0.881213907 0.602280638 0.032610704 0.237004372 1.700153207 0.034691019 0.010082165 17.26750469 -1.237229583 -0.115360508 EDGVITASEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDGVITASEDR 11 0 Q8IWB7;A0A494C0A6;C9JJ54 Q8IWB7 WDFY1 WD repeat and FYVE domain-containing protein 1 0 153.97 7.50E-05 124990000 26484 29107 24776 30798 25729 29868 24496 29438 27568 27119 FALSE TRUE 25448.976 28276.89686 29253.57434 32387.48847 26556.59665 30471.95142 24795.78938 28830.09501 24438.59621 25282.20597 1.00659634 1.118450537 1.15708156 1.281038866 1.050406625 1.205272651 0.980760516 1.140331466 0.966632272 1 14.62583473 1.237417261 24.99993073 0.983316076 1.119178253 0.283854464 0.085215116 37.574168 821394.5675 0.066086962 0.020052986 17.27496837 -1.237417261 0.135862177 RFPTDYASTS(ph)EDEFGSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 RFPTDYASTSEDEFGSNR 18 1 Q5SW79;H0Y2V6;Q5SW79-3 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 RFPTDYAS(0.007)T(0.167)S(0.826)EDEFGSNR;RFPTDYAST(0.016)S(0.984)EDEFGSNR 190.3 1.73E-14 497260000 119645 125408 91661 107806 131458 124588 101101 123161 99297 98347 TRUE FALSE 114969.1411 121831.4866 108226.1817 113369.8806 135686.466 127107.2547 102338.3043 120617.6823 88025.22085 91685.87009 1.253946121 1.328792392 1.18040197 1.236503296 1.479905964 1.386334171 1.116184033 1.315553664 0.960074009 1 16.48441179 1.237472681 24.99999207 0.980036847 1.286012802 0.614657876 0.097279848 19.16786119 440363.7946 0.079575348 0.024190228 17.27717296 -1.237472681 0.305975955 ELPPFWEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELPPFWEQR 9 0 A0A0C4DGA6;Q14527-2;Q14527 A0A0C4DGA6 HLTF Helicase-like transcription factor 0 113.66 0.0041053 37508000 28033 28600 24756 29480 27513 30297 26785 31055 28381 29824 FALSE TRUE 26937.43937 27784.356 29229.95989 31001.46633 28397.98063 30909.6261 27112.80284 30413.7034 25159.30786 27803.99392 0.968833451 0.999293702 1.051286372 1.115000472 1.021363359 1.111697341 0.975140583 1.093860957 0.904881074 1 14.76300451 1.237730517 25 0.95244054 1.044111633 0.302210975 0.054399718 25.31502793 762186.114 0.041238996 0.01261225 17.28743328 -1.237730517 0.091671093 DNEVDGQDY(ph)HFVVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNEVDGQDYHFVVSR 15 0 Q92796-2;Q5JUW8;Q92796-3;Q92796 Q92796-2 DLG3 Disks large homolog 3 1 DNEVDGQDY(1)HFVVSR 98.165 0.0042284 0 27088 25525 26512 28446 26051 27291 31051 37709 39841 48546 TRUE FALSE 26029.37101 24797.05199 31303.30816 29914.10147 26888.95407 27842.84272 31431.01143 36930.29597 35318.41671 45257.93618 0.575133849 0.547905055 0.691664508 0.660969191 0.594126828 0.615203544 0.694486185 0.815996024 0.780380629 1 15.46588318 1.237807019 0.599944104 0.999922955 0.598748403 0.872935499 0.046285776 0.252943848 0.224709525 0.049483226 0.023271305 17.29047876 -1.237807019 -0.401174553 ESIFFNSHNVSKPESSSVLTELDKIEGVFERPSDEVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESIFFNSHNVSKPESSSVLTELDKIEGVFERPSDEVIR 38 3 Q13572-2;Q13572;G3V4M9 Q13572-2 ITPK1 Inositol-tetrakisphosphate 1-kinase 0 137.47 1.33E-09 199050000 121010 119830 94918 112510 90192 120930 107470 121460 165840 164670 FALSE TRUE 116280.7954 116412.5657 112071.794 118316.6546 93093.10759 123375.2875 108785.25 118951.8086 147014.5385 153516.7542 0.757446938 0.758305283 0.730029726 0.770708417 0.606403569 0.803660083 0.708621352 0.774845776 0.957644911 1 17.22803659 1.237852473 3.008750247 1.000196803 0.733787056 0.795202354 0.049341912 0.09769169 1.517305526 0.041925365 0.011956179 17.29228852 -1.237852473 -0.266409746 IDFTPVS(ph)PAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDFTPVSPAPSPTR 14 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 2 IDFTPVS(1)PAPS(0.981)PT(0.019)R 122.33 0.0001599 37897000 137240 147670 123430 154030 145370 142210 131190 158210 132440 144070 TRUE FALSE 131876.5091 143458.5962 145736.5467 161979.5068 150045.9581 145085.5836 132795.5425 154942.9082 117405.9664 134312.0106 0.981866838 1.068099536 1.085059676 1.205994208 1.117144754 1.080213028 0.988709363 1.153604265 0.874128575 1 17.0352288 1.237917396 25 0.937064274 1.087876772 0.418720785 0.069699631 15.9001237 617755.1911 0.054817287 0.016832465 17.29487375 -1.237917396 0.150812497 EVS(ph)PSDVR ddPTM_BT-474_Pertuzumab_2h_R1 3 EVSPSDVR 8 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 EVS(0.998)PS(0.002)DVR;EVS(0.997)PS(0.003)DVR;EVS(0.999)PS(0.001)DVR 129.85 0.0011255 889770000 3048870 2954920 2523160 3347670 3317480 2741410 2992470 3230600 2758770 2749580 TRUE FALSE 2929716.79 2870648.575 2979151.139 3520443.65 3424189.757 2796843.188 3029092.743 3163886.981 2445605.995 2563348.498 1.142925666 1.119882286 1.162210734 1.373376914 1.335826853 1.091089718 1.181693689 1.234278907 0.954066916 1 21.2895982 1.237938822 24.99999564 0.977033353 1.207193752 0.529837856 0.085941506 13.33841126 536074.3494 0.072624327 0.022301227 17.29572702 -1.237938822 0.230160399 EANHNVSAPYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EANHNVSAPYGR 12 0 Q7L576;Q7L576-2;Q7L576-3;Q96F07;Q96F07-2;E7EVJ5;H7C229;E7EW33;A0A0G2JR96;A0A0G2JQT1 Q7L576;A0A0G2JR96 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 92.99 0.0074241 288540000 137640 141660 110810 137800 133240 119620 146280 143340 135130 135090 FALSE TRUE 132260.8766 137619.9955 130835.832 144911.8745 137525.7856 122038.7984 148070.2184 140379.9789 119790.6089 125940.234 1.050187636 1.09274051 1.038872391 1.150640029 1.091992458 0.969021531 1.175718146 1.114655535 0.95117029 1 16.94237973 1.238008481 24.99999988 0.975585109 1.088447259 0.378751029 0.056194462 14.58563726 660131.8083 0.043926786 0.013509648 17.2985014 -1.238008481 0.112862149 HPNYS(ph)PPGSPIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 HPNYS(1)PPGSPIEK;HPNYS(1)PPGSPIEK 204.78 4.84E-08 2412400000 3111000 2588000 2294300 2053950 1816660 2411400 2815700 2376700 5014400 4517300 TRUE FALSE 2989418.681 2514192.774 2708931.046 2159954.606 1875094.519 2460160.16 2850159.379 2327620.314 4445186.334 4211339.247 0.709849885 0.597005519 0.643246931 0.512890194 0.445248983 0.584175251 0.676782185 0.552703114 1.055527962 1 22.00584767 1.238024341 24.99999955 1.027764199 0.587265633 0.848405516 0.073969705 5.0150151 233682.8234 0.060513436 0.018617518 17.29913315 -1.238024341 -0.440498567 TFNGS(ph)IELCR ddPTM_BT-474_Pertuzumab_2h_R1 1 TFNGSIELCR 10 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 TFNGS(1)IELCR 123.26 0.00048974 148310000 118430 139160 115940 128690 116970 138820 112270 138540 114140 121310 TRUE FALSE 113801.6247 135191.2931 136892.9371 135331.7063 120732.4463 141627.0355 113643.9938 135679.1006 101183.3057 113093.5656 1.006260825 1.195393321 1.210439659 1.196634889 1.067544785 1.252299675 1.004867016 1.199706631 0.894686671 1 16.78715733 1.23813695 25 0.947343284 1.144644168 0.447770499 0.086259233 9.144929545 539320.008 0.062559587 0.019286207 17.30361926 -1.23813695 0.197300884 NAQAIEDMVGYAQETQHEK ddPTM_BT-474_Pertuzumab_2h_R1 3 NAQAIEDMVGYAQETQHEK 19 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;; 360.17 2.67E-91 946582000 989204 865911 842821 790908 891298 873219 897028 923491 1162213 1105600 FALSE TRUE 950544.8141 841216.0661 995137.5032 831726.8567 919967.4096 890876.0865 908006.097 904420.5881 1030283.453 1030716.727 0.922217316 0.81614671 0.965481084 0.806940292 0.892551159 0.864326796 0.880946309 0.877467654 0.999579638 1 19.97521646 1.23861707 9.597527104 1.000103122 0.876873805 0.555392598 0.043480542 0.058416052 88.54244378 0.030178929 0.009369215 17.32275926 -1.23861707 -0.123229318 RPLEAGS(ph)PGQDLEPACDGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPLEAGSPGQDLEPACDGAR 20 1 Q9HCM7;A0A3B3IRR3;A0A1B0GUN3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 RPLEAGS(1)PGQDLEPACDGAR;RPLEAGS(1)PGQDLEPACDGAR 119.34 3.21E-05 534010000 216510 249300 206223 235790 245160 264230 239410 266990 211078 231240 TRUE FALSE 208048.5498 242190.2081 243492.0835 247959.1502 253045.794 269572.9116 242339.9712 261476.5632 187117.3104 215577.9088 0.965073606 1.123446319 1.129485321 1.150206677 1.173802063 1.250466308 1.124141024 1.212909823 0.867979986 1 17.71784982 1.238666278 25 0.933989949 1.147549267 0.536661172 0.076829333 1.992932204 472563.1643 0.059248082 0.018473553 17.32472215 -1.238666278 0.213559318 MGEIEDGEADHITTDVQGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 MGEIEDGEADHITTDVQGQK 20 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 244.1 7.10E-30 153100000 350380 309490 270530 285670 317910 329590 333820 324120 445780 413900 FALSE TRUE 336686.7622 300663.6482 319420.7889 300413.4629 328135.8639 336254.5356 337905.389 317426.8087 395176.9233 385866.1843 0.872547987 0.779191493 0.827801974 0.77854312 0.850387718 0.87142784 0.875706146 0.82263443 1.02412945 1 18.55774109 1.238687402 24.99999993 1.012064808 0.834049525 0.814758772 0.033811693 1.306355714 258060.4294 0.026980255 0.008416281 17.32556484 -1.238687402 -0.178015283 GHKHEDGTQS(ph)DSEDPLAK ddPTM_BT-474_Pertuzumab_2h_R1 3 GHKHEDGTQSDSEDPLAK 18 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 GHKHEDGT(0.19)QS(0.81)DSEDPLAK;GHKHEDGT(0.022)QS(0.978)DSEDPLAK;GHKHEDGT(0.024)QS(0.976)DSEDPLAK 235.92 5.03E-24 2938050000 1741270 1520840 1372920 1235830 1553830 1403310 1564610 1423070 2119290 1771970 TRUE FALSE 1673219.243 1477467.132 1621037.184 1299611.334 1603810.353 1431685.89 1583758.165 1393683.107 1878717.084 1651952.894 1.01287346 0.894376067 0.981285357 0.786712103 0.970857195 0.86666266 0.958718721 0.843657899 1.137270373 1 20.65574112 1.238866874 24.99999995 1.068635198 0.91090277 0.418157375 0.072684088 6.757264471 552018.7807 0.05106618 0.015994358 17.3327261 -1.238866874 -0.157732428 APS(ph)PTGPALIS(ph)GASPVHCAADGTVELK ddPTM_BT-474_Pertuzumab_2h_R1 2 APSPTGPALISGASPVHCAADGTVELK 27 0 E7EWD6;Q76L83 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 2 APS(0.996)PT(0.014)GPALIS(0.517)GAS(0.472)PVHCAADGTVELK;APS(0.998)PT(0.01)GPALIS(0.614)GAS(0.378)PVHCAADGTVELK 103.17 0.0012402 947680000 326630 287778 291438 313060 302479 285322 318040 333740 384240 383740 TRUE FALSE 313864.9385 279570.8532 344107.3296 329217.0641 312208.5117 291091.4063 321932.2687 326848.1524 340622.6861 357748.948 0.877332946 0.781472188 0.96186818 0.920246072 0.872702809 0.813675087 0.899883201 0.913624356 0.952127708 1 18.448588 1.238980764 1.369107893 0.997461894 0.873762704 0.432423944 0.047585298 0.384663385 1.391231049 0.045370621 0.014119995 17.33727205 -1.238980764 -0.12369919 GYDFCQVLQWFAER ddPTM_BT-474_Pertuzumab_2h_R1 1 GYDFCQVLQWFAER 14 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 121.56 0.0014935 0 65593 74834 64073 60879 76764 64990 68962 72307 70470 68047 FALSE TRUE 63029.55304 72699.80759 75652.4164 64020.97249 79233.18378 66304.14233 69805.97758 70813.83518 62470.54103 63438.11608 0.99355966 1.14599569 1.192538825 1.009187795 1.248983871 1.0451783 1.100379108 1.116266364 0.984747734 1 15.95306231 1.23899074 24.99953779 0.992373813 1.110097555 0.271680709 0.074566641 13.19946432 767590.2441 0.05311352 0.016686636 17.33767031 -1.23899074 0.117723742 ASPRPYYPQTPNNRPPSTEPSEISLS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPRPYYPQTPNNRPPSTEPSEISLSPER 29 2 Q14686 Q14686 NCOA6 Nuclear receptor coactivator 6 1 ASPRPYYPQTPNNRPPSTEPS(0.003)EIS(0.006)LS(0.991)PER 119.72 3.01E-05 102890000 15043 17525 13394 13189 15482 18443 12355 17777 14107 17029 TRUE FALSE 14455.10293 17025.20416 15814.59375 13869.68587 15979.99259 18815.9301 12506.20419 17409.89874 12505.6325 15875.61066 0.91052264 1.072412553 0.996156563 0.873647393 1.006574987 1.185209848 0.787762087 1.09664435 0.787726077 1 13.95452447 1.239126138 24.99999999 0.893863095 0.992106312 0.09758693 0.11826544 33.11035831 1464318.954 0.084365111 0.02653474 17.34307642 -1.239126138 0.098243217 CVMDDDNEVRDR ddPTM_BT-474_Pertuzumab_2h_R1 1 CVMDDDNEVRDR 12 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 89.43 0.0056541 0 204840 225040 127390 172430 193330 209810 180510 195390 175920 168020 FALSE TRUE 196834.6263 218622.0795 150412.2068 181329.133 199548.635 214052.502 182719.1354 191355.1282 155950.2991 156639.8557 1.256606279 1.395698933 0.960242245 1.157618105 1.273932704 1.366526424 1.166491979 1.221624773 0.995597821 1 17.25709182 1.23915874 22.28870274 0.997798596 1.222888109 0.386859269 0.114312224 4.100372916 153044.9522 0.089687709 0.028211796 17.34437842 -1.23915874 0.225089513 TDSHFDWWEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TDSHFDWWEGK 11 0 H7C499;Q96HL8-4;Q96HL8-3;Q96HL8-2;Q96HL8 H7C499 SH3YL1 SH3 domain-containing YSC84-like protein 1 0 ; 153.34 3.25E-05 333630000 753940 712570 623150 660650 701430 695000 720830 721730 883550 821410 FALSE TRUE 724475.1913 692248.2013 735767.0669 694746.2257 723992.133 709053.3762 729651.7332 706826.0233 783253.1081 765775.1691 0.94606775 0.903983609 0.96081343 0.907245695 0.945436941 0.925928921 0.952827622 0.923020296 1.022823852 1 19.54656135 1.239233963 24.99991936 1.011411955 0.932911035 0.741899527 0.018460123 7.317261221 271767.8944 0.012550641 0.003957864 17.34738282 -1.239233963 -0.078500919 SQPPGEDS(ph)DT(ph)DVDDDSRPPGRPAEVHLER ddPTM_BT-474_Pertuzumab_2h_R1 6 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 2 SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;S(0.016)QPPGEDS(0.984)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER 219.83 3.97E-34 3530050000 288534 274783 212585 260205 230667 298304 244667 276205 247878 248204 TRUE FALSE 277257.7723 266946.4579 251003.8384 273634.2112 238086.6135 304335.9113 247661.3079 270501.2702 219739.9286 231392.922 1.198211985 1.153650058 1.084751583 1.18255221 1.028927815 1.315234315 1.070306325 1.169012725 0.949639802 1 17.81998521 1.239372556 24.99999687 0.974819838 1.147876122 0.460679864 0.075923357 16.94661388 521942.2768 0.053037142 0.016787109 17.35291967 -1.239372556 0.173056283 YQETFNVIER ddPTM_BT-474_Pertuzumab_2h_R1 4 YQETFNVIER 10 0 Q13011;M0R248;M0QZW4 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ;;; 198.62 6.83E-07 2199040000 558580 835180 590430 1043660 668750 646500 963080 808230 716340 685500 FALSE TRUE 536750.0761 811361.4841 697133.835 1097523.418 690260.9511 659572.673 974866.4611 791539.7681 635024.0863 639070.4744 0.839891839 1.26959626 1.090855959 1.717374627 1.080101458 1.03208128 1.525444376 1.238579781 0.993668323 1 19.28561551 1.239526289 21.12904111 0.996833849 1.241182028 0.125276579 0.23700221 6.670274428 146217.038 0.176065881 0.055712614 17.3590634 -1.239526289 0.244348179 LLPETVS(ph)PSAPSWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPETVSPSAPSWR 14 0 B0QXZ6;O95503 B0QXZ6 CBX6 Chromobox protein homolog 6 1 LLPET(0.152)VS(0.815)PS(0.033)APSWR;LLPET(0.162)VS(0.828)PS(0.01)APSWR 108.71 0.00084935 158567000 143806 145382 125890 163197 135339 143347 151928 166427 117078 139245 TRUE FALSE 138185.9025 141235.8477 148641.1234 171619.6167 139692.3018 146245.5746 153787.3403 162990.2243 103787.7963 129813.8121 1.064493063 1.08798783 1.14503319 1.322044349 1.07609737 1.126579461 1.184676251 1.2555692 0.799512737 1 16.98608437 1.23953188 24.99993632 0.899756336 1.162673522 0.573990822 0.088846619 17.17089238 442075.5938 0.068264676 0.021671811 17.35928685 -1.23953188 0.262917186 EESKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESKPR 6 1 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 106.29 0.029414 147941000 356680 391250 261551 325340 320210 322040 389990 397560 259080 328340 FALSE TRUE 342740.5513 380091.9331 308819.0839 342130.8364 330509.8455 328551.8694 394762.8143 389350.2471 229670.3246 306101.2393 1.119696712 1.24171968 1.008878907 1.117704839 1.079740305 1.073343807 1.28964788 1.271965602 0.750308379 1 18.22364936 1.239584076 24.99999335 0.87515417 1.155371908 0.530956571 0.103370034 20.49253496 500682.8872 0.082471417 0.026199674 17.36137332 -1.239584076 0.280217737 EQTLSPT(ph)ITSGLHNIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQTLS(0.152)PT(0.543)IT(0.152)S(0.152)GLHNIAR;EQTLS(0.025)PT(0.972)IT(0.002)S(0.002)GLHNIAR 269 4.49E-27 797050000 254680 319900 265820 330710 327930 306570 324000 322510 297930 285130 TRUE FALSE 244726.824 310776.7652 313859.5871 347777.9827 338478.1663 312769.0554 327965.2089 315850.0558 264110.2354 265817.8911 0.920655954 1.169134116 1.180731612 1.308331735 1.273346067 1.17662906 1.233796595 1.188219704 0.993575844 1 18.02007868 1.239628965 22.76682605 0.996787613 1.190429161 0.358866846 0.098080594 9.145631523 195033.0486 0.075758408 0.024045413 17.36316789 -1.239628965 0.193641548 LEDYQANR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEDYQANR 8 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 93.162 0.026205 177650000 81520 98141 83338 93231 93516 102810 90308 99843 86502 88111 FALSE TRUE 78334.10827 95342.11477 98399.03044 98042.66308 96524.02707 104888.8886 91413.21632 97781.20716 76682.65561 82143.16349 0.953629066 1.160682286 1.197896773 1.193558404 1.17507073 1.276903447 1.112852396 1.190375474 0.9335245 1 16.32585289 1.239737218 24.99975355 0.966762185 1.16380811 0.472748069 0.080412282 24.20651022 514426.5437 0.059622206 0.019007682 17.36749641 -1.239737218 0.197045924 FGEYHKDDPSSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 FGEYHKDDPSSFR 13 1 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;; 157.38 2.83E-05 2186580000 3521570 3722700 2800040 3065160 3396760 3464980 3391560 3489140 4155530 3907660 FALSE TRUE 3383943.151 3616532.241 3306069.515 3223353.275 3506019.87 3535044.27 3433066.926 3417088.04 3683811.656 3642990.708 0.928891513 0.992737158 0.90751522 0.884809634 0.962401541 0.970368731 0.942375977 0.937989777 1.01120534 1 21.79669188 1.239831694 24.99648949 1.005602695 0.941239045 0.44087903 0.029149808 30.46602895 599240.6286 0.022787495 0.00728962 17.37127492 -1.239831694 -0.06436365 VQAGPGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQAGPGSPR 9 0 Q6PK04;I3L0U5;I3L4F6 Q6PK04 CCDC137 Coiled-coil domain-containing protein 137 1 VQAGPGS(1)PR;VQAGPGS(1)PR 120.03 0.00076636 625330000 977440 946780 847460 973150 928540 872350 906690 1023780 837430 906750 TRUE FALSE 939240.5642 919778.7614 1000614.874 1023374.388 958407.3324 889989.5147 917786.3434 1002638.585 742368.4572 845335.0149 1.111086785 1.088064194 1.183690319 1.210613982 1.133760362 1.052824619 1.085707237 1.186084295 0.878194378 1 19.68916368 1.239833382 25 0.939097152 1.132254261 0.663867102 0.054754658 19.24577952 378098.1297 0.04300067 0.013734805 17.37134246 -1.239833382 0.193157109 AVAPS(ph)PSGAIGGLLEQFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVAPSPSGAIGGLLEQFAR 19 0 Q8NCE2;Q8NCE2-2;C9JSR1;Q8NCE2-3 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 AVAPS(0.981)PS(0.019)GAIGGLLEQFAR 59.872 0.036475 0 28146 27865 22764 24887 34143 27551 27805 30570 23471 25619 TRUE FALSE 27046.0232 27070.31748 26877.96118 26171.42105 35241.2406 28108.1001 28145.28591 29938.71882 20806.67048 23883.80231 1.132400229 1.133417415 1.125363576 1.095781179 1.475528902 1.17686873 1.178425677 1.253515601 0.871162397 1 14.54374491 1.239870499 24.99996865 0.935581131 1.19902425 0.489497414 0.106520878 27.56859473 526254.8222 0.081727194 0.026115002 17.37282717 -1.239870499 0.263443119 SLS(ph)DPIPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSDPIPQR 9 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.046)LS(0.954)DPIPQR;S(0.001)LS(0.999)DPIPQR 89.317 0.012786 517550000 585610 735700 492250 637120 576350 654820 623730 639350 607490 569980 TRUE FALSE 562723.7138 714718.5563 581210.525 670001.8396 594888.8212 668060.9091 631363.3943 626147.1991 538530.282 531374.7469 1.058995967 1.345036738 1.093786501 1.260883855 1.119527837 1.257231197 1.188169739 1.178353324 1.01346608 1 19.01937014 1.239895917 4.205159746 0.998337893 1.193196112 0.446364132 0.080683026 0.157501329 5.83295622 0.060861942 0.017764355 17.37384397 -1.239895917 0.194858219 MGPLGLDHMAS(ph)SIER ddPTM_BT-474_Pertuzumab_2h_R1 1 MGPLGLDHMASSIER 15 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 MGPLGLDHMAS(0.576)S(0.424)IER 141.6 3.05E-06 57062000 63074 55283 45221 50227 55007 53212 53868 63382 44763 56688 TRUE FALSE 60608.99835 53706.38297 53393.44064 52819.22149 56776.35011 54287.9831 54527.2527 62073.13955 39681.6919 52848.47127 1.146844874 1.016233425 1.010311923 0.999446535 1.074323415 1.027238476 1.031765941 1.174549387 0.750857895 1 15.68957412 1.240219612 25 0.875428973 1.058724017 0.468650951 0.078639183 34.90112897 526008.6531 0.057049 0.018363083 17.38679813 -1.240219612 0.183295045 RDS(ph)ASYR ddPTM_BT-474_Pertuzumab_2h_R1 5 RDSASYR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 RDS(1)ASYR;RDS(1)ASYR;RDS(0.998)AS(0.001)YR;RDS(1)ASYR;RDS(1)ASYR 133.76 0.001985 1459238000 183906 192952 174098 201108.1 221566 203355.2 193605.3 212357 196603.5 199078 TRUE FALSE 176718.7502 187449.1979 205561.3814 211487.3131 228692.8716 207467.1815 195974.6996 207971.7537 174285.8949 185594.2697 0.952177836 1.009994533 1.107584742 1.13951424 1.232219464 1.117853379 1.055930767 1.120572063 0.939069375 1 17.50179264 1.240241983 24.99921432 0.969534657 1.096233183 0.309392027 0.072954649 53.10125449 789634.5248 0.059199778 0.019057235 17.38769379 -1.240241983 0.126698527 ALEEALSIQT(ph)PPS(ph)SPPTAFGSPEGAGALLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALEEALSIQTPPSSPPTAFGSPEGAGALLR 30 0 E7EMV7;A0A0A0MRZ4;Q15025-7;Q15025-8;Q15025-5;Q15025-6;Q15025-4;Q15025-3;Q15025-2;Q15025;H0YC17 E7EMV7 TNIP1 TNFAIP3-interacting protein 1 2 ALEEALS(0.024)IQT(0.943)PPS(0.379)S(0.349)PPT(0.302)AFGS(0.003)PEGAGALLR 73.266 0.0092253 35310000 18722 23898 19291 27688 26460 27979 21776 26210 20334 21861 TRUE FALSE 17990.32354 23216.45244 22777.31283 29116.981 27311.10993 28544.75455 22042.5012 25668.75434 18025.76957 20380.335 0.88272953 1.13915951 1.117612288 1.428680196 1.340071688 1.400602814 1.081557354 1.25948638 0.884468757 1 14.31489015 1.240281461 24.99966809 0.942234304 1.215230995 0.309040987 0.157442991 52.30948596 760027.5934 0.122463056 0.039438743 17.38927442 -1.240281461 0.272996691 ILQGGVGIPHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILQGGVGIPHIR 12 0 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;P48729-3;A0A590UK94;A0A590UJQ7;E5RG27;D6RGE5 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 131.43 0.00024188 0 99945 102580 68144 101240 79489 93753 96499 97137 88112 87460 FALSE TRUE 96039.0389 99654.51884 80459.13666 106465.0085 82045.83588 95648.7499 97679.98363 95131.087 78109.89516 81536.2563 1.177869126 1.222211116 0.986789685 1.305738249 1.00624973 1.173082433 1.197994464 1.166733565 0.957977453 1 16.3151541 1.240341865 24.99993392 0.978988665 1.154724023 0.377421015 0.090210093 42.78254334 600530.4592 0.06234418 0.020094446 17.39169319 -1.240341865 0.175735358 DGDSYDPYDFS(ph)DTEEEMPQVHT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPY(0.001)DFS(0.999)DTEEEMPQVHT(1)PK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHT(1)PK 267.94 2.19E-44 6580900000 3596820 2811810 2479230 2367910 2738630 2729140 2960070 2804320 3842040 3380680 TRUE FALSE 3456252.298 2731619.932 2927282.011 2490118.119 2826720.521 2784325.081 2996296.222 2746409.812 3405907.726 3151703.532 1.09662989 0.866712209 0.928793581 0.790086407 0.896886554 0.883434959 0.950691012 0.871404872 1.080656125 1 21.5877004 1.240344233 24.99999861 1.04032809 0.904780495 0.311356417 0.07679787 48.82171019 684391.8747 0.054754843 0.017660807 17.39178802 -1.240344233 -0.135547595 S(ph)PPLSPVGTTPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPLSPVGTTPVK 13 0 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 S(1)PPLSPVGTTPVK 125.23 0.00021255 168010000 201870 181880 137900 185400 190420 140810 153270 184890 116530 131330 TRUE FALSE 193980.6972 176692.9605 162821.5976 194968.5162 196545.0322 143657.2747 155145.7641 181071.9569 103302.0029 122434.9021 1.584357841 1.443158425 1.329862602 1.592425957 1.605302318 1.17333597 1.267169422 1.478924341 0.843730024 1 16.90165536 1.240411639 24.99993284 0.92186485 1.427713673 0.679152506 0.140831079 27.01554918 364916.1204 0.109361575 0.035324576 17.39448758 -1.240411639 0.505848823 LDGLVETPTGYIESLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDGLVETPTGYIESLPR 17 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W118;F8VUX1;H0YHC3;F8W020;P55209-3;F8VXI6;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 176.91 2.46E-09 64851000 49759 51184 42077 49459 44525 52327 51136 54521 45879 50368 FALSE TRUE 47814.36327 49724.28243 49681.2499 52011.58492 45957.18706 53385.08779 51761.81766 53395.1223 40671.00826 46956.5305 1.018268657 1.058942854 1.058026421 1.107653917 0.97871769 1.136904435 1.1023348 1.137118133 0.866141681 1 15.51903819 1.240415928 24.99999992 0.933070831 1.077916422 0.503588288 0.056194236 35.97438768 484808.3197 0.041568065 0.01342178 17.39465934 -1.240415928 0.14484559 DTCYS(ph)PKPSVYLSTPSSASK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTCYSPKPSVYLSTPSSASK 20 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 DTCYS(1)PKPSVYLSTPSSASK 198.47 9.40E-22 381520000 558410 574360 506390 492510 600300 568850 528220 586310 574060 569890 TRUE FALSE 536586.7198 557979.8152 597905.9376 517928.5001 619609.1947 580352.5367 534684.5144 574202.4936 508895.1155 531290.8427 1.009967944 1.050234204 1.12538348 0.974849289 1.16623353 1.092344325 1.006387597 1.080768663 0.957846578 1 19.01914232 1.240446097 24.99791008 0.978923269 1.064321451 0.271158069 0.055293084 58.790068 779536.342 0.039577297 0.012791894 17.39586772 -1.240446097 0.085398182 LLLAEDS(ph)EEEVDFLSER ddPTM_BT-474_Pertuzumab_2h_R1 14 LLLAEDSEEEVDFLSER 17 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(0.999)EEEVDFLS(0.001)ER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER 334.43 4.18E-72 2916629000 1123456.8 1211427.6 1006604.9 1218017.2 1257339.2 1278609.5 1177750.8 1278144.3 1185961 1199494.1 TRUE FALSE 1079550.866 1176878.871 1188520.797 1280879.214 1297782.657 1304463.86 1192164.467 1251750.174 1051335.679 1118251.296 0.96539201 1.052427907 1.062838739 1.145430565 1.160546526 1.166521214 1.066097102 1.119381822 0.940160483 1 20.092813 1.240447068 24.99999927 0.97008021 1.0963091 0.405371354 0.059067528 47.16968984 625184.1632 0.046820874 0.01512686 17.39590665 -1.240447068 0.12622889 ELPESGIQLGT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELPESGIQLGTPR 13 0 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 ELPES(0.005)GIQLGT(0.995)PR 77.42 0.0359 0 64483 65756 64154 58022 51084 61816 67939 67611 59830 61993 TRUE FALSE 61962.93307 63880.70326 75748.0549 61016.52237 52727.16325 63065.96187 68770.4578 66214.80922 53038.34923 57794.15889 1.07213141 1.105314179 1.310652432 1.055755868 0.912326856 1.091216882 1.189920558 1.145700716 0.91771124 1 15.81863607 1.240544049 24.99955042 0.958855586 1.113367345 0.278025293 0.097573178 67.25223915 847752.084 0.077631573 0.025133678 17.39979168 -1.240544049 0.154511759 EMDLVGLGLHPLFSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EMDLVGLGLHPLFSSR 16 0 Q8TDD1-2;Q8TDD1;H0YHH7 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 115.31 0.00051539 169270000 538890 543820 453810 479570 522860 509160 492650 547550 514470 524890 FALSE TRUE 517829.583 528310.7861 535823.5619 504320.6652 539678.2667 519455.5641 498679.1981 536242.9012 456069.5224 489338.7328 1.058223166 1.079642282 1.094995197 1.03061669 1.102872572 1.061545979 1.019087934 1.095852147 0.932011901 1 18.90047396 1.240600953 24.99999625 0.966005934 1.067830964 0.646016024 0.030156764 28.5908153 350356.3076 0.021089482 0.006828652 17.40207166 -1.240600953 0.101825031 SLSNTKPTVNEHDLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSNTKPTVNEHDLLK 16 1 O75351 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 ; 196.64 2.73E-11 2531900000 6283000 5699200 5013000 4386800 5263900 5382700 5747300 5244800 7545100 6331700 FALSE TRUE 6037453.414 5536664.396 5918960.614 4613203.274 5433218.124 5491541.882 5817637.177 5136493.047 6688611.88 5902848.319 1.022803414 0.937964877 1.00272958 0.781521568 0.920440071 0.930320683 0.985564402 0.870171952 1.133116001 1 22.49297984 1.240640662 24.99999973 1.066558007 0.928472841 0.360544759 0.071891201 52.8482127 635249.9429 0.052106629 0.016893011 17.40366286 -1.240640662 -0.138085166 VIKDFMIQGGDFTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIKDFMIQGGDFTR 14 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 177.58 1.90E-06 1430400000 1349600 1588200 1114640 1535180 1158700 1155840 1587970 1520520 1770220 1880850 FALSE TRUE 1296856.14 1542906.091 1316080.243 1614410.824 1195970.638 1179211.877 1607404.052 1489120.731 1569272.047 1753458.354 0.739599054 0.87992172 0.75056259 0.920700979 0.682063897 0.672506349 0.916705006 0.849247846 0.894958265 1 20.74177174 1.240794999 0.991636363 0.991024872 0.787677717 0.398045331 0.082436337 0.511202722 1.063686372 0.076581364 0.026521701 17.40984879 -1.240794999 -0.203347155 S(ph)NSAPLIHGLSDTSPVFQAEAPSAR ddPTM_BT-474_Pertuzumab_2h_R1 6 SNSAPLIHGLSDTSPVFQAEAPSAR 25 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.5)NS(0.5)APLIHGLSDTSPVFQAEAPSAR;S(0.5)NS(0.5)APLIHGLSDTSPVFQAEAPSAR;S(0.5)NS(0.5)APLIHGLSDTSPVFQAEAPSAR;S(0.5)NS(0.5)APLIHGLSDTSPVFQAEAPSAR;S(0.5)NS(0.5)APLIHGLSDTSPVFQAEAPSAR;S(0.5)NS(0.5)APLIHGLSDTSPVFQAEAPSAR 278.77 2.33E-53 10492730000 1426536 1484610 1125675 1349157 1404691 1337273 1353515 1467209 1423548 1449106 TRUE FALSE 1370785.396 1442270.376 1329109.513 1418787.154 1449874.162 1364313.576 1370079.721 1436910.621 1261952.799 1350956.76 1.014677477 1.067591813 0.983828315 1.050209153 1.073220258 1.009886931 1.014155125 1.063624436 0.934117832 1 20.36555007 1.240965069 24.99999535 0.967058913 1.035405824 0.425963643 0.031375543 52.07101001 541452.0408 0.022064799 0.007204041 17.41666781 -1.240965069 0.068346911 QGGGGGGGSVPGIER ddPTM_BT-474_Pertuzumab_2h_R1 1 QGGGGGGGSVPGIER 15 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 126.1 0.001064 0 40485 65725 40780 42946 49793 57124 52757 56416 43657 49369 FALSE TRUE 38902.80144 63850.58735 48149.85315 45162.44821 51394.63707 58279.08642 53402.65595 55250.98989 38701.24039 46025.19366 0.845250141 1.387296441 1.046162967 0.981254931 1.116663136 1.266243155 1.160291825 1.200451003 0.840870778 1 15.49013617 1.24098915 24.99985172 0.920435359 1.135924246 0.236367768 0.14643487 78.04897601 803525.5416 0.102968682 0.033605098 17.41763357 -1.24098915 0.215488887 GSDIDNPTLTVMDIS(ph)PPSRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSDIDNPTLTVMDISPPSRSPR 22 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 2 GSDIDNPTLTVMDIS(0.999)PPS(0.119)RS(0.882)PR;GSDIDNPTLTVMDIS(0.992)PPS(0.274)RS(0.734)PR 82.503 0.0024074 80484000 85579 87197 71292 89342 86832 85100 93082 91811 84828 85356 TRUE FALSE 82234.47807 84710.22693 84176.05028 93952.95133 89625.03014 86820.78031 94221.16536 89915.07077 75198.68107 79574.76209 1.033424115 1.064536352 1.057823461 1.180687807 1.126299693 1.091059251 1.184058398 1.129944575 0.945006672 1 16.28002332 1.241022743 24.99997408 0.972503298 1.112341008 0.553481252 0.048754265 45.19743009 458965.5774 0.038300416 0.012514994 17.41898091 -1.241022743 0.13983771 LHVENEDKK ddPTM_BT-474_Pertuzumab_2h_R1 5 LHVENEDKK 9 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;; 211.79 2.97E-06 3989530000 8006830 6825750 6244330 5732360 6728470 6624360 7779000 6723490 10407450 8782680 FALSE TRUE 7693914.232 6631086.293 7372819.335 6028207.787 6944897.348 6758309.098 7874201.729 6584647.582 9226039.908 8187821.261 0.939677844 0.809871892 0.900461686 0.736240765 0.848198456 0.825409945 0.961696827 0.804200211 1.126800356 1 22.96504818 1.241213658 24.99997965 1.063400217 0.851446903 0.593952656 0.069500411 40.15363614 378404.3257 0.048055439 0.015734982 17.42663993 -1.241213658 -0.211953315 MREDYDSVEQDGDEPGPQR ddPTM_BT-474_Pertuzumab_2h_R1 3 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;; 184.2 2.67E-14 1564490000 327079 312652 223908 286243 305473 302502 277339 289114 301960 264100 FALSE TRUE 314296.3911 303735.4711 264373.1564 301016.0355 315298.8165 308618.7977 280733.1576 283143.6949 267682.7667 246212.2718 1.2765261 1.233632544 1.073761086 1.222587458 1.280597487 1.25346635 1.14020782 1.149998304 1.087203188 1 17.90954315 1.241382754 1.023006432 1.003605212 1.217051439 0.601418373 0.057736222 0.351775262 0.772185964 0.056762227 0.01940756 17.43342646 -1.241382754 0.213446227 GYYSPYSVS(ph)GSGSTAGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYSVS(0.877)GS(0.123)GSTAGSR;GYYSPYS(0.001)VS(0.962)GS(0.027)GS(0.009)T(0.001)AGSR;GYYSPYS(0.006)VS(0.984)GS(0.01)GSTAGSR 350.49 2.36E-90 1360640000 772730 853290 617340 830740 740250 739960 760430 825700 759150 786130 TRUE FALSE 742530.8573 828955.0047 728907.0707 873614.591 764060.8135 754922.4982 769736.3698 808649.0065 672974.4746 732884.7149 1.013161882 1.131085132 0.994572619 1.192021846 1.042538885 1.030069918 1.050283017 1.103378185 0.91825421 1 19.48322675 1.241384351 24.99990227 0.959127089 1.071628587 0.359460578 0.058960838 67.40892474 596849.0796 0.040300563 0.013242246 17.43349056 -1.241384351 0.112501498 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR ddPTM_BT-474_Pertuzumab_2h_R1 14 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;;;;;;; 268.96 3.12E-60 17954810000 4050759 3840440 3582105 3984627 4081805 4188242 3921051 4342310 3847067 4075265 FALSE TRUE 3892450.86 3730914.411 4229471.057 4190274.077 4213099.965 4272931.123 3969037.995 4252639.781 3410364.082 3799243.672 1.02453309 0.982015036 1.113240272 1.102923223 1.108931232 1.124679408 1.044691612 1.119338518 0.897642893 1 21.85728081 1.241544097 24.99999875 0.948821431 1.079340364 0.512915278 0.050151334 57.51725925 481999.2502 0.037805745 0.012454668 17.43990429 -1.241544097 0.130518934 EAAATEIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAAATEIRR 9 1 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 100.02 0.0079288 153550000 127520 139050 109400 143800 117960 135380 142010 133100 131660 120530 FALSE TRUE 122536.3774 135084.4301 129171.0136 151221.5352 121754.2905 138117.4764 143747.9609 130351.4385 116714.5088 112366.3957 1.090507323 1.202178189 1.149551988 1.345789675 1.083547174 1.229170656 1.279278915 1.160057129 1.038695848 1 16.77785112 1.241593594 3.291593962 1.004683827 1.199385888 0.466253965 0.07534604 0.193190142 3.687748964 0.063755489 0.018284988 17.44189203 -1.241593594 0.19470206 KGTDLWLGVDALGLNIYEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGTDLWLGVDALGLNIYEK 19 1 P15311;E7EQR4 P15311 EZR Ezrin 0 88.09 0.0041884 179340000 338870 425910 359670 423460 357020 379910 404080 422530 373310 392230 FALSE TRUE 325626.5858 413763.4638 424670.3698 445314.8213 368503.8725 387592.0405 409025.2519 413804.6078 330933.4138 365663.9127 0.890507853 1.131540328 1.161368008 1.217825456 1.007766585 1.059967984 1.118582495 1.131652847 0.90502071 1 18.48015873 1.241706884 24.99976785 0.952510332 1.097233007 0.275963142 0.088381065 92.73643746 736919.4183 0.064218207 0.021219208 17.44644254 -1.241706884 0.144722675 (ac)SESLVVCDVAEDLVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SESLVVCDVAEDLVEK 16 0 P60983;G3V4P8;G3V3X4 P60983 GMFB Glia maturation factor beta 0 ;; 100.93 4.57E-14 77756600 72703.9 72996.5 54211.8 69275.5 69220.7 70702.2 62845.1 70790 91849.6 85405.2 FALSE TRUE 69862.55121 70914.71129 64009.07819 72850.81686 71447.24668 72131.84693 63614.21713 69328.16176 81423.21847 79620.62973 0.877442837 0.890657503 0.803925797 0.914974135 0.897345913 0.90594419 0.798966516 0.870731141 1.02263972 1 16.28085466 1.241839981 24.92297909 1.011319908 0.868667428 0.691838107 0.037718869 40.45765809 307496.4398 0.027695958 0.009170554 17.45179011 -1.241839981 -0.14265248 AKS(ph)PTPESSTIASYVTLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AKSPTPESSTIASYVTLR 18 1 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 AKS(0.707)PT(0.29)PES(0.003)S(0.001)TIASYVTLR;AKS(0.829)PT(0.171)PES(0.001)STIASYVTLR;AKS(0.682)PT(0.318)PESSTIASYVTLR 198.09 1.07E-15 3075120000 450636 434213 377201 420135 404601 427341 431048 433058 545433 493718 TRUE FALSE 433024.6469 421829.6704 445369.6115 441818.2177 417615.3586 435982.1278 436323.2944 424115.201 483517.7325 460278.0401 0.940789282 0.916467078 0.96760995 0.959894193 0.907311065 0.947214705 0.947955923 0.921432621 1.050490552 1 18.81214609 1.24188462 24.99999951 1.025245292 0.938393879 0.727531285 0.021213406 37.78275979 284184.3224 0.014965573 0.004959304 17.45358397 -1.24188462 -0.086851413 VGWSVDFSRPQLGEDEFSYGFDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGWSVDFSRPQLGEDEFSYGFDGR 24 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 227.3 4.12E-33 1600331000 688748 761291 532327 772300 672522 722633 698035 752397 672804 702179 FALSE TRUE 661830.9667 739579.7261 628530.3305 812158.4956 694154.2809 737245.1344 706577.7611 736859.739 596430.1105 654619.7909 1.011015823 1.129785161 0.960145628 1.240656801 1.060393056 1.126218829 1.079371218 1.125630097 0.911109195 1 19.32029769 1.241902892 24.99999014 0.955554574 1.094510984 0.349878589 0.074125704 78.6493064 588328.5911 0.049578163 0.016454183 17.45431832 -1.241902892 0.13895641 EDDRETLVSQCR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDDRETLVSQCR 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 ;; 212.1 2.21E-08 1156410000 1852433 1776190 1330217 1666981 1689364 1652221 1587983 1787659 1689932 1746076 FALSE TRUE 1780037.87 1725534.8 1570616.802 1753014.089 1743703.927 1685630.041 1607417.211 1750743.217 1498098.004 1627812.717 1.093515152 1.060032756 0.964863332 1.076913868 1.071194437 1.035518412 0.987470606 1.075518823 0.920313491 1 20.63450329 1.2419044 24.99999372 0.96015674 1.043690286 0.389950306 0.042707186 80.34086844 600711.1596 0.030391273 0.010075339 17.45437891 -1.2419044 0.083533546 (ac)MNTAPSRPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 3 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.014)RPS(0.933)PT(0.053)R;MNTAPS(0.02)RPS(0.788)PT(0.192)R;MNTAPS(0.127)RPS(0.703)PT(0.17)R 53.769 0.00019214 5313100000 158517 140328 131264 139076 151492 171153 139210 153915 142869 139166 TRUE FALSE 152321.9804 136325.9828 154986.3248 146253.729 156364.8778 174613.8309 140913.6936 150736.6015 126651.1101 129740.1629 1.174054179 1.050761613 1.194590182 1.127281836 1.205215673 1.345873375 1.086122373 1.161834532 0.976190466 1 16.98526563 1.241911336 24.34840763 0.988095149 1.166651878 0.479997974 0.074976706 49.80646739 361956.6884 0.055807706 0.018481504 17.4546577 -1.241911336 0.178556728 DLLHPS(ph)PEEEKRK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 1 DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK 152.94 2.37E-05 2626920000 3262010 2517540 2116930 1687460 2190780 2635260 2451190 2237760 3828300 3027430 TRUE FALSE 3134527.043 2445742.224 2499506.342 1774550.013 2261248.428 2688546.763 2481188.396 2191549.474 3393727.434 2822379.47 1.110597309 0.866553293 0.88560251 0.628742532 0.801185118 0.952581604 0.879112261 0.776490014 1.20243485 1 21.42848054 1.241932073 24.99996776 1.101217451 0.853770693 0.364978969 0.12546219 82.83464048 614272.3773 0.092067613 0.030534893 17.45549115 -1.241932073 -0.247446759 FYPPKVELFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYPPKVELFFK 11 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 110.86 0.0015853 137640000 327090 383890 234620 217410 292070 211410 357200 296570 373760 338490 FALSE TRUE 314306.9612 372941.8331 277021.0531 228630.5562 301464.6968 215684.855 361571.5205 290445.7259 331332.3317 315563.7708 0.996017256 1.181827154 0.877860765 0.72451459 0.955320999 0.683490549 1.145795411 0.920402634 1.049969491 1 18.26757206 1.241950208 24.99997367 1.024984762 0.93681247 0.054391388 0.148925918 279.8275272 2063999.718 0.110596172 0.036680557 17.45622005 -1.241950208 -0.088172291 LGWDPKPGEGHLDALLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGWDPKPGEGHLDALLR 17 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 133.78 1.15E-05 3047500000 5038300 5113500 4099800 4481500 4613200 4599600 4993500 4911200 6142400 5669800 FALSE TRUE 4841397.666 4967667.987 4840725.06 4712790.752 4761587.768 4692607.063 5054611.947 4809782.004 5445140.503 5285779.396 0.915928816 0.939817502 0.915801568 0.891598078 0.900829832 0.88777959 0.956266156 0.909947549 1.030149027 1 22.33368478 1.241962252 24.99996368 1.015074541 0.915282942 0.789574783 0.020715952 34.72955789 255256.9596 0.015394251 0.005109585 17.45670415 -1.241962252 -0.099791598 STSYGYS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 7 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R 149.27 0.00053277 11717548000 6990333 7399191 5333581 7317870 7625195 6372364 6892751 7408159 6575291 6842903 TRUE FALSE 6717143.058 7188173.317 6297477.732 7695546.148 7870466.322 6501217.566 6977106.549 7255177.928 5828891.532 6379427.085 1.052938292 1.126774117 0.98715412 1.20630678 1.233726198 1.019091131 1.09368858 1.13727735 0.913701411 1 22.60499544 1.241983641 24.99482557 0.956850678 1.1090741 0.391216129 0.074949422 81.06354596 591959.8394 0.054740457 0.018161484 17.45756394 -1.241983641 0.152223422 TKVEAFQTTISK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKVEAFQTTISK 12 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 125.53 0.00027689 1134150000 2009970 1841760 1648190 1657710 1802860 1882230 1872070 2030120 2523200 2533100 FALSE TRUE 1931418.15 1789234.808 1946054.597 1743264.612 1860850.629 1920289.98 1894980.953 1988197.313 2236776.914 2361530.881 0.817866989 0.757658866 0.824064852 0.738192596 0.787984881 0.813154719 0.802437507 0.841910359 0.947172418 1 21.17129097 1.24219888 1.575472023 1.002519264 0.788144817 0.894025692 0.025075128 0.096230291 0.441525522 0.02188885 0.006611061 17.46621814 -1.24219888 -0.214374447 DKGS(ph)PAVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKGSPAVK 8 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 DKGS(1)PAVK;DKGS(1)PAVK;DKGS(1)PAVK;DKGS(1)PAVK 119.74 0.00099041 3280500000 7677300 5712160 4872180 4824110 5057170 5701880 6506400 7038300 7835100 9073100 TRUE FALSE 7377262.628 5549254.79 5752691.307 5073082.895 5219838.466 5817175.92 6586027.269 6892956.645 6945692.295 8458570.856 0.872164193 0.656051109 0.680102042 0.599756505 0.61710643 0.687725624 0.778621753 0.814907951 0.821142533 1 23.0119825 1.242497673 0.821119484 0.988310043 0.677352105 0.623337224 0.073970353 0.361257373 0.543162743 0.070807917 0.026924681 17.47823899 -1.242497673 -0.310957937 T(ph)RSYDNLTTACDNTVPLASR ddPTM_BT-474_Pertuzumab_2h_R1 2 TRSYDNLTTACDNTVPLASR 20 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 T(0.662)RS(0.338)YDNLTTACDNTVPLASR;T(0.657)RS(0.343)YDNLTTACDNTVPLASR 241.71 1.52E-29 1091650000 339520 333350 203143 243110 320270 320790 290850 304510 297980 290070 TRUE FALSE 326251.183 323843.1844 239855.459 255656.9362 330571.7754 327276.5936 294409.5093 298221.7621 264154.5596 270423.3005 1.206446273 1.19754172 0.886962989 0.94539537 1.222423418 1.210238145 1.08869875 1.102796103 0.976818784 1 18.04485994 1.242616866 23.95501882 0.988409355 1.104103525 0.161648616 0.108311996 113.3455677 669445.6007 0.084337277 0.028219843 17.48303657 -1.242616866 0.115694171 APQTSSS(ph)PPPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.017)S(0.017)S(0.037)S(0.928)PPPVR;APQT(0.003)S(0.124)S(0.267)S(0.606)PPPVR;APQTS(0.004)S(0.004)S(0.993)PPPVR;APQT(0.004)S(0.087)S(0.087)S(0.821)PPPVR 181.9 1.84E-05 22809200000 1521900 1655790 1310550 1741520 1559480 1626590 1601010 1689100 1623640 1633780 TRUE FALSE 1462422.465 1608568.49 1547395.538 1831400.056 1609642.09 1659480.764 1620603.639 1654219.495 1439331.194 1523122.625 0.960147555 1.056099137 1.015936283 1.2023983 1.056804005 1.089525385 1.064000765 1.086071119 0.944987075 1 20.53860067 1.242643916 24.99026445 0.972493521 1.069963086 0.285258574 0.059223073 114.1791617 698825.5011 0.042069032 0.014125453 17.48412553 -1.242643916 0.097469566 ASIGQS(ph)PGLPSTTFK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASIGQSPGLPSTTFK 15 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ASIGQS(1)PGLPSTTFK;ASIGQS(1)PGLPSTTFK;ASIGQS(1)PGLPSTTFK;ASIGQS(0.999)PGLPS(0.001)TTFK 313.26 3.32E-56 1929440000 4192260 4260390 3671950 3898220 4232480 4040000 3886360 4337390 4192900 4254030 TRUE FALSE 4028421.844 4138887.849 4335553.047 4099407.601 4368621.563 4121691.568 3933922.436 4247821.381 3716939.57 3965900.759 1.015764662 1.043618613 1.09320765 1.033663687 1.10154586 1.039282579 0.991936681 1.071086151 0.937224554 1 21.91921715 1.242697553 24.99942275 0.968612268 1.049255324 0.463517461 0.034488343 80.54167628 486735.6522 0.024261222 0.008143073 17.48628501 -1.242697553 0.080643057 (ac)SRPSS(ph)TGPSANKPCSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRPSSTGPSANKPCSK 16 2 O43255 O43255 SIAH2 E3 ubiquitin-protein ligase SIAH2 1 S(0.012)RPS(0.125)S(0.684)T(0.144)GPS(0.035)ANKPCSK;S(0.002)RPS(0.115)S(0.765)T(0.115)GPS(0.003)ANKPCSK 77.39 0.00011763 533510000 186325 173089 148354 137178 142224 178932 159418 163567 229950 202075 TRUE FALSE 179043.213 168152.6712 175164.8679 144257.773 146798.7641 182550.1276 161369.0052 160189.2843 203847.04 188388.2803 0.950394646 0.892585627 0.92980767 0.765747067 0.77923512 0.969010001 0.856576667 0.850314489 1.08205797 1 17.52334969 1.242705138 24.9982464 1.041029017 0.871179241 0.506415904 0.065822852 76.67742186 462513.4189 0.048428583 0.016266778 17.48659043 -1.242705138 -0.169849776 RNS(ph)LEGYSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSLEGYSR 9 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 RNS(0.679)LEGYS(0.321)R;RNS(0.923)LEGYS(0.077)R 122.86 0.00060793 892220000 866880 890820 743300 952080 960300 891080 893310 968640 859510 909670 TRUE FALSE 833001.3712 865414.6858 877630.8446 1001216.963 991188.9216 909098.2481 904242.595 948637.2455 761942.0282 848057.2407 0.982246635 1.020467304 1.034872179 1.180600689 1.168775967 1.071977462 1.066251842 1.118600491 0.898455896 1 19.69380212 1.242730706 24.99973867 0.949227932 1.083917187 0.406325313 0.063348318 98.17010371 588559.9891 0.048786583 0.016378041 17.48761993 -1.242730706 0.134689255 S(ph)PRPAS(ph)PASNVVVLPSGSTVYVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPRPASPASNVVVLPSGSTVYVK 23 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 2 S(1)PRPAS(0.865)PAS(0.135)NVVVLPSGSTVYVK 156.37 1.05E-08 172260000 231240 228570 217280 255540 216350 226000 209700 259900 294860 301200 TRUE FALSE 222202.8852 222051.4074 256547.3294 268728.45 223309.0942 230569.8748 212266.3713 254532.9742 261388.729 280799.4557 0.79132235 0.790782898 0.913631861 0.957012005 0.795261849 0.82111938 0.755935836 0.906458218 0.930873346 1 18.09918061 1.242826336 2.095605222 0.98973264 0.837303344 0.453227271 0.059486837 0.295475706 2.228361886 0.058224499 0.016899284 17.49147105 -1.242826336 -0.152429296 LDYGQHVVAGTPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDYGQHVVAGTPGR 14 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;; 165.34 3.98E-06 2157030000 2340790 2411150 2032450 2411830 2484300 2455790 2405050 2484250 2560280 2435180 FALSE TRUE 2249309.339 2342386.363 2399758.927 2536304.835 2564209.766 2505447.756 2434483.721 2432949.369 2269647.748 2270243.09 0.990779071 1.031777775 1.057049326 1.117195267 1.129486872 1.103603296 1.072344954 1.0716691 0.999737763 1 21.11441535 1.242910523 6.374440975 0.998894085 1.074455731 0.356212507 0.038520431 0.159698096 27.49303447 0.03365272 0.010445257 17.49486206 -1.242910523 0.075561646 ASDPQS(ph)PPQVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASDPQSPPQVSR 12 0 Q7L7X3-3;Q7L7X3;Q7L7X3-2 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 ASDPQS(1)PPQVSR;ASDPQS(1)PPQVSR 176.43 2.62E-05 611580000 291500 356060 267010 381590 314290 341500 316600 348460 311660 320360 TRUE FALSE 280107.8577 345905.5174 315264.6466 401283.9056 324399.4233 348405.364 320474.6455 341264.1792 276281.6634 298661.7319 0.937876627 1.158184931 1.055591035 1.343606706 1.08617673 1.166555092 1.073035516 1.14264448 0.925065497 1 18.18815287 1.242967211 24.99958874 0.962532717 1.125770257 0.288543016 0.098912547 117.6222632 667328.244 0.06758322 0.022783861 17.4971458 -1.242967211 0.16323754 TQEELRR ddPTM_BT-474_Pertuzumab_2h_R1 4 TQEELRR 7 1 P15924 P15924 DSP Desmoplakin 0 ;;; 127.02 0.0062459 1340330000 1370290 1407130 1128090 1413730 1253130 1328400 1297270 1390230 1322590 1315890 FALSE TRUE 1316737.552 1367000.03 1331960.957 1486692.775 1293438.065 1355261.158 1313146.378 1361521.265 1172455.128 1226763.598 1.073342536 1.114314145 1.08575194 1.211882042 1.05434989 1.104745169 1.07041518 1.109848113 0.955730289 1 20.22642583 1.242975781 24.99859253 0.977865117 1.103605797 0.587381357 0.041977346 65.65389276 371748.9995 0.028997319 0.009764463 17.4974911 -1.242975781 0.12574068 STS(ph)PIIGSPPVR ddPTM_BT-474_Pertuzumab_2h_R1 5 STSPIIGSPPVR 12 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 S(0.001)T(0.101)S(0.898)PIIGSPPVR;S(0.002)T(0.039)S(0.959)PIIGSPPVR;S(0.044)T(0.044)S(0.911)PIIGSPPVR;ST(0.013)S(0.987)PIIGSPPVR;ST(0.001)S(0.999)PIIGSPPVR 258.53 3.22E-21 9951270000 4149140 4113110 3772540 5275240 4739830 4134780 4826360 4733920 4360240 4394170 TRUE FALSE 3986987.022 3995808.13 4454321.898 5547495.769 4892290.937 4218388.085 4885426.437 4636162.898 3865283.835 4096548.952 0.973255066 0.975408369 1.087335206 1.354187594 1.194246912 1.029741896 1.192571234 1.131724032 0.943546356 1 21.96597762 1.243111631 24.9876182 0.971773147 1.123211694 0.219905526 0.109192093 161.6617301 887652.8974 0.084339572 0.028503097 17.50296528 -1.243111631 0.151438547 ESVFTVEGGHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESVFTVEGGHR 11 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;; 199.09 5.14E-08 3323350000 1408070 2124320 1653870 3100550 1296750 1758200 2445060 2112170 1908510 1907520 FALSE TRUE 1353041.068 2063736.474 1952761.099 3260569.757 1338461.141 1793752.009 2474983.376 2068552.951 1691863.946 1778321.971 0.760852697 1.160496528 1.098091983 1.833509235 0.752653998 1.00867674 1.391752121 1.163204968 0.951382243 1 20.76208512 1.243116366 24.01920067 0.97569108 1.162299369 0.049044227 0.293436269 198.6083367 1047198.372 0.207373909 0.069860355 17.50315608 -1.243116366 0.186608288 EDMTYAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDMTYAVR 8 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 95.541 0.02228 107890000 132560 169960 145150 180930 138540 153100 157320 171610 133330 150610 FALSE TRUE 127379.4086 165112.9072 171381.8338 190267.819 142996.2649 156195.7869 159245.3292 168066.1935 118194.9374 140409.0506 0.907202265 1.175942053 1.22058965 1.355096543 1.018426265 1.112433894 1.134152881 1.1969755 0.841790019 1 17.09927641 1.243221149 24.99959994 0.920894979 1.148176203 0.35276348 0.118365941 110.4770253 592636.2642 0.084071852 0.028446843 17.50737964 -1.243221149 0.227281224 QDATVWIPS(ph)PSRQPVYYDELDAASSSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDATVWIPSPSRQPVYYDELDAASSSLR 28 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 QDATVWIPS(0.834)PS(0.166)RQPVYYDELDAASSSLR;QDATVWIPS(0.971)PS(0.029)RQPVYYDELDAASSSLR 154.99 1.39E-08 189382000 213620 209224 193824 201540 180065 216574 205211 231490 194129 223042 TRUE FALSE 205271.4942 203257.1364 228852.3084 211941.5036 185856.9543 220953.2747 207722.4336 226709.6506 172092.2898 207935.1667 0.98718989 0.977502457 1.100594537 1.019267241 0.893821652 1.062606572 0.998976926 1.090290085 0.827624747 1 17.66577425 1.243245184 24.99999963 0.913812381 1.018076278 0.261915927 0.068752683 137.4844467 733740.9294 0.04781379 0.016172101 17.50834854 -1.243245184 0.104263897 SST(ph)PSHGQTTATEPTPAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTPSHGQTTATEPTPAQK 19 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 S(0.134)S(0.134)T(0.731)PS(0.001)HGQTTATEPTPAQK 202.73 1.98E-15 604280000 416350 396790 345610 338730 337040 394790 383680 391550 482500 446840 TRUE FALSE 400078.5817 385473.9377 408069.4151 356211.8959 347881.1977 402772.9243 388375.5906 383464.3557 427728.6228 416575.1288 0.960399587 0.925340739 0.979581801 0.855096407 0.835098338 0.96686743 0.932306237 0.920516683 1.026774268 1 18.66821718 1.24350418 24.97054128 1.013387154 0.920838765 0.409242418 0.043952505 109.0791975 550995.2022 0.032580806 0.011069842 17.51879294 -1.24350418 -0.092548389 (ac)AQHFSLAACDVVGFDLDHTLCR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQHFSLAACDVVGFDLDHTLCR 22 0 Q5TFE4;Q5QPD0 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 92.336 7.71E-18 95988000 10013.9 7002.7 7418.7 10493.4 9031.8 9965.3 10318.5 9837.8 7558.1 8215.9 FALSE TRUE 9622.545717 6802.989852 8759.424118 11034.96563 9322.316049 10166.80519 10444.78089 9634.645992 6700.136174 7659.429775 1.256300534 0.888184898 1.143613085 1.440703284 1.217103143 1.327357975 1.363649932 1.257880322 0.874756525 1 12.90302128 1.243595097 24.97330066 0.937378208 1.23855119 0.411520016 0.143235218 114.2211415 566610.8543 0.10929172 0.037153738 17.52246082 -1.243595097 0.301172982 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI ddPTM_BT-474_Pertuzumab_2h_R1 4 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 36 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;; 264.97 1.23E-62 1799720000 720265 688558 546315 518214 674462 645894 698094 633246 922086 770163 FALSE TRUE 692116.2475 668921 645046.2732 544959.0866 696156.6828 658954.4192 706637.4832 620169.2488 817414.663 717999.174 0.963951314 0.931645919 0.898394172 0.758996816 0.969578668 0.917764871 0.9841759 0.863746466 1.138461843 1 19.45362266 1.243650925 24.99999957 1.069230937 0.909782068 0.459131056 0.068671078 97.11398135 476973.182 0.047986414 0.016337962 17.52471344 -1.243650925 -0.159448869 GCTSSSSLS(ph)PPRGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GCTSSSSLSPPRGDR 15 1 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 GCTSSS(0.003)S(0.001)LS(0.996)PPRGDR;GCT(0.001)S(0.004)S(0.009)S(0.042)S(0.033)LS(0.91)PPRGDR 101.67 0.0010186 963110000 205702 240740 178505 228830 222800 218000 207800 233450 209110 220500 TRUE FALSE 197662.9384 233874.3309 210764.8243 240639.9437 229966.5643 222408.1094 210343.1186 228629.1759 185372.7095 205565.3386 0.961557721 1.137712868 1.025293592 1.170625094 1.118703016 1.081933904 1.023242148 1.112197112 0.901770263 1 17.6492375 1.243660979 24.99997442 0.950885115 1.082225748 0.399851666 0.062632176 102.9872957 504823.2918 0.041828225 0.014220764 17.52511913 -1.243660979 0.131340632 KMQQNIQELEEQLEEEESAR ddPTM_BT-474_Pertuzumab_2h_R1 5 KMQQNIQELEEQLEEEESAR 20 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 266.62 1.48E-36 1205778000 872481 920192 671365 710282 815920 956623 813126 858827 831019 813419 FALSE TRUE 838383.4779 893949.0251 792695.5899 746939.7391 842164.8078 975966.5725 823077.2792 841091.9223 736685.207 758325.4066 1.105572187 1.178846202 1.045323792 0.984985776 1.110558608 1.28700234 1.085387977 1.109143799 0.971463175 1 19.53245753 1.243685328 24.41132638 0.985731549 1.113093031 0.314400516 0.075382621 107.6979131 513041.4744 0.056818989 0.019298801 17.52610173 -1.243685328 0.127361482 ELDEEGS(ph)DPPLPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELDEEGSDPPLPGR 14 0 C9JQV0;Q9BRJ6;H7C0T1;H7C2R9 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR 155.08 5.85E-06 1225550000 2459040 2323760 2145950 1945710 2591860 2255100 2123850 2438510 2147060 2259270 TRUE FALSE 2362937.998 2257488.64 2533770.901 2046128.326 2675229.531 2300699.667 2149842.312 2388153.916 1903334.75 2106247.631 1.121870935 1.071805901 1.202978636 0.971456678 1.270140078 1.092321546 1.020697795 1.133842898 0.903661432 1 21.00624363 1.243802693 24.99996484 0.951830693 1.10924555 0.370301754 0.082820638 115.2244942 549537.741 0.054792512 0.018675563 17.53083868 -1.243802693 0.157414857 RQS(ph)PSPS(ph)TRPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(0.999)PS(0.09)PS(0.807)T(0.104)RPIR 74.141 0.020007 480780000 23072 27676 23731 30872 25048 37169 24524 29275 25622 26307 TRUE FALSE 22170.32073 26886.70758 28019.71959 32465.30762 25853.69167 37920.58265 24824.13205 28670.46102 22713.49798 24525.20346 0.903981114 1.09628887 1.142486734 1.323752836 1.054168285 1.5461883 1.012188628 1.169020313 0.92612883 1 14.58197748 1.243827492 24.87242092 0.963064382 1.161841384 0.173794495 0.167890142 181.4581551 856956.5106 0.115959184 0.039538537 17.53183975 -1.243827492 0.198777001 S(ph)PVREPIDNLTPEER ddPTM_BT-474_Pertuzumab_2h_R1 2 SPVREPIDNLTPEER 15 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;H0Y4X3;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 1 S(1)PVREPIDNLTPEER;S(1)PVREPIDNLTPEER 120.32 8.67E-05 570760000 117015 154858 115592 218680 124497 136454 159442 160225 131002 141930 TRUE FALSE 112441.9244 150441.6015 136482.0457 229966.101 128501.5591 139213.1934 161393.2989 156916.2978 116131.2022 132316.9547 0.849792264 1.13697902 1.031478136 1.737994209 0.971164726 1.052119086 1.219747683 1.185912252 0.877674388 1 17.01363841 1.244039154 24.97898381 0.938837163 1.159180866 0.120143138 0.224994249 241.4767296 1101034.633 0.15700924 0.053685563 17.54038632 -1.244039154 0.220343703 SASS(ph)GAEGDVSSEREP ddPTM_BT-474_Pertuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SAS(0.002)S(0.998)GAEGDVSSEREP;SAS(0.002)S(0.998)GAEGDVSSEREP 354.97 5.84E-87 2139100000 1409150 1539120 1176730 1511980 1500800 1469110 1335610 1500230 1457640 1445810 TRUE FALSE 1354078.86 1495225.805 1389391.287 1590013.469 1549074.595 1498816.411 1351955.595 1469249.726 1292174.818 1347884.001 1.004595988 1.109313415 1.030794405 1.179636725 1.149264027 1.111977299 1.00302073 1.090041669 0.958669156 1 20.36226491 1.244059777 24.99919153 0.97933456 1.086141018 0.361542854 0.056054969 131.0526803 595786.6005 0.040589841 0.01388175 17.54121927 -1.244059777 0.106806458 FCLSS(ph)PTEALK ddPTM_BT-474_Pertuzumab_2h_R1 3 FCLSSPTEALK 11 0 E7EWD6;Q76L83;Q76L83-2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 FCLS(0.035)S(0.963)PT(0.002)EALK;FCLS(0.03)S(0.953)PT(0.016)EALK;FCLS(0.04)S(0.92)PT(0.04)EALK 150.44 3.55E-05 288285000 641760 647300 545900 687490 658780 602120 628780 690820 649050 682280 TRUE FALSE 616679.3097 628839.6378 644556.2735 722971.4413 679970.257 614295.2789 636475.1977 676554.3256 575372.565 636068.5679 0.969517031 0.988634983 1.01334401 1.136625008 1.069020372 0.965768959 1.000639286 1.06364999 0.904576321 1 19.27882277 1.244086559 24.99989315 0.952288158 1.027857067 0.228876171 0.053951061 182.5089122 825716.4041 0.04000573 0.013700442 17.542301 -1.244086559 0.07556891 GTEAS(ph)PPQNNS(ph)GSSSPVFTFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 GT(0.017)EAS(0.983)PPQNNS(0.99)GS(0.008)S(0.002)SPVFTFR 96.379 0.001882 63116000 63042 62032 61270 72709 69417 67702 62908 71447 56347 62254 TRUE FALSE 60578.24894 60262.9081 72342.85194 76461.5202 71649.86085 69070.98083 63677.88692 69971.59448 49950.72479 58037.48113 1.043778051 1.038344651 1.246485039 1.317450701 1.234544633 1.190109899 1.097185572 1.205627693 0.86066321 1 15.82469729 1.244159168 24.99895187 0.93033157 1.175054191 0.532428223 0.090428714 97.76366836 436554.7972 0.068636901 0.023509993 17.54523412 -1.244159168 0.244722621 VGDVYIPR ddPTM_BT-474_Pertuzumab_2h_R1 7 VGDVYIPR 8 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 ;;;;;; 151.29 0.0011062 7894390000 4282050 4632950 3737220 4282100 4338650 4314080 4254530 4591350 4480230 4549610 FALSE TRUE 4114702.752 4500822.802 4412618.788 4503099.694 4478206.618 4401313.653 4306598.211 4496537.018 3971653.073 4241460.862 0.970114516 1.0611492 1.040353532 1.061686018 1.055817032 1.037688145 1.015357291 1.06013875 0.936388005 1 22.01612982 1.24421534 24.99989334 0.968193995 1.03990161 0.459047389 0.030149427 97.94454698 433034.3632 0.019939144 0.006832677 17.54750359 -1.24421534 0.071707615 LLEGEEER ddPTM_BT-474_Pertuzumab_2h_R1 6 LLEGEEER 8 0 P20700;E9PBF6;P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8;Q03252 P20700;P02545;P02545-2;Q03252 LMNB1;LMNA;LMNB2 Lamin-B1;Prelamin-A/C;Lamin-A/C;Lamin-B2 0 ;;;;; 180.93 0.00055023 8260270000 4989200 5533020 4457030 6009950 5340710 5326120 5220740 5694200 5458410 5585640 FALSE TRUE 4794216.548 5375223.687 5262514.467 6320124.24 5512498.787 5433817.796 5284632.978 5576612.78 4838794.18 5207319.628 0.920668768 1.032243855 1.010599472 1.213700078 1.058605805 1.043496114 1.014847053 1.070918088 0.92922934 1 22.31210953 1.244316851 24.98591858 0.964614663 1.049454089 0.172997828 0.07046285 210.9466837 915679.5341 0.050394846 0.01728141 17.55160559 -1.244316851 0.084839426 KNICQFLVEIGLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNICQFLVEIGLAK 14 1 K7EM18;P41567 K7EM18 EIF1 Eukaryotic translation initiation factor 1 0 115.78 0.00064076 40064000 135120 129150 107650 114660 126470 144800 108150 129110 163720 149520 FALSE TRUE 129839.361 125466.7685 127104.7497 120577.6163 130538.0224 147727.9552 109473.5721 126443.8334 145135.192 139392.8772 0.931463383 0.900094545 0.91184537 0.865019926 0.936475557 1.05979558 0.785359871 0.907103978 1.041195181 1 17.08879732 1.244321858 24.945745 1.020597607 0.909481282 0.308088594 0.0649131 143.0846522 619567.5018 0.045726503 0.015689332 17.55180794 -1.244321858 -0.111116324 SLNS(ph)TPPPPPAPAPAPPPALARPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLNSTPPPPPAPAPAPPPALARPR 24 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.025)LNS(0.487)T(0.487)PPPPPAPAPAPPPALARPR;S(0.024)LNS(0.488)T(0.488)PPPPPAPAPAPPPALARPR 89.181 0.0062698 496930000 630430 775150 383730 591880 552150 697360 565330 648950 627440 651710 TRUE FALSE 605792.0986 753043.481 453078.547 622426.9977 569910.4062 711461.097 572248.6776 635548.9557 556215.6416 607569.1012 0.997075226 1.239436764 0.745723484 1.024454661 0.938017429 1.170996181 0.941865998 1.046052135 0.91547717 1 19.21268898 1.244329653 24.98464527 0.957738588 1.012855352 0.02898504 0.127829943 549.8793218 2381505.639 0.085740184 0.029422261 17.55212298 -1.244329653 0.055116763 TVIDKCS(ph)PPLEFLDDSDSHLEIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVIDKCSPPLEFLDDSDSHLEIQK 24 1 Q93075;H7C1W4 Q93075 TATDN2 Putative deoxyribonuclease TATDN2 1 TVIDKCS(1)PPLEFLDDSDSHLEIQK;TVIDKCS(1)PPLEFLDDSDSHLEIQK 243.55 6.63E-38 239150000 406360 358040 284100 290900 310660 364780 322970 347440 469590 422120 TRUE FALSE 390479.0019 347829.0498 335443.1898 305913.3839 320652.661 372156.1015 326922.6035 340265.2426 416284.1119 393529.4364 0.992248523 0.883870475 0.852396692 0.777358326 0.814812391 0.945688091 0.830744979 0.864650039 1.057822042 1 18.58611203 1.24455149 24.99170898 1.028911047 0.865703954 0.525680654 0.060173034 97.13229501 405213.1306 0.043171118 0.014853964 17.56109087 -1.24455149 -0.163207093 KIQVLQQQADDAEER ddPTM_BT-474_Pertuzumab_2h_R1 8 KIQVLQQQADDAEER 15 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;Q5VU61;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;;; 314.06 4.76E-56 30486100000 12619570 13107540 10680660 12189070 12301360 13490040 12607490 13035630 13159300 12792700 FALSE TRUE 12126383.25 12733725.79 12610892.85 12818149.36 12697044.42 13762817.85 12761784.23 12766439.69 11665511.43 11926239.03 1.016781839 1.067706739 1.057407353 1.074785549 1.064631053 1.153994802 1.070059404 1.070449758 0.978138322 1 23.50763582 1.24456017 24.41290631 0.989069143 1.073648098 0.515076229 0.032145143 75.56921166 307513.8994 0.02311937 0.007936586 17.56144184 -1.24456017 0.084578955 EKKDELCR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKKDELCR 8 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 81.338 0.013004 628450000 696820 750410 409660 567000 620540 581110 616500 620700 772680 697680 FALSE TRUE 669587.504 729009.0415 483694.6748 596262.9379 640500.2327 592860.4423 624044.9114 607882.3281 684968.6057 650425.5122 1.029460701 1.120818645 0.743658829 0.916727476 0.984740329 0.911496292 0.959441012 0.934591766 1.053108454 1 19.31102432 1.244610211 24.97098467 1.026554235 0.947540491 0.100000495 0.091463642 303.0932277 1251122.193 0.065197365 0.022440861 17.56346546 -1.244610211 -0.079013744 DVTLS(ph)T(ph)S(ph)LEHRVFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVTLSTSLEHRVFLK 15 1 Q9P2K6 Q9P2K6 KLHL42 Kelch-like protein 42 3 DVT(0.725)LS(0.765)T(0.765)S(0.746)LEHRVFLK 41.202 0.086615 0 17376 21829 14158 18153 22126 22111 16002 21391 16503 19761 TRUE FALSE 16696.92671 21206.45829 16716.66554 19089.87851 22837.70288 22558.09957 16197.83726 20949.26837 14629.64863 18422.56987 0.906329944 1.151112925 0.907401392 1.036222343 1.23965891 1.224481694 0.879238748 1.137152337 0.794115519 1 14.1691867 1.24471837 24.99909028 0.897057749 1.063383087 0.195413508 0.132288114 206.5188152 838445.7408 0.091043595 0.03137873 17.56784011 -1.24471837 0.166325337 LKDLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_BT-474_Pertuzumab_2h_R1 4 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 36 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 244.41 3.40E-50 5094390000 439348 418542 336776 302261 413803 433659 404996 411218 581934 516728 TRUE FALSE 422177.7944 406605.592 397638.9147 317860.7264 427113.3493 442427.8821 409952.4622 402726.2046 515875.292 481729.5523 0.876379272 0.84405366 0.825440152 0.659832317 0.886624761 0.918415488 0.851001273 0.83600062 1.070881555 1 18.87786391 1.24477342 24.99707899 1.035440807 0.836190975 0.58316235 0.067030444 93.56948636 376486.2129 0.049120093 0.016942788 17.5700671 -1.24477342 -0.199249832 EWLTNFMEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EWLTNFMEDR 10 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ;;; 218.6 1.56E-08 570430000 420614 418516 331910 505783 439051 353078 455419 435813 383689 385128 FALSE TRUE 404175.9399 406580.3335 391893.5203 531886.5212 453173.4742 360217.4791 460992.554 426813.3093 340134.2333 359042.9375 1.125703635 1.132400309 1.091494859 1.481400873 1.262170695 1.003271312 1.283948257 1.188752833 0.947335813 1 18.45379686 1.244786702 23.1684801 0.973667802 1.199600632 0.342038101 0.123350743 59.98689987 223241.3593 0.088935264 0.030516122 17.57060445 -1.244786702 0.22593283 LASDLLEWIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LASDLLEWIRR 11 1 O43707;O43707-2;K7EJH8;P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2W4 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ; 178.81 1.18E-05 226087000 453450 539270 363770 428160 410990 498790 425550 471370 444660 449390 FALSE TRUE 435728.6727 523890.5476 429511.331 450257.3889 424209.8666 508875.8755 430758.0082 461636.0448 394184.061 418952.415 1.040043349 1.25047745 1.025203139 1.074722028 1.012549042 1.21463884 1.02817884 1.101881809 0.940880269 1 18.67642687 1.244806817 24.88431003 0.970440118 1.094242667 0.28806434 0.077352336 149.1562177 594244.6544 0.051314653 0.01769344 17.57141826 -1.244806817 0.123802549 TS(ph)PAPWKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPAPWKR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.134)S(0.866)PAPWKR 117.53 0.001263 285470000 545250 551890 412610 432400 476470 490420 527240 507890 672730 599290 TRUE FALSE 523941.0272 536150.6376 487177.8055 454716.2158 491796.0903 500336.6284 533692.5208 497401.894 596364.5107 558699.5545 0.937786728 0.959640353 0.871985312 0.813883262 0.880251445 0.895537905 0.955240641 0.890285109 1.067415404 1 19.09171314 1.244839906 24.99951703 1.033707719 0.900106838 0.598623043 0.043603993 93.95074547 374054.2612 0.032817631 0.011322191 17.57275709 -1.244839906 -0.133600882 GLGTDEDS(ph)LIEIICSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLGTDEDSLIEIICSR 16 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YMM1;H0YN52;H0YLE2 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 GLGTDEDS(1)LIEIICSR;GLGTDEDS(1)LIEIICSR 261.56 8.08E-27 79338000 91744 90732 65056 87249 79298 96062 76202 86759 74572 76014 TRUE FALSE 88158.54305 88144.4122 76813.06636 91751.93135 81848.69219 98004.43946 77134.58287 84967.39633 66106.89919 70865.50407 1.24402619 1.243826786 1.083927467 1.294733348 1.154986382 1.382963979 1.088464463 1.198995159 0.932850194 1 16.1127959 1.244860711 24.72981437 0.966425056 1.208356242 0.559712944 0.086905958 79.69564998 312840.7363 0.057558709 0.019860261 17.57359893 -1.244860711 0.241931186 GIPGLDVEDDEEGGGGAP ddPTM_BT-474_Pertuzumab_2h_R1 3 GIPGLDVEDDEEGGGGAP 18 0 Q9ULX6;Q9ULX6-2 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 ;; 176.95 2.24E-13 220343000 277714 327419 272634 315315 306343 333690 307243 329410 286967 302610 FALSE TRUE 266860.6299 318081.3307 321905.0285 331588.4449 316196.8008 340437.4404 311003.1317 322607.5684 254391.7092 282113.9552 0.945932043 1.127492366 1.141046101 1.175370586 1.120812335 1.206737328 1.102402508 1.143536371 0.901733872 1 18.10591851 1.24489054 24.99641454 0.950866915 1.125948637 0.491546205 0.06879237 102.8792914 406275.0926 0.046805382 0.016164704 17.57480599 -1.24489054 0.175081722 SQATS(ph)PGQTNGDSSLEVLATR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQATSPGQTNGDSSLEVLATR 21 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SQAT(0.025)S(0.975)PGQTNGDSSLEVLATR 180.8 5.05E-18 0 62054 70818 61756 77601 68813 68872 66331 72780 65557 67612 TRUE FALSE 59628.86108 68798.33998 72916.68295 81605.99691 71026.43264 70264.63903 67142.77862 71277.06757 58115.2442 63032.57902 0.946000656 1.091472712 1.156809448 1.294663778 1.126820983 1.114735271 1.065207543 1.130797259 0.921987409 1 15.94381007 1.244896912 24.99082502 0.960993685 1.120563525 0.355406868 0.083203528 146.5567931 578048.6152 0.060929351 0.021044396 17.57506386 -1.244896912 0.15956984 SLDSESIS(ph)PGDFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDSESISPGDFHR 14 0 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 SLDSESIS(1)PGDFHR 182.15 1.00E-06 188070000 177700 213230 162450 238990 222450 218630 204640 223370 188290 203620 TRUE FALSE 170755.2875 207148.8892 191808.3287 251324.3025 229605.3063 223050.8484 207144.4455 218757.3314 166916.1086 189828.636 0.899523334 1.091241519 1.010428841 1.323953581 1.209539883 1.175011595 1.091218111 1.152393738 0.879298888 1 17.53433812 1.24498068 24.99918109 0.939649422 1.12611017 0.292759654 0.111187302 166.668582 649012.5354 0.079812573 0.027588024 17.57845412 -1.24498068 0.186460747 IWLS(ph)TETLANED ddPTM_BT-474_Pertuzumab_2h_R1 2 IWLSTETLANED 12 0 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 IWLS(0.499)T(0.499)ET(0.002)LANED;IWLS(0.497)T(0.497)ET(0.005)LANED 131.45 0.00020814 66952000 142167 165155 126715 160713 149442 160322 149869 161826 150561 155131 TRUE FALSE 136610.9565 160444.9411 149615.2193 169007.4172 154248.9376 163563.8207 151703.1417 158484.2365 133469.9465 144623.8392 0.944595007 1.109394841 1.034512844 1.168599991 1.066552641 1.130960301 1.048949762 1.09583757 0.922876527 1 17.14194585 1.245037724 24.99054283 0.961438251 1.078919086 0.362560207 0.060004958 129.7976836 500811.7706 0.039056307 0.013514569 17.5807632 -1.245037724 0.117480835 VEGGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEGGAR 6 0 A0A494C0Y0 A0A494C0Y0 0 97.64 0.095015 234770000 691180 705720 536300 686410 621560 606620 713150 722060 639670 701360 FALSE TRUE 664167.9215 685593.5566 633221.3399 721835.7024 641553.0419 618886.272 721877.743 707149.2087 567057.3433 653856.2625 1.015770529 1.048538641 0.968441195 1.103966948 0.981183601 0.946517312 1.104031244 1.081505599 0.867250764 1 19.318614 1.245068355 24.99995856 0.933625375 1.033650567 0.296089553 0.060114675 166.6092085 640059.9618 0.042149687 0.014580941 17.58200319 -1.245068355 0.100025192 ITESEEVVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ITESEEVVSR 10 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;; 243.03 5.03E-12 1840330000 649070 683150 576490 706400 685270 650020 694090 696770 680970 668810 FALSE TRUE 623703.6268 663667.2309 680674.567 742857.3887 707312.3319 663163.8498 702584.481 682381.456 603669.1405 623510.903 1.000309095 1.06440357 1.091680296 1.191410423 1.134402508 1.063596236 1.12681988 1.094417841 0.968177361 1 19.25005526 1.245106429 24.24056129 0.984088656 1.099327181 0.460066681 0.048327331 83.60299178 309613.3584 0.035609468 0.012299507 17.58354467 -1.245106429 0.115238525 TPLCATAPCLPS(ph)PTATR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPLCATAPCLPSPTATR 17 0 Q6PI47-3;Q6PI47 Q6PI47-3 KCTD18 BTB/POZ domain-containing protein KCTD18 1 TPLCATAPCLPS(0.997)PT(0.003)AT(0.001)R 128.64 3.80E-05 107620000 55496 66226 52577 65962 57090 59769 59665 66486 53091 60989 TRUE FALSE 53327.15497 64337.29932 62078.83347 69366.30672 58926.3517 60977.57013 60395.19812 65113.04087 47064.33226 56858.16071 0.937897996 1.131540284 1.091819234 1.21998858 1.036374567 1.072450628 1.062208087 1.145183735 0.827749819 1 15.79507981 1.245120474 24.99997604 0.913874893 1.09236408 0.428728926 0.079842747 117.6069998 448219.566 0.052927498 0.018316507 17.58411331 -1.245120474 0.178489187 KNDDGWYEGVCNR ddPTM_BT-474_Pertuzumab_2h_R1 3 KNDDGWYEGVCNR 13 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 ;; 151.3 7.16E-05 1611180000 1073350 1005170 753400 975110 973450 1005460 908870 1029850 966640 1007990 FALSE TRUE 1031402.295 976503.5358 889556.1393 1025435.544 1004761.903 1025791.09 919993.0229 1008583.238 856911.0797 939717.9395 1.097565825 1.039145359 0.946620365 1.091216312 1.069216476 1.091594666 0.979009748 1.073282945 0.911881155 1 19.84186826 1.245182066 24.99994184 0.955940569 1.046224606 0.341322575 0.051333063 155.3232774 586454.8158 0.035018291 0.012123714 17.5866073 -1.245182066 0.090284037 KDGALHMIGSLAEILLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDGALHMIGSLAEILLK 17 1 O95373 O95373 IPO7 Importin-7 0 ; 87.287 0.0029731 50437000 126854 124297 118066 111359 119582 133465 138653 128367 174861 167013 FALSE TRUE 121896.4054 120752.1713 139403.1526 117106.2513 123428.4636 136163.7537 140349.8769 125716.1766 155011.5124 155701.0608 0.782887444 0.775538527 0.895325644 0.752122373 0.792727185 0.874520399 0.901406042 0.807420168 0.995571331 1 17.24841925 1.245218384 0.610949438 1.008846341 0.801562054 0.603231953 0.053858878 0.519627321 0.475198488 0.053399669 0.024821762 17.58807804 -1.245218384 -0.207284287 LMLLLEVISGER ddPTM_BT-474_Pertuzumab_2h_R1 1 LMLLLEVISGER 12 0 O43707;P12814-3;P12814;P12814-2;P12814-4;P35609-2;P35609;G3V2N5;A0A494C1A0;Q08043;A0A494C166;A0A494C033;A0A087WSZ2;G3V5M4;A0A494C0Q3 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 71.349 0.081729 0 75181 75153 57707 60894 60679 75894 62815 68495 62379 57364 FALSE TRUE 72242.8434 73009.71002 68135.93859 64036.74664 62630.79514 77428.62868 63583.74876 67080.55431 55297.99743 53478.68519 1.350871719 1.365211388 1.274076547 1.197425599 1.171135658 1.447840918 1.188954974 1.254341876 1.03401939 1 15.70667638 1.245222211 2.179548984 0.990205305 1.285900023 0.620978073 0.082683836 0.194978014 1.577928598 0.076406968 0.022117262 17.58823303 -1.245222211 0.295694718 KLVILEGELER ddPTM_BT-474_Pertuzumab_2h_R1 4 KLVILEGELER 11 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 148.68 5.57E-05 2270270000 2406810 2749030 2209850 2357380 2319350 2705610 2465150 2663940 2667710 2708700 FALSE TRUE 2312749.204 2670630.356 2609219.053 2479044.664 2393953.999 2760319.288 2495319.243 2608928.708 2364882.745 2525237.336 0.915854194 1.057575982 1.03325696 0.981707592 0.948011486 1.093093013 0.988152364 1.033141983 0.9364992 1 21.26798756 1.245347976 24.99545319 0.968249597 1.009311476 0.079139255 0.051193655 335.8017472 1236673.191 0.033861394 0.011763326 17.59332703 -1.245347976 0.041061879 S(ph)PEPGQTWTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPEPGQTWTR 10 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(1)PEPGQTWTR;S(0.999)PEPGQT(0.001)WTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR 97.779 0.0061115 2789160000 312667 344206 382249 454920 358283 353942 366226 388108 345815 348295 TRUE FALSE 300447.628 334389.5819 451329.8974 478398.4757 369807.4981 361098.9497 370707.9833 380093.4342 306559.531 324704.6694 0.925295064 1.029826835 1.389970456 1.473334143 1.138904158 1.112084253 1.141677402 1.170581978 0.944118024 1 18.30876861 1.245367678 23.12735595 0.972058971 1.179922935 0.219955199 0.150655334 88.36646781 300252.4671 0.114624411 0.039571038 17.59412519 -1.245367678 0.207863963 YIEIDS(ph)DEEPRGELLSLR ddPTM_BT-474_Pertuzumab_2h_R1 6 YIEIDSDEEPRGELLSLR 18 1 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;Y(0.001)IEIDS(0.999)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR 284.45 9.28E-40 4231030000 1455579 1421237 1171066 1220075 1378303 1498999 1278681 1445513 1402386 1436173 TRUE FALSE 1398693.363 1380704.712 1382703.676 1283043.217 1422637.368 1529309.787 1294329.881 1415662.651 1243193.021 1338899.723 1.044658789 1.03122339 1.032716381 0.958281785 1.062542133 1.142213834 0.96671159 1.057332843 0.928518394 1 20.35261648 1.245610837 24.99795076 0.96425919 1.035940203 0.245629625 0.050937508 203.4744407 721477.1259 0.034988167 0.012181525 17.60397881 -1.245610837 0.071681012 GKEQERPPEAVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKEQERPPEAVSK 13 2 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 0 78.505 0.012962 128420000 107780 109040 78978 79959 89501 93004 95456 94456 127560 110180 FALSE TRUE 103567.8384 105930.286 93251.08146 84085.69357 92379.88095 94884.6046 96624.21908 92505.45059 113079.9236 102717.4105 1.008279297 1.031278782 0.907841047 0.818611891 0.89935952 0.923744126 0.940680053 0.900581997 1.100883707 1 16.64832121 1.245630451 24.99895584 1.050441865 0.926058073 0.393637831 0.060314219 151.829969 536885.3755 0.045232055 0.015731377 17.60477387 -1.245630451 -0.124383792 RYDQDLCYTDILFTEQER ddPTM_BT-474_Pertuzumab_2h_R1 1 RYDQDLCYTDILFTEQER 18 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 179.41 1.34E-13 263460000 73468 73395 58399 79412 68564 72481 70325 75289 70809 72225 FALSE TRUE 70596.78934 71301.84646 68952.99838 83510.46284 70769.42333 73946.61548 71185.65839 73734.25584 62771.05918 67333.13642 1.048470235 1.058941411 1.024057426 1.240258026 1.051034113 1.098220273 1.05721584 1.095066408 0.932246179 1 16.03902905 1.245631179 24.96222512 0.966123078 1.085022692 0.393630605 0.05859171 137.3594312 484952.7977 0.039781541 0.013837825 17.60480339 -1.245631179 0.118899615 KPSVGVPPPAS(ph)PSYPR ddPTM_BT-474_Pertuzumab_2h_R1 4 KPSVGVPPPASPSYPR 16 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 KPSVGVPPPAS(0.957)PS(0.043)YPR;KPSVGVPPPAS(0.984)PS(0.016)YPR;KPSVGVPPPAS(0.991)PS(0.009)YPR;KPSVGVPPPAS(0.988)PS(0.012)YPR 131.65 2.66E-05 2423180000 2749510 3299440 2505790 3200970 2984020 3160640 2852340 3086020 2565860 2647210 TRUE FALSE 2642056.109 3205343.202 2958641.994 3366172.445 3080003.713 3224550.306 2887247.79 3022292.609 2274594.33 2467912.109 1.070563291 1.29880768 1.19884415 1.363975821 1.248020018 1.306590415 1.16991516 1.224635431 0.921667478 1 21.23485959 1.245633423 23.97925679 0.960833685 1.239128804 0.66030246 0.078666535 47.54515918 161201.8495 0.052519801 0.01822659 17.60489436 -1.245633423 0.278295119 LGLDYEER ddPTM_BT-474_Pertuzumab_2h_R1 4 LGLDYEER 8 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H3X6;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;; 171.38 0.00067396 4499880000 2620290 3847610 2992280 5334790 2561810 3372540 4224950 3803740 3260530 3389670 FALSE TRUE 2517886.17 3737879.93 3533051.559 5610119.151 2644212.945 3440735.07 4276656.202 3725191.44 2890408.304 3160084.632 0.796778081 1.182841716 1.118024348 1.775306615 0.836753838 1.088811051 1.353335971 1.178826479 0.914661675 1 21.59153177 1.245839804 24.24852942 0.957330818 1.181000523 0.092963149 0.257904294 231.7605728 772072.9434 0.175867199 0.061180392 17.61326236 -1.245839804 0.223669705 AVTGQTTQVS(ph)PPVIAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVTGQTTQVSPPVIAGR 17 0 Q6MZP7-3;Q6MZP7 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 AVTGQTT(0.001)QVS(0.999)PPVIAGR;AVTGQTT(0.002)QVS(0.998)PPVIAGR 174.91 1.08E-13 100330000 138573 146260 119980 161965 141788 149276 143066 151197 144137 144948 TRUE FALSE 133157.414 142088.808 141663.0549 170324.0331 146348.7398 152294.463 144816.8845 148074.7291 127775.172 135130.5429 0.98539835 1.051492912 1.048342232 1.260440678 1.083017478 1.127017325 1.071681364 1.095790234 0.945568406 1 17.04399427 1.245848922 24.94261921 0.972784191 1.09347063 0.321482208 0.068230142 166.8501185 571022.7376 0.04832536 0.016842339 17.61363216 -1.245848922 0.120686439 RVYATILNAGTNTDGFK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVYATILNAGTNTDGFK 17 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 265.6 2.32E-27 3182300000 2582400 2604300 2221100 2381000 2582100 2666300 2578500 2677800 3520000 3199800 FALSE TRUE 2481476.953 2530027.914 2622502.178 2503883.695 2665155.592 2720214.413 2610056.454 2622502.494 3120424.357 2983074.696 0.831852101 0.848127577 0.879127225 0.839363392 0.893425698 0.911882769 0.874955112 0.879127331 1.046042984 1 21.50836867 1.245867234 24.61338513 1.023021509 0.871144787 0.8536694 0.025380553 42.67466774 143760.1235 0.018306703 0.006377702 17.61437484 -1.245867234 -0.151876722 SRS(ph)VS(ph)PCSNVESR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSVSPCSNVESR 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.107)RS(0.893)VS(0.998)PCS(0.002)NVESR 104.89 0.00085109 161870000 135110 129280 102710 106270 117460 133140 115800 125860 119090 120280 TRUE FALSE 129829.7518 125593.061 121271.9818 111754.6074 121238.2076 135832.182 117217.195 123260.947 105571.4025 112133.3285 1.157815911 1.120033292 1.081498101 0.996622583 1.081196904 1.211345314 1.045337694 1.099235604 0.941481038 1 16.77485562 1.245992985 24.99527884 0.970740508 1.096462899 0.449167282 0.056812432 139.3840859 468764.6927 0.040365853 0.014087474 17.61947587 -1.245992985 0.125722391 LEDFRDYR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEDFRDYR 8 1 O43707;O43707-2;K7EJH8;F6THM6;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0;Q08043;A0A087WSZ2 O43707;P12814-3 ACTN4;ACTN2;ACTN1;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ;;; 99.802 0.0059781 3789660000 6776400 7990700 5490920 6985500 6760500 7100800 6922600 7077900 7306100 6801700 FALSE TRUE 6511570.796 7762813.06 6483251.389 7346022.492 6977957.622 7244383.041 7007320.85 6931738.892 6476742.158 6341014.801 1.026897271 1.224222511 1.022431203 1.158493194 1.100448089 1.142464301 1.105078772 1.093159235 1.021404674 1 22.59628231 1.246087257 2.225470475 0.998794033 1.114824586 0.337944434 0.055874713 0.292161133 2.456179628 0.045512796 0.013157155 17.62330094 -1.246087257 0.116030553 LQLEETMPS(ph)PYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQLEETMPSPYGR 13 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 LQLEETMPS(1)PYGR;LQLEETMPS(1)PYGR;LQLEET(0.007)MPS(0.993)PYGR;LQLEETMPS(1)PYGR 272.81 4.20E-32 1029210000 877074 888948 865366 961564 883429 900357 920311 1013778 863168 979628 TRUE FALSE 842796.9784 863596.0734 1021756.886 1011190.433 911845.2961 918562.8354 931574.0413 992843.13 765184.7873 913276.923 0.922827411 0.945601549 1.118781019 1.107211195 0.998432428 1.005787853 1.020034579 1.087121666 0.837845311 1 19.80069285 1.246124497 24.99925475 0.918922643 1.02981067 0.263908407 0.071085917 200.3223011 662097.8429 0.050463152 0.017639816 17.62481216 -1.246124497 0.110888027 VVDFDETWNK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVDFDETWNK 10 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5;Q5T2B7 A0A0A0MTN0 CUL2 Cullin-2 0 ; 138.66 0.010175 0 99052 117329 85810 91641 95050 104580 96911 104400 103036 102934 FALSE TRUE 95180.93833 113982.8918 101317.7758 96370.60299 98107.36957 106694.6793 98097.02581 102244.1035 91339.78524 95962.1885 0.991858771 1.187789624 1.05580935 1.004255994 1.022354441 1.111840829 1.022246651 1.065462398 0.951830994 1 16.55017844 1.246166236 24.96564681 0.97591549 1.059327132 0.257515787 0.055495225 194.4404202 638270.885 0.03755441 0.013128415 17.62650613 -1.246166236 0.083411643 EGLLFEGR ddPTM_BT-474_Pertuzumab_2h_R1 5 EGLLFEGR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;; 137.62 0.0017223 2060567000 1484330 1773750 1322830 1884430 1551510 1588720 1743800 1739280 1599950 1659140 FALSE TRUE 1426320.743 1723164.387 1561894.807 1981685.658 1601415.728 1620845.007 1765141.146 1703363.26 1418330.384 1546764.97 0.922131526 1.114044099 1.009781601 1.281180849 1.035332296 1.047893532 1.14118252 1.10124246 0.916965674 1 20.56082257 1.246240849 24.96407507 0.958482826 1.087819902 0.225053131 0.090798095 203.4244076 661233.1389 0.060139341 0.021037708 17.62953468 -1.246240849 0.129337076 APSPT(ph)KPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPTKPLR 9 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 APS(0.324)PT(0.676)KPLR 114.71 0.002577 1919600000 771670 793090 658070 813190 750400 681680 766580 817080 683970 759470 TRUE FALSE 741512.2833 770471.8497 776997.8877 855158.8334 774537.2975 695464.0367 775961.6353 800207.0125 606328.593 708030.4204 1.047288735 1.08819032 1.097407492 1.207799564 1.093932231 0.982251633 1.095943921 1.130187333 0.856359523 1 19.43345182 1.246307265 24.99135764 0.928179746 1.094930691 0.524471541 0.062704593 117.8841804 380313.4433 0.044107831 0.015438553 17.63223092 -1.246307265 0.166750945 LIQEQHPEEELIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LIQEQHPEEELIK 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 150.12 4.05E-05 808220000 580070 559990 577520 638650 589740 542980 666500 695620 855680 902900 FALSE TRUE 557400.2231 544019.6335 681890.7109 671610.803 608709.5227 553959.4276 674656.8264 681255.2039 758546.7937 841745.7788 0.662195448 0.646299212 0.810091037 0.797878433 0.723151263 0.658107758 0.801497131 0.80933605 0.901159011 1 19.68302506 1.246487074 1.054065949 0.998894453 0.721688226 0.736473653 0.05516074 0.254271363 0.586938548 0.054709044 0.018503821 17.63953265 -1.246487074 -0.277206227 VVETDPSPYCIVAPDTVIHCEGEPIKR ddPTM_BT-474_Pertuzumab_2h_R1 5 VVETDPSPYCIVAPDTVIHCEGEPIKR 27 1 P55072;C9IZA5 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;; 240.75 2.30E-45 11800980000 12396850 11933930 7449100 12650070 9520120 11155770 11752340 12483620 16322780 16716230 FALSE TRUE 11912367.4 11593586 8795318.074 13302941.63 9826343.306 11381347.31 11896168.65 12225828.88 14469886.45 15584024.85 0.764396073 0.74394042 0.564380393 0.853626823 0.630539504 0.73032143 0.763356627 0.784510356 0.92850766 1 23.89356455 1.246511699 1.356973779 1.004168189 0.713534248 0.637301437 0.073484238 0.231024936 0.821426796 0.063715045 0.019901483 17.64053283 -1.246511699 -0.29063394 LQEEER ddPTM_BT-474_Pertuzumab_2h_R1 3 LQEEER 6 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;; 155.53 0.022951 2133560000 2049860 2226130 1846780 2197830 2254600 2450220 2108350 2319430 2139820 2227060 FALSE TRUE 1969749.205 2162642.952 2180534.227 2311260.27 2327121.257 2499765.127 2134152.618 2271532.96 1896916.604 2076219.243 0.94871927 1.041625522 1.05024276 1.113206266 1.120845626 1.203998632 1.027903303 1.094071817 0.913639834 1 20.98552737 1.246607842 24.98502875 0.956819908 1.078585043 0.334679596 0.066547048 176.8885329 549215.8501 0.047382129 0.016630739 17.6444385 -1.246607842 0.121765135 LPSGSGAAS(ph)PTGSAVDIR ddPTM_BT-474_Pertuzumab_2h_R1 9 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LPSGSGAAS(0.96)PT(0.04)GS(0.001)AVDIR;LPSGSGAAS(0.998)PT(0.002)GSAVDIR;LPSGSGAAS(0.837)PT(0.163)GSAVDIR;LPSGSGAAS(0.999)PT(0.001)GSAVDIR;LPSGSGAAS(0.998)PT(0.002)GSAVDIR;LPSGSGAAS(0.995)PT(0.005)GSAVDIR;LPSGSGAAS(0.998)PT(0.002)GSAVDIR;LPSGSGAAS(1)PTGSAVDIR;LPSGSGAAS(1)PTGSAVDIR 404.04 4.02E-147 81543790000 4234492 4842337 3763951 4805863 3943575 4694039 4460438 4736868 4574292 4701072 TRUE FALSE 4069003.371 4704238.29 4444180.674 5053894.165 4070423.671 4788955.685 4515026.175 4639050.02 4055037.549 4382664.206 0.92843147 1.07337411 1.014036318 1.15315569 0.928755542 1.092704223 1.030201257 1.05849999 0.925244864 1 22.06337672 1.246673214 24.98292005 0.962622425 1.038517302 0.154035466 0.067321372 256.2548235 789159.3987 0.042468697 0.014916459 17.64709462 -1.246673214 0.075894877 EIQTAVR ddPTM_BT-474_Pertuzumab_2h_R1 5 EIQTAVR 7 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 0 ;;;; 202.2 0.00073114 28328790000 8561950 8967150 6628350 8962210 7704180 7802590 8536490 8649090 8240980 8384860 FALSE TRUE 8227339.528 8711415.662 7826240.292 9424750.732 7951991.946 7960363.716 8640962.118 8470483.269 7305498.499 7816945.964 1.052500499 1.114427003 1.001188997 1.20568196 1.017276054 1.018347031 1.105414078 1.083605197 0.934571959 1 22.89817363 1.246763352 24.99926104 0.967285972 1.076117899 0.350292072 0.058550097 162.9983567 496776.3455 0.038203849 0.013430786 17.65075764 -1.246763352 0.108831926 AQEDEVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQEDEVKR 8 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 75.378 0.061803 271830000 261480 268350 231790 249950 237410 278810 260260 269860 350540 314530 FALSE TRUE 251261.0725 260696.9207 273679.6091 262849.9495 245046.5083 284447.7292 263445.1397 264287.2967 310748.1688 293226.6029 0.856883618 0.889062991 0.933338266 0.896405534 0.835689892 0.970061128 0.89843533 0.901307364 1.059754353 1 18.16165647 1.247320213 24.90004367 1.029877179 0.898991365 0.667835947 0.037292073 87.45664684 248609.6843 0.024833875 0.008758199 17.67340431 -1.247320213 -0.130885814 IEGVYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IEGVYAR 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ; 124.89 0.0095448 1295230000 935370 955530 811430 905890 904360 650600 1103980 965930 842810 908300 FALSE TRUE 898814.7063 928279.22 958073.4512 952643.0915 933449.5607 663755.5778 1117490.837 945983.208 747137.7421 846780.032 1.061450049 1.096245996 1.131431322 1.12501837 1.102351881 0.783858325 1.319694366 1.117153419 0.882328012 1 19.69162772 1.247382266 24.98985807 0.941163998 1.097055912 0.18651334 0.125796637 265.4845925 752076.2006 0.085452888 0.030166375 17.67592971 -1.247382266 0.155891914 SPGLVPPS(ph)PEFAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 SPGLVPPS(1)PEFAPR 158.93 5.24E-06 392070000 428350 466830 401400 457550 500040 459510 493800 481600 398470 426120 TRUE FALSE 411609.6084 453516.4655 473941.9091 481164.2103 516124.2407 468801.607 499843.2721 471654.7917 353237.3561 397258.5129 1.036125332 1.141615474 1.193031474 1.21121183 1.299215055 1.180092035 1.258231746 1.187274222 0.889187631 1 18.59971861 1.247426147 24.98898477 0.944593813 1.194181792 0.656694413 0.07039654 96.14906186 271017.4835 0.049410541 0.017451356 17.67771577 -1.247426147 0.249587979 TPSS(ph)PCPASK ddPTM_BT-474_Pertuzumab_2h_R1 5 TPSSPCPASK 10 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 TPS(0.037)S(0.963)PCPASK;TPS(0.021)S(0.979)PCPASK;TPS(0.022)S(0.978)PCPASK;T(0.003)PS(0.038)S(0.958)PCPASK;TPSS(0.999)PCPASK 197.94 3.21E-07 4412360000 5653690 5401710 4137720 5467400 4886950 4535050 5221470 5518730 4430850 5104220 TRUE FALSE 5432737.544 5247658.52 4885498.047 5749573.169 5044143.185 4626751.818 5285371.912 5404766.297 3927878.484 4758506.633 1.141689602 1.102795252 1.026687241 1.208272597 1.060026511 0.97231173 1.11072072 1.135811445 0.825443524 1 22.18207745 1.247497355 24.99999732 0.912721744 1.094213663 0.49939498 0.072913371 132.4740573 370595.4843 0.049076975 0.017338808 17.68061451 -1.247497355 0.181491919 NCES(ph)DTEEDIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 NCESDTEEDIAR 12 0 Q9UIK4 Q9UIK4 DAPK2 Death-associated protein kinase 2 1 NCES(1)DTEEDIAR 220.46 3.10E-11 178910000 86399 102650 77207 80243 85543 82760 86526 83748 82113 72065 TRUE FALSE 83022.43156 99722.5225 91160.02236 84384.35085 88294.56828 84433.4639 87584.93107 82018.57453 72791.87649 67183.97336 1.235747566 1.484320107 1.356871554 1.256019057 1.314220697 1.25675008 1.3036581 1.220805654 1.083470846 1 16.0358295 1.247578357 0.803649796 0.98992843 1.336788998 0.731726195 0.066468754 0.289878783 0.419665667 0.062374925 0.024039872 17.6839125 -1.247578357 0.346860568 KDLYANTVLSGGTTMYPGIADR ddPTM_BT-474_Pertuzumab_2h_R1 5 KDLYANTVLSGGTTMYPGIADR 22 1 P60709;A0A2R8Y793;P63261 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;; 234.64 3.07E-30 35033560000 19626260 19553570 17515180 17848600 18178260 19251760 18110270 20202290 18846290 19974350 FALSE TRUE 18859244.06 18995921.33 20680562.65 18769768.38 18762980.24 19641043.78 18331908.9 19785105.65 16706938.17 18621469.48 1.012768841 1.020108609 1.110576298 1.007963867 1.007599334 1.054752623 0.984450176 1.062488955 0.897186883 1 24.15046359 1.247768524 24.99993962 0.948593429 1.032922987 0.401148965 0.041049063 156.9670288 426181.625 0.026495333 0.009383979 17.69165754 -1.247768524 0.084329558 LEIS(ph)PDSSPER ddPTM_BT-474_Pertuzumab_2h_R1 2 LEISPDSSPER 11 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 LEIS(1)PDSSPER;LEIS(0.642)PDS(0.357)SPER 167.84 1.97E-05 179130000 250020 336480 250190 353530 297940 311950 334630 324310 294260 305310 TRUE FALSE 240248.942 326883.9198 295404.8984 371775.7257 307523.5107 318257.8427 338725.302 317612.8852 260856.8384 284631.0818 0.844071352 1.14844773 1.037851863 1.306166998 1.080428423 1.118141563 1.190050292 1.115875621 0.916473481 1 18.11873369 1.247830966 24.91218257 0.958236742 1.114782113 0.209688084 0.112831925 227.0995828 610295.7366 0.07397192 0.026194632 17.6942014 -1.247830966 0.156545371 DSPES(ph)PFEVIIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSPESPFEVIIDK 13 0 O95197-7;O95197-2;O95197 O95197-7 RTN3 Reticulon-3 1 DSPES(1)PFEVIIDK 194.48 1.03E-06 34326000 42610 52232 53556 74824 58991 61299 63834 60241 51555 47665 TRUE FALSE 40944.75409 50742.3945 63234.76055 78685.67561 60888.49909 62538.50778 64615.21959 58997.0023 45702.69254 44436.60709 0.921419451 1.14190524 1.42303305 1.770739954 1.370232857 1.4073646 1.454098857 1.327666673 1.028491947 1 15.43946105 1.247857389 4.282656625 0.999739274 1.369831903 0.299921187 0.206199471 0.251188915 9.748826231 0.185332695 0.055080589 17.69527796 -1.247857389 0.370092629 LKEEPDREAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEEPDREAR 10 2 P26358;P26358-2 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 91.03 0.0058648 38132000 82703 108980 59044 74236 75026 95129 78139 88128 61920 75580 FALSE TRUE 79470.87533 105871.9971 69714.56423 78067.32886 77439.27943 97052.57356 79095.28846 86308.126 54891.10119 70460.89928 1.127871999 1.502563808 0.989407813 1.107952491 1.099039045 1.377396181 1.122541569 1.224908096 0.779029245 1 16.10453527 1.247985859 24.98986484 0.889514611 1.195393056 0.400468452 0.148993476 161.8363321 429096.9171 0.09830164 0.034849414 17.70051321 -1.247985859 0.305878444 EIPYTFEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIPYTFEDR 9 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ;;; 195.06 7.37E-05 1631920000 639080 961280 726860 1483310 745130 820120 1196300 988840 792970 776940 FALSE TRUE 614104.0471 933865.2356 858219.7709 1559863.807 769097.7832 836703.3883 1210940.677 968420.1084 702955.37 724317.1618 0.847838598 1.289304306 1.184867371 2.153564611 1.061824604 1.155161623 1.671837616 1.337011132 0.970507682 1 19.46626203 1.247996936 9.1199923 0.984442251 1.35842003 0.14453068 0.340028613 0.236895015 178.6512497 0.247349589 0.081769843 17.70096471 -1.247996936 0.373977779 DSPAFPDSPWR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSPAFPDSPWR 11 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 0 85.744 0.024866 0 78590 85270 68073 83905 70849 73825 73567 84611 64436 77471 FALSE TRUE 75518.61591 82838.18309 80375.30538 88235.34711 73127.92243 75317.79208 74467.33495 82863.75328 57121.49542 72223.82017 1.045619239 1.14696485 1.112864221 1.22169316 1.012518062 1.042838663 1.031063364 1.147318891 0.790895515 1 16.14018711 1.248073612 24.99935166 0.895447735 1.096471688 0.516330101 0.077288725 130.2932963 342405.9205 0.051421735 0.018240261 17.70409012 -1.248073612 0.201023954 HMDGGQIDGQEITATAVLAPWPRPPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HMDGGQIDGQEITATAVLAPWPRPPPR 27 1 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BV80;H3BPG5 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 0 100.42 0.0018335 362230000 255180 210840 130470 167440 165640 169200 208080 185480 246730 209910 FALSE TRUE 245207.2835 204827.0496 154048.8313 176081.5985 170967.961 172621.3399 210626.5453 181649.7732 218722.2448 195692.6087 1.253022713 1.046677496 0.787198006 0.899786658 0.87365569 0.882104547 1.076313238 0.928240338 1.117682708 1 17.57822974 1.248184578 24.9884621 1.058841369 0.960539022 0.072275914 0.127191465 463.3007208 1202973.678 0.089446552 0.031751529 17.70861428 -1.248184578 -0.098302346 T(ph)PPPPTLSPAAITVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPPPTLSPAAITVGR 16 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C4H9 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 T(0.996)PPPPT(0.004)LSPAAITVGR 88.561 0.068054 165790000 32008 38935 23512 31078 39994 34917 32812 35576 27275 31419 TRUE FALSE 30757.09197 37824.61192 27761.14142 32681.9393 41280.44333 35623.04566 33213.56307 34841.34317 24178.85635 29290.96314 1.050053964 1.291340668 0.947771546 1.115768681 1.409323522 1.216178706 1.133918434 1.189491209 0.825471536 1 14.83816801 1.248226976 24.98906986 0.912735761 1.172719958 0.399846769 0.125638344 168.2025918 434837.9261 0.085575388 0.030379255 17.71034315 -1.248226976 0.259984197 LCWFLDEAAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LCWFLDEAAAR 11 0 M0R1L2;O95336 M0R1L2 PGLS 6-phosphogluconolactonase 0 ; 108.43 0.0048009 251050000 560640 611570 510010 556940 545510 485230 592850 633800 659050 702490 FALSE TRUE 538729.569 594128.6224 602180.1521 585683.7401 563056.8246 495041.6831 600105.4756 620711.8085 584237.407 654909.7266 0.822601264 0.90719163 0.919485736 0.894296903 0.859747232 0.755893008 0.916317855 0.947782241 0.892088456 1 19.32093653 1.248354598 0.998559024 0.986653417 0.868874107 0.35719329 0.051172889 0.57625018 1.211380357 0.050431909 0.017440151 17.71554827 -1.248354598 -0.11777931 LDIDS(ph)PPITAR ddPTM_BT-474_Pertuzumab_2h_R1 8 LDIDSPPITAR 11 0 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 1 LDIDS(1)PPITAR;LDIDS(0.998)PPIT(0.002)AR;LDIDS(1)PPITAR;LDIDS(0.995)PPIT(0.005)AR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR 237.02 1.51E-15 7721851000 2694660 2791880 2400740 2640930 2584120 2812120 2654370 2794070 2975490 2872300 TRUE FALSE 2589349.708 2712258.316 2834607.122 2777228.714 2667240.567 2868982.993 2686854.974 2736371.478 2637724.849 2677756.563 0.966984731 1.012884574 1.058575362 1.037147571 0.996072833 1.071412926 1.003397774 1.021889561 0.985050279 1 21.35259338 1.248445053 24.23547424 0.992525144 1.022472514 0.134675611 0.028736102 229.8813155 563656.675 0.019345953 0.006866455 17.71923849 -1.248445053 0.02994737 GNIIISTPEKWDILSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNIIISTPEKWDILSR 16 1 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 204.07 2.39E-11 1154530000 726800 817120 614210 662990 697440 824970 742880 757410 728670 693910 FALSE TRUE 698395.8525 793816.5376 725211.41 697206.9934 719873.791 841651.4586 751971.5877 741769.2188 645954.4364 646910.8576 1.079585919 1.22708798 1.121037623 1.077748171 1.112786688 1.301031585 1.16240372 1.146632817 0.998521556 1 19.3032074 1.248453288 5.586557877 0.996439945 1.156531709 0.480130274 0.064208948 0.13241447 12.86884481 0.051768306 0.016112959 17.71957448 -1.248453288 0.160091764 IEVIEIMTDR ddPTM_BT-474_Pertuzumab_2h_R1 12 IEVIEIMTDR 10 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;H0YH80;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;;;;;;;;;; 223.84 9.89E-09 6097180000 3943871 4223401 3391188 4020238 4102112 4218889 3981241 4200323 4119192 4137181 FALSE TRUE 3789740.161 4102953.739 4004051.108 4227722.965 4234060.158 4304197.826 4029964.618 4113584.862 3651598.593 3856966.046 0.982570268 1.063777511 1.038134912 1.096126571 1.097769622 1.115954295 1.044853538 1.066533854 0.946754146 1 21.87903501 1.248481708 24.97497749 0.973377075 1.06550019 0.479021428 0.037415268 144.7438046 364378.5069 0.025839527 0.009188123 17.72073408 -1.248481708 0.092123115 NQS(ph)PTEAEKPASSSLPSSPPPQLLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQS(0.862)PT(0.138)EAEKPASSSLPSSPPPQLLTR 188.77 5.80E-18 1672200000 232140 218800 191800 191200 182760 196190 206140 212380 288860 252040 TRUE FALSE 223067.7122 212560.0382 226462.5266 201067.8549 188638.6414 200157.0962 208662.803 207994.2788 256069.8238 234969.1063 0.949349111 0.904629726 0.963797029 0.855720388 0.802823164 0.85184431 0.888043566 0.885198408 1.089802093 1 17.84211156 1.248524427 24.96702976 1.044901044 0.885715438 0.627509137 0.048435235 112.8704944 282832.5437 0.035001546 0.012440781 17.72247723 -1.248524427 -0.159185605 LLTQHENIKNEIDNYEEDYQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLTQHENIKNEIDNYEEDYQK 21 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 194.88 1.25E-18 281420000 156781 146401 119028 114502 132259 130786 133784 138557 194420 166549 FALSE TRUE 150653.8252 142225.7868 140539.0074 120411.4619 136513.2308 133430.5825 135421.2886 135695.7495 172350.2567 155268.4879 0.970279464 0.915999046 0.905135416 0.775504828 0.879207576 0.859353912 0.872174969 0.873942623 1.110014395 1 17.24440554 1.248789223 24.99999309 1.055007196 0.878411562 0.635248916 0.052564991 108.1319308 264292.2146 0.03605001 0.012841675 17.73328621 -1.248789223 -0.176595634 IITDVIGNPEEERR ddPTM_BT-474_Pertuzumab_2h_R1 4 IITDVIGNPEEERR 14 1 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925;J3QWB6 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 ;;; 241.41 3.12E-17 1420900000 927786 1036057 804618 958842 928980 1056108 995210 1010299 966845 982677 FALSE TRUE 891527.0974 1006509.669 950030.3712 1008327.951 958861.4854 1077463.227 1007389.678 989435.9726 857092.8089 916119.4115 0.973155995 1.098666458 1.037015873 1.100651223 1.046655571 1.176116578 1.099627041 1.080029481 0.935568877 1 19.80517613 1.248868982 24.94419618 0.967784445 1.080135801 0.411772762 0.051823855 157.7442822 381716.0371 0.034239362 0.012194789 17.73654322 -1.248868982 0.112351356 KLNTTTMSNATANSSIRPIFGGTVYHS(ph)PVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLNTTTMSNATANSSIRPIFGGTVYHSPVSR 31 2 O43663-2;O43663-4;O43663;O43663-3;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 KLNTTTMSNATANS(0.252)S(0.252)IRPIFGGT(0.093)VYHS(0.337)PVS(0.067)R;KLNTTTMSNATANSSIRPIFGGTVYHS(0.999)PVS(0.001)R 247.4 1.34E-46 1317350000 240045 244600 225051 224594 199824 266230 249360 264530 219132 255320 TRUE FALSE 230663.776 237624.2475 265722.7219 236185.3233 206251.5204 271613.353 252411.7423 259067.3631 194257.054 238026.949 0.969065801 0.998308168 1.116355619 0.992262953 0.866504912 1.141103367 1.060433465 1.088395092 0.8161137 1 17.8607654 1.248888623 24.99843393 0.908056817 1.032345812 0.239768944 0.086021032 249.7935364 604622.6443 0.058419759 0.020811796 17.7373454 -1.248888623 0.124288994 S(ph)PSAGILR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSAGILR 8 0 Q99618;F5GX58;F8WDL1;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 1 S(0.994)PS(0.006)AGILR 109.44 0.0037952 95705000 26816 25845 25984 27918 20891 23807 24203 28480 16691 24221 TRUE FALSE 25768.00107 25107.9259 30679.88681 29358.85133 21562.97799 24288.39385 24499.20355 27891.87805 14796.30765 22580.4901 1.14116217 1.111930069 1.358690032 1.30018663 0.95493844 1.075636257 1.08497218 1.235220225 0.655269553 1 14.46278918 1.248893421 24.99985837 0.827634738 1.158433709 0.489918786 0.134772251 149.4839766 361677.0221 0.092828637 0.033076953 17.73754134 -1.248893421 0.330798971 AAAPRPPVSAASGRPQDDTDSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAAPRPPVSAASGRPQDDTDSSR 23 2 Q8TF74 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 0 ; 203.79 1.04E-24 575650000 250550 236290 232120 240496 266800 253830 251450 255040 257940 239470 FALSE TRUE 240758.229 229551.2406 274069.2475 252908.0274 275381.8643 258962.6165 254527.3203 249773.3349 228659.7326 223250.4836 1.078421982 1.028222814 1.227631148 1.132844253 1.233510718 1.159964415 1.140097509 1.118803108 1.024229506 1 17.76830377 1.24910944 2.458230804 0.998592538 1.145289506 0.447685499 0.057587334 0.261101976 2.647296739 0.054603418 0.015715689 17.74636624 -1.24910944 0.146696968 AES(ph)PSPAPPPGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 AESPSPAPPPGLR 13 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 AES(1)PSPAPPPGLR;AES(0.978)PS(0.022)PAPPPGLR;AES(0.989)PS(0.011)PAPPPGLR;AES(0.984)PS(0.016)PAPPPGLR 257.38 7.07E-24 8905100000 2822790 2936720 2416260 2773460 2730980 2833220 2638560 2884000 2920800 2745070 TRUE FALSE 2712472.246 2852967.621 2852931.931 2916598.603 2818824.452 2890509.65 2670851.487 2824444.392 2589243.029 2559143.964 1.059913895 1.114813258 1.114799312 1.139677425 1.101471622 1.129483019 1.043650347 1.103667645 1.01176138 1 21.28722988 1.249227919 1.09249652 0.995850531 1.108845899 0.617217702 0.02914985 0.285314863 0.699956867 0.025787473 0.00861005 17.75120825 -1.249227919 0.112995368 WLPSS(ph)PSGVAK ddPTM_BT-474_Pertuzumab_2h_R1 3 WLPSSPSGVAK 11 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 WLPS(0.022)S(0.862)PS(0.116)GVAK;WLPS(0.061)S(0.857)PS(0.083)GVAK;WLPS(0.005)S(0.981)PS(0.015)GVAK 146.08 3.77E-05 1338160000 2267320 2357250 2017330 2231590 2325590 2093510 2218450 2374820 2219070 2327260 TRUE FALSE 2178710.628 2290023.538 2381906.406 2346762.627 2400394.714 2135842.207 2245600.055 2325779.137 1967170.477 2169632.607 1.004184128 1.055489086 1.097838592 1.08164056 1.106359992 0.98442575 1.035013968 1.071969111 0.90668368 1 21.04901934 1.249314736 24.99996676 0.953341833 1.056156014 0.479324212 0.042196103 151.5919748 352409.2105 0.028763655 0.010271285 17.75475715 -1.249314736 0.102814181 LIEVDDER ddPTM_BT-474_Pertuzumab_2h_R1 4 LIEVDDER 8 0 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;;; 163.9 0.00077526 6727150000 8352800 8305700 8027900 8172800 8654500 8356300 8323700 8787800 8490500 8625600 FALSE TRUE 8026363.341 8068829.568 9478720.11 8594599.187 8932879.852 8525270.111 8425567.93 8606328.859 7526694.035 8041380.429 0.998132524 1.003413486 1.178742903 1.068796491 1.110863978 1.060174952 1.047776312 1.070255155 0.935995269 1 22.93901175 1.249534113 24.9879535 0.96799764 1.069172089 0.379780625 0.050698264 187.2499577 426396.4234 0.034800269 0.012436716 17.76372795 -1.249534113 0.101174449 LSPWIRPDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSPWIRPDSK 10 1 O14744-2;O14744;G3V580;O14744-4;G3V5L5;G3V2L6;G3V2X6;C9JSX3 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 ; 132.17 0.0002104 1974440000 2801900 2998500 2132670 2658200 2644200 2604700 2903100 3107600 3755700 3944400 FALSE TRUE 2692398.65 2912985.716 2518090.91 2795390.021 2729253.094 2657368.819 2938629.006 3043426.974 3329368.681 3677242.275 0.73217875 0.79216584 0.684776994 0.760186523 0.742201055 0.722652635 0.799139351 0.827638417 0.905398239 1 21.8101928 1.249795393 0.998976092 0.999146432 0.73888693 0.904561411 0.027736115 0.126262766 0.265528195 0.024439152 0.008452373 17.77441814 -1.249795393 -0.260259502 RDPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_BT-474_Pertuzumab_2h_R1 8 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPTPSTVS(0.01)T(0.074)PS(0.915)PS(0.001)ADLLGLR;RDPSSNDINGGMEPTPST(0.001)VS(0.125)T(0.013)PS(0.861)PSADLLGLR;RDPSSNDINGGMEPTPS(0.002)T(0.001)VS(0.22)T(0.141)PS(0.633)PS(0.003)ADLLGLR;RDPSSNDINGGMEPTPS(0.005)T(0.015)VS(0.19)T(0.143)PS(0.523)PS(0.124)ADLLGLR;RDPSSNDINGGMEPTPS(0.002)T(0.001)VS(0.031)T(0.223)PS(0.614)PS(0.13)ADLLGLR;RDPSSNDINGGMEPTPSTVST(0.003)PS(0.96)PS(0.036)ADLLGLR;RDPSSNDINGGMEPTPS(0.001)T(0.01)VS(0.038)T(0.103)PS(0.796)PS(0.052)ADLLGLR;RDPSSNDINGGMEPTPST(0.003)VS(0.081)T(0.037)PS(0.878)PSADLLGLR 263.97 9.82E-60 4178360000 657075 754491 629875 780157 675513 746127 741949 757389 712810 738013 TRUE FALSE 631395.7826 732973.6554 743707.424 820420.9963 697241.4891 761214.1992 751029.1938 741748.6525 631894.7971 688026.7222 0.917690785 1.065327308 1.080928109 1.192426064 1.013393036 1.106373015 1.091569803 1.078081168 0.918416068 1 19.39210507 1.249958056 24.97830783 0.959208039 1.073446635 0.286086733 0.068488226 219.327326 480678.367 0.045367256 0.016249502 17.78107675 -1.249958056 0.114238595 ALSAIADLLTNEHER ddPTM_BT-474_Pertuzumab_2h_R1 5 ALSAIADLLTNEHER 15 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ;;;; 278.16 1.32E-33 1257556000 942253 1119221 850193 1202460 957834 1092727 1072840 1081773 994875 1017777 FALSE TRUE 905428.711 1087301.913 1003841.788 1264519.105 988643.6005 1114822.689 1085969.737 1059434.01 881940.9609 948842.0572 0.954245972 1.145925083 1.057965106 1.332697149 1.041947491 1.174929674 1.144521081 1.116554648 0.929491852 1 19.85580843 1.250060438 21.72149177 0.964746013 1.126607541 0.302385813 0.094697624 43.08922307 81396.06912 0.060933948 0.021673557 17.78526899 -1.250060438 0.161861527 LLEENETEAVTVPTPS(ph)PTPVR ddPTM_BT-474_Pertuzumab_2h_R1 5 LLEENETEAVTVPTPSPTPVR 21 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 LLEENETEAVTVPTPS(0.996)PT(0.004)PVR;LLEENETEAVTVPT(0.039)PS(0.942)PT(0.019)PVR;LLEENETEAVTVPTPS(0.98)PT(0.019)PVR;LLEENETEAVTVPT(0.001)PS(0.994)PT(0.005)PVR;LLEENETEAVTVPTPS(0.988)PT(0.011)PVR 312.27 1.51E-66 2987990000 2728738 2959141 2544558 3134251 2885016 2897420 2693420 2973106 2624409 2783585 TRUE FALSE 2622095.902 2874749.196 3004416.234 3296010.07 2977815.16 2956007.818 2726382.88 2911710.322 2326497.093 2595050.309 1.010421992 1.107781682 1.157748743 1.270114132 1.147498047 1.139094609 1.050608873 1.122024615 0.896513291 1 21.30733108 1.250351116 24.53400321 0.948256675 1.128033332 0.515956595 0.068701639 123.0627133 256076.8229 0.048993975 0.017560567 17.79717683 -1.250351116 0.179776657 EAAELEEAS(ph)AESEDEMIHPEGVASLLPPDFQSSLERPELELSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAAELEEASAESEDEMIHPEGVASLLPPDFQSSLERPELELSR 43 1 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAAELEEAS(0.5)AES(0.5)EDEMIHPEGVASLLPPDFQSSLERPELELSR 64.856 0.0014502 19090000 7173 5074.2 5700.8 5545.9 6057.1 6478.9 5865.4 5502 8958.1 6466.6 TRUE FALSE 6892.67123 4929.488784 6731.061374 5832.124564 6251.932122 6609.907797 5937.18252 5388.381777 7941.214043 6028.611422 1.143326505 0.817682289 1.116519361 0.967407609 1.037043472 1.09642293 0.984834169 0.893801474 1.317254254 1 12.55761003 1.250366788 24.99998862 1.158627224 1.000754467 0.205355057 0.118677171 266.6242222 564593.8646 0.074460989 0.026712681 17.79781909 -1.250366788 -0.157872758 LITPPPPPPS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 6 LITPPPPPPSPER 13 0 Q96HE9;J3QKY4;J3QR53 Q96HE9 PRR11 Proline-rich protein 11 1 LITPPPPPPS(1)PER;LITPPPPPPS(1)PER;LITPPPPPPS(1)PER;LITPPPPPPS(1)PER;LITPPPPPPS(1)PER;LIT(0.001)PPPPPPS(0.999)PER 188.63 6.24E-06 2167870000 1090120 1342550 1189871 1688210 1281900 1463989 1473470 1431670 1243850 1307130 TRUE FALSE 1047516.905 1304261.788 1404907.158 1775338.72 1323133.478 1493591.861 1491502.767 1402105.514 1102653.363 1218596.921 0.85960902 1.070297952 1.152889142 1.456871169 1.08578436 1.225665218 1.223950874 1.150590068 0.904854874 1 20.21678957 1.250402791 21.60266498 0.952427659 1.163446849 0.236553672 0.14333819 51.78171557 94468.99403 0.099542157 0.03545443 17.7992946 -1.250402791 0.21101919 TAENATSGETLEENEAGD ddPTM_BT-474_Pertuzumab_2h_R1 2 TAENATSGETLEENEAGD 18 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 342.48 2.95E-75 2388800000 2960800 3042500 2493500 2970400 2742700 3103600 2892400 3049400 3033900 3056200 FALSE TRUE 2845088.663 2955730.879 2944130.918 3123702.7 2830921.436 3166356.918 2927798.056 2986428.824 2689504.391 2849200.852 0.998556722 1.037389441 1.033318138 1.096343453 0.993584371 1.111314043 1.027585702 1.048163671 0.943950438 1 21.4421259 1.250719686 24.97208292 0.971975222 1.044510638 0.368832734 0.037284239 182.6622634 375153.2003 0.023326923 0.008380682 17.81228709 -1.250719686 0.072535416 KLPDFLTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPDFLTAK 9 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7;Q9BZZ5-3 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ; 104.43 0.0063453 0 1979770 1924510 1770460 1714610 1764810 1444030 1957010 2035000 2283800 2392700 FALSE TRUE 1902398.4 1869624.859 2090421.506 1803101.228 1821576.716 1473229.276 1980960.474 1992976.539 2024552.598 2230640.298 0.852848575 0.838156139 0.937139667 0.808333477 0.816616071 0.660451296 0.888068092 0.893454916 0.907610519 1 21.08902646 1.250727676 1.302118016 0.988663117 0.826586545 0.387835773 0.067588204 0.440277978 1.457803301 0.065659442 0.020747409 17.81261479 -1.250727676 -0.162076572 S(ph)RQPSPLLLLPPPAGLTSDPGPSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 1 S(0.53)RQPS(0.47)PLLLLPPPAGLTSDPGPSVR 50.229 0.083864 376540000 36556 29432 37030 35834 31133 33662 35790 36803 32318 35292 TRUE FALSE 35127.35111 28592.62818 43722.14473 37683.39703 32134.42122 34342.6687 36228.00873 36043.00519 28649.39613 32901.64141 1.067647376 0.869033488 1.328874271 1.145334866 0.976681401 1.043798037 1.101100346 1.095477418 0.870758871 1 15.00587194 1.250760585 24.99217831 0.935379431 1.079450963 0.198998346 0.114837897 308.1699019 631307.655 0.077627241 0.027885016 17.81396459 -1.250760585 0.144071531 S(ph)LS(ph)SSPQAQPPRPAELSDEEVAELFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 2 S(0.774)LS(0.473)S(0.391)S(0.361)PQAQPPRPAELSDEEVAELFQR 44.564 0.083934 105220000 27274 27131 26308 28809 33673 26148 30584 30206 24352 27455 TRUE FALSE 26208.10193 26357.25044 31062.44082 30295.83594 34756.12263 26676.73048 30958.29614 29582.23554 21587.66305 25595.4484 1.023936034 1.029763184 1.213592368 1.183641539 1.357902471 1.042245092 1.209523493 1.155761567 0.843418045 1 14.64359966 1.250875257 24.81748819 0.921709052 1.157005334 0.44329558 0.103129935 156.785977 315972.4802 0.070063368 0.02517273 17.81866884 -1.250875257 0.235296282 SIFKPFIFVDDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIFKPFIFVDDVK 13 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 144.68 3.78E-05 921590000 1792400 1652500 1414300 1203000 1376200 1531400 1549100 1711300 1943600 2020000 FALSE TRUE 1722351.026 1605372.318 1669895.471 1265086.974 1420466.723 1562365.957 1568058.349 1675961.057 1722970.676 1883183.601 0.914595383 0.852477856 0.886740661 0.671781006 0.754290087 0.829640804 0.832663554 0.889961582 0.914924427 1 20.84474223 1.250955451 1.142184844 0.994271896 0.813721819 0.447015568 0.064510222 0.427147764 1.130559847 0.063978199 0.021037165 17.82195944 -1.250955451 -0.180550077 ESIESEIRR ddPTM_BT-474_Pertuzumab_2h_R1 9 ESIESEIRR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;; 197.96 4.35E-05 47436400000 14710066 16541261 12242348 14386908 14929955 16035407 14834294 15530864 15575582 15516528 FALSE TRUE 14135180.36 16069520.43 14454812.61 15129418.05 15410190.56 16359653.92 15015840.53 15210146.23 13807507.23 14465579.74 0.977159617 1.110879807 0.999255673 1.045890889 1.065300585 1.130936624 1.038039318 1.051471597 0.954507699 1 23.78612081 1.251021419 24.17049673 0.977253867 1.054479153 0.314923861 0.04422632 142.7366912 276874.7137 0.028511663 0.010240258 17.82466674 -1.251021419 0.077225285 VTEFGGELHEDGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 VTEFGGELHEDGGK 14 0 C9JUJ0;Q9UFW8 C9JUJ0 CGGBP1 CGG triplet repeat-binding protein 1 0 ;; 198.23 2.23E-08 637300000 956330 900550 762730 769580 874730 879170 841880 901950 1093640 1015190 FALSE TRUE 918955.5663 874867.1957 900572.2778 809298.116 902866.4849 896947.4198 852183.1793 883324.4173 969494.5721 946430.2771 0.970970169 0.924386314 0.951546352 0.855105902 0.953970416 0.94771632 0.90041834 0.933322231 1.024369777 1 19.8521367 1.251123322 14.63793577 1.012186631 0.927985693 0.523894532 0.0314278 1.058710091 1237.577873 0.021053008 0.007349232 17.82884962 -1.251123322 -0.084200938 NLDSTTVAVHGEEIYCK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLDSTTVAVHGEEIYCK 17 0 P21291;E9PS42;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 280.54 6.32E-36 685250000 927660 860130 648710 899710 812890 877860 780430 934440 1073400 1083300 FALSE TRUE 891406.0216 835599.9346 765946.3275 946144.1409 839037.3451 895610.9307 789981.1358 915143.4875 951552.1321 1009927.126 0.882643904 0.827386366 0.758417422 0.936843973 0.830789988 0.886807481 0.782215979 0.906148042 0.942198806 1 19.94581976 1.25142177 2.005579821 0.993268295 0.844601623 0.517067548 0.049897074 0.234762121 1.631285494 0.043826671 0.012807225 17.84110586 -1.25142177 -0.148666672 AS(ph)DPGLPAEEPKEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASDPGLPAEEPKEK 14 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 AS(1)DPGLPAEEPKEK;AS(1)DPGLPAEEPKEK 162.15 2.72E-06 697850000 1536530 1283410 838030 657690 1038210 1223160 1010140 1092240 1541680 1280490 TRUE FALSE 1476480.709 1246808.403 989480.6629 691633.4597 1071604.968 1247893.133 1022502.395 1069684.862 1366674.95 1193761.272 1.2368308 1.044436968 0.828876498 0.579373344 0.897671078 1.045345634 0.856538422 0.896062628 1.144847787 1 20.18708292 1.251460587 24.80527333 1.07242389 0.911875331 0.11280866 0.165055684 390.7840497 751445.6135 0.117862381 0.042425026 17.84270057 -1.251460587 -0.16054856 RTSS(ph)TLDSEGTFNSYR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSSTLDSEGTFNSYR 16 1 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 RT(0.255)S(0.255)S(0.369)T(0.119)LDS(0.001)EGTFNSYR 66.76 0.032875 239370000 55998 61717 44851 55464 62211 64023 48513 59425 44437 53377 TRUE FALSE 53809.53625 59956.89159 52956.57341 58326.50369 64212.07331 65317.58893 49106.71661 58197.85298 39392.69806 49761.72825 1.081343799 1.204879607 1.064202858 1.172115715 1.29039074 1.312606922 0.98683704 1.169530381 0.791626405 1 15.60274897 1.251612616 24.97673619 0.895813224 1.160139667 0.505128828 0.104690571 155.0876227 296784.2004 0.070528612 0.025408406 17.84894766 -1.251612616 0.264326443 VQMTS(ph)PSSTGSPMFK ddPTM_BT-474_Pertuzumab_2h_R1 1 VQMTSPSSTGSPMFK 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 VQMTS(0.419)PS(0.419)S(0.124)T(0.036)GS(0.001)PMFK 193.31 1.03E-07 245410000 330030 370480 356030 514390 587880 499650 377660 454170 278630 368140 TRUE FALSE 317132.0627 359914.2731 420372.5408 540937.7295 606789.6941 509753.2653 382281.9161 444791.2308 247001.0905 343205.5499 0.924029529 1.048684304 1.224841909 1.576133398 1.768006649 1.485271044 1.113857035 1.295990787 0.719688509 1 18.38871336 1.251672767 24.00733131 0.85984443 1.313379906 0.33963762 0.247823923 149.1807759 273143.7188 0.185403787 0.066696461 17.85141994 -1.251672767 0.453535476 YDDYSSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 YDDYSSSR 8 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 190.26 0.00043587 9157200000 8354500 8787300 7587700 8591900 8478600 8359300 8522400 8863500 8970200 8961900 FALSE TRUE 8027996.904 8536694.808 8958966.177 9035328.989 8751321.869 8528330.773 8626699.681 8680465.628 7951940.502 8354902.531 0.960872598 1.021758755 1.072300502 1.081440383 1.047447512 1.020757662 1.032531457 1.038966714 0.951769392 1 22.99419157 1.251705236 24.96763122 0.975884701 1.036849347 0.335537881 0.032867653 218.3229746 414699.4834 0.02297801 0.008281736 17.85275463 -1.251705236 0.060964646 LYPPGDEEEAELADSSGLYHEGSPSPGS(ph)PWK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYPPGDEEEAELADSSGLYHEGSPSPGSPWK 31 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LYPPGDEEEAELADSSGLYHEGS(0.004)PS(0.014)PGS(0.982)PWK;LYPPGDEEEAELADSSGLYHEGS(0.001)PS(0.034)PGS(0.965)PWK 155.11 2.72E-09 223000000 105988 105248 88745 102443 101861 95513 102454 107734 100265 106697 TRUE FALSE 101845.8718 102246.4301 104783.1956 107730.0955 105137.4516 97444.3383 103707.8627 105509.2553 88883.33755 99470.31715 1.023882045 1.027908958 1.053411697 1.08303762 1.056973121 0.979632327 1.042601106 1.060710956 0.893566444 1 16.60197846 1.251723715 24.99367382 0.946783207 1.041887674 0.53252396 0.035309937 144.8641748 275066.5752 0.02338967 0.008432097 17.85351426 -1.251723715 0.095104467 YSLATEEIER ddPTM_BT-474_Pertuzumab_2h_R1 1 YSLATEEIER 10 0 Q66K14-2;Q66K14;H0YB08 Q66K14-2 TBC1D9B TBC1 domain family member 9B 0 111.61 0.0055128 0 63512 71951 67447 82114 77731 93012 72627 80939 65505 75125 FALSE TRUE 61029.88082 69899.02793 79636.17325 86351.91338 80231.28821 94892.76637 73515.83095 79267.58137 58069.14702 70036.71684 0.871398369 0.998034047 1.137063198 1.232952047 1.145560384 1.354900267 1.049675574 1.131800361 0.829124346 1 16.09582383 1.251849151 24.98926959 0.914562186 1.122027421 0.278998032 0.128620667 254.1590209 477954.7164 0.089756695 0.032362882 17.8586716 -1.251849151 0.207465236 DKSDS(ph)PAIQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKSDSPAIQLR 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 DKS(0.012)DS(0.988)PAIQLR 103.88 0.0016203 219020000 399480 336380 276920 267840 317020 325160 280320 326880 451190 383200 TRUE FALSE 383867.88 326786.7718 326965.6041 281663.2545 327217.2362 331734.958 283750.64 320129.8138 399972.8027 357245.5227 1.074521178 0.914740007 0.915240593 0.788430468 0.915944961 0.928590946 0.794273467 0.896105881 1.119602003 1 18.4465564 1.251855909 24.96137315 1.059800978 0.896314303 0.380127476 0.079426805 187.9570724 352885.8183 0.05297717 0.019099642 17.85894947 -1.251855909 -0.163486675 RLVEVDSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLVEVDSSR 9 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 152.07 0.00013044 960170000 342050 428920 315060 444930 355370 369170 377850 393260 350710 369110 FALSE TRUE 328682.3078 416687.6216 371998.3505 467892.8906 366800.7988 376634.8703 382474.2413 385139.0436 310898.8711 344109.8509 0.955166808 1.210914539 1.081045339 1.359719547 1.065941001 1.094519292 1.111488789 1.119232834 0.903487274 1 18.39250967 1.251858927 22.40744198 0.951743779 1.1297597 0.317030501 0.1013608 62.46484285 105257.0889 0.06530155 0.023439011 17.8590736 -1.251858927 0.178015922 MLADLDDLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLADLDDLNR 10 0 Q9BQS8;Q9BQS8-4 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 0 72.643 0.088062 0 15758 20197 18726 20288 22745 19130 19582 21256 18198 20421 FALSE TRUE 15142.15994 19621.00133 22110.20476 21335.06611 23476.61358 19516.82171 19821.65037 20817.05617 16132.23933 19037.86748 0.795370593 1.030630209 1.161380327 1.120664703 1.233153535 1.025157977 1.041169679 1.093455251 0.847376385 1 14.21658426 1.251929854 24.94357695 0.923688179 1.071120983 0.189421922 0.113881152 303.2053888 565710.0691 0.077580255 0.027976287 17.8619905 -1.251929854 0.147432804 RGS(ph)QNSSEHRPPASSTSEDVKAS(ph)PSSANK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSQNSSEHRPPASSTSEDVKASPSSANK 29 3 O15014 O15014 ZNF609 Zinc finger protein 609 2 RGS(0.486)QNS(0.211)S(0.302)EHRPPASS(0.001)T(0.001)SEDVKAS(0.876)PS(0.105)S(0.019)ANK 106.93 0.00021974 178460000 90497 92373 74716 76616 104310 88286 78045 90641 71723 82704 TRUE FALSE 86960.27719 89738.61248 88218.84325 80570.16094 107665.2259 90071.20341 79000.13806 88769.23167 63581.30573 77102.38441 1.127854577 1.16388894 1.144177887 1.044976255 1.396392948 1.168202567 1.024613424 1.151316296 0.824634753 1 16.23448786 1.2520916 24.72427232 0.912317419 1.151431351 0.470910865 0.101903446 148.7016177 271716.0129 0.06840693 0.024669086 17.86864417 -1.2520916 0.239113931 GPS(ph)PSPVGSPASVAQSR ddPTM_BT-474_Pertuzumab_2h_R1 6 GPSPSPVGSPASVAQSR 17 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;A0A087WUV6 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 GPS(0.907)PS(0.093)PVGSPASVAQSR;GPS(0.687)PS(0.313)PVGSPASVAQSR;GPS(0.998)PS(0.002)PVGSPASVAQSR;GPS(0.945)PS(0.055)PVGSPASVAQSR;GPS(0.991)PS(0.009)PVGSPASVAQSR;GPS(0.917)PS(0.083)PVGSPASVAQSR 385.08 1.04E-121 6974030000 1088610 1157400 912340 1121070 1136720 1112690 1080100 1148900 1135000 1152350 TRUE FALSE 1046065.918 1124392.085 1077220.133 1178928.557 1173283.631 1135189.354 1093318.587 1125174.814 1006159.558 1074300.308 0.973718345 1.046627351 1.002717885 1.097391994 1.09213748 1.056677863 1.017702945 1.047355944 0.936571972 1 20.03496591 1.252126062 24.97899771 0.968285992 1.043629083 0.369871924 0.038316613 204.8161857 377146.3597 0.026073228 0.009407737 17.87006209 -1.252126062 0.075343091 T(ph)RWSGAQPLEQPSGSVLWMAAEVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRWSGAQPLEQPSGSVLWMAAEVIR 25 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 T(0.5)RWS(0.5)GAQPLEQPSGSVLWMAAEVIR 94.261 0.017454 121410000 32008 50481 43959 46710 50299 47098 54791 48634 35549 35870 TRUE FALSE 30757.09197 49041.33131 51903.36916 49120.7087 51916.91302 48050.35383 55461.54865 47629.6909 31513.62655 33440.49295 0.919755938 1.46652537 1.552111365 1.468899061 1.552516379 1.436891313 1.658514685 1.424311866 0.942379247 1 15.02930849 1.252128565 8.272195153 0.969811476 1.454877522 0.493566691 0.187066312 0.103381379 45.7552066 0.133574784 0.044683708 17.8701651 -1.252128565 0.485066046 ENPSATLEDLEKPGVDEEPQHVLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENPSATLEDLEKPGVDEEPQHVLLR 25 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 231.21 9.96E-35 888990000 489110 486350 401430 423490 359980 257600 567230 486410 610970 679170 FALSE TRUE 469995.0405 472479.7742 473977.3308 445346.3697 371559.0836 262808.8485 574171.9304 476365.4635 541615.247 633169.211 0.74228979 0.74621407 0.748579246 0.703360748 0.586824307 0.415068901 0.906822253 0.75235096 0.855403639 1 19.27223158 1.252163764 1.099416543 0.98573739 0.677801755 0.425895242 0.117156522 0.456593217 1.131575076 0.113154017 0.037715535 17.87161352 -1.252163764 -0.307935635 TGSPGS(ph)PGAGGVQSTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGSPGSPGAGGVQSTAK 17 0 O43237;O43237-2;J3KRI4;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 T(0.001)GS(0.001)PGS(0.982)PGAGGVQS(0.008)T(0.009)AK;TGSPGS(1)PGAGGVQSTAK 183.53 7.20E-10 241410000 345634 419199 484205 506613 431717 467406 431245 494651 431754 489057 TRUE FALSE 332126.2412 407243.855 571711.6146 532759.3576 445603.5694 476857.2696 436522.7053 484436.284 382743.096 455932.7338 0.728454477 0.89321039 1.253938514 1.168504295 0.977344982 1.04589391 0.957427868 1.062517008 0.839472728 1 18.79846147 1.252257426 24.97442962 0.919736309 1.019708867 0.059933352 0.141035789 581.523703 1060347.473 0.098661499 0.035610082 17.87546819 -1.252257426 0.099972557 APDSGLPSGGGGRPGCAYPGS(ph)PGPGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 APDSGLPSGGGGRPGCAYPGSPGPGAR 27 1 Q6PJ61 Q6PJ61 FBXO46 F-box only protein 46 1 APDSGLPSGGGGRPGCAYPGS(1)PGPGAR 122.77 5.34E-05 359430000 66499 67490 55985 71135 63139 75535 69345 71093 64795 69173 TRUE FALSE 63900.14556 65565.25128 66102.73488 74806.28587 65169.92328 77062.36945 70193.66485 69624.90471 57439.74324 64487.8511 0.99088657 1.016707026 1.025041675 1.160005871 1.010576755 1.1949905 1.088478894 1.079659246 0.890706424 1 15.97673978 1.252438826 24.99220914 0.945353222 1.073705288 0.358930015 0.066966601 207.561345 373785.2111 0.044690777 0.01613569 17.88293615 -1.252438826 0.128352066 RNSLEGYS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSLEGYSR 9 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 RNS(0.027)LEGYS(0.973)R;RNS(0.363)LEGYS(0.637)R 123.38 0.00059239 358350000 746870 802610 648650 856800 845430 817010 790550 824260 792420 772090 TRUE FALSE 717681.4947 779720.3486 765875.4841 901019.5507 872624.0237 833530.502 800224.9874 807238.743 702467.8037 719795.6566 0.99706283 1.083252367 1.064017929 1.251771308 1.21232188 1.158009908 1.111739117 1.121483209 0.975926705 1 19.45722787 1.252504413 8.982767177 0.987740421 1.12879721 0.387819835 0.068710971 0.165455574 91.49832988 0.053414629 0.018061527 17.88563703 -1.252504413 0.141056789 S(ph)PPPGMGLNQNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPPGMGLNQNR 12 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 S(1)PPPGMGLNQNR;S(1)PPPGMGLNQNR 89.44 0.009883 580130000 18472.8 17573.7 20126 20354.9 22761.9 22999.7 22245 21733 16132.6 19275.6 TRUE FALSE 17750.86255 17072.51528 23763.2159 21405.41883 23494.05719 23464.76969 22517.24096 21284.20596 14301.29488 17970.04644 0.98780282 0.950054043 1.322379215 1.191172148 1.307401028 1.305771233 1.253043003 1.184426875 0.79584073 1 14.13330652 1.252621873 24.64985617 0.897920454 1.194972985 0.443117445 0.129765845 157.6208816 276318.0743 0.092243779 0.033307441 17.89047508 -1.252621873 0.297052531 KIEIGDGAELTAEFLYDEVHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIEIGDGAELTAEFLYDEVHPK 22 1 Q6IBS0 Q6IBS0 TWF2 Twinfilin-2 0 145.58 5.96E-08 18646000 26305 24902 23813 22787 24609 26089 25031 24560 37194 28803 FALSE TRUE 25276.97152 24191.81934 28116.53882 23963.0398 25400.57083 26616.53745 25337.33687 24052.82742 32971.89305 26852.14715 0.941338932 0.900926812 1.047087172 0.89240684 0.94594189 0.991225666 0.943586996 0.895750618 1.227905272 1 14.71274983 1.252713249 24.99961631 1.113952694 0.944105915 0.500562812 0.067588931 147.9718931 261384.3659 0.041827574 0.015111839 17.89423964 -1.252713249 -0.169846779 EILERVDGRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EILERVDGRR 10 2 P78545-2;P78545;Q9NZC4-2;Q9NZC4;Q9NZC4-3 P78545-2 ELF3;EHF ETS-related transcription factor Elf-3;ETS homologous factor 0 85.064 0.038016 2132800000 1358100 1260600 2226100 1159600 1892100 841620 2078900 1755400 1471500 1716800 FALSE TRUE 1305023.951 1224648.922 2628405.789 1219447.095 1952961.115 858638.133 2104342.2 1719150.377 1304461.489 1600519.607 0.815375173 0.765157088 1.6422203 0.761907002 1.22020443 0.536474611 1.314786892 1.07412016 0.815023748 1 20.61010892 1.252750079 24.87997595 0.907511804 1.028126906 0.018544041 0.306987522 925.1465947 1622180.554 0.196334241 0.070926568 17.89575722 -1.252750079 0.120615101 LNDSHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNDSHK 6 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 73.039 0.084013 57495000 189400 174330 107260 192480 145070 137680 157040 162140 121140 144040 FALSE TRUE 181998.0386 169358.2791 126644.268 202413.9159 149736.3083 140463.9839 158961.9025 158791.7523 107388.6951 134284.0425 1.355321416 1.261194375 0.943107354 1.507356437 1.115071497 1.046021413 1.183773586 1.182506494 0.799713004 1 17.03492835 1.252757004 24.43095557 0.899856591 1.193913472 0.373637253 0.154954173 156.3584642 269085.2724 0.100339784 0.036229261 17.89604255 -1.252757004 0.294056881 QAS(ph)LDGLQQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 QASLDGLQQLR 11 0 Q3MII6 Q3MII6 TBC1D25 TBC1 domain family member 25 1 QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR 164.93 2.33E-05 1146900000 724640 747480 643140 705850 748790 665720 729580 743580 706220 729150 TRUE FALSE 696320.2677 726162.6023 759369.7046 742279.0031 772875.5104 679181.3145 738508.8183 728224.8132 626052.8663 679764.021 1.024355874 1.068256895 1.117107821 1.091965712 1.136976195 0.999142781 1.086419398 1.071290611 0.920985588 1 19.37467448 1.25284373 24.58253068 0.960492828 1.076142534 0.5417432 0.041896374 117.2731258 201840.2015 0.027467748 0.009922051 17.89961666 -1.25284373 0.115649706 AVCMLSNTTAVAEAWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVCMLSNTTAVAEAWAR 17 0 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 202.4 2.47E-11 51187000 38289 51958 39386 38650 49228 41908 41760 46328 40789 45033 FALSE TRUE 36792.62355 50476.20871 46503.92634 40644.73113 50811.46333 42755.40847 42271.07137 45371.31061 36158.80372 41982.8748 0.876372181 1.202304724 1.107687993 0.96812644 1.210290233 1.018401162 1.006864622 1.080709952 0.861275077 1 15.35751334 1.253140375 24.89590749 0.93063753 1.064076402 0.203489334 0.101037225 273.1602994 466444.0725 0.063262167 0.022874721 17.91184718 -1.253140375 0.133438872 ASILWLIGENCER ddPTM_BT-474_Pertuzumab_2h_R1 1 ASILWLIGENCER 13 0 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 0 129.82 0.00034724 112950000 137490 189630 110960 184600 152200 121130 181760 167800 154120 167360 FALSE TRUE 132116.7388 184221.9381 131012.9403 194127.2281 157095.6512 123579.3316 183984.4333 164334.8714 136624.9437 156024.5581 0.84676887 1.180723985 0.839694352 1.24420944 1.006864901 0.792050515 1.179201758 1.053262854 0.875663071 1 17.2514136 1.253208315 24.96114517 0.937831498 1.026267821 0.041152362 0.15015538 637.3706161 1086153.906 0.094877362 0.034314103 17.91464948 -1.253208315 0.088436323 WIDFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 WIDFVR 6 0 P05455 P05455 SSB Lupus La protein 0 ; 142.63 0.026758 4007600000 2369000 2637500 2186990 2564600 2578400 2183480 2628900 2662100 2444300 2651400 FALSE TRUE 2276416.861 2562281.082 2582227.742 2696959.313 2661336.578 2227631.462 2661073.265 2607126.705 2166833.311 2471818.316 0.920948294 1.03659766 1.04466729 1.091083149 1.076671598 0.901211649 1.076565072 1.054740426 0.876615121 1 21.23714128 1.253359319 24.99852883 0.938307526 1.029832662 0.209702081 0.067101979 294.1238594 496849.7688 0.044225426 0.016001355 17.92087947 -1.253359319 0.091525136 VQVEYKGETK ddPTM_BT-474_Pertuzumab_2h_R1 2 VQVEYKGETK 10 1 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ; 127.17 0.00033113 927970000 2220550 2240620 1323550 1212260 1740470 1908210 2105970 1870500 2940000 2292500 FALSE TRUE 2133768.451 2176719.711 1562744.927 1274824.884 1796453.798 1946795.314 2131743.491 1831873.521 2606263.525 2137226.933 0.99838179 1.018478514 0.731202149 0.596485504 0.840553603 0.910897801 0.997434319 0.857126351 1.21946036 1 21.02730867 1.253800804 24.98904555 1.109730155 0.866598046 0.345729197 0.132535864 239.3281151 392425.2753 0.095777419 0.034688114 17.93910634 -1.253800804 -0.243132109 LALQLHPDRNPDDPQAQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LALQLHPDRNPDDPQAQEK 19 1 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 122.57 1.98E-05 564760000 406540 438440 356090 360740 382260 410050 422130 420380 548560 477080 FALSE TRUE 390651.9673 425936.1205 420443.3842 379357.8346 394555.7401 418341.4919 427296.1532 411699.0061 486289.7686 444766.9467 0.878329584 0.957661363 0.945311668 0.852936212 0.887106704 0.94058584 0.960719218 0.925651084 1.093358605 1 18.76269005 1.253940848 24.63276116 1.046679259 0.920564417 0.623237899 0.039827679 109.8251042 175896.1978 0.026981638 0.009769761 17.94489196 -1.253940848 -0.126114842 SQAFIEMETR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQAFIEMETR 10 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 195.4 8.33E-07 878320000 855800 844800 737400 839630 865630 802280 840640 870880 875630 881650 FALSE TRUE 822354.3899 820707.1311 870664.5834 882963.4049 893473.7751 818502.6513 850928.0038 852896.0237 776232.1533 821935.0602 1.000510174 0.998506051 1.059286342 1.074249594 1.087036943 0.99582399 1.035274008 1.037668382 0.944395964 1 19.64866489 1.254140454 24.97431734 0.972197994 1.037168228 0.383947405 0.032324596 212.4543785 340565.0756 0.022663698 0.008212212 17.95314151 -1.254140454 0.064970235 ERPKDDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPKDDIK 8 2 Q9HAU5 Q9HAU5 UPF2 Regulator of nonsense transcripts 2 0 84.615 0.0097451 184950000 240250 200280 199930 168640 197290 184170 208780 211010 263800 246890 FALSE TRUE 230860.7644 194568.2105 236061.7984 177343.5306 203636.012 187894.0436 211335.1121 206652.5698 233854.5299 230167.9204 1.003010168 0.845331574 1.025606861 0.770496298 0.884728035 0.816334628 0.918177962 0.897833935 1.016017043 1 17.81232725 1.25418843 7.27759256 1.008545197 0.892005626 0.273971615 0.073310131 0.161605972 42.22909649 0.050989371 0.016926836 17.95512487 -1.25418843 -0.116539571 VRPCVVYGGADIGQQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VRPCVVYGGADIGQQIR 17 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 207.53 5.47E-12 2413400000 543050 414280 426260 495310 431890 463860 510810 454400 628000 497630 FALSE TRUE 521827.0056 402465.14 503294.6641 520873.0085 445782.1341 473239.567 517061.4456 445016.4812 556712.0728 463925.0769 1.124808793 0.867521848 1.084861951 1.122752432 0.960892515 1.020077574 1.114536531 0.959242135 1.200004269 1 18.82353231 1.254336642 24.99843895 1.100002289 1.029089255 0.080646388 0.091685545 498.8135066 790419.266 0.057467045 0.020832516 17.96125347 -1.254336642 -0.070913033 S(ph)SSAPLIHGLSDLSQVFQPYTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 S(0.327)S(0.327)S(0.327)APLIHGLS(0.018)DLS(0.001)QVFQPYTLR 60.521 0.038223 5994400 4439.1 5307.4 4145.4 5007.7 4932.9 5843.3 3179.9 5018 6856.2 6091.1 TRUE FALSE 4265.615064 5156.038148 4894.565994 5266.147997 5091.571208 5961.45553 3218.816567 4914.376546 6077.91292 5678.544372 0.751181075 0.907985887 0.861940257 0.927376393 0.896633164 1.04982107 0.566838323 0.865428924 1.070329388 1 12.47130544 1.254353863 14.90853296 1.035164305 0.85229877 0.268254044 0.120070405 2.492559338 2357.826988 0.081876091 0.029038955 17.9619657 -1.254353863 -0.182865534 RNS(ph)IPIVTEQPLISAGENR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSIPIVTEQPLISAGENR 19 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RNS(1)IPIVTEQPLISAGENR 134.68 2.67E-07 0 82544 100810 75696 105380 90630 101010 92198 97318 78917 90657 TRUE FALSE 79318.08922 97934.9975 89375.95105 110818.6744 93545.19626 103052.4914 93326.3467 95308.34929 69958.67301 84516.72064 0.938489906 1.15876476 1.057494308 1.311204145 1.106824727 1.219314836 1.104235304 1.127686315 0.827749497 1 16.36694917 1.254503253 24.3082377 0.913874837 1.133547812 0.42276731 0.099914067 127.5371428 194462.2298 0.063202171 0.022899597 17.96814537 -1.254503253 0.219672975 RLS(ph)PISGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSPISGSR 9 1 E9PQ01 E9PQ01 PCF11 1 RLS(1)PISGSR;RLS(1)PISGSR 95.183 0.0050332 932260000 227440 270220 209327 267570 220470 227895 279870 261650 236192 257910 TRUE FALSE 218551.3934 262513.5902 247157.0454 281379.3198 227561.6178 232503.193 283295.1328 256246.8361 209380.4744 240441.526 0.908958602 1.091798054 1.027929948 1.170260913 0.946432264 0.966984351 1.178228809 1.065734527 0.870816609 1 17.87532656 1.254644065 24.98862012 0.935408292 1.051197919 0.190714782 0.089083055 307.5781072 477883.3904 0.05827764 0.021134115 17.97397219 -1.254644065 0.115789626 SSGSSSSGLGTVSNS(ph)PASQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGSSSSGLGTVSNSPASQR 20 0 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9;Q9UPP1-5;H0Y589 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 SSGSSSSGLGTVS(0.003)NS(0.997)PASQR;SSGSSSSGLGTVSNS(1)PASQR 260.15 2.66E-36 1052460000 512870 491600 402060 493560 470700 437230 470760 517360 400040 498050 TRUE FALSE 492826.4734 477580.0493 474721.1858 519032.6907 485840.493 446071.0902 476521.3017 506676.3352 354629.1363 464316.6299 1.061401728 1.028565463 1.022408321 1.11784213 1.046356003 0.960704531 1.026285235 1.091230214 0.763765744 1 18.82474943 1.254889086 24.9999885 0.881882784 1.044266588 0.490601117 0.066219746 158.5767987 242793.6863 0.041761907 0.01515439 17.98411564 -1.254889086 0.162383804 SGGGYGGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 SGGGYGGDR 9 0 Q92804-2;Q92804;A0A075B7F4;A0A075B7C1 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;;;; 133.05 0.00066955 3637749000 1682075 1758988 1483630 1735869 1632191 1689468 1656583 1775872 1715074 1791732 FALSE TRUE 1616337.649 1708823.384 1751754.944 1825457.407 1684691.906 1723630.201 1676856.758 1739199.623 1520385.99 1670376.396 0.967648761 1.023016961 1.048718689 1.092841956 1.00857023 1.03188132 1.003879582 1.041202227 0.910205624 1 20.6717418 1.255062092 24.98413326 0.955102795 1.028935354 0.380678276 0.036741959 199.8736003 302621.8938 0.024052027 0.008727163 17.99128121 -1.255062092 0.073832558 TFQGHTNEVNAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFQGHTNEVNAIK 13 0 Q9BZK7;A0A0D9SF63;A0A1B0GVH3;O60907;A0A2R8YFW3;Q9BQ87;O60907-2 Q9BZK7;O60907 TBL1XR1;TBL1X;TBL1Y F-box-like/WD repeat-containing protein TBL1XR1;F-box-like/WD repeat-containing protein TBL1X;F-box-like/WD repeat-containing protein TBL1Y 0 174.65 1.96E-05 135940000 340840 309380 274580 318200 322480 337860 320770 338350 431130 407200 FALSE TRUE 327519.596 300556.7853 324202.714 334622.3401 332852.8621 344691.7607 324695.6792 331362.9543 382189.9298 379619.9813 0.862756473 0.791730678 0.854019098 0.881466616 0.876805433 0.907991617 0.855317673 0.872880698 1.006769793 1 18.53419641 1.255266451 5.580159676 1.00549421 0.862263784 0.801382598 0.028004635 0.069223557 6.418765838 0.023589526 0.007503444 17.99974907 -1.255266451 -0.143230425 VNCLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNCLDK 6 0 Q14847;Q14847-2;F6S2S5;K7ESD6;O76041-2 Q14847;O76041-2 LASP1;NEBL LIM and SH3 domain protein 1;Nebulette 0 99.384 0.090404 495990000 720830 665700 658470 791550 666250 621760 731070 820960 891080 956540 FALSE TRUE 692659.1667 646714.8878 777470.1766 832401.9904 687680.5363 634332.4132 740017.0533 804006.8891 789928.3341 891752.6938 0.77673908 0.725217756 0.871845055 0.933444885 0.771156108 0.711332209 0.829845605 0.901602983 0.885815473 1 19.76628414 1.255283383 1.138884075 0.988689179 0.802667138 0.473553697 0.06481952 0.42347985 1.114158483 0.065291522 0.021508195 18.00045085 -1.255283383 -0.18602204 LSDTTEYQPILSSYSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSDTTEYQPILSSYSHR 17 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 0 91.518 0.0035357 201440000 246340 304370 257690 316440 299400 298450 294170 302910 265100 288780 FALSE TRUE 236712.7605 295689.6656 304260.3153 332771.5063 309030.4729 304484.8635 297770.1405 296654.8026 235006.9594 269220.6734 0.879251796 1.098317086 1.130152122 1.236054803 1.147870515 1.130986189 1.106044854 1.101902016 0.872915725 1 18.03842967 1.255545393 22.6252897 0.936458088 1.110845097 0.357613712 0.089329401 70.07043819 93342.89235 0.060314116 0.021849317 18.01131382 -1.255545393 0.174387008 S(ph)LSDSESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.986)LS(0.014)DSESDDSK;S(0.702)LS(0.298)DSESDDSK;S(0.997)LS(0.003)DSESDDSK;S(0.69)LS(0.31)DSESDDSK;S(0.901)LS(0.099)DSESDDSK 308.91 1.54E-45 5964670000 3666630 3226930 3093150 3184570 3154150 3027970 3300020 3419320 4086780 3863320 TRUE FALSE 3523334.046 3134901.116 3652151.012 3348926.039 3255606.099 3089197.628 3340406.632 3348709.847 3622865.868 3601653.895 0.978254477 0.870405988 1.014020536 0.929830055 0.903919753 0.857716404 0.92746464 0.929770029 1.005889509 1 21.78022812 1.255566149 5.904457481 1.003859883 0.924566561 0.332301608 0.043342435 0.167655445 19.13963981 0.032798193 0.010559756 18.01217462 -1.255566149 -0.079293322 ILEEENSLAEYHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILEEENSLAEYHSR 14 0 Q15650 Q15650 TRIP4 Activating signal cointegrator 1 0 145.52 8.56E-06 113370000 92388 83690 129360 96462 105060 113450 96365 109510 88659 103640 FALSE TRUE 88777.37482 81303.24314 152738.2296 101440.4154 108439.3503 115744.0367 97544.3437 107248.5802 78594.80201 96620.37049 0.918826686 0.841471035 1.580807741 1.049886425 1.122323893 1.197925822 1.009562923 1.109999679 0.813439253 1 16.56003976 1.256272914 24.02598191 0.906719715 1.108255419 0.143843125 0.192133867 247.7535523 336071.2155 0.127251788 0.046212861 18.04151125 -1.256272914 0.201535705 GAVAAEGAS(ph)DTEREEPTESQGLAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAVAAEGASDTEREEPTESQGLAAR 25 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 GAVAAEGAS(0.988)DT(0.012)EREEPTESQGLAAR;GAVAAEGAS(1)DTEREEPTESQGLAAR 329.14 5.07E-88 1605750000 660080 667730 507240 614880 660240 632900 629920 648390 596160 586900 TRUE FALSE 634283.3438 648686.9942 598909.5515 646614.0305 681477.2192 645697.6716 637629.1494 635000.5199 528486.4161 547148.7402 1.159252132 1.185577059 1.094600988 1.181788393 1.24550633 1.180113604 1.165367116 1.160562884 0.96589168 1 19.06157355 1.256487557 7.910064449 0.982461825 1.171977324 0.818171736 0.035574141 0.05752314 18.7225165 0.026842833 0.009096642 18.0504302 -1.256487557 0.189515499 LKGAER ddPTM_BT-474_Pertuzumab_2h_R1 1 LKGAER 6 1 O15021-2;H7C1I9;O15021-3;O15021-6;O15021 O15021-2 MAST4 Microtubule-associated serine/threonine-protein kinase 4 0 67.055 0.091002 228920000 408180 406240 338620 400130 370540 389460 390990 410230 408320 418380 FALSE TRUE 392227.8743 394654.433 399816.1666 420780.7573 382458.7556 397335.148 395775.0526 401758.6071 361969.2254 390042.7499 1.005602269 1.011823532 1.025057296 1.078806765 0.980555992 1.018696407 1.014696601 1.030037367 0.928024493 1 18.57327273 1.256488399 24.99967262 0.964012231 1.021183433 0.389814856 0.028343116 196.8626699 274519.9738 0.018082798 0.006575465 18.05046519 -1.256488399 0.057171202 SGLSCQVGSATSHPVSCQEPIDEDQRIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGLSCQVGSATSHPVSCQEPIDEDQRISPK 30 1 Q8TEP8;H0Y966;A0A0A0MR42;K7ENP4;Q8TEP8-1;K7ELX0;Q8TEP8-2 Q8TEP8 CEP192 Centrosomal protein of 192 kDa 1 SGLSCQVGSATSHPVSCQEPIDEDQRIS(1)PK;SGLSCQVGSATSHPVSCQEPIDEDQRIS(1)PK 146.76 2.13E-08 440860000 196092 165120 161654 125870 143448 171565 158197 169056 209073 194788 TRUE FALSE 188428.5078 160410.9393 190868.4738 132366.1658 148062.1352 175034.1618 160133.0622 165564.9345 185339.9095 181594.8353 1.037631426 0.883345273 1.051067744 0.728909308 0.815343316 0.963871916 0.881815069 0.911727111 1.020623242 1 17.47036365 1.256502449 8.494202475 1.010483368 0.904701758 0.163710146 0.09095122 0.27507472 109.1743542 0.064414489 0.022024035 18.05104918 -1.256502449 -0.10578161 QQLS(ph)PSPGQEAGILPETEK ddPTM_BT-474_Pertuzumab_2h_R1 3 QQLSPSPGQEAGILPETEK 19 0 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 QQLS(0.907)PS(0.093)PGQEAGILPETEK;QQLS(0.999)PS(0.001)PGQEAGILPETEK;QQLS(0.961)PS(0.039)PGQEAGILPETEK 294.35 1.29E-49 409500000 431614 402094 366480 391422 447270 404994 422225 433584 401951 431134 TRUE FALSE 414746.0477 390626.6728 432711.0883 411623.3363 461656.8458 413183.2562 427392.3159 424630.3389 356323.2076 401932.9102 1.031878797 0.971870337 1.076575412 1.024109561 1.148591802 1.027990607 1.063342426 1.05647069 0.88652409 1 18.61659518 1.256542341 24.9963008 0.943262054 1.05097959 0.425235764 0.049677246 184.5075894 256484.6764 0.032074815 0.01166314 18.0527073 -1.256542341 0.107717536 LEGVEGVAHIIDPK ddPTM_BT-474_Pertuzumab_2h_R1 3 LEGVEGVAHIIDPK 14 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 111.74 0.00063403 791140000 1522600 1493240 1437120 1289300 1451750 1585320 1523800 1576710 2034580 1927050 FALSE TRUE 1463095.109 1450654.257 1696839.553 1355840.928 1498446.857 1617376.257 1542448.72 1544150.388 1803623.008 1796529.187 0.814400968 0.807476031 0.944509872 0.754700195 0.834078771 0.900278308 0.858571478 0.859518676 1.003948626 1 20.77678094 1.256583963 4.763695325 1.005701619 0.846960896 0.618228968 0.048861361 0.114872307 6.104526993 0.038646145 0.011936161 18.05443754 -1.256583963 -0.158740723 IVPEGEWGQFMDALREPLPATLR ddPTM_BT-474_Pertuzumab_2h_R1 2 IVPEGEWGQFMDALREPLPATLR 23 1 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 209.56 7.46E-25 313810000 58017 57411 35735 37111 60844 55059 42516 50666 41049 37464 FALSE TRUE 55749.6315 55773.69449 42193.10942 39026.30316 62801.10252 56172.3307 43036.32353 49619.72939 36389.28961 34926.52991 1.596197264 1.596886225 1.208053292 1.117382782 1.798091671 1.60829979 1.232195802 1.420688786 1.041881049 1 15.09203569 1.25661838 1.702482888 0.978548344 1.458825012 0.408921852 0.203149407 0.362508591 1.891321775 0.195705461 0.058497354 18.05586836 -1.25661838 0.480276668 VLAPILPDNFST(ph)PTGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 VLAPILPDNFS(0.036)T(0.963)PT(0.001)GSR;VLAPILPDNFS(0.051)T(0.944)PT(0.002)GS(0.002)R;VLAPILPDNFS(0.039)T(0.959)PT(0.002)GSR;VLAPILPDNFS(0.048)T(0.952)PTGSR 281.92 5.92E-35 820920000 397794 424813 414999 429459 403483 444145 429808 479150 352861 465775 TRUE FALSE 382247.7707 412697.7492 489998.5509 451623.4305 416461.3971 453125.9162 435068.1189 469255.3851 312805.6986 434227.6444 0.880293495 0.950417954 1.128437024 1.040061443 0.959085407 1.043521577 1.001935562 1.080666768 0.720372603 1 18.72809205 1.256771121 24.99999959 0.860186113 1.015583895 0.30141328 0.091310208 233.5122257 320575.6093 0.058522772 0.021283151 18.0622197 -1.256771121 0.155397782 QAQT(ph)QTSPEHLVLQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAQTQTSPEHLVLQQK 16 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 QAQT(0.569)QT(0.146)S(0.285)PEHLVLQQK;QAQT(0.428)QT(0.39)S(0.182)PEHLVLQQK 218.37 4.93E-14 1373560000 917270 881670 795700 733020 819780 913630 872340 904280 1198890 1120560 TRUE FALSE 881422.0743 856525.6348 939500.6903 770851.25 846148.9682 932104.2246 883015.9579 885606.302 1062797.033 1044663.473 0.843737813 0.819905794 0.89933334 0.737894327 0.809972771 0.892253102 0.845263552 0.847743149 1.017358279 1 19.99460684 1.256837049 6.196526558 1.010236663 0.836512793 0.722257397 0.042591497 0.073992849 9.990208718 0.03232064 0.010546369 18.06496185 -1.256837049 -0.173723869 RFFPYYVYNIIGGLDEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RFFPYYVYNIIGGLDEEGK 19 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ; 202.03 9.17E-16 371100000 918790 874570 557800 605310 759300 761940 746920 773080 970700 849810 FALSE TRUE 882882.671 849628.1199 658606.8682 636550.1216 783723.5741 777346.9488 756061.0304 757115.6278 860510.2055 792251.6118 1.114396813 1.072422078 0.831310228 0.803469645 0.989235695 0.981186958 0.954319334 0.955650473 1.086157722 1 19.59559916 1.257099458 24.50645789 1.043078833 0.957767261 0.109034693 0.090963935 374.9469043 495645.497 0.064937574 0.023616196 18.07588036 -1.257099458 -0.085311572 TPRPAS(ph)PGPSLPARS(ph)PS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPRPASPGPSLPARSPSPPR 20 2 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 3 T(0.182)PRPAS(0.795)PGPS(0.037)LPARS(0.988)PS(0.999)PPR 78.913 0.0054238 597130000 176400 191210 139480 177270 158450 188280 159750 176920 171940 159860 TRUE FALSE 169506.093 185756.878 164687.1387 186418.9259 163546.6882 192087.1506 161705.0683 173266.5402 152422.092 149032.5398 1.137376396 1.246418254 1.105041482 1.250860558 1.097389123 1.288894028 1.085031957 1.162608786 1.022743706 1 17.18526784 1.257517492 1.50572876 0.993292192 1.1804441 0.472675547 0.06722845 0.286458821 1.212140406 0.055168104 0.016864808 18.09328781 -1.257517492 0.187151909 GIEESLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIEESLRK 8 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PP40;A0A1W2PQ55 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 74.301 0.066273 132400000 106100 134250 83083 162990 97599 121480 138510 124820 107010 105540 FALSE TRUE 101953.4947 130421.3214 98097.94627 171401.9334 100738.3605 123936.4088 140205.1268 122242.4234 94862.67342 98391.68179 1.036200346 1.325531987 0.997014631 1.74203683 1.023850377 1.259622832 1.424969309 1.242406077 0.964133062 1 16.58624873 1.257638437 7.307409764 0.980880512 1.266305275 0.213903628 0.209849665 0.19636808 47.7274654 0.142540049 0.047970442 18.09832727 -1.257638437 0.285424763 ELEEMIENLEPHIDDPDVK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELEEMIENLEPHIDDPDVK 19 0 Q8TF05-2;Q8TF05 Q8TF05-2 PPP4R1 Serine/threonine-protein phosphatase 4 regulatory subunit 1 0 ;;; 191.95 8.52E-15 91427000 132601 115924 101866 112607 120291 126801 130442 128284 180621 163036 FALSE TRUE 127418.8063 112617.961 120275.4522 118418.6608 124160.2693 129365.0031 132038.3882 125634.8906 160117.6613 151993.4265 0.838317875 0.740939681 0.791320092 0.77910383 0.816879204 0.851122355 0.868711176 0.82658108 1.053451225 1 17.2136494 1.258212025 8.701591422 1.02694893 0.814206689 0.841359717 0.036925388 0.067514652 26.35838194 0.028639662 0.009881796 18.12224617 -1.258212025 -0.212742241 RLS(ph)AQAHPAGK ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSAQAHPAGK 11 1 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 RLS(1)AQAHPAGK;RLS(1)AQAHPAGK;RLS(1)AQAHPAGK;RLS(1)AQAHPAGK 119.63 0.00034314 1432760000 1535700 1800720 1877630 1497760 1556390 1809950 1606350 1759340 2339840 1961990 TRUE FALSE 1475683.146 1749365.229 2216959.509 1575059.573 1606452.698 1846548.429 1626008.992 1723009.014 2074231.173 1829102.67 0.806779833 0.956406252 1.212047604 0.861110532 0.878273661 1.009537879 0.888965403 0.941996883 1.134015715 1 20.80270463 1.258419062 24.81936953 1.067007847 0.947786647 0.168302249 0.10882218 344.4862705 430546.5788 0.072510292 0.026398358 18.13088746 -1.258419062 -0.1192212 ALKEPPRDR ddPTM_BT-474_Pertuzumab_2h_R1 8 ALKEPPRDR 9 2 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;;; 111.61 0.0011796 7094410000 13489510 15182560 9784290 11335210 12363180 15296510 12816550 13279990 13826190 12915980 FALSE TRUE 12962325.04 14749568.25 11552528.85 11920221.55 12760852.91 15605815.91 12973402.77 13005753.57 12256698.88 12041169.17 1.076500534 1.224928248 0.959419197 0.989955492 1.059768593 1.296038258 1.077420522 1.080107204 1.0178994 1 23.52147215 1.258602207 2.41185758 1.000066989 1.098388429 0.122989648 0.094105151 0.644669942 6.27597285 0.089139802 0.025780471 18.138535 -1.258602207 0.098321441 YTPSGQAGAAASESLFVSNHAY ddPTM_BT-474_Pertuzumab_2h_R1 1 YTPSGQAGAAASESLFVSNHAY 22 0 P04075;J3KPS3;P04075-2;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 195.46 4.70E-24 0 28233 36491 25482 34349 28219 31345 31388 32377 25498 30787 FALSE TRUE 27129.62315 35450.31241 30087.16424 36121.75601 29126.68976 31978.81738 31772.13573 31708.40364 22603.57394 28701.76907 0.945224773 1.23512639 1.048268634 1.258520195 1.014804687 1.11417583 1.106974823 1.104754329 0.78753243 1 14.80885204 1.258635615 24.47499426 0.893766322 1.108501265 0.411795868 0.100112762 134.1488165 163552.4626 0.059732219 0.021746963 18.13993036 -1.258635615 0.214734944 RLDEELEDAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDEELEDAEK 11 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 194.24 9.62E-07 2146400000 2578200 2195170 1891590 1990690 2107460 2043770 2262610 2323690 2756250 2714610 FALSE TRUE 2477441.094 2132565.901 2233442.391 2093429.749 2175248.365 2085096.43 2290300.498 2275704.989 2443372.055 2530747.047 0.978936673 0.842662606 0.882522967 0.827198337 0.859528165 0.823905507 0.904989893 0.89922262 0.965474625 1 21.27113188 1.258723644 1.46605761 1.000363605 0.867807979 0.513211467 0.042348099 0.280637265 1.134565052 0.037538263 0.011543122 18.14360757 -1.258723644 -0.132555625 MS(ph)PSGGAPQTTPTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSPSGGAPQTTPTLR 15 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 MS(1)PSGGAPQTTPTLR 119.56 0.00021294 87422000 32392 38738 34638 45042 35836 42051 39277 40876 34117 39782 TRUE FALSE 31126.08483 37633.23017 40897.85712 47366.62302 36988.69749 42901.30003 39757.68368 40031.89632 30244.18119 37087.52971 0.839260125 1.014713853 1.102738776 1.27715767 0.997335163 1.15675809 1.071996005 1.079389666 0.815481145 1 15.17864656 1.258999265 24.77363323 0.907740606 1.07480723 0.236086318 0.114275943 251.1253395 304390.1686 0.075783722 0.027601913 18.15512588 -1.258999265 0.167066624 RIS(ph)YVQDENRDPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RISYVQDENRDPIR 14 2 Q9NQS7-2;Q9NQS7;E9PM67 Q9NQS7-2 INCENP Inner centromere protein 1 RIS(0.992)Y(0.008)VQDENRDPIR;RIS(0.996)Y(0.004)VQDENRDPIR 80.459 0.012788 685000000 472230 554880 499800 599540 531000 492560 584440 566990 434560 538780 TRUE FALSE 453774.7295 539055.3657 590124.978 630482.3312 548080.0972 502519.9007 591592.5515 555281.4584 385230.5706 502287.9507 0.903415519 1.073199875 1.174873849 1.255220895 1.091167121 1.000461787 1.177795626 1.105504238 0.766951646 1 18.93815514 1.259059376 24.65726967 0.883475905 1.105149748 0.393088886 0.106154941 166.9439101 200812.475 0.07061748 0.02571915 18.15763896 -1.259059376 0.221673843 GSCLESGGHSNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSCLESGGHSNDR 13 0 A0A096LP25;Q6ZSR9 A0A096LP25 AAK1 Uncharacterized protein FLJ45252 0 106.29 0.0013854 162180000 62401 90565 56973 85707 72674 84732 69794 80458 68727 79661 FALSE TRUE 59962.29993 87982.17487 67269.28846 90130.34854 75011.62521 86445.33909 70648.15985 78796.51418 60925.39909 74265.48952 0.807404628 1.184697973 0.905794722 1.21362357 1.01004687 1.164004165 0.951291916 1.061011174 0.820372955 1 16.18040434 1.259662024 24.9940881 0.910186425 1.04344524 0.134530179 0.128124744 349.5788728 414069.4324 0.076522513 0.027880361 18.18285285 -1.259662024 0.133258815 IRS(ph)EDEEDLGNARPSAPSTLFDFLESK ddPTM_BT-474_Pertuzumab_2h_R1 1 IRSEDEEDLGNARPSAPSTLFDFLESK 27 2 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 IRS(0.951)EDEEDLGNARPS(0.035)APS(0.007)T(0.007)LFDFLESK 120.08 8.77E-05 40385000 47853 45372 38702 44856 59505 51060 41121 50080 47375 43850 TRUE FALSE 45982.85186 44078.03498 45696.31232 47171.02354 61419.03237 52092.46818 41624.2511 49045.8305 41997.18861 40880.00044 1.124825131 1.078229807 1.117815847 1.153889996 1.502422498 1.274277584 1.01820574 1.199751222 1.027328477 1 15.31910759 1.259714443 1.274038 0.996511189 1.195283824 0.217503382 0.126305586 0.698902176 2.225075796 0.125984278 0.040119532 18.18504762 -1.259714443 0.198772635 SLGYHGSSYSPEGVEPVS(ph)PVSS(ph)PSLTHDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 SLGYHGSSYSPEGVEPVS(1)PVS(0.236)S(0.761)PS(0.002)LTHDK 231.93 7.28E-36 93833000 36693 65418 53482 60336 47245 60423 56946 59629 45645 57704 TRUE FALSE 35258.99699 63552.34269 63147.3871 63449.94819 48764.67833 61644.79446 57642.92218 58397.64031 40463.57096 53795.65668 0.655424604 1.181365683 1.17383802 1.179462286 0.906479841 1.145906533 1.071516285 1.085545635 0.752171708 1 15.71520208 1.25972123 24.95685125 0.876085789 1.063164466 0.148788451 0.163912663 330.7910261 390137.2749 0.103500328 0.03771047 18.18533181 -1.25972123 0.187078677 TPLHEIALSIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPLHEIALSIK 11 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 154.15 3.21E-05 471820000 1708200 1867600 1421300 1445600 1588000 1230000 1845900 1666100 2017600 1993700 FALSE TRUE 1641441.655 1814337.877 1678160.527 1520207.589 1639079.462 1254871.443 1868490.676 1631694.453 1788570.506 1858664.923 0.883129409 0.976151136 0.902884918 0.817902985 0.881858501 0.675146675 1.005286458 0.877885213 0.962287761 1 20.82583528 1.259850858 1.280085211 0.997030634 0.870916793 0.203575753 0.084259172 0.678395904 2.177226413 0.077876332 0.024767494 18.19076058 -1.259850858 -0.126113841 TVSAAAAEKEPVPVPVQEIEIDSTTELDGHQEVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSAAAAEKEPVPVPVQEIEIDSTTELDGHQEVEK 35 1 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 0 159.91 1.03E-14 64237000 49091 45119 40917 34190 46103 39125 43312 46469 55081 54230 FALSE TRUE 47172.46945 43832.2503 48311.61209 35954.55 47585.94486 39916.13431 43842.06521 45509.39891 48828.4358 50556.9538 0.933056007 0.866987566 0.955587876 0.711169232 0.941234416 0.789528073 0.867181701 0.900161016 0.96581048 1 15.62562192 1.260038929 2.033930159 0.998540248 0.864129198 0.310501166 0.069354742 0.350348382 2.489689906 0.05964155 0.017448444 18.19863977 -1.260038929 -0.134411051 DQVANSAFVER ddPTM_BT-474_Pertuzumab_2h_R1 8 DQVANSAFVER 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 265.23 1.45E-20 17970570000 2535567 2559329 2229307 2457198 2511309 2653629 2617291 2639507 2548146 2664470 FALSE TRUE 2436474.238 2486339.443 2632192.366 2584014.283 2592087.535 2707287.197 2649322.19 2585000.258 2258891.149 2484003.074 0.980866032 1.000940566 1.059657451 1.040262112 1.043512209 1.089888827 1.066553507 1.040659042 0.909375344 1 21.24423553 1.260107703 24.20204787 0.954687734 1.042565634 0.477930925 0.035725024 116.4840444 130837.8002 0.024297828 0.008851685 18.20152193 -1.260107703 0.0878779 WLVFDEADR ddPTM_BT-474_Pertuzumab_2h_R1 3 WLVFDEADR 9 0 F8WAJ0;Q9H8H2-4;Q9H8H2-2;Q9H8H2 F8WAJ0 DDX31 Probable ATP-dependent RNA helicase DDX31 0 ;; 123.16 0.001316 116665000 199814 211860 187633 207026 204082 192783 195891 214721 178145 211477 FALSE TRUE 192005.048 205817.9602 221542.457 217710.6367 210646.4829 196681.2043 198288.3727 210286.9363 157922.7264 197153.4744 0.9738862 1.043947923 1.123705568 1.104269845 1.068439111 0.997604556 1.00575642 1.066615422 0.801014169 1 17.58895961 1.260261391 24.99953022 0.900507036 1.049975024 0.469412546 0.062708405 166.5622612 191882.4389 0.041057067 0.014965118 18.2079642 -1.260261391 0.149467988 DPGT(ph)PNDDSDIKECNSADHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DPGTPNDDSDIKECNSADHIK 21 1 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 DPGT(0.995)PNDDS(0.005)DIKECNSADHIK 100.08 0.0010874 565320000 133070 99202 97850 87060 100460 97204 104290 104130 165520 121490 TRUE FALSE 127869.4773 96372.85609 115533.6717 91553.17703 103691.3871 99169.53148 105566.3322 101979.6791 146730.8635 113261.3741 1.12897692 0.850888989 1.020062423 0.80833539 0.91550529 0.875581214 0.932059434 0.900392388 1.295506652 1 16.78929641 1.260460113 24.99215178 1.147753383 0.922326744 0.39485962 0.10808497 174.2462744 198854.2691 0.065066462 0.023716849 18.21629761 -1.260460113 -0.225426639 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 176.25 9.91E-16 954720000 88451 84860 68339 76508 88769 85651 80657 97814 99719 107050 FALSE TRUE 84994.23713 82439.87589 80689.37749 80456.58705 91624.3355 87382.9219 81644.10449 95794.10672 88399.31718 99799.40815 0.851650713 0.826055759 0.808515591 0.806183008 0.918084959 0.875585572 0.818082051 0.959866481 0.885769954 1 16.60674364 1.26066038 0.347359182 1.011701378 0.814747902 0.603622994 0.039886221 0.890243824 0.347496041 0.067298819 0.046858059 18.22469968 -1.26066038 -0.196953475 DLVWLEEIQEEAER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLVWLEEIQEEAER 14 0 Q9NQS7-2;Q9NQS7;E9PM67 Q9NQS7-2 INCENP Inner centromere protein 0 ; 173.11 6.40E-06 85395000 38643 38525 35425 39818 40582 37396 41636 41536 33152 40500 FALSE TRUE 37132.78884 37426.30472 41827.08552 41873.01175 41887.35689 38152.17274 42145.55382 40678.26709 29388.72394 37756.89893 0.983470303 0.991244138 1.107799812 1.109016178 1.109396112 1.010468916 1.116234517 1.077373096 0.778366995 1 15.20445266 1.260809848 24.93656459 0.889183489 1.066667095 0.500502599 0.069434752 147.571848 165396.7865 0.044692191 0.016293121 18.230973 -1.260809848 0.177483606 EEWYAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEWYAR 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 185.69 0.0048994 4485200000 2863470 3114810 2741250 3267210 3149610 2785700 3206350 3201250 3182280 3274450 FALSE TRUE 2751562.427 3025978.669 3236654.854 3435831.1 3250920.066 2842028.763 3245590.27 3135143.069 2821040.916 3052668.585 0.901362971 0.991256858 1.060270633 1.125517233 1.064943663 0.930998136 1.063197717 1.027017176 0.92412289 1 21.54163954 1.261478219 24.60570492 0.962061457 1.025062581 0.1110564 0.065230794 356.4747512 382734.3597 0.044905047 0.016371502 18.25905172 -1.261478219 0.063001124 RKDS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RKDSPSR 7 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKDS(0.999)PS(0.001)R 56.563 0.095178 382110000 128630 111100 97160 113350 114760 100230 116230 118470 105470 118740 TRUE FALSE 123602.9974 107931.5368 114718.9733 119200.0071 118451.3596 102256.7193 117652.4575 116023.5531 93497.48777 110697.634 1.116582106 0.975012137 1.036327238 1.076807179 1.070044185 0.923748011 1.06282721 1.048112312 0.844620471 1 16.75626486 1.261567948 24.99069874 0.922310197 1.03677281 0.359532007 0.062086451 202.4306233 219882.1975 0.038947836 0.014201815 18.26282459 -1.261567948 0.114462613 TQMAEVLPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 TQMAEVLPSPR 11 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR 159.41 3.01E-05 5632450000 1620300 1612330 1371690 1782070 1619120 1752400 1733590 1732300 1531090 1722790 TRUE FALSE 1556976.885 1566347.927 1619584.896 1874042.846 1671200.465 1787834.729 1754806.193 1696527.4 1357287.082 1606103.899 0.969412306 0.975246949 1.008393602 1.166825414 1.040530732 1.113150108 1.092585725 1.056299907 0.845080498 1 20.61513379 1.261640187 24.84259634 0.922540297 1.056087834 0.373403488 0.067391207 190.6378463 205201.3067 0.045836154 0.016713568 18.26586261 -1.261640187 0.133547536 TATIMEELADALMYCHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TATIMEELADALMYCHGK 18 0 J3QR41;J3KTD6;J3QLN8;J3KT86;Q96GD4-4;Q96GD4-2;Q96GD4;Q96GD4-5 J3QR41 AURKB Aurora kinase B 0 ; 125.89 6.11E-05 0 260100 244690 199405 223690 232370 268820 228220 251260 236530 255350 FALSE TRUE 249935.0044 237711.6808 235441.9192 235234.6677 239844.3921 274255.7246 231013.0246 246071.3932 209680.106 238054.9171 1.049904818 0.998558163 0.98902355 0.988152946 1.007517068 1.152069144 0.970419042 1.033674903 0.880805608 1 17.8609349 1.262016708 24.98948392 0.940402748 1.022169412 0.265827217 0.055303963 258.2082631 275089.1173 0.03581343 0.013063283 18.28170546 -1.262016708 0.081766664 LQQELEFLEVQEEYIKDEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQQELEFLEVQEEYIKDEQK 20 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 180.63 4.92E-17 152530000 63888 44532 48902 41409 47291 55012 52368 54596 79078 74584 FALSE TRUE 61391.18633 43261.99096 57739.67922 43546.12345 48812.15796 56124.38033 53008.89525 53468.57352 70101.39696 69532.35925 0.882915336 0.622185 0.830400116 0.626271335 0.702006353 0.807169222 0.762362961 0.768973958 1.008183783 1 16.08539692 1.262308415 4.46124569 1.010845759 0.744258975 0.625020551 0.078649399 0.111415201 4.716083862 0.05958281 0.0183665 18.29398907 -1.262308415 -0.266586784 FLKNEVER ddPTM_BT-474_Pertuzumab_2h_R1 1 FLKNEVER 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 83.456 0.016551 491610000 453720 505170 335440 373560 423850 455020 420820 434720 417160 392870 FALSE TRUE 435988.1208 490763.0462 396061.4698 392839.4764 437483.5202 464220.8162 425970.121 425742.8801 369805.7457 366260.565 1.190376913 1.33992871 1.081365311 1.072568313 1.194459797 1.267460547 1.163024802 1.162404367 1.009679395 1 18.48251085 1.26259434 3.185327503 0.994410453 1.186478469 0.485122191 0.074106453 0.216242226 3.761357215 0.068246499 0.019921183 18.30603719 -1.26259434 0.192068016 DEPQEPSNKVPEQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DEPQEPSNKVPEQQR 15 1 P12270 P12270 TPR Nucleoprotein TPR 0 149 3.13E-06 164330000 152280 159550 126960 133000 151420 155800 130830 146110 194280 158690 FALSE TRUE 146328.7292 154999.7902 149904.4962 139864.1459 156290.5618 158950.3827 132431.1367 143092.7774 172226.1489 147941.785 0.989096686 1.04770799 1.013266781 0.945399881 1.056432852 1.074411687 0.895157083 0.967223543 1.164148107 1 17.17467006 1.263530732 24.97821582 1.082074288 0.996777483 0.218374709 0.063105283 283.6255607 283718.6262 0.042135605 0.015372857 18.34554983 -1.263530732 -0.085296805 ALDELFEAIEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDELFEAIEQK 12 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 140.3 0.00013856 3510500 13868 15909 11508 9606.6 13191 11959 12110 14954 18705 19444 FALSE TRUE 13326.02323 15455.2909 13587.75159 10102.39778 13615.30049 12200.81917 12258.2058 14645.19467 16581.68682 18127.04056 0.735146103 0.852609716 0.749584663 0.557310927 0.751104431 0.673072868 0.67623867 0.807919783 0.914748702 1 14.14585579 1.264082874 1.969839787 0.993203585 0.71456533 0.651594864 0.071685271 0.200248951 1.343209287 0.069213718 0.020336908 18.36888834 -1.264082874 -0.278638255 EKPYFPIPEEYTFIQNVPLEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKPYFPIPEEYTFIQNVPLEDR 22 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 224.95 5.91E-26 22032300000 4605930 4652760 4077010 3978240 4612680 4755620 4487490 4807890 4443850 4911260 FALSE TRUE 4425925.163 4520067.84 4813816.4 4183557.443 4761051.041 4851781.895 4542409.245 4708605.391 3939402.778 4578615.986 0.966651315 0.987212698 1.051369325 0.913716603 1.039845022 1.05966124 0.992092208 1.028390546 0.86039161 1 22.12648014 1.264125583 24.99855547 0.93019562 1.006229567 0.248423676 0.051909067 246.1501397 240697.1633 0.032616861 0.011901042 18.37069484 -1.264125583 0.076033947 KEVLAS(ph)PDRLWGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 KEVLASPDRLWGSR 14 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KEVLAS(1)PDRLWGSR;KEVLAS(0.964)PDRLWGS(0.036)R;KEVLAS(0.876)PDRLWGS(0.124)R 192.22 3.14E-07 4124870000 879420 1040392 759728 921807 885002 1009835 925020 968601 911120 982855 TRUE FALSE 845051.2941 1010721.039 897027.7497 969381.5697 913468.8931 1030254.556 936340.6715 948599.0509 807693.4773 916285.3554 0.922257776 1.103063618 0.97898296 1.057947248 0.996926217 1.124381776 1.021887631 1.035265974 0.881486834 1 19.80543744 1.264140632 24.587088 0.94074344 1.033411652 0.252564052 0.061267235 189.2524303 181906.9453 0.036831692 0.013439111 18.37133144 -1.264140632 0.092668212 SLVASLAEPDFVVTDFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLVASLAEPDFVVTDFAK 18 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 218.31 1.85E-18 26246000 72238 83565 69784 67793 69859 75621 74446 87296 87444 94825 FALSE TRUE 69414.8591 81181.80802 82395.52114 71291.80485 72106.07818 77150.10843 75357.09242 85493.30709 77517.72372 88402.41829 0.785214482 0.918321123 0.932050534 0.806446319 0.815657304 0.872714909 0.852432477 0.967092403 0.876873339 1 16.43179822 1.264231243 0.791239276 0.989651661 0.855249619 0.396732845 0.052361663 0.606372389 0.851814249 0.050208707 0.019604514 18.37516481 -1.264231243 -0.134402042 MDTIDQDDELIR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDTIDQDDELIR 12 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 143.79 0.00014541 243560000 383180 423230 403020 469460 474750 491070 422080 465440 384950 460690 FALSE TRUE 368204.902 411159.8948 475854.6791 493688.8869 490020.7649 500999.7719 427245.5413 455828.5013 341252.0898 429487.056 0.857313153 0.957327792 1.107960467 1.149484903 1.140944199 1.166507267 0.994780949 1.061332338 0.794557333 1 18.71225513 1.264362934 24.54805275 0.897278732 1.059792177 0.272033043 0.102551268 204.1695439 194245.4671 0.071164902 0.025966088 18.38073754 -1.264362934 0.162513445 GYYS(ph)PGIVSTR ddPTM_BT-474_Pertuzumab_2h_R1 3 GYYSPGIVSTR 11 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 GYYS(1)PGIVSTR;GYYS(1)PGIVSTR;GYYS(1)PGIVSTR 142.51 3.95E-05 368600000 813710 809170 737470 736900 776960 777510 771810 863780 773010 888900 TRUE FALSE 781909.3136 786093.2639 870747.2339 774931.4973 801951.624 793231.7849 781255.6417 845942.6411 685261.1455 828694.0113 0.943544062 0.94859291 1.050746382 0.935123805 0.967729479 0.957207092 0.942755264 1.020814233 0.826916976 1 19.66047997 1.26516504 24.99991273 0.913457979 0.97200916 0.160982837 0.052318928 310.4515007 291728.996 0.032268683 0.011775696 18.41471661 -1.26516504 0.058551181 VTQHES(ph)DNENEIQIQNK ddPTM_BT-474_Pertuzumab_2h_R1 4 VTQHESDNENEIQIQNK 17 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 VT(0.001)QHES(0.999)DNENEIQIQNK;VT(0.025)QHES(0.975)DNENEIQIQNK;VT(0.028)QHES(0.972)DNENEIQIQNK;VT(0.085)QHES(0.915)DNENEIQIQNK 340.33 1.15E-72 4457700000 3384320 3405370 3086940 3302680 3163830 3417040 3435900 3524330 4232250 4002970 TRUE FALSE 3252057.033 3308252.182 3644818.727 3473131.711 3265597.465 3486134.89 3477949.572 3451551.354 3751822.723 3731845.276 0.871434047 0.886492321 0.976680022 0.930674091 0.875062395 0.934158474 0.931965104 0.924891333 1.005353236 1 21.83145774 1.266049705 4.436492427 1.004684894 0.917388458 0.566732322 0.030171893 0.145419906 5.969217593 0.025200825 0.007813969 18.45226595 -1.266049705 -0.087296436 ERPISLGIFPLPAGDGLLT(ph)PDAQK ddPTM_BT-474_Pertuzumab_2h_R1 5 ERPISLGIFPLPAGDGLLTPDAQK 24 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK 224.78 1.06E-32 4485842000 3289623 3197709 2949838 3113230 3076639 3502176 3311081 3780749 4414643 4598469 TRUE FALSE 3161060.896 3106513.47 3482939.345 3273904.173 3175601.888 3572992.398 3351603 3702675.212 3913511.234 4287010.599 0.737357845 0.724633961 0.812440106 0.763679981 0.740749717 0.833446131 0.781804225 0.863696305 0.912876501 1 22.03154055 1.266480357 0.661808301 1.004096144 0.754540083 0.878963774 0.029091669 0.208779479 0.217122393 0.027717973 0.012205671 18.47057251 -1.266480357 -0.249556061 VLELEGEKGEWGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLELEGEKGEWGFK 14 1 P61201;P61201-2;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 155.98 5.20E-06 304360000 604850 594250 498390 529020 608450 627360 587600 661610 794990 801720 FALSE TRUE 581211.7933 577302.5718 588460.1596 556322.7856 628021.3468 640045.649 594791.2246 647947.5223 704746.0681 747418.7903 0.777625343 0.772395047 0.787323208 0.744325394 0.840253624 0.856341394 0.79579378 0.866913611 0.942906543 1 19.51155731 1.267707537 0.529161958 1.009036769 0.773071202 0.856372986 0.029232944 0.30124238 0.218405178 0.031967302 0.01680983 18.52283835 -1.267707537 -0.235965567 VAHPIRPKPPSATSIPAILK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAHPIRPKPPSATSIPAILK 20 2 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 69.737 0.0117 1632460000 2741900 2568600 2496000 2557900 2655600 2695800 2699500 3034400 3458100 3544600 FALSE TRUE 2634743.517 2495346.043 2947082.723 2689913.526 2741019.786 2750310.923 2732537.289 2971738.58 3065550.986 3304521.085 0.797314785 0.755130919 0.891833536 0.814010096 0.829475653 0.832287297 0.826908716 0.899294785 0.927683893 1 21.65600977 1.267766334 0.923699389 0.999937136 0.816038169 0.775003794 0.032348104 0.233340578 0.426948564 0.030105455 0.010824933 18.52534624 -1.267766334 -0.183898967 KLSDDNTIGKEEIQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSDDNTIGKEEIQQR 16 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 66.965 0.029867 116100000 101650 85217 76757 67752 71332 85639 76160 101340 102740 115830 FALSE TRUE 97677.40562 82786.6946 90628.69735 71248.68884 73626.45856 87370.67926 77092.06886 99247.29359 91077.38592 107984.7309 0.904548308 0.766651858 0.839273262 0.659803365 0.681822864 0.809102162 0.713916386 0.919086363 0.843428373 1 16.7204678 1.267893024 1.120757104 0.983167502 0.764910299 0.436982934 0.07829238 0.404127578 1.031276062 0.072450558 0.024059326 18.53075117 -1.267893024 -0.218257203 KEEEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEEEMR 6 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141;A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 D6RGI3;B1AMS2;A0A087X142 SEPT11;SEPT6;SEPT8 Septin-11;Septin-6;Septin-8 0 91.906 0.075939 774060000 1265600 1389200 1155800 1252000 1258900 1337400 1254200 1382400 1323500 1430100 FALSE TRUE 1216138.953 1349581.376 1364678.771 1316615.87 1299393.662 1364443.144 1269549.275 1353852.957 1173261.829 1333238.053 0.912169398 1.012258368 1.023582223 0.987532472 0.974614892 1.023405491 0.952230003 1.015462283 0.880009257 1 20.34650297 1.268023655 24.9999977 0.940004255 0.989896787 0.164045939 0.042789651 276.7023342 234787.941 0.026087304 0.009523726 18.53632583 -1.268023655 0.049892533 LAIQGPEDS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 6 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 LAIQGPEDS(0.998)PS(0.002)R;LAIQGPEDS(0.993)PS(0.007)R;LAIQGPEDS(0.703)PS(0.297)R;LAIQGPEDS(0.903)PS(0.097)R;LAIQGPEDS(0.697)PS(0.303)R;LAIQGPEDS(1)PSR 289.99 4.49E-36 16246100000 2678130 2810460 2155620 2808900 2486700 2549840 2710580 2764980 2595820 2835290 TRUE FALSE 2573465.719 2730308.433 2545188.486 2953867.666 2566686.964 2601399.512 2743752.889 2707882.197 2301153.396 2643253.283 0.973597852 1.03293485 0.962899962 1.117512152 0.971033302 0.984165811 1.038021179 1.024450519 0.870576199 1 21.33388324 1.268206892 24.99999256 0.935287982 1.014878163 0.262460836 0.052090016 212.5858507 179268.7628 0.032103374 0.011719038 18.54414831 -1.268206892 0.079590181 AAPQS(ph)PSVPK ddPTM_BT-474_Pertuzumab_2h_R1 6 AAPQSPSVPK 10 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 1 AAPQS(0.998)PS(0.002)VPK;AAPQS(0.994)PS(0.006)VPK;AAPQS(0.999)PS(0.001)VPK;AAPQS(0.981)PS(0.019)VPK;AAPQS(0.932)PS(0.068)VPK;AAPQS(0.992)PS(0.008)VPK 233 4.93E-12 12286450000 8301220 7802080 7026620 7686510 7705730 7651130 7871650 8141170 8650630 8500400 TRUE FALSE 7976799.145 7579572.317 8296486.54 8083211.702 7953591.804 7805841.091 7967985.607 7973051.995 7668646.749 7924660.337 1.006579311 0.956453904 1.046920144 1.020007339 1.003650815 0.985006393 1.005467145 1.006106465 0.967694062 1 22.91791767 1.268246269 24.98820377 0.983847001 1.003749179 0.107867143 0.022922827 401.006185 337551.5641 0.015138651 0.005526216 18.54582976 -1.268246269 0.019902178 FYNELTEILVR ddPTM_BT-474_Pertuzumab_2h_R1 2 FYNELTEILVR 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 147.74 8.18E-05 249200000 201405 233430 180917 203664 230367 194772 234336 224260 191849 226289 FALSE TRUE 193533.8699 226772.805 213612.7264 214175.1234 237776.9638 198710.4233 237203.8741 219628.9526 170071.1058 210962.2445 0.917386286 1.074944977 1.012563774 1.01522964 1.127106722 0.941924105 1.124390171 1.041081797 0.806168451 1 17.6866253 1.268262836 24.97718282 0.903084216 1.036995659 0.303342248 0.077727522 183.2333444 154084.7877 0.047117963 0.01719969 18.54653726 -1.268262836 0.133911444 (ac)MELDLS(ph)PPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_BT-474_Pertuzumab_2h_R1 7 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 MELDLS(0.441)PPHLS(0.172)S(0.186)S(0.201)PEDLCPAPGT(0.978)PPGT(0.022)PRPPDT(0.001)PLPEEVKR;MELDLS(0.992)PPHLS(0.004)S(0.002)S(0.002)PEDLCPAPGT(0.836)PPGT(0.161)PRPPDT(0.003)PLPEEVKR;MELDLS(0.737)PPHLS(0.08)S(0.088)S(0.095)PEDLCPAPGT(0.949)PPGT(0.05)PRPPDT(0.001)PLPEEVKR;MELDLS(0.619)PPHLS(0.174)S(0.178)S(0.182)PEDLCPAPGT(0.679)PPGT(0.162)PRPPDT(0.005)PLPEEVKR;MELDLS(0.716)PPHLS(0.092)S(0.098)S(0.105)PEDLCPAPGT(0.871)PPGT(0.115)PRPPDT(0.002)PLPEEVKR;MELDLS(0.812)PPHLS(0.059)S(0.063)S(0.067)PEDLCPAPGT(0.806)PPGT(0.191)PRPPDT(0.004)PLPEEVKR;MELDLS(0.453)PPHLS(0.164)S(0.182)S(0.201)PEDLCPAPGT(0.986)PPGT(0.014)PRPPDTPLPEEVKR 106.06 6.10E-28 2173607000 269929.5 406735 278274 401868 355226 400268 336630 374288 333184 380387 TRUE FALSE 259380.3567 395135.316 328564.302 422608.4556 366652.1669 408361.6932 340749.7786 366558.822 295362.3491 354623.0497 0.731425543 1.114240364 0.92651705 1.191711751 1.033920855 1.151537368 0.960878823 1.033657633 0.832891008 1 18.43592679 1.268323721 24.94693398 0.916445427 1.026293793 0.087615161 0.128856732 373.5885305 313136.0711 0.079941959 0.029181914 18.5491375 -1.268323721 0.109848367 DSQEDWTTFTHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSQEDWTTFTHDR 13 0 O15357;A0A0A0MTP6;O15357-2;F5GY16 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 0 ; 135.89 7.87E-05 683510000 1287370 1258160 1066020 1176180 1205050 1290870 1233590 1390000 1551430 1584470 FALSE TRUE 1237058.157 1222278.509 1258673.527 1236882.791 1243811.528 1316972.276 1248687.043 1361296.014 1375318.171 1477152.436 0.837461407 0.827455907 0.852094542 0.837342688 0.842033292 0.891561523 0.84533391 0.921567728 0.931060422 1 20.49438728 1.268422842 0.606750944 1.002292766 0.835815945 0.90727369 0.016302191 0.183382322 0.165353203 0.015169002 0.007142406 18.55337155 -1.268422842 -0.166476821 TNSS(ph)DSERS(ph)PDLGHSTQIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TNSSDSERSPDLGHSTQIPR 20 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 2 T(0.254)NS(0.328)S(0.375)DS(0.056)ERS(0.978)PDLGHS(0.005)T(0.005)QIPR 52.773 0.068492 549560000 287460 261210 240240 208030 277270 243150 269660 262470 324500 279770 TRUE FALSE 276225.7454 253760.5466 283656.7121 218766.4532 286188.6414 248066.6596 272960.1797 257049.9028 287664.1204 260820.9287 1.059062809 0.972930155 1.087553493 0.838761116 1.097261032 0.951099518 1.046542473 0.985541705 1.10291809 1 17.99270011 1.268591381 24.99961821 1.051459324 1.003499637 0.057042623 0.075653032 492.0344041 409602.4022 0.045326443 0.016546937 18.56057305 -1.268591381 -0.047959687 LKPGGVGAPSSSS(ph)PSPS(ph)PSARPGPPPSEEAMDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKPGGVGAPSSSSPSPSPSARPGPPPSEEAMDFR 34 2 Q92797 Q92797 SYMPK Symplekin 2 LKPGGVGAPS(0.029)S(0.118)S(0.131)S(0.55)PS(0.19)PS(0.926)PS(0.055)ARPGPPPSEEAMDFR 90.372 0.00023921 362840000 119960 127230 108810 125240 100810 137620 122600 129110 123120 133050 TRUE FALSE 115271.8306 123601.525 128474.3875 131703.6514 104052.6452 140402.7707 124100.4155 126443.8334 109143.9338 124038.405 0.929323709 0.996477865 1.035762976 1.061797364 0.838874421 1.13192983 1.00049993 1.01939261 0.879920487 1 16.92042735 1.26859619 24.99369538 0.939960014 1.004276805 0.090245393 0.07815647 396.77697 330173.0238 0.04905618 0.017908146 18.56077857 -1.26859619 0.064316791 RVVLGDGVQLPPGDYSTTPGGTLFSTT(ph)PGGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 RVVLGDGVQLPPGDYSTTPGGTLFS(0.034)T(0.187)T(0.754)PGGT(0.025)R;RVVLGDGVQLPPGDYSTT(0.001)PGGT(0.045)LFS(0.178)T(0.178)T(0.461)PGGT(0.138)R 147.49 2.33E-10 586150000 190663 206531 149791 209820 197952 200979 179141 199706 189943 179169 TRUE FALSE 183211.6792 200640.9381 176861.5658 220648.8353 204319.3059 205042.9331 181333.3811 195582.0013 168381.4669 167033.724 1.096854424 1.201200172 1.05883747 1.320983751 1.223221879 1.227554102 1.085609401 1.170913254 1.008068687 1 17.34977989 1.268923571 1.59874449 0.989149794 1.182961429 0.432769501 0.07548636 0.328200792 1.534090653 0.068481559 0.020745857 18.57477541 -1.268923571 0.193811635 VSPGLPS(ph)PNLENGAPAVGPVQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 VSPGLPS(1)PNLENGAPAVGPVQPR;VSPGLPS(1)PNLENGAPAVGPVQPR 315.82 2.58E-73 1159390000 129327 155519 113398 144666 145367 147792 113528 139938 126889 107646 TRUE FALSE 124272.7579 151083.7504 133891.5411 152132.2296 150042.8616 150780.4555 114917.3896 137048.2314 112485.0927 100355.0405 1.238331002 1.505492396 1.334178537 1.515940094 1.495120332 1.502470177 1.145108298 1.365633761 1.120871379 1 16.61475356 1.269023942 0.876038204 1.001882848 1.428686736 0.586694007 0.114697825 0.359430417 0.600249396 0.103043831 0.038052153 18.57906875 -1.269023942 0.426803888 GLCESVVEADLVEALEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLCESVVEADLVEALEK 17 0 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;B7WPG3;Q8WVV9-5;Q8WVV9-3;Q8WVV9-2;H7BXH8;C9JJZ7 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 0 ; 118.61 0.00037342 24171000 29476 27737 22767.4 26658 29033 32420 25700 33696 34397 37560 FALSE TRUE 28324.04533 26945.96792 26881.97564 28033.82257 29966.87281 33075.55461 26014.52429 33000.16582 30492.39676 35016.02775 0.808888019 0.769532401 0.767704887 0.800599736 0.855804463 0.944583288 0.742931908 0.942430308 0.87081256 1 15.09572781 1.269715202 0.141544561 1.109598985 0.673677582 0.538620339 0.056543911 4.219820579 0.555362365 0.802544497 0.680749564 18.60866431 -1.269715202 -0.435921403 DIPVVIDADGLWLVAQQPALIHGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIPVVIDADGLWLVAQQPALIHGYR 25 0 Q8IW45-2;Q8IW45;Q8IW45-4 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 153.65 9.78E-08 79547000 104820 122400 99821 110380 113370 113570 107760 107200 114550 97020 FALSE TRUE 100723.5185 118909.2718 117860.8752 116076.725 117016.649 115866.4632 109078.7991 104986.2825 101546.7642 90448.74898 1.113597696 1.31465911 1.303068053 1.283342515 1.293734301 1.281017864 1.205973552 1.160726751 1.122699489 1 16.46481293 1.270221267 0.929570265 1.006157656 1.272017612 0.695410401 0.055317328 0.266667518 0.49297396 0.050040345 0.01794807 18.63036088 -1.270221267 0.265859956 YWDAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YWDAEK 6 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 104.11 0.079355 200430000 555580 543610 511640 549600 504200 244100 697250 615220 750990 858330 FALSE TRUE 533867.3194 528106.775 604104.7294 577964.9219 520418.0509 249035.8692 705783.1541 602515.492 665740.7636 800194.5446 0.667171906 0.659972976 0.754947323 0.722280508 0.650364408 0.311219154 0.882014454 0.752961259 0.831973635 1 19.60999127 1.270543083 1.119150354 0.981104912 0.652027883 0.39985107 0.133673552 0.464574763 1.18186324 0.125528593 0.04172888 18.64417125 -1.270543083 -0.329077029 MGSGVER ddPTM_BT-474_Pertuzumab_2h_R1 2 MGSGVER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 113.1 0.014436 833850000 692940 817450 605410 787350 724600 713930 728160 775980 756960 803640 FALSE TRUE 665859.1387 794137.1264 714821.0543 827985.2279 747907.4171 728366.1538 737071.4399 759955.7418 671033.0742 749208.747 0.88874982 1.059967772 0.95410132 1.105146238 0.998263061 0.972180526 0.983799833 1.01434446 0.895655686 1 19.51500822 1.270658606 24.99995802 0.947827573 1.000516711 0.095482049 0.05987533 347.4658757 270628.842 0.036896383 0.013472994 18.64913129 -1.270658606 0.052689138 KEELVAEQALK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEELVAEQALK 11 1 E7ETZ4;Q9Y6E2;B5MCH7;B5MCE7 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 119.01 0.001483 0 288660 256420 269110 222910 277540 260610 290730 292220 358520 356500 FALSE TRUE 277378.8481 249107.1527 317744.1633 234414.4118 286467.3262 265879.7128 294288.0407 286185.5549 317822.3126 332353.9375 0.834588722 0.749523699 0.956041519 0.705315585 0.861934504 0.799989658 0.885465787 0.861086699 0.956276658 1 18.34236092 1.27076222 0.997868089 1.002787987 0.818070598 0.469789038 0.064767163 0.397902642 0.830953221 0.055001324 0.019112635 18.65358111 -1.27076222 -0.184717389 AAVPSGAS(ph)TGIYEALELR ddPTM_BT-474_Pertuzumab_2h_R1 3 AAVPSGASTGIYEALELR 18 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798;P13929-3;P13929-2;P13929;E5RGZ4;P09104-2;F5H0C8;P09104;E5RI09;E5RG95;K7EPM1;K7EKN2;F5H1C3 P06733 ENO1;ENO3;ENO2 Alpha-enolase;Enolase;Beta-enolase;Gamma-enolase 1 AAVPS(0.042)GAS(0.915)T(0.042)GIY(0.001)EALELR;AAVPSGAS(0.983)T(0.017)GIYEALELR;AAVPSGAS(0.99)T(0.01)GIYEALELR 287.54 5.21E-40 120825200 37294.4 37010.5 26094.6 23941 35080.5 34879.8 25053.2 31987.3 24145.4 21034.2 TRUE FALSE 35836.89362 35954.99678 30810.47469 25176.59788 36208.89614 35585.09345 25359.80856 31326.75108 21404.51542 19609.5349 1.827523896 1.833546638 1.571198646 1.283895718 1.846494388 1.814683196 1.293238656 1.597526471 1.091536109 1 14.2592677 1.27120888 1.082923104 0.978606253 1.671015286 0.579358366 0.20052585 0.341210844 0.820180712 0.188965214 0.063574942 18.67277569 -1.27120888 0.692409033 S(ph)RTS(ph)PVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.965)RT(0.035)S(1)PVSR;S(0.797)RT(0.206)S(0.997)PVSR 109.2 0.0020851 310200000 20028.2 30295 21977.1 22689 17367 32497 25119 25221 21568.4 21916 TRUE FALSE 19245.4758 29431.01626 25948.85085 23859.98201 17925.62533 33154.11161 25426.41384 24700.17754 19120.04565 20431.6098 0.941946131 1.440464875 1.270034574 1.167797459 0.877347674 1.622687196 1.244464537 1.208919795 0.935807107 1 14.31851526 1.271272025 6.520322002 0.967198519 1.231556688 0.19820408 0.203509077 0.241781653 30.64946068 0.141950168 0.048626988 18.67549086 -1.271272025 0.264358169 DLLHPS(ph)PEEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 1 DLLHPS(1)PEEEK;DLLHPS(1)PEEEK 165.64 1.38E-05 475140000 1440790 1103050 1470250 1141890 1285760 1256360 1477350 1453410 2144250 2053480 TRUE FALSE 1384482.334 1071592.094 1735956.881 1200823.08 1327117.638 1281764.46 1495430.251 1423396.576 1900843.729 1914395.971 0.723195387 0.559754675 0.906790919 0.627259511 0.69323048 0.669539886 0.781149916 0.743522551 0.992920879 1 20.86845783 1.271881769 2.757209237 1.014309154 0.707087325 0.626282732 0.087503657 0.15904446 2.010421871 0.073832777 0.02150478 18.70172942 -1.271881769 -0.307221829 EELSHS(ph)PEPCTK ddPTM_BT-474_Pertuzumab_2h_R1 2 EELSHSPEPCTK 12 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 EELSHS(1)PEPCTK;EELSHS(1)PEPCTK 171.76 2.42E-05 2248770000 3276100 3181700 2769700 2921600 3081300 3199600 3029700 3212700 3852500 3414100 TRUE FALSE 3148066.39 3090961.031 3270246.402 3072384.126 3180412.813 3264298.104 3066778.375 3146356.622 3415180.351 3182859.966 0.989068455 0.971126931 1.027455319 0.965290386 0.999231146 1.025586466 0.963529155 0.988531276 1.07299108 1 21.60189225 1.272283993 24.9951618 1.036495579 0.990819928 0.316487861 0.02660475 170.3381334 126251.6334 0.016475015 0.006015023 18.71905815 -1.272283993 -0.045675652 MSSPEDDSDTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 114.72 0.00034458 0 280750 305540 245560 256670 285150 273130 254230 302920 355920 352860 FALSE TRUE 269777.9796 296826.2984 289938.1545 269916.7695 294322.1087 278652.8757 257341.3428 296664.5961 315517.4537 328960.4779 0.820092375 0.902315987 0.881376864 0.820514279 0.894703554 0.847070984 0.782286506 0.901824432 0.959134835 1 18.32755474 1.272527547 2.664260616 0.992748134 0.853182613 0.674640821 0.03589721 0.153987384 1.81467749 0.03185995 0.009273375 18.72955882 -1.272527547 -0.139565521 EDPDTPMSFFDFVVDPHSFPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDPDTPMSFFDFVVDPHSFPR 21 0 Q9NXX6 Q9NXX6 NSMCE4A Non-structural maintenance of chromosomes element 4 homolog A 0 ; 217.26 5.88E-25 27735000 37479 36081 31537 34930 33697 37540 35822 37185 35167 38303 FALSE TRUE 36014.27924 35052.00521 37236.43744 36732.74149 34780.89461 38299.08452 36260.40035 36417.11676 31174.98959 35708.70369 1.008557453 0.981609568 1.042783232 1.02867754 0.974017285 1.072542001 1.015449921 1.019838666 0.873036161 1 15.12398814 1.272973869 24.97647828 0.936518072 1.018218461 0.412226625 0.038886192 133.8449117 97142.08276 0.023789449 0.008685838 18.74881696 -1.272973869 0.081700389 S(ph)PQNQYPAELMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQNQYPAELMR 12 0 P33993;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 1 S(1)PQNQYPAELMR;S(1)PQNQYPAELMR 151.03 7.20E-05 250360000 122641 124319 93175 108855 108627 122694 117583 140960 136565 157512 TRUE FALSE 117848.0541 120773.5438 110013.7952 114473.0196 112121.0861 125174.9567 119022.0159 138049.1267 121062.7137 146843.5719 0.802541457 0.822463947 0.749190405 0.77955758 0.763540989 0.852437428 0.810536099 0.940110111 0.824433185 1 17.16392059 1.272994783 0.513268689 0.99515426 0.778136541 0.677406078 0.042518004 0.469033335 0.324191134 0.044929989 0.02427735 18.74971983 -1.272994783 -0.217017719 ESYELR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESYELR 6 0 P35268;K7ERI7;K7EMH1 P35268 RPL22 60S ribosomal protein L22 0 ; 103.28 0.080999 656020000 1346370 1407980 1236980 1360020 1423690 1320420 1334500 1424300 1378520 1471770 FALSE TRUE 1293752.372 1367825.789 1460529.802 1430210.795 1469484.282 1347119.797 1350832.01 1394887.707 1222036.189 1372085.707 0.942909299 0.996895297 1.0644596 1.042362578 1.070985781 0.981804409 0.984509935 1.016618496 0.890641293 1 20.38793917 1.273238078 24.91242605 0.945320612 1.014369924 0.26646585 0.0445497 191.9097477 137868.7717 0.029861895 0.010902966 18.76022654 -1.273238078 0.069049312 VASS(ph)PVMVSNPATR ddPTM_BT-474_Pertuzumab_2h_R1 4 VASSPVMVSNPATR 14 0 P51610-2;P51610;A6NEM2;P51610-4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 VAS(0.001)S(0.999)PVMVSNPATR;VAS(0.001)S(0.999)PVMVSNPATR;VAS(0.003)S(0.997)PVMVSNPATR;VAS(0.002)S(0.998)PVMVSNPATR 345.44 9.70E-82 1672430000 1205410 1252740 1120160 1228840 1153600 1228590 1283580 1286740 1144160 1318620 TRUE FALSE 1158301.245 1217013.082 1322597.83 1292260.58 1190706.592 1253432.932 1299288.836 1260168.369 1014279.754 1229308.693 0.942237903 0.989997947 1.075887478 1.051209177 0.968598529 1.019624232 1.05692642 1.025103277 0.825081413 1 20.22941581 1.273653774 24.94208567 0.912540574 1.01928495 0.360701067 0.055077409 146.437981 104079.2281 0.035146586 0.012833619 18.77819196 -1.273653774 0.106744375 S(ph)PEETATQVPSLESLTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPEETATQVPSLESLTLK 18 0 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 S(0.992)PEET(0.008)ATQVPSLESLTLK 156.83 9.15E-09 49654000 86359 67740 65288 72498 69956 73255 77219 94358 105130 119610 TRUE FALSE 82983.99481 65808.12152 77086.99392 76239.63047 72206.19827 74736.26629 78164.02922 92409.47433 93196.08314 111508.7082 0.744192953 0.590161276 0.691309183 0.683710104 0.647538649 0.67022807 0.700967938 0.8287198 0.835774037 1 16.76679685 1.273887201 0.90457781 0.992655478 0.662540607 0.866127389 0.041328559 0.158377519 0.279122846 0.03612208 0.013138329 18.78828766 -1.273887201 -0.330114871 EVLHGNQR ddPTM_BT-474_Pertuzumab_2h_R1 5 EVLHGNQR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;; 146.58 0.00055098 9679700000 5198780 5169750 4075020 4825310 4994360 4388098 5351040 5027570 5261700 4995260 FALSE TRUE 4995605.93 5022313.792 4811466.762 5074344.827 5155008.125 4476828.348 5416527.628 4923748.923 4664413.875 4656926.591 1.072725935 1.078461018 1.033185013 1.089633845 1.106954989 0.961326802 1.163112092 1.057295799 1.001607774 1 22.15094671 1.274426355 5.334140416 0.999850543 1.071996589 0.248544185 0.048701165 0.225239964 15.14353572 0.03462695 0.011423287 18.81162685 -1.274426355 0.072146045 NFMPALEETPFHSCTAGPNPTLGRPLS(ph)PKPSSPGSVLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFMPALEETPFHSCTAGPNPTLGRPLSPKPSSPGSVLAR 39 2 F8VWK5;F8VUY0;F8VVS9;Q15583-4;Q15583-2;Q15583-3;Q15583 F8VWK5 TGIF1 Homeobox protein TGIF1 1 NFMPALEETPFHSCTAGPNPT(0.018)LGRPLS(0.927)PKPS(0.022)S(0.027)PGS(0.005)VLAR;NFMPALEETPFHSCTAGPNPT(0.014)LGRPLS(0.972)PKPS(0.011)S(0.002)PGSVLAR 215.25 1.11E-39 828520000 307090 248494 218658 203904 230319 254718 212697 258175 308360 298470 TRUE FALSE 295088.5833 241407.1944 258174.3646 214427.5099 237727.4198 259868.5725 215300.0495 252843.596 273356.2656 278254.3611 1.060499401 0.867577398 0.927835825 0.770616888 0.854352898 0.933924527 0.773752651 0.908677927 0.982397058 1 18.08604477 1.275098222 4.070311159 0.995500775 0.878818329 0.219825819 0.078868786 0.288542133 9.035482307 0.062657941 0.019329001 18.84075152 -1.275098222 -0.116682447 GREEYEGPNKKPR ddPTM_BT-474_Pertuzumab_2h_R1 5 GREEYEGPNKKPR 13 3 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;; 166.38 1.48E-05 1882300000 1285070 1230860 986449 982717 1008300 1135120 1136020 1158290 1435610 1234710 FALSE TRUE 1234848.044 1195757.078 1164722.278 1033435.142 1040732.885 1158072.904 1149922.953 1134370.907 1272645.571 1151081.992 1.072771577 1.038811385 1.011849969 0.897794553 0.904134451 1.00607334 0.998993087 0.985482281 1.105608098 1 20.13455917 1.27510568 24.81317849 1.052804074 0.986972108 0.167749973 0.056187721 243.6083229 165403.8042 0.039792653 0.014530208 18.84107509 -1.27510568 -0.065831966 LEQEVSRPIDHDLANWTPAQPLAPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEQEVSRPIDHDLANWTPAQPLAPGR 26 1 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 0 80.102 0.011156 132390000 64098 71867 59726 73855 70144 54482 64033 67119 49711 52643 FALSE TRUE 61592.9793 69817.42353 70519.8168 77666.6654 72400.24546 55583.66337 64816.65501 65732.96919 44068.01569 49077.44272 1.25501607 1.422597015 1.436908952 1.582532852 1.475224491 1.13257049 1.320701557 1.339372338 0.897928116 1 15.58277246 1.275494757 5.907723827 0.947318524 1.375134176 0.667440086 0.119041952 0.101075807 9.032043792 0.093818684 0.031763388 18.85796205 -1.275494757 0.427815652 VSNS(ph)PEPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSNSPEPQK 9 0 O60271;O60271-3;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 VSNS(1)PEPQK 128.85 0.00042574 258770000 508770 468110 399860 469910 465910 511680 521840 562070 624810 685500 TRUE FALSE 488886.7059 454759.9611 472123.5968 494162.1114 480896.4183 522026.5202 528226.434 550463.0581 553884.1882 639070.4744 0.764996547 0.71159595 0.738766092 0.773251357 0.752493563 0.816852822 0.826554277 0.861349538 0.866702829 1 19.28561551 1.275868 0.349399309 1.017929624 0.716226649 0.947919052 0.018213817 0.247979619 0.097907891 0.028748851 0.020199622 18.87417598 -1.275868 -0.301702975 QEQDEDGTEEDNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEQDEDGTEEDNSR 14 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 0 109 0.0018453 17548000 31177 37999 35234 45544 43536 41869 38534 38551 31958 28077 FALSE TRUE 29958.56837 36915.30572 41601.56758 47894.5313 44936.37498 42715.61987 39005.59062 37754.90838 28330.26182 26175.31978 1.144534952 1.410309636 1.589343241 1.829759166 1.716745979 1.631904413 1.490166727 1.442385755 1.082327248 1 14.67591954 1.276435611 2.068510969 0.988663603 1.563017492 0.564765092 0.174480757 0.235526166 1.719280934 0.172927692 0.050781137 18.89886014 -1.276435611 0.57435389 CYSCGEFGHIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 CYSCGEFGHIQK 12 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 122.7 0.00035387 224520000 95990 96544 91835 94710 94792 95585 93723 107430 144570 141430 FALSE TRUE 92238.60468 93790.65965 108431.6274 99597.99445 97841.07077 97517.79419 94870.01011 105211.533 128159.0197 131850.8201 0.699567925 0.711339221 0.822381137 0.755383959 0.742058871 0.739607035 0.71952537 0.797958882 0.972000171 1 17.00854702 1.277094912 2.892504755 1.002240089 0.74435264 0.902391632 0.031760767 0.07334863 1.022213626 0.029268068 0.008577317 18.92757222 -1.277094912 -0.25788745 DRIPQILTK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRIPQILTK 9 1 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ; 158.05 6.12E-05 1545570000 1803450 1699430 1570770 1474420 1420530 1307170 1825770 1732800 2141800 2163910 FALSE TRUE 1732969.18 1650963.92 1854643.081 1550514.993 1466222.638 1333601.873 1848114.319 1697017.074 1898671.843 2017346.448 0.859033996 0.818383933 0.91934783 0.768591332 0.726807554 0.661067351 0.916111519 0.841212513 0.941172918 1 20.94402744 1.277247015 1.325460658 0.99673244 0.80162839 0.43760265 0.074397237 0.395803582 1.342929045 0.072499987 0.022924175 18.93420238 -1.277247015 -0.19510405 RMS(ph)GEPIQTVESIR ddPTM_BT-474_Pertuzumab_2h_R1 4 RMSGEPIQTVESIR 14 1 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 RMS(1)GEPIQTVESIR;RMS(1)GEPIQTVESIR;RMS(1)GEPIQTVESIR;RMS(1)GEPIQTVESIR 202.94 9.64E-09 1369240000 379284 445798 353871 446484 519733 463181 447911 449477 395104 384790 TRUE FALSE 364461.162 433084.2775 417823.3615 469527.0927 536450.684 472546.8372 453392.6688 440195.1429 350253.4503 358727.8306 1.015982399 1.207278166 1.164736399 1.308867204 1.495425329 1.317285131 1.263890421 1.227100619 0.976376574 1 18.45253015 1.277591137 4.498976312 0.983289002 1.260057384 0.451147989 0.115442093 0.181654953 7.367396398 0.09821819 0.031183197 18.94921123 -1.277591137 0.276768381 ELEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEELR 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;P06727;Q9BT92;F5GWH6;A0A499FI31;Q15020-4;Q15020;P61129;O94964-2 Q14980;A0A499FI31;P61129;O94964-2 NUMA1;APOA4;TCHP;SART3;ZC3H6;SOGA1 Nuclear mitotic apparatus protein 1;Apolipoprotein A-IV;Trichoplein keratin filament-binding protein;Squamous cell carcinoma antigen recognized by T-cells 3;Zinc finger CCCH domain-containing protein 6;Protein SOGA1;N-terminal form;C-terminal 80 kDa form 0 104.11 0.079355 149560000 384840 402110 331120 398270 399920 366290 372580 394970 387230 371720 FALSE TRUE 369800.0273 390642.2165 390960.7497 418824.7624 412783.79 373696.6348 377139.7455 386813.7315 343273.2738 346543.0733 1.067111294 1.127254436 1.128173609 1.208579235 1.191147138 1.078355516 1.088291109 1.11620679 0.990564522 1 18.40267516 1.278349917 3.453500131 0.990606783 1.129059637 0.591561453 0.043136567 0.169843367 3.509783492 0.039930367 0.011964529 18.98234739 -1.278349917 0.138452854 GTEAS(ph)PPQNNSGSSSPVFTFR ddPTM_BT-474_Pertuzumab_2h_R1 6 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR 373.47 1.73E-112 2340930000 434831 459560 405337 456522 447004 483180 450382 466669 433449 434742 TRUE FALSE 417837.3238 446453.7988 478590.4126 480083.1551 461382.2896 492950.2307 455893.9096 457032.1221 384245.6867 405296.5371 1.03094225 1.101548515 1.180840123 1.18452321 1.138382018 1.216270522 1.124840377 1.127648722 0.948060621 1 18.62861832 1.278527158 6.331067595 0.973863894 1.141832021 0.635685658 0.049636623 0.103544278 10.68501155 0.036723498 0.012676212 18.99009588 -1.278527158 0.167968127 ELSNS(ph)PLRENSFGS(ph)PLEFR ddPTM_BT-474_Pertuzumab_2h_R1 5 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.012)NS(0.988)PLRENS(0.001)FGS(0.999)PLEFR;ELS(0.005)NS(0.995)PLRENSFGS(1)PLEFR;ELSNS(1)PLRENSFGS(1)PLEFR;ELS(0.029)NS(0.971)PLRENSFGS(1)PLEFR;ELS(0.403)NS(0.597)PLRENS(0.009)FGS(0.991)PLEFR 294.44 6.94E-50 6540590000 2286400 2554700 1870970 2120070 2261710 2547210 2113600 2251090 2291960 2016560 TRUE FALSE 2197044.96 2481842.457 2209095.899 2229487.067 2334459.956 2598716.331 2139466.869 2204604.205 2031786.309 1879976.595 1.168655485 1.320145402 1.175065639 1.18591214 1.241749478 1.38231313 1.13802846 1.17267641 1.080750853 1 20.84228327 1.279614199 1.262610836 1.004679784 1.239049136 0.565355134 0.06858106 0.294725637 0.919965975 0.062510193 0.020038754 19.03768775 -1.279614199 0.234369352 DKVVEDDEDDFPTTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKVVEDDEDDFPTTR 15 1 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2R8YE59;A0A2U3TZL3;A0A2R8YEK8;A0A2R8Y5H3;A0A2R8YFI2 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 163.35 1.41E-06 525510000 633840 620860 516300 555440 588170 600660 604560 668170 763460 776610 FALSE TRUE 609068.8321 603153.6807 609606.895 584106.325 607089.0222 612805.7567 611958.7861 654372.056 676795.2215 724009.513 0.841244239 0.833074248 0.841987411 0.806766091 0.838509731 0.84640567 0.845235836 0.903816931 0.934787747 1 19.46564913 1.279704795 1.007362502 0.998732072 0.831220964 0.962795723 0.010803161 0.077640786 0.164434799 0.009834313 0.003410179 19.04165949 -1.279704795 -0.167511108 GAGGSSS(ph)SPPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GAGGSSSSPPEK 12 0 A0A087WXR4;Q8NG45;Q8NG42;P06401-5;P06401;Q8NG44 A0A087WXR4 PGR;PR Progesterone receptor 1 GAGGS(0.008)S(0.047)S(0.473)S(0.473)PPEK 69.554 0.052093 258890000 401760 364400 378520 463260 351830 403260 455000 473920 573180 604790 TRUE FALSE 386058.775 354007.6688 446926.9841 487168.9041 363146.9315 411414.1935 460568.4261 464133.3864 508115.0094 563827.0346 0.684711359 0.627865723 0.792666823 0.864039633 0.644075061 0.729681566 0.816861196 0.823183987 0.901189511 1 19.10489313 1.279729142 0.698114608 1.003058186 0.718067565 0.652743608 0.066161652 0.419780757 0.47583847 0.066759467 0.028391665 19.04272703 -1.279729142 -0.28499062 EDAIEHFMK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDAIEHFMK 9 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 130.66 0.00035508 1261720000 2438100 2296900 2555100 2856000 2424100 2210960 2902800 2993400 3542500 3787800 FALSE TRUE 2342816.357 2231394.661 3016863.408 3003398.502 2502073.378 2255667.126 2938325.335 2931585.244 3140370.251 3531248.932 0.66345262 0.631899564 0.854333259 0.850520187 0.708551967 0.638773185 0.832092382 0.830183683 0.889308659 1 21.7517471 1.279808215 0.984838522 0.994690329 0.732620442 0.560724787 0.077196873 0.396065388 0.80675927 0.077052575 0.026977686 19.04619449 -1.279808215 -0.262069888 AATSDLEHYDK ddPTM_BT-474_Pertuzumab_2h_R1 2 AATSDLEHYDK 11 0 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 150.06 3.41E-05 1126700000 2019430 2425220 1895970 2278880 2153370 1808510 2496320 2447880 2658560 2843500 FALSE TRUE 1940508.443 2356055.1 2238613.955 2396493.27 2222635.102 1845079.311 2526870.711 2397330.423 2356771.414 2650907.212 0.732016735 0.88877313 0.844470883 0.904027594 0.838443191 0.696018066 0.953209791 0.904343393 0.889043345 1 21.33805474 1.280059269 0.780994025 0.990627959 0.830966854 0.345985659 0.071233856 0.685313012 0.938160311 0.067025238 0.026477291 19.05720779 -1.280059269 -0.159661106 AEAPAGPALGLPSPEAES(ph)GVDRGEPEPMEVEEGELEIVPVRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEAPAGPALGLPSPEAESGVDRGEPEPMEVEEGELEIVPVRR 42 2 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(0.476)PEAES(0.524)GVDRGEPEPMEVEEGELEIVPVRR 68.917 0.0012127 431570000 20215 15455 13604 15599 19465 15365 14943 16244 14100 12335 TRUE FALSE 19424.97545 15014.23853 16062.54542 16404.06626 20091.1094 15675.69083 15125.8769 15908.55572 12499.42711 11499.53946 1.689195947 1.305638246 1.396799017 1.426497671 1.747122958 1.36315814 1.315346319 1.383408073 1.086950234 1 13.48928846 1.280367442 1.048408199 0.988051264 1.48015884 0.600659572 0.137345162 0.328615201 0.745401133 0.126335507 0.043113215 19.07073545 -1.280367442 0.492107576 FWAWDPEEER ddPTM_BT-474_Pertuzumab_2h_R1 3 FWAWDPEEER 10 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 0 ;; 132.9 0.00049188 210315000 176204 184926 139390 184126 170922 163179 158412 173752 149862 154518 FALSE TRUE 169317.7529 179652.0915 164580.8737 193628.7649 176419.8614 166478.5912 160350.6934 170163.9605 132850.294 144052.3582 1.175390358 1.247130514 1.14250732 1.344155468 1.224692629 1.155681123 1.113141745 1.181264664 0.922236162 1 17.13623375 1.281552722 5.97294976 0.960864049 1.198371909 0.688962531 0.06362541 0.096061604 8.136576723 0.047728495 0.016361075 19.12285458 -1.281552722 0.23750786 T(ph)TPDQELAPASEPVWERPWSVEEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPDQELAPASEPVWERPWSVEEIR 25 1 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.5)T(0.5)PDQELAPASEPVWERPWSVEEIR;T(0.5)T(0.5)PDQELAPASEPVWERPWSVEEIR 170.44 1.38E-11 332720000 10432.3 12927.2 6540.2 12193.2 11587.1 10558.9 11952.5 13108.7 17093.7 17877.5 TRUE FALSE 10024.59418 12558.52891 7722.159626 12822.49251 11959.80959 10772.40819 12098.77827 12838.00076 15153.29484 16666.641 0.601476577 0.753512895 0.463330291 0.769350736 0.717589681 0.646345487 0.725927814 0.770281232 0.90919909 1 14.02467575 1.282090504 1.010511767 1.005810701 0.657090225 0.668306345 0.082099787 0.273715857 0.582472045 0.072408148 0.025088563 19.14654884 -1.282090504 -0.348720476 YFAES(ph)DEEEDDVDFAMFN ddPTM_BT-474_Pertuzumab_2h_R1 10 YFAESDEEEDDVDFAMFN 18 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 Y(0.444)FAES(0.556)DEEEDDVDFAMFN;YFAES(1)DEEEDDVDFAMFN;Y(0.007)FAES(0.993)DEEEDDVDFAMFN;Y(0.064)FAES(0.936)DEEEDDVDFAMFN;YFAES(1)DEEEDDVDFAMFN;Y(0.002)FAES(0.998)DEEEDDVDFAMFN;YFAES(1)DEEEDDVDFAMFN;Y(0.093)FAES(0.907)DEEEDDVDFAMFN;Y(0.052)FAES(0.948)DEEEDDVDFAMFN;YFAES(1)DEEEDDVDFAMFN 236.78 3.08E-23 231427400 431872.9 464854.5 332670.6 488677.1 477761.8 438004.1 451079.5 455943.6 423017.2 422243.5 TRUE FALSE 414994.8296 451597.3048 392791.5776 513897.7837 493129.4422 446860.843 456599.9459 446528.2053 374998.0609 393644.5716 1.0542374 1.147220964 0.997833086 1.305486778 1.252727658 1.135188633 1.159929486 1.134343612 0.952631099 1 18.58653406 1.282402156 5.860468737 0.975952507 1.15227702 0.407739203 0.082919237 0.167732041 13.36902207 0.061634339 0.021069579 19.16029344 -1.282402156 0.176324513 RVS(ph)ADSQPFQHGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVSADSQPFQHGDK 14 1 Q96AX9-14;Q96AX9-12;Q96AX9-4;Q96AX9-6;Q96AX9-5;Q96AX9-9;Q96AX9-3;Q96AX9;Q96AX9-13;Q96AX9-2;Q96AX9-11;D6RAZ0;Q96AX9-10;Q96AX9-7;Q96AX9-8;E9PD12;H0YAM8;F2Z2L2;D6RED3 Q96AX9-14 MIB2 E3 ubiquitin-protein ligase MIB2 1 RVS(1)ADSQPFQHGDK;RVS(0.995)ADS(0.005)QPFQHGDK 144.33 4.18E-06 471170000 601620 641960 507210 683140 655810 581540 666010 644040 605970 614150 TRUE FALSE 578108.0253 623651.9293 598874.1298 718396.9373 676904.7242 593299.1372 674160.8296 630740.3489 537182.826 572553.0735 1.009702073 1.08924737 1.045971383 1.254725493 1.18225673 1.036234307 1.177464345 1.101627741 0.938223635 1 19.12704991 1.282486795 7.236348941 0.969356532 1.116659989 0.381921441 0.072664459 0.185056172 24.33741086 0.051099486 0.018113251 19.16402792 -1.282486795 0.147303458 DKPHNIFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKPHNIFK 8 1 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 115.71 0.0014484 2884500000 5764100 5528000 5268700 4634400 4836200 4196100 5951100 5847200 6875200 7223800 FALSE TRUE 5538832.599 5370346.852 6220871.292 4873581.939 4991760.765 4280948.017 6023931.342 5726453.277 6094756.119 6734525.592 0.822453271 0.797435065 0.923728213 0.723671159 0.741219362 0.635671802 0.894484884 0.850312795 0.905001553 1 22.68314489 1.282684037 1.192701177 0.989603978 0.783921852 0.443300662 0.076798553 0.414602878 1.173137219 0.073877776 0.024105591 19.17273355 -1.282684037 -0.205682125 SIEEIVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SIEEIVR 7 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ;;; 154.35 0.003919 999740000 858050 915780 794240 963840 895940 896290 909300 933870 885060 924250 FALSE TRUE 824516.4574 889662.851 937776.8358 1013583.898 924758.7238 914413.5979 920428.2854 914585.2582 784591.6993 861649.7243 0.956904452 1.032511038 1.088350416 1.176329394 1.073242058 1.061235874 1.068216306 1.061435096 0.910569199 1 19.71674198 1.282823527 10.01537958 0.955450417 1.068244768 0.389797824 0.054661534 0.364669223 80.30650666 0.038113399 0.01384803 19.1788926 -1.282823527 0.112794351 RPAAAAAAGSAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPAAAAAAGSASPR 14 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RPAAAAAAGS(0.188)AS(0.812)PR;RPAAAAAAGS(0.38)AS(0.62)PR;RPAAAAAAGS(0.005)AS(0.995)PR;RPAAAAAAGSAS(1)PR;RPAAAAAAGSAS(1)PR;RPAAAAAAGS(0.002)AS(0.998)PR 171.52 1.84E-06 3975785000 685497.1 735117.7 592014.5 726056.5 692194.5 750446 707709 731748.1 733191.1 732713.5 TRUE FALSE 658707.1155 714152.863 699004.6894 763528.363 714459.5647 765620.5323 716370.1544 716637.246 649962.3201 683086.162 0.964310437 1.045479916 1.023303835 1.117762891 1.04592891 1.12082571 1.048725906 1.049116914 0.951508545 1 19.38170804 1.282955834 8.409845472 0.975927959 1.054715195 0.327848775 0.043485645 0.252209349 43.38158042 0.029287841 0.010543986 19.18473628 -1.282955834 0.078787235 TAS(ph)TPTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 T(0.136)AS(0.332)T(0.332)PT(0.198)PPQT(0.001)GGGLEPQANGETPQVAVIVRPDDR 42.709 0.077512 81035000 24613 27297 21510 23767 22332 25194 23887 30049 32966 36054 TRUE FALSE 23651.09675 26518.51629 25397.33549 24993.61772 23050.32906 25703.43994 24179.33625 29428.47765 29223.83788 33612.03047 0.703649747 0.78895907 0.755602537 0.743591428 0.685776156 0.764709528 0.719365534 0.875534064 0.869445775 1 15.03669008 1.283239424 1.127745782 0.990230498 0.736645839 0.84114994 0.036747391 0.157346943 0.404356692 0.033076061 0.010995013 19.19726783 -1.283239424 -0.253584659 RAAEEAEEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 RAAEEAEEAR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 160.67 1.17E-05 780650000 596552 668850 468191 613597 581705 620999 648461 621821 608180 601529 FALSE TRUE 573238.0883 649775.0529 552803.5286 645264.8147 600416.0696 633556.0253 656397.0597 608980.1791 539141.9561 560786.905 1.022203056 1.158684425 0.985763975 1.15064173 1.070667065 1.129762517 1.170492845 1.085938658 0.961402542 1 19.09709314 1.283300998 6.630631646 0.980775442 1.100572414 0.396639503 0.057206938 0.15730596 16.78032643 0.037730752 0.013218743 19.19998979 -1.283300998 0.119796972 EEAEKPVPPASHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEAEKPVPPASHR 13 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 0 ; 76.01 0.017926 471840000 1606520 1573280 1391630 1505770 1521000 1566210 1624670 1679030 2045800 1992230 FALSE TRUE 1543735.422 1528411.595 1643128.498 1583482.97 1569924.346 1597879.839 1644553.197 1644357.444 1813569.361 1857294.488 0.831174287 0.822923669 0.884689266 0.852575066 0.845274864 0.860326593 0.88545635 0.885350953 0.976457623 1 20.82477115 1.283625041 1.342776516 1.004977745 0.851001803 0.889870302 0.018647792 0.119220946 0.413052903 0.017427216 0.005499617 19.21432094 -1.283625041 -0.153975942 NSSYVHGGLDSNGKPADAVYGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSYVHGGLDSNGKPADAVYGQK 23 1 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8;E5RI46 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 202.17 1.28E-24 124700000 149440 119100 118540 126750 116920 124450 124500 136580 184730 172110 FALSE TRUE 143599.7196 115703.3846 139962.8149 133291.5827 120680.838 126966.4643 126023.6682 133759.5753 163760.2249 160452.8364 0.894965292 0.721105262 0.872298789 0.830721262 0.752126548 0.79130084 0.785424995 0.83363796 1.020612839 1 17.29178977 1.284233165 4.493498738 1.013486743 0.805258369 0.72689032 0.049184128 0.090214081 3.52664765 0.036144477 0.011590496 19.24124481 -1.284233165 -0.208228374 GTVTDFPGFDERADAETLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTVTDFPGFDERADAETLRK 20 2 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 118.72 3.46E-05 446420000 393470 430520 264380 380290 426070 375580 340940 385900 376350 340970 FALSE TRUE 378092.7574 418241.9911 312159.3471 399916.8125 439774.9285 383174.4849 345112.5257 377931.0301 333628.3258 317875.7982 1.189435495 1.315740278 0.982016715 1.258091414 1.383480375 1.205422014 1.085683552 1.18892672 1.049555605 1 18.27810365 1.284565224 0.98553318 0.999452567 1.217966794 0.3246845 0.104674129 0.607169072 1.23675155 0.098680913 0.034574805 19.25596217 -1.284565224 0.218514227 TMLTHSSKLQSGLMMSEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TMLTHSSKLQSGLMMSEQK 19 1 F5GX61 F5GX61 RAB6A 0 49.559 0.090564 539600000 31547 58548 58377 72636 74556 68302 46447 59628 18512 27313 FALSE TRUE 30314.10836 56878.26836 68927.02249 76384.75266 76954.16145 69683.11324 47015.43228 58396.66096 16410.59537 25463.06618 1.190512884 2.233755666 2.706941183 2.999825399 3.022187544 2.736634808 1.846416765 2.293386843 0.644486224 1 14.63611853 1.284813227 4.768342855 0.808686523 2.421482244 0.57465377 0.533775665 0.137328236 6.236851459 0.436381308 0.142304605 19.26696139 -1.284813227 1.612795721 ESGT(ph)PPGLFLTQCCFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESGTPPGLFLTQCCFSR 17 0 A0A1B0GW41 A0A1B0GW41 1 ES(0.003)GT(0.997)PPGLFLTQCCFSR;ES(0.002)GT(0.998)PPGLFLTQCCFSR 101.04 0.01326 174133000 78169 85880 77142 62678 81682 87512 78253 84330 76905 87668 TRUE FALSE 75114.06906 83430.78649 91083.27541 65912.81909 84309.37571 89281.5526 79210.68362 82588.55603 68175.06681 81730.16827 0.919049485 1.020807717 1.114438858 0.806468658 1.031557594 1.092394088 0.969173138 1.010502704 0.834148127 1 16.31858108 1.2848372 24.99996892 0.917072685 0.997761222 0.107166914 0.090423364 226.2236844 122212.2695 0.057820496 0.021114273 19.26802497 -1.2848372 0.080688536 RIS(ph)QSQPVR ddPTM_BT-474_Pertuzumab_2h_R1 7 RISQSQPVR 9 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RIS(0.997)QS(0.003)QPVR;RIS(0.992)QS(0.008)QPVR;RIS(0.987)QS(0.013)QPVR;RIS(0.984)QS(0.016)QPVR;RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(1)QSQPVR 160.56 3.99E-05 6444680000 3880167 4055998 3173930 3832472 3967755 3516168 3130754 3740255 2847109 2487992 TRUE FALSE 3728525.784 3940324.908 3747529.755 4030266.339 4095381.443 3587267.326 3169069.104 3663017.427 2523917.122 2319478.086 1.607484807 1.698798076 1.615678017 1.737574657 1.765647827 1.546583841 1.366285426 1.579242093 1.088140103 1 21.14536879 1.284926619 0.825087554 0.979499402 1.675825412 0.816916911 0.108028165 0.226202205 0.339582405 0.101155114 0.038729027 19.27199254 -1.284926619 0.69632601 FLYDDNQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLYDDNQR 8 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ; 143.11 0.0014116 1566720000 1276010 1350540 1054090 1556080 1374590 1379770 1401200 1395100 1326010 1329800 FALSE TRUE 1226142.118 1312023.922 1244587.511 1636389.475 1418804.936 1407669.895 1418348.305 1366290.697 1175486.904 1239731.462 0.989038479 1.058312999 1.003917017 1.319954785 1.144445374 1.135463557 1.144077043 1.102086008 0.94817865 1 20.24159622 1.285592025 6.464040983 0.974254527 1.116995733 0.282578261 0.087821404 0.224944067 21.76499849 0.064194942 0.022457213 19.30154282 -1.285592025 0.142741206 TMLITHMQDLQEVTQDLHYENFR ddPTM_BT-474_Pertuzumab_2h_R1 3 TMLITHMQDLQEVTQDLHYENFR 23 0 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 ;; 253.66 1.18E-43 490886000 186683 202321 170784 184636 201330 191280 217538 183487 202083 172958 FALSE TRUE 179387.222 196551.0032 201648.4679 194165.0861 207805.9623 195147.8127 220200.2951 179697.9293 179143.385 161243.4006 1.112524428 1.218970838 1.250584316 1.204173847 1.288771891 1.210268525 1.365639116 1.114451374 1.111012199 1 17.29888059 1.286314186 2.013865705 1.02179001 1.23434149 0.550414685 0.066957147 0.220012372 1.529956239 0.058750801 0.017346418 19.33366485 -1.286314186 0.21255148 ALS(ph)PGLEESGLGLLAR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALSPGLEESGLGLLAR 16 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR 325.77 5.38E-59 2456700000 411216 460580 383589 490277 441727 451201 475926 460524 425239 424761 TRUE FALSE 395145.2241 447444.7094 452912.0652 515580.2547 455935.5501 460324.5934 481750.5248 451014.0185 376967.6515 395991.5591 0.997862745 1.129934967 1.143741716 1.301998093 1.151376941 1.16246062 1.216567661 1.138948566 0.951958805 1 18.59511015 1.286418553 5.796483089 0.975691191 1.162137505 0.494705479 0.072425619 0.139740114 10.28869392 0.053205299 0.018246651 19.33831156 -1.286418553 0.186446313 DGGSEGSGGNNDGEKEPSLTDAIPSHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGGSEGSGGNNDGEKEPSLTDAIPSHPR 28 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 252.44 1.15E-53 317330000 183350 168100 163070 156630 165990 185160 190660 187500 260290 240130 FALSE TRUE 176184.4793 163305.9526 192540.3765 164713.6931 171329.2191 188904.0621 192993.3541 183628.0595 230742.9704 223865.7812 0.787009423 0.72948153 0.860070599 0.735769854 0.765321159 0.843827319 0.862094033 0.820259615 1.030720145 1 17.7722745 1.28643272 3.995605116 1.019530708 0.799143382 0.778295324 0.045799787 0.0966437 2.789620271 0.038622867 0.012049854 19.33894239 -1.28643272 -0.220387326 RES(ph)EDDPES(ph)EPDDHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RESEDDPESEPDDHEK 16 1 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 2 RES(1)EDDPES(1)EPDDHEK;RES(1)EDDPES(1)EPDDHEK 171.29 1.74E-08 507330000 914420 792860 654280 679290 721960 765810 807000 808710 1052610 958710 TRUE FALSE 878683.4555 770248.4091 772522.9504 714348.2383 745182.4991 781295.2029 816876.3074 792009.8559 933122.1257 893775.7178 0.983114039 0.861791604 0.864336472 0.799247758 0.833746637 0.874151297 0.913961177 0.886139375 1.044022686 1 19.76955332 1.28742147 5.39942959 1.02236091 0.873369415 0.602025781 0.047044725 0.118981445 7.262175084 0.035877541 0.012123744 19.38302119 -1.28742147 -0.148991495 TRNEELAQTWK ddPTM_BT-474_Pertuzumab_2h_R1 4 TRNEELAQTWK 11 1 Q8TAT6;Q8TAT6-2;I3L283;I3L281;I3L3I1 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;; 190.78 1.93E-06 1819340000 748450 743710 598220 667370 758480 750300 717730 816870 874160 911860 FALSE TRUE 719199.7465 722500.119 706331.6613 701813.0457 782877.198 765471.5801 726513.7944 800001.349 774929.0216 850098.91 0.846018902 0.849901241 0.83088174 0.82556634 0.920924835 0.900450019 0.854622663 0.941068551 0.911575127 1 19.69727118 1.287911588 0.236478681 1.030458734 0.809456247 0.741693256 0.027200722 1.164905872 0.279620155 0.103633857 0.082673371 19.40490799 -1.287911588 -0.221002487 VMSQNFTNCHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 VMSQNFTNCHTK 12 0 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8;E5RI46 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 126.51 0.00023603 0 231500 211150 199190 194950 206380 202290 241730 220770 290310 276070 FALSE TRUE 222452.7241 205128.2087 235188.064 205011.3929 213018.4001 206380.4424 244688.364 216211.0224 257355.2259 257371.533 0.864325287 0.797012033 0.913807604 0.796558153 0.827668848 0.801877504 0.950720389 0.840073569 0.99993664 1 17.97349297 1.288585538 1.174472745 1.009521706 0.838960754 0.562873995 0.050979183 0.301682989 0.830262802 0.044102901 0.014479355 19.43504442 -1.288585538 -0.170560952 LIHEQEQQSS(ph)S ddPTM_BT-474_Pertuzumab_2h_R1 2 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.107)S(0.447)S(0.447);LIHEQEQQS(0.104)S(0.448)S(0.448) 126.59 0.00031917 723940000 275270 355240 294160 442520 277130 356810 373420 354730 310850 333670 TRUE FALSE 264512.1441 345108.903 347321.2556 465358.5102 286044.1381 364024.9427 377990.0257 347404.7015 275563.6112 311070.2337 0.850329332 1.109424386 1.116536454 1.495991772 0.919548408 1.170233932 1.215127597 1.116804708 0.885856573 1 18.24688082 1.28889137 7.884009522 0.943522461 1.134590186 0.159438326 0.165270504 0.358235921 48.73355609 0.110024552 0.039572058 19.4487355 -1.28889137 0.191067725 DRPFMGGQKPNLADLAVYGVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRPFMGGQKPNLADLAVYGVLR 22 2 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 161.66 9.62E-12 1216770000 442780 558550 404080 520370 471530 463483 488600 496300 441250 458830 FALSE TRUE 425475.6681 542620.7009 477106.2447 547226.3581 486697.1907 472854.9438 494579.633 486051.2316 391161.1499 427753.0354 0.994675976 1.268537347 1.115377812 1.279304441 1.137799502 1.105439131 1.156227056 1.13628938 0.914455579 1 18.70641857 1.289013583 6.555803207 0.957691596 1.154832384 0.485467711 0.078929871 0.133671347 12.63024717 0.051283636 0.018047584 19.45420926 -1.289013583 0.197140788 AQEQS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQEQSPR 7 0 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 AQEQS(1)PR 89.08 0.019024 11681000 23550 21790 19562 24690 18340 21291 24333 22740 18489 21453 TRUE FALSE 22629.63996 21168.57053 23097.28855 25964.25386 18929.92276 21721.51861 24630.79453 22270.41105 16390.20623 19999.9692 1.131483741 1.058430157 1.154866206 1.298214692 0.946497595 1.086077603 1.231541623 1.113522267 0.819511574 1 14.28771016 1.289614489 9.418153964 0.910255108 1.129137323 0.440437286 0.098212717 0.268814718 47.17600514 0.064828214 0.023567818 19.48114546 -1.289614489 0.218882215 NYGFVHIEDK ddPTM_BT-474_Pertuzumab_2h_R1 3 NYGFVHIEDK 10 0 Q9BWF3;E9PB51;Q9BQ04;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2;E9PLB0;E9PM61;U3KQD5 Q9BWF3 RBM4;RBM4B RNA-binding protein 4;RNA-binding protein 4B 0 ;; 113.69 0.0014551 2758080000 4386040 3773920 3166640 3301510 3254110 3146290 3222870 3716650 4844730 4448430 FALSE TRUE 4214628.708 3666291.497 3738922.29 3471901.327 3358781.403 3209910.139 3262312.447 3639899.879 4294776.561 4147133.874 1.016275055 0.884054291 0.901567782 0.837180914 0.809904263 0.774006877 0.786642666 0.87769047 1.035601138 1 21.98368319 1.28971844 5.497651701 1.018242664 0.853948028 0.474314628 0.065996931 0.155434622 9.681965858 0.051317812 0.017466885 19.48580896 -1.28971844 -0.164294636 S(ph)LLFGVYLDS(ph)NEPRLLS(ph)LGT(ph)DRLLIEYDLLRSYK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLFGVYLDSNEPRLLSLGTDRLLIEYDLLRSYK 34 3 Q8TBY9-2;Q8TBY9 Q8TBY9-2 WDR66 WD repeat-containing protein 66 4 S(0.666)LLFGVY(0.65)LDS(0.666)NEPRLLS(0.581)LGT(0.891)DRLLIEY(0.508)DLLRS(0.035)Y(0.003)K 42.121 0.076493 56964000 41795 64234 38484 49557 54149 60498 51403 53492 41596 49101 TRUE FALSE 40161.60519 62402.10921 45438.91487 52114.64271 55890.75176 61721.31101 52032.08529 52387.37151 36874.19646 45775.34554 0.877363234 1.363225301 0.992650396 1.138487151 1.220979353 1.348352706 1.136683616 1.144445135 0.805547092 1 15.48228316 1.289888524 8.623893563 0.903508473 1.161462042 0.32261803 0.144470075 0.261150363 40.24008157 0.091473029 0.033123818 19.49344173 -1.289888524 0.257953569 EAEDELSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAEDELSAR 9 0 K7EKE6;K7EJE8;P36776-2;P36776;P36776-3 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 ; 99.136 0.010935 0 399000 417670 312350 465060 351220 338370 422470 363640 358260 308540 FALSE TRUE 383406.6389 405758.4605 368798.5932 489061.8023 362517.3103 345212.0732 427640.3142 356130.7069 317591.8267 287642.311 1.332928517 1.410635519 1.282143061 1.700242919 1.26030593 1.200143581 1.486708658 1.238102648 1.10412069 1 18.13391638 1.290703428 1.986116107 1.008187126 1.380721814 0.497054456 0.133134789 0.257714208 1.748436028 0.119549001 0.035389932 19.53005326 -1.290703428 0.372534688 DCDHADEQK ddPTM_BT-474_Pertuzumab_2h_R1 5 DCDHADEQK 9 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ;;;; 195.79 3.07E-05 4913650000 8304497 6407996 7721152 6801048 6771353 6620608 8418072 8386700 9092820 9930510 FALSE TRUE 7979948.076 6225246.228 9116535.922 7152050.902 6989159.719 6754481.23 8521094.883 8213511.714 8060641.194 9257907.713 0.86196021 0.672424744 0.984729618 0.772534262 0.754939446 0.729590469 0.920412597 0.887188765 0.870676339 1 23.14225475 1.290980389 0.78001758 0.988009131 0.800208236 0.312093414 0.086363352 0.690294469 0.940438236 0.079584721 0.031546228 19.54251206 -1.290980389 -0.187800895 GIGT(ph)PQPDVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GIGTPQPDVAK 11 0 Q9Y6X8;H0YKA3 Q9Y6X8 ZHX2 Zinc fingers and homeoboxes protein 2 1 GIGT(1)PQPDVAK;GIGT(1)PQPDVAK 125.89 0.0035641 762560000 1332350 1349000 1221190 1202570 1209670 1446940 1338160 1555990 1669930 1802290 TRUE FALSE 1280280.289 1310527.841 1441886.198 1264634.782 1248580.134 1476198.118 1354536.802 1523858.263 1480366.547 1680219.293 0.761972139 0.779974284 0.858153578 0.752660553 0.743105462 0.878574674 0.806166676 0.906940105 0.881055558 1 20.68021811 1.291298949 0.563267748 0.999540961 0.779745657 0.719319513 0.041492752 0.401434407 0.320329865 0.041706743 0.021022434 19.55685199 -1.291298949 -0.219795304 GIHVEVPPAEAER ddPTM_BT-474_Pertuzumab_2h_R1 1 GIHVEVPPAEAER 13 0 P38117-2;P38117 P38117-2 ETFB Electron transfer flavoprotein subunit beta 0 71.558 0.036692 0 57213 94465 64958 127570 67471 74120 109250 82253 64213 59284 FALSE TRUE 54977.05271 91770.95069 76697.35558 134153.903 69641.26599 75618.75718 110587.0342 80554.44681 56923.80944 55268.64188 0.994724148 1.66045243 1.387719202 2.427305945 1.26005025 1.368203643 2.000900157 1.45750726 1.029947679 1 15.75417354 1.291699602 4.157958441 1.000825959 1.600990106 0.259203552 0.378616086 0.265452917 8.289117534 0.291934363 0.092640806 19.57490226 -1.291699602 0.600164147 RITEAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RITEAEK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 122.19 0.0069993 113690000 83781 100900 74799 116270 101250 79776 102780 98766 88714 96890 FALSE TRUE 80506.7459 98022.43079 88316.84319 122270.7086 104506.7982 81389.12538 104037.8524 96726.44759 78643.55864 90327.554 0.891275611 1.085188588 0.977739785 1.353636883 1.156975846 0.901044275 1.151784232 1.070840993 0.870648602 1 16.46287852 1.292052674 9.626640796 0.935654931 1.080610623 0.148877244 0.13137199 0.583716114 100.3532593 0.087960323 0.032023934 19.59082269 -1.292052674 0.144955692 RDETALQEEEELQLALALSQSEAEEKER ddPTM_BT-474_Pertuzumab_2h_R1 2 RDETALQEEEELQLALALSQSEAEEKER 28 2 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 ; 293.68 1.73E-71 96985000 101608 107707 71949 72869 96062 102843 84516 94562 109537 97578 FALSE TRUE 97637.04703 104635.3018 84951.7848 76629.77782 99151.92147 104922.5559 85550.33209 92609.26165 97102.81898 90968.95515 1.073300742 1.150230885 0.933854683 0.842372848 1.089953395 1.153388601 0.940434371 1.018031498 1.0674281 1 16.47308666 1.292090352 0.004192697 1.67E-07 2.03569834 0.008637127 0.094440651 52816.32588 198.3792631 48275.33049 48031.42462 19.5925224 -1.292090352 2.035698172 ESGADGASTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 ESGADGASTSPR 12 0 O75528-2;O75528 O75528-2 TADA3 Transcriptional adapter 3 1 ESGADGAS(0.022)T(0.197)S(0.781)PR;ESGADGAST(0.011)S(0.989)PR;ESGADGAS(0.001)T(0.126)S(0.873)PR;ESGADGAS(0.013)T(0.42)S(0.567)PR;ESGADGASTS(1)PR;ESGADGASTS(1)PR 215.61 4.30E-11 409234000 940545 996949 830388 974576 970505 990068 949364 997380 932658 1005348 TRUE FALSE 903787.4616 968516.9906 980457.5835 1024873.984 1001722.175 1010087.853 960982.6006 976783.7545 826786.5739 937254.8845 0.964292079 1.033354967 1.046094931 1.093484815 1.068783093 1.077708818 1.025316183 1.042175155 0.882136319 1 19.83808191 1.292187593 11.40184198 0.94118269 1.046128231 0.483825841 0.042436159 0.437944741 91.82406963 0.027815801 0.010157963 19.59690976 -1.292187593 0.104945541 LREQGTESR ddPTM_BT-474_Pertuzumab_2h_R1 1 LREQGTESR 9 1 P42166;P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 108.43 0.0023825 243930000 166740 183910 113180 168400 141680 185010 153730 162690 122880 143370 FALSE TRUE 160223.6165 178665.0669 133634.1437 177091.1442 146237.2659 188751.029 155611.3937 159330.3946 108931.1776 133659.4222 1.198745392 1.336718833 0.999810874 1.324943212 1.094103681 1.412178998 1.164238115 1.192062572 0.814990636 1 17.02820202 1.292502845 7.278067949 0.908666174 1.215755382 0.507520586 0.121311566 0.141772552 15.59297935 0.076468404 0.027358627 19.61114023 -1.292502845 0.307089208 PEQLDIEEEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 PEQLDIEEEGR 11 0 P19532 P19532 TFE3 Transcription factor E3 0 50.108 0.09201 82637000 171290 142970 110580 142580 167090 138940 159310 136700 141470 119660 FALSE TRUE 164595.7974 138892.6356 130564.2658 149938.5709 172464.6016 141749.462 161259.6834 133877.0972 125410.9187 111555.3216 1.47546343 1.245056117 1.17039926 1.344073673 1.546000667 1.270665173 1.445557963 1.200096018 1.12420382 1 16.76739981 1.292556328 1.863283258 1.015998024 1.348406968 0.545444603 0.10929823 0.255736216 1.551238611 0.101661633 0.030302242 19.61355545 -1.292556328 0.332408944 S(ph)IPQLDLGWPDTIAYR ddPTM_BT-474_Pertuzumab_2h_R1 4 SIPQLDLGWPDTIAYR 16 0 A6ND36 A6ND36 FAM83G Protein FAM83G 1 S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR 242.26 6.41E-20 500610000 248916 268992 201520 222687 255086 223774 223891 254098 245134 233021 TRUE FALSE 239188.0875 261320.6115 237939.1468 234179.9028 263291.0729 228298.8636 226631.045 248850.7875 217307.416 217238.2801 1.101040237 1.202921563 1.095291063 1.07798636 1.21199207 1.050914523 1.043237154 1.145519967 1.000318249 1 17.72891882 1.292595546 0.377047144 0.989515212 1.145237682 0.367281517 0.056683895 1.349718341 0.593529377 0.081581284 0.055760987 19.61532672 -1.292595546 0.15572247 IEHAPS(ph)PSSGGTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEHAPSPSSGGTLK 14 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 IEHAPS(0.672)PS(0.328)S(0.001)GGTLK 194.13 1.88E-07 282790000 378860 356630 345450 370910 339160 332120 405190 411500 527220 534370 TRUE FALSE 364053.7323 346459.2616 407880.4995 390052.7095 350069.3894 338835.694 410148.8364 403002.3812 467372.1959 498176.6439 0.730772381 0.695454646 0.818746733 0.782960651 0.702701328 0.680151705 0.823300011 0.808954788 0.938165612 1 18.92629786 1.29306242 1.311766 1.001669434 0.740921852 0.799395581 0.044760237 0.17542342 0.582994853 0.04273871 0.013597645 19.63642484 -1.29306242 -0.260747582 KQEEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 KQEEEER 7 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 110.31 0.010955 224760000 498060 458530 399250 446700 475360 417810 477730 495120 429500 516820 FALSE TRUE 478595.2646 445453.1733 471403.3563 469754.2405 490650.3861 426258.4045 483576.6026 484895.599 380744.9606 481815.3211 0.993316824 0.924530943 0.978390133 0.97496742 1.018337036 0.884692507 1.003655512 1.006393068 0.790230082 1 18.87812074 1.293226138 24.99999462 0.895105396 0.973401306 0.209250303 0.060585779 109.0762373 49883.04121 0.037115092 0.013553099 19.6438287 -1.293226138 0.07829591 TKPSDEEMLFIYGHYK ddPTM_BT-474_Pertuzumab_2h_R1 3 TKPSDEEMLFIYGHYK 16 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5;P07108-6 P07108 DBI Acyl-CoA-binding protein 0 ;; 193.64 2.05E-10 10280070000 4485450 4109480 3999220 4026810 3833520 3578830 4285070 4821640 5907480 6179000 FALSE TRUE 4310153.655 3992281.654 4721968.016 4234634.147 3956828.652 3651196.395 4337511.968 4722071.449 5236887.637 5760490.826 0.748226807 0.693045397 0.819716264 0.735116898 0.686890887 0.633834252 0.752976109 0.819734219 0.909104414 1 22.45776031 1.293598704 1.524682441 0.993305124 0.721249859 0.804986009 0.046225847 0.159753269 0.686378792 0.045365664 0.013946619 19.66068768 -1.293598704 -0.272055265 IEVEKPFAIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEVEKPFAIAK 11 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 128.67 0.0010914 0 642820 533300 508550 683720 457010 435280 762870 722270 890390 1038400 FALSE TRUE 617697.8837 518090.8062 600456.2976 719006.8711 471710.1417 444081.6598 772206.2313 707354.8721 789316.66 968068.2431 0.638072665 0.535180045 0.620262365 0.742723332 0.487269513 0.458729705 0.797677474 0.730686991 0.815352291 1 19.88474923 1.294886397 0.909275425 0.986761599 0.589414624 0.656584898 0.093286938 0.321494791 0.568534538 0.089180838 0.032504304 19.71906856 -1.294886397 -0.397346975 WQPDTEEEYEDSSGNVVNKK ddPTM_BT-474_Pertuzumab_2h_R1 2 WQPDTEEEYEDSSGNVVNKK 20 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 205.62 1.36E-21 1112100000 534330 470420 347379 404359 480457 435394 463061 470256 535620 516049 FALSE TRUE 513447.7929 457004.0822 410158.1127 425228.0164 495911.3357 444197.965 468728.079 460545.0493 474818.6631 481096.5416 1.067244822 0.949921778 0.852548454 0.883872528 1.030793807 0.923303176 0.974291101 0.957281979 0.986950897 1 18.8759669 1.295081951 0.803903877 1.000364268 0.946134933 0.059270451 0.059609725 1.682802966 2.410463429 0.057515557 0.022409145 19.72794965 -1.295081951 -0.054229334 SS(ph)GASHQPSPTELRPTLTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSGASHQPSPTELRPTLTPK 20 1 Q8TBP0 Q8TBP0 TBC1D16 TBC1 domain family member 16 1 S(0.356)S(0.413)GAS(0.231)HQPSPTELRPTLTPK 73.574 0.0089195 78504000 121720 154290 121550 162520 182730 169980 149090 155760 131030 130140 TRUE FALSE 116963.0478 149889.8003 143516.7889 170907.6767 188607.6764 173417.1121 150914.608 152543.5016 116156.0237 121325.5019 0.964043388 1.235435238 1.182907028 1.408670675 1.55455921 1.42935417 1.243882001 1.257307814 0.957391661 1 16.8885233 1.295515893 3.865555667 0.97264809 1.298618687 0.393023175 0.151411012 0.230453228 5.999091633 0.1325062 0.041462719 19.74767146 -1.295515893 0.325970597 EHSNPS(ph)PSQDTDGTK ddPTM_BT-474_Pertuzumab_2h_R1 6 EHSNPSPSQDTDGTK 15 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 EHSNPS(0.998)PS(0.001)QDTDGTK;EHSNPS(0.986)PS(0.014)QDTDGTK;EHSNPS(0.999)PS(0.001)QDTDGTK;EHS(0.004)NPS(0.989)PS(0.008)QDTDGTK;EHS(0.018)NPS(0.938)PS(0.043)QDTDGTK;EHSNPS(0.999)PS(0.001)QDTDGTK 212.47 5.55E-10 2054280000 2760410 2902580 2350780 2461580 2493260 2704550 3193660 2698900 3888190 3645380 TRUE FALSE 2652530.125 2819801.26 2775618.239 2588622.439 2573457.972 2759237.854 3232744.966 2643166.772 3446818.972 3398475.166 0.780505961 0.829725428 0.816724591 0.761701149 0.757239011 0.811904669 0.951233953 0.777750798 1.014225146 1 21.69645615 1.29559243 0.87432256 1.011451809 0.79541613 0.598453367 0.059827416 0.375794274 0.621195729 0.054877618 0.020406808 19.75115196 -1.29559243 -0.216035679 ELPDVQGESDSISPLLLHLEDDDFSENEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELPDVQGESDSISPLLLHLEDDDFSENEK 29 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 0 199.03 3.78E-25 31116000 55978 52453 47906 53838 56686 52394 55593 57601 73428 67998 FALSE TRUE 53790.31787 50957.0918 56563.67986 56616.58563 58509.35667 53453.44258 56273.36376 56411.51922 65092.76128 63392.43489 0.848528976 0.803835535 0.892278076 0.893112652 0.922970647 0.843214852 0.887698412 0.88987778 1.026822229 1 15.95202306 1.29615185 4.406986268 1.014792396 0.872164616 0.755209704 0.032097434 0.099457535 3.495555117 0.026410443 0.008560478 19.77661005 -1.29615185 -0.14262778 YFQDADGCELAENITYLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFQDADGCELAENITYLGR 19 0 Q69YN2 Q69YN2 CWF19L1 CWF19-like protein 1 0 ; 109.35 0.00065046 0 51729 61529 42943 59822 56124 58494 56991 56761 58883 55061 FALSE TRUE 49707.37349 59774.25316 50703.75536 62909.42059 57929.27943 59676.78876 57688.47291 55588.86551 52198.8487 51331.66943 0.968356846 1.164471248 0.987767511 1.225547918 1.128529036 1.162572529 1.123837848 1.08293508 1.01689365 1 15.64756156 1.296597063 2.56744036 1.000516345 1.113230062 0.221594733 0.074029818 0.383758968 4.182104903 0.062358087 0.018382056 19.79689424 -1.296597063 0.112713717 DILYIGDHIFGDILK ddPTM_BT-474_Pertuzumab_2h_R1 2 DILYIGDHIFGDILK 15 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 176.32 8.06E-07 291510000 643160 587040 615400 660760 711730 501320 736050 742250 879680 928760 FALSE TRUE 618024.5961 570298.194 726616.4695 694861.9028 734623.4418 511457.0339 745058.0001 726922.2781 779822.4143 865854.2579 0.713774392 0.658653796 0.839190271 0.802516008 0.848437754 0.590696447 0.860488926 0.839543458 0.900639348 1 19.72376468 1.297508285 1.047860266 0.993982786 0.751925741 0.504277173 0.080329448 0.392724262 0.886176275 0.074563506 0.025544618 19.838475 -1.297508285 -0.242057044 RLS(ph)NVSLTGVSTIR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSNVSLTGVSTIR 14 1 F8WBA3;Q15139;A0A494C0Q1 F8WBA3 PRKD1 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1 1 RLS(1)NVSLTGVSTIR;RLS(0.995)NVS(0.004)LT(0.001)GVSTIR;RLS(1)NVSLTGVSTIR;RLS(1)NVSLTGVSTIR 230.27 5.98E-13 1536410000 904290 1152130 885450 1329630 1217950 1101220 1142630 1152250 916670 1071470 TRUE FALSE 868949.3471 1119272.38 1045470.512 1398252.364 1257126.468 1123487.423 1156613.848 1128455.635 812613.4646 998898.3825 0.869907653 1.12050675 1.04662349 1.399794402 1.258512868 1.124726441 1.157889399 1.129700132 0.813509641 1 19.9299784 1.297673758 8.069996529 0.907741184 1.147643683 0.318747345 0.13499828 0.257807511 30.88687525 0.093156083 0.0337053 19.84603521 -1.297673758 0.239902499 DKPAQIR ddPTM_BT-474_Pertuzumab_2h_R1 5 DKPAQIR 7 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;; 128.1 0.003457 7279990000 6893200 7194600 5837910 6411100 6823790 6656900 7173900 7541300 8296500 8541500 FALSE TRUE 6623806.123 6989417.052 6892950.201 6741977.639 7043283.403 6791507.079 7261696.334 7385569.52 7354716.102 7962976.597 0.831825391 0.877739243 0.865624822 0.84666551 0.884503843 0.852885475 0.911932397 0.927488538 0.923613929 1 22.92487639 1.298384618 0.515150963 1.001074034 0.85246848 0.870811386 0.017041981 0.266063092 0.184600849 0.017590759 0.009580935 19.87854613 -1.298384618 -0.148605554 WAEYHADIYDK ddPTM_BT-474_Pertuzumab_2h_R1 5 WAEYHADIYDK 11 0 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;;;; 170.72 2.57E-05 3975750000 7071390 6612450 6231570 7275320 6547800 5757820 8250750 7546850 9439590 9741510 FALSE TRUE 6795032.261 6423869.4 7357753.32 7650800.137 6758415.934 5874247.065 8351725.147 7391004.91 8368047.317 9081708.851 0.748210758 0.707341482 0.810172781 0.842440587 0.744178881 0.646821778 0.919620446 0.813834162 0.921417704 1 23.11453236 1.299246044 0.904248343 0.997229085 0.759249026 0.579905842 0.066926251 0.377901762 0.661164046 0.062568282 0.022889776 19.91801451 -1.299246044 -0.237980059 KSPEKNER ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPEKNER 8 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 48.794 0.093347 31711000 45500 52690 34807 34781 41666 50346 48648 46092 43414 47126 FALSE TRUE 43721.8097 51187.33279 41097.39918 36576.05158 43006.22473 51364.03061 49243.36878 45140.18409 38485.82473 43934.11404 0.995167665 1.165093092 0.935432524 0.832520522 0.978879981 1.169114974 1.120845836 1.027451789 0.875989549 1 15.42305398 1.299344078 12.63424131 0.938061464 1.030566536 0.109332554 0.102634606 1.836225814 378.044839 0.073709781 0.026942282 19.92251112 -1.299344078 0.092505072 GGNFGFGDSR ddPTM_BT-474_Pertuzumab_2h_R1 10 GGNFGFGDSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;; 209.6 2.15E-07 81195200000 36291550 40314400 34040010 39803500 39655700 38765200 39238700 40115300 39600800 39937900 FALSE TRUE 34873236.1 39164672.78 40191797.02 41857763.41 40931261.6 39549058.9 39718914.95 39286905.04 35105483.2 37232870.46 0.936624968 1.051884324 1.079470815 1.124215321 1.099331346 1.062208162 1.066770154 1.055167237 0.942862658 1 25.15007351 1.301249128 6.906861627 0.971916099 1.063762347 0.3461685 0.048136544 0.207501912 17.95634087 0.033932977 0.012132047 20.01009395 -1.301249128 0.091846248 LDDFLDLNHK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDDFLDLNHK 10 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 ;;; 166.55 5.51E-06 909527000 1826215 1683638 1504579 1592571 1742988 1651422 1674609 1788526 2150291 2031349 FALSE TRUE 1754844.499 1635622.293 1776489.894 1674763.78 1799052.792 1684814.884 1695103.366 1751592.313 1906198.98 1893763.923 0.926643748 0.86368859 0.938073576 0.88435721 0.949987889 0.889664685 0.895097507 0.924926435 1.006566319 1 20.85282506 1.301467731 3.829072645 1.005305812 0.906849547 0.701972524 0.024745017 0.107292866 2.694782768 0.018420102 0.005789036 20.02016864 -1.301467731 -0.098456265 DTILAELLQIHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DTILAELLQIHK 12 0 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 0 ; 137.16 9.72E-05 165585000 447630 443700 405020 408310 437440 442240 467680 476030 567850 560670 FALSE TRUE 430136.1247 431046.1104 478216.1236 429382.928 451510.6549 451182.3958 473403.6077 466199.8141 503390.0486 522695.3215 0.822919408 0.824660357 0.914904159 0.821478422 0.863812313 0.863184301 0.905697044 0.891915032 0.963065916 1 18.99561072 1.301723568 0.650322925 1.003674787 0.846260196 0.765811171 0.027840785 0.314681796 0.315806697 0.026246408 0.011831402 20.03196568 -1.301723568 -0.157414591 QAS(ph)TDAGTAGALTPQHVR ddPTM_BT-474_Pertuzumab_2h_R1 6 QASTDAGTAGALTPQHVR 18 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 QAS(0.948)T(0.052)DAGTAGALTPQHVR;QAS(0.947)T(0.053)DAGTAGALTPQHVR;QAS(0.889)T(0.111)DAGTAGALTPQHVR;QAS(0.93)T(0.07)DAGTAGALTPQHVR;QAS(0.933)T(0.067)DAGTAGALTPQHVR;QAS(0.9)T(0.1)DAGTAGALTPQHVR 330.22 4.55E-75 54312000000 2657888 2921680 2260381 2731454 2735500 2748163 2619027 2786375 2712998 2755879 TRUE FALSE 2554014.799 2838356.547 2668882.129 2872424.668 2823489.842 2803732.739 2651079.436 2728835.383 2405029.841 2569220.861 0.99408145 1.104753815 1.038790463 1.118013913 1.09896735 1.09127743 1.031861245 1.062125652 0.936093069 1 21.29289948 1.302062198 6.635844286 0.968596219 1.069651978 0.510920981 0.03885667 0.140718145 11.18433596 0.025939168 0.009233683 20.04759122 -1.302062198 0.101055759 VGGVS(ph)PEEHPAPEVSTPFPPLPPEPEGGGEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGGVSPEEHPAPEVSTPFPPLPPEPEGGGEEK 32 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 VGGVS(1)PEEHPAPEVSTPFPPLPPEPEGGGEEK;VGGVS(1)PEEHPAPEVSTPFPPLPPEPEGGGEEK 238.05 7.50E-47 507830000 272590 237990 236210 217354 250660 239750 277770 284140 354610 365590 TRUE FALSE 261936.8814 231202.7582 278898.4015 228571.666 258722.7065 244597.9093 281169.4324 278272.4097 314356.1594 340828.2637 0.768530399 0.678355591 0.81829599 0.67063589 0.759099917 0.717657352 0.82495926 0.816459312 0.922330079 1 18.37868545 1.302190379 0.930028735 1.001129574 0.733354947 0.794976957 0.044621099 0.196718207 0.360926466 0.037534818 0.013554189 20.05350909 -1.302190379 -0.267774627 EKDS(ph)PHMQDPNQADEEAMTQIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKDSPHMQDPNQADEEAMTQIIR 23 1 P23511-2;P23511 P23511-2 NFYA Nuclear transcription factor Y subunit alpha 1 EKDS(1)PHMQDPNQADEEAMTQIIR;EKDS(1)PHMQDPNQADEEAMTQIIR;EKDS(1)PHMQDPNQADEEAMTQIIR;EKDS(1)PHMQDPNQADEEAMTQIIR 270 1.89E-45 928340000 777778 786347 688073 665572 770607 773410 723867 827209 933839 926875 TRUE FALSE 747381.5759 763921.1535 812423.0972 699922.2507 795394.274 789048.8801 732725.9009 810126.8451 827833.5117 864096.9307 0.864927937 0.88406882 0.940199031 0.810004325 0.920491956 0.913148574 0.847967253 0.93754163 0.958033158 1 19.72083363 1.302228129 1.813555663 0.994555052 0.885043561 0.534101232 0.036562345 0.247208713 1.430769262 0.03181428 0.009540232 20.05525226 -1.302228129 -0.109511492 (ac)MENGYTYEDYKNTAEWLLSHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 MENGYTYEDYKNTAEWLLSHTK 22 1 P00491;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ; 144.01 1.10E-21 604940000 402880 415690 324490 321120 374580 359190 363810 397700 468940 453490 FALSE TRUE 387135.0042 403834.9282 383132.5612 337693.0417 386628.7059 366453.0679 368262.4156 389487.356 415707.8972 422774.7184 0.91570046 0.955201223 0.906233378 0.798754105 0.9145029 0.86678094 0.871060637 0.921264539 0.983284665 1 18.68952958 1.303036531 2.622134119 0.998966951 0.889650452 0.51921782 0.038829524 0.226622899 2.572285397 0.03604042 0.010674983 20.09261814 -1.303036531 -0.109316499 AERLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AERLEK 6 1 F8VYN8;A0A0A0MS84;A0A338VFC5;Q9Y592-2;Q9Y592 F8VYN8 CEP83 Centrosomal protein of 83 kDa 0 81.784 0.055602 386480000 376190 389390 313470 380060 348430 366570 392070 424100 478470 499550 FALSE TRUE 361488.0789 378284.9785 370121.0021 399674.9421 359637.5674 373982.2966 396868.2699 415342.1868 424156.0915 465715.0335 0.77620015 0.812267054 0.794737072 0.85819635 0.772226665 0.803028182 0.852169763 0.891837619 0.910763151 1 18.82908793 1.303312835 0.797074112 0.997266649 0.800577463 0.87525032 0.023984285 0.18157154 0.255782529 0.022397781 0.008788529 20.10540542 -1.303312835 -0.196689186 IPSKEEEADMS(ph)SPTQR ddPTM_BT-474_Pertuzumab_2h_R1 1 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.5)S(0.5)PTQR 157.97 9.33E-09 793560000 397020 434560 375530 384760 458320 459460 389380 420050 358340 340600 TRUE FALSE 381504.0195 422166.7743 443396.6246 404617.5097 473062.279 468750.596 394145.3489 411375.8207 317662.7455 317530.8586 1.201470689 1.329529911 1.396389083 1.274262009 1.489815135 1.476236351 1.24128203 1.295545959 1.000415351 1 18.27653728 1.303596171 2.24059159 0.978579828 1.353600567 0.690965 0.090004994 0.164453775 1.386845018 0.08238312 0.024344985 20.11852656 -1.303596171 0.375020738 SMDS(ph)SDLSDGAVTLQEYLELK ddPTM_BT-474_Pertuzumab_2h_R1 1 SMDSSDLSDGAVTLQEYLELK 21 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.269)MDS(0.338)S(0.338)DLS(0.055)DGAVTLQEYLELK 174.47 1.91E-12 39323000 10742 10555 7644.2 9130.6 9126.7 8639.9 9336.7 12079 13474 15179 TRUE FALSE 10322.19076 10253.98173 9025.676984 9601.83136 9420.268594 8814.604698 9450.965328 11829.56443 11944.48801 14150.91281 0.729436391 0.724616275 0.637815885 0.678530883 0.66570042 0.622900078 0.66786966 0.835957693 0.844078977 1 13.7886075 1.304641695 1.284684442 0.983291442 0.672219397 0.86369567 0.041546966 0.140333456 0.449084169 0.040230102 0.012905625 20.16701843 -1.304641695 -0.311072045 S(ph)PGLVPPS(ph)PEFAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 2 S(1)PGLVPPS(1)PEFAPR;S(1)PGLVPPS(1)PEFAPR;S(1)PGLVPPS(1)PEFAPR;S(1)PGLVPPS(1)PEFAPR 164.01 6.13E-06 1665610000 1727420 1695440 1577660 1857290 1855760 1770840 1725880 1808240 1570340 1687360 TRUE FALSE 1659910.517 1647087.711 1862778.257 1953144.959 1915452.206 1806647.598 1747001.836 1770899.212 1392081.587 1573073.604 1.055202066 1.047050632 1.184164715 1.241610662 1.217649448 1.148482559 1.110565857 1.125757375 0.884943707 1 20.58515475 1.305379619 6.272733709 0.94363635 1.144526613 0.601357673 0.064740511 0.132806548 9.105221697 0.049455455 0.017502707 20.20131401 -1.305379619 0.200890263 EGAPIEPDPPVSHWKPEAVQYYEDGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EGAPIEPDPPVSHWKPEAVQYYEDGAR 27 1 Q96HS1;Q96HS1-2;F5GXG4 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 ;;; 117.82 0.00027583 784900000 1321770 1619420 1316980 2016620 1169200 1530120 1742500 1583880 1605600 1546120 FALSE TRUE 1270113.767 1573235.727 1554987.582 2120698 1206808.38 1561060.075 1763825.236 1551172.325 1423339.019 1441399.915 0.881166811 1.091463729 1.078803714 1.471276623 0.837247434 1.083016627 1.223689011 1.076156803 0.987469892 1 20.45903923 1.305533292 5.204898286 0.993594244 1.102370586 0.053833083 0.164741765 0.570569187 27.1895461 0.1177193 0.040227175 20.20846338 -1.305533292 0.108776342 DSSGWSSSK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSSGWSSSK 9 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;;; 162.97 0.00014743 374110000 425498 423874 361547 383741 406070 361365 439614 458388 525050 547550 FALSE TRUE 408869.0677 411785.5285 426886.5855 403545.919 419131.6103 368672.0479 444994.1276 448922.1276 465448.5252 510463.9508 0.800975401 0.806688754 0.836271758 0.790547341 0.821079745 0.722229351 0.871744473 0.879439433 0.911814682 1 18.96144956 1.305895458 1.042050067 0.992898519 0.800739741 0.776389881 0.034254535 0.208756617 0.465555763 0.031384582 0.010795585 20.22532261 -1.305895458 -0.192158778 AASDPLLSS(ph)VSPAVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.021)S(0.937)VS(0.042)PAVSK 276.67 2.77E-35 670010000 629970 590990 582060 596320 542350 606520 620710 657680 798500 778630 TRUE FALSE 605350.0759 574135.5438 687251.1899 627096.1467 559795.1803 618784.25 628306.4347 644098.6782 707857.6276 725892.6966 0.833938788 0.79093721 0.946766916 0.863896482 0.771181723 0.852445896 0.865563791 0.887319409 0.975154635 1 19.46939678 1.306109779 1.711137301 1.003044139 0.844811343 0.616406118 0.04426145 0.232174514 1.215226706 0.041560614 0.012572053 20.23530613 -1.306109779 -0.158232796 S(ph)PQVLGSSLSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQVLGSSLSVR 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 S(1)PQVLGSSLSVR;S(1)PQVLGSSLSVR 83.856 0.013179 261770000 52654 51636 45000 54631 60816 53090 56157 55328 38819 51499 TRUE FALSE 50596.22347 50163.39184 53132.50102 57450.51246 62772.20187 54163.51617 56844.26616 54185.45747 34412.42986 48010.92686 1.053848088 1.044832814 1.106675178 1.196613276 1.307456572 1.128149772 1.183986019 1.128606778 0.716762456 1 15.55107517 1.306365601 8.659911477 0.859600231 1.147648708 0.588540804 0.095435086 0.167889361 19.29038805 0.064533988 0.02348125 20.24722928 -1.306365601 0.288048478 LKETAESVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKETAESVLK 10 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 105.25 0.0038641 0 2645200 2457400 2030400 2079200 2307500 2078880 2494100 2550900 2822900 2911500 FALSE TRUE 2541822.66 2387317.358 2397338.446 2186507.761 2381722.833 2120916.378 2524623.542 2498223.024 2502456.227 2714301.512 0.93645553 0.879532855 0.883224813 0.805550803 0.877471726 0.781385697 0.930119049 0.920392599 0.921952191 1 21.37214956 1.30643999 1.025704371 0.990171096 0.863685712 0.443769687 0.045318682 0.430938996 0.93503495 0.04211034 0.014578819 20.25069767 -1.30643999 -0.126485384 S(ph)PLAQMEEERR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 1 S(1)PLAQMEEERR;S(1)PLAQMEEERR;S(1)PLAQMEEERR 144.38 2.25E-05 1930290000 342329 331083 273437 298815 305281 303868 288744 335696 299837 295297 TRUE FALSE 328950.4042 321640.837 322853.1485 314236.878 315100.6406 310012.4192 292277.7354 328763.7603 265800.7608 275296.2712 1.194895967 1.168344328 1.172747989 1.141449816 1.14458739 1.126104679 1.061684324 1.194217992 0.965508031 1 18.07062554 1.306716469 0.307277395 0.974767235 1.195431119 0.573460488 0.050129344 1.193344613 0.400073494 0.101441964 0.077007523 20.2635937 -1.306716469 0.220663884 YQEVDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 YQEVDRR 7 1 Q96MU7-2;Q96MU7 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ; 128.61 0.0059987 756320000 440990 525750 387810 435430 497780 471290 519870 486260 461510 476500 FALSE TRUE 423755.6233 510756.1248 457895.8938 457902.5945 513791.5458 480819.8067 526232.3246 476218.5611 409121.3196 444226.2306 0.953918508 1.149765794 1.030771851 1.030786935 1.156598846 1.082375991 1.184604349 1.072018103 0.920975151 1 18.76093506 1.306842306 7.032680961 0.961308729 1.088659914 0.34125655 0.06762219 0.201305414 16.56832047 0.044280018 0.015900247 20.26946592 -1.306842306 0.127351185 KLENLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLENLK 6 1 P39687;H0YN26 P39687;REV__Q9Y2X3 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 81.784 0.097755 1525800000 1306900 1365400 1137900 1183700 1228600 1189100 1413900 1278700 1324100 1237700 FALSE TRUE 1255824.903 1326460.129 1343543.842 1244790.899 1268119.035 1213144.417 1431203.731 1252294.398 1173793.719 1153869.477 1.088359584 1.149575542 1.164381128 1.078796973 1.099014282 1.051370576 1.240351496 1.085299875 1.017267328 1 20.13804861 1.306853535 3.972893265 1.005656593 1.124077908 0.449291973 0.05046664 0.18947282 5.086736435 0.039450524 0.012589338 20.26999001 -1.306853535 0.118421315 NQS(ph)LVEENEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NQSLVEENEK 10 0 O95239;O95239-2;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 1 NQS(1)LVEENEK 88.092 0.012376 0 261060 244550 205710 220760 224490 246440 217880 244630 326660 270460 TRUE FALSE 250857.4866 237575.6734 242886.373 232153.4501 231710.9247 251423.1856 220546.4806 239578.305 289578.9263 252141.5033 0.994907555 0.942231526 0.963293904 0.920726842 0.918971775 0.997151133 0.874693288 0.950174017 1.148477829 1 17.94387408 1.306922484 9.715824593 1.073848935 0.94248953 0.537512343 0.047810433 0.210973581 28.12601682 0.029331378 0.010705845 20.27320839 -1.306922484 -0.131359405 KTKPPRPDS(ph)PATTPNISVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTKPPRPDSPATTPNISVK 19 3 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 KTKPPRPDS(1)PATTPNISVK;KT(0.001)KPPRPDS(0.999)PATTPNISVK 173.55 3.43E-11 3770100000 2010430 1776870 1416900 1261010 1453870 1812870 1573510 1720460 2148570 1975680 TRUE FALSE 1931860.173 1726195.407 1672965.349 1326090.877 1500635.049 1849527.473 1592767.086 1684931.9 1904673.341 1841865.434 1.048860648 0.937199524 0.908299444 0.71997164 0.814736528 1.004159935 0.864757575 0.914796417 1.034100161 1 20.81273623 1.307960064 5.067667987 1.016962645 0.895322208 0.217919029 0.087318555 0.295128779 13.08773538 0.067455301 0.022957739 20.32170134 -1.307960064 -0.121640437 QEAEDLSLSAPSSPEIS(ph)PQSSPRPHRPNNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEAEDLSLSAPSSPEISPQSSPRPHRPNNDR 31 2 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 QEAEDLSLS(0.001)APS(0.115)S(0.115)PEIS(0.621)PQS(0.121)S(0.027)PRPHRPNNDR 82.157 0.00056804 139850000 20781 23502 21516 29548 28027 27355 24718 26263 22274 25112 TRUE FALSE 19968.85555 22831.74597 25404.41982 31072.97582 28928.51391 27908.13684 25020.50628 25720.65987 19745.5489 23411.14187 0.852963758 0.975251275 1.085142278 1.327272971 1.235672914 1.19208781 1.068743525 1.098650378 0.84342528 1 14.51490768 1.308764791 7.398036422 0.92285733 1.112456055 0.238657872 0.129968533 0.308537739 26.85044327 0.096246129 0.03473422 20.35939138 -1.308764791 0.189598726 SVQEGENPDDGVRGS(ph)PPEDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVQEGENPDDGVRGSPPEDYR 21 1 H7C5M1;Q5TCT4;A2A2V2;P42696-2;P42696 H7C5M1 RBM34 RNA-binding protein 34 1 SVQEGENPDDGVRGS(0.999)PPEDY(0.001)R 64.779 0.014907 105100000 49255 48586 45023 33539 53789 46662 45250 46906 44574 42368 TRUE FALSE 47330.06015 47200.37485 53159.65763 35269.95181 55519.17203 47605.53761 45803.78304 45937.37471 39514.14639 39498.37762 1.198278587 1.194995281 1.345869396 0.892946848 1.405606391 1.205252987 1.159637074 1.16301928 1.000399226 1 15.26950578 1.309031779 2.36255356 0.988510348 1.201936394 0.277814748 0.126588516 0.363359971 3.382321871 0.106584089 0.031564318 20.37191139 -1.309031779 0.213426046 VFKEENQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFKEENQK 8 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 143.04 0.00055437 779890000 832350 721350 671930 635130 754160 667260 786460 836160 1051600 1069600 FALSE TRUE 799820.8418 700777.8043 793362.698 667909.1354 778418.2413 680752.4544 796084.9327 818893.0038 932226.7767 997155.0393 0.802102793 0.702777178 0.795626223 0.669814732 0.780639129 0.682694694 0.798356225 0.821229369 0.934886492 1 19.92745831 1.309513121 1.3589252 1.000387214 0.739550949 0.796323071 0.044948125 0.148383512 0.522584646 0.037231831 0.011784497 20.39450273 -1.309513121 -0.260836265 EALASLPSS(ph)PGLLQSLLER ddPTM_BT-474_Pertuzumab_2h_R1 1 EALASLPSSPGLLQSLLER 19 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 EALASLPS(0.038)S(0.962)PGLLQSLLER 180.78 3.45E-14 134170000 245110 250070 223100 270620 259050 268860 243170 260510 258590 243120 TRUE FALSE 235530.8302 242938.2484 263419.1328 284586.7306 267382.5785 274296.5334 246145.9872 255130.3775 229235.9473 226653.2659 1.039168041 1.071849759 1.162211945 1.255603927 1.179698768 1.210203314 1.086002385 1.125641744 1.011394857 1 17.79012742 1.310003727 1.649734314 0.993611035 1.151562583 0.429593621 0.06217285 0.353523517 1.737464811 0.061650354 0.01877209 20.41755465 -1.310003727 0.157951549 RVGWT(ph)ELLPPSLGLEIEAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVGWTELLPPSLGLEIEAIR 20 1 M0QZW6;Q8N6L0 M0QZW6 CCDC155 Protein KASH5 1 RVGWT(0.5)ELLPPS(0.5)LGLEIEAIR 53.188 0.089193 87382000 11601 6187.8 6128.1 8591.1 7785 11238 7511.8 5802.8 6973.5 3143.5 TRUE FALSE 11147.62009 6011.330002 7235.583989 9034.487701 8035.411595 11465.24006 7603.731655 5682.970152 6181.897515 2930.587945 3.803885194 2.051236856 2.468987154 3.08282429 2.741911093 3.912266165 2.594609613 1.939191131 2.109439345 1 11.51697442 1.310339581 1.171874589 1.144360749 2.936146525 0.53970899 0.566475297 0.341277487 0.931204444 0.525583828 0.173513878 20.43335033 -1.310339581 1.791785776 VDLVDENFTELRGEIAGPPDTPYEGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDLVDENFTELRGEIAGPPDTPYEGGR 27 1 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 217.84 3.07E-34 394510000 184816 193802 116159 131830 174189 187296 141891 145807 164526 124568 FALSE TRUE 177593.1864 188274.9567 137151.5152 138633.7621 179791.9474 191083.2534 143627.5045 142796.0345 145849.6982 116130.8984 1.529250086 1.621230519 1.181007958 1.193771546 1.548183557 1.645412686 1.236772525 1.22961276 1.255907775 1 16.82539235 1.310363926 0.906089777 1.024788043 1.435041382 0.407347726 0.162128953 0.566245848 0.991086842 0.162331564 0.059477916 20.43449579 -1.310363926 0.410253339 EESQDTLTHSS(ph)PSFNLDTLLVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EESQDTLTHSSPSFNLDTLLVPK 23 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 EES(0.001)QDT(0.004)LT(0.02)HS(0.113)S(0.859)PS(0.004)FNLDTLLVPK 95.794 0.0024602 40213000 26429 25644 19795 24966 22226 24077 30262 30794 36161 41638 TRUE FALSE 25396.12546 24912.65823 23372.39684 26254.49825 22940.91948 24563.85344 30632.35541 30158.09314 32056.15488 38817.82117 0.654238819 0.641784043 0.60210481 0.676351672 0.590989365 0.632798356 0.789131241 0.776913599 0.825810257 1 15.24443152 1.310499856 0.664051931 0.994555438 0.623883477 0.902033599 0.038090313 0.186832549 0.193647538 0.037402426 0.016638689 20.44089258 -1.310499856 -0.370671961 GPTSTSIDNIDGT(ph)PVRDER ddPTM_BT-474_Pertuzumab_2h_R1 6 GPTSTSIDNIDGTPVRDER 19 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER 253.09 4.61E-30 3888970000 2967454 3193266 2403529 3073503 2917093 3153527 2838226 3048348 2904195 2917368 TRUE FALSE 2851482.617 3102197.18 2837900.157 3232126.858 3010923.946 3217293.477 2872961.059 2985398.549 2574522.959 2719772.067 1.048427055 1.140609251 1.043433084 1.188381518 1.107050103 1.182927612 1.056324202 1.097664979 0.946595117 1 21.37505432 1.310602007 4.738545332 0.973462046 1.110657867 0.533860132 0.050234518 0.140646935 5.365736071 0.035619197 0.011953938 20.44570109 -1.310602007 0.137195822 DEDFVKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEDFVKPK 8 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 79.906 0.025615 0 239860 229790 261870 287150 259090 248280 279070 320080 409830 428650 FALSE TRUE 230486.006 223236.6142 309195.7343 301969.8459 267423.8651 253300.3917 282485.3421 313470.2361 363307.8165 399617.1537 0.576767048 0.558626205 0.773729885 0.755647857 0.669200165 0.633857654 0.706889931 0.784426377 0.909139693 1 18.60825899 1.310757351 1.363631041 0.999434328 0.6653326 0.769072385 0.063820935 0.198375991 0.702704038 0.063931555 0.020224422 20.45301569 -1.310757351 -0.334101728 CNVWILDGDLYHK ddPTM_BT-474_Pertuzumab_2h_R1 1 CNVWILDGDLYHK 13 0 O43237;B4E2E0;Q9Y6G9;C9JGM7;C9JLW1 O43237;Q9Y6G9 DYNC1LI2;DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 2;Cytoplasmic dynein 1 light intermediate chain 1 0 125.22 0.00020273 444820000 528490 513770 456840 449450 521660 543060 541100 507580 675070 626430 FALSE TRUE 507836.0265 499117.7826 539401.1504 472646.1684 538439.6677 554041.0453 547722.1437 497098.2956 598438.8837 584001.3381 0.869580245 0.854651779 0.92362999 0.809323776 0.92198362 0.948698246 0.937878234 0.851193761 1.024721768 1 19.15561215 1.310787548 0.262300598 1.023481947 0.848097971 0.424411969 0.049157649 2.077589286 0.571246528 0.143748595 0.114482262 20.45443782 -1.310787548 -0.175383976 TENDHINLK ddPTM_BT-474_Pertuzumab_2h_R1 4 TENDHINLK 9 0 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 ;;; 160.36 6.54E-05 4970730000 9773700 9137900 8132700 8721100 9480000 9049900 9085000 9793900 11779400 11206100 FALSE TRUE 9391732.999 8877296.039 9602459.801 9171197.016 9784932.81 9232895.179 9196184.948 9591652.542 10442251.9 10447100.87 0.898979834 0.849737755 0.919150674 0.877870055 0.936617052 0.883775824 0.880261909 0.918116199 0.999535855 1 23.31659931 1.311523939 3.210702398 1.003508325 0.892885301 0.78029155 0.022441356 0.103180651 1.756490585 0.018251008 0.005574002 20.48914985 -1.311523939 -0.110623024 RPAEDYVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPAEDYVPR 9 1 Q969E4;Q5H9L2 Q969E4 TCEAL3;TCEAL5 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5 0 ; 112.36 0.0031678 504080000 179934 218070 148459 209685 202671 194321 190036 199296 177940 191737 FALSE TRUE 172901.9804 211850.8571 175288.8438 220506.868 209190.0968 198250.3038 192361.7174 195180.468 157740.9972 178750.4822 0.967281197 1.185176423 0.980634243 1.233601528 1.170291091 1.109089616 1.076146565 1.091915756 0.882464737 1 17.44758761 1.312090045 6.665321696 0.942398219 1.106357288 0.371155803 0.083449947 0.187822485 13.18412622 0.054413165 0.019469015 20.51587504 -1.312090045 0.163959069 FTDLLQLVEFHQLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTDLLQLVEFHQLNR 15 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 264 4.26E-25 2676200000 1331550 1389120 1257140 1538270 1504370 1315950 1513380 1469600 1403420 1457380 FALSE TRUE 1279511.554 1349503.658 1484333.163 1617660.299 1552759.427 1342559.411 1531901.197 1439252.246 1244109.645 1358670.355 0.941738038 0.993253186 1.092489549 1.190620148 1.142852217 0.988142125 1.127500274 1.059309377 0.915681748 1 20.37376404 1.312705543 7.175732426 0.958661587 1.072275074 0.250943324 0.075136546 0.283176381 22.22142741 0.054001626 0.019462941 20.5449715 -1.312705543 0.113613487 EQAEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EQAEEER 7 0 Q9UII2;A0A0B4J230;Q9UII2-3;Q9UII2-2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 138.83 0.006393 140870000 202500 293310 199050 455340 254620 277360 381550 291240 227140 235610 FALSE TRUE 194586.0761 284945.086 235022.7628 478840.152 262810.0835 282968.4092 386219.523 285225.7922 201356.0194 219651.9248 0.885883774 1.297257405 1.069978162 2.179995246 1.196484318 1.288258272 1.758325238 1.298535364 0.916705008 1 17.74485962 1.312944918 5.130101508 0.959012609 1.396874141 0.18910435 0.343543627 0.303648218 13.31721534 0.247070817 0.084672029 20.55629861 -1.312944918 0.437861531 TALPTSGSS(ph)AGELELLAGEVPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPT(0.022)S(0.028)GS(0.164)S(0.786)AGELELLAGEVPAR;TALPTS(0.001)GS(0.031)S(0.967)AGELELLAGEVPAR 139.11 1.08E-06 103037000 71738 66762 65424 83802 69440 77503 68828 74623 67640 68806 TRUE FALSE 68934.39965 64858.01313 77247.57215 88127.03126 71673.60066 79070.16376 69670.33765 73082.00897 59961.79077 64145.70833 1.074653339 1.011104481 1.204251604 1.373857013 1.117356134 1.23266491 1.08612625 1.139312526 0.934774786 1 15.96906512 1.313611706 4.322530678 0.967045791 1.158925225 0.37636983 0.096174736 0.226810077 7.101430352 0.078000827 0.025632303 20.5878837 -1.313611706 0.191879433 DDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 7 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.001)HS(0.999)AEDS(1)EDEKEDHK;DDSHS(1)AEDS(1)EDEKEDHK;DDS(0.014)HS(0.986)AEDS(1)EDEKEDHK;DDS(0.136)HS(0.864)AEDS(1)EDEKEDHK;DDS(0.012)HS(0.988)AEDS(1)EDEKEDHK;DDS(0.003)HS(0.997)AEDS(1)EDEKEDHK;DDS(0.008)HS(0.992)AEDS(1)EDEKEDHK 241.71 2.99E-20 6063252000 5273567 3394722 3849304 2915363 3761448 2929854 4140878 3936734 6287104 4443341 TRUE FALSE 5067470.171 3297907.852 4544958.86 3065825.234 3882438.391 2989097.655 4191555.304 3855439.067 5573418.312 4142389.556 1.223320526 0.796136579 1.09718287 0.740110314 0.937246084 0.721587773 1.011868934 0.93072827 1.345459725 1 21.9820318 1.313872115 10.80054204 1.172283909 0.924114426 0.248399323 0.166827924 0.483767739 66.0867094 0.101764551 0.037199318 20.60023217 -1.313872115 -0.248169483 YSDEEEDLRTELNLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSDEEEDLRTELNLLR 16 1 Q7Z2Y5;F5H049;Q7Z2Y5-3 Q7Z2Y5 NRK Nik-related protein kinase 0 ; 133.71 2.94E-05 51362000 45102 55295 49737 61331 49560 58844 60532 60101 65031 77432 FALSE TRUE 43339.36398 53718.04074 58725.58229 64496.30026 51154.14241 60033.866 61272.80872 58859.89335 57648.95351 72187.46167 0.60037246 0.744146414 0.813514992 0.893455716 0.708629189 0.831638412 0.848801264 0.815375579 0.798600646 1 16.13946065 1.314430962 0.037042077 1.700264289 2.79E-14 0.560402926 0.067471826 62.63282335 2.132185913 49.40431034 47.4262561 20.62675747 -1.314430962 -1.700264289 NDEWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 NDEWAR 6 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 109.63 0.068384 625140000 622050 557260 467630 530450 530390 511530 548880 566110 667870 609940 FALSE TRUE 597739.5983 541367.4904 552141.1434 557826.5881 547450.476 521873.4871 555597.3576 554419.6307 592056.1975 568628.2205 1.051195802 0.952058781 0.971005524 0.981004051 0.962756431 0.91777627 0.977083686 0.975012514 1.041200869 1 19.11712617 1.315132783 7.144387033 1.020247836 0.970894011 0.246712914 0.032699873 0.261374522 19.73822771 0.021635996 0.007800164 20.6601173 -1.315132783 -0.049353826 ALVLDCHYPEDEVGQEDEAESDIFSIR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALVLDCHYPEDEVGQEDEAESDIFSIR 27 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;;;; 272.44 8.70E-61 1944280000 637783 946047 632565 1369053 605171 793178 1094933 842909 783611 713497 FALSE TRUE 612857.7353 919066.6658 746883.5668 1439709.989 624636.8748 809216.6026 1108333.118 825502.6346 694658.7644 665171.2127 0.921353365 1.381699401 1.122844093 2.16442017 0.939061798 1.216553854 1.666237348 1.241037824 1.04433077 1 19.34336621 1.315225299 3.923806544 1.014671916 1.354880821 0.118261723 0.344978096 0.447874908 11.4737243 0.263820181 0.084639531 20.66451893 -1.315225299 0.340208905 ISYT(ph)PPES(ph)PVPSYASSTPLHVPVPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 2 IS(0.126)Y(0.219)T(0.659)PPES(0.994)PVPS(0.001)YASSTPLHVPVPR;IS(0.136)Y(0.052)T(0.812)PPES(0.991)PVPS(0.007)YASSTPLHVPVPR;IS(0.186)Y(0.059)T(0.757)PPES(0.997)PVPS(0.001)YASSTPLHVPVPR 103.07 0.0084518 2712770000 256620 301113 325273 321750 305714 313614 299815 312970 273588 273519 TRUE FALSE 246591.0067 292525.5521 384057.0668 338355.5561 315547.5685 319955.49 303484.2257 306507.0601 242531.4372 254993.3145 0.967048909 1.147189104 1.506145632 1.326919322 1.237473889 1.254760308 1.190165422 1.202019985 0.951128612 1 17.9600999 1.315226549 3.589392364 0.971570181 1.241623817 0.378652237 0.129190892 0.245075048 5.231378244 0.110718572 0.034739234 20.66457837 -1.315226549 0.270053636 GS(ph)PHSEGGKRS(ph)PEPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPHSEGGKRSPEPNK 16 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 GS(1)PHS(0.001)EGGKRS(0.999)PEPNK 126.02 3.96E-05 514690000 376070 298690 285390 216890 297280 286180 299260 310180 425810 346570 TRUE FALSE 361372.7686 290171.6536 336966.3215 228083.7189 306842.2812 291966.7557 302922.4334 303774.6746 377473.8339 323096.5052 1.118466968 0.898095922 1.042927782 0.705930628 0.949692356 0.903651853 0.937560229 0.940197959 1.168300578 1 18.30160562 1.315922532 8.604843576 1.083422595 0.931023951 0.230326921 0.10713178 0.328156693 32.25090204 0.068211115 0.0248442 20.69772118 -1.315922532 -0.152398643 KLCQPQSTGSLLGDPAASS(ph)PPGER ddPTM_BT-474_Pertuzumab_2h_R1 2 KLCQPQSTGSLLGDPAASSPPGER 24 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 KLCQPQSTGSLLGDPAAS(0.061)S(0.939)PPGER;KLCQPQSTGSLLGDPAAS(0.008)S(0.992)PPGER 179.85 2.25E-17 440060000 338210 336930 247660 294990 328120 360750 315700 326970 318560 313860 TRUE FALSE 324992.3793 327321.0863 292417.6712 310214.4693 338674.2778 368044.6122 319563.631 320217.9552 282398.4043 292601.9826 1.110697803 1.11865642 0.999370095 1.060192643 1.157457221 1.257833624 1.092144449 1.094380675 0.96512813 1 18.15858002 1.316552256 4.193155352 0.982015436 1.112906747 0.399612931 0.0632307 0.231626953 6.758049744 0.053591329 0.017519218 20.72775448 -1.316552256 0.130891311 TVS(ph)PQSNSSRPTCAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSPQSNSSRPTCAR 15 1 Q9H7N4;M0R3G4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 T(0.056)VS(0.936)PQS(0.009)NSSRPTCAR;TVS(0.875)PQS(0.125)NSSRPTCAR 153.06 1.65E-06 293140000 189136 185612 157600 185653 190619 182919 190924 183467 186043 172048 TRUE FALSE 181744.356 180318.5275 186081.8258 195234.5736 196750.4333 186617.7475 193260.585 179678.3423 164924.1786 160395.0357 1.13310462 1.12421514 1.160147039 1.217210824 1.226661613 1.1634883 1.204903781 1.120223837 1.028237426 1 17.29126996 1.316905798 2.437905131 1.001837957 1.176059988 0.799776212 0.032071936 0.129403473 1.279325307 0.031457568 0.009360223 20.74463503 -1.316905798 0.174222031 SIYDDISS(ph)PGLGS(ph)TPLTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 SIYDDIS(0.11)S(0.89)PGLGS(0.544)T(0.449)PLT(0.004)S(0.004)R 88.133 0.0037352 0 41922 48705 40370 44534 41935 45346 36222 47126 35599 36214 TRUE FALSE 40283.64189 47315.98109 47665.75703 46832.40508 43283.87736 46262.92719 36665.29567 46152.83163 31557.95076 33761.19352 1.193193655 1.401490177 1.411850472 1.387166749 1.282060047 1.370298925 1.086018942 1.367037916 0.934740377 1 15.04307829 1.317155461 1.074411238 0.966104362 1.338898059 0.546034043 0.114486386 0.335762553 0.787197945 0.100592905 0.03428372 20.75656391 -1.317155461 0.372793697 TGVELGKPTHFTVNAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGVELGKPTHFTVNAK 16 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 191.51 4.11E-10 2333400000 4998300 5414000 4666600 4799600 4730500 5395300 5384300 5548100 7061900 6780200 FALSE TRUE 4802960.91 5259598.021 5509958.428 5047307.931 4882660.829 5504396.663 5450194.674 5433529.796 6260262.718 6320971.015 0.759845425 0.832087034 0.871694937 0.79850199 0.772454235 0.870815046 0.862240099 0.859603656 0.990395732 1 22.59171477 1.317626616 1.376981122 1.010589013 0.819964538 0.763418926 0.037388381 0.187289201 0.674128845 0.034717169 0.010975509 20.77909439 -1.317626616 -0.190624476 EEYEGPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEYEGPNK 8 0 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 95.531 0.021364 0 111090 102540 97752 102440 104090 101540 118560 123030 129860 141780 FALSE TRUE 106748.48 99615.6596 115417.9609 107726.9407 107438.1494 103593.2084 120010.9727 120489.3875 115118.8372 132177.1143 0.807616966 0.753652855 0.873206844 0.815019614 0.812834733 0.783745423 0.907955763 0.911575261 0.870943792 1 17.01211288 1.31773954 0.424408249 1.004237435 0.792481803 0.692620224 0.038637686 0.576854074 0.300151831 0.049141921 0.031577037 20.78449801 -1.31773954 -0.211755632 VTTEIQLPSQS(ph)PVEEQSPASLSSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 VTTEIQLPSQSPVEEQSPASLSSLR 25 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 VTTEIQLPS(0.036)QS(0.962)PVEEQS(0.002)PASLSSLR;VTTEIQLPS(0.001)QS(0.999)PVEEQSPASLSSLR;VTTEIQLPS(0.001)QS(0.999)PVEEQSPASLSSLR 209.4 1.49E-25 481030000 403961 425392 417040 556224 518951 509664 475066 487071 407321 438252 TRUE FALSE 388173.7575 413260.2367 492408.405 584930.7873 535643.5302 519969.7553 480879.9998 477012.8136 361083.6277 408568.8017 0.950081739 1.011482607 1.205203146 1.431657985 1.311024063 1.27266143 1.176986588 1.167521386 0.883776799 1 18.64021952 1.318452707 5.196014445 0.943322967 1.200616008 0.35777101 0.133164894 0.226212195 9.789102651 0.106866454 0.036871299 20.81865685 -1.318452707 0.257293041 KGLTPSQIGVILR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGLTPSQIGVILR 13 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 172.58 1.07E-06 0 587280 718320 568940 516780 621270 716990 638180 646900 668600 638250 FALSE TRUE 564328.4483 697834.2169 671760.114 543451.0777 641253.7138 731488.029 645990.2377 633541.2889 592703.331 595020.759 0.948418084 1.172789699 1.128969206 0.913331291 1.077699734 1.229348755 1.085660001 1.064738128 0.996105299 1 19.18258048 1.318494563 3.340310939 0.995865126 1.083681167 0.114149293 0.088676037 0.523802553 9.6220963 0.074486789 0.023068542 20.82066341 -1.318494563 0.087816042 SFLSEPSS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 6 SFLSEPSSPGR 11 0 Q69YN4-3;Q69YN4;H0YC41 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR 240.94 1.10E-15 12953300000 9341000 10319000 8023900 10069100 10050500 10240500 9841100 10086500 9849400 9926600 TRUE FALSE 8975943.393 10024712.22 9473997.221 10588767.46 10373783.46 10447569.93 9961538.326 9878210.25 8731337.404 9254262.54 0.969925302 1.083253493 1.023744159 1.14420435 1.120973542 1.128946783 1.076427028 1.067422737 0.943493592 1 23.1416866 1.319357134 5.542258255 0.972531982 1.081111648 0.410939688 0.050244186 0.182327011 8.761035012 0.036244013 0.012669947 20.86205728 -1.319357134 0.108579666 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPT(ph)SPVRTPLEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVPLFPHPPVPSLSTSESKPPPQPSPPTSPVRTPLEVR 38 2 E9PKC0;Q6IQ23;Q6IQ23-2;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 2 TVPLFPHPPVPSLSTSESKPPPQPS(0.981)PPT(0.49)S(0.464)PVRT(0.064)PLEVR 67.58 0.087807 484760000 53381 60655 43561 42482 59664 68206 57007 51272 46511 39949 TRUE FALSE 51294.8115 58925.17879 51433.44171 44674.50111 61583.14675 69585.17205 57704.66872 50213.21528 41231.26627 37243.21865 1.377292655 1.582172028 1.381014949 1.199533841 1.653539865 1.868398452 1.549400691 1.348251228 1.107081175 1 15.18469014 1.320103782 2.284134906 1.013462796 1.517847589 0.540398054 0.169929587 0.244107149 2.139208688 0.165803601 0.04935872 20.89795461 -1.320103782 0.504384793 YEDKPEPEVDALGS(ph)PPALLK ddPTM_BT-474_Pertuzumab_2h_R1 2 YEDKPEPEVDALGSPPALLK 20 1 Q68DQ2 Q68DQ2 CRYBG3 Very large A-kinase anchor protein 1 YEDKPEPEVDALGS(1)PPALLK;YEDKPEPEVDALGS(1)PPALLK 148.85 6.40E-08 247770000 641590 584570 559370 558290 623770 629120 580620 601780 619400 562550 TRUE FALSE 616515.9535 567898.636 660460.6021 587103.4138 643834.1285 641841.2374 587725.8012 589353.0327 549088.3087 524447.9874 1.175552139 1.082850253 1.259344335 1.119469286 1.227641528 1.223841549 1.120656033 1.123758784 1.046983346 1 19.00044017 1.320494334 1.312296542 1.001283284 1.177561461 0.588209727 0.05083514 0.272536206 0.902497095 0.045097188 0.014439546 20.9167562 -1.320494334 0.176278177 GVEGLIDIENPNR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVEGLIDIENPNR 13 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;; 187.42 1.62E-05 600690000 800900 926220 811790 938000 907270 962900 898790 938310 899800 945870 FALSE TRUE 769599.9426 899805.1125 958498.5112 986410.2924 936453.1635 982370.4977 909789.6609 918933.5706 797658.4763 881805.3824 0.872754871 1.020412361 1.086972852 1.118625847 1.06197261 1.11404457 1.031735209 1.042104742 0.904574288 1 19.75010076 1.320889246 7.606707506 0.952941489 1.049138794 0.21630116 0.068895346 0.312068532 24.07704129 0.047450179 0.017200441 20.93578483 -1.320889246 0.096197305 GASDEEIKR ddPTM_BT-474_Pertuzumab_2h_R1 4 GASDEEIKR 9 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;; 132.01 0.00050837 3755660000 4480380 4548890 3780610 4342190 3996350 4208030 4497910 5023860 5904200 6127600 FALSE TRUE 4305281.796 4419160.111 4463850.326 4566290.946 4124896.227 4293119.25 4552956.768 4920115.535 5233979.968 5712572.194 0.753650308 0.773584991 0.781408125 0.799340611 0.722073365 0.751521224 0.79700643 0.861278487 0.916221238 1 22.44570906 1.321466727 1.203578834 0.995259584 0.763901629 0.935041064 0.020776245 0.100830877 0.287467793 0.020508969 0.006731521 20.96364162 -1.321466727 -0.231357955 DTGSEVPSGSGHGPCT(ph)PPPAPANFEDVAPTGSGEPGAT(ph)RESPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTGSEVPSGSGHGPCTPPPAPANFEDVAPTGSGEPGATRESPK 43 1 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 2 DTGSEVPS(0.016)GS(0.018)GHGPCT(0.965)PPPAPANFEDVAPT(0.011)GS(0.009)GEPGAT(0.494)RES(0.486)PK 93.832 0.00011349 317280000 81969 76317 55197 63383 68315 76209 62836 79165 102770 99776 TRUE FALSE 78765.56086 74140.51388 65172.32575 66654.20423 70512.41402 77749.99819 63605.00576 77530.21509 91103.98045 93018.08265 0.84677687 0.79705485 0.700641466 0.716572545 0.758050607 0.835858964 0.683791839 0.833496164 0.979422257 1 16.50522358 1.322002015 3.116211187 0.998870372 0.762245625 0.753496395 0.051259704 0.117528312 1.874234465 0.043605731 0.013364262 20.98949621 -1.322002015 -0.236624747 TPVS(ph)PVKFS(ph)PGDFWGR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 2 T(0.022)PVS(0.978)PVKFS(1)PGDFWGR;T(0.442)PVS(0.558)PVKFS(1)PGDFWGR;T(0.011)PVS(0.989)PVKFS(1)PGDFWGR 143.47 8.02E-07 578836000 1292681 1164283 1100541 952571 1082860 1287611 1153318 1341782 1669020 1670170 TRUE FALSE 1242161.597 1131078.789 1299433.24 1001733.303 1117691.175 1313647.377 1167432.651 1314073.733 1479559.847 1557047.898 0.797767107 0.726425173 0.834549304 0.643354199 0.717827099 0.843678205 0.749773114 0.843952029 0.950233996 1 20.57038189 1.322670797 1.465378598 1.004135547 0.754080234 0.708157559 0.055534922 0.197090045 0.789534571 0.050158481 0.01565952 21.02184342 -1.322670797 -0.250055312 KGFIDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGFIDGR 7 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 72.547 0.082269 1270800000 3749100 4141300 3292600 4167000 3931200 4051500 3781700 4036900 3899500 3935600 FALSE TRUE 3602581.027 4023194.179 3887646.063 4382059.369 4057650.618 4133424.106 3827981.576 3953536.604 3456845.108 3669038.307 0.981887003 1.096525531 1.059581759 1.194334592 1.105916668 1.126568806 1.043320144 1.077540291 0.942166535 1 21.80697054 1.322955414 4.83877611 0.971718582 1.089694114 0.416258776 0.054032911 0.187192252 6.970584557 0.039908069 0.013598454 21.03562472 -1.322955414 0.117975532 AAIELPSLEVLS(ph)DQEEDREQCGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAIELPSLEVLSDQEEDREQCGVK 24 1 Q9BQI3-2;Q9BQI3 Q9BQI3-2 EIF2AK1 Eukaryotic translation initiation factor 2-alpha kinase 1 1 AAIELPS(0.005)LEVLS(0.995)DQEEDREQCGVK;AAIELPSLEVLS(1)DQEEDREQCGVK 270.88 4.14E-52 242310000 128053 119348 111044 119434 120435 131515 127043 138212 173284 169227 TRUE FALSE 123048.5472 115944.3119 131112.121 125598.0031 124308.9012 134174.3234 128597.7902 135357.8739 153613.5268 157765.1046 0.779947806 0.734917346 0.831059069 0.796107627 0.787936607 0.850468954 0.81512189 0.857970933 0.973685069 1 17.26741861 1.323960155 1.37850989 1.008250938 0.794845741 0.865482708 0.029298798 0.132953778 0.479183972 0.027633475 0.008747849 21.08434702 -1.323960155 -0.213405197 VS(ph)LQALEAEAEAGAETEAMLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSLQALEAEAEAGAETEAMLQR 22 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 VS(1)LQALEAEAEAGAETEAMLQR 129.32 9.87E-06 15661000 7474.3 7591.8 4355.9 7591.6 6795.1 4954.6 7145.9 6602.9 3649 5882.4 TRUE FALSE 7182.196093 7375.289297 5143.108026 7983.403386 7013.670563 5054.785407 7233.353662 6466.547808 3234.780818 5483.979809 1.309668588 1.344879003 0.937842262 1.455768195 1.278938072 0.921736692 1.318997136 1.179170608 0.589860089 1 12.42100754 1.32409498 7.609619554 0.798117763 1.218479027 0.453931172 0.186024346 0.180098937 13.3844274 0.119383654 0.043297733 21.09089358 -1.32409498 0.420361264 LAHECLSQSCDSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAHECLSQSCDSAK 14 0 B4DUA7;Q9NX70 B4DUA7 IXL;MED29 Mediator of RNA polymerase II transcription subunit 29 0 ; 157.23 5.35E-06 441530000 367477 334290 249464 271828 308047 281824 303096 318476 444920 353349 FALSE TRUE 353115.5926 324756.3765 294547.6941 285857.0757 317955.6115 287522.6744 306805.3795 311899.3593 394414.5469 329416.3575 1.071943103 0.985853826 0.894150176 0.867768309 0.965208935 0.872824521 0.931360488 0.94682414 1.197313181 1 18.32955267 1.324269945 8.862828574 1.09789271 0.937364066 0.431004814 0.071880248 0.221277779 20.18830098 0.047086382 0.017175512 21.09939218 -1.324269945 -0.160528644 REVLYDS(ph)EGLS(ph)GEER ddPTM_BT-474_Pertuzumab_2h_R1 2 REVLYDSEGLSGEER 15 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 REVLYDS(1)EGLS(1)GEER;REVLY(0.001)DS(0.999)EGLS(1)GEER 101.75 0.0057804 518960000 429120 477740 395920 472530 469280 504130 449550 476050 477870 459920 TRUE FALSE 412349.516 464115.323 467471.5512 496917.3299 484374.8174 514323.854 455051.7274 466219.4011 423624.201 428769.2087 0.961705056 1.082436223 1.09026381 1.158938934 1.129686571 1.199535423 1.061297589 1.087343474 0.98800052 1 18.70984178 1.324471758 2.557880357 0.990200236 1.103698597 0.310143501 0.06000589 0.334756088 3.630875981 0.054239197 0.016248792 21.10919921 -1.324471758 0.113498361 DQELYFFHELSPGSCFFLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQELYFFHELSPGSCFFLPK 20 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 135.73 6.65E-06 357080000 380850 338080 347010 443790 288670 303550 424700 434060 576970 599800 FALSE TRUE 365965.9609 328438.2894 409722.4262 466694.0551 297955.3327 309687.989 429897.6056 425096.5093 511474.7845 559175.0118 0.654474812 0.587362244 0.732726638 0.834611786 0.532848082 0.553830165 0.768806897 0.760220862 0.914695352 1 19.09294037 1.324935452 1.362505707 0.998014583 0.657926473 0.644388432 0.087679093 0.257410129 0.909109681 0.084542518 0.026844938 21.13174939 -1.324935452 -0.34008811 LAEAQIEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAEAQIEELR 10 0 Q9NR28-2;Q9NR28;Q9NR28-3 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 140.17 9.25E-05 131300000 160920 209010 169900 258920 170420 214210 195600 201350 185560 178980 FALSE TRUE 154631.0685 203049.2394 200604.7094 272282.8922 175901.7141 218541.473 197993.8113 197192.0521 164496.0067 166857.5252 0.926725171 1.2169019 1.202251497 1.631828663 1.054203063 1.309748977 1.186604027 1.181798974 0.985847097 1 17.34825723 1.325325422 2.667017735 0.98376797 1.229766801 0.207580263 0.171662209 0.409362213 4.810545839 0.14672 0.044127461 21.15073295 -1.325325422 0.245998831 S(ph)PHS(ph)KSPAEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPHSKSPAEQR 11 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 S(0.995)PHS(0.648)KS(0.357)PAEQR;S(0.999)PHS(0.597)KS(0.404)PAEQR 61.409 0.049784 190104000 615020 574190 447370 438930 510880 562320 569850 567480 739780 701600 TRUE FALSE 590984.3385 557814.6634 528219.7107 461583.2299 527312.9192 573690.4957 576823.9948 555761.3397 655803.2758 654080.0071 0.903535243 0.85282329 0.807576604 0.705698424 0.806190242 0.877095293 0.88188599 0.849684035 1.002634645 1 19.31910759 1.327039786 1.190378609 1.012894917 0.821226316 0.584042105 0.054521094 0.321998319 0.899666041 0.053845351 0.017757615 21.23438981 -1.327039786 -0.1916686 DELHIVEAEAMNYEGSPIK ddPTM_BT-474_Pertuzumab_2h_R1 17 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;;;;;;; 270.95 2.59E-39 18547566200 7343013.3 6758194.3 6556843.8 7345066.5 7077775.8 6962063.8 7698836.2 7891944.3 9767912.2 9587528.8 FALSE TRUE 7056040.222 6565457.216 7741811.331 7724146.262 7305438.886 7102841.5 7793056.86 7728972.892 8659099.757 8938156.935 0.789428992 0.73454262 0.866152987 0.864176622 0.817331687 0.794665114 0.871886332 0.864716624 0.968779114 1 23.09154594 1.327109587 1.163380007 1.005055597 0.813168089 0.745046865 0.038580192 0.227008132 0.609500568 0.037335058 0.012403499 21.23780293 -1.327109587 -0.191887508 VGMADANS(ph)PPKPLSKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 VGMADANSPPKPLSKPR 17 2 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 VGMADANS(1)PPKPLSKPR;VGMADANS(0.99)PPKPLS(0.01)KPR;VGMADANS(1)PPKPLSKPR 149.53 1.68E-07 3354060000 4196280 3650340 3689350 3648430 3816090 3708010 4397790 4835430 5269020 5966490 TRUE FALSE 4032284.738 3546235.877 4356097.614 3836725.91 3938838.001 3782988.503 4451611.47 4735576.681 4670902.939 5562374.318 0.724921501 0.637539956 0.783136367 0.689764063 0.708121708 0.680103187 0.800307785 0.851358864 0.839731861 1 22.4072694 1.327520099 0.69911315 0.993085305 0.697119623 0.824177194 0.04263323 0.238119385 0.267486415 0.039857136 0.017156415 21.25788724 -1.327520099 -0.295965682 GLLPGLLPAPADKLT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLPGLLPAPADKLTPK 17 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GLLPGLLPAPADKLT(1)PK;GLLPGLLPAPADKLT(1)PK 146.78 6.86E-07 876580000 1531480 1182930 1283070 957860 1173760 1399590 1314330 1474070 1696760 1776620 TRUE FALSE 1471628.068 1149193.995 1514949.291 1007295.269 1211515.056 1427890.669 1330415.164 1443629.939 1504150.918 1656287.945 0.888509799 0.693837082 0.914665409 0.608164343 0.731464031 0.862102917 0.80325113 0.871605655 0.908145786 1 20.65952208 1.327794759 0.850104308 0.996235095 0.770392391 0.405290369 0.086736679 0.515302278 0.804442457 0.07743807 0.029455824 21.27133559 -1.327794759 -0.225842704 GTVTDFPGFDERADAETLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GTVTDFPGFDERADAETLR 19 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 217.88 3.19E-19 861520000 902020 1032390 690501 1006300 1050180 986520 788246 955230 895070 790583 FALSE TRUE 866768.0612 1002947.248 815289.8908 1058235.264 1083959.993 1006468.11 797892.7903 935504.1667 793465.406 737036.1092 1.176018448 1.360784411 1.106173606 1.435798396 1.47070134 1.365561467 1.08256947 1.269278608 1.076562459 1 19.49137578 1.328212915 0.993945267 1.004285011 1.31189193 0.407397589 0.122578627 0.495537796 1.012348 0.115314665 0.040652079 21.29182632 -1.328212915 0.307606919 S(ph)PMSTNSSVHTGSDVEQDAEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPMSTNSSVHTGSDVEQDAEKK 22 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 S(0.994)PMS(0.004)T(0.001)NSS(0.001)VHTGSDVEQDAEKK 130.21 6.57E-06 295520000 213500 240040 220060 173790 188930 253560 222500 236630 329010 283890 TRUE FALSE 205156.184 233194.2942 259829.7372 182759.3227 195007.105 258687.1569 225223.0216 231743.5078 291662.1641 264661.8774 0.775163337 0.881102698 0.981742213 0.690538904 0.736815997 0.977425081 0.850983994 0.875621038 1.102018043 1 18.01379087 1.328263725 5.211509105 1.049386174 0.846467778 0.44655947 0.091499689 0.183455585 7.538212002 0.066979612 0.023263749 21.29431748 -1.328263725 -0.202918396 S(ph)PDPFGAVAAQK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPDPFGAVAAQK 12 0 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK 196.7 2.14E-07 6419050000 4641860 4602240 5339410 6011700 5356960 4675620 5351130 5324670 4922940 5041410 TRUE FALSE 4460450.979 4470988.621 6304360.162 6321964.557 5529271.483 4770164.24 5416618.73 5214713.704 4364108.49 4699950.81 0.949042056 0.951284131 1.341367264 1.34511292 1.176453054 1.014939184 1.152484132 1.109525166 0.928543439 1 22.16421423 1.329113584 4.925928213 0.965372494 1.138075296 0.201107652 0.13211091 0.339082466 12.66235304 0.104854822 0.036022422 21.33602858 -1.329113584 0.172702802 TLSDPPS(ph)PLPHGPPNK ddPTM_BT-474_Pertuzumab_2h_R1 3 TLSDPPSPLPHGPPNK 16 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 TLS(0.001)DPPS(0.999)PLPHGPPNK;T(0.001)LS(0.001)DPPS(0.998)PLPHGPPNK;TLS(0.002)DPPS(0.998)PLPHGPPNK 101.92 0.0010029 1001830000 1453890 1655990 1202110 1492530 1387690 1575960 1396280 1430970 1386560 1245360 TRUE FALSE 1397070.371 1608762.787 1419358.018 1569559.652 1432326.309 1607826.991 1413368.092 1401419.969 1229163.522 1161010.658 1.203322607 1.385657208 1.22251937 1.351890822 1.233689199 1.38485119 1.217360136 1.207068996 1.058701325 1 20.14694979 1.329196263 1.446352159 0.997483918 1.295427552 0.718943596 0.06420116 0.17443068 0.682987206 0.052433482 0.0164436 21.3400908 -1.329196263 0.297943634 WLHEINQNCDDVCR ddPTM_BT-474_Pertuzumab_2h_R1 1 WLHEINQNCDDVCR 14 0 F5H157;Q15286-2;Q15286 F5H157 RAB35 Ras-related protein Rab-35 0 192.18 4.03E-07 298580000 135540 173420 113050 192450 127970 120370 178890 143610 143010 128370 FALSE TRUE 130242.947 168474.2314 133480.6498 202382.3676 132086.2713 122803.9639 181079.3093 140644.4033 126776.1043 119675.3856 1.088301879 1.407760089 1.11535592 1.691094343 1.103704581 1.026142204 1.513087328 1.175215794 1.05933316 1 16.86876693 1.329741123 3.49393465 1.021443514 1.279796791 0.193039164 0.2005996 0.369198705 7.353909955 0.155968304 0.04928494 21.36688058 -1.329741123 0.258353277 AASVAAATTS(ph)PTPR ddPTM_BT-474_Pertuzumab_2h_R1 6 AASVAAATTSPTPR 14 0 Q9Y2D9 Q9Y2D9 ZNF652 Zinc finger protein 652 1 AASVAAAT(0.001)T(0.379)S(0.62)PT(0.001)PR;AASVAAAT(0.011)T(0.029)S(0.943)PT(0.017)PR;AASVAAATT(0.001)S(0.994)PT(0.005)PR;AASVAAATT(0.019)S(0.981)PTPR;AASVAAATT(0.002)S(0.997)PT(0.001)PR;AASVAAATT(0.003)S(0.911)PT(0.086)PR 319.82 4.54E-56 11034060000 6782700 7028710 5858490 7440790 6758960 5844310 6400110 6561200 5095960 5286620 TRUE FALSE 6517624.585 6828258.073 6917249.464 7824810.064 6976368.087 5962485.952 6478436.461 6425708.927 4517487.985 4928552.519 1.322421656 1.385448983 1.403505276 1.587648713 1.415500405 1.2097844 1.314470412 1.303772031 0.916595282 1 22.23273257 1.330653081 3.379540846 0.952494356 1.377814449 0.752386468 0.094148848 0.123315456 2.300463831 0.084612591 0.026556062 21.41179521 -1.330653081 0.425320093 ERNEEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERNEEEAKR 9 2 Q96IZ7-2;Q96IZ7;C9J713;H7C5Q0 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 0 143.96 5.66E-05 66793000 85416 87364 71692 67456 80410 79084 71822 82850 111250 92076 FALSE TRUE 82077.84829 84872.46426 84648.33918 70937.41224 82996.46068 80683.13266 72700.97912 81139.11855 98621.3664 85839.61051 0.956176849 0.988733101 0.986122126 0.826394852 0.966878347 0.939928923 0.84693976 0.945240992 1.148902771 1 16.38935591 1.333076144 7.727016659 1.073188678 0.929416381 0.464260531 0.06128457 0.181707302 12.55999481 0.040484138 0.014710121 21.5315921 -1.333076144 -0.143772297 TAFQEALDAAGDKLVVVDFSATWCGPCK ddPTM_BT-474_Pertuzumab_2h_R1 2 TAFQEALDAAGDKLVVVDFSATWCGPCK 28 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 ; 196.15 5.32E-25 415500000 504801 442680 355547 377461 391899 408482 417841 437566 549420 482645 FALSE TRUE 485072.8188 430055.1998 419802.252 396941.8074 404504.7872 416741.7859 422954.6631 428530.1092 487052.145 449955.0243 1.078047344 0.955773748 0.932987142 0.882181076 0.898989378 0.926185426 0.9399932 0.952384319 1.082446286 1 18.77942128 1.333120331 6.472799542 1.040212374 0.940893841 0.340434267 0.052892239 0.217311831 11.90860906 0.037102071 0.013317779 21.53378295 -1.333120331 -0.099318533 MVIENDLSGLIDFTRLPS(ph)PTPENK ddPTM_BT-474_Pertuzumab_2h_R1 1 MVIENDLSGLIDFTRLPSPTPENK 24 1 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 MVIENDLS(0.018)GLIDFT(0.271)RLPS(0.574)PT(0.137)PENK 46.783 0.096941 350980000 84384 81099 65035 68235 73711 93041 67133 74081 73244 62182 TRUE FALSE 81086.17999 78786.13592 76788.2712 71756.61653 76081.98126 94922.35277 67954.59374 72551.20146 64929.64818 57970.35775 1.398752451 1.359076241 1.324612684 1.237815658 1.312429045 1.637429135 1.172230022 1.251522403 1.12004912 1 15.82302777 1.3340902 1.243911257 1.011821393 1.358890284 0.53483371 0.111928435 0.329019564 0.991051251 0.103140339 0.033626651 21.58192603 -1.3340902 0.347068891 LAIQGPEDSPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 LAIQGPEDS(0.497)PS(0.503)R 294 3.47E-36 2179400000 617060 609670 493770 641120 537290 588600 599590 607310 610760 614970 TRUE FALSE 592944.613 592282.8085 583005.2229 674208.28 554572.4208 600501.8953 606927.9618 594768.8363 541429.0853 573317.5341 1.03423422 1.033079879 1.016897597 1.175977081 0.967304134 1.04741589 1.058624454 1.037416093 0.94437908 1 19.12897488 1.334420855 6.202477563 0.972999179 1.04747742 0.254300436 0.050959252 0.260367483 13.35192532 0.033732113 0.012058869 21.59836393 -1.334420855 0.074478241 GRPVS(ph)PQSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GRPVSPQSR 9 1 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GRPVS(1)PQSR;GRPVS(0.999)PQS(0.001)R;GRPVS(1)PQSR;GRPVS(0.999)PQS(0.001)R 82.437 0.011177 705380000 134007 178157 152127 171306 172061 188132 170239 174064 156467 170521 TRUE FALSE 128769.8583 173076.1368 179619.7329 180147.1232 177595.4983 191936.1579 172322.4358 170469.5176 138705.5221 158971.4608 0.810018714 1.088724579 1.129886661 1.133204176 1.11715334 1.207362359 1.083983471 1.072327805 0.872518384 1 17.27840826 1.335543132 6.385125016 0.937840075 1.090016247 0.237623566 0.102309705 0.267633043 14.17266721 0.070077595 0.025136013 21.65424929 -1.335543132 0.152176173 RPGTQGHLGPEKEEEES(ph)DGEPEDSSTS ddPTM_BT-474_Pertuzumab_2h_R1 5 RPGTQGHLGPEKEEEESDGEPEDSSTS 27 2 Q8IYB7;H7C1Q8 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 1 RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.886)DGEPEDS(0.021)S(0.031)T(0.031)S(0.031);RPGTQGHLGPEKEEEES(0.996)DGEPEDS(0.001)S(0.001)T(0.001)S(0.001);RPGTQGHLGPEKEEEES(0.955)DGEPEDS(0.01)S(0.012)T(0.012)S(0.012);RPGTQGHLGPEKEEEES(1)DGEPEDSSTS 148.2 6.50E-08 3560210000 1815840 1577140 1304007 1348030 1582450 1565110 1587340 1630320 1975640 1808240 TRUE FALSE 1744874.965 1532161.511 1539670.072 1417601.99 1633350.941 1596757.597 1606766.342 1596653.322 1751373.63 1685766.294 1.035063384 0.90888133 0.913335424 0.840924388 0.968907106 0.947199859 0.953137067 0.947138004 1.038918405 1 20.68497311 1.335567297 4.57195703 1.018954282 0.935322686 0.311443245 0.047430402 0.240578423 7.765365223 0.035303638 0.011981082 21.65545419 -1.335567297 -0.083631597 EVLYDS(ph)EGLS(ph)GEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EVLYDSEGLSGEER 14 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 EVLY(0.001)DS(0.999)EGLS(1)GEER;EVLYDS(1)EGLS(1)GEER 156.64 8.06E-06 1277210000 972800 1026680 876820 970620 1049240 1041300 954370 997150 907600 876730 TRUE FALSE 934781.9005 997400.0916 1035280.879 1020713.815 1082989.757 1062355.799 966049.8655 976558.504 804573.053 817348.2962 1.143676331 1.220287723 1.266633678 1.248811332 1.325003995 1.299758994 1.181931705 1.194788695 0.984369891 1 19.64059146 1.335630361 2.314998082 0.980975776 1.246972572 0.779553722 0.051650919 0.132823746 1.199529165 0.047805215 0.014344906 21.65859903 -1.335630361 0.265996796 RDEFEFLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 RDEFEFLEK 9 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 ;; 168.22 9.52E-05 1827670000 2187730 2386900 1935670 2098640 2079610 2158150 2198390 2421560 2698570 2717200 FALSE TRUE 2102231.093 2318827.949 2285488.628 2206951.062 2146502.544 2201789.272 2225294.554 2371553.94 2392239.647 2533161.624 0.829884313 0.915388867 0.902227717 0.871223944 0.84736107 0.869186258 0.878465288 0.936203169 0.944369133 1 21.2725077 1.335970595 1.234468949 0.994201396 0.873579432 0.747192653 0.024346189 0.211312361 0.627929731 0.022894523 0.007484304 21.67557341 -1.335970595 -0.120621965 S(ph)PGETSKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPGETSKPR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PGETSKPR;S(1)PGETSKPR;S(1)PGETSKPR;S(1)PGETSKPR 117.14 0.00072709 1940940000 1105260 954760 1308840 1417500 1307070 1148580 1516500 1650580 1736180 2177640 TRUE FALSE 1062065.217 927531.1796 1545376.503 1490657.345 1349113.094 1171805.075 1535059.381 1616494.946 1539096.125 2030146.503 0.523147081 0.456878939 0.761214277 0.734260972 0.664539772 0.577202223 0.756132318 0.796245465 0.758120718 1 20.95315241 1.336025484 0.071846783 1.556903296 2.36E-18 0.691873922 0.081837368 12.02137389 0.813818989 8.771992272 8.178845804 21.67831308 -1.336025484 -1.556903296 GNS(ph)SDHEGCWNEESWTFSQSGTSGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNSSDHEGCWNEESWTFSQSGTSGSK 26 0 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 GNS(0.5)S(0.5)DHEGCWNEESWTFSQSGTSGSK 142.47 1.80E-07 387080000 176460 139660 126580 144980 148510 162220 121380 136650 149090 113680 TRUE FALSE 169563.7481 135677.0335 149455.8218 152462.4352 153286.959 165500.1995 122865.4847 133828.1297 132165.9282 105980.3523 1.599954561 1.280209308 1.410221975 1.438591511 1.44637148 1.56161209 1.159323233 1.262763586 1.247079532 1 16.6934373 1.336290158 0.661508858 1.015130021 1.446611663 0.612902347 0.109380114 0.445539991 0.456031404 0.10407614 0.046787576 21.69152862 -1.336290158 0.431481642 KDAENHEAQLK ddPTM_BT-474_Pertuzumab_2h_R1 3 KDAENHEAQLK 11 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ;; 205.46 1.93E-08 1828790000 2727610 2661920 2468310 2371690 2410430 2703150 2864840 2878510 3635060 3591750 FALSE TRUE 2621011.986 2586004.648 2914388.524 2494093.205 2487963.67 2757809.545 2899900.769 2819067.763 3222423.228 3348477.573 0.782747362 0.772292659 0.870362265 0.744843933 0.743013389 0.82360102 0.866035595 0.841895369 0.962354729 1 21.67507387 1.336358641 0.946427371 1.004499225 0.787668 0.774313089 0.039393485 0.23498832 0.440047327 0.037095697 0.013392002 21.69494939 -1.336358641 -0.216831225 KKS(ph)PASTFALSSQVPDVMVVGEPTLMGGEFGDEDER ddPTM_BT-474_Pertuzumab_2h_R1 1 KKSPASTFALSSQVPDVMVVGEPTLMGGEFGDEDER 36 2 Q86U70-2;Q86U70 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KKS(0.2)PAS(0.2)T(0.2)FALS(0.2)S(0.2)QVPDVMVVGEPTLMGGEFGDEDER 208.5 8.90E-31 232750000 147110 125420 114440 96858 112790 124840 121820 129830 181950 151280 TRUE FALSE 141360.7786 121843.1444 135121.8537 101856.853 116417.9928 127364.3503 123310.8696 127148.9651 161295.7988 141033.6709 1.002319359 0.863929469 0.958082229 0.722216563 0.825462403 0.90307761 0.874336383 0.90155042 1.143668727 1 17.10568011 1.337243051 5.975855158 1.06970096 0.875837525 0.490623764 0.077713056 0.157357249 7.550709268 0.05329701 0.018986994 21.73917464 -1.337243051 -0.193863435 SGPS(ph)PLS(ph)SPNGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGPSPLSSPNGK 12 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 SGPS(1)PLS(0.911)S(0.089)PNGK 177.12 3.46E-05 639960000 1867600 1709000 1470000 1622500 1533400 1646800 1750800 1914100 2045400 2168700 TRUE FALSE 1794612.127 1660260.993 1735661.7 1706237.419 1582723.204 1680099.424 1772226.814 1874573.166 1813214.767 2021812.017 0.887625611 0.821174758 0.858468386 0.843914966 0.782824115 0.830986961 0.876553705 0.927174807 0.896826585 1 20.94721743 1.338442145 0.875705314 0.989278755 0.835412822 0.71138671 0.031092391 0.282787963 0.462987237 0.029732527 0.011159633 21.79927977 -1.338442145 -0.153865933 AVPPVS(ph)PELR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVPPVSPELR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 AVPPVS(1)PELR;AVPPVS(1)PELR;AVPPVS(1)PELR;AVPPVS(1)PELR 124.67 0.00045048 3727500000 1137280 1297630 1017810 1389260 1256400 1217350 1214930 1250160 1003400 1167610 TRUE FALSE 1092833.84 1260622.863 1201750.908 1460959.875 1296813.247 1241965.651 1229798.677 1224343.759 889498.2386 1088526.735 1.003956821 1.158100047 1.104015978 1.342144229 1.191347172 1.140960173 1.129782703 1.124771418 0.817157917 1 20.05394541 1.338547376 5.846039068 0.911216225 1.155845499 0.537819589 0.089356028 0.14545361 6.731318255 0.062289927 0.022139175 21.80456243 -1.338547376 0.244629275 YYDDTYPSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 YYDDTYPSVK 10 0 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8VXB1;F8VUC5;F8W156;F8VXR1 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 148.52 0.012876 0 359390 363020 288500 384520 342320 354110 356520 396930 475160 469630 FALSE TRUE 345344.6415 352667.025 340638.3676 404365.1233 353331.0337 361270.3468 360883.1984 388733.2568 421221.8288 437821.5418 0.788779465 0.80550405 0.778030168 0.923584348 0.807020669 0.825154343 0.824270083 0.887880608 0.962085664 1 18.73998341 1.33880441 1.683804415 0.999550873 0.821723639 0.745813526 0.037356218 0.171037093 0.873440293 0.034077744 0.010435865 21.81747115 -1.33880441 -0.177827234 APVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 APVQPQQSPAAAPGGTDEKPSGK 23 1 Q13200;C9JPC0;F8WBS8 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 APVQPQQS(1)PAAAPGGTDEKPSGK;APVQPQQS(1)PAAAPGGTDEKPSGK 186.35 1.67E-17 1817610000 604844 592685 563837 513681 601102 628230 577473 676810 872450 848070 TRUE FALSE 581206.0278 575782.2041 665734.8884 540192.138 620436.9917 640933.241 584540.2873 662833.637 773413.1336 790629.4635 0.735118098 0.728257965 0.842031469 0.683243116 0.78473801 0.810661973 0.73933532 0.838361922 0.978224528 1 19.59264219 1.339061315 2.411392454 1.002830229 0.762217714 0.818118211 0.042660094 0.108484426 1.058460497 0.036053933 0.0108551 21.830381 -1.339061315 -0.240612516 WVDGVDEIQYDVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 WVDGVDEIQYDVGR 14 0 H3BU86;O14662;F8W9Z6;B7ZBM8;O14662-6;O14662-2;O14662-5;B7ZBM4;B7ZBM5;H0YEW0;E9PND6;Q96NX8;O14662-4;O14662-3 H3BU86;Q96NX8 STX16-NPEPL1;STX16 Syntaxin-16 0 ; 232.42 4.08E-13 245330000 185079 202935 146080 200474 158400 164456 180217 177280 168409 156118 FALSE TRUE 177845.9081 197147.4925 172479.9055 210820.4872 163495.0799 167781.413 182422.5496 173619.106 149291.9163 145543.9888 1.221939219 1.354556063 1.185070623 1.448500133 1.123337908 1.152788338 1.253384293 1.192897814 1.025751167 1 17.15109573 1.339113797 0.505639494 0.984988684 1.287201485 0.495116933 0.091971408 0.7180318 0.482104897 0.096022102 0.054085545 21.83301922 -1.339113797 0.302212801 SEWLDPSQKS(ph)PLHVGETR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SEWLDPS(0.06)QKS(0.938)PLHVGET(0.002)R;SEWLDPS(0.219)QKS(0.78)PLHVGET(0.001)R;SEWLDPS(0.194)QKS(0.806)PLHVGETR;SEWLDPS(0.037)QKS(0.963)PLHVGETR 193.77 6.47E-15 5132210000 1813140 1446430 1270460 1221750 1424380 1510710 1459820 1531840 1939230 1686820 TRUE FALSE 1742280.484 1405179.233 1500060.383 1284804.664 1470196.476 1541257.591 1477685.714 1500206.969 1719096.74 1572570.179 1.107919066 0.893555818 0.9538909 0.817009429 0.934900392 0.980088273 0.93966281 0.953984114 1.093176485 1 20.58469297 1.339132734 6.568000884 1.045501833 0.941717872 0.230866843 0.07181114 0.270804212 14.56767334 0.047601516 0.017133027 21.83397124 -1.339132734 -0.103783961 DSAIPVESDT(ph)DDEGAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 DSAIPVES(0.046)DT(0.954)DDEGAPR;DSAIPVES(0.007)DT(0.993)DDEGAPR 312.09 4.23E-57 1191790000 465520 528700 457960 506590 532710 572260 485540 529620 487970 520110 TRUE FALSE 447326.9637 513621.9937 540723.5593 532735.1706 549845.1009 583831.4893 491482.1838 518683.1619 432577.6913 484882.4864 0.922547166 1.059271077 1.115164136 1.09868924 1.133975997 1.204068007 1.013610921 1.069709005 0.892128925 1 18.88727562 1.339522637 5.577769152 0.947391033 1.082406465 0.328051693 0.074619066 0.225637986 9.744925053 0.053578052 0.018926464 21.85358227 -1.339522637 0.135015432 ASGDPGASGMS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 9 ASGDPGASGMSPR 13 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGAS(0.026)GMS(0.974)PR;ASGDPGASGMS(1)PR;ASGDPGAS(0.001)GMS(0.999)PR 206.66 6.31E-08 3575030000 3079200 3239559 2690822 3228142 3100917 3274889 3143570 3235820 3212828 3243309 TRUE FALSE 2958861.46 3147169.949 3177113.392 3394746.795 3200660.811 3341109.499 3182041.95 3168999.186 2848121.235 3023636.793 0.978577013 1.040855819 1.05075894 1.122736303 1.058546721 1.104996972 1.05238895 1.048075349 0.941952169 1 21.52785342 1.339685297 5.452658699 0.971918668 1.060450762 0.443580482 0.038569332 0.177939 7.43802856 0.027747375 0.009768728 21.86176879 -1.339685297 0.088532094 VVQVSAGDSHTAALTDDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVQVSAGDSHTAALTDDGR 19 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 ; 270.08 9.87E-33 1293530000 236360 239750 205192 263150 229172 259700 249960 242120 248270 231052 FALSE TRUE 227122.7899 232912.5647 242274.7589 276731.203 236543.5255 264951.3119 253019.0853 237120.1374 220087.4304 215402.6422 1.054410417 1.081289265 1.124752957 1.284715917 1.098145886 1.230028143 1.174633155 1.100822789 1.021748982 1 17.71667642 1.339732293 2.56993564 1.002723284 1.151971354 0.415487249 0.065257964 0.275336346 3.028690219 0.058574604 0.017720425 21.86413462 -1.339732293 0.14924807 FENLCK ddPTM_BT-474_Pertuzumab_2h_R1 3 FENLCK 6 0 P08238;Q58FF7;P07900;P07900-2;Q58FG0;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AA5P;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5;Putative heat shock protein HSP 90-beta 2 0 ;; 108.24 0.07115 4012740000 2406140 2213220 1846000 1955030 2053120 1991820 2197670 2218160 2749210 2445070 FALSE TRUE 2312105.389 2150101.133 2179613.264 2055929.333 2119160.469 2032095.965 2224565.743 2172354.221 2437131.206 2279463.231 1.014320107 0.943248877 0.956195842 0.90193573 0.929675215 0.891480037 0.975916484 0.953011302 1.069168905 1 21.12026271 1.34008254 5.576747283 1.033665523 0.943106325 0.48530185 0.036532093 0.160738065 6.925157245 0.02557711 0.009036914 21.88177458 -1.34008254 -0.090559198 NNYHPVEDACWKPGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 NNYHPVEDACWKPGQK 16 1 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 0 150.76 4.26E-07 316870000 431610 359600 324870 340170 353370 331460 340320 387780 469510 446640 FALSE TRUE 414742.204 349344.5601 383581.2357 357726.2145 364736.467 338162.3483 344484.938 379772.2075 416213.1931 416388.675 0.996045832 0.838986699 0.921209578 0.8591161 0.875951938 0.812131474 0.82731582 0.912061807 0.999578562 1 18.6675713 1.340130737 3.483153243 1.002064412 0.872974622 0.489883984 0.049756645 0.187034854 3.681058411 0.039135861 0.012471217 21.88420313 -1.340130737 -0.12908979 IDDIADGAVKPPPNKYPIFFFGTHETAFLGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDDIADGAVKPPPNKYPIFFFGTHETAFLGPK 32 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;M0R0J3 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 83.557 0.00012769 129960000 271460 243420 225210 230380 229520 267940 248560 265830 350370 308350 FALSE TRUE 260851.0431 236477.8999 265910.4568 242269.9394 236902.7192 273357.9304 251601.9516 260340.5176 310597.4665 287465.1799 0.907417877 0.822631458 0.925017969 0.842780122 0.824109269 0.950925363 0.875243227 0.905641921 1.080469873 1 18.13302769 1.340379082 4.958139789 1.038745241 0.878808118 0.679501659 0.043744294 0.107541178 3.898955422 0.03025183 0.010477591 21.89672087 -1.340379082 -0.159937124 LKQDGDSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 LKQDGDSFR 9 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 169.37 5.34E-05 1736040000 2761430 3192630 2366560 2502840 2696410 2684910 2903020 2898220 3466250 3290040 FALSE TRUE 2653510.263 3101579.318 2794250.036 2632011.872 2783142.476 2739200.72 2938548.027 2838370.744 3072775.832 3067202.66 0.865123879 1.011207821 0.911009263 0.858114759 0.907387866 0.893061536 0.958054733 0.925393937 1.001817021 1 21.54849206 1.340424739 1.466078616 1.0059612 0.91292108 0.389432543 0.042061858 0.403359133 1.616891122 0.038263731 0.012003688 21.89902295 -1.340424739 -0.093040119 S(ph)PTTTQSPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPTTTQSPK 9 0 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 S(0.927)PT(0.071)T(0.001)T(0.001)QSPK;S(0.972)PT(0.027)T(0.001)TQSPK;S(0.946)PT(0.053)T(0.001)TQSPK;S(0.986)PT(0.012)T(0.001)TQSPK 150.46 8.94E-05 604405000 586885 576787 546259 728937 733217 612121 589189 645217 557582 585067 TRUE FALSE 563948.8854 560337.5995 644980.1528 766557.5259 756801.5907 624498.506 596399.6712 631893.0435 494287.6289 545439.891 1.033934068 1.027313199 1.182495383 1.405393222 1.38750686 1.144944688 1.093428774 1.158501705 0.906218333 1 19.05706069 1.340574547 3.689438122 0.953091249 1.187328969 0.342946635 0.123962697 0.284642102 6.2380799 0.110178231 0.035615138 21.90657826 -1.340574547 0.23423772 DFLQEVCLRPSADPIFEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFLQEVCLRPSADPIFEPR 19 1 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9;H0YHL2 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 0 109.09 0.00023902 69925000 43508 45265 35629 39903 43848 44938 40470 44246 41811 46542 FALSE TRUE 41807.65926 43974.08652 42067.95286 41962.39861 45258.41074 45846.67715 40965.28397 43332.30464 37064.79057 43389.66888 0.963539486 1.01346905 0.969538463 0.967105758 1.04306882 1.056626573 0.944125296 0.998677928 0.854230777 1 15.40506396 1.341136811 24.96853895 0.926834066 0.994766126 0.247565905 0.047000852 12.23597844 2945.329146 0.029806461 0.010884395 21.93495818 -1.341136811 0.06793206 GVTQYYAYVTER ddPTM_BT-474_Pertuzumab_2h_R1 1 GVTQYYAYVTER 12 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 127.56 0.00048538 0 66590 84452 60381 65940 65502 77993 70659 73396 60998 74636 FALSE TRUE 63987.58918 82043.51165 71293.18987 69343.1713 67608.93132 79570.0719 71523.74598 71880.34695 54073.76276 69580.83724 0.919615108 1.179110728 1.024609543 0.996584319 0.971660216 1.143563013 1.027923043 1.033048032 0.777135845 1 16.08640242 1.341251343 9.464656682 0.889129422 1.040983115 0.315246019 0.087408656 0.285233597 23.46711617 0.054120847 0.019777535 21.94074365 -1.341251343 0.151853693 RNS(ph)VERPAEPVAGAATPSLVEQQK ddPTM_BT-474_Pertuzumab_2h_R1 8 RNSVERPAEPVAGAATPSLVEQQK 24 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 RNS(0.999)VERPAEPVAGAAT(0.001)PSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(0.998)VERPAEPVAGAAT(0.002)PSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK 256.9 3.65E-44 11988160000 2625631 2564556 2157367 2624799 3026060 2632141 2466929 2648790 2332196 2412421 TRUE FALSE 2523018.438 2491417.374 2547251.207 2760265.191 3123395.968 2685364.694 2497120.015 2594091.561 2067454.887 2249025.577 1.121827365 1.107776363 1.132602152 1.227316052 1.388777433 1.194012519 1.110311968 1.153429106 0.919266952 1 21.10086864 1.341337479 3.620534348 0.959215909 1.185097667 0.535152239 0.081542564 0.19261108 4.073944483 0.071407621 0.022991229 21.94509569 -1.341337479 0.225881758 LLS(ph)PRPSLLTPTGDPR ddPTM_BT-474_Pertuzumab_2h_R1 6 LLSPRPSLLTPTGDPR 16 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LLS(0.999)PRPS(0.001)LLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(0.976)PRPS(0.023)LLT(0.001)PTGDPR;LLS(0.998)PRPS(0.002)LLTPTGDPR 118.46 0.00016402 2993332000 3978742 4430810 3245264 4022360 4060910 4296190 4026500 4130230 4002630 4010103 TRUE FALSE 3823248.364 4304447.637 3831755.395 4229954.482 4191532.858 4383061.905 4075777.511 4044939.307 3548268.223 3738495.152 1.022670408 1.151385106 1.024945931 1.131459133 1.121181836 1.172413425 1.09021875 1.081969922 0.949116711 1 21.83402623 1.341361894 4.293445766 0.97514875 1.103933153 0.526013402 0.047518125 0.154912393 4.443518729 0.034329996 0.011528601 21.94632944 -1.341361894 0.128784403 IESFVETLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 IESFVETLKR 10 1 P49770;G3V5E5;H0YJJ8 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 128.81 0.00051266 196150000 124630 138360 99941 116830 109870 137720 128670 150560 145960 169880 FALSE TRUE 119759.3218 134414.1083 118002.5619 122859.6103 113404.0683 140504.7928 130244.7019 147450.8834 129391.2327 158373.8763 0.756181036 0.848713888 0.74508855 0.775756793 0.716052868 0.887171521 0.822387536 0.931030337 0.816998584 1 17.27297486 1.34228897 0.458615791 0.99581786 0.766420098 0.583275027 0.054600194 0.641154446 0.372635904 0.061454099 0.037666888 21.99322768 -1.34228897 -0.229397761 VAIHYINPPNPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAIHYINPPNPAK 13 0 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 ; 122.42 0.00023523 1237070000 2053580 2005760 1764580 1983070 2002050 1874810 2068500 2146300 2478800 2427200 FALSE TRUE 1973323.823 1948557.689 2083478.859 2085416.48 2066447.756 1912719.943 2093814.922 2101978.155 2197417.016 2262803.582 0.872070311 0.861125422 0.920751087 0.92160738 0.913224538 0.845287659 0.9253189 0.928926475 0.971103738 1 21.10967993 1.342702574 1.316260761 0.998845143 0.892232349 0.684244698 0.02534838 0.240731299 0.799325414 0.024208301 0.007789509 22.01418308 -1.342702574 -0.106612794 ELDENVEYEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDENVEYEER 11 0 Q15291;Q15291-2 Q15291 RBBP5 Retinoblastoma-binding protein 5 0 113.63 0.0017429 0 26246 61774 47123 89184 38673 53507 56216 50072 39060 35450 FALSE TRUE 25220.2773 60012.266 55639.17435 93786.79693 39916.95217 54588.9482 56903.98822 49037.9957 34626.07255 33048.93992 0.7631191 1.815860543 1.683538851 2.837815589 1.20781339 1.651760944 1.721809787 1.483799354 1.047721126 1 15.01231638 1.342780354 2.331724916 0.983672164 1.702079012 0.207967006 0.493433683 0.441116169 4.050349889 0.429949916 0.12953281 22.01812605 -1.342780354 0.718406847 RS(ph)PS(ph)PYYSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSPSPYYSR 9 1 P62995;P62995-3;H7BXF3;H7C2L4;Q13595;Q13595-3;Q13595-4 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 2 RS(0.934)PS(0.998)PY(0.064)Y(0.002)S(0.002)R;RS(0.983)PS(0.957)PY(0.045)Y(0.002)S(0.012)R 104.59 0.0021621 1116340000 1056340 1100630 926790 1090330 992880 1228270 1031410 1108470 1031800 1124360 TRUE FALSE 1015057.065 1069241.11 1094281.569 1146602.062 1024816.887 1253106.461 1044032.704 1085579.707 914674.3897 1048206.096 0.968375465 1.020067632 1.043956502 1.09387082 0.977686441 1.195477174 0.996018539 1.035654831 0.872609302 1 19.99949097 1.343536175 7.413944675 0.937035276 1.043576808 0.274813184 0.06824406 0.260006748 15.84842739 0.043865238 0.015926649 22.05647852 -1.343536175 0.106541532 IDRGETHLWSPQVSEDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDRGETHLWSPQVSEDGK 18 1 Q53GG5-2;A0A087WYF8;Q53GG5-3;Q53GG5;A0A2R8Y6L7 Q53GG5-2 PDLIM3 PDZ and LIM domain protein 3 0 124.84 1.86E-05 133350000 286550 259820 218950 227980 213000 259160 237830 272490 335930 324100 FALSE TRUE 275351.3092 252410.188 258519.1355 239746.0751 219851.3384 264400.3928 240740.6347 266862.9863 297796.6347 302148.4183 0.911311437 0.835384773 0.85560314 0.793471223 0.727626971 0.875067936 0.796762849 0.883218214 0.985597199 1 18.20489786 1.34396982 2.629649891 1.001003132 0.825980493 0.654259927 0.047382595 0.164672398 1.895440696 0.04149165 0.012614945 22.07851299 -1.34396982 -0.175022639 VELAQLQEEWNEHNAK ddPTM_BT-474_Pertuzumab_2h_R1 5 VELAQLQEEWNEHNAK 16 0 Q9H307 Q9H307 PNN Pinin 0 ;;;; 353.14 2.68E-87 2919340000 1314483 1314830 1093955 1142079 1219638 1318140 1262204 1333314 1527520 1484100 FALSE TRUE 1263111.551 1277332.336 1291657.003 1201021.834 1258868.764 1344793.694 1277651.23 1305780.6 1354122.333 1383580.585 0.912929514 0.923207762 0.933561093 0.868053402 0.909862987 0.971966294 0.923438247 0.943769097 0.978708684 1 20.39997524 1.344276447 0.614629938 1.001586395 0.911736373 0.603822425 0.023066962 0.512788493 0.465315222 0.023543025 0.01124529 22.09410669 -1.344276447 -0.089850022 GQVLNSDELQELYEGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQVLNSDELQELYEGLR 17 0 O00764;F2Z2Y4;O00764-2 O00764 PDXK Pyridoxal kinase 0 ; 387.87 1.91E-121 216812000 79813 88231 73530 90490 86890 74483 93397 85958 79267 83488 FALSE TRUE 76693.81972 85714.73827 86818.50667 95160.19974 89684.89576 75989.09729 94540.02042 84182.93726 70268.94247 77833.2834 0.9853602 1.101260727 1.115441915 1.22261577 1.152269207 0.976305945 1.214647723 1.081580188 0.902813545 1 16.2480996 1.344289545 5.919933822 0.953685358 1.113111091 0.376838113 0.079991166 0.198472891 9.129574933 0.054760723 0.019530308 22.09477304 -1.344289545 0.159425733 QPPGVPNGPS(ph)SPTNESAPELPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPPGVPNGPSSPTNESAPELPQR 23 0 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 QPPGVPNGPS(0.496)S(0.383)PT(0.112)NES(0.01)APELPQR;QPPGVPNGPS(0.483)S(0.483)PT(0.027)NES(0.007)APELPQR 70.345 0.015044 463860000 444420 485300 409420 619350 557320 534100 519450 518330 467960 472450 TRUE FALSE 427051.5751 471459.7192 483411.3015 651314.7277 575246.7039 544899.8679 525807.1845 507626.3044 414839.1426 440450.5407 0.969578955 1.070403316 1.097538218 1.478746573 1.306041543 1.237142012 1.193793936 1.15251602 0.941851818 1 18.7486205 1.344677272 3.735890662 0.970187441 1.200030832 0.304508345 0.131631792 0.296533269 6.632299134 0.112697762 0.036670981 22.11450752 -1.344677272 0.22984339 SEDPDQQYLILNTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDPDQQYLILNTAR 15 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 185.2 1.01E-06 68666000 38243 38420 39580 35340 34472 41296 40201 39773 34975 39747 FALSE TRUE 36748.42128 37324.29922 46732.98645 37163.90164 35580.82319 42131.03341 40692.99186 38951.67365 31004.78463 37054.90029 0.991729056 1.007270265 1.261182356 1.002941618 0.960219105 1.136989523 1.098181119 1.051188192 0.836725626 1 15.17737672 1.344766953 7.455779203 0.919747127 1.067310432 0.29308099 0.090403685 0.259795303 15.84421711 0.06040736 0.021941919 22.11907459 -1.344766953 0.147563305 RRSPS(ph)PY(ph)YSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSPSPYYSR 10 2 P62995;P62995-3;H7BXF3;Q13595;Q13595-3 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 2 RRS(0.607)PS(0.449)PY(0.374)Y(0.337)S(0.234)R 78.615 0.04836 1156300000 665410 696700 610990 665540 708370 678120 696040 703190 668660 711340 TRUE FALSE 639405.0416 676830.7981 721409.4844 699888.5992 731155.3644 691832.051 704558.3457 688668.8808 592756.5201 663160.3082 0.964178697 1.020614156 1.08783574 1.055383729 1.102531854 1.04323501 1.062425385 1.038465168 0.893835944 1 19.33899813 1.345259032 7.062959885 0.947953089 1.050324905 0.465525544 0.042822932 0.172476356 9.845712486 0.028695939 0.010394233 22.14415088 -1.345259032 0.102371817 KLEELEKEEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEELEKEEELR 12 2 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 90.444 0.0049815 281450000 830930 638820 510670 547480 647720 599100 627160 655130 910090 698570 FALSE TRUE 798456.337 620601.4791 602959.4288 575735.5084 668554.502 611214.2125 634835.3717 641601.3366 806780.3986 651255.2317 1.226026753 0.952931276 0.925841973 0.884039744 1.026562966 0.938517163 0.974787366 0.98517648 1.238808319 1 19.31286353 1.345439939 11.9716323 1.119237685 0.981316375 0.201232941 0.102794919 0.561459013 58.19612598 0.064965818 0.023759308 22.15337702 -1.345439939 -0.13792131 SSQRHS(ph)PPFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSQRHSPPFSK 11 1 Q8WV28-3;Q8WV28;Q8WV28-2 Q8WV28-3 BLNK B-cell linker protein 1 S(0.001)SQRHS(0.998)PPFSK;S(0.066)S(0.066)QRHS(0.869)PPFSK 103.66 0.0016381 935970000 1121750 1435570 1062910 1328260 1147140 1255360 1231520 1227080 1213570 1126970 TRUE FALSE 1077910.77 1394628.949 1255001.481 1396811.658 1184038.8 1280744.239 1246591.71 1201740.369 1075810.621 1050639.318 1.025957007 1.327409821 1.194512198 1.329487326 1.126969817 1.219014192 1.186507766 1.143818196 1.023958082 1 20.00283605 1.345521397 1.733910434 0.994271624 1.210707717 0.444601184 0.083490109 0.283617479 1.527327298 0.070107233 0.021436413 22.15753263 -1.345521397 0.216436092 GHY(ph)EVTGSDDETGKLQGSGVSLASK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHY(0.378)EVT(0.308)GS(0.308)DDET(0.006)GKLQGSGVSLASK 131.59 9.49E-05 20124000 38797 32150 30633 34554 32386 31089 31203 35838 47149 41197 TRUE FALSE 37280.77035 31233.11348 36169.06453 36337.33608 33427.7251 31717.64088 31584.87165 35097.93278 41796.84318 38406.6905 0.970684271 0.813220641 0.941738641 0.94611995 0.87036203 0.825836344 0.822379415 0.913849445 1.088269847 1 15.22907003 1.345583046 5.464033304 1.042063753 0.882672377 0.558419599 0.055887635 0.141141095 5.807507977 0.039257673 0.013860017 22.16067814 -1.345583046 -0.159391376 NQEDNTGKYPDIISR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQEDNTGKYPDIISR 15 1 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ; 197.49 7.66E-09 430720000 518380 502470 369607 420170 463790 463260 466480 512570 599560 593480 FALSE TRUE 498121.1365 488140.0476 436403.2068 441855.0241 478708.2266 472627.4346 472188.9218 501985.2504 531500.4624 553283.071 0.900300701 0.88226095 0.788752141 0.798605718 0.865213941 0.85422356 0.853430995 0.907284673 0.960630264 1 19.07765826 1.345597543 1.364961876 0.999889168 0.844403677 0.733709076 0.032057139 0.209805595 0.742170881 0.031610893 0.01008856 22.16141788 -1.345597543 -0.155485491 KFYEAFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFYEAFSK 8 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 117.7 0.0032532 491690000 1813900 1945000 1522800 1573000 1604500 1138100 1885200 1889100 2100400 2260800 FALSE TRUE 1743010.783 1889530.504 1798003.835 1654182.719 1656110.2 1161113.162 1908271.642 1850089.425 1861971.398 2107674.002 0.826983101 0.896500361 0.853074922 0.784838033 0.785752539 0.550897891 0.905392219 0.877787278 0.883424759 1 21.00722031 1.345912094 1.313622068 0.976282801 0.796111999 0.303329815 0.093751845 0.533145888 1.763527992 0.090498763 0.029159955 22.17747477 -1.345912094 -0.180170802 IFTSIGEDYDER ddPTM_BT-474_Pertuzumab_2h_R1 6 IFTSIGEDYDER 12 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;;;;; 325.95 2.06E-47 9015670000 3557410 4310280 3831750 5428110 3109580 4292880 4257410 4290820 3835570 4257710 FALSE TRUE 3418382.484 4187355.035 4524232.462 5708255.408 3209602.465 4379684.975 4309513.457 4202213.068 3400172.174 3969331.509 0.861198536 1.054927013 1.139797079 1.438089863 0.808600254 1.103381001 1.085702579 1.058670221 0.856610783 1 21.92046463 1.346135271 6.725423927 0.929866622 1.07667306 0.105797986 0.16265115 0.45061003 24.17260247 0.109881185 0.039679245 22.18887434 -1.346135271 0.146806437 TMGYSVTAPEDTRR ddPTM_BT-474_Pertuzumab_2h_R1 2 TMGYSVTAPEDTRR 14 1 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ; 157.09 8.65E-06 218480000 241653 270002 222856 246500 264153 255031 268834 251590 240671 229635 FALSE TRUE 232208.9336 262301.8073 263131.0366 259221.8945 272649.7211 260187.9016 272124.0709 246394.5786 213351.0371 214081.6169 1.084674793 1.225242088 1.229115514 1.210855459 1.273578391 1.21536779 1.271123018 1.150937582 0.996587377 1 17.70780139 1.346957128 3.242389992 0.993648189 1.218294291 0.750694562 0.049343611 0.112007294 1.923070937 0.039560786 0.01247727 22.23090425 -1.346957128 0.224646102 TSCHLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSCHLPR 7 0 D6R9T3;Q96FZ2;E7EMP6;D6RAZ3;D6RAI0;D6RGK7 D6R9T3 HMCES Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein 0 68.422 0.062495 22248000 21968 32032 25348 30026 22292 28185 31527 28179 22510 27245 FALSE TRUE 21109.46627 31118.47872 29928.94746 31575.64546 23009.04243 28754.92001 31912.83686 27597.0938 19954.75917 25399.67188 0.831092085 1.225152784 1.17832024 1.243151707 0.905879514 1.132098089 1.25642713 1.086513792 0.785630589 1 14.63252224 1.34771867 7.055253837 0.895643681 1.119809078 0.267085374 0.141746419 0.254805319 14.39237007 0.092588722 0.033548087 22.26992068 -1.34771867 0.224165397 DPASKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPASKR 6 1 P22626;P22626-2;A0A087WUI2;A0A087X0F8;A0A0A0MQW7;A0A0G2JNL1 P22626 HNRNPA2B1;LILRB4 Heterogeneous nuclear ribonucleoproteins A2/B1 0 88.643 0.081888 843380000 159550 134830 107980 139740 115810 133070 146850 134590 112230 127390 FALSE TRUE 153314.6096 130984.7804 127494.388 146951.9981 119535.1338 135760.7666 148647.1942 131810.6695 99490.12091 118761.7618 1.290942533 1.102920489 1.073530622 1.237367953 1.006511961 1.143135336 1.251641875 1.109874655 0.83772857 1 16.85771088 1.34833818 6.006878332 0.922093474 1.151202851 0.524585262 0.089430998 0.150566585 6.974536225 0.059167378 0.021162941 22.30171082 -1.34833818 0.229109377 T(ph)DSQSVRHSPIAPSSPSPQVLAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDSQSVRHSPIAPSSPSPQVLAQK 24 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 T(0.272)DS(0.232)QS(0.232)VRHS(0.232)PIAPS(0.026)S(0.006)PSPQVLAQK 113.5 0.0020756 863740000 473930 466760 336480 455210 362350 413380 425830 409340 331880 344190 TRUE FALSE 455408.2916 453448.4618 397289.421 478703.4427 374005.3168 421738.8268 431041.4349 400886.986 294206.3738 320877.7047 1.419258131 1.413150416 1.238133454 1.491856354 1.165569659 1.314328857 1.343319989 1.249345093 0.916880074 1 18.29166403 1.349144069 3.60951274 0.956568544 1.335250573 0.733135978 0.090525106 0.112025487 2.348859129 0.069160515 0.022400766 22.34313293 -1.349144069 0.378682028 INEGLEHLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 INEGLEHLAK 10 0 Q99747;J3QS28;J3QKW4 Q99747 NAPG Gamma-soluble NSF attachment protein 0 ; 119.76 0.00064914 668240000 1598770 1679100 1355080 1465880 1497840 1304570 1612140 1631120 2024420 1918390 FALSE TRUE 1536288.301 1631213.712 1599973.1 1541534.242 1546019.384 1330949.299 1631869.852 1597436.802 1794616.329 1788455.737 0.859002697 0.912079443 0.894611517 0.861935921 0.86444375 0.744189119 0.912446318 0.893193368 1.003444643 1 20.77028298 1.349372382 2.138156818 1.008157839 0.862441432 0.588216054 0.045124709 0.218887277 1.719516523 0.041279866 0.012465373 22.35488202 -1.349372382 -0.145716407 VGLQSPS(ph)VEAWEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGLQSPSVEAWEAK 14 0 E9PEZ1;Q8IWT3-3;Q8IWT3 E9PEZ1 CUL9 Cullin-9 1 VGLQS(0.072)PS(0.928)VEAWEAK 126.42 0.00033757 0 183000 201650 163700 167170 161760 201380 191430 201290 278290 247110 TRUE FALSE 175848.1577 195899.1394 193284.2315 175797.6637 166963.1573 205452.0416 193772.7776 197133.2912 246699.6859 230373.0196 0.763319238 0.85035626 0.839005504 0.763100054 0.724751352 0.891823365 0.841126178 0.855713449 1.070870566 1 17.81361224 1.349711536 3.703517037 1.035628517 0.813376474 0.753853426 0.050355881 0.111531564 2.449981336 0.040720208 0.013278223 22.37234646 -1.349711536 -0.222252042 RLSSEVEALR ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSSEVEALR 10 1 P15924 P15924 DSP Desmoplakin 0 ;; 145.91 4.74E-05 419540000 336014 347850 285434 339461 333247 419689 321304 352590 325780 331272 FALSE TRUE 322882.2014 337929.6586 337018.2732 356980.6229 343966.1924 428175.3991 325236.2145 345308.8933 288798.8202 308834.6524 1.045485663 1.094209008 1.091257962 1.155895623 1.113755175 1.386422786 1.053107907 1.118102812 0.935124404 1 18.23647511 1.350116766 3.218177687 0.967242906 1.138339942 0.328249134 0.092778113 0.285803921 4.840067272 0.076543289 0.024166448 22.3932313 -1.350116766 0.171097037 ELSPLISLPSPVPPLS(ph)PIHSNQQTLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSPLISLPSPVPPLSPIHSNQQTLPR 27 0 A0A669KBI3;F5GXF9;P51825;P51825-3;P51825-2;E7ETI4;E7EMC5 A0A669KBI3 AFF1 AF4/FMR2 family member 1 1 ELSPLISLPSPVPPLS(0.998)PIHS(0.002)NQQTLPR;ELSPLISLPSPVPPLS(1)PIHSNQQTLPR 135.02 1.49E-05 299510000 126181 135571 102658 147981 132453 127427 130865 130287 139802 128331 TRUE FALSE 121249.707 131704.6478 121210.5842 155618.3171 136713.471 130003.6612 132466.565 127596.5279 123932.2631 119639.0271 1.013462831 1.100850208 1.013135824 1.300732052 1.142716339 1.086632552 1.107218675 1.066512584 1.035884912 1 16.86832856 1.350625392 1.30006275 1.002291431 1.115006357 0.196374632 0.075456921 0.669313342 2.17308482 0.07056218 0.022826545 22.41947259 -1.350625392 0.112714926 RNEIWLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNEIWLLK 8 1 Q9NRV9;A0A3B3IRV5 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 145.72 0.0009056 1875740000 1726740 1998490 1624680 2089700 1764780 1585610 2047420 2139060 2306600 2468100 FALSE TRUE 1659257.092 1941495.022 1918295.817 2197549.667 1821545.751 1617672.121 2072476.938 2094887.663 2044764.438 2300933.389 0.72112348 0.843785844 0.833703325 0.95506879 0.791655143 0.703050392 0.900711402 0.910451243 0.888667377 1 21.13378779 1.351406086 0.988763066 0.985342985 0.819397447 0.383376755 0.071514057 0.545442284 1.09710987 0.068440415 0.024317169 22.45981043 -1.351406086 -0.165945537 FKYDDAER ddPTM_BT-474_Pertuzumab_2h_R1 5 FKYDDAER 8 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;;; 140.83 0.00058659 4388820000 5927380 5815200 4984260 5107630 5497440 4635780 6042680 6345530 7169640 7614500 FALSE TRUE 5695731.437 5649356.19 5885026.656 5371235.396 5674270.15 4729518.648 6116632.125 6214492.588 6355772.525 7098763.133 0.802355471 0.795822608 0.829021415 0.75664384 0.799332228 0.666245451 0.861647587 0.875433152 0.895335202 1 22.75913624 1.351649123 1.133116337 0.986171731 0.780757634 0.675048086 0.048124776 0.257504743 0.656944789 0.044564 0.015026595 22.47238272 -1.351649123 -0.205414097 NALESYAFNMK ddPTM_BT-474_Pertuzumab_2h_R1 2 NALESYAFNMK 11 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ; 160.18 6.46E-05 519980000 523490 540360 471610 465390 497050 497860 508610 537250 653200 594880 FALSE TRUE 503031.4321 524949.4619 556840.4179 489408.8337 513038.0647 507927.0703 514834.5213 526155.5998 579051.4744 554588.2477 0.907035867 0.946557133 1.004060977 0.882472421 0.925079222 0.915863386 0.928318484 0.948731968 1.044110611 1 19.08105752 1.351862346 4.699311636 1.021155381 0.931640258 0.570335719 0.031405113 0.148760593 4.863916236 0.022963318 0.007923107 22.48341857 -1.351862346 -0.089515123 EAAVGVPPPAQPAPGEPTPPAPPS(ph)PDWTSSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAAVGVPPPAQPAPGEPTPPAPPSPDWTSSSR 32 0 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 EAAVGVPPPAQPAPGEPT(0.001)PPAPPS(0.88)PDWT(0.073)S(0.015)S(0.015)S(0.015)R;EAAVGVPPPAQPAPGEPT(0.002)PPAPPS(0.955)PDWT(0.013)S(0.01)S(0.01)S(0.01)R;EAAVGVPPPAQPAPGEPT(0.001)PPAPPS(0.912)PDWT(0.047)S(0.011)S(0.014)S(0.014)R;EAAVGVPPPAQPAPGEPTPPAPPS(0.972)PDWT(0.005)S(0.006)S(0.008)S(0.008)R 135.84 2.21E-08 3199150000 1255383 1444890 1161423 1463462 1490191 1420337 1458929 1416274 1212913 1352890 TRUE FALSE 1206321.244 1403683.152 1371317.972 1538991.449 1538124.347 1449057.187 1476783.81 1387027.447 1075228.201 1261257.555 0.956443226 1.112923483 1.087262444 1.220203949 1.219516458 1.148898717 1.170882032 1.09971785 0.852504864 1 20.26643148 1.352186432 5.681475665 0.928988521 1.135296316 0.512152804 0.078590678 0.157033338 6.717790608 0.055791927 0.019852995 22.50020276 -1.352186432 0.206307795 TKPYIQVDIGGGQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKPYIQVDIGGGQTK 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 164.57 1.34E-06 1504330000 1704710 1763100 1368610 1458090 1414540 1259270 1545880 1640720 2019130 1908830 FALSE TRUE 1638088.049 1712818.114 1615948.272 1533342.2 1460039.964 1284733.302 1564798.942 1606838.559 1789926.827 1779543.244 0.920510392 0.962504351 0.908069122 0.861649305 0.820457704 0.721945537 0.879326168 0.902949992 1.005834971 1 20.76307556 1.352651796 2.755023873 1.006880686 0.866119481 0.430458037 0.061079129 0.284848929 3.596798715 0.058827555 0.018097566 22.52432558 -1.352651796 -0.140761205 LQALDTGWNELHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQALDTGWNELHK 13 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 165.64 3.50E-05 769820000 718940 768090 666170 822080 740260 690390 707750 844310 1038770 1017670 FALSE TRUE 690843.03 746184.8252 786561.7379 864507.6473 764071.1352 704350.1588 716411.6562 826874.7035 920853.1845 948742.3045 0.728167203 0.786498949 0.829057305 0.911214397 0.805351602 0.742404081 0.755117225 0.871548259 0.970604115 1 19.85565675 1.353018952 2.627173099 0.994845442 0.798416881 0.704015692 0.049308391 0.164756377 1.902004054 0.04646858 0.014212434 22.54337584 -1.353018952 -0.196428561 VGEVCHITCKPEYAYGSAGSPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGEVCHITCKPEYAYGSAGSPPK 23 1 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 230.24 2.47E-33 6651700000 3218500 3211700 3183700 3151800 3096300 3107200 3529200 3661300 4679700 4587900 FALSE TRUE 3092717.462 3120105.461 3759065.411 3314464.776 3195895.301 3170029.713 3572391.405 3585692.876 4148480.075 4277157.447 0.723077768 0.729481086 0.878870011 0.774922321 0.747200762 0.741153383 0.835225603 0.838335488 0.969915213 1 22.02822088 1.353163581 1.435953374 1.005794052 0.771195278 0.775108619 0.044963781 0.178651998 0.690710155 0.0421454 0.013327728 22.5508845 -1.353163581 -0.234598775 TDGCHAYLSK ddPTM_BT-474_Pertuzumab_2h_R1 5 TDGCHAYLSK 10 0 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ;;;; 127.42 0.00035647 4666340000 9430080 9119160 8207110 8414860 8664170 7442830 9678880 9476730 10857840 10894220 FALSE TRUE 9061542.048 8859090.485 9690317.343 8849151.933 8942860.897 7593329.122 9797333.029 9281032.214 9625303.523 10156344.78 0.892205045 0.872271539 0.95411465 0.871292983 0.880519625 0.747643891 0.964651481 0.913816183 0.947713349 1 23.27587794 1.353530592 1.226175484 0.990999368 0.878415685 0.335131697 0.05447033 0.497560111 1.457251638 0.05015686 0.016503726 22.56994973 -1.353530592 -0.112583683 EYCIQAFESFVR ddPTM_BT-474_Pertuzumab_2h_R1 3 EYCIQAFESFVR 12 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 140.78 0.0001395 261892000 176331 179117 153911 190921 181446 167022 186830 182049 178609 181053 FALSE TRUE 169439.7896 174008.7585 181726.1414 200774.4557 187282.3754 170399.2993 189116.4814 178289.6245 158334.0551 168790.119 1.003848984 1.030917921 1.07663969 1.18949176 1.109557695 1.009533616 1.120423888 1.056279986 0.938052867 1 17.36487093 1.353561502 5.406301589 0.970582939 1.078835659 0.378725169 0.054470211 0.21504181 8.592856135 0.040203907 0.014220023 22.57155617 -1.353561502 0.10825272 GIFPVLCKDPVQEAWAEDVDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 GIFPVLCKDPVQEAWAEDVDLR 22 1 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 274.39 1.92E-45 50788997000 7805204 7867660 5208802 5948055 7277967 7923570 6622916 6831912 7210958 6379520 FALSE TRUE 7500167.999 7643282.04 6150148.391 6255034.831 7512069.418 8083790.014 6703969.227 6690830.63 6392400.279 5947429.428 1.261077259 1.285140435 1.03408514 1.051720732 1.263078362 1.359207387 1.127204502 1.12499538 1.07481734 1 22.50383482 1.353876368 1.462049732 1.012457943 1.198050913 0.318397299 0.097296156 0.509972161 2.035289021 0.096398998 0.030378206 22.58792663 -1.353876368 0.18559297 TTGT(ph)PPDSSLVTYELHSRPEQDKFSQAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TTGTPPDSSLVTYELHSRPEQDKFSQAAK 29 2 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.187)T(0.187)GT(0.622)PPDS(0.003)S(0.001)LVTYELHSRPEQDKFSQAAK;T(0.023)T(0.023)GT(0.955)PPDSSLVTYELHSRPEQDKFSQAAK;T(0.049)T(0.049)GT(0.902)PPDSSLVTYELHSRPEQDKFSQAAK 247.76 7.25E-46 2624390000 2809640 2559470 1783710 1603070 2145830 2431110 2252340 2333620 2757000 2522490 TRUE FALSE 2699836.163 2486476.422 2106066.075 1685804.635 2214852.571 2480268.71 2279904.811 2285429.932 2444036.918 2351639.505 1.148065491 1.057337409 0.895573522 0.716863546 0.941833374 1.054697671 0.96949588 0.971845356 1.039290636 1 21.16523549 1.354073647 5.206853658 1.019009473 0.963063137 0.030746922 0.10861827 0.869403255 32.96311394 0.084066123 0.029575036 22.59818956 -1.354073647 -0.055946336 DTGSEVPSGSGHGPCT(ph)PPPAPANFEDVAPTGSGEPGATRES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTGSEVPSGSGHGPCTPPPAPANFEDVAPTGSGEPGATRESPK 43 1 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 2 DTGSEVPSGSGHGPCT(1)PPPAPANFEDVAPT(0.001)GS(0.001)GEPGAT(0.02)RES(0.979)PK 153.94 6.93E-13 308230000 71013 74270 58575 57961 74728 68126 68272 72654 97117 80989 TRUE FALSE 68237.73345 72151.89232 69160.80549 60952.37416 77131.69399 69503.5544 69107.53316 71153.66951 86092.68531 75503.54289 0.903768629 0.95560936 0.915994175 0.807278332 1.021563903 0.920533683 0.915288614 0.942388486 1.140246961 1 16.20425672 1.354425052 6.422099346 1.068424478 0.922025874 0.503203571 0.058797865 0.156668393 7.800445779 0.038308262 0.013809936 22.61648204 -1.354425052 -0.146398603 GYDDRDYYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GYDDRDYYSR 10 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;; 168.22 4.56E-06 22738200000 12471800 14420500 10613000 13090900 13216100 13822600 12810300 13170100 13750200 12775700 FALSE TRUE 11984388.27 14009241.46 12531005.18 13766522.92 13641207.86 14102102.44 12967076.28 12898132.83 12189334.94 11910390.46 1.006212878 1.176220167 1.052107001 1.155841445 1.145319954 1.184016804 1.088719663 1.08293115 1.023420263 1 23.50571737 1.354781868 1.67611199 1.000993134 1.121365897 0.382859406 0.052515048 0.33538761 1.704669226 0.045114788 0.013899193 22.63507134 -1.354781868 0.120372763 RESWER ddPTM_BT-474_Pertuzumab_2h_R1 1 RESWER 6 1 E9PH64;Q9Y6M9;A0A3B3IT57;E7EWZ0;E9PF49 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 94.539 0.07114 89284000 70649 99586 71196 136590 100800 110400 114130 99999 71389 87751 FALSE TRUE 67887.95897 96745.90478 84062.70095 143639.4263 104042.3235 112632.3636 115526.7571 97933.9857 63285.22001 81807.54661 0.82984959 1.182603669 1.027566581 1.75582122 1.271793714 1.376796742 1.412177261 1.197126546 0.773586578 1 16.31994632 1.355960843 5.385093293 0.892401577 1.277436453 0.284239442 0.235716659 0.253202831 10.04250439 0.167905524 0.059416752 22.69660204 -1.355960843 0.385034876 LPVEEAYKR ddPTM_BT-474_Pertuzumab_2h_R1 4 LPVEEAYKR 9 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 114.5 0.0026114 1747860000 1138430 1421120 1035290 1449080 1298960 1342650 1350170 1307410 1240110 1228010 FALSE TRUE 1093938.897 1380591.049 1222389.933 1523867.192 1340742.228 1369799.303 1366693.784 1280411.527 1099337.912 1144835.789 0.95554219 1.205929324 1.067742592 1.331079275 1.171121868 1.196502866 1.193790234 1.118423742 0.960258163 1 20.12670925 1.356011073 3.774065897 0.97996108 1.166066229 0.367454861 0.092595532 0.225552523 5.118228509 0.069020933 0.022729592 22.69922724 -1.356011073 0.186105149 ALVVPEPEPDSDS(ph)NQERK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALVVPEPEPDSDSNQERK 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDS(0.047)DS(0.953)NQERK 188.44 2.32E-14 113280000 148150 147060 134760 152920 128990 149810 190960 185960 241780 266670 TRUE FALSE 142360.1342 142865.9928 159114.1297 160812.2195 133139.0805 152839.2608 193297.0256 182119.861 214334.148 248608.2034 0.572628466 0.574663229 0.640019628 0.646850013 0.535537761 0.614779636 0.777516683 0.73255773 0.862136265 1 17.92351438 1.356377132 0.698969006 0.999496935 0.588354854 0.894732869 0.045403749 0.18988152 0.211518348 0.044378781 0.019261844 22.71836812 -1.356377132 -0.411142081 DAGADLDKPEPTCGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAGADLDKPEPTCGR 15 1 I3L4X3;G5E9C2;Q15653-2;Q15653 I3L4X3 NFKBIB NF-kappa-B inhibitor beta 0 ; 70.451 0.042543 485410000 476720 446050 406400 411120 453750 459150 469970 517420 587530 605960 FALSE TRUE 458089.2554 433329.0907 479845.5203 432337.9525 468345.2808 468434.3276 475721.6334 506735.0962 520836.0575 564917.7895 0.810895433 0.767065755 0.8494077 0.765311273 0.829050332 0.82920796 0.842107723 0.897006796 0.921967881 1 19.10768141 1.356536673 0.674422802 1.000699569 0.79792864 0.879944323 0.02359899 0.184917905 0.194267535 0.020696727 0.009223988 22.72671539 -1.356536673 -0.202770929 MADFHKEEMDDQDKDK ddPTM_BT-474_Pertuzumab_2h_R1 1 MADFHKEEMDDQDKDK 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 140.81 1.00E-06 300220000 140590 117650 112600 68523 109510 81614 123170 114920 169670 130020 FALSE TRUE 135095.5874 114294.7372 132949.3248 72059.48024 113032.4886 83264.291 124677.3913 112546.8618 150409.7729 121213.6296 1.114524727 0.942919848 1.09681828 0.594483314 0.932506427 0.686921853 1.028575679 0.928500056 1.240865185 1 16.8871924 1.356572621 6.475295844 1.11897859 0.909223154 0.197614966 0.16465516 0.316613067 15.89841475 0.110288619 0.039804438 22.72859664 -1.356572621 -0.209755437 FDDAVVQSDMK ddPTM_BT-474_Pertuzumab_2h_R1 3 FDDAVVQSDMK 11 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;; 193.21 2.45E-06 503679000 894710 837780 825710 833114 719280 567753 994250 964990 1214430 1290870 FALSE TRUE 859743.744 813887.3347 974934.1648 876111.1134 742416.2944 579233.3547 1006417.929 945062.6193 1076572.998 1203438.225 0.714406212 0.676301714 0.81012398 0.728006719 0.616912675 0.481315403 0.836285493 0.785302145 0.894581022 1 20.19873066 1.356694054 1.301040265 0.986539533 0.684424491 0.570356782 0.090968705 0.309771046 1.006518017 0.08762796 0.028389129 22.73495264 -1.356694054 -0.302115043 EAELTEINRR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAELTEINRR 10 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ; 164.33 9.92E-06 1552580000 767690 883710 636960 801310 722980 797470 796350 802530 738120 817960 FALSE TRUE 737687.8261 858507.456 752072.8411 842665.7051 746235.3083 813595.3898 806095.9695 785957.4751 654331.7121 762558.8406 0.967384793 1.12582454 0.986248931 1.105050076 0.978593741 1.066928015 1.057093468 1.030684366 0.858073734 1 19.54048914 1.356734829 7.773111853 0.929958864 1.042950111 0.361659546 0.058879002 0.205356151 12.74873715 0.035005302 0.012753389 22.7370873 -1.356734829 0.112991247 LFEELAMDVYDEVDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFEELAMDVYDEVDRR 16 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 ;;; 258.36 1.69E-26 351566000 82664.6 109946 73742.4 98869.3 101413 110418.2 90599.3 99568.4 80823.8 101439.3 FALSE TRUE 79433.97604 106810.4477 87069.29207 103971.9564 104675.0412 112650.9317 91708.08133 97512.27775 71649.02107 94568.72586 0.839960307 1.129447888 0.920698585 1.099432772 1.106867416 1.191207036 0.969750628 1.031126061 0.7576397 1 16.52907554 1.35679382 8.67013091 0.879300067 1.041990067 0.235764024 0.112950447 0.32063637 22.46333882 0.071639423 0.026167501 22.74017592 -1.35679382 0.16269 QPPGVPNGPSS(ph)PTNESAPELPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPPGVPNGPSSPTNESAPELPQR 23 0 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 QPPGVPNGPS(0.264)S(0.696)PT(0.036)NES(0.003)APELPQR 78.272 0.008866 264940000 150080 147710 120430 190510 176200 172370 171280 161070 144510 146740 TRUE FALSE 144214.7077 143497.4554 142194.38 200342.2439 181867.633 175855.4395 173376.1759 157743.8482 128105.8306 136801.1691 1.05419207 1.048949043 1.039423719 1.464477572 1.3294304 1.285481993 1.267358876 1.153088451 0.936438128 1 17.06172103 1.356940361 4.039567199 0.96916086 1.216035216 0.351700325 0.130411313 0.265551684 6.779008851 0.10960838 0.036715477 22.74785029 -1.356940361 0.246874356 VLS(ph)PLRS(ph)PPLIGSESAYESFLSADDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSPLRSPPLIGSESAYESFLSADDK 26 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 VLS(0.745)PLRS(0.766)PPLIGS(0.212)ES(0.212)AY(0.059)ES(0.005)FLSADDK;VLS(1)PLRS(0.999)PPLIGS(0.001)ESAYESFLSADDK 129.9 4.31E-05 53708000 56680 56624 55547 60654 66912 57585 50622 57951 57378 47442 TRUE FALSE 54464.88294 55009.13896 65585.57854 63784.36021 69064.28525 58749.40815 51241.52718 56754.2916 50864.68999 44228.71108 1.231437263 1.243742755 1.482873385 1.442148293 1.561526067 1.328309298 1.158558003 1.283200216 1.150037809 1 15.43269558 1.356981868 0.814088977 1.014811431 1.385901281 0.546135687 0.109066177 0.462034909 0.664060405 0.110631955 0.043448495 22.75002446 -1.356981868 0.371089849 LAAAILGGVDQIHIKPGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAAAILGGVDQIHIKPGAK 19 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 249.69 2.60E-25 1028050000 2488700 2213000 2034200 2064500 2201200 2295400 2308000 2498100 2793500 2817200 FALSE TRUE 2391438.853 2149887.407 2401825.191 2171049.092 2272003.597 2341814.561 2336245.994 2446513.362 2476393.591 2626388.535 0.910542679 0.81857173 0.914497287 0.826629063 0.865067589 0.891648181 0.889527944 0.931512352 0.942889279 1 21.32464893 1.357348059 0.78529202 0.998057582 0.864588182 0.673857316 0.02943136 0.300419658 0.406204824 0.025111369 0.010080319 22.76921506 -1.357348059 -0.1334694 ALDLDSSCK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALDLDSSCK 9 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 154.12 0.00017788 718050000 1041770 966740 811460 866990 939920 1006920 930830 1037690 1206110 1171230 FALSE TRUE 1001056.477 939169.5217 958108.8728 911735.4578 970153.3804 1027280.612 942221.776 1016261.339 1069197.449 1091901.549 0.916801041 0.860122895 0.877468187 0.834997861 0.888498951 0.940817982 0.862918252 0.930726163 0.979206825 1 20.05841135 1.357464089 1.832582182 1.00042793 0.881685702 0.693408314 0.028319505 0.183718623 1.096019469 0.025796858 0.00787699 22.77529912 -1.357464089 -0.118742228 AQQNNVEHK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQQNNVEHK 9 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 155.15 7.40E-05 1684830000 2041580 1780390 1731110 1811280 1800590 1654510 1983450 1972230 2347700 2274500 FALSE TRUE 1961792.797 1729615.02 2043960.085 1904760.378 1858507.613 1687965.326 2007724.054 1931502.761 2081198.938 2120446.089 0.925179285 0.815684506 0.963929286 0.89828286 0.876470108 0.796042557 0.946840415 0.910894538 0.981491088 1 21.01593637 1.357794782 1.465853316 1.000384957 0.883708516 0.405789015 0.049255545 0.36705634 1.471967159 0.043708843 0.013783258 22.79264791 -1.357794782 -0.116676441 KPPPSKEELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPPSKEELLK 11 2 D3DQV9;P78344;H0Y3P2;P78344-2;E9PKF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 72.705 0.025627 587970000 560330 536240 485740 467130 497480 487070 579520 593670 785050 773530 FALSE TRUE 538431.6841 520946.9602 573524.0232 491238.6353 513481.896 496918.8891 586612.3391 581410.507 695934.4152 721138.1241 0.746641546 0.722395534 0.795303984 0.681199092 0.712043753 0.689075882 0.813453511 0.806240147 0.965050095 1 19.45991609 1.357902552 1.388835 1.006954909 0.728140222 0.869213035 0.037935949 0.124027549 0.452142003 0.0339643 0.010834152 22.79830463 -1.357902552 -0.278814688 EIQELQSKPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIQELQSKPDR 11 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;H0Y8L4;H0Y9I0;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 67.997 0.053301 399110000 203430 217570 182130 164180 203540 216680 166280 206600 184350 176300 FALSE TRUE 195479.7307 211365.1166 215044.9425 172653.3495 210087.049 221061.4181 168314.9844 202333.6378 163423.3609 164359.044 1.189345752 1.285996265 1.308385211 1.050464552 1.278220193 1.344990898 1.024068894 1.231046573 0.994307079 1 17.32649132 1.357935042 1.04292689 0.988655654 1.232668071 0.399622872 0.102322295 0.473044072 1.04228583 0.091167331 0.031739193 22.80001022 -1.357935042 0.244012417 GHQAFDVGQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHQAFDVGQPR 11 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 ; 124.39 0.00035022 334780000 84333 111090 91477 141155 97191 106757 115198 110240 111839 108730 FALSE TRUE 81037.17312 107921.822 108008.9288 148440.0265 100317.2368 108915.6997 116607.8276 107963.5055 99143.50559 101365.6203 0.799454222 1.064678751 1.065538084 1.464402093 0.989657406 1.074483631 1.150368609 1.06508997 0.978078222 1 16.6292089 1.358051343 4.333700572 0.989858491 1.096212253 0.055601057 0.155145162 0.64308595 18.44078713 0.115876676 0.039472861 22.80611676 -1.358051343 0.106353762 TLRDS(ph)PNVEAAHLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLRDSPNVEAAHLAR 15 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 T(0.006)LRDS(0.994)PNVEAAHLAR;T(0.132)LRDS(0.868)PNVEAAHLAR;T(0.033)LRDS(0.967)PNVEAAHLAR;T(0.004)LRDS(0.996)PNVEAAHLAR 225.29 6.16E-13 2811740000 588030 629300 591480 587840 557240 602881 689010 690610 772050 815140 TRUE FALSE 565049.1375 611352.9801 698373.5934 618178.4928 575164.1307 615071.6669 697442.3105 676348.6622 684410.1207 759929.8417 0.743554347 0.804486081 0.918997459 0.813467848 0.756864778 0.809379541 0.917771973 0.890014611 0.900622772 1 19.53550671 1.358225021 0.600265944 0.996504845 0.806364466 0.589503897 0.049947566 0.549372787 0.478579121 0.052505779 0.025693877 22.81523893 -1.358225021 -0.190140378 CQEVISWLDANTLAEKDEFEHK ddPTM_BT-474_Pertuzumab_2h_R1 4 CQEVISWLDANTLAEKDEFEHK 22 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;; 323.03 4.52E-68 9606280000 7083770 6031020 4913760 4901052 5355204 5712410 5721650 6293020 8575790 7679640 FALSE TRUE 6806928.437 5859021.215 5801785.738 5153995.881 5527459 5827918.844 5791673.264 6163066.938 7602302.272 7159491.142 0.950755899 0.818357213 0.810362863 0.719882989 0.772046349 0.814012997 0.808950406 0.860824717 1.061849525 1 22.77142562 1.358280614 3.694791954 1.030960287 0.809961505 0.693220968 0.056711897 0.126419851 2.762711031 0.04559217 0.014965637 22.81815964 -1.358280614 -0.220998782 GGFGFR ddPTM_BT-474_Pertuzumab_2h_R1 8 GGFGFR 6 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;;;; 128.66 0.038452 6196224000 5221640 5668620 4841276 5920650 5662480 5365700 5561240 5641480 5524070 5544120 FALSE TRUE 5017572.536 5506956.508 5716202.267 6226215.456 5844618.812 5474198.13 5629300.119 5524981.467 4897000.732 5168611.814 0.970777593 1.065461425 1.105945363 1.204620444 1.130790824 1.05912348 1.089131922 1.068948814 0.947449897 1 22.30134542 1.358611228 4.263869124 0.974663098 1.092796169 0.387339037 0.057008293 0.22696952 6.338131785 0.045272746 0.015373184 22.83553694 -1.358611228 0.11813307 TNSMSSSGLGS(ph)PNRSS(ph)PSIICMPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNSMSSSGLGSPNRSSPSIICMPK 24 1 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 2 T(0.047)NS(0.058)MS(0.058)S(0.169)S(0.149)GLGS(0.52)PNRS(0.117)S(0.877)PS(0.004)IICMPK;T(0.027)NS(0.033)MS(0.154)S(0.139)S(0.154)GLGS(0.493)PNRS(0.219)S(0.774)PS(0.007)IICMPK 79.209 0.010857 641960000 272640 219676 213527 211280 193137 240530 242410 277960 367040 370820 TRUE FALSE 261984.9274 213411.0556 252116.0788 222184.1861 199349.427 245393.6814 245376.6861 272220.0289 325375.158 345704.0311 0.75783012 0.617323017 0.729283017 0.642700594 0.576647679 0.709837489 0.709788328 0.787436664 0.94119573 1 18.3991779 1.3586573 1.431743601 1.004897403 0.667509809 0.844598967 0.050370493 0.13164974 0.506436374 0.044586821 0.014131712 22.83795961 -1.3586573 -0.337387594 ELEAENYHDIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEAENYHDIKR 12 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 125.36 0.00019906 112220000 248890 234720 212090 249940 252620 207480 262640 277350 341100 345410 FALSE TRUE 239163.1036 228026.0154 250419.3809 262839.4334 260745.7517 211675.3878 265854.2669 271622.6256 302379.758 322015.073 0.742707791 0.70812218 0.777663538 0.816233324 0.809731511 0.65734621 0.825595723 0.843509041 0.939023615 1 18.29676869 1.358866052 1.365805865 0.997355549 0.757387999 0.761523351 0.047187089 0.189483329 0.670656228 0.044125772 0.014133742 22.8489397 -1.358866052 -0.239967551 TRNEMTAEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TRNEMTAEEK 10 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;; 130.99 0.00023889 2110410000 2857400 2678500 2094936 2345319 2513420 2598280 2500310 2646107 3216910 2818480 FALSE TRUE 2745729.649 2602111.803 2473537.537 2466361.195 2594266.437 2650819.002 2530909.542 2591463.966 2851739.863 2627581.839 1.044964464 0.990306663 0.941374118 0.93864296 0.987320889 1.008843554 0.963208645 0.98625433 1.085309626 1 21.32530427 1.359206711 8.469457886 1.042215576 0.980026594 0.31775464 0.035128516 0.270153758 18.47561931 0.023501036 0.008582341 22.86686938 -1.359206711 -0.062188982 LPLS(ph)PIITLEEDTKCPATGDDLQSLGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPLSPIITLEEDTKCPATGDDLQSLGQR 28 1 A0A1W2PQQ1;Q5HYW2;A0A0J9YW69;A0A0J9YY72;Q5HYW2-2 A0A1W2PQQ1 NHSL2 NHS-like protein 2 1 LPLS(0.964)PIIT(0.036)LEEDTKCPATGDDLQSLGQR 97.916 0.0010884 29551000 17328 20185 13956 21570 24496 24772 20260 20085 16963 16994 TRUE FALSE 16650.8026 19609.34356 16478.15965 22683.23028 25283.93609 25272.90681 20507.94794 19670.23773 15037.43135 15842.98124 1.050989227 1.237730656 1.040092101 1.431752644 1.595907721 1.595211559 1.294450055 1.241574261 0.949154147 1 13.95155622 1.359208137 2.989298554 0.968939893 1.330018596 0.359945406 0.180731716 0.304496621 4.502549753 0.166614868 0.052214669 22.86694448 -1.359208137 0.361078702 SGLS(ph)DIILGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGLSDIILGK 10 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;K7EJR2;M0R330;M0QX30;M0R1V5 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 S(0.008)GLS(0.992)DIILGK 84.507 0.015602 49007000 66969 62842 52584 53002 57286 59824 60083 69694 75542 79705 TRUE FALSE 64351.77744 61049.80769 62087.09852 55737.43957 59128.65622 61033.68227 60818.31373 68254.79455 66966.78886 74306.50936 0.866031496 0.821594342 0.835553965 0.750101708 0.795739925 0.82137733 0.81847895 0.918557407 0.901223721 1 16.18120098 1.359517892 1.04505353 0.989672804 0.809965469 0.763782084 0.032874348 0.218378901 0.482684465 0.031051809 0.01080612 22.88325981 -1.359517892 -0.179707335 YLLDRDDPSDALSK ddPTM_BT-474_Pertuzumab_2h_R1 1 YLLDRDDPSDALSK 14 1 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 0 63.681 0.061243 271680000 340510 351400 254020 372090 374740 374440 336050 354220 312210 352710 FALSE TRUE 327202.4927 341378.4161 299927.0646 391293.6095 386793.8524 382011.4333 340162.6804 346905.2332 276769.2297 328820.6375 0.995078944 1.03819036 0.912129685 1.189991031 1.176306497 1.16176234 1.034493099 1.05499836 0.841702734 1 18.32694132 1.35960662 6.289928621 0.922280605 1.073674831 0.310714239 0.089206428 0.254999755 12.35811314 0.064443917 0.023224637 22.88793546 -1.35960662 0.151394227 IFCSEDEQSR ddPTM_BT-474_Pertuzumab_2h_R1 4 IFCSEDEQSR 10 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;; 191.17 1.91E-06 1158590000 463866 489596 477134 654601 575123 605727 569744 553772 521636 511345 FALSE TRUE 445737.6039 475633.2014 563362.7276 688385.0361 593622.3536 617975.215 576716.6975 542336.4147 462422.0682 476711.1477 0.935026601 0.997738785 1.181769569 1.444029659 1.245245379 1.29633053 1.209782277 1.137662539 0.970025707 1 18.86275584 1.359851326 3.322823181 0.98299143 1.194914864 0.255090743 0.13517136 0.360025433 6.489786653 0.120254783 0.038549898 22.90083545 -1.359851326 0.211923434 S(ph)EDEDSLEEAGSPAPGPCPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEDEDSLEEAGSPAPGPCPR 20 0 Q8TBB5-3;Q8TBB5;Q8TBB5-2 Q8TBB5-3 KLHDC4 Kelch domain-containing protein 4 1 S(1)EDEDSLEEAGSPAPGPCPR;S(1)EDEDSLEEAGSPAPGPCPR 379.06 1.22E-112 333240000 75081 80691 71789 74701 71823 75641 75170 80064 90872 85955 TRUE FALSE 72146.75151 78389.77168 84762.86924 78556.32756 74133.25202 77170.51285 76089.95295 78410.65042 80556.59153 80133.19129 0.900335433 0.978243477 1.057774786 0.980321965 0.925125417 0.963028074 0.949543525 0.978504028 1.005283706 1 16.29011231 1.359885527 4.185101449 1.002439913 0.967773949 0.125354151 0.038881639 0.527642424 14.28763987 0.030741164 0.01040512 22.90263895 -1.359885527 -0.034665964 NSDMHLLDLESMGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSDMHLLDLESMGK 14 0 Q9Y3P9;Q9Y3P9-2;Q9Y3P9-3 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 162.29 4.46E-06 98580000 138130 135910 139080 151310 132880 142690 160650 156420 208930 196760 FALSE TRUE 132731.7269 132033.9799 164214.8498 159119.1272 137154.2059 145575.2896 162616.0828 153189.8723 185213.1423 183433.2699 0.723596799 0.719792979 0.895229365 0.867449658 0.747706269 0.793614428 0.886513569 0.835125887 1.009703105 1 17.4848958 1.360140898 1.377267245 1.015836308 0.798487956 0.616430648 0.061447842 0.274830452 0.987174453 0.058324898 0.01865259 22.91610996 -1.360140898 -0.217348352 DSGRLS(ph)PDLSVCGQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSGRLSPDLSVCGQPR 16 1 Q8TF76;Q8TF76-2 Q8TF76 GSG2 Serine/threonine-protein kinase haspin 1 DS(0.005)GRLS(0.995)PDLSVCGQPR;DS(0.003)GRLS(0.997)PDLSVCGQPR 164.98 4.35E-09 1033440000 284960 275800 207990 311920 246230 259900 270960 273950 244050 277480 TRUE FALSE 273823.4482 267934.454 245578.4197 328018.2286 254150.2116 265155.3561 274276.0895 268292.8368 216346.4671 258686.0324 1.058516556 1.035751531 0.949330033 1.268016775 0.982465923 1.025008399 1.060266327 1.037136927 0.836328367 1 17.98084263 1.36060858 7.457468406 0.919307022 1.052895124 0.27389456 0.087500304 0.272493929 16.18012497 0.056132964 0.020432208 22.9408011 -1.36060858 0.133588101 IKEDDAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKEDDAPR 8 1 P25490;A0A494C032;H0YJV7 P25490 YY1 Transcriptional repressor protein YY1 0 ; 83.998 0.016201 492210000 564740 601580 501690 606470 624860 595440 592100 604970 619880 602630 FALSE TRUE 542669.3364 584423.5274 592356.543 637769.9894 644959.1894 607480.2048 599346.2969 592477.1581 549513.8211 561813.3333 0.965924631 1.040245029 1.054365406 1.135199098 1.147995519 1.081284777 1.066806822 1.054580094 0.978107475 1 19.09973134 1.360677821 3.380623954 0.988676801 1.073770496 0.304541916 0.047859471 0.308885499 5.749605814 0.041655751 0.013415651 22.94445895 -1.360677821 0.085093695 NLS(ph)SDEATNPISR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLSSDEATNPISR 13 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NLS(0.5)S(0.5)DEATNPISR;NLS(0.975)S(0.025)DEATNPISR 246.8 7.26E-12 201880000 388560 411510 321520 348730 362710 369360 396210 396690 461930 449170 TRUE FALSE 373374.6456 399774.1377 379625.8162 366727.9971 374376.8966 376828.7123 401058.9365 388498.2129 409493.643 418747.3158 0.89164666 0.954690628 0.906574924 0.875773965 0.894040111 0.89989523 0.957758823 0.927762873 0.977901535 1 18.67572042 1.361167962 0.932318074 0.999696121 0.905522619 0.653084259 0.023352654 0.328302464 0.594634506 0.022318764 0.008164024 22.97036848 -1.361167962 -0.094173502 KPYPDDENLVEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPYPDDENLVEVK 13 1 E9PLK3;P55786;P55786-2;A6NEC2;A6NEC2-2 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 77.146 0.04288 676700000 593860 512160 470180 383080 504000 575670 472280 552770 686970 638270 FALSE TRUE 570651.2947 497553.6983 555151.9851 402850.8047 520211.6177 587310.4418 478059.9039 541355.1063 608988.0456 595039.4044 0.959014295 0.836169327 0.93296676 0.67701534 0.874247342 0.987011007 0.803408817 0.909780264 1.023441542 1 19.18262568 1.361449105 4.011747299 1.011240861 0.865572939 0.31961511 0.083004508 0.255749674 6.451597886 0.061972752 0.020798938 22.98524327 -1.361449105 -0.145667921 STVLSLDWHPNNVLLAAGSCDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 STVLSLDWHPNNVLLAAGSCDFK 23 0 A0A1W2PNV4;E9PF58;Q92747;Q92747-2;C9JEY1;C9K057;O15143 A0A1W2PNV4;Q92747;C9JEY1 ARPC1A;ARPC1B Actin-related protein 2/3 complex subunit 1A;Actin-related protein 2/3 complex subunit 1B 0 ; 272.24 1.23E-51 728800000 1275290 1349630 1116220 1176770 1197150 1255840 1277180 1365710 1570430 1541970 FALSE TRUE 1225450.257 1311139.874 1317945.784 1237503.241 1235657.417 1281233.945 1292810.511 1337507.611 1392161.37 1437530.998 0.852468752 0.912077635 0.91681208 0.860853256 0.859569232 0.89127396 0.899327049 0.930420014 0.9684392 1 20.45516164 1.362051228 1.257518067 0.999213525 0.882879257 0.805388826 0.020075002 0.180914278 0.553306388 0.019221427 0.006293801 23.01713305 -1.362051228 -0.116334268 ATDCVGHDVVTLLR ddPTM_BT-474_Pertuzumab_2h_R1 8 ATDCVGHDVVTLLR 14 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;;; 223.03 3.67E-12 8192917000 4974122 6017764 4642916 6942900 5345587 5766888 5990624 5922752 5684225 6050753 FALSE TRUE 4779727.813 5846143.263 5481994.202 7301223.901 5517532.661 5883498.427 6063939.049 5800445.101 5038975.608 5640930.11 0.847329735 1.036379311 0.971824521 1.294329793 0.978124627 1.043001475 1.074989218 1.028278136 0.893288077 1 22.42750163 1.362130178 7.325221839 0.947713751 1.041526864 0.092877255 0.108337196 0.489786923 28.55527738 0.071462532 0.026000677 23.02131768 -1.362130178 0.093813113 S(ph)ET(ph)PPHWR ddPTM_BT-474_Pertuzumab_2h_R1 2 SETPPHWR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 S(1)ET(1)PPHWR;S(1)ET(1)PPHWR 139.31 0.0011856 1915140000 1517700 1396860 1554960 1569630 1480540 1417300 1526800 1697780 2212300 2064870 TRUE FALSE 1458386.606 1357022.92 1835975.862 1650638.792 1528162.914 1445958.777 1545485.435 1662720.25 1961168.979 1925014.516 0.757597719 0.704941656 0.953746503 0.857468232 0.793844878 0.751141753 0.802843523 0.863744266 1.018781398 1 20.87643789 1.362333274 2.952658143 1.013373932 0.805675717 0.616542514 0.063971863 0.17961565 2.599708886 0.056197629 0.017614618 23.03208604 -1.362333274 -0.207698215 CGAQDKEHPR ddPTM_BT-474_Pertuzumab_2h_R1 2 CGAQDKEHPR 10 1 Q96GX9 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 0 ; 180.97 1.17E-06 328390000 600020 566410 457390 488070 524880 521250 557900 556120 691210 583670 FALSE TRUE 576570.555 550256.5414 540050.5476 513259.3512 541763.2419 531790.0321 564727.7471 544635.9277 612746.7386 544137.511 1.0596045 1.011245375 0.992489098 0.943253021 0.995636638 0.977308165 1.037840134 1.000915976 1.126088031 1 19.05361176 1.362381231 24.97308895 1.063213201 1.001024294 0.259214079 0.041039686 8.635021634 1848.314724 0.026329912 0.009614861 23.03462951 -1.362381231 -0.062188907 AQLS(ph)PGIYDDTSAR ddPTM_BT-474_Pertuzumab_2h_R1 4 AQLSPGIYDDTSAR 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR 255.72 2.86E-24 4897890000 3295390 3507720 2881830 3490970 3401340 3442250 3244230 3457710 3199190 3512810 TRUE FALSE 3166602.516 3407683.26 3402640.787 3671139.38 3510747.19 3511854.653 3283933.857 3386307.08 2836031.363 3274884.25 0.966935706 1.040550749 1.039011008 1.120998209 1.072021764 1.072359933 1.002763337 1.034023441 0.865994382 1 21.64301249 1.363077983 6.668126394 0.933748292 1.04640459 0.446634639 0.04925287 0.181978682 9.504305814 0.033373722 0.012088096 23.07161432 -1.363077983 0.112656299 ETMQSLNDR ddPTM_BT-474_Pertuzumab_2h_R1 7 ETMQSLNDR 9 0 P05783;F8VZY9;CON__Q92764;C4AM86;CON__Q497I4;Q92764 P05783 KRT18;KRT35 "Keratin, type I cytoskeletal 18;Keratin, type I cuticular Ha5" 0 ;;;;;; 278.8 5.99E-21 19774540000 4298700 4514320 3985740 4592940 4327370 4208700 4529880 4539960 4408550 4657080 FALSE TRUE 4130702.052 4385576.014 4706051.88 4829982.184 4466563.786 4293802.798 4585318.026 4446208.239 3908109.886 4341651.824 0.951412554 1.010116931 1.083931202 1.112475707 1.028770608 0.988979073 1.056122926 1.024082174 0.90014355 1 22.0498126 1.363792283 7.368411194 0.950939929 1.035538976 0.312631182 0.04860817 0.257745193 15.18348943 0.033698708 0.012267238 23.10959224 -1.363792283 0.084599047 (ac)ASNSWNASSS(ph)PGEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASNSWNASSSPGEAR 15 0 Q99594 Q99594 TEAD3 Transcriptional enhancer factor TEF-5 1 ASNSWNAS(0.12)S(0.12)S(0.76)PGEAR 63.408 2.94E-06 150520000 17801 33736 25249 33754 41471 36223 27032 31938 21487 30233 TRUE FALSE 17105.31724 32773.88231 29812.05596 35496.04799 42804.95238 36955.45388 27362.8257 31278.46914 19047.88584 28185.29198 0.606888062 1.16280088 1.057716769 1.25938195 1.518698206 1.311160938 0.97081931 1.109744372 0.675809421 1 14.78265489 1.364841151 5.736681662 0.840049074 1.142439957 0.186561696 0.236949585 0.3300751 14.27949192 0.168998073 0.060492857 23.16547185 -1.364841151 0.302390883 QREFESR ddPTM_BT-474_Pertuzumab_2h_R1 2 QREFESR 7 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 152.63 0.0016423 11294400000 431550 538720 374920 457600 426430 439750 478920 468280 465940 481220 FALSE TRUE 414684.5489 523356.2331 442676.3841 481216.7908 440146.5082 448642.0463 484781.1662 458609.8544 413048.4446 448626.5408 0.924342435 1.16657439 0.986736949 1.072644498 0.981097791 1.000034562 1.080589582 1.022253061 0.920695516 1 18.77515545 1.365370331 7.364108835 0.961358731 1.033952998 0.150460313 0.065277959 0.359768653 21.26915021 0.040268977 0.01466297 23.19371576 -1.365370331 0.072594267 IDLPEVQIEHDPELEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDLPEVQIEHDPELEK 16 0 Q14966;Q14966-3;Q14966-4;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 0 ; 159.19 9.22E-09 127740000 381640 350030 311120 341070 341310 326200 389830 428010 459410 512260 FALSE TRUE 366725.0869 340047.4871 367346.3048 358672.6636 352288.5461 332795.9875 394600.8562 419171.4439 407259.7028 477564.1739 0.76790745 0.712045638 0.769208255 0.751046002 0.737677919 0.696861293 0.826278179 0.877727993 0.852785291 1 18.86533509 1.365833739 0.798694682 0.988225656 0.737022584 0.844523376 0.034407165 0.206179235 0.286094262 0.032935902 0.01311378 23.21847754 -1.365833739 -0.251203072 MNSEEEDEVWQVIIGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 MNSEEEDEVWQVIIGAR 17 0 Q9NR28-2;Q9NR28;Q9NR28-3;H7BZK7;A0A2U3TZH2;H7BZQ7 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ;;; 213.67 1.07E-12 195989000 103598 110308 96035.3 123405 84937.8 107930.5 103177 103693 95378 91896.6 FALSE TRUE 99549.27563 107162.1238 113391.015 129773.9468 87669.90148 110112.9287 104439.711 101551.7033 84551.0893 85672.36143 1.161976558 1.250836583 1.323542542 1.514770279 1.023316038 1.285279486 1.219059557 1.185349646 0.98691209 1 16.38654223 1.365933531 2.177504348 0.981812665 1.259989356 0.429736563 0.117622409 0.284843412 2.336522345 0.103439033 0.03149854 23.22381329 -1.365933531 0.278176691 TVVLHIDGLDDTSRR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVVLHIDGLDDTSRR 15 1 Q9NVT9;E5RJ86 Q9NVT9 ARMC1 Armadillo repeat-containing protein 1 0 ;;; 201.3 4.21E-09 1100730000 451248 497340 373039 468865 488742 544768 446467 481675 488125 460357 FALSE TRUE 433612.7293 483156.3501 440455.4455 493063.1788 504462.8303 555783.5822 451930.9967 471728.2429 432715.0964 429176.6103 1.010336348 1.12577512 1.026280172 1.148858458 1.175420137 1.294999701 1.053018701 1.099147138 1.008244825 1 18.71121193 1.366217676 1.849362906 0.997559338 1.126136593 0.253644015 0.077526938 0.472709684 2.87731686 0.072269192 0.02212882 23.23901285 -1.366217676 0.128577255 SQAPGQPGASQWGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQAPGQPGASQWGSR 15 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 148.96 4.00E-06 59567000 62093 63878 46994 58943 58088 64448 56961 60163 53635 58700 FALSE TRUE 59666.33691 62056.26198 55486.86118 61985.05529 59956.45327 65751.18272 57658.10576 58920.61303 47546.57966 54724.19672 1.090309963 1.133982145 1.013936513 1.132680953 1.095611391 1.201501103 1.053612647 1.076683013 0.868840157 1 15.73989125 1.366364434 4.963382878 0.936200097 1.102008595 0.584544171 0.055856627 0.135156217 4.782819427 0.03821165 0.013428065 23.24686715 -1.366364434 0.165808498 SGTPPRQGS(ph)ITSPQANEQSVTPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGTPPRQGSITSPQANEQSVTPQR 24 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.037)GT(0.274)PPRQGS(0.319)IT(0.319)S(0.052)PQANEQSVTPQR 63.713 0.027036 345780000 44996 37165 37303 29489 35623 37998 42782 41802 66919 49704 TRUE FALSE 43237.50657 36105.09059 44044.4819 31010.93082 36768.84615 38766.34559 43305.57891 40938.77409 59322.63567 46337.50381 0.933099607 0.779176426 0.950514773 0.669240427 0.793500796 0.836608415 0.934568662 0.883491141 1.280229421 1 15.49989271 1.366532586 5.568995888 1.13723688 0.842276434 0.566599513 0.102525078 0.137472921 5.726850409 0.068808214 0.024566935 23.25586971 -1.366532586 -0.294960447 QELMQVHGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QELMQVHGEK 10 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 ; 117.23 0.00098484 466250000 712070 664330 583970 647910 711660 646000 746910 757470 888770 908000 FALSE TRUE 684241.5172 645383.9588 689506.3693 681348.7127 734551.1902 659062.5626 756050.908 741827.9798 787880.5556 846500.3512 0.808318055 0.762414284 0.814537606 0.804900685 0.867750603 0.778573289 0.89314896 0.876346925 0.930750418 1 19.69115114 1.366649742 0.462473888 1.007506373 0.78782166 0.821993727 0.029701436 0.340312709 0.199741693 0.031435163 0.019372342 23.26214411 -1.366649742 -0.219684713 STMKPVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 STMKPVQK 8 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 78.934 0.026759 1719500000 1405950 1425810 1133680 1314540 1111020 976170 1352520 1357460 1722680 1615510 FALSE TRUE 1351003.92 1385147.295 1338561.195 1382383.567 1146756.967 995908.8262 1369072.544 1329427.977 1527128.588 1506090.069 0.897027308 0.919697516 0.8887657 0.917862481 0.761413272 0.661254494 0.909024349 0.882701509 1.013968965 1 20.52237662 1.36734957 2.297127033 1.011698279 0.847180011 0.379472802 0.078068752 0.337541569 3.060278879 0.074539884 0.022753321 23.29965927 -1.36734957 -0.164518268 GLPWQSSDQDIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLPWQSSDQDIAR 13 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 ;;; 179.19 2.20E-06 419424000 341362 376015 306496 357513 344415 330597 359774 359621 369085 368826 FALSE TRUE 328021.1956 365291.4204 361886.6452 375964.2888 355493.4213 337281.8978 364177.0218 352194.7007 327188.0181 343845.0865 0.953979593 1.062372082 1.05247002 1.09341184 1.033876694 0.980912367 1.059131092 1.02428307 0.951556474 1 18.3913992 1.367506013 6.030964556 0.976723963 1.03613873 0.247094168 0.039704158 0.272203876 12.63201886 0.027036317 0.009734237 23.30805388 -1.367506013 0.059414767 LQSTFVFEEIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQSTFVFEEIGR 12 0 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7EPL9 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 76.655 0.035336 0 57737 80185 41864 51954 68427 68638 60129 58655 49527 47677 FALSE TRUE 55480.57421 77898.20231 49429.75606 54635.35217 70628.0166 70025.90739 60864.87669 57443.75375 43904.90259 44447.79432 1.248218839 1.752577456 1.112085691 1.229202776 1.589010606 1.57546417 1.369356514 1.292387049 0.987785857 1 15.43982421 1.367555986 2.418598535 0.978358213 1.418071815 0.449674754 0.181280477 0.259784285 2.593304259 0.15731726 0.048183685 23.31073599 -1.367555986 0.439713602 RSYDVPPPPMEPDHPFYSNISK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 122.3 1.24E-05 62811000 50396 55722 30622 33073 47697 52495 43636 44458 45039 41754 FALSE TRUE 48426.4686 54132.86312 36156.07658 34779.90149 49231.21732 53556.48487 44170.03042 43539.92676 39926.36154 38925.96439 1.244065995 1.390662093 0.928842153 0.893488499 1.264739823 1.375855055 1.134718975 1.118531742 1.025699997 1 15.24844516 1.367695693 2.095234419 1.002650995 1.174301454 0.149289405 0.155244583 0.680016421 5.201901913 0.149205241 0.045470497 23.31823596 -1.367695693 0.171650459 KRNEDEDS(ph)PNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRNEDEDSPNK 11 2 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 1 KRNEDEDS(1)PNK 67.275 0.031525 24666000 56038 50817 39818 33731 40224 40176 47044 51657 58796 62278 TRUE FALSE 53847.97301 49367.74892 47013.99835 35471.86095 41517.84149 40988.38625 47619.73854 50590.2649 52121.72457 58059.85559 0.927456199 0.850290591 0.809750522 0.61095331 0.715086889 0.705967761 0.820183551 0.871346723 0.897723979 1 15.82525336 1.368215512 1.280999521 0.984245496 0.767276407 0.434658956 0.08282758 0.412752924 1.30353303 0.082963992 0.027076091 23.34616291 -1.368215512 -0.216969089 WKEPGSGGPQNLS(ph)GPGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 WKEPGSGGPQNLSGPGGR 18 1 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR 255.2 8.99E-31 3449750000 1224960 1359840 1141920 1092390 1103290 1291350 1208700 1390020 1507560 1547250 TRUE FALSE 1177087.209 1321058.695 1348290.346 1148768.379 1138778.325 1317461.982 1223492.432 1361315.601 1336428.109 1442453.379 0.816031371 0.915841519 0.934720224 0.796398965 0.789473227 0.91334805 0.84820241 0.943750156 0.92649657 1 20.46009326 1.368294597 1.059178572 0.992163018 0.858432737 0.456929539 0.049760348 0.441453069 0.996725245 0.047256217 0.016396891 23.35041464 -1.368294597 -0.13373028 S(ph)SPVNRPSSATNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPVNRPSSATNK 13 1 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80;A0A0A0MR72 Q96L91-4 EP400 E1A-binding protein p400 1 S(0.65)S(0.35)PVNRPSSATNK 154.6 0.00012174 30320000 90929 90299 68915 79380 79718 75250 98274 95699 111340 119470 TRUE FALSE 87375.39415 87723.76093 81369.47351 83476.81131 82282.20187 76771.60656 99476.70661 93722.78221 98701.14998 111378.1905 0.784492851 0.787620633 0.730569182 0.749489743 0.738764039 0.689287608 0.893143498 0.841482357 0.886180226 1 16.76510723 1.368324686 0.820851702 0.989713447 0.749407769 0.756531646 0.044291754 0.267861016 0.389025413 0.041886266 0.016418677 23.35203246 -1.368324686 -0.240305678 QTPPARQS(ph)PPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QTPPARQSPPAR 12 1 Q9Y5V3;Q9Y5V3-2 Q9Y5V3 MAGED1 Melanoma-associated antigen D1 1 QTPPARQS(1)PPAR 83.751 0.0076447 171990000 108250 123690 88644 97519 123240 110570 109800 111650 96989 111230 TRUE FALSE 104019.4703 120162.4823 104663.9427 102551.9673 127204.1265 112805.8012 111143.7652 109344.3885 85979.21533 103696.293 1.003116575 1.158792458 1.009331574 0.988964642 1.22669888 1.087847963 1.071820043 1.05446767 0.829144541 1 16.6620048 1.368382866 6.336693162 0.916247806 1.079091682 0.402315833 0.078595771 0.193504043 9.592802313 0.051898284 0.018763772 23.35516105 -1.368382866 0.162843876 LSPS(ph)PTSQR ddPTM_BT-474_Pertuzumab_2h_R1 9 LSPSPTSQR 9 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 LS(0.013)PS(0.96)PT(0.027)SQR;LSPS(0.943)PT(0.057)SQR;LSPS(1)PTSQR;LSPS(0.999)PT(0.001)SQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LS(0.052)PS(0.948)PTSQR;LS(0.001)PS(0.998)PT(0.001)SQR;LS(0.002)PS(0.994)PT(0.004)SQR 266.68 1.51E-15 51205220000 5709240 5608620 5037500 5895870 5374710 5956500 5747830 5822840 5757500 5885140 TRUE FALSE 5486116.589 5448667.649 5947888.309 6200156.557 5547592.428 6076944.511 5818173.663 5702596.319 5103932.737 5486534.226 0.99992388 0.99309827 1.084088436 1.130067963 1.011128738 1.107610791 1.060446071 1.039380433 0.93026536 1 22.38746367 1.368445211 5.408938365 0.966328632 1.056282696 0.37887283 0.045365156 0.212387051 8.521716027 0.032449678 0.011555745 23.358514 -1.368445211 0.089954064 T(ph)SFDQDSDVDIFPSDFPTEPPSLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSFDQDSDVDIFPSDFPTEPPSLPR 25 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 T(0.38)S(0.38)FDQDS(0.241)DVDIFPSDFPTEPPSLPR 69.639 0.013251 0 13092 16205 11799 15420 15085 14645 14050 14913 13369 15232 TRUE FALSE 12580.35017 15742.84927 13931.34177 16215.82805 15570.22272 14941.13193 14221.9481 14605.04134 11851.40717 14200.32307 0.885919996 1.108626134 0.981058086 1.141933741 1.096469612 1.052168451 1.001522855 1.028500638 0.83458715 1 13.79363613 1.369013669 7.272504261 0.917825663 1.042296909 0.272612544 0.078078992 0.259054976 15.28119764 0.04978775 0.018134447 23.3891085 -1.369013669 0.124471246 QAGGHKDPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAGGHKDPEK 10 1 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8Y6Q1 Q15813-2 TBCE Tubulin-specific chaperone E 0 ; 87.184 0.0078404 384700000 855140 774740 683350 663290 742020 691510 825000 822580 1020840 996850 FALSE TRUE 821720.1834 752645.1737 806846.546 697522.4764 765887.7472 705492.806 835096.5968 805593.4355 904958.5229 929332.4616 0.884204757 0.809877202 0.868200111 0.75056291 0.824126756 0.759139313 0.898598329 0.866851712 0.973772638 1 19.82583528 1.369509348 1.316448395 1.002760344 0.818572303 0.667882399 0.044846749 0.224565428 0.744342501 0.039102456 0.012676428 23.41581874 -1.369509348 -0.18418804 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_BT-474_Pertuzumab_2h_R1 4 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR 32 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 371.75 6.82E-148 1162865000 271786 346484 260788 325556 322864 328580 315684 320336 322445 315403 FALSE TRUE 261164.3026 336602.6156 307918.1928 342357.9842 333249.2138 335224.1127 319547.4352 313720.9497 285842.3954 294040.4739 0.888191681 1.144749262 1.047196628 1.164322651 1.133344704 1.140061123 1.08674643 1.06693118 0.972119218 1 18.16565523 1.369530767 3.360650566 0.98577105 1.093209618 0.211510329 0.075049285 0.339289673 6.275685536 0.057426612 0.018609221 23.41697363 -1.369530767 0.107438568 GKTPQVGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKTPQVGDR 9 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 73.327 0.040343 314520000 676030 721420 572210 677260 702390 708440 699440 692760 703590 678000 FALSE TRUE 649610.0002 700845.8079 675621.0757 712213.4698 724983.0122 722765.1422 707999.9559 678454.2639 623721.4129 632078.4561 1.027736342 1.108795595 1.068887998 1.126780169 1.146982634 1.143473781 1.120114045 1.073370335 0.986778472 1 19.26974412 1.370384038 3.201562594 0.992179204 1.108134427 0.630473165 0.033916957 0.159471023 2.699257173 0.028643051 0.009187593 23.46302688 -1.370384038 0.115955223 S(ph)SSEDAESLAPR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSSEDAESLAPR 12 0 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 S(0.637)S(0.093)S(0.271)EDAESLAPR;S(0.803)S(0.099)S(0.099)EDAESLAPR;S(0.737)S(0.131)S(0.131)EDAESLAPR;S(0.811)S(0.094)S(0.094)EDAESLAPR;S(0.81)S(0.095)S(0.095)EDAESLAPR;S(0.967)S(0.011)S(0.023)EDAESLAPR 284.12 3.01E-28 9823720000 2720480 2794730 2397760 2634240 2622580 2598900 2521110 2719390 2582830 2494690 TRUE FALSE 2614160.634 2715027.037 2831088.57 2770193.442 2706937.667 2651451.539 2551964.098 2663233.646 2289637.967 2325722.424 1.124020909 1.167390832 1.217294265 1.191110948 1.163912615 1.140055026 1.097278021 1.145121025 0.984484624 1 21.14924749 1.370662401 1.05793181 0.985600422 1.170725529 0.753075803 0.036153143 0.227996454 0.513408363 0.0337624 0.011727322 23.47807044 -1.370662401 0.185125106 KIAEAGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KIAEAGSR 8 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6;E5RGY7 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 0 71.614 0.077426 140190000 152780 179630 147410 199390 160830 167370 187130 171860 146490 162750 FALSE TRUE 146809.1887 174507.1283 174050.2661 209680.5418 166003.243 170754.3361 189420.1529 168311.0309 129861.0693 151726.7975 0.967589055 1.150140457 1.147129373 1.381961164 1.094093105 1.125406578 1.248429124 1.109303259 0.855887499 1 17.21111639 1.371354704 5.30975068 0.931812046 1.163810587 0.427014272 0.105301571 0.185586678 7.289272667 0.073030152 0.025985108 23.51552634 -1.371354704 0.231998541 DIILREDLEELQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIILREDLEELQAR 14 1 Q9UHQ9;H7C0R7 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 ; 155.28 5.37E-06 122009000 88894 154623 82781 161777 106146 133587 130863 119644 97798 102684 FALSE TRUE 85419.9242 150213.3034 97741.36815 170126.3304 109560.2825 136288.2207 132464.5405 117173.3096 86696.38104 95729.12122 0.892308663 1.569149508 1.021020217 1.777163816 1.144482276 1.423686115 1.383743409 1.224009038 0.905642713 1 16.54667025 1.371876461 3.749730332 0.953998092 1.328038509 0.25342533 0.244168472 0.279165365 6.295431984 0.169747316 0.056555636 23.54379466 -1.371876461 0.374040417 FAEHGETLAMK ddPTM_BT-474_Pertuzumab_2h_R1 1 FAEHGETLAMK 11 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4;Q6N069;Q6N069-5;Q6N069-4;Q6N069-3;Q6N069-2 A0A0B4J1W3;Q6N069 NAA15;NAA16 "N-alpha-acetyltransferase 15, NatA auxiliary subunit;N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 112.15 0.001565 257770000 697260 728680 599010 674680 663620 562800 757420 729110 915300 884280 FALSE TRUE 670010.3083 707898.7599 707264.4319 709500.3157 684965.94 574180.2016 766689.5325 714053.6237 811398.9813 824386.928 0.812737667 0.858697216 0.857927762 0.860639939 0.830879186 0.696493579 0.930011754 0.866163205 0.984245327 1 19.6529621 1.37188251 1.497327625 1.003412388 0.829909351 0.564213882 0.054772862 0.273971134 1.142528892 0.049268307 0.015543147 23.54412259 -1.37188251 -0.173503036 QISLS(ph)PSSGGHFVFQDGSGLTQIAQGAQVQLQHPGTPITVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QISLSPSSGGHFVFQDGSGLTQIAQGAQVQLQHPGTPITVR 41 0 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80;A0A0A0MR72;Q6ZTU2-2;Q6ZTU2-6;Q6ZTU2 Q96L91-4 EP400;EP400NL E1A-binding protein p400;EP400 N-terminal-like protein 1 QIS(0.018)LS(0.722)PS(0.101)S(0.159)GGHFVFQDGSGLTQIAQGAQVQLQHPGTPITVR 175.83 1.49E-20 78825000 17808 22740 22715 31087 31363 28522 27508 25937 19340 23071 TRUE FALSE 17112.04367 22091.47746 26820.10579 32691.4038 32371.81938 29098.73438 27844.65113 25401.39189 17144.60428 21508.38062 0.795598887 1.027110216 1.24696072 1.519937943 1.505079343 1.35290215 1.294595424 1.180999738 0.797112743 1 14.39261129 1.372869881 4.674322817 0.903204574 1.261949034 0.304554378 0.20735514 0.270950923 8.815800772 0.164315068 0.05739672 23.59771116 -1.372869881 0.358744459 WDAWNELK ddPTM_BT-474_Pertuzumab_2h_R1 4 WDAWNELK 8 0 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ;;; 167.23 0.00073018 1775679000 1506320 1406169 1282713 1468714 1273811 890301 1492758 1626019 1792936 1988450 FALSE TRUE 1447451.349 1366066.437 1514527.773 1544514.506 1314784.288 908303.4962 1511026.819 1592441.139 1589409.422 1853770.51 0.780814745 0.736912379 0.816998525 0.833174601 0.70924868 0.489976236 0.815109967 0.859028197 0.857392764 1 20.82203122 1.372954135 1.424198211 0.968662757 0.736916634 0.422327389 0.094950524 0.39900667 1.521544399 0.092542509 0.029494047 23.60228961 -1.372954135 -0.231746123 WLKEDKLECSEELGDLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 WLKEDKLECSEELGDLVK 18 2 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 189.55 1.81E-14 5382000000 3010900 2387500 1796800 1534950 2140530 2486300 2215640 2394300 3308500 2708600 FALSE TRUE 2893230.699 2319410.838 2121521.73 1614168.953 2209382.091 2536574.689 2242755.665 2344856.868 2932932.95 2525144.109 1.145768548 0.918526126 0.840158675 0.63923835 0.874952872 1.004526704 0.888169375 0.928603187 1.161491314 1 21.26793429 1.373457742 5.664638684 1.078420879 0.894575957 0.238788017 0.125556649 0.293739294 12.70469708 0.090829114 0.032593471 23.62967467 -1.373457742 -0.183844922 VAEIEHAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 VAEIEHAEK 9 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 196.79 2.91E-05 12056500000 14969700 14363800 12406600 13433100 13564600 14694100 15345700 15238000 18587700 18287800 FALSE TRUE 14384667.57 13954158.49 14648748.6 14126383.9 14000917.68 14991224.77 15533505.27 14923329.97 16477702.22 17049151.02 0.843717529 0.818466472 0.859206924 0.828568173 0.821209083 0.879294503 0.911101395 0.875312205 0.966482273 1 24.02319656 1.373621117 0.606780933 1.003273373 0.831635438 0.857657719 0.022161814 0.24974809 0.220449698 0.021776541 0.010615509 23.63856543 -1.373621117 -0.171637936 AVEYLLMGIPGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEYLLMGIPGDR 13 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ; 171.62 1.47E-06 340190000 466380 503720 395930 504550 540320 490280 528450 490260 461590 463160 FALSE TRUE 448153.354 489354.3988 467483.3584 530589.886 557699.8835 500193.7975 534917.3292 480135.9597 409192.2383 431789.7607 1.037897131 1.133316358 1.082664299 1.22881535 1.29160053 1.158419775 1.238837457 1.111966988 0.947665451 1 18.71996951 1.373651195 4.179255026 0.975753897 1.169762356 0.530279896 0.071640613 0.174060637 4.732344389 0.056191974 0.019214136 23.64020267 -1.373651195 0.19400846 VALSEPQPERR ddPTM_BT-474_Pertuzumab_2h_R1 3 VALSEPQPERR 11 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1;H7C1K0 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;; 118.28 0.0011895 1050490000 916050 1037000 703480 930130 965960 1058200 953640 945170 967350 912030 FALSE TRUE 880249.7533 1007425.775 830614.4848 978134.1208 997030.9807 1079597.529 965310.9316 925651.9092 857540.4835 850257.3957 1.035274445 1.184848001 0.976897689 1.150397663 1.172622532 1.269730242 1.135316125 1.088672576 1.008565745 1 19.69754012 1.373914462 2.5829908 0.999640817 1.135109009 0.308164221 0.075709498 0.345069738 3.917047828 0.066338983 0.020541101 23.65453753 -1.373914462 0.135468192 LLSSNEDDANILSS(ph)PTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLSSNEDDANILSSPTDR 18 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 1 LLSSNEDDANILSS(1)PTDR;LLSSNEDDANILS(0.006)S(0.992)PT(0.001)DR 365.02 1.75E-90 1307220000 806820 976630 765900 982100 974510 1007550 961200 950350 883410 937950 TRUE FALSE 775288.5824 948777.4686 904315.1674 1032786.299 1005855.999 1027923.351 972963.4531 930724.9404 783129.0004 874421.8111 0.886629968 1.085034084 1.034186426 1.18110766 1.150309824 1.175546331 1.112693486 1.064388981 0.895596371 1 19.73796986 1.374714351 5.208019047 0.949867105 1.095286559 0.304885726 0.083759254 0.244228598 9.389825629 0.060133905 0.02138272 23.69814491 -1.374714351 0.145419453 TSVLPEHKDPPPEVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSVLPEHKDPPPEVGR 16 1 O15327;D6RJC3;E7EQN9;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ;; 118.24 0.00017285 1196220000 2731080 2669630 2174520 2239300 2357290 2759960 2583330 2751170 3421140 3262990 FALSE TRUE 2624346.374 2593494.766 2567504.136 2354870.541 2433114.374 2815768.282 2614945.565 2694357.378 3032786.53 3041984.781 0.862708581 0.852566647 0.844022676 0.774123052 0.799844361 0.92563523 0.859618227 0.88572349 0.996976234 1 21.5365815 1.37527661 1.087119355 1.010912785 0.836313693 0.705635705 0.038591859 0.261182573 0.616292238 0.037283347 0.01283498 23.72884559 -1.37527661 -0.174599092 S(ph)WRT(ph)S(ph)QRDT(ph)SDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SWRTSQRDTSDVK 13 2 Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9;Q8NFP9-3 Q5T321 NBEA Neurobeachin 4 S(0.956)WRT(0.969)S(0.975)QRDT(0.591)S(0.508)DVK 41.014 0.088586 253940000 562850 469410 451260 456970 463250 499140 478010 531910 699330 614360 TRUE FALSE 540853.1997 456022.8864 532812.7202 480554.2765 478150.857 509232.9528 483860.0294 520925.8726 619944.9902 572748.85 0.94431128 0.79620044 0.930272877 0.839031412 0.834835124 0.889103405 0.844803144 0.909518845 1.082402855 1 19.12754313 1.375277792 4.420508288 1.039124737 0.86733046 0.681539832 0.046414652 0.106466034 3.179652278 0.030679722 0.010624553 23.72891018 -1.375277792 -0.171794277 LKQDILDEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKQDILDEMR 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 94.191 0.007544 80134000 121980 121560 105630 113660 115620 99698 127640 126250 143290 144640 FALSE TRUE 117212.8867 118093.2278 124719.6907 119526.0062 119339.0223 101713.9619 129202.0965 123642.8934 127024.3199 134843.404 0.869251912 0.87578053 0.924922444 0.886406029 0.885019354 0.754311734 0.958164009 0.916936904 0.942013596 1 17.04092543 1.375686144 1.164288174 0.989811241 0.874616569 0.404158577 0.04833282 0.448045827 1.193342393 0.044506242 0.014968202 23.75123214 -1.375686144 -0.115194671 RDINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDINVSVGSQQPDTKDSPVCPHFTTNGNENSSIEK 35 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RDINVSVGSQQPDTKDS(1)PVCPHFTTNGNENSSIEK 202.5 6.98E-28 893670000 540100 371510 279590 254800 310580 296650 359080 368640 468410 435260 TRUE FALSE 518992.2949 360914.8985 330118.1324 267950.2585 320570.0878 302648.4663 363474.5285 361027.4552 415238.0605 405779.4525 1.279000924 0.889436112 0.81354078 0.660334714 0.790010647 0.74584473 0.895744046 0.889713496 1.023309726 1 18.63033629 1.375870441 2.441982092 1.015195754 0.851138296 0.109988436 0.154971655 0.606407898 6.205047472 0.137511136 0.042376042 23.76131333 -1.375870441 -0.164057459 EHPFLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHPFLVK 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 108.09 0.0073318 1552860000 3181500 3262000 2404300 2938600 3103400 2697200 3101000 3100400 3556800 3359000 FALSE TRUE 3057163.463 3168970.954 2838810.493 3090261.498 3203223.679 2751739.232 3138950.966 3036375.657 3153046.975 3131491.938 0.976264197 1.011968422 0.906536101 0.986833611 1.022906571 0.878731061 1.002381941 0.96962589 1.006883312 1 21.57841873 1.375876636 1.980421648 1.003650458 0.96785526 0.08524741 0.042947546 0.830336045 5.756113999 0.036794483 0.011271344 23.76165226 -1.375876636 -0.035795199 RTDLTVLVAHNDDPTDQMFVFFPEEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTDLTVLVAHNDDPTDQMFVFFPEEPK 27 1 P19388;A0A087WVZ9;A0A0A0MQR7 P19388 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" 0 94.899 0.0032894 107540000 66707 59056 51955 61565 66607 52842 51439 64168 85149 72059 FALSE TRUE 64100.01669 57371.7807 61344.42423 64742.37703 68749.47465 53910.50144 52068.52587 62842.90838 75483.24249 67178.37975 0.954176283 0.854021501 0.913157246 0.963738293 1.023386913 0.802497792 0.77507862 0.935463294 1.123624041 1 16.03570938 1.376195659 6.262278481 1.05839136 0.897179242 0.419834847 0.075776843 0.205199047 10.2915316 0.054211232 0.019641832 23.77911347 -1.376195659 -0.161212118 RGEEGHDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGEEGHDPK 9 1 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 63.184 0.050458 49640000 124080 108800 116770 116570 121100 112710 129290 135580 161220 162250 FALSE TRUE 119230.8164 105697.1305 137872.9365 122586.1917 124995.2915 114989.0734 130872.2897 132780.2256 142918.9815 151260.663 0.788247348 0.698774741 0.911492346 0.810430083 0.826356893 0.760204743 0.86521034 0.877823903 0.944852275 1 17.20667732 1.376553517 1.043221532 0.999520358 0.800628397 0.62947678 0.052052971 0.302386261 0.663380505 0.047603287 0.01665053 23.79871551 -1.376553517 -0.198891961 FESPEVAER ddPTM_BT-474_Pertuzumab_2h_R1 4 FESPEVAER 9 0 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 166.82 0.00014064 4941610000 2488780 2533480 2132100 2376020 2458530 2520700 2451940 2464730 2435890 2382830 FALSE TRUE 2391515.726 2461227.631 2517417.898 2498646.677 2537610.85 2571670.281 2481947.575 2413832.464 2159377.979 2221438.802 1.076561607 1.107943027 1.133237565 1.124787536 1.142327598 1.157659747 1.11727029 1.086607681 0.972062781 1 21.08306297 1.376852204 3.072251001 0.984902035 1.124110916 0.85512913 0.022072137 0.089547903 1.411295957 0.018985799 0.006069093 23.81508875 -1.376852204 0.139208881 RLREEFSFIPSAALDLLDHMLTLDPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLREEFSFIPSAALDLLDHMLTLDPSK 27 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 47.52 0.070836 2178100000 972340 1269600 721120 933640 1001600 1080600 889520 857980 984640 730970 FALSE TRUE 934339.8778 1233392.251 851442.4252 981825.2723 1033817.374 1102450.472 900406.2118 840262.4132 872867.7951 681460.7508 1.37108392 1.809924122 1.249437219 1.440765695 1.517060773 1.617775449 1.321288439 1.233031267 1.280877577 1 19.37827104 1.377153201 0.804960314 1.02251037 1.506072227 0.510319562 0.150097063 0.441705563 0.618805063 0.136906494 0.054416837 23.83160003 -1.377153201 0.483561857 LLGHS(ph)PVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLGHSPVLR 9 0 P30305;G8JLH2;B4DIG0;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 LLGHS(1)PVLR;LLGHS(1)PVLR 115 0.0010425 0 66143 68852 73281 69034 69578 74039 71217 72620 61799 72926 TRUE FALSE 63558.05844 66888.40837 86524.50683 72596.85301 71816.03956 75536.11931 72088.57495 71120.37162 54783.8366 67986.65706 0.934860768 0.983846114 1.272668941 1.067810305 1.056325501 1.111043292 1.060334161 1.046093082 0.80580277 1 16.05296401 1.377500919 6.511192485 0.904230562 1.072610736 0.329629985 0.093694932 0.233586938 12.43034153 0.06345423 0.023058044 23.8506884 -1.377500919 0.168380174 SCT(ph)PSPDQISHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.123)CT(0.864)PS(0.013)PDQISHR;S(0.02)CT(0.979)PSPDQISHR 160.8 0.00024679 1346730000 355520 380410 315300 365750 287010 348960 335460 387200 443920 440720 TRUE FALSE 341625.8854 369561.0793 372281.7238 384626.4013 296241.9373 356016.2103 339565.4598 379204.1847 393528.0627 410869.6418 0.831470254 0.89946066 0.906082333 0.936127575 0.721011988 0.866494318 0.826455462 0.922930648 0.95779299 1 18.64832121 1.377986245 2.100409298 0.99004129 0.857525821 0.443055635 0.056207755 0.298984942 2.313637207 0.05068914 0.015529282 23.87735659 -1.377986245 -0.13251547 APSEEELHGDQTDFGQGS(ph)QSPQKQEEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.5)QS(0.5)PQKQEEQR 139.54 8.45E-08 87080000 31267 23594 24466 24714 25597 30302 31547 28653 39318 39051 TRUE FALSE 30045.05107 22921.12222 28887.55044 25989.4925 26420.35075 30914.7272 31933.08162 28061.30554 34854.78547 36406.04099 0.825276527 0.629596671 0.793482336 0.713878571 0.725713372 0.849164764 0.877136891 0.770787067 0.957390162 1 15.15189024 1.378234841 0.454973311 1.009212959 0.721638371 0.613404928 0.06656629 0.614867732 0.352084518 0.07373488 0.046351587 23.89102822 -1.378234841 -0.287574588 EIISHDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIISHDTR 8 0 P00387-2;P00387;P00387-3;B1AHF3 P00387-2 CYB5R3 NADH-cytochrome b5 reductase 3;NADH-cytochrome b5 reductase 3 membrane-bound form;NADH-cytochrome b5 reductase 3 soluble form 0 ; 118.5 0.0018756 1234190000 1602040 2549450 1638430 3333220 2110850 2152840 2393160 2106090 1703120 1645800 FALSE TRUE 1539430.506 2476742.182 1934530.748 3505247.884 2178747.407 2196371.9 2422448.208 2062598.506 1509788.958 1534328.5 1.003325237 1.614218977 1.26083218 2.284548507 1.420000611 1.43148739 1.57883283 1.344300458 0.984006331 1 20.54917597 1.378444391 2.71502923 0.977713176 1.529753216 0.30582896 0.308828868 0.316765845 3.965330327 0.25347213 0.079295861 23.90255857 -1.378444391 0.55204004 GGDVS(ph)PSPYSSSSWR ddPTM_BT-474_Pertuzumab_2h_R1 8 GGDVSPSPYSSSSWR 15 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 GGDVS(0.999)PS(0.001)PYSSSSWR;GGDVS(0.998)PS(0.002)PYSSSSWR;GGDVS(0.999)PS(0.001)PYSSSSWR;GGDVS(0.881)PS(0.119)PYSSSSWR;GGDVS(0.98)PS(0.02)PYSSSSWR;GGDVS(0.999)PS(0.001)PYSSSSWR;GGDVS(0.999)PS(0.001)PYSSSSWR;GGDVS(0.991)PS(0.009)PYSSSSWR 372.76 1.24E-97 12500600000 2760033 3008435 2538061 2961527 3088152 3181666 3022444 3006008 3030589 2950690 TRUE FALSE 2652167.859 2922637.379 2996745.082 3114371.763 3187485.214 3246001.466 3059433.574 2943932.884 2686569.242 2750837.138 0.964131181 1.062453803 1.089393858 1.13215418 1.158732798 1.18000496 1.112182736 1.070195267 0.976636968 1 21.3914393 1.37904917 3.391596776 0.988128255 1.104002995 0.376301548 0.056213341 0.263511139 4.993946109 0.048071431 0.015739292 23.93586737 -1.37904917 0.11587474 RPPES(ph)PPIVEEWNSR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPPESPPIVEEWNSR 15 1 Q9BTL3;A0A3B3IU46 Q9BTL3 FAM103A1 RNMT-activating mini protein 1 RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR 191.71 1.01E-07 10227430000 672182 715230 542715 680980 647435 615306 662190 664948 618531 669432 TRUE FALSE 645912.3843 694832.3407 640795.6731 716125.4594 668260.3348 627747.9089 670294.0793 651216.5914 548317.954 624090.7744 1.034965442 1.113351405 1.026766777 1.14747003 1.070774256 1.00585994 1.074032988 1.043464538 0.87858686 1 19.25139636 1.379243273 5.87196101 0.940778477 1.067405289 0.530966751 0.047480863 0.146977836 6.821642618 0.030949587 0.01117563 23.94656765 -1.379243273 0.126626812 EVYQQQQYGSGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVYQQQQYGSGGR 13 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ;;; 357.65 6.61E-76 3293070000 711940 835490 702720 763760 833190 845130 827420 801260 804510 778450 FALSE TRUE 684116.5977 811662.6432 829717.1359 803177.7451 859990.313 862219.1076 837546.2135 784713.701 713185.3976 725724.8881 0.942666579 1.118416436 1.143294311 1.106724819 1.185008709 1.188079838 1.154082252 1.08128261 0.982721427 1 19.46906322 1.379639463 3.466106852 0.991111519 1.124883514 0.372330491 0.065365508 0.24640863 4.86069794 0.052232977 0.017197799 23.96842311 -1.379639463 0.133771995 LQAEAPHIVVGTPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQAEAPHIVVGTPGR 15 0 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;; 186.85 3.65E-07 1665130000 2163030 2376810 1933930 2287020 2296220 2420170 2176530 2337320 2417270 2304080 FALSE TRUE 2078496.396 2309025.706 2283434.171 2405053.376 2370080.002 2469107.496 2203167.025 2289053.525 2142871.644 2148022.609 0.967632458 1.074954098 1.063040101 1.119659247 1.103377586 1.149479286 1.025672177 1.06565616 0.997601997 1 21.03457775 1.379939597 1.666848813 0.995688113 1.078809264 0.258714427 0.047788235 0.46968994 2.381014568 0.043490012 0.013532817 23.98499303 -1.379939597 0.083121151 EEDEHPYELLLTAETK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEDEHPYELLLTAETK 16 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 0 ; 230.16 2.51E-15 105059000 149954 137377 120713 122782 140474 152616 147857 154017 198926 194792 FALSE TRUE 144093.6319 133459.1425 142528.5243 129118.7937 144992.4738 155702.0001 149666.5182 150836.4951 176344.7544 181598.5643 0.793473409 0.734912982 0.784854907 0.711012194 0.798423018 0.857396647 0.824161351 0.830604007 0.9710691 1 17.47039327 1.380104318 0.601243955 1.009056626 0.75797422 0.815520986 0.037726316 0.29811199 0.258939315 0.037780096 0.018600312 23.99409189 -1.380104318 -0.251082405 EPSVPASCAVSATYERS(ph)PS(ph)PAHLPDDPK ddPTM_BT-474_Pertuzumab_2h_R1 4 EPSVPASCAVSATYERSPSPAHLPDDPK 28 1 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 2 EPSVPASCAVS(0.001)AT(0.003)Y(0.022)ERS(0.976)PS(0.998)PAHLPDDPK;EPSVPASCAVS(0.004)AT(0.024)Y(0.004)ERS(0.967)PS(1)PAHLPDDPK;EPSVPAS(0.001)CAVS(0.021)AT(0.138)Y(0.005)ERS(0.835)PS(1)PAHLPDDPK;EPSVPASCAVSAT(0.002)Y(0.005)ERS(0.993)PS(1)PAHLPDDPK 176.6 1.16E-13 1454850000 894200 812030 747810 734970 839170 954070 869010 853540 1152270 1078340 TRUE FALSE 859253.6754 788871.6995 882955.9019 772901.8898 866162.6652 973361.9491 879645.2043 835914.1007 1021469.14 1005303.071 0.854721029 0.784710325 0.878298224 0.768824757 0.861593573 0.96822737 0.87500499 0.831504573 1.016080791 1 19.93919907 1.380174963 0.335698994 1.017660076 0.808858007 0.482827289 0.05813439 1.264966998 0.480834983 0.100999826 0.078362593 23.99799524 -1.380174963 -0.208802069 YIGTGHADTTK ddPTM_BT-474_Pertuzumab_2h_R1 4 YIGTGHADTTK 11 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ;;; 167.12 1.96E-05 1289060000 3311210 3247440 3125100 3213870 3392360 2793300 3568930 3715500 4116760 4290560 FALSE TRUE 3181804.252 3154826.191 3689875.087 3379738.216 3501478.34 2849782.44 3612607.633 3638773.627 3649442.664 3999956.55 0.795459704 0.788715115 0.922478792 0.844943732 0.875379094 0.712453349 0.903161719 0.909703288 0.912370577 1 21.9315529 1.380754007 1.096047218 0.987052481 0.831065127 0.465672388 0.057390633 0.413571479 0.988821322 0.053105161 0.018254637 24.03001308 -1.380754007 -0.155987355 AVTHTSPEDVSFAESR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVTHTSPEDVSFAESR 16 0 Q9BTW9-4;Q9BTW9;J3KR97;A0A0J9YVR1;A0A0J9YWI5;I3L439;A0A0J9YVU1 Q9BTW9-4 TBCD Tubulin-specific chaperone D 0 101.42 0.0030727 0 25854 36529 27994 35410 33366 38305 34718 34350 26398 35063 FALSE TRUE 24843.5971 35487.22869 33053.13852 37237.51434 34439.24769 39079.55334 35142.88927 33640.6605 23401.40971 32688.15178 0.760018409 1.085629708 1.01116572 1.139174665 1.053569744 1.195526551 1.075095634 1.029139265 0.715898833 1 14.99648019 1.381001713 8.35740673 0.858804242 1.054623431 0.258290615 0.125483483 0.30573797 23.24813115 0.079940365 0.029290907 24.04372282 -1.381001713 0.19581919 RPAS(ph)PS(ph)SPEHLPATPAESPAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.993)PS(0.869)S(0.138)PEHLPATPAESPAQR;RPAS(0.995)PS(0.538)S(0.468)PEHLPATPAESPAQR 149.66 6.29E-08 4049970000 599709 617560 550217 647077 719340 643800 626550 641410 599350 610210 TRUE FALSE 576271.7093 599947.7935 649653.4514 680472.7215 742478.2244 656818.0771 634217.9063 628164.6594 531314.3007 568879.9332 1.012993561 1.054612333 1.141986935 1.196162286 1.30515805 1.154581202 1.114853714 1.104213073 0.933965622 1 19.11776467 1.381034817 3.311765538 0.967260573 1.144483947 0.440231299 0.076108628 0.240964827 4.380342129 0.066677401 0.021748686 24.04555565 -1.381034817 0.177223374 S(ph)PDNSIK ddPTM_BT-474_Pertuzumab_2h_R1 5 SPDNSIK 7 0 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 S(1)PDNSIK;S(0.998)PDNS(0.002)IK;S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK 174.42 0.00086728 7085100000 7719750 6473180 6214940 6438390 6202950 6029870 6993240 7412660 8213760 8430470 TRUE FALSE 7418053.635 6288571.244 7338117.909 6770676.079 6402473.52 6151798.103 7078825.363 7259585.981 7281368.4 7859466.758 0.943836759 0.80012696 0.93366613 0.861467615 0.814619327 0.782724616 0.900675018 0.923674112 0.9264456 1 22.906 1.3815574 1.268517417 0.986302737 0.856901542 0.416254645 0.051563143 0.393085059 1.218565395 0.046817722 0.01537916 24.07450689 -1.3815574 -0.129401195 VSGAGFS(ph)PSSK ddPTM_BT-474_Pertuzumab_2h_R1 8 VSGAGFSPSSK 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VSGAGFS(0.995)PS(0.004)SK;VSGAGFS(0.986)PS(0.013)S(0.001)K;VSGAGFS(0.832)PS(0.167)SK;VSGAGFS(0.834)PS(0.153)S(0.013)K;VSGAGFS(0.866)PS(0.133)S(0.001)K;VSGAGFS(0.99)PS(0.009)SK;VSGAGFS(0.952)PS(0.045)S(0.003)K;VSGAGFS(0.986)PS(0.014)SK 253.72 2.14E-20 18824820000 13200280 13049610 12522690 13419930 13821340 13059560 13173690 13551330 13245380 13211030 TRUE FALSE 12684398.46 12677447.9 14785818.65 14112534.2 14265915.95 13323633.25 13334913.56 13271490.3 11741819.99 12316235.17 1.029892519 1.029328177 1.200514479 1.145848061 1.158301685 1.08179432 1.082710209 1.077560644 0.953361139 1 23.55405798 1.382072324 3.145347595 0.976583308 1.106882535 0.470528681 0.052651547 0.226640568 3.749840108 0.045295873 0.014617125 24.10306791 -1.382072324 0.130299227 ATSSSNPS(ph)SPAPDWYKDFVTDADAEVLEHSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 ATSSSNPS(0.5)S(0.5)PAPDWYKDFVTDADAEVLEHSGK 313.19 2.65E-104 404340000 262440 272250 253340 224100 276130 285450 290600 278150 360390 347650 TRUE FALSE 252183.5547 264485.6966 299124.1735 235665.8279 285011.9722 291221.9946 294156.4497 272406.1053 319480.0381 324103.3558 0.778096092 0.816053558 0.922928344 0.727131712 0.879386057 0.898546681 0.907600753 0.840491468 0.985735051 1 18.30609443 1.382105596 0.205086414 1.051526521 0.762165149 0.511811018 0.0575057 2.40103934 0.507237898 0.290398793 0.255139413 24.10491454 -1.382105596 -0.289361372 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_BT-474_Pertuzumab_2h_R1 14 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 38 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;; 397.79 3.05E-180 7497608000 1272552 1214291.3 1067654.6 1175938.5 1160195.7 1250204.8 1232196.7 1318294.5 1524275 1488422 FALSE TRUE 1222819.261 1179660.901 1260603.536 1236628.827 1197514.448 1275484.798 1247276.692 1291071.258 1351245.692 1387609.852 0.881241409 0.850138747 0.908471163 0.891193461 0.86300515 0.919195547 0.89886699 0.930428143 0.973793671 1 20.40417056 1.382192123 0.824854378 1.002999569 0.879995336 0.839286466 0.017813153 0.202132202 0.294672965 0.016271046 0.006383224 24.10971756 -1.382192123 -0.123004233 KAAALEAMKDYTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAAALEAMKDYTK 13 2 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 119.54 0.0001914 1510150000 1552770 1708940 937520 1056730 1468960 1790660 1252320 1337520 1227580 1102040 FALSE TRUE 1492086.032 1660202.704 1106950.719 1111267.962 1516210.432 1826868.372 1267646.267 1309899.745 1088230.265 1027397.849 1.452296238 1.615929706 1.077431416 1.08163353 1.475777308 1.778150863 1.233841659 1.274968354 1.059210184 1 19.97056353 1.382195149 1.769422286 1.003866901 1.392385697 0.324741695 0.206663067 0.441660944 2.498694772 0.198550301 0.061435721 24.10988557 -1.382195149 0.388518796 RPLDDGVGNQLGALVHQR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPLDDGVGNQLGALVHQR 18 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;; 222.3 3.75E-19 1975660000 921064 1050440 816832 977259 984710 981836 997280 1003798 994430 1042520 FALSE TRUE 885067.8006 1020482.48 964451.7127 1027695.454 1016384.091 1001689.397 1009485.011 983069.2205 881546.4754 971909.1918 0.910648657 1.049977187 0.99232698 1.057398636 1.045760345 1.030640933 1.038661862 1.011482584 0.907025556 1 19.890462 1.383051918 8.122736803 0.953979539 1.021377395 0.23821365 0.045306545 0.306995669 22.90839161 0.028313458 0.01037835 24.1574961 -1.383051918 0.067397855 SLGYHGSSYSPEGVEPVS(ph)PVS(ph)SPSLTHDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 SLGYHGSSYSPEGVEPVS(1)PVS(0.604)S(0.326)PS(0.059)LT(0.011)HDK 159.54 3.41E-12 126740000 34329 66290 37772 53972 44194 53804 46008 51147 41801 60574 TRUE FALSE 32987.38473 64399.4741 44598.24063 56757.50139 45615.54015 54891.95374 46571.05967 50090.79658 37055.92572 56471.26903 0.584144562 1.140393606 0.78975099 1.005068637 0.807765452 0.972033296 0.824685906 0.887013829 0.656190774 1 15.78522943 1.383246057 22.64184702 0.809264313 0.884880504 0.009409024 0.160065134 30.9223381 7436.958727 0.094236316 0.034414868 24.16829741 -1.383246057 0.075616191 QIEIQFAQGDR ddPTM_BT-474_Pertuzumab_2h_R1 4 QIEIQFAQGDR 11 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 ;;; 146.9 8.27E-05 820240000 345094 338812 306540 354922 334115 325237 349958 343972 326478 342082 FALSE TRUE 331607.345 329149.4135 361938.5969 373239.567 344862.1124 331813.515 354240.8907 336868.858 289417.5861 318912.4814 1.039806731 1.032099503 1.134915119 1.17035108 1.081369129 1.04045321 1.110777757 1.056305029 0.907514139 1 18.28280104 1.383286195 5.11554463 0.955731498 1.087382529 0.559252178 0.046561628 0.154301975 5.905548025 0.034231489 0.012209639 24.17053121 -1.383286195 0.131651031 QSETVDQNS(ph)DSDEMLAILK ddPTM_BT-474_Pertuzumab_2h_R1 3 QSETVDQNSDSDEMLAILK 19 0 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 QS(0.031)ET(0.237)VDQNS(0.644)DS(0.087)DEMLAILK;QS(0.011)ET(0.069)VDQNS(0.46)DS(0.46)DEMLAILK;QS(0.107)ET(0.084)VDQNS(0.405)DS(0.405)DEMLAILK 96.544 0.0008112 75291000 99792 87646 79558 87154 90609 95040 95237 98418 106888 109931 TRUE FALSE 95892.01831 85146.42189 93935.90036 91652.02838 93523.52077 96961.77392 96402.53889 96385.63391 94754.52235 102485.2755 0.935666298 0.830816149 0.916579479 0.8942946 0.912555685 0.946104438 0.940647702 0.940482752 0.924567182 1 16.64505712 1.383989303 0.136042729 1.054840322 0.829309351 0.520147836 0.028309233 4.07790961 0.551539726 0.418468804 0.381228031 24.20969418 -1.383989303 -0.225530971 DSRDPMYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSRDPMYR 8 1 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 60.717 0.082564 135660000 43258 60468 33476 70946 73262 62476 48197 53397 29895 34474 FALSE TRUE 41567.42954 58743.51184 39525.85787 74607.53156 75618.53876 63739.30753 48786.8493 52294.33329 26501.44493 32139.04527 1.293362301 1.827792685 1.229839204 2.321398502 2.35285579 1.983235873 1.51799311 1.627127777 0.824587187 1 14.97203945 1.38404043 2.161246034 0.89243527 1.823883499 0.464111612 0.364973012 0.276203787 2.264296018 0.334165369 0.102751368 24.21254437 -1.38404043 0.931448228 SSFATCVLVSEEDKHAIIVEPEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSFATCVLVSEEDKHAIIVEPEKR 24 2 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 193.77 2.39E-18 1270290000 841460 643010 603790 576410 631290 387990 697990 721400 1014520 947060 FALSE TRUE 808574.8129 624671.9844 712908.2842 606158.5892 651596.0162 395835.4236 706532.2104 706502.8379 899355.9428 882914.7826 0.915801648 0.707511072 0.807448576 0.686542576 0.738005557 0.448328006 0.800226958 0.80019369 1.018621458 1 19.75191467 1.384132076 2.294847534 1.01780883 0.719723207 0.481820829 0.113728109 0.246729982 2.263101977 0.098538339 0.030378817 24.21765434 -1.384132076 -0.298085622 KEDINLSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEDINLSVR 9 1 Q15645;Q15645-2;H0YAL2 Q15645 TRIP13 Pachytene checkpoint protein 2 homolog 0 ; 94.465 0.013955 287150000 440030 496350 435560 461310 467260 420780 518360 519870 571540 589550 FALSE TRUE 422833.1411 482194.584 514275.381 485118.2644 482289.8423 429288.4599 524703.8447 509134.5028 506661.1753 549619.2534 0.769320104 0.877324768 0.935693897 0.882644233 0.877498085 0.781065178 0.954667875 0.926340371 0.921840296 1 19.06807302 1.384464178 0.744247722 0.993818689 0.861913025 0.402521161 0.053237281 0.642970989 0.787738682 0.050979944 0.021345018 24.23618051 -1.384464178 -0.131905664 QVEELFER ddPTM_BT-474_Pertuzumab_2h_R1 4 QVEELFER 8 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 191.85 0.00041647 1670370000 1450900 1520210 1251040 1588090 1505770 1475540 1488170 1523660 1438040 1571180 FALSE TRUE 1394197.224 1476855.099 1477130.757 1670051.515 1554204.46 1505376.43 1506382.67 1492195.889 1274799.728 1464762.579 0.951824715 1.008255618 1.008443811 1.14015168 1.061062374 1.027727258 1.028414223 1.018728844 0.870311507 1 20.48223541 1.384643088 7.14345581 0.935552275 1.034082615 0.339295488 0.053460231 0.243102534 15.40407237 0.036453127 0.013338837 24.24616675 -1.384643088 0.09853034 QPPGPVPT(ph)PPLPSER ddPTM_BT-474_Pertuzumab_2h_R1 2 QPPGPVPTPPLPSER 15 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 QPPGPVPT(1)PPLPSER;QPPGPVPT(1)PPLPSER 127.2 0.00089019 291680000 344520 371710 315380 388840 404950 392680 329450 385820 344370 345930 TRUE FALSE 331055.7775 361109.1947 372376.1816 408908.079 417975.5845 400620.2586 333481.9076 377852.6822 305278.5613 322499.853 1.026530011 1.119718944 1.154655353 1.267932606 1.296048915 1.242233926 1.034052898 1.171636758 0.946600622 1 18.29893898 1.384760903 1.573619414 0.973410403 1.178823019 0.388634142 0.089807398 0.388310223 1.775484626 0.085549046 0.026884268 24.25274516 -1.384760903 0.205412616 GWDSSHEDDLPVYLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWDSSHEDDLPVYLAR 16 0 Q14195-2 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 0 198.78 3.98E-11 157440000 97231 119530 114240 162560 134410 112270 131930 126820 118020 121480 FALSE TRUE 93431.10503 116121.1214 134885.7093 170949.7411 138733.4197 114540.1763 133544.5988 124201.1227 104622.8644 113252.0514 0.824983776 1.025333493 1.191022216 1.509462645 1.224996969 1.011373965 1.179180396 1.09667879 0.923805468 1 16.78917766 1.385065352 4.153230682 0.963986619 1.147736358 0.143877716 0.167558045 0.438318195 11.9697095 0.133127926 0.045883128 24.26975276 -1.385065352 0.183749739 ANVSS(ph)PHREFPPATAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ANVSSPHREFPPATAR 16 1 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.399)S(0.601)PHREFPPATAR 103.41 0.0026986 0 22237 27189 15024 25182 16476 20993 20800 20581 14801 18307 TRUE FALSE 21367.95346 26413.59634 17739.17101 26481.64604 17005.9655 21417.49284 21054.55662 20155.99516 13120.85253 17067.05058 1.252000359 1.547636846 1.03938117 1.551624044 0.996420877 1.254902992 1.233637676 1.180988775 0.768782659 1 14.05892614 1.385605461 4.266255261 0.888570591 1.265507588 0.417378858 0.177676613 0.194015241 5.55153174 0.121412979 0.042093785 24.29995453 -1.385605461 0.376936997 VLAGETLSVNDPPDVLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLAGETLSVNDPPDVLDR 18 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7EQR9;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;; 308.84 9.88E-61 921086000 1430150 1518040 1257510 1528360 1467380 1530010 1506760 1512510 1504280 1537640 FALSE TRUE 1374258.157 1474746.986 1484770.03 1607238.843 1514579.61 1560947.85 1525200.18 1481276.14 1333520.441 1433494.273 0.958677117 1.028777731 1.035769768 1.121203532 1.056564814 1.088911117 1.063973682 1.033332443 0.930258645 1 20.45110471 1.386427699 5.317934531 0.966328152 1.052975407 0.380104964 0.042835007 0.210158622 8.64273311 0.03058709 0.01098584 24.34600456 -1.386427699 0.086647256 KVNAEGSVDSVFSQVCTHLDALK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVNAEGSVDSVFSQVCTHLDALK 23 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 259.77 6.94E-44 411280000 512340 470880 345590 385870 426410 471380 428600 479340 548830 533140 FALSE TRUE 492317.1864 457450.9634 408045.8006 405784.7969 440125.8649 480911.6266 433845.335 469441.4615 486529.1193 497029.9529 0.990518144 0.920369005 0.82096823 0.816419201 0.885511753 0.967570714 0.872875633 0.944493302 0.978872835 1 18.92297327 1.386484946 1.097356086 1.003542537 0.889536102 0.332032104 0.052744025 0.548258215 1.311934554 0.051521376 0.01773035 24.34921394 -1.386484946 -0.114006435 EALPWGLEPQDVQSSDEMRS(ph)PEGYLR ddPTM_BT-474_Pertuzumab_2h_R1 3 EALPWGLEPQDVQSSDEMRSPEGYLR 26 1 Q9H5H4 Q9H5H4 ZNF768 Zinc finger protein 768 1 EALPWGLEPQDVQSSDEMRS(1)PEGYLR;EALPWGLEPQDVQSSDEMRS(1)PEGYLR;EALPWGLEPQDVQSSDEMRS(0.999)PEGYLR 208.15 1.42E-25 337897000 111257 102668 91063 94993 102245 104197 96251 102278 89274 99938 TRUE FALSE 106908.9534 99740.00916 107520.1098 99895.60011 105533.8033 106303.9347 97428.94853 100165.9236 79139.98979 93169.11024 1.147472088 1.070526582 1.154031733 1.072196567 1.132712366 1.140978318 1.045721573 1.075097994 0.84942305 1 16.5075641 1.38661889 4.446187168 0.926358326 1.106495055 0.682405254 0.049192524 0.110621314 3.400713621 0.033266786 0.011634939 24.35672485 -1.38661889 0.180136728 NPLPSKETIEQEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NPLPSKETIEQEK 13 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;; 148.72 3.57E-05 4226620000 4070600 3998690 2193800 2142740 3010750 3822140 2999670 3473870 4024370 2890720 FALSE TRUE 3911516.452 3884651.276 2590268.461 2253327.068 3107593.508 3899426.29 3036380.859 3402133.371 3567540.389 2694928.96 1.45143583 1.441467042 0.961163912 0.836135981 1.153126318 1.446949566 1.126701633 1.262420428 1.323797563 1 21.36181581 1.38691597 0.013683415 3.73E-05 2.357908569 0.05940502 0.203144677 2701.908604 35.71382498 3088.876432 3056.095354 24.37339181 -1.38691597 2.357871249 WGRDDIENIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 WGRDDIENIAR 11 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ;;; 225.15 5.19E-12 2589120000 1177180 1232520 936450 1227330 1126720 1286130 1142060 1182780 1099980 1141870 FALSE TRUE 1131174.504 1197369.736 1105687.346 1290672.648 1162961.972 1312136.43 1156036.872 1158355.18 975114.8819 1064530.128 1.0626045 1.124787082 1.038662333 1.21243412 1.092465062 1.232596801 1.08595975 1.088137526 0.916004964 1 20.02178535 1.387110537 3.609677143 0.959243228 1.12308456 0.520651289 0.061188047 0.171642536 3.673696832 0.044976446 0.015049207 24.38431372 -1.387110537 0.163841332 DFS(ph)PVPWSQYFESMEDVEVENETGK ddPTM_BT-474_Pertuzumab_2h_R1 3 DFSPVPWSQYFESMEDVEVENETGK 25 0 Q9Y570;Q9Y570-4 Q9Y570 PPME1 Protein phosphatase methylesterase 1 1 DFS(0.997)PVPWS(0.002)QYFESMEDVEVENETGK;DFS(0.99)PVPWS(0.003)QY(0.003)FES(0.004)MEDVEVENETGK;DFS(0.959)PVPWS(0.04)QY(0.001)FESMEDVEVENETGK 151.89 8.83E-08 57640000 84362 61222 75336 75263 73143 66827 93249 91764 122168 127392 TRUE FALSE 81065.03977 59476.0085 88950.89104 79147.33245 75495.71102 68178.28773 94390.20916 89869.04133 108300.0008 118763.6264 0.682574642 0.500793133 0.748974191 0.666427381 0.635680413 0.574067076 0.79477372 0.756705096 0.911895368 1 16.85773353 1.387298216 0.979656865 1.000513517 0.635488881 0.74569935 0.071886929 0.231898706 0.454278687 0.063777714 0.022961634 24.39485358 -1.387298216 -0.365024636 TTS(ph)PEPR ddPTM_BT-474_Pertuzumab_2h_R1 4 TTSPEPR 7 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 T(0.081)T(0.079)S(0.84)PEPR;T(0.015)T(0.067)S(0.918)PEPR;T(0.103)T(0.06)S(0.837)PEPR;T(0.024)T(0.217)S(0.758)PEPR 104.06 0.0086403 2422050000 2447810 2537820 2029090 2469620 2425660 2430310 2427700 2464810 2416060 2482730 TRUE FALSE 2352146.879 2465443.858 2395791.7 2597077.384 2503683.557 2479452.533 2457410.919 2413910.812 2141798.998 2314572.486 1.016233837 1.065183257 1.035090374 1.122054894 1.081704536 1.071235638 1.061712664 1.04291865 0.925354039 1 21.14231431 1.387734191 4.727658605 0.963899573 1.065535967 0.621180482 0.031292069 0.129089931 4.407648837 0.022025932 0.007792256 24.41935516 -1.387734191 0.101636394 GLYNEHTVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLYNEHTVDR 10 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 0 ; 133.89 0.0001851 915200000 412750 449620 375300 492220 437110 416730 425310 436090 403380 408880 FALSE TRUE 396619.2737 436797.2778 443125.0585 517623.5332 451170.0401 425156.5661 430515.071 427084.5891 357589.9935 381186.1934 1.040486987 1.145889556 1.162489792 1.357928336 1.183594915 1.115351431 1.129408878 1.120409387 0.938097968 1 18.54013634 1.387837799 2.819504841 0.967860678 1.167552921 0.481692102 0.077888564 0.232159913 3.149482451 0.068154552 0.021615242 24.42518146 -1.387837799 0.199692243 T(ph)PSPGPVESK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSPGPVESK 10 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 T(0.792)PS(0.208)PGPVESK 103.91 0.0112 0 236850 237190 195170 203000 203390 225750 211980 234320 295110 258090 TRUE FALSE 227593.6401 230425.5734 230441.5605 213476.8543 209932.2241 230314.8197 214574.2747 229481.2101 261610.35 240609.3344 0.945905281 0.957675121 0.957741565 0.8872343 0.87250241 0.957214816 0.891795304 0.953750239 1.08728263 1 17.87633309 1.388110557 5.386965068 1.041726097 0.924850234 0.632770215 0.035784044 0.127011376 5.367717762 0.024891926 0.008963955 24.4405265 -1.388110557 -0.116875863 AADKLIQNLDANHDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AADKLIQNLDANHDGR 16 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;; 212.35 2.84E-12 1999240000 4668730 6501260 3458660 3833460 4038650 5921790 4269790 4290720 4230940 3490900 FALSE TRUE 4486270.87 6315850.43 4083716.799 4031305.33 4168556.845 6041532.651 4322044.967 4202115.133 3750661.429 3254458.234 1.37850006 1.940676443 1.254806947 1.238702432 1.280875816 1.856386599 1.328038235 1.291187298 1.152468755 1 21.63398597 1.388162504 1.464472903 1.023477986 1.48021408 0.328888593 0.230680018 0.456002859 1.831031886 0.212676947 0.06774653 24.44345007 -1.388162504 0.456736093 STLTSR ddPTM_BT-474_Pertuzumab_2h_R1 8 STLTSR 6 0 H0YDZ5;M0R104;Q9Y2N7-4;Q9Y2N7-6;Q9Y2N7-7;Q9Y2N7-5;Q9Y2N7-3;Q9Y2N7-2;Q9Y2N7 H0YDZ5 HIF3A Hypoxia-inducible factor 3-alpha 0 ;;;;;;; 132.96 0.034132 7227450000 2019816 2192552 1607585 2363011 1829662 2066772 2146607 2078822 2012735 2089910 FALSE TRUE 1940879.358 2130022.564 1898111.37 2484966.281 1888514.74 2108563.546 2172877.819 2035893.599 1784257.761 1948358.534 0.996161294 1.093239528 0.974210515 1.275415298 0.96928502 1.082225632 1.115235097 1.044927596 0.915774858 1 20.89382775 1.388447258 5.510425375 0.959906034 1.07375394 0.21640537 0.085624499 0.290560206 12.74980104 0.05532488 0.019975179 24.45948215 -1.388447258 0.113847905 GIPDEWR ddPTM_BT-474_Pertuzumab_2h_R1 3 GIPDEWR 7 0 Q6NZY4;Q6NZY4-2;F5GX80;F5H6J5 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 0 ;; 146.94 0.0050827 619450000 779810 946280 813930 1017840 942520 1025100 937040 943070 944220 910090 FALSE TRUE 749334.1631 919293.0209 961025.2568 1070370.844 972837.0118 1045828.224 948507.7758 923595.2749 837036.1041 848448.7937 0.883181364 1.08349853 1.132685041 1.261562103 1.14660663 1.232635643 1.117931669 1.088569259 0.986548759 1 19.69446807 1.388473676 2.670743133 0.990764542 1.131421752 0.21522268 0.095861121 0.413536446 5.068734697 0.08360104 0.026284674 24.46097007 -1.388473676 0.14065721 IFCGDLGNEVNDDILAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFCGDLGNEVNDDILAR 17 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7EQ03 K7EP90 RBM42 RNA-binding protein 42 0 ; 188.25 9.80E-10 89488000 57048 68083 53632 63169 60216 60433 61525 62670 64673 62769 FALSE TRUE 54818.50109 66141.3395 63324.49544 66429.15966 62152.90233 61654.99667 62277.96135 61375.8426 57331.59217 58517.59972 0.936786563 1.130281143 1.082144444 1.135199666 1.062123235 1.053614587 1.064260353 1.048844158 0.979732464 1 15.83658297 1.388590926 2.927027303 0.989272726 1.071136434 0.248140463 0.051555492 0.330691245 4.816915658 0.040382574 0.012907131 24.46757487 -1.388590926 0.081863708 ESVPSAS(ph)PTGIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESVPSASPTGIPK 13 0 Q5THJ4-2;Q5THJ4;H3BLS7;A0A2R8YD87 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 ESVPS(0.001)AS(0.999)PTGIPK;ESVPS(0.001)AS(0.986)PT(0.013)GIPK 214.58 3.21E-11 829500000 617480 616210 608940 707880 674380 634980 666010 673630 662650 693570 TRUE FALSE 593348.1989 598636.2941 718989.0038 744413.7716 696072.0452 647819.7307 674160.8296 659719.3051 587428.7501 646593.8861 0.91765204 0.925830428 1.111963814 1.151284891 1.076521229 1.001895849 1.042634092 1.020299324 0.908497223 1 19.30250034 1.388816941 6.418056921 0.954930115 1.035861605 0.15318231 0.072292138 0.410032241 22.87832268 0.053298967 0.019466969 24.48031155 -1.388816941 0.08093149 ATSSS(ph)NPS(ph)SPAPDWYKDFVTDADAEVLEHSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 2 AT(0.179)S(0.187)S(0.315)S(0.339)NPS(0.502)S(0.469)PAPDWY(0.006)KDFVT(0.003)DADAEVLEHSGK 50.85 0.097027 34937000 17000 15840 13893 14932 14627 18054 15042 17125 22439 19082 TRUE FALSE 16335.62121 15388.25871 16403.77415 15702.64231 15097.49074 18419.06425 15226.0885 16771.36277 19891.81879 17789.55914 0.918270154 0.865016304 0.922101218 0.882688671 0.848671438 1.035386212 0.855900271 0.942764384 1.118173791 1 14.11874314 1.389542693 5.55929058 1.056548776 0.905224265 0.535868537 0.056817131 0.145832671 6.523314064 0.036850567 0.013327089 24.52125497 -1.389542693 -0.151324511 VLEVHENLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLEVHENLDR 10 0 A6NKD9;G3V5D5;G3V2D7;H0YJE0 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 0 109.6 0.0019973 100170000 85725 99399 85078 102380 101120 96191 87678 100050 94918 91680 FALSE TRUE 82374.77223 96564.23784 100453.4871 107663.8441 104372.6166 98136.04793 88751.02959 97983.93254 84143.30657 85470.43194 0.963780928 1.129797003 1.175301035 1.259661869 1.221154664 1.148187106 1.038382837 1.146407363 0.984472696 1 16.38313779 1.389638204 1.144213336 0.989829163 1.152484633 0.298392798 0.082262694 0.566753995 1.459857702 0.078505706 0.026655865 24.52664834 -1.389638204 0.16265547 AESSQTCHSEQGDKK ddPTM_BT-474_Pertuzumab_2h_R1 4 AESSQTCHSEQGDKK 15 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ;;; 241.93 4.32E-18 953460000 819619 727433 603928 600892 654761 686019 686627 735118 912133 813685 FALSE TRUE 787587.3833 706687.3231 713071.2239 631904.1081 675821.9822 699890.7742 695030.1466 719937.5564 808591.4858 758573.3902 1.038248103 0.931600465 0.940016132 0.833016444 0.890911797 0.922640819 0.916233229 0.949067771 1.065937055 1 19.53292924 1.389969331 4.431884859 1.031565015 0.921543623 0.416670587 0.050210068 0.202835689 6.248522205 0.03719946 0.01303896 24.54535574 -1.389969331 -0.110021392 EDDSDKYCK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDDSDKYCK 9 1 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 102.61 0.0032439 204050000 497700 462470 384510 421330 451340 480710 431600 510140 633770 602760 FALSE TRUE 478249.3338 449280.8084 453999.5104 443074.8918 465857.761 490430.2856 436882.0499 499605.4307 561827.0866 561934.5283 0.851076611 0.799525186 0.807922431 0.788481343 0.82902498 0.872753427 0.777460768 0.889081211 0.9998088 1 19.10004252 1.391083862 2.918177864 1.003227907 0.818508429 0.873425968 0.02743556 0.080367117 1.167259778 0.022109986 0.007077194 24.60842744 -1.391083862 -0.184719478 AGRPQYDTK ddPTM_BT-474_Pertuzumab_2h_R1 3 AGRPQYDTK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 150.35 7.79E-05 1750300000 1635210 1619440 1388290 1238240 1355200 888900 1647150 1475830 1761800 1741210 FALSE TRUE 1571304.185 1573255.157 1639184.885 1302145.715 1398791.239 906874.167 1667308.314 1445353.595 1561807.85 1623276.296 0.967983201 0.969185074 1.009800297 0.802171336 0.861708658 0.558669014 1.0271254 0.890392842 0.962133097 1 20.63047715 1.391146789 1.559156927 0.988118542 0.876826814 0.085439319 0.127904835 1.007644446 4.537588925 0.119545484 0.037710964 24.61199332 -1.391146789 -0.111291728 ALHQYTLEPSEKPFDMK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALHQYTLEPSEKPFDMK 17 1 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 123.02 3.30E-05 919050000 322950 350950 267920 259230 310100 309800 285800 333710 433910 379410 FALSE TRUE 310328.757 340941.2496 316339.1038 272608.8914 320074.6481 316064.3683 289297.7059 326818.7719 384654.3559 353712.2228 0.877348129 0.963894453 0.894340324 0.770708146 0.904901294 0.893563603 0.817890045 0.923967991 1.087478269 1 18.43221655 1.391270933 4.833854014 1.040789728 0.876599791 0.61496607 0.052679892 0.13669937 4.894545071 0.037687321 0.01341704 24.61902972 -1.391270933 -0.164189936 GGVTEISAADKAEEFRR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGVTEISAADKAEEFRR 17 2 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 152.68 1.15E-07 297550000 182330 199830 156190 151050 183790 192050 174920 182460 181540 180270 FALSE TRUE 175204.342 194131.0441 184417.0074 158845.7086 189701.7723 195933.3826 177060.7233 178692.1372 160932.3403 168060.1523 1.042509718 1.155128336 1.097327385 0.945171752 1.128773059 1.165852701 1.053555652 1.063262973 0.957587733 1 17.35861817 1.391312562 3.006003999 0.979014155 1.086013665 0.309903932 0.061045637 0.312454519 4.798860504 0.05034972 0.016217922 24.62138969 -1.391312562 0.10699951 RLS(ph)PPSSSAASSYSFSDLNSTR ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSPPSSSAASSYSFSDLNSTR 22 1 P50402 P50402 EMD Emerin 1 RLS(0.994)PPS(0.002)S(0.002)S(0.002)AASSYSFSDLNSTR;RLS(0.977)PPS(0.007)S(0.007)S(0.01)AASSYSFSDLNSTR;RLS(0.982)PPS(0.014)S(0.003)S(0.001)AASSYSFSDLNSTR 197.56 1.22E-22 2782060000 749020 1034220 723860 1307200 989220 898540 853440 921900 778440 696000 TRUE FALSE 719747.4703 1004725.058 854677.6042 1374664.749 1021039.16 916709.0944 863884.654 902862.4428 690074.7547 648859.3001 1.10925045 1.548448266 1.317200207 2.118586801 1.573591007 1.412801041 1.3313898 1.39146105 1.063519864 1 19.30754615 1.391390732 1.057823808 0.987384529 1.533720284 0.349339614 0.246822852 0.524717446 1.175265104 0.229664301 0.080219389 24.62582177 -1.391390732 0.546335755 SQSSDTEQQS(ph)PTSGGGK ddPTM_BT-474_Pertuzumab_2h_R1 11 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSSDTEQQS(0.5)PT(0.5)S(0.001)GGGK;SQSSDTEQQS(0.723)PT(0.277)SGGGK;SQSSDTEQQS(0.998)PT(0.002)SGGGK;SQSSDTEQQS(0.855)PT(0.131)S(0.014)GGGK;SQSSDTEQQS(1)PTSGGGK;SQSSDTEQQS(0.95)PT(0.05)SGGGK;SQSSDTEQQS(0.924)PT(0.075)SGGGK;SQSSDTEQQS(0.999)PT(0.001)SGGGK;SQSSDT(0.002)EQQS(0.981)PT(0.008)S(0.008)GGGK;SQSSDT(0.002)EQQS(0.998)PTSGGGK;SQSSDTEQQS(0.499)PT(0.499)S(0.002)GGGK 456.93 7.07E-184 9270685000 4672331 4397757 4391411 4332410 4274613 5039379 4986473 4908587 6513796 6190671 TRUE FALSE 4489731.139 4272337.276 5185036.654 4556006.199 4412109.809 5141278.696 5047498.948 4807222.963 5774377.186 5771371.339 0.777931427 0.7402638 0.898406349 0.789414843 0.764482053 0.89082445 0.874575322 0.832942932 1.00052082 1 22.46048273 1.392100619 0.581683272 1.011018383 0.793032615 0.633353033 0.053408893 0.496899986 0.408667441 0.053344042 0.027132528 24.66610747 -1.392100619 -0.217985768 NTDKNGEELHGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 NTDKNGEELHGGK 13 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 154.47 2.61E-05 792730000 1111858 1002950 945528 822446 975366 952957 1074998 1085926 1431870 1325410 FALSE TRUE 1068405.36 974346.848 1116405.943 864892.5366 1006739.533 972226.4435 1088154.147 1063501.249 1269330.12 1235638.8 0.864658313 0.788536948 0.903505088 0.699955793 0.814752283 0.786820909 0.880640966 0.860689425 1.027266318 1 20.23682565 1.393195128 1.837424056 1.020062746 0.813103923 0.644491236 0.055923455 0.193000558 1.177114328 0.047301039 0.014663214 24.72834937 -1.393195128 -0.206958823 S(ph)PTFSEELPVLGDGQQLR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPTFSEELPVLGDGQQLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 S(0.937)PT(0.063)FSEELPVLGDGQQLR;S(0.929)PT(0.071)FSEELPVLGDGQQLR;S(0.999)PT(0.001)FSEELPVLGDGQQLR;S(0.499)PT(0.499)FS(0.001)EELPVLGDGQQLR;S(0.973)PT(0.027)FSEELPVLGDGQQLR 352.72 1.97E-90 885380000 132733 146334 121658 144587 139552 142573 124247 140563 125070 121084 TRUE FALSE 127545.6476 142160.6976 143644.3069 152049.1524 144040.8168 145455.9237 125767.572 137660.3249 110872.5779 112882.8728 1.129893707 1.259364632 1.27250754 1.34696388 1.276020119 1.288556183 1.114142197 1.219497001 0.982191321 1 16.78446708 1.393319406 1.230662706 0.980881977 1.261446872 0.654431703 0.070267026 0.25055292 0.734825043 0.063286862 0.021037489 24.73542665 -1.393319406 0.280564895 CFLAQPVTLLDIYTHWQQTSELGR ddPTM_BT-474_Pertuzumab_2h_R1 2 CFLAQPVTLLDIYTHWQQTSELGR 24 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 ; 168.57 1.03E-11 266950000 204152 205019 164883 132091 186715 253180 192745 191288 188772 182470 FALSE TRUE 196173.5141 199172.0589 194681.0259 138908.2323 192720.8575 258299.4731 195103.871 187337.836 167343.394 170111.1444 1.153207892 1.170834866 1.144434285 0.816573381 1.132911417 1.518415939 1.146919984 1.101267272 0.983729753 1 17.37611813 1.393375816 3.028456235 0.990921279 1.153835935 0.142563787 0.15747035 0.554518193 8.657204551 0.136376776 0.044074944 24.73863975 -1.393375816 0.162914657 KLPIDVTEGEVISLGLPFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPIDVTEGEVISLGLPFGK 20 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7;K7ELW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 163.85 3.05E-11 1059030000 3298700 3270100 2608100 2662000 3000400 3234600 3024200 3256400 3923000 3596700 FALSE TRUE 3169783.157 3176839.95 3079441.687 2799386.139 3096910.591 3300005.828 3061211.064 3189154.202 3477677.487 3353092.305 0.945331315 0.947435877 0.918388582 0.834867008 0.923598371 0.984167905 0.912951624 0.951108383 1.037155309 1 21.67706077 1.393383058 3.88364143 1.017677772 0.923880988 0.505969964 0.036802047 0.191611331 4.719183696 0.029226741 0.010001268 24.73905226 -1.393383058 -0.093796784 NKQDDDLNCEPLS(ph)PHNITPEPVSK ddPTM_BT-474_Pertuzumab_2h_R1 5 NKQDDDLNCEPLSPHNITPEPVSK 24 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73;F8WE35;F5H8I0;F5H2W9;F5H2H9;F5GZ10;F5H502;F5H1K9 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK 228.84 1.98E-33 10187540000 8625890 7064360 5797940 5782440 6618160 6972370 6741330 7537980 10238790 8746950 TRUE FALSE 8288780.682 6862891.37 6845756.732 6080872.421 6831039.127 7113356.099 6823832.413 7382318.079 9076525.484 8154511.286 1.016465658 0.841606704 0.839505458 0.745706543 0.837700616 0.872321571 0.836816846 0.905304784 1.11306799 1 22.95916699 1.393659421 4.308599756 1.053956042 0.851766983 0.571948838 0.068149002 0.146939979 4.349154925 0.049281386 0.017237743 24.75479997 -1.393659421 -0.202189058 RPILQLS(ph)PPGPR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPILQLSPPGPR 12 1 Q8N3X1-2;Q8N3X1;F5GXL1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 RPILQLS(1)PPGPR;RPILQLS(1)PPGPR;RPILQLS(1)PPGPR;RPILQLS(1)PPGPR;RPILQLS(1)PPGPR;RPILQLS(1)PPGPR 123.92 0.00020347 6104200000 1498620 1634440 1292754 1595320 1547390 1474610 1551320 1560360 1538310 1586590 TRUE FALSE 1440052.274 1587827.371 1526383.405 1677654.656 1597163.205 1504427.625 1570305.518 1528138.021 1363687.498 1479128.846 0.97358136 1.073488206 1.031947561 1.134218064 1.079799917 1.017103837 1.061642143 1.03313381 0.921953149 1 20.4963163 1.394302634 5.178636066 0.96210855 1.055004082 0.408040279 0.043590366 0.190881361 7.762845099 0.029766485 0.010723334 24.79149025 -1.394302634 0.092895532 SLGNILQAKPTSS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGNILQAKPTSSPAK 16 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SLGNILQAKPTS(0.099)S(0.901)PAK;SLGNILQAKPT(0.008)S(0.066)S(0.926)PAK 209.85 6.79E-12 3654700000 5522700 4842200 4657400 3623500 3970500 2697000 5101300 5219300 5849900 6512200 TRUE FALSE 5306866.778 4704105.197 5499095.783 3810509.269 4098214.738 2751535.188 5163731.235 5111519.631 5185843.877 6071122.894 0.874116184 0.774832808 0.905779026 0.627644891 0.67503406 0.453216849 0.850539731 0.84193974 0.854181997 1 22.53353195 1.394559239 1.40104962 0.964486155 0.727813758 0.293741853 0.126926762 0.518363551 1.921853843 0.121449346 0.039116498 24.80614279 -1.394559239 -0.236672397 QSGEAFVELGSEDDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 QSGEAFVELGSEDDVK 16 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 322.01 7.80E-58 332640000 403720 365700 285900 346550 335890 341580 339400 388280 441530 438270 FALSE TRUE 387942.1761 355270.5941 337568.4898 364435.487 346694.2069 348486.9816 343553.6787 380261.8823 391409.3654 408585.5825 0.94947593 0.86951329 0.826187962 0.891944069 0.84852286 0.852910618 0.840836519 0.93067866 0.957961764 1 18.64027877 1.395846124 2.06070052 0.989134736 0.866654349 0.641257529 0.033592881 0.188547145 1.427281297 0.029222267 0.009038472 24.8797564 -1.395846124 -0.122480386 DGSGDSHPDFPEDADIDLKDVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGSGDSHPDFPEDADIDLKDVDK 23 1 Q08752 Q08752 PPID Peptidyl-prolyl cis-trans isomerase D 0 ; 172.91 2.68E-12 589310000 1244070 1031770 846260 686700 918280 971630 955980 1014140 1381580 1080330 FALSE TRUE 1195450.369 1002344.93 999198.007 722140.6693 947817.3102 991277.0243 967679.5692 993197.6546 1224748.83 1007158.287 1.186953813 0.995220853 0.992096297 0.71700812 0.941080784 0.984231612 0.960801874 0.986138592 1.216044038 1 19.94185901 1.396049053 7.935259032 1.108240587 0.961891033 0.180962183 0.117023925 0.395805639 32.68316359 0.0787671 0.029068397 24.89138446 -1.396049053 -0.146349554 ELSNS(ph)PLRENSFGSPLEFR ddPTM_BT-474_Pertuzumab_2h_R1 8 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELS(0.001)NS(0.999)PLRENSFGSPLEFR;ELS(0.001)NS(0.999)PLRENSFGSPLEFR;ELS(0.001)NS(0.999)PLRENSFGSPLEFR;ELS(0.001)NS(0.999)PLRENSFGSPLEFR;ELSNS(0.502)PLRENS(0.248)FGS(0.25)PLEFR;ELSNS(1)PLRENSFGSPLEFR 272.79 1.41E-39 35087714000 2404318 2499450 1628400 2076932 2182125 2460140 2067114 2102579 2181913 1901847 TRUE FALSE 2310354.594 2428168.133 1922688.104 2184122.709 2252315.032 2509885.716 2092411.959 2059160.009 1934231.384 1773033.209 1.303052071 1.369499523 1.084406143 1.231856628 1.270317454 1.415588667 1.180131285 1.161377011 1.090916613 1 20.75778813 1.396471933 1.357167175 1.013691569 1.269927913 0.529032895 0.08620477 0.326498134 1.14258235 0.080956267 0.026273617 24.91563344 -1.396471933 0.256236343 AIAGVSGFGYDHLILNVEWAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIAGVSGFGYDHLILNVEWAK 21 0 O75821;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 100.67 0.00065509 11286900 25133.5 24030.2 26000 26439 23548 23385.4 26419 30066.9 35436 36375 FALSE TRUE 24151.25503 23344.88222 30698.77837 27803.51996 24305.44281 23858.26881 26742.32362 29446.00801 31413.45384 33911.28885 0.71218924 0.68841035 0.905267225 0.819889804 0.716736038 0.703549456 0.788596498 0.86832465 0.92634208 1 15.049478 1.396921196 1.518856878 0.989191419 0.76120886 0.641277258 0.061943861 0.252171136 1.083845278 0.060212137 0.019115705 24.94142118 -1.396921196 -0.227982558 IFHTVTTTDDPVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFHTVTTTDDPVIR 14 0 O15371-2;O15371;O15371-3;B0QYA5;B0QYA4 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 155.08 5.94E-06 962800000 505710 521320 455650 489890 524760 517200 538780 518310 487160 522590 FALSE TRUE 485946.2941 506452.464 537996.0909 515173.2816 541639.382 527658.1384 545373.7508 507606.7174 431859.6391 487194.5138 0.997437944 1.039528258 1.104273705 1.057428331 1.111751809 1.083054352 1.119416856 1.041897441 0.886421392 1 18.89413836 1.396962943 5.853139864 0.945267018 1.074555919 0.588271983 0.042840527 0.133828928 6.79403303 0.028573897 0.010441665 24.94381882 -1.396962943 0.129288901 RRS(ph)PS(ph)PTPTPGPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSPSPTPTPGPSR 14 2 F8WD88;P49450-2;P49450 F8WD88 CENPA Histone H3-like centromeric protein A 2 RRS(0.996)PS(0.653)PT(0.326)PT(0.024)PGPSR 93.753 0.021823 199000000 130640 137010 107430 138480 121710 113990 125010 116410 109690 96836 TRUE FALSE 125534.4444 133102.6089 126844.9908 145626.9694 125624.9127 116294.9559 126539.9098 114006.0928 97238.45106 90277.21147 1.390544107 1.474376609 1.405061019 1.613108857 1.391546223 1.288198362 1.401681639 1.262844642 1.077109599 1 16.46207424 1.396983818 0.860143277 0.984806373 1.452801928 0.809770468 0.07533337 0.222843277 0.347282049 0.070743611 0.027214315 24.94501781 -1.396983818 0.467995555 AAPEASS(ph)PPASPLQHLLPGK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.423)S(0.577)PPASPLQHLLPGK;AAPEAS(0.079)S(0.921)PPASPLQHLLPGK;AAPEAS(0.095)S(0.905)PPASPLQHLLPGK 261.46 1.42E-36 13734700000 1555500 1812250 1382180 1736480 1540050 1605220 1565170 1514850 1458380 1295790 TRUE FALSE 1494709.34 1760566.404 1631970.672 1826099.941 1589587.107 1637678.648 1584325.019 1483567.818 1292830.816 1208024.989 1.237316574 1.457392372 1.350941154 1.511640866 1.315856146 1.355666201 1.311500203 1.22809365 1.070202047 1 20.20421887 1.39705525 1.156697707 0.992859759 1.38196258 0.779943149 0.07035653 0.180469576 0.473325332 0.060322788 0.020453441 24.94912105 -1.39705525 0.389102821 VLT(ph)PEEQLADKLR ddPTM_BT-474_Pertuzumab_2h_R1 3 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 VLT(1)PEEQLADKLR;VLT(1)PEEQLADKLR;VLT(1)PEEQLADKLR 147.17 6.89E-05 485080000 695630 661920 553219 527594 567427 703170 593880 690760 820500 790060 TRUE FALSE 668444.0105 643042.6897 653197.9796 554823.1896 585678.8048 717388.5792 601148.0811 676495.5646 727360.2798 736548.5325 0.907535595 0.873048633 0.886836306 0.753274448 0.795166617 0.973986842 0.816169003 0.918467059 0.987525258 1 19.49042106 1.397255205 2.643008038 0.998354275 0.857510503 0.462915347 0.058263124 0.246777709 2.994443578 0.049687147 0.015701285 24.9606106 -1.397255205 -0.140843772 CKDDEFTHLYTLIVRPDNTYEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 CKDDEFTHLYTLIVRPDNTYEVK 23 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 263.57 3.85E-44 4056840000 1683660 1769120 1483560 1504030 1577990 1828580 1754960 1831950 2508300 2093470 FALSE TRUE 1617860.706 1718666.43 1751672.294 1581653.169 1628747.481 1865555.14 1776437.725 1794119.592 2223568.3 1951677.412 0.828959077 0.880609889 0.897521426 0.810407068 0.83453724 0.955872691 0.910210732 0.919270562 1.139311387 1 20.89628318 1.397471387 4.190757816 1.06776678 0.876924348 0.685393662 0.051859913 0.121317513 3.450234444 0.038203442 0.013336417 24.97303851 -1.397471387 -0.190842433 FAGHSEAGGGSGDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FAGHSEAGGGSGDR 14 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;; 208.27 8.27E-09 1092570000 674240 721490 618880 699650 710470 698360 675790 710310 716400 692270 FALSE TRUE 647889.9554 700913.8116 730725.3829 735759.0203 733322.9128 712481.3177 684060.5202 695641.8503 635077.2754 645381.9363 1.003886101 1.086044979 1.132237117 1.140036588 1.136261912 1.103968484 1.059931308 1.077876233 0.984033236 1 19.29979367 1.398213677 1.675228191 0.988715197 1.101624937 0.497112915 0.039703485 0.294567301 1.517332897 0.037176442 0.011646806 25.01575856 -1.398213677 0.112909739 IRQEVGPPLPPLLAPLIAT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 IRQEVGPPLPPLLAPLIATPPR 22 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 IRQEVGPPLPPLLAPLIAT(1)PPR 66.01 0.036133 120180000 91096 106870 96220 98071 78361 111010 93638 94698 105560 92748 TRUE FALSE 87535.86761 103822.1722 113609.0944 103132.4561 80881.55273 113254.6983 94783.96985 92742.45321 93577.27134 86466.09535 1.012372159 1.200726965 1.313914939 1.192750241 0.935413498 1.309816267 1.096198105 1.072587502 1.082242363 1 16.39984692 1.398731089 0.820584063 1.004585235 1.165033796 0.158449113 0.112245773 0.99542093 1.430520082 0.10423518 0.041199113 25.04557974 -1.398731089 0.160448561 TALPTS(ph)GSSAGELELLAGEVPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPT(0.115)S(0.509)GS(0.363)S(0.012)AGELELLAGEVPAR 90.22 0.0058617 12962000 14754 10792 9465.6 10895 12943 10303 12524 10982 10921 10002 TRUE FALSE 14177.39737 10484.22273 11176.24448 11457.29226 13359.32335 10511.33372 12677.27246 10755.21786 9681.293865 9324.555631 1.520436783 1.124367009 1.198581994 1.228722602 1.432703485 1.127274493 1.359557813 1.153429535 1.038257934 1 13.18681926 1.399050897 2.681653993 1.010569597 1.272659565 0.433920242 0.121106497 0.251800775 3.147150385 0.09491261 0.030105414 25.06402971 -1.399050897 0.262089968 LSMPQSAAVST(ph)TPPHNRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSMPQSAAVSTTPPHNRR 18 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.105)T(0.501)T(0.393)PPHNRR 60.564 0.050791 227720000 240660 187420 142680 173910 210890 207520 175370 194260 218950 203700 TRUE FALSE 231254.7411 182074.9651 168465.4499 182885.5159 217673.4684 211716.1966 177516.2305 190248.4631 194095.7139 189903.2176 1.217750516 0.958777673 0.887112141 0.963045905 1.146233704 1.114863662 0.934772105 1.001818008 1.022077016 1 17.53490482 1.399141028 0.005630075 1.38E-07 2.02125051 0.02298216 0.097085639 20528.25902 112.354977 20204.04416 20122.34169 25.0692319 -1.399141028 2.021250372 RTFS(ph)LTEVR ddPTM_BT-474_Pertuzumab_2h_R1 3 RTFSLTEVR 9 1 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 RT(0.104)FS(0.892)LT(0.003)EVR;RT(0.098)FS(0.897)LT(0.005)EVR;RT(0.297)FS(0.702)LT(0.001)EVR 112.82 0.0011645 679040000 533480 542260 460090 499140 500560 497630 429410 558870 475310 462370 TRUE FALSE 512631.0118 526795.2757 543238.4976 524900.6752 516660.967 507692.4196 434665.248 547329.1392 421354.8015 431053.2681 1.189252118 1.222111778 1.26025839 1.217716496 1.198601206 1.177795083 1.008379428 1.269748265 0.977500538 1 18.71750664 1.399198317 0.442580354 0.989265536 1.234391488 0.483644917 0.076461743 0.867264996 0.476469766 0.087429259 0.056890911 25.07253911 -1.399198317 0.245125952 IEWLESHQDADIEDFK ddPTM_BT-474_Pertuzumab_2h_R1 3 IEWLESHQDADIEDFK 16 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 344.47 1.72E-72 2739350000 3379620 3507339 3384047 4017138 3636024 3511371 3965612 4152616 5702916 5148432 FALSE TRUE 3247540.714 3407313.126 3995619.571 4224462.974 3752980.014 3582373.327 4014144.346 4066863.028 5055544.884 4799724.115 0.676609871 0.709897703 0.832468591 0.88014704 0.781915778 0.746370675 0.836328141 0.847311831 1.053299057 1 22.19452005 1.399380333 2.406224777 1.030315142 0.782005882 0.718831662 0.060100862 0.16033666 1.632196928 0.054544435 0.017050694 25.08304937 -1.399380333 -0.24830926 S(ph)RS(ph)PHEAGFCVYLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 2 S(1)RS(1)PHEAGFCVY(0.001)LK;S(1)RS(1)PHEAGFCVYLK;S(1)RS(1)PHEAGFCVYLK;S(1)RS(1)PHEAGFCVYLK 162.33 2.54E-06 1191316000 1911970 1755452 1458143 1497513 1531874 1636323 1632043 1739169 2170780 1849675 TRUE FALSE 1837248.099 1705388.228 1721661.876 1574799.825 1581148.118 1669410.572 1652016.43 1703254.552 1924362.155 1724394.865 1.065445123 0.988977793 0.998415103 0.913247805 0.916929266 0.968113862 0.958026763 0.987740446 1.115963747 1 20.71765874 1.400230232 7.235810343 1.057764172 0.970356464 0.326914225 0.048154263 0.250404608 18.69606712 0.032446117 0.012006685 25.13218411 -1.400230232 -0.087407707 FAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPR 39 1 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 ; 136.36 1.88E-09 166932000 27207.5 27261.9 21980 24289.8 19121.7 26725.6 24282.3 26750 35879 29500.9 FALSE TRUE 26144.20082 26484.4173 25952.27494 25543.39949 19736.76685 27266.00994 24579.47405 26197.60315 31806.16634 27502.77777 0.950602192 0.962972451 0.943623774 0.928757077 0.717628125 0.991391131 0.893708783 0.952543898 1.156471052 1 14.74728972 1.400540166 5.570343846 1.076551876 0.91323735 0.405623054 0.078877535 0.195282512 9.299263102 0.053190301 0.019421364 25.15012605 -1.400540166 -0.163314527 GSGS(ph)PTHSLSQK ddPTM_BT-474_Pertuzumab_2h_R1 6 GSGSPTHSLSQK 12 0 I3L2R2;I3L419;I3L156;Q9BSJ6-2;Q9BSJ6 I3L2R2 FAM64A Protein FAM64A 1 GS(0.004)GS(0.995)PT(0.001)HSLSQK;GSGS(0.99)PT(0.009)HSLSQK;GSGS(0.999)PT(0.001)HSLSQK;GSGS(1)PTHSLSQK;GSGS(0.916)PT(0.084)HSLSQK;GSGS(0.996)PT(0.004)HSLSQK 279.75 5.68E-28 5421870000 3754330 4021610 3176400 3819690 3756580 3314380 3779720 3668690 3064980 3625380 TRUE FALSE 3607606.633 3906917.62 3750446.139 4016824.659 3877413.807 3381399.034 3825977.344 3592930.269 2717056.32 3379829.783 1.067392994 1.155951001 1.109655331 1.188469514 1.147221622 1.000464299 1.132002967 1.063050656 0.803903301 1 21.68851916 1.400916716 5.407580565 0.904086899 1.113700223 0.616899135 0.06588236 0.124010157 5.614286497 0.043513462 0.015847556 25.17194165 -1.400916716 0.209613323 LLQQQQAVPVPPAPS(ph)SPPPLWAGLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLQQQQAVPVPPAPSSPPPLWAGLAK 26 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 LLQQQQAVPVPPAPS(0.5)S(0.5)PPPLWAGLAK;LLQQQQAVPVPPAPS(0.5)S(0.5)PPPLWAGLAK 52.237 0.072572 172006000 320780 327330 257644 305050 329010 341660 323920 320260 311845 318530 TRUE FALSE 308243.563 317994.8689 304206.0021 320793.6671 339592.9054 348568.5993 327884.2299 313646.5191 276445.663 296955.6794 1.038012014 1.070849595 1.024415504 1.080274564 1.14358111 1.173806812 1.104152076 1.056206501 0.930932399 1 18.1798881 1.401075119 4.290534012 0.96715096 1.091398046 0.545959888 0.044893695 0.174861783 5.234363322 0.035977944 0.012661036 25.18112441 -1.401075119 0.124247085 WGGRPGLRPGSSLLDQDCRPDSDGLNLSSMNSAGVSGS(ph)PEPPTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 WGGRPGLRPGSSLLDQDCRPDSDGLNLSSMNSAGVSGSPEPPTSPR 46 3 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 2 WGGRPGLRPGSSLLDQDCRPDSDGLNLS(0.001)SMNS(0.001)AGVS(0.019)GS(0.979)PEPPT(0.225)S(0.775)PR 63.576 0.0010983 121560000 22564 31636 17284 23474 22381 29900 20453 24238 17958 19935 TRUE FALSE 21682.17393 30733.77225 20407.60328 24685.49595 23100.90519 30504.59849 20703.30993 23737.47683 15919.48313 18584.78469 1.166662638 1.653706124 1.098081232 1.328263758 1.243000959 1.641374866 1.113992455 1.27725326 0.856586901 1 14.18183435 1.401148622 2.178893878 0.928539366 1.33671822 0.384902325 0.19008117 0.288323653 2.435917837 0.153436456 0.04766699 25.18538661 -1.401148622 0.408178854 TLDKVS(ph)LEETAQLPSAPQGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLDKVSLEETAQLPSAPQGSR 21 1 Q9BRP8-2;Q9BRP8 Q9BRP8-2 WIBG Partner of Y14 and mago 1 T(0.067)LDKVS(0.928)LEET(0.005)AQLPSAPQGSR 61.415 0.029736 211610000 64990 93573 65280 92798 84355 92542 84930 83086 65578 81562 TRUE FALSE 62450.11895 90904.38966 77077.54815 97587.3159 87068.35518 94413.26265 85969.39875 81370.24507 58133.86037 76037.73309 0.821304324 1.19551683 1.013674988 1.283406434 1.14506774 1.241663301 1.130614962 1.070129813 0.764539631 1 16.2144279 1.401441083 5.353162661 0.884333227 1.126925026 0.326680915 0.133119643 0.214135257 9.547973589 0.087045659 0.031684455 25.20235257 -1.401441083 0.242591799 (ac)MDRNPS(ph)PPPPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 MDRNPSPPPPGR 12 1 J3KND1;E9PRZ1;Q96ER3;E9PL53;E9PMD2 J3KND1 SAAL1 Protein SAAL1 1 MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR 78.043 6.95E-05 790900000 115254.2 162203 123796 178272 147701 178388 168215 152542 119436 146943 TRUE FALSE 110749.9384 157577.1293 146168.691 187472.6393 152451.9368 181995.1276 170273.6655 149391.9544 105878.126 136990.4197 0.808450245 1.150278462 1.066999366 1.368509124 1.112865681 1.328524491 1.24296039 1.090528481 0.772887084 1 17.06371548 1.401861924 5.519715267 0.890616452 1.163514525 0.315061939 0.154897575 0.22924677 10.82409701 0.104500852 0.038173804 25.22678603 -1.401861924 0.272898072 TS(ph)PYGSSLDLSTGSSSRPPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPYGSSLDLSTGSSSRPPPK 21 1 J3KNZ9 J3KNZ9 FBRS 1 T(0.021)S(0.978)PYGS(0.001)SLDLSTGSSSRPPPK 141.53 9.38E-08 558200000 117070 102980 99943 76731 89717 93293 104600 106400 138010 123440 TRUE FALSE 112494.775 100043.1112 118004.9233 80691.09611 92602.82878 95179.44838 105880.1261 104202.8028 122343.6834 115079.2989 0.977541366 0.869340639 1.025422682 0.701178204 0.804687113 0.827077062 0.920062315 0.905486946 1.063125033 1 16.81226881 1.40257646 2.718656448 1.031501767 0.869813675 0.325090888 0.087243147 0.313354204 4.036756507 0.073264833 0.02335916 25.26832535 -1.40257646 -0.161688092 QRS(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_BT-474_Pertuzumab_2h_R1 4 QRSPSPAPAPAPAAAAGPPTR 21 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR 170.04 1.04E-10 4073480000 1165510 1322010 1085830 1322280 1275080 1360500 1323460 1242570 1266690 1170760 TRUE FALSE 1119960.581 1284307.569 1282063.635 1390523.029 1316094.106 1388010.242 1339656.899 1216910.495 1122900.662 1091463.382 1.026109166 1.176684065 1.17462817 1.273998791 1.205806926 1.271696572 1.227395184 1.114934788 1.028802871 1 20.0578323 1.402842158 2.505473501 1.007459157 1.19844297 0.541388159 0.065789027 0.215337309 2.37613621 0.057400474 0.018074308 25.28378903 -1.402842158 0.190983813 APSQAAES(ph)SPAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 APSQAAESSPAKK 13 1 Q8NFH8-3;Q8NFH8-2;Q8NFH8-4;Q8NFH8 Q8NFH8-3 REPS2 RalBP1-associated Eps domain-containing protein 2 1 APSQAAES(0.679)S(0.321)PAKK 68.481 0.030817 291330000 181020 151220 130740 138980 145590 134830 158550 176840 213340 217770 TRUE FALSE 173945.5383 146907.3537 154367.6263 146152.7745 150273.0346 137556.355 160490.3823 173188.1922 189122.5376 203020.2439 0.856789131 0.723609384 0.760355831 0.719892616 0.74018744 0.677549944 0.790514183 0.853058734 0.931545219 1 17.63126407 1.403094496 1.475613458 0.991969372 0.744413343 0.79304779 0.044466899 0.155007949 0.632546641 0.039401961 0.012600653 25.29848392 -1.403094496 -0.247556029 (ac)GT(ph)PQKDVIIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTPQKDVIIK 10 1 P53611;Q5T4U8 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 1 GT(1)PQKDVIIK 59.8 0.0155 283970000 438840 413770 390800 362570 381370 435380 450930 518030 597480 650200 TRUE FALSE 421689.6476 401969.6847 461426.2533 381282.2812 393637.1124 444183.6819 456448.6162 507332.4995 529656.5752 606161.3749 0.69567225 0.663139721 0.76122675 0.629011179 0.649393262 0.732781237 0.753015014 0.836959464 0.873788066 1 19.2093424 1.403200739 0.838098425 0.993818298 0.67930954 0.892477651 0.03594589 0.160900912 0.239348362 0.033617947 0.013142595 25.30467354 -1.403200739 -0.314508758 CSLHSAS(ph)PASVR ddPTM_BT-474_Pertuzumab_2h_R1 2 CSLHSASPASVR 12 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 CSLHSAS(1)PASVR;CSLHSAS(1)PASVR 144.55 4.07E-05 937330000 512080 748220 527950 858870 592600 629140 644990 666530 619100 672760 TRUE FALSE 492067.3475 726881.4982 623362.3092 903196.3836 611661.5172 641861.6419 652883.5806 652765.9226 548822.3635 627193.366 0.784554452 1.158943219 0.993891745 1.440060486 0.975235949 1.023387167 1.040960597 1.040773002 0.875044912 1 19.25855077 1.40355508 4.6911126 0.93834166 1.068648828 0.081259294 0.158778923 0.498215197 17.66628348 0.108708914 0.038959355 25.32532804 -1.40355508 0.130307167 NPEVGLKPVWYSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 NPEVGLKPVWYSPK 14 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 158.17 4.66E-06 1071060000 1418180 1258740 1130060 1104460 1118730 1134820 1307540 1478680 1643420 1780860 FALSE TRUE 1362755.958 1222841.968 1334286.98 1161461.313 1154714.966 1157766.838 1323542.066 1448144.741 1456865.851 1660240.766 0.820818273 0.736544959 0.803670773 0.699574024 0.695510549 0.697348759 0.797198872 0.872249839 0.877502758 1 20.66296104 1.403709793 1.149465638 0.981699811 0.741008998 0.763761245 0.045399907 0.211027121 0.546646949 0.043433779 0.014785472 25.33435158 -1.403709793 -0.240690813 SSS(ph)FTLLQSLAIEDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSFTLLQSLAIEDSR 16 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.158)S(0.158)S(0.682)FT(0.002)LLQSLAIEDSR;S(0.059)S(0.031)S(0.91)FT(0.001)LLQSLAIEDSR;SS(0.029)S(0.971)FTLLQSLAIEDSR;S(0.028)S(0.028)S(0.944)FT(0.001)LLQSLAIEDSR 311.1 1.22E-57 328679000 307339 356759 295587 369868 416395 356517 302651 343213 324021 281402 TRUE FALSE 295327.8521 346584.5826 349006.1462 388956.9318 429788.7233 363726.018 306354.9335 336125.5316 287239.4945 262342.3919 1.125734388 1.321115433 1.330345979 1.482630882 1.638274014 1.38645537 1.167767555 1.281247492 1.094903086 1 18.00109143 1.403850838 1.086938522 1.009724039 1.381507482 0.465060214 0.133658018 0.433234269 1.01530817 0.13189867 0.045768385 25.34258067 -1.403850838 0.371783443 NPQTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPQTAR 6 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 113.08 0.061517 25853000 22185 21838 15148 21242 18755 17698 20280 19589 16778 19649 FALSE TRUE 21317.98567 21215.20162 17885.58057 22338.30217 19358.27161 18055.86569 20528.19271 19184.4803 14873.43178 18318.15573 1.163762662 1.158151614 0.976385441 1.219462401 1.0567806 0.985681416 1.120647352 1.04729322 0.811950286 1 14.16098664 1.403979079 5.792598891 0.907644016 1.092507371 0.445904789 0.083874762 0.178256026 9.308611124 0.054622953 0.020083863 25.35006513 -1.403979079 0.184863355 FLRT(ph)AEADGGLAR ddPTM_BT-474_Pertuzumab_2h_R1 3 FLRTAEADGGLAR 13 1 Q8NC60 Q8NC60 NOA1 Nitric oxide-associated protein 1 1 FLRT(1)AEADGGLAR;FLRT(1)AEADGGLAR;FLRT(1)AEADGGLAR 84.289 0.015864 490950000 28963.7 31644 36946.7 41165.1 43337.8 35559.2 36497.9 35328.7 35540.4 31664.4 TRUE FALSE 27831.76658 30741.5441 43623.79056 43289.63574 44731.7997 36278.23139 36944.57222 34599.15 31506.00279 29519.74198 0.942818762 1.041389322 1.477783599 1.466463893 1.515318112 1.228948119 1.251520838 1.172068171 1.067285846 1 14.84939249 1.404408157 1.413058724 1.004400242 1.293867388 0.237010003 0.174283417 0.601142972 2.265721144 0.173338936 0.055920944 25.37512305 -1.404408157 0.289467146 S(ph)PSLSSK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPSLSSK 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3;Q9UPU5 A9Z1X7;Q8IYB3;Q9UPU5 SRRM1;USP24 Serine/arginine repetitive matrix protein 1;Ubiquitin carboxyl-terminal hydrolase 24 1 S(0.996)PS(0.004)LSSK;S(0.992)PS(0.008)LSSK;S(0.966)PS(0.034)LSSK;S(0.975)PS(0.025)LSSK;S(0.982)PS(0.018)LSSK;S(0.978)PS(0.022)LSSK 114.89 0.0060865 11679700000 5579370 5506390 5913850 6167880 5490170 4784930 6857390 6493080 7708440 7933910 TRUE FALSE 5361322.052 5349353.149 6982614.248 6486205.026 5666766.304 4881684.563 6941312.79 6358995.629 6833410.208 7396539.209 0.72484197 0.723223794 0.944038022 0.876924308 0.766137533 0.659995766 0.938454133 0.859725805 0.92386588 1 22.81841897 1.404438907 1.048849789 0.989287704 0.796339487 0.381285834 0.086032556 0.537789039 1.182639256 0.082630393 0.029061146 25.37691976 -1.404438907 -0.192948218 WGNNNR ddPTM_BT-474_Pertuzumab_2h_R1 1 WGNNNR 6 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 119.22 0.049309 535390000 174990 186200 133720 186040 154610 174500 181880 173240 167870 175420 FALSE TRUE 168151.1973 180889.7583 157886.1786 195641.5467 159583.1711 178028.5096 184105.9018 169662.5335 148814.1014 163538.6472 1.028204649 1.106097925 0.965436497 1.196301609 0.975813203 1.088602068 1.125763879 1.037446111 0.909962898 1 17.31927209 1.404973451 5.86505325 0.957233122 1.069603998 0.305129506 0.068098962 0.227396164 12.23310708 0.042253568 0.015568364 25.40817375 -1.404973451 0.112370876 SRGS(ph)PSSYNSSSSSPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 SRGS(0.799)PS(0.041)S(0.016)YNS(0.069)S(0.069)S(0.003)S(0.003)SPR;SRGS(0.874)PS(0.062)S(0.062)YNSSSSSPR;SRGS(0.538)PS(0.039)S(0.003)YNS(0.004)S(0.006)S(0.069)S(0.121)S(0.219)PR 263.84 1.50E-26 297967000 309671 332400 256317 298168 259112 308861 342005 356710 384313 426252 TRUE FALSE 297568.715 322920.2775 302639.1836 313556.4862 267446.5728 315106.381 346190.5595 349343.8138 340687.3994 397381.5724 0.748823639 0.812620161 0.761583336 0.789056433 0.673022081 0.792956702 0.871179198 0.879114277 0.857330644 1 18.60016545 1.405691573 0.675716976 0.987529985 0.758847359 0.733023228 0.043755285 0.343947534 0.357143058 0.043740801 0.019755924 25.45022187 -1.405691573 -0.228682626 NNQFQALLQYADPVSAQHAK ddPTM_BT-474_Pertuzumab_2h_R1 1 NNQFQALLQYADPVSAQHAK 20 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7EK45;A0A087WU68;K7EKJ7 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 251.75 4.63E-36 605880000 709410 695160 602900 599550 672810 602530 649620 739330 912280 870870 FALSE TRUE 681685.4729 675334.7174 711857.4414 630492.8474 694451.5447 614713.5694 657570.2439 724062.5771 808721.799 811885.1992 0.839632837 0.831810603 0.876795688 0.776578817 0.855356823 0.757143461 0.809930079 0.891828768 0.996103636 1 19.63091622 1.405750262 2.584388097 1.002472992 0.821117642 0.815253079 0.03345224 0.108764463 1.277506807 0.027909872 0.008846593 25.45366135 -1.405750262 -0.181355351 ATSACAPISS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSACAPISSPK 12 0 A0A087X1U1;F5GXM9;E7EUN2;Q9UPQ3-2;Q9UPQ3;H7C211 A0A087X1U1 AGAP1 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1" 1 ATSACAPIS(0.32)S(0.68)PK 63.181 0.076054 76975000 309180 310310 279210 294880 323910 326730 300520 314190 299680 306890 TRUE FALSE 297096.9038 301460.2626 329669.458 310098.7921 334328.8593 333336.7045 304197.8537 307701.8667 265661.5828 286104.067 1.038422512 1.053673462 1.152271135 1.083867124 1.168556822 1.165089011 1.063241977 1.075489314 0.928548782 1 18.12618048 1.405923636 3.066699118 0.965191391 1.106656472 0.562715057 0.047629777 0.182064615 2.958900864 0.038996153 0.012778156 25.46382468 -1.405923636 0.141465081 NVIPDT(ph)PPSTPLVPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVIPDTPPSTPLVPSR 16 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 NVIPDT(0.903)PPS(0.048)T(0.048)PLVPS(0.001)R;NVIPDT(0.959)PPS(0.017)T(0.017)PLVPS(0.006)R 108.36 0.011804 239390000 358070 398250 358320 453150 404000 380150 380050 401730 356430 404560 TRUE FALSE 344076.2285 386892.2999 423076.3948 476537.1258 416995.0269 387836.8935 384701.1656 393434.1351 315969.5607 377158.7909 0.912284791 1.025807456 1.121746079 1.263492029 1.105621921 1.028311955 1.019997876 1.043152499 0.837762683 1 18.52481253 1.405948274 4.59926147 0.919391318 1.072886975 0.281679341 0.092967462 0.273190338 9.423300246 0.070103345 0.025103816 25.46526936 -1.405948274 0.153495657 RYDFQNPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RYDFQNPSR 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 ; 172.56 9.00E-05 1238970000 303560 365690 307610 364470 312760 297930 372790 332650 275020 329890 FALSE TRUE 291696.5396 355260.8792 363201.9697 383280.3404 322820.2094 303954.3487 377352.3155 325780.6613 243800.8826 307546.2565 0.948463958 1.155146167 1.180966967 1.246252661 1.049663921 0.988320756 1.226977431 1.059289959 0.79272915 1 18.23044389 1.405986364 6.415871086 0.900125763 1.117299645 0.409812471 0.102710674 0.193830833 12.40223079 0.0674989 0.025041018 25.46750287 -1.405986364 0.217173882 TDCEPVGLEPAVEQSSAASELAEASSEELAEAPTEAPS(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDCEPVGLEPAVEQSSAASELAEASSEELAEAPTEAPSPEAR 42 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 TDCEPVGLEPAVEQSSAASELAEASSEELAEAPT(0.001)EAPS(0.999)PEAR 184.18 1.77E-27 31879000 52733 51202 38276 46603 53110 52695 49225 50396 49764 51365 TRUE FALSE 50672.13606 49741.76909 45193.32465 49008.18641 54818.33138 53760.529 49827.43027 49355.30499 44114.99935 47886.0028 1.058182623 1.038753836 0.943768993 1.023434481 1.144767326 1.122677314 1.040542692 1.030683333 0.921250402 1 15.54731639 1.40646273 4.570455827 0.961393747 1.05217085 0.306771813 0.054527952 0.28014231 9.568885975 0.042487604 0.015206632 25.49545285 -1.40646273 0.090777103 VTAGWPSEPGQGDLNPES(ph)PAALGQDLLEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTAGWPSEPGQGDLNPESPAALGQDLLEPR 30 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 VTAGWPSEPGQGDLNPES(1)PAALGQDLLEPR;VTAGWPSEPGQGDLNPES(1)PAALGQDLLEPR 136.92 1.62E-06 122428000 137870 123490 84236 129676 117031 103397 101361 119718 91916 90039 TRUE FALSE 132481.888 119968.1861 99459.31902 136368.5939 120795.4084 105487.7582 102601.4862 117245.7815 81482.08102 83940.57833 1.578281811 1.429203712 1.184877696 1.624584874 1.439058567 1.256695633 1.222310928 1.39677119 0.970711456 1 16.35708078 1.406649106 0.630059434 0.976115939 1.444281615 0.548596655 0.142006392 0.56260619 0.522172558 0.138368005 0.066092201 25.50639645 -1.406649106 0.468165676 TIS(ph)PPTLGTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TISPPTLGTLR 11 0 Q9UQ84;Q9UQ84-4 Q9UQ84 EXO1 Exonuclease 1 1 T(0.001)IS(0.998)PPT(0.001)LGTLR;TIS(1)PPTLGTLR 119.55 0.0005991 221430000 222480 243660 203544 260730 233870 200130 258320 235490 198670 240020 TRUE FALSE 213785.2356 236711.0554 240328.9286 274186.3065 241392.6409 204176.7657 261481.3974 230627.0492 176117.8145 223763.2316 0.955408242 1.057863947 1.074032257 1.225341199 1.078785997 0.912467899 1.16856284 1.030674466 0.78707218 1 17.77161347 1.406728509 7.843556389 0.895826815 1.070116173 0.331540821 0.097336794 0.264534215 24.36173343 0.062820136 0.023447477 25.51106025 -1.406728509 0.174289358 QAYVDKLEELMK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAYVDKLEELMK 12 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 151.44 5.74E-05 826520000 729170 658490 552690 494090 550620 558890 604850 681730 802760 801780 FALSE TRUE 700673.2303 639710.5099 652573.3775 519590.0441 568331.1924 570191.1387 612252.3352 667652.0373 711634.0502 747474.7264 0.937387186 0.85582895 0.873037381 0.695127241 0.760334995 0.762823302 0.819094363 0.893210183 0.952050986 1 19.51166527 1.406965314 1.790550836 0.991269678 0.809340268 0.511408766 0.063805464 0.289537524 1.696013106 0.061403011 0.019192522 25.52497435 -1.406965314 -0.18192941 SMGFIGHYLDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SMGFIGHYLDQK 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 168.98 4.51E-05 2692000000 4751200 4672000 4259100 4552500 4665200 3800500 5461800 4981900 6081900 6078400 FALSE TRUE 4565517.851 4538759.134 5028814.113 4787455.071 4815260.395 3877348.714 5528643.142 4879022.024 5391508.209 5666704.554 0.805674234 0.800952139 0.887431851 0.844839364 0.849746153 0.684233434 0.975636384 0.86099813 0.951436264 1 22.43407856 1.40700483 1.022029283 0.994213818 0.824097139 0.438352448 0.066771449 0.446710334 0.937618484 0.059294377 0.021083254 25.52729694 -1.40700483 -0.17011668 S(ph)RPTSFADELAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRPTSFADELAAR 13 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 S(0.914)RPT(0.077)S(0.009)FADELAAR;S(0.993)RPT(0.006)S(0.001)FADELAAR 145.71 2.54E-05 152934000 118100 122810 107494 147433 152676 138760 118053 128840 99511 106613 TRUE FALSE 113484.5214 119307.579 126920.557 155042.0348 157586.9622 141565.8223 119497.7679 126179.409 88214.92846 99392.00655 1.141787206 1.200373986 1.276969461 1.559904465 1.585509415 1.424317983 1.202287509 1.269512643 0.887545503 1 16.60084221 1.40728588 2.095535464 0.939384417 1.358119145 0.522582892 0.146604741 0.263655338 2.080227243 0.140967559 0.043897083 25.54382206 -1.40728588 0.418734728 DLESCS(ph)DDDNQGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLESCSDDDNQGSK 14 0 A0A0A0MRK1;E9PAV9;Q5T3I0;Q5T3I0-3;F8W895 A0A0A0MRK1 GPATCH4 G patch domain-containing protein 4 1 DLESCS(1)DDDNQGSK 444.14 3.61E-141 0 397410 325640 304560 288890 294590 345470 366810 390100 492650 498050 TRUE FALSE 381878.7778 316353.066 359600.7669 303799.6475 304065.7549 352455.6401 371299.1305 382044.2987 436726.4374 464316.6299 0.822453372 0.681330466 0.774473159 0.654294135 0.654867251 0.759084679 0.799667956 0.822809855 0.940578927 1 18.82474943 1.407463985 1.061268358 1.001490182 0.717829545 0.776458551 0.051505208 0.204971039 0.459938901 0.046736053 0.016377522 25.55429975 -1.407463985 -0.283660638 GLDDLDADADDGWAGLHEEVDYSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDDLDADADDGWAGLHEEVDYSEK 25 0 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 0 ; 295.04 5.88E-63 433830000 440040 432420 353240 423220 416000 453420 472510 466570 559660 574030 FALSE TRUE 422842.7503 420087.805 417078.3258 445062.4349 429381.0178 462588.4631 478292.7187 456935.1665 496129.7431 535150.4368 0.790138102 0.784990119 0.779366505 0.831658547 0.802355727 0.86440827 0.893753767 0.853844331 0.927084627 1 19.02958498 1.40778883 0.25844193 1.032551538 0.74825991 0.909882656 0.020339844 0.515226554 0.142836766 0.057587034 0.049893708 25.57342112 -1.40778883 -0.284291628 DKPEEQWWNAEDSEGKR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKPEEQWWNAEDSEGKR 17 2 P46108-2;P46108 P46108-2 CRK Adapter molecule crk 0 ;; 233.49 2.32E-20 1435980000 840070 706030 687980 650470 738810 695020 727590 791960 1053440 875320 FALSE TRUE 807239.1357 685894.7157 812313.29 684040.8347 762574.4946 709073.7806 736494.4641 775605.7492 933857.9076 816033.7967 0.989222675 0.840522437 0.995440744 0.838250618 0.934488863 0.868926978 0.902529365 0.950457876 1.144386313 1 19.63826938 1.408010948 5.012554626 1.070672397 0.908813075 0.526240245 0.060516473 0.13791214 5.632222356 0.037548416 0.013653534 25.58650384 -1.408010948 -0.161859322 VIS(ph)HDRDSPPPPPPPPPPPQPQPSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VISHDRDSPPPPPPPPPPPQPQPSLK 26 1 Q69YN4-3;Q69YN4;Q69YN4-4;Q69YN4-2 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 VIS(0.571)HDRDS(0.429)PPPPPPPPPPPQPQPSLK 115.45 0.00071821 2373100000 394170 356740 310120 370280 365870 350880 385090 429650 436610 472040 TRUE FALSE 378765.4006 346566.1245 366165.5826 389390.1952 377638.5408 357975.034 389802.8466 420777.5774 387047.8632 440068.3104 0.860696832 0.787528019 0.832065327 0.884840344 0.858136185 0.813453333 0.885778043 0.956164231 0.879517689 1 18.74736796 1.408500148 0.442725198 1.001914752 0.823151227 0.65167239 0.035515217 0.582739469 0.319919702 0.042847225 0.028012399 25.61534135 -1.408500148 -0.178763525 S(ph)PSGLRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSGLRPR 8 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4 P49815 TSC2 Tuberin 1 S(0.994)PS(0.006)GLRPR 61.48 0.051901 361110000 57923 65737 53930 73221 62789 56623 68252 59773 62730 56117 TRUE FALSE 55659.30512 63862.24512 63676.35067 76999.94458 64808.66521 57767.95586 69087.28839 58538.66666 55609.15339 52316.14561 1.063903017 1.220698589 1.217145299 1.471819907 1.238788991 1.104208943 1.320572982 1.11894074 1.062944388 1 15.67496863 1.408625519 2.289725545 1.017769526 1.237323519 0.371272291 0.106508482 0.317303413 2.968126318 0.093142825 0.029164921 25.62273703 -1.408625519 0.219553993 YELHLK ddPTM_BT-474_Pertuzumab_2h_R1 6 YELHLK 6 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 96.666 0.041949 10454130000 17922800 17778600 17370900 17332000 16791600 15462600 19829100 19192700 22193000 22342200 FALSE TRUE 17222357.16 17271571.74 20510208.04 18226506.6 17331717.06 15775264.37 20071774.46 18796364.04 19673743.68 20828942.89 0.826847394 0.829210192 0.984697502 0.875056727 0.832097776 0.757372299 0.963648254 0.90241565 0.94453875 1 24.31208629 1.408649193 1.110419435 0.990038752 0.861132117 0.352116587 0.061534883 0.542191397 1.318800041 0.05820315 0.020072342 25.62413377 -1.408649193 -0.128906634 SGSLDSELSVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSLDSELSVSPK 13 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7 Q12802-2 AKAP13 A-kinase anchor protein 13 1 SGSLDSELS(0.001)VS(0.999)PK 161.49 4.41E-05 108780000 367600 289640 303180 277140 288720 302130 344620 367760 420070 446130 TRUE FALSE 353233.7856 281379.7508 357971.3702 291443.2286 298006.941 308239.2756 348837.5626 360165.6275 372385.4147 415913.2177 0.84929685 0.676534764 0.860687651 0.700730864 0.716512311 0.741114402 0.838726801 0.865963408 0.895344026 1 18.66592301 1.408869198 0.958975785 0.988867753 0.754095951 0.635012089 0.05872636 0.294327659 0.551887846 0.05124634 0.018734858 25.63711773 -1.408869198 -0.234771801 ERVPYTDDGLEAIIFTAQGDMR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERVPYTDDGLEAIIFTAQGDMR 22 1 P35250;P35250-2;H7C5P4;A0A087WVY3 P35250 RFC2 Replication factor C subunit 2 0 ; 208.46 6.26E-23 153858000 151913 158038 129719 155388 163184 164114 153257 157849 159047 156339 FALSE TRUE 145976.072 153530.911 153162.1089 163407.5933 168432.9616 167432.4975 155132.605 154589.363 140992.6513 145750.0203 1.001550955 1.053385177 1.050854803 1.121149712 1.155629078 1.148764832 1.0643745 1.060647283 0.967359394 1 17.15313656 1.409396842 2.746584292 0.983511018 1.088730427 0.426262267 0.04573213 0.270789367 3.588155864 0.041357502 0.013284582 25.66828436 -1.409396842 0.105219409 AVLS(ph)PGSVFSPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVLSPGSVFSPGR 13 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 AVLS(0.981)PGS(0.019)VFSPGR;AVLS(0.997)PGS(0.003)VFSPGR 209.11 4.25E-08 418590000 368820 434890 370410 530090 520960 444370 459160 421420 339160 349510 TRUE FALSE 354406.1066 422487.363 437351.3267 557448.0084 537717.1515 453355.4659 464779.3374 412717.5297 300659.9787 325837.3764 1.08767788 1.296620319 1.342238056 1.710816649 1.650262341 1.391355009 1.42641505 1.266636548 0.922730173 1 18.31379258 1.409526844 2.790629238 0.95694218 1.426378753 0.533335423 0.166661595 0.216247691 2.954065148 0.148298718 0.047785681 25.67596911 -1.409526844 0.469436573 VDDSTGTVIS(ph)DVEEDAGELSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDDSTGTVISDVEEDAGELSR 21 0 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 VDDSTGTVIS(1)DVEEDAGELSR;VDDSTGTVIS(1)DVEEDAGELSR 204.05 5.78E-22 80088000 79116 79607 62983 65828 74682 85421 80013 76663 79787 77154 TRUE FALSE 76024.05925 77336.6863 74365.42915 69225.39097 77084.21435 87148.27115 80992.22303 75079.88226 70729.91425 71928.29086 1.056942384 1.075191491 1.033882889 0.962422298 1.07168144 1.21159936 1.126013451 1.043815742 0.983339287 1 16.1342717 1.409595923 4.435238408 0.993706602 1.076223437 0.239299579 0.060133573 0.349301794 11.40236562 0.047993721 0.017142982 25.68005346 -1.409595923 0.082516834 ADKDYHFK ddPTM_BT-474_Pertuzumab_2h_R1 8 ADKDYHFK 8 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;; 117.31 0.0019182 46585000000 112404640 107073910 88106180 90978430 95556380 97922660 103561470 106115280 127344210 117309620 FALSE TRUE 108011742.4 104020266.9 104028926.6 95673837.68 98630037.74 99902723.28 104828886.2 103923962.4 112888629.2 109364134.9 0.98763404 0.951136924 0.951216107 0.874819133 0.901849933 0.913487071 0.95853075 0.950256338 1.032227148 1 26.70456446 1.409778412 2.546964004 1.016158283 0.93108276 0.501179874 0.031595121 0.235434001 2.702743854 0.028154988 0.008932354 25.69084634 -1.409778412 -0.085075523 RQEQIQAMPLADSQAVR ddPTM_BT-474_Pertuzumab_2h_R1 3 RQEQIQAMPLADSQAVR 17 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 172.84 2.49E-09 1282920000 448330 498980 398180 455050 427840 509200 470530 460940 443690 448000 FALSE TRUE 430808.7679 484749.579 470139.9835 478535.185 441601.8622 519496.3729 476288.4869 451421.4279 393324.1713 417656.561 1.031490483 1.160641599 1.125661674 1.145762403 1.057332515 1.243836256 1.140383108 1.080843617 0.941740674 1 18.67195758 1.410535478 3.587647217 0.9723452 1.131689297 0.552082094 0.056056428 0.161003426 3.540321522 0.040806469 0.013937848 25.73566994 -1.410535478 0.159344097 EYCLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYCLSPR 7 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 EYCLS(1)PR 85.764 0.021578 488450000 444300 541650 397410 599620 474790 441780 488020 477930 335910 471870 TRUE FALSE 426936.2648 526202.6723 469230.8273 630566.4601 490062.0515 450713.0943 493992.5347 468060.5785 297778.905 439909.8246 0.970508593 1.19616031 1.066652303 1.433399358 1.114005699 1.024557919 1.122940446 1.063992101 0.676908967 1 18.7468483 1.410572045 5.385797696 0.839266304 1.135075945 0.412312478 0.138000216 0.184375205 8.754929852 0.091696717 0.033741918 25.73783691 -1.410572045 0.295809641 SISDAPAPAYHDPLYLEDQVSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SISDAPAPAYHDPLYLEDQVSHR 23 0 Q9H6H4;E5RGS2 Q9H6H4 REEP4 Receptor expression-enhancing protein 4;Receptor expression-enhancing protein 0 153.56 2.86E-08 305300000 84828 138060 77020 131180 109130 97208 113620 103330 115970 102230 FALSE TRUE 81512.82798 134122.664 90939.2273 137950.2155 112640.2656 99173.61236 115010.5155 101196.1994 102805.5718 95305.87104 0.85527604 1.407286482 0.954182846 1.447447193 1.181881707 1.040582404 1.206751633 1.061804465 1.078690858 1 16.54027747 1.410638394 0.937762867 1.005899294 1.172486585 0.073797768 0.173329768 1.209871045 2.180284696 0.146815806 0.054257279 25.74176933 -1.410638394 0.166587291 KDTFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDTFFK 6 1 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 91.065 0.077472 1390300000 1078300 1089100 864980 948760 980130 1145400 1111000 1218900 1321800 1448700 FALSE TRUE 1036158.844 1058039.934 1021301.127 997725.6173 1011656.772 1168560.773 1124596.75 1193729.289 1171754.805 1350578.259 0.767196449 0.783397724 0.756195445 0.738739581 0.749054537 0.86522996 0.832677961 0.883865323 0.867594897 1 20.36514581 1.410647229 0.455832513 1.000428703 0.748664039 0.866971695 0.028391129 0.321314383 0.183687121 0.03378987 0.021562697 25.74229299 -1.410647229 -0.251764665 FGWDCHGLPVEYEIDK ddPTM_BT-474_Pertuzumab_2h_R1 4 FGWDCHGLPVEYEIDK 16 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 166.35 6.71E-09 2191510000 2043180 1861400 1578290 1576930 1858590 1526930 2010740 1966920 2432600 2388610 FALSE TRUE 1963330.267 1808314.695 1863522.112 1658315.546 1918373.235 1557805.571 2035348.038 1926302.415 2156461.446 2226827.317 0.881671539 0.812058789 0.836850751 0.744698762 0.861482712 0.699562808 0.914012515 0.865043463 0.968400841 1 21.08655826 1.410882183 1.2995664 0.999258418 0.810966024 0.563928292 0.057798351 0.277639896 0.897746024 0.049028228 0.016153081 25.75622338 -1.410882183 -0.188292395 GTPSQS(ph)PVVGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 GTPS(0.003)QS(0.997)PVVGR;GTPS(0.005)QS(0.995)PVVGR;GTPS(0.003)QS(0.997)PVVGR;GTPS(0.043)QS(0.957)PVVGR;GT(0.002)PS(0.057)QS(0.94)PVVGR;GT(0.004)PS(0.05)QS(0.946)PVVGR 200.98 4.72E-08 14953990000 5508410 5836550 4958860 5695680 5648170 5664010 5996920 5694580 5463330 5713260 TRUE FALSE 5293135.247 5670097.309 5855036.311 5989634.727 5829848.518 5778540.163 6070312.101 5576984.933 4843155.683 5326295.811 0.993774179 1.064547954 1.099269834 1.124540382 1.094540882 1.084907855 1.139687377 1.047066316 0.909291533 1 22.34470112 1.410946224 5.259924359 0.957139297 1.087573469 0.600100355 0.042221919 0.131152621 5.961554823 0.028805604 0.010575559 25.76002167 -1.410946224 0.130434172 DPDAGIDEAQVEQDAQALFQAGELK ddPTM_BT-474_Pertuzumab_2h_R1 3 DPDAGIDEAQVEQDAQALFQAGELK 25 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;; 223.85 8.95E-34 83772000 130518 114291 110042 120810 84665 76879 102886 144020 163151 184864 FALSE TRUE 125417.2123 111031.5326 129929.0373 127045.0186 87388.32662 78433.54605 104145.1496 141045.9367 144630.7825 172342.9966 0.727718647 0.64424743 0.753897981 0.737163802 0.507060503 0.455101441 0.604290001 0.818402485 0.839203132 1 17.39492315 1.411330723 1.863429174 0.953653984 0.631821518 0.59920907 0.097494901 0.249699825 1.581427251 0.095970961 0.029991457 25.78283816 -1.411330723 -0.321832465 DSEGTWR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSEGTWR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 124.34 0.0096679 1148100000 912700 1060110 830410 1135340 997510 1039480 1020660 1033780 987330 1078050 FALSE TRUE 877030.675 1029876.701 980483.5594 1193935.033 1029595.815 1060498.998 1033151.142 1012432.082 875252.4376 1005032.713 0.872638933 1.024719581 0.975573776 1.18795639 1.024440102 1.055188536 1.027977626 1.007362316 0.870869601 1 19.93881103 1.411610083 6.627298756 0.934780055 1.028359461 0.163647215 0.078506646 0.345405804 24.7695614 0.051237386 0.01918677 25.79942836 -1.411610083 0.093579406 DGELPVEDDIDLSDVELDDLGKDEL ddPTM_BT-474_Pertuzumab_2h_R1 7 DGELPVEDDIDLSDVELDDLGKDEL 25 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;;; 260.06 4.57E-45 2664616000 1402978 1269264 1105813 1155183 1042186 998039 1234551 1420590 2032237 1850870 FALSE TRUE 1348148.069 1233065.833 1305658.008 1214802.133 1075708.859 1018220.032 1249659.804 1391254.32 1801545.976 1725508.926 0.781304604 0.714609942 0.75667995 0.704025412 0.623415413 0.590098386 0.724226798 0.806286365 1.044066448 1 20.71859051 1.41197173 2.573036023 1.026710249 0.695518086 0.836537135 0.056139074 0.109103899 1.280630213 0.05101844 0.016238575 25.82092107 -1.41197173 -0.331192163 S(ph)RSPSLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPSLNR 8 1 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.539)RS(0.459)PS(0.002)LNR;S(0.589)RS(0.406)PS(0.005)LNR 57.836 0.065864 289620000 123964 123223 109230 128000 142059 160619 134171 132029 120195 127782 TRUE FALSE 119119.3498 119708.8007 128970.2908 134606.0953 146628.4567 163866.8262 135813.0248 129302.555 106550.9675 119127.2113 0.999934008 1.004882087 1.082626626 1.129935754 1.230856117 1.375561674 1.140067188 1.08541578 0.894430133 1 16.86214347 1.412128956 3.927805768 0.949506145 1.141264412 0.333668858 0.105512167 0.278739827 7.291469393 0.087000409 0.030395579 25.83027059 -1.412128956 0.191758267 ISMQDVDLSLGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 15 ISMQDVDLSLGSPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLS(0.001)LGS(0.999)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK 296.47 1.26E-43 4876238000 5783832 5483302 5286266 5578621 5743486 5742182 5216056 5499879 5182623 4790787 TRUE FALSE 5557793.451 5326923.596 6241611.859 5866534.298 5928230.443 5858292.854 5279891.654 5386304.577 4594313.364 4466302.729 1.244383506 1.192692014 1.397489655 1.313510224 1.327323919 1.311664974 1.182161616 1.205987346 1.028661433 1 22.09064961 1.412185194 1.199328734 0.991263864 1.297249012 0.770066316 0.058363957 0.20149243 0.562807508 0.054466021 0.018346311 25.83361567 -1.412185194 0.305985147 NLFAEIIEEHLANR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLFAEIIEEHLANR 14 0 Q9NWY4 Q9NWY4 C4orf27 UPF0609 protein C4orf27 0 ; 165.86 3.90E-06 176340000 221202 224280 170155 224723 211188 237100 204643 283530 267690 308370 FALSE TRUE 212557.1813 217883.754 200905.7936 236320.981 217981.0538 241894.3244 207147.4822 277675.0064 237302.9534 287483.8252 0.739370923 0.757899175 0.698842077 0.822032268 0.758237628 0.841418902 0.72055352 0.96588045 0.825448017 1 18.13312126 1.413544029 0.394439655 1.009995941 0.726884111 0.614877134 0.059659991 0.666792618 0.312702428 0.073992842 0.053225374 25.91457129 -1.413544029 -0.283111829 SCSPSPVS(ph)PQVQPQAADTISDSVAVPASLLGMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCSPSPVSPQVQPQAADTISDSVAVPASLLGMR 33 0 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.035)CS(0.035)PS(0.16)PVS(0.77)PQVQPQAADTISDSVAVPASLLGMR 91.398 0.00017295 188660000 76611 82655 65273 81960 75548 77716 71499 77436 62537 82716 TRUE FALSE 73616.95742 80297.76033 77069.28309 86189.96542 77978.07003 79287.47077 72374.02615 75836.91954 55438.06194 77113.57164 0.954656306 1.041292196 0.999425671 1.117701639 1.011210716 1.028190876 0.938538115 0.983444521 0.718914463 1 16.23469717 1.413677515 6.791755909 0.854368099 1.012515093 0.373867918 0.078063722 0.195661016 15.03034762 0.048475118 0.018233875 25.92253769 -1.413677515 0.158146995 KKAENAEGQTPAIGPDGEPLDETSQMS(ph)DLPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKAENAEGQTPAIGPDGEPLDETSQMSDLPVK 32 2 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KKAENAEGQTPAIGPDGEPLDET(0.01)S(0.008)QMS(0.982)DLPVK 117.17 7.26E-07 159120000 109060 86666 63664 65164 72052 84371 79837 96904 109160 114700 TRUE FALSE 104797.8146 84194.37053 75169.501 68527.12185 74369.61802 86077.03943 80814.06909 94902.89854 96768.61444 106931.2668 0.980048378 0.787369055 0.702970265 0.640852053 0.695489918 0.804975401 0.755757146 0.887513085 0.90496089 1 16.70632424 1.413741836 1.253990265 0.988161632 0.754810075 0.443009345 0.087144167 0.388896177 1.177884471 0.082896108 0.027589031 25.92637725 -1.413741836 -0.233351557 EKELQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKELQK 6 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;Q9NTJ3;E9PD53;Q9NTJ3-2;O95202 E7EPN9;Q9NTJ3;O95202 PRRC2C;SMC4;LETM1 "Protein PRRC2C;Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein;LETM1 and EF-hand domain-containing protein 1, mitochondrial" 0 66.258 0.092919 720830000 1026900 979340 890980 904590 853390 945310 968550 1052100 1287400 1219700 FALSE TRUE 986767.6127 951410.1821 1051999.906 951275.9983 880840.0644 964424.8159 980403.4046 1030373.767 1141259.749 1137088.633 0.867801844 0.836707144 0.925169662 0.836589137 0.774645036 0.848152719 0.862204912 0.906150794 1.003668242 1 20.11691328 1.414379584 2.128734766 1.007512291 0.848339532 0.743954755 0.035196912 0.156751415 1.282895849 0.032127772 0.010052642 25.9644773 -1.414379584 -0.15917276 GKTPEEIRK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKTPEEIRK 9 2 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ; 81.338 0.01213 338560000 799400 835290 656450 686020 744290 736640 810740 833770 1009540 980520 FALSE TRUE 768158.5642 811468.347 775085.1177 721425.5744 768230.7638 751535.3655 820662.0786 816552.3581 894941.2515 914108.507 0.840336304 0.887715562 0.84791369 0.789212187 0.840415288 0.822151156 0.897773155 0.893277277 0.97903175 1 19.8020059 1.414664023 1.235712021 1.002971338 0.83973587 0.820346325 0.026979714 0.172274156 0.507947188 0.025408142 0.008492493 25.98148814 -1.414664023 -0.163235468 SDPES(ph)PIKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDPESPIKK 9 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 SDPES(1)PIKK;S(0.014)DPES(0.986)PIKK 69.815 0.033181 897170000 2699000 2255700 2213700 1840900 2270200 2391700 2215800 2405900 2874200 2544600 TRUE FALSE 2593520.096 2191369.645 2613764.833 1935909.07 2343223.045 2440061.813 2242917.623 2356217.324 2547932.866 2372251.976 1.093273448 0.923750793 1.101807422 0.816063845 0.987763133 1.028584585 0.945480348 0.993240747 1.074056589 1 21.17782583 1.414752029 9.372113031 1.03632468 0.981607394 0.060069798 0.079976971 0.882234359 120.8213547 0.048428646 0.018330778 25.98675364 -1.414752029 -0.054717285 VPLHCVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPLHCVDR 8 0 Q8NFH3 Q8NFH3 NUP43 Nucleoporin Nup43 0 111.04 0.0033105 123050000 76099 69352 85858 86479 76014 72647 77909 95634 105880 112050 FALSE TRUE 73124.96695 67374.14886 101374.4505 90942.19155 78459.05934 74115.97211 78862.47365 93659.12448 93860.94629 104460.7537 0.700023352 0.644970924 0.970454902 0.870587166 0.751086476 0.709510218 0.75494835 0.896596293 0.898528327 1 16.67260149 1.415580889 1.714132003 0.97386286 0.775501146 0.408790498 0.089618001 0.380077925 2.060051661 0.085521931 0.026935803 26.03639721 -1.415580889 -0.198361713 IQDPTEDAEAEDT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 IQDPTEDAEAEDTPR 15 0 O96028;O96028-5;O96028-3;H0Y9L4 O96028 WHSC1 Histone-lysine N-methyltransferase NSD2 1 IQDPTEDAEAEDT(1)PR;IQDPTEDAEAEDT(1)PR;IQDPTEDAEAEDT(1)PR 238.08 1.04E-16 1780090000 844710 842810 662260 843860 764990 736790 806720 791250 642610 829000 TRUE FALSE 811697.7993 818773.884 781945.1139 887411.7157 789596.5981 751688.3986 816592.8807 774910.411 569663.6068 772851.0916 1.050264156 1.059419975 1.011766849 1.148231173 1.021667184 0.972617373 1.056597952 1.002664575 0.737093617 1 19.55983095 1.415755158 7.338104627 0.866487992 1.043041589 0.480957645 0.072530604 0.168485193 15.40127233 0.043997352 0.016660802 26.04684692 -1.415755158 0.176553597 SAS(ph)PDYNR ddPTM_BT-474_Pertuzumab_2h_R1 6 SASPDYNR 8 0 Q14669-3;Q14669;Q14669-2;G5E9G6;C9JLD7;C9JLJ5;C9JSX9;F8W9P3 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 SAS(1)PDYNR;S(0.055)AS(0.937)PDY(0.008)NR;S(0.01)AS(0.99)PDYNR;S(0.022)AS(0.978)PDYNR;S(0.001)AS(0.999)PDYNR;S(0.02)AS(0.98)PDYNR 154.85 0.0004389 1032062000 1904620 1908550 1374610 1874080 1942180 1744750 1642260 1834110 1661140 1636030 TRUE FALSE 1830185.345 1854120.023 1623032.605 1970801.493 2004651.984 1780030.04 1662358.469 1796234.988 1472574.351 1525220.231 1.199948249 1.215640853 1.06413 1.292142245 1.314336083 1.167064273 1.089913729 1.177688934 0.965483096 1 20.54058614 1.415940979 1.21079723 0.979742547 1.206217498 0.528318079 0.07603991 0.352202421 1.000491309 0.070977129 0.023869839 26.05799398 -1.415940979 0.226474951 DGASSS(ph)PESASR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGASSSPESASR 12 0 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;G5E9M9;Q14135-5 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 DGASS(0.447)S(0.553)PESASR;DGAS(0.001)S(0.017)S(0.981)PESASR;DGAS(0.214)S(0.214)S(0.573)PESASR 192.4 7.75E-05 214236000 329690 367216 305313 400340 380688 387963 359118 364548 342099 346304 TRUE FALSE 316805.3503 356743.3592 360489.8508 421001.5954 392933.1753 395807.8777 363512.9935 357019.9564 303265.3557 322848.5216 0.981281713 1.104986814 1.116591301 1.304022064 1.217082158 1.225986341 1.125955267 1.105843554 0.939342557 1 18.3004979 1.416482501 2.768726532 0.969478985 1.160861239 0.424482338 0.083329177 0.259658472 3.528064086 0.072351617 0.023415781 26.09050594 -1.416482501 0.191382254 IIEQLS(ph)PQAATSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IIEQLSPQAATSR 13 0 Q03468;P0DP91;D6R9X7 Q03468 ERCC6 DNA excision repair protein ERCC-6 1 IIEQLS(1)PQAATSR;IIEQLS(1)PQAATSR 220.34 2.20E-11 356010000 315710 316340 271350 359470 354350 307750 349070 328100 273540 339350 TRUE FALSE 303371.7042 307318.2929 320388.9811 378022.2898 365747.9896 313972.9159 353342.0231 321324.6203 242488.886 316365.5222 0.958927831 0.971402607 1.012717754 1.19489092 1.156093075 0.992437209 1.116879047 1.015675217 0.766483289 1 18.27123286 1.416514927 7.481009422 0.883311512 1.05900625 0.363347514 0.0909984 0.236010251 22.59760266 0.060265135 0.022869737 26.09245404 -1.416514927 0.175694738 DIYDKDNYELDEDTD ddPTM_BT-474_Pertuzumab_2h_R1 3 DIYDKDNYELDEDTD 15 1 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 ;; 224.25 9.45E-12 1214540000 2325470 2177110 1815230 1804480 2048360 2108060 2131300 2238920 2622300 2521530 FALSE TRUE 2234588.061 2115020.954 2143282.441 1897609.429 2114247.36 2150686.418 2157383.487 2192685.52 2324627.498 2350744.527 0.950587372 0.899723866 0.911746222 0.807237625 0.899394781 0.914895852 0.917744766 0.93276215 0.98888989 1 21.16468633 1.416856618 1.181699524 1.003630893 0.893629342 0.546778209 0.034222877 0.333449182 0.906126467 0.032044262 0.010857388 26.11299094 -1.416856618 -0.110001551 GDRDESDDGGVAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDRDESDDGGVAQR 14 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 0 ; 120.32 0.00012442 73609000 56852 71333 60867 77860 67068 64084 70256 64871 60682 58972 FALSE TRUE 54630.16099 69298.65268 71867.02088 81878.36393 69225.30313 65379.82239 71115.81394 63531.39118 53793.63376 54977.77391 0.99367721 1.260484879 1.307201361 1.489299368 1.259150711 1.189204614 1.293537531 1.155583187 0.978461475 1 15.74656087 1.417043046 2.740692136 0.985374153 1.26457254 0.453299248 0.115565789 0.240520263 3.207507826 0.097368161 0.031464783 26.12420275 -1.417043046 0.279198386 HGS(ph)VSADEAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGSVSADEAAR 11 0 A0A1B0GU90;A0A1B0GW73;H3BNF1;A0A1B0GTV3;A0A0S2Z5D0;H3BUV4;A0A1B0GUD2;H3BUT1;A0A1B0GTU6;Q9NWW5;Q9NWW5-2 A0A1B0GU90 CLN6 Ceroid-lipofuscinosis neuronal protein 6 1 HGS(0.987)VS(0.013)ADEAAR 72.681 0.029391 27568000 17766 18860 14983 19999 19193 18595 16820 18525 16832 16603 TRUE FALSE 17071.68508 18322.13127 17690.7614 21031.15079 19810.36028 18971.00364 17025.84819 18142.45228 14921.30193 15478.46402 1.10293147 1.183717663 1.142927449 1.35873629 1.279866029 1.225638643 1.099970137 1.172109342 0.964004045 1 13.91797469 1.417090527 1.444508204 0.977219041 1.213899245 0.539810946 0.077214294 0.302680851 1.190161107 0.072480614 0.023391693 26.12705906 -1.417090527 0.236680204 RNPLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNPLPK 6 1 P22059 P22059 OSBP Oxysterol-binding protein 1 0 121.87 0.084632 0 458330 460870 424870 459100 429320 398850 497200 493900 584340 577970 FALSE TRUE 440417.9569 447726.4388 501653.4602 482794.206 443129.4677 406915.0203 503284.8823 483700.7924 518008.173 538823.5771 0.817369498 0.830933274 0.931016165 0.896015369 0.822401778 0.755191565 0.934043913 0.897697898 0.961368795 1 19.03945345 1.417403553 1.298411404 0.994452517 0.850642767 0.5144178 0.050310906 0.355850379 1.148619287 0.047964789 0.015840802 26.14589742 -1.417403553 -0.14380975 LNS(ph)SENGEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNSSENGEDR 10 0 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 LNS(0.5)S(0.5)ENGEDR;LNS(0.5)S(0.5)ENGEDR 225.92 3.43E-09 1050100000 583010 543090 481380 581890 529000 541760 526470 550400 550610 517740 TRUE FALSE 560225.3246 527601.6049 568376.0742 611921.4126 546015.7654 552714.7584 532913.0973 539034.0477 488107.0611 482673.0086 1.160672577 1.093082885 1.177559267 1.267776324 1.131233269 1.145112216 1.104087214 1.116768574 1.011258248 1 18.88068663 1.417754662 0.99903857 0.993293845 1.164994978 0.640784557 0.044355333 0.322975749 0.649224071 0.042510775 0.01530404 26.16704384 -1.417754662 0.171701133 YEFGIFNQK ddPTM_BT-474_Pertuzumab_2h_R1 1 YEFGIFNQK 9 0 P11216;P11217 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 109.21 0.0057821 112060000 233660 293490 225940 305430 289120 241340 286390 250170 199980 213780 FALSE TRUE 224528.3089 285119.9526 266772.384 321193.2789 298419.8074 246220.0602 289894.9265 245003.9021 177279.1088 199300.4902 1.12658182 1.430603368 1.338543542 1.611603055 1.497336043 1.235421247 1.454562035 1.229319114 0.889506637 1 17.60458573 1.418568719 3.344541166 0.94702447 1.390936966 0.637106597 0.13097816 0.144706881 2.82913746 0.100072025 0.033874804 26.21613828 -1.418568719 0.443912497 YLHSCPESVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 YLHSCPESVKK 11 1 Q5TFE4;Q5TFE4-2;H0YDA5 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 139.86 2.52E-05 265430000 723230 705400 604000 556500 611870 417580 723910 665830 865470 806460 FALSE TRUE 694965.372 685282.6827 713156.2359 585221.0317 631551.3542 426023.7537 732769.4271 652080.3778 767225.4739 751837.7459 0.924355522 0.911476827 0.948550721 0.778387405 0.840010172 0.56664321 0.974637721 0.867315297 1.02046682 1 19.52006182 1.419045139 1.853615411 1.011584833 0.840345598 0.2430114 0.110369967 0.486776058 3.068184355 0.099232926 0.031142366 26.2449131 -1.419045139 -0.171239235 VGGSSVDLHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;;; 177.06 2.37E-06 2193050000 1861180 2572690 2058560 2888340 2068120 2298270 2493160 2389140 2321060 2447080 FALSE TRUE 1788443.028 2499319.4 2430587.584 3037407.574 2134642.958 2344742.594 2523672.038 2339803.424 2057582.999 2281337.092 0.783945097 1.095550241 1.065422376 1.331415504 0.935698177 1.027793132 1.106224962 1.025628099 0.901919759 1 21.12144821 1.420245698 6.114086074 0.95254136 1.057837909 0.077060288 0.132041854 0.489547507 32.26565309 0.085814376 0.032436893 26.3175646 -1.420245698 0.105296549 ETDEFFK ddPTM_BT-474_Pertuzumab_2h_R1 4 ETDEFFK 7 0 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;; 148.33 0.0048655 687130000 1338560 1206080 1226500 1411850 1287170 1284070 1502510 1663590 1872230 2039440 FALSE TRUE 1286247.595 1171683.779 1448155.833 1484715.748 1328572.992 1310034.775 1520898.167 1629236.285 1659702.299 1901306.912 0.676507084 0.616251785 0.761663372 0.780892205 0.698768296 0.689018047 0.799922494 0.856903362 0.872927084 1 20.85856 1.420270961 0.588846286 1.003352758 0.687895325 0.822202321 0.045387176 0.308373167 0.256491345 0.048470982 0.024637938 26.31909556 -1.420270961 -0.315457433 S(ph)RSPIIHS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPIIHSPK 10 1 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 2 S(0.611)RS(0.39)PIIHS(0.999)PK;S(0.562)RS(0.449)PIIHS(0.989)PK 77.324 0.018971 1977440000 3773900 3096700 3040700 2965100 3232400 3257700 3667500 3610700 4314100 4328100 TRUE FALSE 3626411.816 3008385.148 3590222.13 3118129.166 3336373.082 3323572.926 3712383.962 3536137.783 3824381.454 4034953.932 0.898749249 0.74558104 0.889780203 0.772779372 0.826867701 0.823695383 0.920056096 0.876376247 0.947812917 1 21.94412077 1.420591601 0.74366559 0.998116294 0.820282909 0.583761859 0.048130815 0.384543157 0.464878906 0.041204104 0.017440138 26.33853413 -1.420591601 -0.177833386 ELEVQHPAAK ddPTM_BT-474_Pertuzumab_2h_R1 6 ELEVQHPAAK 10 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;; 123.51 0.00046005 7233950000 11621280 11676980 10245520 11056730 11245480 12071120 11921090 12752580 15026000 14826110 FALSE TRUE 11167107.53 11343963.96 12097113.37 11627369.16 11607201.08 12315206.32 12066983.87 12489234.77 13320311.47 13821924.36 0.807927119 0.820722474 0.87521195 0.841226508 0.83976737 0.890990718 0.873032115 0.903581472 0.963708896 1 23.72045515 1.420939315 0.486160993 1.007887463 0.82712746 0.887225831 0.019569836 0.275586996 0.172323895 0.021621274 0.013086151 26.35963031 -1.420939315 -0.180760003 GALSPGGFDDSTLPLVDKS(ph)LEGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GALSPGGFDDSTLPLVDKSLEGEK 24 1 C9JJX6;E9PDC3;O00192-2;O00192 C9JJX6 ARVCF Armadillo repeat protein deleted in velo-cardio-facial syndrome 1 GALSPGGFDDSTLPLVDKS(1)LEGEK 93.411 0.0048908 62571000 19416 26260 23002 40597 31820 34448 29568 27353 18081 22108 TRUE FALSE 18657.20125 25511.09051 27158.97308 42692.21604 32843.5192 35144.56216 29929.86203 26788.15099 16028.52068 20610.60547 0.905223346 1.237765215 1.317718352 2.071371271 1.5935252 1.705168837 1.452158311 1.299726543 0.777683155 1 14.33109927 1.421051199 3.207044346 0.8923675 1.488158174 0.372898165 0.294001073 0.265822592 4.81832509 0.243397932 0.081751015 26.366422 -1.421051199 0.595790674 S(ph)STPLHSPSPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.333)S(0.333)T(0.333)PLHSPSPIR;S(0.333)S(0.333)T(0.333)PLHSPSPIR 139.74 3.81E-05 520280000 296740 338300 297560 334750 281840 314680 343130 368890 410170 427690 TRUE FALSE 285143.0727 328652.0152 351335.7112 352026.4876 290905.6396 321043.0452 347329.3276 361272.2926 363609.2212 398722.1754 0.715142248 0.824263198 0.881154179 0.882886655 0.729594835 0.80517981 0.871106121 0.906075245 0.91193629 1 18.60502432 1.421413887 0.919568939 0.990992579 0.810034828 0.577042783 0.053336219 0.396858217 0.68877856 0.051512802 0.019273988 26.38845036 -1.421413887 -0.180957751 LKAEATEAAR ddPTM_BT-474_Pertuzumab_2h_R1 5 LKAEATEAAR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 174.24 2.89E-06 2972430000 3029550 3241880 2640170 2990140 2952780 2607610 3280540 3303560 3695570 3778080 FALSE TRUE 2911151.837 3149424.757 3117307.449 3144461.484 3047758.85 2660337.661 3320688.23 3235340.332 3276064.387 3522187.276 0.826518185 0.89416732 0.885048751 0.892758175 0.865302896 0.755308407 0.942791501 0.918559996 0.930122146 1 21.74804019 1.421649056 1.125995065 0.986442211 0.861991392 0.477452866 0.045794191 0.404130608 1.005384897 0.042346896 0.014591585 26.40274349 -1.421649056 -0.12445082 TTSIS(ph)PALAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TTSISPALAR 10 0 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 T(0.001)T(0.001)S(0.058)IS(0.94)PALAR;TTSIS(1)PALAR;TTS(0.025)IS(0.975)PALAR 133.49 0.00020542 646520000 586500 612420 544650 617070 535810 652490 608180 616690 608220 652910 TRUE FALSE 563578.9316 594954.3812 643080.3707 648917.0566 553044.8153 665683.7949 615623.0888 603955.136 539177.4155 608687.8241 0.925891581 0.977437625 1.056502767 1.066091732 0.90858531 1.093637442 1.011393796 0.992224769 0.88580286 1 19.21534298 1.422573193 8.360217578 0.94110111 1.007519258 0.140800513 0.060950974 0.443778874 56.90963816 0.037762678 0.01459908 26.4589858 -1.422573193 0.066418147 EEGLREWGS(ph)GSPPCVPGPQEGLRPMSDSVGGAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEGLREWGSGSPPCVPGPQEGLRPMSDSVGGAFR 34 2 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 EEGLREWGS(0.647)GS(0.353)PPCVPGPQEGLRPMSDSVGGAFR 85.416 0.00032833 419380000 54835 58868 37688 52190 45809 60029 49818 51635 50203 49562 TRUE FALSE 52691.98758 57189.14228 44499.05997 54883.53215 47282.48809 61242.82751 50427.68759 50568.71921 44504.16591 46205.12159 1.140392791 1.237723012 0.963076352 1.187823563 1.023317036 1.325455391 1.091387401 1.094439695 0.963186858 1 15.49576516 1.422836891 2.503781516 0.981013789 1.139759119 0.283867564 0.097418243 0.347623477 3.926713166 0.076969645 0.024605451 26.4750562 -1.422836891 0.15874533 SVTS(ph)SPVEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVTSSPVEKK 10 1 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3;F8VVB8 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 SVT(0.008)S(0.496)S(0.496)PVEKK 111.79 0.0010451 231400000 365790 385380 280620 277960 320680 401160 333500 382140 523380 432880 TRUE FALSE 351494.5224 374389.3397 331334.2764 292305.5489 330994.9634 409271.7301 337581.4728 374248.6755 463968.0966 403560.652 0.870983136 0.927715172 0.82102721 0.724316277 0.820186413 1.014151722 0.836507402 0.927366614 1.149686161 1 18.62242599 1.423281524 4.426406389 1.072356493 0.86110698 0.535979228 0.078968346 0.162738611 5.550832269 0.057498025 0.020860941 26.5021754 -1.423281524 -0.211249513 VPLDLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPLDLSPR 8 0 R4GNG2;Q9UKV5 R4GNG2 AMFR E3 ubiquitin-protein ligase AMFR 1 VPLDLS(1)PR;VPLDLS(1)PR 108.57 0.0039706 132595000 151663 248340 160605 353490 228970 189294 195758 208531 147640 132612 TRUE FALSE 145735.8423 241257.5864 189629.8961 371733.6613 236335.028 193121.6544 198153.745 204224.762 130880.5262 123630.0711 1.178805779 1.951447444 1.533849285 3.006822352 1.911630608 1.562092884 1.602795688 1.651902002 1.058646371 1 16.91567017 1.424086993 1.002654276 0.967919287 1.907542317 0.322373159 0.452209271 0.581544256 1.174424991 0.420152102 0.151300781 26.55137354 -1.424086993 0.93962303 ELDTVTLEDIKEHVK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELDTVTLEDIKEHVK 15 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 254.18 6.55E-25 2051838000 3066250 2872289 2238534 2123309 2591067 2817396 2644029 2906100 3762509 3284250 FALSE TRUE 2946417.56 2790374.13 2643086.89 2232893.232 2674411.023 2874365.677 2676387.418 2846088.019 3335404.752 3061804.822 0.962313972 0.911349446 0.863244734 0.729273537 0.873475345 0.938781485 0.874120845 0.929545867 1.089359037 1 21.54595089 1.424164475 3.719978485 1.042952468 0.87696479 0.52116973 0.062345971 0.182515939 4.428695439 0.048715085 0.017024976 26.556111 -1.424164475 -0.165987678 SES(ph)PFRETEPLVSPHQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SESPFRETEPLVSPHQDK 18 1 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 S(0.031)ES(0.969)PFRETEPLVSPHQDK 173.89 4.35E-12 66131000 105920 112190 90087 96796 89564 103230 102710 113590 145380 133100 TRUE FALSE 101780.5293 108990.451 106367.7249 101791.6532 92444.9074 105317.3813 103966.9957 111244.3268 128877.0719 124085.0184 0.820248331 0.878353023 0.857216497 0.820337978 0.745012642 0.848751788 0.837869043 0.896516986 1.038619114 1 16.92096941 1.424463908 2.677050729 1.020808077 0.829820832 0.818004815 0.035213139 0.110921974 1.42897213 0.030421185 0.009848818 26.57442695 -1.424463908 -0.190987245 DILQDVHDK ddPTM_BT-474_Pertuzumab_2h_R1 5 DILQDVHDK 9 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ;;;; 143.24 0.00010242 2315430000 2352970 2399820 2048380 2103090 2347990 2261790 2510990 2555490 3145810 3074370 FALSE TRUE 2261013.331 2331379.483 2418567.832 2211630.727 2423515.231 2307524.943 2541720.247 2502718.238 2788710.837 2866140.182 0.788870463 0.813421304 0.843841431 0.771640808 0.845567585 0.805098424 0.886809467 0.873201616 0.972984802 1 21.45067774 1.424750326 0.919047641 1.004926449 0.810037829 0.86251511 0.026680955 0.162115648 0.280788446 0.022654829 0.008486785 26.59195861 -1.424750326 -0.19488862 DQDKTDTLEHELR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDKTDTLEHELR 13 1 B8ZZD4;Q86VP1-2;Q86VP1;Q86VP1-4;Q86VP1-3 B8ZZD4 TAX1BP1 Tax1-binding protein 1 0 188.25 3.76E-06 300520000 253330 240310 228390 240680 237950 246870 288990 306860 360920 391040 FALSE TRUE 243429.5835 233456.5941 269665.1535 253101.5236 245603.8779 251861.8805 292526.7461 300523.2338 319949.8747 364554.5125 0.667745358 0.64038871 0.739711468 0.694276206 0.673709608 0.690875773 0.802422508 0.824357465 0.877646178 1 18.47577503 1.426910077 0.69026616 0.997775658 0.673763634 0.929130813 0.028812894 0.153704813 0.164066944 0.028226292 0.012626092 26.72453006 -1.426910077 -0.324012024 ALS(ph)PVIPLIPR ddPTM_BT-474_Pertuzumab_2h_R1 7 ALSPVIPLIPR 11 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR 174.42 1.16E-05 3740931000 1414373 1483057 1135759 1358887 1312322 1363298 1341042 1375564 1420160 1366887 TRUE FALSE 1359097.739 1440761.666 1341015.916 1429019.321 1354534.029 1390864.82 1357454.073 1347158.123 1258949.391 1274306.526 1.066539103 1.130624098 1.052349563 1.121409403 1.062957775 1.091468019 1.065249252 1.057169602 0.987948633 1 20.28128092 1.427147359 1.845707241 0.991089574 1.087048618 0.674985701 0.024559716 0.171204015 1.076351864 0.019508014 0.006149773 26.73913533 -1.427147359 0.095959043 ACRPPGS(ph)PGRAPPPTPAPSGCDPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ACRPPGSPGRAPPPTPAPSGCDPR 24 2 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 ACRPPGS(0.979)PGRAPPPT(0.021)PAPSGCDPR;ACRPPGS(1)PGRAPPPTPAPSGCDPR;ACRPPGS(1)PGRAPPPTPAPSGCDPR 92.231 0.0045454 1441340000 583860 708110 375949 597930 529207 636510 528475 533983 505571 454808 TRUE FALSE 561042.1057 687915.3961 443891.3472 628789.239 546229.4238 649380.6683 534942.6351 522956.0644 448180.6996 424003.4491 1.32320175 1.622428774 1.046905039 1.482981425 1.288266463 1.531545721 1.261646895 1.233376911 1.057021353 1 18.69371647 1.427458971 1.513018735 1.000786159 1.376551706 0.452110902 0.149586816 0.318578277 1.369515195 0.125054144 0.040206896 26.75832785 -1.427458971 0.375765547 SISAS(ph)KASPPGDLQNPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SISASKASPPGDLQNPK 17 1 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 SIS(0.009)AS(0.576)KAS(0.415)PPGDLQNPK 103.26 0.00054962 541490000 671540 634110 500970 500490 588720 647500 575320 666100 817910 766420 TRUE FALSE 645295.4744 616025.8037 591506.423 526320.3489 607656.7135 660592.8936 582360.9383 652344.8022 725064.2858 714509.6907 0.903130472 0.862165778 0.827849406 0.736617509 0.850452725 0.924540146 0.815049741 0.912996438 1.014771801 1 19.44659405 1.427991355 2.944145055 1.008302921 0.844768892 0.637162932 0.048426331 0.165958452 2.582703438 0.040474185 0.013410086 26.79114994 -1.427991355 -0.163534029 GTVQALHATGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GTVQALHATGAR 12 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;;; 166.48 5.18E-05 5602600000 2308010 2982860 2421830 3475730 2640620 2543230 2942250 2824140 2740260 2885500 FALSE TRUE 2217810.418 2897791.753 2859508.554 3655112.842 2725557.94 2594655.853 2978258.136 2765820.522 2429197.173 2690062.515 0.824445679 1.077220971 1.062989629 1.358746431 1.013195019 0.964533664 1.107133429 1.028162173 0.90302629 1 21.35920827 1.428028325 5.522687547 0.952985435 1.065384197 0.095956805 0.127930239 0.446404716 24.93791937 0.086097983 0.03263541 26.79343069 -1.428028325 0.112398762 YISSQIERPIR ddPTM_BT-474_Pertuzumab_2h_R1 3 YISSQIERPIR 11 1 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 185.99 3.85E-06 449500000 606100 683420 548400 606790 646480 637770 634960 639910 636680 653410 FALSE TRUE 582412.9419 663929.5307 647508.0791 638106.5046 667274.6163 650666.1464 642730.8304 626695.6349 564406.7556 609153.9587 0.956101382 1.089920736 1.062962934 1.047529111 1.095412099 1.068147284 1.055120502 1.028796786 0.926542047 1 19.21644738 1.428168649 4.255902237 0.964059571 1.056409491 0.441085055 0.039786481 0.17266496 5.531875237 0.026530161 0.009607434 26.80208925 -1.428168649 0.092349921 GGDISVCEWYQR ddPTM_BT-474_Pertuzumab_2h_R1 6 GGDISVCEWYQR 12 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;;;; 291.87 8.90E-36 8791830000 1684270 2016990 1772720 2481830 1545060 1893990 2077350 1874660 1766080 1755560 FALSE TRUE 1618446.866 1959467.42 2093089.938 2609917.544 1594758.258 1932287.775 2102773.231 1835947.616 1565602.002 1636654.358 0.988875176 1.197239607 1.278883307 1.594666297 0.974401376 1.180632775 1.284799824 1.121768691 0.956586829 1 20.64231824 1.428876256 3.517691008 0.980806449 1.219769602 0.247004784 0.162937942 0.325593926 7.162327895 0.123219712 0.042691478 26.84579419 -1.428876256 0.238963154 TSKEPPSS(ph)PLQPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSKEPPSSPLQPQK 14 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 TSKEPPS(0.023)S(0.977)PLQPQK;TSKEPPS(0.152)S(0.848)PLQPQK 143.71 5.48E-06 1678590000 1880890 1922190 1534470 1464730 1799990 1859340 1443980 1633120 1633800 1348310 TRUE FALSE 1807382.739 1867371.023 1811782.863 1540324.891 1857888.313 1896937.129 1461651.859 1599395.501 1448337.873 1256987.763 1.437868206 1.485592047 1.441368736 1.225409615 1.478048051 1.509113442 1.162821073 1.272403399 1.152229096 1 20.26153917 1.429062863 0.679650192 1.003176616 1.433817276 0.679669214 0.095233827 0.380679901 0.395990073 0.091747003 0.041553391 26.85733172 -1.429062863 0.430640659 IDRDSYS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDRDSYSPR 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 IDRDS(0.094)YS(0.906)PR 156.02 0.00018922 1121500000 1088200 1009300 881190 980770 1011700 952960 1017800 1013500 871060 1099600 TRUE FALSE 1045671.941 980515.7522 1040440.635 1031387.657 1044242.249 972229.5041 1030256.141 992570.8708 772180.9206 1025123.113 1.02004523 0.956485851 1.01494213 1.006111017 1.018650576 0.948402677 1.005007231 0.968245529 0.753256766 1 19.96736575 1.429317419 12.0330493 0.871183209 0.992834529 0.378402105 0.060014193 0.548570823 135.3422188 0.032684607 0.013165932 26.87307841 -1.429317419 0.12165132 KKPLKQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKPLKQPK 8 3 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 67.125 0.026243 1147200000 886350 917280 690390 581880 751700 738320 834000 839820 1149300 920620 FALSE TRUE 851710.4621 891120.0725 815158.8306 611910.8965 775879.1132 753249.3363 844206.7415 822477.4235 1018836.282 858265.5874 0.992362358 1.038280091 0.949774572 0.712962171 0.904008182 0.877641312 0.983619469 0.958301761 1.187087421 1 19.71106463 1.429941911 3.970005359 1.093160587 0.920324149 0.33317357 0.093802925 0.249499894 6.985163376 0.070640423 0.02523985 26.91174822 -1.429941911 -0.172836438 CMALMANDEESDDETSLEGGISPDLVLERSLDYGYGGDFVALDRMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 CMALMANDEESDDETSLEGGISPDLVLERSLDYGYGGDFVALDRMAK 47 2 Q6NV75 Q6NV75 GPR153 Probable G-protein coupled receptor 153 0 14.225 0.091895 22323000 3373.5 5429.9 3864.6 4400.9 3196.6 4225.1 4288.8 3923.5 2089.9 4054.1 FALSE TRUE 3241.65989 5275.044568 4563.019188 4628.030976 3299.421542 4310.534417 4341.287617 3842.478354 1852.663314 3779.512196 0.857692666 1.395694549 1.207303734 1.22450484 0.872975498 1.1405002 1.148637018 1.016659864 0.490185828 1 11.88398433 1.429984713 5.870606079 0.740515324 1.125339624 0.38015632 0.188922318 0.177646719 11.56506759 0.117401515 0.045036784 26.91440063 -1.429984713 0.3848243 GPSAGGGPGSGTS(ph)PQVEWTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPSAGGGPGSGTSPQVEWTAR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3;A0A2R8Y454 Q7Z406 MYH14 Myosin-14 1 GPSAGGGPGS(0.001)GT(0.203)S(0.796)PQVEWTAR 136.49 5.09E-06 127790000 156770 184890 189960 204950 179800 219230 190600 192190 179460 185990 TRUE FALSE 150643.2551 179617.1182 224289.9976 215527.4941 185583.4303 223662.9808 192932.6198 188221.2093 159088.4532 173392.7316 0.868797981 1.035897621 1.293537483 1.243001895 1.070306861 1.289921317 1.112691507 1.085519604 0.917503587 1 17.4036839 1.430175282 3.170030966 0.960260153 1.140217846 0.22695213 0.122907407 0.355614231 6.408605361 0.098020711 0.03312787 26.92621333 -1.430175282 0.179957693 RYS(ph)DHAGPAIPSVVAYPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RYSDHAGPAIPSVVAYPK 18 1 H0YIY6;P27448-6;P27448-7;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 RY(0.452)S(0.513)DHAGPAIPS(0.035)VVAYPK;RY(0.447)S(0.553)DHAGPAIPS(0.001)VVAYPK 123.03 1.64E-05 305130000 504320 529130 449030 505270 530700 515290 439120 532380 456200 460280 TRUE FALSE 484610.6168 514039.7305 530179.7096 531347.0453 547770.4475 525709.5169 444494.0819 521386.167 404414.0885 429104.8256 1.129352522 1.197935096 1.235548234 1.238268632 1.276542268 1.22513075 1.035863629 1.215055473 0.942459894 1 18.7109706 1.430284214 1.098536426 0.976905012 1.214427205 0.56278549 0.073130752 0.333657751 0.79245968 0.065469486 0.022809529 26.93296791 -1.430284214 0.237522193 KQS(ph)LPATSIPTPASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQSLPATSIPTPASFK 16 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 KQS(1)LPATSIPTPASFK 114.1 0.00037365 360010000 731340 645580 615450 609060 690370 602060 695160 749520 860560 866150 TRUE FALSE 702758.4243 627168.6905 726675.5056 640493.6596 712576.378 614234.0657 703667.576 734042.1501 762872.8366 807484.889 0.870305357 0.776694027 0.899924587 0.793195846 0.882464041 0.760675616 0.871431262 0.909047538 0.944751842 1 19.62307574 1.43032131 1.375292915 0.991188826 0.831539054 0.620581519 0.044253465 0.234132236 0.841274493 0.036522646 0.011960729 26.93526854 -1.43032131 -0.159649772 STKPNSSTPAS(ph)PPGTASGR ddPTM_BT-474_Pertuzumab_2h_R1 4 STKPNSSTPASPPGTASGR 19 1 Q8WV28-3;Q8WV28 Q8WV28-3 BLNK B-cell linker protein 1 STKPNSST(0.001)PAS(0.991)PPGT(0.007)ASGR;STKPNSSTPAS(0.998)PPGT(0.001)ASGR;S(0.008)T(0.008)KPNS(0.01)S(0.043)T(0.134)PAS(0.781)PPGT(0.007)AS(0.007)GR;STKPNSST(0.002)PAS(0.989)PPGT(0.007)AS(0.001)GR 123.85 1.84E-05 1060770000 683250 698940 621713 747980 784740 685489 620021 672058 603247 530907 TRUE FALSE 656547.8346 679006.9155 734070.369 786583.3374 809981.8748 699350.0572 627609.0025 658179.7674 534768.9296 494948.196 1.326498086 1.371874715 1.483125658 1.589223567 1.636498287 1.412976273 1.26802968 1.329795265 1.080454346 1 18.91691801 1.43055816 1.026142794 0.9979883 1.476063535 0.732832294 0.098656978 0.265247144 0.55725439 0.099315852 0.035495465 26.9499622 -1.43055816 0.478075235 FDKDHDVMLFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FDKDHDVMLFLK 12 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 120.87 0.00023212 432110000 1957100 1861000 1600100 1564600 1649400 1237300 1904700 1785300 2243900 2078500 FALSE TRUE 1880614.368 1807926.102 1889273.664 1645349.194 1702454.449 1262319.054 1928010.288 1748432.931 1989181.879 1937721.344 0.970528799 0.93301656 0.974997602 0.849115482 0.878585796 0.651445089 0.994988415 0.902313915 1.026557242 1 20.88592969 1.43072987 1.926850906 1.012264965 0.885665318 0.197082126 0.093235255 0.539358226 3.695750663 0.083176863 0.026244711 26.96061965 -1.43072987 -0.126599648 KSEAPAEVTHFS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSEAPAEVTHFSPK 14 1 Q6PID6 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 1 KSEAPAEVTHFS(1)PK;KSEAPAEVTHFS(1)PK 155.28 2.77E-06 1081970000 2834300 2501000 2055250 2053510 2274600 2439600 2345200 2537300 3219000 2648700 TRUE FALSE 2723532.423 2429673.929 2426679.394 2159491.897 2347764.575 2488930.384 2373901.259 2484903.868 2853592.615 2469301.19 1.102956753 0.983952034 0.982739329 0.87453564 0.950780968 1.007949291 0.961365616 1.006318662 1.155627603 1 21.23567139 1.430793842 6.991819818 1.080039435 0.977713247 0.265313573 0.063605386 0.239792046 23.67034396 0.039991295 0.015676948 26.96459129 -1.430793842 -0.102326188 QAS(ph)VHDSGEEGEA ddPTM_BT-474_Pertuzumab_2h_R1 6 QASVHDSGEEGEA 13 0 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA 219.95 2.27E-11 6529162000 4764761 5739677 4409696 5729319 5239551 6216496 5592235 5415745 4995999 5426529 TRUE FALSE 4578548.872 5575987.032 5206626.16 6025009.84 5408085.916 6342197.808 5660674.445 5303907.973 4428874.138 5058985.357 0.905033035 1.102194736 1.029183876 1.19095222 1.069006043 1.253650161 1.118934736 1.048413387 0.875447115 1 22.27041663 1.431116001 4.527415629 0.93942757 1.100799059 0.312489019 0.091860211 0.230421703 8.478606817 0.06276667 0.023114994 26.98460103 -1.431116001 0.161371489 EKNGVYISEENFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKNGVYISEENFR 13 1 P52732 P52732 KIF11 Kinesin-like protein KIF11 0 87.148 0.0077524 222440000 114060 131880 92508 130120 109730 142200 122480 121450 110300 123880 FALSE TRUE 109602.4091 128118.9115 109226.2534 136835.5088 113259.5651 145075.3814 123978.9469 118942.0151 97779.20642 115489.4973 0.949024904 1.109355522 0.945767849 1.18483076 0.980691472 1.256178136 1.073508413 1.029894647 0.846650204 1 16.81740213 1.431529092 4.791010072 0.923577421 1.07422396 0.252971556 0.099805615 0.248840677 10.35017204 0.063930759 0.023818146 27.01028037 -1.431529092 0.150646539 SRS(ph)WEDSPER ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSWEDSPER 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(0.004)RS(0.946)WEDS(0.05)PER;S(0.015)RS(0.865)WEDS(0.12)PER 172.21 9.96E-06 662370000 536240 610030 461980 633040 581370 519180 570540 539700 537240 500370 TRUE FALSE 515283.148 592632.5417 545470.0627 665711.2703 600070.294 529678.1753 577522.4392 528555.0064 476254.7675 466479.4942 1.10462122 1.270436427 1.169333421 1.427096536 1.286380862 1.135480084 1.238044644 1.133072328 1.020955419 1 18.83145414 1.431629528 1.396866007 0.990004245 1.244034244 0.520526675 0.085250433 0.307296624 1.137059671 0.077123584 0.025190017 27.01652756 -1.431629528 0.254029999 ENAGS(ph)LEAINEPIPQPMPFPPSIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENAGSLEAINEPIPQPMPFPPSIIR 25 0 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 ENAGS(1)LEAINEPIPQPMPFPPSIIR 73.672 0.021806 21318000 10912 13812 9354.5 14167 14018 11744 12609 10837 11654 9353.6 TRUE FALSE 10485.54698 13418.09528 11045.06624 14898.16057 14468.9017 11981.47173 12763.31271 10613.21216 10331.08678 8720.072341 1.202461008 1.538759629 1.266625529 1.708490479 1.659263953 1.374010588 1.463670508 1.21710139 1.184747829 1 13.09012439 1.431725168 1.255611408 1.025605015 1.477483627 0.510189216 0.151428363 0.330573176 1.002519763 0.136578272 0.045712882 27.02247775 -1.431725168 0.451878612 VAS(ph)YWLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 VASYWLIK 8 0 F2Z2J7;Q6ZT98-3;Q6ZT98 F2Z2J7 TTLL7 Tubulin polyglutamylase TTLL7 1 VAS(0.575)Y(0.425)WLIK 53.166 0.089084 239810000 9026.6 0 9883.2 8586.6 10516 5399.3 9467 6692.7 0 7271.2 TRUE FALSE 8673.830493 0 11669.31409 9029.755455 10854.25669 5508.477545 9582.859978 6554.493406 0 6778.715147 1.279568518 0 1.721464 1.332074775 1.601226258 0.81261381 1.413669076 0.966922678 0 1 12.72679613 1.431762424 8.348118838 0.489894271 1.151684691 0.210622995 0.508536407 0.336827387 49.71678849 0.30619389 0.122292571 27.02479597 -1.431762424 0.66179042 NPVDYMDLPFSS(ph)SPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPVDYMDLPFSSSPSR 16 0 Q9BX66-6;Q9BX66-5;A0A0U1RQI5;Q9BX66-4;Q9BX66-9;Q9BX66-8;Q9BX66-10;Q9BX66-2;Q9BX66;Q9BX66-12;A0A3B3IT56;Q9BX66-3;Q9BX66-11 Q9BX66-6 SORBS1 Sorbin and SH3 domain-containing protein 1 1 NPVDYMDLPFS(0.134)S(0.43)S(0.43)PS(0.006)R 98.227 0.0029427 46472000 86047 112280 83595 96735 97633 115890 101280 99949 85711 104010 TRUE FALSE 82684.18811 109077.8843 98702.47606 101727.5049 100773.4541 118233.3752 102519.4949 97885.01822 75981.44661 96965.31006 0.852719267 1.124916573 1.017915335 1.049112357 1.039273262 1.219336845 1.057280123 1.00948492 0.783594118 1 16.56518109 1.431829123 5.539073229 0.889897032 1.056651486 0.285169819 0.099148803 0.216268578 12.46544754 0.062362595 0.023818016 27.02894678 -1.431829123 0.166754454 AEASSGDHPTDTEMKEEQK ddPTM_BT-474_Pertuzumab_2h_R1 11 AEASSGDHPTDTEMKEEQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;;;;;;; 328.27 2.05E-75 13741986000 8014723 7565292 6712486 6244960 6836734 7541757 7548750 8114225 10768928 9436901 FALSE TRUE 7701498.764 7349537.279 7925581.539 6567263.134 7056643.758 7694256.494 7641133.861 7946663.418 9546484.44 8797731.29 0.875395998 0.835390061 0.900866516 0.746472348 0.802098123 0.874572801 0.868534581 0.903262802 1.085107527 1 23.06870011 1.432241694 2.912680186 1.041784571 0.841577673 0.732960257 0.046986784 0.126180412 1.936922902 0.037530861 0.01245408 27.05463591 -1.432241694 -0.200206898 EATNPPVIQEEKPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EATNPPVIQEEKPKK 15 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 126.63 4.67E-05 222630000 228760 209100 166460 151840 181300 203020 179220 212590 290410 235210 FALSE TRUE 219819.8063 203136.6727 196543.0249 159676.4806 187131.6792 207125.2035 181413.348 208199.9422 257443.8743 219279.0172 1.002466215 0.926384455 0.896314784 0.7281886 0.853395284 0.94457375 0.827317407 0.949474988 1.174047009 1 17.74240824 1.432276668 5.119189995 1.084927195 0.88101308 0.505860841 0.079712552 0.154037862 7.440103075 0.054092577 0.020417143 27.05681472 -1.432276668 -0.203914115 VNDFLAEIFKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNDFLAEIFKK 11 1 Q14008;Q14008-3;Q14008-2;H0YDX5 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 120.87 0.00067889 57633000 86985 95521 70907 63287 78642 79424 86786 92841 106120 109660 FALSE TRUE 83585.53003 92796.8346 83721.47222 66553.24965 81171.59135 81030.0077 87848.11303 90923.80091 94073.70249 102232.6305 0.817601284 0.907702699 0.818931018 0.650998114 0.793989071 0.792604155 0.859296221 0.889381408 0.920192526 1 16.64149622 1.432328248 1.039923662 0.989947695 0.796371727 0.547926169 0.060212862 0.390757047 0.840397875 0.059868529 0.021296267 27.06002838 -1.432328248 -0.193575968 DLDNAEEKADALNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDNAEEKADALNK 14 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 ; 153.24 5.88E-06 521930000 458090 458110 308510 264290 374520 427880 368840 427810 585310 476740 FALSE TRUE 440187.3364 445045.1513 364264.6198 277930.0386 386566.7759 436532.0268 373353.9743 418975.574 518868.0626 444449.9752 0.990409182 1.00133913 0.819585195 0.625334805 0.869764422 0.982184838 0.840035989 0.942683311 1.167438613 1 18.76166152 1.432843272 4.68287608 1.081706703 0.873772708 0.355650365 0.110430528 0.228321951 9.091090225 0.080766124 0.03001896 27.09213755 -1.432843272 -0.207933995 RSDSAS(ph)SEPVGIYQGFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSDSASSEPVGIYQGFEK 18 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 RS(0.04)DS(0.134)AS(0.799)S(0.027)EPVGIYQGFEK;RS(0.124)DS(0.315)AS(0.509)S(0.052)EPVGIYQGFEK 172.77 6.10E-12 658590000 593100 606530 478450 523740 562850 656450 490840 585850 553320 532940 TRUE FALSE 569920.9963 589232.3583 564916.5581 550770.2842 580954.5814 669723.8688 496847.0467 573751.9928 490509.4333 496843.4991 1.147083533 1.185951631 1.137011069 1.108538776 1.169290898 1.347957395 1.00000714 1.154794203 0.987251386 1 18.92243196 1.432896658 1.36728002 0.991956909 1.168509536 0.378557896 0.081690848 0.415100795 1.475580793 0.0713056 0.023402838 27.09546809 -1.432896658 0.176552626 SPS(ph)PAHLPDDPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.08)PS(0.92)PAHLPDDPK;S(0.011)PS(0.989)PAHLPDDPK;S(0.099)PS(0.901)PAHLPDDPK 215.34 4.37E-11 6188800000 4218750 4122550 3328110 3530090 3772310 3953630 4021790 4291190 5313660 4985940 TRUE FALSE 4053876.586 4004978.91 3929573.51 3712278.368 3893649.777 4033575.107 4071009.869 4202575.427 4710475.593 4648237.843 0.872131918 0.861612303 0.84538994 0.798642086 0.837661477 0.867764354 0.875817892 0.904122287 1.013389537 1 22.14825246 1.433107015 1.741216022 1.013158421 0.846911772 0.883233671 0.022241592 0.109924168 0.619832186 0.020934854 0.006641777 27.10859534 -1.433107015 -0.166246649 IIEVVDAIMTTAQSHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 IIEVVDAIMTTAQSHQR 17 0 Q01813;Q01813-2;Q5VSR5 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 232.74 4.76E-17 1136040000 344240 344350 303260 355510 337460 354270 321530 324320 327510 288980 FALSE TRUE 330786.7202 334529.4752 358065.828 373857.9137 348314.7074 361433.5821 325464.9803 317622.6787 290332.4378 269407.1272 1.227832105 1.241724666 1.329088179 1.3877061 1.29289344 1.341588791 1.208078582 1.178969101 1.077671704 1 18.03942849 1.433168911 1.156718913 1.004944521 1.304786016 0.826335895 0.047588922 0.179056502 0.466875255 0.046147483 0.015820191 27.1124592 -1.433168911 0.299841495 DFVDHIDLVDPVDGVVLVDPEYLK ddPTM_BT-474_Pertuzumab_2h_R1 5 DFVDHIDLVDPVDGVVLVDPEYLK 24 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;; 200.23 1.55E-24 809842000 720042 656414 575190 616570 677960 709378 716124 714074 914278 879210 FALSE TRUE 691901.9626 637693.7154 679139.628 648391.2516 699767.1991 723722.1092 724888.1397 699328.1224 810492.9944 819660.3236 0.844132554 0.77799754 0.828562282 0.791048722 0.853728281 0.882953692 0.88437627 0.8531926 0.988815697 1 19.64466664 1.433180558 0.484965351 1.009139455 0.805294074 0.77844553 0.032955612 0.403236351 0.250636763 0.035623977 0.02173276 27.1131863 -1.433180558 -0.203845381 LISWYDNEFGYSNR ddPTM_BT-474_Pertuzumab_2h_R1 20 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;; 420.69 2.65E-152 98833426700 10125451.99 11613475.7 8870391 11125927 10636488.9 10995311 10350327.15 10510137 10025275.3 9847112 FALSE TRUE 9729738.132 11282270.74 10473467.97 11700137.43 10978621.23 11217643.72 10476997.55 10293099 8887248.077 9180158.333 1.059866048 1.228984331 1.140880973 1.274502792 1.195907611 1.221944471 1.141265452 1.121233276 0.968093115 1 23.13008761 1.433212096 2.064182637 0.979810898 1.18820764 0.64380763 0.057105845 0.176736276 1.38812689 0.046650144 0.014754264 27.1151553 -1.433212096 0.208396742 MGPSGGEGMEPERRDSQDGSS(ph)YR ddPTM_BT-474_Pertuzumab_2h_R1 1 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.001)QDGS(0.187)S(0.813)YR 223.15 1.19E-32 7279300000 656320 710630 428370 553690 689910 744360 629740 589890 584850 523780 TRUE FALSE 630670.2888 690363.5282 505785.988 582266.0073 712101.5817 759411.4692 637446.9465 577708.5654 518460.2799 488303.9141 1.291552803 1.413798883 1.035801626 1.192425435 1.45831635 1.555202503 1.305430754 1.183092227 1.061757371 1 18.89741982 1.433292568 2.184135571 1.01811568 1.322905356 0.430006806 0.135008425 0.317659691 2.786705045 0.126396253 0.040100609 27.12018 -1.433292568 0.304789676 EPGS(ph)GTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQK 40 1 Q9HAF1-3;Q9HAF1-2;Q9HAF1;Q9HAF1-4;B1AK63 Q9HAF1-3 MEAF6 Chromatin modification-related protein MEAF6 1 EPGS(0.397)GT(0.218)ES(0.251)DT(0.066)S(0.066)PDFHNQENEPS(0.003)QEDPEDLDGSVQGVKPQK;EPGS(0.575)GT(0.09)ES(0.112)DT(0.112)S(0.112)PDFHNQENEPSQEDPEDLDGSVQGVKPQK 152.95 7.18E-14 532820000 73710 91673 75796 80292 82472 87756 103244 94613 127805 129503 TRUE FALSE 70829.33171 89058.5758 89494.02327 84435.87974 85124.78678 89530.48645 104507.531 92659.20849 113297.1122 120731.6465 0.586667488 0.737657262 0.741264001 0.699368245 0.705074347 0.741566019 0.865618369 0.7674807 0.938420998 1 16.88144436 1.433570016 0.395115829 1.020253316 0.662940364 0.792551343 0.052963253 0.481497086 0.225934684 0.06735795 0.049001745 27.13751124 -1.433570016 -0.357312953 STELKTEIKEEEDQPSTSATQSS(ph)PAPGQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 STELKTEIKEEEDQPSTSATQSSPAPGQSK 30 2 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 STELKTEIKEEEDQPSTSAT(0.002)QS(0.102)S(0.896)PAPGQSK 164.74 1.69E-12 292200000 279970 216010 140910 117620 167210 205870 178920 203690 277660 218180 TRUE FALSE 269028.4629 209849.6063 166375.5715 123690.3823 172588.4615 210032.8325 181109.6765 199483.7303 246141.2008 203402.4743 1.322641054 1.031696429 0.817962378 0.608106577 0.848507188 1.032597235 0.890400557 0.98073404 1.21011901 1 17.6339777 1.433683351 5.685263708 1.105701148 0.924253487 0.11846288 0.179560922 0.394565987 24.46462497 0.124359485 0.047859777 27.14459405 -1.433683351 -0.181447661 LTAIIEEAEEAPGARPQLQDAWR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTAIIEEAEEAPGARPQLQDAWR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 246.22 1.30E-37 1880210000 575303 590580 470851 628151 543146 619754 543773 584987 608773 569792 FALSE TRUE 552819.5227 573737.2366 555944.2497 660569.9484 560616.7844 632285.8505 550427.8566 572906.814 539667.6412 531199.4803 1.040700421 1.080078686 1.046582819 1.243544041 1.055379015 1.190298323 1.036198033 1.078515389 1.015941584 1 19.01889421 1.433775417 1.3515903 1.001435895 1.106144942 0.245793568 0.064164189 0.552612208 1.92243622 0.055832733 0.018375678 27.15034904 -1.433775417 0.104709046 YSPTS(ph)PTYS(ph)PTSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPTS(0.917)PT(0.234)Y(0.107)S(0.738)PT(0.002)S(0.001)PK;YSPTS(0.773)PT(0.03)Y(0.197)S(1)PTSPK 205.26 1.83E-08 1771200000 1114410 1079150 953140 1067230 997970 1082900 1094840 1123320 1302590 1229810 TRUE FALSE 1070857.625 1048373.699 1125393.6 1122309.868 1030070.611 1104796.98 1108238.979 1100123.049 1154725.444 1146513.873 0.934011921 0.914401232 0.981578703 0.978889043 0.89843711 0.96361414 0.966616284 0.959537495 1.007162208 1 20.12882238 1.434082471 1.269716777 1.005317966 0.945636856 0.413638846 0.025679864 0.42939474 1.329329576 0.023624521 0.007890911 27.16955157 -1.434082471 -0.05968111 CRHENLLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 CRHENLLLR 9 1 Q6ZMV8 Q6ZMV8 ZNF730 Putative zinc finger protein 730 0 68.735 0.052194 582950000 23701 18205 11853 22499 22583 13675 14363 21678 33546 24668 FALSE TRUE 22774.73872 17685.81122 13995.10077 23660.17609 23309.4027 13951.51787 14538.77869 21230.34172 29737.99872 22997.21439 0.990325973 0.769041455 0.608556347 1.028827913 1.013575049 0.606661208 0.63219738 0.923170144 1.293113079 1 14.4891715 1.434411227 6.007173545 1.141213946 0.805314509 0.391595051 0.167432912 0.189681635 13.48457504 0.110639007 0.042991785 27.19012641 -1.434411227 -0.335899437 NPSPT(ph)TRPVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPSPTTRPVSR 11 1 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4;A0A0U1RQR2 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 NPS(0.454)PT(0.545)T(0.001)RPVSR 162.96 3.96E-05 708500000 129530 124540 84789 131350 134300 118810 123980 120270 100710 126430 TRUE FALSE 124467.8244 120988.2411 100112.2584 138128.9892 138619.8815 121212.4196 125497.3043 117786.3825 89277.82301 117866.7835 1.056004251 1.026482929 0.849367866 1.171907684 1.176072489 1.028384894 1.064738518 0.999317865 0.757446843 1 16.84679768 1.434578723 5.968117046 0.875748304 1.050607636 0.316979655 0.100958321 0.216443455 15.16610327 0.065792969 0.025551678 27.20061497 -1.434578723 0.174859332 AKS(ph)PAPGLASGDRPPSVSSVHSEGDCNRR ddPTM_BT-474_Pertuzumab_2h_R1 2 AKSPAPGLASGDRPPSVSSVHSEGDCNRR 29 3 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 AKS(0.999)PAPGLAS(0.001)GDRPPSVSSVHSEGDCNRR;AKS(0.993)PAPGLAS(0.006)GDRPPSVSSVHSEGDCNRR 53.674 0.049736 542210000 121261 101780 93163 86545 103261 109255 101534 108484 141210 111951 TRUE FALSE 116521.9861 98877.33405 109999.6265 91011.59782 106582.4838 111464.211 102776.6035 106243.7675 125180.4328 104368.4591 1.116448275 0.947387122 1.053954686 0.872022052 1.021213543 1.067987512 0.984747733 1.017968153 1.199408652 1 16.67132626 1.434726184 19.91255535 1.102702449 1.005859561 0.174950063 0.077663202 12.60165147 5920.248715 0.041098508 0.017913754 27.2098523 -1.434726184 -0.096842888 DRFVNDYDKDNDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRFVNDYDKDNDGR 14 2 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 81.311 0.0077955 238480000 132840 131180 109930 137370 138320 136480 139680 170610 199900 209950 FALSE TRUE 127648.4659 127438.8748 129796.7964 144459.6822 142769.1884 139239.7191 141389.4456 167086.8439 177208.19 195729.8995 0.65216641 0.651095592 0.663142405 0.738056283 0.729419413 0.711387067 0.722370195 0.853660296 0.905371078 1 17.57850463 1.434745532 0.799042991 1.005322814 0.677332821 0.937632133 0.027977013 0.136865396 0.185711738 0.028719518 0.011651137 27.21106454 -1.434745532 -0.327989992 VSQGSKDPAEGDGAQPEETPR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSQGSKDPAEGDGAQPEETPR 21 1 Q14697;F5H6X6 Q14697 GANAB Neutral alpha-glucosidase AB 0 ;; 199.28 7.39E-22 2125110000 1237310 1385720 1154610 1156570 1227570 1401220 1286040 1403520 1768720 1557370 FALSE TRUE 1188954.557 1346200.622 1363273.711 1216260.716 1267055.904 1429553.628 1301778.942 1374536.822 1567942.321 1451887.943 0.818902425 0.927206972 0.938966205 0.837709771 0.872695383 0.984617054 0.896611167 0.946723766 1.079933426 1 20.46949868 1.435060761 3.714825587 1.03857074 0.900468063 0.56684142 0.049246257 0.159688152 3.967934209 0.035542025 0.01257158 27.23082258 -1.435060761 -0.138102677 SMGTGDTPGLEVPSS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 7 SMGTGDTPGLEVPSSPLR 18 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.018)S(0.982)PLR;SMGTGDTPGLEVPS(0.167)S(0.833)PLR;SMGTGDTPGLEVPS(0.065)S(0.935)PLR;SMGTGDTPGLEVPSS(1)PLR;SMGTGDTPGLEVPS(0.191)S(0.809)PLR;SMGTGDTPGLEVPS(0.031)S(0.969)PLR;SMGTGDTPGLEVPS(0.097)S(0.903)PLR 284.5 1.59E-39 2389190000 2035127 2191385 1953331 2295250 2232458 2261610 2272391 2239413 2169929 2356980 TRUE FALSE 1955591.987 2128888.845 2306341.363 2413708.128 2304267.039 2307341.304 2300201.201 2193168.339 1923607.757 2197339.645 0.889981661 0.96884833 1.049606222 1.098468383 1.048662206 1.050061291 1.04681186 0.998101656 0.875425773 1 21.06732646 1.435454058 6.643242942 0.936263008 1.025251561 0.228240373 0.060706514 0.263158585 24.13820223 0.040066116 0.015824525 27.25549403 -1.435454058 0.088988554 LTEGCSFR ddPTM_BT-474_Pertuzumab_2h_R1 5 LTEGCSFR 8 0 P42677;C9J1C5;H0YMV8;Q71UM5 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ;;;; 161.9 0.00080229 3458180000 1302890 1419940 1192270 1302230 1221380 1314080 1433650 1380550 1374520 1505910 FALSE TRUE 1251971.618 1379444.701 1407739.711 1369438.246 1260666.797 1340651.598 1451195.438 1352041.16 1218490.252 1403913.374 0.891772699 0.982571095 1.002725479 0.97544355 0.897966228 0.954938974 1.033678761 0.963051699 0.8679241 1 20.42102249 1.435671794 25 0.927803928 0.966302388 0.043821697 0.050364619 129.5513481 78145.61494 0.027473797 0.012308271 27.26916216 -1.435671794 0.03849846 RNS(ph)SS(ph)PVSPASVPGQR ddPTM_BT-474_Pertuzumab_2h_R1 3 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.989)S(0.011)S(0.747)PVS(0.253)PASVPGQR;RNS(0.892)S(0.289)S(0.819)PVSPASVPGQR;RNS(0.949)S(0.176)S(0.875)PVSPASVPGQR 165.16 1.54E-09 1029550000 653590 728350 553510 710620 720860 678860 671010 689330 693140 679930 TRUE FALSE 628046.9802 707578.1711 653541.5698 747295.1834 744047.1166 692587.0143 679222.0211 675095.0946 614457.6531 633877.7355 0.990801451 1.116269166 1.031021494 1.178926379 1.173802257 1.092619247 1.07153475 1.065024147 0.969363047 1 19.27384507 1.436031208 2.167559972 0.983546012 1.099266134 0.369091387 0.055103679 0.317327714 2.750872821 0.047751399 0.015170148 27.29173893 -1.436031208 0.115720121 EEASGSSVTAEEAKK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEASGSSVTAEEAKK 15 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 206.06 6.55E-09 1013030000 878830 780480 597020 571270 679620 796970 676130 786730 1024470 854700 FALSE TRUE 844484.352 758221.4746 704914.7946 600753.3132 701480.5945 813085.2794 684404.6812 770483.7506 908176.4605 796810.4077 1.059830976 0.951570747 0.884670667 0.753947623 0.880360733 1.020425024 0.858930399 0.966959948 1.139764807 1 19.60387697 1.436746404 5.434159062 1.068391196 0.912622728 0.33189524 0.086365428 0.215021593 12.21520633 0.058499689 0.022490546 27.33671997 -1.436746404 -0.155768468 QKLPDGSEIPLPPILLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKLPDGSEIPLPPILLGR 18 1 Q96KP4;J3QKT2;A0A087WYZ1;J3KSV5;J3QRD0;J3QKQ0;J3QLU1;J3QR27;A0A087WVS2;J3QL02;J3KRD5;J3QQN6 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 158.45 4.15E-11 306080000 668970 712280 559990 635930 620910 652800 667410 752000 842520 858190 FALSE TRUE 642825.9128 691966.4718 661192.6499 668750.4235 640882.134 666000.0633 675577.9632 736470.9372 746880.6617 800064.0269 0.803468087 0.86488887 0.826424671 0.835871132 0.801038558 0.832433456 0.844404873 0.920514999 0.933526114 1 19.60975593 1.436946227 1.17282392 0.992136993 0.82641064 0.901881683 0.019229238 0.119426796 0.319210407 0.017191358 0.005875661 27.34930075 -1.436946227 -0.165726353 KVGWIFTDLVSEDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVGWIFTDLVSEDTR 15 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ; 105.39 0.0021147 315060000 426450 406090 305980 353230 419540 452390 389910 385500 378420 362670 FALSE TRUE 409783.8625 394508.7108 361277.3925 371460.2426 433034.8851 461537.6358 394681.8352 377539.2903 335463.3481 338106.0379 1.211998062 1.166819479 1.068532803 1.098650131 1.280766495 1.365067713 1.16733152 1.116629838 0.992183843 1 18.36711625 1.437636685 2.434112057 0.993276337 1.194104914 0.492240994 0.079818167 0.269511886 2.939459485 0.074556413 0.024015254 27.3928163 -1.437636685 0.200828577 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 15 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNY(0.001)EGS(0.999)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNY(0.003)EGS(0.997)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNY(0.005)EGS(0.995)PIK 244.19 1.30E-45 2102194800 2338357 2022816 1663274.9 1593466.9 1873192 1964697 1853290.1 2001094 2607944 2089810 TRUE FALSE 2246971.423 1965127.268 1963865.674 1675705.918 1933444.922 2004424.519 1875971.219 1959770.71 2311901.131 1948265.307 1.153319014 1.008654859 1.008007311 0.860101502 0.992393035 1.028825239 0.962893099 1.00590546 1.186645947 1 20.89375872 1.437756168 24.90404807 1.094307561 0.996655257 0.170920348 0.07942076 67.00939295 42397.62781 0.042856322 0.019414234 27.40035363 -1.437756168 -0.097652304 DLEEDHACIPIK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLEEDHACIPIK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 142.1 6.11E-05 4742630000 4197430 4319050 3852390 4304340 4029890 3982290 4790300 4936150 5724050 5965260 FALSE TRUE 4033389.795 4195874.923 4548602.569 4526487.503 4159515.072 4062814.632 4848925.124 4834216.778 5074279.841 5561227.627 0.725269682 0.754487175 0.817913395 0.813936743 0.747949077 0.730560751 0.871916319 0.869271517 0.912438796 1 22.40697196 1.437932335 0.863722693 0.993669153 0.766952532 0.812147191 0.036872334 0.232964068 0.360694196 0.036020523 0.013983469 27.41147055 -1.437932335 -0.226716621 VEAIDVEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEAIDVEEAKR 11 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 165.7 3.41E-05 826460000 1142520 1053370 1067050 1170410 1142630 1144110 1247260 1472310 1673580 1805690 FALSE TRUE 1097869.055 1023328.919 1259889.671 1230815 1179383.732 1167244.688 1262524.341 1441906.284 1483602.215 1683389.008 0.652177869 0.607898064 0.748424556 0.731153046 0.700600827 0.693389753 0.749989655 0.856549661 0.881318702 1 20.68293717 1.438118038 0.742498433 1.000692914 0.677010789 0.886829846 0.03766955 0.19502578 0.233739327 0.038017312 0.016191872 27.42319412 -1.438118038 -0.323682125 KS(ph)PVGKSPPSTGSTYGSSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPVGKSPPSTGSTYGSSQK 20 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(0.363)PVGKS(0.363)PPS(0.078)T(0.078)GS(0.098)T(0.021)YGSSQK 79.237 0.0040781 721100000 551810 554190 446280 432480 443330 513570 450770 542570 667720 606450 TRUE FALSE 530244.6551 538385.0438 526932.7234 454800.3446 457590.1121 523954.7373 456286.6581 531365.7399 591923.2249 565374.6013 0.937864301 0.952262522 0.932006359 0.804423021 0.809357391 0.926739079 0.807051921 0.939847207 1.046957581 1 19.10884755 1.438302393 4.644810148 1.019540798 0.881532365 0.509241274 0.055440105 0.169626503 6.785146966 0.039989552 0.014963156 27.43483753 -1.438302393 -0.138008433 YRADTLGELDLER ddPTM_BT-474_Pertuzumab_2h_R1 4 YRADTLGELDLER 13 1 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ;;; 166.79 3.01E-05 1294510000 860990 1156340 799580 1213000 947170 977670 1147120 983140 919760 936020 FALSE TRUE 827341.5589 1123362.315 944081.8926 1275603.075 977636.5832 997439.1573 1161158.798 962837.8154 815352.7007 872622.5317 0.948109324 1.287340488 1.081890346 1.461803963 1.120343044 1.143036217 1.330654155 1.103384087 0.934370442 1 19.7349982 1.438715843 4.608126191 0.974043694 1.201580605 0.310689206 0.135262235 0.223287567 8.791700516 0.086679879 0.032400079 27.46096807 -1.438715843 0.227536911 LGAPQTHLGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGAPQTHLGLK 11 0 Q96C19;H0Y4Y4;Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2;C9JTV4 Q96C19;Q9BUP0 EFHD2;EFHD1;PP1187 EF-hand domain-containing protein D2;EF-hand domain-containing protein D1 0 ; 132.32 0.0001849 1218750000 2063550 2178160 1858990 2284400 1880860 1459060 2311900 2400300 2841700 2982700 FALSE TRUE 1982904.185 2116041.009 2194950.846 2402298.158 1941359.57 1488563.193 2340193.724 2350732.966 2519122.129 2780679.072 0.713100697 0.760979946 0.789357847 0.863924996 0.698160241 0.535323622 0.841590728 0.845380896 0.905937745 1 21.40700582 1.439140894 1.487564003 0.97708498 0.738616558 0.516883871 0.08470018 0.327402948 1.366780782 0.080598951 0.026110841 27.48785772 -1.439140894 -0.238468422 LKEEPDR ddPTM_BT-474_Pertuzumab_2h_R1 5 LKEEPDR 7 1 P26358;P26358-2 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;;;; 111.17 0.0060554 2381400000 3754320 3516430 3182850 3397420 3582000 3542240 3865240 4091980 4444100 4684010 FALSE TRUE 3607597.024 3416144.859 3758061.797 3572761.253 3697218.283 3613866.52 3912543.963 4007479.183 3939624.399 4366757.831 0.82615001 0.782306918 0.860606872 0.818172519 0.846673534 0.827585742 0.895983729 0.917724165 0.902185226 1 22.05813109 1.439148765 0.428331417 1.004186235 0.806804249 0.856284268 0.022608971 0.327725209 0.171194456 0.026152099 0.017883852 27.48835586 -1.439148765 -0.197381986 DGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYK 36 3 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 206.64 2.77E-30 1021880000 590510 587800 346060 334770 435300 568290 462730 502650 608240 523410 FALSE TRUE 567432.2164 571036.5195 408600.7401 352047.5198 449301.8198 579781.2132 468393.0282 492270.1018 539195.1452 487958.9745 1.162868696 1.170255184 0.837366995 0.721469505 0.920777859 1.188176145 0.959902477 1.00883502 1.10500098 1 18.89640033 1.439346418 8.799735684 1.054260772 0.989213643 0.023694713 0.144335001 1.03573775 193.620524 0.094438813 0.039151372 27.50086907 -1.439346418 -0.065047129 DEMEEWSASEANLFEEALEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEMEEWSASEANLFEEALEK 20 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;Q13330-2 E7ESY4 MTA1 Metastasis-associated protein MTA1 0 194.49 3.52E-18 5787200 11078 9223.4 10244 10365 9810.6 12206 9066.3 11404 15436 12163 FALSE TRUE 10645.05951 8960.357663 12095.31868 10899.93889 10126.16686 12452.81368 9177.256091 11168.50341 13683.76999 11339.18918 0.938784894 0.790211498 1.066682854 0.961262637 0.893023893 1.098210241 0.809339711 0.984947269 1.206767943 1 13.46902986 1.440359126 10.90920474 1.101237702 0.938455408 0.292589355 0.102265161 0.392447329 109.5338898 0.056022348 0.023911075 27.56507166 -1.440359126 -0.162782294 DDS(ph)HS(ph)AEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 DDS(1)HS(1)AEDS(1)EDEKEDHK;DDS(1)HS(1)AEDS(1)EDEKEDHK 135.64 5.84E-05 1145640000 881890 522410 586220 475050 595510 455130 703770 694800 1200180 792750 TRUE FALSE 847424.7638 507511.3783 692162.9944 499567.3874 614665.12 464333.0404 712382.9478 680452.1372 1063940.598 739056.3364 1.146630808 0.686701884 0.936549706 0.675953054 0.831689128 0.628278275 0.963908856 0.920704016 1.439593365 1 19.49532482 1.440507326 3.890321757 1.219579285 0.827383584 0.405391684 0.178647452 0.183485974 5.076982828 0.117766924 0.042421954 27.57447969 -1.440507326 -0.392195701 VLAPILPDNFS(ph)TPTGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 VLAPILPDNFS(0.488)T(0.488)PT(0.012)GS(0.012)R 96.673 0.0023743 21598000 29731 30057 27404 27828 27601 26745 30637 28054 23520 28747 TRUE FALSE 28569.07965 29199.80379 32356.5124 29264.20641 28488.81123 27285.80222 31011.94477 27474.6751 20850.1082 26799.94008 1.066012818 1.089547353 1.207335251 1.091950442 1.063017721 1.018129225 1.157164705 1.025176736 0.777990851 1 14.70994215 1.441644427 5.617568199 0.88896024 1.097130853 0.584307653 0.070068938 0.117525133 7.4475007 0.043419009 0.0169641 27.64677173 -1.441644427 0.208170613 FKMPDVHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKMPDVHFK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 75.294 0.023234 326200000 1197800 1225900 1005000 1079100 1053900 1173700 1123200 1204300 1461700 1243300 FALSE TRUE 1150988.652 1190938.532 1186625.856 1134792.48 1087799.651 1197433.018 1136946.058 1179430.784 1295773.944 1159090.184 0.993010439 1.027477024 1.023756281 0.979037262 0.938494404 1.033080113 0.980895252 1.017548764 1.117923318 1 20.14456139 1.44168008 8.115662306 1.062173217 0.997835887 0.303032681 0.037360326 0.208492995 33.74058594 0.021567524 0.008935736 27.6490415 -1.44168008 -0.064337329 (ac)MELDLS(ph)PPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLS(1)PPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 116.84 8.57E-28 161880000 71111 101250 78697 105480 78550 101060 88602 90971 89733 88018 TRUE FALSE 68331.9035 98362.44913 92919.29851 110923.8354 81076.63209 103103.5024 89686.33778 89092.41706 79546.88603 82056.46246 0.832742498 1.198716666 1.132382456 1.351798897 0.988059071 1.256494606 1.092983235 1.085745283 0.969416468 1 16.32432934 1.442084827 2.330141346 0.983769966 1.134296037 0.132502489 0.134685231 0.526501445 5.300854983 0.106934133 0.034362568 27.67482144 -1.442084827 0.15052607 DGDDVIIIGVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGDDVIIIGVFK 12 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 187.97 2.28E-05 128904000 396880 377640 418960 450010 419650 375100 449650 483270 603810 584290 FALSE TRUE 381369.4908 366870.0769 494675.3917 473235.07 433148.4234 382684.779 455152.9512 473290.3056 535268.0202 544715.5179 0.700125989 0.673507666 0.908135303 0.868774717 0.795182823 0.702540622 0.83557919 0.86887612 0.982656089 1 19.05514344 1.442264767 1.711778994 1.002959111 0.782150724 0.580181142 0.070990965 0.269188213 1.476074701 0.067355482 0.02149681 27.68629023 -1.442264767 -0.220808387 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR 32 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 147.54 3.61E-10 184060000 47060 49287 27725 34969 40965 55885 42864 42135 40896 41166 FALSE TRUE 45220.84317 47881.38302 32735.52424 36773.75428 42282.67643 57015.03299 43388.58245 41264.89753 36253.65753 38377.79015 1.178307636 1.247632624 0.852980959 0.958204058 1.101748596 1.485625742 1.130564899 1.075228599 0.944652034 1 15.22798402 1.442351779 3.386987721 0.974488712 1.133890025 0.142964133 0.158567789 0.513027108 10.78626818 0.128330615 0.044687913 27.6918378 -1.442351779 0.159401314 NQEYETLDHLECDLNLMFENAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NQEYETLDHLECDLNLMFENAK 22 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 0 ; 215.42 1.43E-25 82190000 112709 99469 83030 88533 95098 97339 95237 103206 128480 106622 FALSE TRUE 108304.2077 96632.24151 98035.36799 93102.19874 98156.91354 99307.26127 96402.53889 101074.76 113895.489 99400.39697 1.089575203 0.972151465 0.986267369 0.936638098 0.987490156 0.999063025 0.969840582 1.016844632 1.145825293 1 16.60096399 1.442507815 7.172226314 1.07634141 0.989461622 0.29698781 0.049278961 0.186079524 22.27336068 0.028334212 0.011563243 27.70178888 -1.442507815 -0.086879788 VNPHKVS(ph)PASSVDSNIPSSQGYKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNPHKVSPASSVDSNIPSSQGYKK 24 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 VNPHKVS(0.97)PAS(0.03)SVDSNIPSSQGYKK 169.13 5.01E-12 830550000 249290 245520 172280 164620 198980 233450 200880 228090 303360 231760 TRUE FALSE 239547.4712 238518.01 203414.8283 173116.0579 205380.3724 238170.5189 203338.4295 223379.8618 268923.8446 216062.6888 1.108694299 1.103929657 0.94146208 0.801230693 0.950559181 1.102321369 0.941108484 1.033865972 1.244656568 1 17.72109043 1.442624455 8.49726331 1.128514408 0.990909999 0.189721503 0.105647329 0.30423012 55.70137694 0.065121248 0.027254866 27.70922985 -1.442624455 -0.137604409 AS(ph)DPGLPAEEPK ddPTM_BT-474_Pertuzumab_2h_R1 6 ASDPGLPAEEPK 12 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK 210.41 4.61E-08 5704310000 3927080 3261250 3898880 3959090 3505000 3610420 4575990 5100750 6098690 6742810 TRUE FALSE 3773605.372 3168242.343 4603494.346 4163419.109 3617741.508 3683425.166 4631992.334 4995417.73 5406392.279 6286113.473 0.600308185 0.504006547 0.732327593 0.662320069 0.575513236 0.585962246 0.736861076 0.79467508 0.860053243 1 22.58373688 1.442936075 0.912576003 0.991242877 0.607018913 0.822534595 0.060314228 0.210421515 0.357897827 0.057660645 0.021788059 27.72911922 -1.442936075 -0.384223965 FESPATGILS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 FESPATGILSPR 12 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR 187.63 1.07E-05 2097987000 1196468 1290065 1054750 1367396 1334019 1261823 1286638 1254820 1149821 1253729 TRUE FALSE 1149708.708 1253273.609 1245366.788 1437967.471 1376928.933 1287337.926 1302384.261 1228907.528 1019298.141 1168812.818 0.983655116 1.072262034 1.065497202 1.230280374 1.178057694 1.101406406 1.114279584 1.051415171 0.872079879 1 20.15661247 1.443093912 4.045823213 0.937531783 1.109621186 0.486437489 0.068780094 0.177688125 5.37198497 0.050668812 0.018493726 27.73919875 -1.443093912 0.172089403 EYFGEFGEIEAIELPMDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EYFGEFGEIEAIELPMDPK 19 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 131.48 1.55E-05 39368000 243480 217300 196204 209368 227240 228860 230760 262400 305040 307590 FALSE TRUE 233964.5324 211102.8168 231662.4273 220173.5076 234549.381 233487.706 233584.1099 256981.3483 270413.138 286756.6553 0.815899224 0.736174079 0.807871145 0.767806094 0.817938753 0.814236398 0.814572585 0.896165245 0.943005622 1 18.12946744 1.443295313 0.927283299 1.002123321 0.784747386 0.907277909 0.023339301 0.127367242 0.222768275 0.020002085 0.007500465 27.75206559 -1.443295313 -0.217375935 KETS(ph)PQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KETSPQVK 8 1 Q9GZR2;A0A0C4DG22 Q9GZR2 REXO4 RNA exonuclease 4 1 KET(0.149)S(0.851)PQVK 57.836 0.055545 0 304940 251730 248650 206660 245230 270720 272420 302010 424330 368920 TRUE FALSE 293022.6077 244550.9069 293586.5862 217325.7474 253118.0457 276194.1439 275753.9575 295773.388 376161.8373 343932.7198 0.851976537 0.711042866 0.85361633 0.631884479 0.735952211 0.803047015 0.801767153 0.859974556 1.093707623 1 18.39176685 1.443347428 2.592117305 1.04732934 0.765075403 0.716271869 0.068206733 0.133542067 1.661654664 0.053436328 0.017478052 27.75539601 -1.443347428 -0.282253937 SIVDYKPNLDLLEQQHQLIQEALIFDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIVDYKPNLDLLEQQHQLIQEALIFDNK 28 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 322.45 1.76E-83 1553700000 2043300 1741400 2142200 2682000 2175100 1774500 2920600 3222600 3812700 4454800 FALSE TRUE 1963445.577 1691736.977 2529343.193 2820418.341 2245064.067 1810381.606 2956343.176 3156052.184 3379898.28 4153072.428 0.472769404 0.407345888 0.609029396 0.679116098 0.540579079 0.435913805 0.71184484 0.759931891 0.813830806 1 21.9857476 1.443557334 0.791448256 0.993147268 0.520548952 0.773069176 0.084599967 0.282072673 0.375460528 0.08463774 0.034628397 27.76881415 -1.443557334 -0.472598316 LLDPS(ph)SPLALALSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDPSSPLALALSAR 15 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 LLDPS(0.623)S(0.377)PLALALSAR 83.633 0.0090617 74841000 238060 235980 226880 242290 228170 254490 243780 240730 206330 261120 TRUE FALSE 228756.352 229250.0814 267882.2629 254794.6159 235509.2953 259635.9622 246763.4526 235758.8414 182908.2834 243434.1098 0.939705418 0.941733603 1.100430269 1.046667684 0.967445751 1.066555391 1.013676566 0.968470859 0.751366699 1 17.89317181 1.443594989 6.363219616 0.869223152 1.011205588 0.338591244 0.074370502 0.174351324 15.38579206 0.044589559 0.017899628 27.77122195 -1.443594989 0.141982436 TASTPT(ph)PPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 TAS(0.001)T(0.04)PT(0.959)PPQTGGGLEPQANGETPQVAVIVRPDDR 165.49 3.98E-14 1061400000 80229 73920 67989 66714 67275 70369 83777 88407 99843 108790 TRUE FALSE 77093.56198 71811.87398 80276.12471 70157.11754 69438.96147 71791.90939 84802.28799 86581.36456 88509.24122 101421.5564 0.760129944 0.708053362 0.791509493 0.691737733 0.684656832 0.707856514 0.836136725 0.853678129 0.872686679 1 16.63000479 1.444208333 0.873244073 0.985505151 0.722136252 0.830053102 0.039589884 0.209787979 0.330331456 0.038022488 0.014700568 27.81047027 -1.444208333 -0.263368899 EEGLGFPSFLDPDRHFLSAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEGLGFPSFLDPDRHFLSAFR 21 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 62.663 0.023583 114550000 126900 186680 123910 124950 161690 181820 150080 140250 111550 119150 FALSE TRUE 121940.6077 181356.0692 146303.2934 131398.6845 166890.9057 185496.525 151916.7239 137353.7885 98887.31166 111079.8644 1.097774186 1.632663761 1.317100036 1.182920822 1.502440669 1.669938346 1.367635123 1.236531835 0.890236158 1 16.7612378 1.44442554 2.779568132 0.945673428 1.407122848 0.515614961 0.171731745 0.201443004 2.880462807 0.13573082 0.045081656 27.82438283 -1.44442554 0.461449421 VIEPLKDFHKDEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIEPLKDFHKDEVR 14 2 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 242.26 1.07E-17 4209900000 4475300 4298600 3379900 3434800 3975900 4062100 4041300 4337600 5276700 4850900 FALSE TRUE 4300400.328 4176008.137 3990723.115 3612070.44 4103788.434 4144238.445 4090758.638 4248027.044 4677711.138 4522344.222 0.950922822 0.923416691 0.882445678 0.798716387 0.907447163 0.916391641 0.904565959 0.939341818 1.034355394 1 22.10863938 1.444662764 2.613346396 1.017629303 0.895233375 0.59401504 0.038765983 0.19236805 2.43727696 0.033501792 0.0109876 27.83958546 -1.444662764 -0.122395928 MQAS(ph)IEK ddPTM_BT-474_Pertuzumab_2h_R1 4 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK 121.6 0.0046385 10253400000 6353500 5336110 5903740 4668510 4979900 5440750 5662260 5950400 6519910 6457420 TRUE FALSE 6105198.196 5183929.367 6970677.146 4909452.361 5140083.006 5550765.693 5731556.432 5827522.161 5779797.15 6020053.192 1.014143563 0.861110226 1.157909561 0.815516442 0.853826842 0.922045955 0.952077374 0.968018384 0.960090711 1 22.5213448 1.444876149 1.40281403 0.988668975 0.935908847 0.03647239 0.091181225 1.54036673 5.755269304 0.080509295 0.026411515 27.85326746 -1.444876149 -0.052760128 SQDSYPGSPSLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQDSYPGSPSLSPR 14 0 A0A0D9SEU5;Q6VN20;R4GMX8;Q6VN20-2;Q6VN20-3 A0A0D9SEU5 RANBP10 Ran-binding protein 10 1 SQDSYPGSPSLS(1)PR;SQDSYPGSPS(0.01)LS(0.99)PR 231.83 2.24E-09 0 245590 296250 231258 295690 282350 291750 286750 274986 243364 280570 TRUE FALSE 235992.0713 287801.2401 273051.4649 310950.5963 291432.0442 297649.3849 290259.3323 269307.443 215738.339 261566.744 0.90222506 1.100297521 1.04390742 1.188800195 1.114178507 1.137948121 1.109695093 1.02959359 0.824792692 1 17.9968196 1.444915139 4.800898726 0.912567704 1.089925388 0.410842234 0.081407643 0.172138159 7.619246325 0.052986398 0.020185294 27.85576813 -1.444915139 0.177357683 TSS(ph)PHKEESPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.096)S(0.088)S(0.816)PHKEESPK;T(0.012)S(0.474)S(0.514)PHKEESPK 175.29 6.05E-06 942050000 1249210 1018410 844670 788380 982380 875100 972370 1096060 1661320 1146810 TRUE FALSE 1200389.492 989365.9439 997320.6586 829068.3863 1013979.145 892795.1216 984270.1549 1073425.978 1472733.918 1069135.537 1.122766432 0.925388699 0.932829023 0.775456766 0.94841029 0.835062619 0.920622429 1.004013 1.377499734 1 20.02801333 1.44492431 5.282660774 1.194087255 0.919040558 0.433194166 0.119457648 0.151071424 8.382750769 0.073654475 0.028633761 27.85635639 -1.44492431 -0.275046697 ATPELGSSENSASS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATPELGSSENSASSPPR 17 0 Q9BX63 Q9BX63 BRIP1 Fanconi anemia group J protein 1 ATPELGSSENSAS(0.003)S(0.997)PPR;ATPELGSSENSAS(0.003)S(0.997)PPR 261.02 2.99E-27 796110000 878230 989430 729410 1052760 883020 891590 995210 910070 767110 971440 TRUE FALSE 843907.8007 961212.4252 861230.6126 1107093.07 911423.1402 909618.5607 1007389.678 891276.7365 680030.8888 905643.5035 0.931832225 1.061358494 0.950959853 1.22243804 1.006381801 1.004389207 1.112346827 0.984136399 0.75088143 1 19.78858374 1.445479927 7.209431561 0.871439725 1.042514915 0.318831532 0.095975443 0.176729355 22.12253083 0.054405575 0.022442266 27.89201739 -1.445479927 0.171075189 LPS(ph)SPLGCR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSSPLGCR 9 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 LPS(0.564)S(0.436)PLGCR 104.42 0.0034222 700100000 263680 319150 238410 343230 340920 323930 324440 302630 244710 313310 TRUE FALSE 253375.0941 310048.1545 281495.9904 360944.1414 351886.0014 330480.0865 328410.5938 296380.5847 216931.5467 292089.2346 0.867457832 1.061484361 0.96373285 1.235732436 1.204720886 1.131435354 1.124350215 1.014691915 0.742689291 1 18.15604966 1.445721964 5.351897686 0.869551935 1.089078554 0.338822081 0.117077606 0.197374488 11.35109373 0.077152802 0.030122984 27.90756621 -1.445721964 0.219526619 KKEPELFQTVAEGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKEPELFQTVAEGLR 15 2 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 ; 209.66 1.28E-09 931120000 1139490 1100630 941780 1001510 1021570 1160710 1146720 1224600 1384420 1435360 FALSE TRUE 1094957.471 1069241.11 1111980.596 1053198.051 1054429.727 1184180.351 1160753.902 1199311.582 1227266.446 1338141.789 0.818267152 0.799049188 0.830988618 0.787060131 0.787980568 0.884943854 0.867437152 0.896251498 0.917142306 1 20.35179956 1.445737033 0.534087765 0.999442249 0.799894109 0.884691808 0.021914909 0.248670335 0.177271841 0.022981651 0.012885128 27.90853456 -1.445737033 -0.19954814 DRT(ph)PPHLLYSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRTPPHLLYSDR 12 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 DRT(1)PPHLLYSDR;DRT(1)PPHLLYSDR 120.59 0.00063606 1379120000 347420 310000 301160 311080 318920 267050 339970 337270 417530 379400 TRUE FALSE 333842.4423 301159.1035 355586.3113 327134.8761 329178.3514 272449.934 344130.6546 330305.2566 370133.7448 353702.9001 0.943849887 0.85144652 1.00532484 0.924886044 0.930663422 0.77027905 0.972937045 0.933849444 1.046453803 1 18.43217852 1.446588137 2.274257082 1.021698612 0.910494339 0.307522778 0.062968421 0.348842484 3.366601629 0.051726581 0.016632294 27.96328167 -1.446588137 -0.111204273 RAGELTEDEVER ddPTM_BT-474_Pertuzumab_2h_R1 4 RAGELTEDEVER 12 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;; 200.81 2.50E-07 4566700000 2612250 2996400 2049150 2499430 2561870 2904980 2547630 2642550 2644140 2605890 FALSE TRUE 2510160.382 2910945.606 2419476.988 2628425.882 2644274.875 2963720.686 2578808.658 2587980.419 2343988.312 2429390.749 1.033246868 1.198220421 0.99591924 1.081928003 1.088451858 1.219944007 1.061504272 1.065279606 0.96484615 1 21.21216312 1.446941898 2.446862654 0.982791435 1.100801581 0.319761469 0.065092908 0.318788091 3.558526045 0.051975109 0.01688287 27.98606886 -1.446941898 0.118010147 AESGDSLGSEDRDLLYSIDAYR ddPTM_BT-474_Pertuzumab_2h_R1 2 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 ; 318.69 1.56E-67 1730500000 885790 1046890 748600 1005800 921510 943690 984330 916840 785460 931830 FALSE TRUE 851172.3475 1017033.722 883888.6725 1057709.459 951151.206 962772.0584 996376.525 897906.9336 696297.8737 868716.3241 0.979804712 1.170731681 1.017465251 1.217554487 1.094892751 1.10826979 1.14695269 1.033602004 0.801525025 1 19.72852562 1.447054505 4.967276226 0.901199273 1.10698516 0.510885366 0.078955612 0.130918935 6.329969206 0.047308144 0.018227154 27.99332618 -1.447054505 0.205785887 NSVHEQEAINS(ph)DPELSNCENFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSVHEQEAINSDPELSNCENFQK 23 0 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 NSVHEQEAINS(1)DPELSNCENFQK 203.19 1.25E-24 260700000 148000 163360 100720 135370 136730 147220 150920 160780 199840 196760 TRUE FALSE 142215.9964 158701.1327 118922.3445 142356.4619 141128.0446 150196.8893 152767.0041 157459.8368 177155.001 183433.2699 0.775300993 0.86517093 0.648313932 0.776066752 0.769369944 0.818809419 0.83282059 0.858403914 0.965773554 1 17.4848958 1.447132123 0.892638058 1.006189374 0.767686885 0.715313461 0.051201762 0.279624307 0.456981066 0.046721601 0.017873203 27.99832965 -1.447132123 -0.238502489 RPLQEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPLQEDR 7 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 0 ;; 114.5 0.0094467 206836000 187892 202723 160929 207014 190587 161184 199765 186420 167601 194219 FALSE TRUE 180548.9729 196941.5385 190012.4501 217698.0173 196717.4039 164443.2509 202209.7838 182570.3619 148575.6371 181064.3741 0.997153492 1.087687953 1.049419308 1.202323861 1.086450081 0.908203238 1.116783933 1.008317416 0.820568032 1 17.46614319 1.447465159 5.933250541 0.909280877 1.064010577 0.352286467 0.082550745 0.181645106 13.69869447 0.051281587 0.020524652 28.01980829 -1.447465159 0.1547297 SKFDS(ph)DEEEEDTENVEAASSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SKFDSDEEEEDTENVEAASSGK 22 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.084)KFDS(0.916)DEEEEDTENVEAASSGK;S(0.043)KFDS(0.957)DEEEEDTENVEAASSGK;S(0.297)KFDS(0.703)DEEEEDTENVEAASSGK 303.37 3.46E-56 1677490000 1168250 916860 948910 795230 896670 993420 999800 1111210 1387480 1324770 TRUE FALSE 1122593.498 890712.0505 1120399.145 836271.9156 925512.2049 1013507.633 1012035.851 1088263.125 1229979.087 1235042.148 0.908951569 0.721199719 0.907174826 0.677120143 0.74937702 0.820625948 0.819434262 0.881154645 0.995900496 1 20.23612885 1.447544831 1.686450508 1.009134345 0.792347194 0.560614088 0.069478718 0.238558613 1.274138866 0.058042727 0.01859679 28.02494899 -1.447544831 -0.216787151 SGLS(ph)LEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 S(0.131)GLS(0.869)LEELR;S(0.199)GLS(0.801)LEELR;S(0.003)GLS(0.997)LEELR;S(0.001)GLS(0.999)LEELR 119.27 0.00089554 469370000 1079670 1396180 1057680 1350630 1297070 1380460 1242260 1264710 1137850 1234850 TRUE FALSE 1037475.303 1356362.313 1248826.304 1420336.176 1338791.435 1408373.847 1257463.149 1238593.297 1008686.038 1151212.51 0.901202249 1.178203244 1.084792159 1.233774098 1.162940311 1.223383029 1.092294549 1.075903264 0.876194473 1 20.13472274 1.447869395 3.166963187 0.940014719 1.13403566 0.372673928 0.093963383 0.231443882 4.30775923 0.068944332 0.023727657 28.0459009 -1.447869395 0.194020941 QIGLDQIWDDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QIGLDQIWDDLR 12 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJ59;A0A590UJ97 A0A590UJ56 CUL1 Cullin-1 0 77.379 0.034037 0 19053 24075 21841 26076 25781 27940 25746 23602 18376 23347 FALSE TRUE 18308.3877 23388.40457 25788.15455 27421.78548 26610.26928 28504.96594 26061.08725 23114.61045 16290.03352 21765.68689 0.841158277 1.074553938 1.184807752 1.259863087 1.222578888 1.309628595 1.197347337 1.061974775 0.748427265 1 14.40976793 1.447944112 4.534681429 0.875737491 1.164062336 0.404367433 0.134318864 0.19040179 7.4886134 0.094262686 0.035622831 28.05072636 -1.447944112 0.288324845 KKWNLDELPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKWNLDELPK 10 2 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 79.659 0.014816 784190000 1591300 1426500 1118100 968250 1276800 1163600 1250900 1454800 1761900 1708300 FALSE TRUE 1529110.237 1385817.617 1320165.542 1018221.499 1317869.432 1187128.789 1266208.888 1424757.872 1561896.498 1592595.319 0.960137342 0.87016306 0.828939735 0.639347288 0.827497994 0.745405173 0.795060034 0.894613876 0.980724029 1 20.60294829 1.448246324 2.371464266 0.995325245 0.804326956 0.462263579 0.078028424 0.26164832 2.749863839 0.068031163 0.022019006 28.07025279 -1.448246324 -0.19099829 IAQVS(ph)PGPR ddPTM_BT-474_Pertuzumab_2h_R1 6 IAQVSPGPR 9 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 IAQVS(1)PGPR;IAQVS(1)PGPR;IAQVS(1)PGPR;IAQVS(1)PGPR;IAQVS(1)PGPR;IAQVS(1)PGPR 162.1 6.72E-05 7018900000 5166050 5772020 4593750 6096810 5568960 5114510 5211130 5085960 3704900 4538120 TRUE FALSE 4964155.055 5607407.641 5423942.812 6411467.095 5748090.656 5217928.896 5274905.368 4980933.149 3284335.284 4230749.09 1.173351326 1.32539357 1.28202895 1.515444891 1.358646077 1.23333452 1.24680175 1.177317076 0.776301126 1 22.0124817 1.448493879 2.960913486 0.891052477 1.311426682 0.714169689 0.102892235 0.128412004 2.094587926 0.080851346 0.027366424 28.08625785 -1.448493879 0.420374206 ELQEESGLTVDALHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELQEESGLTVDALHK 15 0 P36639-4;P36639-3;P36639-2;P36639 P36639-4 NUDT1 "7,8-dihydro-8-oxoguanine triphosphatase" 0 166.92 1.34E-06 212590000 195390 214510 191540 187260 203900 179490 223700 207850 191700 226130 FALSE TRUE 187753.9428 208392.3848 226155.5388 196924.511 210458.6287 183119.4108 226437.7075 203557.8249 169939.0197 210814.0137 0.890614146 0.988512961 1.072772795 0.934114899 0.998314225 0.868630162 1.074111268 0.96558014 0.806108743 1 17.68561125 1.448790605 25 0.897317529 0.978955695 0.119028664 0.076923148 30.3970053 26828.0291 0.039015669 0.01802865 28.10545402 -1.448790605 0.081638166 LCDDGPQLPTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 LCDDGPQLPTSPR 13 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 LCDDGPQLPTS(1)PR;LCDDGPQLPT(0.001)S(0.999)PR;LCDDGPQLPTS(1)PR;LCDDGPQLPTS(1)PR 278.62 2.70E-32 4779700000 4743920 5275420 4274610 5649100 5543100 5116960 4907400 5084990 4698050 4686590 TRUE FALSE 4558522.362 5124970.187 5047127.115 5940650.728 5721398.846 5220428.437 4967458.229 4979983.18 4164747.06 4369163.085 1.043339942 1.1729867 1.155170228 1.359677039 1.309495373 1.194834877 1.136935869 1.139802539 0.953213917 1 22.05892553 1.449071633 1.756797525 0.972523614 1.208560737 0.500276897 0.085042589 0.292333036 1.693682248 0.079478757 0.025415827 28.12364666 -1.449071633 0.236037123 QTIDNSQGAYQEAFDISKK ddPTM_BT-474_Pertuzumab_2h_R1 2 QTIDNSQGAYQEAFDISKK 19 1 P27348 P27348 YWHAQ 14-3-3 protein theta 0 ; 312.74 2.27E-61 516610000 690760 580510 510980 472160 552050 710970 521110 656710 821220 740950 FALSE TRUE 663764.3355 563954.4232 603325.4527 496528.2342 569807.1896 725346.3005 527487.5001 643148.709 727998.5484 690764.7965 0.960912222 0.81642033 0.873416618 0.718809408 0.824893209 1.050062632 0.763628232 0.931067582 1.053902214 1 19.39783504 1.449600867 4.733887635 1.021801442 0.857295705 0.359235509 0.08972351 0.206033362 8.992759642 0.059015868 0.0225925 28.15793922 -1.449600867 -0.164505737 GFAVSER ddPTM_BT-474_Pertuzumab_2h_R1 1 GFAVSER 7 0 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 143.37 0.020113 0 357100 405710 340530 436540 389010 391670 395990 396800 400510 400470 FALSE TRUE 343144.1372 394139.548 402071.346 459069.8817 401522.8599 399589.8358 400836.2441 388605.9413 355045.7839 373345.8102 0.919105365 1.055695651 1.076940828 1.229610375 1.075471718 1.070294148 1.07363263 1.040873985 0.95098371 1 18.51015302 1.449705115 3.262475397 0.976363706 1.07690983 0.217766506 0.070839558 0.353112381 6.998820459 0.055110924 0.019155925 28.16469906 -1.449705115 0.100546124 AES(ph)KPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AESKPR 6 1 E9PD25;O43897 E9PD25 TLL1 Metalloendopeptidase;Tolloid-like protein 1 1 AES(1)KPR;AES(1)KPR 98.392 0.024216 137555000 303917 319164 263235 334436 348630 366550 338070 313130 262680 302230 TRUE FALSE 292039.5876 310061.7552 310807.4201 351696.282 359844.0006 373961.8921 342207.4018 306663.7561 232861.6676 281759.6929 1.036484618 1.10044752 1.103093977 1.248213605 1.277130866 1.327237009 1.214536395 1.088387601 0.82645486 1 18.10410572 1.449879745 3.976200509 0.916413762 1.189766831 0.575299592 0.092662915 0.157435088 4.679228656 0.071253209 0.026130283 28.17602638 -1.449879745 0.273353069 AS(ph)GQAFELILS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 AS(1)GQAFELILS(1)PR;AS(1)GQAFELILS(1)PR;AS(1)GQAFELILS(1)PR 161.51 6.15E-05 454691000 223782 232079 240872 233249 237366 270615 247347 243239 220734 252094 TRUE FALSE 215036.352 225460.3341 284402.9286 245287.0088 245001.093 276087.0207 250374.1066 238216.0296 195677.2017 235019.4488 0.914972582 0.959326282 1.210125077 1.043688129 1.042471566 1.174741163 1.065333562 1.013601346 0.832600037 1 17.84242063 1.450076681 4.760999199 0.91526017 1.06235606 0.275887112 0.090521874 0.236570214 10.48218889 0.060730221 0.023299274 28.188806 -1.450076681 0.147095891 EDLAAATPAS(ph)PLVLLPLETR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDLAAATPASPLVLLPLETR 20 0 A0A1B0GTL5 A0A1B0GTL5 1 EDLAAAT(0.004)PAS(0.996)PLVLLPLETR 95.767 0.001237 7440200 6246.2 8256.9 9216 13784 12499 10840 9482 10386 9015.1 9417.8 TRUE FALSE 6002.091598 8021.421296 10881.53621 14495.39389 12901.04169 11059.19223 9598.043552 10171.52547 7991.743642 8779.924017 0.683615438 0.913609421 1.239365647 1.650970312 1.469379651 1.259599993 1.093180708 1.15849812 0.910229249 1 13.09999274 1.450426946 1.917469136 0.956632616 1.214030578 0.103216466 0.255542746 0.786043706 5.423012791 0.245787856 0.078480195 28.21154987 -1.450426946 0.257397962 NQYVTLHDMILK ddPTM_BT-474_Pertuzumab_2h_R1 1 NQYVTLHDMILK 12 0 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 119.56 0.00050435 909730000 812620 801730 674550 708250 679550 793150 801950 803670 986360 926710 FALSE TRUE 780861.912 778865.4454 796456.1903 744802.8674 701408.3429 809188.0364 811764.504 787073.9337 874392.548 863943.1063 0.903834878 0.901524001 0.921885 0.862097124 0.811868673 0.936621903 0.939604122 0.911025191 1.012095058 1 19.72057678 1.450444341 1.081124382 1.008480892 0.8878462 0.577622965 0.036344753 0.351888838 0.808419979 0.034627215 0.012208398 28.21267986 -1.450444341 -0.120634692 RSS(ph)SSGDQSSDSLNSPTLLAL ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.114)S(0.616)S(0.206)S(0.038)GDQS(0.013)S(0.013)DSLNSPTLLAL 176.1 8.86E-13 151440000 146420 150410 116200 156800 117810 147360 143790 139090 137510 137220 TRUE FALSE 140697.7445 146120.4541 137199.9249 164892.4668 121599.4656 150339.7202 145549.745 136217.7429 121900.4413 127925.9672 1.099837255 1.14222669 1.072494724 1.288967912 0.950545603 1.175208783 1.137765445 1.064816987 0.952898336 1 16.96494962 1.450464188 3.360689047 0.978066608 1.12369853 0.343446308 0.080709948 0.244739289 5.155996094 0.055908292 0.019606677 28.21396922 -1.450464188 0.145631922 DSYGGPPRR ddPTM_BT-474_Pertuzumab_2h_R1 4 DSYGGPPRR 9 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 131.11 0.00054911 1374170000 581912 666494 463009 565351 559265 668477 571936 580999 564830 557785 FALSE TRUE 559170.2357 647486.2437 546685.0259 594528.8329 577254.2666 681994.0629 578935.5239 569001.1676 500712.8664 520005.7251 1.075315537 1.245152144 1.051305783 1.143312091 1.110092137 1.311512605 1.113325288 1.094220967 0.962898757 1 18.98816798 1.45053207 2.476540578 0.981248526 1.154133938 0.443673161 0.074072712 0.243891096 2.8027768 0.058596859 0.019129148 28.2183795 -1.45053207 0.172885411 GLNVIGAS(ph)DQSPLQS(ph)PSNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLNVIGASDQSPLQSPSNLR 20 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 2 GLNVIGAS(0.559)DQS(0.441)PLQS(0.997)PS(0.003)NLR 125.23 3.73E-05 78107000 89396 101360 90538 105230 102820 105830 101970 97167 100740 92180 TRUE FALSE 85902.30549 98469.31204 106900.2306 110660.9329 106127.2987 107969.9551 103217.9394 95160.46749 89304.41754 85936.56649 0.999601322 1.145837169 1.243943469 1.287704844 1.234949254 1.256391307 1.201094523 1.107333832 1.039189965 1 16.39098452 1.450618412 2.032885738 1.009941734 1.203399275 0.464522612 0.076098007 0.286344513 2.220145661 0.069594012 0.022251742 28.22399015 -1.450618412 0.193457541 WLDDLLAS(ph)PPPSGGGAR ddPTM_BT-474_Pertuzumab_2h_R1 9 WLDDLLASPPPSGGGAR 17 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 WLDDLLAS(0.974)PPPS(0.026)GGGAR;WLDDLLAS(0.978)PPPS(0.022)GGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(0.999)PPPS(0.001)GGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(0.987)PPPS(0.013)GGGAR;WLDDLLAS(1)PPPSGGGAR 209.31 4.60E-12 8111430000 1482987 1751865 1483937.8 2103127 2096006 2014537 1849047 1788004 1553443 1693332 TRUE FALSE 1425030.229 1701903.525 1752118.37 2211669.637 2163425.937 2055272.318 1871676.19 1751081.093 1377102.663 1578641.115 0.902694232 1.078081338 1.109890243 1.400995841 1.37043557 1.30192499 1.185624885 1.109233172 0.872334218 1 20.5902518 1.450677912 3.237045123 0.938701861 1.202984371 0.332636446 0.142035132 0.286373445 5.599322251 0.117184532 0.040689965 28.22785723 -1.450677912 0.264282509 LGAGEGGEASVS(ph)PEKTSTTSK ddPTM_BT-474_Pertuzumab_2h_R1 6 LGAGEGGEASVSPEKTSTTSK 21 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LGAGEGGEAS(0.06)VS(0.94)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEAS(0.001)VS(0.999)PEKTSTTSK;LGAGEGGEAS(0.001)VS(0.999)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK 280.75 3.32E-45 12327780000 4841530 4041320 2806810 2736661 3321920 3720760 3537220 3872720 5032370 4047730 TRUE FALSE 4652317.655 3926065.51 3314063.004 2877900.402 3428772.574 3795996.316 3580509.556 3792746.979 4461116.455 3773573.642 1.232867859 1.040410466 0.878229318 0.762645883 0.908627444 1.005942027 0.948837865 1.005080949 1.182199389 1 21.8475 1.450955785 5.383972867 1.093919813 0.960264377 0.133768982 0.121751708 0.341408824 20.4381276 0.082481462 0.0326016 28.24592395 -1.450955785 -0.133655436 ILGSAS(ph)PEEEQEKPILDRPTR ddPTM_BT-474_Pertuzumab_2h_R1 5 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 ILGS(0.001)AS(0.999)PEEEQEKPILDRPTR;ILGS(0.003)AS(0.997)PEEEQEKPILDRPTR;ILGS(0.001)AS(0.999)PEEEQEKPILDRPTR;ILGSAS(0.997)PEEEQEKPILDRPT(0.003)R;ILGS(0.001)AS(0.999)PEEEQEKPILDRPTR 272.96 5.55E-45 5422950000 2624690 2456910 2150670 2233040 2378030 2496710 2523390 2654390 3254930 3049900 TRUE FALSE 2522114.213 2386841.332 2539343.91 2348287.462 2454521.495 2547195.187 2554272.002 2599575.919 2885443.992 2843327.556 0.887029075 0.839453522 0.89308877 0.825894103 0.863256676 0.895850069 0.898338989 0.914272403 1.014812376 1 21.43914888 1.451008048 1.399503032 1.013323301 0.865691102 0.829932451 0.024055893 0.142695942 0.531191243 0.020829887 0.006853468 28.24932321 -1.451008048 -0.147632199 DQIYDIFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQIYDIFQK 9 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 129.85 0.00087862 1053040000 1014720 931500 1052580 1034340 958580 889290 1208020 1217420 1353380 1477460 FALSE TRUE 975063.6206 904934.532 1242804.621 1087722.411 989413.5963 907272.0531 1222804.11 1192279.852 1199749.976 1377390.318 0.707906544 0.656992081 0.902289354 0.789698023 0.718324779 0.658689146 0.887768771 0.865607835 0.871031225 1 20.39350601 1.451227645 0.843565841 0.984808596 0.745210927 0.523704515 0.07649513 0.460370656 0.681291672 0.073801282 0.029138299 28.26361088 -1.451227645 -0.239597669 ALVVPEPEPDS(ph)DSNQER ddPTM_BT-474_Pertuzumab_2h_R1 1 ALVVPEPEPDSDSNQER 17 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDS(1)DSNQER 170.91 1.42E-13 0 43927 44613 37950 42800 53111 44727 43422 44841 42501 43158 TRUE FALSE 42210.28428 43340.68092 44808.40919 45008.91313 54819.36355 45631.41058 43953.41142 43915.01768 37676.46466 40234.87022 1.049097065 1.077192015 1.113671026 1.118654363 1.362483916 1.134125954 1.092420857 1.091466617 0.936413227 1 15.29615876 1.451249007 2.235999678 0.968272893 1.141670879 0.379183341 0.082840092 0.321538794 3.017416645 0.073721235 0.023745472 28.26500113 -1.451249007 0.173397986 AAPEAS(ph)SPPASPLQHLLPGK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.995)S(0.005)PPASPLQHLLPGK;AAPEAS(0.872)S(0.128)PPASPLQHLLPGK;AAPEAS(0.5)S(0.5)PPASPLQHLLPGK;AAPEAS(0.891)S(0.109)PPASPLQHLLPGK 272.1 1.31E-44 1587184000 764960 893500 800052 933538 869450 834461 793216 800251 735291 656874 TRUE FALSE 735064.5175 868018.2548 944639.1935 981718.0081 897416.6489 851334.3732 802923.6147 783725.5372 651823.8483 612383.3389 1.200333959 1.417442637 1.542561878 1.603110251 1.465449159 1.390198458 1.311145428 1.279795656 1.064404935 1 19.22407551 1.451260621 1.062621438 0.991833994 1.452148617 0.700286417 0.102193977 0.265947965 0.591990529 0.098525507 0.034963478 28.26575698 -1.451260621 0.460314624 ERS(ph)PSPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERSPSPLR 8 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 ERS(0.752)PS(0.248)PLR;ERS(0.976)PS(0.024)PLR 62.166 0.049271 494580000 139459 178166 164889 243310 206930 178371 218040 184423 141611 192824 TRUE FALSE 134008.7881 173084.8801 194688.1102 255867.2583 213586.0914 181977.7838 220708.4387 180614.6006 125535.913 179763.8587 0.745471248 0.962845821 1.083021424 1.423352058 1.188148123 1.012315741 1.227768698 1.004732552 0.698337885 1 17.45574347 1.451355828 6.662076048 0.847283555 1.1003213 0.219606859 0.180776708 0.237954951 25.18394062 0.114224638 0.047283697 28.27195415 -1.451355828 0.253037745 YDDMAAAMK ddPTM_BT-474_Pertuzumab_2h_R1 2 YDDMAAAMK 9 0 P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;P61981 P31946-2;P61981 YWHAB;YWHAG "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 122.52 0.0013577 3219600000 8362500 7391200 6849700 6162500 6921200 6081400 8050400 8507400 11344600 10893200 FALSE TRUE 8035684.255 7180410.213 8087593.161 6480547.364 7143826.684 6204370.075 8148923.203 8331719.217 10056808.57 10155393.86 0.791272536 0.707053839 0.796383998 0.638138456 0.703451464 0.610943323 0.802423157 0.820423051 0.990292322 1 23.27574286 1.451577186 1.670817322 1.008243917 0.711337414 0.769792292 0.059672161 0.156526081 0.822557354 0.051841352 0.016657282 28.28636792 -1.451577186 -0.296906503 DGRHPQGEQMYR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGRHPQGEQMYR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 119.25 0.00032295 484255000 141897.1 183990.4 107755.1 143177.9 143423 147059 152293 143744.5 133546.7 144552 FALSE TRUE 136351.6045 178743.1739 127228.8436 150567.3286 148036.331 150032.6337 154156.8073 140776.1258 118387.0385 134761.3643 1.011800416 1.326368094 0.944104746 1.117288545 1.098507216 1.113320829 1.143924359 1.044632685 0.878493915 1 17.04004741 1.451822231 4.438708504 0.941063739 1.109387612 0.32356756 0.096449612 0.209772035 7.968932212 0.060526976 0.022896071 28.30233264 -1.451822231 0.168323873 TLGEIPTYGLAGNREEQEELMDFER ddPTM_BT-474_Pertuzumab_2h_R1 2 TLGEIPTYGLAGNREEQEELMDFER 25 1 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 85.777 5.00E-05 164620000 38228 36518 32010 34121.4 38866 38253 37961 34059 34629 30966 FALSE TRUE 36734.0075 35476.54239 37794.91906 35882.40954 40116.16019 39026.50187 38425.57807 33355.66975 30698.0611 28868.64524 1.272453459 1.228895298 1.309203073 1.242954397 1.389610072 1.35186468 1.331048886 1.155428995 1.06337034 1 14.81721579 1.45205086 2.210632126 1.019713425 1.303954172 0.841068932 0.047973258 0.117056847 1.074782405 0.043737793 0.014080175 28.31723596 -1.45205086 0.284240748 VQIS(ph)PDSGGLPER ddPTM_BT-474_Pertuzumab_2h_R1 3 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 VQIS(0.982)PDS(0.018)GGLPER;VQIS(0.922)PDS(0.078)GGLPER;VQIS(0.968)PDS(0.032)GGLPER 212.43 1.46E-08 3877900000 2141990 2274960 1708730 2196590 2145600 2256910 2017530 2180040 2188180 2120670 TRUE FALSE 2058278.663 2210080.368 2017535.521 2309956.273 2214615.173 2302546.267 2042221.136 2135021.412 1939786.98 1977035.132 1.04109362 1.117876123 1.020485417 1.168394145 1.120169863 1.164646105 1.032971596 1.07991071 0.98115959 1 20.91490708 1.452258688 1.593681209 0.989889681 1.102140205 0.400604255 0.049528842 0.351841682 1.685480211 0.042706954 0.013789815 28.33079023 -1.452258688 0.112250524 ISKPGAVS(ph)TPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISKPGAVSTPVK 12 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ISKPGAVS(0.662)T(0.338)PVK 79.771 0.013406 1460300000 1717500 1478700 1609300 1462700 1495400 1522900 1837000 2194500 2423000 2800800 TRUE FALSE 1650378.201 1436528.924 1900136.309 1538190.122 1543500.899 1553694.081 1859481.756 2149182.808 2147951.198 2611099.321 0.632062591 0.550162497 0.727715064 0.589096749 0.591130673 0.595034463 0.712145164 0.823095005 0.822623322 1 21.31622591 1.452561959 0.930758584 0.981304321 0.609514221 0.853596576 0.051782825 0.176143053 0.309214856 0.047452889 0.017810679 28.35058068 -1.452561959 -0.3717901 LSAIYGGTYMLNKPIEEIIVQNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSAIYGGTYMLNKPIEEIIVQNGK 24 1 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 256.53 6.55E-44 415680000 416220 398820 329250 341950 385480 361870 384700 427760 513210 495270 FALSE TRUE 399953.6622 387446.0441 388752.7991 359598.0805 397879.3143 369187.2593 389408.0737 418926.6065 454952.5524 461724.9218 0.866216319 0.839127424 0.841957583 0.778814536 0.861723714 0.799582699 0.843376771 0.907307764 0.985332459 1 18.81667408 1.452564515 1.948753861 1.000276856 0.830241391 0.868649481 0.024936974 0.100539039 0.717727322 0.020965327 0.006704202 28.35074758 -1.452564515 -0.170035465 MQSINEDLKDILHAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 MQSINEDLKDILHAAK 16 1 Q8N3C0;Q8N3C0-4;E5RFZ0;Q8N3C0-3 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 0 ; 124.29 5.01E-05 118853000 328250 326710 277800 243540 309610 341210 327780 339680 452070 420480 FALSE TRUE 315421.6271 317392.5507 328004.6396 256109.1286 319568.8868 348109.5 331791.4697 332665.4893 400752.9088 392000.5151 0.804645951 0.80967381 0.83674543 0.653338755 0.815225681 0.888033272 0.846405698 0.848635337 1.022327506 1 18.58049602 1.45288658 0.915276626 1.017810284 0.790423308 0.633354989 0.059740213 0.347936134 0.592975929 0.056558791 0.021402831 28.37177975 -1.45288658 -0.227386976 IILDLISES(ph)PIKGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IILDLISESPIKGR 14 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLISES(1)PIKGR;IILDLISES(1)PIKGR 286.57 4.98E-34 3170400000 1124530 1122100 878400 857510 953430 1132360 929290 1063500 1343010 1089240 TRUE FALSE 1080582.124 1090098.807 1037146.42 901766.1939 984097.9418 1155257.095 940662.929 1041538.353 1190557.135 1015464.805 1.064125629 1.073497379 1.02135142 0.888032938 0.969110832 1.137663354 0.926337304 1.025676467 1.172425799 1 19.95370881 1.453046278 25 1.090492497 1.009456714 0.122527088 0.078645179 22.10104122 22955.1028 0.042205861 0.019525265 28.38221453 -1.453046278 -0.081035783 DIDDDLEGEVTEECGK ddPTM_BT-474_Pertuzumab_2h_R1 4 DIDDDLEGEVTEECGK 16 0 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5 A0A0J9YVP6 PUF60 Poly(U)-binding-splicing factor PUF60 0 ;;; 377.71 2.46E-104 889188000 997600 881080 656823 782340 796363 730888 826210 979870 1203570 1194020 FALSE TRUE 958612.6891 855952.4611 775525.527 822716.6612 821978.7391 745667.0561 836321.4051 959635.3421 1066945.779 1113147.962 0.861172748 0.768947607 0.696695815 0.73909012 0.738427206 0.669872363 0.751311985 0.862091451 0.958494123 1 20.08621394 1.453280137 2.010685797 0.991087571 0.741095282 0.794972341 0.047693865 0.136777252 1.040182677 0.042694525 0.013669768 28.39750189 -1.453280137 -0.249992289 S(ph)LESCLLDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLESCLLDLR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(1)LESCLLDLR;S(1)LESCLLDLR;S(0.999)LES(0.001)CLLDLR;S(1)LESCLLDLR;S(0.996)LES(0.004)CLLDLR;S(1)LESCLLDLR 198.81 3.04E-07 499243000 371797 380193 347152 365812 364908 361378 380750 385077 392535 422965 TRUE FALSE 357266.7622 369350.2679 409890.0888 384691.6012 376645.5972 368685.3108 385409.7324 377125.0254 347976.0724 394317.2038 0.906038993 0.936683118 1.039493293 0.975589189 0.955184287 0.934996767 0.977410391 0.956400131 0.882477531 1 18.58899713 1.453510575 23.91616428 0.933972153 0.962508838 0.025275848 0.042423467 22.81737739 23119.30856 0.022602974 0.010455303 28.41257371 -1.453510575 0.028536686 SGS(ph)IVELIAGGGSSCS(ph)PVLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.12)GS(0.88)IVELIAGGGS(0.016)S(0.139)CS(0.844)PVLS(0.001)R;S(0.091)GS(0.909)IVELIAGGGS(0.039)S(0.08)CS(0.88)PVLSR;S(0.359)GS(0.641)IVELIAGGGS(0.013)S(0.106)CS(0.881)PVLSR;S(0.397)GS(0.603)IVELIAGGGS(0.202)S(0.164)CS(0.634)PVLS(0.001)R 207.13 5.61E-22 292559000 631134 622812 479702 543843 572447 584014 561545 625789 712708 686860 TRUE FALSE 606468.5855 605050.0116 566394.8223 571910.8024 590860.2776 595823.1632 568417.3557 612866.2385 631804.3758 640338.3604 0.947106441 0.94489109 0.884524272 0.893138437 0.922731347 0.930481758 0.887682811 0.957097492 0.986672695 1 19.28847491 1.453884988 3.006311904 0.993384999 0.915724038 0.682020745 0.021350714 0.146979269 2.495854818 0.017212508 0.005881045 28.43707925 -1.453884988 -0.07766096 DLSLEEIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSLEEIQK 9 0 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN2 Stathmin;Stathmin-2 0 ; 159.37 0.00015379 862340000 1026780 893690 891950 899570 923070 953190 1052290 1075990 1199250 1251430 FALSE TRUE 986652.3024 868202.8362 1053145.206 945996.9155 952761.3849 972464.1549 1065168.24 1053770.43 1063116.168 1166669.531 0.845699897 0.744172032 0.902693675 0.810852508 0.81665061 0.833538657 0.912999107 0.90322958 0.911240192 1 20.15396453 1.454240875 0.495402443 1.000216897 0.810918731 0.659508533 0.039869222 0.489842526 0.312411581 0.040742672 0.024601679 28.46039184 -1.454240875 -0.189298166 AKWDAWNELKGTSKEDAMK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKWDAWNELKGTSKEDAMK 19 3 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 109.89 0.00010796 296930000 885740 749420 584150 509320 607830 659400 630930 771150 1025700 896260 FALSE TRUE 851124.3016 728047.2754 689718.8993 535606.0662 627381.404 672733.5198 638651.5101 755225.483 909266.8361 835555.5119 1.018632861 0.871333221 0.825461492 0.641017932 0.750855443 0.805133244 0.764343603 0.903860333 1.088218345 1 19.67237615 1.454478265 3.640010132 1.040728842 0.80557374 0.495574236 0.093049574 0.187175941 4.681783075 0.071030663 0.02558653 28.47595283 -1.454478265 -0.235155102 APQTS(ph)SSPPPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.141)S(0.356)S(0.356)S(0.147)PPPVR;APQT(0.029)S(0.355)S(0.355)S(0.26)PPPVR 130.15 0.00023236 9379000000 408310 440110 352160 479780 427200 396640 433880 434700 453450 455580 TRUE FALSE 392352.7938 427558.4937 415803.1458 504541.5033 440941.276 404660.3326 439189.9532 425723.2931 401976.257 424723.1608 0.923784785 1.00667572 0.978998049 1.18793028 1.038185144 0.952762575 1.034061699 1.002354786 0.946442987 1 18.69616326 1.454611212 5.512706301 0.972844847 1.020223068 0.061544637 0.067693227 0.507718168 32.80941867 0.044240241 0.017720526 28.48467129 -1.454611212 0.047378221 DLGTESQIFISR ddPTM_BT-474_Pertuzumab_2h_R1 3 DLGTESQIFISR 12 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;; 172.17 0.00032965 212983000 310117 381891 365693 457813 430367 399203 411966 384793 331145 372890 FALSE TRUE 297997.2848 370999.8426 431781.8599 481440.7838 444210.1454 407275.1582 417007.7631 376846.8901 293554.8079 347633.8282 0.857216015 1.067214444 1.242059388 1.384907753 1.27781047 1.171563655 1.199560369 1.084034002 0.84443683 1 18.40720895 1.454695385 3.790165614 0.924993417 1.181088352 0.33941963 0.136469043 0.24749458 6.736753466 0.103664452 0.037771687 28.49019257 -1.454695385 0.256094935 AIYHDLEQSIR ddPTM_BT-474_Pertuzumab_2h_R1 5 AIYHDLEQSIR 11 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;;;; 254.53 1.94E-20 3025960000 1943929 2129930 1819685 2264304 2144013 2010145 2226211 2084450 2046342 2113001 FALSE TRUE 1867958.106 2069186.482 2148542.558 2381165.001 2212977.125 2050791.509 2253456.036 2041405.379 1814049.835 1969885.56 0.948257169 1.050409488 1.0906941 1.208783418 1.123403902 1.041071396 1.143952766 1.036306586 0.920890975 1 20.90968039 1.454699761 4.925326563 0.962841983 1.089779155 0.355517506 0.067389471 0.202537816 9.89445739 0.045670556 0.017812713 28.49047968 -1.454699761 0.126937172 NCEEVGLFNELAS(ph)PFENEFKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NCEEVGLFNELASPFENEFKK 21 1 B8ZZU6;E9PBF9;P15336-5;P15336;E9PEK8;H7C2N6;P15336-3;P15336-7;P15336-4;C9JCI8 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 NCEEVGLFNELAS(1)PFENEFKK 122.04 1.76E-05 23965000 18903 15279 13889 12393 15514 18268 12874 17081 21929 18722 TRUE FALSE 18164.24986 14843.25788 16399.05126 13032.60422 16013.0219 18637.39148 13031.55586 16728.27138 19439.71185 17453.94226 1.040696112 0.850424371 0.939561448 0.74668542 0.917444418 1.067804121 0.746625356 0.958423669 1.113771981 1 14.09126531 1.454732596 8.923833239 1.050700447 0.898446993 0.263878495 0.102911365 0.190192629 48.07787186 0.056069162 0.024694301 28.49263377 -1.454732596 -0.152253453 EKPHAGVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKPHAGVSPR 10 1 A0A0C4DH79;A0A087WWP8;Q5VWQ0-4;Q5VWQ0 A0A0C4DH79 RSBN1 Round spermatid basic protein 1 1 EKPHAGVS(1)PR;EKPHAGVS(1)PR 115.1 0.00076769 1415150000 2885000 2850700 2668100 2773400 2740800 2718600 2973800 2904900 2965500 3089800 TRUE FALSE 2772251.01 2769400.827 3150285.022 2916535.506 2828960.321 2773571.955 3010194.254 2844912.8 2628868.872 2880525.094 0.962411685 0.961422219 1.093649567 1.012501336 0.982098829 0.962870263 1.045015806 0.987636874 0.912635296 1 21.4579004 1.454783881 14.18291174 0.954247108 1.003660538 0.148743061 0.043960908 0.674780554 421.0188466 0.023943871 0.010978352 28.4959986 -1.454783881 0.04941343 RLPDGLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLPDGLTR 8 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 99.013 0.014479 188040000 164704 177785 153421 171997 177558 184126 171103 175902 166086 185072 FALSE TRUE 158267.1856 172714.7459 181147.5875 180873.7858 183269.3143 187849.1539 173197.0097 172269.5622 147232.6136 172536.9086 0.917294664 1.00103072 1.049906301 1.048319384 1.062203536 1.088747651 1.003825854 0.998450498 0.853339814 1 17.39654549 1.45482419 4.462571243 0.924674935 1.027798316 0.321389531 0.05518998 0.209082277 8.118835684 0.037148199 0.014139194 28.49864357 -1.45482419 0.103123381 IAEIEAEMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IAEIEAEMAR 10 0 Q9Y295;F8WEE0 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 ; 101.11 0.010428 21634000 66033 76840 61155 69504 71460 63862 72034 70363 74420 71839 FALSE TRUE 63452.35736 74648.59843 72207.06889 73091.10977 73758.5758 65153.3334 72915.57364 68909.97946 65972.15359 66973.28054 0.947427942 1.114602687 1.078147409 1.091347313 1.101313467 0.972825773 1.088726326 1.028917486 0.985051845 1 16.03129802 1.454857591 4.101252107 0.994144338 1.05936255 0.189948115 0.052176856 0.317079557 10.21367143 0.034694643 0.012917711 28.50083549 -1.454857591 0.065218212 AVS(ph)PAVPFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVSPAVPFSR 10 0 I3L2J0 I3L2J0 CIC 1 AVS(1)PAVPFSR;AVS(1)PAVPFSR 156.01 1.23E-05 1833810000 2425290 2585720 1879700 2259470 2212750 2477200 1944600 2392820 2163980 2079520 TRUE FALSE 2330506.986 2511977.797 2219403.604 2376081.517 2283925.113 2527290.681 1968398.596 2343407.431 1918334.063 1938672.258 1.202114992 1.295720711 1.144805985 1.225623108 1.178087273 1.303619356 1.015333349 1.20876926 0.989509214 1 20.8866375 1.455359025 0.838948856 0.990722739 1.220759136 0.504814532 0.078210176 0.436495091 0.638991769 0.066881626 0.026520536 28.53376138 -1.455359025 0.230036397 RLPQDHADSCVVS(ph)S(ph)DDEELSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLPQDHADSCVVSSDDEELSR 21 1 D6RA71;P78317 D6RA71 RNF4 E3 ubiquitin-protein ligase RNF4 2 RLPQDHADS(0.091)CVVS(0.93)S(0.952)DDEELS(0.027)R 80.406 0.0043803 0 143840 163680 135610 153490 153950 189580 144730 156120 150510 144200 TRUE FALSE 138218.5738 159012.0067 160117.7436 161411.6373 158901.9416 193413.4375 146501.249 152896.0674 133424.7358 134433.2056 1.028157985 1.182832813 1.19105799 1.200682797 1.182014078 1.438732616 1.089769811 1.137338553 0.992498358 1 17.03653001 1.455674123 1.886364358 0.993027279 1.198892367 0.363772671 0.099414131 0.346780405 2.325727452 0.085889739 0.027514971 28.5544713 -1.455674123 0.205865088 ELCESLEEDYKDIEHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELCESLEEDYKDIEHLK 17 1 Q96BD8-2;Q96BD8 Q96BD8-2 SKA1 Spindle and kinetochore-associated protein 1 0 ; 202.34 6.41E-12 55821000 70141 53850 61361 58089 60409 56364 71988 70323 94292 89876 FALSE TRUE 67399.81218 52314.25072 72450.29767 61086.98025 62352.11035 57503.7187 72869.01068 68870.80548 83588.36746 83788.61847 0.804402954 0.624359868 0.864679464 0.729060598 0.744159666 0.686295105 0.869676718 0.821958957 0.997610045 1 16.35446667 1.455708332 1.273875962 1.011421373 0.745209793 0.648382466 0.069783735 0.238067683 0.741106852 0.058527324 0.019685884 28.55672057 -1.455708332 -0.26621158 KEDLYLKPIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEDLYLKPIQR 11 2 P13639 P13639 EEF2 Elongation factor 2 0 ; 192.05 8.78E-07 21301000000 13159100 13137600 11478200 12038700 11965000 12068800 14397100 14741800 15944700 17295000 FALSE TRUE 12644827.82 12762928.51 13552566.07 12660018.75 12349865.09 12312839.4 14573296.02 14437376.68 14134724.5 16123594.25 0.784243738 0.79156845 0.840542491 0.785185893 0.765949881 0.763653514 0.903849092 0.895419251 0.876648487 1 23.94267005 1.45587815 0.719861422 0.986953266 0.788128762 0.761688564 0.0358258 0.305782258 0.346085382 0.035706635 0.015625208 28.56788903 -1.45587815 -0.198824504 S(ph)VEDDKEGHLVCR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEDDKEGHLVCR 13 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BQG1 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 S(1)VEDDKEGHLVCR 69.805 0.028288 668690000 552590 500830 375370 417790 441100 446130 485890 540210 702910 658850 TRUE FALSE 530994.1719 486546.8188 443207.7091 439352.192 455288.3821 455151.0543 491836.4672 529054.4747 623118.6036 614225.5027 0.864493854 0.792130605 0.721571649 0.715294611 0.741239789 0.74101621 0.800742504 0.861335898 1.01447856 1 19.22840889 1.45612358 1.937017567 1.014974212 0.760656063 0.832176817 0.042549147 0.124830804 0.883212022 0.038797979 0.012434109 28.58403796 -1.45612358 -0.254318149 SSS(ph)LDMNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLDMNR 8 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.007)S(0.036)S(0.957)LDMNR 121.5 0.003427 0 388940 440610 369560 451610 438210 418190 450000 423140 385300 446670 TRUE FALSE 373739.7948 428044.2342 436347.7128 474917.6462 452305.4226 426646.0883 455507.2346 414402.0111 341562.3593 416416.643 0.897514067 1.027922974 1.047863288 1.140486708 1.086184787 1.024565409 1.093873749 0.99516198 0.820241854 1 18.6676682 1.456616452 5.907880525 0.907647115 1.048640014 0.355406816 0.072123873 0.165150187 12.92051233 0.044109151 0.018037267 28.61649584 -1.456616452 0.140992899 LLELQELVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLELQELVLR 10 0 Q08379;Q08379-2;A0A087WYC0;Q9NVV4-2 Q08379;Q9NVV4-2 GOLGA2;MTPAP "Golgin subfamily A member 2;Poly(A) RNA polymerase, mitochondrial" 0 100.48 0.0092755 61183000 88724 117460 86293 116440 105580 131360 110250 104900 77690 108780 FALSE TRUE 85256.56799 114110.1558 101888.0647 122449.4824 108976.0766 134016.1892 111599.2725 102733.7783 68870.9569 101412.2337 0.840693128 1.12521095 1.004692047 1.207442908 1.074585113 1.321499234 1.100451774 1.013031412 0.679118824 1 16.62987217 1.456619918 4.675072553 0.836505798 1.1030719 0.346456946 0.13833485 0.188839712 8.209348298 0.088231062 0.034085438 28.61672421 -1.456619918 0.266566102 QKVENLFNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QKVENLFNEK 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 170.04 4.06E-06 2264530000 3996800 3822300 3171000 3060000 3437300 3566800 3469900 3912800 4705300 4376500 FALSE TRUE 3840600.637 3713291.746 3744070.239 3217926.967 3547863.876 3638923.14 3512365.674 3831999.313 4171174.07 4080075.757 0.941306208 0.910103627 0.917647235 0.788692946 0.869558334 0.891876366 0.860857955 0.939198079 1.022327603 1 21.96016451 1.456880751 3.166346302 1.010155909 0.88172211 0.627386187 0.039337896 0.157503918 2.984091422 0.031122503 0.010815959 28.63391631 -1.456880751 -0.128433799 TVKPVENKDDDDSIADFLNS(ph)DEEEDRVSLQNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVKPVENKDDDDSIADFLNSDEEEDRVSLQNLK 33 3 Q15649-2;Q15649 Q15649-2 ZNHIT3 Zinc finger HIT domain-containing protein 3 1 TVKPVENKDDDDSIADFLNS(1)DEEEDRVSLQNLK 136.82 1.37E-08 1283900000 182620 157070 118360 86468 108910 126640 120790 147750 190100 169550 TRUE FALSE 175483.0085 152590.5174 139750.2849 90930.62384 112413.1891 129200.7476 122268.2642 144698.9109 168520.645 158066.2275 1.110186605 0.965358128 0.884124883 0.575269147 0.711177782 0.817383635 0.773525541 0.915432178 1.066139476 1 17.27016963 1.45688993 3.792819017 1.029417595 0.826067034 0.251023098 0.136062466 0.31588817 8.659596712 0.105216909 0.038455731 28.63452148 -1.45688993 -0.203350562 GSS(ph)PGPRPVEGTPASR ddPTM_BT-474_Pertuzumab_2h_R1 5 GSSPGPRPVEGTPASR 16 1 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 GS(0.042)S(0.956)PGPRPVEGT(0.001)PASR;GS(0.017)S(0.983)PGPRPVEGTPASR;GS(0.021)S(0.979)PGPRPVEGTPASR;GS(0.055)S(0.945)PGPRPVEGTPASR;GS(0.161)S(0.827)PGPRPVEGT(0.007)PAS(0.005)R 170.89 3.10E-09 12730051000 7761727 8507935 6841058 8733268 8100943 8086643 8509554 8042618 7520795 8220786 TRUE FALSE 7458390.128 8265297.024 8077389.359 9183993.008 8361517.189 8250160.462 8613696.467 7876535.128 6667065.881 7663984.842 0.973173914 1.078459469 1.053941197 1.198331312 1.091014317 1.076484444 1.123918777 1.027733652 0.86992159 1 22.86966328 1.457239193 4.779384257 0.935779007 1.087123888 0.490326032 0.060576218 0.146076047 6.70260881 0.039067992 0.015194221 28.65755886 -1.457239193 0.151344881 AFGGEEVILKGS(ph)PEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AFGGEEVILKGSPEEK 16 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 AFGGEEVILKGS(1)PEEK 127.17 4.10E-05 140630000 166540 130990 136500 125750 132600 155980 144830 161770 217190 181750 TRUE FALSE 160031.4327 127254.2935 161168.5864 132239.9726 136865.1994 159134.0225 146602.4729 158429.393 192535.5017 169439.9106 0.944473071 0.75102904 0.951184322 0.780453508 0.807750659 0.939176738 0.865218072 0.935018157 1.136305496 1 17.37041421 1.458312451 3.542776521 1.066462693 0.860582984 0.551141356 0.072832475 0.149193472 3.561532575 0.049201671 0.017673467 28.72846696 -1.458312451 -0.205879709 YQYGGLNSGRPVTPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YQYGGLNSGRPVTPPR 16 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 ; 121.45 9.00E-05 893500000 265140 303060 195648 245800 262260 284490 279790 264760 268890 272080 FALSE TRUE 254778.0357 294417.0255 231005.9458 258485.7675 270695.8311 290242.5827 283214.1537 259292.6135 238366.7345 253651.7793 1.004440168 1.160713425 0.910720778 1.019057577 1.067194687 1.144256049 1.116547081 1.022238497 0.939740045 1 17.95248975 1.458323151 5.837843423 0.971934853 1.060914373 0.20862336 0.070272832 0.262600221 20.04111171 0.044386353 0.01817303 28.72917474 -1.458323151 0.08897952 KKDQVTAQEIFQDNHEDGPTAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KKDQVTAQEIFQDNHEDGPTAK 22 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;; 306.4 1.05E-56 5130980000 2641078 2299141 1913439 1762175 2111679 2339228 2107070 2313191 2781228 2355654 FALSE TRUE 2537861.752 2233571.75 2259239.992 1853121.063 2179603.073 2386528.793 2132856.953 2265422.797 2465514.657 2196103.456 1.155620308 1.017061261 1.028749345 0.843822297 0.992486518 1.086710549 0.971200581 1.031564697 1.122676917 1 21.06651459 1.459640557 9.917811634 1.066627751 1.009543968 0.050163307 0.080327423 0.371080803 137.8084492 0.044973704 0.020307665 28.81645529 -1.459640557 -0.057083783 SLDNEWDRDYGRPLDEQESQFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLDNEWDRDYGRPLDEQESQFR 22 2 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ;;; 174.01 1.75E-12 640653000 227642 242870 167706 186092 222060 235497 182004 202615 223730 185452 FALSE TRUE 218745.499 235943.5854 198014.2048 195696.2304 229202.7616 240258.9107 184231.4194 198430.9294 198333.1084 172891.1709 1.265220762 1.364694242 1.14531126 1.131904131 1.325705416 1.389654021 1.065591831 1.14772159 1.147155794 1 17.39950467 1.460425062 0.814948663 1.020403027 1.260269474 0.407343534 0.095639769 0.594802574 0.827117998 0.092802328 0.037482493 28.86855607 -1.460425062 0.239866447 GKPQER ddPTM_BT-474_Pertuzumab_2h_R1 4 GKPQER 6 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 79.027 0.062227 278781000 591988 625627 474654 596993 548645 563364 667609 591505 515278 664321 FALSE TRUE 568852.4545 607784.7305 560434.5364 627803.8803 566292.6647 574755.6061 675779.3986 579290.215 456785.8017 619325.947 0.918502539 0.981364875 0.904910474 1.013688968 0.914369352 0.928034113 1.091153054 0.935355959 0.737553148 1 19.24033936 1.460907336 24.99999511 0.858002277 0.96578623 0.182924504 0.079332261 6.683162365 10308.18921 0.039569199 0.01831628 28.90063173 -1.460907336 0.107783953 LAGFLDLTEQEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAGFLDLTEQEFR 13 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 147.37 8.08E-06 23567000 16537.9 23503 23044 33530 30757 26486 24563 25620 18679.5 26437 FALSE TRUE 15891.58058 22832.71745 27208.56341 35260.48732 31746.32684 27021.56507 24863.60934 25090.93805 16559.08147 24646.39844 0.644783075 0.926411926 1.103956973 1.430654763 1.288071639 1.096369724 1.008813089 1.018036696 0.671866176 1 14.58908922 1.461097494 3.881416741 0.833754249 1.087048399 0.15448881 0.210615784 0.376043192 10.94324214 0.157649166 0.058323671 28.91328879 -1.461097494 0.253294151 MREESGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 MREESGAR 8 1 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;F8VXH9;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2;PCBP3 Poly(rC)-binding protein 3;Poly(rC)-binding protein 2 0 ; 146.27 0.00050702 450239000 368194 435091 272349 316330 362912 351795 346702 326187 360241 311584 FALSE TRUE 353804.5714 422682.6307 321568.5227 332655.8292 374585.3941 358908.5359 350945.0428 319451.1245 319347.9519 290480.1381 1.217999185 1.45511715 1.107024132 1.145193029 1.289538749 1.235569971 1.20815504 1.099734827 1.099379648 1 18.14808 1.461120757 0.852079241 1.003237746 1.250657289 0.459555822 0.088388931 0.496093593 0.744442663 0.082797821 0.032602115 28.9148376 -1.461120757 0.247419543 VAPLWHSSS(ph)EVISMADR ddPTM_BT-474_Pertuzumab_2h_R1 1 VAPLWHSSSEVISMADR 17 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 VAPLWHS(0.02)S(0.413)S(0.567)EVISMADR 82.36 0.0047292 540340000 61782 83408 56537 85911 78192 59257 74898 68682 56226 68128 TRUE FALSE 59367.49114 81029.2855 66754.49356 90344.87701 80707.11669 60455.21714 75814.62413 67263.6927 49843.4602 63513.62988 0.934720488 1.275777902 1.051026271 1.422448649 1.270705467 0.951846356 1.193674874 1.059043434 0.784767936 1 15.9547786 1.461166555 4.186723248 0.893873909 1.162736814 0.325302475 0.150382748 0.218837135 7.508396257 0.099936357 0.037767778 28.91788691 -1.461166555 0.268862904 IDTHNIIVNQLVFPDPEKPCK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDTHNIIVNQLVFPDPEKPCK 21 1 O43681 O43681 ASNA1 ATPase ASNA1 0 ; 188.32 1.54E-17 681590000 1111290 997770 898660 910470 944810 1093260 1048290 1196190 1410130 1432670 FALSE TRUE 1067859.558 969314.5765 1061067.853 957459.4658 975200.6717 1115366.466 1061119.287 1171488.258 1250057.954 1335633.985 0.799515114 0.725733687 0.794430109 0.71685767 0.730140654 0.835083922 0.794468618 0.877102763 0.935928532 1 20.34909328 1.461189835 0.880345804 1.001121726 0.754871145 0.865532717 0.032519207 0.16882119 0.268069862 0.028796591 0.011141343 28.91943709 -1.461189835 -0.246250581 VNNVVWDLDRPLEEDCTLELLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VNNVVWDLDRPLEEDCTLELLK 22 1 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 284.45 6.00E-46 1618690000 1104310 1037250 914833 1013148 1064834 999390 1030901 1253720 1526450 1510540 FALSE TRUE 1061152.344 1007668.646 1080163.673 1065436.69 1099085.353 1019598.351 1043517.475 1227830.244 1353173.795 1408229.78 0.753536361 0.715556978 0.767036522 0.756578724 0.780473022 0.724028397 0.74101364 0.871896235 0.960904118 1 20.42545133 1.461225808 2.046435648 0.991672731 0.747458958 0.95685013 0.019972848 0.057464787 0.456410576 0.017700587 0.005702982 28.92183258 -1.461225808 -0.244213773 KDEESGSGSNPFQHLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEESGSGSNPFQHLEK 17 1 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ; 228.39 9.38E-16 455860000 622810 627010 550450 576660 621960 669150 690760 686550 873220 870760 FALSE TRUE 598469.8966 609128.2887 649928.5597 606421.4917 641965.9082 682680.6715 699213.7275 672372.5026 774095.7264 811782.6496 0.737229229 0.750358842 0.800618934 0.747024455 0.790810088 0.840964847 0.861331205 0.828266658 0.953575106 1 19.63073398 1.461616899 0.375645507 1.016601703 0.736427004 0.885843758 0.0281668 0.362659496 0.158907508 0.039053845 0.030019597 28.94788901 -1.461616899 -0.280174699 S(ph)LSGSS(ph)PCPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)LSGS(0.142)S(0.858)PCPK;S(1)LSGS(0.012)S(0.988)PCPK;S(1)LSGS(0.001)S(0.999)PCPK;S(0.999)LS(0.001)GS(0.031)S(0.969)PCPK 243.4 3.02E-12 3742470000 6548100 6011700 4936460 5195320 5603600 6070000 5904500 6272400 7607500 6929200 TRUE FALSE 6292193.013 5840252.202 5828588.133 5463451.088 5783844.883 6192739.559 5976761.037 6142872.748 6743928.493 6459879.112 0.974041914 0.904080727 0.902275109 0.845751289 0.89534878 0.958646354 0.925212521 0.950926889 1.043971315 1 22.62307574 1.462361206 2.483025455 1.02208465 0.911837004 0.583775682 0.035244894 0.194112125 2.281985549 0.029808601 0.009836552 28.99754333 -1.462361206 -0.110247646 STTTIGLVQALGAHLYQNVFACVR ddPTM_BT-474_Pertuzumab_2h_R1 2 STTTIGLVQALGAHLYQNVFACVR 24 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 214.26 1.51E-32 249720000 305601 355250 246103 218915 311542 460038 295013 285900 256097 234422 FALSE TRUE 293657.7751 345118.6178 290579.2866 230213.2294 321563.0314 469340.2836 298623.4573 279996.0651 227025.9422 218544.3891 1.343698533 1.579169427 1.329612203 1.053393456 1.471385436 2.147574163 1.366420152 1.281186244 1.038809292 1 17.73756681 1.462677373 2.299693544 1.013440997 1.477596609 0.319899759 0.262724989 0.372908222 3.756987914 0.232308155 0.07575833 29.01866126 -1.462677373 0.464155612 SIKPSDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 SIKPSDSPR 9 1 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 SIKPS(0.002)DS(0.998)PR;S(0.001)IKPS(0.028)DS(0.97)PR;SIKPS(0.006)DS(0.994)PR;SIKPS(0.005)DS(0.995)PR 98.182 0.0063768 1655140000 3348220 3281520 2892660 2996640 2871720 3050670 3141460 3482280 3858910 3870680 TRUE FALSE 3217367.861 3187934.263 3415428.009 3151296.95 2964091.482 3112356.638 3179906.127 3410369.701 3420862.715 3608515.396 0.891604305 0.883447599 0.946491184 0.873294583 0.821415778 0.862503356 0.881222824 0.945089414 0.947997262 1 21.78297398 1.462913226 1.602132701 0.986080402 0.878949793 0.624854088 0.030751913 0.255149951 1.24054385 0.029651195 0.00961993 29.03442475 -1.462913226 -0.10713061 YNTEGRVS(ph)PSPSQESLSSSK ddPTM_BT-474_Pertuzumab_2h_R1 6 YNTEGRVSPSPSQESLSSSK 20 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 YNTEGRVS(0.992)PS(0.008)PSQESLSSSK;YNTEGRVS(0.97)PS(0.03)PSQESLSSSK;YNTEGRVS(0.954)PS(0.046)PSQESLSSSK;YNTEGRVS(0.999)PS(0.001)PSQESLSSSK;YNTEGRVS(0.999)PS(0.001)PSQESLSSSK;YNTEGRVS(0.892)PS(0.108)PSQESLSSSK 315.06 1.27E-66 6963740000 3058120 2961150 2591310 2628030 2919700 3030970 2996080 3182110 3711250 3628590 TRUE FALSE 2938605.289 2876700.901 3059617.36 2763662.943 3013614.802 3092258.29 3032746.923 3116398.316 3289964.459 3382822.367 0.86868448 0.850384853 0.904456997 0.816969572 0.890858128 0.91410602 0.896513796 0.921242081 0.972550167 1 21.68979599 1.463396585 0.615373757 1.003518833 0.862362151 0.776771381 0.024201288 0.313915847 0.275868743 0.022898802 0.011372917 29.06675734 -1.463396585 -0.141156681 RDELLAQHAAGALGLPDLVAVLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDELLAQHAAGALGLPDLVAVLTR 24 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 195.24 3.31E-19 610280000 440190 471390 378840 481380 446110 431970 451990 457980 457410 499330 FALSE TRUE 422986.8881 457946.4187 447304.8153 506224.0795 460459.5333 440704.7294 457521.5888 448522.553 405486.7344 465509.9343 0.908652763 0.983752193 0.960892093 1.087461388 0.98915082 0.946713908 0.982839581 0.963508015 0.87105925 1 18.82845243 1.463799417 6.617866797 0.929538706 0.981604105 0.100537848 0.051628538 0.280519187 31.00701747 0.030141601 0.012873674 29.09373084 -1.463799417 0.052065399 RPS(ph)QEQSASASSGQPQAPLNR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPSQEQSASASSGQPQAPLNR 21 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(0.973)QEQS(0.027)ASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR 328.75 3.06E-80 7410600000 1327836 1383426 1102324 1551650 1409335 1452343 1416484 1385329 1379934 1392767 TRUE FALSE 1275942.701 1343972.045 1301538.468 1631730.842 1454667.54 1481710.371 1433819.355 1356721.472 1223289.677 1298433.651 0.982678399 1.035071792 1.002391202 1.256691739 1.120324893 1.141152164 1.104268481 1.044890874 0.942127214 1 20.30834086 1.463805212 3.547292734 0.972622555 1.094959572 0.28939753 0.074652147 0.288841057 7.002145519 0.056770087 0.020539547 29.09411909 -1.463805212 0.122337017 QATVSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 QATVSWDSGGSDEAPPKPSRPGYPSPR 27 2 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1;E5RJQ2;E5RG80;E5RHK7 E7ESA6 PTK2 Focal adhesion kinase 1 1 QATVSWDSGGSDEAPPKPSRPGYPS(1)PR;QATVSWDSGGSDEAPPKPS(0.296)RPGYPS(0.704)PR;QATVSWDSGGSDEAPPKPS(0.001)RPGYPS(0.999)PR;QATVSWDSGGSDEAPPKPS(0.055)RPGYPS(0.945)PR 302.3 2.88E-71 3179740000 1000381 1014655 825428 926873 838229 919395 993666 1101587 1249714 1291139 TRUE FALSE 961285.0045 985718.0329 974601.2011 974709.0266 865191.397 937985.7968 1005826.782 1078838.843 1107851.706 1203689.006 0.798615756 0.818914212 0.809678577 0.809768156 0.718783168 0.779259254 0.835620145 0.89627706 0.920380348 1 20.19903126 1.463951864 1.205201111 0.987119199 0.789219844 0.85223527 0.029175242 0.164486397 0.461027199 0.028835353 0.009868774 29.1039452 -1.463951864 -0.197899355 LEQTSVR ddPTM_BT-474_Pertuzumab_2h_R1 5 LEQTSVR 7 0 O15234 O15234 CASC3 Protein CASC3 0 ;;;; 99.919 0.02367 7994590000 3587950 4285520 3113080 4414050 3641100 3587330 4298390 3907740 3921720 4029280 FALSE TRUE 3447728.947 4163301.166 3675682.806 4641859.649 3758219.288 3659868.27 4350994.983 3827043.803 3476542.787 3756373.277 0.917834489 1.108329992 0.978519049 1.235729068 1.000491435 0.974308995 1.158296757 1.018813499 0.925505143 1 21.840909 1.464022376 11.12949058 0.965775622 1.05689732 0.133815267 0.091205887 0.217756751 125.3475613 0.047186838 0.021632959 29.10867089 -1.464022376 0.091121698 VEPPKEEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEPPKEEQK 9 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 81.338 0.019809 0 269160 266560 236430 196960 248770 235040 238060 271930 323780 304850 FALSE TRUE 258640.9296 258957.9698 279158.1604 207125.1292 256771.913 239792.6698 240973.4495 266314.5505 287025.8518 284202.238 0.91005944 0.911174985 0.982251802 0.728794856 0.903483079 0.843739555 0.847894271 0.937060005 1.009935227 1 18.11655839 1.464114739 3.208957433 1.003538026 0.875348127 0.413176746 0.06180829 0.231386823 4.571107618 0.045957119 0.01616135 29.11486222 -1.464114739 -0.128189898 GNIYYQSYEHRS(ph)PS(ph)PNIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNIYYQSYEHRSPSPNIR 18 1 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 2 GNIYYQSY(0.033)EHRS(0.974)PS(0.993)PNIR;GNIYYQSY(0.121)EHRS(0.88)PS(0.999)PNIR 134.69 1.33E-05 401100000 210764 264704 160282 209372 219125 224775 182015 194185 171325 146963 TRUE FALSE 202527.1099 257154.9011 189248.5229 220177.714 226173.3546 229320.1045 184242.554 190175.0119 151876.9043 137009.0651 1.478202261 1.87691888 1.381284681 1.607030264 1.650791168 1.673758626 1.344747181 1.388046928 1.108517193 1 17.06391183 1.46418013 1.033667721 0.997101686 1.614715555 0.713912658 0.134978319 0.238705391 0.503804129 0.116070446 0.041790885 29.1192463 -1.46418013 0.617613869 RGS(ph)QNSSEHRPPASSTSEDVK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGSQNSSEHRPPASSTSEDVK 21 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGS(0.969)QNS(0.026)S(0.005)EHRPPASSTSEDVK;RGS(0.989)QNS(0.009)S(0.001)EHRPPASSTSEDVK;RGS(0.731)QNS(0.134)S(0.134)EHRPPASSTSEDVK;RGS(0.601)QNS(0.227)S(0.169)EHRPPAS(0.001)S(0.001)T(0.001)SEDVK 184 2.14E-17 691786000 264768 289661 230427 285850 331845 294065 239320 260737 225336 198320 TRUE FALSE 254420.5738 281400.1519 272070.2847 300602.7528 342519.0958 300011.1958 242248.8697 255352.6898 199756.802 184887.6098 1.376082336 1.522006544 1.471544173 1.625867483 1.852580042 1.622667934 1.310249346 1.381123863 1.08042287 1 17.49628902 1.464482219 1.235131079 1.00117967 1.575612211 0.697418837 0.133687201 0.250314952 0.734769525 0.12972716 0.044116832 29.13950826 -1.464482219 0.574432541 GFGFVTYATVEEVDAAMNAR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFGFVTYATVEEVDAAMNAR 20 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;A0A2R8Y4L2;F8W646;F8VYN5 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;; 196.93 1.21E-21 76241000 70051.4 90169 84344.4 91591.7 99275.4 95289 95675 89981.6 85366.4 92464.2 FALSE TRUE 67313.71384 87597.4684 99587.30931 96318.75861 102468.6834 97215.80887 96845.89927 88123.44852 75675.96416 86201.51738 0.780887807 1.016194042 1.155284876 1.117367322 1.188710901 1.127773754 1.123482535 1.022295792 0.877895964 1 16.39542564 1.465156535 4.890803049 0.9396089 1.081541108 0.181372204 0.11153123 0.290306006 14.43670808 0.074448211 0.029552155 29.18478749 -1.465156535 0.141932207 DPNTKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DPNTKR 6 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;A0A2R8Y4L2;F8W646;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;; 113.25 0.042167 2164020000 3823080 3645610 2917960 3104600 3226600 3390900 3762130 3374290 2962310 3813370 FALSE TRUE 3673669.807 3541640.772 3445300.282 3264828.778 3330386.519 3459466.321 3808172.072 3304609.732 2626040.988 3555087.053 1.033355795 0.996217735 0.969118401 0.918354102 0.936794646 0.973103125 1.071189542 0.92954397 0.73867136 1 21.76145346 1.465301212 9.405763519 0.857554094 0.981106561 0.292815649 0.071842442 0.120867968 41.16053223 0.037655096 0.017081229 29.19451143 -1.465301212 0.123552467 GFAFVTFDDHDTVDKIVVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFAFVTFDDHDTVDKIVVQK 20 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 347.2 3.20E-95 759600000 1129700 1227500 573730 618020 862160 1279200 816740 761360 918150 650960 FALSE TRUE 1085550.075 1192492.902 677415.7736 649916.0863 889892.1594 1305066.3 826735.5084 745637.6499 813925.4612 606869.8994 1.78876902 1.964989371 1.116245466 1.070931491 1.466363977 2.150487776 1.362294471 1.228661449 1.34118608 1 19.21102774 1.465425016 0.057572348 1.75E-15 2.70245637 0.22550293 0.328936759 50.52857541 2.933571318 67.86048204 66.31440105 29.20283506 -1.465425016 2.70245637 DSSGSVSPNT(ph)LSQEEGDQICLYHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSGSVSPNTLSQEEGDQICLYHIR 25 0 H7C4T3;H7C4L8;G5E9U9;Q9H0J9 H7C4T3 PARP12 Poly [ADP-ribose] polymerase 12 1 DS(0.018)S(0.018)GS(0.018)VS(0.244)PNT(0.668)LS(0.034)QEEGDQICLYHIR 59.614 0.03699 0 20995 21994 20913 26741 27860 24181 22602 24127 21583 22892 TRUE FALSE 20174.49219 21366.75265 24692.44431 28121.10621 28756.1422 24669.95639 22878.61004 23628.76902 19132.98832 21341.50445 0.945317245 1.001183056 1.157015166 1.317672158 1.347428072 1.155961448 1.072024238 1.107174477 0.896515443 1 14.38137426 1.465691696 2.084980452 0.951045874 1.155430945 0.27109627 0.12101583 0.437420836 3.625265318 0.11395351 0.036876696 29.22077268 -1.465691696 0.204385071 AFITNIPFDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AFITNIPFDVK 11 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 163.34 5.60E-05 205421000 565280 553370 428840 416490 523890 508550 561880 516780 519540 528450 FALSE TRUE 543188.2326 537588.4294 506340.9275 437985.0988 540741.3976 518833.2294 568756.4555 506108.3124 460563.9973 492657.6108 1.102567424 1.091200902 1.027774496 0.889025338 1.09760082 1.053131461 1.154465988 1.027302332 0.93485615 1 18.91022582 1.466233353 25 0.971978274 1.056867698 0.224219404 0.067562229 4.02214889 9240.033218 0.037942559 0.017564724 29.25723994 -1.466233353 0.084889424 DKTEFAQDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKTEFAQDK 9 1 Q9UJA5;Q9UJA5-2;Q9UJA5-3 Q9UJA5 TRMT6 tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 0 ; 131.43 0.00030394 983230000 745650 687730 584500 585910 651580 619820 715170 766100 922440 921940 FALSE TRUE 716509.1736 668116.6138 690132.1521 616148.8853 672538.6624 632353.1851 723922.4644 750279.7673 817728.4784 859496.1826 0.833638576 0.777335173 0.802949642 0.71687216 0.782480104 0.735725414 0.842263734 0.872929726 0.951404433 1 19.71313171 1.466260059 1.285160251 0.996010477 0.774465738 0.846913222 0.033445635 0.144022817 0.455870942 0.02964219 0.009989327 29.25903906 -1.466260059 -0.221544739 S(ph)RSPITTNHRPSPDPEQR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSPITTNHRPSPDPEQR 18 2 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.5)RS(0.5)PITTNHRPSPDPEQR;S(0.499)RS(0.499)PIT(0.001)TNHRPSPDPEQR;S(0.499)RS(0.499)PIT(0.002)TNHRPSPDPEQR 119.02 4.48E-05 787140000 164584 172572 175595 187980 167109 174368 179938 175438 170971 175674 TRUE FALSE 158151.8753 167650.4155 207328.9226 197681.6703 172484.2127 177893.8404 182140.1351 171815.144 151563.0888 163775.4435 0.965662934 1.023660275 1.265934124 1.207028759 1.053175061 1.086205823 1.112133365 1.04908978 0.925432321 1 17.32135953 1.46676386 3.444902018 0.96416441 1.106270187 0.30423963 0.082887186 0.28313947 6.503823175 0.06405156 0.023061629 29.29300054 -1.46676386 0.142105778 TVAISDAAQLPHDYCT(ph)TPGGTLFSTTPGGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCT(0.495)T(0.495)PGGT(0.01)LFSTTPGGTR 138.33 1.82E-06 410420000 122680 125730 87893 113110 91003 128460 102660 110500 95718 106690 TRUE FALSE 117885.53 122144.3035 103777.2203 118947.6207 93930.19414 131057.5492 103916.3838 108218.1364 84852.49392 99463.79127 1.185210502 1.228027827 1.043366827 1.195888666 0.944365713 1.317640797 1.044765964 1.088015397 0.853099332 1 16.6018838 1.466845834 2.617211926 0.930314363 1.138881944 0.363276915 0.107295383 0.266017 3.501783846 0.07919679 0.026517343 29.29853019 -1.466845834 0.208567581 KAEEIANEMIEAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KAEEIANEMIEAAK 14 1 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 193.17 4.65E-07 2092410000 3983840 3568480 3264090 3092220 3554800 3636070 3901310 4296320 5331510 5325150 FALSE TRUE 3828147.128 3466710.444 3853983.672 3251809.845 3669143.37 3709593.827 3949055.399 4207599.491 4726299.336 4964472.847 0.771108483 0.698303838 0.776312771 0.655016141 0.739080157 0.747228143 0.795463188 0.847542049 0.952024411 1 22.2432091 1.467054551 1.086654373 1.003383241 0.7256387 0.892594637 0.033520374 0.125762699 0.290617403 0.028588705 0.010115418 29.3126141 -1.467054551 -0.277744541 ICDLLSDFDEFSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ICDLLSDFDEFSSR 14 0 Q8N142;Q8N142-2 Q8N142 ADSSL1 Adenylosuccinate synthetase isozyme 1 0 ; 184.55 2.98E-06 59681000 76385 77447 66564 89650 84519 82122 80158 80703 85619 80352 FALSE TRUE 73399.78975 75238.28739 78593.59551 94276.84724 87237.63039 83782.56311 81138.99758 79036.45485 75899.89006 74909.68747 0.979843759 1.004386614 1.049177992 1.258540122 1.164570743 1.118447639 1.083157604 1.055089902 1.013218619 1 16.19286468 1.467070998 1.842048071 1.002120637 1.099622542 0.179319019 0.074788538 0.624574447 4.028897238 0.072216191 0.023304222 29.31372423 -1.467070998 0.097501904 IGDEDVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 IGDEDVGR 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;; 132.08 0.0022738 1321270000 2684420 2851930 2379210 3385800 2381190 2261230 3234050 3250000 3616600 3924700 FALSE TRUE 2579509.899 2770595.749 2809186.172 3560541.544 2457783.139 2306953.62 3273629.271 3182886.364 3206058.73 3658876.573 0.705000523 0.757225802 0.767772871 0.973124256 0.671731634 0.63050873 0.894708856 0.869908099 0.87624129 1 21.80296932 1.46719212 1.08866294 0.974332603 0.763413046 0.385961111 0.094220882 0.513394549 1.190374996 0.08875292 0.031384355 29.3219008 -1.46719212 -0.210919557 AQHEDQVEQYKK ddPTM_BT-474_Pertuzumab_2h_R1 6 AQHEDQVEQYKK 12 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 233.37 3.50E-16 21874670000 26284720 24077670 20006900 20097680 21765610 23502890 22907980 24418050 29072190 26066250 FALSE TRUE 25257484.08 23390998.43 23622591.88 21134923.67 22465720.61 23978134.54 23188334.71 23913808.73 25772036.87 24300759.67 1.039370144 0.962562436 0.972092733 0.869722756 0.92448635 0.986723661 0.954222626 0.984076591 1.060544494 1 24.53449808 1.467416836 3.895159111 1.029954549 0.955968694 0.299243008 0.04312106 0.250076605 7.451366106 0.030798115 0.011506115 29.33707668 -1.467416836 -0.073985855 GTSKEDAMK ddPTM_BT-474_Pertuzumab_2h_R1 2 GTSKEDAMK 9 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 68.557 0.052651 1324780000 637520 597020 467850 460230 440840 373210 518260 589420 723530 709100 FALSE TRUE 612605.0136 579993.5741 552400.9023 483982.5255 455020.019 380756.5619 524602.6209 577248.271 641397.9077 661072.0254 0.926684219 0.877353075 0.835613793 0.732117692 0.688306268 0.575968347 0.793563486 0.87320027 0.970239071 1 19.33444794 1.467845749 2.285019674 0.989487384 0.769460941 0.448592602 0.093191569 0.295470453 2.958464833 0.087003349 0.028469509 29.36606457 -1.467845749 -0.220026443 SALPVSPSISSAPVPVEIENLPQS(ph)PGTDQHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SALPVSPSISSAPVPVEIENLPQSPGTDQHDR 32 0 Q9HCM4-2;Q9HCM4-4;Q9HCM4-3;Q9HCM4 Q9HCM4-2 EPB41L5 Band 4.1-like protein 5 1 SALPVSPSISSAPVPVEIENLPQS(0.925)PGT(0.075)DQHDR 102.17 4.29E-06 178830000 25345 24958 28490 42878 33935 35589 33024 31177 24049 32051 TRUE FALSE 24354.48938 24246.22228 33638.77676 45090.93872 35026.55009 36308.63396 33428.15759 30533.18406 21319.05834 29880.15722 0.81507233 0.811448952 1.125789818 1.509059621 1.172234464 1.215141999 1.118741021 1.021854866 0.713485481 1 14.86690012 1.467927641 4.32585921 0.854949093 1.118242169 0.199775297 0.198431347 0.316669754 11.90873143 0.144290617 0.055612055 29.37160243 -1.467927641 0.263293076 KSES(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSESPFR 7 1 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 KS(0.005)ES(0.995)PFR 68.847 0.037572 273000000 138960 140840 137080 150770 142040 108920 167890 170510 210680 216710 TRUE FALSE 133529.2896 136823.3811 161853.4053 158551.2578 146608.8456 111122.437 169944.688 166988.9089 186764.4896 202032.0387 0.660931258 0.677236056 0.801127417 0.784782744 0.725671268 0.550023837 0.84117692 0.826546671 0.92443006 1 17.62422457 1.467960567 1.341489773 0.986363589 0.711849366 0.647222731 0.074234415 0.260998321 0.897112016 0.068668139 0.022940488 29.37382931 -1.467960567 -0.274514223 EELMESR ddPTM_BT-474_Pertuzumab_2h_R1 1 EELMESR 7 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 129.68 0.0084605 187730000 417990 510310 364870 499240 364280 422370 463130 460230 549760 502550 FALSE TRUE 401654.4887 495756.4584 430810.1255 525005.8362 375997.397 430910.6108 468797.9235 450726.0897 487353.5496 468511.8409 0.857298479 1.058151396 0.919528789 1.120581788 0.802535527 0.919743266 1.00061062 0.962037777 1.040216078 1 18.83772598 1.467973293 2.027041643 1.017663629 0.955029379 0.075678807 0.087619828 0.907876131 7.121416331 0.071348397 0.023086771 29.37469007 -1.467973293 -0.062634249 SIRDEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIRDEIK 7 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 85.161 0.019165 221650000 226670 226980 211690 254570 202900 121410 330310 239600 330050 340980 FALSE TRUE 217811.4858 220506.7526 249947.092 267708.3882 209426.4628 123864.9934 334352.4326 234652.1763 292584.1077 317885.1209 0.685189307 0.693668052 0.786281193 0.84215451 0.658811781 0.389653322 1.051802713 0.738166592 0.920408312 1 18.27814596 1.468012737 1.072804192 0.979054601 0.705833034 0.288577501 0.153460479 0.625670606 1.411878968 0.138522968 0.049250664 29.37735808 -1.468012737 -0.273221567 ELLVHLDDPER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLVHLDDPER 11 0 Q86Y56;H0Y650;Q86Y56-2;E9PGY2;Q86Y56-3 Q86Y56 DNAAF5 "Dynein assembly factor 5, axonemal" 0 ; 132.76 0.0001757 342210000 225300 250181 240932 276976 259634 278220 288719 232122 303220 335170 FALSE TRUE 216495.0269 243046.0828 284473.7719 291270.7646 267985.3634 283845.799 292252.4295 227328.5996 268799.7368 312468.6374 0.692853621 0.777825528 0.910407439 0.932159999 0.857639236 0.908397724 0.935301642 0.727524533 0.860245492 1 18.25335187 1.468134044 0.019472366 1.752607558 3.21E-06 0.267472184 0.080108588 488.7076229 9.574661421 431.280067 427.8926688 29.38556489 -1.468134044 -1.752604349 TS(ph)SPHKEESPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.018)S(0.491)S(0.491)PHKEESPK 148.41 2.11E-05 237100000 259300 197500 180550 169030 193610 191820 223220 220230 317650 228950 TRUE FALSE 249166.2693 191867.4934 213179.4013 177753.6586 199837.6415 195698.7318 225951.8331 215682.1735 281591.7037 213443.0126 1.167366719 0.898916723 0.998764957 0.832792118 0.936257594 0.916866425 1.058604966 1.010490674 1.319282839 1 17.70349141 1.468194504 3.809033922 1.163231089 0.964702767 0.280584299 0.11401944 0.227833389 6.483048497 0.074726186 0.027764577 29.38965606 -1.468194504 -0.198528322 EQLRQEQALLEEIER ddPTM_BT-474_Pertuzumab_2h_R1 4 EQLRQEQALLEEIER 15 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 268.12 1.35E-25 473996000 347385 425069 247106 300359 355147 396049 294185 312010 332055 265574 FALSE TRUE 333808.8101 412946.4483 291763.551 315860.564 366570.6258 404057.3821 297785.324 305566.8845 294361.5085 247586.4364 1.348251604 1.667888008 1.178431077 1.275758755 1.480576364 1.631985128 1.202752979 1.234182651 1.188924211 1 17.91757276 1.468221509 1.105637532 1.036509805 1.418609362 0.432545566 0.15208879 0.443733157 1.058410589 0.140629138 0.049484086 29.39148364 -1.468221509 0.382099557 EGQHYPER ddPTM_BT-474_Pertuzumab_2h_R1 2 EGQHYPER 8 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ; 108.15 0.0038667 1018800000 426810 440320 358680 426020 401170 387200 421560 410930 413130 416370 FALSE TRUE 410129.7933 427762.5047 423501.4548 448006.9433 414073.9974 395029.4493 426719.1774 402444.1519 366233.2144 388168.889 1.056575643 1.102001002 1.091023693 1.154154689 1.066736694 1.017674163 1.099313184 1.036775907 0.943489354 1 18.56632497 1.468536239 3.658459033 0.973032149 1.084011214 0.607825079 0.035753688 0.14400177 3.764753131 0.026024967 0.009559318 29.41279111 -1.468536239 0.110979065 DIGKPEVEYDCDNLQHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIGKPEVEYDCDNLQHSK 18 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 0 204.23 6.58E-16 745860000 694090 586720 508950 487590 556200 536120 542860 643300 779030 738350 FALSE TRUE 666964.1954 569987.3201 600928.5865 512754.5783 574090.6781 546960.7137 549503.6831 630015.6302 690597.7804 688340.8968 0.968944601 0.828059647 0.873010146 0.74491372 0.834020877 0.794607318 0.798301664 0.915266887 1.003278729 1 19.3927637 1.469132671 3.041636226 1.000397943 0.831107821 0.590531361 0.055664202 0.162727845 2.91337638 0.041879573 0.014590317 29.45321253 -1.469132671 -0.169290122 ENLWLNLTDGSILCGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENLWLNLTDGSILCGR 16 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 88.282 0.014384 63977000 104731 114565 90408 120283 121041 135215 114989 109307 96601 101394 FALSE TRUE 100637.9967 111297.7184 106746.7367 126490.82 124934.3937 137949.1399 116396.2698 107049.7723 85635.25946 94526.49407 1.064653859 1.177423531 1.129278492 1.338152031 1.321686527 1.459370109 1.231361333 1.132484319 0.905939232 1 16.52843113 1.469356701 2.927018873 0.955587922 1.252641478 0.531479021 0.108500552 0.202822292 3.361066946 0.09020863 0.031109993 29.4684098 -1.469356701 0.297053556 GEAVLRPGLDAEPELSPEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEAVLRPGLDAEPELSPEEQR 21 1 C9JQV0;Q9BRJ6 C9JQV0 C7orf50 Uncharacterized protein C7orf50 0 ; 266.53 4.71E-37 559570000 216510 215650 251860 224080 254660 231780 244660 235930 214660 251330 FALSE TRUE 208048.5498 209499.8731 297376.7046 235644.7957 262851.3702 236466.7504 247654.2223 231057.9631 190292.6967 234307.1952 0.887930691 0.894124796 1.269174446 1.005708747 1.121823723 1.009216768 1.056963795 0.986132597 0.812150461 1 17.83804173 1.469368493 5.145391125 0.902341962 1.038573121 0.172597425 0.111300929 0.274327872 15.63092802 0.069580207 0.028226217 29.46920995 -1.469368493 0.136231159 SLSSS(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 SLSS(0.041)S(0.959)PQAQPPRPAELSDEEVAELFQR;SLS(0.001)S(0.136)S(0.863)PQAQPPRPAELSDEEVAELFQR;SLS(0.023)S(0.137)S(0.839)PQAQPPRPAELSDEEVAELFQR 237.41 2.81E-45 2504120000 374270 466426 372775 500377 473272 478146 465116 425672 349431 412071 TRUE FALSE 359643.1146 453123.9872 440143.7348 526201.5169 488495.2237 487814.4397 470808.2287 416881.7244 309765.0578 384161.0641 0.936177943 1.17951565 1.145727081 1.369741929 1.271589626 1.269817494 1.225549054 1.085174328 0.806341628 1 18.55135178 1.470597128 3.740899218 0.90612138 1.207292528 0.506258825 0.115486048 0.166173916 4.576327644 0.082267773 0.030502544 29.55269749 -1.470597128 0.301171147 ELEEEEENS(ph)DEDELDSHTMVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEEEEENSDEDELDSHTMVK 21 0 A0A087WZ06;Q13188;Q13188-2;E5RFQ9 A0A087WZ06 STK3 Serine/threonine-protein kinase 3;Serine/threonine-protein kinase 3 36kDa subunit;Serine/threonine-protein kinase 3 20kDa subunit 1 ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK 317.17 6.06E-67 1607420000 720810 710040 577750 638420 638390 641420 691910 726930 891370 818060 TRUE FALSE 692639.9483 689790.3544 682162.277 671368.9327 658924.3941 654389.9519 700377.8016 711918.6415 790185.4145 762652.0675 0.908199135 0.904462708 0.894460667 0.880308284 0.863990832 0.858045208 0.918345116 0.933477626 1.036102108 1 19.5406655 1.470834665 2.204688421 1.018496128 0.886959341 0.855188347 0.020720178 0.102721231 0.959722904 0.017753331 0.005797747 29.56886569 -1.470834665 -0.131536787 SMSSIPPYPASSLAS(ph)SSPPGSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPAS(0.001)S(0.006)LAS(0.622)S(0.247)S(0.124)PPGSGR 158.58 2.21E-11 186850000 56700 62258 52702 60687 59792 65400 63726 60136 53158 66887 TRUE FALSE 54484.10131 60482.4628 62226.42375 63819.06334 61715.26398 66722.43281 64505.89785 58894.17059 47123.7267 62356.68391 0.873749178 0.969943541 0.997911047 1.023451847 0.989713694 1.070012525 1.034466457 0.944472459 0.755712519 1 15.92825659 1.471054555 6.454210676 0.868411968 0.99625581 0.284077365 0.073155868 0.152715402 15.91802505 0.041331118 0.0178298 29.58384071 -1.471054555 0.127843842 QNEEFRPFIR ddPTM_BT-474_Pertuzumab_2h_R1 1 QNEEFRPFIR 10 1 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 0 63.408 0.086518 0 127040 165460 120250 159070 167940 170200 163640 150920 140830 152580 FALSE TRUE 122075.1363 160741.2428 141981.8499 167279.6218 173341.9426 173641.5606 165642.6753 147803.4493 124843.5688 142245.6207 0.858199611 1.130025951 0.998145667 1.175991366 1.218610048 1.22071639 1.164483479 1.039072054 0.87766195 1 17.11802471 1.471937741 4.507116718 0.940776936 1.116337658 0.282453297 0.10761883 0.232181775 9.691582201 0.072034455 0.028276494 29.64406389 -1.471937741 0.175560723 RFTDEESR ddPTM_BT-474_Pertuzumab_2h_R1 4 RFTDEESR 8 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;; 113.74 0.0044744 578079000 550366 678641 496960 626608 579421 580555 626493 599023 586346 637991 FALSE TRUE 528857.0883 659286.8231 586771.7268 658947.314 598058.6027 592294.2199 634160.2087 586652.9657 519786.4602 594779.3013 0.889165254 1.108456232 0.986536898 1.107885417 1.005513476 0.995821843 1.066210958 0.986337225 0.873914844 1 19.18199492 1.471950718 6.172305516 0.934094984 1.026053372 0.205973775 0.066887005 0.189847259 17.48990229 0.036071571 0.015425204 29.64494973 -1.471950718 0.091958388 GLGPPS(ph)PPAPPR ddPTM_BT-474_Pertuzumab_2h_R1 6 GLGPPSPPAPPR 12 0 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR 156.73 6.88E-05 8754250000 792810 936520 725608 977260 846180 920500 862140 861560 812222 837180 TRUE FALSE 761826.1087 909811.3665 856741.5067 1027696.506 873398.1482 939113.1407 872691.1272 843768.4849 720021.9637 780477.0529 0.976103149 1.165711872 1.097715177 1.316754287 1.119056793 1.203255287 1.11815091 1.081093264 0.92254085 1 19.57399669 1.471959296 2.671622323 0.962444753 1.149822931 0.416909078 0.083599665 0.236158239 3.268399758 0.063791071 0.021563413 29.64553527 -1.471959296 0.187378178 VAYTEADYYHTELWMEQALR ddPTM_BT-474_Pertuzumab_2h_R1 4 VAYTEADYYHTELWMEQALR 20 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;; 364.95 5.83E-112 484251000 489688 574030 445874 564080 527347 546630 493380 443546 488430 368389 FALSE TRUE 470550.4516 557659.2264 526453.3502 593192.2364 544309.5952 557683.2331 499418.132 434386.6201 432985.4741 343437.6849 1.370118867 1.623756655 1.53289337 1.727219413 1.584886048 1.623826556 1.454173942 1.264819323 1.260739555 1 18.38968883 1.47216059 1.051490517 1.037323695 1.589076218 0.793602465 0.095405267 0.193871594 0.42131045 0.085320601 0.030599069 29.65927905 -1.47216059 0.551752524 ERQEQEEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERQEQEEAR 9 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 190.57 3.37E-05 186780000 199600 205400 169050 220840 208490 190850 231650 204360 203490 211350 FALSE TRUE 191799.4113 199542.1931 199601.0955 232237.5789 215196.2702 194709.1178 234485.002 200139.8946 180390.6683 197035.0762 0.973427752 1.012724216 1.01302316 1.178661096 1.09217239 0.988195206 1.190067304 1.015757693 0.91552566 1 17.58809296 1.472679755 10.71076618 0.960272882 1.065392245 0.255901572 0.072529217 0.11679237 66.41164848 0.039560452 0.018230332 29.69475561 -1.472679755 0.105119364 RQEQPSIESTS(ph)PISR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RQEQPSIES(0.106)T(0.031)S(0.863)PISR;RQEQPSIES(0.181)T(0.181)S(0.637)PIS(0.001)R 154.75 1.48E-06 1243740000 342950 416170 326910 397160 364490 466940 396250 370710 318500 355610 TRUE FALSE 329547.1348 404301.2391 385989.9091 417657.4752 376214.1519 476381.8467 401099.426 363054.709 282345.2153 331524.218 0.994036384 1.219522488 1.164288725 1.25980985 1.134801416 1.436944334 1.209864632 1.095107655 0.851657888 1 18.33875474 1.472865074 3.460048942 0.929271721 1.209065552 0.496291287 0.110018429 0.173596364 4.078748853 0.077662043 0.028210978 29.70742944 -1.472865074 0.279793831 EEDCHS(ph)PTSKPPKPDQPLK ddPTM_BT-474_Pertuzumab_2h_R1 6 EEDCHSPTSKPPKPDQPLK 19 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 EEDCHS(0.976)PT(0.021)S(0.003)KPPKPDQPLK;EEDCHS(0.999)PT(0.001)SKPPKPDQPLK;EEDCHS(0.977)PT(0.019)S(0.004)KPPKPDQPLK;EEDCHS(0.884)PT(0.113)S(0.003)KPPKPDQPLK;EEDCHS(0.962)PT(0.033)S(0.006)KPPKPDQPLK;EEDCHS(0.866)PT(0.133)S(0.001)KPPKPDQPLK 167.72 9.10E-12 4527120000 3747640 3061180 4020660 3581600 3526580 3570280 4481800 4692990 6260130 6321860 TRUE FALSE 3601178.086 2973878.144 4747282.701 3766446.805 3640015.648 3642473.508 4536649.609 4596078.117 5549506.287 5893674.791 0.611024227 0.504588096 0.805487725 0.639065937 0.61761393 0.618030963 0.769748887 0.779832325 0.94160375 1 22.49073603 1.473070044 1.045832259 1.004833632 0.632164081 0.759051192 0.073764396 0.226196294 0.486629659 0.066951021 0.024066655 29.72145346 -1.473070044 -0.372669551 DFYAAYPLTEVPNGSNEDRGEVLEQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFYAAYPLTEVPNGSNEDRGEVLEQEK 27 1 P35227;A0A087X259;J3KT13 P35227 PCGF2 Polycomb group RING finger protein 2 0 191.18 4.72E-18 81576000 80981 74895 74178 64323 82535 75510 77298 86885 119500 93174 FALSE TRUE 77816.17299 72759.06793 87583.61468 67642.71774 85189.81323 77036.86394 78243.99605 85090.79439 105934.861 86863.24199 0.89584698 0.837627819 1.008293182 0.778726607 0.980734903 0.886875302 0.900772228 0.979594964 1.219559143 1 16.40645818 1.473393153 4.151865564 1.11086491 0.900121878 0.52749192 0.078876313 0.132945945 4.6231871 0.048003854 0.018435394 29.74357406 -1.473393153 -0.210743032 AADESER ddPTM_BT-474_Pertuzumab_2h_R1 2 AADESER 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ; 133.81 0.0075265 351460000 364020 370740 304420 392580 349780 377830 428250 354410 301230 380260 FALSE TRUE 349793.696 360166.8582 359435.4658 412841.1008 361030.9914 385469.9815 433491.0516 347091.3096 267035.6333 354504.6515 0.98671116 1.015972165 1.013909026 1.164557641 1.018409744 1.087348163 1.222807796 0.979088168 0.753264117 1 18.43544503 1.473685169 7.468547416 0.872390974 1.071904416 0.44081079 0.088723434 0.101970827 16.29054024 0.048602716 0.021684629 29.76358014 -1.473685169 0.199513442 KGGPDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGGPDDR 7 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 84.498 0.034476 269900000 1345400 1326200 1029400 1102200 1148800 1198900 1358000 1190300 1040300 1349100 FALSE TRUE 1292820.281 1288378.074 1215435.479 1159084.674 1185752.195 1223142.579 1374619.61 1165719.889 922209.5053 1257724.255 1.027904388 1.024372448 0.96637675 0.921572967 0.942775962 0.972504565 1.092941958 0.926848539 0.733236639 1 20.26238423 1.473847001 8.670189736 0.854416364 0.988407681 0.309661741 0.07547267 0.10947626 28.28796643 0.039851891 0.018133019 29.77467304 -1.473847001 0.133991318 SLENETLNKEEDCHS(ph)PTSKPPKPDQPLK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLENETLNKEEDCHSPTSKPPKPDQPLK 28 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SLENETLNKEEDCHS(0.841)PT(0.151)S(0.009)KPPKPDQPLK;SLENETLNKEEDCHS(0.947)PT(0.023)S(0.03)KPPKPDQPLK;SLENETLNKEEDCHS(0.975)PT(0.022)S(0.003)KPPKPDQPLK 201.7 1.64E-25 4451680000 2440340 1839950 1607280 1320740 1841090 1872150 2099830 2136020 3228250 2640160 TRUE FALSE 2344968.815 1787476.427 1897751.25 1388903.55 1900310.332 1910006.156 2125528.348 2091910.441 2861792.594 2461339.612 0.952720544 0.726220965 0.771023731 0.564287652 0.772063442 0.776002688 0.863565652 0.849907274 1.162697167 1 21.2310123 1.474732625 2.141420193 1.078293134 0.760908175 0.563963894 0.103437419 0.207635986 1.835952447 0.085264064 0.027845734 29.8354522 -1.474732625 -0.317384959 INHLEYEDQYKDDNFGEGNDGGILDDK ddPTM_BT-474_Pertuzumab_2h_R1 2 INHLEYEDQYKDDNFGEGNDGGILDDK 27 1 O60216 O60216 RAD21 Double-strand-break repair protein rad21 homolog 0 ; 167.67 4.66E-12 671810000 391060 303900 289135 282644 327090 321640 362600 368730 532410 438960 FALSE TRUE 375776.9429 295233.0695 341388.1263 297231.2907 337611.1469 328143.7812 367037.6073 361115.5966 471973.0488 409228.8482 0.918256239 0.721437579 0.834223022 0.726320473 0.824993517 0.801858868 0.896900619 0.882429472 1.153323015 1 18.64254832 1.474984203 2.297242856 1.073443436 0.808385721 0.65905397 0.071676719 0.152646394 1.559805917 0.054322259 0.017895831 29.85274033 -1.474984203 -0.265057715 EEEMRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEMRR 6 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 103.71 0.05524 217500000 237030 273840 189930 253520 240140 247670 237630 245420 266110 246640 FALSE TRUE 227766.6055 266030.3513 224254.576 266604.1976 247864.3212 252678.0571 240538.187 240351.9912 235902.3084 229934.8531 0.990570166 1.156981413 0.975296146 1.159477104 1.077976296 1.098911512 1.046114514 1.045304737 1.025952809 1 17.81086564 1.475826321 1.206544025 1.004856726 1.078532563 0.159301163 0.056704479 0.712523321 1.999142414 0.046508542 0.015981535 29.91068239 -1.475826321 0.073675838 EEMQSNVEVVHTYR ddPTM_BT-474_Pertuzumab_2h_R1 6 EEMQSNVEVVHTYR 14 0 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ;;;;; 288.45 1.92E-34 19488460000 7461470 8275200 5784770 7235520 6570030 6832610 5649770 5967380 5635830 3932100 FALSE TRUE 7169867.503 8039199.398 6830206.621 7608946.054 6781360.982 6970770.056 5718913.575 5844151.518 4996074.206 3665775.365 1.955893853 2.193042017 1.863236544 2.075671665 1.849911767 1.901581347 1.560082931 1.594247038 1.362896989 1 21.80568695 1.476036665 0.491398455 0.981664579 2.072953883 0.913883309 0.099996817 0.201751591 0.126530935 0.096159632 0.059090462 29.9251727 -1.476036665 1.091289304 NSS(ph)SPVS(ph)PASVPGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 NS(0.212)S(0.606)S(0.182)PVS(1)PASVPGQR 152.11 4.22E-06 292740000 725640 761960 663170 889550 768870 884160 768020 761780 720180 712430 TRUE FALSE 697281.1866 740229.6468 783019.5711 935459.7821 793601.4018 902038.321 777419.2585 746048.9768 638428.1856 664176.4815 1.049843236 1.114507465 1.178932999 1.408450627 1.194865256 1.358130476 1.170501034 1.123269188 0.96123275 1 19.34120711 1.47695871 2.31332511 0.97965689 1.219155745 0.449833622 0.100385482 0.267283704 2.777976371 0.086264818 0.028496521 29.9887739 -1.47695871 0.239498855 LGEAS(ph)DSELADADK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGEASDSELADADK 14 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 LGEAS(0.998)DS(0.002)ELADADK;LGEAS(0.858)DS(0.142)ELADADK 220.25 4.94E-12 656370000 714700 557460 667270 474460 574620 639290 586580 732090 956860 862290 TRUE FALSE 686768.7339 541561.7866 787860.5323 498946.9375 593103.1742 652216.8818 593758.7415 716972.0857 848241.2643 803886.3303 0.85431075 0.673679557 0.980064597 0.620668518 0.737794825 0.811329733 0.738610322 0.89188242 1.055175629 1 19.61663199 1.477281886 3.1345331 1.025145103 0.772437567 0.535634045 0.094324914 0.168448941 3.258652294 0.065645945 0.023278948 30.01109804 -1.477281886 -0.252707536 QTFCEVPDLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 QTFCEVPDLDR 11 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ;; 116.75 0.0022047 379510000 391070 457940 347875 418180 412160 385450 430010 415730 418910 450770 FALSE TRUE 375786.552 444879.9996 410743.7509 439762.3199 425417.5007 393244.0631 435272.591 407145.0302 371357.093 420238.9464 0.894221146 1.058635815 0.977405246 1.046457792 1.012322881 0.935763014 1.035774039 0.968841736 0.883680811 1 18.68085035 1.477860637 7.654733103 0.936648563 0.996774192 0.128849985 0.054312971 0.18650847 31.6036977 0.027982562 0.012604471 30.05111824 -1.477860637 0.060125629 ETIELVHTEPTDVAQLPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETIELVHTEPTDVAQLPSR 19 0 Q6IBS0;H0Y858;D6RG15 Q6IBS0 TWF2 Twinfilin-2 0 165.74 2.13E-11 250730000 220120 309360 231360 300250 280070 295450 298100 273630 260060 279890 FALSE TRUE 211517.467 300537.3557 273171.8986 315745.9385 289078.7059 301424.2014 301748.237 267979.4449 230539.0791 260932.801 0.810620459 1.151780667 1.046905171 1.210066106 1.107866488 1.155179419 1.156421254 1.027005589 0.883518968 1 17.99331879 1.477907662 4.867075173 0.943184515 1.099189983 0.234158688 0.107012382 0.225619383 11.43634398 0.064923114 0.026326832 30.05437229 -1.477907662 0.156005467 SFLIWVNEEDHTR ddPTM_BT-474_Pertuzumab_2h_R1 7 SFLIWVNEEDHTR 13 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;;;;;; 257.91 6.46E-24 2525879000 2084502 2515374 2202769 2996036 2334441 2521012 2528696 2413149 2474168 2329487 FALSE TRUE 2003037.357 2443637.996 2600858.359 3150661.777 2409530.415 2571988.59 2559642.938 2363316.63 2193310.821 2171708.771 0.922332398 1.125214407 1.197609179 1.450775454 1.109508995 1.184315607 1.178630843 1.088229077 1.009947029 1 21.05039922 1.477915845 2.187636023 1.000110764 1.176600122 0.219775397 0.121529614 0.452244234 4.194419928 0.104479821 0.034285987 30.05493862 -1.477915845 0.176489358 LIDAEEEKR ddPTM_BT-474_Pertuzumab_2h_R1 3 LIDAEEEKR 9 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 ;; 150.61 0.00060556 329000000 792840 760020 696210 724350 782770 787000 887260 935630 1071550 1154280 FALSE TRUE 761854.9363 738344.9737 822030.6341 761733.7903 807948.5079 802913.6792 898118.5533 916308.9135 949912.1363 1076099.587 0.707978095 0.68613071 0.763898289 0.707865517 0.750812023 0.746133247 0.834605425 0.8515094 0.88273627 1 20.03738017 1.478000845 0.498631574 1.003692556 0.701657096 0.944255073 0.021993983 0.167050242 0.106909081 0.022252559 0.01349667 30.06082154 -1.478000845 -0.30203546 EYDQALADLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EYDQALADLKK 11 1 Q08752;H0Y8J0 Q08752 PPID Peptidyl-prolyl cis-trans isomerase D 0 ; 95.631 0.012208 312400000 415800 404830 363250 399450 381280 370970 410290 446730 576620 506170 FALSE TRUE 399550.0763 393284.6448 428897.3555 420065.6624 393544.2175 378471.2676 415311.2518 437504.8694 511164.515 471886.6551 0.846707725 0.833430318 0.908899099 0.89018339 0.833980392 0.802038505 0.880108067 0.927139737 1.083235793 1 18.84808085 1.47821327 2.835348934 1.040085699 0.856106468 0.803753633 0.036018281 0.103476699 1.633938525 0.028189808 0.009731503 30.07552869 -1.47821327 -0.18397923 ALYDVGDIVHSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALYDVGDIVHSVR 13 0 Q9Y4C1 Q9Y4C1 KDM3A Lysine-specific demethylase 3A 0 ; 160.38 4.40E-05 154554000 198024 194913 164578 203704 202345 195863 200398 193778 206389 192967 FALSE TRUE 190285.0032 189354.2721 194320.9056 214217.1879 208853.6107 199823.4841 202850.5307 189776.4166 182960.586 179897.1732 1.057743153 1.052569469 1.080177649 1.190775731 1.160961048 1.110765003 1.12759154 1.054916057 1.017028688 1 17.45681299 1.478217019 2.438141208 1.006385707 1.11302701 0.511392604 0.040760955 0.250745068 2.908369732 0.036988745 0.012340945 30.07578829 -1.478217019 0.106641302 SQLDIIIHSLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQLDIIIHSLKK 12 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 187.57 6.70E-06 1448700000 4591800 4593200 3801800 3707500 4115300 4495600 4312100 4543100 5309200 4976500 FALSE TRUE 4412347.379 4462206.433 4488869.831 3898844.519 4247672.362 4586504.112 4364872.77 4449283.397 4706521.874 4639437.222 0.951052287 0.961799076 0.967546195 0.840370142 0.915557676 0.988590618 0.940819449 0.959013601 1.014459653 1 22.14551838 1.478445189 1.218506427 1.009040231 0.933768377 0.328459928 0.038269814 0.542534327 1.550668586 0.036441619 0.012501624 30.09159368 -1.478445189 -0.075271854 LGVSVS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 8 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 LGVSVS(1)PSR;LGVSVS(0.997)PS(0.003)R;LGVSVS(1)PSR;LGVS(0.001)VS(0.998)PS(0.001)R;LGVSVS(0.989)PS(0.011)R;LGVSVS(0.998)PS(0.002)R;LGVS(0.004)VS(0.995)PS(0.001)R;LGVSVS(0.5)PS(0.5)R 190.66 3.86E-05 46805390000 12936840 14641930 11870690 13847160 13939790 13597310 14165880 13756670 13980150 14181500 TRUE FALSE 12431253.99 14224356.49 14015987.75 14561813.59 14388176.01 13872256.92 14339246.28 13472589.96 12393181.98 13220974.37 0.940267611 1.075893205 1.060132737 1.101417579 1.088284085 1.049261313 1.084583169 1.019031546 0.937387944 1 23.65632517 1.47857353 4.415491699 0.969600368 1.060231631 0.382445796 0.044589195 0.176755063 7.14741454 0.0283045 0.011162324 30.10048752 -1.47857353 0.090631263 EKNGNEEGEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKNGNEEGEER 11 1 A0A0G2JP90;A0A087WW46;J3KN36;A0A0G2JN29;A0A087X117;Q5JPE7-3;Q5JPE7-2;Q15155;P69849;Q5JPE7 A0A0G2JP90 NOMO1;NOMO3;NOMO2 Nodal modulator 2;Nodal modulator 1;Nodal modulator 3 0 64.121 0.064121 92054000 109710 124480 113260 113950 102080 118020 120820 132800 176870 151300 FALSE TRUE 105422.4119 120929.9523 133728.6015 119830.9732 105363.4959 120406.4453 122298.6313 130057.6336 156792.4591 141052.3162 0.747399367 0.857341131 0.948078025 0.849549843 0.746981678 0.853629692 0.867044474 0.922052449 1.111590815 1 17.10587083 1.479048226 2.862453358 1.054202704 0.841015597 0.65811296 0.061587402 0.150967501 2.434244368 0.047857469 0.016577276 30.13340618 -1.479048226 -0.213187107 KGSMSNGHGS(ph)PGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGSMSNGHGSPGEK 14 1 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 KGSMSNGHGS(1)PGEK 116.96 0.00015582 87180000 153500 160100 132990 141980 142120 154230 159560 160280 190270 183170 TRUE FALSE 147501.0503 155534.1048 157024.2513 149307.6048 146691.4189 157348.6363 161512.743 156970.162 168671.3473 170763.7327 0.863772699 0.910814622 0.919540987 0.874351962 0.859031461 0.921440599 0.945825793 0.919224237 0.987746898 1 17.38164208 1.479252721 0.792275804 1.001850147 0.889236628 0.729732282 0.023656201 0.318342817 0.419196519 0.022780643 0.009414207 30.14759838 -1.479252721 -0.112613519 VIPSQEHLNGPLPVPFT(ph)NGEIQKENSREALAEAALESPRPALVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVR 44 3 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 VIPSQEHLNGPLPVPFT(0.333)NGEIQKENS(0.333)REALAEAALES(0.333)PRPALVR 74.889 0.00050425 491950000 28676 37711 21119 22412 30103 35433 26928 28724 23712 28376 TRUE FALSE 27555.31022 36635.5192 24935.67309 23568.68601 31071.29033 36149.47954 27257.55292 28130.83936 21020.31317 26454.06825 1.041628454 1.384872786 0.942602584 0.890928601 1.174537317 1.366499822 1.030372821 1.063384244 0.794596618 1 14.69120198 1.479982678 2.959072521 0.900555169 1.124341387 0.220413071 0.160257438 0.365734922 6.321869461 0.123424191 0.043184981 30.19831273 -1.479982678 0.223786218 IDPWSFVSAGPRPSPLPS(ph)PQPAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDPWSFVSAGPRPSPLPSPQPAPR 24 1 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 IDPWSFVSAGPRPS(0.172)PLPS(0.828)PQPAPR;IDPWSFVSAGPRPS(0.036)PLPS(0.964)PQPAPR 117.88 0.00037881 620630000 250090 275078 211025 241540 288060 275930 225359 262530 211695 248074 TRUE FALSE 240316.2063 267233.0448 249161.9117 254005.9083 297325.7115 281509.4937 228117.0109 257108.6638 187664.2711 231271.727 1.039107587 1.155493792 1.077355693 1.098300737 1.285612017 1.217223987 0.986359266 1.111716798 0.811444933 1 17.81922938 1.480052795 2.079793309 0.915702983 1.13517069 0.416805003 0.095714122 0.283348538 2.3728783 0.079185029 0.025899733 30.20318862 -1.480052795 0.219467708 RLS(ph)ASSTGSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSASSTGSTR 11 1 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 1 RLS(0.564)AS(0.053)S(0.061)T(0.061)GS(0.131)T(0.131)R;RLS(0.999)ASSTGSTR 86.578 0.0048466 266870000 304160 342518 301152 345358 322607 354600 321209 332059 349063 324258 TRUE FALSE 292273.0909 332749.722 355576.8655 363181.9678 332983.9471 361770.255 325140.0518 325201.8656 309438.8316 302295.7168 0.966844962 1.10074243 1.176255056 1.20141288 1.101517251 1.196742907 1.075569496 1.075773977 1.02362956 1 18.20560101 1.480206755 1.513653621 1.004468324 1.126486192 0.301520898 0.064490222 0.457270841 1.997431508 0.058185926 0.019164111 30.21389776 -1.480206755 0.122017868 DLLDDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLDDLK 7 0 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 112.17 0.014922 155679000 480630 421510 393600 440000 348090 309770 377450 519240 596070 647350 FALSE TRUE 461846.4482 409488.9475 464732.2756 462708.4527 359286.631 316033.7616 382069.346 508517.5125 528406.6325 603504.4079 0.765274358 0.678518569 0.770056141 0.76670269 0.595333897 0.52366438 0.633084599 0.842607785 0.875563833 1 19.20300478 1.48068581 2.329136451 0.947027059 0.675166045 0.64150184 0.080651761 0.198348986 2.101243702 0.072940137 0.024198968 30.247244 -1.48068581 -0.271861014 QGANINEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 QGANINEIR 9 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;; 143.37 0.00023752 1175340000 938510 1017710 811270 982770 971840 992710 997280 978330 1001490 1023610 FALSE TRUE 901831.9916 988685.9072 957884.5356 1033490.877 1003100.116 1012783.276 1009485.011 958127.1436 887805.0538 954279.983 0.9450392 1.036054329 1.003777249 1.083005927 1.05115913 1.061306215 1.057849928 1.00403148 0.930340225 1 19.86405309 1.480780406 4.959997269 0.964807156 1.036236104 0.327901001 0.039178386 0.182040008 9.702779548 0.024327417 0.009968248 30.25383306 -1.480780406 0.071428949 TSLFEEDEEDDLFAIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSLFEEDEEDDLFAIAK 17 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 0 161.1 7.00E-09 23278000 25704 24701 24985 27521 24118 22668 27811 31206 40052 38690 FALSE TRUE 24699.45926 23996.55166 29500.34529 28941.36211 24893.77737 23126.36249 28151.35934 30561.58519 35505.46487 36069.49184 0.684774251 0.665286658 0.817875268 0.802377872 0.690161577 0.641161306 0.780475629 0.84729736 0.984362769 1 15.13849148 1.480882127 1.812043815 1.002839054 0.722485846 0.793503908 0.054701937 0.154980381 0.976671153 0.050991502 0.016603235 30.26091996 -1.480882127 -0.280353209 LFIGGLSFETTEESLR ddPTM_BT-474_Pertuzumab_2h_R1 6 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 331.48 3.38E-71 1922461000 351706.1 358363.6 252192.2 298280 337315 330274.5 337322.2 317808.5 307574 323454.3 FALSE TRUE 337961.0368 348143.421 297768.9405 313674.2665 348165.0433 336952.8767 341450.45 311245.6434 272659.489 301546.4522 1.120759453 1.154526669 0.98747287 1.040218727 1.154598374 1.117416154 1.13233118 1.032164833 0.904203936 1 18.20202074 1.481681234 4.25316863 0.953637326 1.098510017 0.550702412 0.053712498 0.145496193 5.441601716 0.036779102 0.014408684 30.31665165 -1.481681234 0.144872691 HYCESLRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HYCESLRPR 9 1 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 120.99 0.00037643 299630000 28542 35275 30029 34604 33938 28424 41727 32044 28432 35115 FALSE TRUE 27426.54709 34268.99154 35455.90829 36389.91659 35029.64659 28998.75275 42237.66751 31382.2802 25204.51856 32736.62977 0.83779385 1.046808782 1.083065317 1.111596302 1.070044376 0.885819736 1.290226508 0.958628925 0.76991794 1 14.99861818 1.481926158 12.53401438 0.878050887 1.050493857 0.209422838 0.127116207 0.09926106 89.57646187 0.065074781 0.030152526 30.33375382 -1.481926158 0.172442971 RPS(ph)PQPSPR ddPTM_BT-474_Pertuzumab_2h_R1 7 RPSPQPSPR 9 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(0.989)PQPS(0.011)PR;RPS(1)PQPSPR;RPS(0.994)PQPS(0.006)PR;RPS(0.988)PQPS(0.012)PR 128.85 0.0002486 3345630000 1461861 1817360 1367685 1812265 1548559 1510961 1755553 1569767 1532067 1561481 TRUE FALSE 1404729.856 1765530.672 1614856.103 1905796.214 1598369.807 1541513.667 1777037.983 1537350.763 1358153.177 1455720.501 0.964972228 1.212822565 1.109317415 1.309177285 1.097992235 1.058935191 1.220727455 1.056075505 0.932976609 1 20.47330195 1.482083045 4.580480099 0.971049314 1.142716696 0.365836145 0.09106155 0.180403055 7.993561182 0.055869661 0.022404477 30.34471372 -1.482083045 0.171667381 SAAAGALGS(ph)PGLPLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAAAGALGSPGLPLRK 16 1 O75145-2;O75145;A0A0C4DGR8;A0A0C4DGR7 O75145-2 PPFIA3 Liprin-alpha-3 1 SAAAGALGS(1)PGLPLRK 121.26 6.11E-05 625260000 358280 370650 299670 271630 294380 360640 327840 372990 463170 420920 TRUE FALSE 344278.0215 360079.4249 353827.0351 285648.8569 303849 367932.3879 331852.204 365287.6262 410592.8834 392410.7135 0.877341035 0.917608548 0.901675268 0.72793338 0.774313722 0.937620649 0.845675698 0.930880869 1.04633454 1 18.5820049 1.482110595 2.777673128 1.022974587 0.85381818 0.543373623 0.061488438 0.204334986 3.115488877 0.050777373 0.017507508 30.34663879 -1.482110595 -0.169156407 QVEEKPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVEEKPQR 8 1 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 93.649 0.0099582 631240000 819460 996790 748280 962800 1015320 1002770 934900 927460 856790 955570 FALSE TRUE 787434.5972 968362.5252 883510.8414 1012490.223 1047978.69 1023046.696 946341.5859 908307.6269 759530.7912 890848.3928 0.883915382 1.087011587 0.991763412 1.136546052 1.176382759 1.148395961 1.062292522 1.019598435 0.852592649 1 19.7648204 1.482133673 3.763361394 0.926129372 1.075805017 0.294164934 0.086511082 0.242915183 6.956138329 0.060362848 0.022776132 30.34825139 -1.482133673 0.149675645 MGPSGGEGMEPERRDS(ph)QDGSSYR ddPTM_BT-474_Pertuzumab_2h_R1 31 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.999)QDGS(0.001)S(0.001)YR;MGPSGGEGMEPERRDS(0.997)QDGS(0.002)S(0.001)YR;MGPS(0.001)GGEGMEPERRDS(0.868)QDGS(0.045)S(0.045)Y(0.041)R;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.991)QDGS(0.004)S(0.004)YR;MGPSGGEGMEPERRDS(0.999)QDGSS(0.001)YR;MGPSGGEGMEPERRDS(0.919)QDGS(0.04)S(0.04)YR;MGPSGGEGMEPERRDS(0.863)QDGS(0.055)S(0.082)YR;MGPSGGEGMEPERRDS(0.643)QDGS(0.261)S(0.096)YR;MGPSGGEGMEPERRDS(0.738)QDGS(0.131)S(0.131)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.583)QDGS(0.344)S(0.072)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.998)QDGS(0.001)S(0.001)YR;MGPSGGEGMEPERRDS(0.889)QDGS(0.055)S(0.055)Y(0.001)R;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.999)QDGS(0.001)SYR;MGPSGGEGMEPERRDS(0.989)QDGS(0.005)S(0.005)YR;MGPSGGEGMEPERRDS(0.893)QDGS(0.054)S(0.054)YR;MGPSGGEGMEPERRDS(0.947)QDGS(0.027)S(0.027)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.453)QDGS(0.094)S(0.453)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR 357.89 3.01E-102 54489567600 9510367.6 11127501.8 6456895.3 8258373.3 10421060.9 10389665.2 8806459.3 8877461.9 8539673.6 8017584.3 TRUE FALSE 9138691.92 10810156.34 7623799.914 8684588.936 10756263.79 10599751.35 8914235.383 8694139.209 7570285.654 7474546.174 1.222641711 1.446262568 1.019968268 1.161888459 1.439052424 1.418113033 1.192612257 1.163166165 1.012808735 1 22.83355456 1.482290099 1.845766688 0.99842024 1.279142206 0.410030824 0.127514704 0.342830473 2.246653573 0.114237758 0.037230048 30.35918431 -1.482290099 0.280721966 RPGAPSLS(ph)PAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPGAPSLSPAPR 12 1 Q5QP82-2;Q5QP82 Q5QP82-2 DCAF10 DDB1- and CUL4-associated factor 10 1 RPGAPS(0.054)LS(0.946)PAPR;RPGAPS(0.197)LS(0.803)PAPR 88.768 0.0060026 457960000 158939 196764 151825 182575 174740 188759 173350 180079 178098 181611 TRUE FALSE 152727.4882 191152.4834 179263.1548 191997.7176 180360.6708 192575.8363 175471.5092 176360.3057 157881.0617 169310.3252 0.902056552 1.129006652 1.05878454 1.133998871 1.065266814 1.137413422 1.036389889 1.041639401 0.932495177 1 17.36931043 1.482340134 2.599267475 0.967840974 1.073792633 0.244490292 0.066935637 0.327010113 4.353240301 0.049419072 0.016772111 30.36268221 -1.482340134 0.10595166 LNQPGT(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 3 LNQPGTPTR 9 0 P36507;G5E9C7;M0R1B6 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 LNQPGT(0.996)PT(0.004)R;LNQPGT(0.999)PT(0.001)R;LNQPGT(0.632)PT(0.368)R 145.95 0.0010727 23523700000 7910400 8059400 6705900 8818900 7734000 7835200 8056000 7724900 7625300 7548400 TRUE FALSE 7601252.823 7829553.803 7917805.302 9274044.486 7982771.134 7993633.112 8154591.738 7565378.115 6759707.912 7037140.145 1.080162206 1.112604502 1.12514532 1.317871223 1.134377172 1.135920693 1.158793426 1.075064296 0.960575997 1 22.74655781 1.482344356 2.750264872 0.980622181 1.154740493 0.558539556 0.060761953 0.191687199 2.865073939 0.048823192 0.01679535 30.36297735 -1.482344356 0.174118312 LKGDDLQAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKGDDLQAIK 10 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;P07910-2;G3V4C1;B2R5W2;G3V2D6;A0A0G2JNQ3;O60812;B2RXH8;A0A0G2JPF8;P0DMR1;B7ZW38 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2;HNRNPCL4;HNRNPCL3 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3 0 ; 109.6 0.0029378 0 7297000 6880000 8445000 7811000 6652300 6685100 8603500 9734100 10850100 12043900 FALSE TRUE 7011825.173 6683789.136 9971199.358 8214126.646 6866277.271 6820277.302 8708792.207 9533087.433 9618442.135 11228155.93 0.62448591 0.595270424 0.888053161 0.731565067 0.611523149 0.607426308 0.775620882 0.849034115 0.85663596 1 23.42061767 1.482574679 1.174739545 0.972074985 0.68267634 0.588332831 0.086742445 0.331304283 0.883078995 0.08321384 0.028879433 30.37908432 -1.482574679 -0.289398645 VLDILEDYCMWR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLDILEDYCMWR 12 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 132.78 0.00040691 422030000 350380 383240 313110 384130 340680 357050 375630 351300 319450 367090 FALSE TRUE 336686.7622 372310.3704 369695.9421 403954.9953 351638.2816 364269.7956 380227.0723 344045.5322 283187.3752 342226.6673 0.983812176 1.087905783 1.080266319 1.180372642 1.027501113 1.064410902 1.111038702 1.005314796 0.827484829 1 18.38459266 1.483035331 4.677752749 0.912209123 1.07774549 0.521057782 0.062069618 0.124072357 5.781867651 0.037468792 0.015144496 30.41132423 -1.483035331 0.165536367 STELDSNWNWFQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 STELDSNWNWFQLR 14 0 Q8N6H7;G5E9L0;A0A0D9SF70;E9PQP3;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48;H0YDX1;E9PMR9;E9PM63 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 142.76 2.17E-05 119150000 109650 104890 115920 112800 101800 109640 104320 121620 144570 131980 FALSE TRUE 105364.7568 101898.6399 136869.3226 118621.6215 105074.4895 111856.9959 105596.6994 119108.5045 128159.0197 123040.877 0.856339448 0.828168998 1.112389036 0.96408303 0.853980335 0.909104345 0.858224534 0.968040113 1.041597092 1 16.90877817 1.483035384 5.084988603 1.01765223 0.915707692 0.241957134 0.07765265 0.259196092 14.70996905 0.050279936 0.020830623 30.4113279 -1.483035384 -0.101944538 NEEPVRS(ph)PERR ddPTM_BT-474_Pertuzumab_2h_R1 9 NEEPVRSPERR 11 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR 106.14 0.0018677 14016423000 4251244 4503706 3534250 4153621 4036574 4128328 4107977 4140405 4071057 4194281 TRUE FALSE 4085100.684 4375264.714 4172967.594 4367989.878 4166414.069 4211805.621 4158251.651 4054904.19 3608927.677 3910198.612 1.044729716 1.118936696 1.06720093 1.117076218 1.065524921 1.077133424 1.063437453 1.037007219 0.922952524 1 21.89881046 1.483375599 2.977211833 0.962435951 1.080956917 0.719124815 0.028796424 0.110505674 1.946655491 0.019819326 0.006972687 30.43516071 -1.483375599 0.118520967 KGFSEGLWEIENNPTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGFSEGLWEIENNPTVK 17 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 182.31 1.21E-09 1405310000 2034500 2009950 1377220 1412850 1593230 1969380 1636030 1846470 2121800 1970800 FALSE TRUE 1954989.491 1952628.194 1626114.29 1485767.358 1644477.69 2009202.213 1656052.225 1808339.749 1880942.159 1837315.961 1.064046431 1.062761243 0.885048802 0.808661869 0.89504349 1.093552909 0.901343188 0.984229054 1.023744527 1 20.80916832 1.483500067 7.738546476 1.009517251 0.955902166 0.05625638 0.08702643 0.377612723 63.56151277 0.051987044 0.023591904 30.4438846 -1.483500067 -0.053615085 QPPLLGDHPAEYGEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPPLLGDHPAEYGEGR 16 0 A0A3B3ITJ4 A0A3B3ITJ4 0 ; 178.12 2.84E-09 721590000 221700 261210 219860 260310 241760 261190 256740 251740 258520 261700 FALSE TRUE 213035.7189 253760.5466 259593.5928 273744.6303 249536.43 266471.4408 259882.0609 246541.481 229173.8934 243974.8259 0.873187298 1.040109551 1.064017944 1.122019984 1.022795811 1.092208755 1.065200313 1.010520164 0.939334182 1 17.89637277 1.483717029 4.596255608 0.969974738 1.045061074 0.156942945 0.063930386 0.300361803 13.45531355 0.040840822 0.016437721 30.45909735 -1.483717029 0.075086336 IGPLGLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 IGPLGLSPK 9 0 P30050 P30050 RPL12 60S ribosomal protein L12 1 IGPLGLS(1)PK;IGPLGLS(1)PK;IGPLGLS(1)PK 110.93 0.0023149 2059970000 4926900 4280020 3610270 3451340 3776710 4128940 4170420 4659900 5599780 5395580 TRUE FALSE 4734351.301 4157958.02 4262726.099 3629464.071 3898191.307 4212429.996 4221458.847 4563671.437 4964116.451 5030132.561 0.941198118 0.826610029 0.847438124 0.721544418 0.774967908 0.837439162 0.839234115 0.907266634 0.986875871 1 22.26216499 1.483723273 1.684161844 1.002968571 0.819235444 0.619052405 0.052537624 0.23152577 1.25749437 0.047642079 0.015574765 30.4595353 -1.483723273 -0.183733126 RGS(ph)MS(ph)S(ph)VTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSMSSVTK 9 1 E9PDV9;B3KU01;H0Y8V9;A0A0A0MQU6;Q9H2E6;Q9H2E6-2 E9PDV9 SEMA6A Semaphorin-6A 3 RGS(0.995)MS(0.995)S(0.995)VT(0.015)K 41.189 0.076904 0 63839 98257 76929 130410 114010 122700 103480 91152 69782 78156 TRUE FALSE 61344.1013 95454.80656 90831.78158 137140.4757 117677.2352 125181.0781 104746.4192 89269.67935 61860.63991 72862.42451 0.841916828 1.310069041 1.246620356 1.88218381 1.615060657 1.718047113 1.437591734 1.225181291 0.849006059 1 16.15288738 1.483871166 2.894125564 0.929254334 1.457723479 0.356294155 0.271141486 0.275578103 4.585072314 0.217821106 0.076070256 30.46990963 -1.483871166 0.528469145 RFDEILEASDGIMVAR ddPTM_BT-474_Pertuzumab_2h_R1 34 RFDEILEASDGIMVAR 16 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 322.68 4.56E-58 27020258900 9208453.6 10187868.9 8168050.2 9849280 9939373.2 10268666.3 9673668.9 9578026 9393346.2 9456715.7 FALSE TRUE 8848577.053 9897320.854 9644198.568 10357602.52 10259082.17 10476305.77 9792058.154 9380236.416 8327052.919 8816203.922 1.003672003 1.122628394 1.093917365 1.174836995 1.163662077 1.188301208 1.110688709 1.063976798 0.944516823 1 23.07172616 1.484004426 2.771506783 0.973452126 1.127468572 0.5727158 0.051084773 0.178227757 2.714121412 0.040303209 0.0139158 30.47926049 -1.484004426 0.154016446 DGVVEITGK ddPTM_BT-474_Pertuzumab_2h_R1 6 DGVVEITGK 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 173.48 0.00012889 3079320000 3767980 3396140 3280890 3399520 3342520 3646660 3634330 4032510 4879970 4661940 FALSE TRUE 3620723.176 3299285.412 3873819.806 3574969.635 3450035.191 3720397.964 3678808.018 3949237.259 4326016.264 4346182.651 0.833081227 0.759122586 0.891315464 0.822553933 0.793808146 0.856015097 0.846445792 0.908668037 0.995359977 1 22.05131738 1.484337223 1.530397017 1.007895912 0.824072578 0.809073524 0.032996086 0.146124521 0.653402583 0.028216296 0.009300791 30.50262554 -1.484337223 -0.183823334 GTEPS(ph)PGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 2 GTEPS(0.971)PGGT(0.042)PQPS(0.278)RPVS(0.709)PAGPPEGVPEEAQPPR;GT(0.258)EPS(0.717)PGGT(0.026)PQPS(0.042)RPVS(0.958)PAGPPEGVPEEAQPPR;GTEPS(0.994)PGGT(0.006)PQPS(0.027)RPVS(0.973)PAGPPEGVPEEAQPPR;GTEPS(0.999)PGGT(0.008)PQPS(0.054)RPVS(0.939)PAGPPEGVPEEAQPPR 234.67 6.06E-47 2072090000 771211 894442 764868 1121022 1002469 1039111 947678 921134 856943 903081 TRUE FALSE 741071.2215 868933.3899 903096.662 1178878.08 1034714.326 1060122.536 959275.9668 902112.261 759666.4232 841914.5195 0.880221453 1.032092178 1.072670255 1.400234884 1.229001641 1.259180727 1.139398294 1.071501014 0.902308258 1 19.68331424 1.484761515 3.092203137 0.953366854 1.154458424 0.24202428 0.134089425 0.346478683 6.615344693 0.107131263 0.038166438 30.53244019 -1.484761515 0.201091571 DTPGFIVNR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTPGFIVNR 9 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;;; 134.08 0.00060219 436060000 444489 636300 513838 729370 541710 593800 627960 521650 468320 452360 FALSE TRUE 427117.8785 618153.347 606699.9569 767012.8731 559134.5941 605807.0428 635645.1623 510877.7452 415158.277 421721.2543 1.012796662 1.465786561 1.438627887 1.818767409 1.325839256 1.436510578 1.507263757 1.21141095 0.984437642 1 18.68593021 1.484793324 2.86434427 0.993891353 1.442083625 0.46875181 0.18638776 0.21133676 3.448231191 0.141082644 0.049180865 30.53467653 -1.484793324 0.448192272 ERPLQQVS(ph)PVASVPWR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPLQQVSPVASVPWR 16 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 ERPLQQVS(1)PVASVPWR;ERPLQQVS(1)PVASVPWR 140.48 1.03E-06 1299890000 607220 688870 603320 785030 799360 730230 693170 664310 631230 596650 TRUE FALSE 583489.1711 669224.1021 712353.3448 825545.4924 825072.1404 744995.7509 701653.2218 650591.7664 559575.4167 556238.3641 1.04899124 1.203124677 1.280662016 1.484157774 1.483306787 1.339346221 1.261425438 1.169627642 1.005999321 1 19.08534373 1.484827193 1.866161787 0.992405355 1.314847945 0.494558468 0.1198999 0.294877854 1.980820548 0.11361823 0.037095646 30.53705796 -1.484827193 0.32244259 RIQLVEEELDR ddPTM_BT-474_Pertuzumab_2h_R1 7 RIQLVEEELDR 11 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;;;; 297.32 1.91E-35 11050500000 4421300 5100574 3712358 4397871 4472660 4986550 4492568 4462289 4287806 4371220 FALSE TRUE 4248510.708 4955110.624 4383263.672 4624845.649 4616527.171 5087381.458 4547549.391 4370141.173 3801072.239 4075153.376 1.042540075 1.215932302 1.075607043 1.134888732 1.132847465 1.24839018 1.115921039 1.072386919 0.932743357 1 21.95842293 1.485534515 2.755821245 0.967999307 1.142393974 0.56630885 0.059108845 0.169537465 2.558718727 0.043317274 0.014958692 30.5868332 -1.485534515 0.174394667 QAS(ph)PTEVVER ddPTM_BT-474_Pertuzumab_2h_R1 6 QASPTEVVER 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 QAS(1)PTEVVER;QAS(0.997)PT(0.003)EVVER;QAS(0.807)PT(0.193)EVVER;QAS(0.807)PT(0.193)EVVER;QAS(1)PTEVVER;QAS(0.922)PT(0.078)EVVER 228.76 2.04E-09 4426910000 1387350 1525830 1189276 1351550 1443800 1551320 1476310 1432890 1453000 1485040 TRUE FALSE 1333130.828 1482314.822 1404204.629 1421303.657 1490241.138 1582688.753 1494377.523 1403300.321 1288061.531 1384456.918 0.962926914 1.070683243 1.014263868 1.02661458 1.076408459 1.143183824 1.079396191 1.013610682 0.930373141 1 20.40088873 1.485795327 4.553943841 0.965698232 1.055453014 0.353811989 0.047475944 0.194106397 8.543656859 0.03149673 0.012682648 30.60520744 -1.485795327 0.089754783 VTSSITIYPSDSS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTSSITIYPSDSSSPR 16 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 VTSSITIYPSDS(0.059)S(0.471)S(0.471)PR 215.48 1.69E-14 78521000 94258 105360 96509 96920 89129 104060 97703 99860 92743 108160 TRUE FALSE 90574.29315 102355.236 113950.3231 101922.0528 91995.91523 106164.1645 98898.71854 97797.8561 82215.20345 100834.2269 0.898249493 1.015084254 1.130075835 1.010788261 0.912348099 1.052858417 0.980805046 0.969887499 0.815350164 1 16.6216259 1.486276514 4.384234018 0.902737341 1.003343048 0.185202639 0.074905197 0.267156659 10.79612146 0.047768954 0.019024363 30.63913595 -1.486276514 0.100605707 LPVWVVEDHQEVLPFIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPVWVVEDHQEVLPFIYR 18 0 Q49AR2;E5RFG1;B4DR92;E5RHP8 Q49AR2 C5orf22 UPF0489 protein C5orf22 0 ; 211.12 3.37E-16 387090000 164718 197512 138074 158162 187203 160685 186831 166046 156542 172730 FALSE TRUE 158280.6385 191879.1511 163027.0432 166324.7598 193224.5545 163934.1608 189117.4937 162617.0921 138772.0084 161030.8432 0.982921254 1.191567698 1.012396383 1.032875171 1.19992264 1.018029574 1.174417831 1.00985059 0.861772848 1 17.29697752 1.486421609 5.714815139 0.930978236 1.088299151 0.378834249 0.080661111 0.135748743 10.23937693 0.043824894 0.01884943 30.64937406 -1.486421609 0.157320914 ELQGDGPPSSPT(ph)NDPTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELQGDGPPSSPTNDPTVK 18 0 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 ELQGDGPPS(0.304)S(0.304)PT(0.391)NDPTVK 89.374 0.032453 816290000 458030 574570 437540 567640 521080 583890 483500 530500 472340 504830 TRUE FALSE 440129.6812 558183.8262 516613.211 596935.9684 537841.0114 595696.6559 489417.2176 519544.9896 418721.9434 470637.4144 0.935177841 1.186016685 1.097688359 1.268356382 1.142792721 1.265723118 1.039902912 1.103917737 0.889691152 1 18.84425649 1.486486868 2.055337325 0.949845715 1.147635099 0.342055013 0.099199999 0.315923378 2.599018254 0.079048166 0.025959277 30.65397987 -1.486486868 0.197789383 SQGDEAGGHGEDRPEPLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 SQGDEAGGHGEDRPEPLSPK 20 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 SQGDEAGGHGEDRPEPLS(1)PK;SQGDEAGGHGEDRPEPLS(1)PK;SQGDEAGGHGEDRPEPLS(1)PK;SQGDEAGGHGEDRPEPLS(1)PK;SQGDEAGGHGEDRPEPLS(1)PK 200.74 8.02E-22 7909290000 7474730 6935500 6219865 6113601 6566650 6329396 6720420 7189990 8356230 7777260 TRUE FALSE 7182609.288 6737706.331 7343932.966 6429124.68 6777872.261 6457380.724 6802666.51 7041514.194 7407665.803 7250499.253 0.990636512 0.929274812 1.012886521 0.886714757 0.934814559 0.890611874 0.93823422 0.971176459 1.021676652 1 22.78964891 1.487135108 3.096095017 1.009927935 0.938826375 0.363950358 0.036932107 0.246434891 4.739304111 0.026977357 0.009640939 30.699769 -1.487135108 -0.071101559 MKETAEAYLGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 MKETAEAYLGKK 12 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 91.441 0.0046661 1091160000 1317490 1263460 908730 917950 1042400 1074530 1056430 1175330 1353910 1272510 FALSE TRUE 1266001.034 1227427.358 1072957.726 965325.5095 1075929.743 1096257.733 1069358.906 1151059.025 1200219.813 1186321.764 1.067164974 1.034649616 0.904440733 0.813713057 0.90694597 0.924081279 0.901407138 0.970275569 1.011715244 1 20.17806393 1.487332315 4.193974098 1.003500795 0.932366472 0.146040537 0.067295267 0.394214124 14.45432937 0.048912907 0.019240959 30.71371254 -1.487332315 -0.071134323 KDS(ph)ISEDEMVLR ddPTM_BT-474_Pertuzumab_2h_R1 3 KDSISEDEMVLR 12 1 Q8N5D0-5;Q8N5D0-3;Q8N5D0-6;Q8N5D0-2;Q8N5D0-4;Q8N5D0 Q8N5D0-5 WDTC1 WD and tetratricopeptide repeats protein 1 1 KDS(0.999)IS(0.001)EDEMVLR;KDS(0.79)IS(0.21)EDEMVLR;KDS(0.979)IS(0.021)EDEMVLR 199.05 1.08E-07 1174700000 709870 669250 552290 636760 640690 680310 729990 753580 833910 884410 TRUE FALSE 682127.4956 650163.6453 652101.0886 669623.2599 661298.3757 694066.3343 738923.836 738018.3097 739248.0328 824508.1229 0.827314464 0.788547289 0.790897106 0.812148772 0.802051984 0.841794417 0.896199583 0.895101321 0.896592783 1 19.65317418 1.487485872 0.471161358 0.998998529 0.790011033 0.916858458 0.018274239 0.231237711 0.13635223 0.020528912 0.013201385 30.72457415 -1.487485872 -0.208987496 AVNENHK ddPTM_BT-474_Pertuzumab_2h_R1 4 AVNENHK 7 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;H0Y562 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ;;; 108.92 0.0071435 325187000 420881 424809 361114 496413 397012 322851 509616 423433 388442 526888 FALSE TRUE 404432.5052 412693.8633 426375.3327 522032.9344 409782.2515 329379.2684 515852.8331 414688.9606 344347.6926 491201.4065 0.82335372 0.840172397 0.868025472 1.062767589 0.834244866 0.67055848 1.050185985 0.844234066 0.701031569 1 18.90595517 1.487555656 24.99999637 0.824545581 0.880319686 0.00343996 0.126219052 3.02221579 7222.448265 0.066401974 0.030740445 30.7295115 -1.487555656 0.055774106 LENNDNKPVTNSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LENNDNKPVTNSR 13 1 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 ;;; 214.18 2.85E-11 4032460000 3599190 3489190 2702550 2983530 3245860 3474020 3231270 3664930 4111540 4030590 FALSE TRUE 3458529.676 3389681.717 3190960.903 3137510.341 3350266.035 3544267.065 3270815.249 3589247.915 3644815.216 3757594.549 0.920410553 0.902088204 0.84920309 0.834978415 0.891598599 0.943227647 0.870454544 0.955198297 0.969986295 1 21.84137798 1.488222662 0.936349598 1.001903503 0.880818039 0.631870318 0.031000202 0.337449785 0.592162207 0.029715892 0.011243641 30.77674325 -1.488222662 -0.121085464 TVSSDGCS(ph)TPSREEGGCSLASTPATTLHLLQLSGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQR 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 TVSSDGCS(0.494)T(0.494)PS(0.013)REEGGCSLASTPATTLHLLQLSGQR 253.1 3.98E-62 801600000 106870 137790 82422 108250 109720 110320 110870 108340 107610 107610 TRUE FALSE 102693.4022 133860.3641 97317.48887 113836.7955 113249.2434 112550.746 112226.8602 106102.7411 95394.56394 100321.4789 1.023643226 1.334314103 0.970056363 1.13472007 1.128863377 1.121900786 1.118672307 1.057627363 0.950888733 1 16.61427099 1.489340733 2.815921476 0.976292897 1.122587959 0.287927055 0.089294983 0.291336074 4.627466542 0.063088584 0.021999009 30.85607863 -1.489340733 0.146295062 TSALS(ph)PNAK ddPTM_BT-474_Pertuzumab_2h_R1 4 TSALSPNAK 9 0 P50616 P50616 TOB1 Protein Tob1 1 TSALS(1)PNAK;TSALS(1)PNAK;TSALS(1)PNAK;TSALS(1)PNAK 173.72 5.79E-05 1067290000 1496820 1419300 1459840 1455340 1692270 1521920 1373890 1493730 1545520 1361000 TRUE FALSE 1438322.62 1378822.954 1723665.562 1530450.272 1746703.401 1552694.265 1390704.077 1462883.954 1370079.049 1268818.258 1.13359231 1.086698544 1.358481052 1.206201331 1.376637979 1.2237326 1.096062473 1.152949955 1.079807167 1 20.27505401 1.489412742 0.993427807 1.015373919 1.230972364 0.408959774 0.088814173 0.511525675 0.998022946 0.084052213 0.030997314 30.86119525 -1.489412742 0.215598445 RGVGS(ph)PPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGVGSPPGR 9 1 O96028;O96028-5;O96028-3;H0Y9L4;O96028-6 O96028 WHSC1 Histone-lysine N-methyltransferase NSD2 1 RGVGS(1)PPGR 53.448 0.08669 137310000 59607 86165 63584 110140 81797 86197 79995 73009 50527 63529 TRUE FALSE 57277.49254 83707.65856 75075.04322 115824.3386 84428.07479 87939.9624 80974.00274 71501.33864 44791.38679 59226.12424 0.967098443 1.413357022 1.267600137 1.955629211 1.425520847 1.484817106 1.367200771 1.207260133 0.756277527 1 15.85394606 1.489525937 2.744860938 0.881991427 1.43093266 0.43808023 0.237146394 0.227240922 3.425225969 0.182590986 0.063254276 30.86924 -1.489525937 0.548941233 SFSSQRPGMER ddPTM_BT-474_Pertuzumab_2h_R1 2 SFSSQRPGMER 11 1 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 0 ; 140.63 3.51E-05 541410000 263940 253100 214800 252620 249270 226200 265490 245450 254400 248620 FALSE TRUE 253624.933 245881.8358 253619.1382 265657.7485 257287.9959 230773.919 268739.146 240381.3717 225521.5785 231780.746 1.094245046 1.060838055 1.094220045 1.146159692 1.110049046 0.995656123 1.159454142 1.037106731 0.972995309 1 17.8224012 1.489679424 5.32061416 0.990744762 1.09233735 0.506691681 0.043009288 0.126452544 8.029260782 0.025375688 0.010762092 30.88015159 -1.489679424 0.101592589 QDEGVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QDEGVLK 7 0 Q02790;F5H120 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 84.476 0.08212 0 318110 302020 246370 275000 285730 301690 336820 324230 402140 403310 FALSE TRUE 305677.9095 293406.6853 290894.5395 289192.783 294920.7649 307790.3785 340942.1039 317534.5372 356490.7531 375993.4545 0.812987316 0.780350514 0.773669158 0.769143131 0.784377391 0.818605683 0.9067767 0.84452145 0.94813021 1 18.52034802 1.489815127 0.619072723 1.00014963 0.777032484 0.868834103 0.02779104 0.232934205 0.20483019 0.026984721 0.013456687 30.88980217 -1.489815127 -0.223117147 DFLMLAQTHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFLMLAQTHSK 11 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 133.05 0.00016976 412050000 1075000 1089600 911310 976420 1026200 859390 1059800 1120600 1344600 1276600 FALSE TRUE 1032987.812 1058525.675 1076003.989 1026813.153 1059208.655 876767.4546 1072770.149 1097459.218 1191966.645 1190134.745 0.867958705 0.889416664 0.90410266 0.862770504 0.889990532 0.736695957 0.901385456 0.922130224 1.001539238 1 20.18269349 1.489895222 2.135735493 1.002130607 0.86259384 0.592069117 0.045186984 0.212003647 1.896929905 0.03824002 0.012638578 30.89549956 -1.489895222 -0.139536767 AIEIYTDMGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AIEIYTDMGR 10 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R0I4;M0R027 P54920 NAPA Alpha-soluble NSF attachment protein 0 128.28 0.00077647 244570000 128140 153210 100260 141570 148820 114640 146110 133820 140490 135890 FALSE TRUE 123132.1471 148840.6008 118379.2123 148876.4447 153606.9305 116958.0993 147898.1379 131056.5702 124542.1642 126686.0493 0.971947171 1.174877594 0.934429742 1.175160529 1.212500756 0.923212146 1.167438236 1.034498834 0.983077181 1 16.95089814 1.490062231 7.253951203 0.996713574 1.082007827 0.111504067 0.100467941 0.252714714 33.95357214 0.053013511 0.024001883 30.90738281 -1.490062231 0.085294253 VPVHDVTDASK ddPTM_BT-474_Pertuzumab_2h_R1 4 VPVHDVTDASK 11 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 196.48 6.03E-08 3717840000 5577700 5493300 4475940 5078320 5200300 5496500 5491100 6013100 7356600 6970800 FALSE TRUE 5359717.318 5336636.463 5284841.925 5340412.704 5367572.372 5607642.996 5558301.724 5888927.384 6521509.609 6498661.507 0.824741727 0.821190095 0.813220064 0.821771175 0.825950446 0.862891996 0.855299467 0.90617543 1.003515817 1 22.63171117 1.490192238 1.328954028 1.012200463 0.825512942 0.957875104 0.014234791 0.073589091 0.248705209 0.013056192 0.004411126 30.91663638 -1.490192238 -0.186687522 LELKAS(ph)PNVEAPQPHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LELKASPNVEAPQPHR 16 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 LELKAS(1)PNVEAPQPHR;LELKAS(1)PNVEAPQPHR;LELKAS(1)PNVEAPQPHR 167.16 3.88E-09 1348350000 1098050 1186290 1102020 1113090 1184490 1247380 1075750 1145930 1228570 1085850 TRUE FALSE 1055136.992 1152458.171 1301179.528 1170536.708 1222590.197 1272602.878 1088915.35 1122266.145 1089107.884 1012304.412 1.042311956 1.13845021 1.285363881 1.156309006 1.207729791 1.257134576 1.075679743 1.108625164 1.075869937 1 19.94921176 1.490391216 1.098718062 1.016549312 1.180439245 0.395211215 0.068598434 0.467255873 1.097001223 0.063121462 0.02242704 30.93080447 -1.490391216 0.163889933 IDADKDGFVTEGELK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDADKDGFVTEGELK 15 1 O43852-2;O43852-4;O43852-8;O43852-7 O43852-2 CALU Calumenin 0 ; 127.29 9.39E-05 295890000 569300 472340 460500 448750 519960 500250 586620 642830 811270 834270 FALSE TRUE 547051.1266 458869.3257 543722.5938 471910.0413 536684.9856 510365.3977 593799.231 629555.3359 719178.0307 777764.1498 0.703363773 0.589985185 0.699084155 0.606752113 0.690035644 0.65619558 0.763469531 0.809442472 0.92467367 1 19.56897321 1.491172848 0.946526265 1.001717001 0.649140635 0.912560445 0.03736715 0.117284518 0.209637177 0.030328499 0.011429035 30.98652311 -1.491172848 -0.352576366 KKPEEEGSAHQDTAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKPEEEGSAHQDTAEK 16 2 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 0 ; 159.4 5.49E-09 592800000 520840 465340 441802 384889 434089 406558 492500 516790 578600 600680 FALSE TRUE 500484.997 452068.9588 521645.4492 404753.1674 448051.8669 414778.8813 498527.3623 506118.1059 512919.7537 559995.4086 0.893730537 0.807272617 0.931517368 0.722779439 0.800099179 0.740682647 0.890234732 0.903789742 0.915935641 1 19.09505547 1.491504803 1.266248537 0.978820922 0.818125158 0.453564424 0.062393987 0.37908414 1.16585003 0.055875156 0.01908505 31.01021687 -1.491504803 -0.160695764 ISPPIKEEETKGDSVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISPPIKEEETKGDSVEK 17 2 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;A0A087WTC9;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 57.338 0.058157 50906000 87565 75640 53223 52043 77069 78543 58270 88074 112830 106650 FALSE TRUE 84142.86299 73482.82126 62841.58004 54728.94547 79547.99438 80131.19327 58983.12569 86255.24112 100022.0114 99426.50051 0.846282053 0.739066757 0.63204055 0.550446261 0.800068332 0.80593396 0.593233448 0.867527678 1.005989459 1 16.60134281 1.49197874 3.810158331 0.994080747 0.708912278 0.628822743 0.091097727 0.133326428 4.001750383 0.06388072 0.024527428 31.04407615 -1.49197874 -0.285168469 KYDVDTLDMVFLDHWK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYDVDTLDMVFLDHWK 16 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 302.62 3.13E-46 5875700000 4950700 4708200 4482700 4567000 4797400 4578700 5665200 5355800 5862800 6278500 FALSE TRUE 4757221.171 4573926.746 5292823.607 4802703.417 4951712.728 4671284.451 5734532.412 5245200.858 5197279.523 5853251.603 0.812748451 0.781433476 0.904253561 0.820518875 0.845976401 0.798066574 0.979717395 0.896117443 0.887930312 1 22.48080686 1.492013755 0.173103329 1.061451336 0.745595422 0.549532526 0.047631663 2.65812575 0.479915077 0.363228419 0.350184208 31.04657917 -1.492013755 -0.315855913 QKWDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 QKWDQK 6 1 O15371-2;O15371;B0QYA5;B0QYA6 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 78.616 0.063217 1135780000 1283220 1391570 1251080 1321240 1326320 1292010 1464060 1560920 1829060 1839290 FALSE TRUE 1233070.344 1351883.786 1477177.986 1389429.355 1368982.287 1318135.327 1481977.604 1528686.457 1621432.777 1714713.25 0.71911169 0.788402251 0.861472311 0.810298372 0.79837389 0.768720559 0.86427139 0.891511427 0.945599958 1 20.70953591 1.492062266 1.048822244 0.996603065 0.793816274 0.803763219 0.035769267 0.20872319 0.449402876 0.033652493 0.012160307 31.05004728 -1.492062266 -0.202786791 IPGGNIYIS(ph)PLKSPYK ddPTM_BT-474_Pertuzumab_2h_R1 2 IPGGNIYISPLKSPYK 16 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 IPGGNIYIS(0.996)PLKS(0.004)PYK;IPGGNIY(0.003)IS(0.996)PLKS(0.001)PYK 156.87 7.35E-08 1768100000 1887720 1942070 1650430 1719520 1910620 2064730 2558500 2098900 2711700 2992400 TRUE FALSE 1813945.815 1886684.065 1948699.415 1808264.633 1972076.827 2106480.255 2589811.688 2055556.982 2403879.184 2789722.083 0.650224561 0.676298215 0.698528153 0.648188092 0.706907989 0.75508606 0.928340391 0.736832172 0.861691277 1 21.41168997 1.493248964 0.246518041 1.05047668 0.592187971 0.769114496 0.055749193 0.968486117 0.256693592 0.173182825 0.162369667 31.13500673 -1.493248964 -0.458288709 S(ph)PQGQLDTSESKPDSFFLEPLMPAVLKPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQGQLDTSESKPDSFFLEPLMPAVLKPAK 30 2 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.988)PQGQLDT(0.004)S(0.004)ES(0.004)KPDSFFLEPLMPAVLKPAK;S(0.967)PQGQLDT(0.009)S(0.009)ES(0.014)KPDSFFLEPLMPAVLKPAK 128.59 5.74E-06 1485730000 405188 374618 358866 341346 346100 380503 363861 410114 516659 425944 TRUE FALSE 389352.805 363934.2614 423721.0691 358962.908 357232.6208 388197.0314 368314.0398 401645.0026 458010.0363 397094.4335 0.980504314 0.916492982 1.067053661 0.903973659 0.899616289 0.977593737 0.927522546 1.011459665 1.153403316 1 18.59912261 1.493315017 4.825030626 1.079628633 0.953949989 0.419770611 0.057976374 0.144244418 7.318585562 0.034076156 0.014127263 31.13974249 -1.493315017 -0.125678644 RLTLEDLEDSWDR ddPTM_BT-474_Pertuzumab_2h_R1 6 RLTLEDLEDSWDR 13 1 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;;; 233.19 2.00E-16 1113272000 851470 942831 594833 701912 829343 918215 731601 759394 733234 672697 FALSE TRUE 818193.6111 915942.383 702332.5551 738137.7624 856019.5708 936781.9364 740554.5519 743712.2485 650000.3503 627134.633 1.304653846 1.460519536 1.119907143 1.177000477 1.364969379 1.493749328 1.180854179 1.185889296 1.03646062 1 19.25841567 1.493441067 1.622564996 1.006027696 1.30940212 0.510402792 0.111972153 0.308442781 1.559218386 0.10219148 0.033673497 31.14878183 -1.493441067 0.303374425 SQLDDHPES(ph)DDEENFIDANDDEDMEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SQLDDHPESDDEENFIDANDDEDMEK 26 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 SQLDDHPES(1)DDEENFIDANDDEDMEK;SQLDDHPES(1)DDEENFIDANDDEDMEK;SQLDDHPES(1)DDEENFIDANDDEDMEK 335.77 2.44E-95 1134980000 773510 645770 713960 706130 695010 707260 837930 820670 1047270 1022440 TRUE FALSE 743280.374 627353.2719 842988.454 742573.4539 717365.6278 721561.2818 848184.838 803722.8777 928388.3001 953189.2281 0.779782599 0.65816236 0.884387306 0.779040963 0.75259519 0.756996891 0.889838883 0.843193412 0.973981108 1 19.86240312 1.493621542 0.898135707 1.005102722 0.766221783 0.663206266 0.058691423 0.312609463 0.508668052 0.052511839 0.020308747 31.16172871 -1.493621542 -0.238880939 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGS(ph)PTEFLEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.08)T(0.419)GS(0.441)PT(0.06)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGS(0.001)DT(0.012)T(0.229)GS(0.635)PT(0.123)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.005)T(0.159)GS(0.82)PT(0.016)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTT(0.004)GS(0.97)PT(0.027)EFLEEK 142.04 4.48E-14 2480280000 1464770 1335190 1155880 1003170 1208820 1327940 1323420 1469400 1835500 1741120 TRUE FALSE 1407525.169 1297111.688 1364773.228 1054943.724 1247702.793 1354791.857 1339616.41 1439056.377 1627141.735 1623192.392 0.867133912 0.799111489 0.840795728 0.649919091 0.768672155 0.834646505 0.825297369 0.886559341 1.002433072 1 20.63040258 1.493894254 1.44070196 1.012537533 0.788050356 0.678198423 0.056004845 0.226658486 0.899681997 0.051212942 0.017093885 31.18130263 -1.493894254 -0.224487177 LMHNASDS(ph)EVDQDDVVEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LMHNAS(0.428)DS(0.572)EVDQDDVVEWK 69.122 0.078271 68652000 67341 86565 73158 102440 90157 104440 95821 85080 76038 86439 TRUE FALSE 64709.23927 84096.25096 86379.27799 107726.9407 93056.98178 106551.8484 96993.68606 83323.06827 67406.48502 80584.40954 0.802999484 1.043579663 1.071910541 1.336821121 1.154776492 1.322238991 1.203628427 1.03398497 0.836470546 1 16.29821313 1.494077127 4.479098442 0.919742621 1.142867727 0.252239358 0.147627015 0.243615162 10.46120997 0.098450804 0.039938428 31.19443521 -1.494077127 0.223125106 GDLSYLDQGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDLSYLDQGHR 11 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 208.56 1.92E-08 236910000 247000 292860 248790 284800 262670 272930 301850 274610 277720 290530 FALSE TRUE 237346.9669 284507.9195 293751.8873 299498.5621 271119.0191 278448.8316 305544.1306 268939.2075 246194.3899 270852.1443 0.876297168 1.050417822 1.084547025 1.105764043 1.000985315 1.028047359 1.128084592 0.992937339 0.908962307 1 18.04714599 1.494261574 7.714401798 0.953162348 1.043075147 0.199874397 0.068480479 0.160591847 24.13178823 0.037227726 0.017021635 31.20768645 -1.494261574 0.089912799 MEVEDGLGS(ph)PKPEEIKDFSYVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEVEDGLGSPKPEEIKDFSYVHK 23 2 F8VRB8;H0YHC1;A0A3B3IS46;A0A3B3IRX3;Q71F56 F8VRB8 MED13L Mediator of RNA polymerase II transcription subunit 13-like 1 MEVEDGLGS(1)PKPEEIKDFSYVHK 148.22 5.15E-08 145390000 489720 347620 339650 260650 338720 352150 357580 418800 571610 473040 TRUE FALSE 470581.201 337706.218 401032.3105 274102.1777 349615.2364 359270.7143 361956.171 410151.6336 506723.2292 441000.5795 1.067076151 0.765772731 0.909369124 0.621546072 0.792777272 0.814671751 0.820761214 0.930047834 1.149030756 1 18.75042103 1.49434083 3.300339932 1.072306665 0.819174325 0.432203454 0.111732113 0.191838318 4.271783605 0.076969075 0.028296968 31.21338221 -1.49434083 -0.25313234 FGAPPHAGGGIGLER ddPTM_BT-474_Pertuzumab_2h_R1 2 FGAPPHAGGGIGLER 15 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 164.81 1.46E-06 1251690000 1390640 1510830 1321580 1562020 1468100 1524960 1504660 1480140 1511520 1493150 FALSE TRUE 1336292.251 1467742.608 1560418.904 1642636.039 1515322.77 1555795.736 1523074.479 1449574.592 1339938.586 1392017.621 0.959967914 1.054399446 1.120976402 1.180039689 1.088580164 1.117655203 1.09414885 1.041347875 0.962587374 1 20.40874604 1.494390618 3.041093422 0.982453814 1.092468847 0.379917369 0.053910838 0.248379503 4.667458203 0.041860232 0.01500508 31.21696075 -1.494390618 0.110015033 VVQLHEYSEELEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVQLHEYSEELEK 13 0 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 154.65 4.63E-05 1009130000 1126980 1138170 1008970 1119090 1127520 1123560 1112640 1258230 1543600 1385220 FALSE TRUE 1082936.376 1105710.506 1191313.323 1176846.369 1163787.705 1146279.153 1126256.821 1232247.111 1368376.999 1291397.816 0.838576899 0.856212154 0.922499101 0.911296546 0.901184508 0.887626678 0.872122291 0.954196372 1.059609195 1 20.30050206 1.494510353 3.409520153 1.027994422 0.886816771 0.815120548 0.027710601 0.089429958 2.132193493 0.020284223 0.007537067 31.22556841 -1.494510353 -0.141177651 ERSPALK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSPALK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 82.241 0.022823 320930000 234850 207790 186640 198570 213890 213930 217470 240800 276650 272220 FALSE TRUE 225671.8024 201864.0326 220369.9998 208818.2215 220769.9661 218255.8112 220131.4629 235827.3959 245245.8518 253782.2969 0.889233824 0.795422041 0.86834268 0.822824224 0.869918701 0.860011962 0.867402753 0.929250774 0.966363118 1 17.95323191 1.494590873 1.120212771 1.000566199 0.845766037 0.826333968 0.02469463 0.156451879 0.380598958 0.020254774 0.00716199 31.23135833 -1.494590873 -0.154800161 YGDSLYR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGDSLYR 7 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3;Q5T3R7 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ; 111.28 0.036031 265550000 463290 491760 451920 513580 447840 501000 515240 472810 454760 480070 FALSE TRUE 445184.1146 477735.4863 533591.9969 540085.9253 462245.1803 511130.5633 521545.6612 463046.3083 403137.5513 447554.4313 0.994703847 1.067435496 1.192239334 1.206749141 1.032824497 1.14205229 1.165323422 1.034614509 0.900756474 1 18.77170363 1.494658418 4.35988546 0.952486893 1.116628082 0.482695423 0.068096312 0.15224982 6.162157097 0.044702603 0.01799591 31.23621607 -1.494658418 0.164141189 SEAPAEVTHFS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEAPAEVTHFSPK 13 0 Q6PID6 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 1 SEAPAEVTHFS(1)PK;SEAPAEVTHFS(1)PK 180.62 8.21E-06 1122930000 2126600 1878530 1551510 1641370 1754320 1788680 1736700 1944400 2324800 2034360 TRUE FALSE 2043490.121 1824956.164 1831902.37 1726081.302 1810749.296 1824848.335 1757954.254 1904247.461 2060898.45 1896570.985 1.077465667 0.962239841 0.965902349 0.910106353 0.954749023 0.962182987 0.92691192 1.004047555 1.086644511 1 20.85496194 1.49466019 5.460249695 1.044582875 0.962991016 0.314970685 0.045911969 0.162009469 10.90879464 0.026737847 0.011500954 31.23634347 -1.49466019 -0.081591859 ETVYCLNDDDETEVLKEDIIQGFR ddPTM_BT-474_Pertuzumab_2h_R1 8 ETVYCLNDDDETEVLKEDIIQGFR 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;; 296.45 5.09E-62 12127343900 1608125 1559406 1204902.4 1287092 1436625.5 1519810.7 1355956.2 1567726.7 1835069 1684750.6 FALSE TRUE 1545277.697 1514933.268 1422655.067 1353518.972 1482835.864 1550542.314 1372550.798 1535352.596 1626759.66 1570640.941 0.98385166 0.964531885 0.905779946 0.861762187 0.944096022 0.98720355 0.873879422 0.977532519 1.035729821 1 20.58292198 1.49505957 5.740996681 1.015152508 0.931400782 0.423318984 0.040754321 0.140291431 10.59053092 0.024554782 0.01070081 31.26508189 -1.49505957 -0.083751726 EYTAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EYTAGR 6 0 P07237;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ; 187.21 0.0042292 874500000 711730 818930 721480 878390 731380 870160 847690 790610 774600 811580 FALSE TRUE 683914.8047 795574.9182 851867.4852 923723.8132 754905.5019 887755.2314 858064.2838 774283.6272 686670.6554 756610.9637 0.903918708 1.051498004 1.125898944 1.220870246 0.99774592 1.173331175 1.134089149 1.023357662 0.907561069 1 19.52919216 1.495348827 4.532827094 0.95510499 1.091541058 0.269443143 0.087442929 0.223194678 9.859435732 0.055559854 0.022665455 31.28591252 -1.495348827 0.136436068 AQVPGPLT(ph)PEMEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQVPGPLTPEMEAR 14 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 AQVPGPLT(1)PEMEAR 125.98 0.00098481 284990000 178960 214000 172810 208240 229440 234760 210580 192730 193220 174440 TRUE FALSE 171966.0453 207896.9295 204040.6111 218987.2914 236820.146 239507.008 213157.141 188750.0581 171286.4756 162625.0234 1.05743902 1.278382165 1.254669219 1.346578077 1.456234354 1.472756179 1.310727811 1.160645848 1.053260267 1 17.31118974 1.495659999 2.284870875 1.021306154 1.320957842 0.52650086 0.109032995 0.238030705 2.471573928 0.095641418 0.032059757 31.30833694 -1.495659999 0.299651688 ASFNNPDR ddPTM_BT-474_Pertuzumab_2h_R1 6 ASFNNPDR 8 0 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;;;; 173.48 0.00064568 5785900000 4492220 4861660 4173270 4954850 4602240 4590330 4777280 4761160 4932800 4990590 FALSE TRUE 4316659.076 4723010.217 4927472.723 5210570.402 4750275.229 4683149.618 4835745.782 4662840.382 4372849.224 4652572.894 0.927800418 1.015139435 1.05908555 1.119933104 1.020999636 1.006572003 1.039370235 1.002206841 0.939877638 1 22.14959732 1.495836559 4.338975788 0.969440793 1.029996213 0.185998672 0.047101677 0.290568484 11.65653203 0.031439767 0.01265896 31.32106777 -1.495836559 0.06055542 NFGSYVTHETK ddPTM_BT-474_Pertuzumab_2h_R1 4 NFGSYVTHETK 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ;;; 169.23 1.71E-05 2285250000 2011590 1984230 2058930 2379650 1958540 1973970 2286440 2594430 3064110 3133280 FALSE TRUE 1932974.839 1927641.703 2431024.452 2502464.022 2021538.218 2013885.026 2314422.137 2540854.114 2716285.079 2921060.155 0.66173743 0.659911676 0.832240462 0.856697188 0.692056346 0.689436341 0.792322655 0.869839709 0.929897001 1 21.47806064 1.496064578 1.408918988 0.987684838 0.736703323 0.681204513 0.064042929 0.249065591 0.945723593 0.061920248 0.020758928 31.3375167 -1.496064578 -0.250981514 LLEQALVIEEQLRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEQALVIEEQLRR 14 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;Q12873-3;Q12873;Q12873-2;H7C0J3;I3L229;H7C3H7 Q14839-2;Q12873-3;H7C0J3 CHD4;CHD3 Chromodomain-helicase-DNA-binding protein 4;Chromodomain-helicase-DNA-binding protein 3 0 ; 204.82 2.10E-08 607440000 323790 367660 238710 278660 315710 336280 311920 297090 293060 282840 FALSE TRUE 311135.9288 357174.6968 281850.2071 293041.676 325865.0989 343079.812 315737.3703 290954.9877 259793.0574 263682.9949 1.179962056 1.354560983 1.068897929 1.111340821 1.235821442 1.301107082 1.197412713 1.103427196 0.985247674 1 18.00844501 1.496433018 2.50635086 0.992347697 1.208626208 0.547687695 0.078122388 0.210896949 2.661852614 0.064087114 0.021878658 31.36411361 -1.496433018 0.216278511 SECDS(ph)S(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 SECDS(1)S(1)PEPK 170.4 6.34E-06 152260000 430410 359040 318400 321120 348230 353940 396490 403840 529570 483050 TRUE FALSE 413589.1014 348800.5307 375941.9628 337693.0417 359431.1342 361096.9093 401342.3632 395500.5629 469455.4337 450332.5932 0.9184081 0.774539831 0.834809579 0.749874752 0.798145947 0.801844936 0.891213226 0.878241035 1.042463816 1 18.78063137 1.496563158 1.509110065 1.023635501 0.811592858 0.703158832 0.049959366 0.188946339 0.82429981 0.041641503 0.013835349 31.37351351 -1.496563158 -0.212042644 RSTS(ph)PIIGSPPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.33)T(0.33)S(0.34)PIIGSPPVR;RS(0.113)T(0.265)S(0.622)PIIGSPPVR 120.59 0.00015784 2486670000 1472020 1642570 1114340 1305370 1436160 1515500 1323820 1274150 1282340 1105730 TRUE FALSE 1414491.831 1595725.512 1315726.026 1372740.302 1482355.391 1546144.448 1340021.305 1247838.357 1136774.139 1030837.922 1.372176751 1.547988755 1.276365564 1.331674236 1.438010146 1.499890929 1.29993404 1.210508782 1.102767093 1 19.97538609 1.496580614 1.370565067 1.016878583 1.40845494 0.775267751 0.076960335 0.183749424 0.660362519 0.069877744 0.023539836 31.37477454 -1.496580614 0.391576357 NPDTQWITKPVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 NPDTQWITKPVHK 13 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 231.26 1.63E-12 6822200000 5912200 5378950 5315060 5669730 5475660 6178180 5998600 6873400 8553300 8244500 FALSE TRUE 5681144.688 5225547.613 6275609.575 5962345.445 5651789.577 6303107.033 6072012.661 6731461.888 7582365.242 7686092.672 0.739146004 0.679870493 0.816488929 0.775731662 0.735326754 0.820066489 0.789999929 0.875797649 0.986504531 1 22.87381894 1.496590793 1.16319135 1.012797857 0.755022781 0.856407142 0.037782936 0.155061338 0.404936536 0.034393667 0.012032548 31.37550996 -1.496590793 -0.257775075 VVVS(ph)PTKK ddPTM_BT-474_Pertuzumab_2h_R1 3 VVVSPTKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VVVS(0.5)PT(0.5)KK;VVVS(0.907)PT(0.093)KK;VVVS(0.982)PT(0.018)KK 101.38 0.0033291 48520200000 12349300 10332900 8459900 8050500 9436900 8979400 9919900 11475900 13192500 13443800 TRUE FALSE 11866675.7 10038215.81 9988792.119 8465987.27 9740446.459 9160969.62 10041302.7 11238918.65 11694942.71 12533239.45 0.946816324 0.800927474 0.796984065 0.675482767 0.777169103 0.730933902 0.80117377 0.89672895 0.93311412 1 23.57925602 1.497029971 1.710388701 0.98093666 0.78176615 0.551903825 0.065767064 0.259626832 1.466618465 0.058452047 0.019251783 31.4072543 -1.497029971 -0.199170511 (ac)TECFLPPTS(ph)SPSEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.1)S(0.417)S(0.369)PS(0.114)EHR 56.514 0.0061747 0 93888 91225 86393 95085 82774 89204 72791 80628 59224 52255 TRUE FALSE 90218.75316 88623.35232 102006.1369 99992.34825 85436.50088 91007.766 73681.83803 78963.00362 52501.13981 48715.72231 1.851943251 1.819194053 2.09390587 2.052568319 1.753776745 1.868139518 1.512485796 1.620893623 1.077704226 1 15.57209984 1.497176824 0.822596163 0.969418012 1.93768428 0.86441558 0.130412947 0.188752601 0.26331136 0.119681472 0.048612617 31.41787621 -1.497176824 0.968266268 RT(ph)PTMPQEEAAACPPHILPPEK ddPTM_BT-474_Pertuzumab_2h_R1 5 RTPTMPQEEAAACPPHILPPEK 22 1 Q9NYV4 Q9NYV4 CDK12 Cyclin-dependent kinase 12 1 RT(0.999)PT(0.001)MPQEEAAACPPHILPPEK;RT(0.957)PT(0.043)MPQEEAAACPPHILPPEK;RT(0.797)PT(0.203)MPQEEAAACPPHILPPEK;RT(0.823)PT(0.177)MPQEEAAACPPHILPPEK;RT(0.954)PT(0.046)MPQEEAAACPPHILPPEK 191.51 9.03E-18 4182800000 1568160 1483150 1152790 1275140 1425900 1444090 1360460 1515540 1766410 1625930 TRUE FALSE 1506874.574 1440852.014 1361124.797 1340950.128 1471765.368 1473290.489 1377109.716 1484243.569 1565894.542 1515804.313 0.99410891 0.950552787 0.897955485 0.884645938 0.970946814 0.97195296 0.908500988 0.97917888 1.033045314 1 20.53165209 1.497185079 4.490972519 1.01482751 0.939011962 0.454887037 0.03382625 0.162194676 7.034529644 0.022376749 0.009126331 31.41847338 -1.497185079 -0.075815547 YYEAADTVTQFDNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 YYEAADTVTQFDNVR 15 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2;F8VZW6 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 253.54 2.63E-24 182450000 181620 200570 175230 219130 200990 192730 190750 188470 164220 177650 FALSE TRUE 174522.0896 194849.94 206897.959 230439.3256 207455.0259 196627.1326 193084.4556 184578.0286 145578.4341 165617.6073 1.053765312 1.176504982 1.249250985 1.391393882 1.252614558 1.18723568 1.165844977 1.114483126 0.879003365 1 17.33749653 1.498330232 2.252011473 0.940317043 1.221432679 0.599848271 0.086587523 0.198611214 2.00704027 0.074306903 0.024911636 31.50142731 -1.498330232 0.281115635 MTLS(ph)PPHS(ph)PQGAAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 MTLSPPHSPQGAAPR 15 0 Q05GC8 Q05GC8 BCAR2 2 MT(0.012)LS(0.988)PPHS(1)PQGAAPR 135.38 1.55E-05 257200000 166730 197950 155760 188550 190440 193090 189200 173270 166630 163550 TRUE FALSE 160214.0073 192304.6598 183909.2969 198281.0881 196565.6756 196994.4121 191515.4862 169691.9139 147714.861 152472.6128 1.05077236 1.261240666 1.206179218 1.300437399 1.289186772 1.291998664 1.256064828 1.112933732 0.968796023 1 17.2181906 1.498634022 2.807481287 0.986029666 1.242838023 0.679640195 0.069288014 0.137766338 2.21054116 0.05241631 0.01844788 31.52347032 -1.498634022 0.256808356 KEELKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEELKR 6 2 E7ETZ8;Q49MG5;H0Y945;P08579 E7ETZ8;P08579;REV__Q92817 MAP9;SNRPB2 Microtubule-associated protein 9;U2 small nuclear ribonucleoprotein B 0 81.784 0.03429 469010000 879770 766650 693620 688480 728800 741280 798220 852490 1023500 977520 FALSE TRUE 845387.6158 744785.8926 818972.5635 724012.5353 752242.5139 756269.1895 807988.8551 834885.7836 907316.5709 911311.6997 0.927660224 0.817268003 0.898674475 0.794472995 0.825450298 0.829868847 0.886621839 0.91613636 0.995616068 1 19.79758506 1.499041972 1.605403069 1.004279485 0.847151645 0.696775898 0.038004894 0.186342602 0.923765449 0.031735281 0.010498849 31.55309554 -1.499041972 -0.15712784 KDEET(ph)EES(ph)EYDS(ph)EHENSEPVTNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDEETEESEYDSEHENSEPVTNIR 24 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 3 KDEET(1)EES(0.982)EY(0.019)DS(1)EHENSEPVTNIR 163.51 7.34E-12 207680000 90701 76681 75730 71694 84620 73030 85972 94297 120800 112610 TRUE FALSE 87156.30464 74494.13296 89416.0956 75394.13593 87341.87915 74506.71664 87024.15105 92349.734 107087.2904 104982.8244 0.830195845 0.709584005 0.851721185 0.718156864 0.831963511 0.709703869 0.828937034 0.879665169 1.020045813 1 16.67979379 1.499088678 1.926269317 1.0144708 0.776611558 0.75443594 0.05168917 0.134352142 0.975919547 0.038914893 0.012848753 31.55648903 -1.499088678 -0.237859241 RKDS(ph)AQDDQAK ddPTM_BT-474_Pertuzumab_2h_R1 10 RKDSAQDDQAK 11 2 Q13045-3;Q13045;Q13045-2;J3KS54 Q13045-3 FLII Protein flightless-1 homolog 1 RKDS(1)AQDDQAK;RKDS(1)AQDDQAK;RKDS(1)AQDDQAK;RKDS(1)AQDDQAK;RKDS(1)AQDDQAK;RKDS(1)AQDDQAK;RKDS(1)AQDDQAK;RKDS(1)AQDDQAK;RKDS(1)AQDDQAK;RKDS(1)AQDDQAK 256.35 8.95E-21 7581084000 8564952 6767068 5995331 5431108 6202978 6263820 6703535 7207660 8076832 7976800 TRUE FALSE 8230224.207 6574077.846 7078820.677 5711408.135 6402502.421 6390478.732 6785574.867 7058819.302 7159983.892 7436524.231 1.106729966 0.884025607 0.951899094 0.768021183 0.860953615 0.859336773 0.912465912 0.949209481 0.962813227 1 22.82619704 1.499256008 1.75569849 0.98746039 0.89770832 0.121549333 0.081858148 0.684047341 4.08681205 0.070569572 0.023262981 31.56864982 -1.499256008 -0.08975207 S(ph)SPVRPSSEKNDCCR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPVRPSSEKNDCCR 15 2 B3KV94;A0A3B3ISE6;A0A3B3ITA8;A0A3B3ITJ7;A0A3B3ITE7;A0A3B3IT25;A0A3B3IS40;Q9UGL1;Q9UGL1-2 B3KV94 KDM5B Lysine-specific demethylase 5B 1 S(0.5)S(0.5)PVRPSSEKNDCCR 53.278 0.081521 71835000 43940 48206 38281 45965 46703 49028 38728 44618 40412 38086 TRUE FALSE 42222.77622 46831.21208 45199.22826 48337.25916 48205.24441 50019.37975 39201.96485 43696.62271 35824.59918 35506.4013 1.189159551 1.318951242 1.272988154 1.361367455 1.3576494 1.408742591 1.104081614 1.230668868 1.008961705 1 15.11579152 1.499839507 1.189844719 0.993962439 1.312922741 0.663011513 0.080921481 0.254709257 0.694330182 0.071088966 0.024744072 31.6110926 -1.499839507 0.318960302 QAESFEDLRR ddPTM_BT-474_Pertuzumab_2h_R1 2 QAESFEDLRR 10 1 Q8NI27;A0A0C4DG98 Q8NI27 THOC2 THO complex subunit 2 0 ; 122.86 0.00076535 1199160000 818120 743040 800460 768950 811370 782460 773760 729000 644950 649080 FALSE TRUE 786146.9659 721849.2267 945120.9281 808635.6017 837468.4529 798281.8773 783229.5063 713945.8952 571737.9799 605117.2335 1.299164728 1.192908063 1.5618807 1.336328825 1.383977197 1.319218547 1.294343415 1.179847236 0.944838369 1 19.20685515 1.500019312 1.913495894 0.964648812 1.349790741 0.728862998 0.089530879 0.161216577 1.155582669 0.07530446 0.024873066 31.6241828 -1.500019312 0.385141929 ALWEDEGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALWEDEGVR 9 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJR6;A0A590UJI6;A0A590UJQ9;A0A590UKB4;A0A590UJQ2;A0A590UJG5;A0A590UJ22;S4R3E3;S4R3V9;Q5JWE9;A0A590UKA4;A0A590UJY8;A0A590UJB7;H0Y7F4;A0A590UJC9;P63092-2;A0A590UJB0;A0A590UJS2;A0A590UJJ0;A0A590UK28;A0A590UKA9;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 ; 104.06 0.0077283 256350000 1236990 1767160 1371300 2228180 1777210 1720770 1846960 1629860 1475970 1631140 FALSE TRUE 1188647.063 1716762.327 1619124.414 2343176.637 1834375.574 1755565.148 1869563.649 1596202.821 1308424.073 1520661.435 0.781664502 1.128957628 1.0647501 1.54089305 1.206301108 1.154474696 1.229441088 1.049676664 0.860430891 1 20.53626755 1.500102026 4.177151205 0.933052193 1.169035823 0.206294293 0.177896337 0.282590406 10.49797122 0.117490323 0.047014577 31.63020638 -1.500102026 0.23598363 KFAETQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFAETQPK 8 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 127.4 0.0018889 2600000000 5804800 5742700 4991900 4781200 5022600 5337200 5700000 6319400 7328900 7413300 FALSE TRUE 5577941.998 5578923.819 5894047.374 5027958.305 5184156.49 5445121.841 5769758.305 6188902.182 6496953.997 6911190.588 0.807088435 0.807230498 0.852826629 0.727509716 0.75011048 0.787870306 0.834842887 0.895490018 0.940062919 1 22.72050283 1.5002066 1.255202454 0.99125838 0.78755392 0.833600042 0.03275857 0.170912705 0.516641868 0.031702173 0.010889091 31.63782358 -1.5002066 -0.20370446 LTPSPDIIVLS(ph)DNEASSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR 381.64 4.59E-109 226990000 139628 156726 124292 162092 155088 151643 171291 148046 143700 156829 TRUE FALSE 134171.1834 152256.3279 146754.3293 170457.5875 160076.5464 154709.3254 173387.3105 144988.7984 127387.7784 146206.8321 0.917680668 1.041376287 1.003744675 1.165866089 1.094863653 1.058153871 1.185904297 0.991669105 0.871284718 1 17.1576512 1.500829872 7.157021545 0.934009673 1.069127218 0.322507561 0.077505444 0.130413142 15.58820886 0.042992572 0.0195818 31.68326076 -1.500829872 0.135117545 DFS(ph)PEALKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFSPEALKK 9 1 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 1 DFS(1)PEALKK 92.112 0.0063069 217310000 186880 168080 169600 113120 134780 165600 172420 186460 257110 222550 TRUE FALSE 179576.523 163286.523 200250.4927 118958.1368 139115.3211 168948.5455 174530.1275 182609.5358 227923.9507 207476.4903 0.865527091 0.787012171 0.965171969 0.573357187 0.670511251 0.814302118 0.841204357 0.880145676 1.098553144 1 17.66258834 1.501316515 2.036483836 1.049277007 0.779329774 0.490894771 0.104075062 0.26229759 2.148493709 0.089107013 0.029585898 31.71878293 -1.501316515 -0.269947233 LCS(ph)PLSEPGDPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LCSPLSEPGDPSK 13 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 LCS(0.997)PLS(0.003)EPGDPSK 150.22 4.63E-05 174380000 339490 325790 267260 278300 294450 295670 297590 337180 408990 368640 TRUE FALSE 326222.3555 316498.7882 315559.8272 292663.0964 303921.2517 301648.65 301231.9954 330217.1152 362563.1698 343671.6844 0.949226748 0.920933561 0.918201416 0.851577565 0.884336026 0.877723315 0.876510952 0.960850516 1.054969572 1 18.39067147 1.501496866 3.601227178 1.025514033 0.896095346 0.762105594 0.029218367 0.098312333 2.665363845 0.020996538 0.008014476 31.73195768 -1.501496866 -0.129418687 SAS(ph)PSNIK ddPTM_BT-474_Pertuzumab_2h_R1 4 SASPSNIK 8 0 E7EUC4;Q9NRH2 E7EUC4 SNRK SNF-related serine/threonine-protein kinase 1 SAS(0.996)PS(0.004)NIK;SAS(1)PSNIK;S(0.008)AS(0.955)PS(0.038)NIK;SAS(0.832)PS(0.168)NIK 164.1 0.00034828 684144000 1328420 1389720 1159450 1195500 1207920 1272160 1383750 1490860 1613170 1701630 TRUE FALSE 1276503.878 1350086.546 1368988.407 1257199.898 1246773.844 1297883.947 1400684.746 1460073.22 1430049.705 1586377.084 0.80466611 0.851050207 0.862965319 0.792497516 0.785925273 0.818143403 0.88294565 0.920382193 0.901456355 1 20.59730431 1.501562212 0.891398779 0.985005809 0.818810161 0.79063726 0.029082132 0.24977614 0.40005029 0.029001489 0.011287302 31.73673258 -1.501562212 -0.166195649 NSPNNISGISNPPGT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 NSPNNISGISNPPGTPR 17 0 Q9BWW4-2;Q9BWW4;Q9NW25;A0A087WVT6;Q9BWW4-3 Q9BWW4-2 SSBP3 Single-stranded DNA-binding protein 3 1 NSPNNISGISNPPGT(1)PR;NSPNNISGISNPPGT(1)PR;NSPNNISGIS(0.001)NPPGT(0.999)PR;NSPNNISGISNPPGT(1)PR 316.72 2.87E-57 1632260000 871690 920440 750870 901990 839240 840380 758690 883950 832990 771530 TRUE FALSE 837623.3911 894189.9524 886568.912 948541.812 866234.9168 857373.0594 767975.0752 865696.1236 738432.4674 719273.5859 1.164540736 1.243184749 1.232589281 1.318749681 1.204319099 1.191998533 1.06770927 1.203570019 1.026636431 1 19.4561811 1.501621297 0.628801924 0.998950363 1.240329137 0.65033077 0.057306026 0.433934107 0.389375828 0.055057877 0.027202955 31.74105059 -1.501621297 0.241378774 DVVVDLVCYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVVVDLVCYR 10 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7;Q9ULD0-3;Q9ULD0-2;Q9ULD0 Q02218 OGDH;OGDHL "2-oxoglutarate dehydrogenase, mitochondrial;2-oxoglutarate dehydrogenase-like, mitochondrial" 0 110.87 0.0042539 36905000 49373 64532 55360 88987 62469 52954 79410 58541 48583 60539 FALSE TRUE 47443.44858 62691.61054 65364.78348 93579.62973 64478.37212 54024.76616 80381.84333 57332.10789 43068.06152 56438.63961 0.840619988 1.110792375 1.158156609 1.658077345 1.142450856 0.957230127 1.424234246 1.015830791 0.763095316 1 15.78439559 1.501640866 6.500671709 0.882852772 1.190310232 0.237025762 0.220912455 0.179737379 17.462189 0.126404404 0.05686058 31.7424808 -1.501640866 0.30745746 TPS(ph)PAAEDAREPEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 T(0.066)PS(0.934)PAAEDAREPEAK;T(0.063)PS(0.937)PAAEDAREPEAK;T(0.033)PS(0.967)PAAEDAREPEAK 128.79 4.23E-05 966170000 894440 841960 723910 748860 802140 792400 745200 875420 1051540 898950 TRUE FALSE 859484.2959 817948.1252 854736.6403 787508.7543 827941.5616 808422.8709 754319.9805 857342.2711 932173.5876 838063.3158 1.025560098 0.975998006 1.019895065 0.939676919 0.987922447 0.964632213 0.900075169 1.023004175 1.112294942 1 19.67669972 1.501881781 7.313211088 1.059974134 0.973527509 0.389108092 0.042469981 0.105430812 13.06587513 0.022538204 0.010295007 31.76009412 -1.501881781 -0.086446625 EMDTART(ph)PLSEAEFEEIMNR ddPTM_BT-474_Pertuzumab_2h_R1 5 EMDTARTPLSEAEFEEIMNR 20 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 EMDT(0.107)ART(0.893)PLSEAEFEEIMNR;EMDT(0.001)ART(0.999)PLSEAEFEEIMNR;EMDT(0.008)ART(0.992)PLSEAEFEEIMNR;EMDT(0.057)ART(0.942)PLSEAEFEEIMNR;EMDT(0.266)ART(0.733)PLSEAEFEEIMNR 324.12 6.94E-67 1365617000 451191 498765 397111 439410 476475 466458 446182 455095 468768 442935 TRUE FALSE 433557.9569 484540.7105 468877.7914 462088.0028 491801.2511 475890.1004 451642.5088 445697.1292 415555.4219 412934.6179 1.049943352 1.173407822 1.135477073 1.119034304 1.190990607 1.152458718 1.093738546 1.079340675 1.006346777 1 18.65555384 1.502762113 1.486082791 0.996907299 1.13875771 0.659435078 0.036808734 0.214077949 0.906631142 0.03120911 0.010421289 31.82453838 -1.502762113 0.14185041 DLASLPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLASLPEK 8 0 Q6V0I7-2;Q6V0I7-3;Q6V0I7 Q6V0I7-2 FAT4 Protocadherin Fat 4 0 69.198 0.05454 126180000 213900 306270 286970 263600 270760 292340 257230 245230 178150 205070 FALSE TRUE 205540.5515 297535.4795 338831.8626 277204.4276 279469.2413 298251.3151 260378.0577 240165.9148 157927.1589 191180.4262 1.075112947 1.556307229 1.77231461 1.449962389 1.461808862 1.560051523 1.361949352 1.256226485 0.826063431 1 17.5445753 1.503220531 2.140892978 0.91237993 1.487024275 0.607498942 0.173370411 0.18923113 1.727528806 0.140801609 0.047075409 31.85814842 -1.503220531 0.574644346 REGS(ph)YDR ddPTM_BT-474_Pertuzumab_2h_R1 5 REGSYDR 7 1 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 REGS(1)YDR;REGS(0.999)Y(0.001)DR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR 96.015 0.0079886 690483000 739748 788181 587520 654278 730003 724810 681795 717591 700577 720462 TRUE FALSE 710837.8303 765702.8496 693697.9333 688045.366 753484.2095 739466.1548 690139.0112 702772.4951 621050.436 671664.467 1.058322816 1.140007976 1.032804276 1.024388515 1.121816393 1.100945771 1.027505615 1.046314834 0.924643876 1 19.35738118 1.503335345 2.165465302 0.964949845 1.076023756 0.500375525 0.042147591 0.234490848 2.19367369 0.033940139 0.011365289 31.86657182 -1.503335345 0.111073911 VS(ph)PFGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPFGLR 7 0 J3KNZ9;H3BRE6 J3KNZ9 FBRS 1 VS(1)PFGLR;VS(1)PFGLR 135 0.0085878 252880000 581650 657270 518780 613530 567190 606570 513320 646860 534460 569180 TRUE FALSE 558918.475 638525.3031 612535.0862 645194.3568 585434.1815 618835.261 519602.1637 633502.115 473790.3414 530628.9316 1.053313232 1.203336767 1.154356745 1.215904973 1.103283569 1.166229778 0.979219437 1.193870287 0.892884487 1 19.01734381 1.503756 0.899182558 0.972352098 1.152296414 0.360056892 0.083824271 0.5698066 0.926074537 0.072124975 0.027967138 31.89745254 -1.503756 0.179944316 DKFTDSAIAMNSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKFTDSAIAMNSK 13 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9;H3BUE3 Q8WWM7 ATXN2L Ataxin-2-like protein 0 92.935 0.0053307 349280000 283770 260680 194400 207790 255400 244740 252850 286250 321060 328620 FALSE TRUE 272679.9547 253245.6616 229532.4044 218514.0668 263615.1729 249688.8105 255944.4539 280338.8375 284614.6148 306362.2747 0.89005722 0.826621561 0.749218893 0.713253833 0.860468781 0.815011609 0.835430714 0.915056652 0.929013258 1 18.22487913 1.503770884 0.954512497 0.994446158 0.799933229 0.647794842 0.047998557 0.319670233 0.577922837 0.045871879 0.017290922 31.89854578 -1.503770884 -0.19451293 KDS(ph)GSSSVFAESPGGK ddPTM_BT-474_Pertuzumab_2h_R1 6 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 KDS(0.863)GS(0.062)S(0.054)S(0.022)VFAESPGGK;KDS(0.963)GS(0.036)S(0.001)SVFAESPGGK;KDS(0.996)GS(0.004)SSVFAESPGGK;KDS(0.697)GS(0.302)S(0.001)SVFAESPGGK;KDS(0.963)GS(0.032)S(0.004)S(0.001)VFAESPGGK;KDS(0.989)GS(0.003)S(0.007)S(0.001)VFAESPGGK 246.34 2.10E-20 6054430000 7330840 7262320 6879070 6898130 8060330 7441540 6797160 7238330 7331750 6678220 TRUE FALSE 7044342.668 7055205.744 8122270.973 7254143.316 8319597.835 7592013.037 6880345.677 7088855.956 6499480.477 6225898.211 1.131458053 1.133202874 1.304594245 1.165156106 1.336288766 1.219424536 1.105116956 1.13860775 1.043942618 1 22.56985056 1.503986264 1.117665708 1.006096309 1.21526143 0.54277362 0.067471485 0.354194292 0.856598185 0.061799993 0.021942479 31.91436915 -1.503986264 0.209165121 S(ph)RS(ph)PLAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPLAIR 8 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(1)PLAIR;S(1)RS(1)PLAIR 97.463 0.0046738 2392900000 102406 115667 91831 103845 93465 108393 86061 112364 131116 117441 TRUE FALSE 98403.8603 112368.2904 108426.9045 109204.4529 96471.38661 110584.7807 87114.24026 110043.6441 116232.2614 109486.6165 0.898775243 1.026319874 0.990321082 0.997422849 0.881124924 1.010030123 0.795661087 1.005087633 1.061611593 1 16.740395 1.504245403 12.8051814 1.031630684 0.946744803 0.227387165 0.067924321 0.158907531 58.75997951 0.035489666 0.016461492 31.9334178 -1.504245403 -0.084885881 LSLCGEESFGTGSDHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSLCGEESFGTGSDHIR 17 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ; 246.34 1.20E-20 497310000 472480 543890 434900 542970 542780 489660 475950 472460 478870 415310 FALSE TRUE 454014.9592 528378.7897 513496.1043 570992.7468 560239.0116 499561.2607 481774.8185 462703.5359 424510.6852 387180.6838 1.172617794 1.364682723 1.326244118 1.474744921 1.446970459 1.290253573 1.244315222 1.195058419 1.096414937 1 18.56264745 1.504282312 1.017306665 1.009551537 1.358405408 0.694711888 0.078874674 0.275058756 0.558264675 0.07442712 0.027320517 31.93613183 -1.504282312 0.34885387 VGS(ph)LDNVGHLPAGGAVK ddPTM_BT-474_Pertuzumab_2h_R1 6 VGSLDNVGHLPAGGAVK 17 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK 175.33 8.01E-10 11527770000 15393500 10967540 10407750 8579690 9909680 10246510 11083940 12934770 16615800 15043600 TRUE FALSE 14791905 10654756.5 12288661.94 9022488.829 10228433.86 10453701.45 11219588.57 12667662.48 14729644.04 14024683.57 1.054705079 0.759714573 0.876216699 0.643329226 0.729316551 0.745378774 0.799988714 0.90324052 1.050265695 1 23.74146489 1.504286853 2.667771261 1.02397294 0.791275976 0.42315204 0.103727803 0.234026209 3.407934071 0.078917382 0.027566558 31.93646572 -1.504286853 -0.232696964 NKEDQYDHLDAADMTK ddPTM_BT-474_Pertuzumab_2h_R1 1 NKEDQYDHLDAADMTK 16 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 148.56 8.39E-07 203970000 324530 279270 257280 232810 301470 310860 288820 339310 431490 392060 FALSE TRUE 311847.0088 271305.493 303776.2192 244825.352 311167.0563 317145.8022 292354.6656 332303.1299 382509.0642 365505.427 0.853193922 0.742274869 0.831112746 0.669826859 0.851333615 0.86769109 0.799864089 0.909160591 1.046520888 1 18.4795333 1.504290891 2.386299766 1.025010642 0.798969362 0.700900407 0.057717772 0.145945593 1.680277876 0.045272889 0.015417828 31.93676269 -1.504290891 -0.22604128 FFMT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 FFMTPPR 7 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 FFMT(1)PPR 105.52 0.088401 53437000 207570 217210 192470 213900 200290 195070 210920 198920 175990 206460 TRUE FALSE 199457.9349 211015.3835 227253.6105 224939.4046 206732.5097 199014.4491 213501.3021 194812.2325 156012.353 192476.2803 1.036272805 1.096318898 1.180683719 1.168660389 1.074067461 1.033968699 1.109234352 1.012136312 0.810553658 1 17.55432114 1.504483908 3.864537472 0.90412073 1.101021841 0.603371992 0.062680958 0.124146189 3.929426149 0.041691142 0.01635767 31.95095972 -1.504483908 0.196901111 IMHFPTWVDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IMHFPTWVDLK 11 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 162.38 2.52E-05 395700000 690990 680480 699380 729650 690200 595970 789280 785840 899130 913970 FALSE TRUE 663985.3469 661073.3767 825773.5236 767307.3239 712400.9098 608020.9217 798939.4447 769612.1294 797064.5319 852065.9978 0.779265161 0.77584762 0.969142679 0.900525694 0.836086537 0.713584304 0.937649721 0.903230655 0.935449289 1 19.70060565 1.504537533 1.262932976 0.982554757 0.839976795 0.351335701 0.072073381 0.517865557 1.584132133 0.067508854 0.023197178 31.95490517 -1.504537533 -0.142577962 GSVILDSGHLS(ph)TASSSDDLKGEEGSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSVILDSGHLSTASSSDDLKGEEGSFR 27 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 GSVILDS(0.001)GHLS(0.197)T(0.197)AS(0.197)S(0.197)S(0.197)DDLKGEEGS(0.012)FR 51.595 0.051161 48451000 62859 80463 68051 87659 94943 85738 81865 74982 68607 69076 TRUE FALSE 60402.40079 78168.27402 80349.32949 92183.0915 97996.92782 87471.6811 82866.88836 73433.5955 60819.02098 64397.42099 0.93796304 1.213841685 1.247710362 1.43147179 1.521752367 1.358310314 1.286804457 1.140318888 0.944432557 1 15.97471529 1.504815505 2.604204149 0.973252125 1.299209656 0.419970135 0.146303218 0.261118262 3.617823841 0.121958797 0.042367121 31.9753646 -1.504815505 0.325957532 GLGMEVFPVDLIYRPWK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLGMEVFPVDLIYRPWK 17 1 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 165.75 2.22E-09 138690000 105500 118750 90039 85118 106440 110910 102570 103450 99923 107350 FALSE TRUE 101376.9434 115363.3663 106311.0502 89510.95018 109863.7393 113152.6762 103825.2823 101313.7213 88580.15995 100079.0889 1.012968288 1.152721988 1.062270364 0.894402129 1.097769179 1.130632557 1.03743233 1.012336568 0.885101583 1 16.61078103 1.505024199 3.399766724 0.942560995 1.057249787 0.272887613 0.072224314 0.276120785 6.677025153 0.051076038 0.019212979 31.99073357 -1.505024199 0.114688792 GSRPAS(ph)PAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSRPASPAAK 10 1 A0A590UJ53;Q9P2N6-8;Q9P2N6-6;Q9P2N6-2;Q9P2N6-5;Q9P2N6-4;Q9P2N6-3;Q9P2N6 A0A590UJ53 KANSL3 KAT8 regulatory NSL complex subunit 3 1 GS(0.001)RPAS(0.999)PAAK;GS(0.005)RPAS(0.995)PAAK;GS(0.036)RPAS(0.964)PAAK;GS(0.04)RPAS(0.96)PAAK 81.327 0.012925 2122710000 1865760 1874530 1627570 1635650 1801120 1842410 1926620 2107540 2494480 2483500 TRUE FALSE 1792844.036 1821070.24 1921708.104 1720066.093 1859054.661 1879664.793 1950198.552 2064018.563 2211317.088 2315290.333 0.774349554 0.786540769 0.830007398 0.742915939 0.802946669 0.811848417 0.842312743 0.891472889 0.955092783 1 21.14276169 1.50524195 0.955589439 1.001547448 0.786469105 0.928864114 0.0206972 0.115315134 0.208809809 0.018311319 0.006902101 32.00677741 -1.50524195 -0.215078344 NRSAEEGELAES(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(0.001)AEEGELAES(0.999)K 260.47 1.35E-23 497750000 642160 620460 468220 516270 714150 598730 483770 534340 536800 423550 TRUE FALSE 617063.6773 602765.0883 552837.7695 542914.7566 737121.2833 610836.7308 489690.522 523305.6923 475864.7144 394862.5812 1.562730192 1.526518634 1.40007637 1.374946076 1.866779275 1.546960284 1.240154285 1.325285598 1.205140059 1 18.59099113 1.505379172 0.9495245 1.035280757 1.538748631 0.603888613 0.142336359 0.369552163 0.661524857 0.136674558 0.051666455 32.01689207 -1.505379172 0.503467873 SKVS(ph)SPIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKVSSPIEK 9 1 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(0.089)KVS(0.627)S(0.284)PIEK 73.848 0.033475 0 204200 210070 168400 179530 196090 201500 173150 188230 200410 174360 TRUE FALSE 196219.6382 204079.0093 198833.626 188795.5648 202397.4129 205574.4681 175269.0615 184342.9847 177660.297 162550.4419 1.207130759 1.25548111 1.223211846 1.16145833 1.245136036 1.264681078 1.07824414 1.13406634 1.092954869 1 17.31052795 1.505460135 0.697193713 1.007255248 1.229122361 0.734147208 0.043324909 0.323361246 0.341359895 0.041018979 0.018670587 32.02286137 -1.505460135 0.221867113 ARQPQS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ARQPQSPPR 9 1 O95613-2;O95613 O95613-2 PCNT Pericentrin 1 ARQPQS(1)PPR;ARQPQS(1)PPR 84.479 0.0093651 175705000 34125 45838 30775 38357 39617 36482 42207 35011 26077 39147 TRUE FALSE 32791.35727 44530.74512 36336.72709 40336.60937 40891.31678 37219.69104 42723.54189 34288.01062 23116.84828 36495.53882 0.898503169 1.220169548 0.995648462 1.105247673 1.120446994 1.019842212 1.170651079 0.939512382 0.633415728 1 15.1554325 1.505466238 5.2807518 0.806048514 1.077807017 0.434391969 0.119118849 0.115569136 7.164232411 0.063064045 0.027261445 32.02331137 -1.505466238 0.271758503 TSDANETEDHLESLICK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSDANETEDHLESLICK 17 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ;; 191.35 2.47E-10 504860000 965910 880900 754280 795560 770340 902990 937450 1017430 1294840 1250680 FALSE TRUE 928161.1693 855777.5945 890595.1749 836618.9469 795118.6857 921249.0765 948922.7935 996419.715 1147855.192 1165970.33 0.796041842 0.733961725 0.763823189 0.71753022 0.681937323 0.790113653 0.813848148 0.854584109 0.984463466 1 20.15309965 1.505515309 1.183671744 1.009182793 0.741917572 0.891052597 0.033313287 0.13077144 0.352729342 0.030446382 0.010635871 32.02692988 -1.505515309 -0.267265221 GVSAVAGPHDIGAS(ph)PGDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GVSAVAGPHDIGASPGDKK 19 1 Q8IYB7;Q8IYB7-3;Q8IYB7-2;Q8IYB7-4;Q8IYB7-5;C9JGP4 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 1 GVSAVAGPHDIGAS(1)PGDKK 81.949 0.0024222 201840000 153390 132140 124620 101970 113560 139760 136520 166670 188280 202290 TRUE FALSE 147395.3492 128371.4966 147141.6062 107232.6839 117212.7605 142586.043 138190.7726 163228.2063 166907.2437 188588.7181 0.781570344 0.680695525 0.78022486 0.568606039 0.621525835 0.756068785 0.73276267 0.865524767 0.885033025 1 17.52488385 1.505805086 1.079461872 0.984881242 0.68767018 0.716955907 0.064630498 0.246064929 0.557246862 0.059389523 0.021343071 32.04830651 -1.505805086 -0.297211061 MCINTEWGAFGDDGSLEDIRTEFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 MCINTEWGAFGDDGSLEDIRTEFDR 25 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 290.56 7.26E-63 558440000 255830 256960 150579 234437 231512 257490 194203 203313 188198 159888 FALSE TRUE 245831.8808 249631.7524 177791.9749 246536.3217 238958.7937 262696.6242 196579.7144 199114.5155 166834.552 149058.6433 1.649229292 1.674721752 1.192765283 1.653955223 1.603119339 1.762370959 1.318807887 1.335813281 1.119254464 1 17.18552051 1.505830221 1.283436994 1.018496741 1.572854782 0.63175697 0.155603737 0.271989081 0.858720779 0.139482446 0.047785543 32.05016139 -1.505830221 0.554358041 KIEFPMPNEEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 KIEFPMPNEEAR 12 1 P17980;E9PM69;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;; 93.823 0.011153 902370000 959710 1062290 844510 946100 980000 993450 995560 996290 1003520 1096880 FALSE TRUE 922203.4722 1031994.529 997131.743 994928.3344 1011522.59 1013538.24 1007743.961 975716.2633 889604.6167 1022587.341 0.901833453 1.009199399 0.975106676 0.972951938 0.989179652 0.991150779 0.985484487 0.954164231 0.869954655 1 19.96379264 1.505851349 5.724852776 0.927897243 0.976904396 0.134451704 0.039660623 0.203294615 14.92969555 0.021030443 0.009271428 32.05172062 -1.505851349 0.049007153 KKEEMLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKEEMLKK 8 3 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;D6RDA2 H0Y993 DEK Protein DEK 0 92.838 0.0050353 470080000 954360 844950 619700 599200 695190 700370 714820 819780 1000300 890850 FALSE TRUE 917062.5561 820852.8533 731693.5752 630124.7838 717551.4177 714531.9613 723568.181 802851.2565 886750.1376 830511.936 1.104213578 0.988369724 0.881015123 0.758718516 0.863986882 0.860351225 0.871231526 0.966694423 1.067715103 1 19.66364138 1.505885098 3.898720568 1.031894213 0.897997744 0.259975943 0.087297232 0.271273919 8.7686229 0.062258421 0.024545218 32.05421148 -1.505885098 -0.133896469 VTPLPSLAS(ph)PAVPAPGYCSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTPLPSLASPAVPAPGYCSR 20 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3;H7C3V8 C9JWC4 HJURP Holliday junction recognition protein 1 VTPLPS(0.001)LAS(0.999)PAVPAPGYCSR 130.27 1.72E-05 61773000 45655 45104 40798 46662 44184 45952 39615 43133 35219 36194 TRUE FALSE 43870.75213 43817.67808 48171.10615 49070.23141 45605.21849 46881.18092 40099.82022 42242.28848 31221.08677 33742.54814 1.300161207 1.298588296 1.427607244 1.454253876 1.351564153 1.389378796 1.188405216 1.251899776 0.925273534 1 15.04228131 1.505943813 1.312855228 0.958509613 1.368795799 0.79923787 0.07482392 0.17095552 0.564449142 0.065968856 0.022496367 32.05854539 -1.505943813 0.410286186 KSIKPSDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSIKPSDSPR 10 2 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 KSIKPS(0.027)DS(0.972)PR 77.527 0.032259 0 399970 363200 337370 317900 355170 383600 373530 431690 501480 500330 TRUE FALSE 384338.7302 352841.8916 398340.2638 334306.8571 366594.3656 391356.6548 378101.3719 422775.4506 444554.0928 466442.2035 0.823979321 0.756453616 0.853997046 0.716716572 0.785937385 0.839024968 0.810607121 0.906383358 0.953074335 1 18.8313388 1.505979426 1.122203358 1.000052722 0.788614152 0.800438412 0.037107181 0.179281527 0.436771128 0.031713048 0.011253854 32.0611744 -1.505979426 -0.21143857 KPSDGS(ph)PDTKPSR ddPTM_BT-474_Pertuzumab_2h_R1 6 KPSDGSPDTKPSR 13 2 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 KPS(0.004)DGS(0.996)PDTKPSR;KPS(0.02)DGS(0.98)PDTKPSR;KPS(0.032)DGS(0.965)PDT(0.003)KPSR;KPS(0.002)DGS(0.998)PDTKPSR;KPS(0.021)DGS(0.951)PDT(0.028)KPSR;KPS(0.005)DGS(0.994)PDT(0.001)KPSR 156.11 3.28E-05 2739212000 1538290 1363150 1235930 1221430 1298770 1331480 1536920 1654730 1862510 2000490 TRUE FALSE 1478171.926 1324274.297 1459290.044 1284468.149 1340546.117 1358403.438 1555729.287 1620559.247 1651085.673 1864995.03 0.792587595 0.710068539 0.782463235 0.688724703 0.718793399 0.728368395 0.834173422 0.868934888 0.885302988 1 20.83074036 1.506057357 0.893124069 0.985302968 0.731976118 0.846183124 0.03631681 0.186093252 0.298639378 0.032977065 0.012840298 32.06692802 -1.506057357 -0.25332685 TLCDSSSLLFHQIS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLCDSSSLLFHQISPSR 17 0 A0A0A0MRS1;A0A0A0MR11;Q06730;Q06730-2;Q06730-3 A0A0A0MRS1 ZNF33A Zinc finger protein 33A 1 TLCDSSSLLFHQIS(1)PSR;TLCDSSSLLFHQIS(0.917)PS(0.083)R;TLCDSSSLLFHQIS(0.999)PS(0.001)R;TLCDSSSLLFHQIS(0.847)PS(0.153)R 253.83 3.26E-27 597160000 342072 363858 302047 396258 343928 323738 345233 328273 270000 327403 TRUE FALSE 328703.4481 353481.1261 356633.6119 416708.9229 354990.7565 330284.2042 349458.0647 321494.0478 239350.7319 305227.7032 1.076912235 1.158089919 1.168418227 1.36523952 1.163035834 1.082091176 1.144909394 1.053292491 0.784171061 1 18.21952638 1.506067814 3.152596872 0.893070695 1.169468233 0.588639199 0.090062194 0.151926511 3.144448736 0.065591926 0.024104899 32.06770013 -1.506067814 0.276397538 NNIFEESYR ddPTM_BT-474_Pertuzumab_2h_R1 2 NNIFEESYR 9 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;K7ERN1;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 0 ; 132.84 0.00068331 201857000 384570 569460 399230 535290 469920 465440 482950 438260 349590 427580 FALSE TRUE 369540.5792 553219.5584 471379.7418 562916.381 485035.4036 474851.5157 488860.4866 429209.7778 309906.0088 398619.6258 0.92705064 1.387838236 1.18253019 1.412164241 1.216787564 1.191239681 1.226383387 1.076740206 0.777447945 1 18.60465322 1.506244602 3.290286731 0.89088909 1.230909672 0.486642194 0.134746364 0.163293465 3.695984558 0.088347407 0.032926621 32.08075662 -1.506244602 0.340020582 DKFNECGHVLYADIK ddPTM_BT-474_Pertuzumab_2h_R1 3 DKFNECGHVLYADIK 15 1 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 148.03 2.17E-06 12227800000 15662140 13310250 11132050 11263400 12807870 10295060 13255440 14036420 17664620 15870770 FALSE TRUE 15050046.25 12930654.7 13143859.07 11844705.42 13219846.77 10503233.17 13417664.04 13746563.02 15659406.39 14795828.61 1.01718171 0.873939206 0.888348967 0.800543568 0.893484719 0.709877996 0.906854519 0.929083689 1.058366301 1 23.81868716 1.506288714 2.525411179 1.027051037 0.862713956 0.405699145 0.075531853 0.250924763 3.266086803 0.058229743 0.020111444 32.08401524 -1.506288714 -0.16433708 GPVS(ph)PSVSFQPLAR ddPTM_BT-474_Pertuzumab_2h_R1 6 GPVSPSVSFQPLAR 14 0 Q7Z434;Q7Z434-4 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 1 GPVS(0.996)PS(0.004)VSFQPLAR;GPVS(0.998)PS(0.002)VSFQPLAR;GPVS(0.983)PS(0.017)VSFQPLAR;GPVS(0.86)PS(0.14)VSFQPLAR;GPVS(0.998)PS(0.002)VSFQPLAR;GPVS(0.997)PS(0.003)VSFQPLAR 245.93 1.14E-17 3787290000 1376900 2206110 1642420 3154990 1827080 1981760 2156250 1828430 1604010 1616420 TRUE FALSE 1323089.226 2143193.903 1939241.829 3317819.412 1885849.688 2021832.545 2182638.833 1790672.282 1421929.509 1506938.434 0.877998196 1.422217295 1.286875287 2.201695396 1.251444416 1.341682248 1.448392837 1.188284963 0.943588323 1 20.52318905 1.506828541 2.601273946 0.970961407 1.424027864 0.236342849 0.310407831 0.369841067 5.128188599 0.240048534 0.08354288 32.12392039 -1.506828541 0.453066458 DEQIEHWK ddPTM_BT-474_Pertuzumab_2h_R1 3 DEQIEHWK 8 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ;; 119.68 0.0016475 686280000 802920 750070 785070 864700 812530 718310 925850 955430 1137360 1152660 FALSE TRUE 771540.9987 728678.738 926949.6128 909327.2706 838665.7654 732834.7204 937180.8293 935700.0366 1008251.661 1074589.312 0.717986854 0.678099745 0.862608257 0.846209115 0.780452361 0.681967253 0.872129305 0.870751297 0.938266973 1 20.03535396 1.506842147 1.142004319 0.992031475 0.767568277 0.62556873 0.062733868 0.313622998 0.789746654 0.059678181 0.021071896 32.12492681 -1.506842147 -0.224463198 VTYIDYEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTYIDYEGR 9 0 Q9P2I0;H0YJF4 Q9P2I0 CPSF2 Cleavage and polyadenylation specificity factor subunit 2 0 76.679 0.080842 210860000 240280 320820 244410 309700 289850 296210 302700 283160 259170 309340 FALSE TRUE 230889.592 311670.5277 288580.3239 325683.6541 299173.2885 302199.5691 306404.5331 277312.647 229750.1081 288388.1263 0.800621007 1.080732871 1.000666455 1.129324076 1.03739808 1.047891857 1.062472776 0.961595232 0.79666979 1 18.13765224 1.506867312 5.06662064 0.891866065 1.028927804 0.216983172 0.093949925 0.197493643 11.20057429 0.053119894 0.022750163 32.12678836 -1.506867312 0.137061739 TS(ph)MTEEYRVPDGMVGLIIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSMTEEYRVPDGMVGLIIGR 20 1 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 T(0.131)S(0.868)MT(0.001)EEYRVPDGMVGLIIGR 98.74 0.00045819 17166000 15540 12193 11399 14941 14531 15202 12243 13087 13539 11464 TRUE FALSE 14932.67962 11845.26758 13459.05287 15712.1068 14998.40281 15509.39486 12392.8335 12816.74888 12002.10948 10687.53307 1.397205466 1.108325701 1.259322688 1.470134099 1.403354985 1.451166958 1.15955978 1.199224254 1.123000921 1 13.38364126 1.50718083 1.18847882 1.029482426 1.335009482 0.512250036 0.108902193 0.390578285 1.061573507 0.104252452 0.036402544 32.14998909 -1.50718083 0.305527057 KYSSCSTIFLDDSTVSQPNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KYSSCSTIFLDDSTVSQPNLK 21 1 Q8ND76-3;Q8ND76-2;Q8ND76;R4GNF3 Q8ND76-3 CCNY Cyclin-Y 0 47.752 0.063837 3004500000 895210 452810 441000 296610 587780 479100 516270 616960 841730 694120 FALSE TRUE 860224.2035 439896.3021 520698.51 311918.0776 606686.4775 488787.7303 522588.2667 604219.5604 746180.3392 647106.6341 1.329339182 0.679789511 0.804656424 0.482019595 0.937537101 0.755343408 0.807576741 0.933724874 1.153102595 1 19.30364394 1.507230092 3.337606471 1.074105904 0.810263651 0.181537055 0.206564768 0.328707957 7.678991462 0.138911038 0.052078399 32.15363606 -1.507230092 -0.263842253 ET(ph)PHSPGVEDAPIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETPHSPGVEDAPIAK 15 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 ET(0.543)PHS(0.457)PGVEDAPIAK;ET(0.537)PHS(0.463)PGVEDAPIAK 91.457 0.020682 7333900 35141 38830 32093 39058 37883 39408 38036 35961 37405 34580 TRUE FALSE 33767.65087 37722.60642 37892.919 41073.78806 39101.5411 40204.85676 38501.49595 35218.39278 33158.94121 32237.8658 1.04745305 1.17013349 1.175416488 1.274085211 1.212907248 1.247131464 1.194294194 1.092454228 1.028571228 1 14.97646862 1.507338821 2.276524448 1.011055749 1.194436456 0.606670472 0.056979612 0.195675204 2.046334812 0.048056198 0.016272771 32.16168703 -1.507338821 0.183380707 QVVSVVQDEEVGLPFEASPESPPPAS(ph)PDGVTEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEASPES(0.072)PPPAS(0.925)PDGVT(0.002)EIR;QVVSVVQDEEVGLPFEASPES(0.004)PPPAS(0.985)PDGVT(0.011)EIR 178.89 5.83E-20 1359140000 418620 434893 320322 384901 341758 381173 363569 361370 320778 330727 TRUE FALSE 402259.8676 422490.2774 378211.3109 404765.7867 352750.9564 388880.5792 368018.4662 353907.5832 284364.6263 308326.5657 1.304655234 1.370268814 1.226658203 1.312782717 1.144082268 1.261261994 1.193599602 1.147833572 0.922283896 1 18.23409967 1.507355819 1.684132333 0.956918264 1.266905165 0.770820702 0.064010654 0.159348855 0.876295466 0.055230803 0.018319114 32.16294578 -1.507355819 0.309986901 NTVGNVPLEWYDDFPHVGYDLDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NTVGNVPLEWYDDFPHVGYDLDGR 24 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 149.44 1.44E-07 251860000 92870 94431 79588 103200 91158 90489 81036 103969 119673 118004 FALSE TRUE 89240.53773 91737.92034 93971.32203 108526.1644 94090.17986 92318.74958 82027.74281 101822.0038 106088.2228 110011.484 0.811192927 0.833894036 0.854195568 0.986498504 0.855275981 0.83917375 0.745628909 0.925557952 0.964337712 1 16.74729461 1.507568264 6.035308221 0.971399616 0.850705563 0.483982988 0.056910367 0.130913826 10.6586868 0.034522153 0.015406926 32.17868292 -1.507568264 -0.120694053 TEGT(ph)PPPPGQPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TEGTPPPPGQPAK 13 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;A0A494C150;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 TEGT(1)PPPPGQPAK;TEGT(1)PPPPGQPAK;TEGT(1)PPPPGQPAK 175.21 0.00020845 1169290000 2084520 2147070 1795940 1778880 1930610 1982570 1945130 2085260 2393220 2138640 TRUE FALSE 2003054.654 2085837.666 2120506.308 1870688.21 1992709.824 2022658.924 1968935.083 2042198.652 2121551.699 1993788.008 1.004647759 1.046168227 1.063556557 0.938258332 0.999459228 1.014480434 0.987534821 1.024280738 1.06408088 1 20.92708059 1.507586238 7.403276599 1.035951116 1.008509292 0.07623533 0.034702083 0.287114858 34.66034619 0.019515625 0.008948033 32.18001467 -1.507586238 -0.027441824 VNPFRPGDSEPPPAPGAQR ddPTM_BT-474_Pertuzumab_2h_R1 3 VNPFRPGDSEPPPAPGAQR 19 1 Q15942;H0Y2Y8;C9IZ41 Q15942 ZYX Zyxin 0 ;; 89.049 0.0025734 371130000 316732 369210 292690 325460 315202 359330 338250 324966 329630 319499 FALSE TRUE 304353.7633 358680.4923 345585.5939 342257.0296 325340.7586 366595.8988 342389.6047 318255.3385 292211.7843 297859.0481 1.02180466 1.204195389 1.160231982 1.149057018 1.092264145 1.230769725 1.149502111 1.068476316 0.981040483 1 18.18427026 1.507802832 2.805963046 0.992057881 1.148318257 0.559694084 0.054489584 0.168347171 2.740997462 0.039048342 0.013880589 32.19606767 -1.507802832 0.156260376 GHGADVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHGADVK 7 0 Q9C0J8;C9J8B4 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 0 60.972 0.09429 102540000 175280 232940 196240 262030 221430 208110 264220 202050 163640 216180 FALSE TRUE 168429.8638 226296.7793 231704.9333 275553.3997 228552.497 212318.1268 267453.6034 197877.5969 145064.2732 201537.936 0.835722877 1.122849542 1.149683965 1.367253258 1.134042064 1.053489636 1.327063324 0.981837964 0.719786439 1 17.6206919 1.508005661 6.008826673 0.855877939 1.146579775 0.366475185 0.150632796 0.1334699 10.7561668 0.084555629 0.037719632 32.21110776 -1.508005661 0.290701835 KKKEPIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKKEPIEK 8 3 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 77.662 0.014295 863020000 1485600 1210900 925350 849320 1113200 1226800 1085400 1265800 1550300 1365300 FALSE TRUE 1427541.11 1176366.318 1092581.329 893153.507 1149007.089 1251606.737 1098683.45 1239660.788 1374316.443 1272827.015 1.121551549 0.924215391 0.858389488 0.701708478 0.902720539 0.983328231 0.863183635 0.973942864 1.079735445 1 20.27960493 1.5082418 4.215265524 1.038329662 0.901737708 0.214000801 0.101119641 0.276313496 10.58329918 0.067242255 0.027288919 32.2286267 -1.5082418 -0.136591954 IET(ph)DEEESCDNAHGDANQPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IETDEEESCDNAHGDANQPAR 21 0 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 IET(1)DEEESCDNAHGDANQPAR;IET(1)DEEESCDNAHGDANQPAR 378.43 2.78E-112 2137430000 238772 255745 206483 196795 226861 232268 219082 244842 277166 263304 TRUE FALSE 229440.5263 248451.403 243799.0713 206951.6135 234158.1901 236964.6181 221763.1911 239785.9271 245703.2777 245470.1856 0.934698142 1.012144927 0.99319219 0.843082483 0.953917029 0.965349896 0.903422102 0.976843386 1.000949574 1 17.90518828 1.508324401 6.012593431 0.997189855 0.945215726 0.214711513 0.044247116 0.230086059 18.54644243 0.026074975 0.011636367 32.23475703 -1.508324401 -0.051974129 EGS(ph)PIPHDPEFGSK ddPTM_BT-474_Pertuzumab_2h_R1 6 EGSPIPHDPEFGSK 14 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(0.996)PIPHDPEFGS(0.004)K;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK 243.2 1.68E-17 12430270000 24091500 19306300 17326600 15396820 18124400 17670900 18508800 21083300 27203500 22264600 TRUE FALSE 23149977.55 18755703.23 20457902.05 16191451.73 18707387.79 18028217.71 18735316.23 20647922.49 24115472.73 20756598.81 1.115306884 0.903601953 0.985609552 0.780062855 0.901274238 0.868553556 0.90261976 0.994764252 1.16182198 1 24.30706673 1.50864282 4.060604476 1.082174984 0.916665164 0.332153932 0.089133021 0.194248544 6.874428811 0.056272646 0.022570679 32.2583998 -1.50864282 -0.16550982 AFVEDS(ph)EDEDGAGEGGSSLLQK ddPTM_BT-474_Pertuzumab_2h_R1 3 AFVEDSEDEDGAGEGGSSLLQK 22 0 A0A494C108;Q8N9T8;H0YFD2;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK 236.48 1.10E-30 675060000 395307 384759 313384 348525 363715 379201 372976 430301 443501 467578 TRUE FALSE 379857.9654 373786.05 370019.46 366512.417 375414.2233 386868.704 377540.5919 421415.134 393156.6258 435908.5256 0.871416692 0.857487358 0.848846577 0.840801213 0.861222484 0.887499742 0.8661005 0.9667513 0.901924607 1 18.73366589 1.508981043 0.660313344 0.992714163 0.8510786 0.767773689 0.024121257 0.286175899 0.27657727 0.022164017 0.010540222 32.28353201 -1.508981043 -0.141635563 DS(ph)MALSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSMALSK 7 0 F8VW93;F8VXS0;P20132 F8VW93 SDS L-serine dehydratase/L-threonine deaminase 1 DS(1)MALSK 75.311 0.04596 92071000 61276 109830 93178 145680 135200 100120 113710 89978 52184 77544 TRUE FALSE 58881.26618 106697.7559 110017.3373 153198.5623 139548.8308 102144.495 115101.617 88119.92286 46260.29109 72291.87581 0.814493545 1.475930106 1.521849255 2.119167065 1.930352882 1.412945699 1.592179145 1.218946415 0.639909956 1 16.14154591 1.509123658 3.105443719 0.826225763 1.578784132 0.430146041 0.33437337 0.215347529 4.343269831 0.251762437 0.092415376 32.29413508 -1.509123658 0.752558369 GTPQQIDYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTPQQIDYAR 10 0 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ; 150.61 4.95E-05 535570000 382720 413490 320520 389640 401660 385580 388760 370490 361240 361270 FALSE TRUE 367762.8793 401697.67 378445.0939 409749.3671 414579.7587 393376.6918 393517.7612 362839.252 320233.5496 336800.8611 1.091929748 1.192685995 1.123646456 1.216592397 1.230934379 1.167980065 1.168398916 1.077310939 0.950809771 1 18.3615363 1.510058807 2.626086904 0.976015741 1.173894104 0.78499259 0.040733979 0.108784592 1.5466703 0.030994709 0.010849563 32.36374768 -1.510058807 0.197878363 LDNVLLDTYQDAS(ph)S ddPTM_BT-474_Pertuzumab_2h_R1 1 LDNVLLDTYQDASS 14 0 Q9HD40-3;Q9HD40 Q9HD40-3 SEPSECS O-phosphoseryl-tRNA(Sec) selenium transferase 1 LDNVLLDTYQDAS(0.5)S(0.5) 104.45 0.0011085 6038400 24946 25825 22216 23848 23308 24177 27349 24490 25323 26004 TRUE FALSE 23971.08274 25088.49629 26230.92539 25078.79814 24057.72299 24665.8755 27683.70524 23984.27294 22448.4392 24242.72592 0.988794858 1.034887594 1.082012208 1.03448755 0.992368724 1.017454703 1.141938631 0.989338947 0.925986594 1 14.56526431 1.51033995 8.993467622 0.961289563 1.041497978 0.345236126 0.045098801 0.112767073 18.69871107 0.024284873 0.011249813 32.38470538 -1.51033995 0.080208415 GDAASS(ph)PAPAASVGSSQGGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDAASSPAPAASVGSSQGGAR 21 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 GDAAS(0.002)S(0.998)PAPAASVGSSQGGAR;GDAAS(0.002)S(0.998)PAPAASVGSSQGGAR;GDAASS(1)PAPAASVGSSQGGAR;GDAAS(0.052)S(0.948)PAPAASVGSSQGGAR 462.71 1.73E-223 2191370000 803740 919380 725431 971220 868620 880700 940440 851130 810870 897770 TRUE FALSE 772328.9522 893160.1826 856532.5188 1021344.781 896559.9512 898508.3574 951949.386 833553.8681 718823.437 836963.2382 0.922775239 1.067143862 1.02338129 1.220298257 1.071205891 1.073533838 1.137384944 0.995926499 0.858847085 1 19.67480473 1.510571429 5.126017116 0.927760666 1.076677535 0.357519729 0.078172999 0.154864199 8.984041481 0.04571459 0.019725445 32.40197098 -1.510571429 0.148916869 FY(ph)HKGIAS(ph)LT(ph)PEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYHKGIASLTPEDK 14 1 A0A087X0F3 A0A087X0F3 INTS7 3 FY(1)HKGIAS(1)LT(1)PEDK 56.959 0.034353 0 55401 59947 81149 78067 75775 76613 89116 98259 132130 145280 TRUE FALSE 53235.86767 58237.37025 95814.42945 82096.04723 78212.37169 78162.16735 90206.62827 96229.91731 117131.1563 135440.0562 0.393058517 0.429986312 0.70743052 0.606143039 0.577468541 0.577097866 0.666026217 0.710498209 0.864819165 1 17.04729495 1.510872137 0.097601787 1.460786173 4.89E-17 0.811854046 0.075463975 4.507341372 0.451388858 3.167827581 3.116197299 32.42441408 -1.510872137 -1.460786173 ETDEFFKK ddPTM_BT-474_Pertuzumab_2h_R1 6 ETDEFFKK 8 1 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;; 96.711 0.014026 5907420000 7102830 6653720 5760910 5583180 6044430 6542220 6514040 7743020 8947220 9071150 FALSE TRUE 6825243.551 6463962.42 6802034.588 5871328.589 6238854.58 6674508.171 6593760.77 7583123.931 7931569.095 8456752.931 0.807076145 0.764355122 0.804331715 0.694276945 0.737736414 0.789251883 0.779703608 0.896694511 0.937897697 1 23.0116724 1.511039427 1.372185206 0.991568149 0.760890061 0.870492126 0.032352634 0.13009543 0.469362456 0.029125281 0.009875993 32.43690632 -1.511039427 -0.230678088 SGSGS(ph)ESTGAEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSGSESTGAEER 13 0 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 SGS(0.005)GS(0.992)ES(0.002)TGAEER 193 2.35E-06 51902000 123590 102060 85994 109120 117970 107980 106700 106540 103900 106530 TRUE FALSE 118759.9662 99149.34873 101535.0287 114751.6963 121764.6122 110163.4296 108005.8265 104339.9118 92105.70758 99314.62821 1.195795305 0.998335799 1.022357235 1.155435995 1.226049117 1.109236691 1.087511764 1.050599631 0.927413305 1 16.59971861 1.511172282 2.542687722 0.964775924 1.112079822 0.428602671 0.068369039 0.26758003 3.559362182 0.05588159 0.019428868 32.44683063 -1.511172282 0.147303898 FNPDGEEEDVTVQE ddPTM_BT-474_Pertuzumab_2h_R1 1 FNPDGEEEDVTVQE 14 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;E7EWM2;E7EMW0 Q5SW79 CEP170 Centrosomal protein of 170 kDa 0 83.204 0.020061 91633000 81161 87597 73771 82681 93822 96395 92619 83748 84859 81955 FALSE TRUE 77989.13839 85098.81933 87103.06073 86948.17632 96839.86984 98344.17295 93752.49903 82018.57453 75226.16208 76404.11485 1.020745264 1.113798903 1.140031017 1.138003843 1.267469298 1.287158069 1.227060862 1.073483734 0.9845826 1 16.22136272 1.511242168 3.798320819 0.997960324 1.173807118 0.48849831 0.07377044 0.182568871 5.632086583 0.054565834 0.02147554 32.45205235 -1.511242168 0.175846794 LKEVLEYNAIGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKEVLEYNAIGGK 13 1 P14324-2;P14324;A0A087WVN4;A0A087X1D8 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ; 141.46 3.64E-05 1956770000 1543910 1344620 1142290 1092050 1273090 1295660 1213590 1430460 1753550 1506120 FALSE TRUE 1483572.29 1306272.754 1348727.213 1148410.831 1314040.096 1321859.133 1228442.277 1400920.501 1554494.355 1404109.151 1.056593278 0.930321374 0.960557242 0.817892847 0.935853238 0.94142192 0.874890871 0.997729058 1.107103643 1 20.42122366 1.511498297 5.111552313 1.054140354 0.928642564 0.38894972 0.062139046 0.145501262 8.386710647 0.036164544 0.015609467 32.47119687 -1.511498297 -0.12549779 APSGHLAPS(ph)PPAFDGELDLQR ddPTM_BT-474_Pertuzumab_2h_R1 3 APSGHLAPSPPAFDGELDLQR 21 0 Q9P2Y4;G3V2Q8;G3V452;G3V2W3;G3V2E3;G3V4M7;G3V3F2 Q9P2Y4 ZNF219 Zinc finger protein 219 1 APSGHLAPS(1)PPAFDGELDLQR;APS(0.004)GHLAPS(0.996)PPAFDGELDLQR;APS(0.001)GHLAPS(0.999)PPAFDGELDLQR 88.001 0.0014072 520650000 448730 501500 379890 495850 517840 478010 454640 456420 406410 437490 TRUE FALSE 431193.1355 487197.711 448544.5736 521440.8779 534496.7939 487675.6897 460204.0203 446994.7675 360276.0406 407858.4126 1.057212803 1.194526571 1.099755601 1.278485037 1.31049594 1.195698494 1.128342597 1.095955738 0.883336054 1 18.63770888 1.512410367 2.249415878 0.94366693 1.18988568 0.589183741 0.077950732 0.196227359 2.012630457 0.064303299 0.021833768 32.53946194 -1.512410367 0.24621875 ESLKELEEEAEEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESLKELEEEAEEEQR 15 1 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 ; 192.24 1.30E-07 1236570000 637970 655220 530010 497740 564740 629110 610680 691140 756970 782720 FALSE TRUE 613037.4271 636533.7671 625794.597 523428.421 582905.375 641831.0352 618153.6845 676867.7175 671041.9391 729705.6772 0.840116017 0.872315766 0.857598641 0.717314443 0.798822584 0.879575225 0.847127416 0.927590039 0.919606302 1 19.47695515 1.512541718 0.914449573 0.989869537 0.820570636 0.629508737 0.044129959 0.357502952 0.596990274 0.043125527 0.016630938 32.54930485 -1.512541718 -0.169298901 S(ph)PLS(ph)PTETFSWPDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 2 S(1)PLS(0.986)PT(0.008)ET(0.006)FSWPDVR;S(0.999)PLS(0.44)PT(0.3)ET(0.25)FS(0.01)WPDVR 113.59 0.0021143 29811000 18822.4 22536 20266.8 23255.3 21616.4 23562.9 19971.3 22399.7 19579.2 21941.5 TRUE FALSE 18086.7998 21893.29535 23929.46159 24455.50882 22311.71114 24039.35798 20215.71474 21937.13837 17356.6513 20455.38266 0.884207355 1.070295076 1.169836907 1.195553719 1.090750122 1.1752094 0.988283381 1.072438425 0.848512667 1 14.32019291 1.512773624 2.028557471 0.93256237 1.096670785 0.263531507 0.097164098 0.38883494 3.193715768 0.080105301 0.026838536 32.56669029 -1.512773624 0.164108415 GDNIYEWR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDNIYEWR 8 0 R4GN77;R4GND1;A0A1B0GX65;Q969T4;A0A087X283;H7C061;B7Z306;P51965-2;C9J180;Q96LR5;C9J2P0;P51965-3;P51965 R4GN77;C9J180;C9J2P0 UBE2E3;UBE2E2;UBE2E1 Ubiquitin-conjugating enzyme E2 E3;Ubiquitin-conjugating enzyme E2 E1;Ubiquitin-conjugating enzyme E2 E2 0 ;;; 115.71 0.0056081 3004120000 3469500 4000490 3158080 3880150 3802730 3530280 3754040 3725070 3739100 3971430 FALSE TRUE 3333908.104 3886399.942 3728815.307 4080405.006 3925048.264 3601664.68 3799983.064 3648146.003 3314653.044 3702441.509 0.900462059 1.04968571 1.007123353 1.102084934 1.060124314 0.97278098 1.026345198 0.985335216 0.89526142 1 21.82004551 1.512807012 4.354246447 0.94502062 1.020583182 0.191078391 0.056227714 0.25106454 10.349681 0.034474987 0.014222344 32.56919404 -1.512807012 0.075562562 DFTVLVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFTVLVDR 8 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 0 84.368 0.040715 84707000 104890 140880 122390 190220 165450 143850 150780 140290 121370 143500 FALSE TRUE 100790.7828 136862.2403 144508.5956 200037.277 170771.8495 146758.7456 152625.2907 137392.9625 107592.5864 133780.6172 0.753403482 1.0230349 1.080190827 1.495263523 1.276506665 1.097010528 1.14086251 1.027002008 0.80424645 1 17.02950958 1.512977824 3.6052882 0.902059637 1.136514855 0.185688606 0.182533461 0.336858972 9.341015611 0.131232267 0.05085756 32.58200632 -1.512977824 0.234455218 SQTTTERDS(ph)DT(ph)DVEEEELPVENR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 2 SQTTTERDS(1)DT(1)DVEEEELPVENR;SQTTTERDS(1)DT(1)DVEEEELPVENR 251.8 4.30E-43 1496430000 540390 540840 427640 486900 577750 489980 457310 487040 458030 414000 TRUE FALSE 519270.9614 525415.7727 504924.0608 512028.9674 596333.8534 499887.7313 462906.6966 476982.4538 406036.3546 385959.4112 1.34540303 1.361323905 1.308230985 1.326639414 1.545068823 1.295182127 1.199366263 1.23583579 1.052018276 1 18.55808961 1.513060474 0.980900143 0.999100658 1.36797638 0.760077208 0.07289407 0.245360921 0.46481679 0.068172811 0.025472961 32.58820755 -1.513060474 0.368875722 GGPAS(ph)PGGLQGLETR ddPTM_BT-474_Pertuzumab_2h_R1 6 GGPASPGGLQGLETR 15 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR 235.53 1.16E-17 7079990000 2418570 2552640 2269120 2757350 2492620 2469560 2465100 2403290 2042160 2402470 TRUE FALSE 2324049.611 2479841.206 2679200.46 2899657.164 2572797.386 2519496.195 2495268.631 2353661.222 1810342.558 2239748.567 1.037638619 1.107196247 1.196205904 1.294635124 1.1486992 1.124901354 1.114084263 1.050859573 0.808279369 1 21.09490535 1.513218848 2.938704927 0.90551018 1.151863201 0.599695247 0.077593519 0.155845403 2.821228387 0.058274824 0.021127614 32.60009364 -1.513218848 0.246353021 ETDLLLDDSLVSIFGNRR ddPTM_BT-474_Pertuzumab_2h_R1 6 ETDLLLDDSLVSIFGNRR 18 1 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;;;; 268.2 3.33E-31 4306105000 2363959.6 2686883 1716307 2034217.8 2474975 2589318.8 2156826 2297694.4 2351659.2 2199869.4 FALSE TRUE 2271573.445 2610255.728 2026481.854 2139204.024 2554584.819 2641676.6 2183221.882 2250246.208 2084708.707 2050870.286 1.107614392 1.272755154 0.988108252 1.043071343 1.245610137 1.288075905 1.064534357 1.097215276 1.016499542 1 20.96780482 1.513334331 1.699342655 1.005886751 1.15084549 0.253269321 0.094246625 0.517921753 2.911772106 0.084396801 0.028094756 32.6087635 -1.513334331 0.144958738 QEEDSYEIFICHANVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEEDSYEIFICHANVIR 17 0 Q96HS1;Q96HS1-2;F5GXG4 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 ; 198.07 1.45E-11 508560000 519790 687910 573290 861980 522580 652750 733620 614860 608520 597430 FALSE TRUE 499476.0321 668291.4803 676896.2558 906466.8911 539389.2603 665949.0522 742598.261 602162.9261 539443.3607 556965.534 0.896780863 1.199879417 1.215328803 1.627509847 0.968442798 1.195673721 1.333293024 1.081149352 0.968539933 1 19.08722853 1.514454523 4.905444373 0.993779643 1.212441171 0.18763039 0.186397412 0.262723162 13.89496387 0.111405938 0.047716597 32.69298106 -1.514454523 0.218661528 VNIDFEPFKPINTSLYLCDNK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNIDFEPFKPINTSLYLCDNK 21 1 B7Z7P8;P62495-2;P62495;I3L492;D6RJE8 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 187.83 2.50E-17 258930000 300530 277320 242100 239900 288880 267850 312910 352400 407990 436910 FALSE TRUE 288784.9553 269411.1051 285852.8555 252281.2677 298172.0876 273266.1105 316739.4862 345122.8169 361676.6856 407317.6965 0.708991919 0.661427449 0.701793362 0.619372224 0.732038137 0.670891819 0.777622698 0.847306218 0.88794739 1 18.63579497 1.514580829 0.869199435 0.992578898 0.673782154 0.918614473 0.032035815 0.124621719 0.190144644 0.027175605 0.010761341 32.70249053 -1.514580829 -0.318796743 TVSLT(ph)PS(ph)PTTQVETPDLVDHDNTSPLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 T(0.092)VS(0.099)LT(0.814)PS(0.972)PT(0.012)T(0.011)QVET(0.001)PDLVDHDNTSPLFR 70.073 0.021072 82579000 26175 25661 23097 24733 24034 26851 27093 31015 31153 34575 TRUE FALSE 25152.05206 24929.1734 27271.14169 26009.47309 24807.07544 27393.94562 27424.57224 30374.52941 27616.64204 32233.20445 0.780314973 0.773400406 0.846057417 0.806915525 0.76961245 0.849867274 0.850817432 0.942336635 0.856776188 1 14.97626 1.514774532 0.444517128 0.999852491 0.780579371 0.762042717 0.034518452 0.441261311 0.238801202 0.039607381 0.02728237 32.7170797 -1.514774532 -0.21927312 LYTLQDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYTLQDK 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 101.99 0.020244 1317640000 1863490 1879720 1777090 1789900 1737810 1571900 2149400 1987480 2401300 2380900 FALSE TRUE 1790662.751 1826112.226 2098249.694 1882276.954 1793708.237 1603684.895 2175705 1946437.843 2128714.491 2219639.522 0.806735838 0.822706664 0.945311017 0.848010199 0.808107902 0.722497901 0.980206461 0.876916195 0.959036127 1 21.08189397 1.514800594 1.13865284 0.988969387 0.837230293 0.41558634 0.06599242 0.469066141 1.173201417 0.06015402 0.021322627 32.71904314 -1.514800594 -0.151739094 EVQAEQPSSSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 EVQAEQPSSSSPR 13 0 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSS(0.013)S(0.987)PR;EVQAEQPSS(0.001)S(0.319)S(0.679)PR;EVQAEQPS(0.005)S(0.03)S(0.275)S(0.691)PR;EVQAEQPSSS(0.006)S(0.994)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR 303.44 4.17E-41 4054753000 4543312 4763766 4024861 4885079 4728732 4852706 4502966 4737381 4818776 4681790 TRUE FALSE 4365754.344 4627908.058 4752242.915 5137198.513 4880835.959 4950831.04 4558074.645 4639552.427 4271768.75 4364688.193 1.000244267 1.060306682 1.088793221 1.176990952 1.118255358 1.134292032 1.044307049 1.062974541 0.978711093 1 22.05744716 1.514912041 1.648571825 0.98952582 1.096764981 0.407938131 0.046830643 0.362345192 1.911873176 0.042807078 0.014277314 32.72744043 -1.514912041 0.107239161 ARS(ph)PDLGPQEQMNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARSPDLGPQEQMNPK 15 1 H3BUW4;H3BMU4;A0A0C4DGM2;C9K0J8;Q8IWY8-4;Q8IWY8-3;Q8IWY8-2;Q8IWY8 H3BUW4 ZSCAN29 Zinc finger and SCAN domain-containing protein 29 1 ARS(1)PDLGPQEQMNPK;ARS(1)PDLGPQEQMNPK 234.62 7.08E-18 1181270000 597030 560580 483240 532820 540860 593880 582380 630140 694440 714040 TRUE FALSE 573697.4075 544592.8073 570572.2176 560318.9041 558257.2531 605888.6605 589507.3406 617127.3888 615610.0825 665677.4348 0.861824928 0.818103151 0.857130177 0.841727351 0.838630279 0.910183565 0.88557507 0.927066709 0.924787367 1 19.34446374 1.515167675 0.444598507 1.001848861 0.831901666 0.875636469 0.018324774 0.282561413 0.152939658 0.019658326 0.013541485 32.74671007 -1.515167675 -0.169947195 DLEEALEMGVDWSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DLEEALEMGVDWSLR 15 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;; 115.14 0.0012823 23505000 60371 61534 49978.1 59304 63207 61853 68465 58772 59315 60702 FALSE TRUE 58011.63458 59779.11057 59010.25443 62364.68655 65240.11056 63103.71004 69302.89515 57558.33766 52581.80987 56590.59947 1.025110798 1.056343476 1.042757189 1.102032619 1.152843602 1.11509174 1.224636173 1.017100688 0.929161563 1 15.7882748 1.515427699 7.035547806 0.967184237 1.10218705 0.503881826 0.056432247 0.102284627 10.63731719 0.032991205 0.015108151 32.76632234 -1.515427699 0.135002813 RSS(ph)DSWEVWGSASTNR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSDSWEVWGSASTNR 16 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 RS(0.372)S(0.619)DS(0.009)WEVWGSASTNR 114.75 0.00073857 0 69231 89825 60570 78142 81947 77678 80244 73597 63335 79343 TRUE FALSE 66525.37598 87263.27895 71516.34637 82174.91798 84582.89968 79248.70238 81226.05008 72077.19623 56145.47632 73969.02794 0.89936799 1.179727264 0.966841776 1.110936838 1.143490756 1.071376826 1.098108929 0.974424002 0.759040343 1 16.1746337 1.515492801 4.41015442 0.874399376 1.07126318 0.385473372 0.094632431 0.149157251 6.328549179 0.053819966 0.022367958 32.77123448 -1.515492801 0.196863804 VYSEDGACR ddPTM_BT-474_Pertuzumab_2h_R1 1 VYSEDGACR 9 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 81.548 0.048788 307710000 459220 661210 385150 473730 515560 545540 492510 458960 456250 406530 FALSE TRUE 441273.1747 642352.9382 454755.1726 498179.2621 532143.4556 556571.1926 498537.4847 449482.3156 404458.4128 378995.361 1.16432342 1.694883379 1.199896409 1.314473245 1.404089628 1.468543549 1.315418435 1.185983687 1.067185655 1 18.53182066 1.515755285 1.701606172 1.014844614 1.380515258 0.489118614 0.13893258 0.272543584 1.538523023 0.1121039 0.037376831 32.79104709 -1.515755285 0.365670644 S(ph)VQEGENPDDGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVQEGENPDDGVR 13 0 H7C5M1;Q5TCT4;A2A2V2;P42696-2;P42696 H7C5M1 RBM34 RNA-binding protein 34 1 S(1)VQEGENPDDGVR;S(1)VQEGENPDDGVR 276.63 3.21E-32 2934200000 1389460 1213080 1147640 1041410 1412960 1146310 996480 1206290 922080 900500 TRUE FALSE 1335158.367 1178484.146 1355044.077 1095157.295 1458409.142 1169489.174 1008675.22 1181379.69 817409.3441 839508.3329 1.590405139 1.403778974 1.614092468 1.304522245 1.737218184 1.393064402 1.201507097 1.407228069 0.973676272 1 19.67918512 1.515963352 0.849985509 0.975549848 1.514965636 0.630757749 0.145350084 0.349236877 0.512240584 0.126545939 0.05074733 32.8067608 -1.515963352 0.539415788 LLLEVTYEAIVDGGINPDSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLLEVTYEAIVDGGINPDSLR 21 0 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 147.35 2.33E-07 69974000 28034 38256 33466 21245 33247 30742 30514 24299 26008 19691 FALSE TRUE 26938.40029 37164.97634 39514.05065 22341.457 34316.41995 31363.6243 30887.43946 23797.21716 23055.68087 18357.31103 1.467448051 2.024532693 2.152496658 1.2170332 1.869359837 1.708508629 1.682568836 1.296334584 1.255939981 1 14.16406713 1.516037044 1.059440719 1.018659923 1.77137033 0.510203899 0.252417339 0.373787928 0.815634336 0.224980464 0.081678172 32.81232799 -1.516037044 0.752710406 TSKEPVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSKEPVSR 8 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 89.047 0.012935 347680000 297490 357550 238520 324400 305470 332550 316580 303940 300830 303860 FALSE TRUE 285863.7619 347353.0241 281625.8698 341142.3229 315295.72 339274.3888 320454.4007 297663.5328 266681.0396 283279.2915 1.0091234 1.226185727 0.994163281 1.204261423 1.113020716 1.197667457 1.131231298 1.050777595 0.941406758 1 18.11186562 1.516087056 3.139997128 0.972829702 1.129026695 0.409430101 0.074016396 0.196715347 4.110350885 0.048082689 0.017860414 32.81610677 -1.516087056 0.156196993 ELVEAELFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELVEAELFAR 10 0 Q9UBS8;Q9UBS8-2 Q9UBS8 RNF14 E3 ubiquitin-protein ligase RNF14 0 88.948 0.02756 17370000 15637 16002 15249 16823 16935 18576 17973 16565 17240 16655 FALSE TRUE 15025.88875 15545.63863 18004.83351 17691.23705 17479.72965 18951.61945 18192.95895 16222.92696 15282.98748 15526.94202 0.967730074 1.00120414 1.159586575 1.139389651 1.125767691 1.220563549 1.17170264 1.044824341 0.984288307 1 13.9224861 1.516351079 4.601970636 0.997064045 1.115498923 0.313429494 0.072098298 0.219082652 10.15900144 0.04866315 0.020510565 32.83606291 -1.516351079 0.118434879 RTS(ph)SPHKEESPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSSPHKEESPKK 13 3 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 RT(0.003)S(0.897)S(0.1)PHKEESPKK 104.44 0.0010931 82446000 104180 82261 70170 58671 77627 84596 70896 91227 122680 88166 TRUE FALSE 100108.5304 79914.99682 82851.27992 61699.01734 80123.94295 86306.58908 71763.64646 89343.13057 108753.8807 82194.43829 1.217947741 0.972267692 1.007991315 0.750647107 0.974809788 1.05002955 0.873096136 1.086972944 1.323129435 1 16.32675316 1.51644828 5.916180729 1.175441418 0.973295864 0.236792717 0.133960244 0.169180587 12.89738264 0.074031236 0.033154642 32.84341287 -1.51644828 -0.202145555 EAALPPVS(ph)PLKAALSEEELEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAALPPVSPLKAALSEEELEK 21 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAALPPVS(1)PLKAALSEEELEK;EAALPPVS(1)PLKAALSEEELEK 120.08 2.64E-05 139639000 282347 267548 191013 163001 256860 294471 186609 198861 192970 141105 TRUE FALSE 271312.5671 259917.793 225533.2982 171413.5011 265122.1352 300425.4054 188892.7768 194754.4509 171064.8546 131547.8327 2.062463224 1.975842458 1.714458487 1.303050743 2.015404814 2.283773129 1.435924659 1.480483919 1.300400403 1 17.00522795 1.516512296 1.24566494 1.071328532 1.855734158 0.538949015 0.267737794 0.355753951 1.058834251 0.252220855 0.087379485 32.84825445 -1.516512296 0.784405626 LTAT(ph)PTPLGGMTGFHMQTEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTATPTPLGGMTGFHMQTEDR 21 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LT(0.008)AT(0.984)PT(0.008)PLGGMTGFHMQTEDR;LT(0.001)AT(0.755)PT(0.243)PLGGMTGFHMQTEDR;LT(0.001)AT(0.973)PT(0.027)PLGGMTGFHMQTEDR;LT(0.005)AT(0.993)PT(0.002)PLGGMTGFHMQTEDR 239.13 2.39E-29 1613190000 935545 1006920 795121 919014 859476 906607 786064 952874 834676 804096 TRUE FALSE 898982.8671 978203.6275 938817.0521 966444.4227 887121.8261 924939.2147 795684.0864 933196.8189 739927.0797 749633.8617 1.199229268 1.304908539 1.252367456 1.289221942 1.183406822 1.233854635 1.061430289 1.244870151 0.987051303 1 19.5158266 1.516523952 0.537989885 0.989371592 1.266601065 0.622300095 0.06836853 0.507137651 0.358124702 0.065363236 0.03745686 32.84913608 -1.516523952 0.277229474 CNEIINWLDKNQTAEKEEFEHQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 CNEIINWLDKNQTAEKEEFEHQQK 24 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 271.51 3.97E-52 3984440000 1362180 1052870 823878 843360 940595 1003086 1034166 1210090 1700340 1350280 FALSE TRUE 1308944.5 1022843.178 972771.0817 886885.9107 970850.0924 1023369.086 1046822.433 1185101.219 1507324.532 1258824.333 1.03981506 0.812538455 0.772761581 0.704535087 0.771235562 0.812956232 0.831587383 0.941434947 1.197406574 1 20.26364554 1.516539255 3.144892102 1.097069583 0.812221823 0.575983187 0.094196319 0.14954328 3.137322618 0.066715464 0.024807572 32.85029355 -1.516539255 -0.284847759 GLPSPYNMSSAPGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 16 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMSS(0.008)APGS(0.991)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSS(0.001)APGS(0.999)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMS(0.001)S(0.007)APGS(0.992)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(0.999)R;GLPSPYNMSS(0.001)APGS(0.999)R;GLPSPYNMS(0.001)S(0.013)APGS(0.986)R;GLPSPYNMS(0.005)S(0.151)APGS(0.844)R;GLPSPYNMSS(0.005)APGS(0.995)R;GLPSPYNMSS(0.015)APGS(0.985)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R 181.08 6.32E-07 36861710000 8411160 8921100 7115920 8597470 8359120 8724850 6930910 8257840 7761040 6935090 TRUE FALSE 8082442.568 8666678.963 8401925.037 9041186.457 8627998.686 8901272.445 7015732.55 8087312.718 6880039.276 6465370.177 1.250112886 1.340476837 1.299527298 1.39840198 1.334494151 1.376761454 1.08512465 1.250866153 1.064136946 1 22.62430154 1.516953717 0.835402937 1.006130028 1.334594869 0.697881139 0.073558669 0.300258267 0.427245559 0.06532571 0.026462217 32.88165869 -1.516953717 0.328464841 RYDLEQGLGDLLTER ddPTM_BT-474_Pertuzumab_2h_R1 3 RYDLEQGLGDLLTER 15 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 ;; 168.41 2.01E-06 350453000 240485 252116 177985 196138 247128 247409 197570 224923 218071 203592 FALSE TRUE 231086.5803 244925.8985 210150.8488 206260.7057 255077.0966 252411.7795 199987.9208 220278.2614 193316.4943 189802.5325 1.217510522 1.290424818 1.107207823 1.086712084 1.343907761 1.329865182 1.053663079 1.16056545 1.018513777 1 17.53413972 1.517321371 1.282104732 1.003352831 1.217877308 0.424720679 0.092294406 0.430938701 1.35775987 0.085342771 0.029390879 32.9095066 -1.517321371 0.214524476 SSAIPDFRDPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSAIPDFRDPQK 12 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 0 ; 66.267 0.053369 627710000 914930 894710 709680 750540 830320 878630 853520 948350 1003700 1037950 FALSE TRUE 879173.5241 869193.7468 837934.9627 789275.4593 857027.9969 896396.5006 863965.6331 928766.2411 889764.1839 967648.722 0.908566822 0.898253392 0.865949537 0.815663207 0.885680906 0.926365612 0.892850487 0.959817566 0.919511558 1 19.88412389 1.517433076 0.650687045 0.992100022 0.873175543 0.59784891 0.030234427 0.470657486 0.443133873 0.030232765 0.01459361 32.91797235 -1.517433076 -0.118924479 GPGEPDS(ph)PTPLHPPTPPILSTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPGEPDSPTPLHPPTPPILSTDR 23 0 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 GPGEPDS(0.928)PT(0.072)PLHPPTPPILSTDR 115.12 0.0003886 184180000 66853 61354 46726 56179 68254 57430 50623 54521 40890 42043 TRUE FALSE 64240.31085 59604.24399 55170.42761 59078.40492 70449.4519 58591.27395 51242.53942 53395.1223 36248.33862 39195.39016 1.63897618 1.520695259 1.407574396 1.507279419 1.797391265 1.494851147 1.307361381 1.362280668 0.924811272 1 15.25839637 1.517554466 1.277480425 0.951501188 1.554850569 0.769766611 0.121938079 0.199299037 0.62344667 0.110709362 0.038159516 32.92717452 -1.517554466 0.60334938 KGDDS(ph)DEEDLCISNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGDDSDEEDLCISNK 15 1 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 KGDDS(1)DEEDLCISNK 166.27 8.44E-07 90642000 197750 147070 141570 135320 153700 154510 144240 204140 254790 251130 TRUE FALSE 190021.7114 142875.7076 167154.8482 142303.8814 158643.9001 157634.2981 146005.2523 199924.4377 225867.3074 234120.7414 0.811639798 0.610265057 0.713968558 0.607822616 0.677615743 0.673303429 0.623632282 0.853937316 0.964747104 1 17.83689323 1.517630599 2.750650494 0.980893438 0.67059279 0.824386393 0.057947688 0.088302399 1.401232703 0.040384642 0.014431824 32.93294727 -1.517630599 -0.310300648 SVFDIPIFTEEFLNHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVFDIPIFTEEFLNHSK 17 0 Q9NP66 Q9NP66 HMG20A High mobility group protein 20A 0 178.12 8.89E-14 0 98171 104280 84803 83768 104010 113730 96559 95546 98239 91462 FALSE TRUE 94334.36879 101306.0365 100128.7885 88091.27652 107355.5761 116029.6985 97740.71793 93572.94171 87087.32057 85267.19727 1.106338332 1.188100931 1.174294356 1.033120348 1.259048961 1.360777676 1.146287448 1.097408437 1.021346114 1 16.37970322 1.517958162 2.24286575 1.010187449 1.185643162 0.414364163 0.081878826 0.299796729 3.075807008 0.069907504 0.023848953 32.95779607 -1.517958162 0.175455714 DLVASVPDMQGDGEDNHMDGDK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLVASVPDMQGDGEDNHMDGDK 22 0 E9PQX9;C9JCC6;Q14919;Q14919-2;E9PMW2 E9PQX9 DRAP1 Dr1-associated corepressor 0 ;;; 275.02 2.01E-45 1492700000 1400990 1305180 1287830 1318520 1377820 1313810 1466880 1477940 1849670 1677350 FALSE TRUE 1346237.762 1267957.544 1520569.529 1386568.975 1422138.832 1340376.138 1484832.116 1447420.023 1639703.216 1563741.59 0.860908075 0.810848514 0.972391818 0.886699557 0.90944619 0.857159614 0.949538034 0.925613306 1.04857684 1 20.5765707 1.518203317 1.59356694 1.022611961 0.887411564 0.558388155 0.045612331 0.265113581 1.303987021 0.038582495 0.012915874 32.97640567 -1.518203317 -0.135200397 VSASS(ph)PTTK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSASSPTTK 9 0 Q9BVI0;Q5JWZ0;Q5JXL1 Q9BVI0 PHF20 PHD finger protein 20 1 VSAS(0.066)S(0.911)PT(0.019)T(0.004)K 76.068 0.038263 199940000 439260 401030 360850 356370 405490 399730 362080 422680 467870 455660 TRUE FALSE 422093.2336 389593.017 426063.6221 374762.2984 418532.9541 407812.8145 366511.2434 413951.5103 414759.3591 424797.7423 0.99363342 0.917125912 1.002979959 0.882213489 0.985252303 0.960016436 0.862789998 0.974467303 0.976369029 1 18.69641657 1.518448516 12.9595847 0.983902279 0.942812567 0.152297802 0.043990408 0.220022849 56.23103827 0.022344238 0.010365662 32.99502911 -1.518448516 -0.041089712 VVLVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VVLVDR 6 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 106.76 0.074087 68721000 111080 122190 114750 132580 118830 119380 130300 120080 118410 126930 FALSE TRUE 106738.8708 118705.2608 135487.8776 139422.4697 122652.2749 121793.9454 131894.6504 117600.306 104968.5932 118332.918 0.902021792 1.00314657 1.144971998 1.178222189 1.036501735 1.029248221 1.114606591 0.993808891 0.887061647 1 16.85249194 1.518518449 5.213069811 0.941942445 1.062012546 0.264133574 0.07773601 0.197506456 11.77595272 0.047730974 0.020857184 33.00034261 -1.518518449 0.120070101 EQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_BT-474_Pertuzumab_2h_R1 6 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;;;;; 362.07 4.93E-121 6502881000 494667 478260 392716.5 403282 457457.4 453793 462320 506143 634035 552670 FALSE TRUE 475334.8668 464620.4931 463689.1075 424095.4323 472171.9327 462969.0054 467978.0105 495690.9702 562062.0049 515237.1686 0.922555467 0.901760435 0.899952751 0.823107218 0.916416675 0.898555138 0.908276885 0.962063687 1.09088016 1 18.97487715 1.518947936 2.903353075 1.044405606 0.89411677 0.754984188 0.033783592 0.105317033 1.876772983 0.023928543 0.008700611 33.03299379 -1.518947936 -0.150288836 KGVAINFVTEEDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGVAINFVTEEDKR 14 2 Q14240;Q14240-2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 189.37 4.08E-07 3321300000 2815200 2658600 2278650 2110600 2455540 2416640 2454780 2757280 3333700 2983920 FALSE TRUE 2705178.872 2582779.331 2690452.743 2219528.319 2534524.674 2465506.117 2484822.332 2700341.204 2955272.352 2781816.441 0.97245053 0.928450667 0.96715682 0.797870157 0.911104211 0.886293603 0.893237345 0.970711498 1.062353471 1 21.4075958 1.519526977 3.559243973 1.029697089 0.906519878 0.513745381 0.048076487 0.159881636 4.362133416 0.032642448 0.01269934 33.07706575 -1.519526977 -0.123177211 TVHTEWTQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVHTEWTQR 9 0 C9JIF9;P13798;H7C393 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 101.65 0.003842 274430000 44975 43979 32400 42509 36681 26640 59527 35909 38176 35925 FALSE TRUE 43217.32728 42724.76198 38255.40073 44702.89458 37860.87768 27178.67905 60255.50923 35167.4666 33842.42053 33491.76775 1.290386569 1.275679513 1.142232952 1.334742762 1.130453249 0.81150327 1.799114029 1.050033156 1.01046982 1 15.03151891 1.519622906 17.28115626 1.013625076 1.246146906 0.180076895 0.230161913 0.2981885 111.107303 0.119646008 0.055425723 33.08437284 -1.519622906 0.23252183 DRGEEDADGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 DRGEEDADGSK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 121.21 0.00037976 707020000 853920 748940 780920 796830 788960 828180 940720 999480 1151300 1223570 FALSE TRUE 820547.8623 727580.9645 922049.6155 837954.4918 814337.6149 844926.367 952232.8128 978840.3887 1020609.251 1140696.514 0.719339327 0.637839211 0.808321586 0.734598977 0.713895068 0.740710922 0.834781908 0.858107636 0.894724616 1 20.12148358 1.519790683 0.610249335 0.999959772 0.708928509 0.836968676 0.040639621 0.264299033 0.225052283 0.03944307 0.020132168 33.09715647 -1.519790683 -0.291031263 YKDDDDDQLFYTR ddPTM_BT-474_Pertuzumab_2h_R1 2 YKDDDDDQLFYTR 13 1 O60568;H7C2V1 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 ; 215.96 2.58E-11 1314590000 1498210 1508180 1387890 1306090 1401800 1440750 1561930 1637070 2136450 1874610 FALSE TRUE 1439658.297 1465168.183 1638712.596 1373497.461 1446890.17 1469882.952 1581045.367 1603263.932 1893929.153 1747640.995 0.823772331 0.838369086 0.937671181 0.785915108 0.827910409 0.841066876 0.904673998 0.917387459 1.083706069 1 20.73697742 1.519882877 1.973524979 1.040361444 0.847060973 0.726444445 0.045784705 0.154347474 1.202162816 0.0368345 0.012382338 33.10418322 -1.519882877 -0.193300472 FFEDYGLFMR ddPTM_BT-474_Pertuzumab_2h_R1 1 FFEDYGLFMR 10 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 107.69 0.0052345 109080000 107350 152580 98404 173490 110880 137050 159700 109820 108420 85202 FALSE TRUE 103154.6433 148228.5678 116187.7918 182443.8397 114446.5559 139821.2449 161654.4564 107552.1786 96112.61613 79431.19265 1.298666681 1.866125421 1.462747668 2.296879017 1.440826357 1.760281323 2.035150814 1.354029507 1.210010991 1 16.27741804 1.520011316 3.972545212 1.138860428 1.742651432 0.453845409 0.283490172 0.163363442 5.602512946 0.172141758 0.069556135 33.11397497 -1.520011316 0.603791004 QPS(ph)SPSHNTNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPSSPSHNTNLR 12 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 QPS(0.498)S(0.498)PS(0.003)HNTNLR 107.65 0.0018792 290710000 123750 146680 125660 191540 181490 170030 180080 146130 127670 148820 TRUE FALSE 118913.7132 142496.83 148369.5573 201425.4024 187327.7907 173468.1231 182283.8729 143112.3644 113177.4368 138740.2888 0.857095759 1.027076066 1.069404991 1.451816225 1.350204704 1.250308216 1.313849599 1.03151266 0.815750333 1 17.08202727 1.520024524 4.864387217 0.910228628 1.195932579 0.314021082 0.168247941 0.198024196 10.28179272 0.109629932 0.047138933 33.11498206 -1.520024524 0.285703951 WDKDNLQILR ddPTM_BT-474_Pertuzumab_2h_R1 2 WDKDNLQILR 10 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 108.98 0.0018959 2033400000 3127400 3038600 2858900 2923600 2956900 2539400 3520900 3398900 3989400 4089700 FALSE TRUE 3005177.75 2951942.103 3375566.826 3074487.346 3052011.374 2590748.408 3563989.827 3328711.527 3536540.037 3812700.976 0.788201794 0.774239082 0.885347906 0.806380402 0.800485376 0.679504746 0.934767728 0.87305864 0.927568162 1 21.86238196 1.520466095 1.11400365 0.983064316 0.798406242 0.550599698 0.060099476 0.351358843 0.842125598 0.053895007 0.019273099 33.148669 -1.520466095 -0.184658074 EAEILEVLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAEILEVLR 9 0 P36551 P36551 CPOX "Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial" 0 ;;; 117.89 0.0025086 97259000 171606 204267 160803 200029 152415 162980 168456 179905 161583 149045 FALSE TRUE 164899.4478 198441.5052 189863.6791 210352.5207 157317.5669 166275.5673 170517.6149 176189.8989 143240.7753 138950.0494 1.186753431 1.428149943 1.36641678 1.513871507 1.132187916 1.19665713 1.227186429 1.268008897 1.030879628 1 17.08420682 1.52050297 0.449861678 0.98819927 1.365855454 0.497056661 0.110949624 0.815130573 0.447661054 0.126793251 0.086611258 33.15148367 -1.52050297 0.377656184 S(ph)SPQKEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPQKEVK 8 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 1 S(0.806)S(0.194)PQKEVK 55.649 0.074246 153240000 512090 495370 360220 362570 433710 480360 426860 505450 612960 559150 TRUE FALSE 492076.9567 481242.5326 425319.7671 381282.2812 447660.676 490073.2083 432084.0404 495012.2809 543379.3505 521278.2725 0.943981329 0.923196991 0.815916929 0.731437125 0.858774861 0.940137416 0.828893248 0.949612341 1.04239785 1 18.9916942 1.520576696 3.494595058 1.01846771 0.861602698 0.517185874 0.061737225 0.175016907 4.604306749 0.045150033 0.017478509 33.15711199 -1.520576696 -0.156865012 LENNENKPVTNSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LENNENKPVTNSR 13 1 Q9Y5A9;Q9Y5A9-2 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 0 ;;; 276.51 2.82E-32 1334980000 706430 733840 570562 666760 608932 685220 696180 807960 920430 938670 FALSE TRUE 678821.9346 712911.6017 673675.2455 701171.5635 628518.8508 699075.6179 704700.0591 791275.3437 815946.6452 875093.0448 0.77571401 0.814669487 0.769832705 0.801253727 0.718230884 0.798858615 0.805285864 0.904218527 0.932411302 1 19.73907689 1.520942406 1.291216738 0.989206657 0.7772486 0.898296661 0.026017219 0.115842736 0.370167932 0.022774581 0.007844562 33.18504459 -1.520942406 -0.211958057 LDMSEFQER ddPTM_BT-474_Pertuzumab_2h_R1 1 LDMSEFQER 9 0 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2R8Y602 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 75.387 0.057838 0 64429 78613 68237 76877 70750 71199 80128 71329 69270 76412 FALSE TRUE 61911.04345 76371.03421 80568.94382 80844.63118 73025.738 72638.69256 81108.63043 69856.03122 61406.76 71236.54718 0.86909102 1.072076585 1.131005741 1.134875768 1.025116192 1.01968295 1.13858172 0.980620678 0.862012021 1 16.12032997 1.521189848 5.926624749 0.927686936 1.059865397 0.283147022 0.081162979 0.15889816 11.99562999 0.045541016 0.020470864 33.20395741 -1.521189848 0.13217846 YRPCS(ph)LGR ddPTM_BT-474_Pertuzumab_2h_R1 1 YRPCSLGR 8 1 P40938;P40938-2 P40938 RFC3 Replication factor C subunit 3 1 Y(0.002)RPCS(0.998)LGR 59.265 0.060389 79722000 119970 145350 145430 131620 136470 137020 147990 132950 129060 134390 TRUE FALSE 115281.4398 141204.7603 171712.4361 138412.924 140859.6815 139790.6383 149801.1459 130204.536 114409.6499 125287.6456 0.920134138 1.127044567 1.370545637 1.104761154 1.124290275 1.115757564 1.195657762 1.039244815 0.913175831 1 16.93488463 1.52135884 4.176638572 0.959568087 1.142499111 0.322685522 0.105421575 0.205282489 7.818757507 0.067222057 0.027658991 33.21688019 -1.52135884 0.182931023 DEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_BT-474_Pertuzumab_2h_R1 3 DEPPPLSPAPLTPATPSSLDPFFSR 25 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 DEPPPLS(1)PAPLTPATPSSLDPFFSR;DEPPPLS(1)PAPLTPATPSSLDPFFSR;DEPPPLS(1)PAPLTPATPSSLDPFFSR 147.41 1.53E-07 190933000 101321 113353 108966 138566 137259 126508 118244 117506 118879 109760 TRUE FALSE 97361.2633 110120.2834 128658.5801 145717.4079 141674.0604 129066.0784 119691.1054 115079.46 105384.3543 102325.8574 0.951482506 1.076172594 1.257341823 1.424052644 1.384538219 1.261324182 1.169705375 1.124637144 1.029889775 1 16.64281123 1.521456658 1.635518233 1.00571299 1.234108214 0.2861867 0.129140649 0.496746627 2.584641945 0.124233771 0.041620091 33.22436259 -1.521456658 0.228395223 SYS(ph)PDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYSPDHR 7 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 S(0.179)Y(0.001)S(0.82)PDHR 93.429 0.015673 281940000 630060 705360 466840 616390 668460 589370 566730 592480 493890 531960 TRUE FALSE 605436.5586 685243.8234 551208.3728 648201.9618 689961.623 601287.4652 573665.8113 580245.081 437825.6778 495929.8754 1.220810822 1.381735317 1.111464342 1.307043584 1.391248354 1.212444531 1.156747838 1.170014371 0.882837876 1 18.91977661 1.521496637 1.527197738 0.943941428 1.270709794 0.640441165 0.090959709 0.224861741 1.012656084 0.076794456 0.025836018 33.22742122 -1.521496637 0.326768366 LIGEYGLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LIGEYGLR 8 0 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;; 153.73 0.0010153 499870000 466355 613224 583133 588984 562193 450616 603975 509130 444131 513667 FALSE TRUE 448129.331 595735.4519 688518.1048 619381.5348 580276.4484 459727.7643 611366.6267 498616.2876 393715.1108 478875.8766 0.935794332 1.244028946 1.437779889 1.293407259 1.211747087 0.960014456 1.276670337 1.041222396 0.822165263 1 18.86929224 1.521735566 4.174285852 0.913173796 1.200233948 0.375456923 0.147464468 0.186553717 7.099603345 0.095857969 0.03945242 33.24570649 -1.521735566 0.287060151 VIEETEER ddPTM_BT-474_Pertuzumab_2h_R1 1 VIEETEER 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 112.94 0.0068495 478880000 530380 593840 458040 550410 539960 578320 532040 559690 554060 587260 FALSE TRUE 509652.1632 576904.2646 540818.017 578816.7261 557328.3038 590014.0266 538551.2647 548132.2059 491165.4316 547484.3571 0.930898128 1.053736526 0.987823688 1.057229706 1.017980325 1.077681981 0.983683383 1.001183319 0.897131444 1 19.06245822 1.522073968 2.900103581 0.949080761 1.020148998 0.223399983 0.04687064 0.2937234 5.248753458 0.031565494 0.011514884 33.27162162 -1.522073968 0.071068237 NSNPVIAELSQAINSGTLLSKPS(ph)PPLPPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSNPVIAELSQAINSGTLLSKPSPPLPPKR 30 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 NSNPVIAELSQAINSGTLLSKPS(1)PPLPPKR;NSNPVIAELSQAINSGTLLS(0.01)KPS(0.99)PPLPPKR 208.52 4.78E-26 1674440000 646230 663760 559430 534730 644620 593750 691760 726550 942900 884150 TRUE FALSE 620974.6172 644830.2147 660531.4455 562327.4794 665354.7877 605756.0318 700225.9658 711546.4886 835865.945 824265.733 0.753367018 0.782308652 0.801357401 0.682216252 0.807209085 0.734903815 0.849514832 0.863248902 1.014073389 1 19.65274999 1.522267583 1.384207891 1.015534572 0.762497933 0.841948462 0.040664778 0.135193017 0.497054965 0.033362058 0.011358977 33.28645787 -1.522267583 -0.253036639 TGS(ph)PTFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGSPTFVR 8 0 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;Q9UPP1-5;B0QZZ4;Q5JPR8;B0QZZ2;B0QZZ3;B0QZE1 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 T(0.085)GS(0.905)PT(0.009)FVR;T(0.132)GS(0.793)PT(0.075)FVR 118.67 0.0019322 370320000 470540 437500 398910 374750 431240 438030 403520 461010 532710 477910 TRUE FALSE 452150.7766 425022.9284 471001.9107 394090.8924 445111.2262 446887.2667 408458.3985 451489.9824 472238.9941 445540.73 1.01483601 0.953948539 1.057146696 0.884522707 0.999035994 1.003022253 0.916770053 1.013352881 1.059923285 1 18.7651978 1.522569664 7.928246958 1.032054185 0.975684591 0.180326899 0.048500912 0.175800674 20.93902082 0.0247741 0.011456137 33.30961894 -1.522569664 -0.056369594 LEEQLSINVYDYNCHVDLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEQLSINVYDYNCHVDLIR 20 0 A0A499FI31;Q15020-4;Q15020;Q15020-2;A0A494C0L2;F8W667 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 89.859 0.0023932 0 10926 13837 8528.8 13456 11530 10719 11127 13322 16991 13990 FALSE TRUE 10498.99984 13442.38231 10070.14388 14150.46577 11900.87292 10935.74552 11263.17555 13046.89604 15062.25291 13042.44484 0.804987099 1.030664302 0.772105537 1.084955002 0.912472552 0.838473588 0.863578546 1.000341286 1.154864222 1 13.67092671 1.522611936 4.500037719 1.078859418 0.906860971 0.35057975 0.097230486 0.174756909 7.757772906 0.055945523 0.023595632 33.31286129 -1.522611936 -0.171998447 GGNVFAALIQDQS(ph)EEEEEEEKHPPKPAKPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGNVFAALIQDQSEEEEEEEKHPPKPAKPEK 31 3 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 GGNVFAALIQDQS(1)EEEEEEEKHPPKPAKPEK 133.85 1.85E-06 7170000000 961910 729320 737100 594110 806410 693360 705430 858050 1084800 887910 TRUE FALSE 924317.4938 708520.5077 870310.3667 624772.0883 832348.91 707380.2143 714063.2634 840330.9676 961658.0519 827771.0648 1.116634216 0.855937756 1.051390177 0.754764348 1.005530328 0.854560209 0.862633757 1.01517316 1.161743981 1 19.65887229 1.522833462 5.094748286 1.083922236 0.924547624 0.248655229 0.107300907 0.183626608 10.4294875 0.058278846 0.025431954 33.32985788 -1.522833462 -0.159374612 DKPYACDICGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKPYACDICGK 11 1 Q92785 Q92785 DPF2 Zinc finger protein ubi-d4 0 93.206 0.0085936 150900000 164710 144870 124190 132990 137710 136930 128480 167770 191040 197490 FALSE TRUE 158272.9511 140738.4494 146633.8956 139853.6298 142139.5672 139698.8184 130052.3767 164305.4909 169353.9401 184113.8264 0.859647286 0.764409997 0.796430656 0.759604168 0.77202006 0.758763321 0.70636942 0.892412559 0.91983282 1 17.49023845 1.52354949 3.314465994 0.953310395 0.773398283 0.776200908 0.041065568 0.096583544 2.287351645 0.027935118 0.010660217 33.38485469 -1.52354949 -0.179912112 NS(ph)PVTKT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPVTKTPPR 10 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(1)PVT(0.4)KT(0.6)PPR;NS(1)PVT(0.428)KT(0.572)PPR 115.82 0.0026874 4169100000 2713700 2271360 1864560 1649320 1933260 2113760 2053240 2381870 3078000 2489800 TRUE FALSE 2607645.604 2206583.037 2201527.469 1734441.603 1995445.064 2156501.675 2078368.165 2332683.552 2728598.344 2321163.628 1.123421706 0.950636573 0.948458541 0.747229356 0.859674449 0.929060601 0.895399247 1.004962995 1.175530372 1 21.1464168 1.523786047 4.101868281 1.090018635 0.9160405 0.319114519 0.096706056 0.203209648 7.474932269 0.062812284 0.025769627 33.40304413 -1.523786047 -0.173978135 ERPDCLDTVLAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ERPDCLDTVLAR 12 1 Q9P253 Q9P253 VPS18 Vacuolar protein sorting-associated protein 18 homolog 0 ;; 168.31 4.28E-05 490400000 294077 311709 289115 281091 325749 344764 318075 312681 307284 336692 FALSE TRUE 282584.1457 302819.3645 341364.5118 295598.1402 336227.0124 351735.3643 321967.697 306224.0281 272402.4086 313887.5509 0.900271912 0.964738371 1.087537594 0.941732602 1.071170269 1.120577618 1.025742168 0.975585133 0.867834381 1 18.25988829 1.524222289 4.423358062 0.930074039 1.019432482 0.175692523 0.07054722 0.26750474 11.47705892 0.044136828 0.018553446 33.43661383 -1.524222289 0.089358443 FRDGPPLR ddPTM_BT-474_Pertuzumab_2h_R1 8 FRDGPPLR 8 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;;;; 143.7 0.00054464 6822160000 2843870 3149910 2577230 3127980 2905880 3147240 2968270 2935670 3030370 2891780 FALSE TRUE 2732728.416 3060077.651 3042992.791 3289415.423 2999350.269 3210879.349 3004596.576 2875047.389 2686375.102 2695917.165 1.013654445 1.135078515 1.128741206 1.220147067 1.112552829 1.191015581 1.114498849 1.066445003 0.99646055 1 21.36234474 1.524363694 2.139315164 0.99688859 1.136921093 0.519774801 0.051111696 0.226004494 2.107173388 0.040960931 0.013953179 33.44750245 -1.524363694 0.140032502 ELDRNELFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDRNELFEK 10 1 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1;A0A2R8YGE5 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 61.233 0.097455 0 336290 340920 271040 426500 354940 316100 336630 312600 276670 279720 FALSE TRUE 323147.415 331197.2954 320022.9573 448511.7161 366356.9674 322491.7586 340749.7786 306144.7008 245263.5815 260774.3153 1.239184215 1.27005336 1.227202752 1.719922898 1.404881332 1.236669947 1.306684588 1.173983337 0.94052047 1 17.99244225 1.524422857 1.629257556 0.959052585 1.358632701 0.535246314 0.138588041 0.287830264 1.487292351 0.125569871 0.042153292 33.45205922 -1.524422857 0.399580115 DDGSSMSFYVRPS(ph)PAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDGSSMSFYVRPSPAKR 17 2 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 DDGSSMSFYVRPS(1)PAKR;DDGSSMSFYVRPS(1)PAKR 250.86 8.74E-22 905780000 394860 344000 312110 300390 333600 338000 347340 381150 416390 419240 TRUE FALSE 379428.4347 334189.4568 368515.2198 315893.1639 344330.547 344834.5916 351590.8508 373279.1193 369123.1528 390844.5014 0.970791282 0.85504454 0.942869142 0.808232335 0.880991151 0.88228078 0.89956709 0.955057876 0.944424577 1 18.57623522 1.525023739 1.272885433 0.986897151 0.885847851 0.398754468 0.043195134 0.39308654 1.220785403 0.036439331 0.012611076 33.49837495 -1.525023739 -0.1010493 HGGTIPIVPTAEFQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HGGTIPIVPTAEFQDR 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 156.5 1.57E-07 2379700000 1286830 1958910 1214700 2722600 1247250 1469950 2476000 1546010 1659780 1363200 FALSE TRUE 1236539.261 1903043.805 1434223.311 2863113.712 1287368.929 1499673.396 2506302.029 1514084.353 1471368.733 1270869.25 0.972987002 1.497434772 1.128537268 2.252878266 1.012982987 1.180037519 1.972116352 1.191376968 1.157765626 1 20.27738418 1.525039343 10.70796619 1.111251707 1.438042676 0.122868068 0.390715595 0.238035959 41.47396433 0.203191182 0.094361114 33.49957852 -1.525039343 0.326790969 (ac)GDPERPEAAGLDQDER ddPTM_BT-474_Pertuzumab_2h_R1 2 GDPERPEAAGLDQDER 16 1 Q7LG56;Q7LG56-5 Q7LG56 RRM2B Ribonucleoside-diphosphate reductase subunit M2 B 0 ; 71.153 0.00010338 837550000 47354 79646 73651 90911 69622 90875 78524 68448 43806 73554 FALSE TRUE 45503.35333 77374.57406 86961.37406 95602.9276 71861.45486 92712.55476 79485.0002 67034.52488 38833.32653 68572.12206 0.663583858 1.128367793 1.268173879 1.394195261 1.047968951 1.352044416 1.15914453 0.977576935 0.566313618 1 16.06533455 1.525079676 3.871157361 0.777116999 1.160785419 0.306891381 0.214858472 0.206251531 6.747123866 0.13678523 0.055138176 33.50268976 -1.525079676 0.383668419 LGAGPGDAGEVQAHPFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGAGPGDAGEVQAHPFFR 18 0 P23443-5;P23443;P23443-3;P23443-2;P23443-4 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 0 ; 229.92 1.62E-19 611490000 397250 410220 376570 365060 403660 413180 388120 378900 354710 363250 FALSE TRUE 381725.0308 398520.9272 444624.5758 383900.7903 416644.0905 421534.7827 392869.9287 371075.5826 314444.8079 338646.754 1.127207116 1.176804214 1.31294504 1.13363198 1.230320638 1.244762508 1.160117214 1.095760046 0.928533359 1 18.36942164 1.525117054 2.26247631 0.964820158 1.204108136 0.734726532 0.055775482 0.134569664 1.418700031 0.043005249 0.014794701 33.50557333 -1.525117054 0.239287978 TTWDRPEPLPPGWER ddPTM_BT-474_Pertuzumab_2h_R1 2 TTWDRPEPLPPGWER 15 1 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UK95 A0A590UJQ1 ITCH E3 ubiquitin-protein ligase Itchy homolog 0 ; 144.33 3.88E-06 1044560000 478010 498200 397810 433570 448610 485410 494060 462930 464830 510110 FALSE TRUE 459328.8407 483991.8238 469703.1162 455946.5997 463039.9481 495225.3228 500106.4541 453370.3337 412064.4471 475559.7953 0.965869792 1.017730743 0.987684663 0.958757666 0.973673453 1.041352376 1.051616346 0.953340333 0.866482935 1 18.85926723 1.5251581 6.807356086 0.92586567 0.999019128 0.303213958 0.041767072 0.133548965 12.51584014 0.022780838 0.010442079 33.50874015 -1.5251581 0.073153458 SLATMDS(ph)PPHQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLATMDSPPHQK 12 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.007)LAT(0.007)MDS(0.986)PPHQK 65.956 0.038232 246780000 362200 509020 499320 722770 579630 589140 605900 507610 401880 541830 TRUE FALSE 348044.8236 494503.248 589558.2313 760072.2463 598274.3254 601052.8145 613315.1854 497127.6761 356260.2672 505131.3715 0.689018428 0.978959684 1.167138421 1.504702122 1.184393524 1.189894052 1.21416966 0.98415522 0.705282402 1 18.94629912 1.525189649 4.491138367 0.84824495 1.145281215 0.231740492 0.204564425 0.238517094 10.55557936 0.131933574 0.055774931 33.51117446 -1.525189649 0.297036265 QVAGDAPVEQATAETAS(ph)PVHR ddPTM_BT-474_Pertuzumab_2h_R1 4 QVAGDAPVEQATAETASPVHR 21 0 Q92766;Q92766-2;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 QVAGDAPVEQATAET(0.004)AS(0.996)PVHR;QVAGDAPVEQATAET(0.015)AS(0.985)PVHR;QVAGDAPVEQATAET(0.001)AS(0.999)PVHR;QVAGDAPVEQATAET(0.002)AS(0.998)PVHR 293.77 5.42E-55 4281400000 1672600 1504780 1206290 1877740 1543210 1243290 1450680 1411070 1126140 1119190 TRUE FALSE 1607232.943 1461865.148 1424293.437 1974650.386 1592848.751 1268430.176 1468433.856 1381930.911 998305.3084 1043386.264 1.54040071 1.401077623 1.365068226 1.892540139 1.526614645 1.215686097 1.40737319 1.324467226 0.956793608 1 19.99284192 1.525230238 0.9046172 0.96016635 1.520826806 0.586662085 0.165421995 0.398189389 0.649704667 0.157541595 0.061330909 33.51430655 -1.525230238 0.560660456 NCQHANAERPTVAR ddPTM_BT-474_Pertuzumab_2h_R1 3 NCQHANAERPTVAR 14 1 Q9Y5J1;F6VJE8 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 ;; 191.01 3.23E-07 181164000 134936 177475 146048 214822 190918 218618 182755 154032 105225 138450 FALSE TRUE 129662.5519 172413.5868 172442.1224 225908.9892 197059.0509 223038.6057 184991.6104 150851.1854 93280.29914 129072.6582 1.004570246 1.335787061 1.336008143 1.750246662 1.526729624 1.728008154 1.433236233 1.168730756 0.722696042 1 16.9778239 1.525592797 3.055319593 0.8684378 1.46171543 0.548101248 0.211025334 0.170668074 3.422184759 0.156972813 0.058449663 33.54229675 -1.525592797 0.593277631 SQSSHSYDDSTLPLIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQSSHSYDDSTLPLIDR 17 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 0 ;;; 242.26 2.13E-20 3547680000 854400 1326050 1018550 1504200 991480 1205710 1118680 1127330 927660 1145720 FALSE TRUE 821009.1034 1288232.352 1202624.643 1581831.942 1023371.855 1230090.282 1132370.74 1104050.242 822355.9259 1068119.364 0.768649208 1.206075272 1.125927198 1.480950534 0.958106265 1.151641215 1.060153742 1.033639384 0.769910137 1 20.02664145 1.525967454 2.812392996 0.886524819 1.122971954 0.184571882 0.179423107 0.361991474 6.100254436 0.127690122 0.046357863 33.57124551 -1.525967454 0.236447135 ELSEALTR ddPTM_BT-474_Pertuzumab_2h_R1 5 ELSEALTR 8 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;;; 188.98 0.00045163 1083161000 1336010 1483910 1191110 1653400 1463620 1595680 1514000 1444220 1351800 1557220 FALSE TRUE 1283797.252 1441590.34 1406370.073 1738732.172 1510698.667 1627945.743 1532528.785 1414396.352 1198349.331 1451748.102 0.8843113 0.993003082 0.968742491 1.197681725 1.040606607 1.121369293 1.055643732 0.974271191 0.825452659 1 20.46935972 1.525975409 4.355048637 0.908379416 1.041740521 0.238408338 0.088877262 0.227755403 9.477942163 0.055690463 0.023346264 33.5718604 -1.525975409 0.133361105 IRLDETDDPDDYGDRESGCSFVLALMQK ddPTM_BT-474_Pertuzumab_2h_R1 2 IRLDETDDPDDYGDRESGCSFVLALMQK 28 2 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 180.42 8.38E-18 1343040000 898860 1004620 663690 617160 911650 1024680 805060 808970 795220 750090 FALSE TRUE 863731.5575 975969.2212 783633.5467 649011.7016 940974.0502 1045399.732 814912.5651 792264.4868 704949.9594 699285.7362 1.235162556 1.39566585 1.12061995 0.928106592 1.345621684 1.494953604 1.165349903 1.132962458 1.008100013 1 19.41552255 1.52612288 2.154771539 1.004628331 1.2449525 0.295731088 0.147151974 0.408159221 3.872815852 0.127472957 0.043539911 33.58326218 -1.52612288 0.24032417 ASEDTTS(ph)GSPPKK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDT(0.003)T(0.014)S(0.729)GS(0.254)PPKK;ASEDT(0.021)T(0.015)S(0.482)GS(0.482)PPKK;ASEDTT(0.001)S(0.499)GS(0.499)PPKK 148.52 4.59E-05 3018820000 1491380 1184830 1073740 974430 1040790 1065760 1154630 1299680 1653560 1407060 TRUE FALSE 1433095.221 1151039.808 1267788.703 1024720.449 1074267.956 1087310.397 1168760.707 1272841.154 1465854.801 1311758.573 1.092499222 0.877478396 0.966480212 0.781180676 0.818952495 0.82889521 0.890987665 0.970331874 1.11747301 1 20.32307079 1.52657174 3.34244213 1.0576784 0.886648089 0.361498104 0.08687214 0.216872433 5.251791811 0.059926343 0.023017869 33.61798973 -1.52657174 -0.171030311 MEDQFAALHENPDIIIATPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEDQFAALHENPDIIIATPGR 21 0 Q8TDD1-2;Q8TDD1;F8VRX4 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ; 124.31 2.50E-05 663090000 421220 497610 420610 485150 448630 487190 512180 469910 501870 482720 FALSE TRUE 404758.2567 483418.65 496623.5834 510188.6496 463060.5914 497041.3156 518448.2121 460206.1943 444899.8216 450024.9444 0.899412936 1.074204121 1.103546791 1.133689712 1.028966499 1.104475034 1.152043278 1.022623746 0.988611469 1 18.77964545 1.526983719 7.378660267 0.998026258 1.075196861 0.182402348 0.066426334 0.19551336 20.46957709 0.036444155 0.016812694 33.64989545 -1.526983719 0.077170603 T(ph)S(ph)DKKGRY(ph)QK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSDKKGRYQK 10 3 R4GMW8;A0A494BZX4;A0A494C000;A0A494C0L8;A0A494C1S8;A0A494C0D0;Q86UB2 R4GMW8 BIVM-ERCC5;BIVM Basic immunoglobulin-like variable motif-containing protein 3 T(1)S(1)DKKGRY(1)QK 40.002 0.075479 116700000 30751 31864 23361 31799 29616 27334 29274 19396 27093 15913 TRUE FALSE 29549.21692 30955.26992 27582.85236 33440.1502 30568.62554 27886.71221 29632.26397 18995.46582 24017.51622 14835.19834 1.991831606 2.086609779 1.859284368 2.254108738 2.060547142 1.879766726 1.997429579 1.280432212 1.618954845 1 13.85673659 1.527339432 0.875996786 1.07509713 2.065013708 0.785494194 0.172334771 0.221524185 0.341231334 0.150792756 0.059713974 33.67746799 -1.527339432 0.989916578 LSLPEDFYHFWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSLPEDFYHFWK 12 0 Q9NWY4 Q9NWY4 C4orf27 UPF0609 protein C4orf27 0 146.16 6.11E-05 178900000 400880 475770 373750 482750 476420 466890 500370 442980 446130 462400 FALSE TRUE 385213.1664 462201.5054 441294.939 507664.7854 491744.482 476330.8357 506493.6777 433832.3082 395487.1927 431081.2361 0.893597619 1.072191194 1.023693221 1.177654564 1.140723466 1.104967685 1.174937889 1.006381795 0.917430775 1 18.71760024 1.527429735 6.036618318 0.959481201 1.088103431 0.291447607 0.080195628 0.163365373 12.52754802 0.046018614 0.020826398 33.68447129 -1.527429735 0.12862223 WEETWR ddPTM_BT-474_Pertuzumab_2h_R1 1 WEETWR 6 0 O43663-2;O43663-4;O43663;O43663-3;H0YL53 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 125.86 0.041275 155040000 97485 125330 104430 131370 123950 123730 112700 109890 78347 109950 FALSE TRUE 93675.17842 121755.7111 123302.824 138150.0214 127936.9643 126231.9054 114079.2563 107620.7331 69453.37702 102502.9886 0.913877534 1.187825963 1.202919308 1.347765791 1.248129114 1.231494878 1.112935905 1.049927759 0.677574166 1 16.64530645 1.52746507 2.893429702 0.840619013 1.191207541 0.50685334 0.130362411 0.175670982 3.151040635 0.093146871 0.034167029 33.68721202 -1.52746507 0.350588528 LKDISTLEPLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDISTLEPLKK 12 2 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 121.24 0.00021362 850380000 1598100 1547600 1167200 975080 1312000 1527300 1285000 1480500 1759900 1522100 FALSE TRUE 1535644.485 1503463.963 1378139.004 1025403.996 1354201.672 1558183.052 1300726.214 1449927.158 1560123.53 1419006.811 1.082196698 1.059518497 0.97119971 0.722620912 0.954330635 1.098080037 0.916645504 1.021790132 1.099447527 1 20.43645008 1.527555794 6.18310972 1.053194623 0.969871911 0.087823941 0.103102199 0.333041141 26.56748579 0.061550915 0.027949291 33.69424999 -1.527555794 -0.083322712 KVGIVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVGIVGK 7 1 Q6P4E4;E9PEL3;P61513;G5E9R3 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 91.626 0.04513 0 674100 534880 535070 583110 606650 581280 617660 653630 714820 718310 FALSE TRUE 647755.4267 519625.7461 631769.0516 613204.377 626163.4482 593033.8799 625219.1078 640132.3121 633676.6304 669658.2239 0.967292573 0.775956641 0.943420134 0.915697523 0.935049292 0.885576939 0.93363911 0.955908983 0.94626872 1 19.35306544 1.527737607 0.300974584 1.01035541 0.876339285 0.271486126 0.049167479 1.801518482 0.59865902 0.089623459 0.081817586 33.70835871 -1.527737607 -0.134016125 SLEAQVAHADQQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLEAQVAHADQQLR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 145.46 8.57E-06 781360000 483490 622790 457930 719190 634020 656540 626200 571230 521990 580880 FALSE TRUE 464594.6763 605028.639 540688.1376 756307.4821 654413.8291 669815.6886 633863.6229 559433.9009 462735.8836 541536.4802 0.857919444 1.117244472 0.998433453 1.396595631 1.208439049 1.236880087 1.170491086 1.033049335 0.854487002 1 19.046699 1.528400496 3.716351344 0.928672001 1.149843187 0.274005239 0.138915801 0.247975993 7.492085124 0.093135444 0.037177866 33.75984908 -1.528400496 0.221171186 ACSPSNIPAVIITDMGTQEDGALEETQGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ACSPSNIPAVIITDMGTQEDGALEETQGSPR 31 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 ACSPSNIPAVIITDMGTQEDGALEET(0.031)QGS(0.969)PR;ACSPSNIPAVIITDMGTQEDGALEET(0.034)QGS(0.966)PR 109.38 7.32E-05 56496000 50731 52310 49562 64478 53379 56155 55432 52997 55107 51433 TRUE FALSE 48748.37643 50818.17002 58518.9559 67805.71731 55095.98401 57290.49257 56110.3934 51902.59343 48851.48439 47949.3971 1.016662969 1.059829176 1.220431527 1.414109904 1.149044354 1.194811531 1.170200186 1.082445173 1.018813319 1 15.54922505 1.528602405 1.931534826 1.003500643 1.183133517 0.313381354 0.099538236 0.408140659 3.054724804 0.089281477 0.030173802 33.77554807 -1.528602405 0.179632874 RPLPVES(ph)PDTQR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPLPVESPDTQR 12 1 P57682 P57682 KLF3 Krueppel-like factor 3 1 RPLPVES(0.998)PDT(0.002)QR;RPLPVES(0.999)PDT(0.001)QR;RPLPVES(0.999)PDT(0.001)QR 162.79 3.78E-05 2951680000 1110290 1088540 1010260 1206430 1125040 1090720 1126080 1085080 1085440 1075680 TRUE FALSE 1066898.639 1057495.905 1192836.455 1268693.997 1161227.933 1112775.106 1139861.304 1062672.719 962225.4017 1002823.235 1.063895013 1.05451875 1.189478278 1.265122259 1.157958743 1.109642324 1.136652267 1.05968099 0.959516461 1 19.9356359 1.528842905 2.386020442 0.97923237 1.143760023 0.547939647 0.058149677 0.221544141 2.633867395 0.05010239 0.01748496 33.79425717 -1.528842905 0.164527653 DKEAPCSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKEAPCSR 8 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;H7BZT5;H7C1R1;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 68.657 0.064507 0 175460 189760 137060 163090 162410 173350 173260 160980 161720 159240 FALSE TRUE 168602.8292 184348.2306 161829.7909 171507.0944 167634.0651 176855.2558 175380.4077 157655.7067 143362.2236 148454.533 1.135720317 1.241782429 1.090096662 1.155283648 1.129194655 1.191309233 1.181374554 1.061979743 0.965697852 1 17.17966162 1.529367989 3.230523431 0.986019537 1.160609892 0.768873459 0.039499007 0.09578004 2.170610376 0.02662546 0.010143922 33.83514088 -1.529367989 0.174590355 LEVNGRESEEENLNKS(ph)EISQVFEIALK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEVNGRESEEENLNKSEISQVFEIALK 27 2 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5;Q5JW28 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 LEVNGRES(0.215)EEENLNKS(0.504)EIS(0.281)QVFEIALK 49.312 0.060227 15614000 14208 12821 9802.7 9661.9 12364 15644 11252 15739 20890 17827 TRUE FALSE 13652.73565 12455.35763 11574.26595 10160.55182 12761.69929 15960.3324 11389.70534 15413.98415 18518.65478 16619.56141 0.821485917 0.749439611 0.696424272 0.611361008 0.767872206 0.960334151 0.685319249 0.927460344 1.114268561 1 14.02059469 1.529531664 3.807466336 1.052334065 0.756744522 0.642183929 0.091323297 0.120966609 3.845636439 0.061454666 0.024767833 33.84789494 -1.529531664 -0.295589544 ETRPFPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETRPFPR 7 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 0 ; 98.418 0.02223 281970000 171467 212206 166795 204244 186112 177818 203248 183672 175484 197754 FALSE TRUE 164765.8801 206154.0927 196938.5668 214785.0573 192098.4615 181413.6018 205735.4098 179879.109 155563.792 184359.9454 0.893718425 1.118215197 1.068228602 1.165031031 1.04197504 0.984018526 1.115944189 0.975695174 0.843804719 1 17.49216572 1.530392489 5.189634885 0.917778103 1.058820619 0.317448355 0.079817899 0.156176655 9.126553174 0.044450824 0.019614387 33.91505215 -1.530392489 0.141042516 RGPGLYYVDSEGNR ddPTM_BT-474_Pertuzumab_2h_R1 6 RGPGLYYVDSEGNR 14 1 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;;; 271.08 9.63E-33 9865090000 3541790 3679950 3298200 3621350 3664580 3705250 3661690 3675100 3750390 3881620 FALSE TRUE 3403372.931 3575001.429 3894258.108 3808248.307 3782454.544 3780172.694 3706502.858 3599207.901 3324661.45 3618714.42 0.940492268 0.987920298 1.076144082 1.052376028 1.045248147 1.044617578 1.024259565 0.994609544 0.91874104 1 21.78704583 1.530572518 3.727436436 0.958174608 1.027376506 0.289359359 0.040229949 0.230847935 7.036672752 0.02719319 0.010894594 33.92911393 -1.530572518 0.069201898 DLVHSNKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLVHSNKK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 133.86 0.00058504 2583500000 4225200 3946600 3354980 3253890 3470800 3780170 3750700 4019000 4649400 4355000 FALSE TRUE 4060074.513 3834046.832 3961299.517 3421823.653 3582441.434 3856607.627 3796602.189 3936006.246 4121619.604 4060031.971 1.000010478 0.944339074 0.975681853 0.842807071 0.882367789 0.949895876 0.935116328 0.969452032 1.015169248 1 21.95305966 1.531199967 2.159066544 1.008347419 0.929393911 0.334207504 0.042069118 0.348207816 3.335633029 0.035762393 0.012276796 33.97816861 -1.531199967 -0.078953508 ADIKS(ph)PSLDVTVPEAELNLETPEISVGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADIKSPSLDVTVPEAELNLETPEISVGGK 29 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ADIKS(0.785)PS(0.213)LDVT(0.002)VPEAELNLETPEISVGGK;ADIKS(0.482)PS(0.482)LDVT(0.035)VPEAELNLETPEISVGGK 178.34 7.64E-18 630840000 760990 755160 710370 715160 859680 884230 703720 736580 751240 652970 TRUE FALSE 731249.6695 733623.5762 838749.6611 752069.4933 887332.3879 902109.7364 712332.3359 721369.3656 665962.3847 608743.7603 1.201243803 1.205143484 1.377836975 1.235445096 1.457645147 1.481920301 1.170167782 1.185013158 1.093994597 1 19.21547555 1.531258036 1.457700364 1.029864102 1.319748483 0.53697589 0.099645334 0.313295001 1.283163667 0.091767108 0.031181935 33.98271208 -1.531258036 0.289884381 DSSFTEVPRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 DSSFTEVPRSPK 12 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK 168.05 2.88E-05 7459600000 6420810 5546180 4667980 4565700 4943570 5310470 5048510 5690070 6536590 6043810 TRUE FALSE 6169877.647 5388008.377 5511587.825 4801336.324 5102584.419 5417851.342 5110295.176 5572568.066 5794583.707 5634457.365 1.09502606 0.956260386 0.97819319 0.852138194 0.905603519 0.961556897 0.90697202 0.989015926 1.028419124 1 22.42584525 1.531297954 5.588464757 1.012739906 0.946886419 0.156029311 0.059941268 0.252962783 16.86861843 0.035003112 0.015685605 33.98583575 -1.531297954 -0.065853486 AAEELDMENEFLLPPVFGEEYEEQPRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAEELDMENEFLLPPVFGEEYEEQPRPR 28 1 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 ; 143.05 1.03E-07 103089000 38712 41100 32972 41431 38805 45754 40231 39913 41631 40016 FALSE TRUE 37199.09224 39927.86824 38930.77386 43569.25888 40053.19807 46679.17723 40723.35901 39088.7826 36905.22341 37305.68068 0.997142836 1.07028923 1.043561547 1.167898778 1.073648767 1.251261909 1.091612813 1.047797062 0.989265515 1 15.18710771 1.531312445 2.831262779 0.996951914 1.103334251 0.289281036 0.065699529 0.309129375 5.327364325 0.049267011 0.018031842 33.98696978 -1.531312445 0.106382337 TT(ph)PPESAPQNGPSPMAALMSVADTLGTAHSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 T(0.261)T(0.739)PPESAPQNGPSPMAALMSVADTLGTAHSPK 202.35 2.49E-26 155950000 68329 56402 52091 48105 55160 56687 54790 64993 78210 72404 TRUE FALSE 65658.62714 54793.47018 61505.00246 50587.70481 56934.2715 57833.24998 55460.53641 63650.87184 69331.92868 67500.01259 0.972720221 0.811754962 0.911185052 0.749447339 0.843470532 0.856788729 0.821637423 0.942975703 1.027139493 1 16.04260015 1.531421675 3.350604196 1.010299984 0.849194583 0.570897413 0.056610944 0.140367943 3.441895214 0.036640834 0.014168331 33.99551894 -1.531421675 -0.161105401 NLYPSSS(ph)PYTR ddPTM_BT-474_Pertuzumab_2h_R1 1 NLYPSSSPYTR 11 0 Q9Y2Z0;Q9Y2Z0-2 Q9Y2Z0 SUGT1 Suppressor of G2 allele of SKP1 homolog 1 NLYPS(0.139)S(0.2)S(0.66)PYTR 116.9 0.000972 264500000 309020 340250 330260 387270 330870 403800 368360 343360 310360 370600 TRUE FALSE 296943.1568 330546.4031 389945.3286 407257.0511 341512.734 411965.1127 372868.0999 336269.496 275129.2339 345498.9319 0.859461866 0.956721925 1.128644093 1.178750536 0.988462489 1.192377384 1.079216361 0.973286644 0.796324412 1 18.39832173 1.531455283 4.299783585 0.893549737 1.060478806 0.256198951 0.106814157 0.220762529 8.981473626 0.067321126 0.028286423 33.99814983 -1.531455283 0.166929069 NGYGFVEFEDS(ph)RDADDAVYELNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 NGYGFVEFEDS(1)RDADDAVYELNGK;NGYGFVEFEDS(1)RDADDAVYELNGK 255.33 4.73E-44 263020000 330560 285130 273410 285890 305090 303370 273270 373040 477190 426680 TRUE FALSE 317641.3497 276998.3716 322821.269 300644.8172 314903.4969 309504.3493 276614.36 365336.5936 423021.3917 397780.5836 0.798534074 0.696359709 0.811556125 0.755805662 0.791651252 0.778078071 0.695394324 0.918437472 1.063454098 1 18.60161333 1.5318508 3.816561755 1.025226147 0.762669849 0.879598046 0.040790633 0.054857081 1.757185214 0.024809283 0.010034657 34.0291264 -1.5318508 -0.262556298 RLDDNIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDDNIR 7 1 E7EVT8;F6VX93;Q5VIR6-2;Q5VIR6-3;Q5VIR6-1;Q5VIR6;I3L0S6 E7EVT8 VPS53 Vacuolar protein sorting-associated protein 53 homolog 0 ; 110.31 0.010955 372700000 149121 209280 167643 236340 201143 176551 215087 177163 152899 186250 FALSE TRUE 143293.1865 203311.5393 197939.8193 248537.5357 207612.9473 180120.9822 217719.299 173504.5221 135542.5465 173635.1216 0.825254621 1.170912529 1.1399757 1.431378246 1.195685212 1.037353391 1.253889749 0.999247851 0.780617108 1 17.40569927 1.532302799 4.764486215 0.88861681 1.158458582 0.322186758 0.153604884 0.17554161 8.726116046 0.091339267 0.039551557 34.0645612 -1.532302799 0.269841772 HVPGASFFDIEECR ddPTM_BT-474_Pertuzumab_2h_R1 1 HVPGASFFDIEECR 14 0 Q16762;B1AH48 Q16762 TST Thiosulfate sulfurtransferase 0 182.02 1.57E-06 145900000 93945 140170 102880 260840 102180 115230 203490 123080 129430 104290 FALSE TRUE 90273.52554 136172.4888 121472.7046 274301.9837 105466.7125 117560.0296 205980.3715 120538.355 114737.649 97226.34541 0.928488314 1.400571916 1.249380546 2.821272182 1.084754467 1.209137596 2.118565401 1.239770501 1.180108627 1 16.56905967 1.532334701 9.062947357 1.130769652 1.554788289 0.112739015 0.528313768 0.262629513 34.89105237 0.284539956 0.132164677 34.06706355 -1.532334701 0.424018637 RGFGFVTFDDHDPVDK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGFGFVTFDDHDPVDK 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 154.82 2.07E-07 7649300000 9163920 8396700 6514010 7158650 7798890 8011750 7857170 8476070 9766940 8999940 FALSE TRUE 8805783.875 8157234.337 7691236.51 7528108.784 8049748.38 8173753.074 7953328.397 8301036.192 8658237.918 8390366.047 1.049511288 0.972214358 0.916674728 0.897232462 0.959403718 0.974183132 0.947911969 0.989353283 1.031926124 1 23.00030232 1.532939053 3.681279728 1.015436637 0.956709515 0.25434547 0.038661047 0.267603866 7.976183856 0.02662111 0.010650452 34.11450331 -1.532939053 -0.058727122 AEDQTESSCESHR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 0 76.322 0.015094 0 2750.6 4370 3973.2 5578.5 4627 6585.4 4033.8 4453.1 2926.9 4315.9 FALSE TRUE 2643.103511 4245.371879 4691.245623 5866.407054 4775.831657 6718.5613 4083.166851 4361.141929 2594.650583 4023.580249 0.656903391 1.055122954 1.165938128 1.458006723 1.186960707 1.669796769 1.014809349 1.083895849 0.644861149 1 11.97426409 1.533013257 2.637413755 0.831401119 1.199659172 0.198542439 0.26667955 0.379583121 5.635930832 0.202350501 0.072702361 34.12033269 -1.533013257 0.368258053 S(ph)PERPTGDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPERPTGDLR 10 1 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(1)PERPTGDLR;S(0.998)PERPT(0.002)GDLR;S(1)PERPTGDLR;S(1)PERPTGDLR 107.37 0.0013885 5394130000 3781290 3905290 3076410 3850800 3643610 3922560 3786730 3805500 3956280 4059540 TRUE FALSE 3633513.006 3793914.953 3632385.721 4049540.249 3760810.025 4001876.851 3833073.134 3726915.095 3507179.68 3784583.74 0.960082602 1.002465585 0.95978474 1.070009419 0.993718275 1.057415326 1.012812346 0.984762223 0.926701567 1 21.8517032 1.533292245 4.387142442 0.961052085 1.009398162 0.186132674 0.037326453 0.248732084 10.53781435 0.022214905 0.009409708 34.14225844 -1.533292245 0.048346077 YLGDAFGS(ph)PQTDHGFETDPDPFLLDEPAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 YLGDAFGSPQTDHGFETDPDPFLLDEPAPR 30 0 Q9H8N7 Q9H8N7 ZNF395 Zinc finger protein 395 1 YLGDAFGS(0.813)PQT(0.187)DHGFETDPDPFLLDEPAPR;YLGDAFGS(0.702)PQT(0.298)DHGFETDPDPFLLDEPAPR;YLGDAFGS(0.987)PQT(0.013)DHGFETDPDPFLLDEPAPR;YLGDAFGS(0.995)PQT(0.005)DHGFETDPDPFLLDEPAPR 272.89 1.87E-71 720367000 429381 476367 360778 463944 469152 436546 420694 399227 404386 354377 TRUE FALSE 412600.3158 462781.4796 425978.6101 487888.2054 484242.7002 445373.2592 425842.579 390982.8229 358481.7966 330374.7301 1.24888582 1.400777473 1.289380123 1.476772165 1.465737709 1.348085125 1.288968375 1.183452568 1.085076321 1 18.33374382 1.533304712 1.246350188 1.010330054 1.379399107 0.798575534 0.06645885 0.181074535 0.53914027 0.060295476 0.021038672 34.14323854 -1.533304712 0.369069052 RRDELSEEINNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RRDELSEEINNLR 13 2 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;A0A087WYS2;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ;;; 203.87 4.64E-08 2514550000 1350680 1453780 1037730 1450150 1454430 1616310 1297040 1323700 1232150 1219410 FALSE TRUE 1297893.932 1412319.618 1225270.895 1524992.415 1501213.062 1648992.896 1312913.564 1296365.132 1092281.498 1136818.275 1.141689891 1.242344225 1.077807177 1.341456633 1.320539171 1.450533416 1.154901881 1.140345085 0.96082331 1 20.11657022 1.533364676 2.039909112 0.98197047 1.257469368 0.518263424 0.102326586 0.250836922 2.124863521 0.086949318 0.0296703 34.14795305 -1.533364676 0.275498898 YKETDLLILFK ddPTM_BT-474_Pertuzumab_2h_R1 2 YKETDLLILFK 11 1 P05455 P05455 SSB Lupus La protein 0 ; 135.6 0.00010641 1102020000 3502000 3277800 3033300 2874800 2981200 2577900 3301300 3510800 4027200 4041100 FALSE TRUE 3365137.968 3184320.353 3581484.785 3023168.773 3077093.005 2630026.904 3341702.297 3438300.753 3570049.139 3767392.698 0.89322729 0.845231864 0.950653429 0.802456504 0.816769913 0.698102671 0.887006629 0.912647295 0.947618002 1 21.84513499 1.533613715 1.876832203 0.977871158 0.837359889 0.428534385 0.06295157 0.327831983 2.312245454 0.055076328 0.018649458 34.16754025 -1.533613715 -0.140511269 FSGWYDADLSPAGHEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 4 FSGWYDADLSPAGHEEAKR 19 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;; 202.03 3.71E-16 7932000000 6922500 7875400 5460250 6256600 6279050 6932610 6189330 6102350 6834500 5736370 FALSE TRUE 6651961.047 7650801.303 6447038.638 6579503.876 6481021.346 7072792.124 6265076.872 5976334.34 6058676.213 5347840.55 1.243859271 1.430633773 1.20554055 1.230310405 1.211895023 1.322551048 1.171515271 1.117522911 1.13292013 1 22.35052502 1.53364529 0.368943562 0.98147496 1.322263707 0.647679479 0.065801079 0.702413529 0.297776825 0.090276985 0.073701804 34.17002451 -1.53364529 0.340788746 AVPAPS(ph)PGPTHNS(ph)PELGRPPAAGVLAPDMSDKDK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVPAPSPGPTHNSPELGRPPAAGVLAPDMSDKDK 34 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 2 AVPAPS(0.936)PGPT(0.075)HNS(0.989)PELGRPPAAGVLAPDMSDKDK;AVPAPS(0.958)PGPT(0.046)HNS(0.996)PELGRPPAAGVLAPDMSDKDK;AVPAPS(0.929)PGPT(0.088)HNS(0.984)PELGRPPAAGVLAPDMSDKDK 161.02 1.85E-14 682829000 509585 391872 379509 350283 367553 422469 403000 463551 545353 518353 TRUE FALSE 489669.8548 380696.1942 448094.7184 368361.1476 379375.676 431011.6126 407932.0346 453978.5099 483446.8137 483244.4896 1.013296303 0.787792106 0.927262965 0.762266628 0.785059497 0.891912111 0.84415248 0.939438565 1.000418679 1 18.88239376 1.533724932 2.394385155 1.001567542 0.852670258 0.394644008 0.070858251 0.255884803 3.083892322 0.052476745 0.018420198 34.17629123 -1.533724932 -0.148897284 QERLS(ph)PEVAPPAHR ddPTM_BT-474_Pertuzumab_2h_R1 5 QERLSPEVAPPAHR 14 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR 133.3 2.75E-05 6254200000 4684850 4850800 3854620 4550820 4467260 4706760 4370530 4419840 4619230 4254170 TRUE FALSE 4501760.883 4712459.933 4551235.58 4785688.366 4610953.475 4801933.912 4424017.854 4328568.759 4094874.376 3966031.277 1.135079521 1.188205439 1.147554132 1.206669346 1.162611476 1.210765518 1.115477298 1.091410646 1.032486657 1 21.91926462 1.533874147 1.315025179 1.004192488 1.175073909 0.857188553 0.025431003 0.131168555 0.434910095 0.021031829 0.007262465 34.18803557 -1.533874147 0.170881421 SSQEEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSQEEVR 7 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 87.323 0.045195 217620000 329090 326530 254210 360500 316750 306960 324710 308680 299250 317820 FALSE TRUE 316228.799 317217.6841 300151.4019 379105.4482 326938.5514 313166.9415 328683.8981 302305.6501 265280.3946 296293.7683 1.067281303 1.070618818 1.013019624 1.279491804 1.103427025 1.056947445 1.109317621 1.020290274 0.895328971 1 18.17666876 1.534489537 3.469471822 0.948051524 1.100664058 0.430643973 0.070439296 0.188821361 4.996658384 0.047502726 0.018657576 34.23651396 -1.534489537 0.152612534 VLISSLQDCLHGIESK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLISSLQDCLHGIESK 16 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 184.22 1.86E-09 256470000 331970 379950 266040 316210 346940 322590 309090 360640 413870 384650 FALSE TRUE 318996.2454 369114.198 314119.346 332529.636 358099.6402 329112.9908 312872.7359 353192.658 366889.2127 358597.3129 0.889566748 1.029327841 0.875966815 0.927306547 0.998612168 0.917778742 0.872490464 0.984928345 1.023123151 1 18.45200515 1.534721743 6.559778192 1.009143775 0.933539043 0.332071916 0.047920506 0.149899298 12.87804688 0.025830791 0.01184617 34.25482416 -1.534721743 -0.075604731 S(ph)RNSPLLER ddPTM_BT-474_Pertuzumab_2h_R1 1 SRNSPLLER 9 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 S(0.763)RNS(0.237)PLLER 84.169 0.0094925 453860000 129460 142640 112940 187440 153920 123640 154210 140210 134670 152670 TRUE FALSE 124400.5601 138572.0469 133350.7703 197113.8009 158870.9766 126140.0855 156097.2681 137314.6145 119382.8262 142329.5249 0.874032005 0.97360015 0.936915727 1.384911535 1.116219398 0.886253823 1.096731463 0.964765495 0.838777662 1 17.11887544 1.534890933 5.340583587 0.913789301 1.042145589 0.102580013 0.144047936 0.328203871 20.11289354 0.086433305 0.038506023 34.26817158 -1.534890933 0.128356288 SAMPFTAS(ph)PASSTTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 SAMPFT(0.002)AS(0.998)PASSTTAR;SAMPFTAS(1)PASSTTAR 328 1.91E-71 1737160000 719480 746100 731790 685590 691460 773260 767920 719450 682950 785330 TRUE FALSE 691361.9262 724821.9585 864040.7316 720973.3821 713701.4389 788895.847 777318.0347 704593.1061 605424.3792 732138.8996 0.944304321 0.990006075 1.180159574 0.984749455 0.974816991 1.077522103 1.06170842 0.962376274 0.826925573 1 19.48175785 1.535125285 4.794386961 0.907599546 1.031980436 0.290373564 0.074261337 0.180226603 9.060152511 0.043417027 0.018881399 34.28666824 -1.535125285 0.12438089 VS(ph)EGGPAEIAGLQIGDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSEGGPAEIAGLQIGDK 17 0 O14907 O14907 TAX1BP3 Tax1-binding protein 3 1 VS(1)EGGPAEIAGLQIGDK 265.43 1.57E-27 87632000 101430 84172 89131 70369 86286 93371 88615 108150 132850 125800 TRUE FALSE 97466.00346 81771.49697 105238.9544 74000.75252 89061.46755 95259.02559 89699.49688 105916.6647 117769.425 117279.4539 0.831057787 0.697236338 0.897334962 0.630977976 0.759395312 0.812239675 0.76483556 0.903113556 1.004177808 1 16.83959077 1.535393301 2.175888371 1.006395609 0.766333141 0.653040801 0.068667493 0.164401105 1.608760651 0.05155825 0.01779216 34.30783409 -1.535393301 -0.240062468 IKELNNTCEPVVTQPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKELNNTCEPVVTQPKPK 18 2 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 95.954 0.00094634 424540000 229600 204060 154000 138410 168070 200930 187750 217170 264990 253190 FALSE TRUE 220626.9782 198240.4086 181831.2257 145553.3567 173476.1242 204992.9423 190047.7407 212685.3636 234909.4461 236041.2158 0.934696839 0.839855056 0.770336761 0.616643819 0.734939971 0.868462491 0.805146423 0.901051805 0.995205203 1 17.84867927 1.535688414 1.385858849 1.010451019 0.782814055 0.512305544 0.07954673 0.340621334 1.257223248 0.07553999 0.025890234 34.33115496 -1.535688414 -0.227636964 AGDSAVLVLPPS(ph)PGPR ddPTM_BT-474_Pertuzumab_2h_R1 6 AGDSAVLVLPPSPGPR 16 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR 265.27 4.66E-27 2199310000 2755310 2960150 2284210 2721430 2676020 2497020 2203140 2539010 2097970 1877910 TRUE FALSE 2647629.439 2875729.42 2697017.559 2861883.328 2762096.614 2547511.455 2230102.686 2486578.556 1859817.241 1750717.483 1.512311075 1.642600504 1.540521292 1.634691694 1.577694083 1.455124245 1.273822137 1.420319715 1.062317169 1 20.73951486 1.535819979 0.663886147 0.987770185 1.597210962 0.860394254 0.080989701 0.224720163 0.216995934 0.075121243 0.035897439 34.3415568 -1.535819979 0.609440777 ELSKEDLSPAFDHS(ph)PNK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELSKEDLSPAFDHSPNK 17 1 K7EIY0;K7ENP9;K7EIE9;D3DUJ3;K7EQG9;P17706-3;P17706-2;P17706-4;P17706 K7EIY0 PTPN2 Protein-tyrosine-phosphatase;Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 2 1 ELSKEDLSPAFDHS(1)PNK;ELSKEDLSPAFDHS(1)PNK;ELSKEDLSPAFDHS(1)PNK 209.56 2.52E-12 1778000000 2411660 2011960 1679610 1527180 1784870 1750370 2047100 2123160 2402660 2451090 TRUE FALSE 2317409.661 1954580.871 1983152.89 1605997.943 1842281.965 1785763.681 2072153.022 2079316.004 2129920.11 2285075.491 1.014150154 0.855368183 0.867871936 0.702820519 0.806223677 0.781490015 0.906820379 0.909955059 0.932100545 1 21.1238104 1.536007537 1.295690439 0.980095329 0.835030265 0.300730356 0.076626132 0.52175157 1.679008307 0.070235584 0.0243436 34.35639104 -1.536007537 -0.145065064 ESTLEAIGYICQDIDPEQLQDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESTLEAIGYICQDIDPEQLQDK 22 0 Q14974;Q14974-2;J3KTM9;J3QRG4 Q14974 KPNB1 Importin subunit beta-1 0 ; 197.4 2.01E-22 181531000 335530 333550 274160 310000 313970 336460 330260 374110 447390 428040 FALSE TRUE 322417.1167 324037.4806 323706.8107 325999.1372 324069.1302 343263.4517 334301.8207 366384.4978 396604.1628 399048.4695 0.807964799 0.812025369 0.811196723 0.816941204 0.812104681 0.860204907 0.837747407 0.918145353 0.993874662 1 18.60620447 1.536065315 1.339565285 1.009153238 0.816398107 0.963916954 0.013756318 0.065778045 0.226463811 0.012053644 0.004153414 34.36096203 -1.536065315 -0.192755132 TAWVFDDKYK ddPTM_BT-474_Pertuzumab_2h_R1 2 TAWVFDDKYK 10 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 136.5 0.00010582 1754910000 2651470 2346470 2099640 1600300 1999420 1489020 2473980 2343680 2926900 2867000 FALSE TRUE 2547847.621 2279550.973 2479091.654 1682891.675 2063733.16 1519129.005 2504257.307 2295282.189 2594650.583 2672815.536 0.953244841 0.852865056 0.927520669 0.629632555 0.772119562 0.568362831 0.936936079 0.858750691 0.970755575 1 21.34992884 1.536100202 1.62986673 0.986609468 0.791353913 0.268481036 0.119511523 0.492473025 2.55856609 0.104847107 0.035463301 34.36372242 -1.536100202 -0.195255555 RATVVESSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RATVVESSEK 10 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 172.13 6.11E-06 597790000 825800 839760 712620 756340 782360 664360 844060 888560 1095610 1027800 FALSE TRUE 793526.823 815810.867 841406.2861 795374.798 807525.3199 677793.8144 854389.8588 870210.9255 971240.946 958186.1905 0.828155144 0.851411631 0.878123996 0.830083762 0.842764515 0.707371721 0.891674152 0.908185626 1.013624445 1 19.8699465 1.536126063 1.977735426 1.006967264 0.828732121 0.695875086 0.046184955 0.174185273 1.381260433 0.038331437 0.013065466 34.36576873 -1.536126063 -0.178235143 AKEEQQDDTVYMGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKEEQQDDTVYMGK 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;E7EWF7 E7EX90 DCTN1 Dynactin subunit 1 0 150.57 6.54E-06 164980000 221670 202230 167290 169550 182570 208520 199750 225010 262440 259130 FALSE TRUE 213006.8913 196462.5984 197523.0243 178300.4958 188442.5299 212736.4173 202194.6003 220363.4649 232648.9114 241578.8943 0.881728066 0.81324405 0.817633614 0.738063217 0.780045502 0.880608457 0.836971296 0.91218012 0.963034921 1 17.88213489 1.536128602 1.033572409 1.000898286 0.808505059 0.746191939 0.038878107 0.242236389 0.502463423 0.03648006 0.013459965 34.36596965 -1.536128602 -0.192393227 VDDNEETIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDDNEETIKK 10 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 104.87 0.004209 508650000 630040 560130 449620 515470 516340 554800 533040 637830 803600 708710 FALSE TRUE 605417.3403 544155.6408 530876.3357 542073.4685 532948.545 566018.4361 539563.503 624658.5876 712378.697 660708.4404 0.916315432 0.823594202 0.803495617 0.820442778 0.806631961 0.856684131 0.816643878 0.945437578 1.078204323 1 19.33365425 1.536160939 3.226726717 1.036697148 0.832516776 0.835951157 0.03653199 0.074509814 1.70196101 0.024260193 0.009314369 34.3685286 -1.536160939 -0.204180372 FIEIAAR ddPTM_BT-474_Pertuzumab_2h_R1 8 FIEIAAR 7 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;A0A1W2PPE9;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;; 187.72 0.0013498 3463920000 2885991 3228640 2888127 3442370 3361850 3174100 3117237 3050290 2665281 3032330 FALSE TRUE 2773203.281 3136562.348 3410075.795 3620031.128 3469986.958 3238282.477 3155386.679 2987300.446 2362729.475 2826947.588 0.980988573 1.109522639 1.206274856 1.280544126 1.227467737 1.145504957 1.116181528 1.056722968 0.835788214 1 21.43081371 1.536697975 2.575910044 0.919766112 1.161920758 0.534822852 0.085795548 0.195064241 2.766371584 0.067592798 0.02423009 34.41105398 -1.536697975 0.242154646 TDS(ph)YSAGQSVEILDGVELGEPAHKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDSYSAGQSVEILDGVELGEPAHKK 25 1 P42345;B1AKP8;B1AKQ2 P42345 MTOR Serine/threonine-protein kinase mTOR 1 T(0.106)DS(0.67)Y(0.085)S(0.139)AGQSVEILDGVELGEPAHKK 184.43 8.86E-18 219520000 293330 225030 223280 168920 234090 273220 234800 293760 391680 330890 TRUE FALSE 281866.3393 218612.3647 263631.6628 177637.9814 241619.7174 278744.6956 237673.5526 287693.7533 347218.1285 308478.5256 0.91373083 0.708679362 0.854619174 0.575852018 0.783262683 0.903611346 0.770470334 0.932621656 1.125582819 1 18.23481054 1.537351971 3.023649604 1.061184936 0.782554569 0.564701254 0.09734005 0.156002991 3.117018663 0.067260694 0.025308243 34.462912 -1.537351971 -0.278630366 NPDELAEALDER ddPTM_BT-474_Pertuzumab_2h_R1 2 NPDELAEALDER 12 0 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 131.17 0.00047327 689500000 598490 824550 954140 769960 911710 892000 848660 706380 538150 620510 FALSE TRUE 575100.3491 801034.6413 1126574.323 809697.7279 941035.9801 910036.8512 859046.1549 691793.0062 477061.4681 578482.305 0.994153744 1.384717621 1.947465485 1.399693164 1.626732524 1.573145528 1.484999882 1.195875829 0.82467772 1 19.1419133 1.537562382 2.7421655 0.917400849 1.507675243 0.503140081 0.228800919 0.194440825 3.158901355 0.169467547 0.061877662 34.47961296 -1.537562382 0.590274394 GQRDS(ph)SYYWEIEASEVMLSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQRDSSYYWEIEASEVMLSTR 21 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 GQRDS(0.497)S(0.497)Y(0.003)Y(0.003)WEIEASEVMLSTR 87.339 0.0015861 21016000 13915 12031 11162 10705 11728 15496 11981 11100 8697.9 10397 TRUE FALSE 13371.18642 11687.88766 13179.2217 11257.48633 12105.24177 15809.33974 12127.62706 10870.78112 7710.550857 9692.801929 1.379496508 1.205831683 1.359691634 1.161427461 1.248889832 1.631039183 1.251199308 1.121531338 0.795492461 1 13.24269806 1.537657299 2.824058971 0.90364861 1.32028689 0.618831864 0.132046353 0.153556643 2.656841564 0.095831397 0.035303388 34.48714945 -1.537657299 0.41663828 FVLINWTGEGVNDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVLINWTGEGVNDVR 15 0 Q9UJU6-2;Q9UJU6-3;Q9UJU6-6;F8WBG8;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 122.45 0.00025319 86624000 61370 65725 56808 50370 56320 49192 47606 72451 94266 80856 FALSE TRUE 58971.59255 63850.58735 67074.46929 52969.60174 58131.58395 50186.69594 48188.61647 70954.86153 83565.31888 75379.5511 0.782328784 0.847054492 0.889823146 0.702705189 0.771185064 0.665786612 0.639279695 0.941301195 1.108594011 1 16.20188558 1.538001612 4.769585748 1.047530083 0.760878747 0.718805222 0.076444182 0.08852776 4.404230979 0.049062865 0.021365581 34.51450202 -1.538001612 -0.286651336 RLNLEEWILEQLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLNLEEWILEQLTR 14 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 ; 228.73 2.48E-12 721240000 190622 208655 163491 152881 198702 203163 171879 160966 155958 133692 FALSE TRUE 183172.2815 202704.3637 193037.4605 160771.2067 205093.4303 207271.0951 173982.5066 157641.9958 138254.3017 124636.9218 1.469647027 1.626358874 1.548798364 1.289916378 1.645527083 1.662999151 1.395914663 1.264809766 1.109256388 1 16.92737198 1.538183705 1.527215995 1.024849417 1.537111569 0.770144088 0.105323449 0.175089644 0.792132707 0.093521417 0.031772747 34.52897651 -1.538183705 0.512262152 GDVPTKRPPVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDVPTKRPPVLR 12 2 P62424;Q5T8U2;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 76.326 0.017671 387760000 254260 291250 192840 187170 252180 263830 205940 205930 183630 160650 FALSE TRUE 244323.2381 282943.8352 227690.4777 196829.8661 260291.5987 269164.8234 208460.3553 201677.4735 162785.0922 149769.0324 1.631333488 1.889201196 1.520277417 1.314222727 1.737953398 1.797199455 1.391878895 1.346589948 1.086907551 1 17.19237982 1.538327594 1.353275064 1.007805 1.63877345 0.688852301 0.157413999 0.240397112 0.845166668 0.145214277 0.050012217 34.5404184 -1.538327594 0.630968451 SLS(ph)DS(ph)ESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 S(0.002)LS(0.998)DS(1)ESDDSK 211.52 1.32E-08 572530000 818270 665290 569520 547530 634980 595740 649780 700950 865710 723870 TRUE FALSE 786291.1038 646316.5806 672444.9329 575788.0889 655404.7084 607786.271 657732.202 686475.1375 767438.2302 674841.6401 1.165149062 0.957730736 0.996448489 0.853219562 0.971197788 0.900635401 0.974646736 1.017238855 1.137212324 1 19.36418947 1.539121156 3.776325344 1.071293926 0.967260627 0.168103138 0.082096539 0.28876533 9.127027185 0.051636658 0.020989445 34.6035899 -1.539121156 -0.104033299 SAEPS(ph)PTVMSTSLGSNLSELDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 S(0.009)AEPS(0.984)PT(0.008)VMSTSLGSNLSELDR;S(0.002)AEPS(0.866)PT(0.121)VMS(0.005)T(0.005)S(0.001)LGSNLSELDR 245.75 6.93E-31 134128000 56630 68144 53240 64229 66228 73315 55234 59578 49977 50866 TRUE FALSE 54416.83699 66200.59984 62861.65232 67543.86639 68358.28377 74797.47953 55909.97021 58347.69348 44303.82048 47420.80051 1.147530965 1.396024511 1.325613478 1.424351037 1.441525302 1.577313726 1.179017849 1.230424051 0.934269772 1 15.5332324 1.539208564 1.689764765 0.968231277 1.380090072 0.627488069 0.118494551 0.215620206 1.2126944 0.099147315 0.033591122 34.61055502 -1.539208564 0.411858795 TPVVESARPNS(ph)TSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPVVESARPNSTSSR 15 1 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 TPVVESARPNS(0.953)T(0.033)S(0.014)SR;TPVVESARPNS(0.994)T(0.004)S(0.002)SR 164.97 8.79E-07 1753430000 518600 567210 459690 545860 491850 560010 570510 524660 549490 541270 TRUE FALSE 498332.5387 551033.7262 542766.2087 574031.9 507670.8019 571333.7859 577492.072 513825.5877 487114.1989 504609.3008 0.987561145 1.092000733 1.075616735 1.137576932 1.006067072 1.132229995 1.144434062 1.018264203 0.96532941 1 18.94480727 1.539208743 5.688046883 0.985308794 1.083568761 0.403647161 0.050002388 0.132813165 9.029188253 0.027687868 0.012508665 34.61056933 -1.539208743 0.098259967 VRLDDDDEGVPSSALR ddPTM_BT-474_Pertuzumab_2h_R1 4 VRLDDDDEGVPSSALR 16 1 Q00535;Q00535-2 Q00535 CDK5 Cyclin-dependent-like kinase 5 0 ;;; 301.43 5.43E-46 868760000 763047 809595 610162 688599 750747 806693 706557 763791 759420 781637 FALSE TRUE 733226.2796 786506.1433 720431.8464 724137.6769 774895.4591 823004.8852 715204.0559 748018.4489 673213.8253 728696.0298 1.006216927 1.079333647 0.988658943 0.993744507 1.063400139 1.129421393 0.981484771 1.026516433 0.923860976 1 19.4749576 1.539574218 2.209870109 0.966013622 1.038814644 0.243925989 0.047943775 0.393662353 4.00312215 0.037764126 0.013120047 34.63970767 -1.539574218 0.072801021 RKPS(ph)IVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKPSIVTK 8 2 P46100;P46100-4;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LNN3;A0A087WWG0;A0A096LNL6;A0A096LNL7 P46100 ATRX Transcriptional regulator ATRX 1 RKPS(1)IVTK 98.156 0.0060815 465050000 752700 628350 551820 610630 731290 565730 486580 680930 506520 491730 TRUE FALSE 723283.6518 610430.0732 651546.1492 642144.6875 754812.607 577169.4482 492534.9116 666868.5575 449021.9731 458424.6891 1.577758941 1.331582019 1.421271944 1.400763752 1.64653568 1.259027845 1.074407473 1.454695991 0.979489072 1 18.80632522 1.539881589 0.577042005 0.988522308 1.465094809 0.525391919 0.152530483 0.641908122 0.498875143 0.149884456 0.081105079 34.66423254 -1.539881589 0.476572501 KDEQEHEFYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEQEHEFYK 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 134.38 0.00011175 1419630000 3128600 2891600 2421880 2759400 2765800 2468990 3361300 3383400 4199000 4253600 FALSE TRUE 3006330.853 2809134.399 2859567.59 2901812.965 2854764.469 2518914.669 3402436.595 3313531.608 3722347.124 3965499.883 0.758121534 0.708393515 0.721111505 0.731764733 0.719900278 0.635207349 0.858009506 0.835589889 0.938682949 1 21.91907131 1.540165362 1.147058482 0.990887643 0.715663518 0.832571566 0.044371685 0.164680765 0.416261965 0.038398609 0.013718301 34.68688991 -1.540165362 -0.275224124 NDIHTLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDIHTLLK 8 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2;H0YAH9 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 140.75 0.00064449 846620000 1937850 1695540 1710690 1768860 1765340 1889100 1993960 2209600 2699500 2667900 FALSE TRUE 1862116.68 1647184.859 2019849.737 1860151.077 1822123.764 1927298.896 2018362.679 2163970.988 2393064.077 2487200.757 0.748679685 0.662264538 0.812097589 0.747889398 0.732600197 0.774886744 0.811499704 0.870042751 0.962151556 1 21.24609153 1.54071327 0.980568104 1.005655314 0.738990823 0.878975628 0.034698046 0.153677657 0.288805308 0.030773176 0.011610135 34.73067864 -1.54071327 -0.266664491 LPS(ph)VEEAEVPKPLPPASKDEDEDIQSILR ddPTM_BT-474_Pertuzumab_2h_R1 4 LPSVEEAEVPKPLPPASKDEDEDIQSILR 29 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR 211.25 3.81E-26 767210000 732756 654242 734667 722427 930775 796353 622847 731885 733469 607487 TRUE FALSE 704119.0854 635583.6587 867437.6695 759711.544 960714.2232 812455.8033 630469.5879 716771.319 650208.6741 566341.3644 1.243276811 1.12226247 1.531651622 1.3414375 1.696351853 1.434569068 1.113232456 1.265617107 1.148086145 1 19.11131238 1.540912527 1.069837533 1.042741494 1.387111289 0.360638686 0.162588912 0.558410038 1.234697187 0.154486654 0.056409593 34.74661695 -1.540912527 0.344369795 VPFSPGPAPPPHMGELDQER ddPTM_BT-474_Pertuzumab_2h_R1 1 VPFSPGPAPPPHMGELDQER 20 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 92.492 0.0016448 169130000 74242 79309 68337 56717 76572 75831 70453 69957 64215 70599 FALSE TRUE 71340.54056 77047.18497 80687.01605 59644.17117 79035.00792 77364.35478 71315.22489 68512.3635 56925.58241 65817.26685 1.083918309 1.170622675 1.225924745 0.906208568 1.200824825 1.17544162 1.083533673 1.04094817 0.864903469 1 16.0061785 1.540917381 2.700637206 0.934333177 1.124576025 0.402544223 0.090607005 0.232849858 3.678036663 0.064940246 0.023696601 34.74700534 -1.540917381 0.190242848 YWGPAS(ph)PTHK ddPTM_BT-474_Pertuzumab_2h_R1 5 YWGPASPTHK 10 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.889)PT(0.111)HK;YWGPAS(0.971)PT(0.029)HK;YWGPAS(0.966)PT(0.034)HK;YWGPAS(0.882)PT(0.118)HK;YWGPAS(0.949)PT(0.051)HK 167.11 5.60E-06 6687510000 3543440 3565220 3674120 4217670 4174250 3861530 4021320 3764350 3753630 3792440 TRUE FALSE 3404958.447 3463543.416 4338115.214 4435344.454 4308518.542 3939612.782 4070534.117 3686614.857 3327533.659 3535574.661 0.963056582 0.979626722 1.22699013 1.254490395 1.218619024 1.114277921 1.15130764 1.042720126 0.941157797 1 21.75351329 1.540929274 3.303683161 0.97274069 1.135218942 0.323113773 0.09289742 0.265683713 6.415330705 0.069692564 0.027125194 34.74795687 -1.540929274 0.162478252 LLDSDQELYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDSDQELYR 10 0 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 125.97 0.0073611 0 106680 112310 79675 103290 101670 101260 102610 102980 100730 116690 FALSE TRUE 102510.8277 109107.0288 94074.04486 108620.8093 104940.3079 103307.5466 103865.7719 100853.427 89295.55269 108786.4824 0.942312183 1.002946565 0.864758588 0.99847708 0.964644739 0.949635877 0.954767262 0.927076828 0.820833166 1 16.73113978 1.540969191 5.064208941 0.899728834 0.953836126 0.090013832 0.053852565 0.267052177 14.81243694 0.028855664 0.012775656 34.7511508 -1.540969191 0.054107291 EQSEVSVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQSEVSVSPR 10 0 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 EQSEVSVS(1)PR;EQSEVSVS(1)PR;EQSEVSVS(1)PR;EQSEVSVS(1)PR 197.38 3.32E-07 14462800000 3399030 3703040 2890240 3538350 3520630 3640090 3603430 3422160 3456840 3542580 TRUE FALSE 3266192.15 3597432.925 3412570.661 3720964.668 3633874.261 3713695.114 3647529.854 3351491.2 3064434.015 3302637.901 0.988964654 1.089260474 1.03328635 1.126664436 1.100294483 1.1244633 1.104429236 1.014792206 0.927874659 1 21.65518737 1.541166598 3.977448979 0.964815173 1.083319263 0.548759374 0.043067396 0.129041139 4.530407549 0.026977195 0.011180546 34.76695041 -1.541166598 0.11850409 DGEEKEPPMEEDVGDTDVLQGYQWLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGEEKEPPMEEDVGDTDVLQGYQWLLR 27 1 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 0 76.198 0.014345 41924000 30637 25522 22615 25321 30525 25141 26821 29768 36152 31438 FALSE TRUE 29439.67217 24794.13755 26702.03357 26627.81984 31506.86435 25649.36825 27149.24342 29153.2804 32048.17652 29308.67626 1.004469527 0.845965793 0.911062422 0.90853028 1.075001275 0.875145913 0.926321038 0.994697957 1.093470624 1 14.83904019 1.541379452 3.764569698 1.047018177 0.933284888 0.324580032 0.06475517 0.208316579 6.558916419 0.040696057 0.016567951 34.7839944 -1.541379452 -0.113733289 QGYACPYYHNS(ph)KDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGYACPYYHNSKDR 14 1 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPYYHNS(1)KDR 62.203 0.047786 87774000 98581 70802 63399 67277 60088 79061 77143 83786 102110 97162 TRUE FALSE 94728.34553 68782.79628 74856.6096 70749.17403 62020.78509 80659.66759 78087.09911 82055.78982 90518.90088 90581.1312 1.045784528 0.759350158 0.826404005 0.781058628 0.684698726 0.89046876 0.86206805 0.905881708 0.999312988 1 16.46692294 1.541404747 1.334563278 1.007755979 0.819537135 0.348907517 0.089263957 0.430105015 1.469902219 0.076689871 0.026511389 34.78602035 -1.541404747 -0.188218844 LFNPNDDGKEEPPTTLLWVQYYLAQHYDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFNPNDDGKEEPPTTLLWVQYYLAQHYDK 29 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 228.41 4.33E-35 310370000 485640 401720 380610 330960 419980 457640 459920 431870 613930 543160 FALSE TRUE 466660.6519 390263.3389 449394.6936 348040.8853 433489.0381 466893.7944 465548.6385 422951.7336 544239.2402 506371.2894 0.921578023 0.770705897 0.887480596 0.687323497 0.856069543 0.922038441 0.91938198 0.8352601 1.074782974 1 18.94983608 1.541931777 0.797989869 1.021686867 0.825224041 0.419062521 0.079403565 0.575510719 0.750526392 0.072027372 0.030229572 34.82825996 -1.541931777 -0.196462825 TKDGVVEITGK ddPTM_BT-474_Pertuzumab_2h_R1 6 TKDGVVEITGK 11 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 164.68 2.05E-05 29551160000 33908100 30347460 28374760 26741390 27068940 31511510 30919110 35170700 44088100 39959600 FALSE TRUE 32582933.96 29481980.15 33502710.33 28121516.34 27939637.04 32148694.32 31297507.32 34444412.75 39083403.72 37253100.7 0.874636832 0.791396678 0.899326759 0.7548772 0.74999494 0.862980362 0.840131606 0.924605257 1.049131562 1 25.15085718 1.542067898 2.117033796 1.026233078 0.819740227 0.734799852 0.048145176 0.144145021 1.335827035 0.038255029 0.013226672 34.83917788 -1.542067898 -0.206492851 EIHITNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIHITNPR 8 0 Q92609;Q92609-2;C9J3F6;C9J397;C9JWX0;C9JW04;C9JDR8 Q92609 TBC1D5 TBC1 domain family member 5 0 ; 124.23 0.0013137 488810000 99901 112489 110762 128478 112546 111837 117065 111583 102381 121451 FALSE TRUE 95996.75847 109280.9239 130779.1573 135108.765 116166.1443 114098.4208 118497.6765 109278.7721 90759.1381 113225.0156 0.847840541 0.965165898 1.155037662 1.193276629 1.025975962 1.007713889 1.046567986 0.965146893 0.801582032 1 16.78883321 1.542360432 4.045573684 0.895437137 1.040596084 0.219511874 0.100433737 0.254200038 9.235419372 0.065672096 0.027401252 34.86265291 -1.542360432 0.145158946 YIENHIPSNDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YIENHIPSNDLR 12 0 Q8IY18 Q8IY18 SMC5 Structural maintenance of chromosomes protein 5 0 105.17 0.0010042 0 165520 195370 158000 184890 171120 179680 195870 171840 163610 189800 FALSE TRUE 159051.2954 189798.2389 186554.1147 194432.1951 176624.2302 183313.2527 198267.1157 168291.4439 145037.6787 176944.6769 0.898875842 1.072641699 1.054307583 1.098830428 0.998189 1.035991904 1.12050342 0.951096393 0.819678112 1 17.43293884 1.542558202 5.931034537 0.902317168 1.042148073 0.371989369 0.070300662 0.122663315 8.897130754 0.037161608 0.016920447 34.87853236 -1.542558202 0.139830905 (ac)S(ph)KGPAVGIDLGTTYSCVGVFQHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKGPAVGIDLGTTYSCVGVFQHGK 24 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 1 S(1)KGPAVGIDLGTTYSCVGVFQHGK;S(1)KGPAVGIDLGTTYSCVGVFQHGK 150.83 1.87E-61 914070000 1457090 1283330 1019190 949730 1096580 792660 1268860 1288760 1574510 1547420 TRUE FALSE 1400145.312 1246730.685 1203380.305 998745.6791 1131852.492 808688.1283 1284388.688 1262146.656 1395778.226 1442611.865 0.970562731 0.864217684 0.834167758 0.692317666 0.784585597 0.560572215 0.890321728 0.874903837 0.967535523 1 20.46025176 1.542589419 1.865867553 0.984533844 0.787408033 0.332939436 0.105257876 0.386814177 2.70908961 0.090733952 0.030933625 34.88103947 -1.542589419 -0.197125811 AREEEEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AREEEEQK 8 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 116.3 0.0020949 101630000 115340 90999 97605 105620 107710 99736 125170 127480 137630 153160 FALSE TRUE 110832.3853 88403.79762 115244.3947 111071.0609 111174.59 101752.7303 126701.8679 124847.4935 122006.8194 142786.3368 0.77621142 0.619133452 0.807110801 0.777882978 0.778608041 0.712622318 0.887352885 0.874365827 0.854471248 1 17.12349841 1.542795445 0.331482672 1.018096636 0.695932355 0.660355619 0.057477579 0.763432986 0.283693621 0.090821704 0.080028694 34.89759075 -1.542795445 -0.322164281 LSDVDANTAIKHEEQS(ph)NEDIPIAEQSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSDVDANTAIKHEEQSNEDIPIAEQSSK 28 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LS(0.007)DVDANT(0.016)AIKHEEQS(0.978)NEDIPIAEQSSK 146.59 5.23E-08 153670000 231670 205790 175460 149580 198040 211710 189160 236570 303480 260220 TRUE FALSE 222616.0803 199921.0707 207169.5251 157299.8417 204410.1365 215990.9213 191474.9967 231684.7468 269030.2227 242595.0676 0.917644709 0.824093716 0.853972536 0.648404946 0.842598073 0.890335172 0.789278193 0.955026617 1.10896823 1 17.88819069 1.543290026 3.577821917 1.0520362 0.821831479 0.622296994 0.072965406 0.123981978 3.532428331 0.047876086 0.019201248 34.93735526 -1.543290026 -0.230204722 YSCPESPSQELGGPLPS(ph)PGPR ddPTM_BT-474_Pertuzumab_2h_R1 3 YSCPESPSQELGGPLPSPGPR 21 0 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 YSCPESPSQELGGPLPS(1)PGPR;YSCPESPSQELGGPLPS(1)PGPR;YSCPESPSQELGGPLPS(1)PGPR 252.1 2.62E-36 414180000 235385 305087 218822 344017 275949 312732 254912 246362 180621 205145 TRUE FALSE 226185.894 296386.2175 258368.0031 361771.7586 284825.1502 319055.6553 258031.6893 241274.5386 160117.6613 191250.3464 1.182669199 1.549729049 1.35094136 1.891613612 1.489279133 1.668261843 1.34918286 1.26156393 0.837215013 1 17.54510284 1.543473519 1.954704617 0.919834353 1.524700658 0.600963005 0.186809422 0.199679107 1.551374765 0.14793649 0.05068262 34.95211966 -1.543473519 0.604866305 LSQECEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSQECEK 7 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 99.305 0.024721 148340000 100920 81137 78036 84862 85409 77696 94682 98234 128510 113400 FALSE TRUE 96975.93483 78823.0522 92138.8411 89241.73799 88156.25805 79267.06635 95840.74664 96205.43357 113922.0836 105719.317 0.917296267 0.745587982 0.871542153 0.844138427 0.833870863 0.749787916 0.906558511 0.910008088 1.077590045 1 16.68987948 1.543646049 1.977773184 1.03616161 0.829379641 0.655691 0.057080027 0.168621452 1.344875155 0.043015909 0.01475824 34.96600772 -1.543646049 -0.206781969 LFEELGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFEELGK 7 0 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 121.52 0.010306 43027000 445728 453000 380736 423507 388964 437932 399804 479890 545170 536030 FALSE TRUE 428308.457 440080.8835 449543.4646 445364.247 401475.3803 446787.2851 404696.9209 469980.1038 483284.5871 499724.2107 0.857089666 0.880647513 0.89958312 0.891220072 0.803393896 0.894067719 0.809840533 0.940478956 0.967102607 1 18.93077259 1.544268498 4.487014277 0.976189515 0.864501772 0.702038689 0.032574051 0.091932441 4.077839413 0.019267369 0.008305629 35.01615837 -1.544268498 -0.111687743 VEVGKDQEFTVDTR ddPTM_BT-474_Pertuzumab_2h_R1 5 VEVGKDQEFTVDTR 14 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ;;;; 197.47 2.13E-08 3086169000 5834470 5434230 4867190 4942880 4943450 5592570 5280320 5888600 6617500 6397920 FALSE TRUE 5606452.462 5279251.081 5746799.503 5197982.629 5102460.559 5705655.597 5344942.136 5766998.352 5866309.143 5964583.18 0.939957126 0.88509975 0.963487193 0.871474581 0.855459704 0.956589157 0.89611327 0.966873657 0.983523738 1 22.50798989 1.544454401 1.868394408 0.996576817 0.908005027 0.500212766 0.034024571 0.259926346 1.828006651 0.027411299 0.009360377 35.03115049 -1.544454401 -0.08857179 KDGNASGTTLLEALDCILPPTRPTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDGNASGTTLLEALDCILPPTRPTDK 26 2 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 215.79 2.31E-34 994190000 1000380 913350 976090 1097280 1078450 984630 1222530 1404360 1627820 1756500 FALSE TRUE 961284.0436 887302.1523 1152491.176 1153910.752 1113139.324 1004539.893 1237491.688 1375359.475 1443036.698 1637530.69 0.587032688 0.541853754 0.703798214 0.704665115 0.679766999 0.613447979 0.755705951 0.839898442 0.881227269 1 20.64309052 1.54478454 0.677868122 1.004769896 0.621272482 0.859906685 0.050463657 0.241372483 0.24017696 0.051614243 0.024330978 35.05779037 -1.54478454 -0.383497415 AEFAER ddPTM_BT-474_Pertuzumab_2h_R1 5 AEFAER 6 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;A0A494C034;A0A2R8Y6A3;A0A494C0I0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;; 144.9 0.026088 11429890000 7700080 8329130 6658320 8142630 7656400 7777070 8071630 7810980 7966610 8381490 FALSE TRUE 7399152.361 8091591.367 7861626.538 8562872.11 7902675.059 7934327.684 8170413.022 7649680.533 7062273.832 7813804.217 0.946933421 1.03555082 1.006120235 1.095864687 1.011373569 1.015424429 1.045638308 0.978995675 0.903820167 1 22.89759368 1.545505085 4.838812105 0.94866464 1.024132899 0.328491454 0.041210998 0.156441702 7.977614623 0.02304353 0.010136422 35.1160036 -1.545505085 0.075468259 EPVQTLYSQSPALELDKFLEDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPVQTLYSQSPALELDKFLEDVR 23 1 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 0 ; 136.77 9.18E-06 207786000 155647 157689 143901 138756 164253 146780 158674 170721 204942 187077 FALSE TRUE 149564.1432 153191.8641 169907.1118 145917.2138 169536.3469 149747.9922 160615.8999 167195.5517 181677.8433 174406.1082 0.857562529 0.878362953 0.974203906 0.836651969 0.972078035 0.858616672 0.920930474 0.958656514 1.041694269 1 17.41209104 1.546528131 2.420678937 1.019897915 0.899803232 0.538342438 0.044929557 0.191191264 2.395818613 0.031812416 0.01134703 35.19882217 -1.546528131 -0.120094683 ATLENITNLRPVGEDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATLENITNLRPVGEDFR 17 1 Q9NWV4 Q9NWV4 C1orf123 UPF0587 protein C1orf123 0 ; 112.3 0.00042648 885490000 566280 586640 523450 534920 583570 540460 560070 562900 565320 578360 FALSE TRUE 544149.1515 569909.6016 618049.0591 562527.2853 602341.059 551388.4715 566924.3042 551275.9183 501147.2436 539187.1621 1.009202722 1.056979175 1.14626071 1.043287609 1.117127969 1.02262908 1.051442512 1.022420334 0.92944951 1 19.04042662 1.546599991 2.348429358 0.965180098 1.067677295 0.458215994 0.042315837 0.228052424 2.672820469 0.031855804 0.011284158 35.20464677 -1.546599991 0.102497197 ELREELGEAAAAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELREELGEAAAAFR 14 1 Q96DE0-3;Q96DE0;Q96DE0-2;Q96DE0-4 Q96DE0-3 NUDT16 U8 snoRNA-decapping enzyme 0 ; 190.44 5.51E-07 187326000 151527 188534 131531 188236 182596 201008 157830 164824 152497 148041 FALSE TRUE 145605.1573 183157.1949 155301.5776 197950.8825 188469.3662 205072.5195 159761.5708 161420.3268 135186.1799 138014.0512 1.055002415 1.327090925 1.125259176 1.434280646 1.365581001 1.485881457 1.157574677 1.169593425 0.979510265 1 17.07445563 1.546613958 1.80567612 0.989937967 1.297204451 0.446427084 0.12825313 0.298512703 1.948947216 0.106822457 0.036458978 35.20577898 -1.546613958 0.307266485 FNVWDTAGQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 FNVWDTAGQEK 11 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 234.39 3.95E-15 1383470000 1919250 1748470 1625290 1620550 1510600 1355600 1856280 1827240 2197400 2110270 FALSE TRUE 1844243.588 1698605.348 1919016.057 1704186.78 1559189.821 1383011.161 1878997.71 1789506.855 1947960.364 1967339.533 0.937430249 0.863402234 0.975437145 0.866239279 0.792537228 0.702985498 0.955095792 0.909607531 0.990149555 1 20.90781454 1.546694392 1.779796947 0.993597895 0.862575999 0.30795923 0.074954922 0.439232768 2.77778701 0.066399864 0.022647576 35.21229993 -1.546694392 -0.131021896 DTLVQGLNEAGDDLEAVAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DTLVQGLNEAGDDLEAVAK 19 0 E7ETZ4;Q9Y6E2;Q75MG1;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;;; 295.09 2.70E-49 161064000 260835 251320 222063 228763 223835 259354 252449 286390 337503 328913 FALSE TRUE 250641.2798 244152.5997 262194.7239 240569.4858 231034.8561 264598.3156 255538.5464 280475.9464 299191.0744 306635.4295 0.817391781 0.796230886 0.855069893 0.784545629 0.753451277 0.86290849 0.833362755 0.914688648 0.975722456 1 18.22616487 1.546830718 1.248990183 1.002966264 0.806697229 0.858945919 0.029006293 0.144952113 0.433160623 0.025656453 0.009002654 35.22335488 -1.546830718 -0.196269035 DEDDEDGDGDGDGATGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEDDEDGDGDGDGATGK 17 0 F8VQZ7;P50579-3;P50579;F8VY03;G3V1U3 F8VQZ7 METAP2 Methionine aminopeptidase 2 0 312.62 8.47E-58 173950000 443800 347320 466750 373870 346960 386920 543020 556790 750850 774740 FALSE TRUE 426455.8054 337414.7737 551102.1078 393165.4755 358120.2835 394743.7875 549665.6412 545292.0919 665616.6558 722266.1697 0.59044134 0.46716126 0.763018027 0.544349842 0.495828683 0.546535064 0.761029194 0.754973879 0.921566984 1 19.46217107 1.547304522 1.082741162 0.993730112 0.567951359 0.769843098 0.083520827 0.217095428 0.49047878 0.07487963 0.027299831 35.26180359 -1.547304522 -0.425778753 RPPQADAS(ph)PPYAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPPQADASPPYAR 13 1 Q9P2Y4 Q9P2Y4 ZNF219 Zinc finger protein 219 1 RPPQADAS(1)PPYAR 70.451 0.018491 0 158760 187470 187790 215840 199180 162890 164790 183590 152810 142460 TRUE FALSE 152555.4837 182123.5392 221727.8304 226979.5283 205586.8056 166183.7474 166806.7493 179798.8023 135463.6494 132811.0573 1.148665531 1.371298014 1.66949827 1.709040895 1.547964528 1.251279455 1.255970344 1.353793923 1.019972675 1 17.01901574 1.547374477 0.827101376 0.993284891 1.48483842 0.487892358 0.169075348 0.523365699 0.724504088 0.168620176 0.069387262 35.26748392 -1.547374477 0.491553528 RQLIPTLLS(ph)PQDLGPPGGSAPGPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQLIPTLLSPQDLGPPGGSAPGPTR 25 1 A0A087WTE6 A0A087WTE6 SRCIN1 1 RQLIPT(0.056)LLS(0.944)PQDLGPPGGSAPGPTR;RQLIPT(0.112)LLS(0.888)PQDLGPPGGSAPGPTR 120.69 0.00011656 306900000 431560 527710 368650 398690 465550 558210 438300 441610 415880 428010 TRUE FALSE 414694.1581 512660.2275 435273.2556 419266.4387 480524.8386 569497.3887 443664.0465 432490.5992 368671.0459 399020.5015 1.039280329 1.28479671 1.090854365 1.05073909 1.204261026 1.427238416 1.111882835 1.083880647 0.92394011 1 18.60610335 1.547754896 2.514678296 0.966684922 1.180876317 0.357260407 0.111951915 0.283494263 3.868438827 0.085853452 0.030956127 35.29838988 -1.547754896 0.214191395 DIAAYR ddPTM_BT-474_Pertuzumab_2h_R1 3 DIAAYR 6 0 P26583;P09429;P23497 P26583;P09429;P23497 HMGB2;HMGB1;SP100 High mobility group protein B2;High mobility group protein B1;Nuclear autoantigen Sp-100 0 ;; 131.42 0.035677 11557690000 2448340 2651170 2208120 2587560 2359960 2277920 2404160 2472130 2302230 2289820 FALSE TRUE 2352656.166 2575561.227 2607176.403 2721104.282 2435870.257 2323981.103 2433582.829 2421079.652 2040890.502 2134728.452 1.102086855 1.206505317 1.221315246 1.274684037 1.141067968 1.088654204 1.139996437 1.134139403 0.956042208 1 21.02562113 1.548282972 0.792366387 0.980125206 1.191645793 0.604476181 0.057944277 0.416356574 0.535303622 0.055751467 0.0235517 35.34133675 -1.548282972 0.211520587 S(ph)LPS(ph)SPERR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.869)S(0.131)PERR 89.44 0.042363 329680000 305790 365190 286190 404680 358910 361400 340930 345580 342700 339070 TRUE FALSE 293839.3887 354775.1388 337910.8993 425565.5833 370454.6661 368707.7556 345102.4033 338443.6522 303798.1327 316104.4869 0.929564119 1.12233503 1.068984824 1.346281375 1.171937386 1.166411016 1.091735226 1.070670194 0.961068714 1 18.27004199 1.548430011 1.89192342 0.98078238 1.140056795 0.257359246 0.0984359 0.434983744 3.153198342 0.083096171 0.028498351 35.35330425 -1.548430011 0.159274415 LS(ph)LHEEEGSSGSEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSLHEEEGSSGSEQK 15 0 Q12955;A0A087WY90;H0Y951;A0A087WX55;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 LS(1)LHEEEGSSGSEQK 152.01 1.87E-06 309750000 138790 144800 128740 119920 145660 138730 154790 155710 195550 187620 TRUE FALSE 133365.9334 140670.4458 152006.1818 126109.0856 150345.2862 141535.2157 156684.3663 152494.5341 173351.9838 174912.3303 0.762473024 0.804234016 0.869042117 0.720984538 0.859546528 0.809178035 0.895787999 0.8718341 0.991079265 1 17.41627247 1.548722502 0.805365818 1.008119788 0.798831482 0.727291081 0.044553574 0.286927526 0.379232509 0.038517615 0.01611082 35.3771222 -1.548722502 -0.209288305 AETEQGEQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 AETEQGEQQR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 163.88 1.47E-05 68794000 54167 64110 57495 77288 67977 66427 67539 64873 64287 68560 FALSE TRUE 52050.09376 62281.64557 67885.62547 81276.84294 70163.54194 67770.19945 68365.56249 63533.34988 56989.40927 63916.37013 0.814346836 0.974424008 1.062100763 1.271612308 1.097739778 1.060294871 1.069609591 0.994007478 0.891624621 1 15.96389786 1.548772881 3.94672158 0.944292732 1.057957846 0.125342858 0.109469127 0.365490053 12.71361152 0.073186712 0.030507912 35.38122624 -1.548772881 0.113665114 DASSS(ph)PASTASSASSTSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DASSSPASTASSASSTSLK 19 0 Q04724;A0A669KBK8 Q04724 TLE1 Transducin-like enhancer protein 1 1 DASSS(1)PASTASSASSTSLK;DAS(0.004)S(0.188)S(0.808)PASTASSASSTSLK 315.94 1.14E-61 761510000 565890 541220 524530 493360 510070 601960 591680 652510 815560 791020 TRUE FALSE 543774.3932 525784.9355 619324.2391 518822.3687 526476.8648 614132.0436 598921.1568 639035.4405 722981.0479 737443.5108 0.737377691 0.712983337 0.839826007 0.703541846 0.713921618 0.832785203 0.812158692 0.866555107 0.980388379 1 19.49217302 1.548938494 0.932943295 1.009660796 0.746650936 0.822153331 0.043007854 0.204897647 0.350836656 0.038877949 0.015034249 35.39472109 -1.548938494 -0.263009861 DQQNLPYGVTPAS(ph)PSGHSQGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DQQNLPYGVTPASPSGHSQGR 21 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 DQQNLPYGVTPAS(0.725)PS(0.275)GHSQGR;DQQNLPYGVTPAS(0.998)PS(0.001)GHSQGR;DQQNLPYGVTPAS(1)PSGHSQGR;DQQNLPYGVTPAS(0.959)PS(0.035)GHS(0.006)QGR 347.77 2.97E-95 2029580000 1031150 1269450 1028290 1324430 1364840 1291790 1190510 1198560 1139600 1173330 TRUE FALSE 990851.518 1233246.529 1214124.877 1392783.991 1408741.318 1317910.879 1205079.818 1173809.317 1010237.386 1093859.314 0.905830855 1.127427004 1.109946098 1.27327525 1.287863348 1.204826674 1.101677155 1.073089841 0.923553306 1 20.06099577 1.549070223 2.17737194 0.964034333 1.157524885 0.325843343 0.102785819 0.338672249 3.362504552 0.085558658 0.029923351 35.40545855 -1.549070223 0.193490552 TKDLGHNDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKDLGHNDK 9 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 0 ; 120.09 0.00043343 136568000 424620 407420 345280 317430 354380 356180 361390 406590 479660 425690 FALSE TRUE 408025.381 395800.7805 407679.7767 333812.6003 365778.9545 363382.2036 365812.7989 398193.7744 425211.0077 396857.6371 1.028140428 0.997336938 1.027269576 0.841139414 0.921688082 0.915648761 0.921773363 1.003366792 1.071444689 1 18.59826204 1.549304629 4.666647343 1.036516527 0.948815235 0.279384277 0.056215179 0.210510421 10.04372932 0.035391813 0.015483662 35.42457341 -1.549304629 -0.087701292 AVTFSPDLGPVPHEGLGEYNR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVTFSPDLGPVPHEGLGEYNR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 0 ; 176.73 2.93E-14 956890000 300330 302491 266367 296960 299812 311068 308914 295138 309140 299870 FALSE TRUE 288592.7716 293864.2528 314505.4422 312286.1412 309455.7253 317358.0081 312694.5819 289043.2972 274047.7232 279559.5378 1.032312379 1.051168761 1.125003442 1.117064879 1.106940324 1.135207228 1.118525894 1.033923934 0.980283933 1 18.09279604 1.549315549 3.603339892 0.99292314 1.099557881 0.662918586 0.031393191 0.123896844 3.605073895 0.022274656 0.009016945 35.42546417 -1.549315549 0.106634741 APS(ph)PDPDLVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 APSPDPDLVQR 11 0 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 APS(1)PDPDLVQR;APS(1)PDPDLVQR 128.68 0.00027364 415940000 412720 472220 355260 417310 424660 433520 423220 424300 416980 455500 TRUE FALSE 396590.4461 458752.748 419463.3847 438847.4191 438319.5746 442286.0714 428399.493 415538.0567 369646.1785 424648.5793 0.933926229 1.08031151 0.987789446 1.033436683 1.032193668 1.041534325 1.008832983 0.978545736 0.870475486 1 18.6959099 1.549549463 3.609445755 0.932337384 1.020097295 0.322544317 0.046597086 0.184347741 5.383512665 0.027300064 0.011060484 35.44454965 -1.549549463 0.08775991 MEPGEELEEEGS(ph)PGGREDGFTAEHLAAEAMAADMDPWLVFDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEPGEELEEEGSPGGREDGFTAEHLAAEAMAADMDPWLVFDAR 43 1 Q9H3H3-1;Q9H3H3;Q9H3H3-3 Q9H3H3-1 C11orf68 UPF0696 protein C11orf68 1 MEPGEELEEEGS(0.988)PGGREDGFT(0.012)AEHLAAEAMAADMDPWLVFDAR;MEPGEELEEEGS(0.998)PGGREDGFT(0.002)AEHLAAEAMAADMDPWLVFDAR;MEPGEELEEEGS(0.784)PGGREDGFT(0.216)AEHLAAEAMAADMDPWLVFDAR 99.983 1.74E-05 62697000 15766.8 15896 13657 18034.5 16249.6 18300.9 16314.3 14603.3 13427.6 13354 TRUE FALSE 15150.61602 15442.66164 16125.1237 18965.26271 16772.28314 18670.95674 16513.95928 14301.73675 11903.35514 12449.52169 1.216963704 1.240422085 1.29524042 1.5233728 1.347223095 1.499732858 1.326473394 1.14877801 0.956129516 1 13.60380269 1.549821361 2.540951174 0.981272582 1.357241156 0.720280499 0.093784333 0.140673329 1.968599103 0.075188193 0.027246636 35.4667473 -1.549821361 0.375968574 ILQINKDDVTALHCK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILQINKDDVTALHCK 15 1 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 180.74 3.71E-07 1549200000 2675640 2613910 2057680 2204220 2434570 2780470 2571470 2718240 3335040 3223430 FALSE TRUE 2571073.031 2539363.846 2429548.549 2317980.058 2512880.155 2836693.008 2602940.419 2662107.394 2956460.241 3005104.215 0.855568675 0.845016899 0.808473975 0.771347645 0.836203997 0.943958281 0.866173095 0.885861921 0.983812883 1 21.51898359 1.550065154 0.591923344 1.00433075 0.821619681 0.6932386 0.039223387 0.450918375 0.362852531 0.041157814 0.021836763 35.48666237 -1.550065154 -0.182711069 YRPDLVDMER ddPTM_BT-474_Pertuzumab_2h_R1 1 YRPDLVDMER 10 1 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;E9PNZ4;E9PLY5;A0A5F9ZGX0;E9PLY0 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 71.153 0.047584 0 79467 69276 62934 87582 83627 84913 86237 74247 68592 81797 FALSE TRUE 76361.34178 67300.31631 74307.57376 92102.11752 86316.9384 86629.99904 87292.3942 72713.7735 60805.72372 76256.81633 1.001370703 0.882548204 0.974438448 1.207788653 1.131924234 1.13602958 1.144715953 0.953538018 0.797380833 1 16.21857868 1.5501552 5.386669325 0.891605216 1.067636296 0.326679889 0.101302722 0.173905295 10.68870336 0.06317583 0.028491263 35.49402081 -1.5501552 0.17603108 ISMPDLDLNLKGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISMPDLDLNLKGPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 64.104 0.058176 332970000 299420 315930 281190 309380 273030 320540 341220 307070 309410 356350 FALSE TRUE 287718.3354 306919.9857 332007.288 325347.1389 281812.2579 327021.5384 345395.9524 300728.8972 274287.074 332214.0971 0.866062993 0.923862017 0.999377483 0.979329721 0.848285068 0.984369842 1.039678796 0.905226177 0.825633459 1 18.34175377 1.55041433 11.75839107 0.897384047 0.950015582 0.054126397 0.068027343 0.276311661 49.17389465 0.036203474 0.016822472 35.51520536 -1.55041433 0.052631536 WRCPVPT(ph)LPGCQK ddPTM_BT-474_Pertuzumab_2h_R1 4 WRCPVPTLPGCQK 13 1 E5RJ64 E5RJ64 C8orf58 1 WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK 86.313 0.014362 1357410000 1326690 2429510 2888490 1928300 2859950 2887610 1998320 1608530 495943 757740 TRUE FALSE 1274841.488 2360222.754 3410504.397 2027819.794 2951942.889 2945999.453 2022776.038 1575313.293 439645.6298 706417.5949 1.804657043 3.341115469 4.827887105 2.870568073 4.178750516 4.170337027 2.863428166 2.230002912 0.622359399 1 19.43016175 1.550459424 1.927989244 0.794335106 3.563133057 0.631931166 0.802337419 0.194072569 1.469266092 0.651959997 0.224386791 35.51889316 -1.550459424 2.768797951 WDS(ph)YENLSADGEVLHTQGPVDGSLYAK ddPTM_BT-474_Pertuzumab_2h_R1 2 WDSYENLSADGEVLHTQGPVDGSLYAK 27 0 Q68CZ2;E9PCX8;C9JHU5;Q68CZ2-3 Q68CZ2 TNS3 Tensin-3 1 WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(0.999)YENLS(0.001)ADGEVLHTQGPVDGSLYAK 199.29 3.41E-25 1226610000 116405 113049 97931 100715 119095 118281 123615 127798 159448 157932 TRUE FALSE 111855.7639 109824.9532 115629.3102 105912.9132 122925.7988 120672.7229 125127.8373 125158.9266 141348.1315 147235.125 0.759708418 0.745915441 0.785337807 0.719345423 0.834894519 0.819591948 0.849850451 0.850061605 0.960016379 1 17.16776236 1.550769063 0.490107966 1.009240664 0.747498322 0.881364861 0.029412812 0.265752966 0.162742443 0.030156261 0.019222106 35.54422613 -1.550769063 -0.261742342 S(ph)PDKPGGSPSASR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 S(0.991)PDKPGGS(0.003)PS(0.003)AS(0.003)R;S(1)PDKPGGSPSASR;S(1)PDKPGGSPSASR 81.346 0.0092773 823880000 791170 809710 808780 848130 747040 693740 880920 945300 1136400 1114680 TRUE FALSE 760250.2017 786617.8636 954944.5372 891902.0909 771069.22 707767.8981 891700.9625 925779.2247 1007400.636 1039181.731 0.731585419 0.756958904 0.91893892 0.858273452 0.741996512 0.681081929 0.858079907 0.890873268 0.969417193 1 19.98701654 1.550893027 1.769662015 0.989334587 0.789282943 0.592687666 0.065500724 0.258341538 1.616703993 0.059368422 0.020309445 35.55437322 -1.550893027 -0.200051644 FRAESVVPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 FRAESVVPAR 10 1 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 0 ;; 127.83 0.00031526 595670000 413610 518360 406277 464070 460620 499550 474340 448539 430510 462830 FALSE TRUE 397445.6639 503576.8803 479700.2915 488020.7083 475436.2606 509651.2433 480145.1148 439276.5129 381640.3096 431482.1119 0.92111736 1.167086344 1.111750124 1.131033466 1.101867835 1.181164246 1.112781044 1.018064251 0.884486979 1 18.71894122 1.551127168 3.482235907 0.942898663 1.110169368 0.448210049 0.071933951 0.160753775 4.376905353 0.044620094 0.017891774 35.57354677 -1.551127168 0.167270704 MPLLELGGETTPPLSTERS(ph)PEAVGSECPSR ddPTM_BT-474_Pertuzumab_2h_R1 7 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGETTPPLS(0.002)T(0.007)ERS(0.99)PEAVGSECPSR;MPLLELGGETTPPLS(0.035)T(0.035)ERS(0.929)PEAVGSECPSR;MPLLELGGETTPPLST(0.004)ERS(0.996)PEAVGSECPSR;MPLLELGGETTPPLS(0.001)T(0.009)ERS(0.99)PEAVGSECPSR;MPLLELGGETT(0.001)PPLS(0.017)T(0.017)ERS(0.965)PEAVGSECPSR;MPLLELGGETTPPLS(0.002)T(0.007)ERS(0.991)PEAVGSECPSR;MPLLELGGETTPPLS(0.35)T(0.06)ERS(0.59)PEAVGSECPSR 189.76 1.64E-18 3396530000 761517 865959 708125 959852 963849 1027589 854310 868526 754076 919157 TRUE FALSE 731756.0737 841262.6972 836098.9397 1009390.077 994852.0784 1048367.554 864765.3013 850590.6346 668476.4538 856901.6777 0.853955702 0.981749387 0.975723308 1.177953204 1.160987432 1.223439726 1.00917681 0.992635044 0.7801087 1 19.70877015 1.551180568 3.081443635 0.889446677 1.064204466 0.230565609 0.116312909 0.310580343 6.582499144 0.084965125 0.032694227 35.57792115 -1.551180568 0.174757789 KVVDYSQFQES(ph)DDADEDYGR ddPTM_BT-474_Pertuzumab_2h_R1 50 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.001)QFQES(0.999)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.001)QFQES(0.999)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDY(0.002)S(0.003)QFQES(0.995)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(0.999)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR 342.14 1.03E-80 3.75235E+11 57456640.3 59372869.2 46333920.7 53165556.8 56268103 57813044.5 53325552.4 57423533.3 59357718.4 58246539.8 TRUE FALSE 55211171.28 57679613.1 54707490.86 55909437.56 58078017.63 58982063.87 53978166.46 56237717.27 52619679.06 54301449.78 1.016753171 1.062211292 1.007477537 1.029612244 1.069548196 1.086196853 0.994046507 1.035657749 0.96902899 1 25.69448738 1.551182503 1.658503419 0.988262634 1.042328857 0.333851127 0.028622074 0.402514155 2.184116729 0.023949622 0.008182218 35.57807966 -1.551182503 0.054066224 TPVSPVKFS(ph)PGDFWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 TPVS(0.001)PVKFS(0.999)PGDFWGR;TPVS(0.001)PVKFS(0.999)PGDFWGR 107.78 0.00066696 460220000 430520 419400 308290 300160 314600 358670 367740 455220 568840 542330 TRUE FALSE 413694.8024 407439.1226 364004.8609 315651.2936 324719.3947 365922.5531 372240.5121 445819.5479 504267.668 505597.506 0.818229516 0.80585667 0.719949874 0.624313391 0.642248806 0.723742797 0.736238822 0.881767696 0.997369769 1 18.94762982 1.551279403 2.104421663 1.003127977 0.717527279 0.793066083 0.057142826 0.141442731 1.303627664 0.05168755 0.018010864 35.58601871 -1.551279403 -0.285600698 QPSS(ph)PGPTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPSSPGPTPR 10 0 Q13424-2;Q13424 Q13424-2 SNTA1 Alpha-1-syntrophin 1 QPS(0.194)S(0.806)PGPTPR;QPS(0.056)S(0.944)PGPTPR 109.15 0.0029239 0 539150 610680 469180 675710 623560 616570 638380 567160 568110 575250 TRUE FALSE 518079.4219 593264.0043 553971.2629 710583.4741 643617.3737 629037.4678 646192.6854 555447.9478 503620.5345 536287.8051 0.966047367 1.106241833 1.03297382 1.325003976 1.20013427 1.172947551 1.204936378 1.035727351 0.939086307 1 19.03264792 1.551521955 4.385798245 0.97345211 1.148149749 0.367620077 0.093909446 0.181674271 7.73268622 0.058972555 0.025436896 35.60589895 -1.551521955 0.174697639 YQEQGGEAS(ph)PQSR ddPTM_BT-474_Pertuzumab_2h_R1 4 YQEQGGEASPQSR 13 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4 Q9UJU6-2 DBNL Drebrin-like protein 1 YQEQGGEAS(0.92)PQS(0.08)R;YQEQGGEAS(0.984)PQS(0.016)R;YQEQGGEAS(1)PQSR;YQEQGGEAS(0.997)PQS(0.003)R 206.19 6.70E-08 722130000 615386 697140 596491 734830 712230 761410 686029 680588 650510 701333 TRUE FALSE 591336.0348 677258.2498 704290.1926 772754.6644 735139.5248 776806.2319 694424.8281 666533.62 576666.832 653831.0912 0.904417123 1.035830597 1.077174521 1.181887302 1.12435694 1.18808396 1.062085969 1.019427844 0.881981355 1 19.31855846 1.551643495 3.002182651 0.942048348 1.089665357 0.32081704 0.080694355 0.258332367 5.187259949 0.058954181 0.022504046 35.6158649 -1.551643495 0.147617009 YGS(ph)PPQRDPNWNGER ddPTM_BT-474_Pertuzumab_2h_R1 1 YGSPPQRDPNWNGER 15 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 YGS(1)PPQRDPNWNGER 149.36 2.04E-06 1113000000 578090 504370 434530 398730 438300 495040 502390 529080 636460 597210 TRUE FALSE 555497.6037 489985.8614 513059.2371 419308.5031 452398.3176 505050.048 508538.3991 518154.3131 564211.7291 556760.4348 0.997731823 0.880065879 0.921508076 0.753121948 0.812554717 0.907122734 0.913388178 0.930659366 1.013383304 1 19.08669717 1.551768715 1.401534692 1.009654572 0.873052983 0.384311351 0.061773644 0.420124446 1.589941443 0.056212834 0.019402354 35.62613546 -1.551768715 -0.136601588 GILSLPHQAS(ph)PVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GILSLPHQASPVSR 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 GILSLPHQAS(1)PVSR;GILSLPHQAS(0.999)PVS(0.001)R;GILSLPHQAS(1)PVSR;GILSLPHQAS(1)PVSR 209.25 4.44E-09 2961750000 1733620 1988950 1626940 2082750 1907080 1985870 1856050 1854490 1747100 1854320 TRUE FALSE 1665868.214 1932227.093 1920964.249 2190240.977 1968422.96 2026025.652 1878764.895 1816194.133 1548776.532 1728725.255 0.963639658 1.117717861 1.111202745 1.266968809 1.138655755 1.171976661 1.086792068 1.050597328 0.895906697 1 20.72127717 1.552174529 2.399186803 0.950097338 1.131527332 0.451534922 0.075522647 0.231891804 2.866653319 0.057998121 0.020768327 35.65944088 -1.552174529 0.181429995 PAWLWGAEMGANEHGVCIANEAINTR ddPTM_BT-474_Pertuzumab_2h_R1 2 PAWLWGAEMGANEHGVCIANEAINTR 26 0 Q12765;Q12765-2;Q12765-3;C9K052;B8ZZP4;C9J7U9 Q12765 SCRN1 Secernin-1 0 ; 195.24 3.11E-19 648410000 144023 157829 129729 119982 156722 133936 126379 157038 180399 165394 FALSE TRUE 138394.4219 153327.8715 153173.9161 126174.2854 161763.1055 136644.2777 127925.664 153795.1104 159920.8618 154191.7171 0.897547706 0.994397587 0.99339912 0.818294833 1.04910373 0.886197263 0.829653281 0.997427834 1.037155983 1 17.23436574 1.552177767 8.387883541 1.017637892 0.927730094 0.251231817 0.069587785 0.165824309 19.79894284 0.036982101 0.017225794 35.65970675 -1.552177767 -0.089907798 DSCPLDCK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSCPLDCK 8 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 140.09 0.0015242 435540000 327750 299080 243930 250990 288130 301090 307910 317880 377130 369340 FALSE TRUE 314941.1677 290550.5312 288013.5772 263943.624 297397.9631 307178.2461 311678.2947 311315.6669 334319.7835 344324.2728 0.914664438 0.8438282 0.836460279 0.766555381 0.863714779 0.892119059 0.905188275 0.904135118 0.970944571 1 18.39340836 1.552190876 0.76525014 0.999641811 0.842041569 0.67113792 0.036550278 0.365305892 0.442224425 0.035418522 0.015322542 35.66078309 -1.552190876 -0.157600242 RPMEEDGEEKSPSK ddPTM_BT-474_Pertuzumab_2h_R1 3 RPMEEDGEEKSPSK 14 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;; 149.3 4.23E-06 611997000 1069060 1041269 891650 762081 1003317 1032185 887389 1078880 1286760 1083660 FALSE TRUE 1027279.953 1011573.028 1052790.99 801412.0917 1035589.602 1053056.488 898249.132 1056600.751 1140692.399 1010262.743 1.016844341 1.001296974 1.042096224 0.793270956 1.025069577 1.042359025 0.889124278 1.045867284 1.129104688 1 19.94629912 1.552300019 7.410469131 1.071525567 0.973873673 0.197241217 0.079261545 0.181475385 18.32026937 0.042267393 0.019645636 35.66974617 -1.552300019 -0.097651894 ARQEELYSELQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 ARQEELYSELQAR 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 297.03 9.03E-41 3337130000 1100190 1320500 1103070 1457160 1449800 1483920 1408940 1278790 1214480 1352670 FALSE TRUE 1057193.358 1282840.633 1302419.287 1532364.202 1496434.134 1513925.879 1426183.029 1252382.54 1076617.322 1261052.456 0.838342095 1.017277772 1.032803418 1.215147074 1.186654946 1.200525697 1.130946633 0.993124857 0.853745074 1 20.26619686 1.552477087 4.313068655 0.92518519 1.09620629 0.26105316 0.110579364 0.227572261 9.391699906 0.071723247 0.030821238 35.68429218 -1.552477087 0.1710211 RPS(ph)GSQHSPSLQTFAPEADGTIFFPER ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RPS(0.245)GS(0.245)QHS(0.167)PS(0.245)LQT(0.097)FAPEADGTIFFPER 110.55 0.00065635 375940000 71154 119880 116470 149910 123980 128370 137220 111420 104810 114470 TRUE FALSE 68373.22302 116461.1398 137518.7199 157646.8731 127967.9293 130965.7294 138899.3394 109119.1381 92912.4082 106716.8449 0.640697568 1.09130981 1.288631799 1.477244508 1.199135238 1.227226399 1.301569021 1.022510908 0.870644257 1 16.70342839 1.552606255 5.043482424 0.938099703 1.190385478 0.184028345 0.206534085 0.246474751 13.50421181 0.124102868 0.055390755 35.694907 -1.552606255 0.252285775 DMDDEESWIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DMDDEESWIK 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 190.02 2.20E-06 144550000 281410 272010 284910 308650 261970 253890 335300 334590 422670 410620 FALSE TRUE 270412.1861 264252.5411 336399.5748 324579.4635 270396.503 259023.8298 339403.5017 327680.5996 374690.2736 382808.3417 0.706390527 0.690299851 0.878767619 0.847890258 0.706349558 0.676641028 0.886614697 0.855991273 0.978793388 1 18.54626274 1.552641395 1.334002428 0.998181767 0.759884901 0.619372191 0.070532368 0.289846909 0.990151948 0.065290158 0.022699285 35.69779532 -1.552641395 -0.238296866 LEMQS(ph)DEECDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEMQSDEECDR 11 0 E7EPU0;E7EUI1;A0A0A0MSL2;A0A0A0MT14;B4DWF2;Q9UKS7-3;Q9UKS7-6;Q9UKS7-4;Q9UKS7-7;Q9UKS7-2;Q9UKS7 E7EPU0 IKZF2;ZNFN1A2 Zinc finger protein Helios 1 LEMQS(1)DEECDR 206.45 0.00089603 0 53451 51367 41050 53597 50892 50302 56531 45579 41886 47518 TRUE FALSE 51362.07583 49902.06345 48468.64815 56363.14759 52528.9874 51319.1409 57222.84329 44637.77772 37131.27688 44299.56354 1.159426227 1.126468513 1.094111189 1.27231835 1.185767606 1.158457032 1.291724765 1.007634707 0.838186066 1 15.43500486 1.553430818 5.045734938 0.919706351 1.180356719 0.72552264 0.067657285 0.073456724 4.026833011 0.038223447 0.017072139 35.7627427 -1.553430818 0.260650369 SSS(ph)LSDLTHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLSDLTHR 10 0 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 S(0.277)S(0.277)S(0.445)LSDLTHR 146.16 1.88E-05 353540000 164990 208210 176040 219820 224420 219320 197570 197550 182510 195050 TRUE FALSE 158542.0084 202272.0547 207854.344 231164.9365 231638.6731 223754.8007 199987.9208 193470.5235 161792.2299 181839.0898 0.871880785 1.112368385 1.143067446 1.271260964 1.273866216 1.230509903 1.099807093 1.06396553 0.889754948 1 17.47230284 1.553543013 2.391960961 0.947916014 1.157139416 0.32310747 0.11219125 0.311922964 3.835736381 0.089810569 0.032184032 35.7719828 -1.553543013 0.209223402 RGQSS(ph)PPPAPPICLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGQSSPPPAPPICLR 15 1 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 RGQS(0.289)S(0.711)PPPAPPICLR 64.249 0.040572 538900000 240420 256000 215040 207110 224730 299300 268550 231760 232150 242520 TRUE FALSE 231024.1206 248699.1307 253902.5115 217798.9719 231958.6445 305352.0511 271836.5952 226974.075 205797.3053 226093.9044 1.021806055 1.099981582 1.122995829 0.963312003 1.0259394 1.350554107 1.202317223 1.003892943 0.910229339 1 17.78656257 1.553544136 5.755261168 0.955840265 1.112407822 0.287518955 0.103506044 0.18777958 12.87674956 0.062710397 0.028618278 35.77207531 -1.553544136 0.156567557 ST(ph)TPMAPGVFLTQR ddPTM_BT-474_Pertuzumab_2h_R1 1 STTPMAPGVFLTQR 14 0 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 S(0.038)T(0.481)T(0.481)PMAPGVFLTQR 112.62 0.0034691 0 142240 149990 121990 122190 121700 135170 122120 125110 120080 106250 TRUE FALSE 136681.1035 145712.4321 144036.3067 128496.2405 125614.591 137903.23 123614.5411 122526.4348 106449.0218 99053.59286 1.379870226 1.471046409 1.454125009 1.297239573 1.268147751 1.392208258 1.247956157 1.236971131 1.074660885 1 16.59592168 1.553576162 0.411158921 0.973544386 1.44151842 0.833951881 0.059501041 0.404493395 0.195794588 0.073987611 0.055932864 35.77471326 -1.553576162 0.467974034 SQLIDELADKFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQLIDELADKFNR 13 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 0 ; 169.04 2.66E-05 1243870000 1568240 1642660 1264070 1311830 1521810 1554910 1402560 1640550 1829690 1810660 FALSE TRUE 1506951.447 1595812.945 1492515.568 1379533.704 1570760.401 1586351.346 1419724.949 1606672.069 1621991.262 1688022.385 0.892731909 0.945374279 0.884179962 0.817248465 0.930532921 0.93976914 0.841058129 0.951807324 0.960882555 1 20.68690261 1.55375866 5.758219176 0.973022661 0.894821522 0.45443554 0.039715976 0.135845246 9.322758342 0.022664792 0.010345169 35.78974963 -1.55375866 -0.078201139 VTFLIGDSMS(ph)PDSDTELR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTFLIGDSMSPDSDTELR 18 0 A0A087WX11;J3KNG8;Q8TF40-3;Q8TF40 A0A087WX11 FNIP1 Folliculin-interacting protein 1 1 VTFLIGDS(0.413)MS(0.587)PDSDTELR 138.97 2.29E-06 0 31950 36430 31385 37772 36149 39183 37338 35323 36063 36504 TRUE FALSE 30701.35868 35391.05207 37056.96766 39721.41745 37311.76541 39975.30711 37794.95361 34593.56771 31969.27943 34031.55157 0.90214396 1.039948237 1.088900328 1.167193843 1.096387432 1.174654263 1.110585673 1.016514561 0.939401172 1 15.05458531 1.554035084 4.039074512 0.971139123 1.088348161 0.283167625 0.072978368 0.22691877 8.281237019 0.047452443 0.020033147 35.81253663 -1.554035084 0.117209039 SKVDEAVAVLQAHQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKVDEAVAVLQAHQAK 16 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;Q9H361;H0YB75;H0YAS6;H0YAS7;H0YC10 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 185.33 1.01E-09 3518600000 5066900 5013800 5050300 5000400 4868500 5209000 5976300 6424900 7760900 7974400 FALSE TRUE 4868879.946 4870811.333 5963001.553 5258471.243 5025099.724 5314329.549 6049439.747 6292223.57 6879915.168 7434286.785 0.654922266 0.65518206 0.802094636 0.707326929 0.675935684 0.714840536 0.813721601 0.846378913 0.925430424 1 22.82576291 1.554268798 0.889165257 0.997459 0.696889288 0.865409392 0.041369761 0.188527028 0.295654946 0.039329126 0.015595082 35.83181428 -1.554268798 -0.300569712 IPFDLMDTVPAEQLYEAHLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IPFDLMDTVPAEQLYEAHLEK 21 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 110.38 0.00027356 100550000 47370 62810 59262 55893 53276 62171 64157 47589 47652 38947 FALSE TRUE 45518.72803 61018.7203 69971.96168 58777.64443 54989.67092 63428.14022 64942.17256 46606.27052 42242.74473 36309.085 1.253645693 1.680535885 1.927119939 1.618813705 1.514487928 1.746894482 1.788592925 1.283598045 1.1634208 1 15.14804295 1.55438881 3.320133749 1.103031181 1.656251751 0.642293664 0.173789649 0.130938594 3.249793 0.117576849 0.046563546 35.84171731 -1.55438881 0.55322057 ACFCDDHTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ACFCDDHTR 9 0 Q9Y3S2;D6RBR7 Q9Y3S2 ZNF330 Zinc finger protein 330 0 100.57 0.0045715 161380000 162340 183550 193480 128780 162250 160000 181720 185010 159580 173390 FALSE TRUE 155995.5733 178315.3337 228446.1399 135426.3512 167468.9186 163235.3096 183943.9437 181189.4788 141465.1474 161646.1409 0.965043598 1.103121502 1.413248338 0.83779514 1.036021755 1.009831158 1.137942067 1.120901977 0.875153262 1 17.30247954 1.554589896 0.362152945 0.981776543 1.101885539 0.044804747 0.149715377 4.765314793 1.96660985 0.213675258 0.179283641 35.8583165 -1.554589896 0.120108995 FNEGER ddPTM_BT-474_Pertuzumab_2h_R1 2 FNEGER 6 0 P35579 P35579 MYH9 Myosin-9 0 ; 117.62 0.052495 1142510000 1193210 1291320 1105370 1411560 1328960 1319480 1276290 1314090 1341420 1363800 FALSE TRUE 1146578.034 1254492.818 1305134.948 1484410.781 1371707.205 1346160.79 1291909.619 1286953.582 1189147.625 1271428.611 0.90180292 0.986679714 1.026510601 1.167514061 1.078870802 1.058778116 1.016108657 1.012210651 0.93528462 1 20.27801903 1.554933659 2.504445809 0.968729419 1.040153044 0.127651775 0.065698644 0.524827787 7.155791756 0.052879017 0.019197495 35.88671113 -1.554933659 0.071423624 VNGEDPYPHK ddPTM_BT-474_Pertuzumab_2h_R1 4 VNGEDPYPHK 10 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ;;; 91.855 0.009865 2461560000 5210800 4928700 4199330 4651180 4944800 5297800 5133200 5357100 6526100 6338800 FALSE TRUE 5007156.175 4788138.302 4958242.345 4891227.957 5103853.983 5404925.146 5196021.637 5246474.013 5785284.488 5909467.43 0.847310901 0.8102487 0.839033704 0.82769353 0.863674103 0.914621361 0.879270712 0.887808263 0.978985764 1 22.49459669 1.555100107 0.403193234 1.009778907 0.817992123 0.844679982 0.023592549 0.405125692 0.191179682 0.030092653 0.023168363 35.90046771 -1.555100107 -0.191786784 RGAYGGGYGGYDDYNGYNDGYGFGSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 RGAYGGGYGGYDDYNGYNDGYGFGSDR 27 1 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ;; 273.92 1.27E-60 1511270000 638040 678610 517610 517460 604500 660040 589920 611590 636850 618120 FALSE TRUE 613104.6914 659256.7072 611153.6412 544166.1726 623944.2915 673386.461 597139.6174 598960.4528 564557.4579 576254.1818 1.063948359 1.144038044 1.060562614 0.944316223 1.082758809 1.168558047 1.036243443 1.039403221 0.979702145 1 19.13634579 1.555110103 2.199416623 0.991836137 1.073814196 0.244026486 0.057115912 0.438883266 4.480721924 0.04722016 0.01664556 35.90129402 -1.555110103 0.081978059 DKDPPIPVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDPPIPVAK 10 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 83.182 0.014393 1529120000 2898000 3022500 2616900 2719600 2689300 2705600 3017500 3097200 3668500 3476800 FALSE TRUE 2784742.956 2936301.259 3089832.043 2859958.882 2775803.777 2760309.086 3054429.068 3033241.738 3252067.26 3241313.239 0.859140339 0.905898641 0.953265487 0.882345726 0.856382451 0.851602077 0.94234307 0.93580642 1.003317797 1 21.62814702 1.555232094 1.544853935 1.0031485 0.889229121 0.662286369 0.031420759 0.238794942 1.111971077 0.028507022 0.009780851 35.91137995 -1.555232094 -0.11391938 AVDFAER ddPTM_BT-474_Pertuzumab_2h_R1 3 AVDFAER 7 0 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ;; 141.83 0.0058871 2242160000 2506800 2642620 2576160 2687380 2826740 2449960 2742510 2612590 2650610 2727990 FALSE TRUE 2408831.485 2567255.065 3041729.418 2826076.004 2917664.659 2499499.87 2776073.658 2558639.104 2349723.865 2543220.807 0.947157823 1.009450323 1.196014679 1.111219284 1.147232144 0.982808831 1.091558251 1.006062508 0.923916578 1 21.27822529 1.555326044 3.834648354 0.961748576 1.073013619 0.26243217 0.073174528 0.24655334 8.15214765 0.047726727 0.019850382 35.91914942 -1.555326044 0.111265044 AYINKVEELKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYINKVEELKK 11 2 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 140.14 2.18E-05 2938000000 8331700 6961000 6172500 6374200 6472300 5765400 7058300 8761100 10879500 10643800 FALSE TRUE 8006087.953 6762479.096 7288008.057 6703173.226 6680487.407 5881980.338 7144681.587 8580180.223 9644504.771 9922885.945 0.806830593 0.681503257 0.73446456 0.675526582 0.67324037 0.592769117 0.720020529 0.864685966 0.971945543 1 23.24232834 1.555747551 2.231782604 0.987601631 0.690841907 0.840847036 0.051283663 0.104781285 1.106026877 0.041152288 0.014557697 35.95402789 -1.555747551 -0.296759725 EQTLS(ph)PTITSGLHNIAR ddPTM_BT-474_Pertuzumab_2h_R1 3 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQT(0.04)LS(0.893)PT(0.064)IT(0.003)SGLHNIAR;EQT(0.003)LS(0.867)PT(0.127)IT(0.003)SGLHNIAR;EQTLS(0.563)PT(0.418)IT(0.019)SGLHNIAR 239.32 1.80E-20 9654170000 2018420 2348380 1884780 2533930 2470870 2371520 2327010 2277470 2213210 2441170 TRUE FALSE 1939537.915 2281406.502 2225401.673 2664706.431 2550347.778 2419473.759 2355488.644 2230439.449 1961975.679 2275827.382 0.852234194 1.002451469 0.977842911 1.170873702 1.120624437 1.06311831 1.03500321 0.980056513 0.862093362 1 21.1179597 1.555890267 3.7337402 0.928074129 1.038186818 0.17607703 0.086251498 0.30296115 9.516389499 0.057299068 0.023641254 35.96584487 -1.555890267 0.110112688 YNGGVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 YNGGVGR 7 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ;; 122.98 0.021463 461440000 511110 550480 526090 490260 539180 525360 524890 528300 496090 573520 FALSE TRUE 491135.2561 534780.8494 621166.1658 515562.3774 556523.2144 535983.1392 531313.7608 517390.4204 439775.943 534674.9796 0.918567868 1.000198008 1.161764043 0.964253794 1.040862647 1.002446644 0.993713529 0.967672773 0.822510796 1 19.02830264 1.556155829 3.373166376 0.907377822 1.015918024 0.2303148 0.071650921 0.258336147 6.634770224 0.045872034 0.018301028 35.987844 -1.556155829 0.108540202 SVCLIGDKEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVCLIGDKEQR 11 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 101.64 0.0024676 111850000 749150 689060 703560 655670 700990 727860 697930 818820 926460 917750 FALSE TRUE 719872.3898 669408.6835 830708.9426 689509.2073 723537.98 742577.8279 706471.4761 801911.0809 821292.1448 855589.9751 0.841375438 0.782394258 0.970919444 0.805887431 0.845659721 0.867913194 0.825712662 0.937260959 0.95991324 1 19.70656005 1.556574333 2.805234265 0.978144794 0.849563086 0.561125728 0.048218956 0.172280514 3.013331737 0.033134278 0.012449517 36.02254006 -1.556574333 -0.128581708 RPNKQEESES(ph)PVERPLK ddPTM_BT-474_Pertuzumab_2h_R1 3 RPNKQEESESPVERPLK 17 3 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 RPNKQEES(0.02)ES(0.98)PVERPLK;RPNKQEES(0.007)ES(0.993)PVERPLK;RPNKQEES(0.002)ES(0.998)PVERPLK 262.94 1.25E-26 2885970000 1307220 1184940 1171650 1079490 1189490 1326240 1311800 1445690 1830850 1726250 TRUE FALSE 1256132.397 1151146.671 1383393.218 1135202.608 1227751.026 1353057.481 1327854.201 1415835.996 1623019.584 1609329.55 0.780531494 0.715295802 0.859608412 0.705388532 0.762895969 0.840758489 0.825097756 0.8797676 1.008506669 1 20.61802835 1.556589955 1.056347222 1.016666061 0.768855206 0.791356735 0.045514345 0.199923666 0.430155718 0.039331658 0.014510354 36.02383584 -1.556589955 -0.247810856 GEAACQELLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEAACQELLR 10 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;O60936-1 H3BM67 NOL3 Nucleolar protein 3 0 90.696 0.024789 284460000 143400 209820 159510 230210 202600 186790 198040 168290 136640 169390 FALSE TRUE 137795.7695 203836.139 188337.0053 242091.1657 209116.813 190567.0218 200463.6728 164814.7527 121129.2 157917.0644 0.87258315 1.290779687 1.192632386 1.533027267 1.324219227 1.206753827 1.269423754 1.043679182 0.767043134 1 17.26880755 1.556845636 3.376208745 0.884658662 1.254249575 0.439350037 0.162949341 0.176864848 4.554196174 0.106996588 0.042733595 36.04505029 -1.556845636 0.369590914 LLVLEAFQVSHPCR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLVLEAFQVSHPCR 14 0 A0A0C4DFM0;G3V4T6;O43708-2;O43708;G3V3B9;A0A0A0MR33;G3V267;G3V5T0;O43708-3 A0A0C4DFM0 GSTZ1 Maleylacetoacetate isomerase 0 ; 179.39 1.87E-06 235760000 247390 271270 227050 288500 233200 217587 285250 233860 231010 244590 FALSE TRUE 237721.7253 263533.6452 268082.9857 303389.5196 240701.0898 221986.7582 288740.9748 229030.7093 204786.7133 228023.7014 1.042530771 1.155729179 1.175680353 1.330517475 1.055596801 0.973524931 1.26627615 1.004416242 0.898093979 1 17.79882426 1.557011209 6.107134584 0.950107697 1.142124502 0.391207713 0.101684058 0.136032439 10.27554093 0.057322259 0.026383992 36.05879496 -1.557011209 0.192016806 DDGLFSGDPNWFPKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDGLFSGDPNWFPKK 15 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 159.22 2.85E-06 1955520000 6544900 6938800 5113200 5417600 4944000 5424400 5263900 6830600 8316000 7432900 FALSE TRUE 6289118.072 6740912.218 6037268.983 5697202.985 5103028.25 5534085.085 5328321.183 6689545.723 7372002.544 6929463.062 0.907590966 0.972789978 0.87124629 0.822170915 0.736424771 0.798631154 0.768937093 0.965377211 1.063863459 1 22.72431214 1.557048305 4.688201296 1.027605992 0.840173528 0.593623453 0.065852064 0.121863118 5.860950356 0.043936294 0.019368593 36.06187508 -1.557048305 -0.187432464 KASHTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KASHTPK 7 1 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 63.486 0.051376 77097000 77050 79435 66534 70123 76585 76107 75056 66682 52669 69095 FALSE TRUE 74038.80082 77169.59158 78558.17384 73742.05643 79048.42608 77645.93569 75974.55778 65304.9934 46690.23593 64415.13411 1.149400709 1.198004051 1.219560821 1.14479396 1.227171645 1.20539896 1.179451985 1.013814444 0.724833326 1 15.97511206 1.55725014 3.325126557 0.861275217 1.190870784 0.787316159 0.068361388 0.07663362 1.914177468 0.041045398 0.016316566 36.07863847 -1.55725014 0.329595568 QPLLLSEDEEDT(ph)KR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPLLLSEDEEDTKR 14 1 Q99613-2;Q99613;B5ME19;H3BPE4 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 QPLLLSEDEEDT(1)KR 241.64 3.68E-17 317530000 344990 336470 290610 339830 373960 357070 347090 422710 513570 485730 TRUE FALSE 331507.4094 326874.205 343129.6916 357368.667 385988.763 364290.2 351337.7912 413980.8908 455271.6867 452831.0745 0.73207743 0.721845791 0.757743253 0.789187596 0.852390184 0.804472618 0.775869438 0.914206012 1.005389675 1 18.78861344 1.557278709 2.235286762 1.005657303 0.776012702 0.873149859 0.0353883 0.103369556 1.09645464 0.031439008 0.011142555 36.08101194 -1.557278709 -0.229644601 EKDECT(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDECTPTR 9 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.981)PT(0.019)R 97.594 0.041942 217500000 270100 240400 208840 215920 216270 266130 256140 282410 358190 341710 TRUE FALSE 259544.1934 233544.0274 246582.0336 227063.6571 223226.521 271511.3309 259274.7179 276578.1348 317529.7729 318565.6773 0.814727423 0.733111079 0.774038295 0.712768742 0.700723703 0.852293107 0.813881521 0.86819816 0.996748223 1 18.28123131 1.557483217 1.007840768 1.01290728 0.752371567 0.824388992 0.04232638 0.191444491 0.376940585 0.03818334 0.014334975 36.09800639 -1.557483217 -0.260535713 AVT(ph)PSSEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 AVTPSSEAK 9 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5 Q99700 ATXN2 Ataxin-2 1 AVT(0.981)PS(0.018)S(0.001)EAK;AVT(0.881)PS(0.114)S(0.005)EAK;AVT(0.951)PS(0.046)S(0.003)EAK;AVT(0.944)PS(0.056)SEAK 155.53 0.00081698 2918960000 4587470 4357740 3833440 3795900 4053940 4247150 4351810 4837500 5629060 5473340 TRUE FALSE 4408186.601 4233461.522 4526227.882 3991806.854 4184338.662 4333030.283 4405068.753 4737603.935 4990072.708 5102625.807 0.86390552 0.829663331 0.887038959 0.782304446 0.820036354 0.84917657 0.863294492 0.928463915 0.977942122 1 22.28280842 1.557530601 1.459625518 0.998814874 0.836273155 0.846822606 0.025828825 0.136438292 0.562907811 0.022330991 0.007700866 36.10194505 -1.557530601 -0.162541719 DDDWGNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDDWGNIK 8 0 P54578-2;P54578 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14 0 ; 129.56 0.004859 183750000 728500 660410 626750 786750 627560 618500 779190 922880 1123480 1156500 FALSE TRUE 700029.4146 641575.7534 740017.667 827354.2618 647746.0373 631006.4938 788725.9603 903822.2055 995947.2604 1078169.225 0.649276012 0.595060347 0.686365044 0.767369577 0.600783274 0.585257378 0.731541897 0.838293456 0.923739277 1 20.0401522 1.55773444 1.529477818 0.981252941 0.649839089 0.851409291 0.052745864 0.139791166 0.637437516 0.048192212 0.016568981 36.11889374 -1.55773444 -0.331413852 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_BT-474_Pertuzumab_2h_R1 3 ERSPSPLRGNVVPSPLPTR 19 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 ERS(1)PS(1)PLRGNVVPS(0.957)PLPT(0.043)R;ERS(0.999)PS(0.999)PLRGNVVPS(0.983)PLPT(0.019)R;ERS(1)PS(1)PLRGNVVPS(0.991)PLPT(0.009)R 109.08 0.00017319 3780330000 1830310 1976880 1294600 1630050 1894960 1881430 1430720 1603630 1546180 1312680 TRUE FALSE 1758779.462 1920501.318 1528563.018 1714177.076 1955913.109 1919473.804 1448229.579 1570514.48 1370664.129 1223771.014 1.437180192 1.569330614 1.249059669 1.400733516 1.59826723 1.568490985 1.183415494 1.283340152 1.12003317 1 20.2229022 1.557758403 1.083632287 1.025433764 1.461095677 0.643510177 0.117093797 0.306662112 0.692564208 0.108133704 0.039574618 36.1208867 -1.557758403 0.435661913 DFDS(ph)S(ph)EDEKHSK ddPTM_BT-474_Pertuzumab_2h_R1 4 DFDSSEDEKHSK 12 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 2 DFDS(1)S(1)EDEKHSK;DFDS(1)S(1)EDEKHSK;DFDS(1)S(1)EDEKHSK;DFDS(1)S(1)EDEKHSK 203.04 7.38E-08 3253210000 7558800 5413590 4656330 3672090 5291270 4876610 5273260 6150760 8592200 5958160 TRUE FALSE 7263393.739 5259199.714 5497832.411 3861607.005 5461468.505 4975218.395 5337795.733 6023744.657 7616849.477 5554608.516 1.307633782 0.94681735 0.989778559 0.695207771 0.98323194 0.895691997 0.960967045 1.084458903 1.371266662 1 22.4052538 1.557823433 3.957818223 1.19729144 0.956666018 0.217494883 0.163733832 0.232187945 8.17143467 0.098759519 0.04159369 36.12629572 -1.557823433 -0.240625422 AGAPGESLECPAELRPQVPQPPS(ph)PAAVPRPPSNPPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGAPGESLECPAELRPQVPQPPSPAAVPRPPSNPPAR 37 2 O43734-5;O43734-2;O43734 O43734-5 TRAF3IP2 Adapter protein CIKS 1 AGAPGESLECPAELRPQVPQPPS(1)PAAVPRPPSNPPAR 304.24 5.66E-93 383450000 66358 67525 66106 83327 82365 82537 76109 73781 73930 74487 TRUE FALSE 63764.656 65599.25311 78052.82472 87627.51646 85014.34503 84205.95469 77040.44471 72257.39657 65537.77634 69441.92914 0.918244305 0.944663461 1.124001388 1.261881943 1.224250911 1.212609669 1.109422587 1.040544199 0.943778163 1 16.08351941 1.55827535 2.965907624 0.974246037 1.121324444 0.220718356 0.106383072 0.371626258 7.334165858 0.084053387 0.032205565 36.16390749 -1.55827535 0.147078407 ISRGYDFAAVLEWFAER ddPTM_BT-474_Pertuzumab_2h_R1 1 ISRGYDFAAVLEWFAER 17 1 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9NZN3 A0A024R571;Q9NZN3 EHD1;EHD3 EH domain-containing protein 1;EH domain-containing protein 3 0 54.501 0.076014 6138100000 3766000 6637100 5030500 8236500 6315600 7186900 6458000 5771600 4753300 6099900 FALSE TRUE 3618820.556 6447816.406 5939623.253 8661586.752 6518747.01 7332224.042 6537034.936 5652414.443 4213725.311 5686748.34 0.636360243 1.133831853 1.0444674 1.523117647 1.146304816 1.28935265 1.149520701 0.993962473 0.740972707 1 22.43917253 1.558388569 3.628729794 0.868164356 1.149527335 0.187260204 0.216573441 0.29089679 8.661191347 0.138722083 0.056855757 36.17333658 -1.558388569 0.281362979 DEPIHILNVAIK ddPTM_BT-474_Pertuzumab_2h_R1 4 DEPIHILNVAIK 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;; 160.15 5.95E-05 1357170000 2154633 2154874 2179873 2093749 2221949 2311588 2821893 2562904 3318170 3444390 FALSE TRUE 2070427.56 2093419.103 2573824.542 2201807.637 2293420.008 2358329.893 2856428.171 2509979.137 2941505.253 3211098.397 0.644772381 0.651932406 0.801540228 0.685686754 0.714216671 0.734430902 0.889548627 0.781657497 0.916043325 1 21.61463544 1.558564394 0.322129712 1.028615535 0.643052649 0.781502015 0.053157118 0.624979535 0.223921707 0.08836524 0.080011385 36.18798435 -1.558564394 -0.385562885 GDLS(ph)DVEEEEEEEMDVDEATGAVKK ddPTM_BT-474_Pertuzumab_2h_R1 3 GDLSDVEEEEEEEMDVDEATGAVKK 25 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(1)DVEEEEEEEMDVDEATGAVKK 360.26 1.03E-103 923770000 834530 675340 562010 480891 544080 614794 600462 684755 829780 699619 TRUE FALSE 801915.645 656079.9644 663577.7088 505709.8421 561580.8273 627225.5559 607810.6336 670614.57 735586.8531 652233.182 1.229492254 1.005897864 1.017393361 0.775351295 0.861012354 0.961658458 0.931891615 1.028182234 1.127797348 1 19.31502831 1.558603034 4.73516625 1.068143727 0.960744907 0.100703511 0.114446732 0.337378973 16.51677594 0.070060074 0.030994492 36.19120419 -1.558603034 -0.107398821 LVES(ph)PKEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVESPKEGK 9 1 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PKEGK;LVES(1)PKEGK 73.082 0.027209 1202890000 1413900 1105900 708950 574690 961180 1053160 879800 1064150 1328960 1001300 TRUE FALSE 1358643.225 1074360.815 837073.0355 604349.8198 992097.2276 1074455.617 890567.2556 1042174.931 1178102.032 933481.0591 1.455458803 1.150918708 0.896722036 0.647415193 1.062793099 1.151020266 0.954028201 1.11643929 1.262052423 1 19.83226122 1.558736406 6.832958371 1.149154296 1.033123067 0.028073564 0.203893816 0.439160633 39.71567023 0.117663657 0.0546494 36.20232026 -1.558736406 -0.116031229 KKPAPGPHSS(ph)PPEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKPAPGPHSSPPEEK 15 2 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 1 KKPAPGPHS(0.225)S(0.775)PPEEK 101.92 0.0008306 1048500000 2512400 2227300 2051500 1913700 2127700 2287000 2427100 2471300 3313900 2863200 TRUE FALSE 2414212.63 2163779.585 2422251.685 2012466.286 2196139.403 2333244.707 2456803.576 2420266.791 2937719.965 2669272.914 0.904445783 0.810625086 0.907457485 0.753938002 0.822748169 0.874112458 0.920401793 0.906713877 1.100569354 1 21.34801539 1.559081338 1.518950246 1.045163388 0.844122911 0.64437271 0.055535259 0.219683055 0.987237284 0.045710783 0.01573476 36.23108483 -1.559081338 -0.201040477 TPASTPVSGTPQAS(ph)PMIER ddPTM_BT-474_Pertuzumab_2h_R1 6 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVSGT(0.211)PQAS(0.789)PMIER;TPASTPVS(0.138)GT(0.322)PQAS(0.54)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER 371.01 5.57E-108 6526650000 1585010 1690150 1674280 2142130 1735530 1979690 1835250 1804070 1789740 1867390 TRUE FALSE 1523066.057 1641948.577 1976859.64 2252685.586 1791354.899 2019720.688 1857710.338 1766815.324 1586576.218 1740910.012 0.874867768 0.943155341 1.135532352 1.293970148 1.02897616 1.160152262 1.067091536 1.014880328 0.911348782 1 20.7314102 1.559135353 3.170257397 0.956412883 1.079686757 0.146698675 0.110948868 0.408434098 9.273464832 0.079984064 0.031357616 36.23559134 -1.559135353 0.123273875 VGDDVEFEVSSDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGDDVEFEVSSDRR 14 1 O75534-2;O75534;O75534-3;O75534-4;E9PLD4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;; 169.52 5.32E-06 1432700000 1301800 1416940 1313830 1420110 1445220 1574210 1539690 1391310 1465710 1401790 FALSE TRUE 1250924.217 1376530.259 1551268.307 1493402.047 1491706.814 1606041.605 1558533.187 1362578.962 1299328.746 1306845.515 0.957208945 1.053322863 1.18703266 1.142753317 1.141456122 1.228945263 1.192591756 1.042647311 0.994248158 1 20.31765718 1.559229367 4.931957651 1.00310343 1.13303748 0.357859604 0.073007243 0.177216071 9.322959056 0.045451546 0.020294325 36.24343632 -1.559229367 0.129934049 EVMNADDPDLQRPDEEAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVMNADDPDLQRPDEEAIK 19 1 Q13573;G3V3A4;G3V5R3 Q13573 SNW1 SNW domain-containing protein 1 0 174.02 4.84E-12 249480000 131180 123700 133900 138290 138830 134830 153860 174520 198170 210700 FALSE TRUE 126053.3406 120172.1971 158098.7086 145427.1635 143295.593 137556.355 155742.9847 170916.101 175674.5724 196429.1013 0.641724366 0.61178408 0.804863982 0.740354471 0.729502869 0.700285009 0.792871238 0.870115985 0.894340865 1 17.58364916 1.559376289 0.421159669 1.018438621 0.662527187 0.808720741 0.049529644 0.445271933 0.222014914 0.062605923 0.04645248 36.25569952 -1.559376289 -0.355911434 AIELDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIELDKK 7 1 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ; 81.548 0.043137 923140000 938150 920190 813650 743490 873820 799430 987440 926730 1192430 1089000 FALSE TRUE 901486.0608 893947.0822 960694.6545 781861.608 901927.2139 815595.0223 999524.5861 907592.7016 1057070.345 1015241.06 0.88795272 0.880526919 0.946272459 0.7701241 0.88838725 0.8033511 0.984519466 0.893967686 1.041201333 1 19.95339089 1.559787994 1.301605452 1.015050163 0.868366956 0.459453056 0.059366104 0.362713922 1.178179265 0.049342516 0.017285248 36.29008575 -1.559787994 -0.146683207 (ac)AAGAAEAAVAAVEEVGSAGQFEELLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGAAEAAVAAVEEVGSAGQFEELLR 26 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 88.133 1.04E-24 29157000 9027.1 14207 10215 15794 16116 16049 14440 11760 8187 12735 FALSE TRUE 8674.310952 13801.83027 12061.07773 16609.13023 16634.38578 16373.52178 14616.72104 11517.15189 7257.646083 11872.44711 0.730625361 1.162509308 1.0158881 1.398964349 1.401091588 1.37911937 1.231146444 0.970073969 0.611301614 1 13.53532971 1.560076898 3.892192297 0.799915198 1.203183798 0.348106125 0.211668652 0.191790248 6.548140802 0.135650894 0.056965679 36.31423489 -1.560076898 0.4032686 KAALLAQYADVT(ph)DEEDEADEKDDSGATTMNIGSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAALLAQYADVTDEEDEADEKDDSGATTMNIGSDK 35 2 Q96MW1 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 1 KAALLAQYADVT(1)DEEDEADEKDDSGATTMNIGSDK 322.86 3.50E-105 271320000 118700 78365 78171 51267 90905 81611 77508 103560 140290 107250 TRUE FALSE 114061.0728 76130.10693 92298.2386 53912.89601 93829.04188 83261.23034 78456.56609 101421.4498 124364.8673 99985.86197 1.14077201 0.761408717 0.923112896 0.539205193 0.938423093 0.832730035 0.784676599 1.014357908 1.243824526 1 16.60943649 1.56010256 4.189167723 1.125142642 0.837632876 0.348391832 0.154281591 0.169475493 6.64336977 0.08860723 0.038037068 36.31638067 -1.56010256 -0.287509766 VSSPLSPLSPGIKS(ph)PTIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSSPLSPLSPGIKSPTIPR 19 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 VSSPLSPLSPGIKS(1)PTIPR;VSSPLSPLSPGIKS(0.987)PT(0.013)IPR 193.11 3.63E-15 1999600000 588800 590100 429160 376950 447480 537850 456590 610750 770460 668050 TRUE FALSE 565789.045 573270.9258 506718.7586 396404.4347 461873.6006 548725.6955 462177.885 598137.7991 683000.6108 622802.3785 0.908456783 0.920470033 0.813610828 0.636485101 0.74160539 0.881059088 0.742093963 0.960397423 1.096657037 1 19.24841493 1.560306326 4.154696622 1.044513994 0.805288893 0.58148174 0.084633552 0.128042584 4.94328578 0.055475857 0.023762894 36.33342393 -1.560306326 -0.239225101 QTNPSAMEVEEDDPVPEIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 QTNPSAMEVEEDDPVPEIRR 20 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 84.946 0.0043572 267080000 36044 47550 25510 41750 35742 49281 38360 33221 35158 27288 FALSE TRUE 34635.36063 46193.92056 30120.22447 43904.7225 36891.67389 50277.49559 38829.46115 32534.97474 31167.01123 25439.75945 1.361465728 1.815815933 1.183982283 1.725830882 1.450158126 1.976335337 1.526329729 1.278902609 1.22512995 1 14.63479741 1.560364213 2.155044499 1.106645263 1.588879404 0.438520711 0.218912881 0.261719093 2.563242346 0.163570842 0.057742031 36.33826713 -1.560364213 0.482234141 EDCSPADKPYIDEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDCSPADKPYIDEAR 15 1 Q96DG6 Q96DG6 CMBL Carboxymethylenebutenolidase homolog 0 ; 143.97 3.94E-06 1548980000 2070550 1871030 1794150 2209100 1712880 1228250 2368900 2186400 2758300 2773600 FALSE TRUE 1989630.617 1817670.056 2118392.816 2323111.916 1767976.341 1253086.057 2397891.307 2141250.076 2445189.348 2585741.602 0.769462276 0.702958894 0.819259285 0.898431581 0.683740533 0.484613797 0.927351482 0.828099016 0.945643349 1 21.30214668 1.560833578 1.538729077 0.975430537 0.742269876 0.380674222 0.114384542 0.415380851 1.92023977 0.101104669 0.034819433 36.37756104 -1.560833578 -0.233160661 FYGDEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 FYGDEEK 7 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;; 135.16 0.0072219 2027880000 1931410 1989310 1902540 2026460 1742290 1687520 1955910 2251000 2708650 2548950 FALSE TRUE 1855928.362 1932576.827 2246371.3 2131045.843 1798332.34 1721642.811 1979847.012 2204516.063 2401175.408 2376307.346 0.781013603 0.813268885 0.945320185 0.896788813 0.756775988 0.724503425 0.833161171 0.927706623 1.010465002 1 21.18029001 1.560943402 2.701578161 1.002268888 0.82232562 0.60470005 0.060574419 0.185582526 3.007522271 0.049005759 0.018296171 36.38676129 -1.560943402 -0.179943269 QPHRPDPGRPVGLEQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPHRPDPGRPVGLEQLR 17 2 Q9BV57 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 92.211 0.0020208 246040000 172100 188410 198130 229150 193880 242860 169600 195310 149640 166640 FALSE TRUE 165374.1417 183036.7313 233936.4984 240976.459 200116.3263 247770.7956 171675.6155 191276.7802 132653.4945 155353.3244 1.064503398 1.178196424 1.505835162 1.551150965 1.288136749 1.594885701 1.105065606 1.231237124 0.853882561 1 17.24519359 1.561031544 1.666604933 0.938814789 1.357498557 0.435947014 0.176973507 0.326788698 1.798617073 0.150782561 0.051877655 36.39414693 -1.561031544 0.418683768 VQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTSLR 41 1 Q96K17;Q96K17-2;E9PL10 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4;Transcription factor BTF3 0 ; 196.22 2.35E-35 155036000 89340 89723 75246 95942 85626 86052 80949 100296 120009 104440 FALSE TRUE 85848.49403 87164.18789 88844.62604 100893.5781 88380.23805 87792.0304 81939.67808 98224.85255 106386.0814 97366.18577 0.881707477 0.895220319 0.912479269 1.036228104 0.90770977 0.901668579 0.841561959 1.008818942 1.092638893 1 16.57113321 1.561109062 5.756303068 1.047483446 0.914820338 0.553111791 0.051194928 0.104208505 7.144859446 0.029479425 0.013512134 36.40064353 -1.561109062 -0.132663108 SDQGWR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDQGWR 6 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 96.666 0.097591 234910000 314610 340480 308400 348290 328190 306320 352320 309170 309510 313250 FALSE TRUE 302314.6934 330769.8438 364134.7403 366265.2886 338746.5294 312514.0003 356631.7976 302785.5315 274375.7224 292033.2985 1.035206242 1.132644275 1.246894591 1.254190158 1.159958577 1.070131392 1.221202511 1.036818517 0.939535744 1 18.15577335 1.561622765 4.31706465 0.973807224 1.162126282 0.568804684 0.068431349 0.12341348 5.115659046 0.042907307 0.018598978 36.44372531 -1.561622765 0.188319058 KGVEPSPS(ph)PIKPGDIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGVEPSPSPIKPGDIKR 17 3 Q92890;Q92890-1;Q92890-3 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 KGVEPS(0.03)PS(0.97)PIKPGDIKR 111.83 0.0027091 179940000 240130 205810 125900 113490 144130 178080 159800 200490 256440 216040 TRUE FALSE 230745.4541 199940.5003 148652.9306 119347.2325 148766.0723 181680.8996 161755.6802 196349.8114 227330.0063 201407.4184 1.14566512 0.992716663 0.738070781 0.59256622 0.738632537 0.902056643 0.803126724 0.974888676 1.128707215 1 17.6197573 1.561626096 3.718664692 1.063165553 0.835060684 0.271614571 0.146088153 0.257287379 8.057621743 0.100700369 0.041747741 36.4440049 -1.561626096 -0.228104869 TGRDT(ph)PENGETAIGAENSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGRDTPENGETAIGAENSEK 20 1 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 T(0.322)GRDT(0.678)PENGETAIGAENSEK;T(0.184)GRDT(0.816)PENGETAIGAENSEK 159.66 4.07E-11 776500000 715700 625670 633940 689790 672010 680930 749780 817880 1028180 976950 TRUE FALSE 687729.6528 607826.5042 748507.0599 725390.1446 693625.812 694698.8711 758956.0319 800990.4922 911465.3169 910780.3063 0.755099389 0.667368958 0.821830528 0.796449088 0.761573134 0.762751309 0.833303077 0.879455217 1.000752114 1 19.79674357 1.56191744 1.265344412 1.012370401 0.759340448 0.847391316 0.039632011 0.155297741 0.476148097 0.035686181 0.01257794 36.46846129 -1.56191744 -0.253029953 SQSSHS(ph)YDDSTLPLIDR ddPTM_BT-474_Pertuzumab_2h_R1 7 SQSSHSYDDSTLPLIDR 17 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 SQSSHS(1)YDDSTLPLIDR;SQSS(0.004)HS(0.996)YDDSTLPLIDR;SQSSHS(1)YDDSTLPLIDR;SQSS(0.002)HS(0.998)YDDSTLPLIDR;SQSSHS(1)YDDSTLPLIDR;SQS(0.001)S(0.004)HS(0.994)YDDSTLPLIDR;S(0.001)QS(0.006)S(0.059)HS(0.934)YDDSTLPLIDR 329.64 6.04E-72 7552020000 1854964 2568340 1841423 2789090 1978090 2239160 2263980 2177330 1999310 2372850 TRUE FALSE 1782469.956 2495093.458 2174209.098 2933035.269 2041717.061 2284437.349 2291687.264 2132367.375 1772356.711 2212134.756 0.805769156 1.127912055 0.98285563 1.325884538 0.922962336 1.032684534 1.035961873 0.963940994 0.801197443 1 21.07700784 1.562165662 3.693209019 0.895540469 1.041775124 0.132189707 0.134900138 0.324816701 10.04260352 0.081237179 0.033623281 36.48931094 -1.562165662 0.146234655 KYPDYESK ddPTM_BT-474_Pertuzumab_2h_R1 4 KYPDYESK 8 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 105.52 0.0070092 1084880000 2076430 2430450 1928680 2199120 2190740 2327010 2551000 2579400 3281960 3215950 FALSE TRUE 1995280.82 2361135.946 2277235.379 2312616.847 2261207.142 2374063.737 2582219.901 2526134.489 2909405.66 2998130.842 0.665508253 0.787535992 0.7595517 0.771352876 0.754205624 0.791847942 0.861276588 0.842569795 0.970406501 1 21.51563191 1.562335119 0.626105879 1.009153328 0.740065393 0.863038817 0.035746432 0.232106168 0.202620381 0.032607275 0.01652607 36.50355142 -1.562335119 -0.269087935 SEPVKEES(ph)SELEQPFAQDTSSVGPDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDRK 27 2 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 SEPVKEES(0.909)S(0.091)ELEQPFAQDTSSVGPDRK 349.99 1.90E-110 459840000 266180 215350 195270 141040 231910 269660 247890 246070 396920 338140 TRUE FALSE 255777.3913 209208.4288 230559.6328 148319.0913 239369.5958 275112.71 250923.752 240988.5685 351863.3056 315237.4766 0.811380024 0.663653418 0.731383956 0.470499551 0.759331024 0.872715747 0.795983253 0.764466748 1.116184882 1 18.26607953 1.562445867 0.849041881 1.042788331 0.690061906 0.535730543 0.114050363 0.450985403 0.65019564 0.106316856 0.043323879 36.51286129 -1.562445867 -0.352726425 AS(ph)TDNEELLQFPLELCSDSLPSHPFPPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASTDNEELLQFPLELCSDSLPSHPFPPAK 29 0 Q86YS7;Q86YS7-5;H0YFC4;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 AS(0.876)T(0.124)DNEELLQFPLELCSDSLPSHPFPPAK;AS(0.951)T(0.049)DNEELLQFPLELCSDSLPSHPFPPAK 203.58 1.70E-25 229747000 171213 185630 150035 168935 164070 180682 165049 185018 210180 191569 TRUE FALSE 164521.8067 180336.0142 177149.662 177653.7556 169347.4606 184335.5138 167068.919 181197.3136 186321.2475 178593.861 0.921206394 1.009754832 0.991913502 0.994736071 0.948226661 1.032149217 0.935468432 1.014577504 1.043267929 1 17.44632296 1.562511997 8.291213039 1.023706807 0.979539234 0.252905849 0.033674155 0.152819087 18.89623652 0.016761263 0.007833006 36.51842148 -1.562511997 -0.044167573 SEGEASEEGLYLDSEAVLDYVMTRPDLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEGEASEEGLYLDSEAVLDYVMTRPDLDK 29 1 Q7L211 Q7L211 ABHD13 Alpha/beta hydrolase domain-containing protein 13 0 53.844 0.062711 18222000 5709.4 7274.2 5273.3 6993.7 5759.4 6618.5 7855.3 9643.3 10105 12137 FALSE TRUE 5486.270336 7066.746938 6226.302614 7354.645695 5944.656332 6752.330605 7951.435511 9444.162485 8957.922764 11314.95018 0.484869155 0.624549541 0.550272208 0.649993644 0.52538069 0.59676185 0.702737121 0.834662313 0.791689103 1 13.46594261 1.562541829 0.747043597 0.982481728 0.558969542 0.871179342 0.054299049 0.192937038 0.223542389 0.049248907 0.021732369 36.52093006 -1.562541829 -0.423512186 DRDVSEEHKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRDVSEEHKK 10 2 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 ; 149.38 1.41E-05 531654000 267860 282420 203638 217912 280390 301050 291100 301410 427790 405190 FALSE TRUE 257391.7351 274365.6581 240439.9165 229158.4644 289408.999 307137.4373 294662.5689 295185.7782 379229.0726 377746.1204 0.681388163 0.726322901 0.636511942 0.606646772 0.766146847 0.813078999 0.780054521 0.781439603 1.003925791 1 18.52705741 1.562636933 0.599141975 1.016379995 0.670276328 0.789450948 0.058596256 0.345506777 0.281965006 0.060259791 0.031769575 36.52892847 -1.562636933 -0.346103667 KGDRS(ph)PEPGQTWTR ddPTM_BT-474_Pertuzumab_2h_R1 9 KGDRSPEPGQTWTR 14 2 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 KGDRS(0.968)PEPGQT(0.028)WT(0.004)R;KGDRS(1)PEPGQTWTR;KGDRS(0.971)PEPGQT(0.022)WT(0.007)R;KGDRS(0.991)PEPGQT(0.008)WTR;KGDRS(1)PEPGQTWTR;KGDRS(1)PEPGQTWTR;KGDRS(1)PEPGQTWTR;KGDRS(0.999)PEPGQT(0.001)WTR;KGDRS(0.894)PEPGQT(0.087)WT(0.019)R 205 6.71E-09 76136150000 16533591 17111702 13513912 15431546 13777549 15424250 13874556 14405292 13544329 12048170 TRUE FALSE 15887439.98 16623693.01 15956176.51 16227969.94 14220716.38 15736138.9 14044356.97 14107817.69 12006833.55 11232136.71 1.414462839 1.480011634 1.42058247 1.444780308 1.26607401 1.400992465 1.250372687 1.256022611 1.068971457 1 23.42112907 1.562999236 0.522821347 0.982467943 1.449808219 0.874640694 0.05486559 0.249915015 0.166965495 0.052963732 0.031824914 36.55941486 -1.562999236 0.467340276 QAENDSSNDDKTK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAENDSSNDDKTK 13 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 194.77 6.67E-07 519120000 319426 241383 210023 204183 234289 244519 266405 273186 346867 318980 FALSE TRUE 306942.4788 234498.9932 247978.828 214720.9091 241825.1185 249463.3417 269665.3441 267544.6136 307492.1123 297375.2005 1.032172415 0.788562707 0.833892092 0.722053852 0.813198673 0.838884148 0.906818536 0.899687039 1.034020698 1 18.18192481 1.563156393 1.356844153 1.017929251 0.830728513 0.423011642 0.077274684 0.36997342 1.309678538 0.066147397 0.023066135 36.57264688 -1.563156393 -0.187200737 EIELTHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIELTHR 7 0 O43395;O43395-3 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 ; 161.12 0.0013209 908080000 741570 778600 641250 707610 758210 646150 696480 714030 638010 652430 FALSE TRUE 712588.6246 756395.0903 757138.1395 744129.8369 782598.5132 659215.5957 705003.7306 699285.031 565585.7796 608240.335 1.171557662 1.243579301 1.244800938 1.223414157 1.286660006 1.083807761 1.159087436 1.149685397 0.929872202 1 19.21428197 1.563255046 0.941763147 0.968689553 1.224938091 0.696747882 0.059740713 0.288535595 0.500531251 0.053643583 0.020760032 36.58095557 -1.563255046 0.256248538 RPES(ph)PSEIS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 2 RPES(1)PSEIS(1)PIK;RPES(0.996)PS(0.004)EIS(1)PIK;RPES(0.99)PS(0.01)EIS(1)PIK;RPES(0.978)PS(0.022)EIS(1)PIK 180.62 6.72E-05 1108830000 1948490 1814690 1952820 2166440 1960620 1869530 2282310 2567480 2773920 3014430 TRUE FALSE 1872340.857 1762936.818 2305738.014 2278250.228 2023685.123 1907333.178 2310241.592 2514460.641 2459036.231 2810259.971 0.666251833 0.627321613 0.820471429 0.810690204 0.72010602 0.678703464 0.822073978 0.894743072 0.875020908 1 21.42227217 1.563313027 0.798133849 0.990833007 0.716943766 0.688564816 0.062070966 0.35572212 0.460678795 0.061951971 0.026185284 36.58583964 -1.563313027 -0.273889241 KDGSS(ph)PPLLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDGSSPPLLEK 11 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;Q6W2J9-3 H7BYY2 BCOR BCL-6 corepressor 1 KDGS(0.138)S(0.862)PPLLEK 91.441 0.0065779 514100000 977920 904690 777440 677050 832840 822220 857520 931340 1099000 1015700 TRUE FALSE 939701.8053 878889.127 917940.7021 711992.6316 859629.055 838845.8517 868014.5863 912107.5035 974246.1274 946905.7343 0.992392137 0.928169611 0.96941086 0.751915007 0.907829601 0.885881056 0.91668532 0.963250586 1.028873405 1 19.85286129 1.563471198 2.416491975 1.013830688 0.903045757 0.334067588 0.060719174 0.304050274 3.862610152 0.04657657 0.016913463 36.59916678 -1.563471198 -0.110784931 TTGT(ph)PPDSSLVTYELHSRPEQDK ddPTM_BT-474_Pertuzumab_2h_R1 4 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.168)T(0.168)GT(0.664)PPDSSLVTYELHSRPEQDK;T(0.009)T(0.009)GT(0.981)PPDSSLVTYELHSRPEQDK;T(0.02)T(0.02)GT(0.96)PPDSSLVTYELHSRPEQDK;T(0.154)T(0.154)GT(0.691)PPDSSLVTYELHSRPEQDK 288.34 7.32E-53 1523130000 1309650 1126320 940620 1131990 1163620 1139410 1271800 1404090 1689760 1686340 TRUE FALSE 1258467.43 1094198.456 1110610.958 1190412.14 1201048.894 1162449.651 1287364.669 1375095.051 1497945.529 1572122.69 0.800489325 0.696000677 0.706440385 0.757200534 0.763966389 0.739414079 0.818870357 0.874674133 0.952817193 1 20.58428238 1.56360301 1.02576246 1.001311595 0.736590112 0.912709247 0.028713214 0.12275869 0.249469661 0.025197066 0.00941858 36.61027662 -1.56360301 -0.264721483 VTEGQQER ddPTM_BT-474_Pertuzumab_2h_R1 4 VTEGQQER 8 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 160.26 0.0008244 1567400000 583612 602427 493141 572922 576833 569736 582025 568063 582120 595782 FALSE TRUE 560803.7978 585246.3718 582262.5486 602490.5731 595387.3573 581256.4523 589147.9961 556332.3005 516040.178 555429.1545 1.00967656 1.053683205 1.048311101 1.084729831 1.071941133 1.046499716 1.060707727 1.001626033 0.929083707 1 19.08324338 1.563739908 3.628805024 0.964088161 1.054934435 0.684785302 0.02457806 0.098766933 2.955031122 0.015218671 0.006273432 36.62181868 -1.563739908 0.090846273 GEPAAAAAPEAGAS(ph)PVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEPAAAAAPEAGASPVEK 18 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK 341.1 2.02E-75 7750100000 3869320 4457750 4720720 5555700 5721700 4695400 4036340 4342340 3773680 3198200 TRUE FALSE 3718102.697 4330619.335 5573859.116 5842430.343 5905743.677 4790344.205 4085737.936 4252669.162 3345307.667 2981583.065 1.247023013 1.452456376 1.869429425 1.959506146 1.980740951 1.606644558 1.370325041 1.426312488 1.12199043 1 21.5076471 1.563924991 1.094758223 1.020435641 1.704709843 0.538825141 0.222282645 0.393068037 0.904309592 0.21918694 0.080157139 36.63742912 -1.563924991 0.684274203 FEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 4 FEEAKR 6 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 167.98 0.010409 2163350000 2710070 2649720 2268730 2215000 2370120 2271290 2559900 2700440 3206850 2977130 FALSE TRUE 2604157.468 2574152.58 2678739.979 2329316.415 2446357.062 2317217.04 2591228.822 2644674.97 2842821.832 2775486.333 0.938270687 0.927460009 0.965142558 0.839246221 0.88141564 0.834886849 0.933612532 0.95286903 1.024260793 1 21.40430916 1.564074536 2.171484744 1.010759878 0.899152899 0.543254288 0.040138473 0.227903665 2.277242742 0.033093523 0.011742681 36.65004701 -1.564074536 -0.11160698 GEIPS(ph)PQLTRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEIPSPQLTRPK 12 1 Q8IWZ3-6;H7C0V5 Q8IWZ3-6 ANKHD1;ANKHD1-EIF4EBP3 Ankyrin repeat and KH domain-containing protein 1 1 GEIPS(1)PQLTRPK 106.19 0.00118 583860000 567840 509790 521390 536020 497450 483340 602680 654890 743810 786740 TRUE FALSE 545648.185 495251.2883 615616.7713 563684.0564 513450.931 493113.466 610055.7781 641366.2926 659375.8071 733453.399 0.743943904 0.675232113 0.839339994 0.768534248 0.700045745 0.672317378 0.831758062 0.874447229 0.899001638 1 19.48434578 1.564093049 1.228568403 0.974914263 0.736300151 0.738850063 0.052087524 0.225572801 0.651470506 0.047815354 0.016970619 36.65160939 -1.564093049 -0.238614112 GQGS(ph)QSKGSGDDGKDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQGSQSKGSGDDGKDPR 17 2 O60663-2;O60663;O60663-3 O60663-2 LMX1B LIM homeobox transcription factor 1-beta 1 GQGS(0.409)QS(0.327)KGS(0.264)GDDGKDPR 57.496 0.080421 56348000 116040 96873 76399 67969 85479 93416 92146 104380 132560 115100 TRUE FALSE 111505.0285 94110.27689 90205.99879 71476.88824 88228.50967 95304.93552 93273.71031 102224.5165 117512.3445 107304.1745 1.039149027 0.877042085 0.840656938 0.666114702 0.82222812 0.888175469 0.869245868 0.952661134 1.095133019 1 16.71134668 1.564594506 2.447411156 1.047147458 0.848287136 0.422686081 0.08855754 0.250776687 3.281028234 0.069430931 0.025325183 36.69395351 -1.564594506 -0.198860322 TAPTALGITLSSS(ph)PTSTPELR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 TAPTALGITLS(0.005)S(0.033)S(0.585)PT(0.165)S(0.165)T(0.047)PELR;TAPTALGITLS(0.001)S(0.012)S(0.984)PT(0.001)S(0.001)TPELR 245.48 3.34E-30 200254000 230532 235296 210840 238640 218619 257350 234530 239137 252440 249380 TRUE FALSE 221522.5546 228585.5885 248943.4781 250956.239 225651.0787 262553.7933 237400.2483 234198.7374 223784.0695 232489.2705 0.952829153 0.983209195 1.070774052 1.079431487 0.970587065 1.129315743 1.02112346 1.007352885 0.962556547 1 17.82680461 1.565012431 3.164083212 0.982046549 1.032783802 0.119938501 0.051533268 0.434044465 9.880889066 0.034966785 0.013792194 36.72928138 -1.565012431 0.050737253 FAQPGSFEYEYAMR ddPTM_BT-474_Pertuzumab_2h_R1 6 FAQPGSFEYEYAMR 14 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;; 147.24 1.88E-05 2060060000 1067968 1061008 872314 998902 976170 993278 1002154 1011463 1068367 1027968 FALSE TRUE 1026230.63 1030749.091 1029960.544 1050455.452 1007569.395 1013362.762 1014418.66 990575.9356 947090.4571 958342.8117 1.070838762 1.075553631 1.074730808 1.096116587 1.051366361 1.057411554 1.05851335 1.033634231 0.988258529 1 19.87018229 1.565128997 1.294355512 0.991245471 1.072871102 0.859948406 0.012144241 0.144208038 0.463068875 0.010861832 0.003818759 36.73914095 -1.565128997 0.08162563 AQYDELAR ddPTM_BT-474_Pertuzumab_2h_R1 10 AQYDELAR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;; 199.8 0.00029067 33754001000 14524850 16529350 13258260 15527790 15105970 14714260 15356920 15422050 15817830 16908270 FALSE TRUE 13957202.8 16057949.12 15654322.51 16329181.1 15591867.24 15011792.42 15544862.58 15103579.28 14022256.25 15763057.81 0.885437519 1.018707748 0.99310189 1.03591456 0.989139761 0.952340123 0.986157811 0.958163033 0.889564475 1 23.91004409 1.565309765 4.596396316 0.938822746 0.983288315 0.084029659 0.045742902 0.303976669 14.11702437 0.025753146 0.011376243 36.75443614 -1.565309765 0.044465569 MQMLEDEDDLAYAETEKK ddPTM_BT-474_Pertuzumab_2h_R1 3 MQMLEDEDDLAYAETEKK 18 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 231 1.65E-19 540650000 454740 416802 378183 305265 395159 418225 426751 475478 629654 545074 FALSE TRUE 436968.2581 404915.2151 446529.0807 321019.7632 407869.6481 426681.796 431973.7064 465659.2131 558178.3176 508155.6525 0.859910258 0.796833043 0.87872501 0.631735103 0.802647075 0.839667519 0.850081475 0.916371216 1.098439651 1 18.95491095 1.56608558 1.88665563 1.049311807 0.799670419 0.656535936 0.069175758 0.187223643 1.362404541 0.055784602 0.019416396 36.82015228 -1.56608558 -0.249641388 SEFLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEFLVR 6 0 Q96QR8;Q00577 Q96QR8;Q00577 PURB;PURA Transcriptional activator protein Pur-beta;Transcriptional activator protein Pur-alpha 0 ; 112.56 0.06256 581190000 596530 869200 711050 1011390 913200 777620 835090 702390 576760 656730 FALSE TRUE 573216.9481 844411.267 839552.5522 1063587.959 942573.9073 793344.0092 845310.0812 687885.401 511288.6228 612249.0921 0.936247935 1.379195621 1.371259775 1.737181766 1.539526835 1.295786338 1.380663674 1.123538458 0.83509903 1 19.2237592 1.566601944 2.619643557 0.919030684 1.396763874 0.476834047 0.194061051 0.21167866 3.226298263 0.145998594 0.054370957 36.86395644 -1.566601944 0.47773319 ELCQQIHAECKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELCQQIHAECKR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 134.68 9.16E-05 137720000 216220 213910 145870 167010 189340 202770 188730 215850 256110 234570 FALSE TRUE 207769.8834 207809.4962 172231.9539 175629.4061 195430.2931 206870.1483 191039.7342 211392.6221 227037.4665 218682.365 0.950098941 0.950280084 0.787589589 0.803125602 0.893671939 0.945984594 0.873594605 0.966665154 1.038206563 1 17.73847736 1.566616334 2.952454974 1.018253049 0.883985566 0.497941115 0.054461915 0.198935671 3.925910683 0.04099405 0.015835992 36.86517788 -1.566616334 -0.134267483 AESPES(ph)SAIESTQSTPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(0.117)PES(0.766)S(0.117)AIESTQSTPQK;AESPES(0.879)S(0.121)AIESTQSTPQK 488.87 5.72E-240 2251800000 1359036 1367500 977993 1088342 1295029 1266036 1202471 1344080 1589960 1359200 TRUE FALSE 1305923.371 1328500.239 1154738.09 1144511.461 1336684.784 1291636.115 1217187.2 1316324.278 1409474.406 1267140.173 1.030606872 1.048424055 0.911294673 0.903224036 1.054883123 1.019331675 0.960578179 1.038815047 1.112327141 1 20.2731447 1.566958131 5.436410055 1.06196373 0.989522368 0.200158201 0.055814229 0.216880494 13.50156846 0.03255848 0.014863414 36.89420287 -1.566958131 -0.072441362 S(ph)HWIFEARK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHWIFEARK 9 1 I3L3Y3;A0A087WYU4;A6NH52-2;A6NH52 I3L3Y3 TVP23A Golgi apparatus membrane protein TVP23 homolog;Golgi apparatus membrane protein TVP23 homolog A 1 S(1)HWIFEARK 50.791 0.097352 2420400000 1531000 2309400 1916900 3205500 2501800 2621300 2563900 2091100 1629000 2295000 TRUE FALSE 1471166.827 2243538.173 2263326.471 3370936.239 2582272.669 2674304.482 2595277.775 2047918.054 1444082.749 2139557.606 0.68760328 1.048599097 1.057847877 1.575529553 1.206918973 1.249933386 1.212997382 0.957168925 0.674944552 1 21.02888109 1.56718636 4.190947242 0.830667632 1.162678878 0.248045925 0.22067001 0.227589079 8.95313891 0.137518153 0.059426135 36.91359646 -1.56718636 0.332011246 DGVYFLYEALHGPPKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGVYFLYEALHGPPKK 16 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 170.49 3.41E-09 1239910000 1729720 1638320 1376380 1384540 1521860 1739500 1694190 1741650 2174320 2082570 FALSE TRUE 1662120.63 1591596.718 1625122.483 1455996.275 1570812.009 1774673.882 1714924.004 1705684.319 1927500.309 1941515.679 0.856094364 0.819770211 0.837038043 0.749927642 0.809064807 0.914066212 0.883291349 0.878532343 0.992781222 1 20.88875193 1.567335906 0.725269172 1.005295166 0.815955089 0.729290372 0.038913017 0.342678684 0.377448962 0.038159375 0.017223124 36.92630951 -1.567335906 -0.189340078 KELEEMIENLEPHIDDPDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KELEEMIENLEPHIDDPDVK 20 1 Q8TF05-2;Q8TF05 Q8TF05-2 PPP4R1 Serine/threonine-protein phosphatase 4 regulatory subunit 1 0 ; 185.61 2.32E-17 59088000 196876 171613 154636 151839 176841 177895 211242 204369 283810 268110 FALSE TRUE 189181.8683 166718.7653 182582.1651 159675.429 182529.2514 181492.1588 213827.2428 200148.7087 251593.0786 249950.6709 0.756876817 0.667006672 0.730472795 0.638827767 0.730261098 0.726111909 0.855477771 0.800752837 1.006570927 1 17.93128387 1.567515075 0.897482627 1.014292183 0.698739049 0.835469788 0.048954896 0.18970799 0.301282893 0.041791636 0.016570317 36.94154672 -1.567515075 -0.315553134 LGVEPSDDDCVSVQHVCTIVSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 LGVEPSDDDCVSVQHVCTIVSFR 23 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 309.21 3.98E-73 1159320000 447563 546048 354714 599900 429895 526867 549159 472871 477178 519421 FALSE TRUE 430071.7432 530475.2457 418818.7104 630860.9109 443722.9631 537520.6117 555879.7721 463106.0486 423010.7539 484240.153 0.888137302 1.095479675 0.864898765 1.302785213 0.916328314 1.110028998 1.147942335 0.95635615 0.873555717 1 18.88536319 1.567621076 7.485306556 0.930424495 1.049151302 0.119415037 0.128676372 0.22817418 24.58240663 0.065145446 0.030485511 36.95056434 -1.567621076 0.118726807 EYS(ph)GRK ddPTM_BT-474_Pertuzumab_2h_R1 1 EYSGRK 6 1 O00237 O00237 RNF103 E3 ubiquitin-protein ligase RNF103 1 EYS(1)GRK 66.994 0.069903 0 185110 235640 263610 169730 254200 271790 238140 202770 176320 191770 TRUE FALSE 177875.6966 228919.7779 311250.191 178489.7856 262376.5739 277285.78 241054.4286 198582.7286 156304.8928 178781.2471 0.994934868 1.280446253 1.740955475 0.998369731 1.467584426 1.550977994 1.348320545 1.110758158 0.874280135 1 17.44783589 1.567673279 3.095590073 0.944228743 1.353286133 0.361155727 0.217311269 0.226156529 4.934595077 0.14533944 0.057086805 36.95500615 -1.567673279 0.40905739 TQAQVNS(ph)PIVTENK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQAQVNSPIVTENK 14 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 TQAQVNS(0.999)PIVT(0.001)ENK 126.63 0.0003238 0 95062 177180 158080 251610 234070 250830 230210 165270 123550 182780 TRUE FALSE 91346.87194 172126.9999 186648.5725 264595.6223 241599.0741 255901.9545 233027.3788 161857.1167 109525.122 170400.1478 0.536072727 1.0101341 1.095354522 1.552789864 1.417833712 1.501770731 1.36753038 0.949864885 0.642752506 1 17.37856706 1.568118113 4.877856196 0.813925054 1.230396762 0.235143212 0.290876287 0.219946535 11.34469719 0.179795619 0.080626004 36.9928774 -1.568118113 0.416471708 IS(ph)PGATLPESR ddPTM_BT-474_Pertuzumab_2h_R1 4 ISPGATLPESR 11 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 IS(1)PGATLPESR;IS(1)PGATLPESR;IS(1)PGATLPESR;IS(1)PGATLPESR 262.24 1.04E-20 2942960000 2190900 2159650 1677500 1784340 1943100 2080640 1886520 2065850 1977370 1917080 TRUE FALSE 2105277.206 2098058.897 1980661.566 1876430.001 2005601.576 2122711.966 1909607.796 2023189.476 1752907.247 1787234.464 1.177952445 1.17391363 1.108227043 1.049907015 1.12218157 1.187707606 1.068470777 1.132022416 0.98079311 1 20.76929748 1.568322506 0.018503619 6.80E-07 2.164622661 0.466907812 0.050864093 262.9868608 4.973102287 289.9445702 290.2430233 37.01029156 -1.568322506 2.16462198 NQDDFECVTTLEGHENEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 NQDDFECVTTLEGHENEVK 19 0 O76071 O76071 CIAO1 Probable cytosolic iron-sulfur protein assembly protein CIAO1 0 ; 172.57 8.09E-12 423300000 371870 343660 283870 331800 314460 365690 326520 407130 505060 445170 FALSE TRUE 357336.9093 333859.1533 335171.6237 348924.2378 324574.8915 373084.5024 330516.0494 398722.6232 447727.7062 415018.2394 0.861014952 0.804444532 0.807606972 0.840744345 0.7820738 0.898959291 0.796389214 0.960735181 1.078814528 1 18.66281522 1.568460441 3.583403576 1.036695573 0.827365428 0.843533632 0.037555381 0.06266232 1.836839168 0.022122016 0.009127388 37.02204811 -1.568460441 -0.209330145 SPPGSGAST(ph)PVGPWDQAVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 SPPGS(0.007)GAS(0.041)T(0.952)PVGPWDQAVQR 111.22 0.00040037 0 46718 59540 40392 57616 52577 48626 50634 48704 41187 52763 TRUE FALSE 44892.20891 57841.9775 47691.73292 60589.56866 54268.18695 49609.25104 51253.67404 47698.24538 36511.62443 49189.31501 0.912641473 1.175905326 0.969554728 1.231762806 1.103251528 1.008537139 1.041967631 0.969687123 0.742267389 1 15.58605734 1.568661166 3.149676431 0.866996748 1.070521827 0.339558666 0.106157547 0.206731039 4.68024037 0.066665444 0.026364702 37.0391632 -1.568661166 0.203525079 EGKPEIEGKPESEGEPGSETR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGKPEIEGKPESEGEPGSETR 21 2 Q96EI5;Q96EI5-2;D6RD44 Q96EI5 TCEAL4 Transcription elongation factor A protein-like 4 0 90.193 0.0012366 312690000 151150 147160 117120 128790 139690 148160 132690 172590 225710 180890 FALSE TRUE 145242.8909 142963.1409 138286.1893 135436.8673 144183.2557 151155.8967 134313.8999 169025.9562 200088.3471 168638.1592 0.861269428 0.847750839 0.820017189 0.80312112 0.854985944 0.896332701 0.796462085 1.00229958 1.186495085 1 17.3635715 1.568760197 4.072630302 1.094738351 0.84143885 0.807946656 0.050889486 0.063077664 2.35602931 0.028673513 0.012309113 37.04761009 -1.568760197 -0.2532995 TDFKEEPEPGFKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDFKEEPEPGFKR 13 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8 P47897 QARS Glutamine--tRNA ligase 0 122.45 0.00013213 395560000 675060 641410 472470 440550 570070 593110 541720 658290 774590 725040 FALSE TRUE 648677.9089 623117.6148 557855.839 463286.8383 588406.8193 605103.0906 548349.7314 644696.0815 686661.7905 675932.395 0.95967868 0.921863813 0.825313069 0.685404105 0.870511346 0.895212443 0.811249373 0.953787814 1.015873474 1 19.36651943 1.568821687 3.916566087 1.003134278 0.850446417 0.454601213 0.070210893 0.172955265 6.008464099 0.046496955 0.019733969 37.05285585 -1.568821687 -0.152687861 KLPS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPSPAR 7 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 KLPS(1)PAR;KLPS(1)PAR 82.417 0.015035 4230500000 926320 873750 884000 840010 932770 872540 1091000 1104510 1224980 1332110 TRUE FALSE 890118.3903 848831.5055 1043758.464 883363.0168 962773.3942 890183.3566 1104351.984 1081701.483 1085925.406 1241885.003 0.716747837 0.683502501 0.840463056 0.711308225 0.775251647 0.71680015 0.889254626 0.871015818 0.874417038 1 20.24410016 1.569025086 0.51730084 0.99870951 0.722878618 0.735099285 0.050288702 0.405662597 0.266467632 0.050314383 0.03063386 37.0702134 -1.569025086 -0.275830892 KEEPSNNVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEEPSNNVK 9 1 Q14974;Q14974-2;J3KTM9;J3QRG4 Q14974 KPNB1 Importin subunit beta-1 0 ; 169.37 9.38E-05 821150000 1507090 1582060 1265270 1166190 1356960 1418310 1526490 1660900 2029450 1959730 FALSE TRUE 1448191.257 1536941.198 1493932.435 1226377.206 1400607.851 1446989.2 1545171.641 1626601.835 1799075.344 1826995.742 0.792662634 0.841239617 0.817698915 0.671253456 0.766618016 0.792004692 0.845744523 0.890315066 0.984717864 1 20.80104184 1.569855879 1.291868492 1.00379 0.778583679 0.790796102 0.042909471 0.19584041 0.626345127 0.040604293 0.01431392 37.14119549 -1.569855879 -0.225206321 IFIEWMK ddPTM_BT-474_Pertuzumab_2h_R1 2 IFIEWMK 7 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31;C9JXD9;C9J7L5;F8WDJ9 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 123.96 0.009755 175353000 500870 460580 450290 462030 500170 430300 533430 463530 476460 513160 FALSE TRUE 481295.4467 447444.7094 531667.4196 485875.4237 516258.4223 439000.9608 539958.2759 453957.9435 422374.2583 478403.2161 1.006045592 0.935287837 1.11133747 1.015619058 1.079128243 0.91763798 1.128667738 0.948902366 0.882883401 1 18.86786756 1.569931709 9.444230925 0.933899908 1.025614908 0.23279082 0.069371747 0.147127558 24.16104082 0.034818831 0.016307893 37.14768113 -1.569931709 0.091715 NSSQSGGKPGS(ph)SPITK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.577)S(0.423)PITK 87.16 0.0039752 4056200000 1474600 1195300 1174700 925830 1107300 1184900 1236200 1370100 1690600 1531700 TRUE FALSE 1416971.002 1161211.214 1386994.421 973612.1973 1142917.31 1208859.49 1251328.985 1341806.956 1498690.176 1427956.595 0.992306774 0.813197837 0.971314133 0.681821983 0.80038659 0.846565991 0.876307438 0.939669288 1.049534826 1 20.4455207 1.570079136 2.140700998 1.024698288 0.846082987 0.401003041 0.083332665 0.278320115 2.704086534 0.06406624 0.02280827 37.16029356 -1.570079136 -0.178615301 SDQWKPLNLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDQWKPLNLEEK 12 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 190.03 6.53E-06 3143700000 1940120 1793050 1776970 1462730 1654250 1668050 1964800 2193830 2561430 2658430 FALSE TRUE 1864297.965 1741913.97 2098108.007 1538221.671 1707460.454 1701779.114 1988845.81 2148526.644 2270667.205 2478372.168 0.7522268 0.702846002 0.846566966 0.620658064 0.68894433 0.686651963 0.802480691 0.866910415 0.916192989 1 21.24096142 1.57012032 1.281894399 0.980743354 0.716031213 0.745300168 0.057066684 0.207738984 0.65390219 0.050339766 0.017771785 37.1638176 -1.57012032 -0.264712141 RS(ph)SSSGDQSSDSLNSPTLLAL ddPTM_BT-474_Pertuzumab_2h_R1 3 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.478)S(0.478)S(0.037)S(0.007)GDQSSDSLNSPTLLAL;RS(0.422)S(0.422)S(0.085)S(0.028)GDQS(0.022)S(0.022)DSLNSPTLLAL;RS(0.387)S(0.387)S(0.113)S(0.113)GDQS(0.001)S(0.001)DSLNSPTLLAL 133.21 1.09E-05 442550000 385300 410580 313047 403316 299413 382883 377053 355220 361301 362180 TRUE FALSE 370242.05 398870.6604 369621.5566 424131.1871 309043.8911 390625.1566 381667.4874 347884.5829 320287.6252 337649.226 1.09652865 1.181316673 1.094690964 1.2561296 0.915280911 1.156896348 1.130366836 1.03031358 0.948580955 1 18.36516572 1.570128126 3.428280549 0.976512917 1.11903242 0.338430912 0.082743041 0.218335404 5.875909119 0.051374205 0.020929501 37.16448563 -1.570128126 0.142519503 NEEQKAEQEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NEEQKAEQEEGK 12 1 Q9H307 Q9H307 PNN Pinin 0 ; 138.77 6.26E-05 206540000 951660 821190 606910 513360 665080 680480 671320 807110 1009280 810230 FALSE TRUE 914468.0751 797770.4652 716592.1376 539854.5711 686472.9022 694239.7718 679535.815 790442.8965 894710.7656 755352.4004 1.210650915 1.056156656 0.948685855 0.714705574 0.908811439 0.919093884 0.899627531 1.046455795 1.184494502 1 19.52679035 1.570278369 4.825788637 1.099051537 0.943617343 0.176991414 0.125523719 0.253620022 12.83931076 0.076952693 0.034487891 37.1773448 -1.570278369 -0.155434194 TIEDAIAVLSVAEEAADRHPER ddPTM_BT-474_Pertuzumab_2h_R1 5 TIEDAIAVLSVAEEAADRHPER 22 1 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ;;;; 146.99 4.89E-08 428116000 208889 218537 192883 208668 210503 234077 218981 214049 226349 219978 FALSE TRUE 200725.3869 212304.5387 227741.2488 219437.3805 217274.0202 238810.1973 221660.955 209628.8133 200654.8105 205078.6941 0.978772504 1.035234497 1.110506626 1.070015495 1.059466568 1.164480778 1.080858038 1.022187186 0.97842836 1 17.64581809 1.570394525 3.580038275 0.991392316 1.074329954 0.350884037 0.04550243 0.217435346 6.372401211 0.030402426 0.012565548 37.18728953 -1.570394525 0.082937638 ACRTPES(ph)FLGPSASSLVNLDSLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ACRTPESFLGPSASSLVNLDSLVK 24 1 Q9H201 Q9H201 EPN3 Epsin-3 1 ACRT(0.352)PES(0.648)FLGPSASSLVNLDSLVK 283.77 1.20E-52 7432700000 1667300 1618200 1269000 1479800 1553400 1617000 1503100 1733800 1852200 1843800 TRUE FALSE 1602140.073 1572050.52 1498336.529 1556172.655 1603366.522 1649696.848 1521495.387 1697996.424 1641946.021 1718917.784 0.932063236 0.914558297 0.871674342 0.905321168 0.932776737 0.959729932 0.885147272 0.987828761 0.9552208 1 20.71306911 1.570757557 0.597683116 1.000133883 0.90616962 0.517060942 0.027658888 0.563694489 0.457073936 0.026621286 0.014109789 37.21838786 -1.570757557 -0.093964263 VREMEEEAEKLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VREMEEEAEKLK 12 2 Q92843-2;Q86U42-2;Q86U42 Q92843-2 PABPN1 Polyadenylate-binding protein 2 0 ; 155.08 4.05E-05 235290000 568120 700110 473520 607940 594000 694290 594350 568570 529150 557860 FALSE TRUE 545917.2423 680143.5483 559095.5974 639315.8563 613106.5495 708329.0195 601623.8331 556828.8308 469083.1104 520075.6453 1.049688151 1.307778117 1.075027455 1.229274745 1.178879563 1.361973063 1.156800628 1.070668923 0.901951696 1 18.98836195 1.570893119 2.672197444 0.954916046 1.202175513 0.528881839 0.092132366 0.17269101 2.761071617 0.062268982 0.023438421 37.23000708 -1.570893119 0.247259467 TSS(ph)EASMDAAYLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSEASMDAAYLDK 14 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 TSS(1)EASMDAAYLDK;TSS(1)EASMDAAYLDK 334.01 1.65E-43 146070000 769520 716900 615610 510570 639430 633170 582560 738600 851600 786380 TRUE FALSE 739446.3077 696454.7139 726864.4212 536920.5789 659997.8467 645973.1312 589689.5435 723347.6519 754929.9382 733117.7822 1.008632345 0.949990207 0.991470182 0.732379697 0.900261681 0.881131446 0.804358533 0.986673178 1.029752594 1 19.48368547 1.571113954 6.980723384 1.012119708 0.894333059 0.299192979 0.0778642 0.159000996 15.37466279 0.043778704 0.020483665 37.24894304 -1.571113954 -0.117786649 GLVLDHGAR ddPTM_BT-474_Pertuzumab_2h_R1 6 GLVLDHGAR 9 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;; 198.65 2.60E-05 7718110000 4900970 5543020 4760360 5610720 5202860 4805770 5733080 5281910 5440560 6016810 FALSE TRUE 4709434.674 5384938.497 5620662.946 5900289.932 5370214.717 4902945.962 5803243.148 5172836.713 4822970.437 5609286.099 0.839578262 0.96000425 1.002028216 1.051878943 0.957379357 0.874076643 1.034577849 0.922191634 0.859818942 1 22.41938574 1.571181286 12.92702722 0.917528538 0.962842913 0.038198624 0.069178435 0.345542192 99.37168578 0.036863289 0.017157897 37.25471852 -1.571181286 0.045314375 LQPS(ph)PNRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQPSPNRR 8 1 O43150;O43150-2 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 LQPS(1)PNRR;LQPS(1)PNRR 72.2 0.028646 415310000 274010 310130 285770 344350 319110 323300 279660 284560 243840 244180 TRUE FALSE 263301.3863 301285.396 337414.9959 362121.9448 329374.463 329837.3475 283082.5627 278683.7366 216160.3055 227641.4711 1.156649467 1.323508386 1.482221118 1.590755599 1.446900081 1.448933474 1.243545657 1.224222174 0.949564701 1 17.79640388 1.571308761 1.462442854 0.969005848 1.414125377 0.668097464 0.11558907 0.235331733 0.97682671 0.105327084 0.036615672 37.26565519 -1.571308761 0.445119529 TGCTFPEKPDFH ddPTM_BT-474_Pertuzumab_2h_R1 2 TGCTFPEKPDFH 12 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ; 147.71 6.00E-05 547400000 1464870 1311240 1229380 1326460 1307920 1452620 1464130 1476590 1678860 1705350 FALSE TRUE 1407621.261 1273844.719 1451556.313 1394918.76 1349990.435 1481992.972 1482048.461 1446097.9 1488282.851 1589845.126 0.885382631 0.801238246 0.913017432 0.877392859 0.849133298 0.932161849 0.932196751 0.909584133 0.936118133 1 20.6004548 1.571549112 0.168494018 1.048705902 0.798207932 0.631540813 0.031289897 2.268960135 0.398853597 0.24176693 0.246265469 37.28628473 -1.571549112 -0.25049797 IYHLPDAES(ph)DEDEDFKEQTR ddPTM_BT-474_Pertuzumab_2h_R1 15 IYHLPDAESDEDEDFKEQTR 20 1 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0 Q15019-2 2-Sep Septin-2 1 IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(0.981)DEDEDFKEQT(0.019)R;IYHLPDAES(1)DEDEDFKEQTR 281.24 5.66E-45 1.90844E+11 13329171 11885420 10197000 10757022 11361728 11361155 11956642 12647695 15128710 13553750 TRUE FALSE 12808252.26 11546459.46 12039824.73 11312193.19 11727188.3 11590885.34 12102970.96 12386515.68 13411362.27 12635742.44 1.013652527 0.913793512 0.952838726 0.895253544 0.928096497 0.917309402 0.957836156 0.980276049 1.061383004 1 23.5910071 1.571600968 2.451205905 1.029675387 0.935394158 0.529204826 0.033858241 0.180943823 2.390660023 0.02374969 0.008733761 37.29073715 -1.571600968 -0.094281229 FMERDPDELR ddPTM_BT-474_Pertuzumab_2h_R1 3 FMERDPDELR 10 1 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 ;; 168.22 4.56E-06 1919930000 1416830 1597090 1137510 1469560 1591630 1633910 1495180 1478440 1475500 1576790 FALSE TRUE 1361458.717 1551542.557 1343083.361 1545404.168 1642826.224 1666948.78 1513478.46 1447909.697 1308007.426 1469992.609 0.926167049 1.055476434 0.913666744 1.051300638 1.117574479 1.133984463 1.02958236 0.984977536 0.889805444 1 20.48737747 1.571666423 3.655288212 0.94292898 1.036488315 0.196687698 0.070903381 0.292724172 8.939657175 0.046638798 0.019430577 37.29635785 -1.571666423 0.093559334 YLLSQSS(ph)PAPLTAAEEELR ddPTM_BT-474_Pertuzumab_2h_R1 5 YLLSQSSPAPLTAAEEELR 19 0 Q12792;Q12792-3;Q12792-4;F8VS81 Q12792 TWF1 Twinfilin-1 1 YLLS(0.001)QS(0.47)S(0.53)PAPLTAAEEELR;YLLSQSS(1)PAPLTAAEEELR;YLLSQSS(1)PAPLTAAEEELR;YLLSQS(0.033)S(0.967)PAPLTAAEEELR;YLLSQS(0.033)S(0.967)PAPLTAAEEELR 264.01 2.78E-31 530414000 656148 728159 646093 822212 801517 790242 703964 705393 632895 671150 TRUE FALSE 630505.0108 707392.6183 762856.3774 864646.4599 827298.5222 806221.2347 712579.322 690826.388 561051.4129 625692.4127 1.007691636 1.130575669 1.219219479 1.38190338 1.322212808 1.288526468 1.138865212 1.104099033 0.896688855 1 19.25509408 1.571898516 2.008193216 0.95177442 1.228227006 0.503544193 0.103777549 0.261149963 2.196352794 0.089481444 0.031564305 37.31629484 -1.571898516 0.276452586 RKGS(ph)GS(ph)EQEGEDEEGGER ddPTM_BT-474_Pertuzumab_2h_R1 3 RKGSGSEQEGEDEEGGER 18 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 2 RKGS(1)GS(1)EQEGEDEEGGER;RKGS(1)GS(1)EQEGEDEEGGER;RKGS(1)GS(1)EQEGEDEEGGER 158.37 6.07E-09 1223960000 2644530 2470200 1987660 1985260 2227100 2350080 2299490 2587730 3167650 2716930 TRUE FALSE 2541178.844 2399752.315 2346874.377 2087719.507 2298736.694 2397600.228 2327631.846 2534292.471 2808071.652 2532909.911 1.003264598 0.947429004 0.926552645 0.824237569 0.907547751 0.946579354 0.918955639 1.000545839 1.108634634 1 21.27236433 1.572143222 3.468426799 1.055331238 0.922190802 0.536240054 0.048873647 0.146284299 4.035699866 0.032337961 0.013253319 37.33732691 -1.572143222 -0.133140437 ALFPGDSEIDQLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALFPGDSEIDQLFR 14 0 G3V5T9;P24941;P24941-2;E7ESI2;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 0 ; 204.17 3.26E-08 87766000 76724 82564 70876 79484 80154 83271 86593 77007 74525 87240 FALSE TRUE 73725.54126 80209.35556 83684.86983 83586.17877 82732.2262 84954.79667 87652.75104 75416.77854 66065.23443 81331.15709 0.906485828 0.986206989 1.028939865 1.027726418 1.01722672 1.044554138 1.077726595 0.927280285 0.812299207 1 16.31152052 1.572180641 6.094971216 0.895154463 1.014102804 0.367388877 0.059754012 0.123319663 9.390639106 0.032153865 0.014923004 37.34054406 -1.572180641 0.11894834 GLAITFVSDENDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLAITFVSDENDAK 14 0 O00148;Q13838-2;Q13838;A0A0G2JJZ9;H0Y400 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ; 186.46 2.47E-06 181931000 331200 346080 266729 298310 287660 313280 296100 341740 386050 368250 FALSE TRUE 318256.3378 336210.1372 314932.8637 313705.8148 296912.8451 319614.7362 299723.7604 334682.9496 342227.2225 343308.0995 0.927028341 0.979324804 0.917347607 0.913773416 0.864858259 0.930985132 0.873045992 0.974876358 0.996851583 1 18.38914437 1.572287206 5.592242355 0.994438241 0.916395981 0.578875596 0.029827661 0.106597768 6.979241662 0.017476629 0.008036047 37.34970761 -1.572287206 -0.078042259 WKPDYDSAASEYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 WKPDYDSAASEYGK 14 1 Q99747;J3KTJ6 Q99747 NAPG Gamma-soluble NSF attachment protein 0 ; 179.25 1.72E-06 1330490000 860210 864250 730270 743600 807550 876550 874250 986030 1112380 1142570 FALSE TRUE 826592.0422 839602.4362 862246.0338 781977.2851 833525.5791 894274.4416 884949.333 965668.1359 986107.2859 1065182.716 0.776009627 0.788223864 0.809481811 0.734125022 0.782518873 0.839550274 0.830795806 0.906575108 0.925763506 1 20.02266949 1.572537293 0.766526543 0.996632134 0.7761553 0.919591962 0.021907556 0.151635886 0.182794237 0.020555761 0.008944588 37.37122144 -1.572537293 -0.220476834 GSAADSEESPAIEAIHLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSAADSEESPAIEAIHLLR 19 0 P13716;P13716-2;B7ZBK6 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ;; 192.55 7.23E-15 226021000 300656 343336 276992 324286 331539 294867 339142 307923 313403 332526 FALSE TRUE 288906.0311 333544.3934 327050.6161 341022.4393 342203.253 300829.4128 343292.5212 301564.2824 277826.8053 310003.7178 0.931943762 1.075936753 1.054989335 1.100059192 1.103868223 0.970405822 1.107381949 0.972776341 0.896204753 1 18.24192599 1.572779663 5.820748347 0.944149751 1.051362351 0.343282803 0.059319964 0.136831667 9.61275993 0.03143578 0.014528104 37.39208331 -1.572779663 0.1072126 ELSEES(ph)EDEELQLEEFPMLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSEESEDEELQLEEFPMLK 20 0 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 ELS(0.37)EES(0.63)EDEELQLEEFPMLK 80.316 0.0041803 14776000 29132 29418 26730 37239 30481 31800 37278 41430 50246 53864 TRUE FALSE 27993.48923 28579.02744 31560.70561 39160.90925 31461.44905 32443.01779 37734.21932 40574.45602 44542.28473 50215.7433 0.5574644 0.569124851 0.628502209 0.779853223 0.626525607 0.646072639 0.751442015 0.808002697 0.887018329 1 15.61585212 1.572854667 0.326504436 1.040961885 0.550507278 0.848076244 0.053737187 0.526680451 0.191232493 0.094317537 0.085668249 37.39854167 -1.572854667 -0.490454606 TS(ph)PQVLGSILK ddPTM_BT-474_Pertuzumab_2h_R1 4 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 T(0.212)S(0.788)PQVLGSILK;T(0.136)S(0.864)PQVLGSILK;T(0.039)S(0.961)PQVLGSILK;T(0.069)S(0.931)PQVLGSILK 153.18 3.42E-05 1214630000 4889000 4387570 4582990 4055850 4262030 4140150 5046230 5505310 6469610 6629080 TRUE FALSE 4697932.475 4262440.799 5411238.241 4265172.905 4399122.066 4223866.67 5107987.272 5391623.425 5735206.996 6180086.507 0.760172608 0.689705685 0.875592637 0.690147767 0.711822085 0.683464004 0.826523588 0.872418763 0.928014032 1 22.5591956 1.572948403 1.345172708 0.981633282 0.737172425 0.724560916 0.05630081 0.210358864 0.731614182 0.048715796 0.017096308 37.40661445 -1.572948403 -0.244460856 FNNDSHS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 FNNDSHSPK 9 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 FNNDSHS(1)PK;FNNDSHS(1)PK;FNNDS(0.004)HS(0.996)PK;FNNDS(0.108)HS(0.892)PK 138.45 8.78E-05 690840000 2894650 2564430 2375970 2316060 2493140 2472480 2586850 2767440 3256140 2922890 TRUE FALSE 2781523.878 2491294.967 2805360.632 2435592.134 2573334.112 2522475.24 2618508.644 2710291.397 2886516.638 2724920.057 1.020772654 0.914263507 1.029520343 0.893821501 0.944370498 0.925706144 0.960948795 0.994631527 1.059303237 1 21.37778247 1.573312565 3.101851566 1.029531333 0.952808805 0.325696405 0.042688435 0.22245006 4.90223335 0.02683762 0.010616211 37.43799353 -1.573312565 -0.076722528 IVEHAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IVEHAEK 7 0 Q7Z2Z2-2;Q7Z2Z2 Q7Z2Z2-2 EFTUD1 Elongation factor Tu GTP-binding domain-containing protein 1 0 75.189 0.044144 220730000 452920 486840 423930 466180 460260 480830 488500 464720 488150 488660 FALSE TRUE 435219.3857 472955.7999 500543.5813 490239.6057 475064.6809 490552.712 494478.4091 455123.3696 432737.2585 455562.6229 0.955344806 1.038179552 1.098737157 1.076119025 1.042808731 1.076806321 1.085423571 0.9990358 0.949896319 1 18.79728986 1.573329609 4.944189084 0.97481062 1.055686264 0.408803371 0.039314547 0.143884356 7.601033427 0.022986662 0.010373617 37.43946281 -1.573329609 0.080875645 VLTANSNPSS(ph)PSAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 VLTANSNPSSPSAAK 15 0 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.001)S(0.977)PS(0.021)AAK;VLTANSNPS(0.058)S(0.941)PS(0.001)AAK;VLTANSNPS(0.031)S(0.506)PS(0.463)AAK;VLTANSNPS(0.001)S(0.999)PSAAK 379.44 3.99E-98 3314460000 3675150 3347840 3022090 3399700 3251550 3421420 3936740 4141540 4522490 4904960 TRUE FALSE 3531521.075 3252362.881 3568248.889 3575158.924 3356139.059 3490603.457 3984919.002 4056015.752 4009115.895 4572742.69 0.772298228 0.711249922 0.780330128 0.781841264 0.733944437 0.763350071 0.871450521 0.886998466 0.876742071 1 22.12462831 1.573704175 0.629362271 0.991175503 0.744520434 0.866613668 0.030655661 0.23248279 0.203780403 0.03003441 0.015216882 37.47176722 -1.573704175 -0.246655068 SPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPGPNHTSNSSNASNATVVPQNSSAR 28 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.427)PS(0.573)PGPNHTSNSSNASNATVVPQNSSAR;S(0.036)PS(0.956)PGPNHT(0.003)S(0.004)NS(0.001)SNASNATVVPQNSSAR 264.97 3.68E-54 436550000 68911 118057 79817 152550 122204 126253 126950 96799 71515 114283 TRUE FALSE 66217.88193 114690.1299 94241.70742 160423.1238 126134.8026 128805.9222 128503.6521 94800.06682 63396.91702 106542.5106 0.621516065 1.076472943 0.884545585 1.505719387 1.183891781 1.208962708 1.206125624 0.889786305 0.5950387 1 16.70106966 1.573792404 4.884795226 0.781489648 1.111263252 0.21873238 0.235741138 0.209770412 10.85066885 0.135820758 0.061173236 37.47938054 -1.573792404 0.329773604 KDISENKR ddPTM_BT-474_Pertuzumab_2h_R1 3 KDISENKR 8 2 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;; 107.15 0.0022822 2466730000 1290570 1355890 1021000 1284750 1239440 1020580 1607040 1448620 1812280 1863200 FALSE TRUE 1240133.098 1317221.345 1205517.412 1351056.101 1279307.713 1041216.827 1626707.436 1418705.491 1606557.572 1737003.804 0.713949558 0.758329568 0.69402117 0.777808372 0.73650254 0.599432669 0.936501942 0.816754395 0.924901585 1 20.72816948 1.57379675 0.962415934 0.98517495 0.722015096 0.632492401 0.071591814 0.320047649 0.576085417 0.062064769 0.023883517 37.47975556 -1.57379675 -0.263159854 ESEPES(ph)PMDVDNSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESEPESPMDVDNSK 14 0 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 ESEPES(1)PMDVDNSK 283.34 1.99E-33 112550000 130490 126510 105300 131490 135600 129900 124080 127990 130490 128790 TRUE FALSE 125390.3065 122902.0587 124330.0524 138276.2147 139961.6971 132526.667 125598.5282 125346.9618 115677.3223 120066.9386 1.044336668 1.023612829 1.035506142 1.151659368 1.165697225 1.103773183 1.04607088 1.043975663 0.963440258 1 16.87347942 1.574026111 1.867656045 0.983472205 1.086595772 0.421459204 0.046257406 0.347313257 2.479633868 0.042399029 0.01484321 37.49955474 -1.574026111 0.103123567 EKVELAAECCR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKVELAAECCR 11 1 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4;M0R2C7 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 0 79.466 0.017249 0 87923 108950 75382 101510 86329 98298 93290 94281 100280 95604 FALSE TRUE 84486.87196 105842.8527 89005.20426 106748.9433 89105.85069 100285.6529 94431.71093 92334.0644 88896.63481 89128.65592 0.947920409 1.187528877 0.998614905 1.197694974 0.999744131 1.125178562 1.059498878 1.035963837 0.997396784 1 16.44360173 1.574026292 2.028998199 0.998495017 1.080113511 0.134057479 0.076325828 0.530184179 4.57049423 0.053948068 0.019099525 37.49957035 -1.574026292 0.081618494 KMLGEDS(ph)DEEEEMDTSER ddPTM_BT-474_Pertuzumab_2h_R1 2 KMLGEDSDEEEEMDTSER 18 1 A0A087X0M4;A0A087WWF4;Q9BWU0;H7C256 A0A087X0M4 SLC4A1AP Kanadaptin 1 KMLGEDS(1)DEEEEMDTSER;KMLGEDS(1)DEEEEMDTSER 241.82 3.18E-24 722180000 502040 447160 338350 351780 439170 400300 416710 461090 554260 485070 TRUE FALSE 482419.7218 434407.4346 399497.3716 369935.408 453296.3019 408394.3403 421809.8216 451568.3304 491342.7284 452215.7768 1.066791002 0.960619812 0.883422012 0.818050645 1.002389401 0.903096179 0.932762286 0.99856828 1.086522748 1 18.7866518 1.57405126 3.502051849 1.043701998 0.933525227 0.290918224 0.066314336 0.234845617 6.613439945 0.043161961 0.017780896 37.50172629 -1.57405126 -0.11017677 KKAEEEAEAKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKAEEEAEAKPK 12 3 Q9BUQ8;F8VVA2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 134.21 6.55E-05 543380000 738300 620460 582440 476390 624670 619620 606800 744020 962110 788980 FALSE TRUE 709446.4198 602765.0883 687699.8643 500976.545 644763.0779 632149.1409 614226.1999 728655.727 852895.3063 735541.6818 0.964522388 0.81948461 0.934957027 0.681098784 0.876582652 0.859433471 0.835066476 0.990638253 1.159547212 1 19.48844757 1.574108207 3.577681947 1.080172114 0.849629049 0.571259785 0.080275358 0.12403831 3.641431262 0.048196638 0.019993035 37.50664404 -1.574108207 -0.230543065 GQVQEVGWHDVAGWLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQVQEVGWHDVAGWLGR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 157.51 2.29E-08 3129400000 2376200 2812900 2179500 2627600 2773000 2593400 2912400 2521400 2641820 2690000 FALSE TRUE 2283335.477 2732678.846 2573384.133 2763210.751 2862196.063 2645840.325 2948042.822 2469332.209 2341931.669 2507803.904 0.910492034 1.089670066 1.026150461 1.101844824 1.141315738 1.055042749 1.175547585 0.984659209 0.933857574 1 21.25799311 1.574154753 8.283028736 0.965293606 1.074222349 0.301963545 0.06890333 0.131491653 17.75043165 0.036044553 0.016949429 37.51066409 -1.574154753 0.108928743 VPAS(ph)PLPGLER ddPTM_BT-474_Pertuzumab_2h_R1 6 VPASPLPGLER 11 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER 163.93 2.45E-05 28532700000 4353780 4676230 3820770 4730220 3927450 4174360 4056170 4297170 3947160 3831610 TRUE FALSE 4183629.464 4542868.499 4511268.132 4974347.221 4053779.996 4258768.419 4105810.622 4208431.938 3499094.945 3572091.642 1.171198806 1.271767064 1.262920603 1.39255868 1.134847703 1.192233808 1.149413574 1.178142209 0.979564719 1 21.76833766 1.574331935 0.724182036 0.984368469 1.259053142 0.62505009 0.071357964 0.412187735 0.451792196 0.066463615 0.030103728 37.52597069 -1.574331935 0.274684674 S(ph)KSQEEPKDTFEHDPSESIDEFNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSQEEPKDTFEHDPSESIDEFNK 24 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.498)KS(0.498)QEEPKDT(0.005)FEHDPSESIDEFNK 172.52 2.78E-12 227740000 150950 113810 112200 72774 107800 91309 116740 133290 175320 152170 TRUE FALSE 145050.7071 110564.2502 132477.0359 76529.87486 111267.4849 93155.33054 118168.699 130537.5149 155418.4086 141863.3904 1.022467507 0.779371267 0.933835259 0.539461764 0.784328392 0.656655183 0.832975292 0.920163508 1.095549798 1 17.11414281 1.574339657 2.50844704 1.044170651 0.78063681 0.389553496 0.127781515 0.249384416 3.477585681 0.092617525 0.034375247 37.52663791 -1.574339657 -0.263533842 NKEPGAEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NKEPGAEEK 9 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;; 113.22 0.0016735 1212950000 1864530 1593490 1514170 1410430 1370080 1496220 1634340 2137500 2671720 2614230 FALSE TRUE 1791662.106 1548045.225 1787814.202 1483222.461 1414149.867 1526474.594 1654341.542 2093359.878 2368437.546 2437165.874 0.735141635 0.635182546 0.733562791 0.608584946 0.580243587 0.626331843 0.67879727 0.858932049 0.971799898 1 21.21677301 1.574511098 2.085146646 0.990780398 0.649352583 0.892776263 0.046987056 0.088903124 0.815864526 0.038471088 0.013690092 37.54145477 -1.574511098 -0.341427815 WGTDEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 WGTDEEK 7 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;; 171.47 0.0021788 2084700000 2256710 1964290 1663570 1824630 1483870 1318020 1686730 2250970 2612560 2718010 FALSE TRUE 2168515.278 1908270.372 1964214.105 1918799.373 1531600.026 1344671.267 1707372.706 2204486.683 2315993.142 2533916.762 0.855795783 0.753091183 0.775169151 0.757246411 0.604439755 0.530669076 0.673807732 0.869991752 0.913997325 1 21.2729377 1.574534125 3.166075673 0.946524772 0.703015598 0.574635645 0.088779486 0.17152571 3.947886695 0.06634173 0.026456264 37.54344536 -1.574534125 -0.243509174 LTALADLEDWEELEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTALADLEDWEELEK 15 0 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 ; 269.2 1.75E-25 44008000 92608 91679 80758 83672 83417 89717 92207 110987 121787 128400 FALSE TRUE 88988.77698 89064.40468 95352.76705 87990.32195 86100.18356 91531.13921 93335.45685 108695.0797 107962.2503 119703.3536 0.743410893 0.744042685 0.796575569 0.735069814 0.719279627 0.764649748 0.77972299 0.908037046 0.901915001 1 16.86910405 1.574632764 1.220314804 0.980316157 0.746737086 0.914025679 0.026215519 0.112551937 0.320420212 0.023193904 0.008284301 37.55197335 -1.574632764 -0.233579072 DKLCS(ph)PLSEPGDPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKLCSPLSEPGDPSK 15 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 DKLCS(0.999)PLS(0.001)EPGDPSK;DKLCS(1)PLSEPGDPSK 179.95 3.93E-07 1160650000 1941610 1614710 1335820 1252720 1459960 1608330 1492680 1802520 2265540 1869740 TRUE FALSE 1865729.735 1568660.052 1577232.389 1317373.029 1506920.939 1640851.535 1510947.864 1765297.332 2008365.397 1743100.844 1.070351002 0.899925014 0.904842881 0.755764093 0.864505886 0.941340565 0.866816093 1.012733909 1.152179694 1 20.73322461 1.574648845 4.068587904 1.078496206 0.895677792 0.440509606 0.08134727 0.15079381 5.637360226 0.049450196 0.0213367 37.55336385 -1.574648845 -0.182818413 DIVTESNKFDLVSFIPLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIVTESNKFDLVSFIPLLR 19 1 Q08AM6 Q08AM6 VAC14 Protein VAC14 homolog 0 ; 205.62 3.67E-16 147966000 318320 346120 270820 277284 338950 301340 319400 317980 342320 335210 FALSE TRUE 305879.7025 336248.9965 319763.1984 291594.6605 349852.6346 307433.3013 323308.9127 311413.6019 303461.2687 312505.9281 0.97879648 1.075976377 1.023222824 0.933085213 1.119507194 0.983767902 1.034568895 0.996504622 0.971057639 1 18.25352403 1.574842576 4.759042037 0.98497583 1.022312214 0.083856618 0.049246747 0.371921581 18.38245016 0.026909328 0.012066033 37.57011944 -1.574842576 0.037336384 LLQDLHEAQAER ddPTM_BT-474_Pertuzumab_2h_R1 1 LLQDLHEAQAER 12 0 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2 Q9H8M2 BRD9 Bromodomain-containing protein 9 0 142.38 6.13E-05 91669000 131640 141830 120720 139990 132560 131300 139530 129120 131850 132000 FALSE TRUE 126495.3633 137785.1473 142536.7894 147214.9007 136823.9128 133954.976 141237.6099 126453.6269 116882.9408 123059.5224 1.027920154 1.11966262 1.158275171 1.1962902 1.111851485 1.088538078 1.147717845 1.027580998 0.949808178 1 16.90899677 1.57493435 3.693342452 0.977179439 1.12390773 0.655323557 0.043788608 0.112680614 3.518461567 0.028296967 0.011866764 37.57805952 -1.57493435 0.146728291 TSFDDRLEDDDFDLIEENLGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSFDDRLEDDDFDLIEENLGVK 22 1 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 237.15 1.49E-30 71286000 83412 79971 65178 61047 73461 81480 81513 87682 102670 104710 FALSE TRUE 80152.16682 77690.30538 76957.11448 64197.64299 75823.93978 83127.58143 82510.58048 85871.33606 91015.33203 97617.89843 0.821080643 0.795861278 0.788350453 0.657642133 0.776742186 0.851560859 0.845240287 0.879667944 0.932363158 1 16.57485807 1.575281269 0.764312964 0.99444396 0.767389112 0.74303236 0.044721203 0.319106118 0.382451642 0.044431837 0.019389533 37.6080893 -1.575281269 -0.227054849 QAQAQES(ph)EEEEESR ddPTM_BT-474_Pertuzumab_2h_R1 8 QAQAQESEEEEESR 14 0 H0YLQ7;Q9NVM6 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 1 QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR 332.06 1.95E-68 2191506800 766188.8 844887.7 679425.1 856583.5 807447.8 861379.4 790305.1 820819.1 845911.2 834773.5 TRUE FALSE 736245.2946 820792.33 802212.3293 900791.8771 833420.0918 878797.0816 799977.0902 803868.8987 749886.9069 778233.5473 0.94604672 1.054686389 1.030811807 1.157482712 1.070912575 1.129220251 1.027939611 1.032940435 0.963575664 1 19.56984365 1.57531199 2.12262721 0.98412822 1.066348798 0.231608046 0.055066224 0.411242382 3.932469064 0.043307839 0.015474362 37.61074964 -1.57531199 0.082220577 GGPPS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGPPSPTK 8 0 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 GGPPS(0.997)PT(0.003)K 92.428 0.011316 0 741460 634340 563450 559810 596510 655770 686190 704910 822970 816930 TRUE FALSE 712482.9235 616249.2443 665277.9489 588701.8612 615697.2859 669030.1187 694587.7985 690353.3622 729549.8958 761598.6035 0.935509756 0.809152277 0.87352832 0.772981802 0.808427541 0.878455023 0.912012962 0.906453031 0.957919162 1 19.53867131 1.575475064 0.888619513 0.993893019 0.838702872 0.59182289 0.043622552 0.366765121 0.570857799 0.039385456 0.015738141 37.62487484 -1.575475064 -0.155190147 SPQQTVPYVVPLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 SPQQTVPYVVPLS(1)PK 89.982 0.0064928 42932000 144310 141240 93541 128740 122800 118660 118620 137570 156260 145540 TRUE FALSE 138670.2057 137211.9735 110445.9395 135384.2868 126749.9735 121059.3865 120071.707 134729.1314 138522.0199 135682.4462 1.022020236 1.011272846 0.814003157 0.997802521 0.934166335 0.892225855 0.884946509 0.992973927 1.020928085 1 17.04987456 1.575761838 6.595230418 1.009002093 0.935277981 0.212786662 0.060453471 0.198472622 17.53444043 0.033344259 0.015602022 37.64972754 -1.575761838 -0.073724113 DKDDDGGEDDDANCNLICGDEYGPETR ddPTM_BT-474_Pertuzumab_2h_R1 5 DKDDDGGEDDDANCNLICGDEYGPETR 27 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;; 310.59 4.89E-82 7836080000 4519600 3524820 2686330 2737040 3324270 3268170 3379370 3763080 4604710 3998870 FALSE TRUE 4342969.035 3424295.585 3171809.588 2878298.962 3431198.164 3334254.637 3420727.741 3685371.083 4082002.625 3728022.973 1.164952326 0.918528563 0.85080205 0.772071144 0.920380102 0.894376097 0.917571529 0.988559113 1.094951038 1 21.82997932 1.575812502 3.133632341 1.047309902 0.910251348 0.217699976 0.09634925 0.303719535 6.852129924 0.065779953 0.026181407 37.65411993 -1.575812502 -0.137058554 DFSNSPLHR ddPTM_BT-474_Pertuzumab_2h_R1 3 DFSNSPLHR 9 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;O95758-7 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 ;; 167.67 5.98E-05 1417590000 828290 1073090 940670 1100210 952610 937250 1075030 972360 964410 1106310 FALSE TRUE 795919.5111 1042486.524 1110669.994 1156991.97 983251.5658 956201.8372 1088186.539 952280.4262 854934.2199 1031378.638 0.771704475 1.01076994 1.076878998 1.121791675 0.953337144 0.927110376 1.055079578 0.92330827 0.828923722 1 19.97614264 1.57611097 6.909480478 0.902624058 0.993868124 0.09277915 0.098842049 0.25378729 24.48662222 0.053977038 0.025324342 37.68000658 -1.57611097 0.091244065 SSQPPADRDPAPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSQPPADRDPAPFR 14 1 Q10570 Q10570 CPSF1 Cleavage and polyadenylation specificity factor subunit 1 0 ; 101.72 0.0027906 340220000 354370 342400 296510 349530 327270 358920 348720 345630 362970 369410 FALSE TRUE 340520.8286 332635.0872 350095.9528 367569.2852 337796.9368 366177.6083 352987.7397 338492.6197 321767.1673 344389.5317 0.988766491 0.965868752 1.016569671 1.067306789 0.980857157 1.063265793 1.02496652 0.982877203 0.934311696 1 18.39368176 1.576267763 4.535893997 0.964736042 1.015832276 0.25507422 0.034127485 0.208804661 9.487734736 0.020185728 0.008966832 37.69361259 -1.576267763 0.051096234 GKIEVLDS(ph)PASK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKIEVLDSPASK 12 1 Q8N5I9 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 GKIEVLDS(0.979)PAS(0.021)K 143.86 3.79E-05 620570000 785010 710010 583130 531490 589000 700360 690450 803670 881770 933340 TRUE FALSE 754330.9413 689761.21 688514.5627 558920.2626 607945.7199 714521.7591 698899.9336 787073.9337 781675.1663 870124.0505 0.866923447 0.792715946 0.791283223 0.642345493 0.69868856 0.82117229 0.803218729 0.904553705 0.89834911 1 19.73086157 1.576320375 1.067618698 0.980170206 0.758967846 0.619853937 0.060404716 0.327090055 0.715346863 0.057732493 0.021388631 37.6981792 -1.576320375 -0.22120236 GAEEMETVIPVDVMR ddPTM_BT-474_Pertuzumab_2h_R1 5 GAEEMETVIPVDVMR 15 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;; 257.13 2.07E-24 479394000 497230 568158 474065 565174 570314 551827 533577 554222 562293 568817 FALSE TRUE 477797.7019 551954.6901 559739.091 594342.6979 588658.6678 562985.32 540107.0749 542777.122 498463.856 530290.5179 0.901011211 1.040853403 1.055532905 1.120786961 1.110068251 1.06165451 1.018511659 1.023546723 0.939982593 1 19.01642343 1.576670846 2.034561244 0.972422281 1.052255774 0.185572154 0.058597936 0.481384543 4.181997591 0.047961824 0.017031034 37.72861353 -1.576670846 0.079833493 SPGQLQRPTGVAVDTNGDIIVADYDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGQLQRPTGVAVDTNGDIIVADYDNR 27 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 161.39 1.20E-11 372310000 135840 154970 128840 154090 145760 173620 151360 146860 154040 146140 FALSE TRUE 130531.2226 150550.4073 152124.254 162042.6034 150448.5028 177130.7154 153212.389 143827.2897 136554.025 136241.8076 0.958084929 1.10502356 1.116575423 1.189375025 1.104275592 1.300120121 1.124562215 1.05567661 1.002291641 1 17.05580996 1.576727387 2.96529389 1.005538067 1.134894966 0.293200007 0.079940877 0.281883697 5.671744449 0.056056143 0.02193791 37.7335258 -1.576727387 0.129356899 AVEQHNGK ddPTM_BT-474_Pertuzumab_2h_R1 6 AVEQHNGK 8 0 Q9BRA2;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;;;; 104.01 0.0046619 2631630000 4233610 4220460 3077360 3854410 3724310 3850220 4182940 3723130 3548090 4389170 FALSE TRUE 4068155.841 4100096.613 3633507.408 4053336.562 3844105.813 3928074.086 4234132.071 3646246.064 3145325.698 4091887.606 0.994200289 1.002006166 0.887978302 0.990578665 0.939445601 0.959966271 1.034762554 0.891091451 0.768673532 1 21.96433509 1.57711908 6.841523907 0.867395142 0.96945907 0.264639381 0.064342651 0.13755486 13.0676664 0.032581494 0.015289542 37.76757324 -1.57711908 0.102063928 EDEEESLNEVGYDDIGGCR ddPTM_BT-474_Pertuzumab_2h_R1 6 EDEEESLNEVGYDDIGGCR 19 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 555.03 0 8200110000 2005980 1884430 1556570 2509390 1761250 1893420 2324540 2645290 3128860 3297060 FALSE TRUE 1927584.084 1830687.901 1837876.825 2638899.919 1817902.206 1931706.25 2352988.416 2590663.837 2773684.93 3073747.189 0.627112109 0.595588312 0.597927127 0.858528615 0.591428668 0.628453198 0.765511368 0.842835691 0.902379005 1 21.55156708 1.577235484 1.04568407 0.989687223 0.647488796 0.723376771 0.075768124 0.257158122 0.540393058 0.069103053 0.025789751 37.77769745 -1.577235484 -0.342198427 DITVFVPQWR ddPTM_BT-474_Pertuzumab_2h_R1 1 DITVFVPQWR 10 0 O15037 O15037 KHNYN Protein KHNYN 0 97.635 0.013782 63863000 47517 59242 56626 70282 68035 67055 62163 54080 45127 52381 FALSE TRUE 45659.98311 57552.47616 66859.57784 73909.26244 70223.40756 68410.89804 62923.76939 52963.2291 40004.37215 48833.18821 0.935019498 1.178552502 1.369142181 1.513504753 1.438026271 1.400909925 1.288545182 1.084574467 0.819204594 1 15.57557435 1.578402782 2.864808277 0.913489011 1.319490173 0.50482132 0.157457184 0.191277734 3.581786902 0.117299191 0.045492937 37.87937306 -1.578402782 0.406001162 RMEEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 RMEEEER 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 101.25 0.014744 200160000 203850 182920 172610 218510 223060 220500 212370 199170 200840 208630 FALSE TRUE 195883.3166 177703.3007 203804.4667 229787.3273 230234.9275 224958.6611 214969.0476 195057.0699 178041.4852 194499.3043 1.00711577 0.913644917 1.047841623 1.181430073 1.183731368 1.156603937 1.105243273 1.0028677 0.915383661 1 17.56940547 1.57894451 4.028323212 0.957736231 1.08698459 0.297318637 0.080766942 0.243737327 8.966013021 0.056222222 0.024284787 37.92665231 -1.57894451 0.129248359 FSPPS(ph)PLPQAVFSTSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 FSPPSPLPQAVFSTSSR 17 0 Q99594;A0A1X7SBS4 Q99594 TEAD3 Transcriptional enhancer factor TEF-5 1 FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR 218.05 5.01E-15 1592500000 398308 418612 329715 417740 425578 381337 396241 371204 353059 367281 TRUE FALSE 382741.683 406673.5956 389301.835 439299.6115 439267.1029 389047.8954 401090.3159 363538.5077 312981.2225 342404.7307 1.117804892 1.187698531 1.136963949 1.282983476 1.282888534 1.136222314 1.171392448 1.061721627 0.914068044 1 18.38534311 1.579018946 2.27213938 0.956564075 1.194199332 0.724795261 0.057524198 0.14217433 1.591580232 0.045000906 0.016374558 37.93315329 -1.579018946 0.237635257 MIEYDPERR ddPTM_BT-474_Pertuzumab_2h_R1 3 MIEYDPERR 9 1 O60832;O60832-2;C9IYT0;H7C0M1;H7BZF2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ;; 112.75 0.0030661 853050000 885340 948630 779340 948220 879570 904440 923370 896620 906310 975200 FALSE TRUE 850739.934 921576.0012 920184.0743 997157.7478 907862.1679 922728.3965 934670.4783 878104.4837 803429.4884 909148.8354 0.935754302 1.013669011 1.012137989 1.096803635 0.998584756 1.014936565 1.028072018 0.965853389 0.883716128 1 19.79415697 1.579221499 4.417064586 0.937019894 1.016503507 0.304097339 0.04513901 0.174033627 7.551037504 0.025823263 0.011426694 37.95084923 -1.579221499 0.079483614 S(ph)PDALESAQSEEEVDELSLIDHNEIMSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPDALESAQSEEEVDELSLIDHNEIMSR 28 0 Q13905-2;Q13905;Q13905-4;Q13905-3;H0Y6R4 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 S(1)PDALESAQSEEEVDELSLIDHNEIMSR;S(1)PDALESAQSEEEVDELSLIDHNEIMSR 146.39 5.67E-08 97024000 16700.6 16893.7 15774.9 22159 19806.5 19869.2 19123.5 16718.8 15719.8 16175.9 TRUE FALSE 16047.92209 16411.90822 18625.77534 23302.62865 20443.59406 20270.96884 19357.53911 16373.55094 13935.35421 15080.29189 1.064165217 1.088301761 1.235107084 1.545237242 1.355649759 1.344202685 1.283631594 1.085758224 0.92407722 1 13.88037673 1.579487609 3.01583565 0.967012622 1.281967704 0.488524238 0.130311786 0.201811988 4.218341396 0.098517294 0.038887572 37.97411042 -1.579487609 0.314955083 KPENSAESNTEETKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPENSAESNTEETKR 15 2 J3KND1;E9PRZ1;Q96ER3 J3KND1 SAAL1 Protein SAAL1 0 121.82 6.34E-05 87401000 91778 90495 79002 80118 87838 92130 95986 103760 122840 122730 FALSE TRUE 88191.21429 87914.1712 93279.41879 84252.89958 90663.38904 93992.93172 97160.70538 101617.3197 108895.7182 114417.3878 0.77078507 0.768363733 0.815255623 0.736364474 0.792391705 0.821491677 0.849177798 0.888128297 0.951740992 1 16.80394679 1.579523502 0.773604913 1.001752372 0.77285929 0.940300874 0.01960266 0.124978188 0.152651006 0.017707011 0.007677024 37.97724901 -1.579523502 -0.228893082 SNLNSLDEQEGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNLNSLDEQEGVK 13 0 O75223;M0QZK8;B8ZZK2;H7BZK5 O75223 GGCT Gamma-glutamylcyclotransferase 0 161.87 2.21E-06 0 60047 54704 47377 53461 53296 55115 56302 66248 80933 75485 FALSE TRUE 57700.29685 53143.89548 55939.0778 56220.12862 55010.31424 56229.46306 56991.04072 64879.95565 71745.82514 70372.33371 0.819928711 0.755181656 0.794901559 0.798895328 0.781703709 0.799027972 0.809850089 0.921952594 1.019517491 1 16.10272074 1.579787095 2.121821484 1.011888467 0.789927377 0.963739897 0.017119898 0.043858254 0.420148251 0.012452424 0.004469166 38.00030609 -1.579787095 -0.221961089 VDLVCHGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDLVCHGK 8 0 Q99447-3;Q99447;Q99447-4;I3L1L9;Q99447-2;I3L3V9 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 105.57 0.0043629 127930000 119940 165530 132150 198120 161970 172140 156660 151630 131410 158450 FALSE TRUE 115252.6122 160809.2465 156032.4447 208344.9969 167179.9121 175620.7887 158577.2519 148498.7875 116492.8877 147718.0404 0.780220289 1.088622934 1.056285639 1.41042351 1.131750135 1.188891948 1.073513103 1.005285388 0.788616525 1 17.1724865 1.580206835 2.878222626 0.894309693 1.118907909 0.22458884 0.153409429 0.314924709 5.965968559 0.107064404 0.041670817 38.03705065 -1.580206835 0.224598216 APQTSSS(ph)PPPVRR ddPTM_BT-474_Pertuzumab_2h_R1 1 APQTSSSPPPVRR 13 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.049)S(0.171)S(0.171)S(0.608)PPPVRR 64.798 0.063905 83109000 82961 91836 61698 81859 79184 91669 86525 78135 79484 80978 TRUE FALSE 79718.7924 89216.9272 72848.20106 86083.7528 81731.02527 93522.60999 87583.91883 76521.48495 70461.30954 75493.28793 1.055971923 1.181786218 0.964962622 1.140283529 1.082626383 1.238820199 1.160155045 1.013619714 0.933345354 1 16.20406076 1.580335804 4.553817698 0.968565106 1.118147462 0.433740999 0.072057375 0.147752125 6.765989143 0.041876717 0.018677313 38.0483479 -1.580335804 0.149582356 IDLPEVQIEHDPELEKES(ph)PGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDLPEVQIEHDPELEKESPGLK 22 1 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 IDLPEVQIEHDPELEKES(1)PGLK;IDLPEVQIEHDPELEKES(1)PGLK 231.74 5.63E-27 750130000 2034820 1423780 1461160 1146490 1452960 1414730 1499220 1885960 2468630 2077800 TRUE FALSE 1955296.985 1383175.188 1725224.115 1205660.486 1499695.778 1443336.81 1517567.903 1847014.267 2188401.472 1937068.755 1.009410213 0.714055804 0.890636489 0.622414916 0.774208852 0.745113877 0.783435228 0.953509916 1.129748991 1 20.88544373 1.580500914 3.165147162 1.062378515 0.782899359 0.542861392 0.10220097 0.144265079 3.336360863 0.064002447 0.025691447 38.06281583 -1.580500914 -0.279479156 VLEDSDLKK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLEDSDLKK 9 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 111.06 0.003506 1588250000 3042040 3016990 2349050 2384750 2272880 2151870 2824150 3076890 3996060 3538650 FALSE TRUE 2923153.714 2930948.399 2773575.589 2507827.233 2345989.249 2195382.286 2858712.792 3013351.146 3542444.022 3298974.084 0.886079623 0.888442384 0.840738823 0.760183975 0.711126911 0.665474244 0.866545999 0.913420679 1.073801713 1 21.65358601 1.580751756 2.260688582 1.032868296 0.794455353 0.630008416 0.071979424 0.191315592 2.119598593 0.060551093 0.022048022 38.08480675 -1.580751756 -0.238412943 IDQLEGDHQLIQEALIFDNK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDQLEGDHQLIQEALIFDNK 20 0 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8;H0YJ11;H0YJW3 P12814-3 ACTN1 Alpha-actinin-1 0 ; 269.85 1.16E-37 497850000 748250 721600 716880 946390 738290 693430 988600 1056870 1247040 1346530 FALSE TRUE 719007.5628 701020.6745 846436.1629 995233.3013 762037.7683 707451.6297 1000698.783 1035045.265 1105481.247 1255328.324 0.57276455 0.558436117 0.674274727 0.792807174 0.607042599 0.563559044 0.797161001 0.824521558 0.880631167 1 20.25963331 1.580820023 0.959145179 0.985435189 0.629835334 0.746755062 0.073441211 0.271161618 0.484143941 0.070796033 0.027353934 38.09079376 -1.580820023 -0.355599856 DRGFGAPR ddPTM_BT-474_Pertuzumab_2h_R1 3 DRGFGAPR 8 1 P17844;P17844-2;J3QRQ7;J3KRX8;J3QR02;X6RLV5;J3QKN9 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 111.82 0.0028818 719510000 809180 967340 748300 1003780 779220 709620 947740 758850 681210 861300 FALSE TRUE 777556.351 939752.4103 883534.4558 1055585.206 804284.319 723969.0026 959338.7256 743179.4823 603881.8967 802963.3838 0.968358417 1.170355248 1.10034215 1.314611883 1.001645075 0.90162144 1.194747787 0.925545918 0.752066544 1 19.61497467 1.580876896 5.539027245 0.86512172 1.0935037 0.351909495 0.125454674 0.145455802 9.401558568 0.069386993 0.032042679 38.09578228 -1.580876896 0.22838198 TADGIVSHLK ddPTM_BT-474_Pertuzumab_2h_R1 6 TADGIVSHLK 10 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 152.54 1.78E-05 6661810000 6023850 6482480 5453050 6409780 5902960 5719860 6481850 6572350 7553690 7235370 FALSE TRUE 5788431.282 6297606.017 6438537.437 6740589.514 6092834.069 5835519.488 6561176.819 6436628.676 6696226.779 6745311.945 0.858141377 0.933627098 0.954520338 0.999299894 0.903269429 0.865122256 0.972701763 0.954237362 0.992723069 1 22.68545373 1.581114704 1.60496039 0.996273835 0.925740341 0.328174503 0.040952327 0.474521507 2.41653104 0.035797997 0.012489233 38.11664824 -1.581114704 -0.070533495 TS(ph)SPHKEESPKK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.283)S(0.359)S(0.359)PHKEESPKK;T(0.307)S(0.347)S(0.347)PHKEESPKK 104.41 0.0011169 335800000 638680 469170 377590 332830 440190 428260 444040 540220 766760 498130 TRUE FALSE 613719.6795 455789.731 445828.9124 350007.3962 454349.1111 436919.7106 449474.2943 529064.2682 679720.6193 464391.2114 1.321557481 0.981477943 0.960028746 0.753690827 0.978375774 0.940844055 0.967878554 1.13926417 1.463681057 1 18.82498114 1.581252704 4.095384504 1.250770457 0.974901909 0.260713097 0.167546985 0.197321613 7.486633266 0.097910823 0.042570555 38.12876199 -1.581252704 -0.275868548 GTVIIIANHGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTVIIIANHGDR 12 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 136.99 0.00010019 1751170000 2178160 2316250 2197260 2724800 2311320 2309620 2361800 2407330 2437260 2447830 FALSE TRUE 2093035.099 2250192.818 2594353.76 2865427.255 2385665.707 2356322.099 2390704.415 2357617.794 2160592.463 2282036.294 0.917178708 0.986046026 1.136859114 1.255644909 1.04541094 1.032552421 1.047618928 1.033120201 0.946782691 1 21.12189031 1.581330737 1.553516463 0.975116873 1.069821323 0.127463536 0.085794604 0.794606562 3.766308328 0.078717843 0.027469994 38.13561347 -1.581330737 0.09470445 GYDSGPEGGAAAS(ph)PPPDAELAACHPAAWSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GYDSGPEGGAAASPPPDAELAACHPAAWSR 30 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR;GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR 214.76 1.23E-34 951040000 293380 330000 296710 411700 384380 387040 332490 300360 292350 253040 TRUE FALSE 281914.3853 320588.7231 350332.0973 432947.8863 396743.9318 394866.214 336559.1121 294157.461 259163.6536 235901.3754 1.195051893 1.358994718 1.485078655 1.835291912 1.681821189 1.673861432 1.426694149 1.246951021 1.098610185 1 17.8478243 1.581628598 1.792598291 1.036204212 1.547105641 0.570150575 0.169679743 0.261428773 1.705946304 0.153703177 0.053939092 38.16177776 -1.581628598 0.510901429 DYDRDKDDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYDRDKDDK 9 2 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 168.74 3.32E-05 225330000 278930 213310 215520 163970 191150 191210 216820 249440 312320 275690 FALSE TRUE 268029.1072 207226.6077 254469.2582 172432.5114 197298.5133 195076.3972 219473.508 244288.9768 276866.743 257017.2707 1.042844734 0.80627503 0.990086221 0.670898539 0.767646909 0.759001123 0.853925137 0.950476893 1.07723011 1 17.97150578 1.582027734 2.79649342 1.035982368 0.832547808 0.366508684 0.104567642 0.240145584 4.282308092 0.07284106 0.028155811 38.19686625 -1.582027734 -0.20343456 ILLSQTTGVAIPLHAS(ph)SLDDVSLASTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILLSQTTGVAIPLHASSLDDVSLASTPK 28 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 ILLSQTTGVAIPLHAS(0.424)S(0.424)LDDVS(0.056)LAS(0.056)T(0.04)PK;ILLSQTTGVAIPLHAS(0.213)S(0.213)LDDVS(0.213)LAS(0.213)T(0.147)PK 166.06 1.07E-11 521450000 518470 527270 493300 524750 526720 547420 499560 527950 497680 526220 TRUE FALSE 498207.6192 512232.7759 582450.2834 551832.4104 543662.4272 558489.2075 505673.7647 517047.648 441185.4528 490578.6507 1.015550959 1.044139966 1.187271975 1.124860223 1.108206455 1.138429499 1.030770018 1.053954646 0.899316455 1 18.90412493 1.582066323 1.838611237 0.955176588 1.102175294 0.495390977 0.055669996 0.264270187 1.82686224 0.0454365 0.015990577 38.20026035 -1.582066323 0.146998705 QGSGSSQPMEVQEGYGFGSGDDPYSSAEPHVSGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QGSGSSQPMEVQEGYGFGSGDDPYSSAEPHVSGVK 35 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 228.49 2.94E-37 222810000 63837 105520 90464 144870 141450 122730 111380 87416 55463 79855 FALSE TRUE 61342.17946 102510.6729 106812.8572 152346.7581 145999.8677 125211.6847 112743.1018 85610.82905 49167.07276 74446.34972 0.823978337 1.376973798 1.434762854 2.046396615 1.961142061 1.681904958 1.514420817 1.14996678 0.660436313 1 16.18391349 1.582629814 2.796491753 0.836514439 1.580986753 0.438271275 0.328068535 0.221307655 3.94833842 0.245626632 0.095009668 38.24985681 -1.582629814 0.744472315 S(ph)RS(ph)PLDKDTYPPSASVVGASVGGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPLDKDTYPPSASVVGASVGGHR 25 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 2 S(0.646)RS(0.942)PLDKDT(0.077)Y(0.335)PPSASVVGASVGGHR;S(0.997)RS(0.997)PLDKDT(0.002)Y(0.004)PPSASVVGASVGGHR 199.59 3.79E-25 1562680000 559870 648240 544110 646780 589060 595120 603050 699280 808010 773440 TRUE FALSE 537989.6614 629752.8299 642442.7807 680160.3933 608007.6499 607153.7341 610430.3063 684839.6236 716288.0923 721054.2199 0.746115405 0.873377913 0.890977076 0.943286059 0.843220431 0.842036171 0.846580312 0.949775488 0.993390057 1 19.45974822 1.583270829 3.149095946 0.993069692 0.859509984 0.609419579 0.046965336 0.151751596 3.4811365 0.032081705 0.012896407 38.306355 -1.583270829 -0.133559708 YQHVTGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 YQHVTGTR 8 0 Q99797 Q99797 MIPEP Mitochondrial intermediate peptidase 0 ; 99.442 0.0068105 77247000 80547 105506 74023 134834 78770 80970 110452 82292 83155 82861 FALSE TRUE 77399.13419 102497.0722 87400.60273 141792.7989 81303.70859 82607.26888 111803.7446 80592.64144 73715.59301 77248.75067 1.001946744 1.326844399 1.131417686 1.835535173 1.052492214 1.069367053 1.447321072 1.043287312 0.954262592 1 16.23722398 1.583680733 6.349589622 0.985192345 1.269586589 0.221815247 0.231211717 0.195008423 16.29622689 0.124125639 0.058243549 38.34252704 -1.583680733 0.284394244 DYLIDGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYLIDGSR 8 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ; 104.44 0.016093 0 663200 811510 673490 823580 740180 815010 820740 726040 706810 795640 FALSE TRUE 637281.4108 788366.5294 795204.6247 866085.0625 763988.5619 831490.0606 830784.4616 711047.0203 626575.892 741750.5941 0.859158612 1.062845835 1.072064695 1.167623012 1.029980384 1.120983343 1.120032081 0.958606607 0.844725838 1 19.50057465 1.584029004 5.152642461 0.916436769 1.066950119 0.321314362 0.085325677 0.156420307 8.900675618 0.047399272 0.021704622 38.37328723 -1.584029004 0.15051335 KPSPSESPEPWKPFPAVS(ph)PEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPSPSESPEPWKPFPAVS(1)PEPR 83.088 0.0018721 448990000 207560 220080 173460 219360 216400 196650 222170 204020 207910 226000 TRUE FALSE 199448.3257 213803.5339 204808.0806 230681.1959 223360.7025 200626.3977 224888.9829 199806.9157 184308.9284 210692.8187 0.946630867 1.01476422 0.972069584 1.09486976 1.060124896 0.952222287 1.067378491 0.948332824 0.87477556 1 17.68478162 1.584082178 6.509437417 0.929547415 1.016007408 0.280406476 0.054423567 0.146525585 12.86724832 0.028720397 0.013505324 38.37798585 -1.584082178 0.086459993 HNSTTSSTSSGGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 HNSTTSSTSSGGYR 14 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12 A0A0A0MRT6 ABI1 Abl interactor 1 0 78.505 0.013108 0 4216.7 5829 5394.2 7657.6 5260.1 5083.7 6841.1 4866.7 5161.8 4422.9 FALSE TRUE 4051.906702 5662.762627 6369.051933 8052.809654 5429.295894 5186.495897 6924.823428 4766.200944 4575.854104 4123.333043 0.982677523 1.373345924 1.544636794 1.952985502 1.316725047 1.257840646 1.679423747 1.155909769 1.109746425 1 12.00959528 1.584425413 6.115676932 1.080805476 1.452566169 0.309453068 0.245297905 0.170145988 13.241787 0.138867843 0.064988014 38.40832901 -1.584425413 0.371760693 LLQTCFS(ph)SPADDSMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQTCFS(0.777)S(0.223)PADDSMDR 288 2.30E-36 130000000 100740 116760 87290 121140 105030 116550 110590 109480 114940 114350 TRUE FALSE 96802.96943 113430.1191 103065.2448 127392.0499 108408.3853 118906.7209 111943.4335 107219.1997 101892.4931 106604.9726 0.908053039 1.064022778 0.966795846 1.194991629 1.016916778 1.115395632 1.050077034 1.005761711 0.955794937 1 16.70191521 1.584632615 3.548514041 0.97839876 1.05015823 0.118081927 0.073979137 0.373293442 10.87082107 0.044937737 0.018794133 38.42665795 -1.584632615 0.07175947 DGELPVEDDIDLSDVELDDLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGELPVEDDIDLSDVELDDLGK 22 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ; 179.95 5.49E-17 52277000 49334 41933 54410 57522 41679 38563 64009 70551 94283 94953 FALSE TRUE 47405.97274 40737.1119 64243.09734 60490.71731 43019.64289 39342.77028 64792.36129 69094.0972 83580.38911 88521.74873 0.535529103 0.460193257 0.725732357 0.683343 0.485978231 0.444441856 0.731937204 0.780532447 0.944179146 1 16.43374433 1.584652467 1.487089402 0.986816741 0.564793078 0.752903953 0.092918126 0.196076557 0.845204182 0.083922031 0.029388608 38.42841451 -1.584652467 -0.422023663 LEQGEEPWIMGGEFPCQHS(ph)PEAWR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEQGEEPWIMGGEFPCQHSPEAWR 24 0 I3L0D1;Q9NYW8 I3L0D1 RBAK-RBAKDN;RBAK RB-associated KRAB zinc finger protein 1 LEQGEEPWIMGGEFPCQHS(1)PEAWR;LEQGEEPWIMGGEFPCQHS(1)PEAWR;LEQGEEPWIMGGEFPCQHS(1)PEAWR 125.02 6.56E-05 280763000 215612 241788 177226 236615 225264 200850 203576 192899 175670 164016 TRUE FALSE 207185.6447 234892.443 209254.6806 248826.7285 232509.8211 204911.3246 206067.424 188915.5682 155728.6781 152907.0502 1.354977709 1.536177976 1.36850904 1.6273071 1.520595818 1.340103836 1.347664635 1.235492856 1.018453223 1 17.2222954 1.584661505 1.065393374 0.98056812 1.47748851 0.817402197 0.083779688 0.185951844 0.404392916 0.073511001 0.027344995 38.42921427 -1.584661505 0.496920389 ALDIDLDKPLADSEKLPIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDIDLDKPLADSEKLPIQK 20 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 103.85 0.00015707 195380000 261780 248260 192470 168610 235130 241170 245580 269890 337150 323880 FALSE TRUE 251549.3482 241179.8679 227253.6105 177311.9823 242693.17 246046.6226 248585.4815 264316.6772 298878.1454 301943.3191 0.833101222 0.798758749 0.752636658 0.587235985 0.803770624 0.814876856 0.823285252 0.875385082 0.989848513 1 18.20391823 1.584836189 1.017821046 1.00987218 0.753404677 0.664114801 0.064363003 0.309134581 0.616112637 0.060908221 0.02302003 38.44467456 -1.584836189 -0.256467503 LKETAENSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKETAENSLK 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 170.04 4.06E-06 1456790000 2114680 2046150 1874630 1787950 1954130 2084340 2278710 2483600 3067500 3045700 FALSE TRUE 2032035.968 1987795.805 2213417.342 1880226.314 2016986.366 2126486.783 2306597.535 2432312.792 2719290.26 2839412.026 0.715653786 0.700073039 0.779533693 0.662188614 0.710353534 0.748918002 0.812350414 0.856625516 0.957694845 1 21.43716078 1.584918434 0.989506439 1.002302097 0.712685461 0.925454351 0.029287224 0.119339354 0.225545215 0.025981105 0.009926054 38.45195575 -1.584918434 -0.289616635 EKEHNKEPDSSVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEHNKEPDSSVSK 14 2 Q8WXA9-2;Q8WXA9 Q8WXA9-2 SREK1 Splicing regulatory glutamine/lysine-rich protein 1 0 ; 134.9 2.16E-05 268060000 275354 240340 218376 187775 226670 233700 242346 267844 335728 292942 FALSE TRUE 264592.8613 233485.7385 257841.4009 197466.0903 233961.0464 238425.5741 245311.9028 262312.9278 297617.5649 273100.7774 0.968846972 0.854943515 0.944125474 0.723052099 0.856683927 0.873031474 0.898246813 0.960498649 1.089771943 1 18.0590739 1.585332576 2.322797758 1.044002134 0.867414771 0.523139462 0.06530905 0.20195803 2.386912666 0.048031924 0.017689747 38.48864097 -1.585332576 -0.176587364 RAT(ph)SLPSIPNPFPELCS(ph)PPS(ph)QSPILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 3 RAT(0.52)S(0.473)LPS(0.007)IPNPFPELCS(0.976)PPS(0.603)QS(0.421)PILGGPSSAR 101.04 2.69E-05 101860000 54300 65699 43246 49365 50286 61271 47054 46084 34872 38868 TRUE FALSE 52177.89597 63825.32885 51061.5142 51912.73357 51903.49486 62509.9416 47629.86093 45132.3493 30913.47676 36235.43574 1.439968774 1.761406412 1.409159657 1.432651009 1.432396045 1.725105282 1.31445531 1.245530746 0.853128329 1 15.14511362 1.585563775 1.845854687 0.930475327 1.524288884 0.746736674 0.134608339 0.150490994 1.051032439 0.104684739 0.036969758 38.50913605 -1.585563775 0.593813557 TKS(ph)DES(ph)GEEKNGDEDCQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKSDESGEEKNGDEDCQR 18 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 2 T(0.181)KS(0.82)DES(1)GEEKNGDEDCQR 108.64 0.001896 237010000 689300 427920 398060 295120 426510 389450 419240 562790 791270 558160 TRUE FALSE 662361.3939 415716.1406 469998.2968 310351.1786 440229.0815 397324.9458 424370.7845 551168.1898 701448.3469 520355.326 1.272902113 0.798908207 0.903225687 0.596421643 0.846016288 0.763564676 0.815540388 1.059215044 1.348018002 1 18.98913758 1.585644047 3.970714051 1.182480611 0.842950727 0.344775625 0.1791579 0.174465306 6.271683069 0.104903163 0.04540085 38.51625448 -1.585644047 -0.339529884 ASSVSTKES(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASSVSTKESPAR 12 1 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVSTKES(1)PAR;ASSVSTKES(1)PAR;ASSVS(0.001)T(0.058)KES(0.941)PAR;ASSVST(0.001)KES(0.999)PAR;ASSVSTKES(1)PAR 230.57 1.45E-11 4614440000 5690510 5235530 4790370 4845240 5020330 5040790 5574930 5830560 6487650 6564530 TRUE FALSE 5468118.578 5086217.811 5656096.42 5095303.417 5181813.474 5142718.228 5643157.661 5710156.898 5751199.17 6119908.536 0.893496781 0.831093762 0.924212574 0.832578361 0.846714202 0.840325995 0.922098366 0.933046117 0.939752471 1 22.54507866 1.586066499 1.059997761 0.986026332 0.861158205 0.669916569 0.031124802 0.274011721 0.589940965 0.027108439 0.010106483 38.55373868 -1.586066499 -0.124868128 AQAGSNQSRGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQAGSNQSRGK 11 1 Q96PY0 Q96PY0 PSMG3-AS1 Putative uncharacterized protein PSMG3-AS1 0 64.439 0.062286 1804300000 3100200 4142300 3320900 4435000 3896300 4556200 4010000 3586700 2997500 3901500 FALSE TRUE 2979040.757 4024165.66 3921060.503 4663890.881 4021628.028 4648329.486 4059075.58 3512633.392 2657236.367 3637247.93 0.819037034 1.106376507 1.078029482 1.282258172 1.105678828 1.277979829 1.115974401 0.965739334 0.730562342 1 21.79441584 1.58613403 3.632808973 0.860580017 1.122974139 0.354679091 0.134968494 0.186766983 5.694121354 0.083133154 0.035073135 38.5597341 -1.58613403 0.262394123 VQELETSLAELR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQELETSLAELR 12 0 Q08379;Q08379-2;B7ZC06 Q08379 GOLGA2 Golgin subfamily A member 2 0 ; 179.6 4.77E-05 118264000 59726 82417 70526 114096 100819 107860 99590 79621 68703 87583 FALSE TRUE 57391.84189 80066.54785 83271.61704 119984.5082 104061.9347 110041.0031 100808.8122 77976.79853 60904.12347 81650.9254 0.70289273 0.980595718 1.01984903 1.469481303 1.274473427 1.347700624 1.234631594 0.955002018 0.745908551 1 16.31718162 1.586209706 4.675164645 0.866718496 1.159937971 0.226735298 0.210670788 0.232298788 11.15299447 0.130615222 0.058841173 38.5664537 -1.586209706 0.293219476 KIESER ddPTM_BT-474_Pertuzumab_2h_R1 7 KIESER 6 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;;;; 114.6 0.040317 3849480000 6666400 7380410 6305650 8356490 7304110 7591330 7213460 7076350 6906030 7091840 FALSE TRUE 6405869.718 7169927.933 7445221.223 8787769.45 7539053.332 7744831.894 7301740.481 6930220.9 6122086.427 6611503.36 0.968897597 1.084462571 1.126101103 1.329163576 1.140293353 1.171417675 1.104399421 1.048206516 0.92597494 1 22.65654693 1.586591288 2.297227139 0.964513499 1.141525518 0.382629092 0.085826472 0.285519302 3.292931819 0.067614576 0.024868867 38.60035401 -1.586591288 0.177012019 KAQLNIGNVLPVGTMPEGTIVCCLEEKPGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAQLNIGNVLPVGTMPEGTIVCCLEEKPGDR 31 2 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 148.89 7.43E-09 750150000 655070 572440 467020 450530 555070 593050 496940 631840 749400 639720 FALSE TRUE 629469.1402 556114.5717 551420.9028 473781.9073 572924.3307 605041.8773 503021.7004 618792.2832 664331.2537 596391.1946 1.055463504 0.932466101 0.924595983 0.794414659 0.960651894 1.014505048 0.843442534 1.037561065 1.113918615 1 19.18589943 1.586718539 6.886532258 1.062319056 0.930896276 0.343734915 0.075044332 0.131139411 13.00936153 0.040261063 0.01903885 38.61166583 -1.586718539 -0.131422779 DVQNFPAATDEKDKFVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVQNFPAATDEKDKFVEK 18 2 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 110.41 0.00018799 196830000 150400 127630 91617 83614 120000 118330 124890 139070 181880 162130 FALSE TRUE 144522.2017 123990.1174 108174.2299 87929.32856 123859.909 120722.7137 126418.4412 136198.1559 161233.7449 151148.7907 0.956158505 0.820318289 0.715680419 0.581740206 0.819456831 0.798701155 0.836384073 0.90108664 1.06672203 1 17.20560991 1.586737472 1.609304617 1.035818401 0.773758982 0.529475493 0.091512345 0.287603075 1.475191514 0.08064327 0.028249224 38.61334915 -1.586737472 -0.262059419 DELHIVEAEAMNYEGS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 23 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNY(0.001)EGS(0.999)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNY(0.015)EGS(0.985)PIK;DELHIVEAEAMNY(0.001)EGS(0.999)PIK;DELHIVEAEAMNY(0.016)EGS(0.984)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNY(0.013)EGS(0.987)PIK;DELHIVEAEAMNY(0.009)EGS(0.991)PIK;DELHIVEAEAMNY(0.013)EGS(0.987)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK 329.41 2.05E-75 14564937800 5448608.2 4537390.74 5930503.3 6053888.5 5484478.2 4940936.2 6921166.2 7300585.2 9447991.5 9381650.8 TRUE FALSE 5235670.568 4407988.799 7002277.17 6366330.411 5660891.422 5040845.315 7005869.502 7149825.564 8375495.114 8746223.235 0.598620733 0.503987685 0.800605814 0.7278948 0.647238387 0.576345376 0.801016543 0.817475769 0.957612776 1 23.06022874 1.587089913 1.220787976 0.998320756 0.647348282 0.714839596 0.082638418 0.244927837 0.697124498 0.075675636 0.027187472 38.64469755 -1.587089913 -0.350972475 ERPDLEAPAPGSPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPDLEAPAPGSPFR 15 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 149.97 3.04E-08 0 68886 70429 69510 90590 87994 72779 93005 73762 76814 80176 FALSE TRUE 66193.85896 68420.43388 82072.00324 95265.36076 90824.40692 74250.64124 94143.22301 72238.78892 68094.39675 74745.60811 0.885588607 0.915377313 1.098017734 1.274527871 1.215113626 0.993377981 1.259515113 0.966461987 0.911015356 1 16.18970119 1.587198257 11.74061548 0.952047302 1.094567896 0.183086617 0.128139506 0.183758009 68.18976354 0.072588204 0.034327439 38.65433956 -1.587198257 0.142520594 MGAGLGHGMDR ddPTM_BT-474_Pertuzumab_2h_R1 24 MGAGLGHGMDR 11 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;;;;;;;;;;;;;;;;; 172.8 1.29E-05 24214278000 11869840 12914460 10307012 12416480 12283657 11780090 12232276 12030815 12480212 12678265 FALSE TRUE 11405953.53 12546152.25 12169718.35 13057296.02 12678771.98 12018291.49 12381978.25 11782374.47 11063510.66 11819554.82 0.965007033 1.061474179 1.02962578 1.104719782 1.072694545 1.016814227 1.047584147 0.996854336 0.936034464 1 23.49467236 1.58742214 3.43135603 0.967114493 1.045419429 0.394009573 0.037699354 0.183362205 5.012559592 0.023688456 0.009831536 38.67427136 -1.58742214 0.078304936 SEPDKADPFSFEGPEIVDCDGCTIDWK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEPDKADPFSFEGPEIVDCDGCTIDWK 27 1 Q99733;Q99733-2;C9JZI7;E9PP22;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 117.08 0.00050543 291670000 98993 82843 74451 67609 79382 85134 77098 99544 116120 112840 FALSE TRUE 95124.24412 80480.39875 87905.95185 71098.30859 81935.39412 86855.46781 78041.54839 97488.38161 102938.5444 105197.2463 0.904246522 0.765042828 0.835629781 0.675857126 0.778873944 0.82564393 0.741859232 0.9267199 0.978528888 1 16.68273741 1.587523949 3.829881498 0.981059921 0.787201558 0.674415582 0.057765437 0.102308892 3.445903012 0.0345062 0.014807281 38.68333862 -1.587523949 -0.193858363 RAS(ph)GQAFELILS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR 176.65 7.67E-06 4096870000 669138 718088 695287 728685 720011 817520 720252 700043 629801 747421 TRUE FALSE 642987.3472 697608.8333 820940.8275 766292.5202 743170.8077 834050.8145 729066.6594 685586.8674 558308.6308 696797.5099 0.922775036 1.00116436 1.178162688 1.099734872 1.066552043 1.196977318 1.046310656 0.98391119 0.801249463 1 19.41037994 1.587578646 3.150380483 0.898888113 1.080243411 0.381948079 0.087535377 0.201927877 4.651705462 0.057937494 0.023404295 38.68821086 -1.587578646 0.181355298 WGTLTDCVVMR ddPTM_BT-474_Pertuzumab_2h_R1 2 WGTLTDCVVMR 11 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 171.56 3.35E-05 374340000 269520 284450 253090 262520 278500 248950 291230 266840 263560 314450 FALSE TRUE 258986.8604 276337.7645 298828.993 276068.6887 287458.2054 253983.9396 294794.1599 261329.6608 233641.7737 293152.0214 0.883455823 0.942643217 1.019365282 0.941725346 0.980577258 0.866389863 1.005601662 0.891447582 0.796998679 1 18.16128948 1.587683831 8.505199398 0.881197615 0.949000022 0.110833701 0.064484591 0.181721671 29.49412334 0.032201539 0.01533625 38.6975822 -1.587683831 0.067802408 VERLSSGPEQIT(ph)LEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VERLSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 38 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 VERLS(0.285)S(0.285)GPEQIT(0.43)LEASSTEGHPGAPSPQHTDQTEAFQK 106.97 2.40E-05 132070000 31605 42483 32493 36849 32906 32806 45731 34468 39767 37247 TRUE FALSE 30369.84166 41271.42644 38365.2079 38750.78131 33964.45137 33469.3598 46290.66966 33756.22375 35252.81688 34724.22751 0.874600929 1.18854844 1.10485418 1.115958052 0.978119711 0.963861897 1.333094297 0.972123102 1.015222495 1 15.08365498 1.587807139 24.99999999 0.99523904 1.083351119 0.09243276 0.120355729 2.207846754 2743.165475 0.062314045 0.028905968 38.70857101 -1.587807139 0.088112079 FAELPEFRPEEVLPS(ph)PTLQSLAT(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 3 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.998)PT(0.009)LQS(0.071)LAT(0.551)S(0.372)PR;FAELPEFRPEEVLPS(0.996)PT(0.004)LQS(0.006)LAT(0.596)S(0.398)PR;FAELPEFRPEEVLPS(0.997)PT(0.003)LQSLAT(0.56)S(0.44)PR 179.63 5.20E-17 923050000 694600 773370 639560 759990 792150 760850 702290 654010 559210 602930 TRUE FALSE 667454.2641 751314.2448 755142.7189 799213.175 817630.2242 776234.9083 710884.8351 640504.465 495730.8252 562093.0141 1.187444511 1.336636866 1.34344797 1.421852176 1.454617303 1.380972346 1.264710319 1.139499067 0.881937353 1 19.10044936 1.587888898 2.020528993 0.941845636 1.357307327 0.817401566 0.076238834 0.119533425 1.0277944 0.06153055 0.022061906 38.71585884 -1.587888898 0.415461691 SYDPPCPGHWT(ph)PEAPGSGTTCPGLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SYDPPCPGHWTPEAPGSGTTCPGLPR 26 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;J3QLT7 H3BM67 NOL3 Nucleolar protein 3 1 SYDPPCPGHWT(1)PEAPGSGTTCPGLPR;SYDPPCPGHWT(1)PEAPGSGTTCPGLPR;SYDPPCPGHWT(1)PEAPGSGTTCPGLPR;SYDPPCPGHWT(1)PEAPGSGTTCPGLPR 206.03 1.17E-24 3140380000 572870 614560 449067 520035 549090 608330 512048 539196 511174 520497 TRUE FALSE 550481.6071 597033.3505 530223.3963 546874.0687 566751.9785 620630.8494 518314.5966 528061.4142 453147.6705 485243.2746 1.134444589 1.230379444 1.092696023 1.127010094 1.167974928 1.279009688 1.068154107 1.088240563 0.933856674 1 18.88834869 1.587934292 1.854705462 0.971867436 1.165757717 0.613591216 0.059916526 0.206906398 1.462120101 0.047107299 0.016679927 38.71990578 -1.587934292 0.193890281 SKVSS(ph)PIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKVSSPIEK 9 1 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(0.01)KVS(0.04)S(0.95)PIEK 73.927 0.02576 444670000 505860 540350 444790 418980 456310 548260 433320 474260 473000 440300 TRUE FALSE 486090.4319 524939.7471 525173.4473 440603.608 470987.6256 559346.1928 438623.0998 464466.3653 419307.023 410478.0888 1.184205552 1.278849618 1.279418955 1.073391297 1.147412343 1.362670038 1.068566415 1.131525355 1.021508905 1 18.64694569 1.588010166 1.294730419 1.004826834 1.213226598 0.461441409 0.084117207 0.383484599 1.231607206 0.073418012 0.02611367 38.72667096 -1.588010166 0.208399764 EGYGGFR ddPTM_BT-474_Pertuzumab_2h_R1 3 EGYGGFR 7 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;; 144.9 0.005404 1233140000 1269540 1356310 1264690 1369700 1502250 1442210 1328610 1355550 1215490 1433090 FALSE TRUE 1219924.973 1317629.367 1493247.616 1440390.381 1550571.236 1471372.474 1344869.927 1327557.419 1077512.671 1336025.538 0.913100041 0.986230674 1.117678947 1.078115904 1.160585027 1.101305651 1.006619925 0.993661709 0.806506044 1 20.34951615 1.588154267 2.62138196 0.903958366 1.060616065 0.33791001 0.080790254 0.261121219 4.059495059 0.058868869 0.022474145 38.73952284 -1.588154267 0.156657699 VYEFLDKLDVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYEFLDKLDVVR 12 1 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 167.98 4.35E-05 1251160000 3401500 3282200 2862200 2598900 2982200 2214950 3140500 3271500 3798400 3701900 FALSE TRUE 3268565.619 3188594.87 3379463.209 2733029.54 3078125.171 2259737.807 3178934.378 3203942.382 3367221.556 3451167.016 0.947089957 0.923917868 0.979223316 0.791914598 0.891908493 0.654774978 0.921118672 0.928364917 0.975676211 1 21.71865286 1.588239265 2.341762019 0.983070607 0.867703043 0.221420594 0.087308856 0.431380007 5.202789008 0.067285274 0.024909895 38.7471055 -1.588239265 -0.115367564 IGTLQDRPPS(ph)PFREPPGSER ddPTM_BT-474_Pertuzumab_2h_R1 2 IGTLQDRPPSPFREPPGSER 20 2 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 IGTLQDRPPS(1)PFREPPGSER;IGTLQDRPPS(1)PFREPPGSER 149.09 5.37E-08 475800000 213062 266600 239259 354860 264380 303980 273500 260240 235990 266630 TRUE FALSE 204735.3015 258996.829 282498.4236 373174.3671 272884.0228 310126.6839 276847.1748 254865.9531 209201.4046 248570.9126 0.823649474 1.041943429 1.13649027 1.501279306 1.097811566 1.247638674 1.113755314 1.025324928 0.841616593 1 17.92329796 1.588350668 2.85528979 0.922278774 1.151495294 0.216930965 0.164012068 0.338388485 6.342622876 0.116749579 0.045751402 38.757046 -1.588350668 0.229216521 RSS(ph)PSARPPDVPGQQPQAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.168)S(0.796)PS(0.036)ARPPDVPGQQPQAAK 88.976 0.001689 469170000 197670 229560 196070 293880 241290 222100 220950 209780 176840 192310 TRUE FALSE 189944.8379 223013.1736 231504.2106 309047.182 249051.312 226591.0142 223654.0522 205447.9697 156765.8646 179284.6724 1.059459436 1.243905408 1.291266049 1.72377916 1.389138896 1.263861607 1.247480051 1.14593159 0.874396358 1 17.45189263 1.588376355 1.672201923 0.93576929 1.341264949 0.465537211 0.161776009 0.320165878 1.789619475 0.142465894 0.050027766 38.75933839 -1.588376355 0.405495659 KS(ph)STPEEVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSTPEEVKK 10 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.629)S(0.225)T(0.147)PEEVKK 137.4 7.26E-05 258560000 272080 209410 195300 151550 217800 227540 196410 262960 340840 262590 TRUE FALSE 261446.8128 203437.8318 230595.0544 159371.5137 224805.7348 232141.0147 198813.7243 257529.7841 302149.2721 244804.5454 1.067981856 0.831021464 0.941955771 0.651015337 0.918307029 0.948270851 0.812132487 1.051981219 1.234246985 1 17.90127082 1.588413964 4.696300463 1.124580842 0.877669242 0.423981629 0.115366198 0.13379468 6.477858635 0.063459171 0.028659975 38.76269498 -1.588413964 -0.246911599 KLS(ph)SGDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSSGDLR 8 1 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 KLS(0.97)S(0.03)GDLR 82.417 0.012451 328840000 651610 681560 611260 579160 578550 652870 566260 718420 817180 755130 TRUE FALSE 626144.3608 662122.5761 721728.2794 609050.517 597159.5862 666071.4787 573190.0593 703584.3759 724417.1523 703984.3725 0.889429347 0.940535901 1.025204973 0.86514778 0.848256878 0.946145262 0.814208499 0.99943181 1.029024479 1 19.42518388 1.588480409 8.726405072 1.013525159 0.907812404 0.42772646 0.055885127 0.107889839 18.83601319 0.030249024 0.014422398 38.76862594 -1.588480409 -0.105712755 DKPLKDVIIADCGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKPLKDVIIADCGK 14 2 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 143.59 5.11E-06 4138600000 4149250 3980460 3005310 3557590 2693480 2606190 4007030 4612420 6216240 5799520 FALSE TRUE 3987092.723 3866941.178 3548436.37 3741197.646 2780118.23 2658888.947 4056069.232 4517171.915 5510598.496 5406713.345 0.737433718 0.715211059 0.656301924 0.691954133 0.514197453 0.491775461 0.750191285 0.835474646 1.019214104 1 22.36632044 1.588876205 1.972649714 1.008478269 0.638138445 0.768488247 0.080124223 0.152503175 1.241530718 0.068926718 0.024638443 38.80397404 -1.588876205 -0.370339823 EDAFYSWESSKDPAEQQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDAFYSWESSKDPAEQQGK 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 222.51 2.20E-19 837640000 769560 675280 813740 737100 714230 707920 924550 1134450 1347720 1472180 FALSE TRUE 739484.7444 656021.6756 960800.9195 775141.8193 737203.8566 722234.6274 935864.9195 1111023.211 1194732.476 1372467.937 0.538799286 0.477986886 0.700053454 0.564779547 0.537137398 0.526230601 0.681884723 0.809507589 0.870499371 1 20.38834102 1.588890285 1.208019465 0.97543082 0.556584832 0.874103819 0.058634037 0.144450763 0.402401616 0.052832803 0.019038625 38.8052321 -1.588890285 -0.418845988 MDEIGNHYTEMVK ddPTM_BT-474_Pertuzumab_2h_R1 1 MDEIGNHYTEMVK 13 0 Q8WVV4-1;Q8WVV4 Q8WVV4-1 POF1B Protein POF1B 0 113.35 0.0008291 79416000 98655 96623 82767 86843 93120 102060 99980 106150 123130 123610 FALSE TRUE 94799.45353 93867.40664 97724.83804 91324.97764 96115.28937 104123.7231 101203.5851 103957.9654 109152.7986 115237.7846 0.822642104 0.814554072 0.84802774 0.792491612 0.834060544 0.903555405 0.878215296 0.902117008 0.94719626 1 16.81425431 1.58943406 0.484301003 1.002857822 0.811615512 0.888521578 0.020581852 0.273177716 0.162695756 0.022356704 0.014682871 38.85385005 -1.58943406 -0.19124231 TQPDGTSVPGEPAS(ph)PISQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TQPDGTSVPGEPASPISQR 19 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR 407.94 1.30E-147 9148800000 3835730 4074050 3226260 4047170 4261880 4130650 3650280 3897760 3713440 3728810 TRUE FALSE 3685825.431 3957862.083 3809316.95 4256044.929 4398967.241 4214174.573 3694953.219 3817269.894 3291905.859 3476254.377 1.060286455 1.138542136 1.09581076 1.224319186 1.265433068 1.21227451 1.062912209 1.098098551 0.946969209 1 21.72910223 1.589443841 1.611666534 0.978184277 1.164479716 0.534341088 0.065527973 0.291750798 1.502159202 0.058170748 0.020417592 38.85472513 -1.589443841 0.18629544 IMIMTDQDQDGSHIK ddPTM_BT-474_Pertuzumab_2h_R1 4 IMIMTDQDQDGSHIK 15 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ;;; 265.46 3.28E-25 2694610000 1226250 1235960 941800 1228430 1199650 1207550 1222190 1158070 1205820 1213110 FALSE TRUE 1178326.794 1200711.631 1112004.21 1291829.42 1238237.832 1231967.488 1237147.527 1134155.45 1068940.369 1130944.979 1.041895774 1.061688812 0.983252263 1.142256647 1.094870091 1.089325751 1.093906025 1.002838751 0.945174512 1 20.10909731 1.589486391 4.300781732 0.972880258 1.072583808 0.509814622 0.040925344 0.13444605 5.58254054 0.024659014 0.010930586 38.85853214 -1.589486391 0.099703551 VYYTAGYNS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 VYYTAGYNSPVK 12 0 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 1 VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK 215.96 4.22E-11 580560000 779440 741330 729420 624630 730480 585410 797900 822890 978980 962960 TRUE FALSE 748978.6231 720187.9942 861242.4199 656867.2292 753976.5526 597247.3913 807664.9389 805897.0339 867850.2946 897737.8615 0.834295461 0.802225265 0.959347329 0.731691574 0.839862709 0.665280386 0.899666789 0.8976975 0.966707913 1 19.77593472 1.589698231 1.753464712 0.983929682 0.812015081 0.447741121 0.075286082 0.309024174 1.923060615 0.060129642 0.021202205 38.87749111 -1.589698231 -0.1719146 S(ph)IDKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIDKDR 6 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(1)IDKDR;S(1)IDKDR 138.4 0.0074622 764690000 1867150 1556440 1470550 1590110 1614400 1660550 1790160 1984220 2140950 2267900 TRUE FALSE 1794179.714 1512051.855 1736311.097 1672175.768 1666328.642 1694127.459 1812068.514 1943245.164 1897918.332 2114293.113 0.848595544 0.715157159 0.821225348 0.790891177 0.788125654 0.801273697 0.857056433 0.919099226 0.897660935 1 21.01174397 1.58989897 0.749275874 0.990019956 0.783221437 0.779499759 0.035741404 0.247706109 0.285735454 0.030863129 0.013720719 38.89546515 -1.58989897 -0.206798519 FSESESRS(ph)PLEDETDNTWMFK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSESESRSPLEDETDNTWMFK 21 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 FSESES(0.135)RS(0.865)PLEDETDNTWMFK;FS(0.001)ES(0.007)ES(0.141)RS(0.85)PLEDETDNTWMFK 168.55 6.45E-12 110947000 94117 104083 93951 91396 102810 115536 103431 99894 98730 108714 TRUE FALSE 90438.80359 101114.6547 110930.0356 96112.95851 106116.977 117872.2171 104696.8195 97831.15399 87522.58431 101350.7039 0.892335229 0.997670966 1.094516676 0.948320582 1.047027528 1.163013304 1.033015218 0.965273552 0.863561681 1 16.62899658 1.590009578 4.114054455 0.927241354 1.029599653 0.199410324 0.076393221 0.250869979 9.630992375 0.046226348 0.020273326 38.90537247 -1.590009578 0.102358299 AQHTLPQDPAIVQSSLGSASAS(ph)PFQPHVPYSPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQHTLPQDPAIVQSSLGSASASPFQPHVPYSPFR 34 0 Q9BX40;Q9BX40-2;Q5TBQ1;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 1 AQHTLPQDPAIVQSSLGSAS(0.079)AS(0.902)PFQPHVPY(0.003)S(0.016)PFR 168.49 3.02E-14 624160000 112430 108610 113620 106920 108380 145480 122370 100600 84127 106700 TRUE FALSE 108036.1113 105512.5491 134153.6615 112438.154 111866.1411 148421.7053 123867.6007 98522.57484 74577.25565 99473.11396 1.086083536 1.060714247 1.348642423 1.130337129 1.124586702 1.492078607 1.245236986 0.990444261 0.749722741 1 16.60201902 1.590121459 3.952202788 0.873319138 1.215350882 0.514042036 0.135785529 0.138168082 4.935382109 0.083436904 0.036206611 38.91539646 -1.590121459 0.342031744 EQELSEEDKQLQDELEMLVER ddPTM_BT-474_Pertuzumab_2h_R1 4 EQELSEEDKQLQDELEMLVER 21 1 Q13200;C9JPC0 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 260.56 1.22E-36 203390000 246457 201088 220145 231724 235565 227246 268644 301322 348755 367608 FALSE TRUE 236825.188 195353.1671 259930.0986 243683.3034 243142.1622 231841.0698 271931.7456 295099.5954 309165.7945 342709.5827 0.691037543 0.5700254 0.758455881 0.711048992 0.709469984 0.676494272 0.793475757 0.861077747 0.902121826 1 18.38662701 1.590646548 0.775612687 0.998743112 0.673058225 0.845011192 0.046809148 0.214247695 0.261860154 0.043227093 0.018782707 38.96247601 -1.590646548 -0.325684887 EAARSPDKPGGS(ph)PSASR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(0.006)PDKPGGS(0.609)PS(0.325)AS(0.059)R 131.13 2.20E-05 552710000 397090 366760 301890 281820 339710 331980 350200 363830 414600 394020 TRUE FALSE 381571.2838 356300.3639 356448.2385 296364.764 350637.0807 338692.8631 354485.8524 356316.7834 367536.3461 367332.6744 1.038762164 0.969966433 0.970368996 0.806802075 0.954549119 0.922033041 0.965026737 0.970011132 1.000554461 1 18.4867277 1.591728679 1.655114113 1.000675365 0.941006102 0.131254941 0.05492142 0.72385656 3.956962179 0.047029699 0.016549248 39.05967978 -1.591728679 -0.059669263 LTWHSYPSEDDDKKDDKN ddPTM_BT-474_Pertuzumab_2h_R1 2 LTWHSYPSEDDDKKDDKN 18 3 P83916 P83916 CBX1 Chromobox protein homolog 1 0 ; 98.507 0.00052957 561790000 507990 377000 285906 272112 342606 355468 372240 437340 601590 458510 FALSE TRUE 488137.1892 366248.3291 337575.5741 286155.7329 353626.2331 362655.8065 376795.5845 428308.7762 533300.0253 427454.7093 1.141962361 0.856812011 0.789734133 0.669441058 0.827283512 0.848407559 0.881486568 1.001998029 1.247617616 1 18.70541204 1.591730944 2.92905356 1.125470941 0.846184369 0.418836119 0.124859251 0.200345645 3.975307111 0.085261355 0.033809971 39.05988357 -1.591730944 -0.279286572 IINLGPVHPGPLS(ph)PEPQPMGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 IINLGPVHPGPLSPEPQPMGVR 22 0 Q86T03-2;Q86T03 Q86T03-2 TMEM55B "Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase" 1 IINLGPVHPGPLS(1)PEPQPMGVR;IINLGPVHPGPLS(1)PEPQPMGVR 200.99 1.02E-22 228320000 120204 215932 152958 318000 166226 167957 212934 160927 156108 147939 TRUE FALSE 115506.2948 209773.8308 180600.9131 334412.0181 171572.8103 171353.2056 215539.95 157603.8012 138387.2743 137918.9598 0.837493953 1.520993424 1.309471254 2.424699394 1.244011777 1.242419504 1.562801448 1.142727595 1.003395578 1 17.07346127 1.592030605 3.712113785 1.016226923 1.467864117 0.191252426 0.381300284 0.304994657 9.718174343 0.235867919 0.100723131 39.08684392 -1.592030605 0.451637194 ERDQGGFGDRNEYGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDQGGFGDRNEYGSR 16 2 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 184.21 1.05E-09 153480000 47836 60879 32521 42561 39175 60608 48863 43968 43534 44951 FALSE TRUE 45966.51623 59142.79053 38398.26813 44757.57831 40435.09945 61833.53529 49461.00001 43060.04544 38592.20283 41906.42873 1.096884598 1.41130591 0.916285861 1.068036091 0.96489013 1.47551431 1.180272371 1.027528395 0.920913664 1 15.35488396 1.592156836 3.992117194 0.964269096 1.160049752 0.196586703 0.166328924 0.291670773 10.61933832 0.101266737 0.044141556 39.09820651 -1.592156836 0.195780656 QVDVPTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QVDVPTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK 40 1 P30049 P30049 ATP5D "ATP synthase subunit delta, mitochondrial" 0 237.84 7.48E-51 213040000 106480 165310 112500 204970 110210 132390 198700 129440 149550 134570 FALSE TRUE 102318.6439 160595.5207 132831.2525 215548.5263 113755.0047 135067.0165 201131.75 126767.0188 132573.711 125455.454 0.815577487 1.280099952 1.058792171 1.718127983 0.906736225 1.076613349 1.603212484 1.010454426 1.056739318 1 16.93681567 1.592981601 25 1.025146604 1.215411041 0.092674037 0.266100296 2.219625496 3718.009645 0.136901861 0.063784406 39.17252815 -1.592981601 0.190264436 LEDNPSSGS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEDNPSSGSPPR 12 0 Q05D32-2;Q05D32;H0YMH7 Q05D32-2 CTDSPL2 CTD small phosphatase-like protein 2 1 LEDNPS(0.034)S(0.075)GS(0.891)PPR 62.68 0.079775 178480000 135700 120410 144350 152940 129890 138690 141500 139550 129540 167790 TRUE FALSE 130396.694 116976.0247 170437.256 160833.2517 134068.0298 141494.4068 143231.7193 136668.2437 114835.1623 156425.4338 0.833602892 0.747806938 1.089575089 1.028178396 0.857073089 0.904548598 0.915654928 0.873695795 0.734120785 1 17.25511558 1.593084921 4.90079431 0.848545914 0.913370216 0.02323449 0.108368692 0.493704755 25.78363299 0.062710838 0.028648401 39.18184852 -1.593084921 0.064824302 EDEEESLNEVGYDDIGGCRK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDEEESLNEVGYDDIGGCRK 20 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 264.92 2.15E-36 6730790000 2311190 2193640 1243190 1594302 1557640 1827521 1712534 2093291 2539530 2209280 FALSE TRUE 2220866.14 2131079.535 1467862.088 1676584.117 1607742.905 1864474.727 1733492.503 2050063.809 2251253.201 2059643.498 1.078276965 1.03468369 0.712677747 0.814016658 0.78059281 0.905241479 0.84164687 0.995348861 1.093030519 1 20.97396321 1.593121021 4.18467788 1.0461939 0.875249847 0.296545193 0.106064077 0.215766595 8.548052495 0.066900799 0.029542841 39.18510558 -1.593121021 -0.170944053 IEPIPGES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEPIPGESPK 10 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 IEPIPGES(1)PK 93.162 0.006807 0 240620 218950 178420 174520 205300 207420 206860 244110 293470 269980 TRUE FALSE 231216.3044 212705.7604 210664.4629 183526.9981 211903.6609 211614.1745 209391.6146 239069.0432 260156.5159 251694.0141 0.918640458 0.845096619 0.836986385 0.729167115 0.841909815 0.840759663 0.831929259 0.949840003 1.033622181 1 17.94131138 1.593124267 2.756651491 1.015155956 0.830927456 0.742651845 0.044053767 0.115995011 2.021241209 0.031543354 0.01229483 39.18539846 -1.593124267 -0.184228499 ALEEGDGSVSGSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALEEGDGSVSGSSPR 15 0 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 ALEEGDGSVSGS(0.263)S(0.737)PR;ALEEGDGSVSGS(0.019)S(0.981)PR;ALEEGDGSVSGS(0.021)S(0.979)PR 247.9 2.67E-18 2986030000 2732910 3071520 2553590 3255640 3149660 3217150 2967230 3029650 3100220 3080520 TRUE FALSE 2626104.856 2983923.257 3015080.517 3423663.971 3250971.674 3282202.977 3003543.848 2967086.669 2748296.023 2871873.637 0.914422147 1.039016208 1.049865314 1.192136007 1.132003732 1.14287862 1.045848191 1.033153629 0.95696969 1 21.45356084 1.593176352 2.273816196 0.980843244 1.082165817 0.213442503 0.071781166 0.426007597 4.816643431 0.057292166 0.021170804 39.19009821 -1.593176352 0.101322572 RQLEEAEEEAQR ddPTM_BT-474_Pertuzumab_2h_R1 3 RQLEEAEEEAQR 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 259.7 4.43E-21 542380000 627100 748020 618530 831390 736730 891230 791860 687360 650250 727690 FALSE TRUE 602592.2387 726687.202 730312.1301 874298.1375 760427.5895 909251.2812 801551.0196 673165.7758 576436.3461 678402.9081 0.888251261 1.071173477 1.076516803 1.288759419 1.120908505 1.34028211 1.181526509 0.992280204 0.84969616 1 19.37178283 1.593550429 4.262752319 0.92390734 1.145566383 0.345482855 0.121969831 0.183719712 7.520879325 0.07452074 0.033068283 39.22386889 -1.593550429 0.221659043 KAEEELGELEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAEEELGELEAK 12 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 106.52 0.0030667 412390000 564100 508920 441360 444420 498800 510600 456610 566410 636950 610920 FALSE TRUE 542054.3484 494406.0999 521123.57 467356.5695 514844.355 520924.6818 462198.1298 554713.4356 564646.1063 569541.8442 0.95173753 0.868076867 0.914987328 0.820583376 0.903962299 0.91463812 0.811526202 0.973964321 0.991404077 1 19.11944232 1.593677471 6.95081745 0.990974286 0.883805717 0.585164054 0.040650436 0.082069811 8.472424259 0.02068341 0.00984873 39.23534457 -1.593677471 -0.10716857 TTPQQGASGPGRS(ph)PVGQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TTPQQGASGPGRSPVGQAR 19 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 TTPQQGASGPGRS(1)PVGQAR;TTPQQGASGPGRS(1)PVGQAR;TTPQQGASGPGRS(1)PVGQAR 249.12 3.41E-25 1435490000 90986 112126 80707 97101 86324 98705 93659 92310 91557 93680 TRUE FALSE 87430.16653 108928.2763 95292.55022 102112.3942 89100.68986 100700.8827 94805.22686 90403.76624 81163.8332 87334.97016 1.001090014 1.247246963 1.091115621 1.169203975 1.020217786 1.153041932 1.085535687 1.035138228 0.929339451 1 16.41427182 1.593919015 2.362150731 0.965921594 1.11641383 0.413486784 0.069293525 0.23075282 2.847488351 0.047100423 0.017585692 39.25717241 -1.593919015 0.150492236 S(ph)DDEQSSADKER ddPTM_BT-474_Pertuzumab_2h_R1 1 SDDEQSSADKER 12 1 A6NGV6;P27540-3;P27540-4;P27540 A6NGV6 ARNT Aryl hydrocarbon receptor nuclear translocator 1 S(1)DDEQSSADKER 126.63 0.00017201 49873000 49245 42247 44308 41171 40458 36201 44182 51387 67015 53764 TRUE FALSE 47320.45096 41042.15692 52315.44123 43295.84024 41759.36831 36933.00902 44722.71253 50325.84049 59407.73815 50122.51639 0.944095675 0.81883672 1.043751292 0.863800211 0.833145886 0.736854645 0.892267902 1.004056542 1.185250511 1 15.61317123 1.593923974 3.317755347 1.093496596 0.872729318 0.506371362 0.087040256 0.15674913 4.026925746 0.056086854 0.023189892 39.25762064 -1.593923974 -0.220767278 AEGFVDALHR ddPTM_BT-474_Pertuzumab_2h_R1 6 AEGFVDALHR 10 0 Q96I24;A0A494C1K6 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;;;; 174.41 3.11E-06 5400950000 3912934 4356574 3619833 4051549 4084310 3755922 4229696 3937382 4069626 4265174 FALSE TRUE 3760012.213 4232328.775 4274017.346 4260649.929 4215685.54 3831869.316 4281460.285 3856073.686 3607659.118 3976289.966 0.945608154 1.064391383 1.074875671 1.07151389 1.060205764 0.963679548 1.076747501 0.969766722 0.907292765 1 21.92299154 1.593947988 5.58915097 0.949230267 1.0384849 0.350043996 0.048620062 0.139920849 9.25998125 0.026134378 0.012190941 39.2597914 -1.593947988 0.089254633 SLTPAVPVESKPDKPSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLTPAVPVESKPDKPSGK 18 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 108.49 0.00021924 339950000 161680 141070 138130 125750 165070 145130 145800 185380 234400 201590 FALSE TRUE 155361.3669 137046.8217 163093.1637 132239.9726 170379.6265 148064.628 147584.344 181551.8382 207791.8947 187936.1297 0.826671099 0.729220198 0.867811654 0.703643162 0.906582607 0.787845468 0.785289897 0.966029462 1.105651665 1 17.51988292 1.594009988 3.447529328 1.050382208 0.80053995 0.741956276 0.061431439 0.086592693 2.399240782 0.035726947 0.014950071 39.26539657 -1.594009988 -0.249842258 QIELACDSQEDVDSWK ddPTM_BT-474_Pertuzumab_2h_R1 2 QIELACDSQEDVDSWK 16 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ; 308.84 3.09E-57 209850000 195905 196716 151838 166257 185319 199597 186793 206991 232549 232947 FALSE TRUE 188248.816 191105.8523 179278.5042 174837.5437 191279.9539 203632.9881 189079.0286 202716.5635 206151.0124 217169.2922 0.866829809 0.879985611 0.825524191 0.805074888 0.880787297 0.937669346 0.870652691 0.933449483 0.949264099 1 17.72846059 1.594278034 0.548849681 0.999535165 0.846083295 0.716199174 0.030133744 0.444372679 0.315156202 0.031975676 0.018553154 39.2896386 -1.594278034 -0.15345187 APVHFVEPLSPT(ph)GVAGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 APVHFVEPLSPTGVAGHR 18 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 APVHFVEPLS(0.375)PT(0.625)GVAGHR 108.69 0.0014127 286440000 163860 155970 136150 196890 184270 174290 175870 143660 127150 141760 TRUE FALSE 157456.17 151521.8883 160755.3336 207051.5165 190197.2119 177814.2632 178022.3497 140693.3708 112716.4651 132158.4689 1.191419448 1.146516675 1.216383142 1.566691247 1.439160225 1.345462494 1.347037016 1.064580817 0.852888702 1 17.01190935 1.594484559 3.373218917 0.931191132 1.326124956 0.645136604 0.121145137 0.132971696 3.531363381 0.085796215 0.035678218 39.3083269 -1.594484559 0.394933824 IQELEDLLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IQELEDLLAK 10 0 P20700;E9PBF6 P20700 LMNB1 Lamin-B1 0 ; 141.95 8.52E-05 155232000 242746 256468 204207 225972 227710 249625 221873 275017 316296 297821 FALSE TRUE 233259.218 249153.7837 241111.7475 237634.442 235034.499 254672.5885 224588.3481 269337.8028 280391.4041 277649.3184 0.840121702 0.897368613 0.868403888 0.855879796 0.846515671 0.917245502 0.808892129 0.9700647 1.009876076 1 18.08290433 1.594579018 5.192606969 1.000140211 0.865188221 0.817228405 0.028665082 0.054704164 3.166341503 0.01488168 0.006872202 39.31687736 -1.594579018 -0.13495199 ERELSWR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERELSWR 7 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 ; 143.73 0.0037039 175680000 190395 264160 276350 315410 273970 295220 316380 239800 219124 268590 FALSE TRUE 182954.1529 256626.4154 326292.5924 331688.3479 282782.4939 301189.5507 320251.9531 234848.0462 194249.9622 250398.1601 0.730652944 1.024873407 1.303095008 1.324643711 1.129331357 1.202842507 1.278970872 0.93789845 0.775764335 1 17.93386444 1.594831589 5.774449072 0.879168861 1.152060422 0.28967263 0.170681795 0.168106879 11.83778996 0.097600904 0.045741725 39.33974935 -1.594831589 0.272891562 DFSSVFQFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFSSVFQFLR 10 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 ; 121.73 0.00118 136875000 228927 305890 225251 242188 225774 238831 271190 225515 231680 228602 FALSE TRUE 219980.2797 297166.3167 265958.8664 254687.3517 233036.2258 243660.3265 274508.9043 220858.0364 205380.6577 213118.5829 1.032196614 1.394370742 1.247938414 1.195049949 1.09345803 1.143308683 1.288057102 1.036315245 0.963691926 1 17.70129687 1.594921146 5.16125803 0.987762341 1.201797775 0.480570823 0.095759362 0.124089818 7.105933982 0.053371924 0.024628794 39.34786255 -1.594921146 0.214035434 QLPLEPES(ph)PSGQVGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLPLEPESPSGQVGPR 16 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 QLPLEPES(0.992)PS(0.008)GQVGPR;QLPLEPES(0.993)PS(0.007)GQVGPR 344.18 1.10E-72 328550000 291420 298070 337650 389110 387870 343490 317550 333930 272870 320270 TRUE FALSE 280030.9842 289569.3354 398670.866 409192.0137 400346.1908 350435.6031 321436.2719 327034.2288 241894.9416 298577.8276 0.937882717 0.969828663 1.335232657 1.370470195 1.340843672 1.173682607 1.076557742 1.095306478 0.810157082 1 18.18774751 1.595056485 1.766561341 0.915060756 1.193671897 0.320860183 0.149369294 0.41889401 2.655007025 0.132525961 0.04696792 39.36012648 -1.595056485 0.278611141 QITEEDLEGKTEEEIEMMK ddPTM_BT-474_Pertuzumab_2h_R1 1 QITEEDLEGKTEEEIEMMK 19 1 B8ZZ98;Q8WVK2 B8ZZ98 SNRNP27 U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein 0 258.87 4.38E-31 67792000 85651 67256 59579 44996 62542 62268 58006 77408 95610 79356 FALSE TRUE 82303.66423 65337.92473 70346.25063 47318.24895 64553.72023 63527.10162 58715.89478 75809.49775 84756.75363 73981.14744 1.112495103 0.883169929 0.950867256 0.639598744 0.87256987 0.858693111 0.793660234 1.024713733 1.145653407 1 16.17487006 1.595185505 5.116619833 1.076073364 0.867351957 0.346099206 0.116506061 0.156410444 8.819882344 0.065313631 0.030102708 39.37182124 -1.595185505 -0.208721406 ETEELVASR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETEELVASR 9 0 Q8TEV9 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 0 76.064 0.036489 312380000 286170 426630 416310 734520 487110 494810 501980 411610 291760 475560 FALSE TRUE 274986.16 414462.9301 491546.4778 772428.6652 502778.3355 504815.3972 508123.3814 403110.1097 258640.628 443349.8976 0.62024636 0.934843861 1.108710029 1.742255202 1.1340441 1.138638804 1.146100144 0.909236952 0.583378116 1 18.75808622 1.595211638 3.813280507 0.779262652 1.13552262 0.18825042 0.27645097 0.285823128 9.588227433 0.176505489 0.076179637 39.37419049 -1.595211638 0.356259968 ATNS(ph)PKPHMVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATNSPKPHMVPR 12 1 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 AT(0.03)NS(0.97)PKPHMVPR;AT(0.064)NS(0.936)PKPHMVPR 103.88 0.0013316 736400000 294070 280198 267709 192502 206868 268720 278540 280820 364320 319890 TRUE FALSE 282577.4193 272207.0274 316089.9715 202437.0513 213522.0971 274153.7025 281948.8558 275020.9689 322963.921 298223.5654 0.947535514 0.912761629 1.059909438 0.678809708 0.715979962 0.919289199 0.945427822 0.922197307 1.08295909 1 18.18603474 1.595225786 1.523489384 1.034728739 0.870792129 0.245244467 0.107729471 0.572917158 2.606940084 0.09659337 0.034035843 39.37547323 -1.595225786 -0.163936611 KFS(ph)HS(ph)TLRHFGLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFSHSTLRHFGLGK 14 2 Q7Z449 Q7Z449 CYP2U1 Cytochrome P450 2U1 2 KFS(0.667)HS(0.667)T(0.667)LRHFGLGK 51.211 0.089204 208790000 209830 399160 307950 620160 531480 590660 509340 359870 230650 450030 TRUE FALSE 201629.6116 387776.3476 363603.4153 652166.5319 548575.5369 602603.5499 515573.4553 352438.5587 204467.579 419549.0673 0.480586485 0.924269359 0.866652899 1.554446387 1.307536066 1.436312453 1.228875227 0.840041335 0.487350813 1 18.67848002 1.595227871 4.800846593 0.721120628 1.132753562 0.196684248 0.313679053 0.236831976 11.93745774 0.188973167 0.086130298 39.37566227 -1.595227871 0.411632934 VDIDT(ph)PDINIEGSEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 VDIDTPDINIEGSEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDIDT(1)PDINIEGSEGK;VDIDT(0.999)PDINIEGS(0.001)EGK;VDIDT(1)PDINIEGSEGK 374.74 1.90E-103 385400000 356185 494352 492122 351558 413035 559392 360197 578856 710917 572695 TRUE FALSE 342264.8964 480253.565 581059.3926 369701.9505 426320.6459 570703.2895 364605.1986 566902.4213 630216.6826 533905.8575 0.641058515 0.899509826 1.08831807 0.692447826 0.798494041 1.068921199 0.682901664 1.061802213 1.180389152 1 19.02622585 1.595634225 7.286756601 1.098990895 0.852458439 0.353070381 0.149409561 0.129723809 15.02783061 0.077307978 0.036994348 39.41252187 -1.595634225 -0.246532457 LLS(ph)FQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLSFQR 6 0 Q13946-3;Q13946-2;Q13946;A1E5M1;Q9NP56 Q13946-3;A1E5M1 PDE7A;PDE7B "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A;cAMP-specific 3,5-cyclic phosphodiesterase 7B" 1 LLS(1)FQR;LLS(1)FQR;LLS(1)FQR 90.709 0.051107 213850000 265940 324701 299823 404300 380608 349783 361157 301407 283870 301952 TRUE FALSE 255546.7708 315440.8454 354007.6856 425165.9715 392850.602 356855.8519 365576.9474 295182.8401 251646.2677 281500.5221 0.90780212 1.120569309 1.257573815 1.51035589 1.395559053 1.267691617 1.29867236 1.048604947 0.893946007 1 18.10277807 1.595681973 3.684666491 0.951613001 1.262382493 0.404054407 0.15275007 0.193479892 6.092044892 0.102501815 0.043826987 39.41685528 -1.595681973 0.310769492 VDVNAPDVQAPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDVNAPDVQAPDWHLK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 244.97 4.34E-20 1942980000 1603040 1694500 1424600 1573900 1404530 1594620 1574810 1667860 1871190 1754390 FALSE TRUE 1540391.425 1646174.519 1682056.91 1655129.168 1449707.983 1626864.309 1594082.996 1633418.108 1658780.356 1635563.603 0.941810775 1.006487621 1.028426475 1.011962583 0.886366009 0.994681165 0.974638341 0.998688223 1.014194956 1 20.64135643 1.595713025 3.953008987 1.007030572 0.979295979 0.092904478 0.038249974 0.48671481 17.43687151 0.0238048 0.01038072 39.41967371 -1.595713025 -0.027734593 VEGQKEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEGQKEEK 8 1 A0A1W2PNT1 A0A1W2PNT1 0 84.476 0.01047 329320000 281410 536680 395330 698940 550640 576440 514060 390460 251780 373410 FALSE TRUE 270412.1861 521374.4119 466774.9251 735012.3772 568351.8357 588096.0118 520351.2201 382396.8646 223198.9899 348118.6081 0.776781763 1.497691878 1.340850257 2.111384913 1.632638481 1.689355289 1.494752673 1.098467177 0.641157883 1 18.40921941 1.595772606 3.030896365 0.825782816 1.536807564 0.424807232 0.324412082 0.198770063 4.250239567 0.218885618 0.088136915 39.42508203 -1.595772606 0.711024748 QFDQLLAFFDS(ph)RK ddPTM_BT-474_Pertuzumab_2h_R1 1 QFDQLLAFFDSRK 13 1 Q9BXT8-2;Q9BXT8-1;Q9BXT8-4;Q9BXT8-5;Q9BXT8 Q9BXT8-2 RNF17 RING finger protein 17 1 QFDQLLAFFDS(1)RK 79.148 0.022559 618090000 564150 805630 530840 820290 737680 847050 736090 677850 591930 763060 TRUE FALSE 542102.3943 782654.2212 626774.5965 862625.2652 761408.1471 864177.9314 745098.4896 663852.1606 524736.588 711377.2665 0.762046272 1.100195716 0.881072008 1.212612921 1.070329603 1.214795541 1.047402728 0.933192824 0.737634744 1 19.44025535 1.595836933 3.89366363 0.860272952 1.051307327 0.193828372 0.142666133 0.249492342 8.697223878 0.083436787 0.036240117 39.43092204 -1.595836933 0.191034374 ELENAEFIPMPDS(ph)PSPLSAAFSESEKDTLPYEELQGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELENAEFIPMPDSPSPLSAAFSESEKDTLPYEELQGLK 38 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 ELENAEFIPMPDS(0.779)PS(0.176)PLS(0.04)AAFS(0.004)ES(0.001)EKDTLPYEELQGLK;ELENAEFIPMPDS(0.819)PS(0.171)PLS(0.008)AAFS(0.001)ES(0.001)EKDTLPYEELQGLK 137.69 1.18E-09 63733000 218939 227000 219435 206502 233897 243359 211064 215532 213412 202116 TRUE FALSE 210382.6218 220526.1823 259091.7858 217159.593 241420.5094 248279.8857 213647.0644 211081.1889 189186.3645 188426.5033 1.116523515 1.170356497 1.37502836 1.15248964 1.281244969 1.317648427 1.133848268 1.120230887 1.004032666 1 17.52364238 1.595947336 1.606658279 0.999623559 1.23481827 0.57190109 0.077285758 0.255176986 1.306299645 0.063982278 0.022562275 39.44094714 -1.595947336 0.235194711 EKNLEEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKNLEEAK 8 1 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 98.249 0.0069828 1268120000 2062650 2007060 1775090 1507130 1960680 1590730 2255430 1999580 2663310 2436830 FALSE TRUE 1982039.358 1949820.614 2095888.25 1584913.16 2023747.053 1622895.65 2283032.627 1958287.974 2360982.214 2271781.334 0.872460447 0.858278297 0.922574818 0.697652162 0.890819474 0.714371417 1.00495263 0.862005487 1.03926473 1 21.11539255 1.596001978 1.268117711 1.010875598 0.834848998 0.370255968 0.086369171 0.44278964 1.361697174 0.07041035 0.025230816 39.44590986 -1.596001978 -0.1760266 GFSDKLDFLEGDQKPLAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFSDKLDFLEGDQKPLAQR 19 2 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 81.665 0.003124 590700000 1036800 844390 791060 687360 771990 791570 869910 952620 1186300 1045400 FALSE TRUE 996280.7098 820308.8239 934022.139 722834.732 796821.7595 807576.0877 880556.2188 932948.0641 1051636.197 974594.1269 1.022251912 0.841692764 0.958370375 0.741677702 0.817593435 0.828628108 0.903510697 0.957268301 1.079050415 1 19.894442 1.596531402 2.341628704 1.037645803 0.864475191 0.434927269 0.075845897 0.237444628 2.876025372 0.055444624 0.0207145 39.49402548 -1.596531402 -0.173170612 GFAFVYFENVDDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFAFVYFENVDDAK 14 0 P62995;P62995-3;H7BXF3 P62995 TRA2B Transformer-2 protein homolog beta 0 ; 194.96 1.95E-07 328330000 415330 385460 321350 354070 403780 393830 360790 430530 491410 455800 FALSE TRUE 399098.4444 374467.0582 379425.0934 372343.5951 416767.9504 401793.5124 365205.4559 421639.405 435627.197 424928.26 0.939213703 0.881247715 0.89291565 0.876250488 0.98079603 0.94555611 0.859452031 0.992260211 1.025178219 1 18.69685977 1.596537168 6.010860423 1.011004548 0.911796362 0.609020054 0.035092814 0.0910493 6.941335839 0.019615816 0.009246942 39.49454987 -1.596537168 -0.099208186 DGFIDKEDLHDMLASLGK ddPTM_BT-474_Pertuzumab_2h_R1 3 DGFIDKEDLHDMLASLGK 18 1 J3QRS3;P19105;O14950;J3KTJ1;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;; 228.39 1.47E-19 10344860000 21363030 19790580 17614360 17878480 19239840 20148360 21664550 22382770 28195900 26533900 FALSE TRUE 20528139.17 19226172.04 20797666.68 18801190.5 19858706.93 20555773.64 21929687.24 21920557.98 24995219.64 24736735.32 0.829864528 0.777231586 0.840760368 0.760051407 0.802802256 0.830981671 0.886523099 0.886154042 1.010449411 1 24.56015177 1.596581891 1.022008711 1.011921838 0.801387814 0.86975347 0.029273434 0.153787975 0.308098172 0.024902969 0.009441692 39.49861709 -1.596581891 -0.210534023 ASPAEGSAGSPGS(ph)PTCCR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPAEGSAGSPGSPTCCR 18 0 A4D1S0-2;A4D1S0 A4D1S0-2 KLRG2 Killer cell lectin-like receptor subfamily G member 2 1 ASPAEGSAGSPGS(1)PTCCR 330.54 7.26E-75 201130000 105170 131950 99856 155280 124830 136850 129170 117140 109840 121460 TRUE FALSE 101059.8401 128186.9152 117902.2005 163294.0194 128845.2703 139617.2008 130750.8211 114721.0181 97371.42369 113233.406 0.892491392 1.132059166 1.0412316 1.4421011 1.137873308 1.233003631 1.15470183 1.013137572 0.85991782 1 16.78894012 1.596582375 3.379660863 0.930550393 1.157313744 0.302692454 0.134906823 0.231852902 6.188340915 0.085927873 0.035831394 39.49866116 -1.596582375 0.226763351 RVEDQSIWPSMDDDEEESGAKVDSPLPSDKAPT(ph)PPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVEDQSIWPSMDDDEEESGAKVDSPLPSDKAPTPPGK 37 3 Q12893 Q12893 TMEM115 Transmembrane protein 115 1 RVEDQSIWPSMDDDEEES(0.001)GAKVDS(0.003)PLPS(0.061)DKAPT(0.935)PPGK 66.865 0.0028037 35703000 39276 43550 36656 25316 27577 39287 34025 49721 73017 47239 TRUE FALSE 37741.0505 42307.99664 43280.55461 26622.56179 28464.03925 40081.41006 34441.40813 48694.24397 64728.41627 44039.46045 0.856982581 0.96068381 0.982767594 0.604516075 0.646330335 0.910124912 0.782057904 1.105695744 1.469782227 1 15.42650917 1.59678565 4.005506716 1.249781096 0.821184208 0.545487314 0.15736557 0.124510778 4.569977084 0.094680461 0.041470466 39.51715311 -1.59678565 -0.428596888 RS(ph)PERPTGDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RSPERPTGDLR 11 2 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.998)PERPT(0.002)GDLR;RS(1)PERPTGDLR;RS(1)PERPTGDLR;RS(1)PERPTGDLR 118.37 0.0005749 6577980000 4647920 5153720 3996750 4842780 4823650 5141850 4646170 4842650 4898400 4935180 TRUE FALSE 4466274.148 5006740.952 4719051.632 5092716.456 4978807.083 5245821.73 4703031.218 4742647.585 4342354.168 4600915.863 0.970735888 1.088205284 1.025676577 1.10689189 1.082133912 1.14016902 1.022194571 1.030805111 0.943802125 1 22.13348964 1.596802887 2.153552365 0.975186965 1.068898732 0.356834578 0.047346744 0.289843787 2.897135134 0.034876874 0.012777056 39.51872161 -1.596802887 0.093711767 EAVCIVLSDDTCSDEKIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAVCIVLSDDTCSDEKIR 18 1 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 118.72 8.62E-05 143700000 182680 188200 150250 184060 166970 204550 181220 213140 232110 241110 FALSE TRUE 175540.6636 182832.7203 177403.5173 193559.3587 172340.7417 208686.1411 183437.8246 208738.5845 205761.8459 224779.4049 0.780946385 0.813387331 0.789233859 0.861108066 0.766710552 0.928404189 0.816079323 0.928637499 0.915394566 1 17.77815033 1.59685028 0.366517632 1.011032418 0.780220201 0.699940274 0.041036522 0.593806108 0.246360394 0.050710873 0.043352088 39.52303434 -1.59685028 -0.230812217 T(ph)PLSEAEFEEIMNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPLSEAEFEEIMNR 14 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 T(1)PLSEAEFEEIMNR;T(0.995)PLS(0.005)EAEFEEIMNR 236.4 3.24E-16 173588000 15302.5 18347.2 15863.5 20501.7 17121.5 20176.8 22893.4 20233.9 20735 27846 TRUE FALSE 14704.46138 17823.95582 18730.38733 21559.79519 17672.2286 20584.78872 23173.57628 19816.06289 18381.24973 25959.96562 0.566428384 0.686593969 0.721510483 0.830501685 0.680749307 0.792943605 0.892665908 0.763331631 0.708061405 1 14.66400085 1.596975106 0.04719115 1.612600312 2.63E-16 0.59007403 0.074225972 31.75885142 1.528963079 25.55138544 25.78662265 39.53439581 -1.596975106 -1.612600312 RFPVAPLIPYPLITK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFPVAPLIPYPLITK 15 1 P49756;P49756-2;P49756-3;H0YE46 P49756 RBM25 RNA-binding protein 25 0 79.81 0.030204 53125000 133030 166780 109770 128010 137470 126590 145180 115150 107050 117960 FALSE TRUE 127831.0405 162023.5977 129607.8808 134616.6114 141891.8474 129149.7365 146956.7563 112772.1123 94898.13279 109970.4641 1.162412485 1.4733374 1.178569917 1.224116062 1.290272334 1.174403851 1.336329326 1.025476369 0.862942005 1 16.74675657 1.597380953 4.266480678 0.934562493 1.263262446 0.688369246 0.093614111 0.0857463 3.52048582 0.05154451 0.022946319 39.5713579 -1.597380953 0.328699953 DAFDRNPELQNLLLDDFFK ddPTM_BT-474_Pertuzumab_2h_R1 3 DAFDRNPELQNLLLDDFFK 19 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 323.47 2.80E-62 2189012000 2223176 1925999 2074600 2080134 2363387 2067863 2378148 2646616 3171771 3103509 FALSE TRUE 2136291.824 1871071.394 2449526.369 2187489.965 2439407.489 2109676.607 2407252.487 2591962.455 2811724.853 2893305.571 0.738356793 0.646689867 0.84661862 0.756052173 0.843121277 0.729157897 0.832007691 0.895848154 0.971803629 1 21.46428727 1.597508147 1.120425098 1.005378661 0.75756098 0.732953363 0.054511383 0.235388834 0.563472549 0.048089361 0.017717039 39.58294903 -1.597508147 -0.247817681 KYHNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYHNPK 6 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 81.672 0.039767 3139000000 6500000 6307000 5758300 5912300 6173400 6330200 6883500 6586200 8099100 7677400 FALSE TRUE 6245972.814 6127130.535 6798952.903 6217434.512 6371973.018 6458200.981 6967742.332 6450192.668 7179724.122 7157402.86 0.872659111 0.856055004 0.949918991 0.868671868 0.89026329 0.902310672 0.973501488 0.901191786 1.003118626 1 22.77100475 1.597629647 0.536108763 1.005128017 0.880860923 0.589814827 0.033616732 0.572671922 0.39220946 0.032761951 0.019484535 39.59402447 -1.597629647 -0.124267094 SAIVHLINYQDDAELATR ddPTM_BT-474_Pertuzumab_2h_R1 4 SAIVHLINYQDDAELATR 18 0 P14923;C9JTX4;C9J826;C9JK18;C9JKY1 P14923 JUP Junction plakoglobin 0 ;;; 228.63 2.32E-19 1919380000 587540 663470 491980 662620 512180 639100 644560 565570 611340 560650 FALSE TRUE 564578.2872 644548.4852 580891.73 696817.8976 528654.7349 652023.0399 652448.3181 553890.7819 541943.2461 522676.6761 1.080167364 1.233168639 1.11137871 1.333171977 1.011437393 1.247469171 1.248282825 1.059719722 1.036861354 1 18.99555926 1.597744659 5.271037842 1.027949062 1.181727118 0.371767798 0.089228975 0.14874623 8.854788874 0.046411311 0.021528923 39.60451132 -1.597744659 0.153778055 NDDLNKPINK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDDLNKPINK 10 1 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 96.015 0.0058324 0 225220 187810 166150 167040 189920 166600 179990 211510 251940 221320 FALSE TRUE 216418.1534 182453.8427 196177.001 175660.9544 196028.9493 169968.7661 182192.7715 207142.2446 223340.8274 206329.7993 1.048894315 0.884282558 0.95079335 0.85136008 0.950075801 0.823772265 0.883017248 1.003937605 1.082445814 1 17.65459267 1.597883959 4.407988011 1.0416374 0.909437569 0.427301743 0.062015645 0.140727521 6.11816293 0.034560682 0.015507363 39.6172165 -1.597883959 -0.13219983 TNTMNGSKS(ph)PVISRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNTMNGSKSPVISRPK 16 2 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2 A0A0U1RRM6 ENAH Protein enabled homolog 1 TNT(0.001)MNGS(0.167)KS(0.831)PVIS(0.002)RPK;TNTMNGS(0.002)KS(0.998)PVISRPK 137.43 9.49E-06 1032720000 412760 326940 285660 275790 270000 313120 310820 381090 480160 402090 TRUE FALSE 396628.8829 317615.9913 337285.1165 290023.555 278684.7952 319451.5009 314623.9081 373220.3583 425654.2498 374856.0862 1.058083082 0.847301146 0.899772283 0.773693067 0.743444766 0.852197717 0.839319194 0.995636384 1.135513776 1 18.5159773 1.597922098 3.61262459 1.06811943 0.852246683 0.504663047 0.085247033 0.146325011 4.444647993 0.053304894 0.02270881 39.62069574 -1.597922098 -0.215872747 EKELAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKELAK 6 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 ; 83.801 0.051597 881910000 616010 589700 448940 485660 554380 605770 631680 637530 831830 803880 FALSE TRUE 591935.6482 572882.3334 530073.4446 510724.9708 572212.1362 618019.0844 639410.6888 624364.7827 737404.1457 749432.4916 0.789845189 0.764421532 0.707299791 0.68148229 0.763527259 0.82464944 0.853193177 0.833116778 0.983950061 1 19.515439 1.598195243 0.729588787 1.006508524 0.736693284 0.836902337 0.040314777 0.252842557 0.278265653 0.040188274 0.018258066 39.64562264 -1.598195243 -0.269815239 FLQEFYQDDELGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLQEFYQDDELGKK 14 1 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 229.17 2.22E-12 1055980000 1506680 1340030 1057560 1059210 1233750 1345670 1387380 1473270 1820510 1758020 FALSE TRUE 1447797.28 1301813.656 1248684.617 1113875.955 1273434.689 1372880.369 1404359.171 1442846.46 1613853.337 1638947.74 0.883370009 0.794298454 0.7618819 0.67962872 0.776983096 0.837659638 0.856866352 0.880349278 0.984688711 1 20.64433842 1.598361252 0.983220669 1.004871591 0.777693682 0.718795312 0.049718336 0.280329758 0.521829933 0.047534293 0.018300965 39.66078008 -1.598361252 -0.227177909 LNEQASEEILKVEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNEQASEEILKVEQK 15 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ; 169.61 1.08E-06 957400000 833540 815160 597550 532530 676220 779630 668140 772170 916160 734190 FALSE TRUE 800964.3353 791912.4349 705540.5774 560013.9371 697971.2304 795394.6528 676316.8972 756224.4197 812161.3577 684462.6574 1.170208961 1.156984134 1.030794843 0.818180409 1.019736026 1.162071655 0.988099044 1.104843941 1.186567812 1 19.38461231 1.598384201 10.58513981 1.110146639 1.046988281 0.035548016 0.107391874 0.304450351 108.3872807 0.059101966 0.028716109 39.66287588 -1.598384201 -0.063158358 EAAVSASDILQESAIHS(ph)PGTVEK ddPTM_BT-474_Pertuzumab_2h_R1 5 EAAVSASDILQESAIHSPGTVEK 23 0 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 EAAVSASDILQESAIHS(1)PGTVEK;EAAVSASDILQESAIHS(0.979)PGT(0.021)VEK;EAAVSASDILQESAIHS(0.992)PGT(0.008)VEK;EAAVSASDILQESAIHS(1)PGTVEK;EAAVSASDILQESAIHS(0.974)PGT(0.026)VEK 294.46 8.23E-62 4056940000 1574693 1482119 1435559 1459286 1421217 1579013 1740734 1660363 1985858 1991558 TRUE FALSE 1513152.257 1439850.417 1694996.445 1534599.925 1466931.736 1610941.725 1762037.623 1626075.924 1760431.725 1856668.003 0.814982676 0.77550236 0.91292382 0.826534374 0.790088337 0.86765201 0.949032148 0.875803278 0.948167213 1 20.82428443 1.598642459 0.433545 1.004332438 0.81037721 0.640944892 0.042792889 0.642748615 0.329327393 0.049653802 0.036608981 39.68646883 -1.598642459 -0.193955228 NQCTQVVQER ddPTM_BT-474_Pertuzumab_2h_R1 2 NQCTQVVQER 10 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 152.07 4.35E-05 114187000 80410 72976 68000 63530 82361 78345 64396 82916 88673 88595 FALSE TRUE 77267.4883 70894.79593 80289.11265 66808.79091 85010.21636 79929.18958 65184.09751 81203.75562 78607.21279 82594.38174 0.935505378 0.858348891 0.972089275 0.808878153 1.029249382 0.967731556 0.789207403 0.983163188 0.951725906 1 16.33375603 1.598752544 25 0.975594884 0.910417503 0.16624123 0.071256937 1.404238717 3841.179144 0.036170887 0.017115701 39.69652987 -1.598752544 -0.065177381 T(ph)TPDQELVPASEPVWERPWSVEEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPDQELVPASEPVWERPWSVEEIR 25 1 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 T(0.5)T(0.5)PDQELVPASEPVWERPWSVEEIR;T(0.56)T(0.44)PDQELVPASEPVWERPWSVEEIR 212.21 1.54E-25 235903000 20011.9 13969.9 11287.8 19636.7 20989.7 14930.4 16171.7 20428.8 25106.6 23897.3 TRUE FALSE 19229.81282 13571.49213 13327.75656 20650.15244 21664.85276 15232.30292 16369.6141 20006.93814 22256.60402 22278.71459 0.863147322 0.609168544 0.598228255 0.926900534 0.972446264 0.68371552 0.734764748 0.898029285 0.999007548 1 14.44337838 1.598902793 0.365228213 1.031366607 0.711152124 0.312278145 0.12461533 1.539852302 0.635802493 0.182134583 0.156335593 39.71026575 -1.598902793 -0.320214482 AALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFAR 39 0 O75390;B4DJV2;A0A0C4DGI3;F8VPA1;F8VX68;F8VPF9;F8VRI6;F8VR34;F8W1S4;H0YH82;F8VRP1 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 400.47 4.32E-181 700770000 78310 114249 76794 158569 94815 123644 136710 94471 103609 92441 FALSE TRUE 75249.55862 110990.7304 90672.38407 166752.7651 97864.81058 126144.1664 138383.0979 92520.14084 91847.74068 86179.88873 0.873168436 1.287895958 1.052129278 1.934938273 1.135587572 1.463730903 1.605747001 1.073569973 1.065767687 1 16.39506362 1.598985796 9.580678204 1.047088859 1.344134238 0.182923364 0.280743666 0.167728911 42.93059544 0.144187043 0.070089209 39.7178559 -1.598985796 0.297045378 ERENS(ph)ESKEEDVEIDIELAPGDQTSTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERENSESKEEDVEIDIELAPGDQTSTPK 28 2 H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5;A0A2R8YFJ4 H0Y4W2 TRRAP Transformation/transcription domain-associated protein 1 ERENS(0.5)ES(0.5)KEEDVEIDIELAPGDQTSTPK 141.75 6.42E-08 137720000 255780 207190 182990 158250 204380 183560 192420 245600 317240 249200 TRUE FALSE 245783.8348 201281.1441 216060.3636 166417.3015 210954.0683 187271.709 194774.8935 240528.2742 281228.2452 232321.462 1.057947177 0.866390657 0.930006043 0.716323408 0.908026604 0.806088716 0.838385278 1.035325243 1.21051341 1 17.82576291 1.599083592 4.158953198 1.110139794 0.869570353 0.500626717 0.095989095 0.125527219 4.93059696 0.054521348 0.024155061 39.72680072 -1.599083592 -0.240569441 NTLETSSLNFKVT(ph)PDIEESLLEPENEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTLETSSLNFKVTPDIEESLLEPENEK 27 1 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 1 NT(0.007)LET(0.169)S(0.169)S(0.169)LNFKVT(0.486)PDIEESLLEPENEK 85.658 0.013648 52804000 54686 45074 39392 33699 42108 42197 42947 52152 66970 54181 TRUE FALSE 52548.81066 43788.53365 46511.01067 35438.20943 43462.44206 43050.25225 43472.59823 51075.04298 59367.84636 50511.27261 1.040338284 0.866906165 0.92080457 0.701590112 0.860450347 0.852289994 0.860651415 1.011161278 1.175338559 1 15.62431777 1.599199271 3.561708204 1.089862132 0.86576825 0.506604968 0.087665787 0.143086701 4.233625157 0.053719636 0.022818074 39.73738385 -1.599199271 -0.224093883 VGDTEKPEPERS(ph)PPNRK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGDTEKPEPERSPPNRK 17 3 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 VGDTEKPEPERS(1)PPNRK 100.21 0.0076851 279070000 131040 106680 96751 109970 112000 120000 124530 136560 181760 160880 TRUE FALSE 125918.8119 103637.5909 114236.0579 115645.5649 115602.5817 122426.4822 126054.0354 133739.9883 161127.3668 149983.4543 0.839551353 0.690993492 0.761657734 0.771055484 0.770768897 0.816266586 0.840452942 0.89169828 1.074300946 1 17.19444383 1.599252487 1.365141916 1.039393405 0.768530996 0.833130658 0.044989918 0.143575537 0.51536257 0.037008454 0.013155996 39.74225328 -1.599252487 -0.270862409 AAQDRDQIYR ddPTM_BT-474_Pertuzumab_2h_R1 5 AAQDRDQIYR 10 1 P62995;P62995-3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;;; 199.68 2.50E-07 18709400000 8689590 9871600 6655470 8702730 8614440 8820650 8136340 8429810 8512290 8151270 FALSE TRUE 8349991.216 9590071.633 7858261.479 9151878.938 8891531.286 8999009.587 8235914.963 8255731.478 7546010.526 7599177.223 1.098802011 1.261988154 1.034093725 1.204324978 1.170064999 1.184208411 1.083790353 1.086398071 0.993003625 1 22.85741179 1.599547496 1.359866919 0.993772925 1.159346872 0.513228085 0.060019138 0.304255545 1.083172623 0.047805521 0.017003775 39.76925874 -1.599547496 0.165573947 RLDEVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLDEVSR 7 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 113.94 0.0096466 724120000 1977470 2277980 1630080 2594010 2275090 2826100 2282010 2145080 1947400 2331150 FALSE TRUE 1900188.286 2213014.241 1924671.717 2727887.167 2348270.336 2883245.678 2309937.921 2100783.348 1726339.316 2173259.134 0.874349615 1.018292852 0.885615381 1.255205661 1.080529376 1.326692079 1.06289116 0.966651107 0.794355026 1 21.05142878 1.599908801 3.642151993 0.893504544 1.079621566 0.203021392 0.140561662 0.282706091 8.728977854 0.089088966 0.038115191 39.80235799 -1.599908801 0.186117022 LIHEQEQQS(ph)SS ddPTM_BT-474_Pertuzumab_2h_R1 1 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.457)S(0.457)S(0.085) 92.856 0.010157 440270000 141000 197380 161250 234010 162710 180770 210410 167540 172790 180270 TRUE FALSE 135489.5641 191750.9157 190391.462 246087.2841 167943.7149 184425.2933 212985.0605 164080.2405 153175.6036 168060.1523 0.806196842 1.140965976 1.132876886 1.464280978 0.999307168 1.097376687 1.267314456 0.976318527 0.911433207 1 17.35861817 1.599960515 7.595400867 0.952692625 1.136863303 0.18488723 0.16064796 0.185319786 24.10745521 0.084688686 0.040843494 39.80709768 -1.599960515 0.184170678 LAHPNKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAHPNKPK 8 1 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ; 91.065 0.0076617 2812200000 5666100 5690300 5006700 4881600 5076900 5113600 5792200 5728000 6945400 6420700 FALSE TRUE 5444662.548 5528018.215 5911522.063 5133539.961 5240203.099 5217000.496 5863086.676 5609714.798 6156987.309 5985820.27 0.909593389 0.923518911 0.987587632 0.857616789 0.875436091 0.87155983 0.979495944 0.937167263 1.028595419 1 22.51311753 1.600090997 1.462328007 1.010325963 0.908272566 0.482287868 0.040721914 0.348346056 1.44986112 0.035494741 0.012562176 39.81905943 -1.600090997 -0.102053397 SQSTFQLSSEPEREPEWR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSTFQLSSEPEREPEWR 18 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 0 131.11 1.61E-05 341400000 62705 52445 55323 55981 62706 52638 67915 54815 56014 62321 FALSE TRUE 60254.41928 50949.31995 65321.09675 58870.18612 64722.99544 53702.37643 68746.16409 53683.05109 49655.52555 58099.94316 1.037082241 0.87692547 1.124288479 1.013257207 1.113994127 0.924310309 1.183239782 0.923977687 0.854657042 1 15.82624913 1.600134439 24.99999728 0.916958344 1.034975112 0.237224593 0.092049469 0.871782629 2810.202322 0.045101306 0.021488565 39.82304264 -1.600134439 0.118016768 RDS(ph)DGVDGFEAEGK ddPTM_BT-474_Pertuzumab_2h_R1 6 RDSDGVDGFEAEGK 14 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK 245.71 1.19E-17 2194430000 2840110 2589200 2558810 2641430 2849700 2629160 2890220 3298790 3551010 3689890 TRUE FALSE 2729115.361 2515358.551 3021243.887 2777754.519 2941363.189 2682323.417 2925591.377 3230668.834 3147914.232 3439970.464 0.793354301 0.731215159 0.878276113 0.807493712 0.85505478 0.779751874 0.850469912 0.939155981 0.915099204 1 21.71396475 1.600194564 0.942577753 0.990275045 0.80377857 0.708682707 0.041571561 0.278002314 0.478231024 0.037442322 0.014682769 39.82855629 -1.600194564 -0.186496475 SLENETLNKEEDCHSPT(ph)SKPPKPDQPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLENETLNKEEDCHSPTSKPPKPDQPLK 28 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SLENETLNKEEDCHS(0.091)PT(0.788)S(0.12)KPPKPDQPLK;SLENETLNKEEDCHS(0.354)PT(0.572)S(0.073)KPPKPDQPLK 226.1 7.44E-35 4430200000 4014400 2936300 3031300 2187070 2924700 3240900 3539200 3837200 5606700 4567900 TRUE FALSE 3857512.81 2852559.599 3579123.341 2299944.945 3018775.632 3306433.219 3582513.788 3757960.479 4970250.921 4258512.064 0.90583583 0.669848895 0.840463356 0.54008182 0.708880376 0.776429224 0.841259514 0.882458573 1.167133225 1 22.02191801 1.600290067 1.665287752 1.078549579 0.734291529 0.601141429 0.105382981 0.22205414 1.232758027 0.083365152 0.029537288 39.83731568 -1.600290067 -0.344258049 SAMDSPVPASMFAPEPSS(ph)PGAAR ddPTM_BT-474_Pertuzumab_2h_R1 5 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.131)S(0.869)PGAAR;SAMDSPVPASMFAPEPS(0.066)S(0.934)PGAAR;SAMDSPVPASMFAPEPSS(1)PGAAR;SAMDSPVPASMFAPEPS(0.018)S(0.982)PGAAR;SAMDSPVPASMFAPEPS(0.007)S(0.993)PGAAR 354.15 9.84E-102 2822808000 1251338 1319516 1116437 1340200 1353792 1366671 1291278 1238559 1200179 1269180 TRUE FALSE 1202434.328 1281884.696 1318202.001 1409367.883 1397337.949 1394306.024 1307081.046 1212982.324 1063939.711 1183217.308 1.016241327 1.083389067 1.114082757 1.191131902 1.180964764 1.178402323 1.104683846 1.025156001 0.899192147 1 20.17428363 1.600562782 2.782444689 0.950938288 1.130056548 0.624667048 0.054854606 0.151273093 2.701566465 0.040094319 0.015806388 39.86233934 -1.600562782 0.17911826 YQLDKDGVVLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 YQLDKDGVVLFK 12 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6 P07237 P4HB Protein disulfide-isomerase 0 ; 180.54 1.76E-05 9515900000 8670800 8952600 7924100 9460500 8752800 8556100 9597700 10908700 13230900 12698200 FALSE TRUE 8331935.55 8697280.614 9356161.141 9948757.539 9034341.761 8729110.204 9715159.524 10683431.53 11728983.7 11838139.6 0.703821363 0.734683059 0.790340497 0.840398734 0.763155535 0.737371791 0.820666072 0.902458654 0.990779303 1 23.49693904 1.600724294 1.665930078 1.001845886 0.765065862 0.873678045 0.035505575 0.122539322 0.680934704 0.031645716 0.011216482 39.87716669 -1.600724294 -0.236780023 DLISHDEMFSDIYK ddPTM_BT-474_Pertuzumab_2h_R1 8 DLISHDEMFSDIYK 14 0 Q5W0H4;A0A0B4J2C3;P13693 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;;; 321.86 3.00E-56 10069000000 6625227 6405119 5875014 5937485 6344486 6245102 7008494 7303164 7898345 8242550 FALSE TRUE 6366305.804 6222451.277 6936759.719 6243919.312 6548562.154 6371382.241 7094266.046 7152351.111 7001757.988 7684274.747 0.828484927 0.809764289 0.90272146 0.812558051 0.852203021 0.829145554 0.923218687 0.93077764 0.911180068 1 22.87347767 1.600778652 0.611772398 0.993223133 0.832034629 0.727632676 0.031238751 0.360092139 0.299411776 0.029635695 0.015555138 39.88215819 -1.600778652 -0.161188504 FKGQILMPNIGYGSNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKGQILMPNIGYGSNKK 17 2 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 84.829 0.0029172 462700000 701980 633240 492030 464170 585640 583110 520530 646720 731260 667260 FALSE TRUE 674545.8455 615180.6152 580950.7661 488125.8693 604477.6425 594900.8837 526900.4018 633365.006 648250.4305 622065.8859 1.084363989 0.988931605 0.933905522 0.78468516 0.971726076 0.956330989 0.847017034 1.018163864 1.04209288 1 19.24670787 1.600938327 13.23043477 1.023148319 0.935700822 0.194352818 0.076312105 0.133276836 116.2964446 0.040613009 0.019871419 39.89682415 -1.600938327 -0.087447497 ERDHS(ph)PTPSVFNSDEER ddPTM_BT-474_Pertuzumab_2h_R1 3 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.683)PT(0.283)PS(0.034)VFNSDEER;ERDHS(0.333)PT(0.333)PS(0.333)VFNSDEER;ERDHS(0.675)PT(0.163)PS(0.163)VFNSDEER 189.37 2.17E-10 2411940000 788520 865980 693730 865480 869480 870160 879040 819100 863580 868040 TRUE FALSE 757703.7666 841283.0983 819102.4429 910147.5265 897447.6138 887755.2314 889797.9545 802185.2988 765550.0188 809246.8776 0.936307309 1.039587698 1.012178688 1.124684632 1.108991136 1.097014095 1.099538323 0.991273888 0.946003055 1 19.62622037 1.60110927 5.463728984 0.971962931 1.062768474 0.321052264 0.053947528 0.168031462 10.69563275 0.03148837 0.014718145 39.91253115 -1.60110927 0.090805543 VPLSNENSQVPQS(ph)PEDWR ddPTM_BT-474_Pertuzumab_2h_R1 4 VPLSNENSQVPQSPEDWR 18 0 Q8IZT6;Q8IZT6-2 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 VPLSNENSQVPQS(1)PEDWR;VPLSNENS(0.001)QVPQS(0.999)PEDWR;VPLSNENSQVPQS(1)PEDWR;VPLSNENS(0.002)QVPQS(0.998)PEDWR 144.23 1.05E-07 495078000 269555 341446 317379 397764 393351 413055 359071 326537 286520 340099 TRUE FALSE 259020.4926 331708.2944 374736.4454 418292.6477 406003.4921 421407.2551 363465.4183 319793.8968 253995.4508 317063.7918 0.816934949 1.046187874 1.181896057 1.319269682 1.280510429 1.329092965 1.14634792 1.008610586 0.801086271 1 18.27441361 1.601125151 3.200410882 0.900977835 1.174243748 0.331591585 0.149019465 0.237957316 5.710165434 0.103315305 0.042563998 39.91399062 -1.601125151 0.273265914 KKGEDEDKGPPCGPVNCNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKGEDEDKGPPCGPVNCNEK 20 3 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 136.49 2.32E-06 2272200000 2777100 2089600 2023900 1489600 2240300 2153800 2151900 2589300 3407100 2620400 FALSE TRUE 2668567.862 2030006.654 2389663.751 1566478.435 2312361.284 2197351.312 2178235.596 2535830.05 3020340.292 2442917.974 1.092368999 0.830976183 0.978200569 0.641232514 0.946557072 0.899478138 0.891653187 1.038033236 1.236365823 1 21.22017399 1.601226258 3.539410701 1.123608149 0.889764704 0.359357237 0.120988088 0.182794794 5.349670796 0.071349782 0.030310042 39.92328401 -1.601226258 -0.233843445 KTVSLTPSPTTQVETPDLVDHDNTS(ph)PLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTVSLTPSPTTQVETPDLVDHDNTSPLFR 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 KTVSLTPSPTTQVETPDLVDHDNT(0.052)S(0.948)PLFR;KTVSLTPSPTTQVETPDLVDHDNT(0.095)S(0.905)PLFR 275.07 1.84E-71 581770000 354610 389470 240560 290780 330450 351420 257820 254510 225480 177703 TRUE FALSE 340751.4492 378362.6969 284034.5432 305787.1906 341079.2244 358525.9532 260975.2783 249254.2796 199884.4557 165667.0175 2.056845438 2.283874621 1.714490594 1.845794022 2.058823956 2.164135979 1.575300154 1.504549809 1.206543455 1 17.33792688 1.602103612 1.131937244 1.029284688 2.016052741 0.819204787 0.170308567 0.18992198 0.463608611 0.155537907 0.057263584 40.00401782 -1.602103612 0.986768052 ATLYVTAIEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATLYVTAIEDR 11 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;;; 225.67 1.23E-11 1340920000 607810 711020 609220 691670 692940 630360 739320 663820 735700 695940 FALSE TRUE 584056.1132 690742.4058 719319.606 727367.1716 715229.0444 643106.3111 748368.0193 650111.885 652186.4203 648803.3639 0.900205125 1.064640605 1.108686616 1.121090321 1.102381837 0.991219138 1.153458907 1.002016822 1.005214302 1 19.30742177 1.602174695 25 1.00269931 1.066734435 0.139947506 0.068527016 0.997873294 4365.901719 0.035163836 0.016976254 40.01056599 -1.602174695 0.064035126 MATGLER ddPTM_BT-474_Pertuzumab_2h_R1 4 MATGLER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 138.33 0.0065044 1010790000 938620 996400 934990 947390 959330 901930 1014580 933890 938680 1046840 FALSE TRUE 901937.6927 967983.6476 1103963.492 996284.9114 990187.7207 920167.6426 1026996.734 914604.8451 832124.9817 975936.5944 0.924176527 0.99185096 1.131183622 1.02085004 1.014602513 0.942855968 1.052319115 0.93715601 0.852642463 1 19.89642789 1.602244531 5.757289454 0.916822558 1.012636613 0.254824443 0.063191585 0.169849568 11.94177721 0.034484805 0.016245136 40.01700037 -1.602244531 0.095814055 MLDEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 MLDEQK 6 0 H3BV99 H3BV99 SNAP23 Synaptosomal-associated protein 0 95.445 0.032873 583640000 242600 608030 523410 898470 798440 763370 643440 378410 122470 282770 FALSE TRUE 233118.9238 590689.5797 618001.8302 944840.1444 824122.5477 778805.8644 651314.6112 370595.7013 108567.719 263617.736 0.884306676 2.240705002 2.344310514 3.584129651 3.126202964 2.95429995 2.470678267 1.405807162 0.411837688 1 18.00808791 1.602401762 2.86939288 0.728461919 2.587404719 0.537528901 0.686441255 0.176110907 3.36492887 0.491930093 0.196185019 40.03149063 -1.602401762 1.8589428 KDEET(ph)EESEY(ph)DS(ph)EHENSEPVTNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDEETEESEYDSEHENSEPVTNIR 24 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 3 KDEET(0.967)EES(0.423)EY(0.611)DS(0.996)EHENS(0.004)EPVTNIR 86.191 0.0046411 227040000 236700 221820 201030 192610 194980 218690 235250 248790 323910 287530 TRUE FALSE 227449.5023 215493.9108 237360.5929 202550.6252 201251.7088 223112.0616 238129.0599 243652.3996 287141.0947 268055.337 0.84851697 0.803915763 0.885491017 0.755629891 0.750784189 0.832335831 0.888357839 0.908963061 1.071200812 1 18.03217133 1.602562652 1.544729407 1.033940469 0.81209244 0.769095177 0.046293539 0.169947215 0.797958737 0.039062659 0.013832207 40.0463236 -1.602562652 -0.221848029 LGAGGGS(ph)PEKS(ph)PSAQELK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 2 LGAGGGS(1)PEKS(0.965)PS(0.035)AQELK 86.617 0.0019429 372610000 166140 134010 114000 115710 142320 151550 153270 189100 224390 234040 TRUE FALSE 159647.0651 130188.166 134602.3359 121681.807 146897.8521 154614.4448 155145.7641 185195.0189 198918.1879 218188.2623 0.731694104 0.596678138 0.616909152 0.55769181 0.673261937 0.708628609 0.71106375 0.848785434 0.911681434 1 17.73521397 1.602801096 0.890633993 0.999496539 0.626394075 0.888208642 0.045352728 0.158015045 0.244979212 0.040713799 0.016411691 40.06831658 -1.602801096 -0.373102464 NKQGLETDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 NKQGLETDNK 10 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 51.268 0.094768 1582700000 1217500 1602500 1290000 1781600 1376800 1688700 1726900 1351200 1136200 1743400 FALSE TRUE 1169918.754 1556798.269 1523131.696 1873548.59 1421086.022 1722846.671 1748034.319 1323297.248 1007223.339 1625317.965 0.719809157 0.957842282 0.937128444 1.152727423 0.874343392 1.060005924 1.075502982 0.814177457 0.619708488 1 20.63229055 1.602887228 6.569931557 0.780808408 0.973214447 0.199008414 0.141393446 0.166751853 15.3971735 0.072986702 0.034908281 40.07626391 -1.602887228 0.19240604 NCPS(ph)PVLIDCPHPNCNKK ddPTM_BT-474_Pertuzumab_2h_R1 4 NCPSPVLIDCPHPNCNKK 18 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK 236.04 3.89E-24 6119100000 3813440 3277420 2596940 2617830 2965770 3045630 3052290 3523400 4188450 3776580 TRUE FALSE 3664406.549 3183951.191 3066264.827 2752936.52 3061166.685 3107214.725 3089644.838 3450640.559 3712994.715 3520788.873 1.040791334 0.904328918 0.870902783 0.781909004 0.869454772 0.88253367 0.877543343 0.980075967 1.054591698 1 21.74746729 1.603015469 3.379480605 1.02584955 0.88412976 0.461770813 0.061299614 0.174313327 4.66832766 0.040291418 0.016911676 40.08809959 -1.603015469 -0.14171979 NIDDASQMDLFHRDS(ph)DDDQTEEQLDESEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NIDDASQMDLFHRDSDDDQTEEQLDESEAR 30 1 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 NIDDASQMDLFHRDS(1)DDDQTEEQLDESEAR;NIDDASQMDLFHRDS(1)DDDQTEEQLDESEAR 311.16 1.83E-92 414100000 161152 193629 150563 192279 169735 183510 175485 156285 126476 169519 TRUE FALSE 154854.0017 188106.8905 177773.0834 202202.5422 175194.6804 187220.6979 177632.6379 153057.6601 112118.9747 158037.3271 0.979857129 1.190268742 1.124880347 1.279460656 1.108565195 1.184661253 1.123991662 0.968490564 0.709446159 1 17.26990583 1.60342655 3.231570389 0.850185754 1.149370629 0.589235112 0.09764912 0.122174122 2.99340269 0.0583083 0.024152843 40.12606291 -1.60342655 0.299184875 QAQEYEALLNIK ddPTM_BT-474_Pertuzumab_2h_R1 3 QAQEYEALLNIK 12 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 183.07 3.74E-05 346020000 513650 497660 433720 449190 475340 498990 465530 535540 608690 562100 FALSE TRUE 493575.9901 483467.2241 512102.852 472372.7497 490629.7428 509079.9197 471227.2954 524480.9119 539594.063 524028.4663 0.941887744 0.922597254 0.97724243 0.901425743 0.93626544 0.971473789 0.89923988 1.000863399 1.029703724 1 18.99928566 1.603869806 5.920484456 1.014721422 0.937040697 0.654009312 0.024909282 0.076059605 5.652521482 0.012695832 0.006009015 40.16703788 -1.603869806 -0.077680725 GEPNVS(ph)YICSR ddPTM_BT-474_Pertuzumab_2h_R1 6 GEPNVSYICSR 11 0 A0A3B3ITW1;P49841;P49841-2;P49840;A8MT37 A0A3B3ITW1;P49840 GSK3B;GSK3A Glycogen synthase kinase-3 beta;Glycogen synthase kinase-3 alpha 1 GEPNVS(0.999)Y(0.001)ICSR;GEPNVS(0.627)Y(0.373)ICSR;GEPNVS(0.66)Y(0.34)ICSR;GEPNVS(0.625)Y(0.372)ICS(0.003)R;GEPNVS(0.602)Y(0.398)ICSR;GEPNVS(0.805)Y(0.194)ICS(0.001)R 259.4 1.41E-20 23322090000 1196112 1222963 987687 1162575 1168095 1052907 1287364 1128862 1244882 1238717 TRUE FALSE 1149366.621 1188085.293 1166184.012 1222575.635 1205667.837 1074197.501 1303119.146 1105550.605 1103568.214 1154817.594 0.995279797 1.028807752 1.009842609 1.058674237 1.044033138 0.930188028 1.128419893 0.957337861 0.955621234 1 20.13923356 1.604111326 25 0.967353051 1.026537925 0.222569843 0.048546448 0.498890961 3299.63202 0.023183405 0.011372137 40.18938185 -1.604111326 0.059184874 AIHYALNCCGLAGGVEQFISDICPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIHYALNCCGLAGGVEQFISDICPK 25 0 A6NNI4;A0A2R8Y478;G8JLH6;P21926 A6NNI4 CD9 Tetraspanin;CD9 antigen 0 58.964 0.010744 0 45021 39028 22688 35237 32782 35443 31886 38584 47465 34034 FALSE TRUE 43261.52955 37914.95965 26788.22629 37055.58579 33836.4628 36159.68174 32276.23041 37787.22692 42076.97219 31728.84687 1.363476263 1.194968094 0.84428616 1.167883155 1.06642586 1.139646893 1.01725192 1.190942333 1.326142496 1 14.95350747 1.604169877 17.70483781 1.194042372 1.107236779 0.025816179 0.145636331 0.238052446 810.6984612 0.072847467 0.036078418 40.19480049 -1.604169877 -0.086805593 LFPDT(ph)PLALDANKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFPDTPLALDANKK 14 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 LFPDT(1)PLALDANKK;LFPDT(1)PLALDANKK 213.99 1.53E-10 1787190000 2849600 2402100 2422200 2214810 2481440 2617200 2724500 3092600 3692800 3618900 TRUE FALSE 2738234.482 2333594.46 2859945.422 2329116.61 2561257.771 2670121.577 2757843.246 3028736.729 3273608.825 3373788.68 0.811620034 0.691683648 0.847695482 0.690356401 0.759163663 0.791431186 0.817432124 0.897725678 0.970306423 1 21.68593818 1.604473172 1.180288291 1.002282636 0.758386626 0.795159633 0.04504781 0.174086536 0.4619477 0.036328803 0.013254939 40.22288077 -1.604473172 -0.24389601 EAAFS(ph)PGQQDWSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAAFSPGQQDWSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR 246.8 3.41E-17 1223180000 772660 880990 876970 1077470 939120 988700 981050 909630 921380 980680 TRUE FALSE 742463.593 855865.0278 1035457.987 1133078.356 969327.6477 1008692.191 993056.3834 890845.8226 816788.8051 914257.6701 0.812094464 0.936131088 1.132566913 1.239342466 1.060234636 1.103290926 1.086188736 0.974392506 0.893390159 1 19.8022413 1.604673558 4.645056156 0.943213949 1.060517273 0.137929778 0.110775858 0.305156317 14.56558103 0.068055049 0.03102742 40.24144417 -1.604673558 0.117303324 HPVSCK ddPTM_BT-474_Pertuzumab_2h_R1 3 HPVSCK 6 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;; 103.28 0.034817 201892000 507210 697820 460310 1013460 488180 519190 885680 505930 552130 577630 FALSE TRUE 487387.6724 677918.8568 543498.2565 1065764.792 503882.7531 529688.3775 896519.2168 495482.3687 489454.5171 538506.6056 0.905072783 1.258886799 1.009269433 1.979111827 0.935703941 0.983624661 1.66482492 0.920104533 0.908910888 1 19.03860452 1.60470012 25 0.93583343 1.248613885 0.15612246 0.324884371 0.562689409 4404.973669 0.161322598 0.079564441 40.24390542 -1.60470012 0.312780455 EDLQLDKPASGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDLQLDKPASGVK 13 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 135.02 8.09E-05 548600000 890410 836770 715580 763740 865350 801210 860170 922530 1061600 1022000 FALSE TRUE 855611.7928 812906.1389 844901.224 803156.7129 893184.7686 817411.0152 870697.0178 903479.4331 941091.6186 952779.0297 0.898017028 0.853194826 0.88677563 0.842962206 0.93745217 0.85792297 0.913849897 0.948257051 0.987733346 1 19.86178213 1.604806592 1.300042012 1.001222118 0.878040858 0.760988458 0.025601089 0.18185685 0.588737722 0.02055992 0.00737399 40.2537729 -1.604806592 -0.123181261 LSNKVEAIDVEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSNKVEAIDVEEAKR 15 2 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ;; 151.04 1.73E-06 1901841000 3681520 3250900 2448970 2353350 2895080 3139050 2980830 3362260 3967120 3608990 FALSE TRUE 3537642.128 3158187.515 2891553.356 2474806.676 2988202.877 3202523.742 3017310.289 3292828.156 3516789.169 3364549.893 1.051445882 0.938665681 0.859417589 0.735553567 0.888143429 0.951843142 0.896794634 0.978683111 1.045248037 1 21.68198208 1.604983459 2.580946388 1.023242326 0.89653708 0.293430406 0.075787051 0.318849961 4.832119904 0.057327121 0.022210563 40.2701696 -1.604983459 -0.126705247 QADPQPQAWPPPDS(ph)PVRVDTVR ddPTM_BT-474_Pertuzumab_2h_R1 3 QADPQPQAWPPPDSPVRVDTVR 22 1 Q63ZY3-3;Q63ZY3;Q63ZY3-2;K7ERU2 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 QADPQPQAWPPPDS(0.999)PVRVDT(0.001)VR;QADPQPQAWPPPDS(1)PVRVDTVR;QADPQPQAWPPPDS(1)PVRVDTVR 193.34 4.54E-18 1234500000 392100 438180 348400 432130 400570 422340 336010 367290 308510 291104 TRUE FALSE 376776.2985 425683.5354 411363.6301 454432.2811 413454.6978 430880.0042 340122.1909 359705.3331 273489.2382 271387.2668 1.388334475 1.568546456 1.51578088 1.674479007 1.523485986 1.587694254 1.253272473 1.325431872 1.007745284 1 18.04999351 1.605065375 1.098154021 0.986470907 1.549260754 0.820201024 0.09541169 0.177013314 0.40680932 0.08078072 0.030028446 40.27776609 -1.605065375 0.562789847 SKVGST(ph)ENIK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKVGSTENIK 10 1 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 S(0.001)KVGS(0.387)T(0.613)ENIK;SKVGS(0.323)T(0.677)ENIK;SKVGS(0.452)T(0.548)ENIK;SKVGS(0.278)T(0.722)ENIK 166.79 8.79E-06 15591960000 9227590 7264860 6788810 5582300 5962370 6612530 6942180 8338720 10062340 9189160 TRUE FALSE 8866965.581 7057673.306 8015698.983 5870403.172 6154155.046 6746239.887 7027140.475 8166522.518 8920105.348 8566770.008 1.035041862 0.823842977 0.935673419 0.685252804 0.718375192 0.78748932 0.820278876 0.953279067 1.041244873 1 23.03031993 1.605160064 3.121108921 1.017133876 0.821413475 0.407211198 0.094996334 0.209224502 4.779000193 0.064156238 0.026340998 40.28654875 -1.605160064 -0.195720401 DEEEETHMK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEEEETHMK 9 0 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 114.97 0.0015521 98289000 83968 77354 101570 98350 96474 94762 119980 132830 169170 174870 FALSE TRUE 80686.43773 75147.93966 119925.9584 103425.8553 99577.17383 96678.15257 121448.3511 130087.0141 149966.5308 163025.8991 0.494930181 0.460957063 0.735625192 0.634413647 0.610805856 0.593023275 0.744963541 0.797953054 0.919893904 1 17.31474165 1.605197214 0.696177189 1.012932783 0.567691393 0.814487927 0.071312265 0.278549181 0.283277317 0.070278072 0.033147189 40.28999506 -1.605197214 -0.445241389 GKTEESGEDRGDGPPDRDPT(ph)LSPSAFILR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKTEESGEDRGDGPPDRDPTLSPSAFILR 29 3 Q9H7N4;M0R3G4;M0R2L3;M0R232 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GKTEESGEDRGDGPPDRDPT(0.622)LS(0.344)PS(0.034)AFILR;GKTEESGEDRGDGPPDRDPT(0.883)LS(0.095)PS(0.023)AFILR 114.62 0.00022369 949270000 1153670 1169550 870390 1024010 1065210 1051820 920980 1051090 1005360 923490 TRUE FALSE 1108583.301 1136195.579 1027688.835 1076859.279 1099473.447 1073088.521 932251.2287 1029384.624 891235.7476 860941.1997 1.287641132 1.319713332 1.193680631 1.250793061 1.277059859 1.246413253 1.08282799 1.195650324 1.035187708 1 19.71555518 1.605227705 0.572084262 0.993860922 1.280537152 0.769592496 0.050890563 0.353252083 0.265226549 0.04898988 0.027423066 40.29282384 -1.605227705 0.286676229 LTPRPSPSPMIESTPMSIAGDAT(ph)PLLDEMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTPRPSPSPMIESTPMSIAGDATPLLDEMDR 31 1 Q7KZ85;Q7KZ85-3;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 LTPRPSPSPMIESTPMSIAGDAT(1)PLLDEMDR 89.823 0.00091178 57835000 24920 24271 19061 22469 18830 24934 16750 20797 17937 15700 TRUE FALSE 23946.09885 23578.81484 22505.74671 23628.62778 19435.68405 25438.18256 16954.99151 20367.53468 15900.86696 14636.62502 1.636039649 1.610946159 1.537632254 1.614349466 1.327880166 1.737981436 1.158394882 1.391545842 1.086375236 1 13.83729531 1.605299954 0.606131402 0.985262442 1.602599286 0.678813347 0.138857298 0.390232756 0.319446948 0.122030602 0.064705269 40.29952745 -1.605299954 0.617336843 RSGS(ph)PLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSGSPLEK 8 1 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RS(0.179)GS(0.821)PLEK 74.962 0.014609 0 119600 119050 100960 93393 87194 111370 108050 138170 165160 160470 TRUE FALSE 114925.8998 115654.8106 119205.7178 98213.02392 89998.6742 113621.9777 109372.3482 135316.7412 146411.7292 149601.224 0.76821497 0.773087328 0.796823145 0.656498799 0.601590494 0.759498985 0.731092603 0.904516271 0.978680022 1 17.19076245 1.605544045 2.203561764 0.991956686 0.721888547 0.794565532 0.055668912 0.130878386 1.38368446 0.045855258 0.017043394 40.32218381 -1.605544045 -0.27006814 YLEEIATQMR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLEEIATQMR 10 0 Q01813;Q01813-2;B1APP6;H0Y3Y3 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 143.03 8.07E-05 262700000 353480 382060 335050 401130 387480 375410 392920 355900 359730 373230 FALSE TRUE 339665.6108 371164.0229 395600.9881 421832.3674 399943.6461 383001.0474 397728.6725 348550.5406 318894.9585 347950.7997 0.97618862 1.066714096 1.13694519 1.212333375 1.149425857 1.100733344 1.14306009 1.001723637 0.916494398 1 18.4085238 1.605680654 4.165507214 0.958361669 1.116020449 0.526071301 0.061291819 0.134376358 5.30685638 0.038192498 0.017015938 40.33486932 -1.605680654 0.15765878 S(ph)RT(ph)PPVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTPPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RT(0.998)PPVT(0.002)R 85.672 0.037985 2846100000 406180 291180 215810 217450 291350 309580 253510 336300 425940 296480 TRUE FALSE 390306.0365 282875.8315 254811.6677 228672.6206 300721.5373 315839.9197 256612.5312 329355.2875 377589.0769 276399.1455 1.412110142 1.023432366 0.921897451 0.827327523 1.087997348 1.142694993 0.928412896 1.191593002 1.366100739 1 18.07639363 1.605700173 7.432195642 1.213750556 1.040053127 0.11186392 0.170933787 0.211030063 26.20860587 0.089634866 0.043491416 40.33668214 -1.605700173 -0.173697429 SLFSDHGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLFSDHGK 8 0 P50135;P50135-3;P50135-2 P50135 HNMT Histamine N-methyltransferase 0 102.51 0.0049505 382170000 383890 318980 351560 262730 344290 339240 368150 325850 348050 352280 FALSE TRUE 368887.1544 309883.0027 415094.7124 276289.5268 355364.4005 346099.6652 372655.5298 319121.0836 308540.8231 328419.7618 1.123218507 0.943557723 1.26391515 0.841269494 1.082043293 1.053833251 1.134692772 0.971686606 0.939470942 1 18.32518141 1.605878659 9.40625881 0.965287606 1.05815577 0.134474437 0.107268331 0.191669873 48.07689235 0.051470716 0.025414969 40.35326307 -1.605878659 0.092868164 KGDMDELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGDMDELEK 9 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 96.229 0.01204 664030000 425150 401200 391630 356060 395380 409340 347290 466510 539150 463480 FALSE TRUE 408534.668 389758.1688 462406.2528 374436.2993 408097.7568 417617.1353 351540.2389 456876.4055 477947.9523 432088.0868 0.945489312 0.902034055 1.070166632 0.866573994 0.94447815 0.966509256 0.813584659 1.05736867 1.106135455 1 18.72096593 1.60588517 12.13262241 1.062206277 0.933618431 0.414769413 0.067593337 0.070572225 48.00262908 0.03261984 0.016288289 40.35386804 -1.60588517 -0.128587846 ESLWPFLIDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESLWPFLIDKR 11 1 Q9NZL9;Q9NZL9-2;Q9NZL9-4 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ; 122.18 0.00063527 286210000 586880 818220 659510 1170940 946870 911250 914950 674150 523810 694360 FALSE TRUE 563944.0808 794885.1667 778698.1277 1231372.354 977326.9335 929676.0993 926147.4318 660228.5669 464349.2848 647330.3787 0.871184328 1.227943555 1.202937717 1.90223168 1.509780733 1.436169427 1.43071832 1.019925201 0.717329667 1 19.30414268 1.606047422 3.765433927 0.859937944 1.385216992 0.407429045 0.255573776 0.181254442 5.97129887 0.163469333 0.070992481 40.36894707 -1.606047422 0.525279048 LTHDDTGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTHDDTGAR 9 0 Q5JRX3-3;Q5JRX3;Q5JRX3-2 Q5JRX3-3 PITRM1 "Presequence protease, mitochondrial" 0 119.75 0.00077709 265960000 83294 124520 74950 184470 83612 109820 140770 94955 104140 97408 FALSE TRUE 80038.77839 120968.8115 88495.13225 193990.5188 86301.45591 112040.6356 142492.7854 92994.14607 92318.46379 90810.4694 0.881382719 1.33210204 0.974503632 2.136213149 0.950346986 1.233785448 1.569122881 1.02404653 1.016605953 1 16.47057101 1.606253349 11.7536802 1.01304293 1.302417169 0.124772643 0.343639707 0.16613456 98.67742196 0.168271284 0.084064345 40.38809317 -1.606253349 0.289374239 QSFCLS(ph)PNSVDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSFCLSPNSVDHR 13 0 P15622-2;P15622-3;P15622;E9PPG5;E9PL28 P15622-2 ZNF250 Zinc finger protein 250 1 QS(0.001)FCLS(0.999)PNSVDHR 112.56 0.00018304 0 70641 81569 66826 75313 75986 71186 74868 64199 64816 60097 TRUE FALSE 67880.27162 79242.73198 78902.94474 79199.91296 78430.1587 72625.42969 75784.25698 62873.26822 57458.35941 56026.57666 1.211572715 1.414377546 1.408312794 1.413613283 1.399874191 1.296267486 1.352648359 1.122204353 1.025555421 1 15.77382372 1.606556395 1.877514072 1.001209565 1.368809059 0.846113065 0.061099418 0.110039784 0.804028512 0.047577738 0.017158428 40.41628529 -1.606556395 0.367599494 LQAALDDEEAGGRPAMEPGNGS(ph)LDLGGDSAGR ddPTM_BT-474_Pertuzumab_2h_R1 6 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR 235.13 8.57E-47 10683540000 4621660 4621470 3713020 4511390 5254880 4755990 4794060 4531310 4679570 4887580 TRUE FALSE 4441040.418 4489670.2 4384045.31 4744223.379 5423907.988 4852159.376 4852731.14 4437736.865 4148364.832 4556539.853 0.974651942 0.985324467 0.962143524 1.041189923 1.190356754 1.064878073 1.065003555 0.973926929 0.91041996 1 22.11950726 1.607013338 4.870981673 0.951576782 1.041864326 0.242589349 0.064274248 0.227593251 11.81058675 0.039948666 0.018407467 40.45883173 -1.607013338 0.090287544 FTENDSEKVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FTENDSEKVDR 11 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 100.02 0.0027197 0 403610 391870 281870 298160 336150 362800 321370 374810 404680 390540 FALSE TRUE 387836.475 380694.2513 332810.1792 313548.0733 346962.57 370136.0646 325303.0222 367070.0425 358742.423 364088.3779 1.065226188 1.045609457 0.914091741 0.861186713 0.952962498 1.016610491 0.893472689 1.008189398 0.985316875 1 18.47392916 1.607180211 24.99999979 0.997566814 0.962128173 0.0580757 0.061749618 0.258925969 8254.478458 0.033057636 0.016713724 40.47438059 -1.607180211 -0.03543864 TDSEEQDKS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 TDSEEQDKSR 10 1 Q9NRF9 Q9NRF9 POLE3 DNA polymerase epsilon subunit 3 1 TDSEEQDKS(1)R 67.275 0.038432 77239000 119830 168250 115440 221810 185370 180240 160080 136690 93174 139620 TRUE FALSE 115146.9111 163451.6747 136302.5759 233257.6407 191332.5944 183884.5763 162039.1069 133867.3037 82597.27814 130163.413 0.884633465 1.255742078 1.047165043 1.792036911 1.469941437 1.412720917 1.244889813 1.028455697 0.634566014 1 16.98996446 1.607274952 2.805376668 0.81797243 1.322505657 0.389840999 0.244584136 0.228066747 4.159026501 0.170542317 0.067919415 40.48321097 -1.607274952 0.504533227 TGKPMINLYTDKDTGKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGKPMINLYTDKDTGKPK 18 3 Q92804-2;Q92804;A0A075B7D9 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 120.4 2.02E-05 1500800000 756220 642080 657120 527030 659940 610540 700840 837630 1092800 957730 FALSE TRUE 726666.0864 623768.5071 775876.2016 554230.0815 681167.5694 622885.5371 709417.0896 820332.6478 968749.9254 892862.094 0.813861504 0.698616854 0.868976527 0.620734249 0.762903447 0.697627933 0.794542734 0.918767471 1.0849939 1 19.76807784 1.607313143 2.303664941 1.040702798 0.743383373 0.754272936 0.067925558 0.11715002 1.372639732 0.046334546 0.017444717 40.4867712 -1.607313143 -0.297319425 IEEVLSGVLDTELR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEEVLSGVLDTELR 14 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8;J3QSZ5 P18583-7 SON Protein SON 0 121.08 0.00027143 8935600 10916 9439.5 8659.5 8795.7 9032.6 11740 10295 9227.7 10243 8731.2 FALSE TRUE 10489.39065 9170.294702 10224.46428 9249.647131 9323.141782 11977.39084 10420.99329 9037.14477 9080.257582 8139.828047 1.288650152 1.126595629 1.256103227 1.136344291 1.145373309 1.47145502 1.28024735 1.110237798 1.115534325 1 12.9907826 1.60820376 4.220196525 1.073438885 1.24004888 0.381915361 0.098905352 0.199684436 8.076984285 0.06029518 0.026998758 40.56988349 -1.60820376 0.166609995 KYEGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYEGGR 6 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 119.89 0.033075 8122400000 3998710 4034650 3497190 4091470 3536170 3897760 4370920 3514320 3351330 4151560 FALSE TRUE 3842435.992 3919585.732 4129210.028 4302631.257 3649914.12 3976575.378 4424412.626 3441748.064 2970901.068 3870371.143 0.992782307 1.012715729 1.066877019 1.111684409 0.943039823 1.027440323 1.143149446 0.889255303 0.76760108 1 21.88404049 1.608629687 6.982826985 0.866346099 1.040270114 0.473390383 0.07531551 0.093619398 9.973019065 0.038261068 0.018522688 40.60969122 -1.608629687 0.173924015 TKSNSLS(ph)EQLAINTSPDAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKSNSLSEQLAINTSPDAVK 20 1 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 T(0.26)KS(0.17)NS(0.17)LS(0.4)EQLAINTSPDAVK 163.71 1.16E-11 161250000 230990 209450 160150 156110 203520 236790 162620 239920 284330 220390 TRUE FALSE 221962.6554 203476.6911 189092.6675 164166.8558 210066.4056 241578.056 164610.1922 234965.5682 252054.0504 205462.789 1.080305862 0.99033354 0.920325614 0.79901016 1.022406085 1.175775221 0.801167905 1.143591836 1.226762528 1 17.64851761 1.608869055 25 1.138902198 0.972156705 0.251711146 0.120395826 0.134635332 3130.986421 0.058907335 0.030303653 40.63208001 -1.608869055 -0.166745494 LT(ph)IHMDEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTIHMDEELR 10 0 O94915;A0A669KB90;A0A6E1XQM6;F2Z2S2 O94915 FRYL Protein furry homolog-like 1 LT(1)IHMDEELR 107.15 0.0065821 969640000 217170 314920 240570 1056800 531210 394280 478000 371680 205670 447560 TRUE FALSE 208682.7563 305938.7899 284046.3505 1111341.575 548296.8521 402252.6117 483849.907 364004.6781 182323.2038 417246.3626 0.500142781 0.733232971 0.680764114 2.663514112 1.314084199 0.964064993 1.159626423 0.872397487 0.436967749 1 18.67053995 1.608878034 3.449999664 0.700936253 1.17034748 0.083073354 0.577591571 0.493656285 13.80199773 0.380903537 0.161805781 40.63292009 -1.608878034 0.469411228 DQLKEVWEETDGLDPNDFDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQLKEVWEETDGLDPNDFDPK 21 1 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 90.316 0.0019886 42682000 52078 51184 36475 33805 37658 44417 41941 50589 63503 50963 FALSE TRUE 50042.73418 49724.28243 43066.84388 35549.6801 38869.30377 45315.14217 42454.2865 49544.31947 56294.40567 47511.23062 1.053282214 1.046579552 0.90645608 0.748237409 0.818107703 0.953777488 0.893563184 1.042791753 1.18486524 1 15.53598095 1.608967109 4.065435482 1.098420581 0.913011917 0.365773703 0.0966501 0.187586954 7.10629343 0.061889556 0.027483923 40.64125485 -1.608967109 -0.185408664 GSEGDCS(ph)PEDKNSVTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSEGDCSPEDKNSVTAK 17 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GSEGDCS(1)PEDKNSVTAK 188.19 2.57E-10 453850000 843750 688290 528100 553240 687990 717430 653570 842630 1059000 896450 TRUE FALSE 810775.3172 668660.6431 623539.4175 581792.7827 710119.8232 731936.9261 661568.5852 825229.396 938786.7597 835732.643 0.970137189 0.800089178 0.746099154 0.696147013 0.849697363 0.875802725 0.791603141 0.987432288 1.12330991 1 19.67268196 1.609012311 3.638367504 1.06123495 0.813584276 0.643114756 0.075558669 0.113302309 3.5063601 0.047327611 0.020414766 40.64548511 -1.609012311 -0.247650675 AIGSTSKPQES(ph)PKGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIGSTSKPQESPKGK 15 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGS(0.009)T(0.05)S(0.04)KPQES(0.901)PKGK 113.54 0.00035312 1063700000 1309000 1009000 631170 572420 818310 826190 878270 963740 1164500 1044200 TRUE FALSE 1257842.833 980224.3079 745236.4593 601962.6648 844631.6843 842896.1279 889018.531 943838.4322 1032310.842 973475.4039 1.292115679 1.006932794 0.765542156 0.618364534 0.867645634 0.865862789 0.913241904 0.9695555 1.060438546 1 19.892785 1.609033959 2.43207258 1.029013552 0.887447173 0.081845661 0.163910091 0.6503926 8.631357616 0.126213921 0.048304013 40.64751119 -1.609033959 -0.141566378 FKMPDMNIK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKMPDMNIK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 65.347 0.077024 0 346010 410920 293980 320220 351510 317460 411480 385380 491610 465790 FALSE TRUE 332487.5467 399200.9639 347108.7255 336746.5926 362816.6384 323879.2587 416515.8153 377421.7683 435804.4938 434241.6284 0.765674051 0.919306068 0.799344657 0.77548206 0.835517865 0.745850323 0.959179839 0.869151513 1.003599069 1 18.72813851 1.609135844 1.128225341 1.002320268 0.814327174 0.582558006 0.060081202 0.323946867 0.78480758 0.050346642 0.018610636 40.65704811 -1.609135844 -0.187993093 AQLGGPEAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 AQLGGPEAAK 10 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;; 136.63 0.00026164 1060050000 1309440 1043810 958570 908390 1014010 1052040 1092410 1201570 1424880 1325360 FALSE TRUE 1258265.637 1014041.561 1131804.922 955272.1168 1046626.553 1073312.97 1105779.24 1176757.16 1263133.596 1235592.187 1.01835027 0.820692759 0.916002007 0.773128972 0.847064722 0.868662801 0.89493868 0.952383134 1.022290048 1 20.23677122 1.609433631 1.955779323 1.011981585 0.868158246 0.443589878 0.060997134 0.262900557 2.111986171 0.045573995 0.01658983 40.68493544 -1.609433631 -0.143823339 GMPVTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GMPVTAR 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 77.496 0.08815 97565000 238630 327010 307440 432970 376100 338520 372830 298980 252840 351860 FALSE TRUE 229304.0758 317683.995 363001.247 455315.6336 388197.5981 345365.1063 377392.8051 292805.9585 224138.6632 328028.2088 0.699037673 0.968465475 1.106615947 1.388038045 1.183427485 1.05285185 1.150488875 0.892624325 0.683290818 1 18.32346036 1.609574565 4.806715301 0.826338182 1.089589754 0.238891507 0.179402792 0.208910871 10.60174483 0.106105704 0.048860051 40.69814036 -1.609574565 0.263251572 GGEGPGHDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGEGPGHDFR 10 0 P78332;P78332-3 P78332 RBM6 RNA-binding protein 6 0 94.616 0.0079824 176900000 220330 226080 181920 231120 211240 196860 202570 199410 181980 179230 FALSE TRUE 211719.26 219632.4198 214796.9908 243048.1309 218034.7264 200840.6441 205049.1123 195292.1138 161322.3933 167090.5925 1.267092641 1.31445114 1.285512174 1.454588959 1.304889301 1.201986546 1.227173291 1.168779827 0.965478612 1 17.35027098 1.609639454 0.985451848 0.972649861 1.321870443 0.803097621 0.061779776 0.218874191 0.408076167 0.057040906 0.022038815 40.70422157 -1.609639454 0.349220582 AYINKVEELK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYINKVEELK 10 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 146.16 2.66E-05 2213900000 5873800 5228400 4410300 4900300 4718200 4635600 5593700 6290300 7820000 7467300 FALSE TRUE 5644245.402 5079291.151 5207339.317 5153205.07 4869965.188 4729335.008 5662157.374 6160403.107 6932306.384 6961533.12 0.810776205 0.729622493 0.748016166 0.74023997 0.699553547 0.679352511 0.813349197 0.884920462 0.995801681 1 22.73097363 1.609804127 1.738502945 1.001265317 0.734597825 0.892577355 0.036005688 0.099460592 0.609709204 0.029660533 0.010625402 40.71965848 -1.609804127 -0.266667492 VFPLS(ph)PASNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VFPLSPASNLR 11 0 A0A2R8YH03;Q5VWN6;J3KPH3 A0A2R8YH03 FAM208B Protein FAM208B 1 VFPLS(0.941)PAS(0.059)NLR;VFPLS(0.998)PAS(0.002)NLR;VFPLS(0.998)PAS(0.002)NLR;VFPLS(1)PASNLR 178.52 7.87E-06 276914000 377721 399513 386949 383121 342491 393717 353446 363339 303532 342974 TRUE FALSE 362959.2457 388119.2804 456879.2919 402893.9207 353507.5341 401678.2275 357771.5779 355835.9227 269076.3199 319744.0655 1.135155535 1.213843578 1.428890607 1.260051285 1.105595294 1.256249203 1.118931097 1.112877332 0.841536557 1 18.28655806 1.609955085 1.543644431 0.927387212 1.235750106 0.592355222 0.09627349 0.255521512 1.198754012 0.081415774 0.028978914 40.7338148 -1.609955085 0.308362894 QMEKDETVSDCSPHIANIGR ddPTM_BT-474_Pertuzumab_2h_R1 5 QMEKDETVSDCSPHIANIGR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;; 233.89 1.01E-29 6278350000 4250090 4536050 3206520 3733730 3806810 4361870 3869210 3876130 4433690 3980960 FALSE TRUE 4083991.784 4406686.295 3786009.493 3926428.253 3929259.501 4450070 3916562.549 3796086.561 3930396.099 3711326.033 1.1004131 1.187361675 1.02012312 1.057958319 1.058721186 1.199051218 1.05530005 1.02283834 1.059027437 1 21.82350331 1.610178501 0.013883919 1.08E-07 2.119684828 0.232813628 0.056223767 715.1632127 10.08767471 767.5484201 770.1939181 40.75477512 -1.610178501 2.119684719 RGGGS(ph)GGGEES(ph)EGEEVDED ddPTM_BT-474_Pertuzumab_2h_R1 2 RGGGSGGGEESEGEEVDED 19 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 2 RGGGS(1)GGGEES(1)EGEEVDED;RGGGS(1)GGGEES(1)EGEEVDED 100.28 0.00044195 556110000 861630 849700 724210 713980 771900 826000 781930 851120 939300 887500 TRUE FALSE 827956.547 825467.3879 855090.857 750828.5934 796728.8645 842702.2859 791499.4932 833544.0746 832674.6019 827388.8345 1.00068615 0.997677698 1.033481262 0.90746764 0.962943699 1.018508168 0.956623368 1.007439356 1.006388493 1 19.65820596 1.610264111 25 1.005187368 0.982724213 0.084150028 0.033425368 0.630906279 6482.724814 0.01664152 0.008677675 40.76280967 -1.610264111 -0.022463155 DPDASKPEDWDER ddPTM_BT-474_Pertuzumab_2h_R1 3 DPDASKPEDWDER 13 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;; 105.19 0.0013427 1549290000 1671360 1689770 1541310 1560930 1605180 1620870 1772450 1960260 2360230 2256840 FALSE TRUE 1606041.403 1641579.414 1819859.003 1641489.784 1656812.072 1653645.102 1794141.773 1919779.946 2092306.585 2103982.217 0.763334115 0.780224947 0.864959309 0.780182347 0.787464865 0.785959638 0.852736187 0.912450652 0.994450699 1 21.00469108 1.610338431 1.499763075 1.004008386 0.795105549 0.89960678 0.027018841 0.109114993 0.480313202 0.023091725 0.008221785 40.7697859 -1.610338431 -0.208902837 VLEDSDLK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLEDSDLK 8 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 143.61 0.0013928 1050860000 1887820 2132140 1654170 1915510 1576680 1542570 2033480 2068180 2445920 2401250 FALSE TRUE 1814041.907 2071333.455 1953115.316 2014369.701 1627395.344 1573761.822 2058366.337 2025471.36 2168269.416 2238611.199 0.81034255 0.925276107 0.872467411 0.899830083 0.726966498 0.703008108 0.919483623 0.904789256 0.968577937 1 21.09417255 1.610358293 1.793798037 0.981924857 0.831501245 0.430939487 0.069971723 0.353902297 2.330542239 0.060737486 0.021843863 40.77165057 -1.610358293 -0.150423612 KNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKK 36 2 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 308.45 9.89E-110 349820000 401420 345943 279102 233428 327456 358380 302791 358276 394040 373584 FALSE TRUE 385732.0626 336077.0444 329541.94 245475.2471 337988.9196 365626.6891 306496.6468 350877.4754 349310.2312 348280.8229 1.107531731 0.964959947 0.946196053 0.704819878 0.970449411 1.049804253 0.880027342 1.007455629 1.002955684 1 18.40989151 1.61047159 24.99999998 1.003909841 0.942678393 0.063256436 0.100231454 0.760569357 7206.447086 0.050579635 0.026424857 40.78228824 -1.61047159 -0.061231448 LEDHEYKPLDPK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEDHEYKPLDPK 12 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ;;; 178.15 1.34E-05 1623010000 4041400 3445960 3077590 2739480 3288820 3406120 3485370 4045450 4952380 4519330 FALSE TRUE 3883457.62 3347684.595 3633778.974 2880864.891 3394607.882 3474994.08 3528025.001 3961910.044 4390206.584 4213231.754 0.921728936 0.794564551 0.862468335 0.683766064 0.805701675 0.824781138 0.837367894 0.940349422 1.042004533 1 22.00649584 1.610600443 2.132255466 1.021987418 0.810758717 0.675638582 0.057454122 0.159992462 1.569970098 0.042907159 0.015911898 40.79438993 -1.610600443 -0.211228701 LGDLWTLDIDTLTWNKPSLSGVAPLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGDLWTLDIDTLTWNKPSLSGVAPLPR 27 1 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 0 ; 329.97 3.09E-95 298020000 216000 195180 171715 179179 183439 193151 182492 210155 228840 228394 FALSE TRUE 207558.4812 189613.6575 202747.7203 188426.4497 189339.482 197056.6456 184725.3917 205815.2258 202863.0426 212924.6709 0.974797708 0.890519904 0.952203985 0.884944186 0.88923224 0.925475872 0.86756218 0.966610515 0.952745596 1 17.69998359 1.610740391 8.254271701 0.970851357 0.911459378 0.424087175 0.032575298 0.102540831 16.98964559 0.015907824 0.00785376 40.80753774 -1.610740391 -0.059391979 EEFASTCPDDEEIELAYEQVAK ddPTM_BT-474_Pertuzumab_2h_R1 4 EEFASTCPDDEEIELAYEQVAK 22 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;;; 308.95 3.85E-67 967280000 827725 801989 584990 646340 705113 751232 671323 799188 886417 817938 FALSE TRUE 795376.5919 779117.0589 690710.706 679697.6849 727793.6 766422.4257 679538.8517 782684.4885 785794.6583 762538.3307 1.043064407 1.021741501 0.905804572 0.891361991 0.954435431 1.005093639 0.891153696 1.026419862 1.030498569 1 19.54045033 1.610895599 25 1.02134962 0.958353218 0.226803146 0.050719368 0.435677901 3560.125055 0.025884983 0.013575018 40.8221241 -1.610895599 -0.062996402 DYGHSSSR ddPTM_BT-474_Pertuzumab_2h_R1 8 DYGHSSSR 8 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;;;;;; 172.21 0.00028488 394097000 230642 306223 243732.8 327073 264967 261906 269007 259712.9 217980 279673 FALSE TRUE 221628.2557 297489.8199 287780.7388 343953.2767 273489.9042 267201.9188 272299.1881 254349.7379 193235.8242 260730.4986 0.85002812 1.140985889 1.103747894 1.319190806 1.048937143 1.024820342 1.044370297 0.975527371 0.741132416 1 17.99219982 1.610949434 2.537098811 0.868352509 1.088905788 0.297015918 0.124761318 0.281402447 4.112044159 0.087015915 0.033775674 40.82718478 -1.610949434 0.220553279 YSVEAS(ph)SPGHGSPLSSLLPSASVPESMTISELR ddPTM_BT-474_Pertuzumab_2h_R1 1 YSVEASSPGHGSPLSSLLPSASVPESMTISELR 33 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 Y(0.01)S(0.011)VEAS(0.493)S(0.438)PGHGS(0.034)PLS(0.011)S(0.004)LLPSASVPESMTISELR 64.726 0.0034331 73897000 28863 34903 33367 46880 37022 37994 39790 32703 31570 33904 TRUE FALSE 27735.00205 33907.60061 39397.15914 49299.48242 38212.84625 38762.26471 40276.96192 32027.67162 27986.30595 31607.65188 0.877477459 1.072765568 1.246443719 1.559732517 1.208974536 1.226356987 1.274278838 1.013288546 0.885428189 1 14.94798624 1.611096189 4.351347859 0.944798673 1.219256886 0.321810985 0.162950981 0.199536096 8.523812685 0.100604314 0.045458379 40.84098324 -1.611096189 0.274458213 KMEES(ph)DEEAVQAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KMEESDEEAVQAK 13 1 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 KMEES(1)DEEAVQAK;KMEES(1)DEEAVQAK;KMEES(1)DEEAVQAK;KMEES(1)DEEAVQAK 160.55 1.87E-05 2233080000 1493280 1402520 1128200 994100 1307840 1293610 1236140 1460500 1668350 1577550 TRUE FALSE 1434920.967 1362521.503 1332090.837 1045405.62 1349907.861 1319767.681 1251268.251 1430340.165 1478965.902 1470701.133 0.975671354 0.926443498 0.905752234 0.710821251 0.91786688 0.897373131 0.850797094 0.972556648 1.005619611 1 20.48807267 1.611321867 4.504845079 0.998751326 0.881436542 0.370054831 0.065814358 0.178229632 8.086618966 0.039056304 0.017780796 40.86221146 -1.611321867 -0.117314784 DRPGGSMVVSDVVPGGPAEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRPGGSMVVSDVVPGGPAEGR 21 1 O95049;O95049-4;O95049-3;K7ESC0 O95049 TJP3 Tight junction protein ZO-3 0 72.99 0.013749 254380000 186200 179740 218600 152990 183340 203500 247230 161190 180260 191660 FALSE TRUE 178923.0981 174613.9912 258105.8827 160885.8322 189237.2976 207614.9094 250255.6747 157861.3702 159797.6405 178678.6975 1.001367822 0.97725131 1.444525208 0.900419773 1.059092663 1.161945505 1.400590435 0.883492954 0.894329558 1 17.44700812 1.611425847 25 0.916669423 1.130827188 0.246614532 0.167115433 0.460544325 3209.735351 0.080141733 0.042221861 40.87199602 -1.611425847 0.214157765 FVEVGR ddPTM_BT-474_Pertuzumab_2h_R1 6 FVEVGR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;;;; 145 0.026058 2048040000 1803790 1688540 1740540 1477970 2016320 1715300 1640220 1743990 1683910 1662560 FALSE TRUE 1733295.893 1640384.492 2055094.296 1554248.209 2081176.764 1749984.541 1660293.503 1707975.997 1492759.596 1549953.33 1.118289086 1.058344442 1.32590721 1.002770973 1.342735115 1.12905628 1.071189352 1.101953177 0.963099706 1 20.56379335 1.611434554 1.291689605 0.984703981 1.163600034 0.29836973 0.10279806 0.512581428 1.636670297 0.083635585 0.030131038 40.87281542 -1.611434554 0.178896053 GPPHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPPHSK 6 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 103.28 0.034817 120046000 136171 135201 108437 126303 123726 136494 148122 119942 120684 149036 FALSE TRUE 130849.2868 131345.1999 128033.9781 132821.513 127705.7592 139254.0022 149934.7613 117465.1558 106984.4583 138941.659 0.941757049 0.945326267 0.921494525 0.955951685 0.919132247 1.002248017 1.079120276 0.845427906 0.769995544 1 17.0841197 1.611454625 25 0.855775863 0.962997975 0.273188406 0.069102626 0.376814165 2605.3645 0.032588762 0.017173209 40.87470438 -1.611454625 0.107222112 AAARPLLTDLYQATMALGYWR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAARPLLTDLYQATMALGYWR 21 1 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 100.97 0.00055785 84650000 30590 28191 28467 25214 31913 28409 32225 25747 27211 25481 FALSE TRUE 29394.50898 27387.02028 33611.62014 26515.29756 32939.51063 28983.44944 32619.37919 25215.31545 24122.12136 23755.14917 1.23739526 1.152887742 1.414919346 1.116191583 1.386626133 1.220091241 1.373149836 1.061467359 1.015448111 1 14.53595265 1.611489232 5.487656594 1.018023176 1.268538561 0.596011825 0.093251311 0.091405956 5.885045386 0.047139701 0.022213991 40.87796163 -1.611489232 0.250515384 NADGYKLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 NADGYKLDK 9 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 97.911 0.0058099 894030000 1230240 1136160 792790 747280 920060 1087590 938520 1150770 1364870 1194880 FALSE TRUE 1182160.861 1103757.829 936064.7885 785847.2104 949654.5655 1109581.815 950005.8885 1127006.197 1209935.68 1113949.713 1.061233597 0.990850678 0.840311531 0.70546022 0.852511163 0.996078909 0.852826548 1.011720892 1.086167235 1 20.08725268 1.611491662 4.854344918 1.044583221 0.895792663 0.285452517 0.096652647 0.204115992 10.5456016 0.058827108 0.027173917 40.87819043 -1.611491662 -0.148790558 STPST(ph)KQR ddPTM_BT-474_Pertuzumab_2h_R1 2 STPSTKQR 8 1 Q9NQ75-2;Q9NQ75 Q9NQ75-2 CASS4 Cas scaffolding protein family member 4 1 S(0.011)T(0.011)PS(0.001)T(0.976)KQR;S(0.003)T(0.003)PS(0.003)T(0.992)KQR 72.643 0.073758 598630000 491420 734620 510520 631720 628890 726310 634870 522270 395430 576840 TRUE FALSE 472214.7631 713669.3569 602782.3205 664323.1449 649118.818 740996.4858 642639.729 511484.942 350542.4442 537770.113 0.878097819 1.327090033 1.120892191 1.23532924 1.207056328 1.377905666 1.195008264 0.951121919 0.651844414 1 19.03663005 1.611568921 3.602724481 0.819651773 1.203652212 0.505694294 0.149139849 0.132978465 4.04391082 0.085622514 0.036919399 40.88546312 -1.611568921 0.384000439 TGIIVTTSEAVLLQLVADKDHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGIIVTTSEAVLLQLVADKDHPK 23 1 Q96CN7 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ; 246.73 7.77E-38 1072740000 1278470 1102680 1004890 1056140 1097560 1105620 1310270 1274690 1737150 1545410 FALSE TRUE 1228505.979 1071232.646 1186495.977 1110647.512 1132864.014 1127976.394 1326305.476 1248367.206 1539956.015 1440738.004 0.852692145 0.743530498 0.823533476 0.770887912 0.786308136 0.782915694 0.920573673 0.866477599 1.068866102 1 20.45837658 1.611737864 1.217020553 1.029014426 0.791925779 0.761167424 0.049156305 0.19097845 0.538973859 0.039555968 0.014392362 40.90137083 -1.611737864 -0.237088648 AVEQLAEGLLSHYLPDLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEQLAEGLLSHYLPDLQR 19 0 H3BST1;Q9UL45;H3BPR6;H3BN13;Q9UL45-2 H3BST1 BLOC1S6 Biogenesis of lysosome-related organelles complex 1 subunit 6 0 ; 147.06 1.09E-07 162369000 109634 122199 105784 122395 124419 130512 118754 112724 115913 109532 FALSE TRUE 105349.3821 118714.0042 124901.522 128711.8206 128421.0501 133151.0421 120207.347 110396.21 102755.0422 102113.3001 1.031691092 1.162571419 1.22316605 1.260480471 1.257632943 1.303953961 1.17719579 1.081114898 1.006284608 1 16.63981126 1.611933718 2.398243241 1.006356063 1.211658858 0.579696024 0.069715969 0.192964934 2.482433474 0.053808182 0.020581219 40.91982029 -1.611933718 0.205302795 RAPFDLFENRK ddPTM_BT-474_Pertuzumab_2h_R1 1 RAPFDLFENRK 11 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 136.7 5.27E-05 906500000 218830 321480 144090 424010 154930 242550 513770 397630 595130 669730 FALSE TRUE 210277.8817 312311.7052 170130.2683 445893.2069 159913.4642 247454.5272 520057.6709 389418.8015 527573.3374 624368.5906 0.336784849 0.500204062 0.272483707 0.714150605 0.256120289 0.396327636 0.832933749 0.623700179 0.844970976 1 19.25203844 1.611972247 0.711428252 0.987672666 0.402750278 0.630450427 0.152481682 0.404531149 0.425170068 0.136352191 0.063416934 40.9234507 -1.611972247 -0.584922389 GNAEGSS(ph)DEEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNAEGSSDEEGK 12 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.279)S(0.721)DEEGK 136.08 0.00024497 0 283500 225770 261550 282360 250220 233600 285610 315810 398160 360450 TRUE FALSE 272420.5066 219331.2607 308817.9031 296932.6334 258268.5535 238323.5521 289105.3806 309288.4131 352962.546 336036.4004 0.810687492 0.652700899 0.919001343 0.883632348 0.768573146 0.709219453 0.860339476 0.920401518 1.050369976 1 18.35825799 1.61252968 2.109613793 1.022432464 0.794332487 0.598167321 0.074994805 0.203116566 1.945391537 0.058400687 0.021649483 40.9760112 -1.61252968 -0.228099976 ELEATFGCR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEATFGCR 9 0 A0A0G2JM25;A0A0G2JNK1;K7ERG0;A0A0G2JMB6;A0A0G2JPH3;A0A0G2JNK3;Q8WX94;Q8WX94-2;Q8WX94-3;Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 A0A0G2JM25;Q9NX02 NLRP7;NLRP2 "NACHT, LRR and PYD domains-containing protein 7;NACHT, LRR and PYD domains-containing protein 2" 0 106.93 0.0066456 164800000 31702 37082 27308 32270 32504 34217 38065 31250 34278 36287 FALSE TRUE 30463.05079 36024.45767 32243.16306 33935.45857 33549.52068 34908.89118 38530.85086 30604.67658 30386.90515 33829.24917 0.90049444 1.064890843 0.953114948 1.003139573 0.991731165 1.031914454 1.138980374 0.904680929 0.898243558 1 15.04598354 1.612627749 25 0.926092884 1.012190974 0.227433933 0.065120118 0.55773422 2913.366714 0.030097728 0.016007703 40.98526514 -1.612627749 0.08609809 EAFNMIDQNR ddPTM_BT-474_Pertuzumab_2h_R1 6 EAFNMIDQNR 10 0 J3QRS3;P19105;O14950;J3KTJ1;P24844-2;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;;;;; 196.27 7.83E-07 3538180000 2355780 2425350 2102740 2446710 2386650 2505150 2487530 2362810 2521320 2474770 FALSE TRUE 2263713.513 2356181.393 2482751.893 2572984.996 2463418.765 2555805.849 2517973.136 2314017.148 2235110.324 2307151.624 0.981172408 1.021251212 1.076111283 1.115221457 1.06773163 1.107775416 1.091377398 1.002975758 0.968774787 1 21.13768139 1.61288612 4.887151947 0.985092277 1.067890148 0.449863404 0.038336957 0.144905483 7.579053343 0.023301021 0.010786852 41.00965544 -1.61288612 0.08279787 VSPLNLSSVT(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 1 VSPLNLSSVTP 11 0 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 1 VSPLNLSSVT(1)P 118.4 0.0081052 23741000 49567 50349 52076 58953 56105 49470 59665 50912 49999 61551 TRUE FALSE 47629.86684 48913.09582 61487.29162 61995.57139 57909.66828 50470.31729 60395.19812 49860.64941 44323.32313 57382.09595 0.830047527 0.852410408 1.071541403 1.080399215 1.009194023 0.879548167 1.052509448 0.868923461 0.772424262 1 15.80831304 1.612988107 9.288880823 0.86419961 0.969851139 0.133339079 0.099651169 0.174064947 41.44964318 0.052140313 0.026164857 41.01928698 -1.612988107 0.105651529 RSEDDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSEDDLR 7 1 P15924 P15924 DSP Desmoplakin 0 72.968 0.08044 121520000 280770 327010 253280 319680 307590 333380 290690 286640 292110 271340 FALSE TRUE 269797.198 317683.995 299053.3302 336178.7231 317483.9117 340121.172 294247.5512 280720.7838 258950.8974 252961.9001 1.066552702 1.255857087 1.182207004 1.328969789 1.255066125 1.344554938 1.16320897 1.109735433 1.023675491 1 17.94856058 1.613005103 1.860560148 1.011403075 1.24108989 0.585012113 0.074876111 0.218975626 1.568955521 0.058675754 0.021257049 41.02089226 -1.613005103 0.229686814 LLELDPEHQR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLELDPEHQR 10 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;; 192.12 7.18E-07 1785600000 2108210 2478690 1864590 2415060 2064260 2130350 1940650 1832740 1837840 1476330 FALSE TRUE 2025818.822 2408000.188 2201562.891 2539701.536 2130658.798 2173427.137 1964400.255 1794893.279 1629216.108 1376336.854 1.471891722 1.74957183 1.599581443 1.845261593 1.548064917 1.579138951 1.42726706 1.304109 1.183733548 1 20.39240218 1.613054291 0.822876515 1.01172226 1.666601753 0.838797673 0.097190313 0.196673543 0.264202147 0.083422894 0.035229624 41.02553854 -1.613054291 0.654879493 LDRPAGGPSAES(ph)PRPSSAYNGDLNGLLVPDPLCSGDSTSANK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDRPAGGPSAESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK 42 2 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 LDRPAGGPS(0.153)AES(0.828)PRPS(0.009)S(0.009)AY(0.001)NGDLNGLLVPDPLCSGDSTSANK;LDRPAGGPS(0.009)AES(0.989)PRPS(0.001)S(0.001)AYNGDLNGLLVPDPLCSGDSTSANK;LDRPAGGPS(0.045)AES(0.895)PRPS(0.03)S(0.03)AYNGDLNGLLVPDPLCSGDSTSANK;LDRPAGGPS(0.17)AES(0.825)PRPS(0.002)S(0.002)AYNGDLNGLLVPDPLCSGDSTSANK 365.24 2.98E-176 5596760000 1214275 1231168 1056564 1075794 1119232 1270373 1173301 1407344 1571994 1559997 TRUE FALSE 1166819.791 1196056.294 1247508.618 1131315.857 1155233.114 1296060.812 1187660.209 1378281.855 1393547.831 1454337.014 0.802303579 0.822406556 0.857785098 0.777891126 0.794336597 0.891169516 0.81663342 0.947704584 0.958201447 1 20.47193019 1.613241651 1.172956506 0.998820605 0.816805549 0.808607433 0.03248012 0.178299396 0.466718727 0.027587237 0.010121578 41.0432413 -1.613241651 -0.182015056 FQRPGDPQSAQDK ddPTM_BT-474_Pertuzumab_2h_R1 3 FQRPGDPQSAQDK 13 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;H7C561;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 ;; 97.69 0.0033405 1206850000 991260 890350 806090 879440 867180 942340 889240 1046840 1179440 1160260 FALSE TRUE 952520.4633 864958.0897 951768.3944 924828.0038 895073.6323 961394.7604 900122.7851 1025222.388 1045554.916 1081674.557 0.880598011 0.799647255 0.879902729 0.85499654 0.827488847 0.888802232 0.832156751 0.947810394 0.966607663 1 20.04483507 1.613306928 3.384783521 0.978357951 0.851428586 0.802156264 0.027453897 0.078041865 2.10576242 0.01609835 0.006830463 41.04941082 -1.613306928 -0.126929365 VEQSAER ddPTM_BT-474_Pertuzumab_2h_R1 1 VEQSAER 7 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 92.653 0.036086 95874000 108410 142510 106550 153570 116560 126670 131340 120870 108240 143830 FALSE TRUE 104173.2173 138445.7543 125805.9552 161495.7661 120309.2583 129231.3542 132947.3782 118373.9923 95953.04898 134088.266 0.776900324 1.032497164 0.938232397 1.204398945 0.897239273 0.963778249 0.991491517 0.882806496 0.715596165 1 17.03282347 1.613343665 4.49675032 0.841171024 0.978519061 0.136238549 0.120225458 0.255160276 11.55044205 0.065345333 0.029781405 41.05288331 -1.613343665 0.137348037 ELGDHVTNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELGDHVTNLR 10 0 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 0 ; 164.97 6.00E-06 604710000 322150 388500 324440 386060 344800 363820 368800 360230 360570 407590 FALSE TRUE 309560.0218 377420.3604 383073.5251 405984.6029 355890.8051 371176.6897 373313.4847 352791.1246 319639.6052 379983.5663 0.814666868 0.99325443 1.008131822 1.06842674 0.936595255 0.976823007 0.982446395 0.928437848 0.841193235 1 18.5355775 1.613648045 4.809108514 0.910165605 0.973819539 0.071966041 0.070854164 0.31773615 16.16257374 0.038956882 0.017991574 41.08166579 -1.613648045 0.063653934 LFIGGLSFETTDDSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 329.15 3.96E-71 553363000 310450 291780 254949 269908 299504 274381 295832 293638 328025 308018 FALSE TRUE 298317.2708 283458.7201 301023.9556 283837.9842 309137.8182 279929.1718 299452.4805 287574.2727 290788.9772 287155.6665 1.038869525 0.987125637 1.04829537 0.988446398 1.076551342 0.974834226 1.042822815 1.001457767 1.012652756 1 18.13147351 1.61402835 25 1.005290905 1.021085407 0.06651894 0.030100355 1.612375637 6516.55721 0.012891272 0.006921165 41.1176561 -1.61402835 0.015794502 DKVQAGDVITIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKVQAGDVITIDK 13 1 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 132.81 0.00010441 142160000 383980 350520 326200 294530 358880 355250 359970 427000 544540 458060 FALSE TRUE 368973.6371 340523.5128 385151.5963 309730.7286 370423.7011 362433.3984 364375.4205 418182.3008 482726.1021 427035.1882 0.864035675 0.797413239 0.901920045 0.725304933 0.86743133 0.848720219 0.853267905 0.979268951 1.130412939 1 18.70399543 1.614034369 2.774327913 1.06536743 0.833521956 0.749694263 0.054228054 0.099889455 1.781862539 0.03401422 0.013604874 41.11822601 -1.614034369 -0.231845474 ACRT(ph)PESFLGPSASSLVNLDSLVK ddPTM_BT-474_Pertuzumab_2h_R1 4 ACRTPESFLGPSASSLVNLDSLVK 24 1 Q9H201 Q9H201 EPN3 Epsin-3 1 ACRT(0.998)PES(0.002)FLGPSASSLVNLDSLVK;ACRT(0.961)PES(0.038)FLGPSASSLVNLDSLVK;ACRT(0.962)PES(0.038)FLGPSASSLVNLDSLVK;ACRT(0.984)PES(0.016)FLGPSASSLVNLDSLVK 316.73 1.87E-73 6430374000 4972496 5410688 3931084 4418310 4247823 4668366 4091971 5327824 5645906 5604191 TRUE FALSE 4778165.359 5256380.476 4641518.325 4646339.509 4384458.085 4762763.559 4142049.765 5217802.573 5005006.42 5224614.152 0.914548945 1.006080128 0.888394471 0.889317254 0.839192705 0.911601014 0.792795342 0.998696252 0.957966708 1 22.31689306 1.614167724 25 0.983751856 0.894704168 0.398797867 0.052699995 0.583316913 2305.606056 0.025835383 0.013882272 41.1308537 -1.614167724 -0.089047689 REEEGLQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 REEEGLQLR 9 1 C9JYI4;P52294;C9J352;C9JWD9;F2Z3G4;C9J4U1 C9JYI4 KPNA1 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed" 0 72.096 0.076515 397860000 478710 692100 603950 758260 708670 607720 681350 506890 367780 550850 FALSE TRUE 460001.484 672361.9856 713097.1998 797393.8895 731465.0141 620008.5148 689688.5651 496422.5444 326031.1563 513540.4389 0.895745396 1.309267849 1.388590159 1.552738264 1.424357186 1.207321698 1.343007313 0.966666901 0.63486949 1 18.97011836 1.614220934 3.622943764 0.811330438 1.31758663 0.55123803 0.182411543 0.132145918 4.065421203 0.112339381 0.048633585 41.13589342 -1.614220934 0.506256192 KESFGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KESFGVK 7 1 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5 Q68EM7 ARHGAP17 Rho GTPase-activating protein 17 0 ; 60.682 0.062343 2173500000 3389900 5718200 4244000 7512200 5497000 6280300 5987300 4732200 3967500 5491800 FALSE TRUE 3257418.96 5555122.535 5010985.207 7899905.542 5673815.997 6407291.969 6060574.368 4634478.416 3517126.033 5119835.494 0.636235083 1.085019732 0.978739495 1.542999878 1.108202794 1.251464422 1.183743965 0.90520065 0.68696075 1 22.28766603 1.614349497 4.649499777 0.830443655 1.127212649 0.20286271 0.225198722 0.227703723 10.92613906 0.12799581 0.058766552 41.14807258 -1.614349497 0.296768994 DSPRPGKPDER ddPTM_BT-474_Pertuzumab_2h_R1 2 DSPRPGKPDER 11 2 A0A0A0MR03;Q9Y5B0;K7EJD2;A0A0J9YWJ4;A0A0J9YWB6;Q9Y5B0-4 A0A0A0MR03 CTDP1 RNA polymerase II subunit A C-terminal domain phosphatase 0 ; 76.655 0.019549 270560000 824130 778320 677390 649610 677490 751530 737140 830300 972370 886680 FALSE TRUE 791922.0885 756123.0757 799809.4415 683136.4499 699282.0811 766726.4515 746161.3398 813154.0148 861990.6341 826624.3738 0.958019281 0.914711808 0.967560922 0.826417018 0.845949023 0.927539129 0.902660705 0.983704377 1.042783955 1 19.65687238 1.614403311 3.070767528 1.020779095 0.903788327 0.558807728 0.042531347 0.160029045 3.546650254 0.028969619 0.011954443 41.15317157 -1.614403311 -0.116990769 QQPPEPEWIGDGESTS(ph)PSDKVVK ddPTM_BT-474_Pertuzumab_2h_R1 4 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.063)T(0.213)S(0.722)PS(0.002)DKVVK;QQPPEPEWIGDGEST(0.047)S(0.953)PSDKVVK;QQPPEPEWIGDGES(0.06)T(0.295)S(0.638)PS(0.007)DKVVK;QQPPEPEWIGDGEST(0.01)S(0.988)PS(0.002)DKVVK 266 2.65E-44 3206760000 1356480 1141092 902659 797871 1065353 1215307 960930 1185800 1316860 1119720 TRUE FALSE 1303467.262 1108549.173 1065789.561 839049.2179 1099621.047 1239881.34 972690.1488 1161312.816 1167375.574 1043880.367 1.248674947 1.0619504 1.020988223 0.803779096 1.053397575 1.187761912 0.931802321 1.112496079 1.118303984 1 19.99352495 1.614429441 25 1.086551011 1.039186553 0.012601129 0.119638111 2.547673927 9669.749319 0.058160942 0.031299836 41.15564773 -1.614429441 -0.047364458 KSS(ph)PSTGSLDSGNESK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSPSTGSLDSGNESK 16 1 Q15057;A0A0U1RQT1;A0A087X1H5 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 KS(0.027)S(0.684)PS(0.108)T(0.178)GS(0.003)LDSGNESK 119.45 0.00050183 0 84067 79528 63202 60465 75652 78470 77570 88492 113530 96693 TRUE FALSE 80781.5687 77259.93931 74624.00732 63585.6059 78085.41529 80056.71716 78519.32486 86664.60928 100642.5504 90143.89698 0.896140187 0.857073434 0.827832053 0.705378933 0.866230748 0.888099138 0.871044269 0.961402959 1.116465493 1 16.4599422 1.614463378 2.069094829 1.058792007 0.837172505 0.692669803 0.057526935 0.163342758 1.496376388 0.045064227 0.016668456 41.15886382 -1.614463378 -0.221619502 ILHLLTQEALSIHGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILHLLTQEALSIHGVK 16 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 ; 224.59 4.43E-15 110040000 139231 248670 173958 359760 158503 222060 282680 183036 224810 189289 FALSE TRUE 133789.6986 241578.1751 205396.0803 378327.2567 163601.3929 226550.2053 286139.5224 179256.2426 199290.5113 176468.2874 0.75815151 1.36896084 1.163926297 2.143882406 0.927086647 1.283801235 1.621478434 1.015798619 1.129327621 1 17.42904942 1.614569057 24.99999999 1.054413333 1.333118545 0.110437118 0.357540668 1.25197181 4653.235406 0.165517906 0.089145282 41.1688805 -1.614569057 0.278705212 LRPVDQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRPVDQLR 8 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 67.897 0.068455 0 89147 109860 77773 81998 95604 87930 114240 84535 96257 104760 FALSE TRUE 85663.03668 106726.9004 91828.31115 86229.92661 98679.18949 89708.00485 115638.1033 82789.32271 85330.3089 97664.51189 0.87711529 1.092791008 0.94024236 0.882919752 1.01038942 0.91853226 1.184034006 0.847690948 0.873708446 1 16.57554681 1.614658671 24.99999998 0.895522772 0.985525337 0.120126439 0.09696983 1.032097564 3785.577525 0.043625744 0.023507835 41.17737627 -1.614658671 0.090002564 TRPKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRPKSPR 7 2 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1;U3KPT1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 TRPKS(1)PR 68.335 0.049402 1727400000 630070 529830 433080 471440 527630 529160 503040 561080 616180 579860 TRUE FALSE 605446.1678 514719.7672 511347.1898 495771.0749 544601.6981 539859.9778 509196.354 549493.5019 546233.8296 540585.5657 1.11998212 0.952152258 0.94591351 0.917100097 1.007429226 0.998657774 0.941934795 1.016478309 1.010448418 1 19.04416347 1.614758715 25 1.010098393 0.979611611 0.043537412 0.05310387 1.760227249 6362.84633 0.024929832 0.013440725 41.18686298 -1.614758715 -0.030486782 ITEANLTGHEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ITEANLTGHEEK 12 0 E9PJN1;O75676-2;O75676;E9PKU3 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 0 88.087 0.0072429 0 119570 192710 125910 91687 185420 206130 148020 107280 73923 88522 FALSE TRUE 114897.0722 187214.0995 148664.7379 96418.97706 191384.2027 210298.0898 149831.513 105064.6305 65531.57095 82526.32609 1.392247512 2.268537912 1.801421981 1.168342051 2.319068493 2.548254597 1.815560199 1.27310442 0.794068682 1 16.3325668 1.615012439 2.904538924 0.920238649 1.92875421 0.521401922 0.396304811 0.179395763 3.535212135 0.272018786 0.110445402 41.21093222 -1.615012439 1.008515561 VVEHNIR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVEHNIR 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ;;; 182.26 0.00065984 1229168000 1307630 1462370 1388990 1484300 1440110 1299040 1584070 1400680 1518200 1635110 FALSE TRUE 1256526.374 1420664.639 1640011.391 1560904.901 1486432.446 1325307.479 1603456.323 1371755.469 1345860.301 1524362.543 0.82429628 0.931972939 1.075867023 1.023972222 0.975117404 0.869417505 1.051886462 0.89988794 0.882900401 1 20.53977463 1.615147185 25 0.918544452 0.967348657 0.040185036 0.078580919 1.732335921 5928.867439 0.037731403 0.020384523 41.22372051 -1.615147185 0.048804205 GSSAGFDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSSAGFDR 8 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4;G3V4S5;G3V2S7 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;; 125.58 0.0029213 1354166000 1158520 1248990 1098860 1333540 1236560 1194470 1298560 1202210 1295690 1259470 FALSE TRUE 1113243.758 1213370.028 1297448.446 1402364.159 1276335.075 1218623.002 1314452.166 1177383.943 1148608.703 1174164.975 0.948115283 1.033389731 1.10499672 1.194350188 1.087015115 1.037863527 1.119478262 1.002741496 0.978234514 1 20.1632037 1.615167232 6.010788123 0.989802106 1.078024658 0.274450375 0.060676344 0.183228071 14.06320458 0.034794153 0.016653479 41.22562341 -1.615167232 0.088222552 T(ph)PPVPDSGSANGSFFAPSR ddPTM_BT-474_Pertuzumab_2h_R1 5 TPPVPDSGSANGSFFAPSR 19 0 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 1 T(0.998)PPVPDS(0.001)GS(0.001)ANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR;T(0.995)PPVPDS(0.005)GSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR 130.47 0.00019556 2274920000 52529.2 44115 56588.3 69377 46201.2 52865.4 58291.1 47687.9 42085.5 54868.5 TRUE FALSE 50476.30079 42856.88339 66815.06461 72957.55528 47687.30356 53934.37461 59004.48392 46703.1282 37308.13048 51152.20762 0.98678636 0.837830572 1.306200997 1.426283609 0.932262864 1.054389969 1.153508063 0.913022729 0.729355236 1 15.64250888 1.615275401 4.697429668 0.85240315 1.101344763 0.251205891 0.17357119 0.217181891 10.61218313 0.102871794 0.047355188 41.23589273 -1.615275401 0.248941613 EVMNGAILQQVFVVDYVVQSQMCGDCHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVMNGAILQQVFVVDYVVQSQMCGDCHR 28 0 C9JA08;Q96D46;C9J0B9;C9IZW9;C9K0C2 C9JA08 NMD3 60S ribosomal export protein NMD3 0 221.69 2.32E-34 48931000 42793 49340 47885 49482 48648 50465 56504 45656 53816 47524 FALSE TRUE 41120.60225 47932.87151 56538.8847 52035.77195 50212.8071 51485.43688 57195.51285 44713.18765 47707.0333 44305.15715 0.928122252 1.081880183 1.276124233 1.174485665 1.133340007 1.162064197 1.290944814 1.009209549 1.076782848 1 15.43518702 1.615327082 25 1.032244498 1.15246974 0.245017538 0.097097418 0.893332341 2983.881165 0.047104843 0.025471631 41.24080007 -1.615327082 0.120225242 TIEDLDENQLKDEFFK ddPTM_BT-474_Pertuzumab_2h_R1 3 TIEDLDENQLKDEFFK 16 1 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ;; 241.93 5.76E-20 888210000 1472090 1177027 1350010 1181820 1460950 1368550 1493080 1788510 2321690 2113550 FALSE TRUE 1414559.095 1143459.342 1593986.838 1242813.872 1507942.784 1396223.019 1511352.76 1751576.643 2058141.485 1970397.376 0.717905491 0.580319156 0.808967195 0.630742756 0.765298818 0.708599715 0.767029422 0.888945887 1.044531174 1 20.91005518 1.615606883 1.660302441 1.028778934 0.699903157 0.808504996 0.062088731 0.132260518 0.730913677 0.047102184 0.01688639 41.26737865 -1.615606883 -0.328875777 NQVEEDAEDS(ph)GEADDEEKPEIHKPGQNSFSK ddPTM_BT-474_Pertuzumab_2h_R1 6 NQVEEDAEDSGEADDEEKPEIHKPGQNSFSK 31 2 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK;NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK;NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK;NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK;NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK;NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK 371.39 2.13E-137 5107180000 2125716 1659581 1549790 1294574 1536326 1634279 1771965 1951159 2592685 2122267 TRUE FALSE 2042640.669 1612251.375 1829871.528 1361387.119 1585743.321 1667325.241 1793650.838 1910866.885 2298374.268 1978523.966 1.032406331 0.814875838 0.924867002 0.688082198 0.801477944 0.842711673 0.906560076 0.965804265 1.161661071 1 20.91599311 1.615708295 2.21524207 1.078507929 0.846099498 0.476383248 0.092728951 0.223319537 2.396175483 0.067238708 0.025297373 41.27701613 -1.615708295 -0.232408431 RIEEEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RIEEEQK 7 1 Q06124;Q06124-1 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 91.853 0.044607 0 280110 182560 147430 111310 158170 181260 181890 213880 325320 172350 FALSE TRUE 269162.9915 177353.5675 174073.8806 117054.7224 163257.6817 184925.2014 184116.0242 209463.3033 288391.0375 160676.581 1.675184958 1.103792267 1.083380537 0.728511409 1.016063951 1.150915711 1.145879649 1.303633062 1.794854208 1 17.29380014 1.615714201 3.775772017 1.436717664 1.107243275 0.124441111 0.283000195 0.296304564 9.850083884 0.167122103 0.073252594 41.27757747 -1.615714201 -0.329474389 IHDVLCK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHDVLCK 7 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 101.64 0.0089085 710490000 1049900 1710550 1055250 2380900 1050310 1312610 2165400 1214880 1768480 1355800 FALSE TRUE 1008868.747 1661766.789 1245957.149 2503778.534 1084094.175 1339151.874 2191900.813 1189792.303 1567729.564 1263970.458 0.798174309 1.314719642 0.985748631 1.980883744 0.857689488 1.059480358 1.734139274 0.941313379 1.240321365 1 20.26953131 1.615741897 24.9999999 1.068107492 1.2523738 0.053548379 0.358813385 2.093264176 6624.488762 0.162940291 0.088284135 41.28020986 -1.615741897 0.184266307 IREIADGLCLEVEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IREIADGLCLEVEGK 15 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ; 114.91 0.00051915 981180000 1430870 1426140 1110530 1137090 1306110 1415490 1294830 1479700 1747050 1515410 FALSE TRUE 1374950.018 1385467.884 1311227.475 1195775.351 1348122.214 1444112.178 1310676.517 1449143.678 1548732.208 1412769.931 0.973229957 0.98067481 0.928125271 0.846404871 0.95424045 1.022184962 0.927735287 1.025746405 1.096238088 1 20.43009511 1.615826664 4.440936175 1.051802745 0.947431719 0.442675236 0.048125838 0.148869939 6.601421496 0.028762398 0.013098197 41.28826792 -1.615826664 -0.104371026 QAGEVTYADAHK ddPTM_BT-474_Pertuzumab_2h_R1 5 QAGEVTYADAHK 12 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 ;;;; 218.5 3.42E-11 10031300000 6368140 6080830 5415970 5872270 6181380 6339450 6089320 6458670 7846010 7350580 FALSE TRUE 6119266.048 5907410.682 6394756.257 6175338.558 6380209.701 6467638.022 6163842.92 6325296.207 6955363.838 6852718.669 0.892969104 0.862053583 0.933170697 0.901151624 0.931047955 0.94380615 0.899474094 0.923034567 1.014978751 1 22.70824503 1.615897843 0.177822995 1.039632578 0.847605132 0.599727381 0.028381092 2.481945408 0.458408048 0.195247511 0.205212257 41.29503544 -1.615897843 -0.192027446 CLELFSELAEDKENYKK ddPTM_BT-474_Pertuzumab_2h_R1 2 CLELFSELAEDKENYKK 17 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 271.68 7.27E-36 22610000000 8364900 6481200 6007700 5439100 7182100 6979200 7199500 8974600 11841600 10145000 FALSE TRUE 8037990.46 6296362.522 7093425.031 5719812.603 7413118.769 7120324.206 7287609.635 8789271.374 10497391.21 9457870.114 0.849873213 0.66572732 0.750002373 0.604767515 0.783804248 0.752846478 0.77053391 0.929307684 1.109910697 1 23.1730839 1.615915481 2.268148227 1.055411843 0.729734387 0.784494158 0.067680281 0.110190818 1.248491922 0.047127447 0.017840287 41.29671254 -1.615915481 -0.325677456 DYTGEDVTPQNFLAVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYTGEDVTPQNFLAVLR 17 0 Q99538-3;Q99538-2;Q99538;G3V2T4;G3V4E4;H0YJN9 Q99538-3 LGMN Legumain 0 150.68 6.47E-07 12079000 19619 19844 21251 24523 19348 20456 22515 20022 19329 23074 FALSE TRUE 18852.26779 19278.06855 25091.52843 25788.63497 19970.34599 20869.63434 22790.5453 19608.5387 17134.85295 21511.17743 0.876394045 0.89618844 1.166441424 1.198848136 0.92837066 0.970176291 1.059474563 0.911551158 0.796555791 1 14.39279887 1.616165129 5.432538116 0.885006311 1.016870442 0.171477049 0.110819511 0.23714879 15.00151598 0.063884586 0.030162218 41.32045823 -1.616165129 0.13186413 S(ph)SMEMEGIFNHK ddPTM_BT-474_Pertuzumab_2h_R1 5 SSMEMEGIFNHK 12 0 O75962-5;O75962;E7EPJ7;O75962-4;O75962-2;E7EWP2 O75962-5 TRIO Triple functional domain protein 1 S(0.5)S(0.5)MEMEGIFNHK;S(0.5)S(0.5)MEMEGIFNHK;S(0.5)S(0.5)MEMEGIFNHK;S(0.5)S(0.5)MEMEGIFNHK;S(0.5)S(0.5)MEMEGIFNHK 296.1 1.81E-36 865876000 879579 937927 758236 850718 851802 891339 970192 961082 1083420 1101940 TRUE FALSE 845204.0803 911178.2403 895266.1121 894623.6579 879200.9849 909362.4853 982065.4999 941235.3208 960434.7037 1027304.622 0.822739489 0.886960129 0.871470928 0.870845549 0.855832794 0.885192635 0.955963284 0.916218326 0.93490741 1 19.97043261 1.616230798 0.337653347 1.007784805 0.841060461 0.800588402 0.022142371 0.572882463 0.214356714 0.034451117 0.031627707 41.32670667 -1.616230798 -0.166724344 RPNKQEES(ph)ESPVERPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPNKQEESESPVERPLK 17 3 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 RPNKQEES(0.675)ES(0.325)PVERPLK 100.67 0.0070545 385900000 267960 239380 227390 249490 217400 245630 269250 282190 360460 323090 TRUE FALSE 257487.827 232553.1168 268484.4313 262366.2088 224392.8684 250596.8069 272545.162 276362.6779 319542.092 301206.8265 0.854853889 0.772071203 0.891362372 0.871050008 0.744979359 0.831975855 0.904843908 0.917517976 1.060872676 1 18.20039494 1.616276071 1.562354627 1.028279982 0.828310253 0.719991837 0.047894351 0.189326032 0.91278104 0.039360021 0.014075938 41.33101506 -1.616276071 -0.199969729 KGDIVDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGDIVDIK 8 1 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 ; 85.377 0.026914 827280000 1170460 1080350 951230 887770 1078490 1087280 1074540 1204480 1358070 1329330 FALSE TRUE 1124717.129 1049539.476 1123138.421 933587.9161 1113180.61 1109265.547 1087690.542 1179607.067 1203907.587 1239293.295 0.907547175 0.846885463 0.906273297 0.753322817 0.898238226 0.895079116 0.877669997 0.951838497 0.971446866 1 20.24108623 1.616515816 1.077251854 0.99985751 0.8604803 0.571245011 0.042809 0.330012939 0.728937432 0.03667917 0.013780596 41.35383738 -1.616515816 -0.139377211 DRPYDYK ddPTM_BT-474_Pertuzumab_2h_R1 4 DRPYDYK 7 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ;;; 74.301 0.042457 1633360000 2904440 3603830 3006890 4010490 3658430 3768610 3494790 3209670 2957160 3272260 FALSE TRUE 2790931.274 3501052.297 3550301.911 4217471.87 3776106.723 3844813.876 3537560.285 3143389.193 2621475.594 3050626.916 0.914871386 1.147650104 1.1637942 1.382493496 1.23781335 1.260335656 1.159617476 1.030407611 0.859323564 1 21.54067432 1.616529524 2.827507918 0.93133771 1.19361964 0.438216009 0.115872098 0.207442044 3.859050324 0.080603632 0.032516796 41.35514269 -1.616529524 0.26228193 EVIKPYDWTYTTDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVIKPYDWTYTTDYK 15 1 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 176.83 7.09E-07 1261930000 2530400 2035150 1865220 1874930 2150610 2182340 2252970 2484200 3069100 2822300 FALSE TRUE 2431509.17 1977109.515 2202306.746 1971695.362 2219786.324 2226468.41 2280542.521 2432900.402 2720708.635 2631143.107 0.924126538 0.751426066 0.837015189 0.749368347 0.843658529 0.846198143 0.866749708 0.924655293 1.034040538 1 21.32725829 1.616554833 1.394885998 1.021550866 0.818180731 0.70298686 0.048775869 0.198240048 0.745270114 0.038773102 0.013900308 41.35755281 -1.616554833 -0.203370135 IEEVLSPEGSPSKS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 3 IEEVLSPEGSPSKSPSK 17 1 Q9UEY8-2;Q9UEY8 Q9UEY8-2 ADD3 Gamma-adducin 1 IEEVLSPEGSPS(0.01)KS(0.961)PS(0.029)K;IEEVLSPEGSPS(0.002)KS(0.998)PSK;IEEVLSPEGS(0.001)PS(0.129)KS(0.869)PSK 235.5 2.22E-20 2082130000 2122870 1566810 1668810 1397400 1432590 1530700 1506080 2023480 2517330 2025710 TRUE FALSE 2039905.893 1522126.113 1970401.089 1469519.981 1478670.558 1561651.803 1524511.858 1981694.431 2231573.252 1888506.857 1.080168645 0.805994485 1.04336454 0.778138547 0.78298395 0.826924084 0.807257782 1.049344578 1.181660126 1 20.84881459 1.61659135 5.015993876 1.097544597 0.87022414 0.423616342 0.108251711 0.131217305 7.193507391 0.058563419 0.027304508 41.36103045 -1.61659135 -0.227320457 VADEEKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VADEEKPK 8 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 90.629 0.013736 0 175440 175280 192010 175370 166870 178180 201310 239350 291050 287430 FALSE TRUE 168583.6108 170281.186 226710.4782 184420.8667 172237.5251 181782.9217 203773.692 234407.3389 258011.2242 267962.1101 0.629132271 0.635467402 0.846054236 0.688234865 0.642768207 0.678390395 0.760457111 0.874777926 0.962864579 1 18.03166949 1.616662002 1.567668498 0.992948037 0.689027803 0.806011762 0.058452019 0.160041078 0.777479756 0.050676765 0.018129777 41.3677597 -1.616662002 -0.303920234 ECEDVMDWINDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ECEDVMDWINDK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A5F9ZHC3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 152.85 0.00014419 69572000 139974 119830 154657 197586 143370 129289 196583 225528 259380 289620 FALSE TRUE 134503.6613 116412.5657 182606.9602 207783.4371 147981.6263 131903.3122 198988.8416 220870.768 229936.2698 270003.7794 0.498154736 0.431151616 0.676312608 0.769557514 0.548072425 0.488523947 0.736985393 0.818028431 0.851603893 1 18.04262008 1.617057698 1.105094921 0.970550523 0.57242126 0.688468886 0.098463779 0.291345467 0.676587164 0.094268587 0.035165834 41.40546804 -1.617057698 -0.398129263 TAASGVEANSRPLDHAQPPSSLVIDKESEVYK ddPTM_BT-474_Pertuzumab_2h_R1 1 TAASGVEANSRPLDHAQPPSSLVIDKESEVYK 32 2 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 0 73.126 0.0016524 109210000 112820 98210 83593 81231 93761 105310 93209 104000 129950 86999 FALSE TRUE 108410.8697 95409.14696 98700.11462 85423.34164 96776.90772 107439.4404 94349.71962 101852.3637 115198.6208 81106.48024 1.336648679 1.176344315 1.216920206 1.053224618 1.193208082 1.324671469 1.163282137 1.255785769 1.42033806 1 16.30752957 1.617082028 12.56450618 1.253689921 1.206185753 0 0.122315223 0.365511006 246.1331174 0.056967101 0.029803076 41.40778774 -1.617082028 -0.047504169 T(ph)SPLKDNPS(ph)PEPQLDDIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 2 T(0.864)S(0.136)PLKDNPS(1)PEPQLDDIKR 211.3 2.57E-16 605950000 865800 633420 612180 443270 625970 560910 667610 771660 1025900 826510 TRUE FALSE 831963.5788 615355.4818 722814.5439 466147.2178 646104.8935 572251.9845 675780.4109 755724.9513 909444.1329 770529.7415 1.079729352 0.798613536 0.938074814 0.604969792 0.838520382 0.742673454 0.877033519 0.980786218 1.180284269 1 19.55549112 1.617209534 2.729818212 1.088878437 0.827246517 0.4010422 0.123598627 0.213614 3.680377272 0.081249223 0.032457061 41.41994656 -1.617209534 -0.26163192 KCLELFTELAEDKENYKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KCLELFTELAEDKENYKK 18 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 186.56 2.08E-14 1768700000 2555000 2028600 1649100 1174100 1811700 2027500 1717600 2166400 2595900 2095400 FALSE TRUE 2455147.775 1970746.314 1947129.054 1234695.442 1869974.976 2068497.439 1738620.503 2121663.083 2301224.315 1953476.692 1.256809352 1.008840455 0.996750595 0.632050255 0.957254818 1.05888002 0.890013436 1.086095929 1.178014729 1 20.89761261 1.617248703 6.713818612 1.10270971 0.963979479 0.107507872 0.15159732 0.260611611 25.23067714 0.082446708 0.040113724 41.42368238 -1.617248703 -0.138730231 KAAPGAAGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAAPGAAGSR 10 1 Q92522 Q92522 H1FX Histone H1x 0 70.808 0.084776 80795000 72739 71471 76017 77853 78252 76250 95863 62961 57253 87054 FALSE TRUE 69896.27946 69432.71706 89754.96289 81871.00266 80769.04665 77791.82724 97036.20007 61660.83335 50753.87946 81157.75504 0.861239686 0.855527818 1.105932056 1.00878841 0.995210459 0.95852611 1.195649141 0.759765143 0.625373132 1 16.30844134 1.617530938 11.95766702 0.768584744 0.994271576 0.335354222 0.128725892 0.084382034 46.75672427 0.061239485 0.031935264 41.45061112 -1.617530938 0.225686832 SPVDIVTGGIS(ph)PVRDLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPVDIVTGGISPVRDLDR 18 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;H0Y9N9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 SPVDIVTGGIS(1)PVRDLDR;SPVDIVT(0.002)GGIS(0.998)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR 157.63 1.81E-09 308317000 187419 209615 157510 187998 201313 209992 200556 188961 192151 206504 TRUE FALSE 180094.4583 203636.9854 185975.5608 197700.5993 207788.4155 214238.1821 203010.4643 185058.8893 170338.824 192517.3001 0.935471556 1.057759408 0.966019992 1.02692381 1.07932334 1.112825611 1.054505045 0.96125849 0.88479749 1 17.55462857 1.617580161 4.739687768 0.937045547 1.035955727 0.330273437 0.055215575 0.16750768 8.320888709 0.031625266 0.014606164 41.45530941 -1.617580161 0.09891018 QELSFAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 QELSFAAR 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 153.73 0.0010151 1646300000 2185760 2692880 2460630 2951730 2657860 2302110 2834310 2315830 2135220 2732920 FALSE TRUE 2100338.083 2616081.699 2905320.577 3104069.139 2743352.481 2348660.241 2868997.134 2268007.301 1892838.777 2547816.894 0.824367751 1.02679345 1.140317652 1.218325048 1.076746326 0.921832431 1.126060958 0.890176726 0.74292575 1 21.28083017 1.617694992 5.641891661 0.85486504 1.052869312 0.292735686 0.120368561 0.16116566 10.93999187 0.066380659 0.03155397 41.466272 -1.617694992 0.198004272 GDYGPPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDYGPPGR 8 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 ;;; 117.18 0.0049536 622750000 825580 1053040 861530 1065160 1058060 1166790 995730 967170 898970 1024110 FALSE TRUE 793315.4209 1023008.33 1017227.636 1120133.035 1092093.461 1190383.293 1007916.042 947197.6015 796922.6944 954746.1175 0.830917672 1.071497764 1.065443071 1.17322607 1.143857451 1.24680611 1.055690118 0.992093693 0.834695926 1 19.86475762 1.617771897 3.04162219 0.917252872 1.095475919 0.273081265 0.108828677 0.263429149 5.728172348 0.072165687 0.029802893 41.47361552 -1.617771897 0.178223047 S(ph)RSPS(ph)SPELNNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPSSPELNNK 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.989)RS(0.25)PS(0.705)S(0.057)PELNNK;S(1)RS(0.017)PS(0.796)S(0.187)PELNNK 198.61 2.17E-06 755610000 1594240 1400690 1185120 1216050 1312410 1389830 1366020 1562470 1907900 1607080 TRUE FALSE 1531935.338 1360743.693 1399297.547 1278810.486 1354624.86 1417933.315 1382737.761 1530204.448 1691323.191 1498231.04 1.022496062 0.908233548 0.933966464 0.853546918 0.904149509 0.946404978 0.922913572 1.021340773 1.128880089 1 20.51482869 1.618269979 3.528787918 1.067575167 0.923660699 0.569289443 0.049540803 0.123637765 3.623070366 0.029436325 0.012699272 41.52120784 -1.618269979 -0.143914468 EEFKPNKPKPCGLCNQFGHEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEFKPNKPKPCGLCNQFGHEVK 22 3 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 96.303 0.00089022 946580000 927650 755020 662800 565020 763780 695630 770010 943560 1192000 1069300 FALSE TRUE 891396.4124 733487.5688 782582.7039 594180.7499 788347.6773 709696.1152 779433.6127 924075.1563 1056689.157 996875.3586 0.894190437 0.735786638 0.785035659 0.596043171 0.790818702 0.711920612 0.781876697 0.92697161 1.060001281 1 19.92705361 1.618790914 2.44329505 1.028173272 0.747413986 0.709396532 0.072067469 0.129620148 1.742254533 0.049773555 0.019284873 41.5710423 -1.618790914 -0.280759286 RNPDELAEALDER ddPTM_BT-474_Pertuzumab_2h_R1 1 RNPDELAEALDER 13 1 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 77.527 0.04122 150840000 42948 52387 45535 52169 52645 56085 53471 45927 42926 50497 FALSE TRUE 41269.54468 50892.97405 53764.18742 54861.44834 54338.37424 57219.07713 54125.39409 44978.5914 38053.22044 47076.79321 0.876643073 1.081062889 1.142052883 1.165360778 1.154249696 1.215441266 1.149725595 0.955430231 0.808322272 1 15.52272843 1.618816156 4.363601255 0.898345609 1.119293961 0.45248045 0.096647711 0.139742931 6.018279674 0.056586753 0.025730195 41.57345856 -1.618816156 0.220948352 NTEESSS(ph)PVRK ddPTM_BT-474_Pertuzumab_2h_R1 5 NTEESSSPVRK 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 NTEESS(0.007)S(0.993)PVRK;NTEESS(0.009)S(0.991)PVRK;NTEESS(0.004)S(0.996)PVRK;NTEESS(0.021)S(0.979)PVRK;NTEES(0.007)S(0.04)S(0.953)PVRK 202.32 2.48E-08 10861340000 6755990 6492830 5177560 5511740 5768120 5815000 5981050 6630660 7614810 7068670 TRUE FALSE 6491958.442 6307660.846 6113260.266 5796201.562 5953656.818 5932583.284 6054247.879 6493734.554 6750408.693 6589902.685 0.985137225 0.95717056 0.927670796 0.87955799 0.903451402 0.90025355 0.918715825 0.985406745 1.024356355 1 22.65182573 1.618871003 3.504338742 1.010644663 0.922378263 0.618208839 0.028727672 0.134294864 3.88385321 0.019537241 0.008417251 41.57870927 -1.618871003 -0.0882664 KRT(ph)SIETNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRTSIETNIR 10 2 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46;H0YLC5;Q9UKI9-3;Q9UKI9;Q9UKI9-2 A0A0C4DG88 POU2F1;POU2F3 "POU domain protein;POU domain, class 2, transcription factor 1;POU domain, class 2, transcription factor 3" 1 KRT(0.5)S(0.5)IETNIR 75.462 0.06258 71648000 103380 109860 104960 99376 90953 127130 103200 106600 107510 109400 TRUE FALSE 99339.79531 106726.9004 123928.6068 104504.8073 93878.58585 129700.6557 104462.9925 104398.6727 95305.91552 101990.2406 0.974012756 1.046442285 1.215102603 1.024654974 0.920466364 1.271696733 1.024244986 1.02361434 0.934461131 1 16.63807158 1.618970781 2.68484006 0.971331448 1.074021368 0.136929393 0.100229866 0.458920231 7.624370159 0.067842612 0.027021412 41.58826289 -1.618970781 0.10268992 LHRQTAEYSAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHRQTAEYSAFK 12 1 Q5BJF6-9;Q5BJF6-3;Q5BJF6-4;Q5BJF6-8;Q5BJF6-5;Q5BJF6-6;Q5BJF6-10;Q5BJF6-7;Q5BJF6-2;Q5BJF6 Q5BJF6-9 ODF2 Outer dense fiber protein 2 0 69.451 0.045546 361950000 416750 701580 512080 933930 706040 822340 744620 585840 471390 695720 FALSE TRUE 400462.9493 681571.6253 604624.2472 982130.2392 728750.4178 838968.2782 753732.8823 573742.1993 417879.7834 648598.2647 0.617428339 1.05083788 0.932201457 1.514235071 1.123577502 1.293509903 1.162095126 0.884587934 0.644281377 1 19.30696564 1.619106297 4.571618007 0.806353696 1.114547558 0.201388021 0.233132945 0.231456225 10.80748055 0.133689768 0.06138359 41.60124208 -1.619106297 0.308193862 DLELALS(ph)PIHNSSALPTTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLELALSPIHNSSALPTTGR 20 0 A0A087WUU7;Q96GX5-2;Q96GX5-3;Q96GX5 A0A087WUU7 MASTL Serine/threonine-protein kinase greatwall 1 DLELALS(1)PIHNSSALPTTGR;DLELALS(1)PIHNSSALPTTGR;DLELALS(1)PIHNSSALPTTGR;DLELALS(1)PIHNSSALPTTGR 265.62 7.53E-37 2013170000 435153 774780 605283 986230 712498 744750 757189 646530 510982 804730 TRUE FALSE 418146.7397 752684.033 714671.1025 1037129.448 735416.1452 759809.3553 766455.7055 633178.9296 452977.4656 750224.9203 0.557361837 1.003277834 0.952609122 1.382424684 0.980260886 1.012775415 1.021634559 0.843985467 0.603788882 1 19.51696366 1.619113905 4.41238717 0.780007623 1.001987403 0.122493262 0.206421266 0.286528017 12.58209037 0.117176014 0.053416472 41.60197085 -1.619113905 0.221979779 TEELIES(ph)PKLESSEGEIIQTVDR ddPTM_BT-474_Pertuzumab_2h_R1 4 TEELIESPKLESSEGEIIQTVDR 23 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 TEELIES(1)PKLESSEGEIIQTVDR;TEELIES(0.988)PKLES(0.012)SEGEIIQTVDR;TEELIES(1)PKLESSEGEIIQTVDR;TEELIES(1)PKLESSEGEIIQTVDR 255.95 8.82E-44 1829300000 608688 468467 426457 358452 458926 477046 465857 543560 663183 560845 TRUE FALSE 584899.8 455106.7798 503527.2664 376951.7507 473687.7716 486692.197 471558.2973 532335.296 587901.2461 522858.4686 1.118657983 0.870420596 0.963027849 0.720944143 0.905957922 0.930829711 0.901885167 1.018125034 1.124398439 1 18.99606095 1.619124146 3.68629808 1.064930228 0.908580496 0.285508178 0.096115935 0.215103206 6.84825466 0.056805971 0.024817372 41.60295179 -1.619124146 -0.156349732 DGPLNMILDDGGDLTNLIHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGPLNMILDDGGDLTNLIHTK 21 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 232.29 2.25E-26 575860000 577710 561630 468990 494790 539810 555380 570700 639770 740650 730000 FALSE TRUE 555132.4545 545612.8623 553746.9256 520326.1712 557173.4789 566610.1641 577684.3973 626558.5259 656574.5171 680556.4498 0.815703759 0.801715805 0.813667883 0.7645599 0.818702812 0.832568943 0.848841264 0.920656216 0.964761288 1 19.37635531 1.61928539 1.035514353 1.000716955 0.801065148 0.959704494 0.014671116 0.084274684 0.172309129 0.013016541 0.004958451 41.61840094 -1.61928539 -0.199651807 GPEEEHPSVTLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPEEEHPSVTLFR 13 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;A0A1B0GV31;C9JYZ0;A0A1B0GVA5;F8WC59;A0A1B0GTG3;A0A1B0GVZ3;A0A1B0GVG0;A0A1B0GU36;A0A1B0GUT4 A0A1B0GW23 ACY1 Aminoacylase-1 0 ; 210.41 3.02E-08 561200000 640380 909300 715780 1113740 839000 872800 937840 792290 735750 943730 FALSE TRUE 615353.2416 883367.6543 845137.3684 1171220.255 865987.197 890448.614 949317.5665 775928.9346 652230.7445 879810.3265 0.699415798 1.004043289 0.960590417 1.331219036 0.984288512 1.012091569 1.079002528 0.881927515 0.741331086 1 19.74683301 1.619688275 5.705490014 0.852672438 1.018949889 0.13350351 0.155690665 0.241808764 16.76565256 0.084000112 0.040056213 41.65702728 -1.619688275 0.166277451 EKFEVK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKFEVK 6 1 P33316-2;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMP1 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;; 85.256 0.055182 1537700000 1911940 1829360 1524640 1580560 1701960 1886930 1958440 2166260 2510430 2595580 FALSE TRUE 1837219.271 1777188.444 1800176.363 1662132.891 1756705.089 1925085.017 1982407.975 2121525.974 2225456.511 2419779.055 0.759250836 0.734442444 0.743942452 0.686894486 0.725977475 0.795562311 0.819251646 0.876743672 0.919694096 1 21.20644389 1.619803462 0.791711014 0.994140607 0.726570891 0.946528808 0.021642491 0.126243783 0.158297708 0.021195117 0.009184941 41.66807735 -1.619803462 -0.267569717 IPSIVS(ph)SPLNSPLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.57)S(0.43)PLNSPLDR 113.4 0.00072201 35656000 49809 47467 50492 59399 56972 50561 51066 51962 47963 51036 TRUE FALSE 47862.40921 46113.28764 59617.02759 62464.58951 58804.55612 51583.37806 51690.96098 50888.96654 42518.44132 47579.28626 1.005950551 0.969188301 1.253003823 1.312852596 1.235927664 1.084156197 1.086417327 1.069561369 0.893633441 1 15.53804601 1.620081958 1.53852235 0.952038189 1.150558427 0.324340122 0.106001471 0.477209245 2.223854502 0.097352136 0.03489852 41.69480602 -1.620081958 0.198520238 STVTGERQS(ph)GDGQESTEPVENK ddPTM_BT-474_Pertuzumab_2h_R1 4 STVTGERQSGDGQESTEPVENK 22 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK;STVT(0.001)GERQS(0.999)GDGQESTEPVENK;STVT(0.001)GERQS(0.999)GDGQESTEPVENK 312.91 1.80E-67 2423510000 1346849 1335690 981176 970819 1147616 1240029 1141355 1274268 1434758 1306266 TRUE FALSE 1294212.652 1297597.429 1158496.329 1020923.085 1184530.111 1265103.236 1155323.244 1247953.92 1271890.287 1217791.44 1.062753941 1.06553338 0.951309306 0.838339843 0.972687171 1.038850491 0.948703699 1.024768182 1.044423737 1 20.21583565 1.62023718 8.346801361 1.026559272 0.98090767 0.076993078 0.063680021 0.30078345 49.64177493 0.035411205 0.017800264 41.70971098 -1.62023718 -0.045651602 HEPVGVCGQIIPWNFPLLMQAWK ddPTM_BT-474_Pertuzumab_2h_R1 2 HEPVGVCGQIIPWNFPLLMQAWK 23 0 P05091;P05091-2;F8VP50 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ; 191.79 1.11E-17 429560000 226115 334180 207708 441920 213290 235510 422710 217440 331900 247240 FALSE TRUE 217278.1758 324649.5136 245245.456 464727.5442 220150.6666 240272.1736 427883.2514 212949.788 294224.1034 230494.2146 0.942662167 1.408493112 1.063998315 2.016222164 0.955124479 1.042421711 1.856373064 0.923883441 1.276492358 1 17.81437101 1.62036393 25 1.075127988 1.325808563 0.100372627 0.355971005 1.923244817 3837.965062 0.159114124 0.087461221 41.72188584 -1.62036393 0.250680575 AALEEVYPDLTPEETRR ddPTM_BT-474_Pertuzumab_2h_R1 4 AALEEVYPDLTPEETRR 17 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ;;; 250.17 5.22E-21 1867500000 533909 565525 469501 562920 550021 607680 529249 540620 526267 550730 FALSE TRUE 513043.246 549396.7807 554350.2747 591972.3687 567712.925 619967.706 535726.1076 529456.0081 466527.3765 513428.5666 0.999249515 1.070054953 1.079702827 1.152979026 1.105729135 1.207505282 1.043428711 1.031216497 0.908650992 1 18.96980404 1.620421857 2.351336729 0.958251263 1.101657972 0.481187848 0.057750326 0.219060399 2.698099544 0.042014809 0.01613672 41.72745115 -1.620421857 0.143406709 DTATYWPLNWR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTATYWPLNWR 11 0 E9PCJ7;Q8N806 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 130.66 0.0024834 0 92922 103740 72287 77326 80379 90102 109000 69993 87241 68501 FALSE TRUE 89290.50551 100781.4368 85350.86892 81316.80413 82964.46353 91923.92417 110333.9746 68547.62009 77337.76742 63861.36626 1.398192847 1.578128416 1.336502394 1.273333298 1.299133864 1.439429338 1.727710838 1.073381672 1.211025882 1 15.9626558 1.620840908 13.60261523 1.106269214 1.42511224 0.566174039 0.136477454 0.073483743 54.79989873 0.067510597 0.035991009 41.76773339 -1.620840908 0.318843026 EKLEAEMEAAR ddPTM_BT-474_Pertuzumab_2h_R1 6 EKLEAEMEAAR 11 1 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;;;;; 163.51 2.18E-05 3066340000 3441780 3475400 2917370 3042790 3151360 3106280 3410290 3595740 4132210 3987290 FALSE TRUE 3307271.433 3376284.995 3444603.656 3199828.757 3252726.356 3169091.11 3452026.149 3521486.712 3663138.844 3717227.297 0.889714609 0.90828048 0.926659411 0.860810626 0.875041018 0.852541655 0.928656193 0.947342315 0.985449248 1 21.82579548 1.620980408 1.638048304 0.9943976 0.887485579 0.78367153 0.022118623 0.168407718 0.903178589 0.019287075 0.006937122 41.78115178 -1.620980408 -0.106912021 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR ddPTM_BT-474_Pertuzumab_2h_R1 3 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR 35 2 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 ;; 187.68 1.11E-20 1386940000 232550 219102 162692 182474 184078 207729 180852 228032 249179 243181 FALSE TRUE 223461.6889 212853.4255 192094.0635 191891.505 189999.036 211929.4227 183065.3209 223323.0595 220893.2446 226710.1343 0.985671371 0.938879182 0.847311322 0.846417853 0.838070326 0.934803481 0.807486271 0.985059888 0.974342172 1 17.79048936 1.621133151 9.121325774 0.985735511 0.884877015 0.441911045 0.051955354 0.097857231 20.66704208 0.026765811 0.013639651 41.79584891 -1.621133151 -0.100858496 LEQTSVRDPS(ph)PEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEQTSVRDPSPEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK 48 3 O15234 O15234 CASC3 Protein CASC3 1 LEQTS(0.001)VRDPS(0.998)PEADAPVLGS(0.001)PEKEEAASEPPAAAPDAAPPPPDRPIEK;LEQT(0.017)S(0.014)VRDPS(0.97)PEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK 140.08 3.98E-15 1453760000 373500 321580 233139 233503 282890 277550 273400 353520 413690 389180 TRUE FALSE 358903.2071 312408.8533 275272.4034 245554.1178 291989.4138 283162.2512 276745.951 346219.6885 366729.6455 362820.492 0.989203242 0.861056253 0.758701368 0.676792307 0.804776522 0.780447239 0.762762736 0.954245133 1.010774346 1 18.46889642 1.621193949 4.21652439 0.998831721 0.799559807 0.54963561 0.076683618 0.131788641 5.351518223 0.047280054 0.021377169 41.80170051 -1.621193949 -0.199271914 T(ph)SPSKSPFLHSGMK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSPSKSPFLHSGMK 14 1 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;H0YEW5 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 T(0.58)S(0.419)PS(0.001)KSPFLHSGMK;T(0.852)S(0.147)PS(0.001)KSPFLHSGMK;T(0.5)S(0.5)PSKSPFLHSGMK 210.43 8.49E-09 2524820000 2345580 2148040 1575700 1477670 1757980 1777370 1863420 2102000 2388440 2311700 TRUE FALSE 2253912.14 2086780.002 1860464.041 1553932.726 1814527.023 1813309.639 1886225.091 2058592.965 2117314.304 2155126.5 1.045837514 0.968286549 0.863273706 0.721040146 0.841958476 0.841393598 0.875227088 0.955207486 0.982454767 1 21.03934112 1.621247325 2.844021416 0.988130931 0.872848047 0.249014258 0.080212445 0.344517117 6.496028515 0.058858189 0.023912779 41.80683834 -1.621247325 -0.115282884 EFWEIVHSFTDEQKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFWEIVHSFTDEQKR 15 1 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG63;S4R306 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 91.441 0.0036529 164510000 127750 140450 112320 120770 133170 131560 122000 143890 156710 153800 FALSE TRUE 122757.3888 136444.5035 132618.7225 127002.9542 137453.534 134220.2333 123493.0725 140918.6212 138920.9378 143382.989 0.856150298 0.951608726 0.924926475 0.885760264 0.958646036 0.936095936 0.861281198 0.982812691 0.968880191 1 17.12951435 1.621273047 9.487345581 0.982434138 0.914778833 0.492234309 0.033887537 0.086766035 20.58351329 0.016272666 0.008338824 41.80931454 -1.621273047 -0.067655305 LYAYEPADTALLLDNMKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYAYEPADTALLLDNMKK 18 1 O95994 O95994 AGR2 Anterior gradient protein 2 homolog 0 168.32 3.37E-11 723560000 850460 905210 618160 628650 675650 817130 743090 862910 899200 934950 FALSE TRUE 817223.083 879394.2971 729875.2629 661094.7018 697382.8959 833652.9285 752184.1577 845090.607 797126.5858 871625.0037 0.937585635 1.008913573 0.837373021 0.758462296 0.800095102 0.956435307 0.862967623 0.969557554 0.914529278 1 19.73334806 1.621405484 1.134794 0.977452736 0.874905714 0.196295772 0.073165092 0.82442396 2.016905225 0.070007639 0.02598592 41.82206613 -1.621405484 -0.102547022 EGLGVNEVHYVDNQDCIDLIEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGLGVNEVHYVDNQDCIDLIEAK 23 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 190.24 1.58E-17 162530000 102700 104380 100910 118260 91679 109450 108650 105120 112040 110110 FALSE TRUE 98686.37046 101403.1846 119146.6817 124363.4128 94627.9383 111663.154 109979.6912 102949.2353 99321.68891 102652.1516 0.961366799 0.987833017 1.160683725 1.211503225 0.921831026 1.087781914 1.071382231 1.002894081 0.967555841 1 16.64740434 1.621629651 4.205341761 0.984302544 1.060552014 0.123088938 0.082844388 0.363828375 14.70798911 0.04986846 0.022541669 41.84365871 -1.621629651 0.07624947 CALGWDHQEK ddPTM_BT-474_Pertuzumab_2h_R1 6 CALGWDHQEK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 183.78 1.63E-06 6479370000 8137340 7609400 6422450 7380070 7389120 7301550 8119220 8355960 9748750 9479400 FALSE TRUE 7819323.756 7392387.362 7583129.582 7760956.297 7626797.755 7449192.344 8218585.443 8183406.506 8642112.77 8837351.795 0.884803948 0.836493503 0.858077143 0.878199316 0.863018462 0.842921332 0.929982831 0.926002121 0.977907519 1 23.07518268 1.621742387 1.032529399 0.998350003 0.859107987 0.871088847 0.019256968 0.152477464 0.309874401 0.0163811 0.006252706 41.85452209 -1.621742387 -0.139242017 TSS(ph)TLDSEGTFNSYR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSTLDSEGTFNSYR 15 0 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 TSS(0.999)T(0.001)LDSEGTFNSYR;TSS(1)TLDSEGTFNSYR 343.37 9.57E-70 598890000 964860 977660 832830 774600 875230 863480 759850 1082140 1231580 1091960 TRUE FALSE 927152.2045 949778.094 983340.9072 814577.1988 903382.5678 880940.1572 769149.2716 1059793.431 1091776.202 1018000.577 0.910758035 0.932983847 0.965953193 0.800173612 0.8874087 0.865363122 0.755548955 1.041053861 1.072471103 1 19.95730695 1.621794837 8.667828005 1.044432917 0.877517506 0.609660209 0.05993137 0.071140205 12.8978877 0.031164511 0.015789364 41.85957715 -1.621794837 -0.166915411 SPSKPLPEVTDEYKNDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSKPLPEVTDEYKNDVK 18 2 P05455;E7ERC4;E9PGX9;E9PFL9 P05455 SSB Lupus La protein 0 142.98 6.12E-08 665140000 614700 467950 475700 391130 449300 474420 468710 632440 778210 697300 FALSE TRUE 590676.8444 454604.5242 561669.5719 411316.2662 463752.1425 484013.0975 474446.2132 619379.893 689870.8633 650071.2499 0.908634007 0.69931492 0.864012325 0.632724899 0.713386637 0.74455392 0.72983725 0.952787703 1.061223463 1 19.31023833 1.621895066 3.600416994 1.025592246 0.750968106 0.692600318 0.076765995 0.097766921 2.98014637 0.044762401 0.019482576 41.86923886 -1.621895066 -0.27462414 ERLDQPMTEIVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERLDQPMTEIVSR 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 209.39 3.49E-08 1973230000 401176 450479 297238 377722 442378 503893 382136 376729 331006 373457 FALSE TRUE 385497.5984 437631.78 350955.5186 397216.2777 456607.4901 514082.0617 386812.6947 368949.4145 293431.5866 348162.4247 1.107234931 1.256975908 1.008022387 1.140893587 1.311478372 1.476558138 1.11101218 1.059704863 0.842800847 1 18.40940098 1.622342325 2.564552678 0.928974993 1.211477304 0.440850014 0.127194305 0.234690852 3.521404205 0.09293903 0.036660767 41.91238017 -1.622342325 0.282502311 RQGLAETAS(ph)PVAVSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RQGLAETASPVAVSLR 16 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 RQGLAET(0.007)AS(0.993)PVAVSLR 58.366 0.067755 313100000 122860 119650 117850 118490 118680 136400 130740 117890 121020 128210 TRUE FALSE 118058.4954 116237.6991 139148.1166 124605.2831 122497.45 139158.1015 132340.0352 115455.5303 107282.317 119526.2225 0.987720459 0.972487013 1.164163927 1.042493275 1.024858373 1.164247464 1.107205034 0.965943103 0.897563018 1 16.86696764 1.622348979 5.406785895 0.943988499 1.067295963 0.375874512 0.065971044 0.14783827 9.281712925 0.03701191 0.017540264 41.91302236 -1.622348979 0.123307464 TDSS(ph)PNQAR ddPTM_BT-474_Pertuzumab_2h_R1 6 TDSSPNQAR 9 0 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 TDS(0.001)S(0.999)PNQAR;TDS(0.002)S(0.998)PNQAR;TDS(0.007)S(0.993)PNQAR;TDS(0.194)S(0.805)PNQAR;TDS(0.115)S(0.885)PNQAR;TDS(0.017)S(0.983)PNQAR 227.36 2.13E-07 2221252000 1547784 1480608 1318438 1547866 1457980 1615099 1560101 1496319 1541359 1659337 TRUE FALSE 1487294.89 1438382.51 1556709.075 1627751.55 1504877.251 1647757.408 1579193.983 1465419.49 1366390.388 1546948.627 0.961437804 0.929819184 1.006309484 1.052233747 0.972803637 1.065166211 1.02084449 0.947296804 0.883281038 1 20.56099386 1.622434325 5.384780303 0.933769909 1.001811177 0.240887796 0.046444819 0.188392592 11.74100219 0.025971918 0.012301151 41.92125973 -1.622434325 0.068041269 LIFAGKQLEDGRTLSDYNIQKESTLHLVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LIFAGKQLEDGRTLSDYNIQKESTLHLVLR 30 3 M0R2S1;P62987;P0CG48;Q96C32;Q5PY61;J3QKN0;F5GXK7;F5H747;F5H388;B4DV12;F5H265;F5H2Z3;F5GYU3;F5H6Q2;M0R1M6;J3QTR3;J3QS39;P0CG47;P62979;A0A2R8Y422 M0R2S1;P62979 UBA52;UBC;UBB;RPS27A Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40;Polyubiquitin-C;Ubiquitin;Polyubiquitin-B;Ubiquitin;Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 164.62 1.96E-12 629420000 572210 588920 443900 305620 444110 450940 514320 323620 512040 235770 FALSE TRUE 549847.4006 572124.5782 524122.6045 321393.0848 458395.2015 460058.3158 520614.402 316937.1339 453915.3658 219801.0879 2.501568149 2.602919684 2.384531439 1.4621997 2.085500149 2.0930666 2.368570634 1.441927048 2.065118832 1 17.745839 1.622531017 0.09453234 3.08E-16 3.642439724 0.564211722 0.331367614 8.388545446 0.808536056 14.33047282 14.77827889 41.93059421 -1.622531017 3.642439724 APGLITPGS(ph)PPPAQQNQYVHISSSPQNTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 APGLITPGSPPPAQQNQYVHISSSPQNTGR 30 0 P54253 P54253 ATXN1 Ataxin-1 1 APGLIT(0.06)PGS(0.94)PPPAQQNQYVHISSSPQNTGR 84.852 4.73E-07 0 20361 32350 23248 37145 33757 32249 30311 24541 16542 28433 TRUE FALSE 19565.26961 31427.40967 27449.43075 39062.0579 34842.82456 32901.09688 30681.95509 24034.21977 14664.22151 26507.20758 0.738111306 1.185617518 1.035545923 1.473639114 1.314466054 1.241213235 1.157494805 0.90670508 0.553216383 1 14.69409708 1.62273024 3.465344041 0.764700311 1.181221191 0.373026153 0.206800541 0.186085812 5.271983479 0.12676381 0.054646367 41.94983333 -1.62273024 0.41652088 SINDPEHPLTLEELNVVEQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SINDPEHPLTLEELNVVEQVR 21 0 Q9Y3D0;J3KS95;H3BNV7 Q9Y3D0 FAM96B Mitotic spindle-associated MMXD complex subunit MIP18 0 195.13 1.19E-18 151820000 162050 158900 160410 165330 165560 170760 161680 163220 151850 178000 FALSE TRUE 155716.9068 154368.3276 189399.6553 173862.7011 170885.3878 174212.8842 163658.6882 159849.45 134612.6246 165943.9015 0.938370772 0.930244054 1.141347489 1.047719739 1.029778053 1.049829989 0.986229001 0.963274026 0.811193563 1 17.34033608 1.622953289 2.782243727 0.902950479 1.023164169 0.278057064 0.071309595 0.271812974 4.886903652 0.047821179 0.019338246 41.97138386 -1.622953289 0.12021369 TS(ph)SLDTLAAPYLAGHWPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.207)S(0.479)S(0.314)LDTLAAPYLAGHWPR 259.77 6.67E-31 224860000 126330 135960 114850 130890 134070 115770 119700 141260 152940 142030 TRUE FALSE 121392.8839 132082.5539 135605.9498 137645.2486 138382.4833 118110.9487 121164.9244 138342.9316 135578.8924 132410.1816 0.916794181 0.997525661 1.024135366 1.039536741 1.04510455 0.892008056 0.915072564 1.044805845 1.023931021 1 17.01465454 1.623028669 25 1.025774501 0.980307206 0.142728284 0.052000696 1.84826057 3040.266033 0.026291219 0.014508074 41.9786694 -1.623028669 -0.045467295 S(ph)KS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKSPFR 6 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 2 S(1)KS(1)PFR;S(1)KS(1)PFR;S(1)KS(1)PFR 70.552 0.051534 2075250000 1421690 1389660 1122650 1228457 1389540 1239490 1318210 1419120 1594040 1513120 TRUE FALSE 1366128.783 1350028.257 1325537.828 1291857.813 1434235.816 1264553.337 1334342.648 1389814.676 1413091.262 1410635.035 0.968449492 0.95703582 0.939674541 0.915798758 1.016730608 0.896442599 0.945916283 0.985240436 1.001741221 1 20.42791335 1.623104142 3.676720168 0.998890098 0.94793696 0.34650218 0.030040942 0.203903651 6.468435256 0.01748625 0.007661374 41.98596525 -1.623104142 -0.050953137 RFS(ph)EGVLQSPSQDQEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK 259.16 6.02E-27 18199900000 4418870 4465550 3771090 3180710 3784390 3782720 3543020 4706470 5613890 4577190 TRUE FALSE 4246175.675 4338196.886 4452609.85 3344866.824 3906118.341 3859209.19 3586380.539 4609279.75 4976624.743 4267172.844 0.995079372 1.016644285 1.043456643 0.783860168 0.915387889 0.904394861 0.840458231 1.080171795 1.166258065 1 22.02484912 1.623132877 6.823536658 1.096153053 0.929669948 0.415756241 0.083122795 0.118998472 11.83672889 0.04526849 0.022212246 41.9887433 -1.623132877 -0.166483105 TIDLGAAAHYTGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIDLGAAAHYTGDK 14 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 214.42 6.88E-12 873120000 1415980 1437970 1175380 1312120 1408500 1405540 1381750 1541730 1688540 1677560 FALSE TRUE 1360641.936 1396960.504 1387797.312 1379838.67 1453805.682 1433960.982 1398660.27 1509892.737 1496864.018 1563937.367 0.870010504 0.893233024 0.887373971 0.882285122 0.929580501 0.916891566 0.894319875 0.965443226 0.95711251 1 20.57675131 1.623534529 0.409318027 1.005913973 0.875822686 0.835314996 0.016386158 0.392989285 0.185716045 0.01963363 0.015508941 42.02759407 -1.623534529 -0.130091287 RREEGPPPPS(ph)PDGAS(ph)SDAEPEPPSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RREEGPPPPSPDGASSDAEPEPPSGR 26 2 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9JWF0;C9IYK2;C9JJ64;F8WCB7 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 2 RREEGPPPPS(1)PDGAS(0.544)S(0.456)DAEPEPPSGR 119.54 0.0017987 419730000 117890 130540 97901 113350 138790 147030 131690 110550 112190 110440 TRUE FALSE 113282.7285 126817.127 115593.8885 119200.0071 143254.3064 150003.0473 133301.6616 108267.1039 99454.66154 102959.8004 1.100261733 1.231714965 1.122708941 1.157733471 1.391361539 1.456908878 1.294696193 1.051547336 0.965956238 1 16.65172164 1.623577064 4.252470122 0.991034761 1.254477294 0.529770266 0.106666082 0.145348497 5.9968329 0.069126647 0.03136902 42.03171047 -1.623577064 0.263442533 KDEEVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEEVLK 7 1 O00148;O00148-2;O00148-3;K7EQN7;A0A0G2JJL7;F6QYI9;A0A0D9SEM9;A0A140T9N3;A0A140T9K2;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4;F6R6M7 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ; 97.431 0.019245 1832050000 1585070 1389600 1330110 1290650 1285600 1331400 1670120 1738800 2007260 2135910 FALSE TRUE 1523123.712 1349969.969 1570490.465 1357260.601 1326952.492 1358321.82 1690559.428 1702893.172 1779404.26 1991242.913 0.764911052 0.677953433 0.788698584 0.68161478 0.666394081 0.682147724 0.848997085 0.855191077 0.893614861 1 20.9252378 1.623708202 1.046217797 0.974434288 0.709025588 0.798402377 0.047991419 0.208207887 0.433865497 0.043045606 0.016372223 42.04440412 -1.623708202 -0.265408701 TSFSQEQSCDS(ph)AGEGSER ddPTM_BT-474_Pertuzumab_2h_R1 1 TSFSQEQSCDSAGEGSER 18 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 TSFSQEQSCDS(1)AGEGSER 389.24 1.44E-126 325400000 153420 164030 104450 162350 141050 146990 142900 144860 182250 154100 TRUE FALSE 147424.1768 159352.025 123326.4385 170728.903 145587.0013 149962.2385 144648.8529 141868.5904 161561.7441 143662.6697 1.026182912 1.109209687 0.858444568 1.188401296 1.013394792 1.043849726 1.006864575 0.987511861 1.12459099 1 17.13232571 1.623747435 0.0025649 0.024114297 2.036483629 0.001149601 0.08546389 167176.2475 440.3285842 172656.2131 172798.6962 42.04820253 -1.623747435 2.012369332 PYQYPALT(ph)PEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 PYQYPALTPEQK 12 0 P04075;J3KPS3;H3BQN4;H3BUH7;H3BR04;H3BMQ8 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 1 PYQYPALT(1)PEQK 135.58 0.00067785 0 165820 120040 113390 114930 131330 118130 122050 154930 185270 163010 TRUE FALSE 159339.5711 116616.5767 133882.0953 120861.5511 135554.3487 120518.6695 123543.6844 151730.6414 164238.9263 151969.1875 1.048499197 0.767369877 0.880981846 0.795303002 0.891985744 0.793046745 0.812952194 0.998430299 1.080738333 1 17.21341931 1.623898151 4.54328653 1.039619464 0.850286864 0.506510205 0.077567235 0.115662733 5.354439257 0.040810076 0.018778354 42.06279732 -1.623898151 -0.1893326 DVDDDGEEKELMER ddPTM_BT-474_Pertuzumab_2h_R1 2 DVDDDGEEKELMER 14 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ; 203.11 1.41E-08 851980000 722410 614210 517660 476960 615500 547560 575660 653130 767100 665020 FALSE TRUE 694177.4185 596693.3322 611212.6773 501575.9628 635298.1165 558632.0384 582705.0993 639642.6373 680022.0239 619977.6031 1.119681445 0.962443368 0.985862512 0.809022714 1.024711398 0.901051966 0.939880887 1.031718943 1.096849339 1 19.24185657 1.624122243 4.779485224 1.052783286 0.958329597 0.175596587 0.078710569 0.238555464 12.05685833 0.043028455 0.019993882 42.08450695 -1.624122243 -0.094453689 EKDECT(ph)PTRK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDECTPTRK 10 2 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.999)PT(0.001)RK 143.21 5.53E-05 2507700000 2487400 2102100 1578400 1578200 1898600 2046700 1973000 2347700 2858800 2537000 TRUE FALSE 2390189.658 2042150.166 1863651.991 1659651.091 1959670.193 2088085.676 1997146.164 2299219.175 2534281.009 2365166.73 1.010579773 0.863427572 0.787957977 0.701705749 0.828554777 0.882849251 0.844399737 0.972117164 1.071502054 1 21.17351046 1.624249101 2.737745693 1.035824395 0.837794012 0.522353409 0.075204203 0.18679032 3.24193245 0.053634896 0.02161663 42.09680166 -1.624249101 -0.198030383 GADNDGS(ph)GS(ph)ESGYTTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 GADNDGS(1)GS(0.999)ES(0.001)GYTTPK;GADNDGS(1)GS(0.963)ES(0.037)GYTTPK 237.83 4.59E-20 295260000 823180 753340 605420 602610 624820 738290 751860 887210 1000640 1044160 TRUE FALSE 791009.2155 731855.4808 714832.8615 633710.7743 644917.9027 753218.7296 761061.4876 868888.8035 887051.5422 973438.1132 0.812593225 0.751825382 0.734338272 0.651002633 0.662515566 0.773771562 0.781828323 0.892597888 0.911256227 1 19.89272974 1.624267987 1.165498748 0.981679913 0.721973256 0.807212755 0.046005294 0.197802798 0.51042859 0.043354619 0.016013618 42.09863236 -1.624267987 -0.259706657 RPEPSTLENITDDKYATVSS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPEPSTLENITDDKYATVSSPSK 23 2 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 RPEPSTLENITDDKYAT(0.001)VS(0.084)S(0.819)PS(0.096)K;RPEPSTLENITDDKYATVS(0.015)S(0.975)PS(0.01)K 243.55 1.11E-37 1444370000 1117000 955860 999020 799570 932310 994680 1032310 1194960 1455190 1352600 TRUE FALSE 1073346.405 928599.8087 1179565.137 840835.9035 962298.5979 1014793.111 1044943.719 1170283.658 1290002.932 1260987.197 0.851195323 0.736407008 0.935429907 0.666807645 0.76313114 0.804760836 0.828671156 0.928069421 1.023010332 1 20.2661222 1.624316739 1.860586235 1.014413871 0.789965864 0.634922047 0.066791821 0.192696003 1.382770207 0.050219948 0.018382996 42.10335837 -1.624316739 -0.224448007 GGAEGELQALR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGAEGELQALR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 117.53 0.0019609 254670000 317240 363600 314290 400150 346720 357320 364760 339700 327320 384500 FALSE TRUE 304841.9101 353230.484 371089.1943 420801.7895 357872.5637 364545.2552 369224.042 332685.0763 290164.0058 358457.4725 0.850426992 0.985418107 1.035239109 1.173923887 0.998368262 1.016983277 1.030035835 0.928101942 0.809479584 1 18.45144244 1.624353477 4.369820397 0.894692103 1.018328367 0.222839603 0.085369851 0.218614874 9.461787736 0.049418413 0.022568351 42.10692014 -1.624353477 0.123636264 KSEEWPDWS(ph)EPEEPENQTVNIQIWPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSEEWPDWSEPEEPENQTVNIQIWPR 26 1 Q8IZE3;Q8IZE3-2;X6RHX1 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 1 KSEEWPDWS(1)EPEEPENQTVNIQIWPR 180.48 1.32E-17 97190000 49060 48921 41262 42430 44005 47160 40336 54016 59145 55501 TRUE FALSE 47142.68096 47525.82098 48718.96127 44619.81738 45420.46079 48113.60751 40829.64403 52900.55072 52431.10756 51741.86783 0.911112856 0.918517691 0.941577166 0.862354207 0.877828008 0.92987767 0.789102631 1.022393527 1.013320735 1 15.65904451 1.625004181 10.90518835 1.013766389 0.893490073 0.645921684 0.041241556 0.057298451 19.33940647 0.019544568 0.010278884 42.17005629 -1.625004181 -0.120276317 SAYQEYDS(ph)DSDVPEELKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAYQEYDSDSDVPEELKR 18 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 SAYQEYDS(0.993)DS(0.007)DVPEELKR;SAYQEYDS(0.995)DS(0.005)DVPEELKR 203.72 7.05E-16 2225400000 1532300 1288940 1215040 1217510 1333180 1316700 1633410 1663190 1963530 2072700 TRUE FALSE 1472416.022 1252180.693 1434624.756 1280345.837 1376062.945 1343324.576 1653400.16 1628844.545 1740638.306 1932314.183 0.761996178 0.648021271 0.742438662 0.662597133 0.712132094 0.695189524 0.855658037 0.842950158 0.900805015 1 20.88189826 1.625026196 0.807562495 0.987470621 0.694092975 0.849080282 0.042087153 0.192346724 0.249167804 0.035945992 0.015417854 42.172194 -1.625026196 -0.293377646 TGGVPLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGGVPLIK 8 0 A0A0C4DH79;A0A087WWP8;Q5VWQ0-4;Q5VWQ0;A0A0C4DGT8 A0A0C4DH79 RSBN1 Round spermatid basic protein 1 0 74.255 0.041451 222170000 391680 762800 650830 1269100 1000200 1024500 846350 575040 296270 549640 FALSE TRUE 376372.7126 741045.6909 768449.4586 1334598.403 1032372.341 1045216.092 856707.8845 563165.223 262638.6717 512412.3932 0.734511338 1.446190023 1.499669931 2.604539665 2.014729454 2.039794716 1.671910937 1.099046843 0.512553317 1 18.96694584 1.625078344 3.030031964 0.76299199 1.759944578 0.414013909 0.469790362 0.212351215 4.586052558 0.323336128 0.134442095 42.17725821 -1.625078344 0.996952587 KFDEVLVNHFCEEFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFDEVLVNHFCEEFGK 16 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 235.95 6.64E-20 1334900000 2028600 1965700 1748400 1716500 2054800 2094200 2261400 2157500 2774900 2750200 FALSE TRUE 1949320.069 1909640.161 2064374.773 1805088.771 2120894.508 2136546.159 2289075.69 2112946.871 2459904.985 2563926.504 0.760287031 0.744810804 0.805161446 0.704032962 0.827205657 0.83331022 0.892800822 0.824105866 0.959428822 1 21.28992348 1.625346763 0.407626508 1.00973161 0.739270424 0.794967487 0.039987964 0.452026724 0.212389454 0.046831948 0.037175954 42.20333418 -1.625346763 -0.270461185 S(ph)LSDS(ph)ESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 S(1)LS(0.002)DS(0.998)ESDDSK 309.49 2.08E-45 489840000 1658000 1405300 1369600 1321100 1424800 1385000 1595400 1845100 2367400 2141100 TRUE FALSE 1593203.527 1365222.22 1617117.187 1389282.129 1470629.986 1413005.649 1614924.982 1806998.04 2098662.677 1996081.39 0.798165613 0.683951179 0.810145916 0.69600475 0.736758528 0.707889797 0.809047662 0.905272726 1.051391335 1 20.92873912 1.625476103 1.900819331 1.026145232 0.738429893 0.874727336 0.042954951 0.0900347 0.678833024 0.03046639 0.011204587 42.21590494 -1.625476103 -0.287715339 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(ph)PPGSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPSPPGSGR 40 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.987)PPGS(0.013)GR;LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.84)PPGS(0.16)GR 143.22 2.09E-13 346950000 656130 722230 634350 898550 918410 813540 696560 704390 622010 625350 TRUE FALSE 630487.7142 701632.7075 748991.156 944924.2732 947951.4917 829990.3362 705084.7096 689844.1003 551402.0325 582994.4875 1.081464281 1.203498013 1.284731112 1.620811677 1.626004211 1.423667554 1.209419171 1.183277227 0.945810028 1 19.15312272 1.625497559 1.661586374 0.977037744 1.378254945 0.462942182 0.164085503 0.344236454 1.907294092 0.149092781 0.053874224 42.21799065 -1.625497559 0.401217201 VCGTLLEYLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VCGTLLEYLGK 11 0 F8VWW7;Q8NCJ5 F8VWW7 SPRYD3 SPRY domain-containing protein 3 0 84.268 0.016088 277660000 420490 759950 535530 893590 721120 603780 701430 436540 276920 431430 FALSE TRUE 404056.7859 738276.9701 632312.1838 939708.287 744315.4797 615988.8453 710014.3102 427525.2964 245485.2025 402208.8618 1.004594439 1.8355562 1.572099085 2.336368927 1.850569568 1.531514851 1.765287585 1.062943503 0.6103426 1 18.61758534 1.625706168 3.425852363 0.807646163 1.725777661 0.567483905 0.326914491 0.134507877 3.72884209 0.200460836 0.086391927 42.2382745 -1.625706168 0.918131498 KIVEPEVVGES(ph)DSEVEGDAWR ddPTM_BT-474_Pertuzumab_2h_R1 1 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 KIVEPEVVGES(0.977)DS(0.023)EVEGDAWR 101.3 0.00034428 120790000 38902 40049 25197 32257 34586 35302 40992 31526 40012 33460 TRUE FALSE 37381.66683 38906.84173 29750.6584 33921.78764 35698.4901 36015.83063 41493.67236 30874.97708 35470.0055 31193.7244 1.198371389 1.247265034 0.95373858 1.087455515 1.144412563 1.15458578 1.330192953 0.989781685 1.137087866 1 14.92896819 1.625866648 25 1.04757568 1.151991592 0.220605176 0.100067728 1.478891446 2048.976015 0.047527035 0.026286681 42.25388518 -1.625866648 0.104415912 QTVEHCQYRPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QTVEHCQYRPPR 12 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 0 ; 112.43 0.00076587 191624000 118465 142911 105156 154420 135335 131051 136164 119227 104128 137840 FALSE TRUE 113835.2568 138835.3182 124160.0284 162389.6347 139688.1732 133700.941 137830.4158 116764.9208 92307.82598 128503.974 0.885850089 1.080397079 0.966196021 1.263693484 1.087033878 1.040442072 1.072577069 0.908648325 0.718326625 1 16.97145345 1.625889914 4.025158609 0.846719197 1.062503703 0.359633893 0.110963805 0.165674047 6.208498409 0.062761869 0.028182902 42.25614883 -1.625889914 0.215784507 EEKREERR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEKREERR 8 3 Q9H1J1;Q9H1J1-2;Q9BZI7-2;Q9BZI7 Q9H1J1;Q9BZI7-2 UPF3A;UPF3B Regulator of nonsense transcripts 3A;Regulator of nonsense transcripts 3B 0 86.136 0.019869 43756000 29464 35473 23162 25793 27133 31578 31964 26703 29327 27608 FALSE TRUE 28312.51431 34461.34477 27347.88864 27124.17982 28005.75759 32216.5288 32355.18499 26151.57372 25997.92191 25738.08557 1.100024096 1.338924167 1.062545564 1.053853821 1.088105699 1.251706492 1.257093691 1.016065226 1.010095403 1 14.65161713 1.625947376 7.31225268 1.007125272 1.163206234 0.391332973 0.089088764 0.13073264 15.06086797 0.04816484 0.023949512 42.26174024 -1.625947376 0.156080961 DEVQEVVYFSAADHEPESK ddPTM_BT-474_Pertuzumab_2h_R1 5 DEVQEVVYFSAADHEPESK 19 0 Q12765;Q12765-2;C9K052;B8ZZP4;C9J7U9 Q12765 SCRN1 Secernin-1 0 ;;;; 276.08 1.85E-39 3082680000 3630622 3336011 2893048 3040146 3417228 3523264 3550222 3735353 4633894 4367511 FALSE TRUE 3488733.278 3240871.233 3415886.129 3197048.299 3527146.242 3594506.812 3593670.679 3658216.655 4107873.78 4071695.59 0.856825664 0.795951259 0.838934555 0.785188438 0.866259809 0.882803425 0.882598072 0.89845043 1.008885289 1 21.95719828 1.62605481 0.725633049 1.011468161 0.822189973 0.826044088 0.029434995 0.24304775 0.26264384 0.026889664 0.012388948 42.27219606 -1.62605481 -0.189278188 WESGSLLER ddPTM_BT-474_Pertuzumab_2h_R1 3 WESGSLLER 9 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ;; 109.21 0.0057821 630130000 467720 529390 468810 565290 565030 538570 527320 523210 541100 538620 FALSE TRUE 449440.9853 514292.3155 553534.3956 594464.6846 583204.7031 549460.2544 533773.4999 512405.5307 479676.5965 502138.7876 0.895053313 1.024203523 1.102353392 1.183865296 1.161441254 1.094239816 1.062999938 1.020446027 0.955266967 1 18.93772664 1.62642534 2.406723156 0.978573248 1.083573528 0.210572571 0.075510679 0.410180818 5.330975537 0.058160049 0.022632935 42.30827708 -1.62642534 0.10500028 T(ph)T(ph)S(ph)WAKSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSWAKSK 8 1 F5H1N7 F5H1N7 KIAA1211 3 T(1)T(1)S(1)WAKSK 67.334 0.087566 775300000 906360 1331600 984920 1575200 1244900 1496900 1341100 1114200 1007900 1237200 TRUE FALSE 870938.4492 1293624.072 1162916.953 1656496.261 1284943.339 1527168.344 1357512.783 1091191.381 893487.4175 1153403.342 0.755103109 1.121571288 1.008248295 1.436181256 1.114045098 1.32405403 1.176962762 0.946062267 0.774653051 1 20.13746568 1.62646924 4.35526815 0.880536079 1.146218809 0.254953766 0.177934765 0.20965604 9.030343136 0.101551721 0.046415786 42.31255399 -1.62646924 0.26568273 IEHAPS(ph)PSSGGTLKNDK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEHAPSPSSGGTLKNDK 17 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 IEHAPS(0.812)PS(0.152)S(0.035)GGTLKNDK;IEHAPS(0.967)PS(0.027)S(0.006)GGTLKNDK 98.175 0.001143 576270000 888700 818990 568220 487640 583230 758890 654250 780380 930940 769760 TRUE FALSE 853968.6215 795633.2071 670909.994 512807.1588 601990.1226 774235.2758 662256.9072 764264.8803 825263.594 717623.4696 1.189995391 1.108705666 0.934905312 0.714590841 0.838866269 1.078887897 0.922847336 1.064994266 1.149995268 1 19.45286755 1.626620987 5.525560181 1.084858421 0.963447195 0.107106244 0.133121966 0.316740506 20.69633419 0.078684207 0.037533411 42.32734098 -1.626620987 -0.121411226 NSADGLNMFDGTDSCYFHSGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSADGLNMFDGTDSCYFHSGPR 22 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 211.43 3.30E-23 264200000 109450 126560 96543 107560 108300 115060 90441 113590 109140 98256 FALSE TRUE 105172.573 122950.6327 113990.4677 113111.1845 111783.5679 117386.592 91547.84401 111244.3268 96750.88475 91601.0336 1.148159239 1.34224067 1.244423378 1.234824325 1.220330857 1.281498553 0.999419334 1.214444013 1.056220448 1 16.48307626 1.626707629 0.54053664 1.003637604 1.261875587 0.503533133 0.079590981 0.626472904 0.430059169 0.074674697 0.044593687 42.33578622 -1.626707629 0.258237983 PTGDFDSKPSWADQVEEEGEDDKCVTSELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 PTGDFDSKPSWADQVEEEGEDDKCVTSELLK 31 2 O75821;K7ENA8;K7ER90;K7EL20;K7EL60;K7ENH0 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 187.92 9.47E-19 299310000 112170 77038 79051 57983 85485 78723 88520 100830 131930 111210 FALSE TRUE 107786.2724 74840.95167 93337.27418 60975.50958 88234.70266 80314.833 89603.33424 98747.82526 116953.8595 103677.6476 1.039628838 0.721861977 0.900264197 0.588125898 0.851048463 0.774659098 0.864249298 0.95245048 1.128052788 1 16.66174536 1.626730184 2.245696682 1.062159975 0.805722681 0.423225807 0.115029709 0.236415149 2.621303245 0.078711549 0.030072916 42.33798489 -1.626730184 -0.256437293 DMLPSPEQTLS(ph)PLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DMLPSPEQTLSPLSK 15 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 DMLPSPEQT(0.002)LS(0.998)PLSK 158.17 1.93E-06 76667000 39603 39276 39561 40368 48468 41674 36758 39847 34681 35468 TRUE FALSE 38055.27098 38155.88694 46710.55273 42451.39732 50027.01724 42516.67683 37207.8554 39024.14553 30744.15827 33065.72077 1.150897972 1.15394088 1.412657932 1.283849144 1.512957107 1.28582338 1.125269752 1.180199452 0.929789448 1 15.01304873 1.626782838 1.361245556 0.972045568 1.302140822 0.545535799 0.112998252 0.322025117 1.14851175 0.100203025 0.03621055 42.34311835 -1.626782838 0.330095254 GIPILSLDWLHQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIPILSLDWLHQSR 14 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 0 ; 216.34 6.16E-12 331450000 87776 150502 114879 165286 140289 148401 159238 119150 116897 141255 FALSE TRUE 84345.61688 146209.8303 135640.1908 173816.4303 144801.5231 151401.7699 161186.8023 116689.5109 103627.3426 131687.673 0.640497436 1.110277272 1.030014334 1.319914205 1.099582974 1.149703434 1.224008281 0.886108078 0.786917562 1 17.00676078 1.626789377 7.402415355 0.873851785 1.093017324 0.197420903 0.174505791 0.171145059 20.20869711 0.088967569 0.044365122 42.34375587 -1.626789377 0.21916554 QDENDDDDDWNPCK ddPTM_BT-474_Pertuzumab_2h_R1 4 QDENDDDDDWNPCK 14 0 Q14974;Q14974-2 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 326.01 6.65E-57 2512700000 2025790 1736590 1464000 1400010 1663290 1765260 1736490 1951610 2335420 2156910 FALSE TRUE 1946619.887 1687064.153 1728577.367 1472264.684 1716791.233 1800954.767 1757741.684 1911308.571 2070312.912 2010820.565 0.968072399 0.838992888 0.8596378 0.73217109 0.853776445 0.895631763 0.87414149 0.950511749 1.029586105 1 20.93935292 1.626876071 1.580290934 1.018954987 0.850306791 0.562808139 0.055446311 0.26302428 1.301650599 0.046301167 0.016694264 42.35220934 -1.626876071 -0.168648197 ESTESSNT(ph)TIEDEDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESTESSNTTIEDEDVK 16 0 E9PF82;E9PBG7;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;H0Y9J2 E9PF82;Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 ESTESS(0.001)NT(0.807)T(0.192)IEDEDVK 185.33 1.88E-08 285610000 676110 545490 516390 530280 542740 532900 609350 703650 809090 823960 TRUE FALSE 649686.8737 529933.1593 609713.16 557647.8143 560197.725 543675.6031 616807.4076 689119.3816 717245.4952 768152.4553 0.845778555 0.689880187 0.793739779 0.725959815 0.729279352 0.707770442 0.802975247 0.897112776 0.933728051 1 19.55103315 1.627060561 1.612085408 0.976638171 0.745572945 0.802064993 0.044262535 0.13920471 0.720421814 0.034018378 0.012280481 42.3702046 -1.627060561 -0.231065225 EFEEESKQPGVSEQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFEEESKQPGVSEQQR 16 1 O94776 O94776 MTA2 Metastasis-associated protein MTA2 0 139.04 2.45E-05 0 106680 90257 83750 78159 103780 87679 87815 102600 114050 106710 FALSE TRUE 102510.8277 87682.95873 98885.48801 82192.79536 107118.178 89451.92945 88889.70624 100481.2741 101103.5221 99482.43665 1.030441464 0.881391346 0.993999457 0.826204083 1.076754667 0.899173085 0.893521603 1.01004034 1.016295193 1 16.60215422 1.627082342 8.383176137 1.010577518 0.941772138 0.152701027 0.070791101 0.190654896 30.27817719 0.033164605 0.016863231 42.37232963 -1.627082342 -0.06880538 AAETTVVEVEEIVDIGAFAPEDIHIPQIYVHR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAETTVVEVEEIVDIGAFAPEDIHIPQIYVHR 32 0 P55809;E9PDW2 P55809 OXCT1 "Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial" 0 207.88 2.09E-27 288310000 30433 55080 41012 62047 33670 44346 58412 34715 37983 40058 FALSE TRUE 29243.64471 53509.17233 48423.78071 65249.25311 34753.02613 45242.7065 59126.86353 33998.12312 33671.32908 37344.83598 0.783070643 1.432839934 1.296666043 1.747209524 0.930597905 1.211484943 1.583267458 0.910383517 0.901632801 1 15.18862114 1.627114405 9.794425547 0.927735473 1.290332821 0.259602863 0.267328167 0.130359208 31.14763656 0.128001372 0.066617069 42.37545795 -1.627114405 0.362597347 LGMLS(ph)PEGTCK ddPTM_BT-474_Pertuzumab_2h_R1 10 LGMLSPEGTCK 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LGMLS(0.998)PEGT(0.002)CK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(0.947)PEGT(0.053)CK;LGMLS(0.892)PEGT(0.108)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK 186.14 4.36E-06 8168540000 9258990 8895830 8123710 8745710 8883020 9970770 10410960 10987230 13330810 13722020 TRUE FALSE 8897138.434 8642129.638 9591845.108 9197077.141 9168750.406 10172385.8 10538372.44 10760339.86 11817552.34 12792615.36 0.695490186 0.675556123 0.749795475 0.718936424 0.71672212 0.795176398 0.823785609 0.841136824 0.923779227 1 23.60880791 1.62723498 0.493686138 1.007272048 0.689024532 0.95607605 0.020924761 0.158867477 0.096012943 0.021807298 0.014291492 42.38722446 -1.62723498 -0.318247516 S(ph)TSGSPRPAGAKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.298)T(0.298)S(0.242)GS(0.162)PRPAGAKPK 65.467 0.030308 573460000 1601300 1512600 1273800 1194900 1215600 1459200 1334500 1623200 1885800 1712100 TRUE FALSE 1538719.426 1469462.129 1504003.996 1256568.932 1254700.878 1488706.024 1350832.01 1589680.353 1671731.89 1596137.942 0.964026595 0.920636049 0.942276952 0.78725585 0.786085491 0.932692585 0.846312825 0.995954241 1.047360536 1 20.60615391 1.627350354 4.765190643 1.02277266 0.881254906 0.510573602 0.059328664 0.130939737 6.593385837 0.035265831 0.016414317 42.3984865 -1.627350354 -0.141517754 SKGHYEVTGS(ph)DDETGK ddPTM_BT-474_Pertuzumab_2h_R1 5 SKGHYEVTGSDDETGK 16 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVTGS(1)DDETGK;SKGHYEVT(0.003)GS(0.997)DDETGK;SKGHYEVTGS(1)DDETGK;SKGHYEVTGS(1)DDETGK;SKGHYEVTGS(1)DDETGK 220.36 6.98E-15 5294290000 4399350 4421180 3985780 3879020 3513020 4125100 4253640 4843740 5687100 5388390 TRUE FALSE 4227418.538 4295092.275 4706099.109 4079216.687 3626019.479 4208512.348 4305697.319 4743715.076 5041524.25 5023429.546 0.841540326 0.855011947 0.936829922 0.8120382 0.721821506 0.837776724 0.857123063 0.944318027 1.003602062 1 22.26024121 1.627438743 2.139016418 1.002158715 0.834022936 0.658447117 0.049273235 0.18948069 1.877635853 0.040194917 0.015182892 42.40711644 -1.627438743 -0.168135779 CAGGHDDATLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 CAGGHDDATLAR 12 0 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 0 ; 194.5 3.00E-06 335320000 403830 414470 395230 439510 408860 405630 488050 390770 464260 449240 FALSE TRUE 388047.8771 402649.7214 466656.8528 462193.1638 422011.3532 413832.1165 494022.9019 382700.4629 411559.1511 418812.5747 0.926543042 0.961407908 1.114237922 1.103579959 1.007637733 0.988108146 1.179579917 0.913775006 0.98268098 1 18.67594523 1.627589554 24.99999913 0.961168824 1.039708005 0.172102116 0.074863104 1.450421024 1833.795503 0.035221744 0.019496998 42.42184509 -1.627589554 0.078539181 VDVEVPDVS(ph)LEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDVEVPDVSLEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDVEVPDVS(1)LEGPEGK 199.08 4.10E-11 27652000 54235 62019 40826 43470 52729 51718 44248 63315 76578 58963 TRUE FALSE 52115.43624 60250.27884 48204.16637 45713.49191 54425.07617 52763.77339 44789.52026 62007.52312 67885.18648 54969.38349 0.948081149 1.096069758 0.876927542 0.83161733 0.990097991 0.959875662 0.814808488 1.128037449 1.234963577 1 15.74634068 1.62759607 7.380736011 1.13936698 0.935363002 0.461897195 0.093251354 0.098692546 11.53805181 0.047605417 0.023751526 42.42248164 -1.62759607 -0.204003978 RADAGEKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 RADAGEKPK 9 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 ;; 104.22 0.0018534 492320000 884070 810630 687420 759730 831090 810650 910470 1003300 1111130 1180390 FALSE TRUE 849519.567 787511.6261 811652.0856 798939.7563 857822.7646 827041.8984 921612.6042 982581.5044 984999.1806 1100441.134 0.771980927 0.715632669 0.737569744 0.726017714 0.779526263 0.751554875 0.837493779 0.892897834 0.89509484 1 20.06965054 1.627967256 0.711900243 0.992395342 0.732603789 0.935257401 0.022465888 0.133174779 0.13937658 0.019907958 0.009309018 42.45875505 -1.627967256 -0.259791554 RKQGGS(ph)PDEPDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKQGGSPDEPDSK 13 2 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 RKQGGS(0.5)PDEPDS(0.5)K;RKQGGS(0.918)PDEPDS(0.082)K 90.561 0.0054611 262140000 417690 342800 242910 206967 292040 354060 294660 357680 449610 327980 TRUE FALSE 401366.213 333023.6796 286809.2405 217648.5917 301433.7318 361219.3358 298266.1372 350293.783 398572.1577 305765.6225 1.312659709 1.089146899 0.938003554 0.711815115 0.985832643 1.181360196 0.975473092 1.145628407 1.30352181 1 18.22206669 1.628053509 5.392896411 1.174006227 1.019183557 0.099077602 0.163913212 0.298494367 18.67211613 0.093346694 0.044401242 42.4671884 -1.628053509 -0.15482267 IIVEKPFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IIVEKPFGR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 121.83 0.00054982 5537800000 10388800 10742800 12073100 15997200 12699600 13516600 13676700 11441800 10580100 13194500 FALSE TRUE 9982794.211 10436425.86 14254977.73 16822817.41 13108094.17 13789914.91 13844079.55 11205522.83 9379091.403 12300824.76 0.811554868 0.848433017 1.158863573 1.367617028 1.065627258 1.121056123 1.125459456 0.910957033 0.762476629 1 23.55225171 1.62822745 4.960325223 0.868520509 1.078673048 0.214466768 0.157291136 0.230728246 12.45989324 0.094037766 0.044111967 42.48420047 -1.62822745 0.210152539 ALDMSYDHKPEDEVELAR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALDMSYDHKPEDEVELAR 18 1 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;;;; 276.4 2.54E-39 4949270000 3410244 3036160 2722884 2835063 3119944 3151564 3182495 3378990 3992018 3734257 FALSE TRUE 3276967.894 2949571.69 3214969.709 2981380.941 3220299.832 3215290.783 3221443.326 3309212.676 3538860.853 3481332.447 0.94129703 0.847253669 0.923488279 0.85639076 0.925019337 0.923580506 0.925347801 0.950559226 1.016524824 1 21.73120816 1.628258134 1.000096953 1.011539188 0.896065335 0.656708804 0.029484307 0.28035247 0.535240375 0.024349245 0.009425795 42.48720229 -1.628258134 -0.115473853 DLDDNLFGQHLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLDDNLFGQHLAK 13 0 O14656;A0A494BZT7;O14656-2 O14656 TOR1A Torsin-1A 0 167.73 3.14E-05 313990000 804990 893250 731380 804620 806720 822370 907470 905170 1072100 1037400 FALSE TRUE 773530.1008 867775.3846 863556.6355 846146.5346 832668.8814 838998.8848 918575.8893 886477.9232 950399.7026 967135.974 0.79981525 0.897263061 0.892900956 0.874899246 0.860963612 0.867508714 0.949789806 0.916601126 0.982695017 1 19.88335921 1.62827108 0.752652097 1.001621607 0.864047489 0.724172392 0.030040596 0.325951664 0.374063664 0.026986792 0.012126863 42.48846874 -1.62827108 -0.137574118 QEKPVNGEDKGDSGVDT(ph)QNSEGNADEEDPLGPNCYYDK ddPTM_BT-474_Pertuzumab_2h_R1 1 QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDK 38 2 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 QEKPVNGEDKGDSGVDT(0.5)QNS(0.5)EGNADEEDPLGPNCYYDK 208.9 4.04E-29 351270000 408610 299730 258470 198870 265720 302390 274690 344030 401490 366200 TRUE FALSE 392641.0695 291181.9939 305181.2786 209133.7045 274267.1251 308504.533 278051.7384 336925.6603 355914.5384 341396.9478 1.150101288 0.85291329 0.893919177 0.612582233 0.803367244 0.90365346 0.814452912 0.986902966 1.042524078 1 18.38109063 1.628314107 4.638011237 1.019012356 0.852517868 0.228581737 0.124701729 0.229142528 11.0164329 0.071620176 0.033189427 42.49267844 -1.628314107 -0.166494487 DDGSSMSFYVRPS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 3 DDGSSMSFYVRPSPAK 16 1 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 DDGSSMSFYVRPS(1)PAK;DDGSSMSFYVRPS(1)PAK;DDGSSMSFYVRPS(1)PAK 172.83 2.69E-09 2917800000 3125700 2746530 2476490 2442980 2617380 2723790 2867410 3249010 3515600 3671800 TRUE FALSE 3003544.188 2668201.654 2924046.832 2569062.491 2701570.405 2778866.9 2902502.221 3181916.808 3116523.827 3423105.715 0.877432495 0.779468084 0.854208744 0.750506325 0.789216177 0.811796985 0.847914865 0.929540912 0.910437505 1 21.70687442 1.628373703 1.174862459 0.977238581 0.805274321 0.727556304 0.03800893 0.219100617 0.574344917 0.031953582 0.011805596 42.49850991 -1.628373703 -0.17196426 TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_BT-474_Pertuzumab_2h_R1 6 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.134)T(0.866)PGGT(0.005)LFS(0.052)T(0.316)T(0.553)PGGT(0.074)R;TVAISDAAQLPHDY(0.004)CT(0.308)T(0.688)PGGT(0.009)LFS(0.245)T(0.043)T(0.703)PGGT(0.002)R;TVAISDAAQLPHDYCT(0.025)T(0.975)PGGTLFS(0.268)T(0.024)T(0.706)PGGT(0.001)R;TVAISDAAQLPHDYCT(0.039)T(0.953)PGGT(0.009)LFS(0.003)T(0.028)T(0.874)PGGT(0.094)R;TVAISDAAQLPHDYCT(0.005)T(0.976)PGGT(0.015)LFS(0.005)T(0.009)T(0.987)PGGT(0.003)R;TVAISDAAQLPHDYCT(0.147)T(0.832)PGGT(0.021)LFS(0.073)T(0.228)T(0.699)PGGTR 216.75 1.39E-34 24878840000 4501086 4590389 3537892 4606683 4774895 5129835 4163963 4576711 4598075 4469385 TRUE FALSE 4325178.583 4459475.6 4177267.784 4844434.462 4928483.834 5233563.778 4214922.825 4482200.318 4076120.803 4166669.573 1.038042136 1.070273397 1.002543569 1.16266346 1.182835295 1.256054431 1.011580772 1.075727326 0.97826831 1 21.99046326 1.628575411 1.841112514 0.99735937 1.112627206 0.263011501 0.075652729 0.478542589 3.352819272 0.063508433 0.023298725 42.51825288 -1.628575411 0.115267836 EKEEFAVPENSSVQQFK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKEEFAVPENSSVQQFK 17 1 Q9UMX0;Q9UMX0-2;Q9UMX0-4;Q9UHD9 Q9UMX0;Q9UHD9 UBQLN1;UBQLN2 Ubiquilin-1;Ubiquilin-2 0 ;; 209.73 3.66E-12 1135400000 786240 807710 771400 827408 744949 748564 928554 1073080 1305240 1316800 FALSE TRUE 755512.8716 784674.9016 910809.1397 870110.626 768910.9611 763700.477 939917.9216 1050920.523 1157074.627 1227611.963 0.615432966 0.639188054 0.741935699 0.708783111 0.626346911 0.622102505 0.765647411 0.856068982 0.942541016 1 20.22742318 1.628624215 1.450714342 0.985429888 0.662260535 0.900735994 0.041659029 0.118688724 0.485934742 0.037765199 0.013619137 42.52303116 -1.628624215 -0.323169353 HGSGTQYVSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGSGTQYVSTR 11 0 Q96B23-2;Q96B23 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 0 109.24 0.0019558 198580000 29083 39041 34149 55418 38685 36839 43261 33951 31166 38837 FALSE TRUE 27946.40421 37927.58891 40320.48394 58278.12962 39929.33816 37583.90982 43790.44106 33249.89999 27628.16634 36206.5354 0.771860768 1.047534333 1.113624474 1.609602493 1.102821292 1.038042149 1.209462341 0.918339731 0.763071253 1 15.14396251 1.628703039 5.104973471 0.869810593 1.137546701 0.217438942 0.202604472 0.219788083 12.48121982 0.115687507 0.054555063 42.53074977 -1.628703039 0.267736108 MGPAIER ddPTM_BT-474_Pertuzumab_2h_R1 1 MGPAIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 81.784 0.061099 625470000 452220 532360 464650 617470 519520 558080 520870 460510 413440 460610 FALSE TRUE 434546.7424 517177.614 548622.5911 649337.7007 536230.8326 569364.76 527244.5629 451000.3076 366508.0245 429412.4744 1.011956495 1.204384234 1.277612142 1.51215379 1.24875467 1.325915743 1.227827775 1.050272953 0.853510427 1 18.71200458 1.628852089 2.686251283 0.928919589 1.27193083 0.559884555 0.120888616 0.172649866 2.873787821 0.084755708 0.034144738 42.54534884 -1.628852089 0.343011241 KLVIPSELGYGER ddPTM_BT-474_Pertuzumab_2h_R1 2 KLVIPSELGYGER 13 1 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 ; 109.55 0.0018092 2634400000 1003800 1180480 953420 1110750 1063200 1160170 1011070 1037650 1005200 991110 FALSE TRUE 964570.3862 1146813.866 1125724.203 1168075.941 1097398.794 1183629.432 1023443.777 1016222.165 891093.9101 923981.2369 1.043928543 1.241165751 1.218340977 1.264177122 1.18768515 1.281010247 1.107645628 1.099829871 0.964406932 1 19.81750403 1.628861788 1.642467326 0.984250626 1.207971048 0.617417109 0.066694343 0.215904961 1.165535873 0.051681477 0.018707307 42.54629898 -1.628861788 0.223720422 S(ph)PYQEFTDHLVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPYQEFTDHLVK 12 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 S(1)PYQEFTDHLVK;S(1)PYQEFTDHLVK;S(0.999)PY(0.001)QEFTDHLVK 162.59 4.01E-05 301712000 254123 253473 264427 245439 260748 265245 256626 307065 344010 341554 TRUE FALSE 244191.5922 246244.1982 312214.841 258106.1362 269135.1962 270608.4356 259766.6658 300724.0004 304959.427 318420.2434 0.766884635 0.773330852 0.98051191 0.810583314 0.84522012 0.849846834 0.815798214 0.944424881 0.957726254 1 18.28057253 1.629276722 3.917282625 0.971586816 0.837920745 0.537610516 0.056736553 0.145712005 5.205896321 0.033672455 0.015066036 42.58696805 -1.629276722 -0.133666071 LEMDGHLNR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEMDGHLNR 9 0 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;G3V1E2;Q9BRK5-4;Q9BRK5-3 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 ;; 120.12 0.0007167 274210000 439580 588790 472930 606880 515070 461260 575450 520150 559200 628730 FALSE TRUE 422400.7276 571998.2857 558398.9713 638201.1495 531637.6943 470586.9932 582492.5292 509408.7207 495721.9604 586145.5571 0.720641354 0.975863894 0.952662636 1.088810009 0.907006268 0.802850056 0.993767712 0.869082286 0.84573184 1 19.16089945 1.629515546 25 0.893049434 0.925532914 0 0.103058984 4.658210323 5364.586561 0.047497115 0.02630834 42.61039359 -1.629515546 0.03248348 SVEST(ph)SPEPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVESTSPEPSK 11 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 1 SVEST(0.973)S(0.027)PEPSK 241.15 1.15E-14 597050000 911960 853930 774660 794850 812280 884360 854470 962050 1101600 1039600 TRUE FALSE 876319.595 829576.7525 914658.2942 835872.3038 838407.7239 902242.3651 864927.2595 942183.3313 976550.9863 969186.966 0.904180128 0.855951206 0.943737717 0.86244691 0.865062938 0.930927052 0.8924256 0.972137848 1.007598142 1 19.88641548 1.629708318 2.223409867 1.005439482 0.891592612 0.742492462 0.02723234 0.130328669 1.4123173 0.019121215 0.007310317 42.62931143 -1.629708318 -0.11384687 RFDTEEEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFDTEEEFK 9 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 144.77 0.00015837 296200000 230230 209990 186480 212040 221250 196330 203320 243400 287480 243780 FALSE TRUE 221232.3571 204001.2908 220181.0842 222983.4098 228366.7072 200299.9271 205808.291 238373.7049 254846.4756 227268.5635 0.973440205 0.897622125 0.96881452 0.981144978 1.004831921 0.881335826 0.905573071 1.048863518 1.121345037 1 17.79403861 1.629821827 5.549671818 1.067905268 0.945379659 0.547546973 0.046572092 0.100872022 6.644249716 0.025281524 0.012096279 42.64045472 -1.629821827 -0.122525609 ESDVPLKTEEFEVTK ddPTM_BT-474_Pertuzumab_2h_R1 4 ESDVPLKTEEFEVTK 15 1 Q969H8;M0QXF7;M0QYN0 Q969H8 MYDGF Myeloid-derived growth factor 0 ;;; 202.41 2.84E-11 1083960000 1652540 1577770 1326881 1287471 1437142 1421650 1515901 1761440 2216130 1858600 FALSE TRUE 1587956.91 1532773.544 1566677.913 1353917.533 1483368.978 1450396.737 1534453.05 1725065.648 1964564.213 1732715.367 0.916455721 0.884607809 0.904174998 0.781384848 0.856095009 0.837065778 0.8855771 0.995585127 1.133806655 1 20.72460325 1.629870092 2.918985437 1.067384869 0.862473559 0.755673155 0.047074953 0.098744144 1.970258843 0.030219461 0.012492632 42.64519379 -1.629870092 -0.20491131 SYQNS(ph)PSS(ph)DDGIRPLPEYSTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 SYQNS(0.999)PS(0.426)S(0.575)DDGIRPLPEYSTEK;SYQNS(0.999)PS(0.207)S(0.794)DDGIRPLPEYSTEK 243.75 5.04E-31 2299000000 1247840 1177190 1089560 1184160 1183520 1257910 1266450 1355190 1572010 1555920 TRUE FALSE 1199073.033 1143617.694 1286467.729 1245274.64 1221588.996 1283345.802 1281949.194 1327204.853 1393562.015 1450536.153 0.82664126 0.788410335 0.886891186 0.85849266 0.842163771 0.884738929 0.883776107 0.91497537 0.960722015 1 20.46815482 1.629898533 0.359232872 1.013525071 0.812522374 0.845939711 0.023265446 0.444777633 0.178572292 0.032533032 0.028857912 42.64798661 -1.629898533 -0.201002696 S(ph)LSGS(ph)SPCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.987)LS(0.017)GS(0.537)S(0.459)PCPK 95.273 0.011015 98650000 344150 301890 265940 287790 300890 335580 318440 334900 426850 383520 TRUE FALSE 330700.2375 293280.3928 314001.2738 302642.8764 310568.4001 342365.6575 322337.164 327984.198 378395.7775 357543.8488 0.924922184 0.820264126 0.878217525 0.84644968 0.868616258 0.957548728 0.90153184 0.917325802 1.05831992 1 18.44776066 1.630064158 0.853858642 1.022726284 0.86843498 0.619629614 0.042275329 0.368105308 0.525085687 0.037782959 0.015726405 42.66425421 -1.630064158 -0.154291304 GQDHCGIESEVVAGIPR ddPTM_BT-474_Pertuzumab_2h_R1 3 GQDHCGIESEVVAGIPR 17 0 P07858;R4GMQ5 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ;; 217.4 9.32E-18 404120000 393299 482160 412058 467590 392482 456460 418108 393870 363724 377342 FALSE TRUE 377928.4403 468409.2689 486526.0468 491722.3759 405106.54 465689.9339 423224.9308 385736.4469 322435.5764 351784.2902 1.074318697 1.331524124 1.383023803 1.397795153 1.151576552 1.323794004 1.203080815 1.096514135 0.916571846 1 18.42433153 1.630113276 1.88222614 0.957812228 1.283749748 0.622175063 0.097760636 0.198491953 1.463430521 0.075464958 0.027826743 42.66907975 -1.630113276 0.32593752 AGDEKPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 AGDEKPEK 8 1 Q8WW12;Q8WW12-2;G5E9V9;A0A0B4J1Z9 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ;; 89.247 0.012805 1602640000 2579680 2047080 1808670 1695460 1905130 1904160 1964920 2229510 2499970 2409620 FALSE TRUE 2478863.254 1988699.283 2135536.903 1782962.894 1966410.237 1942663.42 1988967.279 2183469.839 2216183.886 2246414.291 1.103475554 0.885277168 0.950642502 0.79369282 0.875355113 0.864784126 0.885396468 0.971980034 0.986542819 1 21.09919259 1.630683308 4.377519553 0.988998441 0.90186032 0.179649381 0.075864631 0.271141105 11.80650533 0.043066287 0.019765011 42.72512166 -1.630683308 -0.087138121 VGINYQPPTVVPGGDLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGINYQPPTVVPGGDLAK 18 0 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 146.47 1.66E-06 0 120960 135350 113360 124540 115420 122360 131530 142660 169430 159020 FALSE TRUE 116232.7495 131489.9505 133846.6737 130967.5243 119132.5891 124834.203 133139.7035 139714.0211 150197.0167 148249.4338 0.784035032 0.886950777 0.90284779 0.88342681 0.803595576 0.842055176 0.898079002 0.942425327 1.013137203 1 17.17766707 1.630688772 1.76307626 1.007383209 0.854625794 0.747809449 0.035851707 0.172151817 1.092090365 0.029433129 0.01075012 42.72565917 -1.630688772 -0.152757414 HADIVTTTTHK ddPTM_BT-474_Pertuzumab_2h_R1 4 HADIVTTTTHK 11 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ;;; 153.95 1.86E-05 997720000 1219370 1704730 1185200 2508690 1134610 1320140 2266360 1131310 1762420 1430650 FALSE TRUE 1171715.672 1656112.77 1399392.005 2638163.792 1171105.761 1346834.135 2294096.392 1107948.053 1562357.47 1333750.801 0.878511691 1.241695801 1.049215493 1.978003529 0.878054401 1.009809429 1.72003375 0.830700947 1.171401336 1 20.34705771 1.630731613 25 1.000764443 1.24908048 0.099856832 0.34400725 1.961231198 2138.203474 0.155031685 0.085894591 42.72987411 -1.630731613 0.248316037 ELKDDLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELKDDLK 7 1 P12429;D6RA82;D6RFG5;D6RCA8;D6RAZ8 P12429 ANXA3 Annexin A3;Annexin 0 ;; 109.21 0.0064555 2132100000 2255510 1957050 1766680 1549020 1702730 1562280 1812120 2272740 2731850 2505880 FALSE TRUE 2167362.176 1901236.85 2085958.376 1628965.108 1757499.857 1593870.372 1834297.267 2225807.125 2421741.841 2336154.516 0.927747784 0.813831807 0.892902572 0.697284832 0.752304629 0.682262394 0.785178058 0.952765371 1.036635986 1 21.15570427 1.63122816 3.485709423 1.012665907 0.787886603 0.626880562 0.072821145 0.128507873 3.688375694 0.047108239 0.0205055 42.77875686 -1.63122816 -0.224779303 IPTRPFEEGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IPTRPFEEGKK 11 2 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 86.814 0.0079809 780040000 817600 769340 635420 582590 705820 724460 697880 828780 932210 916320 FALSE TRUE 785647.2881 747399.1765 750254.5288 612657.5397 728523.3413 739109.0776 706420.8642 811665.4034 826389.4289 854256.8302 0.919685111 0.874911561 0.878254059 0.717181904 0.852815354 0.865207103 0.826942015 0.950142129 0.967378193 1 19.70431035 1.631268187 3.786429685 0.977484299 0.845824338 0.564652932 0.050493933 0.139523232 4.686281501 0.031195102 0.013867733 42.78269975 -1.631268187 -0.131659961 TEKPERPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 TEKPERPSR 9 2 Q02241;H7BYN4;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 TEKPERPS(1)R 86.772 0.010956 106010000 152720 145820 161290 155860 136770 170040 169260 180120 212480 208760 TRUE FALSE 146751.5336 141661.3564 190438.6909 163903.9533 141169.3313 173478.3253 171331.4545 176400.4591 188360.1612 194620.4993 0.754039447 0.727885073 0.978513012 0.842172093 0.725356948 0.891367179 0.880336117 0.9063817 0.9678331 1 17.57030415 1.631354271 0.687009797 1.004617369 0.80860581 0.468161873 0.071231921 0.627563781 0.61924482 0.068741765 0.033077335 42.79118081 -1.631354271 -0.196011558 KSPLSWIEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPLSWIEEK 10 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 127.17 0.00058218 1984260000 3933200 3736000 3185400 3356900 3580500 3822500 3711500 3979500 4538600 4381800 FALSE TRUE 3779486.196 3629452.938 3761072.639 3530150.011 3695670.034 3899793.569 3756922.447 3897321.934 4023397.155 4085016.783 0.925207018 0.888479321 0.920699434 0.864170259 0.90468907 0.954657906 0.919683479 0.954052857 0.984915698 1 21.96191057 1.631489207 0.733271492 1.00177449 0.900018461 0.729056926 0.020813684 0.318810531 0.34991608 0.01910923 0.008755589 42.80447816 -1.631489207 -0.10175603 AQNDLIWNIKDELK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQNDLIWNIKDELK 14 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 225.32 2.57E-12 1337570000 2412500 2317400 2135410 1929930 2222300 2352800 2337400 2697000 3276000 2970200 FALSE TRUE 2318216.833 2251310.021 2521326.089 2029533.919 2293782.298 2400375.228 2366005.8 2641306.008 2904122.214 2769025.708 0.83719585 0.813033268 0.910546291 0.732941523 0.828371615 0.866866357 0.854454256 0.953875581 1.048788462 1 21.40094702 1.631508192 1.973148354 1.026649196 0.829883604 0.7613536 0.04383079 0.138112585 1.135585331 0.03260643 0.012147356 42.80634938 -1.631508192 -0.196765592 HLSVNDLPVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLSVNDLPVGR 11 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ; 199.19 5.11E-08 672270000 156111 299460 208814 455450 195774 247913 301250 194813 167691 209634 FALSE TRUE 150010.0095 290919.694 246551.3348 478955.8291 202071.2485 252925.9707 304936.7876 190790.0435 148655.4207 195435.3025 0.767568641 1.488572895 1.261549637 2.450712963 1.033954695 1.294167264 1.560295319 0.976231219 0.760637504 1 17.57633157 1.63159093 4.876102415 0.878185005 1.425983045 0.229716797 0.416537052 0.217125182 11.40011934 0.228269825 0.107000951 42.81450531 -1.63159093 0.547798041 RREEEGLQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RREEEGLQLR 10 2 C9JYI4;P52294;C9J352;C9JWD9;F2Z3G4;C9J4U1 C9JYI4 KPNA1 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed" 0 ;;; 209.21 5.60E-08 1654300000 398833 489847 346037 406305 418207 434463 437378 407033 426236 438933 FALSE TRUE 383246.1654 475877.0432 408573.5835 427274.4497 431659.008 443248.1395 442730.7628 398627.6263 377851.4762 409203.6769 0.936565791 1.162934426 0.998460196 1.044160827 1.054875682 1.083196864 1.081932514 0.974154556 0.923382407 1 18.64245958 1.631661608 5.256765633 0.9580468 1.05478449 0.315066824 0.057912269 0.150944633 9.032371671 0.029057062 0.013798433 42.82147357 -1.631661608 0.09673769 AKSDESIKEEDKDQDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKSDESIKEEDKDQDEK 17 3 P26358;P26358-2;K7ENQ6 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 68.82 0.015801 104710000 333450 188260 177630 113080 195950 190490 191020 246620 310320 249350 FALSE TRUE 320418.4054 182891.0091 209731.6924 118916.0724 202252.9097 194341.8383 193357.7599 241527.2108 275093.7746 232461.3024 1.378373097 0.786758945 0.902221962 0.511552121 0.8700498 0.836018022 0.831784722 1.038999646 1.183395996 1 17.82663105 1.631691927 4.173800361 1.096824359 0.8561738 0.166332979 0.204233742 0.270340045 10.83183545 0.115801435 0.05265846 42.82446308 -1.631691927 -0.240650558 AKIELLGSYDPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKIELLGSYDPQK 13 1 P24666;P24666-3;P24666-2 P24666;P24666-2 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ; 91.207 0.0060537 851800000 2241300 2012700 1501550 1582920 1777880 1909500 1853330 2008210 2424600 1954670 FALSE TRUE 2153707.518 1955299.767 1772913.487 1664614.691 1835067.125 1948111.398 1876011.607 1966739.762 2149369.573 1822278.46 1.181876187 1.072997245 0.972910302 0.91347987 1.007017953 1.06905253 1.029486793 1.079275097 1.179495681 1 20.797312 1.631710907 4.215435931 1.100907751 1.029864616 0.076291767 0.077638025 0.364603055 14.86735568 0.046328017 0.021111837 42.82633467 -1.631710907 -0.071043135 DGKLDKDEIR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGKLDKDEIR 10 2 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ;; 91.937 0.0055168 1670160000 4341110 4040690 3187840 3411250 3612110 3726260 3820910 4311330 5223500 4515060 FALSE TRUE 4171454.622 3925453.477 3763953.601 3587305.021 3728296.799 3801607.53 3867671.44 4222299.529 4630550.179 4209250.965 0.991020649 0.932577675 0.894209833 0.852243084 0.885738776 0.90315535 0.918850283 1.003099973 1.10008888 1 22.0051321 1.631757544 3.042855475 1.051083641 0.906923299 0.665077171 0.04082353 0.122548239 2.670771447 0.026913617 0.011285617 42.83093387 -1.631757544 -0.144160342 IDGATQS(ph)SPAEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDGATQSSPAEPK 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 IDGATQS(0.5)S(0.5)PAEPK 178.68 4.95E-07 0 156610 148960 140270 132030 150700 191390 170260 183060 255130 244370 TRUE FALSE 150489.5081 144711.8066 165619.9093 138844.0841 155547.4024 195260.0369 172343.6928 179279.747 226168.712 227818.6022 0.660567252 0.635206279 0.7269815 0.609450162 0.682768663 0.857085572 0.75649526 0.786940773 0.992757877 1 17.79752603 1.63175874 0.538528823 1.016030012 0.648399892 0.791988582 0.060497361 0.364605961 0.248553492 0.061651256 0.037034338 42.83105187 -1.63175874 -0.36763012 SPPVLGSAAAS(ph)PVHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPVLGSAAASPVHLK 16 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 SPPVLGS(0.13)AAAS(0.87)PVHLK 73.294 0.022847 144560000 78048 83716 70751 82584 65266 71919 72318 85812 95691 88852 TRUE FALSE 74997.79787 81328.50165 83537.27955 86846.17014 67365.34016 73373.25146 73203.04932 84039.95221 84828.55885 82833.9749 0.905398998 0.981825413 1.008490534 1.048436589 0.813257365 0.885786919 0.883732181 1.014558969 1.024079298 1 16.337935 1.632034468 7.92563833 1.015324348 0.93552061 0.244986353 0.06447094 0.184421758 24.69867233 0.035656322 0.01808888 42.85825335 -1.632034468 -0.079803737 KSST(ph)PEEVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSSTPEEVKK 10 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KSS(0.214)T(0.786)PEEVKK;KS(0.156)S(0.156)T(0.688)PEEVKK 185.57 6.84E-05 854200000 2158560 1748970 1643730 1246970 1735370 1798890 1672880 2160280 2657030 2226270 TRUE FALSE 2074201.089 1699091.088 1940788.576 1311326.271 1791189.752 1835264.788 1693353.206 2115669.463 2355415.094 2075482.75 0.999382476 0.818648619 0.935102243 0.631817475 0.863023194 0.884259235 0.815884018 1.019362586 1.134875775 1 20.98501551 1.632063614 4.221352046 1.070008973 0.845397376 0.488162132 0.095102456 0.132194705 5.404690256 0.053129917 0.024225092 42.8611297 -1.632063614 -0.224611597 LIGEPDLVVSVIPNNS(ph)NENIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIGEPDLVVSVIPNNSNENIPR 22 0 A0A0A0MSU3;Q9H9A7 A0A0A0MSU3 RMI1 RecQ-mediated genome instability protein 1 1 LIGEPDLVVSVIPNNS(1)NENIPR;LIGEPDLVVSVIPNNS(1)NENIPR 78.088 0.0058492 36001000 32842.6 36919 34442.3 32601.4 34613.7 41155 39006.4 33012.9 30105.6 41677 TRUE FALSE 31559.07488 35866.10627 40666.78977 34283.96216 35727.0811 41987.1823 39483.77199 32331.17208 26688.1385 38854.17967 0.812244015 0.923095188 1.046651612 0.882375138 0.919517061 1.080634893 1.016203979 0.832115679 0.686879474 1 15.24578218 1.632198682 6.367709451 0.816476429 0.957089738 0.197081708 0.103184786 0.173676344 14.75973834 0.053275752 0.026097709 42.87446188 -1.632198682 0.140613309 AVPMAPAPAS(ph)PGSSNDSSAR ddPTM_BT-474_Pertuzumab_2h_R1 7 AVPMAPAPASPGSSNDSSAR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(0.805)PGS(0.164)S(0.03)NDSSAR;AVPMAPAPAS(0.898)PGS(0.085)S(0.017)NDSSAR;AVPMAPAPAS(0.999)PGS(0.001)SNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(0.998)PGS(0.001)SNDSSAR 372.51 3.49E-112 1671670000 3742888 3892338 3274893 3696778 3560317 3660042 3436024 3416051 3498076 3184032 TRUE FALSE 3596611.799 3781332.331 3866739.015 3887569.156 3674837.83 3734050.557 3478075.09 3345508.353 3100989.078 2968374.677 1.211643472 1.273872992 1.302645197 1.309662552 1.237996624 1.257944486 1.171710269 1.127050564 1.044675762 1 21.50124177 1.632215149 0.974370704 0.999988932 1.275021539 0.922554278 0.028217251 0.125876479 0.228541562 0.025507279 0.009989451 42.87608759 -1.632215149 0.275032607 SKEGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_BT-474_Pertuzumab_2h_R1 13 SKEGHSLEMENENLVENGADSDEDDNSFLK 30 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK 411.74 5.69E-175 19055730000 4565787 4515199 3393573 3335544 3849534 4220067 4010956 4236342 4750877 4406041 TRUE FALSE 4387350.996 4386429.945 4006867.131 3507691.826 3973357.757 4305399.646 4060043.279 4148860.057 4211577.36 4107615.919 1.068101566 1.067877336 0.975472685 0.853948347 0.967314821 1.048150492 0.988418431 1.010040895 1.025309436 1 21.96986986 1.632378725 4.606735744 1.014197824 0.993108614 0.014113983 0.059108225 0.934248044 44.48542598 0.036769996 0.01706582 42.89223973 -1.632378725 -0.021089211 TTQIPQWCVEYMR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTQIPQWCVEYMR 13 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 131.26 1.48E-05 229690000 191741 186166 149064 182071 159382 159595 175243 187371 216432 194565 FALSE TRUE 184247.5497 180856.728 176003.1807 191467.7061 164508.6668 162822.1202 177387.6763 183501.7234 191863.5467 181386.9392 1.015770763 0.997076905 0.970318929 1.055576035 0.906948799 0.89765074 0.977951759 1.011658966 1.057758334 1 17.46871105 1.632419484 3.713584042 1.030028782 0.972739425 0.195454411 0.045845774 0.300562951 9.738734026 0.02894137 0.012817544 42.89626548 -1.632419484 -0.057289357 RGT(ph)SPRPPEGGLGYSQLGDDDLK ddPTM_BT-474_Pertuzumab_2h_R1 3 RGTSPRPPEGGLGYSQLGDDDLK 23 2 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 RGT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK;RGT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK;RGT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK 196.55 1.49E-22 1381060000 952130 791080 927020 934620 953480 916960 1068020 1199710 1408550 1437800 TRUE FALSE 914919.707 768519.1729 1094553.135 982855.8502 984149.5501 935501.5595 1081090.748 1174935.569 1248657.309 1340416.525 0.682563733 0.573343553 0.816576873 0.733246593 0.734211741 0.697918551 0.806533438 0.876545124 0.931544252 1 20.35424995 1.632457339 0.82140196 1.003405524 0.69520535 0.773890353 0.057391813 0.269122064 0.358282215 0.05349397 0.022776733 42.90000463 -1.632457339 -0.308200174 TLEGELHDLR ddPTM_BT-474_Pertuzumab_2h_R1 9 TLEGELHDLR 10 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;; 248.45 7.94E-13 46247230000 14476010 15655781 11992493 15228386 14626687 13109109 14587206 13815111 14056436 14858353 FALSE TRUE 13910271.53 15209293.45 14159803.26 16014324.83 15097167.67 13374184.17 14765728.59 13529824.13 12460808.31 13851983.52 1.004207918 1.097986684 1.022222069 1.15610337 1.089892119 0.965506792 1.065964926 0.976742725 0.89956852 1 23.72358924 1.632586941 3.568134174 0.946042054 1.0594569 0.405763583 0.05504611 0.17661353 5.304540787 0.0330107 0.014475369 42.91280876 -1.632586941 0.113414845 RPSGPDGAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSGPDGAAR 10 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C528 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 0 ; 123.67 0.0037497 36684000 126012 128061 99053 135307 123997 113874 141593 112607 135259 129454 FALSE TRUE 121087.3117 124408.8257 116954.0805 142290.2105 127985.4761 116176.6103 143325.8575 110281.6261 119904.9654 120685.9653 1.003325544 1.030847501 0.969077724 1.179012076 1.06048351 0.962635631 1.187593414 0.913789983 0.99352866 1 16.88089839 1.63271203 24.99999999 0.965256786 1.052956616 0.217301681 0.075415974 1.17402093 1177.584774 0.033745528 0.01870242 42.92517063 -1.63271203 0.08769983 IQEY(ph)IIAFAKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQEYIIAFAKEK 12 1 V9GZ60;P31513 V9GZ60 FMO3 Dimethylaniline monooxygenase [N-oxide-forming] 3 1 IQEY(1)IIAFAKEK 63.727 0.082184 2404800000 1962500 3797200 4098100 3528900 4976700 6277400 4302300 2340800 1001300 2184500 TRUE FALSE 1885803.33 3688907.574 4838717.832 3711026.952 5136780.075 6404333.329 4354952.834 2292461.662 887636.6218 2036541.869 0.925983089 1.811358573 2.375948123 1.822219817 2.522305165 3.144709876 2.138405746 1.125663899 0.435854836 1 20.95769004 1.633340864 3.621788425 0.736707742 2.151158333 0.522789765 0.554698699 0.150255941 4.644255118 0.352625323 0.155324557 42.98736888 -1.633340864 1.414450591 IGTDIQDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 IGTDIQDNK 9 0 P14324-2;P14324;A0A087X090 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 101.9 0.0085444 181610000 163200 155740 138900 142690 153220 159110 162610 162920 196870 184910 FALSE TRUE 156821.9636 151298.4477 164002.3198 150054.248 158148.4605 162327.3132 164600.0698 159555.6451 174522.1429 172385.881 0.909714663 0.877673083 0.951367472 0.870455557 0.91740959 0.941650861 0.954834983 0.925572583 1.012392325 1 17.39528209 1.633425826 0.612650761 1.005731789 0.901827884 0.623245302 0.027033759 0.472892025 0.389745578 0.02502156 0.013283393 42.99577942 -1.633425826 -0.103903905 ATIS(ph)DEEIER ddPTM_BT-474_Pertuzumab_2h_R1 4 ATISDEEIER 10 0 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 1 ATIS(1)DEEIER;ATIS(1)DEEIER;ATIS(1)DEEIER;ATIS(1)DEEIER 233.13 4.89E-12 7511450000 1605140 1704680 1438380 1450020 1592580 1628670 1546430 1520820 1530620 1534830 TRUE FALSE 1542409.354 1656064.195 1698327.263 1524855.706 1643806.782 1661602.823 1565355.673 1489414.536 1356870.434 1430874.597 1.07794866 1.15737899 1.186915517 1.065680884 1.148812611 1.161249789 1.093985228 1.040911998 0.948280469 1 20.44846581 1.633690601 2.127160073 0.975467627 1.133439183 0.729636925 0.038131204 0.13849869 1.355021577 0.027418591 0.010411154 43.02200048 -1.633690601 0.157971556 RRS(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_BT-474_Pertuzumab_2h_R1 3 RRSLEPAENVHGAGGGAFPASQTPSKPASADGHR 34 3 P12931;P12931-2 P12931 SRC Proto-oncogene tyrosine-protein kinase Src 1 RRS(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;RRS(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;RRS(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR 201.31 2.48E-27 2451725000 817550 1155002 629881 949537 795216 988913 906780 825725 904746 783516 TRUE FALSE 785599.2422 1122062.474 743714.5083 998542.7184 820794.8448 1008909.498 917877.4449 808673.4902 802043.0271 730447.7634 1.075503659 1.536129659 1.018162483 1.367028237 1.123687259 1.3812206 1.256595599 1.107092842 1.098015583 1 19.47842158 1.633920822 3.025380208 1.059275987 1.258298321 0.247249377 0.147803068 0.285004812 6.135636948 0.086018177 0.036093688 43.04481268 -1.633920822 0.199022334 KYPYVEVNSILGIDSAYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYPYVEVNSILGIDSAYDR 19 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 139 6.85E-07 460450000 508490 648490 547360 525710 547030 630380 582250 573990 611210 597380 FALSE TRUE 488617.6486 629995.7001 646280.128 552841.9561 564625.7167 643126.7155 589375.7497 562136.9059 541828.0032 556918.9205 0.877358679 1.131216191 1.160456404 0.992679429 1.013838273 1.154794157 1.058279272 1.009369381 0.972902847 1 19.08710778 1.634472785 3.597823864 0.988024453 1.062298959 0.108820826 0.080476713 0.390203591 11.91085455 0.047889102 0.021080484 43.09955486 -1.634472785 0.074274506 GT(ph)EANGKKPS(ph)QQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTEANGKKPSQQK 13 2 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 2 GT(1)EANGKKPS(1)QQK 73.848 0.067508 531800000 260850 201510 216520 242200 213960 178750 243660 290550 375550 329240 TRUE FALSE 250655.6936 195763.1321 255649.9805 254699.971 220842.2177 182364.4475 246641.984 284550.041 332919.1384 306940.2815 0.81662691 0.63778899 0.83289811 0.829803015 0.719495716 0.594136575 0.803550393 0.927053431 1.084638148 1 18.22759847 1.63447653 2.555738594 1.036872926 0.74009018 0.705635088 0.078350319 0.132451763 1.971867545 0.05456894 0.02180217 43.09992655 -1.63447653 -0.296782746 FVDILGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVDILGLR 8 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 96.253 0.021106 35306000 97984 105930 92092 109990 117380 106940 106720 106020 109750 112050 FALSE TRUE 94154.67695 102908.9801 108735.073 115666.5971 121155.6343 109102.4001 108026.0713 103830.65 97291.64011 104460.7537 0.901340203 0.985144913 1.040917944 1.107273239 1.159819645 1.044434357 1.03413069 0.993968034 0.931370267 1 16.67260149 1.634499038 2.912876097 0.964816538 1.045103161 0.167127575 0.066206104 0.394727506 7.838384453 0.047118186 0.019566205 43.10216036 -1.634499038 0.080286623 EGVKFDESEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGVKFDESEK 10 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 117.09 0.00091531 2225030000 6440300 6288300 4631100 4324800 4823300 5666200 5422100 6198200 7664700 6177600 FALSE TRUE 6188605.956 6108963.841 5468042.788 4548003.446 4978445.825 5780774.446 5488457.282 6070205.004 6794635.389 5759185.65 1.074562678 1.060733967 0.949447217 0.789695579 0.864435725 1.003748585 0.952991901 1.054004051 1.179790999 1 22.4574334 1.634681739 3.631479396 1.097251854 0.951764166 0.280673882 0.089507428 0.24049799 7.473158923 0.058070706 0.025627205 43.12029652 -1.634681739 -0.145487688 MGVMSS(ph)PTENSFTLDADF ddPTM_BT-474_Pertuzumab_2h_R1 5 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.007)S(0.832)PT(0.16)ENSFTLDADF;MGVMS(0.084)S(0.737)PT(0.179)ENSFTLDADF;MGVMS(0.008)S(0.833)PT(0.159)ENSFTLDADF;MGVMS(0.008)S(0.834)PT(0.157)ENSFTLDADF;MGVMS(0.02)S(0.702)PT(0.278)ENSFTLDADF 230.14 5.05E-19 253950000 247146 286789 215642 317906 317117 252098 259745 230606 173002 221114 TRUE FALSE 237487.2611 278610.0585 254613.3063 334313.1668 327317.3563 257195.5943 262923.837 225843.9055 153363.5382 206137.7518 1.152080388 1.351572218 1.235160974 1.621794959 1.587857408 1.247687976 1.275476397 1.095597015 0.743985693 1 17.65324922 1.634731198 1.923146472 0.872926563 1.376532428 0.616975674 0.153103026 0.205117113 1.589441649 0.121821384 0.045295308 43.12520748 -1.634731198 0.503605866 TDDIPVWDQEFLK ddPTM_BT-474_Pertuzumab_2h_R1 4 TDDIPVWDQEFLK 13 0 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;; 208.72 1.02E-07 259060000 555400 517225 496380 498934 490937 498200 541394 644110 722240 744560 FALSE TRUE 533694.354 502474.2494 586086.9079 524684.0435 506728.4345 508273.9453 548019.7417 630808.9034 640254.3431 694130.288 0.768867694 0.723890397 0.844347118 0.755886975 0.730019196 0.732245738 0.789505589 0.908775938 0.922383527 1 19.40484696 1.634737997 1.848588138 0.967412127 0.758676317 0.847597667 0.035776972 0.118547657 0.838557092 0.028480333 0.010514326 43.12588268 -1.634737997 -0.20873581 KADIDLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KADIDLTK 8 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 97.456 0.013178 1605600000 2399200 2360100 2204800 1946800 2229300 2318300 2312100 2685200 3027400 2983100 FALSE TRUE 2305436.612 2292792.259 2603256.406 2047274.581 2301007.459 2365177.614 2340396.171 2629749.682 2683742.244 2781051.98 0.828980051 0.824433443 0.93606895 0.736151139 0.827387433 0.850461491 0.841550675 0.9455953 0.965009738 1 21.40719928 1.63478503 1.887664497 0.987556874 0.832211162 0.651354476 0.045881019 0.192657712 1.43008772 0.034893758 0.012929731 43.13055337 -1.63478503 -0.155345713 RNS(ph)GSSLVSSSSASSNLSHLEEDSWILWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSGSSLVSSSSASSNLSHLEEDSWILWGR 30 1 O60447-2;O60447 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 1 RNS(0.761)GS(0.098)S(0.14)LVSSSSASSNLSHLEEDSWILWGR;RNS(0.391)GS(0.304)S(0.304)LVS(0.001)S(0.001)SSASSNLSHLEEDSWILWGR 153.01 7.40E-09 79004000 48884 66632 57609 90048 72259 77670 74684 59202 53027 66678 TRUE FALSE 46973.55924 64731.7206 68020.22781 94695.38807 74583.27636 79240.54062 75598.00513 57979.45801 47007.59727 62161.83967 0.755665525 1.041341777 1.094244124 1.523368494 1.199824149 1.274745745 1.216148131 0.932717859 0.756213097 1 15.92374158 1.634817506 4.56257085 0.869279292 1.170698645 0.28282002 0.190725642 0.201233907 9.43591462 0.112486733 0.052200697 43.13377875 -1.634817506 0.301419353 EFGGGHIKDEVFGTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFGGGHIKDEVFGTVK 16 1 Q12792;Q12792-3;Q12792-4;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 ; 217.37 8.60E-15 961620000 2743200 2432200 2176800 2050100 2558600 2431800 2599500 2893000 3360700 3311100 FALSE TRUE 2635992.711 2362836.037 2570196.183 2155905.907 2640899.693 2480972.662 2631313.459 2833258.539 2979207.425 3086836.248 0.853946403 0.765455582 0.832631204 0.698419266 0.855536051 0.803726684 0.85243053 0.917851908 0.965132967 1 21.55769752 1.634860001 1.084879129 0.999593652 0.794434671 0.744930862 0.043084492 0.215971881 0.482151319 0.035381615 0.013373962 43.1379995 -1.634860001 -0.205158981 HFNYPST(ph)PPSER ddPTM_BT-474_Pertuzumab_2h_R1 1 HFNYPSTPPSER 12 0 Q9BX63;Q9BX63-2 Q9BX63 BRIP1 Fanconi anemia group J protein 1 HFNYPS(0.206)T(0.792)PPS(0.002)ER 82.007 0.05929 239050000 130100 134430 107890 127720 121750 119110 138410 108460 99252 136140 TRUE FALSE 125015.5482 130596.188 127388.123 134311.6445 125666.1993 121518.4858 140103.903 106220.2631 87985.32906 126919.1165 0.985001721 1.02897177 1.003695318 1.058245977 0.990128223 0.957448248 1.103883377 0.836913036 0.693239375 1 16.95354986 1.635236672 6.4986188 0.819970777 1.015683455 0.496444359 0.079698843 0.089200479 7.844859481 0.038311814 0.018878961 43.17542999 -1.635236672 0.195712678 IDWPVGSPATIHYPALDGHLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDWPVGSPATIHYPALDGHLSR 22 0 O15498;O15498-2 O15498 YKT6 Synaptobrevin homolog YKT6 0 ; 187.19 1.69E-17 824530000 219891 261543 188009 282386 226218 209301 277626 190401 217494 191522 FALSE TRUE 211297.4166 254084.0497 221986.4085 296959.9753 233494.5074 213533.2096 281023.67 186469.1528 192804.9929 178550.0443 1.183407248 1.42304109 1.243272772 1.66317503 1.307725844 1.195929188 1.573921032 1.044352319 1.079837273 1 17.44596897 1.635396498 7.759626746 1.043313529 1.368641335 0.508101155 0.14802675 0.09302039 11.6421146 0.071973458 0.036526999 43.19132212 -1.635396498 0.325327807 EKYDTDFYILDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKYDTDFYILDK 12 1 P14868;P14868-2 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 108.17 0.0015822 514410000 193030 183360 181290 193430 182350 181680 177660 220730 244650 239110 FALSE TRUE 185486.1742 178130.7523 214053.1358 203412.9455 188215.4534 185353.6941 179834.2562 216171.8484 216878.3577 222914.8667 0.832094229 0.799097678 0.96024612 0.912514039 0.844337823 0.831499921 0.806739626 0.969750701 0.972920115 1 17.76613331 1.635619874 6.029063832 0.981523848 0.858239229 0.605663805 0.046464069 0.101959927 7.794424045 0.026618334 0.012962638 43.21354295 -1.635619874 -0.123284619 DSENT(ph)PVKGGTVADLDEQDEETVTAGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSENTPVKGGTVADLDEQDEETVTAGGK 28 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 DS(0.01)ENT(0.915)PVKGGT(0.076)VADLDEQDEETVTAGGK 110.78 0.0010186 138490000 55344 46753 43258 36392 33958 46586 43137 54562 61703 61996 TRUE FALSE 53181.09529 45419.65022 51075.68287 38270.19548 35050.28991 47528.00084 43664.92351 53435.27563 54698.73412 57796.9557 0.920136617 0.785848487 0.883708878 0.662148984 0.606438341 0.822327063 0.755488295 0.924534432 0.946394727 1 15.81870588 1.635658777 3.080900623 0.967395534 0.771073764 0.466705613 0.088872042 0.198337447 4.435545694 0.05951275 0.025149632 43.21741408 -1.635658777 -0.196321771 ALPSLNTGSSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALPSLNTGSSSPR 13 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 ALPSLNTGSS(0.002)S(0.998)PR;ALPS(0.003)LNT(0.007)GS(0.08)S(0.231)S(0.678)PR;ALPSLNTGSSS(1)PR;ALPSLNTGSS(0.001)S(0.999)PR;ALPSLNTGS(0.001)S(0.192)S(0.807)PR;ALPSLNTGSS(0.039)S(0.961)PR 198.04 1.35E-07 56729540000 15684460 16388360 13742870 18011800 16517080 17263270 16664580 15993240 16350780 17125380 TRUE FALSE 15071493.96 15920980.02 16226512.32 18941391.16 17048366.88 17612345.15 16868526.11 15662974.01 14494708 15965462.76 0.944006083 0.997213815 1.016350892 1.186397879 1.067827919 1.103152813 1.056563557 0.981053556 0.907878977 1 23.92845103 1.635780393 3.776051842 0.951616406 1.057218169 0.294629565 0.064323462 0.226165218 7.566281254 0.040369288 0.018003666 43.22951794 -1.635780393 0.105601763 LGVADIIDCVVLTSS(ph)PEATETSQQLQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.004)S(0.173)S(0.822)PEATETSQQLQLR 160 5.76E-12 31798000 20759 20053 15087 18482 17369 19989 18857 17846 16620 20778 TRUE FALSE 19947.71533 19481.10807 17813.55651 19435.85823 17927.68966 20393.19128 19087.77761 17477.47386 14733.36728 19370.68755 1.029788709 1.005700392 0.919614054 1.003364397 0.925506109 1.052786135 0.985394946 0.902263991 0.760601152 1 14.24158754 1.636325459 4.16331467 0.867018185 0.98737577 0.323764735 0.066596662 0.167609839 6.699196985 0.035746664 0.016303602 43.28380766 -1.636325459 0.120357586 EENKGGEDKLK ddPTM_BT-474_Pertuzumab_2h_R1 4 EENKGGEDKLK 11 2 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 100.55 0.0022176 7022730000 7468760 5486560 5387170 4068040 5245830 5153760 5943410 6786070 9184830 7129870 FALSE TRUE 7176872.602 5330088.681 6360751.456 4277992.032 5414566.886 5257972.558 6016147.229 6645935.283 8142206.604 6646957.554 1.079722947 0.801883965 0.956941789 0.643601527 0.814593269 0.791034472 0.905097886 0.999846205 1.224952399 1 22.66426271 1.636393368 2.580182724 1.112282855 0.842374059 0.428178112 0.11978582 0.209994781 3.193031463 0.07897516 0.031710147 43.29057636 -1.636393368 -0.269908796 FIIHAPPGEFNEVFNDVR ddPTM_BT-474_Pertuzumab_2h_R1 6 FIIHAPPGEFNEVFNDVR 18 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ;;;;; 179.46 8.36E-14 4314337000 1417358 1562482 1287827 1507496 1459884 1551635 1476363 1462548 1546827 1501058 FALSE TRUE 1361966.082 1517921.543 1520565.986 1585298.049 1506842.495 1583010.123 1494431.172 1432345.873 1371237.684 1399390.005 0.973256975 1.08470229 1.086592002 1.132849344 1.076785235 1.131214399 1.06791614 1.023550167 0.979882434 1 20.41636666 1.636576403 2.667752327 0.991785302 1.084291996 0.435226076 0.041656524 0.213616159 3.499180668 0.028022758 0.011365192 43.30882516 -1.636576403 0.092506694 GVKPVFSIGDEEEYDT(ph)DEIDSSSMSDDDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 GVKPVFSIGDEEEYDTDEIDSSSMSDDDRK 30 2 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 GVKPVFSIGDEEEYDT(1)DEIDSSSMSDDDRK 175.67 1.38E-11 141840000 71316 55126 57799 52937 63828 60676 58218 73265 90017 71241 TRUE FALSE 68528.89188 53553.86045 68244.56503 55669.08491 65881.08559 61902.91029 58930.4893 71752.05215 79798.64754 66415.78362 1.031816357 0.806342371 1.027535344 0.838190591 0.991949233 0.932051192 0.887296454 1.080346391 1.201501258 1 16.01923852 1.636969383 5.062989163 1.112435397 0.928882255 0.442191756 0.083761758 0.115656066 6.497071251 0.041330842 0.019573433 43.34803172 -1.636969383 -0.183553142 AGDWQCPNPGCGNQNFAWR ddPTM_BT-474_Pertuzumab_2h_R1 5 AGDWQCPNPGCGNQNFAWR 19 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2 B0QYK0 EWSR1 RNA-binding protein EWS 0 ;;;; 242.07 5.03E-24 757960000 357958 398368 309640 391701 370780 409476 398547 355078 359797 397760 FALSE TRUE 343968.6056 387006.9347 365598.8359 411916.7356 382706.4754 417755.8853 403424.5374 347745.5152 318954.353 370819.3609 0.927590741 1.043653529 0.985921649 1.110828557 1.032056348 1.126575172 1.087927384 0.937776049 0.860134034 1 18.50035705 1.637030871 5.657289672 0.920619819 1.047488072 0.393424624 0.063549582 0.129603283 8.833931178 0.03374516 0.016281432 43.35416946 -1.637030871 0.126868253 KLDDDSDS(ph)PSFFEEKPEEPVVLALDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDDDSDSPSFFEEKPEEPVVLALDPK 27 2 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 KLDDDS(0.125)DS(0.751)PS(0.125)FFEEKPEEPVVLALDPK;KLDDDS(0.014)DS(0.982)PS(0.004)FFEEKPEEPVVLALDPK 164.17 5.61E-12 195462000 131420 94287 90742 65872 104670 91874 100914 133735 179531 142320 TRUE FALSE 126283.9611 91598.02708 107141.0979 69271.66181 108036.8056 93731.75523 102149.0157 130973.3255 159151.3935 132680.5396 0.951789625 0.690365198 0.807511774 0.522093609 0.814262633 0.706446895 0.769886948 0.987132897 1.199508187 1 17.01759726 1.637104135 3.019471354 1.100200611 0.741261664 0.62189446 0.112826933 0.125851085 2.697238552 0.068262716 0.028725751 43.36148382 -1.637104135 -0.358938947 HPECNLR ddPTM_BT-474_Pertuzumab_2h_R1 3 HPECNLR 7 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;K7EMK2;H0YH35 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;; 101.64 0.0089085 364063000 117916 156491 127077 193306 165067 174041 168861 131399 112761 154166 FALSE TRUE 113307.7124 152028.0299 150042.6407 203282.5458 170376.53 177560.2283 170927.5714 128685.5647 99960.84401 143724.1995 0.788369062 1.057776146 1.043962264 1.414393307 1.185440799 1.235423324 1.18927482 0.89536463 0.695504615 1 17.13294347 1.637710244 4.680040082 0.833332062 1.141099701 0.350433566 0.166255767 0.165610555 8.127524148 0.095497311 0.044618045 43.4220421 -1.637710244 0.307767639 NAAEELKPR ddPTM_BT-474_Pertuzumab_2h_R1 5 NAAEELKPR 9 1 P78406 P78406 RAE1 mRNA export factor 0 ;;;; 111.06 0.0019942 5630360000 8054970 8244920 6812530 6907590 7755970 7845260 7576170 8939820 10167260 9690920 FALSE TRUE 7740172.867 8009782.954 8043705.715 7264091.548 8005447.819 8003896.532 7668889.435 8755209.593 9013115.269 9034545.357 0.856730755 0.886572886 0.89032767 0.804035097 0.886093047 0.88592134 0.848840659 0.96908137 0.997627984 1 23.10702057 1.637950077 4.025433802 0.994607898 0.866456218 0.838013508 0.025006659 0.065162748 2.453314851 0.014538588 0.006591199 43.44602791 -1.637950077 -0.128151679 REEDEPEER ddPTM_BT-474_Pertuzumab_2h_R1 2 REEDEPEER 9 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 245.08 2.18E-10 342670000 303140 305460 268870 322300 302200 315690 301800 291730 304170 291200 FALSE TRUE 291292.9537 296748.5799 317460.79 338933.9416 311920.5375 322073.4681 305493.5187 285705.6736 269641.8968 271476.7646 1.072994052 1.093090159 1.169384755 1.248482323 1.148976922 1.186375816 1.125302635 1.05241299 0.993241161 1 18.0504692 1.638002445 2.158546761 0.997256092 1.15551116 0.657221162 0.045721417 0.183013917 1.851747326 0.036512445 0.013977927 43.45126701 -1.638002445 0.158255068 DLESLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLESLR 6 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 153.61 0.023518 1735560000 1837770 2173400 1877880 2278500 2061770 2202380 2229400 1938930 1927510 2176700 FALSE TRUE 1765947.917 2111416.76 2217254.689 2396093.658 2128088.705 2246913.633 2256684.064 1898890.418 1708707.146 2029270.17 0.870237952 1.040480854 1.092636516 1.180766215 1.048696588 1.107252088 1.112066839 0.935750422 0.842030386 1 20.95252952 1.638421166 5.32048959 0.911562864 1.069897862 0.363326905 0.083672787 0.145328232 8.900124273 0.045821462 0.02190571 43.49318035 -1.638421166 0.158334998 ERQEGEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERQEGEAK 8 1 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;A0A494C0Y7;E7ESD9 Q92878-2 RAD50 DNA repair protein RAD50 0 87.149 0.014163 119650000 110770 139970 91490 103810 99882 121650 105320 97246 79597 100210 FALSE TRUE 106440.9859 135978.1926 108024.2782 109167.6465 103094.7952 124109.8463 106608.9377 95237.83612 70561.48226 93422.68744 1.139348362 1.455515746 1.156295983 1.168534641 1.10353061 1.328476516 1.141146124 1.01942942 0.75529279 1 16.51148533 1.638509783 2.545521593 0.879420982 1.223058474 0.590021332 0.114157438 0.158972332 2.34407979 0.075450486 0.03024748 43.502056 -1.638509783 0.343637493 TEIKEEEDQPSTSATQSS(ph)PAPGQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TEIKEEEDQPSTSATQSSPAPGQSK 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 TEIKEEEDQPSTSATQS(0.171)S(0.829)PAPGQSK 211.73 7.19E-26 542400000 206130 174950 165720 146600 172070 168640 180080 225220 283790 245520 TRUE FALSE 198074.2117 169960.5973 195669.2904 154166.0436 177604.7878 172050.0163 182283.8729 220569.1283 251575.3489 228890.7117 0.865365878 0.742540385 0.854859024 0.673535603 0.775937068 0.751668843 0.79637951 0.963643857 1.099106849 1 17.80429939 1.638604851 2.859232587 1.047926351 0.774187729 0.797613207 0.056618511 0.086586914 1.650783893 0.034791527 0.014434385 43.51157971 -1.638604851 -0.273738622 KKT(ph)GGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKTGGSK 7 2 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 KKT(1)GGSK 91.626 0.026153 405850000 490500 1035400 780110 1375100 1211700 1200600 939540 641900 285880 537640 TRUE FALSE 471330.7177 1005871.406 921093.2305 1446069.076 1250675.431 1224876.955 951038.3716 628644.5407 253428.1009 501225.1639 0.940357252 2.006825431 1.837683534 2.885068787 2.495236714 2.443765882 1.897427424 1.254215841 0.505617274 1 18.93509932 1.6388719 2.545633839 0.766792622 2.137390642 0.541764546 0.498696332 0.187753973 2.768561562 0.35532992 0.14250896 43.53834331 -1.6388719 1.37059802 QCVENADLPEGEKKPIDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 QCVENADLPEGEKKPIDQR 19 2 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 147.53 5.88E-08 959680000 1079800 886500 734990 639520 882650 892590 872360 1006600 1230600 1064100 FALSE TRUE 1037600.222 861217.888 867819.0428 672525.7038 911041.2389 910638.7814 883036.2026 985813.3582 1090907.447 992027.5592 1.045938908 0.868139075 0.87479328 0.677930464 0.918362832 0.91795714 0.890132733 0.993735859 1.099674537 1 19.92002067 1.638874466 2.64715727 1.051394765 0.876485601 0.376032571 0.087769317 0.243799111 3.923759705 0.06011832 0.024389759 43.53860058 -1.638874466 -0.174909164 QGEVIVSIEEKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QGEVIVSIEEKPK 13 1 P49321;P49321-3;P49321-4;E9PPR5 P49321 NASP Nuclear autoantigenic sperm protein 0 133.66 6.03E-06 0 75300 55535 56354 54857 67933 58989 63222 72159 88111 74767 FALSE TRUE 72357.19275 53951.19617 66538.42139 57688.17634 70118.12664 60181.798 63995.72975 70668.89143 78109.00867 69702.96449 1.03807913 0.774015805 0.954599591 0.827628735 1.005956162 0.863403708 0.918120631 1.01385776 1.120598087 1 16.0889324 1.6391795 3.292387945 1.062141457 0.905965888 0.378424719 0.079243322 0.180554476 4.627881114 0.04442489 0.019193337 43.56919145 -1.6391795 -0.156175569 RAS(ph)PSPPPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RASPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RAS(0.719)PS(0.281)PPPKR;RAS(0.8)PS(0.2)PPPKR 73.466 0.02343 175757000 783020 1207700 900040 1616400 1227400 1374490 1259000 824850 532330 932370 TRUE FALSE 752418.7127 1173257.578 1062697.249 1699822.598 1266880.436 1402283.13 1274408.019 807816.5593 471902.1301 869219.7494 0.865625422 1.349782468 1.222587556 1.955572913 1.457491545 1.613266531 1.466151706 0.929358266 0.542903139 1 19.72936143 1.639240445 3.908723688 0.762749273 1.438433737 0.487182696 0.281239317 0.143662596 5.128170387 0.166415903 0.075032019 43.5753059 -1.639240445 0.675684464 EKENLSYDLVPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKENLSYDLVPLK 13 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;R4GN69 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 116.08 0.00055948 385560000 1103300 1061500 1007800 879460 959850 1056800 1167800 1242200 1542400 1487500 FALSE TRUE 1060181.816 1031227.059 1189931.878 924849.036 990724.447 1078169.22 1182091.886 1216548.136 1367313.218 1386750.3 0.764508085 0.74362851 0.858072198 0.666918216 0.714421657 0.777478988 0.852418698 0.877265457 0.985983719 1 20.40327661 1.639296644 1.162372857 1.002771168 0.751034139 0.79211995 0.048007025 0.201612397 0.51642635 0.042594705 0.015857962 43.58094512 -1.639296644 -0.25173703 FDDTNPEKEKEDFEK ddPTM_BT-474_Pertuzumab_2h_R1 3 FDDTNPEKEKEDFEK 15 2 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 162.4 8.98E-07 791740000 2339540 1676170 1258060 975620 1546840 1573840 1522430 1949960 2578590 1824730 FALSE TRUE 2248108.19 1628367.273 1485419.427 1025971.865 1596595.513 1605664.123 1541061.954 1909692.645 2285879.274 1701139.412 1.321530837 0.957221531 0.873190884 0.603108633 0.938544779 0.943875682 0.905899859 1.122596203 1.343734239 1 20.69806995 1.639482694 4.153892595 1.188794292 0.921000825 0.236366531 0.180737353 0.223000203 8.889109499 0.105450512 0.048187341 43.59961901 -1.639482694 -0.267793467 RSEEVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSEEVVR 7 1 O14907;A0A087X282 O14907 TAX1BP3 Tax1-binding protein 3 0 ; 114.5 0.0094467 525226000 469768 509237 437055 503504 438290 469991 502323 448902 437188 526410 FALSE TRUE 451408.9472 494714.0594 516040.5607 529489.9018 452387.9959 479494.54 508470.5791 439632.0168 387560.2511 490755.7818 0.919824002 1.008065677 1.051522121 1.078927486 0.921818983 0.977053267 1.036096971 0.895826464 0.789721213 1 18.90464574 1.639485086 5.609252427 0.878724854 1.000378306 0.323430896 0.067865682 0.143133168 9.611243805 0.035518117 0.017142996 43.59985907 -1.639485086 0.121653452 SSS(ph)PPPR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSSPPPR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.001)S(0.004)S(0.995)PPPR;S(0.007)S(0.007)S(0.986)PPPR;S(0.001)S(0.005)S(0.994)PPPR;S(0.214)S(0.214)S(0.571)PPPR;S(0.009)S(0.009)S(0.983)PPPR 126.04 0.0041866 1429459000 1414567 1578967 1278580 1813338 1640019 1721711 1686482 1413620 1328261 1622473 TRUE FALSE 1359284.158 1533936.407 1509647.848 1906924.591 1692771.701 1756525.176 1707121.671 1384428.253 1177482.38 1512581.459 0.898651871 1.014118214 0.998060527 1.260708692 1.119127628 1.161276417 1.128614701 0.915275171 0.778458822 1 20.52858141 1.639525965 4.933355211 0.877193446 1.087880572 0.3886008 0.106042317 0.149830705 8.060202945 0.060585372 0.028612036 43.6039633 -1.639525965 0.210687126 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR 34 1 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 368.85 1.53E-148 1269600000 961680 997830 854320 1067840 892580 1009110 1027750 928670 1006810 964060 FALSE TRUE 924096.4824 969372.8654 1008714.628 1122951.35 921290.6463 1029514.896 1040327.912 909492.64 892521.1497 898763.3575 1.028186646 1.078562958 1.122336174 1.249440513 1.025064761 1.145479382 1.157510376 1.011937828 0.99305467 1 19.77758178 1.63953672 5.655989409 0.998660098 1.116699181 0.416818026 0.061606858 0.137584635 9.373534905 0.033254217 0.016072982 43.60504311 -1.63953672 0.118039083 RRKDS(ph)AQDDQAK ddPTM_BT-474_Pertuzumab_2h_R1 4 RRKDSAQDDQAK 12 3 Q13045-3;Q13045;Q13045-2;J3KS54 Q13045-3 FLII Protein flightless-1 homolog 1 RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK 174.87 0.00016139 924182000 545299 477993 334772 289507 344159 431533 387688 456745 534273 456431 TRUE FALSE 523988.1122 464361.1076 395272.7474 304448.491 355229.1868 440258.8929 392432.6417 447313.0561 473624.5689 425516.5218 1.231416609 1.091288079 0.928924559 0.715479835 0.834818787 1.034645825 0.922250069 1.051223709 1.113058 1 18.69885562 1.639894529 5.664611646 1.064464214 0.957217312 0.081361886 0.134606118 0.358054698 24.45892139 0.078660663 0.038038933 43.64098345 -1.639894529 -0.107246902 ELAYLSELPPTPLHVSEDS(ph)SSPER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELAYLSELPPTPLHVSEDSSSPER 24 0 Q96EB6;B0QZ35;E9PC49 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 ELAYLSELPPTPLHVS(0.001)EDS(0.613)S(0.089)S(0.298)PER 171.31 4.42E-12 69295000 48440 74969 66835 90701 74883 87217 76574 65917 63052 67571 TRUE FALSE 46546.91125 72830.95752 78913.57124 95382.08948 77291.6797 88980.5875 77511.13552 64555.79091 55894.6013 62994.35598 0.738906058 1.156150521 1.252708596 1.514137068 1.226961979 1.412516822 1.230445717 1.024786902 0.887295384 1 15.94293495 1.639917113 3.554221443 0.947245414 1.237318448 0.261169683 0.19227249 0.252466765 7.531341252 0.119754459 0.052816946 43.64325289 -1.639917113 0.290073034 KWDKDEYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KWDKDEYEK 9 2 Q96NC0;R4GNG8 Q96NC0 ZMAT2 Zinc finger matrin-type protein 2 0 ; 122.69 0.00032549 1094000000 2398770 1985430 1768130 1573530 1977340 1873170 2012410 2303040 2857270 2434220 FALSE TRUE 2305023.416 1928807.48 2087670.423 1654740.072 2040942.937 1911046.781 2037038.476 2255481.419 2532924.688 2269348.111 1.015720508 0.849939007 0.919942786 0.729169784 0.899352077 0.842112663 0.897631556 0.99388957 1.116146384 1 21.1138465 1.63997395 2.809158069 1.058256348 0.871592326 0.506605459 0.072796302 0.169317559 3.10549723 0.045920409 0.018982023 43.64896496 -1.63997395 -0.186664022 S(ph)QS(ph)IEQESQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSIEQESQEK 11 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 S(1)QS(1)IEQESQEK;S(1)QS(1)IEQESQEK 194 1.03E-06 360240000 1184260 960870 952620 865800 965010 892100 957450 1242330 1513410 1310250 TRUE FALSE 1137977.81 933466.9284 1124779.625 910484.0418 996050.423 910138.8732 969167.5595 1216675.451 1341614.042 1221505.6 0.931618987 0.764193736 0.920814137 0.745378524 0.815428454 0.745095948 0.79342048 0.996045741 1.098328195 1 20.22022905 1.640039691 4.064808601 1.048153272 0.813040167 0.695400846 0.065593651 0.087607843 3.359473791 0.035972558 0.016369841 43.6555728 -1.640039691 -0.235113105 LEKPAKYDDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEKPAKYDDIK 11 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 132.47 0.00072222 1042300000 1297740 1109840 928500 765930 985410 1057530 976500 1185650 1437520 1110180 FALSE TRUE 1247022.886 1078188.45 1096300.604 805459.7391 1017106.608 1078913.981 988450.6991 1161165.913 1274338.756 1034986.52 1.204868723 1.041741539 1.059241433 0.778232106 0.982724498 1.042442544 0.955037269 1.121914045 1.231261211 1 19.98118055 1.640625832 6.116937644 1.135193731 1.004066987 0.156703449 0.113009365 0.216773703 16.94735905 0.060282092 0.029541126 43.7145319 -1.640625832 -0.131126745 S(ph)PGLLDTTPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGLLDTTPIR 11 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 S(1)PGLLDTTPIR;S(1)PGLLDTTPIR 132.86 0.00018218 715960000 327810 408250 359750 440670 427330 391790 374840 365580 351150 340490 TRUE FALSE 314998.8228 396607.1097 424764.8276 463413.0315 441075.4575 399712.2622 379427.404 358030.6452 311288.9241 317428.309 0.992346347 1.249438372 1.338144127 1.459898246 1.389527793 1.259220589 1.195316842 1.127910256 0.980658988 1 18.27607127 1.640750791 1.467658326 0.986054717 1.294689357 0.486604435 0.116628648 0.337756822 1.418348727 0.103027464 0.037452506 43.72711159 -1.640750791 0.308634641 VGDTEKPEPERS(ph)PPNR ddPTM_BT-474_Pertuzumab_2h_R1 5 VGDTEKPEPERSPPNR 16 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 VGDTEKPEPERS(1)PPNR;VGDT(0.002)EKPEPERS(0.998)PPNR;VGDT(0.077)EKPEPERS(0.923)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR 156.08 1.56E-07 8463060000 3720030 3446640 2835360 2856800 3043590 3216420 3366360 3522440 4191560 3830090 TRUE FALSE 3574647.115 3348345.202 3347772.624 3004239.79 3141489.836 3281458.216 3407558.521 3449700.383 3715751.681 3570674.593 1.001112541 0.937734625 0.93757427 0.841364765 0.879802893 0.919002315 0.954317856 0.966120069 1.040630162 1 21.76776523 1.640857576 1.709683314 1.018431792 0.916938689 0.463832719 0.041129063 0.314456467 1.859811746 0.034871021 0.012797223 43.73786466 -1.640857576 -0.101493103 FSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_BT-474_Pertuzumab_2h_R1 5 FSGEEGEIEDDESGTENREEKDNIQPTTE 29 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.965)GT(0.035)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.982)GT(0.018)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.997)GT(0.003)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.999)GT(0.001)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.998)GT(0.002)ENREEKDNIQPTTE 278.63 2.30E-71 3655700000 1961980 1782410 1305180 1211660 1706450 1702410 1426850 1818090 1961900 1662480 TRUE FALSE 1885303.653 1731577.412 1541055.06 1274193.918 1761339.514 1736833.897 1444312.217 1780545.806 1739193.337 1549878.749 1.216420093 1.117234115 0.994306852 0.822124904 1.136436973 1.120625661 0.931887232 1.148829099 1.122147999 1 20.56372392 1.640943272 24.9999988 1.1016446 1.04600856 0.025088562 0.112542271 2.460315457 1848.906281 0.053743173 0.029799707 43.74649594 -1.640943272 -0.05563604 FS(ph)QIQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSQIQPK 7 0 Q86V21;Q86V21-2 Q86V21 AACS Acetoacetyl-CoA synthetase 1 FS(1)QIQPK;FS(1)QIQPK 56.729 0.077199 639340000 611830 896680 695400 1094050 892020 880260 833720 681920 507440 713440 TRUE FALSE 587919.0072 871107.5643 821074.2491 1150514.052 920712.6334 898059.4603 843923.3148 667838.1137 449837.5386 665118.0733 0.883931787 1.309703644 1.234478932 1.729789187 1.384284491 1.350225616 1.26883233 1.00408956 0.676327342 1 19.34325095 1.641032599 2.811638861 0.835905955 1.33091193 0.467362386 0.207090621 0.19141085 3.516603814 0.137605585 0.056963615 43.75549481 -1.641032599 0.495005975 TDKLDEALEDYK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDKLDEALEDYK 12 1 Q99614;H0YB37 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 125.53 0.00027689 221020000 673190 537130 486550 368570 524290 562780 587290 672960 901270 789830 FALSE TRUE 646880.9905 521811.5783 574480.4082 387591.9419 541154.264 574159.7972 594477.4307 659063.1408 798961.608 736334.1106 0.878515583 0.708661423 0.780189862 0.526380533 0.734930321 0.779754447 0.807347401 0.895059907 1.085053098 1 19.49000101 1.641071094 1.489126756 1.044838051 0.725003959 0.653888492 0.087443035 0.226934593 0.983995673 0.072432602 0.026338581 43.75937332 -1.641071094 -0.319834092 INEELESQYQQSMDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 INEELESQYQQSMDSK 16 0 E9PM92;O00193;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 256.77 2.78E-26 103960000 81529 69742 63593 68676 68275 75067 72653 83354 91723 91347 FALSE TRUE 78342.75654 67753.02644 75085.66972 72220.37659 70471.12738 76584.90617 73542.14915 81632.71077 81310.98957 85159.98633 0.91994797 0.795596962 0.881701289 0.848055286 0.827514546 0.899306229 0.863576338 0.9585806 0.954802755 1 16.3778881 1.641123511 1.170790821 0.993446338 0.854008823 0.67468442 0.034735185 0.23413562 0.608460245 0.027530769 0.010243335 43.76465521 -1.641123511 -0.139437514 FRPPETTER ddPTM_BT-474_Pertuzumab_2h_R1 1 FRPPETTER 9 1 Q96P70 Q96P70 IPO9 Importin-9 0 62.78 0.073304 581090000 314250 473950 395060 486510 423040 342150 480130 341100 314090 439260 FALSE TRUE 301968.7626 460433.41 466456.1301 511618.8394 436647.4658 349068.5074 486005.9746 334056.1658 278435.82 409508.5289 0.737393097 1.124356094 1.139063285 1.249348434 1.06627197 0.852408394 1.186803058 0.815748982 0.679926791 1 18.64353397 1.641155638 7.065922123 0.807859951 1.057013065 0.272541831 0.162097058 0.145429298 14.74383691 0.081812221 0.041099177 43.76789278 -1.641155638 0.249153115 RMEDEGGFPVPQENGQPES(ph)PRR ddPTM_BT-474_Pertuzumab_2h_R1 2 RMEDEGGFPVPQENGQPESPRR 22 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PRR;RMEDEGGFPVPQENGQPES(1)PRR 185.48 2.78E-17 2480100000 633200 690080 574470 701260 749060 716450 704080 620500 619220 652800 TRUE FALSE 608453.844 670399.5941 678289.508 737452.1126 773154.1952 730937.1099 712696.7417 607686.4582 548928.7416 608585.2745 0.999784039 1.101570515 1.114534867 1.211748203 1.270412262 1.201043043 1.171071289 0.998523105 0.901975063 1 19.2150999 1.641232293 3.94694597 0.951035031 1.158164842 0.581836827 0.072722473 0.129600806 4.712370301 0.046165887 0.020894072 43.77561869 -1.641232293 0.207129811 EEMQDAHVILNDITEECRPPSSLITR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEMQDAHVILNDITEECRPPSSLITR 26 1 Q9H0C8;E9PC05 Q9H0C8 ILKAP Integrin-linked kinase-associated serine/threonine phosphatase 2C 0 ;;; 173.59 2.12E-12 267318000 210520 240308 187814 227463 237249 248798 222467 227718 240353 231091 FALSE TRUE 202292.6457 233454.6511 221756.1677 239202.3927 244880.3295 253828.866 225189.6177 223015.5437 213069.1351 215439.0007 0.938978759 1.083622976 1.0293223 1.110302182 1.136657377 1.178193666 1.045259293 1.035167927 0.98899983 1 17.71691992 1.641258553 2.40304698 0.998434985 1.081933224 0.215174486 0.06119183 0.399157471 5.163575526 0.044528558 0.017610861 43.77826574 -1.641258553 0.083498238 KPPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPPSPK 6 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 1 KPPS(1)PK;KPPS(1)PK 66.621 0.061818 2394360000 1786620 1248970 1220430 1029190 1214970 1236340 1443660 1502570 1721090 1753570 TRUE FALSE 1716796.915 1213350.598 1440988.849 1082306.619 1254050.613 1261339.642 1461327.943 1471541.404 1525719.079 1634799.142 1.050157705 0.742201636 0.881447031 0.662042566 0.76709767 0.77155634 0.893888372 0.900135905 0.933276168 1 20.64068196 1.641916788 1.323500361 0.975050247 0.80549837 0.271865824 0.098727761 0.522744756 1.754239671 0.081551864 0.029807643 43.84466825 -1.641916788 -0.169551877 GEEKPAGHRTS(ph)PVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEEKPAGHRTSPVAK 15 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GEEKPAGHRT(0.27)S(0.73)PVAK 104.29 0.00073333 513580000 966480 918990 840700 774490 870400 949110 893950 1029700 1217300 1060000 TRUE FALSE 928708.8931 892781.305 992633.1913 814461.5217 898397.2065 968301.6545 904890.4275 1008436.335 1079117.207 988205.2558 0.939793517 0.903437115 1.004480785 0.824182544 0.909120045 0.979858839 0.915690766 1.020472548 1.091997033 1 19.9144512 1.641996662 3.908289135 1.049042141 0.924878267 0.517270006 0.049931583 0.133417183 4.76501836 0.028333612 0.012803431 43.85273274 -1.641996662 -0.124163874 T(ph)PDRER ddPTM_BT-474_Pertuzumab_2h_R1 1 TPDRER 6 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 T(1)PDRER 97.431 0.066413 63430000 80045 81504 55837 71882 71157 78472 70876 62732 50697 68758 TRUE FALSE 76916.75291 79179.58572 65927.98799 75591.83863 73445.82953 80058.75761 71743.40169 61436.56228 44942.0891 64100.95942 1.199931383 1.235232459 1.028502359 1.179262203 1.145783623 1.248947884 1.119225084 0.958434364 0.701114141 1 15.96805833 1.642070501 3.030033055 0.845814897 1.167867928 0.680422943 0.089401612 0.110305283 2.379357688 0.053550575 0.022678044 43.86018924 -1.642070501 0.322053032 RDSS(ph)ESQLASTESDKPTTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RDS(0.285)S(0.593)ES(0.023)QLAS(0.098)T(0.002)ESDKPTTGR 237.71 1.04E-29 3465200000 525920 515330 392980 521160 534990 449420 446200 566390 578450 605640 TRUE FALSE 505366.465 500633.293 464000.2278 548057.1301 552198.4392 458507.5803 451660.7291 554693.8486 512786.7811 564619.4634 0.895056756 0.886673814 0.821792832 0.970666379 0.97800107 0.81206478 0.799938292 0.9824207 0.90819891 1 19.10691934 1.642186879 12.79791753 0.958784379 0.883385011 0.276514262 0.06115968 0.176875801 53.27381864 0.030255419 0.016491346 43.87194398 -1.642186879 -0.075399368 AWYDNHR ddPTM_BT-474_Pertuzumab_2h_R1 1 AWYDNHR 7 0 Q5F1R6;Q5F1R6-3;Q5F1R6-2 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 0 75.189 0.044144 66369000 186480 230040 196080 267980 211040 241840 221510 205880 199950 207920 FALSE TRUE 179192.1554 223479.4844 231516.0178 281810.4799 217828.2933 246730.1705 224220.9056 201628.5061 177252.5143 193837.3932 0.924445756 1.152922461 1.194382642 1.453849927 1.123768173 1.272871898 1.156747426 1.040194065 0.914439218 1 17.56448738 1.642253234 2.659303632 0.959863815 1.195857765 0.352121633 0.12572035 0.257420737 4.182107373 0.085621815 0.034916114 43.87864763 -1.642253234 0.235993951 LFLDGEEEKEWAFEESK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFLDGEEEKEWAFEESK 17 1 Q9NRN7;E9PLW6 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 189.64 3.13E-10 35667000 113650 89394 85095 68843 98235 102720 90185 116330 142000 117890 FALSE TRUE 109208.4324 86844.57065 100473.5594 72395.99548 101394.818 104797.0688 91288.71101 113927.7448 125880.7553 109905.2053 0.993660237 0.790177048 0.914183811 0.658713073 0.922566112 0.953522342 0.83061317 1.036600082 1.145357538 1 16.74590019 1.642294583 4.450543795 1.077768241 0.862790324 0.467864343 0.095190478 0.13262812 5.980623003 0.051955468 0.024122612 43.88282552 -1.642294583 -0.214977917 SEPHS(ph)PGIPEIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEPHSPGIPEIFR 13 0 Q9UJJ2;Q8ND82 Q9UJJ2 ZNF280C Zinc finger protein 280C 1 S(0.001)EPHS(0.999)PGIPEIFR 57.499 0.073497 56928000 33229 61018 37814 79176 42377 67491 55585 39796 30445 41840 TRUE FALSE 31930.37394 59277.82638 44647.83097 83262.28285 43740.09469 68855.71426 56265.26586 38974.19869 26989.01124 39006.13953 0.81859867 1.519705028 1.144635986 2.134594293 1.12136436 1.765253242 1.442472045 0.999181133 0.691917005 1 15.2514136 1.642423153 3.717374442 0.847059987 1.44399494 0.324051655 0.349443002 0.196980903 6.406061697 0.196151199 0.08765718 43.89581865 -1.642423153 0.596934954 LVVLDEELEGISPDELKDELPER ddPTM_BT-474_Pertuzumab_2h_R1 6 LVVLDEELEGISPDELKDELPER 23 1 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;;;;; 279.19 6.58E-52 1371119000 569192 540466 500582 519445 545053 522914 589041 668604 767637 773361 FALSE TRUE 546947.3474 525052.4389 591048.3028 546253.6187 562585.1247 533487.6794 596249.86 654797.0938 680498.066 720980.5706 0.758615932 0.728247695 0.819783954 0.75765373 0.780305528 0.739947373 0.826998513 0.908203522 0.943850769 1 19.45960086 1.642478243 1.390060853 0.985584236 0.763826352 0.91536707 0.025893435 0.101489566 0.378465517 0.021421633 0.007805992 43.90138721 -1.642478243 -0.221757884 EWDFDLK ddPTM_BT-474_Pertuzumab_2h_R1 3 EWDFDLK 7 0 Q96EY4;H0Y9X1 Q96EY4 TMA16 Translation machinery-associated protein 16 0 ;; 129.4 0.008525 241338000 953110 897770 783720 791850 866020 837270 871350 958290 1072930 1038790 FALSE TRUE 915861.4075 872166.4786 925355.6378 832717.4734 893876.3198 854200.1731 882013.842 938500.9766 951135.4845 968431.828 0.945715931 0.900596669 0.955519646 0.859861737 0.92301419 0.882044712 0.910765029 0.969093486 0.982139844 1 19.88529097 1.642550636 3.07406568 0.988103424 0.90943873 0.614943425 0.02666462 0.134806269 2.997335303 0.016095471 0.006847562 43.90870569 -1.642550636 -0.078664694 QKLEEDAEMK ddPTM_BT-474_Pertuzumab_2h_R1 5 QKLEEDAEMK 10 1 P05455 P05455 SSB Lupus La protein 0 ;;;; 128.08 0.00030922 4281930000 6374080 5454580 4835120 3976530 4893710 5225250 5348070 6186730 7758260 6525390 FALSE TRUE 6124973.907 5299020.719 5708933.741 4181759.19 5051120.627 5330908.135 5413521.28 6058971.864 6877574.85 6083419.523 1.006830761 0.871059558 0.938441565 0.68740273 0.830309435 0.87630125 0.889881301 0.995981264 1.130544232 1 22.53645107 1.64265874 2.668335629 1.066357935 0.863372399 0.484952661 0.082349986 0.194898315 3.189937925 0.055839402 0.022804163 43.91963678 -1.64265874 -0.202985536 GAGSIAGASAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 GAGSIAGASASPK 13 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GAGSIAGASAS(1)PK 196.37 1.49E-07 223190000 180710 143840 151680 134290 161390 167480 169200 203450 270620 220480 TRUE FALSE 173647.6534 139737.824 179091.9501 141220.723 166581.2559 170866.5603 171270.7202 199248.6864 239900.3521 205546.6932 0.844808791 0.679834941 0.871295701 0.687049355 0.81043024 0.831278566 0.833244834 0.969359727 1.167133114 1 17.64910664 1.642849194 2.211468458 1.084727795 0.785048377 0.735811567 0.071170101 0.12449306 1.331165819 0.04754066 0.018408963 43.93890142 -1.642849194 -0.299679418 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(ph)PFAK ddPTM_BT-474_Pertuzumab_2h_R1 3 AASGEDSTEEALAAAAAPWEGGPVPGVDRSPFAK 34 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK 285.14 1.53E-74 563410000 190257 163843 154488 167144 185671 195870 174945 167060 154508 186155 TRUE FALSE 182821.5461 159170.3581 182407.4182 175770.3219 191643.2763 199830.6256 177086.0292 163610.1526 136968.8996 173546.556 1.053443815 0.917162297 1.051057551 1.012813656 1.104275883 1.151452556 1.020394949 0.942745027 0.789234328 1 17.40496321 1.643019209 3.410697588 0.888286621 1.045496536 0.410547539 0.074530162 0.182605518 5.022728347 0.045870932 0.02007938 43.95610574 -1.643019209 0.157209915 DPHLACVAYER ddPTM_BT-474_Pertuzumab_2h_R1 6 DPHLACVAYER 11 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;; 114.72 0.0012195 18827700000 1070570 1152370 1120969 1205880 1253990 1034791 1294956 1074135 1192290 1198517 FALSE TRUE 1028730.941 1119505.536 1323553.034 1268115.611 1294325.727 1055715.183 1310804.059 1051953.737 1056946.238 1117340.376 0.920696113 1.00193778 1.184556705 1.134941186 1.158398779 0.944846535 1.173146596 0.941480107 0.945948308 1 20.09163731 1.643086836 9.654720777 0.957816524 1.075833022 0.24363002 0.089769006 0.152414769 27.17216137 0.04427636 0.023440594 43.96295099 -1.643086836 0.118016498 VYSLDDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYSLDDIR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ; 81.191 0.054673 532750000 1007830 1289880 1143560 1424040 1288470 898610 1337270 985020 878790 1229700 FALSE TRUE 968442.8894 1253093.885 1350226.73 1497534.875 1329914.808 916780.5099 1353635.91 964678.9928 779033.4434 1146411.324 0.844760401 1.09305784 1.177785584 1.306280603 1.160067752 0.799695965 1.180759368 0.841477202 0.679540953 1 20.12869333 1.643335521 5.919298354 0.814442343 1.084947081 0.310436582 0.162664961 0.154945927 11.41975274 0.087331863 0.042648863 43.9881321 -1.643335521 0.270504738 LNAS(ph)PAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNASPAAR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 LNAS(1)PAAR;LNAS(1)PAAR 110.74 0.0035326 971410000 1140780 1179050 1016540 1200030 1106140 1109330 1200920 1103310 1150510 1241910 TRUE FALSE 1096197.056 1145424.648 1200251.391 1261963.692 1141719.998 1131761.413 1215617.218 1080526.263 1019908.928 1157794.33 0.946797742 0.989316167 1.036670642 1.089972251 0.986116419 0.977515077 1.04994228 0.933262701 0.880906826 1 20.14294757 1.643373697 6.717256429 0.929160241 1.011664386 0.329874784 0.047036318 0.134468036 12.36536678 0.024434858 0.012192019 43.99199899 -1.643373697 0.082504145 SDYDGIGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SDYDGIGSR 9 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;; 159.46 0.00015364 2578110000 2470760 3346720 2779710 4026440 3524650 3375350 3299270 2785330 2437600 2914590 FALSE TRUE 2374199.968 3251274.822 3282065.431 4234245.051 3638023.568 3443601.89 3339647.453 2727811.962 2160893.867 2717182.223 0.873772818 1.1965612 1.207893016 1.558322079 1.33889569 1.267343007 1.229084831 1.003912045 0.795270133 1 21.37367989 1.643391203 3.061765371 0.896270324 1.255418956 0.424857 0.165084323 0.200540311 4.420533055 0.109014671 0.04636782 43.99377238 -1.643391203 0.359148632 S(ph)AEDVSTVPTQPDNPFSHPDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SAEDVSTVPTQPDNPFSHPDK 21 0 A0A0U1RR07;Q9HCH5-7;Q9HCH5-13;Q9HCH5;Q9HCH5-15;Q9HCH5-12 A0A0U1RR07;Q9HCH5-12 SYTL2 Synaptotagmin-like protein 2 1 S(1)AEDVSTVPTQPDNPFSHPDK;S(1)AEDVSTVPTQPDNPFSHPDK;S(1)AEDVSTVPTQPDNPFSHPDK;S(1)AEDVSTVPTQPDNPFSHPDK 285.95 1.31E-45 3411350000 2524860 2112490 1926950 1961460 2156020 2236040 2477650 2472060 2995550 2962960 TRUE FALSE 2426185.68 2052243.854 2275192.73 2062691.186 2225370.341 2281254.261 2507972.222 2421011.097 2655507.722 2762276.08 0.878328454 0.742953924 0.823665942 0.74673607 0.805629226 0.825860339 0.907936842 0.87645515 0.961347688 1 21.39742609 1.643535957 0.765957145 0.996968702 0.792119403 0.739426546 0.041043882 0.283198343 0.333142892 0.035330783 0.015778991 44.00843827 -1.643535957 -0.204849299 DELIHELK ddPTM_BT-474_Pertuzumab_2h_R1 3 DELIHELK 8 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ;; 128.36 0.0011368 454910000 641870 607930 672530 702770 671150 657520 796380 882990 1038350 1069600 FALSE TRUE 616785.0108 590592.4316 794071.1313 739040.0439 692738.1493 670815.5049 806126.3367 864755.9479 920480.8611 997155.0393 0.618544746 0.592277438 0.796336678 0.741148583 0.694714585 0.672729394 0.808426278 0.867223164 0.923107064 1 19.92745831 1.643560179 0.8759216 0.99869983 0.679685264 0.801878186 0.056025234 0.250743694 0.37298975 0.054167974 0.022361284 44.01089283 -1.643560179 -0.319014566 LAAQLGAPT(ph)SPIPDSAIVNTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAAQLGAPTSPIPDSAIVNTR 21 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LAAQLGAPT(0.5)S(0.5)PIPDSAIVNTR;LAAQLGAPT(0.626)S(0.374)PIPDSAIVNTR 187.47 3.20E-16 562090000 423961 411714 418931 582330 509890 511940 445336 442315 431069 410257 TRUE FALSE 407392.1354 399972.3198 494641.1508 612384.1211 526291.0749 522291.7776 450786.1552 433181.0407 382135.8543 382469.928 1.065161221 1.045761485 1.293281156 1.601130118 1.376032562 1.365576061 1.178618559 1.132588497 0.999126536 1 18.54498679 1.64380603 1.729876948 1.001219386 1.295166758 0.360168842 0.150712563 0.415114281 2.521623113 0.134140492 0.049424405 44.03581416 -1.64380603 0.293947372 DFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_BT-474_Pertuzumab_2h_R1 3 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDAS(0.013)AS(0.012)PLS(0.975)PHRR;DFTNEAPPAPLPDASASPLS(1)PHRR;DFTNEAPPAPLPDASAS(0.002)PLS(0.998)PHRR 278.37 2.46E-52 2109020000 551542 639851 513145 626323 601925 616846 609895 581842 590505 637302 TRUE FALSE 529987.1289 621603.076 605881.7163 658647.6051 621286.4643 629319.0488 617359.0775 569826.7594 523473.348 594136.9679 0.892028535 1.04622858 1.019767746 1.10857873 1.045695686 1.059215438 1.039085448 0.959083158 0.881065102 1 19.18043603 1.643927253 4.148946556 0.935018715 1.035053534 0.297566261 0.058463678 0.186119877 7.416933698 0.032739501 0.015008017 44.04810742 -1.643927253 0.100034819 VETVSQPSES(ph)PKDTIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VETVSQPSESPKDTIDK 17 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 VETVSQPS(0.035)ES(0.965)PKDTIDK 98.562 0.0022125 0 119540 82139 99941 92937 109790 84446 109320 140020 172130 167130 TRUE FALSE 114868.2446 79796.47614 118002.5619 97733.48971 113321.4951 86153.55598 110657.8909 137128.5381 152590.524 155810.1362 0.737232169 0.512139185 0.757348429 0.627260152 0.727305025 0.552939353 0.710209833 0.880100239 0.979336311 1 17.24942957 1.644030179 2.258279361 0.986804644 0.651331215 0.774165609 0.0743513 0.113982151 1.278594244 0.049263989 0.01920805 44.05854786 -1.644030179 -0.335473429 EIQSSNLETAMSVIGDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIQSSNLETAMSVIGDRR 18 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 64.346 0.05785 2629500000 909820 1393800 1084500 1498000 1303900 1422900 1180500 1087800 870350 1040400 FALSE TRUE 874263.2285 1354050.189 1280493.275 1575311.96 1345841.128 1451672.013 1194947.312 1065336.55 771551.5168 969932.7813 0.90136476 1.396024771 1.320187645 1.624145497 1.387561235 1.496672801 1.231989819 1.098361217 0.795469059 1 19.88752524 1.644037432 2.225188995 0.904501674 1.36566641 0.483590409 0.183747719 0.222202906 2.40949815 0.130929807 0.050847663 44.05928371 -1.644037432 0.461164736 PWIS(ph)LPR ddPTM_BT-474_Pertuzumab_2h_R1 3 PWISLPR 7 0 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 1 PWIS(1)LPR;PWIS(1)LPR;PWIS(1)LPR 70.919 0.035893 771840000 872080 1370890 1129080 1682070 1419170 1091870 1313470 871830 547470 957440 TRUE FALSE 837998.1495 1331793.559 1333129.872 1768881.834 1464818.892 1113948.359 1329544.639 853826.4058 485323.5008 892591.736 0.938837002 1.492052308 1.493549423 1.981736737 1.641084981 1.247993136 1.489532767 0.95656992 0.543723946 1 19.76764092 1.644440254 3.2708397 0.761455967 1.492423306 0.539346422 0.271468395 0.150351356 3.799868053 0.171771085 0.074475138 44.10016903 -1.644440254 0.730967339 RRFS(ph)DSEER ddPTM_BT-474_Pertuzumab_2h_R1 2 RRFSDSEER 9 2 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RRFS(0.986)DS(0.014)EER;RRFS(0.984)DS(0.016)EER 96.82 0.005599 543370000 245610 267910 200837 303360 277730 272950 252100 254320 242500 258840 TRUE FALSE 236011.2897 260269.4691 237132.7135 319016.446 286663.4377 278469.236 255185.2752 249068.2031 214972.4166 241308.5362 0.978047828 1.078575475 0.982695089 1.322027189 1.187953987 1.153996623 1.057506208 1.03215662 0.890861219 1 17.88051943 1.64460741 2.103413581 0.949226501 1.119476722 0.305538055 0.098316883 0.359513133 3.424353263 0.075705365 0.028996066 44.11714604 -1.64460741 0.170250221 RGDDWNDREWDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDDWNDREWDR 12 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 212.95 8.02E-09 3092200000 463790 532530 348090 431790 457930 529430 463490 427450 451490 419570 FALSE TRUE 445664.5741 517342.7658 410997.6062 454074.7336 472659.7343 540135.4373 469162.3293 418623.0081 400238.748 391152.1502 1.139363733 1.322612609 1.050735899 1.160864726 1.208378208 1.380883212 1.199436917 1.07023062 1.023230341 1 18.57737037 1.644692283 3.261259213 1.020310881 1.212444704 0.476057942 0.086758542 0.18377587 4.616643181 0.055093529 0.023874436 44.12576854 -1.644692283 0.192133823 VLGSQEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLGSQEAK 8 0 Q8N3D4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 0 60.478 0.092043 196670000 216350 357510 239930 451040 342380 368260 334970 268270 227090 277820 FALSE TRUE 207894.8028 347314.1648 283290.6882 474318.2285 353392.9636 375706.4695 339069.4631 262730.1308 201311.6952 259003.0039 0.802673327 1.340965779 1.093773755 1.831323271 1.364435772 1.450587305 1.309133322 1.014390284 0.777256218 1 17.9826093 1.644783679 3.282265659 0.88955026 1.334852557 0.332998894 0.250725387 0.221551495 5.638910274 0.154414764 0.067035179 44.13505567 -1.644783679 0.445302297 SESGGLGVSMVEYVLSS(ph)SPADKLDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SESGGLGVSMVEYVLSSSPADKLDSR 26 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 1 SESGGLGVSMVEYVLS(0.046)S(0.538)S(0.415)PADKLDS(0.002)R;SESGGLGVSMVEYVLS(0.012)S(0.552)S(0.434)PADKLDS(0.002)R 86.869 0.0076196 138772000 60878 60572 49425 47985 53915 60249 59877 62328 80840 70872 TRUE FALSE 58498.82046 58844.54587 58357.19695 50461.5116 55649.22494 61467.27606 60609.79264 61040.90502 71663.38211 66071.77631 0.885382893 0.890615466 0.883239413 0.763737778 0.842254107 0.930310633 0.917332574 0.923857484 1.084629264 1 16.01174651 1.644787348 1.192627894 1.035690409 0.859663349 0.643651006 0.048821625 0.292552369 0.789216405 0.043969352 0.01633038 44.13542856 -1.644787348 -0.17602706 NSVTPDMMEEMYK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSVTPDMMEEMYK 13 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 128.68 0.00037815 63699000 59112 54154 44702 43477 51298 41882 44987 62883 75389 62286 FALSE TRUE 56801.83769 52609.58094 52780.64579 45720.85318 52948.04676 42728.88274 45537.56436 61584.44408 66831.15678 58067.31374 0.97820674 0.906010241 0.908956216 0.787376757 0.911839094 0.73585086 0.784220268 1.060569882 1.150925581 1 15.82543867 1.644803654 5.748910386 1.084678462 0.857714047 0.61159503 0.077122841 0.090321439 6.329237631 0.042092579 0.020476887 44.13708567 -1.644803654 -0.226964416 RNELVIR ddPTM_BT-474_Pertuzumab_2h_R1 3 RNELVIR 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 119.41 0.0076786 2580460000 1852450 2534400 2289800 2774110 2467290 2344200 2560260 2046960 1822870 2374310 FALSE TRUE 1780054.206 2462121.393 2703617.796 2917282.15 2546652.624 2391601.33 2591593.228 2004689.561 1615945.44 2213495.869 0.804182303 1.112322561 1.22142437 1.31795238 1.150511577 1.080463426 1.170814576 0.905666728 0.730042221 1 21.07789525 1.644901384 4.548766753 0.851734597 1.132690233 0.392077838 0.138781675 0.152581119 7.158636028 0.078787471 0.036799731 44.14701902 -1.644901384 0.280955635 KENQWCEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 KENQWCEEK 9 1 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;;; 199.68 3.90E-05 8260630000 10207700 9730920 7839550 8709360 8941380 9164160 9823920 10802590 13254100 12045960 FALSE TRUE 9808771.799 9453403.689 9256331.075 9158851.113 9228987.608 9349465.594 9944148.072 10579512.74 11749550.13 11230076.4 0.873437673 0.841793355 0.824244711 0.815564453 0.821809868 0.832538022 0.885492468 0.942069525 1.046257364 1 23.42086441 1.64494154 1.74994305 1.023437873 0.833811134 0.921870786 0.021585098 0.080527957 0.502206171 0.016900313 0.006242921 44.15110122 -1.64494154 -0.189626739 LPSEGPRPAHVVVGDVLQAADVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPSEGPRPAHVVVGDVLQAADVDK 24 1 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 141.45 1.67E-07 2848900000 1513410 1216040 1359920 1359480 1457400 1148720 1282800 1749220 1960590 1984980 FALSE TRUE 1454264.264 1181359.73 1605687.795 1429642.926 1504278.595 1171947.905 1298499.29 1713097.996 1738032.043 1850535.537 0.785861301 0.638388027 0.867688171 0.772556321 0.81288825 0.633302027 0.701688384 0.925730937 0.9392049 1 20.81951141 1.645387985 4.740577407 0.957564877 0.744965421 0.650035804 0.070955126 0.099967869 5.039805285 0.039835605 0.018753959 44.19651091 -1.645387985 -0.212599456 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGS(ph)AR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR 45.187 0.04843 63057000 38308 40620 33174 40556 37285 39667 39940 36587 37851 39268 TRUE FALSE 36810.88101 39461.55737 39169.27975 42649.10002 38484.30589 40469.09392 40428.79767 35831.46566 33554.31316 36608.34338 1.005532554 1.077938899 1.069954992 1.16501038 1.051244124 1.105460946 1.104360207 0.97877867 0.916575569 1 15.15988487 1.645534424 4.623786855 0.955563204 1.084792836 0.610907574 0.043093333 0.097906508 4.727877109 0.023427409 0.010980413 44.21141589 -1.645534424 0.129229632 TQT(ph)PPLGQTPQLGLK ddPTM_BT-474_Pertuzumab_2h_R1 6 TQTPPLGQTPQLGLK 15 0 D3DQV9;P78344;H0Y3P2;P78344-2;E9PKF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 T(0.184)QT(0.816)PPLGQTPQLGLK;T(0.066)QT(0.934)PPLGQTPQLGLK;T(0.036)QT(0.964)PPLGQTPQLGLK;T(0.006)QT(0.994)PPLGQTPQLGLK;T(0.004)QT(0.996)PPLGQTPQLGLK;T(0.171)QT(0.829)PPLGQTPQLGLK 169.4 1.34E-05 6090069000 3031780 2929030 2555970 2390217 2498840 2874700 3255860 3785860 4857930 4712960 TRUE FALSE 2913294.686 2845496.932 3017890.636 2513576.386 2579217.458 2932828.404 3295706.189 3707680.668 4306478.153 4393747.021 0.663054717 0.647624207 0.686860354 0.572080362 0.587020019 0.667500516 0.75009011 0.843853925 0.98013794 1 22.06702038 1.645807436 1.279300671 1.005525366 0.632044606 0.942481742 0.034778366 0.095450252 0.297963516 0.031990355 0.011760881 44.23921746 -1.645807436 -0.37348076 KESETSREDEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KESETSREDEYK 12 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YHI8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ; 142.1 3.32E-05 918940000 554270 465070 371770 342150 460400 426230 425910 511730 598090 528370 FALSE TRUE 532608.5156 451806.659 438957.109 359808.4025 475209.1841 434848.6626 431122.414 501162.5967 530197.3306 492583.0293 1.081256324 0.917219295 0.891133236 0.730452292 0.964729103 0.882792619 0.875227908 1.017417505 1.076361342 1 18.9100074 1.645854105 4.795479819 1.040335378 0.90074787 0.318656824 0.083733532 0.177386001 9.124797419 0.04665163 0.022015214 44.24397162 -1.645854105 -0.139587508 ALPESLGQHALR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALPESLGQHALR 12 0 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ;; 171.32 3.88E-05 807940000 405379 514160 386555 516898 450165 453805 459247 460355 459680 499314 FALSE TRUE 389536.3405 499496.6602 456414.0874 543575.1677 464644.9661 462981.248 464867.4022 450848.5084 407499.0535 465495.018 0.836821718 1.073044052 0.980491884 1.167735737 0.998173875 0.994599792 0.998651724 0.968535625 0.875410128 1 18.8284062 1.645875173 2.741542195 0.934569057 1.014992031 0.09724785 0.082770905 0.457829717 7.947405158 0.052562835 0.021715725 44.24611795 -1.645875173 0.080422973 NKEVTWEVLEGEVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 NKEVTWEVLEGEVEK 15 1 P05455 P05455 SSB Lupus La protein 0 ;; 221.85 1.35E-12 731640000 2256460 2019500 1668180 1362700 1717870 1958980 1711570 2161650 2516520 2123570 FALSE TRUE 2168275.049 1961905.837 1969657.234 1433029.11 1773126.849 1998591.918 1732516.706 2117011.172 2230855.2 1979738.712 1.095232939 0.990992309 0.994907672 0.723847597 0.895636802 1.009523078 0.875123922 1.069338675 1.126843247 1 20.9168786 1.645895721 6.642412946 1.075445995 0.937661759 0.251315708 0.097944617 0.174774609 15.68011818 0.052604465 0.026249859 44.24821148 -1.645895721 -0.137784236 DIISDTSGDFRK ddPTM_BT-474_Pertuzumab_2h_R1 4 DIISDTSGDFRK 12 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YN52 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ;;; 222.72 3.87E-11 2744560000 2854020 2510770 1285126 3602460 2368390 1922330 1790280 3164100 3243410 2948110 FALSE TRUE 2742481.743 2439165.298 1517376.856 3788383.392 2444571.415 1961200.83 1812189.982 3098760.229 2875231.694 2748431.884 0.997835078 0.887475259 0.552088216 1.378379946 0.889442241 0.713570833 0.659354155 1.127464809 1.046135329 1 21.39017729 1.645993645 12.40998663 1.064453598 0.871919703 0.141809497 0.213099818 0.231400423 60.19591406 0.101784285 0.055439492 44.25818956 -1.645993645 -0.192533895 YEPERDEWHLVAPMLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 YEPERDEWHLVAPMLTR 17 1 K7EQX2;Q14145 K7EQX2 KEAP1 Kelch-like ECH-associated protein 1 0 96.143 0.0014386 265510000 87251 111870 75690 93644 102440 111410 107770 90980 97347 102390 FALSE TRUE 83841.13446 108679.5771 89368.86671 98476.97806 105735.0756 113662.7865 109088.9215 89101.23121 86296.57667 95455.0341 0.878331198 1.138542123 0.936240478 1.031658298 1.107695122 1.190746906 1.14283047 0.933436691 0.904054747 1 16.54253366 1.646015084 7.906195174 0.938444643 1.064412461 0.240220321 0.093123817 0.161087727 19.51923757 0.047312704 0.024334561 44.26037443 -1.646015084 0.125967818 SHHCTLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHHCTLAR 8 0 Q9HCN6-3 Q9HCN6-3 0 ; 92.692 0.02698 947390000 990390 1152850 913980 1112500 1118800 1026260 1121160 1040730 1132020 1108510 FALSE TRUE 951684.4639 1119971.847 1079156.517 1169916.258 1154787.218 1047011.68 1134881.091 1019238.562 1003517.835 1033429.63 0.920899146 1.083742728 1.044247703 1.132071526 1.117431883 1.013142695 1.098169685 0.986267988 0.971055799 1 19.97900872 1.646036523 6.592081778 0.982880033 1.06211727 0.250541772 0.05731128 0.169501356 15.00578022 0.029240896 0.014573749 44.26255947 -1.646036523 0.079237237 GTFVER ddPTM_BT-474_Pertuzumab_2h_R1 1 GTFVER 6 0 P09012;M0R221;M0R2B8;M0R268;M0QXK2;M0QZG7 P09012 SNRPA U1 small nuclear ribonucleoprotein A 0 99.279 0.090682 769290000 666520 737830 570120 675380 680100 677020 661900 677400 714930 687100 FALSE TRUE 640471.6615 716787.8108 673153.3663 710236.4427 701976.0342 690709.8083 670000.5302 663411.4533 633774.1436 640562.105 0.999858806 1.118998151 1.050879159 1.108770621 1.095875058 1.078287028 1.045957176 1.035670777 0.989403117 1 19.28897893 1.646144906 1.470145943 0.99446235 1.078358233 0.481113411 0.032191771 0.300114153 1.264776095 0.024864902 0.00907233 44.27360704 -1.646144906 0.083895883 GPASTPTYS(ph)PAPTQPAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GPAST(0.001)PT(0.001)YS(0.998)PAPTQPAPR;GPASTPT(0.01)YS(0.99)PAPTQPAPR 401.1 2.37E-128 501170000 236380 274990 235720 280510 252460 272580 265130 250570 247350 275120 TRUE FALSE 227142.0083 267147.5544 278319.8476 294987.1547 260580.6052 278091.7544 268374.7402 245395.6419 219271.865 256485.8773 0.885592652 1.041568281 1.085127378 1.150110711 1.01596473 1.084238077 1.046352895 0.956760834 0.854908142 1 17.96851986 1.646305972 3.75534012 0.92188064 1.050379567 0.31853035 0.071759074 0.195773076 6.493616105 0.042028721 0.018890191 44.29002978 -1.646305972 0.128498927 AHQNTLEVYPPFLFFLAVGGVYHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHQNTLEVYPPFLFFLAVGGVYHPR 25 0 Q5VV87;Q5VV89;O14880 Q5VV87 MGST3 Microsomal glutathione S-transferase 3 0 152.47 7.18E-08 45574000 29448 42041 22873 31079 21490 32833 37403 20772 26989 16802 FALSE TRUE 28297.1396 40842.03184 27006.65991 32682.99091 22181.24537 33496.90576 37860.7491 20343.05094 23925.32187 15663.98557 1.806509555 2.607384414 1.724124411 2.086505427 1.416066509 2.138466331 2.417057199 1.298714867 1.527409595 1 13.93516372 1.646342206 7.278349005 1.303578727 2.019915082 0.503942264 0.341284941 0.104911389 11.00255735 0.170102823 0.086273676 44.29372509 -1.646342206 0.716336354 EDITQSAQHALR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDITQSAQHALR 12 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 275.63 7.83E-28 7091800000 2911200 3294300 2661400 3216800 2979600 2904300 3129300 2969300 3061300 3308700 FALSE TRUE 2797427.085 3200349.789 3142374.183 3382819.434 3075441.54 2963026.936 3167597.309 2907982.917 2713794.058 3084598.802 0.906901437 1.03752546 1.018730274 1.096680525 0.997031296 0.960587462 1.026907391 0.942742672 0.87978834 1 21.55665143 1.646576496 5.239869376 0.931169034 1.0092334 0.230239415 0.054096318 0.187649569 11.23621797 0.028772793 0.013795905 44.31762682 -1.646576496 0.078064367 EPPADVWT(ph)PPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EPPADVWTPPAR 12 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 1 EPPADVWT(1)PPAR 106.54 0.021358 243500000 104790 98806 110400 108980 121670 116190 108600 98097 86813 102380 TRUE FALSE 100694.6909 95988.14962 130351.7358 114604.4709 125583.626 118539.4414 109929.0793 96071.26267 76958.35219 95445.71141 1.054994399 1.005683212 1.365716007 1.20072939 1.315759757 1.241956707 1.151744564 1.006554001 0.806304977 1 16.54239276 1.646598328 2.737181494 0.902830766 1.200620494 0.535741215 0.110668851 0.178254892 3.082717583 0.075667995 0.03127204 44.31985475 -1.646598328 0.297789728 (ac)MELDLSPPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_BT-474_Pertuzumab_2h_R1 11 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLSPPHLSSSPEDLCPAPGT(0.96)PPGT(0.04)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.774)PPGT(0.221)PRPPDT(0.004)PLPEEVKR;MELDLSPPHLS(0.004)S(0.004)S(0.004)PEDLCPAPGT(0.753)PPGT(0.186)PRPPDT(0.051)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.996)PPGT(0.003)PRPPDTPLPEEVKR;MELDLSPPHLS(0.001)S(0.001)S(0.001)PEDLCPAPGT(0.834)PPGT(0.154)PRPPDT(0.01)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.978)PPGT(0.021)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.841)PPGT(0.156)PRPPDT(0.002)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.888)PPGT(0.107)PRPPDT(0.004)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.801)PPGT(0.195)PRPPDT(0.004)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.963)PPGT(0.037)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.797)PPGT(0.202)PRPPDT(0.001)PLPEEVKR 154.84 5.62E-67 16089190000 1925114 3246832 2154469 3422530 2708719 3197167 2681348 2614290 2430615 2646811 TRUE FALSE 1849878.417 3154235.53 2543829.474 3599167.183 2795847.407 3261815.907 2714163.139 2560303.998 2154701.775 2467540.133 0.74968524 1.27829148 1.030917163 1.458605327 1.133050429 1.321889708 1.099946908 1.03759366 0.873218533 1 21.23464212 1.64686584 2.498323809 0.941369096 1.173709306 0.185643737 0.181271732 0.373562651 5.270048952 0.117910795 0.04745622 44.34716282 -1.64686584 0.23234021 TNLESILSY(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 TNLESILSYPK 11 0 H9KV48;E9PGN7;P05155-2;P05155;P05155-3 H9KV48 SERPING1 Plasma protease C1 inhibitor 1 TNLESILS(0.004)Y(0.996)PK 85.813 0.086705 72586000 71258 116190 79088 149080 125430 127080 103950 87427 57678 87842 TRUE FALSE 68473.15858 112876.375 93380.9609 156774.0367 129464.5699 129649.6447 105222.1712 85621.6019 51130.63525 81892.3831 0.836135865 1.378350106 1.140288722 1.914390945 1.580911007 1.583170983 1.284883492 1.045538042 0.624363748 1 16.32144165 1.646995707 2.575916107 0.816135205 1.420789898 0.407308837 0.283640728 0.234796369 3.547869148 0.196001073 0.07960662 44.36042591 -1.646995707 0.604654693 LSSEVEALRR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSSEVEALRR 10 1 P15924 P15924 DSP Desmoplakin 0 ;;; 142 5.86E-05 3117460000 1600644 1843500 1381359 1679370 1552502 1586540 1572634 1555590 1529670 1511177 FALSE TRUE 1538089.063 1790925.185 1631001.299 1766042.487 1602439.637 1618620.926 1591880.365 1523466.523 1356028.274 1408823.636 1.091754158 1.271220286 1.157704384 1.253558247 1.137430972 1.148916646 1.129935873 1.081374903 0.962525216 1 20.42605959 1.647245685 1.126943858 0.97652724 1.187153566 0.679871838 0.052082773 0.245201034 0.589333619 0.042292002 0.015918271 44.38596693 -1.647245685 0.210626325 GVQKPAGPST(ph)SPDGNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVQKPAGPSTSPDGNSR 17 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GVQKPAGPS(0.128)T(0.436)S(0.436)PDGNSR 99.569 0.0025039 546960000 296190 278560 253060 288780 270110 269530 283800 310420 354310 331350 TRUE FALSE 284614.5673 270615.7415 298793.5713 303683.9704 278798.3335 274980.0813 287273.2293 304009.7185 314090.2142 308907.3694 0.921358943 0.876041715 0.967259447 0.983090727 0.902530535 0.890170027 0.929965607 0.984145244 1.01677799 1 18.23681476 1.647385211 3.138840346 1.006731065 0.923861645 0.568967091 0.030766329 0.163789389 3.799306612 0.02072449 0.008913253 44.40022905 -1.647385211 -0.08286942 TEESEPLPSCPGS(ph)PPLPDDLLPLDCK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEESEPLPSCPGSPPLPDDLLPLDCK 26 0 O94864;O94864-2 O94864 SUPT7L STAGA complex 65 subunit gamma 1 TEESEPLPS(0.001)CPGS(0.999)PPLPDDLLPLDCK;TEESEPLPS(0.002)CPGS(0.998)PPLPDDLLPLDCK 141.84 1.87E-07 133556000 301135 262955 257853 286980 262740 280317 311499 347475 408850 408074 TRUE FALSE 289366.3113 255455.7809 304452.773 301791.0722 271191.2707 285985.2018 315311.2179 340299.5198 362439.062 380434.7845 0.760620014 0.671483763 0.800275856 0.793279386 0.712845622 0.751732527 0.828818054 0.894501591 0.952696958 1 18.53728964 1.64744014 1.174825958 0.993934441 0.744824176 0.868988248 0.035895954 0.151110934 0.39514985 0.031771396 0.011850386 44.40584509 -1.64744014 -0.249110264 TVSLTPS(ph)PTTQVETPDLVDHDNT(ph)SPLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TVS(0.002)LT(0.069)PS(0.817)PT(0.051)T(0.06)QVETPDLVDHDNT(0.586)S(0.414)PLFR 159.84 1.80E-11 321000000 154750 167770 151830 201210 182120 179360 161820 168180 167340 158800 TRUE FALSE 148702.1989 162985.3639 179269.0584 211594.4722 187978.0552 182986.7821 163800.4016 164707.0242 148344.2647 148044.3346 1.004443698 1.100922669 1.210914683 1.429264233 1.269741634 1.236026915 1.106428031 1.112552025 1.002025948 1 17.17566976 1.647461122 1.437724201 1.0014012 1.213786392 0.35460877 0.106169626 0.470893719 1.889474332 0.097243582 0.035514886 44.40799055 -1.647461122 0.212385193 TIHWIK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIHWIK 6 0 P78406;E9PQ57;E9PPG9;B0QZ36 P78406 RAE1 mRNA export factor 0 ; 112.27 0.02714 4050600000 5131700 5142700 4387300 5185600 4883200 5041700 5184800 4968100 5353900 5316800 FALSE TRUE 4931147.491 4996035.231 5180182.705 5453229.437 5040272.563 5143646.628 5248253.133 4865506.999 4746147.717 4956688.4 0.994847183 1.007938129 1.04508944 1.100175964 1.016862904 1.037718374 1.058822486 0.981604371 0.957523922 1 22.24094514 1.64759034 5.846644498 0.975857899 1.038026058 0.449334359 0.029162665 0.125268973 9.032744845 0.016070575 0.007855575 44.42120552 -1.64759034 0.062168159 TT(ph)PPESAPQNGPSPMAALMSVADTLGTAHS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 T(0.46)T(0.539)PPESAPQNGPSPMAALMSVADTLGT(0.001)AHS(0.999)PK;T(0.468)T(0.532)PPESAPQNGPSPMAALMSVADTLGT(0.001)AHS(0.999)PK;T(0.481)T(0.508)PPES(0.011)APQNGPS(0.138)PMAALMS(0.108)VADT(0.069)LGT(0.157)AHS(0.528)PK 168.4 6.87E-14 318059000 313134 246763 223476 199673 249553 235996 255741 287952 361239 296954 TRUE FALSE 300896.3771 239725.5608 263863.0844 209978.1475 257580.0989 240768.0008 258870.8349 282005.6906 320232.6632 276841.0411 1.086892232 0.865932161 0.953121269 0.758479114 0.930425987 0.869697643 0.935088359 1.01865565 1.156738401 1 18.07869831 1.647603547 2.893682124 1.080493146 0.9052833 0.381636814 0.085761009 0.204800934 3.996823018 0.052579536 0.022108517 44.42255635 -1.647603547 -0.175209846 TESSTEGKEQEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 TESSTEGKEQEEK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 189.09 5.07E-06 3889520000 4229420 3617640 2508040 2250360 2941780 3254770 3132660 3877650 4945560 3840720 FALSE TRUE 4064129.591 3514468.449 2961298.619 2366501.349 3036405.025 3320583.679 3170998.43 3797575.172 4384160.762 3580584.613 1.135046376 0.981534813 0.827043329 0.660925967 0.848019347 0.927385899 0.885609132 1.060601992 1.224425963 1 21.77176373 1.647675706 3.672282285 1.12062797 0.885607898 0.353498857 0.124241877 0.201251467 6.39641167 0.078050098 0.03494167 44.4299379 -1.647675706 -0.235020072 RS(ph)PPEEPPDFCCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPPEEPPDFCCPK 14 1 A0A087X0G7;A0A087WUW6;A0A087X1B1;Q9Y6K9;Q9Y6K9-2;Q9Y6K9-3 A0A087X0G7 IKBKG NF-kappa-B essential modulator 1 RS(1)PPEEPPDFCCPK 140.28 6.12E-06 231610000 248860 234260 192460 237930 214610 287370 243290 272630 333660 333780 TRUE FALSE 239134.2761 227579.1342 227241.8032 250209.5958 221513.1256 293180.8183 246267.4558 267000.0952 295784.3156 311172.7833 0.768493547 0.731359381 0.730275318 0.804085734 0.71186536 0.942180146 0.791417081 0.8580445 0.950546871 1 18.24735636 1.647810878 0.398717624 1.011810011 0.726298101 0.691573912 0.054516752 0.594550624 0.269940706 0.063941646 0.052491025 44.44376867 -1.647810878 -0.285511911 LQEGYDHSYYFIATFITDHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQEGYDHSYYFIATFITDHIR 21 0 P10768;X6RA14 P10768 ESD S-formylglutathione hydrolase 0 78.794 0.0048178 31007000 25771 23123 19258 21650 22641 26384 27477 19546 21090 24063 FALSE TRUE 24763.84083 22463.55468 22738.34899 22767.35909 23369.26833 26917.50256 27813.27175 19142.36827 18695.95162 22433.19158 1.103892897 1.00135349 1.013602942 1.01489612 1.04172731 1.199896255 1.239826783 0.853305612 0.833405784 1 14.45334727 1.648037677 9.389322364 0.882755742 1.080898153 0.50802362 0.086069972 0.094099826 14.96853561 0.044909406 0.02376737 44.46698429 -1.648037677 0.198142411 RSS(ph)RSS(ph)PELTR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.314)S(0.683)RS(0.378)S(0.624)PELTR 82.663 0.090121 3116500000 2883300 3521300 2425600 3272000 3172400 3269700 3031300 3017400 2875800 3215900 TRUE FALSE 2770617.448 3420875.972 2863959.877 3440868.312 3274443.127 3335815.574 3068397.956 2955089.636 2549351.24 2998084.229 0.92412929 1.141020635 0.955263314 1.147689007 1.092178497 1.112649052 1.023452886 0.985659311 0.850326757 1 21.51560948 1.648068972 2.615983209 0.924852691 1.064835788 0.315708105 0.077776893 0.249266562 3.897208635 0.048520093 0.019820071 44.47018868 -1.648068972 0.139983097 DSENLAS(ph)PSEYPENGER ddPTM_BT-474_Pertuzumab_2h_R1 5 DSENLASPSEYPENGER 17 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 DSENLAS(1)PSEYPENGER;DSENLAS(0.999)PS(0.001)EYPENGER;DSENLAS(0.803)PS(0.197)EYPENGER;DSENLAS(1)PSEYPENGER;DSENLAS(0.996)PS(0.004)EYPENGER 422.16 1.98E-160 3104040000 1634270 1729700 1414582 1729130 1778900 1674000 1554330 1671710 1664610 1604290 TRUE FALSE 1570400.922 1680370.65 1670228.435 1818370.607 1836119.934 1707849.427 1573352.355 1637188.604 1475650.451 1495630.009 1.049992921 1.123520282 1.116739049 1.215789062 1.227656521 1.141892992 1.051966292 1.094648138 0.986641377 1 20.51232189 1.64819656 1.247546022 0.996447125 1.147951869 0.526064419 0.053312501 0.36797292 1.089383401 0.049112314 0.018138926 44.48325517 -1.64819656 0.151504743 ALRPPT(ph)SPGVFGALQNFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALRPPTSPGVFGALQNFK 18 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ALRPPT(0.5)S(0.5)PGVFGALQNFK 113.17 0.00041199 424460000 318820 253490 204550 260480 299970 216760 194050 277300 185630 196150 TRUE FALSE 306360.1619 246260.7134 241516.7352 273923.404 309618.8075 221143.0357 196424.8419 271573.6581 164558.0606 182864.5858 1.675338943 1.346683462 1.320740887 1.497957644 1.693158936 1.209326753 1.074154633 1.485107994 0.899890265 1 17.48041618 1.648453455 0.608278651 0.979680805 1.487563444 0.472962345 0.188855807 0.716248538 0.581012893 0.183822546 0.098814758 44.50957576 -1.648453455 0.507882639 NINPSTANS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 NINPSTANSPK 11 0 P46937-6;P46937-7;P46937;P46937-9;P46937-4;H0YCI3 P46937-6 YAP1 Transcriptional coactivator YAP1 1 NINPSTANS(1)PK;NINPSTANS(1)PK;NINPSTANS(1)PK;NINPSTANS(1)PK 230.23 2.05E-12 1426290000 1894440 1488990 1491670 1127920 1222060 1294450 1391810 1726080 1973420 1884930 TRUE FALSE 1820403.19 1446525.463 1761247.951 1186132.086 1261368.67 1320624.666 1408843.387 1690435.845 1749405.635 1757262.012 1.035931567 0.823170053 1.002268267 0.674988748 0.717803413 0.751524051 0.801726423 0.961971427 0.995529194 1 20.74489789 1.648558841 4.322492542 0.991666713 0.822842378 0.306538689 0.107873907 0.210354341 9.040271002 0.063464487 0.029433609 44.52037777 -1.648558841 -0.168824334 FDDVWPMDPHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 FDDVWPMDPHPR 12 0 O00165-3;O00165;O00165-2;O00165-5;E9PIQ7 O00165-3 HAX1 HCLS1-associated protein X-1 0 122.39 0.00035932 156160000 278390 335160 287560 385630 258320 320100 342330 293470 321210 312310 FALSE TRUE 267510.211 325601.565 339528.4887 405532.4105 266629.0974 326572.6413 346519.5369 287409.7419 284747.5874 291156.9655 0.918783483 1.118302509 1.166135552 1.392830873 0.915757234 1.121637742 1.190146821 0.987129885 0.97798652 1 18.15143761 1.64879957 6.956948268 0.985557999 1.122197656 0.174991929 0.128131712 0.217124543 20.93396342 0.0657432 0.033146184 44.54506226 -1.64879957 0.136639657 EKQSDDEVYAPGLDIESSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQSDDEVYAPGLDIESSLK 20 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 163.64 1.76E-11 275690000 606640 551850 477440 485420 535790 502450 513030 648320 746210 695870 FALSE TRUE 582931.8381 536111.7783 563724.0286 510472.5844 553024.1719 512609.8833 519308.6146 634931.9654 661503.3692 648738.1051 0.898562661 0.826391689 0.868954705 0.786870049 0.852461367 0.790164597 0.800490384 0.97871847 1.019677068 1 19.30727666 1.649053826 4.672467295 1.006039547 0.830808836 0.837070428 0.033956507 0.057153882 2.817145626 0.01858486 0.008748557 44.57114858 -1.649053826 -0.175230711 LES(ph)PSFTGTGDTEIAHATEDLENNGSKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LESPSFTGTGDTEIAHATEDLENNGSKK 28 1 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 LES(0.831)PS(0.052)FT(0.058)GT(0.058)GDTEIAHATEDLENNGSKK 76.423 0.0038316 82793000 28830 30260 22204 29243 24838 23582 25879 33872 39336 36896 TRUE FALSE 27703.29173 29397.01443 26216.75673 30752.23473 25636.93683 24058.8442 26195.71494 33172.53136 34870.74219 34397.00106 0.805398461 0.854638879 0.762181467 0.894038253 0.745324768 0.699445982 0.761569734 0.964401847 1.013772745 1 15.06999517 1.649063941 4.416183913 1.000886326 0.789490881 0.761258841 0.0525149 0.082387415 3.679080975 0.031440227 0.014646713 44.57218675 -1.649063941 -0.211395445 HGWEELVYYTVPLIQEMESR ddPTM_BT-474_Pertuzumab_2h_R1 2 HGWEELVYYTVPLIQEMESR 20 0 O75323;O75323-2 O75323 GBAS Protein NipSnap homolog 2 0 ; 170.06 9.85E-12 195851000 338801 495110 333291 589660 322953 401376 504430 314558 378550 296506 FALSE TRUE 325560.2824 480989.9476 393524.0977 620092.4233 333341.0765 409492.0977 510603.3652 308062.2674 335578.591 276423.3845 1.177759555 1.740047964 1.4236281 2.243270497 1.205907659 1.481394559 1.847178617 1.114458055 1.214002179 1 18.07652014 1.649455752 7.206299002 1.119413851 1.593211819 0.348341076 0.299560079 0.137066805 13.98191374 0.145661085 0.073929889 44.61241686 -1.649455752 0.473797968 RDAYVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDAYVSR 7 1 P00390-5;P00390-4;P00390-2;P00390-3;P00390;A0A2R8YF59;H0YC68 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 91.069 0.026738 31282000 55446 61650 53040 65132 52339 42542 71787 39842 41139 57408 FALSE TRUE 53279.10902 59891.80236 62625.50787 68493.47033 54022.53147 43402.22839 72665.55078 39019.24878 36469.07319 53519.70503 0.995504534 1.119060771 1.170139257 1.279780415 1.009395165 0.810957915 1.357734516 0.729063226 0.681413942 1 15.70778254 1.649548515 9.400237798 0.779471824 1.09981781 0.413682683 0.163830625 0.10146688 15.88927841 0.07790891 0.041277335 44.62194691 -1.649548515 0.320345986 GPPQEEEEEEDEEEEATKEDAEAPGIR ddPTM_BT-474_Pertuzumab_2h_R1 6 GPPQEEEEEEDEEEEATKEDAEAPGIR 27 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;; 346.89 4.06E-110 10426230000 3191912 3075776 2365045 2547221 2873128 2733439 2764019 3096516 3459495 3239519 FALSE TRUE 3067168.55 2988057.88 2792461.242 2678683.381 2965544.771 2788711.009 2797845.891 3032571.863 3066787.631 3020103.493 1.015583922 0.989389234 0.924624354 0.886950857 0.981934817 0.923382598 0.92640729 1.004128458 1.015457794 1 21.52616656 1.649550966 6.040309792 1.008442473 0.948250139 0.342951598 0.035935312 0.158301622 12.05246572 0.019908142 0.009799213 44.62219877 -1.649550966 -0.060192334 GAPS(ph)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GAPSPGVLGPHASEPQLAPPACTPAAPAVPGPPGPR 36 0 O96013;O96013-4;O96013-3;M0R0L9 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 GAPS(1)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR 114.71 6.37E-06 683960000 47507 73009 63094 83739 66011 73690 67781 54690 47448 53148 TRUE FALSE 45650.37392 70926.8548 74496.48932 88060.77983 68134.30376 75180.06229 68610.52415 53560.63239 42061.90196 49548.23862 0.921331922 1.43147076 1.503514381 1.777273669 1.375110512 1.517310491 1.384721759 1.080979544 0.848908117 1 15.59654615 1.649561191 2.762097385 0.92866321 1.440470019 0.504122679 0.202731985 0.184211648 3.246153132 0.134662413 0.055985511 44.62324934 -1.649561191 0.511806809 LLKEEDMTK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLKEEDMTK 9 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 123.8 0.00049936 1160160000 1647050 1424980 1371670 1210690 1437670 1402560 1569230 1767340 2145630 2039740 FALSE TRUE 1582681.465 1384340.966 1619561.282 1273173.856 1483913.961 1430920.724 1588434.706 1730843.811 1902067.078 1901586.593 0.832295238 0.727992599 0.851689472 0.669532411 0.780355713 0.752487806 0.835320733 0.910210357 1.000252676 1 20.85877221 1.649584625 1.578866888 1.005006315 0.766567457 0.78002479 0.048986851 0.150096147 0.741278649 0.037005528 0.01357213 44.62565719 -1.649584625 -0.238438858 TS(ph)PLKDNPSPEPQLDDIKR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 1 T(0.164)S(0.836)PLKDNPSPEPQLDDIKR;T(0.433)S(0.567)PLKDNPSPEPQLDDIKR;T(0.132)S(0.78)PLKDNPS(0.088)PEPQLDDIKR;T(0.113)S(0.887)PLKDNPSPEPQLDDIKR 228.48 5.36E-20 3255770000 2110670 1592250 1364850 1096230 1397860 1397690 1480580 1814560 2193580 1882890 TRUE FALSE 2028182.683 1546840.589 1611508.756 1152806.562 1442823.436 1425952.249 1498699.781 1777088.702 1944573.995 1755360.183 1.155422518 0.881209796 0.918050194 0.656735052 0.821952925 0.812341685 0.853784765 1.012378382 1.107792015 1 20.74333566 1.649810446 3.932479967 1.055267635 0.860916401 0.296163042 0.119234117 0.213611734 7.731352082 0.070724337 0.032208141 44.64886732 -1.649810446 -0.194351234 EQKMNRDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQKMNRDNK 9 2 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;A0A0C4DGG3 Q8NHM5-4 KDM2B Lysine-specific demethylase 2B 0 49.418 0.094455 118510000 114280 165520 115170 171570 133960 162060 146320 126640 96148 160770 FALSE TRUE 109813.8113 160799.5317 135983.7809 180424.7483 138268.9451 165336.9642 148110.7079 124024.8397 85233.68213 149880.9047 0.732673795 1.072848686 0.907278891 1.203787425 0.922525423 1.103122273 0.988189311 0.827489266 0.568676058 1 17.19345707 1.649834453 3.978376799 0.761301535 1.000289949 0.240531926 0.154456461 0.201545588 7.453784238 0.082526429 0.037676106 44.65133552 -1.649834453 0.238988414 SKPPPTYES(ph)EEEDKCKPMSYEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKPPPTYESEEEDKCKPMSYEEK 23 3 O60885;O60885-2;O60885-3 O60885 BRD4 Bromodomain-containing protein 4 1 SKPPPTYES(1)EEEDKCKPMSYEEK;SKPPPT(0.001)YES(0.999)EEEDKCKPMSYEEK;SKPPPT(0.003)YES(0.996)EEEDKCKPMSYEEK;SKPPPT(0.002)YES(0.998)EEEDKCKPMSYEEK 188.17 1.22E-16 2138380000 793861 491893 488676 312239 516914 427880 497014 626502 819058 582759 TRUE FALSE 762836.0345 477864.6933 576990.6237 328353.6922 533541.0083 436532.0268 503096.606 613564.5148 726081.9696 543288.2139 1.404109301 0.879578612 1.062034127 0.604382138 0.982058868 0.803499902 0.926021572 1.129353627 1.336458165 1 19.05135822 1.650039651 4.300332348 1.185826101 0.93531538 0.166182412 0.206394071 0.252538994 10.76225866 0.112623115 0.052237552 44.67243762 -1.650039651 -0.250510721 DGDKSPMS(ph)SLQISNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGDKSPMSSLQISNEK 16 1 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 DGDKS(0.249)PMS(0.686)S(0.065)LQISNEK 291.33 9.37E-46 1775500000 1447800 1058200 1169800 850170 1169000 1154600 1260100 1457200 1844800 1669500 TRUE FALSE 1391218.375 1028021.172 1381208.882 894047.3756 1206601.947 1177946.803 1275521.481 1427108.311 1635386.038 1556423.278 0.893856058 0.660502311 0.887424971 0.574424315 0.775240234 0.756829341 0.819520948 0.916915296 1.050733474 1 20.56980303 1.650050824 1.729699731 1.027610734 0.751958274 0.57932905 0.090556452 0.218593914 1.32716992 0.066039702 0.024462429 44.67358692 -1.650050824 -0.27565246 SGYSS(ph)PGSPGTPGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 SGYS(0.03)S(0.969)PGS(0.002)PGTPGSR;SGYSS(1)PGSPGTPGSR;SGYS(0.023)S(0.976)PGS(0.001)PGTPGSR;SGYS(0.004)S(0.995)PGSPGTPGSR 291.2 6.78E-44 858720000 1329850 1393470 1041980 1258490 1165680 1266800 1105330 1196760 1232060 1076440 TRUE FALSE 1277877.992 1353729.6 1230288.965 1323440.82 1203175.156 1292415.564 1118857.359 1172046.488 1092201.714 1003531.76 1.273380717 1.348965378 1.225959171 1.318783194 1.198940785 1.287867126 1.11491973 1.167921669 1.088357895 1 19.93665485 1.650478215 0.468938969 0.99457828 1.308856773 0.796489327 0.04747487 0.35085739 0.196323724 0.045689213 0.031938589 44.71757203 -1.650478215 0.314278493 GDTSGDYKK ddPTM_BT-474_Pertuzumab_2h_R1 5 GDTSGDYKK 9 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 125.75 0.00079034 9161690000 13535160 11980670 9486510 10386390 8819980 8369000 9974080 12829410 14350670 14205480 FALSE TRUE 13006190.98 11638993.02 11200933.38 10922432.83 9103682.667 8538226.914 10096145.77 12564478.2 12721642.1 13243330.19 0.982093688 0.878856969 0.845779213 0.824749718 0.687416423 0.644719024 0.762357023 0.948740084 0.960607485 1 23.65876261 1.650654576 4.978312842 0.971619652 0.79870461 0.415727329 0.090297105 0.168087477 9.250663016 0.05553473 0.026465544 44.7357349 -1.650654576 -0.172915042 EPAFEDITLESER ddPTM_BT-474_Pertuzumab_2h_R1 1 EPAFEDITLESER 13 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 137.01 1.12E-05 0 100220 144590 105500 114130 159170 138010 130850 98825 83895 103600 FALSE TRUE 96303.2916 140466.4348 124566.1968 120020.263 164289.8476 140800.6568 132451.3814 96784.22922 74371.59132 96583.07972 0.997103135 1.454358622 1.28973105 1.242663449 1.701021008 1.457819083 1.37137252 1.002082658 0.770027126 1 16.55948285 1.650698425 3.595780612 0.885064545 1.373854 0.561662218 0.177461744 0.132441272 4.04047031 0.105401962 0.047082873 44.74025189 -1.650698425 0.488789454 AFALNDLDDYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AFALNDLDDYEK 12 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 167.18 0.00011613 400920000 922980 954870 878400 906930 966670 939010 1047910 1134850 1300680 1312010 FALSE TRUE 886908.9212 927638.0425 1037146.42 953736.766 997763.8185 957997.4256 1060734.636 1111414.951 1153032.259 1223146.394 0.725104473 0.758403121 0.847933187 0.779740488 0.815735404 0.783223848 0.867218054 0.908652436 0.942677234 1 20.22216565 1.650776496 0.7291165 1.001868584 0.775963718 0.860943089 0.03094868 0.220607564 0.238384731 0.029143604 0.013504955 44.74829533 -1.650776496 -0.225904866 ETVVEEPVDITPYLDQLDESLRDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETVVEEPVDITPYLDQLDESLRDK 24 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 0 ; 131.65 4.99E-05 89542000 79111 77811 56220 55795 68483 75730 63124 78601 85028 77296 FALSE TRUE 76019.25466 75591.90646 66380.20461 58674.58664 70685.81789 77261.31249 63896.53039 76977.86188 75375.97791 72060.67307 1.054934008 1.049003614 0.921171032 0.81423867 0.980920867 1.072170286 0.886704601 1.068236787 1.046007131 1 16.13692451 1.650776531 12.05437372 1.042532801 0.968455755 0.14377928 0.077520263 0.227858714 51.1667524 0.038633935 0.021029153 44.74829901 -1.650776531 -0.074077045 HYSNWETVLILEELRGDEGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HYSNWETVLILEELRGDEGTR 21 1 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 150.83 4.07E-08 50135000 18175 28640 14193 26602 16746 24394 25712 18652 21024 22846 FALSE TRUE 17464.70091 27823.21524 16757.99082 27974.93241 17284.6503 24887.26339 26026.67115 18266.82968 18637.44366 21298.62007 0.819992133 1.306338868 0.786811106 1.313462202 0.811538505 1.168491823 1.221988611 0.857653201 0.875054046 1 14.37847234 1.650890819 10.76865791 0.900398342 1.063899671 0.112575446 0.192232712 0.214896756 40.73453846 0.08340876 0.044951309 44.76007637 -1.650890819 0.163501329 LYDAYELK ddPTM_BT-474_Pertuzumab_2h_R1 3 LYDAYELK 8 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ;; 123.92 0.0030874 525980000 1214420 1299200 1022240 1218900 1082750 806280 1080640 1375420 1519840 1557600 FALSE TRUE 1166959.124 1262148.088 1206981.508 1281807.575 1117577.637 822583.534 1093865.196 1347017.096 1347314.135 1452102.365 0.803634201 0.869186718 0.831195883 0.882725355 0.76962731 0.566477649 0.753297579 0.927632328 0.927836885 1 20.46971173 1.651055754 4.763225203 0.951946745 0.782840678 0.460241448 0.084372944 0.164770664 8.40865338 0.052102763 0.024644941 44.77707846 -1.651055754 -0.169106067 SLSGSS(ph)PCPK ddPTM_BT-474_Pertuzumab_2h_R1 7 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSGS(0.016)S(0.984)PCPK;SLSGS(0.074)S(0.926)PCPK;SLSGS(0.021)S(0.979)PCPK;SLSGS(0.053)S(0.947)PCPK;SLSGS(0.011)S(0.989)PCPK;SLSGS(0.084)S(0.916)PCPK;SLSGS(0.208)S(0.792)PCPK 209.19 2.05E-07 9701190000 13568429 12966041 10918611 11609460 11303256 12572594 12878463 13869557 16941332 14966776 TRUE FALSE 13038159.79 12596262.21 12891846.89 12208625.62 11666835.49 12826820.46 13036073.48 13583145.8 15018223.02 13953062.93 0.934429943 0.90275965 0.923943865 0.874978181 0.836148705 0.919283496 0.934280419 0.973488464 1.0763388 1 23.73407852 1.6514009 1.877890118 1.0368769 0.897358319 0.73207517 0.032900481 0.158840158 1.164033483 0.025531118 0.00960003 44.81267822 -1.6514009 -0.139518581 QLLDLDPEVECLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLLDLDPEVECLK 13 0 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 150.68 0.00010321 27811000 151720 138540 116620 116080 133900 132020 123010 149490 158380 156530 FALSE TRUE 145790.6147 134588.9748 137695.8282 122070.9027 138207.0151 134689.5349 124515.4332 146402.9793 140401.3664 145928.0837 0.999057967 0.922296596 0.943586901 0.836514121 0.947089906 0.922985703 0.853265732 1.003254312 0.962127117 1 17.15489803 1.651553258 10.35504921 0.986763892 0.917364628 0.342273117 0.044764979 0.127012737 22.48996067 0.020992968 0.011269497 44.828402 -1.651553258 -0.069399263 HSQELPAILDDTTLSGSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSQELPAILDDTTLSGSDR 19 0 Q15021;F5GZK7 Q15021 NCAPD2 Condensin complex subunit 1 0 63.125 0.040878 140900000 43238 73576 56132 94183 69849 43782 80777 49080 52827 62741 FALSE TRUE 41548.21116 71477.68452 66276.30105 99043.79592 72095.75652 44667.30204 81765.57309 48066.48085 46830.30043 58491.49619 0.710329088 1.222018399 1.133092934 1.693302486 1.232585268 0.763654633 1.39790531 0.821768701 0.80063434 1 15.83593927 1.651645146 8.687671251 0.858521143 1.172420333 0.192310578 0.271297847 0.181310808 24.61419719 0.134060127 0.070306598 44.83788777 -1.651645146 0.31389919 TPTVPDS(ph)PGYMGPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPTVPDSPGYMGPTR 15 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 TPTVPDS(1)PGYMGPTR 142.13 1.34E-05 0 93414 108120 91786 130160 119210 118560 107100 96424 85457 97028 TRUE FALSE 89763.27761 105036.5235 108373.772 136877.5732 123044.4979 120957.3644 108410.7218 94432.8107 75756.27962 90456.20714 0.992339613 1.161186466 1.198079993 1.513191604 1.360265943 1.33719253 1.198488476 1.043961644 0.837491224 1 16.46493188 1.651689732 2.524905793 0.921375 1.267914079 0.507123947 0.135076856 0.209054765 3.015193154 0.098573346 0.040011832 44.84249128 -1.651689732 0.346539079 SES(ph)PKEPEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 7 SESPKEPEQLRK 12 2 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 S(0.016)ES(0.984)PKEPEQLRK;SES(1)PKEPEQLRK;S(0.003)ES(0.997)PKEPEQLRK;S(0.032)ES(0.968)PKEPEQLRK;S(0.001)ES(0.999)PKEPEQLRK;S(0.042)ES(0.958)PKEPEQLRK;S(0.014)ES(0.986)PKEPEQLRK 155.61 5.14E-05 30926450000 19719690 16192960 13789510 13657616 16048560 16567099 15349667 18435340 21764250 17711630 TRUE FALSE 18949022.71 15731152.64 16281581.2 14362487.2 16564776.51 16902097.09 15537520.82 18054643.79 19293663.58 16512005.52 1.147590623 0.952709991 0.986045043 0.869820881 1.003195916 1.023624724 0.940983262 1.093425251 1.168462762 1 23.97701202 1.65171733 6.350497627 1.099793738 0.985162319 0.248872303 0.076966335 0.158220365 13.07003019 0.038614224 0.019201314 44.84534097 -1.65171733 -0.114631419 ITNDFYPEEDGKTK ddPTM_BT-474_Pertuzumab_2h_R1 3 ITNDFYPEEDGKTK 14 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;; 197.88 2.08E-08 1443740000 1003880 879490 681640 634490 747790 902750 756550 950850 1103450 928780 FALSE TRUE 964647.2598 854407.8063 804827.511 667236.1049 771843.3445 921004.2235 765808.8852 931214.6152 978190.982 865872.9033 1.11407489 0.986758915 0.929498438 0.770593585 0.891404895 1.063671377 0.884435674 1.075463398 1.129716588 1 19.72379575 1.651756247 6.758177257 1.078306673 0.945048376 0.246747271 0.095123715 0.174744992 15.96767423 0.050817336 0.025546807 44.84935971 -1.651756247 -0.133258297 YCPDNLEVYFEDEDRAELYR ddPTM_BT-474_Pertuzumab_2h_R1 1 YCPDNLEVYFEDEDRAELYR 20 1 O95801 O95801 TTC4 Tetratricopeptide repeat protein 4 0 102.9 0.00026739 22119000 24552 48724 47252 73094 68293 70620 51128 35513 16584 31897 FALSE TRUE 23592.4807 47334.43923 55791.48752 76866.3901 70489.70637 72047.98479 51753.71976 34779.64414 14701.45385 29736.58778 0.793382242 1.591791216 1.876189963 2.584909562 2.370470576 2.422873307 1.740405461 1.169590956 0.494389402 1 14.85995149 1.651820991 2.698579436 0.762085569 1.97290934 0.484865011 0.494916702 0.206455637 3.453178476 0.352072591 0.145748084 44.85604627 -1.651820991 1.210823771 VTGLTEGLVDVILYHQPDDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTGLTEGLVDVILYHQPDDK 20 0 O43390-2;O43390-4 O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 205.24 8.83E-22 699550000 880540 720030 691110 652120 794380 741890 729150 832000 927470 857720 FALSE TRUE 846127.5233 699495.4494 816008.9507 685775.9914 819931.9541 756891.5241 738073.5558 814818.9093 822187.4939 799625.8604 1.058154276 0.874778423 1.020488445 0.857621077 1.025394494 0.946557086 0.923023619 1.019000197 1.028215237 1 19.6089656 1.652070952 7.225999182 1.018124165 0.955644458 0.156293738 0.061100169 0.200507587 20.37848036 0.028006048 0.014248634 44.88187087 -1.652070952 -0.062479707 EGIIHTLIVDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGIIHTLIVDNR 12 0 Q9NVQ4;Q9NVQ4-3;Q9NVQ4-2 Q9NVQ4 FAIM Fas apoptotic inhibitory molecule 1 0 86.911 0.010845 291680000 74436 129990 129310 181160 168780 149580 141660 90648 46557 101910 FALSE TRUE 71526.95883 126282.8125 152679.1935 190509.6893 174208.962 152604.6101 143393.6775 88776.08712 41272.04454 95007.54493 0.752855564 1.329187198 1.607021775 2.005205897 1.83363292 1.606236749 1.509287263 0.934410916 0.434408073 1 16.53575447 1.652177845 3.329915739 0.707052133 1.554323048 0.498888687 0.338534772 0.164647804 4.307492015 0.218306436 0.095833512 44.89291898 -1.652177845 0.847270915 EKDLLPS(ph)PAGPVPSKDPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKDLLPSPAGPVPSKDPK 18 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 EKDLLPS(1)PAGPVPSKDPK;EKDLLPS(1)PAGPVPSKDPK;EKDLLPS(0.999)PAGPVPS(0.001)KDPK 177.7 4.83E-14 2215840000 2770100 2359110 2075620 1658600 2195000 2211980 2350780 2819010 3398650 3189210 TRUE FALSE 2661841.429 2291830.493 2450730.706 1744200.545 2265604.168 2256707.751 2379549.549 2760796.458 3012849.5 2973201.966 0.895277704 0.770829065 0.824273202 0.586640452 0.762008163 0.759015962 0.800332294 0.928560014 1.013334962 1 21.50358604 1.652323622 2.052600912 1.008124737 0.760651423 0.646069291 0.072771344 0.182111455 1.63749041 0.054689424 0.020988008 44.90799047 -1.652323622 -0.247473314 NLDFGIDMDSR ddPTM_BT-474_Pertuzumab_2h_R1 6 NLDFGIDMDSR 11 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;;;;; 180.19 1.58E-05 1171845000 1275558 1348101 1234965 1415711 1388317 1303009 1360532 1303993 1338563 1393818 FALSE TRUE 1225707.783 1309654.479 1458150.647 1488776.014 1432973.477 1329356.735 1377182.598 1277065.089 1186614.94 1299413.465 0.943277729 1.007881259 1.122160641 1.145729249 1.102784845 1.023043681 1.059849412 0.982801181 0.913192738 1 20.30942913 1.652345278 3.245631573 0.95375951 1.062779092 0.342786627 0.05896624 0.231861059 5.755165828 0.039049285 0.017032024 44.91022991 -1.652345278 0.109019581 DAMEQCHNYNAR ddPTM_BT-474_Pertuzumab_2h_R1 3 DAMEQCHNYNAR 12 0 Q92785;J3KMZ8;Q92785-2;E9PN04 Q92785 DPF2 Zinc finger protein ubi-d4 0 ;; 212.68 1.74E-08 1128750000 1247150 1166050 975190 1134060 1075430 991800 1058860 1130020 986280 968530 FALSE TRUE 1198409.999 1132795.396 1151428.526 1192588.973 1110022.183 1011854.876 1071818.645 1106684.692 874321.6292 902930.6004 1.327244861 1.254576371 1.275212652 1.320798046 1.229354927 1.120634161 1.187044325 1.22565864 0.968315426 1 19.78425558 1.652484222 0.425193911 0.97940718 1.309742688 0.726236551 0.061964518 0.574260898 0.282456067 0.073839086 0.057123606 44.92460035 -1.652484222 0.330335509 GVNWAAFHPTMPLIVSGADDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVNWAAFHPTMPLIVSGADDR 21 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 221.14 4.42E-25 3505100000 2865600 3535000 2736100 3133000 2746200 3033500 3259300 2746900 2755200 3148600 FALSE TRUE 2753609.184 3434185.261 3230574.134 3294694.505 2834534.017 3094839.448 3299188.288 2690175.555 2442441.247 2935342.518 0.938087861 1.169943623 1.100578251 1.122422506 0.965656989 1.054336736 1.123953429 0.916477562 0.832080492 1 21.48509743 1.652652787 5.892102971 0.902623392 1.070335216 0.444117794 0.077299144 0.113644895 8.302772803 0.039275045 0.019290669 44.94204051 -1.652652787 0.167711824 DSYDSYATHNE ddPTM_BT-474_Pertuzumab_2h_R1 6 DSYDSYATHNE 11 0 Q14011 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ;;;;; 228.2 8.01E-12 6615990000 5639500 5945360 4509570 5630010 5613920 5326140 5715790 5428920 5803000 5966140 FALSE TRUE 5419102.105 5775804.154 5324549.614 5920575.491 5794496.835 5433838.2 5785741.548 5316810.905 5144267.768 5562048.024 0.974299769 1.038431191 0.957300187 1.064459614 1.041791946 0.97694917 1.040217834 0.955908845 0.924887334 1 22.40718477 1.6527205 6.775572851 0.954728129 1.013680093 0.297307072 0.037046099 0.139827143 12.80948192 0.0179836 0.009050976 44.94904824 -1.6527205 0.058951964 NVATETQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NVATETQLK 9 0 Q5T3J3 Q5T3J3 LRIF1 Ligand-dependent nuclear receptor-interacting factor 1 0 ; 62.558 0.081834 1513160000 1624550 3173900 1654520 2598400 2656100 2870100 2640400 1801910 1502350 2043100 FALSE TRUE 1561060.79 3083383.48 1953528.569 2732503.735 2741535.869 2928135.388 2672714.005 1764699.929 1331809.526 1904719.017 0.819575368 1.618812776 1.025625591 1.434596762 1.439338739 1.537305693 1.403206447 0.926488323 0.699215745 1 20.86114676 1.65275606 4.584809313 0.840701288 1.341583938 0.433052016 0.236025503 0.134434708 6.427668249 0.123408876 0.058042912 44.95272882 -1.65275606 0.50088265 TDGS(ph)ISGDRQPVTVADYISR ddPTM_BT-474_Pertuzumab_2h_R1 3 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 TDGS(0.999)IS(0.001)GDRQPVTVADYISR;T(0.001)DGS(0.997)IS(0.002)GDRQPVTVADYISR;TDGS(0.998)IS(0.002)GDRQPVTVADYISR 211.49 1.62E-22 1217680000 474940 441030 358110 423320 397760 465240 419050 487950 504120 515820 TRUE FALSE 456378.8197 428452.2562 422828.4431 445167.5959 410554.3116 474647.4716 424178.4593 477873.662 446894.411 480883.052 0.949043261 0.890969758 0.879274995 0.925729435 0.853750844 0.987033063 0.882082364 0.99374195 0.92932036 1 18.87532656 1.652804639 0.680371214 0.99204451 0.901465419 0.314467292 0.041228679 0.707654504 0.682649053 0.035438762 0.017325003 44.95775732 -1.652804639 -0.090579091 EENSGLLQELEELRK ddPTM_BT-474_Pertuzumab_2h_R1 3 EENSGLLQELEELRK 15 1 A0A3B3ISJ8;J3KP58;P30622-2;P30622-1;P30622;F5H0N7;A0A3B3ITA2 A0A3B3ISJ8;J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 0 ;; 224.06 1.90E-12 406280000 257171 249479 222044 229156 257247 262972 259960 306704 332554 346840 FALSE TRUE 247120.473 242364.1032 262172.2901 240982.7686 265521.5834 268289.474 263141.4682 300370.4552 294803.8641 323348.2179 0.76425494 0.749545196 0.810804809 0.745273223 0.821162971 0.829723064 0.813802129 0.928938026 0.911722557 1 18.30272913 1.652811214 0.578389852 1.001522635 0.76272924 0.890573131 0.026356973 0.209717539 0.157523958 0.024290981 0.013717517 44.95843798 -1.652811214 -0.238793395 EDKS(ph)PSEESAPTTSPESVSGSVPSSGSSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDKSPSEESAPTTSPESVSGSVPSSGSSGR 30 1 P54725-2;P54725;A0A494C0B4;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 EDKS(0.85)PS(0.149)EESAPTTSPESVSGSVPSSGSSGR;EDKS(0.952)PS(0.047)EES(0.001)APTTSPESVSGSVPSSGSSGR;EDKS(0.641)PS(0.179)EES(0.179)APTTSPESVSGSVPSSGSSGR 180.22 4.39E-18 3267890000 677779 552839 502248 493262 524582 593261 559464 679263 809580 713931 TRUE FALSE 651290.6474 537072.573 593015.386 518719.3109 541455.6564 605257.1439 566310.8878 665235.9817 717679.8724 665575.8175 0.978537126 0.806929217 0.890980968 0.779354203 0.813514617 0.9093737 0.850858569 0.999489411 1.078284177 1 19.34424349 1.65294477 3.552074235 1.039920171 0.85665793 0.638656794 0.057021088 0.110388621 3.286802139 0.032663046 0.014578674 44.97226593 -1.65294477 -0.183262241 TYDATTHFETTCDDIK ddPTM_BT-474_Pertuzumab_2h_R1 4 TYDATTHFETTCDDIK 16 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;; 268.61 1.50E-27 8781800000 8755000 8105800 7215000 7129000 7845000 6503700 8234100 8857300 10645700 9735300 FALSE TRUE 8412844.921 7874630.52 8518910.997 7496928.544 8097341.55 6635209.27 8334871.379 8674393.66 9437244.766 9075919.46 0.926941337 0.867639974 0.938627875 0.826024138 0.892178648 0.731078465 0.918350082 0.955759215 1.039811427 1 23.11361238 1.653091972 2.483735606 1.014785424 0.86582036 0.532846275 0.05693764 0.19113287 2.655157906 0.038359801 0.015520177 44.98751164 -1.653091972 -0.148965064 NTPENLHEMAK ddPTM_BT-474_Pertuzumab_2h_R1 3 NTPENLHEMAK 11 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;; 126.12 0.00031413 847080000 1509090 1361390 1108820 1167520 1179800 1233720 1394900 1419180 1755460 1596940 FALSE TRUE 1450113.094 1322564.49 1309208.44 1227775.847 1217749.338 1258666.664 1411971.203 1389873.437 1556187.54 1488777.831 0.97402921 0.888355846 0.879384695 0.824687083 0.817952358 0.845436194 0.948409611 0.93356672 1.045278555 1 20.50569705 1.6531029 1.572091006 1.017939316 0.87054243 0.58479178 0.047144554 0.262676305 1.28461098 0.039862982 0.014654942 44.9886437 -1.6531029 -0.147396886 KQTDAQSASS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQTDAQSASSPK 12 1 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H4P8;H0YFK8;F5H4Q7 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 KQTDAQS(0.003)AS(0.047)S(0.95)PK 75.911 0.019929 109570000 94899 73245 80613 70003 87458 80292 89209 94978 101850 105990 TRUE FALSE 91190.24216 71156.12431 95181.56233 73615.86322 90271.166 81915.55925 90300.76643 93016.67111 90288.41499 98811.20289 0.922873515 0.720122033 0.963266912 0.745015353 0.91357218 0.82901085 0.913871745 0.941357542 0.913746745 1 16.592387 1.653121888 0.646248623 0.991523914 0.837612507 0.296050869 0.073305466 0.762147962 0.677627597 0.062207247 0.031743612 44.9906107 -1.653121888 -0.153911407 FLPS(ph)PVVIK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLPSPVVIK 9 0 Q13618;Q13618-2;Q13618-3;A0A087WTG3;H7C399 Q13618 CUL3 Cullin-3 1 FLPS(1)PVVIK;FLPS(1)PVVIK 100.88 0.0045754 316750000 897880 848830 712760 820330 750590 776920 757840 904830 1003500 884870 TRUE FALSE 862789.8569 824622.1995 841571.5873 862667.3296 774733.409 792629.8547 767114.6726 886144.9443 889586.887 824936.9667 1.045885797 0.999618435 1.020164717 1.045737268 0.939142553 0.960836872 0.929907015 1.074197157 1.078369527 1 19.65392436 1.653126628 10.62587297 1.056935122 0.992061278 0.283134995 0.042772463 0.138690421 24.94782732 0.021260026 0.011451785 44.99110171 -1.653126628 -0.064873844 RMKVT(ph)NEDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RMKVTNEDFK 10 2 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 1 RMKVT(1)NEDFK 71.349 0.082403 442890000 285910 534850 660320 542220 725010 766020 643440 275230 134090 238160 TRUE FALSE 274736.3211 519596.6017 779654.5127 570204.0392 748330.6051 781509.4492 651314.6112 269546.4043 118868.6654 222029.2111 1.237388179 2.340217304 3.511495217 2.568148742 3.370415098 3.519849688 2.933463611 1.214013251 0.535373993 1 17.76038997 1.653196077 3.926203327 0.801319276 2.838738337 0.635671118 0.650920175 0.113784894 4.108680038 0.393303267 0.179551795 44.99829695 -1.653196077 2.037419061 QICVVMLETLSQS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 3 QICVVMLETLSQSPPK 16 0 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15366-8 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 1 QICVVMLETLSQS(1)PPK;QICVVMLETLSQS(1)PPK;QICVVMLET(0.001)LS(0.117)QS(0.882)PPK 267.39 2.70E-27 1295410000 794335 616268 556667 548875 558443 518115 615012 710270 815663 789315 TRUE FALSE 763291.51 598692.64 657269.1099 577202.5045 576405.8263 528591.6403 622538.7008 695602.6763 723072.3558 735853.992 1.037286633 0.81360249 0.893205876 0.784398143 0.783315484 0.718337668 0.846008458 0.945299861 0.982630201 1 19.48906001 1.653359092 3.122211344 0.984855333 0.830923657 0.384064243 0.080149331 0.2180087 4.990083939 0.050797523 0.021952421 45.01519044 -1.653359092 -0.153931676 WGDWRPHLAMVLSNLNNNMDVESR ddPTM_BT-474_Pertuzumab_2h_R1 1 WGDWRPHLAMVLSNLNNNMDVESR 24 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 48.641 0.088568 211340000 106530 126990 104660 110140 137840 118600 136770 103040 113190 119000 FALSE TRUE 102366.6898 123368.3695 123574.3901 115824.3386 142273.7488 120998.1733 138443.8322 100912.188 100341.1457 110940.024 0.922720999 1.112027608 1.113884653 1.044026623 1.282438417 1.090662945 1.247916011 0.909610295 0.904462989 1 16.75942042 1.653537063 8.485713007 0.930329694 1.118158517 0.411534454 0.097267775 0.106636242 13.77975133 0.046742063 0.024453182 45.03364114 -1.653537063 0.187828823 PEINTNHLDK ddPTM_BT-474_Pertuzumab_2h_R1 3 PEINTNHLDK 10 0 Q13907 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ;; 126.71 0.0003754 2584730000 3512880 2871030 2724390 2661340 3068810 2795240 3315970 3332160 4432160 3652390 FALSE TRUE 3375592.766 2789151.035 3216747.877 2798692.076 3167521.061 2851761.668 3356551.833 3263349.732 3929039.778 3405010.372 0.991360494 0.819131436 0.944710155 0.821933495 0.930252984 0.837519231 0.985768461 0.958396414 1.153899504 1 21.69922776 1.653691886 1.809846028 1.068143597 0.891652786 0.483126328 0.069483844 0.243083804 1.636354481 0.048269198 0.018064976 45.04969823 -1.653691886 -0.176490811 QLVARPDVVEMHDVTAQDPK ddPTM_BT-474_Pertuzumab_2h_R1 4 QLVARPDVVEMHDVTAQDPK 20 1 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;; 201.67 7.43E-22 1753790000 2781410 2540670 2040830 2112750 2224290 2207400 2328920 2589030 2972170 2688880 FALSE TRUE 2672709.422 2468212.579 2409653.379 2221789.281 2295836.308 2252035.14 2357422.02 2535565.626 2634781.722 2506759.763 1.066200863 0.984622705 0.96126219 0.886319189 0.91585813 0.898384909 0.940425985 1.011491274 1.051070693 1 21.25739231 1.653857837 4.354242341 1.026837003 0.94639546 0.299270528 0.049276071 0.207586055 9.064357715 0.029805321 0.013896453 45.06691577 -1.653857837 -0.080441543 TQDPS(ph)SPGTTPPQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQDPSSPGTTPPQAR 15 0 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 TQDPS(0.705)S(0.295)PGT(0.001)TPPQAR 195.23 1.98E-08 1391100000 429500 456570 352300 463090 437530 403450 433720 404030 397090 449710 TRUE FALSE 412714.6652 443549.0706 415968.4469 486990.1304 451603.5498 411608.0354 439027.9951 395686.6393 352014.0079 419250.7411 0.984410103 1.057956557 0.992171047 1.161572497 1.077168161 0.981770561 1.047172854 0.943794728 0.839626442 1 18.67745381 1.654215399 3.768649714 0.911829124 1.045657975 0.421251479 0.062003524 0.16028512 5.355052428 0.035620135 0.016132917 45.10403534 -1.654215399 0.133828851 EKDGTTDSGIK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDGTTDSGIK 11 1 Q9NW64;Q9NW64-2 Q9NW64 RBM22 Pre-mRNA-splicing factor RBM22 0 90.861 0.0064906 0 135140 132320 124340 128810 137770 133460 153190 160650 193450 191010 FALSE TRUE 129858.5794 128546.3632 146811.0039 135457.8995 142201.4972 136158.6526 155064.785 157332.5214 171490.367 178072.7226 0.729244645 0.721875655 0.824444091 0.760688653 0.798558561 0.764623861 0.870794711 0.8835296 0.963035576 1 17.44210701 1.65424303 0.772126825 1.005032298 0.757247079 0.885448858 0.030842048 0.1835414 0.218159741 0.027830559 0.012413814 45.10690511 -1.65424303 -0.247785218 QENSADDLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 QENSADDLHR 10 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 142.08 3.64E-05 40364000 63500 83632 61875 67650 79589 88808 82808 66678 71842 72721 FALSE TRUE 61018.3498 81246.89724 73057.1889 71141.42461 82149.05247 90603.75861 83821.42907 65301.076 63686.79735 67795.5419 0.900034841 1.198410618 1.077610516 1.049352548 1.211717617 1.336426498 1.236385561 0.963206048 0.939395063 1 16.04890279 1.654252878 6.845789598 0.961837858 1.149691171 0.336347544 0.113308844 0.147467438 13.69756296 0.060548787 0.030561503 45.10792797 -1.654252878 0.187853312 GGDGPSHESEDFPRPLVTLPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGDGPSHESEDFPRPLVTLPGR 22 1 Q15637-6;Q15637-2 Q15637-6 SF1 Splicing factor 1 0 141.78 7.19E-08 106260000 77700 102610 89962 112950 93337 100540 92726 89801 80241 90348 FALSE TRUE 74663.3981 99683.66327 106220.1346 118779.363 96339.26937 102572.9877 93860.80853 87946.57797 71132.37808 84228.64949 0.88643708 1.1834888 1.261092695 1.410201443 1.143782667 1.217792144 1.114357277 1.044140901 0.844515239 1 16.36202341 1.654321915 2.028699061 0.925289662 1.193679914 0.380386519 0.128869248 0.300632725 2.630296186 0.097126295 0.037244618 45.11509903 -1.654321915 0.268390252 ASDADRPCR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASDADRPCR 9 1 Q86U44;H0YFV6;Q86U44-2 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 108.3 0.0024015 115070000 237200 258590 207860 266750 268750 271380 236370 243320 236750 237050 FALSE TRUE 227929.9618 251215.2664 245424.9258 280516.9995 277394.5878 276867.4895 239262.7668 238295.357 209875.1325 220994.3924 1.031383463 1.136749506 1.110548205 1.269339898 1.25521098 1.252825859 1.082664425 1.078286894 0.94968533 1 17.75365024 1.654475278 1.85657604 0.980859579 1.176293845 0.509989078 0.074372324 0.273007981 1.948215532 0.060941172 0.02293015 45.13103335 -1.654475278 0.195434265 NREEEWDPEYTPK ddPTM_BT-474_Pertuzumab_2h_R1 3 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;; 122.34 0.0002154 2916730000 4814910 4576330 3510910 3909480 4256120 4610790 4174040 5125970 5852530 5421300 FALSE TRUE 4626737.994 4445817.549 4145409.537 4111248.731 4393021.965 4704023.333 4225123.15 5020116.928 5188175.33 5054110.522 0.915440605 0.879643912 0.820205557 0.813446543 0.869197843 0.930732186 0.835977593 0.99327407 1.026525896 1 22.26902578 1.654514054 4.909617098 1.011965503 0.865796772 0.759062891 0.036236595 0.075808053 4.086542122 0.020962506 0.009991455 45.1350631 -1.654514054 -0.146168731 LYHEADK ddPTM_BT-474_Pertuzumab_2h_R1 3 LYHEADK 7 0 O75663 O75663 TIPRL TIP41-like protein 0 ;; 127.84 0.0038154 800690000 1472360 1357890 1406630 1450250 1426500 1335820 1697730 1650210 1996190 1962130 FALSE TRUE 1414818.543 1319164.307 1660839.331 1525097.576 1472384.668 1362831.196 1718507.328 1616132.587 1769590.88 1829233.187 0.77344898 0.721156994 0.907942925 0.833736009 0.804919066 0.745028685 0.939468702 0.883502769 0.967394913 1 20.80280757 1.65451631 0.972709388 0.995178726 0.800793078 0.603270139 0.057712837 0.364672852 0.656670878 0.051931165 0.020540231 45.13529761 -1.65451631 -0.194385649 AAVGRPLDKHEGALETLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAVGRPLDKHEGALETLLR 19 2 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 239.18 1.69E-24 1667200000 632170 789960 513540 559910 665540 762600 702480 640860 742200 646380 FALSE TRUE 607464.0975 767431.1143 606348.1016 588807.0222 686947.6985 778020.2945 711077.1604 627626.017 657948.5676 602600.1069 1.008071672 1.273532987 1.006219705 0.977110717 1.139972746 1.291105471 1.180014992 1.04152988 1.091849404 1 19.2008414 1.654641437 8.381232792 1.050026727 1.127356377 0.111963838 0.103427198 0.296220021 37.32371082 0.053185255 0.027788515 45.1483036 -1.654641437 0.07732965 EHAALEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EHAALEPR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 74.92 0.03973 322250000 104090 160170 99489 183400 72978 46946 201970 89882 110360 97168 FALSE TRUE 100022.0477 155602.1084 117468.8754 192865.296 75325.40365 47895.28029 204441.7693 88025.90529 97832.39547 90586.72481 1.104157899 1.717714254 1.296755961 2.129067988 0.831528061 0.528722949 2.256862357 0.971730742 1.07998601 1 16.46701202 1.654647361 0.332916276 0.96483387 1.502245116 0.061149971 0.519591283 4.192333588 1.526944621 0.798258047 0.759628281 45.14891944 -1.654647361 0.537411246 MILVFWS(ph)NY(ph)PYEPVCLASHRNNMEASVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 MILVFWSNYPYEPVCLASHRNNMEASVPK 29 1 Q1A5X7 Q1A5X7 WHAMMP3 "Putative WASP homolog-associated protein with actin, membranes and microtubules-like protein 1" 2 MILVFWS(0.635)NY(0.55)PY(0.345)EPVCLAS(0.462)HRNNMEAS(0.008)VPK 41.205 0.071423 695280000 148060 256820 203400 318980 250310 311190 245200 205220 143430 242680 TRUE FALSE 142273.6515 249495.7451 240158.9046 335442.596 258361.4485 317482.475 248200.8309 200982.1353 127148.4277 226243.0674 0.628853088 1.102777415 1.061508347 1.482664639 1.141964045 1.403280457 1.097053862 0.88834605 0.561999221 1 17.78751406 1.654770764 3.407482159 0.768840103 1.153397021 0.274100148 0.236113412 0.234341514 6.418846048 0.142253013 0.062968437 45.16175017 -1.654770764 0.384556919 DYENDEDVNKQLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYENDEDVNKQLDK 14 1 A6NKE1;A0A087WWM0;O43617 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 144.29 8.11E-06 211310000 298960 275530 195170 155970 238250 233330 227970 284300 355580 271270 FALSE TRUE 287276.3127 267672.1542 230441.5605 164019.6304 245913.5276 238048.0925 230759.9651 278429.1056 315216.0491 252896.6413 1.135943567 1.058425105 0.911208466 0.648563894 0.97238748 0.941286097 0.912467496 1.100960077 1.246422442 1 17.94818835 1.654888635 4.580357663 1.13767322 0.93366114 0.272172642 0.130935233 0.204059075 9.754483817 0.076113948 0.03584585 45.17400909 -1.654888635 -0.20401208 S(ph)KTPTGPELDTSYK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKTPTGPELDTSYK 14 1 Q8NF91;Q8NF91-4;A0A0C4DG40;E7ENN3;H0Y325;Q8NF91-2;Q8NF91-8;Q8NF91-11;Q8NF91-3;Q8NF91-9;A0A5F9ZH87;A0A5F9ZHE1;Q5JV20;F8WAI0;H0Y326;A0A5F9ZH86 Q8NF91 SYNE1 Nesprin-1 1 S(0.675)KT(0.324)PTGPELDTSYK 184.83 7.56E-07 1027400000 283990 235150 207570 232220 247950 254900 265760 301850 367130 349530 TRUE FALSE 272891.3568 228443.7522 245082.5164 244204.902 255925.5369 260054.2526 269012.4504 295616.692 325454.9415 325856.0218 0.837459917 0.701057329 0.752119034 0.749425776 0.78539453 0.798064898 0.825556173 0.907200335 0.998769149 1 18.31387513 1.654917032 1.134199065 1.012894897 0.760418913 0.883983482 0.033252637 0.133078363 0.323649582 0.02758998 0.010407561 45.17696298 -1.654917032 -0.252475984 LSETSIKDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSETSIKDR 9 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 128.87 0.00036958 1279710000 1956380 2127000 1525640 1649870 1822040 2141590 1801430 1804370 1886420 1773980 FALSE TRUE 1879922.507 2066340.043 1801357.086 1735019.988 1880647.571 2184894.417 1823476.439 1767109.129 1672281.51 1653826.755 1.136710663 1.249429565 1.089205433 1.049094159 1.137149079 1.321114446 1.102580082 1.068497123 1.01115882 1 20.65737668 1.654943916 2.400244953 1.01239069 1.159515163 0.410452429 0.073977293 0.276226478 3.549461609 0.053683142 0.021549425 45.17975963 -1.654943916 0.147124473 MS(ph)SPEDDSDTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 MS(0.584)S(0.416)PEDDSDTKR 112.02 0.00080771 602930000 418860 374110 304730 305340 362020 341810 342140 392510 437150 407310 TRUE FALSE 402490.4881 363440.7491 359801.4897 321098.634 373664.7021 348721.6324 346327.2117 384404.5313 387526.5647 379722.5309 1.059959458 0.957121897 0.9475379 0.845613857 0.984046696 0.918359075 0.912053364 1.012330057 1.020551938 1 18.53458608 1.654979582 6.784327951 1.012950759 0.94349477 0.243646193 0.051835224 0.176670692 16.16312536 0.026706029 0.013464965 45.18347013 -1.654979582 -0.069455989 DLSLLSHGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLSLLSHGGR 10 0 A6NP24;Q08257;Q08257-2 A6NP24 CRYZ Quinone oxidoreductase 0 ;;; 154.24 1.48E-05 936470000 594870 719160 603630 838620 666240 721990 729340 663050 693790 712030 FALSE TRUE 571621.8227 698650.2609 712719.3687 881901.2787 687670.2147 736589.1325 738265.8811 649357.7858 615033.8678 663803.5739 0.861130981 1.05249548 1.073690165 1.328557594 1.035954372 1.109649242 1.112175213 0.978237857 0.926529913 1 19.34039687 1.6550567 4.943313594 0.960362093 1.089128886 0.185601546 0.108406504 0.247287073 13.49347721 0.060408789 0.028837511 45.19149411 -1.6550567 0.128766793 MGPSGGEGMEPERRDSQDGS(ph)SYR ddPTM_BT-474_Pertuzumab_2h_R1 4 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.225)QDGS(0.669)S(0.106)YR;MGPSGGEGMEPERRDS(0.185)QDGS(0.715)S(0.1)YR;MGPSGGEGMEPERRDSQDGS(0.863)S(0.137)YR;MGPSGGEGMEPERRDS(0.11)QDGS(0.445)S(0.445)YR 230.3 3.15E-33 65255000000 12637680 14595340 8171070 9859620 13546450 13439890 11511280 10768990 10873200 10270620 TRUE FALSE 12143785.49 14179095.19 9647764.113 10368476.17 13982183.87 13711653.78 11652158.49 10546606.59 9638919.92 9574981.759 1.268282885 1.480848272 1.007601305 1.082871637 1.460283081 1.432029233 1.216937931 1.101475372 1.006677627 1 23.19083831 1.655110318 2.44192705 1.011095224 1.284398537 0.383849292 0.145354504 0.29206206 3.901635027 0.106395289 0.042930727 45.19707382 -1.655110318 0.273303313 EEYEGPNKKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEYEGPNKKPR 11 2 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 188.96 1.64E-06 11071280000 14038900 13106010 10291330 10235050 11961090 12272330 11407300 13737370 15069250 14368410 FALSE TRUE 13490244.27 12732239.43 12151202.26 10763282.16 12345829.32 12520484.92 11546905.95 13453688.51 13358651.92 13395224.79 1.007093533 0.950505842 0.907129402 0.803516352 0.921658988 0.934697634 0.862016586 1.004364519 0.997269708 1 23.67521546 1.655136481 7.392414577 1.001022236 0.910876062 0.388733021 0.050532784 0.132370716 13.81150526 0.026749545 0.01369224 45.1997967 -1.655136481 -0.090146175 S(ph)SPNPFITGLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.952)S(0.048)PNPFITGLTR 190.37 0.00011095 0 118930 129020 116460 110750 119340 140170 133080 151480 175420 179200 TRUE FALSE 114282.0841 125340.4759 137506.9126 116465.8208 123178.6795 143004.3334 134708.6728 148351.8851 155507.057 167062.6244 0.684067334 0.750260427 0.823086032 0.6971387 0.737320391 0.85599238 0.806336386 0.888001644 0.930830924 1 17.35002948 1.655162007 0.594434035 1.00321373 0.732519406 0.816792046 0.041937741 0.303112347 0.236964037 0.040665606 0.022394145 45.20245341 -1.655162007 -0.270694324 DPPHNNFFFFDGMK ddPTM_BT-474_Pertuzumab_2h_R1 2 DPPHNNFFFFDGMK 14 0 Q9UBE0;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 168.41 3.49E-06 2168480000 2910200 2796800 2377400 2341800 2590200 2390500 2704500 2803300 3211500 3022200 FALSE TRUE 2796466.167 2717038.002 2807049.065 2462660.579 2673516.135 2438837.548 2737598.48 2745410.875 2846943.984 2817503.702 0.992533271 0.964342301 0.996289397 0.874057619 0.948895341 0.865602251 0.97163971 0.974412517 1.010449066 1 21.42598608 1.655395035 2.341776535 1.00200397 0.941015326 0.256795131 0.041615563 0.372447359 4.524733026 0.029600237 0.011804128 45.22671405 -1.655395035 -0.060988644 AS(ph)PGGVSTSSSDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPGGVSTSSSDGK 14 0 P54259 P54259 ATN1 Atrophin-1 1 AS(1)PGGVSTSSSDGK 156.96 5.69E-06 100440000 155370 134350 139310 137790 137530 141280 144570 163010 191720 169460 TRUE FALSE 149297.9686 130518.4695 164486.4159 144901.3584 141953.7774 144136.7784 146339.2909 159643.7865 169956.7494 157982.3233 0.94502958 0.826158692 1.041169749 0.91719982 0.898542156 0.912360164 0.926301677 1.010516767 1.075795987 1 17.26940362 1.655631511 3.493656021 1.039404277 0.922482472 0.460625891 0.052489597 0.162111975 4.667811382 0.030264845 0.013489206 45.25134692 -1.655631511 -0.116921805 ICDQISDAVLDAHLQQDPDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 ICDQISDAVLDAHLQQDPDAK 21 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;; 262.94 1.01E-36 2360960000 1632999 1501478 1476552 1481121 1587023 1590867 1769964 1871292 2137826 2197250 FALSE TRUE 1569179.594 1458657.318 1743397.792 1557561.832 1638071.036 1623035.421 1791625.349 1832649.166 1895148.955 2048428.3 0.766040771 0.712086099 0.851090464 0.760369222 0.799672137 0.792332063 0.874634152 0.894661124 0.925172218 1 20.96608597 1.655765027 0.574048904 1.001459569 0.761158995 0.83995626 0.033274091 0.269863966 0.200264262 0.031253938 0.017800646 45.26526077 -1.655765027 -0.240300574 YDEMVESMKK ddPTM_BT-474_Pertuzumab_2h_R1 2 YDEMVESMKK 10 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 147.72 4.23E-05 3200500000 7806700 7347800 6206600 5909800 6491900 6914700 7218000 7926000 9589800 8702800 FALSE TRUE 7501605.533 7138247.938 7328270.685 6214805.486 6700717.859 7054519.972 7306336.043 7762325.33 8501206.108 8113351.604 0.924600079 0.879814938 0.90323593 0.765997308 0.825887769 0.869495162 0.900532406 0.956734739 1.047804474 1 22.95186658 1.656050525 1.82843735 1.023799538 0.859016652 0.690627589 0.043054989 0.187815266 1.293898907 0.034992959 0.013148314 45.2950272 -1.656050525 -0.164782886 S(ph)PSSESSPQHPTPPARPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSSESSPQHPTPPARPR 18 1 O14733;O14733-4;O14733-2;O14733-3 O14733 MAP2K7 Dual specificity mitogen-activated protein kinase kinase 7 1 S(0.88)PS(0.061)S(0.036)ES(0.018)S(0.005)PQHPTPPARPR;S(0.707)PS(0.112)S(0.112)ES(0.031)S(0.037)PQHPTPPARPR 82.034 0.0035985 442290000 284848 311349 276296 262232 296843 290415 287900 238640 236737 226291 TRUE FALSE 273715.8252 302469.6314 326228.8334 275765.8249 306391.2247 296287.3903 291423.4063 233712.0006 209863.6082 210964.109 1.297452095 1.433749242 1.546371252 1.307169386 1.452338154 1.404444536 1.381388558 1.107828254 0.994783469 1 17.68663805 1.656191229 2.522158033 0.999929873 1.412780776 0.867633488 0.066978616 0.079294202 1.138651978 0.04434099 0.018083286 45.30970439 -1.656191229 0.412850903 RGS(ph)PSAAFTFPDTDDFGK ddPTM_BT-474_Pertuzumab_2h_R1 3 RGSPSAAFTFPDTDDFGK 18 1 Q9ULT0;Q9ULT0-4;H7C055;Q9ULT0-3 Q9ULT0 TTC7A Tetratricopeptide repeat protein 7A 1 RGS(0.85)PS(0.057)AAFT(0.092)FPDTDDFGK;RGS(0.996)PS(0.004)AAFTFPDTDDFGK;RGS(0.997)PS(0.003)AAFTFPDTDDFGK 242.64 2.91E-24 373810000 392360 416995 342780 351899 350858 402482 419011 469865 552001 549807 TRUE FALSE 377026.1374 405102.7109 404727.9711 370060.5496 362143.6662 410620.4618 424138.982 460162.1236 489340.1607 512568.0822 0.735563041 0.790339323 0.78960822 0.721973456 0.70652793 0.801104236 0.827478333 0.897758053 0.954683246 1 18.96738412 1.656278604 1.102907243 0.995028746 0.752530381 0.914794926 0.027437631 0.133236209 0.306261557 0.025985552 0.009875985 45.3188211 -1.656278604 -0.242498365 RSES(ph)PPAELPSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSESPPAELPSLR 13 1 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 RS(0.005)ES(0.995)PPAELPSLR;RS(0.01)ES(0.99)PPAELPSLR 103.88 0.00096511 768520000 353300 434510 354346 428840 455580 435020 387290 353870 301380 344340 TRUE FALSE 339492.6454 422118.2002 418384.2046 450972.4838 470234.1444 443816.4025 392029.7709 346562.4608 267168.6059 321017.5451 1.057551684 1.314938098 1.303306349 1.404821919 1.464823813 1.382530049 1.221209796 1.079574827 0.832255464 1 18.29229262 1.656428697 2.188145336 0.920372494 1.32772294 0.675765681 0.110910624 0.159671527 1.661032845 0.081603924 0.031970499 45.33448615 -1.656428697 0.407350446 MKPAGS(ph)VNDMALDAFDLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 MKPAGSVNDMALDAFDLDR 19 1 H0YJN0;Q9UI08-5;Q9UI08;Q9UI08-2 H0YJN0 EVL Ena/VASP-like protein 1 MKPAGS(1)VNDMALDAFDLDR 174.86 2.23E-12 65117000 158610 123860 88798 96326 136220 117350 90611 146780 142160 129450 TRUE FALSE 152411.3458 120327.6341 104845.7739 101297.3964 140601.64 119722.8974 91719.92452 143748.9417 126022.5928 120682.2362 1.262914499 0.997061687 0.868775532 0.839372882 1.165056635 0.992050704 0.760011808 1.191135881 1.044251389 1 16.88085381 1.656648718 25 1.088486195 0.980982786 0.079220705 0.146814818 1.010414355 503.0368212 0.06809366 0.037760684 45.35745913 -1.656648718 -0.107503409 ALELDHK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALELDHK 7 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7ELJ8;K7EJV7;K7EN19;K7EJL5;K7EJE9 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ;; 114.78 0.0058274 750110000 1996730 2435410 2644610 2572460 3403710 3705260 3021690 2393280 2260650 2694860 FALSE TRUE 1918695.584 2365954.491 3122549.856 2705224.969 3513193.423 3780182.896 3058670.346 2343857.932 2004030.489 2512334.732 0.76371017 0.941735375 1.242887668 1.076777284 1.398377923 1.50464938 1.217461315 0.932940146 0.797676545 1 21.26059726 1.656870295 4.923490733 0.890240689 1.176569483 0.241608144 0.204871503 0.225886208 12.26020788 0.122268293 0.058397512 45.38060646 -1.656870295 0.286328794 NSYNNSQAPS(ph)PGLGSK ddPTM_BT-474_Pertuzumab_2h_R1 3 NSYNNSQAPSPGLGSK 16 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 NSYNNSQAPS(1)PGLGSK;NSYNNSQAPS(1)PGLGSK;NSYNNS(0.001)QAPS(0.999)PGLGSK 377.81 1.09E-104 657220000 1727670 1611840 1362464 1330161 1427980 1388540 1506260 1759660 2048870 1896780 TRUE FALSE 1660150.746 1565871.901 1608691.553 1398810.769 1473912.274 1416617.23 1524694.06 1723322.406 1816290.867 1768309.401 0.938834994 0.885519186 0.909734208 0.791044128 0.833514923 0.801113894 0.862232627 0.974559319 1.02713409 1 20.75393929 1.656878962 3.398083943 1.010457084 0.856631501 0.691253306 0.043388795 0.116294882 3.165486552 0.028134331 0.012470845 45.38151208 -1.656878962 -0.153825583 YKAEDEVQR ddPTM_BT-474_Pertuzumab_2h_R1 5 YKAEDEVQR 9 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ;;;; 133.81 0.00024314 20705420000 13184100 12879400 11325700 11439800 11838400 12131000 12439600 13841700 15724300 14890500 FALSE TRUE 12668850.8 12512092.12 13372505.93 12030209.45 12219192.89 12376297.13 12591839.55 13555864.06 13939343.39 13881953.17 0.91261299 0.901320727 0.963301472 0.86660784 0.880221446 0.891538603 0.90706541 0.976509853 1.00413416 1 23.72670723 1.657116593 2.97896355 1.000212407 0.902085104 0.752941958 0.023989253 0.109250378 2.259549659 0.015788967 0.006763124 45.40635002 -1.657116593 -0.098127303 IDHLTNNR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDHLTNNR 8 0 Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3;H7C5R6 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 0 78.192 0.031262 135390000 252060 340290 337340 517160 413410 444400 418720 322140 310820 350000 FALSE TRUE 242209.2165 330585.2624 398304.8421 543850.6896 426707.7081 453386.0725 423844.4206 315487.6964 275537.0167 326294.1883 0.742303189 1.013150936 1.220692419 1.666749544 1.307739223 1.389500913 1.298964051 0.966881139 0.844443532 1 18.31581377 1.657458147 4.789308267 0.918567345 1.25027332 0.258798843 0.229491816 0.220676391 11.4260398 0.136465388 0.064892401 45.44207429 -1.657458147 0.331705975 LKPEGLHQLLAGFEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKPEGLHQLLAGFEDK 16 1 Q9BY32;Q9BY32-3;Q9BY32-2 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 ; 202.41 1.83E-11 2313700000 4775600 4169300 3654000 3629400 4162300 4147000 4377800 4914400 5654200 5548400 FALSE TRUE 4588964.272 4050395.646 4314359.083 3816713.769 4296184.16 4230855.181 4431376.826 4812915.923 5012358.92 5172601.926 0.887167491 0.78304801 0.834079085 0.737871157 0.830565395 0.817935585 0.856701693 0.930463235 0.969020812 1 22.30245874 1.657856992 1.319971483 0.995649938 0.809424821 0.787739792 0.036019945 0.170100181 0.566908319 0.028946707 0.010683236 45.48382624 -1.657856992 -0.186225117 DIMLATGKLS(ph)PDAIPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIMLATGKLSPDAIPGK 17 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 DIMLATGKLS(1)PDAIPGK 124.86 2.96E-05 176760000 383320 377860 349780 294890 363310 360070 406420 407910 526200 475540 TRUE FALSE 368339.4306 367083.8028 412993.0268 310109.3082 374996.1961 367350.8621 411393.8895 399486.516 466467.982 443331.2522 0.830844721 0.828012465 0.931567591 0.699497964 0.845860052 0.828614857 0.927960498 0.901101634 1.052188357 1 18.75802554 1.657975661 1.219480975 1.021856752 0.826899639 0.602169525 0.060086219 0.295810276 0.834317576 0.049849836 0.018572102 45.49625619 -1.657975661 -0.194957113 SILVS(ph)PTGPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SILVSPTGPSR 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 SILVS(0.983)PT(0.017)GPSR;SILVS(0.993)PT(0.007)GPSR;SILVS(0.933)PT(0.067)GPSR 195.77 6.58E-08 536320000 380071 437334 382438 427440 427527 419200 403070 392490 344291 428770 TRUE FALSE 365217.4051 424861.6625 451553.0539 449500.2296 441278.7942 427676.5112 408002.8912 384384.9443 305208.5291 399729.026 0.91366246 1.062874184 1.129647898 1.124512358 1.103944836 1.069916077 1.020698685 0.961613792 0.76353857 1 18.60866281 1.658085831 2.504083451 0.879262031 1.071177558 0.45231346 0.079350589 0.203576017 2.873935222 0.05262972 0.021463573 45.50779898 -1.658085831 0.191915527 SCYLSSLDLLLEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCYLSSLDLLLEHR 14 0 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 217.68 5.67E-12 949290000 839860 959550 729650 1017580 799930 712410 942170 723270 756190 811710 FALSE TRUE 807037.3427 932184.5735 861513.986 1070097.426 825660.4749 726815.4183 953700.5583 708334.2217 670350.4814 756732.1587 1.066476868 1.23185537 1.138466201 1.414103277 1.091086807 0.960465879 1.260288131 0.936043504 0.885849073 1 19.52942323 1.658196353 6.483023903 0.930807326 1.165823167 0.430385831 0.118521213 0.123002356 10.46081368 0.061612641 0.030883022 45.51938158 -1.658196353 0.235015841 DELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_BT-474_Pertuzumab_2h_R1 28 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNY(0.004)EGS(0.995)PIKVTLATLK;DELHIVEAEAMNYEGS(0.998)PIKVT(0.001)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.019)EGS(0.98)PIKVTLATLK;DELHIVEAEAMNY(0.002)EGS(0.998)PIKVTLATLK;DELHIVEAEAMNY(0.396)EGS(0.592)PIKVT(0.012)LATLK;DELHIVEAEAMNY(0.02)EGS(0.978)PIKVT(0.002)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.001)EGS(0.999)PIKVTLATLK;DELHIVEAEAMNY(0.101)EGS(0.899)PIKVTLATLK;DELHIVEAEAMNY(0.004)EGS(0.996)PIKVTLATLK;DELHIVEAEAMNY(0.085)EGS(0.913)PIKVT(0.002)LATLK;DELHIVEAEAMNY(0.121)EGS(0.879)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.014)EGS(0.986)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.063)EGS(0.923)PIKVT(0.012)LAT(0.002)LK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.035)EGS(0.755)PIKVT(0.189)LAT(0.021)LK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.003)EGS(0.997)PIKVTLATLK;DELHIVEAEAMNY(0.003)EGS(0.994)PIKVT(0.003)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.018)EGS(0.981)PIKVT(0.001)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.453)EGS(0.523)PIKVT(0.025)LATLK 277.73 6.49E-61 39186718000 12480584.6 10395389.6 10747051.3 9485865.9 10753640.6 10750338.1 12116530.7 13135320.2 17111549.5 14782439.4 TRUE FALSE 11992829.56 10098923.27 12689282.54 9975432.576 11099541.22 10967717.3 12264816.43 12864071.25 15169118.14 13781211.61 0.870230419 0.73280373 0.92076683 0.723842929 0.80541113 0.795845649 0.889966483 0.933449947 1.100710051 1 23.7161994 1.658227015 1.737394153 1.047102687 0.807354076 0.689461451 0.062664114 0.171649662 1.052022865 0.045043149 0.016813501 45.52259545 -1.658227015 -0.239748611 PGWLSS(ph)PTLGR ddPTM_BT-474_Pertuzumab_2h_R1 6 PGWLSSPTLGR 11 0 Q5XPI4;Q5XPI4-2;C9JS59;C9J266 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 1 PGWLS(0.042)S(0.815)PT(0.143)LGR;PGWLS(0.297)S(0.695)PT(0.007)LGR;PGWLS(0.036)S(0.962)PT(0.002)LGR;PGWLS(0.02)S(0.98)PTLGR;PGWLS(0.003)S(0.996)PT(0.001)LGR;PGWLS(0.001)S(0.999)PTLGR 260.22 1.30E-20 1063327000 2446013 2310716 2064665 2210467 2342113 2295492 2370965 2575318 3040895 2704937 TRUE FALSE 2350420.108 2244816.642 2437795.894 2324549.467 2417449.192 2341908.421 2399981.579 2522136.783 2695705.348 2521729.208 0.932066814 0.890189413 0.966715969 0.921807726 0.958647417 0.928691476 0.951720578 1.000161625 1.06899081 1 21.26598193 1.658588452 2.568060703 1.035028986 0.933865051 0.723886399 0.025344649 0.115850633 1.730019697 0.015988099 0.006572461 45.56049685 -1.658588452 -0.101163935 SDPYSTGHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDPYSTGHLR 10 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 0 ; 152.54 1.78E-05 458240000 180473 221826 192517 260200 231457 234006 230850 200439 201023 214682 FALSE TRUE 173419.9156 215499.7397 227309.1044 273628.9532 238902.0246 238737.7617 233675.2114 196299.8646 178203.7118 200141.3969 0.866486985 1.076737462 1.13574257 1.367178192 1.193666219 1.192845485 1.167550616 0.980805908 0.890389068 1 17.61066008 1.658629382 4.245674802 0.942989507 1.152662876 0.334525877 0.119942059 0.194912424 8.149955328 0.071693818 0.033386878 45.56479091 -1.658629382 0.209673368 RGS(ph)RSS(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGS(0.905)RS(0.099)S(0.995)PEPK 92.269 0.047133 1405400000 3613600 2958800 2439400 2317500 2847800 2729300 2697200 3292200 3854600 3220100 TRUE FALSE 3472376.517 2874417.921 2880253.844 2437106.453 2939402.073 2784488.316 2730209.14 3224214.92 3417041.968 3001999.759 1.156687807 0.95750105 0.959445062 0.811827664 0.979148004 0.927544484 0.909463478 1.074022378 1.138255244 1 21.51749243 1.65897485 6.092032182 1.081375149 0.951820572 0.261015992 0.086454774 0.166585395 12.85952474 0.04483521 0.022241386 45.60105071 -1.65897485 -0.129554577 SNNIAELS(ph)PGAINSCR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNNIAELSPGAINSCR 16 0 Q9Y2I9;F8VZ81;Q9Y2I9-2;Q9Y2I9-3 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 SNNIAELS(1)PGAINSCR;SNNIAELS(1)PGAINSCR 248.94 1.83E-20 561600000 513670 568340 472660 643760 686620 599510 512460 519200 406200 476250 TRUE FALSE 493595.2085 552131.4997 558080.1763 676984.5307 708705.7559 611632.503 518731.6388 508478.3386 360089.8789 443993.1633 1.111718038 1.243558562 1.256956689 1.524763412 1.596208713 1.377571894 1.168332492 1.145239118 0.811025729 1 18.76017794 1.659030679 1.731112142 0.91793188 1.355124189 0.571519471 0.145883018 0.260035713 1.580502757 0.124102408 0.046331386 45.60691317 -1.659030679 0.437192309 RFS(ph)FCCSPEPEAEAEAAAGPGPCER ddPTM_BT-474_Pertuzumab_2h_R1 2 RFSFCCSPEPEAEAEAAAGPGPCER 25 1 Q13501;E7EMC7;E3W990;D6RBF1;C9J6J8 Q13501 SQSTM1 Sequestosome-1 1 RFS(0.863)FCCS(0.137)PEPEAEAEAAAGPGPCER;RFS(0.949)FCCS(0.051)PEPEAEAEAAAGPGPCER 195.19 2.87E-19 1455950000 475360 509710 387270 512610 490420 538890 493880 486110 513940 514970 TRUE FALSE 456782.4057 495173.5699 457258.3038 539065.8635 506194.8047 549786.725 499924.2512 476071.6586 455599.6858 480090.6232 0.95145038 1.031416874 0.952441647 1.122841892 1.054373446 1.145172804 1.041312259 0.991628738 0.948986845 1 18.87294723 1.659049649 3.891645899 0.973995144 1.046351382 0.190895123 0.059233963 0.290790689 10.33337875 0.035318248 0.016172847 45.60890534 -1.659049649 0.072356238 S(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLESLQTAVAEVTLNGDIPFHRPRPR 28 2 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.333)S(0.333)S(0.333)LES(0.001)LQTAVAEVTLNGDIPFHRPRPR 71.988 0.0051055 54177000 26377 27412 18189 20557 27564 22880 20594 20365 25093 18794 TRUE FALSE 25346.15768 26630.2366 21476.15691 21617.94923 28450.62109 23342.64928 20846.03553 19944.45563 22244.54784 17521.06564 1.446610509 1.519898227 1.225733489 1.233826165 1.623795132 1.332261961 1.189769844 1.138312934 1.269588751 1 14.0968029 1.659091739 0.582723828 1.023470836 1.417742541 0.481678897 0.127738226 0.674414331 0.511151434 0.129632584 0.072869221 45.61332576 -1.659091739 0.394271705 SGEHDFGAAFDGDGDR ddPTM_BT-474_Pertuzumab_2h_R1 5 SGEHDFGAAFDGDGDR 16 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ;;;; 204.52 2.50E-11 2173960000 1179310 1326680 1110823 1354140 1185600 1156730 1162290 1164630 1211226 1065240 FALSE TRUE 1133221.261 1288844.385 1311573.426 1424027.328 1223735.901 1180119.873 1176514.453 1140579.984 1073732.702 993090.346 1.141105908 1.297811816 1.320698999 1.433935325 1.232250324 1.188330828 1.184700322 1.148515831 1.081203444 1 19.92156545 1.659171185 0.724695761 1.009161 1.295015072 0.63290833 0.071796682 0.416978395 0.444890175 0.069278913 0.032348494 45.62167066 -1.659171185 0.285854072 GVGISVLEMSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVGISVLEMSHR 12 0 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 114.76 0.00022442 0 412630 557580 464530 610420 481960 452380 536460 403560 356670 476160 FALSE TRUE 396503.9634 541678.3643 548480.9044 641923.8494 497462.6811 461527.4335 543025.358 395226.345 316182.3169 443909.2591 0.893209491 1.220245699 1.235569867 1.446069971 1.120640471 1.039688684 1.223280089 0.890331384 0.712267903 1 18.75990528 1.659247312 4.698408083 0.840144897 1.176729678 0.456094253 0.150084481 0.134114711 6.726020183 0.083230653 0.039494208 45.62966838 -1.659247312 0.336584781 VCEVCSAYLGLHDNDRR ddPTM_BT-474_Pertuzumab_2h_R1 6 VCEVCSAYLGLHDNDRR 17 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;;;; 179.81 5.81E-10 10257980000 3762380 4154580 3016980 3926010 3741520 4172220 3726230 3702320 3840300 3746210 FALSE TRUE 3615342.03 4036095.446 3562215.398 4128631.847 3861869.389 4256585.147 3771832.717 3625865.798 3404365.244 3492475.86 1.035180249 1.155654501 1.01996851 1.182150432 1.105768384 1.218787278 1.0799882 1.038193518 0.974771303 1 21.73581871 1.659262176 2.503577684 0.991456476 1.1198195 0.446147098 0.058080438 0.21725263 3.06382237 0.037521918 0.015321364 45.63123007 -1.659262176 0.128363024 IKKPEGKPDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKKPEGKPDQK 11 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;D6RBK5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 97.463 0.002737 4861990000 9267700 8084800 7044400 6060120 6890500 7837700 8065600 9492600 12046800 10382900 FALSE TRUE 8905508.038 7854229.42 8317479.782 6372883.519 7112139.19 7996183.664 8164309.225 9296574.493 10679297.77 9679656.935 0.920023106 0.811416094 0.859274232 0.658379069 0.734751163 0.826081308 0.843450267 0.960423965 1.103272341 1 23.20652449 1.659520256 2.121704543 1.0521072 0.79665203 0.671001464 0.070535007 0.168658652 1.633398387 0.053013294 0.02066748 45.65835455 -1.659520256 -0.25545517 S(ph)SVSRVFDCLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSVSRVFDCLK 11 1 A0A494C0P0;A0A494C0K7;Q6P2C8-4;Q6P2C8-2;Q6P2C8 A0A494C0P0 MED27 Mediator of RNA polymerase II transcription subunit 27 1 S(0.551)S(0.448)VS(0.001)RVFDCLK 54.343 0.080106 376350000 404250 349760 434460 335970 395880 373590 394270 466180 523660 520810 TRUE FALSE 388451.4631 339785.1873 512976.5865 353309.452 408613.8397 381144.2458 399095.1942 456553.2201 464216.3122 485535.0748 0.800048201 0.699815945 1.056518083 0.727670297 0.841574298 0.784998377 0.821969853 0.940309452 0.956092229 1 18.88921599 1.660017403 3.094690337 0.972170801 0.818753037 0.358624094 0.090604763 0.236154425 5.287815358 0.054206531 0.023533889 45.71065059 -1.660017403 -0.153417763 DKS(ph)PAPEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKSPAPEEK 9 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 DKS(1)PAPEEK 75.669 0.022775 329600000 483100 420490 366870 322810 395980 385570 441120 533260 675080 613680 TRUE FALSE 464219.9179 408498.0369 433171.57 339470.2628 408717.0563 393366.4896 446518.5585 522247.9946 598447.7486 572114.907 0.811410282 0.714013972 0.757140855 0.593360282 0.714396796 0.687565531 0.780470065 0.912837593 1.04602719 1 19.12594541 1.660145096 1.97787405 1.023403478 0.710044054 0.841208618 0.054294194 0.108936646 0.898028263 0.040338938 0.015466416 45.7240926 -1.660145096 -0.313359424 TSS(ph)VLGMSVESAPAVEEEKGEELEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSVLGMSVESAPAVEEEKGEELEQK 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.001)S(0.006)S(0.994)VLGMSVESAPAVEEEKGEELEQK 273.75 8.80E-61 59976000 77178 44072 43783 34472 48350 40172 38217 63145 73251 55042 TRUE FALSE 74161.79844 42815.10971 51695.56205 36251.10405 49905.22166 40984.30536 38684.71108 61841.03368 64935.85357 51313.95631 1.445255906 0.834375534 1.007436685 0.706457008 0.972546754 0.798697047 0.753882839 1.205150375 1.26546184 1 15.64706364 1.660241124 8.212649489 1.176125268 0.918881931 0.197757095 0.205480508 0.166034761 19.78701185 0.097696029 0.05103962 45.73420395 -1.660241124 -0.257243337 S(ph)IAIGS(ph)QPVLTVGT(ph)T(ph)HIS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 2 SIAIGSQPVLTVGTTHISK 19 0 Q96DZ1;Q96DZ1-3 Q96DZ1 ERLEC1 Endoplasmic reticulum lectin 1 5 S(0.999)IAIGS(0.999)QPVLT(0.024)VGT(0.993)T(0.993)HIS(0.991)K;S(1)IAIGS(0.999)QPVLT(0.02)VGT(0.994)T(0.994)HIS(0.993)K 52.465 0.039687 1505850000 73403 109216 83081 123373 90228 116650 88485 78974 45847 81979 TRUE FALSE 70534.32961 106101.2666 98095.58483 129740.2953 93130.26556 119008.7429 89567.9059 77343.1593 40642.64077 76426.48931 0.922904221 1.388278692 1.2835286 1.697582821 1.218560036 1.557166161 1.171948453 1.01199414 0.531787357 1 16.22178514 1.660300431 2.43303357 0.770780921 1.350425945 0.499598388 0.225109642 0.190159144 2.513573589 0.145971211 0.059175923 45.74044975 -1.660300431 0.579645024 DFDTALK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFDTALK 7 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 127.84 0.0088763 2388100000 2302560 2211120 1915880 2072050 2201860 2175180 2228390 2525510 2854300 2775800 FALSE TRUE 2212573.41 2148061.023 2262122.135 2178988.749 2272684.827 2219163.63 2255661.703 2473357.336 2530291.83 2587792.594 0.855004151 0.830074647 0.874151252 0.84202604 0.87823299 0.857550808 0.871654749 0.955778814 0.977779995 1 21.30329056 1.660313138 1.887529257 0.992374226 0.855155784 0.94191543 0.01381333 0.064411158 0.476980284 0.010160839 0.003856789 45.74178815 -1.660313138 -0.137218442 EGPAHEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGPAHEPK 8 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;; 81.548 0.022576 705650000 2188930 2304660 1721660 1821440 2148620 2094170 2040300 2235920 2549480 2232840 FALSE TRUE 2103384.196 2238933.353 2032802.26 1915444.737 2217732.314 2136515.552 2065269.802 2189747.471 2260073.719 2081607.758 1.010461355 1.075578886 0.976553941 0.920175633 1.065393951 1.026377589 0.99215128 1.051950091 1.085734673 1 20.98926681 1.660328849 6.876518587 1.051877359 1.010255359 0.112236139 0.045820234 0.262332354 24.35211636 0.023726282 0.012032412 45.7434429 -1.660328849 -0.041621999 GGS(ph)DDSSKDPIDVNYEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 1 GGS(1)DDSSKDPIDVNYEK;GGS(1)DDSSKDPIDVNYEK;GGS(0.934)DDS(0.028)S(0.038)KDPIDVNYEK 189.79 2.03E-10 1112980000 1578960 1338170 1185930 1041660 1233440 1356840 1297840 1625380 1990440 1667850 TRUE FALSE 1517252.498 1300006.702 1400253.932 1095420.197 1273114.718 1384276.234 1313723.354 1591815.335 1764493.596 1554885.034 0.975797223 0.836078986 0.900551424 0.704502374 0.818783826 0.890275618 0.844900636 1.023751146 1.134806469 1 20.56837648 1.660478995 3.672070493 1.071157248 0.847866413 0.619379063 0.072092866 0.11566183 3.672073282 0.042041032 0.019038346 45.75926022 -1.660478995 -0.223290835 GAPS(ph)SPATGVLPS(ph)PQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GAPSSPATGVLPSPQGK 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 2 GAPS(0.5)S(0.5)PATGVLPS(1)PQGK;GAPS(0.5)S(0.5)PATGVLPS(1)PQGK 165.66 3.57E-09 167890000 381270 411870 374720 398770 457380 423650 412720 390160 347500 468390 TRUE FALSE 366369.5469 400123.8709 442440.2396 419350.5675 472092.0431 432216.4933 417770.9908 382103.0597 308053.2568 436665.5281 0.839016417 0.916316597 1.013224565 0.960347315 1.081129635 0.989811344 0.956729954 0.875047456 0.705467313 1 18.73616912 1.660857783 3.789468663 0.836071955 0.970834891 0.221291867 0.088965859 0.227074961 7.666280405 0.050582278 0.023069976 45.79918846 -1.660857783 0.134762936 FEAFEHENK ddPTM_BT-474_Pertuzumab_2h_R1 3 FEAFEHENK 9 0 Q9UBQ0;F8VXU5;Q9UBQ0-2;Q05DG7 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;; 166.07 6.10E-05 2890770000 3277900 3023050 3195810 3541000 3327900 3118590 3961500 4327400 4949700 5193400 FALSE TRUE 3149796.044 2936835.574 3773363.957 3723751.434 3434944.926 3181650.027 4009982.022 4238037.678 4387830.807 4841646.392 0.650563009 0.606577874 0.779355544 0.769108508 0.709458033 0.657142172 0.82822695 0.875329864 0.906268333 1 22.20706629 1.661037716 0.914195569 0.990123091 0.691964389 0.789415376 0.054826613 0.252785583 0.404725219 0.05259137 0.021413726 45.81816757 -1.661037716 -0.298158702 EIDSWFSER ddPTM_BT-474_Pertuzumab_2h_R1 3 EIDSWFSER 9 0 H0Y6F5;Q9H4I2;Q9H4I2-2;Q9Y6X8 H0Y6F5;Q9Y6X8 ZHX3;ZHX2 Zinc fingers and homeoboxes protein 3;Zinc fingers and homeoboxes protein 2 0 ;; 154.49 0.00017583 514905000 293274 375241 299790 392327 363328 354450 344151 321148 292089 347163 FALSE TRUE 281812.5278 364539.4941 353968.7218 412575.0435 375014.7751 361617.2219 348362.8229 314516.1816 258932.2813 323649.3408 0.870734132 1.126340913 1.093679724 1.274759412 1.158707057 1.117311782 1.076358821 0.971780696 0.800039576 1 18.30407204 1.661118486 2.729442581 0.896618771 1.115098036 0.388569626 0.104476003 0.221619601 3.782196176 0.067965523 0.028522112 45.8266896 -1.661118486 0.218479265 MTQNPNYYNLQGISHR ddPTM_BT-474_Pertuzumab_2h_R1 2 MTQNPNYYNLQGISHR 16 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 199.08 3.91E-11 1367140000 298880 311300 259490 267630 312790 322500 329470 281090 319000 316130 FALSE TRUE 287199.4392 302422.0288 306385.6153 281442.4164 322851.1744 329021.171 333502.1524 275285.3933 282788.4574 294718.2335 0.974488194 1.026139527 1.039588259 0.954954205 1.095457076 1.116392315 1.131596605 0.934062986 0.959521418 1 18.16897679 1.661228825 10.49468514 0.960602559 1.047834114 0.322103734 0.055538766 0.140300314 22.68824958 0.028422255 0.01532856 45.83833407 -1.661228825 0.087231555 NRPT(ph)SISWDGLDSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.495)S(0.495)IS(0.011)WDGLDSGK;NRPT(0.56)S(0.438)IS(0.001)WDGLDSGK 153.19 4.36E-06 1863850000 1970520 1574660 1452250 1580470 1595600 1355830 1560390 1993570 2291620 2156000 TRUE FALSE 1893509.9 1529752.239 1714703.88 1662038.246 1646923.923 1383245.812 1579486.52 1952402.083 2031484.905 2009972.2 0.942057756 0.761081292 0.853098307 0.826896136 0.819376469 0.688191514 0.785825058 0.971357755 1.010702986 1 20.93874412 1.661234044 4.525373463 1.000167329 0.806923756 0.650464813 0.061639921 0.098400166 4.624832414 0.03434713 0.016213561 45.83888488 -1.661234044 -0.193243574 VEYQEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEYQEDR 7 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 0 ; 67.981 0.06369 198181000 153176 231570 211758 348490 299680 337320 300230 207988 187908 254950 FALSE TRUE 147189.7126 224965.8503 250027.3811 366475.6107 309319.4794 344140.8415 303904.3045 203692.9751 166577.4716 237682.0094 0.619271576 0.946499278 1.051940707 1.54187358 1.301400473 1.44790446 1.278617197 0.856997867 0.700841734 1 17.85867318 1.66131783 5.704536059 0.828002565 1.185952279 0.239074751 0.25694248 0.203313595 14.15810493 0.146704319 0.072060416 45.84772917 -1.66131783 0.357949714 EMEEQMR ddPTM_BT-474_Pertuzumab_2h_R1 2 EMEEQMR 7 0 P23246;P23246-2;H0Y9K7;H0Y9U2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 99.799 0.023876 413840000 1133060 1451390 1159350 1564440 1512810 1616130 1371680 1222500 1086770 1261710 FALSE TRUE 1088778.763 1409997.778 1368870.335 1645180.936 1561470.908 1648809.256 1388467.03 1197254.948 963404.4257 1176253.258 0.925632941 1.198719552 1.163754766 1.398662171 1.327495501 1.401746813 1.180415035 1.017854735 0.819045065 1 20.16576729 1.661324375 2.879351014 0.912068104 1.24442262 0.484839886 0.136105534 0.188168267 3.608024074 0.090146436 0.038422765 45.84842008 -1.661324375 0.332354516 SVPVNNLPERS(ph)PTDSPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVPVNNLPERSPTDSPR 17 1 P49454 P49454 CENPF Centromere protein F 1 SVPVNNLPERS(0.945)PT(0.054)DSPR;SVPVNNLPERS(0.994)PT(0.006)DSPR;SVPVNNLPERS(0.948)PT(0.051)DS(0.001)PR 146.72 2.58E-07 1786610000 565920 691020 667600 835660 830500 758820 685140 652470 552860 644950 TRUE FALSE 543803.2207 671312.7862 788250.1707 878788.5127 857213.7867 774163.8603 693524.9483 638996.2665 490101.6506 601266.962 0.904428906 1.116497045 1.31098201 1.461561283 1.425679176 1.287554296 1.153439307 1.062749672 0.815114885 1 19.19764616 1.661379995 2.071226189 0.912718993 1.261396903 0.420651424 0.156260395 0.293402137 2.68755619 0.124019123 0.04814383 45.85429224 -1.661379995 0.34867791 SSLFPIDDGLLDDGHSDQVGVLNS(ph)PTCYSAHQNGER ddPTM_BT-474_Pertuzumab_2h_R1 2 SSLFPIDDGLLDDGHSDQVGVLNSPTCYSAHQNGER 36 0 A0A5K1VW61;A0A5K1VW79;A0A5K1VW71;A0A5K1VW93;Q7Z5Q1-7;Q7Z5Q1-5;Q7Z5Q1-4;Q7Z5Q1-6;Q7Z5Q1-3;Q7Z5Q1;Q7Z5Q1-8;Q7Z5Q1-9 A0A5K1VW61 CPEB2 Cytoplasmic polyadenylation element-binding protein 2 1 SSLFPIDDGLLDDGHS(0.003)DQVGVLNS(0.615)PT(0.157)CY(0.175)S(0.051)AHQNGER;SSLFPIDDGLLDDGHSDQVGVLNS(0.815)PT(0.168)CY(0.002)S(0.014)AHQNGER 99.453 0.00029339 59370000 16863.8 20035.4 20669.7 21179.9 21511.5 26172 16809.3 17915.8 15415.5 13943 TRUE FALSE 16204.74405 19464.01001 24405.17458 22272.99718 22203.43693 26701.21577 17015.01724 17545.83247 13665.59707 12998.62819 1.246650324 1.497389549 1.877519245 1.713488289 1.708136936 2.054156437 1.308985609 1.349821859 1.051310713 1 13.66607176 1.661580299 1.669027733 1.038181463 1.677180474 0.558637414 0.221275455 0.263444593 1.47341305 0.17939358 0.066782733 45.87544592 -1.661580299 0.63899901 SLEPSPS(ph)PGPQEEDGEVALVLLGRPSPGAVGPEDVALCSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLEPSPSPGPQEEDGEVALVLLGRPSPGAVGPEDVALCSSR 41 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 S(0.006)LEPS(0.109)PS(0.885)PGPQEEDGEVALVLLGRPSPGAVGPEDVALCSSR 89.905 0.00014852 35225000 6303.3 8280.2 6996.5 6986.1 5284.4 6814.1 6273.4 5501.3 4923.2 4128.2 TRUE FALSE 6056.960067 8044.056803 8260.923186 7346.653458 5454.377525 6951.885771 6350.175746 5387.696233 4364.338976 3848.593337 1.5738114 2.090129068 2.146478587 1.908919134 1.417239248 1.806344595 1.649999153 1.399913101 1.134008869 1 11.91011552 1.661584897 0.601642782 0.964127902 1.930484559 0.70026898 0.199587852 0.40738959 0.323630349 0.196837091 0.107457213 45.87593166 -1.661584897 0.966356657 RSET(ph)PPHWR ddPTM_BT-474_Pertuzumab_2h_R1 5 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 RS(0.245)ET(0.755)PPHWR;RS(0.082)ET(0.918)PPHWR;RS(0.077)ET(0.923)PPHWR;RS(0.016)ET(0.984)PPHWR;RS(0.18)ET(0.82)PPHWR 96.82 0.0041661 3350180000 856780 850194 773422 878519 898760 926940 927660 816217 843250 932080 TRUE FALSE 823296.0904 825947.2995 913196.5601 923859.4709 927669.4316 945683.3619 939012.9806 799361.8337 747527.7952 868949.3914 0.947461496 0.950512547 1.050920306 1.063191344 1.067575904 1.088306605 1.08063023 0.919917594 0.860266205 1 19.72891263 1.661634849 6.398778625 0.916409527 1.03690633 0.432488085 0.056633976 0.122377993 10.19885193 0.031162616 0.015618042 45.8812086 -1.661634849 0.120496803 TLS(ph)SPTEPVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLSSPTEPVKR 11 1 J3QQN1;P40306 J3QQN1 PSMB10 Proteasome subunit beta type-10 1 T(0.002)LS(0.494)S(0.494)PT(0.01)EPVKR 90.793 0.0068738 216990000 146150 165140 141340 219250 173300 168020 166760 155180 149240 154270 TRUE FALSE 140438.2964 160430.3689 166883.2821 230565.5188 178874.3519 171417.4795 168800.8588 151975.4788 132298.9009 143821.1555 0.97647871 1.11548519 1.160352811 1.603140498 1.243727679 1.191879449 1.173685875 1.056697662 0.919884842 1 17.13391638 1.661671921 1.9321445 0.95882618 1.226214398 0.315880235 0.150630013 0.387806746 3.028941735 0.120760627 0.046126135 45.88512516 -1.661671921 0.267388218 TGYES(ph)GEYEMLGEGLGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGYESGEYEMLGEGLGVK 18 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 1 T(0.002)GYES(0.998)GEYEMLGEGLGVK 152.71 4.04E-08 37909000 46494 47996 42654 43541 50363 46937 48090 54013 63916 56539 TRUE FALSE 44676.96308 46627.20107 50362.52663 45788.15623 51982.97163 47886.0983 48678.53981 52897.61267 56660.52364 52709.56317 0.8476064 0.884606099 0.955472283 0.868687833 0.986215186 0.908489758 0.923523871 1.003567654 1.074957185 1 15.68577712 1.66175857 2.97618009 1.038636939 0.91154771 0.626836449 0.041387197 0.136524334 2.810255454 0.025412337 0.010936836 45.89428094 -1.66175857 -0.127089229 IES(ph)PKLER ddPTM_BT-474_Pertuzumab_2h_R1 7 IESPKLER 8 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 1 IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER 125.97 0.00075045 34195120000 35641200 30654900 22490000 19868300 26189400 29564800 26404700 31201400 36604900 30131500 TRUE FALSE 34248302.5 29780652.27 26554443.29 20893705.34 27031805.84 30162620.51 26727848.62 30557080.19 32449665.21 28090666.67 1.219205756 1.060161819 0.945311964 0.743795282 0.9623056 1.073759511 0.951485023 1.087801886 1.155176045 1 24.74358753 1.661962441 6.206478962 1.092295408 0.986879698 0.096844608 0.119208954 0.298321532 23.73300912 0.065643798 0.032730933 45.91583015 -1.661962441 -0.10541571 RQEELDR ddPTM_BT-474_Pertuzumab_2h_R1 3 RQEELDR 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;; 170.24 0.0062886 51304000 346641 377389 295341 373237 351066 350543 336527 333384 315582 332883 FALSE TRUE 333093.8865 366626.2352 348715.6885 392499.8063 362358.3567 357631.2196 340645.5181 326499.5039 279758.4544 310336.5379 1.073331193 1.181382759 1.123669455 1.264755381 1.167630338 1.152398045 1.097664878 1.052082059 0.901467988 1 18.24347404 1.662082266 1.709052508 0.953211833 1.1638906 0.698607281 0.053242146 0.17821688 1.051712215 0.040598203 0.015167823 45.92850046 -1.662082266 0.210678767 VEPFLPGHYEVLDLKPNGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEPFLPGHYEVLDLKPNGK 19 1 P08243-2;P08243;P08243-3;F8WEJ5;C9J057 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 181.41 1.89E-14 333980000 387980 405180 379650 317050 388640 384480 418130 419530 531560 470400 FALSE TRUE 372817.3127 393624.6631 448261.2003 333412.9885 401140.9586 392254.449 423247.2 410866.5589 471219.5373 438539.389 0.850134154 0.897581091 1.022168616 0.760280597 0.914720476 0.894456596 0.965129269 0.936897732 1.07452044 1 18.7423469 1.662155154 1.31334427 1.029774527 0.891842824 0.392968577 0.066690596 0.434982746 1.433675793 0.054559401 0.020196127 45.93620927 -1.662155154 -0.137931703 GLGHPPS(ph)SPLLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLGHPPSSPLLKK 13 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 GLGHPPS(0.586)S(0.414)PLLKK 128.22 0.00010278 858210000 467130 474990 379840 407420 431340 467480 406050 427140 404380 420370 TRUE FALSE 448874.0432 461443.7503 448485.5375 428446.995 445214.4428 476932.7659 411019.3614 418319.4097 358476.4777 391897.9655 1.14538498 1.177458907 1.144393636 1.093261596 1.136046834 1.21698199 1.048791771 1.067419192 0.914718905 1 18.58011856 1.662219894 1.701077556 0.964399643 1.147241874 0.718410702 0.045265531 0.173268747 1.011695326 0.034153926 0.012753258 45.9430575 -1.662219894 0.182842231 HSMNPFCEIAVEEAVR ddPTM_BT-474_Pertuzumab_2h_R1 3 HSMNPFCEIAVEEAVR 16 0 P38117-2;P38117;M0QY67 P38117-2 ETFB Electron transfer flavoprotein subunit beta 0 ;; 166.76 6.56E-09 444728000 248796 323409 223042 457176 260091 268458 373801 229573 288493 260251 FALSE TRUE 239072.7773 314185.692 263350.6509 480770.9081 268457.0632 273886.4047 378375.6885 224832.2373 255744.4841 242623.968 0.985363397 1.294949112 1.085427187 1.981547463 1.106473798 1.128851395 1.559514881 0.926669526 1.054077576 1 17.88836255 1.662588243 9.328478365 0.994337401 1.307931248 0.213307431 0.274323728 0.179193872 24.88211507 0.130426933 0.069448827 45.98204082 -1.662588243 0.313593847 SVS(ph)VDSGEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSVDSGEQR 10 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 SVS(0.999)VDS(0.001)GEQR 142.89 3.66E-05 172540000 125580 178560 134480 201010 239000 224780 155370 159150 122300 142070 TRUE FALSE 120672.1948 173467.6436 158783.5275 211384.1502 246687.6521 229325.2056 157271.4645 155863.4969 108417.0167 132447.4724 0.911094735 1.309708978 1.198841508 1.595984781 1.862531973 1.731442673 1.187425186 1.176794801 0.818566144 1 17.01506079 1.66279259 2.084910423 0.930736408 1.438217627 0.353624398 0.266295074 0.341655822 3.175734934 0.210755841 0.08207058 46.00368173 -1.66279259 0.507481219 MIS(ph)S(ph)KPR ddPTM_BT-474_Pertuzumab_2h_R1 1 MISSKPR 7 1 J3KT09;G9BQT7;O75952-4;O75952-3;O75952-2;O75952;J3KRI0 J3KT09 CABYR Calcium-binding tyrosine phosphorylation-regulated protein 2 MIS(1)S(1)KPR 50.04 0.09113 121450000 86844 136440 140100 231170 158810 167900 158910 124450 98213 144100 TRUE FALSE 83450.04047 132548.8648 165419.1865 243100.7114 163918.2679 171295.053 160854.7881 121880.064 87064.27198 134339.9786 0.621185453 0.986667306 1.231347423 1.809593197 1.220174884 1.275086201 1.197370952 0.907250881 0.648089071 1 17.03552918 1.662886966 3.633897425 0.811882551 1.214743712 0.226832797 0.287326502 0.27531083 8.557354864 0.179094859 0.081094849 46.01367976 -1.662886966 0.40286116 ADKNEVAAEVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADKNEVAAEVAK 12 1 P56192;H0YIP0 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 121.28 0.00034572 364900000 463730 445420 344750 415400 411810 434160 436650 498920 578090 549200 FALSE TRUE 445606.9189 432717.0577 407053.9939 436838.8438 425056.2426 442939.0127 441993.8533 488617.1276 512467.6468 512002.1948 0.870322283 0.84514688 0.795023924 0.853197209 0.830184415 0.865111551 0.863265544 0.954326236 1.000909082 1 18.96579047 1.663035905 1.694214867 1.005577959 0.839784294 0.917181015 0.019555263 0.086305188 0.499277921 0.015380681 0.005743965 46.02946265 -1.663035905 -0.165793665 GNVVPS(ph)PLPTRR ddPTM_BT-474_Pertuzumab_2h_R1 10 GNVVPSPLPTRR 12 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 GNVVPS(0.998)PLPT(0.002)RR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(0.999)PLPT(0.001)RR;GNVVPS(1)PLPTRR 137.79 5.27E-05 54519380000 6622960 7526310 5118740 6359000 6232960 7180230 5954290 6043230 5787180 5744080 TRUE FALSE 6364127.401 7311667.008 6043810.184 6687188.752 6433448.819 7325419.17 6027160.382 5918435.189 5130243.588 5355028.345 1.188439536 1.365383437 1.128623379 1.248768134 1.201384643 1.367951521 1.125514188 1.105210805 0.95802361 1 22.35246278 1.663177868 1.804882452 0.984488007 1.245594439 0.649028009 0.076466969 0.189348788 1.265051783 0.055242174 0.020842488 46.04451135 -1.663177868 0.261106432 AGTFIAPPVYSNITPYQS(ph)HLRSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AGTFIAPPVYS(0.001)NIT(0.136)PY(0.104)QS(0.436)HLRS(0.322)PVR 80.067 0.014457 622030000 371160 446330 202620 399200 450880 432710 355190 318030 262460 318620 TRUE FALSE 356654.6569 433601.1054 239237.9413 419802.7598 465382.9647 441459.6927 359536.9215 311462.5694 232666.6411 297039.5836 1.200697404 1.45974183 0.805407611 1.413288945 1.566737197 1.486198194 1.210400705 1.04855577 0.783284969 1 18.18029567 1.663212851 2.569924638 0.897420035 1.319283514 0.406961607 0.206880047 0.248001435 3.699824044 0.142140953 0.058745131 46.04822039 -1.663212851 0.421863479 RSPES(ph)CSKPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(0.249)PES(0.614)CS(0.137)KPEK 106.42 0.0018377 2655800000 2814600 2460900 2174000 1913300 2354600 2308200 2442900 2801900 3272700 3084000 TRUE FALSE 2704602.32 2390717.541 2566890.16 2012045.642 2430337.847 2354873.385 2472796.941 2744039.786 2901196.816 2875117.933 0.940692654 0.831519818 0.892794738 0.699813256 0.845300229 0.819052797 0.860068004 0.954409471 1.009070544 1 21.4551897 1.663256748 2.290750605 1.003843208 0.834186222 0.584059081 0.057792361 0.184997414 2.13087377 0.040155743 0.016050132 46.05287507 -1.663256748 -0.169656986 ECYQSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ECYQSHR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 164.53 0.0011942 390890000 372050 420600 363080 445710 429480 375460 443100 376370 396600 441070 FALSE TRUE 357509.8747 408604.8998 428696.6327 468713.1465 443294.6142 383052.0584 448522.7903 368597.828 351579.6307 411195.936 0.869439222 0.99369878 1.042560481 1.139877867 1.078061759 0.931556041 1.090776321 0.896404355 0.85501728 1 18.64946648 1.663503755 7.806860305 0.90686066 1.023726437 0.250369417 0.081303765 0.156000071 17.22086798 0.041012286 0.021289421 46.07907527 -1.663503755 0.116865776 RGPEVTSQGVQTS(ph)SPACK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGPEVTSQGVQTSSPACK 18 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 RGPEVTSQGVQT(0.011)S(0.646)S(0.343)PACK 184.95 3.41E-14 570930000 581120 547060 555730 541330 615010 669290 682630 774920 896120 987000 TRUE FALSE 558409.1879 531458.3844 656162.7731 569268.1062 634792.3552 682823.5024 690984.2301 758917.6312 794396.2144 920149.6109 0.606867819 0.577578231 0.71310444 0.618669072 0.689879502 0.742078782 0.750947696 0.824776343 0.86333375 1 19.81150893 1.663644961 0.352795056 1.023375225 0.577676095 0.93385461 0.031725693 0.26755334 0.104110754 0.042640366 0.039206416 46.09405985 -1.663644961 -0.44569913 S(ph)PPWEP ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPWEP 6 0 F5H8F7;Q9UBL3-2;Q9UBL3-3;Q9UBL3;H0YAQ0 F5H8F7 ASH2L Set1/Ash2 histone methyltransferase complex subunit ASH2 1 S(1)PPWEP;S(1)PPWEP 79.597 0.029756 831600000 990567 912718 669254 730664 850947 871079 816119 967687 1066400 1041023 TRUE FALSE 951854.5465 886688.1763 790203.0853 768373.6566 878318.4831 888692.8142 826106.9085 947703.9253 945346.7427 970513.585 0.980774057 0.913627784 0.814211256 0.7917186 0.905003801 0.915693328 0.851205919 0.976497331 0.974068532 1 19.88838888 1.663701677 5.583263683 0.983340516 0.879264176 0.44895829 0.051577697 0.141012884 9.507204706 0.029243232 0.014332789 46.10007979 -1.663701677 -0.104076341 ASEDTTSGS(ph)PPKK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTTS(0.001)GS(0.999)PPKK;ASEDTTS(0.004)GS(0.996)PPKK;ASEDT(0.001)T(0.009)S(0.006)GS(0.984)PPKK;ASEDTTS(0.019)GS(0.981)PPKK 149.73 2.69E-05 29247050000 3352070 2753570 2443800 2191530 2548180 2595720 2757930 3118580 3841220 3226680 TRUE FALSE 3221067.398 2675040.88 2885449.022 2304635.126 2630144.524 2648207.237 2791682.372 3054180.233 3405180.809 3008134.09 1.070785844 0.889269162 0.959215559 0.76613444 0.874344177 0.8803488 0.928044525 1.015307211 1.131991031 1 21.52043745 1.663726274 2.860562696 1.067989303 0.901166676 0.408032083 0.07811836 0.206524855 3.898062475 0.049370112 0.021058992 46.1026908 -1.663726274 -0.166822627 DKYGVFPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKYGVFPLR 9 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 100.88 0.0039781 665060000 1002800 1277400 1151900 1158300 1215200 1306500 1264100 944620 863020 1055000 FALSE TRUE 963609.4673 1240969.803 1360073.954 1218080.002 1254288.012 1332918.325 1279570.434 925113.2669 765053.5877 983543.9103 0.979732025 1.261732994 1.382829927 1.238460214 1.275274036 1.355219946 1.300979469 0.940591729 0.777854023 1 19.90762994 1.663987864 4.519870101 0.8813898 1.265233978 0.66193925 0.114667419 0.090994628 4.275731407 0.062871475 0.029730873 46.1304684 -1.663987864 0.383844178 VNTLIRPDGEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNTLIRPDGEKK 12 2 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 112.15 0.00073367 2211400000 3111200 2732800 2450800 2143100 2600200 2928600 2577400 3357800 3933000 3452700 FALSE TRUE 2989610.864 2654863.22 2893714.078 2253705.648 2683837.794 2987818.299 2608942.992 3288460.257 3486542.328 3218845.554 0.92878357 0.824787389 0.898991278 0.70015961 0.833788931 0.928226673 0.810521334 1.021627227 1.083165461 1 21.61811192 1.66414572 4.931547824 1.044615651 0.844805281 0.632060852 0.065852947 0.094500282 5.179088877 0.035482918 0.017034343 46.14723872 -1.66414572 -0.19981037 DDGVFVQEVTQNS(ph)PAAR ddPTM_BT-474_Pertuzumab_2h_R1 5 DDGVFVQEVTQNSPAAR 17 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR 329.79 5.98E-72 2055551000 1007745 996229 922546 927752 848561 1030456 903805 909772 857184 910436 TRUE FALSE 968361.2113 967817.5243 1089270.584 975633.3919 875855.7352 1051292.526 914866.0359 890984.8903 759880.0659 848771.3588 1.140897606 1.140257048 1.283349836 1.149465497 1.031910097 1.238605091 1.077871003 1.049734868 0.895270626 1 19.69501645 1.66438529 1.922297475 0.951963677 1.160725077 0.582245435 0.070249037 0.214869617 1.657705501 0.051993301 0.019889178 46.17270201 -1.66438529 0.2087614 MEES(ph)DEEAVQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 MEESDEEAVQAK 12 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 MEES(1)DEEAVQAK;MEES(1)DEEAVQAK 214.23 4.65E-11 84354000 378920 344690 283230 303020 302020 304910 297820 378190 403700 402740 TRUE FALSE 364111.3875 334859.7787 334415.9614 318658.8985 311734.7476 311075.4891 301464.8102 370380.2443 357873.6684 375462.0611 0.969768787 0.891860492 0.890678436 0.848711312 0.830269633 0.828513774 0.802916836 0.986465166 0.95315534 1 18.51830761 1.664428523 7.613813472 0.977381892 0.864788483 0.570683239 0.045086876 0.095386805 10.17045039 0.02397525 0.01240058 46.17729863 -1.664428523 -0.112593409 ENAEVDGDDDAEEMEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENAEVDGDDDAEEMEAK 17 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 297.56 7.79E-46 248270000 319020 302730 271510 275490 305040 299310 305920 366990 426120 404000 FALSE TRUE 306552.3457 294096.4368 320577.8967 289708.0719 314851.8886 305362.2533 309663.9405 359411.5283 377748.644 376636.7202 0.813920495 0.780849081 0.851159432 0.769197628 0.835956432 0.810760706 0.822182023 0.954265766 1.002952245 1 18.52281414 1.664479616 2.686107841 0.999637266 0.809654419 0.928283131 0.022389028 0.051543289 0.847386771 0.013587392 0.005696671 46.18273152 -1.664479616 -0.189982848 KPDGVKES(ph)TESSNTTIEDEDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPDGVKESTESSNTTIEDEDVK 22 2 Q13557;D6R938;Q13557-8;Q13557-12;H0Y9J2 Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 KPDGVKES(0.174)T(0.174)ES(0.174)S(0.174)NT(0.174)T(0.128)IEDEDVK;KPDGVKES(0.953)T(0.029)ES(0.006)S(0.007)NT(0.002)T(0.003)IEDEDVK 88.517 0.0021029 1222530000 194178 158425 131847 113483 159641 144614 150563 204270 262250 201518 TRUE FALSE 186589.3091 153906.8741 155674.6858 119339.8712 164775.9977 147538.1942 152405.635 200051.7531 232480.4794 187869.0064 0.993188353 0.819224401 0.828634211 0.635229161 0.8770792 0.785324823 0.811233518 1.064847028 1.237460526 1 17.51936755 1.664516658 3.93984193 1.127443115 0.814571061 0.626686929 0.099037908 0.104928388 3.818888101 0.055099198 0.025410774 46.18667069 -1.664516658 -0.312872055 RLAPEYEAAATR ddPTM_BT-474_Pertuzumab_2h_R1 3 RLAPEYEAAATR 12 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 188.13 1.54E-05 1684960000 779920 1015270 630139 802570 767230 774430 764440 698790 706150 641550 FALSE TRUE 749439.8642 986315.4937 744019.1347 843990.7339 791908.6497 790089.5052 773795.4454 684359.7423 625990.8124 598097.2471 1.25304015 1.649088837 1.243976859 1.411126264 1.324046639 1.321005086 1.293761924 1.14422821 1.046637174 1 19.19002055 1.664680862 0.866608813 0.984740761 1.394345544 0.638016225 0.105806659 0.322550593 0.468013889 0.088395179 0.036997247 46.20413688 -1.664680862 0.409604783 GGTLKDDDWGNIK ddPTM_BT-474_Pertuzumab_2h_R1 4 GGTLKDDDWGNIK 13 1 P54578-2;P54578 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14 0 ;;; 187.57 6.25E-06 4282380000 6648860 6306960 5174410 5455680 5611020 5925680 6279560 7269230 8549780 8218060 FALSE TRUE 6389015.2 6127091.676 6109540.991 5737248.299 5791503.554 6045501.31 6356411.134 7119117.86 7579244.818 7661443.476 0.833917945 0.799730716 0.797439935 0.748846913 0.75592851 0.789081239 0.829662341 0.92921365 0.989271126 1 22.8691848 1.664899942 1.751859035 0.998783559 0.784831651 0.934658219 0.022409198 0.081585656 0.509127187 0.019135457 0.00719371 46.22745052 -1.664899942 -0.213951907 KLDPELHLDIK ddPTM_BT-474_Pertuzumab_2h_R1 3 KLDPELHLDIK 11 1 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;; 141.58 2.47E-05 10586350000 32782120 30050290 25766620 25666150 27217750 29685660 31128150 32291720 38290440 36732620 FALSE TRUE 31500958.51 29193285.15 30423221.41 26990783.08 28093233.65 30285924.38 31509105.61 31624884.7 33943869.78 34244686.93 0.919878712 0.852490934 0.888407053 0.788174327 0.820367659 0.884397759 0.920116621 0.923497556 0.991215655 1 25.02937684 1.664928792 1.099447946 0.999817479 0.853922008 0.688441567 0.035801722 0.278290927 0.634817325 0.032509349 0.012416595 46.23052142 -1.664928792 -0.145895471 DDIIENAPTTHTEEYSGEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDIIENAPTTHTEEYSGEEK 20 0 O14744-2;O14744;G3V580;O14744-3;O14744-5;G3V5L5;G3V2X6;H0YJX6 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 ; 280.62 1.01E-44 209790000 580360 463200 463480 444380 494020 548180 608840 603260 832730 779940 FALSE TRUE 557678.8896 449989.9895 547241.1461 467314.5051 509910.602 559264.5752 616291.166 590802.4702 738201.9815 727113.9691 0.766975898 0.618871331 0.752620867 0.642697741 0.701280162 0.769156692 0.847585375 0.812530766 1.015249346 1 19.47182199 1.66494228 0.818670652 1.014977334 0.69009716 0.808141404 0.055371299 0.227986827 0.298932437 0.047395897 0.020471702 46.23195722 -1.66494228 -0.324880173 EIQGHEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIQGHEPR 8 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 89.698 0.015843 0 184850 204150 155080 213890 173910 193410 192500 179260 191120 184880 FALSE TRUE 177625.8576 198327.8419 183106.4057 224928.8885 179503.9731 197320.8827 194855.8726 175558.2184 169424.8588 172357.9129 1.030563985 1.150674422 1.06236147 1.305010514 1.041460587 1.144832166 1.130530472 1.018567789 0.982982771 1 17.39504801 1.664944336 3.764368999 0.993982371 1.127277694 0.374315089 0.073251714 0.184670111 6.151429005 0.04035524 0.018446171 46.23217609 -1.664944336 0.133295323 GNLYSFGCPEYGQLGHNSDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNLYSFGCPEYGQLGHNSDGK 21 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 128.32 1.06E-05 725950000 374610 489620 461910 622350 656280 664950 527950 420330 360120 394390 FALSE TRUE 359969.827 475656.517 545387.4121 654469.5581 677389.8422 678395.7446 534411.21 411650.0386 319240.6873 367677.614 0.979036562 1.293678208 1.483330481 1.780009261 1.842347253 1.84508308 1.453477693 1.119595055 0.868262508 1 18.48808182 1.664989474 2.871452113 0.946987693 1.554096891 0.48882276 0.252438152 0.205171771 3.901120338 0.178576073 0.07635866 46.23698147 -1.664989474 0.607109197 GFGS(ph)EEGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFGSEEGSR 9 0 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 1 GFGS(1)EEGSR;GFGS(1)EEGSR;GFGS(1)EEGSR;GFGS(1)EEGSR 230.61 8.77E-08 2939780000 2322180 2526050 2007970 2535960 2511400 2309650 2148500 2376320 2262480 2173710 TRUE FALSE 2231426.638 2454009.527 2370854.846 2666841.2 2592181.462 2356352.705 2174793.986 2327248.162 2005652.755 2026482.686 1.101132842 1.210969896 1.169935901 1.315995058 1.279153027 1.16277959 1.073186562 1.148417491 0.989721141 1 20.95054642 1.665081299 0.997529212 0.997607658 1.214050115 0.585178289 0.065920397 0.376937245 0.710577731 0.060780198 0.023921819 46.24675868 -1.665081299 0.216442457 YFEQLLEEER ddPTM_BT-474_Pertuzumab_2h_R1 3 YFEQLLEEER 10 0 O15460-2;O15460 O15460-2 P4HA2 Prolyl 4-hydroxylase subunit alpha-2 0 ;; 129.16 0.00072253 88946000 110342 137939 120983 166376 136506 130823 142750 127246 137706 132971 FALSE TRUE 106029.7127 134005.1148 142847.3194 174962.6853 140896.8395 133468.3307 144497.0172 124618.3256 122074.1922 123964.7557 0.855321434 1.080993658 1.152322033 1.411390554 1.136587884 1.076663523 1.16562983 1.005272224 0.984749185 1 16.91957048 1.665192667 5.308292354 0.993308681 1.13425216 0.174476059 0.127415424 0.262038811 16.28926264 0.071816534 0.03493164 46.25861943 -1.665192667 0.140943479 ESHRLPVDIAYKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESHRLPVDIAYKR 13 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 178.67 8.65E-06 259160000 495000 542460 342950 410760 455170 511020 466120 441480 491930 433000 FALSE TRUE 475654.8527 526989.5719 404928.6939 431959.3728 469810.9564 521353.1745 471824.516 432363.2837 436088.1687 403672.5243 1.178318622 1.30548784 1.003111853 1.070073752 1.163841798 1.291525043 1.168829899 1.071074343 1.080301835 1 18.62282587 1.665340346 3.757022952 1.050521859 1.168538263 0.285283586 0.086340183 0.275796629 9.151062971 0.053282048 0.024353578 46.27435205 -1.665340346 0.118016404 IVQPMIDQS(ph)NRAGKS(ph)PIVTVFK ddPTM_BT-474_Pertuzumab_2h_R1 1 IVQPMIDQSNRAGKSPIVTVFK 22 2 H0YNY8 H0YNY8 MEIS1 2 IVQPMIDQS(0.983)NRAGKS(0.983)PIVT(0.035)VFK 46.362 0.091117 356980000 47752 144270 113550 155490 187150 214670 134740 71235 26298 54297 TRUE FALSE 45885.79905 140155.5609 134071.0109 163514.8575 193169.8497 219010.7745 136388.9884 69763.97236 23312.76129 50619.41583 0.906486144 2.768810318 2.648608419 3.230279427 3.816121671 4.326616001 2.69440068 1.378205797 0.460549789 1 15.62740324 1.665505814 3.076718385 0.778561979 3.012978373 0.5351947 0.852288301 0.168827395 3.720953586 0.559191729 0.243802384 46.29198606 -1.665505814 2.234416393 KLDEAVAEAHLGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KLDEAVAEAHLGK 13 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;; 120.7 0.00016565 3015280000 7175800 6902700 5957740 5988580 6447500 7218600 7284400 8054300 9131500 9380500 FALSE TRUE 6895361.803 6705841.754 7034436.147 6297651.331 6654889.693 7364565.038 7373548.666 7887975.89 8094930.402 8745150.38 0.788478357 0.766806912 0.804381382 0.720130708 0.76098059 0.842131321 0.84315859 0.901982876 0.925647936 1 23.06005176 1.66569474 0.761718299 0.993082306 0.76583433 0.900454938 0.025723198 0.176490348 0.204288929 0.024235999 0.010955983 46.31212837 -1.66569474 -0.227247977 RRET(ph)PS(ph)PRPMR ddPTM_BT-474_Pertuzumab_2h_R1 6 RRETPSPRPMR 11 3 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR 91.076 0.008408 8856350000 3045530 3205070 2249155 2669940 2866000 3129090 2719230 2674804 2764950 2579450 TRUE FALSE 2926507.321 3113664.542 2655627.341 2807735.923 2958187.493 3192362.344 2752508.75 2619568.363 2451084.468 2404741.554 1.216973739 1.294802153 1.104329626 1.167583235 1.230147784 1.327528249 1.144617286 1.089334676 1.019271474 1 21.19745042 1.665920291 2.035873116 1.013804402 1.218840272 0.663547695 0.060333767 0.187869778 1.652147093 0.04609621 0.017899621 46.33618685 -1.665920291 0.20503587 EYTINIHKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYTINIHKR 9 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 137.95 9.75E-05 404480000 2200700 2535100 1678900 1949200 1967300 2410800 2277800 2006400 2169600 2220500 FALSE TRUE 2114694.211 2462801.43 1982314.577 2049798.446 2030579.991 2459548.028 2305676.398 1964967.139 1923316.104 2070103.557 1.021540301 1.189699627 0.957591986 0.990191258 0.980907445 1.188128014 1.113797612 0.949212001 0.929091734 1 20.98127151 1.665930115 7.188865777 0.954139077 1.06253701 0.265150701 0.078757471 0.173362051 17.08695232 0.041188801 0.021116493 46.33723498 -1.665930115 0.108397933 SKQEALKNDLVEALK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKQEALKNDLVEALK 15 2 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 130.56 3.32E-05 501030000 857280 808990 683860 461140 663480 715290 697700 830970 975160 857340 FALSE TRUE 823776.5498 785918.3973 807448.7144 484939.4907 684821.4368 729753.6539 706238.6613 813810.1791 864463.925 799271.5982 1.030659105 0.983293287 1.01023071 0.606726789 0.856806921 0.913023377 0.883602849 1.018189788 1.081564673 1 19.6083263 1.665950191 4.174277904 1.043302348 0.893006486 0.231269653 0.113186954 0.261131471 10.61050231 0.067712553 0.031612314 46.33937701 -1.665950191 -0.150295862 FYS(ph)TSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FYSTSLK 7 0 A0A0C4DH43 A0A0C4DH43 1 FYS(0.333)T(0.333)S(0.333)LK;FY(0.001)S(0.333)T(0.333)S(0.333)LK 77.674 0.039238 96989000 128344 327640 245810 478250 389730 434960 346670 208998 120123 241940 TRUE FALSE 123328.1746 318296.028 290233.335 502932.5398 402266.0194 443755.1892 350912.6512 204682.1183 106487.1406 225553.1883 0.546780897 1.411179467 1.286762281 2.229773578 1.783464124 1.967408187 1.555786703 0.907467191 0.472115431 1 17.78310815 1.665998962 3.810904641 0.726067282 1.579799919 0.377595609 0.440376494 0.188291613 6.424026895 0.264825105 0.121471429 46.34458123 -1.665998962 0.853732637 RST(ph)SPIIGSPPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.26)T(0.45)S(0.29)PIIGSPPVR 73.168 0.022011 351890000 191180 190040 142820 182430 192300 193680 178150 167680 169390 167650 TRUE FALSE 183708.4742 184620.2453 168630.751 191845.2342 198485.5041 197596.3423 180330.253 164217.3494 150161.5573 156294.9162 1.175396352 1.181230009 1.078926654 1.22745665 1.269942164 1.264253164 1.153781949 1.050689001 0.960757784 1 17.25391133 1.666076038 2.500487909 0.983961341 1.197959863 0.744747393 0.052116211 0.134844269 1.889185732 0.038550972 0.015854848 46.3528069 -1.666076038 0.213998522 RSS(ph)LS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSLSPGR 8 1 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 RS(0.114)S(0.935)LS(0.951)PGR;RS(0.121)S(0.917)LS(0.962)PGR 48.944 0.084275 0 349770 353340 299690 357190 327250 362630 358940 340030 374160 361070 TRUE FALSE 336100.6017 343263.0892 353850.6496 375624.6187 337776.2935 369962.6271 363332.8151 333008.2617 331686.9254 336614.4073 0.998473608 1.019751626 1.051204708 1.115889904 1.003451683 1.099069496 1.079373928 0.989287013 0.985361643 1 18.3607374 1.666101338 6.760872639 0.990167427 1.053368796 0.365123392 0.036698907 0.14020626 12.68378921 0.019029177 0.009654355 46.35550729 -1.666101338 0.063201369 KHEPEPLPHWDDWERPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KHEPEPLPHWDDWERPR 17 2 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 0 ; 119.8 3.29E-05 369820000 15119 24461.7 19267.9 26976.9 14856.2 17971.3 27687.8 14466.2 22489.7 17486.5 FALSE TRUE 14528.13277 23764.07627 22750.03814 28369.18104 15334.06317 18334.692 28026.65158 14167.46791 19936.76354 16302.12378 0.891180374 1.457728857 1.395526034 1.740213817 0.940617515 1.124681192 1.719202477 0.869056579 1.222954985 1 13.99277231 1.666162734 13.88225371 1.035817515 1.325305072 0.185887085 0.281214732 0.214325496 45.68948592 0.128827552 0.070824843 46.36206097 -1.666162734 0.289487557 VNYDTTESK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNYDTTESK 9 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 112.04 0.0047155 364970000 219660 208490 170904 191899 187336 188609 199586 222510 252500 240310 FALSE TRUE 211075.4444 202544.0693 201790.1545 201802.9304 193361.8326 192422.8032 202028.5932 217915.0907 223837.2586 224033.5897 0.94215981 0.904079025 0.900713839 0.900770865 0.863093043 0.858901576 0.901778137 0.972689368 0.999123653 1 17.77335553 1.666340632 3.066993137 0.99673004 0.893270789 0.80188375 0.021823126 0.096366319 2.108445214 0.01474133 0.00642734 46.38105595 -1.666340632 -0.103459251 EKEAAEQAER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEAAEQAER 10 1 Q969G3;Q969G3-4;Q969G3-2;B4DGM3;Q969G3-5;A0A2R8Y855;A0A2R8Y7I9;A0A2U3TZQ7;A0A2R8YES3;A0A2R8Y4T4;A0A2R8Y765;A0A2R8Y7U4;Q969G3-6;Q969G3-3 Q969G3 SMARCE1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 0 138.45 5.87E-05 911000000 1085500 1019700 839000 900370 1034500 1047000 1023400 1117600 1354900 1251900 FALSE TRUE 1043077.46 990619.1544 990625.9635 946838.2036 1067775.632 1068171.057 1035924.675 1094521.169 1201097.432 1167107.698 0.893728541 0.84878127 0.848787104 0.811268922 0.914890403 0.915229211 0.887599899 0.937806486 1.029123049 1 20.15450626 1.666468052 0.866176145 1.017904941 0.859465526 0.750181892 0.032045908 0.281047507 0.407237259 0.029771391 0.012472717 46.39466589 -1.666468052 -0.158439415 TTAPTEGKS(ph)PLKKEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 TTAPTEGKSPLKKEDR 16 3 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 TTAPTEGKS(1)PLKKEDR;TTAPTEGKS(1)PLKKEDR;TTAPTEGKS(1)PLKKEDR 114.4 0.0032398 2566260000 2558290 1753880 1315040 996550 1469320 1506470 1499040 1903590 2263470 1836570 TRUE FALSE 2458309.198 1703861.06 1552696.981 1047982.065 1516582.012 1536931.856 1517385.7 1864280.201 2006530.375 1712177.478 1.435779427 0.995142782 0.90685516 0.612075605 0.885762155 0.897647513 0.88623155 1.088835839 1.171917281 1 20.70740082 1.666618702 5.760572742 1.100252461 0.929362467 0.093627063 0.19547403 0.309227491 21.99262858 0.106488281 0.052565709 46.41076228 -1.666618702 -0.170889994 KPAPPRPKPPS(ph)GK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPAPPRPKPPSGK 13 3 Q9UBC2;Q9UBC2-2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 KPAPPRPKPPS(1)GK 126.63 0.00013297 915820000 771660 581990 617080 529260 511350 461340 669810 766420 1028700 848460 TRUE FALSE 741502.6741 565392.215 728600.0829 556575.172 527798.0371 470668.6109 678007.3351 750593.1592 911926.2887 790993.0485 0.937432605 0.714787843 0.921120716 0.703641041 0.66726002 0.595035079 0.857159663 0.948925102 1.152887867 1 19.59330549 1.666677007 2.438759627 1.069803823 0.756375052 0.571976698 0.108469915 0.179612059 2.378573601 0.074205663 0.030315164 46.41699345 -1.666677007 -0.313428772 GEMMDLQHGSLFLR ddPTM_BT-474_Pertuzumab_2h_R1 11 GEMMDLQHGSLFLR 14 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;;;;;;; 226.88 2.24E-12 16551100000 6108514 10825222 9283935 14901140 9772543 10032490 10324422 8627025 7905831 8695042 FALSE TRUE 5869786.52 10516497.27 10961748.57 15670189.62 10086885.72 10235353.82 10450775.36 8448873.919 7008394.209 8106119.061 0.724117975 1.297352924 1.352280727 1.933130948 1.244354499 1.262670058 1.289245234 1.042283472 0.864580714 1 22.95057993 1.666736474 2.418827873 0.929171069 1.329004932 0.23651587 0.274627305 0.368094271 4.785473931 0.193167918 0.078730218 46.42334972 -1.666736474 0.399833863 LEGVDGGQS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEGVDGGQSPR 11 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 LEGVDGGQS(1)PR;LEGVDGGQS(1)PR;LEGVDGGQS(1)PR 168.76 1.86E-05 1591080000 1313620 1391570 1201350 1470070 1403220 1530880 1373890 1406740 1456750 1471640 TRUE FALSE 1262282.278 1351883.786 1418460.669 1545940.489 1448355.846 1561835.442 1390704.077 1377690.327 1291385.847 1371964.512 0.920054613 0.985363524 1.033890204 1.126807928 1.055680255 1.138393471 1.013658928 1.004173443 0.941267676 1 20.38781173 1.666745938 2.723300292 0.972731308 1.045514032 0.165471355 0.06123482 0.417360125 7.061133535 0.042336932 0.017865769 46.42436134 -1.666745938 0.072782725 ITSEIPQTER ddPTM_BT-474_Pertuzumab_2h_R1 3 ITSEIPQTER 10 0 F8VZQ9;H0YHG0;P82979 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 ;; 152.54 4.15E-05 936810000 358820 396550 298704 407450 348617 363715 383700 360858 391160 398840 FALSE TRUE 344796.9177 385240.7823 352686.4574 428478.5433 359830.5824 371069.5665 388395.8354 353406.1562 346757.1567 371826.2116 0.927306648 1.036077528 0.948525 1.152362394 0.967738613 0.997965057 1.044562818 0.950460579 0.93257857 1 18.50426895 1.666827201 7.856477024 0.956245351 1.012428435 0.119410685 0.061032263 0.228076762 25.26761238 0.028758279 0.014967225 46.43304891 -1.666827201 0.056183084 YMTISDEWDIPEKQPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 YMTISDEWDIPEKQPFK 17 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 278.2 7.36E-36 309760000 382600 387130 372740 335380 390520 401580 424170 476510 564910 558510 FALSE TRUE 367647.569 376089.4314 440102.4096 352689.002 403081.4305 409700.2227 429361.1193 466669.902 500783.7851 520681.6202 0.706089009 0.722302107 0.845242836 0.677360192 0.774141846 0.78685363 0.82461355 0.896267285 0.961785025 1 18.99004196 1.666956812 0.923108246 1.003485984 0.743038568 0.834427053 0.041704186 0.19750285 0.321488805 0.036119344 0.01467801 46.4469084 -1.666956812 -0.260447416 FAVVMADPPWDIHMELPYGTLTDDEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 FAVVMADPPWDIHMELPYGTLTDDEMR 27 0 Q86U44;Q86U44-2 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 52.79 0.095009 54925000 46059 48832 48573 41524 59645 51688 56307 43005 43543 54045 FALSE TRUE 44258.96336 47439.35917 57351.2216 43667.05862 61563.53559 52733.16677 56996.10191 42116.93172 38600.18119 50384.48401 0.878424464 0.941546988 1.138271488 0.866676706 1.221874885 1.046615199 1.131223293 0.835910748 0.766112464 1 15.6206919 1.666988853 7.609010629 0.850897961 1.03379307 0.275940311 0.121038661 0.144005981 15.30610027 0.058620809 0.030355198 46.45033532 -1.666988853 0.182895109 SENLGQGDKPDYFSSVATVVYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SENLGQGDKPDYFSSVATVVYLR 23 1 P27694 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 134.56 1.70E-05 683930000 322810 345040 316230 336980 322790 340130 326490 389650 437470 405670 FALSE TRUE 310194.2283 335199.797 373379.7955 354371.5782 333172.8335 347007.6616 330485.6823 381603.5913 387810.2396 378193.6096 0.82019955 0.886317983 0.987271562 0.937011016 0.88095839 0.917539728 0.873853164 1.009016498 1.025427796 1 18.52876546 1.667105974 5.851710656 1.014390764 0.904737738 0.595616811 0.041755205 0.102864844 7.503630166 0.02287471 0.011325311 46.46286376 -1.667105974 -0.109653026 TGSES(ph)SQTGTSTTSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 TGS(0.022)ES(0.965)S(0.013)QTGTSTTSSR;TGS(0.323)ES(0.676)S(0.001)QTGTSTTSSR;TGS(0.321)ES(0.678)S(0.001)QTGTSTTSSR;TGS(0.065)ES(0.934)S(0.001)QTGTSTTSSR;TGS(0.288)ES(0.711)SQTGTSTTSSR 395.44 1.08E-121 9720190000 5221210 4607330 4300720 4350310 4502820 4593890 4941650 5063060 6126390 5503290 TRUE FALSE 5017159.341 4475933.459 5077955.773 4574830.02 4647657.295 4686781.603 5002127.391 4958506.042 5430947.891 5130547.266 0.977899448 0.872408581 0.98974934 0.891684607 0.905879442 0.913505199 0.974969556 0.966467276 1.05855138 1 22.29068129 1.668282698 1.625791778 1.024928555 0.924675468 0.490600752 0.039075732 0.274821278 1.447541276 0.028785231 0.010741104 46.58892589 -1.668282698 -0.100253088 LAGSALTDKHS(ph)DKS ddPTM_BT-474_Pertuzumab_2h_R1 1 LAGSALTDKHSDKS 14 2 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 LAGSALTDKHS(0.999)DKS(0.001) 83.253 0.0044892 89017000 131770 145660 109150 121780 116850 146290 134370 151110 189250 169450 TRUE FALSE 126620.2827 141505.9194 128875.833 128065.0804 120608.5864 149248.084 136014.4603 147989.5257 167767.1334 157973.0006 0.801531162 0.895760155 0.815809237 0.810677014 0.763475948 0.944769571 0.860998144 0.936802651 1.061998777 1 17.26931848 1.668376015 1.181281707 1.032299619 0.830413258 0.695042652 0.050423371 0.251520169 0.663384684 0.04278182 0.01611342 46.59893756 -1.668376015 -0.20188636 LTLYDIAHTPGVAADLSHIETK ddPTM_BT-474_Pertuzumab_2h_R1 4 LTLYDIAHTPGVAADLSHIETK 22 0 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 ;;; 242.34 6.05E-31 10305548000 3370642 4750404 3454624 6779620 3415894 4066208 6358940 3002643 5086458 4104729 FALSE TRUE 3238913.584 4614927.129 4078951.404 7129517.001 3525769.333 4148429.512 6436762.61 2940637.373 4509064.612 3826712.049 0.846395951 1.205977108 1.065915426 1.863092104 0.921357366 1.084071511 1.682060873 0.76845013 1.178313015 1 21.86767391 1.668505174 19.74347668 0.980321439 1.236358562 0.123181884 0.313113846 0.399488658 121.7825769 0.140859912 0.07802591 46.61279815 -1.668505174 0.256037123 NS(ph)PEDLGLSLTGDSCK ddPTM_BT-474_Pertuzumab_2h_R1 8 NSPEDLGLSLTGDSCK 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK 357.37 1.70E-87 4532577000 3498780 2884760 2548230 2438859 2843150 2939810 2982980 3394560 4167820 3566850 TRUE FALSE 3362043.809 2802489.469 3008751.846 2564728.805 2934602.502 2999254.972 3019486.602 3324461.15 3694706.547 3325264.072 1.011060697 0.842787041 0.904815913 0.771285753 0.882517129 0.901959937 0.908044154 0.999758539 1.111101695 1 21.66503748 1.668534465 2.438277919 1.057182926 0.880649705 0.556085626 0.061779089 0.174451211 2.306646905 0.040517979 0.016585525 46.61594206 -1.668534465 -0.176533221 KGEFVNEYVGELIDEEECMAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGEFVNEYVGELIDEEECMAR 21 1 O96028;O96028-4;O96028-2 O96028 WHSC1 Histone-lysine N-methyltransferase NSD2 0 112.32 0.00036475 19392000 43652 39355 36510 36046 36555 43288 39295 40236 41318 44303 FALSE TRUE 41946.03158 38232.63393 43108.16916 37906.33838 37730.82477 44163.31302 39775.90396 39405.11254 36627.75386 41302.31835 1.015585402 0.925677673 1.043722747 0.917777498 0.913528012 1.06926959 0.963042888 0.954065392 0.886820772 1 15.33393514 1.668614011 3.642169934 0.938164988 0.977675188 0.061211889 0.055961052 0.497212652 15.49705476 0.031530195 0.014359678 46.62448102 -1.668614011 0.0395102 SAS(ph)PDGGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SASPDGGPR 9 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(0.047)AS(0.953)PDGGPR;S(0.162)AS(0.838)PDGGPR 94.363 0.0092024 245300000 583640 651100 535290 701510 633960 671770 627120 590230 588720 610900 TRUE FALSE 560830.7036 632531.2655 632028.8105 737715.0152 654351.8991 685353.6497 634794.8822 578041.5442 521890.9737 569523.1989 0.984737241 1.110633012 1.109750773 1.295320395 1.148946874 1.203381444 1.114607594 1.014956977 0.916364732 1 19.11939508 1.668649087 2.789187561 0.959402824 1.14692404 0.491724549 0.076410019 0.19165841 3.411866345 0.050580051 0.021536264 46.6282468 -1.668649087 0.187521216 EVMNADDPDLQRPDEEAIKEITEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVMNADDPDLQRPDEEAIKEITEK 24 2 Q13573;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 ; 197.28 1.06E-24 657350000 988620 850500 693970 616660 799870 813010 747950 952770 1096780 933080 FALSE TRUE 949983.6374 826244.5727 819385.8163 648485.8965 825598.545 829449.6192 757103.6358 933094.9665 972278.1325 869881.6605 1.092083763 0.949835604 0.941950904 0.745487491 0.949092943 0.953520067 0.870352452 1.072668857 1.117713106 1 19.73045962 1.668699831 6.574512205 1.072224091 0.925166848 0.339869429 0.085367591 0.141892074 12.35412218 0.044265154 0.022381373 46.63369537 -1.668699831 -0.147057243 LLHVAVSDVNDDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLHVAVSDVNDDVR 14 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 125.47 9.11E-05 872340000 645390 540400 582540 449750 522630 513750 460380 667500 678320 648690 FALSE TRUE 620167.4453 524988.3211 687817.9365 472961.6514 539440.8686 524138.377 466014.2682 653715.8917 601319.9573 604753.6485 1.025487728 0.868102776 1.137352273 0.78207325 0.892001015 0.866697337 0.770585294 1.080962295 0.994322165 1 19.20598804 1.668869921 11.7502664 1.027442431 0.906828262 0.213223752 0.104627015 0.179382954 31.40933992 0.048567059 0.026471606 46.65196286 -1.668869921 -0.120614168 IQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_BT-474_Pertuzumab_2h_R1 8 IQPQPPDEDGDHSDKEDEQPQVVVLK 26 1 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK 252.75 9.50E-53 12288230000 2556912 1991200 1880788 1671257 1940993 1871517 2164701 2289430 2925750 2431788 TRUE FALSE 2456985.052 1934412.926 2220688.23 1757510.774 2003426.803 1909360.356 2191193.258 2242152.47 2593631.126 2267080.833 1.083765968 0.853261559 0.979536414 0.77523075 0.883703295 0.842210974 0.966526304 0.989004202 1.144039987 1 21.1124044 1.669210698 2.213721309 1.068398976 0.899519006 0.349894559 0.087063835 0.277540624 2.950063987 0.058585037 0.023339718 46.68858355 -1.669210698 -0.168879971 EKEESPQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEESPQPR 9 1 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 0 60.436 0.087311 1696700000 1011600 1706000 1420000 2032500 2146800 2252700 1619500 1266000 811630 1239200 FALSE TRUE 972065.5536 1657346.55 1676625.588 2137397.569 2215853.772 2298251.137 1639319.925 1239856.658 719497.165 1155267.88 0.841420047 1.43459935 1.451287287 1.850131563 1.91804326 1.989366429 1.418995502 1.073220055 0.622796823 1 20.13979599 1.66922554 2.75586267 0.821703117 1.598901275 0.480190989 0.321572163 0.202960795 3.517923457 0.220539693 0.093639158 46.69017914 -1.66922554 0.777198158 LSDDNTIGKEEIQQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSDDNTIGKEEIQQR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 216.39 2.02E-12 968090000 1339400 1299950 1187960 1474580 1228740 1266460 1463010 1704020 1921710 1999890 FALSE TRUE 1287054.767 1262876.699 1402650.798 1550683.251 1268263.538 1292068.689 1480914.754 1668831.392 1703565.537 1864435.669 0.690318679 0.677350643 0.752319225 0.831717219 0.680239903 0.693007922 0.794296515 0.895086604 0.913716448 1 20.83030759 1.669341003 1.489982662 0.969838189 0.722365715 0.813118332 0.046885889 0.166746002 0.72276109 0.040743619 0.015114689 46.70259397 -1.669341003 -0.247472473 VTPTEEHVEGPLPSPVTNGT(ph)SPAQLNGGSACSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTPTEEHVEGPLPSPVTNGTSPAQLNGGSACSSR 34 0 H3BN50;Q15599-3;H3BQS0;H3BUQ9;Q15599;Q15599-2 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 VTPTEEHVEGPLPSPVT(0.002)NGT(0.884)S(0.114)PAQLNGGSACSSR 281.4 1.82E-73 317490000 56402 73281 77221 73025 66127 79038 69616 72548 74033 74039 TRUE FALSE 54197.74748 71191.09763 91176.55247 76793.829 68254.03501 80636.20251 70467.98143 71049.85845 65629.08421 69024.27258 0.785198387 1.031392218 1.320934637 1.11256267 0.988841062 1.16822966 1.020915959 1.029345994 0.950811675 1 16.07481616 1.669378704 2.102386746 0.980025389 1.075565947 0.059099407 0.129513436 0.827661409 7.823150664 0.096092596 0.037755369 46.70664844 -1.669378704 0.095540558 EVIRNDGVLLLQALTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVIRNDGVLLLQALTR 16 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 151.95 5.42E-07 300790000 327160 426610 313120 410280 397230 476510 360620 299870 263320 260670 FALSE TRUE 314374.2255 414443.5005 369707.7493 431454.6 410007.2637 486145.3587 365033.3754 293677.5797 233429.0175 243014.5887 1.293643428 1.705426422 1.521339732 1.775426744 1.687171399 2.000478083 1.50210478 1.208477159 0.960555573 1 17.8906834 1.669639591 2.453245041 0.997052581 1.668493539 0.716709796 0.173342972 0.131937494 1.767366577 0.116793443 0.047951986 46.73471417 -1.669639591 0.671440958 IDDPTDSKPEDWDKPEHIPDPDAK ddPTM_BT-474_Pertuzumab_2h_R1 7 IDDPTDSKPEDWDKPEHIPDPDAK 24 2 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;;; 185.14 1.46E-17 38464580000 19984520 14645930 14884210 11561090 14097000 12715430 16832920 19681030 26686890 21683180 FALSE TRUE 19203502.86 14228242.42 17574117.84 12157759.24 14550442.81 12972544.71 17038926.31 19274609.85 23657506.13 20214558.91 0.949983769 0.703861137 0.869379239 0.601435792 0.719800164 0.641742655 0.842903691 0.953501382 1.170320176 1 24.26889139 1.669895268 2.331883978 1.080530705 0.744941941 0.612379412 0.105928926 0.163306027 1.95173436 0.070367969 0.028473428 46.76223585 -1.669895268 -0.335588763 CNKEVYFAER ddPTM_BT-474_Pertuzumab_2h_R1 1 CNKEVYFAER 10 1 P50238 P50238 CRIP1 Cysteine-rich protein 1 0 75.479 0.035452 133960000 463770 619820 385570 570870 655560 589800 495270 373720 283200 306240 FALSE TRUE 445645.3557 602143.3405 455251.076 600332.6691 676646.6828 601726.1601 501331.2624 366002.5514 251052.3233 285498.092 1.560939874 2.109097599 1.594585353 2.10275545 2.370056759 2.107636362 1.755988136 1.281978975 0.879348515 1 18.12312158 1.670039438 2.173981938 0.947459005 1.984297397 0.761962686 0.234536176 0.133410798 1.360432133 0.171101422 0.067882973 46.77776181 -1.670039438 1.036838393 RT(ph)SSPHKEESPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSSPHKEESPK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 RT(0.418)S(0.418)S(0.163)PHKEESPK 134.14 0.0071838 186070000 74516 61985 66318 59098 65218 67444 64552 80205 101680 69413 TRUE FALSE 71603.83234 60217.24849 78303.13784 62148.05486 67315.7962 68807.76389 65342.00669 78548.73872 90137.71268 64711.59568 1.10650698 0.930548039 1.210032561 0.96038514 1.040243182 1.063298829 1.009741855 1.213827876 1.392914388 1 15.98173663 1.670223717 5.543938286 1.230339107 1.045129567 0.270144448 0.115142681 0.152341734 10.23864157 0.055723305 0.02738825 46.79761463 -1.670223717 -0.18520954 FKIDSNIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKIDSNISPK 10 1 Q9H501 Q9H501 ESF1 ESF1 homolog 1 FKIDSNIS(1)PK 153.52 0.0065799 0 474480 408760 343860 313110 386070 363030 370780 494890 573390 524660 TRUE FALSE 455936.797 397102.565 406003.1511 329269.6446 398488.2922 370370.7153 375317.7166 484670.3486 508301.171 489124.3109 0.932149122 0.811864297 0.830061279 0.673181924 0.814697375 0.757211832 0.767325827 0.990894007 1.039206516 1 18.89984165 1.670411958 4.717538759 1.017555502 0.794123584 0.707972927 0.062402621 0.084627149 4.316924357 0.034535452 0.016526615 46.81790304 -1.670411958 -0.223431918 DGS(ph)FGEGLTMK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGSFGEGLTMK 11 0 Q9ULT0;Q9ULT0-4;G5E9G4 Q9ULT0 TTC7A Tetratricopeptide repeat protein 7A 1 DGS(1)FGEGLTMK 92.295 0.010596 56583000 133460 118550 107970 101630 108130 109270 115390 145210 178670 147710 TRUE FALSE 128244.2357 115169.0701 127482.5808 106875.1365 111608.0997 111479.5143 116802.1773 142211.3628 158388.1306 137705.4701 0.931293692 0.836343465 0.925762649 0.776113951 0.810484141 0.80955037 0.848202887 1.032721232 1.150194909 1 17.07122634 1.670489524 3.787291617 1.079419777 0.844351667 0.744567259 0.057330773 0.084335275 2.839948152 0.032369754 0.014887884 46.82626562 -1.670489524 -0.23506811 GKEKCSEKSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GKEKCSEKSR 10 3 Q5VUJ6-2;Q5VUJ6 Q5VUJ6-2 LRCH2 Leucine-rich repeat and calponin homology domain-containing protein 2 0 67.726 0.075953 1569500000 1267000 2050900 1220100 2303500 1816300 2183200 1737000 1433800 1148000 1492100 FALSE TRUE 1217484.239 1992410.34 1440599.211 2422383.911 1874722.939 2227345.8 1758257.926 1404191.529 1017683.853 1391038.738 0.875233885 1.432318372 1.035628392 1.741420886 1.347714401 1.601210476 1.263989189 1.009455374 0.731599937 1 20.40773117 1.670560071 2.994796645 0.868222524 1.352100283 0.387378344 0.242768796 0.207876662 4.308971266 0.146245267 0.06364328 46.83387273 -1.670560071 0.483877758 NQTAEKEEFEHQQK ddPTM_BT-474_Pertuzumab_2h_R1 5 NQTAEKEEFEHQQK 14 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;; 214.65 4.08E-12 27187690000 14941980 11809600 12900120 12823450 12064990 10809100 15105040 17671050 22139350 21398070 FALSE TRUE 14358030.9 11472801.77 15231458.65 13485269.79 12453071.36 11027667.41 15289900 17306136.64 19626183.8 19948759.66 0.719745545 0.575113539 0.763529107 0.675995401 0.624252915 0.552799653 0.76645868 0.867529457 0.983829779 1 24.24979571 1.670640889 1.881251286 0.989811531 0.654218575 0.824117029 0.062632374 0.122817769 0.900590706 0.046988529 0.017997674 46.84258879 -1.670640889 -0.335592957 KASVVDPSTESSPAPQEGSEQPASPAS(ph)PLSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 KASVVDPSTESSPAPQEGSEQPASPASPLSSR 32 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 KASVVDPSTESSPAPQEGSEQPASPAS(1)PLSSR;KASVVDPSTESSPAPQEGSEQPAS(0.002)PAS(0.969)PLS(0.015)S(0.015)R;KASVVDPSTESSPAPQEGSEQPASPAS(1)PLSSR;KASVVDPSTESSPAPQEGSEQPASPAS(0.929)PLS(0.036)S(0.036)R 340.48 3.37E-117 4413780000 1451761 1614301 1292247 1354653 1541410 1719694 1503310 1500477 1633285 1519381 TRUE FALSE 1395024.575 1568262.716 1525784.779 1424566.804 1590990.853 1754467.391 1521707.957 1469491.626 1447881.334 1416471.972 0.98485858 1.107161135 1.077172588 1.005714785 1.123206731 1.238617796 1.074294436 1.037430782 1.022174362 1 20.43387062 1.670655555 3.296796613 1.017112867 1.091987781 0.188802931 0.065108284 0.361668728 9.183595779 0.041258362 0.01840419 46.84417068 -1.670655555 0.074874915 RPPESPPIVEEWNSR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPPESPPIVEEWNSR 15 1 Q9BTL3;A0A3B3IU46 Q9BTL3 FAM103A1 RNMT-activating mini protein 0 ;;; 164.8 2.34E-06 1540780000 358058 405692 335914 384897 413928 403659 414231 367554 397983 408587 FALSE TRUE 344064.6975 394122.0614 396621.1322 404761.5803 427242.37 411821.2615 419300.4829 359963.8815 352805.6383 380913.0386 0.903263114 1.034677266 1.041238005 1.062608888 1.121627056 1.081142465 1.100777449 0.945002783 0.926210454 1 18.53910215 1.67075751 7.299978677 0.951717388 1.05276714 0.341870527 0.058215232 0.136184339 13.71827355 0.030173004 0.015545968 46.85516916 -1.67075751 0.101049753 DVDASPS(ph)PLSVQDLK ddPTM_BT-474_Pertuzumab_2h_R1 3 DVDASPSPLSVQDLK 15 0 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 1 DVDASPS(1)PLSVQDLK;DVDAS(0.018)PS(0.953)PLS(0.029)VQDLK;DVDAS(0.005)PS(0.833)PLS(0.162)VQDLK 188.27 3.21E-07 166740000 329209 279138 247830 236913 268882 291622 259398 343875 369139 379004 TRUE FALSE 316343.1483 271177.2575 292618.3939 249140.1083 277530.8337 297518.7966 262572.5903 336773.8611 327235.8883 353333.7215 0.895309814 0.767481961 0.828164356 0.705112739 0.785463761 0.842033405 0.743129156 0.953132522 0.926138289 1 18.43067192 1.670847859 6.076561475 0.956338882 0.793657362 0.668639752 0.052953305 0.078947694 6.13507797 0.026380345 0.013174365 46.86491771 -1.670847859 -0.16268152 IDGDKDGFVTVDELKDWIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDGDKDGFVTVDELKDWIK 19 2 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 195.56 4.93E-16 896720000 1983800 1901500 1323500 1123200 1539200 1614200 1691400 1802500 2246100 1977800 FALSE TRUE 1906270.903 1847271.082 1562685.891 1181168.487 1588709.766 1646840.23 1712099.859 1765277.745 1991132.144 1843841.844 1.033858142 1.001859833 0.847516231 0.640601845 0.861630172 0.893156989 0.928550279 0.957391086 1.079882285 1 20.81428348 1.670891849 1.663469187 1.036854067 0.873211085 0.266453009 0.101464293 0.506849701 2.810266158 0.08779244 0.032920508 46.86966495 -1.670891849 -0.163642982 NRPTSISWDGLDSGK ddPTM_BT-474_Pertuzumab_2h_R1 5 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ;;;; 207.79 2.93E-09 11748490000 13197340 11763650 10508300 11238350 10844210 8994640 11666760 13633550 15950370 15051470 FALSE TRUE 12681573.36 11428162.22 12407383.57 11818362.59 11193023.86 9176517.784 11809541.3 13352012.43 14139750.87 14032020.53 0.903759607 0.814434542 0.884219314 0.842242396 0.797677272 0.653969809 0.841613741 0.951538832 1.007677464 1 23.74221943 1.67095689 3.20120988 0.996923797 0.814646408 0.599561086 0.06340925 0.150525038 3.593123566 0.041188734 0.018245934 46.87668477 -1.67095689 -0.182277389 KNQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KNQKPSQVNGAPGSPTEPAGQK 22 2 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 KNQKPSQVNGAPGS(0.999)PT(0.001)EPAGQK;KNQKPSQVNGAPGS(1)PTEPAGQK 166.79 5.89E-12 1182760000 765463 670887 609717 528168 617597 708319 662194 812274 978160 847916 TRUE FALSE 735547.8597 651753.9596 719906.425 555426.8138 637462.5684 722641.6955 670298.1283 795500.258 867123.3776 790485.8941 0.93050093 0.8244979 0.910713816 0.702639754 0.806418651 0.914174055 0.847957102 1.006343395 1.096949843 1 19.59238019 1.67098123 3.142887176 1.051333404 0.843428606 0.628043519 0.066053427 0.13104607 3.009163766 0.040533455 0.017872614 46.87931208 -1.67098123 -0.207904798 DAEQSGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAEQSGSPR 9 0 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5 P08651-3 NFIC Nuclear factor 1 C-type 1 DAEQS(0.041)GS(0.959)PR;DAEQS(0.021)GS(0.979)PR 81.92 0.020894 114177000 127078 137011 111728 154119 149619 138654 142138 121727 115287 141660 TRUE FALSE 122111.6513 133103.5804 131919.735 162073.1001 154431.631 141457.6789 143877.5274 119213.2949 102200.1031 132065.242 0.924631261 1.007862314 0.998898218 1.227219953 1.169358634 1.071119673 1.089442802 0.902684863 0.773860719 1 17.01089129 1.671137239 4.57787946 0.872784576 1.074691758 0.417486074 0.095630992 0.151592868 7.328521244 0.055013188 0.026207117 46.89615532 -1.671137239 0.201907182 KFGGPGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFGGPGAR 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ; 103.56 0.0076141 3982500000 4869100 4590200 3987700 4407800 4853700 4550000 4706600 4383700 4693900 4660400 FALSE TRUE 4678810.189 4459291.99 4708366.096 4635287.086 5009823.669 4642004.117 4764200.779 4293175.063 4161068.15 4344746.957 1.076888996 1.026364029 1.083691672 1.066871588 1.153076052 1.0684176 1.096542751 0.988130058 0.957723935 1 22.05084072 1.671190148 4.946341822 0.977222773 1.081262979 0.680778755 0.03127601 0.088908256 4.936051121 0.017285359 0.008341498 46.90186887 -1.671190148 0.104040206 GFGFGQGAGALVHS(ph)E ddPTM_BT-474_Pertuzumab_2h_R1 5 GFGFGQGAGALVHSE 15 0 P21291;E9PP21 P21291 CSRP1 Cysteine and glycine-rich protein 1 1 GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E 170.95 1.17E-06 3354310000 3504950 4186620 3399350 4439690 4425460 4300440 4246000 3892720 4160470 4145630 TRUE FALSE 3367972.679 4067221.697 4013688.163 4668822.933 4567808.94 4387397.843 4297963.818 3812333.972 3688190.888 3864842.788 0.871438468 1.052364073 1.03851266 1.208024023 1.181887386 1.135207325 1.112066921 0.986413725 0.954292604 1 21.8819783 1.671235009 5.168613406 0.975335469 1.092760075 0.226955501 0.088379706 0.22505773 13.48034532 0.050455918 0.024526938 46.90671391 -1.671235009 0.117424605 KDDS(ph)HS(ph)AEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 KDDS(1)HS(1)AEDS(1)EDEKEDHK;KDDS(1)HS(1)AEDS(1)EDEKEDHK 148.02 5.35E-08 2141680000 3062800 1735310 1662200 1219340 1959380 1460640 2089340 2502500 3691300 2436900 TRUE FALSE 2943102.39 1685820.658 1962596.515 1282270.284 2022405.237 1490175.142 2114909.968 2450822.5 3272279.099 2271846.592 1.295467044 0.742048633 0.863877219 0.564417636 0.890203258 0.655931235 0.930921117 1.078779927 1.440360943 1 21.11543399 1.671349285 2.790415889 1.225865126 0.823779604 0.344688326 0.209301366 0.225518803 4.009968532 0.127246442 0.054346288 46.91905807 -1.671349285 -0.402085521 AGGAS(ph)PAASSTAQPPTQHR ddPTM_BT-474_Pertuzumab_2h_R1 13 AGGASPAASSTAQPPTQHR 19 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 AGGAS(0.999)PAAS(0.001)STAQPPTQHR;AGGAS(0.994)PAAS(0.002)S(0.002)T(0.002)AQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(0.999)PAAS(0.001)STAQPPTQHR;AGGAS(0.993)PAAS(0.006)STAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR 185.46 2.38E-14 14743683000 1049845.1 1068249.4 910642.5 1084594.2 1023314.4 1067437.3 989238.6 1057178.3 1084999.4 1047702.8 TRUE FALSE 1008815.993 1037783.973 1075215.857 1140570.237 1056230.237 1089021.614 1001345.198 1035347.199 961834.8168 976740.9562 1.032838837 1.062496629 1.100819875 1.167730532 1.081382152 1.114954387 1.02519014 1.060001828 0.984738902 1 19.89761647 1.671382653 1.243734625 0.995435663 1.09402187 0.484332183 0.037915626 0.387614704 1.137444046 0.033359253 0.012485528 46.92266313 -1.671382653 0.098586207 FCYHER ddPTM_BT-474_Pertuzumab_2h_R1 1 FCYHER 6 0 P28331-4;P28331;P28331-2;F8WDL5;C9JPQ5 P28331-4 NDUFS1 "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial" 0 89.703 0.049864 116320000 98652 158870 122790 189140 125210 111870 137840 102900 87149 86576 FALSE TRUE 94796.57077 154339.1832 144980.8844 198901.5381 129237.4934 114132.088 139526.9272 100775.079 77256.21088 80712.13041 1.174502151 1.912217933 1.796271313 2.464332648 1.601215241 1.414063629 1.728698356 1.248574143 0.957182155 1 16.3004979 1.671386273 1.092073458 0.93060515 1.800850431 0.4795139 0.319606902 0.406680149 0.914360437 0.281525486 0.10804753 46.92305422 -1.671386273 0.870245281 IISSS(ph)PNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IISSSPNKK 9 1 B9EGE7;Q8TCN5-2;Q8TCN5 B9EGE7 ZNF507 Zinc finger protein 507 1 IISS(0.014)S(0.986)PNKK 164.33 0.00037525 0 247690 220060 179100 167730 196970 200400 197070 229290 253700 240180 TRUE FALSE 238010.001 213784.1043 211467.3541 176386.5654 203305.7189 204452.2253 199481.8016 224555.0814 224901.0396 223912.3947 1.062960366 0.954766727 0.944420046 0.787748109 0.907969919 0.913090254 0.890892181 1.00287026 1.00441532 1 17.77257487 1.671389782 6.343670871 1.003320162 0.919132235 0.241783554 0.063941728 0.196340376 16.28386547 0.034524957 0.017374778 46.92343334 -1.671389782 -0.084187927 LDQPVS(ph)APPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 LDQPVSAPPSPR 12 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR 148.41 8.66E-05 9644620000 11886670 11633330 9018010 10215430 10819550 10319320 8337770 10061470 8184680 7585670 TRUE FALSE 11422125.79 11301558.82 10647765.01 10742649.57 11167570.65 10527983.72 8439810.123 9853697.128 7255589.439 7071885.814 1.615145676 1.598096903 1.505647191 1.519064341 1.579150307 1.488709518 1.193431334 1.393362024 1.025976611 1 22.75366355 1.671462666 0.64809373 0.984376664 1.585631857 0.844193128 0.0876231 0.251573365 0.223343387 0.080193797 0.041116966 46.9313088 -1.671462666 0.601255193 KEEEPDKAVTEDGKVDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEEEPDKAVTEDGKVDYR 18 3 Q92620 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 62.765 0.021401 93342000 356070 275070 212380 161090 266350 247770 238260 336620 398670 342410 FALSE TRUE 342154.3907 267225.2729 250761.7904 169403.8742 274917.3896 252780.0792 241175.8972 329668.6794 353414.653 319218.2657 1.071850917 0.837124005 0.78554963 0.530683524 0.861220736 0.791872228 0.755520354 1.032737518 1.107125409 1 18.28418368 1.671802111 5.073937782 1.058122706 0.796627512 0.432115644 0.126648207 0.141075569 8.192683856 0.069763104 0.033821402 46.96800473 -1.671802111 -0.261495194 TAADKDRGEEDADGSK ddPTM_BT-474_Pertuzumab_2h_R1 6 TAADKDRGEEDADGSK 16 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;;; 280.54 1.02E-35 3785880000 7615430 6266920 5231770 4243390 5933420 6367070 6467290 7155410 9474410 8022280 FALSE TRUE 7317810.576 6088193.578 6177267.219 4462391.866 6124273.843 6495816.518 6546438.63 7007648.283 8398914.697 7478923.83 0.978457696 0.814046742 0.825956696 0.596662296 0.818871001 0.868549629 0.875318265 0.936986182 1.123011129 1 22.83439926 1.671809039 1.504623522 1.058684101 0.806415856 0.49938195 0.094316651 0.313506236 1.38831339 0.078505378 0.029188095 46.96875398 -1.671809039 -0.252268245 EYSGFAGVSRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EYSGFAGVSRPR 12 1 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 128.36 0.00021702 216400000 199821 238060 180108 221648 211389 188342 231964 189698 212069 218170 FALSE TRUE 192011.7744 231270.7619 212657.5221 233087.2798 218188.5192 192150.4043 234802.8448 185780.67 187995.8162 203393.1516 0.944042476 1.137062679 1.045549078 1.145993747 1.072742703 0.944724062 1.15442847 0.913406713 0.92429767 1 17.63391158 1.672015219 8.917005945 0.939937959 1.064371405 0.347766942 0.073472165 0.118395234 15.23925768 0.03365195 0.017869412 46.99105755 -1.672015219 0.124433446 IDVDAPDIDIHGPDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 IDVDAPDIDIHGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 229.68 2.96E-15 4181343000 4529545 4231721 3923907 3790119 3550508 4338263 4216298 4565749 5359125 4905284 FALSE TRUE 4352525.374 4111036.46 4633044.282 3985727.496 3664713.314 4425985.65 4267898.316 4471464.688 4750779.597 4573044.746 0.951778436 0.898971405 1.01312026 0.871569757 0.801372722 0.967842192 0.933272809 0.977787215 1.038865758 1 22.1247236 1.672287553 1.690547548 1.019712576 0.914203191 0.359655098 0.05450503 0.389174537 2.23752645 0.043866434 0.016505024 47.02053353 -1.672287553 -0.105509385 WPGS(ph)PTSR ddPTM_BT-474_Pertuzumab_2h_R1 4 WPGSPTSR 8 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 WPGS(0.963)PT(0.037)SR;WPGS(0.968)PT(0.032)S(0.001)R;WPGS(0.966)PT(0.034)SR;WPGS(0.679)PT(0.32)S(0.001)R 108.26 0.0048133 2631870000 4159990 4618700 3668930 5052770 4897440 4504400 3962450 4189070 3962090 3693970 TRUE FALSE 3997412.992 4486979.198 4331987.266 5313544.065 5054970.605 4595482.054 4010943.648 4102564.241 3512330.154 3443774.122 1.160765152 1.302924942 1.257918526 1.542942097 1.467857771 1.334431903 1.164694172 1.191298876 1.019907238 1 21.71555909 1.672308306 1.244416781 1.007572747 1.350768637 0.592669129 0.106235225 0.324598673 0.95352375 0.097258974 0.036418045 47.02278054 -1.672308306 0.34319589 AEAPAGPALGLPS(ph)PEAESGVDRGEPEPMEVEEGELEIVPVRR ddPTM_BT-474_Pertuzumab_2h_R1 3 AEAPAGPALGLPSPEAESGVDRGEPEPMEVEEGELEIVPVRR 42 2 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(0.999)PEAES(0.001)GVDRGEPEPMEVEEGELEIVPVRR 345.13 5.38E-136 1963020000 141706 147778 98880.8 111128 140152 162377 111244 118411 117595 99320 TRUE FALSE 136167.9729 143563.5161 116750.7602 116863.3294 144660.1164 165660.3742 112605.4373 115965.7715 104246.1086 92592.96793 1.470608145 1.550479689 1.260903098 1.262118841 1.562322924 1.789124789 1.216133794 1.252425255 1.125853409 1 16.49861501 1.672386816 1.753322811 1.074434089 1.463527365 0.50481248 0.158680477 0.305152873 1.905509416 0.129684695 0.049080733 47.03128192 -1.672386816 0.389093276 KFDGVEGPRT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFDGVEGPRTPK 12 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YAN4 Q6PKG0 LARP1 La-related protein 1 1 KFDGVEGPRT(1)PK;KFDGVEGPRT(1)PK 68.919 0.082598 1072820000 783800 741650 567430 519930 648580 738730 592830 795600 867670 740550 TRUE FALSE 753168.2295 720498.8682 669977.2234 546763.6496 669442.1647 753667.6267 600085.2309 779170.582 769175.7392 690391.8889 1.09092856 1.043608536 0.970430323 0.791961288 0.969655315 1.091651914 0.869195077 1.128591738 1.114114681 1 19.39705599 1.672688538 10.24915813 1.090129976 0.975166384 0.209827062 0.093154507 0.173344498 26.04209064 0.045657486 0.024625904 47.06396781 -1.672688538 -0.114963591 KPPAPPS(ph)PVQSQS(ph)PSTNWS(ph)PAVPVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 KPPAPPS(1)PVQSQS(0.999)PS(0.001)TNWS(1)PAVPVKK 161.55 1.26E-11 3428200000 3505700 3016300 2332600 2245100 2586000 2925200 2757000 3202400 3606100 3428000 TRUE FALSE 3368693.368 2930278.077 2754152.708 2360969.88 2669181.039 2984349.548 2790740.991 3136269.321 3196750.646 3195818.507 1.05409408 0.916910041 0.861798848 0.738768449 0.835210458 0.933829484 0.873247647 0.981366531 1.000291675 1 21.60775405 1.672790469 3.89800126 0.997993707 0.881533578 0.292499212 0.075420823 0.240029599 8.553016158 0.046172522 0.021400904 47.07501522 -1.672790469 -0.116460129 RFDSELSQAHEEAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RFDSELSQAHEEAQR 15 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 154.46 1.61E-06 272870000 73844 99350 66784 70324 73454 83910 77715 69652 60898 81305 FALSE TRUE 70958.09484 96516.63527 78853.3544 73953.43007 75816.71462 85606.71769 78666.09942 68213.66186 53985.11435 75798.13993 0.936145595 1.273337781 1.040307249 0.975662861 1.000245055 1.129403937 1.037836806 0.899938467 0.712222152 1 16.20987482 1.672879446 3.539103707 0.843444538 1.06254715 0.378653377 0.109226937 0.178864344 5.249690598 0.061651301 0.028015759 47.0846608 -1.672879446 0.219102611 ECYLEGDQTSLYHAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ECYLEGDQTSLYHAAK 16 0 A0A2R8YF87;Q96AX1 A0A2R8YF87 VPS33A Vacuolar protein sorting-associated protein 33A 0 82.349 0.010241 210720000 113020 119090 120350 108410 114440 118230 129480 108020 125030 117520 FALSE TRUE 108603.0534 115693.6698 142099.9222 114005.0531 118121.0665 120620.6916 131064.615 105789.3493 110837.1186 109560.2657 0.991263144 1.055982012 1.297002351 1.040569337 1.078137824 1.100952894 1.196278725 0.96558135 1.011654342 1 16.74136514 1.673049348 9.035612012 0.992262514 1.109526328 0.29749383 0.081620375 0.147883187 19.33171137 0.039633552 0.021086623 47.10308461 -1.673049348 0.117263814 TREQENEEKEKEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TREQENEEKEKEEK 14 3 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 89.541 0.0026759 161200000 88377 57671 51768 37385 64137 54982 54702 79662 102120 69403 FALSE TRUE 84923.12913 56026.27955 61123.62917 39314.44433 66200.02485 56093.77371 55371.45944 78016.95186 90527.76572 64702.27299 1.312521573 0.865908985 0.944690601 0.607620761 1.023148365 0.866952135 0.855788474 1.205783789 1.399143516 1 15.98152877 1.673302992 5.443889791 1.231849504 0.913369306 0.305729202 0.188667553 0.154583164 10.13194897 0.096152938 0.04720472 47.13060249 -1.673302992 -0.318480198 TMSS(ph)DDEDCSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TMSSDDEDCSAK 12 0 Q9NVR2;H0YBW3 Q9NVR2 INTS10 Integrator complex subunit 10 1 TMS(0.016)S(0.984)DDEDCSAK 135.04 0.0002388 0 234350 230050 165120 212570 197050 222570 215740 244740 288790 258250 TRUE FALSE 225191.3429 223489.1992 194960.8571 223540.7632 203388.2922 227070.5179 218380.2907 239686.0335 256007.7699 240758.4975 0.935341204 0.928271283 0.809777678 0.928485455 0.844781365 0.943146432 0.907051227 0.995545478 1.06333846 1 17.87722719 1.673429041 2.387430097 1.033867737 0.895596683 0.631597643 0.042536525 0.155928262 1.960624136 0.027929328 0.0114227 47.14428368 -1.673429041 -0.138271054 VS(ph)PENLVDK ddPTM_BT-474_Pertuzumab_2h_R1 4 VSPENLVDK 9 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 VS(1)PENLVDK;VS(1)PENLVDK;VS(1)PENLVDK;VS(1)PENLVDK 216.84 6.17E-07 3574080000 3249010 2813190 2603510 2409520 2638320 2859850 2931740 3403030 4208440 3657860 TRUE FALSE 3122035.097 2732960.576 3074022.172 2533875.616 2723183.959 2917678.126 2967619.511 3332756.241 3730715.534 3410109.884 0.915523313 0.801428889 0.901443729 0.743048084 0.798561938 0.855596513 0.870241609 0.977316378 1.094016223 1 21.7013868 1.673544642 2.208879788 1.047932725 0.832535893 0.728889749 0.05237374 0.133262035 1.406500362 0.035704736 0.01428089 47.15683423 -1.673544642 -0.215396833 LVHSGSGCRS(ph)PSLGSDLTFATR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVHSGSGCRSPSLGSDLTFATR 22 1 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 LVHS(0.006)GS(0.077)GCRS(0.822)PS(0.095)LGSDLTFATR;LVHS(0.049)GS(0.21)GCRS(0.728)PS(0.013)LGSDLTFATR 165.17 7.93E-12 220620000 80940 101994 64364 75229 84811 85551 69398 72325 54525 63543 TRUE FALSE 77776.77532 99085.23098 75996.00657 79111.57771 87539.02284 87280.89984 70247.31348 70831.46348 48335.55059 59239.17601 1.312928041 1.672630135 1.282867381 1.335460468 1.477721817 1.473364515 1.185825297 1.19568617 0.815938942 1 15.85426395 1.673551698 1.475050022 0.920539148 1.425963075 0.697653089 0.128285546 0.202596408 0.858478637 0.100261915 0.037291995 47.1576004 -1.673551698 0.505423927 EQIVPKPEEEVAQKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQIVPKPEEEVAQKK 15 2 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 115.31 0.00030225 483120000 436810 360680 307380 224620 335246 370690 316920 420110 484670 411180 FALSE TRUE 419738.9823 350393.7595 362930.4036 236212.6651 346029.4921 378185.6058 320798.5618 411434.5817 429652.2935 383330.4124 1.094979602 0.914077642 0.94678218 0.616211648 0.90269251 0.986578663 0.83687219 1.073315783 1.120840611 1 18.54822894 1.67374654 6.350816999 1.073873341 0.894955362 0.286739424 0.118536654 0.166299264 13.86863109 0.062067501 0.031281201 47.17876196 -1.67374654 -0.178917978 LAEQFVLLNLVYETTDKHLSPDGQYVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAEQFVLLNLVYETTDKHLSPDGQYVPR 28 1 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 236.79 2.27E-45 1103330000 390625 642933 276820 301054 430274 670010 430202 342570 323284 306708 FALSE TRUE 375358.9431 624597.1803 326847.5318 316591.433 444114.154 683558.0613 435466.9408 335495.8098 286586.1556 285934.394 1.31274499 2.18440731 1.143085752 1.107217039 1.553202984 2.390611538 1.522961036 1.173331424 1.00227941 1 18.12532464 1.673859958 3.382045902 1.029677803 1.618608706 0.297580785 0.388513618 0.266628736 7.12301141 0.241218514 0.10860215 47.19108452 -1.673859958 0.588930903 RLS(ph)DCESTDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSDCESTDVK 11 1 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 RLS(0.802)DCES(0.196)T(0.002)DVK;RLS(1)DCESTDVK 168 0.00034209 564980000 804790 804440 687280 849550 967410 789720 804800 778360 758270 793400 TRUE FALSE 773337.9171 781498.1588 811486.7845 893395.3773 998527.6212 805688.6795 814649.3831 762286.594 672194.3685 739662.3113 1.045528352 1.05656074 1.097104411 1.207842232 1.349977694 1.089265557 1.101380144 1.030587313 0.90878548 1 19.49650724 1.673870583 1.928737655 0.955358203 1.145553403 0.424978131 0.086194412 0.318780417 2.471996026 0.069973262 0.027032679 47.19223902 -1.673870583 0.190195199 DKQNKPTGFALGSIEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKQNKPTGFALGSIEGR 17 2 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 ; 204.63 4.84E-12 3168800000 2639700 2634400 2021950 2219740 2376650 2559500 2414600 2721800 3110700 2784400 FALSE TRUE 2536537.606 2559269.491 2387361.343 2334301.047 2453097.106 2611254.844 2444150.597 2665593.879 2757586.377 2595810.108 0.977166087 0.985923232 0.919697992 0.899257245 0.945021787 1.005949871 0.941575268 1.026883234 1.062322074 1 21.30775342 1.674082946 4.920713768 1.035306326 0.953069225 0.531455765 0.032696079 0.122379829 6.755702731 0.018700134 0.009034114 47.21532089 -1.674082946 -0.0822371 EVIEYAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVIEYAR 7 0 H3BS10;H3BP20;P06865;H3BU85;H3BTD4;P06865-2 H3BS10 HEXA Beta-hexosaminidase;Beta-hexosaminidase subunit alpha 0 114.78 0.013557 344500000 237460 291130 231590 278250 276810 263850 281590 254340 268250 289410 FALSE TRUE 228179.8007 282827.2574 273443.4647 292610.5158 285713.845 269185.2278 285036.1827 249087.7901 237799.3846 269808.0029 0.845711759 1.048253774 1.013474255 1.084513849 1.058952447 0.997691784 1.056440801 0.923203861 0.881365201 1 18.04157362 1.674324812 6.874692098 0.926578993 1.019746676 0.220072348 0.067994812 0.166573157 15.55680002 0.033306246 0.017018036 47.24162322 -1.674324812 0.093167683 NRVPSAGDVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ;;; 127.71 0.00025616 1945750000 2048990 1849240 1647980 1625750 1692280 1666060 1849010 2111520 2435770 2341350 FALSE TRUE 1968913.206 1796501.486 1945806.645 1709655.152 1746713.723 1699748.875 1871638.737 2067916.374 2159271.601 2182768.279 0.902025755 0.823038113 0.891439858 0.783250869 0.800228655 0.778712468 0.85746103 0.947382456 0.989235377 1 21.05772755 1.674435193 2.489727977 0.991252731 0.828100028 0.753903586 0.038792883 0.123893844 1.709593479 0.026719683 0.011076057 47.25363181 -1.674435193 -0.163152703 S(ph)LTSSLENIFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 S(0.999)LT(0.001)SSLENIFSR 97.273 0.00526 16580000 12855 16073 13248 19660 16494 17795 15707 12271 10026 12725 TRUE FALSE 12352.61239 15614.61378 15642.2083 20674.65496 17024.54449 18154.82709 15899.22696 12017.59956 8887.890512 11863.12442 1.041261303 1.31623114 1.318557216 1.742766427 1.435081003 1.530357978 1.340222559 1.013021455 0.749203178 1 13.53419641 1.674459127 3.005294036 0.874854155 1.409017084 0.601408673 0.176990826 0.146742391 3.054512258 0.113598385 0.049687892 47.25623607 -1.674459127 0.534162929 RS(ph)SRSS(ph)PELTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.908)S(0.102)RS(0.334)S(0.478)PELT(0.179)R;RS(0.608)S(0.39)RS(0.053)S(0.948)PELT(0.001)R 115.11 0.011787 849120000 948110 1048600 825950 1014410 1048810 1032420 945270 964310 967160 958030 TRUE FALSE 911056.813 1018694.955 975217.5382 1066763.822 1082545.926 1053296.24 956838.497 944396.6615 857372.0515 893141.7748 1.020058448 1.140574748 1.09189556 1.194394722 1.212065046 1.179315837 1.071317594 1.057387179 0.959950677 1 19.76852968 1.674549376 1.810630805 0.984204466 1.141385403 0.5506747 0.055105401 0.249619842 1.676123136 0.043629784 0.016641463 47.26605713 -1.674549376 0.157180937 ANS(ph)PEKPPEAGAAHKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ANSPEKPPEAGAAHKPR 17 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 ANS(1)PEKPPEAGAAHKPR;ANS(1)PEKPPEAGAAHKPR 160.52 1.61E-09 19184700000 8350100 6498200 6248800 5346130 6114900 6335500 6938000 8110200 9966300 8869100 TRUE FALSE 8023768.86 6312877.698 7378097.164 5622044.41 6311591.312 6463608.151 7022909.319 7942721.536 8834967.406 8268387.957 0.97041514 0.763495585 0.892325953 0.679944439 0.763340006 0.781725311 0.849368626 0.96061307 1.068523569 1 22.97917465 1.674656348 2.328896386 1.033009973 0.803100073 0.591605958 0.076172343 0.174018804 2.068001931 0.051111223 0.020780043 47.27770082 -1.674656348 -0.2299099 GVEPSPS(ph)PIKPGDIKR ddPTM_BT-474_Pertuzumab_2h_R1 6 GVEPSPSPIKPGDIKR 16 2 Q92890;Q92890-1;Q92890-3 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPS(0.002)PS(0.998)PIKPGDIKR;GVEPS(0.035)PS(0.965)PIKPGDIKR;GVEPSPS(1)PIKPGDIKR;GVEPS(0.003)PS(0.997)PIKPGDIKR;GVEPS(0.025)PS(0.975)PIKPGDIKR;GVEPS(0.04)PS(0.96)PIKPGDIKR 205.65 1.15E-11 4055840000 4673240 3880620 3255210 2762550 3675980 4144840 3773580 4535740 5448080 4903870 TRUE FALSE 4490604.614 3769948.517 3843498.859 2905125.537 3794221.235 4228651.505 3819762.201 4442075.384 4829636.799 4571726.517 0.98225574 0.824622493 0.840710582 0.635454795 0.829931804 0.924957232 0.835518526 0.971640663 1.056414197 1 22.12430767 1.674680115 1.647774831 1.035117816 0.826864257 0.456692771 0.085409143 0.317591909 1.722726752 0.06946097 0.026095625 47.28028817 -1.674680115 -0.20825356 IRLEETLEQLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IRLEETLEQLAK 12 1 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ; 167.3 4.52E-05 651630000 1788190 1699060 1478640 1624920 1697070 1751650 1767230 1963820 2197900 2191180 FALSE TRUE 1718305.558 1650604.472 1745863.14 1708782.316 1751657.798 1787069.563 1788857.889 1923266.431 1948403.606 2042769.427 0.841164713 0.808022898 0.854655017 0.836502786 0.857491685 0.87482686 0.875702302 0.941499518 0.953804957 1 20.96209494 1.674834644 0.660196375 1.002071951 0.830885759 0.947857919 0.013159919 0.127414122 0.116334448 0.011732392 0.00592963 47.29711428 -1.674834644 -0.171186192 RQLHGES(ph)PTRR ddPTM_BT-474_Pertuzumab_2h_R1 3 RQLHGESPTRR 11 2 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;Q9UQ26-2;A0A0J9YXG4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 RQLHGES(0.936)PT(0.064)RR;RQLHGES(0.968)PT(0.032)RR;RQLHGES(0.988)PT(0.012)RR 104.7 0.0013386 256151000 75854 87558 60777 86918 75317 78018 78082 72723 73239 77576 TRUE FALSE 72889.54182 85060.93157 71760.75588 91403.8484 77739.63971 79595.57741 79037.59087 71221.24464 64925.21576 72321.70842 1.007851493 1.176146601 0.992243649 1.263850791 1.074914316 1.100576565 1.092861225 0.984783769 0.897727905 1 16.14214114 1.67503324 3.123260748 0.946190315 1.106387157 0.416771663 0.076706904 0.183582429 4.146021298 0.043389583 0.019182099 47.31874739 -1.67503324 0.160196842 NLFASFPTEESSINYTFKT(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLFASFPTEESSINYTFKTPEK 22 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NLFASFPTEESS(0.001)INYT(0.024)FKT(0.974)PEK 92.924 0.0032323 498770000 228070 173860 159530 103410 145420 165940 161730 207870 245040 220080 TRUE FALSE 219156.7723 168901.683 188360.6197 108747.0025 150097.5664 169295.4205 163709.3001 203577.4119 217224.0865 205173.7856 1.068151916 0.823212783 0.918054025 0.530023863 0.731563079 0.825131827 0.79790554 0.992219407 1.058732166 1 17.64648689 1.675033954 3.868728078 1.028568991 0.803585329 0.343654697 0.128856535 0.206352942 7.241018846 0.076153777 0.035315514 47.31882523 -1.675033954 -0.224983661 RYS(ph)DLTTLVAFPSSSVYPTKDEENNPLETEYGLSVYK ddPTM_BT-474_Pertuzumab_2h_R1 1 RYSDLTTLVAFPSSSVYPTKDEENNPLETEYGLSVYK 37 2 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 1 RY(0.031)S(0.958)DLT(0.005)T(0.005)LVAFPSSSVYPTKDEENNPLETEYGLSVYK 143.24 2.37E-13 337900000 77201 65333 52594 60417 51892 64255 58514 76402 85790 78543 TRUE FALSE 74183.89957 63469.76681 62098.90575 63535.12861 53561.15331 65554.28012 59230.11184 74824.272 76051.47886 73223.21265 1.013119978 0.866798444 0.848076771 0.867691082 0.731477784 0.895266375 0.808898021 1.021865462 1.038625268 1 16.16001345 1.675085443 6.163717548 1.023913223 0.858078676 0.537411741 0.067187608 0.100916693 8.071587858 0.034465657 0.017294496 47.32443557 -1.675085443 -0.165834547 KCLELFSELAEDKENYKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KCLELFSELAEDKENYKK 18 3 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 228.63 1.02E-19 4541500000 2670800 2144300 1599450 1283010 1759070 2056300 1802420 2305800 2762700 2115400 FALSE TRUE 2566422.183 2083146.663 1888506.195 1349226.3 1815652.084 2097879.795 1824478.555 2258184.424 2449089.878 1972122.074 1.301350569 1.056297017 0.957601063 0.684149484 0.920659075 1.063767716 0.925134696 1.145053065 1.241855112 1 20.91131743 1.675226479 6.352966346 1.145972174 0.977567589 0.143910628 0.155455207 0.237738291 19.89210862 0.083443081 0.042089307 47.33980656 -1.675226479 -0.168404585 NKSEDSTKDDIDLDALAAEIEGAGAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 NKSEDSTKDDIDLDALAAEIEGAGAAK 27 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 118.01 0.00024442 49682000 415290 314660 265340 190180 273580 315210 290060 371510 452030 366260 FALSE TRUE 399060.0077 305686.2049 313292.8405 199995.2126 282379.9492 321583.7622 293609.841 363838.1887 400717.4495 341452.884 1.16871178 0.895251495 0.917528758 0.585718329 0.826995355 0.941810063 0.85988391 1.065558986 1.173565866 1 18.38132699 1.675228457 4.407232119 1.096441928 0.874934987 0.287372784 0.139561728 0.204763621 9.250823095 0.079546129 0.037767341 47.34002216 -1.675228457 -0.221506941 EVSGHSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSGHSVR 8 0 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 136.39 0.00079292 285370000 358400 443480 372640 441620 422970 428280 450020 372650 387600 432560 FALSE TRUE 344393.3318 430832.3846 439984.3373 464412.0611 436575.2142 436940.115 455527.4794 364954.6473 343601.273 403262.3259 0.854018116 1.068367554 1.091062341 1.15163761 1.082608481 1.083513353 1.129605842 0.90500556 0.852053988 1 18.62135911 1.675249624 6.658656844 0.908434251 1.071227916 0.390096426 0.083395967 0.122171728 10.93538189 0.042187553 0.021450018 47.34232949 -1.675249624 0.162793665 LADS(ph)PPPQVWQLISK ddPTM_BT-474_Pertuzumab_2h_R1 1 LADSPPPQVWQLISK 15 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 1 LADS(1)PPPQVWQLISK 124.96 9.79E-05 224350000 150580 128940 121020 107110 130970 137130 145550 177780 187630 208910 TRUE FALSE 144695.1671 125262.7574 142891.0061 112637.9599 135182.769 139902.8626 147331.2844 174108.7809 166331.029 194760.3396 0.742939591 0.643163581 0.733676098 0.578341361 0.694098035 0.718333429 0.756474777 0.89396425 0.854029261 1 17.5713404 1.675274702 0.924220575 0.974622238 0.670882309 0.812957557 0.050822225 0.2027958 0.330205634 0.043219816 0.017614802 47.34506333 -1.675274702 -0.303739928 LEDLASLVYLNESSVLHTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEDLASLVYLNESSVLHTLR 20 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;H0YEV9 Q92614 MYO18A Unconventional myosin-XVIIIa 0 124.08 2.75E-05 59419000 41039 58660 47721 50385 50344 59040 52458 46977 45307 52338 FALSE TRUE 39435.15051 56987.07423 56345.24625 52985.37589 51963.36048 60233.82925 53099.9967 46006.90853 40163.9393 48793.10064 0.808211612 1.167933037 1.154778965 1.085919427 1.064973527 1.23447431 1.088268546 0.942897826 0.82314792 1 15.57438954 1.675447804 4.001477976 0.904566582 1.097407955 0.305672188 0.113065136 0.19206472 7.204286849 0.061776194 0.028841373 47.36393803 -1.675447804 0.192841373 ARS(ph)PVLWGWSLPS ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSPVLWGWSLPS 13 1 A1IGU5 A1IGU5 ARHGEF37 Rho guanine nucleotide exchange factor 37 1 ARS(1)PVLWGWSLPS 90.367 0.018476 193290000 381320 414290 368270 344260 386860 353650 342090 386570 355370 335540 TRUE FALSE 366417.5928 402474.8548 434824.5811 362027.2999 399303.7032 360801.0453 346276.5998 378587.1944 315029.8874 312813.5769 1.171360899 1.286628473 1.390043825 1.157326045 1.27649096 1.153405964 1.10697433 1.210264587 1.007085084 1 18.25494361 1.67551752 0.500458084 0.993308931 1.277466132 0.578250521 0.07531044 0.622317717 0.377375511 0.076411668 0.050484376 47.37154184 -1.67551752 0.284157202 S(ph)KS(ph)PTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSPTLR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.996)KS(0.902)PT(0.103)LR;S(1)KS(0.869)PT(0.131)LR 107.55 0.0042399 1421930000 2370100 1890430 1537890 1505930 1656250 1610560 1740070 2159800 2590500 2149700 TRUE FALSE 2277473.872 1836516.787 1815820.933 1583651.228 1709524.785 1643126.627 1761365.497 2115199.375 2296437.3 2004098.904 1.136407922 0.916380316 0.906053553 0.790206124 0.853014181 0.819883002 0.878881523 1.055436621 1.145870244 1 20.93452228 1.675668954 4.635690565 1.080607799 0.891791572 0.394820716 0.09422935 0.155303675 7.711004672 0.052759642 0.025269184 47.38806264 -1.675668954 -0.188816226 EFSDFIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFSDFIR 7 0 A6NHR9;A6NHR9-2;J3KTL8;A6NHR9-3 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 0 ; 99.139 0.025003 147827000 399060 479510 414410 545370 494300 426460 476320 416050 398430 472760 FALSE TRUE 383464.294 465834.8443 489303.1055 573516.6111 510199.6084 435083.3134 482149.3466 407458.4221 353201.8968 440739.5441 0.870047399 1.056939071 1.110186531 1.301259709 1.157598893 0.987166501 1.093955269 0.924488006 0.801384631 1 18.74956682 1.677023781 3.873736557 0.889299981 1.09090152 0.325688171 0.114028314 0.206223023 7.251612168 0.068048611 0.03162049 47.53612545 -1.677023781 0.201601539 T(ph)TGTPPDSSLVTYELHSRPEQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.35)T(0.35)GT(0.3)PPDSSLVTYELHSRPEQDK 137.35 1.15E-05 65403000 73878 59596 58855 66123 67209 63521 70976 78510 91777 88690 TRUE FALSE 70990.76608 57896.38043 69491.40772 69535.61595 69370.83852 64805.43814 71844.62552 76888.74106 81358.85972 82682.9473 0.858590174 0.700221537 0.840456345 0.840991017 0.838998134 0.783782391 0.868917085 0.929922597 0.983985965 1 16.3353022 1.67715182 1.475664246 0.998222855 0.808301393 0.742291381 0.043151896 0.186043347 0.788765652 0.03455357 0.012885196 47.55014216 -1.67715182 -0.189921462 LRLS(ph)PSPTSQR ddPTM_BT-474_Pertuzumab_2h_R1 7 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 LRLS(0.378)PS(0.207)PT(0.207)S(0.207)QR;LRLS(0.709)PS(0.289)PT(0.001)SQR;LRLS(0.979)PS(0.021)PTSQR;LRLS(0.971)PS(0.029)PTSQR;LRLS(0.998)PS(0.002)PTSQR;LRLS(0.496)PS(0.496)PT(0.007)SQR;LRLS(0.993)PS(0.007)PTSQR 157.5 5.80E-05 80232900000 3292660 3677530 3018180 4105760 3745490 3802330 3927660 3339710 3539450 3846370 TRUE FALSE 3163979.207 3572650.445 3563632.265 4317658.766 3865967.087 3879215.718 3975727.878 3270743.821 3137666.475 3585851.934 0.882350768 0.996318451 0.993803517 1.20408172 1.078116765 1.081811461 1.108726169 0.912124617 0.875012837 1 21.77388449 1.677189199 7.096667296 0.920282651 1.053206163 0.293466881 0.084788522 0.15463276 15.16473788 0.044503331 0.022888967 47.55423494 -1.677189199 0.132923512 NRPLSDEELDAMFPEGYK ddPTM_BT-474_Pertuzumab_2h_R1 3 NRPLSDEELDAMFPEGYK 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 197.45 1.68E-15 1823070000 2054520 1945470 1598020 1637560 1896610 1817890 1805990 2199140 2542000 2242200 FALSE TRUE 1974227.087 1889987.1 1886817.762 1722074.668 1957616.183 1854648.981 1828092.246 2153726.99 2253442.817 2090333.797 0.944455421 0.904155644 0.902639456 0.823827597 0.93650889 0.887250153 0.87454561 1.030326828 1.078030131 1 20.99530191 1.677350534 5.092199875 1.043497615 0.895238262 0.757884549 0.036176193 0.067590091 3.979915174 0.01887437 0.009189056 47.57190401 -1.677350534 -0.148259352 S(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPLRGNVVPSPLPTR 17 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 S(1)PS(1)PLRGNVVPS(0.999)PLPT(0.001)R;S(1)PS(1)PLRGNVVPS(1)PLPTR 110.94 0.00089806 353660000 202568 214270 150954 164141 175636 211465 152823 180282 184472 157836 TRUE FALSE 194651.4186 208159.2294 178234.7458 172612.3367 181285.4914 215740.9672 154693.2936 176559.1137 163531.5119 147145.6271 1.322848816 1.414647744 1.211281295 1.173071467 1.232014128 1.466173147 1.051293855 1.199893718 1.111358286 1 17.16688514 1.677475603 0.036844936 7.80E-07 2.356442281 0.45184669 0.104842832 64.14526714 2.347918336 73.51586321 75.04843159 47.58560582 -1.677475603 2.356441501 GAQEVGER ddPTM_BT-474_Pertuzumab_2h_R1 1 GAQEVGER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 88.136 0.034498 120240000 148730 156070 118940 145110 140790 152040 144190 139530 147400 144520 FALSE TRUE 142917.4672 151619.0364 140435.1038 152599.1445 145318.6382 155114.353 145954.6404 136648.6567 130667.77 134731.5317 1.060757385 1.125341889 1.042332868 1.132616416 1.078579278 1.151284714 1.083299793 1.014229223 0.96983808 1 17.039728 1.677920932 3.074171942 0.986673616 1.099041591 0.685425733 0.032004388 0.111604026 2.430574492 0.018290464 0.008077507 47.63442558 -1.677920932 0.112367976 QQDS(ph)QPEEVMDVLEMVENVK ddPTM_BT-474_Pertuzumab_2h_R1 7 QQDSQPEEVMDVLEMVENVK 20 0 Q9H307 Q9H307 PNN Pinin 1 QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK 143.57 5.58E-07 168444000 142940.6 121864.6 120093.6 118620.6 127543.4 140111.7 118113.3 151640.5 164467.8 145072 TRUE FALSE 137354.3233 118389.1409 141797.185 124742.6234 131645.9493 142944.8546 119558.8059 148509.0707 145798.1048 135246.1442 1.015587721 0.875360563 1.048437911 0.922337743 0.973380425 1.056923696 0.884008979 1.098065099 1.078020417 1 17.04522794 1.678007157 10.15886346 1.065221621 0.969539151 0.299147088 0.063223307 0.127451113 19.16792348 0.027855173 0.015024035 47.6438838 -1.678007157 -0.095682469 RLKEDILENEDEQNS(ph)PPKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLKEDILENEDEQNSPPKK 19 3 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 RLKEDILENEDEQNS(1)PPKK;RLKEDILENEDEQNS(1)PPKK 202.73 3.85E-16 793310000 971450 761040 628200 505640 676920 665690 667130 861380 1026170 816790 TRUE FALSE 933484.66 739335.8843 741729.7142 531736.141 698693.7466 679150.7079 675294.5365 843592.202 909683.4837 761468.0858 1.225901226 0.970934827 0.974078531 0.698303909 0.917561431 0.891896483 0.886832356 1.107849715 1.194644268 1 19.53842405 1.678199093 5.858505547 1.115156811 0.929067884 0.24428459 0.129710318 0.184092865 13.70772103 0.068890023 0.034333395 47.66494468 -1.678199093 -0.186088927 IDASKNEEDEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDASKNEEDEGK 12 1 Q14103-2;Q14103-4;D6RBQ9 Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 100.54 0.0028956 694900000 589240 509770 333340 295660 412830 470140 413360 544390 681400 479600 FALSE TRUE 566211.8494 495231.8587 393581.9531 310919.048 426109.0519 479646.5529 418418.8233 533148.1563 604050.3287 447116.2648 1.266363794 1.107613159 0.880267582 0.69538747 0.953016218 1.07275577 0.935816601 1.192415034 1.350991624 1 18.7702905 1.678243095 5.587650866 1.206502794 0.978794136 0.22391214 0.162637766 0.199952535 13.80005535 0.089613162 0.044315127 47.66977425 -1.678243095 -0.227708658 HDDSWPFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HDDSWPFLK 9 0 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 80.239 0.024676 33843000 87576 106920 76853 116790 87451 92290 106680 81867 92382 91351 FALSE TRUE 84153.4331 103870.7463 90742.04669 122817.5459 90263.94084 94156.16703 107985.5818 80176.41784 81895.18266 85163.7154 0.988137174 1.219659638 1.065501267 1.442134662 1.059887305 1.105590175 1.267976406 0.941438704 0.961620595 1 16.37795127 1.678330886 7.635397035 0.964430585 1.166536262 0.351707457 0.121831795 0.129368753 13.98698424 0.057796313 0.030086153 47.67941146 -1.678330886 0.202105677 RPPEEDWR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPPEEDWR 8 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 0 68.224 0.091494 174740000 180320 164430 144930 168870 169070 164050 147400 175670 159890 162180 FALSE TRUE 173272.895 159740.6174 171122.075 177585.4009 174508.2901 167367.2034 149203.9253 172042.3531 141739.9575 151195.4041 1.14601959 1.056517679 1.131794157 1.174542321 1.15419044 1.106959595 0.986828443 1.137880838 0.937462076 1 17.20605476 1.678350029 0.871976533 0.987745272 1.128866371 0.462139872 0.057470072 0.544531776 0.796188702 0.051529957 0.021617619 47.68151313 -1.678350029 0.141121099 NS(ph)PEDKR ddPTM_BT-474_Pertuzumab_2h_R1 5 NSPEDKR 7 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(1)PEDKR;NS(1)PEDKR;NS(1)PEDKR;NS(1)PEDKR;NS(1)PEDKR 108.47 0.004438 4480667000 3320120 2568870 2793540 2714250 2547670 2758360 3413690 3506220 3930240 4254930 TRUE FALSE 3190366.04 2495608.343 3298394.82 2854332.768 2629618.119 2814135.929 3455467.759 3433815.332 3484095.632 3966739.801 0.804279131 0.629133361 0.831512775 0.719566423 0.662916715 0.709432953 0.871110265 0.86565177 0.878327243 1 21.91952234 1.678376317 0.97144269 0.968072848 0.722434759 0.644087709 0.065105244 0.315391494 0.56365069 0.056413355 0.022553342 47.68439945 -1.678376317 -0.245638088 LKDEDDEDDCFILEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKDEDDEDDCFILEK 15 1 A6NHR9;A6NHR9-2 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 0 ; 129.32 6.07E-05 451430000 671510 568520 387910 383730 469700 531670 492640 615960 713900 641720 FALSE TRUE 645266.6468 552306.3662 458013.966 403534.3513 484808.3271 542420.7317 498669.0757 603240.2107 632861.0649 598255.7328 1.078579964 0.92319444 0.765582243 0.674518152 0.810369714 0.906670345 0.833538315 1.008331684 1.057843712 1 19.19040279 1.678529357 4.412704883 1.030195347 0.84814232 0.358797767 0.101332468 0.190158351 8.626129687 0.060488742 0.028798686 47.70120573 -1.678529357 -0.182053027 RPAS(ph)PELLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPASPELLR 9 1 Q99929 Q99929 ASCL2 Achaete-scute homolog 2 1 RPAS(1)PELLR;RPAS(1)PELLR;RPAS(1)PELLR;RPAS(1)PELLR 118.87 0.0005635 944590000 298719 469123 380124 701301 558325 631501 526455 419179 356760 502268 TRUE FALSE 287044.7312 455744.0714 448820.8626 737495.2287 576284.0307 644270.3829 532897.9138 410522.8072 316262.1005 468248.941 0.613017363 0.973294398 0.958509082 1.57500672 1.230721482 1.375914234 1.13806539 0.876719136 0.675414449 1 18.83691621 1.678618654 4.268293761 0.821487178 1.143028732 0.192103783 0.254167604 0.270340827 11.50493989 0.149248855 0.070666715 47.7110148 -1.678618654 0.321541553 LVIASTLYEDGTLDDGEYNPTDDRPSR ddPTM_BT-474_Pertuzumab_2h_R1 6 LVIASTLYEDGTLDDGEYNPTDDRPSR 27 1 C9JLU1;P52434;P52434-3;P52434-4 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ;;;;; 280.21 4.22E-61 1417215000 207391 216864 177576 204717 225188 233701 227180 200588 217972 225207 FALSE TRUE 199285.9304 210679.2511 209667.9334 215282.4689 232431.3765 238426.5943 229960.2968 196445.7877 193228.7324 209953.5293 0.949190667 1.003456583 0.998639718 1.02538152 1.107061059 1.135616034 1.095291408 0.935663184 0.920340482 1 17.67971051 1.678735838 7.583693657 0.94638645 1.046510855 0.360318269 0.056411143 0.141377892 15.1727735 0.031230349 0.016242572 47.72389023 -1.678735838 0.100124405 Y(ph)LS(ph)S(ph)VET(ph)QEGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 YLSSVETQEGKR 12 1 P17405-2;E9PQT3;H0YEP5 P17405-2 SMPD1 Sphingomyelin phosphodiesterase 4 Y(1)LS(1)S(1)VET(1)QEGKR 42.475 0.067301 450550000 190490 319880 228770 365770 323920 345810 292640 228570 180290 252450 TRUE FALSE 183045.4402 310757.3356 270113.828 384647.4335 334339.181 352802.5151 296221.4159 223849.9496 159824.235 235351.3366 0.777753986 1.320397581 1.147704669 1.634354149 1.420596058 1.49904615 1.258634942 0.951130989 0.679087858 1 17.84445652 1.679136594 3.301109198 0.834199813 1.318445866 0.41686798 0.227724613 0.187836358 4.75053935 0.137065234 0.061686512 47.76794892 -1.679136594 0.484246053 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 MESEGGADDSAEEGDLLDDDDNEDRGDDQVK 31 1 B4DY08 B4DY08 HNRNPC 1 MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK 391.64 1.31E-155 1226400000 567830 498120 627860 597000 439530 708190 742970 766190 924590 1006400 TRUE FALSE 545638.5758 483914.1053 741328.2687 627811.2415 453667.8816 722510.087 752062.6891 750367.9088 819634.4194 938235.6316 0.581558148 0.515770334 0.790130159 0.669140268 0.483532991 0.77007317 0.80157123 0.799764882 0.87359123 1 19.83959077 1.679140198 0.52395218 1.001275634 0.594544235 0.675199337 0.088490169 0.502348152 0.324353796 0.091348901 0.05761948 47.76834539 -1.679140198 -0.406731399 DLLHPSPEEEK ddPTM_BT-474_Pertuzumab_2h_R1 7 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;;;;; 215.08 1.31E-11 15459300000 14914320 14953390 13664480 13616990 14053320 15569240 16273410 16279480 19620110 19174920 FALSE TRUE 14331451.89 14526933.96 16133955.5 14319764.49 14505357.8 15884060.7 16472568.86 15943303.05 17392917.37 17876185.59 0.801706372 0.812641706 0.902539047 0.801052574 0.811434729 0.888559845 0.921481195 0.891873883 0.972965809 1 24.09153559 1.67925796 0.589567068 1.001942917 0.821744447 0.757878808 0.033764192 0.376720895 0.288633638 0.033307932 0.018669699 47.78129986 -1.67925796 -0.18019847 LKEELEEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEELEEAR 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 159.83 6.00E-05 777450000 1370900 1498700 1237100 1301600 1441900 1440100 1731900 1810800 2056000 2243700 FALSE TRUE 1317323.712 1455958.543 1460671.489 1368775.732 1488280.023 1469219.809 1753095.51 1773406.347 1822611.499 2091732.201 0.629776466 0.69605399 0.69830712 0.65437427 0.711506006 0.702393838 0.838107053 0.847817109 0.871340748 1 20.99626673 1.679309946 0.587817214 0.994035986 0.658913986 0.93286282 0.028997318 0.168881728 0.128817721 0.027702812 0.015572486 47.78701968 -1.679309946 -0.335122 ADRDQSPFS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 3 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(0.179)PFS(0.821)K;ADRDQS(0.283)PFS(0.717)K;ADRDQS(0.25)PFS(0.75)K 130.99 0.00068908 1297732000 2059640 1908720 1586050 1675100 1731910 1913540 1822600 2035230 2317260 2090710 TRUE FALSE 1979146.992 1854285.174 1872684.516 1761552.112 1787618.458 1952233.09 1844905.524 1993201.789 2054214.36 1949104.349 1.015413563 0.951352438 0.960792334 0.903775168 0.917148668 1.00160522 0.94654015 1.022624463 1.053927339 1 20.8943799 1.679339661 4.741732348 1.030469889 0.954747101 0.46149711 0.033947565 0.13647219 7.088071689 0.018726237 0.009025758 47.79028945 -1.679339661 -0.075722788 RPEGPGAQAPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 1 RPEGPGAQAPS(0.075)S(0.925)PR;RPEGPGAQAPS(0.022)S(0.978)PR;RPEGPGAQAPS(0.246)S(0.754)PR;RPEGPGAQAPS(0.041)S(0.959)PR;RPEGPGAQAPS(0.045)S(0.955)PR;RPEGPGAQAPS(0.005)S(0.995)PR 201.65 1.86E-08 41567170000 6291830 6981150 5693410 7184230 6729830 6604880 6369800 5739600 5388520 5639660 TRUE FALSE 6045938.328 6782054.437 6722335.836 7555008.971 6946301.094 6738435.199 6447755.518 5621075.254 4776837.8 5257680.805 1.149924948 1.289932708 1.278574354 1.436947059 1.321172082 1.281636419 1.226349746 1.069116872 0.908544656 1 22.32599513 1.679343356 1.973401718 0.952969435 1.299440959 0.795177726 0.069656321 0.130143913 1.061161434 0.052512563 0.02050618 47.79069606 -1.679343356 0.346471524 CCLTYCFNKPEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 CCLTYCFNKPEDK 13 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ; 218.16 2.24E-11 4400600000 4981900 4288400 3571100 3482800 3894700 4201100 4409800 5108100 6469800 5606800 FALSE TRUE 4787201.84 4166099.031 4216477.209 3662547.725 4019976.563 4286049.12 4463768.452 5002615.95 5735375.428 5227046.442 0.915852173 0.797027361 0.806665343 0.700691636 0.769072287 0.819975328 0.853975281 0.957063612 1.097249755 1 22.31756455 1.67969751 1.923416728 1.048993309 0.79630929 0.759574733 0.055721486 0.144805531 1.113796063 0.041992631 0.016303512 47.82968385 -1.67969751 -0.252684019 AVDIPHMDIEALKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVDIPHMDIEALKK 14 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 159.02 3.23E-06 4637100000 8523970 7362400 6084760 5742690 7768560 7222870 7098440 8465630 9501460 9090020 FALSE TRUE 8190843.829 7152431.561 7184411.487 6039070.919 8018442.788 7368921.38 7185312.832 8290811.782 8422894.094 8474344.849 0.966545966 0.844009972 0.847783707 0.712629829 0.946202088 0.869556469 0.847890068 0.978342507 0.993928645 1 23.01467041 1.680040684 4.396569972 0.993638203 0.858449321 0.456463353 0.064326709 0.15099957 6.807004497 0.035525651 0.016923567 47.86749313 -1.680040684 -0.135188882 SDS(ph)LILDHQWELEK ddPTM_BT-474_Pertuzumab_2h_R1 9 SDSLILDHQWELEK 14 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 S(0.004)DS(0.996)LILDHQWELEK;S(0.003)DS(0.997)LILDHQWELEK;S(0.008)DS(0.992)LILDHQWELEK;S(0.002)DS(0.998)LILDHQWELEK;SDS(1)LILDHQWELEK;S(0.132)DS(0.868)LILDHQWELEK;SDS(1)LILDHQWELEK;SDS(1)LILDHQWELEK;SDS(1)LILDHQWELEK 307.55 1.27E-45 16519126000 8284490 7321699 6768337 6724821 7284504 7232507 7942431 8470251 9827616 9538996 TRUE FALSE 7960722.972 7112891.313 7991526.057 7071889.818 7518816.687 7378753.247 8039632.846 8295337.357 8712026.232 8892911.304 0.895176248 0.799838328 0.898640027 0.795227747 0.845484277 0.829734267 0.904049593 0.932803339 0.979659634 1 23.08422437 1.680356395 1.324181626 0.995246555 0.841774859 0.751583977 0.03341852 0.183788837 0.615408745 0.025633932 0.009588989 47.90230313 -1.680356395 -0.153471696 YLDIHER ddPTM_BT-474_Pertuzumab_2h_R1 1 YLDIHER 7 0 P62072 P62072 TIMM10 Mitochondrial import inner membrane translocase subunit Tim10 0 85.064 0.021085 228950000 321250 405280 364700 476580 321760 408770 417980 344720 375520 373570 FALSE TRUE 308695.1948 393721.8112 430609.4027 501176.3509 332109.7026 417035.6095 423095.3643 337601.4115 332892.5439 348267.7712 0.886373131 1.130514632 1.236431959 1.439054637 0.953604468 1.197456796 1.214856496 0.969373107 0.955852282 1 18.40983745 1.680387214 6.360623653 0.971219212 1.15863343 0.23664212 0.144114899 0.191399316 16.24048197 0.074560531 0.037714986 47.90570261 -1.680387214 0.187414218 KET(ph)PPPLVPPAAR ddPTM_BT-474_Pertuzumab_2h_R1 6 KETPPPLVPPAAR 13 1 Q9BQA1;Q9BQA1-2 Q9BQA1 WDR77 Methylosome protein 50 1 KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR 80.488 0.010344 10683960000 3964740 3726950 3312030 3389150 3489030 3705780 3897510 4448710 5091290 5050110 TRUE FALSE 3809793.578 3620661.035 3910587.497 3564064.438 3601257.819 3780713.411 3945208.893 4356842.584 4513348.104 4708061.552 0.809206408 0.769034346 0.830615202 0.757013136 0.764913071 0.803029733 0.837968843 0.925400515 0.958642544 1 22.16670175 1.680542574 1.354965344 0.990998598 0.78521899 0.932251509 0.021245716 0.092094864 0.323990658 0.017491256 0.006536611 47.92284293 -1.680542574 -0.205779608 DVAEAKPELSLLGDGDH ddPTM_BT-474_Pertuzumab_2h_R1 6 DVAEAKPELSLLGDGDH 17 1 H7C5G1;Q2TAA2-2;Q2TAA2 H7C5G1 IAH1 Isoamyl acetate-hydrolyzing esterase 1 homolog 0 ;;;;; 257.35 3.63E-27 2944244000 3040270 2964680 2434220 2513970 2823730 2061410 2817660 3047190 3553820 3322280 FALSE TRUE 2921452.887 2880130.229 2874137.703 2643716.293 2914557.84 2103093.123 2852143.366 2984264.462 3150405.252 3097259.016 0.943238157 0.929896471 0.927961687 0.853566421 0.94101198 0.679017516 0.920860461 0.963517887 1.017159119 1 21.56256061 1.680760125 3.045180539 1.001771894 0.880592027 0.322276599 0.074231728 0.264526697 5.630081362 0.046361385 0.020485026 47.94685499 -1.680760125 -0.121179867 PKPRPS(ph)PSSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 PKPRPSPSSTR 11 2 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 1 PKPRPS(0.961)PS(0.017)S(0.017)T(0.004)R;PKPRPS(0.762)PS(0.016)S(0.028)T(0.194)R;PKPRPS(0.787)PS(0.058)S(0.058)T(0.098)R;PKPRPS(0.862)PS(0.052)S(0.052)T(0.034)R 98.582 0.0042632 1189410000 664293 540483 634604 653331 570096 534106 692582 746273 923220 855110 TRUE FALSE 638331.6951 525068.954 749291.0595 687049.4912 588433.6556 544905.9893 701058.0257 730862.2018 818419.9361 797192.638 0.800724523 0.65864752 0.939912166 0.861836222 0.738132325 0.683531136 0.879408555 0.916794971 1.026627564 1 19.60456886 1.681025553 1.975350044 1.007276459 0.785469558 0.561653478 0.080140083 0.235128168 1.920244397 0.060694849 0.02374612 47.97616757 -1.681025553 -0.221806901 ADAETLRK ddPTM_BT-474_Pertuzumab_2h_R1 6 ADAETLRK 8 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 140.5 0.0010399 7416050000 6244870 6572980 4924720 6158720 5083180 5019980 5411760 6986600 7541210 7495930 FALSE TRUE 6000813.576 6385525.046 5814726.454 6476572.277 5246685.101 5121487.435 5477990.738 6842324.268 6685163.456 6988223.984 0.858703669 0.913755063 0.832074997 0.926783728 0.750789487 0.732873967 0.783888832 0.979122061 0.956632683 1 22.73649442 1.681348435 6.427373702 0.976386746 0.829184496 0.565689138 0.060158193 0.110348565 9.533693812 0.033885669 0.017178141 48.01184938 -1.681348435 -0.14720225 LHLDEDYPCSLVGNWNTWYGEQDQAVHLWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHLDEDYPCSLVGNWNTWYGEQDQAVHLWR 30 0 Q9BPW8;H7C2U6 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 ; 237.13 1.03E-45 1117420000 303450 463340 337550 721070 342230 376860 690800 196503 422950 354130 FALSE TRUE 291590.8385 450125.9969 398552.7938 758284.5091 353238.1388 384480.3674 699254.217 192445.1444 374938.4892 330144.4597 0.883221965 1.363421326 1.207207276 2.296826395 1.069950225 1.164582219 2.118024993 0.582911931 1.135680088 1 18.33273791 1.68143233 13.09869504 0.897728824 1.438576242 0.237283934 0.44088057 0.175858865 35.74780853 0.200945128 0.110276054 48.02112503 -1.68143233 0.540847418 ELTNDGELILTMTADDVVCTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELTNDGELILTMTADDVVCTR 21 0 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ; 389.53 8.59E-131 92757000 97530 111095 79002 96121 100157 98430 96066 97368 101344 100111 FALSE TRUE 93718.41977 107926.6794 93279.41879 101081.8163 103378.6409 100420.322 97241.68444 95357.31677 89839.85399 93330.3928 1.004157563 1.156393712 0.999453833 1.083053583 1.107663193 1.075965921 1.041908017 1.021717727 0.962600192 1 16.51005935 1.681457669 1.835644016 0.982731729 1.073179987 0.381631203 0.044379282 0.308260547 2.131560479 0.031118314 0.011977367 48.02392687 -1.681457669 0.090448257 FRDPSSVGVAQHLTNTVFIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FRDPSSVGVAQHLTNTVFIDR 21 1 Q8WXA9-2;A0A087WY03;E5RFV3 Q8WXA9-2 SREK1 Splicing regulatory glutamine/lysine-rich protein 1 0 ; 143.14 8.40E-08 502650000 197367 234462 208893 214160 192929 214069 217768 198240 197818 224870 FALSE TRUE 189653.6794 227775.3733 246644.6119 225212.8233 199134.7365 218397.6219 220433.1099 194146.2747 175362.53 209639.3546 0.904666396 1.086510564 1.176518657 1.074286952 0.949891956 1.041777782 1.051487257 0.92609651 0.836496231 1 17.67755005 1.68156328 4.511820365 0.907351215 1.045715319 0.322305837 0.079014059 0.18100375 8.580736906 0.044088052 0.021116221 48.0356067 -1.68156328 0.138364104 KACQVTQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KACQVTQSR 9 1 E9PQX9;C9JCC6;Q14919;Q14919-2 E9PQX9 DRAP1 Dr1-associated corepressor 0 79.659 0.035667 0 23867 26678 22139 24674 24833 22949 28083 20023 25172 20475 FALSE TRUE 22934.25125 25917.16956 26140.00978 25947.4281 25631.776 23413.0445 28426.68815 19609.51805 22314.58009 19088.21001 1.201487789 1.357757985 1.369432218 1.35934318 1.342806684 1.226570982 1.489227546 1.027310473 1.169024234 1 14.2203942 1.681819194 8.344604238 1.075469892 1.33403128 0.674799831 0.08554712 0.066867956 8.163696806 0.038956315 0.020561952 48.06392066 -1.681819194 0.258561387 EGS(ph)VMLQVDVDTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGSVMLQVDVDTVK 14 0 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 1 EGS(0.992)VMLQVDVDT(0.008)VK 55.314 0.086117 1220600000 157550 286630 217880 379680 316320 335350 290230 230880 174490 298270 TRUE FALSE 151392.7718 278455.593 257255.7627 399275.3303 326494.7201 342131.0068 293781.9216 226112.2473 154682.6267 278067.9072 0.544445324 1.001394213 0.925154453 1.435891449 1.174154628 1.230386527 1.056511427 0.813154778 0.556276444 1 18.08507772 1.681851469 4.097461567 0.752592989 1.072747736 0.197644091 0.239456939 0.256136323 10.06520681 0.137181795 0.064672752 48.06749265 -1.681851469 0.320154747 DKADFCIIHYAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKADFCIIHYAGK 13 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ; 124.7 0.00012539 7878000000 21715000 20906000 18845900 20057900 20866000 21241000 23408000 23819000 29431000 27968000 FALSE TRUE 20866353.79 20309781.35 22251773.35 21093090.62 21537173.84 21670507.57 23694474.11 23327129.33 26090116.26 26073702.45 0.800283498 0.778937375 0.853418244 0.808979494 0.826011338 0.831125062 0.908749885 0.894661177 1.000629516 1 24.63609212 1.682007672 0.809962039 1.008861274 0.808184462 0.888469011 0.025140644 0.172725821 0.221223839 0.021929706 0.009596223 48.08478431 -1.682007672 -0.200676813 ERHAS(ph)EMR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERHASEMR 8 1 P49754-2;P49754-3;P49754 P49754-2 VPS41 Vacuolar protein sorting-associated protein 41 homolog 1 ERHAS(1)EMR;ERHAS(1)EMR 50.297 0.094753 1098590000 346490 346830 309730 314880 338110 377460 329560 344590 340080 369720 TRUE FALSE 332948.7877 336938.748 365705.1009 331130.9945 348985.6152 385092.4998 333593.2539 337474.0961 301475.5441 344678.5351 0.965969023 0.977544911 1.061003409 0.960695143 1.012495934 1.117251179 0.967838783 0.979098092 0.874657147 1 18.39489193 1.682049832 2.640310107 0.938402588 1.013501321 0.212887501 0.054197545 0.3389367 5.290820307 0.034338438 0.014602754 48.08945246 -1.682049832 0.075098733 ELEEKNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEEKNR 7 1 P32780 P32780 GTF2H1 General transcription factor IIH subunit 1 0 68.915 0.055776 312020000 199740 230720 151570 179950 195020 210430 174940 187240 173210 180530 FALSE TRUE 191933.94 224140.0915 178962.0707 189237.2411 201292.9954 214685.0388 177080.9681 183373.4286 153547.927 168302.5423 1.140410224 1.331768899 1.063335516 1.1243873 1.196018745 1.275589993 1.052158605 1.089546397 0.912332784 1 17.36069744 1.682052679 1.653002947 0.966232898 1.18354087 0.520000662 0.082417761 0.277648699 1.515001028 0.063243422 0.023913927 48.08976763 -1.682052679 0.217307972 EAENPEGEEKEAATLEVERPLPMEVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAENPEGEEKEAATLEVERPLPMEVEK 27 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;; 275.6 3.96E-61 3286870000 2977640 2636150 1799390 1645030 2284290 2388720 2183970 2718730 3205660 2552780 FALSE TRUE 2861270.537 2560969.583 2124579.8 1729930.195 2357766.262 2437021.555 2210698.078 2662587.275 2841766.916 2379877.937 1.202276172 1.07609283 0.892726374 0.726898707 0.990708904 1.024011155 0.92891238 1.118791529 1.194080954 1 21.18245615 1.682138689 6.354244366 1.117788403 0.970804397 0.174529469 0.124543471 0.221457673 18.85717327 0.0675673 0.034201292 48.09929254 -1.682138689 -0.146984006 EGQT(ph)IKLCIGNITNK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGQTIKLCIGNITNK 15 1 F5H2U7;A0A1W2PNT6;F5GYH1;A0A1W2PRM0;A0A1W2PRL5;A0A1W2PR09;Q8NC96 F5H2U7 NECAP1 Adaptin ear-binding coat-associated protein 1 1 EGQT(1)IKLCIGNITNK 69.188 0.081482 107310000 211070 306810 213680 252810 253310 352860 252450 222550 197980 227510 TRUE FALSE 202821.151 298060.0792 252296.7293 265857.5544 261457.9462 359995.071 255539.5586 217954.2647 175506.1404 212100.5451 0.956250023 1.40527729 1.189514762 1.253450595 1.232707564 1.697284988 1.204803875 1.027598796 0.827466711 1 17.6943888 1.682349082 3.145868897 0.921560282 1.294902269 0.41408603 0.180681781 0.196692449 4.479492147 0.107625891 0.048031383 48.12259985 -1.682349082 0.373341987 SPGS(ph)TPTT(ph)PTSSQAPQK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 2 SPGS(1)TPT(0.008)T(0.869)PT(0.121)S(0.003)SQAPQK;SPGS(0.994)T(0.006)PTT(0.84)PT(0.16)SSQAPQK;SPGS(1)TPTT(0.983)PT(0.017)SSQAPQK;SPGS(0.987)T(0.013)PTT(0.993)PT(0.007)SSQAPQK;SPGS(0.962)T(0.038)PT(0.207)T(0.792)PT(0.001)SSQAPQK;SPGS(0.96)T(0.04)PT(0.309)T(0.69)PTSSQAPQK 377.56 2.02E-104 5816600000 4959100 4914490 4364490 4806080 4955550 4771380 4009080 4368400 4204120 3623090 TRUE FALSE 4765292.889 4774333.557 5153250.431 5054122.365 5114949.766 4867860.573 4058144.32 4278191.013 3726885.923 3377694.887 1.410812121 1.413488701 1.525670791 1.496322946 1.5143315 1.441178299 1.201453789 1.26660079 1.103381462 1 21.68760758 1.682424017 0.874601899 1.018405287 1.479962702 0.88020741 0.060549901 0.182870472 0.268576089 0.056687148 0.023784404 48.13090385 -1.682424017 0.461557416 KAAAPAPEEEMDECEQALAAEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAAAPAPEEEMDECEQALAAEPK 23 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 181.69 6.69E-17 738890000 816410 697500 565650 593610 682330 712360 675770 804370 911610 848860 FALSE TRUE 784503.7946 677607.9829 667875.5378 624246.2832 704277.7641 726764.4073 684040.2754 787759.4784 808127.8546 791365.9561 0.991328713 0.856251116 0.843952829 0.788821251 0.889952062 0.918367036 0.864379204 0.995442718 1.02118097 1 19.59398548 1.682509608 4.434135651 1.009984994 0.875060296 0.574386166 0.049846759 0.119869142 5.499356986 0.028174074 0.013466341 48.14039039 -1.682509608 -0.134924699 SPFIEEQLHTVLEKS(ph)PENSPPVKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPFIEEQLHTVLEKSPENSPPVKPK 25 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SPFIEEQLHTVLEKS(1)PENSPPVKPK;SPFIEEQLHTVLEKS(1)PENSPPVKPK 273.43 2.87E-53 2225500000 1116120 914770 773840 695970 934400 845110 881310 1054360 1239330 1071040 TRUE FALSE 1072500.796 888681.6553 913690.102 731889.0951 964455.8246 862198.7032 892095.7354 1032587.098 1098646.454 998497.5068 1.074114646 0.890018903 0.915064981 0.732990408 0.965907093 0.8634961 0.89343812 1.034140887 1.100299647 1 19.9293993 1.682718223 4.407107065 1.05483566 0.898732027 0.369541849 0.083400752 0.165809308 7.518386084 0.044930336 0.021457615 48.16352042 -1.682718223 -0.156103633 DKASPEPEKDFS(ph)EK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKASPEPEKDFSEK 14 2 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 DKAS(0.009)PEPEKDFS(0.991)EK 123.14 8.24E-05 1339900000 1217000 852650 924500 632220 950240 978860 961080 1264000 1590700 1305600 TRUE FALSE 1169438.295 828333.2568 1091577.715 664848.95 980805.3326 998653.2199 972841.9845 1237897.958 1410130.405 1217170.549 0.960784251 0.680540009 0.896815747 0.546224973 0.805807644 0.820471068 0.799265136 1.017029174 1.158531486 1 20.2150999 1.68281803 3.061948709 1.083835961 0.777245554 0.553351566 0.11243047 0.146346432 3.144886661 0.064877209 0.028769347 48.17459034 -1.68281803 -0.306590407 ENVEYIEREES(ph)DGEYDEFGRK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENVEYIEREESDGEYDEFGRK 21 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 ENVEY(0.001)IEREES(0.998)DGEY(0.001)DEFGRK;ENVEYIEREES(1)DGEYDEFGRK 207.13 2.00E-22 1212730000 2494250 2061300 1887590 1827590 2256140 2243590 2028100 2486420 2652760 2614770 TRUE FALSE 2396771.952 2002513.742 2228719.502 1921912.139 2328710.792 2288956.927 2052920.494 2435074.558 2351629.806 2437669.299 0.983222767 0.821487042 0.91428296 0.788422014 0.955302179 0.938994033 0.842165299 0.998935565 0.964704198 1 21.21707099 1.682946871 7.790618489 0.985833563 0.89054681 0.359756386 0.058436466 0.129749848 14.62900166 0.02744675 0.014352904 48.1888843 -1.682946871 -0.095286752 DLLDDLKSELTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLDDLKSELTGK 13 1 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 209.22 3.62E-08 3166600000 2103400 1739640 1488240 1446510 1386940 1394690 1691950 2426800 2822000 2878000 FALSE TRUE 2021196.803 1690027.17 1757198.074 1521164.554 1431552.185 1422891.587 1712656.59 2376685.732 2501658.391 2683070.497 0.753314833 0.629885489 0.654920576 0.566949156 0.533549971 0.530322103 0.638319639 0.885808157 0.932386381 1 21.35545353 1.683129375 2.911232846 0.955789077 0.60607212 0.849652208 0.063090636 0.085730459 1.652762589 0.042310719 0.018518948 48.20913901 -1.683129375 -0.349716957 CEDRPVVFTHLLTADHGPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 CEDRPVVFTHLLTADHGPPR 20 1 H0YF29;Q6P1X6-2;Q6P1X6 H0YF29 C8orf82 UPF0598 protein C8orf82 0 ; 156.39 1.22E-08 105147000 41964 52396 40180 69508 32052 44042 67411 27679 46945 38466 FALSE TRUE 40324.00049 50901.71738 47441.4198 73095.31621 33082.98169 44932.55942 68235.99598 27107.41898 41616.00041 35860.66356 1.124463311 1.419430438 1.322937589 2.038314659 0.922542374 1.252976241 1.902809073 0.755909576 1.160491644 1 15.13011456 1.683130286 11.67666486 0.97215056 1.4191088 0.28723431 0.327334599 0.151062308 27.41426063 0.14990087 0.081767778 48.2092401 -1.683130286 0.44695824 DAAGLECKPRPLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DAAGLECKPRPLHK 14 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 151.74 4.12E-06 362850000 993100 975360 575970 680900 713840 961700 774750 893320 984170 857160 FALSE TRUE 954288.5541 947543.6878 680060.5914 716041.3306 736801.3119 981146.2329 784231.6223 874872.6298 872451.1476 799103.7897 1.194198509 1.18575797 0.851029116 0.896055481 0.922034561 1.227808259 0.981388941 1.09481727 1.091787023 1 19.60802337 1.683233442 14.74016429 1.06982057 1.032993749 0.006591126 0.126530166 0.883833743 209.7966209 0.062740291 0.034581555 48.22069238 -1.683233442 -0.036826821 ATLLNVPDLSDSIHSANAS(ph)ER ddPTM_BT-474_Pertuzumab_2h_R1 1 ATLLNVPDLSDSIHSANASER 21 0 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ATLLNVPDLSDSIHSANAS(1)ER 158.61 1.52E-11 120530000 329360 322360 273370 317340 318010 319530 351030 335450 410080 399540 TRUE FALSE 316488.2471 313166.6084 322774.0401 333717.9554 328239.0805 325991.1155 355326.0101 328522.8403 363529.4376 372478.7999 0.849681236 0.840763578 0.866556808 0.895938119 0.881228893 0.875193744 0.953949621 0.881990707 0.975973499 1 18.50679879 1.683476113 0.169998894 1.052055482 0.787878004 0.764124542 0.025285267 1.711478446 0.295403063 0.17993448 0.197837443 48.24764417 -1.683476113 -0.264177479 SLPPDDIQDDFDWDSIV ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPPDDIQDDFDWDSIV 17 0 Q9UPW0-2;Q9UPW0;F6VXT0 Q9UPW0-2 FOXJ3 Forkhead box protein J3 0 ; 98.531 0.0041989 30562000 28202 24641 22450.5 24209 28400 27803 25546 25141 25478 26386 FALSE TRUE 27099.83466 23938.26281 26507.80476 25458.42939 29313.51179 28365.19571 25858.63959 24621.82956 22585.84425 24598.85272 1.101670674 0.973145499 1.077603296 1.034943771 1.191661747 1.153110514 1.051213237 1.000934062 0.918166571 1 14.58630341 1.683587024 2.77310201 0.960206033 1.085405071 0.431962259 0.059609269 0.232541966 4.033902282 0.040129823 0.017337141 48.2599674 -1.683587024 0.125199038 SKPVNKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKPVNKDR 8 2 P62316;P62316-2;K7EJB5 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 71.223 0.027727 170400000 684030 604790 411780 428290 575280 697690 579940 491090 549650 471520 FALSE TRUE 657297.3514 587541.9814 486197.806 450394.0982 593784.4037 711797.7698 587037.4792 480948.8199 487256.0363 439583.5304 1.495272925 1.336587794 1.106041906 1.02459275 1.350788559 1.619254864 1.335440112 1.09410109 1.108449254 1 18.74577781 1.683613819 4.795126287 1.070294861 1.316976417 0.345227785 0.161785482 0.217351067 11.57703317 0.097190878 0.047072307 48.26294495 -1.683613819 0.246681556 EGS(ph)PANWK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGSPANWK 8 0 O96019-2;O96019 O96019-2 ACTL6A Actin-like protein 6A 1 EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK 123.51 0.0014102 6541900000 8501300 7184970 6890370 6270780 7220080 7742590 7386180 8846880 10488380 8931090 TRUE FALSE 8169059.797 6980061.69 8135613.134 6594415.707 7452320.43 7899150.475 7476574.28 8664188.836 9297783.073 8326179.319 0.981129457 0.838327091 0.977112409 0.792009811 0.895046833 0.948712509 0.897959796 1.040595993 1.116692629 1 22.9892232 1.683615331 4.045783556 1.064517375 0.901132212 0.551644654 0.061129226 0.119100011 4.562213028 0.032251392 0.015194077 48.26311301 -1.683615331 -0.163385162 KS(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSLPEEDVAEIQHAEEFLIKPESK 24 2 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 KS(1)LPEEDVAEIQHAEEFLIKPESK;KS(1)LPEEDVAEIQHAEEFLIKPESK;KS(1)LPEEDVAEIQHAEEFLIKPESK 176.18 3.74E-13 172484000 186060 134578 159381 113229 126806 163626 158664 187953 217727 216801 TRUE FALSE 178788.5695 130739.9672 188184.6921 119072.7623 130884.8302 166934.6298 160605.7775 184071.7049 193011.5437 202116.8752 0.884580119 0.646853298 0.93106868 0.589128256 0.647570026 0.825931183 0.794618348 0.910719131 0.954950167 1 17.62483025 1.683615663 1.306252298 0.991341524 0.742169088 0.455079487 0.101489384 0.367029356 1.193251168 0.082250954 0.030856601 48.26314994 -1.683615663 -0.249172437 IMGVEEEDDDDDDDDNLPQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IMGVEEEDDDDDDDDNLPQLK 21 0 Q6AI12;K7ERW4 Q6AI12 ANKRD40 Ankyrin repeat domain-containing protein 40 0 ; 158.15 2.42E-11 56371000 154181 155120 140751 161772 161095 156777 180036 196453 228863 232472 FALSE TRUE 148155.4361 150696.1295 166187.8367 170121.0723 166276.767 159947.1384 182239.3344 192396.1769 202883.4317 216726.4644 0.683605652 0.695328694 0.766809154 0.78495754 0.767219488 0.738013878 0.840872548 0.887737349 0.936126708 1 17.72551581 1.683670985 0.607556259 1.008222046 0.718834926 0.911118351 0.029458211 0.211412108 0.169235689 0.030732397 0.016775768 48.26929826 -1.683670985 -0.28938712 KECSEAMEVETSVISIDS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KECSEAMEVETSVISIDSPQK 21 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KECSEAMEVETSVISIDS(1)PQK;KECSEAMEVETSVISIDS(1)PQK 187.51 1.75E-17 510130000 462610 398510 370355 341060 391070 398040 438330 484090 566530 558760 TRUE FALSE 444530.6898 387144.885 437286.387 358662.1475 403649.1217 406088.6415 443694.4137 474093.3723 502219.8895 520914.6875 0.853365629 0.743202091 0.83945874 0.688523776 0.774885277 0.779568423 0.851760229 0.910117115 0.964111594 1 18.99068759 1.683786473 1.2826275 0.992338779 0.774726732 0.774166403 0.044183054 0.183592703 0.57412825 0.035484555 0.01333255 48.28213577 -1.683786473 -0.217612047 ERLNS(ph)SENGEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERLNSSENGEDR 12 1 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 ERLNS(0.974)S(0.026)ENGEDR;ERLNS(0.661)S(0.339)ENGEDR 185.13 8.13E-06 1341020000 1177650 1295290 1050950 1342760 1372350 1320990 1128060 1160140 1032810 1077920 TRUE FALSE 1131626.136 1258349.597 1240880.043 1412060.005 1416492.884 1347701.323 1141865.536 1136182.704 915569.7387 1004911.518 1.126095298 1.252199397 1.234815226 1.405158543 1.409569756 1.341114415 1.136284653 1.130629596 0.91109488 1 19.93863705 1.683947371 1.619709161 0.964685275 1.296482652 0.670567336 0.090274306 0.220150801 1.147260114 0.075538904 0.028531328 48.30002668 -1.683947371 0.331797378 DLLVSSGSNNSLPCGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLLVSSGSNNSLPCGSPK 18 0 Q5THK1-4;Q5THK1-2;Q5THK1;Q5THK1-3 Q5THK1-4 PRR14L Protein PRR14L 1 DLLVSSGSNNSLPCGS(1)PK 319.36 1.79E-61 151320000 175080 144890 115780 132760 130800 136790 134850 165100 185190 169210 TRUE FALSE 168237.68 140757.8791 136704.0215 139611.7595 135007.3008 139555.9875 136500.3346 161690.6273 164168.0076 157749.256 1.066487946 0.892288703 0.866590594 0.885023252 0.855834786 0.884669704 0.865299388 1.024985039 1.040689584 1 17.26727368 1.684102289 6.130493691 1.025257066 0.897585097 0.468919231 0.057998994 0.114319688 9.274874614 0.029813383 0.01501722 48.31725902 -1.684102289 -0.127671969 DDDRTPGLHGDCDDDKYR ddPTM_BT-474_Pertuzumab_2h_R1 3 DDDRTPGLHGDCDDDKYR 18 2 O95159 O95159 ZFPL1 Zinc finger protein-like 1 0 ;; 185.27 3.24E-14 3992790000 2628720 2882990 2012140 2341620 2372220 2648800 2527300 3134580 3880200 3044700 FALSE TRUE 2525986.716 2800769.948 2375778.458 2462471.289 2448524.611 2702360.551 2558229.853 3069849.828 3439735.963 2838479.757 0.889908307 0.986714787 0.836989748 0.867531742 0.86261831 0.952045032 0.901267605 1.081511968 1.21182332 1 21.43668702 1.684133542 3.903858585 1.117928193 0.899068957 0.67488834 0.062998506 0.096079417 3.423801055 0.034186195 0.016010351 48.3207362 -1.684133542 -0.218859236 TAS(ph)LTSAASVDGNR ddPTM_BT-474_Pertuzumab_2h_R1 6 TASLTSAASVDGNR 14 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4 Q9UN36 NDRG2 Protein NDRG2 1 TAS(0.5)LT(0.5)S(0.001)AASVDGNR;T(0.018)AS(0.98)LT(0.002)SAASVDGNR;TAS(1)LTSAASVDGNR;TAS(1)LTSAASVDGNR;TAS(0.999)LTSAASVDGNR;TAS(0.997)LT(0.003)SAASVDGNR 397.29 1.84E-114 4742356000 2033668 1915209 1861277 1867710 1803272 1868200 1724920 1979172 1839049 1765155 TRUE FALSE 1954190.006 1860589.115 2197651.158 1964102.737 1861275.882 1905976.284 1746030.087 1938301.407 1630287.867 1645599.48 1.187524687 1.130645177 1.335471471 1.193548467 1.131062512 1.15822611 1.0610298 1.177869482 0.99069542 1 20.65018181 1.684173534 0.510705053 0.994144272 1.214508893 0.537560641 0.065678918 0.693712518 0.431442416 0.066965106 0.043482979 48.325186 -1.684173534 0.220364621 QAREQTGK ddPTM_BT-474_Pertuzumab_2h_R1 1 QAREQTGK 8 1 Q9Y5B6-2;Q9Y5B6 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 0 62.2 0.074004 256090000 177870 251380 279750 456140 343690 411500 318530 138000 63207 121620 FALSE TRUE 170918.6438 244210.8885 330307.048 479681.4401 354745.101 419820.8119 322428.2654 135150.2518 56032.00635 113382.5691 1.507450794 2.153866247 2.913208359 4.230645363 3.128744602 3.70269271 2.843719877 1.191984384 0.494185366 1 16.79083934 1.684266567 3.480113546 0.773182823 2.995172956 0.631317101 0.715323285 0.133666251 3.758381014 0.455718937 0.208629821 48.33553913 -1.684266567 2.221990134 ERGT(ph)PPVDPK ddPTM_BT-474_Pertuzumab_2h_R1 3 ERGTPPVDPK 10 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERGT(1)PPVDPK;ERGT(1)PPVDPK;ERGT(1)PPVDPK 105.95 0.015802 2680240000 2297220 2086820 1838880 1726500 1816240 2060180 2195080 2546250 2898110 2977970 TRUE FALSE 2207442.103 2027305.937 2171206.522 1815604.872 1874661.009 2101838.251 2221944.046 2493669.048 2569128.703 2776269.439 0.795110904 0.730226652 0.782059007 0.653972862 0.675244622 0.757072862 0.800334439 0.898208586 0.925388821 1 21.40471616 1.684314634 1.273093057 0.979811855 0.72581508 0.839301337 0.041906222 0.165500538 0.509399879 0.037138737 0.013967915 48.34088908 -1.684314634 -0.253996775 KPMS(ph)PITAQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPMSPITAQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR 48 2 B1AKL4;Q9NRA8;B0QYZ7;H7C0J7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 KPMS(0.686)PIT(0.284)AQMS(0.03)QLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR;KPMS(0.594)PIT(0.405)AQMS(0.001)QLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR 167.09 1.18E-21 515100000 98134 93248 79986 74431 89393 83597 84328 105189 124273 100003 TRUE FALSE 94298.81479 90588.65834 94441.24948 78272.39283 92268.40703 85287.38862 85360.03129 103016.8104 110166.05 93229.70774 1.01146745 0.97167159 1.012995233 0.839564928 0.989688901 0.914809138 0.915588318 1.104978369 1.181662506 1 16.50850212 1.68437542 5.960917296 1.10847095 0.950036082 0.509446937 0.064581455 0.100456754 7.806495186 0.032106044 0.016100794 48.34765557 -1.68437542 -0.158434868 YCFPNYVGRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 YCFPNYVGRPK 11 1 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 ; 188.87 2.70E-06 2313600000 2132130 2154200 1868200 1916720 1959780 1775380 2053640 2263920 2576440 2448240 FALSE TRUE 2048804.002 2092764.325 2205825.298 2015642.149 2022818.104 1811279.4 2078773.061 2217169.261 2283973.333 2282418.524 0.897646063 0.916906476 0.966442076 0.883116802 0.886260816 0.793578996 0.910776459 0.971412227 1.000681211 1 21.12213193 1.684598214 3.198018968 0.99595515 0.892030711 0.558088155 0.04027887 0.172199013 4.051476711 0.026348466 0.011834147 48.37246445 -1.684598214 -0.10392444 GQPSSSNAGNKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQPSSSNAGNKR 12 1 Q9H0H5;F8VRD2;F8W1E5;F8VQZ5;F8W1T4;F8VZ66;F8VV37;F8VV47;F8VWY4;F8VVE5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 0 96.745 0.008517 24085000 18846 19130 14345 22059 19874 22010 20375 17841 18258 20470 FALSE TRUE 18109.47748 18584.43113 16937.4606 23197.46763 20513.26526 22455.05728 20624.35534 17472.57712 16185.42838 19083.54867 0.948957545 0.973845664 0.887542506 1.215574107 1.074918801 1.176670947 1.08074005 0.915583229 0.848135149 1 14.22004185 1.684637587 5.799957647 0.910265024 1.053813612 0.259903848 0.099754207 0.191753148 14.2708948 0.054826024 0.027377337 48.37685006 -1.684637587 0.143548587 SLPS(ph)HMEEAPNVFQLYQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPSHMEEAPNVFQLYQR 18 0 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(0.041)LPS(0.959)HMEEAPNVFQLYQR;S(0.065)LPS(0.935)HMEEAPNVFQLYQR 146.16 9.00E-08 70976000 25279.8 28513 28704 28404 30066 33796 32463 26230 31357 26478.2 TRUE FALSE 24291.83747 27699.83716 33891.45132 29869.93384 31033.1002 34479.37828 32860.2919 25688.34133 27797.48482 24684.80793 0.984080473 1.122141085 1.372967998 1.210053322 1.25717406 1.396785358 1.33119496 1.040653887 1.126096865 1 14.5913358 1.684709234 7.633593666 1.063495742 1.245177308 0.333000357 0.118417956 0.153772673 17.03006515 0.06169566 0.032184564 48.38483163 -1.684709234 0.181681567 SLSDSESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 0 ; 265.31 1.43E-20 885660000 722980 685480 520860 635890 559010 612080 599250 740830 846860 721970 FALSE TRUE 694725.1423 665930.7816 614990.9885 668708.3591 576991.0643 624456.677 606583.8008 725531.6016 750728.0031 673070.3288 1.032173181 0.989392569 0.913709849 0.993519296 0.857252266 0.927773295 0.901219048 1.077943226 1.115378246 1 19.36039773 1.684870523 6.7205939 1.072446653 0.943534794 0.495549442 0.054878528 0.102139324 9.522835046 0.027900708 0.014270422 48.40280416 -1.684870523 -0.128911859 IFDIDEAEEGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 IFDIDEAEEGVK 12 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 157.75 0.00017282 65581000 115740 112990 108980 112120 105620 108960 101240 128920 135500 122420 FALSE TRUE 111216.7528 109767.6358 128675.1102 117906.5266 109017.3632 111163.2459 102479.0054 126257.7569 120118.6081 114128.3844 0.974488104 0.96179085 1.127459317 1.033104318 0.955216915 0.974019272 0.897927417 1.106278317 1.052486713 1 16.80029812 1.684900218 15.39802694 1.0592978 0.993232677 0.180738323 0.061333367 0.246755539 63.19772749 0.029866525 0.016481786 48.40611387 -1.684900218 -0.066065123 KEDS(ph)DEEEDDDS(ph)EEDEEDDEDEDEDEDEIEPAAMK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEDSDEEEDDDSEEDEEDDEDEDEDEDEIEPAAMK 35 1 P19338;C9J1H7;C9JWL1 P19338 NCL Nucleolin 2 KEDS(1)DEEEDDDS(1)EEDEEDDEDEDEDEDEIEPAAMK 219.66 6.43E-37 223820000 85134 60357 54741 56148 58830 48585 76055 103200 139160 124690 TRUE FALSE 81806.86916 58635.67746 64633.91641 59045.80501 60722.32038 49567.42199 76985.78384 101068.8839 123363.1402 116244.6352 0.70374748 0.504416202 0.556016338 0.507944344 0.522366647 0.426406104 0.662273865 0.869449878 1.061237277 1 16.82680461 1.685064586 2.156771954 1.02539427 0.534797214 0.887518834 0.071102194 0.081300483 0.808046126 0.048504947 0.019503427 48.42443766 -1.685064586 -0.490597055 RGEEWDPQKAEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGEEWDPQKAEEK 13 2 I3L0X5;O75391;I3L4C3 I3L0X5 SPAG7 Sperm-associated antigen 7 0 64.244 0.035401 255280000 509940 410630 312050 296760 387240 363770 382960 453880 533090 469730 FALSE TRUE 490010.981 398919.2344 368444.3765 312075.8192 399695.9263 371125.6786 387646.779 444507.2194 472575.8581 437914.7687 1.118964274 0.910951772 0.841360929 0.712640544 0.912725386 0.847483815 0.885210563 1.015054187 1.079150309 1 18.74029058 1.685174523 3.851364218 1.041541961 0.880696341 0.310403779 0.096346672 0.217772965 7.545699918 0.056459728 0.026400855 48.43669729 -1.685174523 -0.16084562 S(ph)QEEPKDTFEHDPSESIDEFNK ddPTM_BT-474_Pertuzumab_2h_R1 3 SQEEPKDTFEHDPSESIDEFNK 22 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.653)QEEPKDT(0.263)FEHDPS(0.071)ES(0.013)IDEFNK;S(0.935)QEEPKDT(0.065)FEHDPSESIDEFNK;S(0.991)QEEPKDT(0.009)FEHDPSESIDEFNK 195.86 1.33E-22 1236490000 1080820 875780 772460 669320 815710 759820 868790 937100 1098440 1001910 TRUE FALSE 1038580.359 850803.6119 912060.7053 703863.6854 841948.053 775184.081 879422.5119 917748.5575 973749.6962 934049.7433 1.111911188 0.910876126 0.976458387 0.753561243 0.901395305 0.829917343 0.941515715 0.98254784 1.042503039 1 19.83313986 1.685355889 2.675394471 1.018412892 0.90815098 0.186429164 0.088265883 0.382442176 6.125252178 0.05701974 0.024428494 48.45692925 -1.685355889 -0.110261913 QEGGDNDLIER ddPTM_BT-474_Pertuzumab_2h_R1 1 QEGGDNDLIER 11 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A096LNY6 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 114.76 0.0017922 0 76549 94058 74860 86680 86029 87642 93551 79751 88249 93877 FALSE TRUE 73557.38045 91375.55793 88388.86725 91153.56519 88796.20091 89414.18129 94695.90512 78104.11398 78231.34349 87518.62717 0.840476854 1.044069827 1.009943484 1.041533307 1.014597735 1.021658865 1.082008576 0.892428464 0.893882206 1 16.41730249 1.685584388 9.640733776 0.920727076 1.011219348 0.22421705 0.066447098 0.147213239 21.8399862 0.030463703 0.016365746 48.48243103 -1.685584388 0.090492272 DGLPRTPS(ph)RR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLPRTPSRR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.157)PS(0.843)RR;DGLPRT(0.269)PS(0.731)RR 82.069 0.0099761 2677105000 427265 436312 279554 338441 361206 425811 346041 339764 346214 316366 TRUE FALSE 410567.0114 423868.809 330075.6264 355907.9806 372824.519 434421.1902 350275.9533 332747.7547 306913.2382 294938.249 1.392043971 1.437144251 1.119134692 1.206720328 1.264076532 1.472922524 1.187624713 1.12819465 1.040601682 1 18.1700534 1.685650506 1.979637113 1.02733777 1.304175757 0.559473031 0.10342969 0.247743514 2.029417564 0.079636241 0.03131464 48.48981262 -1.685650506 0.276837987 AAGLATMISTMRPDIDNMDEYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAGLATMISTMRPDIDNMDEYVR 23 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 235.25 3.96E-37 939740000 456380 529770 436880 449950 471910 523890 502120 460620 498720 497210 FALSE TRUE 438544.165 514661.4783 515833.9343 473171.9734 487089.4137 534483.4147 508265.0948 451108.036 442107.3964 463533.5238 0.946089425 1.110300446 1.112829834 1.020793425 1.050818093 1.153063128 1.096501264 0.973193982 0.953776531 1 18.82231416 1.685859769 6.034995877 0.972074785 1.07368401 0.377727477 0.055215873 0.137797788 10.96725301 0.028372169 0.014267873 48.51318292 -1.685859769 0.101609226 KKEGETVEPYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKEGETVEPYK 11 2 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 98.803 0.0029522 1331170000 3493800 3176300 2946000 2581200 3136300 3243000 3273600 3776400 4512500 4134800 FALSE TRUE 3357258.433 3085715.034 3478407.733 2714416.041 3237181.938 3308575.682 3313663.296 3698416.02 4000259.918 3854746.313 0.870941473 0.800497564 0.902370079 0.704175015 0.839791176 0.858312172 0.859632003 0.959444726 1.037749204 1 21.87820449 1.685977366 1.745594795 1.022529891 0.82517972 0.70292287 0.05048904 0.175126704 1.07949772 0.037350434 0.014293808 48.52632087 -1.685977366 -0.197350172 GLTMLDHEQVTPEDPGAQFLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLTMLDHEQVTPEDPGAQFLIR 22 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QZS6;A0A590UKA0 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ;;; 209.01 6.20E-23 1426770000 930330 1035470 817100 1047740 1014120 1101310 1009700 969490 1031670 1019970 FALSE TRUE 893971.6751 1005939.409 964768.1463 1101813.987 1046740.091 1123579.243 1022057.011 949469.6927 914559.1467 950886.5234 0.940145489 1.057896378 1.014598611 1.158722897 1.100804423 1.181612332 1.074846457 0.99850999 0.961796307 1 19.85891366 1.686082783 4.016058109 0.981487047 1.080999145 0.28192954 0.06489229 0.233165804 8.795033684 0.038159693 0.017993533 48.53810118 -1.686082783 0.099512097 NEEPSEEEIDAPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 NEEPSEEEIDAPKPK 15 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 108.34 0.00099108 307730000 210510 145860 130680 114980 152420 150910 147930 188360 220560 191070 FALSE TRUE 202283.0365 141700.2156 154296.783 120914.1316 157322.7277 153961.5036 149740.4116 184470.3002 195522.9535 178128.6587 1.135600739 0.795493643 0.866209761 0.678802235 0.883197173 0.86432753 0.840630658 1.035601466 1.097650175 1 17.44256012 1.68611113 4.773061149 1.054086704 0.856821982 0.355389859 0.109241709 0.161536614 8.553005963 0.057427258 0.027844596 48.54126952 -1.68611113 -0.197264722 EDKENAFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDKENAFK 8 1 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 101.11 0.008225 276070000 618660 605700 643220 652190 678580 619520 774000 913680 1056490 1104400 FALSE TRUE 594482.0832 588426.029 759464.1624 685849.6041 700407.142 632047.1189 783472.4435 894812.1887 936561.6844 1029598.004 0.57739242 0.57151046 0.737631735 0.666133385 0.680272435 0.613877568 0.760949847 0.869088892 0.909638209 1 19.97364973 1.686177871 1.154959441 0.983843494 0.639479955 0.871399309 0.049849001 0.157935432 0.396793339 0.044862701 0.017127574 48.54872967 -1.686177871 -0.344363539 VKEPS(ph)VQEATSTSDILK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKEPSVQEATSTSDILK 17 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VKEPS(0.999)VQEAT(0.001)STSDILK;VKEPS(0.977)VQEAT(0.021)S(0.003)TSDILK 202.17 6.56E-12 665690000 872100 653900 684750 527330 606000 624730 646030 839060 1034460 765460 TRUE FALSE 838017.3678 635251.4122 808499.5572 554545.5645 625492.5404 637362.4686 653936.3084 821733.1178 917032.4376 713614.7124 1.174327481 0.890188222 1.132963689 0.777093794 0.876512955 0.89314648 0.916371674 1.151508095 1.285052594 1 19.44478583 1.686449606 5.357909705 1.166422386 0.944393672 0.313318211 0.130166317 0.156238735 10.21556795 0.066370537 0.03276491 48.57911577 -1.686449606 -0.222028714 (ac)S(ph)EGESQTVLSSGSDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEGESQTVLSSGSDPK 16 0 F8W6G1;Q9UHY1;C9JHZ6;C9JDW7 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 S(0.993)EGES(0.007)QTVLSSGSDPK 98.407 8.75E-72 210360000 650410 591230 550000 569690 592850 597130 644390 707280 806090 796410 TRUE FALSE 624991.2581 574368.6993 649397.2347 599091.7692 611919.5587 609204.3777 652276.2376 692674.4208 714586.0426 742468.4413 0.841774846 0.773593418 0.874646246 0.806891897 0.824169116 0.820512151 0.878523855 0.932934496 0.962446352 1 19.50197018 1.68648112 1.230478591 0.992450487 0.820732277 0.870151078 0.024991558 0.134089065 0.384071687 0.019855668 0.007505332 48.58264104 -1.68648112 -0.171718209 NYQQNYQNS(ph)ESGEKNEGSESAPEGQAQQR ddPTM_BT-474_Pertuzumab_2h_R1 3 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(0.965)ES(0.032)GEKNEGS(0.003)ESAPEGQAQQR;NYQQNYQNS(0.898)ES(0.099)GEKNEGS(0.003)ES(0.001)APEGQAQQR;NYQQNYQNS(0.997)ES(0.003)GEKNEGSESAPEGQAQQR 141.46 4.89E-08 7003880000 686790 526164 439626 391744 436843 478343 420530 624873 649510 610725 TRUE FALSE 659949.4875 511158.3179 519076.1976 411961.9548 450894.4518 488015.4232 425676.5719 611969.1542 575780.3478 569360.0518 1.159107467 0.897776927 0.911683558 0.723552616 0.791932013 0.857129723 0.747640391 1.074836832 1.011276337 1 19.11898175 1.686482411 9.097482721 1.030732197 0.863632483 0.283646676 0.115129584 0.149513345 20.83004324 0.057009549 0.030443072 48.58278539 -1.686482411 -0.167099713 RADAGSHT(ph)EGSPSQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RADAGSHTEGSPSQPR 16 1 Q86V15;Q86V15-2 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 RADAGS(0.003)HT(0.927)EGS(0.062)PS(0.007)QPR;RADAGS(0.008)HT(0.957)EGS(0.034)PS(0.001)QPR 78.794 0.011805 100690000 59784 54652 46171 57697 54857 45689 40493 46390 32261 28970 TRUE FALSE 57447.57519 53093.37847 54515.12677 60674.74908 56621.52522 46612.86288 40988.56545 45432.03029 28598.86653 27007.8361 2.127070639 1.965850884 2.01849295 2.246560919 2.096485073 1.725901428 1.517654554 1.682179577 1.058909956 1 14.72109043 1.686499857 0.702579291 0.980020445 2.104361848 0.876529363 0.145999324 0.222155369 0.223365157 0.141019866 0.068110492 48.58473714 -1.686499857 1.124341403 up S(ph)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR 40 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR 227.2 3.43E-40 509455000 50127.2 101480.8 42044.5 134222.3 47260 50633 108834.5 32497.4 74524.5 39624.5 TRUE FALSE 48168.17361 98586.66694 49642.87642 141149.529 48780.16082 51656.83395 110166.4492 31826.31733 66064.79119 36940.69732 1.30393244 2.668781969 1.343853257 3.820976301 1.320499188 1.398371923 2.982251478 0.861551612 1.788401302 1 15.17292348 1.686533305 11.18895944 1.251225251 2.117279064 0.198830295 0.82905796 0.190410244 34.05910007 0.370339904 0.201490103 48.58847905 -1.686533305 0.866053813 LTEEELLDREFDLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTEEELLDREFDLLR 15 1 H0Y9P1;Q9NSY1;Q9NSY1-2;Q9NSY1-3 H0Y9P1 BMP2K BMP-2-inducible protein kinase 0 ; 104.41 0.0012728 58553000 62648 74636 55602 71750 71169 77045 63753 62451 59937 59719 FALSE TRUE 60199.6469 72507.45436 65650.51826 75453.0261 73458.21552 78602.90269 64533.22828 61161.36503 53133.20304 55674.17894 1.081284862 1.302353366 1.179191494 1.355260689 1.319430604 1.411837663 1.159123125 1.098558905 0.954359885 1 15.76472076 1.686559104 2.073981046 0.985679272 1.275847001 0.617203705 0.091481926 0.18829281 1.712402593 0.065006228 0.025897361 48.59136552 -1.686559104 0.290167729 HYPCTLVGTWNTWYGEQDQAVHLWR ddPTM_BT-474_Pertuzumab_2h_R1 2 HYPCTLVGTWNTWYGEQDQAVHLWR 25 0 O75323;H7C333 O75323 GBAS Protein NipSnap homolog 2 0 ; 279.16 2.01E-53 977440000 42532 46616 37716 76968 39158 49673 60019 30252.8 34427.7 39596 FALSE TRUE 40869.80242 45286.55732 44532.12019 80940.3277 40417.55263 50677.42209 60753.53048 29628.06911 30519.61183 36914.12765 1.107158831 1.226808276 1.206370651 2.192665325 1.09490743 1.37284626 1.645807021 0.802621408 0.82677321 1 15.17188544 1.686643511 7.470358703 0.863822264 1.408117507 0.378737679 0.310213471 0.128827282 14.00248025 0.153927582 0.080091743 48.60081042 -1.686643511 0.544295243 IENIYMR ddPTM_BT-474_Pertuzumab_2h_R1 1 IENIYMR 7 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 89.296 0.041823 81904000 158180 179240 147940 183080 146660 152510 180770 142080 158740 165000 FALSE TRUE 151998.1507 174128.2507 174676.0489 192528.7807 151377.4521 155593.8567 182982.3173 139145.9983 140720.5007 153824.403 0.988127681 1.131993671 1.135554863 1.251614028 0.98409257 1.011503075 1.189553242 0.904576879 0.914812591 1 17.23092487 1.686650457 8.151671401 0.933549619 1.099441395 0.41975301 0.085413188 0.113323337 13.794505 0.042198115 0.022230893 48.6015877 -1.686650457 0.165891776 SYS(ph)PDGKES(ph)PSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SYSPDGKESPSDK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.001)YS(0.999)PDGKES(0.937)PS(0.063)DK 157.22 2.71E-05 411980000 1015100 678060 690440 577820 782760 775420 861750 1079200 1442300 1232100 TRUE FALSE 975428.7697 658722.3927 815217.8668 607641.3594 807938.1863 791099.5237 872296.3543 1056914.143 1278576.151 1148648.77 0.849196722 0.573475905 0.709719009 0.529005363 0.703381406 0.688721866 0.759410864 0.920136922 1.113113237 1 20.13150629 1.68675113 1.810673691 1.058832378 0.666744685 0.760573144 0.085984613 0.14055175 0.940793851 0.060811895 0.023453203 48.61285526 -1.68675113 -0.392087693 MLLYTEVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLLYTEVTR 9 0 P50395;V9GYF8;Q5SX90;V9GYJ7;Q5SX86;G5E9U5;P31150 P50395;Q5SX86;G5E9U5;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 156.51 0.00016462 547940000 401540 449540 361050 471250 530000 448480 466260 389080 387280 446100 FALSE TRUE 385847.3729 436719.5593 426299.7665 495571.269 547047.9313 457548.5729 471966.2294 381045.362 343317.598 415885.2497 0.927773642 1.050096294 1.025041804 1.191605784 1.315381904 1.100179853 1.134847244 0.916227162 0.825510398 1 18.66582599 1.686801127 5.081149063 0.899770019 1.112214612 0.41269036 0.10466711 0.150613621 8.963718409 0.059546041 0.029163695 48.61845197 -1.686801127 0.212444593 GLDDS(ph)TGGTPLTPAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDDSTGGTPLTPAAR 16 0 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8;I3L2R3;I3L522 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 GLDDS(0.63)T(0.368)GGT(0.001)PLT(0.001)PAAR;GLDDS(0.832)T(0.167)GGTPLTPAAR 59.502 0.065191 833800000 367750 649340 598700 1055980 775870 756780 630640 457970 243030 418900 TRUE FALSE 353377.9234 630821.459 706898.408 1110479.254 800826.5632 772082.6101 638357.961 448512.7595 215442.2533 390527.5299 0.904873271 1.615305992 1.81011159 2.84353642 2.050627682 1.977024796 1.634604252 1.148479237 0.551669823 1 18.57506473 1.68681207 2.229927311 0.78094094 1.900294049 0.475183285 0.46169972 0.245843485 2.630176232 0.339904471 0.138229132 48.6196771 -1.68681207 1.11935311 DIPNENEAQFQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIPNENEAQFQIR 13 0 Q10567-4;Q10567-3;Q10567-2;Q10567 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 79.82 0.045294 47801000 57637 49690 50427 50497 54566 52399 61650 62681 71636 73533 FALSE TRUE 55384.48232 48272.88985 59540.28064 53103.15622 56321.16495 53458.54368 62404.49114 61386.61545 63504.1816 68552.54441 0.807912861 0.704173569 0.868534949 0.774634358 0.821576579 0.779818519 0.910316191 0.895468082 0.926357762 1 16.06492259 1.68688926 0.593851042 0.998317799 0.777458247 0.7190069 0.04397393 0.364820576 0.281869969 0.039718895 0.022180273 48.62831938 -1.68688926 -0.220859552 DDVFLDGTGWEGGDEWIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDVFLDGTGWEGGDEWIR 18 0 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 145 2.19E-07 26586000 17868 14995 14251 14257 15042 14629 16004 18681 23175 19048 FALSE TRUE 17169.69881 14567.35728 16826.47271 14992.80548 15525.83959 14924.8084 16199.86174 18295.23082 20544.27116 17757.86199 0.966878716 0.820332835 0.947550596 0.844291136 0.874307932 0.840462011 0.912264199 1.030260897 1.156911297 1 14.11617027 1.687213561 3.035243415 1.082192449 0.880523527 0.678604871 0.056134946 0.108325092 2.27376985 0.031262247 0.013895644 48.66464514 -1.687213561 -0.201668922 DIKEES(ph)DEEEEDDEESGR ddPTM_BT-474_Pertuzumab_2h_R1 3 DIKEESDEEEEDDEESGR 18 1 Q96EV2;A8MTF7;Q96EV2-2;H7BXM6;H7C0H2 Q96EV2 RBM33 RNA-binding protein 33 1 DIKEES(1)DEEEEDDEESGR;DIKEES(1)DEEEEDDEESGR;DIKEES(1)DEEEEDDEESGR 278.76 2.08E-39 3435490000 1725820 1362660 1248170 1125280 1370160 1392860 1370540 1688890 2015820 1671900 TRUE FALSE 1658373.046 1323798.271 1473742.084 1183355.836 1414232.441 1421024.584 1387313.078 1654013.831 1786992.565 1558660.724 1.063973077 0.849317783 0.945518202 0.759213226 0.907338216 0.911695895 0.890067388 1.061176307 1.14649233 1 20.5718755 1.687656174 4.509682833 1.08234221 0.897971761 0.475231703 0.079280247 0.128345888 6.100931719 0.041276728 0.019862933 48.71426716 -1.687656174 -0.184370449 GPSS(ph)VEDIK ddPTM_BT-474_Pertuzumab_2h_R1 4 GPSSVEDIK 9 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 GPS(0.017)S(0.983)VEDIK;GPS(0.044)S(0.956)VEDIK;GPS(0.034)S(0.966)VEDIK;GPS(0.039)S(0.961)VEDIK 180.19 5.13E-05 4130230000 7058500 6568100 6286700 5703400 6257100 6857300 6322800 7437700 8358800 7374400 TRUE FALSE 6782646.016 6380784.219 7422846.537 5997753.157 6458365.304 6995959.304 6400180.318 7284108.896 7409944.067 6874925.32 0.98657741 0.92812415 1.079698497 0.872409936 0.939408794 1.017605134 0.930945431 1.059518258 1.077821754 1 22.71291261 1.687736631 7.304653597 1.051103432 0.965574692 0.300023337 0.056224706 0.143728477 15.24276344 0.02680321 0.013904459 48.72329286 -1.687736631 -0.08552874 DSAYISSS(ph)PLGSHQVFDFR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSAYISSSPLGSHQVFDFR 19 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 DSAYISS(0.027)S(0.973)PLGSHQVFDFR;DSAYIS(0.01)S(0.167)S(0.823)PLGSHQVFDFR;DSAYISS(0.095)S(0.905)PLGSHQVFDFR 228.3 3.50E-26 1441640000 751100 874734 723622 941630 872790 872240 792250 754090 744258 709637 TRUE FALSE 721746.1816 849787.4428 854396.5923 990227.6371 900864.083 889877.2904 801945.7925 738517.778 659772.952 661572.6539 1.090955283 1.284496023 1.291462982 1.496778368 1.361700907 1.345093823 1.212180987 1.116306385 0.997279661 1 19.33554008 1.687943689 1.68681553 0.997687459 1.319486993 0.63044557 0.09555399 0.229088008 1.30670903 0.077972772 0.029717306 48.74652807 -1.687943689 0.321799534 TQASS(ph)SPAALKPPAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQASSSPAALKPPAGR 16 1 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 1 T(0.045)QAS(0.112)S(0.421)S(0.421)PAALKPPAGR 76.301 0.016407 289890000 192460 182590 173510 157910 188070 195210 210040 226690 272160 273230 TRUE FALSE 184938.4504 177382.712 204867.1167 166059.754 194119.4424 199157.2799 212610.5324 222008.7723 241265.5378 254723.8887 0.726034968 0.696372503 0.804271314 0.651920614 0.762077885 0.781855526 0.834670566 0.871566359 0.947164944 1 17.95857474 1.687979632 0.751640023 1.000873562 0.720293352 0.868188841 0.037612403 0.195382483 0.219672675 0.032659991 0.015027996 48.75056262 -1.687979632 -0.280580211 DVPDSQQHPAPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVPDSQQHPAPEK 13 0 O60885;O60885-2;O60885-3;M0QZD9 O60885 BRD4 Bromodomain-containing protein 4 0 100.11 0.0025499 375330000 892960 771550 687760 646640 695040 786240 732600 885700 1006100 894450 FALSE TRUE 858062.136 749546.1494 812053.5311 680013.1679 717396.5928 802138.3115 741565.7779 867409.9855 891891.7459 833868.1048 1.029014218 0.898878546 0.9738393 0.815492479 0.860323819 0.961948667 0.889308242 1.040224444 1.069583716 1 19.66945968 1.688317017 5.877257431 1.041948129 0.915374461 0.452931357 0.059253004 0.120567227 9.264989967 0.030497084 0.01529176 48.78844953 -1.688317017 -0.126573668 AAATGNAS(ph)PGKLEHSK ddPTM_BT-474_Pertuzumab_2h_R1 5 AAATGNASPGKLEHSK 16 1 H0Y6H0;Q8NB78 H0Y6H0 KDM1B Lysine-specific histone demethylase 1B 1 AAAT(0.009)GNAS(0.991)PGKLEHSK;AAATGNAS(1)PGKLEHSK;AAATGNAS(1)PGKLEHSK;AAAT(0.001)GNAS(0.999)PGKLEHSK;AAATGNAS(1)PGKLEHSK 225.83 3.93E-15 1520550000 2078540 1785590 1428950 1275520 1598070 1587070 1601750 1807420 2050310 1807560 TRUE FALSE 1997308.359 1734666.721 1687193.052 1341349.74 1649473.373 1619161.643 1621352.696 1770096.145 1817567.404 1685132.351 1.185253109 1.029394944 1.001222872 0.795990736 0.978839064 0.960851319 0.962151545 1.050419656 1.078590298 1 20.68443048 1.688338153 6.532807769 1.048380043 0.981145816 0.067630054 0.090967422 0.34226464 31.03894484 0.048175439 0.0245659 48.79082408 -1.688338153 -0.067234227 EKEDDEEEEDEDASGGDQDQEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEDDEEEEDEDASGGDQDQEER 23 1 O60216;E5RI01;E5RFZ5 O60216 RAD21 Double-strand-break repair protein rad21 homolog 0 226.14 9.53E-33 256260000 244220 189170 187310 169790 204910 204800 208400 242630 278370 266910 FALSE TRUE 234675.6124 183775.0568 221161.0837 178552.8822 211501.1162 208941.1963 210950.4615 237619.6057 246770.6046 248831.948 0.94310885 0.738550891 0.888796979 0.717564138 0.849975729 0.839687982 0.84776277 0.954940102 0.991715922 1 17.9248122 1.688365292 1.86637108 1.000019417 0.822897176 0.560191388 0.061657178 0.212116258 1.519549588 0.042135805 0.016380511 48.79387304 -1.688365292 -0.177122241 STHSELLEDYYQSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 STHSELLEDYYQSGR 15 0 A0A3B3ITW3;P28288 A0A3B3ITW3 ABCD3 ATP-binding cassette sub-family D member 3 0 ; 132.08 4.96E-05 345410000 116259 204467 161019 243590 168290 207200 195338 158162 168141 163939 FALSE TRUE 111715.4697 198635.8014 190118.7151 256161.7091 173703.2007 211389.726 197728.6049 154895.8994 149054.3386 152835.2655 0.730953484 1.299672564 1.243945332 1.676064148 1.136538744 1.383121397 1.293736784 1.013482712 0.975261423 1 17.22161795 1.688418387 4.876484791 0.990437203 1.27055719 0.216207988 0.22115986 0.230466067 12.73937428 0.117304958 0.057159771 48.79983874 -1.688418387 0.280119987 LQDGTPQAALS(ph)PLTPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQDGTPQAALSPLTPAR 17 0 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6 A0A087WVP4 SMTN Smoothelin 1 LQDGTPQAALS(1)PLTPAR 161.95 3.04E-09 137570000 82102 118420 100140 121590 101100 105290 118610 96222 100710 123450 TRUE FALSE 78893.36307 115042.7775 118237.5256 127865.2745 104351.9733 107419.0359 120061.5847 94234.98207 89277.82301 115088.6215 0.685500982 0.999601664 1.02736069 1.111015779 0.906709733 0.933359306 1.043209859 0.818803639 0.7757311 1 16.81238568 1.68860679 9.052742611 0.849083249 0.965166726 0.105750193 0.12010231 0.214725175 30.24997767 0.056923078 0.030391159 48.82101344 -1.68860679 0.116083477 GPPPSWGR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPPPSWGR 8 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;; 125.5 0.0029293 895240000 340280 341423 296028 295855 337437 313991 311941 332757 347920 328327 FALSE TRUE 326981.4814 331685.9503 349526.8447 311124.112 348290.9676 320340.1132 315758.6273 325885.4517 308425.5802 306089.1198 1.068255812 1.083625418 1.141912019 1.016449432 1.13787438 1.046558314 1.031590497 1.064675059 1.007633268 1 18.22359224 1.688687707 0.602436228 0.999462928 1.090879034 0.400799641 0.036838966 0.731457056 0.577153932 0.033335687 0.018378915 48.83011044 -1.688687707 0.091416106 RPDPDS(ph)DEDEDYER ddPTM_BT-474_Pertuzumab_2h_R1 3 RPDPDSDEDEDYER 14 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 1 RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER 191.18 1.29E-07 1471310000 990831 1269745 1176747 1677560 1546430 1521940 1490550 1128120 1106140 1363820 TRUE FALSE 952108.2291 1233533.116 1389411.359 1764139.073 1596172.325 1552714.67 1508791.797 1104823.928 980575.6245 1271447.257 0.748838164 0.970180327 1.092779392 1.387504722 1.255397986 1.22121831 1.186672738 0.86894987 0.771227921 1 20.27804019 1.688816376 5.868631305 0.863453844 1.134936153 0.293036278 0.171489422 0.177369915 13.61786468 0.096125733 0.048201017 48.84457963 -1.688816376 0.271482309 KAEGGGGGGRPGAPAAGDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAEGGGGGGRPGAPAAGDGK 20 2 Q00839 Q00839 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 108.25 0.0001208 757850000 210300 175240 185170 153470 165790 174630 174670 204270 224420 212740 FALSE TRUE 202081.2435 170242.3268 218634.3381 161390.6051 171122.7859 178161.1382 176807.6637 200051.7531 198944.7824 198330.9303 1.018909371 0.858375073 1.102371364 0.813744003 0.862814417 0.898302337 0.891478013 1.008676523 1.00309509 1 17.59755016 1.688890866 6.696358878 1.004326525 0.918333063 0.186112692 0.079271224 0.214832547 20.25776082 0.039052897 0.019996921 48.85295809 -1.688890866 -0.085993462 YYGGGSEGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 YYGGGSEGGR 10 0 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 193.86 1.23E-06 3617300000 2832100 3233680 2487660 3199260 3067000 2880400 3062880 2812210 2912580 3151900 FALSE TRUE 2721418.401 3141458.613 2937235.5 3364374.192 3165652.84 2938643.662 3100364.442 2754136.881 2581956.129 2938419.006 0.926150558 1.069098249 0.99959723 1.14496067 1.077332006 1.000076455 1.055113119 0.93728528 0.878688888 1 21.4866087 1.688920706 5.138461645 0.929386567 1.042637319 0.356622068 0.061154946 0.149959995 9.141578001 0.031707322 0.015578105 48.85631488 -1.688920706 0.113250752 GLHQSIEEFR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLHQSIEEFR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 196.48 3.33E-07 3363960000 1343620 2323400 1859050 2823040 2040370 2328310 2330810 1823220 1705870 2365430 FALSE TRUE 1291109.845 2257138.907 2195021.689 2968737.433 2106000.354 2375390.023 2359335.15 1785569.87 1512226.789 2205217.319 0.585479641 1.023544885 0.995376587 1.346233501 0.955008078 1.077168224 1.06988782 0.809702452 0.685749552 1 21.07248941 1.688937498 6.216215725 0.8103012 1.021113058 0.147259969 0.189179718 0.221696332 18.67644172 0.095779936 0.048469839 48.85820398 -1.688937498 0.210811858 DTWHQVYR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTWHQVYR 8 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1;H7C141 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ;;; 93.162 0.011264 1037430000 319155 512491 421062 614020 456514 514760 527101 331163 321828 392340 FALSE TRUE 306682.0698 497875.2585 497157.2699 645709.6458 471198.1874 525168.7999 533551.8197 324324.3683 285295.4347 365766.4623 0.83846416 1.361183459 1.359220489 1.765360448 1.288248749 1.43580359 1.45872264 0.886697939 0.779993422 1 18.48056327 1.689043326 5.634605211 0.870697255 1.37393806 0.485552357 0.220319227 0.116974058 8.394450203 0.115197154 0.057405334 48.87011103 -1.689043326 0.503240805 YLQSLLAEVER ddPTM_BT-474_Pertuzumab_2h_R1 1 YLQSLLAEVER 11 0 O95232;J3KPP4;D6RDI2;D6RHH0;U3KQT3 O95232 LUC7L3 Luc7-like protein 3 0 103.08 0.0064718 81391000 103370 114030 96355 89338 100050 102170 96111 84923 88757 78441 FALSE TRUE 99330.18612 110777.976 113768.4919 93948.74489 103268.1991 104235.9474 97287.23517 83169.31037 78681.67746 73128.1212 1.358303543 1.514847835 1.555742032 1.284714325 1.412154414 1.425388013 1.330366945 1.137309547 1.075942827 1 16.15813868 1.689088118 1.31631161 1.010149173 1.435157347 0.835837065 0.071359572 0.159287674 0.526099904 0.061083524 0.022981619 48.87515166 -1.689088118 0.425008174 IKEEVLSES(ph)EAENQQAGAAALAPEIVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKEEVLSESEAENQQAGAAALAPEIVIK 28 1 Q9UJX5;Q9UJX5-3 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 1 IKEEVLS(0.424)ES(0.576)EAENQQAGAAALAPEIVIK 181.44 8.41E-18 76636000 148700 122730 114390 101440 125990 143880 145420 152380 175010 186680 TRUE FALSE 142888.6396 119229.8606 135062.8176 106675.3306 130042.5828 146789.3522 147199.6935 149233.2997 155143.5985 174035.9973 0.821029223 0.685087352 0.776062537 0.612949805 0.74721658 0.843442474 0.84580027 0.857485245 0.891445453 1 17.40902622 1.689124374 0.607106725 0.98643688 0.719420162 0.679016244 0.058604124 0.418457214 0.334018574 0.056048076 0.030684501 48.87923206 -1.689124374 -0.267016718 LDPELHLDIK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDPELHLDIK 10 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;;; 164.33 6.19E-06 1716760000 4364650 4227480 3991660 4208680 4226610 4265620 4764750 4891890 5612150 5594860 FALSE TRUE 4194074.653 4106916.41 4713041.756 4425890.479 4362562.749 4351873.759 4823062.436 4790870.762 4975082.26 5215915.149 0.80409181 0.787381752 0.903588655 0.848535751 0.836394501 0.834345198 0.92468192 0.918510103 0.953827299 1 22.31448897 1.689377691 0.585361835 1.002569479 0.824132482 0.772652539 0.031335317 0.360416682 0.27232376 0.031326062 0.017754664 48.90775086 -1.689377691 -0.178436997 ATTVPDFQETRPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATTVPDFQETRPR 13 1 B7ZC38;Q9NR46 B7ZC38 SH3GLB2 Endophilin-B2 0 ;;; 153.32 3.79E-05 2419760000 1681210 2134070 1567320 2015770 1953590 2030130 1817700 1773450 1718960 1779060 FALSE TRUE 1615506.455 2073208.413 1850569.589 2119804.131 2016428.997 2071180.62 1839945.556 1736827.638 1523830.867 1658562.682 0.974040036 1.250003051 1.115767049 1.278097087 1.215768942 1.248780431 1.109361483 1.047188422 0.91876592 1 20.66150211 1.689508153 2.128565377 0.963695223 1.185367727 0.504546698 0.085950413 0.216642635 2.085179258 0.057776296 0.023251282 48.92244498 -1.689508153 0.221672504 KIQALQQQADEAEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KIQALQQQADEAEDR 15 1 P67936;A0A2R8Y5V9;A0A2R8YGX3;A0A590UJB9;A0A590UK79 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;; 271.43 3.43E-33 7719330000 4581630 4469280 3655020 4116900 4019000 4593330 4115440 4285590 4507660 4364250 FALSE TRUE 4402574.834 4341820.51 4315563.419 4329373.702 4148274.785 4686210.28 4165805.986 4197091.069 3995969.334 4068655.46 1.082071185 1.0671389 1.060685394 1.064079705 1.019568952 1.151783513 1.023877796 1.031567089 0.982135099 1 21.95612069 1.689559656 2.090146054 0.995556272 1.069959135 0.459401885 0.033708978 0.257312583 2.3774806 0.022814076 0.009135498 48.928247 -1.689559656 0.074402864 GLDISHISQR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLDISHISQR 10 0 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ;;; 147.3 2.71E-05 1323270000 894430 1392980 1101050 1436670 1203640 1097190 1383690 1078850 1110930 1509180 FALSE TRUE 859474.6868 1353253.574 1300034.228 1510816.711 1242356.174 1119375.934 1400624.012 1056571.37 984821.8838 1406961.894 0.610872754 0.961826742 0.924001022 1.073814946 0.88300627 0.795597904 0.995495342 0.750959479 0.699963437 1 20.42415183 1.689733238 10.8554536 0.795064651 0.898838614 0.049811275 0.138360114 0.269799836 48.33543981 0.063382111 0.034417417 48.94780688 -1.689733238 0.103773963 EHPDPGSKDPEEDYPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHPDPGSKDPEEDYPK 16 1 F5H8F7;Q9UBL3-2;Q9UBL3-3;Q9UBL3 F5H8F7 ASH2L Set1/Ash2 histone methyltransferase complex subunit ASH2 0 71.781 0.023845 271220000 284870 234510 204870 181500 194040 222530 217450 255290 289580 260340 FALSE TRUE 273736.9655 227822.0044 241894.5663 190867.2368 200281.4728 227029.7091 220111.2181 250018.1723 256708.0924 242706.9399 1.127849766 0.938671158 0.996652862 0.786410297 0.825198789 0.935406747 0.906901213 1.030123705 1.057687483 1 17.88885584 1.689770249 5.564102028 1.033922557 0.924423591 0.202906824 0.088273902 0.225900648 15.89472689 0.048069769 0.023918001 48.9519785 -1.689770249 -0.109498966 VGS(ph)TENIK ddPTM_BT-474_Pertuzumab_2h_R1 6 VGSTENIK 8 0 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VGS(0.992)T(0.008)ENIK;VGS(0.98)T(0.02)ENIK;VGS(0.614)T(0.386)ENIK;VGS(0.5)T(0.5)ENIK;VGS(0.5)T(0.5)ENIK;VGS(0.988)T(0.012)ENIK 157.14 0.00040041 6954700000 8962570 6315800 6177070 5110300 5627490 5569480 6350270 8033050 9537160 8309890 TRUE FALSE 8612302.856 6135679.568 7293403.957 5374043.195 5808503.327 5682098.702 6427986.504 7867164.71 8454541.58 7747053.749 1.111687505 0.792001678 0.941442282 0.693688642 0.749769334 0.733452857 0.829733046 1.015504083 1.09132347 1 22.88521632 1.690025405 4.087565731 1.04721551 0.824980741 0.386284865 0.115076118 0.175267823 6.84566444 0.064232769 0.030486575 48.98074713 -1.690025405 -0.222234769 AGNYEEALQLYQHAVQYFLHVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGNYEEALQLYQHAVQYFLHVVK 23 0 O75351;K7EKZ3;K7EL71 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 162.49 9.57E-12 195330000 23760 26017 23041 25995 30546 24975 27102 22317 23263 24304 FALSE TRUE 22831.43293 25275.02063 27205.02124 27336.60507 31528.53983 25480.01161 27433.68238 21856.14615 20622.28177 22657.86843 1.007660231 1.115507432 1.200687581 1.206495004 1.391505116 1.124554664 1.21077949 0.964616165 0.910159834 1 14.46772452 1.690054238 5.050090701 0.949388875 1.185095336 0.53634825 0.094036755 0.120004267 7.098561386 0.052248861 0.025623518 48.98399899 -1.690054238 0.235706462 DREPEREER ddPTM_BT-474_Pertuzumab_2h_R1 3 DREPEREER 9 2 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 0 ;; 157.97 3.78E-05 198391000 93561 101011 74631.9 83414 86272.5 89228.1 90107.4 84999.9 92093 89250.9 FALSE TRUE 89904.53268 98130.26518 88119.54451 87719.00654 89047.53331 91032.35332 91210.16132 83244.62236 81638.98873 83205.85705 1.080507261 1.179367278 1.059054586 1.054240767 1.070207513 1.094061843 1.096198808 1.000465896 0.981168774 1 16.34439747 1.69009623 4.533109201 0.990745187 1.090831571 0.64092505 0.033154871 0.108303081 5.207760821 0.018888694 0.009114571 48.98873555 -1.69009623 0.100086384 AETEKQS(ph)PPHGEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 AETEKQSPPHGEAK 14 1 Q9Y6D6;E5RJN9 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 AETEKQS(1)PPHGEAK;AET(0.005)EKQS(0.995)PPHGEAK;AET(0.004)EKQS(0.996)PPHGEAK 174.23 1.55E-06 1296410000 1546580 1222190 1560170 1452330 1492650 1611430 1957040 2104110 3021570 2751500 TRUE FALSE 1486137.944 1187334.338 1842127.425 1527284.925 1540662.443 1644014.219 1980990.841 2060659.393 2678574.041 2565138.454 0.579359738 0.462873392 0.718139569 0.595400581 0.600615706 0.640906621 0.772274431 0.803332619 1.044222013 1 21.29060527 1.690107443 1.005521258 1.032819501 0.58679795 0.853598925 0.067919591 0.176132863 0.335547053 0.05853972 0.023233339 48.99000038 -1.690107443 -0.446021551 S(ph)LELSSLAGPGEDPLSADSLGKPTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLELSSLAGPGEDPLSADSLGKPTR 25 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(0.996)LELS(0.004)SLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR 288.61 8.90E-55 1039510000 566990 581000 480319 511229 566504 579550 564950 679960 778470 739300 TRUE FALSE 544831.404 564430.4489 567123.3279 537613.59 584726.1156 591268.8981 571864.0271 665918.5884 690101.3492 689226.5525 0.790496829 0.818933117 0.82284022 0.78002449 0.848380135 0.857873069 0.829718508 0.966182434 1.001269244 1 19.39461876 1.690197141 2.402694777 1.002411444 0.81919626 0.924389033 0.022142407 0.066202156 0.833773808 0.015493276 0.006463689 49.00011974 -1.690197141 -0.183215184 TSFSVGS(ph)DDELGPIRK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSFSVGSDDELGPIRK 16 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 TSFSVGS(1)DDELGPIRK;TSFSVGS(1)DDELGPIRK;TS(0.001)FS(0.006)VGS(0.993)DDELGPIRK 255.19 8.16E-27 778530000 441721 444401 360685 447776 435888 419535 441902 484607 568853 500954 TRUE FALSE 424458.055 431727.1186 425868.8029 470885.773 449908.7334 428018.2851 447310.1289 474599.6961 504279.1923 467023.9394 0.908857168 0.924421817 0.911877887 1.008269027 0.963352615 0.916480397 0.957788437 1.016221346 1.079771613 1 18.83313698 1.690212439 3.046227046 1.041833472 0.941210015 0.61271983 0.033388757 0.144142861 3.038476676 0.020700602 0.009238733 49.0018458 -1.690212439 -0.100623457 FDKEEEIRK ddPTM_BT-474_Pertuzumab_2h_R1 2 FDKEEEIRK 9 2 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 104.79 0.0018011 218906000 316370 325020 271880 278160 344390 357310 363480 398740 528500 510570 FALSE TRUE 304005.9106 315750.7478 321014.7639 292515.8709 355467.6171 364535.053 367928.377 390505.8797 468506.8957 475988.6391 0.638683123 0.66335774 0.674416861 0.614543808 0.746798532 0.765848222 0.772977224 0.820410085 0.984281676 1 18.86056761 1.690404698 0.60746323 1.016633002 0.647169113 0.914053724 0.037521437 0.19627912 0.156748671 0.036386324 0.019919977 49.02354334 -1.690404698 -0.369463889 SS(ph)DTEEESR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSDTEEESR 9 0 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 S(0.407)S(0.589)DT(0.003)EEESR;S(0.123)S(0.874)DT(0.003)EEESR;S(0.224)S(0.775)DTEEESR 150.15 9.01E-05 84242000 111942 110675 85138 106927 106288 116423 100169 105152 102578 107639 TRUE FALSE 107567.1829 107518.6574 100524.3305 112445.5153 109706.85 118777.1528 101394.8982 102980.5745 90933.77548 100348.5147 1.071935975 1.071452405 1.001752052 1.120549872 1.093258335 1.183646347 1.010427494 1.026229185 0.906179586 1 16.61465974 1.690429757 2.125445936 0.959901597 1.085344889 0.480489494 0.052608018 0.244541286 2.344715493 0.036847688 0.01483666 49.02637204 -1.690429757 0.125443293 KADPDAAHRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KADPDAAHRPR 11 2 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 0 ; 88.338 0.0073417 99522000 220238 225512 178482 217900 214769 201095 219648 209061 233550 222970 FALSE TRUE 211630.8555 219080.6186 210737.6677 229145.8451 221677.2399 205161.2787 222336.1179 204743.8173 207038.3831 207868.0433 1.018101927 1.053940832 1.013805029 1.102362063 1.066432514 0.986978448 1.069602207 0.984970148 0.996008717 1 17.66530846 1.690523268 7.941498911 0.99326383 1.044434715 0.358602734 0.031055699 0.131994349 15.93650756 0.015096194 0.007932749 49.03692942 -1.690523268 0.051170885 AYT(ph)PPPPLGPHPNLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYTPPPPLGPHPNLGK 16 0 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 AYT(1)PPPPLGPHPNLGK;AY(0.002)T(0.998)PPPPLGPHPNLGK 123.41 0.00032398 885490000 866500 834710 708070 658110 725650 800640 832170 853930 1000860 964200 TRUE FALSE 832636.222 810904.8881 836033.9999 692075.136 748991.1913 816829.4894 842354.3454 836296.0471 887246.5687 898893.8752 0.926289794 0.902114154 0.930069748 0.769918625 0.833236505 0.908705145 0.937100996 0.93036127 0.987042623 1 19.77779127 1.690564962 1.105334612 0.995414078 0.87453287 0.485220186 0.046148265 0.446790318 1.026104804 0.04312008 0.016655703 49.04163736 -1.690564962 -0.120881209 NLANTVTEEILEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NLANTVTEEILEK 13 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;; 267.75 3.10E-24 165257000 238254 214536 182830 171385 193058 201887 188429 238848 254478 246117 FALSE TRUE 228942.7703 208417.6433 215871.448 180230.2004 199267.8859 205969.2935 190735.0505 233915.7053 225590.7243 229447.2764 0.997801211 0.908346556 0.940832471 0.785497232 0.868469171 0.897675914 0.831280517 1.019474753 0.98319199 1 17.80780316 1.690676831 8.068359656 1.000085724 0.888255533 0.459224654 0.054991607 0.109741591 13.54836584 0.027537738 0.014502021 49.05427155 -1.690676831 -0.111830191 DLCPS(ph)EGES(ph)DAEAESK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLCPSEGESDAEAESK 16 0 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 2 DLCPS(1)EGES(1)DAEAESK 193.06 6.35E-10 261970000 227950 192680 173420 195150 187690 183560 212080 276120 343600 305620 TRUE FALSE 219041.462 187184.9551 204760.8517 205221.7149 193727.2193 187271.709 214675.4985 270418.0255 304595.9685 284920.0852 0.768782102 0.656973533 0.718660643 0.720278161 0.679935285 0.657278018 0.753458635 0.949101308 1.069057551 1 18.1201978 1.690733807 2.586473286 1.032285532 0.699128793 0.937611874 0.035841534 0.049912471 0.738583452 0.021985129 0.00938036 49.06070747 -1.690733807 -0.33315674 ASHGYGGK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASHGYGGK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 135.84 0.0020865 1707050000 3746050 3919783 3267145 3731505 3535001 3477460 3929719 3415104 3612235 4162256 FALSE TRUE 3599650.225 3807994.627 3857590.779 3924088.42 3648707.518 3547776.624 3977812.077 3344580.909 3202189.227 3880342.694 0.927662969 0.981355238 0.994136622 1.011273676 0.940305485 0.914294665 1.025118756 0.861929261 0.825233614 1 21.88775264 1.690771512 8.906394635 0.883546027 0.970035389 0.281636772 0.053594182 0.125280726 17.62376495 0.024745293 0.013192044 49.06496712 -1.690771512 0.086489362 GHS(ph)PFTLRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHSPFTLRPK 10 1 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 GHS(0.993)PFT(0.007)LRPK 61.11 0.056758 456560000 341680 443400 434210 426910 529250 544470 474590 317770 273550 369960 TRUE FALSE 328326.7679 430754.6661 512681.4059 448942.8763 546273.8069 555479.5564 480398.1744 311207.9385 242497.7508 344902.2797 0.951941426 1.248918002 1.486454095 1.301652389 1.58385096 1.610541853 1.392852998 0.902307572 0.70309118 1 18.39582814 1.690826109 4.464481826 0.838628512 1.383958151 0.592703224 0.189495887 0.115191803 5.375984914 0.108436385 0.052234042 49.07113567 -1.690826109 0.545329639 RKS(ph)LSDSESDDS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 2 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.965)LS(0.036)DS(0.188)ES(0.008)DDS(0.804)K;RKS(0.94)LS(0.058)DS(0.002)ES(0.004)DDS(0.995)K 250.46 2.04E-16 1072730000 2633100 1990550 1871630 1632390 2004210 2183800 2265300 2795000 3674100 3075100 TRUE FALSE 2530195.541 1933781.463 2209875.175 1716637.844 2068677.235 2227957.932 2293023.419 2737282.273 3257031.571 2866820.738 0.882578917 0.674538675 0.770845259 0.598794972 0.721592811 0.777152859 0.799848902 0.954814592 1.136112743 1 21.45102027 1.690987318 1.914444106 1.070296484 0.729557073 0.752854337 0.076613873 0.140635599 1.065891983 0.054409203 0.021329202 49.08935409 -1.690987318 -0.340739412 RSS(ph)DTEEESR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.206)S(0.794)DTEEESR;RS(0.212)S(0.726)DT(0.062)EEESR 159.58 4.68E-06 208302000 109079 158539 136523 200903 179783 187092 167279 106174 95889 107253 TRUE FALSE 104816.0721 154017.6229 161195.743 211271.6279 185565.8835 190875.1284 169326.2104 103981.4698 85004.08272 99988.65878 1.048279609 1.540350924 1.612140267 2.112955914 1.855869313 1.908967785 1.693454163 1.039932639 0.850137243 1 16.60947685 1.691030572 3.949905452 0.931801626 1.708281403 0.604168991 0.266767241 0.127600405 4.64337065 0.160224398 0.075670581 49.09424348 -1.691030572 0.776479777 NVHSEDFENR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVHSEDFENR 10 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 202.16 2.29E-07 953720000 515860 573770 533880 619050 546250 544070 588970 517030 581480 529340 FALSE TRUE 495699.6209 557406.6414 630363.9921 650999.2447 563820.6273 555071.4682 596177.991 506353.1498 515472.8282 493487.3303 1.004482973 1.129525739 1.277366111 1.319181273 1.142523005 1.124793757 1.208091788 1.026071226 1.044551291 1 18.91265352 1.691162565 5.860249818 1.025600078 1.177248651 0.402392023 0.082716895 0.151651105 11.70148263 0.045793776 0.022987002 49.10916676 -1.691162565 0.151648573 QYQDFLEDLEEDEAIRK ddPTM_BT-474_Pertuzumab_2h_R1 3 QYQDFLEDLEEDEAIRK 17 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ;; 288.21 9.79E-37 527714000 447530 463720 391124 410550 443310 468980 465530 497996 582000 567450 FALSE TRUE 430040.0328 450495.1596 461808.8073 431738.5347 457569.4688 478463.0969 471227.2954 487712.2086 515933.7999 529016.1061 0.812905369 0.851571728 0.872957935 0.81611605 0.864944306 0.904439565 0.890761718 0.921923176 0.975270496 1 19.01295212 1.691195371 0.554339767 1.005118239 0.835280433 0.881976521 0.020144991 0.251760055 0.175504536 0.019937279 0.011933018 49.11287654 -1.691195371 -0.169837806 VGVNGFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGVNGFGR 8 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 143.02 0.0014148 11662500000 4177800 4865700 4145600 4735400 4658000 4325500 4648300 4255800 4684600 4339900 FALSE TRUE 4014526.957 4726935 4894802.138 4979794.561 4807828.8 4412964.574 4705187.286 4167916.243 4152823.847 4045954.707 0.992232303 1.168311398 1.209801516 1.230808282 1.188305146 1.090710325 1.162936223 1.030144068 1.026413825 1 21.94804874 1.691325773 4.105205502 1.016979466 1.154925398 0.461383761 0.064229908 0.162150695 6.387179388 0.036888444 0.017541218 49.12762537 -1.691325773 0.137945932 GLLGELILLQQQIQEHEEEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLGELILLQQQIQEHEEEAR 21 0 O60313-10;O60313-9;O60313-2;E5KLJ9;A0A2R8YE54 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ; 84.166 0.0030865 133060000 141409 199817 153716 169960 192734 216260 176705 153690 143689 163521 FALSE TRUE 135882.5799 194118.4148 181495.9006 178731.656 198933.4641 220632.9254 178867.5686 150516.2478 127378.0271 152445.577 0.891351409 1.273362065 1.190561931 1.172429266 1.304947431 1.447289778 1.173320815 0.987344144 0.835563941 1 17.21793477 1.691329563 3.38239354 0.918269428 1.223095357 0.446339587 0.137205552 0.177115662 4.657702533 0.080795616 0.037018698 49.12805415 -1.691329563 0.304825929 KVEEAEPEEFVVEK ddPTM_BT-474_Pertuzumab_2h_R1 7 KVEEAEPEEFVVEK 14 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;;; 175.26 3.87E-06 10714900000 11780850 10727480 8871520 9936720 9847370 10691940 10965890 12875080 14886000 14425320 FALSE TRUE 11320441.36 10421542.77 10474801.01 10449555.31 10164119.6 10908138.35 11100093.84 12609205.1 13196203.69 13448280.23 0.841776135 0.77493498 0.778895207 0.777017963 0.755793263 0.811117717 0.825391325 0.937607254 0.981255853 1 23.68091836 1.691388691 1.622560349 0.997716632 0.785061717 0.935940097 0.021839198 0.077127374 0.40296509 0.016912792 0.006427895 49.13474327 -1.691388691 -0.212654914 KS(ph)REDLSAQPVQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSREDLSAQPVQTK 14 2 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 KS(0.999)REDLS(0.001)AQPVQTK;KS(0.992)REDLS(0.008)AQPVQTK 156.73 4.33E-06 731060000 579850 500190 416630 435350 458990 454380 431490 639740 689970 660670 TRUE FALSE 557188.8209 485925.0709 491924.3089 457818.4657 473753.8302 463567.8749 436770.7037 626529.1454 611647.4982 615922.2324 0.904641514 0.788939001 0.798679254 0.743305634 0.769177999 0.752640269 0.709132875 1.017221189 0.99305962 1 19.23238868 1.691589673 6.784689842 1.003343253 0.779225753 0.811347513 0.049036639 0.053053586 5.16660036 0.025254368 0.012972105 49.15748703 -1.691589673 -0.2241175 LLPPVGTGRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPPVGTGRSPR 12 1 Q9NWZ5;Q9NWZ5-4;Q9NWZ5-3;Q9NWZ5-2 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 LLPPVGT(0.11)GRS(0.89)PR;LLPPVGT(0.06)GRS(0.94)PR 136.39 6.70E-05 469510000 639990 742170 444770 590170 645850 668450 604950 543080 511280 578890 TRUE FALSE 614978.4833 721004.0383 525149.8329 620628.7444 666624.3518 681966.517 612353.5591 531865.2082 453241.6379 539681.2647 1.139521646 1.335981227 0.973074048 1.149991273 1.235218629 1.263646826 1.134657805 0.985517273 0.839832078 1 19.04174808 1.691685263 2.975900965 0.918437911 1.181770772 0.558972459 0.096828202 0.15858623 3.174337543 0.058835959 0.026139746 49.168308 -1.691685263 0.26333286 YASICQQNGIVPIVEPEILPDGDHDLK ddPTM_BT-474_Pertuzumab_2h_R1 4 YASICQQNGIVPIVEPEILPDGDHDLK 27 0 H3BPS8;P04075;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;; 258.05 6.06E-53 8127523000 3948188 3333941 3051112 3438045 3232431 2712496 3720748 3814167 4644349 4285432 FALSE TRUE 3793888.448 3238860.267 3602515.81 3615482.914 3336405.079 2767344.528 3766283.627 3735403.119 4117141.972 3995175.874 0.949617381 0.810692788 0.901716451 0.904962142 0.835108437 0.692671516 0.942707842 0.934978393 1.030528343 1 21.92982758 1.691771115 2.183172496 1.005538661 0.852556176 0.440758693 0.070050612 0.263053186 2.675553763 0.048947024 0.019885937 49.17802855 -1.691771115 -0.152982485 TTQSMQDFPVVDS(ph)EEEAEEEFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TTQSMQDFPVVDSEEEAEEEFQK 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 TTQSMQDFPVVDS(1)EEEAEEEFQK;TTQSMQDFPVVDS(1)EEEAEEEFQK 211.87 2.63E-25 268970000 436620 399540 385610 367940 426800 406560 430310 471310 556980 512000 TRUE FALSE 419556.4077 388145.5104 455298.3048 386929.4275 440528.4096 414780.9218 435576.2625 461577.2838 493753.9655 477321.784 0.878980222 0.813173677 0.95386031 0.810625956 0.922917043 0.86897547 0.912542183 0.967014914 1.034425794 1 18.86460265 1.691804375 1.743676043 1.018223611 0.874324679 0.650695549 0.041972594 0.190359759 1.168728005 0.029478744 0.011336622 49.18179498 -1.691804375 -0.143898932 IYHPNIDEK ddPTM_BT-474_Pertuzumab_2h_R1 3 IYHPNIDEK 9 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ;; 142.43 0.00010435 831710000 2196970 2149000 1798650 2055640 2073070 1939000 2225280 2327800 2661640 2601710 FALSE TRUE 2111109.984 2087712.624 2123706.066 2161731.827 2139752.179 1978207.909 2252513.642 2279730.117 2359501.786 2425493.864 0.87038356 0.860737129 0.875576763 0.891254296 0.882192369 0.815589739 0.928682474 0.939903477 0.972792313 1 21.2098471 1.691991729 1.56516956 0.987036597 0.868671532 0.80207265 0.023587515 0.155417318 0.749266107 0.018548241 0.007022985 49.20301652 -1.691991729 -0.118365065 RNEVLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNEVLDR 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 96.668 0.020143 1841670000 1407100 1583110 1430300 2259900 1837770 1800920 1753040 1484130 1316250 1771490 FALSE TRUE 1352108.976 1537961.253 1688787.027 2376533.71 1896883.541 1837335.836 1774494.228 1453482.197 1166834.818 1651505.404 0.818713019 0.93124809 1.022574327 1.439010556 1.148578464 1.112521843 1.074470736 0.880095332 0.706528005 1 20.65535026 1.692175959 3.872062143 0.836367205 1.089393823 0.262029422 0.165203694 0.245875812 8.580090462 0.099385622 0.046822402 49.22389308 -1.692175959 0.253026618 GAGATSGS(ph)PPAGR ddPTM_BT-474_Pertuzumab_2h_R1 3 GAGATSGSPPAGR 13 0 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGAT(0.011)S(0.124)GS(0.865)PPAGR;GAGAT(0.009)S(0.08)GS(0.911)PPAGR;GAGATS(0.006)GS(0.994)PPAGR 137.39 6.43E-05 581940000 425453 457550 412087 524267 454016 440594 452648 432050 413564 461866 TRUE FALSE 408825.8264 444501.122 486560.2877 551324.4827 468619.837 449503.1126 458187.6416 423128.0165 366617.9485 430583.4044 0.949469539 1.032322931 1.130002417 1.280412754 1.088336968 1.043939706 1.06410892 0.98268538 0.851444679 1 18.71593319 1.692196598 2.142411148 0.923089141 1.094347511 0.360928636 0.086645075 0.313716212 3.058638899 0.064697921 0.026155749 49.22623241 -1.692196598 0.17125837 SDDDGFEIVPIEDPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDDDGFEIVPIEDPAK 16 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 ; 138.45 1.52E-05 57198000 177805 144766 147089 143498 147514 158258 160443 178279 202528 195423 FALSE TRUE 170856.184 140637.4154 173671.2543 150903.949 152258.9218 161458.0852 162406.5494 174597.4763 179537.8705 182186.8261 0.937807566 0.771940641 0.953259124 0.82829232 0.835729591 0.886222613 0.891428611 0.958343037 0.985460224 1 17.47505912 1.692455212 1.513532913 0.99798277 0.863846656 0.520016077 0.049317763 0.274663933 1.229109954 0.036367375 0.013733471 49.2555544 -1.692455212 -0.134136114 KLEPGGFGEKPVRPGGGDT(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEPGGFGEKPVRPGGGDTSPR 22 3 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065 Q5JSZ5 PRRC2B Protein PRRC2B 1 KLEPGGFGEKPVRPGGGDT(0.604)S(0.396)PR 73.805 0.014179 2220700000 1030000 962590 1002000 908650 954670 1073700 1036800 1210700 1289200 1335500 TRUE FALSE 989746.4613 935137.8757 1183083.689 955545.5354 985377.8276 1095410.95 1049488.669 1185698.622 1142855.421 1245045.395 0.794948092 0.751087373 0.950233376 0.76747847 0.791439277 0.879816072 0.842932051 0.952333647 0.917922692 1 20.24776691 1.692552707 0.800624249 0.991557189 0.811296227 0.553051323 0.055705604 0.437457213 0.547481275 0.04934599 0.021836255 49.26661303 -1.692552707 -0.180260962 TLLSESSSQSSKS(ph)PSLSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLLSESSSQSSKSPSLSSK 19 1 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 TLLSESSSQS(0.005)S(0.283)KS(0.708)PS(0.004)LSSK 163.71 1.52E-11 237160000 153920 154420 130650 101840 121350 163490 162810 157460 221670 200690 TRUE FALSE 147904.6362 150016.0928 154261.3613 107095.9746 125253.333 166795.8798 164802.5175 154208.396 196506.9509 187097.0875 0.790523456 0.801808808 0.824498998 0.572408561 0.669456348 0.891493727 0.880839566 0.824215908 1.050294013 1 17.51342758 1.692638532 0.917508052 1.015085566 0.743618281 0.556445269 0.088939428 0.448609862 0.717802299 0.084671926 0.034875477 49.27635008 -1.692638532 -0.271467285 EILS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EILSPLR 7 0 A0A140T9S5;Q9Y334-2;Q9Y334 A0A140T9S5 VWA7 von Willebrand factor A domain-containing protein 7 1 EILS(1)PLR 66.962 0.069706 216090000 211560 252580 326410 433860 455100 365090 312320 288200 214590 286870 TRUE FALSE 203292.0013 245376.6657 385399.548 456251.5666 469738.7048 372472.3699 316142.2656 282248.5693 190230.6428 267440.0394 0.760140485 0.917501606 1.441068992 1.705995735 1.756426248 1.392732258 1.182105216 1.055371402 0.71130203 1 18.02885595 1.692864462 2.152443669 0.864330538 1.345981128 0.274461081 0.299175538 0.403866229 3.977168072 0.234662597 0.09505854 49.30199141 -1.692864462 0.48165059 TPSNEHAAVWVPDSEATVCMR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSNEHAAVWVPDSEATVCMR 21 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 0 ;; 172.42 5.63E-12 922180000 853203 1037889 820082 1099702 978502 1019074 1018544 878025 925592 964418 FALSE TRUE 819858.8835 1008289.422 968289.06 1156457.752 1009976.405 1039680.375 1031009.246 859893.4769 820522.6766 899097.1098 0.911869112 1.121446628 1.076957149 1.286243432 1.123322936 1.15636049 1.146716228 0.956396665 0.912607401 1 19.77811742 1.693067208 5.426536342 0.949168172 1.124314104 0.40510306 0.089023763 0.139830449 9.490950386 0.0468179 0.023254208 49.32501301 -1.693067208 0.175145932 S(ph)LDLPSIGGSSVGKEDSEDALSVQFDMK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDLPSIGGSSVGKEDSEDALSVQFDMK 28 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.989)LDLPS(0.004)IGGS(0.004)S(0.004)VGKEDSEDALSVQFDMK 47.807 0.066274 17551000 9276.7 8969.7 9170.9 6912 8823.9 8914.4 7918.8 12149 13558 11827 TRUE FALSE 8914.156308 8713.892938 10828.28564 7268.729148 9107.728757 9094.655276 8015.712643 11898.1189 12018.95268 11025.94676 0.808470828 0.79030791 0.982073093 0.65923855 0.826026913 0.824841211 0.726986337 1.079101792 1.090060831 1 13.42861492 1.693116835 6.796299126 1.062713065 0.805563939 0.67270547 0.080873267 0.071746089 7.061009648 0.039208686 0.020157263 49.33064965 -1.693116835 -0.257149125 ADQDRLDLEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ADQDRLDLEER 11 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 157.56 2.78E-05 298750000 529260 797070 544250 877110 832120 962350 692470 594860 465010 601080 FALSE TRUE 508575.9341 774338.344 642608.0818 922377.7522 858885.8955 981809.3764 700944.655 582575.9331 412224.0143 560368.3162 0.907574392 1.381838198 1.146760199 1.646020529 1.532716734 1.752078674 1.250864181 1.039630394 0.735630482 1 19.09601586 1.693119631 2.763819543 0.87727576 1.403432855 0.442833062 0.236554171 0.213633866 3.641272213 0.152781642 0.06661879 49.33096725 -1.693119631 0.526157096 TLEENKEEEGSEPPKAETQEGEPIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLEENKEEEGSEPPKAETQEGEPIAK 26 2 Q9UNP9-2;Q9UNP9;Q9UNP9-3;E9PKY5;E9PEQ6;E9PIB0 Q9UNP9-2 PPIE Peptidyl-prolyl cis-trans isomerase E;Peptidyl-prolyl cis-trans isomerase 0 100.94 0.0025151 66188000 95404 66365 55041 43749 61171 55910 61034 76514 91263 72901 FALSE TRUE 91675.50621 64472.33518 64988.13308 46006.89113 63138.62077 57040.53851 61780.95235 74933.95916 80903.20685 67963.35034 1.348896218 0.948633857 0.956223211 0.676936774 0.929009833 0.839283794 0.909033355 1.102564232 1.190394624 1 16.05246935 1.693158795 5.442492495 1.111542377 0.929823065 0.150473283 0.163737339 0.24912017 17.00229411 0.086664947 0.043067364 49.33541609 -1.693158795 -0.181719312 AS(ph)PDMDGYPALK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPDMDGYPALK 12 0 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 AS(1)PDMDGYPALK;AS(1)PDMDGYPALK 105.65 0.0014258 71030000 281289 262407 306392 330340 270563 274408 374540 403040 452480 497340 TRUE FALSE 270295.9149 254923.4093 361763.8501 347388.887 279265.9046 279956.7178 379123.7326 394717.0832 401116.3674 463654.7188 0.58296811 0.549813037 0.780244081 0.749240486 0.60231438 0.60380431 0.817685483 0.851316868 0.865118699 1 18.82269131 1.693230565 0.992524429 0.970354087 0.645512497 0.705801646 0.077036576 0.303295966 0.563128484 0.072657462 0.029008377 49.34356975 -1.693230565 -0.32484159 LLHGDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLHGDIK 7 0 Q96KB5;Q96KB5-2;E5RFX4 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 0 134.44 0.0031745 426650000 1225400 1131700 1095500 1125400 1164700 1147200 1306900 1331800 1546200 1527900 FALSE TRUE 1177510.013 1099425.024 1293481.219 1183482.029 1202163.633 1170397.17 1322894.233 1304297.865 1370681.858 1424413.972 0.826662779 0.771843752 0.908079564 0.830855392 0.843970683 0.821669257 0.928728768 0.915673316 0.96227774 1 20.44193706 1.693268231 0.788417146 0.998167534 0.828871716 0.734292794 0.035434082 0.301617616 0.367455875 0.031565619 0.014105503 49.34784938 -1.693268231 -0.169295818 VKIEPGVDPDDTYNETPYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKIEPGVDPDDTYNETPYEK 20 1 Q9H4A4;A6NKB8;C9JMZ3 Q9H4A4 RNPEP Aminopeptidase B 0 ; 84.166 0.0025795 1788280000 988060 856000 743110 633220 802660 937140 865590 915710 1163750 1051010 FALSE TRUE 949445.5228 831587.7181 877406.5074 665900.5601 828478.2879 956089.6129 876183.3493 896800.2685 1031645.979 979824.1566 0.968995831 0.848711182 0.895473439 0.679612312 0.845537725 0.975776731 0.894225095 0.915266543 1.0528889 1 19.90216333 1.693303574 0.949818256 1.019598958 0.852229464 0.361310792 0.079012563 0.605133979 1.033050549 0.072274121 0.029342423 49.35186551 -1.693303574 -0.167369495 STSHTSDFNPNSGSDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 STSHTSDFNPNSGSDQR 17 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 0 185.25 5.90E-10 133030000 35626 66559 44903 76247 54159 67709 61769 47782 41274 64011 FALSE TRUE 34233.69653 64660.80249 53017.97096 80182.11681 55901.07342 69078.12237 62524.9475 46795.285 36588.74855 59675.47795 0.573664388 1.083540588 0.888438145 1.343635938 0.936751164 1.157562951 1.047749421 0.784162718 0.613128706 1 15.8648506 1.69332948 5.519518473 0.771998456 1.019292175 0.164716653 0.207201846 0.216923114 15.18850205 0.103432978 0.051513505 49.35480948 -1.69332948 0.247293719 VDYIMQLPVPMDAALNKEELLEYEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDYIMQLPVPMDAALNKEELLEYEEK 26 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 300.89 1.15E-70 166310000 280910 246690 226380 182310 245020 223130 252420 287610 359170 302390 FALSE TRUE 269931.7266 239654.6427 267291.9018 191719.0409 252901.2908 227641.8415 255509.1915 281670.753 318398.5274 281908.856 0.957514179 0.85011392 0.948150071 0.680074559 0.897103037 0.807501562 0.906353902 0.99915539 1.129437833 1 18.10486927 1.693377813 2.516982706 1.064627374 0.855065119 0.526240151 0.079820408 0.183118965 2.54653773 0.049934757 0.021194304 49.36030255 -1.693377813 -0.209562255 SS(ph)PSIICMPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPSIICMPK 10 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 S(0.384)S(0.615)PS(0.001)IICMPK;S(0.048)S(0.952)PS(0.001)IICMPK;S(0.078)S(0.921)PSIICMPK 171.63 4.16E-06 876820000 2107660 2080670 2005720 1887910 1839470 1761610 2067850 2554330 2930640 2871540 TRUE FALSE 2025290.317 2021331.329 2368198.221 1985345.261 1898638.223 1797230.961 2093156.967 2501582.193 2597966.033 2677048.038 0.756538653 0.75505979 0.884630454 0.741617346 0.709228298 0.671348043 0.781889954 0.934455474 0.970459251 1 21.3522116 1.69347155 3.045195344 0.977824167 0.754331924 0.781492847 0.051741384 0.1081314 2.268701092 0.034318933 0.015367622 49.37095754 -1.69347155 -0.223492243 EVSS(ph)RPST(ph)PGLSVVSGISATSEDIPNKIEDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.117)S(0.883)RPS(0.243)T(0.757)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.135)S(0.864)RPS(0.196)T(0.805)PGLSVVSGISATSEDIPNKIEDLR 211.77 2.61E-27 749180000 243003 207622 173257 177288 185427 206101 183226 236679 261091 221166 TRUE FALSE 233506.1741 201700.8238 204568.394 186437.8549 191391.4279 210268.5034 185468.3746 231791.4959 231453.0443 206186.2298 1.132501304 0.978245851 0.992153521 0.90422069 0.928245441 1.019798963 0.899518725 1.124185141 1.122543656 1 17.65358846 1.693904094 9.255903283 1.091312453 0.97653985 0.302592003 0.071015115 0.126827723 19.40093894 0.033474987 0.017929479 49.42015394 -1.693904094 -0.114772603 RPEGIER ddPTM_BT-474_Pertuzumab_2h_R1 1 RPEGIER 7 1 Q9H5V9-2;Q9H5V9 Q9H5V9-2 CXorf56 UPF0428 protein CXorf56 0 80.455 0.04789 85358000 38374 49158 45591 57259 56635 55473 51913 38265 36373 40686 FALSE TRUE 36874.30166 47756.06197 53830.30787 60214.14385 58456.71621 56594.70207 52548.32682 37474.81438 32244.08953 37930.30098 0.972159479 1.259047799 1.419190106 1.587494491 1.541161412 1.492070999 1.38539177 0.987991485 0.85008789 1 15.2110632 1.693920483 3.96811985 0.923701631 1.396659017 0.586989895 0.166668598 0.132406051 4.856941268 0.10099826 0.04786539 49.42201895 -1.693920483 0.472957386 VLT(ph)PEEQLADK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLTPEEQLADK 11 0 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 VLT(1)PEEQLADK;VLT(1)PEEQLADK 220.99 9.77E-11 340440000 796370 651240 802390 710650 678980 696270 898780 1040490 1286410 1277430 TRUE FALSE 765246.98 632667.2728 947399.7221 747326.7317 700820.0083 710349.0565 909779.5385 1019003.518 1140382.13 1190908.528 0.642574104 0.531247579 0.79552686 0.62752656 0.588475094 0.596476589 0.763937378 0.855652213 0.957573233 1 20.18363118 1.693992397 1.49026155 0.986286263 0.630988146 0.814649147 0.06684638 0.155733236 0.673305328 0.054046401 0.020410854 49.43020337 -1.693992397 -0.355298117 AGEVS(ph)PPIFQEDAALDLSVAAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGEVSPPIFQEDAALDLSVAAHR 23 0 Q9Y5P3-2;Q9Y5P3 Q9Y5P3-2 RAI2 Retinoic acid-induced protein 2 1 AGEVS(1)PPIFQEDAALDLSVAAHR;AGEVS(1)PPIFQEDAALDLSVAAHR 184.75 2.09E-17 92723000 76526 86423 60832 68504 72640 72503 73649 68952 72948 72008 TRUE FALSE 73535.27932 83958.30066 71825.6956 72039.49965 74976.53157 73969.06034 74550.33849 67528.1171 64667.24886 67130.83402 1.095402439 1.25066673 1.069935994 1.07312088 1.116871743 1.101864164 1.110523049 1.005918042 0.963301735 1 16.03468795 1.694077587 3.095869023 0.981055774 1.119242758 0.594503623 0.048401371 0.15048174 3.268016879 0.029727672 0.013376005 49.43990035 -1.694077587 0.138186984 SEEPAGQILSHLS(ph)SELK ddPTM_BT-474_Pertuzumab_2h_R1 3 SEEPAGQILSHLSSELK 17 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SEEPAGQILSHLS(0.921)S(0.079)ELK;SEEPAGQILSHLS(0.987)S(0.013)ELK;SEEPAGQILSHLS(0.886)S(0.114)ELK 226.16 1.39E-15 264491000 365350 346257 285454 302561 330551 328328 326795 362762 406740 370585 TRUE FALSE 351071.7181 336382.0894 337041.8877 318176.2095 341183.4731 334967.0171 330794.415 355270.8379 360568.5804 345484.9479 1.016170806 0.973651939 0.975561713 0.920955345 0.987549458 0.969556038 0.957478515 1.028325084 1.043659304 1 18.39826333 1.694249483 6.296102114 1.027023897 0.970442005 0.484388884 0.024649615 0.106837278 9.383690887 0.012427532 0.006317623 49.45947278 -1.694249483 -0.056581893 RDTDS(ph)DTQDANDSSCK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDTDSDTQDANDSSCK 16 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 RDT(0.04)DS(0.938)DT(0.022)QDANDSSCK 134.86 1.59E-05 152220000 114940 105460 78370 85157 82546 91788 89311 110290 121020 112880 TRUE FALSE 110448.0177 102452.3841 92533.20233 89551.96298 85201.16706 93644.01625 90404.01473 108012.473 107282.317 105234.5371 1.049541537 0.973562358 0.879304503 0.850975027 0.809631224 0.889860106 0.85907172 1.026397569 1.0194592 1 16.68324874 1.69450791 6.988476915 1.016685785 0.897809697 0.394594951 0.064159499 0.137471761 14.22175926 0.035115826 0.018138742 49.48891248 -1.69450791 -0.118876088 ETEFKDDSLPIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETEFKDDSLPIKR 13 2 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 113.72 0.0004496 285000000 502560 517820 389430 404070 484300 506930 467670 583260 660790 612780 FALSE TRUE 482919.3996 503052.2806 459808.6638 424924.1011 499877.9493 517180.4719 473393.4854 571215.4772 585779.8895 571275.8648 0.845334854 0.880576813 0.804880255 0.743815952 0.875020249 0.905307757 0.828660048 0.999894293 1.025388828 1 19.12382805 1.694537702 4.618172565 1.013009807 0.840505157 0.763650225 0.042776184 0.082861023 4.144784324 0.02497908 0.012130552 49.49230744 -1.694537702 -0.17250465 MEVDEAEKKEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MEVDEAEKKEEK 12 2 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 76.262 0.017768 290220000 663400 475150 394990 294380 460320 430760 461190 534430 684840 486010 FALSE TRUE 637473.5946 461599.1872 466373.4795 309572.9871 475126.6109 439470.2623 466834.1812 523393.8337 607099.8343 453092.1098 1.406940401 1.018775603 1.029312737 0.683245151 1.048631394 0.96993581 1.030329531 1.155159894 1.339903788 1 18.78944484 1.694687226 3.85141602 1.191523201 1.011074749 0.103327025 0.180761482 0.355270892 12.23843177 0.101682495 0.0479724 49.5093502 -1.694687226 -0.180448452 LNPEDIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNPEDIKK 8 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 80.688 0.039766 429780000 716790 732070 511390 529970 589750 673400 648010 732390 904400 753680 FALSE TRUE 688777.0543 711192.0804 603809.5488 557321.8152 608719.8443 687016.6094 655940.5402 717265.8906 801736.3036 702632.5823 0.98028055 1.01218204 0.859353187 0.793190964 0.866341613 0.977775052 0.933547001 1.020826402 1.141046293 1 19.42241095 1.694773734 2.163193771 1.074053653 0.910438941 0.454532008 0.069648267 0.265147486 2.636970611 0.052374141 0.021287581 49.51921305 -1.694773734 -0.163614713 GS(ph)PTRPNPPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSPTRPNPPVR 11 1 Q14195-2;Q14195;H0YBT4 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 1 GS(0.979)PT(0.021)RPNPPVR;GS(0.997)PT(0.003)RPNPPVR;GS(0.853)PT(0.147)RPNPPVR;GS(0.883)PT(0.117)RPNPPVR 109 0.0012039 1719520000 648340 699090 552690 795790 707170 731070 704290 637600 681230 659770 TRUE FALSE 623002.156 679152.6377 652573.3775 836860.8173 729916.7653 745852.7363 712909.3117 624433.3372 603899.6263 615083.1902 1.012874626 1.104163873 1.060951409 1.360565255 1.186696006 1.212604649 1.15904535 1.015201435 0.981817803 1 19.23042202 1.694845665 3.988360551 0.993348567 1.162731347 0.399308411 0.088702742 0.191601157 7.099528775 0.052393468 0.024873495 49.52741543 -1.694845665 0.16938278 KEVLASPDRLWGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 KEVLASPDRLWGSR 14 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KEVLAS(0.202)PDRLWGS(0.798)R 160.45 3.74E-06 3348000000 652200 738990 613560 608890 590260 694280 679190 606390 640650 674230 TRUE FALSE 626711.303 717914.7287 724443.9406 640314.8859 609246.249 708318.8173 687502.1304 593867.8346 567926.0978 628563.8016 0.997052807 1.142150927 1.152538436 1.018695134 0.969267157 1.126884519 1.093766661 0.944801201 0.903529755 1 19.26169967 1.694861701 5.768845313 0.942429245 1.073411175 0.443555354 0.062350452 0.129105343 9.81481489 0.033304837 0.016712424 49.52924422 -1.694861701 0.130981931 HLEEAFTSEHWLVR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLEEAFTSEHWLVR 14 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 ;; 262.64 8.28E-25 315027000 48629 78472 50290 91248 53108 54044 74684 48120 65710 51830 FALSE TRUE 46728.52492 76234.05539 59378.5217 95957.32022 54816.26705 55136.80671 75598.00513 47126.30518 58250.87628 48319.50793 0.967073692 1.57770761 1.228872649 1.985891916 1.134454166 1.141087918 1.564544184 0.975305983 1.205535378 1 15.56031814 1.695057962 1.007782835 1.019437985 1.395702422 0.152064332 0.289095159 0.869860584 1.662867741 0.244008045 0.096987977 49.5516319 -1.695057962 0.376264437 MPLPS(ph)PTESR ddPTM_BT-474_Pertuzumab_2h_R1 4 MPLPSPTESR 10 0 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 MPLPS(0.996)PT(0.004)ES(0.001)R;MPLPS(0.999)PT(0.001)ESR;MPLPS(1)PTESR;MPLPS(0.938)PT(0.062)ESR 192.5 7.09E-07 1786830000 1181410 1541530 1268460 1706800 1584340 1576970 1554980 1374510 1465050 1494050 TRUE FALSE 1135239.191 1497567.074 1497698.939 1794888.153 1635301.735 1608857.414 1574010.31 1346125.888 1298743.666 1392856.663 0.815043803 1.075176731 1.075271404 1.288638092 1.174063189 1.155077516 1.130059074 0.966449689 0.932431671 1 20.40961537 1.695103254 5.433569827 0.960702885 1.111835419 0.224133483 0.114274718 0.216434914 14.79796922 0.062422933 0.031051394 49.55679986 -1.695103254 0.151132534 AALSEEELEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AALSEEELEKK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 176.42 1.39E-05 1126470000 815950 750390 641110 621690 646650 726570 831030 1071470 1307830 1300230 FALSE TRUE 784061.7719 728989.6119 756972.8384 653775.4954 667450.0845 741261.7432 841200.3937 1049343.77 1159370.621 1212164.264 0.646827988 0.60139507 0.624480412 0.539345627 0.550626763 0.611519218 0.693965677 0.865677863 0.956446792 1 20.20915379 1.695125984 1.525230601 0.991255392 0.59009272 0.964289787 0.030273194 0.066007241 0.300328366 0.026231273 0.009931676 49.55939362 -1.695125984 -0.401162672 RLEAFEHPNVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEAFEHPNVVR 12 1 F8W1L8;F8VYH9;F8VTV8;F8VWX7;P11802;F8VYY1;Q96BE9 F8W1L8 CDK4 Cyclin-dependent kinase 4 0 ; 88.021 0.0066347 189638000 143722 166020 133761 154244 150683 141234 163644 143305 160095 170429 FALSE TRUE 138105.1853 161285.2722 157934.5882 162204.5513 155529.8555 144089.8482 165646.7242 140345.7017 141921.6868 158885.692 0.869210963 1.015102556 0.994013911 1.020888346 0.978878926 0.906877431 1.042552807 0.883312398 0.893231385 1 17.27762969 1.695330777 12.57806672 0.916641622 0.976835002 0.130218438 0.057546592 0.199930102 47.90181302 0.025651674 0.014057308 49.58276905 -1.695330777 0.06019338 NYQQNYQNSESGEKNEGS(ph)ESAPEGQAQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNSESGEKNEGS(0.988)ES(0.012)APEGQAQQR 135.15 4.07E-06 2009500000 51464 53132 38867 42109 48354 46892 41104 57647 59086 55366 TRUE FALSE 49452.72998 51616.72738 45891.13149 44282.25054 49909.35032 47840.18837 41607.04305 56456.5693 52378.80499 51616.01151 0.958088945 1.000013869 0.889087129 0.857916938 0.966935431 0.926847832 0.806087914 1.09378016 1.014778234 1 15.65553104 1.695358229 11.06059133 1.039559032 0.917608641 0.482362335 0.05739581 0.09908772 19.80552779 0.027355477 0.014879759 49.58590327 -1.695358229 -0.121950391 EKDEMVEQEFNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDEMVEQEFNR 12 1 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 139.86 5.40E-05 747310000 786840 744630 620730 659670 696830 711690 758140 856310 989870 960130 FALSE TRUE 756089.4229 723393.8815 732909.7191 693715.6478 719244.1698 726080.8594 767418.3441 838626.8993 877504.1075 895099.5399 0.844698706 0.808171437 0.818802475 0.775015087 0.803535403 0.811173313 0.857355311 0.936909094 0.980342485 1 19.7716886 1.695582235 1.54130438 0.995989494 0.807422384 0.952894762 0.016427164 0.071497719 0.332926089 0.013440306 0.005095281 49.61148591 -1.695582235 -0.18856711 IFQIHTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFQIHTSR 8 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 163.32 0.0003366 493390000 349230 557290 448200 757310 553230 523490 550750 475780 420660 592070 FALSE TRUE 335581.7055 541396.6348 529199.7102 796394.8599 571025.1454 534075.3265 557490.2432 465954.9767 372908.4404 551968.5715 0.607972488 0.98084685 0.958749714 1.44282646 1.034524744 0.967582855 1.010003598 0.844169398 0.675597234 1 19.0742266 1.69568424 4.129279534 0.814589708 1.015825364 0.111142719 0.202401985 0.34699959 13.81552712 0.114626822 0.054774951 49.62313983 -1.69568424 0.201235656 TPS(ph)PSPPCSSSPSPSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSPSPPCSSSPSPSGR 17 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 TPS(1)PSPPCSSSPSPSGR 184.87 6.41E-10 456020000 35891 46219 38278 39520 38524 42573 42083 38861 40482 44226 TRUE FALSE 34488.34004 44900.87937 45195.68609 41559.63194 39763.15945 43433.85523 42598.02434 38058.50677 35886.65307 41230.53363 0.836475714 1.089020088 1.096170292 1.007981908 0.964410497 1.053439076 1.033166942 0.923066073 0.870390216 1 15.33142551 1.695912657 5.943702979 0.922261445 1.017358447 0.185223269 0.075700289 0.199127085 15.99782158 0.037827778 0.019078462 49.64924595 -1.695912657 0.095097002 RLDPDAIPSPIQVIEDDR ddPTM_BT-474_Pertuzumab_2h_R1 3 RLDPDAIPSPIQVIEDDR 18 1 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 ;; 152.04 6.95E-08 217646000 68849 64267 69682 76156 64583 72225 72418 68331 71754 77350 FALSE TRUE 66158.30496 62434.16808 82275.08747 80086.42029 66660.37085 73685.43899 73304.27315 66919.94097 63608.78674 72111.0156 0.917450745 0.865806251 1.140950336 1.110598979 0.924413147 1.021833327 1.016547507 0.928012737 0.882095283 1 16.13793204 1.695990448 6.185253585 0.928739179 1.002105693 0.102164075 0.08409746 0.301441832 25.91210802 0.045048553 0.022858035 49.65813997 -1.695990448 0.073366514 TKADVTPPPDGSTTHNLEVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKADVTPPPDGSTTHNLEVSPK 22 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 TKADVTPPPDGSTTHNLEVS(1)PK;TKADVTPPPDGSTTHNLEVS(1)PK 236.77 1.01E-30 1648350000 831490 713790 687350 608400 725600 748710 757060 918590 1102790 984690 TRUE FALSE 798994.4515 693433.4081 811569.435 639799.5969 748939.583 763849.4292 766325.1267 899620.7955 977605.9025 917996.0692 0.870368053 0.755377317 0.884066351 0.696952436 0.815841819 0.832083551 0.834780401 0.979983276 1.064934737 1 19.80812845 1.696089933 2.431445061 1.03441321 0.805852293 0.759928811 0.052719248 0.112431573 1.445865322 0.032796885 0.013817125 49.66951655 -1.696089933 -0.228560917 RLS(ph)STSLASGHSVR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSSTSLASGHSVR 14 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3;M0QZ82 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 RLS(0.882)S(0.117)T(0.001)SLASGHSVR;RLS(0.743)S(0.244)T(0.012)SLASGHSVR;RLS(0.76)S(0.228)T(0.012)SLASGHSVR;RLS(0.923)S(0.074)T(0.003)SLASGHSVR 222.44 2.38E-12 7739280000 1011720 1262660 971380 1305920 1065910 1043570 1151930 1016950 1044820 1132630 TRUE FALSE 972180.8639 1226650.173 1146929.974 1373318.688 1100195.963 1064671.7 1166027.664 995949.6271 926216.4138 1055915.961 0.920699089 1.161692993 1.086194372 1.300594686 1.041935157 1.00829208 1.104280745 0.943209179 0.877168684 1 20.01006359 1.696301128 4.601797464 0.929425393 1.095306907 0.325207333 0.097720618 0.182375378 9.067103339 0.05260495 0.025570108 49.69367643 -1.696301128 0.165881513 ELLDLAMQNAWFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLDLAMQNAWFR 13 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 194.5 2.24E-06 156282000 149455 151785 133927 129433 149685 147750 154208 130071 134168 157619 FALSE TRUE 143614.1334 147456.2404 158130.5881 136113.0526 154499.754 150737.6062 156095.2436 127384.9884 118937.8111 146943.3247 0.977343705 1.003490568 1.076133185 0.926296263 1.051424107 1.025821394 1.062281964 0.866898776 0.809412822 1 17.1649003 1.696602343 7.116931451 0.879406408 1.017197922 0.469429884 0.060482698 0.095235777 10.26467524 0.028410415 0.014725331 49.72815464 -1.696602343 0.137791515 AS(ph)PPGDLQNPK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPPGDLQNPK 11 0 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK 138.42 6.07E-05 1957910000 1080380 1008870 1043340 1059470 1110020 1147460 1195910 1376940 1623210 1615850 TRUE FALSE 1038157.555 980098.0154 1231894.747 1114149.374 1145724.801 1170662.427 1210545.904 1348505.708 1438950.006 1506407.04 0.68916138 0.650619646 0.817770174 0.739607121 0.760567875 0.777122249 0.803598146 0.895180168 0.955219916 1 20.52268022 1.696624269 0.645156827 1.012429531 0.714934674 0.860272404 0.039738658 0.245751232 0.214918692 0.03847383 0.020004409 49.73066532 -1.696624269 -0.297494857 VIEPPAASCPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIEPPAASCPSSPR 14 0 A0A0A0MRX4;Q3MIN7;Q3MIN7-2 A0A0A0MRX4 RGL3 Ral guanine nucleotide dissociation stimulator-like 3 1 VIEPPAASCPS(0.006)S(0.994)PR;VIEPPAASCPS(0.008)S(0.992)PR 201.37 1.88E-08 880130000 665840 740720 543970 721240 697650 700220 661000 668820 666220 693270 TRUE FALSE 639818.2367 719595.3908 642277.4795 758463.2828 720090.5458 714378.9282 669089.5157 655008.6333 590593.4986 646314.2054 0.989949209 1.11338322 0.993754236 1.173520985 1.114149341 1.105312126 1.035238759 1.013452324 0.913786969 1 19.30187618 1.696635624 2.04802378 0.959722993 1.083402133 0.413935548 0.057084233 0.272025836 2.39204403 0.039429307 0.015812617 49.73196554 -1.696635624 0.123679139 GSDHSASLEPGELAELVR ddPTM_BT-474_Pertuzumab_2h_R1 7 GSDHSASLEPGELAELVR 18 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;;; 253.02 1.70E-30 5633195000 2360394 3595560 2864411 4101820 3311617 3626540 3446311 3052887 3001547 3538730 FALSE TRUE 2268147.193 3493018.149 3382073.786 4313515.422 3418138.168 3699871.124 3488487.985 2989843.817 2660823.968 3299048.665 0.68751553 1.058795581 1.025166383 1.307502817 1.036098135 1.121496376 1.057422408 0.906274542 0.806542806 1 21.65361863 1.69678673 4.690956105 0.889302385 1.055281817 0.145592828 0.149578352 0.2756679 14.24905488 0.080343063 0.039177162 49.74927203 -1.69678673 0.165979432 ESTQLSPADLTEGKPTDPSKLES(ph)PSFTGTGDTEIAHATEDLENNGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK 47 2 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 ES(0.001)T(0.001)QLS(0.021)PADLT(0.005)EGKPT(0.035)DPS(0.142)KLES(0.701)PS(0.029)FT(0.029)GT(0.029)GDT(0.006)EIAHATEDLENNGSK 128.34 5.76E-11 713700000 178000 159130 134200 124930 176950 164080 161990 204510 260600 194610 TRUE FALSE 171043.5632 154591.7682 158452.9253 131377.6523 182641.7575 167397.81 163972.4821 200286.797 231017.7805 181428.8914 0.942758135 0.85207911 0.87336104 0.724127515 1.006685077 0.922663468 0.903783741 1.103941029 1.273324104 1 17.46904469 1.696788974 3.534132659 1.15188944 0.884919369 0.581018147 0.092067575 0.127444221 3.654858882 0.051523074 0.023959772 49.74952903 -1.696788974 -0.266970072 ASS(ph)PFRR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSPFRR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.028)S(0.972)PFRR;AS(0.399)S(0.601)PFRR 121.85 0.0026939 4180200000 1507460 1676040 1268450 1578910 1411680 1646960 1595460 1513350 1657780 1684220 TRUE FALSE 1448546.797 1628240.98 1497687.132 1660397.734 1457087.969 1680262.66 1614985.717 1482098.794 1469595.764 1570146.279 0.922555316 1.036999547 0.953851976 1.057479648 0.927995046 1.070131288 1.028557491 0.943924024 0.935961053 1 20.58246754 1.696800427 8.864171809 0.955452602 1.001454516 0.108862734 0.051239866 0.218006457 32.47377771 0.023058229 0.01229809 49.750841 -1.696800427 0.046001915 FLIVAHDDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLIVAHDDGR 10 0 Q16658 Q16658 FSCN1 Fascin 0 ; 135.86 0.00013302 433340000 869980 1231520 906270 1345890 1175240 1111970 1061540 893050 799930 861120 FALSE TRUE 835980.2198 1196398.255 1070053.149 1415351.544 1213042.662 1134454.795 1074531.444 874608.2054 709125.3 802795.5754 1.041336357 1.490290047 1.332908628 1.763028581 1.511023104 1.413130354 1.338487003 1.089453196 0.883319891 1 19.61467314 1.69683579 2.044658589 0.939776803 1.442360065 0.57173683 0.171087602 0.207830713 1.820645528 0.122288255 0.049029971 49.7548923 -1.69683579 0.502583262 EAFLNTEDKGDSLDSVEALIK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAFLNTEDKGDSLDSVEALIK 21 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 162.85 1.65E-11 38695000 74280 66088 55993 55977 60030 65607 64252 81926 96502 85363 FALSE TRUE 71377.05548 64203.23495 66112.18066 58865.97968 61960.91947 66933.61849 65038.3352 80234.19947 85547.49753 79581.28798 0.896907518 0.806762954 0.830750323 0.739696242 0.778586538 0.84107232 0.81725663 1.008204334 1.074970005 1 16.28014163 1.696889314 3.694972838 1.039598248 0.811474348 0.841963124 0.042135949 0.068704444 2.164710664 0.024251154 0.01137825 49.76102455 -1.696889314 -0.2281239 VAGTGEGGLEEMVEELNSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 VAGTGEGGLEEMVEELNSGK 20 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;; 285.73 9.24E-45 260180000 181930 168560 144255 164012 156623 174631 164211 185533 203270 193873 FALSE TRUE 174819.9745 163752.8338 170325.0874 172476.679 161660.921 178162.1585 166220.6633 181701.6787 180195.6418 180741.809 0.967235945 0.906004176 0.94236684 0.954271067 0.894430137 0.985727428 0.91965807 1.005310723 0.996978191 1 17.46357074 1.696959528 6.833934947 1.000622863 0.938216792 0.54518492 0.025981803 0.090942105 9.227742943 0.012089099 0.006229412 49.76907034 -1.696959528 -0.062406071 YMWDSQSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YMWDSQSGR 9 0 Q9UKD2 Q9UKD2 MRTO4 mRNA turnover protein 4 homolog 0 ; 126.24 0.0011143 517350000 416540 449560 413770 484200 444040 403260 474460 406010 438970 478850 FALSE TRUE 400261.1563 436738.989 488547.4433 509189.62 458322.9499 411414.1935 480266.5834 397625.7516 389139.9659 446417.063 0.896608104 0.978320555 1.094374485 1.140614153 1.026669874 0.921591551 1.07582488 0.890704645 0.871695995 1 18.76803265 1.696997784 8.245307267 0.911979382 1.021543682 0.249744389 0.077367009 0.158244997 21.2789375 0.039331844 0.020800339 49.77345456 -1.696997784 0.1095643 QEASES(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QEASESPVK 9 0 Q01167;Q01167-2;E9PPI7;Q01167-3 Q01167 FOXK2 Forkhead box protein K2 1 QEAS(0.001)ES(0.999)PVK 124.33 0.0014908 0 305790 289100 247740 286880 265030 258090 272720 322650 347940 347050 TRUE FALSE 293839.3887 280855.1511 292512.1289 301685.9112 273554.9306 263308.7566 276057.6289 315987.1647 308443.3099 323543.9944 0.908189903 0.868058613 0.904087648 0.932441697 0.845495313 0.813826748 0.853230577 0.976643579 0.953327261 1 18.30360237 1.697116658 6.25901293 0.973794857 0.874698258 0.650399103 0.034044392 0.093525887 8.241126926 0.018974904 0.009650524 49.7870802 -1.697116658 -0.0990966 NQESLGS(ph)PHICDLGK ddPTM_BT-474_Pertuzumab_2h_R1 4 NQESLGSPHICDLGK 15 0 A4D1E1;A0A087WUA7 A4D1E1 ZNF804B Zinc finger protein 804B 1 NQES(0.005)LGS(0.995)PHICDLGK;NQESLGS(1)PHICDLGK;NQES(0.004)LGS(0.996)PHICDLGK;NQES(0.001)LGS(0.999)PHICDLGK 103.08 0.001574 3065610000 3805840 3552190 3152110 2940210 3250210 3475590 3632570 4109970 5294950 4251880 TRUE FALSE 3657103.565 3450885.019 3721766.395 3091954.59 3354755.956 3545868.811 3677026.478 4025097.683 4693889.474 3963896.38 0.92260322 0.870579018 0.938916167 0.780029116 0.846327864 0.894541247 0.927629314 1.015439683 1.184160489 1 21.91848782 1.697144926 2.215748103 1.093538718 0.874426218 0.680024412 0.059481959 0.148228889 1.552271009 0.039593955 0.016244551 49.79032095 -1.697144926 -0.2191125 NCSASTS(ph)QER ddPTM_BT-474_Pertuzumab_2h_R1 3 NCSASTSQER 10 0 H7BZV4;A0A0C4DG62;Q66PJ3-4;Q66PJ3-3;F8WEP2 H7BZV4 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 NCSAST(0.004)S(0.996)QER;NCSAS(0.002)T(0.006)S(0.993)QER;NCS(0.044)AS(0.033)T(0.012)S(0.911)QER 143.25 3.60E-05 473330000 1128160 1136540 920390 1095960 1040010 1080330 1036310 1169290 1255710 1165730 TRUE FALSE 1084070.26 1104126.992 1086724.947 1152522.627 1073462.866 1102175.013 1048992.672 1145143.753 1113167.065 1086774.069 0.997512078 1.01596737 0.9999548 1.060498829 0.987751638 1.014171247 0.965235279 1.053709125 1.024285633 1 20.05162062 1.697320146 25 1.029737127 1.007745122 0.104052478 0.025986073 1.136747507 680.5986849 0.01154201 0.006400631 49.81041335 -1.697320146 -0.021992005 VIEHGEQNR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIEHGEQNR 9 0 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 0 64.297 0.088436 0 116350 127240 79557 112170 93504 110110 104950 97441 99615 100820 FALSE TRUE 111802.9134 123611.2398 93934.71964 117959.1071 96511.64108 112336.4996 106234.4095 95428.8093 88307.12282 93991.3716 1.189501882 1.315133907 0.999397264 1.254999317 1.026813839 1.195178852 1.13025704 1.015293294 0.939523717 1 16.5202407 1.697342557 2.706947388 0.970063314 1.16121866 0.447308337 0.089909393 0.211185348 3.4246454 0.05404797 0.023532969 49.81298385 -1.697342557 0.191155346 LTVENS(ph)PKQEAGISEGQGTAGEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTVENSPKQEAGISEGQGTAGEEEEK 26 1 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LT(0.001)VENS(0.999)PKQEAGISEGQGTAGEEEEK 201.63 2.95E-25 215630000 296200 214150 174680 110660 206590 214500 181720 233560 266050 194100 TRUE FALSE 284624.1765 208042.6517 206248.5617 116371.1759 213235.155 218837.337 183943.9437 228736.9044 235849.1194 180953.4341 1.572913926 1.149702699 1.13978805 0.643100124 1.178397945 1.209357192 1.016526404 1.264065009 1.303369127 1 17.46525896 1.697461516 12.51901701 1.212090412 1.117331276 0.008965969 0.226362161 0.530797498 132.1003145 0.107585379 0.058947851 49.82663018 -1.697461516 -0.094759135 DVFSPIGER ddPTM_BT-474_Pertuzumab_2h_R1 1 DVFSPIGER 9 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 99.136 0.012892 185690000 196970 262450 191820 233320 213120 257940 237810 204580 230880 206450 FALSE TRUE 189272.1946 254965.183 226486.141 245361.6732 219975.1984 263155.7235 240720.3899 200355.3515 204671.4703 192466.9576 0.983400979 1.324721844 1.17675337 1.274824916 1.142924485 1.367277411 1.250710215 1.040985705 1.06341095 1 17.55425126 1.697474275 5.640893925 1.037926516 1.224871332 0.401692916 0.101532731 0.136652479 10.06543317 0.049597725 0.024843923 49.82809404 -1.697474275 0.186944816 S(ph)EDEDS(ph)LEEAGSPAPGPCPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEDEDSLEEAGSPAPGPCPR 20 0 Q8TBB5-3;Q8TBB5;Q8TBB5-2 Q8TBB5-3 KLHDC4 Kelch domain-containing protein 4 2 S(1)EDEDS(1)LEEAGSPAPGPCPR;S(1)EDEDS(1)LEEAGSPAPGPCPR 373.26 4.50E-112 312670000 541910 496730 418040 496310 501790 482020 543600 597800 668610 678880 TRUE FALSE 520731.5581 482563.7467 493589.1272 521924.6186 517930.5311 491766.7747 550252.7394 585455.2211 592712.1958 632898.8529 0.822772163 0.762465826 0.779886272 0.824657236 0.818346452 0.777006898 0.869416553 0.925037577 0.936503824 1 19.27161543 1.697487175 1.070994004 0.987944462 0.79342851 0.897892286 0.02396708 0.137997088 0.297196678 0.020909369 0.008169033 49.82957404 -1.697487175 -0.194515953 AQDPDQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQDPDQLR 8 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2;E9PKK8;E9PPK9;E9PQF2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 123.72 0.003107 552320000 346760 415060 340130 421360 399640 391540 388050 372580 346590 437480 FALSE TRUE 333208.2358 403222.8952 401599.0572 443106.4401 412494.7835 399457.2071 392799.072 364886.0928 307246.5562 407849.0899 0.816989038 0.988657092 0.984675624 1.086447049 1.011390717 0.979424049 0.963099052 0.894659573 0.753333926 1 18.63767591 1.697561802 3.33014804 0.862976326 0.983560426 0.200853778 0.083863401 0.271266572 6.850398547 0.048095089 0.022098903 49.83813726 -1.697561802 0.120584101 LKPDEGGEVPVLNVSYKPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKPDEGGEVPVLNVSYKPQK 20 2 P61221;D6R9I9 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 116.98 4.89E-05 748660000 146260 146580 101550 109840 137400 147850 126000 183610 208840 186440 FALSE TRUE 140543.9975 142399.6819 119902.344 115508.8556 141819.5958 150839.6283 127542.0257 179818.3893 185133.3587 173812.2527 0.808596605 0.819272978 0.689838271 0.664561064 0.815935549 0.867830811 0.733791914 1.034555312 1.065134108 1 17.40717026 1.69760841 5.559440268 1.039261435 0.771439681 0.793947275 0.060989678 0.066266028 4.755465188 0.034184009 0.017088308 49.84348611 -1.69760841 -0.267821754 LSLDGNPK ddPTM_BT-474_Pertuzumab_2h_R1 4 LSLDGNPK 8 0 B8ZZZ7;Q9NUQ6;Q9NUQ6-4;Q9NUQ6-3;F8VT91 B8ZZZ7 SPATS2L SPATS2-like protein 0 ;;; 89.298 0.014004 5430240000 5876830 10230760 7933730 13640700 11451630 12497200 10119610 7176440 5145240 8430770 FALSE TRUE 5647156.986 9938988.742 9367531.496 14344698.16 11819982.08 12749901.95 10243456.81 7028244.006 4561173.926 7859746.439 0.718490988 1.264543178 1.191836349 1.825084088 1.503863028 1.622177261 1.303280824 0.894207474 0.580320747 1 22.90605134 1.69776613 3.50213223 0.777584788 1.376851545 0.404162535 0.291350245 0.193388267 5.433793907 0.174433504 0.081043996 49.86159076 -1.69776613 0.599266757 LS(ph)PGESAYQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LSPGESAYQK 10 0 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 LS(0.997)PGES(0.003)AYQK;LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK 241.92 2.56E-12 1154100000 1736970 1647010 1479830 1611760 1642290 1557670 1515520 1654230 1577850 1552350 TRUE FALSE 1669087.292 1600038.887 1747268.2 1694943.127 1695115.749 1589167.155 1534067.387 1620069.572 1398739.083 1447207.952 1.153315451 1.105603991 1.20733734 1.171181463 1.171300743 1.098091779 1.060018628 1.119444908 0.966508705 1 20.46484081 1.697816247 0.782220067 0.989591095 1.1611531 0.700997207 0.040207271 0.352017928 0.422522523 0.037072384 0.016679455 49.86734505 -1.697816247 0.171562005 SKDQDDQKPGPSER ddPTM_BT-474_Pertuzumab_2h_R1 4 SKDQDDQKPGPSER 14 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;; 136.01 1.66E-05 3116956000 1253982 1192654 1040871 931498 1028877 1057167 1134613 1311822 1565835 1366877 FALSE TRUE 1204974.997 1158640.676 1228979.544 979572.7234 1061971.763 1078543.641 1148498.733 1284732.417 1388087.975 1274297.203 0.945599656 0.909238969 0.964437135 0.768716058 0.833378399 0.846383119 0.901280118 1.008188995 1.089296886 1 20.28127036 1.69786228 3.029265064 1.046003975 0.876285207 0.603657297 0.056765729 0.151736077 3.130359037 0.036241768 0.016281307 49.87263107 -1.69786228 -0.169718768 KAVIFCLSADKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAVIFCLSADKK 12 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 155.98 4.09E-05 2343100000 4039700 3715600 2968600 2896100 3127200 2721500 3690300 3848500 4692100 4375900 FALSE TRUE 3881824.058 3609634.726 3505092.056 3045568.068 3227789.228 2776530.595 3735462.995 3769027.13 4159472.479 4079516.395 0.951540252 0.884819272 0.859193031 0.746551251 0.791218594 0.680602877 0.91566319 0.923890669 1.019599402 1 21.95996671 1.69791124 2.104675744 1.000319294 0.820574969 0.489092493 0.074294919 0.260046831 2.428254401 0.055492081 0.02245123 49.87825377 -1.69791124 -0.179744325 RDEMDELEGFQQQELSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDEMDELEGFQQQELSK 17 1 Q92805;R4GNH1 Q92805 GOLGA1 Golgin subfamily A member 1 0 157.88 1.45E-08 269760000 187360 164980 160760 203430 181110 170860 188220 173620 183740 201810 FALSE TRUE 180037.7641 160274.9319 189812.9081 213929.0467 186935.5676 174314.9063 190523.4927 170034.6863 162882.6055 188141.2289 0.956928819 0.851886282 1.008885236 1.137066277 0.993591722 0.926510937 1.012662104 0.9037609 0.865746474 1 17.52145651 1.698006207 7.76626074 0.914179395 0.983781996 0.117015829 0.075047227 0.251605785 31.27430996 0.039122752 0.020535253 49.88916178 -1.698006207 0.069602601 EDKAPQVDVDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDKAPQVDVDK 11 1 P41250 P41250 GARS Glycine--tRNA ligase 0 119.01 0.00090017 0 280290 274340 251320 234360 256760 264080 263400 341290 400400 347010 FALSE TRUE 269335.9569 266516.0918 296739.1146 246455.3477 265018.9186 269419.8785 266623.568 334242.2422 354948.2706 323506.7036 0.832551394 0.823834835 0.917258008 0.761824546 0.819206884 0.832810806 0.824167057 1.033184903 1.097189847 1 18.30343608 1.698049027 4.483983499 1.053679202 0.829898923 0.845304329 0.041776373 0.057628481 2.719675158 0.022036992 0.010686958 49.89408087 -1.698049027 -0.223780278 SGMSHEEDQLIPNLYR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGMSHEEDQLIPNLYR 16 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 171.08 5.05E-09 1137300000 533730 615890 457170 586410 604320 601350 580680 546340 579260 588620 FALSE TRUE 512871.2415 598325.4202 539790.7887 616674.6904 623758.5016 613509.709 587786.5355 535057.8881 513504.8333 548752.2431 0.934613476 1.090337994 0.983669398 1.123776163 1.136685106 1.118008567 1.071132816 0.975044558 0.935768081 1 19.06579541 1.698085831 4.553002383 0.964384136 1.07046884 0.331384957 0.061637708 0.185348135 9.025157036 0.033881683 0.016468238 49.89830936 -1.698085831 0.106084705 IILHNTMESLLER ddPTM_BT-474_Pertuzumab_2h_R1 2 IILHNTMESLLER 13 0 O15498 O15498 YKT6 Synaptobrevin homolog YKT6 0 ; 172.57 2.32E-05 754370000 546230 711570 556860 644790 670980 590110 717580 571110 733500 613810 FALSE TRUE 524882.7277 691276.7203 657496.9893 678067.6892 692562.6811 602042.4285 726361.9587 559316.3789 650236.1551 572236.102 0.917248538 1.208027103 1.148995995 1.184943919 1.210274358 1.052087463 1.269339624 0.977422391 1.136307466 1 19.12625099 1.698310785 14.27119327 1.043163149 1.145253223 0.181790289 0.100345641 0.225557792 69.26719453 0.043606456 0.024016881 49.92416209 -1.698310785 0.102090074 EVDEISPEDDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVDEISPEDDQR 12 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 ; 199.59 3.95E-07 374160000 266760 278090 218780 269170 273960 268870 259180 257640 255930 275330 FALSE TRUE 256334.7243 270159.1455 258318.4127 283061.896 282772.1722 274306.7356 262351.9224 252319.644 226877.8993 256681.6539 0.998648405 1.052506642 1.00637661 1.102774163 1.101645435 1.06866514 1.022090665 0.983006149 0.883888256 1 17.96962066 1.698322724 2.428801823 0.941169051 1.055827309 0.53082875 0.042137562 0.191245601 2.448376822 0.027900678 0.01177818 49.92553461 -1.698322724 0.114658258 IKDPDASKPEDWDER ddPTM_BT-474_Pertuzumab_2h_R1 10 IKDPDASKPEDWDER 15 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;;;; 156.49 5.57E-06 79678824700 81272970 74619436 65871430 63842204 68339125 73130665 76162000 86884591 105948629 93641531 FALSE TRUE 78096732.48 72491362.75 77775862.7 67137107.8 70537315.02 74609417.15 77094093.34 85090393.83 93921784.81 87299106.7 0.894587991 0.830379204 0.890912469 0.769046905 0.80799584 0.854641244 0.883102889 0.974699479 1.075861923 1 26.37946356 1.698430135 2.033140409 1.038538074 0.838862601 0.804765333 0.03936902 0.120115451 1.038133547 0.027959333 0.011210438 49.93788391 -1.698430135 -0.199675473 QFT(ph)DVNRFTLRCMVCQK ddPTM_BT-474_Pertuzumab_2h_R1 1 QFTDVNRFTLRCMVCQK 17 2 Q5VVQ6-2;Q5VVQ6 Q5VVQ6-2 YOD1 Ubiquitin thioesterase OTU1 1 QFT(0.5)DVNRFT(0.5)LRCMVCQK 63.037 0.076475 697430000 332930 227770 248870 214080 280380 263820 266950 338540 423080 320590 TRUE FALSE 319918.7275 221274.2226 293846.3451 225128.6945 289398.6773 269154.6212 270217.014 331549.0307 375053.7321 298876.1537 1.070405663 0.740354223 0.983170927 0.753250775 0.96828962 0.900555691 0.904110316 1.109319116 1.254880081 1 18.18918827 1.698531648 4.036513603 1.143591452 0.895383205 0.451128912 0.110032058 0.138560416 5.253560797 0.055491349 0.02648838 49.94955777 -1.698531648 -0.248208247 TIEELSNAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TIEELSNAR 9 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;; 78.113 0.030692 9335230000 2456570 4397130 3421290 5749530 4736450 4872850 3866460 2704720 1752160 2432810 FALSE TRUE 2360564.529 4271728.158 4039593.209 6046263.932 4888802.216 4971382.366 3913778.894 2648866.587 1553262.142 2268033.612 1.04079786 1.883450111 1.781099358 2.665861697 2.155524588 2.191935049 1.725626496 1.167913285 0.684849702 1 21.11301059 1.698595487 2.432844909 0.852769567 1.981730272 0.570263627 0.393983979 0.187567935 2.409400922 0.269560989 0.113883582 49.95690071 -1.698595487 1.128960705 GQSQTS(ph)PDHR ddPTM_BT-474_Pertuzumab_2h_R1 6 GQSQTSPDHR 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQS(0.252)QT(0.252)S(0.496)PDHR;GQS(0.001)QT(0.064)S(0.936)PDHR;GQS(0.019)QT(0.029)S(0.952)PDHR;GQS(0.179)QT(0.104)S(0.717)PDHR;GQSQT(0.009)S(0.991)PDHR;GQSQT(0.014)S(0.986)PDHR 145.83 3.12E-05 453785000 356496 393468 324473 432387 386054 373751 402724 340017 358311 391891 TRUE FALSE 342563.7422 382246.6779 383112.489 454702.5449 398471.7775 381308.5013 407652.6568 332995.5301 317637.0374 365347.8735 0.937637159 1.04625401 1.048623837 1.244574221 1.090664012 1.043686111 1.115793156 0.91144784 0.869409843 1 18.47891128 1.69880186 6.443180131 0.918098738 1.078917959 0.426060996 0.078420089 0.122298235 11.40365891 0.040798272 0.020855969 49.98064542 -1.69880186 0.160819221 FKEPPAYGPMCDILWSDPLEDFGNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKEPPAYGPMCDILWSDPLEDFGNEK 26 1 Q08209-3;Q08209-2;Q08209;E7ETC2;Q08209-5 Q08209-3 PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 0 158.18 1.90E-11 95248000 121500 125350 103860 118570 122150 110440 129680 152490 177960 174460 FALSE TRUE 116751.6457 121775.1407 122629.8124 124689.4119 126079.0657 112673.1725 131267.0626 149341.0282 157758.7269 162643.6688 0.717837015 0.748723523 0.753978395 0.766641658 0.775185819 0.692760888 0.807083753 0.918209908 0.969965373 1 17.31135514 1.698878202 2.013075169 0.984202098 0.745361774 0.942015424 0.024718919 0.064030204 0.541156042 0.017729096 0.007092805 49.98943198 -1.698878202 -0.238840324 ASEPLLS(ph)PPPFGESR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASEPLLSPPPFGESR 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR 292.27 6.34E-44 1166540000 283303 337618 282533 375207 387177 353539 305192 304692 278076 283613 TRUE FALSE 272231.2056 327989.4652 333592.998 394571.4782 399630.8998 360687.8008 308927.031 298400.0037 246509.9783 264403.6389 1.02960461 1.240487713 1.261680813 1.492307292 1.511442511 1.364155964 1.168391752 1.128577523 0.932324454 1 18.01238251 1.698885863 1.727909696 0.975122907 1.323421951 0.506558997 0.133272416 0.298030369 1.789318599 0.110631561 0.042736205 49.99031377 -1.698885863 0.348299044 VMES(ph)MLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VMESMLK 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 VMES(1)MLK;VMES(1)MLK 59.641 0.068128 950270000 589000 833030 650530 968630 852390 905310 788890 650140 554780 733220 TRUE FALSE 565981.2288 809272.8 768095.242 1018621.11 879807.8985 923615.9885 798544.6718 636714.3818 491803.7002 683558.3563 0.827992553 1.183911794 1.12367179 1.490174322 1.287099909 1.351188205 1.168217263 0.931470409 0.719475807 1 19.38270498 1.698980252 3.300880531 0.851612332 1.223577538 0.420954975 0.173371368 0.19119121 4.729597066 0.103888962 0.047709035 50.00117978 -1.698980252 0.371965206 MAEDEAETIGNLIEECGGLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MAEDEAETIGNLIEECGGLEK 21 0 O00629;H7C4F6 O00629 KPNA4 Importin subunit alpha-3 0 174.2 3.31E-12 38417000 86351 81149 58523 70779 76576 79659 74416 93048 102970 98198 FALSE TRUE 82976.30745 78834.70997 69099.40794 74431.91267 79039.13658 81269.75956 75326.72527 91126.52628 91281.27729 91546.96199 0.906379695 0.861139553 0.75479739 0.813046234 0.863372578 0.887738465 0.82282059 0.995407431 0.997097832 1 16.48222439 1.699296092 5.456095377 0.998417987 0.84259242 0.753966659 0.040054879 0.075683093 5.26968915 0.022437449 0.011198258 50.03755632 -1.699296092 -0.155825568 S(ph)SPPLRTPDVLESSGPAVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPPLRTPDVLESSGPAVR 19 1 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 S(0.564)S(0.436)PPLRTPDVLESSGPAVR;S(0.571)S(0.429)PPLRTPDVLESSGPAVR;S(0.572)S(0.428)PPLRTPDVLESSGPAVR;S(0.851)S(0.149)PPLRTPDVLESSGPAVR 182.02 1.83E-14 2321400000 275215 315588 185567 214175 239460 280090 227663 214597 189038 211635 TRUE FALSE 264459.2935 306587.7392 219103.0848 225228.5974 247162.4484 285753.6117 230449.2079 210165.497 167579.1988 197300.7729 1.340386505 1.553910482 1.110502922 1.141549493 1.252719108 1.44831471 1.168009656 1.065203617 0.849359059 1 17.59003708 1.699372564 2.219067072 0.932415255 1.298775226 0.570254616 0.131515517 0.211418666 2.217656941 0.094285909 0.038788891 50.04636783 -1.699372564 0.366359971 ADGTTPFYADSTAET(ph)Y(ph)GKIVHY(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 ADGTTPFYADSTAETYGKIVHYK 23 1 Q09013-5 Q09013-5 DMPK Myotonin-protein kinase 3 ADGT(0.003)T(0.003)PFY(0.011)ADS(0.012)T(0.012)AET(0.987)Y(0.986)GKIVHY(0.986)K 40.012 0.072583 582200000 52140 130080 89434 166590 148140 172740 114740 66635 35881 58259 TRUE FALSE 50102.31116 126370.2458 105596.7132 175187.7299 152905.0576 176232.9212 116144.2224 65258.96396 31807.93931 54313.06604 0.922472525 2.326700645 1.944223019 3.225517222 2.815253654 3.244761049 2.138421395 1.20153342 0.58564065 1 15.72901169 1.699535895 2.967060513 0.821217087 2.4561237 0.523077973 0.640749499 0.178164688 3.508348643 0.405093666 0.18132191 50.06519308 -1.699535895 1.634906613 DRNVIPDT(ph)PPSTPLVPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 DRNVIPDTPPSTPLVPSR 18 1 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 DRNVIPDT(0.995)PPS(0.002)T(0.002)PLVPSR;DRNVIPDT(0.816)PPS(0.082)T(0.102)PLVPSR;DRNVIPDT(1)PPSTPLVPSR 102.66 0.00090226 807427000 298481 350929 277400 332959 296109 326649 309134 280687 272513 294409 TRUE FALSE 286816.0325 340920.8485 327532.3507 350143.0539 305633.6149 333254.0666 312917.2744 274890.7154 241578.4667 274468.4162 1.044987385 1.242113221 1.193333482 1.275713464 1.113547486 1.214180018 1.140084818 1.001538608 0.880168546 1 18.06628062 1.699891862 2.646314116 0.938820496 1.184853701 0.688017995 0.067152041 0.123938698 1.908233901 0.040274992 0.017468571 50.10624546 -1.699891862 0.246033206 AVSELDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVSELDAK 8 0 F8W8M5;E7EQI0;P07101-6;P07101-5;P07101-3;P07101-4;P07101-2;P07101 F8W8M5 TH Tyrosine 3-monooxygenase 0 ; 75.38 0.038541 900350000 981470 1394240 1172840 1848950 1536970 1745650 1446160 1177950 961530 1430870 FALSE TRUE 943113.0673 1354477.64 1384798.278 1944374.531 1586408.036 1780948.239 1463858.539 1153624.921 852381.1455 1333955.9 0.707004682 1.015384122 1.038113987 1.457600308 1.189250736 1.335087793 1.097381509 0.864814887 0.6389875 1 20.34727954 1.699946699 3.765526023 0.802267517 1.138512837 0.28741113 0.205271414 0.230740424 7.543948275 0.120502628 0.056908281 50.11257268 -1.699946699 0.33624532 DFIS(ph)RFEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFISRFEEK 9 1 F6XZQ7 F6XZQ7 GSTM2 1 DFIS(1)RFEEK 66.435 0.038601 165360000 156270 315490 229010 503320 401200 366190 302020 207540 118080 207940 TRUE FALSE 150162.7956 306492.5341 270397.2013 529296.4055 414104.9624 373594.6127 305716.2111 203254.2265 104676.0534 193856.0386 0.774609843 1.581031658 1.394835071 2.730358102 2.13614683 1.927175524 1.577027021 1.048480243 0.539967979 1 17.56462615 1.699970158 2.570977629 0.771476742 1.790747484 0.407897465 0.487744331 0.250048525 3.616589424 0.332232198 0.142895685 50.11527969 -1.699970158 1.019270742 DSEHIDDETR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSEHIDDETR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 79.693 0.02624 42585000 45190 47325 34704 38061 43165 40532 38961 48589 49613 50991 FALSE TRUE 43423.92484 45975.33734 40975.78479 40025.33277 44553.44143 41351.58481 39437.81637 47585.62017 43981.14023 47537.33415 0.91346992 0.967141683 0.861970607 0.841976806 0.937230541 0.869875973 0.829617754 1.001015749 0.925191558 1 15.53677338 1.69997216 10.0991189 0.97144378 0.890140895 0.442484375 0.044433465 0.11366056 21.50142126 0.021473747 0.011603429 50.11551066 -1.69997216 -0.081302885 QRQEEPPPGPQRPDQSAAAAGPGDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 QRQEEPPPGPQRPDQSAAAAGPGDPK 26 2 Q9BQ61;K7EN60;K7ELS0;K7ERU7 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 ; 214.11 1.39E-27 1251220000 507570 493670 411780 400590 439670 472090 471950 518720 626130 527440 FALSE TRUE 487733.6033 479591.015 486197.806 421264.4979 453812.3848 481635.9833 477725.8653 508008.2507 555054.3474 491716.019 0.991900984 0.97534145 0.988777642 0.856723152 0.9229156 0.97950029 0.971548306 1.033133417 1.128810789 1 18.90746583 1.699977036 2.53319122 1.068463402 0.951017134 0.480692368 0.047746286 0.207347991 2.904272041 0.031531121 0.013502513 50.11607336 -1.699977036 -0.117446268 NGLS(ph)PPPCK ddPTM_BT-474_Pertuzumab_2h_R1 1 NGLSPPPCK 9 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 1 NGLS(1)PPPCK 93.561 0.0097718 541660000 878220 842330 784710 796350 845080 880700 833230 1053500 1179700 1092800 TRUE FALSE 843898.1915 818307.5731 926524.5528 837449.7189 872262.7657 898508.3574 843427.318 1031744.857 1045785.402 1018783.683 0.828338936 0.803220141 0.909441885 0.822009356 0.856180542 0.881942234 0.827876744 1.012722204 1.026503879 1 19.95841633 1.700066525 5.485228378 1.015923013 0.848433307 0.864461933 0.030073992 0.048164644 3.394181593 0.015377595 0.007684435 50.12640113 -1.700066525 -0.167489706 DDLITDLLNEAKQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDLITDLLNEAKQR 14 1 P36543;C9J8H1;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 71.806 0.036836 131040000 54823 116520 88578 142850 128740 131220 101810 68457 44864 63925 FALSE TRUE 52680.45655 113196.9637 104586.015 150222.5056 132881.039 133873.3583 103055.9812 67043.33903 39771.22681 59595.30281 0.883969945 1.899427612 1.754937219 2.520710501 2.229723363 2.246374328 1.729263488 1.1249769 0.667355059 1 15.862911 1.700095049 2.687085019 0.844769991 1.9557264 0.535574423 0.417896014 0.184834189 2.940482546 0.273009159 0.118964226 50.12969352 -1.700095049 1.110956408 VKTSEDADELHK ddPTM_BT-474_Pertuzumab_2h_R1 3 VKTSEDADELHK 12 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 ;; 120.14 0.00026566 656960000 1938140 1790950 1484700 1260390 1572400 1472410 1781920 1772720 2175640 1987530 FALSE TRUE 1862395.346 1739873.86 1753018.317 1325438.879 1622977.674 1502183.139 1803727.67 1736112.713 1928670.468 1852912.823 1.005117631 0.938993912 0.946087854 0.715327166 0.875906116 0.810714417 0.973455226 0.936964055 1.040885704 1 20.82136358 1.700334862 1.703654196 1.011957509 0.882403516 0.286055439 0.079279196 0.461605774 2.684019327 0.0631589 0.024365982 50.15738225 -1.700334862 -0.129553993 LWCSTTADYDRDHEWGFCR ddPTM_BT-474_Pertuzumab_2h_R1 1 LWCSTTADYDRDHEWGFCR 19 1 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 178.88 2.22E-14 64129000 9109.3 14529 9906.1 11623 11946 11398 9583.3 14320 16166 10027 FALSE TRUE 8753.298485 14114.64715 11696.35263 12222.86442 12330.25394 11628.47537 9700.583292 14024.287 14330.90345 9347.862359 0.936395739 1.509933138 1.251232868 1.307557167 1.319045303 1.243971608 1.037732791 1.500266741 1.533067444 1 13.19042078 1.700380458 19.72366023 1.387340695 1.248054086 0.046955684 0.20064308 0.643321987 320.1890094 0.087231367 0.048322535 50.1626484 -1.700380458 -0.13928661 NRPTS(ph)ISWDGLDSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.29)S(0.587)IS(0.123)WDGLDSGK;NRPT(0.005)S(0.95)IS(0.045)WDGLDSGK;NRPT(0.1)S(0.543)IS(0.354)WDGLDS(0.002)GK 195.08 6.56E-08 1066070000 1448400 1235320 1113120 1209600 1173110 1054470 1215780 1515400 1672200 1662610 TRUE FALSE 1391794.927 1200089.883 1314285.545 1272027.601 1210844.149 1075792.106 1230659.079 1484106.46 1482378.866 1549999.944 0.897932243 0.774251566 0.847926189 0.820662998 0.781189802 0.694059448 0.793973628 0.957488074 0.956373497 1 20.56383673 1.700408647 4.607627399 0.971135437 0.797715655 0.701028081 0.050825445 0.094876721 4.738670545 0.028418387 0.013863758 50.1659045 -1.700408647 -0.173419783 GGTTSWGTSGQPS(ph)PSYDSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGTTSWGTSGQPSPSYDSSR 20 0 Q99081;Q99081-3;H0YNQ5 Q99081 TCF12 Transcription factor 12 1 GGTTSWGT(0.001)SGQPS(0.999)PSYDSSR 207.82 1.31E-24 269970000 203960 217180 177920 229640 238310 258290 226800 197010 207290 209230 TRUE FALSE 195989.0177 210986.239 210074.1018 241491.7479 245975.4576 263512.8008 229575.6462 192941.6747 183759.3082 195058.6657 1.004769601 1.081655297 1.076979077 1.238046754 1.261033221 1.350941266 1.176956919 0.989146901 0.942072005 1 17.57354857 1.700427723 4.651029051 0.970350545 1.176465382 0.460224345 0.095670845 0.162074619 8.252399998 0.057999901 0.02833291 50.16810802 -1.700427723 0.206114837 EVDDKDAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVDDKDAPR 9 1 Q8WXA9-2;Q8WXA9 Q8WXA9-2 SREK1 Splicing regulatory glutamine/lysine-rich protein 1 0 ;;; 100.02 0.0045099 1213450000 3175800 2936250 2402760 2653820 2927540 2942500 2852340 3316720 3739370 3424820 FALSE TRUE 3051686.225 2852511.025 2836992.181 2790783.968 3021706.983 3001999.366 2887247.79 3248228.573 3314892.394 3192853.891 0.955786368 0.89340481 0.888544317 0.874071932 0.946396887 0.940224473 0.904284345 1.017343319 1.038222389 1 21.6064151 1.700504753 5.101721898 1.022099177 0.913402337 0.76116515 0.02659802 0.073390734 4.501999121 0.014591115 0.007220309 50.17700707 -1.700504753 -0.108696841 IANEVIGEMNLKPEEVFLAQGTLRPDLIESASLVASGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IANEVIGEMNLKPEEVFLAQGTLRPDLIESASLVASGK 38 2 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 177.6 2.29E-23 301460000 228730 230180 184800 175240 196530 213880 207040 244240 283690 245240 FALSE TRUE 219790.9787 223615.4918 218197.4709 184284.1574 202851.5659 218204.8001 209573.8175 239196.3586 251486.7005 228629.6764 0.96134055 0.978068531 0.954370729 0.806037783 0.8872495 0.954402786 0.916651857 1.046217457 1.099974004 1 17.80265315 1.700580763 4.595754059 1.05731266 0.921040404 0.554609445 0.051648019 0.126244515 6.272388687 0.029661629 0.0144671 50.18578974 -1.700580763 -0.136272256 DINTDFLLVVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DINTDFLLVVLR 12 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 122.33 0.00083869 214629000 204989 257360 208200 234356 272100 294450 260170 207875 196355 262786 FALSE TRUE 196977.8033 250020.3448 245826.3714 246451.1412 280852.3436 300403.9807 263354.0383 203582.3086 174065.6036 244987.2702 0.80403281 1.020544229 1.003425081 1.005975295 1.146395661 1.226202409 1.074970296 0.830991376 0.710508768 1 17.90234726 1.700605481 5.786384469 0.827332675 1.047891253 0.337552947 0.122446636 0.150735213 11.74730206 0.06521212 0.032847104 50.18864615 -1.700605481 0.220558578 DRHEASGFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRHEASGFAR 10 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 59.367 0.095814 41671000 22149 29323 27883 32138 29782 35562 35489 20200 23410 26815 FALSE TRUE 21283.39259 28486.73675 32922.07835 33796.64603 30739.96508 36281.08801 35923.325 19782.86294 20752.59494 24998.79617 0.8513767 1.139524342 1.31694655 1.351930941 1.229657815 1.451313406 1.437002196 0.791352624 0.830143772 1 14.609571 1.700676304 8.027237957 0.862008622 1.26195663 0.510457234 0.16992977 0.096292976 12.91905613 0.087167157 0.045978844 50.19683142 -1.700676304 0.399948007 MVVS(ph)AGPWSSEKAEMNILEINETLR ddPTM_BT-474_Pertuzumab_2h_R1 2 MVVSAGPWSSEKAEMNILEINETLR 25 1 A0A087WUL8;A0A087WVE3;A0A075B762;A0A087WVU4;A0A087WZJ2;A0A087X002;A0A087WYI5;A0A075B757;A0A075B7F7;A0A087WV19;A0A087X230;A0A087WUR2 A0A087WUL8 NBPF19;NBPF14;NBPF10;NOTCH2NL 1 MVVS(0.75)AGPWS(0.125)S(0.125)EKAEMNILEINETLR;MVVS(0.333)AGPWS(0.333)S(0.333)EKAEMNILEINETLR 64.315 0.024627 1481420000 138287 338460 292814 560230 522470 440990 359050 143556 61046 91182 TRUE FALSE 132882.5912 328807.4522 345732.0034 589143.5374 539275.722 449907.1199 363444.1613 140591.5184 54116.31401 85006.16192 1.56321128 3.86804256 4.067140494 6.930598019 6.343960365 5.29264126 4.275503717 1.653897968 0.636616367 1 16.3752798 1.700879634 2.857940843 0.866833145 4.79643704 0.58062932 1.384347941 0.173788984 3.152927567 0.932200198 0.413659931 50.22033828 -1.700879634 3.929603895 SPDLEAS(ph)LDTLENNCHVGSDIDFRPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPDLEASLDTLENNCHVGSDIDFRPK 26 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.028)PDLEAS(0.902)LDT(0.071)LENNCHVGSDIDFRPK;S(0.003)PDLEAS(0.922)LDT(0.074)LENNCHVGSDIDFRPK;S(0.166)PDLEAS(0.716)LDT(0.119)LENNCHVGSDIDFRPK 203.29 2.56E-25 697520000 413782 339981 380027 388203 423286 392131 454206 488006 589750 593943 TRUE FALSE 397610.942 330285.0748 448706.3326 408238.2034 436901.3786 400060.1575 459764.7089 477928.5056 522804.0524 553714.7116 0.718079064 0.596489614 0.81035653 0.73727173 0.789036971 0.722502309 0.830327783 0.863131312 0.944175839 1 19.07878333 1.700935095 0.4546293 1.016755362 0.686272663 0.772555414 0.053101215 0.424499677 0.224345036 0.056311144 0.041705038 50.22675203 -1.700935095 -0.330482699 DGDSYDPYDFS(ph)DTEEEMPQVHTPK ddPTM_BT-474_Pertuzumab_2h_R1 10 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 DGDSYDPYDFS(0.998)DT(0.002)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.997)DT(0.003)EEEMPQVHTPK;DGDSYDPYDFS(0.997)DT(0.003)EEEMPQVHTPK;DGDSYDPYDFS(0.997)DT(0.003)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK 283.64 1.31E-52 19715800000 10104580 9126900 8104950 8705900 9047790 9542010 10122020 9835400 12585290 11504360 TRUE FALSE 9709681.842 8866609.748 9569694.759 9155212.542 9338820.382 9734955.98 10245896.31 9632295.553 11156660.64 10725159.45 0.905318181 0.826711229 0.892265966 0.85362018 0.870739538 0.907674709 0.955314124 0.898102783 1.040232613 1 23.35449576 1.701373314 0.766393936 1.012565392 0.866139501 0.682386333 0.035197134 0.34651856 0.401176509 0.03062888 0.013984414 50.27745822 -1.701373314 -0.14642589 NSSQSGGKPGSS(ph)PITK ddPTM_BT-474_Pertuzumab_2h_R1 5 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.289)S(0.711)PITK;NSSQSGGKPGS(0.03)S(0.97)PITK;NSSQSGGKPGS(0.023)S(0.977)PITK;NSSQSGGKPGS(0.026)S(0.974)PITK;NSSQSGGKPGS(0.027)S(0.973)PITK 245.82 2.29E-20 16005260000 8490220 7017250 6065870 5397460 5614660 5918350 6574840 8114580 9425830 8615300 TRUE FALSE 8158412.816 6817124.901 7162107.644 5676023.557 5795260.638 6038023.092 6655304.859 7947011.087 8355849.295 8031778.057 1.015766715 0.848769084 0.891721309 0.706695767 0.721541432 0.751766676 0.828621609 0.989446052 1.04034863 1 22.93728797 1.701457422 3.720299277 1.018526279 0.814892788 0.50162776 0.085259838 0.165005934 5.249411733 0.051729093 0.024411272 50.2871962 -1.701457422 -0.203633491 (ac)MDSAGQDINLNS(ph)PNKGLLSDSMTDVPVDTGVAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDSAGQDINLNSPNKGLLSDSMTDVPVDTGVAAR 34 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 MDSAGQDINLNS(1)PNKGLLSDSMTDVPVDTGVAAR 108.52 1.41E-46 173430000 107850 92104 93647 88235 93841 105410 101680 93644 98786 108690 TRUE FALSE 103635.1028 89477.2841 110571.0961 92788.81892 96859.48099 107541.4624 102924.3903 91710.21868 87572.22742 101328.3295 1.022765334 0.883043119 1.091216017 0.915724353 0.955897344 1.06131684 1.015751377 0.905079746 0.864242289 1 16.62867806 1.701508515 7.415737909 0.914117983 0.990081543 0.176838662 0.067220019 0.189767118 22.65106065 0.031789343 0.016597965 50.29311262 -1.701508515 0.07596356 VPTLAVPAISLPDDVRR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPTLAVPAISLPDDVRR 17 1 P26358;P26358-2;K7EJL0;K7EMU8;K7EIZ6 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 90.754 0.0059719 290410000 61153 69889 56603 69717 61762 74156 67062 59171 59630 66221 FALSE TRUE 58763.07315 67895.83415 66832.42123 73315.10272 63748.63082 75655.48513 67882.72482 57949.09817 52861.05239 61735.79269 0.951847714 1.099780714 1.082555489 1.187562345 1.03260407 1.225471997 1.099568368 0.9386629 0.856246435 1 15.91381955 1.70162806 4.537802622 0.91951743 1.102924311 0.483847786 0.078047449 0.130144073 6.300569656 0.04078248 0.019873357 50.30695839 -1.70162806 0.183406881 VKELLVDCYKPTEAFISGLLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKELLVDCYKPTEAFISGLLDK 22 2 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 0 ; 192.18 6.53E-18 1865160000 1731220 1530400 1219500 1021920 1252670 1484640 1338940 1572690 1782010 1534160 FALSE TRUE 1663562.008 1486754.49 1439890.778 1074661.414 1292963.268 1514660.438 1355326.348 1540213.402 1579723.696 1430249.977 1.163126751 1.03950674 1.006740641 0.75138013 0.904012088 1.059017978 0.947615012 1.07688406 1.104508807 1 20.44783589 1.701778731 7.168496074 1.067395602 0.976048546 0.103302059 0.10460335 0.278665162 31.55943811 0.055388014 0.028786873 50.32441458 -1.701778731 -0.091347056 ALAMPGRPES(ph)PPVFR ddPTM_BT-474_Pertuzumab_2h_R1 7 ALAMPGRPESPPVFR 15 1 Q63ZY3-3;Q63ZY3;Q63ZY3-2;K7ERU2 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR 149.12 2.07E-06 8553250000 2626340 2873350 2473250 2921130 2827570 2916070 2791040 2655750 2761700 2796620 TRUE FALSE 2523699.729 2791404.871 2920221.292 3071889.869 2918521.357 2975034.933 2825197.582 2600907.834 2448203.394 2607202.436 0.967972296 1.070651374 1.120059283 1.178232203 1.119407268 1.141083213 1.083612666 0.997585687 0.93901546 1 21.31407117 1.701785461 3.098612041 0.969126493 1.104127236 0.507394454 0.053879503 0.178220702 3.838102175 0.033995707 0.015422788 50.3251944 -1.701785461 0.135000743 AQRPGAHAEDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQRPGAHAEDAR 12 1 E7EMB8;Q99952-2;Q99952 E7EMB8 PTPN18 Tyrosine-protein phosphatase non-receptor type 18 0 ; 93.959 0.0041331 105919000 73819 88119 67006 79806 79952 72463 78979 72107 75193 78955 FALSE TRUE 70934.07187 85605.9324 79115.47474 83924.79722 82523.72869 73928.25151 79945.56863 70617.96525 66657.40587 73607.30752 0.963682469 1.16300861 1.074831799 1.140169367 1.121135 1.004360219 1.086109129 0.959387969 0.905581363 1 16.16756138 1.701789587 4.138067921 0.945935872 1.083747741 0.46844651 0.060260367 0.14237595 5.678222742 0.031873826 0.01532263 50.32567247 -1.701789587 0.13781187 KLTS(ph)DEEGEPSGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLTSDEEGEPSGKR 14 2 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.092)S(0.908)DEEGEPSGKR 190.55 3.08E-07 766900000 681280 595500 484820 415740 505650 563230 516460 641530 728300 605570 TRUE FALSE 654654.8244 578516.9231 572437.7588 437196.3912 521914.6915 574618.8965 522780.592 628282.1813 645626.4373 564554.2045 1.159596048 1.02473229 1.013964211 0.774409946 0.924472243 1.017827681 0.92600602 1.112881945 1.143603984 1 19.10675258 1.701823287 7.667956516 1.095075316 0.972381416 0.198215765 0.098529102 0.18441195 23.28860219 0.050529361 0.026503415 50.32957781 -1.701823287 -0.1226939 KAPEPEEEIEEVEES(ph)EDEGEDPALDSLSQAIAFQQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPEPEEEIEEVEESEDEGEDPALDSLSQAIAFQQAK 37 1 G3V1V1;Q8TBF4 G3V1V1 ZCRB1 Zinc finger CCHC-type and RNA-binding motif-containing protein 1 1 KAPEPEEEIEEVEES(1)EDEGEDPALDSLSQAIAFQQAK 139.54 2.67E-13 37555000 70925 62386 58144 57264 65745 64875 64175 77494 86870 82889 TRUE FALSE 68153.17259 60606.81236 68651.91421 60219.4019 67859.74763 66186.81695 64960.39285 75893.72182 77008.88179 77274.8542 0.881957958 0.784301866 0.888412083 0.779288457 0.878160798 0.856511703 0.840640769 0.982127014 0.996558099 1 16.23771141 1.701936526 4.171322912 0.996002208 0.842344098 0.786236054 0.035550124 0.07189141 2.915965395 0.018016163 0.008672914 50.34270258 -1.701936526 -0.15365811 EERS(ph)PQTLAPVGEDAMK ddPTM_BT-474_Pertuzumab_2h_R1 4 EERSPQTLAPVGEDAMK 17 1 Q92797 Q92797 SYMPK Symplekin 1 EERS(0.999)PQT(0.001)LAPVGEDAMK;EERS(1)PQTLAPVGEDAMK;EERS(0.999)PQT(0.001)LAPVGEDAMK;EERS(0.998)PQT(0.002)LAPVGEDAMK 239.19 1.71E-20 3167100000 3363690 3317750 2588000 2831410 3099480 3032490 2981190 3548840 3987730 3510350 TRUE FALSE 3232233.276 3223131.018 3055709.17 2977539.409 3199177.589 3093809.026 3017674.695 3475555.214 3535059.608 3272590.868 0.987668 0.984886638 0.93372783 0.90984163 0.97756723 0.945369938 0.922105701 1.062019468 1.080202125 1 21.64200182 1.70201286 7.042303816 1.052699376 0.9514439 0.661301402 0.031269839 0.071887305 7.922300177 0.015720887 0.008150981 50.35155177 -1.70201286 -0.101255475 SECDSS(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.108)S(0.892)PEPK;SECDS(0.058)S(0.942)PEPK;SECDS(0.046)S(0.954)PEPK 270.06 6.98E-19 996810000 3137940 2728300 2202550 2304280 2480890 2532610 2656550 3098190 3630750 3274490 TRUE FALSE 3015305.836 2650491.555 2600599.78 2423204.167 2560690.08 2583821.109 2689061.654 3034211.294 3218602.481 3052705.876 0.987748561 0.868243343 0.851899884 0.793788942 0.838826334 0.846403556 0.880878068 0.993941578 1.054344117 1 21.54165716 1.702053863 2.969065843 1.027453916 0.859791541 0.673062864 0.04803768 0.129523891 2.545494403 0.030095051 0.013508549 50.35630585 -1.702053863 -0.167662375 AQLGGPEAAKS(ph)DETAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQLGGPEAAKSDETAAK 17 1 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(1)DETAAK 232.81 1.40E-17 1237830000 736850 537590 516390 420890 502520 556080 564580 710990 881780 711140 TRUE FALSE 708053.0874 522258.4596 609713.16 442612.1833 518684.0122 567324.3186 571489.4989 696307.808 781684.0311 662973.8544 1.067995491 0.787751215 0.91966396 0.667616348 0.782359679 0.855726534 0.862009105 1.050279439 1.179057102 1 19.33859245 1.702294999 3.28320289 1.097455499 0.837812739 0.495552579 0.105331066 0.160518474 3.907897224 0.060392994 0.027794576 50.38427325 -1.702294999 -0.25964276 SGS(ph)PLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSPLEK 7 0 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.019)GS(0.981)PLEK;S(0.002)GS(0.998)PLEK 81.547 0.028222 400030000 1766020 1682930 1506430 1426730 1491320 1631660 1784190 2064500 2467100 2388500 TRUE FALSE 1697001.986 1634934.484 1778675.411 1500363.706 1539289.662 1664653.283 1806025.451 2021867.354 2187045.151 2226724.768 0.762106755 0.734232855 0.79878548 0.673798454 0.691279715 0.747579273 0.811068111 0.908000568 0.982180278 1 21.08649182 1.702308203 1.491153944 0.997891744 0.731499677 0.909280526 0.033000641 0.107749247 0.465861697 0.027937375 0.010615585 50.38580518 -1.702308203 -0.266392067 CPPGVVPACHNSK ddPTM_BT-474_Pertuzumab_2h_R1 4 CPPGVVPACHNSK 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 141.13 3.97E-05 1464400000 1014930 1660510 1375060 2198190 1759910 1909690 1833270 1375990 1363080 1777050 FALSE TRUE 975265.4135 1613153.881 1623563.93 2311638.849 1816519.103 1948305.24 1855706.107 1347575.326 1208348.873 1656688.821 0.588683524 0.973721716 0.980005364 1.395336783 1.096475742 1.176023654 1.120129552 0.813414872 0.729375884 1 20.65987121 1.702466218 6.804922686 0.829731567 1.061809404 0.16544801 0.201751036 0.211522209 22.08902639 0.104414628 0.053883963 50.40414099 -1.702466218 0.232077837 DQVAEKDPTQHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQVAEKDPTQHK 12 1 A0MZ66;A0MZ66-3;A0MZ66-6;A0MZ66-5;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 0 53.967 0.082806 47557000 127250 109970 119400 129550 118440 115270 141660 156180 187790 184060 FALSE TRUE 122276.9293 106833.7633 140978.236 136236.091 122249.7302 117600.8384 143393.6775 152954.8284 166472.8665 171593.4523 0.712596709 0.622598135 0.821582841 0.793946909 0.712438199 0.685345722 0.835659377 0.891379166 0.970158618 1 17.38863498 1.702469047 1.45230577 0.990572887 0.726715434 0.783345886 0.054836125 0.184258651 0.751786742 0.046534701 0.017656511 50.40446936 -1.702469047 -0.263857453 MES(ph)EGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MESEGGADDSAEEGDLLDDDDNEDRGDDQLELIKDDEK 38 2 P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 2 MES(1)EGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK 160.19 5.42E-18 696750000 56172 52062 63213 60194 50094 60768 69838 88910 107200 108600 TRUE FALSE 53976.73614 50577.24273 74636.99527 63300.61955 51705.319 61996.7706 70692.69833 87073.97743 95031.10542 101244.4253 0.533132921 0.499555828 0.737196098 0.625225729 0.510697936 0.612347499 0.698237934 0.860037253 0.938630499 1 16.62748295 1.702559307 1.41090437 0.986491948 0.584147475 0.858024915 0.064282329 0.145770447 0.558354553 0.055104597 0.020888828 50.4149461 -1.702559307 -0.402344473 QIILEKEETEELKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QIILEKEETEELKR 14 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 117.4 0.00017189 182080000 416780 339160 241680 241850 323450 324180 300140 354170 394630 341170 FALSE TRUE 400491.7768 329487.4889 285356.9521 254331.9075 333854.063 330735.1417 303813.2031 346856.2657 349833.2568 318062.252 1.259161608 1.035921386 0.897173275 0.799629336 1.049650063 1.039844054 0.95520044 1.090529491 1.099889266 1 18.27894964 1.702626377 9.095148708 1.070557178 0.99745028 0.047105227 0.114779995 0.338273115 56.63732982 0.057716925 0.03089311 50.42273252 -1.702626377 -0.073106899 GPESESEDHR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPESESEDHR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 177.06 2.37E-06 788299500 1020913.4 1278261.5 950045.4 1303904.8 1237463.3 1220252.9 1251570.8 1085797 1182101.6 1229056.6 FALSE TRUE 981014.9756 1241806.734 1121739.737 1371199.483 1277267.431 1244927.25 1266887.898 1063374.913 1047914.382 1145811.502 0.856174837 1.083779253 0.978991514 1.196705986 1.11472736 1.086502665 1.105668686 0.92805397 0.914560886 1 20.12793829 1.702710878 7.26401003 0.941910886 1.066347083 0.252014594 0.088239191 0.159849648 18.64120545 0.043541988 0.022678325 50.43254421 -1.702710878 0.124436197 RCS(ph)SSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 RCSSSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 36 2 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RCS(0.745)S(0.128)S(0.128)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR;RCS(0.739)S(0.112)S(0.149)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR;RCS(0.605)S(0.163)S(0.232)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 217.77 3.06E-39 328270000 41182 44625 30446.1 39094 41472.1 36048.4 31568.6 39863.2 34753.1 32479.3 TRUE FALSE 39572.56191 43352.33869 35948.38754 41111.64603 42806.08776 36777.32335 31954.94597 39040.01099 30808.07378 30279.44808 1.306911599 1.431741377 1.1872207 1.357740931 1.413701057 1.214596886 1.055334492 1.289323732 1.017458234 1 14.88605129 1.702731507 0.551149779 0.998037489 1.349716083 0.574894246 0.09904843 0.596926409 0.411147684 0.097253321 0.058844729 50.43493987 -1.702731507 0.351678594 EKQEEEEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKQEEEEAK 9 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ;; 138.22 0.00013019 951470000 2145430 1639360 1489740 1353020 1611110 1572630 1744170 2033700 2502770 2147450 FALSE TRUE 2061584.224 1592607.058 1758969.157 1422849.524 1662932.816 1604429.656 1765515.674 1991703.384 2218666.042 2002001.299 1.029761681 0.795507505 0.878605403 0.710713587 0.830635234 0.801412895 0.881875389 0.99485619 1.108224077 1 20.93301148 1.702758604 2.56689985 1.054322021 0.83494044 0.541047131 0.080489162 0.175565293 2.522719506 0.049995656 0.021556486 50.43808673 -1.702758604 -0.219381581 GSSDGRGS(ph)DSESDLPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSDGRGSDSESDLPHR 17 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 GSSDGRGS(0.994)DS(0.006)ESDLPHR 131.56 1.61E-05 179300000 126150 142470 122030 149320 141580 149650 134000 118920 112850 120970 TRUE FALSE 121219.9185 138406.8951 144083.5355 157026.4231 146134.0493 152676.0255 135639.9321 116464.2604 100039.7411 112776.5942 1.074867701 1.227266137 1.277601409 1.392367133 1.295783495 1.353791775 1.202731233 1.032698862 0.887061201 1 16.78310815 1.702851145 2.584308209 0.946047867 1.275198892 0.716910926 0.084401384 0.131448057 1.916345967 0.056325742 0.024336704 50.44883535 -1.702851145 0.329151025 SKVGS(ph)TENIK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKVGSTENIK 10 1 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 S(0.005)KVGS(0.948)T(0.047)ENIK;SKVGS(0.98)T(0.02)ENIK;SKVGS(0.5)T(0.5)ENIK;SKVGS(0.5)T(0.5)ENIK 183.06 1.04E-06 11727860000 9157740 7551770 6659780 5322870 6048780 7009710 7216390 8710990 10285620 9267380 TRUE FALSE 8799845.396 7336400.914 7863350.392 5597583.959 6243344.502 7151451.139 7304706.339 8531105.012 9118039.538 8639692.098 1.018536922 0.849150737 0.910142434 0.647891603 0.72263507 0.82774375 0.845482253 0.987431602 1.05536626 1 23.04254847 1.702960972 2.867809306 1.028093595 0.821446694 0.443053766 0.094367361 0.21839173 3.980401525 0.061509603 0.027379944 50.46159477 -1.702960972 -0.206646901 DMGYGNWISKPQEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DMGYGNWISKPQEEK 15 1 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 176.49 7.26E-07 1852150000 1537030 1481270 1261780 1167900 1431560 1480480 1461450 1617820 2017440 1675540 FALSE TRUE 1476961.168 1439025.63 1489811.714 1228175.459 1477607.428 1510416.32 1479335.662 1584411.452 1788428.669 1562054.183 0.945524927 0.921239254 0.953751624 0.786256631 0.945938651 0.966942335 0.947045037 1.014312735 1.14492102 1 20.57501307 1.70298208 1.916027768 1.073824395 0.916977767 0.522189034 0.058257065 0.238106698 1.798585924 0.042040146 0.016671683 50.46404748 -1.70298208 -0.156846628 ILWQGTEDLSVPGVEHEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILWQGTEDLSVPGVEHEAR 19 0 O43924;B8ZZK5;C9IZ52 O43924 PDE6D "Retinal rod rhodopsin-sensitive cGMP 3,5-cyclic phosphodiesterase subunit delta" 0 ; 168.09 1.67E-11 464520000 179144 249610 201591 280940 236950 278720 239940 231180 239760 243920 FALSE TRUE 172142.8544 242491.3672 238022.9781 295439.3471 244571.7119 284355.9094 242876.4575 226406.0522 212543.45 227399.0811 0.757007696 1.06636916 1.046719173 1.299210822 1.075517591 1.250470793 1.068062616 0.995633101 0.934671543 1 17.7948669 1.703208813 3.547338761 0.968533887 1.094186365 0.105866455 0.136422774 0.420744247 12.0665973 0.079280361 0.037134156 50.49040021 -1.703208813 0.125652479 NS(ph)EEEEEEKKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSEEEEEEKKK 11 2 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 NS(1)EEEEEEKKK;NS(1)EEEEEEKKK 162.4 1.31E-05 1461180000 1291570 775760 850750 566800 815310 718380 936190 1227680 1680590 1228370 TRUE FALSE 1241094.016 753636.0843 1004499.45 596052.6159 841535.1866 732906.1358 947647.3733 1202327.979 1489816.469 1145171.406 1.083762667 0.658098937 0.877160786 0.520492053 0.734855221 0.639996888 0.827515749 1.049910933 1.300955002 1 20.12713212 1.703296348 2.866437947 1.155928837 0.742930267 0.518810782 0.158298327 0.164287615 2.989886655 0.092411402 0.041144401 50.50057786 -1.703296348 -0.41299857 GSAVHQLSEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSAVHQLSEELR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 151.78 6.50E-05 2373010000 3395920 3960420 3402740 4273400 4025800 3970720 3835840 3586090 3603260 3778930 FALSE TRUE 3263203.692 3847472.699 4017690.812 4493950.686 4155293.513 4051010.679 3882784.157 3512035.988 3194233.031 3522979.705 0.926262416 1.09210754 1.140424058 1.275610722 1.179482671 1.149881923 1.10213072 0.996893619 0.90668505 1 21.74836473 1.703343991 2.713825237 0.952135622 1.134769564 0.41916364 0.084941385 0.232743784 3.767271163 0.056514585 0.024780947 50.50611825 -1.703343991 0.182633942 GVTIPYRPKPS(ph)SSPVIFAGGQLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 GVTIPYRPKPSSSPVIFAGGQLTK 24 2 F8VZX2 F8VZX2 PCBP2 1 GVT(0.105)IPYRPKPS(0.298)S(0.298)S(0.298)PVIFAGGQLTK;GVT(0.081)IPYRPKPS(0.306)S(0.306)S(0.306)PVIFAGGQLTK 165.34 7.50E-12 2181440000 1208960 1155920 934410 959430 1023760 1084200 1221980 1460070 1825300 1698420 TRUE FALSE 1161712.507 1122954.293 1103278.673 1008946.297 1056690.17 1106123.267 1236934.957 1429919.044 1618099.596 1583384.501 0.733689452 0.709211372 0.696785065 0.637208648 0.667361699 0.698581593 0.781196833 0.903077581 1.021924615 1 20.5945802 1.703561843 1.602619238 1.015519492 0.686952499 0.958792748 0.026901542 0.067799777 0.343728504 0.022648796 0.008678311 50.53145965 -1.703561843 -0.328566994 TREEECHFYAGGQVYPGEASR ddPTM_BT-474_Pertuzumab_2h_R1 2 TREEECHFYAGGQVYPGEASR 21 1 Q13162;A6NG45 Q13162 PRDX4 Peroxiredoxin-4 0 ; 124.86 1.45E-05 1948300000 439566 553479 388088 515594 473534 477466 498830 445721 469250 511510 FALSE TRUE 422387.2748 537694.3208 458224.1346 542203.8681 488765.6512 487120.6897 504934.8308 436516.7056 415982.7073 476864.9721 0.885758652 1.12756095 0.96090961 1.137017604 1.024956077 1.021506544 1.058863327 0.915388488 0.872328084 1 18.86322129 1.703742001 6.458302675 0.920738104 1.035371023 0.273640551 0.075092617 0.145772092 14.02546567 0.034644142 0.017755451 50.55242584 -1.703742001 0.114632918 RRLS(ph)ESSALK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRLSESSALK 10 2 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RRLS(0.958)ES(0.04)S(0.002)ALK;RRLS(0.923)ES(0.075)S(0.002)ALK 101.32 0.002687 572320000 235878 281340 238510 348710 332200 350380 303640 226900 209973 257040 TRUE FALSE 226659.627 273316.4587 281614.0626 366706.9649 342885.5147 357464.9237 307356.0371 222214.4357 186137.7453 239630.4519 0.94587155 1.140574817 1.175201484 1.530302022 1.430892911 1.49173413 1.28262512 0.927321357 0.776769997 1 17.87045173 1.703782359 4.220390977 0.878750162 1.299865744 0.50847918 0.172818487 0.150070733 6.234318889 0.103331366 0.049919288 50.55712378 -1.703782359 0.421115582 VLYIDIDIHHGDGVEEAFYTTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLYIDIDIHHGDGVEEAFYTTDR 23 0 Q92769;Q92769-3;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ; 72.876 0.011735 17625500 7825.4 9459.6 10000.4 9726.2 8632.9 8920.5 12476.7 5819.9 8928.4 8860 FALSE TRUE 7519.574717 9189.82147 11807.69474 10228.17035 8910.585069 9100.878622 12629.39359 5699.717031 7914.885463 8259.904308 0.910370682 1.112582074 1.429519556 1.238291627 1.078775823 1.10181405 1.528999988 0.690046376 0.95822968 1 13.01190935 1.703812738 12.75559179 0.870488535 1.19845344 0.385831155 0.183162842 0.121906973 36.36478073 0.084958586 0.046597936 50.56066038 -1.703812738 0.327964905 ITKPGSIDSNNQLFAPGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 194.19 3.34E-15 485650000 341120 333300 266520 269060 305630 325020 309110 350740 388370 370250 FALSE TRUE 327788.6533 323794.6103 314686.0927 282946.2188 315460.8665 331592.1271 312892.9806 343497.0964 344283.8658 345172.6377 0.949636841 0.938065695 0.911677399 0.819723779 0.913921997 0.960655889 0.906482573 0.995145788 0.997425138 1 18.39695858 1.703846356 4.930392569 0.998330993 0.91313007 0.526261336 0.036112906 0.136205883 7.83699994 0.020694395 0.010219449 50.56457434 -1.703846356 -0.085200923 EVEERPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVEERPEK 8 1 Q32MZ4-3 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 96.331 0.0082232 971430000 1596730 1556340 1504980 1559630 1637510 1594740 1813360 1914350 2172260 2247520 FALSE TRUE 1534328.026 1511954.707 1776963.364 1640122.691 1690181.996 1626986.735 1835552.442 1874818.004 1925674.152 2095293.469 0.732273569 0.721595676 0.848073738 0.782765143 0.806656453 0.776495875 0.876035968 0.894775854 0.919047465 1 20.99872089 1.704058009 0.374153304 1.014928197 0.736060301 0.839547967 0.033532518 0.44406753 0.183185355 0.044513201 0.040034541 50.58922304 -1.704058009 -0.278867896 DEDDDEEEEEEGGSWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEDDDEEEEEEGGSWGR 17 0 O00165-3;O00165;O00165-2;Q5VYD6;O00165-4;O00165-6 O00165-3 HAX1 HCLS1-associated protein X-1 0 ; 357.54 1.28E-87 624170000 228470 219659 204460 228310 184026 229310 230040 212230 245350 225641 FALSE TRUE 219541.1398 213394.5404 241410.4702 240093.1065 189945.3634 233946.8053 232855.2983 207847.3763 217498.8966 210358.1341 1.043654151 1.014434461 1.147616522 1.141354041 0.902961819 1.112135769 1.106946966 0.988064366 1.03394574 1 17.68248808 1.704099017 10.12896789 1.00890034 1.066338625 0.136756831 0.068584107 0.244551654 50.09895513 0.033014338 0.017849568 50.59400003 -1.704099017 0.057438285 NYVPPKGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 NYVPPKGDK 9 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 113.93 0.0015697 1966210000 3006400 2794500 1937700 1910300 2395000 2486900 2155000 3061900 3279100 2857700 FALSE TRUE 2888906.564 2714803.596 2287885.494 2008890.812 2472037.35 2537186.822 2181373.535 2998670.695 2906870.315 2664145.434 1.084365188 1.019014789 0.858768994 0.754046978 0.927891293 0.952345465 0.81878921 1.125565691 1.09110797 1 21.34524141 1.704185029 9.166036201 1.079306798 0.913902227 0.364457961 0.093902757 0.122997371 21.36256055 0.047719203 0.02556687 50.60402114 -1.704185029 -0.165404571 KNLQYYDISAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNLQYYDISAK 11 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 100.22 0.006718 1208100000 486780 477130 468890 407880 520320 457610 464300 542880 599640 545090 FALSE TRUE 467756.0994 463522.7196 553628.8534 428930.7357 537056.5653 466863.1877 469982.2423 531669.3383 531571.3811 508170.5688 0.920470661 0.912140033 1.089454776 0.844068433 1.056843112 0.918713551 0.924851361 1.046241894 1.046049129 1 18.9549533 1.704291176 7.784967356 1.033837897 0.954729094 0.212012084 0.068925739 0.177605387 23.57086923 0.031639108 0.016638037 50.61639097 -1.704291176 -0.079108803 FLEANKIEFEEVDITMSEEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLEANKIEFEEVDITMSEEQR 21 1 Q9UJC5 Q9UJC5 SH3BGRL2 SH3 domain-binding glutamic acid-rich-like protein 2 0 92.29 0.0017234 31817000 56059 56297 38757 48662 54106 49228 49424 56196 60439 58073 FALSE TRUE 53868.1523 54691.46468 45761.25204 51173.45165 55846.36863 50223.42389 50028.8657 55035.53296 53578.2181 54139.66398 0.994984977 1.010192171 0.845244478 0.945211844 1.031524109 0.927664123 0.924070488 1.016547369 0.989629676 1 15.72439831 1.704375298 9.484593692 1.001755058 0.953750401 0.162821238 0.049725155 0.217155539 40.05206987 0.024542034 0.013192964 50.62619625 -1.704375298 -0.048004658 QNS(ph)PAGNKENIKPNETSPSFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QNSPAGNKENIKPNETSPSFSK 22 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 QNS(1)PAGNKENIKPNETSPSFSK 148.3 3.74E-08 159490000 230070 181210 160960 140340 168380 184290 205010 249800 309060 295700 TRUE FALSE 221078.61 176042.0682 190049.0525 147582.9642 173796.0956 188016.4701 207518.9737 244641.5427 273976.8045 275671.9756 0.801962585 0.638592544 0.689402875 0.535357154 0.630445279 0.682029683 0.752775008 0.887437115 0.993850767 1 18.07259309 1.70444658 1.499527673 1.005498491 0.653565282 0.826076817 0.062330167 0.14664411 0.641659259 0.050355329 0.019172131 50.63450631 -1.70444658 -0.35193321 DFYELEPEKFQNK ddPTM_BT-474_Pertuzumab_2h_R1 3 DFYELEPEKFQNK 13 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;; 210.56 2.64E-08 1235700000 1296240 1195100 942620 867700 1005380 1063510 1080470 1247590 1459370 1262960 FALSE TRUE 1245581.508 1161016.918 1112972.402 912482.101 1037718.961 1085014.901 1093693.115 1221826.831 1293708.436 1177418.594 1.057891827 0.9860698 0.945264843 0.774985299 0.88135092 0.9215201 0.928890643 1.037716609 1.098766779 1 20.16719589 1.70461621 3.900413166 1.055054822 0.92229959 0.359454576 0.071645 0.20743573 7.276221349 0.043141835 0.020595551 50.65428734 -1.70461621 -0.132755232 EEHLCTQR ddPTM_BT-474_Pertuzumab_2h_R1 6 EEHLCTQR 8 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 168.27 0.00030783 12381920000 3630990 3728010 3346160 3797100 3528910 3582210 4001480 3520990 3869060 4370070 FALSE TRUE 3489086.897 3621690.805 3950885.547 3993068.786 3642420.595 3654644.741 4050451.309 3448280.326 3429860.529 4074081.266 0.856410726 0.888958901 0.969761104 0.980115154 0.894047113 0.89704758 0.99419993 0.846394586 0.841873371 1 21.95804333 1.704655075 24.40857201 0.883112653 0.92582884 0.037820937 0.058549052 1.506991126 1076.027248 0.026617879 0.014760162 50.6588207 -1.704655075 0.042716187 SLRDDYEVSCPELDQLVEAALAVPGVYGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLRDDYEVSCPELDQLVEAALAVPGVYGSR 30 1 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ; 192.22 1.41E-18 156049000 131424 150525 114093 145455 148655 156703 142659 139983 145299 152711 FALSE TRUE 126287.8048 146232.1744 134712.1431 152961.95 153436.6231 159871.642 144404.9035 137092.3021 128805.2667 142367.7479 0.88705347 1.027143974 0.946226551 1.07441434 1.077748474 1.122948451 1.014309109 0.962944937 0.90473628 1 17.11926283 1.704958982 3.925020703 0.94798035 1.027216498 0.164920331 0.066969381 0.31001528 11.01826593 0.038579399 0.018443396 50.69428271 -1.704958982 0.079236147 KS(ph)SGTGTEPVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSGTGTEPVAK 12 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 KS(0.625)S(0.374)GT(0.001)GTEPVAK 133.71 9.70E-05 509210000 602330 511410 394080 443610 529030 467910 526950 587480 657980 660160 TRUE FALSE 578790.2777 496825.0875 465299.0223 466504.7653 546046.7304 477371.4608 533398.9717 575348.3327 583288.8689 615446.7752 0.940439208 0.807259226 0.756034544 0.757993679 0.887236317 0.775650276 0.866685785 0.934846612 0.94774868 1 19.23127457 1.705019317 1.627278453 0.978863596 0.816236894 0.564389678 0.055504799 0.259118416 1.358556733 0.043200339 0.016607873 50.70132595 -1.705019317 -0.162626702 DLDANGDAQVDFSEFIVFVAAITSACHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLDANGDAQVDFSEFIVFVAAITSACHK 28 0 P25815 P25815 S100P Protein S100-P 0 271 2.04E-61 557800000 407560 454210 384630 384760 448530 392740 446230 387720 451990 416480 FALSE TRUE 391632.1046 441256.3755 454141.197 404617.5097 462957.3748 400681.4719 451691.0962 379713.4465 400681.9901 388271.4386 1.008655455 1.136463648 1.169648735 1.042099597 1.192354958 1.031962261 1.163338457 0.977958739 1.031963596 1 18.56670606 1.705082456 8.955634472 1.004925641 1.107836863 0.37925525 0.060281584 0.111131618 18.82733369 0.026798502 0.014325699 50.70869762 -1.705082456 0.102911221 KVEEEGS(ph)PGDPDHEASTQGR ddPTM_BT-474_Pertuzumab_2h_R1 5 KVEEEGSPGDPDHEASTQGR 20 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR 211.49 1.25E-22 5375220000 5116180 4589120 3881800 4257800 4452830 4745250 4756320 4773590 5750000 5349210 TRUE FALSE 4916234.029 4458242.791 4583327.61 4477545.568 4596059.321 4841202.206 4814529.267 4675013.698 5097284.106 4986903.242 0.985829039 0.893990233 0.919072897 0.897860927 0.921625927 0.970783264 0.965434666 0.937458272 1.02213415 1 22.24971278 1.705086452 0.731767777 1.00536385 0.92199914 0.462540595 0.030590842 0.574745224 0.614727172 0.02786301 0.013153495 50.70916415 -1.705086452 -0.08336471 QKEDVEVVGGS(ph)DGEGAIGLSSDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKEDVEVVGGSDGEGAIGLSSDPK 24 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 1 QKEDVEVVGGS(1)DGEGAIGLSSDPK 150.98 7.18E-08 1052100000 327170 247960 242200 224390 284930 240890 268140 337420 406080 336570 TRUE FALSE 314383.8347 240888.4236 285970.9277 235970.7948 294095.0322 245760.9608 271421.5775 330452.1591 359983.5008 313773.8141 1.001944141 0.767713597 0.911391948 0.75204107 0.937283543 0.783242418 0.865023037 1.053154037 1.147270692 1 18.25936543 1.705109054 4.077885634 1.081141486 0.85321001 0.576467195 0.081273651 0.111266043 4.291605844 0.040609729 0.019538837 50.71180332 -1.705109054 -0.227931476 TCDISFSDPDDLLNFK ddPTM_BT-474_Pertuzumab_2h_R1 5 TCDISFSDPDDLLNFK 16 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;;;; 352.15 6.81E-87 404651000 792086 761732 619850 661324 729379 787156 720062 819451 900429 885944 FALSE TRUE 761130.4034 740008.1492 731870.6835 695455.0109 752840.1379 803072.8336 728874.3342 802529.0505 798216.0748 825938.2238 0.921534301 0.895960652 0.886108261 0.842018193 0.911496909 0.972315859 0.882480449 0.971657477 0.966435566 1 19.65567435 1.705182366 0.660431032 0.999534642 0.889260681 0.55885116 0.031854631 0.511251634 0.462687774 0.030194047 0.015442294 50.72036452 -1.705182366 -0.110273961 VAAQSPPS(ph)PASAEALLPALPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 VAAQSPPSPASAEALLPALPLR 22 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 VAAQSPPS(0.999)PAS(0.001)AEALLPALPLR;VAAQSPPS(1)PASAEALLPALPLR;VAAQS(0.001)PPS(0.999)PASAEALLPALPLR 202.62 1.45E-22 275355000 241183 291539 244293 296044 298931 314086 244755 251130 220399 229417 TRUE FALSE 231757.3017 283224.5932 288442.1794 311322.8663 308546.3871 320437.0341 247750.3849 245944.0777 195380.2295 213878.3822 1.08359386 1.324231978 1.348627086 1.455606981 1.442625402 1.498220768 1.158370389 1.149924902 0.913510882 1 17.70643114 1.705183717 1.776721875 0.971073069 1.36039234 0.622282268 0.11925012 0.219243775 1.398068907 0.09204663 0.03594976 50.72052233 -1.705183717 0.389319271 QDWVDGEPTEAEKDFWELASLDCYNHLAEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 QDWVDGEPTEAEKDFWELASLDCYNHLAEWK 31 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 228.46 1.35E-35 118180000 99929 93617 70634 65853 74999 87965 82619 95481 110550 95664 FALSE TRUE 96023.6642 90947.13482 83399.13504 69251.68122 77411.41095 89743.71257 83630.11604 93509.28398 98000.82746 89184.59207 1.076684458 1.019762862 0.935129411 0.776498267 0.867990862 1.00626925 0.937719331 1.048491469 1.098853795 1 16.44450686 1.705235576 4.462968382 1.057398551 0.940648812 0.249506635 0.081493086 0.245576676 11.48420049 0.048186396 0.023501662 50.72657923 -1.705235576 -0.116749738 LYKEELEQTYHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYKEELEQTYHAK 13 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 183 6.45E-06 4163500000 1496450 1550370 1256400 1695300 1317450 1393090 1746930 1715080 2106910 2036670 FALSE TRUE 1437967.08 1506154.966 1483459.428 1782794.636 1359826.976 1421259.234 1768309.452 1679662.999 1867742.41 1898724.527 0.757333178 0.793245647 0.781292603 0.938943281 0.716179181 0.748533668 0.931314378 0.884627009 0.983682669 1 20.85659918 1.705261931 1.238385819 0.991807481 0.794734845 0.591558682 0.064133276 0.318901313 0.923660488 0.054093805 0.020653805 50.72965757 -1.705261931 -0.197072636 TSTTAEKTDEEEKEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSTTAEKTDEEEKEDR 16 2 Q9NUU7;I3L0H8;H3BTB3 Q9NUU7 DDX19A ATP-dependent RNA helicase DDX19A 0 66.673 0.030324 393960000 131220 101670 87188 58595 97124 85785 88932 125750 146910 118180 FALSE TRUE 126091.7773 98770.47115 102944.8111 61619.09497 100248.0817 87519.63148 90020.37642 123153.2186 130233.3927 110175.5633 1.144462288 0.896482561 0.934370635 0.559280961 0.909893979 0.794365182 0.817063001 1.117790686 1.182053341 1 16.74944475 1.705311403 6.085302906 1.112370862 0.856327017 0.35754301 0.143273036 0.142986518 12.45748613 0.07347242 0.037371021 50.73543667 -1.705311403 -0.256043845 QNGSNDSDRYS(ph)DNEEGKKK ddPTM_BT-474_Pertuzumab_2h_R1 5 QNGSNDSDRYSDNEEGKKK 19 3 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 QNGSNDS(0.069)DRYS(0.93)DNEEGKKK;QNGSNDS(0.001)DRYS(0.999)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK 284.33 4.79E-40 3433030000 3062250 2254188 1415174 1082367 1706254 1916107 1818286 2262854 2810243 1900200 TRUE FALSE 2942573.885 2189900.765 1670927.422 1138228.091 1761137.209 1954851.996 1840538.728 2216125.274 2491235.996 1771497.761 1.661065539 1.236186019 0.943228639 0.642523019 0.99415153 1.10350238 1.038973217 1.250989599 1.406287973 1 20.75653821 1.705342447 6.258860917 1.246077048 1.068485705 0.043576107 0.258947063 0.383337086 35.17513632 0.138725398 0.07083914 50.73906349 -1.705342447 -0.177591343 S(ph)QGGEEEGPLSDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SQGGEEEGPLSDK 13 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK 224.36 1.49E-11 1936680000 1099160 946550 934160 891530 927420 1009310 995080 1201350 1382380 1266410 TRUE FALSE 1056203.612 919555.3208 1102983.492 937541.9701 957251.3066 1029718.94 1007258.087 1176541.703 1225458.018 1180634.923 0.894606446 0.778865086 0.934229092 0.794099812 0.810793657 0.872173879 0.853149494 0.996533035 1.037965246 1 20.17113149 1.705587955 3.445912018 1.019839032 0.84500826 0.736861329 0.044805911 0.094404189 2.536361802 0.024310198 0.011346042 50.76775452 -1.705587955 -0.174830772 SSVNSHMTQSTDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSVNSHMTQSTDSR 14 0 Q9NXV6 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 0 ;; 179.56 1.85E-06 547720000 350465 471000 346060 468703 387420 408229 415832 382305 383713 436280 FALSE TRUE 336768.4403 457567.5412 408600.7401 492892.818 399881.7161 416483.6701 420921.0764 374410.2682 340155.5089 406730.367 0.827989419 1.124989866 1.004598558 1.211841697 0.983161693 1.023979776 1.034889722 0.920536794 0.836316972 1 18.63371318 1.705596229 4.269659517 0.906017507 1.038286021 0.201495721 0.099982407 0.238471576 10.14638667 0.051703335 0.025064247 50.76872173 -1.705596229 0.132268515 IILDLISES(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 2 IILDLISESPIK 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLISES(1)PIK;IILDLISES(1)PIK 270.8 1.12E-27 668900000 2008770 1723620 2111720 1909710 2014590 1986770 2082870 2547100 3010700 2716300 TRUE FALSE 1930265.048 1674464.045 2493354.779 2008270.362 2079391.117 2026943.851 2108360.786 2494501.495 2668937.958 2532322.582 0.762250853 0.66123647 0.984611833 0.793054715 0.821139902 0.800428771 0.832579862 0.985064665 1.053948647 1 21.27202976 1.705789739 2.882183902 1.027214023 0.806045024 0.613270117 0.075359997 0.153821074 2.82264646 0.046274496 0.020687264 50.79134796 -1.705789739 -0.221168999 SVVS(ph)FDK ddPTM_BT-474_Pertuzumab_2h_R1 6 SVVSFDK 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 SVVS(1)FDK;SVVS(1)FDK;SVVS(1)FDK;SVVS(1)FDK;SVVS(1)FDK;SVVS(1)FDK 135.43 0.0032289 2680104000 4946170 4260530 4450370 3687720 4030390 3465340 3629450 5835720 5936460 5902250 TRUE FALSE 4752868.208 4139023.856 5254650.857 3878043.671 4160031.155 3535411.549 3673868.295 5715210.343 5262577.948 5502485.35 0.863767535 0.752209882 0.954959536 0.704780372 0.756027666 0.64251176 0.667674344 1.038659802 0.956400174 1 22.39165197 1.705819832 8.08895356 0.995661084 0.763158881 0.597163952 0.088343074 0.084681768 12.19687043 0.045030375 0.023800976 50.79486757 -1.705819832 -0.232502203 SLYVAEYHSEPVEDEKP ddPTM_BT-474_Pertuzumab_2h_R1 4 SLYVAEYHSEPVEDEKP 17 1 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ;;; 305.89 9.76E-47 2245590000 2907370 2724960 2452590 2525060 2674590 2691760 2932220 3046780 3638590 3425110 FALSE TRUE 2793746.766 2647246.809 2895827.571 2655378.649 2760620.616 2746189.231 2968105.385 2983862.928 3225552.517 3193124.249 0.874925793 0.829045976 0.906894735 0.831592648 0.864551581 0.860032062 0.929530189 0.934465024 1.010155655 1 21.60653726 1.705825329 1.175482156 1.006877214 0.859107927 0.83765557 0.024597513 0.158056668 0.410659832 0.019389966 0.007457732 50.7955104 -1.705825329 -0.147769287 KPS(ph)PSES(ph)PEPWKPFPAVSPEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 KPS(0.994)PS(0.012)ES(0.995)PEPWKPFPAVSPEPR;KPS(0.953)PS(0.05)ES(0.997)PEPWKPFPAVSPEPR 177.85 3.35E-17 934000000 587970 492310 440760 407120 497160 464130 479780 592720 688000 583600 TRUE FALSE 564991.4824 478269.8008 520415.1367 428131.512 513151.6029 473515.0266 485651.6912 580480.1249 609901.1243 544072.2522 1.038449361 0.879055675 0.95651843 0.786901942 0.943168119 0.870316442 0.892623524 1.066917349 1.120992886 1 19.05343873 1.705884806 5.369187406 1.071579428 0.905176234 0.516400439 0.067528316 0.107404464 7.367493437 0.03336729 0.016691986 50.80246745 -1.705884806 -0.166403193 VSQGSAESLS(ph)PSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSQGSAESLSPSFR 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 VSQGSAESLS(0.999)PS(0.001)FR;VSQGSAES(0.008)LS(0.978)PS(0.013)FR;VSQGSAESLS(0.999)PS(0.001)FR;VSQGSAESLS(0.975)PS(0.025)FR 310.24 1.11E-55 1280300000 1105830 1292780 1206600 1479750 1404350 1407590 1156510 1154710 964750 1056850 TRUE FALSE 1062612.941 1255911.18 1424659.461 1556120.075 1449522.193 1436052.434 1170663.715 1130864.835 855235.6246 985268.6082 1.078500758 1.274689125 1.445960471 1.579386638 1.471194942 1.457523788 1.18816707 1.147773131 0.868022809 1 19.91015757 1.70617819 1.687447289 0.945876141 1.391324325 0.608001144 0.13881579 0.243631086 1.384437243 0.11357219 0.043958843 50.83679814 -1.70617819 0.445448184 SPHAAHLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPHAAHLKK 9 1 Q15048 Q15048 LRRC14 Leucine-rich repeat-containing protein 14 0 53.775 0.090484 338890000 447070 751790 626100 1005000 735100 955140 740410 622940 507100 739510 FALSE TRUE 429598.0101 730349.6853 739250.1975 1056868.17 758745.1591 974453.5852 749471.3591 610076.0713 449536.1339 689422.329 0.623127497 1.059364709 1.072274811 1.532976415 1.100552052 1.413434907 1.087100501 0.884909069 0.65204754 1 19.3950285 1.70622929 3.533001549 0.813319316 1.150328243 0.224121637 0.239558818 0.276757469 7.836504812 0.138816551 0.065165948 50.84278009 -1.70622929 0.337008927 FENAFLSHVVSQHQALLGTIR ddPTM_BT-474_Pertuzumab_2h_R1 2 FENAFLSHVVSQHQALLGTIR 21 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 216.38 3.59E-25 1444480000 271286 396490 302020 437300 268878 302538 439880 214225 320230 313300 FALSE TRUE 260683.8432 385182.4934 356601.7324 459869.1054 277526.7051 308655.5256 445263.383 209801.1789 283878.8329 292079.9119 0.892508634 1.318757222 1.220904683 1.574463312 0.950173886 1.056750269 1.5244574 0.71830061 0.971921797 1 18.15600361 1.70624101 12.09748551 0.886641221 1.220476389 0.311249563 0.219888923 0.134809095 39.26722054 0.100234891 0.054839711 50.84415218 -1.70624101 0.333835168 AIPTESITDS(ph)PISAQDLLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIPTESITDSPISAQDLLSR 20 0 Q9UDV7-2;Q9UDV7 Q9UDV7-2 ZNF282 Zinc finger protein 282 1 AIPTESIT(0.001)DS(0.998)PISAQDLLSR;AIPTESITDS(1)PISAQDLLSR 161.22 6.27E-11 71447000 54256 55572 46142 59491 41801 54604 54614 49827 56176 52887 TRUE FALSE 52135.61554 53987.14097 54480.88582 62561.33764 43145.56713 55708.13029 55282.38247 48798.05504 49799.13599 49304.91638 1.057412107 1.094964659 1.104978769 1.268866114 0.875076367 1.129869684 1.121234687 0.989719862 1.010023739 1 15.58944389 1.706259245 7.29397327 1.00065377 1.093414176 0.181041225 0.090709021 0.215096499 26.05845441 0.043858848 0.022881253 50.84628702 -1.706259245 0.092760406 AQQMHTGPVLDVCWSDDGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 AQQMHTGPVLDVCWSDDGSK 20 0 P78406;E9PQ57;E9PPG9;B0QZ36 P78406 RAE1 mRNA export factor 0 ;;; 296.04 1.28E-54 2742350000 2460890 2258530 1829340 2038720 2088600 2300220 2145160 2472370 2757540 2501960 FALSE TRUE 2364715.698 2194118.936 2159942.431 2143938.584 2155781.716 2346732.024 2171413.11 2421314.696 2444515.62 2332500.021 1.013811652 0.940672633 0.926020327 0.919159084 0.924236526 1.006101609 0.930938088 1.038077031 1.048023836 1 21.15344566 1.706389768 6.741635579 1.031862618 0.950018241 0.524163476 0.033527088 0.097214161 10.26434349 0.0168482 0.008696769 50.86157076 -1.706389768 -0.081844377 NPEHFVVCNR ddPTM_BT-474_Pertuzumab_2h_R1 3 NPEHFVVCNR 10 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ;; 104.79 0.0026344 1330030000 992080 1127120 884270 1067830 1074280 1081680 1060500 982560 1018990 1084390 FALSE TRUE 953308.4168 1094975.641 1044077.259 1122940.834 1108835.192 1103552.311 1073478.716 962269.7926 903318.5272 1010943.299 0.942989006 1.083122705 1.03277529 1.110785179 1.096832228 1.091606534 1.061858481 0.951853376 0.893540249 1 19.94727065 1.706522617 4.39508938 0.939553264 1.064803779 0.50006076 0.050845678 0.129156399 5.844538208 0.026886202 0.013100083 50.87713151 -1.706522617 0.125250515 GPTSTSIDNIDGTPVRDER ddPTM_BT-474_Pertuzumab_2h_R1 2 GPTSTSIDNIDGTPVRDER 19 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 0 ; 98.391 0.0011172 556630000 314940 350020 266630 334880 345850 331170 330190 316060 341690 332110 FALSE TRUE 302631.7966 340037.7723 314815.9722 352163.1969 356974.5793 337866.4843 334230.964 309533.2506 302902.7837 309615.8939 0.977442704 1.098256837 1.016795256 1.137419635 1.152959478 1.091243993 1.079501959 0.999733078 0.978317941 1 18.24012001 1.706749232 3.888135188 0.988954729 1.083451494 0.394791924 0.048939805 0.189555646 6.589314293 0.027897062 0.013338707 50.90368608 -1.706749232 0.094496766 GDEASEEGQNGSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDEASEEGQNGSSPK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5 P35611 ADD1 Alpha-adducin 1 GDEASEEGQNGSS(1)PK 145.04 4.33E-06 248940000 464900 380550 346020 345430 373810 398950 390990 512690 606170 517980 TRUE FALSE 446731.194 369697.0866 408553.5112 363257.6837 385833.9381 407017.0423 395775.0526 502102.7723 537360.1229 482896.7532 0.925107057 0.765582051 0.846047335 0.752247103 0.798998824 0.84286556 0.819585242 1.039772517 1.112784709 1 18.88135524 1.706760783 4.179731152 1.062990225 0.816628401 0.803495151 0.051931997 0.067119122 2.726415281 0.026732219 0.01293192 50.90503996 -1.706760783 -0.246361824 KKVEEVLEEEEEEYVVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKVEEVLEEEEEEYVVEK 18 2 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ; 93.153 0.0012385 225527000 694220 603470 440720 449560 497530 549400 538930 684740 827640 648810 FALSE TRUE 667089.1149 586259.6265 520367.9078 472761.8455 513533.5043 560509.2444 545525.5866 670599.8797 733689.7769 604865.5208 1.102871782 0.969239618 0.860303472 0.781598271 0.849004426 0.92666754 0.901895657 1.108675989 1.212979996 1 19.2062549 1.70684843 4.728037702 1.123719895 0.905752458 0.471448086 0.093526176 0.137972745 7.293076635 0.052042412 0.025621001 50.91531444 -1.70684843 -0.217967437 KQEDSVTELTVEDSGESLEDLMAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KQEDSVTELTVEDSGESLEDLMAK 24 1 Q9GZZ9-2;Q9GZZ9 Q9GZZ9-2 UBA5 Ubiquitin-like modifier-activating enzyme 5 0 ;;; 247.34 9.31E-38 348567000 360995 337303 289837 277916 334474 339678 354753 407161 467659 466961 FALSE TRUE 346886.9163 327683.4487 342216.9933 292259.2781 345232.66 346546.5219 359094.5733 398752.9831 414572.3109 435333.3155 0.796830621 0.752718519 0.786103386 0.671345995 0.793030645 0.796048705 0.824872714 0.915971668 0.952310095 1 18.73176091 1.706898402 1.032282487 0.996627516 0.755722797 0.871800493 0.033579563 0.15791664 0.315723499 0.028781048 0.011415226 50.92117333 -1.706898402 -0.240904719 DKDDKISWEEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDDKISWEEYK 12 2 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ; 147.35 3.68E-05 1356840000 2202500 1858560 1662310 1241250 1452560 1691320 1784590 2149600 2724800 2151900 FALSE TRUE 2116423.865 1805555.689 1962726.395 1305311.061 1499282.912 1725519.649 1806430.346 2105210.009 2415492.127 2006149.896 1.054967961 0.900010359 0.978354807 0.650654801 0.747343414 0.860115016 0.900446347 1.049378221 1.204043692 1 20.93599798 1.706926778 2.861972029 1.108796595 0.858594932 0.426579623 0.114855614 0.217528927 3.925999117 0.073679553 0.032914746 50.92450052 -1.706926778 -0.250201664 IEGYEDQVLITEHGDLGNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEGYEDQVLITEHGDLGNGK 20 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ; 295.66 1.32E-54 712160000 997430 1199390 915930 1067420 1113510 1056650 1043220 1279810 1393210 1317820 FALSE TRUE 958449.3329 1165184.572 1081458.926 1122509.674 1149327.06 1078016.187 1055987.238 1253381.476 1235058.642 1228562.878 0.780138608 0.948412648 0.880263392 0.913677024 0.935505281 0.877461143 0.859530479 1.020201326 1.005287287 1 20.22854027 1.707411955 7.010172421 1.008743735 0.890104388 0.617301265 0.044337135 0.08211912 9.36934973 0.021036625 0.010920934 50.98142323 -1.707411955 -0.118639347 IQCRS(ph)ENSK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQCRSENSK 9 1 Q9UKB1-2;Q9UKB1-3;Q9UKB1 Q9UKB1-2 FBXW11 F-box/WD repeat-containing protein 11 1 IQCRS(1)ENSK 79.201 0.016722 431830000 951700 1295700 915090 1320900 1059400 1255200 1138300 1048400 1002000 1204200 TRUE FALSE 914506.5118 1258747.905 1080467.119 1389071.807 1093476.563 1280581.004 1152230.856 1026750.174 888257.1607 1122638.461 0.814604651 1.121240674 0.962435509 1.237327826 0.974023785 1.140688697 1.026359683 0.914586671 0.791222812 1 20.09846196 1.707507473 3.731782787 0.884394728 1.049718073 0.219369652 0.118149828 0.245612925 7.808561677 0.061877333 0.029393817 50.99263719 -1.707507473 0.165323345 DLQSS(ph)PPSLPLGFLGEGDAVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLQSSPPSLPLGFLGEGDAVTK 22 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLQS(0.177)S(0.662)PPS(0.161)LPLGFLGEGDAVTK 145.65 5.88E-08 137970000 73276 64048 57133 61525 61606 64996 64494 80120 89428 85673 TRUE FALSE 70412.29291 62221.41375 67458.20402 64700.31262 63587.61294 66310.26365 65283.29686 78465.494 79276.50835 79870.2914 0.881583023 0.779030759 0.844596944 0.810067317 0.796135983 0.830224386 0.817366454 0.982411515 0.992565658 1 16.28537136 1.707536967 4.444042509 0.994003788 0.820163884 0.895167973 0.02648223 0.0456405 2.114411209 0.013238941 0.006466798 50.99610031 -1.707536967 -0.173839905 VDCTAHSDVCSAQGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDCTAHSDVCSAQGVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 262.42 6.95E-27 2508200000 2068700 2120970 2030380 2131690 2094400 2129500 2468000 2555300 3011400 3003300 FALSE TRUE 1987852.917 2060482.012 2397314.832 2241706.776 2161768.278 2172559.949 2498204.122 2502532.162 2669558.497 2799883.816 0.70997693 0.735916969 0.856219397 0.800642785 0.772092137 0.775946465 0.892252781 0.893798574 0.953453312 1 21.41693553 1.707733821 0.748699537 1.001377315 0.767371183 0.809628876 0.039594883 0.275551592 0.306052346 0.038168448 0.017749461 51.01922071 -1.707733821 -0.234006132 RKPEEESPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RKPEEESPR 9 2 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;; 185.61 2.40E-05 591715000 402534 370656 346823 337492 362873 369084 367668 419347 470473 429021 FALSE TRUE 386802.5263 360085.2538 409501.6311 354910.0026 374545.1396 376547.1314 372167.631 410687.3379 417066.8774 399963.0255 0.96709571 0.900296354 1.023848718 0.88735703 0.936449411 0.941454853 0.93050509 1.026813259 1.042763583 1 18.60950711 1.707870381 5.768348263 1.02627658 0.9403896 0.515860585 0.036375626 0.105108716 8.356420724 0.017523093 0.008861734 51.0352658 -1.707870381 -0.08588698 GASWIDTADGSANHR ddPTM_BT-474_Pertuzumab_2h_R1 3 GASWIDTADGSANHR 15 0 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-2;E9PBT8;J3QT17;Q8NBJ7-5 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 ;; 212.55 8.18E-10 1826620000 1414920 1804180 1423830 1947960 1688860 1903700 1809590 1527550 1604140 1788730 FALSE TRUE 1359623.362 1752726.553 1681147.754 2048494.449 1743183.716 1942194.118 1831736.304 1496005.559 1422044.752 1667577.724 0.815328331 1.051061386 1.00813757 1.22842517 1.045338811 1.164679817 1.098441337 0.897112942 0.852760703 1 20.66932257 1.707875915 6.623690541 0.906989457 1.066509041 0.263536982 0.107694799 0.161830127 16.71912862 0.054155462 0.027904194 51.03591608 -1.707875915 0.159519584 LMLSTSEYSQS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 LMLSTSEYSQSPK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LMLSTSEYSQS(1)PK;LMLSTSEYSQS(1)PK 297.72 9.71E-41 420660000 498640 376820 348230 346020 389030 397830 432830 457990 574830 512700 TRUE FALSE 479152.5975 366073.4625 411162.9073 363878.1337 401543.5033 405874.3952 438127.103 448532.3465 509577.7083 477974.3723 1.002465038 0.765885126 0.860219566 0.761292142 0.840094211 0.84915514 0.916633042 0.938402501 1.066119311 1 18.86657374 1.707940339 1.436609747 1.029812709 0.838896121 0.536658338 0.066285975 0.278239398 1.107665802 0.050368647 0.019176064 51.04348746 -1.707940339 -0.190916589 HPASLEFQAQITTLLVDLGTPQAEIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPASLEFQAQITTLLVDLGTPQAEIAR 27 0 Q92797;A0A087WUE9;M0R3C7;Q92797-2 Q92797 SYMPK Symplekin 0 116.72 0.00060096 50109000 67957 70323 61529 69704 59602 71843 65054 60066 60144 61058 FALSE TRUE 65301.16531 68317.45689 72648.65901 73301.43179 61519.15246 73295.71468 65850.15031 58825.61611 53316.70526 56922.48728 1.147194517 1.200183972 1.276273446 1.287741195 1.080753063 1.287640758 1.156838948 1.033433691 0.936654525 1 15.79671108 1.707973274 2.51571414 0.970778191 1.213432048 0.715856103 0.063512494 0.129492184 1.771131009 0.040158751 0.017305611 51.0473585 -1.707973274 0.242653857 S(ph)DSELVSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDSELVSK 8 0 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 1 S(0.929)DS(0.071)ELVSK;S(0.977)DS(0.023)ELVSK;S(0.998)DS(0.002)ELVSK;S(0.994)DS(0.006)ELVSK 164.85 0.00034373 1035050000 650630 591200 697360 863030 653770 709110 1048370 1123700 1400870 1513840 TRUE FALSE 625202.6603 574339.5548 823388.4647 907571.0817 674799.1058 723448.69 1061200.266 1100495.202 1241849.111 1411306.268 0.442995737 0.406956001 0.583422949 0.643071672 0.478137964 0.51260928 0.751927692 0.779770647 0.879928856 1 20.42859967 1.707998786 0.759667036 0.998448789 0.491717942 0.860128116 0.070700445 0.227543835 0.259030723 0.069039907 0.031792603 51.05035725 -1.707998786 -0.506730847 down EIKDSLAEVEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIKDSLAEVEEK 12 1 Q32MZ4-2;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 138.77 6.26E-05 318000000 420780 380850 292890 243020 302520 367160 333260 382580 438560 379920 FALSE TRUE 404335.4524 369988.5309 345821.7383 255562.2913 312250.8305 374584.2268 337338.5356 374679.5893 388776.5074 354187.68 1.14158531 1.04461152 0.976379919 0.721544836 0.881597097 1.057586833 0.952428768 1.057856076 1.097656777 1 18.4341545 1.708047203 5.417005484 1.058836567 0.961802777 0.108158931 0.108558487 0.33743998 23.68261846 0.061225932 0.030712084 51.05604892 -1.708047203 -0.097033789 TKPPRPDS(ph)PATTPNISVK ddPTM_BT-474_Pertuzumab_2h_R1 4 TKPPRPDSPATTPNISVK 18 2 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 TKPPRPDS(1)PATTPNISVK;TKPPRPDS(1)PATTPNISVK;TKPPRPDS(0.999)PAT(0.001)TPNISVK;T(0.001)KPPRPDS(0.999)PATTPNISVK 230.24 1.14E-19 3338470000 2085306 1872310 1672460 1598832 1725269 1745216 1920053 2184144 2591650 2390050 TRUE FALSE 2003809.936 1818913.552 1974710.726 1681347.911 1780763.844 1780505.463 1943551.183 2139040.663 2297456.757 2228169.785 0.899307562 0.81632628 0.88624787 0.754586981 0.799204736 0.799088775 0.872263504 0.959998954 1.031095912 1 21.08742774 1.708098414 2.183494474 1.013999156 0.824040219 0.781400815 0.041007245 0.124332336 1.250212873 0.02827948 0.011681972 51.06206963 -1.708098414 -0.189958937 EQDDTAAMLADFIDCPPDDEKPPPPTEPDS ddPTM_BT-474_Pertuzumab_2h_R1 1 EQDDTAAMLADFIDCPPDDEKPPPPTEPDS 30 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 132.37 6.51E-06 40792000 89592 81408 60520 65327 73225 77259 72695 88355 96809 90529 FALSE TRUE 86090.64559 79086.32355 71457.31026 68698.5343 75580.34863 78821.22991 73584.66316 86530.43837 85819.64818 84397.3902 1.020062888 0.937070724 0.846676776 0.813988847 0.895529452 0.933929707 0.871883159 1.025273864 1.016851919 1 16.36491077 1.708251544 6.876953555 1.015075722 0.899488107 0.475411504 0.053366026 0.11521961 12.7834725 0.028488071 0.014755781 51.08007704 -1.708251544 -0.115587615 QTDPST(ph)PQQESSKPLGGIQPSSQTIQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 QTDPSTPQQESSKPLGGIQPSSQTIQPK 28 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 QTDPS(0.035)T(0.949)PQQES(0.013)S(0.003)KPLGGIQPSSQTIQPK;QTDPS(0.01)T(0.99)PQQESSKPLGGIQPSSQTIQPK 309.09 2.05E-82 2249790000 713770 625820 576910 531960 585920 635370 621240 767020 872330 804450 TRUE FALSE 685875.0793 607972.2263 681170.4703 559414.5194 604766.6489 648217.6167 628842.921 751180.769 773306.7555 749963.885 0.914544144 0.810668672 0.90827103 0.745921944 0.806394363 0.864331776 0.838497604 1.00162259 1.031125326 1 19.5164616 1.708298468 4.177077878 1.016456199 0.837820798 0.73034146 0.047229309 0.088186309 3.57337855 0.025375668 0.01229277 51.08559643 -1.708298468 -0.178635401 QFEDELHPDLK ddPTM_BT-474_Pertuzumab_2h_R1 6 QFEDELHPDLK 11 0 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 ;;;;; 151.78 3.33E-05 3157230000 10258030 9871430 7661860 8964940 8996010 9168350 10072730 10580670 12595940 11898250 FALSE TRUE 9857134.847 9589906.482 9046528.539 9427621.628 9285374.832 9353740.319 10196003.08 10362175.47 11166101.7 11092370.93 0.888640933 0.864549747 0.815563111 0.849919434 0.837095594 0.843258883 0.919190599 0.934171381 1.00664698 1 23.40306443 1.70836022 1.315345066 1.004650427 0.847833735 0.880796665 0.022091587 0.131926214 0.434032875 0.018522582 0.007053646 51.09286076 -1.70836022 -0.156816692 KDPSGASNPSADSPLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDPSGASNPSADSPLHR 17 1 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 0 ; 160.97 1.96E-09 1231080000 955670 1059180 848170 976280 970160 1024290 1044010 933640 1057270 1039010 FALSE TRUE 918321.3599 1028973.223 1001453.186 1026665.928 1001366.077 1045001.846 1056786.907 914360.0077 937253.142 968636.9272 0.948055287 1.062289899 1.033878803 1.059907896 1.033788873 1.078837505 1.091004149 0.943965672 0.967600053 1 19.88559648 1.708369843 9.492003992 0.967781232 1.045790424 0.427063062 0.038842126 0.097551642 19.35725198 0.018159298 0.009766482 51.0939929 -1.708369843 0.078009192 QFEQNDLSFVGQDVDGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QFEQNDLSFVGQDVDGDR 18 0 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 ; 298.79 4.47E-49 916040000 405900 408740 351190 493100 364300 382120 447150 480980 561020 544140 FALSE TRUE 390036.9793 397083.1354 414657.8452 518548.9501 376018.0403 389846.7282 452622.3555 471047.5949 497335.3616 507284.9131 0.768871632 0.782761571 0.817406224 1.022204557 0.741236395 0.768496595 0.892244858 0.928566142 0.98038666 1 18.95243673 1.708374893 1.828769376 0.987191285 0.822261957 0.459169411 0.074875761 0.318819368 2.165552147 0.057488178 0.022659017 51.09458702 -1.708374893 -0.164929328 T(ph)ISAQDTLAYATALLNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 T(0.5)IS(0.5)AQDTLAYATALLNEK 126.22 0.00031347 33208000 43415 48788 39566 40206 45021 48977 41171 54771 57081 54112 TRUE FALSE 41718.2938 47396.61401 46716.45634 42281.03648 46469.14135 49967.3485 41674.86301 53639.95971 50601.40418 50446.94604 0.826973624 0.939533861 0.926051228 0.838128763 0.921148751 0.990493031 0.826112704 1.063294489 1.003061794 1 15.62247931 1.70845908 9.731143496 1.023418805 0.900876481 0.542137112 0.053097391 0.083149213 17.29645315 0.024361423 0.01313141 51.10449247 -1.70845908 -0.122542324 LAAFADALEFADEEKES(ph)PVEFTGHK ddPTM_BT-474_Pertuzumab_2h_R1 3 LAAFADALEFADEEKESPVEFTGHK 25 1 Q5SY16 Q5SY16 NOL9 Polynucleotide 5-hydroxyl-kinase NOL9 1 LAAFADALEFADEEKES(1)PVEFTGHK;LAAFADALEFADEEKES(0.999)PVEFT(0.001)GHK;LAAFADALEFADEEKES(0.998)PVEFT(0.002)GHK 254.75 4.59E-45 351998000 473198 407047 354005 324526 344590 354107 379774 446106 513615 451932 TRUE FALSE 454704.899 395438.4181 417981.5783 341274.8258 355674.0503 361267.2862 384421.7878 436893.7552 455311.5784 421322.2431 1.079233073 0.938565254 0.992070998 0.81000904 0.844185315 0.857460749 0.9124175 1.036958676 1.080673014 1 18.68456456 1.708467397 4.766778977 1.045949135 0.91297679 0.346889394 0.075050946 0.183252932 9.863269426 0.042223066 0.020838979 51.10547122 -1.708467397 -0.132972344 APGPS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 2 APGPSPAK 8 0 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 APGPS(1)PAK;APGPS(1)PAK 91.584 0.01299 366560000 396820 373270 364110 414570 400160 363510 410320 494770 544450 567060 TRUE FALSE 381311.8357 362624.7051 429912.7766 435966.0074 413031.5098 370860.4213 415341.6189 484552.8266 482646.3185 528652.5211 0.721290111 0.685941503 0.813223733 0.824674034 0.7812911 0.701520198 0.785660906 0.916580944 0.91297459 1 19.01196024 1.708471487 2.676790618 0.949504875 0.757051497 0.770972314 0.046533766 0.124368223 1.941977786 0.031410727 0.013792463 51.10595256 -1.708471487 -0.192453378 RNEDEDSPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNEDEDSPNK 10 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 ; 136.49 0.00018654 847590000 1200440 1122150 1192400 1205500 1218800 1222670 1337050 1501050 1679460 1727810 FALSE TRUE 1153525.478 1090147.381 1407893.205 1267715.999 1258003.809 1247393.225 1353413.218 1470052.793 1488814.742 1610783.89 0.716126778 0.676780658 0.874042268 0.787018052 0.780988571 0.774401354 0.840220235 0.912631919 0.924279633 1 20.61933152 1.708518618 0.436972448 1.014199149 0.731944816 0.749760884 0.047569199 0.505081264 0.252851523 0.055638901 0.04313299 51.11149899 -1.708518618 -0.282254333 TQSPCFGDDDPAKKEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQSPCFGDDDPAKKEPR 17 2 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ; 170.61 1.03E-09 2394280000 2482030 2007340 1309540 1404212 1705940 1809950 1672310 2201480 2497720 2051050 FALSE TRUE 2385029.524 1950092.629 1546203.009 1476683.55 1760813.109 1846548.429 1692776.23 2156018.669 2214189.297 1912130.557 1.247315208 1.019853285 0.808628367 0.772271299 0.920864479 0.965702066 0.885282767 1.127547835 1.157969726 1 20.8667496 1.708568108 7.442687374 1.105516961 0.936568311 0.216833818 0.128539674 0.17765462 22.80489962 0.06670192 0.034914629 51.11732369 -1.708568108 -0.16894865 LLLERPS(ph)PIRDR ddPTM_BT-474_Pertuzumab_2h_R1 8 LLLERPSPIRDR 12 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR 151.8 3.46E-05 18481428000 3066100 3200972 2621772 3186736 3255344 3206349 3025757 2885502 2845936 3029923 TRUE FALSE 2946273.422 3109683.413 3095584.521 3351203.827 3360055.096 3271183.574 3062787.119 2825915.375 2522877.276 2824703.616 1.043038075 1.100888389 1.095897107 1.186391311 1.189524832 1.158062586 1.084286189 1.000428986 0.893147607 1 21.42966807 1.708629972 2.473852562 0.946610898 1.13061 0.698204578 0.048795305 0.143441219 1.890916304 0.033454549 0.014354099 51.1246058 -1.708629972 0.183999102 AEDEKQR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEDEKQR 7 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 85.212 0.019131 18369000 50634 64869 47068 46714 48303 64774 56206 43519 47436 46225 FALSE TRUE 48655.1673 63018.99963 55574.23462 49124.91514 49856.70986 66083.77466 56893.86584 42620.31744 42051.26415 43094.13958 1.129043712 1.462356605 1.289600748 1.139944216 1.156925521 1.533474744 1.320222805 0.989004952 0.975800064 1 15.39520407 1.708656249 5.544778731 0.985414505 1.295381246 0.548334002 0.125335021 0.113263226 8.345349084 0.066495703 0.03347135 51.12769919 -1.708656249 0.309966741 TNT(ph)PQGVLPSSQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNTPQGVLPSSQLK 14 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 TNT(1)PQGVLPSSQLK;T(0.01)NT(0.99)PQGVLPSSQLK 301.65 7.29E-43 777549000 688554 563776 495748 463921 482024 491957 538733 650219 761248 654928 TRUE FALSE 661644.5484 547697.6605 585340.6915 487864.0184 497528.7397 501904.7076 545326.1756 636791.7504 674834.3185 610569.1432 1.083652123 0.897028071 0.958680434 0.799031566 0.814860602 0.822027633 0.893144014 1.042947809 1.105254542 1 19.21979516 1.708912338 4.401020069 1.058878401 0.887815958 0.42528465 0.081634391 0.161460953 7.322184916 0.045703184 0.022322866 51.15785632 -1.708912338 -0.171062443 LTPS(ph)PDIIVLSDNEASSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPS(1)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR 346.37 1.32E-90 339652000 61966 70787 56491 66019 73259 74404 69081 62894 66057 69288 TRUE FALSE 59544.30021 68768.22407 66700.18034 69426.2485 75615.44227 75908.49986 69926.43394 61595.21692 58558.48629 64595.06204 0.921808855 1.06460497 1.032589462 1.074791885 1.170607162 1.175144004 1.082535286 0.953559219 0.906547412 1 15.97913626 1.708938601 5.014327395 0.946158477 1.080331863 0.381782547 0.07024732 0.16472199 9.871667276 0.039407772 0.019585584 51.16095005 -1.708938601 0.134173386 NSQEDSEDS(ph)EDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NSQEDS(0.039)EDS(0.961)EDKDVK 274.1 4.77E-33 281710000 553130 363890 319820 227710 350500 313510 332380 477130 589900 392960 TRUE FALSE 531513.0681 353512.2135 377618.5884 239462.1404 361774.1508 319849.387 336447.7659 467277.0988 522937.0251 366344.4692 1.450855992 0.964972159 1.03077464 0.653652943 0.987524533 0.873083706 0.918391826 1.275512907 1.427446213 1 18.48284131 1.708996695 6.393532718 1.262508323 0.967349847 0.223564493 0.210934213 0.172893574 16.84120425 0.104958934 0.05385097 51.16779421 -1.708996695 -0.295158476 AQSPGS(ph)PLHAR ddPTM_BT-474_Pertuzumab_2h_R1 4 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 AQS(0.109)PGS(0.891)PLHAR;AQS(0.001)PGS(0.999)PLHAR;AQSPGS(1)PLHAR;AQSPGS(1)PLHAR 111.81 0.0010374 1591580000 733490 936940 791670 1052670 955460 943130 971370 799760 828290 969540 TRUE FALSE 704824.3999 910219.3886 934742.3796 1106998.425 986193.2386 962200.7348 983257.9166 783244.6765 734265.9917 903872.1922 0.779783255 1.007022228 1.034153266 1.224728932 1.091075981 1.064531848 1.087828484 0.866543615 0.812355992 1 19.78575926 1.709023152 6.872765397 0.880706563 1.049458271 0.259794159 0.113261672 0.161239171 17.97650914 0.058188341 0.030146022 51.17091141 -1.709023152 0.168751708 SGS(ph)PSDNS(ph)GAEEMEVSLAKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 2 S(0.003)GS(0.844)PS(0.153)DNS(1)GAEEMEVSLAKPK 187.51 1.62E-17 380710000 922030 752910 683870 582720 783720 753200 843520 907830 1152700 1039200 TRUE FALSE 885996.0482 731437.744 807460.5216 612794.249 808929.0656 768430.2201 853843.2501 889082.9933 1021850.329 968814.0584 0.914516094 0.754982587 0.833452523 0.63251998 0.834968339 0.793165844 0.881328303 0.917702407 1.054743498 1 19.88586027 1.709146445 1.366980328 1.026677202 0.786757846 0.618500786 0.071184784 0.254606325 0.909797004 0.056072187 0.021344664 51.18544044 -1.709146445 -0.239919356 VT(ph)RSPPTQVAISSDSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTRSPPTQVAISSDSAR 17 1 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 VT(0.595)RS(0.404)PPT(0.002)QVAISSDSAR 83.606 0.0088732 450590000 102360 76784 67918 80889 82619 77922 70261 103390 106220 94702 TRUE FALSE 98359.65804 74594.1955 80192.29343 85063.69098 85276.51517 79497.63623 71120.87514 101254.9604 94162.35091 88287.74919 1.11408048 0.844898598 0.908306013 0.963482383 0.965892957 0.900437909 0.805557688 1.146874411 1.066539263 1 16.42992564 1.709151004 11.38763088 1.078542067 0.926633012 0.371269015 0.084525184 0.107833745 30.4714836 0.038205756 0.020834036 51.18597776 -1.709151004 -0.151909055 T(ph)QLASWSDPTEETGPVAGILDTETLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQLASWSDPTEETGPVAGILDTETLEK 27 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 T(0.31)QLAS(0.31)WS(0.31)DPT(0.057)EET(0.013)GPVAGILDTETLEK 68.689 0.0090009 0 4921.8 5164.3 3368.3 5421.9 6577.5 4458.9 3584 4143.1 2774.3 2724.5 TRUE FALSE 4729.450615 5017.01922 3977.026737 5701.724909 6789.071261 4549.062013 3627.862064 4057.543537 2459.373095 2539.967188 1.862012484 1.975229934 1.565778785 2.244802584 2.67289723 1.790992433 1.428310602 1.597478722 0.968269632 1 11.31059414 1.70926559 1.156972754 0.999734565 2.032336441 0.626818408 0.304235269 0.327523844 0.823227088 0.277382857 0.107173956 51.19948472 -1.70926559 1.032601877 NKIFMEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 NKIFMEFR 8 1 F5H5U2;Q8NHQ9 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 0 ; 60.973 0.05342 483220000 216462 497290 352710 583100 571170 576300 438460 223490 128159 210220 FALSE TRUE 208002.4257 483107.7761 416452.543 613193.8609 589542.2018 587953.1809 443826.0046 218874.8534 113610.9276 195981.6122 1.061336436 2.465066854 2.124957226 3.12883364 3.008150588 3.000042577 2.264630849 1.11681321 0.579701975 1 17.58035878 1.709337401 3.146401137 0.802875495 2.512530351 0.609504127 0.568097098 0.145080079 3.192184463 0.348467335 0.159927437 51.20795128 -1.709337401 1.709654857 VQPGCY(ph)LPSNPEAIVLDIDY(ph)KSGT(ph)PMQS(ph)AAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VQPGCYLPSNPEAIVLDIDYKSGTPMQSAAK 31 1 P42356;P42356-2;A8MTF1 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 4 VQPGCY(0.713)LPS(0.287)NPEAIVLDIDY(0.573)KS(0.485)GT(0.974)PMQS(0.967)AAK 42.735 0.067652 7591300000 66279 90969 82299 146270 123700 120280 104050 61131 42843 71692 TRUE FALSE 63688.7434 88374.65319 97172.26003 153819.0122 127678.9228 122712.144 105323.395 59868.62349 37979.64225 66836.23698 0.952907379 1.322256566 1.453885862 2.301431367 1.910324827 1.836012163 1.575842683 0.895750961 0.568249261 1 16.02834289 1.709450249 3.64209039 0.768869452 1.655151439 0.518178605 0.354320459 0.164102603 4.937750299 0.218221731 0.103393875 51.22125904 -1.709450249 0.886281988 VPEEAAQDRPMS(ph)PGDCPPETTETPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VPEEAAQDRPMSPGDCPPETTETPK 25 1 P13994 P13994 CCDC130 Coiled-coil domain-containing protein 130 1 VPEEAAQDRPMS(1)PGDCPPETTETPK;VPEEAAQDRPMS(1)PGDCPPETTETPK 150.04 1.08E-07 995480000 1216768 1038433 831175 928026 991813 880193 906107 1221160 1272340 1235170 TRUE FALSE 1169215.361 1008817.908 981386.8119 975921.5331 1023715.566 897991.1055 917196.2085 1195942.619 1127909.297 1151510.836 1.01537504 0.876081993 0.852260162 0.847513981 0.889019481 0.779837304 0.796515482 1.038585641 0.97950385 1 20.13509656 1.709498282 8.672079286 1.005060034 0.862212871 0.523219541 0.06143252 0.09059377 15.53234048 0.030482031 0.016249958 51.22692438 -1.709498282 -0.142847164 NDSYTLHK ddPTM_BT-474_Pertuzumab_2h_R1 4 NDSYTLHK 8 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QSE0 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;;; 93.111 0.011301 2292170000 2866990 2888940 2467240 2631490 2687380 2598550 3116770 3121680 3842760 3601100 FALSE TRUE 2754944.861 2806550.26 2913125.151 2767301.514 2773822.018 2651094.461 3154913.964 3057216.217 3406545.995 3357194.289 0.820609302 0.835980887 0.867726113 0.82428995 0.826232198 0.789675614 0.939747209 0.910646198 1.014700283 1 21.6788246 1.709576085 1.321978067 1.004249463 0.830624132 0.818160363 0.032119318 0.164825179 0.548050454 0.02569526 0.009790681 51.23610244 -1.709576085 -0.173625331 KGS(ph)ITEYTAAEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KGSITEYTAAEEK 13 1 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.949)IT(0.051)EYTAAEEK;KGS(0.916)IT(0.084)EYTAAEEK;KGS(0.791)IT(0.209)EYTAAEEK 258.38 3.81E-24 3546040000 4392990 3356960 3566690 2842920 3463600 3187780 3671130 4716170 5608960 5038880 TRUE FALSE 4221307.094 3261222.788 4211270.224 2989643.442 3575009.84 3252239.096 3716058.387 4618779.441 4972254.375 4697592.169 0.898610808 0.694232847 0.896474209 0.63642039 0.761030271 0.692320444 0.791055982 0.983222739 1.058468721 1 22.16349004 1.709599563 3.278560848 1.027549886 0.758822283 0.669274364 0.080014823 0.114085026 2.739201432 0.043833991 0.020318851 51.23887228 -1.709599563 -0.268727603 RQS(ph)PSPSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 RQSPSPSTR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RQS(0.988)PS(0.011)PSTR 75.479 0.023365 172570000 40176 39272 31345 35486 40873 39055 41376 32200 35882 38818 TRUE FALSE 38605.8775 38152.00101 37009.73877 37317.43671 42187.71716 39844.71886 41882.37186 31535.05875 31808.82579 36188.82228 1.066790104 1.054248207 1.022684255 1.031186824 1.165766513 1.101022812 1.157328955 0.871403289 0.87896825 1 15.14325654 1.709703589 8.408371821 0.908457368 1.083392839 0.657152139 0.055642604 0.068424037 11.11662563 0.027951959 0.014851625 51.25114697 -1.709703589 0.174935471 RIESLIDRDYMER ddPTM_BT-474_Pertuzumab_2h_R1 2 RIESLIDRDYMER 13 2 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ; 162.41 2.27E-05 215100000 87140 104420 64025 67516 81439 90591 75295 64819 64868 57126 FALSE TRUE 83734.47246 101442.0438 75595.74173 71000.50885 84058.5594 92422.81209 76216.48273 63480.465 57504.45659 53256.80514 1.572277425 1.904771486 1.419456941 1.333172515 1.578362787 1.735417884 1.43111256 1.19196908 1.07975791 1 15.70067826 1.709935204 2.069543939 1.046251738 1.585547374 0.693996583 0.149906572 0.177933553 1.588344611 0.111738612 0.04553363 51.27848719 -1.709935204 0.539295636 TENSWGEPSS(ph)PSTLVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TENSWGEPSSPSTLVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR 45 1 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0;K7ELY5 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 TENSWGEPS(0.174)S(0.763)PS(0.031)T(0.031)LVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR;TENSWGEPS(0.013)S(0.928)PS(0.046)T(0.013)LVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR 248.15 3.29E-56 347970000 74736 77828 73050 93508 82689 101306 74610 77589 75541 71458 TRUE FALSE 71815.23449 75608.42164 86251.75999 98333.95909 85348.76678 103354.4767 75523.0995 75986.76004 66965.90237 66618.08601 1.078014077 1.134953376 1.294719875 1.476085024 1.281165099 1.551447706 1.133672611 1.140632591 1.00522105 1 16.02362628 1.709948319 2.060931083 1.02040898 1.299463965 0.403818284 0.137982638 0.314513523 2.781849309 0.101986729 0.041511568 51.28003567 -1.709948319 0.279054985 DGEDLKDHSTESK ddPTM_BT-474_Pertuzumab_2h_R1 4 DGEDLKDHSTESK 13 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 187.57 4.11E-06 2261440000 3062440 2419500 2091900 1856690 2278280 2139830 2556760 2615380 3379030 2778540 FALSE TRUE 2942756.459 2350498.229 2469952.864 1952513.993 2351562.945 2183098.829 2588050.394 2561371.489 2995456.68 2590347.011 1.136047196 0.907406698 0.953522001 0.753765416 0.907817731 0.842782384 0.999113394 0.988814039 1.156392046 1 21.30471395 1.710065589 2.045497447 1.071041602 0.912725352 0.256955183 0.100199073 0.380938532 3.313770524 0.069810769 0.028358668 51.29388438 -1.710065589 -0.158316249 KTTYHT(ph)MVDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTTYHTMVDLK 11 1 S4R407;Q5T2K3;Q9H8W5-2;Q9H8W5 S4R407 TRIM45 Tripartite motif-containing protein 45 1 KT(0.231)T(0.231)Y(0.189)HT(0.35)MVDLK 68.069 0.028279 832320000 551850 993710 707600 1361400 1035700 1137600 1018200 704340 573790 977550 TRUE FALSE 530283.0919 965370.3637 835479.0605 1431662.017 1069014.231 1160603.051 1030661.036 689795.1329 508655.7647 911339.6678 0.581872062 1.059287111 0.916759239 1.570942282 1.173014046 1.27351315 1.130929633 0.756902346 0.558140705 1 19.79762934 1.710396876 5.150398017 0.740197588 1.12017797 0.249985754 0.257988845 0.199484025 12.67149576 0.136916494 0.068361793 51.33302721 -1.710396876 0.379980382 DKADKDEQIR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKADKDEQIR 10 2 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;A0A494BZX5;A0A494C122;A0A494C0Y7;H7C0P8 Q92878-2 RAD50 DNA repair protein RAD50 0 ;; 117.79 0.00051217 1327800000 1356032 1169031 1130860 1019018 1157175 1244426 1224443 1497616 1808348 1506157 FALSE TRUE 1303036.77 1135691.38 1335231.558 1071609.641 1194396.585 1269589.146 1239428.1 1466689.706 1603071.916 1404143.645 0.927993924 0.808814244 0.950922338 0.763176649 0.85062279 0.904173267 0.882693237 1.044543919 1.141672308 1 20.4212591 1.710478129 3.273106429 1.078478043 0.864997795 0.679192056 0.060719596 0.109549932 2.617365112 0.033361193 0.015472341 51.3426321 -1.710478129 -0.213480248 TGKPEEASLDSR ddPTM_BT-474_Pertuzumab_2h_R1 5 TGKPEEASLDSR 12 1 Q9BY42;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ;;;; 116.19 0.0007922 4307100000 10362070 9597690 8126820 8382840 8588820 9099830 9210110 10470050 11889300 10902680 FALSE TRUE 9957108.849 9323973.278 9595517.154 8815479.377 8865087.195 9283834.797 9322826.081 10253839.81 10539676.51 10164231.77 0.979622373 0.917331825 0.944047457 0.86730405 0.872184676 0.913382832 0.917218959 1.008816017 1.036937837 1 23.27699784 1.710497314 3.929151599 1.020077133 0.912814238 0.677240369 0.031437424 0.109315839 3.87065125 0.018215258 0.008757609 51.34490016 -1.710497314 -0.107262895 SS(ph)PTQETQAPFIAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPTQETQAPFIAK 14 0 O15231-5 O15231-5 ZNF185 Zinc finger protein 185 1 S(0.01)S(0.99)PTQETQAPFIAK;S(0.205)S(0.795)PTQETQAPFIAK;S(0.205)S(0.795)PTQETQAPFIAK 308.03 1.26E-55 738340000 1113600 1071990 993200 1062420 1051120 1155840 1243280 1310260 1395470 1534840 TRUE FALSE 1070079.281 1041417.895 1172693.334 1117251.624 1084930.229 1179211.877 1258495.633 1283202.673 1237062.096 1430883.92 0.747844927 0.727814381 0.819558678 0.780812202 0.758223791 0.824114284 0.87952322 0.896790198 0.864543992 1 20.44847521 1.710684879 0.30549911 1.017276195 0.717767323 0.867796129 0.028609678 0.511693542 0.165701293 0.052337794 0.054478654 51.36708009 -1.710684879 -0.299508872 TASGAVDEDALTLEELEEQQRR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASGAVDEDALTLEELEEQQRR 22 1 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 0 203.26 2.10E-22 57478000 39983 41842 22005 34131 36646 38136 36415 30922 33080 34292 FALSE TRUE 38420.42016 40648.70713 25981.793 35892.505 37824.75187 38907.13605 36860.65766 30283.44989 29324.89708 31969.3723 1.20178838 1.27148906 0.812708888 1.12271535 1.183155913 1.217012824 1.152999106 0.947264451 0.917280978 1 14.9644028 1.71080275 5.806117011 0.94899082 1.134369136 0.33141399 0.118474465 0.175507464 14.28557964 0.063133562 0.032015484 51.3810234 -1.71080275 0.185378316 RDS(ph)DGVDGFEAEGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSDGVDGFEAEGKK 15 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGKK;RDS(1)DGVDGFEAEGKK 192.94 5.93E-08 1295030000 1772070 1496800 1311240 1115910 1321750 1420340 1352850 1603640 1726320 1612760 TRUE FALSE 1702815.545 1454112.73 1548210.236 1173502.249 1364265.289 1449060.248 1369406.583 1570524.274 1530355.391 1503526.329 1.132547873 0.967134863 1.029719405 0.780499966 0.907377053 0.963774442 0.910796543 1.04456054 1.017844092 1 20.5199187 1.710920294 9.553922407 1.022524357 0.950971176 0.105240058 0.0855656 0.243158785 51.32916454 0.041973191 0.022593049 51.39493184 -1.710920294 -0.071553181 KVEEEEDESALKR ddPTM_BT-474_Pertuzumab_2h_R1 6 KVEEEEDESALKR 13 2 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;;;;; 138.28 2.86E-05 3278540000 4821740 3941740 3621430 3355240 3761860 4090590 4243190 4550980 5541940 5052290 FALSE TRUE 4633301.07 3829325.435 4275902.959 3528404.338 3882863.643 4173304.532 4295119.429 4457000.673 4912842.205 4710093.898 0.983696115 0.813004054 0.907816925 0.749115498 0.824370751 0.886034254 0.911896773 0.946265779 1.043045491 1 22.16732439 1.710947489 1.409693995 1.020407094 0.853212805 0.519290865 0.060297464 0.305497694 1.166578743 0.04778726 0.018219549 51.39815021 -1.710947489 -0.167194289 DILIQYDR ddPTM_BT-474_Pertuzumab_2h_R1 8 DILIQYDR 8 0 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;;;;;; 196.95 0.00034426 9483110000 5039420 6064060 5690260 7208690 6649340 6113200 6447350 5190040 5319000 5985050 FALSE TRUE 4842473.895 5891118.946 6718616.561 7580731.355 6863222.06 6236813.092 6526254.598 5082863.86 4715209.419 5579677.233 0.867877064 1.055817156 1.204122798 1.358632594 1.230039261 1.117773096 1.169647334 0.910960195 0.845068491 1 22.41175024 1.711094362 5.351936721 0.907128738 1.153239101 0.401556081 0.124883067 0.153571619 10.58543256 0.069771428 0.035024686 51.41553539 -1.711094362 0.246110363 STPFIVPS(ph)SPTEQEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.816)S(0.184)PTEQEGR 211.75 6.58E-12 5150400000 943260 977270 791920 988870 1054600 1052300 956990 967130 987830 1033100 TRUE FALSE 906396.3564 949399.2164 935037.5602 1039905.699 1088522.167 1073578.227 968701.9299 947158.4275 875695.6797 963127.2168 0.941097231 0.985746431 0.970834947 1.079717903 1.130195625 1.114679565 1.005788138 0.983419855 0.909221196 1 19.87736685 1.711392632 2.879067093 0.954669637 1.038356055 0.21571177 0.061402759 0.368736341 6.696822956 0.041599371 0.018700063 51.45085929 -1.711392632 0.083686417 KKDQEDDEQQR ddPTM_BT-474_Pertuzumab_2h_R1 4 KKDQEDDEQQR 11 2 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;;; 131.69 0.00011139 270206000 122930 112812 92996 85249 99420.1 109020.4 113775.3 128149 160008 142973 FALSE TRUE 118125.7597 109594.7122 109802.4459 89648.71111 102618.0378 111224.8672 115167.7162 125502.6784 141844.5626 133289.3114 0.886235802 0.822231814 0.823790331 0.672587398 0.769889474 0.834462014 0.864043148 0.941580965 1.064185576 1 17.02420157 1.711538744 1.5489523 1.032711551 0.795226242 0.736440311 0.054972693 0.194205179 0.911502672 0.0457399 0.017562665 51.46817204 -1.711538744 -0.23748531 FRKVQHELDEAEER ddPTM_BT-474_Pertuzumab_2h_R1 2 FRKVQHELDEAEER 14 2 P13533;P12883 P13533 MYH6;MYH7 Myosin-6;Myosin-7 0 ; 63.76 0.037414 998890000 200370 488050 312030 517460 529990 667000 415800 242630 151577 234690 FALSE TRUE 192539.3189 474131.2919 368420.7621 544166.1726 547037.6097 680487.197 420888.6848 237619.6057 134370.6144 218794.2373 0.880001783 2.167019103 1.683868674 2.487113826 2.500237742 3.110169653 1.923673539 1.086041427 0.61414147 1 17.73921521 1.711554944 3.326771604 0.82799563 2.173293995 0.501468043 0.556625231 0.173038858 4.273044921 0.333809286 0.155556546 51.47009189 -1.711554944 1.345298365 WDGS(ph)EEDEDNSK ddPTM_BT-474_Pertuzumab_2h_R1 6 WDGSEEDEDNSK 12 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK 311.99 2.69E-46 7330420000 4847740 4130550 3641550 3666490 4089480 4418620 4472490 4976250 6116670 5625110 TRUE FALSE 4658284.961 4012750.758 4299659.091 3855717.988 4221021.838 4507967.524 4527225.67 4873488.699 5422331.265 5244116.289 0.888287884 0.765191033 0.819901553 0.73524647 0.804906224 0.859623867 0.863296201 0.929325063 1.033983795 1 22.32226825 1.71158608 1.187817372 1.021462179 0.801619144 0.792884536 0.041632935 0.186926762 0.495898567 0.034300597 0.013213534 51.47378215 -1.71158608 -0.219843035 SKQQS(ph)LQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKQQSLQR 8 1 D6RD21;D6RED4;Q9BW11-3;Q9BW11-2;Q9BW11;Q9BW11-4 D6RD21 MXD3 Max dimerization protein 3 1 SKQQS(1)LQR 53.597 0.082108 208700000 167930 295410 162960 294430 249970 270260 239300 134270 86707 177150 TRUE FALSE 161367.1099 286985.196 192410.497 309625.5676 258010.5121 275724.8424 242228.625 131497.2776 76864.38487 165151.4727 0.977085504 1.737708973 1.165054685 1.874797497 1.562265887 1.669526998 1.466705813 0.796222252 0.465417496 1 17.33343031 1.711688162 3.990798092 0.702401654 1.518278137 0.600311146 0.276281698 0.111893013 4.092726968 0.14256798 0.068802631 51.48588261 -1.711688162 0.815876483 GRDPDAHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRDPDAHPK 9 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61 Q641Q2 FAM21A WASH complex subunit FAM21A 0 61.353 0.053912 90493000 123510 119380 108220 115780 119590 130670 133280 132980 161830 162780 FALSE TRUE 118683.0927 115975.3993 127777.7613 121755.4197 123436.721 133312.2369 134911.1205 130233.9165 143459.7368 151754.7656 0.782071602 0.764229043 0.842001639 0.802316943 0.813396011 0.878471502 0.889007472 0.858186667 0.945339254 1 17.2113823 1.711689349 0.209209232 1.048140649 0.720466398 0.874622815 0.024804865 0.861996696 0.183355596 0.103118322 0.116484045 51.4860233 -1.711689349 -0.327674251 TVKPVENKDDDDSIADFLNS(ph)DEEEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVKPVENKDDDDSIADFLNSDEEEDR 26 2 Q15649-2;Q15649 Q15649-2 ZNHIT3 Zinc finger HIT domain-containing protein 3 1 TVKPVENKDDDDSIADFLNS(1)DEEEDR 132.57 2.84E-05 149390000 115740 87844 97853 90644 85961 94670 108780 129710 160170 147840 TRUE FALSE 111216.7528 85338.77513 115537.2138 95322.1477 88726.01363 96584.29226 110111.2822 127031.4432 141988.1731 137826.6651 0.806932046 0.619174635 0.838279108 0.691608896 0.643750711 0.700766373 0.798911314 0.921675374 1.03019378 1 17.07249551 1.711763972 1.897083467 1.014527598 0.713893206 0.782867256 0.063849313 0.133385836 0.981404805 0.044596903 0.017787599 51.49487072 -1.711763972 -0.300634392 DCDINDDEFLHLPAHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCDINDDEFLHLPAHLR 17 0 Q9BSF4 Q9BSF4 C19orf52 Uncharacterized protein C19orf52 0 ; 92.773 0.0018656 109437000 61085 117112 71782 196284 65635 89470 157259 54957 113796 101807 FALSE TRUE 58697.73067 113772.0804 84754.60418 206414.2408 67746.20938 91279.1447 159183.5827 53822.11874 100878.3552 94911.52121 0.618446843 1.198717279 0.892985415 2.174807001 0.713782779 0.961728814 1.67717871 0.567076769 1.06286733 1 16.5342956 1.711971918 24.9999985 0.857759335 1.179049417 0.084167699 0.452400293 2.020290575 1890.65516 0.203034623 0.112592905 51.51953308 -1.711971918 0.321290082 KPPAPPS(ph)PVQSQS(ph)PSTNWSPAVPVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(0.995)PVQS(0.086)QS(0.389)PS(0.289)T(0.187)NWS(0.054)PAVPVKK 120.15 0.00013069 186030000 135030 119840 102750 108890 107680 115640 113410 141360 157530 143100 TRUE FALSE 129752.8783 116422.2805 121319.2107 114509.8259 111143.625 117978.32 114797.9455 138440.8666 139647.8548 133407.7095 0.972604048 0.872680304 0.909386804 0.858344891 0.833112459 0.884344094 0.860504583 1.037727633 1.046774997 1 17.02548252 1.712017431 6.209995482 1.03132235 0.881971914 0.755919268 0.037313601 0.06270798 5.870087703 0.018892529 0.009671245 51.52493243 -1.712017431 -0.149350437 KEESEKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEESEKPR 8 2 P83916;J3KS05;K7ELA4 P83916 CBX1 Chromobox protein homolog 1 0 ;;; 105.78 0.0024304 922080000 991940 962290 711890 895880 825600 907530 988360 1035330 1215450 1191960 FALSE TRUE 953173.8882 934846.4314 840544.3589 942116.4742 852156.1738 925880.8784 1000455.845 1013950.074 1077477.212 1111227.488 0.857766658 0.841273674 0.756410697 0.847816028 0.766860236 0.833205522 0.900315963 0.912459496 0.969627933 1 20.08372276 1.712161876 1.070848579 0.993422386 0.812440121 0.801761347 0.033285495 0.203359288 0.436841879 0.028552468 0.01123668 51.54207229 -1.712161876 -0.180982265 EHINLGCDMDFDIAGPSIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EHINLGCDMDFDIAGPSIR 19 0 P21796;C9JI87 P21796 VDAC1 Voltage-dependent anion-selective channel protein 1 0 ; 252.55 7.46E-31 1057290000 423650 620390 406510 845600 353930 447380 712330 323269 556330 464110 FALSE TRUE 407093.2896 602697.0846 479975.3998 889241.5173 365314.4799 456426.3301 721047.7076 316593.3822 493177.7507 432675.4163 0.940874555 1.392954307 1.109319785 2.055216182 0.844315314 1.054893144 1.666486425 0.731711048 1.139833076 1 18.72292563 1.712249602 15.78688046 0.952999935 1.294172203 0.162653103 0.351041315 0.290673419 158.9282902 0.157806097 0.087151287 51.5524847 -1.712249602 0.341172268 ETPHS(ph)PGVEDAPIAK ddPTM_BT-474_Pertuzumab_2h_R1 10 ETPHSPGVEDAPIAK 15 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 ETPHS(1)PGVEDAPIAK;ET(0.002)PHS(0.998)PGVEDAPIAK;ET(0.009)PHS(0.991)PGVEDAPIAK;ET(0.015)PHS(0.985)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.004)PHS(0.996)PGVEDAPIAK;ET(0.002)PHS(0.998)PGVEDAPIAK;ET(0.031)PHS(0.969)PGVEDAPIAK;ET(0.001)PHS(0.999)PGVEDAPIAK;ET(0.006)PHS(0.994)PGVEDAPIAK 371.6 1.39E-97 99374970000 21079990 21769420 18467500 20572750 21131660 21221860 21246680 19928780 21553770 21364090 TRUE FALSE 20256160.69 21148577.46 21804988.06 21634512.09 21811379.04 21650980.55 21506703.23 19517243.73 19107076.39 19917081.16 1.017024559 1.061831163 1.094788332 1.086229048 1.095109211 1.087055898 1.079811999 0.979924898 0.959331151 1 24.2475029 1.712259632 5.000438937 0.976248974 1.076728477 0.771838065 0.023557416 0.072456301 4.331672546 0.012868471 0.006411464 51.55367535 -1.712259632 0.100479504 VIHDNFGIVEGLMTTVHAITAT(ph)QK ddPTM_BT-474_Pertuzumab_2h_R1 3 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAIT(0.001)AT(0.998)QK 318.18 1.84E-73 7430355000 3757785 3778882 3228346 2986959 3379594 3688234 2887933 2740291 3916113 2591278 TRUE FALSE 3610926.608 3671111.985 3811779.936 3141116.312 3488301.71 3762812.618 2923276.388 2683703.033 3471572.27 2415768.433 1.494732094 1.519645648 1.577874719 1.30025555 1.44397189 1.557604846 1.210081375 1.110910713 1.437046789 1 21.20405074 1.712344056 0.301963598 0.973078049 1.589732735 0.564651089 0.125287918 1.101290369 0.351687031 0.231580628 0.242747819 51.56369798 -1.712344056 0.616654686 S(ph)RSPAVNGENK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPAVNGENK 11 1 Q8IZD2-6;Q8IZD2-5;Q8IZD2-7;Q8IZD2;Q8IZD2-8;Q8IZD2-2 Q8IZD2-6 KMT2E Histone-lysine N-methyltransferase 2E 1 S(0.5)RS(0.5)PAVNGENK 71.98 0.028795 81122000 136170 132930 118370 134150 130910 119220 125270 159690 175220 159330 TRUE FALSE 130848.3259 129138.9666 139762.0921 141073.4976 135120.839 121630.7101 126803.0917 156392.3457 155329.7602 148538.4372 0.880905497 0.869397639 0.940915327 0.949744054 0.909669185 0.818850073 0.853671912 1.052874587 1.045720981 1 17.18047678 1.712442446 7.273393065 1.035671925 0.890792753 0.738364402 0.039131745 0.067177333 8.586779152 0.021456635 0.011211986 51.57538116 -1.712442446 -0.144879172 VSPPAPGS(ph)APET(ph)PEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSPPAPGSAPETPEDK 16 0 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 2 VSPPAPGS(1)APET(1)PEDK 202.03 1.67E-10 143490000 226790 222820 189620 191980 205990 214360 231780 260990 317020 294800 TRUE FALSE 217926.7961 216465.3918 223888.5521 201888.1108 212615.8554 218694.5061 234616.593 255600.4653 281033.2187 274832.9334 0.792942801 0.787625373 0.814635092 0.734584856 0.77361855 0.795736171 0.853669864 0.930021239 1.022560197 1 18.06819537 1.712504246 1.490361709 1.014676917 0.78072988 0.946360071 0.021872335 0.078114054 0.336744995 0.017692616 0.006773228 51.58272083 -1.712504246 -0.233947037 DMDLTEVITGTLWNLSSHDSIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DMDLTEVITGTLWNLSSHDSIK 22 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ; 104.63 0.00031518 131275000 102962 169792 140468 238216 191284 190218 168865 120708 97838 132726 FALSE TRUE 98938.13121 164949.6984 165853.6923 250510.3563 197436.8236 194064.3383 170931.6204 118215.3376 86731.84041 123736.3498 0.799588248 1.3330739 1.340379707 2.024549429 1.595625084 1.568369672 1.381417996 0.955380838 0.700940674 1 16.91690985 1.712586763 3.180053649 0.843115411 1.467582002 0.424930326 0.293970153 0.207424367 4.644586581 0.181796808 0.083928849 51.59252257 -1.712586763 0.624466592 EAALVQQEEEKAEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAALVQQEEEKAEQR 15 1 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 199.15 6.90E-09 833870000 1032770 958520 779320 742200 884960 939580 836350 1002950 1087230 939300 FALSE TRUE 992408.2066 931183.9481 920160.4599 780505.0309 913425.5421 958578.9514 846585.5015 982238.732 963812.2084 875680.3744 1.133299587 1.063383371 1.050794887 0.891312691 1.043103818 1.09466762 0.966774552 1.12168636 1.100643838 1 19.74004485 1.71261716 21.79187543 1.083342513 1.033587503 0.058141987 0.069548123 1.134257723 940.8147092 0.032544885 0.018039821 51.59613378 -1.71261716 -0.04975501 ARSPYS(ph)PAEEDALFMDLPTGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSPYSPAEEDALFMDLPTGPR 22 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 ARS(0.021)PY(0.079)S(0.9)PAEEDALFMDLPTGPR 140.46 7.84E-08 87475000 35596 43427 34431 39852 44407 41817 35211 38051 36213 34666 TRUE FALSE 34204.86897 42188.50448 40653.44761 41908.7665 45835.39148 42662.56839 35641.92275 37265.23355 32102.25206 32318.04094 1.058383119 1.305416518 1.257918068 1.296760734 1.418260208 1.320085226 1.102849112 1.153078357 0.993322959 1 14.98005213 1.71276692 1.404974236 1.005257031 1.279696501 0.551192372 0.09460419 0.30369879 1.150981182 0.077748507 0.029677281 51.61392894 -1.71276692 0.274439471 LSPLEACAHSFFDELR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSPLEACAHSFFDELR 16 0 P49840;A8MT37 P49840 GSK3A Glycogen synthase kinase-3 alpha 0 ;;; 224.33 7.90E-15 650551000 383170 497197 375163 491130 482654 489583 471593 403498 400254 484785 FALSE TRUE 368195.2928 483017.4284 442963.2996 516477.2782 498179.0042 499482.7037 477364.4962 395165.6253 354818.8439 451950.0801 0.814681331 1.068740663 0.980115546 1.142775056 1.102287678 1.105172287 1.056232795 0.874356799 0.785084149 1 18.7858039 1.712970508 5.488277478 0.871707259 1.046641187 0.324134675 0.099339964 0.154623333 11.28222284 0.050522108 0.025477871 51.63813014 -1.712970508 0.174933928 KKEDDVGIER ddPTM_BT-474_Pertuzumab_2h_R1 2 KKEDDVGIER 10 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 0 ; 92.781 0.0051933 450290000 462870 433770 358890 386320 454670 457790 448390 494280 610030 570840 FALSE TRUE 444780.5287 421399.3043 423749.4065 406258.0215 469294.8735 467046.8275 453877.5309 484072.9453 540781.9519 532176.4983 0.835776345 0.791841251 0.796257271 0.763389632 0.881840658 0.877616409 0.852870302 0.909609776 1.0161703 1 19.02154527 1.713208914 0.693728257 1.015844734 0.80250216 0.812518805 0.034732723 0.279910302 0.273504899 0.033230691 0.016382772 51.6664847 -1.713208914 -0.213342573 WGQPPS(ph)PTPVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_BT-474_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 WGQPPS(0.666)PT(0.334)PVPRPPDADPNT(0.12)PS(0.88)PKPLEGRPER 95.977 3.51E-05 1331700000 476260 410640 345120 352210 368940 419040 372060 456480 488600 438700 TRUE FALSE 457647.2327 398928.9493 407490.8612 370387.6003 380807.2902 427513.2759 376613.3816 447053.5285 433136.1764 408986.4582 1.118978938 0.975408699 0.996343162 0.905623139 0.931099997 1.045299343 0.920845603 1.093076603 1.059047721 1 18.64169355 1.71323271 12.28524809 1.056421715 0.982115476 0.184121316 0.063025657 0.170880974 62.85459539 0.029080843 0.015925547 51.66931571 -1.71323271 -0.074306239 AVSTGLPHMIQELQNHIHDEGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVSTGLPHMIQELQNHIHDEGLR 23 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 79.177 0.004404 76578000 32686 36600 32355 38460 39718 43761 45453 24448 36072 27506 FALSE TRUE 31408.59498 35556.20384 38202.26823 40444.92521 40995.56554 44645.8774 46009.26741 23943.14026 31977.25779 25642.99412 1.224841172 1.3865855 1.48977409 1.577230998 1.598704322 1.741055557 1.794223685 0.933710788 1.247017319 1 14.6462771 1.713259189 9.442006854 1.073696604 1.547041183 0.627452421 0.170724942 0.075750664 16.38237424 0.087267323 0.046934976 51.67246611 -1.713259189 0.473344579 RGS(ph)ASGSEPAGDSDR ddPTM_BT-474_Pertuzumab_2h_R1 5 RGSASGSEPAGDSDR 15 1 P50747;A0A0C4DG27 P50747 HLCS Biotin--protein ligase;Biotin--[methylmalonyl-CoA-carboxytransferase] ligase;Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase;Biotin--[methylcrotonoyl-CoA-carboxylase] ligase;Biotin--[acetyl-CoA-carboxylase] ligase 1 RGS(0.752)AS(0.247)GS(0.001)EPAGDSDR;RGS(0.99)AS(0.01)GSEPAGDSDR;RGS(0.961)AS(0.03)GS(0.009)EPAGDSDR;RGS(0.968)AS(0.031)GS(0.001)EPAGDSDR;RGS(0.997)AS(0.003)GSEPAGDSDR 152 1.78E-06 252429000 161718 174440 142036 172591 183000 182599 155149 166788 169704 158851 TRUE FALSE 155397.8818 169465.142 167705.0648 181498.4422 188886.3612 186291.2769 157047.7599 163343.7695 150439.9134 148091.8803 1.049334248 1.144324332 1.132439297 1.22557997 1.275467371 1.257943896 1.060475156 1.102989369 1.015855245 1 17.17613302 1.713319319 1.606520016 1.0167226 1.179385676 0.464660135 0.06892839 0.349676365 1.778287223 0.057595387 0.022249444 51.67962091 -1.713319319 0.162663077 KDEELDPMDPSSYSDAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEELDPMDPSSYSDAPR 18 1 O60828-2;O60828;O60828-5;O60828-4;H7C053 O60828-2 PQBP1 Polyglutamine-binding protein 1 0 ; 120.32 7.77E-05 638400000 1641590 1666610 1479890 1357750 1540320 1631080 1561550 1782910 1981690 1823100 FALSE TRUE 1577434.848 1619079.915 1747339.043 1427823.64 1589865.792 1664061.555 1580660.716 1746092.285 1756736.859 1699619.813 0.928110414 0.952612991 1.028076414 0.840084135 0.935424369 0.979078699 0.930008408 1.027342863 1.033605778 1 20.69678064 1.713334432 6.419099475 1.022520997 0.942918375 0.386267132 0.045146997 0.138961371 13.99926035 0.022731325 0.011694348 51.68141935 -1.713334432 -0.079602622 T(ph)PSPAAEDAREPEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 T(0.567)PS(0.433)PAAEDAREPEAK;T(0.624)PS(0.376)PAAEDAREPEAK;T(0.909)PS(0.091)PAAEDAREPEAK 225.85 6.01E-12 2771300000 1994760 1837490 1601890 1592090 1607060 1737670 1622950 2095080 2325470 1905480 TRUE FALSE 1916802.574 1785086.584 1891387.157 1674257.956 1658752.544 1772806.878 1642812.148 2051815.866 2061492.395 1776420.142 1.079025467 1.004878599 1.064718369 0.942489851 0.933761392 0.997965985 0.924788066 1.155028485 1.160475692 1 20.7605414 1.713434085 9.583784226 1.116754925 0.991869368 0.392363006 0.063651085 0.098842789 22.11568989 0.03013576 0.016229645 51.69327951 -1.713434085 -0.124885557 DIDIHEVR ddPTM_BT-474_Pertuzumab_2h_R1 9 DIDIHEVR 8 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;; 177.97 0.00025206 32623110000 39736270 39927060 35968530 39902920 41520910 41621910 39748880 39217450 41083770 41172140 FALSE TRUE 38183332.64 38788379.34 42468843.49 41962314.48 42856467.78 42463533.54 40235338.68 38407595.95 36420112.67 38383514.29 0.994784697 1.010547889 1.106434475 1.09323795 1.116533193 1.106296136 1.048245306 1.000627396 0.948847789 1 25.19398347 1.713519538 2.716102603 0.974877311 1.073123117 0.493254861 0.040189408 0.212359942 3.397679171 0.027357162 0.012126149 51.70345172 -1.713519538 0.098245806 KSES(ph)PFRETEPLVSPHQDK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSESPFRETEPLVSPHQDK 19 2 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 KS(0.185)ES(0.806)PFRET(0.01)EPLVSPHQDK;KS(0.229)ES(0.764)PFRET(0.007)EPLVSPHQDK;KS(0.109)ES(0.862)PFRET(0.029)EPLVSPHQDK 186.96 1.01E-14 842830000 594770 545800 407530 361160 442740 522360 500380 586360 729760 617500 TRUE FALSE 571525.7308 530234.3184 481179.7365 379799.5109 456981.1342 532922.4771 506503.8001 574251.4611 646920.7042 575676.175 0.992790315 0.92106351 0.835851399 0.659745057 0.793816305 0.925733077 0.879841519 0.997525147 1.123757995 1 19.13489798 1.713562687 1.891133155 1.065300699 0.845420519 0.475538083 0.089026308 0.287747874 2.100616048 0.070149645 0.028004234 51.70858895 -1.713562687 -0.219880181 GILHLSPDVYQEMEASR ddPTM_BT-474_Pertuzumab_2h_R1 1 GILHLSPDVYQEMEASR 17 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0;E5RJN7;E5RJ67 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 0 244.36 1.65E-20 213770000 66136 120970 90441 146270 103770 121860 116550 93847 89632 123150 FALSE TRUE 63551.332 117520.054 106785.7005 153819.0122 107107.8563 124324.0927 117976.3738 91909.02665 79457.35113 114808.9408 0.553539921 1.02361413 0.93011659 1.339782522 0.932922606 1.082878144 1.027588731 0.80053893 0.692083304 1 16.80887547 1.713581904 6.466708232 0.81069426 0.999203009 0.108193016 0.195571838 0.247722137 25.36671356 0.096367157 0.04963015 51.71087708 -1.713581904 0.188508749 QLENLEQQKYDDEDISEDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLENLEQQKYDDEDISEDIK 20 1 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 ; 92.563 0.0014908 257860000 248450 227850 219270 226783 227747 242868 244385 293680 335670 321900 FALSE TRUE 238740.2993 221351.9411 258896.9666 238487.2978 235072.6891 247778.9574 247375.8567 287615.4054 297566.1488 300097.4263 0.795542642 0.737600265 0.86270972 0.794699577 0.783321243 0.825661721 0.824318488 0.958406771 0.991565148 1 18.19507142 1.713865813 2.084459849 0.998957372 0.798301439 0.886658338 0.029783624 0.087975318 0.795669828 0.020553439 0.008425003 51.74469279 -1.713865813 -0.200655933 S(ph)DVKFEDRFDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDVKFEDRFDK 11 2 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 1 S(1)DVKFEDRFDK 56.094 0.095428 1518700000 1449700 2304900 1645400 2304900 2206100 2687200 2010200 1871900 1648500 2087500 TRUE FALSE 1393044.121 2239166.509 1942760.382 2423856.165 2277061.21 2741537.025 2034801.429 1833244.611 1461369.191 1946111.766 0.715808899 1.150584745 0.998277908 1.24548662 1.170056751 1.408725374 1.045572749 0.942003765 0.750917402 1 20.89216314 1.713922273 3.215982355 0.872933703 1.124842551 0.225298298 0.177980866 0.293311853 6.712165137 0.103959484 0.048188193 51.75142022 -1.713922273 0.251908848 NDKDKPLPPLLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDKDKPLPPLLAR 13 2 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 89.541 0.0041634 1501940000 2395100 2175750 1914940 1795750 2097800 1940510 2009200 2587100 2853500 2615800 FALSE TRUE 2301496.844 2113699.74 2261012.256 1888428.873 2165277.642 1979748.442 2033789.191 2533675.481 2529582.643 2438629.536 0.943766493 0.866757213 0.927165124 0.774381203 0.887907577 0.811828288 0.833988583 1.038975147 1.037296812 1 21.21763918 1.71397933 6.559357057 1.027722515 0.861798829 0.696209704 0.048831168 0.070181727 7.413663121 0.024228381 0.012502991 51.75821976 -1.71397933 -0.165923685 EDFEWVYTDQPHADR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDFEWVYTDQPHADR 15 0 O15121 O15121 DEGS1 Sphingolipid delta(4)-desaturase DES1 0 69.805 0.048567 169250000 166090 305660 259830 256760 284380 305310 212210 175040 105840 135650 FALSE TRUE 159599.0192 296942.8761 306787.0609 270011.4144 293527.341 311483.5774 214807.0895 171425.3628 93825.48692 126462.3047 1.262028393 2.348074209 2.425917048 2.13511382 2.321065884 2.463054728 1.698585915 1.355545143 0.741924538 1 16.94834789 1.714030105 1.914035401 0.893485846 2.180191292 0.689543854 0.341940933 0.168282192 1.261336271 0.241496742 0.096741653 51.76427138 -1.714030105 1.286705445 MEISAELPQT(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEISAELPQTPQR 13 0 Q8IWV7;H3BS20;H3BNQ6;A0A087WTJ9;Q8IWV7-2 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 MEISAELPQT(1)PQR;MEISAELPQT(1)PQR;MEISAELPQT(1)PQR 163.64 0.0004292 801910000 1155400 1196350 1082920 1294300 1240470 1409200 1205630 1164200 1121230 1283030 TRUE FALSE 1110245.691 1162231.269 1278627.733 1361098.978 1280370.844 1437694.99 1220384.861 1140158.863 993952.671 1196129.235 0.928198775 0.971660281 1.068971225 1.137919664 1.070428518 1.201956233 1.020278432 0.953207086 0.830974314 1 20.18994184 1.714053893 3.1773468 0.911896986 1.065137748 0.34867259 0.082019206 0.234722656 5.233829055 0.050335725 0.023268431 51.76710675 -1.714053893 0.153240762 TKEYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 TKEYVSNDAAQSDDEEKLQSQPTDTDGGR 29 2 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR 368.79 9.93E-137 2988630000 1672260 1335120 1056750 875020 1196380 1235530 1210290 1529700 1802990 1442140 TRUE FALSE 1606906.23 1297043.685 1247728.232 920179.8871 1234862.649 1260513.263 1225101.891 1498111.16 1598322.134 1344462.573 1.195203394 0.964730228 0.928049807 0.684422092 0.918480495 0.937559206 0.911220524 1.114282532 1.188818615 1 20.35859816 1.714141802 5.60056246 1.114063775 0.924949751 0.273413416 0.123165643 0.183253585 13.99687753 0.065400233 0.033092059 51.77758638 -1.714141802 -0.189114024 QMEDGHTLFDYEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QMEDGHTLFDYEVR 14 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 182.1 1.56E-06 56515000 52677 57361 45350 54139 54469 50606 52423 46618 46619 49199 FALSE TRUE 50618.3246 55725.12044 53545.75381 56933.12028 56221.04485 51629.28799 53064.56836 45655.32201 41327.00656 45866.70791 1.103596201 1.214936127 1.167420908 1.241273309 1.225748422 1.125637534 1.156929956 0.9953913 0.901024042 1 15.48515974 1.714356962 2.452461007 0.94549966 1.184517418 0.816849518 0.046138678 0.097798413 1.257380776 0.029310522 0.012617305 51.80324463 -1.714356962 0.239017759 RLS(ph)PQPQIR ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSPQPQIR 9 1 A0A0A0MR27;J3QT39;Q49A88-5;Q49A88-6;Q49A88;C9JU82;Q49A88-2;Q49A88-3 A0A0A0MR27 CCDC14 Coiled-coil domain-containing protein 14 1 RLS(1)PQPQIR;RLS(1)PQPQIR;RLS(1)PQPQIR 116.74 0.00077502 433170000 308804 303130 253748 277107 292791 283773 271202 322643 328294 324470 TRUE FALSE 296735.5983 294485.0292 299605.9082 291408.5255 302208.8884 289511.0845 274521.0512 315980.3093 291027.4414 302493.3579 0.980965666 0.973525605 0.990454502 0.963355121 0.999059584 0.957082451 0.907527534 1.044585942 0.962095312 1 18.20654394 1.714368449 25 1.004077596 0.969203014 0.219963055 0.029841456 1.284765254 1321.911804 0.013430846 0.007448053 51.80461485 -1.714368449 -0.034874581 LMLPDS(ph)PLVEEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LMLPDSPLVEEGR 13 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR 208.15 5.06E-08 65371000 112341 131883 111186 143383 131056 140460 119622 110123 99963 109033 TRUE FALSE 107950.5895 128121.826 131279.7835 150783.0138 135271.5353 143300.1974 121085.9698 107848.9216 88615.61932 101648.0978 1.062003046 1.260444895 1.291512447 1.483382543 1.330782751 1.409767625 1.19122711 1.061002851 0.87178827 1 16.63322369 1.714486094 2.213127626 0.941985174 1.311276396 0.647206344 0.109434376 0.173445954 1.786793165 0.076683373 0.032008103 51.81864999 -1.714486094 0.369291223 LAGS(ph)PPGSGQWKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAGSPPGSGQWKPK 14 1 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 LAGS(0.998)PPGS(0.002)GQWKPK;LAGS(0.982)PPGS(0.018)GQWKPK 128.59 4.41E-05 2750500000 4770000 4407900 4197100 4074600 4198400 4447900 4888900 5596300 6191300 6471300 TRUE FALSE 4583583.126 4282191.008 4955609.334 4284890.594 4333445.349 4537839.585 4948731.821 5480734.449 5488489.58 6032993.087 0.759752756 0.709795444 0.821418036 0.710242915 0.718291118 0.752170526 0.820278053 0.908460257 0.90974571 1 22.5244425 1.714707251 1.208951019 0.974241875 0.74118328 0.866541296 0.034703729 0.147010588 0.404407598 0.02891607 0.011132212 51.84504443 -1.714707251 -0.233058594 ILEPDDFLDDLDDEDYEEDTPKR ddPTM_BT-474_Pertuzumab_2h_R1 4 ILEPDDFLDDLDDEDYEEDTPKR 23 1 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 0 ;;; 222.93 2.47E-32 387540000 197166 193399 152632 148211 178229 175639 170120 216317 240046 214855 FALSE TRUE 189460.5347 187883.4499 180215.9977 155860.1875 183961.8976 179190.5409 172201.9794 211849.9784 212796.9844 200302.6795 0.945871195 0.937997686 0.899718357 0.778123328 0.918419554 0.894598821 0.859708816 1.057649248 1.062377123 1 17.61182219 1.714709197 6.834168665 1.043920413 0.88976313 0.674720042 0.047392238 0.074717582 8.617700234 0.024544591 0.012736326 51.84527672 -1.714709197 -0.154157283 ERPDLPPIQYEPVLCSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPDLPPIQYEPVLCSR 17 1 F5H365;Q15436;G3V4V1;G3V1W4;G3V3G5;G3V2R6;G3V5X8;G3V4Q2 F5H365 SEC23A Protein transport protein Sec23A 0 ; 159.18 2.96E-09 1136750000 569050 733650 586070 691930 637880 720110 722340 609500 682210 729610 FALSE TRUE 546810.8969 712727.0203 691985.8861 727640.5902 658397.9895 734671.1176 731180.213 596913.612 604768.3809 680192.8648 0.803905664 1.04783078 1.017337761 1.069756282 0.967957801 1.080092361 1.074960134 0.877565236 0.889113091 1 19.37558435 1.714756945 10.30963783 0.913691428 1.014127497 0.183615782 0.082471672 0.152816237 41.04914416 0.037899568 0.020534213 51.85097715 -1.714756945 0.100436069 SEALSS(ph)VLDQEEAMEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEALSSVLDQEEAMEIK 17 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEALS(0.018)S(0.982)VLDQEEAMEIK 191.96 2.24E-10 18057000 67841 51584 47132 49945 46694 49525 51426 68556 73351 74858 TRUE FALSE 65189.69872 50112.87483 55649.80085 52522.66744 48195.95492 50526.42943 52055.36677 67140.29464 65024.50199 69787.80098 0.934113094 0.718074995 0.797414449 0.752605279 0.690607158 0.724000882 0.745909257 0.96206348 0.931745965 1 16.09068725 1.714956862 5.509612189 0.960916053 0.760250946 0.659207425 0.065179143 0.088091472 6.512162968 0.03296509 0.016657238 51.87485098 -1.714956862 -0.200665107 KLVPLLLEDGGEAPAALEAALEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLVPLLLEDGGEAPAALEAALEEK 24 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 172.61 8.36E-12 205336000 368310 337200 256360 236370 307250 325250 308660 377490 440780 376930 FALSE TRUE 353916.038 327583.3862 302689.9547 248569.084 317132.9753 331826.7778 312437.4734 369694.6996 390744.5023 351400.1954 1.00715948 0.932223119 0.861382431 0.707367518 0.902483776 0.944298786 0.889121513 1.052061736 1.111964385 1 18.42275547 1.715019189 4.252108593 1.064895818 0.886924848 0.481356675 0.077097482 0.156055976 6.537944764 0.044485962 0.021751419 51.88229625 -1.715019189 -0.17797097 EKEPIVGSTDYGKDEDSAEALLK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKEPIVGSTDYGKDEDSAEALLK 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 237.97 2.03E-37 1429380000 1543000 1338920 1258390 1114430 1353340 1353310 1472660 1853300 2344930 2002000 FALSE TRUE 1482697.854 1300735.313 1485809.066 1171945.866 1396871.41 1380674.855 1490682.854 1815028.707 2078743.377 1866402.757 0.794414736 0.69692102 0.796081693 0.627916917 0.748429783 0.73975183 0.79869302 0.972474296 1.113769989 1 20.83182891 1.715171276 2.208425056 1.05890599 0.731491377 0.864573684 0.052876547 0.085879579 0.880118014 0.033606103 0.014028105 51.90046822 -1.715171276 -0.327414613 QKEECTIR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKEECTIR 8 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 79.974 0.024305 76632000 147090 123010 110830 91186 97055 101820 111750 141900 160860 144740 FALSE TRUE 141341.5602 119501.8752 130859.4464 95892.12039 100176.8622 103878.8702 113117.6299 138969.7154 142599.8472 134936.6309 1.047466201 0.885614784 0.96978445 0.710645581 0.742399314 0.769834473 0.838301869 1.02988873 1.056791223 1 17.04192252 1.715314627 5.234585005 1.033672834 0.844766362 0.408428096 0.097125644 0.159407294 10.55940209 0.054352243 0.027303559 51.91760221 -1.715314627 -0.188906472 VDHSQNQK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDHSQNQK 8 0 E7EQ69;Q9GZZ1 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ;;; 163.99 0.00033272 459487000 657380 648740 558954 552010 608200 594890 662650 552310 564574 754090 FALSE TRUE 631688.8628 630238.5704 659969.4217 580499.3023 627763.3054 606919.0834 670759.7089 540904.6055 500485.9264 703014.8126 0.89854275 0.896479788 0.938770293 0.825728408 0.89295886 0.863309097 0.954118885 0.769407125 0.711913771 1 19.42319556 1.715321859 11.28108005 0.806389523 0.893317913 0.126237154 0.076855103 0.158936487 52.50181346 0.033699418 0.01837049 51.91846677 -1.715321859 0.086928389 SVEDRFDQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVEDRFDQQK 10 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 184.36 1.43E-06 1230750000 1395830 1413630 1218480 1312260 1301300 1317740 1370240 1444720 1679010 1455900 FALSE TRUE 1341279.42 1373314.656 1438686.441 1379985.896 1343157.496 1344385.606 1387009.407 1414886.027 1488415.824 1357290.596 0.988203576 1.011805917 1.059969357 1.016721032 0.98958727 0.990492095 1.021895688 1.042434119 1.096608072 1 20.3722982 1.715350173 3.384436325 1.053596668 1.011269274 0.229658121 0.029407761 0.277412703 7.063005798 0.016845792 0.007910655 51.92185175 -1.715350173 -0.042327394 TKYDEETTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKYDEETTAK 10 1 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3;P39880-9;Q13948-9;Q13948-10;Q13948-2;Q13948;A0A2R8Y8D0 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1;Protein CASP 0 97.911 0.0054283 0 142490 163120 128210 141270 123000 119930 134810 177010 195760 179870 FALSE TRUE 136921.3333 158467.9773 151380.399 148560.9616 126956.4067 122355.0668 136459.8451 173354.6816 173538.1455 167687.2447 0.816528016 0.945021058 0.902754406 0.88594074 0.757102348 0.729662337 0.81377594 1.033797663 1.034891746 1 17.35541343 1.715360363 6.245261099 1.025132484 0.837423302 0.65606969 0.06193098 0.094718633 9.127660341 0.035851334 0.018400752 51.92307004 -1.715360363 -0.187709182 IACEEEFS(ph)DS(ph)EEEGEGGRK ddPTM_BT-474_Pertuzumab_2h_R1 2 IACEEEFSDSEEEGEGGRK 19 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 2 IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK 175.86 6.13E-12 1429900000 3285300 3055300 2253550 2337700 2833700 2749300 2651500 3225100 3611700 3052500 TRUE FALSE 3156906.844 2968165.835 2660816.615 2458348.977 2924848.534 2804892.73 2683949.85 3158500.558 3201714.957 2845751.456 1.109340325 1.043016539 0.935013706 0.863866369 1.027794795 0.985642201 0.943142749 1.109900357 1.125085942 1 21.44037823 1.715376952 8.593668866 1.086819657 0.983867279 0.259261082 0.070162724 0.142874317 26.47898586 0.035170548 0.018749088 51.92505347 -1.715376952 -0.102952378 TPS(ph)PGPVESK ddPTM_BT-474_Pertuzumab_2h_R1 5 TPSPGPVESK 10 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 T(0.048)PS(0.952)PGPVESK;TPS(1)PGPVESK;T(0.003)PS(0.997)PGPVESK;T(0.027)PS(0.973)PGPVESK;T(0.05)PS(0.95)PGPVESK 232.17 3.59E-10 2812710000 3536870 3166550 2675310 2770980 2984770 3156970 3093780 3506930 3930250 3667980 TRUE FALSE 3398645.21 3076243.094 3158798.029 2913990.61 3080777.838 3220806.096 3131642.605 3434510.67 3484104.497 3419544.448 0.993888298 0.899606115 0.9237482 0.852157547 0.90093224 0.94188163 0.91580696 1.004376671 1.018879722 1 21.70537271 1.715450688 4.189939439 1.010694941 0.915053274 0.590082652 0.034080555 0.122901231 4.981844318 0.018663252 0.009109662 51.9338702 -1.715450688 -0.095641666 NGNYCVLQMDQSYKPDENEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGNYCVLQMDQSYKPDENEVR 21 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 310.92 1.44E-66 1427240000 907460 702170 664000 638560 699160 676350 746030 924680 1109990 942720 FALSE TRUE 871995.4599 682144.7991 783999.5706 671516.1581 721649.1164 690026.2604 755160.1383 905585.0349 983988.5887 878868.7347 0.992179407 0.776162323 0.892055366 0.764068776 0.821111376 0.785130058 0.8592411 1.03039851 1.119608139 1 19.74528818 1.715705873 3.508069917 1.064302089 0.833086085 0.663591913 0.068264849 0.108067246 2.970181164 0.036395005 0.017226572 51.96439476 -1.715705873 -0.231216005 YPSS(ph)IS(ph)SSPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 YPSSISSSPQK 11 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 YPS(0.097)S(0.902)IS(0.419)S(0.297)S(0.285)PQK 101.89 0.0043092 97238000 332690 273190 305360 300720 286970 248920 291650 360320 378740 398840 TRUE FALSE 319688.107 265398.8887 360545.3447 316240.1952 296200.6507 253953.3329 295219.2999 352879.2661 335747.023 371826.2116 0.859778297 0.713771328 0.969660915 0.850505385 0.796610463 0.682989324 0.793971191 0.949043545 0.902967603 1 18.50426895 1.715722284 6.032214321 0.944319398 0.808265276 0.407152455 0.07773722 0.151863417 13.63669935 0.040742074 0.020826211 51.96635837 -1.715722284 -0.136054122 SSILLDVKPWDDETDMAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSILLDVKPWDDETDMAK 18 1 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 ;; 241.02 5.13E-24 6316242000 7624557 6296119 6093720 4802458 6276702 6340036 7111614 7888287 9944440 9036790 FALSE TRUE 7326580.883 6116559.851 7194990.758 5050313.433 6478597.82 6468235.872 7198648.059 7725391.117 8815588.862 8424720.164 0.869652729 0.726025284 0.854033204 0.599463642 0.768998577 0.767768632 0.85446732 0.916990828 1.046395452 1 23.00619734 1.715730614 1.487009368 1.023429568 0.758428614 0.668951917 0.071982464 0.21608497 0.926394433 0.055273533 0.021206894 51.9673551 -1.715730614 -0.265000954 SGPKPFSAPKPQTSPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.005)S(0.029)PS(0.967)PK;SGPKPFSAPKPQT(0.022)S(0.023)PS(0.955)PK 180.9 3.98E-14 98062000000 4164000 3093500 2327930 2034450 2400570 2801350 3276300 3562500 4560200 4220600 TRUE FALSE 4001266.276 3005276.409 2748638.736 2139448.208 2477786.514 2857995.216 3316396.339 3488933.13 4042545.214 3934735.003 1.016908705 0.763781146 0.698557523 0.543733747 0.629721319 0.726350114 0.842851256 0.886700916 1.027399612 1 21.90783505 1.715917574 1.517761911 1.01055823 0.718281683 0.473440701 0.11654608 0.34309538 1.538418565 0.098005509 0.037676146 51.98973141 -1.715917574 -0.292276547 GAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_BT-474_Pertuzumab_2h_R1 6 GAGDGSDEEVDGKADGAEAKPAE 23 2 P35579;P35579-2 P35579 MYH9 Myosin-9 1 GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE 219.43 1.64E-32 4946710000 8529970 6953000 5399580 5045820 6445590 6853460 6703040 7978470 9856230 7652760 TRUE FALSE 8196609.342 6754707.248 6375404.219 5306235.375 6652918.256 6992041.657 6785073.809 7813711.806 8737392.091 7134431.749 1.148880476 0.946775789 0.893610654 0.743750247 0.932508501 0.980041845 0.951032128 1.095211515 1.22467947 1 22.76636709 1.71593026 3.356560089 1.126689733 0.932182286 0.332666872 0.10593991 0.225149602 5.626212398 0.062533187 0.029329593 51.99125005 -1.71593026 -0.194507447 TEVEVEELPPIDHGIPITDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 TEVEVEELPPIDHGIPITDRR 21 1 J3KT25;A0A3B3ITH3;Q9P2X3-2;Q9P2X3 J3KT25 IMPACT Protein IMPACT 0 95.666 0.00090389 284140000 61530 75862 55721 57288 66169 68756 69409 54707 64641 58653 FALSE TRUE 59125.33957 73698.49004 65791.02421 60244.64055 68297.38598 70146.29343 70258.4481 53577.28133 57303.22468 54680.38007 1.081289843 1.347805007 1.203192519 1.101759726 1.249029101 1.282842097 1.284893192 0.979826425 1.047966832 1 15.73873565 1.715943138 7.70645351 1.012717925 1.224369622 0.603993948 0.078574721 0.078811049 11.74851085 0.038015398 0.020025638 51.99279186 -1.715943138 0.211651697 KKPVPVLLGSLLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKPVPVLLGSLLNR 14 2 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ; 209.21 3.91E-09 428310000 1136700 1172620 984890 1109510 1158720 1124820 1339850 1399790 1527610 1652020 FALSE TRUE 1092276.507 1139178.026 1162881.532 1166771.944 1195991.281 1147564.631 1356247.485 1370883.847 1354202.117 1540127.214 0.709211874 0.73966489 0.755055505 0.757581538 0.776553567 0.745110287 0.880607441 0.890110788 0.87927939 1 20.55461809 1.715977693 0.500048139 0.998308143 0.721608528 0.908163354 0.026831764 0.23485646 0.140427654 0.027849977 0.01876772 51.99692877 -1.715977693 -0.276699615 RSIQFVDWCPTGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSIQFVDWCPTGFK 14 1 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 74.296 0.053619 820280000 552650 542540 374940 385440 313110 398970 418000 618220 603390 755920 FALSE TRUE 531051.827 527067.2904 442699.9985 405332.6046 323181.4675 407037.4468 423115.609 605453.541 534895.6968 704720.8651 0.753563366 0.747909302 0.628191984 0.575167594 0.458595003 0.577586768 0.600401705 0.859139513 0.759017823 1 19.4266924 1.715987145 5.327425218 0.858243633 0.61555156 0.582651353 0.097489923 0.123114456 8.482336188 0.054438141 0.027419719 51.99806054 -1.715987145 -0.242692073 GTQEVAPPTPLTPT(ph)SHTANTSPRPVSGMER ddPTM_BT-474_Pertuzumab_2h_R1 2 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.005)PT(0.369)S(0.369)HT(0.083)ANT(0.083)S(0.083)PRPVS(0.008)GMER;GTQEVAPPTPLTPT(0.2)S(0.2)HT(0.2)ANT(0.2)S(0.2)PRPVS(0.002)GMER 109.97 0.00034227 813380000 77255 55763 61611 48281 48631 62787 56409 77770 84122 78412 TRUE FALSE 74235.78919 54172.69384 72745.47823 50772.7882 50195.26028 64056.59616 57099.35022 76164.02232 74572.82323 73101.0854 1.015522393 0.74106552 0.995135405 0.694555873 0.686655472 0.876274214 0.781101264 1.04190002 1.020132914 1 16.15760521 1.716034211 6.960736664 1.021699958 0.821797815 0.405527879 0.106965432 0.120168827 14.54498406 0.051730405 0.026919565 52.00369601 -1.716034211 -0.199902144 KSST(ph)PEEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.013)S(0.081)T(0.906)PEEVK;KS(0.01)S(0.152)T(0.837)PEEVK 93.011 0.0056773 1116180000 3802400 3297000 3091500 2461700 3011900 3156000 3173600 3776200 4499700 3567800 TRUE FALSE 3653798.004 3202972.788 3650202.82 2588748.632 3108780.499 3219816.482 3212439.466 3698220.15 3988912.92 3326149.728 1.098506773 0.962967109 1.097425888 0.778301894 0.934648393 0.968031131 0.965813246 1.111862199 1.199258376 1 21.66542168 1.716185728 5.00803587 1.117830428 0.967330814 0.279462081 0.095671625 0.187797329 11.30135814 0.049549384 0.024777965 52.02184226 -1.716185728 -0.150499615 T(ph)SPKPAVVETVTTAKPQQIQALMDEVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPKPAVVETVTTAKPQQIQALMDEVTK 28 2 P56192;H0YIP0;H0YI94 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 1 T(0.5)S(0.5)PKPAVVETVTTAKPQQIQALMDEVTK;T(0.5)S(0.5)PKPAVVETVTTAKPQQIQALMDEVTK 169.13 2.18E-10 5357400000 476710 357019 396344 289793 406660 401130 464540 498890 754290 538680 TRUE FALSE 458079.6462 346837.1677 467972.1774 304749.2515 419740.5882 409241.1234 470225.1795 488587.7472 668666.1614 502194.7238 0.912155434 0.690642795 0.93185403 0.606834833 0.835812422 0.814905263 0.936340342 0.972904979 1.331487827 1 18.93788735 1.716319969 1.6997127 1.15372896 0.794369883 0.558111467 0.123472855 0.23032196 1.325933545 0.08642161 0.033782728 52.03792478 -1.716319969 -0.359359077 IDPHAPNEMLYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDPHAPNEMLYGR 13 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 ; 85.909 0.009069 606690000 1071130 1208360 1039040 1237940 1151900 1206300 1161930 1135830 1188730 1209180 FALSE TRUE 1029269.055 1173898.756 1226817.641 1301830.232 1188951.91 1230692.213 1176150.047 1112374.714 1053790.354 1127281.162 0.913054427 1.041354008 1.088297829 1.154840759 1.054707512 1.091734923 1.043351106 0.986776637 0.934807029 1 20.10441596 1.71641882 3.01972345 0.965897261 1.062466121 0.285321015 0.059304323 0.277659807 5.536128708 0.036581888 0.016739117 52.04977061 -1.71641882 0.096568859 SNS(ph)LSEQLAINTSPDAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 S(0.066)NS(0.933)LS(0.002)EQLAINTSPDAVK;S(0.176)NS(0.775)LS(0.05)EQLAINTSPDAVK 318.9 1.91E-61 200685000 338220 335430 298920 272280 325900 359510 316720 407830 445880 415470 TRUE FALSE 325001.9885 325863.8648 352941.4934 286332.4034 336382.8695 366779.5385 320596.1141 399408.168 395265.5717 387329.8468 0.839083255 0.841308429 0.911216877 0.739246938 0.868466172 0.946943649 0.827708261 1.031183554 1.020488286 1 18.56320315 1.716445191 6.597245105 1.018438911 0.854994638 0.673902562 0.052090188 0.077079295 8.376931912 0.026255931 0.013575628 52.05293121 -1.716445191 -0.163444273 TEAEIAHIALETLEGHQR ddPTM_BT-474_Pertuzumab_2h_R1 6 TEAEIAHIALETLEGHQR 18 0 O75955;A0A140T9R1;A0A140T9X0;A2AB09;A0A140T9C3;A0A140T959;A2AB13;A2AB11;A0A0G2JJQ6;A0A140T910;A2AB12;A0A140T957;A2AB10;A0A140T9B1 O75955 FLOT1 Flotillin-1 0 ;;;;; 306.26 1.83E-50 516515000 243203 343639 258756 396860 268012 301183 383866 247703 363530 318526 FALSE TRUE 233698.3579 333838.7522 305518.9652 417341.9922 276632.8494 307273.1266 388563.8669 242587.8465 322263.5984 296951.9503 0.78699048 1.124218083 1.028849835 1.405419266 0.931574449 1.034757059 1.308507543 0.816926261 1.085238195 1 18.17986998 1.716546182 24.99999992 0.958579324 1.091770278 0.089736841 0.17606541 2.025250682 2290.445384 0.078438553 0.043498155 52.06503706 -1.716546182 0.133190954 NSQGSEMFGDDDKRK ddPTM_BT-474_Pertuzumab_2h_R1 6 NSQGSEMFGDDDKRK 15 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;;; 207.79 1.81E-09 1423820000 918204 722697 683094 529798 649736 689248 677983 826761 934277 786405 FALSE TRUE 882319.5726 702086.3892 806544.2811 557140.9383 670635.3485 703185.0668 686280.3588 809688.0964 828221.7918 733141.0889 1.203478547 0.957641578 1.100121509 0.759936862 0.914742549 0.959140167 0.936082248 1.104409654 1.129689502 1 19.48373134 1.71655168 7.693020435 1.086484216 0.968725524 0.140430029 0.113992242 0.208039251 31.13150486 0.0558256 0.029406687 52.06569617 -1.71655168 -0.117758692 AKIDDPTDSKPEDWDKPEHIPDPDAK ddPTM_BT-474_Pertuzumab_2h_R1 3 AKIDDPTDSKPEDWDKPEHIPDPDAK 26 3 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;; 118.01 0.00040392 6010800000 4561120 3088340 2656415 1842644 2893420 2854520 3075180 3784770 4863950 3475690 FALSE TRUE 4382866.388 3000263.567 3136488.282 1937743.078 2986489.482 2912240.35 3112814.973 3706613.177 4311814.787 3240278.42 1.352620306 0.925927707 0.967968759 0.598017462 0.921676811 0.898762382 0.96066281 1.143918113 1.330692684 1 21.62768635 1.716561675 3.597610348 1.185734869 0.928278606 0.209033681 0.186435547 0.278265325 8.064437979 0.105358964 0.050164268 52.06689452 -1.716561675 -0.257456263 SS(ph)SPVTELASRS(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.383)S(0.548)S(0.069)PVTELAS(0.007)RS(0.993)PIR 199.7 4.15E-09 933110000 762970 876770 688000 799790 816650 804890 750300 717060 735080 684060 TRUE FALSE 733152.2889 851765.378 812336.9045 841067.2577 842918.2889 821165.4273 759482.3958 702252.4604 651636.8001 637728.0069 1.149631631 1.335624857 1.273798384 1.318849492 1.321752032 1.287642096 1.190918993 1.101178642 1.021809914 1 19.28258172 1.716586265 1.49187631 1.005279056 1.287980798 0.827941079 0.049880758 0.139308669 0.601436109 0.038074803 0.014621398 52.06984267 -1.716586265 0.282701742 RQVQDESQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RQVQDESQR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 130.79 0.00056338 186520000 76977 108870 107710 120000 106380 111600 110580 66785 63160 80829 FALSE TRUE 73968.65374 105765.1342 127175.593 126193.2144 109801.8093 113856.6285 111933.3111 65405.86641 55990.34159 75354.37983 0.981610543 1.403569831 1.687700082 1.6746633 1.457139048 1.510949048 1.485425417 0.867976972 0.743027037 1 16.20140375 1.717039773 4.947314729 0.848424188 1.47583616 0.659450167 0.192637755 0.096221403 5.639060132 0.104840825 0.052391501 52.12424443 -1.717039773 0.627411972 MKGDYDVTVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 MKGDYDVTVPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 114.82 0.0011004 1421200000 2687900 2817800 2137970 2412700 2305810 2679600 2504800 2813000 3168900 2775400 FALSE TRUE 2582853.896 2737439.103 2524348.738 2537219.736 2379978.473 2733783.348 2535454.492 2754910.567 2809179.757 2587419.686 0.998235389 1.057980318 0.975623998 0.980598451 0.919826994 1.056567422 0.97991621 1.064732785 1.085707036 1 21.30308265 1.717063591 7.639735039 1.055765854 0.9960657 0.250662195 0.042831243 0.153355086 22.75699776 0.020797825 0.010948249 52.12710321 -1.717063591 -0.059700154 IFVGGLS(ph)PDTPEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IFVGGLSPDTPEEK 14 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IFVGGLS(0.998)PDT(0.002)PEEK;IFVGGLS(0.823)PDT(0.177)PEEK 165.78 4.10E-06 198121000 527359 474228 410018 387031 442989 479176 453233 509073 579041 498506 TRUE FALSE 506749.2273 460703.4818 484117.3734 407005.7163 457238.1435 488865.267 458779.801 498560.4647 513310.6932 464741.7446 1.090388873 0.991310738 1.041691174 0.875767501 0.983854256 1.051907372 0.987171491 1.072768845 1.104507394 1 18.82606971 1.717088535 7.030612072 1.065918885 1.00044047 0.155501181 0.058684107 0.205073628 25.57480866 0.02908521 0.015160448 52.13009725 -1.717088535 -0.065478415 LAPWQAS(ph)PPHPCR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAPWQASPPHPCR 13 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 LAPWQAS(1)PPHPCR 90.348 0.0045295 152590000 130970 164340 132570 189050 140150 168940 139130 127830 105720 123890 TRUE FALSE 125851.5476 159653.1841 156528.348 198806.8932 144658.052 172356.0825 140832.7146 125190.2658 93719.10881 115498.82 1.089634921 1.382292773 1.355237639 1.721289388 1.252463463 1.492275701 1.21934332 1.08390948 0.811429146 1 16.81751859 1.717134764 1.98127179 0.912652636 1.388951237 0.575309661 0.16195753 0.20860504 1.684231931 0.112491472 0.045607245 52.13564657 -1.717134764 0.476298601 LEKPAKYDDIKK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEKPAKYDDIKK 12 3 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 138.77 8.39E-05 67881200000 46834100 40882100 31819800 25162400 36664900 39906100 35873400 45472000 55209700 38534900 FALSE TRUE 45003771.59 39716182.54 37570345.69 26461034.48 37844259.81 40713028.68 36312429.4 44532987.31 48942526.31 35924896.9 1.252718184 1.105533654 1.045802464 0.736565356 1.053427096 1.133281713 1.010787296 1.239613504 1.362356765 1 25.09848068 1.717274191 6.773101246 1.224381318 1.041929141 0.173723975 0.148691289 0.195470847 22.57866193 0.07550575 0.039181968 52.15238703 -1.717274191 -0.182452177 VQFVITAQEWDPSFEEALMDNPSLAFVRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQFVITAQEWDPSFEEALMDNPSLAFVRPR 30 1 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 0 88.518 0.0010691 100360000 19846 21049 17731 20613 19302 23299 22945 15561 16865 21445 FALSE TRUE 19070.39638 20448.70313 20935.38612 21676.8394 19922.86636 23770.12174 23225.80777 15239.65991 14950.5559 19992.51105 0.953876996 1.022818148 1.047161413 1.084247964 0.996516461 1.188951287 1.161725394 0.762268425 0.74780781 1 14.28717206 1.717366136 8.71892849 0.819448396 1.065451569 0.558293413 0.092530591 0.074994046 14.8369069 0.044655016 0.023848027 52.16342948 -1.717366136 0.246003173 MATIDENGNQNGSGRPGFAFCQPLEHDLLS(ph)PVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MATIDENGNQNGSGRPGFAFCQPLEHDLLSPVEK 34 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 MATIDENGNQNGSGRPGFAFCQPLEHDLLS(1)PVEK 133.85 1.79E-08 45234000 22794 22467 22152 26451 25293 27255 20539 22292 20025 19648 TRUE FALSE 21903.18528 21826.26316 26155.35917 27816.13928 26106.57232 27806.11477 20790.36243 21831.66241 17751.84595 18317.22346 1.195769945 1.191570502 1.427910689 1.518578367 1.425247247 1.518031094 1.135017131 1.191865266 0.969134104 1 14.16091321 1.717416916 1.56921688 1.000252197 1.375934936 0.596344492 0.12223388 0.273482988 1.319200333 0.102363009 0.039545923 52.16952897 -1.717416916 0.37568274 RNPGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNPGVK 6 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 107.65 0.049838 573060000 1243700 1460900 1169800 1511700 1510400 1499300 1460800 1146100 1150100 1378700 FALSE TRUE 1195094.829 1419236.562 1381208.882 1589719.018 1558983.388 1529616.873 1478677.707 1122432.634 1019545.47 1285319.421 0.929803759 1.104189775 1.074603604 1.236827976 1.212915142 1.190067503 1.15043598 0.873271357 0.793223422 1 20.2936955 1.717450758 5.598389459 0.874530971 1.135425521 0.571873483 0.094453008 0.102262237 7.874098158 0.049995339 0.025359917 52.17359442 -1.717450758 0.26089455 DELDVSNFAEEFTEMDPTYSPAALPQS(ph)SEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DELDVSNFAEEFTEMDPTYSPAALPQSSEK 30 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 DELDVSNFAEEFTEMDPTYSPAALPQS(0.794)S(0.206)EK 100.66 0.00030129 12279000 24630 19548 23356 19691 20077 18967 21109 25327 28387 25457 TRUE FALSE 23667.43237 18990.51018 27576.94875 20707.25487 20722.79494 19350.52574 21367.33826 24803.9886 25164.62677 23732.77472 0.997246746 0.80018078 1.161977438 0.872517231 0.873172024 0.815350332 0.900330388 1.045136479 1.060332265 1 14.53459316 1.71750532 6.30034587 1.039022107 0.914826402 0.230449502 0.098380646 0.195739677 19.43594055 0.049154506 0.025287473 52.18014961 -1.71750532 -0.124195706 NDLSPTTVMSEGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDLSPTTVMSEGAR 14 0 P30043;M0R192;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 166.45 4.06E-07 371790000 329972 286179 279740 248195 286837 295054 312925 411456 484613 460405 FALSE TRUE 317076.3294 278017.4551 330295.2408 261004.3737 296063.3726 301020.194 316754.6698 402959.2898 429601.7639 429221.3593 0.738724489 0.647725117 0.769521911 0.608088037 0.689768499 0.701316902 0.737975087 0.938814626 1.000886267 1 18.71136234 1.717584244 2.29240723 1.001576825 0.689718976 0.907119916 0.041705452 0.06919901 0.767082918 0.026166643 0.011072523 52.18963318 -1.717584244 -0.311857848 VEEESTGDPFGFDS(ph)DDESLPVSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEEESTGDPFGFDSDDESLPVSSK 24 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 VEEESTGDPFGFDS(0.994)DDES(0.006)LPVSSK 148.3 1.05E-07 85839000 337190 306090 285310 291410 303790 352650 313920 375820 433790 413780 TRUE FALSE 324012.242 297360.6129 336871.8637 306449.705 313561.6812 359780.8246 317761.8469 368059.1857 384547.9778 385754.312 0.839944576 0.770854929 0.873280876 0.794416797 0.812853341 0.932668316 0.823741529 0.954128507 0.996872791 1 18.55732276 1.717594098 0.866689241 1.013845922 0.819523425 0.719251229 0.042681803 0.282160745 0.404247472 0.036312297 0.015532371 52.19081727 -1.717594098 -0.194322497 RS(ph)YSPDGKES(ph)PSDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSYSPDGKESPSDKK 15 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 RS(0.624)Y(0.078)S(0.298)PDGKES(0.98)PS(0.02)DKK 78.554 0.032401 517790000 415330 254160 261460 192070 245930 261860 261100 369230 427890 345700 TRUE FALSE 399098.4444 246911.6056 308711.6381 201982.7557 253840.5618 267154.9886 264295.4199 361605.2715 379317.7211 322285.4311 1.23833846 0.766127109 0.957882698 0.626720094 0.787626549 0.82893908 0.820066297 1.122003158 1.176962048 1 18.29797945 1.717594614 6.102993785 1.111387564 0.84779469 0.326821177 0.1556626 0.146592721 13.60673363 0.076534158 0.039224625 52.19087933 -1.717594614 -0.263592874 TEMEDLMSSKDDVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEMEDLMSSKDDVGK 15 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 218.78 1.73E-12 861870000 1424320 1202940 839290 734210 960430 1130460 1032830 1229710 1432050 1167330 FALSE TRUE 1368656 1168633.329 990968.3729 772102.6661 991323.1032 1153318.676 1045470.082 1204316.059 1269489.688 1088265.699 1.257648753 1.073849272 0.910594144 0.709479924 0.910920103 1.059776741 0.960675397 1.106637891 1.166525499 1 20.0535994 1.717676662 5.971058902 1.102192674 0.973532674 0.108535537 0.138105331 0.300997748 26.66757622 0.075615454 0.038654959 52.20074033 -1.717676662 -0.12866 KPSKYPLCSADAAVSTT(ph)PPGS(ph)PPPPPPLPEPPVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 KPSKYPLCSADAAVS(0.022)T(0.025)T(0.953)PPGS(1)PPPPPPLPEPPVLK 199.09 3.59E-27 1797900000 2921400 2689000 2024100 2029600 2496600 2561900 2420300 2867100 3172000 2894200 TRUE FALSE 2807228.458 2612312.353 2389899.896 2134347.899 2576905.406 2613703.373 2449920.355 2807893.383 2811927.858 2698173.256 1.040418161 0.968178136 0.885747381 0.791034414 0.955055573 0.968693677 0.907992231 1.040664597 1.042159858 1 21.36355156 1.717782351 6.954227377 1.030235498 0.927728652 0.333040714 0.062334693 0.15007806 18.40188185 0.03309729 0.017233978 52.21344528 -1.717782351 -0.102506846 NDKSEEEQS(ph)S(ph)SSVKKDETNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVKKDETNVK 21 3 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 2 NDKS(0.006)EEEQS(0.855)S(0.38)S(0.38)S(0.38)VKKDETNVK 72.086 0.023149 355050000 180780 107280 101080 72736 82903 100950 111840 154920 206310 136680 TRUE FALSE 173714.9177 104220.4794 119347.4045 76489.91368 85569.65029 102991.2782 113208.7314 151720.8479 182890.5537 127422.5419 1.363298167 0.817912419 0.936627089 0.600285574 0.671542484 0.808265764 0.888451366 1.190690797 1.435307686 1 16.959261 1.717884657 3.73902968 1.245557678 0.846919711 0.338445604 0.215747762 0.20200592 6.352446911 0.120208636 0.057730747 52.22574662 -1.717884657 -0.398637967 RPLEMEQQQAYRPEMK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPLEMEQQQAYRPEMK 16 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0QYZ0;M0R0K8;M0QZV6;M0R203 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ;;; 261.17 4.53E-27 2121020000 2438440 2269040 1978340 1847680 1804150 1956250 2240240 2334030 2788180 2561790 FALSE TRUE 2343143.069 2204329.201 2335870.046 1943038.986 1862182.123 1995806.715 2267656.727 2285831.465 2471677.495 2388277.681 0.981101606 0.922978604 0.978056306 0.813573313 0.779717592 0.835667783 0.949494586 0.957104562 1.034920485 1 21.18753916 1.717966078 1.999638572 1.011253238 0.884914125 0.382413599 0.064233288 0.349948725 2.881733152 0.050250371 0.020440424 52.23553874 -1.717966078 -0.126339114 AREEEEQKEGGDGAAGDPK ddPTM_BT-474_Pertuzumab_2h_R1 4 AREEEEQKEGGDGAAGDPK 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;; 123.53 1.75E-05 3795580000 4041900 3067510 2886690 2453590 3190760 3051840 3174370 3963530 4685700 3921700 FALSE TRUE 3883938.079 2980027.618 3408379.097 2580220.074 3293393.693 3113550.296 3213218.89 3881681.72 4153798.98 3656079.766 1.062323124 0.815088239 0.932249654 0.705734076 0.90079919 0.851608962 0.878870018 1.061705972 1.13613467 1 21.80186612 1.718061387 4.289265588 1.077908295 0.870096055 0.473875229 0.09035311 0.139453217 5.938845732 0.046294327 0.022733979 52.24700344 -1.718061387 -0.20781224 RKAS(ph)PEPEGEAAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKASPEPEGEAAGK 14 2 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 RKAS(1)PEPEGEAAGK;RKAS(1)PEPEGEAAGK 103.99 0.00085359 1075370000 1405760 1308320 1059970 906880 1141290 1180780 1173040 1352210 1597970 1270690 TRUE FALSE 1350821.345 1271007.995 1251530.158 953684.1855 1178000.629 1204656.181 1187396.014 1324286.391 1416575.145 1184625.034 1.140294444 1.072920087 1.056477891 0.805051521 0.994408015 1.016909271 1.00233912 1.11789499 1.195800446 1 20.17599905 1.718201993 5.601011873 1.117724088 1.008006769 0.165868621 0.092504225 0.239641693 18.50673045 0.049203639 0.024974448 52.26392149 -1.718201993 -0.109717319 DREDYVPYTGEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DREDYVPYTGEK 12 1 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 ;;; 198.48 1.67E-07 4324980000 4640490 4465330 3734860 3705560 4046280 4043890 4232700 4739660 5415240 4946310 FALSE TRUE 4459134.52 4337983.16 4409832.284 3896804.396 4176432.271 4125660.226 4284501.049 4641784.365 4800524.658 4611292.018 0.967003283 0.940730525 0.956311651 0.845056956 0.905696767 0.894686394 0.92913245 1.006612539 1.041036794 1 22.1367396 1.718443417 3.444350585 1.021620303 0.916728358 0.634090643 0.033603276 0.133961526 3.522899025 0.020192673 0.009548216 52.29298313 -1.718443417 -0.104891945 GAEADQIIEYLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GAEADQIIEYLK 12 0 Q12904;Q12904-2;A0A5F9ZHC5;D6R937 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 165.7 0.0004128 33029000 92983 92460 76763 89476 86980 99340 93266 107660 111062 119927 FALSE TRUE 89349.12156 89823.13133 90635.78168 94093.86708 89777.79069 101348.7229 94407.41721 105436.7834 98454.70737 111804.2375 0.799156844 0.803396484 0.810664996 0.84159482 0.802990949 0.906483736 0.844399276 0.943048186 0.880599068 1 16.77061534 1.718463863 0.281830592 1.017721446 0.768169785 0.799012343 0.029105879 0.64341142 0.189517711 0.054616133 0.059215841 52.295445 -1.718463863 -0.249551661 AQTPPGPSLSGSKS(ph)PCPQEK ddPTM_BT-474_Pertuzumab_2h_R1 5 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQTPPGPSLS(0.001)GS(0.011)KS(0.988)PCPQEK;AQTPPGPS(0.001)LS(0.003)GS(0.157)KS(0.839)PCPQEK;AQTPPGPSLSGS(0.018)KS(0.982)PCPQEK;AQTPPGPSLS(0.014)GS(0.205)KS(0.781)PCPQEK;AQTPPGPS(0.004)LS(0.014)GS(0.067)KS(0.914)PCPQEK 200.63 8.11E-22 14660420000 6852390 6039460 5034110 4641160 5321380 5280120 5399120 6542440 7441300 6188230 TRUE FALSE 6584591.023 5867220.514 5943885.66 4880690.824 5492547.02 5386887.644 5465196.046 6407336.328 6596594.82 5769095.67 1.141355838 1.017008705 1.030297641 0.846006221 0.952063778 0.933749057 0.947322832 1.110630971 1.143436545 1 22.45991376 1.718469833 7.555890725 1.093996293 0.976312593 0.256666494 0.079811205 0.152072579 22.41053058 0.040461033 0.021281203 52.29616386 -1.718469833 -0.1176837 EAEDS(ph)DS(ph)DDNIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAEDSDSDDNIKR 13 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 EAEDS(1)DS(1)DDNIKR;EAEDS(1)DS(1)DDNIKR 149.3 5.85E-07 965450000 1351720 1131650 1060870 1057850 1095070 1099410 1295530 1410580 1749940 1605520 TRUE FALSE 1298893.288 1099376.45 1252592.808 1112445.765 1130293.921 1121640.823 1311385.084 1381451.03 1551294.148 1496776.7 0.867793631 0.734495967 0.836860173 0.743227607 0.755152001 0.749370847 0.876139429 0.922950651 1.036423233 1 20.51342758 1.718531601 1.669112285 1.01530308 0.77949564 0.810416221 0.045157433 0.13358311 0.738207388 0.03250796 0.012689192 52.30360227 -1.718531601 -0.23580744 S(ph)PQEGGSHVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQEGGSHVGR 11 0 Q8TC76 Q8TC76 FAM110B Protein FAM110B 1 S(1)PQEGGSHVGR;S(1)PQEGGSHVGR 112.03 0.001018 85257000 78817 92589 82000 109540 94875 104111 91726 83546 69411 102720 TRUE FALSE 75736.7445 89948.45237 96819.22408 115193.3725 97926.74054 106216.1958 92848.57023 81820.7459 61531.75427 95762.68291 0.790879518 0.939285008 1.011032911 1.202904608 1.022598131 1.10916061 0.969569434 0.854411587 0.642544177 1 16.54717595 1.718669889 3.296346977 0.803453832 1.018585468 0.276486084 0.129025105 0.247574496 5.923761926 0.075078432 0.035170406 52.32025949 -1.718669889 0.215131636 VLEESSIENQDVSQERPHS(ph)NGELQDSGPLAQQLAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLEESSIENQDVSQERPHSNGELQDSGPLAQQLAGK 36 1 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 1 VLEESSIENQDVS(0.021)QERPHS(0.979)NGELQDSGPLAQQLAGK;VLEESSIENQDVSQERPHS(1)NGELQDSGPLAQQLAGK 296.38 2.79E-92 240720000 110655 112523 86910 106014 103258 106867 101591 137650 139015 154245 TRUE FALSE 106330.4803 109313.9542 102616.5703 111485.3952 106579.3873 109027.924 102834.301 134807.4794 123234.6 143797.8488 0.739444165 0.760191861 0.713616867 0.775292511 0.741175117 0.758202747 0.715131012 0.937479111 0.856998912 1 17.13368257 1.718679877 6.708734845 0.921774171 0.744555528 0.839747693 0.037527948 0.046119692 5.275391273 0.017183037 0.00891251 52.32146278 -1.718679877 -0.177218643 VTNLSEDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTNLSEDTR 9 0 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 89.886 0.027461 185070000 428030 525850 456120 641600 545850 542880 555140 424870 451500 492520 FALSE TRUE 411302.1144 510853.2729 538551.0303 674713.0529 563407.761 553857.4056 561933.9694 416096.286 400247.6128 459161.1817 0.895768481 1.112579402 1.172901917 1.469447069 1.227037004 1.206237434 1.223827257 0.906209633 0.871693054 1 18.80864115 1.718865194 6.047508095 0.917390522 1.196705976 0.434496864 0.135647202 0.132576087 12.1335715 0.072748177 0.037275173 52.34379356 -1.718865194 0.279315454 NENTEGS(ph)PQEDGVELEGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NENTEGSPQEDGVELEGLK 19 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK 376.5 2.93E-108 578350000 974780 857310 819990 865400 888170 1010110 1021960 1109540 1446240 1341980 TRUE FALSE 936684.5199 832860.3582 968180.4336 910063.3977 916738.7947 1030535.116 1034467.052 1086627.611 1282068.898 1251086.499 0.748696849 0.665709652 0.773871698 0.727418446 0.732754126 0.823712123 0.82685494 0.868547148 1.024764394 1 20.25475011 1.718892379 0.802906038 1.021236325 0.724324448 0.883436229 0.038009223 0.180023675 0.224890619 0.033361154 0.014896434 52.34707015 -1.718892379 -0.296911877 DLDEEGS(ph)EKELHENVLDK ddPTM_BT-474_Pertuzumab_2h_R1 5 DLDEEGSEKELHENVLDK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK 280.55 1.72E-39 2266360000 1607680 1193270 1437190 1289270 1365030 1257400 1751580 1939590 2577300 2359930 TRUE FALSE 1544850.088 1159239.108 1696922.203 1355809.379 1408937.43 1282825.49 1773016.36 1899536.789 2284735.709 2200089.839 0.702175912 0.526905351 0.771296778 0.616251825 0.640399953 0.583078685 0.805883618 0.863390556 1.038473824 1 21.06913101 1.71898556 1.55391451 1.016597514 0.640381949 0.817757345 0.070372815 0.138353191 0.652893754 0.051512174 0.019900769 52.35830281 -1.71898556 -0.376215565 NAS(ph)AS(ph)FQELEDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NASASFQELEDKK 13 1 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 2 NAS(1)AS(1)FQELEDKK;NAS(1)AS(1)FQELEDKK 140.32 0.00013753 435050000 2036070 1246930 1356170 1001740 1241630 979940 1027680 1892870 1933600 1540860 TRUE FALSE 1956498.133 1211368.777 1601260.087 1053439.921 1281568.157 999755.0582 1040257.055 1853781.573 1714105.834 1436496.18 1.361993273 0.843280194 1.114698465 0.73333987 0.89214867 0.695967781 0.724162772 1.290488342 1.193254711 1 20.45412273 1.719006156 11.09222706 1.178391049 0.89916645 0.243594161 0.202006037 0.133445131 47.60346268 0.094395395 0.051412039 52.36078591 -1.719006156 -0.279224598 DAS(ph)PSKEER ddPTM_BT-474_Pertuzumab_2h_R1 4 DASPSKEER 9 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DAS(0.912)PS(0.088)KEER;DAS(0.969)PS(0.031)KEER;DAS(0.971)PS(0.029)KEER;DAS(0.97)PS(0.03)KEER 151.79 4.97E-05 8636320000 9470900 7473910 6399450 6185030 6927280 6793460 7339970 8348610 9710900 8411720 TRUE FALSE 9100766.757 7260761.405 7555972.97 6504240.14 7150102.252 6930828.416 7429798.748 8176208.286 8608559.343 7841986.712 1.160518003 0.925882901 0.963527898 0.829412288 0.911771789 0.883810273 0.947438324 1.042619503 1.09775235 1 22.90278777 1.71902807 4.136456307 1.055035547 0.937169545 0.22720922 0.08407987 0.247977861 9.728447506 0.045710285 0.022350366 52.36342795 -1.71902807 -0.117866003 YDDMATCMK ddPTM_BT-474_Pertuzumab_2h_R1 4 YDDMATCMK 9 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;; 162.97 0.00014743 2123690000 2349490 2490250 1942740 2084970 2297010 2173510 2479740 2447600 2769210 2741440 FALSE TRUE 2257669.333 2419230.508 2293836.334 2192575.552 2370895.413 2217459.861 2510087.8 2397056.205 2454860.89 2555759.827 0.883365217 0.946579754 0.89751639 0.857895773 0.927667533 0.867632333 0.982129766 0.937903546 0.960520963 1 21.28532084 1.71907234 0.866826671 0.988704077 0.898459713 0.514768879 0.031967206 0.462769987 0.662976082 0.027652814 0.011834845 52.36876596 -1.71907234 -0.090244364 TLSDVEDQKELASPVS(ph)PELR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLSDVEDQKELASPVSPELR 20 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 TLSDVEDQKELAS(0.002)PVS(0.998)PELR;TLSDVEDQKELAS(0.03)PVS(0.97)PELR 162.87 1.24E-11 518510000 473870 469540 373160 406030 422310 465450 441330 514080 569050 542690 TRUE FALSE 455350.6365 456149.1789 440598.3129 426985.257 435893.9847 474861.7179 446731.1286 503464.0684 504453.8297 505933.1229 0.900021398 0.901599754 0.870862754 0.843955925 0.861564434 0.938585944 0.882984545 0.995119801 0.997076109 1 18.94858717 1.719438917 4.516131093 0.998730333 0.884799756 0.816142735 0.024271746 0.075141902 3.588138869 0.01401531 0.006940858 52.4129877 -1.719438917 -0.113930576 TS(ph)PLKDNPS(ph)PEPQLDDIKR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 2 T(0.449)S(0.551)PLKDNPS(1)PEPQLDDIKR;T(0.009)S(0.991)PLKDNPS(1)PEPQLDDIKR;T(0.457)S(0.543)PLKDNPS(1)PEPQLDDIKR 193.88 2.31E-15 898360000 1086030 815600 766420 579100 741480 715870 800660 1056730 1255650 1048100 TRUE FALSE 1043586.747 792339.8866 904929.1429 608987.4204 765330.3776 730345.3819 810458.7166 1034908.156 1113113.876 977111.2534 1.068032676 0.81090038 0.92612703 0.623252898 0.783258175 0.747453659 0.829443642 1.05915079 1.139188472 1 19.89816331 1.719513223 4.332440035 1.078865918 0.816471176 0.481742265 0.113334775 0.145492103 6.327171589 0.061090279 0.030087075 52.42195619 -1.719513223 -0.262394742 YVDEENS(ph)DGETSNHR ddPTM_BT-474_Pertuzumab_2h_R1 3 YVDEENSDGETSNHR 15 0 A0A494C108;Q8N9T8;H0YFD2;H0YH26;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 YVDEENS(1)DGETSNHR;YVDEENS(1)DGETSNHR;YVDEENS(1)DGETSNHR 259.55 4.68E-25 6731970000 2093480 2375490 1933460 2568230 2367970 2518580 2353820 2121210 2141770 2423960 TRUE FALSE 2011664.487 2307743.351 2282879.232 2700776.658 2444137.906 2569507.413 2382626.753 2077406.272 1898645.249 2259783.03 0.890202493 1.021223418 1.010220539 1.195148659 1.081580786 1.137059345 1.054360849 0.919294571 0.840189179 1 21.10775283 1.719520703 4.546776263 0.907748974 1.062630585 0.350430655 0.084111195 0.181228202 8.786441046 0.046116042 0.022860252 52.422859 -1.719520703 0.154881611 MSVQPTVSLGGFEITPPVVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 MSVQPTVSLGGFEITPPVVLR 21 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 ; 174.95 5.45E-12 142609000 65238 60172 47959 62106 57683 59816 59267 57931 63119 60252 FALSE TRUE 62688.42684 58455.95347 56626.25814 65311.2981 59538.42608 61025.5205 59992.32727 56734.70461 55953.99574 56171.07837 1.116026764 1.040677074 1.008103454 1.162721101 1.059948069 1.086422449 1.068028762 1.0100341 0.996135331 1 15.77753988 1.71958013 3.142575931 0.998839407 1.077124031 0.44099361 0.039155041 0.211698982 4.56878867 0.022862638 0.010600403 52.43003286 -1.71958013 0.078284624 MMENGIKPVYVFDGKPPQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 MMENGIKPVYVFDGKPPQLK 20 2 P39748;P39748-2;F5H1Y3 P39748 FEN1 Flap endonuclease 1 0 ; 132.14 7.36E-06 880860000 826640 706190 643130 661160 749290 752380 786750 873730 1020810 991490 FALSE TRUE 794333.9949 686050.1526 759357.8973 695282.5468 773391.5933 767593.6391 796378.4818 855687.1702 904931.9284 924335.4992 0.859356798 0.742209028 0.821517618 0.75219717 0.836700088 0.830427523 0.861568643 0.925732238 0.979008087 1 19.81805707 1.719580405 0.952142901 1.004760946 0.795277461 0.836429356 0.032974379 0.178552802 0.304641286 0.026580423 0.01090768 52.43006602 -1.719580405 -0.209483484 KQVSS(ph)PCAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQVSSPCAQR 10 1 Q6NSI8-3;Q6NSI8-2;Q6NSI8 Q6NSI8-3 KIAA1841 Uncharacterized protein KIAA1841 1 KQVS(0.143)S(0.857)PCAQR 65.563 0.042015 32548000 69419 66771 56049 58605 59090 61511 63005 72319 79513 77365 TRUE FALSE 66706.02873 64866.75646 66178.3011 61629.61107 60990.68351 62754.79456 63776.07404 70825.58738 70487.01759 72124.99964 0.924866954 0.899365779 0.917550107 0.854483347 0.845624732 0.870083811 0.884243665 0.981983885 0.977289677 1 16.13821179 1.719625798 4.57537555 0.986190062 0.883354037 0.785206688 0.024248965 0.084178233 4.139093403 0.014268586 0.007079581 52.43554647 -1.719625798 -0.102836024 EDEKDDKPIR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDEKDDKPIR 10 2 P35998;C9JLS9 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 129.82 0.00016481 1600370000 2931770 2036060 2138210 1753640 2012710 1698300 2139650 2612260 3075900 2597030 FALSE TRUE 2817193.187 1977993.562 2524632.111 1844145.571 2077450.645 1732640.79 2165835.677 2558315.918 2726736.727 2421130.845 1.163585683 0.816970948 1.042749142 0.761687694 0.858049721 0.715632859 0.894555402 1.056661569 1.126224439 1 21.20724962 1.719697897 4.567839196 1.071152883 0.882270061 0.266405124 0.126565327 0.211444426 10.35777621 0.065756813 0.032621734 52.44425216 -1.719697897 -0.188882822 AIS(ph)SPTVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AISSPTVSR 9 0 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 AIS(0.5)S(0.5)PT(0.001)VSR 80.986 0.023665 54088000 107410 125080 93964 113790 107310 106130 96717 130480 125760 119620 TRUE FALSE 103212.2985 121512.8409 110945.385 119662.7155 110761.7236 108276.0213 97900.65158 127785.5424 111484.252 111518.0309 0.925521171 1.089625058 0.994864993 1.073034689 0.993218072 0.970928382 0.877890784 1.145873375 0.9996971 1 16.76691747 1.719712647 24.99999998 1.059452345 0.996028326 0.120506159 0.069879325 1.757817374 2322.322971 0.031577957 0.017511586 52.44603341 -1.719712647 -0.063424019 S(ph)PSFGDPQLS(ph)PEARPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSFGDPQLSPEARPR 16 1 O95425-2;O95425-3 O95425-2 SVIL Supervillin 2 S(0.995)PS(0.006)FGDPQLS(1)PEARPR;S(0.997)PS(0.003)FGDPQLS(1)PEARPR 105.51 0.00072731 969590000 336640 383220 286910 360440 369640 365010 352000 337060 334530 383270 TRUE FALSE 323483.7366 372290.9408 338761.0193 379042.3516 381529.8063 372390.7523 356307.8813 330099.5932 296555.5569 357310.7815 0.905328788 1.041924734 0.948085076 1.060819799 1.067781399 1.042204074 0.997193199 0.92384448 0.829965319 1 18.44681992 1.71971806 3.594775103 0.904510919 1.014429573 0.313695661 0.061363395 0.207835307 5.980754237 0.033366695 0.015936091 52.44668705 -1.71971806 0.109918654 AALAPAKES(ph)PRK ddPTM_BT-474_Pertuzumab_2h_R1 3 AALAPAKESPRK 12 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AALAPAKES(1)PRK;AALAPAKES(1)PRK;AALAPAKES(1)PRK 94.487 0.0026324 124090000 670850 640520 489520 433450 523990 516430 530580 647170 694400 664290 TRUE FALSE 644632.4403 622252.9967 577987.1533 455820.4064 540844.6142 526872.5684 537073.3968 633805.7133 615574.6232 619297.0466 1.040909922 1.004773073 0.933295511 0.73602871 0.87332019 0.850759052 0.867230677 1.023427638 0.993989276 1 19.24027204 1.719938975 7.87612082 1.005261299 0.896868416 0.264416872 0.079825421 0.170970795 28.11182819 0.042972365 0.022717634 52.47337219 -1.719938975 -0.108392882 LDQPVSAPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 LDQPVSAPPSPR 12 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVS(0.107)APPS(0.893)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR 179.97 2.10E-05 25144600000 6058620 7698450 6177140 7921360 7739640 8278020 8097700 6458050 7187070 8018360 TRUE FALSE 5821842.432 7478897.744 7293486.608 8330182.339 7988592.55 8445407.236 8196802.075 6324689.011 6371223.944 7475269.335 0.778813735 1.000485388 0.975682117 1.114365512 1.068669528 1.129779658 1.096522641 0.846081757 0.852306942 1 22.83369413 1.7200086 9.674354347 0.888711266 1.030011341 0.230207016 0.102727662 0.140884624 37.3534775 0.050505056 0.027238528 52.48178529 -1.7200086 0.141300074 YNLDAS(ph)EEEDSNKKK ddPTM_BT-474_Pertuzumab_2h_R1 2 YNLDASEEEDSNKKK 15 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNKKK;YNLDAS(1)EEEDSNKKK 179.78 3.42E-07 1756390000 2059300 1336770 1324260 1010770 1380890 1265090 1420120 1879150 2386780 1651650 TRUE FALSE 1978820.279 1298646.628 1563583.24 1062935.961 1425307.581 1290670.987 1437499.853 1840344.896 2115842.741 1539782.274 1.285129925 0.843396271 1.015457358 0.690315753 0.925655273 0.838216551 0.933573452 1.195198131 1.374118131 1 20.55429494 1.720026448 4.518293052 1.217420251 0.918459224 0.325681765 0.167310186 0.173875954 8.308363057 0.084994371 0.042119949 52.48394215 -1.720026448 -0.298961027 DLTDEEKQEYLNEYEAEKIEYNESMK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLTDEEKQEYLNEYEAEKIEYNESMK 26 2 Q969G3;Q969G3-4;Q969G3-2;B4DGM3;Q969G3-5;A0A2R8Y855;A0A2R8Y7I9;A0A2U3TZQ7;J3QKS7;A0A2R8YES3;A0A2R8Y4T4;A0A2R8Y765;A0A2R8Y7U4;Q969G3-6;Q969G3-3;J3QR61;J3QKX6;A0A2R8YD78;J3KT85 Q969G3 SMARCE1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 0 ; 370 7.90E-127 307030000 330280 270850 224270 145217 255850 247310 230420 291280 340950 240080 FALSE TRUE 317372.2925 263125.6232 264800.5779 152711.6668 264079.6476 252310.7776 233239.9489 285264.9662 302246.7854 223819.1678 1.417985312 1.175617021 1.183100538 0.682299324 1.179879499 1.127297453 1.042091038 1.274533227 1.350406171 1 17.77197407 1.720150627 10.09104822 1.232785772 1.106703784 0.041000411 0.191672297 0.283802942 83.57477787 0.091668981 0.0496054 52.49895118 -1.720150627 -0.126081987 LMNIFS(ph)S(ph)LKETIY(ph)HLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMNIFSSLKETIYHLMK 17 1 A0A0A0MT16;Q86UQ4-3;Q86UQ4;Q86UQ4-4 A0A0A0MT16 ABCA13 ATP-binding cassette sub-family A member 13 3 LMNIFS(0.998)S(0.998)LKET(0.164)IY(0.84)HLMK 42.908 0.06696 167370000 50642 98937 63787 107090 95939 102400 80446 55260 36118 62322 TRUE FALSE 48662.85465 96115.41363 75314.72983 112616.9277 99024.96506 104470.5982 81430.52221 54118.86169 32018.03606 58100.87543 0.837558028 1.654285119 1.296275302 1.938300015 1.704362703 1.798089915 1.401536924 0.931463791 0.551076655 1 15.82627228 1.720293233 3.008566564 0.767991852 1.559421148 0.523537044 0.305136298 0.167111091 3.28505797 0.179011677 0.082158658 52.51619267 -1.720293233 0.791429296 RRPPS(ph)PEPSTK ddPTM_BT-474_Pertuzumab_2h_R1 3 RRPPSPEPSTK 11 2 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RRPPS(0.657)PEPS(0.172)T(0.172)K;RRPPS(0.663)PEPS(0.289)T(0.048)K;RRPPS(0.994)PEPS(0.003)T(0.004)K 99.069 0.0039771 436301000 393856 387424 331644 351099 350334 376282 359515 412907 438827 427852 TRUE FALSE 378463.6721 376375.0468 391579.4482 369219.2615 361602.8113 383890.6799 363914.8521 404380.3262 389013.1987 398873.2029 0.948832033 0.943595719 0.981714102 0.925655719 0.906560803 0.96243788 0.912357234 1.013806701 0.975280354 1 18.60557068 1.72035404 10.24281298 0.995245728 0.940921122 0.559697692 0.022809686 0.076634667 23.52820986 0.010703899 0.005798831 52.5235461 -1.72035404 -0.054324606 FGPPEDMPQTSSSHSDLGQLASQGGLGMYETPLFLAHEEESGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 FGPPEDMPQTSSSHSDLGQLASQGGLGMYETPLFLAHEEESGGR 44 0 P12270 P12270 TPR Nucleoprotein TPR 0 193.05 6.18E-29 52881000 10808 13074 8672 14746 10929 13358 13277 10099 11410 12758 FALSE TRUE 10385.61141 12701.14232 10239.22331 15507.04283 11280.54121 13628.10791 13439.4879 9890.452121 10114.78463 11893.8893 0.873188841 1.067871241 0.860881 1.303782341 0.948431663 1.14580753 1.129948965 0.831557439 0.850418596 1 13.53793293 1.720428265 9.75068698 0.88289141 1.05056288 0.217418687 0.132360212 0.140810543 38.43551362 0.06018052 0.032478933 52.53252368 -1.720428265 0.167671469 ELEKPIQSKPQSPVIQAAAVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEKPIQSKPQSPVIQAAAVSPK 23 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 ELEKPIQSKPQSPVIQAAAVS(1)PK;ELEKPIQSKPQSPVIQAAAVS(1)PK 281.27 4.48E-52 2244100000 1096420 970310 845940 713760 910340 956550 1064740 1208380 1601700 1386990 TRUE FALSE 1053570.694 942637.7088 998820.1758 750597.2391 939621.9128 975892.0964 1077770.607 1183426.531 1419881.731 1293047.932 0.814796318 0.72900446 0.772454099 0.580486787 0.726672144 0.75472229 0.833511721 0.915222477 1.098089016 1 20.30234432 1.720461616 1.497010729 1.047811112 0.723076588 0.794366859 0.064102275 0.162313752 0.705521514 0.050964934 0.019633762 52.53655805 -1.720461616 -0.324734524 LEHAFCTETRPYNQGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEHAFCTETRPYNQGAR 17 1 Q9BV20 Q9BV20 MRI1 Methylthioribose-1-phosphate isomerase 0 112.67 0.0002702 317600000 109310 142120 108530 125900 122320 133020 130730 118910 129710 135700 FALSE TRUE 105038.0444 138066.8768 128143.7852 132397.7141 126254.5339 135709.7555 132329.9128 116454.4669 114985.8646 126508.9181 0.830281737 1.091360821 1.01292294 1.046548465 0.997989199 1.072728765 1.046012525 0.920523775 0.908915089 1 16.94887956 1.720540081 8.339051565 0.937094971 1.019767318 0.166369489 0.071298332 0.163939166 30.96583439 0.032458032 0.017266236 52.54605074 -1.720540081 0.082672347 YADSPGASS(ph)PEQPK ddPTM_BT-474_Pertuzumab_2h_R1 3 YADSPGASSPEQPK 14 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 YADSPGAS(0.016)S(0.984)PEQPK;YADSPGAS(0.022)S(0.978)PEQPK;YADSPGAS(0.169)S(0.831)PEQPK 314.52 8.17E-56 1569890000 2230960 2017290 1618430 1764950 1837610 1882290 1889420 2218740 2418830 2327330 TRUE FALSE 2143771.617 1959758.864 1910916.303 1856039.281 1896718.395 1920351.193 1912543.287 2172922.244 2144254.559 2169697.866 0.988050756 0.903240444 0.880729217 0.855436745 0.874185491 0.885077698 0.881479084 1.001486095 0.988273341 1 21.04906273 1.720754124 6.20321796 0.995780466 0.8924015 0.650206313 0.033867051 0.086412299 8.435106227 0.017786405 0.009151958 52.57195459 -1.720754124 -0.103378965 GEEGHDPKEPEQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEEGHDPKEPEQLR 14 1 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 119.31 0.00011703 3287500000 3711900 3367720 2760570 2854490 3214890 3445860 3238200 3270050 3790800 3529390 FALSE TRUE 3566834.844 3271675.923 3259466.408 3001810.571 3318299.857 3515537.65 3277830.06 3202522.325 3360484.276 3290341.272 1.084031883 0.99432723 0.990616516 0.912309795 1.008497169 1.068441648 0.996197595 0.97331008 1.021317851 1 21.6498058 1.720762813 0.00199167 4.63E-06 1.998293855 0.004864466 0.045241839 220440.5422 415.4141087 208224.9825 208556.8633 52.57300641 -1.720762813 1.998289224 SEPFS(ph)PSLRPEPPKHPESIK ddPTM_BT-474_Pertuzumab_2h_R1 4 SEPFSPSLRPEPPKHPESIK 20 2 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 S(0.03)EPFS(0.81)PS(0.16)LRPEPPKHPESIK;S(0.011)EPFS(0.91)PS(0.079)LRPEPPKHPESIK;SEPFS(0.874)PS(0.126)LRPEPPKHPESIK;SEPFS(0.972)PS(0.028)LRPEPPKHPESIK 146.5 6.92E-08 2601050000 2089810 1813940 1609390 1525700 1887310 1835930 1702000 2215190 2461380 2027870 TRUE FALSE 2008137.915 1762208.207 1900242.574 1604441.56 1948017.04 1873053.762 1722829.585 2169445.552 2181974.461 1890520.559 1.06221427 0.932128561 1.005142507 0.848677129 1.030413042 0.990760854 0.911299048 1.147538725 1.154165953 1 20.85035211 1.720990816 9.018387826 1.111247444 0.967340294 0.423649757 0.070049161 0.08854132 20.27360756 0.031719611 0.017004379 52.60061428 -1.720990816 -0.14390715 VYAILTHGIFSGPAISR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYAILTHGIFSGPAISR 17 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;B7ZB02;P11908;P11908-2;H7C540;A0A0B4J207;P21108 B1ALA9;P11908;A0A0B4J207 PRPS1;PRPS2;PRPS1L1 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2;Ribose-phosphate pyrophosphokinase 3 0 ; 203.04 1.00E-11 1189150000 434520 488110 466880 527710 506650 467510 536840 439310 486910 558350 FALSE TRUE 417538.478 474189.5807 551255.6017 554945.1763 522946.8574 476963.3725 543410.0085 430238.095 431638.0181 520532.4572 0.802137258 0.910970246 1.059022534 1.066110612 1.004638328 0.916299005 1.043950288 0.826534617 0.829224023 1 18.9896286 1.721018158 11.84042361 0.87189932 0.975611159 0.1609295 0.088745789 0.162205736 72.40372763 0.042730151 0.023361438 52.60392598 -1.721018158 0.103711838 RGS(ph)LGEEGSEPPPPPPLPLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSLGEEGSEPPPPPPLPLAR 21 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 RGS(0.999)LGEEGS(0.001)EPPPPPPLPLAR 101.47 0.00032901 201030000 34550 39210 29745 32928 30284 31927 30587 41934 46097 36562 TRUE FALSE 33199.7478 38091.76919 35120.58317 34627.41803 31258.11236 32572.58581 30961.33286 41068.04825 40864.26181 34085.62317 0.974010293 1.11753184 1.030363535 1.015895114 0.917046821 0.955610688 0.908339938 1.204849565 1.198870902 1 15.05687574 1.721205054 10.42905904 1.149507582 0.992085753 0.423190483 0.077462526 0.091914217 30.2176815 0.037539686 0.020364757 52.62656864 -1.721205054 -0.157421829 SPAVATSTAAPPPPSS(ph)PLPSK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPAVATSTAAPPPPSSPLPSK 21 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 SPAVATSTAAPPPPS(0.021)S(0.979)PLPSK;SPAVATSTAAPPPPSS(1)PLPSK;SPAVATSTAAPPPPSS(1)PLPSK;SPAVATSTAAPPPPS(0.007)S(0.993)PLPSK;SPAVATSTAAPPPPS(0.02)S(0.98)PLPSK;SPAVATSTAAPPPPS(0.031)S(0.969)PLPSK 323.38 3.27E-67 33090060000 11463700 11500400 10088600 11173900 11165400 11287900 10680800 11094700 11562300 10973200 TRUE FALSE 11015685.93 11172419.85 11911834.44 11750586.32 11524545.23 11516149.07 10811514.83 10865590.57 10249796.18 10229975.39 1.076804734 1.09212578 1.164404995 1.148642677 1.126546721 1.12572598 1.056846611 1.06213262 1.00193752 1 23.28629934 1.721415637 1.162012908 0.999765807 1.125098015 0.754286949 0.026829602 0.235382869 0.59597724 0.024175713 0.009396194 52.65209262 -1.721415637 0.125332207 (ac)AS(ph)GADSKGDDLSTAILK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASGADSKGDDLSTAILK 17 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 AS(0.986)GADS(0.014)KGDDLSTAILK 80.522 9.17E-05 86852000 340590 297910 224320 216420 260830 292660 249510 357460 394430 318040 TRUE FALSE 327279.3663 289413.8985 264859.614 227589.4621 269219.8338 298577.7857 252563.578 350078.3261 349655.96 296498.8675 1.103813208 0.976104566 0.893290474 0.767589651 0.907996162 1.007011555 0.851819706 1.180707127 1.179282616 1 18.17766707 1.721443894 8.784896472 1.132297954 0.926056789 0.442133238 0.097460537 0.094615282 20.52272717 0.048096565 0.02572224 52.6555185 -1.721443894 -0.206241165 MWGTS(ph)PEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 MWGTSPEDK 9 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 MWGT(0.108)S(0.892)PEDK 133.85 0.00027825 140640000 491790 387820 404860 397750 421890 402360 399290 507940 528190 518820 TRUE FALSE 472570.3031 376759.7533 478027.2081 418277.9252 435460.475 410495.9949 404176.6305 497450.8615 468232.0856 483679.8593 0.977031179 0.778944473 0.988313238 0.864782598 0.900307231 0.848693587 0.835628407 1.028471316 0.968061987 1 18.88369294 1.721451567 9.325121291 0.997208217 0.883210849 0.425748661 0.060586685 0.093042076 23.33015735 0.026820006 0.014421883 52.6564489 -1.721451567 -0.113997367 GNLLHFPSS(ph)QGEEEKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNLLHFPSSQGEEEKEK 17 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GNLLHFPS(0.126)S(0.874)QGEEEKEK 212.18 1.09E-12 257190000 569820 406440 453570 355170 422290 381630 470430 561550 688260 593880 TRUE FALSE 547550.8044 394848.7291 535540.1886 373500.3663 435873.3414 389346.8201 476187.2631 549953.7963 610131.6102 553655.9786 0.988972982 0.713166198 0.967279699 0.674607303 0.787263857 0.703228783 0.860077885 0.993313208 1.102004916 1 19.07863029 1.721479664 2.843923173 1.04940074 0.801380952 0.500734116 0.101481653 0.177179122 3.087811574 0.058032494 0.0262699 52.6598556 -1.721479664 -0.248019788 S(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 S(1)LPEEDVAEIQHAEEFLIKPESK 299.72 4.66E-62 61406000 84131 64188 73860 61373 68224 80912 77162 87864 104970 100040 TRUE FALSE 80843.06751 62357.42109 87208.14501 64540.46788 70418.48692 82548.09608 78106.33164 86049.5777 93054.24567 93264.20169 0.866817772 0.668610463 0.935065582 0.692017588 0.755043046 0.885099476 0.837473867 0.922643159 0.997748804 1 16.50903581 1.721521591 1.015538984 1.009658792 0.785344258 0.525866461 0.076992799 0.375891039 0.726033395 0.062797047 0.025209533 52.66493965 -1.721521591 -0.224314534 KPSGDS(ph)QPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSGDSQPSSPR 12 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 2 KPS(0.031)GDS(0.969)QPS(0.544)S(0.457)PR 58.831 0.036286 0 53102 58110 45621 58184 52708 67533 48908 53655 49760 51589 TRUE FALSE 51026.71513 56452.7597 53865.72953 61186.88321 54403.40069 68898.56353 49506.55073 52547.0055 44111.45341 48094.83108 1.060960481 1.173780184 1.119989993 1.272213289 1.131169389 1.432556514 1.029352835 1.092570747 0.917176595 1 15.55359423 1.721667274 2.054053769 0.977505615 1.191170096 0.393759696 0.107826469 0.29458696 2.566067261 0.072238737 0.029711502 52.68260898 -1.721667274 0.213664481 RKPDYEPVENTDEAQKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKPDYEPVENTDEAQKK 17 3 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 0 168.32 9.25E-10 56083000 149860 123510 102960 88231 119380 116470 117880 139210 166320 131040 FALSE TRUE 144003.3055 119987.6157 121567.1623 92784.61248 123219.9661 118825.1032 119322.6507 136335.2649 147440.0509 122164.5441 1.178765137 0.982180359 0.995110024 0.759505249 1.008639348 0.972664402 0.976737167 1.115997001 1.206897238 1 16.89846611 1.721667605 4.842855532 1.122299575 0.974156114 0.223218367 0.10572549 0.220980156 12.35325069 0.055455605 0.027765849 52.68264905 -1.721667605 -0.148143462 DMWAHLLELQPQTGES(ph)S(ph)S(ph)GISRDDY(ph)IGQVAKEIENK ddPTM_BT-474_Pertuzumab_2h_R1 2 DMWAHLLELQPQTGESSSGISRDDYIGQVAKEIENK 36 2 A0A1C7CYW8;A0A669KB38;Q8IVF4;A0A0J9YY17 A0A1C7CYW8 DNAH10 "Dynein heavy chain 10, axonemal" 4 DMWAHLLELQPQT(0.627)GES(0.688)S(0.694)S(0.688)GIS(0.627)RDDY(0.675)IGQVAKEIENK;DMWAHLLELQPQT(0.629)GES(0.687)S(0.693)S(0.687)GIS(0.629)RDDY(0.674)IGQVAKEIENK 64.53 0.0022721 1270710000 545940 488970 456860 382440 433010 473210 495880 584600 711560 615320 TRUE FALSE 524604.0612 475025.0544 539424.7648 402177.7742 446938.1599 482778.6304 501948.7278 572527.8057 630786.6919 573643.8283 0.91451182 0.828083614 0.940347892 0.701093177 0.77912136 0.841599973 0.875018091 0.998054503 1.099613838 1 19.12979573 1.721851617 2.391319735 1.05178584 0.831135847 0.64661382 0.066364601 0.161788454 1.954565435 0.043876281 0.018886577 52.70497568 -1.721851617 -0.220649993 VTHVEPWEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTHVEPWEK 9 0 Q5VTL8;Q5VTL8-2 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 107.79 0.0027168 320020000 472340 616170 457880 873430 666640 746070 661250 496350 481000 604410 FALSE TRUE 453880.4306 598597.4349 540629.1015 918507.827 688083.081 761156.0466 669342.5753 486100.199 426398.8965 563472.7723 0.805505524 1.062336042 0.95945914 1.630083781 1.221146992 1.350830216 1.187888054 0.862686225 0.756733808 1 19.10398637 1.721877824 5.149950207 0.855530785 1.188163717 0.285779783 0.21640315 0.200302625 12.88771966 0.117098769 0.05905992 52.70815621 -1.721877824 0.332632932 DKDAYSSFGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DKDAYSSFGSR 11 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;O15523-2;O15523;O15523-3;C9J8G5;C9J081 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 179.67 6.38E-06 9161700000 6100000 6006600 5093800 5625100 5846500 5843400 6234500 6903100 7852000 7693800 FALSE TRUE 5861605.256 5835297.649 6014362.971 5915412.085 6034557.982 5961557.552 6310799.676 6760548.573 6960673.878 7172692.073 0.817211334 0.813543589 0.838508458 0.824712956 0.841324 0.83114645 0.879836972 0.942539914 0.970440918 1 22.77408327 1.721913044 1.189578562 0.996636638 0.824584763 0.983377628 0.008488155 0.05009475 0.133126775 0.007176647 0.002780197 52.71243078 -1.721913044 -0.172051875 EEEEQKEGGDGAAGDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEEQKEGGDGAAGDPK 17 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 147.53 3.15E-06 0 289910 203640 225150 189810 244530 219980 244760 319960 404330 312100 FALSE TRUE 278579.9967 197832.3866 265839.6134 199606.1168 252395.5295 224428.1463 247755.4461 313352.7142 358432.1535 290961.189 0.957447272 0.679927063 0.913660046 0.686023169 0.867454283 0.771333617 0.851506852 1.076957086 1.231889912 1 18.1504672 1.721965762 3.328336422 1.12729658 0.808334007 0.638403593 0.098626092 0.11344006 2.754628555 0.050894682 0.02397417 52.71882988 -1.721965762 -0.318962573 VSNQDSKS(ph)PLGFYCDQNPVESSMCQSNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSNQDSKSPLGFYCDQNPVESSMCQSNSR 29 1 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 VSNQDS(0.208)KS(0.792)PLGFYCDQNPVESSMCQSNSR 199.29 2.25E-25 975390000 147770 114970 74670 76737 104760 114420 92551 124030 132260 106520 TRUE FALSE 141994.985 111691.1682 88164.53003 80697.40577 108129.7005 116733.6508 93683.66682 121468.7372 117246.3993 99305.30552 1.42988317 1.124725085 0.887812887 0.812619279 1.088861264 1.17550266 0.943390349 1.223184769 1.180666014 1 16.59958318 1.722026624 24.99973679 1.15182794 1.056842073 0.028134282 0.169981007 3.049812737 4592.982437 0.081900507 0.04541792 52.72621836 -1.722026624 -0.094985867 AKDDATLSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 AKDDATLSGK 10 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;; 86.772 0.013434 661640000 1350170 1220690 1154590 1112340 1153320 1175590 1252980 1447530 1619390 1591830 FALSE TRUE 1297403.864 1185877.116 1363250.097 1169748.001 1190417.585 1199361.235 1268314.344 1417638 1435563.636 1484013.936 0.874253154 0.799101065 0.918623514 0.78823249 0.802160651 0.808187313 0.854651235 0.9552727 0.967351856 1 20.50107321 1.722044998 2.663568974 0.980380474 0.83050932 0.743640244 0.037869934 0.12077635 1.832405026 0.023261039 0.010342277 52.72844917 -1.722044998 -0.149871154 KETKPEPMEEDLPENKK ddPTM_BT-474_Pertuzumab_2h_R1 3 KETKPEPMEEDLPENKK 17 3 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 189.87 1.45E-10 1004450000 936570 709840 702420 567420 713700 727470 790360 1017710 1275780 1063050 FALSE TRUE 899967.809 689596.0582 829362.9192 596704.6142 736656.8087 742179.9418 800032.6621 996693.9329 1130958.803 991048.6766 0.908096474 0.695824609 0.836853869 0.602094154 0.743310421 0.74888344 0.807258696 1.005696245 1.141173819 1 19.91859639 1.72216235 2.620821805 1.074210355 0.750345071 0.720750843 0.082497852 0.11900876 1.744831424 0.04919743 0.021773556 52.74269901 -1.72216235 -0.323865284 (ac)METMAS(ph)PGKDNYR ddPTM_BT-474_Pertuzumab_2h_R1 4 METMASPGKDNYR 13 1 O60684;S4R3E5 O60684 KPNA6 Importin subunit alpha-7 1 METMAS(1)PGKDNYR;METMAS(1)PGKDNYR;MET(0.03)MAS(0.97)PGKDNYR;METMAS(1)PGKDNYR 134.68 2.94E-23 1763250000 1607060 1417140 1292820 1242670 1394740 1409840 1510140 1668320 1813330 1872120 TRUE FALSE 1544254.319 1376724.555 1526461.333 1306804.348 1439603.079 1438347.931 1528621.545 1633868.609 1607488.38 1745319.645 0.88479742 0.788809407 0.874602734 0.748747859 0.824836346 0.824117195 0.875840451 0.936142909 0.921028068 1 20.73505985 1.722182944 1.147657768 0.976826935 0.819100334 0.684384262 0.039544899 0.2482935 0.612750872 0.031810226 0.01239494 52.7452001 -1.722182944 -0.157726601 SLRVDIAEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLRVDIAEGR 10 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 113.77 0.0013174 669010000 227550 348010 187206 265797 264190 322570 218920 203611 162451 169162 FALSE TRUE 218657.0944 338085.0955 221038.2886 279514.815 272687.9113 329092.5864 221599.2084 199406.3617 144010.2435 157704.5071 1.386498703 2.143788417 1.40159779 1.772395857 1.729106646 2.086767161 1.405154568 1.264430329 0.913165047 1 17.26686437 1.722320701 1.966764859 0.981307857 1.75071245 0.624040272 0.242628307 0.185823935 1.471710712 0.160559595 0.065285649 52.76193335 -1.722320701 0.769404594 ELSDIAHR ddPTM_BT-474_Pertuzumab_2h_R1 17 ELSDIAHR 8 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;;;;;;;; 225.99 3.32E-06 1.34962E+11 86791750.2 96401615 74431025 96439474.3 86605297.9 80723500.3 85313037 82832672.6 82304997.9 78646946.1 FALSE TRUE 83399832.65 93652335.33 87882366.93 101416727.1 89391035.96 82355784.78 86357123.47 81122148.96 72962079.59 73320118.39 1.137475423 1.277307476 1.198611907 1.383204629 1.219188375 1.12323584 1.177809384 1.106410502 0.995116773 1 26.12770578 1.722344296 0.88332603 0.988274204 1.245078177 0.648259265 0.066672084 0.344303343 0.510217774 0.059352241 0.025200898 52.7647999 -1.722344296 0.256803973 DLDKELDEYMHGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDKELDEYMHGGK 14 1 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 0 ; 161.66 2.74E-06 270600000 455570 364390 374520 339950 395950 424440 442610 490030 639820 566550 FALSE TRUE 437765.8207 353997.954 442204.0952 357494.8602 408686.0913 433022.4676 448026.7936 479910.7093 567190.3159 528177.0639 0.828823989 0.670225911 0.837226993 0.67684662 0.773767207 0.819843377 0.848251134 0.908617095 1.073863965 1 19.01066213 1.722358441 1.174291554 1.037768731 0.756202206 0.762564135 0.058735469 0.198551876 0.513677656 0.04613273 0.017909669 52.76651855 -1.722358441 -0.281566525 NWTEDMEGGIS(ph)SPVKK ddPTM_BT-474_Pertuzumab_2h_R1 3 NWTEDMEGGISSPVKK 16 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 NWTEDMEGGIS(0.569)S(0.431)PVKK;NWTEDMEGGIS(0.5)S(0.5)PVKK;NWTEDMEGGIS(0.5)S(0.5)PVKK 324.91 1.23E-58 2373170000 2419550 2037570 1852200 1730320 1888940 1935250 2099820 2347100 2731710 2545470 TRUE FALSE 2324991.311 1979460.499 2186933.742 1819622.023 1949699.471 1974382.081 2125518.225 2298631.565 2421617.733 2373063.05 0.979742747 0.834137339 0.921565798 0.766781996 0.821596152 0.831997313 0.895685526 0.968634847 1.020460764 1 21.178319 1.722426817 2.256353041 1.008460967 0.855398209 0.556787277 0.055202735 0.200149597 2.134499585 0.036688134 0.015525399 52.7748268 -1.722426817 -0.153062758 RMEDEGGFPVPQENGQPES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 11 RMEDEGGFPVPQENGQPESPR 21 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR 232.18 1.62E-26 9206270000 2330563 2906823 2466798 2852926 3112178 3074912 2715954 2537309 2461198 2671351 TRUE FALSE 2239482.021 2823923.254 2912603.272 3000165.853 3212284.032 3137088.827 2749192.657 2484912.682 2181813.121 2490418.017 0.899239407 1.133915365 1.169523852 1.204683644 1.289857369 1.259663561 1.103908114 0.997789393 0.876083094 1 21.24795649 1.722499154 2.75068638 0.93941388 1.166764016 0.431389391 0.103655448 0.225159248 3.652847506 0.066599574 0.02989982 52.7836178 -1.722499154 0.227350136 GHVQPIR ddPTM_BT-474_Pertuzumab_2h_R1 3 GHVQPIR 7 0 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ;; 97.596 0.02764 85453000 114726 111375 96321 115423 110882 109786 119495 100614 122470 108372 FALSE TRUE 110242.3811 108198.694 113728.3473 121379.9949 114448.6202 112005.9481 120957.4156 98536.28574 108567.719 101031.8679 1.091164435 1.070936293 1.125668066 1.201403056 1.132797231 1.108619987 1.197220422 0.975299059 1.074588853 1 16.6244509 1.72253865 11.26056785 1.019894997 1.131621857 0.579072178 0.04523523 0.073608493 30.66251004 0.021605415 0.011779809 52.78841842 -1.72253865 0.11172686 EDEIPVLKDELIHELK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDEIPVLKDELIHELK 16 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 160.25 5.32E-09 40044000 96286 78056 85606 79838 80585 83798 103880 114310 137380 139370 FALSE TRUE 92523.03667 75829.9193 101076.9085 83958.44875 83177.08971 85492.45297 105151.3145 111949.4586 121785.1983 129930.3458 0.71209721 0.583619776 0.777931498 0.646180446 0.64016677 0.657986804 0.809289884 0.861611334 0.937311431 1 16.98737889 1.722547172 1.215531118 0.982661853 0.665697382 0.842394138 0.052242759 0.157981374 0.439096031 0.04230287 0.016349249 52.78945425 -1.722547172 -0.316964471 GLGLDDALEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLGLDDALEPR 11 0 Q9Y230;X6R2L4;M0R0Z0;A0A1W2PS48 Q9Y230 RUVBL2 RuvB-like 2 0 ; 125.97 0.00073803 282440000 441560 510120 455470 535330 514390 526990 515300 470310 498210 528200 FALSE TRUE 424303.347 495571.8771 537783.5609 562958.4455 530935.8215 537646.0989 521606.3955 460597.9341 441655.2895 492424.5435 0.861661655 1.006391504 1.09211364 1.14323799 1.078207471 1.091834487 1.059261571 0.93536754 0.896899424 1 18.90954315 1.722584795 5.658910291 0.937107452 1.054353016 0.279847863 0.07510517 0.184704476 14.75559922 0.040372039 0.020588897 52.79402759 -1.722584795 0.117245564 KWESPAQNTAHLDQFER ddPTM_BT-474_Pertuzumab_2h_R1 4 KWESPAQNTAHLDQFER 17 1 P17612-2;P17612;Q15136 P17612-2 PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit alpha 0 ;;; 147.06 2.69E-07 2291030000 1542120 1812750 1296230 1682570 1675640 1642350 1626040 1626480 1768000 1691730 FALSE TRUE 1481852.245 1761052.145 1530487.595 1769407.639 1729538.482 1675559.442 1645939.964 1592892.62 1567304.052 1577147.62 0.939577391 1.116605778 0.970414929 1.121903629 1.096624349 1.062398612 1.043618202 1.009983212 0.993758626 1 20.58888627 1.722715362 2.557826323 0.997576588 1.055691773 0.141405138 0.055333287 0.452286447 6.29501102 0.033193385 0.014593443 52.80990206 -1.722715362 0.058115185 S(ph)PS(ph)PSPTPEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPSPTPEAK 11 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 S(1)PS(0.714)PS(0.286)PTPEAK;S(0.999)PS(0.658)PS(0.343)PTPEAK 138.42 8.46E-05 1477630000 3028000 2562400 2315800 2267000 2434900 2362700 2606500 3041000 3579400 3136200 TRUE FALSE 2909662.412 2489322.861 2734316.575 2384000.142 2513220.77 2410475.413 2638399.127 2978202.287 3173081.518 2923782.381 0.99517065 0.851404974 0.93519839 0.815382211 0.859578602 0.824437355 0.902392444 1.018612844 1.085265969 1 21.4794045 1.722836467 3.358391369 1.045106055 0.87669807 0.628486108 0.053588322 0.125154014 3.093104923 0.029708126 0.014034574 52.82463033 -1.722836467 -0.168407985 FNDPHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 FNDPHVK 7 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 62.2 0.086891 916580000 2292700 2281400 1876230 2054130 2201490 2253400 2340800 2380200 2722100 2695500 FALSE TRUE 2203098.749 2216336.706 2215306.498 2160143.895 2272302.925 2298965.292 2369447.411 2331048.038 2413098.62 2512931.384 0.876704698 0.881972632 0.881562669 0.859611173 0.90424392 0.914853985 0.942901754 0.927621046 0.960272388 1 21.26093985 1.722977161 0.433947609 1.001087849 0.867415494 0.91481412 0.0120592 0.271061564 0.13385645 0.014024861 0.011036363 52.84174625 -1.722977161 -0.133672355 KLEEVVQILGDKFPCTLVAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEEVVQILGDKFPCTLVAQK 21 2 Q9BY32 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 175.61 8.28E-13 321020000 138810 121290 103860 92121 122850 118590 118580 142850 162840 147250 FALSE TRUE 133385.1517 117830.928 122629.8124 96875.37585 126801.5818 120987.9711 120031.2175 139900.0976 144355.0859 137276.6263 0.971652315 0.858346618 0.893304386 0.705694614 0.923693896 0.881344292 0.874374762 1.019110837 1.051563472 1 17.06672648 1.723038481 4.148907537 1.029580596 0.867921458 0.528779704 0.065190191 0.139892443 5.494681678 0.035074111 0.017229613 52.84920775 -1.723038481 -0.161659138 TKECS(ph)VEK ddPTM_BT-474_Pertuzumab_2h_R1 6 TKECSVEK 8 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 TKECS(1)VEK;TKECS(1)VEK;TKECS(1)VEK;TKECS(1)VEK;TKECS(1)VEK;T(0.115)KECS(0.885)VEK 126.34 0.00074077 7085580000 14195740 10774370 9454390 7822890 9271460 8543650 10209320 12585630 14819110 12526300 TRUE FALSE 13640954.79 10467095.52 11163008.58 8226630.29 9569684.931 8716408.457 10334264.71 12325732.34 13136906.76 11677882.54 1.168101729 0.896317931 0.955910332 0.704462496 0.819470901 0.746403162 0.884943368 1.05547665 1.124939107 1 23.47727537 1.723189011 4.415069208 1.070629634 0.870320326 0.303917423 0.122519972 0.21035376 9.510013022 0.067466474 0.033441301 52.8675288 -1.723189011 -0.200309308 NSSS(ph)PVSLDAALPESSNVYRDPSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSSSPVSLDAALPESSNVYRDPSAK 25 1 Q70EL1-7;Q70EL1;H7C296;H7C1E9;Q70EL1-6;R4GN32 Q70EL1-7 USP54 Inactive ubiquitin carboxyl-terminal hydrolase 54 1 NSS(0.033)S(0.966)PVSLDAALPESSNVYRDPSAK;NSS(0.027)S(0.973)PVSLDAALPESSNVYRDPSAK 270.93 3.87E-53 856180000 796540 681410 623600 588980 608490 716740 685050 777820 884080 833790 TRUE FALSE 765410.3362 661976.854 736298.3919 619377.3284 628062.6335 731232.9739 693433.8468 761757.7452 783722.9448 777316.6606 0.984682788 0.851617992 0.947230941 0.796814683 0.807988128 0.940714397 0.89208669 0.979983813 1.008241537 1 19.56814291 1.723264624 1.701735665 1.008556582 0.880487379 0.430865314 0.056609357 0.319591016 1.840404112 0.04257101 0.016743457 52.87673423 -1.723264624 -0.128069203 GGS(ph)DGYGSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSDGYGSGR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GGS(1)DGYGSGR 82.912 0.017404 64817000 184200 190010 149740 179270 171910 176750 158660 166180 167160 153580 TRUE FALSE 177001.2604 184591.1008 176801.3489 188522.1462 177439.6413 180324.0061 160601.7285 162748.3249 148184.6976 143177.8898 1.236233196 1.28924306 1.234836951 1.316698734 1.239294988 1.259440311 1.121693641 1.136686154 1.034969141 1 17.1274492 1.723354275 0.898605554 1.00244458 1.271607782 0.894623025 0.033239501 0.149424345 0.228507697 0.027344961 0.011521962 52.88765056 -1.723354275 0.269163202 SQS(ph)IEQESQEK ddPTM_BT-474_Pertuzumab_2h_R1 5 SQSIEQESQEK 11 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 SQS(1)IEQESQEK;SQS(1)IEQESQEK;SQS(1)IEQESQEK;SQS(1)IEQESQEK;SQS(1)IEQESQEK 322.02 3.89E-46 3887790000 3861130 3455710 2914190 2662770 2874320 3197360 3235270 3876690 4534810 3878050 TRUE FALSE 3710232.771 3357156.534 3440848.959 2800195.879 2966775.113 3262012.81 3274864.202 3796634.997 4020037.38 3615386.219 1.026234141 0.9285748 0.951723758 0.774521921 0.820597008 0.902258462 0.905813101 1.050132618 1.11192474 1 21.78571834 1.723411251 4.027608968 1.064221264 0.895431486 0.502992417 0.069329222 0.155360746 5.705946553 0.0400422 0.019587864 52.89458946 -1.723411251 -0.168789777 DLPYDQASWESEDVEIQDYDLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPYDQASWESEDVEIQDYDLFK 23 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 127.28 4.68E-05 31937000 14530 15345 12094 13440 13150 15716 15034 15817 19731 18200 FALSE TRUE 13962.15154 14907.37562 14279.65483 14133.64001 13572.98169 16033.78829 15217.99059 15490.37342 17491.2196 16967.29779 0.822885984 0.878594565 0.841598645 0.832992984 0.799949518 0.94498184 0.89690125 0.91295465 1.030878329 1 14.0504692 1.723537579 0.824044271 1.013867124 0.840958741 0.737475791 0.037476387 0.307373802 0.401575264 0.033817617 0.014901028 52.90997773 -1.723537579 -0.172908383 NS(ph)SEKLPTELSK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSSEKLPTELSK 12 1 P38432 P38432 COIL Coilin 1 NS(0.984)S(0.016)EKLPTELSK;NS(0.986)S(0.014)EKLPTELSK 203.59 7.46E-08 1102210000 1599340 1319450 1130270 943450 1253920 1349840 1285060 1678340 1946530 1686090 TRUE FALSE 1536836.025 1281820.578 1334534.932 992141.5676 1294253.476 1377134.69 1300786.949 1643681.692 1725568.075 1571889.622 0.977699708 0.81546475 0.849000409 0.631177631 0.823374273 0.876101394 0.827530718 1.045672463 1.097766694 1 20.58406848 1.723596841 4.322705926 1.057511744 0.821854599 0.591103017 0.083315392 0.122502158 5.275524564 0.045659065 0.022576264 52.91719809 -1.723596841 -0.235657145 EMGVDVHFPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EMGVDVHFPK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 86.624 0.015574 0 167060 198230 160160 185160 162710 185250 182080 180990 202740 188650 FALSE TRUE 160531.1105 192576.6745 189104.4747 194716.1298 167943.7149 188995.8819 184308.3495 177252.4933 179725.8052 175872.5675 0.912769472 1.094978468 1.075235766 1.107143272 0.954917059 1.074618314 1.047965309 1.007846168 1.021909259 1 17.42417094 1.723672827 7.142811268 1.011456026 1.042677087 0.04327112 0.058171004 0.407730702 55.90417104 0.027789795 0.014552673 52.92645759 -1.723672827 0.031221061 S(ph)MDDLLSACDTSSPLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMDDLLSACDTSSPLTR 17 0 J3QR65;Q9NYA4 J3QR65 MTMR4 Myotubularin-related protein 4 1 S(1)MDDLLSACDTSSPLTR 193.77 1.17E-10 143460000 19946 19409 17792 18351 17581 20897 18029 24406 26409 22947 TRUE FALSE 19166.48827 18855.47432 21007.41018 19298.09731 18146.50883 21319.55166 18249.6443 23902.00757 23411.16104 21392.77925 0.895932597 0.881394329 0.981986021 0.902084628 0.848253919 0.996576995 0.85307496 1.117293237 1.094348741 1 14.3848363 1.723759328 8.912402306 1.077175261 0.911155005 0.655190691 0.053717325 0.058795359 13.81699671 0.0244476 0.013097455 52.93700023 -1.723759328 -0.166020255 TVAISDAAQLPHDYCTT(ph)PGGT(ph)LFSTTPGGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.011)CT(0.471)T(0.518)PGGT(0.371)LFS(0.164)T(0.15)T(0.312)PGGT(0.004)R 84.408 0.0012467 193760000 53072 57952 40447 46751 46131 59296 52989 41603 47903 44529 TRUE FALSE 50997.88757 56299.2657 47756.67264 49163.82471 47614.84551 60495.00575 53637.49523 40743.88351 42465.25227 41513.01117 1.228479605 1.356183619 1.150402519 1.184299171 1.146986069 1.4572541 1.292064674 0.981472612 1.022938377 1 15.34127596 1.723760189 6.709439356 1.003565111 1.259317447 0.62896215 0.090603646 0.08848719 10.49764194 0.0473049 0.024602241 52.93710521 -1.723760189 0.255752336 EVEEDEYK ddPTM_BT-474_Pertuzumab_2h_R1 5 EVEEDEYK 8 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 167.24 0.00073 2912130000 2654990 2735270 2260920 2250580 2248410 2453260 2602440 2889680 3505510 3023920 FALSE TRUE 2551230.056 2657262.778 2669518.538 2366732.704 2320732.15 2502866.598 2634289.439 2830007.098 3107579.201 2819107.205 0.90497802 0.942590184 0.946937574 0.839532707 0.823215288 0.887822426 0.93444103 1.003866434 1.10232743 1 21.42680691 1.723958751 2.297843997 1.051565006 0.89147667 0.688557249 0.043863006 0.162099578 1.794771549 0.031273856 0.013327762 52.96131389 -1.723958751 -0.160088335 MDY(ph)VEINIDHK ddPTM_BT-474_Pertuzumab_2h_R1 1 MDYVEINIDHK 11 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 1 MDY(1)VEINIDHK 133.05 0.00098547 185810000 121060 196540 192210 317840 246730 251250 214820 138460 108790 151900 TRUE FALSE 116328.8414 190934.8716 226946.6227 334243.7605 254666.2945 256330.4471 217449.0314 135600.7526 96440.61528 141611.6777 0.82146362 1.348298917 1.602598221 2.360283883 1.798342472 1.810093993 1.535530367 0.957553465 0.681021628 1 17.11158071 1.724021954 3.256225551 0.832700478 1.652846135 0.449236144 0.372383053 0.203668667 4.702408058 0.23193775 0.108941841 52.96902192 -1.724021954 0.820145658 TAVPS(ph)PVEAAAASDPAAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAVPSPVEAAAASDPAAAR 19 0 Q147X3;Q147X3-2;J3KNC2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 TAVPS(1)PVEAAAASDPAAAR;TAVPS(1)PVEAAAASDPAAAR 214.24 4.56E-19 421850000 123089 126035 115963 113459 124818 120111 132870 116997 133302 145825 TRUE FALSE 118278.5458 122440.6052 136920.0937 119314.6326 128832.8843 122539.7267 134496.1028 114580.9711 118170.1158 135948.1429 0.870026933 0.900641985 1.007149423 0.877648124 0.947661966 0.901371097 0.989319162 0.842828513 0.86922935 1 17.05269692 1.724087336 25 0.889504266 0.927537933 0.016438926 0.057064436 2.277612103 3917.974764 0.024849787 0.013780431 52.97699689 -1.724087336 0.038033667 TADEDRGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TADEDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 92.732 0.0090079 238850000 849280 1193090 914820 1342400 1175550 1189580 1113420 856060 812340 961220 FALSE TRUE 816089.1987 1159064.241 1080148.324 1411681.425 1213362.633 1213634.123 1127046.367 838382.0618 720126.5688 896115.7132 0.910696227 1.293431444 1.205367017 1.575333859 1.354024503 1.354327465 1.257701824 0.935573442 0.803608907 1 19.77332551 1.724088823 3.724741425 0.891344614 1.296643893 0.517532314 0.161655387 0.152742491 4.712240417 0.09100402 0.043956872 52.97717837 -1.724088823 0.405299279 EAEAAIYHLQLFEELRR ddPTM_BT-474_Pertuzumab_2h_R1 24 EAEAAIYHLQLFEELRR 17 1 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;; 281.72 3.54E-36 42618392100 14105748.9 14914550.5 11142208.4 13722080.9 14169165.3 14253022.5 13681384.1 13128461.8 14164502 13432727.8 FALSE TRUE 13554480.64 14489202.12 13155853.31 14430279.14 14624929.37 14541228.38 13848820.97 12857354.48 12556607.12 12522917.18 1.082374054 1.157014928 1.050542228 1.152309716 1.167853237 1.161169412 1.105878189 1.026706021 1.002690262 1 23.57806734 1.724180611 2.801412309 1.003946256 1.129500689 0.700051534 0.035107557 0.132172072 2.222420262 0.021693562 0.009806094 52.98837621 -1.724180611 0.125554433 SPQPVPS(ph)PRPQSQPPHSSPSPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPQPVPSPRPQSQPPHSSPSPR 22 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 SPQPVPS(0.984)PRPQS(0.016)QPPHSSPSPR;SPQPVPS(0.738)PRPQS(0.007)QPPHS(0.156)S(0.087)PS(0.013)PR;SPQPVPS(0.387)PRPQS(0.045)QPPHS(0.158)S(0.387)PS(0.023)PR 140.8 7.67E-08 844300000 174121 318159 204863 325521 251549 300766 271999 219551 219227 260492 TRUE FALSE 167316.1588 309085.4168 241886.3013 342321.1778 259640.302 306847.6946 275327.8051 215017.1951 194341.27 242848.6448 0.688972998 1.272749193 0.99603727 1.409607116 1.069144537 1.263534721 1.133742399 0.885395903 0.800256761 1 17.88969791 1.724255833 5.165003756 0.880968446 1.135616374 0.224545929 0.188269393 0.205749314 13.3476425 0.091633575 0.046337527 52.99755485 -1.724255833 0.254647928 IKPHLMSQELPEDWDKQPVK ddPTM_BT-474_Pertuzumab_2h_R1 4 IKPHLMSQELPEDWDKQPVK 20 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;; 219.87 5.35E-25 8377160000 10510410 9986950 8738400 8883850 9223840 9626450 10793290 11648060 14492000 13247900 FALSE TRUE 10099651.56 9702131.964 10317623.26 9342346.563 9520533.19 9821103.415 10925381.51 11407523.49 12846928.92 12350607.93 0.817745297 0.78555906 0.83539396 0.756428073 0.77085543 0.795191902 0.884602731 0.923640646 1.040185956 1 23.55807872 1.724330784 1.450467751 1.019068902 0.791815875 0.907668332 0.028426792 0.104198887 0.422429532 0.022413986 0.008638058 53.00670197 -1.724330784 -0.227253027 LAQFEPSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAQFEPSQR 9 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 71.692 0.097325 0 215370 196770 222420 191130 181440 186890 194920 227890 233630 240820 FALSE TRUE 206953.1023 191158.3123 262616.2417 200994.2422 187276.1824 190669.0438 197305.4893 223183.9919 207109.3019 224509.0469 0.921802953 0.851450375 1.169735676 0.895261215 0.834158734 0.849271094 0.878830907 0.994097988 0.922498691 1 17.77641406 1.72453181 13.28087224 0.968347911 0.915443519 0.075541893 0.092359739 0.341741647 234.9486663 0.045077441 0.024773144 53.03124346 -1.72453181 -0.052904392 S(ph)PSPAHLPDDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.5)PS(0.5)PAHLPDDPK;S(0.543)PS(0.457)PAHLPDDPK 126.48 0.00018465 3621900000 5177100 5155000 4725100 4601900 4844200 5124400 5032900 5040200 5421300 5451200 TRUE FALSE 4974773.208 5007984.447 5579030.679 4839404.61 5000018.092 5228018.879 5094494.136 4936118.109 4805896.752 5081985.369 0.978903489 0.98543858 1.097805341 0.952266537 0.983871013 1.028735524 1.002461394 0.97129719 0.945673079 1 22.27696079 1.724599448 4.552504339 0.968447867 1.005393919 0.122629751 0.038713273 0.33949808 16.44068896 0.020342961 0.010139124 53.03950321 -1.724599448 0.036946053 SLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR ddPTM_BT-474_Pertuzumab_2h_R1 7 SLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR 40 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ;;;;;; 245.17 3.13E-51 1173071000 166899.5 348737.8 143851.8 483854.2 188464.3 217371.6 406669.9 101246.9 317608.7 195458.9 FALSE TRUE 160376.883 338792.1394 169849.0202 508825.9732 194526.4254 221767.0027 411646.8479 99156.11613 281555.0919 182220.2946 0.880126351 1.859244823 0.932108142 2.792367197 1.067534359 1.217026913 2.259061477 0.544155174 1.545135752 1 17.47532412 1.724725827 24.99999996 1.021260606 1.572728824 0.139476848 0.617659068 1.681449125 3025.743665 0.268232845 0.148748479 53.05493995 -1.724725827 0.551468218 EEEEEETPKESLTEAEVATEKEGEDGDQPT(ph)TPPKPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEEEETPKESLTEAEVATEKEGEDGDQPTTPPKPLK 37 3 P18858;P18858-2 P18858 LIG1 DNA ligase 1 1 EEEEEETPKESLTEAEVAT(0.001)EKEGEDGDQPT(0.499)T(0.499)PPKPLK 80.652 0.0008678 143210000 385220 225800 203610 115600 257560 220950 217010 295280 348470 240170 TRUE FALSE 370165.1765 219360.4051 240406.8563 121566.1299 265844.6513 225417.7604 219665.8333 289182.3648 308913.1465 223903.072 1.65323849 0.979711458 1.073709504 0.542940875 1.18732025 1.006764929 0.981075567 1.291551573 1.379673551 1 17.7725148 1.72483102 8.43669947 1.248980046 1.041034371 0.064834134 0.271115729 0.25355828 52.8460678 0.128453794 0.068476424 53.06779218 -1.72483102 -0.207945675 GGVTGS(ph)PEASISGS(ph)KGDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGVTGSPEASISGSKGDLK 19 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 GGVT(0.009)GS(0.991)PEAS(0.002)IS(0.11)GS(0.888)KGDLK;GGVT(0.123)GS(0.877)PEAS(0.003)IS(0.212)GS(0.785)KGDLK 202.44 3.14E-16 716190000 1544640 1127280 907260 719040 680920 789060 1004140 1592260 1794580 1783020 TRUE FALSE 1484273.761 1095131.078 1071222.064 756149.7406 702822.4102 805015.3338 1016428.966 1559379.275 1590866.802 1662254.467 0.892928123 0.658822761 0.644439275 0.454894094 0.422812767 0.484291274 0.611476152 0.938111045 0.957053708 1 20.66470982 1.724995884 3.87265515 0.970404973 0.581163313 0.643640663 0.126018104 0.129863921 4.358513719 0.075478101 0.036745599 53.08794132 -1.724995884 -0.38924166 SGLSLEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 0 70.256 0.052925 1319900000 111470 241100 177340 328330 252720 313980 216990 124060 70618 132720 FALSE TRUE 107113.6292 234224.0641 209389.2829 345275.1506 260848.9683 320328.8907 219645.5885 121498.1176 62601.74069 123730.7562 0.865699301 1.893014084 1.692297771 2.790536171 2.108198288 2.58891888 1.775189899 0.98195567 0.50595133 1 16.91684464 1.725260725 3.178870771 0.754668007 2.022620258 0.519257466 0.50251418 0.171839101 3.76179754 0.298932489 0.139793235 53.12032519 -1.725260725 1.267952251 MVQFEENGRK ddPTM_BT-474_Pertuzumab_2h_R1 4 MVQFEENGRK 10 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 152.07 3.00E-05 1819770000 1439680 1410020 1121400 1022150 1266000 1442680 1353010 1227360 1457580 1276860 FALSE TRUE 1383415.714 1369807.61 1324061.925 1074903.284 1306722.04 1471851.978 1369568.541 1202014.587 1292121.629 1190377.135 1.1621659 1.150734141 1.112304569 0.902993894 1.097737853 1.236458543 1.150533307 1.009776273 1.085472487 1 20.18298729 1.725296863 10.63190284 1.036624584 1.113018935 0.175974402 0.083241633 0.206471317 80.92303487 0.042706132 0.023204274 53.12474557 -1.725296863 0.076394351 GALKEEVASR ddPTM_BT-474_Pertuzumab_2h_R1 1 GALKEEVASR 10 1 Q9P2M7;Q9P2M7-2 Q9P2M7 CGN Cingulin 0 77.379 0.019934 54784000 159300 249580 147840 244960 238660 238400 214210 147040 138730 169600 FALSE TRUE 153074.3799 242462.2228 174557.9767 257602.415 246336.7156 243220.6113 216831.5661 144003.5726 122981.952 158112.8409 0.968133764 1.533475848 1.104008856 1.629231462 1.557980454 1.53827235 1.371372273 0.910764564 0.777811285 1 17.27059501 1.725327408 4.250784959 0.874257697 1.405293752 0.547658027 0.203663254 0.129275887 5.346092781 0.107153272 0.052954096 53.12848205 -1.725327408 0.531036055 EAMEDGEIDGNKVTLDWAKPK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAMEDGEIDGNKVTLDWAKPK 21 2 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 240.71 3.19E-30 6585350000 5416860 4330220 3699660 3038300 4205220 4385060 4121560 5101030 5738820 4993230 FALSE TRUE 5205163.123 4206726.365 4368270.86 3195107.027 4340484.72 4473728.918 4172000.884 4995691.948 5087373.213 4655034.085 1.118179379 0.903693999 0.938397181 0.68637672 0.932428129 0.961051807 0.896234229 1.07318053 1.09287561 1 22.1503603 1.725390939 6.520454605 1.061300002 0.912689117 0.271761687 0.101123312 0.16850457 18.89423593 0.051150078 0.026545152 53.13625453 -1.725390939 -0.148610885 DADSDENDKGEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DADSDENDKGEKK 13 2 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4 Q5T1Z4 PUM1 Pumilio homolog 1 0 ; 85.909 0.0051008 193390000 218295 151976 127041 88676 138036 139941 136799 199745 233309 175418 FALSE TRUE 209763.7901 147641.7933 150000.1347 93252.57899 142476.0533 142770.7029 138473.1871 195620.1959 206824.7404 163536.7826 1.282670398 0.902804806 0.917225668 0.570223882 0.871217172 0.873018905 0.846740317 1.196184692 1.264698603 1 17.31925564 1.725475654 6.708529442 1.170587093 0.881737339 0.314816923 0.173253839 0.144895728 17.38627002 0.087231555 0.045411255 53.14662056 -1.725475654 -0.288849754 AQPYDPNFYDETYDYGGFTMMFDDRR ddPTM_BT-474_Pertuzumab_2h_R1 12 AQPYDPNFYDETYDYGGFTMMFDDRR 26 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;; 232.87 7.73E-37 5895882000 1689920 1795362 1496916.9 1687758.7 1740630 1843690 1674055 1638287 1780599 1613842 FALSE TRUE 1623876.058 1744160.034 1767443.083 1774864.129 1796618.945 1880970.675 1694542.586 1604455.801 1578472.866 1504535.044 1.07932086 1.159268467 1.174743712 1.179676164 1.194135658 1.25020064 1.126289875 1.066413047 1.049143304 1 20.52088628 1.725482011 2.333877375 1.030914874 1.17402963 0.67563508 0.041816059 0.164329969 1.877844969 0.028483829 0.012214795 53.14739844 -1.725482011 0.143114757 IKEELIAQGLLESEDRPAEDS(ph)EDEVLAELR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKEELIAQGLLESEDRPAEDSEDEVLAELR 30 2 O75528-2;O75528 O75528-2 TADA3 Transcriptional adapter 3 1 IKEELIAQGLLESEDRPAEDS(1)EDEVLAELR;IKEELIAQGLLESEDRPAEDS(1)EDEVLAELR 307.89 1.92E-92 153062000 222768 200316 182151 169921 193450 212701 195574 238504 259760 243692 TRUE FALSE 214061.9803 194603.1838 215069.7376 178690.6432 199672.4949 217001.96 197967.4931 233578.8091 230273.1338 227186.5238 0.942230097 0.856578905 0.946665912 0.78653716 0.878892338 0.955170916 0.871387483 1.028136727 1.013586237 1 17.79351773 1.72553766 6.939990839 1.014573714 0.889853216 0.578328184 0.047962681 0.087479912 11.38459677 0.023296783 0.012172672 53.15420898 -1.72553766 -0.124720498 EKFPEFCSSPS(ph)PPVEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.006)S(0.066)PS(0.928)PPVEVK 133.1 1.30E-05 915620000 757110 697810 533320 514930 541350 679850 632390 776560 896880 799720 TRUE FALSE 727521.3042 677909.142 629702.7876 541505.599 558763.0144 693597.0328 640129.378 760523.7646 795069.9424 745554.2521 0.975812695 0.909268695 0.844610283 0.726312804 0.749459899 0.930310612 0.858595302 1.020078368 1.066414604 1 19.50795381 1.725539517 3.271066627 1.039002229 0.8496704 0.536721852 0.073251767 0.175312843 4.075562821 0.046042404 0.021682473 53.15443635 -1.725539517 -0.189331829 DLQGLTVEHAIDSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLQGLTVEHAIDSFR 15 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ;;; 234.77 1.16E-17 1086830000 660532 723343 589806 682862 692128 662065 670563 640592 668161 668771 FALSE TRUE 634717.6792 702713.9659 696397.0644 718104.5897 714390.9257 675452.4079 678769.5506 627363.5513 592314.1644 623474.5445 1.018033029 1.127093274 1.116961503 1.151778522 1.145822122 1.08336806 1.088688474 1.006237635 0.950021408 1 19.24997113 1.725580535 2.121814673 0.972767055 1.112064134 0.686318981 0.037351571 0.158254544 1.474610833 0.02559204 0.010665638 53.15945691 -1.725580535 0.139297079 EESDDEAAVEEEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EESDDEAAVEEEEEEK 16 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 405.54 1.85E-139 2386200000 323207 300096 452150 482140 373460 365612 593900 661750 850950 883540 FALSE TRUE 310575.7131 291537.5559 533863.563 507023.3032 385472.6801 373004.9251 601168.3259 648084.6312 754353.7235 823697.0488 0.377050899 0.353937842 0.648130965 0.615545854 0.467978707 0.452842372 0.729841544 0.786799749 0.915814527 1 19.65175429 1.725647809 1.080366842 0.988281089 0.484437979 0.804477295 0.093933905 0.221975149 0.484373767 0.086981881 0.034388893 53.16769211 -1.725647809 -0.503843111 down LNEELKVDEETQEVLENLKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNEELKVDEETQEVLENLKDR 21 2 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;Q9BRK5-2 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 253.93 1.26E-36 57877000 129010 119660 91373 81930 98122 96581 112430 139960 162380 158670 FALSE TRUE 123968.1466 116247.414 107886.1337 86158.41712 101278.1832 98533.93399 113805.952 137069.7771 143947.3032 147923.1396 0.838057838 0.78586362 0.729339128 0.582453951 0.684667615 0.666115756 0.769358684 0.926628366 0.973122282 1 17.17448822 1.725782572 2.393864466 0.98253204 0.710695288 0.754792129 0.064931896 0.139656611 1.683618511 0.046460542 0.02008426 53.18419275 -1.725782572 -0.271836752 VRS(ph)PHYVHSTR ddPTM_BT-474_Pertuzumab_2h_R1 3 VRSPHYVHSTR 11 1 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 VRS(0.999)PHY(0.001)VHSTR;VRS(1)PHYVHSTR;VRS(1)PHYVHSTR 119.54 0.00034538 235833000 94038 122440 107575 159912 141159 167652 158412 70401 85932 118355 TRUE FALSE 90362.891 118948.1311 127016.1955 168165.0775 145699.5074 171042.0383 160350.6934 68947.19475 76177.35962 110338.7104 0.8189591 1.0780272 1.151148088 1.524080505 1.320474989 1.550154408 1.453258723 0.624868593 0.690395595 1 16.7515795 1.725799756 8.88920557 0.75030312 1.281037445 0.50099962 0.227480975 0.087379952 21.22666552 0.116881121 0.062625176 53.18629722 -1.725799756 0.530734325 LTPVSLSNS(ph)PIKGADCQEVPQDKDGYK ddPTM_BT-474_Pertuzumab_2h_R1 3 LTPVSLSNSPIKGADCQEVPQDKDGYK 27 2 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 LTPVSLS(0.012)NS(0.988)PIKGADCQEVPQDKDGYK;LTPVSLSNS(1)PIKGADCQEVPQDKDGYK;LTPVSLS(0.016)NS(0.984)PIKGADCQEVPQDKDGYK 291.4 8.65E-71 3388870000 2955690 2340270 1761250 1415300 2017120 2234950 2047430 2566120 2825660 2520340 TRUE FALSE 2840178.367 2273527.791 2079547.054 1488343.803 2082002.497 2280142.22 2072487.061 2513128.725 2504902.923 2349635.127 1.20877422 0.96760887 0.885051057 0.633436139 0.886096089 0.970423958 0.882046339 1.069582548 1.066081663 1 21.16400531 1.725859455 7.522289533 1.049328089 0.909373756 0.154639004 0.133435734 0.218568718 34.68236788 0.069143408 0.036444096 53.19360885 -1.725859455 -0.139954333 TPEEREWR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPEEREWR 8 1 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2;E9PJG2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 0 ;; 65.246 0.059068 6777500000 3162030 3798770 3149310 3549370 3396580 3476300 3588180 3316990 3690620 3634640 FALSE TRUE 3038454.372 3690432.799 3718460.373 3732553.411 3505834.08 3546593.168 3632093.22 3248492.997 3271676.29 3388462.595 0.896705891 1.089117172 1.097388644 1.101547769 1.034638566 1.046667351 1.071900048 0.9586923 0.965534132 1 21.69219942 1.725997215 7.939891865 0.972566482 1.053176844 0.258993086 0.056431234 0.143040092 26.01429254 0.027056545 0.014341279 53.21048471 -1.725997215 0.080610362 KVVGDVAYDEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVVGDVAYDEAK 12 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 170.52 6.56E-05 1149020000 1762660 1563200 1367390 1339190 1406630 1443930 1604360 1786110 2082120 1978960 FALSE TRUE 1693773.298 1518619.067 1614507.79 1408305.756 1451875.531 1473127.254 1623994.638 1749226.204 1845766.467 1844923.277 0.918072486 0.823133995 0.875108364 0.763341096 0.786957133 0.79847616 0.880250501 0.948129511 1.000457033 1 20.81512939 1.726028126 1.984798589 0.998135538 0.825152031 0.733450999 0.042312444 0.158531999 1.277852733 0.030834469 0.012612987 53.21427206 -1.726028126 -0.172983507 KSS(ph)TPEEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KSS(0.5)T(0.5)PEEVK;KS(0.007)S(0.619)T(0.374)PEEVK;KS(0.032)S(0.862)T(0.106)PEEVK;KSS(0.5)T(0.5)PEEVK 162.93 3.88E-05 9176500000 15955600 12913000 12646600 9952200 12083900 12798600 12753200 15350300 18024700 14276700 TRUE FALSE 15332037.51 12544733.88 14932121.94 10465834.23 12472589.62 13057396.46 12909277.48 15033310.94 15978611.62 13309726.39 1.151942351 0.942523799 1.121895485 0.786329781 0.937103382 0.981041689 0.969913062 1.12949812 1.200521419 1 23.66597758 1.726258116 6.005316573 1.123233354 0.978382781 0.223366441 0.105836157 0.186850471 17.31736239 0.052036319 0.026787454 53.2424603 -1.726258116 -0.144850573 LQVEEVHQLSR ddPTM_BT-474_Pertuzumab_2h_R1 6 LQVEEVHQLSR 11 0 Q9NR28-2;Q9NR28;Q9NR28-3 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ;;;;; 203.69 3.58E-08 5237570000 4670140 5472240 4456040 5838580 4368890 4958280 4666510 4572110 4379750 4234860 FALSE TRUE 4487625.766 5316177.073 5261345.552 6139909.813 4509419.315 5058539.819 4723620.145 4477694.331 3882579.141 3948029.16 1.136674929 1.346539465 1.332651138 1.555183502 1.142195037 1.281282284 1.196450166 1.134159387 0.983422104 1 21.91270121 1.726289547 0.971864719 0.980068563 1.320935969 0.544295818 0.110771105 0.391340056 0.693536933 0.096088344 0.039246066 53.24631375 -1.726289547 0.340867406 NLEQILNGGES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 7 NLEQILNGGESPK 13 0 Q13033-2;Q13033;G3V340;G3V3G7 Q13033-2 STRN3 Striatin-3 1 NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK 291.59 1.56E-40 999120000 2858280 2365340 2449380 2385760 2646670 2438030 2430060 3014810 3215800 2941460 TRUE FALSE 2746575.258 2297882.819 2892037.452 2508889.36 2731802.544 2487328.637 2459799.801 2952553.12 2850755.866 2742232.294 1.001583733 0.837960673 1.054628909 0.91490767 0.996196621 0.907045199 0.897006357 1.07669694 1.039574901 1 21.38691936 1.726335943 10.61513198 1.042431794 0.943821869 0.33614756 0.060789885 0.099482618 40.13135114 0.026848677 0.014587677 53.25200236 -1.726335943 -0.098609925 RGEAHLAVNDFELAR ddPTM_BT-474_Pertuzumab_2h_R1 6 RGEAHLAVNDFELAR 15 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 196.22 5.87E-09 7613310000 2216340 2319447 1795572 2310414 2520401 2598063 2307271 2167972 2341422 2257622 FALSE TRUE 2129722.983 2253298.643 2120071.803 2429654.743 2601471.987 2650597.614 2335508.073 2123202.621 2075633.591 2104711.251 1.011883688 1.070597518 1.007298175 1.154388633 1.236023224 1.259364016 1.109657238 1.008785704 0.986184489 1 21.00519089 1.726358386 4.097725032 0.995390969 1.126674351 0.343077503 0.078170639 0.239897971 9.114620529 0.048141491 0.02368769 53.25475441 -1.726358386 0.131283382 QQPTTEGGDGETKPSQGPADGSRPEPQRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQPTTEGGDGETKPSQGPADGSRPEPQRPR 30 3 Q9Y2T7;I3L2D6 Q9Y2T7 YBX2 Y-box-binding protein 2 0 ; 225.56 3.37E-35 342130000 140870 123685 113920 118651 115659 146693 134392 149829 187967 173461 FALSE TRUE 135364.6447 120157.6249 134507.8781 124774.5923 119379.2768 149659.233 136036.7295 146734.9788 166629.7742 161712.332 0.837070637 0.743033159 0.831772546 0.771583656 0.738219994 0.925465802 0.841226688 0.90738274 1.030408579 1 17.30307018 1.726424799 0.877553257 1.019008496 0.788555902 0.729354829 0.05019818 0.282175664 0.412784286 0.04339647 0.01851778 53.26289884 -1.726424799 -0.230452594 LWLFGYDEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LWLFGYDEQR 10 0 Q9NT62;Q9NT62-2 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 ; 166.16 1.31E-05 525060000 337620 397150 338030 345270 363940 375990 423240 311000 388660 412410 FALSE TRUE 324425.4371 385823.6709 399119.5404 363089.4261 375646.4606 383592.7754 428419.7377 304577.7413 344540.9462 384477.1034 0.843809512 1.003502335 1.038084029 0.944372039 0.977032071 0.99769992 1.114291941 0.792186943 0.896128646 1 18.55253816 1.726437998 25 0.881018467 0.989119332 0.21213682 0.079928446 1.100166123 2258.785256 0.035574454 0.019727822 53.26451759 -1.726437998 0.108100865 YWGPASPT(ph)HK ddPTM_BT-474_Pertuzumab_2h_R1 1 YWGPASPTHK 10 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.3)PT(0.7)HK 91.245 0.037827 2168500000 752290 696450 656880 773500 819260 746910 731620 651690 684990 651470 TRUE FALSE 722889.6751 676587.9279 775592.8282 813420.4277 845612.2419 762013.0319 740573.7844 638232.3738 607232.8069 607345.3566 1.190244837 1.114008563 1.277021088 1.339304596 1.39230873 1.254661822 1.219361894 1.050855772 0.999814686 1 19.21215759 1.726473197 2.400749769 1.000612419 1.264336461 0.708514592 0.07098185 0.162782806 1.972834432 0.052557053 0.022755196 53.26883479 -1.726473197 0.263724042 WSEPNEEELIK ddPTM_BT-474_Pertuzumab_2h_R1 3 WSEPNEEELIK 11 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ;; 220.94 2.04E-11 239810000 329043 313028 270544 303056 309091 313282 300684 359708 374155 379467 FALSE TRUE 316183.6358 304100.7479 319437.319 318696.7565 319033.1927 319616.7767 304363.8607 352279.9041 331682.493 353765.3621 0.893766518 0.859611428 0.902963809 0.900870437 0.901821453 0.903471088 0.860355177 0.995801008 0.937577639 1 18.43243327 1.726508653 9.242695286 0.973907164 0.889925914 0.769515783 0.022217003 0.046706337 12.79499161 0.010136646 0.005450425 53.27318383 -1.726508653 -0.083981251 MDAEVPDVNIEGPDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 MDAEVPDVNIEGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 154.72 7.64E-07 142150000 232790 221310 188420 201660 196680 235640 210120 262810 283500 268230 FALSE TRUE 223692.3094 214998.4555 222471.6854 212067.6968 203006.3908 240404.8022 212691.5114 257382.8817 251318.2685 250062.5432 0.894545447 0.859778729 0.889664172 0.848058626 0.811822467 0.961378698 0.85055326 1.02927403 1.005021645 1 17.93192945 1.72653554 7.245908922 1.011489237 0.873785435 0.736118476 0.037723558 0.059991597 8.741915582 0.018173017 0.009543853 53.27648208 -1.72653554 -0.137703802 GVVPLAGTNGETTTQGLDGLSER ddPTM_BT-474_Pertuzumab_2h_R1 5 GVVPLAGTNGETTTQGLDGLSER 23 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;; 422.83 6.06E-179 1804092000 266101 297392 204700 313225 285139 261640 254957 260618 259719 247167 FALSE TRUE 255701.4787 288910.6713 241693.8435 329390.5798 294310.7549 266930.5401 258077.24 255236.1472 230236.788 230426.1589 1.109689455 1.253810213 1.048899329 1.429484314 1.277245415 1.158421168 1.119999748 1.107670016 0.999178171 1 17.81394498 1.726584428 1.171722136 0.999220918 1.2218575 0.422058282 0.097633041 0.452147383 1.16383471 0.082826669 0.03224197 53.28247973 -1.726584428 0.222636582 AIQDHLLEVEQSKDQMEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIQDHLLEVEQSKDQMEK 18 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 246.68 1.57E-24 342160000 763550 689040 592130 507900 630850 677920 630660 752610 851390 704130 FALSE TRUE 733709.6219 669389.2538 699141.0629 534112.7799 651141.8632 691628.0069 638378.2057 737068.3405 754743.7765 656438.6479 1.117712408 1.019728585 1.065051647 0.813652245 0.991931028 1.05360647 0.972487235 1.122828985 1.149755242 1 19.32430065 1.726629242 8.670503293 1.100909512 1.001822525 0.177655153 0.083606863 0.164770076 38.0379151 0.040636607 0.021727424 53.28797811 -1.726629242 -0.099086988 IVAHAVEVPAVQS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 IVAHAVEVPAVQSPR 15 0 Q96FF9;B5MBX0;H0YCL8 Q96FF9 CDCA5 Sororin 1 IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR 190.46 1.39E-07 10555140000 2758900 3058790 2417000 3202900 3100650 2813970 2756010 2458580 2099580 2590060 TRUE FALSE 2651079.138 2971556.304 2853805.666 3368202.053 3200385.223 2870870.401 2789738.875 2407809.464 1861244.481 2414632.929 1.097922217 1.23064515 1.18187971 1.394912664 1.32541273 1.188946927 1.155346985 0.997174119 0.77081881 1 21.20337246 1.726761964 2.025056979 0.8832293 1.243521266 0.700200367 0.093194465 0.161556791 1.359636971 0.066039418 0.027184559 53.3042656 -1.726761964 0.360291966 SRS(ph)PITTNHRPS(ph)PDPEQRPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 2 S(0.116)RS(0.884)PITT(0.001)NHRPS(0.999)PDPEQRPLR;S(0.272)RS(0.728)PIT(0.086)T(0.035)NHRPS(0.88)PDPEQRPLR 146.1 1.61E-07 1529420000 180625 211465 173991 208191 180642 202128 199464 169833 189040 180485 TRUE FALSE 173565.9753 205434.2252 205435.0441 218935.7625 186452.514 206215.1666 201905.1001 166325.8892 167580.9717 168260.5902 1.031530765 1.220928947 1.220933814 1.301170775 1.108117556 1.225570209 1.199954784 0.988501758 0.995960917 1 17.36033778 1.726782732 5.639078459 0.994186727 1.192625637 0.616242938 0.069238414 0.095042624 7.598467437 0.034666909 0.0177378 53.30681466 -1.726782732 0.19843891 SS(ph)LGSLQTPEAVTTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSLGSLQTPEAVTTR 15 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.021)S(0.957)LGS(0.021)LQTPEAVTTR;S(0.001)S(0.999)LGSLQTPEAVTTR;S(0.021)S(0.979)LGSLQTPEAVTTR 319.53 1.74E-56 871180000 1089620 1169100 981640 976100 1028580 1135490 1020350 1212330 1248160 1216130 TRUE FALSE 1047036.446 1135758.413 1159044.184 1026476.638 1061665.21 1158450.386 1032837.349 1187294.962 1106474.11 1133760.432 0.923507662 1.00176226 1.022300789 0.905373489 0.936410533 1.021777047 0.910983766 1.047218556 0.975932903 1 20.11268439 1.726826054 25 1.009585217 0.963613679 0.192540298 0.044083359 1.436139662 3045.862094 0.01995054 0.01106351 53.31213235 -1.726826054 -0.045971538 QSQQPMKPIS(ph)PVKDPVSPASQK ddPTM_BT-474_Pertuzumab_2h_R1 2 QSQQPMKPISPVKDPVSPASQK 22 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 QSQQPMKPIS(1)PVKDPVSPASQK;QSQQPMKPIS(1)PVKDPVSPASQK 141.78 6.25E-08 1658000000 2199550 1691640 1486740 1286830 1594840 1606650 1746710 2227420 2767680 2226780 TRUE FALSE 2113589.154 1643396.083 1755426.99 1353243.451 1646139.477 1639137.564 1768086.759 2181422.999 2453504.569 2075958.207 1.018127025 0.791632547 0.845598425 0.651864496 0.792954054 0.789581196 0.851696702 1.050802945 1.181866071 1 20.98534597 1.726863732 3.108381372 1.098975473 0.807778266 0.615102871 0.093747396 0.13722669 2.856928414 0.054182839 0.025241134 53.31675782 -1.726863732 -0.291197208 AS(ph)PAPGSGHPEGPGAHLDMNSLDR ddPTM_BT-474_Pertuzumab_2h_R1 10 ASPAPGSGHPEGPGAHLDMNSLDR 24 0 O94826 O94826 TOMM70A Mitochondrial import receptor subunit TOM70 1 AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.999)PAPGS(0.001)GHPEGPGAHLDMNSLDR;AS(0.737)PAPGS(0.263)GHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.997)PAPGS(0.003)GHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR 292.37 1.27E-61 13651300000 1284947 1503712 1130935 1817729 981276 1471829 1829354 960927 1765630 1456616 TRUE FALSE 1234729.851 1460827.606 1335320.112 1911542.212 1012839.634 1501590.391 1851742.181 941083.5216 1565203.085 1357958.101 0.909254748 1.075753077 0.983329391 1.407659198 0.745854849 1.105770782 1.363622471 0.693013666 1.152615153 1 20.37300754 1.726978914 25 0.925823841 1.080475683 0.076273934 0.212072027 1.994173223 4285.064602 0.093593612 0.051902404 53.33090021 -1.726978914 0.154651842 EVEELILTESKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVEELILTESKK 12 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7;Q9BZZ5-3 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ; 162.32 0.00010101 141689000 237238 231688 173919 176439 204944 216249 190119 241369 238696 235835 FALSE TRUE 227966.4767 225080.4851 205350.0321 185545.0379 211536.2099 220621.7029 192445.7332 236384.6458 211600.2308 219861.6854 1.036863136 1.02373674 0.933996443 0.843917109 0.962133123 1.003456799 0.875303639 1.075151614 0.96242431 1 17.74623669 1.727093366 24.99999974 1.016318991 0.954054812 0.152087641 0.062916797 1.582549481 3434.427259 0.030003476 0.016638425 53.34495652 -1.727093366 -0.062264179 WRPHS(ph)PGWR ddPTM_BT-474_Pertuzumab_2h_R1 2 WRPHSPGWR 9 1 Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 WRPHS(1)PGWR;WRPHS(1)PGWR 93.766 0.0055577 447830000 346310 409390 326690 423570 361680 355050 417350 343580 403860 431300 TRUE FALSE 332775.8223 397714.598 385730.1502 445430.4985 373313.7657 362229.3543 422457.6541 336484.9529 358015.5059 402087.6668 0.827620068 0.989124091 0.959318532 1.107794482 0.928438737 0.900871586 1.050660562 0.83684475 0.890391662 1 18.61715056 1.72714461 24.99999975 0.896218809 0.968348295 0.086430235 0.081861962 1.675063619 3651.474718 0.036845399 0.020432651 53.35125131 -1.72714461 0.072129486 TDSREDEIS(ph)PPPPNPVVK ddPTM_BT-474_Pertuzumab_2h_R1 8 TDSREDEISPPPPNPVVK 18 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDS(0.006)REDEIS(0.993)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDS(0.002)REDEIS(0.998)PPPPNPVVK;TDS(0.002)REDEIS(0.998)PPPPNPVVK 222.57 4.18E-19 44627695200 8107481 7815870 6333391.4 6605341 6964599 7425975 7520923.8 8301486 9422289 8987062 TRUE FALSE 7790631.679 7592969.04 7477976.112 6946243.441 7188621.652 7576133.302 7612967.115 8130057.413 8352710.254 8378360.286 0.929851595 0.906259552 0.89253456 0.829069556 0.857998631 0.904250121 0.908646424 0.970363787 0.996938538 1 22.99823649 1.727156222 1.657040479 1.001262352 0.883207088 0.764708334 0.025842858 0.179634353 0.974314682 0.021677447 0.008511527 53.35267785 -1.727156222 -0.118055264 AS(ph)AGTPSLSAGVSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASAGTPSLSAGVSPK 15 0 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 AS(0.32)AGT(0.32)PS(0.32)LS(0.005)AGVS(0.033)PK;AS(0.328)AGT(0.328)PS(0.328)LS(0.007)AGVS(0.011)PK 65.716 0.03911 562870000 1066460 1550780 1279200 1896740 1405760 1566900 1428180 1189210 933950 1478990 TRUE FALSE 1024781.564 1506553.273 1510379.896 1994630.979 1450977.547 1598583.792 1445658.494 1164652.398 827931.9114 1378816.69 0.743232637 1.092642179 1.095417474 1.446625206 1.052335352 1.159388194 1.048477658 0.844675298 0.600465542 1 20.39499924 1.727237325 3.170941931 0.779801583 1.110339626 0.322686814 0.183407729 0.234599499 5.090183934 0.105902558 0.049594129 53.36264223 -1.727237325 0.330538043 VLQQGHFEDDDPDGFLG ddPTM_BT-474_Pertuzumab_2h_R1 2 VLQQGHFEDDDPDGFLG 17 0 Q6SPF0;E9PIW9 Q6SPF0 SAMD1 Atherin 0 ; 129.34 7.89E-05 292480000 310310 316620 256860 340500 334250 309180 309110 305630 318120 315020 FALSE TRUE 298182.7421 307590.3076 303280.3158 358073.2458 345001.4548 315431.8314 312892.9806 299318.6337 282008.3513 293683.4148 1.015320332 1.047353347 1.032677708 1.219249123 1.174739319 1.074053949 1.065409093 1.019188073 0.960246092 1 18.16390227 1.727316991 1.85702196 0.980718107 1.097699022 0.369904612 0.059858244 0.376245098 2.620739658 0.047820712 0.01924524 53.37243177 -1.727316991 0.116980915 FQEKPDRR ddPTM_BT-474_Pertuzumab_2h_R1 5 FQEKPDRR 8 2 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;;; 105.1 0.0025044 783932000 1172990 1255150 958870 1109530 1146410 1220400 1185260 1114450 1225690 1229410 FALSE TRUE 1127148.254 1219354.351 1132159.139 1166792.976 1183285.319 1245077.324 1199765.566 1091436.218 1086554.81 1146140.966 0.983428992 1.063878168 0.987800954 1.018018735 1.032408189 1.086321283 1.04678709 0.952270489 0.948011494 1 20.12835306 1.72732075 7.831190513 0.963445539 1.032457188 0.453433148 0.032298074 0.098607566 17.6143539 0.015823849 0.008379478 53.37289376 -1.72732075 0.06901165 RSLSGSS(ph)PCPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSLSGSSPCPK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.078)LS(0.078)GS(0.124)S(0.719)PCPK;RS(0.131)LS(0.053)GS(0.035)S(0.781)PCPK 80.632 0.014626 358080000 738560 715270 561020 580680 556510 632370 664980 788310 904080 858010 TRUE FALSE 709696.2587 694871.1999 662408.7938 610648.9644 574410.6496 645156.9547 673118.2242 772031.123 801452.6286 799896.2185 0.887235422 0.868701694 0.828118422 0.76341024 0.71810647 0.806550825 0.841506946 0.965164112 1.001945765 1 19.60945331 1.727356333 2.540621539 0.99976026 0.809140364 0.758360495 0.045227575 0.136679146 1.864244733 0.032609396 0.014374681 53.37726691 -1.727356333 -0.190619896 EVSEEHNLLPQPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EVSEEHNLLPQPPR 14 0 C9IZD2;C9J8Z7;C9JLE1;F8W8R3;A0A087WWF6;P49005 C9IZD2 POLD2 DNA polymerase delta subunit 2 0 ;; 112.15 0.00061003 535600000 344450 399210 324470 376300 346640 382570 370000 349100 359270 399410 FALSE TRUE 330988.5132 387824.9217 383108.9468 395720.8881 357789.9904 390305.8275 374528.1707 341890.963 318487.1758 372357.6049 0.888899565 1.041538877 1.0288737 1.062744208 0.960877355 1.048201574 1.00582925 0.91817908 0.855326094 1 18.5063293 1.727373228 4.890493198 0.914473709 1.010024979 0.283735589 0.057872907 0.178928209 10.21549212 0.028652514 0.01444697 53.37934348 -1.727373228 0.09555127 VWYVSNIDGTHIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VWYVSNIDGTHIAK 14 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7EPY4;K7ENA0 P06744 GPI Glucose-6-phosphate isomerase 0 ; 234.22 3.32E-17 15883800000 10654100 10217200 7990900 10325100 9226800 8072500 8428200 8863000 8541900 7057900 FALSE TRUE 10237725.99 9925815.46 9435033.387 10857979.65 9523588.402 8235731.481 8531346.833 8679975.953 7572259.323 6579862.146 1.555918006 1.508514197 1.433925693 1.650183455 1.447384184 1.251657147 1.296584433 1.319172919 1.150823399 1 22.64962593 1.727620403 0.393103821 0.986143788 1.578040484 0.828903193 0.077219685 0.460722326 0.200421172 0.099488056 0.086730027 53.40973251 -1.727620403 0.591896696 LKTEKEPDATPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKTEKEPDATPPSPR 15 2 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 LKTEKEPDATPPS(1)PR;LKTEKEPDATPPS(1)PR;LKTEKEPDAT(0.001)PPS(0.999)PR 140.35 2.59E-06 2108630000 2669210 2474800 1723660 1700940 2130770 2331030 2058610 2433520 2616130 2287080 TRUE FALSE 2564894.322 2404221.127 2035163.705 1788725.717 2199308.152 2378165.024 2083803.885 2383266.962 2319157.89 2132174.034 1.202947921 1.127591411 0.954501683 0.838921068 1.031486228 1.115370971 0.977314164 1.117763805 1.087696338 1 21.02389377 1.727629868 24.99999995 1.078175493 1.031240559 0.01862871 0.099698486 3.410979313 7764.804281 0.049579994 0.027494554 53.4108965 -1.727629868 -0.046934935 IKGS(ph)SPGIQDTLEAEDGAFETDEAPEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKGSSPGIQDTLEAEDGAFETDEAPEDR 28 1 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 1 IKGS(0.5)S(0.5)PGIQDT(0.001)LEAEDGAFETDEAPEDR;IKGS(0.5)S(0.5)PGIQDTLEAEDGAFETDEAPEDR 147.27 4.93E-08 218080000 92429 89482 77780 68934 89872 92592 85310 99191 113173 107470 TRUE FALSE 88816.77249 86930.06097 91836.57621 72491.692 92762.8145 94464.27368 86354.0493 97142.67119 100326.0755 100190.9612 0.886474902 0.867643747 0.916615383 0.723535249 0.925860112 0.942842274 0.861894609 0.9695752 1.001348568 1 16.61239283 1.727707183 0.923767652 1.011517197 0.863535133 0.455040117 0.057560163 0.4924841 0.792297077 0.050539625 0.021075912 53.42040583 -1.727707183 -0.147982064 TSLDIEEYS(ph)DTEVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSLDIEEYSDTEVQK 15 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 1 TSLDIEEYS(1)DTEVQK 423.45 3.62E-153 134420000 248230 219580 172050 160560 183880 206320 180930 234620 235880 228980 TRUE FALSE 238528.8972 213317.7934 203143.2622 168846.5208 189794.6672 210491.9318 183144.2755 229775.015 209103.8913 213470.9806 1.117383245 0.999282398 0.951620036 0.790957723 0.889088843 0.986044713 0.857935233 1.076375882 0.979542468 1 17.70368044 1.727723635 24.99979221 1.021144963 0.938227984 0.142474558 0.08606305 1.6188903 3717.038464 0.041707736 0.023128991 53.42242961 -1.727723635 -0.082916979 TAS(ph)PLPLRPDAPVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 TASPLPLRPDAPVEK 15 1 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 T(0.001)AS(0.999)PLPLRPDAPVEK;TAS(1)PLPLRPDAPVEK;TAS(1)PLPLRPDAPVEK;TAS(1)PLPLRPDAPVEK 218.66 5.02E-12 6191780000 7569920 6889700 5985420 5805740 6123510 6592900 7044220 8592430 9871960 9672440 TRUE FALSE 7274079.157 6693212.502 7067118.539 6105374.937 6320478.26 6726212.955 7130429.272 8414993.318 8751336.487 9017317.023 0.806678876 0.742262081 0.783727413 0.677072229 0.7009267 0.745921757 0.790748429 0.933203668 0.970503362 1 23.10426681 1.72774102 1.974106354 0.987418386 0.739116721 0.894747652 0.034958791 0.09323105 0.741903851 0.025921353 0.01060457 53.42456814 -1.72774102 -0.248301665 LDT(ph)PDINIVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDTPDINIVLK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 LDT(1)PDINIVLK;LDT(1)PDINIVLK 212.17 7.66E-08 105043000 430630 320800 261530 246910 265430 267820 277160 424410 444860 419330 TRUE FALSE 413800.5035 311651.0981 308794.2887 259653.0547 273967.797 273235.5039 280551.967 415645.7852 394361.3578 390928.4056 1.058507127 0.797207605 0.789899849 0.664195927 0.700813226 0.69894001 0.717655619 1.063227382 1.008781537 1 18.57654489 1.727796283 7.647500399 1.024035929 0.766692949 0.536673477 0.105487037 0.091189429 15.41345028 0.053635749 0.02834 53.43136673 -1.727796283 -0.257342981 YYGTKDPVPGYSVPAAEHSTITAWGK ddPTM_BT-474_Pertuzumab_2h_R1 2 YYGTKDPVPGYSVPAAEHSTITAWGK 26 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 169.6 4.81E-12 580260000 596870 737880 466940 624850 610620 686840 653260 603360 674140 679100 FALSE TRUE 573543.6605 716836.3849 551326.445 657098.5834 630261.1469 700728.3754 661254.7913 590900.4052 597614.4534 633103.9521 0.905923362 1.132257005 0.870830838 1.037899987 0.995509734 1.106814091 1.044464798 0.933338677 0.943943647 1 19.27208288 1.727985371 10.71404421 0.954708774 1.016309835 0.092742266 0.077012374 0.200177327 87.58647798 0.034463234 0.018738353 53.4546353 -1.727985371 0.061601061 LADVAAPPGGPPPPHS(ph)PYSGPPSR ddPTM_BT-474_Pertuzumab_2h_R1 6 LADVAAPPGGPPPPHSPYSGPPSR 24 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LADVAAPPGGPPPPHS(0.989)PYS(0.011)GPPSR;LADVAAPPGGPPPPHS(0.994)PYS(0.006)GPPSR;LADVAAPPGGPPPPHS(0.934)PYS(0.066)GPPS(0.001)R;LADVAAPPGGPPPPHS(1)PYSGPPSR;LADVAAPPGGPPPPHS(0.999)PYS(0.001)GPPSR;LADVAAPPGGPPPPHS(0.996)PYS(0.004)GPPSR 229.7 1.66E-33 5129410000 1778790 2400990 2390450 3311430 2760660 2791020 2712550 2212950 2271310 2665780 TRUE FALSE 1709272.92 2332516.116 2822457.49 3482333.299 2849459.136 2847456.337 2745746.998 2167251.809 2013480.411 2485224.346 0.687774093 0.938553543 1.135695252 1.401214866 1.146560125 1.145754242 1.104828625 0.872054796 0.810180543 1 21.24494466 1.728015076 5.984079577 0.881589142 1.094389833 0.184920308 0.176194204 0.235690097 21.78136871 0.095703549 0.0493199 53.45829162 -1.728015076 0.212800691 ERDYIAPWER ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDYIAPWER 10 1 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 0 153.74 1.43E-05 190520000 150980 216930 170760 209360 208940 210690 188800 163140 146790 179570 FALSE TRUE 145079.5347 210743.3688 201620.1305 220165.0947 215660.7449 214950.2962 191110.5909 159771.102 130127.0146 167407.564 0.866624729 1.258864079 1.20436691 1.315144247 1.288237758 1.283993931 1.141588745 0.954384009 0.777306661 1 17.35300519 1.728131989 2.864249347 0.883263668 1.213809525 0.503159457 0.130432023 0.178242281 3.11971562 0.07721765 0.03525859 53.47268467 -1.728131989 0.330545857 ESPFSTSAS(ph)PLLSGSQHFDVPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESPFSTSASPLLSGSQHFDVPPR 23 0 O14980 O14980 XPO1 Exportin-1 1 ES(0.001)PFS(0.013)T(0.246)S(0.049)AS(0.69)PLLSGSQHFDVPPR;ES(0.003)PFS(0.035)T(0.041)S(0.008)AS(0.911)PLLS(0.002)GSQHFDVPPR 194.11 2.63E-18 1151230000 283200 379550 360330 477200 416190 439940 400310 360500 360470 408830 TRUE FALSE 272132.2309 368725.6056 425449.6465 501828.3492 429577.1293 448835.8882 405209.1135 353055.549 319550.9568 381139.58 0.71399625 0.967429323 1.116256796 1.316652417 1.127086117 1.177615529 1.063151493 0.926315627 0.83840927 1 18.53995991 1.728247369 4.078740627 0.908555479 1.083799544 0.161154108 0.151543462 0.328948267 12.32682568 0.087495336 0.043107953 53.48689282 -1.728247369 0.175244065 DSIKLDDDSER ddPTM_BT-474_Pertuzumab_2h_R1 1 DSIKLDDDSER 11 1 Q86VP6;Q86VP6-2;F5H6I6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 153.75 2.95E-05 1888200000 2135800 1988800 1524900 1419100 1664300 1818400 1773700 2014300 2335500 1952400 FALSE TRUE 2052330.575 1932081.371 1800483.351 1492339.921 1717833.721 1855169.294 1795407.071 1972704.001 2070383.831 1820162.209 1.127553668 1.061488565 0.989188404 0.819893916 0.943780567 1.019232948 0.986399488 1.083806702 1.137472156 1 20.7956356 1.72832539 5.307616692 1.083152863 0.987338207 0.168417707 0.081254134 0.267145541 18.52077449 0.044983989 0.02290685 53.49650251 -1.72832539 -0.095814656 EALLGVQEDVDEYVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EALLGVQEDVDEYVK 15 0 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 200.16 1.64E-08 61004000 45643 49858 39442 41664 48722 51028 43266 61240 60955 63018 FALSE TRUE 43859.2211 48436.09866 46570.04678 43814.28403 50289.18738 52059.82112 43795.50225 59975.3726 54035.64394 58749.73473 0.746543304 0.824447955 0.792685227 0.745778415 0.855990033 0.886128616 0.745458723 1.020862015 0.919759795 1 15.84229472 1.728442008 9.351740698 0.975464789 0.803748511 0.724064631 0.050981228 0.053182508 15.71602956 0.023978144 0.0129094 53.51086957 -1.728442008 -0.171716278 T(ph)TPTQPSEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 TTPTQPSEQK 10 0 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 1 T(0.663)T(0.337)PTQPSEQK;T(0.989)T(0.011)PTQPSEQK;T(0.657)T(0.343)PTQPSEQK 208.03 1.36E-06 1466800000 2781990 2366130 2127080 1957200 1954120 2158250 2334020 2630350 3028240 2821010 TRUE FALSE 2673266.755 2298650.289 2511490.673 2058211.327 2016976.044 2201891.294 2362584.435 2576032.353 2684486.891 2629940.48 1.016474242 0.874031297 0.954961031 0.782607569 0.7669284 0.837239972 0.898341408 0.97950215 1.020740549 1 21.32659872 1.728450787 2.689058673 1.008365713 0.867174956 0.40646756 0.069712261 0.253011705 3.880241838 0.045661281 0.020489466 53.51195117 -1.728450787 -0.141190757 LTS(ph)DEEGEPSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTSDEEGEPSGK 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 LT(0.006)S(0.994)DEEGEPSGK;LT(0.01)S(0.99)DEEGEPSGK 182.03 1.83E-05 390310000 519290 512670 497640 513310 530810 512250 565500 684130 763480 780400 TRUE FALSE 498995.5727 498049.1536 587574.6179 539801.9906 547883.9857 522608.046 572420.7582 670002.4764 676812.9512 727542.8129 0.685864205 0.684563361 0.807615177 0.7419522 0.753060818 0.718319303 0.786786355 0.920911408 0.930272335 1 19.47267262 1.728509407 1.818411819 0.969988836 0.733039575 0.881461885 0.036164617 0.107647332 0.715685222 0.027389419 0.010978371 53.5191746 -1.728509407 -0.236949261 ISINQT(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISINQTPGK 9 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 ISINQT(1)PGK;ISINQT(1)PGK;ISINQT(1)PGK 187.58 0.00045129 372140000 1103560 961730 1074960 1015320 1030540 1033570 1259390 1398140 1469300 1642450 TRUE FALSE 1060431.655 934302.402 1269229.184 1067720.787 1063688.255 1054469.494 1274802.792 1369267.92 1302511.224 1531205.399 0.692546967 0.610174444 0.828908509 0.697307355 0.694673788 0.688653197 0.832548522 0.894241832 0.850644352 1 20.54623639 1.728701 0.855608897 0.972135942 0.694880392 0.725950557 0.059810852 0.295944664 0.413172283 0.053685144 0.023226277 53.54279032 -1.728701 -0.277255549 SGGGGGGGGSSWGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGGGGGGGGSSWGGR 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;;; 172.13 2.43E-06 347992000 225739 249159 212808 255787 229328 244755 245560 229016 239429 269102 FALSE TRUE 216916.8703 242053.2293 251267.1395 268988.1977 236704.5434 249704.1138 248565.2367 224286.7396 212250.0237 250875.4818 0.864639576 0.964834138 1.001561163 1.072198031 0.943514056 0.995330879 0.990791268 0.894016179 0.846037333 1 17.93661196 1.728721454 7.230627456 0.903329688 0.979846968 0.175014291 0.060773107 0.176759092 26.13739273 0.029623072 0.015570158 53.54531212 -1.728721454 0.076517281 DVT(ph)PPPETEVVLIK ddPTM_BT-474_Pertuzumab_2h_R1 8 DVTPPPETEVVLIK 14 0 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(0.96)PPPET(0.04)EVVLIK;DVT(1)PPPETEVVLIK;DVT(0.979)PPPET(0.021)EVVLIK 163.99 3.37E-05 12142037000 1826230 1514960 1649450 1668280 1607070 1621450 1786140 1978270 2323890 2154480 TRUE FALSE 1754858.913 1471754.824 1947542.307 1754380.131 1658762.866 1654236.83 1807999.316 1937418.033 2060091.75 2008555.151 0.873692172 0.732743048 0.969623516 0.873453801 0.825848803 0.823595424 0.900149202 0.96458294 1.025658543 1 20.93772664 1.728742311 2.079498601 1.010930076 0.85032146 0.582258211 0.05616186 0.208720574 1.857594692 0.038437541 0.015973558 53.54788365 -1.728742311 -0.160608616 TGLYNYYDDEKEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TGLYNYYDDEKEK 13 1 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 ;; 179.41 1.26E-05 2270970000 2333840 2109240 1833840 1627770 1985310 2058100 2266880 2752430 3697020 2896820 FALSE TRUE 2242630.953 2049086.54 2165255.682 1711779.405 2049169.299 2099716.192 2294622.756 2695591.359 3277349.789 2700615.801 0.83041466 0.75874789 0.801763687 0.633847808 0.758778534 0.777495337 0.849666493 0.99813952 1.213556474 1 21.36485698 1.728766008 2.045454877 1.108307117 0.757327149 0.801320513 0.069975765 0.117649412 1.01040665 0.046983306 0.019432547 53.55080555 -1.728766008 -0.350979967 VEGQATDEKKEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEGQATDEKKEPK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 ; 151.07 2.51E-05 566070000 764470 550270 426510 326280 452750 499890 495950 640740 764470 578200 FALSE TRUE 734593.6672 534576.8384 503589.8447 343119.3499 467313.1149 509998.1183 502019.5845 627508.4951 677690.5705 539037.999 1.362786424 0.991723848 0.934238116 0.636540189 0.866939095 0.946126468 0.931325037 1.164126641 1.257222259 1 19.04002745 1.728836887 5.691550548 1.157680631 0.937552274 0.184433872 0.177360904 0.231342786 18.98058586 0.093593358 0.048024671 53.55954596 -1.728836887 -0.220128357 EVVEEAENGR ddPTM_BT-474_Pertuzumab_2h_R1 8 EVVEEAENGR 10 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;; 247.5 2.41E-12 41548100000 20319060 21327736 17495680 20528221 19993047 21302350 19528180 20603910 21030290 21227620 FALSE TRUE 19524968.67 20719489.85 20657538.57 21587684.95 20636141.51 21733098.11 19767171.71 20178432.06 18643019.65 19789854.39 0.986615075 1.046975356 1.043844899 1.090846073 1.042763686 1.098193937 0.998853823 1.019635196 0.942049359 1 24.23825766 1.728840276 1.876844487 0.976695726 1.051024444 0.409034718 0.034805586 0.29924621 2.131680306 0.024267938 0.009806164 53.55996392 -1.728840276 0.074328718 WKDSDEADLVLAK ddPTM_BT-474_Pertuzumab_2h_R1 5 WKDSDEADLVLAK 13 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;; 181.26 1.11E-05 16994270000 11415530 10344440 8197650 8919890 9155500 9974200 10472720 11552720 13537750 12929320 FALSE TRUE 10969398.47 10049426.7 9679147.711 9380246.592 9449994.972 10175885.16 10600888.28 11314152.29 12001001.37 12053605.64 0.910051216 0.833727849 0.803008494 0.778210842 0.783997358 0.844219187 0.879478606 0.938652934 0.995635807 1 23.52296143 1.728844212 1.405155676 1.001640493 0.819526651 0.799832699 0.034923836 0.177932382 0.672817323 0.030009667 0.01158326 53.56044941 -1.728844212 -0.182113842 WVEISNEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 WVEISNEVR 9 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 78.264 0.070408 127770000 67975 96241 62125 88180 89590 103810 85853 71579 74610 78900 FALSE TRUE 65318.46185 93496.30091 73352.36946 92730.98037 92471.74371 105909.1093 86903.6947 70100.86864 66140.58559 73556.03272 0.888009582 1.271089501 0.997231182 1.260684908 1.257160566 1.439842599 1.181462505 0.953026775 0.899186418 1 16.16655605 1.728876549 4.799220376 0.942490396 1.197440731 0.349459575 0.145888795 0.182486624 9.956209041 0.076762773 0.038683375 53.56443752 -1.728876549 0.254950335 TVQSNS(ph)PISALAPTGK ddPTM_BT-474_Pertuzumab_2h_R1 4 TVQSNSPISALAPTGK 16 0 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 TVQS(0.003)NS(0.997)PISALAPTGK;TVQSNS(1)PISALAPTGK;TVQS(0.016)NS(0.982)PIS(0.002)ALAPTGK;TVQS(0.002)NS(0.997)PIS(0.001)ALAPTGK 272.21 3.77E-35 535346000 804890 998400 817060 980380 860860 930810 763400 1138370 1070250 886480 TRUE FALSE 773434.0089 969926.6095 964720.9174 1030977.529 888550.3437 949631.6159 772742.7176 1114862.262 948759.7069 826437.92 0.935864619 1.173623071 1.16732412 1.247495431 1.075156793 1.14906588 0.935028148 1.348996984 1.148010859 1 19.65654693 1.728886453 24.99999982 1.198196921 1.110122462 0.034093604 0.124289996 1.925757717 4951.398823 0.055195167 0.030608419 53.56565907 -1.728886453 -0.088074459 YQELPNSGPPHDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 YQELPNSGPPHDRR 14 1 P19525-2;P19525;C9JZT2;F8WBH4 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 53.169 0.097861 167650000 134010 163370 117600 163230 148090 177460 162470 129640 142250 160490 FALSE TRUE 128772.741 158710.8476 138852.936 171654.3199 152853.4493 181048.3628 164458.3565 126962.8887 126102.3764 149619.8694 0.860666044 1.060760501 0.928038078 1.147269548 1.021611969 1.210055613 1.099174576 0.848569707 0.842818383 1 17.19094225 1.729065268 8.852688089 0.886490415 1.051891336 0.305147299 0.102770392 0.117128001 29.94023588 0.049198474 0.02636816 53.58771857 -1.729065268 0.165400921 DVHNIYGLYVHMATADGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVHNIYGLYVHMATADGLR 19 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 174.2 2.86E-12 1183010000 444720 549760 420900 504460 538410 463340 595600 338820 477650 485020 FALSE TRUE 427339.8507 534081.3831 496965.9929 530495.2411 555728.4466 472709.0523 602889.131 331823.2486 423429.1745 452169.1634 0.945088443 1.181153927 1.099070952 1.173222953 1.229027744 1.045425231 1.333326506 0.733847585 0.936439741 1 18.78650308 1.729231214 16.24748955 0.877246955 1.144105514 0.497896607 0.116514428 0.089342812 133.0100707 0.050110994 0.027691939 53.60819858 -1.729231214 0.266858558 KWDLSELPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KWDLSELPK 9 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 110.86 0.0035581 901650000 2029280 1967680 1674300 1588890 1712510 1446360 1813800 2187500 2460300 2352300 FALSE TRUE 1949973.494 1911563.693 1976883.255 1670892.803 1767594.439 1475606.39 1835997.827 2142327.361 2181017.058 2192976.626 0.889190277 0.871675361 0.901461161 0.761929144 0.806025207 0.672878303 0.837217235 0.976903874 0.994546423 1 21.064459 1.729257677 4.040121392 0.993010396 0.815699 0.60906976 0.062802311 0.13861793 5.074604594 0.037041735 0.018242593 53.61146523 -1.729257677 -0.177311395 GRAEGEWEDQEALDYFS(ph)DKESGK ddPTM_BT-474_Pertuzumab_2h_R1 17 GRAEGEWEDQEALDYFSDKESGK 23 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 GRAEGEWEDQEALDYFS(0.999)DKES(0.001)GK;GRAEGEWEDQEALDYFS(0.997)DKES(0.003)GK;GRAEGEWEDQEALDYFS(0.998)DKES(0.002)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDY(0.002)FS(0.989)DKES(0.008)GK;GRAEGEWEDQEALDYFS(0.996)DKES(0.004)GK;GRAEGEWEDQEALDY(0.006)FS(0.98)DKES(0.014)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.998)DKES(0.002)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDY(0.009)FS(0.99)DKES(0.002)GK 246.35 7.27E-38 10528503400 4366128 3328650 2760900 2472806 3228346 3148909 3108953 4012051 4494647 3768320 TRUE FALSE 4195494.891 3233720.161 3259856.046 2600427.814 3332188.681 3212582.097 3147001.297 3929200.745 3984433.516 3513088.33 1.194246912 0.920477898 0.927917473 0.740211338 0.948506945 0.914460952 0.895793388 1.118446329 1.134168328 1 21.74430842 1.729309403 7.676512936 1.092776955 0.926040063 0.279037921 0.109189001 0.139578985 24.236817 0.053290603 0.028185429 53.617851 -1.729309403 -0.166736892 QEKPVNGEDKGDSGVDTQNS(ph)EGNADEEDPLGPNCYYDK ddPTM_BT-474_Pertuzumab_2h_R1 1 QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDK 38 2 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 QEKPVNGEDKGDS(0.007)GVDT(0.072)QNS(0.921)EGNADEEDPLGPNCYYDK 89.677 0.00027771 537100000 247650 186820 160340 150120 174680 168040 164660 243480 253810 227100 TRUE FALSE 237971.5642 181492.0765 189317.0047 157867.7112 180298.7408 171437.8839 166675.1583 238452.0529 224998.5529 211718.3147 1.124000843 0.857233711 0.894192857 0.745649763 0.85159728 0.809745176 0.787249599 1.126270315 1.062725977 1 17.69178655 1.729365325 9.639740298 1.068147268 0.860341869 0.444486616 0.100010557 0.085213235 28.14169524 0.047582454 0.025682744 53.62475546 -1.729365325 -0.207805399 SLIGVEYKPVSATGAEDKDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLIGVEYKPVSATGAEDKDK 20 2 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 147.35 6.92E-08 597050000 525720 418230 347980 265570 343650 405780 376120 477300 561740 422660 FALSE TRUE 505174.2812 406302.4899 410867.7268 279276.0995 354703.8143 413985.1496 380723.0691 467443.5882 497973.6302 394032.8617 1.282061296 1.031138591 1.04272452 0.708763473 0.900188408 1.050636101 0.966221618 1.186306102 1.263787056 1 18.58795643 1.729401822 6.926409502 1.167140524 0.987605727 0.176902014 0.148102625 0.198874236 26.51679127 0.075598878 0.03957841 53.62926213 -1.729401822 -0.179534798 TQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYR 36 1 P11388;P11388-2;P11388-3;P11388-4;J3KTB7 P11388 TOP2A DNA topoisomerase 2-alpha 0 138.8 4.69E-10 24478000 12947 14017 11431 10450 12796 14477 13953 10209 11938 12696 FALSE TRUE 12441.01693 13617.24888 13496.83598 10989.32575 13207.59496 14769.73486 14123.76099 9998.180582 10582.84829 11836.08861 1.051108802 1.150485547 1.140312178 0.928459233 1.115874965 1.247856056 1.193279423 0.844719984 0.894117021 1 13.53090478 1.729468309 9.687117431 0.904849853 1.117832009 0.532197164 0.08800098 0.076938937 25.85331237 0.044189091 0.02386048 53.63747304 -1.729468309 0.212982156 IHYLDTTTLIEPVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 IHYLDTTTLIEPVSR 15 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 0 122.78 0.00010677 907680000 216750 254510 192950 245590 218330 225470 255150 185710 236940 220440 FALSE TRUE 208279.1704 247251.624 227820.3571 258264.9293 225352.7827 230029.1579 258272.602 181875.0236 210043.5645 205509.4025 1.013477573 1.203115872 1.108564155 1.256706147 1.096557043 1.119312086 1.256743482 0.884996119 1.02206304 1 17.64884488 1.729533338 12.83116412 0.966621627 1.151818292 0.532996453 0.07787357 0.063202421 51.74538767 0.033920085 0.018618009 53.64550495 -1.729533338 0.185196664 TVS(ph)PGSVS(ph)PIHGQGQVVENLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 2 T(0.002)VS(0.998)PGS(0.294)VS(0.706)PIHGQGQVVENLK 232.44 8.79E-27 826400000 466200 471640 377710 437400 426290 458930 446830 538810 576060 587030 TRUE FALSE 447980.3886 458189.289 445970.5991 459974.2664 440002.005 468209.879 452298.4392 527683.3852 510668.0838 547269.9352 0.818572993 0.837227225 0.814900601 0.840488828 0.803994476 0.855537366 0.826463158 0.96421044 0.933119199 1 19.06189308 1.729555251 5.099473834 0.96220624 0.828261299 0.903476965 0.020571631 0.043144719 2.718601124 0.009864106 0.005008275 53.6482118 -1.729555251 -0.133944941 MSES(ph)PTPCSGSSFEETEALVNTAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 MSESPTPCSGSSFEETEALVNTAAK 25 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 MS(0.114)ES(0.711)PT(0.174)PCSGSSFEETEALVNTAAK;MS(0.091)ES(0.442)PT(0.442)PCS(0.01)GS(0.013)S(0.002)FEETEALVNTAAK;MS(0.036)ES(0.197)PT(0.197)PCS(0.143)GS(0.143)S(0.143)FEET(0.143)EALVNTAAK 185.06 1.14E-17 235124000 150666 144034 117315 133127 143969 143139 131749 171707 173761 175514 TRUE FALSE 144777.8061 139926.2913 138516.4302 139997.7004 148599.8936 146033.3687 133361.3837 168161.1904 154036.3797 163626.2804 0.884807781 0.855157808 0.846541459 0.855594224 0.908166422 0.892481136 0.815036456 1.027715047 0.94139144 1 17.32004496 1.72958349 10.64390547 0.986987829 0.866613099 0.764284108 0.03160095 0.042413634 19.16261318 0.014487126 0.00787457 53.65170025 -1.72958349 -0.12037473 SYSMIVNNLLKPISVEGSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSMIVNNLLKPISVEGSSK 20 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 189.79 1.88E-17 821420000 665610 673580 618790 630350 715930 741220 720740 803510 979570 974880 FALSE TRUE 639597.2253 654370.1579 730619.1179 662882.439 738958.5386 756207.9762 729560.6317 786917.2377 868373.3203 908850.5093 0.703743046 0.71999757 0.803893611 0.729363556 0.8130694 0.832048801 0.802728968 0.865837923 0.955463315 1 19.79368349 1.729659951 0.322404225 1.026579792 0.696559191 0.877497055 0.032319075 0.455874512 0.15609004 0.051167604 0.05237521 53.66114696 -1.729659951 -0.330020602 EFS(ph)AHK ddPTM_BT-474_Pertuzumab_2h_R1 3 EFSAHK 6 0 Q5SVQ8-2;Q5SVQ8 Q5SVQ8-2 ZBTB41 Zinc finger and BTB domain-containing protein 41 1 EFS(1)AHK;EFS(1)AHK;EFS(1)AHK 63.653 0.071609 958130000 579898 892410 1133980 717738 1060040 887290 1166750 364493 570932 858470 TRUE FALSE 557234.945 866959.3406 1338915.411 754780.5442 1094137.149 905231.6117 1181029.036 356966.0922 506122.1929 800325.0623 0.696260771 1.083259017 1.672964492 0.943092476 1.367115939 1.131079925 1.475686682 0.446026382 0.632395781 1 19.61022656 1.729775341 11.72942746 0.659829402 1.203998388 0.38860393 0.287880044 0.082051879 51.05089549 0.13093054 0.07156929 53.67540629 -1.729775341 0.544168987 SFDFEIETK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFDFEIETK 9 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 158.37 0.00015556 278700000 391020 369560 336790 345940 365950 381720 363490 429630 468780 431680 FALSE TRUE 375738.5061 359020.5106 397655.4449 363794.0049 377721.1141 389438.6399 367938.4994 420757.9904 415566.0597 402441.9291 0.933646519 0.892105133 0.988106398 0.903966457 0.938572964 0.96768903 0.914264824 1.045512309 1.032611241 1 18.6184211 1.729888697 8.164282318 1.028117724 0.934846877 0.680768682 0.028810575 0.059362117 12.25697026 0.013277882 0.007065847 53.68941815 -1.729888697 -0.093270847 KRGHT(ph)ASESDEQQWPEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRGHTASESDEQQWPEEK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 KRGHT(0.333)AS(0.333)ES(0.333)DEQQWPEEK 96.718 0.07343 383230000 211190 170050 97398 109710 86635 151100 120490 190210 186290 187910 TRUE FALSE 202936.4613 165200.3405 114999.9852 115372.1462 89421.69345 154155.3455 121964.5927 186282.097 165143.1402 175182.6883 1.158427601 0.943017498 0.656457475 0.658581892 0.510448232 0.87996906 0.696213729 1.06335905 0.94269098 1 17.41850069 1.730019542 9.748404827 0.999368211 0.775357244 0.245554365 0.172481715 0.14323819 49.73959803 0.087138738 0.047077722 53.7055962 -1.730019542 -0.224010967 QPSKEEEEEEEEEQLNQTLAEMK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPSKEEEEEEEEEQLNQTLAEMK 23 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 69.133 0.022638 53974000 32852 26905 30945 26286 28744 28763 25453 40148 39031 37077 FALSE TRUE 31568.10752 26137.69574 36537.44987 27642.62361 29668.57686 29344.60757 25764.50143 39318.92977 34600.36451 34565.74177 0.913277306 0.756173437 1.057042262 0.79971157 0.858323165 0.84895061 0.745376784 1.137511529 1.001001649 1 15.07705527 1.730062891 13.09471741 1.050485485 0.85604368 0.486222703 0.090402534 0.070585983 63.47744091 0.040094595 0.022024986 53.71095708 -1.730062891 -0.194441805 YHNEMK ddPTM_BT-474_Pertuzumab_2h_R1 1 YHNEMK 6 0 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 86.512 0.053492 94267000 225090 313530 230350 421150 245440 261370 330830 181200 236430 253020 FALSE TRUE 216293.2339 304588.4314 271979.3691 442885.602 253334.8005 266655.0805 334878.7965 177458.1567 209591.4576 235882.73 0.916952394 1.291270587 1.153027901 1.877566882 1.073986215 1.13045614 1.419683401 0.752315172 0.888540918 1 17.84771027 1.730113032 9.88169459 0.870495966 1.273560623 0.334307251 0.249021053 0.106244965 38.57095585 0.11733724 0.063457579 53.71715857 -1.730113032 0.403064657 S(ph)PSPS(ph)PTPEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPSPTPEAK 11 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 S(1)PS(0.402)PS(0.59)PT(0.008)PEAK 100.07 0.00629 176590000 417100 366730 342230 346770 358030 355700 379080 433380 502700 445640 TRUE FALSE 400799.2709 356271.2195 404078.5739 364666.8413 369546.3601 362892.4977 383719.2944 424430.5516 445635.6035 415456.4059 0.964720402 0.857541765 0.972613656 0.877749954 0.889494914 0.873479125 0.923609045 1.021600692 1.072641069 1 18.66433758 1.730137068 3.445147599 1.03955845 0.90439121 0.679517468 0.038876779 0.108220991 2.785452628 0.020534035 0.009827641 53.72013165 -1.730137068 -0.13516724 EGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTR 34 0 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 332.33 1.38E-117 1241980000 173576 248928 187686 367838 192975 196671 283462 144542 238503 179860 FALSE TRUE 166792.458 241828.8172 221605.0353 386822.1633 199182.2161 200647.8224 286931.0927 141557.1572 211429.1393 167677.922 0.994719257 1.442222174 1.321611293 2.306935574 1.187885762 1.196626365 1.711203773 0.844220608 1.260924138 1 17.35533322 1.730167079 13.92743545 1.042004216 1.459168177 0.225607111 0.353351158 0.13942274 152.3738066 0.164204983 0.09039687 53.72384399 -1.730167079 0.417163961 EAYSGCSGPVDSECPPPPSS(ph)PVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.216)S(0.784)PVHK;EAYSGCSGPVDSECPPPPS(0.212)S(0.788)PVHK 174.86 1.53E-12 2249720000 584950 641110 544150 825290 836080 835030 695290 648280 679500 646520 TRUE FALSE 562089.5073 622826.1705 642490.0096 867883.3158 862973.2725 851914.8787 703799.167 634892.7915 602366.0087 602730.6245 0.932571674 1.033340841 1.06596543 1.439919062 1.431772731 1.413425574 1.167684432 1.053360765 0.99939506 1 19.20115384 1.730194608 3.117041547 1.009638731 1.227188975 0.229268754 0.165523693 0.374194031 7.78844158 0.1098486 0.05138075 53.7272495 -1.730194608 0.217550244 HCCGVAQMR ddPTM_BT-474_Pertuzumab_2h_R1 4 HCCGVAQMR 9 0 O00170;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 ;;; 141.52 0.00010652 280700000 162919 193681 173895 258888 280081 219257 227510 127787 143250 150731 FALSE TRUE 156551.9454 188157.4075 205321.6948 272249.2407 289090.0597 223690.5268 230294.3354 125148.1538 126988.8606 140521.8551 1.114075424 1.338990347 1.461137092 1.937415646 2.057260484 1.591855776 1.638850663 0.890595656 0.903694735 1 17.100435 1.730221504 5.887439763 0.924667556 1.608722695 0.579315694 0.256935765 0.113332077 10.12576236 0.145211024 0.074856699 53.73057699 -1.730221504 0.684055139 RQS(ph)PLPPQK ddPTM_BT-474_Pertuzumab_2h_R1 11 RQSPLPPQK 9 1 Q01105;B2REB7 Q01105 SET Protein SET 1 RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK 94.767 0.0025546 14651970000 9350710 9111590 8135220 8253520 8682710 9305080 8798670 9988990 11026680 9929130 TRUE FALSE 8985273.915 8851736.374 9605435.221 8679485.156 8961997.253 9493235.093 8906350.755 9782713.866 9774977.514 9256621.181 0.970686143 0.956259979 1.037682653 0.937651545 0.968171547 1.025561585 0.962160013 1.056834203 1.055998439 1 23.14205425 1.730245837 9.217293579 1.041505004 0.980779313 0.398858145 0.032397434 0.09391681 27.64555897 0.014943204 0.008038125 53.73358748 -1.730245837 -0.060725691 TTDGVYEGVAIGGDRYPGSTFMDHVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTDGVYEGVAIGGDRYPGSTFMDHVLR 27 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 226.03 9.21E-35 533350000 419110 433950 336440 413150 455730 454250 442060 395010 447500 442100 FALSE TRUE 402730.7178 421574.1709 397242.1921 434472.721 470388.9693 463435.2462 447470.0625 386852.9055 396701.6761 412156.1732 0.97713135 1.022850556 0.963814733 1.054145854 1.141288181 1.124416608 1.085680845 0.938607573 0.962503298 1 18.65283158 1.730256231 9.720832285 0.96409725 1.054381142 0.334381766 0.05529219 0.121293342 41.99619049 0.029726241 0.016057051 53.73487347 -1.730256231 0.090283892 LDS(ph)PDPFK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDSPDPFK 8 0 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 LDS(1)PDPFK;LDS(1)PDPFK;LDS(1)PDPFK;LDS(1)PDPFK 85.958 0.017175 650700000 1733310 1382120 1806750 1918610 1925220 1683520 2198660 2616990 2938130 3164090 TRUE FALSE 1665570.329 1342703.291 2133269.916 2017629.692 1987146.45 1717561.928 2225567.859 2562948.242 2604605.8 2949783.366 0.564641576 0.455187085 0.723195452 0.683992498 0.673658436 0.582267141 0.754485188 0.868859819 0.882982062 1 21.49217758 1.730443881 0.561279227 1.014982581 0.575361164 0.781326372 0.073193009 0.368442017 0.258317561 0.07577413 0.045562228 53.75809632 -1.730443881 -0.439621417 SPDKPGGS(ph)PSASR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 SPDKPGGS(0.999)PS(0.001)ASR;SPDKPGGS(0.998)PS(0.002)ASR;SPDKPGGS(0.998)PS(0.002)ASR 138.05 3.25E-05 686480000 844030 843080 668980 802560 770490 790940 785220 899370 962320 940090 TRUE FALSE 811044.3745 819036.1839 789879.5674 843980.2178 795273.5106 806933.3487 794829.7572 880797.6952 853081.468 876416.867 0.925409363 0.934528094 0.901260116 0.962989474 0.907414657 0.920718643 0.90690833 1.004998567 0.973374087 1 19.74125772 1.73059722 8.48691292 0.991008001 0.923269652 0.754995177 0.018252614 0.049740206 11.57115464 0.008321633 0.004445075 53.77708032 -1.73059722 -0.067738348 SDPVDPDKEPEKEDVSASGPS(ph)PEATQLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDPVDPDKEPEKEDVSASGPSPEATQLAK 29 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 SDPVDPDKEPEKEDVSASGPS(1)PEATQLAK 243.84 7.61E-46 237480000 386270 266560 250480 188060 293440 256500 302940 369940 467480 392630 TRUE FALSE 371174.1414 258957.9698 295747.3079 197765.7991 302878.7641 261686.6057 306647.4703 362300.6097 414413.6302 366036.8204 1.014034984 0.707464264 0.80797147 0.540289359 0.827454363 0.714918804 0.837750339 0.989792801 1.13216378 1 18.48162925 1.73078226 2.405231857 1.066334637 0.76059241 0.526301393 0.116182828 0.193355779 2.340967352 0.072048988 0.031345798 53.799998 -1.73078226 -0.305742227 LNKDNDTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNKDNDTLK 9 1 Q9H8Y8;Q9H8Y8-3 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 128.01 0.00039146 398290000 578350 520890 438320 377880 495540 473650 456890 551630 578580 537780 FALSE TRUE 555747.4426 506034.7272 517534.1744 397382.4321 511479.4941 483227.5275 462481.5565 540238.6477 512902.024 501355.6816 1.108489368 1.009332787 1.032269491 0.792615795 1.020192875 0.96384173 0.922461984 1.077555651 1.023030241 1 18.93547495 1.730898129 24.99998647 1.037942262 0.975610094 0.089431546 0.079795595 1.6314117 5290.770056 0.037183243 0.020619919 53.81435368 -1.730898129 -0.062332169 IQTYLQSTKPIIDLYEEMGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQTYLQSTKPIIDLYEEMGK 20 1 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 0 266.14 9.49E-37 279750000 380650 377100 325080 297950 341180 339380 350150 398130 470430 373660 FALSE TRUE 365773.7772 366345.4772 383829.1874 313327.2352 352154.3646 346242.4961 354435.2404 389908.4764 417028.7586 348351.6754 1.05001297 1.051654127 1.101843954 0.899456662 1.010916236 0.993945259 1.01746386 1.119295539 1.197148709 1 18.41018498 1.730996375 5.425600201 1.118649924 1.016470508 0.260390512 0.06644747 0.185478365 13.58077954 0.033484685 0.01713628 53.82652901 -1.730996375 -0.102179416 DLEDKEGEIQAGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLEDKEGEIQAGAK 14 1 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 230.86 6.89E-13 564300000 727390 600880 566100 485150 580630 641340 631090 821190 991690 830400 FALSE TRUE 698962.7946 583743.4907 668406.8628 510188.6496 599306.4913 654308.3342 638813.4682 804232.1395 879117.5087 774156.2684 0.902870419 0.754038318 0.86340044 0.659025407 0.774141495 0.845188964 0.825173798 1.038849871 1.135581464 1 19.56226529 1.731024105 3.057108026 1.076401608 0.795091907 0.737049113 0.069911055 0.106215455 2.119393173 0.039961268 0.018616495 53.82996594 -1.731024105 -0.281309701 VVPEDGS(ph)PEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVPEDGSPEKR 11 1 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 VVPEDGS(1)PEKR;VVPEDGS(1)PEKR;VVPEDGS(1)PEKR;VVPEDGS(1)PEKR 125.84 0.00019596 4318930000 5396600 4887000 3878020 3941050 4738100 4636800 4416780 5355400 5770400 5167900 TRUE FALSE 5185694.906 4747627.545 4578864.48 4144448.063 4890505.29 4730559.273 4470833.875 5244809.119 5115368.383 4817873.53 1.07634517 0.985419712 0.950391174 0.860223507 1.015075481 0.981877013 0.927968293 1.088614943 1.061748166 1 22.19996509 1.731116197 11.6190719 1.055499499 0.968660923 0.287629173 0.056728915 0.103896917 66.31497204 0.027033985 0.014770994 53.84138182 -1.731116197 -0.086838576 HKSETDTSLIR ddPTM_BT-474_Pertuzumab_2h_R1 3 HKSETDTSLIR 11 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;; 234.26 1.03E-15 1621572000 5394314 9335042 6865101 11988144 8893109 8301022 8289951 5994465 4953842 6689139 FALSE TRUE 5183498.245 9068815.742 8105777.464 12606853.55 9179163.928 8468874.352 8391405.9 5870677.203 4391502.624 6236077.657 0.831211305 1.454249969 1.29981984 2.021599833 1.471945096 1.358045043 1.345622419 0.941405403 0.704209098 1 22.57220746 1.73115388 2.729236303 0.837676873 1.43116606 0.419113378 0.279009482 0.22806094 3.592697358 0.173317905 0.078314974 53.84605376 -1.73115388 0.593489187 IHQLEDLEATFADLCDGDDEETVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHQLEDLEATFADLCDGDDEETVQR 25 0 Q49AR2;Q49AR2-2 Q49AR2 C5orf22 UPF0489 protein C5orf22 0 ; 128.58 0.00010991 176325000 168638 265736 187576 350560 240779 249770 247431 200273 197431 226968 FALSE TRUE 162047.4405 258157.4695 221475.1558 368652.4436 248523.8752 254820.5205 250459.1346 196137.2926 175019.4606 211595.2552 0.765836835 1.220053206 1.046692449 1.742252884 1.174524802 1.204282772 1.183670845 0.926945608 0.827142652 1 17.69094775 1.731168338 3.80589209 0.900900674 1.210023761 0.227612922 0.22890795 0.279416255 8.916118764 0.126114924 0.061612802 53.84784632 -1.731168338 0.309123087 RGSLT(ph)LTISGESPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.255)LT(0.745)LTISGESPK 200.67 1.11E-08 1014200000 833330 808070 646870 628890 806400 744430 749480 962230 1009500 1053800 TRUE FALSE 800762.5423 785024.6348 763773.7985 661347.0883 832338.5884 759482.8846 758652.3604 942359.6142 894905.7922 982425.1874 0.815087553 0.799068107 0.77743711 0.673178067 0.84722847 0.773069435 0.772224053 0.959217685 0.910914952 1 19.90598802 1.731300946 5.743867868 0.951075663 0.778282834 0.749281793 0.046832587 0.073969797 6.231852375 0.023442723 0.012068114 53.86429074 -1.731300946 -0.172792828 MKDTDSEEEIREAFR ddPTM_BT-474_Pertuzumab_2h_R1 10 MKDTDSEEEIREAFR 15 2 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;;;;;; 238.83 4.94E-18 14018720000 13052040 13292550 6905017 11117650 12157220 11117520 10913410 12863380 14366110 11959180 FALSE TRUE 12541951.85 12913459.49 8152907.173 11691433.25 12548268.02 11342323.87 11046971.58 12597746.71 12735329.42 11149174.09 1.124922057 1.158243596 0.731256603 1.048636711 1.125488572 1.017324134 0.990833177 1.129926451 1.142266622 1 23.41043351 1.731306606 11.58345043 1.101300511 1.025820142 0.053629969 0.117747167 0.248577032 158.2487055 0.056344869 0.03078139 53.86499275 -1.731306606 -0.075480369 DSLRDESQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSLRDESQR 9 1 Q96MW1;Q86WV7 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 0 84.896 0.013846 417430000 315310 533740 588490 512980 595900 684240 481540 306820 215430 281590 FALSE TRUE 302987.3366 518518.2578 694843.2339 539454.9593 615067.6647 698075.8016 487433.2306 300484.0598 190975.2896 262517.6585 1.154159832 1.975174778 2.646843789 2.054928276 2.342957301 2.659157504 1.856763592 1.144624181 0.727475975 1 18.00205494 1.731318021 2.814342731 0.883758143 2.16404747 0.631519643 0.405698265 0.151481596 2.542853455 0.251213114 0.114517288 53.86640858 -1.731318021 1.280289327 NQKPEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQKPEVR 7 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ; 101.33 0.0083363 2322400000 4843600 4227300 3794700 3387400 4367000 3947100 3850700 4724800 4927700 4379100 FALSE TRUE 4654306.757 4106741.543 4480486.703 3562224.12 4507468.521 4026913.066 3897826.018 4627231.229 4368328.155 4082499.657 1.140062988 1.005938001 1.097486119 0.872559564 1.10409526 0.986384178 0.954764567 1.133430892 1.07001311 1 21.96102133 1.731411206 25 1.078791094 1.021165791 0.056340002 0.080027379 1.600624195 5561.503306 0.035084122 0.019455892 53.8779677 -1.731411206 -0.057625303 IRQPS(ph)VDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR ddPTM_BT-474_Pertuzumab_2h_R1 7 IRQPSVDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR 40 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 IRQPS(0.989)VDLT(0.011)DDDQTSSVPHSAISDIMSSDQETYSCKPHGR;IRQPS(0.779)VDLT(0.219)DDDQT(0.001)SSVPHSAISDIMSSDQETYSCKPHGR;IRQPS(1)VDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR;IRQPS(1)VDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR;IRQPS(0.999)VDLT(0.001)DDDQTSSVPHSAISDIMSSDQETYSCKPHGR;IRQPS(0.934)VDLT(0.066)DDDQTSSVPHSAISDIMSSDQETYSCKPHGR;IRQPS(0.998)VDLT(0.002)DDDQTSSVPHSAISDIMSSDQETYSCKPHGR 333.09 2.29E-130 5918710000 1336347 1408745 921152 1450655 1354143 1375608 1382466 1223439 1390696 1388200 TRUE FALSE 1284121.082 1368568.972 1087624.657 1525523.478 1397700.239 1403423.736 1399385.032 1198174.557 1232830.02 1294175.978 0.992230658 1.057482905 0.840399355 1.178760466 1.079992415 1.084414918 1.081294242 0.925820428 0.952598442 1 20.30360237 1.731451112 10.60357527 0.955484464 1.045551617 0.179741949 0.083475389 0.152819541 72.38506333 0.039731878 0.021594696 53.88291863 -1.731451112 0.090067152 QKVDDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKVDDDR 7 1 Q13618;Q13618-2;Q13618-3;A0A087WTG3 Q13618 CUL3 Cullin-3 0 75.109 0.040458 260480000 377480 323790 310200 319210 337840 372440 332490 433470 455610 442810 FALSE TRUE 362727.6643 314555.8262 366260.0404 335684.4664 348706.9304 379970.992 336559.1121 424518.693 403891.0629 412818.0843 0.878662244 0.761972012 0.887218982 0.813153491 0.844698776 0.920432041 0.81527221 1.028343256 0.978375411 1 18.65514665 1.731510064 8.038089748 1.00061012 0.845856529 0.73129027 0.043359388 0.054967523 11.10490977 0.020146585 0.010711576 53.89023335 -1.731510064 -0.154753591 KLSEIMEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSEIMEK 8 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 112.75 0.0047803 353240000 778260 845240 715050 790320 803860 775570 891960 965940 1145400 1098900 FALSE TRUE 747844.7388 821134.5828 844275.4412 831108.5099 829716.8869 791252.5568 902876.0733 945993.0014 1015378.994 1024470.524 0.729981704 0.801520945 0.82410906 0.811256635 0.809898252 0.772352682 0.881309957 0.923396993 0.99112563 1 19.96644705 1.731633295 1.369254722 0.999863772 0.793774523 0.894361172 0.028174876 0.121539559 0.434428697 0.022794529 0.00880898 53.90552679 -1.731633295 -0.206089249 RLS(ph)NLPTVDPIAVCHELYNTIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSNLPTVDPIAVCHELYNTIR 22 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;Q86U86-6;C9JQF1;C9JPI5;C9JCJ2;C9J053 Q86U86-8 PBRM1 Protein polybromo-1 1 RLS(1)NLPTVDPIAVCHELYNTIR;RLS(1)NLPTVDPIAVCHELYNTIR 217.57 5.88E-26 2387300000 509410 489580 347920 479510 544320 395000 412290 404210 325240 351070 TRUE FALSE 489501.694 475617.6577 410796.8834 504257.5686 561828.5471 402987.1706 417335.7283 395862.9222 288320.1187 327291.7162 1.495612843 1.45319186 1.255139874 1.540697621 1.716598738 1.231278247 1.275118519 1.209510973 0.880927028 1 18.32021756 1.731656197 1.135564528 0.947558218 1.465675738 0.685113496 0.134447159 0.282745869 0.681939244 0.117767426 0.046214199 53.90836961 -1.731656197 0.51811752 VVPQQITHT(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 5 VVPQQITHTSPR 12 0 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 VVPQQIT(0.017)HT(0.491)S(0.491)PR;VVPQQIT(0.002)HT(0.787)S(0.211)PR;VVPQQITHT(0.787)S(0.213)PR;VVPQQITHT(0.62)S(0.379)PR;VVPQQITHT(0.516)S(0.484)PR 151.38 0.00024483 3056900000 1571420 1705709 1367463 1577687 1621780 1674590 1555800 1477031 1502194 1547516 TRUE FALSE 1510007.169 1657063.849 1614593.983 1659111.615 1673946.027 1708451.357 1574840.346 1446529.794 1331671.235 1442701.363 1.046652625 1.148584102 1.119146363 1.150003499 1.160285884 1.184203052 1.091591362 1.002653654 0.923040117 1 20.46034126 1.731847509 2.649559095 0.962069758 1.136386568 0.771668304 0.039007031 0.107256188 1.587113149 0.023645356 0.010600616 53.93212215 -1.731847509 0.17431681 DNVKNEDKDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DNVKNEDKDQK 11 2 Q8IX12-2;Q8IX12 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 159.64 1.60E-05 662740000 2152230 1671420 1256070 929320 1444450 1639710 1532870 1981390 2392950 1860240 FALSE TRUE 2068118.472 1623752.738 1483069.79 977282.3166 1490912.046 1672866.06 1551629.722 1940473.604 2121312.348 1734244.288 1.192518543 0.936288359 0.855167753 0.563520562 0.859689754 0.964608084 0.894700783 1.118915955 1.223191198 1 20.7258757 1.731961863 4.140163491 1.132105168 0.882268744 0.295974499 0.153178101 0.229004263 8.816713295 0.08660717 0.042942181 53.94632482 -1.731961863 -0.249836425 PTVEELYR ddPTM_BT-474_Pertuzumab_2h_R1 1 PTVEELYR 8 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-3;E9PQK6 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 110.67 0.012402 0 70065 73180 53718 59343 67829 60468 61346 73579 77683 70766 FALSE TRUE 67326.78234 71092.97805 63426.03755 62405.69934 70010.78139 61690.70439 62096.7707 72059.56794 68864.75151 65972.95579 1.020520932 1.077607896 0.961394511 0.945928504 1.061204255 0.935090806 0.941245848 1.0922592 1.043833048 1 16.00958712 1.732063308 24.99999915 1.051736911 0.992699916 0.183485921 0.051177515 1.01571975 3881.297517 0.024160993 0.013398434 53.95892734 -1.732063308 -0.059036995 DGVIEASINHEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DGVIEASINHEK 12 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 135.02 0.00013516 3846710000 8069000 9632400 10151500 7494300 9767000 9989100 10100700 7744300 8616500 9935500 FALSE TRUE 7753654.559 9357693.383 11986101.87 7881081.721 10081164.43 10191086.45 10224315.39 7584377.499 7638391.043 9262559.735 0.837096308 1.010270773 1.29403774 0.850853538 1.088377804 1.100245152 1.103832599 0.8188209 0.824652284 1 23.14297951 1.732167954 9.766895724 0.868612127 1.046036227 0.231913882 0.132056522 0.126068187 46.40730639 0.061512134 0.033247512 53.97193067 -1.732167954 0.1774241 DLGHAQMVVDELFSSHSDLDSDSELDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLGHAQMVVDELFSSHSDLDSDSELDR 27 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 0 139.4 1.36E-07 75185000 6199.6 7951 6685.4 7562.3 6637 8524.4 8366.9 5543.2 7599.5 6465.3 FALSE TRUE 5957.312778 7724.245265 7893.600496 7952.591209 6850.485133 8696.769209 8469.296625 5428.730983 6736.83662 6027.399472 0.988371985 1.28152204 1.309619602 1.319406694 1.136557344 1.442872544 1.405132788 0.900675492 1.117702029 1 12.55731997 1.732178203 12.39235177 1.009223768 1.274608309 0.455292477 0.131653961 0.074130554 62.26635388 0.061254166 0.033573958 53.9732044 -1.732178203 0.265384542 KLDDDSDSPSFFEEKPEEPVVLALDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDDDSDSPSFFEEKPEEPVVLALDPK 27 2 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 169.91 3.29E-12 208867000 187331 144613 132715 105066 141251 134520 148461 196526 237398 196486 FALSE TRUE 180009.8974 140488.7788 156699.5527 110488.4689 145794.4667 137240.0866 150277.9101 192467.6694 210449.5743 183177.8282 0.982705708 0.766952967 0.855450434 0.603175995 0.795917651 0.749217784 0.820393557 1.050714878 1.148881261 1 17.48288537 1.732217369 3.57296855 1.082945678 0.785471685 0.630438571 0.094970951 0.122839929 3.405673884 0.051831529 0.025048 53.97807214 -1.732217369 -0.297473994 TGS(ph)ESSQTGTSTTSSR ddPTM_BT-474_Pertuzumab_2h_R1 6 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 T(0.009)GS(0.975)ES(0.016)SQTGTSTTSSR;T(0.001)GS(0.998)ES(0.002)SQTGTSTTSSR;T(0.01)GS(0.989)ES(0.001)SQTGTSTTSSR;T(0.021)GS(0.975)ES(0.001)S(0.001)QT(0.002)GTSTTSSR;T(0.018)GS(0.982)ESSQTGTSTTSSR;TGS(0.685)ES(0.31)S(0.005)QTGTSTTSSR 387.22 2.59E-121 2264835000 678437.8 613330.5 555195.6 591763.7 609150.4 625012.8 646165.3 682567 811000.3 726839.9 TRUE FALSE 651923.7007 595838.9147 655531.7952 622304.6955 628744.2758 637650.987 654073.2642 668471.7529 718938.9459 677610.3862 0.96209225 0.879323763 0.967416983 0.918381282 0.92788465 0.941028945 0.96526452 0.98651344 1.060991627 1 19.37009646 1.732255363 1.612621709 1.028707899 0.930809044 0.651606921 0.027819129 0.199821724 1.019479939 0.01963021 0.007704264 53.98279458 -1.732255363 -0.097898856 EQGIHSLEVLITR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQGIHSLEVLITR 13 0 Q9H078-5;Q9H078-3;Q9H078-2;A0A2R8Y602;A0A2R8YDH5;F5H7A5 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 ; 216.54 2.73E-11 198312000 215423 259770 218302 287130 210606 248600 239570 230555 235990 243690 FALSE TRUE 207004.031 252361.6139 257754.0275 301948.8137 217380.3333 253626.8623 242501.9293 225793.9587 209201.4046 227184.6592 0.911170814 1.110821544 1.134557361 1.329089802 0.956844243 1.116390795 1.067422114 0.993878545 0.920843006 1 17.79350589 1.732266899 2.349951564 0.958606459 1.100401076 0.20787353 0.106640729 0.407159639 4.686372582 0.069567443 0.030096291 53.98422843 -1.732266899 0.141794617 GGQS(ph)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGQSDDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR 37 0 A0A669KBG8;A0A669KB10;Q92538 A0A669KBG8 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR 122.48 1.03E-08 145225000 4627.1 3648.8 2088.9 4437.6 6078.4 5476.9 5836.4 1488.2 4075.8 2445.9 TRUE FALSE 4446.267816 3544.739797 2466.410697 4666.625068 6273.917256 5587.646671 5907.827609 1457.46815 3613.132271 2280.237014 1.949914763 1.554548836 1.081646637 2.046552634 2.751432073 2.450467489 2.590883128 0.639173972 1.584542417 1 11.15496807 1.732270711 14.34610009 1.08925141 2.044620536 0.440054481 0.509445411 0.090955029 127.9209139 0.263247497 0.145054279 53.98470231 -1.732270711 0.955369126 T(ph)PQAPASANLVGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPQAPASANLVGPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(1)PQAPASANLVGPR 91.1 0.061367 172970000 71440 88271 86284 84762 78085 103930 92594 52236 72401 49698 TRUE FALSE 68648.04582 85753.59751 101877.4382 89136.57698 80596.67494 106031.5358 93727.19307 51157.30835 64182.34201 46331.91019 1.481658009 1.850853918 2.198861168 1.923870106 1.739550012 2.288520706 2.022951195 1.104148483 1.385272952 1 15.49971854 1.732574647 6.990025341 1.190526658 1.943293678 0.694167293 0.232382147 0.072608747 10.13253822 0.115591153 0.060688888 54.02249608 -1.732574647 0.75276702 (ac)ADDIDIEAMLEAPYKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADDIDIEAMLEAPYKK 16 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;F8WF24;F2Z2Z5;A8MYG5;F2Z3E6;F8WF73;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 ; 66.289 0.0006901 42099000 89412 91534 76629 78198 84532 88334 84594 100472 107188 104457 FALSE TRUE 85917.68019 88923.53994 90477.5649 82233.80815 87251.04855 90120.174 85629.28668 98397.21809 95020.46761 97382.03435 0.882274444 0.91314112 0.929099146 0.844445371 0.895966583 0.925429157 0.879312979 1.010424754 0.975749462 1 16.57136802 1.732643929 7.947340057 0.99363742 0.89681934 0.773671475 0.024672917 0.052570397 10.42823321 0.0119306 0.006339498 54.03111489 -1.732643929 -0.09681808 S(ph)RWSGSHQFEQLSGSILWMAPEVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRWSGSHQFEQLSGSILWMAPEVIR 25 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.571)RWS(0.355)GS(0.074)HQFEQLSGSILWMAPEVIR;S(0.329)RWS(0.329)GS(0.329)HQFEQLS(0.012)GSILWMAPEVIR 167.65 7.47E-12 402410000 282837 276166 244204 238388 278769 266800 283190 256493 309169 274332 TRUE FALSE 271783.4173 268290.0161 288337.0951 250691.2332 287735.8581 272194.8788 286655.7639 251196.3299 274073.4313 255751.2493 1.062686568 1.049027197 1.127412264 0.980215088 1.125061398 1.064295402 1.120838177 0.982190041 1.071640635 1 17.96438176 1.732753934 24.99999993 1.019512456 1.074408666 0.242567506 0.04666708 0.841909445 3597.095763 0.020011166 0.011097209 54.04480253 -1.732753934 0.054896209 SQSSSLLDMGNMSAS(ph)DLDVADR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSSSLLDMGNMSASDLDVADR 22 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 SQSSSLLDMGNMS(0.242)AS(0.757)DLDVADR 60.541 0.035041 26364000 26438 27048 24403 26785 27331 28043 26925 26036 28825 26382 TRUE FALSE 25404.77373 26276.61752 28813.16494 28167.37706 28210.12644 28610.04867 27254.5162 25498.3475 25552.90684 24595.12364 1.032919131 1.068366962 1.171499089 1.145242344 1.146980468 1.163240693 1.108126822 1.036723697 1.038941996 1 14.58608469 1.732855842 3.158279102 1.024110867 1.124383133 0.525892357 0.041250333 0.190888831 4.063845214 0.025834499 0.012155343 54.05748569 -1.732855842 0.100272266 DHSVAESLNYVASWNMSMLQTQDLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHSVAESLNYVASWNMSMLQTQDLVK 26 0 Q13011 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ; 311.4 9.23E-82 598450000 270440 334910 235100 468660 257740 327300 427600 195129 394690 318680 FALSE TRUE 259870.9058 325358.6947 277587.7998 492847.5988 266030.4412 333918.2303 432833.0967 191099.518 349886.4459 297095.5197 0.874704896 1.095131609 0.934338559 1.658886001 0.895437405 1.123942328 1.456881938 0.643225849 1.177690078 1 18.18056732 1.732969932 25 0.915596346 1.147147914 0.113854957 0.263425379 1.138221718 5049.601515 0.117024943 0.064896322 54.07168855 -1.732969932 0.231551568 KKDELS(ph)DYAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKDELSDYAEK 11 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 1 KKDELS(1)DYAEK;KKDELS(1)DYAEK 130.29 0.00083215 959200000 1663590 1419120 1332190 1051410 1468810 1428660 1463310 1837400 2263250 1761120 TRUE FALSE 1598575.064 1378648.087 1572946.367 1105673.396 1516055.608 1457548.484 1481218.426 1799457.048 2006335.348 1641837.774 0.973649827 0.839698117 0.958040065 0.673436447 0.923389407 0.887754264 0.902171 1.096001735 1.22200584 1 20.64688015 1.73309765 3.464385386 1.126242014 0.872682003 0.554910106 0.092898153 0.140295422 3.632379143 0.049742021 0.023907532 54.08759242 -1.73309765 -0.253560011 KVEEVLEEEEEEYVVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVEEVLEEEEEEYVVEK 17 1 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ; 239.93 4.26E-20 502530000 592062 572803 446462 546124 531828 589870 626996 666167 876509 787030 FALSE TRUE 568923.5625 556467.2193 527147.6149 574309.5251 548934.7306 601797.5756 634669.3646 652410.4187 777011.3729 733723.7571 0.775392042 0.758415158 0.718455154 0.782732629 0.748149048 0.820196388 0.864997703 0.889177176 1.058997157 1 19.48487747 1.733215819 1.014243406 1.029410995 0.75580383 0.900333682 0.033749988 0.1397408 0.268724717 0.028361773 0.011454879 54.10231127 -1.733215819 -0.273607164 LTEQHFIELDENR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTEQHFIELDENR 13 0 Q8IY18 Q8IY18 SMC5 Structural maintenance of chromosomes protein 5 0 124.45 0.00021168 103470000 74494 103890 68772 106370 100120 83098 100240 76946 79958 114240 FALSE TRUE 71582.69212 100927.1589 81200.63022 111859.7684 103340.4507 84778.29849 101466.7671 75357.03821 70881.50305 106502.423 0.672122662 0.947651293 0.762429886 1.050302568 0.970310795 0.796022251 0.952717921 0.707561725 0.665538877 1 16.70052673 1.733253714 15.4405786 0.765416055 0.883897448 0.072395916 0.134029356 0.166803789 326.6006375 0.059269771 0.032719935 54.10703233 -1.733253714 0.118481394 S(ph)KSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_BT-474_Pertuzumab_2h_R1 18 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.498)KS(0.498)PLPPEEEAKDEEEDQT(0.001)LVNLDT(0.001)Y(0.001)T(0.001)S(0.001)DLHFQVSK;S(0.575)KS(0.425)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.498)KS(0.498)PLPPEEEAKDEEEDQT(0.003)LVNLDTYTSDLHFQVSK;S(0.548)KS(0.452)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.522)KS(0.471)PLPPEEEAKDEEEDQT(0.006)LVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.435)KS(0.435)PLPPEEEAKDEEEDQT(0.13)LVNLDTYTSDLHFQVSK;S(0.496)KS(0.496)PLPPEEEAKDEEEDQT(0.007)LVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQT(0.001)LVNLDTYTSDLHFQVSK;S(0.493)KS(0.493)PLPPEEEAKDEEEDQT(0.013)LVNLDTYTSDLHFQVSK;S(0.496)KS(0.496)PLPPEEEAKDEEEDQT(0.009)LVNLDTYTSDLHFQVSK 207.62 9.37E-31 50043732000 854360.9 643700.1 592081.4 524119.7 645372.5 618197.2 681648.5 791196.3 988627.3 765369.9 TRUE FALSE 820971.5315 625342.4034 699083.6798 551169.5805 666131.4926 630697.5709 689990.7182 774857.8199 876402.4736 713530.715 1.150576302 0.876405725 0.979752749 0.772453896 0.933570873 0.883910892 0.967009133 1.085948795 1.228261735 1 19.44461601 1.733259827 3.121089339 1.125091513 0.925638073 0.3525841 0.104015318 0.215363602 4.469035151 0.057674503 0.027068654 54.1077939 -1.733259827 -0.19945344 RKHDNEGSGSK ddPTM_BT-474_Pertuzumab_2h_R1 3 RKHDNEGSGSK 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 189.33 1.55E-06 153991000 155681 142565 98281 122050 123438 139473 134418 116758.1 119500 146916 FALSE TRUE 149596.8144 138499.1858 116042.5629 128349.0151 127408.4954 142293.2396 136063.0477 114347.0044 105934.861 136965.2485 1.092224605 1.011199464 0.847240919 0.937091829 0.930224979 1.038900314 0.993412922 0.834861439 0.773443353 1 17.06345037 1.733294483 7.901108103 0.854598145 0.973667021 0.26318951 0.082169561 0.145117406 28.52294425 0.040267102 0.021391055 54.11211177 -1.733294483 0.119068876 NGQLDLSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NGQLDLSGK 9 0 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 65.224 0.067163 469500000 541170 894960 617820 1038900 684620 725230 718910 582120 454780 617180 FALSE TRUE 520020.4781 869436.6171 729473.8173 1092517.754 706641.4241 739894.6475 727708.2356 570099.0186 403155.281 575377.8489 0.903789534 1.511070714 1.267816998 1.898783131 1.228134565 1.28592828 1.264748438 0.990825454 0.700679183 1 19.13415016 1.733402481 1.973250071 0.841602796 1.37313723 0.409862303 0.24565453 0.284262687 2.251731541 0.168304701 0.069211622 54.12556981 -1.733402481 0.531534434 AEIIHHLADLLTDQRDEILLANK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEIIHHLADLLTDQRDEILLANK 23 1 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 82.586 0.0055127 36499000 50166 72568 49132 91763 46560 55908 85535 29245 71615 52110 FALSE TRUE 48205.45726 70498.43169 58011.24534 96498.89943 48057.64468 57038.49807 86581.80292 28641.08053 63485.56543 48580.54329 0.99227909 1.45116598 1.194125084 1.986369293 0.98923646 1.174101692 1.782232084 0.589558671 1.306810528 1 15.568091 1.733594482 24.99999996 0.946419333 1.365524617 0.223428632 0.342557387 0.745342458 3718.910396 0.15049391 0.083456465 54.14950384 -1.733594482 0.419105284 FYYNVESCGSLRPETIVLSALSGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYYNVESCGSLRPETIVLSALSGLK 25 1 P19387 P19387 POLR2C DNA-directed RNA polymerase II subunit RPB3 0 129.78 8.90E-05 61162000 25230 21677 22752 14039 21294 23533 20654 25943 25123 28574 FALSE TRUE 24243.98371 21058.79318 26863.79252 14763.55447 21978.94085 24008.85338 20906.76983 25407.26798 22271.14236 26638.65753 0.910105311 0.790535077 1.008451439 0.554215409 0.825076895 0.901278653 0.784828207 0.953774339 0.836045973 1 14.70123376 1.733612734 11.10153354 0.920114392 0.82320649 0.142429165 0.117244215 0.182213859 108.8294795 0.053599344 0.02921774 54.15177963 -1.733612734 -0.096907902 AQGPLAMLQHFDTIYSILHHFR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQGPLAMLQHFDTIYSILHHFR 22 0 Q15021;F5GZK7 Q15021 NCAPD2 Condensin complex subunit 1 0 ; 129.02 5.48E-06 122604000 45770 54124 53273 62508 60179 40433 63105 34523 47834 50241 FALSE TRUE 43981.2578 52580.43651 62900.61615 65734.04537 62114.71219 41250.58296 63877.29787 33810.08799 42404.08486 46838.13232 0.939005371 1.122598915 1.342936045 1.403430114 1.326156896 0.88070512 1.363788322 0.721849619 0.90533253 1 15.51539593 1.733675974 12.86394379 0.86287902 1.200427833 0.402084699 0.179225395 0.077210452 80.78180991 0.085153225 0.046748517 54.15966553 -1.733675974 0.337548813 DAEPRPPHGELQYLGQIQHILR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAEPRPPHGELQYLGQIQHILR 22 1 P04818;P04818-2;P04818-3 P04818 TYMS Thymidylate synthase 0 ; 171.06 4.16E-12 112436000 33694 32413 27725 34527 33506 33609 35354 27471 29409 37044 FALSE TRUE 32377.20123 31488.61298 32735.52424 36308.94261 34583.75092 34288.59701 35786.67283 26903.71425 26070.61361 34534.97688 0.937519123 0.911789027 0.947894778 1.051367219 1.001412308 0.992865787 1.036244297 0.779028008 0.75490462 1 15.07577064 1.733772591 10.37429532 0.82712711 0.982382388 0.420648152 0.073344197 0.075991084 35.74759971 0.034197313 0.018564929 54.1717158 -1.733772591 0.155255278 GGSAAATSNPHHDNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSAAATSNPHHDNVR 16 0 Q9GZY8-5;Q9GZY8-2;Q9GZY8 Q9GZY8-5 MFF Mitochondrial fission factor 0 79.81 0.010012 24817000 7935.1 15547 10117 21725 10860 17543 19529 6258.1 13651 13189 FALSE TRUE 7624.987519 15103.61478 11945.36695 22846.22985 11209.32176 17897.73148 19768.00174 6128.868048 12101.39571 12295.69728 0.620134617 1.228365861 0.971507892 1.85806704 0.911645879 1.455609313 1.607717016 0.498456322 0.984197596 1 13.58586593 1.733808223 24.99999998 0.799896879 1.245553242 0.211867373 0.359634918 0.727026804 3789.167156 0.161059979 0.089315918 54.17616049 -1.733808223 0.445656363 MSMTGAGKS(ph)PPSVQSLAMR ddPTM_BT-474_Pertuzumab_2h_R1 2 MSMTGAGKSPPSVQSLAMR 19 1 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7;Q96KQ7-3 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 MSMT(0.001)GAGKS(0.996)PPS(0.003)VQSLAMR;MSMT(0.001)GAGKS(0.993)PPS(0.004)VQS(0.001)LAMR 94.276 0.00098253 1481560000 1177090 1231840 675560 864440 1160190 1019080 997530 1170910 1273460 1154420 TRUE FALSE 1131088.021 1196709.129 797648.7198 909053.852 1197508.565 1039686.496 1009738.071 1146730.299 1128902.16 1076230.105 1.050972293 1.111945414 0.741150722 0.844664954 1.112688225 0.966044799 0.938217641 1.065506618 1.048941257 1 20.03755514 1.733944324 10.26468495 1.04195612 0.964379995 0.082682784 0.108857287 0.243473977 110.8449918 0.054366491 0.029494393 54.19314106 -1.733944324 -0.077576125 YADSPGAS(ph)SPEQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 YADSPGASSPEQPK 14 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 YADSPGAS(0.656)S(0.344)PEQPK 294 1.54E-43 367770000 459100 423600 348490 373390 400710 391980 397240 456120 506980 446520 TRUE FALSE 441157.8644 411519.3427 411469.8951 392660.7026 413599.2011 399906.1042 402101.5419 446700.9626 449429.7558 416276.8027 1.059770474 0.988571403 0.988452617 0.943268278 0.993567738 0.960673527 0.965947512 1.073086369 1.079641606 1 18.66718364 1.733974611 8.967903071 1.056306461 0.983677746 0.413827426 0.035256896 0.088719653 25.75468037 0.016654793 0.008946178 54.19692054 -1.733974611 -0.072628716 VT(ph)SPEKAEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTSPEKAEEAK 11 1 P56211;H3BMD8;P56211-2;H3BTD3 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 VT(0.897)S(0.103)PEKAEEAK 107.99 0.0070205 0 224430 180740 213010 176210 174000 188070 213000 227800 257790 258650 TRUE FALSE 215659.0275 175585.4722 251505.6454 185304.2192 179596.868 191872.9043 215606.7577 223095.8504 228526.7599 241131.4051 0.894363085 0.728173388 1.043023182 0.768478163 0.744809113 0.795719264 0.894146317 0.925204456 0.94772707 1 17.87946004 1.734028336 1.737717714 0.971252298 0.828877819 0.311190751 0.08646624 0.42808223 2.570716731 0.063645536 0.025371987 54.20362555 -1.734028336 -0.142374478 AGLAS(ph)PEEEDAVGKEPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGLASPEEEDAVGKEPLK 18 1 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 AGLAS(1)PEEEDAVGKEPLK 120.64 2.42E-05 276800000 388730 349780 301580 290140 326620 341910 365480 391490 470430 438650 TRUE FALSE 373538.0018 339804.6169 356082.2146 305114.1602 337126.0289 348823.6545 369952.8536 383405.5947 417028.7586 408939.8448 0.913430194 0.830940348 0.87074473 0.746110129 0.82439027 0.852995028 0.904663261 0.937559887 1.019780205 1 18.64152911 1.734149552 1.349124608 1.010305589 0.834592323 0.725777122 0.041301672 0.215060881 0.744356736 0.034030775 0.013171687 54.21875642 -1.734149552 -0.175713266 S(ph)CPELTSGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCPELTSGPR 10 0 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(1)CPELTSGPR 147.19 2.87E-05 388330000 81347 78715 60512 79129 71408 65998 61300 97104 90418 81866 TRUE FALSE 78167.86931 76470.12527 71447.86448 83212.85717 73704.90317 67332.52478 62050.20774 95098.76847 80154.1277 76321.1429 1.024196787 1.001952046 0.936147727 1.090298887 0.965720643 0.882226369 0.813014656 1.246034386 1.050221795 1 16.21979516 1.734152422 25 1.116445905 0.962191488 0.31746255 0.092690035 0.532522609 2989.949506 0.04312717 0.023916248 54.21911475 -1.734152422 -0.154254417 EAIESAIGGNAYQHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAIESAIGGNAYQHSK 16 0 P63172 P63172 DYNLT1 Dynein light chain Tctex-type 1 0 115.73 0.000483 304390000 55399 81724 77324 102420 90482 112260 94874 61344 62760 88494 FALSE TRUE 53233.94583 79393.31154 91298.16686 107705.9085 93392.4357 114529.9741 96035.09639 60077.22496 55635.74791 82500.22256 0.645258209 0.962340574 1.106641461 1.305522641 1.13202647 1.388238365 1.164058634 0.728206823 0.674370883 1 16.33211039 1.734160362 7.707475997 0.779994978 1.115660214 0.305515875 0.205117591 0.137155589 25.34365536 0.104914339 0.055631531 54.22010595 -1.734160362 0.335665237 (ac)ASCAS(ph)IDIEDATQHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASCASIDIEDATQHLR 16 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 AS(0.002)CAS(0.998)IDIEDATQHLR;AS(0.002)CAS(0.998)IDIEDATQHLR 96.414 2.50E-12 255270000 111181 89683 95229 82476 97308 102012 92515 116995 119628 118132 TRUE FALSE 106835.9236 87125.32865 112438.9987 86732.59624 100438.0002 104074.7525 93647.22624 114579.0124 106048.331 110130.8144 0.970082026 0.79110764 1.020958569 0.787541586 0.911988173 0.945010287 0.850327193 1.04039013 0.962930598 1 16.74885866 1.734276445 12.01959562 1.000259788 0.89568838 0.306894387 0.071855916 0.091443782 75.69996401 0.030761768 0.016838734 54.23460051 -1.734276445 -0.104571408 S(ph)GSFDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSFDSR 7 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.5)GS(0.5)FDS(0.001)R 71.692 0.056253 109940000 231310 216830 195850 211800 227910 223690 217630 264680 285410 269480 TRUE FALSE 222270.1495 210646.2207 231244.4517 222731.0234 235240.9321 228213.1651 220293.421 259214.2655 253011.4533 251227.8796 0.884735205 0.838466738 0.920456965 0.88656969 0.936364756 0.908391081 0.876866936 1.031789409 1.007099426 1 17.93863705 1.73445958 7.65723657 1.013208224 0.894062397 0.814104547 0.02620205 0.048953649 8.904107047 0.013209085 0.007001163 54.25747508 -1.73445958 -0.119145827 YEDHTIFHDISLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YEDHTIFHDISLR 13 0 P82675 P82675 MRPS5 "28S ribosomal protein S5, mitochondrial" 0 ; 127.71 0.00010045 280790000 57369 97314 61902 130402 65187 75230 129034 15895.5 95800 64870 FALSE TRUE 55126.95606 94538.7 73089.0684 137132.0628 67283.79906 76751.20214 130613.1567 15567.25237 84925.18563 60476.29712 0.911546485 1.56323559 1.208557268 2.267534049 1.112564794 1.269112128 2.159741302 0.257410806 1.404272247 1 15.88408219 1.734518895 25 0.845057792 1.496079673 0.249665386 0.484262531 0.579066437 3542.714887 0.211166866 0.11710268 54.26488604 -1.734518895 0.65102188 DYKDEQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYKDEQGR 8 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6;C9JQF1;C9JPI5;C9JCJ2;C9J053 Q86U86-8 PBRM1 Protein polybromo-1 0 76.1 0.033449 382310000 299390 255870 221850 222760 243740 257110 238190 287530 302950 270460 FALSE TRUE 287689.5078 248572.8381 261943.23 234256.6703 251580.1185 262308.9404 241105.0405 281592.405 268560.3861 252141.5033 1.140984344 0.985846578 1.038873912 0.92906827 0.997773533 1.04032433 0.956229091 1.11680307 1.065117732 1 17.94387408 1.734595033 25 1.069913704 1.00996828 0.110781407 0.060162329 0.782459283 4877.884063 0.026655603 0.014781845 54.2744003 -1.734595033 -0.059945425 KVELSES(ph)EEDKGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.154)ES(0.846)EEDKGGK 169.25 1.75E-06 329560000 388540 306100 269120 205360 281740 277660 315880 376430 467020 401020 TRUE FALSE 373355.4272 297370.3277 317755.9705 215958.6542 290802.423 283274.4754 319745.8339 368656.589 414005.8475 373858.5582 0.998654221 0.795408641 0.849936329 0.577648015 0.777840754 0.757704937 0.855258832 0.986085729 1.107386305 1 18.51213303 1.734679558 2.341142421 1.053524374 0.785927492 0.533273746 0.100413391 0.206442752 2.351205742 0.066274349 0.028706487 54.28496448 -1.734679558 -0.267596881 EQVYDAMGEKEEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 EQVYDAMGEKEEAK 14 1 P49321;P49321-3;P49321-4;E9PPR5;E9PNB5 P49321 NASP Nuclear autoantigenic sperm protein 0 ;; 176.33 2.04E-06 2402480000 2055950 1758400 1439490 1448310 1707620 1659520 1715250 2145060 2449100 2164610 FALSE TRUE 1975601.201 1708252.154 1699637.864 1523057.453 1762547.148 1693076.631 1736241.743 2100763.761 2171088.435 2017999.037 0.978990161 0.846507913 0.842239185 0.754736462 0.873413275 0.838987829 0.860377885 1.041013263 1.075861978 1 20.94449406 1.734865595 4.55138245 1.045741442 0.85071756 0.702549875 0.05429104 0.09310144 4.444616978 0.028558135 0.014395469 54.30822335 -1.734865595 -0.195023883 ETCSTLAES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 ETCSTLAESPR 11 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 ETCSTLAES(1)PR;ETCSTLAES(1)PR;ETCSTLAES(1)PR;ETCSTLAES(1)PR 243.26 8.63E-16 3288510000 1193450 1311440 1164310 1410820 1329840 1383490 1316470 1168080 1168850 1359120 TRUE FALSE 1146808.655 1274039.015 1374726.717 1483632.589 1372615.511 1411465.116 1332581.354 1143958.74 1036167.048 1267065.592 0.905090204 1.005503601 1.084968865 1.170920116 1.083302648 1.113963732 1.051706685 0.902840979 0.817769068 1 20.27305978 1.734936842 4.382906818 0.893290714 1.066489401 0.4425683 0.077901808 0.160208702 6.996435679 0.042810592 0.021473963 54.31713345 -1.734936842 0.173198687 SSS(ph)ASSPEMK ddPTM_BT-474_Pertuzumab_2h_R1 7 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SS(0.012)S(0.987)ASSPEMK;SSS(0.995)AS(0.005)SPEMK;SS(0.01)S(0.99)ASSPEMK;SS(0.003)S(0.997)ASSPEMK;SS(0.002)S(0.998)ASSPEMK;S(0.003)S(0.053)S(0.943)AS(0.001)SPEMK;S(0.001)S(0.041)S(0.958)ASSPEMK 229.24 1.80E-09 3290290000 5313830 5266150 3953100 4376970 4843050 4851840 4672600 5385630 5820230 5283330 TRUE FALSE 5106159.649 5115964.558 4667513.106 4602865.946 4998831.102 4949947.529 4729784.677 5274414.858 5159541.891 4925485.353 1.036681521 1.03867217 0.94762501 0.934499976 1.01489107 1.00496645 0.960267738 1.070841649 1.047519487 1 22.23183446 1.735010911 16.76638558 1.044229287 0.99051836 0.259435282 0.037176778 0.106088858 342.0281152 0.018044915 0.009977442 54.32639806 -1.735010911 -0.053710927 RNMEELKKEVVMDDHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNMEELKKEVVMDDHK 16 3 E9PRA5;Q13733 E9PRA5 ATP1A4 Sodium/potassium-transporting ATPase subunit alpha-4 0 53.403 0.066467 461650000 303500 428000 288680 431290 348520 445680 357230 358000 308560 421930 FALSE TRUE 291638.8845 415793.8591 340850.8977 453548.9286 359730.4623 454691.955 361601.8876 350607.1749 273533.5624 393352.3053 0.74141903 1.057052046 0.866528283 1.153034881 0.914524861 1.15594074 0.919282492 0.891331181 0.69539077 1 18.58546251 1.735021183 3.031122663 0.838950427 0.98592387 0.120290011 0.138300881 0.387399705 7.538301771 0.075380492 0.035180868 54.32768294 -1.735021183 0.146973444 TKPIWTR ddPTM_BT-474_Pertuzumab_2h_R1 3 TKPIWTR 7 1 P08238;P07900;P07900-2;Q58FG0;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA5P;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ;; 78.516 0.032033 853690000 484260 509680 455070 483640 475030 444080 470530 560810 583580 584330 FALSE TRUE 465334.5838 495144.4254 537311.272 508600.7184 490309.7714 453059.6019 476288.4869 549229.0775 517334.445 544752.8086 0.854212363 0.90893414 0.986339608 0.933635789 0.900059189 0.83167924 0.874320388 1.008217064 0.949668247 1 19.0552422 1.735108353 10.34780175 0.983204311 0.901096358 0.468118419 0.042627131 0.092420877 44.63078229 0.022107759 0.012001785 54.33858855 -1.735108353 -0.082107953 GDS(ph)ETDLEALFNAVMNPK ddPTM_BT-474_Pertuzumab_2h_R1 8 GDSETDLEALFNAVMNPK 18 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 GDS(0.994)ET(0.006)DLEALFNAVMNPK;GDS(0.996)ET(0.004)DLEALFNAVMNPK;GDS(0.5)ET(0.5)DLEALFNAVMNPK;GDS(0.994)ET(0.006)DLEALFNAVMNPK;GDS(0.5)ET(0.5)DLEALFNAVMNPK;GDS(0.979)ET(0.021)DLEALFNAVMNPK;GDS(0.998)ET(0.002)DLEALFNAVMNPK;GDS(0.895)ET(0.105)DLEALFNAVMNPK 400.08 1.47E-127 3599254000 1736099 1685660 1444281 1433337 1449175 1595447 1509246 1879861 2046728 1758120 TRUE FALSE 1668250.332 1637586.627 1705294.705 1507311.694 1495789.03 1627708.031 1527716.604 1841041.213 1814392.018 1639040.966 1.01782101 0.999112689 1.040422259 0.919630275 0.912600149 0.99308563 0.932079573 1.123242952 1.106983935 1 20.64442048 1.735232686 11.13077099 1.085104838 0.973440104 0.469557235 0.050006894 0.069384486 44.16604097 0.023939593 0.013053451 54.3541472 -1.735232686 -0.111664733 LLNQADPCVQILIQETGEHVLVTAGEVHLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLNQADPCVQILIQETGEHVLVTAGEVHLQR 31 0 Q7Z2Z2-2;Q7Z2Z2 Q7Z2Z2-2 EFTUD1 Elongation factor Tu GTP-binding domain-containing protein 1 0 218.63 4.19E-35 80563000 32943 25963 24713 27291 31184 31502 30991 23330 31343 22216 FALSE TRUE 31655.55114 25222.56066 29179.18884 28699.49178 32187.06168 32138.99202 31370.27713 22848.22735 27785.07404 20711.29053 1.528420022 1.21781695 1.408854209 1.385693071 1.554082863 1.551761923 1.514646182 1.103177386 1.341542382 1 14.33812983 1.735259724 9.203215268 1.170391536 1.446189782 0.553076678 0.124330832 0.082333362 26.57280532 0.059988495 0.032298874 54.35753126 -1.735259724 0.275798245 MLFKDDYPSSPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 MLFKDDYPSSPPK 13 1 P63279;H3BQQ9;B0QYN7;H3BPC4 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 ; 164.33 3.39E-05 766440000 2128010 2085250 1572200 1516630 1798110 1959420 1783330 2073010 2269200 1908720 FALSE TRUE 2044845.017 2025780.712 1856331.513 1594903.456 1855947.841 1999040.815 1805154.926 2030201.619 2011609.929 1779440.694 1.149150417 1.138436767 1.043210667 0.896294808 1.042995053 1.123409632 1.014450738 1.140921204 1.130473151 1 20.76299242 1.735324613 24.99999954 1.103282878 1.056468528 0.026747197 0.077712011 1.216247158 9265.707223 0.037916193 0.021026576 54.36565357 -1.735324613 -0.046814351 S(ph)PNELVDDLFK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPNELVDDLFK 11 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK 178.68 7.80E-06 334045000 427046 374819 397710 400745 385010 369084 452731 517231 584288 607486 TRUE FALSE 410356.5702 364129.5291 469585.044 421427.4975 397394.1963 376547.1314 458271.6574 506549.9991 517962.0758 566340.4321 0.724575797 0.642951674 0.829156842 0.744123982 0.701687843 0.664877713 0.809180541 0.894426692 0.914577251 1 19.11131 1.735327383 1.718872853 0.958530146 0.719886623 0.783532109 0.051772298 0.158787773 0.930609801 0.039305653 0.015650244 54.36600028 -1.735327383 -0.238643523 FGNDVQHFK ddPTM_BT-474_Pertuzumab_2h_R1 3 FGNDVQHFK 9 0 P62993;J3KT38 P62993 GRB2 Growth factor receptor-bound protein 2 0 ;; 79.974 0.025425 1199150000 2097240 2208770 2039100 2020820 2175210 2171710 2225950 2090540 2364070 2297980 FALSE TRUE 2015277.542 2145778.042 2407610.73 2125114.762 2245177.605 2215623.464 2253191.842 2047369.618 2095710.685 2142335.768 0.940691731 1.001606786 1.12382511 0.991961575 1.048004537 1.034209248 1.051745425 0.955671678 0.978236333 1 21.03075318 1.735346246 11.84342654 0.975744344 1.029831402 0.195961035 0.04565326 0.12194276 99.52095602 0.021373161 0.011691899 54.36836163 -1.735346246 0.054087058 S(ph)TSATDTHHVEMAR ddPTM_BT-474_Pertuzumab_2h_R1 3 STSATDTHHVEMAR 14 0 H3BTL2;H3BS02;O14874-2;O14874-3;O14874;H3BQP2;H3BNP3 H3BTL2 BCKDK "[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial" 1 S(0.979)T(0.02)S(0.001)ATDTHHVEMAR;S(0.37)T(0.37)S(0.26)ATDTHHVEMAR;S(0.978)T(0.021)S(0.001)ATDTHHVEMAR 207.05 6.43E-09 2958140000 706577 889841 600285 1182500 636038 776417 1096680 375618 902216 692229 TRUE FALSE 678963.1897 864463.6059 708769.8528 1243528.967 656496.7399 792116.6837 1110101.498 367861.357 799800.2221 645343.7133 1.052095458 1.339539827 1.098282726 1.92692505 1.017282305 1.227433796 1.720170934 0.570023926 1.239339914 1 19.29970823 1.735353133 25 0.914287445 1.336720873 0.2582915 0.312850636 0.484495153 3723.312391 0.137261631 0.076118524 54.3692238 -1.735353133 0.422433429 AEIIHHLADLLTDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEIIHHLADLLTDQR 15 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 ; 134.61 1.97E-05 127048000 51643 81556 77618 157042 68026 70193 116357 39605 86855 77514 FALSE TRUE 49624.73447 79230.10273 91645.2992 165146.9564 70214.11807 71612.35055 117781.0118 38787.14291 76995.58453 72263.90774 0.686715347 1.096399367 1.268202926 2.285331109 0.971634669 0.990983643 1.629873272 0.536742949 1.065477732 1 16.14098765 1.735470905 24.99999886 0.842626406 1.284616278 0.156983993 0.431970453 0.666676573 5315.399414 0.20364246 0.112930026 54.38396964 -1.735470905 0.441989872 SRS(ph)PAYSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSPAYSR 8 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 S(0.201)RS(0.799)PAYSR;S(0.014)RS(0.986)PAYSR;S(0.11)RS(0.89)PAYSR 65.842 0.03829 638188000 122203 157059 129223 200648 170569 166448 195953 106362 144729 186338 TRUE FALSE 117427.1717 152579.8311 152576.4707 211003.4673 176055.5068 169813.6926 198351.1314 104165.5875 128299.9707 173717.1613 0.675967595 0.878323304 0.87830396 1.214638011 1.013460648 0.977529746 1.141805047 0.599627502 0.738556684 1 17.40638076 1.735502173 24.99999982 0.748465649 0.973167737 0.204727138 0.167401333 0.499878877 4025.581571 0.078266131 0.043402507 54.38788534 -1.735502173 0.224702087 DMVVDIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DMVVDIQR 8 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 114.89 0.0059752 171620000 463570 604110 665430 595390 647010 595970 591750 485850 474890 504440 FALSE TRUE 445453.1719 586881.3743 785688.0034 626118.1493 667821.6642 608020.9217 598992.0135 475817.0277 420982.4781 470273.8295 0.94722084 1.247956696 1.670703225 1.331390586 1.420069803 1.292908267 1.273709009 1.011787171 0.895185851 1 18.84314152 1.735525385 2.514028566 0.94246157 1.335138122 0.466397161 0.16896502 0.2273985 3.002016573 0.110097443 0.048772473 54.39079233 -1.735525385 0.392676552 SISASKAS(ph)PPGDLQNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SISASKASPPGDLQNPK 17 1 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 SIS(0.009)AS(0.06)KAS(0.93)PPGDLQNPK;SIS(0.009)AS(0.474)KAS(0.517)PPGDLQNPK 170.91 1.08E-09 899040000 1168810 1084870 901380 913280 1019910 1182980 1064030 1175630 1414950 1322940 TRUE FALSE 1123131.613 1053930.57 1064279.417 960414.4902 1052716.331 1206900.666 1077051.917 1151352.83 1254330.808 1233336.095 0.910645214 0.854536386 0.862927325 0.778712708 0.853551871 0.978565916 0.873283383 0.933527231 1.017022702 1 20.23413457 1.735582579 0.784299408 1.010202285 0.854185183 0.57163034 0.047075495 0.462676895 0.552511209 0.044097778 0.020116704 54.3979557 -1.735582579 -0.156017103 SET(ph)PPVPPPPPYLASYPGFPENGAPGPPISR ddPTM_BT-474_Pertuzumab_2h_R1 1 SETPPVPPPPPYLASYPGFPENGAPGPPISR 31 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.193)ET(0.807)PPVPPPPPYLASYPGFPENGAPGPPISR 114.92 0.00022778 167560000 191080 181590 156210 172270 167990 184420 176560 209240 222010 222310 TRUE FALSE 183612.3823 176411.231 184440.6219 181160.8753 173393.5509 188149.0988 178720.7941 204919.1209 196808.3555 207252.7457 0.885934619 0.851188873 0.889930897 0.874106033 0.836628486 0.907824396 0.862332576 0.988740198 0.94960554 1 17.66103169 1.735600435 7.023951635 0.975919789 0.872400904 0.824341171 0.022558251 0.047861468 6.89647261 0.01040953 0.005478938 54.40019232 -1.735600435 -0.103518885 SNGELSES(ph)PGAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNGELSESPGAGK 13 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 SNGELS(0.001)ES(0.999)PGAGK 199.19 1.26E-07 379710000 325920 316720 286530 312210 302400 322150 357110 382380 432050 441970 TRUE FALSE 313182.6861 307687.4557 338312.3448 328323.1955 312126.9706 328664.0937 361480.419 374483.7194 383005.4953 412034.9782 0.76008762 0.746750815 0.82107676 0.79683331 0.757525422 0.797660663 0.877305176 0.908863905 0.929546071 1 18.65240729 1.735767739 0.823966295 0.991085286 0.771575829 0.915259327 0.023586139 0.16073247 0.20936197 0.022393948 0.009919243 54.42115309 -1.735767739 -0.219509457 SIDTGMGLER ddPTM_BT-474_Pertuzumab_2h_R1 2 SIDTGMGLER 10 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 186.67 3.06E-06 238330000 532640 556300 475560 581350 531830 508040 612250 470220 621240 618120 FALSE TRUE 511823.8399 540434.8687 561504.2708 611353.5432 548936.7949 518312.9169 619742.8986 460509.7927 550719.4397 576254.1818 0.888191107 0.937841122 0.974403811 1.060909513 0.9525949 0.899451897 1.075467941 0.799143515 0.955688405 1 19.13634579 1.735810836 25 0.900097318 0.968916509 0.076080496 0.074620789 0.63676861 5692.448079 0.033299411 0.018466198 54.42655372 -1.735810836 0.068819191 T(ph)KSPTDDEVTPSAVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.659)KS(0.329)PT(0.012)DDEVTPSAVVR 117.74 0.00052719 2668700000 328580 316780 244770 274310 264160 290450 259610 361930 356870 332780 TRUE FALSE 315738.7303 307745.7446 289005.3839 288467.172 272656.9463 296323.098 262787.1848 354456.019 316359.6137 310240.5142 1.017722431 0.991958595 0.931552685 0.929817863 0.878856674 0.955139914 0.847043416 1.142520086 1.019723728 1 18.24302757 1.73604572 25 1.062416791 0.936291977 0.464198512 0.057921097 0.256305202 2500.541714 0.026448637 0.014667149 54.45599783 -1.73604572 -0.126124814 GFPTDATLDDIKEWLEDKGQVLNIQMR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFPTDATLDDIKEWLEDKGQVLNIQMR 27 2 P05455;E7ERC4;E9PGX9 P05455 SSB Lupus La protein 0 ;; 188.3 4.86E-18 1481560000 2040720 1736430 1375110 1147450 1605220 1717420 1549970 1803120 1945800 1735970 FALSE TRUE 1960966.406 1686908.717 1623622.966 1206670.032 1656853.359 1752147.409 1568938.997 1765884.942 1724920.941 1618391.206 1.211676385 1.042336804 1.003232692 0.745598486 1.023765671 1.082647634 0.9694436 1.091136022 1.065824465 1 20.62612895 1.736121546 24.99999936 1.059236904 1.005141652 0.024768657 0.111177659 1.1845906 11907.91152 0.053786565 0.029827429 54.46550641 -1.736121546 -0.054095252 SS(ph)SKSEGSPSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSKSEGSPSQR 12 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 S(0.093)S(0.452)S(0.452)KS(0.004)EGSPSQR 81.632 0.010371 46627000 51300 43870 34217 32162 33162 45503 37079 48371 50126 44425 TRUE FALSE 49295.13928 42618.87055 40400.77305 33821.88467 34228.68585 46423.10184 37532.78389 47372.12195 44435.90663 41416.05518 1.190242264 1.029042249 0.975485784 0.816637039 0.826459345 1.120896272 0.906237538 1.143810576 1.072914995 1 15.33790253 1.73614925 24.99999947 1.0819134 0.975519943 0.114066567 0.115321085 0.614176675 6243.173346 0.055372866 0.030707196 54.46898091 -1.73614925 -0.106393458 EKQEEEVDYES(ph)EEEEEREGEENDDEDMQEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQEEEVDYESEEEEEREGEENDDEDMQEER 31 2 B9ZVN9;O95602 B9ZVN9 POLR1A DNA-directed RNA polymerase;DNA-directed RNA polymerase I subunit RPA1 1 EKQEEEVDYES(1)EEEEEREGEENDDEDMQEER 330.94 5.88E-106 276700000 38091 32187 37469 30273 36409 30790 30997 48680 49468 43128 TRUE FALSE 36602.36161 31269.05827 44240.48179 31835.39316 37580.12855 31412.5949 31376.35056 47674.74099 43852.60003 40206.90215 0.910350205 0.777703743 1.100320578 0.791789257 0.93466859 0.781273692 0.780372247 1.185735246 1.090673434 1 15.29515556 1.736201237 11.76888924 1.101371281 0.869834783 0.495563758 0.103426204 0.06207377 50.98083331 0.046831084 0.02561179 54.47550148 -1.736201237 -0.231536498 SLTDPSQESHTEAIS(ph)DAETSSSDISFSGIATR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLTDPSQESHTEAISDAETSSSDISFSGIATR 32 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 SLTDPSQESHTEAIS(1)DAETSSSDISFSGIATR;SLTDPSQESHTEAIS(1)DAETSSSDISFSGIATR 274.27 1.31E-73 534160000 114310 127714 105797 112368 116214 117836 110860 113952 115558 112898 TRUE FALSE 109842.6388 124071.7218 124916.8713 118167.3259 119952.1289 120218.7247 112216.7378 111598.8514 102440.3403 105251.3179 1.043622455 1.17881395 1.186843774 1.12271588 1.139673415 1.14220636 1.066178933 1.060308352 0.973292709 1 16.68347877 1.736352601 1.261280386 0.987629904 1.14078009 0.67341741 0.039934455 0.242968728 0.728488056 0.032056082 0.012450747 54.49449106 -1.736352601 0.153150186 GHAGGSHSNQHQMK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHAGGSHSNQHQMK 14 0 Q9Y4J8;Q9Y4J8-2;Q9Y4J8-15;Q9Y4J8-14;Q9Y4J8-13;Q9Y4J8-4;K7ER73;Q9Y4J8-16;Q9Y4J8-5;Q9Y4J8-7;Q9Y4J8-9;Q9Y4J8-3 Q9Y4J8 DTNA Dystrobrevin alpha 0 39.424 0.086077 5113800 11792 20915 16951 24258 21255 16421 21322 5555 8441 10560 FALSE TRUE 11331.1556 20318.52468 20014.42277 25509.95829 21938.68638 16753.04387 21582.94501 5440.287309 7482.813068 9844.761794 1.150983217 2.063891956 2.033002239 2.591221486 2.228462896 1.701721608 2.192327805 0.552607308 0.760080663 1 13.26514058 1.736379686 7.743708698 0.757001915 2.01948207 0.695880219 0.369853831 0.063490135 12.14036676 0.182126304 0.096723364 54.49788979 -1.736379686 1.262480155 SSVKT(ph)PETVVPTALELQPSTSTDRPVTSEPTSQATR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSVKTPETVVPTALELQPSTSTDRPVTSEPTSQATR 36 2 Q14676;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SS(0.002)VKT(0.985)PET(0.013)VVPTALELQPSTSTDRPVTSEPTSQATR;SSVKT(0.997)PET(0.003)VVPTALELQPSTSTDRPVTSEPTSQATR 233.83 7.67E-48 820270000 14516.4 17936.6 7841.4 12672.9 16696.6 13091.4 13350.6 17438.3 19106.1 16337.8 TRUE FALSE 13949.08304 17425.06573 9258.515411 13326.94989 17233.6613 13356.11708 13513.98864 17078.19301 16937.25563 15231.22625 0.915821406 1.144035644 0.607864085 0.874975505 1.131469063 0.876890465 0.887255459 1.121261856 1.112008669 1 13.89474448 1.736417339 8.795569544 1.085322897 0.921177226 0.201356698 0.143780661 0.166732298 47.24728093 0.069429349 0.037262701 54.50261486 -1.736417339 -0.16414567 NEDEDS(ph)PNKLYTLVTYVPVTTFK ddPTM_BT-474_Pertuzumab_2h_R1 1 NEDEDSPNKLYTLVTYVPVTTFK 23 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 1 NEDEDS(1)PNKLYTLVTYVPVTTFK 134.04 1.25E-05 98113000 124720 91006 100180 77408 105330 96045 100210 148820 166100 146330 TRUE FALSE 119845.8045 88410.59798 118284.7545 81403.03616 108718.0351 97987.09571 101436.4 145746.815 147245.0243 136418.9388 0.878512951 0.648081555 0.867069892 0.596713601 0.79694239 0.718280736 0.743565379 1.068376695 1.07935911 1 17.05768442 1.736698402 5.613012931 1.054968327 0.744551993 0.722806866 0.084772284 0.071044445 5.676460321 0.038993665 0.020143272 54.53789882 -1.736698402 -0.310416334 LHAVNAEECNVLQGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LHAVNAEECNVLQGR 15 0 A0A0C4DGA2;O75521-2;O75521 A0A0C4DGA2 ECI2 "Enoyl-CoA delta isomerase 2, mitochondrial" 0 ;;; 278.64 1.26E-33 4643260000 1497960 1863420 1390970 2046300 1609390 1840050 2016640 1306180 1827680 1779170 FALSE TRUE 1439418.067 1810277.086 1642349.221 2151909.788 1661157.491 1877257.072 2041320.244 1279206.927 1620209.429 1658665.231 0.86781711 1.09140594 0.990163169 1.297374387 1.001502569 1.131787799 1.230700569 0.771226708 0.976815212 1 20.66159131 1.736704457 24.99999999 0.901614425 1.090173435 0.27069997 0.12808441 0.28575163 3744.98614 0.057017865 0.031619327 54.53865927 -1.736704457 0.18855901 LEHVVEEEKVDISEDGMK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEHVVEEEKVDISEDGMK 18 1 P40937-2;P40937 P40937-2 RFC5 Replication factor C subunit 5 0 211.16 2.00E-16 108990000 173890 138910 117200 113420 143980 136640 147810 165700 215230 163070 FALSE TRUE 167094.1866 134948.4228 138380.6471 119273.6198 148611.2475 139402.9544 149618.943 162278.2371 190797.9927 152025.1237 1.099122188 0.88767185 0.910248542 0.784565188 0.977544 0.916973136 0.98417248 1.067443546 1.25504251 1 17.21395024 1.736972494 2.380546426 1.133206089 0.923832321 0.416693351 0.094402079 0.232125947 2.730632081 0.058539673 0.025542984 54.57232972 -1.736972494 -0.209373767 AKSPT(ph)PDGS(ph)ER ddPTM_BT-474_Pertuzumab_2h_R1 1 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.29)PT(0.734)PDGS(0.975)ER 148.08 0.00087766 523300000 1129700 964010 800630 785110 876700 842700 886620 1060800 1169800 1031700 TRUE FALSE 1085550.075 936517.3787 945321.6509 825629.6212 904899.8517 859739.9714 897470.7208 1038894.109 1037009.208 961822.0401 1.128639218 0.973690911 0.982844655 0.858401645 0.940818378 0.89386595 0.93309436 1.08013132 1.0781716 1 19.87541046 1.736993058 8.681231761 1.057989992 0.953226773 0.269166592 0.070319825 0.132155583 36.17723624 0.034671221 0.018592441 54.57491379 -1.736993058 -0.104763219 HDLDDLSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HDLDDLSLR 9 0 J3QLQ2;H7C1R0;J3QKK3;O43502 J3QLQ2 RAD51C DNA repair protein RAD51 homolog 3 0 144.65 9.91E-05 73993000 58681 72064 63267 100310 77118 64959 86210 52634 75265 69673 FALSE TRUE 56387.68164 70008.80528 74700.75427 105487.0111 79598.57051 66272.51549 87265.06377 51547.08951 66721.23274 64953.98565 0.868117346 1.077821547 1.150056513 1.624026764 1.225460912 1.020299445 1.343490517 0.793593942 1.027207677 1 15.98713043 1.737045944 24.99999988 0.932423928 1.193287932 0.244932409 0.198196499 0.289614019 4612.954804 0.095274743 0.052834616 54.58155997 -1.737045944 0.260864004 EKQSEDTNTESK ddPTM_BT-474_Pertuzumab_2h_R1 4 EKQSEDTNTESK 12 1 O95232;J3KPP4;H0YBV7;H0YAR4 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 137.62 8.11E-05 850070000 1061290 891220 787355 764922 839990 893291 926591 1054820 1263950 1117070 FALSE TRUE 1019813.613 865803.2782 929647.5631 804399.7161 867009.0412 911353.9561 937930.8978 1033037.598 1120471.695 1041409.854 0.979262497 0.831376115 0.892681743 0.772414159 0.832533933 0.875115549 0.900635705 0.991960653 1.075918084 1 19.99010653 1.737118658 2.091692808 1.039442981 0.858557232 0.647303266 0.052982669 0.17239583 1.543518182 0.035558006 0.014920991 54.59069929 -1.737118658 -0.180885749 SKDKEEGKEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SKDKEEGKEER 11 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 0 134.98 5.68E-05 153470000 315950 247500 173620 154310 230250 228170 218300 271490 304620 253440 FALSE TRUE 303602.3247 240441.5423 204996.9962 162273.9576 237656.2004 232783.7537 220971.6207 265883.6366 270040.8147 236274.2831 1.28495713 1.01763738 0.867622974 0.686803301 1.005848784 0.985226791 0.935233483 1.125317716 1.142912429 1 17.85010308 1.737125315 8.247566759 1.098807985 0.958197474 0.123130095 0.144291934 0.216901488 50.55292127 0.072980014 0.038976859 54.59153617 -1.737125315 -0.14061051 NKS(ph)EDEDEDEGDATR ddPTM_BT-474_Pertuzumab_2h_R1 2 NKSEDEDEDEGDATR 15 1 Q9BZI1 Q9BZI1 IRX2 Iroquois-class homeodomain protein IRX-2 1 NKS(1)EDEDEDEGDATR;NKS(1)EDEDEDEGDATR 216.61 1.32E-12 867970000 958260 772370 668570 575610 674620 655750 694720 891310 1007490 797250 TRUE FALSE 920810.1398 750342.7638 789395.4713 605317.3011 696319.765 669009.7143 703222.1912 872904.137 893123.9589 743251.5474 1.238894346 1.009540803 1.062083858 0.814417815 0.936856126 0.900112104 0.946142922 1.174439717 1.201644264 1 19.50349104 1.737145903 8.874424624 1.138921082 0.97875128 0.223359801 0.116694027 0.139551852 41.13360755 0.057052718 0.030648609 54.59412415 -1.737145903 -0.160169802 DSPNVEAAHLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSPNVEAAHLAR 12 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 123.02 0.0003482 288320000 164330 187680 179420 189610 173340 191460 195240 163560 179070 205630 FALSE TRUE 157907.8019 182327.5502 211845.1852 199395.7948 178915.6385 195331.4524 197629.4055 160182.4288 158742.7243 191702.4969 0.823712807 0.951096376 1.105072644 1.040131443 0.933298425 1.018930142 1.030917222 0.835578208 0.82806811 1 17.5485096 1.737164229 11.32239093 0.875095906 0.990682048 0.218830549 0.083714055 0.108589559 78.45914593 0.039851015 0.021753191 54.59642792 -1.737164229 0.115586143 ESPGAAATSSSGPQAQQHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESPGAAATSSSGPQAQQHR 19 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 0 124.29 2.96E-05 51270000 31194 44933 40685 49067 46716 37754 39063 33019 27890 29378 FALSE TRUE 29974.90399 43651.55483 48037.68453 51599.35375 48218.66257 38517.41175 39541.06468 32337.14611 24724.04412 27388.20189 1.094445853 1.593808714 1.753955397 1.88399932 1.76056328 1.406350512 1.443726201 1.180696208 0.90272608 1 14.74126693 1.737194376 1.358549773 0.940225485 1.621773551 0.602122332 0.207078644 0.285349642 1.002025901 0.175673725 0.06813744 54.60021791 -1.737194376 0.681548066 SDKVPENK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDKVPENK 8 1 Q9UBF2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ; 109.66 0.0032602 466450000 1099830 1025060 827130 858010 969380 941090 1023020 1155940 1399210 1212940 FALSE TRUE 1056847.428 995826.2924 976610.7904 902291.9989 1000560.988 960119.4846 1035540.025 1132069.435 1240377.547 1130786.493 0.934612709 0.880649263 0.863656222 0.797933124 0.884836345 0.849072296 0.915769715 1.001134557 1.096915779 1 20.10889513 1.737219083 2.314994078 1.049152674 0.866926591 0.777467991 0.039564778 0.117805154 1.306851614 0.025558928 0.011060094 54.60332421 -1.737219083 -0.182226083 HTQSMS(ph)SARER ddPTM_BT-474_Pertuzumab_2h_R1 1 HTQSMSSARER 11 1 K7EJR8;B5MDG7;Q9P0W2-2;Q9P0W2-3;Q9P0W2 K7EJR8 HMG20B SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related 1 HT(0.004)QS(0.004)MS(0.496)S(0.496)ARER 79.089 0.017018 348360000 178630 259210 199600 305020 257070 284170 247310 196580 192550 222950 TRUE FALSE 171648.9421 251817.5846 235672.1601 320762.1188 265338.89 289916.1121 250336.6538 192520.5543 170692.5312 207849.3979 0.825833242 1.211538677 1.133860201 1.543242954 1.276592055 1.394837392 1.204413658 0.926250238 0.821231781 1 17.66517904 1.73723657 4.016767669 0.8992784 1.245899334 0.388705748 0.178414176 0.192205496 6.831229169 0.098080716 0.048680744 54.60552288 -1.73723657 0.346620935 RS(ph)SDTEEESR ddPTM_BT-474_Pertuzumab_2h_R1 3 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.499)S(0.499)DT(0.003)EEESR;RS(0.498)S(0.498)DT(0.004)EEESR;RS(0.5)S(0.5)DTEEESR 151.3 1.23E-05 369204000 88841 104205 86466 117981 121557 122235 104753 81348 82833 83486 TRUE FALSE 85368.9955 101233.1754 102092.3296 124070.0135 125466.9913 124706.6754 106034.9985 79668.13537 73430.1451 77831.41886 1.096844909 1.300672362 1.311711018 1.594086493 1.612035257 1.602266505 1.362367539 1.023598651 0.943451195 1 16.24806504 1.737237771 3.550078584 0.974900037 1.429692177 0.617678743 0.152927014 0.148598414 4.019401269 0.094572559 0.045882198 54.60567388 -1.737237771 0.45479214 KGDVEGSQS(ph)QDEGEGSGESER ddPTM_BT-474_Pertuzumab_2h_R1 2 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 KGDVEGSQS(1)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER 283.29 2.33E-45 684920000 730260 670790 604950 585370 589330 688170 660470 743140 881060 710850 TRUE FALSE 701720.6319 651659.726 714277.922 615581.0159 608286.3347 702085.2689 668553.0294 727793.8993 781045.7625 662703.4963 1.058875705 0.983335277 1.077824285 0.928893569 0.91788611 1.059425931 1.008826773 1.098219495 1.178574984 1 19.33800401 1.737259726 3.928850056 1.105326881 1.001966643 0.271791196 0.064437445 0.227607942 7.695056146 0.034303845 0.0169634 54.60843442 -1.737259726 -0.103360238 MEVEELS(ph)PLALGR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEVEELSPLALGR 13 0 P30305;G8JLH2;B4DIG0;P30305-3;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 MEVEELS(1)PLALGR;MEVEELS(1)PLALGR;MEVEELS(1)PLALGR 146.59 4.10E-05 118808000 204396 227104 235926 290088 300665 288358 260339 226936 215317 273261 TRUE FALSE 196407.9783 220627.2163 278563.0763 305059.4764 310336.1628 294188.7963 263525.1066 222249.6923 190875.1168 254752.7891 0.770974791 0.86604436 1.093464285 1.197472568 1.218185536 1.154801081 1.034434628 0.872413186 0.74925624 1 17.95873842 1.737266637 4.150029879 0.855293446 1.060415497 0.230671914 0.144083886 0.276689331 10.59372909 0.084764379 0.04229229 54.60930349 -1.737266637 0.205122051 AAVS(ph)PQKR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAVSPQKR 8 1 E9PJF5;G5E9I4;Q9HCU9 E9PJF5 BRMS1 Breast cancer metastasis-suppressor 1 1 AAVS(1)PQKR;AAVS(1)PQKR;AAVS(1)PQKR;AAVS(1)PQKR 129.16 0.00067546 1966532000 3088850 2942590 2441100 2723470 2759300 2875660 2775310 3121260 3382120 3078200 TRUE FALSE 2968134.327 2858670.214 2882261.072 2864028.613 2848055.39 2933807.815 2809275.074 3056804.89 2998195.917 2869710.772 1.034297378 0.996152728 1.004373367 0.998019954 0.99245381 1.022335715 0.978940143 1.065196158 1.044772855 1 21.45247391 1.737508556 24.99999866 1.041720853 1.003578943 0.331646064 0.02100951 0.136301289 3054.724518 0.008982558 0.004981381 54.63973149 -1.737508556 -0.03814191 MLLHSEQHPGQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 MLLHSEQHPGQLK 13 0 J3QKT4;J3KQ22;E2QRB3;P32322-2;P32322;P32322-3 J3QKT4 PYCR1 "Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 1, mitochondrial" 0 ; 126.83 0.00010639 879940000 2366500 3265200 2096920 3541300 2481800 2646900 3251300 2066610 3115200 2702460 FALSE TRUE 2274014.564 3172079.693 2475880.09 3724066.917 2561629.351 2700422.132 3291090.382 2023933.781 2761575.556 2519419.977 0.90259448 1.259051576 0.982718289 1.478144554 1.016753608 1.071842788 1.306288912 0.803333227 1.096115606 1 21.2646602 1.737592055 25 0.955636053 1.148489442 0.181098516 0.173743906 0.209610073 5065.965775 0.074960835 0.041569621 54.65023764 -1.737592055 0.192853389 KDS(ph)SSVVEWTQAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 KDS(0.566)S(0.11)S(0.324)VVEWTQAPK 145.88 5.18E-06 236430000 330830 319810 234840 193390 291760 254330 235320 366860 371630 291310 TRUE FALSE 317900.7978 310689.3319 277280.812 203370.8811 301144.7254 259472.7269 238199.9166 359284.2128 329444.1204 271579.3142 1.170563372 1.144009561 1.020993859 0.748845256 1.108864739 0.955421541 0.877091531 1.322943958 1.213067797 1 18.05101407 1.737664971 24.99999972 1.203119678 1.002134401 0.239963865 0.140688159 0.165369556 4288.96248 0.065862208 0.03652393 54.65941392 -1.737664971 -0.200985276 LEELHVIDVK ddPTM_BT-474_Pertuzumab_2h_R1 6 LEELHVIDVK 10 0 Q16531;F5GY55;F5H2L3;F5GWI0 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;;; 178.84 2.17E-06 3914880000 10240000 9558600 8751600 9038800 9658300 9141400 10253700 10972300 12491400 12201600 FALSE TRUE 9839809.479 9285998.087 10333208.8 9505293.551 9968967.991 9326245.371 10379187.85 10745718.17 11073428.64 11375174.76 0.865024906 0.816338938 0.908400004 0.835617364 0.876379326 0.819877106 0.912442056 0.944664007 0.973473276 1 23.43938537 1.737690376 1.585545109 0.987659905 0.8544871 0.788519681 0.027872595 0.151505878 0.743717409 0.019987309 0.007857717 54.66261141 -1.737690376 -0.133172804 SSSFS(ph)DTLEESSPIAAIFDTENLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.216)S(0.216)S(0.216)FS(0.282)DT(0.068)LEESSPIAAIFDTENLEK 202.47 3.66E-25 358000000 88023 82507 65414 68553 81397 78404 72219 89966 93900 76712 TRUE FALSE 84582.96385 80153.98114 77235.76493 72091.02855 84015.20843 79989.3826 73102.83773 88108.17066 83240.86566 71516.22791 1.182710083 1.120780325 1.079975373 1.008037346 1.17477125 1.11847877 1.022185312 1.232002487 1.163943738 1 16.12598302 1.737741193 25 1.154691276 1.100878039 0.008018915 0.076225629 0.29635786 8318.246562 0.034052033 0.018883433 54.669008 -1.737741193 -0.053813236 SKT(ph)PTGPELDTSYK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKTPTGPELDTSYK 14 1 Q8NF91;Q8NF91-4;A0A0C4DG40;E7ENN3;H0Y325;Q8NF91-2;Q8NF91-8;Q8NF91-11;Q8NF91-3;Q8NF91-9;A0A5F9ZH87;A0A5F9ZHE1;Q5JV20;F8WAI0;H0Y326;A0A5F9ZH86 Q8NF91 SYNE1 Nesprin-1 1 S(0.206)KT(0.736)PT(0.058)GPELDTSYK 160.76 7.60E-06 779140000 249860 222270 189160 208990 176430 193780 211720 309570 357650 294950 TRUE FALSE 240095.195 215931.0772 223345.4198 219775.9989 182105.0312 197698.3644 214311.0927 303177.2713 317051.0714 274972.7738 0.873159883 0.785281664 0.812245579 0.799264581 0.662265681 0.718974325 0.779390227 1.102571964 1.153027142 1 18.06892925 1.737906417 5.20994273 1.096418235 0.770970146 0.831374107 0.063718659 0.061963225 4.097044036 0.033838304 0.01738092 54.6898103 -1.737906417 -0.325448089 RLS(ph)LESEGAGEGAAASPELSALEEAFRR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSLESEGAGEGAAASPELSALEEAFRR 28 2 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 RLS(0.999)LES(0.001)EGAGEGAAASPELSALEEAFRR;RLS(0.773)LES(0.227)EGAGEGAAASPELSALEEAFRR 192.79 1.38E-18 107697000 20303.4 19516 17525.6 18487.2 18772.7 20772.9 19724.8 15058.7 18613.7 14239.3 TRUE FALSE 19509.92068 18959.42279 20692.86577 19441.32661 19376.54094 21192.94227 19966.198 14747.73258 16500.75081 13274.85953 1.469689426 1.428220219 1.558801111 1.46452221 1.459641882 1.596472055 1.504060963 1.110952063 1.243007565 1 13.69640897 1.738047297 5.873047501 1.133858553 1.498747419 0.850472142 0.072704187 0.053179533 4.779955099 0.035182696 0.018275092 54.70755393 -1.738047297 0.364888866 LGSQHS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 5 LGSQHSPGR 9 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 LGS(0.022)QHS(0.978)PGR;LGS(0.001)QHS(0.999)PGR;LGSQHS(1)PGR;LGS(0.006)QHS(0.994)PGR;LGSQHS(1)PGR 132.17 0.00020131 5199253000 2216130 2696080 2229090 3000030 2349010 2519460 2611040 2260730 2375300 2729670 TRUE FALSE 2129521.19 2619190.438 2631936.149 3154861.908 2424568.04 2570405.207 2642994.689 2214045.135 2105665.902 2544787.02 0.836817059 1.029237582 1.034246139 1.239735146 0.952758726 1.010066928 1.038591705 0.870031605 0.827442881 1 21.27911349 1.73805862 7.176626777 0.887975666 1.02661278 0.223787937 0.101995977 0.170321999 26.43676145 0.049959504 0.026390725 54.70898032 -1.73805862 0.138637113 AKDYPAHTEEDK ddPTM_BT-474_Pertuzumab_2h_R1 4 AKDYPAHTEEDK 12 1 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YC67;H0YB03;H0YC27;H0YBD9;H0YAP5 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ;;; 150.69 4.11E-05 679250000 766960 693320 689770 714340 646110 598712 755450 777380 922670 846900 FALSE TRUE 736986.3553 673547.1924 814426.7829 751207.173 666892.7149 610818.3668 764695.4231 761326.8313 817932.3697 789538.7087 0.933439168 0.853089513 1.031522298 0.95145072 0.844661202 0.773639544 0.96853443 0.964267898 1.035962342 1 19.59065047 1.738083437 2.442051921 1.009006117 0.902120929 0.305167328 0.068175572 0.354477631 4.391484987 0.046036006 0.020265899 54.71210656 -1.738083437 -0.106885187 KQSTDEEVTSLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQSTDEEVTSLAK 13 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7;E5RJ93 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 0 97.797 0.005794 251730000 123870 106240 99938 104260 104030 125120 116640 106370 120430 122980 FALSE TRUE 119029.0235 103210.1392 117999.0197 109640.8711 107376.2194 127650.0121 118067.4752 104173.4223 106759.2913 114650.4551 1.038190589 0.900215696 1.029206728 0.95630559 0.936552928 1.113384261 1.029803808 0.908617609 0.93117198 1 16.80688256 1.738109374 24.9999979 0.939713537 0.997947883 0.138978387 0.060552724 0.142953409 6511.229937 0.02824048 0.015660787 54.71537424 -1.738109374 0.058234345 GTT(ph)PPPPSWEPNSQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 GTTPPPPSWEPNSQTK 16 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 GT(0.02)T(0.98)PPPPSWEPNSQTK;GT(0.383)T(0.617)PPPPSWEPNSQTK 146 1.30E-05 364890000 306060 320570 251940 298170 295780 305340 292350 343950 363990 346550 TRUE FALSE 294098.8368 311427.6575 297471.1624 313558.5894 305294.0323 311514.184 295927.8668 336847.3123 322671.3812 323077.8598 0.910303284 0.963939954 0.920741404 0.970535677 0.944954979 0.964207774 0.915964551 1.04261961 0.998741855 1 18.30152236 1.738111923 12.75199475 1.014936139 0.943708069 0.676728749 0.022845725 0.038657594 48.33757639 0.009796886 0.005377424 54.71569535 -1.738111923 -0.07122807 VTQQEKT(ph)PPPRPSPLEAGSDGCEEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTQQEKTPPPRPSPLEAGSDGCEEPK 26 2 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 VTQQEKT(1)PPPRPSPLEAGSDGCEEPK;VT(0.002)QQEKT(0.997)PPPRPS(0.001)PLEAGSDGCEEPK 189.2 4.27E-16 829650000 956120 755660 600140 497140 675710 719170 688560 848110 983540 760180 TRUE FALSE 918753.7734 734109.3167 708598.648 522797.455 697444.8258 733712.1101 696986.8033 830596.2321 871892.6625 708692.3315 1.296407104 1.035864626 0.999867808 0.737693117 0.984129212 1.035304148 0.98348292 1.172012445 1.230283755 1 19.43479991 1.73815788 7.618982732 1.149146499 1.000394736 0.139388591 0.137527414 0.207879665 38.4347038 0.068780863 0.036515504 54.72148572 -1.73815788 -0.148751762 SRS(ph)IDKDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSIDKDR 8 2 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.099)RS(0.901)IDKDR;S(0.056)RS(0.944)IDKDR;S(0.004)RS(0.996)IDKDR 65.842 0.049794 1397600000 2189770 1904680 1379140 1558990 1703150 1837190 1681290 2022280 2125010 1911530 TRUE FALSE 2104191.367 1850360.391 1628381.277 1639449.661 1757933.367 1874339.241 1701866.13 1980519.211 1883787.774 1782060.37 1.180763235 1.038326435 0.913763251 0.919974254 0.986461175 1.051782123 0.954999145 1.111364825 1.057084151 1 20.76511478 1.738305479 24.99999578 1.06499389 1.001865692 0.074599052 0.076918414 0.123058674 7941.487309 0.036919958 0.020473933 54.7400865 -1.738305479 -0.063128198 VLGIVVGVLLQDHDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLGIVVGVLLQDHDVR 16 0 A5YKK6-3;A5YKK6-2;A5YKK6;H3BMZ2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 169.04 3.65E-12 0 59219 67919 64399 74692 71820 70859 79367 54299 76859 68907 FALSE TRUE 56904.65601 65982.01662 76037.33185 78546.86307 74130.15553 72291.81753 80338.31709 53177.70667 68134.28854 64239.86751 0.885815277 1.027119438 1.183647084 1.222712096 1.153958724 1.125341946 1.250599047 0.827799134 1.060623117 1 15.9711813 1.73862128 25 0.953214389 1.125399279 0.293812957 0.112190543 0.044715996 4268.519063 0.053150684 0.029474741 54.77990561 -1.73862128 0.17218489 ELSVQDQPSLSPT(ph)SLQNSSSHTTTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSVQDQPSLSPTSLQNSSSHTTTAK 26 0 O95628-3;O95628-2;O95628;O95628-8;O95628-4;O95628-7;O95628-9;O95628-10;O95628-6 O95628-3 CNOT4 CCR4-NOT transcription complex subunit 4 1 ELSVQDQPSLS(0.258)PT(0.726)S(0.016)LQNSSSHTTTAK 254.65 5.16E-52 853820000 385680 560740 428090 666260 546750 584520 504930 420580 373360 454990 TRUE FALSE 370607.1992 544748.2442 505455.3858 700645.7584 564336.7103 596339.3949 511109.4844 411894.876 330977.7381 424173.122 0.873716839 1.284259223 1.19162521 1.651791974 1.33043958 1.405886804 1.204954906 0.971053692 0.780289275 1 18.69429368 1.738624265 2.807560625 0.88685655 1.302873125 0.43880152 0.188981152 0.21629262 3.569900486 0.115136062 0.052830106 54.78028213 -1.738624265 0.416016574 LAPVPS(ph)PEPQKPAPVSPESVK ddPTM_BT-474_Pertuzumab_2h_R1 5 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK 203.72 3.44E-22 3290800000 4240880 3733310 3094010 2967130 3340320 3420820 3406000 4164850 4631760 3921230 TRUE FALSE 4075141.721 3626839.654 3653166.433 3120263.935 3447764.426 3489991.324 3447683.647 4078844.392 4105982.023 3655641.599 1.114754171 0.992121234 0.999322919 0.853547551 0.943135243 0.954686402 0.943113145 1.115767036 1.123190529 1 21.8016932 1.73869255 9.033447879 1.08803598 0.967117398 0.337185677 0.06890057 0.108063112 34.51872229 0.033713136 0.018143889 54.78889609 -1.73869255 -0.120918583 MPLLELGGETT(ph)PPLSTER ddPTM_BT-474_Pertuzumab_2h_R1 4 MPLLELGGETTPPLSTER 18 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.243)T(0.757)PPLSTER;MPLLELGGET(0.189)T(0.809)PPLS(0.001)TER;MPLLELGGET(0.036)T(0.964)PPLSTER;MPLLELGGET(0.064)T(0.936)PPLSTER 129.88 0.00022644 686034000 244970 256099 237112 313013 285068 279507 260457 265968 253950 281081 TRUE FALSE 235396.3016 248795.3073 279963.4129 329167.6384 294237.4711 285158.823 263644.5507 260475.6679 225122.6606 262043.1335 0.898311276 0.949444101 1.068386754 1.256158229 1.122858925 1.0882133 1.006111273 0.994018291 0.85910536 1 17.99944478 1.738901872 2.048425106 0.933569008 1.068413957 0.213943152 0.097164385 0.482455416 4.125399517 0.073360725 0.030647657 54.81530971 -1.738901872 0.134844949 NAGFTPQER ddPTM_BT-474_Pertuzumab_2h_R1 2 NAGFTPQER 9 0 P27695;G3V3M6;G3V5Q1 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 118.5 0.0022801 533190000 411780 400530 323070 368530 362320 313050 354860 422680 430950 440300 FALSE TRUE 395687.1824 389107.2766 381455.9357 387549.8775 373974.3519 319380.0855 359202.8828 413951.5103 382030.3627 410478.0888 0.963966636 0.947936777 0.929296706 0.944142667 0.911070194 0.778068536 0.875084183 1.008461893 0.930696115 1 18.64694569 1.738904912 15.65365896 0.976901713 0.906124242 0.282036219 0.0530357 0.08733363 322.7932973 0.026964883 0.01489105 54.81569334 -1.738904912 -0.07077747 STLTTLPFPGAEANS(ph)PGKAEAEKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 STLTTLPFPGAEANSPGKAEAEKPR 25 2 Q96GV9 Q96GV9 C5orf30 UNC119-binding protein C5orf30 1 STLTTLPFPGAEANS(1)PGKAEAEKPR;STLTTLPFPGAEANS(1)PGKAEAEKPR 299.33 2.03E-63 1516630000 1794150 1352180 1248730 1070890 1269310 1300880 1340650 1635160 1814750 1635550 TRUE FALSE 1724032.634 1313617.15 1474403.289 1126158.761 1310138.509 1327184.685 1357057.276 1601393.375 1608747.188 1524772.742 1.130681699 0.86151668 0.966965928 0.738574825 0.859235264 0.87041475 0.890006254 1.050250526 1.055073418 1 20.5401628 1.738906137 6.245454286 1.038631514 0.894009707 0.286444176 0.095055956 0.171457299 18.16150327 0.046809008 0.024463 54.81584799 -1.738906137 -0.144621807 EQEELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQEELRR 7 1 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 103.56 0.013385 387230000 244080 293810 218140 308350 286110 273850 251710 231860 201041 235480 FALSE TRUE 234541.0838 285430.8265 257562.7505 324263.9805 295312.988 279387.4346 254790.5023 227072.01 178219.6685 219530.7299 1.068374728 1.300186205 1.173242355 1.477077859 1.34520114 1.272657522 1.16061429 1.03435182 0.811821054 1 17.74406338 1.738951092 1.921325748 0.90882713 1.2805918 0.63671325 0.110840441 0.192819918 1.436909006 0.078454084 0.032192702 54.82152241 -1.738951092 0.37176467 GFPTDATLDDIKEWLEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFPTDATLDDIKEWLEDK 18 1 P05455;E7ERC4;E9PGX9 P05455 SSB Lupus La protein 0 ; 192.16 1.72E-14 1473150000 1299640 990060 1095690 896470 1072400 965850 1172360 1326360 1610220 1441390 FALSE TRUE 1248848.632 961824.4582 1293705.556 942736.9241 1106894.72 985380.1488 1186707.692 1298970.202 1427434.576 1343763.371 0.929366478 0.715769218 0.962748043 0.701564683 0.823727409 0.73329886 0.883122518 0.96666588 1.062266323 1 20.35784768 1.739003146 2.338767571 1.026723011 0.809634973 0.537153994 0.082731524 0.190472362 2.154398746 0.049331133 0.021450958 54.8280936 -1.739003146 -0.217088038 SKGESDDFHMDFDSAVAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKGESDDFHMDFDSAVAPR 19 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 214.69 2.55E-19 829510000 1014980 949510 743690 994860 916660 965780 1009590 848730 1022280 1027370 FALSE TRUE 975313.4595 922430.9045 878091.3263 1046204.844 946145.2014 985308.7333 1021945.664 831203.4289 906235.0601 957785.3148 1.018300703 0.963087333 0.916793474 1.092316647 0.987846845 1.028736522 1.066988237 0.867838978 0.946177652 1 19.86934279 1.739016958 25 0.927725028 1.008115402 0.2565408 0.05568966 0.089626583 4493.990506 0.025538261 0.01416227 54.82983744 -1.739016958 0.080390374 ESDHIHIIALAQALSVSIQVEYMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESDHIHIIALAQALSVSIQVEYMDR 25 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 159.51 1.35E-11 37226000 21308.9 25818.7 24863.4 23089.7 26038.7 23577 28456.7 17130.6 26830.5 20918.4 FALSE TRUE 20476.12463 25082.37596 29356.76946 24281.36218 26876.25843 24053.74309 28804.96161 16776.84712 23784.81412 19501.57814 1.049972699 1.2861716 1.505353529 1.245097295 1.378158129 1.233425466 1.47705798 0.860281512 1.219635352 1 14.25130326 1.739036599 25 1.026843992 1.314381879 0.441058101 0.146524963 0.065374765 3170.693333 0.06437391 0.035698642 54.83231712 -1.739036599 0.287537887 NCPS(ph)PVLIDCPHPNCNK ddPTM_BT-474_Pertuzumab_2h_R1 1 NCPSPVLIDCPHPNCNK 17 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 NCPS(1)PVLIDCPHPNCNK 123.36 0.00043424 0 26961 24103 23816 22852 25746 23440 25358 28222 31329 30079 TRUE FALSE 25907.33431 23415.60604 28120.08098 24031.39446 26574.14347 23913.97286 25668.33879 27639.20584 27772.66326 28041.72254 0.923885267 0.835027378 1.002794352 0.856987099 0.947664447 0.85279971 0.915362412 0.985645793 0.990405037 1 14.77528735 1.739062384 3.819825695 0.993022428 0.903097503 0.425171528 0.046618366 0.181918224 5.751943815 0.023469858 0.011571 54.83557272 -1.739062384 -0.089924926 S(ph)PTESVNTPVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPTESVNTPVGK 12 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 S(1)PTESVNTPVGK 189.99 0.00011048 0 125820 139190 142450 149200 136240 132760 169330 151770 210450 203320 TRUE FALSE 120902.8153 135220.4375 168193.8838 156900.2299 140622.2833 135444.4982 171402.3112 148635.8965 186560.5983 189548.9553 0.637844799 0.71338002 0.887337435 0.827755709 0.74187844 0.714562093 0.904264077 0.784155714 0.984234379 1 17.53221098 1.739094869 0.042681355 1.696417663 3.07E-11 0.543631592 0.078235341 45.6857138 1.871611522 36.00968473 37.32845665 54.83967456 -1.739094869 -1.696417663 ILEHMPVSNQKPDTDEAEDPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILEHMPVSNQKPDTDEAEDPEK 22 1 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 237.95 9.26E-31 405660000 609330 472990 444540 394830 493600 528170 511430 610850 753430 605970 FALSE TRUE 585516.71 459500.7883 524878.2667 415207.2236 509477.0923 538849.9593 517689.0333 598235.734 667903.785 564927.1122 1.036446468 0.813380662 0.929107942 0.734974857 0.901845709 0.953839792 0.916381994 1.058960919 1.182283113 1 19.10770522 1.739256985 2.471748261 1.10126377 0.887308103 0.485626677 0.08622134 0.201628687 2.557511104 0.052584174 0.023260121 54.86014925 -1.739256985 -0.213955666 SGEISLPIKEEPS(ph)PISK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGEISLPIKEEPSPISK 17 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5;I3L2A0 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 SGEISLPIKEEPS(0.998)PIS(0.002)K;SGEISLPIKEEPS(0.992)PIS(0.008)K 190.91 1.65E-10 483270000 1107350 965400 896400 806480 1046290 1030820 815840 921410 854180 822260 TRUE FALSE 1064073.538 937867.7372 1058399.42 848102.5294 1079944.868 1051663.887 825824.494 902382.5615 757217.0674 766567.5978 1.388101377 1.223463841 1.380699397 1.106363655 1.408805787 1.371912783 1.077301593 1.177172847 0.98780208 1 19.54805349 1.73925939 1.244795817 1.002782888 1.30388823 0.576569007 0.102811296 0.318343998 0.928040427 0.081774379 0.031848147 54.86045304 -1.73925939 0.301105343 SILDADPEAQALLEISGHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SILDADPEAQALLEISGHSR 20 0 Q6P9B6 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 ; 145.52 1.44E-07 111940000 131273 158471 131498 155022 132392 176347 156152 132871 152769 149704 FALSE TRUE 126142.706 153951.5622 155262.6138 163022.704 136650.5089 179912.8572 158063.0349 130127.1674 135427.3036 139564.4147 0.903831441 1.103086073 1.112479955 1.168082167 0.979121427 1.289102652 1.132545393 0.932380705 0.970356977 1 17.09057161 1.739267844 9.210018911 0.965334399 1.104476052 0.267514771 0.098660112 0.127772565 43.96251457 0.046567253 0.02510147 54.86152106 -1.739267844 0.139141653 GPAGNNDCR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPAGNNDCR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 131.22 0.0026551 264005000 698203 740548 523094 801921 672780 695481 690286 651735 682435 703497 FALSE TRUE 670916.4549 719428.2961 617628.722 843308.2389 694420.5797 709544.1023 698733.9266 638276.4445 604967.8398 655848.5216 1.022974716 1.096942773 0.941724654 1.285827765 1.05881245 1.081871925 1.065389192 0.97320711 0.922420071 1 19.32300311 1.739283847 3.164733062 0.95658272 1.083406072 0.285728385 0.082814815 0.273471124 5.773880582 0.046297469 0.021934778 54.86354254 -1.739283847 0.126823352 LALDMEIHAYR ddPTM_BT-474_Pertuzumab_2h_R1 8 LALDMEIHAYR 11 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 196.88 5.90E-08 5927040000 7706030 8591410 6919870 7681510 7555060 7733160 8136350 7462210 8326980 8788930 FALSE TRUE 7404869.828 8346391.399 8170444.441 8077953.652 7798075.366 7889529.794 8235925.085 7308112.756 7381736.14 8193647.943 0.903732975 1.018641691 0.997168111 0.985880002 0.951722044 0.962883669 1.005159746 0.891924184 0.900909606 1 22.96607448 1.739465463 25 0.921891677 0.976610072 0.18652604 0.040802469 0.173324827 4750.499667 0.017906729 0.009930158 54.88649052 -1.739465463 0.054718394 SKETQEELNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKETQEELNK 10 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ; 132.76 0.00019606 214389000 352730 404930 317370 332570 358110 412880 372900 504430 555890 516590 FALSE TRUE 338944.9216 393381.7929 374725.8189 349733.9776 369628.9334 421228.7165 377463.6617 494013.3442 492787.6977 481600.8992 0.703787975 0.816821135 0.778083719 0.726190458 0.767500505 0.874642712 0.783768598 1.025773301 1.023228359 1 18.87747856 1.739517493 5.014732348 1.019295816 0.780529659 0.855692364 0.044655336 0.060315523 3.617390581 0.023484169 0.012038481 54.8930666 -1.739517493 -0.238766157 RVGMADANS(ph)PPKPLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVGMADANSPPKPLSK 16 2 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 RVGMADANS(1)PPKPLSK 84.919 0.003822 349020000 261090 205730 209470 192090 222870 203120 203480 270720 263170 272910 TRUE FALSE 250886.3141 199862.7818 247325.8886 202003.7879 230038.816 207227.2256 205970.2491 265129.5374 233296.0449 254425.5626 0.986089258 0.785545209 0.97209528 0.793960268 0.904149778 0.814490586 0.809550137 1.042071145 0.916952064 1 17.9568841 1.739558615 21.20514752 0.984534244 0.864149378 0.362991006 0.072657413 0.067059395 1183.008549 0.030801051 0.017070939 54.89826444 -1.739558615 -0.120384866 TS(ph)SPHKEES(ph)PKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 2 T(0.324)S(0.51)S(0.167)PHKEES(1)PKK 95.197 0.0033157 552620000 1335000 755770 849840 545560 847430 646290 916430 1178600 1543200 1124500 TRUE FALSE 1282826.724 734216.1796 1003424.993 573716.417 874688.3556 659358.4266 927645.5445 1154261.498 1368022.406 1048336.613 1.223678261 0.700363004 0.95715916 0.54726355 0.834358301 0.628956786 0.884873744 1.101040909 1.304945748 1 19.9996706 1.73958833 3.263477563 1.164063212 0.803091403 0.363504024 0.18902766 0.209588755 4.715814492 0.102071753 0.048730488 54.90202078 -1.73958833 -0.360971809 TSKPFNPLLGETFELDRLEENGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSKPFNPLLGETFELDRLEENGYR 24 2 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 120.67 7.46E-05 248270000 95662 81184 73614 66581 84246 81827 77388 106200 117960 92620 FALSE TRUE 91923.42328 78868.71181 86917.68733 70017.25339 86955.8491 83481.598 78335.09749 104006.9329 104569.6753 86346.7649 1.064584451 0.913395098 1.006611972 0.810884501 1.007053932 0.966817901 0.907215199 1.204526111 1.211043349 1 16.39785451 1.739595378 9.535854729 1.153271526 0.951339395 0.496233413 0.08480466 0.069580673 27.20733545 0.037938304 0.020501663 54.90291175 -1.739595378 -0.201932131 FVSAIEGMHPNQEDHETFVDINPLTGIILK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVSAIEGMHPNQEDHETFVDINPLTGIILK 30 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PRF6;Q14108-2 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ; 183.25 3.36E-18 642700000 271170 522100 307360 558250 315000 433840 618220 123414 553650 393270 FALSE TRUE 260572.3766 507210.2192 362906.7892 587061.3494 325132.2611 442612.542 625785.9613 120865.4578 490801.9731 366633.4726 0.710716277 1.383425838 0.989835398 1.601221365 0.88680463 1.207234405 1.706843505 0.329662911 1.338672025 1 18.48397898 1.739668452 25 0.835304045 1.212573795 0.133103626 0.369911419 0.274557648 6192.713573 0.159079039 0.088217279 54.91215043 -1.739668452 0.377269751 AFEDEKK ddPTM_BT-474_Pertuzumab_2h_R1 4 AFEDEKK 7 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;; 121.62 0.0070879 6372280000 8762340 6572650 5889200 5163740 6046900 6218750 6759570 7736540 9189550 8005380 FALSE TRUE 8419898.066 6385204.457 6953509.445 5430241.24 6241404.03 6344497.386 6842295.64 7576777.745 8146390.81 7463168.482 1.128193486 0.855562148 0.931710099 0.72760534 0.836294135 0.850107753 0.916808411 1.015222658 1.09154588 1 22.83135682 1.739784483 2.814697996 1.047853132 0.879464713 0.313243325 0.097739861 0.272778775 4.517062612 0.058721767 0.026994128 54.92682341 -1.739784483 -0.168388419 KEEELQAALAR ddPTM_BT-474_Pertuzumab_2h_R1 6 KEEELQAALAR 11 1 P35579;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 P35579;P35749;Q7Z406 MYH9;MYH11;MYH14 Myosin-9;Myosin-11;Myosin-14 0 ;;;;; 215.72 2.02E-11 8500620000 6587910 6326010 5470410 7254790 6332750 6172840 7949610 8249950 9452800 9868880 FALSE TRUE 6330447.194 6145598.389 6459034.776 7629210.581 6536448.655 6297659.054 8046899.705 8079585.65 8379757.773 9200451.967 0.688058284 0.66796701 0.702034509 0.829221283 0.710448647 0.684494531 0.874620044 0.87817269 0.910798492 1 23.1332733 1.73982208 0.719617382 0.995863964 0.701986995 0.797455215 0.050405084 0.287482237 0.296182781 0.048189412 0.023358407 54.93157864 -1.73982208 -0.293876969 NLPFDFTWK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLPFDFTWK 9 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 101.65 0.0089381 396560000 172690 193440 153560 160790 181270 160210 162080 199560 201240 185940 FALSE TRUE 165941.0839 187923.2806 181311.7079 169088.3912 187100.7142 163449.556 164063.5835 195439.0163 178396.0789 173346.1182 0.957281799 1.084092811 1.045951936 0.975438002 1.079347586 0.94290866 0.946450865 1.127449627 1.02913224 1 17.403296 1.739838955 24.99999997 1.063414246 1.008543713 0.114001947 0.057710173 0.363313078 7124.28876 0.026358044 0.014616888 54.93371313 -1.739838955 -0.054870533 INRLDLLITYLNTR ddPTM_BT-474_Pertuzumab_2h_R1 1 INRLDLLITYLNTR 14 1 Q14790-3;Q14790-2;Q14790;Q14790-4;Q14790-9;E7EQ01;E7EVN1;E7ETB7;E7EQ06;A0A0A0MS31;Q14790-6;Q14790-5;Q14790-8;Q14790-7 Q14790-3 CASP8 Caspase-8;Caspase-8 subunit p18;Caspase-8 subunit p10 0 156.17 5.15E-06 122040000 75027 63971 59658 63762 63505 67906 65749 71743 76530 75037 FALSE TRUE 72094.86189 62146.60971 70439.52769 67052.76446 65547.696 69279.10585 66553.65593 70261.48198 67842.63524 69954.67715 1.030593876 0.888383911 1.006930924 0.958517246 0.937002337 0.990342729 0.951382504 1.004385766 0.969808425 1 16.0941329 1.739922824 25 0.99048766 0.964255274 0.083804938 0.037830767 0.49231536 9068.479122 0.015961962 0.008851773 54.94432261 -1.739922824 -0.026232386 SNVVSPT(ph)KNEDNGAPENSVEKPHEKPEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNVVSPTKNEDNGAPENSVEKPHEKPEAR 29 3 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 SNVVS(0.197)PT(0.803)KNEDNGAPENSVEKPHEKPEAR 109.27 0.00020385 167230000 91780 69113 81680 51500 72918 77565 82053 102110 124500 111950 TRUE FALSE 88193.13613 67141.96491 96441.39296 54157.92117 75263.47369 79133.41744 83057.18916 100001.3928 110367.2819 104367.5268 0.845024682 0.643322372 0.924055556 0.518915441 0.721138806 0.758218767 0.795814481 0.958165781 1.0574868 1 16.67131337 1.740028278 1.944704386 1.032178145 0.728520449 0.585498292 0.102877377 0.206021008 1.57474916 0.068799509 0.028352117 54.95766572 -1.740028278 -0.303657696 MAKPEEVLVVENDQGEVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MAKPEEVLVVENDQGEVVR 19 1 O14980 O14980 XPO1 Exportin-1 0 134.07 9.53E-06 103390000 185520 169270 171750 178830 173540 161960 169260 207990 225840 189180 FALSE TRUE 178269.6733 164442.5853 202789.0456 188059.4377 179122.0717 165234.9422 171331.4545 203694.9338 200203.59 176366.6701 1.010790039 0.932390373 1.149815016 1.066298057 1.015623142 0.936883041 0.9714503 1.154951407 1.135155468 1 17.42821842 1.740038971 24.99987475 1.108856653 1.013490742 0.225604425 0.07089732 0.313383555 5324.319539 0.033846009 0.018769308 54.95901888 -1.740038971 -0.095365912 LQGPPT(ph)PAGK ddPTM_BT-474_Pertuzumab_2h_R1 5 LQGPPTPAGK 10 0 P78411-3;P78411-2;P78411 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 LQGPPT(1)PAGK;LQGPPT(1)PAGK;LQGPPT(1)PAGK;LQGPPT(1)PAGK;LQGPPT(1)PAGK 129.54 0.0033588 3875360000 5494100 5244420 4711430 4760260 4974490 5192580 4885140 5796530 5759750 5816110 TRUE FALSE 5279384.498 5094854.276 5562890.206 5005937.589 5134498.989 5297577.525 4944925.805 5676829.63 5105927.327 5422179.689 0.973664615 0.939632135 1.025950914 0.923233437 0.946943717 0.977019912 0.911981175 1.046964497 0.941674312 1 22.37044149 1.740048092 24.99999961 0.999235175 0.958001737 0.180071199 0.038213197 0.356923934 6027.228102 0.016556077 0.009181227 54.96017311 -1.740048092 -0.041233437 TIDDLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIDDLEEK 8 0 P67936;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ; 176.09 0.00061035 769520000 1108110 950810 831050 830600 955130 1019200 925860 1165990 1231470 1150540 FALSE TRUE 1064803.836 923693.8297 981239.2216 873467.3655 985852.6239 1039808.922 937190.9516 1141911.899 1091678.688 1072612.901 0.992719587 0.861162334 0.914812064 0.814336062 0.919113152 0.969416759 0.873745739 1.064607649 1.017775087 1 20.03269808 1.740094322 10.14768984 1.029383854 0.904422855 0.545500404 0.050544992 0.065695899 32.61539065 0.02342066 0.012709183 54.96602382 -1.740094322 -0.124960999 AEIIHHLADLLTDQRDEILLANKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEIIHHLADLLTDQRDEILLANKK 24 2 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 176.46 1.17E-13 63453000 238180 347590 209240 388190 209600 288610 375560 120840 326560 226720 FALSE TRUE 228871.6623 337677.0735 247054.3225 408224.5324 216341.9744 294445.8919 380156.2156 118344.6118 289490.2779 211364.0525 1.082831539 1.597608816 1.168856859 1.931381082 1.023551412 1.393074596 1.798585006 0.559908889 1.369628726 1 17.68937051 1.740144048 25 0.9527556 1.427008284 0.279148216 0.331803924 0.285013878 4523.754052 0.142136828 0.078822089 54.97231779 -1.740144048 0.474252684 SRNTDEMVELR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRNTDEMVELR 11 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 203.61 3.29E-08 1712650000 1285370 1586270 739290 1033520 937930 1360560 1031840 1484970 1352530 1399300 FALSE TRUE 1235136.319 1541031.133 872896.1484 1086860.091 968099.3703 1388071.455 1044467.967 1454304.851 1198996.465 1304524.165 0.946809843 1.181297499 0.669129919 0.833146768 0.742109189 1.064044265 0.800650532 1.114816337 0.919106366 1 20.31509224 1.740157879 24.99999997 1.017438333 0.892356722 0.121044772 0.148224377 0.527458493 8299.88389 0.068726552 0.038112282 54.97406842 -1.740157879 -0.125081611 RGS(ph)LTLTISGESPK ddPTM_BT-474_Pertuzumab_2h_R1 5 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.994)LT(0.006)LTISGESPK;RGS(0.996)LT(0.003)LTISGESPK;RGS(0.768)LT(0.116)LT(0.116)ISGESPK;RGS(0.996)LT(0.004)LTISGESPK;RGS(0.951)LT(0.049)LTISGESPK 239.7 2.41E-17 2710730000 4221930 3811460 3320960 3097850 3717480 3704010 3831940 4640710 5193180 5091270 TRUE FALSE 4056932.308 3702760.893 3921131.346 3257730.41 3837056.12 3778907.62 3878836.428 4544877.717 4603671.978 4746433.748 0.854732737 0.780114311 0.82612158 0.686353288 0.808408233 0.796157246 0.817210696 0.957535269 0.969922308 1 22.17841252 1.740169881 2.461861766 0.98487909 0.788683225 0.80060136 0.041507853 0.108830414 1.367453733 0.025955888 0.011477577 54.97558773 -1.740169881 -0.196195865 SKT(ph)PVDDPMSLLYNMNDCYSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKTPVDDPMSLLYNMNDCYSK 21 1 Q02363 Q02363 ID2 DNA-binding protein inhibitor ID-2 1 S(0.489)KT(0.511)PVDDPMSLLYNMNDCYSK 161.91 3.12E-11 110680000 176860 141850 118000 101620 149240 123570 115600 192240 191590 144330 TRUE FALSE 169948.1157 137804.5769 139325.2249 106864.6204 154040.4401 126068.6701 117014.7474 188270.1768 169841.5064 134554.4005 1.263043906 1.02415511 1.035456472 0.794211263 1.144819044 0.936934575 0.86964638 1.399212334 1.262251593 1 17.03783005 1.740210979 25 1.251822919 1.005398587 0.273095952 0.154931516 0.279428895 4256.468208 0.069223897 0.038388209 54.98079044 -1.740210979 -0.246424332 EVADVLVDGYNVHYGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVADVLVDGYNVHYGAR 17 0 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2U3TZY2 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 ; 222.64 3.30E-15 1174760000 1054640 1208310 1163390 1581410 1148560 1301950 1325330 1076660 1163880 1349460 FALSE TRUE 1013423.503 1173850.182 1373640.452 1663026.76 1185504.475 1328276.321 1341549.785 1054426.595 1031761.222 1258059.872 0.805544732 0.933063845 1.091872082 1.321897945 0.942327549 1.055813281 1.066364022 0.838137054 0.820120922 1 20.26276915 1.740248364 8.83645625 0.873955281 1.038292516 0.194295241 0.133799573 0.16197276 48.86494761 0.066771995 0.035897677 54.98552343 -1.740248364 0.164337235 NSNS(ph)PPS(ph)PSSMNQR ddPTM_BT-474_Pertuzumab_2h_R1 3 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 2 NS(0.001)NS(0.999)PPS(0.99)PS(0.009)S(0.001)MNQR;NS(0.002)NS(0.998)PPS(0.962)PS(0.034)S(0.003)MNQR;NSNS(1)PPS(1)PSSMNQR 311.58 1.42E-55 524791000 408904 434401 348997 388840 377756 383325 388515 436578 458690 449833 TRUE FALSE 392923.5796 422012.3088 412068.5213 408908.079 389906.8648 391076.0941 393269.7628 427562.5117 406621.4342 419365.4102 0.936947993 1.006311676 0.982600165 0.975063916 0.92975447 0.932542562 0.937773486 1.019546442 0.969611285 1 18.67784835 1.740348989 25 0.99657086 0.958817437 0.319348637 0.026091896 0.371837836 5229.1133 0.012926041 0.007168161 54.99826492 -1.740348989 -0.037753423 ADEIEMIMTDLER ddPTM_BT-474_Pertuzumab_2h_R1 3 ADEIEMIMTDLER 13 0 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3;P39880-9;Q13948-9;Q13948-10;Q13948-2;Q13948 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1;Protein CASP 0 ;; 174.1 4.78E-05 40143200 52784.7 54480.5 44510.3 51472.3 54045.3 51302.2 47853.3 63997 60353.8 61782.3 FALSE TRUE 50721.81557 52926.76948 52554.30134 54128.79157 55783.71616 52339.56563 48438.943 62675.43959 53502.68965 57597.72979 0.880621784 0.918903743 0.912437027 0.939773004 0.968505466 0.90870883 0.840987018 1.088158159 0.928902751 1 15.81372433 1.740373709 24.99999978 1.010395892 0.913774028 0.454101194 0.047873208 0.24343496 3376.89968 0.021333061 0.01183036 55.00139556 -1.740373709 -0.096621864 VQAMQISS(ph)EKEEDDNEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 1 VQAMQIS(0.208)S(0.792)EKEEDDNEKR 135.64 4.16E-06 307220000 288690 268710 260590 264740 293420 229440 258170 334190 364330 294810 TRUE FALSE 277407.6756 261046.6539 307684.4098 278403.2631 302858.1208 234079.434 261329.5617 327288.8597 322972.7858 274842.2561 1.009334152 0.949805381 1.119494557 1.012956548 1.101934342 0.851686481 0.950834727 1.190824382 1.17512056 1 18.06824431 1.74039194 13.82019805 1.136374771 1.000926651 0.291896994 0.086569331 0.079124686 153.8192359 0.040457625 0.022271506 55.00370444 -1.74039194 -0.135448119 IDGATQSS(ph)PAEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDGATQSSPAEPK 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 IDGATQS(0.183)S(0.817)PAEPK;IDGATQS(0.013)S(0.987)PAEPK 305.2 2.46E-41 3252900000 3483400 3120900 3309800 3072500 3142900 3818900 4064400 4194900 5317700 5311400 TRUE FALSE 3347264.877 3031894.988 3907954.486 3231072.093 3243994.233 3896120.775 4114141.343 4108273.849 4714056.99 4951654.147 0.675989231 0.612299425 0.78922202 0.652523782 0.655133444 0.786832169 0.830862015 0.829677059 0.952016609 1 22.23947912 1.740407568 0.657774665 1.003097542 0.667856359 0.836595103 0.050153645 0.261456354 0.232701768 0.046520367 0.024223557 55.00568381 -1.740407568 -0.335241182 AEEKENDTVTIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEEKENDTVTISPK 14 1 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 AEEKENDT(0.006)VT(0.02)IS(0.974)PK 71.742 0.024569 116440000 153220 122820 104020 83933 127290 123920 119140 163550 190060 146960 TRUE FALSE 147231.993 119317.2939 122818.7279 88264.79219 131384.3985 126425.7473 120598.071 160172.6353 168485.1856 137006.2683 1.074636911 0.870889306 0.896446049 0.64423908 0.958966331 0.922773453 0.880237616 1.169089833 1.229762606 1 17.06388238 1.740416695 6.174544538 1.148067363 0.885697285 0.478722876 0.114258902 0.115870359 11.92613276 0.056475839 0.029534571 55.00683974 -1.740416695 -0.262370078 GTVIVQPEPVLNEDKDDFKGPEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTVIVQPEPVLNEDKDDFKGPEFR 24 2 P46100;A0A096LNW1;A0A096LNN3;A0A087WWG0;A0A096LNL6;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 0 ; 104.53 0.0017066 199934000 222363 194670 162926 154953 193164 186053 193007 229770 268580 233309 FALSE TRUE 213672.8081 189118.2022 192370.3525 162950.1429 199377.2955 189815.1191 195369.0774 225025.1692 238091.9244 217506.7736 0.982373121 0.869481897 0.884433847 0.749172728 0.916648673 0.872686013 0.898220658 1.03456626 1.094641424 1 17.7307008 1.74052371 3.374826485 1.053529277 0.875362805 0.618321846 0.058150029 0.133520534 3.217942904 0.032432693 0.015617731 55.02039575 -1.74052371 -0.178166472 AEVAAEFLNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEVAAEFLNDR 11 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 90.05 0.015936 0 56692 62259 55411 56900 57700 55768 64559 52585 68272 65051 FALSE TRUE 54476.41396 60483.43428 65425.00031 59836.61582 59555.9729 56895.66717 65349.09235 51499.10137 60522.04878 60645.03783 0.898283123 0.997335255 1.078818691 0.98666961 0.982041978 0.938175145 1.077567014 0.849189039 0.997971985 1 15.88810198 1.740540542 24.99999999 0.935408073 0.994605309 0.080760318 0.064950149 0.593884153 7545.812703 0.028927242 0.016041664 55.02252825 -1.740540542 0.059197236 AELAESRCR ddPTM_BT-474_Pertuzumab_2h_R1 1 AELAESRCR 9 1 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 60.019 0.089805 202220000 63066 128520 105190 159140 133790 127440 106710 52100 24589 49739 FALSE TRUE 60601.311 124854.7354 124200.1729 167353.2345 138093.4769 130016.9241 108015.9489 51024.11679 21797.75981 46370.13323 1.306903966 2.692567969 2.678451932 3.609073833 2.978069444 2.803893693 2.329429341 1.100365974 0.470081889 1 15.50090825 1.740543076 2.549025049 0.725645983 2.730223104 0.689978008 0.550551858 0.143399675 1.934947758 0.353920916 0.158208815 55.02284923 -1.740543076 2.004577121 HYDDFFER ddPTM_BT-474_Pertuzumab_2h_R1 2 HYDDFFER 8 0 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 ; 184.49 0.00021773 628400000 109097 118422 106660 131274 120758 102812 131027 88493 114400 125777 FALSE TRUE 104833.3686 115044.7205 125935.8346 138049.0669 124642.2907 104890.9291 132630.5476 86665.58863 101413.7916 117258.0118 0.894040135 0.981124605 1.074006226 1.177310316 1.062974622 0.894531022 1.13110009 0.739101639 0.864877291 1 16.83932697 1.740563211 25 0.848599768 1.032123759 0.33248612 0.104574366 0.324448751 4075.818112 0.048376282 0.02682717 55.02540031 -1.740563211 0.183523991 QKLEAQLTENNIVKEELALLDGSNVVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 QKLEAQLTENNIVKEELALLDGSNVVFK 28 2 O15212;A2AB88 O15212 PFDN6 Prefoldin subunit 6 0 ; 175.11 5.54E-13 278530000 462430 399640 298660 299220 340060 402070 374730 428370 506260 460930 FALSE TRUE 444357.7244 388242.6585 352634.5057 314662.7801 350998.3387 410200.1309 379316.0578 419524.0098 448791.4872 429710.8005 1.034085538 0.903497557 0.820632168 0.732266398 0.816824567 0.954595813 0.882724049 0.976293845 1.044403554 1 18.71300651 1.740625532 1.410188373 1.02580689 0.863268635 0.368825882 0.078068937 0.445944917 1.695885939 0.066901561 0.026041169 55.03329706 -1.740625532 -0.162538254 VGPGNHGTEGSGGERHS(ph)DTDSDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGPGNHGTEGSGGERHSDTDSDRR 24 2 Q99442 Q99442 SEC62 Translocation protein SEC62 1 VGPGNHGTEGS(0.002)GGERHS(0.998)DTDSDRR;VGPGNHGTEGSGGERHS(0.999)DT(0.001)DSDRR 208.88 2.80E-25 564980000 92695 177739 89706 221328 111265 116651 170421 74527 160214 102183 TRUE FALSE 89072.37692 172670.0577 105917.8697 232750.7646 114843.9398 119009.7631 172506.6632 72987.99141 142027.1784 95262.05439 0.935024732 1.812579614 1.11185792 2.443268373 1.205558084 1.249288228 1.810864402 0.766181161 1.490910303 1 16.53961404 1.740630269 25 1.082572518 1.520304739 0.160087183 0.444665031 0.565279853 6871.387665 0.19378017 0.107460973 55.03389735 -1.740630269 0.437732221 TPQS(ph)PAPCVLLR ddPTM_BT-474_Pertuzumab_2h_R1 4 TPQSPAPCVLLR 12 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 TPQS(1)PAPCVLLR;TPQS(1)PAPCVLLR;TPQS(1)PAPCVLLR;T(0.016)PQS(0.984)PAPCVLLR 139.7 6.19E-05 1965000000 786340 881360 845270 1021440 1053420 1005620 814620 807510 691610 749660 TRUE FALSE 755608.9635 856224.4757 998029.0919 1074156.641 1087304.211 1025954.325 824589.5632 790834.6363 613101.3323 698884.8605 1.081163731 1.225129523 1.428030779 1.536957948 1.55577016 1.467987623 1.179864681 1.131566415 0.877256565 1 19.41469527 1.740638608 1.802871966 0.95441097 1.387997591 0.58574859 0.144569781 0.251442647 1.631264047 0.115477229 0.046690573 55.03495406 -1.740638608 0.433586621 GTWESHPETTELVVLQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTWESHPETTELVVLQGR 18 0 P36915;A0A140T8Y2;P36915-2 P36915 GNL1 Guanine nucleotide-binding protein-like 1 0 ; 146.88 8.06E-08 684900000 399180 460480 380280 451190 446550 442460 456070 392110 443790 458320 FALSE TRUE 383579.6043 447347.5613 449005.0553 474475.97 460913.6863 451406.8444 461651.5211 384012.7915 393412.8197 427277.5782 0.897729307 1.046971768 1.050850965 1.110463067 1.078721913 1.05647211 1.08044874 0.898743138 0.920742955 1 18.70481409 1.740678396 10.5909237 0.933647795 1.050317452 0.40405429 0.058717968 0.080749763 47.7917919 0.027850998 0.015153533 55.03999629 -1.740678396 0.116669657 VETGVLKPGMVVTFAPVNVTTEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VETGVLKPGMVVTFAPVNVTTEVK 24 1 P68104;A0A087WVQ9;Q5VTE0 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ; 284.43 1.58E-52 1429550000 1485710 1165930 1164600 1111420 1299980 1336720 1468890 1564450 1902150 1876300 FALSE TRUE 1427646.811 1132678.818 1375069.126 1168780.519 1341795.037 1363749.394 1486866.715 1532143.561 1686225.906 1749216.53 0.816163572 0.647534938 0.786105724 0.668173722 0.767083442 0.779634408 0.850018674 0.875902745 0.963989236 1 20.73827746 1.740694583 0.820634067 1.001031537 0.726042053 0.795025909 0.048623076 0.227457218 0.293814322 0.039536933 0.017590137 55.04204778 -1.740694583 -0.274989484 AT(ph)PPPSPLLSELLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATPPPSPLLSELLK 14 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128 BRD8 Bromodomain-containing protein 8 1 AT(1)PPPSPLLSELLK;AT(0.999)PPPS(0.001)PLLSELLK 96.734 0.036375 568690000 405778 409694 316120 327800 370209 355605 353816 429425 457796 403564 TRUE FALSE 389919.7471 398009.9283 373249.9161 344717.7973 382117.1087 362795.5767 358146.106 420557.2237 405828.9173 376230.2508 1.036385953 1.057889224 0.992078429 0.916241574 1.015646955 0.964291351 0.951933305 1.117818737 1.078671682 1 18.52125633 1.74070505 25 1.07422395 0.990367157 0.339991257 0.0473288 0.356480748 4182.255886 0.022497191 0.012475829 55.04337438 -1.74070505 -0.083856793 SLGTADVHFER ddPTM_BT-474_Pertuzumab_2h_R1 8 SLGTADVHFER 11 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ;;;;;;; 228.06 3.54E-12 23399600000 10450860 10629880 9643420 9472790 10600730 9568720 9268810 9548440 8942640 8701250 FALSE TRUE 10042428.84 10326726.23 11386200.51 9961681.827 10941712.11 9762206.074 9382244.469 9351261.377 7927508.998 8111906.587 1.237986253 1.273033179 1.403640487 1.228032118 1.348845921 1.203441629 1.156601641 1.152782182 0.97726828 1 22.95160961 1.740723869 0.894526803 0.983983593 1.300373438 0.792711065 0.058463133 0.234668867 0.354608004 0.050113778 0.021323708 55.04575955 -1.740723869 0.316389845 SGT(ph)PTQDEMMDKPTSSSVDTMSLLSK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGTPTQDEMMDKPTSSSVDTMSLLSK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.125)GT(0.743)PT(0.125)QDEMMDKPT(0.002)S(0.003)S(0.001)SVDTMSLLSK;S(0.205)GT(0.757)PT(0.038)QDEMMDKPTSSSVDTMSLLSK;S(0.001)GT(0.999)PTQDEMMDKPTSSSVDTMSLLSK 301.3 1.91E-70 2653710000 1687040 1260291 1298938 947213 1222002 1102537 1368227 1671921 2085151 1683244 TRUE FALSE 1621108.612 1224348.735 1533684.991 996098.7764 1261308.804 1124831.054 1384971.771 1637395.247 1848453.4 1569236.385 1.033055713 0.780219441 0.977344781 0.634766557 0.803772342 0.716801538 0.882576892 1.043434414 1.177931775 1 20.58163126 1.740739869 3.062558854 1.09359979 0.819065907 0.481731714 0.115875683 0.180774677 3.555322215 0.065298193 0.030729306 55.04778759 -1.740739869 -0.274533883 FNLLAHLADDLGHVVPNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 FNLLAHLADDLGHVVPNSR 19 0 Q8N5N7;Q8N5N7-2 Q8N5N7 MRPL50 "39S ribosomal protein L50, mitochondrial" 0 139.11 3.47E-07 88733000 58034 77939 43209 104760 52771 61885 81086 35243 68100 53158 FALSE TRUE 55765.96712 75716.25603 51017.82748 110166.6762 54468.42714 63136.3571 82078.35472 34515.21973 60369.5735 49557.56131 1.125276661 1.527844672 1.029466062 2.223004386 1.099094179 1.274000484 1.656222634 0.696467276 1.218170788 1 15.59681757 1.740869339 25 0.961636769 1.421467616 0.257397961 0.348360318 0.479868333 5229.143333 0.152795908 0.084733068 55.06420063 -1.740869339 0.459830847 TTPPESAPQNGPSPMAALMSVADTLGTAHS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 TTPPESAPQNGPSPMAALMSVADT(0.074)LGT(0.213)AHS(0.714)PK;TTPPESAPQNGPSPMAALMSVADT(0.005)LGT(0.048)AHS(0.947)PK 280.31 7.72E-74 775320000 512120 395490 382830 378220 440180 400460 435390 499910 598450 488130 TRUE FALSE 492105.7842 384211.0124 452015.897 397739.9795 454338.7895 408557.5756 440718.4331 489586.6838 530516.4649 455068.5203 1.081388323 0.844292662 0.993291948 0.874022179 0.998396437 0.897793535 0.968466096 1.075852673 1.165794691 1 18.79572426 1.740902519 3.63716094 1.093889605 0.943944976 0.387623609 0.074426057 0.176284707 4.983780336 0.037034219 0.018124483 55.06840771 -1.740902519 -0.149944629 AASLTEDRDR ddPTM_BT-474_Pertuzumab_2h_R1 3 AASLTEDRDR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;; 201.61 2.18E-07 4650100000 2383520 2625430 2070600 2478910 2348400 2420300 2604940 2057760 2399030 2715120 FALSE TRUE 2290369.403 2550555.307 2444803.48 2606846.842 2423938.419 2469240.124 2636820.035 2015266.537 2126702.172 2531222.504 0.904847124 1.007637734 0.96585878 1.029876606 0.957615703 0.975512868 1.041717996 0.79616333 0.840187762 1 21.2714029 1.741023164 25 0.862405788 0.98406562 0.373162583 0.060968659 0.334547462 3417.610999 0.026188113 0.014522617 55.08370756 -1.741023164 0.121659831 SLGNILQAKPTS(ph)SPAKGPPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGNILQAKPTSSPAKGPPQK 21 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SLGNILQAKPT(0.021)S(0.674)S(0.305)PAKGPPQK 146.5 8.53E-08 1237200000 1012100 812870 569530 476730 631720 666830 696930 808620 877890 869460 TRUE FALSE 972546.0131 789687.7435 672456.7401 501334.0924 652039.8475 680313.7595 705459.2378 791921.7144 778235.6076 810570.6998 1.19982873 0.974236724 0.829608991 0.618495207 0.804420697 0.839302185 0.870324128 0.976992771 0.96010824 1 19.6285785 1.741075468 4.609548733 0.977395554 0.863880811 0.098422406 0.138353021 0.443926198 21.58524448 0.078155562 0.039749046 55.09034192 -1.741075468 -0.113514743 RLS(ph)SASTGKPPLSVEDDFEK ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 RLS(0.989)S(0.011)ASTGKPPLSVEDDFEK;RLS(0.492)S(0.492)AS(0.013)T(0.003)GKPPLSVEDDFEK;RLS(0.942)S(0.046)AS(0.005)T(0.007)GKPPLSVEDDFEK;RLS(0.982)S(0.018)ASTGKPPLSVEDDFEK 258.09 1.59E-36 2229370000 1227575 1225512 972534 960336 1206219 1072198 1009811 1410116 1294323 1326982 TRUE FALSE 1179600.012 1190561.598 1148292.528 1009899.056 1245018.13 1093878.578 1022169.369 1380996.612 1147396.879 1237104.327 0.953517004 0.962377684 0.928209935 0.816341059 1.006397037 0.884225004 0.826259634 1.116313783 0.927485948 1 20.23853574 1.741134781 25 1.021903677 0.912673664 0.313025505 0.070020393 0.468053439 4573.796731 0.031265785 0.017338459 55.09786637 -1.741134781 -0.109230013 SQSDLDDQHDYDS(ph)VAS(ph)DEDTDQEPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 SQSDLDDQHDYDS(1)VAS(1)DEDTDQEPLR;SQSDLDDQHDYDS(1)VAS(1)DEDTDQEPLR 261.25 4.29E-53 1214900000 715820 777410 676760 825000 818620 801900 833380 685300 812210 838660 TRUE FALSE 687844.963 755239.028 799065.5864 867578.3489 844951.6558 818114.9674 843579.1537 671148.3155 720011.3259 781856.8112 0.879758228 0.96595568 1.022010137 1.10963841 1.080698721 1.04637442 1.078943282 0.858403106 0.920899218 1 19.57654489 1.741311869 25 0.916488773 1.02980063 0.29649589 0.069764961 0.532079703 4864.113481 0.034143604 0.018934314 55.12033762 -1.741311869 0.113311856 AMTLS(ph)PQEEVAAGQMASSSR ddPTM_BT-474_Pertuzumab_2h_R1 6 AMTLSPQEEVAAGQMASSSR 20 0 Q9Y6A5;A0A494BZT8 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 AMTLS(1)PQEEVAAGQMASSSR;AMTLS(1)PQEEVAAGQMASSSR;AMTLS(1)PQEEVAAGQMASSSR;AMTLS(1)PQEEVAAGQMASSSR;AMT(0.002)LS(0.998)PQEEVAAGQMASSSR;AMTLS(1)PQEEVAAGQMASSSR 449.72 7.01E-198 2834120000 663577 699680 652291 698084 693648 791879 700074 634868 642709 713543 TRUE FALSE 637643.6772 679725.8115 770174.4938 734112.1989 715959.8179 807891.3359 708641.715 621757.7539 569751.3688 665214.0971 0.958554066 1.021815104 1.157784384 1.103572823 1.076284795 1.214483186 1.065283671 0.934673148 0.856493227 1 19.34345922 1.741315289 4.033094797 0.918985935 1.092313555 0.487073646 0.072909032 0.158226862 5.621761289 0.040004449 0.019958929 55.12077167 -1.741315289 0.17332762 SDKTEEIAEEEETVFPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDKTEEIAEEEETVFPK 17 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;; 178.88 8.64E-10 539781000 1604330 1183530 1162913 973333 1196330 1169410 1223779 1538660 1667600 1593800 FALSE TRUE 1541631.01 1149776.883 1373077.248 1023566.833 1234811.041 1193056.271 1238755.973 1506886.133 1478301.039 1485850.506 1.037541128 0.773817338 0.924101881 0.688876053 0.83104662 0.802945025 0.833701619 1.014157297 0.994919094 1 20.50285754 1.741332299 5.901354354 1.00275617 0.834188713 0.417291011 0.086910796 0.137336522 12.52039128 0.041455406 0.021622181 55.12293058 -1.741332299 -0.168567457 REDEGEPGDEGQLEDEGS(ph)QEK ddPTM_BT-474_Pertuzumab_2h_R1 1 REDEGEPGDEGQLEDEGSQEK 21 1 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 REDEGEPGDEGQLEDEGS(1)QEK 247.78 1.22E-30 389540000 259450 231850 206470 207680 212160 214200 205700 285950 292780 243100 TRUE FALSE 249310.4072 225237.865 243783.7219 218398.3897 218984.3191 218531.2708 208217.4181 280045.0326 259544.8418 226634.6205 1.100054381 0.993836972 1.075668498 0.96365855 0.966243898 0.964244873 0.918736148 1.23566749 1.145212683 1 17.79000874 1.74143707 25 1.14556142 0.996575935 0.381453375 0.074421911 0.41743032 3649.52269 0.033441363 0.018545005 55.13623036 -1.74143707 -0.148985485 ALNFGGIGVVVGHELTHAFDDQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALNFGGIGVVVGHELTHAFDDQGR 24 0 B4DKB2;A0A3B3ISF9;P42892-3;P42892-4;P42892;P42892-2 B4DKB2 ECE1 Endothelin-converting enzyme 1 0 178.39 2.33E-17 56027000 28347 40084 22845 44997 32105 31495 44296 10471 33417 25921 FALSE TRUE 27239.1679 38940.84357 26973.59968 47319.30056 33137.68648 32131.85048 44838.1077 10254.77019 29623.64226 24165.34758 1.127199508 1.611433208 1.116209878 1.958146904 1.371289462 1.32966639 1.855471251 0.424358481 1.225872798 1 14.56065213 1.741464742 25 0.851459521 1.480578816 0.422330951 0.319806823 0.408696551 3539.029654 0.136717334 0.075816733 55.13974357 -1.741464742 0.629119294 HTGMASIDSSAPETTSDSS(ph)PTLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTGMASIDSSAPETTSDSSPTLSR 24 0 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2;S4R3B3;H7C453;S4R3U7 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 HTGMASIDSSAPETTSDS(0.008)S(0.991)PT(0.001)LSR 259.71 3.56E-44 522400000 168510 193870 144820 227380 224030 180540 219240 135110 183100 204870 TRUE FALSE 161924.4429 188341.0174 170992.1955 239115.109 231236.1284 184190.6425 221923.1247 132319.9313 162315.2556 190993.9724 0.847798707 0.986109745 0.89527535 1.251951075 1.210698565 0.964379347 1.161937845 0.692796373 0.849844912 1 17.54316758 1.741468388 25 0.824792618 1.048572207 0.283222789 0.142845334 0.566665921 4900.767701 0.067329026 0.037337322 55.14020647 -1.741468388 0.22377959 LQNAHTGLDLTVPQHQEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQNAHTGLDLTVPQHQEVR 19 0 Q53T59;F6TR53;B5MC96;A0A494C0K6 Q53T59 HS1BP3 HCLS1-binding protein 3 0 58.997 0.042968 439080000 50944 57129 54515 49387 47037 55719 57125 45909 54843 57191 FALSE TRUE 48953.05216 55499.73686 64367.07318 51935.86899 48549.98782 56845.67636 57824.11284 44960.96311 48617.45256 53317.40263 0.918143978 1.040930993 1.207243227 0.974088504 0.910584264 1.066174899 1.084526064 0.843269944 0.911849606 1 15.70231888 1.741485279 25 0.907242464 1.030926944 0.243195948 0.088573947 0.644171658 5538.808938 0.042017189 0.023300578 55.14235111 -1.741485279 0.12368448 SSTAISSIAADGEFLHELEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTAISSIAADGEFLHELEEK 21 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 218.88 5.27E-25 134716000 175862 159426 144489 151107 162455 171262 168982 192854 232450 204985 FALSE TRUE 168989.1186 154879.3266 170601.3764 158905.6504 167680.5126 174725.035 171050.0523 188871.4975 206063.2505 191101.1834 0.884291325 0.810457182 0.892727996 0.83152625 0.877443612 0.9143064 0.89507584 0.988332433 1.078293953 1 17.54397719 1.741517331 1.569746568 1.042831713 0.863087466 0.813791494 0.033525766 0.140286297 0.673054967 0.024781197 0.009757243 55.14642085 -1.741517331 -0.179744247 TKEQILEEFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKEQILEEFSK 11 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 191.06 1.82E-06 3663000000 6000000 5280800 4622400 3953200 4938100 4921600 5027200 5901000 6708000 5808800 FALSE TRUE 5765513.367 5130196.754 5457770.505 4157225.126 5096938.471 5021118.124 5088724.377 5779142.288 5946535.962 5415364.802 1.064658352 0.947340935 1.007830627 0.767672221 0.941199468 0.9271985 0.939682655 1.067175066 1.098085942 1 22.3686271 1.741520676 5.522885821 1.061773625 0.937302675 0.322527615 0.07444308 0.177288447 13.56583591 0.037794318 0.019605495 55.14684564 -1.741520676 -0.12447095 SS(ph)SPVTELASRS(ph)PIRQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.278)S(0.361)S(0.361)PVTELAS(0.088)RS(0.912)PIRQDR 158.05 2.49E-11 964350000 157370 187810 108170 102420 137100 173010 133530 109120 109030 105230 TRUE FALSE 151219.8064 182453.8427 127718.7252 107705.9085 141509.946 176508.3807 135164.1801 106866.6339 96653.37149 98102.67837 1.541444219 1.859825294 1.30188826 1.097889581 1.442467712 1.799220813 1.377782771 1.089334518 0.985226633 1 16.5820049 1.741535026 3.090042343 1.007600428 1.497490831 0.5200884 0.207488651 0.202017667 4.040974988 0.13044588 0.061574983 55.14866787 -1.741535026 0.489890403 FAALDNEEEDKEEEIIK ddPTM_BT-474_Pertuzumab_2h_R1 2 FAALDNEEEDKEEEIIK 17 1 Q5STZ8;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ; 171.46 1.57E-09 268680000 427460 294960 332830 280180 350580 327580 366550 488600 578760 524610 FALSE TRUE 410754.3906 286548.0296 392979.7848 294640.1234 361856.7241 334203.892 371035.9485 478510.2393 513061.5912 489077.6974 0.839855084 0.585894698 0.803511971 0.602440318 0.739875742 0.683334967 0.75864418 0.978393089 1.049039026 1 18.89970415 1.741595635 2.80992589 1.025217051 0.704654297 0.766745248 0.07467765 0.098390141 1.618738657 0.040183683 0.018496156 55.15636471 -1.741595635 -0.320562754 GSVIS(ph)PTELEAPILVPHTAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSVISPTELEAPILVPHTAQR 21 0 Q8N1B4-2;Q8N1B4 Q8N1B4-2 VPS52 Vacuolar protein sorting-associated protein 52 homolog 1 GS(0.03)VIS(0.933)PT(0.038)ELEAPILVPHTAQR;GS(0.059)VIS(0.899)PT(0.042)ELEAPILVPHTAQR 239.51 4.05E-30 264120000 91564 127735 106628 121378 106644 130876 118438 93545 103071 106988 TRUE FALSE 87985.57765 124092.1229 125898.0515 127642.3331 110074.3011 133522.4024 119887.4797 91613.26306 91370.81219 99741.60746 0.882135148 1.244135983 1.262242055 1.279730058 1.103594617 1.338683081 1.201980625 0.918505981 0.916075192 1 16.60590783 1.7416447 6.249424675 0.939593756 1.199041443 0.454798499 0.12106991 0.121759464 12.96800668 0.058816244 0.030829381 55.16259642 -1.7416447 0.259447687 DENKVDGMNAPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DENKVDGMNAPK 12 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 116.19 0.00020952 0 677440 606560 494930 478860 576460 601420 606020 740930 875610 788960 FALSE TRUE 650964.8959 589261.5027 584374.8607 503574.022 595002.3594 613581.1245 613436.654 725629.5366 776214.4237 735523.0365 0.88503672 0.801146223 0.794502458 0.684647519 0.808951358 0.834210615 0.834014196 0.986549028 1.055323063 1 19.488411 1.741681854 2.152416108 1.032413381 0.795848852 0.796447918 0.048619251 0.124886971 1.183570642 0.033953081 0.014432093 55.16731586 -1.741681854 -0.236564529 LKEEEEDKK ddPTM_BT-474_Pertuzumab_2h_R1 4 LKEEEEDKK 9 2 P27797 P27797 CALR Calreticulin 0 ;;; 125.22 0.0002856 3877110000 5501450 4882010 3953070 3185510 4859220 4432670 5014090 6707660 8838200 6568130 FALSE TRUE 5286447.252 4742779.855 4667477.685 3349914.553 5015521.224 4522301.624 5075453.933 6569144.477 7834924.589 6123264.705 0.863338024 0.774550846 0.76225313 0.54707982 0.819092668 0.738544199 0.828880373 1.072817328 1.279533871 1 22.54586962 1.741701268 2.702694767 1.151072406 0.747989879 0.730053418 0.100255396 0.117812975 1.789589046 0.059649186 0.027157418 55.169782 -1.741701268 -0.403082527 RKAS(ph)PEPPDSAEGALK ddPTM_BT-474_Pertuzumab_2h_R1 4 RKASPEPPDSAEGALK 16 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RKAS(0.998)PEPPDS(0.002)AEGALK;RKAS(0.993)PEPPDS(0.007)AEGALK;RKAS(1)PEPPDSAEGALK;RKAS(1)PEPPDSAEGALK 171.47 2.56E-09 3092050000 6982830 6239330 5032870 4625370 5776270 5835680 5602060 6698730 7291210 6200730 TRUE FALSE 6709933.284 6061390.417 5942421.565 4864085.9 5962068.97 5953681.448 5670619.686 6560398.885 6463542.408 5780749.034 1.160737691 1.048547581 1.027967402 0.841428312 1.031366166 1.029915226 0.980948948 1.134870039 1.118115035 1 22.46282501 1.741742259 25 1.095180484 1.01315222 0.120368546 0.080964975 0.977611858 7725.034844 0.038296418 0.021237116 55.17498943 -1.741742259 -0.082028264 YGDGIQLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGDGIQLTR 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 93.098 0.022401 369710000 321380 362360 297400 335580 337380 360980 329960 334360 360980 336280 FALSE TRUE 308820.1143 352025.8476 351146.7956 352899.324 348232.1341 368279.2629 333998.1492 327455.3492 320003.0638 313503.4561 0.985061275 1.122877087 1.120073125 1.125663265 1.110776061 1.174721541 1.065373101 1.044503156 1.020732172 1 18.25812182 1.74174343 2.237256933 1.015989708 1.10883786 0.399249444 0.046347938 0.278351211 2.861184465 0.030185532 0.012982897 55.17513826 -1.74174343 0.092848151 QQQS(ph)PPKGK ddPTM_BT-474_Pertuzumab_2h_R1 2 QQQSPPKGK 9 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 QQQS(1)PPKGK;QQQS(1)PPKGK 95.417 0.0058182 306040000 1096850 893490 687080 695550 815950 864960 858200 987820 1182740 936740 TRUE FALSE 1053983.889 868008.54 811250.64 731447.4189 842195.7728 882450.0838 868702.9083 967421.1718 1048480.314 873293.7654 1.206906463 0.993947941 0.928955035 0.83757316 0.964389998 1.010484809 0.994743055 1.107784356 1.200604373 1 19.73610752 1.74178647 3.890033075 1.117714023 0.981403335 0.207275385 0.09814898 0.277753645 9.086639286 0.054346963 0.02696109 55.18060653 -1.74178647 -0.136310689 KQPGQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQPGQLR 7 1 Q8WZA0-2;Q8WZA0;K7ES95 Q8WZA0-2 LZIC Protein LZIC 0 76.847 0.063577 300060000 132470 163100 133660 178990 168150 135160 173990 122370 163750 167690 FALSE TRUE 127292.9259 158448.5477 157815.3353 188227.6954 173558.6975 137893.0278 176119.3417 119843.0167 145161.7865 156332.2069 0.814246331 1.013537458 1.00948703 1.204023784 1.110191565 0.882051309 1.12657107 0.766591984 0.928546902 1 17.2542555 1.741802667 25 0.879852549 1.026909002 0.17845968 0.120234841 0.806496881 6253.771128 0.055384214 0.030713434 55.1826646 -1.741802667 0.147056453 EPTGVEENKTDSLFVLPSRDDAT(ph)PVRDEPMDAESITFK ddPTM_BT-474_Pertuzumab_2h_R1 6 EPTGVEENKTDSLFVLPSRDDATPVRDEPMDAESITFK 38 3 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 EPTGVEENKTDS(0.007)LFVLPS(0.195)RDDAT(0.798)PVRDEPMDAESITFK;EPTGVEENKTDS(0.002)LFVLPS(0.176)RDDAT(0.822)PVRDEPMDAESITFK;EPTGVEENKTDS(0.001)LFVLPS(0.122)RDDAT(0.877)PVRDEPMDAESITFK;EPT(0.001)GVEENKT(0.001)DS(0.012)LFVLPS(0.014)RDDAT(0.973)PVRDEPMDAESITFK;EPT(0.007)GVEENKT(0.007)DS(0.03)LFVLPS(0.147)RDDAT(0.801)PVRDEPMDAES(0.007)IT(0.002)FK;EPT(0.001)GVEENKT(0.005)DS(0.013)LFVLPS(0.047)RDDAT(0.935)PVRDEPMDAESITFK 154.05 5.96E-14 2916350000 1109517 968594 732825 743126 913747 958548 878376 1045847 1139224 961668 TRUE FALSE 1066155.849 940970.6475 865262.7791 781478.8219 943138.5021 977930.4973 889125.8282 1024249.894 1009904.068 896533.3698 1.189198177 1.049565671 0.96512055 0.8716673 1.051983712 1.090790962 0.991737573 1.142455963 1.126454521 1 19.77399776 1.741855665 24.99999487 1.101634311 1.025358372 0.085724467 0.085680624 1.177639046 8984.350283 0.041143821 0.022816268 55.18939907 -1.741855665 -0.076275939 RKGDEVDGVDEVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKGDEVDGVDEVAK 14 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 112.84 0.00032073 1647110000 2974500 2776100 1975820 1816860 2239180 2537000 2352630 2806500 3173100 2599300 FALSE TRUE 2858253.252 2696928.346 2332894.626 1910628.362 2311205.258 2588299.878 2381422.19 2748544.794 2812902.991 2423247.096 1.179513743 1.112939886 0.962714298 0.788457919 0.953763759 1.068112238 0.98274014 1.134240416 1.160799076 1 21.20851009 1.741857109 9.107369675 1.109280876 1.001180285 0.13000671 0.106465998 0.199788502 67.96300698 0.055029184 0.029665847 55.18958257 -1.741857109 -0.108100591 SLLENQSLSSS(ph)CESLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLENQSLSSSCESLK 16 0 Q14789;Q14789-2;Q14789-4;Q14789-3;E7EU81 Q14789 GOLGB1 Golgin subfamily B member 1 1 SLLENQSLS(0.001)S(0.04)S(0.96)CESLK 210.98 8.69E-12 85956000 142590 161670 117150 145890 143110 155570 135770 194860 200740 174080 TRUE FALSE 137017.4252 157059.3299 138321.611 153419.4004 147713.2631 158715.732 137431.5939 190836.0729 177952.8368 162289.4065 0.844278305 0.967773148 0.852314479 0.945344515 0.910184258 0.977979619 0.846830343 1.175899752 1.09651542 1 17.30820931 1.741895294 13.91577804 1.10100367 0.911068966 0.658748105 0.060622701 0.038604595 75.64235178 0.02587151 0.014245702 55.19443529 -1.741895294 -0.189934704 TGSGSPFAGNS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 6 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR 321.05 3.70E-56 7472720000 2569820 2618550 2266880 2669540 2631050 2479720 2546940 2668030 2808060 2719990 TRUE FALSE 2469388.593 2543871.518 2676555.642 2807315.279 2715680.113 2529861.637 2578110.214 2612934.248 2489300.801 2535762.655 0.973824813 1.003197801 1.055522936 1.107089133 1.07095201 0.997672883 1.016700127 1.030433287 0.981677365 1 21.27398829 1.741914702 1.071944057 0.996227268 1.039559491 0.148494142 0.037148155 1.056323896 2.263849388 0.035234678 0.014074574 55.19690182 -1.741914702 0.043332223 DYSDHPSGGSYR ddPTM_BT-474_Pertuzumab_2h_R1 5 DYSDHPSGGSYR 12 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;;; 130.99 0.00020664 3583313000 2247990 3513520 2958270 4444830 3130530 3277060 3225810 3018170 2699330 3345100 FALSE TRUE 2160136.066 3413317.85 3492895.195 4674228.209 3231226.341 3343324.398 3265288.428 2955843.735 2392913.375 3118533.397 0.692676906 1.09452663 1.120044184 1.498854626 1.03613652 1.072082281 1.047058989 0.947831355 0.767320105 1 21.57243628 1.741968133 2.158724143 0.878747609 1.103083786 0.153471809 0.189583495 0.503610223 4.801106021 0.129962382 0.055305609 55.20369309 -1.741968133 0.224336178 S(ph)KSYDEGLDDYREDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSYDEGLDDYREDAK 16 2 Q5T5U3;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 S(0.617)KS(0.383)YDEGLDDYREDAK;S(0.5)KS(0.5)YDEGLDDYREDAK 107.78 0.00057464 515930000 878590 737830 570900 520540 641190 625310 626130 866490 959450 730820 TRUE FALSE 844253.7315 716787.8108 674074.3296 547405.1318 661814.4587 637954.1966 633792.7662 848596.6787 850537.2583 681320.9105 1.239142552 1.052056087 0.989363924 0.803446839 0.971369656 0.936349064 0.930241178 1.245516857 1.248365117 1 19.37797496 1.742012149 10.97466138 1.183028899 0.981490158 0.297700412 0.122322195 0.097440012 67.58675673 0.059002082 0.032172512 55.20928834 -1.742012149 -0.201538741 YIIEELNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIIEELNVR 9 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 93.551 0.021688 130514000 115766 121995 108307 126027 126349 124376 127009 110908 126460 126402 FALSE TRUE 111241.7367 118515.822 127880.4842 132531.2686 130413.1303 126890.9679 128563.3741 108617.711 112104.791 117840.68 0.944001144 1.005729279 1.085198119 1.124664832 1.10669024 1.07680105 1.090993146 0.921733574 0.951325052 1 16.84647813 1.742032714 10.36817115 0.953698357 1.065430123 0.448718912 0.05281101 0.084615586 46.7238773 0.027017371 0.014685728 55.21190275 -1.742032714 0.111731766 VIFHPEFLSSTSPLLPVDYEEFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIFHPEFLSSTSPLLPVDYEEFVR 24 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 0 ; 200.29 1.55E-24 568540000 235650 259498 252483 286840 254237 252888 254443 247111 261084 243805 FALSE TRUE 226440.5375 252097.3711 298112.2946 301643.8468 262414.764 258001.5686 257556.9495 242008.0715 231446.8389 227291.8702 0.996254452 1.109135012 1.311583623 1.327121144 1.154527717 1.135111293 1.133155134 1.064745832 1.018280322 1 17.79418656 1.74205313 1.14737189 1.000747906 1.186812101 0.357367198 0.089331614 0.547440378 1.346774429 0.0821906 0.032380193 55.21449823 -1.74205313 0.186064195 RVATPVDWK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVATPVDWK 9 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 112.85 0.0030409 767090000 890200 938960 762210 805900 830260 682190 851150 920160 1005100 1010400 FALSE TRUE 855409.9998 912181.7801 899958.3023 847492.5956 856966.0669 695984.3492 861566.6283 901158.3744 891005.2617 941964.708 0.908112578 0.968382119 0.955405542 0.899707376 0.909764516 0.73886457 0.914648522 0.956679552 0.945900896 1 19.84531348 1.742116505 4.133607491 0.96468439 0.897921952 0.218286313 0.059643173 0.349530988 13.11185104 0.034318408 0.017206106 55.22255606 -1.742116505 -0.066762438 EPPS(ph)SPLQPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EPPSSPLQPQK 11 0 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EPPS(0.605)S(0.395)PLQPQK 143.42 0.0015137 0 455110 452370 472710 531890 534410 451900 479340 470630 458110 473400 TRUE FALSE 437323.798 439468.8505 558139.2124 559340.9066 551599.783 461037.7276 485206.3063 460911.326 406107.2734 441336.1963 0.990908522 0.995768881 1.264657685 1.26738054 1.249840343 1.044640642 1.099402928 1.044354236 0.920176674 1 18.75151855 1.742160606 1.369983561 0.963964889 1.148042686 0.320489403 0.100057425 0.531050134 1.897165987 0.088567119 0.034473192 55.22816404 -1.742160606 0.184077797 DGHPVVVNILIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGHPVVVNILIGR 13 0 A1L0T0;M0R026 A1L0T0 ILVBL Acetolactate synthase-like protein 0 ; 145 4.16E-05 779670000 401210 533430 350040 603490 369200 433290 496350 347890 483090 394530 FALSE TRUE 385530.2696 518217.0987 413300.0146 634636.1912 381075.6533 442051.4207 502424.4798 340705.9499 428251.6485 367808.1317 1.048183105 1.408933229 1.123683733 1.725454487 1.036071855 1.20185331 1.365996117 0.926314349 1.164334368 1 18.48859385 1.742220443 19.45679362 1.03432153 1.277943086 0.237718542 0.19894793 0.210487101 1099.549589 0.087291167 0.048351673 55.23577381 -1.742220443 0.243621556 ELLSNWYHFLVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLSNWYHFLVTR 13 0 J3QLV0;J3QLD4;J3QL54;J3KT10;Q9BW27-2;Q9BW27-3;Q9BW27;J3KTC7 J3QLV0 NUP85 Nuclear pore complex protein Nup85 0 ; 148.72 4.08E-05 206890000 162236 188155 152589 177688 196564 160718 180165 165098 179057 191513 FALSE TRUE 155895.6378 182789.0036 180165.2266 186858.499 202886.6596 163967.8281 182369.9132 161688.6686 158731.2 178541.6539 0.873161161 1.023789125 1.009093523 1.046582099 1.136354767 0.918372965 1.021441827 0.905607543 0.889042957 1 17.44590117 1.742247437 8.836662242 0.924047148 1.008488496 0.171040139 0.072109301 0.163785734 50.3139846 0.034183605 0.018392927 55.23920725 -1.742247437 0.084441348 ILENEKDLEEAEEYKEAR ddPTM_BT-474_Pertuzumab_2h_R1 5 ILENEKDLEEAEEYKEAR 18 2 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;;; 224.89 2.45E-19 4678069000 3638841 3092396 2346026 1853851 2728928 2956013 2598974 3356344 3556815 2877134 FALSE TRUE 3496631.071 3004203.894 2770005.085 1949528.472 2816706.447 3015785.608 2630781.021 3287034.324 3153060.273 2682263.151 1.303612238 1.120025786 1.032711904 0.726822225 1.050123082 1.124343675 0.980806458 1.225470484 1.175522346 1 21.35501935 1.742303141 25 1.153165335 1.041129037 0.060543743 0.146223674 1.601954833 10755.67312 0.070511868 0.039102388 55.24629277 -1.742303141 -0.112036298 SEPVKEESSELEQPFAQDTSS(ph)VGPDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDRK 27 2 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 SEPVKEESSELEQPFAQDT(0.011)S(0.247)S(0.742)VGPDRK 210.21 7.35E-26 668780000 256740 170770 159750 130880 144580 146830 134700 245210 205220 197200 TRUE FALSE 246706.317 165899.8068 188620.3786 137634.7325 149230.547 149799.0032 136348.4989 240146.3278 181924.286 183843.4684 1.341936807 0.902397068 1.025983573 0.74865174 0.81172613 0.814818196 0.741655388 1.306254337 0.98956078 1 17.4881184 1.742344712 24.99999685 1.121772254 0.902502047 0.171607762 0.184435066 1.000249283 6641.728045 0.085011811 0.047143271 55.25158129 -1.742344712 -0.219270207 QVEELYHSLLELGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QVEELYHSLLELGEK 15 0 A0A0D9SGF6;Q13813;Q13813-2 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 153.74 2.60E-06 390671000 601184 564080 514799 505517 593229 577701 593857 626992 751900 697640 FALSE TRUE 577689.0646 547992.9907 607834.6309 531606.793 612310.7495 589382.51 601124.7996 614044.3961 666547.4642 650388.2214 0.888221904 0.842562907 0.934572016 0.81736842 0.941454241 0.906201082 0.92425536 0.944119798 1.024845534 1 19.3109416 1.742394946 0.793416975 1.014067471 0.87828516 0.631191218 0.036609131 0.36882878 0.448690338 0.030830096 0.014003709 55.25797248 -1.742394946 -0.135782311 EIFVDFAPFLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIFVDFAPFLSR 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 88.681 0.013763 0 70160 81238 64709 57096 72020 67945 72256 56533 65416 65672 FALSE TRUE 67418.06963 78921.17178 76403.35574 60042.7314 74336.58871 69318.89445 73140.29054 55365.57379 57990.24993 61223.97695 1.101171028 1.289056604 1.247931931 0.980706161 1.214174453 1.132218093 1.194634752 0.904311947 0.947182016 1 15.90180914 1.742401591 8.345402297 0.946999533 1.167099596 0.582504819 0.083380028 0.077518825 19.6596 0.040038648 0.021458448 55.258818 -1.742401591 0.220100063 LSGEHS(ph)ESSTPRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSGEHSESSTPRPR 14 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 LSGEHS(0.939)ES(0.038)S(0.022)T(0.001)PRPR;LSGEHS(0.734)ES(0.121)S(0.139)T(0.006)PRPR 141.1 5.91E-06 1364550000 298260 312120 219812 319090 270430 309520 248940 268230 247239 247410 TRUE FALSE 286603.6695 303218.6432 259536.9181 335558.2731 279128.6265 315778.7065 251986.6022 262690.9568 219173.4652 230652.7003 1.242576692 1.314611287 1.12522818 1.454820484 1.210168475 1.369065725 1.092493614 1.138902586 0.950231517 1 17.81536266 1.742420309 1.395443393 0.98511269 1.282749358 0.599526349 0.096139307 0.260991531 0.969991199 0.071177001 0.027726508 55.26119972 -1.742420309 0.297636668 TNS(ph)TGGSSGSSVGGGSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 TNSTGGSSGSSVGGGSGK 18 0 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 TNS(0.996)T(0.004)GGSSGSSVGGGSGK;TNS(0.972)T(0.028)GGSSGSSVGGGSGK;T(0.007)NS(0.97)T(0.022)GGSSGSSVGGGSGK 271.66 6.10E-39 608755000 1157180 964511 864551 942584 1102838 1015481 989686 1106982 1250255 1184977 TRUE FALSE 1111956.126 937004.0906 1020794.598 991230.8732 1138311.786 1036014.722 1001798.073 1084122.435 1108331.294 1104717.452 1.006552512 0.848184383 0.92403229 0.897270946 1.030409888 0.937809681 0.906836469 0.981357208 1.003271281 1 20.075246 1.742429683 0.488442224 1.00718269 0.921478051 0.182452459 0.050900146 1.441999422 0.827914705 0.051750976 0.036221525 55.26239245 -1.742429683 -0.085704639 VHYRS(ph)PPLATGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHYRSPPLATGYR 13 1 Q86U06-3;Q86U06-5;Q86U06-2;Q86U06 Q86U06-3 RBM23 Probable RNA-binding protein 23 1 VHY(0.01)RS(0.99)PPLATGYR;VHYRS(0.995)PPLAT(0.005)GYR 110.74 0.00062682 867950000 625800 721070 519261 633124 625177 556863 691648 459158 624304 635038 TRUE FALSE 601343.0441 700505.7896 613103.0136 665799.6055 645286.386 568123.1514 700112.5951 449676.2268 553435.6272 592026.3106 1.015737026 1.18323422 1.035600957 1.124611514 1.089962345 0.959624836 1.182570069 0.759554464 0.934815932 1 19.17530177 1.742471369 25 0.881359917 1.083348763 0.488410916 0.086888863 0.49182174 3159.606346 0.036984583 0.020509846 55.26769713 -1.742471369 0.201988846 HRSES(ph)ESK ddPTM_BT-474_Pertuzumab_2h_R1 1 HRSESESK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HRS(0.042)ES(0.958)ESK 171.09 0.00017648 281730000 178500 130120 121290 119400 121430 149390 157340 82585 131380 126480 TRUE FALSE 171524.0227 126409.105 143209.8011 125562.2483 125335.9062 152410.7682 159265.574 80879.59089 116466.2932 117913.3969 1.454661023 1.072050405 1.214533758 1.064868383 1.062948821 1.292565324 1.350699565 0.685923678 0.987727402 1 16.84736812 1.742550126 25 0.872496362 1.201690865 0.50617364 0.14619911 0.551073776 3470.125558 0.065900682 0.036545291 55.27772059 -1.742550126 0.329194503 DLHQGIEAASDEEDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLHQGIEAASDEEDLR 16 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ;;; 197.1 4.42E-11 1934750000 919310 1108640 839390 1172180 1099840 1032550 1123970 848220 1065620 1030150 FALSE TRUE 883382.3488 1077022.673 991086.4451 1232676.35 1135217.352 1053428.868 1137725.481 830703.9606 944655.285 960377.0229 0.9198287 1.121458185 1.031976423 1.28353378 1.182053845 1.096890954 1.184665453 0.864976921 0.983629619 1 19.87324136 1.742585828 19.37959814 0.943472929 1.122197394 0.38406332 0.097066101 0.161179579 766.7135403 0.044992982 0.02492138 55.2822649 -1.742585828 0.178724466 DEILPTTPISEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEILPTTPISEQK 13 0 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 194.5 8.96E-07 0 107650 89821 88283 88544 102870 95745 106080 108560 117940 122930 FALSE TRUE 103442.919 87259.39302 104237.7019 93113.76645 106178.907 97681.0295 107378.2388 106318.1981 104551.9456 114603.8416 0.902613015 0.761400245 0.909548061 0.812483815 0.926486455 0.852336432 0.936951478 0.927701869 0.912290061 1 16.80629588 1.742585876 0.303472801 1.008686776 0.821600324 0.458483772 0.047625328 1.199670088 0.381060736 0.075238709 0.080440434 55.28227111 -1.742585876 -0.187086452 FSETHADPHNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSETHADPHNSR 12 0 O00767 O00767 SCD Acyl-CoA desaturase 0 76.522 0.017862 208910000 170090 489710 250190 831650 316380 432530 533060 173260 406970 353960 FALSE TRUE 163442.6948 475743.9503 295404.8984 874571.5562 326556.65 441276.0529 539583.7477 169682.1205 360772.4718 329985.9739 0.495301945 1.441709612 0.895204408 2.650329484 0.989607668 1.337256998 1.635171766 0.514210099 1.093296383 1 18.33204518 1.742707914 25 0.841110048 1.371072505 0.135663632 0.551998876 1.348726127 8168.725699 0.247485702 0.137243458 55.2978077 -1.742707914 0.529962456 LSDLDSETR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSDLDSETR 9 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 120.15 0.0016539 856150000 2668050 2428700 2093020 2056720 2177320 2306550 2441290 2653290 3065500 2896200 FALSE TRUE 2563779.656 2359435.854 2471275.273 2162867.566 2247355.475 2353190.021 2471167.237 2598498.634 2717517.292 2700037.794 0.949534729 0.873852899 0.915274326 0.801050848 0.832342229 0.87153966 0.915234314 0.96239343 1.006473797 1 21.36454817 1.742800155 1.761264971 1.002609822 0.870834233 0.648587372 0.038591381 0.215252404 1.326161713 0.029640614 0.01194153 55.30955387 -1.742800155 -0.131775589 VLRPPGGGSNFSLGFDEPTEQPVRK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLRPPGGGSNFSLGFDEPTEQPVRK 25 2 Q9UK76;J3KT51;Q9UK76-2 Q9UK76 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 169.56 5.48E-12 721710000 182040 207950 182140 160320 183580 199210 185190 233360 254730 221490 FALSE TRUE 174925.6755 202019.4696 215056.7497 168594.1344 189485.0174 203238.1627 187456.4106 228541.0345 225814.1183 206488.285 0.847145762 0.97835802 1.04149613 0.816482806 0.91765505 0.984260016 0.90783073 1.106799034 1.09359288 1 17.65570041 1.742804301 9.228613578 1.073382202 0.931456312 0.472209491 0.067189982 0.087743931 31.52223227 0.031818137 0.017174328 55.31008188 -1.742804301 -0.141925889 MGS(ph)PAPLLPGDLLGGGSDSI ddPTM_BT-474_Pertuzumab_2h_R1 9 MGSPAPLLPGDLLGGGSDSI 20 0 Q9UPQ9-1;Q9UPQ9;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI 191.96 2.04E-17 429131900 773052 707982 616396 586566 610830 691477 688751 819915 917061 881420 TRUE FALSE 742840.2732 687791.0465 727792.4689 616838.7416 630477.9017 705459.1387 697180.1408 802983.4687 812960.0799 821720.6383 0.904005861 0.837013231 0.885693306 0.750667213 0.767265506 0.858514568 0.84843937 0.97719764 0.989338763 1 19.64828848 1.742806711 2.726306578 0.995391811 0.830104288 0.713936266 0.044466451 0.137204704 2.117900917 0.0285286 0.013035108 55.3103888 -1.742806711 -0.165287524 TKPFPWGDGNHTLFHNPHVNPLPTGYEDE ddPTM_BT-474_Pertuzumab_2h_R1 2 TKPFPWGDGNHTLFHNPHVNPLPTGYEDE 29 1 P12074 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 ; 145.52 3.93E-08 1260800000 304316 507840 301797 831870 317241 431660 675600 24831 519860 318623 FALSE TRUE 292422.9943 493356.9004 356338.4313 874802.9104 327445.3449 440388.461 683868.1949 24318.23117 460847.6722 297042.3804 0.98444873 1.660897343 1.199621518 2.945044102 1.102352279 1.482577874 2.302257994 0.081867884 1.551454279 1 18.18030926 1.742817014 25 0.81736776 1.67008506 0.237041035 0.64709802 0.997652376 5886.983312 0.285182711 0.158148299 55.31170092 -1.742817014 0.8527173 S(ph)LEDVTAEYIHK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLEDVTAEYIHK 12 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 S(1)LEDVTAEYIHK;S(1)LEDVTAEYIHK;S(1)LEDVTAEYIHK 218.21 6.66E-08 85870000 224772 219093 187220 180474 195483 194793 208632 231824 266230 240380 TRUE FALSE 215987.6617 212844.6822 221054.8187 189788.2848 201770.8882 198731.8479 211185.3008 227036.7534 236008.6865 224098.8485 0.963805317 0.949780347 0.986416575 0.846895404 0.900365573 0.886804414 0.942375663 1.013109862 1.053145467 1 17.77377571 1.742855685 3.255771717 1.028294944 0.921724439 0.563410947 0.039425325 0.166334526 3.698762638 0.023745362 0.011367171 55.31662628 -1.742855685 -0.106570505 DTLRT(ph)PPRER ddPTM_BT-474_Pertuzumab_2h_R1 2 DTLRTPPRER 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DT(0.006)LRT(0.994)PPRER;DTLRT(1)PPRER 129.77 0.014024 2266460000 540250 637190 463620 561730 613690 718720 546550 577130 557640 593790 TRUE FALSE 519136.4327 619017.9651 547406.4472 590720.9526 633429.8962 733253.0108 553238.8424 565212.0638 494339.045 553572.0744 0.937793752 1.118224697 0.988862106 1.067107573 1.144259123 1.324584539 0.999398033 1.021027053 0.892998523 1 19.07841164 1.742860896 2.643996663 0.958100799 1.0948241 0.220291068 0.103014902 0.381656049 5.532923918 0.064913075 0.029399107 55.31729008 -1.742860896 0.136723301 AASDPLLSSVS(ph)PAVSK ddPTM_BT-474_Pertuzumab_2h_R1 3 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.027)S(0.194)VS(0.779)PAVSK;AASDPLLS(0.2)S(0.116)VS(0.684)PAVSK;AASDPLLS(0.096)S(0.327)VS(0.577)PAVSK 305.9 1.82E-46 1136210000 1287070 1279070 1206620 1359470 1152240 1307990 1286840 1494560 1577400 1599710 TRUE FALSE 1236769.881 1242592.176 1424683.075 1429632.41 1189302.846 1334438.454 1302588.733 1463696.814 1398340.165 1491360.217 0.829289844 0.83319386 0.955291055 0.958609727 0.797461829 0.894779436 0.87342328 0.981450891 0.937627375 1 20.50819733 1.742878517 7.228228829 0.968777191 0.879387983 0.424784277 0.050808712 0.13901425 22.51505438 0.025710264 0.013641272 55.31953445 -1.742878517 -0.089389209 PAS(ph)TPPIMASAIKDEDDEDRIIAELEVFER ddPTM_BT-474_Pertuzumab_2h_R1 1 PASTPPIMASAIKDEDDEDRIIAELEVFER 30 2 A0A087WTE6 A0A087WTE6 SRCIN1 1 PAS(0.858)T(0.141)PPIMAS(0.001)AIKDEDDEDRIIAELEVFER 296.05 2.70E-81 50309000 17018 12436 8536.6 7514.7 10457 7359.5 8065.1 16833 14737 11702 TRUE FALSE 16352.91775 12081.33746 10079.35352 7902.534568 10793.3589 7508.314132 8163.803106 16485.39267 13064.11754 10909.41312 1.498973187 1.107423225 0.92391345 0.724377607 0.989362011 0.688241801 0.748326516 1.511116363 1.197508739 1 13.41328587 1.742888152 25 1.276687397 0.941351647 0.203931948 0.250462346 1.083088875 6285.700612 0.119256681 0.066133924 55.32076179 -1.742888152 -0.33533575 DISGPS(ph)PSKK ddPTM_BT-474_Pertuzumab_2h_R1 5 DISGPSPSKK 10 1 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DIS(0.012)GPS(0.962)PS(0.026)KK;DIS(0.002)GPS(0.499)PS(0.499)KK;DIS(0.025)GPS(0.967)PS(0.008)KK;DISGPS(0.994)PS(0.006)KK;DIS(0.051)GPS(0.915)PS(0.034)KK 170 2.73E-06 11269810000 9378490 7043470 6909570 5843310 7051090 6711260 7387360 8613590 10155890 8439030 TRUE FALSE 9011968.242 6842597.132 8158283.002 6144883.929 7277894.713 6846966.275 7477768.721 8435716.356 9003035.944 7867446.981 1.145475561 0.869735398 1.036967014 0.781051839 0.925064348 0.870290743 0.950469541 1.072230468 1.144340212 1 22.90746412 1.742889873 4.060110617 1.083372384 0.930423482 0.269782294 0.098994156 0.226022082 8.121929295 0.050349068 0.025192134 55.32098102 -1.742889873 -0.152948902 TIAPTGHLHTVEFHQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TIAPTGHLHTVEFHQQR 17 0 Q96FX7;H0Y2Q1 Q96FX7 TRMT61A tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 0 73.279 0.0092489 73372000 30092 42217 33391 51827 34325 36342 43606 19726 30493 28464 FALSE TRUE 28915.97137 41013.01249 39425.49648 54501.79768 35429.0948 37076.86014 44139.66327 19318.65121 27031.56248 26536.10793 1.089683968 1.545554932 1.485730183 2.053873079 1.335127777 1.397222993 1.663381208 0.728013741 1.018670958 1 14.69566916 1.74290207 10.81535319 0.911632224 1.520332293 0.554417032 0.24401774 0.064263477 42.22133915 0.114337587 0.062306753 55.32253474 -1.74290207 0.60870007 SEQSVAQLEEEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEQSVAQLEEEKK 13 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;G5E9S8;G3V2P7 Q07866-6 KLC1 Kinesin light chain 1 0 112.96 0.00056761 0 53488 48361 46089 41722 57763 49574 46543 63163 63061 56281 FALSE TRUE 51397.62983 46981.79163 54418.30754 43875.27742 59620.99935 50576.42025 47112.60716 61858.66198 55902.57965 52469.03774 0.979580187 0.895419349 1.037150859 0.836212732 1.136308229 0.96392887 0.897912544 1.178955526 1.065439392 1 15.67917871 1.742917628 25 1.095064516 0.96571344 0.268455598 0.088126407 0.91472083 5272.538047 0.03852092 0.021361631 55.32451658 -1.742917628 -0.129351076 TGSCS(ph)ELDACPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSCSELDACPSK 13 0 A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9;H0Y9Z7 A0A1B0GUA8 KIF13A Kinesin-like protein KIF13A 1 T(0.006)GS(0.356)CS(0.638)ELDACPSK 200.76 1.13E-07 244500000 462230 392660 268860 306850 392330 350910 354670 461130 512810 425460 TRUE FALSE 444165.5406 381461.7213 317448.9828 322686.5653 404949.6508 358005.6406 359010.5576 451607.5044 454597.9587 396643.2152 1.119811265 0.961725063 0.80033887 0.81354364 1.020941832 0.902588591 0.905122144 1.138573627 1.146113034 1 18.59748235 1.743018375 8.286806977 1.104580665 0.925790056 0.376219907 0.095521077 0.114010182 28.35814443 0.047295699 0.025344055 55.33735222 -1.743018375 -0.178790609 IEYARPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEYARPTR 8 1 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;Q8WVV9-3;Q8WVV9-2;H7BXH8 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 0 62.107 0.074538 261580000 191670 223600 152870 147870 183530 207510 186730 157560 156680 196980 FALSE TRUE 184179.3245 217223.1469 180497.0096 155501.5884 189433.4091 211705.9944 189015.2576 154306.3309 138894.3433 183638.3691 1.002945764 1.182885406 0.982893773 0.84678158 1.031556804 1.152841835 1.029279766 0.840272823 0.756347074 1 17.486508 1.743179132 5.780471611 0.849496689 1.034413863 0.35191933 0.103183685 0.164890126 14.21511736 0.053337367 0.027833843 55.35783946 -1.743179132 0.184917174 QAEVANQETKEDLPAENGETK ddPTM_BT-474_Pertuzumab_2h_R1 1 QAEVANQETKEDLPAENGETK 21 1 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 0 247.85 1.78E-30 292320000 339440 292610 257370 213970 285800 266060 263040 350040 370190 304870 FALSE TRUE 326174.3095 284265.0493 303882.4842 225013.0173 294993.0166 271439.9155 266259.1622 342811.5517 328167.5832 284220.8833 1.147608528 1.000155393 1.069177186 0.791683618 1.037900569 0.955031567 0.936803654 1.206144839 1.154621642 1 18.11665304 1.743185981 25 1.136003364 0.987270309 0.253025046 0.100374446 1.007571984 5469.635648 0.045243878 0.025090053 55.35871255 -1.743185981 -0.148733055 SGS(ph)IVELIAGGGS(ph)SCSPVLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.383)GS(0.617)IVELIAGGGS(0.616)S(0.066)CS(0.317)PVLSR 150.94 9.74E-08 53061000 85869 74995 63471 69651 80539 69391 69365 91385 86309 89014 TRUE FALSE 82513.14455 72856.21603 74941.6216 73245.69646 83129.61008 70794.13356 70213.90962 89497.86781 76511.56416 82985.00249 0.994313937 0.877944374 0.903074283 0.882637757 1.001742575 0.853095516 0.846103603 1.078482438 0.921992672 1 16.34056301 1.743225572 25 1.004223635 0.907508479 0.322865887 0.060788964 0.932488916 5018.937039 0.026935188 0.014936956 55.36375931 -1.743225572 -0.096715155 GDVTDTEQLAQEMLIISHHPSLVAVQSGLWPALLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDVTDTEQLAQEMLIISHHPSLVAVQSGLWPALLAR 36 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 136.45 2.48E-09 313830000 41632 51119 40585.1 49652 48021 55553 53706 35501.4 48874 47487.4 FALSE TRUE 40004.97541 49661.13617 47919.73038 52214.54567 49565.63908 56676.31972 54363.27009 34768.28368 43326.02842 44271.0361 0.903637659 1.121752291 1.082417187 1.179429041 1.11959519 1.280212182 1.227964712 0.785350576 0.978654042 1 15.43407552 1.743300676 25 0.908386936 1.135709173 0.438705129 0.108131264 0.757746037 4013.569595 0.050409838 0.02795479 55.37333445 -1.743300676 0.227322237 SSS(ph)SPELQTLQDILGDPGDKADVGRLS(ph)PEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSSPELQTLQDILGDPGDKADVGRLSPEVK 31 2 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 2 S(0.117)S(0.132)S(0.562)S(0.188)PELQT(0.001)LQDILGDPGDKADVGRLS(1)PEVK 109.68 5.95E-05 126420000 109930 92596 81920 71575 84984 96088 82600 110810 112460 92364 TRUE FALSE 105633.8141 89955.25274 96724.7663 75268.99433 87717.58754 98030.9652 83610.88351 108521.7348 99694.01227 86108.10401 1.2267581 1.044678126 1.123294577 0.874122072 1.018691429 1.138463868 0.970999007 1.260296415 1.157777348 1 16.3938614 1.743312088 25 1.163018732 1.053471388 0.096075158 0.108833662 1.533106398 8100.870449 0.048999571 0.027172739 55.37478945 -1.743312088 -0.109547344 GREETVAEDVCIDLTCDSGSQAVPS(ph)PATR ddPTM_BT-474_Pertuzumab_2h_R1 2 GREETVAEDVCIDLTCDSGSQAVPSPATR 29 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GREETVAEDVCIDLTCDSGS(0.002)QAVPS(0.792)PAT(0.206)R;GREETVAEDVCIDLTCDSGSQAVPS(0.971)PAT(0.029)R 166.19 2.68E-12 408750000 186386 195076 138386 175016 175287 200499 174543 165880 178632 167292 TRUE FALSE 179101.8291 189512.6235 163395.4286 184048.5967 180925.2655 204553.2272 176679.1094 162454.52 158354.4442 155961.1638 1.148374535 1.215127015 1.04766741 1.180092481 1.160066141 1.311565149 1.132840414 1.041634443 1.015345361 1 17.2508273 1.743378272 3.214485324 1.015220867 1.175147757 0.565979845 0.061934626 0.168751316 3.650004197 0.035952369 0.017167569 55.38322891 -1.743378272 0.15992689 TEGSMGVTLEASAEADLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TEGSMGVTLEASAEADLK 18 0 O75410-3;E7ET87;E7EVI4;E5RJU4;E5RIP3;E5RI10 O75410-3 TACC1 Transforming acidic coiled-coil-containing protein 1 0 52.453 0.076437 335010000 146790 293800 214530 379580 328850 325590 297950 176630 171770 265930 FALSE TRUE 141053.2845 285421.1117 253300.3432 399170.1693 339427.7589 332173.6529 301596.4012 172982.5288 152271.3897 247918.3242 0.568950621 1.151270736 1.021708839 1.610087397 1.369111218 1.339851154 1.216515165 0.697739989 0.614199818 1 17.91950538 1.743462217 6.60489658 0.745681396 1.20529468 0.322074319 0.27126569 0.155901243 19.42786597 0.137526889 0.072532352 55.393935 -1.743462217 0.459613284 SHHGEHERPEFIAYPHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SHHGEHERPEFIAYPHLR 18 1 P12074;H0YIV9 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 ;;; 217.88 2.75E-19 8863200000 680872 1611500 1022540 2927160 805610 1319400 1823810 37550.1 1121950 514257 FALSE TRUE 654262.7695 1565541.598 1207335.724 3078231.078 831523.1773 1346079.172 1846130.332 36774.67731 994590.9396 479425.9153 1.364679607 3.265450506 2.518294664 6.420660586 1.734414329 2.807689632 3.850710346 0.076705652 2.074545634 1 18.87094837 1.743491008 25 1.049251924 3.178162597 0.325622535 1.375464998 1.047053617 5331.123845 0.620241796 0.343955681 55.39760741 -1.743491008 2.128910673 EKESELGDRPLQVGER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKESELGDRPLQVGER 16 2 A6NHR9;A6NHR9-2 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 0 198.07 2.34E-11 242640000 155890 148720 122120 151600 151940 154070 143550 183610 190240 172650 FALSE TRUE 149797.6465 144478.6512 144189.8005 159424.0942 156827.2881 157185.401 145306.8078 179818.3893 168644.7528 160956.2617 0.930672997 0.897626782 0.895832191 0.990480845 0.974347232 0.97657214 0.90277201 1.117187908 1.04776758 1 17.29630918 1.743645336 25 1.06221289 0.939991188 0.620294739 0.041696445 0.604517246 2984.191455 0.019756119 0.010955812 55.41729657 -1.743645336 -0.122221702 TSS(ph)FAEPGGGGGGGGGGPGGSASGPGGTGGGK ddPTM_BT-474_Pertuzumab_2h_R1 4 TSSFAEPGGGGGGGGGGPGGSASGPGGTGGGK 32 0 P49840 P49840 GSK3A Glycogen synthase kinase-3 alpha 1 T(0.032)S(0.14)S(0.828)FAEPGGGGGGGGGGPGGSASGPGGTGGGK;T(0.122)S(0.122)S(0.755)FAEPGGGGGGGGGGPGGSASGPGGTGGGK;T(0.039)S(0.151)S(0.81)FAEPGGGGGGGGGGPGGSASGPGGTGGGK;T(0.188)S(0.188)S(0.623)FAEPGGGGGGGGGGPGGSASGPGGTGGGK 330.17 3.79E-117 1414100000 3138570 2838150 2397380 2414410 2629320 2671640 2577320 3329850 3382040 3140920 TRUE FALSE 3015911.215 2757208.741 2830639.895 2539017.989 2713894.466 2725662.391 2608862.013 3261087.434 2998124.998 2928182.691 1.029960058 0.941610901 0.966688282 0.867096851 0.926818697 0.930837546 0.890949196 1.113689881 1.02388591 1 21.48157414 1.743687179 25 1.052881805 0.934420529 0.510133495 0.049039217 0.709512949 3473.816735 0.022236457 0.012331175 55.42263615 -1.743687179 -0.118461275 S(ph)KDAS(ph)PINRWS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 3 S(1)KDAS(1)PINRWS(0.981)PT(0.019)R;S(1)KDAS(0.999)PINRWS(0.577)PT(0.425)R 66.76 0.035972 584540000 550080 459160 372980 334000 401410 429660 400450 529190 559220 449210 TRUE FALSE 528582.2655 446065.2064 440385.7829 351237.78 414321.7172 438348.0196 405350.8269 518262.0416 495739.69 418784.6066 1.262181697 1.065142317 1.051580636 0.838707475 0.989343234 1.046714738 0.967921983 1.237538423 1.183758147 1 18.67584889 1.743693559 25 1.160424063 1.025240723 0.1518457 0.114229506 1.502108547 7345.23225 0.05363598 0.029743926 55.42345032 -1.743693559 -0.13518334 VSCHDS(ph)DDDIMR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSCHDSDDDIMR 12 0 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101;F5GWN9 Q76FK4-2 NOL8 Nucleolar protein 8 1 VSCHDS(1)DDDIMR;VSCHDS(1)DDDIMR 104.94 0.0035542 216770000 894900 988860 906270 810890 850610 929240 856290 884720 831990 904490 TRUE FALSE 859926.3186 960658.681 1070053.149 852740.1301 877970.6432 948029.8695 866769.5332 866450.2228 737545.9832 843228.0867 1.019802746 1.139263144 1.268996095 1.011280511 1.041201849 1.124286399 1.027918243 1.027539567 0.874669612 1 19.6855634 1.743740209 1.476945385 0.943902166 1.104374388 0.379837984 0.077976687 0.408628367 1.716409615 0.062133069 0.024323213 55.42940405 -1.743740209 0.160472222 SLADELALVDVLEDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLADELALVDVLEDK 15 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;;; 218.06 4.63E-12 126877000 296612 240938 274942 280666 299754 314391 327394 388187 462489 475898 FALSE TRUE 285020.0751 234066.6841 324630.1355 295151.2059 309395.8596 320748.2014 331400.7457 380170.8028 409989.1876 443665.0046 0.64242181 0.527575269 0.731701018 0.665256901 0.697363679 0.722951322 0.746961654 0.856887063 0.924096297 1 18.75911124 1.743758014 0.51442909 1.015679384 0.613923058 0.876970644 0.046570589 0.264012424 0.162758256 0.046202763 0.030603021 55.43167649 -1.743758014 -0.401756326 YLAEVATGEKR ddPTM_BT-474_Pertuzumab_2h_R1 3 YLAEVATGEKR 11 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 155.48 5.05E-05 3015510000 2326800 2225860 1909880 1760070 1857610 2196020 1991780 2335250 2405090 2275420 FALSE TRUE 2235866.084 2162380.652 2255037.801 1850907.424 1917361.713 2240425.029 2016155.999 2287026.271 2132074.266 2121303.777 1.054005611 1.019363976 1.063043316 0.872532941 0.903860038 1.056154735 0.950432475 1.078122943 1.005077297 1 21.0165198 1.743773878 24.99999986 1.034200658 0.98742797 0.069707694 0.064337934 2.556514873 12307.96507 0.030952428 0.01716442 55.43370143 -1.743773878 -0.046772689 SHGLES(ph)VPVLPGSGEAGVSFDLPAQADTLHSANK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHGLESVPVLPGSGEAGVSFDLPAQADTLHSANK 34 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 S(0.42)HGLES(0.58)VPVLPGSGEAGVSFDLPAQADTLHSANK 73.128 0.0058029 103520000 44161 56432 59681 68029 59134 62593 79230 14660 53264 56357 TRUE FALSE 42435.1393 54822.61461 70466.6843 71539.98484 61036.09881 63858.67335 80199.64044 14357.26588 47217.69402 52539.89019 0.807674686 1.043447453 1.341203494 1.361631792 1.161709676 1.215432181 1.52645238 0.273264101 0.898701803 1 15.68112556 1.743775547 25 0.668880748 1.211389548 0.42591704 0.255212477 0.820342194 3948.15327 0.115153682 0.063858581 55.43391435 -1.743775547 0.5425088 AEGSDVANAVLDGADCIMLSGETAK ddPTM_BT-474_Pertuzumab_2h_R1 5 AEGSDVANAVLDGADCIMLSGETAK 25 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;; 242.05 1.22E-38 321342000 394384 386695 325151 357885 359754 376836 366459 428152 458821 432404 FALSE TRUE 378971.0373 375666.8372 383913.0186 376355.4877 371325.8141 384455.8821 370943.8349 419310.5116 406737.5636 403116.8919 0.940102102 0.931905471 0.952361527 0.933613786 0.921136825 0.953708192 0.920189261 1.040171027 1.008981692 1 18.62083871 1.743786301 10.31836942 1.017507402 0.936608384 0.871089573 0.014135806 0.027762304 15.20295256 0.006222053 0.003382519 55.43528715 -1.743786301 -0.080899018 ESFNPESYELDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESFNPESYELDK 12 0 P49903;P49903-2;P49903-4;Q5T5U6 P49903 SEPHS1 "Selenide, water dikinase 1" 0 ; 223.31 5.29E-11 200850000 176397 185178 145889 138615 165093 180835 162570 199367 210176 195441 FALSE TRUE 169503.2102 179896.9047 172254.3876 145768.9368 170403.3663 184491.6076 164559.5803 195250.0018 186317.7016 182203.607 0.93029558 0.987339975 0.945395047 0.800033211 0.935235965 1.012557384 0.903163132 1.071603384 1.022579655 1 17.47519199 1.743893348 12.87764047 1.034549483 0.931641206 0.409632642 0.055408513 0.084993513 112.7461463 0.026998847 0.014829808 55.44895273 -1.743893348 -0.102908277 SVFDVLDGEEMRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVFDVLDGEEMRR 13 1 Q8N1G2 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 136.3 0.00011858 293750000 137820 150550 104550 138010 134320 152380 134890 131340 141290 135700 FALSE TRUE 132433.842 146256.4614 123444.5107 145132.7126 138640.5248 155461.228 136540.8242 128627.7831 125251.3515 126508.9181 1.046834041 1.156096057 0.975777143 1.147213294 1.095895268 1.228855881 1.079298015 1.01674874 0.990059463 1 16.94887956 1.743938444 3.450998154 0.999165862 1.108644231 0.357898832 0.06348707 0.2332953 5.850551717 0.034858845 0.016927384 55.45471071 -1.743938444 0.109478368 DRDYSDHPSGGSYR ddPTM_BT-474_Pertuzumab_2h_R1 5 DRDYSDHPSGGSYR 14 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;;; 203.2 9.24E-09 6771620000 3804102 5863720 4488917 6346140 4701050 5444720 5077200 4273350 3912270 5109290 FALSE TRUE 3655433.488 5696492.447 5300164.157 6673665.046 4852263.543 5554815.969 5139336.292 4185103.829 3468165.511 4763233.237 0.767426936 1.195929774 1.112724045 1.401078787 1.01869115 1.166186011 1.078959613 0.878626685 0.728111629 1 22.18350976 1.744000262 3.481615519 0.845879723 1.122992638 0.31013049 0.161230467 0.228582256 5.840259925 0.086717989 0.042193159 55.4626048 -1.744000262 0.277112915 LDEYLNSPLPDEIDENSMEDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDEYLNSPLPDEIDENSMEDIK 22 0 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 175.85 1.02E-12 91837000 104290 83388 75562 74827 91129 82710 87825 100670 115800 101690 FALSE TRUE 100214.2315 81009.85589 89217.73427 78688.83044 94060.24705 84382.45287 88899.82862 98591.12932 102654.8695 94802.44572 1.057084875 0.854512299 0.941091061 0.83002954 0.992171102 0.890087299 0.937737713 1.039963986 1.082829337 1 16.53263666 1.744028035 3.985982463 1.047983272 0.922723609 0.389037404 0.064093413 0.176466827 6.064108716 0.031853703 0.015908879 55.46615165 -1.744028035 -0.125259663 GSSPT(ph)PPCS(ph)PVQPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSSPTPPCSPVQPSK 15 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 2 GS(0.001)S(0.046)PT(0.955)PPCS(0.998)PVQPSK;GSS(0.001)PT(0.999)PPCS(1)PVQPSK 328.34 4.53E-68 2209860000 800570 869150 652670 925470 891700 897420 771330 745900 736660 710610 TRUE FALSE 769282.8393 844362.693 770621.9876 973233.6176 920382.3403 915566.4473 780769.7673 730496.9043 653037.4451 662479.7518 1.161217135 1.27454868 1.163238553 1.469076776 1.389298824 1.38202933 1.178556424 1.102670538 0.985747026 1 19.33751683 1.744038153 1.91582886 1.001422537 1.307893663 0.638919544 0.09395764 0.211099976 1.558627034 0.070400478 0.02899984 55.46744392 -1.744038153 0.306471126 TEIKEEEDQPSTSATQS(ph)SPAPGQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEIKEEEDQPSTSATQSSPAPGQSK 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 TEIKEEEDQPSTSAT(0.003)QS(0.981)S(0.016)PAPGQSK;TEIKEEEDQPSTSAT(0.004)QS(0.891)S(0.105)PAPGQSK 244.04 5.85E-39 1047040000 1282360 992120 1065110 864450 1003590 992830 1139660 1417130 1681970 1543720 TRUE FALSE 1232243.953 963825.709 1257599.07 909064.3681 1035871.384 1012905.703 1153607.5 1387865.77 1491039.817 1439162.469 0.856222963 0.669712926 0.87384093 0.631662086 0.719773761 0.703816091 0.801582535 0.964356561 1.036046901 1 20.45679804 1.744043786 2.517933141 1.016450366 0.739302565 0.72494992 0.071476027 0.124728052 1.633344857 0.042167034 0.018843805 55.46816337 -1.744043786 -0.277147801 LSEGS(ph)QPAEEEEDQETPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 LSEGS(1)QPAEEEEDQETPSR 362.25 1.23E-91 305370000 165180 184530 144990 180090 170780 188830 179120 161720 181690 180380 TRUE FALSE 158724.583 179267.3851 171192.9183 189384.4665 176273.2938 192648.272 181312.1241 158380.4255 161065.3129 168162.7019 0.943875075 1.066035352 1.018019551 1.126197809 1.048230623 1.145606426 1.078194642 0.941828501 0.957794511 1 17.35949823 1.744047061 8.850333891 0.963615926 1.064723367 0.386328158 0.054248105 0.105253632 32.88455191 0.025868824 0.013932141 55.46858159 -1.744047061 0.101107441 DKPHVNVGTIGHVDHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKPHVNVGTIGHVDHGK 17 1 P49411;H3BNU3 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 215.45 1.89E-15 2388200000 918030 1142120 882290 1490520 815900 1007280 1543150 136627.4 1273650 837950 FALSE TRUE 882152.3727 1109547.856 1041739.429 1567445.916 842144.1645 1027647.892 1562035.531 133805.9964 1129070.592 781194.9001 1.129234679 1.420321428 1.33352052 2.006472284 1.078020561 1.31548208 1.999546504 0.171283756 1.445312292 1 19.57532301 1.744050318 25 0.810645906 1.461604429 0.298386568 0.416025386 1.149460031 5254.326887 0.181001785 0.100374607 55.46899769 -1.744050318 0.650958523 KGAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_BT-474_Pertuzumab_2h_R1 11 KGAGDGSDEEVDGKADGAEAKPAE 24 3 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE 176.98 5.17E-17 1.61467E+11 22968010 15920090 13107400 8960930 14138360 13536840 14746300 19428610 23678820 16347790 TRUE FALSE 22070394.78 15466064.62 15476198.75 9423404.671 14593133.19 13810564.18 14926769.63 19027402.41 20990899.62 15240539.62 1.448137358 1.014797704 1.01546265 0.618311746 0.957520767 0.906172913 0.979412147 1.248473012 1.37730685 1 23.86141065 1.744127989 5.791642853 1.233585622 0.97372455 0.178743855 0.208652369 0.233661567 20.23494416 0.10581805 0.055294708 55.47891884 -1.744127989 -0.259861072 S(ph)PPGPAGSSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPGPAGSSPK 11 0 Q9H9D4 Q9H9D4 ZNF408 Zinc finger protein 408 1 S(1)PPGPAGSSPK 72.006 0.035807 0 95256 86038 77817 83334 89079 79904 82644 99322 99857 97576 TRUE FALSE 91533.29021 83584.28048 91880.26293 87634.87773 91944.30693 81519.71363 83655.42199 97270.96599 88521.65199 90967.09061 1.006224225 0.918840868 1.010038491 0.963369029 1.010742526 0.896145112 0.919622926 1.069298417 0.973117326 1 16.47305709 1.744136984 25 1.019101831 0.960541474 0.231758769 0.04429935 1.442483206 6490.957634 0.020014842 0.011099191 55.48006786 -1.744136984 -0.058560357 KET(ph)ES(ph)EAEDNLDDLEK ddPTM_BT-474_Pertuzumab_2h_R1 6 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK 303.76 3.25E-46 2971800000 6504850 4720630 4333820 3117230 4530160 4423940 4431180 6535500 7199080 5740640 TRUE FALSE 6250633.271 4586002.254 5117037.679 3278110.614 4675876.711 4513395.098 4485410.106 6400539.641 6381870.619 5351821.34 1.167945055 0.856904961 0.956130139 0.61252243 0.873698207 0.843338148 0.838109089 1.195955402 1.192467053 1 22.35159852 1.74418538 8.405325461 1.142340126 0.868739686 0.407410184 0.138019669 0.103194533 27.07011316 0.065591614 0.035206813 55.4862507 -1.74418538 -0.273600439 NTS(ph)ASDEDER ddPTM_BT-474_Pertuzumab_2h_R1 1 NTSASDEDER 10 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-4 Q32MZ4-2;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NT(0.06)S(0.936)AS(0.004)DEDER 99.991 0.0045296 28472000 23307 25677 29160 33729 34001 31232 28691 27834 29594 26913 TRUE FALSE 22396.13667 24944.7171 34429.86066 35469.75773 35094.67304 31863.53244 29042.12904 27259.21817 26234.61319 25090.15854 0.892626351 0.994203248 1.37224564 1.413692053 1.398742578 1.269961383 1.157510782 1.086450615 1.045613687 1 14.61483397 1.744249144 2.001852971 1.029103423 1.235038004 0.20158467 0.160210206 0.543484233 4.407426383 0.124270496 0.051830857 55.49439796 -1.744249144 0.205934581 LDHFNFER ddPTM_BT-474_Pertuzumab_2h_R1 2 LDHFNFER 8 0 Q9UHL4;R4GNE8;R4GMV4 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 ; 138.4 0.00070713 512730000 331140 351920 308950 389370 325870 324380 360380 304150 346990 369380 FALSE TRUE 318198.6827 341883.5862 364784.1376 409465.4324 336351.9045 330939.1859 364790.4382 297869.1962 307601.1499 344361.5636 0.924024968 0.992804141 1.059305614 1.189056723 0.976740554 0.961022428 1.059323911 0.864989673 0.893250532 1 18.3935646 1.744275257 14.51923028 0.909930563 1.025605451 0.27994789 0.075733424 0.114838188 227.9603558 0.036577567 0.020166294 55.49773475 -1.744275257 0.115674888 THLTEDTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 THLTEDTPK 9 0 Q15738;C9JDR0 Q15738 NSDHL "Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating" 0 ; 102.61 0.0035568 217330000 163937 205859 140809 205708 179597 179427 206431 135114 195072 192183 FALSE TRUE 157530.1608 199988.1029 166256.3186 216324.6145 185373.9006 183055.1369 208957.3643 132323.8487 172928.2444 179166.2742 0.879240033 1.116215112 0.927944276 1.207395842 1.034647293 1.021705327 1.166276216 0.738553331 0.965183013 1 17.45093957 1.74427791 25 0.880213485 1.052623058 0.259736817 0.113770544 1.233993708 5415.462865 0.04876629 0.027043348 55.4980738 -1.74427791 0.172409573 VKDDIESLHDK ddPTM_BT-474_Pertuzumab_2h_R1 5 VKDDIESLHDK 11 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 188.09 1.98E-06 3735830000 3361770 3417450 3723550 3248770 3474650 3627940 4222920 4559280 5752820 5429200 FALSE TRUE 3230388.312 3319987.672 4396478.315 3416439.409 3586415.273 3701299.432 4274601.358 4465129.275 5099783.991 5061475.448 0.63823056 0.655932782 0.868615952 0.674988834 0.708571109 0.73126887 0.844536618 0.88217938 1.007568651 1 22.27112657 1.744287624 1.133277805 1.011063393 0.710127798 0.778634013 0.061732059 0.219267546 0.525788436 0.052756702 0.020854342 55.49931514 -1.744287624 -0.300935595 KHHEEEIVHHK ddPTM_BT-474_Pertuzumab_2h_R1 2 KHHEEEIVHHK 11 1 Q9UII2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 165.7 8.66E-06 201971000 158349 194003 153412 314420 133597 172721 266170 3429.5 198350 104641 FALSE TRUE 152160.546 188470.2244 181136.961 330647.2539 137894.2688 176213.537 269427.4681 3358.679627 175834.1396 97553.57187 1.559763965 1.931966414 1.85679476 3.389391568 1.413523526 1.806325833 2.761841139 0.034429079 1.802436714 1 16.57390708 1.744293967 24.99999999 0.89426971 2.098343188 0.378066485 0.679165311 1.096501421 4798.549092 0.301500592 0.167197461 55.50012577 -1.744293967 1.204073478 IREESGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 IREESGAR 8 1 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;; 139.74 0.00060261 3971523000 1268530 1419130 1027066 1210200 1201260 1187673 1219580 1159110 1203520 1176550 FALSE TRUE 1218954.445 1378657.802 1212679.673 1272658.567 1239899.619 1211688.562 1234505.585 1135173.973 1066901.455 1096861.221 1.111311461 1.256911792 1.105590799 1.160273099 1.130407016 1.10468721 1.125489316 1.034929444 0.972685911 1 20.06494957 1.74437009 1.101561754 0.977959555 1.155539958 0.701129872 0.042505698 0.248868013 0.563274123 0.034647856 0.013772502 55.50985459 -1.74437009 0.177580403 ACPDSLGS(ph)PAPSHAYHGGVL ddPTM_BT-474_Pertuzumab_2h_R1 3 ACPDSLGSPAPSHAYHGGVL 20 0 E9PNA7;Q5XXA6-2;Q5XXA6 E9PNA7 ANO1 Anoctamin;Anoctamin-1 1 ACPDS(0.007)LGS(0.993)PAPSHAYHGGVL;ACPDSLGS(1)PAPSHAYHGGVL;ACPDSLGS(1)PAPSHAYHGGVL 214.94 7.92E-25 1152960000 673140 914290 654883 1060810 803650 880860 1026980 510730 934020 858860 TRUE FALSE 646832.9446 888215.3444 773234.9259 1115558.531 829500.1321 898671.5927 1039548.488 500183.247 827993.9653 800688.6472 0.80784578 1.109314273 0.965712363 1.393248843 1.035983381 1.122373342 1.298318007 0.624691319 1.034102292 1 19.61088183 1.744410669 25 0.856254808 1.108655953 0.223005704 0.184192416 1.45384335 6235.026861 0.081572329 0.045236056 55.51504151 -1.744410669 0.252401146 ERQEQLER ddPTM_BT-474_Pertuzumab_2h_R1 4 ERQEQLER 8 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ;;; 197.27 0.0001326 1567166000 667716 681560 542619 644487 680069 612328 648197 580372 601544 678816 FALSE TRUE 641620.9205 662122.5761 640682.3238 677749.0513 701944.037 624709.6917 656129.8288 568387.1154 533259.247 632839.1877 1.013876721 1.046273033 1.012393569 1.070965681 1.10919812 0.987153931 1.036803412 0.898154107 0.842645742 1 19.27147941 1.744457726 5.119862854 0.902639601 1.041124282 0.585907068 0.048185118 0.106303459 6.660332658 0.023799353 0.012302201 55.52105712 -1.744457726 0.138484681 EKPTDMQNFGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKPTDMQNFGLR 12 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 82.069 0.014544 632170000 311530 305860 303190 293360 316150 268620 297970 351830 368340 345100 FALSE TRUE 299355.0632 297137.1723 357983.1774 308500.3448 326319.2519 274051.6804 301616.646 344564.5876 326527.5874 321726.0696 0.930465671 0.923571946 1.112695586 0.958891349 1.014276687 0.851816829 0.9374952 1.070987464 1.014924242 1 18.29547332 1.744472219 25 1.03330062 0.963418839 0.177828614 0.065998651 2.054804859 8720.277316 0.031476605 0.017455366 55.52290991 -1.744472219 -0.069881781 ECHGLVDALVTSINHALDAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ECHGLVDALVTSINHALDAGK 21 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 234.23 5.23E-30 291000000 258060 240723 214233 247491 235781 233365 262030 220989 276389 275691 FALSE TRUE 247974.7299 233857.8157 252949.6687 260264.0402 243365.11 238083.8002 265236.8015 216425.4999 245014.4794 257018.203 0.964813881 0.909888144 0.984170248 1.012628822 0.946878887 0.926330499 1.031976718 0.842062925 0.953296212 1 17.97151101 1.744496286 24.99999991 0.916519289 0.965768184 0.07294912 0.050812476 2.095441521 8856.566056 0.022497085 0.012475952 55.52598681 -1.744496286 0.049248895 EIKHS(ph)PGPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIKHSPGPTR 10 1 A0A087WY28;H7C1H4;Q96CV9-3;Q96CV9-2;Q96CV9 A0A087WY28 OPTN Optineurin 1 EIKHS(0.99)PGPT(0.01)R 52.576 0.090367 104180000 111710 115700 100610 114810 127960 136400 108420 102630 93551 106020 TRUE FALSE 107344.2497 112400.3493 118792.4651 120735.3579 132075.9496 139158.1015 109746.8764 100510.6546 82931.48268 98839.17097 1.086049677 1.137204493 1.201876381 1.221533494 1.336271322 1.407924612 1.110358123 1.016911146 0.839054819 1 16.59279529 1.744525747 2.562944544 0.927445123 1.230064715 0.623663324 0.096941703 0.173807531 2.358604861 0.064539646 0.029008749 55.52975365 -1.744525747 0.302619592 SLGNILQAKPTSS(ph)PAKGPPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGNILQAKPTSSPAKGPPQK 21 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SLGNILQAKPTS(0.028)S(0.971)PAKGPPQK 217.93 4.43E-25 1495900000 1320400 960470 751910 702550 806510 828840 868580 1097100 1182000 1062000 TRUE FALSE 1268797.308 933078.336 887796.8631 738808.6897 832452.1266 845599.7127 879209.9419 1074444.502 1047824.315 990069.7941 1.281523096 0.942436929 0.896701292 0.746218796 0.840801458 0.854080912 0.888028245 1.085220969 1.058333788 1 19.9171707 1.744545444 9.188335546 1.05207925 0.908822464 0.153396763 0.133637029 0.184947812 66.06905084 0.066053734 0.035668813 55.53227229 -1.744545444 -0.143256786 ENGKGDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENGKGDIK 8 1 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 62.823 0.07041 618320000 683090 607600 472210 523880 533010 568790 543540 705150 707740 676780 FALSE TRUE 656394.0876 590271.8429 557548.8513 550917.5096 550154.7507 580291.3235 550192.0051 690588.4061 627400.3223 630941.0878 1.040341326 0.93554193 0.883678147 0.873167908 0.871958985 0.919723465 0.872018031 1.094537064 0.99438812 1 19.26714578 1.744673986 24.99999941 1.034467257 0.910513746 0.491205236 0.053900276 0.970251496 3981.279962 0.025195369 0.013972152 55.548711 -1.744673986 -0.123953511 HEDLQTDESSMDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEDLQTDESSMDDR 14 0 A0A0D9SEU5;Q6VN20;R4GMX8;Q6VN20-2;Q6VN20-3 A0A0D9SEU5 RANBP10 Ran-binding protein 10 0 59.248 0.077682 33793000 11111 13626 9800.9 13579 10284 12793 12964 7103 9043.6 10254 FALSE TRUE 10676.76984 13237.39982 11572.14065 14279.81382 10614.7942 13051.68323 13122.65731 6956.320568 8017.008442 9559.487447 1.116876809 1.384739495 1.210539866 1.493784462 1.110393654 1.365312031 1.372736497 0.727687609 0.838644173 1 13.22271755 1.744684097 9.699976818 0.842794431 1.297237204 0.702660645 0.130405459 0.048656102 21.16149117 0.05746362 0.0311354 55.55000427 -1.744684097 0.454442773 YLDEDTIYHLQPSGR ddPTM_BT-474_Pertuzumab_2h_R1 6 YLDEDTIYHLQPSGR 15 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;;;; 203.04 5.61E-09 5591330000 3516710 4432530 4283400 4174900 4545990 4549000 4297250 3567680 3500640 4247480 FALSE TRUE 3379273.085 4306118.584 5057505.664 4390367.089 4692215.897 4640983.897 4349841.031 3494006.161 3103262.023 3959794.396 0.853396098 1.087460144 1.277214208 1.108736124 1.184964528 1.172026482 1.098501739 0.882370601 0.783692715 1 21.91699409 1.744684658 4.262195621 0.872096445 1.12385053 0.4453892 0.113394388 0.16158908 6.465446739 0.060157967 0.03039456 55.5500761 -1.744684658 0.251754085 SEPVKEESSELEQPFAQDTSSVGPDRK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEPVKEESSELEQPFAQDTSSVGPDRK 27 2 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ; 277.59 3.37E-61 795780000 712380 625160 493420 469350 564850 593360 546060 716130 727140 644890 FALSE TRUE 684539.402 607331.0489 582591.9701 493573.2097 583018.9132 605358.1457 552742.8456 701341.6652 644598.1156 601211.0259 1.138600878 1.010179492 0.969030748 0.820965 0.969740887 1.006897944 0.919382416 1.166548242 1.072166158 1 19.19751194 1.744705558 25 1.092571609 0.972353833 0.235715272 0.08394225 1.585580135 6472.651154 0.039653502 0.021989745 55.55274938 -1.744705558 -0.120217775 KDCEVVMMIGLPGAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDCEVVMMIGLPGAGK 16 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 196.64 7.28E-11 1708990000 4761900 4148500 3811300 3418500 4154200 4325700 3992800 4678600 4822200 4533100 FALSE TRUE 4575799.683 4030188.842 4500086.692 3594929.195 4287823.616 4413168.618 4041665.081 4581985.275 4274804.072 4226069.099 1.082755529 0.953649537 1.064839828 0.850655564 1.014612756 1.044272707 0.95636512 1.084219204 1.011531987 1 22.01088493 1.744706776 25 1.039176561 0.993441407 0.056710982 0.066166836 3.072026412 12538.12889 0.029221592 0.016204707 55.55290529 -1.744706776 -0.045735154 WGQPPS(ph)PTPVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_BT-474_Pertuzumab_2h_R1 2 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 WGQPPS(0.955)PT(0.045)PVPRPPDADPNT(0.599)PS(0.401)PKPLEGRPER;WGQPPS(0.948)PT(0.05)PVPRPPDADPNT(0.606)PS(0.397)PKPLEGRPER 123.17 9.71E-08 2713400000 771760 546310 459730 498750 639550 576750 561510 687770 759970 588280 TRUE FALSE 741598.766 530729.7737 542813.4376 524490.5473 660121.7066 588412.2802 568381.9273 673567.3092 673701.3917 548435.2716 1.352208372 0.96771634 0.989749321 0.956339926 1.203645609 1.072892847 1.036370118 1.228161907 1.228406389 1 19.06496183 1.7447434 25 1.173018882 1.074119531 0.048324087 0.128020704 2.817705584 11431.80043 0.05749208 0.031882229 55.55759014 -1.7447434 -0.098899351 APNYPTEGNHR ddPTM_BT-474_Pertuzumab_2h_R1 2 APNYPTEGNHR 11 0 Q9GZT8-2;Q9GZT8;B8ZZI0;E7EXA3;Q6X734;Q9GZT8-3 Q9GZT8-2 NIF3L1 NIF3-like protein 1 0 ; 96.604 0.0068882 499420000 300640 326930 249158 347950 310610 312690 321210 286560 327210 319510 FALSE TRUE 288890.6564 317606.2765 294186.3931 365907.7412 320601.0527 319012.806 325141.0641 280642.4359 290066.4926 297869.3031 0.969857093 1.066260515 0.987635819 1.228417086 1.076314509 1.070982484 1.091556131 0.942166356 0.973804583 1 18.18431993 1.744800437 10.01166919 0.969690319 1.073180719 0.312876018 0.066489081 0.114872032 56.20654667 0.031583839 0.017145388 55.56488725 -1.744800437 0.1034904 SELISS(ph)TFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SELISSTFK 9 0 H0YHG7;Q92730 H0YHG7 RND1 Rho-related GTP-binding protein Rho6 1 SELIS(0.058)S(0.593)T(0.349)FK;SELIS(0.059)S(0.47)T(0.47)FK 72.485 0.048901 1296373000 362439 634260 507400 809540 625500 709520 535920 404840 279774 409980 TRUE FALSE 348274.4832 616171.5258 599098.4671 851320.4564 645619.7756 723866.9805 542478.7493 396479.9125 248015.2284 382211.6894 0.911208351 1.612121091 1.567451974 2.22735327 1.689168054 1.89389022 1.419314909 1.037330682 0.648894933 1 18.54401238 1.744887888 2.471539032 0.830966612 1.670845153 0.525341618 0.321681163 0.202894079 2.554656237 0.206196568 0.09170434 55.57607701 -1.744887888 0.839878541 EEPLS(ph)EEEPCTSTAIASPEKK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK 242.43 2.92E-30 2227530000 2099670 1835850 1595150 1567600 1662230 1795950 1752000 2374830 2665820 2161850 TRUE FALSE 2017612.575 1783493.355 1883429.089 1648504.024 1715697.138 1832265.34 1773441.5 2325788.931 2363207.29 2015425.974 1.001084933 0.884921291 0.934506706 0.817943226 0.851282637 0.909120634 0.879933832 1.153993727 1.172559707 1 20.94265336 1.744911537 7.410774709 1.12008722 0.893488914 0.701447272 0.063105254 0.063490264 11.15804738 0.029905192 0.015923462 55.57910346 -1.744911537 -0.226598306 HHVLHDQNVDKR ddPTM_BT-474_Pertuzumab_2h_R1 3 HHVLHDQNVDKR 12 1 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ;; 198.49 7.43E-08 278865000 159100 247521 147311 290309 137081 162838 242343 16749 165138 89255 FALSE TRUE 152882.1961 240461.9434 173933.3746 305291.8823 141490.3349 166130.6959 245308.8661 16403.1273 146392.2266 83209.67935 1.837312646 2.889831391 2.090302186 3.668946746 1.700407164 1.996530899 2.948080897 0.197130039 1.759317278 1 16.34446374 1.744946347 25 0.963817067 2.45154983 0.503624812 0.664956665 0.98700674 3876.758045 0.289881091 0.160754042 55.58355847 -1.744946347 1.487732763 HYAHTDCPGHADYVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HYAHTDCPGHADYVK 15 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 85.457 0.0045887 66924000 36538 49119 37938 62300 32972 35483 56776 11449 45311 34680 FALSE TRUE 35110.05457 47718.17421 44794.24053 65515.31047 34032.57432 36200.49057 57470.84167 11212.57415 40167.48524 32331.09271 1.08595323 1.475922099 1.385484893 2.026387139 1.05262679 1.119680392 1.777571893 0.346804677 1.242379452 1 14.98063465 1.745026152 25 0.81763908 1.416578403 0.334641748 0.356642525 1.366479335 5300.794313 0.158838625 0.088084101 55.59377332 -1.745026152 0.598939322 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNKK ddPTM_BT-474_Pertuzumab_2h_R1 3 YKLDEDEDEDDADLSKYNLDASEEEDSNKK 30 3 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLS(0.151)KY(0.003)NLDAS(0.837)EEEDS(0.009)NKK;YKLDEDEDEDDADLSKYNLDAS(1)EEEDSNKK;YKLDEDEDEDDADLSKYNLDAS(1)EEEDSNKK 206.64 8.70E-26 1022231000 603787 337903 314557 195986 380410 346432 318790 551463 616145 359605 TRUE FALSE 580190.3365 328266.3373 371404.4472 206100.8609 392646.2331 353437.0924 322691.4474 540075.0963 546202.8027 335248.633 1.730627001 0.979172784 1.10784776 0.614770175 1.17120905 1.054253642 0.962543663 1.610968825 1.62924692 1 18.35487192 1.745027743 14.02064203 1.462840412 1.068792483 0.18364688 0.306529719 0.131579161 221.5786717 0.138009652 0.076019052 55.59397698 -1.745027743 -0.394047929 DDEEADAIYAALDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDEEADAIYAALDKR 15 1 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 171.21 1.76E-06 195428000 99422 81413 92112 94731 85715 89571 101156 124569 151450 133782 FALSE TRUE 95536.47832 79091.18095 108758.6874 99620.07826 88472.10082 91382.18699 102393.9774 121996.6066 134258.0309 124720.826 0.766002611 0.634145744 0.872017055 0.798744536 0.709361088 0.732693889 0.820985401 0.978157462 1.076468424 1 16.92834286 1.745102714 2.386160463 1.038461343 0.753015023 0.796757988 0.06050335 0.114656705 1.342563589 0.039065841 0.017192623 55.6035749 -1.745102714 -0.28544632 HAGVYSTGLAMVGAICDFCEAWVCHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HAGVYSTGLAMVGAICDFCEAWVCHGR 27 0 Q9Y3S2;D6RBR7;D6R8Y9;D6R9C8 Q9Y3S2 ZNF330 Zinc finger protein 330 0 88.79 0.0042203 99142000 98985 115530 98841 88587 93213 119980 118260 61091 94857 102670 FALSE TRUE 95116.55677 112235.1975 116703.7674 93158.98569 96211.2808 122406.0778 119707.3013 59829.4495 84089.23103 95716.06945 0.993736551 1.172584689 1.21927037 0.973284697 1.005173753 1.278845637 1.25064999 0.625072152 0.878527833 1 16.54647353 1.745113692 25 0.807356243 1.128069594 0.496708908 0.134376419 1.013858636 3880.221604 0.061946311 0.034352433 55.60498044 -1.745113692 0.32071335 VIPDSDAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIPDSDAHR 9 0 Q5EBL8;Q5EBL8-2 Q5EBL8 PDZD11 PDZ domain-containing protein 11 0 131.5 0.0013017 0 93334 123030 105330 130560 116180 106380 120300 99129 112690 126980 FALSE TRUE 89686.40409 119521.3049 124365.4741 137298.2172 119917.0352 108531.0765 121772.2674 97081.95151 99897.90364 118379.5315 0.757617495 1.009645023 1.050565689 1.159813825 1.012987919 0.916806099 1.028659819 0.820090689 0.84387818 1 16.85306013 1.745117962 24.99999993 0.873628396 0.998388729 0.156442195 0.106950614 2.11468406 8087.994775 0.050217951 0.027848352 55.60552715 -1.745117962 0.124760332 SWAQASVTHGAHGDGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SWAQASVTHGAHGDGGR 17 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 0 ; 159.26 1.87E-09 577530000 320680 464390 372990 711450 386370 439590 535640 164620 353510 373230 FALSE TRUE 308147.4711 451146.0519 440397.5901 748168.0198 398797.9419 448478.811 542195.3225 161220.5395 313381.0268 347950.7997 0.885606446 1.296580012 1.26568926 2.1502121 1.146133138 1.288914443 1.558252842 0.46334292 0.900647526 1 18.4085238 1.745121051 25 0.756570039 1.381603995 0.387568331 0.334466555 1.296724087 4957.216226 0.154171423 0.085496042 55.60592263 -1.745121051 0.625033956 SLETENRR ddPTM_BT-474_Pertuzumab_2h_R1 7 SLETENRR 8 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 164.71 0.00052672 15778344000 5829505 6425380 4831252 5732419 5503819 5671910 5734346 5459878 5899924 5859387 FALSE TRUE 5601681.5 6242134.454 5704366.707 6028269.832 5680854.337 5786599.906 5804524.642 5347129.611 5230189.362 5462525.499 1.025474664 1.142719508 1.044272783 1.103568273 1.039968479 1.059326846 1.062608246 0.978874993 0.957467267 1 22.38113668 1.745159089 3.865575756 0.974472224 1.070951426 0.603154738 0.033234999 0.122582132 3.921216393 0.016789112 0.008350136 55.61079314 -1.745159089 0.096479201 LESADKSDQNNTAEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LESADKSDQNNTAEGK 16 1 Q9NXG2 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 0 99.566 0.0021438 218330000 132410 124060 93812 92993 112100 112660 113010 138080 157800 132880 FALSE TRUE 127235.2708 120521.9303 110765.9152 97792.37987 115705.7983 114938.0624 114393.0502 135228.5997 139887.2056 123879.9192 1.027085516 0.972893194 0.894139388 0.789412687 0.934015771 0.927818351 0.923418831 1.091610332 1.129216151 1 16.91858282 1.745192702 5.591475389 1.082416663 0.919750641 0.528502968 0.064379581 0.123307426 9.707232546 0.033999844 0.017738272 55.61509744 -1.745192702 -0.162666022 EIQGHQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIQGHQPR 8 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 185.55 0.00021217 576650000 999681 1090907 847431 1027648 990701 1069691 1036048 1006153 1115496 1119394 FALSE TRUE 960612.3613 1059795.4 1000580.633 1080685.036 1022567.797 1091320.885 1048727.465 985375.5889 988869.5706 1043576.447 0.920500231 1.015541701 0.958799554 1.035559052 0.979868605 1.045750781 1.004935928 0.944229425 0.947577509 1 19.99310486 1.745268483 24.91451405 0.959420478 0.996861049 0.11749454 0.037266646 2.322850692 8655.129429 0.016425971 0.009108996 55.62480264 -1.745268483 0.037440571 DLQYITVS(ph)KEELSSGDSLSPDPWK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLQYITVSKEELSSGDSLSPDPWK 24 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 DLQYIT(0.17)VS(0.829)KEELSSGDSLSPDPWK 148.02 1.02E-07 67188000 120860 98977 96260 97279 93403 86987 92409 142080 140520 119290 TRUE FALSE 116136.6576 96154.27287 113656.3233 102299.5808 96407.39232 88745.93674 93539.92898 139145.9983 124568.7587 111210.382 1.044296903 0.864615975 1.021993821 0.919874377 0.866892016 0.798000466 0.841107883 1.251196118 1.120118072 1 16.76293195 1.745388541 25 1.141144302 0.90545066 0.534043724 0.091860574 0.997768073 3664.468559 0.042319608 0.023468384 55.64018195 -1.745388541 -0.235693642 S(ph)SEMLVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSEMLVK 7 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 S(0.993)S(0.007)EMLVK;S(0.997)S(0.003)EMLVK;S(0.991)S(0.009)EMLVK;S(0.996)S(0.004)EMLVK 137.14 0.0030549 802990000 1773910 1648570 1468950 1416870 1566660 1543200 1498920 1999020 1963600 1864890 TRUE FALSE 1704583.636 1601554.398 1734421.942 1489994.83 1617053.042 1574404.561 1517264.231 1957739.538 1740700.36 1738579.339 0.980446274 0.921185684 0.997608739 0.8570186 0.930100229 0.90556958 0.872703475 1.126057059 1.001219974 1 20.72947747 1.745402966 25 1.050733068 0.923283641 0.523797852 0.051773502 0.998687181 3660.086936 0.022836691 0.012664103 55.64203004 -1.745402966 -0.127449427 LQGS(ph)GVSLASK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQGSGVSLASK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LQGS(0.763)GVS(0.237)LASK;LQGS(0.994)GVS(0.006)LASK 122.66 0.00040497 366260000 865920 880970 819850 861260 731090 786250 843480 1082290 1110950 1191210 TRUE FALSE 832078.8891 855845.5982 968015.1325 905709.7318 754606.1738 802148.5137 853802.7606 1059940.333 984839.6135 1110528.286 0.749264021 0.770665285 0.871670848 0.815566558 0.679501984 0.722312546 0.768825767 0.954446948 0.886820828 1 20.08281471 1.745404898 6.096848108 0.939616008 0.768664872 0.68955475 0.054856524 0.09575874 9.533706493 0.029303304 0.015398689 55.64227746 -1.745404898 -0.170951136 HDIAFVEFDNEVQAGAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 HDIAFVEFDNEVQAGAAR 18 0 P09012;M0R268 P09012 SNRPA U1 small nuclear ribonucleoprotein A 0 ;;; 156.83 8.73E-09 1214960000 382600 726820 548950 901710 693480 910490 733620 456685 457611 670860 FALSE TRUE 367647.569 706091.8052 648157.4763 948247.3612 715786.414 928900.7316 742598.261 447254.2952 405664.9177 625422.0547 0.58783915 1.128984499 1.036352127 1.516171926 1.144485406 1.485238208 1.187355411 0.715123958 0.648625859 1 19.25447057 1.745503539 6.9504334 0.765294612 1.176155514 0.29879151 0.255374711 0.15565468 22.56304766 0.125793331 0.066727474 55.65491698 -1.745503539 0.410860903 STHHLASHGFYEFLNWFDER ddPTM_BT-474_Pertuzumab_2h_R1 1 STHHLASHGFYEFLNWFDER 20 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 122.57 1.05E-05 103290000 26747 58515 38726 73975 41366 36712 56838 15894 49662 25045 FALSE TRUE 25701.69767 56846.20949 45724.64966 77792.85862 42696.57496 37454.34179 57533.60045 15565.78335 44024.57796 23348.67984 1.100777339 2.434664824 1.958339828 3.331788313 1.828650495 1.604131028 2.464105073 0.666666529 1.885527501 1 14.51105336 1.745540007 25 1.188814096 2.127883871 0.312266684 0.624323209 1.707517601 6134.644859 0.279818606 0.155173874 55.65959057 -1.745540007 0.939069775 S(ph)FTLDDESLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFTLDDESLK 10 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.949)FT(0.051)LDDESLK;S(0.999)FT(0.001)LDDESLK 252.69 4.82E-17 146779000 279790 251190 209171 233880 256760 197668 219860 297390 279220 270920 TRUE FALSE 268855.4975 244026.3071 246972.8527 245950.5748 265018.9186 201664.9824 222550.7124 291248.7926 247524.1162 252570.3471 1.064477681 0.966171643 0.97783788 0.973790382 1.049287542 0.798450747 0.881143472 1.153139297 0.980020493 1 17.94632574 1.745557978 25 1.056976057 0.957653951 0.175371998 0.083763759 2.278392547 8164.561011 0.039348432 0.021820729 55.66189377 -1.745557978 -0.099322106 TLLEGSGLESIISIIHSSLAEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLLEGSGLESIISIIHSSLAEPR 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 343.45 1.85E-87 3527300000 291240 549530 449500 769860 428390 626510 573880 378860 398490 651990 FALSE TRUE 279858.0188 533857.9424 530734.6491 809592.5669 442169.5534 639178.4615 580903.3151 371036.4086 353255.0858 607830.1366 0.460421427 0.878301207 0.873162775 1.33193884 0.727455792 1.051574154 0.955700088 0.610427793 0.581174023 1 19.21330868 1.745569363 24.65423785 0.696812538 0.911465224 0.08813865 0.234735905 2.599120915 9172.723698 0.106534951 0.059077293 55.6633529 -1.745569363 0.214652686 GGS(ph)PDLWK ddPTM_BT-474_Pertuzumab_2h_R1 5 GGSPDLWK 8 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 GGS(1)PDLWK;GGS(1)PDLWK;GGS(1)PDLWK;GGS(1)PDLWK;GGS(1)PDLWK 132.01 0.0010286 20659200000 15676650 15341980 12546690 14206120 14198380 14969990 14432420 16993640 17983700 16823220 TRUE FALSE 15063989.19 14904441.75 14814155.98 14939299.56 14655083.79 15272693.45 14609048.27 16642715.4 15942265.77 15683768.32 0.960482766 0.950309992 0.944553355 0.952532532 0.934410882 0.973789789 0.931475649 1.061142644 1.016481845 1 23.9027689 1.745678635 21.23599771 1.029051411 0.949933134 0.785179791 0.018247581 0.203225708 610.351734 0.007676144 0.00425443 55.67736 -1.745678635 -0.079118277 AVTTVTQSTPVPGPSVPPPEELQVS(ph)PGPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVTTVTQSTPVPGPSVPPPEELQVSPGPR 29 0 P51610-2;P51610;H7C1C4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR;AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR;AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR;AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR 166.88 2.66E-12 1796620000 685360 730820 715430 840070 764250 872580 760390 690160 656550 806080 TRUE FALSE 658575.3735 709977.7291 844724.1157 883426.1134 788832.7953 890224.1655 769695.8803 675907.9548 582021.1965 751483.4836 0.876367063 0.944768241 1.124075424 1.17557622 1.049700775 1.184622397 1.024235259 0.89943155 0.774496325 1 19.51938187 1.745747718 3.6606181 0.873848268 1.064120355 0.343223741 0.103270967 0.222635001 6.309281385 0.058833945 0.028977062 55.68621728 -1.745747718 0.190272087 EHYPVSSPS(ph)SPS(ph)PPAQPGGVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EHYPVSSPSSPSPPAQPGGVSR 22 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 EHYPVS(0.104)S(0.123)PS(0.422)S(0.356)PS(0.995)PPAQPGGVSR;EHYPVSS(0.001)PS(0.541)S(0.458)PS(1)PPAQPGGVSR 120.57 3.14E-06 580510000 134808 191617 122904 170431 145965 153586 167482 124595 160283 161653 TRUE FALSE 129539.5543 186152.2708 145115.4868 179226.9643 150660.0968 156691.6142 169531.6948 122022.0697 142088.3458 150704.0983 0.859562253 1.235217043 0.962916659 1.189264037 0.999708027 1.039730279 1.124930886 0.809679837 0.942830005 1 17.20135913 1.745755297 25 0.903443792 1.063878103 0.247396785 0.11185315 1.742262525 6071.627093 0.046732005 0.025915294 55.68718917 -1.745755297 0.160434312 QPS(ph)MSETMPLYTLCK ddPTM_BT-474_Pertuzumab_2h_R1 4 QPSMSETMPLYTLCK 15 0 A0A0A0MR03;Q9Y5B0;K7EJD2 A0A0A0MR03 CTDP1 RNA polymerase II subunit A C-terminal domain phosphatase 1 QPS(0.994)MS(0.006)ETMPLYTLCK;QPS(0.999)MS(0.001)ETMPLYTLCK;QPS(0.997)MS(0.003)ETMPLYTLCK;QPS(0.991)MS(0.007)ET(0.002)MPLYTLCK 241.79 7.09E-18 318153000 310299 310532 251033 316493 309919 252627 290068 324256 332787 337605 TRUE FALSE 298172.172 301675.9314 296400.2473 332827.2417 319887.8261 257735.291 293617.939 317560.0003 295010.4149 314738.7126 0.947364147 0.958496427 0.941734319 1.057471573 1.016359962 0.818886526 0.932894262 1.008963904 0.93731849 1 18.26379511 1.745827617 25 0.981873954 0.954329489 0.045226387 0.060466901 6.553635213 22610.88984 0.029755302 0.01650082 55.69646311 -1.745827617 -0.027544465 SKAEVACIAVYETDVFVVGTER ddPTM_BT-474_Pertuzumab_2h_R1 3 SKAEVACIAVYETDVFVVGTER 22 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5;C9J6M0;Q86UP8-4;A0A087WW90;A0A0D9SF80;A0A494C0I1;A0A494C1N8;Q86UP8-3;Q86UP8;Q6EKJ0;Q86UP8-2;Q6EKJ0-2;Q86UP8-5 A0A494C1K3;A0A087WW90 GTF2I;GTF2IRD2;GTF2IRD2B General transcription factor II-I;General transcription factor II-I repeat domain-containing protein 2A;General transcription factor II-I repeat domain-containing protein 2B 0 ;; 177.5 5.80E-17 353424000 521158 511145 425190 456820 464804 413042 478559 519763 582075 540143 FALSE TRUE 500790.5692 496567.6451 502031.2913 480396.5349 479754.8428 421393.9922 484415.7482 509029.7124 516000.2863 503558.6335 0.994502995 0.986116833 0.996966903 0.954003175 0.95272886 0.836832027 0.961984794 1.01086483 1.024707456 1 18.94180025 1.745893286 4.77722052 1.013607561 0.952651576 0.26970913 0.043126061 0.256480393 13.45789842 0.024248617 0.012460961 55.70488554 -1.745893286 -0.060955986 KEPVGDDESVPENVLSFDDLTADALANLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEPVGDDESVPENVLSFDDLTADALANLK 29 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 165.46 7.58E-12 47939000 52260 53140 42391 42060 44448 49711 45943 60371 64493 54197 FALSE TRUE 50217.62142 51624.49923 50051.99668 44230.72164 45877.71029 50716.19048 46505.26418 59124.31775 57172.02502 50526.18892 0.99389292 1.021737446 0.990614922 0.875401897 0.907998629 1.003760457 0.920418998 1.170171727 1.131532503 1 15.62474374 1.745904517 14.50663982 1.112380489 0.95926949 0.5389932 0.059645226 0.081018975 139.1652432 0.028131589 0.015510389 55.70632614 -1.745904517 -0.153111 AHGVDK ddPTM_BT-474_Pertuzumab_2h_R1 7 AHGVDK 6 0 P30043;M0R192;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;; 121.68 0.019546 4161990000 6800810 6405980 5176070 5738750 5557150 5668010 6392720 4595450 5507690 6814820 FALSE TRUE 6535026.827 6223287.723 6111500.99 6034927.575 5735900.777 5782621.046 6470956.02 4500552.352 4882480.121 6353246.171 1.028612248 0.97954456 0.961949345 0.9498967 0.902829927 0.91018369 1.018527513 0.708386269 0.768501643 1 22.59906249 1.745919988 25 0.80024299 0.959963186 0.376172114 0.079825709 1.356970878 4622.793504 0.035088338 0.019458297 55.70831055 -1.745919988 0.159720196 EAANEAGDS(ph)SQDEAEDDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAANEAGDSSQDEAEDDVK 19 0 A0A0C4DH01;Q9NVU0-3;Q9NVU0-2;Q9NVU0-5;Q9NVU0-4;Q9NVU0 A0A0C4DH01 POLR3E DNA-directed RNA polymerase III subunit RPC5 1 EAANEAGDS(0.98)S(0.02)QDEAEDDVK 254.4 2.63E-29 0 57672 49369 37598 39547 44537 48916 45836 57091 61018 57118 TRUE FALSE 55418.11448 47961.04446 44392.79496 41588.02541 45969.57305 49905.11503 46396.95468 55912.0509 54091.49245 53249.34698 1.040728528 0.900687937 0.833677735 0.78100536 0.863288954 0.937196752 0.871314998 1.050004443 1.015815132 1 15.70047621 1.745992544 8.320304731 1.023072719 0.884561661 0.460351286 0.065377967 0.105976172 27.04901273 0.033149816 0.017802014 55.71761834 -1.745992544 -0.138511058 MTIAGTTDTPTDVTHHPIPSEEDINFILNEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MTIAGTTDTPTDVTHHPIPSEEDINFILNEVR 32 0 P43304;P43304-2 P43304 GPD2 "Glycerol-3-phosphate dehydrogenase, mitochondrial" 0 73.126 0.0015911 39894000 10949 16023 11876 27336 10536 15042 20954 5403.6 17401 15825 FALSE TRUE 10521.10098 15566.03973 14022.25738 28746.81424 10874.90001 15346.15955 21210.44132 5292.013772 15425.71143 14753.15865 0.713142265 1.055098782 0.95045798 1.948519291 0.737123504 1.040194843 1.437688146 0.35870378 1.045587036 1 13.84873625 1.746009203 25 0.74697978 1.1299278 0.128267602 0.379818193 2.805531167 9442.805769 0.170966559 0.094809853 55.71975557 -1.746009203 0.38294802 EIETTGQIMHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIETTGQIMHR 11 0 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 0 ; 78.83 0.028808 1315150000 1321860 1398960 1266030 1439390 1624640 1801390 1575710 1194250 1503870 1455990 FALSE TRUE 1270200.25 1359063.031 1494829.784 1513677.09 1676898.021 1837815.34 1594994.01 1169588.32 1333156.982 1357374.5 0.935777303 1.001243968 1.101265556 1.115150675 1.235398205 1.353948626 1.17505818 0.861654849 0.982158558 1 20.37238739 1.746012508 24.99999647 0.941131699 1.136943662 0.349714058 0.114163305 1.899735878 6391.248449 0.059157117 0.032805662 55.72017963 -1.746012508 0.195811963 DYDEEEQGYDS(ph)EKEKK ddPTM_BT-474_Pertuzumab_2h_R1 5 DYDEEEQGYDSEKEKK 16 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK 249.28 1.20E-20 10357770000 5553280 3435160 3701390 2175230 3830670 3162160 3883210 5310670 6775070 4742840 TRUE FALSE 5336251.678 3337192.6 4370313.51 2287493.881 3953886.979 3226101.042 3930733.886 5201002.809 6005992.457 4421603.222 1.206859008 0.754747188 0.9884002 0.517344901 0.894220214 0.729622465 0.888983857 1.176270811 1.35832913 1 22.07613814 1.746038868 3.867532642 1.206489428 0.836191298 0.384675073 0.187045038 0.182583224 5.834015659 0.095782944 0.047688087 55.72356179 -1.746038868 -0.37029813 VDSPLPSDKAPT(ph)PPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDSPLPSDKAPTPPGK 16 1 Q12893 Q12893 TMEM115 Transmembrane protein 115 1 VDSPLPSDKAPT(1)PPGK;VDSPLPSDKAPT(1)PPGK 122.57 0.00014972 453770000 657760 673930 689200 736330 580660 761380 822930 1224690 1607020 1301690 TRUE FALSE 632054.012 654710.1762 813753.7712 774332.0795 599337.4562 776775.6253 833001.2635 1199399.724 1424597.827 1213525.377 0.520841199 0.539510907 0.670570049 0.638084785 0.493881272 0.640098378 0.686430856 0.98835982 1.173933281 1 20.21077285 1.746045731 2.23630472 1.094398339 0.585071703 0.91140015 0.066171401 0.073216495 0.748714268 0.043338728 0.018714326 55.72444236 -1.746045731 -0.509326637 QS(ph)SSWTR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSSSWTR 7 0 Q92934;F5H1R6 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 QS(0.548)S(0.226)S(0.226)WTR 70.816 0.058744 285870000 410670 479430 419710 444710 460860 432300 459480 441320 495710 483800 TRUE FALSE 394620.5624 465757.1258 495560.9334 467661.5364 475683.9804 441041.4022 465103.2537 432206.5878 439439.079 451031.7951 0.874928479 1.032648099 1.098727271 1.036870441 1.054657312 0.977849914 1.031198374 0.958261906 0.974297342 1 18.78286961 1.746067913 14.06260993 0.974957448 1.020053322 0.081473706 0.056304401 0.247752163 388.8013465 0.02646976 0.014582165 55.72728862 -1.746067913 0.045095874 KDS(ph)S(ph)DRENPPHDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSSDRENPPHDSR 14 2 Q92613 Q92613 JADE3 Protein Jade-3 2 KDS(1)S(1)DRENPPHDSR 108.17 0.00045113 98923000 102370 124170 85565 107740 92562 101310 91818 137150 126730 112260 TRUE FALSE 98369.26722 120628.7932 101028.4989 113300.4743 95539.34079 103358.5576 92941.69615 134317.8046 112344.1417 104656.5302 0.93992479 1.152616019 0.965333923 1.082593452 0.912884658 0.987597787 0.888063993 1.283415419 1.073455631 1 16.67530281 1.746160127 25 1.143977112 0.99569429 0.247716045 0.099930427 1.914074268 6314.053543 0.04388299 0.024335357 55.73912249 -1.746160127 -0.148282822 ELFGKDEQQR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELFGKDEQQR 10 1 G3XA94;Q9NPL8 G3XA94 TIMMDC1 "Complex I assembly factor TIMMDC1, mitochondrial" 0 ;;; 52.79 0.088821 38852120000 16260540 25720750 25356900 19540830 23738060 27807120 20330010 12771770 8144850 13049440 FALSE TRUE 15625060.12 24987219.39 29939455.89 20549334.58 24501616.26 28369399.02 20578814.74 12508028.49 7220280.774 12165589.81 1.284365195 2.053925851 2.460995017 1.689135908 2.014009732 2.331937824 1.691559149 1.028148136 0.593500265 1 23.53630293 1.746205588 2.757934236 0.800717326 1.987849479 0.700655159 0.322215259 0.128064424 2.012850517 0.191055344 0.087870875 55.74495742 -1.746205588 1.187132153 REDFQDISVPVQEDELSKVEESSEIS(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 REDFQDISVPVQEDELSKVEESSEISPEPK 30 2 O94782 O94782 USP1 Ubiquitin carboxyl-terminal hydrolase 1 1 REDFQDISVPVQEDELSKVEESSEIS(1)PEPK;REDFQDISVPVQEDELSKVEES(0.001)SEIS(0.999)PEPK 297.32 2.41E-81 482340000 204827 175081 130288 123918 151304 148221 152044 190522 202460 176213 TRUE FALSE 196822.1344 170087.8613 153833.9398 130313.4228 156170.8306 151218.1302 153904.76 186587.6541 179477.5896 164277.9366 1.198104496 1.035366434 0.936424836 0.793249694 0.950650062 0.920501763 0.936855936 1.13580471 1.092524007 1 17.32577921 1.746214936 24.99477522 1.085720786 0.959602008 0.190244789 0.101421423 2.564048941 8395.708998 0.049553315 0.027479727 55.74615729 -1.746214936 -0.126118779 DDDDIDLFGS(ph)DDEEESEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DDDDIDLFGSDDEEESEEAKR 21 1 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(0.999)DDEEES(0.001)EEAKR;DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR 327.1 3.37E-80 1439935000 863527 624532 824530 753208 777759 704693 1029406 1145438 1490670 1428500 TRUE FALSE 829779.4102 606720.9588 973540.9126 792081.1551 802776.3246 718942.3753 1042004.179 1121784.305 1321455.391 1331746.423 0.623076132 0.455582946 0.731025739 0.59476875 0.602799685 0.539849301 0.782434374 0.842340768 0.992272529 1 20.34488797 1.746217591 1.405245936 0.998865386 0.590638281 0.830866186 0.072709623 0.149071584 0.562069987 0.055897312 0.021839695 55.74649809 -1.746217591 -0.408227105 EAETEPHEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAETEPHEGK 10 0 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 ;; 136.96 0.00010389 535153000 1081930 981710 1003470 1005270 975090 1016510 1061350 1222050 1360820 1322240 FALSE TRUE 1039646.979 953712.592 1184819.351 1057152.105 1006454.655 1037064.529 1074339.119 1196814.24 1206345.419 1232683.507 0.843401387 0.773688126 0.961170766 0.857602214 0.816474504 0.841306404 0.871544977 0.970901479 0.978633535 1 20.233371 1.746235981 2.817344218 0.987477612 0.849548129 0.650160711 0.044424127 0.15438988 2.53394741 0.026960224 0.01247454 55.74885877 -1.746235981 -0.137929483 SES(ph)PKEPEQLR ddPTM_BT-474_Pertuzumab_2h_R1 9 SESPKEPEQLR 11 1 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 S(0.001)ES(0.999)PKEPEQLR;SES(1)PKEPEQLR;S(0.016)ES(0.984)PKEPEQLR;SES(1)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;SES(1)PKEPEQLR;S(0.049)ES(0.951)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;S(0.006)ES(0.994)PKEPEQLR 197.79 1.33E-07 38194510000 27009400 22583470 19661070 18794070 21019660 20031490 21077320 26784410 28680010 24013290 TRUE FALSE 25953842.79 21939411.55 23214262.71 19764034.2 21695776.45 20436540.45 21335270.55 26231302.57 25424375.5 22386848.48 1.159334366 0.980013402 1.036959835 0.882841291 0.969130446 0.912881528 0.953026978 1.17172824 1.135683548 1 24.41614811 1.746262412 24.99999968 1.115643197 0.979399589 0.296495359 0.08195103 1.816346199 5911.885164 0.037531147 0.020813046 55.75225163 -1.746262412 -0.136243608 S(ph)PLHIKDDVLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLHIKDDVLPK 12 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 S(1)PLHIKDDVLPK 153.74 4.28E-05 115360000 512820 440920 397970 340380 453130 416180 437940 510790 566940 533550 TRUE FALSE 492778.4274 428345.3933 469892.0318 357947.0526 467705.338 424595.4447 443299.6407 500242.008 502583.348 497412.1833 0.990684274 0.861147772 0.944673347 0.719618587 0.940277206 0.853608856 0.891211867 1.005689094 1.010396136 1 18.92408232 1.746263172 4.435118013 1.007194227 0.880923087 0.388996514 0.068480986 0.181047952 7.92353183 0.034221062 0.017423627 55.75234927 -1.746263172 -0.12627114 LGS(ph)PVDNLEDMDRDDLTDDSVFTR ddPTM_BT-474_Pertuzumab_2h_R1 10 LGSPVDNLEDMDRDDLTDDSVFTR 24 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR 279.28 2.23E-52 3579718000 724799 688013 569021 624329 646950 667828 645054 786740 810481 798432 TRUE FALSE 696473.0538 668391.5429 671855.7525 656550.6945 667759.7343 681331.9397 652948.3638 770493.5441 718478.5947 744353.4895 0.935675138 0.897949096 0.90260308 0.882041535 0.897100294 0.915333843 0.877201992 1.035117797 0.965238432 1 19.50562839 1.746264607 13.53344108 0.999519082 0.900721437 0.810570176 0.021926475 0.038869004 54.24630663 0.009493402 0.005224078 55.7525335 -1.746264607 -0.098797645 TLSVAAAFNEDEDS(ph)EPEEMPPEAK ddPTM_BT-474_Pertuzumab_2h_R1 5 TLSVAAAFNEDEDSEPEEMPPEAK 24 0 Q8WW12 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 T(0.004)LS(0.004)VAAAFNEDEDS(0.992)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK 123.72 7.15E-05 1039240000 647408 607320 519585 520231 563108 594295 576582 692900 761474 673521 TRUE FALSE 622106.5796 589999.8282 613485.5676 547080.1843 581220.8802 606312.0521 583638.383 678591.3729 675034.6639 627902.8228 0.990768885 0.939635572 0.977039034 0.871281613 0.925654192 0.965614471 0.929504315 1.080726743 1.075062318 1 19.26018177 1.746265529 8.573961094 1.057053106 0.941426507 0.643408029 0.037132528 0.066039592 18.6541768 0.017598806 0.009470529 55.75265183 -1.746265529 -0.115626599 SAS(ph)PHDVDLCLVSPCEFEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.008)AS(0.992)PHDVDLCLVSPCEFEHR;S(0.133)AS(0.867)PHDVDLCLVSPCEFEHR 287.53 1.16E-45 4100300000 289960 321790 286270 381120 323130 304340 347340 251145 307880 356020 TRUE FALSE 278628.0426 312612.8643 338005.357 400789.6489 333523.7699 310493.9633 351590.8508 245958.768 272930.7531 331906.4483 0.839477642 0.941870415 1.018375385 1.207538 1.004872824 0.935486385 1.059307081 0.741048477 0.822312295 1 18.34041713 1.746322254 25 0.833122088 1.004958915 0.271891032 0.108076507 1.982121069 6401.569937 0.051080336 0.028326729 55.75993442 -1.746322254 0.171836827 RDYEVDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDYEVDGR 8 1 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;F8VYC1;E9PIW2;E9PN83;A0A3B3ISW2;B7Z2T4;A0A3B3ITF1;F8W750;Q15700-2;Q15700-4;Q15700;Q15700-3;B5MCC5;H7C325;Q15700-5;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;C9JUA9;Q12959-8;A0A590UJX2;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1;DLG2 Disks large homolog 2;Disks large homolog 1 0 98.044 0.01251 268050000 218120 265220 208100 268430 245170 244210 252640 211190 233590 252700 FALSE TRUE 209595.6293 257656.1853 245708.2992 282283.7045 253056.1157 249148.0935 255731.8839 206828.8527 207073.8425 235584.4039 0.889683807 1.093689485 1.042973538 1.198227471 1.074163279 1.05757465 1.085521281 0.877939495 0.878979419 1 17.84588451 1.746348081 8.642745715 0.910726765 1.068959167 0.415247997 0.077912818 0.099834742 28.98024315 0.036594568 0.019703636 55.76325048 -1.746348081 0.158232402 AQHPNIVTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQHPNIVTVR 10 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 0 ; 68.355 0.066135 240070000 253940 263950 245950 303320 275240 269970 296040 218100 285790 286340 FALSE TRUE 244015.7441 256422.4044 290398.6361 318974.3815 284093.3446 275428.9784 299663.0261 213596.1588 253348.3173 266945.9368 0.914101735 0.960578039 1.087855615 1.194902554 1.064235508 1.031778126 1.122560732 0.800147631 0.949062272 1 18.02618806 1.746443709 25 0.900907443 1.056438291 0.335364634 0.087715539 1.846458987 5871.300302 0.04210787 0.023350955 55.77553036 -1.746443709 0.155530848 SAVCIADPLPTPS(ph)QEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAVCIADPLPTPSQEK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 SAVCIADPLPTPS(1)QEK 237.59 9.61E-20 70816000 373680 345380 304530 277020 303830 295860 309390 401810 384790 412470 TRUE FALSE 359076.1725 335530.1006 359565.3452 291317.0354 313602.9679 301842.4919 313176.4074 393512.4831 341110.2524 384533.0395 0.933797972 0.872565075 0.935070094 0.757586489 0.815542322 0.784958536 0.814433027 1.023351553 0.887076577 1 18.55274804 1.746444967 24.99999982 0.967360441 0.842599283 0.448364405 0.063629316 1.653695483 5257.519262 0.030244632 0.016772198 55.77569195 -1.746444967 -0.124761158 SLS(ph)GSSPCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLS(0.958)GS(0.042)SPCPK 112.94 0.0016306 572080000 195920 170370 141620 158050 179380 170620 161670 205000 213590 176790 TRUE FALSE 188263.2298 165511.2144 167213.8843 166206.9794 185149.9206 174070.0533 163648.5658 200766.6784 189344.1586 164815.8558 1.142264067 1.004219003 1.014549744 1.008440472 1.123374445 1.056148709 0.992917611 1.218127208 1.14882247 1 17.33049552 1.746460283 25 1.142451624 1.047402543 0.172907025 0.069525221 2.208428975 7007.50477 0.030683623 0.017015711 55.77765897 -1.746460283 -0.095049081 GGVTGSPEASISGS(ph)KGDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGVTGSPEASISGSKGDLK 19 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVTGSPEASIS(0.013)GS(0.987)KGDLK;GGVTGSPEASIS(0.009)GS(0.991)KGDLK 184.34 1.52E-14 1594980000 1292670 947200 752610 629850 541850 570640 662620 1280770 1160320 932710 TRUE FALSE 1242151.027 920186.7834 888623.3687 662356.634 559279.0973 582178.7318 670729.3418 1254321.652 1028605.338 869536.7209 1.428520495 1.058249481 1.021950364 0.761735092 0.64319204 0.669527483 0.771364021 1.442517172 1.182934905 1 19.72988743 1.746483585 25 1.242597415 0.893009898 0.242487736 0.240305348 2.339701765 7402.150078 0.119049747 0.066019216 55.78065177 -1.746483585 -0.349587517 KYCEDESR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYCEDESR 8 1 Q92797;A0A087WUE9 Q92797 SYMPK Symplekin 0 ; 107.21 0.0064904 269600000 554140 544820 417030 504750 551040 489720 546370 600920 697420 646970 FALSE TRUE 532483.5962 529282.267 492396.5978 530800.208 568764.702 499622.4739 553056.6395 588510.792 618251.8054 603150.1456 0.882837549 0.877529867 0.81637483 0.880046555 0.942990242 0.828355058 0.916946872 0.975728508 1.025037978 1 19.20215766 1.746496918 2.250259294 1.010549724 0.8726393 0.749361471 0.03347217 0.136958152 1.41814645 0.021995118 0.009520018 55.78236434 -1.746496918 -0.137910423 SLS(ph)ELESLKLPAESNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSELESLKLPAESNEK 17 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 S(0.048)LS(0.95)ELES(0.002)LKLPAESNEK 83.905 0.0032793 161630000 105870 93720 77681 75594 82327 89844 82092 119350 119180 99690 TRUE FALSE 101732.4834 91047.19736 91719.6847 79495.4154 84975.12272 91660.70724 83096.66645 116885.3808 105651.186 92937.90751 1.094628512 0.979656201 0.986892078 0.855360504 0.914321454 0.986257488 0.894109505 1.25767175 1.136793251 1 16.50397954 1.746529124 25 1.151705386 0.956006091 0.460868714 0.08474002 1.35615436 4265.900313 0.038307573 0.021243588 55.78650121 -1.746529124 -0.195699295 S(ph)CETSSQDLGFSYYPAENLIEYK ddPTM_BT-474_Pertuzumab_2h_R1 4 SCETSSQDLGFSYYPAENLIEYK 23 0 S5FZ81;Q8WUB8-3;Q8WUB8-2;Q8WUB8 S5FZ81 PHF10 PHD finger protein 10 1 S(0.974)CET(0.026)S(0.001)SQDLGFSYYPAENLIEYK;S(0.87)CET(0.129)SSQDLGFSYYPAENLIEYK;S(0.907)CET(0.092)S(0.001)SQDLGFSYYPAENLIEYK;S(0.881)CET(0.113)S(0.003)S(0.003)QDLGFSYYPAENLIEYK 276.36 5.99E-52 385165000 428778 383103 357223 338132 357585 346039 361662 463689 485326 432673 TRUE FALSE 412020.8817 372177.2775 421781.1425 355583.033 369087.0463 353036.1457 366088.1277 454113.6601 430233.8271 403367.6723 1.021452412 0.922675026 1.045649345 0.881535774 0.915013948 0.875221714 0.907579246 1.125805788 1.066604631 1 18.62173594 1.746607544 20.06632446 1.072018064 0.936441471 0.481411721 0.059587367 0.367308211 922.4984579 0.027591067 0.015286823 55.79657539 -1.746607544 -0.135576593 EHGVGGVSQCPEPGLR ddPTM_BT-474_Pertuzumab_2h_R1 3 EHGVGGVSQCPEPGLR 16 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 174.87 3.72E-09 1880790000 639120 790400 595870 708930 738100 797490 792180 582480 790750 755610 FALSE TRUE 614142.4838 767858.5659 703556.9641 745517.9623 761841.6568 813615.7942 801874.9358 570451.5844 700987.3751 704431.8617 0.871826669 1.090039516 0.99875801 1.058325159 1.08149801 1.154995733 1.138328601 0.80980378 0.995110263 1 19.42610064 1.746624005 25 0.919858501 1.060190131 0.273622032 0.089383699 2.045710813 6359.036294 0.04072446 0.02258374 55.79869024 -1.746624005 0.14033163 SEAEDLAEPLSSTEGVAPLSQAPS(ph)PLAIPAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEAEDLAEPLSSTEGVAPLSQAPSPLAIPAIK 32 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 SEAEDLAEPLSSTEGVAPLS(0.008)QAPS(0.992)PLAIPAIK 142.04 3.88E-10 115610000 105630 87155 90343 95495 91484 105600 98861 128070 137440 136820 TRUE FALSE 101501.8628 84669.42473 106669.9898 100423.5084 94426.66594 107735.3044 100070.8905 125425.3097 121838.3874 127553.0595 0.795761883 0.663797678 0.83627935 0.787307719 0.740293226 0.844631283 0.784543239 0.983318708 0.955197687 1 16.96073798 1.746713081 4.631903677 0.978369 0.777051849 0.778526937 0.048960514 0.081812874 3.970777049 0.025099757 0.012861926 55.810136 -1.746713081 -0.201317152 TATNDEESPLSVS(ph)SPEGTGTWLHYTSGVGTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TATNDEESPLSVSSPEGTGTWLHYTSGVGTGR 32 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 TATNDEESPLSVS(0.978)S(0.021)PEGTGTWLHYTSGVGTGR 244.03 4.19E-47 78628000 50392 50426 43164 52614 40019 49905 46171 59357 55275 60857 TRUE FALSE 48422.62493 48987.89985 50964.69498 55329.41485 41306.24748 50914.11329 46736.05451 58131.25721 49000.41373 56735.10118 0.853486183 0.86344959 0.898292132 0.975223692 0.728054531 0.89740059 0.823759076 1.024608329 0.863670157 1 15.79195397 1.746745986 25 0.961366092 0.864669708 0.295582586 0.07065732 2.333234119 7144.422648 0.031306576 0.01736105 55.81436476 -1.746745986 -0.096696384 VIPNLPSEGQPALVEVHSMEALLQHTSEQEEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIPNLPSEGQPALVEVHSMEALLQHTSEQEEMR 33 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 111.61 3.79E-06 84365000 16062 29845 19482 35206 28243 34409 30177 17907 28098 22207 FALSE TRUE 15434.27928 28993.84982 23002.83077 37022.98588 29151.46174 35104.77356 30546.31515 17537.21419 24908.43284 20702.90011 0.745512909 1.400472865 1.111092197 1.788299498 1.408085901 1.695645217 1.475460684 0.847089736 1.203137372 1 14.33754526 1.746831187 25 1.015882065 1.3952811 0.245747195 0.286019488 2.547840769 7720.976454 0.132101059 0.073256954 55.82531565 -1.746831187 0.379399036 ELEDS(ph)PQENVSVTEIIKPCDDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEDSPQENVSVTEIIKPCDDPK 23 1 Q5F1R6;Q5F1R6-3;Q5F1R6-2;A0A2R8Y534;A0A2R8Y4Q0 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 1 ELEDS(0.945)PQENVS(0.053)VT(0.002)EIIKPCDDPK;ELEDS(0.999)PQENVS(0.001)VTEIIKPCDDPK 184.19 2.07E-17 325470000 422740 339380 319000 278570 361800 371630 381840 450780 538530 509300 TRUE FALSE 406218.8534 329701.2147 376650.3961 292947.0311 373437.6256 379144.6132 386513.0721 441471.2355 477398.3321 474804.6574 0.855549429 0.694393388 0.793274435 0.616984325 0.786507924 0.798527578 0.814046506 0.929795504 1.005462614 1 18.85697456 1.746883174 1.245103132 1.01394432 0.744736565 0.735466661 0.060539328 0.208925656 0.6087671 0.047849795 0.018722661 55.83199855 -1.746883174 -0.269207755 QLSST(ph)SPLAPYPTSQMVSSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLSSTSPLAPYPTSQMVSSDR 21 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 QLSST(0.5)S(0.5)PLAPYPTSQMVSSDR 253.95 2.50E-35 166950000 123050 169770 152980 170260 139690 163660 140420 118880 108770 111380 TRUE FALSE 118241.07 164928.3258 180626.889 179047.139 144183.2557 166969.3173 142138.502 116425.0865 96422.8856 103836.1334 1.13872759 1.588351958 1.739537896 1.72432402 1.388565338 1.608007847 1.368873217 1.121238654 0.92860628 1 16.66394904 1.746905204 1.879568915 0.963443557 1.54716964 0.662329444 0.165687632 0.189995634 1.344141908 0.119301279 0.049019723 55.8348308 -1.746905204 0.583726083 KDFALDSEESR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDFALDSEESR 11 1 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4;H3BNB1;H3BTH2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 96.866 0.010732 322360000 588700 540640 379070 434930 505280 462070 479160 586570 576850 619960 FALSE TRUE 565692.9532 525221.4765 447576.3814 457376.7894 521532.7901 471413.372 485024.1034 574457.1245 511368.4064 577969.557 0.978759082 0.908735538 0.774394388 0.791351004 0.902353392 0.815637028 0.839186247 0.993922807 0.884767027 1 19.14063398 1.746959649 25 0.954661182 0.854758503 0.339431829 0.064256598 2.282153711 6809.785514 0.030452864 0.016887726 55.84183085 -1.746959649 -0.099902679 SRPTS(ph)EGS(ph)DIESTEPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 SRPT(0.038)S(0.962)EGS(0.863)DIES(0.117)T(0.02)EPQK;S(0.001)RPT(0.048)S(0.946)EGS(0.694)DIES(0.245)T(0.066)EPQK 218.25 5.63E-14 668010000 1704900 1554500 1322920 1334060 1526250 1516370 1456580 1721520 1806630 1606440 TRUE FALSE 1638270.623 1510167.182 1562001.072 1402910.996 1575343.217 1547032.04 1474406.062 1685970.01 1601548.936 1497634.388 1.093905586 1.008368394 1.042978904 0.936751324 1.051887717 1.032983786 0.984489989 1.125755407 1.069385792 1 20.51425404 1.746970769 25 1.076630589 1.0202716 0.129458105 0.048820483 2.859053448 8519.901709 0.021479598 0.011911709 55.8432607 -1.746970769 -0.056358989 TEYGDLELCIEVVDNVQDAIDHIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 TEYGDLELCIEVVDNVQDAIDHIHK 25 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 92.336 0.0070782 15982000 17338 22792 14218 28535 12727 17385 25648 867.29 22966 7438.9 FALSE TRUE 16660.41179 22141.99448 16787.50888 30007.69477 13136.37551 17736.53661 25961.8879 849.3801584 20358.99596 6935.056677 2.402346883 3.192763305 2.420673638 4.326957394 1.894198725 2.557518624 3.743572563 0.122476311 2.935663962 1 12.75969196 1.746995227 25 1.322957044 2.923320212 0.379531058 0.926221369 1.875126698 5571.583528 0.398317986 0.220887746 55.84640572 -1.746995227 1.600363168 FHDNFGFDDLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 FHDNFGFDDLVR 12 0 O00165-3;O00165;O00165-2;O00165-5;O00165-4 O00165-3 HAX1 HCLS1-associated protein X-1 0 ; 145.81 6.42E-05 211003000 181432 238650 213880 269090 211367 192992 247720 129859 205576 207893 FALSE TRUE 174341.4369 231843.9357 252532.8737 282977.7671 218165.8115 196894.4305 250751.6715 127177.3663 182239.8743 193812.2219 0.899537888 1.196229698 1.302977032 1.460061519 1.125655592 1.015903066 1.293786682 0.656188578 0.94029093 1 17.56430003 1.747054418 25 0.842044721 1.191665086 0.427175443 0.168703658 1.718486679 5070.481986 0.078921925 0.043766181 55.85401766 -1.747054418 0.349620365 QAFEELRDDLVELSK ddPTM_BT-474_Pertuzumab_2h_R1 4 QAFEELRDDLVELSK 15 1 Q15397 Q15397 KIAA0020 Pumilio domain-containing protein KIAA0020 0 ;;; 102.38 0.0014191 106037000 90834 83724 77430 79514 78877 83820 83414 90186 97534 93088 FALSE TRUE 87284.10686 81336.27349 91423.32342 83617.72707 81414.15034 85514.89783 84434.84548 88323.62758 86462.34922 86783.06685 1.005773477 0.937236681 1.053469608 0.963525836 0.938134054 0.985386907 0.97294148 1.017751859 0.996304375 1 16.40512595 1.747066647 25 1.005528247 0.978736799 0.114465777 0.032032887 4.119010812 12135.82649 0.014463993 0.008021019 55.8555904 -1.747066647 -0.026791448 ILEQEEEEEQAGKPGEPSKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILEQEEEEEQAGKPGEPSKK 20 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 274.95 9.53E-45 964120000 884990 662220 620980 530880 689870 659600 671630 916960 1028550 834920 FALSE TRUE 850403.6124 643334.134 733204.8996 558278.7804 712060.2951 672937.5639 679849.6088 898024.4556 911793.316 778370.1247 1.092544004 0.826514422 0.941974616 0.717240761 0.914809385 0.86454701 0.873427162 1.153724208 1.171413556 1 19.57009681 1.747077644 7.253048234 1.119583028 0.882828054 0.50272407 0.098957465 0.096330201 15.90583097 0.045732465 0.024366986 55.85700482 -1.747077644 -0.236754974 SELCSS(ph)PLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SELCSSPLGK 10 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 SELCS(0.104)S(0.896)PLGK;SELCS(0.182)S(0.818)PLGK 177.57 2.42E-06 1616350000 2615300 2660900 2147500 2294200 2344200 2499100 2457300 2736600 2914500 2911600 TRUE FALSE 2513091.185 2585013.737 2535601.021 2412603.937 2419603.322 2549633.514 2487373.172 2680088.254 2583658.179 2714394.739 0.925838512 0.95233523 0.934131276 0.888818381 0.891396998 0.939300934 0.916363835 0.987361276 0.951835834 1 21.37219911 1.747139494 8.304231053 0.976569454 0.921157609 0.601993135 0.021758767 0.089321112 22.70123272 0.011002464 0.005912575 55.86496024 -1.747139494 -0.055411845 VSS(ph)PIEK ddPTM_BT-474_Pertuzumab_2h_R1 4 VSSPIEK 7 0 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 VS(0.001)S(0.999)PIEK;VS(0.007)S(0.993)PIEK;VS(0.003)S(0.997)PIEK;VS(0.004)S(0.996)PIEK 139.78 0.0027993 1015420000 3685630 3638820 3405400 3619520 3623470 3554350 3336010 3318210 3568560 3107650 TRUE FALSE 3541591.505 3535044.416 4020831.533 3806323.861 3740022.203 3626221.392 3376837.088 3249687.804 3163472.029 2897166.097 1.222433021 1.220173196 1.38784985 1.313809334 1.29092433 1.251644286 1.165565582 1.121678114 1.091919456 1 21.46621097 1.747199954 0.922676497 1.019994385 1.293491279 0.811214736 0.047328091 0.235530593 0.376696585 0.044429742 0.018702369 55.87273803 -1.747199954 0.273496894 EKQS(ph)DDEVYAPGLDIESSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQSDDEVYAPGLDIESSLK 20 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 1 EKQS(0.998)DDEVY(0.002)APGLDIESSLK 143.54 1.01E-07 59816000 105220 73750 71440 66599 76925 85214 77763 106900 107260 99527 TRUE FALSE 101107.8861 71646.72221 84350.79717 70036.18237 79399.36249 86937.08546 78714.68686 104692.4776 95084.29447 92785.94764 1.089689642 0.772172123 0.909090216 0.75481454 0.855726158 0.936963923 0.84834707 1.128322556 1.024770419 1 16.50161871 1.747236276 24.99907912 1.057605454 0.874199136 0.41023493 0.093092525 1.738000195 5020.108896 0.040576533 0.022501739 55.87741107 -1.747236276 -0.183406318 VSFELFADKVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSFELFADKVPK 12 1 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 162.31 5.75E-05 78125000000 30500000 29260000 24382500 23390200 25835700 23110700 26947000 31276000 35276000 32135000 FALSE TRUE 29308026.28 28425533.45 28788960.14 24597371.03 26666728.75 23578014.19 27276785.45 30630139.67 31271616.37 29958467.83 0.978288558 0.948831349 0.960962366 0.821049033 0.89012325 0.787023366 0.910486665 1.0224201 1.0438323 1 24.83646051 1.74726234 4.584856954 1.025718019 0.895394054 0.493388469 0.056910519 0.160745873 7.599289906 0.031714856 0.016241083 55.88076466 -1.74726234 -0.130323965 GLYDGPVCEVSVT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLYDGPVCEVSVTPK 15 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 1 GLYDGPVCEVSVT(1)PK;GLYDGPVCEVSVT(1)PK 250.08 1.17E-17 693020000 824220 650390 591990 581590 614250 613830 605340 854140 829920 745830 TRUE FALSE 792008.5712 631841.514 698975.7617 611605.9296 634007.9091 626242.0632 612748.332 836501.7105 735710.9609 695314.2698 1.139065608 0.908713572 1.005265953 0.879610783 0.911829279 0.90066045 0.881253785 1.203055578 1.058098464 1 19.40730567 1.747312097 25 1.102873031 0.941741174 0.3452509 0.087629099 1.923545692 5507.990855 0.038930591 0.021588928 55.88716726 -1.747312097 -0.161131858 TIHLSSIRPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TIHLSSIRPPR 11 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 83.045 0.010381 195920000 118720 189370 147760 235200 176310 181210 189910 124030 162540 174280 FALSE TRUE 114080.2911 183969.353 174463.5189 247338.7002 181981.1713 184874.1904 192234.1754 121468.7372 144089.1406 162475.8604 0.702136864 1.132287299 1.073781167 1.52231045 1.120050516 1.137856356 1.1831553 0.74761098 0.886834144 1 17.30986586 1.747453861 24.99999994 0.861616282 1.13850084 0.249371726 0.194182558 2.659505656 7493.681318 0.090273734 0.050061274 55.90541311 -1.747453861 0.276884559 GSFS(ph)DTGLGDGK ddPTM_BT-474_Pertuzumab_2h_R1 7 GSFSDTGLGDGK 12 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GSFS(0.975)DT(0.025)GLGDGK;GSFS(0.988)DT(0.012)GLGDGK;GSFS(0.999)DT(0.001)GLGDGK;GSFS(0.995)DT(0.005)GLGDGK;GSFS(0.997)DT(0.003)GLGDGK;GSFS(0.991)DT(0.009)GLGDGK;GSFS(1)DTGLGDGK 258.02 3.36E-21 7264890000 13847790 13222510 10590910 11310220 12786440 12789360 12245000 14759690 15564030 13813890 TRUE FALSE 13306603.06 12845416.96 12504923.03 11893941.81 13197727.45 13047969.62 12394857.97 14454897.24 13797266.56 12878262.93 1.033260707 0.997449503 0.971010074 0.923567245 1.024806492 1.013177763 0.962463497 1.122426008 1.071360838 1 23.61843467 1.747466211 25 1.074626822 0.988738995 0.40398753 0.041319296 1.789623464 5035.606158 0.018804463 0.010427974 55.90700296 -1.747466211 -0.085887828 SQHFFDTSVPLMDDGDDNTLYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQHFFDTSVPLMDDGDDNTLYHR 23 0 H3BU86;O14662;F8W9Z6;B7ZBM8;O14662-6;O14662-2;O14662-5;Q96NX8;O14662-4 H3BU86;Q96NX8 STX16-NPEPL1;STX16 Syntaxin-16 0 274.11 6.33E-52 214490000 86519 151920 107350 185860 117240 129730 150810 81639 132400 130150 FALSE TRUE 83137.74183 147587.3903 126750.533 195452.2569 121011.1311 132353.2295 152655.6579 79953.12612 117370.5071 121334.8246 0.685192748 1.216364641 1.044634411 1.610850451 0.997332229 1.090809913 1.258135564 0.658946237 0.967327455 1 16.88863416 1.747551906 25 0.849621762 1.141152586 0.192705968 0.235205701 2.994728178 8345.995152 0.105264553 0.058374714 55.91803563 -1.747551906 0.291530824 LDRETEELHHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDRETEELHHDR 12 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 64.65 0.037777 77362000 73955 92899 70384 92270 92292 104640 97143 46462 77757 73749 FALSE TRUE 71064.75684 90249.61148 83103.95448 97032.06576 95260.656 106755.8925 98331.86509 45502.54346 68930.35134 68753.91454 1.033610338 1.312646881 1.20871597 1.411295145 1.385530651 1.552724571 1.43020024 0.661817495 1.002566207 1 16.06915424 1.747562746 25 0.870071319 1.341349658 0.623852437 0.158222386 1.307796709 3640.294012 0.074176398 0.041134543 55.91943128 -1.747562746 0.47127834 TPHYGSQTPLHDGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPHYGSQTPLHDGSR 15 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ;; 144.73 2.42E-06 827440000 189146 262125 250726 295720 222362 286561 291351 178758 265269 275609 FALSE TRUE 181753.9652 254649.4516 296037.7656 310982.1446 229514.4757 292355.4598 294916.6407 175066.5848 235156.7752 256941.7569 0.707374182 0.991078502 1.15215903 1.210321547 0.89325487 1.137827744 1.147795688 0.681347349 0.915214319 1 17.97108184 1.747618946 25 0.838556917 1.042465069 0.183503999 0.159449808 3.032374502 8388.212548 0.073713985 0.040878143 55.92666804 -1.747618946 0.203908152 AREQAEAEVASLNR ddPTM_BT-474_Pertuzumab_2h_R1 3 AREQAEAEVASLNR 14 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;; 299.46 8.08E-44 3802010000 1386730 1619630 1002730 1170590 1297900 1506000 1278700 1231150 1312370 1223380 FALSE TRUE 1332535.058 1573439.738 1183945.617 1231004.29 1339648.132 1536452.352 1294349.113 1205726.322 1163395.26 1140519.383 1.168358099 1.379581761 1.03807584 1.07933658 1.174594796 1.34715146 1.13487691 1.057173022 1.02005742 1 20.12125953 1.747634474 2.887202454 1.020178894 1.194585947 0.374403785 0.099185256 0.274177208 4.718214734 0.06091928 0.02841649 55.92866774 -1.747634474 0.174407053 LGIDDLVHFDFMDPPAPETLMR ddPTM_BT-474_Pertuzumab_2h_R1 8 LGIDDLVHFDFMDPPAPETLMR 22 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;;;;;; 144.01 1.03E-07 1751842300 987392.7 946634.6 857268.4 869361.9 889597.7 970630.5 948690.4 915319.6 1032752.5 1010618.2 FALSE TRUE 948804.3017 919637.5081 1012195.87 914229.7718 918212.4179 990257.3137 960300.7569 896417.9304 915518.7659 942168.1291 1.007043512 0.976086411 1.074326162 0.970346739 0.974573847 1.05104098 1.019245639 0.951441577 0.971714854 1 19.84562501 1.747644946 25 0.970623447 1.01016788 0.194014311 0.033354738 3.253527163 8974.152552 0.015271464 0.00846869 55.93001637 -1.747644946 0.039544432 GTVSFHSHSDHR ddPTM_BT-474_Pertuzumab_2h_R1 3 GTVSFHSHSDHR 12 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;; 184.87 7.96E-06 299597000 88658 209483 173818 247552 152952 157048 205316 14433.8 132765 78613 FALSE TRUE 85193.14734 203508.7499 205230.7792 260328.1884 157871.84 160223.6182 207828.7186 14135.73699 117694.0738 73288.47149 1.162435859 2.776818043 2.800314633 3.552102849 2.154115603 2.186204937 2.835762766 0.192878043 1.605901602 1 16.16129866 1.747652325 25 0.910263446 2.533570875 0.536989611 0.664102188 1.565742018 4315.245216 0.301312909 0.167093293 55.93096666 -1.747652325 1.623307428 STASDKEEVKPDDLEWASQQSTETGS(ph)LDGSCR ddPTM_BT-474_Pertuzumab_2h_R1 1 STASDKEEVKPDDLEWASQQSTETGSLDGSCR 32 2 Q93073;Q93073-2 Q93073 SECISBP2L Selenocysteine insertion sequence-binding protein 2-like 1 STASDKEEVKPDDLEWASQQSTET(0.001)GS(0.999)LDGSCR 169.7 1.71E-14 74415000 106180 99920 97694 76740 89505 96229 97147 126200 140700 125370 TRUE FALSE 102030.3682 97070.37943 115349.479 80700.5606 92384.00961 98174.81631 98335.91405 123593.9259 124728.3259 116878.5782 0.872960381 0.830523274 0.986917198 0.690464941 0.79042722 0.839972712 0.841351046 1.057455761 1.06716156 1 16.83465101 1.747656879 5.347843779 1.0466134 0.83377149 0.636883002 0.070980707 0.104262092 7.263072309 0.036204495 0.018874451 55.9315531 -1.747656879 -0.21284191 VTEGLVDVILYHQPDDK ddPTM_BT-474_Pertuzumab_2h_R1 6 VTEGLVDVILYHQPDDK 17 0 O43390;O43390-3;B4DT28 O43390 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 264.52 1.78E-27 3437700000 4638310 4078620 3624900 3670890 4141110 4086640 4060680 4527870 4939380 4506540 FALSE TRUE 4457039.717 3962301.751 4280000.065 3860345.073 4274312.564 4169274.661 4110375.817 4434367.902 4378682.29 4201308.032 1.06086954 0.94311146 1.018730365 0.918843618 1.01737662 0.992375381 0.978356213 1.055473169 1.042218818 1 22.00240713 1.747667243 18.94171232 1.036568708 0.98767026 0.191287743 0.03970317 0.549190185 1150.490908 0.016961759 0.009393372 55.93288784 -1.747667243 -0.048898448 GGHS(ph)SPASSDKNSNSNHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGHSSPASSDKNSNSNHR 18 1 Q13029-5;Q13029-3;Q13029-2;Q13029 Q13029-5 PRDM2 PR domain zinc finger protein 2 1 GGHS(0.5)S(0.5)PASSDKNSNSNHR 62.684 0.029901 31997000 33893 34903 30799 40349 38623 35055 38948 20898 29051 28999 TRUE FALSE 32568.42409 33907.60061 36365.06442 42431.41673 39865.34387 35763.83612 39424.65727 20466.449 25753.25227 27034.8719 1.20468202 1.254217173 1.345116949 1.569506853 1.474589708 1.322877957 1.458289036 0.757038875 0.952593834 1 14.7225339 1.747704778 10.79604489 0.896000921 1.379016131 0.775373409 0.11645099 0.047079446 29.84669395 0.057841684 0.031551224 55.93772228 -1.747704778 0.483015211 ETERAS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETERASPIK 9 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ETERAS(1)PIK;ETERAS(1)PIK 96.059 0.0046175 2862300000 4420900 3806100 4432700 4376500 4454400 4315600 5444900 5889400 6898700 7140200 TRUE FALSE 4248126.34 3697553.755 5233787.495 4602371.689 4597679.821 4402864.389 5511536.315 5767781.832 6115588.498 6656587.894 0.638183767 0.555472836 0.7862568 0.691401024 0.690696179 0.661429618 0.827982204 0.866477229 0.918727221 1 22.66635142 1.747759526 0.797749704 0.997450272 0.657141939 0.811594825 0.057453771 0.251064785 0.307978757 0.052764687 0.023942107 55.94477435 -1.747759526 -0.340308333 S(ph)SSSPELQTLQDILGDPGDKADVGR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSSSPELQTLQDILGDPGDKADVGR 25 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 1 S(0.313)S(0.313)S(0.313)S(0.059)PELQT(0.002)LQDILGDPGDKADVGR;S(0.25)S(0.25)S(0.25)S(0.25)PELQT(0.002)LQDILGDPGDKADVGR;S(0.332)S(0.332)S(0.332)S(0.005)PELQTLQDILGDPGDKADVGR;S(0.325)S(0.325)S(0.325)S(0.009)PELQT(0.015)LQDILGDPGDKADVGR;S(0.34)S(0.34)S(0.308)S(0.011)PELQTLQDILGDPGDKADVGR 113.43 0.0012496 280826000 144237 154521 105065.4 112049 139942 138685 130208 160218 168796 147294 TRUE FALSE 138600.0586 150114.2124 124053.0549 117831.8623 144443.3615 141489.3057 131801.5245 156909.4423 149634.9857 137317.6462 1.009339021 1.093189525 0.903402137 0.858097015 1.051892204 1.030379632 0.959829477 1.142675007 1.089699612 1 17.06715751 1.747826935 24.99999972 1.089109741 0.986744022 0.242055796 0.072814822 2.967670867 8024.524903 0.034981358 0.019399047 55.95345838 -1.747826935 -0.102365719 AS(ph)LGS(ph)LEGEAEAEASSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 AS(1)LGS(1)LEGEAEAEASSPK;AS(1)LGS(1)LEGEAEAEASSPK 214.9 1.43E-18 367820000 1096790 929330 862520 813910 685320 766670 817100 1445320 1364040 1208810 TRUE FALSE 1053926.234 902826.4183 1018396.551 855915.9926 707363.9402 782172.5927 827099.9142 1415473.637 1209199.898 1126936.222 0.935213736 0.801133552 0.903686057 0.759507039 0.627687642 0.694069973 0.733936755 1.25603704 1.072997632 1 20.10397444 1.747848633 24.99976844 1.12383442 0.775068754 0.678041451 0.104154264 1.255558087 3387.022833 0.05024473 0.027863316 55.95625406 -1.747848633 -0.348765667 ICHQIEYYFGDFNLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ICHQIEYYFGDFNLPR 16 0 P05455;E7ERC4;E9PFL9 P05455 SSB Lupus La protein 0 ; 232.93 1.22E-19 4924100000 926530 1037410 813170 985470 934610 879290 971780 825130 961190 936420 FALSE TRUE 890320.1833 1007824.083 960127.9079 1036330.225 964672.5794 897069.8462 983672.9343 808090.7772 852079.7408 872995.4393 1.019845171 1.154443697 1.099808618 1.187096952 1.105014455 1.027576784 1.126779007 0.92565292 0.976041457 1 19.73561459 1.74787978 10.47224106 0.96460979 1.105221775 0.59865544 0.050861646 0.067059236 38.10112338 0.023684259 0.012900581 55.96026729 -1.74787978 0.140611985 FFQTSGLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 FFQTSGLSK 9 0 P0CE72;P0CE71 P0CE72 OCM;OCM2 Oncomodulin-1;Putative oncomodulin-2 0 55.064 0.075721 213640000 364120 734880 424910 610250 652260 814420 514040 307210 203120 289180 FALSE TRUE 349889.7878 713921.9419 501700.6891 641745.0756 673240.5353 830888.1304 520330.9753 300866.0061 180062.6691 269593.581 1.297841686 2.64814147 1.860951908 2.380416749 2.497242452 3.082002647 1.930056989 1.115998404 0.667904141 1 18.04042662 1.74790356 3.000386147 0.859096424 2.313120697 0.64242481 0.456389384 0.138793577 2.58157277 0.260380503 0.122743263 55.96333152 -1.74790356 1.454024273 MIFDVESMKK ddPTM_BT-474_Pertuzumab_2h_R1 2 MIFDVESMKK 10 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 136.48 0.0001871 1349580000 2567680 2546070 1932000 1832990 1961910 2005100 2224860 2422650 2754230 2554380 FALSE TRUE 2467332.227 2473458.576 2281155.377 1927590.834 2025016.617 2045644.496 2252088.502 2372621.431 2441581.357 2381369.567 1.036097992 1.038670608 0.957917414 0.80944632 0.850357981 0.859020172 0.945711465 0.996326426 1.025284521 1 21.1833601 1.747920699 3.240124707 1.01112195 0.922171369 0.210285002 0.070868011 0.391736475 8.53184667 0.046147948 0.022177432 55.96554001 -1.747920699 -0.088950582 S(ph)PGGPGSHVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPGGPGSHVR 10 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 S(1)PGGPGSHVR;S(1)PGGPGSHVR;S(1)PGGPGSHVR 133.32 0.00012898 421278000 238680 257345 195759 235952 248165 258983 252379 205204 248731 253286 TRUE FALSE 229352.1217 250005.7726 231137.0059 248129.511 256147.4526 264219.8137 255467.6897 200966.4657 220496.0996 236130.7136 0.971293053 1.058760077 0.978851935 1.050814217 1.084769739 1.118955724 1.081890982 0.851081431 0.933788308 1 17.84922618 1.747956135 25 0.917211253 1.051083155 0.504511864 0.054621742 1.700105816 4533.688029 0.025654793 0.014226945 55.97010668 -1.747956135 0.133871902 AHGNVQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHGNVQDR 8 0 Q16531;F5GY55;F5H2L3;F5GWI0;F5GZY8 Q16531 DDB1 DNA damage-binding protein 1 0 86.67 0.015869 19604000 19163 33388 19622 39800 30634 35645 32445 19235 23399 28292 FALSE TRUE 18414.08877 32435.80693 23168.13189 41854.08277 31619.37043 36365.76632 32842.07162 18837.79053 20742.84362 26375.75764 0.698144449 1.229758302 0.878387351 1.586839072 1.198804253 1.378757222 1.24516126 0.714208509 0.786435935 1 14.68692492 1.747994638 10.44035253 0.816681116 1.189248821 0.292185208 0.241226264 0.120322524 67.54054565 0.112073961 0.061038552 55.975069 -1.747994638 0.372567705 RVT(ph)QEQGVSLLEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVTQEQGVSLLEDK 14 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RVT(0.5)QEQGVS(0.5)LLEDK;RVT(0.5)QEQGVS(0.5)LLEDK 89.013 0.0037023 52717000 137676 111290 110088 107831 120923 112023 113057 138262 151039 114408 TRUE FALSE 132295.4697 108116.1182 129983.3505 113396.1708 124812.5981 114288.1818 114440.6254 135406.8414 133893.6859 106659.0443 1.240358665 1.013661044 1.218680998 1.063165075 1.17020173 1.071528276 1.072957537 1.269529859 1.255343013 1 16.70264678 1.748114483 25 1.201539985 1.118803475 0.039127775 0.09696189 4.511999846 11832.29654 0.041002618 0.022738304 55.99051774 -1.748114483 -0.08273651 LFIHESIHDEVVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFIHESIHDEVVNR 14 0 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GUY0 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ; 166.45 2.20E-06 117209000 88830 113175 96155 138700 105516 86843 120039 59718 83873 124260 FALSE TRUE 85358.42539 109947.3598 113532.3475 145858.3236 108910.018 88599.02496 121508.0732 58484.80243 74352.08866 115843.7595 0.736840946 0.949100411 0.980047159 1.259095218 0.940145748 0.764814828 1.048896149 0.504859327 0.641830764 1 16.8218208 1.748172442 25 0.672170225 0.958847539 0.26070925 0.179575347 2.638823881 6878.242313 0.082317333 0.04564927 55.99799045 -1.748172442 0.286677314 EKT(ph)PSPKEEDEEPES(ph)PPEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 EKT(0.681)PS(0.321)PKEEDEEPES(0.998)PPEKK 92.363 0.00315 440630000 670470 318870 291410 169350 325160 289720 319880 483120 562950 295070 TRUE FALSE 644267.2912 309776.1398 344074.2694 178090.1738 335619.0667 295578.3369 323794.7871 473143.4032 499046.2761 275084.6461 2.342069252 1.126112068 1.250794162 0.647401359 1.220057431 1.074499581 1.177073282 1.719992046 1.814155327 1 18.06951609 1.748219974 24.99986249 1.577116821 1.22434166 0.050058178 0.450210352 5.359839662 13901.74087 0.204180442 0.113228422 56.00411955 -1.748219974 -0.352775161 GNDS(ph)DGEGESDDPEKKK ddPTM_BT-474_Pertuzumab_2h_R1 3 GNDSDGEGESDDPEKKK 17 2 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 GNDS(0.995)DGEGES(0.005)DDPEKKK;GNDS(1)DGEGESDDPEKKK;GNDS(0.99)DGEGES(0.01)DDPEKKK 143.31 2.89E-07 1522340000 1111220 821550 658010 474090 738230 751800 771660 986750 1235890 821580 TRUE FALSE 1067792.294 798120.1984 776927.0444 498557.8417 761975.8384 767001.9111 781103.8059 966373.2677 1095596.948 765933.6548 1.394105465 1.042022626 1.014352927 0.650915179 0.99483269 1.001394711 1.01980609 1.261693179 1.430407114 1 19.54685991 1.748270829 4.828074025 1.260169757 1.00089559 0.196396859 0.19388217 0.251293825 13.45385692 0.100628616 0.051934874 56.01067788 -1.748270829 -0.259274167 PGRPLS(ph)PANVPALPGETVTSPVR ddPTM_BT-474_Pertuzumab_2h_R1 3 PGRPLSPANVPALPGETVTSPVR 23 1 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 1 PGRPLS(1)PANVPALPGETVTSPVR;PGRPLS(1)PANVPALPGETVTSPVR;PGRPLS(1)PANVPALPGETVTSPVR 150.62 4.96E-08 793090000 279284 236700 247719 269388 222092 236507 249278 303205 312659 316987 TRUE FALSE 268369.2725 229949.5478 292487.3338 283291.147 229235.7909 241289.3336 252328.7387 296943.7108 277167.2611 295517.1881 0.908134225 0.778125798 0.989747282 0.958628325 0.775710517 0.816498475 0.853854696 1.004827207 0.93790572 1 18.17288252 1.748296063 9.769701512 0.977297997 0.867714098 0.359809195 0.068517398 0.127642111 56.59424741 0.033827739 0.018362463 56.01393241 -1.748296063 -0.109583899 HQPWQS(ph)PERPLSR ddPTM_BT-474_Pertuzumab_2h_R1 6 HQPWQSPERPLSR 13 1 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-2;V9GYS7;J3QRS2;V9GYU5;J3QL08 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 1 HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(0.99)PERPLS(0.01)R 132.4 7.22E-05 12808000000 728522 929770 770364 1227590 967210 947640 1005260 753049 886510 1081430 TRUE FALSE 700050.5548 903253.8699 909585.9115 1290946.067 998321.188 966801.9301 1017562.673 737498.275 785877.1014 1008183.783 0.694367998 0.89592184 0.902202482 1.280467003 0.990217463 0.958954058 1.009302758 0.731511742 0.77949786 1 19.94332722 1.748301261 25 0.813488041 0.970079544 0.118221881 0.150729503 4.298379145 11055.44807 0.071735173 0.03978096 56.01460288 -1.748301261 0.156591503 RVEHHDHAVVSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVEHHDHAVVSGR 13 1 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ; 122.97 0.00014859 111635000 23326.64 30512 24485.5 46434.2 16821.34 20191.36 35438.9 759.2 25723.2 17138.4 FALSE TRUE 22415.00912 29641.82763 28910.57453 48830.67463 17362.41368 20599.64313 35872.61186 743.5222547 22803.21018 15977.6009 1.402902054 1.855211418 1.809444027 3.056195666 1.086672135 1.289282619 2.245181368 0.046535288 1.427198634 1 13.96376318 1.748340644 25 0.76133262 1.820443526 0.358015647 0.609506705 2.474651896 6339.126265 0.277580597 0.153932761 56.01968262 -1.748340644 1.059110906 DAHVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DAHVAK 6 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 76.592 0.07465 304070000 702010 691130 567230 637260 609990 659530 773190 319830 610760 704160 FALSE TRUE 674574.6731 671419.6491 669741.079 670149.065 629610.8823 672866.1485 782652.5305 313225.3987 541429.0853 656466.616 1.027584125 1.022778056 1.020221078 1.020842566 0.959090481 1.024981518 1.19221985 0.477138351 0.824762558 1 19.32436212 1.748340662 25 0.721748117 1.03273422 0.451845723 0.133870426 1.745263817 4470.70019 0.057482076 0.031876863 56.01968499 -1.748340662 0.310986103 S(ph)SSLDGEHHDGYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLDGEHHDGYHR 14 0 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 S(0.456)S(0.456)S(0.087)LDGEHHDGYHR 90.561 0.0095331 741940000 337360 336600 290780 420160 347860 334960 377960 211220 316460 327380 TRUE FALSE 324175.5982 327000.4976 343330.4144 441844.508 359049.2328 341733.1207 382585.5875 206858.2332 280536.7875 305206.261 1.062152517 1.071408222 1.12491275 1.447691494 1.17641503 1.119679261 1.253531256 0.677765366 0.919171142 1 18.21942503 1.748408826 24.99999996 0.843406674 1.181057158 0.55112624 0.129285486 1.708142936 4345.256018 0.060421987 0.03350702 56.02847813 -1.748408826 0.337650484 AVSTCAHLFWSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVSTCAHLFWSGR 13 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 100.11 0.0025499 1056450000 522750 669600 513780 663700 610350 576790 640610 548240 663010 677020 FALSE TRUE 502320.3521 650503.6636 606631.475 697953.6365 629982.4621 588453.089 648449.9768 536918.6524 587747.8844 631164.8324 0.79586239 1.030639906 0.961130031 1.105818323 0.998126685 0.932328702 1.027386102 0.850678975 0.931211396 1 19.2676573 1.748414428 25 0.913538259 0.983920251 0.064753151 0.083318111 5.046081463 12829.14268 0.037173716 0.020614828 56.02920086 -1.748414428 0.070381991 FNYSGSGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 FNYSGSGGR 9 0 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;; 150.62 0.00019731 781030000 677594 759420 577264 607084 618699 655956 671910 561580 662700 614120 FALSE TRUE 651112.8774 737762.0851 681588.446 638415.678 638600.0152 669219.8798 680133.0356 549983.1768 587473.0743 572525.1054 1.137265198 1.288610889 1.190495298 1.115087656 1.115409629 1.168891763 1.187953208 0.960627179 1.026108844 1 19.12697943 1.7484198 8.619703055 0.997033295 1.17272409 0.729930494 0.049124854 0.063433336 18.26667465 0.024979755 0.013466005 56.02989393 -1.7484198 0.175690795 T(ph)SPGRVDLPGSSTTLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPGRVDLPGSSTTLTK 17 1 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-11;O94875-2;O94875-8;H7BZK1;H7BZX1;H7C1R7;O94875-7;O94875 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 T(0.591)S(0.409)PGRVDLPGSSTTLTK;T(0.5)S(0.5)PGRVDLPGSSTTLTK 191.44 3.92E-10 807690000 420670 344615 350449 325146 364020 380603 372369 443540 490220 451840 TRUE FALSE 404229.7513 334786.9176 413782.93 341926.824 375729.0339 388299.0534 376926.1632 434380.744 434572.2808 421236.4743 0.959626661 0.794771911 0.982305558 0.811721788 0.891966999 0.921807766 0.89480894 1.031204016 1.031658717 1 18.68427084 1.748495426 5.358765328 1.023499158 0.890852852 0.526895432 0.055060145 0.118187562 8.261626912 0.025498711 0.013310888 56.03965154 -1.748495426 -0.132646306 DNVSSPGGATIHALHVLESGGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNVSSPGGATIHALHVLESGGFR 23 0 J3QKT4;J3KQ22;E2QRB3;P32322-2;P32322;P32322-3 J3QKT4 PYCR1 "Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 1, mitochondrial" 0 ; 198.39 1.62E-24 708820000 290760 456890 326590 581650 333330 355260 485260 72344 360050 272160 FALSE TRUE 279396.7777 443859.9445 385612.078 611669.0262 344051.8622 362443.6006 491198.757 70850.07112 319178.6335 253726.3608 1.10117363 1.749364722 1.519795092 2.410742913 1.355995731 1.428482242 1.935938999 0.279238117 1.257964023 1 17.95291389 1.748501646 25 0.799815869 1.652649905 0.446657176 0.405625173 2.03742401 5134.394308 0.179368391 0.099469105 56.04045408 -1.748501646 0.852834036 EEPPEPVPS(ph)PIIPILPSTAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEPPEPVPSPIIPILPSTAGK 21 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765;H7C2V8 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 EEPPEPVPS(1)PIIPILPSTAGK;EEPPEPVPS(1)PIIPILPSTAGK 150.09 4.80E-08 83311000 267310 261940 226130 250730 260430 234240 249490 304180 315400 309780 TRUE FALSE 256863.2297 254469.7277 266996.7212 263670.2053 268806.9675 238976.4933 252543.3333 297898.5767 279597.1143 288798.3247 0.889420775 0.881132977 0.924509245 0.912990772 0.930777447 0.827485733 0.874462598 1.031510751 0.968139668 1 18.13970285 1.748543393 11.50445654 0.998915247 0.892276651 0.719180688 0.031014137 0.058266894 44.90640097 0.015082362 0.008252464 56.04584139 -1.748543393 -0.106638596 NT(ph)SLPPLWS(ph)PEAER ddPTM_BT-474_Pertuzumab_2h_R1 1 NTSLPPLWSPEAER 14 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 2 NT(0.537)S(0.464)LPPLWS(1)PEAER 72.819 0.056473 0 38153 36631 30475 34239 35378 35836 34713 39510 41015 39216 TRUE FALSE 36661.93858 35586.31975 35982.51041 36006.07889 36515.9655 36560.62847 35137.82808 38694.10469 36359.14915 36559.86539 1.002791947 0.973371192 0.984207957 0.984852611 0.998799233 1.000020872 0.961103869 1.058376563 0.994509929 1 15.15797314 1.74854583 25 1.022677194 0.986795809 0.328905186 0.020019306 2.341199226 5873.756271 0.008610239 0.004774858 56.04615586 -1.74854583 -0.035881385 KFS(ph)PSQVPVQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFSPSQVPVQTR 12 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 KFS(0.772)PS(0.228)QVPVQTR;KFS(0.807)PS(0.193)QVPVQTR 154.88 4.40E-05 906810000 797030 843920 730560 773030 744360 832050 815800 738070 843450 857160 TRUE FALSE 765881.1864 819852.2279 862588.4432 812926.1709 768303.0154 848874.6211 825784.0044 722828.5966 747705.092 799103.7897 0.958425171 1.025964635 1.079444816 1.017297354 0.961455853 1.062283313 1.033387671 0.904549078 0.935679572 1 19.60802337 1.748585244 25 0.939415977 1.021585515 0.383656004 0.042054438 2.310694943 5774.380028 0.01934254 0.010726457 56.05124244 -1.748585244 0.082169538 DEAQNEGPATESEAPLKEDGLLPKPLS(ph)SGGEEEEKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DEAQNEGPATESEAPLKEDGLLPKPLSSGGEEEEKPR 37 3 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 DEAQNEGPATESEAPLKEDGLLPKPLS(0.5)S(0.5)GGEEEEKPR 85.507 0.00060685 397300000 112910 89180 74339 57942 92636 84646 82827 115550 127910 99407 TRUE FALSE 108497.3524 86636.67372 87773.71096 60932.39356 95615.72107 86357.60012 83840.6616 113163.8521 113390.193 92674.07535 1.170741137 0.934853392 0.947122597 0.657491249 1.031741841 0.931842047 0.904683012 1.221095022 1.223537355 1 16.4998782 1.74858582 9.615857576 1.164135224 0.932224631 0.33685452 0.133074256 0.112993798 47.31726111 0.062446407 0.033873118 56.05131685 -1.74858582 -0.231910594 SILKPSTPIPPQEGEEVGES(ph)SEEQDNAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SILKPSTPIPPQEGEEVGESSEEQDNAPK 29 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;A0A3B3ISZ5;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SILKPSTPIPPQEGEEVGES(0.849)S(0.151)EEQDNAPK 230.67 2.17E-35 251840000 520020 483140 417580 369300 462100 480210 471800 624360 705740 625520 TRUE FALSE 499697.0435 469361.3202 493045.995 388359.6173 476963.8662 489920.1752 477574.0295 611466.7478 625627.3539 583152.9732 0.856888443 0.804868262 0.84548312 0.665965253 0.817905229 0.840122914 0.818951547 1.048552911 1.072835744 1 19.15351486 1.748639263 4.455683528 1.047488622 0.803346396 0.801706908 0.053113984 0.077242143 3.395790709 0.028061225 0.014338037 56.05821478 -1.748639263 -0.244142226 EKELETGPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKELETGPK 9 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 121.6 0.00055563 2736450000 3976210 3408740 2815960 2860250 3143470 3140550 3411990 3975780 4609510 4224660 FALSE TRUE 3820815.317 3311526.073 3324866.613 3007867.845 3244582.567 3204054.073 3453746.954 3893678.754 4086257.749 3938520.015 0.970114485 0.840804683 0.844191879 0.763705106 0.823807561 0.813517276 0.876914918 0.988614692 1.037510977 1 21.90922218 1.74864458 2.701720842 1.018595251 0.83839943 0.692896352 0.049728372 0.137367445 2.062675247 0.030771497 0.014102294 56.05890104 -1.74864458 -0.180195821 RGPFELEAFYSDPQGVPYPEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGPFELEAFYSDPQGVPYPEAK 22 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 152.88 6.09E-08 649640000 1254920 1277480 1138180 1046040 1216140 1274960 1279670 1428370 1666670 1572010 FALSE TRUE 1205876.339 1241047.521 1343874.445 1100026.25 1255258.248 1300740.565 1295330.984 1398873.66 1477476.609 1465536.362 0.822822531 0.846821377 0.916984716 0.750596354 0.856517982 0.88755257 0.883861375 0.954513103 1.008147356 1 20.48299733 1.748752259 1.176875579 1.010823807 0.841340061 0.724812959 0.039898244 0.238642476 0.618098048 0.033126184 0.013050836 56.07280209 -1.748752259 -0.169483746 DAEYIYPSLES(ph)DDDDPALK ddPTM_BT-474_Pertuzumab_2h_R1 1 DAEYIYPSLESDDDDPALK 19 0 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9;Q9UPP1-5;H0Y589 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 DAEYIYPSLES(1)DDDDPALK 134.87 5.72E-06 84048000 162160 134710 133710 123210 132800 118570 126790 178040 172200 154180 TRUE FALSE 155822.6079 130868.2027 157874.3714 129568.8829 137071.6326 120967.5666 128341.6939 174363.4118 152652.5779 143737.2513 1.084079503 0.910468244 1.098353906 0.901428695 0.953626366 0.841588145 0.892890972 1.213070448 1.062025164 1 17.13307448 1.748763939 25 1.109137772 0.952029417 0.314845138 0.0915236 2.662600013 6536.995022 0.041439676 0.022980365 56.07431004 -1.748763939 -0.157108354 HPEAEMAQNSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 HPEAEMAQNSVR 12 0 P14923 P14923 JUP Junction plakoglobin 0 ; 178.22 2.23E-05 618210000 342770 362280 286000 426780 300170 345700 369810 249960 320360 367320 FALSE TRUE 329374.1694 351948.1291 337686.562 448806.1669 309825.2407 352690.2909 374335.8454 244798.2387 283994.0759 342441.0892 0.961841846 1.027762556 0.986115781 1.310608397 0.904754863 1.029929824 1.093139396 0.714862341 0.829322429 1 18.38549629 1.74880939 24.99996601 0.825132116 1.046216722 0.352963132 0.12091691 2.477799791 6056.240376 0.053885379 0.029882217 56.08017886 -1.74880939 0.221084605 ELVGPPLAETVFT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELVGPPLAETVFTPK 15 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK 234.21 1.34E-16 394183000 385157 293784 341795 321782 323867 314449 314404 493292 482691 448033 TRUE FALSE 370104.6386 285405.568 403564.9597 338389.2076 334284.4762 320807.3742 318251.7702 483105.3478 427897.9413 417687.3258 0.886080606 0.683299565 0.966189144 0.81014957 0.800322288 0.768056281 0.761937819 1.1566196 1.024445596 1 18.67206384 1.748822984 13.86482364 1.06651806 0.809850224 0.668578924 0.080455107 0.076147078 94.13338407 0.035621815 0.019619789 56.08193433 -1.748822984 -0.256667836 PSADLTNSSAPS(ph)PSHK ddPTM_BT-474_Pertuzumab_2h_R1 5 PSADLTNSSAPSPSHK 16 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 PSADLTNSSAPS(0.715)PS(0.285)HK;PSADLTNSSAPS(0.997)PS(0.002)HK;PSADLTNSS(0.005)APS(0.978)PS(0.017)HK;PSADLTNSSAPS(0.73)PS(0.27)HK;PSADLTNS(0.054)S(0.084)APS(0.84)PS(0.021)HK 238.45 2.18E-14 1924840000 940215 722767 844896 680141 676901 705816 912550 999296 1184819 1189910 TRUE FALSE 903470.3583 702154.3928 997587.5018 715243.1585 698674.1354 720088.0831 923718.0599 978660.1884 1050323.314 1109316.336 0.814438884 0.632961375 0.899281359 0.644760323 0.629824075 0.649127809 0.832691298 0.882219216 0.94682038 1 20.0812394 1.748834637 1.731086918 0.967713574 0.711590604 0.597886863 0.085715407 0.23772671 1.407115267 0.06278505 0.02532732 56.0834391 -1.748834637 -0.25612297 HQEPVYSVAFSPDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQEPVYSVAFSPDGR 15 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ; 127.75 7.62E-05 205870000 269190 286160 243223 271890 259441 263930 294043 199742 259700 307980 FALSE TRUE 258669.7572 277998.997 287178.8066 285922.2755 267786.1554 269266.8454 297641.5862 195617.2579 230219.9448 287120.2403 0.900910911 0.968231974 1.000203978 0.995827655 0.932662062 0.9378191 1.036644389 0.681307795 0.801824157 1 18.13129551 1.74884848 25 0.798964481 0.967371327 0.363625175 0.082127261 2.152318618 5240.672677 0.035438425 0.019652433 56.08522676 -1.74884848 0.168406846 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR 37 0 P02545;P02545-6;P02545-5;P02545-4 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 ;; 138.8 2.16E-10 3148020000 435490 830560 785910 1394350 1106160 1200800 1213590 27273.4 844670 526469 FALSE TRUE 418470.5693 806873.242 927941.4195 1466312.571 1141740.641 1225080.999 1228442.277 26710.19476 748786.6027 490810.7857 0.852610785 1.643959883 1.890629641 2.987531271 2.326233804 2.496035202 2.502883623 0.054420554 1.525611548 1 18.90480743 1.748890676 25 0.807270017 2.132464972 0.439772049 0.63977878 2.376113512 5761.904589 0.305856582 0.169613188 56.09067628 -1.748890676 1.325194955 ADYEIASK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADYEIASK 8 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;B8ZZ12;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ; 147.19 0.0021368 361640000 532500 534520 461990 484330 510600 508640 505620 576450 590220 594930 FALSE TRUE 511689.3113 519276.0129 545481.8699 509326.3293 527023.9127 518925.0493 511807.9288 564546.1061 523220.7 554634.8612 0.922569689 0.936248421 0.983497267 0.918309261 0.950217791 0.935615638 0.922783555 1.017869856 0.943360644 1 19.08117877 1.748954017 25 0.987190057 0.939677345 0.447259243 0.02473979 2.363984536 5697.476491 0.01080443 0.005991718 56.09885752 -1.748954017 -0.047512712 MCIVLRPS(ph)RVHNSEENTMRALTLK ddPTM_BT-474_Pertuzumab_2h_R1 4 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK;MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK;MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK;MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALT(0.001)LK 71.535 0.030321 1948715000 633719 958328 844131 1231750 1050201 1208892 1070198 579538 791734 984094 TRUE FALSE 608952.5609 930997.4237 996684.2493 1295320.765 1083981.669 1233336.625 1083295.403 567570.3378 701859.6755 917440.4368 0.663751603 1.014776967 1.086374885 1.411885408 1.181528114 1.344323375 1.180780092 0.618645435 0.765019338 1 19.80725497 1.749000802 24.99905726 0.766914847 1.141890498 0.339718481 0.210031576 2.818986929 6763.325758 0.100974904 0.055995905 56.10490125 -1.749000802 0.374975652 TENVFVDEPLIHATTYIPLMDNADS(ph)SPVVDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TENVFVDEPLIHATTYIPLMDNADSSPVVDKR 32 1 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 TENVFVDEPLIHATTYIPLMDNADS(0.5)S(0.5)PVVDKR;TENVFVDEPLIHATTYIPLMDNADS(0.5)S(0.5)PVVDKR 115.87 8.69E-07 74984000 13054.8 22381.1 14875.4 23784.1 14767.6 18452.7 17650.4 25185.2 26535.3 19593 TRUE FALSE 12544.60398 21742.81294 17563.71568 25011.60025 15242.61327 18825.82624 17866.41088 24665.11682 23523.12399 18265.94866 0.686775388 1.190346768 0.961555078 1.369302012 0.834482432 1.030651437 0.978126634 1.350333195 1.287812882 1 14.15686906 1.749001478 25 1.242910009 1.020771237 0.184270448 0.193512362 3.97263641 9530.906455 0.084267901 0.046730996 56.10498857 -1.749001478 -0.222138772 MEAIPCVVGDEEVWTSDVQYQVSPFNHGHK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEAIPCVVGDEEVWTSDVQYQVSPFNHGHK 30 0 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 65.581 0.0056552 33930000 15843 21016 14616 28069 17516 19580 26802 6769.1 25802 18092 FALSE TRUE 15223.83804 20416.64426 17257.43633 29517.64445 18079.41805 19975.92102 27130.01089 6629.315719 22873.06513 16866.61273 0.90260198 1.210476851 1.023171434 1.750063568 1.071905684 1.184346931 1.608503814 0.393043691 1.356114918 1 14.04188265 1.749026914 25 0.864144341 1.249739571 0.174124331 0.327222248 3.912565426 9363.92248 0.143500913 0.079578877 56.10827461 -1.749026914 0.385595229 HSQEELLQR ddPTM_BT-474_Pertuzumab_2h_R1 3 HSQEELLQR 9 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;; 155.5 7.32E-05 1944080000 586910 605980 485410 546470 510060 593400 608680 478980 643950 591820 FALSE TRUE 563972.9083 588698.0437 573134.3849 574673.3822 526466.5431 605398.9546 616129.2079 469088.8956 570851.4957 551735.5043 1.022179838 1.066993223 1.038784672 1.041574047 0.954200951 1.097263 1.116711183 0.850206108 1.034647021 1 19.0736173 1.749028401 25 0.948823869 1.046613343 0.292813884 0.06068628 2.927088019 7004.387218 0.027220668 0.015095365 56.10846676 -1.749028401 0.097789474 KLS(ph)LQER ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSLQER 7 1 Q96RR4-6;Q96RR4-5;Q96RR4-2;Q96RR4-3;Q96RR4-4;Q96RR4-7;Q96RR4;F5H4I7;J3KPJ3;Q8N5S9;Q8N5S9-2 Q96RR4-6;J3KPJ3 CAMKK2;CAMKK1 Calcium/calmodulin-dependent protein kinase kinase 2;Calcium/calmodulin-dependent protein kinase kinase 1 1 KLS(1)LQER;KLS(1)LQER 119.27 0.0029514 807970000 1317210 1265430 1084930 1089780 1398720 1294110 1217690 1640020 1683180 1561950 TRUE FALSE 1265731.977 1229341.175 1281000.985 1146023.676 1443711.099 1320277.791 1232592.454 1606153.014 1492112.463 1456157.735 0.869227245 0.84423627 0.879713066 0.787018912 0.991452412 0.906685972 0.84646905 1.103007576 1.024691506 1 20.47373521 1.749043129 12.66785112 1.046687795 0.876287814 0.662698585 0.054756781 0.069917016 69.65069506 0.025496287 0.014003661 56.11036953 -1.749043129 -0.170399981 ELLNPVVEFVSHPSTTCR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLNPVVEFVSHPSTTCR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 212.83 1.49E-16 1136970000 380000 561900 405640 563430 469310 508360 511860 416090 489180 503980 FALSE TRUE 365149.1799 545875.1622 478948.1714 592508.6898 484405.7824 518639.3875 518124.2958 407497.5961 433650.3372 469844.9857 0.777169473 1.161819704 1.01937487 1.261072711 1.03099064 1.103852128 1.102755827 0.867302213 0.922964702 1 18.84182533 1.749073695 14.57928089 0.922031067 1.074931739 0.203893753 0.121064966 0.226320777 300.1879443 0.053364824 0.029431053 56.11431874 -1.749073695 0.152900672 DSLSPGQERPYSTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSLSPGQERPYSTVR 15 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 ; 176.29 7.36E-07 779350000 167856 159881 152247 167062 157084 147740 158185 192961 190316 197156 FALSE TRUE 161296.0019 155321.3504 179761.4196 175684.0898 162136.7495 150727.404 160120.9153 188976.2879 168712.1255 183802.4485 0.877550888 0.845045056 0.978014281 0.955831064 0.88212508 0.820051121 0.871157684 1.028148914 0.917899228 1 17.48779646 1.749074045 25 0.981598337 0.891168835 0.404865757 0.051126616 2.9387309 7001.648625 0.025095849 0.013916973 56.11436404 -1.749074045 -0.090429501 QEESES(ph)PVERPLKENPPNK ddPTM_BT-474_Pertuzumab_2h_R1 3 QEESESPVERPLKENPPNK 19 2 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 QEES(0.007)ES(0.993)PVERPLKENPPNK;QEES(0.04)ES(0.96)PVERPLKENPPNK;QEES(0.139)ES(0.861)PVERPLKENPPNK 194.77 1.25E-15 1714360000 1379260 1230980 1242650 1185770 1219350 1428670 1498920 1641480 2028070 1973440 TRUE FALSE 1325356.994 1195873.656 1467224.498 1246967.732 1258571.5 1457558.686 1517264.231 1607582.864 1797851.996 1839777.151 0.720389963 0.65001006 0.797501206 0.677781943 0.684089103 0.792247412 0.824700008 0.873792167 0.97721183 1 20.8110996 1.749116916 0.879991854 1.005401551 0.704103722 0.875932931 0.040885052 0.176687247 0.258592304 0.035425436 0.015248019 56.1199036 -1.749116916 -0.301297829 SEPQPEEGS(ph)PAGGQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SEPQPEEGSPAGGQK 15 0 F8WE91;Q9Y6K1;Q9Y6K1-3 F8WE91 DNMT3A DNA (cytosine-5)-methyltransferase 3A 1 SEPQPEEGS(1)PAGGQK;SEPQPEEGS(1)PAGGQK;SEPQPEEGS(1)PAGGQK;SEPQPEEGS(1)PAGGQK 275.31 1.75E-33 835720000 1160956 1073919 976387 993014 1046652 1098208 1070637 1254476 1369539 1254587 TRUE FALSE 1115584.556 1043291.882 1152841.851 1044263.572 1080318.512 1120414.518 1083739.776 1228570.632 1214074.674 1169612.705 0.953806804 0.891997733 0.98566119 0.892828512 0.923654905 0.957936344 0.92658003 1.050408077 1.038014267 1 20.15759946 1.749163561 8.053665237 1.032076378 0.932626676 0.690664584 0.029478292 0.063169516 14.52680182 0.013290758 0.007140928 56.12593141 -1.749163561 -0.099449702 LESESTS(ph)PSLEMK ddPTM_BT-474_Pertuzumab_2h_R1 7 LESESTSPSLEMK 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 LESES(0.119)T(0.218)S(0.585)PS(0.077)LEMK;LESEST(0.213)S(0.787)PSLEMK;LESES(0.001)T(0.187)S(0.813)PSLEMK;LESEST(0.001)S(0.999)PSLEMK;LESEST(0.048)S(0.952)PSLEMK;LESES(0.001)T(0.006)S(0.496)PS(0.496)LEMK;LESEST(0.002)S(0.499)PS(0.499)LEMK 364.3 4.73E-91 2757850000 7921370 7700400 6609430 6893680 7299520 7573400 7337720 8407170 8894100 8265880 TRUE FALSE 7611794.103 7480792.131 7803901.027 7249463.651 7534315.69 7726539.337 7427521.212 8233559.002 7884479.055 7706024.585 0.987771843 0.9707719 1.012701289 0.940752728 0.977717578 1.002662171 0.963859008 1.068457401 1.023157786 1 22.87755536 1.749165469 25 1.035947976 0.979742814 0.471328069 0.024588279 2.046160334 4832.946081 0.010710201 0.005939422 56.12617793 -1.749165469 -0.056205162 LKFS(ph)DDEEEEEVVKDGRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKFSDDEEEEEVVKDGRPK 19 3 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LKFS(1)DDEEEEEVVKDGRPK;LKFS(1)DDEEEEEVVKDGRPK 163.74 1.39E-10 599090000 523380 423310 308320 231817 398300 401180 371310 493510 536710 402310 TRUE FALSE 502925.731 411237.6133 364040.2825 243781.1032 411111.6812 409292.1345 375854.2029 483318.846 475784.9309 375061.1854 1.340916497 1.096454737 0.97061572 0.649976891 1.096118973 1.09126764 1.002114368 1.28864 1.268552837 1 18.51676644 1.749235708 25 1.210568947 1.024877932 0.125628258 0.176719089 4.942891545 11597.92403 0.084571858 0.046899363 56.13525601 -1.749235708 -0.185691015 AQHTLPQDPAIVQSSLGSAS(ph)ASPFQPHVPYS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQHTLPQDPAIVQSSLGSASASPFQPHVPYSPFR 34 0 Q9BX40;Q9BX40-2;Q5TBQ1;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 2 AQHTLPQDPAIVQS(0.001)S(0.004)LGS(0.16)AS(0.437)AS(0.398)PFQPHVPY(0.425)S(0.575)PFR 139.36 1.57E-10 67291000 17863 14762 15008 21655 15648 20562 16268 15059 16891 12995 TRUE FALSE 17164.89421 14341.00221 17720.27945 22772.61715 16151.33213 20977.77773 16467.09265 14748.02639 14973.60449 12114.83708 1.416848952 1.183755268 1.462692345 1.879729542 1.333186078 1.731577371 1.359250029 1.217352433 1.23597242 1 13.56448738 1.749241181 2.294084184 1.139576597 1.496451803 0.39919564 0.192100968 0.305664663 3.284667272 0.127601665 0.055701778 56.13596349 -1.749241181 0.356875206 KREEGS(ph)DIEDEDMEELLNDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KREEGSDIEDEDMEELLNDTR 21 2 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR 313.24 6.99E-67 345130000 370120 347240 292550 285920 322920 346210 330550 391750 414890 384030 TRUE FALSE 355655.3012 337337.0552 345420.2927 300676.3655 333307.0151 353210.6034 334595.3698 383660.2256 367793.4266 358019.306 0.993396991 0.942231465 0.964809123 0.839832826 0.930974977 0.986568594 0.934573539 1.071618818 1.02730054 1 18.44967786 1.749256353 24.99948816 1.037152914 0.940060745 0.485305125 0.042951757 2.276919179 5332.088165 0.020308916 0.011262358 56.13792466 -1.749256353 -0.097092169 LTS(ph)SCPDLPSQTDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTSSCPDLPSQTDKK 15 1 P56962 P56962 STX17 Syntaxin-17 1 LTS(0.734)S(0.265)CPDLPSQTDKK 211.17 9.28E-10 373750000 603270 518870 421020 393680 491100 440400 477010 606930 635820 565640 TRUE FALSE 579693.5414 504072.3356 497107.6795 413997.872 506896.6775 449305.1897 482847.7911 594396.6834 563644.3792 527328.699 1.099302091 0.955897786 0.942690357 0.785085039 0.961253727 0.852040085 0.915648612 1.1271844 1.068867255 1 19.00834299 1.749320635 24.99190262 1.073684133 0.924335374 0.363424486 0.081435231 2.78782982 6487.508801 0.037962206 0.021051933 56.14623442 -1.749320635 -0.149348759 LQGKPQSHELK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQGKPQSHELK 11 1 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 0 73.435 0.026177 402170000 336250 389180 313340 387320 388430 360330 352010 559920 502930 514700 FALSE TRUE 323108.9783 378080.9674 369967.5082 407309.6316 400924.2037 367616.1195 356318.0037 548357.4563 445839.4949 479838.9106 0.67336969 0.787933115 0.7710244 0.848846608 0.835539167 0.766124029 0.742578386 1.142794893 0.929144105 1 18.87219063 1.749324812 25 1.030141525 0.780219591 0.743669732 0.066892608 1.311143208 3050.925291 0.029789398 0.016519785 56.14677453 -1.749324812 -0.249921934 EKTPS(ph)PKEEDEEPES(ph)PPEKK ddPTM_BT-474_Pertuzumab_2h_R1 5 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 EKT(0.438)PS(0.569)PKEEDEEPES(0.992)PPEKK;EKT(0.457)PS(0.561)PKEEDEEPES(0.982)PPEKK;EKT(0.432)PS(0.568)PKEEDEEPES(1)PPEKK;EKT(0.32)PS(0.68)PKEEDEEPES(1)PPEKK;EKT(0.017)PS(0.983)PKEEDEEPES(1)PPEKK 136.16 2.82E-06 2603160000 3339620 1774280 1596130 951860 1825800 1489040 1689370 2596130 2834660 1705050 TRUE FALSE 3209103.958 1723679.272 1884586.197 1000985.609 1884528.515 1519149.409 1710045.015 2542519.008 2512881.281 1589565.445 2.01885614 1.084371378 1.185598368 0.629722804 1.18556208 0.955701078 1.07579403 1.599505712 1.580860536 1 20.60020098 1.749355333 25 1.447839043 1.13260641 0.068527599 0.363600063 5.791979659 13439.28378 0.165222376 0.091624305 56.15072052 -1.749355333 -0.315232633 SKS(ph)NPDFLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSNPDFLKK 10 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.06)KS(0.94)NPDFLKK 79.885 0.020211 729370000 761500 623820 510730 425060 583330 601340 579210 801020 844770 682760 TRUE FALSE 731739.7381 606029.2644 603030.2721 446997.3975 602093.3392 613499.5068 586298.5452 784478.6571 748875.2512 636516.0571 1.149601381 0.952103655 0.947392081 0.702256279 0.945920111 0.963839796 0.921105664 1.232456979 1.176522168 1 19.27983738 1.749443122 24.99959745 1.153630061 0.933006472 0.37503293 0.115034636 2.727374817 6277.142855 0.05374519 0.029804525 56.16207204 -1.749443122 -0.220623588 KLPPPPGSPLGHS(ph)PTASPPPTAR ddPTM_BT-474_Pertuzumab_2h_R1 3 KLPPPPGSPLGHSPTASPPPTAR 23 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 KLPPPPGS(0.001)PLGHS(0.974)PT(0.024)AS(0.001)PPPTAR;KLPPPPGS(0.071)PLGHS(0.922)PT(0.006)AS(0.001)PPPTAR;KLPPPPGS(0.362)PLGHS(0.637)PT(0.001)ASPPPTAR 176 4.10E-13 2722820000 791420 892580 686531 888420 856500 863270 849330 683784 727650 832110 TRUE FALSE 760490.4314 867124.4923 810602.4235 934271.4627 884050.1004 880725.9109 859724.3546 669663.6214 645050.2226 775750.4485 0.980328703 1.117787935 1.044926787 1.204345372 1.139606303 1.135321175 1.108248608 0.863246193 0.831517692 1 19.5652331 1.749445671 6.426674234 0.887113649 1.109346532 0.647723098 0.069357471 0.083506981 9.618447344 0.033473242 0.0177473 56.1624016 -1.749445671 0.222232884 TNTMNGSKS(ph)PVISR ddPTM_BT-474_Pertuzumab_2h_R1 11 TNTMNGSKSPVISR 14 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 TNTMNGS(0.032)KS(0.968)PVISR;TNTMNGSKS(1)PVISR;TNTMNGS(0.007)KS(0.993)PVISR;TNTMNGS(0.002)KS(0.998)PVISR;TNTMNGS(0.003)KS(0.997)PVISR;TNTMNGS(0.088)KS(0.912)PVISR;TNTMNGS(0.14)KS(0.86)PVISR;TNTMNGS(0.009)KS(0.991)PVISR;TNT(0.001)MNGS(0.003)KS(0.996)PVISR;TNTMNGSKS(0.999)PVISR;TNTMNGS(0.001)KS(0.999)PVISR 306.96 2.19E-44 17284780000 12310770 11504230 9253740 9388020 9619080 10591030 10369470 12538550 13350800 11593920 TRUE FALSE 11829651.5 11176140.62 10926096.67 9872536.837 9928486.444 10805187.88 10496374.68 12279624.56 11835273.16 10808653.47 1.094461168 1.033999346 1.010865664 0.913391928 0.9185683 0.999679369 0.971108446 1.136091983 1.094981275 1 23.36568347 1.749481811 25 1.088295467 0.988566353 0.298313829 0.059058976 3.240526951 7431.823199 0.028695983 0.015913493 56.16707539 -1.749481811 -0.099729114 RDS(ph)TEAPKPK ddPTM_BT-474_Pertuzumab_2h_R1 6 RDSTEAPKPK 10 2 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 RDS(0.998)T(0.002)EAPKPK;RDS(0.975)T(0.025)EAPKPK;RDS(0.772)T(0.228)EAPKPK;RDS(0.99)T(0.01)EAPKPK;RDS(0.815)T(0.185)EAPKPK;RDS(0.5)T(0.5)EAPKPK 141.32 1.97E-05 3150500000 2552681 2258366 1926747 2043160 2373427 2071412 2201150 2678326 2937063 2550102 TRUE FALSE 2452919.404 2193959.613 2274953.043 2148607.732 2449770.435 2113297.37 2228088.332 2623017.632 2603659.921 2377381.32 1.031773651 0.922847166 0.956915504 0.903770764 1.030449097 0.888918135 0.937202759 1.103322218 1.095179767 1 21.18094189 1.749507671 9.688792981 1.073092486 0.95069863 0.499040332 0.051693897 0.080838665 34.5108058 0.023086284 0.012533467 56.17041999 -1.749507671 -0.122393856 NNS(ph)FTAPSTVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NNSFTAPSTVGK 12 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 NNS(0.999)FT(0.001)APSTVGK;NNS(0.999)FT(0.001)APSTVGK 194.23 1.88E-06 123860000 494690 417530 288920 280780 390880 329320 300430 535880 451530 375010 TRUE FALSE 475356.9679 405622.4532 341134.271 295271.0894 403453.0102 335979.076 304106.7522 524813.8907 400274.2074 349610.2387 1.359676907 1.160213313 0.975755951 0.844572203 1.154007994 0.961010402 0.869845098 1.501139934 1.144915575 1 18.41538791 1.749512106 25 1.262474602 1.041183883 0.132719798 0.18620716 4.381814845 10021.39064 0.08570845 0.047529818 56.17099362 -1.749512106 -0.221290719 KQGGSPDEPDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQGGSPDEPDSK 12 1 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 80.905 0.030596 112590000 207870 182260 141140 146170 173840 170110 169010 198130 214040 193970 FALSE TRUE 199746.2106 177062.1233 166647.1376 153713.8512 179431.7215 173549.7408 171078.3949 194038.5463 189743.0765 180832.2391 1.104594023 0.979151307 0.921556568 0.850035657 0.992255155 0.959727876 0.946061365 1.073030712 1.049276818 1 17.46429238 1.749531913 12.55184272 1.045259094 0.960109557 0.234407861 0.062378758 0.169438243 160.8631007 0.030125609 0.016542176 56.17355547 -1.749531913 -0.085149537 SFGTRPLS(ph)SGFSPEEAQQQDEEFEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGT(0.001)RPLS(0.724)S(0.245)GFS(0.031)PEEAQQQDEEFEK;SFGTRPLS(0.946)S(0.046)GFS(0.008)PEEAQQQDEEFEK;SFGTRPLS(0.361)S(0.361)GFS(0.278)PEEAQQQDEEFEK;SFGTRPLS(0.45)S(0.256)GFS(0.294)PEEAQQQDEEFEK 343.46 5.39E-89 7399360000 1427310 1242300 981300 1082180 1129020 1206750 1128580 1449360 1458580 1294550 TRUE FALSE 1371529.147 1206870.82 1158642.739 1138031.439 1165335.954 1231151.312 1142391.9 1419430.21 1293008.113 1206868.975 1.136435831 1.000001529 0.960040205 0.942961881 0.965586138 1.02012011 0.946574916 1.17612619 1.071374059 1 20.20283763 1.749544662 25 1.09799918 0.99245636 0.251965038 0.066555616 3.24723758 7404.50574 0.030147642 0.016718484 56.17520449 -1.749544662 -0.10554282 KKEEPSQNDIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 KKEEPSQNDISPK 13 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK 181.72 6.16E-06 20448100000 7637350 5031820 5676750 3964020 5657310 5562350 6239690 7446790 9307480 8034200 TRUE FALSE 7338873.918 4888317.42 6702665.004 4168603.547 5839282.514 5674824.528 6316053.193 7293011.184 8250933.891 7490036.478 0.979818181 0.652642672 0.894877485 0.55655317 0.779606686 0.757649785 0.843260672 0.973695015 1.101587945 1 22.83654131 1.749604196 2.027193228 1.051256483 0.761488958 0.511315332 0.112371846 0.223485438 1.854141337 0.07194323 0.030264811 56.1829056 -1.749604196 -0.289767525 SDHYWVVGIHENPQQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDHYWVVGIHENPQQLR 17 0 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 0 203.99 5.31E-12 214730000 113310 120530 108820 139650 146710 132180 145780 63490 119000 120380 FALSE TRUE 108881.7199 117092.6024 128486.1947 146857.3532 151429.0604 134852.7702 147564.0992 62178.90931 105491.6189 112226.5554 0.970195686 1.043359141 1.144882281 1.308579353 1.349315765 1.201611951 1.314876847 0.554048096 0.939988032 1 16.77605457 1.749626315 25 0.797050977 1.194085679 0.518766046 0.157412933 2.143907195 4852.493315 0.073974719 0.041022889 56.18576709 -1.749626315 0.397034702 LHEVECSVFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHEVECSVFYR 11 0 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 123.01 0.00037892 159990000 114500 128430 100220 140570 134290 121920 137270 84386 114660 141410 FALSE TRUE 110025.2134 124767.3021 118331.9834 147824.8345 138609.5598 124385.3059 138949.9513 82643.39961 101644.2775 131832.1747 0.834585439 0.946410104 0.897595626 1.121310749 1.051409188 0.943512509 1.053991194 0.626883382 0.771012673 1 17.00834299 1.749644081 25 0.766095839 0.981026632 0.321500804 0.116225643 2.814113903 6359.201279 0.05242527 0.02907249 56.18806556 -1.749644081 0.214930793 TLDPNQVSLHPQVLPLPHS(ph)SSPEHNRPTDHPTSILSSPEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLDPNQVSLHPQVLPLPHSSSPEHNRPTDHPTSILSSPEDR 41 1 F5H527;Q76I76;A0A3B3IS79 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 TLDPNQVSLHPQVLPLPHS(0.331)S(0.331)S(0.331)PEHNRPT(0.005)DHPTSILSSPEDR 84.159 0.00012823 93496000 13369 25978 18417 32778 26846 36730 28911 11335 17291 28482 TRUE FALSE 12846.5247 25237.13288 21745.36158 34469.67651 27709.52597 37472.70577 29264.82147 11100.92829 15328.19817 26552.88877 0.48380893 0.950447731 0.818945229 1.298151655 1.04355975 1.411247796 1.102133245 0.418068572 0.577270455 1 14.6965812 1.749682469 25 0.616401064 1.032586296 0.246380803 0.275758539 3.60843124 8125.958468 0.12943318 0.071777201 56.19303238 -1.749682469 0.416185232 GFVPSPTSQPGGHESLVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFVPSPTSQPGGHESLVDR 19 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 181.34 3.17E-14 746200000 133340 235810 206930 278750 185590 228370 225540 174900 195280 249140 FALSE TRUE 128128.9254 229084.9297 244326.8541 293136.3209 191559.6709 232987.7979 228300.226 171288.2539 173112.6331 232265.5259 0.551648485 0.986306206 1.051929051 1.26207417 0.82474431 1.003109682 0.982927729 0.737467402 0.745322115 1 17.82541551 1.749742725 24.99998963 0.80459549 0.966014777 0.080709601 0.183020616 6.116138799 13698.7812 0.084338034 0.046769822 56.20082944 -1.749742725 0.161419286 LHLSGIDANPNALFPPVEFPAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHLSGIDANPNALFPPVEFPAPR 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 193.87 4.81E-18 2318400000 749100 1557730 1129320 1953750 1330370 1582510 1553800 655130 1095310 1362110 FALSE TRUE 719824.3438 1513305.066 1333413.246 2054583.272 1373162.559 1614509.436 1572815.869 641601.3366 970975.0007 1269853.076 0.5668564 1.191716659 1.050053168 1.617969283 1.081355461 1.27141436 1.238580981 0.505256355 0.764635704 1 20.27623015 1.749776456 25 0.718666601 1.164090659 0.299338322 0.269662798 3.217215725 7184.129756 0.121811561 0.067550875 56.20519456 -1.749776456 0.445424058 SHEGETSYIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SHEGETSYIR 10 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;; 187.55 1.22E-06 2476640000 434161 561695 431234 549830 510433 450713 547070 273656 450179 473513 FALSE TRUE 417193.5081 545676.0086 509167.5765 578206.7922 526851.541 459826.7257 553765.2063 268004.908 399076.5672 441441.5427 0.945070791 1.236122919 1.153420164 1.309815086 1.193479748 1.041648058 1.254447424 0.60711302 0.904030384 1 18.75186288 1.749798849 25 0.807120473 1.166788848 0.541624464 0.136108437 1.942635682 4329.29638 0.059196681 0.03282776 56.20809278 -1.749798849 0.359668374 RAVSPS(ph)NPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RAVSPSNPK 9 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 RAVS(0.377)PS(0.623)NPK 144.89 0.00010432 556040000 276980 265570 222800 214610 194300 236630 236700 272440 279800 284310 TRUE FALSE 266155.3154 257996.2036 263064.9162 225686.0478 200549.836 241414.8207 239596.8054 266814.0188 248038.277 265053.4305 1.004157218 0.973374324 0.992497685 0.851473786 0.756639277 0.910815681 0.903956629 1.00664239 0.935804817 1 18.01592369 1.749814699 25 0.978931778 0.910136303 0.160385104 0.070523286 6.222834931 13848.44956 0.036185295 0.020066648 56.21014416 -1.749814699 -0.068795475 (ac)SVCTLSVPVSSLS(ph)PGRR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVCTLSVPVSSLSPGRR 17 1 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SVCTLSVPVS(0.002)S(0.003)LS(0.996)PGRR;SVCTLSVPVS(0.002)S(0.003)LS(0.994)PGRR;SVCTLSVPVS(0.105)S(0.067)LS(0.828)PGRR;SVCTLSVPVS(0.05)S(0.034)LS(0.916)PGRR 153.56 2.63E-22 1127250000 103853 87576 78670 82023 78070 85836 85740 102764 105887 101324 TRUE FALSE 99794.30994 85078.41823 92887.419 86256.21686 80581.19245 87571.66273 86789.31177 100641.8875 93867.15167 94461.23523 1.056457813 0.900670185 0.983339026 0.913138778 0.853060965 0.927064552 0.918782308 1.065430568 0.993710822 1 16.52743478 1.749818068 25 1.023500107 0.932108183 0.3332643 0.053930435 3.169750988 7051.9231 0.024474409 0.013572245 56.21058017 -1.749818068 -0.091391924 RRPAS(ph)PELLR ddPTM_BT-474_Pertuzumab_2h_R1 3 RRPASPELLR 10 2 Q99929 Q99929 ASCL2 Achaete-scute homolog 2 1 RRPAS(1)PELLR;RRPAS(1)PELLR;RRPAS(1)PELLR 118.76 0.00061576 988810000 205469 222121 161792 238008 200786 245266 226893 177482 211036 246586 TRUE FALSE 197439.0443 215786.3266 191031.4134 250291.6214 207244.464 250225.4466 229669.7844 173816.9347 187080.078 229884.5106 0.858861886 0.938672754 0.830988625 1.088771143 0.901515563 1.088483282 0.999065939 0.756105465 0.813800275 1 17.81054974 1.749836238 25 0.834337602 0.960289006 0.168066253 0.099678884 4.23208964 9400.164133 0.044914296 0.024907378 56.21293198 -1.749836238 0.125951403 LRS(ph)PFLQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LRSPFLQK 8 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 LRS(1)PFLQK;LRS(1)PFLQK;LRS(1)PFLQK 109.39 0.002197 3510360000 3169690 3027090 3172490 3208100 3371810 3473370 3011060 3169070 2947530 3239660 TRUE FALSE 3045815.011 2940760.357 3745829.515 3373670.425 3480267.331 3543603.921 3047910.253 3103627.597 2612938.751 3020234.943 1.008469562 0.973685959 1.240244413 1.117022513 1.152316756 1.173287505 1.009163297 1.027611314 0.865144203 1 21.52622935 1.749864196 1.897596485 0.942834635 1.110110417 0.389890405 0.082771938 0.332710599 2.398233629 0.059987987 0.024777099 56.21655078 -1.749864196 0.167275782 STS(ph)PAS(ph)EKADPGAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 STSPASEKADPGAVK 15 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 2 S(0.088)T(0.108)S(0.804)PAS(1)EKADPGAVK 132.13 1.09E-05 0 601390 447970 409540 383510 428810 447260 454890 628140 693310 592570 TRUE FALSE 577887.0139 435194.3342 483552.9882 403302.9971 442603.0631 456303.9036 460457.0799 615168.6895 614608.3554 552434.7061 1.04607297 0.787775151 0.875312472 0.730046452 0.8011862 0.825987033 0.833504982 1.113559092 1.112544792 1 19.07544443 1.749890574 6.717454373 1.082803426 0.835054063 0.618148738 0.083429958 0.086251577 11.30014113 0.039546189 0.021038668 56.21996545 -1.749890574 -0.247749362 VY(ph)ENVGLMQQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VYENVGLMQQQK 12 0 Q06124;Q06124-1 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1 VY(1)ENVGLMQQQK 153.95 0.00044707 0 89819 116870 79041 98586 82697 79593 82813 127640 129530 82918 TRUE FALSE 86308.77418 113536.982 93325.46696 103674.0353 85357.02411 81202.42499 83826.49027 125004.1894 114826.2974 77301.89 1.116515705 1.468747815 1.207285707 1.341157833 1.104203585 1.050458469 1.084404149 1.617090984 1.485426778 1 16.23821607 1.749897957 25 1.427539353 1.203467568 0.121125432 0.191420835 4.633696747 10236.05646 0.086698735 0.04807888 56.2209212 -1.749897957 -0.224071785 AKT(ph)QTPPVSPAPQPTEER ddPTM_BT-474_Pertuzumab_2h_R1 2 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.636)QT(0.364)PPVSPAPQPTEER;AKT(0.62)QT(0.38)PPVSPAPQPTEER 92.95 0.0036209 15871200000 7055000 6761380 5966650 5493210 6027360 6079070 6203990 7821150 8090030 7906720 TRUE FALSE 6779282.8 6568552.062 7044956.382 5776715.226 6221235.508 6201992.96 6279916.285 7659640.519 7171683.711 7371190.812 0.919699812 0.891111386 0.955741964 0.783688196 0.84399328 0.841382772 0.851954107 1.039132036 0.97293421 1 22.81346627 1.749901159 10.28159885 1.003142075 0.868398813 0.634760556 0.046683161 0.073044079 37.89837219 0.02295746 0.01250264 56.22133567 -1.749901159 -0.134743262 RSS(ph)LGEK ddPTM_BT-474_Pertuzumab_2h_R1 4 RSSLGEK 7 1 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 RS(0.043)S(0.957)LGEK;RS(0.016)S(0.984)LGEK;RS(0.118)S(0.882)LGEK;RS(0.2)S(0.8)LGEK 99.174 0.0065673 334980000 1104220 1132590 855570 986420 885430 894560 942000 1226040 1194640 1141130 TRUE FALSE 1061065.862 1100289.642 1010190.531 1037329.254 913910.6601 912648.6161 953528.4778 1200721.846 1059029.476 1063840.249 0.997392102 1.034262093 0.949569761 0.97507991 0.859067573 0.857881263 0.896307955 1.128667436 0.995477918 1 20.02085009 1.749905147 25 1.051361257 0.937866805 0.351597505 0.063583339 3.367206536 7433.596506 0.031877931 0.017678006 56.22185195 -1.749905147 -0.113494452 ATAPQTQHVSPMR ddPTM_BT-474_Pertuzumab_2h_R1 7 ATAPQTQHVSPMR 13 0 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PK06;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;;;;; 189.09 5.55E-06 1487357000 657347 1264776 895674 1451612 1096973 1220829 1085983 945709 827211 1164594 FALSE TRUE 631657.1525 1228705.827 1057542.216 1526529.869 1132258.133 1245514.999 1099273.585 926179.7787 733309.4752 1085715.011 0.581789094 1.131701979 0.97405139 1.406013414 1.042868636 1.147184101 1.012488152 0.853059753 0.675416171 1 20.05021403 1.749909277 3.423009376 0.817537819 1.064245141 0.160947454 0.205904366 0.336880721 8.190571253 0.111703328 0.054474107 56.22238664 -1.749909277 0.246707322 SSS(ph)LDGEHHDGYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLDGEHHDGYHR 14 0 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 S(0.302)S(0.302)S(0.397)LDGEHHDGYHR 117 0.0005501 684010000 459150 393530 344080 452360 429160 411690 426520 267440 345350 393400 TRUE FALSE 441205.9104 382306.9097 406262.91 475706.3538 442964.3212 420014.6539 431739.8793 261917.2705 306147.3158 366754.6676 1.203000123 1.042405028 1.107723898 1.297069665 1.207794638 1.145219655 1.17718987 0.714148431 0.834746884 1 18.4844558 1.749927237 24.99999097 0.830631674 1.166977774 0.722223951 0.090424303 1.4891692 3281.152756 0.041646803 0.023095398 56.22471167 -1.749927237 0.3363461 CLALATHDNPLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 CLALATHDNPLRR 13 1 P16615-5;P16615-2;P16615-3;P16615;H7C5W9;P16615-4 P16615-5 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 0 135.6 5.33E-05 222250000 204390 310400 214030 318210 253640 225580 280030 161550 239970 253290 FALSE TRUE 196402.2128 301547.6959 252709.9821 334632.8562 261798.5609 230141.3822 283457.0909 158213.936 212729.6116 236134.4427 0.831738948 1.277016993 1.070195348 1.417128532 1.108684349 0.974620134 1.20040553 0.670016344 0.900883451 1 17.84924896 1.749930115 25 0.831782147 1.13411629 0.343082562 0.169042895 2.97882873 6561.724101 0.074851522 0.041508995 56.2250843 -1.749930115 0.302334144 SLDGAAAVDSADRS(ph)PRPTSAPAITQGQVAEGGVLDASAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDGAAAVDSADRSPRPTSAPAITQGQVAEGGVLDASAK 39 2 A0A2R8Y4N6;A0A2R8YD30;A0A2U3TZH6;A0A3B3IU06;A0A2R8Y5Z6;A0A2R8Y5G2;A0A2R8Y570;A0A2R8YCW8;A0A2R8Y6G5;A0A3B3ITP0;A0A2R8YFR9;Q4VB86;A0A3B3IUD6;A0A2R8Y7Y3;A0A2R8Y7N0;A0A2R8Y420;P11171-3;P11171-7;P11171-5;P11171-4;P11171-6;P11171-2;P11171 A0A2R8Y4N6 EPB41 Protein 4.1 1 S(0.001)LDGAAAVDS(0.025)ADRS(0.973)PRPT(0.001)S(0.001)APAITQGQVAEGGVLDASAK 107.03 6.89E-06 298440000 58027 49188 42193 58904 41404 53827 49697 65710 68660 60720 TRUE FALSE 55759.24069 47785.2064 49818.21368 61944.0425 42735.79726 54915.41882 50305.20675 64353.06554 60866.00465 56607.38032 0.985017155 0.844151525 0.880065698 1.094275025 0.75495098 0.970110585 0.888668694 1.13683172 1.075230903 1 15.78870254 1.749944341 14.7587942 1.078852534 0.915202183 0.37600676 0.090674897 0.180818443 228.2155279 0.039810501 0.021963212 56.22692609 -1.749944341 -0.163650351 S(ph)PQQTVPYVVPLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 2 S(0.998)PQQT(0.002)VPYVVPLS(1)PK;S(1)PQQTVPYVVPLS(1)PK;S(1)PQQTVPYVVPLS(1)PK;S(0.999)PQQT(0.001)VPYVVPLS(1)PK 180.16 9.36E-07 436192000 1217340 1040600 903930 917560 1027980 1082050 1038600 1265570 1345060 1301400 TRUE FALSE 1169765.007 1010923.107 1067290.259 964915.3816 1061045.91 1103929.792 1051310.697 1239435.537 1192374.428 1213255.019 0.96415427 0.833232166 0.879691608 0.795311263 0.874544835 0.909890975 0.86652079 1.021578743 0.982789611 1 20.2104514 1.749968884 7.546377901 1.00036186 0.871549828 0.647728527 0.04272427 0.078472769 14.65433982 0.02023665 0.010841068 56.2301037 -1.749968884 -0.128812032 TLENPVNVYNPSHSDSLASQQSVASHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLENPVNVYNPSHSDSLASQQSVASHPR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 119.14 7.96E-05 588160000 63263 81604 62569 104140 74228 74089 80504 71432 77096 88823 FALSE TRUE 60790.61202 79276.73382 73876.61014 109514.6779 76615.61103 75587.13034 81489.23203 69956.90424 68344.38529 82806.93909 0.734124612 0.957368243 0.892154824 1.322530202 0.925231772 0.912811549 0.984086997 0.844819347 0.825346113 1 16.33746405 1.750007385 13.92966981 0.876772129 0.96903994 0.04391865 0.145033754 0.463459818 531.3509053 0.068221952 0.037583814 56.23508876 -1.750007385 0.092267811 RQQEVETELK ddPTM_BT-474_Pertuzumab_2h_R1 3 RQQEVETELK 10 1 P08621;P08621-2;M0QYR1;P08621-3;M0QX04 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 205.97 2.55E-07 2136210000 2912980 2718870 2213610 2204490 2576980 2588110 2560710 2907050 3084660 2943810 FALSE TRUE 2799137.521 2641330.49 2613658.568 2318263.993 2659870.902 2640443.357 2592048.735 2847018.402 2734502.329 2744423.127 1.019936574 0.962435589 0.952352625 0.844718138 0.969191258 0.96211234 0.944478535 1.037383184 0.996385106 1 21.3880715 1.750016635 24.99999867 1.012965232 0.948326335 0.300796569 0.042139538 3.787103663 8279.05509 0.020092145 0.011142221 56.23628653 -1.750016635 -0.064638896 ALIFVSHGAGEHSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALIFVSHGAGEHSGR 15 0 A0A0C4DFN3;Q99685-2;Q99685;A0A3B3ITT3;C9JAM4 A0A0C4DFN3 MGLL Monoglyceride lipase 0 178.67 4.06E-07 172570000 65881 92910 61074 91633 98486 92439 108460 31653 86202 96080 FALSE TRUE 63306.29768 90260.29777 72111.43038 96362.19011 101653.8916 94308.17991 109787.3659 30999.35449 76416.71035 89572.41602 0.706761082 1.007679616 0.805062915 1.075802065 1.134879421 1.052870784 1.225682758 0.346081482 0.853127712 1 16.4507669 1.75002424 25 0.672964133 1.003943898 0.238272315 0.211664511 3.486142519 7616.049445 0.094597539 0.052459123 56.23727127 -1.75002424 0.330979766 HHEEEIVHHK ddPTM_BT-474_Pertuzumab_2h_R1 2 HHEEEIVHHK 10 0 Q9UII2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 90.149 0.011028 32613000 77932 108213 91338 162496 66069 97348 109633 11846.1 75469 38892 FALSE TRUE 74886.33128 105126.8712 107844.8084 170882.438 68194.16939 99316.44326 110974.7214 11601.4739 66902.07551 36257.8102 2.065384834 2.899426927 2.974388354 4.712982861 1.880813238 2.739173787 3.060712184 0.31997172 1.845176947 1 15.14600418 1.750065344 25 1.050481406 2.93097872 0.534536112 0.790687887 2.354739039 5125.896486 0.360877438 0.200125467 56.24259418 -1.750065344 1.880497314 EDSEKDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDSEKDEK 8 1 P29374;P29374-3;P29374-2;H7C485 P29374 ARID4A AT-rich interactive domain-containing protein 4A 0 50.04 0.094983 1721200000 1175800 2688400 1985700 3928400 2887600 3013900 2266100 1366600 744270 1351600 FALSE TRUE 1129848.436 2611729.464 2344560.162 4131145.195 2980482.276 3074843.123 2293833.21 1338379.232 659783.5898 1260054.928 0.896666019 2.072710805 1.860680919 3.278543739 2.365359009 2.440245305 1.820423188 1.062159437 0.523614943 1 20.26505519 1.750142233 2.529016035 0.765307932 2.193286062 0.510186553 0.567604502 0.210323666 2.756251738 0.363968428 0.163819284 56.25255239 -1.750142233 1.42797813 HALLEADVAAHQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HALLEADVAAHQDR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 170.11 1.86E-06 946260000 405400 564600 519680 678510 536370 534660 598180 332600 530060 498700 FALSE TRUE 389556.5198 548498.1608 613597.7362 713527.9824 553622.8282 545471.1915 605500.7058 325731.6938 469889.811 464922.6048 0.837895417 1.179762298 1.319784691 1.534724221 1.190784923 1.173251603 1.302368823 0.700614877 1.010683942 1 18.82663105 1.750163798 25 0.883588209 1.231308967 0.385740023 0.181814941 3.067256625 6620.167582 0.085695924 0.047523042 56.25534568 -1.750163798 0.347720758 EQEAGVLAMDALHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQEAGVLAMDALHR 14 0 A0A0A0MTH9;O14981;O14981-2 A0A0A0MTH9 BTAF1 TATA-binding protein-associated factor 172 0 124.78 9.51E-05 81556000 120240 114490 99676 116260 114840 126020 124270 104330 136080 120640 FALSE TRUE 115540.8879 111224.8573 117689.6705 122260.1925 118533.9329 128568.2107 125790.8534 102175.549 120632.7689 112468.9453 1.027313695 0.988938386 1.046419259 1.08705734 1.053925886 1.143144095 1.118449658 0.90847788 1.072587358 1 16.77916718 1.750178358 25 0.986514923 1.065970658 0.262621954 0.055488914 4.174845182 8999.394968 0.026597212 0.014749541 56.25723171 -1.750178358 0.079455735 ASAGTPSLSAGVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASAGTPSLSAGVSPK 15 0 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 ASAGTPSLSAGVS(1)PK;ASAGTPSLSAGVS(1)PK 268.77 1.09E-25 830080000 1042400 883840 732510 737520 767510 750740 822890 974660 1028460 1028440 TRUE FALSE 1001661.856 858633.7486 864890.8516 775583.4956 792197.6562 765920.4772 832960.774 954532.9304 911713.5325 958782.8428 1.044722341 0.895545592 0.902071682 0.808925088 0.826253476 0.798846666 0.868768961 0.995567388 0.950907225 1 19.87084457 1.750223723 7.447343688 0.978856628 0.871726766 0.336777132 0.066558082 0.159925494 28.6491595 0.033890491 0.018147065 56.26310851 -1.750223723 -0.107129863 RGEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGEGDAPFSEPGT(0.004)T(0.013)S(0.047)T(0.05)QRPS(0.924)S(0.958)PET(0.005)ATK;RGEGDAPFSEPGTT(0.002)S(0.043)T(0.037)QRPS(0.872)S(0.956)PET(0.086)AT(0.006)K 144.86 8.95E-08 977670000 537300 503370 455960 464850 501740 489580 489160 624960 646550 617950 TRUE FALSE 516301.722 489014.3805 538362.1148 488840.9642 517878.9228 499479.643 495146.4864 612054.3576 573156.3546 576095.6961 0.896208261 0.848842274 0.934501192 0.848541254 0.898946002 0.867008114 0.859486522 1.062417862 0.994897824 1 19.13594895 1.750251174 11.41755191 1.020272876 0.879166117 0.82081912 0.029973584 0.041324252 29.50602663 0.012926348 0.007073456 56.26666497 -1.750251174 -0.141106759 DQEPKPS(ph)PEPAAVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQEPKPSPEPAAVSR 15 1 Q9H7S9 Q9H7S9 ZNF703 Zinc finger protein 703 1 DQEPKPS(1)PEPAAVSR 96.131 0.0023121 558580000 298800 285000 236770 215890 267100 275850 265540 339730 374340 324510 TRUE FALSE 287122.5657 276872.079 279559.6059 227032.1088 275691.5141 281427.876 268789.758 332714.4568 331846.4926 302530.6487 0.949069349 0.915186875 0.924070362 0.750443335 0.911284577 0.930245835 0.888471165 1.099771075 1.096902063 1 18.20672178 1.750337307 7.351780968 1.072039043 0.893599657 0.644298538 0.057754608 0.081578091 14.03750021 0.028507105 0.015255238 56.27782533 -1.750337307 -0.178439386 DRELDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRELDLR 7 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ; 133.23 0.0030018 2203090000 4930400 5264600 4050900 5004600 4505600 4665300 4977700 3999700 5281800 4508200 FALSE TRUE 4737714.517 5114458.763 4782987.742 5262888.006 4650526.716 4759635.562 5038618.582 3917104.797 4682232.207 4202855.599 1.127260836 1.216900901 1.138032852 1.252217185 1.106515941 1.132476587 1.198855983 0.932010321 1.114059738 1 22.00293846 1.750379365 25 1.013560167 1.167804943 0.581442456 0.059134653 2.11157265 4474.194408 0.025374185 0.014071311 56.28327569 -1.750379365 0.154244777 HYLILPSEEEGR ddPTM_BT-474_Pertuzumab_2h_R1 7 HYLILPSEEEGR 12 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;;;;; 170.04 4.22E-05 4125840000 2156479 2344821 2206529 2818700 2563824 2503739 2668940 1985582 2575452 2729010 FALSE TRUE 2072201.417 2277949.001 2605297.874 2964173.445 2646291.727 2554366.318 2701603.286 1944579.038 2283097.486 2544171.722 0.814489603 0.895359767 1.024025954 1.165083874 1.040138802 1.004007039 1.0618793 0.76432696 0.897383406 1 21.27876462 1.750382019 25 0.866254493 1.005522157 0.191285842 0.1039492 4.660685011 9873.264245 0.050548706 0.028031777 56.28361963 -1.750382019 0.139267664 TEHSHS(ph)PGDSSAPIQNTDCCHSSER ddPTM_BT-474_Pertuzumab_2h_R1 1 TEHSHSPGDSSAPIQNTDCCHSSER 25 0 Q13129 Q13129 RLF Zinc finger protein Rlf 1 TEHSHS(1)PGDSSAPIQNTDCCHSSER 254.85 1.26E-44 268600000 23648 41895 29270 52028 25976 32271 37480 6854.9 25971 18712 TRUE FALSE 22723.81002 40700.19562 34559.74011 54713.17132 26811.54163 32923.54173 37938.69145 6713.34392 23022.88096 17444.61957 1.302625713 2.33310881 1.98111171 3.136392346 1.536951925 1.88731784 2.174807613 0.384837508 1.319769735 1 14.09049452 1.750397249 25 0.877792815 2.074301704 0.516763945 0.508554667 2.444581279 5171.961421 0.227298084 0.126048663 56.28559334 -1.750397249 1.196508889 IHSEVVEDTEAVSAVQQLLDDER ddPTM_BT-474_Pertuzumab_2h_R1 1 IHSEVVEDTEAVSAVQQLLDDER 23 0 Q96GA7;H0YID3 Q96GA7 SDSL Serine dehydratase-like 0 243.23 2.22E-37 340710000 167250 199810 160240 205430 189450 232930 210340 132810 195850 186920 FALSE TRUE 160713.6851 194111.6144 189198.9325 216032.2669 195543.8313 237640.0042 212914.2038 130067.4271 173617.9291 174259.7419 0.922265139 1.113921163 1.085729443 1.239714145 1.122140026 1.363711444 1.221820952 0.746399746 0.996316918 1 17.41087979 1.750449959 25 0.895858334 1.158966604 0.424173479 0.126666156 2.921404653 6153.314368 0.059285852 0.032877054 56.29242516 -1.750449959 0.26310827 KDSGSSSVSSTSSSSSS(ph)SPGDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSGSSSVSSTSSSSSSSPGDK 22 1 Q9H7S9 Q9H7S9 ZNF703 Zinc finger protein 703 1 KDSGSSSVSSTSSSS(0.004)S(0.019)S(0.592)S(0.385)PGDK 162.44 9.94E-12 265220000 138340 105580 98423 91349 95576 108550 106200 135420 149260 128200 TRUE FALSE 132933.5199 102568.9618 116210.2255 96063.53284 98650.28884 110744.9554 107499.7074 132623.5297 132316.6305 119516.8998 1.112257096 0.858196305 0.972332998 0.803765267 0.825408699 0.926604987 0.89945194 1.109663402 1.107095572 1 16.86685511 1.750484913 7.812268845 1.07948593 0.906832453 0.410404756 0.086402227 0.115846268 24.12078323 0.040712847 0.021864556 56.296956 -1.750484913 -0.172653478 YADSPGASS(ph)PEQPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 YADSPGASSPEQPKR 15 1 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 YADSPGAS(0.033)S(0.967)PEQPKR;YADSPGAS(0.01)S(0.99)PEQPKR 206.61 2.33E-09 1247000000 1033230 963930 760740 876310 858970 935930 912410 1026640 1080240 1055180 TRUE FALSE 992850.2293 936439.6602 898222.6406 921536.4641 886599.5501 954855.1459 923576.3465 1005439.525 957615.6839 983711.7187 1.009289826 0.951945212 0.913095395 0.936795249 0.90127985 0.97066562 0.938868907 1.022087575 0.973471868 1 19.90787606 1.750488001 24.99976254 0.998926892 0.9438308 0.388040103 0.030142546 3.308271033 6945.835878 0.013983825 0.007754769 56.2973563 -1.750488001 -0.055096092 SAS(ph)QDCIETTPGAQEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASQDCIETTPGAQEGK 17 0 Q99767;Q99767-2 Q99767 APBA2 Amyloid beta A4 precursor protein-binding family A member 2 1 S(0.012)AS(0.988)QDCIETTPGAQEGK;S(0.001)AS(0.999)QDCIETTPGAQEGK 246.67 1.09E-21 0 331270 309870 239576 297410 294500 273230 286350 370780 364830 353850 TRUE FALSE 318323.6022 301032.811 282872.7125 312759.3657 303972.86 278754.8978 289854.437 363123.2634 323416.0279 329883.4243 0.964957857 0.912543004 0.857492956 0.948090576 0.921455392 0.84501032 0.878657173 1.10076238 0.980394903 1 18.33159676 1.750544617 25 1.033398912 0.902661952 0.603441963 0.045605155 2.079824393 4346.036505 0.020693678 0.011475753 56.3046959 -1.750544617 -0.13073696 LHDVNSDGFLDEQELEALFTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHDVNSDGFLDEQELEALFTK 21 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 109.89 0.00020759 0 65925 75700 51843 69971 60581 71053 74243 46588 70160 70877 FALSE TRUE 63348.57812 73541.11012 61212.18334 73582.2117 62529.64288 72489.74034 75151.60804 45625.94152 62195.73093 66076.43766 0.958716607 1.112970262 0.926384435 1.113592293 0.946322851 1.097058844 1.137343518 0.690502441 0.941269432 1 16.01184829 1.750553076 25 0.849974075 1.041288771 0.335761198 0.103930938 3.059242935 6388.129045 0.044488724 0.024671204 56.3057925 -1.750553076 0.191314696 YSEKEDKYEEEIK ddPTM_BT-474_Pertuzumab_2h_R1 4 YSEKEDKYEEEIK 13 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 123.02 0.00012837 2085690000 1780510 1272680 1195500 866490 1144570 1143730 1232770 1639890 1905900 1422710 FALSE TRUE 1710925.701 1236384.412 1411553.444 911209.6527 1181386.134 1166857.004 1247857.008 1606025.698 1689550.222 1326348.584 1.289951767 0.932171547 1.064240171 0.687006164 0.890705616 0.879751385 0.940821306 1.210862451 1.273835734 1 20.33902856 1.750583695 6.915515701 1.179663565 0.942328056 0.258921289 0.158092055 0.172439751 24.61434435 0.07672992 0.040928412 56.30976244 -1.750583695 -0.237335509 DGHPNVLHDCQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGHPNVLHDCQR 12 0 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 58.268 0.062063 116530000 47665 59726 49688 64435 72073 59139 69491 35714 57800 70294 FALSE TRUE 45802.1991 58022.67296 58667.7269 67760.49807 74391.2935 60334.8311 70341.45165 34976.49342 51238.78632 65532.92477 0.698918891 0.885397274 0.895240478 1.033991666 1.135174323 0.920679663 1.07337574 0.53372398 0.781878521 1 15.9999323 1.750623394 25 0.728408879 0.95380129 0.198562683 0.155665755 4.208315025 8736.22843 0.071389687 0.039589354 56.31490991 -1.750623394 0.225392411 AGAAAGDS(ph)DEESR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGAAAGDSDEESR 13 0 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(1)DEESR;AGAAAGDS(1)DEESR 171.76 1.81E-06 38599000 76245 87428 97397 123543 74476 105451 96748 90787 90385 109826 TRUE FALSE 73265.26111 84934.63904 114998.8045 129919.069 76871.58818 107583.2915 97932.03096 88912.21672 80124.87372 102387.3872 0.715569204 0.829542011 1.123173543 1.268897201 0.75079158 1.050747503 0.956485302 0.868390328 0.78256586 1 16.64367848 1.7506266 5.178649665 0.869274616 0.966105547 0.034647384 0.166118061 0.566275748 36.00095037 0.086711227 0.045244708 56.31532563 -1.7506266 0.096830931 NDKSEEEQSSSSVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDKSEEEQSSSSVKK 15 2 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 211.12 8.66E-10 1029120000 1391950 1154950 1098140 837530 866330 1202920 1207950 1372560 1842760 1434430 FALSE TRUE 1337551.055 1122011.957 1296598.326 880755.0237 894196.2912 1227243.867 1222733.253 1344216.156 1633577.61 1337274.778 1.000206597 0.839028728 0.969582577 0.658619334 0.668670572 0.917720043 0.914347054 1.005190689 1.221572138 1 20.35086451 1.750659392 1.802343313 1.108076409 0.83299906 0.449342666 0.117698756 0.303072646 1.955336332 0.087607232 0.03573228 56.31957803 -1.750659392 -0.27507735 GLALHDILTEIHLFVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLALHDILTEIHLFVHR 17 0 P40937-2;P40937 P40937-2 RFC5 Replication factor C subunit 5 0 ; 310.57 1.45E-58 354200000 159004 194597 179699 228580 206179 172105 226750 87648 200484 170941 FALSE TRUE 152789.9479 189047.2841 212174.6067 240377.0412 212810.9348 175585.081 229525.0343 85838.03817 177725.8968 159363.0138 0.958754131 1.186268254 1.33139178 1.508361542 1.335384728 1.101793175 1.440265397 0.538632121 1.115226755 1 17.28195731 1.750665665 25 0.848961356 1.271149204 0.420140148 0.203989353 2.92250008 6045.723305 0.09231419 0.051193093 56.32039143 -1.750665665 0.422187848 ILS(ph)PSMASK ddPTM_BT-474_Pertuzumab_2h_R1 5 ILSPSMASK 9 0 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91;C9JWI7;Q8IX09 Q9Y6A5 TACC3;ERIC-1s Transforming acidic coiled-coil-containing protein 3 1 ILS(0.992)PS(0.008)MASK;ILS(0.977)PS(0.023)MASK;ILS(0.987)PS(0.013)MASK;ILS(0.998)PS(0.002)MASK;ILS(0.996)PS(0.004)MASK 156.58 7.40E-05 2047970000 3532790 3533230 3498670 3957010 3901840 3742460 3733750 3481280 3478000 4046200 TRUE FALSE 3394724.661 3432465.74 4130957.496 4161231.76 4027346.227 3818135.105 3779444.749 3409390.351 3083192.021 3772147.27 0.89994489 0.909950088 1.095120949 1.103146686 1.067653498 1.012191421 1.001934569 0.903832779 0.817357277 1 21.84695457 1.750682076 3.716498379 0.893486401 1.018904322 0.28247922 0.076506523 0.255223078 7.382026135 0.044182387 0.021940205 56.32251978 -1.750682076 0.12541792 NEDEEEEEEEKDEAEDLLGR ddPTM_BT-474_Pertuzumab_2h_R1 6 NEDEEEEEEEKDEAEDLLGR 20 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;; 327.26 9.05E-80 5702130000 5066710 3887629 3592732 3250076 4072550 3804702 4093510 5379920 6307600 5113480 FALSE TRUE 4868697.372 3776757.627 4242018.592 3417812.812 4203547.269 3881635.681 4143607.6 5268822.772 5591587.692 4767139.445 1.021303746 0.792248196 0.889845712 0.716952556 0.881775605 0.814248403 0.869202096 1.105237812 1.172944017 1 22.1846924 1.750742308 4.52909007 1.105931799 0.846611549 0.626132221 0.083889288 0.105982302 4.816183815 0.040879607 0.020990242 56.33033164 -1.750742308 -0.259320249 WNS(ph)NDFIDAFASPVEAEGTPEPGAEAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 WNSNDFIDAFASPVEAEGTPEPGAEAAK 28 0 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 WNS(1)NDFIDAFASPVEAEGTPEPGAEAAK;WNS(1)NDFIDAFASPVEAEGTPEPGAEAAK 174.86 7.30E-13 79659000 102711 101422 82164 97750 85892 92450 92874 119958 123896 117034 TRUE FALSE 98696.94057 98529.54386 97012.86253 102794.8892 88654.79419 94319.40234 94010.61979 117480.8254 109831.8455 109107.1829 0.904587012 0.903052771 0.889151932 0.942145938 0.812547733 0.864465563 0.861635479 1.07674694 1.006641749 1 16.73538656 1.750749061 12.22234282 1.030189566 0.882463077 0.76231611 0.037163571 0.059852659 50.20016566 0.01754487 0.009627004 56.33120754 -1.750749061 -0.147726488 GHVSELEADLAEQQHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHVSELEADLAEQQHLR 17 0 O00291-3;O00291-4;O00291 O00291-3 HIP1 Huntingtin-interacting protein 1 0 158.29 1.94E-09 118070000 90385 116870 95449 126310 110820 119250 114020 90579 105130 118340 FALSE TRUE 86852.65427 113536.982 112698.7576 132828.8742 114384.6259 121661.3167 115415.4109 88708.512 93196.08314 110324.7264 0.78724559 1.029116371 1.021518577 1.203980998 1.036799543 1.102756569 1.046142734 0.804067365 0.844743388 1 16.75139664 1.750784538 25 0.867551835 1.041417469 0.280130167 0.108386665 3.916682197 8023.427407 0.05010983 0.027788517 56.33580936 -1.750784538 0.173865634 LGDVGMAELCPGLLHPSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGDVGMAELCPGLLHPSSR 19 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 126.43 2.54E-05 391890000 138530 193650 153210 179190 162490 172790 178640 143660 171960 191410 FALSE TRUE 133116.0944 188127.2916 180898.4551 188438.0174 167716.6384 176283.9322 180826.2498 140693.3708 152439.8217 178445.6302 0.745975647 1.054255525 1.013745503 1.055996816 0.93987529 0.987885957 1.013340868 0.788438308 0.854264806 1 17.44512505 1.750837073 25 0.861741084 0.98019194 0.147474154 0.097233284 4.944494421 10085.50168 0.042782647 0.023725214 56.3426245 -1.750837073 0.118450857 T(ph)NSSDSERS(ph)PDLGHSTQIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TNSSDSERSPDLGHSTQIPR 20 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 2 T(0.353)NS(0.353)S(0.294)DS(0.001)ERS(1)PDLGHSTQIPR 99.423 0.0015114 568710000 315180 311260 256160 264000 308660 311770 271340 374880 362570 298660 TRUE FALSE 302862.4172 302383.1696 302453.8102 277625.0716 318588.3292 318074.203 274660.7401 367138.597 321412.5736 278431.4922 1.087744834 1.086023593 1.086277302 0.997103702 1.144225198 1.142378689 0.986457164 1.318595803 1.154368606 1 18.08696287 1.750847108 25 1.188997447 1.078716456 0.125198837 0.087990742 4.755990454 9693.068117 0.038260218 0.021217202 56.34392638 -1.750847108 -0.110280991 EIIDAS(ph)DKEGMS(ph)PAKR ddPTM_BT-474_Pertuzumab_2h_R1 6 EIIDASDKEGMSPAKR 16 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR 143.31 7.64E-07 4275260000 3324670 2374510 2134938 1736543 2321558 2253863 2350759 3466960 3502770 2971040 TRUE FALSE 3194738.221 2306791.3 2520768.788 1826166.192 2396233.021 2299437.654 2379528.292 3395366.064 3105150.234 2769808.814 1.153414706 0.832834125 0.910087648 0.659311279 0.865125784 0.830179196 0.859094779 1.22584853 1.121070241 1 21.40135497 1.750892202 25 1.130921172 0.862603054 0.438961822 0.125043402 2.908967559 5906.973204 0.056581707 0.031377439 56.34977705 -1.750892202 -0.268318118 LHSQEEDFR ddPTM_BT-474_Pertuzumab_2h_R1 3 LHSQEEDFR 9 0 Q4V328-4;Q4V328;Q4V328-2;A0A087WV84;A0A087WW92;A0A087WZF5 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 0 ;; 176.33 5.32E-05 424570000 648487 641220 537270 653488 666231 668993 794054 389272 820017 656382 FALSE TRUE 623143.4111 622933.0334 634366.6405 687214.594 687660.9252 682520.4968 803771.8704 381233.3972 726932.108 611924.6625 1.018333545 1.017989749 1.036674413 1.12303791 1.123767299 1.115366872 1.313514424 0.62300708 1.187943798 1 19.22299452 1.750976907 25 0.902424267 1.10241985 0.196224798 0.152724337 4.693216335 9464.943197 0.067249374 0.037293178 56.36076861 -1.750976907 0.199995584 AHSS(ph)PAS(ph)LQLGAVSPGTLTPTGVVSGPAATPTAQHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 2 AHS(0.469)S(0.515)PAS(0.476)LQLGAVS(0.513)PGT(0.017)LT(0.007)PT(0.003)GVVSGPAATPTAQHLR 66.025 0.0026089 172950000 12707 15350 11009 11594 13209 15679 13730 9858.5 13483 11749 TRUE FALSE 12210.39639 14912.23303 12998.57119 12192.36773 13633.87948 15996.04012 13898.03185 9654.91853 11952.46637 10953.22977 1.114775884 1.361446199 1.186734093 1.113129916 1.244736007 1.46039483 1.268852397 0.881467726 1.091227576 1 13.41906872 1.750989525 25 0.987459251 1.254486603 0.539097556 0.10972263 2.700606695 5440.853238 0.051575967 0.028601522 56.36240607 -1.750989525 0.267027352 GIHDADSEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GIHDADSEAR 10 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 0 120.09 0.00060585 101760000 34039 31884 29951 32844 34663 41994 34909 29876 31733 35501 FALSE TRUE 32708.71825 30974.69954 35363.81196 34539.08278 35777.96688 42843.14745 35336.22678 29259.05016 28130.80288 33096.48565 0.988283729 0.935890894 1.068506558 1.043587623 1.08102012 1.294492349 1.06767308 0.884053083 0.849963442 1 15.01439041 1.751060688 6.53027293 0.901637484 1.071873409 0.366970641 0.09417655 0.162797628 19.59374344 0.049849817 0.02651473 56.3716424 -1.751060688 0.170235925 TGS(ph)CSELDACPSK ddPTM_BT-474_Pertuzumab_2h_R1 3 TGSCSELDACPSK 13 0 A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9;H0Y9Z7 A0A1B0GUA8 KIF13A Kinesin-like protein KIF13A 1 T(0.01)GS(0.989)CS(0.001)ELDACPSK;T(0.001)GS(0.989)CS(0.01)ELDACPSK;TGS(0.999)CS(0.001)ELDACPSK 344.55 9.02E-64 767480000 1225820 1010040 715050 770080 958600 893380 916320 1180550 1301860 1083700 TRUE FALSE 1177913.599 981234.6481 844275.4412 809823.9211 989434.2396 911444.7557 927534.1983 1156171.23 1154078.311 1010300.034 1.165904741 0.971230937 0.835668032 0.801567746 0.979346933 0.902152554 0.918077964 1.144384036 1.142312454 1 19.94635237 1.751115243 9.016935291 1.105604934 0.931180061 0.335782147 0.100016235 0.12889023 42.72972596 0.049008415 0.026534653 56.37872413 -1.751115243 -0.174424872 AELGIPLEEVPPEEINYLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AELGIPLEEVPPEEINYLTR 20 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 68.809 0.047975 25964000 26108 25154 22777 24019 20537 25681 23156 34634 32337 29959 FALSE TRUE 25087.6705 24436.63255 26893.31057 25258.62347 21197.59126 26200.28742 23439.39005 33918.7958 28666.23933 27929.85025 0.898238633 0.874928878 0.962887747 0.904359431 0.758958285 0.938074755 0.839223621 1.21442813 1.026365665 1 14.76952022 1.751142331 25 1.096369512 0.883431417 0.59428556 0.074566814 2.199062633 4376.494904 0.032792211 0.018184971 56.38224064 -1.751142331 -0.212938095 SVAHVTEADLFHTIETLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVAHVTEADLFHTIETLMR 19 0 A5YKK6-3;A5YKK6-2;A5YKK6;H3BMZ2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ; 283.5 4.57E-40 319310000 174987 235175 195749 240409 226778 232918 251178 141558 215190 254229 FALSE TRUE 168148.3146 228468.0393 231125.1987 252816.5373 234072.5203 237627.7615 254251.9915 138634.7778 190762.5334 237009.8434 0.709457093 0.963960129 0.975171307 1.066692141 0.987606747 1.002607141 1.072748658 0.584932574 0.804871775 1 17.85458745 1.751154871 25 0.758318267 0.974260774 0.241307207 0.134198695 3.967400038 7887.900524 0.059896572 0.033215718 56.38386874 -1.751154871 0.215942507 NGETVPIDEQFDKEK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGETVPIDEQFDKEK 15 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 142.39 4.19E-06 601360000 618620 509580 497320 458730 514860 506410 517380 665780 682190 613420 FALSE TRUE 594443.6465 495047.2773 587196.7868 482405.1103 531420.9395 516649.9572 523711.8512 652031.4103 604750.6512 571872.517 1.039468813 0.8656602 1.026796654 0.843553582 0.929264694 0.903435542 0.915784262 1.140169165 1.057492069 1 19.12533405 1.75117621 24.99998731 1.076118965 0.928484606 0.457449473 0.066464872 2.748227237 5454.707976 0.028282632 0.015684207 56.38663914 -1.75117621 -0.14763436 HATAEEVEEEERDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HATAEEVEEEERDR 14 1 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 ; 249.32 2.61E-18 1108370000 74445 88157 83069 89678 87553 86651 93826 55375 87629 80125 FALSE TRUE 71535.6071 85642.84867 98081.41616 94306.29233 90369.22176 88403.14259 94974.27065 54231.4869 77681.72329 74698.06238 0.95766349 1.146520351 1.313038291 1.262499847 1.209793385 1.183473035 1.271442225 0.726009286 1.039942949 1 16.1887832 1.751177105 25 0.902252215 1.198024116 0.51463979 0.11963557 2.641165685 5241.838823 0.054447292 0.030193902 56.38675535 -1.751177105 0.295771901 IVVPPHLGYGEEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IVVPPHLGYGEEGR 14 0 O95302;O95302-3;O95302-2;C9J4P8 O95302 FKBP9 Peptidyl-prolyl cis-trans isomerase FKBP9;Peptidyl-prolyl cis-trans isomerase 0 ; 170.95 3.09E-06 252200000 164502 216270 159706 231520 190201 197513 203610 168704 207520 203309 FALSE TRUE 158073.08 210102.1914 188568.4268 243468.7749 196318.9879 201506.8482 206101.8401 165220.2034 183963.1996 189538.7003 0.833988413 1.108492308 0.994880869 1.284533314 1.035772576 1.063143558 1.087386585 0.871696404 0.97058384 1 17.53213292 1.751185308 25 0.937803781 1.065823795 0.174315877 0.109143623 5.486701531 10882.19897 0.048902325 0.02711894 56.38782047 -1.751185308 0.128020014 EREQCCYNCGKPGHLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EREQCCYNCGKPGHLAR 17 2 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 97.579 0.0012251 57477000 90784 94602 43387 56448 81472 97250 78838 63720 80695 65281 FALSE TRUE 87236.06091 91904.04359 51227.99604 59361.28804 84092.62087 99216.46163 79802.84303 62404.15973 71534.8419 60859.45972 1.43340183 1.51010285 0.841742537 0.975383093 1.381751025 1.63025538 1.311264401 1.025381428 1.1754104 1 15.89319391 1.75118988 9.652865875 1.077590581 1.291991616 0.178471329 0.226226446 0.247903895 102.7505571 0.117971144 0.064092343 56.38841402 -1.75118988 0.214401035 DLEGENIEIVFAKPPDQK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLEGENIEIVFAKPPDQK 18 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;; 240.07 5.58E-24 2923840000 4812890 3982410 3889690 3609590 4253240 4114190 4322580 5315190 6031260 5599200 FALSE TRUE 4624796.938 3868835.566 4592643.509 3795881.372 4390049.327 4197381.741 4375481.027 5205429.469 5346616.65 5219961.197 0.885983011 0.741161748 0.879823304 0.727185745 0.84101187 0.804102096 0.838220987 0.997216123 1.024263677 1 22.31560765 1.751247612 3.280846665 1.013933795 0.810730258 0.764827768 0.048559809 0.092075157 2.043021904 0.024724371 0.011956285 56.39591047 -1.751247612 -0.203203538 QKS(ph)LDSDLSDGPVTVQEFMEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKSLDSDLSDGPVTVQEFMEVK 22 1 Q14161-3;Q14161;Q14161-6;R4GNG3;Q14161-9;Q14161-5;Q14161-11;Q14161-7;Q14161-2 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 1 QKS(0.778)LDS(0.154)DLS(0.068)DGPVTVQEFMEVK 106.37 0.00029594 44332000 36211 26877 18832 17728 34883 30210 25275 45758 38913 37970 TRUE FALSE 34795.83409 26110.49428 22235.36132 18642.9442 36005.04337 30820.8669 25584.32301 44813.08131 34495.75938 35398.25808 0.982981536 0.73762088 0.62814846 0.526662757 1.017141671 0.870688801 0.722756554 1.265968546 0.974504432 1 15.11139075 1.751293974 25 1.098184799 0.778394474 0.42199534 0.158481428 3.415824464 6716.945351 0.074928753 0.041552028 56.4019311 -1.751293974 -0.319790325 DKEISPS(ph)VTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKEISPSVTKK 11 2 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 DKEIS(0.234)PS(0.751)VT(0.015)KK 104.41 0.0013583 272260000 600200 503080 474930 375350 495790 574180 550840 662690 835080 751910 TRUE FALSE 576743.5204 488732.651 560760.4158 394721.8585 511737.5356 585790.313 557581.3447 649005.2199 740285.2193 700982.466 0.822764546 0.69721095 0.799963541 0.563098048 0.73002901 0.835670422 0.795428376 0.925850861 1.056068098 1 19.41901883 1.751303266 1.215223175 1.035108346 0.724951357 0.715865602 0.07341556 0.23394791 0.647488516 0.060653013 0.023844418 56.40313789 -1.751303266 -0.310156989 GHLSRPEAQSLS(ph)PYTTSANR ddPTM_BT-474_Pertuzumab_2h_R1 4 GHLSRPEAQSLSPYTTSANR 20 1 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQS(0.001)LS(0.999)PYTTSANR;GHLSRPEAQS(0.007)LS(0.993)PYTTSANR 211.49 1.62E-22 1758290000 488198 704410 690960 861330 757150 837690 786430 469528 526577 766920 TRUE FALSE 469118.6824 684320.9165 815831.8423 905783.3445 781504.4174 854628.6657 796054.5656 459832.0827 466802.1866 714975.8253 0.65613223 0.957124552 1.141062136 1.266872686 1.093050128 1.195325262 1.113400674 0.643143539 0.652892266 1 19.44753494 1.751332768 11.03667826 0.73900513 1.073954931 0.351166932 0.182051826 0.122877859 76.96373703 0.088165999 0.048193657 56.40696956 -1.751332768 0.3349498 VEHHDHAVVSGR ddPTM_BT-474_Pertuzumab_2h_R1 5 VEHHDHAVVSGR 12 0 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;;;; 193.49 1.58E-06 483329000 275455 365726 320669 570489 251103 240762 436728 9509.76 356737 204873 FALSE TRUE 264689.9141 355295.8526 378621.0215 599932.0057 259179.956 245630.3726 442072.8079 9313.380133 316241.7113 190996.7692 1.38583451 1.860219175 1.982342545 3.141058396 1.356986074 1.286044647 2.31455647 0.048761977 1.655743773 1 17.54318871 1.751398235 25 0.834384767 1.907993478 0.34522875 0.630546999 3.978797697 7760.329532 0.28889493 0.160207491 56.41547319 -1.751398235 1.073608711 ANGTTVHVGIHPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ANGTTVHVGIHPSK 14 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KS10;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 70.529 0.025419 690320000 279920 360250 277620 368090 344080 354560 366250 159760 295930 298630 FALSE TRUE 268980.4169 349976.0227 327792.1096 387087.169 355147.6457 361729.4461 370732.2771 156460.9002 262337.267 278403.5241 0.966153061 1.25708187 1.177399283 1.390381714 1.275657867 1.299299092 1.331636438 0.561993246 0.942291474 1 18.08681795 1.751408618 25 0.802153265 1.249717688 0.598565621 0.152243324 2.222195815 4330.707639 0.067168761 0.037248677 56.41682191 -1.751408618 0.447564422 VAELALSLSS(ph)TSDDEPPSSVSHGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VAELALSLSSTSDDEPPSSVSHGAK 25 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 1 VAELALS(0.115)LS(0.115)S(0.539)T(0.115)S(0.115)DDEPPSSVSHGAK 97.771 0.0052583 130610000 32593 46564 31761 41214 33389 32035 36421 42901 45060 40686 TRUE FALSE 31319.22953 45236.04031 37500.91922 43341.05948 34462.98751 32682.76965 36866.73109 42015.07936 39944.97771 37930.30098 0.825704746 1.19260958 0.988679716 1.142650028 0.908587241 0.861653317 0.971959888 1.107691694 1.053115232 1 15.2110632 1.751473098 25 1.062995245 0.991142722 0.072439094 0.109969921 10.57224365 20500.55434 0.050853614 0.028201421 56.42519876 -1.751473098 -0.071852523 AEGGGGGGRPGAPAAGDGK ddPTM_BT-474_Pertuzumab_2h_R1 5 AEGGGGGGRPGAPAAGDGK 19 1 Q00839 Q00839 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;; 165.06 2.06E-11 521825000 806829 691940 772417 778805 774035 704241 769627 919754 946305 918332 FALSE TRUE 775297.2307 672206.5487 912009.9342 818999.2194 798932.5387 718481.2355 779045.9254 900760.7585 838884.4236 856132.5557 0.90558083 0.785166437 1.065267204 0.956626651 0.933187896 0.839217281 0.909959469 1.052127679 0.979853433 1 19.70747466 1.751477142 25 1.012915753 0.914018529 0.282866361 0.070811262 5.076709353 9841.126152 0.033595181 0.018630117 56.4257242 -1.751477142 -0.098897223 GEES(ph)S(ph)EEEEKGYK ddPTM_BT-474_Pertuzumab_2h_R1 3 GEESSEEEEKGYK 13 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 GEES(1)S(1)EEEEKGYK;GEES(1)S(1)EEEEKGYK;GEES(1)S(1)EEEEKGYK 169.04 1.25E-05 738690000 2008250 1712080 1293290 1068270 1421440 1482820 1494070 1934180 2209840 1724530 TRUE FALSE 1929765.37 1663253.155 1527016.272 1123403.543 1467161.909 1512803.636 1512354.876 1894238.507 1958988.228 1607726.047 1.200307337 1.034537668 0.949798801 0.69875309 0.912569596 0.940958591 0.940679464 1.178209752 1.218483853 1 20.61659016 1.751481294 7.359306186 1.146814437 0.944797347 0.286493353 0.127595244 0.166549691 28.69839394 0.065062469 0.034866018 56.42626374 -1.751481294 -0.202017089 LVINGNPITIFQERDPS(ph)KIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVINGNPITIFQERDPSKIK 20 2 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPIT(0.006)IFQERDPS(0.994)KIK;LVINGNPITIFQERDPS(1)KIK 145.61 1.13E-07 3501700000 1370150 1158010 895450 812950 1194250 1097200 1036870 1273640 1362730 1041790 TRUE FALSE 1316603.023 1124984.689 1057277.734 854906.4469 1232664.136 1119386.136 1049559.525 1247338.889 1208038.603 971228.6354 1.355605648 1.158310873 1.08859819 0.88023192 1.269180182 1.152546471 1.080651339 1.284289655 1.24382515 1 19.88945143 1.751542709 25 1.205108114 1.134778259 0 0.136891321 13.53600863 26106.5868 0.063139837 0.035013673 56.43424363 -1.751542709 -0.070329855 ITELKEEIEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITELKEEIEVK 11 1 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 ; 160.69 2.48E-05 1627440000 1322520 1222460 1019040 929280 1174800 1178120 1141890 1523160 1648590 1435560 FALSE TRUE 1270834.456 1187596.638 1203203.196 977240.2522 1212588.509 1201942.394 1155864.791 1491706.214 1461448.975 1338328.243 0.949568586 0.887373217 0.899034451 0.730194747 0.906047164 0.898092378 0.863663154 1.11460415 1.091995916 1 20.35200057 1.75155132 8.270518443 1.075335602 0.873856109 0.679883406 0.060444148 0.069625875 17.36298867 0.02907379 0.01567774 56.43536261 -1.75155132 -0.201479494 RKS(ph)PPKEYIDEEGVR ddPTM_BT-474_Pertuzumab_2h_R1 3 RKSPPKEYIDEEGVR 15 3 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR 116.09 0.0026309 10170200000 3080730 2880470 2281990 2031850 2492340 2619640 2552560 3055810 3424250 2748110 TRUE FALSE 2960331.666 2798321.816 2694396.356 2136714.022 2572508.38 2672610.916 2583798.993 2992706.456 3035543.496 2561978.062 1.155486735 1.092250499 1.051685959 0.834009492 1.004110229 1.043182592 1.00851722 1.168123373 1.184843672 1 21.28882669 1.751557855 13.56916251 1.131795611 1.022805051 0.168723013 0.090211175 0.271926044 269.2260369 0.043773594 0.024101777 56.43621181 -1.751557855 -0.108990559 KEDLEAEEEYSSLCELLGSPEQRPGMQDPLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 KEDLEAEEEYSSLCELLGSPEQRPGMQDPLSPK 33 2 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 KEDLEAEEEYSSLCELLGS(0.005)PEQRPGMQDPLS(0.995)PK;KEDLEAEEEYSSLCELLGSPEQRPGMQDPLS(1)PK;KEDLEAEEEYSSLCELLGSPEQRPGMQDPLS(1)PK 218.27 4.99E-36 151515000 142547 118422 99278 98797 109458 108062 113224 154755 162061 131561 TRUE FALSE 136976.1056 115044.7205 117219.743 103895.925 112978.816 110247.0877 114609.6692 151559.2552 143664.5147 122650.2563 1.116802441 0.937990054 0.955723588 0.847090974 0.921146188 0.898873684 0.934442965 1.235702719 1.17133481 1 16.90419072 1.751637989 25 1.154198473 0.9383474 0.507843011 0.085474598 2.727489164 5222.049806 0.038548677 0.021377157 56.44662613 -1.751637989 -0.215851073 IEDVGS(ph)DEEDDS(ph)GKDKK ddPTM_BT-474_Pertuzumab_2h_R1 3 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 2 IEDVGS(1)DEEDDS(1)GKDKK;IEDVGS(1)DEEDDS(1)GKDKK;IEDVGS(1)DEEDDS(1)GKDKK 181.69 4.23E-10 1849490000 1363910 870644 811865 482096 811660 730534 846276 1339140 1441650 955560 TRUE FALSE 1310606.889 845814.0856 958587.0653 506977.0323 837767.781 745305.898 856632.9788 1311486.291 1277999.936 890839.0701 1.471204995 0.94945778 1.076049645 0.569100581 0.940425504 0.8366336 0.96160239 1.472192156 1.434602476 1 19.76480531 1.751654869 24.99917887 1.340966236 0.953272661 0.274404823 0.242284111 4.363748166 8343.768576 0.110551361 0.061306359 56.44882017 -1.751654869 -0.387693575 NYQQNYQNS(ph)ESGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NYQQNYQNSESGEK 14 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(1)ESGEK 295.98 1.32E-43 227900000 276730 249700 258630 240860 228430 210370 255820 363840 388430 382640 TRUE FALSE 265915.0857 242578.8005 305370.1942 253290.8135 235777.6584 214623.8255 258950.8017 356326.5769 344337.0548 356723.452 0.745437633 0.680019211 0.856041823 0.710048112 0.660953624 0.601653254 0.725914711 0.998887443 0.965277312 1 18.44444654 1.751658036 5.192977848 0.986660904 0.708500084 0.805454948 0.062272555 0.076697955 4.89658555 0.033615892 0.01757037 56.4492318 -1.751658036 -0.27816082 KLTVDTPGAPETLAPVAAPEEDKDS(ph)EAEVEVESR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLTVDTPGAPETLAPVAAPEEDKDSEAEVEVESR 34 2 P12755 P12755 SKI Ski oncogene 1 KLTVDTPGAPETLAPVAAPEEDKDS(0.995)EAEVEVES(0.005)R 81.573 0.00060205 146270000 127150 102090 78822 77191 79103 98895 86906 146880 131200 118030 TRUE FALSE 122180.8374 99178.49316 93066.88879 81174.83676 81647.41983 100894.7247 87969.58162 143846.8767 116306.726 110035.723 1.110374287 0.901329954 0.845787952 0.737713486 0.742008301 0.916926994 0.79946384 1.307274336 1.056990611 1 16.74761244 1.751669793 25 1.145351079 0.857868176 0.466658735 0.12478283 3.07751829 5877.89183 0.057683402 0.03198865 56.45076003 -1.751669793 -0.287482903 AFSDPFVEAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AFSDPFVEAEK 11 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 0 166.97 0.0018643 0 220800 227560 184850 175280 219720 206210 207750 256480 269440 263200 FALSE TRUE 212170.8919 221070.2116 218256.507 184326.2218 226787.4933 210379.7075 210292.5066 251183.5984 238854.3008 245373.2296 0.864686389 0.900954892 0.889487852 0.751207547 0.924255241 0.857386553 0.857031173 1.023679718 0.9734326 1 17.90461833 1.75168821 8.287384521 0.99750108 0.863720601 0.660401206 0.044480285 0.075619736 18.97230982 0.020939277 0.011293928 56.45315395 -1.75168821 -0.133780479 S(ph)PALSDANK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPALSDANK 9 0 P52701;P52701-3;P52701-2;A0A087WWJ1;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 S(1)PALSDANK;S(1)PALSDANK;S(1)PALSDANK 164.6 6.52E-05 1341390000 1580120 1377340 1311200 1274500 1265270 1172218 1330990 1650800 1614610 1674830 TRUE FALSE 1518367.163 1338059.612 1548163.007 1340277.098 1305968.559 1195921.051 1347279.054 1616710.403 1431326.242 1561392.272 0.972444395 0.856965694 0.991527264 0.858385892 0.836412849 0.765932477 0.862870323 1.035428721 0.916698684 1 20.5744016 1.751698302 25 0.984099866 0.874724569 0.346193385 0.066819744 4.495112838 8566.759574 0.031933112 0.017708551 56.45446583 -1.751698302 -0.109375297 RNDDISELEDLSELEDLKDAK ddPTM_BT-474_Pertuzumab_2h_R1 3 RNDDISELEDLSELEDLKDAK 21 2 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 0 ;; 195.34 2.48E-19 175699000 234816 202332 169334 158676 208206 195726 201474 245995 277603 253123 FALSE TRUE 225639.1311 196561.6895 199936.4206 166865.2874 214903.1351 199683.7138 203939.6991 240915.1173 246090.6712 235978.7538 0.956184095 0.832963503 0.847264499 0.707119962 0.910688491 0.846193611 0.864229071 1.020918678 1.042850966 1 17.84829745 1.751758789 3.918110755 1.02665459 0.846064152 0.619809979 0.060686974 0.127570696 4.132069541 0.03231151 0.016226639 56.46232908 -1.751758789 -0.180590438 RLEEPEEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEEPEEPK 9 1 O75822;O75822-2 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 136.36 0.00031253 986670000 1129180 1030590 973240 900140 1064550 1039750 1077290 1234860 1399060 1327560 FALSE TRUE 1085050.397 1001198.582 1149126.118 946596.3333 1098792.218 1060774.457 1090474.197 1209359.709 1240244.574 1237643.179 0.876706967 0.808955763 0.928479337 0.764837838 0.887810183 0.857092315 0.881089329 0.977147315 1.002101895 1 20.239164 1.751765064 2.18555395 1.002704876 0.852388888 0.695609692 0.041511025 0.147553881 1.430564995 0.025378068 0.010940903 56.46314495 -1.751765064 -0.150315988 YRDELKR ddPTM_BT-474_Pertuzumab_2h_R1 3 YRDELKR 7 2 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;; 132.08 0.0019141 599220000 706110 734110 704160 709410 695340 679890 731670 622430 741660 713980 FALSE TRUE 678514.4406 713173.9016 831417.376 746022.7351 717706.2426 693637.8416 740624.3963 609576.603 657469.8661 665621.4987 1.01936978 1.071440606 1.249084318 1.120791225 1.078249792 1.042090502 1.112681002 0.915800653 0.987753351 1 19.34434251 1.751782152 18.18340569 0.964002798 1.101645517 0.485860914 0.061794737 0.487295255 675.2251463 0.030112564 0.01667025 56.46536657 -1.751782152 0.137642719 EGMS(ph)PAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGMSPAKR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 EGMS(1)PAKR 83.883 0.010931 348630000 450640 390720 480830 512440 468260 441700 582020 653270 748330 785670 TRUE FALSE 433028.4906 379577.0482 567726.677 538887.0898 483322.0082 450631.4766 589142.9349 639779.7462 663382.7157 732455.8711 0.591200791 0.518225142 0.775100179 0.735726357 0.65986502 0.615233619 0.804339153 0.87347207 0.905696496 1 19.48238232 1.751783043 1.056697506 0.981905288 0.646447071 0.752758641 0.072219087 0.260242798 0.541240806 0.066334672 0.026729178 56.46548242 -1.751783043 -0.335458217 DSAPYGEYGSWYK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSAPYGEYGSWYK 13 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 120.03 0.00047003 0 71305 69544 63340 65301 64768 67232 66903 80169 80285 80239 FALSE TRUE 68518.32177 67560.67321 74786.94699 68671.19244 66851.32154 68591.4771 67721.77893 78513.48213 71171.38338 74804.34106 0.915967186 0.903165141 0.999767472 0.918010793 0.89368238 0.916945142 0.905318835 1.04958457 0.951433866 1 16.19083437 1.751807465 25 1.003011006 0.922697663 0.510093746 0.035219185 3.132293485 5920.228623 0.016103541 0.008930172 56.4686578 -1.751807465 -0.080313343 DDYSRDDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDYSRDDYR 9 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 102.06 0.0033248 565180000 791470 807400 526670 581600 668250 798720 700810 619160 700600 741180 FALSE TRUE 760538.4774 784373.7425 621850.9847 611616.4457 689744.8681 814870.6656 709386.7224 606374.1296 621070.8252 690979.2184 1.100667657 1.135162566 0.899956132 0.885144487 0.998213622 1.179298369 1.026639736 0.877557694 0.898827068 1 19.3982828 1.751819605 24.97041769 0.915875518 1.029731665 0.215041801 0.092792086 6.349007564 11974.97981 0.046598792 0.025841295 56.47023624 -1.751819605 0.113856147 QQENVTLLLSLLEEFDFHVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQENVTLLLSLLEEFDFHVR 20 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 101.49 0.0009564 0 38933 47381 42657 32804 51829 44225 45208 33366 46538 34806 FALSE TRUE 37411.45532 46029.74027 50366.0688 34497.01837 53496.12685 45119.2598 45761.26903 32676.98044 41255.20134 32448.55862 1.152946599 1.41854499 1.552182006 1.063129453 1.648644166 1.390485794 1.410271241 1.007039506 1.271403202 1 14.98586677 1.751827097 17.14916975 1.104908377 1.383908336 0.355684025 0.174610411 0.464019282 604.1724914 0.076725736 0.042445732 56.47121047 -1.751827097 0.278999958 QDFVQHFSQIVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDFVQHFSQIVR 12 0 P14324-2;P14324;A0A087WVN4;A0A087X1D8;A0A087WTP2 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ; 188.4 9.25E-06 2022620000 1426070 2301200 1901630 2520200 1810300 1911490 2050800 1638470 1761210 2323800 FALSE TRUE 1370337.608 2235572.029 2245296.843 2650267.824 1868529.944 1950141.637 2075898.304 1604635.022 1561284.824 2166406.956 0.632539331 1.031926168 1.036415082 1.223347172 0.86250182 0.900173272 0.958221768 0.740689563 0.720679381 1 21.04687285 1.751829393 25 0.797417477 0.961143774 0.113977009 0.158432972 6.990011681 13189.67826 0.073045695 0.040507731 56.47150897 -1.751829393 0.163726297 HESVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 HESVSK 6 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 123.99 0.01855 279140000 596380 948400 701910 1084470 757960 933700 871020 585140 661810 922200 FALSE TRUE 573072.8103 921352.5606 828760.7509 1140439.627 782340.4718 952580.0537 881679.8033 573056.6545 586684.1033 859738.5726 0.666566359 1.071665957 0.963968324 1.326495824 0.909974842 1.107988037 1.025520817 0.666547568 0.682398257 1 19.71353851 1.751851235 22.03658625 0.755906091 1.022947506 0.2486129 0.178317891 1.972299264 3281.494336 0.079049308 0.043820514 56.47434927 -1.751851235 0.267041415 TATESFAS(ph)DPILYRPVAVALDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TATESFASDPILYRPVAVALDTK 23 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 1 TATESFAS(1)DPILYRPVAVALDTK;TATES(0.011)FAS(0.989)DPILYRPVAVALDTK 161.2 1.09E-11 186060000 376190 350370 304160 280750 322760 323940 316430 417830 412280 371750 TRUE FALSE 361488.0789 340377.7906 359128.478 295239.5411 333141.8685 330490.2887 320302.565 409201.6645 365479.7028 346571.0414 1.043041789 0.982129924 1.03623337 0.851887509 0.961251313 0.953600415 0.924204641 1.180715108 1.054559265 1 18.40279159 1.751913327 25 1.093901631 0.963159388 0.375692037 0.066314954 3.629848437 6806.150599 0.029954105 0.016611068 56.48242408 -1.751913327 -0.130742243 SNRNS(ph)IER ddPTM_BT-474_Pertuzumab_2h_R1 3 SNRNSIER 8 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 SNRNS(1)IER;SNRNS(1)IER;S(0.011)NRNS(0.989)IER 108.9 0.0022536 1088420000 506060 535640 479733 543260 531590 529940 533240 502083 553850 581850 TRUE FALSE 486282.6157 520364.0716 566431.4247 571297.7137 548689.0751 540655.7499 539765.9506 491714.8106 490979.2699 542440.7812 0.896471343 0.959301162 1.044227212 1.053198309 1.01151885 0.99670926 0.995068898 0.906485699 0.905129715 1 19.04910612 1.751981405 24.99892067 0.929207647 0.997478467 0.216702723 0.04822988 5.454446815 10174.96077 0.02330079 0.012921616 56.4912787 -1.751981405 0.068270819 EVLPGALQVCSSEPAEPPGT(ph)PPASHSHLDAAPLPTVVYSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLPGALQVCSSEPAEPPGTPPASHSHLDAAPLPTVVYSK 40 0 E9PF42;Q8N398 E9PF42 VWA5B2 von Willebrand factor A domain-containing protein 5B2 1 EVLPGALQVCSSEPAEPPGT(0.899)PPAS(0.05)HS(0.05)HLDAAPLPT(0.001)VVYSK 83.484 0.00089599 70723000 21712 30847 21137 27900 20280 29789 26236 14364 24332 18259 TRUE FALSE 20863.47104 29967.27376 24956.92609 29339.92234 20932.32462 30391.35399 26557.08402 14067.37838 21569.93337 17022.30167 1.225655111 1.760471313 1.466131113 1.723616636 1.229700015 1.785384526 1.56013473 0.826408711 1.267157273 1 14.0551385 1.751989924 25 1.030016318 1.546868817 0.546685869 0.210432251 2.757278814 5140.498842 0.089041458 0.049378156 56.49238684 -1.751989924 0.516852499 S(ph)REPTGVEENKTDSLFVLPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SREPTGVEENKTDSLFVLPSR 21 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 S(0.978)REPT(0.022)GVEENKTDSLFVLPSR 177.12 3.43E-17 159220000 79618 65531 62063 58331 62515 59981 60429 92392 83691 77477 TRUE FALSE 76506.44054 63662.12004 73279.16468 61341.4699 64525.85175 61193.85692 61168.54818 90484.07291 74190.74854 72229.41378 1.059214474 0.881387744 1.014533565 0.849258864 0.893345915 0.847215195 0.846864802 1.252731653 1.027154239 1 16.14029884 1.752030123 25 1.114221221 0.910045939 0.437968138 0.092582955 3.223683432 5992.068573 0.040907378 0.022685324 56.49761604 -1.752030123 -0.204175282 KPLSLAGDEETECQSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 KPLSLAGDEETECQSSPK 18 1 Q86TN4;Q86TN4-4;F5H1K3;Q86TN4-2 Q86TN4 TRPT1 tRNA 2-phosphotransferase 1 1 KPLSLAGDEETECQSS(1)PK;KPLSLAGDEETECQS(0.203)S(0.797)PK;KPLSLAGDEETECQS(0.003)S(0.997)PK;KPLSLAGDEETECQS(0.014)S(0.986)PK 232.02 2.91E-20 4744890000 3509350 2766860 2243650 2289800 2522060 2400650 2604630 3261440 3542770 3134890 TRUE FALSE 3372200.722 2687951.862 2649127.465 2407976.852 2603184.35 2449192.788 2636506.241 3194090.124 3140609.602 2922561.108 1.153851228 0.919724776 0.906440402 0.823926947 0.890720246 0.838029624 0.902121853 1.0929079 1.074608703 1 21.47880176 1.752031654 8.716621233 1.061198764 0.910844755 0.33216009 0.088020649 0.134720248 39.74193963 0.042662351 0.023076129 56.49781525 -1.752031654 -0.150354009 NNRPSEGPLQTR ddPTM_BT-474_Pertuzumab_2h_R1 11 NNRPSEGPLQTR 12 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;;;;; 222.74 2.20E-11 11352009000 3226072.3 3299900.3 2996364.3 3246963.3 3229856.6 3114299.9 3318228.4 3695024.8 4034240.8 4012550.1 FALSE TRUE 3099993.828 3205790.374 3537873.983 3414539.465 3333747.871 3177273.178 3358837.872 3618721.247 3576290.697 3740776.508 0.828703298 0.856985272 0.94575925 0.912788951 0.891191405 0.849361936 0.897898569 0.967371678 0.956028966 1 21.83490634 1.752040985 3.483516725 0.973698547 0.883794993 0.622866763 0.03272119 0.159433648 4.001554676 0.019292096 0.009464927 56.49902907 -1.752040985 -0.089903553 HNFAKPNDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 HNFAKPNDSR 10 1 Q9NWX6;E5RIQ8 Q9NWX6 THG1L Probable tRNA(His) guanylyltransferase 0 56.359 0.074875 138620000 334480 373320 279070 376020 339370 341940 353580 298340 354250 330990 FALSE TRUE 321408.1518 362673.2791 329504.1569 395426.4373 350286.1443 348854.2611 357907.2178 292179.1747 314037.0251 308571.7525 1.041599399 1.175328837 1.067836425 1.28147322 1.135185387 1.13054503 1.159883285 0.946875961 1.017711513 1 18.23524647 1.752046033 10.25855247 0.988233614 1.144860554 0.555794144 0.062818974 0.084428616 41.85692312 0.028391943 0.015475578 56.49968578 -1.752046033 0.15662694 TTEYHDRDEQFYWIIEALGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTEYHDRDEQFYWIIEALGIR 21 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 151.48 3.70E-08 1384880000 987400 1019280 814640 887760 938550 1081540 966560 785720 990770 881140 FALSE TRUE 948811.3164 990211.1324 961863.5696 933577.4 968739.3131 1103409.48 978389.0504 769494.6074 878301.9432 821459.603 1.155031012 1.205428884 1.170920111 1.136486075 1.179290265 1.343230362 1.191037328 0.936740656 1.069196757 1 19.6478301 1.752105971 24.99999988 1.001834754 1.199216479 0.685813027 0.060587901 2.363982632 4369.439165 0.028712133 0.015922399 56.5074841 -1.752105971 0.197381725 T(ph)PELPEPSVK ddPTM_BT-474_Pertuzumab_2h_R1 4 TPELPEPSVK 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(1)PELPEPSVK;T(1)PELPEPSVK;T(1)PELPEPSVK;T(1)PELPEPSVK 158.94 8.76E-05 1222960000 1928800 1846990 1599910 1666330 1694980 1806280 1790070 2134640 2149420 2210420 TRUE FALSE 1853420.364 1794315.654 1889049.327 1752329.491 1749500.571 1842804.219 1811977.412 2090558.938 1905426.853 2060706.285 0.899410254 0.870728481 0.91669994 0.850353835 0.848981043 0.894258553 0.879299212 1.014486613 0.92464747 1 20.97470746 1.752126394 25 0.977882464 0.87923904 0.710189882 0.029190978 2.117132005 3907.273998 0.012815912 0.007107098 56.5101414 -1.752126394 -0.098643424 SHVAGQMLHGGGSR ddPTM_BT-474_Pertuzumab_2h_R1 7 SHVAGQMLHGGGSR 14 0 P43155-2;P43155 P43155-2 CRAT Carnitine O-acetyltransferase 0 ;;;;;; 112.96 0.00037696 1911737000 844997 1218557 854081 1457043 989048 1015576 1293449 153582.9 1017029 756010 FALSE TRUE 811973.583 1183804.947 1008432.436 1532241.164 1020861.627 1036111.643 1309278.616 150411.3594 901580.1317 704804.7693 1.152054609 1.679621079 1.430796838 2.173993751 1.448431781 1.470069 1.857647213 0.213408544 1.279191304 1 19.42686416 1.752136073 25 0.772662916 1.609261121 0.48910164 0.35954359 3.042346464 5610.794852 0.155997316 0.086508978 56.51140079 -1.752136073 0.836598205 HLEEIVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 HLEEIVEK 8 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 114.89 0.0025684 1079428000 2575510 2904850 2220010 2823520 2637350 2610840 2897440 2278360 3218720 2680970 FALSE TRUE 2474856.222 2822006.522 2621215.191 2969242.206 2722182.758 2663632.974 2932899.737 2231311.07 2853344.4 2499385.514 0.990185871 1.12908013 1.048743852 1.187988883 1.089140808 1.065715136 1.173448322 0.892743859 1.141618363 1 21.25314201 1.752150971 25 1.002896171 1.098984105 0.200837881 0.078309114 5.712616535 10523.82843 0.033577185 0.018620173 56.51333943 -1.752150971 0.096087935 PASHSHAHQHSPIS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 PASHSHAHQHSPISPR 16 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 PASHSHAHQHS(0.01)PIS(0.99)PR 93.776 0.0019569 72564000 24270 30811 33233 39024 44698 31305 44206 11872 39428 33685 TRUE FALSE 23321.50157 29932.30045 39238.94236 41038.03332 46135.75176 31938.00855 44747.00625 11626.83905 34952.29874 31403.48495 0.742640557 0.95315219 1.249509169 1.3067987 1.469128405 1.017021156 1.424905749 0.370240407 1.113007005 1 14.93863705 1.752172823 25 0.771764262 1.172504162 0.232373762 0.276132216 5.170218572 9509.298878 0.126378361 0.070083548 56.5161831 -1.752172823 0.400739899 AHSSPASLQLGAVS(ph)PGTLTPTGVVSGPAATPTAQHLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 AHSSPAS(0.001)LQLGAVS(0.997)PGT(0.001)LTPTGVVSGPAATPTAQHLR;AHSSPAS(0.002)LQLGAVS(0.997)PGT(0.001)LTPTGVVSGPAATPTAQHLR;AHSSPASLQLGAVS(0.986)PGT(0.011)LT(0.003)PTGVVSGPAATPTAQHLR 234.65 7.56E-50 14623500000 68786 157108 121975 184182 150412 177094 156320 70251 105159 153615 TRUE FALSE 66097.76707 152627.4337 144018.5958 193687.6551 155250.1386 180674.962 158233.0909 68800.2923 93221.79118 143210.5192 0.461542682 1.065755745 1.005642578 1.352468074 1.084069379 1.261603987 1.104898521 0.480413678 0.650942345 1 17.12777794 1.752176893 25 0.666700251 1.068364996 0.265547695 0.252557159 4.72199769 8682.310497 0.115625399 0.064120494 56.51671267 -1.752176893 0.401664745 S(ph)PEASASASPHTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPEASASASPHTPR 14 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(1)PEASASASPHTPR;S(0.994)PEAS(0.005)ASASPHTPR 176 2.41E-06 801490000 290406 392484 453887 613055 466358 493301 499858 263081 407168 463522 TRUE FALSE 279056.6125 381290.7406 535914.4776 644694.842 481358.8286 503275.8842 505975.4117 257648.2854 360947.9956 432127.2421 0.645774173 0.882357564 1.240177488 1.491909741 1.113928449 1.164647435 1.170894502 0.596232453 0.835281742 1 18.72109666 1.752205632 25 0.77742494 1.116234517 0.248201167 0.228818654 5.457532209 10013.56247 0.112300601 0.062276751 56.52045272 -1.752205632 0.338809578 RTS(ph)SEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSSEELR 8 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RTS(0.995)S(0.005)EELR 169.82 0.00018301 243010000 159630 185200 164690 213870 194680 190870 187060 160720 163400 187910 TRUE FALSE 153391.4831 179918.2773 194453.1465 224907.8563 200942.059 194729.5222 189349.2962 157401.0758 144851.517 175182.6883 0.875608684 1.027032289 1.110002069 1.283847499 1.147042901 1.111579712 1.080867625 0.898496748 0.826859768 1 17.41850069 1.752239376 4.323456442 0.895350298 1.100938093 0.390087927 0.103815681 0.193146003 7.823111168 0.057682003 0.029469731 56.52484453 -1.752239376 0.205587795 EELYQNLTR ddPTM_BT-474_Pertuzumab_2h_R1 3 EELYQNLTR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 122.94 0.0013301 425670000 420970 466490 380070 402650 397330 440070 412070 482280 475800 488520 FALSE TRUE 404518.027 453186.1619 448757.1036 423430.8148 410110.4803 448968.5169 417113.0359 472320.7495 421789.1787 455432.1053 0.888207095 0.995068544 0.985343586 0.929734224 0.900486539 0.985807789 0.915862169 1.037082683 0.926129655 1 18.79687647 1.75225554 25 0.990317993 0.946075649 0.18215893 0.043045061 7.168929745 13105.63565 0.019138482 0.01061317 56.52694829 -1.75225554 -0.044242343 LGVIEDHSNR ddPTM_BT-474_Pertuzumab_2h_R1 8 LGVIEDHSNR 10 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;;;;;; 223.31 4.50E-09 36836370000 9201930 11155950 9041000 11348870 10049640 10946630 10676760 9766710 11009320 10917150 FALSE TRUE 8842308.402 10837793.23 10674909.82 11934586.54 10372895.8 11167978.36 10807425.38 9565024.025 9759588.148 10177721.71 0.868790546 1.064854546 1.048850629 1.172618675 1.019176599 1.097296495 1.061870789 0.939800115 0.958916782 1 23.27891131 1.752267096 9.959359503 0.962929344 1.053980954 0.202213271 0.073213883 0.175169208 78.97601347 0.034163106 0.018598866 56.52845236 -1.752267096 0.09105161 GDT(ph)PGHATPGHGGATSSAR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDT(0.778)PGHAT(0.222)PGHGGATSSAR;GDT(1)PGHATPGHGGATSSAR;GDT(0.998)PGHAT(0.002)PGHGGATSSAR 219.78 1.12E-18 706515000 266637.7 332013.7 297940.2 400898.8 340340.6 321312.3 409597.2 121172.9 328349.8 359657.5 TRUE FALSE 256217.2039 322544.9944 351784.6218 421589.2351 351287.9645 327809.4549 414609.9731 118670.6373 291076.9073 335297.5772 0.764148689 0.961966373 1.04917138 1.25735843 1.047690137 0.977667234 1.236543301 0.353926319 0.868115152 1 18.35508253 1.752278305 25 0.681532739 1.045288995 0.302402455 0.203884332 4.151535305 7576.875982 0.090848812 0.050380518 56.52991149 -1.752278305 0.363756256 DLTTGYDDSQPDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLTTGYDDSQPDKK 14 1 Q96G03 Q96G03 PGM2 Phosphoglucomutase-2 0 171.26 4.88E-06 229380000 218080 189200 163730 155460 152450 183620 172400 263440 251340 218860 FALSE TRUE 209557.1925 183804.2012 193319.6532 163483.3092 157353.6927 187332.9222 174509.8828 257999.8719 222808.9369 204036.4173 1.027057793 0.900840172 0.947476219 0.801245736 0.771203959 0.918134737 0.855287919 1.264479525 1.092005731 1 17.63846715 1.752291006 24.99999965 1.139389664 0.884716735 0.56764898 0.091442484 2.734425365 4985.916903 0.041823949 0.023193556 56.53156463 -1.752291006 -0.25467293 DLQVTLIPTFDSVAMHTWYAETHAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLQVTLIPTFDSVAMHTWYAETHAR 25 0 Q66K74-2;Q66K74;M0R1M7 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 0 50.426 0.079356 55675000 39975 49944 34290 40044 48002 51324 49922 32259 46730 51530 FALSE TRUE 38412.73281 48519.64602 40486.96578 42110.67564 49546.02792 52361.80644 50532.96037 31592.84038 41425.40631 48039.8272 0.79960181 1.009987938 0.842779172 0.876578416 1.031353167 1.089966586 1.051897213 0.65763851 0.862313808 1 15.55194334 1.752377459 25 0.807229365 0.959891128 0.15340674 0.11913119 6.101258033 11055.23071 0.055314523 0.030674776 56.54281928 -1.752377459 0.152661763 RKEQEEEEQKER ddPTM_BT-474_Pertuzumab_2h_R1 4 RKEQEEEEQKER 12 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;;; 150.26 2.98E-05 1804060000 1350650 1055160 827390 773649 928750 1006940 995670 1177190 1335470 1134960 FALSE TRUE 1297865.105 1025067.87 976917.7782 813577.1176 958624.0872 1027301.017 1007855.307 1152880.615 1183873.044 1058088.148 1.226613404 0.968792507 0.923285815 0.768912419 0.905996432 0.970903056 0.9525249 1.08958844 1.118879411 1 20.01302839 1.752400178 5.985923029 1.077531876 0.949267801 0.167863769 0.109903773 0.260431929 24.35850654 0.056456025 0.029909795 56.54577718 -1.752400178 -0.128264075 KLGEMWNNTAADDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLGEMWNNTAADDK 14 1 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ; 159.18 7.94E-06 1237490000 730690 615670 693160 631880 656590 593270 665250 841770 853330 804780 FALSE TRUE 702133.827 598111.6944 818429.4313 664491.4025 677709.8136 605266.3259 673391.5285 824387.1553 756463.5559 750271.5338 0.93583962 0.797193639 1.090844307 0.885667885 0.903286055 0.806729695 0.897530425 1.098785064 1.008253041 1 19.5170533 1.752401427 25 1.041811169 0.901345954 0.369949138 0.079551149 4.355553137 7878.39535 0.03621985 0.020085717 56.54593985 -1.752401427 -0.140465214 AQVWLEQVCAHLGLGVQEPHPGER ddPTM_BT-474_Pertuzumab_2h_R1 2 AQVWLEQVCAHLGLGVQEPHPGER 24 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ; 243.88 6.09E-38 558590000 193702 205357 171955 201666 200038 197000 211490 130651 210468 172950 FALSE TRUE 186131.9117 199500.4194 203031.0936 212074.0064 206472.4039 200983.475 214078.2779 127953.0112 186576.555 161235.9425 1.154407069 1.237319771 1.259217334 1.315302303 1.280560654 1.246517817 1.327732977 0.793576229 1.157164787 1 17.29881386 1.752526686 25 0.970640243 1.261619279 0.648105581 0.093239217 2.360480412 4231.317245 0.040008642 0.022186975 56.56225112 -1.752526686 0.290979036 ARAPS(ph)PGDYK ddPTM_BT-474_Pertuzumab_2h_R1 6 ARAPSPGDYK 10 1 P55198 P55198 MLLT6 Protein AF-17 1 ARAPS(0.99)PGDY(0.01)K;ARAPS(0.975)PGDY(0.025)K;ARAPS(0.727)PGDY(0.273)K;ARAPS(0.973)PGDY(0.027)K;ARAPS(0.998)PGDY(0.002)K;ARAPS(0.871)PGDY(0.129)K 110.44 0.0011422 7952310000 6206500 5769190 4428380 4886670 4709400 4949960 5118130 6661520 6519620 6356940 TRUE FALSE 5963943.118 5604658.35 5228686.775 5138871.624 4860882.128 5050051.583 5180767.206 6523957.284 5779540.07 5926378.792 1.006338496 0.945713824 0.882273469 0.86711832 0.820211178 0.852131084 0.87418766 1.100833665 0.975222859 1 22.49871941 1.752530601 25 1.031655716 0.888898735 0.52884798 0.057268608 3.365042913 6030.369149 0.027967797 0.015509585 56.56276101 -1.752530601 -0.142756981 DEKTDTLEDLFPTTK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEKTDTLEDLFPTTK 15 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 143.02 4.09E-06 43718000 145600 124770 107790 93776 121740 125530 121180 167080 179350 163400 FALSE TRUE 139909.791 121211.6818 127270.0508 98615.7906 125655.8777 128068.3026 122663.0371 163629.7396 158990.9399 152332.7725 0.918448399 0.795703248 0.835473869 0.647370812 0.824877508 0.840714053 0.805230779 1.074159795 1.043708043 1 17.21686683 1.752531912 6.779073974 1.042344508 0.805343459 0.717527009 0.065898033 0.075218831 10.07816028 0.032380792 0.017296749 56.56293187 -1.752531912 -0.237001049 SSGS(ph)LGHRPSQEMDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGSLGHRPSQEMDK 15 1 Q5SW79;H0Y2V6;H0YB66 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.01)S(0.04)GS(0.95)LGHRPSQEMDK;S(0.005)S(0.004)GS(0.992)LGHRPSQEMDK 171.85 6.42E-07 840540000 677640 671720 548380 463730 549940 552820 585620 719590 742850 710900 TRUE FALSE 651157.0796 652563.2033 647484.4646 487663.1609 567629.3195 563998.3992 592786.9927 704730.215 658524.7823 662750.1098 0.98250769 0.98462934 0.976966213 0.735817548 0.856475633 0.850997066 0.894435148 1.063342283 0.993624554 1 19.33810548 1.752539127 21.43823113 1.021333139 0.89424502 0.363592229 0.073611332 1.787860967 2752.519954 0.037192168 0.020614853 56.56387144 -1.752539127 -0.127088119 HLTHENVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLTHENVQR 9 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 96.89 0.0070621 82251000 47415 59501 45583 64400 45616 46901 59084 29284 50326 55975 FALSE TRUE 45561.96938 57804.08974 53820.86209 67723.69172 47083.28007 47849.37035 59807.08767 28679.27517 44613.20346 52183.76339 0.873106239 1.107702588 1.031371802 1.297792404 0.90225919 0.916939815 1.146086134 0.549582347 0.854924991 1 15.67131337 1.75254397 25 0.761093075 1.041609762 0.308646274 0.159684169 4.35144085 7790.587281 0.070943582 0.039341952 56.56450231 -1.75254397 0.280516688 EHQTSAYS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHQTSAYSPPR 11 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 EHQTS(0.002)AY(0.009)S(0.989)PPR;EHQT(0.009)S(0.012)AYS(0.978)PPR;EHQTS(0.004)AY(0.188)S(0.807)PPR;EHQT(0.001)S(0.004)AYS(0.995)PPR 119.87 0.00088359 1184510000 396556 468451 426018 541472 498365 558394 540704 327075 483411 537579 TRUE FALSE 381058.1531 455091.2361 503008.9293 569417.4348 514395.3628 569685.1093 547321.2973 320320.787 428536.2099 501168.2955 0.760339703 0.908060706 1.003672686 1.136180081 1.026392466 1.136714182 1.092090825 0.639148146 0.855074461 1 18.93493563 1.752591784 25 0.798742581 1.015437772 0.257388565 0.13460085 5.094792938 9090.311746 0.06376912 0.035363353 56.57073019 -1.752591784 0.216695191 S(ph)LEGIFDDIVPDGKR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLEGIFDDIVPDGKR 15 1 Q13009 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 S(1)LEGIFDDIVPDGKR;S(1)LEGIFDDIVPDGKR;S(1)LEGIFDDIVPDGKR 151.04 1.88E-06 65477000 87962 79313 62088.7 61946 59619.6 57283 66352 95204 87182 89219 TRUE FALSE 84524.34779 77051.0709 73309.50925 65143.04048 61537.31858 58441.30151 67164.03562 93238.00413 77285.46486 83176.11766 1.016209342 0.926360511 0.881376906 0.78319405 0.739843603 0.702621175 0.807491832 1.12097086 0.929178555 1 16.34388173 1.752626942 25 1.023570403 0.830949394 0.422389732 0.096186764 4.37040718 7778.313937 0.048406193 0.026843975 56.57530999 -1.752626942 -0.192621009 FTPNGSSFSISWQSPPVT(ph)FTGIPVSPTHHPVGTGEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 FTPNGSSFSISWQSPPVTFTGIPVSPTHHPVGTGEQR 37 0 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 FTPNGSSFSISWQS(0.09)PPVT(0.327)FT(0.327)GIPVS(0.11)PT(0.141)HHPVGT(0.005)GEQR 128.67 2.67E-08 121530000 45434 61239 45422 57963 61311 70568 67176 25501 61098 50274 TRUE FALSE 43658.38905 59492.52368 53630.76581 60954.47738 63283.124 71994.93331 67998.11998 24974.39544 54162.41118 46868.8972 0.931500241 1.269339098 1.14427198 1.300531504 1.350215767 1.536091899 1.450815446 0.532856477 1.155615225 1 15.51634323 1.752647652 25 0.859009766 1.29033726 0.40557545 0.213215169 3.967969873 7051.668599 0.098149194 0.054428936 56.57800784 -1.752647652 0.431327493 WVPEITHHCPK ddPTM_BT-474_Pertuzumab_2h_R1 2 WVPEITHHCPK 11 0 A0A590UJK8;P60953-1;P60953;A0A494C1M1;Q5JYX0;A0A494BZX6 A0A590UJK8 CDC42 Cell division control protein 42 homolog 0 ; 147.37 2.04E-05 1278300000 866150 1111090 779600 1272170 927000 831390 1232270 504719 1239080 992680 FALSE TRUE 832299.9004 1079402.801 920491.0621 1337826.846 956817.7969 848201.2754 1247350.889 494296.3763 1098424.833 925444.8994 0.899351113 1.16636096 0.994647075 1.445603998 1.033900341 0.916533525 1.347839174 0.534117565 1.186915433 1 19.81978757 1.752660712 25 0.863833195 1.114222344 0.144352398 0.224665411 6.831584286 12129.47111 0.097928744 0.054306693 56.57970929 -1.752660712 0.250389149 GFFDPNTHENLTYVQLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFFDPNTHENLTYVQLLR 18 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 206.8 8.13E-16 1617680000 1772670 1916890 1643910 1849740 1857430 1819780 1861910 1694400 1944240 1967000 FALSE TRUE 1703392.097 1862222.174 1941001.106 1945205.303 1917175.923 1856577.198 1884696.612 1659410.048 1723538.026 1833773.338 0.928900023 1.015513824 1.058473839 1.060766488 1.045481403 1.012435485 1.027769666 0.904915571 0.939886076 1 20.8063839 1.752741781 24.99999757 0.940563312 1.024642091 0.390573257 0.041347828 4.059606562 7166.555175 0.019338522 0.010724249 56.59027198 -1.752741781 0.084078779 TVEDEDQDS(ph)EEEKDNDSYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVEDEDQDSEEEKDNDSYIK 20 1 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 TVEDEDQDS(1)EEEKDNDSYIK 75.97 0.0049061 0 96931 76752 61733 67814 74772 69727 75638 105220 109120 89329 TRUE FALSE 93142.82936 74563.10811 72889.52634 71313.88867 77177.10929 71136.92771 76563.68047 103047.1702 96733.15507 83278.66726 1.118447646 0.895344637 0.875248473 0.856328409 0.926733242 0.854203484 0.919367264 1.237377754 1.161559836 1 16.34565936 1.752766331 25 1.151266278 0.91326446 0.534164863 0.090120849 2.993166006 5274.787525 0.040235611 0.022312711 56.59347099 -1.752766331 -0.238001818 AMAVLTDHPYASLTLPDDAAADCLFLRPGLPGVPPFLLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AMAVLTDHPYASLTLPDDAAADCLFLRPGLPGVPPFLLHR 40 1 O95865 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ; 276.16 2.15E-77 1628620000 518020 559650 465270 574490 578970 474880 591150 399740 571100 594630 FALSE TRUE 497775.2057 543689.33 549354.6389 604139.4977 597593.0959 484482.399 598384.6705 391485.2293 506271.1222 554355.1805 0.897935517 0.980759897 0.990979535 1.089805812 1.077996773 0.873956655 1.079424693 0.70619928 0.913261281 1 19.08045109 1.752796993 25 0.845741364 0.999464806 0.24500282 0.097484049 5.000312373 8792.925432 0.043244058 0.023981141 56.59746673 -1.752796993 0.153723442 FEIINAIYEPTEEECEWKPDEEDEISEELKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FEIINAIYEPTEEECEWKPDEEDEISEELKEK 32 2 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8VV59;F8W543;F8W118;H0YH88;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 61.583 0.010904 82657000 43458 38433 24956 35577 32710 38707 35351 30425 34999 30879 FALSE TRUE 41759.61331 37336.92847 29466.10434 37413.13323 33762.14686 39489.68206 35783.63611 29796.71312 31026.06025 28787.53783 1.450614275 1.29698235 1.023571537 1.299629495 1.172804255 1.371763098 1.24302524 1.035055978 1.077760121 1 14.81315678 1.752821843 4.965769965 1.041785546 1.26021384 0.478680337 0.10888594 0.16662607 9.448296459 0.055866944 0.029104118 56.60070537 -1.752821843 0.218428294 GRES(ph)PAAGPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GRESPAAGPR 10 1 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 GRES(1)PAAGPR;GRES(1)PAAGPR;GRES(1)PAAGPR;GRES(1)PAAGPR 120.84 0.00032153 758704000 194921 182156 166199 171388 173009 178860 182908 151901 187706 179636 TRUE FALSE 187303.2718 176961.0892 196234.8564 180233.3552 178573.9916 182476.6717 185146.4828 148764.1913 166398.4018 167469.0937 1.118434857 1.056679088 1.17176759 1.07621861 1.066310133 1.089614016 1.105556128 0.888308332 0.99360663 1 17.35353535 1.752853659 25 0.95309387 1.096705118 0.695482699 0.04149633 2.254607556 3948.927831 0.018084235 0.01002861 56.60485192 -1.752853659 0.143611248 MVSSCLDAHTGISHEDLIQNFLNAGSFPEIQGFLQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MVSSCLDAHTGISHEDLIQNFLNAGSFPEIQGFLQLR 37 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 105.64 1.24E-05 213970000 21988 28314 22903 27029 24299 22777 27793 11973 23105 24091 FALSE TRUE 21128.68465 27506.51244 27042.08157 28423.96993 25080.5994 23237.56655 28133.13905 11725.75337 20482.21726 22459.29511 0.940754576 1.224727326 1.204048544 1.265577116 1.11671356 1.034652532 1.252627872 0.522089109 0.911970619 1 14.45502503 1.752902408 25 0.771158111 1.152424524 0.509535058 0.149972948 3.082567524 5380.710913 0.065237967 0.0361779 56.6112061 -1.752902408 0.381266412 DLGVLDVIFHPTQPWVFSSGADGTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGVLDVIFHPTQPWVFSSGADGTVR 26 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 205.13 3.52E-25 325800000 178629 210003 181359 201217 201263 204673 203972 172612 185891 215472 FALSE TRUE 171647.9812 204013.9201 214134.6056 211601.8335 207736.8072 208811.6283 206468.2704 169047.5019 164789.433 200877.8895 0.854489171 1.015611626 1.065993904 1.053385387 1.034144712 1.039495331 1.027829747 0.841543598 0.820346298 1 17.61595925 1.752920965 9.231431234 0.874695361 1.018554951 0.389032718 0.071381523 0.110610788 38.94489591 0.033336016 0.01809371 56.61362516 -1.752920965 0.143859589 QLLLQQQQQQQVSGLKS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLLLQQQQQQQVSGLKSPK 19 1 A0A3B3IUB6;Q9H334-8;C9J0F0;Q9H334-3;Q9H334-7;Q9H334-6;Q9H334;Q9H334-4;A0A3B3IRS5;A0A3B3IST0;A0A3B3IST6;A0A3B3IRY1;A0A087WVT2;A0A3B3IU15;A0A3B3IU08;G5E965 A0A3B3IUB6 FOXP1 Forkhead box protein P1 1 QLLLQQQQQQQVSGLKS(1)PK 255.67 3.72E-31 689020000 485130 358580 337160 278330 340830 364850 352550 515010 541790 460810 TRUE FALSE 466170.5833 348353.6495 398092.3121 292694.6447 351793.1065 372227.517 356864.6124 504374.8635 480288.2706 429598.9283 1.085129763 0.810881095 0.926660394 0.681320705 0.8188873 0.866453551 0.830692511 1.174059874 1.117992246 1 18.71263087 1.752921434 10.24595086 1.107123176 0.852440307 0.519709495 0.104218658 0.090879292 44.08157316 0.047943484 0.026142826 56.61368635 -1.752921434 -0.254682869 NNLAGAEELFAR ddPTM_BT-474_Pertuzumab_2h_R1 5 NNLAGAEELFAR 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 251.64 1.13E-20 1899526000 1115129 1131204 997804 1085532 1078253 1108386 1106342 1243480 1308448 1268259 FALSE TRUE 1071548.526 1098943.169 1178129.379 1141556.437 1112935.987 1130798.324 1119881.744 1217801.703 1159918.469 1182358.688 0.906280418 0.929449904 0.996422989 0.965490801 0.941284568 0.956391944 0.94715906 1.029976534 0.981020802 1 20.17323634 1.7529374 25 1.005155369 0.950633782 0.507056195 0.024680243 3.896926696 6785.620103 0.011740135 0.00651038 56.61576757 -1.7529374 -0.054521587 GLTEQEVETILDK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLTEQEVETILDK 13 0 Q13618;Q13618-2;Q13618-3 Q13618 CUL3 Cullin-3 0 100.02 0.0060314 26572000 92443 121080 88997 135660 127580 133130 103040 84386 61313 91100 FALSE TRUE 88830.22536 117626.9169 105080.7376 142661.4289 131683.7266 135821.9798 104301.0343 82643.39961 54353.00529 84929.71586 1.045926322 1.384991293 1.237267034 1.679758697 1.55050238 1.599228002 1.228086463 0.973079902 0.6399763 1 16.3739818 1.75308441 2.5268297 0.821956989 1.422718154 0.615957563 0.192627762 0.168335416 2.193346829 0.12203519 0.055065897 56.63493549 -1.75308441 0.600761165 DNEEETTDDPRK ddPTM_BT-474_Pertuzumab_2h_R1 1 DNEEETTDDPRK 12 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 91.62 0.01314 340140000 189520 150580 130530 119690 145290 136630 147730 172400 192180 157310 FALSE TRUE 182113.3489 146285.6058 154119.6746 125867.2152 149963.3848 139392.7522 149537.9639 168839.8798 170364.5321 146655.2536 1.241778555 0.997479478 1.050897741 0.858252345 1.022557195 0.950479092 1.019656373 1.151270586 1.161666752 1 17.16206923 1.753097247 24.88100244 1.117559573 1.011652608 0.122585793 0.09952786 7.595997218 13019.40649 0.045116861 0.025019139 56.6366095 -1.753097247 -0.105906965 GS(ph)PSYTQASLGLLTPVSGTQEQTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPSYTQASLGLLTPVSGTQEQTK 24 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(0.764)PS(0.132)Y(0.1)T(0.003)QASLGLLTPVSGTQEQTK 181.81 2.07E-17 81408000 153900 148170 131840 146480 140580 164660 174400 174600 196890 212470 TRUE FALSE 147885.4179 143944.3367 155666.4208 154039.8504 145101.8834 167989.538 176534.3594 170994.449 174539.8726 198079.2177 0.746597344 0.726700854 0.785879622 0.777667906 0.732544712 0.848092698 0.891231102 0.863262946 0.881161965 1 17.595718 1.753145678 0.319456475 1.01343392 0.709303253 0.874742585 0.029247031 0.476817882 0.160123059 0.048629756 0.050897306 56.64292584 -1.753145678 -0.304130667 ANS(ph)LGDLYAQK ddPTM_BT-474_Pertuzumab_2h_R1 3 ANSLGDLYAQK 11 0 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 ANS(1)LGDLYAQK;ANS(1)LGDLYAQK;ANS(1)LGDLYAQK 157.86 3.19E-05 990830000 1672300 1540980 1375000 1331010 1291340 1373840 1451510 1850220 1818770 1828430 TRUE FALSE 1606944.667 1497032.759 1623493.087 1399703.586 1332877.124 1401619.986 1469274.014 1812012.31 1612310.855 1704588.808 0.942716895 0.878236882 0.952425054 0.821138552 0.781934692 0.822262812 0.861952165 1.063020186 0.945864978 1 20.70099233 1.753244637 25 1.005221254 0.862999902 0.556229597 0.056088786 3.623372801 6177.064263 0.027392621 0.015190901 56.65583401 -1.753244637 -0.142221352 S(ph)KSEDMDNVQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.909)KS(0.091)EDMDNVQSK 212.95 8.63E-09 1686900000 1315400 1059700 978840 888830 1107400 1018100 1027200 1330800 1369500 1113000 TRUE FALSE 1263992.714 1029478.394 1155738.162 934702.6228 1143020.527 1038686.68 1039771.181 1303318.515 1214040.101 1037615.519 1.218170595 0.992157861 1.113840475 0.900817891 1.101583878 1.001032329 1.002077515 1.256070762 1.170028859 1 19.98484053 1.753270983 25 1.166344862 1.042248801 0.143802321 0.100575227 6.595074321 11223.00417 0.043358723 0.024044959 56.65927107 -1.753270983 -0.124096061 DTSQSDKDLDDALDKLSDSLGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTSQSDKDLDDALDKLSDSLGQR 23 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;A0A0C4DGD1;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5 P20810-6;P20810-5;A0A0C4DGB5 CAST Calpastatin 0 83.934 0.004265 390870000 597780 479860 408670 343070 428730 482270 459390 595510 689140 522420 FALSE TRUE 574418.0967 466174.8626 482525.7598 360775.8838 442520.4898 492021.8298 465012.1522 583212.5104 610911.7163 487036.0281 1.179416026 0.9571671 0.990739354 0.740758102 0.908599086 1.010237029 0.954779781 1.197473034 1.254346046 1 18.89366897 1.75327293 6.903387276 1.167670298 0.954815072 0.341418514 0.118094636 0.149255965 21.07457681 0.057895646 0.030989406 56.65952512 -1.75327293 -0.212855227 AANRT(ph)PPKSPGDPS(ph)KDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AANRTPPKSPGDPSKDR 17 3 O94811 O94811 TPPP Tubulin polymerization-promoting protein 2 AANRT(0.992)PPKS(0.106)PGDPS(0.901)KDR 69.704 0.064763 287200000 362630 294400 262150 205310 322400 294270 282820 363620 391940 286610 TRUE FALSE 348458.0187 286004.0002 309526.3365 215906.0737 332770.2888 300220.341 286281.2358 356111.1199 347448.6143 267197.6494 1.304120824 1.070383669 1.158417139 0.808038821 1.245408743 1.123589005 1.071421236 1.332762922 1.30034308 1 18.02754779 1.753276625 25 1.243418849 1.105768109 0.072105437 0.149493405 9.09925109 15478.47547 0.066306353 0.036770625 56.66000716 -1.753276625 -0.137650739 SLDS(ph)DES(ph)EDEEDDYQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 S(0.005)LDS(0.997)DES(0.998)EDEEDDYQQK 294.22 2.35E-46 510900000 585790 492780 434550 472440 470310 510400 491890 629400 660460 603530 TRUE FALSE 562896.6792 478726.3969 513082.8515 496822.685 485437.9483 520720.6377 497909.897 616402.6701 585487.3497 562652.3755 1.0004342 0.850838666 0.911900267 0.883001133 0.862767082 0.925474876 0.884933431 1.095530201 1.040584516 1 19.10188433 1.753313556 11.98164458 1.050003015 0.899686804 0.681608699 0.044590242 0.075523118 53.9201035 0.019390311 0.01063878 56.66482556 -1.753313556 -0.150316212 GGYDKDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GGYDKDGR 8 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 71.379 0.044591 1820730000 6520900 6765700 5098950 5698400 6088500 6254700 6198000 6060000 6814100 6540300 FALSE TRUE 6266056.019 6572748.86 6020443.691 5992495.107 6284342.132 6381174.319 6273852.978 5934858.882 6040591.935 6097319.656 1.027673859 1.077973476 0.987391843 0.982808094 1.0306729 1.046554007 1.028952611 0.973355379 0.990696286 1 22.53974375 1.753328371 15.53812919 0.986621898 1.025826459 0.305182537 0.026239435 0.426844281 450.4866689 0.012973226 0.007166366 56.66675861 -1.753328371 0.039204561 IAQPGDHVSVTGIFLPILR ddPTM_BT-474_Pertuzumab_2h_R1 2 IAQPGDHVSVTGIFLPILR 19 0 P33993;P33993-3;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 130.85 1.67E-05 719510000 367060 545280 432870 546120 437180 544250 505590 394960 403790 576350 FALSE TRUE 352714.8894 529729.1483 511099.2381 574305.3186 451242.2917 555255.1079 511777.5617 386803.938 357953.452 537313.3011 0.656441761 0.985885045 0.951212704 1.068846272 0.839812249 1.033391704 0.95247514 0.719885283 0.66619131 1 19.03540403 1.753378989 12.30433962 0.770848608 0.936288623 0.155765837 0.135513651 0.225785742 169.6086112 0.060236676 0.033079512 56.6733636 -1.753378989 0.165440015 S(ph)AGEEEDGPVLTDEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SAGEEEDGPVLTDEQK 16 0 H7BZV4;A0A0C4DG62;Q66PJ3-4;Q66PJ3-3;F5H7X4;Q66PJ3-7;F5GYV5;F8WCT1;Q66PJ3-2;Q66PJ3 H7BZV4;F5GYV5;Q66PJ3 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK 428.89 3.38E-160 2642290000 3261040 2915550 2350630 2247350 2755830 2523820 2613910 3316010 3443440 2847660 TRUE FALSE 3133594.952 2832401.369 2775441.13 2363336.003 2844473.775 2574853.37 2645899.812 3247533.235 3052555.127 2654785.452 1.180357136 1.066904057 1.045448373 0.890217325 1.07145147 0.969891321 0.996652973 1.223275211 1.149831195 1 21.34016384 1.753387462 25 1.14525701 1.027179856 0.176772443 0.08804259 6.539185142 11040.33008 0.040313608 0.022356321 56.67446929 -1.753387462 -0.118077153 S(ph)KDVEFQDGWPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKDVEFQDGWPR 12 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 S(1)KDVEFQDGWPR;S(1)KDVEFQDGWPR;S(1)KDVEFQDGWPR 130.21 0.0001335 1290970000 1019500 870150 652920 670390 908970 709680 798520 1160330 1085950 1056540 TRUE FALSE 979656.8129 845334.174 770917.1681 704988.9082 938207.8456 724030.2158 808292.5266 1136368.78 962677.5087 984979.6047 0.994596039 0.858225053 0.782673229 0.7157396 0.952514997 0.735071277 0.820618541 1.153697777 0.977357809 1 19.90973433 1.753391658 25 1.053409044 0.831636029 0.509487809 0.092652197 3.619655914 6109.461504 0.041890596 0.023230442 56.67501692 -1.753391658 -0.221773015 DVSGLHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVSGLHSK 8 0 P52732 P52732 KIF11 Kinesin-like protein KIF11 0 117.04 0.0021563 159080000 272150 320770 293500 348110 296450 305030 327420 278260 331570 356730 FALSE TRUE 261514.0771 311621.9537 346541.9789 366075.9988 305985.5835 311197.9156 331427.0639 272513.8338 293931.5637 332568.3594 0.786346836 0.93701624 1.042017285 1.100754141 0.920068235 0.9357412 0.996568238 0.819422011 0.883822996 1 18.34329139 1.753423049 25 0.883715477 0.965043752 0.072455741 0.088651763 9.947408663 16754.28457 0.042053016 0.023320814 56.67911349 -1.753423049 0.081328274 KVELS(ph)ES(ph)EEDKGGK ddPTM_BT-474_Pertuzumab_2h_R1 8 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK 103.9 0.00058399 7742140000 6836680 4954490 3960540 2871125 4517580 4407150 4499710 6122960 6931720 5162620 TRUE FALSE 6569494.987 4813192.796 4676297.68 3019304.105 4662892.063 4496265.593 4554778.797 5996518.736 6144860.206 4812951.149 1.364961909 1.000050208 0.971607136 0.627329057 0.968821814 0.934201377 0.946358826 1.245913069 1.276734381 1 22.19849035 1.753435999 9.024406825 1.193580054 0.959235659 0.201828648 0.180200556 0.180820082 58.93784734 0.087204596 0.047302279 56.68080363 -1.753435999 -0.234344394 HNGYDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HNGYDPR 7 0 P12532;P12532-2;F8WCN3;C9JSQ1;P17540;C9J8F6;C9J6W7;C9JT96;D6RHV3;D6R998 P12532 CKMT1A;CKMT1B;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ;;; 86.794 0.019815 1078670000 1487120 1670950 1415990 1886310 1325890 1566130 1614230 1192390 1574150 1507820 FALSE TRUE 1429001.706 1623296.142 1671890.892 1983662.685 1368538.456 1597798.222 1633985.43 1167766.73 1395459.091 1405694.008 1.016580919 1.154800499 1.189370433 1.41116251 0.973567823 1.136661473 1.162404776 0.830740348 0.992718958 1 20.42285115 1.753436285 24.99999834 0.929762044 1.153815826 0.395934174 0.117424643 4.661235433 7843.859591 0.054196246 0.030054759 56.68084095 -1.753436285 0.224053781 GLSSAGGGS(ph)PHREDAQPEHSASAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLSSAGGGSPHREDAQPEHSASAR 24 1 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 GLSSAGGGS(1)PHREDAQPEHSASAR;GLSSAGGGS(1)PHREDAQPEHSASAR;GLSS(0.002)AGGGS(0.998)PHREDAQPEHSASAR;GLS(0.323)S(0.323)AGGGS(0.355)PHREDAQPEHSASAR 278.97 2.29E-52 9052630000 1453261 1776988 1424711 1916110 1633203 1809653 1960928 1080365 1837169 1892866 TRUE FALSE 1396465.953 1726310.042 1682187.97 2015000.667 1685736.458 1846245.424 1984926.423 1058055.085 1628621.277 1764660.5 0.791351058 0.978267515 0.953264365 1.141863076 0.955275226 1.046232646 1.124820567 0.599579968 0.922909125 1 20.75095922 1.753481739 25 0.802930002 1.001851539 0.209827342 0.134414982 5.818377786 9761.208548 0.05972142 0.033118637 56.68677355 -1.753481739 0.198921537 FDPYEHEALFHTPVEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FDPYEHEALFHTPVEGK 17 0 Q9HAV7 Q9HAV7 GRPEL1 "GrpE protein homolog 1, mitochondrial" 0 73.593 0.015001 225780000 123890 140230 107300 141620 114430 132050 149130 74771 152730 117610 FALSE TRUE 119048.2418 136230.7777 126691.4969 148929.0252 118110.7449 134720.1415 150955.0975 73226.95272 135392.7307 109644.1699 1.08576901 1.242480816 1.155478645 1.358294064 1.077218651 1.228703191 1.376772679 0.667859976 1.234837482 1 16.74246958 1.753490731 25 0.939833076 1.21678249 0.339423614 0.158569466 4.758934995 7979.016922 0.067930071 0.037671017 56.68794725 -1.753490731 0.276949414 TKDIEDVFYK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKDIEDVFYK 10 1 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 120.96 0.00048127 5341800000 9520600 9116300 6672000 6204200 7659500 8077000 7956900 9154900 10445000 8728300 FALSE TRUE 9148524.426 8856312.05 7877778.818 6524399.506 7905874.774 8240322.474 8054278.922 8965848.116 9259327.389 8137124.467 1.124294518 1.088383505 0.968128096 0.801806527 0.971580907 1.012682368 0.989818818 1.10184478 1.137911485 1 22.95608763 1.753525491 6.617780884 1.08915163 0.988784339 0.167442446 0.086640102 0.257177526 32.00265354 0.045782316 0.024455551 56.69248457 -1.753525491 -0.100367291 KRFDTEEEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KRFDTEEEFK 10 2 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 198.62 1.65E-07 729360000 1040880 917050 744620 690390 867470 941950 890600 1132810 1252450 1175420 FALSE TRUE 1000201.259 890896.6319 879189.398 726021.1106 895372.9604 960996.8744 901499.4292 1109417.078 1110277.127 1095807.756 0.912752491 0.813004495 0.802320838 0.662544234 0.817089453 0.876975791 0.822680278 1.012419442 1.013204296 1 20.06356329 1.753541733 4.022444084 1.012279735 0.809653471 0.676762423 0.061065494 0.120755983 4.127294637 0.034473718 0.017429193 56.69460483 -1.753541733 -0.202626264 AQEPPAGGGGSIHDLPLFTETSPT(ph)SAPWDPLPGPPPVLPHSPHSHL ddPTM_BT-474_Pertuzumab_2h_R1 2 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGSIHDLPLFTET(0.001)S(0.303)PT(0.542)S(0.152)APWDPLPGPPPVLPHSPHSHL;AQEPPAGGGGSIHDLPLFT(0.001)ET(0.009)S(0.093)PT(0.706)S(0.19)APWDPLPGPPPVLPHS(0.001)PHS(0.001)HL 77.701 0.00028711 438560000 20663 28842 25193 36067 25586 33008 33303 5744.9 26380.5 21525.2 TRUE FALSE 19855.46712 28019.4544 29745.93552 37928.42219 26408.99693 33675.44438 33710.57208 5626.265807 23385.89624 20067.27903 0.989444911 1.396275716 1.482310356 1.890063029 1.316022809 1.678127081 1.679877577 0.280370139 1.165374548 1 14.29255739 1.753563106 25 0.759764795 1.502276491 0.492845128 0.312124523 3.678615891 6137.91159 0.139520579 0.077371651 56.69739507 -1.753563106 0.742511696 TPS(ph)SQNLLALLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSSQNLLALLAR 13 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 T(0.104)PS(0.861)S(0.035)QNLLALLAR 88.78 0.0081311 39738000 32565 28320 20116 25465 28502 25392 22549 38661 28268 33034 TRUE FALSE 31292.3238 27512.34133 23751.40868 26779.2517 29418.79271 25905.44364 22824.96141 37862.63684 25059.13515 30796.57776 1.016097439 0.893357098 0.771235326 0.869552842 0.955261748 0.841179297 0.741152526 1.229442997 0.813698696 1 14.91048242 1.753575434 25 1.034409618 0.869003129 0.228595706 0.120118516 6.304563367 10510.75681 0.053185975 0.029494364 56.69900454 -1.753575434 -0.165406489 RQEQPSIES(ph)TSPISR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RQEQPSIES(0.442)T(0.117)S(0.442)PISR;RQEQPSIES(0.581)T(0.183)S(0.237)PISR 134.52 2.12E-05 2929700000 334230 386250 301320 341710 349890 378400 355820 278030 307070 331510 TRUE FALSE 321167.9221 375234.5282 355775.2268 359345.6941 361144.5296 386051.5073 360174.6316 272288.5833 272212.7009 309056.5324 1.039188266 1.214129096 1.15116553 1.162718326 1.168538736 1.249129097 1.165400481 0.881031639 0.88078611 1 18.23751123 1.753586953 6.599210532 0.912611516 1.169515831 0.777090491 0.05966802 0.061457084 7.583273415 0.027942405 0.014924861 56.70050841 -1.753586953 0.256904314 KVVVS(ph)PTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVVVSPTKK 9 2 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.8)PT(0.2)KK 83.617 0.022437 0 847080 720350 567730 556770 566910 575020 642480 825330 853850 747280 TRUE FALSE 813975.1771 699806.3233 670331.4401 585504.9664 585145.175 586647.2984 650342.8624 808286.6471 756924.5276 696666.06 1.168386439 1.004507559 0.962199077 0.840438483 0.839922035 0.842078195 0.933507314 1.160221078 1.086495483 1 19.41010775 1.753595411 25 1.094729069 0.933163874 0.288321439 0.100090944 6.029624374 10039.00724 0.049562933 0.027485004 56.70161273 -1.753595411 -0.161565194 RYEDDGIS(ph)DDEIEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RYEDDGISDDEIEGK 15 1 I3VM54;Q9Y2K7;Q9Y2K7-3 I3VM54 KDM2A Lysine-specific demethylase 2A 1 RYEDDGIS(1)DDEIEGK;RYEDDGIS(1)DDEIEGK 208.27 1.82E-09 1677080000 1354880 1217490 1128450 1198030 1291390 1177970 1269840 1539180 1645300 1446300 TRUE FALSE 1301929.792 1182768.377 1332386.017 1259860.472 1332928.732 1201789.36 1285380.682 1507395.395 1458532.442 1348340.813 0.965579162 0.87720283 0.98816709 0.934378356 0.988569596 0.891309785 0.953305477 1.117963189 1.08172387 1 20.36275377 1.753615525 24.99861493 1.075271631 0.941352462 0.623241984 0.043987471 2.791095197 4640.556658 0.01897642 0.010523538 56.70423877 -1.753615525 -0.133919169 VADAKGDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_BT-474_Pertuzumab_2h_R1 5 VADAKGDSESEEDEDLEVPVPSR 23 1 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 2 VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR 241.5 1.52E-37 3738715000 4685467 4001786 2966006 3163781 3574491 3650587 3737180 4836226 5080371 4311541 TRUE FALSE 4502353.77 3887658.981 3502029.263 3327064.117 3689467.749 3724404.37 3782916.727 4736356.243 4503668.583 4019516.488 1.120123225 0.96719568 0.87125635 0.827727446 0.917888448 0.926580195 0.941137258 1.178339797 1.120450332 1 21.93859054 1.753642433 25 1.113451975 0.93178356 0.437239012 0.082858593 4.285529952 7112.902729 0.039379834 0.021838435 56.70775227 -1.753642433 -0.181668415 KQSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_BT-474_Pertuzumab_2h_R1 4 KQSAGPNSPTGGGGGGGSGGTR 22 1 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 KQSAGPNS(0.984)PT(0.016)GGGGGGGSGGTR;KQSAGPNS(0.985)PT(0.015)GGGGGGGSGGTR;KQSAGPNS(0.885)PT(0.115)GGGGGGGSGGTR;KQS(0.001)AGPNS(0.959)PT(0.039)GGGGGGGSGGTR 207.7 4.76E-23 1156670000 767427 865305 665050 753752 803264 929608 806870 727186 834706 835665 TRUE FALSE 737435.1044 840627.3486 785239.329 792653.231 829101.7161 948405.3107 816744.7164 712169.355 739953.6743 779064.6652 0.946564691 1.079021275 1.00792574 1.017442154 1.064227083 1.217364043 1.048365756 0.914133816 0.949797504 1 19.57138356 1.753649222 24.99980944 0.948712985 1.05879665 0.308072496 0.068126541 5.858310242 9718.866596 0.032592965 0.018074512 56.70863874 -1.753649222 0.110083665 QPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPPPHYEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPPPHYEGR 38 0 P14866;M0QXS5;P14866-2 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 166.74 1.88E-18 1520970000 132018 147784 123373 204267 170621 187759 187523 9909.7 150404 86762 FALSE TRUE 126858.5906 143569.345 145669.2455 214809.2443 176109.1794 191555.6156 189817.9626 9705.061232 133330.7685 80885.53246 1.568371831 1.7749694 1.800930786 2.655718987 2.177264265 2.368230879 2.346748013 0.119985131 1.648388339 1 16.30359406 1.753670349 25 0.865828504 2.109763603 0.578023697 0.459656974 3.346740899 5544.470053 0.209842366 0.116368958 56.71139747 -1.753670349 1.243935098 HISDLYEDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 HISDLYEDLR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;E9PIA2;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ;;;;; 232.88 6.69E-12 4364590000 1591052 2970150 2490100 3714480 2693830 2571270 2851930 1963180 2175490 3034310 FALSE TRUE 1528871.929 2885444.23 2940116.462 3906184.758 2780479.488 2623262.841 2886832.772 1922639.647 1928537.496 2828793.481 0.540467849 1.02002647 1.03935352 1.380866007 0.982920636 0.927343356 1.020517331 0.679667731 0.681752665 1 21.43175542 1.753677233 15.58795709 0.761135506 1.003270865 0.156011671 0.208523861 0.546992191 566.2968191 0.097850205 0.054056565 56.71229634 -1.753677233 0.24213536 S(ph)PQALSNGTK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPQALSNGTK 10 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 S(1)PQALSNGTK;S(1)PQALSNGTK;S(1)PQALSNGTK 137.81 8.54E-05 1588930000 1053760 1143740 871070 984960 1078050 1053480 1041460 1228430 1268210 1204260 TRUE FALSE 1012577.894 1111121.655 1028491.726 1035793.904 1112726.457 1074782.087 1054205.699 1203062.491 1124248.118 1122694.398 0.901917651 0.989691992 0.916092329 0.922596484 0.991121413 0.957323818 0.938996134 1.071585014 1.001383921 1 20.09853384 1.75368506 25 1.029580196 0.947309374 0.541969439 0.03311381 3.518811166 5823.852221 0.014565761 0.008077656 56.7133185 -1.75368506 -0.082270822 TCFVDCLIEQTHPEIR ddPTM_BT-474_Pertuzumab_2h_R1 3 TCFVDCLIEQTHPEIR 16 0 Q15029;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;; 275.83 2.82E-35 874830000 534520 590720 475600 578130 565190 629090 569430 500430 580580 584890 FALSE TRUE 513630.3675 573873.244 561551.4997 607967.3586 583369.8496 641810.6308 576398.8547 490095.9456 514674.9924 545274.8793 0.941965946 1.052447611 1.029850303 1.114974083 1.069863791 1.177040526 1.057079423 0.898805289 0.943881723 1 19.05662417 1.753840742 24.99949902 0.940475575 1.068224692 0.428472076 0.060915718 4.546517356 7447.845561 0.028670102 0.015899124 56.73365224 -1.753840742 0.127749116 AQLYLPSTS(ph)PPHEGLDGFAQELSR ddPTM_BT-474_Pertuzumab_2h_R1 4 AQLYLPSTSPPHEGLDGFAQELSR 24 0 I3L1Z8;I3L1A6;Q8N137-4;Q8N137-5;Q8N137;Q8N137-3;Q8N137-2;I3L465 I3L1Z8 CNTROB Centrobin 1 AQLYLPS(0.032)T(0.159)S(0.809)PPHEGLDGFAQELSR;AQLYLPS(0.029)T(0.152)S(0.82)PPHEGLDGFAQELSR;AQLYLPS(0.004)T(0.05)S(0.946)PPHEGLDGFAQELSR;AQLYLPS(0.189)T(0.142)S(0.669)PPHEGLDGFAQELSR 243.74 6.90E-38 928560000 367928 442724 339161 421570 409638 450540 418972 390133 442161 434435 TRUE FALSE 353548.967 430097.945 400454.9373 443327.2782 422814.3783 459650.2275 424099.5047 382076.6172 391968.737 405010.3305 0.872938146 1.061943147 0.988752402 1.094607334 1.043959491 1.134909885 1.047132561 0.943374992 0.967799356 1 18.62759918 1.753856533 13.40860037 0.967042742 1.040651705 0.159080079 0.066911532 0.336809799 285.5890837 0.030859633 0.016991627 56.73571506 -1.753856533 0.073608963 GTGARPYTGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTGARPYTGK 10 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 83.045 0.014768 1016500000 968340 1152700 898540 1030700 1050100 1224700 1098100 324900 943600 572720 FALSE TRUE 930496.2022 1119826.125 1060926.166 1083894.551 1083877.42 1249464.273 1111538.876 318190.7015 836486.4839 533929.1643 1.742733427 2.097330881 1.9870167 2.030034362 2.030002279 2.340131157 2.081809631 0.595941789 1.566661909 1 19.02628883 1.753860429 25 1.042232425 2.054296383 0.756216492 0.257501978 2.218319119 3629.312974 0.110538664 0.061299622 56.73622401 -1.753860429 1.012063959 NKYETEINITK ddPTM_BT-474_Pertuzumab_2h_R1 1 NKYETEINITK 11 1 P15924;P15924-3 P15924 DSP Desmoplakin 0 105.78 0.0022064 521470000 981490 890540 744190 734520 766530 892410 844750 958800 1100000 900440 FALSE TRUE 943132.2857 865142.6711 878681.6874 772428.6652 791186.1336 910455.1416 855088.3032 939000.4449 975132.6116 839452.3968 1.123508956 1.030603611 1.046732001 0.920157794 0.94250268 1.084582217 1.018626317 1.118586889 1.161629433 1 19.67908899 1.753868544 7.530227408 1.104295615 1.020105528 0.173796993 0.067879699 0.20814924 38.24809059 0.033291719 0.017914417 56.73728427 -1.753868544 -0.084190087 EGCTEVSLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGCTEVSLLR 10 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 108.15 0.0071322 0 85423 125440 102710 162460 131560 137890 132000 94352 114950 119300 FALSE TRUE 82084.57472 121862.574 121271.9818 170844.5801 135791.7469 140678.2303 133615.4555 92403.59823 101901.3579 111219.7047 0.738039855 1.095692299 1.090382159 1.536099925 1.220932453 1.264867863 1.201364954 0.830820388 0.916216763 1 16.76305289 1.753922167 11.04145872 0.907339087 1.178873793 0.261130091 0.189985505 0.184159256 106.5070773 0.093004858 0.050890394 56.74429012 -1.753922167 0.271534706 ERS(ph)PYK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSPYK 6 1 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 ERS(1)PYK 71.692 0.053029 240530000 419670 355730 376270 379120 357400 345200 381670 481970 478110 475070 TRUE FALSE 403268.8324 345584.9287 444270.3591 398686.4286 368896.0956 352180.1805 386340.9916 472017.1511 423836.9572 442893.0858 0.910533141 0.780289735 1.00310972 0.900186617 0.832923582 0.795181031 0.872312086 1.065758681 0.956973524 1 18.75659895 1.75393792 25 1.01030395 0.869049881 0.48757611 0.064295143 4.338334662 7061.972402 0.029885968 0.016573429 56.74634842 -1.75393792 -0.141254069 QKNEGRPET(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKNEGRPETPK 11 2 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 QKNEGRPET(1)PK 122.34 0.018722 196820000 100270 77048 61865 50283 67485 65055 70186 90026 91656 83137 TRUE FALSE 96351.33755 74850.66648 73045.38168 52878.11166 69655.71631 66370.45667 71044.95726 88166.93164 81251.59513 77506.05694 1.243145908 0.965739575 0.942447398 0.682244895 0.898713198 0.856326064 0.916637487 1.137548924 1.048325748 1 16.24202144 1.753938079 24.99999996 1.072231493 0.917739716 0.166658646 0.133585762 8.484389112 13810.80644 0.063925907 0.035450307 56.74636921 -1.753938079 -0.154491777 HIDLVEGDEGR ddPTM_BT-474_Pertuzumab_2h_R1 5 HIDLVEGDEGR 11 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;; 190.53 2.23E-06 7142400000 4440700 5092990 3917200 5993390 4963870 4932610 5101900 3923470 4985110 5078640 FALSE TRUE 4267152.535 4947742.912 4625125.178 6302709.576 5123537.387 5032350.754 5164338.578 3842448.973 4419221.212 4734659.189 0.901258647 1.045005081 0.976865492 1.331185482 1.082134359 1.062874972 1.090751915 0.811557669 0.933376836 1 22.17482915 1.753942674 25 0.899747396 1.075703724 0.282574049 0.112162718 6.114218728 9949.691518 0.052438369 0.029079957 56.74696958 -1.753942674 0.175956328 SSS(ph)LDALGPTRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLDALGPTRK 12 1 Q9H425;Q9H425-3;Q9H425-2;E5RI90 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 S(0.014)S(0.045)S(0.94)LDALGPTRK 92.906 0.0079144 58689000 128900 134010 90597 114390 104160 119810 113930 144240 138590 141450 TRUE FALSE 123862.4455 130188.166 106969.8932 120293.6816 107510.401 122232.6403 115324.3094 141261.3936 122857.8442 131869.4655 0.939280712 0.987250274 0.811180153 0.91221786 0.815278962 0.926921481 0.874533835 1.071221401 0.931662563 1 17.00875102 1.753956118 25 1.005276721 0.894339823 0.398160605 0.05948718 4.962662949 8068.696253 0.026790294 0.014856743 56.74872629 -1.753956118 -0.110936899 EKQEASES(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQEASESPVK 11 1 Q01167;Q01167-2;E9PPI7;Q01167-3 Q01167 FOXK2 Forkhead box protein K2 1 EKQEAS(0.004)ES(0.996)PVK 115.31 0.00069048 589060000 522930 414580 384280 378060 400290 402930 424140 518380 531040 506020 TRUE FALSE 502493.3175 402756.5843 453727.9443 397571.7219 413165.6914 411077.5207 429330.7522 507675.2718 470758.5655 471746.8147 1.065175857 0.853755811 0.961803938 0.842765037 0.87582084 0.871394375 0.910087231 1.076160466 0.997905128 1 18.84765325 1.7539659 24.99999634 1.029152507 0.90569031 0.391237718 0.064315555 4.703828536 7642.996069 0.028224207 0.015651808 56.75000441 -1.7539659 -0.123462196 GFSESER ddPTM_BT-474_Pertuzumab_2h_R1 1 GFSESER 7 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4;C9J188;C9JWF5 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 92.822 0.035798 521930000 611070 827530 673610 974110 883630 870030 839460 739660 821800 852540 FALSE TRUE 587188.7088 803929.6546 795346.3114 1024383.934 912052.7614 887622.6027 849733.5626 724385.7625 728512.7093 794796.7064 0.73879107 1.011490924 1.000691504 1.288862832 1.147529619 1.116791999 1.069120639 0.911410121 0.916602577 1 19.60022637 1.754009117 8.331286079 0.93680766 1.064881248 0.121497256 0.133456602 0.264067937 66.55657094 0.067147612 0.036310616 56.75565203 -1.754009117 0.128073588 LTEVQDDKEEEEEENPLLVPLEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 LTEVQDDKEEEEEENPLLVPLEEK 24 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 ;; 147.41 1.63E-07 188442000 451902 332564 304853 244210 314348 316855 324447 444851 464953 394231 FALSE TRUE 434241.1702 323079.6003 359946.7185 256813.7074 324459.2889 323262.0252 328417.6794 435664.6714 412173.4847 367529.3832 1.181514159 0.87905788 0.979368548 0.69875694 0.882811834 0.879554234 0.893582104 1.185387322 1.121470836 1 18.48750007 1.754030451 16.51005999 1.114710913 0.903979176 0.337379658 0.120332797 0.469762184 505.0485771 0.055063606 0.030448427 56.75844002 -1.754030451 -0.210731738 AHQCGDDDK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHQCGDDDK 9 0 Q9BQ61;K7EN60 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 162.36 6.38E-05 105410000 194530 168570 163030 171890 181720 158390 216670 102950 194050 228570 FALSE TRUE 186927.5525 163762.5486 192493.1476 180761.2635 187565.1888 161592.7543 219321.6723 100824.0465 172022.2575 213088.7503 0.87722863 0.76851804 0.903347302 0.848290974 0.880220981 0.758335455 1.029250357 0.473155182 0.807279865 1 17.7010949 1.75406268 25 0.706578032 0.85978095 0.068701222 0.141709503 8.215239079 13265.04146 0.060450875 0.03352332 56.76265226 -1.75406268 0.153202918 EDLAYMNHIMVSVS(ph)PPEEHAMPIGR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDLAYMNHIMVSVSPPEEHAMPIGR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 EDLAYMNHIMVS(0.001)VS(0.999)PPEEHAMPIGR;EDLAYMNHIMVS(0.025)VS(0.975)PPEEHAMPIGR;EDLAYMNHIMVS(0.015)VS(0.985)PPEEHAMPIGR 220.78 2.00E-33 750475000 207194 235304 208108 269958 249749 260412 257920 169534 247087 241821 TRUE FALSE 199096.6294 228593.3603 245717.7449 283890.5647 257782.4034 265677.7091 261076.5021 166033.0637 219038.7196 225442.2483 0.883138058 1.013977469 1.089936544 1.259260706 1.143452061 1.178473472 1.15806378 0.736477146 0.971595703 1 17.78239838 1.754144376 25 0.880794151 1.110154372 0.381607699 0.116095559 5.091548319 8178.094236 0.055534659 0.03079688 56.77333107 -1.754144376 0.229360222 LAQHITYVHQHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAQHITYVHQHSR 13 0 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 177.21 5.44E-06 437270000 210080 315590 207730 301500 253230 209050 264960 89243 185920 224080 FALSE TRUE 201869.8413 306589.6822 245271.4319 317060.4511 261375.3729 213277.1342 268202.6597 87400.10086 164815.141 208902.862 0.966333536 1.467618391 1.17409321 1.51774106 1.251181388 1.020939264 1.283863022 0.418376752 0.788955879 1 17.67247273 1.754185438 25 0.689135545 1.249111283 0.54589857 0.209447825 3.463249596 5548.065512 0.091763489 0.050887851 56.77869916 -1.754185438 0.559975738 RIPEEILGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RIPEEILGK 9 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 89.827 0.018991 319930000 529170 498570 455260 450830 496700 484240 537210 426090 574120 548800 FALSE TRUE 508489.4514 484351.2718 537535.6092 474097.3903 512676.8066 494031.6646 543784.5367 417291.0926 508948.3045 511629.2872 0.993863065 0.946684023 1.050634947 0.9266424 1.002047419 0.96560474 1.062848727 0.815612208 0.994759912 1 18.96473933 1.754212093 25 0.918600817 0.989869103 0.124518063 0.062182635 7.899801831 12633.76452 0.026555043 0.014726228 56.78218408 -1.754212093 0.071268286 NTVELLTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NTVELLTDR 9 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 61.691 0.087512 700530000 264160 539480 512700 816060 623700 651190 485220 242410 115060 213700 FALSE TRUE 253836.3352 524094.5586 605356.2949 858176.9544 643761.8769 664357.508 491158.2675 237404.1488 101998.8712 199225.9087 1.274113075 2.630654628 3.03854202 4.307556985 3.231316054 3.33469433 2.465333303 1.191632908 0.511975937 1 17.60404575 1.754216514 2.504445181 0.763493531 3.026436601 0.625117357 0.719738129 0.17476287 2.233091801 0.475014354 0.213994939 56.78276208 -1.754216514 2.26294307 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.467)S(0.533)RPS(0.533)T(0.467)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.172)S(0.792)RPS(0.54)T(0.489)PGLS(0.007)VVSGISATSEDIPNKIEDLR;EVS(0.473)S(0.527)RPS(0.527)T(0.473)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.109)S(0.877)RPS(0.606)T(0.408)PGLSVVSGISATSEDIPNKIEDLR 179.43 9.96E-20 5598390000 292048 254219 195388 203639 221216 245409 226842 297372 284468 273329 TRUE FALSE 280634.4413 246968.923 230698.958 214148.8332 228331.6135 250371.3381 229618.1603 291231.1643 252176.3852 254816.1834 1.101321108 0.969204231 0.90535442 0.840405152 0.89606402 0.98255666 0.90111294 1.142906861 0.989640383 1 17.95909738 1.754219886 25 1.05625592 0.937755206 0.266304349 0.076464647 6.451963823 10313.15904 0.036024738 0.019977678 56.78320292 -1.754219886 -0.118500714 KEIHTVPDMGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEIHTVPDMGK 11 1 Q15257;Q15257-2;A6PVN5;Q15257-3;Q15257-4;Q5T948;Q5T949;A6PVN6;Q68CR8 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 ; 140.39 2.51E-05 1645990000 2888800 2911500 2397500 2543900 2557100 2307700 2906300 2987500 3474200 3368600 FALSE TRUE 2775902.502 2828466.871 2830781.582 2675190.984 2639351.444 2354363.275 2941868.169 2925807.081 3079823.381 3140441.722 0.883921037 0.900658927 0.901395992 0.851851816 0.840439555 0.749691758 0.93676891 0.931654633 0.980697511 1 21.58253607 1.754222445 2.119925175 0.979553651 0.859123092 0.563973303 0.045525298 0.237231016 2.153854902 0.032201322 0.013786237 56.78353754 -1.754222445 -0.120430558 HNGSLS(ph)PGLEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 HNGSLSPGLEAR 12 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HNGSLS(1)PGLEAR;HNGS(0.001)LS(0.999)PGLEAR;HNGSLS(1)PGLEAR;HNGSLS(1)PGLEAR 164.48 3.68E-05 9293400000 2845030 3279840 3018710 4267130 4481090 4259380 3861340 2038330 3587960 2841080 TRUE FALSE 2733843.082 3186302.174 3564258.048 4487357.091 4625228.329 4345507.582 3908596.234 1996237.773 3180669.823 2648651.121 1.032164282 1.202990514 1.345688007 1.694204667 1.746258045 1.64064929 1.475693119 0.753680905 1.200864016 1 21.33682639 1.754225395 25 0.973186465 1.463182382 0.457124749 0.230905662 5.07169639 8104.013611 0.117018563 0.064893317 56.78392323 -1.754225395 0.489995917 RNS(ph)LTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSLTPR 7 1 Q9NQ86-4;Q9NQ86;D6RAU9 Q9NQ86-4 TRIM36 E3 ubiquitin-protein ligase TRIM36 1 RNS(1)LTPR;RNS(1)LTPR 86.882 0.012097 409800000 97144 84715 103128 128272 122422 109215 102223 92711 77558 103987 TRUE FALSE 93347.50508 82299.01114 121765.5237 134892.1333 126359.8148 111423.4021 103474.0357 90796.48545 68753.94099 96943.86787 0.962902627 0.848934677 1.256041525 1.391445754 1.303432776 1.149359981 1.067360298 0.936588228 0.709213925 1 16.56486202 1.754258721 2.318717812 0.849651046 1.158133045 0.357319078 0.162599801 0.320942448 3.506157346 0.115604557 0.050870756 56.78828078 -1.754258721 0.308481999 EILQTYGYEHILTLHNLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EILQTYGYEHILTLHNLEK 19 0 A0A2R8YF87;Q96AX1;H3BMM5;A0A2R8Y5U3 A0A2R8YF87 VPS33A Vacuolar protein sorting-associated protein 33A 0 119.5 3.38E-05 119320000 53280 79086 65271 93197 90415 88072 77696 33760 52380 67390 FALSE TRUE 51197.7587 76830.54471 77066.92165 98006.90834 93323.28059 89852.87618 78646.86689 33062.8442 46434.04199 62825.61528 0.81491854 1.222917505 1.226679935 1.559983263 1.485433611 1.430194926 1.251828041 0.526263755 0.739094107 1 15.93906527 1.754272905 25 0.721115554 1.303887698 0.545759291 0.220200499 3.848882708 6131.467797 0.10501235 0.058235082 56.7901355 -1.754272905 0.582772143 SYSEHDDER ddPTM_BT-474_Pertuzumab_2h_R1 1 SYSEHDDER 9 0 Q9UBU9;Q9UBU9-2;E9PQA4 Q9UBU9 NXF1 Nuclear RNA export factor 1 0 61.65 0.087783 52045000 83131 78701 65336 94644 83807 97924 86131 62440 83476 80116 FALSE TRUE 79882.14861 76456.52454 77143.66859 99528.58818 86502.72827 99904.09037 87185.09694 61150.59218 74000.15444 74689.67196 1.069520678 1.023655916 1.032855903 1.332561592 1.158161845 1.33758909 1.167297896 0.818728889 0.990768235 1 16.18862114 1.754277048 25 0.924016471 1.163452179 0.454144066 0.112116333 4.896256272 7797.929296 0.054857388 0.030421474 56.79067723 -1.754277048 0.239435708 DGKPMLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGKPMLR 7 1 Q9Y3F4 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 76.899 0.036032 894700000 779290 708170 645600 662570 718040 687370 731410 804460 911130 849860 FALSE TRUE 748834.4852 687973.685 762274.2813 696765.3171 741136.4087 701269.0924 740361.2144 787847.6199 807702.3422 792298.2252 0.945142197 0.868326677 0.962105249 0.879423044 0.935426062 0.885107489 0.93444765 0.994382664 1.019442322 1 19.59568404 1.754294956 2.867268962 1.00924174 0.912184773 0.677095347 0.028524953 0.123454937 2.070421182 0.015067558 0.00705981 56.79301902 -1.754294956 -0.097056967 TFVNITPAEVGVLVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TFVNITPAEVGVLVGK 16 0 P07737;I3L3D5 P07737 PFN1 Profilin-1 0 ; 180.54 5.70E-09 152149000 389880 383010 335670 376930 372470 363380 374050 454010 473690 460840 FALSE TRUE 374643.0586 372086.9298 396333.0359 396383.4025 384450.8358 370727.7926 378627.7358 444634.5348 419918.6971 429626.8963 0.872019563 0.866069916 0.922505177 0.92262241 0.894848156 0.862906386 0.881294302 1.034931795 0.977403186 1 18.71272479 1.754338792 10.74613781 1.003677571 0.889824221 0.834117589 0.023537813 0.054623901 29.13070197 0.01165253 0.006370766 56.79875185 -1.754338792 -0.11385335 (ac)SAEVPEAASAEEQKEMEDKVTS(ph)PEKAEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEVPEAASAEEQKEMEDKVTSPEKAEEAK 30 3 P56211 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 S(0.021)AEVPEAAS(0.021)AEEQKEMEDKVT(0.145)S(0.812)PEKAEEAK 44.75 0.0052992 538010000 1030400 573770 485410 257940 580870 452540 516440 744390 768160 518210 TRUE FALSE 990130.8288 557406.6414 573134.3849 271252.3143 599554.2111 461690.6689 522760.3472 729018.0864 680961.6972 483111.1751 2.049488565 1.153785443 1.186340566 0.561469757 1.241027411 0.955661331 1.082070493 1.509006879 1.409534145 1 18.8819957 1.754343202 24.99999998 1.356016966 1.145684883 0.015896432 0.369073293 17.42277534 27631.56889 0.170113723 0.094336772 56.79932863 -1.754343202 -0.210332082 GSDFDCELR ddPTM_BT-474_Pertuzumab_2h_R1 8 GSDFDCELR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 193.28 7.86E-05 26537330000 9084300 9944570 8004230 9802050 9385000 9111270 9242300 9251400 9662850 9581800 FALSE TRUE 8729275.513 9660960.6 9450772.414 10307934.98 9686877.048 9295506.122 9355410.032 9060355.357 8565963.778 8932816.151 0.977214281 1.081513426 1.057983536 1.153940124 1.084414689 1.040601974 1.047308024 1.014277603 0.958932058 1 23.09068364 1.754355486 1.479968097 0.979971247 1.072066849 0.394509167 0.042481396 0.387337311 1.630368684 0.033648152 0.013279402 56.80093523 -1.754355486 0.092095602 KETES(ph)EAEDNLDDLEK ddPTM_BT-474_Pertuzumab_2h_R1 5 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KET(0.235)ES(0.765)EAEDNLDDLEK;KET(0.06)ES(0.94)EAEDNLDDLEK;KET(0.028)ES(0.972)EAEDNLDDLEK;KET(0.046)ES(0.954)EAEDNLDDLEK;KET(0.015)ES(0.985)EAEDNLDDLEK 310.88 7.20E-58 25779770000 15033630 11150540 9873400 7800660 10491950 10513720 11055720 14715730 15759060 12290520 TRUE FALSE 14446099.12 10832537.52 11657743.01 8203252.997 10829433.1 10726314.62 11191023.21 14411845.03 13970157.58 11458072.13 1.260779209 0.945406644 1.017426219 0.715936582 0.945135706 0.93613607 0.976693381 1.257789693 1.219241546 1 23.44986099 1.754379822 25 1.180620719 0.959714656 0.269575618 0.13954576 6.259258958 9903.828194 0.063901858 0.035436965 56.80411816 -1.754379822 -0.220906063 HVAEVLEYTKDEQLESLFQR ddPTM_BT-474_Pertuzumab_2h_R1 3 HVAEVLEYTKDEQLESLFQR 20 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;; 258.95 1.70E-36 1607727000 908971 825170 739426 783942 825157 812795 926108 688923 978786 948079 FALSE TRUE 873447.4084 801636.9595 873056.7266 824401.3406 851698.9243 829230.2718 937441.9867 674696.4993 867678.3167 883864.7649 0.988213857 0.906967889 0.987771842 0.932723391 0.963607735 0.938186819 1.06061699 0.763348112 0.981686737 1 19.75346612 1.754433828 25 0.891050722 0.963982011 0.07354225 0.071956586 9.223595085 14544.47518 0.030886096 0.017128093 56.81118238 -1.754433828 0.072931289 SAIDLT(ph)PIVVEDKEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAIDLTPIVVEDKEEK 16 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38;A0A2R8Y7X1 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 SAIDLT(1)PIVVEDKEEK 121.74 0.00015699 110430000 102900 72143 81598 68950 86116 75418 85024 112400 119060 124430 TRUE FALSE 98878.55424 70085.55228 96344.57374 72508.51776 88885.99935 76943.00363 86064.54915 110078.9007 105544.8079 116002.2453 0.852384831 0.604174101 0.830540594 0.62506133 0.766243784 0.663288917 0.741921408 0.948937673 0.909851423 1 16.8237932 1.754437623 4.269905706 0.949460375 0.719155061 0.635324125 0.078678641 0.11143779 4.354500451 0.036848689 0.01883842 56.81167882 -1.754437623 -0.230305314 LKEDILENEDEQNS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 4 LKEDILENEDEQNSPPK 17 1 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK 253.18 3.19E-27 2810000000 4591440 3518800 3134570 2875370 3450100 3437300 3667900 4678020 5491780 4630320 TRUE FALSE 4412001.449 3418447.269 3701056.527 3023768.19 3561075.6 3506804.561 3712788.857 4581417.252 4868376.158 4316704.302 1.022076367 0.791911382 0.857380137 0.700480732 0.824952406 0.812380074 0.860098028 1.061322929 1.127799316 1 22.04149884 1.75447957 3.709134133 1.075241487 0.828046267 0.619770034 0.080561033 0.125778476 3.586264305 0.042499745 0.0211808 56.81716633 -1.75447957 -0.24719522 VVIKLS(ph)PQACSFTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVIKLSPQACSFTK 14 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 VVIKLS(1)PQACSFTK;VVIKLS(1)PQACSFTK 134.21 2.43E-05 996830000 743380 658650 603150 598270 727680 662090 685480 817710 843210 815980 TRUE FALSE 714327.8877 639865.9469 712152.622 629146.7864 751086.4881 675477.9134 693869.1093 800824.0027 747492.3358 760712.9478 0.939024227 0.841139813 0.936164718 0.827048873 0.987345477 0.887953748 0.912130011 1.05272824 0.982620761 1 19.53699264 1.754572605 25 1.014124537 0.902772017 0.522426733 0.047014761 3.993672004 6242.870819 0.020080424 0.011135654 56.82933904 -1.754572605 -0.11135252 LQHFQELGEEKDNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQHFQELGEEKDNR 14 1 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0 Q13439-5 GOLGA4 Golgin subfamily A member 4 0 ; 171.67 1.79E-06 198461000 300930 244450 196429 202512 229060 251410 234690 280160 296210 255100 FALSE TRUE 289169.3229 237478.5253 231928.0898 212963.6686 236427.9229 256493.6825 237562.2064 274374.5981 262585.4826 237821.8498 1.215907299 0.99855638 0.975217753 0.895475621 0.994138777 1.078511847 0.998908244 1.153698024 1.10412682 1 17.85952174 1.754592404 24.99999999 1.100348354 1.015847907 0.092603112 0.086068764 10.55304716 16476.01434 0.040169868 0.022276687 56.83192994 -1.754592404 -0.084500447 DSSGSFS(ph)PCQPFLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSGSFSPCQPFLEK 15 0 Q6ZRI6;H3BMJ2;Q6ZRI6-2 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 1 DS(0.013)S(0.013)GS(0.06)FS(0.914)PCQPFLEK 69.261 0.052641 49526000 111260 116530 96605 104530 105230 116330 111600 137590 135050 140950 TRUE FALSE 106911.8362 113206.6785 114063.6725 109924.8058 108614.8185 118682.2723 112965.7942 134748.7184 119719.6902 131403.331 0.813615876 0.861520615 0.868042474 0.836545048 0.826575839 0.903190744 0.859687448 1.025458924 0.911085657 1 17.00364232 1.754601308 25 0.977770672 0.853977215 0.725854103 0.035508126 2.791636917 4356.041784 0.015550999 0.008623857 56.83309506 -1.754601308 -0.123793457 LPGGELNPGEDEVEGLKR ddPTM_BT-474_Pertuzumab_2h_R1 4 LPGGELNPGEDEVEGLKR 18 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;;; 207.43 1.19E-15 3627630000 1811911 1687699 1471110 1637780 1707721 1753800 1672048 2087399 2112503 1921126 FALSE TRUE 1741099.515 1639567.477 1736972.302 1722306.022 1762651.397 1789263.038 1692511.024 2044293.481 1872700.516 1791006.425 0.972134712 0.915444777 0.969830302 0.961641454 0.984168104 0.999026588 0.945005557 1.141421635 1.045613511 1 20.77233908 1.754604608 25 1.074575355 0.964302407 0.564960056 0.039150398 3.470687219 5414.508603 0.017215464 0.009546851 56.83352692 -1.754604608 -0.110272948 ES(ph)SPKKEETVASK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESSPKKEETVASK 13 2 J3QQY0 J3QQY0 MSL1 1 ES(0.5)S(0.5)PKKEETVASK 56.851 0.062101 81160000 105840 77240 84445 68347 90036 71014 86274 126350 127130 105780 TRUE FALSE 101703.6558 75037.19083 99706.08997 71874.39686 92932.08971 72449.95174 87329.84702 123740.8283 112698.7354 98615.42638 1.031315886 0.760907229 1.011059766 0.728835229 0.942368685 0.734671586 0.885559696 1.254781659 1.142810405 1 16.58952572 1.754669373 24.99997975 1.151783048 0.863922862 0.512543687 0.116441268 3.81139576 5922.092846 0.048970743 0.027157088 56.84200295 -1.754669373 -0.287860187 MFYEEHLHLDDEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 MFYEEHLHLDDEIR 14 0 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 250.8 8.85E-19 52030000 28739 33381 27697 37471 28558 25062 34282 1433.7 26108 17887 FALSE TRUE 27615.84811 32429.00656 32702.46402 39404.8828 29476.59401 25568.77081 34701.55337 1404.093594 23144.32929 16675.49756 1.65607341 1.944709982 1.961108741 2.363040903 1.76765904 1.533313817 2.080990582 0.084201001 1.387924361 1 14.02544219 1.75470815 24.99999863 0.758302309 1.903482787 0.638152635 0.370629521 3.194751523 4952.025853 0.162537457 0.090135795 56.84707842 -1.75470815 1.145180478 INHEGEVNR ddPTM_BT-474_Pertuzumab_2h_R1 5 INHEGEVNR 9 0 Q09028-3;Q09028;Q09028-2;Q09028-4;Q16576;E9PC52;Q16576-2;Q5JP01 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 ;;;; 154.84 7.47E-05 9361630000 5517874 5529569 4666310 5738794 5545208 4953316 5728896 4226738 5722227 5732611 FALSE TRUE 5302229.384 5371871.106 5509616.019 6034973.846 5723574.651 5053475.443 5799007.943 4139454.383 5072663.78 5344336.151 0.992121235 1.005152175 1.030926174 1.129227967 1.070960825 0.945575896 1.085075448 0.774549779 0.949166302 1 22.34957932 1.754731059 25 0.887551532 1.036883392 0.390882562 0.072529155 4.91770809 7611.880025 0.032535838 0.018042877 56.85007729 -1.754731059 0.14933186 MVVNEGSDGGQSVYHVHLHVLGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 MVVNEGSDGGQSVYHVHLHVLGGR 24 0 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ;; 282.86 1.34E-52 4994440000 1162970 1562340 1221190 1699470 1530450 1468840 1491980 646969 1422040 866900 FALSE TRUE 1117519.847 1517783.593 1441886.198 1787179.85 1579678.314 1498540.951 1510239.298 633608.8641 1260615.981 808184.0908 1.382754077 1.878017162 1.784106139 2.211352427 1.954602091 1.854207436 1.86868229 0.783990766 1.559812913 1 19.62432443 1.754743876 25 1.11415336 1.864748506 0.620836089 0.262294346 3.516859558 5439.258957 0.1167761 0.064758836 56.85175497 -1.754743876 0.750595146 HSSLAGCQIINYR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSSLAGCQIINYR 13 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 183.79 1.01E-05 1689070000 915210 1472130 1115120 1681370 1253140 1382640 1347460 1075610 1089770 1410630 FALSE TRUE 879442.5814 1430146.294 1316646.99 1768145.707 1293448.386 1410597.928 1363950.619 1053398.278 966063.8783 1315086.774 0.6687335 1.087491961 1.001186398 1.344508775 0.983546038 1.072627264 1.037156366 0.801010472 0.734600863 1 20.32672657 1.754801683 6.569040702 0.827453037 1.041724796 0.195624305 0.166778284 0.212826094 25.81232824 0.079579476 0.042570701 56.85932279 -1.754801683 0.214271759 PQSPVIQAAAVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 PQSPVIQAAAVSPK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 PQSPVIQAAAVS(1)PK;PQSPVIQAAAVS(1)PK;PQSPVIQAAAVS(1)PK;PQSPVIQAAAVS(1)PK 168.08 3.72E-06 642880000 813650 616620 662090 586520 725450 654950 863950 914170 1253320 1093310 TRUE FALSE 781851.6585 599034.6013 781744.3911 616790.3675 748784.7581 668193.5377 874523.2785 895292.07 1111048.368 1019259.14 0.767078388 0.587715702 0.766973148 0.605135969 0.734636295 0.655567865 0.857998957 0.878375317 1.090054849 1 19.95908946 1.754831279 1.368928913 1.039212677 0.681866508 0.793430464 0.070946126 0.158473745 0.564028292 0.050982509 0.020016728 56.86319773 -1.754831279 -0.35734617 IDS(ph)PGFKPASQQVYR ddPTM_BT-474_Pertuzumab_2h_R1 7 IDSPGFKPASQQVYR 15 1 A0A087X0K9;G5E9E7;Q07157-2 A0A087X0K9 TJP1 Tight junction protein ZO-1 1 IDS(0.999)PGFKPAS(0.001)QQVYR;IDS(1)PGFKPASQQVYR;IDS(0.999)PGFKPAS(0.001)QQVYR;IDS(1)PGFKPASQQVYR;IDS(1)PGFKPASQQVYR;IDS(1)PGFKPASQQVYR;IDS(1)PGFKPASQQVYR 243.97 3.18E-18 7732840000 6731943 6110739 5563651 4618315 5210316 5026460 6202689 7169725 8467915 7950178 TRUE FALSE 6468851.225 5936466.707 6569126.498 4856666.791 5377910.546 5128098.465 6278599.363 7021667.673 7506672.79 7411705.363 0.872788503 0.80095827 0.886317814 0.655269813 0.725596915 0.691891841 0.847119395 0.947375446 1.012813168 1 22.8213741 1.754846416 2.415138494 0.999889695 0.771453862 0.657508803 0.069437068 0.171609802 2.035685421 0.046438157 0.020703181 56.86517977 -1.754846416 -0.228435833 YIASTQRPDGTWR ddPTM_BT-474_Pertuzumab_2h_R1 3 YIASTQRPDGTWR 13 1 Q9BRP8-2;Q9BRP8 Q9BRP8-2 WIBG Partner of Y14 and mago 0 ;; 140.53 3.59E-05 1091430000 804330 1040290 928300 1124840 1047470 1046800 999080 635100 884620 871510 FALSE TRUE 772895.8944 1010621.948 1096064.46 1182893.127 1081162.824 1067967.013 1011307.04 621984.9631 784201.6462 812481.8514 0.951277734 1.243870181 1.349032545 1.455900984 1.33069166 1.3144503 1.24471339 0.765537054 0.965192816 1 19.63197606 1.754857224 25 0.896270991 1.283221485 0.595738152 0.135350394 3.79874726 5834.310403 0.064153788 0.035576771 56.86659496 -1.754857224 0.386950494 YKDLDEDELLGNLS(ph)ETELK ddPTM_BT-474_Pertuzumab_2h_R1 4 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 1 YKDLDEDELLGNLS(0.979)ET(0.021)ELK;YKDLDEDELLGNLS(0.999)ET(0.001)ELK;YKDLDEDELLGNLS(0.999)ET(0.001)ELK;YKDLDEDELLGNLS(0.985)ET(0.015)ELK 254.29 4.07E-31 638510000 1265200 996640 863260 714620 876420 899180 919740 1315970 1350850 1184810 TRUE FALSE 1215754.585 968216.803 1019270.285 751501.6238 904610.8452 917362.0357 930996.0532 1288794.76 1197507.171 1104561.763 1.100666912 0.876561941 0.922782518 0.680361795 0.81897715 0.830521267 0.84286464 1.166792843 1.084146863 1 20.07504266 1.754866137 13.21260573 1.093009987 0.859509088 0.466156171 0.105589081 0.179519318 140.969031 0.050077606 0.027567785 56.86776192 -1.754866137 -0.233500899 KSS(ph)GTGTEPVAK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSSGTGTEPVAK 12 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 KS(0.213)S(0.767)GT(0.019)GTEPVAK;KS(0.015)S(0.983)GT(0.001)GTEPVAK;KS(0.001)S(0.991)GT(0.005)GT(0.003)EPVAK 199.84 1.77E-07 875481000 659130 563420 531740 554120 599450 603310 602400 726160 776560 781870 TRUE FALSE 633370.4709 547351.8132 627837.2465 582718.1996 618731.8537 615509.3416 609772.3514 711164.5422 688408.1644 728913.2485 0.86892435 0.750914892 0.86133329 0.799434227 0.848841553 0.844420571 0.836549963 0.975650455 0.944430858 1 19.4753876 1.75487388 4.587385605 0.970939004 0.827472244 0.782742008 0.034557196 0.078805984 3.645973476 0.016653463 0.008611136 56.86877586 -1.75487388 -0.14346676 ALDYYGLYDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDYYGLYDDR 11 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 0 130.98 0.0024976 0 91192 118150 97315 118090 96954 101580 110240 89313 104730 124030 FALSE TRUE 87628.11582 114780.4777 114901.9853 124184.6391 100072.6135 103634.0172 111589.1501 87468.65534 92841.48946 115629.3376 0.757836356 0.992658784 0.993709621 1.07398902 0.865460406 0.89626058 0.965059148 0.75645729 0.802923301 1 16.81914796 1.754899434 24.99994081 0.829535072 0.940653988 0.108543071 0.100023609 9.39317356 14389.16157 0.045328159 0.025136993 56.87212217 -1.754899434 0.111118916 KPHLQGKPGRPLS(ph)PANVPALPGETVTSPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPHLQGKPGRPLSPANVPALPGETVTSPVR 30 3 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 1 KPHLQGKPGRPLS(1)PANVPALPGETVTSPVR;KPHLQGKPGRPLS(1)PANVPALPGETVTSPVR 143.22 3.31E-08 4886600000 2827700 2848400 2608600 2701600 2277100 2597400 2614600 3182900 3191500 3000100 TRUE FALSE 2717190.358 2767166.421 3080032.048 2841029.9 2350344.99 2649921.208 2646598.257 3117172.003 2829214.3 2796900.555 0.971500525 0.989368898 1.101230447 1.015777946 0.840339134 0.947449205 0.946261122 1.114509416 1.011553412 1 21.41539753 1.754924164 25 1.052307737 0.974228621 0.173930103 0.067664068 9.94808169 15216.18193 0.03363281 0.018650973 56.87536074 -1.754924164 -0.078079117 DISGPS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 DISGPSPSK 9 0 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DIS(0.063)GPS(0.935)PS(0.001)K;DIS(0.001)GPS(0.898)PS(0.101)K;DISGPS(1)PSK;DISGPS(0.999)PS(0.001)K 202.68 2.04E-05 4742870000 4801560 4153230 3821500 3557770 3846250 3889570 4026490 4919400 5313800 4634770 TRUE FALSE 4613909.727 4034783.947 4512130.059 3741386.936 3969968.124 3968219.77 4075767.389 4817812.671 4710599.701 4320852.9 1.067823838 0.933793406 1.04426838 0.865890838 0.918792705 0.918388073 0.943278441 1.115014277 1.090201359 1 22.04288469 1.754927315 12.86196277 1.07632068 0.952220266 0.399057527 0.062841218 0.181140571 136.1521684 0.028864676 0.015878616 56.87577338 -1.754927315 -0.124100413 DEILPTT(ph)PISEQK ddPTM_BT-474_Pertuzumab_2h_R1 6 DEILPTTPISEQK 13 0 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 1 DEILPT(0.012)T(0.988)PISEQK;DEILPT(0.012)T(0.988)PISEQK;DEILPT(0.049)T(0.951)PISEQK;DEILPT(0.011)T(0.989)PISEQK;DEILPT(0.169)T(0.831)PISEQK;DEILPT(0.002)T(0.998)PISEQK 357.57 3.21E-75 35689300000 18016000 15013900 13918400 13377300 14417400 14746200 14966400 18322000 19215000 16603700 TRUE FALSE 17311914.8 14585718.27 16433764.49 14067704.06 14881148.76 15044378.27 15149563.28 17943644.3 17033793.76 15479116.61 1.118404573 0.942283635 1.061673279 0.908818275 0.961369382 0.971914525 0.97870981 1.159216301 1.100437072 1 23.8838198 1.754933498 25 1.100716134 0.9875222 0.284696166 0.067409741 6.006309013 9181.765553 0.029404419 0.016306299 56.8765831 -1.754933498 -0.113193934 CPHVTEHIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 CPHVTEHIPR 10 0 P48449-2;P48449;A0A0G2JQD0;P48449-3 P48449-2 LSS Lanosterol synthase 0 ; 116.52 0.00062437 163350000 154994 186842 151493 249910 153007 165293 206979 95042 187226 187918 FALSE TRUE 148936.6631 181513.4491 178871.155 262807.885 157928.6091 168635.3377 209512.0709 93079.34949 165972.8894 175190.1465 0.850142923 1.03609394 1.021011505 1.500129376 0.901469702 0.962584604 1.195912414 0.531304707 0.947387126 1 17.41856211 1.754952772 25 0.783103237 1.070128327 0.212169014 0.207396787 7.588561905 11586.87265 0.093988791 0.052121935 56.87910737 -1.754952772 0.287025091 EHNSMWASLS(ph)SPDAEAVEPDFSSIER ddPTM_BT-474_Pertuzumab_2h_R1 1 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNS(0.146)MWAS(0.095)LS(0.38)S(0.38)PDAEAVEPDFSSIER 57.432 0.0042978 0 12040 13860 13981 14748 13874 14009 14961 7446.1 10432 16816 TRUE FALSE 11569.46349 13464.72637 16507.67771 15509.14605 14320.26981 14292.27158 15144.09719 7292.335433 9247.803095 15677.03734 0.737987876 0.858882076 1.052984524 0.989290624 0.913455106 0.911669167 0.966005047 0.465160303 0.589894818 1 13.93636532 1.754971158 25 0.634587189 0.923735087 0.320880193 0.150325756 5.356829101 8170.092305 0.06669353 0.036985287 56.88151543 -1.754971158 0.289147898 KSS(ph)LGNDETDKEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSSLGNDETDKEK 13 2 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;A0A0J9YWK3;A0A3B3IU00;O75128-5;O75128-4 H7C1N2;O75128-3 COBL Protein cordon-bleu 1 KS(0.105)S(0.895)LGNDETDKEK;KS(0.003)S(0.997)LGNDETDKEK;KS(0.139)S(0.859)LGNDET(0.001)DKEK 217.35 2.98E-07 516120000 650390 502680 393510 318042 449520 375030 454970 688120 689630 545360 TRUE FALSE 624972.0398 488344.0586 464626.0106 334456.1857 463979.219 382613.3636 460538.059 673910.0815 611346.0936 508422.2814 1.229238101 0.960508767 0.913858475 0.657831488 0.91258632 0.752550345 0.905818009 1.325492816 1.202437651 1 18.95566773 1.754991182 24.99999577 1.202503481 0.892096401 0.377282646 0.158086584 5.54152427 8441.467637 0.073887509 0.040974607 56.88413805 -1.754991182 -0.310407079 TLSLEPEESLDVSET(ph)EGEQILK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLSLEPEESLDVSETEGEQILK 22 0 A0A0C4DGW2;P57768-2;P57768 A0A0C4DGW2 SNX16 Sorting nexin-16 1 TLSLEPEES(0.014)LDVS(0.433)ET(0.553)EGEQILK 65.784 0.083148 23576000 15094 15916 12488 14810 13348 15359 14445 18289 17347 18122 TRUE FALSE 14504.10979 15462.09126 14744.85939 15574.34587 13777.35054 15669.5695 14621.78223 17911.32576 15377.84128 16894.5808 0.85850664 0.915210117 0.872756748 0.921854532 0.81548934 0.927490874 0.865471739 1.060181722 0.910223312 1 14.04427293 1.755022656 25 0.993423469 0.883966867 0.530448347 0.046403957 4.159217922 6323.65672 0.019482124 0.010803976 56.88826074 -1.755022656 -0.109456602 TVQS(ph)PNSSVPSPGLAGPVTMTSVHPPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVQSPNSSVPSPGLAGPVTMTSVHPPIR 28 0 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 T(0.036)VQS(0.957)PNS(0.006)S(0.001)VPSPGLAGPVTMTSVHPPIR 124.69 2.58E-05 165480000 38685 50086 38419 47713 39467 56245 45827 40722 45646 49677 TRUE FALSE 37173.14743 48657.59632 45362.16793 50175.47365 40736.4919 57382.31244 46387.84453 39881.07647 40464.45744 46312.33254 0.802661956 1.050640157 0.979483551 1.083414954 0.879603545 1.23902877 1.001630494 0.86113297 0.873729636 1 15.4991088 1.755038011 24.99557399 0.899706183 1.013137002 0.116448453 0.115321279 10.52799977 15988.98008 0.051082712 0.02832834 56.89027215 -1.755038011 0.113430819 AS(ph)PHATPSTLHFPTSPIIQQPGPYFSHPAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPHATPSTLHFPTSPIIQQPGPYFSHPAIR 31 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;B1AKN6 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 AS(0.968)PHAT(0.03)PS(0.001)T(0.001)LHFPTSPIIQQPGPYFSHPAIR;AS(0.907)PHAT(0.031)PS(0.031)T(0.031)LHFPTSPIIQQPGPYFSHPAIR 172.26 9.40E-13 1099930000 114289 153103 110224 143752 127803 136358 145927 84646 131641 144681 TRUE FALSE 109822.4595 148736.6523 130143.9287 151171.0579 131913.8996 139115.2522 147712.8983 82898.03052 116697.6656 134881.627 0.814213633 1.102719886 0.96487514 1.120768346 0.977997541 1.031387708 1.095129867 0.614598388 0.865185779 1 17.04133432 1.755050117 25 0.790882674 1.019962852 0.32029756 0.122575184 5.34301778 8109.952618 0.052211059 0.028953985 56.89185789 -1.755050117 0.229080178 SPMFPALGEAS(ph)SDDDLFQSAKPKPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPMFPALGEASSDDDLFQSAKPKPAK 26 2 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;Q5SRD0 Q641Q2;A0A0A0MR88 FAM21A;FAM21C;FAM21D WASH complex subunit FAM21A;WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 1 SPMFPALGEAS(0.704)S(0.296)DDDLFQSAKPKPAK 270.45 9.22E-61 580960000 512500 455210 409500 368180 463650 454890 467870 569560 676950 566190 TRUE FALSE 492470.9334 442227.8565 483505.7593 387181.8139 478563.7233 464088.1875 473595.933 557798.387 600105.474 527841.447 0.932990269 0.837804343 0.916005672 0.733519158 0.906642944 0.879218921 0.897231424 1.056753671 1.136904799 1 19.00974511 1.755050755 3.156229472 1.078643198 0.865488396 0.680485498 0.060691461 0.119257894 2.424254246 0.03293342 0.0158355 56.89194156 -1.755050755 -0.213154802 YMEDVTQIVVEPEPTAEEKPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 YMEDVTQIVVEPEPTAEEKPSPR 23 1 O15297-2;O15297 O15297-2 PPM1D Protein phosphatase 1D 1 YMEDVTQIVVEPEPT(0.007)AEEKPS(0.993)PR;YMEDVTQIVVEPEPT(0.014)AEEKPS(0.986)PR;YMEDVTQIVVEPEPT(0.01)AEEKPS(0.99)PR 160.99 1.11E-11 411941000 314095 278040 219452 264982 263792 258463 273462 325952 331853 331120 TRUE FALSE 301819.8201 270110.5714 259111.8581 278657.7528 272277.1092 263689.2989 276808.7098 319220.9773 294182.4387 308692.9475 0.977734745 0.875013743 0.839383796 0.902702038 0.882032167 0.854212256 0.896712128 1.034105184 0.952993715 1 18.235813 1.755080271 25 0.996084928 0.886027531 0.603495965 0.039300443 3.766968415 5707.279033 0.017621594 0.009772106 56.89580827 -1.755080271 -0.110057397 HLMTLVMDPLQTASVQWFER ddPTM_BT-474_Pertuzumab_2h_R1 1 HLMTLVMDPLQTASVQWFER 20 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY6 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 200.99 1.30E-21 102170000 124990 149240 120830 126520 143820 164660 142820 121480 155980 133120 FALSE TRUE 120105.2526 144983.8213 142666.6688 133049.7124 148446.1009 167989.538 144567.8739 118971.3955 138273.8043 124103.6638 0.967781683 1.168247712 1.149576608 1.072085289 1.196145999 1.353622712 1.164896099 0.958645312 1.114179872 1 16.92118618 1.755098681 25 1.023886118 1.159874962 0.263574304 0.098306601 8.122462028 12292.50169 0.046845736 0.025978284 56.89822013 -1.755098681 0.135988845 GGIDNPAITS(ph)DQELDDKK ddPTM_BT-474_Pertuzumab_2h_R1 4 GGIDNPAITSDQELDDKK 18 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GGIDNPAIT(0.141)S(0.859)DQELDDKK;GGIDNPAIT(0.02)S(0.98)DQELDDKK;GGIDNPAIT(0.006)S(0.994)DQELDDKK;GGIDNPAIT(0.026)S(0.974)DQELDDKK 232.87 6.76E-22 5678500000 3925390 3160050 3018270 2312270 3303190 2968730 3194540 4017850 4638800 3752210 TRUE FALSE 3771981.419 3069928.468 3563738.53 2431606.532 3409440.106 3028759.755 3233635.736 3934879.993 4112222.871 3498069.475 1.078303746 0.877606488 1.018772942 0.695128141 0.974663348 0.865837507 0.924405807 1.124871882 1.175569239 1 21.73812751 1.755108583 5.465142408 1.112146846 0.912221109 0.381067232 0.105012141 0.156791135 11.33005884 0.049698711 0.026237411 56.89951741 -1.755108583 -0.199925737 LSSGPEQITLEASS(ph)TEGHPGAPSPQHTDQTEAFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 LSSGPEQITLEAS(0.036)S(0.482)T(0.482)EGHPGAPSPQHTDQTEAFQK;LSSGPEQITLEAS(0.017)S(0.492)T(0.492)EGHPGAPSPQHTDQTEAFQK 211.26 6.13E-28 388430000 89189 116936 77464 102063 114967 116549 112349 80565 111182 113670 TRUE FALSE 85703.39528 113601.0998 91463.46798 107330.4837 118665.018 118905.7006 113723.9607 78901.3046 98561.08547 105971.0297 0.808743631 1.072001472 0.863098795 1.012828544 1.119787345 1.122058557 1.073160854 0.744555421 0.930075756 1 16.69331039 1.755149349 25 0.867732395 1.015569957 0.174156991 0.114581155 8.499246411 12823.38944 0.052973864 0.029377084 56.9048586 -1.755149349 0.147837562 TDS(ph)PWIKPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDSPWIKPAR 10 1 A0A1B0GV09;Q9H9B1-3;Q9H9B1;A0A0C4DGF8;A0A1B0GU48;Q9H9B1-4;A0A1W2PPZ7;A0A0D9SEQ1;A0A1B0GVZ8;A0A1B0GUD1;A0A0D9SER9 A0A1B0GV09 EHMT1 Histone-lysine N-methyltransferase EHMT1 1 T(0.002)DS(0.998)PWIKPAR;T(0.001)DS(0.999)PWIKPAR 189.33 6.20E-07 281450000 650800 504180 485920 438740 467220 496060 509330 673110 655610 628550 TRUE FALSE 625366.0165 489801.28 573736.5532 461383.424 482248.5556 506090.6731 515563.3329 659210.0433 581187.9013 585977.7486 1.067218027 0.835870101 0.979109795 0.787373625 0.822981004 0.863668756 0.879834318 1.124974532 0.991825889 1 19.16048636 1.755156082 25 1.047781752 0.884506437 0.394921939 0.083515206 5.418009306 8171.197669 0.037267674 0.020667185 56.90574085 -1.755156082 -0.163275315 QRS(ph)PLLNQPVPELSHASLIANQSPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 QRSPLLNQPVPELSHASLIANQSPFR 26 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR 226.85 8.77E-35 1496470000 579280 624320 628680 591730 648130 586230 626340 348580 566040 509400 TRUE FALSE 556641.0972 606515.0049 742296.4609 622269.2562 668977.6901 598083.9723 634005.3363 341381.7012 501785.5122 474897.8843 1.172127979 1.277148256 1.56306542 1.310322233 1.408676922 1.259394897 1.335035083 0.718852858 1.056617704 1 18.8572578 1.755169596 25 0.907209549 1.338304856 0.683950871 0.126592277 3.131019839 4718.214777 0.056769847 0.031481998 56.90751161 -1.755169596 0.431095307 EAMEDGEIDGNKVTLDWAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAMEDGEIDGNKVTLDWAK 19 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 235.7 3.29E-24 1334380000 1569430 1331090 1308230 1256210 1384930 1338610 1464780 1833360 2023710 2044400 FALSE TRUE 1508094.941 1293128.616 1544656.262 1321043.149 1429477.531 1365677.611 1482706.416 1795500.475 1793986.925 1905930.967 0.791264199 0.678476104 0.81044712 0.693122244 0.750015376 0.716540963 0.7779434 0.942059553 0.941265427 1 20.86206443 1.755209156 2.779879885 0.966652131 0.738450021 0.860734002 0.0400961 0.076565191 1.204853361 0.02171745 0.010096876 56.9126956 -1.755209156 -0.228202111 IEEDNLTYQHLLPES(ph)PEPSASHALSDYETSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEEDNLTYQHLLPESPEPSASHALSDYETSEK 32 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 IEEDNLT(0.006)Y(0.001)QHLLPES(0.981)PEPS(0.005)AS(0.006)HALS(0.001)DYETSEK;IEEDNLTYQHLLPES(0.997)PEPS(0.003)ASHALSDYETSEK 329.79 1.01E-116 297344000 158871 174149 143794 177421 182315 184622 172757 127685 155848 178669 TRUE FALSE 152662.1457 169182.441 169780.7745 186577.7191 188179.3275 188355.1833 174871.2518 125048.2601 138156.7884 166567.5895 0.91651771 1.015698441 1.019290577 1.120132192 1.129747558 1.130803321 1.049851609 0.750735846 0.829433798 1 17.34574818 1.755251776 25 0.839147346 1.060069187 0.521213749 0.084612981 4.324568526 6484.674314 0.039796345 0.02206927 56.91828107 -1.755251776 0.220921841 S(ph)TENVNKLPELSSFGKPSSSVQGTGLIR ddPTM_BT-474_Pertuzumab_2h_R1 3 STENVNKLPELSSFGKPSSSVQGTGLIR 28 2 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 S(0.812)T(0.188)ENVNKLPELSSFGKPSSSVQGTGLIR;S(0.973)T(0.027)ENVNKLPELSSFGKPSSSVQGTGLIR;S(0.957)T(0.043)ENVNKLPELSSFGKPSSSVQGTGLIR 177.6 9.23E-18 4142670000 3111660 2864300 2221500 2198600 2615240 2545620 2528180 3164800 3266320 2732020 TRUE FALSE 2990052.887 2782612.968 2622974.467 2312070.009 2699361.57 2597094.181 2559120.623 3099445.774 2895541.047 2546977.852 1.173961087 1.092515573 1.029837957 0.90776997 1.059829228 1.019676782 1.004767521 1.216911161 1.136853642 1 21.28035498 1.755272472 25 1.138903923 1.037488457 0.142610542 0.08112265 8.977626228 13445.21585 0.037835896 0.020982171 56.92099353 -1.755272472 -0.101415465 NATDLQNSSMS(ph)EEELTK ddPTM_BT-474_Pertuzumab_2h_R1 1 NATDLQNSSMSEEELTK 17 0 Q5QNY5;P40855;P40855-5;H0YJ60 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 1 NATDLQNSS(0.023)MS(0.976)EEELTK 335.14 3.90E-72 268380000 313890 272120 257040 235500 293390 267170 277790 333360 334630 335140 TRUE FALSE 301622.8318 264359.404 303492.8458 247654.1832 302827.1558 272572.3605 281189.6771 326475.9995 296644.2053 312440.6693 0.965376346 0.846110734 0.971361528 0.792643876 0.969230915 0.872397185 0.899977835 1.044921585 0.949441716 1 18.25322273 1.75530617 25 1.000048583 0.900116846 0.36113686 0.058242171 5.876633772 8783.3265 0.024306314 0.013479178 56.92541032 -1.75530617 -0.099931738 KFNHDGEEEEEDDDYGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KFNHDGEEEEEDDDYGSR 18 1 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 183.56 4.07E-14 205440000 138200 133550 101360 143540 139700 135910 133590 124130 137970 132530 FALSE TRUE 132798.9912 129741.2848 119678.0067 150948.1166 144193.5774 138658.1933 135224.9144 121566.6721 122308.224 123553.6251 1.074828773 1.050080762 0.968632095 1.221721471 1.167052584 1.122251114 1.09446335 0.983918295 0.989920158 1 16.91477781 1.755308414 5.234269828 0.990236449 1.101482561 0.379685094 0.063553092 0.200854805 12.93768779 0.034699295 0.018245795 56.92570449 -1.755308414 0.111246112 PTHSGGGGGGGGGGGGGGGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 PTHSGGGGGGGGGGGGGGGGR 21 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ;; 182.28 4.73E-17 68731000 41058.2 42132.6 34304.6 41509.1 36396.4 40617 42543.3 35543.9 46597.8 42744.7 FALSE TRUE 39453.60015 40931.0195 40504.20432 43651.38963 37567.12326 41438.30357 43063.95763 34809.90604 41308.2131 39849.5634 0.990063549 1.027138468 1.016427807 1.095404464 0.942723585 1.039868446 1.080663223 0.873532934 1.036603907 1 15.2822763 1.75533851 25 0.958107549 1.02686294 0.17150771 0.05601221 8.655595889 12911.84617 0.024537028 0.013607 56.92964949 -1.75533851 0.06875539 TLRES(ph)DSAEGDEAESPEQQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLRESDSAEGDEAESPEQQVR 21 1 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 T(0.425)LRES(0.565)DS(0.01)AEGDEAESPEQQVR 125.12 1.11E-05 0 34733 48634 36233 44212 51746 52068 39289 28230 25915 23924 TRUE FALSE 33375.59596 47247.00594 42781.1091 46493.78662 53410.45708 53120.85063 39769.83053 27647.04063 22973.23784 22303.60617 1.496421507 2.118357255 1.918125202 2.084586065 2.394700511 2.381715774 1.783112122 1.239577153 1.030023471 1 14.44498937 1.755353785 2.538618742 1.041337213 2.077225973 0.767878806 0.240755787 0.12370165 1.621962177 0.154413199 0.069922361 56.93165189 -1.755353785 1.03588876 KGS(ph)FSALVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 KGSFSALVGR 10 1 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 1 KGS(0.848)FS(0.152)ALVGR;KGS(1)FSALVGR;KGS(1)FSALVGR 180.84 1.20E-06 2674790000 2847050 3150240 2330350 2323790 2872090 2715980 2726230 3656110 3809460 3559640 TRUE FALSE 2735784.138 3060398.24 2751496.083 2443721.08 2964473.383 2770898.976 2759594.418 3580610.051 3377026.071 3318542.412 0.824393302 0.92221158 0.829127895 0.736383863 0.89330586 0.834974706 0.831568223 1.078970706 1.017623297 1 21.66211828 1.755409855 9.138031622 1.034365139 0.839623762 0.763351545 0.049305057 0.061979613 20.50629606 0.02350442 0.012778366 56.93900254 -1.755409855 -0.194741376 SGPKPFSAPKPQTS(ph)PS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFSAPKPQT(0.405)S(0.597)PS(0.998)PKR 83.606 0.00478 1661300000 419300 306180 301620 210790 297690 388310 339410 423490 530830 484760 TRUE FALSE 402913.2924 297448.0462 356129.4435 221668.8972 307265.4692 396161.8943 343563.8011 414744.7835 470572.4038 451926.7734 0.891545525 0.658177527 0.788024663 0.490497377 0.679901009 0.876606383 0.760220065 0.917725631 1.041258079 1 18.7857295 1.755453172 1.12832642 1.029730369 0.705189817 0.548958149 0.107725485 0.352819027 0.837299774 0.090940746 0.03619973 56.94468206 -1.755453172 -0.324540552 RDS(ph)LGAYASQDANEQGQDLGKR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDSLGAYASQDANEQGQDLGKR 22 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGAYASQDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR;RDS(0.966)LGAYAS(0.034)QDANEQGQDLGKR;RDS(0.979)LGAY(0.001)AS(0.02)QDANEQGQDLGKR 189.12 1.77E-17 3899250000 1271070 1229330 934260 950090 1083080 1120420 1121070 1386310 1407440 1337120 TRUE FALSE 1221395.179 1194270.712 1103101.565 999124.2588 1117918.252 1143075.66 1134789.99 1357682.214 1247673.312 1246555.671 0.97981599 0.958056459 0.884919615 0.801507932 0.896805716 0.916987252 0.910340401 1.089146875 1.000896583 1 20.24951588 1.755483634 24.99999703 1.035905835 0.903983674 0.557266983 0.050149408 4.621469658 6834.801091 0.024715831 0.013706206 56.94867638 -1.755483634 -0.131922161 AVAFQNPQTHVIENLHAAAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVAFQNPQTHVIENLHAAAYR 21 0 H3BP04;H3BSJ9;H3BRG4;P22695 H3BP04 UQCRC2 "Cytochrome b-c1 complex subunit 2, mitochondrial" 0 80.752 0.0035022 997750000 633310 693410 728270 565000 564950 743690 685550 413880 638560 600550 FALSE TRUE 608559.545 673634.6257 859884.5893 594159.7177 583122.1298 758727.9213 693939.966 405333.2334 566073.3459 559874.2136 1.086957624 1.203189233 1.535853176 1.06123787 1.041523463 1.355175686 1.239456916 0.723971963 1.011072366 1 19.09474321 1.755494095 25 0.891075728 1.221814141 0.440666765 0.157393488 5.443394671 8045.386478 0.072893664 0.040423627 56.95004812 -1.755494095 0.330738413 KET(ph)ESEAEDNLDDLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KET(0.973)ES(0.027)EAEDNLDDLEK;KET(0.568)ES(0.432)EAEDNLDDLEK 148.24 5.57E-07 801460000 449060 386360 345190 327090 369890 417120 382580 494510 525330 403760 TRUE FALSE 431510.2387 375341.3911 407573.5117 343971.1541 381787.8478 425554.4522 387262.1285 484298.1957 465696.7408 376412.9756 1.146374506 0.997153168 1.082782843 0.913813222 1.014279189 1.130552026 1.028822473 1.286613978 1.2371963 1 18.52195684 1.755494862 24.99999921 1.201578914 1.041534975 0.271288596 0.094306654 6.433583419 9508.462703 0.041684619 0.023116415 56.95014866 -1.755494862 -0.160043939 HSCDALNR ddPTM_BT-474_Pertuzumab_2h_R1 6 HSCDALNR 8 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;Q6XYB5;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;;;; 185.47 0.00021261 1393400000 496614 627592 605991 710450 605808 524360 622100 413489 468959 567523 FALSE TRUE 477205.7758 609693.6906 715507.0539 747116.4096 625294.3645 534962.9185 629713.4459 404950.3077 415724.7404 529084.1617 0.901946817 1.152356723 1.352350166 1.412093696 1.181842908 1.011111194 1.190195231 0.765379758 0.785744066 1 19.01313771 1.755552099 8.268994303 0.834966558 1.181569158 0.488454619 0.150096817 0.114347977 27.83898006 0.076043465 0.04117828 56.95765473 -1.755552099 0.3466026 KEAEDSLRR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEAEDSLRR 9 2 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;; 153.12 4.43E-05 1051090000 2320070 2506420 1807540 2102390 2178160 2281410 2290680 2399980 2659090 2600390 FALSE TRUE 2229399.099 2434939.356 2134202.687 2210894.6 2248222.495 2327541.673 2318714.027 2350419.574 2357241.251 2424263.269 0.919619221 1.004403848 0.880351038 0.911986181 0.927383805 0.960102685 0.956461312 0.969539738 0.972353655 1 21.20911495 1.755557319 0.802866038 0.993534236 0.930354798 0.363511019 0.030079492 0.697407975 0.863687438 0.027303527 0.012383022 56.95833942 -1.755557319 -0.063179437 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNK ddPTM_BT-474_Pertuzumab_2h_R1 4 YKLDEDEDEDDADLSKYNLDASEEEDSNK 29 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLSKYNLDAS(1)EEEDSNK;YKLDEDEDEDDADLSKYNLDAS(0.999)EEEDS(0.001)NK;YKLDEDEDEDDADLS(0.003)KYNLDAS(0.997)EEEDSNK;YKLDEDEDEDDADLS(0.001)KY(0.001)NLDAS(0.993)EEEDS(0.005)NK 176.86 7.16E-18 3193030000 1468814 931882 886999 525935 902279 878598 908725 1282488 1455828 984476 TRUE FALSE 1411411.125 905305.6378 1047299.45 553078.5684 931301.6235 896363.8535 919846.2484 1256004.175 1290568.509 917796.5636 1.53782568 0.986390311 1.141101952 0.602615645 1.014714655 0.976647646 1.002233267 1.368499539 1.406159665 1 19.80781488 1.75557262 11.88539086 1.288806784 1.019446213 0.147180993 0.237502186 0.273699327 174.3644067 0.109482243 0.060097729 56.96034617 -1.75557262 -0.269360572 VWS(ph)PLVTEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VWSPLVTEEGK 11 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(1)PLVTEEGK;VWS(1)PLVTEEGK 188.15 3.44E-06 178021000 685960 600890 715450 595110 666380 695000 672590 853360 801430 870690 TRUE FALSE 659151.9248 583753.2055 844747.7301 625823.6984 687814.7179 709053.3762 680821.3576 835737.8178 710455.0263 811717.3908 0.812046079 0.719158185 1.04069192 0.770987176 0.847357376 0.873522465 0.838741864 1.029592106 0.875249236 1 19.630618 1.755573059 25 0.967830645 0.844585769 0.304579259 0.086582398 7.75976753 11415.69852 0.03836779 0.021277084 56.96040379 -1.755573059 -0.123244876 GLSDIHHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLSDIHHR 8 0 D6R9T3;Q96FZ2;E7EMP6;D6RAZ3;D6RAI0;D6RGK7 D6R9T3 HMCES Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein 0 106.04 0.0042717 87792000 162400 211790 191630 254010 215240 246540 240520 86291 185700 219800 FALSE TRUE 156053.2285 205749.9566 226261.8038 267119.4865 222163.3901 251525.2077 243463.5557 84509.0607 164620.1145 204912.7502 0.761559387 1.004085672 1.104186067 1.303576699 1.084185293 1.227474657 1.188132781 0.412414848 0.803366869 1 17.64465023 1.755645053 25 0.686001475 1.10550471 0.407667367 0.194215466 5.317905544 7790.369232 0.088752123 0.049218068 56.96984698 -1.755645053 0.419503235 DLFPYEESK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLFPYEESK 9 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;; 156.92 0.00016235 879456000 1549470 1515060 1321980 1368190 1435210 1441980 1460090 1776720 1912030 1754500 FALSE TRUE 1488914.999 1471851.972 1560891.193 1438802.45 1481374.833 1471137.824 1477959.018 1740030.111 1694984.37 1635666.152 0.910280498 0.899848646 0.954284706 0.879643103 0.905670654 0.899412036 0.903582321 1.063805171 1.03626548 1 20.64144689 1.755655793 8.67341455 1.0362867 0.907519175 0.863966752 0.022858512 0.042087038 11.85562186 0.010471192 0.005682124 56.97125581 -1.755655793 -0.128767525 EQFNEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQFNEFR 7 0 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ;;; 125.49 0.0094078 2909360000 2264470 2677110 2183200 2512500 2378190 2526210 2513420 2445100 2817590 2658090 FALSE TRUE 2175972.009 2600761.444 2577752.805 2642170.426 2454686.641 2577291.697 2544179.986 2394607.831 2497748.996 2478055.197 0.878096667 1.049517157 1.040232198 1.066227431 0.9905698 1.040046122 1.026684147 0.966325461 1.00794728 1 21.24077689 1.75565582 25 0.98856502 1.017719783 0.030408732 0.050677869 19.6282191 28735.86811 0.022738378 0.01260962 56.97125942 -1.75565582 0.029154763 (ac)AENDVDNELLDYEDDEVETAAGGDGAEAPAKK ddPTM_BT-474_Pertuzumab_2h_R1 3 AENDVDNELLDYEDDEVETAAGGDGAEAPAKK 32 1 Q13838-2;Q13838;Q5STU3;F6WLT2;F6S4E6;A0A0A0MT12;F6TRA5;F6R6M7;F6U6E2;F6S2B7;A0A0G2JHN7 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;; 127.92 1.19E-19 618908000 355761 342519 272153 267791 296942 333759 314381 396919 420547 395173 FALSE TRUE 341857.4668 332750.6935 321337.1011 281611.7256 306493.4091 340507.8357 318228.4887 388722.4839 372808.2676 368407.5807 0.92793277 0.903213481 0.872232598 0.764402635 0.831941103 0.924269351 0.863794627 1.055142468 1.011945158 1 18.49094322 1.755696555 8.281893661 1.02368278 0.867577522 0.691182177 0.046720424 0.080743624 19.72973821 0.024120338 0.013064462 56.97660337 -1.755696555 -0.156105259 SPS(ph)FASEWDEIEK ddPTM_BT-474_Pertuzumab_2h_R1 7 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.001)PS(0.999)FASEWDEIEK;S(0.038)PS(0.962)FASEWDEIEK;SPS(1)FASEWDEIEK;SPS(1)FASEWDEIEK;SPS(1)FASEWDEIEK;SPS(1)FASEWDEIEK;S(0.167)PS(0.833)FASEWDEIEK 424.75 4.31E-146 3544772000 1777454 1625620 1287415 1389705 1481745 1470934 1505152 1893161 1882332 1785463 TRUE FALSE 1707989.133 1579258.909 1520079.529 1461427.842 1529406.674 1500677.293 1523572.5 1854066.564 1668657.563 1664532.001 1.026107718 0.94877053 0.913217366 0.877981223 0.91882083 0.901561095 0.915315836 1.113866578 1.002478512 1 20.66668518 1.755721493 25 1.047751107 0.925602777 0.527182631 0.047423678 4.557551446 6646.72317 0.02195107 0.012173162 56.9798751 -1.755721493 -0.12214833 EKQELQDDKR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKQELQDDKR 10 2 P12270 P12270 TPR Nucleoprotein TPR 0 ;; 98.353 0.0030566 199470000 362572 304766 283715 272785 313899 325581 323203 367952 427433 390398 FALSE TRUE 348402.2854 296074.3721 334988.6117 286863.4665 323995.8464 332164.4709 327158.455 360353.6626 378912.5978 363955.9957 0.95726486 0.813489476 0.920409653 0.788181731 0.890206097 0.912650086 0.898895633 0.990102284 1.041094534 1 18.47340451 1.755760479 1.689210701 1.025169531 0.873622099 0.603574808 0.047726748 0.215567846 1.206835511 0.033101166 0.013360241 56.98499032 -1.755760479 -0.151547432 FRTPS(ph)FLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FRTPSFLKK 9 2 P35611;P35611-3;P35612;Q9UEY8-2;Q9UEY8 P35611;Q9UEY8-2 ADD1;ADD2;ADD3 Alpha-adducin;Beta-adducin;Gamma-adducin 1 FRT(0.226)PS(0.774)FLKK 56.956 0.09336 795530000 1039300 792280 494390 492430 702380 584310 583170 1066300 887280 724120 TRUE FALSE 998683.007 769684.9501 583737.2706 517844.3713 724972.6906 596125.1485 590307.0089 1044280.532 786559.6942 675074.7074 1.479366648 1.140147811 0.864700254 0.767091946 1.073914757 0.883050634 0.874432122 1.546911062 1.165144666 1 19.36468764 1.755766434 25 1.289369825 0.999115562 0.157348538 0.228591323 9.394847319 13665.5888 0.106967855 0.059319571 56.98577173 -1.755766434 -0.290254263 VLSAPPHFHFGQT(ph)NRTPEFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSAPPHFHFGQTNRTPEFLR 21 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 VLSAPPHFHFGQT(0.734)NRT(0.266)PEFLR;VLSAPPHFHFGQT(0.746)NRT(0.254)PEFLR 255.12 3.05E-36 3850900000 977960 1151470 848430 1121800 1099220 1175140 1247380 135807 971850 854390 TRUE FALSE 939740.242 1118631.203 1001760.174 1179696.232 1134577.41 1198902.136 1262645.81 133002.538 861529.6623 796521.4043 1.179805385 1.40439566 1.25766887 1.481060303 1.424415469 1.505172528 1.5852001 0.166979239 1.081615205 1 19.60335361 1.755788977 25 0.678885634 1.407149679 0.578037834 0.254649333 3.848639393 5590.832206 0.109661561 0.060813532 56.98872978 -1.755788977 0.728264045 STAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_BT-474_Pertuzumab_2h_R1 24 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 STAPSAAASASASAAASS(1)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.005)S(0.995)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.212)S(0.788)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.002)S(0.998)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.002)S(0.998)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.033)S(0.967)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.042)S(0.958)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.189)S(0.811)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.009)S(0.991)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.014)S(0.986)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.009)S(0.991)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.192)S(0.808)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.005)S(0.995)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.001)S(0.999)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.005)S(0.995)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.166)S(0.834)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.004)S(0.996)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.006)S(0.994)PAGGGAEALELLEHCGVCR;STAPSAAASAS(0.001)AS(0.006)AAAS(0.227)S(0.766)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.19)S(0.81)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.029)S(0.971)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.002)S(0.998)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.005)S(0.995)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.004)S(0.996)PAGGGAEALELLEHCGVCR 357.43 1.54E-145 86640758000 3311546.8 3960954.4 3010330.6 3785516.1 3460519.7 4032123.9 3712848.2 3303441.8 3927150.9 3864485.2 TRUE FALSE 3182127.89 3847991.859 3554364.304 3980887.04 3571830.459 4113656.208 3758287.147 3235224.572 3481357.194 3602740.175 0.883252118 1.068073653 0.986572478 1.104960904 0.991420498 1.141813178 1.043174629 0.897989978 0.96630815 1 21.78066318 1.755827161 25 0.946145286 1.036563268 0.190741115 0.071034822 8.894051071 12891.57903 0.0313248 0.01737112 56.99374054 -1.755827161 0.090417982 GVEFPMADLDALS(ph)PIHT(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVEFPMADLDALSPIHTPQR 20 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-5 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 2 GVEFPMADLDALS(1)PIHT(1)PQR 159.98 4.39E-11 56049000 37692 33982 36427 38417 37399 41277 36418 36306 33996 41179 TRUE FALSE 36218.95497 33012.86663 43010.16921 40399.70597 38601.9728 42111.64922 36863.69438 35556.26841 30136.9166 38389.90965 0.943449862 0.859936033 1.120350884 1.052352202 1.005523929 1.096945776 0.960244364 0.926187864 0.785021816 1 15.22843954 1.755896688 2.831369412 0.886908939 1.012342263 0.238913386 0.085684396 0.326564471 5.325156437 0.051168109 0.023927221 57.00286548 -1.755896688 0.125433324 SSHPEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSHPEDLR 8 0 B0QYR6;Q9UJY5-4;Q9UJY5-3;Q9UJY5;Q9UJY5-6;Q9UJY5-2 B0QYR6 GGA1 ADP-ribosylation factor-binding protein GGA1 0 68.224 0.071619 0 284590 329940 269050 359860 319530 328090 348970 177500 302020 335070 FALSE TRUE 273467.9082 320530.4342 317673.32 378432.4177 329807.9726 334724.2046 353240.7992 173834.563 267735.9558 312375.4105 0.875446335 1.026106484 1.016960072 1.211466732 1.055806448 1.071544665 1.130821401 0.556492468 0.857096771 1 18.25292137 1.755914549 25 0.764091963 1.059475015 0.424368471 0.131353931 5.113345772 7374.222845 0.058244048 0.032299637 57.00520993 -1.755914549 0.295383053 KS(ph)LSDSESDDS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.986)LS(0.013)DS(0.001)ES(0.002)DDS(0.998)K 216.77 2.56E-11 224950000 1085600 775260 684350 605270 721900 709970 798730 1074700 1297800 984880 TRUE FALSE 1043173.552 753150.3439 808027.2683 636508.0572 745120.5691 724326.0798 808505.0967 1052507.069 1150479.185 918173.2004 1.136140274 0.82027045 0.880037958 0.693233103 0.811525068 0.788877392 0.88055837 1.146305587 1.253008892 1 19.8084068 1.755924536 4.260054116 1.152229576 0.844839849 0.514996889 0.121485028 0.142174656 5.499953285 0.062403381 0.031947396 57.00652077 -1.755924536 -0.307389727 EVVHTVSLHEIDVINSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVVHTVSLHEIDVINSR 17 0 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ; 235.24 2.16E-20 593270000 157231 201312 195711 268500 205880 253200 238590 106422 205739 210920 FALSE TRUE 151086.2387 195570.7789 231080.3313 282357.3172 212502.3172 258319.8775 241509.9358 104224.3485 182384.3712 196634.2005 0.768361955 0.994591878 1.175178736 1.435952222 1.080698661 1.313707772 1.22821938 0.530041815 0.927531278 1 17.58515475 1.755946775 25 0.778188063 1.153472006 0.335138084 0.205780973 6.701317799 9646.383329 0.096621914 0.053582396 57.00944002 -1.755946775 0.375283943 LVSDEMVVELIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVSDEMVVELIEK 13 0 F8W1A4;P54819-2;P54819;P54819-6;P54819-3;P54819-5;F8VZG5;A0A5F9ZHP2;P54819-4;G3V213 F8W1A4 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 0 ; 145.91 9.78E-05 13767000 26238 27285 23475.5 25131.8 26281 28291 26823 24147 27984 28683 FALSE TRUE 25212.58995 26506.85851 27718.04506 26428.85521 27126.35223 28863.0634 27151.2679 23648.35601 24807.37364 26740.27486 0.942869514 0.991270982 1.036565451 0.98835391 1.014438048 1.079385442 1.015369813 0.884372211 0.927715731 1 14.70672667 1.755998647 25 0.927049203 1.012106726 0.370651371 0.042516401 6.05717383 8693.18032 0.019676637 0.010911895 57.01624959 -1.755998647 0.085057523 ELHWHPQCPGLLVSTALSGFTIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELHWHPQCPGLLVSTALSGFTIFR 24 0 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 160.69 1.17E-11 94557000 118530 124770 116070 121780 121000 118230 137920 62325 138170 104880 FALSE TRUE 113897.7166 121211.6818 137046.431 128065.0804 124892.0749 120620.6916 139607.9062 61037.96697 122485.5209 97776.38418 1.164879613 1.239682596 1.401631203 1.309775172 1.277323517 1.233638292 1.427828482 0.624260832 1.252710681 1 16.57719843 1.756029611 25 0.928126804 1.29332086 0.475461995 0.16004418 4.93979731 7076.955133 0.068650398 0.038070633 57.02031489 -1.756029611 0.365194057 TRSES(ph)PAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRSESPAVR 9 1 Q9UBC3-4;Q9UBC3-3;Q9UBC3-5;Q9UBC3-2;Q9UBC3-6;Q9UBC3 Q9UBC3-4 DNMT3B DNA (cytosine-5)-methyltransferase 3B 1 T(0.261)RS(0.171)ES(0.568)PAVR 58.781 0.064547 319550000 114710 175560 170900 304930 201890 251660 203940 90118 111330 104250 TRUE FALSE 110227.0064 170553.2007 201785.4316 320667.4738 208383.9752 256748.7376 206435.8787 88257.03181 98692.28513 97189.05464 1.134150412 1.754860167 2.076215603 3.299419621 2.144109498 2.641745396 2.124065096 0.908096412 1.015467076 1 16.56850623 1.756057512 5.164157849 0.971324919 2.214540779 0.517184845 0.526983928 0.147242961 9.132557301 0.281543431 0.147988713 57.02397815 -1.756057512 1.24321586 KLDPAQSAS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 4 KLDPAQSASR 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.005)AS(0.995)R;KLDPAQSAS(1)R;KLDPAQS(0.002)AS(0.998)R;KLDPAQS(0.005)AS(0.995)R 98.337 0.0049244 3972660000 5146500 4888300 4945500 5567800 4319940 3911320 4939000 6148500 5894300 6317200 TRUE FALSE 4945369.09 4748890.47 5839261.862 5855154.825 4458894.793 3990409.57 4999444.959 6021531.326 5225203.775 5889330.417 0.839716698 0.806354905 0.99149843 0.994197033 0.757114048 0.677565918 0.848898704 1.022447528 0.887232233 1 22.48967219 1.756082228 25 0.968718918 0.845106378 0.263395964 0.095666906 10.37019523 14812.09163 0.048488794 0.026889583 57.02722352 -1.756082228 -0.12361254 GEAEAPHHGTGHPESAGEHALEPPAPAGASAST(ph)PPPPAPEAQLPPFPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEAEAPHHGTGHPESAGEHALEPPAPAGASASTPPPPAPEAQLPPFPR 48 0 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 GEAEAPHHGTGHPESAGEHALEPPAPAGASAS(0.178)T(0.822)PPPPAPEAQLPPFPR 132.1 4.89E-11 548160000 37500 48835 50590 67568 49917 59972 63977 308.74 52196 35336 TRUE FALSE 36034.45854 47442.27361 59732.73837 71055.19258 51522.62564 61184.67493 64759.96966 302.3644111 46270.9289 32942.66125 1.093853902 1.440146965 1.813233543 2.156935411 1.564009211 1.857308202 1.965839043 0.009178506 1.404589889 1 15.00766949 1.756131554 25 0.723802469 1.711755577 0.476468333 0.426857598 5.172028017 7366.612854 0.192190931 0.106580692 57.03370096 -1.756131554 0.987953108 VNEASGDGDGEDAVVILEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNEASGDGDGEDAVVILEK 19 0 Q96C86 Q96C86 DCPS m7GpppX diphosphatase 0 ; 183.7 6.17E-14 130628000 246778 235418 186858 206813 230579 217713 223510 279980 300430 275655 FALSE TRUE 237133.6429 228704.1091 220627.3972 217486.6437 237995.7829 222115.306 226245.3822 274198.3152 266326.4459 256984.6413 0.922754145 0.889952442 0.858523669 0.846302108 0.926108976 0.864313544 0.88038484 1.066983279 1.036351607 1 17.97132261 1.756131723 8.054310493 1.037296054 0.882592733 0.853559313 0.028516447 0.046358517 10.36184003 0.013499248 0.007307087 57.03372313 -1.756131723 -0.154703322 GSSPS(ph)HSATSVHTSV ddPTM_BT-474_Pertuzumab_2h_R1 2 GSSPSHSATSVHTSV 15 0 F8WA39;Q13613 F8WA39 MTMR1 Myotubularin-related protein 1 1 GS(0.004)S(0.021)PS(0.739)HS(0.199)AT(0.036)SVHTSV;GSS(0.012)PS(0.986)HS(0.001)ATSVHTSV 144.92 4.36E-06 604530000 183754 358080 282810 485990 325870 401080 340250 181251 247490 335990 TRUE FALSE 176572.6905 347867.909 333920.0581 511072.0021 336351.9045 409190.1124 344414.0813 177508.1035 219395.9728 313233.098 0.563710194 1.110572003 1.06604334 1.631602807 1.073807036 1.30634379 1.099545621 0.56669651 0.700423979 1 18.25687714 1.756141385 24.99999995 0.720105087 1.143971042 0.276396136 0.267805865 7.750154516 11032.50428 0.123420492 0.0684438 57.03499194 -1.756141385 0.423865955 VVTTPAFMCETALHYIHDGIGAMVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VVTTPAFMCETALHYIHDGIGAMVR 25 0 P0DPI2-2;A0A0B4J2D5-2;P0DPI2;A0A0B4J2D5;A0A096LNH5;A0A096LPI6 P0DPI2-2 0 105.72 0.0023552 102470000 97663 117640 80405 120320 88990 105740 104000 54232 95705 80780 FALSE TRUE 93846.22199 114285.0224 94935.9721 126529.7296 91852.44417 107878.1352 105272.7831 53112.09025 84840.96963 75308.69865 1.246153813 1.517554073 1.260624255 1.680147604 1.219679078 1.432479079 1.397883445 0.705258373 1.126575962 1 16.20052889 1.756141555 25 0.9252234 1.399002138 0.616338406 0.162297914 3.834447631 5458.36234 0.068251784 0.03784949 57.03501433 -1.756141555 0.473778738 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR 33 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 307.82 1.57E-104 15726860000 2880594 3780210 3091483 4161650 3654880 4100550 3821760 109616 3513340 844704 FALSE TRUE 2768017.202 3672402.112 3650182.748 4376433.255 3772442.534 4183465.931 3868531.842 107352.3913 3114520.372 787491.4457 3.51498066 4.663418418 4.635203046 5.55743593 4.790455255 5.312395396 4.912474749 0.136321978 3.954989466 1 19.58690473 1.756164236 24.99999999 1.693411094 4.812232878 0.652022513 1.028223963 3.785394311 5381.582982 0.442400605 0.245336484 57.03799309 -1.756164236 3.118821784 KEMQPTHPIR ddPTM_BT-474_Pertuzumab_2h_R1 10 KEMQPTHPIR 10 1 B7Z2E6;H0YB80;P63104-2;P27348;P31946-2;P31946;P63104;E7EX29;B0AZS6 B7Z2E6;P27348;P31946-2;P63104 YWHAZ;YWHAQ;YWHAB "14-3-3 protein zeta/delta;14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;;;;;; 151.07 1.33E-05 11886240000 8280100 8803360 7691450 7846480 7998640 8036930 8340110 7666600 8856750 8918340 FALSE TRUE 7956504.538 8552296.792 9081466.11 8251437.773 8255923.52 8199442.231 8442178.761 7508282.031 7851368.871 8314292.888 0.956967074 1.028625874 1.092271614 0.992440113 0.992979635 0.986186359 1.015381449 0.903057197 0.944321902 1 22.98716214 1.756205912 25 0.940440356 1.011040822 0.31332417 0.040125233 7.127915965 10109.58032 0.018768344 0.010408124 57.04346677 -1.756205912 0.070600465 SSS(ph)ETILSSLAGSDIVK ddPTM_BT-474_Pertuzumab_2h_R1 5 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.102)S(0.102)S(0.755)ET(0.041)ILSSLAGSDIVK;SS(0.031)S(0.967)ET(0.001)ILSSLAGSDIVK;S(0.039)S(0.039)S(0.922)ETILSSLAGSDIVK;S(0.002)S(0.032)S(0.966)ETILSSLAGSDIVK;S(0.001)S(0.001)S(0.997)ETILSSLAGSDIVK 381.5 8.61E-106 461960000 914754 891587 671536 791356 862403 793481 829928 1033796 995356 1040777 TRUE FALSE 879004.4024 866159.8117 792897.4934 832197.978 890142.9757 809525.7295 840084.9071 1012447.751 882367.3598 970284.2468 0.905924635 0.892686668 0.817180631 0.857684726 0.917404337 0.834318121 0.865813198 1.043454797 0.909390586 1 19.88804792 1.756218318 25 0.985664557 0.868934975 0.60759766 0.042021122 4.282527432 6069.671797 0.018616773 0.010324003 57.04509632 -1.756218318 -0.116729581 GAAAHPDSEEQQQR ddPTM_BT-474_Pertuzumab_2h_R1 5 GAAAHPDSEEQQQR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;; 220.31 4.69E-12 573075000 659668 702989 593499 766936 712186 773687 722515 655479 731044 745405 FALSE TRUE 633887.4453 682940.442 700757.4716 806517.6589 735094.1095 789331.4812 731357.3547 641943.1296 648058.9499 694918.0554 0.912175817 0.982763992 1.008403028 1.160593904 1.057814089 1.135862675 1.052436829 0.923768097 0.932568876 1 19.40648334 1.756225398 9.166767958 0.947088425 1.049096165 0.266460748 0.069586054 0.182284894 60.16885888 0.035299249 0.019207774 57.0460263 -1.756225398 0.10200774 NCSETQYESK ddPTM_BT-474_Pertuzumab_2h_R1 2 NCSETQYESK 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 221.91 1.20E-08 362720000 282440 267340 247730 298320 266620 262640 307870 322340 398510 356200 FALSE TRUE 271401.9325 259715.725 292500.3217 313716.331 275196.0744 267950.7607 311637.8052 315683.5664 353272.8155 332074.2567 0.817292901 0.782101351 0.880828055 0.944717408 0.828718483 0.806900129 0.938458188 0.95064149 1.063836803 1 18.34114636 1.756233727 1.693766551 1.025838774 0.847273416 0.689086309 0.049158463 0.210390276 1.184483612 0.038105824 0.015395077 57.04712041 -1.756233727 -0.178565358 ARPTILSSGLPEEPDQNLS(ph)SPEEVFHSGHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARPTILSSGLPEEPDQNLSSPEEVFHSGHSR 31 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 ARPTILSSGLPEEPDQNLS(0.853)S(0.147)PEEVFHSGHSR 119.97 8.91E-06 87236000 42714 49077 43109 48439 52746 60397 57150 7156.9 44707 39241 TRUE FALSE 41044.68966 47677.37201 50899.75525 50938.94259 54442.62299 61618.26872 57849.4188 7009.107514 39632.04879 36583.17212 1.121955459 1.303259648 1.391343405 1.39241459 1.488187597 1.684333675 1.581312266 0.19159376 1.08334096 1 15.15889256 1.756243736 25 0.690284406 1.428768492 0.565068249 0.26529843 4.343615583 6147.391041 0.11911397 0.066055527 57.04843514 -1.756243736 0.738484086 RHT(ph)VEDAVVSQGPEAAGPLSTPQEVSASR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHTVEDAVVSQGPEAAGPLSTPQEVSASR 29 1 Q96NW4 Q96NW4 ANKRD27 Ankyrin repeat domain-containing protein 27 1 RHT(0.996)VEDAVVS(0.004)QGPEAAGPLSTPQEVSASR 85.745 0.0015209 160920000 54819 50320 47227 59122 60277 60233 59599 28459 58387 43365 TRUE FALSE 52676.61287 48884.92287 55761.96946 62173.29351 62215.86445 61450.95253 60328.39039 27871.3117 51759.15254 40427.84992 1.302978342 1.209189283 1.379295945 1.537882762 1.538935772 1.520015352 1.492248302 0.689408706 1.280284572 1 15.30306186 1.756247743 25 0.968928464 1.427960308 0.587770069 0.167001343 4.562368673 6455.520249 0.077732213 0.043106946 57.0489615 -1.756247743 0.459031844 ATFHTPFSHLGQSPEGCSSYTFPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATFHTPFSHLGQSPEGCSSYTFPK 24 0 A0A0C4DGA2;O75521-2;O75521 A0A0C4DGA2 ECI2 "Enoyl-CoA delta isomerase 2, mitochondrial" 0 148.04 9.70E-08 472990000 255410 316790 251290 401020 289680 361000 391510 116690 339080 349560 FALSE TRUE 245428.2948 307755.4594 296703.6929 421716.6903 298997.8203 368299.6673 396301.4165 114280.3107 300589.0599 325883.9898 0.753115533 0.944371215 0.910458022 1.294069986 0.917497728 1.130155757 1.216081271 0.350677892 0.922380569 1 18.31399895 1.756252776 25 0.695334167 1.026685351 0.218918185 0.220970062 8.02274844 11348.54955 0.098611417 0.054685872 57.04962256 -1.756252776 0.331351184 S(ph)REDLSAQPVQTK ddPTM_BT-474_Pertuzumab_2h_R1 6 SREDLSAQPVQTK 13 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(1)REDLSAQPVQTK;S(0.999)REDLS(0.001)AQPVQTK;S(0.978)REDLS(0.022)AQPVQTK;S(1)REDLSAQPVQTK;S(1)REDLSAQPVQTK;S(0.808)REDLS(0.192)AQPVQTK 268.6 5.41E-25 15586120000 13643670 12159890 10772960 10740720 10378910 10406020 11505220 14631910 14351290 14072020 TRUE FALSE 13110460.29 11813101.84 12719873.52 11295049.85 10712757.07 10616436.85 11646024.32 14329755.95 12722191.72 13118909.55 0.999355948 0.900463701 0.96958314 0.860974748 0.816588987 0.809246898 0.887728075 1.092297793 0.969759847 1 23.64514447 1.756259675 25 1.026851106 0.888026143 0.466588801 0.062853425 5.946153574 8407.828078 0.030596549 0.016967443 57.05052884 -1.756259675 -0.138824963 TSYEEFTHK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSYEEFTHK 9 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 150.08 8.61E-05 1388650000 879900 961460 726130 825900 848850 811340 868060 942500 1027070 1016350 FALSE TRUE 845512.5352 934040.1022 857357.8437 868524.798 876154.0312 827745.8507 878683.5779 923037.0456 910481.3194 947511.7092 0.892350487 0.985782121 0.904851977 0.916637535 0.924689397 0.873599601 0.92735907 0.97416954 0.960918277 1 19.85378425 1.756287093 4.012292239 0.976539499 0.918027587 0.483691602 0.028740827 0.183914089 6.199759907 0.015033453 0.0076206 57.05413068 -1.756287093 -0.058511912 GFGFVDFNS(ph)EEDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 1 GFGFVDFNS(1)EEDAK;GFGFVDFNS(1)EEDAK 224.86 3.14E-12 111443000 232030 214292 194942 180273 208644 203046 207743 235952 240960 243370 TRUE FALSE 222962.0111 208180.602 230172.3559 189576.9111 215355.2237 207151.7292 210285.421 231079.5087 213607.231 226886.3331 0.982703577 0.917554615 1.014483123 0.835558971 0.949176712 0.913019865 0.92683159 1.018481394 0.941472446 1 17.79161018 1.756290953 25 0.987100484 0.932606823 0.201843171 0.047731446 10.37904601 14649.99129 0.02088941 0.011584458 57.05463778 -1.756290953 -0.054493661 ITSLSSS(ph)LDTSLDFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ITSLSSSLDTSLDFSK 16 0 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 ITSLS(0.019)S(0.125)S(0.855)LDTSLDFSK 113.52 0.00068684 25897000 63545 69549 67445 72746 60375 66960 67997 90208 89145 94036 TRUE FALSE 61061.59115 67565.53062 79633.81181 76500.42978 62317.01671 68313.97708 68829.16763 88345.17328 79025.63333 87666.85796 0.696518531 0.770707793 0.908368495 0.872626572 0.710838944 0.779245186 0.785121872 1.00773742 0.901431113 1 16.41974392 1.756293013 9.89891719 0.964461758 0.792733898 0.610526758 0.066021366 0.103604108 42.38969588 0.032629232 0.017806823 57.0549085 -1.756293013 -0.171727859 VVDRDSEEAEIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVDRDSEEAEIIR 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 271.56 3.93E-32 7658050000 3237070 3699240 2810730 3654280 3339430 3752380 3247570 3256840 3317630 3283150 FALSE TRUE 3110561.726 3593741.297 3318691.435 3842877.829 3446845.799 3828255.695 3287314.733 3189585.116 2941026.551 3060779.326 1.016264616 1.174126232 1.084263543 1.255522669 1.12613339 1.25074541 1.074012329 1.042082678 0.960875071 1 21.5454676 1.756293508 2.252262648 0.988275165 1.152205329 0.479753352 0.069822256 0.229479043 2.356807253 0.043338752 0.018936999 57.05497353 -1.756293508 0.163930164 FLLVYLHGDDHQDSDEFCR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLLVYLHGDDHQDSDEFCR 19 0 Q96CS3 Q96CS3 FAF2 FAS-associated factor 2 0 136.34 3.48E-06 86474000 51926 56981 45548 65104 45749 54446 54977 37534 59162 42190 FALSE TRUE 49896.67451 55355.95767 53779.53681 68464.02524 47220.55813 55546.93542 55649.82497 36758.90978 52446.17779 39332.43372 1.268588536 1.407387045 1.367307632 1.740650623 1.200550123 1.412242523 1.414858419 0.934569929 1.333407898 1 15.26343184 1.756310713 25 1.091316349 1.406265318 0.434661579 0.163166218 6.19896863 8740.070605 0.071945838 0.03989793 57.05723387 -1.756310713 0.314948969 EGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_BT-474_Pertuzumab_2h_R1 17 EGMNPSYDEYADSDEDQHDAYLER 24 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 1 EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER 314.47 9.18E-74 1.00106E+11 15809763 16961710 13812579 17140224 17326609 17803411 16900750 15551495 18383632 17373887 TRUE FALSE 15191899.98 16477978.64 16308819.28 18024833.01 17883935.11 18163408.17 17107586.43 15230351.19 16296799.17 16197138.16 0.937937297 1.017338895 1.006895115 1.112840604 1.104141666 1.121396137 1.056210441 0.940311248 1.006153001 1 23.94923559 1.756318691 25 0.977795066 1.055111315 0.243657384 0.055059158 9.686200252 13650.65587 0.027572313 0.015290536 57.05828204 -1.756318691 0.07731625 EEEEDGQEGS(ph)IHNLPLVTSQRPFYDGPMPTPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEEEDGQEGSIHNLPLVTSQRPFYDGPMPTPR 32 1 O75717;O75717-2;H3BSQ1 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 EEEEDGQEGS(1)IHNLPLVTSQRPFYDGPMPTPR;EEEEDGQEGS(1)IHNLPLVTSQRPFYDGPMPTPR;EEEEDGQEGS(1)IHNLPLVTSQRPFYDGPMPTPR 169.75 1.96E-14 779120000 167947 145340 134118 176168 142406 121462 127027 207523 158525 170025 TRUE FALSE 161383.4456 141195.0455 158356.106 185260.0516 146986.6183 123918.0449 128581.5944 203237.5775 140529.9066 158509.0553 1.018133918 0.890769586 0.999035076 1.16876636 0.92730739 0.781772654 0.811193999 1.282182757 0.886573365 1 17.27420574 1.756336458 25 1.083504371 0.944560654 0.115340844 0.138330899 12.85189935 18093.91381 0.065611178 0.036385595 57.06061631 -1.756336458 -0.138943717 ATNVTYQAHHVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATNVTYQAHHVSR 13 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 55.885 0.073063 275760000 211280 353750 256920 349100 255660 266050 315460 120927 241320 304630 FALSE TRUE 203022.944 343661.3964 303351.1592 367117.0928 263883.5361 271429.7133 319320.6938 118429.8152 213926.3653 283997.1388 0.714876723 1.210087531 1.068148646 1.292678843 0.929176742 0.955748056 1.124379968 0.417010593 0.753269439 1 18.11551687 1.75637404 25 0.669853903 1.051582318 0.334404282 0.20155589 6.31838227 8876.723623 0.088243668 0.048936146 57.06555429 -1.75637404 0.381728414 EQHVQDIIPINSHFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQHVQDIIPINSHFR 15 0 Q01968-2;Q01968;A0A2R8YF88 Q01968-2 OCRL Inositol polyphosphate 5-phosphatase OCRL-1 0 ; 226.74 4.77E-13 265110000 151690 190163 156647 188803 182869 196092 189315 160535 203747 191430 FALSE TRUE 145761.7871 184739.7374 184956.5975 198547.1455 188751.1475 200057.1146 191631.8936 157219.8962 180618.4947 178464.2756 0.816756108 1.035163686 1.036378832 1.112531597 1.05764107 1.120992501 1.073782935 0.880960044 1.01207087 1 17.44527578 1.756376942 25 0.953743521 1.043171205 0.120366655 0.086154923 12.26365289 17226.45589 0.040110606 0.022243666 57.06593558 -1.756376942 0.089427684 KKVEEEDEEEEEEEEEEEEEEDE ddPTM_BT-474_Pertuzumab_2h_R1 1 KKVEEEDEEEEEEEEEEEEEEDE 23 2 O15347 O15347 HMGB3 High mobility group protein B3 0 59.351 0.050603 0 93228 70779 69487 59619 71896 61754 70194 100660 98519 81107 FALSE TRUE 89584.54669 68760.45222 82044.84663 62695.94373 74208.60013 63002.70819 71053.05517 98581.33582 87335.53615 75613.55065 1.184768417 0.909366795 1.085054807 0.829162805 0.981419329 0.833219809 0.939686796 1.303752237 1.155024931 1 16.20635718 1.756387737 25 1.180182852 0.958702116 0.318467079 0.122994728 6.672509549 9367.027232 0.053984446 0.02993743 57.06735413 -1.756387737 -0.221480736 VSEEIEDIIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSEEIEDIIKK 11 1 O75223;M0QZK8;O75223-3 O75223 GGCT Gamma-glutamylcyclotransferase 0 137.16 0.0022246 0 328370 318340 276070 312760 321790 306280 314890 441130 438350 364730 FALSE TRUE 315536.9374 309261.2549 325961.9901 328901.5811 332140.6676 312473.1914 318743.718 432020.5113 388590.3457 340026.5122 0.927977455 0.909521004 0.958636984 0.967282166 0.976808148 0.91896714 0.937408427 1.270549489 1.142823667 1 18.37528771 1.756445884 25 1.161468424 0.943115981 0.650123748 0.065001518 3.53756609 4949.953815 0.02803009 0.015544194 57.07499519 -1.756445884 -0.218352442 NENLAANFLLQQNFDED ddPTM_BT-474_Pertuzumab_2h_R1 16 NENLAANFLLQQNFDED 17 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;;;;;;;;;;;;;; 305.82 1.47E-46 3508260800 2471037.1 2372851.7 2081446.4 2490631.2 2344261.8 2244162.7 2387554.3 2646276.8 2852785.3 2795012.3 FALSE TRUE 2374466.238 2305180.293 2457610.066 2619172.975 2419667.11 2289541.207 2416773.904 2591630.259 2528949.073 2605703.627 0.911257218 0.884667108 0.943165616 1.005169179 0.928604115 0.878665242 0.927493779 0.994599014 0.970543636 1 21.31324157 1.756450605 6.76297053 0.986461463 0.925955026 0.423367611 0.033542933 0.168856765 22.17653569 0.017794999 0.009559 57.07561563 -1.756450605 -0.060506437 KPPLLNNADSVQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPLLNNADSVQAK 14 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 155.98 9.13E-06 393610000 429770 411340 365970 311430 389260 409930 384870 520500 505390 456340 FALSE TRUE 412974.1133 399608.9859 432108.92 327502.9396 401780.9014 418219.0655 389580.1542 509751.4931 448020.246 425431.6853 0.970717809 0.93930236 1.015695198 0.76981323 0.944407564 0.98304635 0.915729053 1.198198232 1.053095624 1 18.69856796 1.756535179 25 1.100905839 0.933399828 0.435629976 0.077325546 5.765377902 8027.10037 0.034692261 0.019239055 57.08673163 -1.756535179 -0.167506011 LDFLPEMMVDHCSLNS(ph)SPVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDFLPEMMVDHCSLNSSPVSK 21 0 Q92879-4;G5EA30;F5H0D8;E9PKU1;F5H3J7 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 LDFLPEMMVDHCS(0.211)LNS(0.263)S(0.263)PVS(0.263)K 71.052 0.02896 133210000 310830 289500 284320 275710 376290 289340 320430 210840 352510 237850 TRUE FALSE 298682.42 281243.7435 335702.9487 289939.4261 388393.7096 295190.653 324351.5182 206486.0803 312494.5426 221740.2076 1.346992605 1.268347975 1.51394712 1.307563609 1.751570965 1.331245498 1.462754643 0.931207211 1.409282268 1 17.75851087 1.756541376 25 1.114963065 1.427690374 0.403855681 0.174014107 6.792869674 9454.408002 0.076258478 0.042289663 57.08754621 -1.756541376 0.312727309 DLSQAPFSWPAGALVAQACHAATAALHTHR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLSQAPFSWPAGALVAQACHAATAALHTHR 30 0 Q6GMV3 Q6GMV3 PTRHD1 Putative peptidyl-tRNA hydrolase PTRHD1 0 91.615 0.00034502 141300000 41534 47693 34167 53782 43225 52373 52607 3460.8 39746 35519 FALSE TRUE 39910.80536 46332.84234 40341.73694 56557.69547 44615.37138 53432.01794 53250.8202 3389.333271 35234.20071 33113.26649 1.205281435 1.399222947 1.2182953 1.708007136 1.347356395 1.613613624 1.608141565 0.102355751 1.064050891 1 15.01512171 1.756571499 25 0.645682589 1.445625922 0.560795977 0.289915012 4.391375887 6101.740553 0.125675745 0.06969421 57.09150599 -1.756571499 0.799943333 VSALEEDMDDVES(ph)S(ph)EEEEEEDEKLER ddPTM_BT-474_Pertuzumab_2h_R1 2 VSALEEDMDDVESSEEEEEEDEKLER 26 1 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 2 VSALEEDMDDVES(1)S(1)EEEEEEDEKLER;VS(0.001)ALEEDMDDVES(1)S(1)EEEEEEDEKLER 85.489 0.0076118 444020000 284290 244269 212663 200154 244223 240324 242138 287650 295690 282444 TRUE FALSE 273179.6325 237302.6873 251095.9348 210483.9719 252078.6546 245183.5159 245101.3573 281709.927 262124.5108 263313.8163 1.037467902 0.901216239 0.953599543 0.799365468 0.957331667 0.931145655 0.930833637 1.069863826 0.995483315 1 18.0064237 1.756638964 25 1.026627665 0.925982214 0.336381795 0.058667098 7.360492098 10189.05967 0.026302092 0.01458609 57.10037545 -1.756638964 -0.100645451 KNS(ph)LISSLEEEVSILNR ddPTM_BT-474_Pertuzumab_2h_R1 3 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR 146.99 2.55E-07 209412000 91871 86557 73903 69508 83693 86618 82745 98544 103143 91875 TRUE FALSE 88280.57975 84088.47911 87258.91606 73095.31621 86385.06135 88369.47531 83757.65806 96509.03196 91434.63905 85652.22442 1.030686364 0.981743086 1.018758318 0.85339659 1.008555959 1.03172423 0.97788071 1.126754531 1.067510385 1 16.38620309 1.756659754 25 1.076187713 0.984708155 0.28360332 0.056380528 7.972931205 11024.16133 0.025833088 0.014325992 57.10310896 -1.756659754 -0.091479558 S(ph)PTAALNESLVECPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPTAALNESLVECPK 15 0 Q53EZ4 Q53EZ4 CEP55 Centrosomal protein of 55 kDa 1 S(0.902)PT(0.098)AALNESLVECPK;S(0.999)PT(0.001)AALNESLVECPK;S(0.999)PT(0.001)AALNESLVECPK;S(0.999)PT(0.001)AALNESLVECPK 328.56 8.84E-69 2315880000 585040 583085 619640 742160 776160 764620 672480 605590 663720 602800 TRUE FALSE 562175.99 566455.9867 731622.7318 780462.9665 801125.8913 780081.1403 680710.0114 593084.3549 588377.2881 561971.8191 1.000363312 1.007979346 1.301885089 1.388793779 1.425562393 1.388114339 1.211288517 1.05536316 1.046987177 1 19.10013826 1.756706026 3.399046259 1.03212499 1.259904299 0.329013127 0.139604766 0.293748729 6.925918756 0.088471892 0.043369486 57.10919341 -1.756706026 0.227779309 LVNWSCTLNSAISDIEVDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVNWSCTLNSAISDIEVDKK 20 1 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 96.131 0.0018078 49649000 72881 71250 69472 67173 72186 71759 73838 92130 102780 92939 FALSE TRUE 70032.72995 69218.01976 82027.1358 70639.80658 74507.92825 73210.01615 74741.65153 90227.4833 91112.84529 86644.15875 0.808279877 0.798876933 0.946712819 0.815286427 0.859930194 0.844950395 0.862627702 1.041356793 1.051575162 1 16.40281487 1.756715044 4.71815369 1.035547119 0.848002832 0.807923026 0.040854948 0.074188308 3.653235293 0.020572375 0.010704483 57.11037921 -1.756715044 -0.187544287 QEPQGQEIQSENLIMEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QEPQGQEIQSENLIMEK 17 0 Q4VCS5 Q4VCS5 AMOT Angiomotin 0 ; 66.335 0.028937 4302500000 1355760 1951910 1505240 2130000 2031970 2235420 1917770 1468820 1568690 1844300 FALSE TRUE 1302775.4 1896243.438 1777270.352 2239929.555 2097330.16 2280621.724 1941240.243 1438488.354 1390618.888 1719383.918 0.757698956 1.102862146 1.033666962 1.302751254 1.219814922 1.326417969 1.129032453 0.836630108 0.808789051 1 20.71346029 1.756807904 6.499349424 0.868994367 1.139065502 0.328745226 0.157606978 0.17286956 20.17092837 0.079478802 0.042622268 57.12259176 -1.756807904 0.270071135 DLLDDLKSELTGKFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLDDLKSELTGKFEK 16 2 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 154.82 1.79E-07 4034200000 1674100 1381010 967370 958310 1176350 1132940 1200300 1629470 1811910 1336070 FALSE TRUE 1608674.321 1341624.947 1142195.278 1007768.494 1214188.366 1155848.823 1214989.63 1595820.875 1606229.573 1245576.789 1.291509553 1.07711139 0.917001094 0.809077773 0.97480009 0.927962718 0.975443378 1.28119028 1.289546809 1 20.24838253 1.756824339 12.35043341 1.212872074 0.985550945 0.280233083 0.140444446 0.23931224 154.1526385 0.067542996 0.037134895 57.12475344 -1.756824339 -0.227321129 NLSSHVVER ddPTM_BT-474_Pertuzumab_2h_R1 1 NLSSHVVER 9 0 Q9BS34 Q9BS34 ZNF670 Zinc finger protein 670 0 76.221 0.036044 114640000 88890 208470 154950 312210 234670 229240 178780 87367 41584 88607 FALSE TRUE 85416.08053 202524.6397 182952.9118 328323.1955 242218.3737 233875.3899 180967.9631 85562.84092 36863.55865 82605.56897 1.03402327 2.451706855 2.214776971 3.974589118 2.932228138 2.831230301 2.190747735 1.03579991 0.446259969 1 16.33395143 1.756827217 2.645560352 0.715083975 2.627153433 0.557992563 0.69795819 0.189047005 2.687172694 0.440883891 0.202381124 57.12513206 -1.756827217 1.912069458 MCIVLRPSRVHNS(ph)EENTMRALTLK ddPTM_BT-474_Pertuzumab_2h_R1 3 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.113)RVHNS(0.443)EENT(0.443)MRALTLK;MCIVLRPS(0.129)RVHNS(0.435)EENT(0.435)MRALT(0.001)LK;MCIVLRPS(0.051)RVHNS(0.473)EENT(0.473)MRALT(0.002)LK 60.139 0.03725 512358000 163950 231837 217499 297491 252322 292803 256862 160522 180537 254069 TRUE FALSE 157542.6527 225225.2358 256805.9075 312844.5462 260438.1663 298723.6773 260005.554 157207.1646 160043.1966 236860.6803 0.665127925 0.95087642 1.084206577 1.320795607 1.099541578 1.261178837 1.097715136 0.66371153 0.675684949 1 17.8536792 1.756869771 10.96580295 0.754597997 1.082922695 0.325458978 0.188580591 0.17594109 90.77046576 0.091910614 0.050354131 57.13072973 -1.756869771 0.328324698 T(ph)PS(ph)PESHR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSPESHR 8 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 T(1)PS(0.999)PES(0.001)HR;T(1)PS(0.893)PES(0.107)HR;T(1)PS(0.999)PES(0.001)HR 129.85 0.0056924 640630000 567573 607680 471384 638942 581175 611332 594530 490187 621985 582733 TRUE FALSE 545391.6197 590349.5614 556573.5747 671917.8732 599869.0217 623693.5519 601806.036 480064.4672 551379.8704 543263.9749 1.003916411 1.086671653 1.024499323 1.236816546 1.104194369 1.148048795 1.107759881 0.883667037 1.014939138 1 19.05129386 1.756869779 25 0.95751762 1.105229008 0.44948583 0.068438355 6.14562891 8399.956778 0.031403521 0.01741497 57.1307307 -1.756869779 0.147711388 VTVAGGVHISGLHTESAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTVAGGVHISGLHTESAPR 19 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 221.79 1.49E-19 1325980000 387350 662650 506580 798040 582060 694590 692630 263190 523310 704630 FALSE TRUE 372211.9338 643751.8708 598130.2748 839226.94 600782.4885 708635.0857 701106.6131 257755.0345 463906.0427 656904.7825 0.566614742 0.979977446 0.910528117 1.277547313 0.914565557 1.078748556 1.067288033 0.392378076 0.706199825 1 19.32532474 1.756902809 25 0.641796442 0.982584118 0.22981059 0.219305431 8.336104637 11373.39329 0.097911406 0.054297457 57.13507593 -1.756902809 0.340787677 (ac)T(ph)TS(ph)QKHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSQKHR 7 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.643)T(0.414)S(0.942)QKHR 44.135 0.056877 162050000 140530 99940 99551 99401 109320 111590 109260 78850 106250 101740 TRUE FALSE 135037.9322 97089.80905 117542.0802 104531.0975 112836.3771 113846.4263 110597.1566 77221.71995 94188.94544 94849.05918 1.423713987 1.023624376 1.239254044 1.10207838 1.1896415 1.200290517 1.166033248 0.814153779 0.993040376 1 16.53334584 1.756911448 25 0.922576926 1.184184622 0.541043505 0.107824692 5.030917338 6860.714363 0.045316671 0.025130749 57.13621249 -1.756911448 0.261607696 YHDEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 YHDEKK 6 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 94.151 0.029087 209508000 595580 522020 365090 434160 444410 484040 488150 300790 461180 446350 FALSE TRUE 572304.0752 507132.5007 431069.8844 456567.0496 458704.8513 493827.6204 494124.1257 294578.5814 408828.7798 416118.3169 1.375339782 1.218721888 1.035931049 1.097204884 1.102342369 1.186748096 1.187460647 0.707920246 0.982482057 1 18.66663427 1.75693581 24.99999993 0.872679075 1.16354618 0.54884696 0.11351503 5.254180843 7155.670248 0.052477727 0.029101881 57.13941761 -1.75693581 0.290867104 T(ph)T(ph)IEEDKS(ph)VLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTIEEDKSVLK 11 1 Q86TU7 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 3 T(1)T(1)IEEDKS(1)VLK 45.973 0.087907 0 304860 266850 285770 251310 289710 329350 305790 104060 240980 255660 TRUE FALSE 292945.7342 259239.6993 337414.9959 264280.1392 299028.7853 336009.6827 309532.3495 101911.1246 213624.9607 238343.9205 1.229088342 1.087670702 1.41566437 1.108818462 1.2546105 1.409768212 1.298679441 0.427580131 0.896288692 1 17.8626853 1.756944373 25 0.72622655 1.257286292 0.621115705 0.171675555 4.108518203 5592.782634 0.074849516 0.041508393 57.14054427 -1.756944373 0.531059742 FRQCVNT(ph)FGSYICKCHKGFDLMYIGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FRQCVNTFGSYICKCHKGFDLMYIGGK 27 3 H0YAK9;D6RH31;Q6UXI9-2;Q6UXI9-5;Q6UXI9;Q6UXI9-4;Q6UXI9-6;Q6UXI9-3 H0YAK9 NPNT Nephronectin 1 FRQCVNT(0.342)FGS(0.342)Y(0.316)ICKCHKGFDLMY(0.001)IGGK 57.945 0.039649 169550000 91918 139040 221390 101170 197110 199600 161790 57032 73405 82021 TRUE FALSE 88325.74294 135074.7153 261400.0978 106391.3958 203450.2222 203636.0488 163770.0344 55854.26927 65072.37214 76465.64461 1.155103621 1.76647586 3.41852997 1.391362047 2.660674911 2.663105108 2.141746601 0.730449204 0.85100142 1 16.22252408 1.756951214 5.734472839 0.848188238 2.215411364 0.479362393 0.624289493 0.139991145 11.4500558 0.306771014 0.163102351 57.14144438 -1.756951214 1.367223126 EMEKS(ph)FDEQNVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EMEKSFDEQNVPK 13 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 EMEKS(1)FDEQNVPK 59.872 0.058202 601090000 401960 305660 173830 179860 293510 233150 214320 371410 314190 231140 TRUE FALSE 386250.9588 296942.8761 205244.9478 189142.5962 302951.0157 237864.4527 216942.9123 363740.2537 278524.4684 215484.6819 1.792475249 1.378023131 0.952480455 0.877754254 1.405905111 1.103857827 1.006767211 1.688009795 1.292548806 1 17.71722579 1.756969979 25 1.397692847 1.202684437 0.010032276 0.298282801 20.950016 28478.80237 0.139756273 0.077503235 57.14391336 -1.756969979 -0.19500841 VNAVPRPIPEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNAVPRPIPEKK 12 2 Q9HD45 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ; 102.66 0.0013105 839110000 834130 966740 735600 781050 749210 941370 845510 1093800 1155370 1019690 FALSE TRUE 801531.2774 939169.5217 868539.2833 821360.0841 773309.0201 960405.1464 855857.6043 1071212.648 1024217.241 950625.4881 0.843161989 0.987949023 0.913650322 0.864020684 0.813473897 1.010287604 0.90030997 1.126850333 1.077414033 1 19.85851756 1.756992746 12.5428293 1.075803862 0.907219406 0.580500431 0.063520947 0.147515886 96.57038109 0.029255218 0.016092068 57.14690908 -1.756992746 -0.168584456 RPAEDTDRETVAGIPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPAEDTDRETVAGIPNK 17 2 F8W108;F8WCU9;Q68CP9-3;Q68CP9;F8VWP4 F8W108 ARID2 AT-rich interactive domain-containing protein 2 0 70.41 0.018388 109590000 157210 154860 122200 122430 130710 149570 132580 160590 158560 146330 FALSE TRUE 151066.0594 150443.5444 144284.2583 128748.627 134914.4059 152594.4079 134202.5537 157273.7604 140560.9335 136418.9388 1.107368675 1.102805415 1.057655628 0.943773849 0.988971231 1.11857202 0.983753098 1.152873361 1.030362315 1 17.05768442 1.756993496 25 1.077084535 1.043095144 0 0.066173792 26.86202449 36468.82508 0.031155754 0.017277256 57.14700779 -1.756993496 -0.033989391 LVEQLKEER ddPTM_BT-474_Pertuzumab_2h_R1 4 LVEQLKEER 9 1 O95232;J3KPP4 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 182.28 4.24E-05 3352440000 4417640 4314920 3211160 3440230 3828080 3884340 3894750 4267600 4597710 4413560 FALSE TRUE 4244993.745 4191862.706 3791488.044 3617780.683 3951213.67 3962884.016 3942415.116 4179472.569 4075797.236 4114625.65 1.031684072 1.018771345 0.921466098 0.879249047 0.960285092 0.9631214 0.958146731 1.015760102 0.990563318 1 21.97232975 1.757011118 13.94156201 1.002242592 0.959270552 0.165503419 0.041180268 0.586546928 441.5593885 0.021138506 0.011656972 57.1493267 -1.757011118 -0.042972041 T(ph)PPKS(ph)PSSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPPKSPSSAK 10 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 2 T(1)PPKS(0.882)PS(0.102)S(0.016)AK;T(1)PPKS(0.589)PS(0.355)S(0.056)AK 89.231 0.026705 1361980000 4221600 3403400 3180000 2671000 2998900 2929800 3244400 4088200 4491800 3772900 TRUE FALSE 4056615.205 3306338.364 3754696.739 2808850.63 3095362.342 2989042.563 3284105.938 4003777.241 3981909.695 3517358.122 1.153313101 0.940006178 1.067476387 0.798568281 0.88002479 0.849797621 0.933685403 1.138291042 1.132074005 1 21.7460608 1.757048739 9.408968636 1.099956741 0.938583459 0.287344676 0.103050746 0.1676226 58.80715838 0.049565665 0.027017852 57.15427745 -1.757048739 -0.161373281 HNS(ph)WSSSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 HNSWSSSSR 9 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 HNS(0.933)WS(0.056)S(0.009)S(0.001)SR;HNS(0.953)WS(0.046)SSSR;HNS(0.974)WS(0.025)S(0.001)SSR;HNS(0.788)WS(0.141)S(0.06)S(0.011)SR 134.73 0.00025249 1247540000 1180680 1486520 1131510 1450290 1351510 1294860 1313250 840630 1151630 1254550 TRUE FALSE 1134537.72 1444125.905 1335999.027 1525139.641 1394982.547 1321042.956 1329321.946 823270.6967 1020901.79 1169578.211 0.970040062 1.234740774 1.14229131 1.304008254 1.192722755 1.129503734 1.136582345 0.703903928 0.872880309 1 20.15755691 1.757097112 25 0.835441972 1.16665147 0.625736132 0.105593344 4.166728215 5625.226866 0.04654157 0.025809983 57.16064387 -1.757097112 0.331209497 TVDKFNEWFVSAFVTAGHMR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVDKFNEWFVSAFVTAGHMR 20 1 F5H785;P0DI82;P0DI81;P0DI81-3 F5H785 TRAPPC2;TRAPPC2B Trafficking protein particle complex subunit 2B;Trafficking protein particle complex subunit 2 0 80.236 0.0039587 65566000 119640 119750 103130 116390 118880 119130 118940 105820 128990 119300 FALSE TRUE 114964.3365 116334.8472 121767.8851 122396.9018 122703.8832 121538.8902 120395.6233 103634.78 114347.596 111219.7047 1.03366878 1.045991333 1.094840931 1.100496554 1.103256689 1.09278199 1.082502634 0.93180233 1.028123535 1 16.76305289 1.757121056 25 0.981871839 1.080691768 0.649381328 0.031050193 4.371296862 5893.776436 0.014529376 0.008057425 57.16379542 -1.757121056 0.098819929 KRPQS(ph)PS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 KRPQS(1)PS(1)PR;KRPQS(1)PS(1)PR 93.766 0.034445 745748000 1792190 1715980 1450920 1536620 1577420 1664200 1588840 1899310 1899290 1799360 TRUE FALSE 1722149.233 1667041.931 1713133.52 1615925.142 1628159.147 1697851.264 1608284.699 1860088.585 1683690.562 1677487.744 1.026624033 0.993772942 1.0212495 0.963300714 0.970593766 1.012139296 0.95874602 1.108853755 1.003697683 1 20.6778708 1.757184239 25 1.048028629 0.992320466 0.235667459 0.035807318 8.40829041 11298.31932 0.015643402 0.008675183 57.17211241 -1.757184239 -0.055708163 KLHAVVETLVNHR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLHAVVETLVNHR 13 1 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 200.21 4.54E-08 275140000 352870 342190 321200 356330 357050 418950 393530 285710 402360 397100 FALSE TRUE 339079.4503 332431.0762 379247.9851 374720.234 368534.8375 427421.456 398346.1379 279809.9887 356685.7796 370204.0633 0.915925793 0.897967119 1.024429558 1.012199139 0.995491066 1.154556361 1.076017735 0.755826357 0.963484237 1 18.4979612 1.75720023 25 0.882971792 1.012092672 0.203182608 0.091338209 10.15280849 13630.72131 0.043705547 0.024237483 57.17421761 -1.75720023 0.12912088 QS(ph)PLTYEDHGAPFAGHLPR ddPTM_BT-474_Pertuzumab_2h_R1 3 QSPLTYEDHGAPFAGHLPR 19 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 QS(0.997)PLT(0.003)YEDHGAPFAGHLPR;QS(1)PLTYEDHGAPFAGHLPR;QS(0.98)PLT(0.02)YEDHGAPFAGHLPR 278.61 2.49E-39 1589140000 783900 1002330 785860 1120860 967450 1130420 1034520 644745 939130 1039690 TRUE FALSE 753264.3214 973744.5298 927882.3834 1178707.719 998568.9079 1153277.867 1047180.765 631430.7904 832523.8996 969270.8702 0.777145321 1.00461549 0.95729936 1.216076698 1.030226883 1.189840634 1.080379899 0.651449259 0.858917693 1 19.88654037 1.75724806 25 0.804846018 1.044800692 0.289073935 0.140463687 8.113478997 10864.89242 0.064562948 0.035804043 57.18051466 -1.75724806 0.239954674 ETNGNEDEEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETNGNEDEEGR 11 0 Q9BUQ8;H0YIL9 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 135.99 0.00025265 47271000 56634 43745 43349 48031 51344 47533 50684 42322 53125 52533 FALSE TRUE 54420.68067 42497.43543 51183.12859 50509.88567 52995.52639 48494.14983 51304.28595 41448.03591 47094.47272 48974.89312 1.111195496 0.867739217 1.045089133 1.031342438 1.082095805 0.990183883 1.047563 0.846311922 0.9616044 1 15.57975472 1.757250261 25 0.921700732 1.020849254 0.237516162 0.071494399 9.54387794 12778.8579 0.031372358 0.017397638 57.18080442 -1.757250261 0.099148522 AVGMPS(ph)PVSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVGMPSPVSPK 11 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 AVGMPS(1)PVSPK 184.98 4.90E-06 209510000 426520 439920 358960 391840 389210 424930 413400 472410 493800 470180 TRUE FALSE 409851.1269 427373.9123 423832.057 412062.9094 401729.2931 433522.3757 418459.3129 462654.5684 437745.8942 438334.2898 0.935019542 0.974995391 0.96691513 0.940065423 0.916490684 0.989022273 0.954657946 1.055483404 0.998657655 1 18.74167202 1.757251326 25 1.022298765 0.954576421 0.590478144 0.024406194 4.916636101 6582.797805 0.011037409 0.006120957 57.18094467 -1.757251326 -0.067722344 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR 34 0 P46060;H0Y4Q3 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ; 187.04 2.66E-20 615050000 166286 209348 199047 206510 205137 216239 233060 127406 227845 218170 FALSE TRUE 159787.3593 203377.6 235019.2207 217168.0058 211735.4179 220611.5007 235912.258 124775.0216 201980.9908 203393.1516 0.785608355 0.999923539 1.155492301 1.067725261 1.041015473 1.084655501 1.159882996 0.613467172 0.99305699 1 17.63391158 1.757316352 25 0.831978386 1.047374326 0.227947792 0.141028352 8.947537163 11938.11297 0.063430024 0.035175689 57.18950686 -1.757316352 0.215395941 RLS(ph)MSEVKDDNSATK ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSMSEVKDDNSATK 15 2 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 RLS(0.826)MS(0.174)EVKDDNSATK;RLS(0.997)MS(0.003)EVKDDNSATK;RLS(1)MSEVKDDNSATK 242.34 3.33E-18 638527000 425314 386940 308580 275919 348003 354508 343993 514163 472584 427365 TRUE FALSE 408692.2587 375904.8501 364347.2703 290159.2127 359196.8325 361676.3947 348202.8892 503545.3544 418938.2456 398419.1879 1.025784578 0.943490829 0.914482237 0.728276201 0.901555054 0.907778555 0.873961144 1.263858192 1.051501178 1 18.6039276 1.757316661 25 1.127886136 0.895444752 0.495281579 0.094304608 5.661086634 7553.092808 0.043305582 0.02401545 57.18954754 -1.757316661 -0.232441384 HPQHLHQQHHGDAAQHTR ddPTM_BT-474_Pertuzumab_2h_R1 3 HPQHLHQQHHGDAAQHTR 18 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 ;; 88.565 0.00093939 95191200 13482.92 15352.4 13588.48 17126.6 18220 25281.1 19094.2 1614.72 19729.5 4967.4 FALSE TRUE 12955.99258 14914.56458 16044.22061 18010.50588 18806.06285 25792.30116 19327.88053 1581.375468 17489.88987 4630.953573 2.797694335 3.220624942 3.464560885 3.88915708 4.060948258 5.569544318 4.173628654 0.341479448 3.776736172 1 12.17709358 1.757335714 25 1.695358567 3.912821651 0.465597351 1.068058109 6.782793231 9040.493342 0.49395274 0.27392544 57.19205667 -1.757335714 2.217463084 EVLEALGEVMVSRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVLEALGEVMVSRPR 15 1 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ; 242.26 5.86E-18 365890000 595170 613010 444470 573460 625630 545610 579310 426570 590440 536550 FALSE TRUE 571910.0984 595527.555 524795.6162 603056.3393 645753.9571 556642.608 586399.7691 417761.1804 523415.7265 500208.9906 1.143342301 1.190557479 1.049152706 1.205608757 1.290968314 1.112820078 1.172309535 0.835173274 1.04639408 1 18.93217146 1.757358225 25 0.94835892 1.167053415 0.596461024 0.077404279 4.870632973 6484.073171 0.034895275 0.019351567 57.19502114 -1.757358225 0.218694495 DLYDKFEEELGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLYDKFEEELGSR 13 1 Q9NRR4-3;Q9NRR4-2;Q9NRR4-4;Q9NRR4;H7C5U6 Q9NRR4-3 DROSHA Ribonuclease 3 0 95.981 0.0040555 49716000 119330 122470 106210 109390 121290 120190 128970 140300 163730 158490 FALSE TRUE 114666.4517 118977.2755 125404.5096 115035.631 125191.403 122620.3241 130548.3734 137402.756 145144.0568 147755.3311 0.776056274 0.805231693 0.848730862 0.778554859 0.847288568 0.829887647 0.883544251 0.929934338 0.982327038 1 17.17285066 1.757392849 0.908016457 1.005157124 0.806624079 0.917017877 0.021790197 0.135608753 0.210067888 0.018305725 0.007795611 57.19958119 -1.757392849 -0.198533045 NATTGRIVSPGFPGNYSNNLTCHWLLEAPEGQRLHLHFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NATTGRIVSPGFPGNYSNNLTCHWLLEAPEGQRLHLHFEK 40 2 H0YGK0;H0YFX0;H0YF95;A0A0A0MSU7;C9JFF1;Q53EL9-4;Q53EL9-2;Q53EL9-3;Q53EL9 H0YGK0 SEZ6 Seizure protein 6 homolog 0 23.069 0.090046 942060000 3251600 1026600 1120900 566770 1743300 957120 1374500 2532000 2623900 1257900 FALSE TRUE 3124523.877 997322.3731 1323471.564 596021.0676 1799374.828 976473.6222 1391321.542 2479713.315 2326045.872 1172701.313 2.664381666 0.850448757 1.128566627 0.50824627 1.534384594 0.832670358 1.186424478 2.114531031 1.983493876 1 20.16140417 1.757394557 25 1.805916888 1.19114132 0.091984359 0.614767253 13.51384261 17955.67549 0.27107199 0.150325019 57.19980615 -1.757394557 -0.614775568 SGLDLHHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGLDLHHR 8 0 K7ENM7;Q9UK11 K7ENM7 ZNF223 Zinc finger protein 223 0 64.265 0.068081 107290000 145870 149000 135040 166180 156480 161090 171040 86057 153070 165370 FALSE TRUE 140169.2391 144750.6659 159444.7319 174756.5697 161513.3213 164347.3502 173133.2387 84279.89288 135694.1353 154169.3426 0.909190094 0.938906941 1.034218148 1.133536453 1.047635792 1.066018363 1.123006921 0.546670897 0.880162898 1 17.23415638 1.757403902 25 0.766204844 1.037610126 0.392019174 0.126289098 6.39693559 8495.308831 0.05658806 0.031381377 57.20103696 -1.757403902 0.271405282 LSEELSGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSEELSGGR 9 0 B4DXW1;P61158;Q9P1U1-2;Q9P1U1 B4DXW1 ACTR3;ACTR3B Actin-related protein 3;Actin-related protein 3B 0 ; 225.24 6.53E-07 406110000 259870 329070 271630 343040 339840 362860 324970 258979 331340 316184 FALSE TRUE 249713.9931 319685.2458 320719.5834 360744.3355 350771.2622 370197.2778 328947.0801 253630.9931 293727.6723 294768.5761 0.847152693 1.0845296 1.088038582 1.223822228 1.189988658 1.255891258 1.115950297 0.860441084 0.996468742 1 18.16922321 1.757444972 25 0.941933151 1.1253228 0.30481735 0.111552422 9.018195376 11950.33715 0.053661653 0.029758543 57.20644657 -1.757444972 0.183389649 GTDDS(ph)PKDSQEDLQER ddPTM_BT-474_Pertuzumab_2h_R1 2 GTDDSPKDSQEDLQER 16 1 Q969E4;Q5H9L2;Q6IPX3-2;Q6IPX3 Q969E4 TCEAL3;TCEAL5;TCEAL6 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5;Transcription elongation factor A protein-like 6 1 GTDDS(1)PKDSQEDLQER;GTDDS(0.998)PKDS(0.002)QEDLQER 229.59 1.84E-15 1759940000 1467600 1217750 1023270 1045800 1201010 1184420 1100390 1552700 1467510 1205540 TRUE FALSE 1410244.569 1183020.962 1208197.652 1099773.863 1239641.577 1208369.784 1113856.902 1520636.202 1300924.417 1123887.702 1.254791352 1.052614919 1.075016347 0.978544263 1.102994165 1.075169505 0.991074909 1.353014362 1.157521712 1 20.10006646 1.757524092 25 1.205661332 1.072113414 0.113223824 0.107875937 10.98998061 14502.38983 0.047206973 0.026179116 57.21686944 -1.757524092 -0.133547918 GHLDAELDAYMAQTDPETND ddPTM_BT-474_Pertuzumab_2h_R1 2 GHLDAELDAYMAQTDPETND 20 0 X6R700;Q9Y3Y2-4;Q9Y3Y2;Q9Y3Y2-3 X6R700 CHTOP Chromatin target of PRMT1 protein 0 ; 260.19 5.87E-36 153364000 320120 321700 297690 341710 361040 344130 344950 275250 347110 356520 FALSE TRUE 307609.3565 312525.431 351489.2051 359345.6941 372653.1795 351088.5444 349171.6013 269565.9913 307707.528 332372.5828 0.92549558 0.940286435 1.057515641 1.081153238 1.121191093 1.056310185 1.050542732 0.811035582 0.925790946 1 18.34244185 1.757533697 25 0.895229699 1.036690171 0.36946852 0.071263796 7.65070229 10090.75706 0.034773304 0.019283832 57.21813484 -1.757533697 0.141460473 DLS(ph)LEEIQK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLSLEEIQK 9 0 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN2 Stathmin;Stathmin-2 1 DLS(1)LEEIQK;DLS(1)LEEIQK;DLS(1)LEEIQK 183.99 6.31E-05 512040000 1015380 866020 771540 776170 843320 813180 861990 1006460 1063010 960330 TRUE FALSE 975697.827 841321.9575 910974.4408 816228.2267 870446.1537 829623.0568 872539.2915 985676.2493 942341.5613 895285.9937 1.089816923 0.939724248 1.017523392 0.911695517 0.972254855 0.926657026 0.974592809 1.100962437 1.052559258 1 19.77198909 1.75754945 25 1.059931997 0.971717232 0.290743898 0.052953354 8.188885184 10791.60632 0.023168245 0.012848289 57.22021033 -1.75754945 -0.088214765 KT(ph)SPQVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTSPQVK 7 1 E9PSC8;E9PKA8;Q6ZUT1-3;Q6ZUT1;Q6ZUT1-2 E9PSC8 C11orf57 Uncharacterized protein C11orf57 1 KT(0.5)S(0.5)PQVK;KT(0.868)S(0.132)PQVK 77.379 0.022389 1234220000 311781 276705 260571 259546 263806 285885 282668 336569 365113 343315 TRUE FALSE 299596.2538 268813.6443 307661.9761 272941.2002 272291.5596 291665.7906 286127.3755 329618.7325 323666.9029 320061.9693 0.936057022 0.839879992 0.961257524 0.852776107 0.850746373 0.911279123 0.893974927 1.029859103 1.011263237 1 18.28799174 1.757575639 6.251144423 1.014720793 0.890246764 0.694017554 0.036894844 0.083085392 8.635861463 0.017165246 0.009194255 57.22366093 -1.757575639 -0.124474029 SLSQS(ph)FENLLDEPAYGLIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.08)LS(0.241)QS(0.679)FENLLDEPAYGLIQK;S(0.007)LS(0.04)QS(0.953)FENLLDEPAYGLIQK 260.08 1.64E-36 332230000 362200 344830 247490 310910 297800 258710 282080 407400 351770 356280 TRUE FALSE 348044.8236 334995.786 292216.9484 326956.1024 307379.0075 263941.2935 285532.1794 398987.0476 311838.5443 332148.8383 1.047858019 1.008571301 0.87977712 0.984366238 0.925425508 0.794647649 0.859651296 1.201229695 0.938851829 1 18.34147034 1.757597657 25 1.065187372 0.926679736 0.24378396 0.093574807 9.950137384 13079.40988 0.043969539 0.024384003 57.22656224 -1.757597657 -0.138507636 MALIQLGSVEEAIQALIELHNHDLGENHHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 MALIQLGSVEEAIQALIELHNHDLGENHHLR 31 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-7 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 ;;; 236.03 2.92E-46 1006200000 370615 389753 362673 435690 423916 379489 421624 36373.1 412940 126591 FALSE TRUE 356130.9561 378637.626 428216.0787 458176.0131 437551.6431 387162.5276 426783.9606 35621.98277 366064.7824 118016.8788 3.017627306 3.208334518 3.628430806 3.882292243 3.707534444 3.280569114 3.616295948 0.301838035 3.101800235 1 16.84863368 1.757601039 24.99999973 1.447165415 3.489632906 0.636929003 0.695136358 4.568140427 6003.731786 0.297566937 0.165018299 57.2270079 -1.757601039 2.042467491 LIEVDDERK ddPTM_BT-474_Pertuzumab_2h_R1 5 LIEVDDERK 9 1 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;;;; 163.64 0.0001008 2344430000 2068130 1784920 1609280 1510240 1866040 1824570 1800140 2194880 2346290 2189260 FALSE TRUE 1987305.193 1734015.829 1900112.694 1588183.667 1926062.871 1861464.056 1822170.652 2149554.961 2079948.996 2040979.47 0.973701707 0.849599839 0.930980797 0.778147792 0.943695368 0.912044478 0.892792249 1.053197738 1.019093541 1 20.96083024 1.757657718 8.39155181 1.025931384 0.894433131 0.551407692 0.052336546 0.098148355 24.50692355 0.023683314 0.012865129 57.23447696 -1.757657718 -0.131498253 NAEFSFHEALTHLLHSHLLPEVFTLATLR ddPTM_BT-474_Pertuzumab_2h_R1 3 NAEFSFHEALTHLLHSHLLPEVFTLATLR 29 0 O15296-4;O15296;I3L1D5;O15296-3;O15296-2 O15296-4 ALOX15B Arachidonate 15-lipoxygenase B 0 ;; 94.192 0.00044284 200891000 67217 85433 54693 80931 87126 66373 73443 40610 78327 44387 FALSE TRUE 64590.08533 82996.53449 64577.24174 85107.85861 89928.48692 67715.10754 74341.8174 39771.38931 69435.64733 41380.62895 1.560877323 2.005685669 1.560566946 2.05670771 2.173202515 1.636396286 1.796536671 0.961111281 1.677974673 1 15.33666795 1.757668115 25 1.225707373 1.83855717 0.526839832 0.266463715 6.04418865 7915.726775 0.117267386 0.06503153 57.23584714 -1.757668115 0.612849797 TLHS(ph)PPLQLQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLHSPPLQLQQR 12 0 B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;A0A2R8YGT1;F8W9A8;Q6PFW1 B7WPL9 PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 1 TLHS(1)PPLQLQQR;T(0.001)LHS(0.999)PPLQLQQR 171.46 2.47E-05 719460000 336640 375850 324890 358110 354480 313460 362860 269730 364830 361260 TRUE FALSE 323483.7366 365131.126 383604.8501 376592.1 365882.1711 319798.376 367300.7892 264159.9812 323416.0279 336791.5384 0.960486532 1.084145783 1.138997886 1.118175658 1.086375783 0.949543974 1.090587937 0.78434269 0.960285491 1 18.36149637 1.757770841 25 0.895569457 1.063930155 0.416059379 0.078390653 6.794111222 8850.219774 0.035806426 0.019856658 57.24938699 -1.757770841 0.168360698 DNLHAVFCLAENSVGPNATRPDDIHLLYSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DNLHAVFCLAENSVGPNATRPDDIHLLYSGK 31 1 Q8NDH3-3;Q8NDH3-2;Q8NDH3;Q8NDH3-5;Q8NDH3-4 Q8NDH3-3 NPEPL1 Probable aminopeptidase NPEPL1 0 143.01 1.40E-08 450770000 82431 93767 74308 86255 79481 76389 85768 62127 77151 95571 FALSE TRUE 79209.50539 91092.85697 87737.10857 90706.63089 82037.57855 77933.63792 86817.65444 60844.05574 68393.14192 89097.89104 0.889016614 1.02239072 0.984727108 1.018055869 0.920757805 0.874696775 0.974407513 0.682889965 0.767617966 1 16.44310366 1.75779324 25 0.786305651 0.956645743 0.321509195 0.088591333 7.364202374 9581.653513 0.039170735 0.021722601 57.25233977 -1.75779324 0.170340092 S(ph)ASPHDVDLCLVSPCEFEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.566)AS(0.434)PHDVDLCLVSPCEFEHR;S(0.571)AS(0.429)PHDVDLCLVSPCEFEHR 242.9 5.31E-30 3551000000 175122 201656 167698 214229 186191 195063 202801 159546 212444 202781 TRUE FALSE 168278.0386 195904.9683 198004.759 225285.3844 192180.0026 199007.3075 205282.9393 156251.3193 188328.2478 189046.4623 0.890141168 1.036279473 1.047386746 1.191693204 1.016575504 1.052689932 1.085886172 0.826523371 0.996200857 1 17.52838133 1.757800828 25 0.925091657 1.050253289 0.244551768 0.082848026 9.693151153 12606.89788 0.0378526 0.020991315 57.25334003 -1.757800828 0.125161632 SNVVS(ph)PTKNEDNGAPENSVEKPHEKPEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNVVSPTKNEDNGAPENSVEKPHEKPEAR 29 3 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 S(0.003)NVVS(0.807)PT(0.19)KNEDNGAPENSVEKPHEKPEAR;SNVVS(0.946)PT(0.054)KNEDNGAPENSVEKPHEKPEAR 159.78 2.89E-12 1185220000 674320 531200 570740 430101 566430 581760 698310 744960 974860 908400 TRUE FALSE 647966.8289 516050.6961 673885.414 452298.5642 584649.7354 593523.5858 706856.1267 729576.3157 864197.9797 846873.2589 0.765128456 0.609360008 0.79573349 0.534080583 0.69036273 0.700841099 0.834665777 0.8614941 1.020457277 1 19.69178655 1.75780345 1.171767022 1.012551271 0.67295116 0.754182736 0.073572167 0.208887757 0.535576846 0.057746265 0.022883448 57.25368573 -1.75780345 -0.339600111 SSSRPCS(ph)PVHHHEGHAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSRPCSPVHHHEGHAK 17 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 1 S(0.222)S(0.222)S(0.222)RPCS(0.335)PVHHHEGHAK 62.064 0.023209 226030000 37009 49281 44862 60052 46065 52003 55590 3371.7 57474 16616 TRUE FALSE 35562.64736 47875.55413 52969.56135 63151.29092 47546.72256 53054.53629 56270.32705 3302.073217 50949.79247 15490.58352 2.295759054 3.090623027 3.419468433 4.076753522 3.069395191 3.424954019 3.632550509 0.213166484 3.289081551 1 13.91910387 1.757831958 25 1.464282084 3.311913615 0.490094008 0.834459811 6.317073343 8202.688177 0.362918971 0.201260301 57.25744411 -1.757831958 1.84763153 EDALDDSVSSSSVHAS(ph)PLAS(ph)SPVRK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 2 EDALDDSVSSSSVHAS(1)PLAS(0.891)S(0.109)PVRK 276.2 4.62E-53 628350000 135320 212450 214240 272000 254440 268590 231870 158090 200590 243440 TRUE FALSE 130031.5448 206391.134 252957.9337 286037.9526 262624.2937 274021.0738 234707.6944 154825.3863 177819.8641 226951.592 0.57294837 0.909405976 1.114589819 1.260347857 1.157181985 1.207398774 1.03417514 0.682195639 0.783514505 1 17.79202508 1.75792106 25 0.793746152 1.054502749 0.191781133 0.197066648 11.97891568 15482.89413 0.096184148 0.053339872 57.26919251 -1.75792106 0.260756597 QHTFVETESVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QHTFVETESVR 11 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 165.7 2.13E-05 1902020000 387930 385340 318970 370450 382080 322600 371710 224360 320130 378140 FALSE TRUE 372769.2667 374350.4805 376614.9744 389568.9689 394369.9502 329123.193 376259.0982 219726.8876 283790.1845 352528.241 1.05741675 1.061902103 1.068325685 1.105071661 1.118690375 0.93360802 1.067316188 0.623288753 0.805014043 1 18.42737931 1.757943283 25 0.77534729 1.058638286 0.569787968 0.098003542 4.912285832 6341.899764 0.042747769 0.023706269 57.2721231 -1.757943283 0.283290995 ERFTEHEVQIYVGEIVLALEHLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERFTEHEVQIYVGEIVLALEHLHK 24 1 O75582-3;O75582;O75582-2;A0A3B3ISL8;G3V2D1 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 ; 158.69 7.65E-12 170356000 285350 274240 228980 242110 276830 296890 297770 104283 314520 170858 FALSE TRUE 274198.2065 266418.9437 270361.7796 254605.3261 285734.4884 302893.3192 301414.1983 102129.5196 278817.0082 159285.6355 1.72142457 1.672586124 1.697339367 1.598419879 1.793849693 1.901573348 1.892287383 0.641172189 1.750421545 1 17.28125664 1.757947912 25 1.108273172 1.749854921 0.530802003 0.268322827 5.874357144 7582.148774 0.11571497 0.064170697 57.27273361 -1.757947912 0.641581749 KMLEDPQER ddPTM_BT-474_Pertuzumab_2h_R1 3 KMLEDPQER 9 1 Q9BUQ8;H0YIL9 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ;; 90.913 0.017811 757230000 429390 464830 363597 395360 421870 468730 431110 415750 467900 466490 FALSE TRUE 412608.9641 451573.5035 429307.0661 415764.577 435439.8317 478208.0418 436386.0531 407164.6172 414785.9536 434894.2168 0.948757073 1.038352514 0.987152851 0.95601312 1.001254592 1.099596231 1.003430343 0.936238289 0.953762864 1 18.730305 1.757953364 25 0.957606677 1.007155389 0.160902833 0.042733872 13.31468034 17180.6857 0.020243999 0.011226586 57.27345257 -1.757953364 0.049548712 VKGNVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKGNVFK 7 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 121.52 0.0040402 3911300000 4314300 4095800 3491300 3195000 3683700 3666900 3791300 4396400 4460100 4453300 FALSE TRUE 4145692.386 3978991.794 4122255.574 3359894.333 3802189.556 3741047.23 3837699.064 4305612.804 3953808.146 4151674.024 0.998559223 0.958406602 0.992914075 0.809286643 0.915820831 0.901093681 0.924373889 1.037078725 0.9523407 1 21.98526174 1.757970435 25 0.998607049 0.926110975 0.250370521 0.053628062 11.52026088 14852.15237 0.025578326 0.014184707 57.27570383 -1.757970435 -0.072496074 GSGEKPVSAPGDDTES(ph)LHSQGEEEFDMPQPPHGHVLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GSGEKPVSAPGDDT(0.018)ES(0.491)LHS(0.491)QGEEEFDMPQPPHGHVLHR 151.79 6.30E-14 317420000 156100 167980 145010 173290 190720 231120 234780 26576 210800 176350 TRUE FALSE 149999.4394 163189.3749 171216.5327 182233.5177 196854.682 235793.4048 237653.3079 26027.19631 186870.8677 164405.6574 0.912373952 0.992601942 1.041427256 1.108438241 1.197371703 1.434217097 1.445529987 0.158310831 1.136644996 1 17.32690042 1.757990947 25 0.684529468 1.160383078 0.269083896 0.290689908 9.149668509 11783.47052 0.133050437 0.073784492 57.27840912 -1.757990947 0.47585361 HLLSYLVVDEAHCVSQWGHDFRPDYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLLSYLVVDEAHCVSQWGHDFRPDYLR 27 1 O94762-4;O94762;J3KSL7;J3KTQ2;O94762-2;O94762-3 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 0 115.63 0.00024938 43687000 19868 18552 15188 18593 17292 20182 18738 13292 15935 16998 FALSE TRUE 19091.53659 18022.91512 17932.80946 19552.58696 17848.21288 20590.09387 18967.32125 13017.51556 14126.1256 15846.71032 1.204763399 1.13732849 1.13164241 1.233857789 1.126303979 1.299329227 1.196924842 0.821464852 0.891423224 1 13.95189576 1.758020254 9.770194519 0.894716581 1.189269133 0.80687695 0.063987101 0.057931934 22.04427815 0.029446443 0.016086121 57.28227454 -1.758020254 0.294552552 ELLDMMIAEEESLKER ddPTM_BT-474_Pertuzumab_2h_R1 4 ELLDMMIAEEESLKER 16 1 O43663-2;O43663-4;O43663;H0YLA0 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 ;;; 165.45 6.40E-09 173887000 204136 197193 164609 184318 191839 193742 190156 191040 199802 209613 FALSE TRUE 196158.1394 191569.2487 194357.508 193830.6741 198009.6757 197659.596 192483.186 187094.9572 177121.3146 195415.7248 1.003799155 0.980316445 0.994584792 0.991888827 1.013274013 1.011482552 0.984993333 0.957420174 0.906382098 1 17.57618704 1.758037481 3.166679098 0.947731286 0.998237123 0.420096993 0.023070724 0.189300999 3.849647615 0.012332013 0.005951547 57.28454666 -1.758037481 0.050505837 KEPPKEETAQLTGPEAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEPPKEETAQLTGPEAGR 18 2 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 0 128.14 1.35E-05 400000000 110200 92573 87203 89124 108700 97572 99890 123320 127330 112920 FALSE TRUE 105893.2622 89932.90868 102962.5219 93723.70032 112196.4342 99544.97269 101112.4837 120773.3989 112876.0322 105271.8278 1.00590314 0.854292269 0.978063401 0.890301824 1.065778343 0.945599357 0.960489485 1.147252797 1.072233992 1 16.68375988 1.758083031 25 1.085960406 0.955204489 0.402364623 0.064163576 7.123397031 9130.594567 0.028178889 0.015627031 57.29055527 -1.758083031 -0.130755916 RPASVSSSAAVEHEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;; 174.59 2.48E-09 724956000 627031 901923 652141 929555 842130 994723 791963 695011 657873 774048 FALSE TRUE 602525.9353 876201.0391 769997.3855 977529.4449 869217.8763 1014836.981 801655.2801 680658.78 583194.0151 721621.0395 0.834961707 1.214212157 1.067038436 1.354629912 1.204535107 1.406329535 1.110908962 0.943235774 0.808172133 1 19.46088188 1.758085087 3.378189589 0.899511787 1.189464285 0.366326218 0.153847713 0.221426983 5.137887823 0.084491898 0.041416166 57.29082644 -1.758085087 0.289952498 HS(ph)PQQPSNGSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 HSPQQPSNGSLR 12 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 HS(1)PQQPSNGSLR;HS(0.999)PQQPS(0.001)NGSLR;HS(1)PQQPSNGSLR 167.89 5.04E-05 873490000 707224 801049 751781 919830 764919 815356 865011 565833 853479 836720 TRUE FALSE 679584.9042 778203.8668 887644.55 967302.5365 789523.3143 831843.057 875597.2634 554148.3508 756595.642 780048.2091 0.871208851 0.997635605 1.137935501 1.240054814 1.01214682 1.066399547 1.122491217 0.710402696 0.969934464 1 19.57320376 1.758097709 25 0.866788506 1.069145983 0.299872588 0.117122913 8.914086804 11417.2692 0.054485589 0.030215652 57.29249144 -1.758097709 0.202357477 LVEIDNGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVEIDNGK 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 138.54 0.0016302 246030000 415400 431100 363280 397930 412610 404540 397190 500400 488420 457070 FALSE TRUE 399165.7088 418805.4501 428932.7771 418467.215 425881.9754 412720.076 402050.93 490066.5651 432976.6092 426112.2418 0.936761889 0.982852425 1.006619231 0.982058655 0.999459611 0.968571272 0.943532925 1.150087975 1.016109294 1 18.70087397 1.758103443 25 1.069547136 0.976889458 0.416905598 0.042926521 6.69657793 8574.537262 0.018730716 0.010387152 57.29324795 -1.758103443 -0.092657678 VALSDDET(ph)KETENMR ddPTM_BT-474_Pertuzumab_2h_R1 1 VALSDDETKETENMR 15 1 Q15054;H0YD46;Q15054-3;Q15054-2 Q15054 POLD3 DNA polymerase delta subunit 3 1 VALS(0.16)DDET(0.833)KET(0.007)ENMR 245.19 2.81E-17 1203300000 1003600 811320 635440 734700 813230 790630 800890 998700 1100800 921400 TRUE FALSE 964378.2025 788181.948 750278.1433 772617.955 839388.2815 806617.0803 810691.5314 978076.496 975841.7989 858992.7573 1.122684905 0.917565301 0.873439429 0.899446414 0.977177368 0.939026637 0.943769926 1.138631831 1.136030299 1 19.71228644 1.758167638 9.398828374 1.101703999 0.947100275 0.425832005 0.073005429 0.124910497 42.80205171 0.034027178 0.01856773 57.30171733 -1.758167638 -0.154603724 TIDLGAAAHYTGDKASPDQNASTHT(ph)PQSSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 TIDLGAAAHYT(0.006)GDKAS(0.232)PDQNAS(0.232)T(0.232)HT(0.294)PQS(0.001)S(0.002)VK 59.436 0.018016 141260000 79901 74560 66220 65139 88933 82600 79053 62040 77064 84753 TRUE FALSE 76778.38058 72433.6218 78187.42706 68500.8316 91793.61071 84270.22859 80020.47426 60758.85232 68316.0178 79012.60382 0.971723205 0.916735031 0.989556391 0.866960817 1.16175909 1.066541596 1.012755819 0.768976712 0.864621775 1 16.26979518 1.75818197 25 0.856063525 0.998448151 0.254406025 0.092003369 10.14666642 12940.09847 0.043240879 0.023979696 57.30360835 -1.75818197 0.142384625 KDIPSFER ddPTM_BT-474_Pertuzumab_2h_R1 1 KDIPSFER 8 1 K7EJR3;R4GMR5;P48556 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 93.111 0.01812 167450000 127760 112610 96369 120390 119300 102920 111120 139050 136590 127520 FALSE TRUE 122766.998 109398.4731 113785.022 126603.3423 123137.3928 105001.1129 112479.9198 136178.5689 121084.8758 118882.9568 1.032671135 0.920219988 0.957118035 1.064941062 1.035786762 0.883231001 0.946139992 1.14548437 1.018521738 1 16.85918238 1.758189337 25 1.068329856 0.976216063 0.228175208 0.063844889 10.88220861 13872.91811 0.029975104 0.0166227 57.30458039 -1.758189337 -0.092113792 EKNGS(ph)EEDDDEKPGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKNGSEEDDDEKPGKR 16 3 Q6ZU65;Q6ZU65-2;H7C4P8 Q6ZU65 UBN2 Ubinuclein-2 1 EKNGS(1)EEDDDEKPGKR 96.55 0.01865 165510000 275970 169640 155920 112060 175670 154380 178570 241710 292900 209250 TRUE FALSE 265184.7873 164802.0333 184098.2124 117843.43 181320.5851 157501.6694 180755.3931 236718.604 259651.2199 195077.3111 1.359383035 0.844803695 0.943719243 0.604085782 0.929480646 0.807380769 0.926583374 1.213460462 1.331017013 1 17.57368647 1.758194222 4.908976127 1.204406752 0.897454935 0.278701231 0.192847468 0.208134545 11.25137346 0.095313596 0.049952538 57.30522499 -1.758194222 -0.306951817 MMLDQCLELQLFHR ddPTM_BT-474_Pertuzumab_2h_R1 2 MMLDQCLELQLFHR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 136.51 2.66E-05 242240000 192703 229911 174726 186768 195926 189126 201383 171846 205915 215799 FALSE TRUE 185171.9537 223354.1634 206302.875 196407.1189 202228.1377 192950.2573 203847.5854 168297.32 182540.3925 201182.7415 0.920416693 1.110205387 1.025450162 0.976262265 1.005196252 0.95907957 1.013245887 0.83653955 0.907336241 1 17.61814702 1.758199109 25 0.899305617 1.004067867 0.296450061 0.059787903 8.458065321 10777.19007 0.026471326 0.014680024 57.30586987 -1.758199109 0.104762249 IAVDEVHCCSQWGHDFRPDYK ddPTM_BT-474_Pertuzumab_2h_R1 1 IAVDEVHCCSQWGHDFRPDYK 21 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 100.28 0.00045961 513990000 53976 51842 54093 49162 58358 65262 65376 21516 55576 60120 FALSE TRUE 51866.55825 50363.51692 63868.80839 51699.25671 60235.13807 66581.64235 66176.09104 21071.68708 49267.24547 56048.01885 0.925395033 0.898578004 1.139537306 0.922410065 1.074705927 1.187939266 1.180703482 0.37595775 0.8790185 1 15.77437576 1.758269859 25 0.691929712 1.046576566 0.34388308 0.181427717 7.71025738 9789.035286 0.081063942 0.04495488 57.31520623 -1.758269859 0.354646854 MES(ph)GALDDFDK ddPTM_BT-474_Pertuzumab_2h_R1 1 MESGALDDFDK 11 0 Q5QNY5;E9PS71 Q5QNY5 PEX19 1 MES(1)GALDDFDK 58.37 0.055289 0 124760 282130 295800 267590 303710 360840 263110 90000 69221 142320 TRUE FALSE 119884.2413 274083.9286 349257.64 281400.352 313479.108 368136.432 266330.0189 88141.46855 61363.32228 132680.5396 0.903555575 2.065743246 2.632320015 2.120886399 2.362660785 2.774607588 2.007302801 0.664313461 0.462489243 1 17.01759726 1.758282835 4.454690534 0.663412506 2.185616728 0.635416169 0.490419402 0.117417616 5.00460888 0.257269488 0.133026144 57.31691874 -1.758282835 1.522204222 FMFNIADGGFTELHTLWQNEER ddPTM_BT-474_Pertuzumab_2h_R1 1 FMFNIADGGFTELHTLWQNEER 22 0 Q12873-3;Q12873;Q12873-2;H7C0J3;I3L229 Q12873-3;H7C0J3 CHD3 Chromodomain-helicase-DNA-binding protein 3 0 196.43 2.13E-22 94358000 54677 62491 45455 49590 59704 60343 55927 40803 52188 57617 FALSE TRUE 52540.16239 60708.81787 53669.72964 52149.34584 61624.43338 61563.1768 56611.45136 39960.40379 46263.83703 53714.54927 0.978136522 1.130211808 0.999165596 0.970860717 1.147257758 1.146117349 1.053931423 0.743940037 0.861290612 1 15.71302529 1.758305733 25 0.845853553 1.06425615 0.511144909 0.085328274 5.998383445 7601.766152 0.038687862 0.021454812 57.31994075 -1.758305733 0.218402598 DKAS(ph)PEPEKDFSEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DKASPEPEKDFSEK 14 2 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 DKAS(1)PEPEKDFSEK;DKAS(1)PEPEKDFSEK;DKAS(1)PEPEKDFSEK;DKAS(1)PEPEKDFSEK;DKAS(1)PEPEKDFSEK 163.79 2.20E-06 7139320000 10330650 7128950 7281430 4971520 7068560 7092520 7922950 10037490 12638280 9673760 TRUE FALSE 9926916.777 6925639.326 8597346.376 5228100.743 7295926.652 7235935.614 8019913.432 9830212.324 11203635.44 9018547.619 1.100722333 0.767932889 0.953296111 0.579705399 0.80899131 0.802339348 0.889268846 1.089999492 1.242288217 1 23.10446368 1.758311401 2.985254203 1.134489029 0.826251215 0.448332977 0.136724337 0.196335657 3.543800657 0.07659161 0.036416905 57.32068891 -1.758311401 -0.308237814 DLKPENILLDDNMQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLKPENILLDDNMQIR 16 1 J3KNN3;P15735-2;P15735;H3BTI9;H3BP07;H3BTW6 J3KNN3 PHKG2 "Phosphorylase b kinase gamma catalytic chain, liver/testis isoform" 0 ; 130.39 4.58E-05 126916000 99974 94273 88932 92145 88673 97709 95342 117754 118267 126179 FALSE TRUE 96066.90555 91584.42634 105003.9907 96900.61449 91525.24758 99684.74293 96508.82392 115322.3388 104841.826 117632.7839 0.816667789 0.778562092 0.892642231 0.823755175 0.778059011 0.847423138 0.820424551 0.980358833 0.891263664 1 16.84393067 1.75831648 9.085821363 0.950779248 0.822756012 0.69888773 0.040438002 0.08065609 25.1252643 0.01839164 0.010026251 57.32135924 -1.75831648 -0.128023235 CPTEVLLTPPTPLPPPS(ph)PPPTASDR ddPTM_BT-474_Pertuzumab_2h_R1 1 CPTEVLLTPPTPLPPPSPPPTASDR 25 0 Q6ZMT1 Q6ZMT1 STAC2 SH3 and cysteine-rich domain-containing protein 2 1 CPTEVLLTPPTPLPPPS(0.973)PPPT(0.02)AS(0.006)DR 86.543 0.010683 64406000 29852 42714 33507 52659 48855 51954 44647 37665 43269 41503 TRUE FALSE 28685.35084 41495.83854 39562.46026 55376.7373 50426.46544 53004.54548 45193.40334 36887.20459 38357.28452 38691.96484 0.741377466 1.072466563 1.022498093 1.431220604 1.303280039 1.369910928 1.168030715 0.953355683 0.991350134 1 15.23974637 1.758384803 6.902238087 0.980821149 1.174367744 0.15675812 0.185235475 0.288698402 39.90944072 0.096041308 0.051804161 57.33037772 -1.758384803 0.193546595 NHLVTLPEAIHFLTEIEVLDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 NHLVTLPEAIHFLTEIEVLDVR 22 0 Q13045-3;Q13045;Q13045-2;J3KS54;J3QQQ2 Q13045-3 FLII Protein flightless-1 homolog 0 63.69 0.017393 147490000 103690 106490 60211 73826 90380 122830 94459 48564 72043 61981 FALSE TRUE 99637.68016 103453.0095 71092.46709 77636.16871 93287.15478 125313.7068 95615.0175 47561.13643 63864.98067 57782.97166 1.724343302 1.790371912 1.230335946 1.34358214 1.614440242 2.168696125 1.654726553 0.823099523 1.105256079 1 15.81835678 1.758430529 9.257657438 0.978760013 1.643593067 0.608559199 0.246345043 0.108592226 35.54690509 0.127060487 0.069318566 57.3364142 -1.758430529 0.664833054 KATGAATPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KATGAATPK 9 1 P10412 P10412 HIST1H1E Histone H1.4 0 67.385 0.097889 266460000 364770 346150 266590 291300 375380 286220 281960 306870 260930 267000 FALSE TRUE 350514.3851 336278.1409 314768.7433 306334.0279 387454.4386 292007.5645 285410.7108 300533.0273 231310.3203 248915.8522 1.408164173 1.350971173 1.264558848 1.230673038 1.556567953 1.17311759 1.146615245 1.20736797 0.92927115 1 17.92529859 1.75848623 0.90777606 0.975233611 1.345702405 0.629653617 0.106827956 0.372161432 0.576107378 0.093702669 0.039928703 57.34376841 -1.75848623 0.370468793 SAPAS(ph)PNHAGVLSAHSSGAQTPESLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAPASPNHAGVLSAHSSGAQTPESLSR 27 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 S(0.048)APAS(0.952)PNHAGVLSAHSSGAQTPESLSR 182.17 2.68E-17 230310000 22902 51514 38449 57559 40830 56734 46195 28975 42207 43649 TRUE FALSE 22006.96452 50044.87116 45397.58959 60529.62689 42143.33403 57881.20035 46760.34823 28376.65612 37415.83831 40692.61435 0.540809797 1.229826885 1.115622339 1.487484347 1.035650688 1.422400632 1.149111429 0.697341682 0.91947492 1 15.31247935 1.758489114 25 0.847097507 1.162834919 0.186347732 0.25175632 12.33326272 15485.9878 0.112742454 0.062522703 57.34414926 -1.758489114 0.315737412 SHTEEDCTEELFDFLHAR ddPTM_BT-474_Pertuzumab_2h_R1 6 SHTEEDCTEELFDFLHAR 18 0 P07919 P07919 UQCRH "Cytochrome b-c1 complex subunit 6, mitochondrial" 0 ;;;;; 414.82 7.20E-148 2053130000 404080 578861 420535 846290 359729 543570 580406 66250 502664 329665 FALSE TRUE 388288.1069 562352.451 496535.0293 889967.1283 371300.01 554561.3578 587509.1822 64881.91435 445603.6901 307336.4959 1.263397325 1.829761381 1.615607114 2.895741769 1.208122091 1.804411013 1.911615412 0.211110347 1.449888627 1 18.22945957 1.758537968 25 0.825546912 1.805370521 0.38748958 0.518171121 8.12248493 10173.84801 0.229207425 0.12710961 57.35060022 -1.758537968 0.979823609 LQLLEDDKENR ddPTM_BT-474_Pertuzumab_2h_R1 6 LQLLEDDKENR 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;; 186.58 3.62E-06 19600300000 15903800 14988200 13286700 13677200 14453400 15271000 14845100 17001500 18245600 17304300 FALSE TRUE 15282261.91 14560751.21 15687902.25 14383081.93 14918306.74 15579790.08 15026778.77 16650413.08 16174435.98 16132264.35 0.947310408 0.902585706 0.97245507 0.891572418 0.924749708 0.965753458 0.931473626 1.032118785 1.002614117 1 23.94344562 1.75854703 9.717850135 1.012407928 0.933239061 0.67277393 0.02487878 0.083861069 31.11122345 0.011265392 0.006156105 57.35179695 -1.75854703 -0.079168866 RPDHSGGS(ph)PSPPTSEPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RPDHS(0.008)GGS(0.991)PSPPTSEPAR;RPDHS(0.011)GGS(0.988)PS(0.001)PPTSEPAR;RPDHS(0.01)GGS(0.99)PSPPTSEPAR 158.05 2.85E-11 708410000 212974 264182 196786 230744 248873 249388 205509 225199 200891 215564 TRUE FALSE 204650.7406 256647.788 232349.6077 242652.7255 256878.2261 254430.7962 208024.0806 220548.562 178086.6959 200963.6583 1.018347011 1.27708557 1.15617724 1.207445802 1.278232235 1.266053765 1.035132831 1.097454952 0.886163685 1 17.61657511 1.75854913 1.581058839 0.961300243 1.202019857 0.531872833 0.088437807 0.272885273 1.323258489 0.064146533 0.025627857 57.35207423 -1.75854913 0.240719614 AHFPLDVQWNDLDYMDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 AHFPLDVQWNDLDYMDSR 18 0 P10253 P10253 GAA Lysosomal alpha-glucosidase;76 kDa lysosomal alpha-glucosidase;70 kDa lysosomal alpha-glucosidase 0 ;;; 284.72 1.44E-39 734804000 320524 378783 307014 398033 338670 360316 356715 250004 334923 355472 FALSE TRUE 307997.5677 367980.4797 362498.2593 418575.5308 349563.6281 367601.8364 361080.5849 244841.33 296903.9452 331395.5648 0.929395564 1.110396513 1.093853684 1.2630692 1.054822892 1.109253941 1.089575792 0.738818971 0.895920093 1 18.33819477 1.758590934 25 0.855720218 1.099327024 0.502233572 0.097012127 6.219105903 7769.142262 0.043384153 0.024059124 57.35759517 -1.758590934 0.243606806 DREVGIPPEQSLETAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DREVGIPPEQSLETAK 16 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 161.86 7.55E-09 992432000 972620 909660 796707 858683 927930 956950 930030 1168420 1160400 1108830 FALSE TRUE 934608.9351 883717.3875 940689.6776 902999.7325 957777.7112 976300.1847 941411.9853 1144291.719 1028676.257 1033727.956 0.904114984 0.8548839 0.909997327 0.873537111 0.926527821 0.944445953 0.910696068 1.106956343 0.995113125 1 19.97942513 1.758592409 25 1.042201057 0.903153832 0.721300284 0.037087209 4.21050692 5259.536433 0.016762002 0.009295535 57.35778999 -1.758592409 -0.139047226 LEGDLTGPSVDVEVPDVELECPDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEGDLTGPSVDVEVPDVELECPDAK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 223.97 8.83E-34 182223000 201444 190951 149543 168898 184823 181496 181749 218942 227200 221944 FALSE TRUE 193571.3458 185505.2644 176568.7467 177614.846 190767.9996 185165.9735 183973.2986 214420.7712 201409.2085 206911.5352 0.935527087 0.89654385 0.853353809 0.85840959 0.921978562 0.894904063 0.889139885 1.036292012 0.973407347 1 17.65865455 1.758592773 12.25580855 1.003145415 0.891328684 0.774184481 0.027312219 0.103600448 61.05178947 0.012970305 0.007134658 57.35783798 -1.758592773 -0.111816731 ALPS(ph)EDEEGQDDKDFYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALPSEDEEGQDDKDFYLR 18 1 Q8NF91;Q8NF91-4;A0A0C4DG40;E7ENN3;H0Y325;Q8NF91-2;Q8NF91-8;Q8NF91-11;Q8NF91-3;Q8NF91-9;A0A5F9ZH87;A0A5F9ZHE1;Q5JV20;F8WAI0;H0Y326;A0A5F9ZH86;A0A5F9ZHB2 Q8NF91 SYNE1 Nesprin-1 1 ALPS(1)EDEEGQDDKDFYLR 167.16 1.45E-11 173880000 87849 87809 69155 67374 78124 72303 77908 102390 104190 100010 TRUE FALSE 84415.76396 85304.77329 81652.84684 70851.18021 80636.92941 73765.0162 78861.46141 100275.6107 92362.788 93236.23362 0.905396547 0.914931567 0.875763034 0.759910364 0.864866869 0.791162548 0.845824186 1.075500445 0.990631908 1 16.50860311 1.758666094 12.12698512 1.02400318 0.849224582 0.717549423 0.049123933 0.119668212 69.19583808 0.023978594 0.01318703 57.36752247 -1.758666094 -0.174778598 AT(ph)SPSSSVSGDFDDGHHSVSTPGPSR ddPTM_BT-474_Pertuzumab_2h_R1 6 ATSPSSSVSGDFDDGHHSVSTPGPSR 26 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;Q86U86-6;C9JQF1;C9JPI5;C9JCJ2;C9J053;C9J409 Q86U86-8 PBRM1 Protein polybromo-1 1 AT(0.49)S(0.49)PS(0.02)SSVSGDFDDGHHSVSTPGPSR;AT(0.484)S(0.484)PS(0.032)SSVSGDFDDGHHSVSTPGPSR;AT(0.52)S(0.427)PS(0.054)SSVSGDFDDGHHSVSTPGPSR;AT(0.548)S(0.445)PS(0.006)S(0.001)SVSGDFDDGHHSVSTPGPSR;AT(0.448)S(0.448)PS(0.104)S(0.001)SVSGDFDDGHHSVSTPGPSR;AT(0.439)S(0.439)PS(0.119)S(0.003)SVSGDFDDGHHSVSTPGPSR 174.53 4.63E-12 3613700000 148290 237559 172667 303301 219485 267057 252942 86712.1 214268 220323 TRUE FALSE 142494.6629 230784.0499 203871.7679 318954.401 226544.9344 272457.0755 256037.5799 84921.46483 189945.1949 205400.327 0.693741169 1.123581707 0.992558147 1.552842713 1.102943397 1.326468558 1.246529563 0.413443669 0.924756049 1 17.64807895 1.758721454 25 0.725806445 1.162092376 0.297316726 0.255390881 9.37116075 11630.9349 0.11545126 0.064024747 57.37483555 -1.758721454 0.43628593 DVKPKPIADAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVKPKPIADAK 11 2 E7EVA0;P27816-4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 ; 89.013 0.0070585 1918010000 2063100 1622370 1483350 1240650 1529880 1430240 1566970 2003850 2172430 1811290 FALSE TRUE 1982471.771 1576101.596 1751424.342 1304680.095 1579089.98 1459160.433 1586147.048 1962469.797 1925824.854 1688609.715 1.174026037 0.933372337 1.03719902 0.772635668 0.935142067 0.864119411 0.939321285 1.162180805 1.140479554 1 20.68740449 1.758755436 11.89110235 1.112669686 0.942673714 0.289926551 0.106595242 0.241305624 134.8361805 0.049197994 0.027044196 57.37932511 -1.758755436 -0.169995972 AAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK 41 2 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 65.315 0.0010726 153670000 54825 68629 37558 40599 57753 59110 52002 19576 49645 30642 FALSE TRUE 52682.37839 66671.76811 44345.56607 42694.31926 59610.67769 60305.2447 52638.41603 19171.74876 44009.50773 28566.59005 1.844195555 2.333907127 1.552357702 1.494554274 2.086727103 2.111041066 1.842656612 0.67112486 1.540593668 1 14.80204121 1.75878375 25 1.056304988 1.899035275 0.601487884 0.307462819 5.967112438 7383.190683 0.141055325 0.078223984 57.38306617 -1.75878375 0.842730287 TSSKES(ph)S(ph)PIPS(ph)PTSDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSKESSPIPSPTSDRK 17 2 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 3 T(0.381)S(0.407)S(0.408)KES(0.427)S(0.377)PIPS(0.756)PT(0.127)S(0.117)DRK 52.483 0.051375 0 350910 276990 233040 199610 237350 239290 261020 347760 403600 307380 TRUE FALSE 337196.0492 269090.5164 275155.5119 209911.896 244984.5783 244128.6078 264214.4408 340578.6345 357785.02 286560.8788 1.176699522 0.939034377 0.960199149 0.73252112 0.854912852 0.851925806 0.922018532 1.188503594 1.248548028 1 18.12848214 1.758799117 5.991862706 1.162559049 0.908932176 0.417351 0.121378333 0.148135403 13.58395883 0.060587431 0.032420634 57.38509655 -1.758799117 -0.253626873 QLAAEEERR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLAAEEERR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 82.008 0.031537 936880000 334850 399710 341870 468990 440910 376120 391730 318960 306660 363430 FALSE TRUE 321763.6918 388310.6622 403653.5139 493194.6301 455092.2706 383725.4041 396524.1089 312373.3645 271849.2424 338814.5624 0.949674918 1.146086105 1.191370026 1.455647675 1.343189819 1.132552867 1.170327822 0.921959677 0.802354068 1 18.37013636 1.758810316 2.843654019 0.885300445 1.214997568 0.499542189 0.133048305 0.203917474 3.337226443 0.083717419 0.03930214 57.38657637 -1.758810316 0.329697124 SGSGPTQDLNT(ph)ILLTSAQLSSDVAVETPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSGPTQDLNTILLTSAQLSSDVAVETPK 29 0 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 S(0.096)GS(0.096)GPT(0.096)QDLNT(0.711)ILLTSAQLSSDVAVETPK 171.52 8.06E-12 20764000 35891 32915 33513 40256 34372 33497 42106 43642 54242 50552 TRUE FALSE 34488.34004 31976.29643 39569.54459 42333.61698 35477.6066 34174.33229 42621.30582 42740.77745 48084.67556 47128.06801 0.731800422 0.678497927 0.839617372 0.898267609 0.752791449 0.725137561 0.904372015 0.906907057 1.020298043 1 15.52429892 1.75881751 1.458498601 1.005886506 0.775439253 0.677835601 0.064311057 0.249816559 1.017925641 0.05371578 0.021237778 57.38752699 -1.75881751 -0.230447253 FFLDIASDCPTSDAVNHSLSFISDGNVLALHR ddPTM_BT-474_Pertuzumab_2h_R1 1 FFLDIASDCPTSDAVNHSLSFISDGNVLALHR 32 0 H0Y465;P21359-2;P21359-6;P21359;J3KSB5;P21359-4 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 0 103.88 3.51E-06 41014000 25340 37563 34056 45053 44792 30307 43161 25925 47178 37806 FALSE TRUE 24349.68479 36491.74002 40210.67677 47378.19073 46232.77536 30919.8283 43689.21723 25389.63969 41822.55123 35245.36595 0.690862022 1.035362779 1.140878402 1.344238865 1.31174054 0.877273578 1.239573375 0.720368168 1.186611349 1 15.10514596 1.758831008 25 0.942138458 1.101126622 0.058722737 0.214303212 22.50473723 27780.43169 0.099859029 0.055378203 57.38931069 -1.758831008 0.158988165 EKADFTVVAGDEGSSTTGGS(ph)SEENKGPSGSAVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKADFTVVAGDEGSSTTGGSSEENKGPSGSAVSR 34 2 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 EKADFTVVAGDEGSS(0.001)T(0.005)T(0.017)GGS(0.918)S(0.058)EENKGPSGSAVSR 149.71 7.73E-11 230670000 278070 234400 216600 172840 217590 245890 229520 284040 310050 264550 TRUE FALSE 267202.717 227715.1415 255744.4382 181760.2931 224588.98 250862.0643 232328.9344 278174.4747 274854.4238 246631.7929 1.08340743 0.923300029 1.036948381 0.736970246 0.910624609 1.017152174 0.94200724 1.127893819 1.11443225 1 17.91199926 1.758849281 10.29661718 1.089858852 0.945208315 0.287451928 0.093745786 0.194009897 82.04365928 0.044154902 0.024177679 57.39172538 -1.758849281 -0.144650537 HVAVTNMNEHSSR ddPTM_BT-474_Pertuzumab_2h_R1 6 HVAVTNMNEHSSR 13 0 P33176;O60282;Q12840;J3KNA1;A0A0G2JMZ6 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ;;;;; 211.83 1.09E-08 2185143000 360072 611524 484915 800352 561503 634739 610272 321927 505766 616343 FALSE TRUE 345999.9882 594083.9343 572549.9274 841658.2626 579564.2539 647573.8575 617740.6913 315279.095 448353.564 574597.5396 0.602160581 1.033913119 0.996436441 1.464778744 1.008643814 1.12700423 1.075084122 0.548695519 0.780291479 1 19.13219229 1.758857045 25 0.734753271 1.059801759 0.225651891 0.221932673 11.26793497 13891.56914 0.101935148 0.056529362 57.39275131 -1.758857045 0.325048488 YYFSHDTD ddPTM_BT-474_Pertuzumab_2h_R1 4 YYFSHDTD 8 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ;;; 224.29 9.61E-06 2966880000 3184720 3582410 3093260 3671440 3472660 3363260 3494790 3271770 3545040 3819470 FALSE TRUE 3060257.622 3480243.174 3652280.891 3860923.458 3584361.263 3431267.422 3537560.285 3204206.806 3142621.921 3560773.895 0.859436098 0.977383928 1.025698626 1.084293351 1.006624225 0.963629684 0.99348074 0.899862474 0.882567109 1 21.7637594 1.758865671 10.23270388 0.918929729 0.991911287 0.162379206 0.060595552 0.253977382 105.8525672 0.029377714 0.016083501 57.39389132 -1.758865671 0.072981559 IGLDDEEKLDLFR ddPTM_BT-474_Pertuzumab_2h_R1 3 IGLDDEEKLDLFR 13 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;; 211.06 2.27E-08 530504000 996143 933651 864095 890051 966409 945569 967952 1209608 1338312 1219279 FALSE TRUE 957212.6303 907024.1876 1020256.188 935986.6388 997494.4232 964689.053 979798.0861 1184629.172 1186392.432 1136696.147 0.842100708 0.797947798 0.89756281 0.823427299 0.877538316 0.848678035 0.861970095 1.042168723 1.043719938 1 20.11641523 1.758892262 4.985831194 1.032411634 0.848805136 0.894056012 0.028181737 0.049622581 2.782496094 0.013630277 0.007164268 57.39740554 -1.758892262 -0.183606498 NFEDVAFDEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NFEDVAFDEK 10 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;; 174.41 7.24E-06 2371050000 3799260 3909010 3439160 3701300 3714090 3621920 4008090 4587110 5300040 4956090 FALSE TRUE 3650780.719 3797528.862 4060692.716 3892324.537 3833557.078 3695157.704 4057142.204 4492384.576 4698401.679 4620409.61 0.790142223 0.821903074 0.878859897 0.842419799 0.829700698 0.799746779 0.878091457 0.97229141 1.016879904 1 22.13958932 1.758938779 2.37939097 1.006760208 0.83013061 0.910565246 0.023812309 0.07641811 0.875192029 0.015822435 0.007048767 57.40355366 -1.758938779 -0.176629597 TTHFVEGGDAGNREDQINR ddPTM_BT-474_Pertuzumab_2h_R1 7 TTHFVEGGDAGNREDQINR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;;;;;; 239.93 1.59E-24 35654370000 4420754 4247308 3945466 4728400 4231824 4808321 4679284 3407477 4666315 4768623 FALSE TRUE 4247986.046 4126178.934 4658499.473 4972433.291 4367944.462 4905548.545 4736550.477 3337111.409 4136614.484 4445639.917 0.955539838 0.928140608 1.047880521 1.118496636 0.982523224 1.103451615 1.065437275 0.750648157 0.930487975 1 22.08395967 1.758944554 25 0.870211715 1.030188697 0.350988035 0.082312306 8.596254149 10552.2643 0.037916893 0.021027346 57.40431698 -1.758944554 0.159976982 SSLFPFEDAFLDDSHGDQALSSGLS(ph)SPTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALS(0.033)S(0.055)GLS(0.304)S(0.304)PT(0.304)R;SSLFPFEDAFLDDSHGDQALS(0.008)S(0.007)GLS(0.433)S(0.433)PT(0.12)R;SSLFPFEDAFLDDSHGDQALS(0.005)S(0.003)GLS(0.786)S(0.193)PT(0.012)R;SSLFPFEDAFLDDSHGDQALS(0.008)S(0.019)GLS(0.644)S(0.281)PT(0.049)R 218.01 1.54E-34 384453000 116282.5 124694.8 113268.9 129728.9 128061.1 128800.5 121210.4 107285.1 109977.6 113417 TRUE FALSE 111738.0513 121138.6264 133739.1099 136424.2241 132180.3016 131404.9344 122693.8091 105069.6252 97493.40391 105735.1656 1.056772841 1.14567964 1.264849865 1.290244578 1.250107293 1.242774186 1.160387923 0.993705591 0.922052785 1 16.69009574 1.758947778 2.854322205 0.95852125 1.213268276 0.722849539 0.065792804 0.131877806 2.173901098 0.041874815 0.019681547 57.40474315 -1.758947778 0.254747026 YYHSPTNTVHMYPPEMAPSSAPPS(ph)TPPTHK ddPTM_BT-474_Pertuzumab_2h_R1 1 YYHSPTNTVHMYPPEMAPSSAPPSTPPTHK 30 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 YYHSPTNTVHMYPPEMAPSSAPPS(0.436)T(0.436)PPT(0.127)HK 67.911 0.0032664 193440000 130590 133490 122800 135470 137210 138590 149420 64118 141400 126080 TRUE FALSE 125486.3984 129682.9959 144992.6917 142461.6229 141623.4843 141392.3848 151248.6467 62793.94089 125348.8648 117540.4893 1.067601464 1.103304884 1.233555284 1.212021694 1.204891056 1.202924929 1.286779114 0.534232427 1.066431368 1 16.84279828 1.758975462 25 0.824678677 1.188074766 0.502524392 0.144266623 6.271031363 7686.287847 0.062627557 0.0347309 57.40840245 -1.758975462 0.363396088 DIHDDQDYLHSLGK ddPTM_BT-474_Pertuzumab_2h_R1 3 DIHDDQDYLHSLGK 14 0 O75955;A0A140T9R1;O75955-2;A0A140T9X0;A2AB09;A0A140T9C3;A0A140T959;A2AB13;A2AB11;A0A0G2JJQ6;A0A140T910;A2AB12;A0A140T957;A2AB10;A0A140T9B1 O75955 FLOT1 Flotillin-1 0 ;; 241.27 1.14E-17 2785690000 1930160 2424370 1708040 2708430 1840830 1955680 2726620 947570 2817140 2229870 FALSE TRUE 1854727.213 2355229.341 2016720.823 2848212.397 1900041.969 1995225.19 2759989.191 928002.3484 2497350.078 2078838.919 0.892193809 1.132954228 0.970118851 1.370097688 0.913991917 0.95977864 1.327658996 0.446404163 1.201319667 1 20.98734654 1.758986045 25 0.827680331 1.078743833 0.117556821 0.235021888 14.75500233 18075.55549 0.101688365 0.056392241 57.40980151 -1.758986045 0.251063502 VLETAEDIQER ddPTM_BT-474_Pertuzumab_2h_R1 3 VLETAEDIQER 11 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6;A0A1B0GTB7 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 147.3 0.0019149 295502000 284631 304941 208479 293230 290675 300475 298854 254867 330527 301377 FALSE TRUE 273507.3058 296244.3812 246155.7929 308363.6354 300024.8254 306550.8104 302511.4646 249603.9074 293006.9606 280964.4674 0.973458703 1.054383795 0.876110048 1.097518268 1.067839034 1.091066117 1.076689403 0.88838247 1.042861268 1 18.10002816 1.75900508 25 0.966468087 1.034542942 0.109436351 0.072339006 17.9978162 22027.60288 0.033565586 0.018614336 57.41231784 -1.75900508 0.068074854 EGGVIVDYHGCDFFPER ddPTM_BT-474_Pertuzumab_2h_R1 1 EGGVIVDYHGCDFFPER 17 0 A0A087WVD7;D6RDH4;Q9Y3D8-2;Q9Y3D8 A0A087WVD7 TAF9;AK6 Adenylate kinase isoenzyme 6 0 114.29 0.0003706 145760000 85530 113680 77457 101600 115770 117930 104520 83848 112520 96824 FALSE TRUE 82187.39304 110437.9577 91455.20292 106843.5882 119493.8472 120314.6254 105799.147 82116.5095 99747.20132 90266.02424 0.910501972 1.22347205 1.013174156 1.183652311 1.323796503 1.332889384 1.17208161 0.909716698 1.105035944 1 16.46189544 1.759012889 25 0.999485765 1.175218892 0.245078037 0.128404735 12.64714734 15472.97519 0.060837017 0.033738013 57.41335013 -1.759012889 0.175733127 SNS(ph)FNNPLGNR ddPTM_BT-474_Pertuzumab_2h_R1 3 SNSFNNPLGNR 11 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 S(0.007)NS(0.993)FNNPLGNR;SNS(1)FNNPLGNR;SNS(1)FNNPLGNR 191.69 1.80E-06 975430000 1322230 1386910 1006240 1213680 1274860 1256140 1248860 1431760 1501610 1375500 TRUE FALSE 1270555.79 1347356.685 1188089.952 1276318.17 1315867.03 1281540.011 1264143.922 1402193.656 1331153.528 1282336.16 0.990813353 1.050704743 0.926504289 0.995307011 1.026148268 0.999379142 0.985813207 1.093468078 1.038069088 1 20.29034308 1.759043021 25 1.052771473 0.997002001 0.249102001 0.036786727 10.82905167 13229.1289 0.016478985 0.00913884 57.4173337 -1.759043021 -0.055769472 MDMMSLNSQLLDAIQQK ddPTM_BT-474_Pertuzumab_2h_R1 5 MDMMSLNSQLLDAIQQK 17 0 H0YHW1;H0YHP2;Q6ZP65-2;Q6ZP65 H0YHW1 CCDC64 Bicaudal D-related protein 1 0 ;;;; 73.156 0.02038 20641880000 3391390 6846230 7819760 8301320 7539390 8445920 7278700 3056910 3130120 5523700 FALSE TRUE 3258850.729 6650982.224 9232964.582 8729752.12 7781901.326 8616702.289 7367778.908 2993783.74 2774801.9 5149574.879 0.632838789 1.291559474 1.792956661 1.695237437 1.511173545 1.673284201 1.430754787 0.581365222 0.538840966 1 22.29602191 1.759048581 6.264558097 0.674866895 1.46523551 0.506865479 0.326266514 0.127032322 13.19835276 0.164643027 0.088413804 57.41806879 -1.759048581 0.790368615 HTLSDMEYR ddPTM_BT-474_Pertuzumab_2h_R1 4 HTLSDMEYR 9 0 Q8WVV4-1;Q8WVV4 Q8WVV4-1 POF1B Protein POF1B 0 ;;; 163.88 7.90E-05 1121440000 502684 572660 431936 461466 493749 438907 520160 283254 463443 518320 FALSE TRUE 483038.5535 556328.2975 509996.4436 485282.3156 509630.885 447782.0003 526525.8737 277404.7059 410834.8936 483213.7247 0.999637487 1.151308974 1.055426238 1.004280902 1.054669723 0.926674838 1.089633524 0.574082837 0.850213627 1 18.88230191 1.759067584 25 0.767885322 1.039894717 0.455888403 0.113696506 6.654818337 8120.006995 0.049261866 0.027318783 57.42058117 -1.759067584 0.272009395 GIEHQDSQHSFLAFLNTPTDALDQFETVDST(ph)PLSVHTPTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPT(0.001)DALDQFET(0.009)VDS(0.074)T(0.276)PLS(0.276)VHT(0.276)PT(0.086)LR 51.19 0.054839 74894000 7184.5 8345.2 6321.8 7436.8 6848.2 8341 7567.9 4247.4 6479.8 7455.3 TRUE FALSE 6903.721797 8107.203067 7464.289888 7820.614139 7068.478572 8509.660735 7660.518224 4159.689706 5744.24027 6950.345891 0.993291831 1.166445986 1.073945096 1.125212221 1.016996662 1.224350683 1.102177984 0.598486719 0.826468259 1 12.76286906 1.75909469 25 0.772365783 1.104392983 0.584311596 0.111609041 5.288941436 6444.877409 0.047651422 0.026425764 57.42416517 -1.75909469 0.3320272 SDS(ph)DSSTLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDSDSSTLSK 10 0 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 SDS(0.711)DS(0.086)S(0.144)T(0.059)LSK;SDS(0.996)DS(0.001)S(0.001)T(0.001)LSK 132.17 0.003732 254760000 679510 618010 482160 483420 605960 530200 576890 702890 795580 660970 TRUE FALSE 652953.998 600384.9599 569297.0376 508369.3641 625451.2537 540921.0073 583950.1524 688375.0759 705269.0937 616201.9132 1.059642925 0.974331541 0.923880672 0.825004521 1.015010243 0.877830782 0.947660401 1.117125834 1.144542201 1 19.23304364 1.759094788 6.533358948 1.097032374 0.9414617 0.449403893 0.07109979 0.13157004 15.42560159 0.034136921 0.018380655 57.42417816 -1.759094788 -0.155570674 LQSEVAELK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQSEVAELK 9 0 P53990-2;P53990;P53990-4;P53990-5;J3KR23;H3BQF7;H3BMU1;H3BUI0;P53990-3;F5GXM3 P53990-2 IST1 IST1 homolog 0 ; 74.301 0.096497 156906000 408420 386170 351100 356800 367460 344110 376390 430900 470530 432830 FALSE TRUE 392458.4949 375156.8097 414551.5802 375214.4908 379279.6846 351068.14 380996.3734 422001.7644 417117.407 403514.0386 0.972601836 0.929724307 1.02735355 0.929867253 0.939941733 0.870027078 0.94419608 1.04581681 1.033712256 1 18.62225934 1.759097085 8.118012763 1.029069491 0.94370558 0.485211466 0.038501598 0.12545453 27.97805106 0.018985011 0.010320809 57.42448178 -1.759097085 -0.085363911 S(ph)SPRPTAEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPRPTAEKK 10 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.5)S(0.5)PRPTAEKK;S(0.5)S(0.5)PRPTAEKK 62.89 0.042864 237020000 565260 523580 448500 419270 495630 469610 493820 552020 602900 524130 TRUE FALSE 543169.0143 508648.011 529553.9268 440908.5749 511572.3891 479105.836 499863.5169 540620.5941 534461.3196 488630.2083 1.111615707 1.040967182 1.083751921 0.902335892 1.046952031 0.980508016 1.022989386 1.106400269 1.093795084 1 18.89838353 1.759151455 25 1.077168412 1.02391825 0.075282356 0.059871217 18.99751086 23085.66829 0.027284243 0.015130119 57.4316714 -1.759151455 -0.053250162 SVNEILGLAESS(ph)PNEPK ddPTM_BT-474_Pertuzumab_2h_R1 6 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 SVNEILGLAES(0.318)S(0.682)PNEPK;SVNEILGLAES(0.001)S(0.999)PNEPK;SVNEILGLAESS(1)PNEPK;SVNEILGLAES(0.005)S(0.995)PNEPK;SVNEILGLAES(0.148)S(0.852)PNEPK;SVNEILGLAES(0.003)S(0.997)PNEPK 339.66 2.14E-72 557724000 942936 823214 708894 729510 813523 805773 803367 913654 986927 844321 TRUE FALSE 906085.0186 799736.7427 837006.9151 767160.0985 839690.7061 822066.2821 813198.8457 894786.7256 874895.1845 787134.3866 1.151118582 1.016010425 1.063359611 0.974624043 1.066769182 1.044378566 1.033113099 1.136764879 1.111494046 1 19.58625044 1.759162815 25 1.096647247 1.04666388 0.052523112 0.05392821 17.42824173 21167.00942 0.023469746 0.01301532 57.43317361 -1.759162815 -0.049983367 SSSRPCSPVHHHEGHAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSRPCSPVHHHEGHAK 17 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 0 73.464 0.0088138 12732000 9815.3 15229 12179 15193 9483.1 14565 14013 102.84 12970 5396.8 FALSE TRUE 9431.707225 14794.68383 14380.01622 15977.11255 9788.132524 14859.51428 14184.49529 100.7163181 11497.69997 5031.269929 1.874617613 2.940546629 2.858128549 3.175562587 1.945459628 2.953432133 2.819267399 0.020018071 2.285248086 1 12.29670688 1.759163751 25 1.035546757 2.675931057 0.543889388 0.64964676 6.322842032 7678.890348 0.279385852 0.154936974 57.43329737 -1.759163751 1.640384299 HKIPESQFPEFSTSLFSGSLEPVACGSVLSEGS(ph)PLTEQEESSPSHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HKIPESQFPEFSTSLFSGSLEPVACGSVLSEGSPLTEQEESSPSHDR 47 1 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 HKIPESQFPEFSTSLFSGSLEPVACGS(0.004)VLS(0.015)EGS(0.196)PLT(0.196)EQEES(0.196)S(0.196)PS(0.196)HDR 53.527 0.0066224 212880000 8819.7 11403 9972.4 8835.6 11453 14031 11720 5478.2 10390 10829 TRUE FALSE 8475.016373 11077.7976 11774.63451 9291.606375 11821.39615 14314.71643 11863.43287 5365.073256 9210.570758 10095.54218 0.839481052 1.097295955 1.166320174 0.920367248 1.170952083 1.417924483 1.175115972 0.531429928 0.912340377 1 13.30143077 1.759179281 25 0.771603649 1.120586125 0.343107781 0.185827128 9.231525829 11202.94127 0.086636586 0.048045542 57.43535123 -1.759179281 0.348982476 GTPLGTPAT(ph)SPPPAPLCHSDDYVHISLPQATVTPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTPLGTPATSPPPAPLCHSDDYVHISLPQATVTPPR 36 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6W1;Q59IT9 A0A2R8YFV7 TSC1 Hamartin 1 GTPLGT(0.028)PAT(0.486)S(0.486)PPPAPLCHSDDYVHISLPQATVTPPR 82.363 0.0025664 343490000 23548 36074 30371 41369 31387 42109 37556 16083 36207 29090 TRUE FALSE 22627.71813 35045.20484 35859.7153 43504.05905 32396.59136 42960.47283 38015.62156 15750.88043 32096.93315 27119.70839 0.83436436 1.292241212 1.322275107 1.60414922 1.194577423 1.584105264 1.40177103 0.580790922 1.18352796 1 14.72705405 1.759194625 25 0.886505555 1.334531143 0.350359859 0.246121854 9.228694458 11191.16715 0.11101259 0.061563601 57.43738051 -1.759194625 0.448025588 KGDIFLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGDIFLVR 8 1 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 132.84 0.0015152 16703100000 11077300 12695000 8164900 13266600 10802100 11404200 13498900 15386900 16269600 17904400 FALSE TRUE 10644386.87 12332951.03 9640479.057 13951290.82 11149559.36 11634800.74 13664103.58 15069155.14 14422743.22 16691719.04 0.637704651 0.73886644 0.577560588 0.835821091 0.667969508 0.697040293 0.818615719 0.902792283 0.864065779 1 23.99262921 1.759276201 0.72989889 0.986988597 0.677743513 0.707194222 0.067834406 0.332370652 0.348926464 0.059081244 0.028576856 57.44817022 -1.759276201 -0.309245085 SEHPPLCGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEHPPLCGR 9 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;;; 95.815 0.0077896 1757260000 1798620 2374220 1985400 2401990 2142330 2046950 2172760 1818170 2089700 2433420 FALSE TRUE 1728327.942 2306509.57 2344205.945 2525956.992 2211239.99 2088340.731 2199350.887 1780624.154 1852486.017 2268602.296 0.761847039 1.016709528 1.033326092 1.113441962 0.974714693 0.920540694 0.969473976 0.784899212 0.816575924 1 21.11337228 1.75932488 25 0.846649547 0.978034491 0.168385768 0.100622485 13.33851 16073.35336 0.046407547 0.025735993 57.45460986 -1.75932488 0.131384943 SSS(ph)LGNLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSLGNLKK 9 1 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;H0YGH8;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.017)S(0.068)S(0.916)LGNLKK;S(0.004)S(0.131)S(0.865)LGNLKK 110.66 0.0023841 728240000 1574650 1404550 1060980 1179950 1200040 1217690 1307470 1665950 1658990 1548300 TRUE FALSE 1513110.937 1364493.609 1252722.687 1240847.361 1238640.376 1242312.526 1323471.209 1631547.55 1470668.41 1443432.262 1.04827291 0.945311841 0.867877711 0.859650566 0.858121582 0.860665622 0.916891803 1.130324985 1.018869017 1 20.46107198 1.759400434 25 1.060153743 0.90238467 0.507703824 0.06348237 7.315979106 8784.005884 0.030322008 0.016815835 57.46460605 -1.759400434 -0.157769074 TIADLELHYQEFIR ddPTM_BT-474_Pertuzumab_2h_R1 6 TIADLELHYQEFIR 14 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;;; 212.24 2.72E-09 2037037000 1577181 1604819 1405158 1755149 1676102 1657111 1641897 1617473 1745181 1758194 FALSE TRUE 1515543.023 1559051.133 1659101.308 1845732.45 1730015.343 1690618.92 1661991.027 1584071.617 1547075.369 1639109.954 0.924613397 0.951157138 1.012196469 1.12605774 1.055460214 1.03142496 1.013959449 0.966421815 0.943850878 1 20.64448121 1.75940121 4.380230326 0.966047809 1.020433069 0.134182104 0.053114227 0.394079303 16.07925194 0.030554355 0.015778791 57.46470877 -1.75940121 0.05438526 DCHYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DCHYYR 6 0 Q96SZ5 Q96SZ5 ADO 2-aminoethanethiol dioxygenase 0 119.7 0.060326 0 72629 74716 64555 74279 64121 64849 77475 37402 70622 74362 FALSE TRUE 69790.57838 72585.17283 76221.52452 78112.54809 66183.5102 66160.29121 78423.16223 36629.63563 62605.28663 69325.39551 1.006710137 1.047021403 1.099474788 1.126752289 0.954679158 0.95434423 1.131232814 0.528372545 0.903064255 1 16.08109632 1.759421889 25 0.765254372 1.04395865 0.399932328 0.128515425 7.684628658 9217.129192 0.056138054 0.031132159 57.46744505 -1.759421889 0.278704278 IKS(ph)LEEIYLFSLPIK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKSLEEIYLFSLPIK 15 1 P15880;H0YEN5;E9PQD7;E9PPT0;E9PMM9;H3BNG3;H0YE27 P15880 RPS2 40S ribosomal protein S2 1 IKS(0.994)LEEIY(0.006)LFSLPIK;IKS(1)LEEIYLFSLPIK 119.38 0.00013154 178115000 931150 748270 745480 565130 779390 711390 755370 937870 1007390 878870 TRUE FALSE 894759.6286 726930.0722 880204.8191 594296.427 804459.7872 725774.7932 764614.444 918502.6568 893035.3105 819343.3521 1.092044777 0.887210558 1.074280785 0.725332579 0.981834765 0.885800552 0.93320394 1.121022895 1.089940265 1 19.64410863 1.759452051 12.21147745 1.078527905 0.93435683 0.254891628 0.101527724 0.290341227 164.1862804 0.044656382 0.024572221 57.4714363 -1.759452051 -0.144171075 SVSHGSNHTQKPDEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 149.97 5.06E-07 37997000 39990 46444 38312 55278 44178 58627 56657 23749 48383 59801 FALSE TRUE 38427.14659 45119.46259 45235.83065 58130.9042 45599.02549 59812.47811 57350.38531 23258.57485 42890.76468 55750.625 0.689268445 0.809308642 0.811395938 1.042695112 0.81791057 1.072857535 1.02869493 0.417189491 0.769332446 1 15.76670036 1.759453704 25 0.669979532 0.898868112 0.132203434 0.177949244 13.48287187 16147.03154 0.080619011 0.044708274 57.47165509 -1.759453704 0.22888858 KVVQSLEQTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVVQSLEQTAR 11 1 E9PGT1;Q15631;H7C1D4;Q15631-2;A0A0J9YVW2 E9PGT1 TSN Translin 0 95.417 0.012464 314900000 199910 225210 183350 236110 253440 248050 201660 181320 165460 175570 FALSE TRUE 192097.2962 218787.2313 216485.4236 248295.6654 261592.1278 253065.741 204127.9754 177575.6786 146677.6745 163678.4875 1.173625802 1.336688985 1.322626002 1.516971895 1.598207142 1.546114855 1.247127698 1.084905422 0.89613288 1 17.32050519 1.759458417 2.248905284 0.960233551 1.418631769 0.704352205 0.122656424 0.165994064 1.694095713 0.087297796 0.03823992 57.47227877 -1.759458417 0.458398218 HRS(ph)PSGAGEGASCSDGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HRSPSGAGEGASCSDGPR 18 1 Q7Z2K8;Q7Z2K8-2 Q7Z2K8 GPRIN1 G protein-regulated inducer of neurite outgrowth 1 1 HRS(0.977)PS(0.023)GAGEGASCSDGPR;HRS(0.967)PS(0.033)GAGEGASCSDGPR 90.1 0.0016767 128124000 67123 86518 68559 88158 69229 93763 82653 51866 88319 65142 TRUE FALSE 64499.75895 84050.59135 80949.13639 92707.84494 71455.81366 95658.9521 83664.53214 50794.94898 78293.39738 60729.87432 1.062076279 1.384007332 1.332937657 1.52656079 1.176617183 1.575154785 1.377650342 0.836407938 1.289207301 1 15.89011876 1.759538897 25 1.032028181 1.357703739 0.392260638 0.174104253 9.002038435 10736.97441 0.075902523 0.042092771 57.48293002 -1.759538897 0.325675558 TDLCDHALHISHDEL ddPTM_BT-474_Pertuzumab_2h_R1 3 TDLCDHALHISHDEL 15 0 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;; 233.37 7.26E-18 1203130000 568440 911330 775840 1138090 889190 1055910 992770 9053.5 952240 363490 FALSE TRUE 546224.7364 885339.7607 916051.5465 1196826.961 917791.6039 1077261.224 1004919.816 8866.542061 844145.7073 338870.4985 1.61189817 2.61261976 2.70324962 3.531812201 2.708384495 3.178976123 2.96549809 0.026164987 2.491056941 1 18.37037452 1.759552924 25 1.107371541 2.795092058 0.50001974 0.725498541 7.369602937 8784.045693 0.321537626 0.178313533 57.48478664 -1.759552924 1.687720517 SGVSDHWALDDHHALHLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGVSDHWALDDHHALHLTR 19 0 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;D6RD67 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ; 220.34 1.02E-19 510200000 104428.8 160148.9 91391.7 192087 103833 111142.3 140174 52874.1 129577.7 112782.3 FALSE TRUE 100347.607 155581.6102 107908.2132 202000.6331 107172.8827 113389.6735 141889.4913 51782.23136 114868.5827 105143.4544 0.954387581 1.479707996 1.026295111 1.921190761 1.019301519 1.078428269 1.34948478 0.492491251 1.092493902 1 16.68199951 1.759574536 25 0.816847846 1.269666262 0.257601322 0.307829513 11.58081441 13789.30054 0.135256691 0.075008442 57.48764741 -1.759574536 0.452818416 VDKITEYLCEPLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDKITEYLCEPLRK 14 2 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;K7ERB2;K7EN71;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 133.25 2.57E-05 1219890000 3585300 3387880 2660150 2584810 2563630 2789990 2960530 3340590 3611390 3428730 FALSE TRUE 3445182.512 3291260.979 3140898.28 2718212.354 2646091.487 2846405.509 2996761.852 3271605.649 3201440.147 3196499.063 1.077798693 1.029645532 0.982605725 0.850371704 0.827809248 0.89047594 0.937513759 1.023496514 1.00154578 1 21.60806124 1.759612156 8.317716538 1.008781171 0.937241139 0.146058273 0.072399748 0.313364849 74.60200591 0.039263413 0.021378071 57.49262734 -1.759612156 -0.071540031 DS(ph)PRPGKPDER ddPTM_BT-474_Pertuzumab_2h_R1 2 DSPRPGKPDER 11 2 A0A0A0MR03;Q9Y5B0;K7EJD2;A0A0J9YWJ4;A0A0J9YWB6;Q9Y5B0-4 A0A0A0MR03 CTDP1 RNA polymerase II subunit A C-terminal domain phosphatase 1 DS(1)PRPGKPDER;DS(1)PRPGKPDER 64.244 0.054758 500850000 711490 659570 695300 622410 616760 652510 726680 825850 1008010 863420 TRUE FALSE 683684.1842 640759.7094 820956.1769 654532.6547 636598.6455 665704.1993 735573.3272 808795.9089 893584.9307 804939.7943 0.849360647 0.796034329 1.019897615 0.813144858 0.790864919 0.827023591 0.913824031 1.004790563 1.110126418 1 19.61852135 1.759644945 2.345883327 1.055119403 0.851373056 0.61803818 0.066646966 0.180283039 2.004626578 0.042800484 0.018996857 57.49696817 -1.759644945 -0.203746348 LGEMWNNTAADDKQPYEK ddPTM_BT-474_Pertuzumab_2h_R1 5 LGEMWNNTAADDKQPYEK 18 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;;;; 261.31 8.06E-31 9259580000 2885540 2567450 2578850 2250740 2683530 2443400 2614560 3420210 3610550 3280190 FALSE TRUE 2772769.907 2494228.84 3044905.561 2366900.961 2769848.18 2492807.222 2646557.767 3349581.468 3200695.501 3058019.81 0.906720714 0.815635279 0.995711523 0.773997916 0.905765283 0.815170397 0.865448209 1.095343286 1.046656235 1 21.54416632 1.759651573 9.229012645 1.051787113 0.866909268 0.636962821 0.06186686 0.086536418 27.47529906 0.027045633 0.014773845 57.49784574 -1.759651573 -0.184877845 VKGDVDISLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKGDVDISLPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 112.43 0.00079057 0 2200000 2218100 1869000 1919400 1779000 2084100 2045300 2493800 2712200 2341300 FALSE TRUE 2114021.568 2154841.96 2206769.876 2018460.464 1836223.151 2126241.93 2070330.993 2442302.159 2404322.426 2182721.666 0.968525489 0.987227091 1.011017534 0.924744779 0.841253917 0.97412417 0.948508931 1.118925146 1.101524974 1 21.05769674 1.75966656 11.19608372 1.081959512 0.950157383 0.537893648 0.051935222 0.147695903 72.04167239 0.025385778 0.013940819 57.49982987 -1.75966656 -0.131802128 QGGDLGWMTR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGGDLGWMTR 10 0 Q9Y237;Q9Y237-2 Q9Y237 PIN4 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 0 94.465 0.01881 256160000 327980 322330 280910 292500 327410 305250 295510 297900 306470 292220 FALSE TRUE 315162.179 313137.464 331676.6858 307595.9601 337941.44 311422.3641 299126.5398 291748.2609 271680.8104 272427.6791 1.156865485 1.149433365 1.217485268 1.129092172 1.240481294 1.14313775 1.09800348 1.07092004 0.99725847 1 18.05551377 1.759674993 1.209041407 0.996524756 1.17695826 0.815988905 0.033010808 0.175146852 0.479106462 0.026245292 0.010374955 57.50094639 -1.759674993 0.180433504 HIAEEADR ddPTM_BT-474_Pertuzumab_2h_R1 20 HIAEEADR 8 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;P67936;P67936-2 TPM3;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-4 chain 0 ;;;;;;;;;;;;;;;;;;; 172.21 0.00028488 12203145600 3918241.5 4199230.2 3581920 4155818.7 4175207.1 4017002.8 4147822.1 3066833.02 4081379.5 4223388.1 FALSE TRUE 3765112.29 4079472.266 4229252.623 4370301.001 4309506.428 4098229.349 4198584.388 3003501.846 3618078.41 3937334.262 0.956259245 1.03610006 1.074141117 1.109964435 1.094523894 1.040863964 1.066352031 0.762826229 0.918915736 1 21.90878777 1.759693099 24.99999996 0.872263981 1.057315816 0.532722645 0.067767079 6.431625189 7615.138208 0.030318714 0.016813798 57.50334372 -1.759693099 0.185051835 (ac)ASGEHS(ph)PGSGAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASGEHSPGSGAAR 13 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 1 ASGEHS(0.997)PGS(0.003)GAAR;AS(0.011)GEHS(0.97)PGS(0.018)GAAR 88.282 3.16E-32 499000000 9869.4 7209.4 10528.9 5645.7 7510.8 8996.2 8480.1 5907.9 7017 7455.9 TRUE FALSE 9483.692937 7003.794971 12431.70644 5937.075254 7752.391703 9178.109328 8583.882 5785.8998 6220.459578 6950.905252 1.364382421 1.00760904 1.788501784 0.854144178 1.115306773 1.320419283 1.234930083 0.832395147 0.894913591 1 12.76298516 1.759711959 8.199259586 0.900565006 1.236479556 0.292931779 0.235832823 0.183641604 41.89221105 0.107874321 0.05871585 57.50584101 -1.759711959 0.33591455 HVDYVVDQVVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVDYVVDQVVGK 12 0 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 95.417 0.0060585 259050000 958630 973490 724090 991960 968050 898060 946640 816740 1030900 945710 FALSE TRUE 921165.6798 945727.0183 854949.1703 1043155.174 999188.2074 916219.3885 958225.2635 799874.0336 913876.5539 881656.2193 1.044812773 1.072670954 0.969708092 1.183176789 1.133308182 1.039202547 1.086846826 0.907240278 1.036545236 1 19.7498567 1.759742362 25 0.973564435 1.076432586 0.330261003 0.061312387 10.89607368 12871.07528 0.028405493 0.015752756 57.50986683 -1.759742362 0.102868151 S(ph)LHSAHSLASR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 S(0.997)LHS(0.003)AHSLASR;S(1)LHSAHSLASR;S(1)LHSAHSLASR;S(1)LHSAHSLASR 237.48 8.98E-16 2515950000 720010 790390 716080 980010 800360 767110 784390 169149 661550 469267 TRUE FALSE 691871.2132 767848.8511 845491.5851 1030588.434 826104.3063 782621.4898 793989.5995 165656.014 586453.6174 437483.1281 1.581480905 1.755150774 1.932626725 2.355721552 1.888311236 1.788918108 1.814903361 0.37865692 1.340517107 1 18.73886785 1.759758974 25 0.863284949 1.887387714 0.702706208 0.287872478 5.046376818 5956.396807 0.130741695 0.072504728 57.51206673 -1.759758974 1.024102765 RS(ph)SFSMEEES ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSFSMEEES 10 1 P19532 P19532 TFE3 Transcription factor E3 1 RS(0.488)S(0.488)FS(0.024)MEEES;RS(0.695)S(0.304)FS(0.001)MEEES 151.66 2.06E-05 477480000 382660 439940 370370 459190 438660 409180 426080 377940 421540 455160 TRUE FALSE 367705.2241 427393.3419 437304.0978 482888.8509 452769.8973 417453.9 431294.4945 370135.4069 373688.5464 424331.6078 0.866551578 1.007215428 1.030571586 1.137998778 1.067019022 0.983791667 1.016409069 0.872278662 0.880652159 1 18.69483262 1.759772159 15.0601252 0.907424366 1.02135882 0.274436818 0.072040343 0.612770995 438.2549724 0.034553578 0.019092435 57.51381273 -1.759772159 0.113934454 GQS(ph)QTSPDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQSQTSPDHR 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQS(0.481)QT(0.26)S(0.26)PDHR;GQS(0.431)QT(0.284)S(0.284)PDHR 81.017 0.023364 64957000 62792 62388 55770 73957 64377 71379 66397 56884 62291 66602 TRUE FALSE 60338.01922 60608.75532 65848.8796 77773.92963 66447.74467 72822.33229 67209.58635 55709.32552 55219.98683 62090.98722 0.971767754 0.976128067 1.060522349 1.252580014 1.070167308 1.172832573 1.082437071 0.897220805 0.889339811 1 15.92209625 1.759812174 6.799235234 0.921211839 1.088427926 0.419127074 0.083250258 0.152511109 20.01156936 0.04284386 0.023147003 57.51911224 -1.759812174 0.167216087 GLS(ph)PNNSGHDSTDTDSNHEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GLSPNNSGHDSTDTDSNHEER 21 0 Q9UKT9-9;Q9UKT9-6;Q9UKT9-8;Q9UKT9-4;Q9UKT9-3;Q9UKT9-7;Q9UKT9;Q9UKT9-16;Q9UKT9-12;Q9UKT9-11;Q9UKT9-10;Q9UKT9-13;Q9UKT9-5;Q9UKT9-2;Q9UKT9-15 Q9UKT9-9 IKZF3 Zinc finger protein Aiolos 1 GLS(0.999)PNNS(0.001)GHDSTDTDSNHEER;GLS(1)PNNSGHDSTDTDSNHEER 261.23 8.00E-37 516600000 139233 233472 194007 237292 184821 228973 209039 78464 149215 209026 TRUE FALSE 133791.6204 226813.6072 229068.3806 249538.6686 190765.9353 233602.9909 211597.2818 76843.69098 132276.7388 194868.4828 0.686573932 1.163931714 1.175502458 1.280549142 0.978947096 1.198772565 1.085846612 0.394336169 0.678800065 1 17.57214125 1.759850456 25 0.635380726 1.096464648 0.418271962 0.207369537 7.900763646 9285.406263 0.091282379 0.050622016 57.52418259 -1.759850456 0.461083921 KNPEVPVNFAEFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNPEVPVNFAEFSK 14 1 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 123.97 0.00016003 1199600000 824780 852770 646380 617840 808090 746950 731510 861970 871120 810460 FALSE TRUE 792546.6858 828449.8345 763195.2446 649726.7964 834082.9487 762053.8408 740462.4382 844170.0183 772234.1096 755566.8223 1.048943207 1.096461372 1.010096291 0.859919702 1.103916853 1.008585632 0.980009201 1.117267187 1.022059316 1 19.52719983 1.759873425 25 1.05838566 1.015491324 0.031348121 0.070162727 30.55668635 35873.11224 0.032763765 0.018169632 57.52722504 -1.759873425 -0.042894336 SLT(ph)PPPSSTESK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLTPPPSSTESK 12 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 SLT(0.997)PPPS(0.001)S(0.001)T(0.001)ESK;SLT(1)PPPSSTESK;SLT(1)PPPSSTESK 172.92 0.00038528 752050000 1474850 1407900 1190550 1271020 1307750 1347000 1357130 1592010 1700990 1574620 TRUE FALSE 1417211.231 1367748.07 1405708.869 1336617.495 1349814.966 1374237.263 1373738.963 1559134.437 1507900.746 1467969.585 0.965422749 0.931727799 0.957587189 0.910521245 0.919511535 0.936148322 0.935808873 1.062102685 1.027201627 1 20.48539065 1.760041165 12.43225873 1.033156631 0.935595565 0.810294295 0.020616504 0.098170929 55.55795382 0.009321746 0.00513286 57.54944835 -1.760041165 -0.097561066 TASESISNLSEAGS(ph)IK ddPTM_BT-474_Pertuzumab_2h_R1 4 TASESISNLSEAGSIK 16 0 J3KP58;P30622-2;P30622-1;P30622;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK 392.91 1.54E-121 2107440000 2001910 1847820 1626940 1540280 1693600 1737260 1783290 2443720 2320120 2166670 TRUE FALSE 1923673.144 1795121.983 1920964.249 1619774.035 1748076.182 1772388.587 1805114.436 2393256.328 2056749.704 2019919.511 0.952351385 0.88870966 0.951010295 0.801900287 0.865418732 0.877455056 0.893656617 1.184827571 1.018233495 1 20.94586638 1.760042247 25 1.083326509 0.887538349 0.634733246 0.061380717 5.649283766 6580.007872 0.027165814 0.015065001 57.54959178 -1.760042247 -0.19578816 RTDLCDHALHISHDEL ddPTM_BT-474_Pertuzumab_2h_R1 4 RTDLCDHALHISHDEL 16 1 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;; 157.35 3.07E-08 2459060000 1026931 1706451 1453273 2119670 1498345 2115107 1673251 72674.6 1478789 659572 FALSE TRUE 986797.4012 1657784.688 1715911.759 2229066.423 1546540.628 2157875.913 1693728.746 71173.84411 1310923.072 614898.601 1.604813216 2.696029371 2.790560519 3.625095941 2.515114891 3.509319926 2.754484632 0.115748912 2.131933737 1 19.229989 1.760045262 25 1.029378369 2.831630894 0.559616691 0.690749557 6.928974023 8069.39295 0.306614409 0.170037923 57.54999125 -1.760045262 1.802252526 SHPAMS(ph)PGTPGPTMGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHPAMSPGTPGPTMGR 16 0 A0A3F2YNW7;Q8NFD5;Q8NFD5-2;Q8NFD5-3;A0A1B0GUC6;A0A1B0GUG2;A0A1B0GU09;A0A6I8PTU7 A0A3F2YNW7 ARID1B AT-rich interactive domain-containing protein 1B 1 SHPAMS(1)PGTPGPTMGR;SHPAMS(1)PGTPGPTMGR 145.17 8.02E-07 698600000 399290 409100 372800 406420 402660 426900 416930 335910 440750 411090 TRUE FALSE 383685.3054 397432.8686 440173.2529 427395.3849 415611.9246 435532.2105 422032.5141 328973.3411 390717.9078 383246.5081 1.001144948 1.037016281 1.148538196 1.115197075 1.084450649 1.136428385 1.101203808 0.858385749 1.019495023 1 18.54791312 1.760052632 25 0.947182542 1.092060439 0.513778123 0.057475391 7.437975161 8659.195267 0.026438286 0.014661719 57.55096794 -1.760052632 0.144877897 NTADHDES(ph)PPRTPTGNAPS(ph)SESDIDISSPNVSHDESIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTADHDESPPRTPTGNAPSSESDIDISSPNVSHDESIAK 39 1 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 2 NTADHDES(0.519)PPRT(0.493)PT(0.399)GNAPS(0.469)S(0.096)ES(0.024)DIDISSPNVSHDESIAK 146.05 4.10E-13 726470000 168600 184530 145020 142660 157140 162790 165320 127870 179660 151290 TRUE FALSE 162010.9256 179267.3851 171228.34 150022.6997 162194.5508 166081.7253 167343.2356 125229.4398 159265.75 141042.9935 1.148663408 1.271012339 1.214015214 1.063666446 1.149965317 1.177525527 1.186469681 0.887881324 1.129200012 1 17.10577547 1.760073603 25 0.997630569 1.173467005 0.520826686 0.073436733 7.775336829 9043.116684 0.033470073 0.018561427 57.55374697 -1.760073603 0.175836435 HGGSPQPLATTPLSQEPVNPPS(ph)EASPTRDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HGGSPQPLATTPLSQEPVNPPSEASPTRDR 30 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGSPQPLATTPLSQEPVNPPS(0.431)EAS(0.431)PT(0.137)RDR;HGGSPQPLATTPLS(0.005)QEPVNPPS(0.331)EAS(0.331)PT(0.331)RDR 125.54 8.52E-06 338620000 110992 113054 91799 129393 121285 144136 126441 89865 132807 119066 TRUE FALSE 106654.3099 109829.8106 108389.1214 136070.9882 125186.2422 147050.5287 127988.4228 88009.25635 117731.3061 111001.5538 0.960836189 0.989443903 0.976464902 1.2258476 1.127788197 1.324760994 1.153032714 0.792865085 1.060627551 1 16.76022035 1.760125628 25 0.932632039 1.112262837 0.24432487 0.125248512 14.10520356 16365.45397 0.061690758 0.034211603 57.56064184 -1.760125628 0.179630798 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHATPGHGGATSSAR ddPTM_BT-474_Pertuzumab_2h_R1 5 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 IWDPTPSHT(0.018)PAGAAT(0.982)PGRGDT(0.95)PGHAT(0.045)PGHGGAT(0.002)S(0.002)S(0.002)AR;IWDPTPS(0.001)HT(0.001)PAGAAT(0.999)PGRGDT(0.997)PGHAT(0.003)PGHGGATSSAR;IWDPTPSHT(0.054)PAGAAT(0.946)PGRGDT(0.996)PGHAT(0.004)PGHGGATSSAR;IWDPTPSHT(0.018)PAGAAT(0.982)PGRGDT(0.998)PGHAT(0.002)PGHGGATSSAR;IWDPTPSHT(0.001)PAGAAT(0.999)PGRGDT(0.682)PGHAT(0.317)PGHGGATSSAR 154.77 1.12E-13 3641800000 710502 865611 653066 932567 822450 853883 841878 370595 698572 796713 TRUE FALSE 682734.7963 840924.6218 771089.5536 980696.8946 848904.8512 871149.0993 852181.1548 362942.0837 619273.0352 742750.9189 0.919197512 1.132175808 1.038153618 1.3203577 1.142919961 1.172868424 1.147331 0.488645755 0.833756 1 19.50251896 1.760155049 25 0.727383969 1.131749807 0.517512236 0.153036141 6.851288886 7938.315193 0.067249879 0.03729453 57.56454136 -1.760155049 0.404365838 EREES(ph)EDELEEANGNNPIDIEVDQNK ddPTM_BT-474_Pertuzumab_2h_R1 6 EREESEDELEEANGNNPIDIEVDQNK 26 1 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK 318.34 3.01E-82 9977980000 4684844 4132213 3706051 4009917 4374210 4177234 4274754 5536477 5483962 4951537 TRUE FALSE 4501755.117 4014366.331 4375816.856 4216869.297 4514910.437 4261700.534 4327069.718 5422146.815 4861445.624 4616164.989 0.975215385 0.869632334 0.947933375 0.913500559 0.978065223 0.923212351 0.93737328 1.174599874 1.053135154 1 22.13826336 1.760161918 25 1.09137999 0.933351495 0.618432556 0.050275464 5.591296743 6476.350625 0.021432405 0.011885804 57.56545185 -1.760161918 -0.158028495 HCVTFVLHEEDHTLGNSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HCVTFVLHEEDHTLGNSLR 19 0 A0A0R4J2F3;P0DPB6 A0A0R4J2F3 0 275.37 6.79E-40 225370000 19181 32415 28205 30781 23868 27295 31023 8264.2 28566 23243 FALSE TRUE 18431.38531 31490.55594 33302.27092 32369.6111 24635.7359 27846.9236 31402.66875 8093.541382 25323.30744 21668.73091 0.850598283 1.453271817 1.536881466 1.493839729 1.136925647 1.285120191 1.449215872 0.373512478 1.168656695 1 14.40332704 1.760169915 25 0.791146984 1.327831221 0.381276924 0.269870852 9.207682638 10661.22733 0.119770765 0.066420687 57.56651184 -1.760169915 0.536684237 DLEEFFSTVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLEEFFSTVGK 11 0 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;H0Y4X3;A0A0U1RQH7;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 150.61 7.87E-05 94984000 234230 268530 198700 188540 243190 227220 231620 276740 275220 274870 FALSE TRUE 225076.0326 260871.7873 234609.5101 198270.572 251012.4272 231814.5441 234454.6348 271025.2223 243978.1794 256252.8101 0.878335861 1.018025079 0.915539268 0.773730333 0.97954995 0.904632203 0.914934883 1.057647806 0.952099528 1 17.9672083 1.76019498 25 1.007318538 0.913296848 0.293853043 0.064635193 13.07813062 15125.11037 0.029721833 0.016482504 57.56983441 -1.76019498 -0.094021689 NDSVIVADQTPT(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 NDSVIVADQTPTPTR 15 0 B8ZZU6;E9PBF9;P15336-5;P15336;E9PEK8;H7C2N6;P15336-3;P15336-7 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 NDSVIVADQTPT(1)PTR 293.35 1.95E-27 0 200680 200640 169510 178220 191840 211120 199380 196130 253400 230300 TRUE FALSE 192837.2037 194917.9436 200144.2277 187417.9556 198010.7078 215388.991 201820.0721 192079.847 224635.0943 214701.5759 0.898163895 0.907855207 0.932197293 0.872923055 0.922260151 1.003201724 0.940002752 0.89463641 1.04626663 1 17.71197325 1.760218838 0.34843834 1.010081893 0.894231004 0.40137086 0.041357534 1.51816383 0.563597425 0.060108345 0.059465536 57.572997 -1.760218838 -0.115850888 EHLMLEEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHLMLEEELR 10 0 P15924 P15924 DSP Desmoplakin 0 ;;; 157.38 9.28E-06 912790000 611228 707450 666386 680528 651176 619983 656465 398311 632274 567914 FALSE TRUE 587340.534 687274.2187 786816.7739 715650.1316 672121.6674 632519.481 664499.015 390085.7387 560500.9062 529448.6789 1.109343658 1.298094123 1.48610584 1.351689333 1.269474633 1.194675719 1.255077294 0.736777244 1.058650118 1 19.01413132 1.760225712 25 0.911894775 1.288208709 0.635824665 0.120601146 6.21377492 7176.146416 0.056346611 0.031247903 57.5739084 -1.760225712 0.376313934 EKT(ph)PELPEPSVK ddPTM_BT-474_Pertuzumab_2h_R1 7 EKTPELPEPSVK 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EKT(0.999)PELPEPS(0.001)VK;EKT(0.808)PELPEPS(0.192)VK;EKT(0.999)PELPEPS(0.001)VK;EKT(0.999)PELPEPS(0.001)VK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK 175.15 0.00018124 16220620000 9000870 7072370 6537750 5270060 6470290 6419510 6965110 9067810 10325160 8429890 TRUE FALSE 8649106.049 6870672.932 7719266.856 5542048.428 6678412.754 6549316.891 7050351.1 8880556.555 9153091.123 7858926.042 1.100545546 0.87425087 0.982229228 0.705191574 0.849786945 0.833360291 0.897113812 1.129996199 1.164674546 1 22.90590074 1.760242023 5.695199965 1.109615055 0.882776055 0.44985192 0.104015969 0.144093209 11.40759752 0.051092928 0.027290785 57.57607067 -1.760242023 -0.226839001 HESGASIK ddPTM_BT-474_Pertuzumab_2h_R1 8 HESGASIK 8 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 170.3 0.00029602 4964192000 5072167 8619277 6145777 9205774 6628391 8158721 7505700 5666989 6637032 8680176 FALSE TRUE 4873941.106 8373463.659 7256455.616 9680885.099 6841599.216 8323695.929 7597557.002 5549963.697 5883623.952 8092259.948 0.602296656 1.034749713 0.896715585 1.196314152 0.845449758 1.028599672 0.938867146 0.685836062 0.727068086 1 22.94811123 1.760293371 25 0.773688837 0.947338827 0.105538222 0.164137446 17.25114793 19860.86676 0.071681646 0.039752474 57.58287847 -1.760293371 0.17364999 GYLGPPHQGPPMHHASGHDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GYLGPPHQGPPMHHASGHDTR 21 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 0 32.156 0.084465 88751000 74090 97580 67560 101020 88412 81702 85017 49347 74859 81664 FALSE TRUE 71194.48089 94797.11394 79769.59486 106233.6543 91255.85227 83354.07042 86057.46348 48327.96721 66361.32015 76132.82454 0.935135158 1.245154301 1.047768756 1.39537256 1.198640046 1.094850624 1.130359526 0.634784897 0.871651887 1 16.21623098 1.760325261 25 0.803663473 1.158601309 0.499626925 0.142803463 7.452930375 8567.81137 0.063091264 0.034988398 57.58710688 -1.760325261 0.354937836 FGLALAVAGGVVNSALYNVDAGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 FGLALAVAGGVVNSALYNVDAGHR 24 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 211.93 2.50E-25 324540000 189110 250570 180210 218690 208040 275090 251330 134400 248200 235350 FALSE TRUE 181719.3721 243423.9889 212777.9557 229976.6171 214731.7955 280652.5083 254405.8517 131624.593 220025.3765 219409.5349 0.828220033 1.109450367 0.969775338 1.048161454 0.978680328 1.279126308 1.159502261 0.599903706 1.002806814 1 17.7432667 1.760349861 25 0.828781799 1.057844226 0.219606475 0.155175064 12.83216826 14735.05381 0.069923277 0.038777008 57.59036895 -1.760349861 0.229062426 HSSAPPK ddPTM_BT-474_Pertuzumab_2h_R1 3 HSSAPPK 7 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;; 86.086 0.020334 65065000 87992 119604 100150 143608 104729 128756 117979 87375 88195 127443 FALSE TRUE 84553.17536 116193.011 118249.3328 151019.6261 108097.7034 131359.5345 119422.8623 85570.67572 78183.47334 118811.1721 0.71166014 0.977963679 0.995271158 1.271089439 0.909827767 1.105616014 1.005148423 0.720224152 0.658048161 1 16.85831098 1.760367167 8.234690795 0.768845543 1.007470518 0.256541174 0.156641659 0.178064314 40.82317086 0.073158296 0.039864131 57.59266386 -1.760367167 0.238624976 VPSIDVLCNEFHTPHDAAFFLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPSIDVLCNEFHTPHDAAFFLSR 23 0 Q8NI27;A0A0C4DG98 Q8NI27 THOC2 THO complex subunit 2 0 ; 190.37 8.92E-18 334250000 196122 207334 169853 213140 195507 192028 227726 76075 209079 196449 FALSE TRUE 188457.3354 201421.0373 200549.2155 224140.1809 201795.6602 195910.9377 230512.9789 74504.02467 185345.2285 183143.3343 1.029015531 1.099799991 1.095039665 1.223851154 1.101845508 1.069713722 1.258647932 0.406807187 1.012022792 1 17.48261367 1.76037642 24.99999988 0.749612889 1.12400008 0.412360267 0.170602774 8.2197381 9427.142433 0.073007079 0.040487284 57.59389099 -1.76037642 0.374387191 EKT(ph)PS(ph)PKEEDEEPES(ph)PPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKTPSPKEEDEEPESPPEK 19 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 EKT(1)PS(1)PKEEDEEPES(1)PPEK 89.659 0.015467 342690000 166080 97736 106600 72502 89948 83706 108290 145140 186590 118290 TRUE FALSE 159589.41 94948.66497 125864.9913 76243.83691 92841.25911 85398.59267 109615.2854 142142.8083 165409.0854 110278.1129 1.447153979 0.860992834 1.14134154 0.69137778 0.841882914 0.774392945 0.993989492 1.2889485 1.499926695 1 16.75078696 1.760380991 4.369494743 1.29754304 0.942061365 0.254677895 0.230796994 0.230228 9.30805972 0.116201191 0.060056491 57.59449716 -1.760380991 -0.355481675 FYAAEIILGLEHMHNR ddPTM_BT-474_Pertuzumab_2h_R1 1 FYAAEIILGLEHMHNR 16 0 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 92.575 0.0027323 191620000 53503 55341 56900 68017 61197 53262 67135 19458 65186 48685 FALSE TRUE 51412.04361 53762.72886 67183.09573 71527.36552 63165.45708 54338.99413 67956.61821 19056.1855 57786.35856 45387.52159 1.132735206 1.184526649 1.480210714 1.575925784 1.391692141 1.197223207 1.497253338 0.419855168 1.27317722 1 15.47000809 1.760387589 25 0.84576149 1.354165142 0.423531268 0.24026175 8.911111946 10214.83764 0.107355129 0.059535629 57.59537221 -1.760387589 0.508403651 CQFGLAQECLHHAQDYGGLLLLATASGNANMVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 CQFGLAQECLHHAQDYGGLLLLATASGNANMVNK 34 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 86.324 0.00034447 179490000 32429 30945 28439 28526 35864 29619 32426 22013 29801 34939 FALSE TRUE 31161.63883 30062.4789 33578.55992 29998.23028 37017.59813 30217.91647 32822.83909 21558.42386 26418.11542 32572.55041 0.956684031 0.922939055 1.030885193 0.920966578 1.136466063 0.927711097 1.007684037 0.661858638 0.811054556 1 14.99136907 1.76039046 25 0.791538285 0.98649924 0.345295358 0.09911729 9.262432015 10616.15805 0.042778643 0.023723488 57.59575291 -1.76039046 0.194960955 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK 31 0 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ; 210.91 7.73E-27 377830000 287560 323070 287710 352750 390510 377500 331340 44671 262740 202754 FALSE TRUE 276321.8373 313856.3599 339705.5971 370955.4698 403071.1088 385133.3086 335395.038 43748.52824 232914.8567 189021.291 1.461855624 1.660428612 1.797181658 1.962506276 2.132411152 2.037512847 1.774377036 0.231447622 1.232214929 1 17.52818922 1.760428892 25 0.762526176 1.8488029 0.707755868 0.296889925 5.284395787 6046.068842 0.135444393 0.075113045 57.60084991 -1.760428892 1.086276725 QDIVLTTYNILTHDYGTK ddPTM_BT-474_Pertuzumab_2h_R1 1 QDIVLTTYNILTHDYGTK 18 0 A0A0C4DGA6;Q14527-2;Q14527 A0A0C4DGA6 HLTF Helicase-like transcription factor 0 96.487 0.0015836 65101000 146470 144850 101750 116040 126690 129410 122520 151120 147420 138070 FALSE TRUE 140745.7905 140719.0198 120138.4884 122028.8383 130765.0989 132026.7589 124019.4364 147999.3192 130685.4996 128718.3959 1.093439593 1.093231615 0.93334358 0.948029514 1.015900625 1.025702332 0.963494266 1.149791513 1.015282227 1 16.97385873 1.760468043 25 1.070161869 1.009062672 0.079248243 0.063512021 20.99030693 23972.80971 0.030135941 0.016711967 57.60604281 -1.760468043 -0.061099197 QTGIVLNRPVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QTGIVLNRPVLR 12 1 Q13435;E9PPJ0;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 76.073 0.029276 659470000 545590 560730 446530 528370 493480 553750 529570 442580 485050 574380 FALSE TRUE 524267.7396 544738.5294 527227.904 555639.239 509353.2324 564947.2044 536051.0361 433440.5683 429989.1575 535476.731 0.979067267 1.01729636 0.984595359 1.037653378 0.951214503 1.055035955 1.001072512 0.809447999 0.803002507 1 19.03046436 1.760496478 13.49635352 0.854941531 1.004760951 0.520003426 0.057900737 0.230983743 142.0025293 0.024877776 0.01372361 57.60981471 -1.760496478 0.14981942 SSHYDELLAAEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSHYDELLAAEAR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 175.74 1.77E-05 3405170000 2551990 3228130 2828110 3441740 2920120 3034000 3266780 1589680 2833540 3255140 FALSE TRUE 2452255.409 3136066.893 3339212.388 3619368.614 3014048.312 3095349.559 3306759.831 1556852.552 2511888.418 3034666.468 0.808080702 1.033414026 1.100355648 1.19267427 0.993205792 1.019996626 1.089661703 0.513022623 0.827731299 1 21.53310653 1.760509653 25 0.733666205 1.040454602 0.374463808 0.146404933 9.076266993 10346.23642 0.0651555 0.036133347 57.61156236 -1.760509653 0.306788398 IHLDDANESDHFENIQSTNWQTMR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHLDDANESDHFENIQSTNWQTMR 24 0 E1CEI4;P48506;A0A2R8YEL6;B4E2I4;A0A2R8Y648 E1CEI4 GCLC Glutamate--cysteine ligase catalytic subunit 0 ; 170.56 4.51E-12 283820000 102419 126668 115624 131094 131031 143756 136666 31983 115529 106276 FALSE TRUE 98416.35225 123055.5527 136519.8288 137859.7771 135245.7311 146662.8448 138338.5594 31322.53987 102414.6323 99077.83186 0.993323637 1.242008937 1.377904888 1.391429086 1.365045324 1.480279111 1.396261472 0.316140748 1.033678577 1 16.59627468 1.760539824 25 0.722184409 1.330593745 0.546159894 0.222379011 6.96706967 7931.003416 0.09887754 0.054834168 57.61556482 -1.760539824 0.608409336 DTPRPDHPPHDGHSPASR ddPTM_BT-474_Pertuzumab_2h_R1 3 DTPRPDHPPHDGHSPASR 18 1 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 0 ;; 98.165 0.00042782 232163000 189955 225163 206846 262767 248633 248992 242762 70308 213197 179565 FALSE TRUE 182531.3486 218741.5717 244227.6735 276328.4364 256630.5062 254026.7888 245732.994 68856.11523 188995.7704 167402.9026 1.090371468 1.306677293 1.458921379 1.650678883 1.53301109 1.517457493 1.467913579 0.411319721 1.128987415 1 17.35296502 1.760541059 25 0.797186656 1.443917361 0.586796374 0.223795667 6.759922815 7694.764258 0.101968047 0.056548048 57.61572873 -1.760541059 0.646730705 YSPKT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSPKTPPR 8 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 YS(0.028)PKT(0.972)PPR;YS(0.001)PKT(0.999)PPR 85.813 0.026638 710060000 1399090 1334950 1171910 1193610 1242850 1353880 1309400 1476390 1603270 1519600 TRUE FALSE 1344412.016 1296878.533 1383700.206 1255212.355 1282827.399 1381256.381 1325424.829 1445902.031 1421273.511 1416676.138 0.948990372 0.91543755 0.976723027 0.886026327 0.905519169 0.974997986 0.935587742 1.020629904 1.003245182 1 20.43407856 1.760553721 6.973552364 1.00844221 0.934054282 0.601098763 0.027301856 0.105475883 14.83970964 0.013168322 0.007132269 57.61740855 -1.760553721 -0.074387928 S(ph)PPEGDTTLFLSR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPPEGDTTLFLSR 13 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR 177.38 1.63E-05 6683090000 909206 812194 639727 726962 772544 767397 787075 713657 830725 859880 TRUE FALSE 873673.2243 789031.0223 755339.8996 764480.5959 797393.5794 782914.2931 796707.4593 698919.7336 736424.5807 801639.5617 1.089857919 0.98427156 0.942243791 0.953646293 0.994703377 0.976641287 0.993847481 0.871862826 0.918648001 1 19.61259418 1.760555071 25 0.917625517 0.986813187 0.238040711 0.047756864 13.48051873 15334.97799 0.021721772 0.012046025 57.6175876 -1.760555071 0.06918767 AAAHCAHVFTTVSQITAIEAQHLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAHCAHVFTTVSQITAIEAQHLLK 25 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 0 77.19 0.009872 283470000 73306 72747 71819 70303 80121 74613 75803 48184 72838 71641 FALSE TRUE 70441.12048 70672.32679 84798.29091 73931.34626 82698.16473 76121.72598 76730.69979 47188.98356 64569.7356 66788.69126 1.054686342 1.0581481 1.269650435 1.106944078 1.238206097 1.139739746 1.148857664 0.706541522 0.966776476 1 16.02731622 1.760563063 25 0.865419068 1.148515022 0.583937466 0.097529985 6.52532801 7420.291876 0.042987423 0.023839406 57.61864792 -1.760563063 0.283095954 THYSNIEANESEEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 THYSNIEANESEEVR 15 0 A0A0C4DGQ5;K7ELJ7;P04632;U3KQE2;K7EIV0;A0A075B7C0;K7EM73 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ; 205.68 2.35E-12 1819470000 670630 1174680 867470 1398260 969340 1109310 1107260 437670 886710 1077730 FALSE TRUE 644421.0382 1141179.277 1024241.126 1470424.366 1000519.701 1131741.008 1120810.979 428631.9616 786054.3982 1004734.387 0.641384476 1.13580195 1.019414821 1.463495611 0.995805174 1.126408156 1.11552963 0.426612214 0.782350448 1 19.93838273 1.760604764 25 0.682458971 1.0859405 0.296582541 0.231083425 10.98703298 12470.27093 0.102720689 0.056965404 57.62418069 -1.760604764 0.403481529 TYS(ph)GPMNK ddPTM_BT-474_Pertuzumab_2h_R1 3 TYSGPMNK 8 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 TYS(1)GPMNK;TYS(1)GPMNK;TYS(1)GPMNK 93.096 0.044219 740830000 1504300 1534040 1297760 1291230 1433340 1542590 1427920 1880520 1799280 1666950 TRUE FALSE 1445510.293 1490290.681 1532294.101 1357870.535 1479444.683 1573782.227 1445395.312 1841686.605 1595033.278 1554045.992 0.930159275 0.958974631 0.986003058 0.873764703 0.95199543 1.012699904 0.930085287 1.185091442 1.026374564 1 20.56759777 1.760610044 25 1.087706278 0.950556982 0.477582782 0.057324648 7.938435629 9007.956674 0.02521432 0.013983144 57.62488132 -1.760610044 -0.137149296 AAS(ph)GGSGSENVGPPAAAVPGPLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AASGGSGSENVGPPAAAVPGPLSR 24 0 Q9UL54-2 Q9UL54-2 TAOK2 Serine/threonine-protein kinase TAO2 1 AAS(0.964)GGS(0.034)GS(0.002)ENVGPPAAAVPGPLSR 152.07 2.87E-14 0 78252 77368 56927 57126 87723 63595 65022 95446 80661 81390 TRUE FALSE 75193.82533 75161.54039 67214.97523 60074.27971 90544.68996 64880.93447 65817.75869 93475.00675 71504.70144 75877.38281 0.990991288 0.9905658 0.885836764 0.791728411 1.193302755 0.855076072 0.867422627 1.231921862 0.942371742 1 16.2113823 1.760670315 25 1.080441616 0.940049073 0.153522979 0.124578455 17.31743112 19596.93342 0.055953871 0.031030609 57.63287902 -1.760670315 -0.140392543 SKS(ph)EDMDNVQSK ddPTM_BT-474_Pertuzumab_2h_R1 8 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.058)KS(0.942)EDMDNVQSK;S(0.151)KS(0.849)EDMDNVQSK;S(0.347)KS(0.653)EDMDNVQSK;S(0.303)KS(0.697)EDMDNVQSK;S(0.054)KS(0.946)EDMDNVQSK;SKS(1)EDMDNVQSK;S(0.487)KS(0.513)EDMDNVQSK;SKS(1)EDMDNVQSK 248.75 5.10E-17 8823830000 12404930 9823460 9700880 8754930 10241210 9501120 10360620 13326120 13483720 11710370 TRUE FALSE 11920131.62 9543304.539 11454044.81 9206772.986 10570627.82 9693239.156 10487416.37 13050930.97 11953104.63 10917216.21 1.09186549 0.874151831 1.049172664 0.843326065 0.968253043 0.887885608 0.960631004 1.195444948 1.094885766 1 23.38010169 1.76068304 25 1.114448762 0.94802477 0.369196532 0.08459699 9.376934414 10605.11436 0.035871696 0.019893232 57.63456774 -1.76068304 -0.166423992 SEDHLTESHQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDHLTESHQR 11 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 211.37 5.53E-09 65687000 80551 91748 85210 116240 95375 94439 102370 36117 87109 91221 FALSE TRUE 77402.97787 89131.43687 100609.3425 122239.1603 98442.82349 96348.62129 103622.8347 35371.17133 77220.75151 85042.52042 0.910167966 1.048080847 1.183047515 1.437388729 1.157571801 1.132946446 1.218482639 0.415923366 0.908025199 1 16.37589673 1.760686466 25 0.720501343 1.162388562 0.448678288 0.190478992 8.563855922 9684.038716 0.086952692 0.048220966 57.63502242 -1.760686466 0.441887219 AKSEDS(ph)DVELS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 2 AKSEDSDVELSD 12 1 Q5VZL5-2;Q5VZL5-4;Q5VZL5;H7C1I7;Q5VZL5-3 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 2 AKS(0.007)EDS(0.993)DVELS(1)D;AKS(0.008)EDS(0.992)DVELS(1)D 130.95 0.0024787 538270000 2202100 2149730 1614550 1560900 1836520 2010680 1918640 2195000 2448900 2083420 TRUE FALSE 2116039.497 2088421.805 1906335.1 1641458.236 1895593.334 2051337.327 1942120.89 2149672.483 2170911.139 1942308.108 1.089445845 1.075226838 0.981479248 0.84510703 0.975948834 1.056133844 0.999903611 1.106761834 1.117696585 1 20.88934064 1.760740696 10.86625772 1.083733561 1.000124534 0.171307056 0.071004723 0.328965021 146.5851056 0.035918644 0.019726848 57.64221963 -1.760740696 -0.083609027 QLVMNHMHHEDQQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLVMNHMHHEDQQVR 15 0 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 126.48 4.86E-05 45386000 47402 48089 27565 37042 42768 43658 40710 22529 40618 32161 FALSE TRUE 45549.47743 46717.5488 32546.60868 38953.74206 44143.67156 44540.79467 41208.22116 22063.76828 36007.21492 29982.70682 1.519191636 1.558149805 1.085512688 1.299206982 1.472304413 1.485549485 1.37439963 0.735883134 1.200932762 1 14.87184301 1.760744549 25 0.960145023 1.395525913 0.576654239 0.16475173 7.694378223 8678.028312 0.076517597 0.042434131 57.64273111 -1.760744549 0.43538089 STS(ph)GSPRPAGAKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.076)T(0.076)S(0.455)GS(0.392)PRPAGAKPK;S(0.137)T(0.113)S(0.399)GS(0.351)PRPAGAKPK;S(0.033)T(0.115)S(0.506)GS(0.346)PRPAGAKPK 67.605 0.027193 1616680000 2524130 2275560 1831810 1822160 1939260 2187850 2144940 2681020 2954410 2655730 TRUE FALSE 2425484.209 2210663.257 2162858.815 1916201.896 2001638.059 2232089.826 2171190.417 2625656 2619037.763 2475855.042 0.979655177 0.892888808 0.873580553 0.773955609 0.808463349 0.901543018 0.876945694 1.060504737 1.057831625 1 21.23949542 1.760794579 5.557869805 1.04390792 0.867479073 0.66592827 0.054061948 0.105113107 7.769282048 0.028615982 0.015264047 57.64937179 -1.760794579 -0.176428847 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(ph)PHNIGTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGSPHNIGTSR 44 1 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(1)PHNIGTSR;SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(1)PHNIGTSR 173.83 5.12E-21 1566810000 108994 131139 113636 146688 124373 143217 131145 70886 115028 126423 TRUE FALSE 104734.394 127399.0441 134172.553 154258.5853 128373.5705 146112.9459 132749.9917 69422.17933 101970.5037 117860.2576 0.888631979 1.080933019 1.138403697 1.308826134 1.08920151 1.239713444 1.126333799 0.589021106 0.865181408 1 16.8467178 1.760803294 25 0.780929729 1.133585159 0.492172859 0.140965132 7.95740659 8950.954203 0.0637113 0.035332359 57.65052868 -1.760803294 0.35265543 SMGYDDLDY(ph)GMMSDYGTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMGYDDLDYGMMSDYGTAR 19 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 SMGYDDLDY(1)GMMSDYGTAR 178.67 7.24E-15 0 23596 31051 18056 26718 20223 18621 23415 31147 27630 30999 TRUE FALSE 22673.84223 30165.45588 21319.12085 28096.91918 20873.49116 18997.52938 23701.55977 30503.80357 24493.55823 28899.41012 0.784578029 1.043808706 0.7377009 0.972231581 0.722280873 0.657367375 0.820139916 1.055516477 0.847545266 1 14.81875242 1.760833614 25 0.970253016 0.821065733 0.246385791 0.118539018 16.26716306 18273.31943 0.05492732 0.030460762 57.65455356 -1.760833614 -0.149187283 DMLDSHLENK ddPTM_BT-474_Pertuzumab_2h_R1 2 DMLDSHLENK 10 0 Q9GZT8-2;Q9GZT8 Q9GZT8-2 NIF3L1 NIF3-like protein 1 0 ; 90.149 0.011028 342990000 1043070 931890 730310 839320 844770 856900 880010 1048760 1057180 1012870 FALSE TRUE 1002305.671 905313.4096 862293.2627 882637.4058 871942.7943 874227.1051 890779.8256 1027102.74 937173.3585 944267.4127 1.061463795 0.958746852 0.913187569 0.934732464 0.923406635 0.925825771 0.943355466 1.087724437 0.99248724 1 19.84883596 1.760846887 25 1.034389643 0.947617437 0.352492268 0.046150363 10.87353446 12207.23502 0.02132529 0.011826184 57.6563157 -1.760846887 -0.086772207 KQTIDNSQGAYQEAFDISKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQTIDNSQGAYQEAFDISKK 20 2 P27348 P27348 YWHAQ 14-3-3 protein theta 0 ; 169.84 5.73E-12 5150600000 929530 940980 637280 544780 763110 756280 773730 995740 977260 908610 FALSE TRUE 893202.94 914144.1717 752450.6722 572896.1611 787656.1262 771572.4998 783199.1392 975177.621 866325.5418 847069.0354 1.054462981 1.07918497 0.888299112 0.676327592 0.929860606 0.91087322 0.924598948 1.151237479 1.022733102 1 19.69212003 1.760848995 25 1.07110736 0.918283288 0.240587727 0.108591833 15.72463894 17651.68821 0.054301559 0.030114272 57.65659551 -1.760848995 -0.152824072 CCSFDGDADR ddPTM_BT-474_Pertuzumab_2h_R1 1 CCSFDGDADR 10 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 148.52 0.012876 0 306610 305220 282480 294000 298080 307180 299550 303220 308190 336030 FALSE TRUE 294627.3422 296515.4244 333530.4197 309173.3752 307668.0139 313391.3901 303215.9825 296958.401 273205.5632 313270.3888 0.94048896 0.946515965 1.064672665 0.986921798 0.982116488 1.000386252 0.967905022 0.947930004 0.872107844 1 18.25704888 1.760858605 2.741400425 0.930704125 0.987793385 0.184307843 0.043038014 0.360680915 5.469332761 0.025262015 0.011760243 57.65787136 -1.760858605 0.057089259 DQHFVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQHFVK 6 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 70.912 0.089617 228680000 582030 716580 545510 910440 690720 738210 907330 247030 881990 771370 FALSE TRUE 559283.6241 696143.84 644095.7918 957427.9175 712937.6361 753137.112 918434.176 241928.7442 781870.1928 719124.4228 0.777728591 0.968043662 0.89566669 1.33138006 0.991396778 1.047297363 1.277156145 0.33642126 1.087253009 1 19.45588188 1.760882668 25 0.74144262 1.04230023 0.146526465 0.242658893 15.87320881 17791.55914 0.107546488 0.059641954 57.66106609 -1.760882668 0.300857609 KRS(ph)EGEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KRSEGEEK 8 2 Q9H8T0;Q9H8T0-2;H3BSX7;H3BNB8;H3BVH0;H3BRV2;H3BM79 Q9H8T0 AKTIP AKT-interacting protein 1 KRS(1)EGEEK;KRS(1)EGEEK 97.163 0.0066366 126105000 98248 94343 85633 86001 113994 98445 86785 77969 65992 79311 TRUE FALSE 94408.35954 91652.43001 101108.788 90439.52192 117660.7205 100435.6253 87847.10079 76358.9129 58500.86482 73939.19533 1.276837801 1.239564883 1.367458593 1.223160754 1.591317298 1.358354319 1.188099227 1.032725776 0.791202346 1 16.17405172 1.76090342 2.064946375 0.900848157 1.342258127 0.729261544 0.110257308 0.153491587 1.31207355 0.075029932 0.032066732 57.66382142 -1.76090342 0.44140997 TNS(ph)SSSSPVVLK ddPTM_BT-474_Pertuzumab_2h_R1 4 TNSSSSSPVVLK 12 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 T(0.011)NS(0.958)S(0.029)S(0.002)SSPVVLK;TNS(0.65)S(0.251)S(0.097)S(0.002)SPVVLK;T(0.003)NS(0.981)S(0.016)S(0.001)SSPVVLK;TNS(0.821)S(0.086)S(0.086)S(0.004)S(0.004)PVVLK 174.47 3.18E-05 3688560000 2988520 2414100 2057410 1982250 2210150 2132530 2234660 2894660 2757700 2605260 TRUE FALSE 2871725.334 2345252.232 2429229.754 2084554.16 2281241.482 2175651.218 2262008.438 2834884.259 2444657.457 2428803.42 1.182362192 0.965599856 1.000175533 0.858263844 0.939245006 0.895770815 0.931326273 1.167193786 1.00652751 1 21.2118143 1.760918176 25 1.073759381 0.960664718 0.158278641 0.092435114 16.8042154 18805.13467 0.042641121 0.023647413 57.66578069 -1.760918176 -0.113094662 DIHSGDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIHSGDFR 8 0 P78332;P78332-3 P78332 RBM6 RNA-binding protein 6 0 80.438 0.026848 0 47303 59613 52905 56086 58403 61132 57095 46919 58477 58761 FALSE TRUE 45454.34646 57912.89561 62466.11037 58980.60518 60281.58554 62368.13092 57793.74569 45950.10625 51838.93612 54781.06513 0.829745576 1.057169945 1.140286524 1.076660431 1.100409154 1.13849796 1.054994925 0.838795415 0.946292957 1 15.7413897 1.760920874 25 0.914094631 1.06562768 0.289732318 0.090623884 12.32730913 13793.48829 0.041900943 0.023237142 57.66613889 -1.760920874 0.151533049 SEGEGKPQGEGKPASQAKPESQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEGEGKPQGEGKPASQAKPESQPR 24 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 0 ; 135.68 1.14E-05 1047490000 680340 568200 517790 441090 525560 555170 554370 695390 765160 625430 FALSE TRUE 653751.5606 551995.4923 611366.1712 463854.7078 542465.1147 566395.9178 561154.5459 681029.9535 678302.2446 583069.069 1.121224903 0.946706868 1.048531304 0.795539898 0.930361673 0.971404501 0.962415219 1.168009057 1.163330865 1 19.15330727 1.760940693 10.96483066 1.123438169 0.962321855 0.341570892 0.089817819 0.202888449 91.29168954 0.041452173 0.022774429 57.66877056 -1.760940693 -0.161116314 DLNYCFSGMSDHR ddPTM_BT-474_Pertuzumab_2h_R1 16 DLNYCFSGMSDHR 13 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;;;;;;;;;;;; 225.21 1.28E-11 41665640000 8569368 11407987 9249785 11320259 9697660 9674193 10235082 8760777 9435325 10407327 FALSE TRUE 8234467.625 11082642.38 10921426.91 11904498.92 10009594.04 9869811.811 10360342 8579863.893 8364266.462 9702429.472 0.848701621 1.142254361 1.125638371 1.226960624 1.031658521 1.01725159 1.06780905 0.884300568 0.862079594 1 23.20991461 1.76098185 6.204936764 0.905797762 1.074457798 0.322137799 0.098956327 0.178238108 17.84991857 0.048269795 0.025989103 57.67423596 -1.76098185 0.168660036 DAMLELNASNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DAMLELNASNDR 12 0 P35250 P35250 RFC2 Replication factor C subunit 2 0 116.55 0.0019308 60632000 59445 62056 53174 61398 59833 72432 62873 59075 68197 63328 FALSE TRUE 57121.82368 60286.22364 62783.72465 64566.75814 61757.58278 73896.62467 63642.45858 57855.08061 60455.56247 59038.73815 0.967531242 1.021129948 1.063432699 1.093633776 1.046051876 1.251663348 1.077977961 0.979951171 1.023998215 1 15.84937427 1.760987096 11.57724157 1.001805626 1.078477948 0.187994753 0.069335355 0.400790455 197.0861817 0.034267688 0.018850427 57.67493263 -1.760987096 0.076672322 EKT(ph)PS(ph)PKEEDEEPES(ph)PPEKK ddPTM_BT-474_Pertuzumab_2h_R1 4 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 EKT(1)PS(1)PKEEDEEPES(1)PPEKK;EKT(1)PS(1)PKEEDEEPES(1)PPEKK;EKT(1)PS(1)PKEEDEEPES(1)PPEKK;EKT(1)PS(1)PKEEDEEPES(1)PPEKK 145.03 2.53E-07 4344880000 5444410 2700560 2544420 1380000 2899260 2063990 2767120 4245880 4910610 2936190 TRUE FALSE 5231636.438 2623542.673 3004253.294 1451221.965 2992517.331 2105725.292 2800984.842 4158201.094 4353178.14 2737319.236 1.911226272 0.958435041 1.097516598 0.530161753 1.093229205 0.769265515 1.023258378 1.519077877 1.590307072 1 21.38433227 1.76103835 10.5963368 1.413822326 1.022912692 0.128609894 0.363931977 0.316680225 133.3357223 0.166993864 0.091685064 57.68173969 -1.76103835 -0.390909634 YAHQSGFHVDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YAHQSGFHVDR 11 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 184.03 2.94E-06 1057849000 156850 257832 218194 321447 218355 266704 254677 54470 198262 209212 FALSE TRUE 150720.1286 250478.8838 257626.5095 338036.9182 225378.5869 272096.9376 257793.8133 53345.17547 175756.1289 195041.8849 0.772757752 1.284231251 1.32087787 1.733150387 1.155539422 1.395069258 1.321735654 0.273506255 0.901119926 1 17.57342445 1.761060951 25 0.659502325 1.301498626 0.438182867 0.286416432 9.053445595 10067.10993 0.128526196 0.071276939 57.68474153 -1.761060951 0.641996302 RNS(ph)SSPVSPAS(ph)VPGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.978)S(0.023)S(0.115)PVS(0.178)PAS(0.707)VPGQR 207.33 1.18E-11 298810000 540950 604850 494860 666480 655800 648220 613050 518130 641500 628380 TRUE FALSE 519809.0759 587600.2702 584292.2101 700877.1127 676894.4026 661327.4525 620552.6893 507430.4344 568679.6094 585819.2629 0.887319876 1.003040199 0.997393304 1.19640503 1.155466277 1.12889332 1.059290345 0.866189398 0.970742421 1 19.16009611 1.761086517 25 0.933971791 1.067870196 0.254079499 0.089479778 15.0867899 16756.91718 0.044554381 0.024708628 57.68813742 -1.761086517 0.133898404 SEIDLFNIRK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEIDLFNIRK 10 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 118.6 0.0012887 2005890000 4071900 4184700 2837500 3912600 3484800 3574300 3750900 4641200 5055300 4539800 FALSE TRUE 3912765.646 4065356.453 3350299.37 4114529.755 3596891.757 3646574.795 3796804.636 4545357.598 4481443.538 4232315.302 0.924497672 0.960551415 0.791599664 0.97216995 0.849863845 0.861602819 0.897098719 1.073964786 1.058863345 1 22.01301568 1.761118245 7.064347409 1.048653693 0.892369985 0.627121002 0.053057709 0.093732633 13.64552556 0.024485803 0.013282965 57.69235211 -1.761118245 -0.156283708 RAEDGIVLDLPLYPAHPQDFHEVEDLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RAEDGIVLDLPLYPAHPQDFHEVEDLIK 28 1 P30039;P30039-2;A0A0C4DFS0 P30039 PBLD Phenazine biosynthesis-like domain-containing protein 0 34.418 0.096276 8164500 14027 15024 11801 13317 17224 14714 15031 8691.6 14602 13729 FALSE TRUE 13478.80933 14595.53023 13933.70321 14004.29197 17778.0256 15011.52716 15214.95387 8512.115423 12944.44218 12799.1226 1.053104166 1.140353967 1.088645187 1.094160311 1.389003462 1.172855955 1.188749756 0.665054605 1.01135387 1 13.64375729 1.761123965 25 0.862120363 1.164063198 0.490398498 0.124438562 8.529340876 9457.812113 0.056585078 0.031380485 57.69311197 -1.761123965 0.301942834 GQYISPFHDIPIYADKDVFHMVVEVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQYISPFHDIPIYADKDVFHMVVEVPR 27 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 255.96 4.58E-53 6565600000 1634300 2559800 2038870 2526000 2438300 2834400 2535600 1551070 2336300 2642400 FALSE TRUE 1570429.749 2486797.01 2407339.163 2656367.163 2516730.134 2891713.51 2566631.431 1519039.862 2071093.019 2463427.894 0.637497754 1.009486422 0.97723143 1.07832146 1.021637426 1.173857581 1.04189428 0.616636625 0.840736205 1 21.23223581 1.761135742 25 0.781805345 1.003089169 0.18658086 0.157924266 14.82429865 16429.42908 0.071988252 0.039922674 57.69467647 -1.761135742 0.221283824 HIDMVEGDEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIDMVEGDEGR 11 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 151.98 3.32E-05 790860000 630000 705020 553200 712920 656230 697320 675120 593990 705400 636180 FALSE TRUE 605378.9035 684913.5199 653175.5459 749713.8866 677338.2339 711420.2882 683382.3205 581723.8989 625325.9493 593090.9619 1.020718477 1.154820363 1.101307536 1.264079095 1.142047809 1.199512948 1.152238635 0.9808342 1.054350832 1 19.17789386 1.761137792 9.344430206 1.01418244 1.152594479 0.506405525 0.061412913 0.129646603 41.27048027 0.028507491 0.01560593 57.69494872 -1.761137792 0.138412039 HIEIFTDLSSR ddPTM_BT-474_Pertuzumab_2h_R1 6 HIEIFTDLSSR 11 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;; 234.65 1.67E-15 6776430000 4717130 5343230 4509650 5500070 5169830 5061020 5347430 3744780 5323210 5385510 FALSE TRUE 4532779.345 5190846.312 5324644.072 5783929.272 5336122.277 5163357.292 5412873.448 3667448.984 4718941.518 5020744.611 0.90281018 1.033879776 1.060528763 1.15200627 1.062814919 1.028404687 1.078101729 0.730459179 0.939888778 1 22.25946991 1.761141933 24.9999999 0.864580767 1.04974144 0.390662846 0.087088236 9.651557447 10693.66429 0.039193277 0.02173546 57.69549893 -1.761141933 0.185160673 LTDIINNDHENVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTDIINNDHENVK 13 0 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 66.059 0.0569 518500000 310400 291770 266930 271330 292680 308370 296510 352860 374440 349870 FALSE TRUE 298269.2248 283449.0053 315170.1888 285333.3738 302094.318 314605.4527 300138.7781 345573.3177 331935.141 326172.9933 0.914451015 0.86901433 0.966266967 0.874791536 0.926178207 0.964535566 0.9201828 1.059478635 1.017665925 1 18.31527781 1.761205166 11.439495 1.028475185 0.919486706 0.688737622 0.032750548 0.121158123 58.00912889 0.014975219 0.008236964 57.70389988 -1.761205166 -0.108988479 DDQHFTVTGLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDQHFTVTGLHK 12 0 P10586-2;P10586;H0Y6Z7;H0Y7Z9 P10586-2 PTPRF Receptor-type tyrosine-protein phosphatase F 0 68.809 0.029879 21566000 27054 31239 30548 46256 26791 31405 33530 15959 31553 27971 FALSE TRUE 25996.69977 30348.09431 36068.70314 48643.2777 27652.75685 32040.03062 33940.35017 15629.44107 27971.23572 26076.49926 0.996939793 1.163810142 1.383188088 1.865406749 1.060447439 1.22869371 1.301568506 0.599368839 1.072660691 1 14.67046258 1.76122591 25 0.856593359 1.296219878 0.338465037 0.25144187 12.42336287 13713.70087 0.118760974 0.065861089 57.70665623 -1.76122591 0.439626519 EMDEEDKAFK ddPTM_BT-474_Pertuzumab_2h_R1 4 EMDEEDKAFK 10 1 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 ;;; 160.36 6.75E-06 4846140000 6435700 5306800 4243730 3606140 5198710 4851750 4949500 6416100 6729500 5081170 FALSE TRUE 6184185.729 5155455.26 5010666.412 3792253.318 5365931.228 4949855.709 5010073.462 6283605.293 5965595.372 4737017.83 1.30550189 1.088333514 1.057768113 0.800557113 1.132765681 1.044930774 1.057642939 1.326489686 1.259356749 1 22.17554767 1.761243031 25 1.227609125 1.061032785 0.130583011 0.14013432 17.76355531 19593.72622 0.064230973 0.035620899 57.70893119 -1.761243031 -0.166576339 EKLQEEGGGS(ph)DEEETGSPSEDGMQSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKLQEEGGGSDEEETGSPSEDGMQSAR 27 1 Q13610;Q13610-2 Q13610 PWP1 Periodic tryptophan protein 1 homolog 1 EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR 144.51 7.29E-13 386350000 221886 213033 147718 158441 190041 186785 184878 244714 234436 215519 TRUE FALSE 213214.4498 206957.5074 174413.9286 166618.159 196153.8414 190561.9207 187140.5923 239660.5704 207823.8081 200921.7062 1.06118176 1.030040563 0.86806912 0.829269083 0.976270036 0.948438694 0.931410527 1.19280577 1.034352197 1 17.61627391 1.761283882 25 1.093637479 0.945620151 0.339518465 0.079560906 11.86239071 13061.02014 0.037956894 0.021049668 57.7143597 -1.761283882 -0.148017328 IFVGGLNPEATEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IFVGGLNPEATEEK 14 0 Q99729-3;D6R9P3;D6RD18;D6RBZ0;Q99729-2 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 194.96 1.95E-07 186264000 331320 318350 266400 276700 291700 300930 307470 369420 398820 392870 FALSE TRUE 318371.6481 309270.9697 314544.406 290980.5202 301082.7954 307015.0108 311232.9098 361791.3479 353547.6256 366260.565 0.86924905 0.844401498 0.858799544 0.794463145 0.822045353 0.838242061 0.849758177 0.987797712 0.965289904 1 18.48251085 1.761296961 4.44708052 0.98337124 0.837014151 0.910062141 0.020857428 0.053711217 2.255737652 0.011191068 0.005806792 57.71609781 -1.761296961 -0.146357089 EKDDANFK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDDANFK 8 1 Q5VTR2;H3BP71;O75150-4;O75150;O75150-3 Q5VTR2;H3BP71 RNF20;RNF40 E3 ubiquitin-protein ligase BRE1A;E3 ubiquitin-protein ligase BRE1B 0 72.879 0.041051 563730000 819760 713340 626560 608140 653410 675800 695460 936640 983480 914790 FALSE TRUE 787722.8729 692996.2416 739793.3298 639526.1783 674427.5261 689465.139 703971.2475 917298.0567 871839.4735 852830.4585 0.923657059 0.812583832 0.867456506 0.749886653 0.790810787 0.808443381 0.82545275 1.075592514 1.022289325 1 19.70189944 1.761302573 7.719448602 1.035047184 0.82146583 0.803254516 0.046923245 0.061838726 11.64908431 0.022326563 0.012157989 57.71684373 -1.761302573 -0.213581353 AHSEVFTKPSGQQTLS(ph)PDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHSEVFTKPSGQQTLSPDR 19 1 F5H212;P15822;A0A0D9SFF3;P15822-2;P15822-3 F5H212 HIVEP1 Zinc finger protein 40 1 AHSEVFTKPSGQQTLS(1)PDR;AHSEVFTKPSGQQT(0.01)LS(0.99)PDR 277.15 1.03E-39 624940000 613330 518730 494780 548300 545720 532540 555630 446890 561560 588010 TRUE FALSE 589360.3855 503936.3283 584197.7523 576597.8287 563273.5794 543308.3237 562429.9661 437661.5653 497814.0631 548183.559 1.075115034 0.919283915 1.065697325 1.051833495 1.027527313 0.991106564 1.025988388 0.798385063 0.908115639 1 19.06429953 1.761314746 25 0.883008005 1.020196429 0.430200885 0.062195417 9.136948163 10046.53044 0.027011521 0.014979731 57.71846141 -1.761314746 0.137188424 SCDEPLT(ph)PPPHSPTSMLQLIHDPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 S(0.002)CDEPLT(0.997)PPPHS(0.001)PTSMLQLIHDPVS(0.999)PR;SCDEPLT(0.819)PPPHS(0.077)PT(0.038)S(0.066)MLQLIHDPVS(1)PR 173.94 4.26E-12 343980000 160583 187566 151571 185187 161777 172071 172939 104185 157439 170749 TRUE FALSE 154307.2388 182216.8013 178963.2514 194744.5233 166980.7041 175550.3935 175055.4792 102033.5433 139567.1848 159184.0181 0.969363889 1.144692812 1.124253888 1.223392433 1.048979075 1.102814187 1.099705116 0.640978564 0.876766314 1 17.28033597 1.761329314 25 0.806455216 1.107066972 0.568314088 0.103651865 6.968943757 7657.794706 0.045076157 0.024997744 57.72039764 -1.761329314 0.300611756 EIS(ph)SS(ph)PTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 EIS(0.971)S(0.034)S(0.983)PT(0.012)SK;EIS(0.582)S(0.42)S(0.996)PT(0.002)SK;EIS(0.928)S(0.17)S(0.894)PT(0.004)S(0.005)K;EIS(0.986)S(0.015)S(0.993)PT(0.006)SK 136.81 0.00026665 5708480000 8925790 8381380 6540620 6871860 7377060 7427900 7686960 8950580 9775400 8663760 TRUE FALSE 8576960.259 8142351.249 7722655.529 7226517.518 7614349.835 7578097.227 7781035.316 8765747.395 8665737.574 8076955.818 1.061905061 1.008096544 0.956134428 0.894708066 0.942725206 0.938236806 0.963362372 1.085278611 1.072896493 1 22.94538022 1.761399891 10.88645355 1.058843454 0.962882315 0.413038097 0.046818585 0.193874031 84.84127658 0.023356526 0.012835407 57.72977854 -1.761399891 -0.095961138 KELEEDFIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KELEEDFIK 9 1 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 110.66 0.0036088 90564000 221030 225120 184850 188390 211910 192670 219680 242720 279040 262470 FALSE TRUE 212391.9032 218699.798 218256.507 198112.8305 218726.2776 196565.9194 222368.5096 237707.7472 247364.549 244692.6731 0.867994536 0.893773382 0.891961758 0.809639406 0.893881598 0.803317553 0.908766522 0.971454291 1.010919313 1 17.90061138 1.761457365 2.495163858 1.001540559 0.862147195 0.78366745 0.031509992 0.114543906 1.438868003 0.018971396 0.008594933 57.73741885 -1.761457365 -0.139393364 SLSPS(ph)HLTEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSPSHLTEDR 11 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SLS(0.342)PS(0.535)HLT(0.123)EDR 97.439 0.0065725 59171000 88097 90809 75011 92930 87857 90397 89435 81911 96308 95149 TRUE FALSE 84654.07184 88219.21623 88567.15631 97726.12844 90683.00019 92224.88928 90529.53228 80219.50923 85375.5196 88704.47348 0.954338248 0.994529506 0.99845197 1.101704622 1.022304701 1.039687015 1.020574597 0.904345701 0.962471409 1 16.43671924 1.761463041 25 0.94672578 1.021209654 0.31780583 0.041720644 12.44940506 13600.02307 0.019682841 0.010915468 57.73817354 -1.761463041 0.074483874 AIPGDQHPES(ph)PVHTEPMGIQGR ddPTM_BT-474_Pertuzumab_2h_R1 8 AIPGDQHPESPVHTEPMGIQGR 22 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.994)PVHT(0.006)EPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR 259.7 2.03E-37 12057600000 3271090 3397850 2993600 3571450 3438100 3604960 3383160 2047477 3136740 3206030 TRUE FALSE 3143252.186 3300946.645 3534610.112 3755772.963 3548689.609 3677854.761 3424564.124 2005195.884 2780670.425 2988882.732 1.051647879 1.104408215 1.182585745 1.256580903 1.187296367 1.230511562 1.145767309 0.670884763 0.930337746 1 21.51117486 1.761515957 25 0.838286358 1.170683897 0.66425499 0.096543355 6.187890473 6744.199899 0.04342875 0.024084314 57.74520891 -1.761515957 0.33239754 INPPPYLTCESFPHAVDHILQHLL ddPTM_BT-474_Pertuzumab_2h_R1 2 INPPPYLTCESFPHAVDHILQHLL 24 0 Q9H0R4;Q9H0R4-2 Q9H0R4 HDHD2 Haloacid dehalogenase-like hydrolase domain-containing protein 2 0 ; 162.49 1.04E-11 149491000 190372 206477 141776 165002 181711 187000 180070 88244 188751 123409 FALSE TRUE 182932.0518 200588.4781 167398.077 173517.773 187555.8993 190781.2681 182273.7505 86421.73056 167324.7778 115050.3985 1.590016672 1.743483558 1.454997802 1.508189239 1.630206429 1.658240828 1.584294821 0.751164113 1.454360697 1 16.81190646 1.761552651 25 1.053546812 1.596285168 0.653143589 0.175930934 6.620012236 7203.643402 0.075582017 0.041915701 57.7500881 -1.761552651 0.542738356 RTDKDTEITCSER ddPTM_BT-474_Pertuzumab_2h_R1 2 RTDKDTEITCSER 13 2 P16422;B5MCA4 P16422 EPCAM Epithelial cell adhesion molecule 0 ; 95.57 0.0026073 1181050000 194778 286590 226280 332470 283360 286710 277950 127531 224238 280370 FALSE TRUE 187165.8604 278416.7338 267173.8296 349628.8165 292474.5317 292507.4726 281351.6352 124897.4403 198783.4423 261380.2902 0.71606723 1.065178762 1.022165173 1.337625023 1.118961692 1.119087719 1.076407234 0.47783802 0.760514277 1 17.99579083 1.761566393 25 0.697002332 1.078057809 0.370326196 0.186798244 10.59228991 11519.23465 0.084790871 0.047022375 57.75191541 -1.761566393 0.381055477 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR 43 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 161.96 2.51E-20 787100000 555810 671470 478040 559220 555030 512010 551490 105366 590010 189466 FALSE TRUE 534088.3307 652320.333 564432.4619 588081.4112 572883.044 522363.193 558239.2996 103190.1553 523034.5383 176633.2991 3.023712593 3.693076767 3.195504273 3.329391538 3.243346793 2.957331351 3.160442015 0.584205559 2.961132137 1 17.43039782 1.761608685 25 1.509251271 3.239503549 0.633297309 0.597595286 6.982933284 7580.06965 0.252728901 0.140156616 57.75753964 -1.761608685 1.730252278 VREFTMAEIEHFVDPSEKDHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VREFTMAEIEHFVDPSEKDHPK 22 2 P41250 P41250 GARS Glycine--tRNA ligase 0 70.352 0.0056559 323300000 100740 95295 77577 75631 90575 126010 96486 58671 99348 81542 FALSE TRUE 96802.96943 92577.2799 91596.88959 79534.32497 93488.42713 128558.0085 97666.82453 57459.42335 88070.43154 76019.08771 1.273403461 1.217816244 1.204919611 1.046241508 1.229802014 1.69112801 1.284767122 0.755855208 1.158530498 1 16.21407409 1.761641573 25 0.951933577 1.278236416 0.381130722 0.178655637 12.71888438 13786.82948 0.086524674 0.047984247 57.76191367 -1.761641573 0.326302839 YLLEGTAETHELAEGSTADVLHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLLEGTAETHELAEGSTADVLHSR 24 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ; 285.38 7.95E-53 318320000 99022 92669 81099 109006 105265 115208 108158 66515 102561 110780 FALSE TRUE 95152.11077 90026.17085 95755.39334 114631.8127 108650.9443 117537.5847 109481.67 65141.44201 90918.70525 103276.7719 0.921331186 0.871698148 0.927172602 1.109947673 1.052036603 1.138083448 1.060080286 0.630746302 0.880340308 1 16.65615629 1.761643343 25 0.800946235 1.013076666 0.300824977 0.11807472 12.75308009 13822.83868 0.05638929 0.031272176 57.76214905 -1.761643343 0.212130431 S(ph)KSEEAHAEDSVMDHHFR ddPTM_BT-474_Pertuzumab_2h_R1 10 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.811)KS(0.189)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR 266.74 1.76E-31 20891190000 7545710 6036810 4172910 5238200 6692290 6099570 6523550 2081869 6111200 5204690 TRUE FALSE 7250815.311 5864646.089 4927047.663 5508544.13 6907553.586 6222907.485 6603387.156 2038877.678 5417482.196 4852171.71 1.494344336 1.208664169 1.015431431 1.135273947 1.4236004 1.282499437 1.360913741 0.420198995 1.116506694 1 22.21019918 1.76168031 25 0.792096328 1.262602409 0.451960439 0.213699514 9.832456028 10640.16915 0.09607368 0.053279719 57.76706592 -1.76168031 0.470506081 HTEMIHNYMEHLER ddPTM_BT-474_Pertuzumab_2h_R1 1 HTEMIHNYMEHLER 14 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 0 149.3 2.62E-06 42432000 5699.8 7781.2 6929.9 8315.8 5634.2 9582.8 7983.7 2309.4 7152 6290 FALSE TRUE 5477.045515 7559.287795 8182.287085 8744.979435 5815.42916 9776.570782 8081.406909 2261.710083 6340.134944 5863.972697 0.934016203 1.289106922 1.395348769 1.491306301 0.991721732 1.667226518 1.378145385 0.385695875 1.081201307 1 12.51766267 1.761735779 25 0.766837037 1.318282178 0.403016894 0.26736383 10.39512521 11222.10959 0.118378669 0.065649774 57.77444461 -1.761735779 0.551445141 VALS(ph)DDETKETENMR ddPTM_BT-474_Pertuzumab_2h_R1 3 VALSDDETKETENMR 15 1 Q15054;H0YD46;Q15054-3;Q15054-2 Q15054 POLD3 DNA polymerase delta subunit 3 1 VALS(0.999)DDET(0.001)KETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR 297.63 2.39E-44 8332400000 3987530 3417070 2946130 2854510 3252230 3056390 3236050 4017840 3984630 3675340 TRUE FALSE 3831692.919 3319618.509 3478561.227 3001831.603 3356840.932 3118192.3 3275653.748 3934870.2 3532311.507 3426405.948 1.118283407 0.968833979 1.01522157 0.876087553 0.97969738 0.910047539 0.95600282 1.1483958 1.030908643 1 21.70826466 1.76174039 25 1.073849441 0.97009264 0.224761533 0.070417802 14.86858804 16048.26363 0.031841716 0.017658391 57.77505803 -1.76174039 -0.103756801 TPTHQPPKPGS(ph)PGRPACPLSNLLLQSYEER ddPTM_BT-474_Pertuzumab_2h_R1 3 TPTHQPPKPGSPGRPACPLSNLLLQSYEER 30 2 Q96F63 Q96F63 CCDC97 Coiled-coil domain-containing protein 97 1 T(0.005)PT(0.005)HQPPKPGS(0.989)PGRPACPLSNLLLQSYEER;TPTHQPPKPGS(1)PGRPACPLSNLLLQSYEER;T(0.132)PT(0.132)HQPPKPGS(0.715)PGRPACPLS(0.02)NLLLQSYEER 207.62 5.54E-26 3825870000 1190666 1008139 779557 850185 1007617 1007069 992184 1178378 1174957 1175028 TRUE FALSE 1144133.456 979387.8628 920440.2911 894063.1497 1040027.916 1027432.625 1004326.645 1154044.083 1041580.807 1095442.307 1.044448849 0.894057 0.840245338 0.81616635 0.949413684 0.937915779 0.916822947 1.053495994 0.950831277 1 20.06308207 1.761788996 24.99998036 1.005164109 0.909038719 0.284084196 0.063053527 15.21232466 16384.87133 0.030036516 0.016657486 57.78152456 -1.761788996 -0.09612539 QQQLEEEAAKPPEPEKPVS(ph)PPPVEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 QQQLEEEAAKPPEPEKPVSPPPVEQK 26 2 O75376;O75376-2;A0A088AWL3;E7EVU5;E7EW50;J3KS51;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 QQQLEEEAAKPPEPEKPVS(1)PPPVEQK;QQQLEEEAAKPPEPEKPVS(1)PPPVEQK 200.8 2.71E-25 3149400000 3093780 2005540 2030760 1547480 2181720 1918950 2384070 2943900 3738600 2973300 TRUE FALSE 2972871.657 1948343.963 2397763.506 1627345.628 2251897.005 1957752.484 2413246.962 2883107.436 3314209.801 2771915.743 1.072497122 0.702887152 0.865020343 0.587083367 0.812397351 0.706281383 0.870606175 1.040113663 1.195638724 1 21.40245197 1.76182468 2.704901734 1.102047024 0.782673718 0.502667059 0.127851532 0.186086267 2.743516018 0.072495623 0.033649327 57.78627229 -1.76182468 -0.319373306 SLLQDAAIEEVEMEDFDANIEEQKEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLQDAAIEEVEMEDFDANIEEQKEEK 27 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23;U3KQT9 P49750 YLPM1 YLP motif-containing protein 1 0 211.33 9.22E-26 49751000 45843 31414 32961 27867 32904 32263 34255 45191 48386 40547 FALSE TRUE 44051.40488 30518.10348 38917.78591 29305.21921 33962.38704 32915.37997 34674.22294 44257.79006 42893.42413 37800.71557 1.165359021 0.807341951 1.029551566 0.775255673 0.898458839 0.870760764 0.91729012 1.170818843 1.134725189 1 15.20612592 1.761835771 11.53748991 1.113842159 0.914334898 0.343357336 0.112200849 0.22889274 108.5674804 0.048824053 0.026872594 57.78774816 -1.761835771 -0.199507261 LSAKPAPPKPEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSAKPAPPKPEPK 13 2 Q15651;A0A087WZE9;Q15651-2;P05204 Q15651;P05204 HMGN3;HMGN2 High mobility group nucleosome-binding domain-containing protein 3;Non-histone chromosomal protein HMG-17 0 106.13 0.00078643 7203100000 9945800 8172100 7154900 6458200 8554200 7905800 7858300 10463000 10017000 8937500 FALSE TRUE 9557107.14 7939039.709 8447949.59 6791508.476 8829353.612 8065660.693 7954472.226 10246935.39 8879912.155 8332155.164 1.147015022 0.952819475 1.013897296 0.815096256 1.05967225 0.968016142 0.954671639 1.229806118 1.065740133 1 22.99025828 1.761942159 25 1.120865689 0.982425483 0.206448695 0.096652012 15.18256182 16245.60071 0.042512657 0.023576124 57.80190593 -1.761942159 -0.138440206 TAS(ph)QGPQTDSVIQNSENIK ddPTM_BT-474_Pertuzumab_2h_R1 4 TASQGPQTDSVIQNSENIK 19 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 TAS(1)QGPQTDSVIQNSENIK;T(0.059)AS(0.941)QGPQTDSVIQNSENIK;T(0.021)AS(0.979)QGPQTDSVIQNSENIK;T(0.002)AS(0.998)QGPQTDSVIQNSENIK 493.46 5.75E-241 2166260000 2542190 2422000 2028460 2210840 1873800 2116320 2198830 2909780 2766170 2582210 TRUE FALSE 2442838.404 2352926.931 2395047.845 2324941.717 1934072.479 2159113.44 2225739.939 2849692.026 2452165.978 2407314.617 1.014756604 0.977407321 0.994904375 0.965782246 0.803414919 0.896897076 0.924573765 1.183763853 1.018631284 1 21.19899327 1.761997996 25 1.084510281 0.937369696 0.387409359 0.0726555 11.79063946 12586.10731 0.034896867 0.019352535 57.809338 -1.761997996 -0.147140586 FHVLVASQDFVESVLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FHVLVASQDFVESVLVR 17 0 O60784;O60784-4;O60784-2;O60784-3;V9GYF4;B0QY02;V9GZ68;Q6UW50;B0QY01;H7BYN7 O60784 TOM1 Target of Myb protein 1 0 147.64 3.92E-07 90108000 50010 52565 50822 51548 59973 56665 54909 35046 45256 47417 FALSE TRUE 48055.55391 51065.89767 60006.66593 54208.39846 61902.08601 57810.80512 55580.99277 34322.28785 40118.72861 44205.40436 1.087096807 1.155195805 1.3574509 1.226284416 1.400328465 1.307776865 1.257334789 0.776427415 0.907552576 1 15.43193514 1.761998373 11.20548303 0.883044501 1.262425724 0.733387402 0.09968203 0.11037183 49.72473807 0.047681808 0.026232386 57.80938821 -1.761998373 0.379381223 IHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 IHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIR 34 2 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 50.492 0.039853 776120000 244680 263970 198850 255010 278700 282510 261310 168160 283440 211160 FALSE TRUE 235117.6351 256441.8341 234786.6184 268171.0967 287664.6386 288222.5458 264507.9899 164687.4372 251265.0795 196857.9451 1.194351769 1.302674545 1.192670269 1.362256913 1.461280308 1.464114367 1.343649045 0.836580089 1.27637764 1 17.58679541 1.762109376 25 1.026558515 1.336384356 0.509976698 0.131835591 9.915762662 10534.62854 0.061110337 0.033890078 57.82416573 -1.762109376 0.309825841 NHYNEEMSNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NHYNEEMSNLR 11 0 P15924;P15924-3 P15924 DSP Desmoplakin 0 ;;; 252.21 2.22E-20 2047160000 1821280 1831430 1487310 1600180 1534320 1507100 1689490 582700 1600480 1250530 FALSE TRUE 1750102.364 1779199.41 1756100.002 1682765.482 1583672.796 1537574.595 1710166.484 570667.0414 1418800.22 1165830.489 1.50116366 1.526121873 1.50630818 1.443404935 1.358407428 1.318866344 1.466908354 0.48949401 1.216986717 1 20.15292661 1.762176493 24.99999951 0.858717959 1.442948507 0.656332596 0.179466606 6.751663044 7152.644301 0.077935607 0.04322116 57.83310277 -1.762176493 0.584230548 KNHLEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 KNHLEGK 7 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 114.78 0.0037829 5983190000 24366800 25308200 20286800 23687100 23621400 25768000 24785000 20285100 26034600 25693500 FALSE TRUE 23414518.52 24586434.92 23953076.04 24909594.07 24381203.78 26289046.62 25088326.24 19866205.6 23079261.35 23953256.36 0.977508785 1.026433924 0.999992472 1.039925165 1.017865939 1.097514518 1.047386872 0.829373898 0.963512476 1 24.51371846 1.762203938 25 0.914643142 1.030831439 0.432220634 0.050724802 9.887629045 10462.68755 0.022635606 0.012553162 57.83675758 -1.762203938 0.116188297 NLS(ph)NEELTK ddPTM_BT-474_Pertuzumab_2h_R1 4 NLSNEELTK 9 0 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 NLS(1)NEELTK;NLS(1)NEELTK;NLS(1)NEELTK;NLS(1)NEELTK 186.14 4.41E-05 3012880000 3637700 3287910 2829890 2765710 3009880 3109390 3157370 3794630 4155850 3630220 TRUE FALSE 3495534.662 3194142.026 3341314.074 2908448.625 3106695.524 3172263.996 3196010.839 3716269.564 3684095.331 3384341.966 1.032855042 0.943800023 0.987286187 0.85938379 0.917961469 0.937335538 0.944352217 1.098077441 1.088570649 1 21.69044392 1.762217439 8.857178406 1.069097022 0.942799006 0.541960905 0.048693725 0.114262465 31.13361945 0.02301585 0.012601648 57.83855559 -1.762217439 -0.126298017 DFMHVLEHECQHHHSK ddPTM_BT-474_Pertuzumab_2h_R1 5 DFMHVLEHECQHHHSK 16 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;;; 205.42 6.97E-12 3387270000 1385050 2100510 1733850 2396460 1844290 2020000 1957370 110026.2 1880560 803679 FALSE TRUE 1330920.715 2040605.511 2047195.264 2520141.588 1903613.263 2060845.784 1981324.88 107754.1205 1667086.713 749245.1055 1.776348894 2.723548671 2.732343861 3.363574309 2.540708306 2.750562892 2.644428192 0.143816916 2.225021826 1 19.51507823 1.762235107 25 1.064449249 2.680973392 0.580514602 0.592725907 8.146442197 8608.872807 0.258673352 0.143453745 57.84090869 -1.762235107 1.616524143 DNYVPEVSALDQEIIEVDPDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 DNYVPEVSALDQEIIEVDPDTK 22 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ; 173.8 3.34E-12 222050000 1043780 924560 881780 813490 954610 951650 947690 1171510 1251470 1146540 FALSE TRUE 1002987.924 898192.454 1041137.261 855474.3164 985315.8976 970893.015 959288.1137 1147317.909 1109408.372 1068883.825 0.938350736 0.840308772 0.974041554 0.800343589 0.921817577 0.908324172 0.897467144 1.073379429 1.037912958 1 20.02767363 1.762288479 8.690571143 1.04069772 0.895552765 0.633389281 0.048709413 0.090859456 23.53325778 0.021224337 0.011616567 57.84801738 -1.762288479 -0.145144955 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR 29 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 255.95 5.96E-58 1199330000 363570 423300 364740 427310 426800 462840 420530 381090 455700 437850 FALSE TRUE 349361.2825 411227.8985 430656.6316 449363.5203 440528.4096 472198.9419 425676.5719 373220.3583 403970.8465 408194.0295 0.855870633 1.007432419 1.055029227 1.100857651 1.079213261 1.156800217 1.042829001 0.914320963 0.989653981 1 18.63889556 1.762367058 25 0.960481928 1.049747355 0.159117085 0.076771633 21.50842365 22603.24423 0.037220744 0.020641541 57.8584851 -1.762367058 0.089265427 RHVTLPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RHVTLPSSPR 10 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 RHVTLPS(0.512)S(0.488)PR;RHVTLPS(0.5)S(0.5)PR;RHVT(0.004)LPS(0.778)S(0.218)PR;RHVTLPS(0.868)S(0.132)PR 96.734 0.0034107 873480000 675700 870890 736170 886970 841330 801160 933710 533770 900410 978340 TRUE FALSE 649292.897 846053.0699 869212.295 932746.628 868392.1435 817360.0041 945137.0223 522747.463 798199.2316 912076.1604 0.711884517 0.927612305 0.953004072 1.022663094 0.952104858 0.896153238 1.036247918 0.573140145 0.875145373 1 19.79879477 1.762468358 25 0.772278161 0.932713583 0.107344312 0.131080528 18.80808518 19681.63322 0.057911855 0.032116565 57.87198226 -1.762468358 0.160435422 SVTVVEDDEDEDGDDLLHHHHVSGSR ddPTM_BT-474_Pertuzumab_2h_R1 7 SVTVVEDDEDEDGDDLLHHHHVSGSR 26 0 P02545-2;Q3BDU5;Q5TCI8 P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;; 236.98 3.39E-45 7892803000 1113691 1567723 1264718 1954178.7 1505391 1710643.5 1714169 314978.2 1582693.2 1213419 FALSE TRUE 1070166.724 1523013.075 1493280.676 2055034.097 1553813.269 1745233.884 1735147.513 308473.7901 1403032.503 1131233.05 0.946017909 1.346330073 1.320046895 1.816631945 1.373557171 1.5427713 1.533855038 0.272688099 1.24026831 1 20.10946475 1.762473755 25 0.771494845 1.424499306 0.416254453 0.308066029 10.97193475 11478.93497 0.137428547 0.076214838 57.87270144 -1.762473755 0.653004461 TKRPETK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKRPETK 7 2 O75362 O75362 ZNF217 Zinc finger protein 217 0 64.567 0.041028 59327000 112020 128140 98771 93907 106050 113250 118250 130880 143950 146990 FALSE TRUE 107642.1346 124485.5727 116621.1168 98753.55152 109461.1946 115539.9926 119697.1789 128177.2823 127609.3995 137034.2364 0.785512711 0.908426799 0.851036354 0.720648753 0.798787204 0.843146907 0.873483751 0.935366852 0.931222758 1 17.06417685 1.762474707 1.197750272 0.977304525 0.81567454 0.643970092 0.046880952 0.311072204 0.834175668 0.041456141 0.016430871 57.87282823 -1.762474707 -0.161629985 AAS(ph)VPCSVAPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 AASVPCSVAPEK 12 0 Q9C073;D6RFX7 Q9C073 FAM117A Protein FAM117A 1 AAS(1)VPCSVAPEK;AAS(0.984)VPCS(0.016)VAPEK;AAS(0.922)VPCS(0.078)VAPEK 222.74 2.53E-11 726370000 1977580 1888710 1562480 1779660 1738430 1810120 1856340 2000270 2194630 2157710 TRUE FALSE 1900293.987 1834845.84 1844854.893 1871508.466 1794348.18 1846721.867 1879058.444 1958963.725 1945504.803 2011566.38 0.944683708 0.912147796 0.917123547 0.930373705 0.892015395 0.918051666 0.934126988 0.973849904 0.967159137 1 20.93988792 1.762534691 1.899711933 0.984116314 0.917730435 0.784779322 0.014452319 0.139731842 1.001831742 0.009894643 0.004134641 57.88082217 -1.762534691 -0.066385879 LDAVSEVLHSESSVFGQIENHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDAVSEVLHSESSVFGQIENHLR 23 0 A0A590UKC9;A0A590UJN8;A0A590UJW0;P20585 A0A590UKC9 MSH3 DNA mismatch repair protein Msh3 0 234.98 2.55E-37 54572000 34667 39199 27273 32576 39774 38644 39129 23534 39165 38411 FALSE TRUE 33312.17531 38081.0829 32201.83778 34257.25126 41053.36683 39425.40816 39607.87241 23048.01468 34719.15339 35809.38876 0.930263723 1.063438507 0.89925684 0.956655571 1.146441429 1.100979646 1.106075076 0.643630497 0.969554483 1 15.12805027 1.762548203 25 0.835810921 1.029850371 0.258340478 0.118194592 14.61953174 15247.5717 0.054012018 0.029953634 57.88262296 -1.762548203 0.194039451 HLETSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLETSK 6 0 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 77.984 0.070979 90814000 185810 193630 147740 188410 192540 169610 189500 134630 194750 187770 FALSE TRUE 178548.3398 188107.862 174439.9045 198133.8627 198733.224 173039.6304 191819.1577 131849.8435 172642.7965 175052.1707 1.019972155 1.074581716 0.996502379 1.131856074 1.135279975 0.988503197 1.0957828 0.753203133 0.986236251 1 17.41742543 1.762616801 25 0.889604925 1.063621612 0.419537196 0.07945346 10.56643753 10988.90676 0.034772964 0.019284304 57.89176643 -1.762616801 0.174016686 GVAINFVTEEDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVAINFVTEEDKR 13 1 Q14240;Q14240-2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 144.88 6.66E-05 246950000 299540 327440 396380 243610 318150 338260 326680 179830 297760 310690 FALSE TRUE 287833.6456 318101.7318 468014.6834 256182.7413 328383.5837 345099.849 330678.0076 176116.4477 263959.5331 289646.6896 0.993740498 1.098240523 1.615812299 0.884466319 1.133738432 1.191451038 1.141659889 0.608038876 0.911315553 1 18.14393465 1.762651245 24.99999991 0.804095793 1.157732336 0.330098299 0.201302756 13.61847129 14142.6984 0.090765434 0.050336429 57.89635799 -1.762651245 0.353636543 SPITSS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPITSSPPK 9 0 Q52LA3;G3V5T8 Q52LA3;G3V5T8 LIN52 Protein lin-52 homolog 1 SPIT(0.004)S(0.041)S(0.954)PPK 113.44 0.0018873 271190000 582210 497530 459890 474100 466180 310440 554300 590950 697250 704740 TRUE FALSE 559456.5895 483340.9315 543002.3532 498568.3578 481175.1031 316717.3095 561083.6892 578746.676 618101.1031 657007.3321 0.851522597 0.735670529 0.826478377 0.758847479 0.732374023 0.48206054 0.853999129 0.880883131 0.940782656 1 19.32554995 1.762666994 2.558717558 0.947734217 0.73560916 0.467543793 0.09890864 0.244827018 3.22842777 0.062134079 0.028394938 57.89845753 -1.762666994 -0.212125056 HEVTICNYEASANPADHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEVTICNYEASANPADHR 18 0 X6R8S9;Q9GZP4-2;Q9GZP4 X6R8S9 PITHD1 PITH domain-containing protein 1 0 108.14 0.00023121 467760000 60591 75317 44961 73264 55120 69782 68229 39655 71136 59915 FALSE TRUE 58223.03673 73169.0329 53086.45285 77045.16382 56892.98486 71193.03985 69064.00691 38836.11039 63060.93951 55856.90368 1.04236062 1.309937144 0.950400924 1.37933109 1.018548847 1.274561158 1.236445316 0.695278611 1.128973061 1 15.76944798 1.762667501 25 0.913395855 1.175674628 0.291779403 0.163625293 13.95747279 14484.96722 0.06888192 0.038200412 57.89852513 -1.762667501 0.262278773 DLVQPDKPAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 DLVQPDKPASPK 12 1 Q6PJT7-5;Q6PJT7;G3V411;G3V4R5;Q6PJT7-9;Q6PJT7-2;H0YJA2 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK 219.84 8.15E-11 10497520000 10921810 8066490 7290020 5549220 7895240 7435440 8095890 10835850 12397700 10088710 TRUE FALSE 10494973.59 7836441.603 8607488.78 5835615.909 8149197.565 7585789.691 8194969.924 10612085.91 10990365.07 9405392.686 1.115846402 0.83318601 0.915165275 0.620454255 0.866438844 0.806536202 0.871305452 1.128298016 1.168517407 1 23.16505675 1.76266904 5.195047582 1.110983033 0.849862647 0.444835821 0.121000327 0.153103782 9.389373571 0.059584339 0.031646779 57.89873031 -1.76266904 -0.261120385 LADVDKDGLLDDEEFALANHLIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LADVDKDGLLDDEEFALANHLIK 23 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 0 ; 192.45 5.48E-18 112981000 154921 143141 123346 129290 144326 144280 163530 174322 215279 204696 FALSE TRUE 148866.516 139058.7588 145637.366 135962.6724 148968.3769 147197.4405 165531.3291 170722.1898 190841.4304 190831.7576 0.780092988 0.728698203 0.763171538 0.712474035 0.780626761 0.771346668 0.86742024 0.894621482 1.000050688 1 17.54194175 1.762675517 1.012417716 1.008548215 0.746594436 0.939423701 0.024649427 0.10187038 0.194344934 0.019611035 0.008041787 57.89959381 -1.762675517 -0.261953779 REEQTDT(ph)SDGESVTHHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQT(0.014)DT(0.624)S(0.362)DGESVTHHIR;REEQT(0.052)DT(0.474)S(0.474)DGESVTHHIR 178.22 6.85E-14 2316770000 332760 418100 295000 456160 389190 453370 412360 187137 370070 384590 TRUE FALSE 319755.3713 406176.1974 348313.0622 479702.4723 401708.6498 462537.452 417406.585 183272.5556 328061.2051 358541.3767 0.891822791 1.132857248 0.971472429 1.337927791 1.120396908 1.290053205 1.164179679 0.511161521 0.914988412 1 18.45178009 1.762677572 25 0.762732382 1.137647862 0.415405189 0.171806262 10.83518402 11239.9774 0.076360888 0.042348077 57.89986777 -1.762677572 0.37491548 GLDVEDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDVEDVK 8 0 P17844;P17844-2;J3KTA4;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3 P17844;A0A1X7SBZ2 DDX5;DDX17 Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17 0 ; 143.12 0.0014111 757590000 1784050 1658930 1518960 1566530 1638020 1757340 1701950 2008740 2196000 2062100 FALSE TRUE 1714327.354 1611618.941 1793469.861 1647378.801 1690708.401 1792874.619 1722778.973 1967258.817 1946719.286 1922432.13 0.89174922 0.838322932 0.932917128 0.856924297 0.879463246 0.932607498 0.896145537 1.023317695 1.012633557 1 20.87450124 1.76272757 5.074555978 1.013542787 0.888780103 0.798513818 0.028114858 0.075596376 4.36387062 0.01394305 0.007385198 57.90653386 -1.76272757 -0.124762684 NS(ph)PLDCGSASPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPLDCGSASPNK 13 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 NS(0.997)PLDCGS(0.003)ASPNK;NS(1)PLDCGSASPNK 179.97 4.68E-07 0 610530 567450 568560 571390 592390 578010 639640 836100 991390 858300 TRUE FALSE 586669.8126 551266.8816 671311.4395 600879.5064 611444.7623 589697.7582 647468.1057 818834.2428 878851.5634 800166.5765 0.733184602 0.68894015 0.83896461 0.750943021 0.764146842 0.736968746 0.809166647 1.023329725 1.098335758 1 19.60994084 1.762784065 3.008904804 1.055248922 0.754513778 0.90565425 0.041804398 0.062303749 1.132644078 0.023593545 0.011288566 57.91406712 -1.762784065 -0.300735143 EHNGQVTGIDWAPESNR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHNGQVTGIDWAPESNR 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ;;; 149.47 3.24E-07 4439930000 2717110 2734220 2063560 2726670 2578310 2638080 2732590 2001400 2763540 2853350 FALSE TRUE 2610922.337 2656242.723 2436491.196 2867393.765 2661243.683 2691423.785 2766032.254 1960070.391 2449834.525 2660090.063 0.981516518 0.99855368 0.915943121 1.077931084 1.000433677 1.011779196 1.039826543 0.73684362 0.920959241 1 21.34304366 1.762817612 25 0.859862502 1.00317675 0.335646238 0.073224435 11.99887967 12375.22556 0.031879605 0.017679942 57.91854083 -1.762817612 0.143314247 LEGDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEGDLK 6 0 Q09666;P13535;Q9UKX3;Q9Y623;P12882;P11055;P35749;P35749-2;P35749-4;P35749-3;Q9UKX2;P13533;P12883;A0A6E1W127;A7E2Y1 Q09666;P35749;Q9UKX2;P13533;A0A6E1W127 AHNAK;MYH8;MYH13;MYH4;MYH1;MYH3;MYH11;MYH2;MYH6;MYH7;MYH7B Neuroblast differentiation-associated protein AHNAK;Myosin-8;Myosin-13;Myosin-4;Myosin-1;Myosin-3;Myosin-11;Myosin-2;Myosin-6;Myosin-7;Myosin-7B 0 97.071 0.096521 276540000 667660 645220 637740 714190 612360 673730 669150 814870 800930 778910 FALSE TRUE 641567.1091 626818.9573 752993.8044 751049.4315 632057.1155 687353.2822 677339.2579 798042.6497 710011.7842 726153.7319 0.883514166 0.863204208 1.03696197 1.034284337 0.870417775 0.946567169 0.932776667 1.098999585 0.977770619 1 19.46991548 1.762851803 25 1.034518642 0.940562025 0.27793577 0.063954726 17.6426502 18170.3711 0.030626552 0.016985152 57.92310075 -1.762851803 -0.093956618 AKTQT(ph)PPVS(ph)PAPQPTEER ddPTM_BT-474_Pertuzumab_2h_R1 4 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.001)QT(0.999)PPVS(1)PAPQPTEER;AKTQT(1)PPVS(1)PAPQPTEER;AKTQT(1)PPVS(1)PAPQPTEER;AKT(0.008)QT(0.992)PPVS(1)PAPQPTEER 191.2 5.45E-14 24353200000 19087170 19888500 18539180 21085600 22939100 21584600 17593150 16957930 15439720 14850500 TRUE FALSE 18341222.29 19321299.45 21889622.23 22173830.34 23676956.98 22021055.4 17808460.23 16607742.82 13687067.71 13844662.41 1.324786532 1.395577507 1.581087468 1.601615821 1.710186662 1.590580886 1.286305127 1.199577305 0.988616935 1 23.72282654 1.762862687 1.634088737 1.006063645 1.538284877 0.784754542 0.112082942 0.175230178 0.911005548 0.092430955 0.037275772 57.92455248 -1.762862687 0.532221232 RGDINLLMLGDPGTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGDINLLMLGDPGTAK 16 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 139.88 2.81E-06 358990000 323420 380810 264770 329620 314390 359030 340570 301980 385010 335640 FALSE TRUE 310780.3888 369949.6717 312619.8288 346631.7277 324502.6399 366289.8326 344737.9975 295744.0075 341305.2789 312906.8038 0.993204318 1.182299864 0.999082874 1.107779452 1.037058434 1.170603605 1.101727394 0.945150453 1.090756975 1 18.2553735 1.762867779 25 1.007632796 1.087388219 0.190111382 0.068284624 19.8817089 20462.9272 0.029251728 0.016222641 57.92523158 -1.762867779 0.079755424 DKS(ph)HSHTPSRR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKSHSHTPSRR 11 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.333)HS(0.333)HT(0.333)PS(0.001)RR;DKS(0.808)HS(0.187)HT(0.005)PSRR 77.912 0.014873 618200000 20175.5 23998.3 16009.7 21602.8 22971.7 23992 25021 2696.27 22397 18574.9 TRUE FALSE 19387.01915 23313.89198 18903.00892 22717.7231 23710.60559 24477.13468 25327.21448 2640.591082 19854.58646 17316.80548 1.119549398 1.346315982 1.09159908 1.311888796 1.369225151 1.413490191 1.462580065 0.152487194 1.146550181 1 14.07988519 1.762963166 25 0.685729934 1.302941507 0.448282124 0.267923079 10.31099582 10570.91276 0.116300407 0.064497932 57.93795545 -1.762963166 0.617211574 TET(ph)QEKNPLPSK ddPTM_BT-474_Pertuzumab_2h_R1 3 TETQEKNPLPSK 12 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 TET(1)QEKNPLPSK;TET(1)QEKNPLPSK;TET(1)QEKNPLPSK 187 1.78E-05 3812160000 7143600 5272200 3290010 4118000 6496100 4062600 4867400 8858300 7189900 6228600 TRUE FALSE 6864420.214 5121842.018 3884587.993 4330530.474 6705052.956 4144748.556 4926968.697 8675373.009 6373732.695 5806731.374 1.182148746 0.882052516 0.668980144 0.745777649 1.154703485 0.713783416 0.848492617 1.494020035 1.097645523 1 22.46929486 1.762965112 25 1.244022819 0.875119478 0.329224002 0.200478277 13.45295939 13790.9753 0.090679066 0.050288838 57.93821519 -1.762965112 -0.368903341 SSMIT(ph)SLEGLGTDNVFSLHEDNHYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSMITSLEGLGTDNVFSLHEDNHYR 25 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.002)S(0.002)MIT(0.544)S(0.451)LEGLGTDNVFSLHEDNHYR 140.55 7.27E-07 79435000 16518 18997 16801 22879 20451 20123 20833 9315.1 20452 17372 TRUE FALSE 15872.4583 18455.22416 19837.31444 24059.78793 21108.82499 20529.90085 21087.96049 9122.73993 18130.3747 16195.37897 0.980060938 1.139536419 1.224874977 1.485595859 1.303385678 1.267639423 1.302097378 0.563292773 1.119478262 1 13.98329461 1.762967381 25 0.854436689 1.251177383 0.436656759 0.17983375 11.40866524 11694.22894 0.082680676 0.045853162 57.93851783 -1.762967381 0.396740694 TIS(ph)AQDTLAYATALLNEK ddPTM_BT-474_Pertuzumab_2h_R1 4 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 T(0.005)IS(0.995)AQDTLAYATALLNEK;T(0.003)IS(0.997)AQDTLAYATALLNEK;T(0.041)IS(0.959)AQDTLAYATALLNEK;T(0.027)IS(0.973)AQDTLAYATALLNEK 360.62 5.76E-91 3010781000 973408 937295 808848 797451 827138 958810 883003 1082769 1098034 964965 TRUE FALSE 935366.1392 910564.2643 955024.8263 838607.5417 853743.645 978197.7951 893809.4548 1060409.442 973389.7837 899607.061 1.039749664 1.012179988 1.06160219 0.932193152 0.94901839 1.08736118 0.993555402 1.178747353 1.082016611 1 19.77893546 1.763024084 25 1.104717106 1.010358956 0.234836819 0.060447271 15.96875808 16330.493 0.02737031 0.01517929 57.94608296 -1.763024084 -0.09435815 TCVQTLEGHAQNVSCASFHPELPIIITGSEDGTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TCVQTLEGHAQNVSCASFHPELPIIITGSEDGTVR 35 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 234.64 1.86E-47 233023000 45740 64375 58066 66970 61897 60077 65745 39469 61334 69833 FALSE TRUE 43952.43023 62539.08803 68559.81787 70426.32973 63887.97322 61291.7981 66549.60698 38653.95136 54371.62145 65103.14871 0.675119884 0.960615412 1.053095269 1.081765339 0.981334613 0.941456739 1.022217946 0.593733976 0.835161164 1 15.9904397 1.763046346 25 0.768845172 0.967887982 0.173351045 0.140826091 17.68416185 18068.2953 0.063801794 0.035383309 57.94905338 -1.763046346 0.199042811 VHPEEQGWICDPCHLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 VHPEEQGWICDPCHLAR 17 0 Q9BV36-2;Q9BV36-5;C9JKV5;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ;;; 213.99 9.80E-14 1848810000 1168760 1243590 928150 1301420 1196650 1208930 1258040 731462 1219140 1230360 FALSE TRUE 1123083.567 1208124.031 1095887.352 1368586.442 1235141.334 1233375.393 1273436.27 716357.0541 1080748.338 1147026.621 0.979125982 1.053265904 0.955415795 1.193160138 1.076820111 1.07528053 1.110206377 0.624533939 0.942217311 1 20.12946744 1.763097477 25 0.819221063 1.064760463 0.411451981 0.111329139 11.0094762 11225.16041 0.048752312 0.027037192 57.95587638 -1.763097477 0.245539399 GITPLPKPPPGVGLLPTPPEHFPFS(ph)DPEDDFQTDFSDDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GITPLPKPPPGVGLLPTPPEHFPFSDPEDDFQTDFSDDFR 40 1 P61129 P61129 ZC3H6 Zinc finger CCCH domain-containing protein 6 1 GITPLPKPPPGVGLLPT(0.051)PPEHFPFS(0.854)DPEDDFQT(0.075)DFS(0.021)DDFR 61.737 0.0061228 208120000 46633 43061 40397 39456 35426 45610 33775 33533 41524 28946 TRUE FALSE 44810.5308 41832.94244 47697.63653 41492.32889 36565.50946 46532.26545 34188.34855 32840.53183 36810.3696 26985.46164 1.660543422 1.550202958 1.767530872 1.537580844 1.355007743 1.724345726 1.266917313 1.216971282 1.364081523 1 14.71989475 1.76311029 0.409733978 0.996193902 1.686855301 0.681079048 0.131781534 0.59475485 0.269302718 0.151591162 0.129441791 57.95758624 -1.76311029 0.690661398 SAATWDER ddPTM_BT-474_Pertuzumab_2h_R1 1 SAATWDER 8 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 86.794 0.039502 0 431500 414110 340700 379840 396420 362890 394600 430300 463130 449580 FALSE TRUE 414636.503 402299.9883 402272.0688 399443.5879 409171.2093 370227.8844 399429.2328 421414.1546 410557.424 419129.5462 0.989280061 0.959846405 0.959779792 0.953031328 0.976240432 0.883325663 0.952997078 1.005450841 0.979547798 1 18.6770367 1.763139076 10.45414558 0.994176578 0.952132404 0.333663112 0.026815719 0.244475356 94.24127142 0.012804899 0.007043511 57.96142795 -1.763139076 -0.042044175 HFSVEGQLEFR ddPTM_BT-474_Pertuzumab_2h_R1 9 HFSVEGQLEFR 11 0 P08238;Q58FF7;P07900;P07900-2;Q14568;Q58FG1 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AA2P;HSP90AA4P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-alpha A4 0 ;;;;;;;; 196.16 6.14E-08 3255738000 1525144 2332584.9 1927077.1 2378386.1 1978989.4 2146902.1 2089894.5 1621491.9 1956419.1 2354982.1 FALSE TRUE 1465539.686 2266061.862 2275342.8 2501134.892 2042645.391 2190313.931 2115471.254 1588007.526 1734334.606 2195477.065 0.667526758 1.032150096 1.036377394 1.139221599 0.930387944 0.997648286 0.963558804 0.723308638 0.78995797 1 21.06610303 1.763150735 25 0.810654223 0.978323084 0.153217518 0.132494894 19.86902476 20214.36186 0.059768114 0.03314634 57.96298391 -1.763150735 0.167668861 IVDEILDALSHCHHK ddPTM_BT-474_Pertuzumab_2h_R1 1 IVDEILDALSHCHHK 15 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 131.53 1.84E-05 24305000 48818 56805 52570 69005 54564 70909 69092 3348.7 70349 35795 FALSE TRUE 46910.13859 55184.97702 62070.56841 72566.35632 56319.10061 72342.82856 69937.56856 3279.548175 62363.27645 33370.57277 1.405733696 1.653701823 1.860039048 2.174561307 1.687687563 2.167862957 2.095785681 0.098276652 1.86881049 1 15.02628883 1.763262503 25 0.909681624 1.872307294 0.428692801 0.459872994 11.81630048 11967.23434 0.201844337 0.111938863 57.97790294 -1.763262503 0.96262567 YLADPSNLFVVSSDFCHWGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 YLADPSNLFVVSSDFCHWGQR 21 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 107.78 0.00033511 199740000 265100 308020 218330 321810 331630 313360 298750 265790 298920 296960 FALSE TRUE 254739.5989 299235.5712 257787.0877 338418.6527 342297.1801 319696.3539 302406.1919 260301.3436 264987.8548 276846.6347 0.920146995 1.080871261 0.931154854 1.222404791 1.236414452 1.154777822 1.092323886 0.940236618 0.957164804 1 18.07872746 1.76331826 7.042002982 0.962483375 1.097916099 0.246637042 0.09980571 0.232984276 33.06289997 0.051110066 0.027831707 57.98534689 -1.76331826 0.135432723 HILGFDTGDAVLNEAAQILR ddPTM_BT-474_Pertuzumab_2h_R1 2 HILGFDTGDAVLNEAAQILR 20 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ; 260.29 2.50E-36 971250000 996492 1044959 945184 1059270 1058505 1124833 1107965 764918 1141895 1087618 FALSE TRUE 957547.991 1015157.792 1115999.774 1113939.052 1092552.775 1147577.894 1121524.607 749122.176 1012271.867 1013952.664 0.944371493 1.001188545 1.100642874 1.098610508 1.077518521 1.131786458 1.106091681 0.738813756 0.998342332 1 19.95155887 1.76336256 25 0.887277793 1.068860804 0.389072793 0.086299605 12.32142782 12428.42926 0.039314413 0.021803091 57.99126206 -1.76336256 0.181583011 HLDAHTAAHSQS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLDAHTAAHSQSPR 14 0 H7C3X3;H0Y6N5;E9PHI4;O94901-9 H7C3X3 SUN1 1 HLDAHT(0.008)AAHS(0.42)QS(0.572)PR 69.594 0.07783 58603000 41816 64830 40861 71057 46092 56415 56368 12412 50822 40924 TRUE FALSE 40181.78449 62981.11188 48245.49165 74724.26029 47574.59104 57555.74995 57057.84845 12155.68786 45052.89962 38152.18103 1.053197574 1.65078667 1.264553961 1.958584235 1.246969105 1.508583478 1.495533071 0.318610563 1.180873502 1 15.21947791 1.763365121 24.99999509 0.77242096 1.467850507 0.452784888 0.31037647 10.83608653 10929.05646 0.132381688 0.073416648 57.99160402 -1.763365121 0.695429547 FLHDNMVEIPNR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLHDNMVEIPNR 12 0 P49916-3;P49916;P49916-4;P49916-2;K7EJR4 P49916-3 LIG3 DNA ligase 3 0 145.17 6.37E-05 326780000 83822 94972 81955 98766 96005 91780 93413 83155 92315 95087 FALSE TRUE 80546.14357 92263.49155 96766.09158 103863.3251 99093.08801 93635.85448 94556.21624 81437.82019 81835.78822 88646.6728 0.908620042 1.040800389 1.091593046 1.171655087 1.117843286 1.056281658 1.066664019 0.918678814 0.923168187 1 16.43577886 1.763380826 7.243809675 0.941587491 1.070908311 0.390841401 0.06675975 0.160630762 24.71307326 0.033728782 0.018391144 57.99370118 -1.763380826 0.12932082 MALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_BT-474_Pertuzumab_2h_R1 11 MALIQMGSVEEAVQALIDLHNHDLGENHHLR 31 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;;;;; 291.25 1.21E-81 27362771000 7868465.1 8142494.9 7788630.8 7652789.7 8758543.3 7641782.3 7831303 269420.54 7997029.8 2466902 FALSE TRUE 7560956.785 7910278.918 9196209.643 8047751.094 9040269.8 7796304.374 7927144.829 263856.9117 7089240.503 2299816.53 3.287634768 3.439526073 3.99867099 3.499301352 3.93086565 3.38996797 3.446859662 0.114729548 3.082524371 1 21.13308734 1.763416909 25 1.348735087 3.5860324 0.65912662 0.715222284 7.732184045 7782.262683 0.302363429 0.167685686 57.99851963 -1.763416909 2.237297313 TKEVYELLDSPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 157.68 4.36E-05 2272400000 5992000 5183800 4594700 4180500 4958000 5256300 5153000 5695700 6557100 5930200 FALSE TRUE 5757826.015 5035963.099 5425064.499 4396256.106 5117478.573 5362585.987 5216063.955 5578081.805 5812765.498 5528542.272 1.04147273 0.910902522 0.981282991 0.795192637 0.925647001 0.969981909 0.943479076 1.008960686 1.051410157 1 22.3984677 1.763459151 1.897639943 1.029200963 0.93066226 0.276188918 0.060451577 0.401969387 2.873728634 0.04219552 0.017641294 58.00416124 -1.763459151 -0.098538703 LS(ph)GSARPQELVGTFIQQEVGKPEDEASGSFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSGSARPQELVGTFIQQEVGKPEDEASGSFFK 32 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 LS(0.821)GS(0.177)ARPQELVGT(0.002)FIQQEVGKPEDEASGSFFK 136.86 1.28E-08 156210000 84931 69463 101020 85846 92766 78216 87873 128620 110320 114270 TRUE FALSE 81611.80262 67481.98325 119276.5612 90276.52235 95749.90264 79797.58111 88948.41606 125963.9521 97796.9361 106530.3911 0.766089393 0.633452882 1.119648205 0.847425053 0.898803634 0.749059309 0.834958129 1.182422694 0.918019122 1 16.70090554 1.763514991 25 1.049241884 0.838334445 0.316947407 0.132451937 16.69679924 16738.83512 0.060963251 0.033809319 58.01161972 -1.763514991 -0.210907439 KKDEISVDSLDFNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKDEISVDSLDFNKK 15 3 P63151;P63151-2;A0A590UJY3;A0A590UJJ1;E5RFR9 P63151 PPP2R2A Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform 0 165.02 6.35E-07 523720000 576660 444260 388210 348460 437500 442930 474420 570620 665640 620540 FALSE TRUE 554123.4897 431590.1398 458368.1827 366444.0624 451572.5848 451886.3481 480226.0939 558836.4976 590079.3378 578510.2731 0.957845548 0.746037123 0.792325053 0.633427062 0.780578333 0.781120698 0.830108152 0.965992349 1.019998028 1 19.14198305 1.76353305 2.073063694 1.012021703 0.773525043 0.626241392 0.074243287 0.188378942 1.62000748 0.049702696 0.021318235 58.01403204 -1.76353305 -0.23849666 EKVASDT(ph)EEADR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKVASDTEEADR 12 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 EKVAS(0.361)DT(0.639)EEADR 127.32 0.00043942 351330000 501370 468050 358430 414630 441200 448240 448810 581350 627110 563550 TRUE FALSE 481775.9061 454701.6723 423206.2742 436029.104 455391.5987 457303.7199 454302.671 569344.9193 555923.1019 525380.2565 0.917004208 0.865471564 0.80552375 0.829930509 0.866784758 0.870424258 0.864712112 1.083681604 1.058134741 1 19.00300246 1.763543502 6.898597808 1.051908285 0.857245451 0.867605656 0.033481469 0.052666443 7.032169058 0.016500477 0.00898034 58.01542818 -1.763543502 -0.194662833 MDFDEFFHHPFLDAS(ph)PSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDFDEFFHHPFLDASPSVR 19 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 MDFDEFFHHPFLDAS(0.987)PS(0.013)VR 121.33 5.91E-05 18724000 21143 26437 20161 24823 24978 22570 27001 8145.8 23446 25816 TRUE FALSE 20316.70819 25683.04264 23804.54118 26104.118 25781.44005 23026.38086 27331.44631 7977.586383 20784.50837 24067.45933 0.844156748 1.06712729 0.989075783 1.08462292 1.07121569 0.956743317 1.135618261 0.331467741 0.863593788 1 14.55479623 1.76366541 25 0.665031364 1.023633586 0.336197691 0.179218398 12.51710261 12473.36121 0.076577556 0.042468861 58.03171559 -1.76366541 0.358602222 RPPT(ph)PGPDTSVSGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPPTPGPDTSVSGPR 15 1 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 RPPT(0.998)PGPDT(0.001)SVSGPR 85.855 0.0045601 416430000 130040 174090 134660 223650 184100 210130 148690 143190 121110 131060 TRUE FALSE 124957.893 169125.1237 158996.0575 235192.6033 190021.7437 214378.9726 150509.7127 140233.0765 107362.1005 122183.1895 1.022709373 1.384193066 1.301292413 1.924917858 1.555220031 1.754570113 1.231836502 1.147728072 0.878697806 1 16.89868628 1.763756699 2.135180421 0.965915543 1.496097839 0.447459687 0.239435023 0.277808256 2.538663725 0.164845193 0.07135227 58.04391517 -1.763756699 0.530182296 SS(ph)PGAGPSDHHSASR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPGAGPSDHHSASR 15 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 S(0.034)S(0.966)PGAGPSDHHSASR 237.97 6.04E-18 711540000 243790 480980 329380 572350 391150 478500 414860 101120 271960 429260 TRUE FALSE 234262.4173 467262.9213 388906.293 601889.0521 403731.695 488175.5978 419937.1808 99031.83666 241088.2409 400185.8379 0.585384077 1.167614836 0.971814233 1.504023869 1.008860526 1.219872249 1.049355427 0.247464621 0.602440712 1 18.61031059 1.763801691 25 0.544560624 1.092037257 0.351623264 0.277618259 13.23153767 13114.04907 0.121952776 0.06763344 58.04992869 -1.763801691 0.547476633 ISLEVQLEQLRPFSHL ddPTM_BT-474_Pertuzumab_2h_R1 1 ISLEVQLEQLRPFSHL 16 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 0 59.606 0.075309 0 112060 120590 98072 104540 111150 118730 112940 104700 124780 117620 FALSE TRUE 107680.5713 117150.8913 115795.792 109935.3219 114725.2407 121130.8019 114322.1935 102537.9084 110615.4975 109653.4926 0.982007675 1.068373551 1.056015538 1.002570181 1.046252499 1.10466889 1.042576855 0.935108458 1.008773135 1 16.74259224 1.763804382 25 0.975559981 1.045587585 0.371989554 0.036548195 14.1322943 14005.31118 0.016656674 0.009237709 58.0502884 -1.763804382 0.070027604 AAS(ph)SDQLRDNS(ph)PPPAFKPEPPK ddPTM_BT-474_Pertuzumab_2h_R1 5 AASSDQLRDNSPPPAFKPEPPK 22 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 AAS(0.712)S(0.289)DQLRDNS(0.999)PPPAFKPEPPK;AAS(0.985)S(0.015)DQLRDNS(1)PPPAFKPEPPK;AAS(0.906)S(0.094)DQLRDNS(1)PPPAFKPEPPK;AAS(0.863)S(0.139)DQLRDNS(0.998)PPPAFKPEPPK;AAS(0.951)S(0.049)DQLRDNS(1)PPPAFKPEPPK 107.17 0.00024832 3410130000 2819040 2324500 1597840 1740150 1907900 1802760 1880960 3152130 2650870 2216940 TRUE FALSE 2708868.8 2258207.536 1886605.232 1829959.35 1969269.336 1839213.042 1903979.751 3087037.414 2349954.351 2066784.679 1.310668125 1.092618674 0.912821375 0.885413642 0.952817851 0.889890979 0.92122792 1.49364249 1.137009759 1 20.97895666 1.763826053 25 1.259295943 0.985766636 0.239428757 0.168499179 16.97676958 16809.78777 0.077992634 0.04325401 58.05318518 -1.763826053 -0.273529307 DQHLNNSSSS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNSS(0.003)S(0.031)S(0.966)PQR 222.96 1.07E-11 662900000 407410 450190 347530 436730 354220 422110 490750 176570 453480 484160 TRUE FALSE 391487.9668 437351.022 410336.4018 459269.6876 365613.808 430645.3534 496755.9453 172923.7678 402002.8515 451367.412 0.867337686 0.968946828 0.909096206 1.017507413 0.810013746 0.954090486 1.100557843 0.383110883 0.890633309 1 18.78394274 1.763873644 25 0.694632283 0.943935107 0.18098457 0.168641532 17.47017643 17265.79187 0.072813553 0.04038157 58.05954711 -1.763873644 0.249302824 LVEHGLNETIHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEHGLNETIHIR 13 0 Q7Z3B4-2;Q7Z3B4-3;Q7Z3B4 Q7Z3B4-2 NUP54 Nucleoporin p54 0 ; 198.33 7.33E-08 498790000 237230 240450 219850 286060 261650 282770 294650 140986 288770 281560 FALSE TRUE 227958.7893 233592.6014 259581.7855 300823.5909 270066.2099 288487.8031 298256.0148 138074.5898 255990.0402 262489.6904 0.868448544 0.889911528 0.988921832 1.146039642 1.028864065 1.099044319 1.136258016 0.526019097 0.975238455 1 18.00190123 1.763874549 25 0.786103964 1.024048134 0.231467471 0.150241775 17.26887568 17066.23625 0.068688957 0.038093884 58.0596681 -1.763874549 0.237944171 FTDKDQQPS(ph)GS(ph)EGEDDDAEAALK ddPTM_BT-474_Pertuzumab_2h_R1 2 FTDKDQQPSGSEGEDDDAEAALK 23 1 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 2 FTDKDQQPS(1)GS(1)EGEDDDAEAALK;FTDKDQQPS(1)GS(1)EGEDDDAEAALK 151.73 3.97E-08 1120330000 1655710 1437100 1354860 1177260 1550220 1528690 1475610 2000490 1951400 1638280 TRUE FALSE 1591003.023 1396115.315 1599713.341 1238018.53 1600084.234 1559601.159 1493668.957 1959179.182 1729885.253 1527317.836 1.041697402 0.914096124 1.047400418 0.810583429 1.047643258 1.021137266 0.977968646 1.282758006 1.13262951 1 20.54256889 1.763880229 25 1.165926678 0.977786049 0.358910262 0.094864778 13.10850888 12951.77996 0.041205262 0.022851948 58.06042752 -1.763880229 -0.188140629 SHISDQS(ph)PLSSKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHISDQSPLSSKR 13 1 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SHISDQS(0.992)PLS(0.004)S(0.004)KR 69.485 0.029144 184360000 149610 202170 148000 158120 139300 183370 162370 59301 130220 154150 TRUE FALSE 143763.0758 196404.3095 174746.8922 166280.5921 143780.711 187077.867 164357.1326 58076.41363 115437.9715 143709.2832 1.000374315 1.366677957 1.215974976 1.157062289 1.00049703 1.301779975 1.14367791 0.404124301 0.803274284 1 17.13279373 1.763888751 25 0.680024091 1.176928167 0.553569852 0.176242139 9.214082627 9100.849785 0.076431819 0.042388001 58.06156672 -1.763888751 0.496904076 SSEPVKETVQTTQS(ph)PTPVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSEPVKETVQTTQSPTPVEK 20 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 SSEPVKETVQT(0.001)T(0.004)QS(0.995)PTPVEK;SSEPVKETVQT(0.005)T(0.014)QS(0.93)PT(0.05)PVEK;SSEPVKETVQTT(0.003)QS(0.948)PT(0.049)PVEK;SSEPVKETVQTTQS(1)PTPVEK 323.41 3.40E-67 8984600000 4731300 4266450 3444900 3343727 3977677 4051352 4081643 4880620 5514350 4840370 TRUE FALSE 4546395.565 4144775.023 4067470.061 3516297.151 4105622.593 4133273.113 4131595.368 4779833.491 4888384.106 4512527.429 1.007505359 0.918504117 0.901372928 0.779230089 0.909827731 0.915955233 0.915583436 1.059236441 1.083291832 1 22.10550427 1.763988454 4.526061101 1.054080665 0.901578033 0.573611154 0.055397369 0.135948225 5.892187087 0.029398727 0.015348749 58.07489775 -1.763988454 -0.152502633 TAS(ph)PPPPPKR ddPTM_BT-474_Pertuzumab_2h_R1 5 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.009)AS(0.991)PPPPPKR;T(0.004)AS(0.996)PPPPPKR;T(0.028)AS(0.972)PPPPPKR;T(0.027)AS(0.973)PPPPPKR;T(0.001)AS(0.999)PPPPPKR 119.76 0.00039761 8784040000 2521220 2436864 1950717 2166949 2246440 2289557 2274956 2535650 2702930 2445958 TRUE FALSE 2422687.935 2367367.025 2303254.955 2278785.498 2318698.783 2335853.411 2302797.592 2483287.941 2396104.718 2280291.086 1.062446786 1.038186326 1.010070587 0.999339738 1.016843331 1.02436633 1.009870014 1.089022343 1.050788968 1 21.12078657 1.764041209 25 1.055788976 1.022006725 0.115185687 0.026409918 21.65373652 21259.53675 0.012030972 0.006671849 58.08195271 -1.764041209 -0.033782251 TDYNASVSVPDSSGPER ddPTM_BT-474_Pertuzumab_2h_R1 4 TDYNASVSVPDSSGPER 17 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;; 346.54 3.51E-87 1241340000 1414240 1228390 960760 997910 1201360 1179660 1181530 1511930 1532670 1280040 FALSE TRUE 1358969.937 1193357.52 1134390.704 1049412.255 1240002.835 1203513.533 1195989.918 1480708.117 1358687.727 1193341.751 1.138793591 1.000013214 0.95060003 0.879389541 1.039101192 1.00852378 1.002219119 1.240808106 1.138557103 1 20.18657583 1.764116079 25 1.150040603 0.997444114 0.305655189 0.082994692 15.20659356 14885.99443 0.037890744 0.02101394 58.09196658 -1.764116079 -0.152596488 SSTS(ph)PSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.11)S(0.11)T(0.11)S(0.667)PS(0.004)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR;S(0.105)S(0.105)T(0.105)S(0.683)PS(0.003)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 371.56 1.96E-161 398040000 62873 69351 67404 77532 71340 82817 86181 16249.7 88649 57623 TRUE FALSE 60415.85365 67373.17738 79585.40219 81533.43581 73634.71589 84491.61648 87235.70886 15914.13802 78585.93717 53720.14288 1.124640599 1.25415112 1.481481581 1.51774421 1.370709606 1.572810718 1.623891974 0.296241543 1.462876548 1 15.71317552 1.764145401 25 0.853387412 1.424353837 0.36377493 0.299816453 14.21349101 13897.87483 0.132148643 0.073288052 58.09588886 -1.764145401 0.570966425 SEEKIS(ph)DSEGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEEKISDSEGFK 12 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 S(0.001)EEKIS(0.999)DSEGFK 107.98 0.0010633 116700000 211500 149400 117490 107450 121300 115410 141210 195630 216340 192340 TRUE FALSE 203234.3462 145139.2583 138723.0566 112995.5074 125201.7247 117743.6693 142938.1702 191590.1721 191781.9902 179312.6405 1.133407805 0.809420116 0.773637911 0.630159185 0.698231448 0.65663898 0.797144974 1.068469973 1.069539714 1 17.45211767 1.76416018 5.114105403 1.051550503 0.770274252 0.446237537 0.132263119 0.166238901 9.72555463 0.068810662 0.036558934 58.09786594 -1.76416018 -0.281276251 LESEMEDAYHEHQANLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LESEMEDAYHEHQANLLR 18 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 195.89 1.16E-15 231890000 148971 164435 142252 186053 178732 172514 186764 15478.3 171917 126253 FALSE TRUE 143149.0486 159745.4748 167960.1008 195655.2176 184481.0771 176002.3513 189049.6737 15158.6677 152401.7029 117701.7719 1.216201306 1.357205353 1.426997216 1.662296281 1.567360238 1.495324569 1.606175257 0.128788781 1.294812308 1 16.84477651 1.764160731 24.99999989 0.726724643 1.480918403 0.504914023 0.299914173 10.67130331 10428.08829 0.130861274 0.072574134 58.09793968 -1.764160731 0.754193761 RDS(ph)DTYR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSDTYR 7 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BQG1;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 RDS(0.977)DT(0.023)YR;RDS(0.977)DT(0.023)YR 98.634 0.0068104 419320000 237840 225330 192386 248280 236310 197619 230450 250230 284440 252170 TRUE FALSE 228544.9499 218903.809 227154.4298 261093.7606 243911.1258 201614.9916 233270.316 245062.6631 252151.5637 235090.3013 0.972158139 0.931147767 0.966243305 1.110610515 1.037521005 0.85760659 0.992258357 1.042419282 1.072573229 1 17.8428555 1.76419551 4.96519484 1.042998075 0.980643609 0.144441426 0.063862337 0.375707094 20.39287337 0.034153062 0.01807754 58.10259233 -1.76419551 -0.062354466 LGIHEDSTNRR ddPTM_BT-474_Pertuzumab_2h_R1 11 LGIHEDSTNRR 11 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;; 184.24 3.24E-06 42318351000 16316992.9 19653381 15133157 18740107 17655813 19207071 18129685 17416422 19012977 19084763 FALSE TRUE 15679306.78 19092885.82 17868055.11 19707286.17 18223728.26 19595451.14 18351561.51 17056766.8 16854703.56 17792135 0.881249315 1.073108192 1.00426706 1.107640323 1.02425753 1.101354679 1.031442348 0.958668917 0.947312032 1 24.0847363 1.764195836 5.729796667 0.965082635 1.037976277 0.177395255 0.061322163 0.258725925 20.42071903 0.028745881 0.015463097 58.10263598 -1.764195836 0.072893642 TYEIWHR ddPTM_BT-474_Pertuzumab_2h_R1 3 TYEIWHR 7 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;; 107.32 0.0075045 921510000 827570 855960 732620 875170 843600 835450 846380 792630 880050 896690 FALSE TRUE 795227.6495 831548.8589 865020.731 920337.6286 870735.1601 852343.3714 856738.2516 776261.9135 780150.4135 835956.3876 0.951278872 0.994727561 1.034767775 1.100939765 1.041603573 1.019602678 1.024859986 0.928591401 0.93324296 1 19.67306815 1.76424234 9.69107517 0.948582567 1.026762154 0.390469264 0.039809532 0.187963599 60.63010092 0.019832851 0.010910841 58.10885796 -1.76424234 0.078179587 SPFIEEQLHTVLEKS(ph)PENS(ph)PPVKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPFIEEQLHTVLEKSPENSPPVKPK 25 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 2 SPFIEEQLHT(0.008)VLEKS(0.992)PENS(1)PPVKPK;SPFIEEQLHT(0.003)VLEKS(0.997)PENS(1)PPVKPK 111.52 0.0045099 1567960000 846580 578440 559710 425220 502540 574420 652750 802790 982170 875260 TRUE FALSE 813494.7177 561943.4576 660862.0477 447165.6552 518704.6555 586035.166 660738.5498 786212.106 870678.1792 815977.8606 0.99695685 0.688674883 0.809901934 0.548011995 0.635684717 0.718199836 0.809750585 0.96352137 1.067036523 1 19.63817048 1.764250976 2.14900194 1.032870119 0.722334578 0.553464672 0.112008869 0.214329514 1.983840564 0.074640245 0.032385777 58.11001341 -1.764250976 -0.310535541 DLFEDELVPLFEK ddPTM_BT-474_Pertuzumab_2h_R1 7 DLFEDELVPLFEK 13 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;; 253.53 2.03E-23 977628500 2002000 2021746 1659546 1967024 1918547 1801215 2012577 2427421 2624376 2696775 FALSE TRUE 1923759.627 1964087.784 1959462.879 2068542.344 1980258.807 1837636.801 2037207.519 2377293.908 2326467.839 2514120.027 0.765182094 0.781222759 0.779383187 0.822769924 0.78765484 0.73092644 0.810306388 0.945576934 0.925360688 1 21.2616221 1.764254343 3.344727716 0.956271296 0.779756556 0.89627941 0.02738601 0.066438651 1.488641658 0.015199025 0.007477604 58.11046399 -1.764254343 -0.17651474 VALSDDETKET(ph)ENMR ddPTM_BT-474_Pertuzumab_2h_R1 1 VALSDDETKETENMR 15 1 Q15054;H0YD46;Q15054-3;Q15054-2 Q15054 POLD3 DNA polymerase delta subunit 3 1 VALS(0.002)DDET(0.292)KET(0.707)ENMR 132.02 8.87E-06 0 366870 308210 272790 279920 301500 291070 303830 392690 365350 367560 TRUE FALSE 352532.3148 299420.1526 322089.2212 294366.7047 311198.0213 296955.6348 307548.3624 384580.8143 323876.9997 342664.8338 1.028796305 0.873798893 0.939954117 0.859051399 0.908170289 0.866606682 0.897519477 1.122323554 0.945171397 1 18.38643862 1.764288087 25 1.033470985 0.906510414 0.405499808 0.061548785 13.05380818 12693.09343 0.026617785 0.014762113 58.11497923 -1.764288087 -0.12696057 AASSSSPGS(ph)PVASSPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AASSSSPGSPVASSPSR 17 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 AASSSS(0.001)PGS(0.999)PVASSPSR;AASSSSPGS(0.998)PVAS(0.002)SPSR;AASSSS(0.002)PGS(0.998)PVASSPSR 368.02 1.15E-104 243954000 303307 407999 333543 487660 499260 452720 415770 355488 376600 391571 TRUE FALSE 291453.4271 396363.268 393821.6397 512828.191 515319.1513 461874.3086 420858.3176 348147.0486 333849.9468 365049.5474 0.798394161 1.085779371 1.078816951 1.404818044 1.411641666 1.265237313 1.152879987 0.953698069 0.914533244 1 18.47773277 1.764296117 4.048708978 0.948182414 1.188328647 0.254035888 0.167725474 0.292071461 9.795543179 0.096102931 0.049235999 58.11605384 -1.764296117 0.240146234 ETENDDLTNVIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETENDDLTNVIQK 13 0 O95373 O95373 IPO7 Importin-7 0 333.63 3.76E-62 155700000 207630 194800 176110 190020 200560 212000 207610 237690 279370 265440 FALSE TRUE 199515.5901 189244.4947 207936.9945 199826.955 207011.1945 216286.7853 210150.7933 232781.6184 247657.0888 247461.5124 0.806248972 0.764743143 0.840280141 0.807507208 0.836538953 0.874021916 0.849226174 0.940678072 1.000790331 1 17.91684464 1.764300626 0.788428823 1.015313057 0.804319891 0.900999775 0.024465502 0.170481097 0.204098754 0.021940601 0.010099596 58.11665716 -1.764300626 -0.210993166 DAGDKDKEQELSEEDKQLQDELEMLVER ddPTM_BT-474_Pertuzumab_2h_R1 1 DAGDKDKEQELSEEDKQLQDELEMLVER 28 3 Q13200;C9JPC0 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 265.23 2.38E-54 208910000 313320 201660 166720 115960 191320 182890 205030 271580 336350 245220 FALSE TRUE 301075.108 195908.8542 196850.0127 121944.7095 197473.9816 186588.1611 207539.2185 265971.7781 298168.9581 228611.031 1.316975418 0.856952761 0.861069616 0.533415684 0.863799007 0.816181793 0.90782679 1.163424954 1.304263214 1 17.80253549 1.764306739 3.773335997 1.17945835 0.858007288 0.301431973 0.191308473 0.238782968 6.871719472 0.103021813 0.052056135 58.1174752 -1.764306739 -0.321451062 CHTPPLYR ddPTM_BT-474_Pertuzumab_2h_R1 2 CHTPPLYR 8 0 Q02543;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 154.31 0.0004271 1325990000 445850 465630 415840 493220 436060 398160 502860 187381 481640 446480 FALSE TRUE 428425.6891 452350.6883 490991.5383 518675.1433 450086.2659 406211.068 509014.1511 183511.5169 426966.2464 416239.5119 1.029276839 1.086755763 1.179588973 1.246097808 1.081315572 0.975907035 1.222887632 0.440879618 1.025770582 1 18.6670544 1.764370897 25 0.767283274 1.116736982 0.375631974 0.170029608 13.33497125 12924.85214 0.074249105 0.041177678 58.1260615 -1.764370897 0.349453709 S(ph)PSPFTHTHLAQGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPFTHTHLAQGYR 15 0 P38398-7;P38398;P38398-4;P38398-8;Q5YLB2 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 S(0.828)PS(0.172)PFTHTHLAQGYR;S(0.87)PS(0.13)PFTHTHLAQGYR 179.74 4.24E-07 355920000 146196 159046 115843 149090 139802 118728 149634 64383 142319 135465 TRUE FALSE 140482.4987 154510.1638 136778.407 156784.5528 144298.8583 121128.7615 151465.2657 63053.46855 126163.5438 126289.8349 1.11238168 1.223456852 1.083051594 1.241466131 1.142600736 0.959133105 1.199346454 0.499275881 0.99899999 1 16.946379 1.764375497 25 0.784350084 1.135924027 0.448058974 0.152091985 11.76571684 11401.82658 0.06588003 0.036536348 58.1266771 -1.764375497 0.351573943 SAT(ph)PVNCEQPDILVSSTPINEGQTVLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SATPVNCEQPDILVSSTPINEGQTVLDK 28 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.203)AT(0.797)PVNCEQPDILVSSTPINEGQTVLDK 230.85 1.55E-34 125240000 156860 162860 135510 139630 137300 158640 152380 180320 188030 183140 TRUE FALSE 150729.7378 158215.3923 159999.6714 146836.321 141716.3792 161847.8095 154244.872 176596.329 166685.6227 170735.7647 0.882824627 0.926668133 0.937118662 0.860020871 0.830033353 0.947943214 0.903412781 1.034325347 0.976278304 1 17.38140577 1.764412824 11.75915333 1.003802555 0.898671131 0.643718965 0.035879073 0.189141055 84.16395443 0.017328664 0.00956123 58.13167321 -1.764412824 -0.105131423 GDTPGHATPGHGGATSSAR ddPTM_BT-474_Pertuzumab_2h_R1 5 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;;; 235.79 2.08E-24 1007605000 510945 767771 619424 888890 691399 819527 758399 288103 615769 772626 FALSE TRUE 490976.7045 745874.9228 731367.6958 934765.7194 713638.4767 836098.3974 767680.5138 282153.5724 545869.4846 720295.3528 0.681632476 1.035512613 1.015371948 1.297753367 0.99075813 1.160771611 1.065785737 0.391719274 0.757841186 1 19.45822907 1.764485699 24.99999997 0.656920959 1.047805058 0.328554433 0.203056326 14.68809022 14173.26248 0.090474741 0.050176778 58.1414286 -1.764485699 0.390884099 NKPEWFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 NKPEWFFK 8 1 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 99.653 0.0060746 1058050000 2958800 2636500 2403100 2451000 2496800 2457100 2659900 2996400 3278500 3211800 FALSE TRUE 2843166.825 2561309.601 2837393.627 2577496.404 2577111.84 2506784.245 2692452.652 2934523.293 2906338.425 2994261.925 0.949538449 0.855405995 0.947610362 0.860811936 0.860683502 0.837196046 0.899204117 0.980048962 0.970636002 1 21.513769 1.76453629 3.922589219 0.982856972 0.883382555 0.602232357 0.035975062 0.139254545 4.353611451 0.018792659 0.009572299 58.14820198 -1.76453629 -0.099474416 KAPPQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAPPQGR 7 1 I3L0N3;P46459;P46459-2;K7EQD6;I3L2G1 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 81.297 0.068918 128450000 111546 105239 94361 101133 106575 116364 107888 105037 115985 115343 FALSE TRUE 107186.659 102237.6868 111414.1317 106352.4862 110003.0817 118716.9598 109208.3656 102867.9492 102818.869 107530.7159 0.996800385 0.950776584 1.03611448 0.989042855 1.022992182 1.104028359 1.015601586 0.956637817 0.956181387 1 16.7143893 1.764574384 8.614484557 0.967644745 1.017306434 0.225086715 0.03854472 0.257133642 62.71338955 0.019335588 0.010620215 58.15330257 -1.764574384 0.049661689 ETTSGTSTEPVKNS(ph)SPAPPQPAPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETTSGTSTEPVKNSSPAPPQPAPGK 25 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ETTSGT(0.001)S(0.004)T(0.003)EPVKNS(0.496)S(0.496)PAPPQPAPGK 94.384 1.17E-05 0 111300 84776 65920 62304 76290 87510 78182 103640 100450 84874 TRUE FALSE 106950.273 82358.27148 77833.21038 65519.51691 78743.93713 89279.51216 79138.8147 101499.7978 89047.33712 79125.40838 1.351655241 1.040857459 0.983668988 0.828046493 0.995178903 1.128329243 1.000169431 1.282771234 1.125394977 1 16.27185342 1.764600673 25 1.164869761 1.036915219 0.06348506 0.141289736 33.24340372 31936.46256 0.066300764 0.036770248 58.15682285 -1.764600673 -0.127954542 WDDQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 WDDQQK 6 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 110.61 0.066431 1018860000 2246100 2177900 1852400 1832230 1902290 1886920 2018400 2542700 2455100 2366700 FALSE TRUE 2158319.929 2115788.424 2187169.886 1926791.61 1963478.885 1925074.815 2043101.783 2490192.356 2176407.341 2206401.301 0.978208238 0.958931824 0.991283809 0.87327342 0.889901073 0.872495323 0.925988297 1.128621686 0.986405936 1 21.07326378 1.764624152 25 1.050099604 0.925235753 0.478927699 0.052694563 12.88391902 12366.22864 0.025016793 0.013874152 58.15996702 -1.764624152 -0.124863851 KDLGSTEDGDGT(ph)DDFLTDKEDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDLGSTEDGDGTDDFLTDKEDEK 23 2 Q15527 Q15527 SURF2 Surfeit locus protein 2 1 KDLGSTEDGDGT(1)DDFLTDKEDEK 192.18 4.74E-16 120450000 149300 85168 76357 71908 89167 69075 84145 203870 146750 112960 TRUE FALSE 143465.1909 82739.09203 90156.40845 75619.1805 92035.13753 70471.74383 85174.79168 199660.0133 130091.5552 105309.1186 1.362324487 0.785678326 0.856112079 0.718068687 0.873952216 0.66918938 0.808807374 1.895942307 1.235330397 1 16.68427084 1.76465034 25 1.464203329 0.850976477 0.402197774 0.278037831 12.77480104 12249.18085 0.121512676 0.067390218 58.16347422 -1.76465034 -0.613226852 TTGMSQS(ph)TELLPDATDEEVAPPKPPLPGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTGMSQSTELLPDATDEEVAPPKPPLPGIR 30 1 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 TTGMS(0.029)QS(0.78)T(0.191)ELLPDATDEEVAPPKPPLPGIR;TTGMS(0.027)QS(0.94)T(0.033)ELLPDATDEEVAPPKPPLPGIR 188.67 1.96E-18 985810000 729270 712850 616840 666220 656230 647270 689260 855390 835730 805160 TRUE FALSE 700769.3221 692520.216 728316.7095 700603.694 677338.2339 660358.2429 697695.3701 837725.8976 740861.4341 750625.796 0.933580122 0.922590483 0.97027935 0.933359469 0.902364717 0.879743604 0.929484936 1.116036648 0.986991705 1 19.51773435 1.764655265 25 1.044787302 0.923944 0.621979864 0.038991085 9.412715042 9023.720139 0.017633084 0.009779098 58.16413379 -1.764655265 -0.120843302 QGTAVEVEAESLDPTVKPVDVGGDEPEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QGTAVEVEAESLDPTVKPVDVGGDEPEEK 29 1 P49321;P49321-3;P49321-4;E9PPR5 P49321 NASP Nuclear autoantigenic sperm protein 0 112.99 0.00024488 192440000 139660 117930 103370 102490 115820 107770 121760 146480 167900 153380 FALSE TRUE 134201.9328 114566.7519 122051.2585 107779.5212 119545.4555 109949.1832 123250.1353 143455.1368 148840.6959 142991.436 0.938531262 0.80121408 0.853556422 0.753748086 0.836032275 0.768921457 0.861940678 1.003242857 1.040906365 1 17.12556922 1.764749304 3.260713305 1.021746765 0.822313998 0.752644784 0.04873298 0.101709773 2.162277637 0.026069416 0.012753531 58.17672965 -1.764749304 -0.199432767 HYEDGYPGGSDNYGSLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 HYEDGYPGGSDNYGSLSR 18 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;;; 226.65 3.40E-19 4121290000 2143810 2740110 2246880 3075620 2284650 2570130 2636930 1545200 2556030 2565910 FALSE TRUE 2060027.535 2661964.746 2652941.198 3234353.117 2358137.842 2622099.79 2669201.538 1513291.08 2265880.19 2392118.63 0.861172815 1.112806327 1.109034127 1.352087257 0.985794689 1.096141202 1.115831591 0.632615398 0.94722735 1 21.18985751 1.764783981 25 0.824641267 1.098248923 0.331435264 0.147166149 15.75150201 15026.37134 0.065999561 0.036603051 58.18137502 -1.764783981 0.273607656 CQHAAEIITDLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 CQHAAEIITDLLR 13 0 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;; 199.31 1.19E-07 1847386000 2215370 2170630 1849370 2225360 2152610 1947080 2241310 1765970 2494850 2171770 FALSE TRUE 2128790.891 2108725.758 2183592.298 2340211.096 2221850.656 1986451.292 2268739.822 1729502.102 2211645.087 2024674.083 1.051423984 1.041513681 1.078490763 1.15584583 1.097386821 0.981121509 1.120545692 0.854212595 1.092346223 1 20.94925826 1.764804044 25 0.968131605 1.074359459 0.263734525 0.070029381 19.25841901 18357.79199 0.031269608 0.017342046 58.18406295 -1.764804044 0.106227854 ASYDDPYKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASYDDPYKK 9 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ; 101.65 0.0061604 1273970000 5895900 5158300 4394000 4350100 5000100 5213600 5135400 6375800 6953300 6407200 FALSE TRUE 5665481.71 5011190.335 5188093.544 4574609.182 5160932.757 5319022.564 5198248.561 6244137.502 6163990.535 5973234.637 0.948478011 0.838940815 0.868556797 0.765851245 0.864009715 0.89047608 0.870256884 1.045352791 1.031935109 1 22.51008096 1.764820357 5.461464266 1.028619254 0.859578821 0.738337945 0.044102535 0.086779542 6.003571605 0.021947833 0.01176186 58.18624841 -1.764820357 -0.169040433 QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDK ddPTM_BT-474_Pertuzumab_2h_R1 2 QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDK 38 2 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ; 178.15 2.22E-23 631560000 237411 165059 147744 138021 151884 162265 169303 210460 241900 190507 FALSE TRUE 228132.7156 160351.6789 174444.6273 145144.2804 156769.4868 165546.1095 171374.9808 206113.9275 214440.5261 177603.7912 1.284503636 0.902861802 0.982212295 0.817236385 0.882692232 0.932109097 0.964928618 1.16052662 1.20740962 1 17.43830285 1.764855936 6.190960765 1.136973255 0.953972811 0.234054798 0.127030154 0.213295922 20.75936592 0.060477854 0.032779997 58.19101545 -1.764855936 -0.183000443 S(ph)VHS(ph)EHSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVHSEHSAR 9 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 2 S(1)VHS(1)EHSAR;S(1)VHS(1)EHSAR 131.13 0.0001805 167101000 87576 92630 76371 106221 94901 98373 100739 18494 84538 86833 TRUE FALSE 84153.4331 89988.28309 90172.93856 111703.0785 97953.57685 100362.1695 101971.874 18112.09244 74941.60065 80951.72357 1.039550851 1.111628995 1.113910051 1.379872764 1.210024599 1.239778043 1.259662791 0.223739429 0.925756702 1 16.30477418 1.764862758 25 0.641404323 1.196865697 0.499219797 0.214996698 11.1280356 10583.92937 0.093949225 0.052103865 58.19192951 -1.764862758 0.555461374 EAAVSHAGSMHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAAVSHAGSMHR 12 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 182.25 9.90E-06 235240000 217879 333190 232910 310450 224275 248038 295280 141290 277790 295270 FALSE TRUE 209364.0478 323687.7474 275002.0181 326472.3617 231489.0091 253053.4983 298893.725 138372.3121 246256.4438 275271.0999 0.760574023 1.175887144 0.999022484 1.186003041 0.840949192 0.919288289 1.085815856 0.502676497 0.894596069 1 18.07049363 1.764940986 24.99999995 0.74888358 1.000914446 0.192354364 0.175216972 20.12952827 19088.47352 0.076537055 0.042447092 58.20241243 -1.764940986 0.252030866 FNHDGEEEEEDDDYGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 FNHDGEEEEEDDDYGSR 17 0 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 ; 240.21 2.60E-20 941860000 269730 320090 256480 298550 278540 279570 320790 147558 304630 313160 FALSE TRUE 259188.6534 310961.3466 302831.6414 313958.2013 287499.4921 285223.0969 324715.924 144510.8757 270049.6795 291949.3943 0.887786234 1.065120712 1.037274429 1.075385692 0.984757967 0.976960742 1.112233594 0.494986044 0.924987977 1 18.15535879 1.764966697 25 0.755861963 1.021463974 0.315095919 0.13811715 14.82602117 14045.55198 0.059259946 0.032865276 58.20585814 -1.764966697 0.265602011 EES(ph)DGEYDEFGRK ddPTM_BT-474_Pertuzumab_2h_R1 3 EESDGEYDEFGRK 13 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EES(1)DGEYDEFGRK;EES(1)DGEYDEFGRK;EES(1)DGEYDEFGRK 209.66 2.21E-08 1516760000 1054080 876050 914230 823510 905960 832340 955540 1295970 1453680 1282850 TRUE FALSE 1012885.388 851065.9117 1079451.698 866011.4498 935101.0262 849170.4851 967234.1844 1269207.767 1288664.341 1195961.427 0.846921452 0.711616523 0.902580697 0.724113195 0.781882262 0.710031667 0.808750318 1.061244734 1.077513297 1 20.18973943 1.7649876 4.602478836 1.052972024 0.778443421 0.800288669 0.06012917 0.073785342 3.314813246 0.02876271 0.015075369 58.20865972 -1.7649876 -0.274528603 FGDSHHSHAGGHCGGCCH ddPTM_BT-474_Pertuzumab_2h_R1 1 FGDSHHSHAGGHCGGCCH 18 0 F5H2C9;Q86UY6-4;Q86UY6-3;Q86UY6 F5H2C9 NAA40 N-alpha-acetyltransferase 40 0 53.995 0.041616 96150000 15092 35187 34931 53786 45627 51374 40299 902.68 16000 7931.2 FALSE TRUE 14502.18795 34183.50121 41243.80874 56561.90191 47094.63389 52412.81748 40792.19122 884.0393426 14183.74708 7394.01276 1.961342024 4.62313257 5.578000752 7.649689518 6.369293024 7.088548422 5.51692194 0.119561512 1.918274628 1 12.85214182 1.765041172 7.766900901 1.045147152 5.685089869 0.651048237 1.516059499 0.104817802 19.30455232 0.763176963 0.418458262 58.21584054 -1.765041172 4.639942717 APS(ph)IDGKEELDLAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 APSIDGKEELDLAEK 15 1 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;B5MCW3;Q9H0E9-3;Q9H0E9;H0YAH7;H0YA84 H7C128 BRD8 Bromodomain-containing protein 8 1 APS(1)IDGKEELDLAEK 160.77 1.02E-06 431010000 321600 303280 245380 260980 291750 278870 290480 386710 402050 378250 TRUE FALSE 309031.5165 294630.7513 289725.6244 274449.2091 301134.4037 284508.9425 294034.9811 378724.3034 356410.9695 352630.7906 0.876359991 0.835521909 0.821611817 0.778290542 0.853965144 0.806818208 0.833832408 1.073996694 1.010719934 1 18.42779893 1.765051683 8.160479881 1.030466907 0.827321008 0.898612811 0.03057476 0.044774435 9.423319108 0.014030955 0.00770382 58.21724947 -1.765051683 -0.203145899 HYGDQVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HYGDQVDR 8 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-2;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 ; 142.92 0.0006097 610200000 156512 180665 135618 135964 176618 137232 160523 116768 149266 185503 FALSE TRUE 150395.338 175512.6111 160127.1894 142981.1183 182299.0784 140006.9251 162487.5285 114356.7 132321.9495 172938.7166 0.869645277 1.014883275 0.925918687 0.826773328 1.054125311 0.809575368 0.9395671 0.66125563 0.765137802 1 17.39990136 1.765064267 25 0.774087964 0.921259366 0.163256972 0.107092538 21.03751189 19856.63311 0.046162107 0.025601313 58.21893636 -1.765064267 0.147171402 HKFQSQADQDQQASGLQS(ph)PPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 HKFQSQADQDQQASGLQSPPSR 22 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 HKFQSQADQDQQASGLQS(0.953)PPS(0.047)R;HKFQSQADQDQQASGLQS(0.988)PPS(0.012)R;HKFQSQADQDQQASGLQS(1)PPSR;HKFQSQADQDQQASGLQS(0.957)PPS(0.043)R 220.99 5.87E-26 669680000 279008 320101 222025 256046 280838 346090 314713 228982 348814 302436 TRUE FALSE 268104.0589 310972.0329 262149.8564 269260.5647 289871.4093 353088.1769 318564.5518 224253.4417 309218.0971 281951.7403 0.950886342 1.102926453 0.929768535 0.954988128 1.028088739 1.252300044 1.129854887 0.795361083 1.096705758 1 18.10508872 1.765069029 25 0.943424336 1.050558246 0.096700972 0.115113883 34.44341546 32504.18322 0.054991627 0.030498293 58.21957478 -1.765069029 0.10713391 AVS(ph)PLDPSKEVSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVSPLDPSKEVSGK 14 1 Q14865;Q14865-2 Q14865 ARID5B AT-rich interactive domain-containing protein 5B 1 AVS(0.919)PLDPS(0.081)KEVSGK;AVS(0.998)PLDPS(0.002)KEVSGK 112.16 0.00036926 1649780000 2875500 2590600 1803990 1611210 2046400 2370100 2242400 2717200 2836500 2393700 TRUE FALSE 2763122.281 2516718.624 2130011.123 1694364.741 2112224.314 2418025.046 2269843.162 2661088.87 2514512.412 2231572.567 1.238195128 1.12777808 0.954488845 0.75926939 0.946518319 1.083552057 1.017149608 1.192472479 1.126789444 1 21.08962929 1.765072441 25 1.125506048 1.009709978 0.083760447 0.127143425 36.97079776 34884.78472 0.063782867 0.035374056 58.2200321 -1.765072441 -0.11579607 GEVPPKET(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEVPPKETPK 10 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GEVPPKET(1)PK;GEVPPKET(1)PK;GEVPPKET(1)PK;GEVPPKET(1)PK 100.19 0.006765 5334600000 6182680 4936760 4820580 3893270 4397990 4159000 4875200 6729580 6341550 5694090 TRUE FALSE 5941054.03 4795968.438 5691766.039 4094202.131 4539455.343 4243097.83 4934864.156 6590611.821 5621683.83 5308424.213 1.119174691 0.903463673 1.072213864 0.771265062 0.855141782 0.799314007 0.929628824 1.241538272 1.05901179 1 22.33985223 1.765140163 24.9999676 1.122875768 0.913538515 0.320864995 0.117380365 17.44536492 16419.04241 0.054058295 0.029980473 58.22911149 -1.765140163 -0.209337253 ADIDVSGPSVDTDAPDLDIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADIDVSGPSVDTDAPDLDIEGPEGK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 262.94 3.60E-45 288180000 597180 615080 518590 570990 515990 583710 571920 723070 718240 630500 FALSE TRUE 573841.5454 597538.5206 612310.749 600458.8623 532587.287 595513.0161 578919.328 708138.3518 636708.4063 587795.6734 0.97626024 1.016575228 1.041706798 1.021543522 0.906075548 1.013129295 0.984898927 1.204735563 1.083213836 1 19.16495521 1.765176542 25 1.11633776 0.99536912 0.372291021 0.058729349 14.67231568 13790.25999 0.026184479 0.014521614 58.2339892 -1.765176542 -0.12096864 QHGDVVSAIR ddPTM_BT-474_Pertuzumab_2h_R1 6 QHGDVVSAIR 10 0 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;; 193.21 5.98E-07 5560650000 1388243 1401039 1183810 1460292 1238110 1367056 1428431 964357 1386259 1536663 FALSE TRUE 1333988.929 1361082.739 1397750.801 1535657.845 1277934.933 1394698.809 1445912.566 944442.6909 1228896.69 1432583.446 0.931177121 0.950089674 0.975685433 1.071950014 0.892049211 0.973555022 1.009304254 0.659258414 0.857818575 1 20.45018775 1.765197974 24.99999994 0.804482049 0.972106334 0.290026926 0.090608172 15.98405549 15011.04779 0.039443625 0.021875255 58.23686305 -1.765197974 0.167624284 S(ph)PGPPALK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPGPPALK 8 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK 82.749 0.020419 5818610000 4155180 3914140 3784060 3914670 3914650 3854070 4052800 4826420 4854830 5099120 TRUE FALSE 3992790.972 3802512.56 4467923.818 4116706.588 4040568.272 3932001.936 4102399.379 4726752.74 4303730.052 4753752.061 0.839924111 0.799897115 0.939873128 0.865991018 0.849974551 0.82713652 0.862981352 0.994320419 0.905333302 1 22.18063523 1.765240868 12.6721794 0.962401751 0.855381985 0.602906609 0.041403711 0.272486141 129.1984956 0.019013535 0.010507019 58.24261529 -1.765240868 -0.107019766 KS(ph)DNHSPAVVTTTVSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSDNHSPAVVTTTVSSK 17 1 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 KS(0.632)DNHS(0.368)PAVVTTTVSSK 107.21 0.00043814 143480000 77377 73268 73334 101960 92664 97011 119220 115160 172710 182100 TRUE FALSE 74353.0213 71178.46838 86587.08511 107222.1678 95644.62172 98972.62889 120679.05 112781.9058 153104.6849 169766.2048 0.437973043 0.419273485 0.510037232 0.631587235 0.563390233 0.582993706 0.710854379 0.664336615 0.901856085 1 17.37318977 1.765272197 0.224999222 1.109708827 0.30653117 0.896369892 0.057527303 0.706683487 0.158792149 0.194477028 0.228399571 58.24681686 -1.765272197 -0.803177657 down S(ph)STPPLHVHVDENTPVHVHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTPPLHVHVDENTPVHVHIK 21 0 Q5BJF6-9;Q5BJF6-3;Q5BJF6-4 Q5BJF6-9 ODF2 Outer dense fiber protein 2 1 S(0.461)S(0.461)T(0.079)PPLHVHVDENTPVHVHIK 184.34 1.81E-17 143420000 219960 211350 189720 184790 192800 210050 206770 15528 234070 64818 TRUE FALSE 211363.72 205322.5049 224006.6243 194327.034 199001.5871 214297.3549 209300.5131 15207.34137 207499.3549 60427.81913 3.497788321 3.39781425 3.707011564 3.215853838 3.293211471 3.546336075 3.463644992 0.251661265 3.433838221 1 15.88292525 1.765278975 25 1.516607968 3.443278341 0.566381277 0.755156766 11.30769632 10587.13473 0.318260176 0.176506846 58.247726 -1.765278975 1.926670372 FGEYNSNMS(ph)PEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FGEYNSNMSPEEK 13 0 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 1 FGEYNSNMS(1)PEEK 238.12 9.58E-17 212670000 337140 279870 239550 223320 272530 245770 269790 312820 322680 333340 TRUE FALSE 323964.1961 271888.3816 282842.0138 234845.572 281296.175 250739.6378 273091.7707 306360.1577 286050.7192 310762.5849 1.04248134 0.874907067 0.910154657 0.755707358 0.905180317 0.806852723 0.878779441 0.985833471 0.92047992 1 18.24545329 1.765280252 9.133801164 0.964386295 0.875910409 0.227216123 0.072569962 0.270266095 74.86525257 0.033544696 0.018466684 58.24789729 -1.765280252 -0.088475886 RHGAPAAPS(ph)PPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RHGAPAAPSPPPR 13 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR 95.954 0.0027315 526790000 223239 242194 191780 218060 202601 219440 219024 134389 211029 215659 TRUE FALSE 214514.5731 235286.8643 226438.9121 229314.1027 209117.8452 223877.2272 221704.4812 131613.8202 187073.8726 201052.2238 1.066959464 1.170277353 1.126269124 1.14056984 1.040117046 1.113527734 1.10272086 0.654625041 0.930474028 1 17.61721077 1.765292847 25 0.828862617 1.110464972 0.604590515 0.090341642 9.448644055 8841.951924 0.038818272 0.021528657 58.24958659 -1.765292847 0.281602354 LHQLS(ph)GSDQLESTAHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHQLSGSDQLESTAHSR 17 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 LHQLS(0.791)GS(0.209)DQLESTAHSR;LHQLS(0.98)GS(0.02)DQLESTAHSR 214.87 3.73E-15 785900000 165759 174200 171985 214158 188270 207148 206273 95846 181598 217685 TRUE FALSE 159280.955 169231.9866 203066.5153 225210.72 194325.8755 211336.6745 208797.4307 93866.74661 160983.7564 202941.0011 0.784863355 0.833897466 1.000618476 1.109734942 0.95754862 1.041370021 1.028857794 0.462532195 0.793253978 1 17.63070084 1.765312231 25 0.697566626 0.96976333 0.266874832 0.154215352 17.73569786 16584.86505 0.070302749 0.038989895 58.25218641 -1.765312231 0.272196704 TLDGFKK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLDGFKK 7 1 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 114.78 0.0093439 8165900000 8838900 10077400 7703000 7653400 7975200 8135600 8892000 9466500 11137300 9765100 FALSE TRUE 8493466.016 9790002.419 9095103.452 8048392.891 8231729.551 8300107.406 9000822.956 9271013.467 9873040.395 9103701.079 0.932968464 1.075387069 0.99905559 0.884079214 0.904217909 0.911728904 0.988699308 1.018378502 1.084508411 1 23.11802176 1.765459124 2.671342407 1.042473035 0.954178847 0.3081881 0.055265506 0.338885686 4.847151248 0.036163684 0.016780961 58.27189265 -1.765459124 -0.088294188 EEQMKEGEETEGS(ph)EEDDKENDKTEEMPNDSVLENK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEQMKEGEETEGSEEDDKENDKTEEMPNDSVLENK 35 3 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 EEQMKEGEET(0.016)EGS(0.979)EEDDKENDKT(0.005)EEMPNDSVLENK 94.93 0.00026376 804880000 192070 111260 90175 43075 121660 112690 107850 207970 186850 103590 TRUE FALSE 184563.6921 108086.9737 106471.6284 45298.10591 125573.3044 114968.669 109169.9006 203675.3468 165639.5713 96573.75703 1.911116412 1.119216825 1.10249028 0.469051917 1.300283931 1.190475265 1.130430294 2.109013391 1.715161307 1 16.55934358 1.765459782 24.99999987 1.720116861 1.148104019 0.168036773 0.417290616 23.02488793 21412.65221 0.189133023 0.104893948 58.27198089 -1.765459782 -0.572012842 HAHLTDTEIMTLVDETNMYEGVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HAHLTDTEIMTLVDETNMYEGVGR 24 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ; 223.93 4.19E-33 584150000 184894 196408 173806 216710 197735 208160 199059 3916.84 182368 111974 FALSE TRUE 177668.1381 190806.6361 205216.6105 227894.4291 204095.3259 212369.1378 201495.1436 3835.955885 161666.3492 104389.9012 1.701966722 1.82782658 1.965866507 2.183108005 1.955125193 2.034383933 1.930216824 0.036746427 1.548678055 1 16.67162263 1.765494217 25 0.777664467 1.952377226 0.646106053 0.364926745 9.32087021 8657.118922 0.15671957 0.086917054 58.27660144 -1.765494217 1.174712759 KQGGS(ph)PDEPDSK ddPTM_BT-474_Pertuzumab_2h_R1 6 KQGGSPDEPDSK 12 1 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 KQGGS(1)PDEPDSK;KQGGS(1)PDEPDSK;KQGGS(1)PDEPDSK;KQGGS(1)PDEPDSK;KQGGS(0.998)PDEPDS(0.002)K;KQGGS(0.949)PDEPDS(0.051)K 195.36 3.69E-07 5338340000 8496160 6723480 5876410 4871490 6046690 6158790 6655010 8050180 9625870 7712320 TRUE FALSE 8164120.674 6531732.933 6938408.007 5122908.183 6241187.275 6283324.954 6736456.003 7883940.97 8533181.593 7189957.697 1.135489389 0.908452206 0.965013745 0.712508807 0.86804228 0.87390291 0.93692568 1.09652119 1.186819443 1 22.77755185 1.765539246 3.643456818 1.109284975 0.902479433 0.371457173 0.10698988 0.212727855 5.665528141 0.058285273 0.02927181 58.28264407 -1.765539246 -0.206805542 NDS(ph)WGSFDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NDS(0.992)WGS(0.008)FDLR;NDS(0.996)WGS(0.004)FDLR;NDS(1)WGSFDLR;NDS(0.998)WGS(0.002)FDLR;NDS(0.989)WGS(0.011)FDLR;NDS(0.996)WGS(0.004)FDLR 262.3 2.19E-17 2590840000 2136410 1895750 1513460 1556760 1870250 1736470 1817260 2170170 2211720 2029110 TRUE FALSE 2052916.735 1841685.066 1786975.889 1637104.57 1930408.29 1771582.613 1839500.171 2125355.231 1960654.818 1891676.572 1.085236644 0.97357291 0.944651911 0.865425197 1.020474809 0.936514539 0.972417906 1.123529922 1.03646408 1 20.85123402 1.765573322 25 1.065147652 0.966750762 0.26819446 0.060949772 19.90728516 18435.47514 0.02782736 0.015432973 58.2872173 -1.765573322 -0.098396889 AAFTTPDHAPLS(ph)PQSSVASSGSEQTEEQGSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAFTTPDHAPLSPQSSVASSGSEQTEEQGSSR 32 0 M0QZ22;Q5PRF9;A0A087WZT0;M0R0X3 M0QZ22 SAMD4B Protein Smaug homolog 2 1 AAFTTPDHAPLS(1)PQSSVASSGSEQTEEQGSSR;AAFTTPDHAPLS(1)PQSSVASSGSEQTEEQGSSR 441.63 4.02E-231 1523860000 254540 327730 300920 410320 363280 367940 317750 273700 261450 277690 TRUE FALSE 244592.2954 318383.4613 355302.9379 431496.6644 374965.2311 375379.9989 321638.7195 268047.9994 231771.2921 258881.809 0.944802945 1.229840994 1.372452315 1.666770895 1.448403164 1.450005315 1.242415297 1.035406854 0.895278401 1 17.98193407 1.765589704 2.471205487 0.9516447 1.365161745 0.477146972 0.175850971 0.241945967 2.965345952 0.117853239 0.053440265 58.28941602 -1.765589704 0.413517045 SHLEPSGNPLPATPTTSAPSAPPAS(ph)SQGPDTAPRPSPPQEEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTS(0.001)APS(0.044)APPAS(0.295)S(0.295)QGPDT(0.238)APRPS(0.127)PPQEEAR;SHLEPSGNPLPATPTTSAPS(0.007)APPAS(0.338)S(0.338)QGPDT(0.197)APRPS(0.12)PPQEEAR 204.61 6.90E-36 1891100000 106581 126364 107271 155481 128634 140084 154884 45996 143653 145926 TRUE FALSE 102415.6967 122760.2224 126657.2559 163505.393 132771.6294 142916.5945 156779.5167 45046.16653 127346.1137 136042.302 0.752822432 0.902368018 0.931013766 1.201871702 0.975958415 1.050530551 1.152432107 0.33111882 0.936077321 1 17.0536958 1.765594075 25 0.687464185 0.998566946 0.198847928 0.207098044 20.98896634 19422.24779 0.092585963 0.051348758 58.29000271 -1.765594075 0.311102761 PKPRPS(ph)PSSTREPLLSSSENGNGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 PKPRPSPSSTREPLLSSSENGNGGR 25 3 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 1 PKPRPS(0.979)PS(0.016)S(0.004)T(0.001)REPLLSSSENGNGGR 176.01 5.49E-12 207460000 158550 133920 106220 112430 121410 141810 146710 138470 189810 166860 TRUE FALSE 152353.6907 130100.7327 125416.3169 118232.5258 125315.2629 144677.4954 148505.4809 135610.5461 168263.5645 155558.4236 0.979398526 0.836346433 0.806232886 0.760052224 0.805583266 0.930052465 0.95466049 0.871766009 1.0816744 1 17.24709699 1.765620723 0.917254716 1.019936872 0.838021049 0.458674727 0.071815704 0.523228635 0.824926651 0.065076635 0.027698392 58.29357932 -1.765620723 -0.181915823 HQDDLQDVIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQDDLQDVIGR 11 0 E5RG17;Q6P1N9;H0YBX2;G5EA19;U3KQS5;E5RID7 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 ; 116.51 0.00097916 822910000 357878 398240 309176 365830 365774 334433 359568 283994 384908 351948 FALSE TRUE 343891.7321 386882.5851 365050.9808 384710.5301 377539.4529 341195.4644 363968.5007 278129.4247 341214.8575 328110.2485 1.048098112 1.179123745 1.112586341 1.172503852 1.150648158 1.039880546 1.109287206 0.847670641 1.039939652 1 18.32382113 1.765637402 25 0.948899698 1.118889568 0.549547816 0.063280235 11.66369304 10775.7749 0.027997373 0.015527514 58.29581818 -1.765637402 0.16998987 IPVHPNDHVNK ddPTM_BT-474_Pertuzumab_2h_R1 6 IPVHPNDHVNK 11 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ;;;;; 143.97 2.14E-05 4002200000 3809360 4530080 3552480 5138750 3665190 4231630 5170680 778800 5017160 4067480 FALSE TRUE 3660486 4400886.554 4194492.16 5403961.503 3783084.165 4317196.458 5233960.329 762717.5078 4447633.03 3791985.957 0.965321613 1.160575647 1.106146544 1.425100611 0.997652472 1.138505392 1.380268911 0.201139328 1.17290335 1 21.85452219 1.76567087 25 0.711419596 1.167257864 0.272524776 0.272514024 18.35220162 16934.16189 0.117757142 0.065308739 58.30031083 -1.76567087 0.455838268 FTGSFDDDPDPHRDPYGEEVDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 213.72 4.80E-26 6076000000 1533550 1763170 1345210 1695000 1595920 1716930 1638320 1483560 1676460 1641220 FALSE TRUE 1473617.171 1712886.118 1588319.371 1782479.153 1647254.216 1751647.501 1658370.25 1452923.968 1486155.289 1530058.708 0.963111522 1.119490454 1.038077404 1.164974353 1.076595433 1.14482372 1.083860536 0.949587072 0.971306056 1 20.54515558 1.765754682 7.317991451 0.971117429 1.089288764 0.461993561 0.054568186 0.13385067 20.73529191 0.024720962 0.013546079 58.31156299 -1.765754682 0.118171335 YHTSQSGDEMTSLSEYVSR ddPTM_BT-474_Pertuzumab_2h_R1 19 YHTSQSGDEMTSLSEYVSR 19 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;;;;;;;;;; 353.31 7.60E-91 25983266000 3294261.3 5667475 4595587 7473401 5479007 6815673 5726886 1962025 4579592.2 5724172 FALSE TRUE 3165517.926 5505844.162 5426111.799 7859104.121 5655244.236 6953490.578 5796973.344 1921508.498 4059736.093 5336468.732 0.593185885 1.031739234 1.0167982 1.472716232 1.059735289 1.303013458 1.086293884 0.360071162 0.76075328 1 22.34745396 1.765764452 25 0.644578256 1.099017506 0.293699681 0.259014984 18.67985892 17177.16222 0.118444662 0.065690016 58.31287474 -1.765764452 0.45443925 AGVQADEDEDGDEKDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGVQADEDEDGDEKDEK 17 1 P26358;P26358-2 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 193.64 1.23E-17 0 100970 83900 71198 57177 77762 70779 79052 109960 118560 104640 FALSE TRUE 97023.98077 81507.25415 84065.06239 60127.91182 80263.28535 72210.19987 80019.46202 107689.2876 105101.5658 97552.6396 0.994580784 0.835520745 0.86174052 0.616363761 0.822768976 0.740217796 0.820269573 1.10390952 1.077383106 1 16.57389329 1.76579599 6.413450804 1.066506058 0.805144301 0.596564813 0.092980298 0.112500201 12.01255303 0.045491777 0.024760929 58.31710947 -1.76579599 -0.261361757 EHQHEEIQNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EHQHEEIQNVR 11 0 Q6DD88;F5H6I7 Q6DD88 ATL3 Atlastin-3 0 ; 161.99 1.48E-05 871050000 578600 849130 461360 1070650 602670 610060 751630 3907.24 737350 399340 FALSE TRUE 555987.6723 824913.6438 544738.0149 1125906.375 622055.4279 622395.8312 760828.6728 3826.554129 653649.1192 372292.3461 1.493416876 2.215768474 1.463199608 3.02425335 1.670878906 1.67179325 2.043632325 0.010278358 1.755741492 1 18.50607643 1.765806338 25 0.833552232 1.953643819 0.388409802 0.582294624 16.26214988 14930.93686 0.253146184 0.140396458 58.318499 -1.765806338 1.120091587 LTEADYLSSHLTEGPHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LTEADYLSSHLTEGPHR 17 0 K7EIN2;Q9BRJ7;K7ENA3;W4VSQ8;Q9BRJ7-2 K7EIN2 NUDT16L1 Protein syndesmos 0 ;; 210.9 1.71E-12 615360000 413810 564200 462440 572530 534310 528780 586350 249525 554780 567640 FALSE TRUE 397637.8477 548109.5684 546013.1949 602078.3419 551496.5664 539472.2939 593525.9267 244372.2216 491803.7002 529193.2372 0.751403872 1.035745603 1.031784151 1.137728715 1.042145907 1.019424014 1.121567482 0.461782586 0.929346155 1 19.0134351 1.765820818 25 0.742695628 1.026393587 0.25550131 0.166566003 18.55834056 17030.10609 0.073069957 0.0405249 58.32044351 -1.765820818 0.283697958 DKS(ph)HSHTPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.989)HS(0.011)HTPSR 96.745 0.0039444 82629000 41171 42437 40312 46491 46981 44023 55283 3400.8 55973 37209 TRUE FALSE 39561.9918 41226.73831 47597.27514 48890.40608 48492.18653 44913.17522 55959.56989 3330.572292 49619.1797 34688.80129 1.140483105 1.188473997 1.372122223 1.409400275 1.397920503 1.294745669 1.613188344 0.096012897 1.430409177 1 15.08218237 1.765874701 25 0.753016864 1.342756843 0.315726618 0.331665276 17.59525292 16114.44918 0.14328539 0.079467312 58.32767985 -1.765874701 0.589739979 AQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIR 36 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 125.56 6.32E-09 39695000 18235 23680 17714 21816 19959 18528 21935 1900.5 20964 14243 FALSE TRUE 17522.35604 23004.66959 20915.31385 22941.92637 20600.99936 18902.64885 22203.44709 1861.254011 18584.25461 13278.30892 1.319622562 1.732499953 1.575148911 1.727774712 1.551477638 1.423573511 1.67215925 0.140172519 1.399594987 1 13.6967838 1.765875845 25 0.76658302 1.577586821 0.521846661 0.315282373 11.98468636 10975.60373 0.134197573 0.074426655 58.32783348 -1.765875845 0.811003801 KVSVS(ph)ESNVLLDEEVLTDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVSVSESNVLLDEEVLTDPK 20 1 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 KVS(0.177)VS(0.412)ES(0.412)NVLLDEEVLTDPK;KVS(0.382)VS(0.545)ES(0.073)NVLLDEEVLTDPK 162.77 1.26E-11 136039000 264180 220040 211998 176931 240380 217553 226010 284780 284870 249370 TRUE FALSE 253855.5535 213764.6746 250310.7545 186062.4301 248112.041 221952.0707 228775.978 278899.1935 252532.7519 232479.9478 1.091946019 0.919497258 1.076698257 0.800337543 1.067240609 0.954714903 0.984067573 1.19966989 1.086256059 1 17.82674676 1.765883994 24.99999996 1.114929928 0.980845893 0.217944031 0.093406118 21.50671217 19690.02491 0.039787717 0.022066592 58.32892785 -1.765883994 -0.134084035 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGK ddPTM_BT-474_Pertuzumab_2h_R1 8 TGDLGIPPNPEDRSPSPEPIYNSEGK 26 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 TGDLGIPPNPEDRS(1)PS(0.997)PEPIY(0.002)NS(0.001)EGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(0.993)PS(0.978)PEPIY(0.016)NS(0.012)EGK;TGDLGIPPNPEDRS(1)PS(0.999)PEPIY(0.001)NSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK 183.93 9.40E-18 16572770000 9397580 8474420 7566433 7677850 8125210 8328260 8671880 10001330 11511260 10329860 TRUE FALSE 9030312.184 8232737.839 8933855.757 8074104.759 8386564.759 8496663.123 8778009.061 9794799.04 10204550.02 9630209.381 0.937706734 0.854886692 0.927690708 0.838414248 0.870860064 0.882292667 0.911507602 1.017090974 1.059639476 1 23.19913574 1.766011363 2.919702174 1.033721129 0.883625468 0.802613221 0.031258476 0.091666235 1.560611931 0.017077427 0.008129497 58.34603697 -1.766011363 -0.150095661 EKFEGVELNTDEPPMVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKFEGVELNTDEPPMVFK 18 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ; 174.32 5.58E-12 201537000 450300 445850 384310 452810 401930 424440 459450 529260 606090 571210 FALSE TRUE 432701.7782 433134.7945 453763.3659 476179.5784 414858.4435 433022.4676 465072.8865 518330.596 537289.2041 532521.4379 0.812552786 0.81336593 0.852103472 0.89419795 0.779045526 0.813154996 0.873341153 0.973351605 1.008953191 1 19.02248008 1.76605577 2.395112831 1.003348301 0.828963253 0.871005606 0.028817045 0.094051058 1.082336142 0.019102665 0.008583509 58.35200322 -1.76605577 -0.174385048 FHDIDDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 FHDIDDVK 8 0 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;H0Y9D8;D6R967 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ;; 174.52 0.00027147 799640000 1223870 1273570 1142870 1551200 1223230 1217710 1605190 633083 1718090 1377450 FALSE TRUE 1176039.807 1237249.031 1349412.032 1631257.618 1262576.304 1242332.931 1624834.795 620009.6148 1523059.626 1284154.085 0.915808953 0.963473967 1.050817848 1.270297418 0.983196891 0.967432916 1.26529582 0.482815592 1.18604118 1 20.29238689 1.766078913 25 0.836363046 1.057084499 0.113830926 0.20127525 29.67427048 26975.06949 0.088721993 0.049206346 58.35511281 -1.766078913 0.220721453 GSSPSIRPIQGSQGSSS(ph)PVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSPSIRPIQGSQGSSSPVEK 21 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 GSSPSIRPIQGSQGS(0.018)S(0.037)S(0.946)PVEK 206.96 2.38E-22 719250000 225080 201610 193950 209750 201510 196690 204040 263000 253200 229650 TRUE FALSE 216283.6248 195860.2802 229001.0794 220575.2226 207991.7522 200667.2066 206537.1026 257568.9581 224457.7975 214095.6009 1.010219845 0.914826271 1.069620667 1.030265086 0.971490078 0.937278513 0.964695686 1.203055817 1.048399857 1 17.70789563 1.766079619 25 1.104126523 0.985333348 0.315473647 0.06432373 18.03813872 16396.9501 0.029020628 0.0160951 58.35520765 -1.766079619 -0.118793175 LQSIGTENTEENRR ddPTM_BT-474_Pertuzumab_2h_R1 13 LQSIGTENTEENRR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;;;; 268.56 5.23E-25 1.89418E+11 15469026.1 16458168.7 12545181 15549375.2 14309810.1 13878943.1 13755196.5 14201754.2 13595521.8 12889925.3 FALSE TRUE 14864479.46 15988797.84 14812374.27 16351880.32 14770098.14 14159584.84 13923536.71 13908483.01 12052215.16 12016879.18 1.236966706 1.330528302 1.232630707 1.360742675 1.229112644 1.178307997 1.15866495 1.157412237 1.002940529 1 23.51855894 1.76609802 0.662482252 0.990293941 1.291658065 0.819289017 0.04804019 0.270608988 0.24189171 0.043338276 0.022677648 58.35768019 -1.76609802 0.301364124 NHKPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 5 NHKPSR 6 1 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 NHKPS(1)R;NHKPS(1)R;NHKPS(1)R;NHKPS(1)R;NHKPS(1)R 79.596 0.040413 25857480000 17024200 14999590 15521980 16410830 14323540 14699040 16715930 4096442 14715860 14686880 TRUE FALSE 16358875.44 14571816.38 18327147.07 17257794.9 14784269.67 14996264.66 16920504.55 4011849.041 13045377.27 13692124.54 1.194765312 1.064248017 1.33851741 1.260417611 1.079764476 1.095247463 1.235783717 0.29300413 0.952765017 1 23.70684298 1.76612099 25 0.679482408 1.178632111 0.491156503 0.19808351 12.78110172 11600.76907 0.086079192 0.047740537 58.36076687 -1.76612099 0.499149703 KDRNNTEVER ddPTM_BT-474_Pertuzumab_2h_R1 2 KDRNNTEVER 10 2 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 62.303 0.048352 536270000 1001570 721340 777810 787090 854000 735410 990440 882780 1194190 1031410 FALSE TRUE 962427.5371 700768.0895 918377.5693 827711.8092 881469.6856 750280.4941 1002561.301 864550.2845 1058630.558 961551.682 1.000910877 0.728788793 0.95509954 0.860808446 0.916715869 0.780280986 1.042649417 0.899119934 1.100960643 1 19.87500488 1.766129605 1.318898495 1.028845008 0.875958853 0.286787327 0.093002047 0.511366995 1.678226858 0.068438461 0.027058078 58.36192461 -1.766129605 -0.152886154 VNGLPS(ph)PTHSAHCSFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VNGLPSPTHSAHCSFYR 17 0 O15075-2;O15075;Q5VZY9 O15075-2 DCLK1 Serine/threonine-protein kinase DCLK1 1 VNGLPS(0.915)PT(0.083)HS(0.002)AHCSFYR 88.09 0.0028224 267860000 95292 186120 139550 236220 163220 172560 173780 31691 142460 150880 TRUE FALSE 91567.88329 180812.0398 164769.7893 248411.3425 168470.1195 176049.2814 175906.7716 31036.56978 126288.538 140660.7632 0.650983837 1.285447595 1.171398374 1.766031527 1.197705143 1.251587702 1.250574557 0.220648382 0.897823495 1 17.10186042 1.766143573 24.9999863 0.631177291 1.245898661 0.350544699 0.31774479 17.24237017 15637.21016 0.142707842 0.07914728 58.36380165 -1.766143573 0.61472137 S(ph)DSDLLTCSPTEDATMGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSDLLTCSPTEDATMGSR 19 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.998)DS(0.002)DLLTCSPTEDATMGSR 375.67 3.33E-108 331030000 45948 48311 43897 51615 42188 42211 45894 79998 64859 57154 TRUE FALSE 44152.30136 46933.21758 51830.16438 54278.85634 43545.01533 43064.53534 46455.6645 78346.01334 57496.47823 53282.90867 0.828639098 0.880830622 0.972735267 1.018691691 0.817241709 0.808224183 0.871868028 1.470377937 1.079079196 1 15.70138522 1.766160699 25 1.228980798 0.888169625 0.510075834 0.131395657 12.79898712 11600.27681 0.058639373 0.03252234 58.36610323 -1.766160699 -0.340811172 YHDLECQLIQEFTSAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 YHDLECQLIQEFTSAQR 17 0 F8W9B8;A0A0A0MSI8;O00471 F8W9B8 EXOC5 Exocyst complex component 5 0 124.93 4.86E-05 69268000 17255 28825 24193 29729 21014 30979 25839 14957 27808 20549 FALSE TRUE 16580.65552 28002.93922 28565.21327 31263.31725 21689.93439 31605.41661 26155.22541 14648.13272 24651.35242 19157.19793 0.865505257 1.461745049 1.491095586 1.631935807 1.132208086 1.649793291 1.365294941 0.764628145 1.286793221 1 14.22559894 1.766167089 25 0.998389495 1.39075065 0.294376255 0.249315324 20.94645653 18980.28371 0.110408156 0.061234004 58.36696205 -1.766167089 0.392361155 VEAEAGGSGART(ph)PPLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VEAEAGGSGARTPPLSR 17 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGS(0.007)GART(0.993)PPLSR;VEAEAGGS(0.018)GART(0.982)PPLSR 177.08 1.69E-09 4102200000 1506660 1659640 966130 1263670 1457800 1584090 1235340 1233100 1285900 1097910 TRUE FALSE 1447778.061 1612308.692 1140731.182 1328888.16 1504691.461 1616121.385 1250458.46 1207636.054 1139930.023 1023547.578 1.414470703 1.575216167 1.114487697 1.298315964 1.470074761 1.578941146 1.221690606 1.179853365 1.113704969 1 19.96514673 1.766191023 1.961190967 1.075812558 1.398275922 0.516999334 0.134611778 0.278188215 2.127398526 0.096716691 0.040911166 58.37017874 -1.766191023 0.322463364 GREEYEGPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 GREEYEGPNK 10 1 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 108.37 0.0019699 626890000 733540 654230 626750 613210 649390 647170 672740 826420 801400 793540 FALSE TRUE 704872.4458 635572.001 740017.667 644857.8416 670278.2191 660256.2208 680973.1934 809354.1382 710428.4317 739792.829 0.952797078 0.859121603 1.00030392 0.87167355 0.906035031 0.892487998 0.920491747 1.094028093 0.96030727 1 19.49676179 1.766248637 25 1.026428204 0.913013594 0.481038288 0.048971183 13.8330397 12497.63167 0.020916562 0.011600815 58.37792267 -1.766248637 -0.113414611 SFS(ph)KEVEER ddPTM_BT-474_Pertuzumab_2h_R1 3 SFSKEVEER 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(0.26)FS(0.74)KEVEER;S(0.104)FS(0.896)KEVEER;S(0.008)FS(0.992)KEVEER 138.89 7.50E-05 4234500000 8018200 7160200 5386100 4856500 6901400 7177700 6906000 8829600 10306400 9518300 TRUE FALSE 7704839.879 6955998.107 6359488.083 5107144.547 7123389.799 7322838.012 6990517.694 8647265.674 9136460.68 8873617.063 0.868286272 0.783896584 0.716673712 0.57554259 0.80276056 0.8252371 0.787786721 0.974491643 1.029620798 1 23.08109086 1.766250643 1.577459488 1.027482639 0.749249804 0.676228505 0.074829 0.222254343 1.069973613 0.060022266 0.024117742 58.37819228 -1.766250643 -0.278232835 LYNLDVFQYELYNPMALYGSVPVLLAHNPHR ddPTM_BT-474_Pertuzumab_2h_R1 4 LYNLDVFQYELYNPMALYGSVPVLLAHNPHR 31 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 184.66 1.69E-18 2724870000 438656 529568 451825 541011 576788 445214 570631 166311 516249 532237 FALSE TRUE 421512.8386 514465.2391 533479.8283 568932.6425 595340.9098 454216.5321 577614.5529 162876.6197 457646.5778 496188.1139 0.849502087 1.036835073 1.075156404 1.146606754 1.199829043 0.915411956 1.164103969 0.328255787 0.922324749 1 18.92052765 1.76628992 24.99999989 0.682631425 1.059083921 0.31924962 0.196869521 17.16230561 15482.39964 0.085802314 0.047586996 58.38347224 -1.76628992 0.376452496 WASLADSYS(ph)DPGLTEDGLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 WASLADSYSDPGLTEDGLGR 20 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 WASLADS(0.082)YS(0.918)DPGLTEDGLGR;WASLADSYS(1)DPGLTEDGLGR 304.09 4.20E-55 177882000 386370 373640 309550 372450 356160 377080 360480 457090 420230 437480 TRUE FALSE 371270.2332 362984.153 365492.5709 391672.1891 367616.2099 384704.816 364891.6621 447650.9318 372527.2521 407849.0899 0.910312766 0.889996231 0.896146589 0.960336063 0.901353513 0.943252849 0.894673229 1.09758963 0.913394835 1 18.63767591 1.766315568 25 1.012664425 0.914588357 0.435717396 0.046558101 15.42639631 13903.5407 0.020045429 0.011117179 58.3869202 -1.766315568 -0.098076068 DLPVSEQQER ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPVSEQQER 10 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 157.75 2.01E-05 283690000 219920 192430 187330 132090 172530 183390 186370 247230 282390 212160 FALSE TRUE 211325.2833 186942.0848 221184.6981 138907.1807 178079.5841 187098.2715 188650.8518 242124.6141 250334.2711 197790.2142 1.068431439 0.945153356 1.118279279 0.702295517 0.900345777 0.945943014 0.953792646 1.224148601 1.265655493 1 17.59361152 1.766328865 7.050146956 1.182175577 0.942436648 0.393242496 0.121818333 0.154535498 21.44697554 0.057479047 0.031482666 58.38870792 -1.766328865 -0.239738929 AQT(ph)PPGPSLSGSKS(ph)PCPQEK ddPTM_BT-474_Pertuzumab_2h_R1 6 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AQT(1)PPGPS(0.002)LS(0.005)GS(0.106)KS(0.886)PCPQEK;AQT(1)PPGPS(0.004)LS(0.003)GS(0.006)KS(0.987)PCPQEK;AQT(0.996)PPGPS(0.019)LS(0.061)GS(0.279)KS(0.644)PCPQEK;AQT(1)PPGPSLSGS(0.021)KS(0.978)PCPQEK;AQT(1)PPGPSLSGS(0.006)KS(0.993)PCPQEK;AQT(1)PPGPSLS(0.001)GS(0.026)KS(0.974)PCPQEK 155.09 7.78E-08 40378200000 23344800 18913700 17227700 14910050 17932800 18963100 19266600 24114700 27301500 24144000 TRUE FALSE 22432459.41 18374299.79 20341128.62 15679559.47 18509624.8 19346546.87 19502390.41 23616723.02 24202348.18 22508705.37 0.996612601 0.816319708 0.903700514 0.696599791 0.822331826 0.859513977 0.866437678 1.049226183 1.075243901 1 24.42397974 1.766340854 4.0085039 1.048735379 0.843545549 0.585597221 0.073046658 0.13663408 4.452713529 0.038088364 0.019520925 58.39031978 -1.766340854 -0.20518983 KPS(ph)PQAEEMLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSPQAEEMLK 11 1 Q15013;Q15013-3 Q15013 MAD2L1BP MAD2L1-binding protein 1 KPS(1)PQAEEMLK 121.79 0.00024766 276020000 265260 259450 234300 200800 252300 251640 251020 278760 320330 273660 TRUE FALSE 254893.3459 252050.74 276643.222 211163.3121 260415.4586 256728.3332 254092.0578 273003.5086 283967.4813 255124.7644 0.99909292 0.987950898 1.08434484 0.827686456 1.020737674 1.00628543 0.995952151 1.070078435 1.11305338 1 17.96084342 1.766377494 4.249189385 1.069091811 0.987498592 0.199419298 0.065764973 0.293310327 10.88347071 0.033049167 0.017122683 58.39524625 -1.766377494 -0.081593219 GPHHLDNSS(ph)PGPGSEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPHHLDNSSPGPGSEAR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 GPHHLDNS(0.011)S(0.989)PGPGSEAR;GPHHLDNS(0.019)S(0.981)PGPGSEAR 199.28 8.65E-12 1034860000 475690 634630 593460 699870 630610 690580 684880 62433 563750 583560 TRUE FALSE 457099.5089 616530.9738 700711.4234 735990.3746 650894.1434 704544.0008 693261.7663 61143.73673 499755.4634 544034.9614 0.840202453 1.133256165 1.287989694 1.352836539 1.196419696 1.29503442 1.274296351 0.112389352 0.918609095 1 19.05333984 1.766457456 25 0.589887593 1.207909691 0.443053022 0.261645375 14.27938091 12804.24581 0.115381348 0.063992479 58.40599891 -1.766457456 0.618022099 LHSEGDQLLAAEHPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHSEGDQLLAAEHPGR 16 0 O60437;K7EKI8 O60437 PPL Periplakin 0 ; 194.05 1.59E-10 1245630000 229456 265800 224888 275200 259420 256470 254167 130496 242808 234369 FALSE TRUE 220488.6058 258219.6442 265530.2642 289403.105 267764.4799 261655.9991 257277.5718 127801.212 215245.4538 218494.9789 1.009124361 1.181810427 1.215269411 1.324529774 1.225494889 1.197537813 1.177498783 0.584916013 0.98512769 1 17.7372406 1.766461067 25 0.81763006 1.197632446 0.575167277 0.129942828 11.59842734 10398.90208 0.057603907 0.031947959 58.40648459 -1.766461067 0.380002386 VMDRPGNYVEPTIVTGLGHDASIAHTETFAPILYVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VMDRPGNYVEPTIVTGLGHDASIAHTETFAPILYVFK 37 1 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GTY9 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ; 173.04 2.08E-18 718980000 364440 417470 344890 464370 405040 443170 485420 56524 438230 406030 FALSE TRUE 350197.2819 405564.1643 407219.295 488336.1914 418068.4794 452131.201 491360.7152 55356.75965 388483.9676 378529.2264 0.925152557 1.071421005 1.075793536 1.290088472 1.104454954 1.194441986 1.298078671 0.146241705 1.026298474 1 18.53004517 1.766524134 25 0.638622132 1.139019337 0.347820221 0.251001955 16.7999378 15028.4678 0.1092285 0.060579993 58.41496676 -1.766524134 0.500397205 AVSLFSLNDPALSPDIPPAHS(ph)PVHSHLSLER ddPTM_BT-474_Pertuzumab_2h_R1 4 AVSLFSLNDPALSPDIPPAHSPVHSHLSLER 31 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AVSLFSLNDPALSPDIPPAHS(0.693)PVHS(0.125)HLS(0.183)LER;AVSLFSLNDPALSPDIPPAHS(0.605)PVHS(0.162)HLS(0.232)LER;AVSLFSLNDPALSPDIPPAHS(0.771)PVHS(0.114)HLS(0.114)LER;AVSLFSLNDPALSPDIPPAHS(0.849)PVHS(0.057)HLS(0.094)LER 263.86 1.50E-58 1076500000 217480 317570 274111 379354 294433 374123 328551 63720.4 301489 250930 TRUE FALSE 208980.6412 308513.2145 323648.9553 398932.5054 303903.7048 381688.0234 332571.9054 62404.55147 267265.2327 233934.2876 0.89333053 1.31880289 1.383503712 1.705318658 1.299098597 1.63160359 1.421646689 0.26676103 1.142479948 1 17.83574381 1.766554129 24.99999846 0.733881457 1.396086573 0.437099602 0.295976495 15.42030314 13779.51771 0.132309477 0.073381123 58.41900138 -1.766554129 0.662205116 RPAS(ph)PSS(ph)PEHLPATPAESPAQR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.938)PS(0.378)S(0.683)PEHLPAT(0.001)PAESPAQR;RPAS(0.958)PS(0.269)S(0.773)PEHLPATPAESPAQR;RPAS(0.905)PS(0.378)S(0.717)PEHLPATPAESPAQR 191.92 4.39E-17 6068320000 842153 904363 844999 956822 893255 1007235 926977 838501 943823 922064 TRUE FALSE 809240.7297 878571.4527 997709.1162 1006203.698 921987.3583 1027601.982 938321.6218 821185.6613 836684.1699 859611.784 0.941402555 1.022056083 1.160650813 1.170532695 1.072562493 1.195425657 1.091564401 0.955298283 0.973327943 1 19.71332573 1.766581248 6.618281066 0.974020739 1.099666954 0.359851854 0.07129017 0.186945532 21.6777885 0.036197963 0.01977084 58.42264936 -1.766581248 0.125646215 S(ph)SPPVLQGPAPAGFSQHPGLLVPHTHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPPVLQGPAPAGFSQHPGLLVPHTHAR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 S(0.5)S(0.5)PPVLQGPAPAGFSQHPGLLVPHTHAR;S(0.5)S(0.5)PPVLQGPAPAGFSQHPGLLVPHTHAR 128.08 5.14E-05 2899470000 194465 290412 232457 351431 270353 336758 322761 32712 302014 240024 TRUE FALSE 186865.0928 282129.7341 274467.1509 369568.396 279049.1498 343567.4775 326711.0457 32036.48577 267730.6369 223766.9607 0.835087951 1.26081944 1.226575854 1.651577136 1.247052509 1.535380721 1.460050423 0.143168972 1.196470811 1 17.77163751 1.766617782 25 0.696389848 1.329655706 0.350964995 0.328337802 17.86816972 15930.67057 0.145745701 0.080833207 58.42756424 -1.766617782 0.633265858 ASPGS(ph)PGRPGSGASQPVCPEGMHHVVLDGHLEAPSCPLAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPGSPGRPGSGASQPVCPEGMHHVVLDGHLEAPSCPLAPR 41 1 Q96JH8-3;Q96JH8-2;Q96JH8-1;Q96JH8 Q96JH8-3 RADIL Ras-associating and dilute domain-containing protein 1 AS(0.178)PGS(0.735)PGRPGS(0.016)GAS(0.071)QPVCPEGMHHVVLDGHLEAPSCPLAPR;AS(0.034)PGS(0.966)PGRPGSGASQPVCPEGMHHVVLDGHLEAPSCPLAPR 280.78 3.77E-81 567810000 145604 157397 134505 153572 152877 163900 171173 28224 167415 124494 TRUE FALSE 139913.6347 152908.1917 158813.0455 161497.8693 157794.4275 167214.1703 173267.8664 27641.16454 148410.7511 116061.9105 1.20550863 1.317470917 1.368347676 1.391480363 1.359571171 1.440732533 1.49289173 0.238158793 1.278720559 1 16.82453506 1.766676537 25 0.765451338 1.369446991 0.469041358 0.254357581 14.11764596 12560.50536 0.109230141 0.060581125 58.43546945 -1.766676537 0.603995653 ALTHIDHSLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALTHIDHSLSR 11 0 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;; 261.75 6.08E-21 2334150000 842160 972630 903290 1015530 925140 761100 1114760 146557 995730 993390 FALSE TRUE 809247.4561 944891.5447 1066534.597 1067941.625 954897.9683 776489.9635 1128402.766 143530.5467 882698.9048 926106.8105 0.873816548 1.02028355 1.151632387 1.153151681 1.031088377 0.838445366 1.21843696 0.154982714 0.953128618 1 19.82081907 1.766733583 25 0.616622858 1.040583627 0.266850982 0.244772265 19.6916052 17484.16826 0.106376255 0.058998255 58.44314557 -1.766733583 0.42396077 DKEIS(ph)PSVTK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKEISPSVTK 10 1 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 DKEIS(0.986)PS(0.014)VTK;DKEIS(0.997)PS(0.003)VTK;DKEIS(0.976)PS(0.024)VTK;DKEIS(0.985)PS(0.014)VTK 94.09 0.0050515 2828550000 3391040 2730850 3398490 2860540 3437660 3435150 3819210 4532760 5934710 5165610 TRUE FALSE 3258514.408 2652968.832 4012672.742 3008172.812 3548235.456 3504611.087 3865950.634 4439156.922 5261026.601 4815738.634 0.67663855 0.550895519 0.833241388 0.624654501 0.73679984 0.727741132 0.80277418 0.921801879 1.092465144 1 22.19932566 1.766742278 1.329990214 1.051161785 0.68372043 0.790321647 0.07363731 0.175172768 0.585144416 0.056619814 0.022396095 58.44431563 -1.766742278 -0.367441355 HPWDDISYVLPEHMSM ddPTM_BT-474_Pertuzumab_2h_R1 4 HPWDDISYVLPEHMSM 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 225.86 6.49E-15 321828000 214676 318519 237547 331844 275597 271597 289723 136229 256067 298783 FALSE TRUE 206286.2246 309435.15 280477.0271 348970.5086 284461.8278 277088.8774 293268.7167 133415.8235 226999.3477 278546.1613 0.740581825 1.110893608 1.006931942 1.252828282 1.021237652 0.99476825 1.052854993 0.478972042 0.814943371 1 18.08755691 1.766774876 25 0.712669877 1.035652078 0.316226805 0.170448369 18.24759537 16178.30442 0.074810813 0.04149147 58.44870269 -1.766774876 0.322982201 PSSLMNPSLSKPNIS(ph)PSHSRPPGGSDK ddPTM_BT-474_Pertuzumab_2h_R1 3 PSSLMNPSLSKPNISPSHSRPPGGSDK 27 2 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 PSSLMNPSLS(0.006)KPNIS(0.93)PS(0.057)HS(0.006)RPPGGSDK;PSSLMNPSLSKPNIS(0.903)PS(0.091)HS(0.006)RPPGGSDK;PSSLMNPSLS(0.001)KPNIS(0.924)PS(0.057)HS(0.003)RPPGGS(0.015)DK 219.77 1.53E-34 4703170000 2492590 1681080 2081910 1591695 1799186 1731030 2162920 2379950 2692700 2780580 TRUE FALSE 2395176.827 1633137.244 2458157.449 1673842.57 1857058.452 1766032.613 2189390.462 2330803.201 2387035.985 2592248.84 0.923976429 0.630007899 0.948272176 0.645710606 0.71638896 0.681274338 0.844591163 0.899143309 0.920835974 1 21.30577278 1.76678242 1.941921799 0.952707434 0.754356711 0.386493248 0.10306569 0.31468194 2.356371211 0.066973904 0.028265218 58.44971792 -1.76678242 -0.198350723 DMDEPS(ph)PVPNVEEVTLPK ddPTM_BT-474_Pertuzumab_2h_R1 10 DMDEPSPVPNVEEVTLPK 18 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK 248.46 1.75E-24 5326740000 2789433 2459368 2235750 2233680 2399217 2421069 2477518 2979270 3195760 2927900 TRUE FALSE 2680418.874 2389229.233 2639799.759 2348960.492 2476389.994 2470024.674 2507838.606 2917747.033 2832990.723 2729590.725 0.981985632 0.875306767 0.967104605 0.860554101 0.907238573 0.904906604 0.918759938 1.068932059 1.037881136 1 21.38025322 1.766803424 8.680246637 1.039410744 0.913851722 0.673279938 0.037936698 0.093339934 22.31337175 0.016521277 0.009112633 58.45254486 -1.766803424 -0.125559022 RDWGDHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDWGDHGR 8 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 111.39 0.0051988 95439000 143720 192650 167120 211430 194060 178200 164440 141740 120700 133630 FALSE TRUE 138103.2635 187155.8106 197322.3016 222341.9276 200302.1161 181803.3261 166452.4659 138813.0195 106998.642 124579.1211 1.10855866 1.502304792 1.583911492 1.784744713 1.607830545 1.459340253 1.33611848 1.11425589 0.858881015 1 16.92670277 1.766805779 1.638329331 0.928865201 1.530627955 0.66910956 0.164824524 0.215483808 1.124966798 0.128348876 0.051953545 58.45286187 -1.766805779 0.601762754 VSVHVIEGDHR ddPTM_BT-474_Pertuzumab_2h_R1 14 VSVHVIEGDHR 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;;;;;;; 187.85 1.97E-06 58749846000 6990908 11024561 8848020 13601501 10508219 12266990 12055299 3622357 10211997 12286858 FALSE TRUE 6717695.587 10710151.31 10447054.04 14303476.1 10846225.41 12515036.94 12202835.36 3547554.062 9052773.913 11454658.16 0.586459717 0.93500401 0.912035426 1.24870388 0.946883377 1.09257184 1.065316414 0.309704053 0.790313756 1 23.44943107 1.766809592 25 0.629738937 0.980620327 0.208383429 0.228070344 23.08954951 20446.00007 0.102505826 0.056851509 58.453375 -1.766809592 0.350881389 VLTPPHDVDSLPHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLTPPHDVDSLPHLR 15 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 0 ; 179.39 3.89E-07 165218000 116873 114061 103099 126656 124415 122927 125338 59701 122676 114947 FALSE TRUE 112305.474 110808.092 121731.2827 133192.7313 128416.9215 125412.6682 126871.9239 58468.15349 108750.3348 107161.5373 1.048001706 1.034028577 1.135960586 1.242915459 1.198349004 1.170314194 1.18393154 0.54560764 1.014826192 1 16.70942766 1.766814028 25 0.809176303 1.147002928 0.482741177 0.135868759 14.20252934 12574.48978 0.060683001 0.033655911 58.45397205 -1.766814028 0.337826625 FHHTIGGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 FHHTIGGSR 9 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;; 117.89 0.0010783 752599000 518074 626278 506771 620903 565079 586699 568860 194956.3 523872 473879 FALSE TRUE 497827.0953 608417.1646 598355.7928 652947.8782 583255.2792 598562.4558 575821.8788 190930.3843 464404.2468 441782.7532 1.126859507 1.377186321 1.354411842 1.477984085 1.320230984 1.354879636 1.303405066 0.432181616 1.051205017 1 18.75297757 1.766836067 25 0.775020395 1.339598935 0.625706737 0.17674601 10.67455256 9443.553587 0.076064938 0.042187308 58.45693852 -1.766836067 0.56457854 S(ph)FDEQNVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFDEQNVPK 9 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 S(1)FDEQNVPK;S(1)FDEQNVPK 131.17 0.00035725 597790000 660140 507350 394330 440340 577680 395320 461770 841770 669880 547960 TRUE FALSE 634340.999 492880.8747 465594.2028 463066.0002 596261.6018 403313.6413 467421.2794 824387.1553 593838.0308 510846.1811 1.241745603 0.964832259 0.911417605 0.906468556 1.167203796 0.789501138 0.914994174 1.613767873 1.162459567 1 18.96252943 1.766854438 25 1.320672654 0.977996431 0.28288519 0.191925063 19.57092418 17302.73666 0.084499895 0.046865443 58.45941135 -1.766854438 -0.342676223 HCAPS(ph)PDRSPELSSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 HCAPSPDRSPELSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 HCAPS(0.835)PDRS(0.165)PELSSSR;HCAPS(0.999)PDRS(0.001)PELSSSR;HCAPS(1)PDRSPELSSSR 167.05 3.91E-09 809310000 297204 358610 282013 310959 335763 329669 324688 200949 331728 300828 TRUE FALSE 285588.9391 348382.7939 332979.0224 327007.6313 346563.1218 336335.1331 328661.6289 196799.3329 294071.6282 280452.6516 1.018314277 1.242216081 1.187291404 1.165999428 1.235727742 1.199258168 1.171897028 0.70172035 1.048560698 1 18.0973977 1.766855101 25 0.888941543 1.180484962 0.561783321 0.103299661 12.03865626 10643.17798 0.044219408 0.0245251 58.45950063 -1.766855101 0.291543419 LRDDQYTLEHMHAFGMYNYLHCDSWYQDSVYYIDTLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRDDQYTLEHMHAFGMYNYLHCDSWYQDSVYYIDTLGR 38 1 Q96RS6-2;Q96RS6;E5RHQ3;E5RGX7 Q96RS6-2 NUDCD1 NudC domain-containing protein 1 0 40.146 0.044239 243150000 35600 34631 22981 21818 31568 27746 28432 10517 31137 17316 FALSE TRUE 34208.71264 33643.35779 27134.17791 22944.02959 32583.41339 28307.04313 28779.95932 10299.82027 27602.4583 16143.1719 2.119082474 2.084061175 1.680845504 1.421283856 2.018402183 1.753499455 1.782794578 0.638029524 1.709853458 1 13.97863645 1.766882157 25 1.089218314 1.828384968 0.526998818 0.312711783 15.13438553 13367.26985 0.140589254 0.077974032 58.46314262 -1.766882157 0.739166655 EHLASK ddPTM_BT-474_Pertuzumab_2h_R1 5 EHLASK 6 0 Q96TA1;Q96TA1-2;Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q96TA1;Q9P0K7-3 FAM129B;RAI14 Niban-like protein 1;Ankycorbin 0 ;;;; 98.415 0.039961 1434110000 6683440 7118230 5433020 6762370 6371780 6287050 7252250 3956450 7244620 7240980 FALSE TRUE 6422243.776 6915225.05 6414887.571 7111376.726 6576734.09 6414178.459 7341005.205 3874747.925 6422241.11 6750541.975 0.951367135 1.024395534 0.950277414 1.053452708 0.974252751 0.950172369 1.087469011 0.573990642 0.95136674 1 22.6865719 1.76690833 25 0.798089309 0.997181365 0.25618576 0.115574908 19.77831032 17452.82218 0.049367016 0.027379876 58.46666606 -1.76690833 0.199092056 AQSGSDS(ph)SPEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQSGSDSSPEPK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQSGS(0.001)DS(0.649)S(0.35)PEPK 121.04 0.00040208 54148000 205720 178980 145990 157370 175560 177990 182880 206340 233450 224610 TRUE FALSE 197680.235 173875.6656 172373.6405 165491.8846 181207.0468 181589.0798 185118.1401 202079.0069 206949.7347 209396.9646 0.94404537 0.83036383 0.823190732 0.790326091 0.865375709 0.867200153 0.884053599 0.965052226 0.988312964 1 17.675881 1.766913145 1.452872158 1.000580858 0.846108785 0.71393702 0.037477615 0.206515093 0.833074559 0.029570214 0.011756696 58.46731432 -1.766913145 -0.154472074 SDHTLT(ph)SPGGGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDHTLTSPGGGGK 13 0 C9J0Q5;Q9Y618;Q9Y618-4 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SDHT(0.004)LT(0.498)S(0.498)PGGGGK 177.93 0.00016802 278290000 458340 493460 428750 515780 465010 496930 522780 360370 541990 538070 TRUE FALSE 440427.5661 479387.0039 506234.6625 542399.4676 479967.469 506978.2651 529177.938 352928.2336 480465.5674 501626.0396 0.877999807 0.955666106 1.009187368 1.081282519 0.956823273 1.010669752 1.054925176 0.703568407 0.95781624 1 18.93625272 1.766930609 25 0.85670373 0.994357451 0.198921267 0.090754276 23.49941514 20720.11296 0.040472822 0.022446981 58.46966546 -1.766930609 0.137653721 AS(ph)GDYDNDCTNPITPLCTQPDQVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASGDYDNDCTNPITPLCTQPDQVIK 25 0 Q8TAF3-4;Q8TAF3-3;Q8TAF3 Q8TAF3-4 WDR48 WD repeat-containing protein 48 1 AS(0.985)GDY(0.015)DNDCTNPITPLCTQPDQVIK 114.34 0.0011764 100750000 90503 98393 78204 86456 86528 47497 93743 106800 130420 114110 TRUE FALSE 86966.0427 95586.92798 92337.20244 90918.00452 89311.2517 48457.42188 94890.25488 104594.5427 115615.2684 106381.2281 0.817494254 0.898531909 0.867983987 0.854643307 0.839539582 0.455507262 0.891983075 0.983204881 1.086801407 1 16.69888407 1.766943158 3.315690485 1.032771509 0.796092434 0.421829365 0.121122437 0.230614832 5.045076359 0.070193948 0.034550855 58.47135498 -1.766943158 -0.236679075 NAEAVLQS(ph)PGLSGK ddPTM_BT-474_Pertuzumab_2h_R1 5 NAEAVLQSPGLSGK 14 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 1 NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK 350.45 7.07E-82 1783130000 3542510 3265120 2958800 2893580 3087360 3648190 3346690 4030560 4837110 4317220 TRUE FALSE 3404064.793 3172001.974 3493520.978 3042918.011 3186667.738 3721958.901 3387647.793 3947327.527 4288021.552 4024810.844 0.84577013 0.788112062 0.867996314 0.756040005 0.791755902 0.924753745 0.841691181 0.980748582 1.065397038 1 21.94048955 1.766951192 1.328106435 1.040306995 0.817444017 0.765599823 0.047168474 0.188911854 0.629121608 0.036999217 0.014636934 58.47243658 -1.766951192 -0.222862977 TVHRDS(ph)EEEDDYLFDDPLPIPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVHRDSEEEDDYLFDDPLPIPLR 23 1 B3KSJ7;Q96SD1-2;Q96SD1-3;Q96SD1 B3KSJ7 DCLRE1C Protein artemis 1 T(0.21)VHRDS(0.79)EEEDDYLFDDPLPIPLR 119.22 0.00012564 53228000 37017 41262 32868 37417 40309 41045 39836 33654 42396 42411 TRUE FALSE 35570.33472 40085.24816 38807.97874 39348.09585 41605.57559 41874.95802 40323.52488 32959.03314 37583.38382 39538.46519 0.899638733 1.01382914 0.981524663 0.995185212 1.052280997 1.059094171 1.019855593 0.833594146 0.950552421 1 15.27096925 1.767090322 25 0.911278528 1.006390045 0.249847022 0.057191651 22.22711362 19488.49156 0.026061913 0.014454622 58.49117184 -1.767090322 0.095111517 TMFAQVES(ph)DDEEAKNEPEWK ddPTM_BT-474_Pertuzumab_2h_R1 8 TMFAQVESDDEEAKNEPEWK 20 1 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 T(0.152)MFAQVES(0.848)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK 235.69 9.13E-30 4880250000 3866705 2940943 2519841 2086642 2822730 2504248 2804361 4888870 4053123 3373025 TRUE FALSE 3715589.894 2857070.185 2975232.322 2194333.844 2913525.674 2554885.61 2838681.609 4787913.126 3593029.469 3144567.012 1.181590305 0.908573477 0.946150077 0.697817485 0.92652682 0.812476122 0.902725748 1.522598535 1.14261501 1 21.58442995 1.767100043 25 1.273083731 0.900735351 0.405888165 0.168669028 16.30660619 14292.58181 0.074780696 0.041475052 58.49248104 -1.767100043 -0.37234838 SHHANS(ph)PTAGAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHHANSPTAGAAK 13 0 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 SHHANS(0.996)PT(0.003)AGAAK 89.506 0.0047782 15113000 14002 18719 18364 23744 17687 16904 22026 4098.9 22333 16383 TRUE FALSE 13454.78636 18185.15245 21682.7833 24969.43069 18255.91842 17245.81046 22295.56078 4014.256283 19797.85147 15273.36482 0.880931381 1.190644803 1.419646788 1.634834955 1.195278096 1.129142836 1.459767448 0.262827238 1.296233784 1 13.89873031 1.767141189 25 0.780152719 1.280780596 0.269880977 0.309399675 22.62566431 19802.60246 0.138978535 0.077081246 58.49802305 -1.767141189 0.500627877 GDTHPLTLDEILDETQHLDIGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDTHPLTLDEILDETQHLDIGLK 23 0 P29084;E5RH41;E5RIW4 P29084 GTF2E2 Transcription initiation factor IIE subunit beta 0 356.24 4.26E-102 38362000 55636 44747 40606 40328 46438 46565 48712 35001 50035 51304 FALSE TRUE 53461.68361 43470.85937 47944.40748 42409.33291 47931.72044 47506.5762 49308.15203 34278.21712 44355.23656 47829.13438 1.11776398 0.908878238 1.002410102 0.886684099 1.002144845 0.993256031 1.030922944 0.716680692 0.927368583 1 15.54560206 1.767179322 25 0.85226873 0.985367554 0.217953643 0.09037475 24.03034742 21003.97486 0.039104849 0.021688518 58.50315957 -1.767179322 0.133098825 SREDLS(ph)AQPVQTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SREDLSAQPVQTK 13 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.003)REDLS(0.997)AQPVQTK 247.21 7.82E-17 699830000 349270 321030 266100 273130 269880 279490 295960 386860 373960 331260 TRUE FALSE 335620.1423 311874.5387 314190.1894 287226.272 278560.9353 285141.4793 299582.047 378871.2058 331509.6286 308823.4651 1.086770211 1.009879669 1.017377968 0.930066217 0.902007026 0.923315458 0.970075402 1.226821303 1.073459973 1 18.23642285 1.767185003 25 1.122608468 0.973120006 0.358586574 0.073440851 18.86152188 16482.83314 0.034454984 0.019109933 58.50392485 -1.767185003 -0.149488462 VHVQFFDDSPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHVQFFDDSPTR 12 0 P52701;P52701-2;A0A087WWJ1;A0A494C0M1;F8WAX8;C9J7Y7;C9J8Y8;C9JH55 P52701 MSH6 DNA mismatch repair protein Msh6 0 ; 197.07 1.99E-07 895060000 778750 909990 705890 841760 840850 812230 886900 555930 890660 907570 FALSE TRUE 748315.589 884037.9762 833460.0254 885203.3345 867896.7039 828653.8471 897754.1475 544449.8512 789556.0108 846099.4755 0.884429799 1.044839291 0.985061508 1.046216621 1.025762016 0.979381114 1.061050353 0.643482081 0.933171611 1 19.69046776 1.767191646 25 0.822578216 1.006210994 0.289909722 0.099128626 18.92333787 16533.01617 0.042436485 0.023536163 58.50481985 -1.767191646 0.183632778 QAPGLLWDASHQQEQPTSSSHHGGAGAVEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 QAPGLLWDASHQQEQPTSSSHHGGAGAVEIR 31 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 0 166.75 4.36E-13 170770000 19507 35027 26754 50773 35156 38291 37231 8441.5 32268 33321 FALSE TRUE 18744.64487 34028.06426 31589.04294 53393.40061 36286.82467 39065.27026 37686.64412 8267.180075 28605.07192 31064.13899 0.603417493 1.095413083 1.016897425 1.718811541 1.168125879 1.2575681 1.213188111 0.2661326 0.92083904 1 14.92296245 1.767272459 25 0.656683051 1.172195704 0.264414733 0.316460218 23.23413758 20242.1167 0.145185209 0.080524105 58.51570726 -1.767272459 0.515512653 VTSSMSSPS(ph)MQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTSSMSSPSMQPK 13 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 VTSSMS(0.005)S(0.437)PS(0.559)MQPK 189.99 1.87E-05 259540000 338790 342490 288790 297010 310630 313120 321770 404650 398120 361180 TRUE FALSE 325549.7122 332722.5205 340980.7771 312338.7217 320621.6961 319451.5009 325707.9175 396293.8361 352927.0867 336716.9569 0.96683492 0.98813711 1.012662921 0.927600215 0.952199435 0.948724127 0.967304767 1.176934597 1.048141709 1 18.36117685 1.76728884 25 1.092426129 0.966142794 0.518159796 0.047200043 13.63072486 11868.62665 0.020833511 0.011554825 58.51791451 -1.76728884 -0.126283336 GTPKPPGPPAQPPGPPNASS(ph)NPDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTPKPPGPPAQPPGPPNASSNPDLR 25 1 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 GTPKPPGPPAQPPGPPNAS(0.043)S(0.957)NPDLR 195.54 5.47E-25 1150400000 293040 374290 337350 404680 328500 307710 328190 486140 398110 412960 TRUE FALSE 281587.6728 363615.6157 398316.6493 425565.5833 339066.5008 313932.107 332206.4874 476101.0391 352918.2218 384989.8514 0.731415833 0.944481041 1.034615972 1.10539429 0.880715426 0.815429565 0.862896739 1.236658674 0.91669487 1 18.55446089 1.767382821 25 1.074642751 0.919441543 0.200739742 0.124943186 31.9243719 27706.6803 0.059450527 0.032973785 58.53057914 -1.767382821 -0.155201208 ESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR 34 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 43.438 0.041668 474200000 47147 55735 42396 44099 61019 61200 52424 13715 58539 27188 FALSE TRUE 45304.44312 54145.49237 50057.90029 46374.95467 62981.73155 62437.50593 53065.58059 13431.78046 51893.89814 25346.53254 1.787402006 2.136209057 1.974940762 1.829637036 2.484826334 2.463354931 2.093603159 0.529925757 2.04737662 1 14.62950078 1.767406881 25 1.157375266 2.123034629 0.512227677 0.409753142 15.71556184 13627.91305 0.18169168 0.10077193 58.53382182 -1.767406881 0.965659363 NKFDVDAADEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NKFDVDAADEK 11 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ;;; 157.52 2.79E-05 2747580000 6867300 5648430 5697910 5330930 5754130 4930770 6332330 7988740 9258420 8557130 FALSE TRUE 6598918.324 5487342.307 6727649.086 5606059.936 5939216.817 5030473.548 6409826.949 7823769.727 8207442.976 7977547.963 0.827186293 0.687848238 0.843322925 0.702729706 0.744491521 0.630578916 0.803483348 0.980723621 1.028817754 1 22.92751395 1.767417482 3.150147258 1.011586639 0.739060446 0.796483304 0.05972327 0.09365025 1.847546766 0.032316722 0.015714198 58.53525061 -1.767417482 -0.272526193 RVS(ph)LSEIGFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVSLSEIGFGK 11 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RVS(0.859)LS(0.141)EIGFGK;RVS(0.989)LS(0.011)EIGFGK 158.29 1.84E-05 2208940000 5296400 5129300 4162600 4575000 4823600 4704500 4842600 5410900 5644600 5384400 TRUE FALSE 5089410.833 4983017.386 4914874.417 4811116.298 4978755.475 4799628.213 4901865.187 5299163.024 5003848.672 5019709.792 1.013885472 0.992690333 0.979115252 0.958445109 0.991841298 0.956156513 0.976523622 1.055671193 0.996840232 1 22.25917253 1.767429763 25 1.022929238 0.980162334 0.358441619 0.021843249 19.41687668 16824.19395 0.009919888 0.005501671 58.53690588 -1.767429763 -0.042766904 HLAPPPLLS(ph)PLLPSIKPTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLAPPPLLSPLLPSIKPTVR 20 1 Q14676;Q14676-3;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 HLAPPPLLS(0.998)PLLPS(0.001)IKPT(0.001)VR 82.477 0.0023166 337090000 228400 242120 225660 223560 229280 262820 248980 175590 257560 252970 TRUE FALSE 219473.8755 235214.9747 266441.7818 235097.9584 236654.9994 268134.4005 252027.0917 171964.0051 228322.8686 235836.1166 0.930620291 0.997366214 1.129775141 0.996870038 1.003472254 1.136952238 1.068653501 0.729167388 0.968142081 1 17.84742515 1.767454697 25 0.872005767 1.04059875 0.318854355 0.090169794 20.16609109 17458.27619 0.040525027 0.022476787 58.54026676 -1.767454697 0.168592982 ILGSASPEEEQEKPILDRPT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 ILGSAS(0.011)PEEEQEKPILDRPT(0.989)R 121.35 4.80E-05 762500000 433230 401900 326280 326570 377040 346290 371190 479470 442420 447170 TRUE FALSE 416298.8926 390438.2055 385246.0541 343424.3168 389167.834 353292.2211 375732.7343 469568.7769 392198.3364 416882.7776 0.998599403 0.936565928 0.924111224 0.823791088 0.933518617 0.847461781 0.901291093 1.126380849 0.940788052 1 18.66928225 1.767536501 25 1.034169617 0.906210165 0.402150806 0.062595935 18.66497986 16113.07428 0.028254993 0.015671117 58.55129448 -1.767536501 -0.127959451 GPTTGEGALDLSDVHS(ph)PPKS(ph)PEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPTTGEGALDLSDVHSPPKSPEGK 24 1 O95684;O95684-2 O95684 FGFR1OP FGFR1 oncogene partner 2 GPTTGEGALDLS(0.186)DVHS(0.814)PPKS(1)PEGK 73.548 0.035725 116220000 139680 91618 99547 104040 110240 128230 133920 135010 193510 172620 TRUE FALSE 134221.1512 89005.14434 117537.3573 109409.5169 113785.9697 130822.8985 135558.953 132221.9963 171543.5561 160928.2936 0.834043213 0.553073312 0.730370991 0.679865016 0.707060065 0.812926649 0.842356244 0.82162057 1.065962685 1 17.29605847 1.767541986 0.768000299 1.027431254 0.688106054 0.687275009 0.07967464 0.33536648 0.383272741 0.06796905 0.031859499 58.55203398 -1.767541986 -0.339325201 CQSLTEDLEFR ddPTM_BT-474_Pertuzumab_2h_R1 3 CQSLTEDLEFR 11 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;; 234.99 3.81E-15 816680000 679700 765930 681740 932820 691420 672900 848890 951010 1060950 1113210 FALSE TRUE 653136.5726 744086.4263 804945.5832 980962.952 713660.1522 686506.499 859278.9698 931371.3112 940515.4039 1037811.295 0.629340397 0.716976612 0.775618445 0.945222852 0.687658879 0.661494534 0.827972266 0.897438017 0.906248957 1 19.98511271 1.767588574 2.084296942 0.944364838 0.744635612 0.522883261 0.084834504 0.271504472 2.353222711 0.059876271 0.025818522 58.55831537 -1.767588574 -0.199729226 IFQVAQELSGEDMHQFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 IFQVAQELSGEDMHQFHR 18 0 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1 C4P0D6 DISC1;TSNAX Translin-associated protein X 0 127.78 1.43E-05 194900000 161480 196210 174660 187270 195450 190450 201180 22986 181310 157560 FALSE TRUE 155169.1831 190614.2829 206224.9473 196935.0271 201736.8268 194301.0295 203642.101 22511.33107 160728.4489 146888.3209 1.056375226 1.297681679 1.403957415 1.340712631 1.37340277 1.322780656 1.386373674 0.153254738 1.094222114 1 17.16436017 1.767611271 25 0.666567101 1.318553718 0.500544689 0.253404796 14.23921755 12260.74949 0.109078855 0.060498779 58.56137571 -1.767611271 0.651986617 LEALESHPTDELER ddPTM_BT-474_Pertuzumab_2h_R1 2 LEALESHPTDELER 14 0 O15211;O15211-2 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 0 ; 173.44 2.70E-06 266740000 190599 222070 210026 249670 242910 258980 231160 206977 215341 238480 FALSE TRUE 183150.1804 215736.781 247982.3702 262555.4986 250723.4208 264216.753 233989.0052 202702.8526 190896.3925 222327.5372 0.823785405 0.970355646 1.115392062 1.180940076 1.127720947 1.18841218 1.052451748 0.911730752 0.858626848 1 17.76232712 1.767652903 4.624969753 0.913616711 1.076531035 0.268531071 0.106500478 0.25329591 11.38593348 0.058089535 0.030575408 58.56698984 -1.767652903 0.162914324 LCVQNSHQEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LCVQNSHQEAR 11 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 0 ;;; 220.29 9.25E-12 1878570000 1428620 1287150 1128410 1064400 1193420 1013490 1354780 1482250 1771140 1660980 FALSE TRUE 1372787.951 1250441.742 1332338.788 1119333.812 1231807.438 1033983.462 1371360.203 1451641.02 1570087.612 1548480.345 0.886538828 0.807528327 0.860416984 0.722859554 0.795494397 0.667740773 0.885616797 0.937461702 1.013953853 1 20.56242164 1.767697865 2.339361819 0.99603979 0.791660034 0.659797812 0.062084009 0.16777003 1.838235072 0.039530258 0.017660882 58.57305344 -1.767697865 -0.204379756 LHEENFEITTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHEENFEITTLR 12 0 Q96Q11-2;Q96Q11;A0A494C1L4;F8W8C3;A0A494C181;A0A494C1D4 Q96Q11-2 TRNT1 "CCA tRNA nucleotidyltransferase 1, mitochondrial" 0 172.76 3.49E-05 501880000 210050 204600 179120 234100 218790 217710 237220 124810 240580 229260 FALSE TRUE 201841.0138 198765.0083 211490.9685 246181.9291 225827.5791 222112.2454 240123.1693 122232.6299 213270.367 213732.016 0.944364899 0.92997302 0.989514685 1.151825233 1.056592191 1.03920905 1.123477773 0.571896678 0.997840057 1 17.70544351 1.76771138 25 0.812890111 1.033538026 0.260416818 0.130596625 22.79055421 19556.48229 0.058543015 0.032470115 58.57487629 -1.76771138 0.220647915 GFGFITFEDEQSVDQAVNMHFHDIMGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFITFEDEQSVDQAVNMHFHDIMGK 27 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 309.99 3.22E-82 797960000 490490 500520 440380 438220 521060 565950 551100 50709 552030 359461 FALSE TRUE 471321.1085 486245.6597 519966.4622 460836.5867 537820.3681 577393.8968 557844.5267 49661.84143 489365.8687 335114.3863 1.406448448 1.45098414 1.551608894 1.375162051 1.604885944 1.722975558 1.664639148 0.148193702 1.460295018 1 18.3542941 1.76773067 24.99999867 0.78803097 1.53983617 0.476831842 0.318206272 15.79400545 13543.80186 0.137988882 0.076534037 58.57747807 -1.76773067 0.7518052 MDYYDSEHHEDFEFISGTR ddPTM_BT-474_Pertuzumab_2h_R1 3 MDYYDSEHHEDFEFISGTR 19 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;; 230.29 3.50E-20 525690000 385690 444117 392802 537462 472292 489592 498676 190353 446207 499664 FALSE TRUE 370616.8084 431451.218 463790.0592 565200.4782 487483.7011 499491.8857 504778.9461 186422.144 395555.452 465821.3122 0.79562012 0.926216141 0.995639416 1.213341819 1.046503645 1.072282166 1.083632141 0.400200977 0.849157051 1 18.82941712 1.767746769 25 0.689029802 1.0251421 0.312060476 0.176244483 20.43571444 17514.52483 0.079702027 0.044205443 58.57964955 -1.767746769 0.336112298 TS(ph)PTVATQTGASATSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSPTVATQTGASATSTR 17 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.007)S(0.986)PT(0.007)VATQTGASATSTR;T(0.007)S(0.992)PT(0.001)VATQTGASATSTR;T(0.015)S(0.983)PT(0.002)VATQTGASATSTR;T(0.167)S(0.815)PT(0.018)VATQTGASATSTR 271.49 1.37E-35 1407150000 780914 713177 618727 669503 644954 695309 695393 821570 850110 749665 TRUE FALSE 750395.0175 692837.8902 730544.7324 704056.1301 665699.5311 709368.6244 703903.4275 804604.2924 753609.0768 698889.5218 1.073696191 0.991341076 1.045293583 1.007392597 0.95251039 1.014993933 1.007174103 1.151261061 1.078295 1 19.41470489 1.76777271 25 1.091912853 1.011105235 0.26669665 0.045946097 21.66720633 18553.46953 0.02026788 0.011241311 58.58314867 -1.76777271 -0.080807619 QGTEIDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QGTEIDGR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 158.87 0.0013632 0 3051300 3439900 2640800 3230900 3130700 3365600 3113600 3124300 3172400 3440000 FALSE TRUE 2932051.823 3341797.42 3118051.304 3397647.136 3231401.809 3433654.738 3151705.168 3059782.113 2812282.452 3207005.736 0.914264602 1.042030384 0.972262466 1.059445294 1.007607119 1.070673089 0.982756324 0.954093121 0.876918435 1 21.6127955 1.76778983 3.015147757 0.934386898 1.013053083 0.251534359 0.050880077 0.278032893 5.026353917 0.027327783 0.013143083 58.58545814 -1.76778983 0.078666185 ERDLS(ph)RDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDLSRDR 8 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 ERDLS(1)RDR 79.659 0.033558 0 106920 117620 68434 91747 92545 102710 94877 78714 85366 86854 TRUE FALSE 102741.4482 114265.5928 80801.54611 96482.07366 95521.79397 104786.8666 96038.13311 77088.52839 75675.60956 80971.30122 1.268862506 1.411186322 0.997903515 1.191558888 1.179699382 1.294123535 1.186076198 0.952047543 0.934597918 1 16.30512304 1.767798801 4.356635088 0.956028822 1.219913152 0.583044734 0.099520791 0.14286976 5.582051953 0.05218958 0.027204068 58.58666823 -1.767798801 0.26388433 HYFQNTQGLIFVVDSNDRER ddPTM_BT-474_Pertuzumab_2h_R1 6 HYFQNTQGLIFVVDSNDRER 20 1 P61204;F5H423;F5H0C7;P84077;P84085;C9J1Z8;P18085;C9JPM4;C9JAK5 P61204;P84077;P84085;P18085 ARF3;ARF1;ARF5;ARF4 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 ;;;;; 306.11 1.63E-55 6741250000 832590 998382 583386 779443 907619 974547 854274 535243 901007 766822 FALSE TRUE 800051.4623 969909.1229 688816.8276 819670.1466 936813.3894 994253.0081 864728.8608 524190.045 798728.4627 714884.4629 1.119133935 1.356735491 0.963535876 1.146577089 1.310440271 1.390788386 1.209606455 0.733251416 1.117283287 1 19.44735057 1.767804855 25 0.925633471 1.217635897 0.399451091 0.147172451 20.15344585 17238.27375 0.067925343 0.037673915 58.58748493 -1.767804855 0.292002426 FPLGDGQSLLLADALHTHSPLFLEGSSRDS(ph)PPLLDAPAS(ph)PPQASR ddPTM_BT-474_Pertuzumab_2h_R1 1 FPLGDGQSLLLADALHTHSPLFLEGSSRDSPPLLDAPASPPQASR 45 1 Q9BZ71;Q9BZ71-3;Q9BZ71-2 Q9BZ71 PITPNM3 Membrane-associated phosphatidylinositol transfer protein 3 2 FPLGDGQSLLLADALHTHSPLFLEGS(0.102)S(0.141)RDS(0.756)PPLLDAPAS(0.867)PPQAS(0.133)R 89.567 2.87E-05 90403000 17198 19840 24489 19969 20447 23045 22449 10533 25368 15921 TRUE FALSE 16525.88315 19274.18263 28914.70705 20999.60248 21104.69632 23510.98569 22723.73758 10315.48987 22488.33099 14842.65649 1.113404677 1.298566914 1.948081671 1.414814289 1.421894816 1.584014675 1.530975105 0.694989463 1.515114967 1 13.8574617 1.767811779 25 1.043840313 1.484716733 0.309699046 0.274551106 24.38906093 20856.27021 0.124031955 0.068792832 58.58841903 -1.767811779 0.440876421 RAEENALQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RAEENALQQK 10 1 P15924;P15924-3 P15924 DSP Desmoplakin 0 135.56 0.00022608 297560000 449880 462020 412390 410900 400050 370220 435680 479590 537180 499650 FALSE TRUE 432298.1922 448843.642 486918.0466 432106.5982 412917.9716 377706.1021 441011.9822 469686.2989 476201.5784 465808.2605 0.928060382 0.963580254 1.045318617 0.927649067 0.886454807 0.810861752 0.946767199 1.008325396 1.022312438 1 18.8293767 1.767828427 4.351912421 1.011902128 0.928545328 0.308397892 0.055560549 0.278118983 10.83815353 0.032079785 0.016719192 58.59066498 -1.767828427 -0.083356799 QWALEDFEIGRPLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 QWALEDFEIGRPLGK 15 1 A3KFJ0;O14965;A3KFJ1;Q5QPD4;Q5QPD2 A3KFJ0 AURKA Aurora kinase A 0 137.52 1.48E-05 313860000 366000 398520 344860 375760 358360 387880 376540 342730 340140 430090 FALSE TRUE 351696.3154 387154.5998 407183.8734 395153.0186 369886.9749 395723.1994 381148.2092 335652.5057 301528.7332 400959.6212 0.877136491 0.965570046 1.015523389 0.985518236 0.9225043 0.986940276 0.950590007 0.837122962 0.752017703 1 18.61309743 1.767837798 5.392786863 0.846355444 0.96159411 0.282343631 0.067441265 0.186727398 12.29856583 0.031511581 0.01694486 58.59192923 -1.767837798 0.115238666 ILHVDNHIGISIAGLTADAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILHVDNHIGISIAGLTADAR 20 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ; 170.53 5.30E-12 693830000 269730 257740 221560 282140 289990 272190 302350 116181 291090 285690 FALSE TRUE 259188.6534 250389.5076 261600.8206 296701.2792 299317.7917 277693.8683 306050.2497 113781.8217 258046.6835 266339.9618 0.973149698 0.940112426 0.982206421 1.1139946 1.123818557 1.042629376 1.149096244 0.427205219 0.968862058 1 18.02290938 1.767840516 25 0.740369155 1.045299558 0.313723898 0.161122545 20.27271593 17319.15654 0.071117775 0.039445094 58.59229593 -1.767840516 0.304930403 RGS(ph)LPAGASWQNTDLFEMIEK ddPTM_BT-474_Pertuzumab_2h_R1 5 RGSLPAGASWQNTDLFEMIEK 21 1 J3KPC5;P47736-3 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RGS(0.938)LPAGAS(0.062)WQNTDLFEMIEK;RGS(0.996)LPAGAS(0.004)WQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK 274.58 5.85E-45 1259928000 1426110 1279839 1153358 1045888 1293254 1138186 1196081 1744743 1530790 1403677 TRUE FALSE 1370376.045 1243339.245 1361795.447 1099866.405 1334852.689 1161200.901 1210718.997 1708713.447 1357021.137 1308604.707 1.047203971 0.950125915 1.040646912 0.840487887 1.020057992 0.887358035 0.925198412 1.305752179 1.036998515 1 20.31959793 1.767862872 25 1.144942049 0.956611974 0.330462897 0.098551456 19.70507406 16821.36421 0.042610678 0.023633234 58.59531207 -1.767862872 -0.188330075 DKGATKES(ph)SEKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKGATKESSEKDR 13 3 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 DKGAT(0.009)KES(0.958)S(0.033)EKDR 95.205 0.026541 642690000 806740 523310 505520 378690 465620 481270 539490 703970 814450 637700 TRUE FALSE 775211.7089 508385.7112 596878.7092 398234.2363 480597.0902 491001.6091 546092.44 689432.7735 721997.0505 594508.011 1.303955026 0.855136856 1.003987664 0.669855122 0.808394641 0.825895699 0.918561954 1.159669442 1.214444612 1 19.18133672 1.767907543 5.329631514 1.139664915 0.895780177 0.255199968 0.164145629 0.226560585 14.46744898 0.080647263 0.043311196 58.60133948 -1.767907543 -0.243884738 SDVEDHSVHLLFSANR ddPTM_BT-474_Pertuzumab_2h_R1 3 SDVEDHSVHLLFSANR 16 0 P23919-2;P23919;H7C312;G5E9E9;H7C3A4;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 ;; 259.96 5.28E-27 771280000 499168 644762 563862 756180 639940 659041 689688 36937.9 676535 437892 FALSE TRUE 479659.9627 626374.019 665764.4064 795206.5404 660524.2513 672367.2606 698128.6081 36175.11946 599737.5831 408233.1848 1.174965634 1.534353508 1.630843428 1.94792234 1.618007247 1.64701765 1.710122141 0.088613863 1.469105417 1 18.63903394 1.767960967 25 0.76613705 1.621840464 0.469704958 0.364705105 16.42814507 13977.16677 0.159954091 0.088717631 58.6085487 -1.767960967 0.855703414 HIAEDADR ddPTM_BT-474_Pertuzumab_2h_R1 3 HIAEDADR 8 0 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;; 157.68 0.00037306 3912400000 1278210 1391210 1091230 1271000 1285450 1154870 1277900 977900 1368370 1266340 FALSE TRUE 1228256.14 1351534.053 1288439.535 1336596.462 1326797.667 1178222.263 1293539.322 957706.0233 1213038.374 1180569.664 1.040392768 1.144815164 1.091371034 1.132162297 1.12386224 0.998011637 1.095690803 0.811223643 1.027502579 1 20.17105174 1.767970191 25 0.928089471 1.09112086 0.479808556 0.067538734 16.06452661 13663.50861 0.029774172 0.01651393 58.60979353 -1.767970191 0.163031389 AHLTVGQAAAGGS(ph)GNLLTER ddPTM_BT-474_Pertuzumab_2h_R1 6 AHLTVGQAAAGGSGNLLTER 20 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER 288.73 2.31E-46 5465180000 2030666 2925100 2246759 3517730 2151860 2724640 2873670 1465511 2685324 3009138 TRUE FALSE 1951305.328 2841679.012 2652798.33 3699280.467 2221076.531 2779734.088 2908838.833 1435247.686 2380497.277 2805326.403 0.695571583 1.012958424 0.945629117 1.31866312 0.79173551 0.990877241 1.036898533 0.51161522 0.848563388 1 21.41973721 1.767980654 25 0.736649745 0.978341069 0.145491433 0.192086566 31.0139377 26369.17989 0.085135931 0.047220093 58.61120553 -1.767980654 0.241691324 (ac)AAGVAGWGVEAEEFEDAPDVEPLEPTLSNIIEQR ddPTM_BT-474_Pertuzumab_2h_R1 3 AAGVAGWGVEAEEFEDAPDVEPLEPTLSNIIEQR 34 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ;; 148.75 5.27E-60 232759000 8049.7 7193 8230.3 7020.9 4747.3 10075.3 5784 12495.6 7369.9 8323.1 FALSE TRUE 7735.108825 6987.862683 9717.698292 7383.24949 4900.001216 10279.02947 5854.786322 12237.56149 6533.299849 7759.369024 0.996873431 0.900570995 1.252382541 0.951527047 0.631494803 1.324724915 0.754544127 1.577133586 0.841988547 1 12.92172362 1.767993243 25 1.200013295 0.980655712 0.064297748 0.261379197 45.73145672 38865.91599 0.113805221 0.063121569 58.61290449 -1.767993243 -0.219357583 RPAEATSS(ph)PTSPERPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEAT(0.004)S(0.087)S(0.464)PT(0.233)S(0.211)PERPR;RPAEAT(0.215)S(0.215)S(0.543)PT(0.022)S(0.004)PERPR 132.12 3.22E-05 5151150000 159116 186612 142246 160787 169971 184787 166578 159770 174558 165159 TRUE FALSE 152897.5708 181290.0085 167953.0164 169085.2363 175438.2716 188523.5197 168616.6314 156470.6937 154742.9076 153972.6338 0.993017831 1.177417077 1.09079784 1.098151224 1.139412032 1.224396278 1.095107794 1.016224051 1.005002667 1 17.23231443 1.768013793 3.648760203 1.005851772 1.123924578 0.441987377 0.056912614 0.193057493 5.121895758 0.030044175 0.015131097 58.61567802 -1.768013793 0.118072807 VHDRS(ph)EEEEEEEEEEEEEQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 VHDRSEEEEEEEEEEEEEQPR 21 1 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR 347.54 1.74E-95 7557520000 666505 648653 553451.7 769105 650265 798243 731518 267723.8 722100 622062 TRUE FALSE 640457.2477 630154.0515 653472.7337 808798.6012 671181.3643 814384.0204 740470.5361 262195.21 640130.2353 579929.1867 1.104371469 1.086605168 1.126814702 1.394650623 1.157350552 1.404281831 1.276829229 0.452115907 1.103807585 1 19.14551722 1.768031615 25 0.798448081 1.223939218 0.432329122 0.191128535 17.7347956 15052.67743 0.085308097 0.047315637 58.61808352 -1.768031615 0.425491137 KVDQPPEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVDQPPEAK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 99.522 0.008466 445630000 918850 918040 768750 778800 864030 986430 951260 1059680 1310270 1234070 FALSE TRUE 882940.3262 891858.3981 907680.2258 818993.9613 891822.3096 1006376.29 962901.8044 1037797.238 1161533.643 1150485.34 0.767450306 0.77520188 0.788954187 0.711868229 0.775170512 0.874740647 0.836952694 0.902051684 1.009603167 1 20.13381117 1.768078204 0.817820178 1.013899994 0.762574789 0.879865366 0.033235017 0.195028122 0.248918124 0.030727629 0.013862359 58.62437213 -1.768078204 -0.251325206 GSSGENNNPGS(ph)PTVSNFR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSSGENNNPGSPTVSNFR 18 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(0.972)PT(0.028)VSNFR;GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(1)PTVSNFR 481.89 1.24E-239 1595570000 1639540 1874960 1502130 1985060 1873610 1789610 1499120 1434110 1320240 1193890 TRUE FALSE 1575464.964 1821487.977 1773598.306 2087509.184 1933876.367 1825797.14 1517466.679 1404495.127 1170371.89 1113026.767 1.415478056 1.636517675 1.593491153 1.875524692 1.737493136 1.640389247 1.363369439 1.261870037 1.051521783 1 20.08605686 1.768107925 1.327151114 1.020456332 1.664727589 0.822416153 0.116185521 0.173776664 0.577731505 0.098295969 0.038915926 58.62838423 -1.768107925 0.644271256 RS(ph)YDVPPPPMEPDHPFYSNISK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 RS(0.542)Y(0.458)DVPPPPMEPDHPFYSNISK 125.58 9.87E-06 335070000 174580 169590 136160 153420 149230 155270 150380 186160 192490 148970 TRUE FALSE 167757.2206 164753.4592 160767.1409 161338.0246 154030.1185 158409.6658 152220.3954 182315.7309 170639.3422 138880.1292 1.207928172 1.186299726 1.157596423 1.161707046 1.109086803 1.140621532 1.096055975 1.312756058 1.228680756 1 17.08348067 1.768108241 25 1.214142034 1.151276813 0 0.080821101 50.14398803 42449.99488 0.035389189 0.019629666 58.62842689 -1.768108241 -0.06286522 AQVLATIHGHAGAFPAAGDAGEGAPGGGSS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGSSPER 33 0 Q86WR7;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.034)S(0.966)PER 170.44 3.58E-14 227560000 96236 101290 87646 111350 110030 112130 103970 36061 91101 97656 TRUE FALSE 92474.99073 98401.30837 103485.5819 117096.7868 113569.2149 114397.3454 105242.416 35316.32775 80759.59641 91041.67214 1.015743544 1.080838105 1.136683669 1.286188886 1.247442102 1.256538272 1.155980701 0.387913874 0.887061875 1 16.47423944 1.768151382 25 0.698486995 1.174843953 0.547190599 0.168294517 14.09555942 11915.36344 0.075081912 0.041643887 58.63425098 -1.768151382 0.476356957 VAHSFNCTPIEGMLSHQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAHSFNCTPIEGMLSHQLK 19 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 265.64 1.13E-31 2511200000 2373000 2271500 1902460 2028340 2139900 2428500 2372800 1755500 2453400 2549900 FALSE TRUE 2280260.537 2206719.044 2246276.842 2133022.87 2208731.827 2477605.934 2401839.036 1719248.312 2174900.317 2377193.002 0.959223982 0.928287708 0.944928258 0.897286366 0.929134414 1.042240126 1.010367704 0.723226221 0.914902709 1 21.18082761 1.768238071 25 0.850446982 0.956780172 0.155451261 0.076251476 29.2911431 24688.2268 0.03455364 0.019165415 58.64595612 -1.768238071 0.10633319 DAEVERDEER ddPTM_BT-474_Pertuzumab_2h_R1 2 DAEVERDEER 10 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 ; 192.5 6.17E-07 514240000 588900 611200 461490 512060 540190 551780 548570 589690 631420 600850 FALSE TRUE 565885.1369 593769.1744 544891.5088 538487.478 557565.7019 562937.3697 555283.5638 577512.6954 559743.8487 560153.8943 1.01023155 1.060010794 0.972753228 0.9613206 0.995379498 1.004969126 0.991305371 1.030989343 0.999267977 1 19.09546372 1.768292127 25 1.013290005 0.999320903 0.029867512 0.025981462 83.13078098 69939.8834 0.01282919 0.007115242 58.65325612 -1.768292127 -0.013969102 APWNHGEER ddPTM_BT-474_Pertuzumab_2h_R1 1 APWNHGEER 9 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 119.16 0.0019321 0 119350 124570 130970 139060 133150 140310 144540 52932 140670 128430 FALSE TRUE 114685.6701 121017.3856 154639.1924 146236.9033 137432.8907 143147.1643 146308.9238 51838.9357 124701.7313 119731.3217 0.957858549 1.010741248 1.291551703 1.221375503 1.147844096 1.1955699 1.22197702 0.432960523 1.041513027 1 16.86944109 1.768306334 25 0.76839768 1.154147774 0.391153432 0.181549014 19.03709747 16008.69337 0.080966243 0.044908122 58.6551749 -1.768306334 0.385750094 DEVFHIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEVFHIHK 8 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 131.06 0.00059051 318950000 545070 566720 493060 531930 496320 440560 614480 5814.2 678290 315850 FALSE TRUE 523768.0618 550557.7005 582166.9101 559382.971 512284.5835 449468.4251 622000.1901 5694.134738 601293.3628 294457.1982 1.778757881 1.869737619 1.977085001 1.899708937 1.739759078 1.526430421 2.11236198 0.019337733 2.042039952 1 18.16769842 1.768350148 25 0.926970394 1.835548394 0.379436367 0.47774574 20.46512291 17184.22178 0.204190533 0.113254258 58.6610927 -1.768350148 0.908578 SGEWTEDEVLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGEWTEDEVLRR 12 1 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 134.49 0.00023175 181220000 339340 451460 433270 331610 360220 445860 362210 268040 245030 275050 FALSE TRUE 326078.2176 438584.8028 511571.527 348724.4318 371806.8034 454875.5947 366642.8343 262504.8803 217215.2216 256420.6185 1.271653658 1.71041161 1.995048331 1.359970325 1.449987936 1.77394313 1.429849271 1.023727662 0.847105131 1 17.96815275 1.768394796 2.786756509 0.924708211 1.600431947 0.668430989 0.20088596 0.145292036 2.247887464 0.119713254 0.056379159 58.66712364 -1.768394796 0.675723737 HPHTGDTK ddPTM_BT-474_Pertuzumab_2h_R1 4 HPHTGDTK 8 0 P51397;B4DQ75 P51397 DAP Death-associated protein 1 0 ;;; 125.31 0.0012673 222198000 433609 398017 355746 429194 349780 333224 403268 2329 377444 263589 FALSE TRUE 416663.0809 386665.9449 420037.2157 451344.7538 361030.9914 339962.0176 408203.3144 2280.905336 334598.1395 245735.8822 1.695572812 1.573502174 1.709303549 1.836706751 1.469183043 1.383444756 1.661146556 0.009281938 1.361616938 1 17.90674901 1.76846336 25 0.695741606 1.613797357 0.551216534 0.339194448 14.73686179 12327.41472 0.147050538 0.081562275 58.67638638 -1.76846336 0.918055752 RHS(ph)DVSLANADLEDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RHSDVSLANADLEDSR 16 1 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;Q9UQ26-2;D6RDY0;Q9UQ26-5;Q9UQ26-4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 RHS(1)DVSLANADLEDSR;RHS(0.984)DVS(0.016)LANADLEDSR 219.3 7.68E-15 984350000 262430 293910 205301 284540 281920 270130 276360 197676 272750 300630 TRUE FALSE 252173.9455 285527.9746 242403.4576 299225.1435 290988.2128 275592.2137 279742.1763 193593.9215 241788.5635 280268.0623 0.899759835 1.018767434 0.86489861 1.067639106 1.038249633 0.983316513 0.998123632 0.690745567 0.86270466 1 18.09644783 1.768557127 25 0.819557514 0.984043761 0.280834058 0.091457097 22.61567799 18858.88473 0.040089102 0.022235373 58.68905638 -1.768557127 0.164486247 ERS(ph)PS(ph)PLRGNVVPSPLPT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 ERSPSPLRGNVVPSPLPTR 19 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 ERS(1)PS(1)PLRGNVVPS(0.319)PLPT(0.681)R;ERS(1)PS(1)PLRGNVVPS(0.085)PLPT(0.915)R 105.58 0.00052956 3713100000 1213360 1326700 832270 901760 1070020 1236590 873380 938760 883200 795250 TRUE FALSE 1165940.55 1288863.815 982679.7027 948299.9417 1104438.165 1261594.697 884068.6857 919374.2779 782942.8387 741387.0092 1.572647666 1.738449419 1.325461184 1.279088964 1.489691823 1.7016682 1.192452356 1.240073358 1.056051467 1 19.49986731 1.768597358 1.468873429 1.039189529 1.50361273 0.609199842 0.152382569 0.28726095 1.185892939 0.124324888 0.049548212 58.69449331 -1.768597358 0.464423201 HFFLYGEFPGDER ddPTM_BT-474_Pertuzumab_2h_R1 1 HFFLYGEFPGDER 13 0 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 0 123.64 0.00015816 0 106170 109600 79505 103140 95646 100990 102850 68389 104280 104570 FALSE TRUE 102020.759 106474.3153 93873.32208 108463.0678 98722.54045 103032.087 104108.7091 66976.74325 92442.57158 97487.38076 1.046502206 1.092185619 0.962927933 1.11258572 1.012669944 1.056876143 1.06791985 0.687029877 0.94825167 1 16.57292786 1.768702524 25 0.847040516 1.049701936 0.442754564 0.086196085 17.04189719 14142.39053 0.03673153 0.02037362 58.70870814 -1.768702524 0.202661419 VHEIFQVDPETEQEITR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHEIFQVDPETEQEITR 17 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ; 181.41 8.05E-10 235820000 77194 83213 57956 88247 87366 101385 84939 58830 87571 85123 FALSE TRUE 74177.17314 80839.84671 68429.93842 92801.43825 90176.20673 103435.0742 85978.50889 57615.13994 77630.30721 79357.54339 0.934721136 1.018678795 0.862299102 1.169409161 1.136328103 1.303405697 1.083432087 0.726019701 0.978234757 1 16.27607975 1.76879122 25 0.874355651 1.077497912 0.245667751 0.134801546 30.58858887 25309.72366 0.065558169 0.036362807 58.72069949 -1.76879122 0.203142261 S(ph)PVGLDCCNCCLDLAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPVGLDCCNCCLDLAHR 17 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 S(1)PVGLDCCNCCLDLAHR 79.69 0.0083779 179790000 120030 94887 99729 110240 95904 118950 78011 95029 99113 76968 TRUE FALSE 115339.0949 92180.91566 117752.2488 115929.4996 98988.83926 121355.2505 78965.72195 93066.61794 87862.10776 71754.8888 1.607403995 1.284663905 1.64103451 1.615632071 1.379541393 1.69124714 1.100492569 1.297007347 1.224475561 1 16.13078951 1.768907697 0.843081922 1.062102924 1.53203607 0.547485366 0.155560076 0.439600657 0.592573189 0.132515775 0.058809617 58.73645031 -1.768907697 0.469933146 SSS(ph)LEGFHNHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLEGFHNHFK 12 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.181)S(0.181)S(0.638)LEGFHNHFK 205.62 1.67E-07 633710000 553540 591230 515900 616350 562830 673890 637500 36353 616270 433440 TRUE FALSE 531907.0448 574368.6993 609134.6061 648159.8974 580933.9381 687516.5175 645301.9157 35602.29785 546313.6132 404082.7227 1.316332065 1.421413654 1.507450262 1.604027742 1.437660918 1.701425176 1.596954978 0.088106459 1.351984588 1 18.62429114 1.768949246 25 0.725113858 1.51645318 0.506057867 0.312736746 16.3937865 13494.02339 0.134929206 0.074840729 58.74206999 -1.768949246 0.791339322 DDSHSAEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 5 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK;DDSHS(0.001)AEDS(0.999)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK 336.18 1.67E-72 3908741000 2958708 1928462 2245699 1780966 2361809 1721190 2634544 2905691 3827035 3172041 TRUE FALSE 2843078.42 1873464.152 2651546.765 1872881.869 2437778.731 1755993.641 2666786.338 2845687.465 3392606.031 2957195.838 0.96141026 0.633527252 0.896642262 0.633330348 0.82435485 0.593803636 0.901795648 0.96229253 1.147237524 1 21.49579836 1.768956688 2.269336643 1.062039521 0.756579357 0.517206442 0.120455923 0.201881819 2.078077909 0.070222797 0.031116693 58.74307647 -1.768956688 -0.305460164 EKNFDEFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKNFDEFSK 9 1 Q15648;Q15648-3 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 0 79.82 0.021473 0 526060 541740 426230 438450 526280 531570 520800 664910 720330 703800 FALSE TRUE 505500.9936 526290.1056 503259.2424 461078.457 543208.2742 542318.7096 527173.7062 651179.3761 638561.1583 656130.9991 0.770426933 0.802111326 0.767010312 0.702723172 0.827896068 0.826540295 0.803458009 0.992453301 0.973222053 1 19.32362436 1.768983668 3.778247694 0.990044923 0.783415779 0.879930528 0.034349651 0.071373138 2.031304816 0.019579517 0.009944186 58.74672603 -1.768983668 -0.206629143 SGSMDPSGAHPSVR ddPTM_BT-474_Pertuzumab_2h_R1 6 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;;;; 151.54 6.91E-06 2455261000 2274620 3301880 2485070 3417450 2758890 3148540 2858710 2714180 2553220 3181200 FALSE TRUE 2185725.336 3207713.615 2934177.429 3593825.004 2847632.202 3212205.636 2893695.748 2658131.235 2263389.17 2965734.49 0.736992925 1.081591635 0.989359445 1.211782449 0.960177727 1.083106275 0.975709645 0.896280919 0.763179973 1 21.49995801 1.768987439 3.137516098 0.868880927 1.019682948 0.156453277 0.125800333 0.356190971 6.94836432 0.067747825 0.032957088 58.74723613 -1.768987439 0.150802021 HASSSPES(ph)PKPAPAPGSHR ddPTM_BT-474_Pertuzumab_2h_R1 9 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HASSSPES(1)PKPAPAPGSHR;HASS(0.005)S(0.005)PES(0.99)PKPAPAPGSHR;HASS(0.001)S(0.001)PES(0.999)PKPAPAPGSHR;HAS(0.005)S(0.016)S(0.011)PES(0.969)PKPAPAPGSHR;HAS(0.243)S(0.243)S(0.243)PES(0.272)PKPAPAPGSHR;HASS(0.002)S(0.002)PES(0.996)PKPAPAPGSHR;HASSSPES(1)PKPAPAPGSHR;HAS(0.239)S(0.239)S(0.239)PES(0.284)PKPAPAPGSHR;HAS(0.223)S(0.223)S(0.223)PES(0.332)PKPAPAPGSHR 191.42 5.86E-15 4218549000 2095227 2646294 2036676 2670913 2387535 2627934 2525499 1390709 2311113 2719920 TRUE FALSE 2013343.212 2570824.286 2404748.659 2808759.14 2464332.232 2681072.626 2556406.812 1361990.373 2048765.141 2535697.396 0.793999795 1.01385295 0.948357901 1.107687039 0.971855804 1.057331459 1.008167148 0.537126542 0.807969099 1 21.27395116 1.769018425 24.99999824 0.734512765 0.992417107 0.315559216 0.132205387 21.58286118 17724.86755 0.057532639 0.031911613 58.75142775 -1.769018425 0.257904341 GVHIHQAGGS(ph)PPASSTSSSSLTNDVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GVHIHQAGGSPPASSTSSSSLTNDVAK 27 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 GVHIHQAGGS(0.846)PPAS(0.018)S(0.018)T(0.018)S(0.018)S(0.031)S(0.042)S(0.008)LTNDVAK;GVHIHQAGGS(0.505)PPAS(0.002)S(0.002)T(0.482)S(0.007)S(0.001)SSLTNDVAK 251.33 5.56E-47 1323120000 394110 445360 370560 415560 438950 478810 512230 38268.4 513560 369740 TRUE FALSE 378707.7455 432658.7689 437528.4351 437007.1014 453069.2254 488491.8663 518498.824 37478.14417 455262.8218 344697.1805 1.098667952 1.255185111 1.269312486 1.267800046 1.314397828 1.41716235 1.504215449 0.108727736 1.320761664 1 18.39496997 1.769083407 25 0.720393682 1.304003479 0.348581862 0.302128274 21.84659232 17903.23289 0.131012747 0.072668843 58.76021916 -1.769083407 0.583609796 LGIAVIHGEAQDAESDLVDGRHS(ph)PPMVR ddPTM_BT-474_Pertuzumab_2h_R1 24 LGIAVIHGEAQDAESDLVDGRHSPPMVR 28 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.005)DLVDGRHS(0.995)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.034)DLVDGRHS(0.966)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.042)DLVDGRHS(0.958)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.013)DLVDGRHS(0.987)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR 277.33 8.01E-62 41389576000 2668830.2 3109989 2510186.7 3227127.1 3115582.1 3398543 3244701.3 2206798 3286107.8 3427182.9 TRUE FALSE 2564529.365 3021295.159 2963833.275 3393679.516 3215797.628 3467263.868 3284410.925 2161226.85 2913082.619 3195056.75 0.802655341 0.945615492 0.927630871 1.062165646 1.006491552 1.085196333 1.027966381 0.676428314 0.911746754 1 21.60741013 1.769107333 25 0.82932156 0.984625655 0.178908574 0.107549176 31.10300663 25468.86889 0.049529103 0.027472131 58.76345651 -1.769107333 0.155304095 S(ph)TTELDDYSTNK ddPTM_BT-474_Pertuzumab_2h_R1 4 STTELDDYSTNK 12 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.989)T(0.011)TELDDYSTNK;S(0.995)T(0.005)TELDDYSTNK;S(0.841)T(0.136)T(0.022)ELDDYSTNK;S(0.808)T(0.096)T(0.096)ELDDYSTNK 317.04 1.75E-46 1706460000 2574630 2142360 1979340 2094480 2180320 1934960 2100840 3432870 2695750 2692300 TRUE FALSE 2474010.613 2081261.99 2337050.768 2202576.364 2250451.973 1974086.217 2126550.708 3361980.035 2389739.762 2509948.123 0.985681971 0.829205182 0.931115168 0.877538601 0.896612943 0.786504788 0.847248869 1.339461961 0.952107233 1 21.25922612 1.769151329 25 1.130744836 0.876257533 0.447427213 0.109123099 18.1351618 14828.70476 0.047135311 0.026144275 58.7694097 -1.769151329 -0.254487303 TQEHFTHNTVR ddPTM_BT-474_Pertuzumab_2h_R1 3 TQEHFTHNTVR 11 0 Q08209-3;Q08209-2;Q08209;E7ETC2;Q08209-5 Q08209-3 PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 0 ;; 181.98 3.46E-06 829780000 239173 325068 253198 419130 277197 286195 350140 91070 315068 340420 FALSE TRUE 229825.8547 315797.3789 298956.511 440761.3495 286113.2932 291982.059 354425.1181 89189.37268 279302.8015 317363.0502 0.724173323 0.995066624 0.942001631 1.388823775 0.901533096 0.920025374 1.116781295 0.28103263 0.880073472 1 18.27577464 1.769173291 25 0.646341629 1.004333508 0.202372563 0.239534873 29.16868105 23833.43712 0.106432379 0.059035229 58.7723818 -1.769173291 0.357991879 MQAQMQMQMQGGDGDGGALGHHV ddPTM_BT-474_Pertuzumab_2h_R1 1 MQAQMQMQMQGGDGDGGALGHHV 23 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0;H7C1T1 Q15019-2 2-Sep Septin-2 0 157.57 5.19E-09 339090000 151770 191800 158760 166060 146430 173640 169880 70448 158250 160880 FALSE TRUE 145838.6606 186330.0518 187451.4636 174630.3765 151140.0539 177151.1198 171959.0423 68993.22418 140286.1234 149983.4543 0.972364994 1.242337381 1.249814284 1.164330941 1.007711515 1.18113775 1.146520082 0.460005569 0.935343996 1 17.19444383 1.769241602 25 0.744940778 1.143768755 0.479155486 0.159114973 17.21655185 14036.1294 0.069557047 0.038581727 58.78162696 -1.769241602 0.398827977 RPQYS(ph)NPPVQGEVMEGADNQGAGEQGRPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR 30 2 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 RPQYS(1)NPPVQGEVMEGADNQGAGEQGRPVR;RPQYS(1)NPPVQGEVMEGADNQGAGEQGRPVR 119.7 1.96E-05 1609560000 97891 103701 72671 97332 93123 102868 84865 91299 81216 93364 TRUE FALSE 94065.3115 100743.549 85804.26626 102355.3162 96118.38587 104948.0614 85903.60326 89413.64375 71996.70017 87040.37312 1.080708964 1.15743471 0.985798465 1.175952176 1.104296574 1.205740022 0.98693974 1.02726632 0.827164425 1 16.40939712 1.769262168 1.885888582 0.927512812 1.113239227 0.488509808 0.077047761 0.25656545 1.804020849 0.050367156 0.021129968 58.78441058 -1.769262168 0.185726415 CVGAELEYDSEHSDWHGFD ddPTM_BT-474_Pertuzumab_2h_R1 2 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 ; 159.34 3.36E-11 201779000 66544 75081 78932 97779 79447 102799 91425 35533 90408 81261 FALSE TRUE 63943.38691 72939.76339 93196.76823 102825.3859 82002.48491 104877.6662 92543.8865 34799.23113 80145.26286 75757.12009 0.844057784 0.962810668 1.23020474 1.357303258 1.082439311 1.384393521 1.221586649 0.459352614 1.057923833 1 16.20909387 1.769290509 25 0.78517767 1.1640594 0.298392558 0.216757926 26.28959058 21398.96994 0.100459495 0.05572219 58.78824681 -1.769290509 0.37888173 FGESEEVEMEVES(ph)DEEDDKQEK ddPTM_BT-474_Pertuzumab_2h_R1 7 FGESEEVEMEVESDEEDDKQEK 22 1 Q15459;Q15459-2;H7C1L2 Q15459 SF3A1 Splicing factor 3A subunit 1 1 FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK 225.3 3.75E-26 4100200000 3090210 2050580 1958440 1516980 2098010 1931910 2153620 3090660 3372910 2712900 TRUE FALSE 2969441.177 1992099.466 2312373.673 1595271.52 2165494.397 1970974.544 2179976.646 3026836.791 2990031.397 2529152.867 1.17408529 0.787654828 0.914287825 0.630753301 0.85621333 0.77930226 0.861939456 1.196778902 1.182226443 1 21.27022281 1.769602476 7.219406234 1.140520057 0.844884394 0.438301303 0.138482506 0.145799839 20.90417337 0.063430344 0.035014495 58.83049146 -1.769602476 -0.295635663 TSLVLNSDTCFENLTDPSS(ph)PTISSYENLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSLVLNSDTCFENLTDPSSPTISSYENLLR 30 0 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 TSLVLNSDTCFENLTDPS(0.021)S(0.846)PT(0.133)ISSYENLLR;TSLVLNSDTCFENLTDPS(0.001)S(0.896)PT(0.103)ISSYENLLR 263.5 1.21E-58 223630000 44696 45196 40264 51758 45248 51943 43707 33679 34081 34077 TRUE FALSE 42949.23091 43907.05433 47540.60047 54429.23658 46703.44301 52993.32305 44241.89934 32983.51688 30212.26776 31768.93444 1.351925448 1.382075134 1.496449324 1.713284929 1.470097875 1.668086261 1.392615148 1.038231765 0.95100035 1 14.95532908 1.769675013 3.034104901 0.978950011 1.515077083 0.826305064 0.10630777 0.095311152 1.738058732 0.063760306 0.030768811 58.84031826 -1.769675013 0.536127072 AGS(ph)PDVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGSPDVLR 8 0 Q8NDX6 Q8NDX6 ZNF740 Zinc finger protein 740 1 AGS(1)PDVLR;AGS(1)PDVLR 88.364 0.014891 726580000 1873450 1664290 1440210 1730790 1582970 1546700 1560890 1552160 1449160 1452680 TRUE FALSE 1800233.503 1616826.079 1700487.984 1820116.279 1633887.668 1577975.334 1579992.639 1520107.354 1284657.432 1354288.69 1.329283421 1.193856296 1.255631829 1.343964764 1.206454488 1.1651691 1.166658668 1.122439673 0.948584627 1 20.36910388 1.769828272 0.817625745 0.972532757 1.26841241 0.801254885 0.053679548 0.259274436 0.330658574 0.048065351 0.021703846 58.86108614 -1.769828272 0.295879652 HSTPSNSSNPSGPPS(ph)PNSPHR ddPTM_BT-474_Pertuzumab_2h_R1 11 HSTPSNSSNPSGPPSPNSPHR 21 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 1 HSTPSNSSNPSGPPS(0.989)PNS(0.011)PHR;HSTPSNSSNPS(0.001)GPPS(0.991)PNS(0.009)PHR;HSTPSNSSNPSGPPS(0.983)PNS(0.017)PHR;HSTPSNSSNPSGPPS(0.994)PNS(0.006)PHR;HSTPSNSSNPSGPPS(0.998)PNS(0.002)PHR;HSTPSNSSNPS(0.002)GPPS(0.992)PNS(0.006)PHR;HSTPSNSSNPS(0.001)GPPS(0.834)PNS(0.165)PHR;HSTPSNSSNPSGPPS(0.981)PNS(0.018)PHR;HSTPSNSSNPS(0.009)GPPS(0.984)PNS(0.007)PHR;HSTPSNSSNPS(0.001)GPPS(0.953)PNS(0.046)PHR;HSTPSNSSNPS(0.234)GPPS(0.747)PNS(0.019)PHR 248.02 3.12E-30 3286798000 801968.6 1446936 1009856 1533242 1103841 1360557 1317191 515911.5 1177306 1354735 TRUE FALSE 770626.7805 1405670.802 1192359.443 1612372.803 1139347.048 1388068.395 1333311.177 505257.7472 1043663.159 1262977.592 0.61016663 1.112981585 0.944085985 1.276644031 0.902111847 1.099044357 1.055688704 0.40005282 0.826351287 1 20.26839761 1.769858637 25 0.680724362 1.012963135 0.213110719 0.21678666 29.54349181 23610.75066 0.094078539 0.052184743 58.86520183 -1.769858637 0.332238772 ESDQTLAALLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 10 ESDQTLAALLSPK 13 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK 250.52 7.69E-18 9271602000 4022900 3374741 3040282 3016616 3355490 3164176 3399609 4024090 4434630 3859660 TRUE FALSE 3865680.62 3278496.691 3589728.588 3172303.913 3463422.383 3228157.807 3441214.432 3940991.135 3931229.394 3598241.79 1.074324864 0.911138518 0.997634066 0.88162611 0.962531866 0.897148662 0.956359976 1.095254673 1.092541753 1 21.7788607 1.769864236 7.761730255 1.069818083 0.94954112 0.42378606 0.057427886 0.148384411 25.65804788 0.025381468 0.01405551 58.86596066 -1.769864236 -0.120276964 KAPTTDEDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPTTDEDKK 10 2 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 77.64 0.018219 1032900000 938930 741190 753890 608770 726050 783600 905710 936210 1342900 1033300 FALSE TRUE 902235.5776 720051.9869 890134.6932 640188.6927 749404.0576 799444.9289 916794.3499 916876.9363 1190459.622 963313.6706 0.936595841 0.747474067 0.924034113 0.664569301 0.777943966 0.829890568 0.951709062 0.951794794 1.235796458 1 19.87764611 1.769887082 1.534466334 1.102064694 0.807444114 0.574225386 0.098635057 0.25431791 1.152634978 0.071488663 0.02868095 58.86905739 -1.769887082 -0.29462058 GNIWS(ph)AEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNIWSAEK 8 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 GNIWS(1)AEK;GNIWS(1)AEK 96.229 0.0095337 567170000 756380 644550 737750 601370 644270 752850 685980 850180 771060 844830 TRUE FALSE 726819.8334 626168.0651 871077.8362 632406.7778 664993.5297 768073.1428 694375.2284 832623.4859 683532.5013 787608.9116 0.922818194 0.795024099 1.105977628 0.802945178 0.844319458 0.975196105 0.881624393 1.05715346 0.867857754 1 19.58711991 1.769912261 25 0.980154246 0.904122176 0.103243462 0.095551871 58.10630754 46358.28545 0.042141685 0.023375969 58.87247056 -1.769912261 -0.07603207 RS(ph)SDSWEVWGSASTNR ddPTM_BT-474_Pertuzumab_2h_R1 4 RSSDSWEVWGSASTNR 16 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 RS(0.497)S(0.497)DS(0.007)WEVWGSASTNR;RS(0.5)S(0.5)DSWEVWGSASTNR;RS(0.5)S(0.5)DSWEVWGSASTNR;RS(0.49)S(0.49)DS(0.021)WEVWGSASTNR 233.3 7.33E-20 4496900000 1704920 1931180 1450080 1689070 2093390 1894650 1630730 1775630 1669480 1758420 TRUE FALSE 1638289.842 1876104.637 1712141.713 1776243.105 2160725.791 1932961.121 1650687.362 1738962.62 1479967.629 1639320.647 0.999371199 1.144440315 1.04442149 1.083523903 1.318061719 1.179123269 1.006933796 1.060782479 0.902793259 1 20.64466664 1.769934411 1.79104781 0.968033072 1.127429075 0.334809036 0.089927785 0.405767545 2.558111483 0.066738376 0.027636059 58.87547318 -1.769934411 0.159396004 RGERPDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGERPDYK 8 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 81.95 0.012112 624080000 468520 451860 462890 499230 497590 434720 521490 586440 665860 655110 FALSE TRUE 450209.7204 438973.3952 546544.5199 524995.3201 513595.4342 443510.3363 527872.1506 574329.8091 590274.3643 610738.8162 0.737155898 0.718757976 0.894890754 0.859606932 0.840941202 0.726186587 0.864317343 0.940385307 0.966492302 1 19.22019601 1.770083695 2.363156904 0.976492665 0.801839683 0.649999707 0.056647839 0.189342 2.111306469 0.038149544 0.017134347 58.89571449 -1.770083695 -0.174652981 MGVMSSPT(ph)ENSFTLDADF ddPTM_BT-474_Pertuzumab_2h_R1 1 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.005)S(0.32)PT(0.675)ENSFTLDADF 155.02 2.44E-07 78463000 40954 49585 38901 61695 61813 40078 48664 41419 35198 43338 TRUE FALSE 39353.4724 48170.88435 45931.27605 64879.08634 63801.27128 40888.40462 49259.56459 40563.68318 31202.4706 40402.67866 0.97403127 1.192269571 1.136837397 1.605811508 1.579134686 1.012022123 1.219215315 1.003984996 0.772287176 1 15.30216332 1.770085328 1.570125516 0.883895203 1.276946304 0.349779064 0.203222579 0.428497034 2.03998339 0.162675766 0.065512372 58.89593596 -1.770085328 0.3930511 SKLS(ph)PS(ph)PSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 S(0.002)KLS(0.997)PS(0.936)PS(0.065)LR;S(0.015)KLS(0.985)PS(0.934)PS(0.066)LR;S(0.066)KLS(0.926)PS(0.875)PS(0.133)LR;S(0.008)KLS(0.992)PS(0.908)PS(0.092)LR 98.368 0.0073032 1585630000 5611450 5032830 4395880 4469230 4804780 4979390 5002310 5934070 6422430 5949530 TRUE FALSE 5392148.33 4889298.616 5190313.302 4699887.496 4959330.112 5080076.677 5063529.766 5811529.381 5693382.671 5546563.034 0.97216029 0.881500595 0.935771084 0.847351318 0.894126702 0.915896321 0.912913048 1.047771268 1.026470381 1 22.40316264 1.770108537 6.611343257 1.02724544 0.905609609 0.723744266 0.032846286 0.084063257 9.440158023 0.015124303 0.008318267 58.8990835 -1.770108537 -0.121635831 VYADGIFDLFHSGHAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VYADGIFDLFHSGHAR 16 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;C9JPY0;Q9Y5K3-2;Q9Y5K3-4;Q9Y5K3-3;Q9Y5K3;C9JVS0;F8WAZ5;F2Z2B1 P49585 PCYT1A;PCYT1B Choline-phosphate cytidylyltransferase A;Choline-phosphate cytidylyltransferase B 0 124.25 4.83E-05 295580000 381520 429770 343210 439600 392740 378300 428360 30124 374300 363040 FALSE TRUE 366609.7766 417513.3804 405235.6817 462287.8087 405372.8388 385949.4852 433602.3978 29501.92887 331811.0332 338450.9774 1.083199048 1.233600752 1.197324601 1.365892964 1.197729851 1.140340879 1.281137969 0.08716751 0.980381371 1 18.36858736 1.770120608 25 0.597416003 1.2166375 0.471591633 0.249032685 18.40679819 14588.27478 0.106720763 0.059198025 58.90072056 -1.770120608 0.619221497 S(ph)PSWQRPNQGVPSTGR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPSWQRPNQGVPSTGR 16 1 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 1 S(0.987)PS(0.013)WQRPNQGVPSTGR;S(0.998)PS(0.002)WQRPNQGVPSTGR;S(0.999)PS(0.001)WQRPNQGVPSTGR;S(0.841)PS(0.159)WQRPNQGVPSTGR;S(0.989)PS(0.011)WQRPNQGVPSTGR 174.04 2.43E-09 3339470000 201556 226711 145394 179513 203808 212815 202664 140519 212403 203140 TRUE FALSE 193678.9687 220245.4243 171669.9301 188777.6874 210363.6694 217118.2651 205144.2627 137617.2335 188291.9019 189381.1469 1.022694032 1.162974393 0.906478458 0.996813519 1.110795203 1.146461877 1.083234873 0.726668076 0.994248398 1 17.53093319 1.77017047 25 0.879442761 1.061995493 0.320683665 0.100596808 27.01440036 21376.42271 0.045971373 0.025500278 58.90748345 -1.77017047 0.182552732 KGGEFDEFVNDDT(ph)DDDLPISK ddPTM_BT-474_Pertuzumab_2h_R1 7 KGGEFDEFVNDDTDDDLPISK 21 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK 187.75 1.62E-17 3720198000 2497213 2170043 1989094 1917688 2182150 2310292 2313118 2740240 3179908 2961486 TRUE FALSE 2399619.155 2108155.498 2348567.533 2016660.107 2252340.837 2357007.687 2341426.63 2683653.086 2818938.175 2760901.915 0.869143211 0.763574934 0.850652289 0.73043526 0.815798933 0.853709317 0.84806585 0.972020437 1.021020761 1 21.3967082 1.770203628 1.571580647 1.017979759 0.806407363 0.814223041 0.039719176 0.139198048 0.663985646 0.028457748 0.011463282 58.91198119 -1.770203628 -0.211572396 TETQEKNPLPSK ddPTM_BT-474_Pertuzumab_2h_R1 5 TETQEKNPLPSK 12 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;;; 201.95 1.30E-07 12187440000 11624400 10564830 8291600 8307280 9489270 9829390 9887580 11994400 13005000 11310900 FALSE TRUE 11170105.6 10263531.39 9790076.566 8736019.716 9794500.987 10028147 10008587.16 11746711.45 11528726.92 10544802.67 1.059299633 0.973326075 0.928426721 0.828466875 0.928846304 0.951003761 0.949148834 1.113981154 1.09330893 1 23.33002876 1.770221815 9.497859966 1.077500421 0.940905767 0.469956768 0.05980915 0.192443187 51.81299052 0.029135221 0.016194785 58.91444825 -1.770221815 -0.136594654 SLQAMKEILCGTNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLQAMKEILCGTNEK 15 1 Q9H9S4;B7ZBJ5;Q5TAW7;B7ZBJ6;B7ZBJ7 Q9H9S4 CAB39L Calcium-binding protein 39-like 0 67.275 0.07543 439830000 431220 569950 290550 345250 411560 522830 429300 370330 432640 403970 FALSE TRUE 414367.4457 553695.584 343058.8482 363068.3939 424798.2012 533401.9808 434553.9018 362682.5561 383528.521 376608.7521 1.100259735 1.47021433 0.910915762 0.964046618 1.127956264 1.416329222 1.153860338 0.963022113 1.018373893 1 18.522707 1.770223434 7.173822737 0.994059258 1.1664844 0.183366822 0.163888691 0.322134559 45.10118903 0.081080312 0.044804805 58.91466791 -1.770223434 0.172425141 YGAFGLPITVAHVDGQTHMLFGSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGAFGLPITVAHVDGQTHMLFGSDR 25 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 221.83 6.33E-34 780520000 428620 574520 452760 574880 548070 522880 536980 137173 505710 453280 FALSE TRUE 411869.0565 558135.2521 534583.8036 604549.6257 565699.1693 533452.9919 543551.7219 134340.3296 448303.9209 422578.9419 0.974655894 1.320783401 1.265050741 1.430619384 1.338682819 1.262374764 1.286272618 0.317905878 1.06087615 1 18.68886135 1.770395159 25 0.725648176 1.27895525 0.491955484 0.2180228 18.72972244 14716.10594 0.094692852 0.052527041 58.93796808 -1.770395159 0.553307075 AEGLEEADTGASGCHSHPEEQPTSIS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 7 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPTSIS(0.995)PS(0.004)R;AEGLEEADTGASGCHSHPEEQPT(0.006)S(0.022)IS(0.932)PS(0.039)R;AEGLEEADTGASGCHSHPEEQPTSIS(0.991)PS(0.008)R;AEGLEEADTGASGCHSHPEEQPT(0.003)S(0.046)IS(0.839)PS(0.112)R;AEGLEEADTGASGCHSHPEEQPT(0.01)S(0.046)IS(0.797)PS(0.147)R;AEGLEEADTGASGCHSHPEEQPTSIS(0.975)PS(0.024)R;AEGLEEADTGASGCHSHPEEQPT(0.043)S(0.026)IS(0.782)PS(0.15)R 328.52 7.57E-105 7640790000 1655374 2129858 1950542 2583710 2339226 2422597 2444826 59528.6 2200763 1950723 TRUE FALSE 1590680.154 2069116.535 2303048.329 2717055.583 2414469.329 2471583.571 2474746.512 58299.31361 1950941.611 1818598.794 0.87467349 1.137753166 1.266386152 1.494037933 1.327653651 1.359059282 1.360798501 0.032057271 1.07277186 1 20.79439587 1.770400397 25 0.604319778 1.270999425 0.397807482 0.307753019 22.50925395 17682.80527 0.137059715 0.076028424 58.93867889 -1.770400397 0.666679648 GHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYK ddPTM_BT-474_Pertuzumab_2h_R1 2 GHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYK 36 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ; 215.1 3.99E-39 242405000 64809 94428 85662 119850 93961 102013 110059 31844.8 96221 115268 FALSE TRUE 62276.19263 91735.00589 101143.0289 126035.4729 96983.3409 104075.7728 111405.935 31187.19375 85298.39547 107460.7957 0.579524767 0.853660214 0.941208636 1.172850732 0.902499747 0.968499927 1.036712359 0.290219271 0.793762925 1 16.7134509 1.770404885 24.99999999 0.620578083 0.93090741 0.159066715 0.220133031 35.03023339 27515.14802 0.099248556 0.05505474 58.93928803 -1.770404885 0.310329328 DSHGVAQVR ddPTM_BT-474_Pertuzumab_2h_R1 5 DSHGVAQVR 9 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;;; 191.17 3.62E-05 6750720000 1596000 1704830 1606430 1665780 1575680 1312470 1667970 510797 1552830 1521890 FALSE TRUE 1533626.556 1656209.918 1896747.636 1751751.105 1626363.178 1339009.043 1688383.116 500248.8634 1376559.248 1418811.035 1.080923758 1.167322411 1.336857121 1.23466132 1.146285966 0.94375432 1.189998579 0.35258315 0.970220286 1 20.43625103 1.770416219 25 0.709241613 1.158780655 0.443138785 0.192568532 20.96574144 16462.06913 0.085956285 0.047680827 58.9408261 -1.770416219 0.449539042 HCSQVDSVR ddPTM_BT-474_Pertuzumab_2h_R1 3 HCSQVDSVR 9 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 164.97 6.19E-05 853795000 231153 340536 260001 344689 290924 264103 292992 229375 221163 314838 FALSE TRUE 222119.2852 330824.2467 306988.9644 362478.4406 300281.8347 269443.3436 296577.7237 224638.3261 196057.5034 293513.7418 0.756759407 1.127116722 1.045910023 1.234962419 1.023058862 0.917992261 1.010438973 0.765341768 0.667967034 1 18.16306852 1.770444518 5.134378909 0.787816735 1.028168565 0.301924588 0.141056425 0.199872435 11.4489795 0.068574199 0.036795243 58.94466689 -1.770444518 0.24035183 HIVNHAVVNEDPNAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIVNHAVVNEDPNAR 15 0 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 84.753 0.0047458 170940000 101450 95660 90373 110600 107320 119510 114070 27969 102470 107690 FALSE TRUE 97485.22184 92931.87046 106705.4114 116308.0793 110772.0453 121926.5741 115466.0228 27391.43038 90838.03519 100396.0604 0.971006447 0.925652562 1.062844608 1.158492463 1.103350518 1.214455763 1.150105117 0.272833718 0.90479681 1 16.61534313 1.770465785 24.99997179 0.651734607 1.085481684 0.390126195 0.198624772 22.43873134 17591.23571 0.088375109 0.049022821 58.94755345 -1.770465785 0.433747078 S(ph)HS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 S(0.485)HS(0.515)GT(0.515)S(0.485)PDNTAPPPPPPRPQPSHSR;S(0.498)HS(0.537)GT(0.52)S(0.445)PDNTAPPPPPPRPQPSHSR 108.1 0.0045823 1257360000 52587 62398 54758 63787 51541 60907 64375 15148.4 61504 55795 TRUE FALSE 50531.8419 60618.47013 64653.98869 67079.05471 53198.86307 62138.58127 65162.84051 14835.58025 54522.32377 52015.95495 0.971468119 1.165382241 1.242964562 1.289586143 1.022741255 1.19460618 1.252747173 0.28521211 1.048184616 1 15.66666659 1.770466153 25 0.705455475 1.166683588 0.386600165 0.216509814 22.43875852 17591.07344 0.093973242 0.052128458 58.94760345 -1.770466153 0.461228113 HMDFLSDFEMMLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HMDFLSDFEMMLQR 14 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 0 ; 189.3 7.35E-07 125436000 163279 182692 138739 158637 165506 147300 164286 104363 166361 165362 FALSE TRUE 156897.8762 177481.803 163812.2235 166824.2746 170829.6508 150278.5069 166296.5812 102207.8676 147476.3967 154161.8845 1.017747524 1.151269029 1.062598736 1.08213697 1.108118595 0.974809743 1.078713988 0.662990518 0.956633329 1 17.23408659 1.770537596 25 0.839277767 1.069427676 0.456114093 0.09528586 19.8382764 15517.63398 0.041194193 0.022851145 58.95730126 -1.770537596 0.230149908 LLQLTLEHDPHDTLGHGLGPET(ph)SPLSSPAYTPSGEAGSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLQLTLEHDPHDTLGHGLGPETSPLSSPAYTPSGEAGSSAR 41 0 E9PC47;P53667-4;P53667-2;P53667;P53667-3 E9PC47 LIMK1 LIM domain kinase 1 1 LLQLTLEHDPHDTLGHGLGPET(0.492)S(0.492)PLS(0.014)SPAYTPSGEAGSSAR 138.24 6.63E-10 150370000 17822 15781 16946 22007 23006 26086 20259 5033.3 19355 16107 TRUE FALSE 17125.49654 15330.94133 20008.51916 23142.78391 23746.00888 26613.47679 20506.9357 4929.360596 17157.90154 15016.05854 1.140478807 1.020969736 1.332474771 1.541202296 1.581374288 1.772334379 1.365667005 0.328272601 1.142636831 1 13.87421856 1.770622953 25 0.758810506 1.404302562 0.455365153 0.282772021 23.56495167 18383.5609 0.136210349 0.075558776 58.96889001 -1.770622953 0.645492056 S(ph)SS(ph)PFLSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSPFLSK 8 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.998)S(0.002)S(1)PFLSK;S(0.999)S(0.012)S(0.989)PFLSK;S(1)S(0.007)S(0.993)PFLSK;S(0.984)S(0.041)S(0.975)PFLSK 152.69 0.00066227 2548170000 5480440 4540270 4404800 4572780 4563170 4460010 5115240 6356400 7361960 6765640 TRUE FALSE 5266258.346 4410785.945 5200845.344 4808781.724 4709948.507 4550194.458 5177841.837 6225138.119 6526261.165 6307397.177 0.834933682 0.699303662 0.824562842 0.762403506 0.746734093 0.721406046 0.820915774 0.98695832 1.034699573 1 22.58861335 1.770639309 2.852405938 1.0173631 0.7638174 0.88076605 0.040003091 0.070594528 1.13878362 0.021902992 0.010403862 58.9711109 -1.770639309 -0.2535457 NGGS(ph)FEDDLSLGAEANHLHESDAQIENCNNILAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGGSFEDDLSLGAEANHLHESDAQIENCNNILAK 34 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 NGGS(0.991)FEDDLS(0.009)LGAEANHLHESDAQIENCNNILAK;NGGS(0.953)FEDDLS(0.045)LGAEANHLHES(0.001)DAQIENCNNILAK 228.94 1.64E-36 136000000 61779 73217 46468 74677 83830 74126 83716 17036.9 93204 57108 TRUE FALSE 59364.60838 71128.92285 54865.80128 78531.08892 86526.46808 75624.87851 84740.54145 16685.08206 82623.87266 53240.02429 1.115037214 1.336004703 1.030536744 1.475038563 1.625214662 1.420451615 1.591669849 0.313393585 1.551912753 1 15.70022361 1.770652824 25 0.886211638 1.371888968 0.241538302 0.330678736 33.9834387 26486.56801 0.147405148 0.081768107 58.9729461 -1.770652824 0.485677331 S(ph)VS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVSPPPK 7 0 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)VS(1)PPPK;S(1)VS(1)PPPK;S(1)VS(1)PPPK;S(1)VS(1)PPPK 90.15 0.025364 2269460000 4963960 4513440 3973260 3990140 4123730 4368170 4575170 5364920 6171800 5607190 TRUE FALSE 4769962.955 4384721.11 4691316.467 4196071.604 4256373.521 4456497.39 4631162.299 5254132.527 5471203.138 5227410.027 0.912490685 0.838794181 0.897445665 0.802705658 0.814241374 0.852524934 0.885938213 1.005111996 1.046637457 1 22.31766489 1.770671404 2.717447705 1.026205451 0.850922911 0.832573477 0.033095318 0.093661656 1.374383702 0.019799375 0.009276935 58.97546907 -1.770671404 -0.17528254 SGWSSQSDYYASYYSSQYDYGDPGHWDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGWSSQSDYYASYYSSQYDYGDPGHWDR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ; 216.64 3.36E-34 1102060000 437450 501390 383940 461890 444300 427780 448940 381280 452580 424160 FALSE TRUE 420353.9704 487090.8481 453326.4987 485728.1983 458591.313 436430.0047 454434.262 373406.4348 401205.0158 395431.2654 1.063026642 1.231796498 1.146410358 1.228350514 1.159724466 1.103681077 1.149211764 0.944301747 1.014601148 1 18.59306742 1.770716761 8.254114182 0.985207472 1.158520217 0.700465919 0.050379115 0.098792467 19.61552046 0.022788572 0.012662417 58.9816287 -1.770716761 0.173312745 GISHVIVDEIHER ddPTM_BT-474_Pertuzumab_2h_R1 8 GISHVIVDEIHER 13 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;; 242.48 3.57E-17 17833100000 2938740 3167420 2743380 3366740 3348550 3651610 3281430 1672851 3190550 3187490 FALSE TRUE 2823890.792 3077088.283 3239169.792 3540497.855 3456259.152 3725448.056 3321589.122 1638306.042 2828372.14 2971598.463 0.95029353 1.035499352 1.090042895 1.19144558 1.163097637 1.253684878 1.117778584 0.551321473 0.951801589 1 21.50280775 1.770722806 25 0.78953218 1.120742367 0.456040937 0.137517073 21.29366362 16560.07006 0.06259871 0.03472513 58.98244964 -1.770722806 0.331210186 AQHQQALSSLELLNVLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQHQQALSSLELLNVLFR 18 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 205.95 9.07E-16 130400000 117740 113140 91617 106680 126400 118820 114070 98804 128840 112600 FALSE TRUE 113138.5906 109913.358 108174.2299 112185.7676 130465.7708 121222.6218 115466.0228 96763.66287 114214.6233 104973.5017 1.077782381 1.047058126 1.030490821 1.068705585 1.242844801 1.154792589 1.099953997 0.921791322 1.088032899 1 16.67966567 1.770746411 25 0.996216089 1.104183771 0.308977712 0.068146489 35.35256401 27473.48939 0.033806314 0.01875328 58.98565561 -1.770746411 0.107967682 ENQTAVDVFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENQTAVDVFR 10 0 C9J931;Q15382 C9J931 RHEB GTP-binding protein Rheb 0 89.679 0.026402 103760000 86427 96668 85541 93584 95369 106570 90155 149780 106000 126760 FALSE TRUE 83049.33729 93911.12329 101000.1615 98413.88146 98436.6305 108724.9184 91258.34386 146686.9907 93967.32439 118174.4323 0.702769082 0.794682246 0.854670165 0.832784889 0.832977393 0.920037578 0.772234248 1.241275188 0.795157824 1 16.85055841 1.770813663 25 1.035724101 0.821754475 0.378736231 0.113900375 26.30633151 20400.75241 0.049563342 0.027494187 58.99479052 -1.770813663 -0.213969626 AKTQT(ph)PPVSPAPQPT(ph)EER ddPTM_BT-474_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKTQT(1)PPVS(0.206)PAPQPT(0.794)EER 195.18 1.12E-14 661500000 996300 977520 930840 1027600 1126400 1061600 885410 856140 778590 774430 TRUE FALSE 957363.4945 949642.0867 1099063.494 1080634.559 1162631.679 1083066.279 896245.9124 838460.4098 690207.7273 721977.1663 1.326030156 1.315335347 1.522296751 1.496771102 1.610344112 1.500139242 1.241377088 1.161339235 0.955996615 1 19.46159368 1.770814267 1.639673185 0.989247937 1.464334647 0.810741334 0.092770208 0.16073951 0.839438382 0.075413989 0.030631218 58.99487249 -1.770814267 0.475086711 TVEGVLIVHEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVEGVLIVHEHR 12 0 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;;; 144.57 3.65E-05 2107290000 1124100 1250990 1301580 1478830 1450910 1447070 1362230 300936 1313520 1058010 FALSE TRUE 1080168.929 1215312.99 1536804.459 1555152.594 1497579.838 1476330.747 1378901.378 294721.5664 1164414.716 986350.0403 1.095117235 1.232131536 1.558072081 1.576674132 1.518304635 1.496761481 1.397983801 0.298800177 1.180528888 1 19.9117402 1.77083356 25 0.758533021 1.423349466 0.519692636 0.254705638 19.70517716 15272.08097 0.115141848 0.063872917 58.99749335 -1.77083356 0.664816444 DVKPHNVMIDHEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVKPHNVMIDHEHR 14 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YDP2;P68400-2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYW6 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ;;; 261.39 1.07E-24 3822520000 2894350 2833240 2605370 2978250 2743490 2406910 3187000 145681 3512790 1806950 FALSE TRUE 2781235.602 2752438.769 3076218.315 3131957.839 2831736.847 2455579.369 3226003.459 142672.6364 3114032.806 1684563.667 1.651012459 1.633917924 1.826121728 1.859210133 1.680991287 1.457694605 1.915038014 0.084694119 1.848569376 1 20.68394352 1.770849568 25 0.888469777 1.712688641 0.393980666 0.416125289 24.62766599 19077.68497 0.17815883 0.098829862 58.999668 -1.770849568 0.824218864 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 0 159.22 3.64E-18 46744000 17329 15766 13380 17803 15333 17742 16875 3186.7 15156 14853 FALSE TRUE 16651.76352 15316.36912 15798.06364 18721.81496 15826.19987 18100.7554 17081.5213 3120.893531 13435.55442 13846.99308 1.202554477 1.106115171 1.140902111 1.352049131 1.142934049 1.307197548 1.233590657 0.225384205 0.970286787 1 13.7572851 1.770857619 25 0.65420409 1.211739769 0.50690342 0.21298806 18.76726384 14534.32934 0.091770434 0.050907613 59.00076182 -1.770857619 0.557535679 AHINNSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHINNSEK 8 0 Q9NVM9-2;Q9NVM9;H0YH12 Q9NVM9-2 ASUN Protein asunder homolog 0 ; 99.802 0.0065549 140091000 104319 104964 81029 96016 99020 91460 102893 80158 111686 106194 FALSE TRUE 100242.0981 101970.5295 95672.74278 100971.3973 102205.0682 93309.38386 104152.2353 78502.70929 99007.87351 99001.38579 1.012532273 1.029990931 0.966377814 1.019898827 1.032359976 0.942505836 1.052028055 0.79294556 1.000065532 1 16.5951611 1.770901005 25 0.909452162 1.006085225 0.219364947 0.062615881 31.83509813 24621.636 0.026877512 0.014909759 59.00665627 -1.770901005 0.096633063 EIESEIDS(ph)EEELINK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIESEIDSEEELINK 15 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 EIESEIDS(1)EEELINK;EIESEIDS(1)EEELINK 151.72 3.10E-06 81727000 181761 166098 133279 154615 162487 150108 154348 181522 186459 163319 TRUE FALSE 174657.5792 161361.0477 157365.4801 162594.6987 167713.5419 153143.2866 156236.957 177773.5073 165292.956 152257.2587 1.147121528 1.059792151 1.033549937 1.067894563 1.101514262 1.005819282 1.026137988 1.167586418 1.085616262 1 17.21615148 1.770930905 25 1.102402215 1.061309949 0 0.053971791 67.79316667 52383.52845 0.024279542 0.013468845 59.0107189 -1.770930905 -0.041092266 S(ph)PSVPNNQDHAHHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSVPNNQDHAHHVK 15 0 Q7Z2Y5;Q7Z2Y5-2 Q7Z2Y5 NRK Nik-related protein kinase 1 S(0.847)PS(0.153)VPNNQDHAHHVK;S(0.984)PS(0.016)VPNNQDHAHHVK 160.81 2.82E-06 933960000 836670 924610 840220 1096580 826180 975680 1100160 130810 1233000 668890 TRUE FALSE 803972.0114 898241.0281 992066.4446 1153174.625 852754.83 995408.9181 1113624.087 128108.7278 1093035.009 623585.4845 1.289273133 1.440445697 1.590906891 1.849264702 1.367502694 1.59626698 1.785840297 0.205438919 1.752823047 1 19.25022782 1.770939808 25 0.907618418 1.561649875 0.31294748 0.38439205 29.28126012 22619.31157 0.166752124 0.092502961 59.01192855 -1.770939808 0.654031458 KGPGLAVQSGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGPGLAVQSGDK 12 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ; 123.02 0.00055831 1143650000 1867140 1797590 1514050 1619210 1704330 1593830 1782380 2030060 2315000 2128000 FALSE TRUE 1794170.105 1746324.493 1787672.515 1702777.622 1759151.322 1626058.335 1804193.3 1988138.552 2052210.905 1983868.665 0.904379477 0.880262149 0.901104265 0.858311668 0.886727712 0.819640112 0.909431825 1.002152303 1.034448974 1 20.91988509 1.770951552 3.204152016 1.017424125 0.875656548 0.864698419 0.024266637 0.074244814 1.503466025 0.013307216 0.006519773 59.01352431 -1.770951552 -0.141767577 DDDVIRNIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDDVIRNIIR 10 1 M9MMK7;Q0VDD8-2;Q0VDD8;Q0VDD8-4;H7C374;Q0VDD8-3 M9MMK7 DNAH14 "Dynein heavy chain 14, axonemal" 0 72.643 0.043203 175440000 58172 90121 75848 139000 76742 59550 96456 64392 55401 69427 FALSE TRUE 55898.57393 87550.83732 89555.42083 146173.8067 79210.47613 60754.1418 97636.45738 63062.2827 49112.11074 64724.64745 0.863636592 1.352666114 1.383637059 2.258394791 1.223806992 0.93865543 1.508489597 0.974316357 0.758785295 1 15.98202758 1.770991291 1.189295149 0.857024191 1.409399198 0.219383212 0.367818424 0.698970368 1.84506427 0.315867298 0.125926355 59.01892452 -1.770991291 0.552375008 QQELTHQEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQELTHQEHR 10 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ; 117.23 0.00056952 1017600000 240707 326900 270530 346160 319240 352180 331170 35396 294420 281780 FALSE TRUE 231299.9043 317577.1321 319420.7889 364025.3591 329508.6445 359301.3209 335222.9575 34665.06023 260998.6759 262694.7896 0.880489121 1.20892056 1.215938806 1.38573498 1.254340236 1.367751989 1.276092906 0.131959451 0.993543406 1 18.00302806 1.770999942 25 0.621267785 1.238480755 0.439061823 0.262878489 21.55827541 16622.53678 0.115243766 0.063929818 59.02010012 -1.770999942 0.61721297 LLEDS(ph)DS(ph)EDEAAPSPLQPALRPNPTAILDEAPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEDSDSEDEAAPSPLQPALRPNPTAILDEAPKPK 35 2 Q9BW85 Q9BW85 CCDC94 Coiled-coil domain-containing protein 94 2 LLEDS(0.889)DS(0.906)EDEAAPS(0.203)PLQPALRPNPT(0.002)AILDEAPKPK 56.347 0.022897 61856000 26745 25576 19130 21203 19459 19546 22697 28174 27887 32586 TRUE FALSE 25699.77583 24846.59752 22587.21654 22297.28937 20084.91641 19941.23351 22974.77268 27592.19705 24721.38467 30378.9212 0.845973946 0.817889396 0.743516085 0.733972389 0.661146467 0.656416776 0.756273487 0.908267837 0.813767695 1 14.89078302 1.771039115 5.096275971 0.895766777 0.739849476 0.530641697 0.069634186 0.164808663 9.236962952 0.036513392 0.019589523 59.02542397 -1.771039115 -0.155917301 AVQQHQHGYDS(ph)DEEVDSELGTWEHQLR ddPTM_BT-474_Pertuzumab_2h_R1 8 AVQQHQHGYDSDEEVDSELGTWEHQLR 27 0 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 1 AVQQHQHGYDS(1)DEEVDSELGTWEHQLR;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR;AVQQHQHGY(0.004)DS(0.996)DEEVDSELGTWEHQLR;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR 426.3 5.52E-187 12982410000 1403504 1459740 1282727 1535658 1565117 1559711 1507161 745655.4 1500834 1409105 TRUE FALSE 1348653.512 1418109.644 1514544.303 1614913.493 1615460.41 1591249.425 1525606.087 730257.3554 1330465.616 1313665.063 1.026634223 1.079506249 1.152915112 1.229319054 1.229735383 1.211305278 1.161335663 0.555893108 1.012789069 1 20.32516606 1.771074551 25 0.812064423 1.160578383 0.506370395 0.13337471 19.87504766 15289.49503 0.05959979 0.033062446 59.03024033 -1.771074551 0.34851396 TTFFHHEYPWILSASDDQTIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTFFHHEYPWILSASDDQTIR 21 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 215.88 3.70E-25 1462260000 504930 566690 557740 628010 608240 640760 665360 281060 640520 666560 FALSE TRUE 485196.7774 550528.556 658536.0249 660421.6714 627804.592 653716.6062 673502.8747 275256.0128 567810.8549 621413.2975 0.780795614 0.885929796 1.059739191 1.062773639 1.010285095 1.051983614 1.083824368 0.442951597 0.913741076 1 19.24519359 1.771096944 24.99999999 0.727654687 0.995258029 0.2260528 0.163647984 32.03177237 24624.46112 0.073608675 0.040833737 59.0332841 -1.771096944 0.267603342 EKIEAELQDICNDVLELLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKIEAELQDICNDVLELLDK 20 1 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ; 222.06 6.76E-25 10922500000 313169 316905 283690 279597 302009 312289 319599 413098 455016 432224 FALSE TRUE 300930.0093 307867.1797 334959.0936 294027.0347 311723.3938 318603.6975 323510.3482 404567.3819 403364.4913 402949.0835 0.746818945 0.764034942 0.83126903 0.729687811 0.773604921 0.790679792 0.802856642 1.004016136 1.001030919 1 18.62023803 1.77115227 3.686897845 1.005339665 0.774463353 0.941153616 0.025804861 0.045689799 1.227645171 0.013843747 0.007009894 59.04080494 -1.77115227 -0.230876312 IPLNLDGPHPSPPT(ph)PDSVGQLHIMDYNETHHEHS ddPTM_BT-474_Pertuzumab_2h_R1 1 IPLNLDGPHPSPPTPDSVGQLHIMDYNETHHEHS 34 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6S1 A0A2R8YFV7 TSC1 Hamartin 1 IPLNLDGPHPS(0.258)PPT(0.742)PDSVGQLHIMDYNETHHEHS 168.5 1.45E-14 533860000 171370 226740 172170 242680 232910 230600 246850 49959 273500 163470 TRUE FALSE 164672.6709 220273.5972 203284.9489 255204.7439 240401.7617 235262.89 249871.0241 48927.32919 242453.4266 152398.0313 1.080543295 1.445383483 1.333907972 1.674593443 1.577459759 1.543739693 1.63959483 0.321049614 1.590922301 1 17.21748474 1.771167587 24.99999991 0.903754564 1.479259963 0.321304507 0.328621544 29.30531945 22479.65783 0.143931846 0.079846081 59.04288733 -1.771167587 0.575505399 GNVLQPEESLLDPFGAKPFHS(ph)PDLSWHPPHQGLSDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNVLQPEESLLDPFGAKPFHSPDLSWHPPHQGLSDIR 37 1 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 GNVLQPEESLLDPFGAKPFHS(0.962)PDLS(0.036)WHPPHQGLS(0.002)DIR 114.47 4.42E-06 104560000 93144 122880 107810 120510 116130 107090 115900 30510 104230 107350 TRUE FALSE 89503.8295 119375.5827 127293.6652 126729.5355 119865.4269 109255.4332 117318.4189 29879.95784 92398.24737 100079.0889 0.894330979 1.192812445 1.271930696 1.266293858 1.197707016 1.091690926 1.172257064 0.298563448 0.923252284 1 16.61078103 1.771265476 25 0.669955508 1.164673444 0.455404197 0.203274094 21.28432212 16277.97873 0.08909484 0.049425357 59.05619695 -1.771265476 0.494717936 SQEIDDHQHEMSVLQNAHQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQEIDDHQHEMSVLQNAHQQK 21 0 Q15643-2;Q15643 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 282.22 1.56E-45 293730000 257140 259430 203370 249070 249570 284240 276370 2850.1 303710 144890 FALSE TRUE 247090.6845 252031.3104 240123.4829 261924.5325 257597.6457 289987.5275 279752.2987 2791.244439 269234.1141 135076.4712 1.829265173 1.865841683 1.77768549 1.939083322 1.907050453 2.146839674 2.071066087 0.020664179 1.993197717 1 17.04341687 1.77129615 24.99999795 0.910847593 1.932577248 0.462478645 0.455714499 22.67822352 17327.75441 0.195526601 0.108467675 59.06036813 -1.77129615 1.021729655 STS(ph)LNERPK ddPTM_BT-474_Pertuzumab_2h_R1 4 STSLNERPK 9 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 S(0.003)T(0.152)S(0.845)LNERPK;S(0.001)T(0.03)S(0.969)LNERPK;S(0.009)T(0.067)S(0.924)LNERPK;S(0.003)T(0.073)S(0.924)LNERPK 118.61 0.00058258 4139150000 2872540 2633550 2086980 2084880 2196560 2152950 2294300 3242740 2909660 2605150 TRUE FALSE 2760277.961 2558443.733 2464143.711 2192480.907 2267214.347 2196484.124 2322378.33 3175776.286 2579367.595 2428700.87 1.136524467 1.053420684 1.014593333 0.90273814 0.933509093 0.904386436 0.956222464 1.307602894 1.062035933 1 21.21175338 1.771307863 25 1.154836967 0.981262672 0.264473254 0.100663487 32.19303299 24588.93854 0.047106815 0.026132202 59.06196102 -1.771307863 -0.173574295 KLPDSFFKPPEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPDSFFKPPEPK 13 2 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 0 ; 115.06 0.00039011 1021610000 2579190 2280430 2021680 1800960 2058130 2208620 2391000 2801100 3347100 3070100 FALSE TRUE 2478392.403 2215394.369 2387042.548 1893907.761 2124331.621 2253279.81 2420261.773 2743256.306 2967151.24 2862159.392 0.865916975 0.774028999 0.834000564 0.661705902 0.742212899 0.787265662 0.845606915 0.958456861 1.03668274 1 21.44867259 1.771309646 1.83363705 1.019409802 0.77255637 0.786699152 0.051927987 0.146732046 0.971408199 0.037740637 0.015741868 59.06220349 -1.771309646 -0.246853432 AISHEHSPSDLEAHFVPLVK ddPTM_BT-474_Pertuzumab_2h_R1 3 AISHEHSPSDLEAHFVPLVK 20 0 P30153;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;; 83.758 0.0010033 1480990000 1683300 1628730 1432020 1617560 1595070 1749290 1764200 46065.7 2030740 797387 FALSE TRUE 1617514.775 1582280.215 1690817.869 1701042.465 1646376.875 1784661.842 1785790.807 45114.4272 1800218.909 743379.2683 2.175894384 2.12849656 2.274502318 2.288256531 2.214719922 2.400742015 2.402260708 0.060688304 2.421669511 1 19.50373893 1.771325859 25 1.073964004 2.267744183 0.467322745 0.539944125 22.85702819 17448.52811 0.229648663 0.127397522 59.06440849 -1.771325859 1.193780179 EYGSCSHHYQQLLQSLEQGAQEESR ddPTM_BT-474_Pertuzumab_2h_R1 5 EYGSCSHHYQQLLQSLEQGAQEESR 25 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 282.18 1.40E-53 4341690000 711587 972757 872506 1219456 1006510 1163102 1023690 415456 960120 979507 FALSE TRUE 683777.3933 945014.9228 1030187.243 1282392.27 1038885.308 1186620.719 1036218.224 406876.6884 851131.2028 913164.1184 0.748800111 1.034879606 1.128151251 1.404339313 1.137676445 1.299460519 1.134755739 0.445567976 0.932068163 1 19.80051465 1.771336987 25 0.736873986 1.141103871 0.331376208 0.21259601 28.88970126 22046.24062 0.098188621 0.054470419 59.06592187 -1.771336987 0.404229885 DEAQNEGPATESEAPLKEDGLLPKPLSSGGEEEEKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEAQNEGPATESEAPLKEDGLLPKPLSSGGEEEEKPR 37 3 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 344.47 1.00E-130 770080000 638080 484780 480010 360560 494880 507200 522130 668250 799960 631430 FALSE TRUE 613143.1282 470954.549 566758.4848 379168.5448 510798.2646 517455.9315 528519.9831 654450.404 709151.8945 588662.6837 1.04158654 0.800041453 0.962789897 0.644118534 0.867726592 0.879036409 0.897831641 1.111757925 1.204682944 1 19.16708165 1.771359011 3.528970612 1.122665613 0.859336431 0.498933375 0.107780999 0.164317436 4.033357063 0.056108938 0.028141922 59.0689174 -1.771359011 -0.263329182 NHKEDEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 NHKEDEAK 8 1 O14617-5;O14617-2;O14617;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ;;; 133.13 0.00056025 146932000 401170 320080 271646 248599 291095 295159 323699 107894 300789 312326 FALSE TRUE 385491.8329 310951.6318 320738.4749 261429.2242 300458.335 301127.3172 327660.5252 105665.9512 266644.6937 291171.8818 1.32393221 1.067931525 1.101543435 0.897851889 1.031893372 1.034190923 1.125316508 0.362898885 0.915763885 1 18.15151152 1.771361883 24.99999983 0.694313 1.072361355 0.369101205 0.187838227 26.04860566 19863.05413 0.082619701 0.045833356 59.06930805 -1.771361883 0.378048355 KNDMDEPPPLDYGS(ph)GEDDGKSDK ddPTM_BT-474_Pertuzumab_2h_R1 3 KNDMDEPPPLDYGSGEDDGKSDK 23 2 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5;H7C2H0 Q12873-3;H7C2H0 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 KNDMDEPPPLDYGS(1)GEDDGKSDK;KNDMDEPPPLDYGS(1)GEDDGKSDK;KNDMDEPPPLDYGS(1)GEDDGKSDK 209.05 4.74E-25 641402000 996090 756035 690435 538772 754274 654475 758255 954800 1154140 816929 TRUE FALSE 957161.7016 734473.622 815211.9631 566578.0875 778535.9082 667708.9329 767534.7515 935083.0463 1023126.866 761597.6712 1.256781287 0.964385331 1.070397132 0.743933587 1.0222404 0.876721343 1.00779556 1.227791368 1.343395476 1 19.53866954 1.771427314 5.052312384 1.213692228 0.979558485 0.271253616 0.147101113 0.212383639 11.6258499 0.0703958 0.037743156 59.07820805 -1.771427314 -0.234133743 HLDAHTAAHS(ph)QSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLDAHTAAHSQSPR 14 0 H7C3X3;H0Y6N5;E9PHI4;O94901-9 H7C3X3 SUN1 1 HLDAHT(0.086)AAHS(0.54)QS(0.374)PR 66.826 0.090742 47212000 46161 70769 46552 85842 59493 64517 63066 11423 64039 43497 TRUE FALSE 44356.97709 68750.73741 54964.98194 90272.31591 61406.64638 65821.57794 63837.82057 11187.11106 56769.56119 40550.90945 1.093858996 1.695417892 1.355456208 2.226147752 1.514309968 1.623183767 1.574263597 0.275878179 1.399957781 1 15.30744665 1.771444743 25 0.822864362 1.602401493 0.415163016 0.372813672 25.12891482 19113.44192 0.163151588 0.090509145 59.08057905 -1.771444743 0.779537131 LVAFGTSHGFGLFDHQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVAFGTSHGFGLFDHQQR 18 0 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 300 9.60E-50 338230000 222360 172270 205960 133850 176040 194180 185680 93359 186900 171220 FALSE TRUE 213669.9254 167357.0283 243181.5536 140758.0145 181702.4865 198106.4526 187952.4074 91431.10403 165683.8955 159623.1169 1.338590109 1.048451074 1.523473281 0.881814723 1.13832188 1.241088738 1.177476114 0.572793627 1.037969304 1 17.28431007 1.771468776 25 0.828030543 1.187723133 0.35155353 0.198154661 28.83873347 21919.15917 0.086211676 0.047826405 59.08384854 -1.771468776 0.35969259 DGQWFTDWDAVPHSR ddPTM_BT-474_Pertuzumab_2h_R1 6 DGQWFTDWDAVPHSR 15 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;;;; 236.78 1.02E-17 5397010000 3275770 3587520 2764760 3221470 3342290 3579510 3351800 3212410 3478520 3674660 FALSE TRUE 3147749.287 3485207.442 3264413.634 3387730.453 3449797.793 3651890.145 3392820.331 3146072.611 3083652.993 3425772.005 0.918843777 1.017349502 0.952898684 0.98889548 1.007013248 1.066005017 0.990381241 0.918354346 0.900133747 1 21.70799771 1.771476612 8.038343445 0.932207533 0.994551978 0.223036116 0.043719513 0.242314042 44.64189377 0.020236216 0.011257507 59.08491463 -1.771476612 0.062344445 LQQHIQELEAHLEAEEGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQQHIQELEAHLEAEEGAR 19 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 174.2 2.86E-12 487380000 123427 162117 133373 141471 138371 162490 149970 75735 154061 136697 FALSE TRUE 118603.3364 157493.5819 157476.468 148772.3353 142821.8289 165775.6591 151805.3777 74171.04578 136572.6412 127438.3904 0.930671958 1.235840953 1.235706661 1.16740595 1.120712749 1.300829825 1.191206019 0.582014929 1.071675817 1 16.95944043 1.771536494 25 0.842979582 1.177216242 0.414878909 0.152140377 23.99097085 18197.10125 0.066250381 0.036753443 59.09306201 -1.771536494 0.33423666 VIPVLLQLFEVHEEHVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIPVLLQLFEVHEEHVR 17 0 Q8IZE3;Q8IZE3-2;X6RHX1 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 0 141.85 3.52E-07 63776000 35245 39054 34377 39499 44606 43713 44164 9802.7 42276 38644 FALSE TRUE 33867.58643 37940.21816 40589.68861 41537.54812 46040.7925 44596.90681 44704.49224 9600.270819 37477.00572 36026.60746 0.940071487 1.053116594 1.126658641 1.152968627 1.277966363 1.237888049 1.240874326 0.266477237 1.040259085 1 15.13677518 1.771572761 25 0.694054408 1.151432154 0.369894026 0.219709717 25.85991265 19593.12616 0.09740991 0.05403904 59.09799697 -1.771572761 0.457377746 AQHPQPAGQQGHGAS(ph)PHTGLPAGSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQHPQPAGQQGHGASPHTGLPAGSLR 26 0 H7C0J3;I3L229 H7C0J3 CHD3 1 AQHPQPAGQQGHGAS(1)PHTGLPAGSLR 228.84 1.62E-34 355670000 127370 126490 129030 129500 116740 139670 133470 37229 124550 119950 TRUE FALSE 122392.2396 122882.629 152348.5913 136183.5105 120495.0481 142494.2231 135103.4458 36460.20814 110411.6062 111825.6797 1.094491354 1.098876657 1.362375724 1.217819654 1.077525739 1.274253137 1.208161186 0.326045039 0.987354662 1 16.770892 1.771608376 25 0.703348795 1.193514109 0.483938496 0.194697926 21.05056849 15932.06221 0.084716217 0.046997301 59.10284359 -1.771608376 0.490165313 HLEHSTIIYEDPQHHPLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLEHSTIIYEDPQHHPLLR 19 0 P61962;A0A087WWI6 P61962 DCAF7 DDB1- and CUL4-associated factor 7 0 ; 199.08 2.19E-16 544230000 126846 155433 146598 182289 163191 168706 156947 6704.93 144693 113548 FALSE TRUE 121888.7181 151000.203 173091.5197 191696.9571 168440.1867 172117.3509 158867.7643 6566.470852 128268.0572 105857.2928 1.151443749 1.426450639 1.635140244 1.810899864 1.591200589 1.625937584 1.500772976 0.062031351 1.211707326 1 16.69176114 1.771616934 25 0.666485199 1.550583677 0.545414115 0.321451193 19.65042895 14868.51762 0.142529034 0.079070022 59.10400818 -1.771616934 0.884098479 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR 30 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 177.14 3.03E-18 22256400000 2073545 2860406 2172589 2807769 2445037 2905106 2710238 152428 2836506 1641041 FALSE TRUE 1992508.569 2778830.022 2565224.161 2952678.295 2523683.836 2963849.234 2743406.703 149280.3085 2514517.73 1529891.831 1.302385259 1.816357186 1.676735641 1.929991542 1.649583182 1.937293326 1.793203053 0.097575728 1.64359184 1 20.54499822 1.771695748 25 0.826674727 1.743331496 0.475094355 0.38947673 22.33110911 16856.64412 0.166783362 0.09252607 59.11473517 -1.771695748 0.916656769 SHS(ph)PSASQSGSQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SHSPSASQSGSQLR 14 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.001)HS(0.992)PS(0.007)ASQSGSQLR;S(0.007)HS(0.933)PS(0.058)AS(0.001)QSGSQLR;S(0.007)HS(0.992)PSASQSGSQLR 239.16 2.49E-17 728740000 349030 393260 325580 442860 379870 399100 410560 196104 381980 434090 TRUE FALSE 335389.5217 382044.6098 384419.5485 465716.0577 392088.8635 407170.0754 415584.5561 192054.3839 338619.2318 404688.6977 0.8287593 0.944045663 0.94991422 1.150800752 0.968865367 1.006131572 1.026924049 0.474573135 0.836740027 1 18.62645303 1.77182285 25 0.715936157 0.986387826 0.287617802 0.145218312 29.44956595 22145.01535 0.064177347 0.035604104 59.13203835 -1.77182285 0.270451669 LEILSGDHEQR ddPTM_BT-474_Pertuzumab_2h_R1 5 LEILSGDHEQR 11 0 Q4G0J3;Q4G0J3-3;H0YA82;Q4G0J3-2 Q4G0J3 LARP7 La-related protein 7 0 ;;;; 247.3 4.24E-16 2000230000 1334100 1523040 1271870 1462270 1468250 1519500 1418330 1299400 1366790 1401770 FALSE TRUE 1281961.897 1479604.39 1501725.202 1537737.93 1515477.595 1550225.331 1435687.947 1272566.936 1211637.729 1306826.869 0.980973017 1.132211485 1.149138602 1.176695985 1.159662102 1.186251498 1.098606082 0.973783877 0.927160099 1 20.31763659 1.771832416 3.361936178 0.959210449 1.135444952 0.628162342 0.05643792 0.139539565 3.102634932 0.031448985 0.015603208 59.13334079 -1.771832416 0.176234502 DHEDYDPQTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DHEDYDPQTVR 11 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 113.69 0.0008525 0 204310 194830 155950 136790 165820 188620 173060 55545 170660 143740 FALSE TRUE 196325.3393 189273.6392 184133.6341 143849.7483 171153.7509 192434.0256 175177.96 54397.97634 151287.3923 134004.3618 1.465066784 1.412443869 1.37408687 1.073470642 1.277225223 1.436028075 1.307255657 0.405941834 1.128973641 1 17.03192043 1.771875381 25 0.786741867 1.331153539 0.543609415 0.203684293 20.75704828 15583.92878 0.090639879 0.050285184 59.13919124 -1.771875381 0.544411673 SDSVLPASHGHLPQAGS(ph)LER ddPTM_BT-474_Pertuzumab_2h_R1 5 SDSVLPASHGHLPQAGSLER 20 0 Q8N4C8;Q8N4C8-4;Q8N4C8-2;Q8N4C8-3;Q8N4C8-5 Q8N4C8 MINK1 Misshapen-like kinase 1 1 SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPAS(0.002)HGHLPQAGS(0.998)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER 141.48 3.18E-07 2931440000 1364850 1761090 1327180 1822650 1510640 1608310 1605730 550407 1506910 1486300 TRUE FALSE 1311510.153 1710865.437 1567030.949 1916717.185 1559231.108 1640831.13 1625381.404 539040.9031 1335851.894 1385631.577 0.94650712 1.234718857 1.130914577 1.383280532 1.125285489 1.184175619 1.173025666 0.389021809 0.964074373 1 20.40211228 1.771923805 25 0.722945518 1.176619372 0.459460384 0.187146334 22.30248762 16719.89234 0.080811226 0.044832735 59.14578569 -1.771923805 0.453673855 VHLFDIITQYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VHLFDIITQYR 11 0 B4DYU2;Q96MW5;H3BQV3 B4DYU2 COG8 Conserved oligomeric Golgi complex subunit 8 0 96.229 0.0071678 107700000 80083 87847 80105 84473 84248 69675 88910 39233 89507 83647 FALSE TRUE 76953.26782 85341.68957 94581.75543 88832.66165 86957.91343 71083.87624 89998.10718 38422.82484 79346.5406 77981.51418 0.986814229 1.094383592 1.212874056 1.139150254 1.115109322 0.911547781 1.154095405 0.492717091 1.017504487 1 16.25084455 1.772062362 25 0.784691512 1.089038172 0.331298863 0.158287276 29.04227193 21682.52347 0.069746771 0.03869434 59.16465848 -1.772062362 0.30434666 TGS(ph)PGDAPERPPLCDFSEGLSAPMDFYR ddPTM_BT-474_Pertuzumab_2h_R1 4 TGSPGDAPERPPLCDFSEGLSAPMDFYR 28 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 T(0.145)GS(0.855)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.035)GS(0.965)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.03)GS(0.97)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.038)GS(0.962)PGDAPERPPLCDFSEGLSAPMDFYR 213.15 2.00E-26 651900000 288144 272680 212735 246608 263725 240429 250518 382546 314821 305618 TRUE FALSE 276883.0139 264903.4334 251180.9468 259335.4684 272207.9541 245290.6391 253583.9142 374646.2914 279083.8399 284918.2206 0.9717982 0.929752519 0.881589623 0.910210192 0.955389773 0.860915945 0.890023508 1.314925702 0.979522613 1 18.12018836 1.772074893 25 1.130067029 0.912957495 0.448626813 0.091391677 23.07789809 17223.16451 0.039496442 0.021911772 59.16636567 -1.772074893 -0.217109534 EDSLDEEFFHHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDSLDEEFFHHK 12 0 Q5JRA6-2;Q5JRA6;A0A0A0MRH6 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 0 158.05 4.31E-05 43016000 42247 68131 39027 71155 52698 44979 71771 11445 81802 49672 FALSE TRUE 40595.94053 66187.97059 46080.04705 74827.31808 54393.07903 45888.5062 72649.35497 11208.65675 72516.1799 46307.6712 0.876656923 1.429308987 0.995084526 1.615873054 1.17460191 0.99094826 1.568840607 0.242047515 1.565964732 1 15.49896359 1.772115814 25 0.857185464 1.236914024 0.105414218 0.380080114 54.5835515 40686.30606 0.162792819 0.090315353 59.17194078 -1.772115814 0.37972856 LS(ph)SGFDDIDLPSAVK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.989)S(0.011)GFDDIDLPSAVK;LS(0.91)S(0.09)GFDDIDLPSAVK;LS(0.5)S(0.5)GFDDIDLPSAVK 254.2 1.14E-24 410215000 594570 469552 339744 405093 429802 386666 407020 646710 506990 505410 TRUE FALSE 571333.5471 456160.8367 401143.2984 425999.8983 443626.9717 394484.6514 412001.2325 633355.2125 449438.6207 471178.1305 1.212563806 0.968128203 0.851362303 0.904116449 0.941527085 0.837230393 0.874406527 1.344194842 0.953861378 1 18.84591305 1.772182144 25 1.134756912 0.933475629 0.198941078 0.139377049 40.17918743 29890.24653 0.063150827 0.03503529 59.18097889 -1.772182144 -0.201281283 SHVTEEEEEEEEEES(ph)DS ddPTM_BT-474_Pertuzumab_2h_R1 1 SHVTEEEEEEEEEESDS 17 0 O75971-2;O75971 O75971-2 SNAPC5 snRNA-activating protein complex subunit 5 1 SHVTEEEEEEEEEES(0.5)DS(0.5) 211.87 1.46E-17 0 52205 50541 38824 45922 47062 50049 47376 17972 48163 39515 TRUE FALSE 50164.77088 49099.62016 45840.36044 48292.03992 48575.79197 51061.02507 47955.80166 17600.87192 42695.73816 36838.61385 1.361744258 1.332830284 1.244356278 1.310908171 1.318610743 1.386073463 1.301780839 0.47778323 1.158994156 1 15.16893116 1.772315532 25 0.82780219 1.321603709 0.596280272 0.165599083 18.55775023 13750.96248 0.070736521 0.039244438 59.19915828 -1.772315532 0.493801519 YMNSDTTS(ph)PELR ddPTM_BT-474_Pertuzumab_2h_R1 7 YMNSDTTSPELR 12 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 YMNSDTT(0.001)S(0.999)PELR;YMNSDTT(0.001)S(0.999)PELR;YMNSDTT(0.001)S(0.999)PELR;YMNSDTT(0.001)S(0.999)PELR;YMNSDTT(0.033)S(0.967)PELR;YMNSDTT(0.002)S(0.998)PELR;YMNSDT(0.012)T(0.049)S(0.939)PELR 283.03 3.67E-28 4306380000 3955090 4410650 3610500 4214550 4267810 4423730 3892200 4075240 4247880 3973980 TRUE FALSE 3800520.71 4284862.58 4262997.665 4432063.431 4405087.985 4513180.852 3939833.908 3991084.87 3765678.471 3704818.795 1.02583174 1.156564684 1.150662934 1.196296952 1.189015773 1.218192063 1.063434982 1.077268577 1.016427167 1 21.82097155 1.772328466 1.686686722 1.016658664 1.157242426 0.526678183 0.053465584 0.28254588 1.56638412 0.039746744 0.016260224 59.20092137 -1.772328466 0.140583763 GPSFPEPLREEQDLER ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSFPEPLREEQDLER 16 1 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494BZY8;A0A494C0Q8;A0A494C1D8;A0A494C0S8 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 ; 89.982 0.0051122 783980000 401140 491400 416720 561590 501260 536450 473910 420160 414280 471940 FALSE TRUE 385463.0053 477385.7531 492030.5739 590573.7272 517383.4831 547297.3866 479709.8523 411483.5492 367252.6712 439975.0834 0.876101897 1.085029064 1.118314633 1.342289028 1.175938144 1.243928139 1.090311407 0.935242846 0.83471243 1 18.7470623 1.772336922 3.312091581 0.908705033 1.148366961 0.398273284 0.118813874 0.224606857 4.841900691 0.068498178 0.033878865 59.20207402 -1.772336922 0.239661928 EDQKMS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDQKMSPK 8 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 EDQKMS(1)PK 68.735 0.084548 218490000 1082800 752830 673290 557280 720390 709690 770240 1068500 1171300 989790 TRUE FALSE 1040482.979 731360.0255 794968.4803 586041.2876 743561.9986 724040.418 779666.4275 1046435.102 1038338.934 922750.6417 1.127588464 0.792586851 0.861520377 0.635102552 0.805810329 0.784654473 0.844937291 1.134038877 1.125264928 1 19.81558131 1.772353356 5.991911326 1.09611097 0.823484474 0.474672705 0.120077452 0.145569604 12.30527469 0.057326457 0.031417671 59.20431433 -1.772353356 -0.272626496 EGMNPS(ph)YDEYADS(ph)DEDQHDAYLER ddPTM_BT-474_Pertuzumab_2h_R1 1 EGMNPSYDEYADSDEDQHDAYLER 24 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 2 EGMNPS(1)YDEYADS(1)DEDQHDAYLER 174.46 1.52E-12 108630000 50798 63919 48421 61102 57279 55803 56639 53584 55841 58230 TRUE FALSE 48812.758 62096.0927 57171.75182 64255.48154 59121.43105 56931.37489 57332.16502 52477.47167 49502.16378 54286.03023 0.899177151 1.143868734 1.05315772 1.183646718 1.089072655 1.04872975 1.056112683 0.966684641 0.911876657 1 15.72829337 1.772383777 2.551246179 0.949557253 1.077610261 0.314328715 0.072819082 0.282238591 3.651269205 0.042639405 0.019642175 59.20846159 -1.772383777 0.128053008 RIEELNK ddPTM_BT-474_Pertuzumab_2h_R1 4 RIEELNK 7 1 Q9BTC8;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8;H7C3F3;H0YIT0;E9PF88;E7ESY4;Q13330-3;Q13330;Q13330-2;O94776 Q9BTC8;E7ESY4;O94776 MTA3;MTA1;MTA2 Metastasis-associated protein MTA3;Metastasis-associated protein MTA1;Metastasis-associated protein MTA2 0 ;;; 141.52 0.004091 1431410000 1834130 1828090 1519850 1544160 1721750 1709870 1722830 1948070 2015450 1907040 FALSE TRUE 1762450.172 1775954.663 1794520.704 1623854.283 1777131.652 1744444.743 1743914.509 1907841.674 1786664.565 1777874.482 0.991324297 0.99892016 1.00936299 0.91336835 0.999582181 0.981196794 0.980898554 1.073102569 1.004944153 1 20.76172204 1.772501117 25 1.033422815 0.981784227 0.287159656 0.03105877 35.70841916 26314.55693 0.014002668 0.007768304 59.22446098 -1.772501117 -0.051638588 AVDLGPPKPSDQETGEQVS(ph)SPSSHPALHTTTEDSAGVQTEF ddPTM_BT-474_Pertuzumab_2h_R1 2 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF 41 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AVDLGPPKPSDQET(0.001)GEQVS(0.224)S(0.224)PS(0.224)S(0.224)HPALHT(0.034)T(0.034)T(0.034)EDS(0.001)AGVQTEF;AVDLGPPKPS(0.002)DQET(0.032)GEQVS(0.477)S(0.477)PS(0.006)S(0.006)HPALHTTTEDSAGVQTEF 111.51 3.20E-06 1477370000 72421 81779 90040 98880 87001 96139 99471 48241 99530 99146 TRUE FALSE 69590.70725 79446.74299 106312.2309 103983.2086 89799.46618 98082.99645 100688.3559 47244.80649 88231.77166 92430.75311 0.752895599 0.859527163 1.150182459 1.124984977 0.971532343 1.061151112 1.089338261 0.51113731 0.954571598 1 16.49608532 1.772559672 25 0.770862292 1.00754679 0.172619969 0.168956905 43.54012748 32030.6549 0.077877857 0.043207992 59.23244666 -1.772559672 0.236684497 TKLDDLALLEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKLDDLALLEDLEK 14 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ; 136.48 2.45E-05 414250000 1653940 1390350 1216310 1136360 1306580 1331400 1422810 1767480 1990260 1875200 FALSE TRUE 1589302.196 1350698.579 1436124.274 1195007.676 1348607.332 1358321.82 1440222.774 1730980.92 1764334.029 1748191.034 0.909112429 0.77262642 0.821491614 0.68356813 0.771430185 0.776987065 0.823836038 0.990155473 1.009234114 1 20.73743141 1.772616392 3.036306209 1.006306695 0.784821816 0.764805436 0.052533412 0.109091261 1.980795875 0.030007499 0.014522312 59.24018313 -1.772616392 -0.221484879 RLS(ph)QPESAEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RLSQPESAEK 10 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RLS(0.983)QPES(0.017)AEK;RLS(0.5)QPES(0.5)AEK;RLS(0.782)QPES(0.218)AEK;RLS(1)QPESAEK;RLS(0.992)QPES(0.008)AEK;RLS(1)QPESAEK 209.67 9.66E-08 11408270000 9044790 9562620 7990110 10015780 11138070 9131570 8310670 8504440 7661650 7638770 TRUE FALSE 8691309.607 9289903.44 9434100.616 10532695.61 11496336.14 9316216.602 8412378.465 8328820.342 6791931.612 7121389.304 1.220451409 1.304507175 1.324755636 1.479022583 1.614338951 1.308202122 1.181283329 1.169549927 0.953736879 1 22.76372729 1.772779591 1.362066979 0.989014817 1.384539473 0.66901645 0.109031568 0.269750726 0.946968868 0.094946841 0.037735709 59.26244846 -1.772779591 0.395524656 ENYSHHTQDDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 ENYSHHTQDDRR 12 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 136.38 7.21E-05 1771924700 257706 447694.9 363553.6 635871 721508.5 651946.1 510312.7 83985.6 192479 283784.8 FALSE TRUE 247634.5646 434927.0798 429255.8227 668688.3785 744716.4762 665128.8968 516558.0595 82251.26801 170629.5909 264563.8027 0.936010755 1.643940234 1.622503979 2.527512727 2.81488423 2.514058575 1.952489548 0.310893883 0.644946849 1 18.01325616 1.77278926 7.503600542 0.614301528 2.046931233 0.570347363 0.535454809 0.14066188 21.4707235 0.276479854 0.153952461 59.26376789 -1.77278926 1.432629705 GQHHQQQQAAGGSESHPVPPTAPLT(ph)PLLHGEGASQQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GQHHQQQQAAGGSESHPVPPTAPLTPLLHGEGASQQPR 38 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 GQHHQQQQAAGGSESHPVPPT(0.006)APLT(0.994)PLLHGEGASQQPR;GQHHQQQQAAGGSESHPVPPT(0.149)APLT(0.851)PLLHGEGASQQPR;GQHHQQQQAAGGSESHPVPPT(0.003)APLT(0.997)PLLHGEGASQQPR;GQHHQQQQAAGGSESHPVPPTAPLT(1)PLLHGEGASQQPR 268.35 3.24E-63 4526200000 539418 702520 504325 706459 772410 648511 677653 112735 649639 552060 TRUE FALSE 518336.9482 682484.8174 595467.7461 742919.4337 797255.2691 661624.3367 685946.3201 110406.9829 575894.7042 514668.4845 1.007127819 1.326066853 1.15699283 1.44349121 1.549065647 1.285534974 1.332792547 0.214520582 1.118962442 1 18.97328392 1.772831481 25 0.698881665 1.310168222 0.443964171 0.263298397 25.71296507 18765.84082 0.116020254 0.06437199 59.26952964 -1.772831481 0.611286557 AEHLDHVMFR ddPTM_BT-474_Pertuzumab_2h_R1 3 AEHLDHVMFR 10 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77;D6RC77;D6RCD1 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ;; 151.22 1.17E-05 637298000 690440 721355 688718 878553 788895 581521 855775 39693.7 793398 733566 FALSE TRUE 663456.8415 700782.6617 813184.663 923895.2256 814270.5241 593279.7531 866248.2304 38874.01122 703334.7852 683880.9214 0.970135035 1.024714449 1.189073474 1.350959205 1.190661267 0.867519088 1.266665297 0.056843246 1.028446274 1 19.38338562 1.772850601 25 0.597471181 1.123158339 0.30250663 0.286338187 32.49637237 23703.27822 0.125891144 0.069848404 59.27213911 -1.772850601 0.525687157 AEEKS(ph)PISINVK ddPTM_BT-474_Pertuzumab_2h_R1 7 AEEKSPISINVK 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 AEEKS(0.955)PIS(0.045)INVK;AEEKS(0.994)PIS(0.006)INVK;AEEKS(0.979)PIS(0.021)INVK;AEEKS(0.955)PIS(0.045)INVK;AEEKS(0.916)PIS(0.084)INVK;AEEKS(0.988)PIS(0.012)INVK;AEEKS(0.997)PIS(0.003)INVK 230.97 2.75E-12 12719050000 10658730 9169030 8217240 7241710 8504130 8484600 9020370 11224040 12696400 10678140 TRUE FALSE 10242175.05 8907538.242 9702278.06 7615455.521 8777673.065 8656164.425 9130763.986 10992259.65 11255157.9 9954900.067 1.028857646 0.894789318 0.974623351 0.764995677 0.881743966 0.869538053 0.917213023 1.104205927 1.130614855 1 23.2469754 1.772866633 5.159601882 1.087739933 0.898203215 0.548371126 0.071994047 0.131611828 7.531986738 0.03521166 0.018975358 59.27432718 -1.772866633 -0.189536718 NHS(ph)GSRTPPVALNSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.333)GS(0.333)RT(0.333)PPVALNSSR 53.395 0.091673 207500000 54841 75671 52070 72469 56593 65986 59803 43244 44382 44228 TRUE FALSE 52697.75309 73512.93717 61480.20729 76209.13377 58413.36524 67320.28213 60534.887 42350.99629 39343.94142 41232.39817 1.278066652 1.78289259 1.491065522 1.848282835 1.416686097 1.632703532 1.468138883 1.027129107 0.954199687 1 15.33149075 1.772873326 2.923438369 0.972858762 1.585196231 0.736356095 0.156294443 0.110263759 1.85872318 0.082925387 0.039736483 59.27524071 -1.772873326 0.612337468 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVST(ph)PPPFQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGR 47 0 B7Z8Z7;A0AV96;A0AV96-2 B7Z8Z7 RBM47 RNA-binding protein 47 1 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPT(0.136)VS(0.18)T(0.684)PPPFQGR 81.777 0.0001881 103580000 31994 28876 36370 45732 34538 32209 36158 11256 37413 28394 TRUE FALSE 30743.63911 28052.48475 42942.86805 48092.234 35648.94614 32860.28805 36600.51242 11023.55967 33166.03309 26470.84909 1.161414921 1.059750092 1.62227014 1.816799825 1.346724694 1.241376426 1.382672399 0.416441484 1.252926681 1 14.69211685 1.772923893 25 0.832426126 1.383844331 0.378297598 0.282565134 33.07653835 24074.97235 0.133556864 0.074102821 59.28214273 -1.772923893 0.551418205 WGEEHIPGSPFHVTVP ddPTM_BT-474_Pertuzumab_2h_R1 1 WGEEHIPGSPFHVTVP 16 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 84.468 0.0074781 64529000 59653 78014 63784 78435 62476 72419 71431 13388 61597 68292 FALSE TRUE 57321.69481 75789.1171 75311.18767 82483.03975 64485.59728 73883.3618 72305.19395 13111.53312 54604.7668 63666.52201 0.900342802 1.190407685 1.182900923 1.295548071 1.012865086 1.160474288 1.135686255 0.205940779 0.857668443 1 15.95824733 1.772958944 25 0.606773556 1.13372604 0.443173893 0.219055697 24.62111653 17902.36643 0.094719935 0.05255463 59.28692754 -1.772958944 0.526952484 DFGNHQVTGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFGNHQVTGK 10 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 0 90.685 0.010662 176540000 224570 248900 211930 245320 234330 254730 244360 222570 275260 252920 FALSE TRUE 215793.5561 241801.6157 250230.4654 257980.9946 241867.4373 259880.8151 247350.5508 217973.8517 244013.6388 235789.5031 0.915195771 1.025497796 1.061245145 1.094115689 1.02577695 1.102172962 1.049031223 0.924442559 1.034879142 1 17.84713997 1.772999218 25 0.978916694 1.043381379 0.154952082 0.054759911 54.19716279 39361.43866 0.025420058 0.014104135 59.29242568 -1.772999218 0.064464684 FTEDLVGSVVHVLSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTEDLVGSVVHVLSHR 16 0 Q6P9B6;H3BUB0;H3BM75 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 ; 89.466 0.0033428 102563000 122685 134923 102460 151082 119773 104431 138387 38016 132442 129709 FALSE TRUE 117890.3346 131075.1281 120976.8012 158879.3601 123625.6073 106542.6664 140080.6215 37230.95632 117407.7394 120923.6939 0.974915095 1.083949092 1.00043918 1.313881135 1.022343954 0.881073534 1.158421621 0.307888017 0.970924189 1 16.88373743 1.773001509 25 0.687765133 1.061798533 0.286154838 0.209971581 33.78098745 24532.26721 0.091906552 0.050993868 59.29273848 -1.773001509 0.3740334 VSPNELILGWYATGHDITEHSVLIHEYYSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPNELILGWYATGHDITEHSVLIHEYYSR 30 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 181.9 2.24E-18 2194400000 187857 205338 178542 217147 212867 202814 221670 56513 238610 163700 FALSE TRUE 180515.3408 199481.9613 210808.511 228353.9827 219714.0604 206915.038 224382.8638 55345.9868 211523.9931 152612.4532 1.182834932 1.307114571 1.3813323 1.496299797 1.439686315 1.355820143 1.47027886 0.362657081 1.386020529 1 17.21951317 1.773021412 25 0.852537019 1.380013833 0.412095002 0.248262857 28.08214159 20381.89204 0.107561399 0.059680012 59.29545589 -1.773021412 0.527476814 MQEEEEVVDKMDDDVFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 MQEEEEVVDKMDDDVFLR 18 1 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 0 ; 131.67 1.50E-05 134632000 131978 127633 113764 126442 131288 127999 132072 150017 164370 161482 FALSE TRUE 126820.1539 123993.0318 134323.6855 132967.6868 135510.9978 130587.2275 133688.3366 146919.0965 145711.4067 150544.6803 0.842408736 0.823629447 0.892251292 0.883244008 0.900138068 0.867431697 0.888030958 0.975916892 0.967894757 1 17.1998322 1.773155781 2.886343229 0.982961359 0.869426013 0.836932449 0.022447028 0.101966451 1.675857299 0.014160253 0.006763417 59.31380438 -1.773155781 -0.113535346 RKS(ph)QEALHEQSSYILSSAETPARPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RKSQEALHEQSSYILSSAETPARPR 25 3 Q9NVE5;Q9NVE5-3 Q9NVE5 USP40 Ubiquitin carboxyl-terminal hydrolase 40 1 RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR 249 2.37E-39 2031154000 310060 327683 239841 284474 298174 281253 294998 328439 335081 337245 TRUE FALSE 297942.5124 318337.8017 283185.6039 299155.7372 307765.0375 286940.1284 298608.2738 321656.6199 297044.0097 314403.0958 0.947644971 1.012514845 0.900708701 0.95150379 0.978886791 0.912650455 0.949762511 1.023070778 0.944787165 1 18.2622559 1.773164457 24.99998164 0.991304877 0.950664628 0.210013807 0.034382879 52.71347898 38100.96593 0.015368684 0.008527169 59.31498933 -1.773164457 -0.040640249 DKLDETGVALK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKLDETGVALK 11 1 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 100.22 0.0038211 266890000 952120 811180 575360 708030 788540 756940 774080 964460 936180 870240 FALSE TRUE 914910.0978 788045.9406 679340.3508 744571.5132 813904.1052 772245.8454 783553.4226 944543.564 829908.7712 811297.8697 1.127711697 0.971339837 0.837350098 0.917753566 1.003212427 0.951864752 0.965802391 1.164237698 1.022939665 1 19.62987217 1.773233153 25 1.079075798 0.961793221 0.21763022 0.079707374 44.56745136 32149.19822 0.037268562 0.020679178 59.3243725 -1.773233153 -0.117282577 HQADACHAYQIIHR ddPTM_BT-474_Pertuzumab_2h_R1 3 HQADACHAYQIIHR 14 0 Q99538-3;Q99538-2;Q99538;G3V2T4;G3V4E4;G3V4P5;G3V3Z4 Q99538-3 LGMN Legumain 0 ;; 179.65 6.41E-07 672590000 199930 229459 171804 230693 196590 186364 207244 48575 193801 183520 FALSE TRUE 192116.5146 222915.054 202852.8046 242599.0934 202913.4959 190132.4078 209780.3141 47571.90928 171801.523 171090.0269 1.122897214 1.302910859 1.185649498 1.417961629 1.186004231 1.111300356 1.226139932 0.278051913 1.004158606 1 17.38439614 1.773249968 25 0.687693772 1.225477826 0.497198006 0.208624473 23.56402697 16989.91848 0.090223043 0.050061421 59.32666947 -1.773249968 0.537784054 S(ph)PPAPGLQPMR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPPAPGLQPMR 11 0 P15408;P15408-3;P15408-2;C9JCN8 P15408 FOSL2 Fos-related antigen 2 1 S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR 113.22 0.0014899 4512560000 218877 187895 192031 233637 195314 238064 220686 96812 218997 208341 TRUE FALSE 210323.0449 182536.4186 226735.2734 245695.0336 201596.4522 242877.8172 223386.8213 94812.79837 194137.3787 194229.8785 1.082856286 0.939795772 1.167355276 1.26497033 1.037927088 1.250465783 1.150115641 0.488147339 0.999523761 1 17.56740562 1.773252398 25 0.777040951 1.128499098 0.403805243 0.162493614 28.88088424 20821.97239 0.072256141 0.040092005 59.32700135 -1.773252398 0.351458147 LNFSHGTHEYHAETIK ddPTM_BT-474_Pertuzumab_2h_R1 5 LNFSHGTHEYHAETIK 16 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;; 223.97 4.76E-15 6728536400 1669311.2 1758128.9 1541562.8 1667367.9 1554292.7 1325149.4 1703910.1 163203 1744090.7 1200784.8 FALSE TRUE 1604072.673 1707988.785 1820157.49 1753420.957 1604287.936 1351944.829 1724763.062 159832.801 1546108.836 1119454.576 1.432905548 1.525732997 1.625932422 1.5663172 1.433097841 1.207681721 1.540717327 0.142777389 1.381126907 1 20.09436456 1.77327199 25 0.755649199 1.475227887 0.467273315 0.306518775 26.09428225 18802.31742 0.133433023 0.074036242 59.32967787 -1.77327199 0.719578688 APAPPQSGSCDHPLLLLEPGNLAS(ph)SPSMSLASPQPCGLASHEEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 APAPPQSGSCDHPLLLLEPGNLASSPSMSLASPQPCGLASHEEHR 45 0 Q9C073;D6RJ87 Q9C073 FAM117A Protein FAM117A 1 APAPPQSGSCDHPLLLLEPGNLAS(0.399)S(0.399)PS(0.097)MS(0.097)LAS(0.007)PQPCGLAS(0.002)HEEHR 62.489 0.0015887 31230000 8597.2 9393.3 6085 9688.9 10577 8362.9 9915.5 2405.4 9516.7 9105.6 TRUE FALSE 8261.211919 9125.412281 7184.69486 10188.94529 10917.21881 8532.003568 10036.84886 2355.727649 8436.404113 8488.869602 0.973181626 1.074985565 0.846366501 1.200271151 1.28606273 1.005081238 1.182353991 0.277507814 0.993819496 1 13.05135674 1.773282701 24.99999999 0.682160409 1.081449228 0.289092179 0.223813319 34.87325419 25120.27765 0.098865021 0.05485662 59.33114108 -1.773282701 0.399288818 IMGPNYT(ph)PGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 IMGPNYTPGKK 11 1 P13639 P13639 EEF2 Elongation factor 2 1 IMGPNYT(1)PGKK;IMGPNYT(1)PGKK 121.18 0.00024432 1195490000 994980 800610 851580 773450 837180 821680 914710 1217280 1397540 1222190 TRUE FALSE 956095.0816 777777.3867 1005479.449 813367.8472 864108.655 838294.9326 925904.4946 1192142.743 1238897.118 1139409.983 0.839114187 0.682614159 0.88245624 0.713850027 0.758382556 0.735727214 0.812617503 1.04628076 1.087314608 1 20.11985552 1.773306592 3.663332055 1.054150273 0.767525395 0.819334677 0.058214436 0.076986116 2.02880357 0.028771321 0.014579437 59.33440506 -1.773306592 -0.286624879 S(ph)GSGPTQDLNTILLTSAQLSSDVAVETPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSGPTQDLNTILLTSAQLSSDVAVETPK 29 0 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 S(0.304)GS(0.304)GPT(0.304)QDLNT(0.085)ILLT(0.004)SAQLSSDVAVETPK 99.614 0.00052225 23228000 22419 21054 20855 19244 24063 21009 23022 27946 32393 28403 TRUE FALSE 21542.84069 20453.56053 24623.96242 20237.18515 24837.00825 21433.81637 23303.75012 27368.90533 28715.88244 26479.23951 0.813574751 0.772437612 0.929934653 0.764266101 0.937980422 0.8094574 0.880076262 1.033598617 1.084467793 1 14.69257407 1.773321203 3.272652169 1.048839246 0.840541804 0.708666577 0.057859197 0.113781184 2.389877327 0.030006703 0.014811321 59.33640121 -1.773321203 -0.208297441 ELNLQDFSHLDHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELNLQDFSHLDHR 13 0 Q5VZK9;Q5VZK9-2;Q5VZK9-3;A0A0U1RR91;Q5VZK9-4 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 ;;; 131.53 7.48E-05 584536000 251493 285010 246824 330721 299632 311465 325890 11177.9 318030 248978 FALSE TRUE 241664.3755 276881.7939 291430.5874 347789.5504 309269.9354 317763.0357 329878.3393 10947.07246 281928.5677 232114.4983 1.041142959 1.192867296 1.255546679 1.498353412 1.33240249 1.368992622 1.421187999 0.047162381 1.214609901 1 17.82447711 1.773357045 25 0.656692104 1.30690961 0.389752594 0.306781615 29.27022027 21039.16675 0.134262936 0.07449804 59.34129849 -1.773357045 0.650217506 DHAISLSEPR ddPTM_BT-474_Pertuzumab_2h_R1 3 DHAISLSEPR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;; 159.83 7.56E-06 539620000 404980 449700 388100 473570 433130 457000 472340 266172 477510 480790 FALSE TRUE 389152.9339 436874.9963 458238.3032 498011.0045 447062.0198 466240.8531 478120.6382 260675.4552 423305.0667 448225.6651 0.868207611 0.974676442 1.022338387 1.111072041 0.997403885 1.040192228 1.066696255 0.581571908 0.94440167 1 18.77386573 1.773392042 24.99996331 0.798372462 1.014901764 0.273333763 0.120436894 34.96291054 25105.71886 0.053247967 0.029545501 59.34608056 -1.773392042 0.216529302 RGTS(ph)PRPPEGGLGYSQLGDDDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGTSPRPPEGGLGYSQLGDDDLK 23 2 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 RGT(0.402)S(0.597)PRPPEGGLGY(0.001)SQLGDDDLK 158.02 1.10E-10 277020000 91837 70944 77804 80138 72729 72782 88712 107760 115850 128220 TRUE FALSE 88247.90851 68920.74658 91864.91354 84273.93178 75068.39434 74253.70191 89797.68399 105534.7183 102699.1937 119535.5452 0.738256628 0.576571149 0.768515452 0.705011481 0.628000602 0.621185119 0.751221604 0.882873108 0.859151924 1 16.86708016 1.773396102 2.069413176 0.924334211 0.671883997 0.750550677 0.06238826 0.147353144 1.252564635 0.040719069 0.017612179 59.34663535 -1.773396102 -0.252450214 GHIVLLQEAETLIQIEEDSTHIICDNDEMLR ddPTM_BT-474_Pertuzumab_2h_R1 3 GHIVLLQEAETLIQIEEDSTHIICDNDEMLR 31 0 Q9NV88-3;Q9NV88-2;Q9NV88;H0YBK3 Q9NV88-3 INTS9 Integrator complex subunit 9 0 ;; 355.49 6.41E-121 218225000 29773.7 35784.1 25458.8 32736.7 35035.1 40319.9 36954 13917.8 35965 35929.1 FALSE TRUE 28610.11089 34763.5725 30059.77149 34426.24501 36162.03581 41135.196 37406.25411 13630.39257 31882.40398 33495.59005 0.854145601 1.037855206 0.897424749 1.027784402 1.079605875 1.228077963 1.11675161 0.406930958 0.951838852 1 15.03168355 1.773399186 25 0.724522572 1.038295684 0.265499154 0.180601989 36.9523627 26528.87695 0.081501343 0.045223344 59.34705688 -1.773399186 0.313773112 DMGITLHLLLHSDRDPIPDVPAVYFVMPTEENIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DMGITLHLLLHSDRDPIPDVPAVYFVMPTEENIDR 35 1 Q8WVM8;G3V363;H0YJS6;J3KNG4;G3V2M8 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 48.085 0.051429 135610000 62008 70645 54841 51269 68259 74397 64169 21958 70134 46246 FALSE TRUE 59584.65881 68630.27377 64751.98863 53914.99923 70454.61273 75901.35831 64954.31942 21504.55963 62172.68235 43113.71723 1.382034829 1.591843111 1.501888327 1.250530056 1.634157694 1.760492094 1.506581283 0.498786952 1.442062674 1 15.39585934 1.773407294 25 0.932418378 1.523903836 0.491752716 0.249144783 26.50264513 19022.37466 0.110110506 0.061096891 59.34816487 -1.773407294 0.591485458 SSCNYNHHLDVVDNLTLMVEHTDIPEAS(ph)PASTPQIIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSCNYNHHLDVVDNLTLMVEHTDIPEASPASTPQIIK 37 0 D6REL5;Q6UWZ7-2;Q6UWZ7 D6REL5 FAM175A BRCA1-A complex subunit Abraxas 1 S(0.005)S(0.005)CNY(0.005)NHHLDVVDNLT(0.005)LMVEHT(0.005)DIPEAS(0.725)PAS(0.125)T(0.125)PQIIK 46.082 0.033902 70869000 14835 15908 13260 14451 12172 13602 14096 3341.9 12440 13454 TRUE FALSE 14255.2318 15454.31942 15656.37697 15196.81784 12563.52343 13877.04176 14268.51106 3272.888597 11027.86335 12542.7486 1.136531733 1.232131801 1.248241312 1.211601885 1.001656323 1.106379647 1.137590454 0.260938707 0.879222227 1 13.61456591 1.773468639 25 0.638082835 1.154708304 0.509090353 0.193838487 23.52148399 16852.94885 0.084908113 0.047113596 59.35654845 -1.773468639 0.516625469 KPLHLLDCIHVLLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPLHLLDCIHVLLIR 15 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 171.67 4.35E-07 117093000 132608 128555 129744 119135 131553 129864 134966 76561 137282 133952 FALSE TRUE 127425.5328 124888.7373 153191.6269 125283.5716 135784.5217 132489.9391 136617.7543 74979.9886 121698.3229 124879.3117 1.020389454 1.000075477 1.226717419 1.003237205 1.087325994 1.06094386 1.093998296 0.600419618 0.974527495 1 16.93017497 1.773570046 25 0.817256048 1.071398683 0.385486149 0.119365108 29.35166063 20969.27338 0.051668867 0.028670508 59.37040974 -1.773570046 0.254142635 KTET(ph)QEKNPLPSK ddPTM_BT-474_Pertuzumab_2h_R1 4 KTETQEKNPLPSK 13 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 KT(0.029)ET(0.971)QEKNPLPSK;KT(0.203)ET(0.797)QEKNPLPSK;KT(0.203)ET(0.797)QEKNPLPSK;KT(0.137)ET(0.863)QEKNPLPSK 149.34 0.0020829 5529160000 5826830 4435060 2811560 3399960 5206240 3421910 4215480 6975180 5547190 5162590 TRUE FALSE 5599111.042 4308576.431 3319671.435 3575432.343 5373703.438 3491103.365 4267070.305 6831140.095 4917496.247 4812923.181 1.163349347 0.89520989 0.689741205 0.742881656 1.116515522 0.725360292 0.886585999 1.419332875 1.021727558 1 22.19848197 1.773636644 25 1.189538587 0.878024501 0.287404509 0.182364538 38.47187303 27432.68256 0.082541754 0.045801371 59.37951473 -1.773636644 -0.311514086 MLEVHFVGDDDVLNHILDR ddPTM_BT-474_Pertuzumab_2h_R1 5 MLEVHFVGDDDVLNHILDR 19 0 Q13416;C9JK08;B8ZZ80 Q13416 ORC2 Origin recognition complex subunit 2 0 ;;;; 224.65 1.11E-19 244845000 158363 163474 144621 169843 177442 191956 174671 126000 181421 183673 FALSE TRUE 152173.9989 158811.8816 170757.2318 178608.6176 183149.5831 195837.4818 176808.6759 123398.056 160826.8487 171232.6641 0.888697257 0.92746254 0.997223472 1.043075622 1.069594893 1.143692314 1.03256395 0.720645542 0.939229962 1 17.38559841 1.773645632 25 0.857693403 1.018768488 0.260104969 0.09506389 41.00563213 29231.90335 0.045455548 0.025222976 59.38074365 -1.773645632 0.161075085 QSHSSSS(ph)PHPK ddPTM_BT-474_Pertuzumab_2h_R1 3 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.001)S(0.007)S(0.072)S(0.919)PHPK;QS(0.002)HS(0.008)S(0.038)S(0.341)S(0.611)PHPK;QSHSSS(0.017)S(0.983)PHPK 128.76 0.00016686 987449000 1248288 1693302 1229600 1759501 1377628 1587641 1659896 628457 1496847 1791641 TRUE FALSE 1199503.525 1645010.685 1451816.072 1850309.057 1421940.656 1619744.189 1680210.304 615479.1433 1326931.204 1670291.559 0.718140206 0.984864394 0.869199191 1.107776093 0.851312843 0.969737397 1.005938331 0.368486053 0.794430886 1 20.67166852 1.773748166 25 0.654457963 0.93476147 0.196946519 0.178239285 40.18193196 28561.1912 0.07683494 0.042635924 59.39476462 -1.773748166 0.280303507 LHTDDDLNWLDHSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LHTDDDLNWLDHSR 14 0 Q9Y4G6 Q9Y4G6 TLN2 Talin-2 0 ;;; 203.85 8.36E-09 268131000 144154 166981 135408 165820 179315 189160 169290 41630.8 167586 139992 FALSE TRUE 138520.3023 162218.8654 159879.2377 174377.9901 185082.8298 192984.9448 171361.8217 40771.10943 148562.3399 130510.2171 1.061375158 1.242959125 1.225032348 1.336125201 1.418148202 1.478696067 1.313014608 0.312397836 1.138319613 1 16.99380323 1.773777628 25 0.747742981 1.304885343 0.47409223 0.22788119 26.74674419 18995.58879 0.101401134 0.05626752 59.3987941 -1.773777628 0.557142362 LLEELEEGQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LLEELEEGQK 10 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;E5RIF1;D6RG00;H0YBX6 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 ;;; 198.58 6.84E-07 587155000 1398670 1297730 1169870 1236860 1315980 1266330 1326660 1608890 1725170 1649390 FALSE TRUE 1344008.43 1260720.011 1381291.533 1300694.493 1358309.692 1291936.06 1342896.062 1575665.859 1529335.934 1537675.346 0.874052142 0.81988699 0.898298549 0.845883688 0.883352715 0.840187796 0.873328733 1.024706459 0.994576611 1 20.5523195 1.773918464 5.598100398 1.006815454 0.860591182 0.895964313 0.022529926 0.048339994 3.38136506 0.01003727 0.005475742 59.41805945 -1.773918464 -0.146224271 EVS(ph)SRPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.5)S(0.5)RPS(0.552)T(0.448)PGLSVVSGISATSEDIPNK 183.65 8.12E-18 634610000 259400 258860 262880 285600 258660 231610 277720 360260 375920 394160 TRUE FALSE 249262.3612 251477.5663 310388.2637 300339.8502 266980.0338 236293.3129 281118.8204 352820.5051 333247.1376 367463.1921 0.678332869 0.684361241 0.844678516 0.817333155 0.726549052 0.643039406 0.765025794 0.960151963 0.906885764 1 18.48724022 1.773983613 4.551180912 0.950872306 0.736581302 0.7261902 0.061632582 0.114242797 4.810784397 0.03354021 0.017750233 59.42697352 -1.773983613 -0.214291005 HSEHVWVEVVR ddPTM_BT-474_Pertuzumab_2h_R1 3 HSEHVWVEVVR 11 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;; 160.18 1.61E-05 1152810000 725190 999580 837550 1196740 1032310 1149030 1048390 269048 966810 987260 FALSE TRUE 696848.7731 971072.9571 988913.9162 1258503.895 1065515.189 1172264.174 1061220.51 263492.0648 857061.782 920392.0008 0.757121718 1.055064534 1.074448621 1.367356402 1.157675412 1.273657499 1.153009272 0.286282437 0.931192124 1 19.81188892 1.77400077 25 0.665850753 1.132431066 0.341823946 0.235060446 34.07715132 24049.19319 0.106152905 0.058906031 59.42932117 -1.77400077 0.466580312 AGGAAVVITEPEHTK ddPTM_BT-474_Pertuzumab_2h_R1 4 AGGAAVVITEPEHTK 15 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;; 208.27 2.97E-09 2136970000 3388600 3180840 2806530 2949420 3162610 3284640 3227590 3420010 3871710 3737880 FALSE TRUE 3256169.766 3090125.558 3313732.402 3101639.92 3264338.223 3351057.671 3267090.212 3349385.598 3432209.712 3484710.058 0.934416267 0.886766906 0.950934897 0.890071159 0.936760353 0.961646052 0.937550085 0.961166221 0.984934085 1 21.73260719 1.774044902 0.500085739 1.001977122 0.912254972 0.644028988 0.020524316 0.516421658 0.303218228 0.019620298 0.013592327 59.43536063 -1.774044902 -0.08972215 AANQVEETLHTHLPQT(ph)PETNFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AANQVEETLHTHLPQTPETNFR 22 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 AANQVEETLHTHLPQT(0.999)PET(0.001)NFR 139.15 7.36E-07 180100000 95552 95906 79864 109530 94417 95902 97348 26713 98448 79163 TRUE FALSE 91817.7222 93170.85478 94297.20137 115182.8564 97454.00855 97841.20415 98539.37394 26161.36721 87272.59577 73801.2195 1.244122019 1.262456846 1.277718742 1.560717522 1.320493201 1.325739667 1.335199806 0.354484213 1.182535958 1 16.17135704 1.774045909 25 0.781055594 1.335633661 0.513576666 0.214280124 25.27162158 17812.1852 0.093209482 0.051724425 59.43549836 -1.774045909 0.554578066 GTFS(ph)DQELDAQSLDDEDDNMHHAVYPAVNR ddPTM_BT-474_Pertuzumab_2h_R1 4 GTFSDQELDAQSLDDEDDNMHHAVYPAVNR 30 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 GT(0.06)FS(0.94)DQELDAQSLDDEDDNMHHAVYPAVNR;GT(0.038)FS(0.962)DQELDAQSLDDEDDNMHHAVYPAVNR;GT(0.013)FS(0.987)DQELDAQSLDDEDDNMHHAVYPAVNR;GT(0.077)FS(0.923)DQELDAQSLDDEDDNMHHAVYPAVNR 240.48 2.29E-45 1546050000 231713 213574 231200 280754 283236 244620 253858 149420.2 256841 253800 TRUE FALSE 222657.3998 207483.0786 272982.983 295243.7476 292346.5432 249566.384 256964.7901 146334.6207 227685.4864 236609.8999 0.94103163 0.876899397 1.153725956 1.247808091 1.235563445 1.054758842 1.086027213 0.618463643 0.962282164 1 17.85215091 1.774066523 25 0.821302592 1.090623164 0.32359038 0.145606057 39.36694933 27730.87049 0.070384645 0.039058307 59.43831956 -1.774066523 0.269320572 FEEFYGLLQHVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 FEEFYGLLQHVHK 13 0 Q9BYG5-2;Q9BYG5 Q9BYG5-2 PARD6B Partitioning defective 6 homolog beta 0 60.628 0.052259 53318000 66215 67076 67576 72860 68128 61676 73771 31998 79946 62383 FALSE TRUE 63627.2446 65163.05815 79788.48642 76620.31333 70319.39899 62923.13098 74673.83157 31337.23012 70870.86524 58157.74384 1.094045958 1.120453681 1.371932285 1.31745677 1.209114975 1.081938996 1.283987765 0.538831599 1.218597225 1 15.82768368 1.774081069 25 0.872267781 1.212988135 0.34441007 0.181261148 35.5825845 25054.81734 0.080384908 0.044607893 59.4403105 -1.774081069 0.340720355 NEEPS(ph)EEEIDAPKPK ddPTM_BT-474_Pertuzumab_2h_R1 6 NEEPSEEEIDAPKPK 15 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK 189.51 1.54E-07 10659910000 9348740 6977740 6730580 5124540 6657790 6133230 6985080 8911460 9675800 8341720 TRUE FALSE 8983380.905 6778741.687 7946945.527 5389018.124 6871943.862 6257248.113 7070565.499 8727435.237 8577443.748 7776727.874 1.155162049 0.871670167 1.021888081 0.692967301 0.883654922 0.804611941 0.909195437 1.122250306 1.102963083 1 22.89073183 1.774123751 7.285618598 1.083683865 0.895487713 0.294208227 0.119349062 0.215033507 29.95314516 0.055211557 0.030799829 59.44615242 -1.774123751 -0.188196153 TPEPVVPTAPELRPSTSTDRPVT(ph)PKPTSR ddPTM_BT-474_Pertuzumab_2h_R1 6 TPEPVVPTAPELRPSTSTDRPVTPKPTSR 29 3 Q14676;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 TPEPVVPTAPELRPS(0.039)T(0.039)S(0.039)T(0.039)DRPVT(0.746)PKPT(0.048)S(0.048)R;TPEPVVPTAPELRPS(0.113)T(0.113)S(0.113)T(0.113)DRPVT(0.545)PKPT(0.001)S(0.001)R;TPEPVVPTAPELRPS(0.008)T(0.008)S(0.008)T(0.008)DRPVT(0.786)PKPT(0.083)S(0.099)R;TPEPVVPTAPELRPS(0.082)T(0.082)S(0.082)T(0.082)DRPVT(0.588)PKPT(0.049)S(0.034)R;TPEPVVPTAPELRPS(0.049)T(0.049)S(0.049)T(0.217)DRPVT(0.572)PKPT(0.031)S(0.031)R;TPEPVVPTAPELRPS(0.067)T(0.067)S(0.067)T(0.067)DRPVT(0.576)PKPT(0.078)S(0.078)R 130.56 7.41E-06 12423110000 5797170 4402190 3915170 3772590 3983020 4043050 4118490 6520190 5536170 4500840 TRUE FALSE 5570610.187 4276643.851 4622728.311 3967293.822 4111137.456 4124803.241 4168893.313 6385545.798 4907727.191 4195994.098 1.327602007 1.019220655 1.101700385 0.945495568 0.979776749 0.983033614 0.993541272 1.521819538 1.169622043 1 22.00058122 1.774305369 25 1.285371844 1.041551355 0.187156294 0.159830012 44.62570441 31225.08042 0.070781239 0.039280168 59.47101744 -1.774305369 -0.243820489 DHQLDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHQLDTR 7 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 ; 111.74 0.0065113 166658000 404070 457520 378780 421300 423920 392020 450160 236653 451230 458260 FALSE TRUE 388278.4977 444471.9776 447233.9719 443043.3435 437555.7718 399946.913 455669.1927 231766.0329 400008.2621 427221.642 0.908845572 1.040377953 1.046842968 1.037033942 1.024189153 0.936157895 1.066587335 0.542496002 0.936301495 1 18.70462521 1.774413783 25 0.778353837 1.010181104 0.292935514 0.12320986 35.5209656 24779.20222 0.05307596 0.029454632 59.48586519 -1.774413783 0.231827267 ELLTTMGDRFT(ph)DEEVDELYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 1 ELLTTMGDRFT(0.999)DEEVDELYR 141.37 3.10E-07 111670000 37625 47493 50185 40372 49239 62600 46438 46067 48844 45733 TRUE FALSE 36154.5734 46138.54614 59254.54586 42455.60376 50822.81715 63865.81489 47006.32214 45115.70035 43299.43389 42635.46318 0.847992978 1.082163596 1.38979482 0.99578146 1.192031548 1.497950535 1.102516981 1.058173103 1.015573203 1 15.37976631 1.774424666 3.490806597 1.024250079 1.174657831 0.113286933 0.173906711 0.49917836 11.89099387 0.09646983 0.048407073 59.48735594 -1.774424666 0.150407752 S(ph)LHS(ph)AHSLASR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 2 S(1)LHS(1)AHSLASR;S(1)LHS(1)AHSLASR 133.66 8.30E-05 4373000000 2180170 2851600 2573600 3520100 3268800 3059200 3050000 776420 3074600 2498600 TRUE FALSE 2094966.546 2770275.16 3038706.769 3701772.783 3373943.921 3121059.12 3087326.812 760386.6557 2725584.298 2329367.596 0.899371378 1.189282088 1.304520065 1.589175014 1.448437733 1.339874018 1.325392702 0.326434804 1.170096254 1 21.1515069 1.774523202 25 0.764212088 1.313825137 0.389686243 0.263459072 34.36786851 23901.82482 0.120616855 0.066938363 59.50085436 -1.774523202 0.549613049 VDDYEHAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDDYEHAAK 9 0 O43148;O43148-2;K7EP06;K7ERH6 O43148 RNMT mRNA cap guanine-N7 methyltransferase 0 ;;; 142.43 0.00010435 2156260000 4461200 4109430 3846700 4150880 4153550 3823340 4382000 4733900 5444200 5045500 FALSE TRUE 4286851.372 3992233.08 4541884.259 4365107.414 4287152.708 3900650.554 4435628.227 4636143.311 4826197.24 4703763.791 0.911366209 0.848731624 0.965585106 0.928003107 0.911430271 0.829261572 0.94299553 0.985624176 1.026028826 1 22.16538418 1.774533369 2.742250015 1.00908953 0.901245525 0.606848493 0.03754745 0.173282022 2.572548474 0.0224728 0.010593727 59.50224738 -1.774533369 -0.107844005 SIYVGNVDYGATAEELEAHFHGCGSVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIYVGNVDYGATAEELEAHFHGCGSVNR 28 0 Q92843-2;Q86U42-2;Q86U42;B4DEH8;G3V4T2 Q92843-2 PABPN1 Polyadenylate-binding protein 2 0 ; 218.98 1.66E-34 368620000 115209 116037 100241 145398 112557 126080 124290 14652.8 125359 92206 FALSE TRUE 110706.5049 112727.7384 118356.7785 152902.0082 116177.4981 128629.424 125811.0982 14350.21456 111128.7719 85960.80549 1.287871889 1.311385319 1.376869119 1.778740989 1.351517095 1.496372949 1.463586776 0.166939042 1.292784208 1 16.39139138 1.774581252 25 0.736160639 1.442843274 0.472092273 0.295561788 28.72557118 19945.56293 0.128990955 0.071586111 59.50880818 -1.774581252 0.706682635 SAS(ph)DTNLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASDTNLQK 9 0 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 SAS(1)DTNLQK;SAS(0.98)DT(0.02)NLQK 187.76 4.21E-05 812660000 842090 787990 550650 680350 740440 619620 709240 912570 845360 825330 TRUE FALSE 809180.1918 765517.2967 650164.7041 715462.945 764256.9251 632149.1409 717919.8913 893725.1106 749398.2768 769429.664 1.051662328 0.994915237 0.844995631 0.929861401 0.993277178 0.821581453 0.933054605 1.161542312 0.973965928 1 19.55342993 1.774585603 25 1.061532481 0.93433358 0.267021836 0.079424545 45.18390121 31369.58034 0.036503846 0.020259016 59.50940427 -1.774585603 -0.127198901 TQPHHST(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQPHHSTPTK 10 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 TQPHHS(0.247)T(0.752)PTK 96.745 0.012191 206500000 66342 102750 79894 110130 86143 93746 92505 13708 80247 87640 TRUE FALSE 63749.2813 99819.6706 94332.62303 115813.8225 88913.86783 95641.60835 93637.10386 13424.92501 71137.69698 81704.06474 0.780246142 1.221722211 1.154564627 1.417479325 1.088242894 1.170585682 1.146051964 0.164311593 0.870675127 1 16.31812023 1.774601633 24.99999946 0.592462482 1.15343381 0.396541858 0.253979226 31.1295912 21602.56321 0.110769965 0.061474033 59.51160081 -1.774601633 0.560971328 EIGLLSEEVELYGETK ddPTM_BT-474_Pertuzumab_2h_R1 4 EIGLLSEEVELYGETK 16 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;; 314.04 2.18E-57 72553000 154839 148798 133859 134640 151927 153407 159293 173931 189038 195149 FALSE TRUE 148787.7207 144554.4267 158050.299 141588.7865 156813.8699 156508.9946 161242.4754 170339.2641 167579.1988 181931.3844 0.817823275 0.794554646 0.868735757 0.778253774 0.861939629 0.860263858 0.886281803 0.936283009 0.921112096 1 17.47303491 1.774614611 0.523666178 0.997819105 0.807956086 0.83785379 0.025815248 0.288164797 0.180423818 0.024018466 0.015837209 59.51337933 -1.774614611 -0.189863019 HCNGVDWR ddPTM_BT-474_Pertuzumab_2h_R1 6 HCNGVDWR 8 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;;;;; 118.18 0.0019367 2819620000 2132810 2223630 1874330 2100010 2125790 1937100 2275200 1695284 2368040 2507800 FALSE TRUE 2049457.427 2160214.25 2213063.125 2208391.768 2194167.966 1976269.489 2303044.578 1660275.793 2099230.027 2337944.472 0.876606545 0.923980135 0.946584982 0.94458692 0.938503028 0.84530215 0.985072402 0.710143381 0.897895588 1 21.15680923 1.774630828 25 0.838193465 0.922341018 0.049855688 0.077104442 62.58533159 43396.29548 0.033327162 0.018495814 59.51560156 -1.774630828 0.084147554 TQPHHS(ph)TPTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQPHHSTPTK 10 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 T(0.001)QPHHS(0.499)T(0.499)PTK;T(0.006)QPHHS(0.497)T(0.497)PTK 88.087 0.020782 212058000 108557 161589 107252 150216 114436 126276 129972 14350.8 97401 141785 TRUE FALSE 104314.4724 156980.6399 126634.8222 157968.6658 118116.9379 128829.3872 131562.6362 14054.45097 86344.44682 132181.7757 0.789174392 1.187611826 0.958035414 1.195086577 0.893594728 0.974638044 0.995316 0.106326692 0.653225049 1 17.01216376 1.774671839 25 0.493595725 1.007282416 0.369930415 0.23744964 31.39190069 21742.21917 0.101682093 0.056431519 59.52122196 -1.774671839 0.513686691 ILCDLS(ph)DLEYLDEEFHQSLQWMK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILCDLSDLEYLDEEFHQSLQWMK 23 0 A0A2R8YE75;A0A2R8Y6F3;Q9P2P5 A0A2R8YE75 HECW2 E3 ubiquitin-protein ligase HECW2 1 ILCDLS(0.967)DLEY(0.033)LDEEFHQSLQWMK 44.158 0.065232 221290000 169970 122820 118530 98162 123270 122400 126890 168490 164750 131580 TRUE FALSE 163327.3845 119317.2939 139951.0077 103228.1526 127235.0915 124875.0119 128442.9178 165010.6226 146048.2707 122667.9694 1.331459103 0.972685 1.140892838 0.841524915 1.037231578 1.017992003 1.047077884 1.345181007 1.190598258 1 16.90439906 1.77484215 25 1.214859564 1.045265944 0.118116378 0.14225964 59.28386337 40867.51496 0.062491594 0.034682768 59.54456816 -1.77484215 -0.169593619 REEQTDTS(ph)DGESVTHHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQT(0.079)DT(0.3)S(0.622)DGESVTHHIR;REEQT(0.001)DT(0.179)S(0.82)DGESVTHHIR 177.91 4.30E-14 2841170000 474080 562070 428820 588490 577770 632490 596700 164651 583420 544260 TRUE FALSE 455552.4295 546040.3139 506317.313 618862.0394 596354.4968 645279.3812 604002.5931 161250.8993 517192.6075 507396.7854 0.897822853 1.076160373 0.997872528 1.219680647 1.175321787 1.271745111 1.190394994 0.317800396 1.019306039 1 18.95275485 1.77492157 25 0.708339177 1.124145364 0.339151045 0.21016115 36.47423072 25088.67513 0.093629537 0.051965124 59.55545809 -1.77492157 0.415806187 KKPNATRPVT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKPNATRPVTPPR 13 3 F8W0W8;P36873;P36873-2 F8W0W8 PPP1CC Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit 1 KKPNAT(0.071)RPVT(0.929)PPR;KKPNAT(0.015)RPVT(0.985)PPR 82.813 0.011652 8366200000 3147600 2358800 2088500 2263300 2275600 2314800 2258200 3792800 2946500 2684900 TRUE FALSE 3024588.312 2291529.334 2465938.408 2380109.184 2348796.741 2361606.842 2285836.527 3714477.355 2612025.673 2503049.332 1.208361447 0.915495074 0.985173715 0.95088385 0.938374131 0.943491929 0.913220726 1.483980882 1.043537432 1 21.25525529 1.774922015 25 1.226501806 0.973016109 0.252946418 0.146988283 40.64370129 27956.28515 0.063607632 0.035302045 59.55551919 -1.774922015 -0.253485697 RHEQSGGPEHGPER ddPTM_BT-474_Pertuzumab_2h_R1 2 RHEQSGGPEHGPER 14 1 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 0 ; 139.6 4.14E-06 134187000 64583 71182 50744 66689 59502 60404 63732 23059.5 60890 61226 FALSE TRUE 62059.02496 69151.95905 59914.56959 70130.82728 61415.93587 61625.41027 64511.97128 22583.31327 53978.02247 57079.10849 1.08724587 1.211510847 1.049675988 1.228660173 1.075979242 1.079649138 1.130220373 0.395649369 0.945670385 1 15.80067518 1.774924918 25 0.718267641 1.124396324 0.470264123 0.162779396 27.76349774 19095.26698 0.069592983 0.038624365 59.55591729 -1.774924918 0.406128683 RSPGPGPSQS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPGPGPSQSPR 12 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 RS(0.002)PGPGPS(0.034)QS(0.964)PR 82.837 0.005079 0 195200 243640 212210 285810 266460 271970 226650 190260 176290 194400 TRUE FALSE 187571.3682 236691.6257 250561.0676 300560.6884 275030.9279 277469.4197 229423.8105 186331.0645 156278.2983 181233.1148 1.034972932 1.306006499 1.382534686 1.658420364 1.51755339 1.531008392 1.265904472 1.028129239 0.862305426 1 17.46748706 1.774931529 2.530621003 0.935762291 1.415154499 0.604280987 0.159864593 0.186107265 2.361595422 0.104636516 0.048194884 59.55682389 -1.774931529 0.479392208 RQS(ph)IPEEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQSIPEEFK 9 1 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H3G9 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 RQS(1)IPEEFK;RQS(1)IPEEFK 147.73 5.62E-05 994550000 885910 885120 733050 779040 761280 725070 829630 1054870 1113280 1093990 TRUE FALSE 851287.6578 859877.2442 865528.4416 819246.3478 785767.2626 739731.4122 839783.2601 1033086.566 986905.1217 1019893.083 0.834683235 0.843105281 0.848646251 0.803266893 0.77044082 0.725302901 0.823403231 1.012936143 0.967655471 1 19.95998649 1.774940023 5.472258979 0.992214943 0.80436065 0.847547559 0.036265763 0.074635942 4.892360682 0.019736489 0.01075498 59.55798871 -1.774940023 -0.187854293 DVHTLLDR ddPTM_BT-474_Pertuzumab_2h_R1 5 DVHTLLDR 8 0 E9PI41;Q9NPD3 E9PI41 EXOSC4 Exosome complex component RRP41 0 ;;;; 166.16 0.00032007 1085336000 299052 308296 240967 296695 294772 301428 294982 223391 314334 303917 FALSE TRUE 287364.7172 299503.6999 284515.0972 312007.4645 304253.6091 307523.0807 298592.078 218777.8978 278652.1221 283332.4309 1.014231644 1.057075249 1.00417413 1.101206323 1.073839688 1.085379036 1.053857749 0.772159746 0.983481211 1 18.11213622 1.774963508 25 0.895214085 1.057344906 0.476367709 0.064493003 28.18040933 19361.45273 0.028106876 0.015599689 59.56120949 -1.774963508 0.16213082 SHFGGPDYEEGPNSLINEEEFFDAVEAALDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SHFGGPDYEEGPNSLINEEEFFDAVEAALDR 31 0 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2R8YE59;A0A2R8YFA1 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 ;; 255.95 2.00E-58 243188600 56766 67273 59200.8 66729.9 69822.7 69981.1 67697.4 7813.6 64906.1 55197.5 FALSE TRUE 54547.52196 65354.43991 69899.70147 70173.83814 72068.61056 71396.16579 68525.90103 7652.246429 57538.23164 51458.92416 1.060020645 1.270031214 1.358359169 1.36368646 1.400507526 1.387439923 1.331662139 0.148705916 1.118139032 1 15.65113367 1.775001336 25 0.66896403 1.319044313 0.483093913 0.258170314 28.12890593 19305.99623 0.112136153 0.062236922 59.56639765 -1.775001336 0.650080283 EESDDEAAVEEEEEEKKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EESDDEAAVEEEEEEKKPK 19 2 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 252.12 4.30E-31 1106320000 776700 612110 797010 564826 652590 670548 890330 1133500 1601750 1209380 FALSE TRUE 746345.7053 594653.2221 941047.4364 593976.7375 673581.15 684106.94 901226.1249 1110092.829 1419926.055 1127467.615 0.661966424 0.527423772 0.834655846 0.526823768 0.597428379 0.606764159 0.799336595 0.984589547 1.259394093 1 20.10465456 1.775015852 1.993506042 1.127557083 0.626151988 0.79615311 0.103804801 0.123356466 0.969866211 0.066592209 0.028526184 59.56838865 -1.775015852 -0.501405095 QEKPAEKPAETPVAT(ph)SPTATDSTSGDSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.588)S(0.397)PT(0.015)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.583)S(0.401)PT(0.016)ATDSTSGDSSR 176.6 9.83E-14 2596790000 899750 807060 737850 743170 813910 776290 707350 710130 747810 640630 TRUE FALSE 864586.7753 784043.439 871195.9084 781525.0928 840090.1543 791987.1157 716006.7609 695465.5673 662921.7439 597239.5595 1.447638157 1.312778811 1.458704291 1.308562168 1.40662175 1.326079465 1.198860239 1.164466681 1.109976279 1 19.1879502 1.77504633 0.727166808 1.009484921 1.39821738 0.88367403 0.049057133 0.185836526 0.193131956 0.041280007 0.020157252 59.57256911 -1.77504633 0.388732459 VHCCLYFIPATGHSLRPLDIEFMK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHCCLYFIPATGHSLRPLDIEFMK 24 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18 Q9UHD8 9-Sep Septin-9 0 ; 119.06 0.00026591 356100000 168951 181138 144580 186519 181022 214885 187298 31399 203986 124745 FALSE TRUE 162348.2081 175972.1216 170708.8222 196145.2679 186844.737 219230.1219 189590.209 30750.59968 180830.3645 116295.91 1.395992413 1.513141103 1.467883282 1.686605039 1.606632056 1.885106036 1.630239695 0.264416863 1.554915942 1 16.82744083 1.775115108 25 0.86699964 1.604468225 0.469234989 0.317908037 31.06097524 21252.00716 0.139125046 0.07721812 59.58200418 -1.775115108 0.737468585 LGNSGAS(ph)PSSAGK ddPTM_BT-474_Pertuzumab_2h_R1 3 LGNSGASPSSAGK 13 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 LGNSGAS(1)PSSAGK;LGNSGAS(0.984)PS(0.015)S(0.001)AGK;LGNSGAS(0.986)PS(0.013)SAGK 214.41 3.24E-11 710670000 1178830 1142800 963890 978700 1025510 1126820 1100210 1300090 1382930 1279510 TRUE FALSE 1132760.02 1110208.463 1138086.365 1029210.824 1058496.46 1149605.072 1113674.699 1273242.687 1225945.584 1192847.648 0.949626738 0.93072109 0.954091972 0.862818337 0.887369365 0.96374845 0.93362694 1.067397575 1.027746994 1 20.18597836 1.775156037 9.375430591 1.03586177 0.924717231 0.686465992 0.032698118 0.146398347 34.50412421 0.015646297 0.008798822 59.58761963 -1.775156037 -0.111144539 RVS(ph)RT(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 RVSRTPEPK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)RT(1)PEPK;RVS(1)RT(1)PEPK;RVS(1)RT(1)PEPK 98.942 0.0062604 32851910000 40943160 34510040 29101830 29886390 32925440 33270910 33528480 38765970 40256470 35827300 TRUE FALSE 39343056.04 33525847.45 34361178.05 31428830.17 33984516.68 33943670.6 33938811.57 37965439.17 35686724.29 33400685.06 1.17791165 1.0037473 1.028756685 0.940963639 1.01747963 1.016256719 1.016111242 1.136666482 1.068442885 1 24.99337436 1.775170306 25 1.082835966 1.023495538 0.056714899 0.064174237 80.65806504 55103.24093 0.028933769 0.01606016 59.58957742 -1.775170306 -0.059340428 EAAEVLQNNRR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAAEVLQNNRR 11 1 P61081;M0QX69 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;;; 168.3 2.92E-05 3105410000 1854820 2148900 1528440 1821560 1730090 1884820 1688410 1709340 1668530 1664710 FALSE TRUE 1782331.584 2087615.476 1804663.108 1915570.93 1785739.916 1922932.352 1709073.267 1674041.532 1479125.469 1551957.709 1.14844082 1.345149719 1.162830081 1.234293254 1.15063697 1.239036567 1.10123701 1.0786644 0.953070732 1 20.56565781 1.775175665 1.239677601 0.976139994 1.219092381 0.709044133 0.059403165 0.220981908 0.635671283 0.045038093 0.017940499 59.59031273 -1.775175665 0.242952387 GSGEKPVSAPGDDTES(ph)LHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVSAPGDDT(0.021)ES(0.979)LHS(1)QGEEEFDMPQPPHGHVLHR 201.9 9.92E-31 540620000 103660 109320 81306 82811 83813 103230 101830 52075 117450 81604 TRUE FALSE 99608.8526 106202.3006 95999.80284 87084.88563 86508.92126 105317.3813 103076.226 50999.63305 104117.5684 76076.88839 1.309318174 1.395986388 1.261878671 1.144695682 1.137124863 1.384354481 1.354895398 0.670369597 1.368583424 1 16.21517062 1.775176368 25 0.980000482 1.280338613 0.322465806 0.178075903 43.78951849 29910.76695 0.079468543 0.044107921 59.59040923 -1.775176368 0.300338132 HLDGEEDGSSDQSQASGTTGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 ;; 386.42 1.01E-131 865200000 400491 466797 371488 554238 465329 490194 479390 241279 488920 460772 FALSE TRUE 384839.369 453484.4066 438624.1453 582842.2896 480296.7299 500106.0585 485256.9182 236296.5043 433419.8513 429563.502 0.8958847 1.055686539 1.021092675 1.356824513 1.11810414 1.164219158 1.129651183 0.550085152 1.008977367 1 18.71251189 1.775249825 25 0.806725015 1.113089185 0.324569261 0.162905533 40.06091146 27309.09512 0.073708343 0.040911082 59.60048934 -1.775249825 0.30636417 DATNRS(ph)PTQIVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DATNRSPTQIVK 12 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 DAT(0.002)NRS(0.988)PT(0.01)QIVK;DATNRS(0.999)PT(0.001)QIVK;DAT(0.002)NRS(0.997)PT(0.002)QIVK;DATNRS(0.999)PT(0.001)QIVK 161.09 4.02E-05 3460510000 1837050 1939350 1559810 1710150 1762240 1786290 1758460 2034830 2040120 1964240 TRUE FALSE 1765256.055 1884041.637 1841702.365 1798411.046 1818924.05 1822410.008 1779980.559 1992810.049 1808534.13 1831200.275 0.963988526 1.028856135 1.005735085 0.982094133 0.993296077 0.995199724 0.97202943 1.088253468 0.987622247 1 20.80435815 1.775264805 25 1.034599529 0.993414543 0.1868091 0.030241049 53.47054651 36435.43123 0.013206374 0.00732962 59.60254512 -1.775264805 -0.041184986 TFNQVEIKPEMIGHYLGEFSITYKPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFNQVEIKPEMIGHYLGEFSITYKPVK 27 2 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841 K7EM56 RPS15 40S ribosomal protein S15 0 184.88 7.68E-18 1307800000 449410 463310 423690 398610 402330 477860 489850 519900 605130 600070 FALSE TRUE 431846.5604 450096.8524 500260.2079 419182.3099 415271.3098 487522.6566 495844.9308 509163.8833 536438.1793 559426.7244 0.771944817 0.804568021 0.894237236 0.749306909 0.742315824 0.8714683 0.886344733 0.91015295 0.958906959 1 19.09358965 1.775314164 0.922605444 0.990758794 0.797875546 0.728226808 0.043869221 0.305248104 0.485809346 0.040330457 0.017202835 59.60931955 -1.775314164 -0.192883248 HFEELETIMDR ddPTM_BT-474_Pertuzumab_2h_R1 5 HFEELETIMDR 11 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ;;;; 224.66 6.04E-12 2699410000 1374280 1404807 1229413 1526700 1481755 1484465 1460302 808618 1504181 1416938 FALSE TRUE 1320571.618 1364743.28 1451595.277 1605493.17 1529416.995 1514481.899 1478173.613 791919.7557 1333432.679 1320967.527 0.999700289 1.033139159 1.098887934 1.215391853 1.1578006 1.14649442 1.119008289 0.59949979 1.00943638 1 20.33316357 1.775365987 25 0.828565804 1.113960941 0.440365241 0.121525306 32.15819717 21852.67465 0.054580035 0.030294897 59.61643297 -1.775365987 0.285395137 EHNGHITGIDWAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHNGHITGIDWAPK 14 0 A0A1W2PNV4;E9PF58;Q92747 A0A1W2PNV4;Q92747 ARPC1A Actin-related protein 2/3 complex subunit 1A 0 58.752 0.061499 201910000 119490 134920 104620 115180 112910 117490 127880 5130.2 128980 94327 FALSE TRUE 114820.1987 131072.2137 123527.1613 121124.4536 116541.8527 119865.7283 129445.0337 5024.259577 114338.7311 87938.14827 1.305692705 1.490504591 1.404705053 1.377382353 1.325270716 1.363068596 1.472000903 0.057134016 1.300217634 1 16.42420153 1.775455096 24.99999944 0.689403547 1.391415883 0.452264034 0.299756959 30.89491849 20943.49634 0.128014349 0.071055562 59.6286664 -1.775455096 0.702012335 ATISPLHLAAYHGHHQALEVLVQSLLDLDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATISPLHLAAYHGHHQALEVLVQSLLDLDVR 31 0 O15084-2;O15084;O15084-4;O15084-1;B4DIW9 O15084-2 ANKRD28 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit A 0 ; 79.898 0.00054829 134034000 110275 118950 103795 121707 118180 122838 117911 71184 125897 110605 FALSE TRUE 105965.3311 115557.6625 122553.0654 127988.3129 121981.367 125321.8685 119354.0301 69714.02552 111605.7004 103113.6248 1.02765596 1.120682768 1.188524461 1.241235705 1.182980108 1.215376423 1.157500091 0.676089369 1.082356483 1 16.65387545 1.77549152 25 0.886830691 1.167333418 0.488631724 0.112114161 30.12173459 20399.20829 0.049715763 0.027595517 59.63366754 -1.77549152 0.280502727 AQGPRPHQENNHQESYPLS(ph)VSPMENNHCPASSESHPKPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQGPRPHQENNHQESYPLSVSPMENNHCPASSESHPKPSSPR 42 2 P41212 P41212 ETV6 Transcription factor ETV6 2 AQGPRPHQENNHQESYPLS(0.762)VS(0.172)PMENNHCPAS(0.028)S(0.039)ES(0.029)HPKPS(0.512)S(0.459)PR 169.93 2.79E-20 1176800000 348330 424240 302910 408650 367290 376480 400140 23354 385900 322530 TRUE FALSE 334716.8785 412141.0906 357652.5752 429740.4755 379104.2164 384092.6835 405037.033 22871.73174 342094.2498 300684.7558 1.113182069 1.370675043 1.189460284 1.429206061 1.260802914 1.27739327 1.347048778 0.076065485 1.137717304 1 18.1978922 1.775579615 25 0.642921891 1.288109584 0.439108551 0.276594394 31.29599144 21143.98462 0.117939279 0.065465408 59.64576528 -1.775579615 0.645187693 (ac)AYHSGYGAHGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYHSGYGAHGSK 12 0 E9PIZ0;C9JST7;A6NGW1;O95070 E9PIZ0 YIF1A Protein YIF1A 0 ; 62.924 5.61E-05 119030000 175803 279250 178766 312730 217860 246120 243460 131466 242440 246270 FALSE TRUE 168932.4244 271286.0634 211072.9928 328870.0328 224867.6648 251096.715 246439.5363 128751.1812 214919.2276 229589.9135 0.735800723 1.181611418 0.919347848 1.432423697 0.979431811 1.093674853 1.073390083 0.56078762 0.936100477 1 17.80869974 1.775595441 25 0.786863516 1.071289761 0.199390884 0.201489544 52.78725641 35648.51846 0.087578592 0.048613648 59.64793889 -1.775595441 0.284426245 LVDEPGHCADFHPSGTVVAIGTHSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVDEPGHCADFHPSGTVVAIGTHSGR 26 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 173.01 1.45E-12 241740000 99008 162270 144570 204010 172240 154510 165260 48933 146210 171180 FALSE TRUE 95138.6579 157642.2185 170697.0149 214538.9805 177780.256 157634.2981 167282.5013 47922.51645 129612.8538 159585.8261 0.596159823 0.987820926 1.069625161 1.344348591 1.114010312 0.987771295 1.048229065 0.300293062 0.812182741 1 17.283973 1.775603003 25 0.631212171 1.036441379 0.250415089 0.240604816 46.73467245 31554.61331 0.110397267 0.061279666 59.64897738 -1.775603003 0.405229208 AAPEASS(ph)PPAS(ph)PLQHLLPGK ddPTM_BT-474_Pertuzumab_2h_R1 9 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.468)S(0.534)PPAS(0.998)PLQHLLPGK;AAPEAS(0.098)S(0.902)PPAS(1)PLQHLLPGK;AAPEAS(0.455)S(0.545)PPAS(1)PLQHLLPGK;AAPEAS(0.447)S(0.553)PPAS(1)PLQHLLPGK;AAPEAS(0.094)S(0.906)PPAS(1)PLQHLLPGK;AAPEAS(0.472)S(0.531)PPAS(0.997)PLQHLLPGK;AAPEAS(0.431)S(0.569)PPAS(1)PLQHLLPGK;AAPEAS(0.514)S(0.573)PPAS(0.913)PLQHLLPGK;AAPEAS(0.088)S(0.912)PPAS(1)PLQHLLPGK 202.73 5.98E-22 10776704000 6967697 8016830 6994191 9164822 9762433 9302185 7218093 6469055 5923036 5749509 TRUE FALSE 6695391.698 7788197.858 8258196.899 9637819.562 10076450.52 9490281.554 7306430.181 6335466.754 5250677.785 5360089.634 1.249119353 1.45299769 1.540682612 1.798070596 1.879903362 1.770545308 1.363117164 1.1819703 0.979587683 1 22.3538257 1.775639347 2.064148765 1.011555521 1.621319541 0.667315229 0.178003928 0.19917601 1.681260968 0.132511442 0.057386424 59.65396936 -1.775639347 0.60976402 HEEEFDLFMR ddPTM_BT-474_Pertuzumab_2h_R1 5 HEEEFDLFMR 10 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ;;;; 190.86 8.55E-07 777108000 479692 518498 414596 516635 540883 498484 507298 277643 517289 498397 FALSE TRUE 460945.1063 503710.9447 489522.7198 543298.5943 558280.9929 508563.688 513506.4647 271909.575 458568.5214 464640.1273 0.992047564 1.084088341 1.053552397 1.16928901 1.201534177 1.094532431 1.105170291 0.585204676 0.98693267 1 18.82575423 1.77575133 25 0.814690021 1.103986227 0.447098703 0.120835194 32.03348365 21542.26573 0.053355202 0.029617876 59.66935321 -1.77575133 0.289296206 DKNEQAFEEVFQNANFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DKNEQAFEEVFQNANFR 17 1 P27694;I3L4R8 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 ;;; 326.37 1.87E-60 1199260000 1444800 1396710 1150230 1295330 1378800 1347750 1391110 1505840 1662420 1614060 FALSE TRUE 1388335.619 1356877.198 1358102.148 1362182.137 1423150.354 1375002.428 1408134.82 1474743.878 1473709.051 1504738.279 0.922642587 0.901736347 0.902550408 0.905261836 0.945779326 0.913781784 0.935800491 0.980066699 0.979378987 1 20.52108115 1.775784819 0.975815472 0.999740427 0.910930546 0.863469064 0.012720802 0.175799965 0.311532285 0.011136272 0.004651611 59.67395446 -1.775784819 -0.088809881 INMAHLCVIGSHAVNGVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 INMAHLCVIGSHAVNGVAR 19 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 217.26 2.10E-19 1931880000 1009980 910550 779890 848100 956830 998810 993720 637250 1056460 1001960 FALSE TRUE 970508.865 884582.0055 920833.4716 891870.5426 987607.3059 1019006.623 1005881.443 624090.5648 936535.0898 934096.3567 1.038981533 0.946992245 0.985801374 0.954795013 1.057286327 1.090900971 1.076849765 0.668122256 1.002610794 1 19.83321185 1.775825941 25 0.855289759 1.018869195 0.248409166 0.099233184 47.62463024 31963.03032 0.044574211 0.024743473 59.6796051 -1.775825941 0.163579436 KQVDSEHMHQNVPTEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQVDSEHMHQNVPTEEQR 18 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LNN3;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 0 ; 91.475 0.0010223 248110000 323480 338740 252110 324950 315420 383420 333050 29244 336290 246680 FALSE TRUE 310838.044 329079.4669 297671.8852 341720.7084 325565.7708 391173.0151 337125.9655 28640.10118 298115.769 229972.1439 1.351633458 1.430953599 1.294382355 1.485922176 1.415674809 1.700958249 1.465942613 0.124537262 1.296312519 1 17.8110996 1.775857643 25 0.718257774 1.452473088 0.493244435 0.294287912 30.44319453 20414.42197 0.127544443 0.070802366 59.68396172 -1.775857643 0.734215313 QSHSSS(ph)SPHPK ddPTM_BT-474_Pertuzumab_2h_R1 3 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.001)S(0.021)S(0.804)S(0.174)PHPK;QSHS(0.001)S(0.019)S(0.809)S(0.171)PHPK;QSHS(0.002)S(0.054)S(0.472)S(0.472)PHPK 126.71 0.00050461 853446000 1005310 1361940 1048010 1572800 1181501 1404220 1408340 511519 1239220 1576400 TRUE FALSE 966021.3738 1323098.805 1237408.72 1653972.396 1219505.053 1432614.291 1425575.686 500955.9539 1098548.941 1469629.024 0.657323282 0.900294417 0.841987127 1.12543531 0.829804687 0.974813553 0.970024178 0.340872387 0.747500847 1 20.48702059 1.775944136 25 0.626157289 0.906591745 0.165363199 0.190967282 52.68473492 35247.25099 0.083699218 0.046463541 59.69584937 -1.775944136 0.280434456 HNQLQDGHER ddPTM_BT-474_Pertuzumab_2h_R1 1 HNQLQDGHER 10 0 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925;J3QWB6 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 84.687 0.0085305 153400000 54295 65864 56371 64635 56430 61802 65866 26843 65553 64186 FALSE TRUE 52173.09137 63985.62321 66558.49367 67970.8201 58245.1222 63051.67878 66672.08781 26288.68267 58111.69826 59838.62505 0.871896561 1.069303032 1.11229985 1.135902104 0.973369996 1.053695314 1.114198191 0.439326316 0.971140266 1 15.86878941 1.775960618 25 0.744762917 1.051406473 0.302851774 0.162207779 40.68990362 27210.43723 0.070588741 0.039185712 59.69811502 -1.775960618 0.306643556 HPNIVSLQDVLMQDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPNIVSLQDVLMQDSR 16 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 239.18 8.12E-20 504930000 220370 224780 235580 260160 233400 233430 246750 212220 254640 284960 FALSE TRUE 211757.6968 218369.4945 278154.5464 273586.8888 240907.523 238150.1145 249769.8003 207837.5828 225734.3347 265659.4054 0.797102201 0.821990451 1.047034439 1.029840778 0.906828511 0.896449023 0.940188058 0.782346036 0.849713318 1 18.01921827 1.775982858 25 0.853982452 0.92386324 0.024882688 0.089793186 109.4114171 73122.84417 0.043167401 0.023964099 59.70117216 -1.775982858 0.069880788 S(ph)SSLEGFHNHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLEGFHNHFK 12 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.411)S(0.411)S(0.178)LEGFHNHFK 218.11 5.86E-11 668850000 690530 755400 600210 778290 685190 741570 764180 56107 811170 523380 TRUE FALSE 663543.3242 733856.7316 708681.2986 818457.6402 707229.7586 756565.0535 773532.2634 54948.37084 719089.3823 487931.0064 1.359912191 1.504017416 1.45242112 1.677404447 1.449446232 1.550557443 1.585331232 0.112615042 1.473752176 1 18.89631764 1.776098856 25 0.772098166 1.514274003 0.451834087 0.323127565 33.27569304 22170.36838 0.138109021 0.076671345 59.71712017 -1.776098856 0.742175836 GNAEGS(ph)SDEEGKLVIDEPAKEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.863)S(0.137)DEEGKLVIDEPAKEK;GNAEGS(0.882)S(0.118)DEEGKLVIDEPAKEK 220.99 5.07E-26 2167160000 2416070 1785500 1374440 1093780 1577780 1557770 1652110 2054700 2437420 1665880 TRUE FALSE 2321647.313 1734579.288 1622831.882 1150230.117 1628530.727 1589269.177 1672329.016 2012269.727 2160734.3 1553048.464 1.494896887 1.116886774 1.044933188 0.740627317 1.048602645 1.023322333 1.076804141 1.295690234 1.391285817 1 20.56667142 1.776158928 6.994357157 1.256858258 1.061559659 0.102668537 0.195327236 0.353895875 43.37934582 0.093439187 0.05225211 59.72538081 -1.776158928 -0.1952986 (ac)S(ph)KSES(ph)PKEPEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSESPKEPEQLRK 14 3 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 2 S(0.951)KS(0.085)ES(0.964)PKEPEQLRK 55.724 0.0027098 376290000 733400 527670 388070 287090 484640 385880 475390 640930 744700 519010 TRUE FALSE 704737.9172 512621.3682 458202.8816 301906.7493 500228.8857 393682.758 481207.965 627694.5715 660164.778 483856.9904 1.456500435 1.059448098 0.946979977 0.623958639 1.033836228 0.813634536 0.994525189 1.297272921 1.364379953 1 18.88422118 1.776187156 6.73674615 1.246911365 0.970970602 0.185446194 0.217042588 0.274862406 30.59442749 0.104066281 0.058049879 59.72926306 -1.776187156 -0.275940763 DVHEDSITVAFENNWQPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVHEDSITVAFENNWQPDR 19 0 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 Q06787 FMR1 Fragile X mental retardation protein 1 0 198.51 7.38E-16 216090000 134140 153970 121250 165340 149920 144840 153490 122070 167030 160370 FALSE TRUE 128897.6605 149578.9264 143162.5722 173873.2172 154742.313 147768.764 155368.4565 119549.2118 148069.4546 149507.9971 0.862145591 1.000474418 0.957557957 1.162969344 1.035010274 0.988366957 1.039198301 0.799617507 0.990378157 1 17.18986313 1.77621216 25 0.908906413 1.010828784 0.123410395 0.087733865 71.23599781 47319.01761 0.040222204 0.022329694 59.73270193 -1.77621216 0.101922371 KASPEPPDS(ph)AEGALK ddPTM_BT-474_Pertuzumab_2h_R1 1 KASPEPPDSAEGALK 15 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 KAS(0.022)PEPPDS(0.978)AEGALK 159.69 1.86E-06 220140000 301950 242190 210410 212030 244420 236090 248390 316660 348760 297980 TRUE FALSE 290149.4602 235282.9783 248435.7675 222972.8937 252281.9913 240863.9016 251429.8711 310120.8603 309170.2269 277797.5492 1.044463715 0.846958438 0.894305109 0.802645287 0.908150529 0.867048332 0.905083115 1.116355638 1.112933602 1 18.08367435 1.776274678 6.137551689 1.085228542 0.888716737 0.610277138 0.065986882 0.109485399 9.55644125 0.030062169 0.016637432 59.74130128 -1.776274678 -0.196511805 IHHELNQFCSVHTLQEVYIELFDQIDENLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IHHELNQFCSVHTLQEVYIELFDQIDENLK 30 0 E5RJ09;E5RHW4;O94905 E5RJ09 ERLIN2 Erlin-2 0 77.065 0.0013123 122790000 38255 53822 52324 56363 29712 57631 52429 4477.2 55743 36224 FALSE TRUE 36759.95231 52287.04926 61780.11074 59271.90118 30667.71346 58796.33831 53070.64179 4384.744255 49415.28833 33770.51622 1.088522073 1.548304708 1.829409724 1.755137553 0.908120956 1.741055361 1.57150816 0.129839421 1.463267189 1 15.04347661 1.776295417 25 0.776011954 1.504161958 0.320616406 0.412241247 45.76037708 30329.55597 0.183311302 0.101770062 59.74415422 -1.776295417 0.728150004 EWSQHINGASHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EWSQHINGASHSR 13 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 246.96 1.82E-17 4201600000 784190 1250980 1113910 1687730 1279940 1266560 1277970 371480 1090460 1375470 FALSE TRUE 753542.9878 1215303.275 1315218.316 1774833.948 1321110.433 1292170.711 1293610.179 363808.8082 966675.5524 1282308.192 0.587645772 0.947746636 1.025664754 1.384093121 1.030259684 1.007691224 1.008813784 0.283714017 0.753855866 1 20.29031161 1.776315916 25 0.604282219 1.014277094 0.244646247 0.246047075 50.19185605 33248.63307 0.113023298 0.062748204 59.7469742 -1.776315916 0.409994875 KVS(ph)VSESNVLLDEEVLTDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVSVSESNVLLDEEVLTDPK 20 1 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 KVS(0.607)VS(0.16)ES(0.233)NVLLDEEVLTDPK;KVS(0.936)VS(0.025)ES(0.039)NVLLDEEVLTDPK 198.09 9.74E-22 503320000 728120 575200 539310 480630 589860 530620 579650 713920 720970 609370 TRUE FALSE 699664.2654 558795.8592 636775.3139 505435.3719 608833.3826 541349.5 586743.9301 699177.3025 639128.5082 568096.8271 1.231593334 0.983627847 1.12089222 0.88969934 1.071707064 0.952917661 1.032823811 1.230736151 1.125034462 1 19.11577732 1.776352484 25 1.142979056 1.033408726 0.091194285 0.103185885 74.71979934 49448.79541 0.044822417 0.024885001 59.7520052 -1.776352484 -0.10957033 KVYEDSGIPLPAES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 KVYEDSGIPLPAESPK 16 1 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 KVYEDSGIPLPAES(1)PK;KVYEDSGIPLPAES(1)PK;KVYEDSGIPLPAES(1)PK;KVYEDSGIPLPAES(1)PK;KVYEDSGIPLPAES(1)PK 240.13 7.94E-20 4548640000 3741560 2977570 2577950 2337770 2843480 2507610 2855440 3512830 3367290 3266250 TRUE FALSE 3595335.699 2892652.619 3043842.911 2458422.59 2934943.117 2558315.592 2890385.729 3440288.833 2985049.356 3045023.978 1.180724922 0.949960539 0.999612132 0.807357383 0.963848934 0.840162708 0.949216082 1.129806812 0.980304056 1 21.53802216 1.77640255 25 1.049961734 0.947445722 0.110541841 0.101132109 82.81829133 54735.71786 0.046300152 0.025705097 59.75889387 -1.77640255 -0.102516012 SLS(ph)ESAATR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSESAATR 9 0 O14924-5;O14924-4;O14924;E9PBG5 O14924-5 RGS12 Regulator of G-protein signaling 12 1 S(0.007)LS(0.947)ES(0.046)AATR 67.385 0.064093 0 400450 455570 292570 461150 523720 489650 423920 404840 438600 403730 TRUE FALSE 384799.9713 442577.5896 345443.9072 484950.0068 540565.9294 499551.0585 429108.0598 396479.9125 388811.9668 376385.0075 1.02235733 1.175864024 0.917794015 1.288441349 1.436204734 1.327234211 1.140077451 1.053389228 1.033016616 1 18.52184964 1.776402896 3.093641661 1.026950881 1.198055416 0.21951202 0.139090853 0.406194579 7.592092481 0.086211133 0.04207061 59.75894152 -1.776402896 0.171104536 LLEMNLMHAPQVADAILGNQMFTHYDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LLEMNLMHAPQVADAILGNQMFTHYDR 27 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 244.14 1.41E-45 16124350000 897661 1081496 928590 1077950 1093531 1224455 1100771 859087 1205340 1122248 FALSE TRUE 862579.4157 1050652.793 1096406.869 1133583.129 1128705.418 1249214.319 1114242.565 841346.5532 1068514.856 1046237.143 0.824458796 1.004220505 1.047952538 1.083485839 1.078823692 1.194006853 1.065000007 0.804164294 1.021293177 1 19.99677846 1.776471765 25 0.921517158 1.05008982 0.156869901 0.102849304 69.88424485 46103.07202 0.048715551 0.027046708 59.76841852 -1.776471765 0.128572662 KTTTTPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 KTTTTPGR 8 1 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 0 ;;; 111.65 0.0051186 1266390000 1054570 1095890 780070 946826 941975 871513 904388 931930 789986 823045 FALSE TRUE 1013356.239 1064636.29 921046.0016 995691.8033 972274.4814 889135.59 915456.1709 912685.3198 700310.1012 767299.4291 1.320678995 1.387510859 1.200373631 1.297657428 1.267138283 1.158785679 1.19308856 1.189477387 0.912694673 1 19.54943016 1.776516448 0.567213671 0.965554477 1.317246752 0.734683749 0.070558276 0.413832761 0.290609802 0.068094399 0.041355321 59.77456821 -1.776516448 0.351692275 EVLDVAAGMIKPGVTTEEIDHAVHLACIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLDVAAGMIKPGVTTEEIDHAVHLACIAR 30 1 P53582 P53582 METAP1 Methionine aminopeptidase 1 0 69.578 0.0042459 259020000 67138 53958 50386 48145 63065 57464 62480 14844 66926 49085 FALSE TRUE 64514.17274 52419.17067 59491.87103 50629.76922 65093.543 58625.96145 63244.64893 14537.46621 59328.84106 45760.42923 1.409824467 1.14551309 1.300072399 1.106409404 1.422485411 1.281149728 1.382081637 0.317686404 1.296509715 1 15.48181296 1.776590084 24.99999993 0.801038309 1.284547801 0.367629304 0.247842161 40.96558593 26941.12795 0.106328447 0.059035043 59.78470413 -1.776590084 0.483509493 TGQAGSLSGS(ph)PKPFSPQLSAPITTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGQAGSLSGSPKPFSPQLSAPITTK 25 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 TGQAGSLSGS(0.998)PKPFS(0.002)PQLSAPITTK;TGQAGSLS(0.011)GS(0.989)PKPFSPQLSAPITTK 200.8 3.93E-25 6434800000 3190600 2418400 2573000 2085810 2384700 2383400 2587900 3351400 3584600 3038700 TRUE FALSE 3065907.825 2349429.6 3037998.336 2193458.904 2461406.041 2431593.981 2619571.494 3282192.419 3177691.236 2832886.142 1.082255929 0.829341344 1.072403967 0.774284173 0.868868679 0.858345115 0.924700592 1.158603719 1.121715126 1 21.43384119 1.776673635 8.771920846 1.105272399 0.90879465 0.39639851 0.099918944 0.212461824 43.08943191 0.043802386 0.024724768 59.79620684 -1.776673635 -0.196477749 DGLAPEKT(ph)SPDRDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLAPEKTSPDRDKK 15 3 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.5)S(0.5)PDRDKK;DGLAPEKT(0.826)S(0.174)PDRDKK 116.65 0.00044455 1846580000 1578340 1045360 1014090 730130 1049610 987220 1130930 1439560 1751450 1322230 TRUE FALSE 1516656.728 1015547.356 1197358.621 767812.0968 1083371.659 1007182.265 1144770.66 1409832.583 1552632.739 1232674.184 1.230379241 0.823857082 0.971350448 0.622883246 0.878879166 0.817070948 0.92868876 1.143718755 1.259564578 1 20.23336009 1.776697141 3.761558515 1.1539679 0.878652305 0.329909867 0.154865956 0.222370451 6.126296258 0.079730341 0.040773845 59.79944327 -1.776697141 -0.275315595 TGGIGDSRPPSFHPHAGGGS(ph)QENLDNDTETDSLVSAQR ddPTM_BT-474_Pertuzumab_2h_R1 3 TGGIGDSRPPSFHPHAGGGSQENLDNDTETDSLVSAQR 38 1 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR;TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR;TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR 319.52 2.19E-110 1721690000 381852 566210 415710 615980 485530 531210 511410 8054.2 512280 365543 TRUE FALSE 366928.8017 550062.2452 490838.0444 647770.8016 501147.5134 541951.4302 517668.7886 7887.877955 454128.1221 340784.447 1.076718157 1.614106072 1.440318209 1.900822667 1.470570379 1.590305646 1.519050512 0.023146238 1.332596385 1 18.37849997 1.776714102 25 0.686175325 1.532761782 0.451905729 0.363583283 34.93803285 22902.36931 0.15715235 0.087255961 59.80177883 -1.776714102 0.846586457 LVGDRNEWHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVGDRNEWHGR 11 1 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 0 101.35 0.0020126 103560000 140950 157870 80690 116220 122300 148350 119560 93139 102340 92041 FALSE TRUE 135441.5182 153367.7022 95272.47794 122218.1281 126233.8906 151349.7386 121023.211 91215.6471 90722.79224 85806.98109 1.578444043 1.787356929 1.110311501 1.424337817 1.471137767 1.763839454 1.410412178 1.063032937 1.057289175 1 16.38880741 1.776790931 3.591825335 1.037262044 1.513776536 0.593973966 0.178393756 0.161527334 4.049618276 0.099116058 0.050174943 59.81235892 -1.776790931 0.476514492 YSS(ph)TETLKDDDLWSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 YSSTETLKDDDLWSSR 16 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 YS(0.045)S(0.628)T(0.164)ET(0.164)LKDDDLWSSR;YS(0.098)S(0.843)T(0.012)ET(0.047)LKDDDLWSSR;YS(0.001)S(0.827)T(0.103)ET(0.07)LKDDDLWSSR;YS(0.001)S(0.883)T(0.112)ET(0.004)LKDDDLWSSR 193.72 1.99E-10 2115980000 1960960 1930880 1413090 1636320 1878150 1808600 1787650 2324720 2165790 2022400 TRUE FALSE 1884323.515 1875813.193 1668466.797 1720770.671 1938562.4 1845171.131 1809527.795 2276713.72 1919938.599 1885421.047 0.999417885 0.994904134 0.88493061 0.912671827 1.028185404 0.978652028 0.959747319 1.207535963 1.01830761 1 20.84645531 1.776807345 25 1.096866007 0.96441809 0.355978825 0.065759638 42.71021363 27928.84714 0.029823893 0.016559671 59.81461954 -1.776807345 -0.132447918 SST(ph)PLPTISSSAENTR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSTPLPTISSSAENTR 16 0 P42166;P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 S(0.004)S(0.019)T(0.977)PLPTISSSAENTR;SS(0.002)T(0.998)PLPTISSSAENTR;S(0.018)S(0.087)T(0.895)PLPTISSSAENTR;SS(0.001)T(0.999)PLPTISSSAENTR;S(0.003)S(0.003)T(0.994)PLPTISSSAENTR;SS(0.002)T(0.998)PLPTISSSAENTR 411.9 4.99E-139 30378100000 9250200 11675770 6928310 10062810 7426980 8626130 8963260 12722610 11604120 9596100 TRUE FALSE 8888691.957 11342788.47 8180409.736 10582152.83 7665875.557 8800556.259 9072955.057 12459883.66 10286868.95 8946147.6 0.993577611 1.267896415 0.914405854 1.182872595 0.856891245 0.983725806 1.014174532 1.392765268 1.149865775 1 23.09283513 1.776831943 25 1.222405182 1.032554704 0.167072033 0.145185367 64.08642098 41880.12732 0.064008615 0.035541153 59.81800754 -1.776831943 -0.189850478 YS(ph)PSQNSPIHHIPSR ddPTM_BT-474_Pertuzumab_2h_R1 5 YSPSQNSPIHHIPSR 15 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 Y(0.001)S(0.993)PS(0.005)QNSPIHHIPSR;YS(0.999)PS(0.001)QNSPIHHIPSR;YS(0.72)PS(0.28)QNSPIHHIPSR;Y(0.017)S(0.905)PS(0.079)QNSPIHHIPSR;YS(0.933)PS(0.067)QNSPIHHIPSR 240.94 4.73E-18 13175980000 1304450 1522110 1445570 1965790 1810380 1744960 1769350 887250 1712970 1881250 TRUE FALSE 1253470.652 1478700.913 1706816.656 2067244.657 1868612.517 1780244.287 1791003.835 868927.9774 1518520.827 1753831.262 0.714704247 0.843126101 0.973193199 1.178702138 1.065446008 1.015060186 1.021195068 0.495445598 0.86583063 1 20.74207852 1.776932283 25 0.733770419 0.981146566 0.183005159 0.168555598 61.47702126 40069.79326 0.079351696 0.044061935 59.83182961 -1.776932283 0.247376147 TVT(ph)PASSAK ddPTM_BT-474_Pertuzumab_2h_R1 4 TVTPASSAK 9 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 1 TVT(0.978)PAS(0.02)S(0.001)AK;T(0.002)VT(0.947)PAS(0.042)S(0.009)AK;T(0.001)VT(0.999)PASSAK;TVT(1)PASSAK 147.62 0.0010279 1436900000 4067080 3837630 3542660 3578540 3577720 3769030 3760230 4293170 4315240 4252560 TRUE FALSE 3908134.017 3728184.55 4182897.468 3763228.878 3692800.613 3845242.369 3806248.82 4204514.539 3825392.046 3964530.323 0.985774782 0.940384925 1.055080205 0.94922439 0.931459798 0.969911201 0.960075598 1.060532824 0.964904222 1 21.91871853 1.77703237 25 1.014712667 0.970068955 0.162674932 0.038957176 76.49706369 49729.85726 0.017661375 0.009806519 59.84561989 -1.77703237 -0.044643712 AAHTEDINACTLTTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAHTEDINACTLTTSPR 17 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 AAHTEDINACTLTT(0.022)S(0.978)PR;AAHTEDINACTLTT(0.145)S(0.855)PR;AAHTEDINACTLTT(0.035)S(0.965)PR;AAHTEDINACTLTT(0.009)S(0.991)PR 247.16 6.51E-21 2885610000 585570 728810 696990 957510 904900 980650 725210 594760 543170 584950 TRUE FALSE 562685.277 708025.0524 822951.5975 1006927.206 934006.9303 1000479.415 734085.3369 582477.9982 481511.6188 545330.8155 1.031823732 1.298340443 1.509086914 1.846452057 1.712734553 1.834628425 1.346128471 1.06811862 0.882971593 1 19.05677216 1.777036523 2.749186205 0.957279147 1.549266092 0.527038242 0.234443172 0.213712535 3.175867798 0.151704306 0.071725123 59.84619217 -1.777036523 0.591986946 VDDSS(ph)EDKTEFTVK ddPTM_BT-474_Pertuzumab_2h_R1 3 VDDSSEDKTEFTVK 14 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 1 VDDS(0.235)S(0.765)EDKTEFTVK;VDDS(0.231)S(0.769)EDKTEFTVK;VDDS(0.187)S(0.799)EDKT(0.013)EFT(0.001)VK 149.52 4.52E-06 518330000 1036550 831350 769360 618380 815260 765470 835800 1060140 1236920 937660 TRUE FALSE 996040.48 807640.712 908400.4663 650294.6659 841483.5783 780948.3279 846028.7704 1038247.739 1096510.027 874151.453 1.139436967 0.923913939 1.039179725 0.743915329 0.962629045 0.893378745 0.967828593 1.187720657 1.254370765 1 19.73752373 1.777038569 5.307801364 1.165156759 0.943920772 0.38120465 0.112581411 0.172681374 10.3442728 0.052980331 0.028848098 59.84647416 -1.777038569 -0.221235987 HLNRPTLDDSSEEEHAIEITTQEITQLFHR ddPTM_BT-474_Pertuzumab_2h_R1 5 HLNRPTLDDSSEEEHAIEITTQEITQLFHR 30 1 H3BU86;O14662;F8W9Z6;B7ZBM8;O14662-6;O14662-2;O14662-5;B7ZBM4;B7ZBM5;Q96NX8;O14662-4 H3BU86;Q96NX8 STX16-NPEPL1;STX16 Syntaxin-16 0 ;;;; 297.7 1.50E-81 735201000 201973 322384 196571 362220 248960 279425 315639 57028.8 335088 250854 FALSE TRUE 194079.6719 313189.924 232095.7524 380914.2176 256968.0245 285075.1649 319501.8845 55851.13535 297050.215 233863.4351 0.829884637 1.33920005 0.992441389 1.628789115 1.098795219 1.218981346 1.366189992 0.238819443 1.270186658 1 17.83530679 1.777044912 24.99999995 0.756859167 1.219271393 0.213449955 0.318158659 57.30210557 37239.28285 0.136977205 0.076063382 59.84734819 -1.777044912 0.462412226 HQQIPLHS(ph)PPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HQQIPLHSPPSK 12 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;C9JAU4 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HQQIPLHS(0.999)PPS(0.001)K 118.21 0.00041881 132800000 302220 282490 218300 244630 270810 262920 269060 131960 253280 289750 TRUE FALSE 290408.9083 274433.6618 257751.6661 257255.3836 279520.8496 268236.4225 272352.8368 129234.9799 224528.7162 270124.9744 1.075090924 1.015950718 0.954194134 0.952356901 1.034783438 0.9930086 1.008247525 0.478426625 0.8312031 1 18.0432675 1.777067235 25 0.715075593 1.001968973 0.397175699 0.127339257 37.11858955 24108.50544 0.05494944 0.030513122 59.85042451 -1.777067235 0.286893381 AATFPLQVLGFEIDAVNSVQFSNHTGYAHWK ddPTM_BT-474_Pertuzumab_2h_R1 1 AATFPLQVLGFEIDAVNSVQFSNHTGYAHWK 31 0 O00764;O00764-2 O00764 PDXK Pyridoxal kinase 0 225.84 2.07E-35 153500000 146280 175250 152400 184110 139000 157280 174450 84217 180520 168840 FALSE TRUE 140563.2159 170252.0416 179942.0701 193611.9392 143471.0612 160460.3094 176584.9713 82477.88952 160028.1264 157404.3164 0.893007378 1.081622445 1.143183835 1.230029415 0.911481111 1.019414925 1.121855965 0.52398747 1.016669238 1 17.26411558 1.777080199 25 0.796900768 1.061058433 0.250109044 0.159935282 52.31949712 33970.04381 0.071238827 0.039558231 59.85221116 -1.777080199 0.264157665 GLGKPGGQGDAIQLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLGKPGGQGDAIQLSPK 17 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GLGKPGGQGDAIQLS(1)PK;GLGKPGGQGDAIQLS(1)PK 189.84 2.01E-10 1798140000 1965850 1820470 1752900 1574540 1797100 1781800 1969560 2377540 2674190 2655600 TRUE FALSE 1889022.409 1768551.978 2069688.023 1655802.198 1854905.354 1817829.217 1993664.064 2328442.968 2370627.162 2475733.847 0.76301514 0.714354647 0.835989711 0.668812684 0.749234558 0.734258741 0.805282065 0.940506174 0.957545241 1 21.2394248 1.777134619 2.043026754 0.979344311 0.743168309 0.858052796 0.040550477 0.100908867 0.833074901 0.025859686 0.011179433 59.8597114 -1.777134619 -0.236176002 ETPCWIEIHLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETPCWIEIHLHR 12 0 K7EIU8;Q13485 K7EIU8 SMAD4 Mothers against decapentaplegic homolog;Mothers against decapentaplegic homolog 4 0 ; 167.18 2.89E-05 335780000 89374 79659 67193 88493 91234 84302 91615 43134 104520 74857 FALSE TRUE 85881.16527 77387.20331 79336.2698 93060.13434 94168.62447 86006.6442 92736.21178 42243.26783 92655.32778 69786.86871 1.230620701 1.108907804 1.136836647 1.333490613 1.349374549 1.232418731 1.328849015 0.605318287 1.327690001 1 16.09066798 1.777224054 25 0.937158518 1.243174042 0.311308023 0.179712586 51.01170728 32997.62829 0.079513033 0.044155447 59.87203976 -1.777224054 0.306015524 GGAFDGTMNGPFGHGYGEGAGEGIDDVEWVVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGAFDGTMNGPFGHGYGEGAGEGIDDVEWVVGK 33 0 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 0 ; 210.51 1.54E-27 253470000 119505 133542 90432 125340 119504 121647 127986 135096 161256 151572 FALSE TRUE 114834.6125 129733.5129 106775.074 131808.8124 123347.9547 124106.7857 129552.331 132306.2204 142950.8949 141305.8934 0.81266683 0.918104049 0.75563072 0.932790623 0.872914439 0.878284569 0.916821852 0.936310703 1.011641422 1 17.10846211 1.777246939 0.720092575 1.012693456 0.851058617 0.589022099 0.047551792 0.441121205 0.450736621 0.040412948 0.01989435 59.87519468 -1.777246939 -0.161634839 LHSCLPADTLQGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHSCLPADTLQGHR 14 0 O00291-3;O00291-4;O00291;O75146;O75146-2 O00291-3;O75146 HIP1;HIP1R Huntingtin-interacting protein 1;Huntingtin-interacting protein 1-related protein 0 105.99 0.00055955 198540000 43659 46195 52553 46615 51268 51071 58312 11999 50879 63507 FALSE TRUE 41952.75801 44877.56383 62050.49614 49020.80574 52917.08178 52103.69061 59025.6397 11751.21646 45103.42922 59205.61432 0.708594252 0.757995071 1.048050879 0.827975629 0.893784861 0.880046448 0.996960176 0.198481455 0.761810003 1 15.85344637 1.777260561 25 0.567725753 0.874926048 0.150248027 0.212052152 59.36312989 38363.62105 0.092608246 0.051428125 59.87707287 -1.777260561 0.307200294 IAQNDHDLGDMSTVADPSVISHLFSHR ddPTM_BT-474_Pertuzumab_2h_R1 5 IAQNDHDLGDMSTVADPSVISHLFSHR 27 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;;;; 260.46 2.82E-53 2654830000 1447078 1555350 1531045 1950084 1749171 1709210 1785189 194973.8 1801924 1412034 FALSE TRUE 1390524.592 1510992.941 1807738.889 2050728.069 1805434.674 1743771.397 1807036.677 190947.5229 1597377.142 1316395.679 1.05631203 1.147825813 1.373248878 1.557835612 1.37149848 1.324655971 1.372715442 0.145053289 1.213447573 1 20.32816177 1.777264705 25 0.697968813 1.322590282 0.405167851 0.28756202 40.32243802 26055.71873 0.127855225 0.071001787 59.87764413 -1.777264705 0.624621469 VHTGFDQHEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 VHTGFDQHEQK 11 0 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;; 194.96 1.64E-07 1020080000 1176420 1134640 950283 1020230 1125050 970440 1162230 96707 1154520 946770 FALSE TRUE 1130444.206 1102281.178 1122020.277 1072884.193 1161238.255 990062.9617 1176453.718 94709.96666 1023463.73 882644.4246 1.280747008 1.24883945 1.271203041 1.215533869 1.315635405 1.121700805 1.332873902 0.107302515 1.159542508 1 19.75147284 1.777307274 25 0.662818043 1.251250707 0.416092195 0.264417321 37.88761008 24455.46059 0.112780184 0.062630705 59.88351357 -1.777307274 0.588432664 DHAGVMGESNR ddPTM_BT-474_Pertuzumab_2h_R1 3 DHAGVMGESNR 11 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ;; 128.88 0.0002566 717280000 327817 338366 263838 321132 316389 340796 338204 205345 351040 345763 FALSE TRUE 315005.5492 328716.133 311519.3956 337705.661 326565.9395 347687.1286 342343.0417 201104.554 311191.4109 322344.164 0.977233604 1.019767595 0.9664186 1.047655576 1.013097105 1.078620826 1.062042003 0.62388148 0.965401101 1 18.29824234 1.777328208 25 0.823478399 1.023848746 0.326590638 0.100881029 43.28589643 27924.81832 0.043798991 0.024323536 59.88640012 -1.777328208 0.200370347 YVASYLLAALGGNSS(ph)PSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 1 YVASYLLAALGGNS(0.052)S(0.948)PSAK;YVASYLLAALGGNS(0.007)S(0.993)PSAK 306.82 8.86E-51 2456700000 1477570 1301560 1214810 1367570 1320360 1440490 1570220 1832130 2087210 2130080 TRUE FALSE 1419824.931 1264440.783 1434353.19 1438150.452 1362830.579 1469617.695 1589436.822 1794295.875 1850278.671 1985807.784 0.714986084 0.636738758 0.722302129 0.724214329 0.686285243 0.740060396 0.800398122 0.903559695 0.931751142 1 20.92129455 1.777333137 0.979343975 0.992777245 0.690924215 0.951806984 0.024867639 0.0978781 0.174630396 0.021119279 0.008817517 59.88707979 -1.777333137 -0.30185303 GEQGYGFHLHGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEQGYGFHLHGEK 13 0 Q15599;Q15599-2 Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 0 108.63 0.00069436 176240000 245810 268530 236620 274680 236230 242840 272820 19575 282620 202460 FALSE TRUE 236203.4734 260871.7873 279382.4976 288856.2677 243828.5525 247750.3912 276158.8528 19170.76941 250538.1624 188747.2039 1.251427669 1.382122659 1.4801941 1.530387003 1.291826038 1.312604299 1.463114934 0.101568495 1.327374167 1 17.52609575 1.777370958 25 0.717101765 1.389698863 0.428803042 0.299902778 38.18280742 24605.54192 0.129239817 0.071772849 59.89229537 -1.777370958 0.672597098 FHSEDYIDFLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FHSEDYIDFLQR 12 0 O15379;O15379-2 O15379 HDAC3 Histone deacetylase 3 0 ; 289.59 4.37E-36 171255000 183768 210340 172329 209320 200592 178010 203859 105021 207553 203110 FALSE TRUE 176586.1434 204341.3091 203472.6837 220123.0303 207044.2239 181609.4842 206353.8874 102852.2796 183992.4536 189353.1788 0.932575542 1.079154364 1.074567034 1.162499788 1.093428825 0.959104491 1.089783064 0.543176937 0.971689278 1 17.53072012 1.777398484 25 0.790436805 1.059311396 0.342671308 0.133182929 43.2034133 27821.14905 0.058322874 0.032389483 59.89609154 -1.777398484 0.268874592 GAAEEAELEDS(ph)DDEEKPVKQDDFPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GAAEEAELEDSDDEEKPVKQDDFPK 25 2 Q9UBB9;F6XM96 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK 327.79 4.73E-88 2610730000 2884590 1884670 1842820 1364730 1972430 1758670 2032990 2851620 3316360 2426130 TRUE FALSE 2771857.034 1830921.057 2175858.567 1435163.879 2035875.002 1794231.512 2057870.34 2792733.05 2939900.716 2261806.054 1.225506063 0.809495161 0.962000505 0.634521194 0.900110334 0.793273813 0.909835013 1.234735863 1.299802302 1 21.1090438 1.777407247 5.382575347 1.199496205 0.875323502 0.404374677 0.158666566 0.164866439 10.20140436 0.074059126 0.040428183 59.89730014 -1.777407247 -0.324172703 NVPQEESLEDS(ph)DVDADFK ddPTM_BT-474_Pertuzumab_2h_R1 5 NVPQEESLEDSDVDADFK 18 0 O00505 O00505 KPNA3 Importin subunit alpha-4 1 NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEES(0.002)LEDS(0.998)DVDADFK 324.43 5.10E-62 1858550000 1381707 1146729 1092247 983975 1127637 1160348 1183999 1493275 1580320 1455796 TRUE FALSE 1327708.363 1114025.412 1289640.33 1034758.068 1163908.468 1183811.032 1198489.134 1462438.349 1400928.699 1357193.64 0.978274819 0.820830115 0.950225739 0.762424784 0.857584676 0.872249174 0.883064213 1.077545831 1.032224627 1 20.37219514 1.777458935 7.162537971 1.040717698 0.870284105 0.605967596 0.059620444 0.118150185 15.13160121 0.026386775 0.014821845 59.90442929 -1.777458935 -0.170433592 QKGESRPET(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 QKGESRPETPK 11 2 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 QKGES(0.002)RPET(0.998)PK;QKGES(0.001)RPET(0.999)PK 119.62 0.00090415 306600000 498170 385580 351340 316460 365970 373140 423980 519780 615350 561250 TRUE FALSE 478700.9656 374583.6359 414834.9535 332792.5385 377741.7574 380685.1465 429168.7941 509046.3614 545498.0478 523236.0376 0.914885312 0.715898006 0.792825654 0.636027557 0.721933755 0.727559111 0.820220251 0.972880927 1.042546783 1 18.99710238 1.77748094 2.313567264 1.021237664 0.745511221 0.737278285 0.067958838 0.135544662 1.437180002 0.042428228 0.019059001 59.90746463 -1.77748094 -0.275726443 DLEVDGHFVTMQIWDTAGQER ddPTM_BT-474_Pertuzumab_2h_R1 1 DLEVDGHFVTMQIWDTAGQER 21 0 P51151 P51151 RAB9A Ras-related protein Rab-9A 0 88.09 0.0025084 76297000 40114 47049 38831 45624 42231 45117 44957 55603 55866 58275 FALSE TRUE 38546.30053 45707.20859 45848.62549 47978.66011 43589.39847 46029.29665 45507.19721 54454.77862 49524.32589 54327.98234 0.70951099 0.841319825 0.843922846 0.883129799 0.802337885 0.84724841 0.837638271 1.002333904 0.911580437 1 15.72940785 1.7775131 7.886699878 0.967592225 0.827212553 0.655826686 0.048968588 0.130306538 20.91833238 0.022003224 0.012417778 59.91190107 -1.7775131 -0.140379672 GIYETPAGTILYHAHLDIEAFTMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIYETPAGTILYHAHLDIEAFTMDR 25 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ; 181.82 1.35E-17 224477000 226620 201352 178272 166464 232230 200853 205187 132017 247780 160613 FALSE TRUE 217763.4399 195609.6381 210489.716 175055.227 239699.8889 204914.3853 207698.1399 129290.8028 219653.0532 149734.5385 1.454330057 1.306376205 1.405752595 1.169103861 1.600832322 1.368517828 1.387109093 0.8634668 1.466949813 1 17.19204751 1.777540754 25 1.098010754 1.381794286 0.340280164 0.174835846 53.49889363 34325.1974 0.075340932 0.041843028 59.91571609 -1.777540754 0.283783532 SHS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSPLR 6 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.058)HS(0.942)PLR;S(0.431)HS(0.569)PLR 80.098 0.068611 606003000 460813 529416 479094 625500 531280 595180 601770 265540 606710 599530 TRUE FALSE 442803.9185 514317.574 565676.9432 657782.13 548369.1037 607214.9474 609134.6413 260056.5062 537838.8243 558923.2991 0.792244516 0.920193477 1.012083311 1.176873698 0.981116916 1.086401208 1.089835837 0.465281205 0.962276622 1 19.09229079 1.777629975 25 0.752565106 1.013573755 0.205496183 0.168607204 59.07902273 37818.833 0.075963572 0.04219015 59.92802641 -1.777629975 0.261008649 LDGERPGPNR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDGERPGPNR 10 1 E7ESY4;Q13330-3;Q13330;H0Y4T7 E7ESY4 MTA1 Metastasis-associated protein MTA1 0 ;; 123.79 0.00041283 735920000 324990 362066 282017 327402 335196 361549 331228 322997 336571 357111 FALSE TRUE 312289.0315 351740.2322 332983.7453 344299.2565 345977.8838 368859.7685 335281.6673 316326.9991 298364.8711 332923.5539 0.938020239 1.056519516 1.000180797 1.034169113 1.039211193 1.10794134 1.007083048 0.950149052 0.896196342 1 18.34483142 1.777644275 3.736888523 0.941497923 1.031462361 0.366127111 0.046842437 0.206304992 5.591542922 0.024081708 0.012309204 59.92999965 -1.777644275 0.089964438 IMPES(ph)SESPPTEREPGGVVDGLIGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IMPESSESPPTEREPGGVVDGLIGK 25 1 Q5JZB7;A0A087X074;Q5JZB8;Q9BPZ2;Q99865 Q5JZB7 SPIN2B;SPIN2A Spindlin-2B;Spindlin-2A 1 IMPES(0.366)S(0.33)ES(0.299)PPT(0.005)EREPGGVVDGLIGK 60.093 0.045963 89547000 45217 66421 41517 54313 56634 58615 57007 45474 61704 60386 TRUE FALSE 43449.86965 64526.73811 49020.04544 57116.10044 58455.68404 59800.23546 57704.66872 44534.94601 54699.6206 56296.00243 0.771810924 1.146204621 0.870755352 1.014567606 1.038362966 1.062246569 1.025022492 0.791085407 0.971643069 1 15.78074486 1.777798725 25 0.898737643 0.996886519 0.062162292 0.110958894 99.86314358 63651.31062 0.047615203 0.026446712 59.95131657 -1.777798725 0.098148876 SLKESEQES(ph)EEEILAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLKESEQESEEEILAQK 17 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 S(0.006)LKES(0.003)EQES(0.99)EEEILAQK 156.74 3.14E-08 352630000 637840 533760 403000 420640 437520 488180 522900 584370 695190 625390 TRUE FALSE 612912.5076 518537.6874 475831.0647 442349.2808 451593.2281 498051.3341 529299.4066 572302.5553 616274.9457 583031.7783 1.051250602 0.889381517 0.816132297 0.758705267 0.77456023 0.85424389 0.90783972 0.981597533 1.057017762 1 19.15321499 1.777812444 2.012609231 1.027257463 0.849365029 0.450389821 0.077174967 0.290119831 2.321471987 0.05563167 0.023957555 59.95321042 -1.777812444 -0.177892433 GPIAQWADGAIS(ph)PNGHRPQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPIAQWADGAISPNGHRPQLR 21 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;Q5SRD0 Q641Q2;A0A0A0MR88 FAM21A;FAM21C;FAM21D WASH complex subunit FAM21A;WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 1 GPIAQWADGAIS(1)PNGHRPQLR;GPIAQWADGAIS(1)PNGHRPQLR 162.71 1.10E-11 635320000 421750 484760 431150 591730 555210 550700 488480 410120 399790 459350 TRUE FALSE 405267.5437 470935.1194 509068.3959 622269.2562 573068.8339 561835.5313 494458.1644 401650.8787 354407.5153 428237.8154 0.946360945 1.099704656 1.188751618 1.45309273 1.33820231 1.311970852 1.15463452 0.937915486 0.827595094 1 18.70805267 1.77784433 3.163498335 0.904464939 1.231400222 0.496692972 0.135468179 0.203395873 3.958416097 0.082768918 0.040676404 59.95761233 -1.77784433 0.326935282 FWEVISDEHGIDPTGSYHGDSDLQLER ddPTM_BT-474_Pertuzumab_2h_R1 3 FWEVISDEHGIDPTGSYHGDSDLQLER 27 0 Q13885;Q9BVA1 Q13885;Q9BVA1 TUBB2A;TUBB2B Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;; 331.99 1.70E-95 2657280000 1025040 1404480 1038040 1723310 1457230 1483670 1379010 466130 1287790 1380370 FALSE TRUE 984980.3036 1364425.606 1225636.919 1812250.236 1504103.126 1513670.824 1395886.737 456504.2526 1141605.478 1286876.31 0.765404022 1.060261654 0.952412372 1.408255184 1.168801628 1.176236451 1.084709327 0.354738252 0.887113601 1 20.29544196 1.777880132 25 0.680015759 1.10054667 0.317602883 0.22187725 49.5625464 31525.0145 0.100584513 0.055868339 59.96255527 -1.777880132 0.42053091 RSDAEEVDFAGWLCSTIGLNQPS(ph)TPTHAAGV ddPTM_BT-474_Pertuzumab_2h_R1 1 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.461)T(0.461)PT(0.077)HAAGV 82.157 0.00066682 34792000 29381 28818 25849 34825 30644 31899 27477 21428 21095 20090 TRUE FALSE 28232.75804 27996.13886 30520.48931 36622.32242 31629.69209 32544.01964 27813.27175 20985.50431 18700.38404 18729.28641 1.507412372 1.494778725 1.629559645 1.955350654 1.688782552 1.737600618 1.485015026 1.120464702 0.998456836 1 14.19300831 1.777881795 2.247315118 1.003419245 1.673084504 0.842853339 0.122022205 0.114545957 1.145806021 0.086170968 0.038377232 59.96278492 -1.777881795 0.669665259 VADPDHDHTGFLTEYVATR ddPTM_BT-474_Pertuzumab_2h_R1 4 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ;;; 191.93 4.96E-15 2994150000 3854240 4175340 3389460 4230900 4284130 4420730 4498620 355658 4655890 3437920 FALSE TRUE 3703612.04 4056263.391 4002010.82 4449257.256 4421932.932 4510120.189 4553675.457 348313.538 4127372.886 3205066.616 1.155549161 1.265578497 1.24865137 1.388194939 1.379669586 1.407184539 1.420774044 0.108675912 1.287765086 1 21.61192291 1.777933039 25 0.706300103 1.326388109 0.396149927 0.290265173 42.17211385 26788.15378 0.125657929 0.069797242 59.96986058 -1.777933039 0.620088006 LGTGFSDEELEEHHQSLK ddPTM_BT-474_Pertuzumab_2h_R1 4 LGTGFSDEELEEHHQSLK 18 0 P18858;P18858-3;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ;;; 292.13 1.94E-49 1791100000 743445 1166779 965390 1255470 1023180 1207070 1173430 359782 1047710 1269250 FALSE TRUE 714390.3475 1133503.605 1139857.448 1320264.957 1056091.514 1231477.782 1187790.787 352352.376 928778.3532 1183282.567 0.603736054 0.957931467 0.963301142 1.115764733 0.892509992 1.040730098 1.003809927 0.297775346 0.784916789 1 20.1743632 1.777947679 25 0.619679414 0.950138099 0.199517309 0.209198138 58.08359378 36881.56811 0.092120444 0.051169228 59.97188215 -1.777947679 0.330458685 TSVS(ph)PAPDKTK ddPTM_BT-474_Pertuzumab_2h_R1 4 TSVSPAPDKTK 11 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 T(0.002)S(0.015)VS(0.983)PAPDKTK;TS(0.001)VS(0.999)PAPDKTK;TSVS(1)PAPDKTK;TSVS(1)PAPDKTK 185.32 2.74E-06 3204940000 2176880 1901210 1445730 1245310 1554630 1710190 1701280 2042710 2246050 1963050 TRUE FALSE 2091805.123 1846989.352 1707005.571 1309580.598 1604636.086 1744771.214 1722100.774 2000527.325 1991087.82 1830090.875 1.143006149 1.009233682 0.932743611 0.715582279 0.876806779 0.953379549 0.940991946 1.093130047 1.087972104 1 20.80348386 1.777948906 6.496534724 1.067475809 0.930456995 0.22162152 0.103299015 0.283212503 28.19881324 0.052815528 0.02948574 59.97205162 -1.777948906 -0.137018814 GPGPTVKPSGHLFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPGPTVKPSGHLFFR 15 1 F5GXQ0;Q5VW32-2;Q5VW32 F5GXQ0 BROX BRO1 domain-containing protein BROX 0 ; 166.09 8.34E-07 1186570000 763070 842650 739060 866970 752130 803160 804290 778950 796110 896590 FALSE TRUE 733248.3808 818618.447 872624.5823 911714.4256 776322.9445 819400.4455 814133.1416 762864.4103 705738.9304 835863.1607 0.877234953 0.979368975 1.043980191 1.090746032 0.928767986 0.980304533 0.974002899 0.912666626 0.844323525 1 19.67290725 1.777963585 3.568659025 0.908160505 0.987526137 0.159162122 0.064891006 0.34735562 8.568485685 0.035357371 0.017892444 59.97407865 -1.777963585 0.079365632 EQST(ph)PPKS(ph)PQ ddPTM_BT-474_Pertuzumab_2h_R1 3 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 2 EQS(0.003)T(0.997)PPKS(1)PQ;EQST(1)PPKS(1)PQ;EQS(0.003)T(0.997)PPKS(1)PQ 142.08 0.00091243 1626080000 3988490 3626400 3156800 3123200 3223250 3456980 3615750 3966510 4591560 4175740 TRUE FALSE 3832615.401 3522978.623 3727303.983 3284388.726 3326928.764 3526882.504 3660000.63 3884600.182 4070345.358 3892913.41 0.984510827 0.904972254 0.957458744 0.843683992 0.85461155 0.905975071 0.940170059 0.997864523 1.04557819 1 21.89241882 1.778026282 2.236139149 1.023033569 0.905688199 0.577279797 0.040713493 0.206667463 2.046518233 0.027191169 0.012092872 59.98273751 -1.778026282 -0.11734537 RPENSLLEETLHFDHAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPENSLLEETLHFDHAVR 18 1 O00566;U3KQ48 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 0 ; 222.7 2.26E-19 421210000 167146 189964 152869 211811 169910 190155 197212 3548.5 191637 160943 FALSE TRUE 160613.7495 184546.4127 180495.8289 222742.5911 175375.3095 194000.0644 199625.5394 3475.222235 169883.1712 150042.1873 1.070457266 1.229963493 1.202967193 1.484533085 1.168839995 1.292970117 1.330462739 0.023161634 1.132236035 1 17.19500867 1.778027366 24.99999921 0.616643897 1.258456207 0.396631666 0.294918815 41.54095305 26324.13727 0.127126094 0.070615271 59.98288723 -1.778027366 0.64181231 SSDYQFPS(ph)SPFTDTLK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSDYQFPSSPFTDTLK 16 0 Q9UK61-3;Q9UK61 Q9UK61-3 FAM208A Protein FAM208A 1 SSDYQFPS(0.499)S(0.499)PFT(0.001)DTLK;SSDYQFPS(0.463)S(0.216)PFT(0.321)DTLK;SSDYQFPS(0.853)S(0.147)PFTDTLK 192.78 5.03E-10 401336000 677019 632802 572914 591255 585967 661756 641023 752875 818152 813226 TRUE FALSE 650560.349 614755.1065 676452.3042 621769.7414 604815.1607 675137.1597 648868.0312 737327.8682 725278.8149 758145.4787 0.858094346 0.810866943 0.892246044 0.820119303 0.797756074 0.890511358 0.855862166 0.972541404 0.956648605 1 19.53211518 1.77804625 1.577204111 0.987726298 0.839687931 0.780995612 0.031390333 0.158274303 0.758954719 0.022571151 0.009154197 59.98549537 -1.77804625 -0.148038367 SYIYSGSHDGHINYWDSETGENDSFAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYIYSGSHDGHINYWDSETGENDSFAGK 28 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 268.24 1.28E-54 1694280000 305036 443872 407481 508254 394444 479182 447357 19287.3 416428 387872 FALSE TRUE 293114.8559 431213.2052 481121.8811 534485.0498 407131.6495 488871.3884 452831.8888 18889.01051 369156.8392 361601.084 0.810602813 1.19251082 1.330532187 1.47810688 1.125913797 1.351963282 1.252296823 0.052237151 1.020895278 1 18.46403948 1.778140427 25 0.592414204 1.234800498 0.377974725 0.302902252 43.98770355 27794.96005 0.133493629 0.074155391 59.99850475 -1.778140427 0.642386293 LGSSGLGSASS(ph)IQAAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSSGLGSASSIQAAVR 17 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LGS(0.001)S(0.004)GLGS(0.173)AS(0.297)S(0.525)IQAAVR 65.924 0.03769 0 180840 162160 124110 127010 132020 161760 137230 192270 177980 139530 TRUE FALSE 173772.5729 157535.3556 146539.4378 133565.0013 136266.5432 165030.898 138909.4618 188299.5573 157776.4566 130079.5088 1.335895057 1.21106973 1.126537447 1.026795093 1.047563482 1.268692506 1.067881199 1.447572789 1.212923219 1 16.98903419 1.778168593 25 1.268669612 1.151306199 0.009212149 0.138766165 113.6437057 71758.13439 0.062864923 0.034921918 60.00239596 -1.778168593 -0.117363413 EHGAVAVER ddPTM_BT-474_Pertuzumab_2h_R1 4 EHGAVAVER 9 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;; 106.4 0.002942 2018557000 798289 908287 693151 853250 830912 900922 852016 668868 872792 955931 FALSE TRUE 767090.9833 882383.5441 818418.8048 897286.3348 857639.0391 919139.2601 862443.2267 655055.6421 773716.3112 891184.9419 0.860753977 0.990123938 0.918349005 1.006846382 0.962358091 1.031367584 0.967748877 0.735038948 0.868188268 1 19.76536533 1.778168968 24.99999993 0.839616084 0.966218838 0.222184221 0.075745471 55.19160901 34849.34597 0.03292984 0.018291882 60.00244781 -1.778168968 0.126602754 TATPPGYKPGS(ph)PPSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 1 TATPPGYKPGS(0.982)PPS(0.018)FR;TATPPGYKPGS(0.972)PPS(0.028)FR 110.41 0.00054283 819140000 686410 641160 508440 547090 625090 550490 593720 733570 715540 650850 TRUE FALSE 659584.3383 622874.7446 600326.4182 575325.3805 645196.5875 561621.285 600986.123 718421.5231 634314.899 606767.3498 1.087046524 1.026546245 0.989384841 0.948181178 1.063334386 0.925595758 0.990472087 1.184014801 1.045400513 1 19.21078393 1.778313826 25 1.095946358 1.001720178 0.195095464 0.063363953 64.50823645 40583.60664 0.028318163 0.015732032 60.02246481 -1.778313826 -0.09422618 HLWNHSIIEEEFVSLVTGCCYR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLWNHSIIEEEFVSLVTGCCYR 22 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 0 ; 149.94 3.45E-08 291640000 178233 148938 172689 177548 198606 194686 201099 48000 204760 177845 FALSE TRUE 171267.4573 144690.4341 203897.7437 186711.2736 204994.3424 198622.6843 203560.1097 47008.78323 181516.5032 165799.3997 1.03297996 0.872683703 1.229785778 1.12612756 1.236399786 1.197969864 1.227749377 0.283528066 1.094795901 1 17.33907926 1.778367364 24.99999999 0.717434497 1.132079161 0.300964111 0.228382519 52.74489246 33138.36233 0.101427576 0.056348351 60.02986467 -1.778367364 0.414644664 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR 30 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 328.86 1.64E-105 3426197000 564912 667084 514401 622637 615011 582817 636892 160280 658351 539697 FALSE TRUE 542834.6145 648059.4175 607364.7035 654771.3702 634793.3874 594601.9591 644686.4748 156970.162 583617.7545 503142.8415 1.078887683 1.288022732 1.207141697 1.301362786 1.261656403 1.181775651 1.281318985 0.311979321 1.159944466 1 18.94060851 1.778370167 25 0.752460202 1.23232544 0.416935958 0.214290596 41.16782047 25862.94092 0.091594542 0.050885367 60.03025205 -1.778370167 0.479865238 TVSTLHHVLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSTLHHVLQR 11 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 150.04 1.97E-05 428570000 150500 182850 131340 193220 158960 150290 165750 71969 155170 176410 FALSE TRUE 144618.2936 177635.297 155076.0596 203192.1074 164073.0928 153328.9668 167778.4981 70482.815 137555.7521 164461.5936 0.879343867 1.080102005 0.942931759 1.235498836 0.997637741 0.932308653 1.020168262 0.42856702 0.836400458 1 17.32739119 1.778452203 25 0.694795556 1.017402134 0.323885909 0.163652649 48.06260727 30132.34402 0.07141073 0.039673679 60.04159252 -1.778452203 0.322606579 GAGGEENKENERPSAGSK ddPTM_BT-474_Pertuzumab_2h_R1 6 GAGGEENKENERPSAGSK 18 2 Q9UHB9;Q9UHB9-4;Q9UHB9-2;K7EN53;K7EQC2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;;;;; 234.49 5.11E-24 2033590000 1718897 1632214 1455314 1425593 1557252 1672469 1753402 1912358 2391570 2125732 FALSE TRUE 1651720.605 1585664.855 1718321.613 1499168.026 1607342.425 1706287.469 1774860.658 1872867.139 2120089 1981754.278 0.833463877 0.80013192 0.867070974 0.756485323 0.811070496 0.860998504 0.89560077 0.945055176 1.069804175 1 20.91834666 1.778689655 1.28087482 1.033325608 0.815228107 0.852985663 0.03510452 0.148204321 0.456397842 0.027635298 0.011019387 60.07442946 -1.778689655 -0.2180975 AEGEPQEES(ph)PLKSK ddPTM_BT-474_Pertuzumab_2h_R1 5 AEGEPQEESPLKSK 14 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEPQEES(0.999)PLKS(0.001)K;AEGEPQEES(1)PLKSK;AEGEPQEES(1)PLKSK;AEGEPQEES(1)PLKSK;AEGEPQEES(0.999)PLKS(0.001)K 218.14 3.33E-12 3719190000 2774810 2175070 1682550 1505380 1993200 2106600 2089870 2422270 2878730 2310310 TRUE FALSE 2666367.357 2113039.133 1986624.213 1583072.842 2057313.088 2149196.895 2115446.454 2372249.278 2551948.639 2153830.646 1.237965187 0.981060947 0.922367883 0.735003397 0.955187954 0.9978486 0.98217864 1.101409381 1.184841828 1 21.03847339 1.778831949 3.260666938 1.109705133 0.960104987 0.168358784 0.122029865 0.373358465 7.690215305 0.069942419 0.034666781 60.0941157 -1.778831949 -0.149600146 S(ph)LSQSFENLLDEPAYGLIQK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.378)LS(0.311)QS(0.311)FENLLDEPAYGLIQK;S(0.379)LS(0.311)QS(0.311)FENLLDEPAYGLIQK;S(0.333)LS(0.333)QS(0.333)FENLLDEPAYGLIQK 131.71 8.92E-06 296299000 265622 247996 265265 230863 268865 254729 246713 363865 300661 290374 TRUE FALSE 255241.1986 240923.3969 313204.2863 242777.8671 277513.2869 259879.7949 249732.3475 356351.0606 266531.2238 270706.7103 0.942869862 0.889979405 1.156987523 0.896829882 1.02514373 0.960004998 0.922519974 1.316373208 0.984575607 1 18.04637112 1.778846263 25 1.133857768 0.973536557 0.201434477 0.112438655 68.41833363 42474.3908 0.048924053 0.02718441 60.09609648 -1.778846263 -0.160321211 FSTLTDDPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSTLTDDPSPR 11 0 Q14C86-2;Q14C86-6;Q14C86-4;Q14C86-5;Q14C86 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FSTLTDDPS(1)PR 79.492 0.016597 0 277120 322720 308060 307050 315720 334000 285520 277970 261950 276300 TRUE FALSE 266289.844 313516.3416 363733.2948 322896.8873 325875.4205 340753.7088 289014.2792 272229.8224 232214.5342 257585.9549 1.033790232 1.217132905 1.412085123 1.253550053 1.265113312 1.322873792 1.122011017 1.056850411 0.90150309 1 17.97469441 1.778970091 1.923093298 0.959221089 1.256062735 0.606246927 0.095896141 0.213526969 1.55439976 0.066988374 0.028498845 60.1132338 -1.778970091 0.296841646 ALSDHHIYLEGTLLKPNMVTPGHACTQK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALSDHHIYLEGTLLKPNMVTPGHACTQK 28 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;; 239.47 2.00E-45 13940300000 5945600 7042470 5785200 6832490 6213770 6146650 6744050 2171470 6828980 6188670 FALSE TRUE 5713239.379 6841625.651 6830714.331 7185115.628 6413641.555 6270939.474 6826585.701 2126628.386 6053782.82 5769505.869 0.990247607 1.185825235 1.183934029 1.245360658 1.111644862 1.086911014 1.183218434 0.368598011 1.049272322 1 22.46001633 1.779021836 25 0.73982886 1.145196346 0.392495019 0.185585183 44.96545815 27793.55336 0.080157905 0.044544579 60.12039647 -1.779021836 0.405367486 LPETNLFETEETRK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPETNLFETEETRK 14 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ; 174.59 4.04E-06 796820000 580610 555670 432600 487890 533760 531950 549450 608340 680470 662650 FALSE TRUE 557919.1193 539822.8357 510780.4431 513070.0614 550928.8751 542706.3935 556174.3335 595777.5664 603225.8984 617768.1253 0.903120599 0.873827596 0.826815794 0.830522069 0.891805279 0.878495298 0.900296261 0.964403215 0.976460056 1 19.23670591 1.779071251 1.161838906 0.997938465 0.861164776 0.83910493 0.022402384 0.180291483 0.453045896 0.019808749 0.007956983 60.12723745 -1.779071251 -0.136773689 RLAAAEETAVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLAAAEETAVSPR 13 1 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEET(0.014)AVS(0.986)PR;RLAAAEETAVS(1)PR 227.29 9.91E-12 6801180000 3419980 3727000 2916010 3385750 3722900 3498470 3125880 3035390 2792230 2971140 TRUE FALSE 3286323.401 3620709.609 3442997.873 3560488.963 3842650.46 3569211.46 3164135.454 2972708.136 2475267.756 2769902.041 1.186440297 1.307161609 1.243003479 1.285420535 1.387287493 1.288569562 1.142327565 1.073217786 0.89363007 1 21.40140353 1.779106701 1.689556418 0.954525827 1.286280512 0.835270954 0.059272657 0.130583906 0.724566828 0.043174409 0.017768739 60.13214574 -1.779106701 0.331754685 NKS(ph)NEDQSMGNWQIK ddPTM_BT-474_Pertuzumab_2h_R1 4 NKSNEDQSMGNWQIK 15 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(0.999)NEDQS(0.001)MGNWQIK 309.83 2.41E-56 1905990000 2350000 1804240 1696640 1639720 1851710 1699750 1900540 2408160 2689390 2213290 TRUE FALSE 2258159.402 1752784.842 2003260.59 1724346.146 1911271.934 1734120.11 1923799.377 2358430.654 2384101.722 2063381.897 1.094397215 0.849471852 0.970862734 0.835689287 0.926281236 0.840426153 0.932352552 1.142992801 1.15543406 1 20.97657943 1.779155436 6.135942122 1.111155653 0.913525069 0.494584204 0.082031941 0.135048651 11.48762994 0.036393799 0.020253139 60.13889383 -1.779155436 -0.197630585 DTPRPDHPPHDGHS(ph)PASR ddPTM_BT-474_Pertuzumab_2h_R1 7 DTPRPDHPPHDGHSPASR 18 1 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(0.999)PAS(0.001)R;DTPRPDHPPHDGHS(1)PASR;DT(0.001)PRPDHPPHDGHS(0.944)PAS(0.056)R;DTPRPDHPPHDGHS(0.947)PAS(0.053)R;DT(0.001)PRPDHPPHDGHS(0.979)PAS(0.02)R 166.49 1.28E-11 3948124500 427434.7 445267.3 366798.3 438727.4 440754.9 449262.9 441395.2 109335.2 461495.6 362302.8 TRUE FALSE 410730.0794 432568.7126 433086.9122 461370.1737 454932.1816 458347.3037 446797.1265 107077.3899 409108.5542 337763.7087 1.216027859 1.2806844 1.282218608 1.365955435 1.346894797 1.357005776 1.322809749 0.317018635 1.211227091 1 18.3656548 1.779192773 25 0.772187562 1.313367465 0.486142948 0.216617054 39.62190749 24387.57938 0.092997067 0.051683409 60.14406428 -1.779192773 0.541179902 ATLNLEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ATLNLEER 8 0 Q6IE37 Q6IE37 OVOS1 Ovostatin homolog 1 0 69.423 0.053956 784590000 240620 448860 396540 610420 517380 408950 395650 238050 159410 240110 FALSE TRUE 231216.3044 436058.9523 468203.599 641923.8494 534021.9976 417219.2492 400492.0831 233134.1843 141314.4451 223847.1358 1.03292054 1.948021138 2.091622023 2.867688465 2.385654816 1.863857885 1.789132041 1.041488351 0.631298875 1 17.77215433 1.779268016 2.02224382 0.793370013 2.085786061 0.57544826 0.441051131 0.225332649 1.818826145 0.314071599 0.135620554 60.15448547 -1.779268016 1.292416047 GEEHCGHLIEAHK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEEHCGHLIEAHK 13 0 H7C4E5;C9J8T6;Q14061 H7C4E5 COX17 Cytochrome c oxidase copper chaperone 0 ;;; 231.52 7.93E-13 3184770000 3374560 3329610 3410900 3966940 3032370 3355340 3460180 314833 3954520 2052690 FALSE TRUE 3242678.464 3234652.783 4027325.505 4171674.249 3129908.935 3423187.274 3502526.718 308331.5885 3505619.468 1913659.478 1.694490844 1.690296952 2.104515224 2.179945961 1.635562111 1.788817349 1.83027689 0.161121449 1.831893035 1 20.8679027 1.779361741 24.99999854 0.913620006 1.852725496 0.468596978 0.411166817 44.76351378 27438.12357 0.179853914 0.099963792 60.16746875 -1.779361741 0.939105491 EIGDLWGHLHDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EIGDLWGHLHDR 12 0 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ;; 124.12 0.00019006 451030000 346804 409420 368854 440240 424380 437160 474630 3607.6 491370 364117 FALSE TRUE 333250.5163 397743.7425 435514.1229 462960.8392 438030.5681 445999.6747 480438.6639 3533.101799 435591.7376 339455.0313 0.98172213 1.171712615 1.282980315 1.36383555 1.290393507 1.313869684 1.415323444 0.010408159 1.28320896 1 18.37286094 1.779520717 25 0.660443776 1.264704157 0.31491011 0.32408833 55.22138295 33716.91874 0.140946815 0.078345738 60.18949741 -1.779520717 0.60426038 DYFGAHTYELLAKPGQFIHTNWTGHGGTVSSSSYNA ddPTM_BT-474_Pertuzumab_2h_R1 2 DYFGAHTYELLAKPGQFIHTNWTGHGGTVSSSSYNA 36 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 126.04 1.28E-08 814250000 241040 346020 215396 267620 258010 320240 280540 82927 282800 251840 FALSE TRUE 231619.8903 336151.8484 254322.8487 281431.9003 266309.126 326715.4722 283973.3324 81214.52847 250697.7296 234782.6525 0.986528978 1.431757606 1.083226746 1.198691204 1.134279399 1.391565641 1.20951582 0.345913668 1.067786427 1 17.84096629 1.77957034 25 0.73649047 1.213316209 0.398844645 0.220468794 47.0870632 28715.48334 0.094466135 0.052510181 60.19637514 -1.77957034 0.476825739 QVEEALHQLHAR ddPTM_BT-474_Pertuzumab_2h_R1 6 QVEEALHQLHAR 12 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ;;;;; 213.06 7.55E-09 3555155000 1258412 1406921 1142601 1394195 1352091 1323157 1432277 140266.9 1385779 1265795 FALSE TRUE 1209231.868 1366796.991 1349094.418 1466149.571 1395582.235 1349912.141 1449805.634 137370.3395 1228471.178 1180061.577 1.024719295 1.158242093 1.143240695 1.242434801 1.182635095 1.143933645 1.22858473 0.116409467 1.041022944 1 20.17043071 1.779608975 25 0.626144236 1.163148542 0.388680982 0.245483693 46.7705265 28495.59121 0.105341921 0.058557317 60.20173051 -1.779608975 0.537004305 HADHSSLTLGSGSSTTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HADHSSLTLGSGSSTTR 17 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 142.91 3.29E-07 236810000 126349 161481 134364 159173 146853 164465 153204 81771 145064 169839 FALSE TRUE 121411.1414 156875.72 158646.5637 167387.9376 151576.6601 167790.595 155078.9564 80082.40027 128596.9429 158335.6533 0.766795974 0.990779504 1.001963616 1.057171485 0.957312248 1.059714547 0.97943169 0.50577617 0.812179318 1 17.27262663 1.779720364 25 0.720234351 0.981017351 0.283622207 0.138454685 55.8602231 33941.46659 0.060553353 0.033662568 60.21717318 -1.779720364 0.260783 (ac)SQGDSNPAAIPHAAEDIQGDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQGDSNPAAIPHAAEDIQGDDR 22 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 112.5 9.30E-45 256680000 9242.4 14525.4 14948.5 12883.4 13595.2 15861.2 13398.3 12261.9 11934.7 14246.8 FALSE TRUE 8881.19679 14111.14981 17650.02648 13548.31382 14032.50195 16181.92433 13562.2724 12008.68748 10579.92289 13281.85155 0.66867159 1.062438453 1.328882981 1.020062133 1.056517 1.218348532 1.021113085 0.904142577 0.79656988 1 13.69716866 1.77975537 3.655895021 0.885749044 1.072375436 0.149808344 0.165853431 0.369694677 9.525409861 0.088654597 0.045187802 60.22202709 -1.77975537 0.186626391 YIHSADIIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIHSADIIHR 10 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 ; 178.84 1.26E-06 504650000 465140 475350 448860 528360 488470 486910 509480 199184 506510 500350 FALSE TRUE 446961.8146 461793.4834 529978.9868 555628.7229 504182.0812 496755.6538 515715.1686 195070.7808 449013.1083 466460.8488 0.958197919 0.98999409 1.136170352 1.191158324 1.080866878 1.064946083 1.105591541 0.418193255 0.962595488 1 18.83139647 1.779775078 25 0.732259755 1.078612093 0.371527273 0.162058411 49.77713816 30205.13336 0.071352173 0.039667163 60.22475994 -1.779775078 0.346352338 GEVPGGSAHYGGPS(ph)PEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEVPGGSAHYGGPSPEKK 18 1 O94762-4;O94762;J3KS37 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 1 GEVPGGSAHYGGPS(1)PEKK 185.61 2.46E-14 322640000 529200 525300 397920 410300 435220 433600 468430 570970 594680 588230 TRUE FALSE 508518.2789 510318.9583 469832.9957 431475.6322 449219.2466 442367.6891 474162.7865 559179.27 527174.4195 548388.6582 0.927295398 0.93057898 0.856751847 0.786806266 0.819162176 0.806668195 0.864647325 1.019676942 0.961315322 1 19.06483921 1.779790064 6.626566203 0.992462581 0.852489018 0.652745793 0.045974422 0.130367758 13.3915952 0.024193165 0.013583027 60.22683824 -1.779790064 -0.139973563 IEVDEGFCS(ph)PKPSEIK ddPTM_BT-474_Pertuzumab_2h_R1 3 IEVDEGFCSPKPSEIK 16 1 Q9UHV7 Q9UHV7 MED13 Mediator of RNA polymerase II transcription subunit 13 1 IEVDEGFCS(0.999)PKPS(0.001)EIK;IEVDEGFCS(1)PKPSEIK;IEVDEGFCS(1)PKPSEIK 177.4 1.79E-09 1262080000 1238780 912290 903090 888680 1057140 939500 1055070 1465940 1649410 1397630 TRUE FALSE 1190367.108 886272.3824 1066298.452 934544.8813 1091143.868 958497.3337 1067982.262 1435667.827 1462175.892 1302967.275 0.913581738 0.680195427 0.818361652 0.717243556 0.837429987 0.735626559 0.819653941 1.101844884 1.122189267 1 20.31336942 1.779855993 4.526100431 1.084609641 0.780332035 0.781088456 0.069337307 0.077565194 3.140692801 0.031650874 0.016855644 60.23598177 -1.779855993 -0.304277606 SDLQPPNYYEVMEFDPLAPAVTTEAIYEEIDAHQHK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDLQPPNYYEVMEFDPLAPAVTTEAIYEEIDAHQHK 36 0 J3KQU4;I3L4I4;O75674;O75674-3 J3KQU4 TOM1L1 TOM1-like protein 1 0 ;;; 120.43 1.88E-07 223967000 51456 53748.5 49613 50459 50947 57349 57012 8481.3 65269 37628.6 FALSE TRUE 49445.04263 52215.64541 58579.17274 53063.19504 52585.75652 58508.63607 57709.72991 8306.158191 57859.93675 35079.98141 1.409494551 1.488474147 1.66987468 1.51263464 1.499024641 1.667863942 1.645090094 0.236777725 1.649371933 1 15.09836036 1.779921266 25 0.883646473 1.558278768 0.400190775 0.329076864 51.16844815 30939.59695 0.141195224 0.078501103 60.24503566 -1.779921266 0.674632295 SHNWLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHNWLK 6 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 79.939 0.065827 246870000 421800 425520 336510 419140 383950 381970 448590 175380 454150 444570 FALSE TRUE 405315.5897 413384.5862 397324.8426 440771.8656 396300.1004 389693.6951 454079.9786 171758.3417 402596.796 414458.8779 0.977939215 0.997407966 0.958659263 1.063487572 0.956186781 0.940246948 1.095597182 0.414415883 0.971379351 1 18.66086944 1.779946884 25 0.732696447 0.995560193 0.230173658 0.158313091 63.29719496 38249.68261 0.067922479 0.037764013 60.24858955 -1.779946884 0.262863745 KEEPS(ph)PLNLSHHTPDHQGEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 KEEPSPLNLSHHTPDHQGEGR 21 1 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 1 KEEPS(1)PLNLSHHTPDHQGEGR;KEEPS(1)PLNLSHHTPDHQGEGR;KEEPS(1)PLNLSHHTPDHQGEGR 223.44 1.34E-25 1114730000 1053395 1259590 874989 1099740 1040897 1208480 1103810 378986 1105410 1030400 TRUE FALSE 1012227.159 1223667.726 1033118.976 1156497.713 1074378.397 1232916.294 1117318.757 371159.8067 979928.4911 960610.0902 1.053733631 1.27384434 1.07548212 1.203920014 1.118433388 1.283472146 1.163134521 0.38637925 1.020110554 1 19.87359144 1.779996935 25 0.738076453 1.171969876 0.454050474 0.179416826 43.39139319 26189.17409 0.076543177 0.04255796 60.25553338 -1.779996935 0.433893424 EHMQPTHPIR ddPTM_BT-474_Pertuzumab_2h_R1 15 EHMQPTHPIR 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;;;;;;;;;;; 124.42 0.00030517 7861199000 5204436 5440495 4993578 5837751 5457314 5588900 6042913 2828078 5936895 6418761 FALSE TRUE 5001040.887 5285337.409 5896028.626 6139038.029 5632853.461 5701911.387 6116867.977 2769677.201 5262963.569 5984012.6 0.835733683 0.883243028 0.985296827 1.025906601 0.941317112 0.952857517 1.022201721 0.462846151 0.879504092 1 22.51268178 1.780009422 25 0.723254751 0.95108816 0.200562173 0.140942515 66.79117015 40300.11948 0.061810257 0.034366044 60.25726592 -1.780009422 0.227833409 THKHS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 THKHSPEK 8 1 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 T(0.001)HKHS(0.999)PEK;T(0.425)HKHS(0.575)PEK 78.692 0.018098 84183000 210899 153920 148752 133782 150900 137684 167316 9908.9 175245 126413 TRUE FALSE 202656.8339 149530.3523 175634.7954 140686.5051 155753.8355 140468.0648 169363.6633 9704.277752 155351.9223 117850.9349 1.719603108 1.268809216 1.490313127 1.193766559 1.32161731 1.191913029 1.437100719 0.082343664 1.318206957 1 16.84660368 1.780013685 25 0.70440098 1.359069006 0.383098415 0.326987231 52.92657131 31931.28309 0.140680901 0.078219685 60.25785735 -1.780013685 0.654668026 RHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_BT-474_Pertuzumab_2h_R1 7 RHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR 39 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 377.12 3.77E-162 3206845000 824955 954110 853436 917835 979020 1108268 982883 414499 1036203 893509 FALSE TRUE 792714.8466 926899.717 1007670.87 965204.5743 1010511.067 1130677.938 994911.8162 405939.4508 918577.5796 832990.8396 0.951648936 1.112736987 1.209702222 1.158721715 1.213111861 1.357371395 1.194385063 0.487327629 1.102746316 1 19.6679411 1.780108361 24.99999959 0.809855461 1.178641622 0.374932801 0.177925629 53.5127008 32211.29939 0.079525694 0.044219636 60.27099501 -1.780108361 0.368786161 EHIEELLR ddPTM_BT-474_Pertuzumab_2h_R1 5 EHIEELLR 8 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ;;;; 168.27 0.00030783 2016679000 2614360 2816120 2376150 2742810 2631660 2556610 2794020 1649470 2875620 2906200 FALSE TRUE 2512187.921 2735807.015 2805573.162 2884366.753 2716309.734 2608306.406 2828214.053 1615407.868 2549191.673 2709360.485 0.927225423 1.00976117 1.035511213 1.064593201 1.002564904 0.96270187 1.043867757 0.596232165 0.940883167 1 21.36952093 1.78010923 25 0.802772629 1.008223487 0.298926035 0.107000998 56.02258846 33721.39108 0.046377953 0.025788188 60.27111553 -1.78010923 0.205450858 SVGDGETVEFDVVEGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SVGDGETVEFDVVEGEK 17 0 P67809;H0Y449;A0A0D9SEI8;P16989;P16989-3;P16989-2;Q9Y2T7 P67809;P16989;P16989-2;Q9Y2T7 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3;Y-box-binding protein 2 0 ;; 407.63 5.53E-140 1687890000 1396790 1350780 1265580 1160290 1339400 1393930 1436300 1676010 1857410 1872350 FALSE TRUE 1342201.903 1312257.077 1494298.459 1220172.706 1382483.017 1422116.22 1453877.869 1641399.808 1646564.604 1745534.067 0.768934808 0.7517797 0.85606949 0.699025432 0.792011479 0.814716966 0.832912916 0.940342465 0.943301328 1 20.73523708 1.780117627 1.106429929 0.990457394 0.772323918 0.822790009 0.038188852 0.181493357 0.412620668 0.030774873 0.012464671 60.27228093 -1.780117627 -0.218133475 DLDRPESQS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLDRPESQSPK 11 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 DLDRPES(0.078)QS(0.922)PK;DLDRPES(0.008)QS(0.992)PK;DLDRPES(0.023)QS(0.977)PK 142.38 9.91E-05 2338960000 2124710 1795400 1567500 1521710 1768390 1861150 1835460 2220480 2411010 2371450 TRUE FALSE 2041673.984 1744196.95 1850782.119 1600245.635 1825271.87 1898783.728 1857922.909 2174626.312 2137322.253 2210829.579 0.923487728 0.788933243 0.837143729 0.723821343 0.825604962 0.858855764 0.840373643 0.983624578 0.966751247 1 21.07615639 1.780151996 3.044303485 0.985810768 0.821398714 0.682190722 0.048425896 0.13495067 2.427321963 0.027234862 0.013278991 60.27705086 -1.780151996 -0.164412054 VDVADQAQDKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDVADQAQDKDR 12 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 104.7 0.0019245 149950000 151510 124130 156930 167870 159040 145340 182970 191510 230380 249890 FALSE TRUE 145588.8217 120589.9339 185290.7419 176533.7908 164155.666 148278.8744 185209.2416 187555.2516 204228.2282 232964.7277 0.624939334 0.517631725 0.79535964 0.757770468 0.704637426 0.636486372 0.7950098 0.805080037 0.876648711 1 17.82975201 1.780195661 0.063082045 1.581641856 1.10E-15 0.698943548 0.071598253 14.69806812 0.867325748 10.20352241 10.88881204 60.28311163 -1.780195661 -1.581641856 NDKSEEEQS(ph)SSS(ph)VKKDETNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVKKDETNVK 21 3 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 2 NDKSEEEQS(0.996)S(0.043)S(0.178)S(0.783)VKKDETNVK 115.11 0.00023168 534880000 334000 165140 188430 99775 154290 159450 192330 308430 367010 231430 TRUE FALSE 320946.9107 160430.3689 222483.4926 104924.3997 159252.878 162674.1882 194683.7921 302060.8127 325348.5634 215755.04 1.487552322 0.74357646 1.03118561 0.486312624 0.738118924 0.753976307 0.90233717 1.400017412 1.50795348 1 17.71903474 1.780236444 5.496124236 1.338970604 0.850589451 0.329985819 0.274514451 0.19399031 12.4005138 0.12930318 0.07111281 60.28877277 -1.780236444 -0.488381154 TNATNNMNLS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 TNATNNMNLSR 11 0 A0A087X2H1;Q9ULT8;H0YJP0 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 TNATNNMNLS(1)R 122.45 0.00040971 211810000 183400 151580 124770 152350 138150 148840 148620 191030 170830 177300 TRUE FALSE 176232.5252 147257.0868 147318.7145 160212.8018 142593.7202 151849.6468 150438.856 187085.1637 151438.0946 165291.3131 1.06619351 0.890894289 0.891267132 0.969275389 0.862681272 0.918678931 0.910143753 1.131851156 0.916189071 1 17.33465138 1.780273968 24.99999991 1.029692094 0.925392268 0.220771812 0.072468372 76.22280678 45699.09685 0.031614276 0.017580827 60.29398208 -1.780273968 -0.104299826 LVINGNPITIFQERDPS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 2 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPIT(0.001)IFQERDPS(0.999)K;LVINGNPITIFQERDPS(1)K 187.79 2.49E-14 1970020000 1281210 1112690 929950 1063150 1043160 1009100 1056980 1393850 1344050 1089900 TRUE FALSE 1231138.897 1080957.171 1098012.652 1118019.299 1076714.189 1029504.693 1069915.637 1365066.51 1191479.079 1016080.102 1.211655355 1.063850348 1.080635916 1.100325945 1.059674514 1.013212139 1.052983554 1.34346348 1.172623178 1 19.95458271 1.780342857 25 1.20898826 1.079411967 0.124882437 0.093124613 79.734866 47725.92387 0.040861275 0.022723662 60.30354695 -1.780342857 -0.129576293 HLAGYEQQDAHEFLIAALDVLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLAGYEQQDAHEFLIAALDVLHR 23 0 Q9UPT9-2;Q9UPT9 Q9UPT9-2 USP22 Ubiquitin carboxyl-terminal hydrolase 22 0 ; 302.71 1.68E-62 402890000 86093 102490 95521 104980 107526 113013 113834 26983 113492 105579 FALSE TRUE 82728.39038 99567.08555 112783.7696 110398.0304 110984.6714 115298.2003 115227.1345 26425.79162 100608.864 98428.04029 0.840496165 1.011572366 1.145849996 1.121611586 1.127571687 1.171395874 1.170673867 0.268478287 1.022156528 1 16.58678175 1.780353309 25 0.686015853 1.090212282 0.294650505 0.217485367 59.93212569 35863.86544 0.095726777 0.053236108 60.30499826 -1.780353309 0.404196429 VYAEADSQESADHLAHEVSLAVFQLAGGIGERPQPGF ddPTM_BT-474_Pertuzumab_2h_R1 2 VYAEADSQESADHLAHEVSLAVFQLAGGIGERPQPGF 37 1 O95394-4;O95394;A0A494C0G1;A0A087WT27;A0A494C1E2;A0A494C1Q4;H0Y8I3 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 248.55 1.27E-50 589080000 311320 373610 290920 400890 388520 436950 378700 24302 378530 304900 FALSE TRUE 299153.2702 362955.0086 343495.7155 421579.9809 401017.0986 445785.4284 383334.6439 23800.15521 335560.8613 284248.8514 1.052434403 1.276891733 1.208433082 1.483136973 1.410795845 1.568292805 1.348588189 0.083729996 1.180517915 1 18.11679499 1.780387315 25 0.659289669 1.345895238 0.43009267 0.300220467 48.95193627 29269.40367 0.132457565 0.073663242 60.30972037 -1.780387315 0.68660557 DGGTSYS(ph)PQENSHNHSALHSSNSHSSNPSNNPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGGTSYSPQENSHNHSALHSSNSHSSNPSNNPSK 34 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 DGGTS(0.001)Y(0.004)S(0.994)PQENSHNHSALHSSNSHSSNPSNNPSK;DGGT(0.004)S(0.012)Y(0.004)S(0.97)PQENS(0.003)HNHS(0.003)ALHS(0.001)S(0.001)NS(0.001)HS(0.001)S(0.001)NPS(0.001)NNPS(0.001)K 81.426 0.0005876 70427000 5216.8 18234 11238.3 26556 17690.4 19826.1 16002.7 564.71 5370.4 4611.2 TRUE FALSE 5012.921689 17713.98417 13269.3108 27926.55834 18259.42778 20226.99733 16198.54583 553.0485412 4760.774707 4298.879317 1.166099655 4.120605132 3.086690699 6.496241528 4.247485551 4.705179149 3.768085735 0.128649469 1.107445535 1 12.06974489 1.780444682 6.260271703 0.72359978 4.067064403 0.565934385 1.279693714 0.135144466 11.95271541 0.606759983 0.33923875 60.31768732 -1.780444682 3.343464623 AQSGSDSS(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 AQSGSDSSPEPK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQSGSDS(0.095)S(0.905)PEPK;AQSGS(0.003)DS(0.286)S(0.711)PEPK;AQSGS(0.001)DS(0.041)S(0.958)PEPK 228.8 1.02E-11 647497000 2724130 2307740 1940160 2118340 2209930 2195450 2331690 2612170 2932610 2718730 TRUE FALSE 2617667.988 2241925.515 2290790.071 2227667.781 2281014.405 2239843.503 2360225.92 2558227.777 2599712.407 2534587.996 1.0327785 0.884532523 0.903811615 0.878907256 0.89995471 0.883711083 0.931206935 1.009326873 1.025694279 1 21.27331982 1.780561203 3.421473355 1.014971593 0.909798684 0.516189748 0.042353143 0.168805326 3.804750948 0.022424633 0.011263807 60.33387278 -1.780561203 -0.105172909 LWTLSANDMEDDSMDLIDS(ph)DELLDPEDLKKPDPASLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LWTLSANDMEDDSMDLIDSDELLDPEDLKKPDPASLR 37 2 Q6FI81-3;Q6FI81 Q6FI81-3 CIAPIN1 Anamorsin 1 LWTLSANDMEDDSMDLIDS(1)DELLDPEDLKKPDPASLR;LWTLSANDMEDDS(0.061)MDLIDS(0.938)DELLDPEDLKKPDPASLR;LWTLSANDMEDDS(0.001)MDLIDS(0.999)DELLDPEDLKKPDPASLR 184.78 1.82E-23 388407000 173861 158121 152905 146969 166906 153374.1 184381 230440 281335 247829 TRUE FALSE 167066.3199 153611.5439 180538.3349 154554.0877 172274.6831 156475.4294 186637.5098 225681.3335 249399.0303 231043.3211 0.723095215 0.664860352 0.781404691 0.668939864 0.745638014 0.677255801 0.807803095 0.976792285 1.079447045 1 17.81780386 1.780676075 2.257873886 1.04000217 0.711271038 0.923277342 0.039905545 0.062819705 0.63252179 0.023163609 0.010356941 60.34983338 -1.780676075 -0.328731132 QSDEVGDRDHR ddPTM_BT-474_Pertuzumab_2h_R1 4 QSDEVGDRDHR 11 1 P40222 P40222 TXLNA Alpha-taxilin 0 ;;; 129.34 0.00014839 456323000 281751 300249 209474 278177 274297 302432 277028 262733 297775 282345 FALSE TRUE 270739.8594 291686.1925 247330.6115 292533.7483 283120.0121 308547.3823 280418.3515 257307.4717 263972.8304 263221.5217 1.028562778 1.108139603 0.939629138 1.111359536 1.075595986 1.172196636 1.065332157 0.977532043 1.002854283 1 18.00591793 1.78077236 6.735443426 0.9929297 1.073673484 0.280688237 0.057238984 0.256792532 27.17358588 0.026992973 0.015208941 60.36321457 -1.78077236 0.080743784 EGTVSDHIER ddPTM_BT-474_Pertuzumab_2h_R1 1 EGTVSDHIER 10 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 0 91.095 0.010106 0 241450 260740 198490 233390 270140 241120 240340 180100 213720 213170 FALSE TRUE 232013.8671 253303.9505 234361.5584 245435.2859 278829.2984 245995.6116 243281.3528 176380.8721 189459.4016 198731.806 1.167472242 1.274601965 1.179285606 1.235007575 1.403043146 1.237827082 1.224169184 0.887532175 0.953342122 1 17.60046326 1.780804733 6.089846299 0.941183245 1.250998943 0.812147201 0.065850753 0.075949006 6.245466445 0.031702162 0.017682942 60.36771431 -1.780804733 0.309815698 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK ddPTM_BT-474_Pertuzumab_2h_R1 6 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK 29 2 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;;;; 182.97 5.53E-18 10368190000 3192210 2683117 2154159 1955869 2661229 2687185 2734739 2978513 3777050 3204190 FALSE TRUE 3067454.904 2606597.13 2543463.45 2056811.633 2746829.848 2741521.722 2768207.554 2917005.666 3348295.119 2987167.357 1.026877485 0.872598291 0.851463325 0.68854918 0.91954334 0.917766363 0.926699854 0.9765123 1.120893046 1 21.51034664 1.780844323 1.363085913 1.056088589 0.867277768 0.407901151 0.084614796 0.410221736 1.440421512 0.068688248 0.027453723 60.37321766 -1.780844323 -0.18881082 DGIDDESYEAIFKPVMSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGIDDESYEAIFKPVMSK 18 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 ; 223.5 4.67E-19 194250000 619840 547480 507880 506780 525940 545050 604830 649090 785690 715900 FALSE TRUE 595615.9675 531866.4064 599665.2137 532934.9765 542857.3377 556071.2844 612232.0905 635686.0647 696501.7651 667411.4553 0.892426947 0.796909316 0.898494038 0.798510383 0.813377315 0.833176116 0.917323318 0.952465019 1.04358677 1 19.34821692 1.780849447 1.591184076 1.018371795 0.83652228 0.796253953 0.03676412 0.148099397 0.723005704 0.026015692 0.010591495 60.37393 -1.780849447 -0.181849514 SIGEAIQYLHSINIAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIGEAIQYLHSINIAHR 17 0 P49137-2;P49137 P49137-2 MAPKAPK2 MAP kinase-activated protein kinase 2 0 172.93 8.91E-10 122030000 89035 103200 81711 107940 104950 111080 102370 59102 105900 103760 FALSE TRUE 85555.41377 100256.837 96477.99535 113510.7963 108325.8121 113326.1137 103622.8347 57881.52305 93878.67597 96732.24278 0.884456013 1.036436602 0.997371637 1.173453577 1.119852171 1.171544363 1.071233662 0.598368459 0.970500355 1 16.56170923 1.780858888 25 0.81398753 1.071604037 0.335124917 0.130403024 60.3158964 35661.91755 0.058982092 0.032812 60.37524245 -1.780858888 0.257616507 KTDVKEEDKSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTDVKEEDKSK 11 3 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 85.536 0.0066338 768870000 2690600 1942800 1580300 1176500 2063200 1887800 2036000 2625700 3241100 2507900 FALSE TRUE 2585448.377 1887393.246 1865895.364 1237219.306 2129564.702 1925972.609 2060917.177 2571478.377 2873183.916 2338037.699 1.105819798 0.807255267 0.798060427 0.529169956 0.910834202 0.823756011 0.881473031 1.099844702 1.228886907 1 21.15686676 1.780909375 2.916276104 1.131528134 0.818299083 0.437241429 0.142300013 0.21607693 3.573992679 0.082034651 0.039565303 60.38226161 -1.780909375 -0.313229051 KHDSGAADLER ddPTM_BT-474_Pertuzumab_2h_R1 1 KHDSGAADLER 11 1 Q9NX55;Q9NX55-3;J3QT56 Q9NX55;J3QT56 HYPK Huntingtin-interacting protein K 0 159.64 1.85E-05 455890000 458690 754880 606740 799750 550780 670600 696450 280640 607380 820670 FALSE TRUE 440763.8877 733351.5615 716391.4149 841025.1933 568496.3389 684159.9915 704973.3634 274844.6859 538432.7687 765085.2899 0.576097716 0.958522626 0.936354972 1.099256781 0.743049626 0.894227089 0.921431078 0.359234048 0.703755223 1 19.54526106 1.78092105 25 0.618865766 0.885316654 0.131690734 0.197699906 86.27827747 50937.335 0.086834766 0.048310002 60.38388488 -1.78092105 0.266450888 FNGGHS(ph)PTHSPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.945)PT(0.055)HSPEK;FNGGHS(0.499)PT(0.499)HS(0.002)PEK;FNGGHS(0.978)PT(0.022)HSPEK 121.45 0.00015881 1701050000 1773690 1817900 1491180 1697930 1671880 1342530 1697270 442006 1759510 1465380 TRUE FALSE 1704372.234 1766055.272 1760669.397 1785560.371 1725657.539 1369676.876 1718041.698 432878.4216 1559777.801 1366128.507 1.247592906 1.292744615 1.288802179 1.307022261 1.263173654 1.00259739 1.257598893 0.316865082 1.141750423 1 20.38166177 1.780957678 24.99998167 0.748014476 1.235882321 0.426686351 0.217090932 51.63137402 30455.98721 0.0948796 0.052785749 60.38897773 -1.780957678 0.487867845 DVEEGDEKFE ddPTM_BT-474_Pertuzumab_2h_R1 2 DVEEGDEKFE 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 152.28 0.00014936 354950000 1086510 893990 916110 895720 924720 880020 1043450 1181030 1348590 1328330 FALSE TRUE 1044047.988 868494.2805 1081671.456 941948.2165 954464.4586 897814.6073 1056220.053 1156641.318 1195503.717 1238361.026 0.843088539 0.701325593 0.873470202 0.760641038 0.770748141 0.725002312 0.852917712 0.934009787 0.965391911 1 20.24000054 1.781136494 2.129139038 0.977031709 0.77876348 0.744029663 0.049295744 0.139920186 1.252092661 0.030456063 0.013379595 60.41384741 -1.781136494 -0.198268229 YSGGNYRDNYDN ddPTM_BT-474_Pertuzumab_2h_R1 1 YSGGNYRDNYDN 12 1 P98179 P98179 RBM3 RNA-binding protein 3 0 72.321 0.049854 0 113100 157360 71894 124260 127300 170880 111220 73892 69195 74291 FALSE TRUE 108679.927 152872.2469 84886.84507 130673.0735 131394.7201 174335.3107 112581.1436 72366.10438 61340.27369 69259.2044 1.569176659 2.207248094 1.22563991 1.886725015 1.89714452 2.517142843 1.625504431 1.044859019 0.885662407 1 16.07971819 1.781149463 3.42116568 0.95669008 1.880352552 0.605869292 0.326130667 0.151779438 3.415463535 0.176873154 0.088888843 60.41565144 -1.781149463 0.923662472 QEQEEARR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEQEEARR 8 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 113.62 0.0045108 170236000 107617 109616 77418 94181 97738 100863 97628 83428 96231 91654 FALSE TRUE 103411.2087 106489.859 91409.15475 99041.6927 100881.8315 102902.519 98822.80067 81705.18265 85307.26031 85446.19294 1.210249458 1.246279739 1.069786161 1.159111826 1.18064747 1.204296124 1.156550073 0.956217941 0.998374034 1 16.38272859 1.781256174 5.61625785 0.983465355 1.175612707 0.791817226 0.044762397 0.085207225 5.703017956 0.022199762 0.012266443 60.43049809 -1.781256174 0.192147352 FFEEVLLFEDELHDHGVSSLSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 FFEEVLLFEDELHDHGVSSLSVK 23 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 176.46 1.93E-13 282110000 248918 289946 245367 255207 287727 315826 287157 86781 325623 214885 FALSE TRUE 239190.0094 281677.024 289710.2751 268378.2639 296982.0003 322212.2181 290671.3133 84988.94202 288659.6422 200330.6476 1.19397612 1.406060567 1.446160528 1.339676515 1.482459144 1.60840202 1.450957788 0.424243335 1.440916034 1 17.61202362 1.781292639 25 0.895754286 1.425609299 0.411185676 0.250902708 56.20676774 32894.91413 0.109249649 0.060796309 60.43557228 -1.781292639 0.529855013 CPSIAAAIAAVNALHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 CPSIAAAIAAVNALHGR 17 0 Q14498-2;Q14498;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 107.82 0.00153 0 539400 475860 424370 424700 508700 490180 519160 250270 565410 477070 FALSE TRUE 518319.6517 462288.9387 501063.0991 446618.8179 525062.7975 500091.7754 525513.6354 245101.837 501227.0272 444757.624 1.165398014 1.039417682 1.126598111 1.004184738 1.180559409 1.124414172 1.181573079 0.551090805 1.12696669 1 18.76265981 1.781310462 25 0.845173766 1.11313891 0.311297169 0.148134134 64.94722901 37994.40182 0.063756768 0.035480249 60.43805259 -1.781310462 0.267965144 MLPEIDQNKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLPEIDQNKDR 11 1 D3DQV9;P78344;H0Y3P2;P78344-2 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 ; 117.98 0.00071366 825900000 1240990 1201310 968530 1045230 1107940 1130960 1255050 1219930 1467590 1394710 FALSE TRUE 1192490.739 1167049.815 1143564.916 1099174.446 1143577.896 1153828.786 1270409.677 1194738.019 1300995.336 1300245.049 0.91712769 0.897561437 0.879499535 0.845359454 0.879509518 0.887393331 0.977054039 0.918856042 1.000577035 1 20.31035211 1.781315527 0.938344946 0.997024757 0.881266205 0.700295016 0.028221293 0.312811066 0.513656615 0.025073476 0.010653383 60.4387574 -1.781315527 -0.115758552 VHSPSGAVEECHVSELEPDKYAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VHSPSGAVEECHVSELEPDKYAVR 24 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 243.48 7.15E-38 247410000 145480 213970 143770 215640 164420 209200 187160 64330 172260 199200 FALSE TRUE 139794.4808 207867.7851 169752.4371 226769.2062 169708.7186 213430.1673 189450.5201 63001.56302 152705.767 185708.0066 0.752764963 1.119325919 0.91408249 1.221106243 0.913847075 1.149278221 1.020152677 0.339250656 0.822289624 1 17.50267649 1.781335953 25 0.650371734 1.022666015 0.285988264 0.202442377 63.48933829 37119.38619 0.086413115 0.048089456 60.44160013 -1.781335953 0.372294281 AASAPAKES(ph)PRK ddPTM_BT-474_Pertuzumab_2h_R1 4 AASAPAKESPRK 12 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AASAPAKES(1)PRK;AASAPAKES(1)PRK;AASAPAKES(1)PRK;AASAPAKES(1)PRK 128.06 0.00013495 2278490000 2396800 2074980 1700090 1619490 1773590 1810940 1949890 2259300 2449410 2367800 TRUE FALSE 2303130.406 2015803.602 2007334.081 1703072.073 1830639.133 1847558.448 1973753.337 2212644.665 2171363.246 2207426.797 1.043355281 0.913191597 0.909354767 0.771519162 0.829309101 0.836973824 0.894142148 1.002363779 0.983662629 1 21.07393417 1.781367532 4.628755171 0.994928991 0.878049898 0.356959743 0.067292703 0.22990735 9.7207911 0.035972545 0.019271597 60.4459951 -1.781367532 -0.116879092 RRPS(ph)PQPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 RRPSPQPSPR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR 101.3 0.016838 5084441000 654125 705625 572105 690469 648798 713835 653937 650650 679553 690251 TRUE FALSE 628561.0718 685501.2659 675497.0999 726104.1878 669667.1769 728269.2328 661940.0766 637213.8501 602412.9924 643499.685 0.976785361 1.065270554 1.049724057 1.128367589 1.040664343 1.131732074 1.028656411 0.990231798 0.936151185 1 19.29557992 1.781378875 2.836736652 0.968999811 1.066797723 0.446086936 0.044449233 0.212288586 3.327560803 0.024957485 0.011950347 60.44757392 -1.781378875 0.097797911 FEAHPNDLYVEGLPENIPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 FEAHPNDLYVEGLPENIPFR 20 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 94.463 0.0013645 1130700000 79506 74061 75295 83301 83223 83807 83581 62606 94422 81321 FALSE TRUE 76398.81762 71948.85279 88902.48143 87600.17459 85899.94338 85501.63496 84603.88928 61313.16422 83703.61041 75813.05624 1.007726392 0.949029842 1.172653971 1.155476101 1.133049472 1.127795649 1.115954078 0.808741492 1.104079094 1 16.2101587 1.781547065 25 0.950961878 1.097040876 0.260136368 0.093644445 83.45654756 48553.58631 0.043837285 0.02440035 60.47098808 -1.781547065 0.146078999 KDDS(ph)DDDGGGWITPSNIK ddPTM_BT-474_Pertuzumab_2h_R1 5 KDDSDDDGGGWITPSNIK 18 1 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK 264.97 3.22E-31 5036540000 4864510 3862840 3719470 3359650 3826510 4042970 4506240 5647300 6607290 6353420 TRUE FALSE 4674399.571 3752675.585 4391660.968 3533041.939 3949593.169 4124721.623 4561388.713 5530681.282 5857258.139 5923097.204 0.789181641 0.633566436 0.741446716 0.596485558 0.666812148 0.696379188 0.770101951 0.933748188 0.988884352 1 22.49792033 1.781649292 1.800098768 0.998514087 0.68061886 0.869355094 0.050114588 0.103626136 0.656348295 0.033752295 0.014135997 60.48522384 -1.781649292 -0.317895227 KSLDS(ph)DES(ph)EDEEDDYQQK ddPTM_BT-474_Pertuzumab_2h_R1 8 KSLDSDESEDEEDDYQQK 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.264)LDS(0.736)DES(1)EDEEDDYQQK;KS(0.06)LDS(0.94)DES(1)EDEEDDYQQK;KS(0.011)LDS(0.989)DES(1)EDEEDDYQQK;KS(0.004)LDS(0.996)DES(1)EDEEDDYQQK;KS(0.031)LDS(0.969)DES(1)EDEEDDYQQK;KS(0.078)LDS(0.922)DES(1)EDEEDDYQQK;KS(0.165)LDS(0.912)DES(0.923)EDEEDDYQQK;KS(0.037)LDS(0.963)DES(1)EDEEDDYQQK 264.98 1.83E-30 11294430000 11395390 8506710 7565720 5639700 7703510 7264000 8242970 11201590 12262720 9620020 TRUE FALSE 10950045.56 8264106.96 8933013.903 5930765.593 7951300.395 7410883.057 8343849.933 10970273.25 10870707.44 8968447.477 1.220952187 0.92146461 0.996049085 0.661292337 0.886586047 0.826328423 0.930356113 1.223207615 1.212105826 1 23.09642683 1.781708574 7.349742605 1.163009715 0.907923 0.334497986 0.143849053 0.21689914 27.93203623 0.066837135 0.037991761 60.49348068 -1.781708574 -0.255086715 TVQGSGHQEHINIHK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVQGSGHQEHINIHK 15 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 152.07 1.01E-06 4954900000 3362000 3869400 3133340 3805900 3400200 3898800 3755200 64941 3946800 2755910 FALSE TRUE 3230609.323 3759048.501 3699604.239 4002322.955 3509570.521 3977636.407 3801157.261 63599.94566 3498775.81 2569249.761 1.257413496 1.463091895 1.439955078 1.557778857 1.365990405 1.548170391 1.479481411 0.024754287 1.361788902 1 21.29291571 1.781716777 25 0.693681591 1.450409168 0.447325437 0.324690154 51.70517038 29962.84033 0.138831847 0.077284948 60.49462331 -1.781716777 0.756727577 DAVAHCHEAER ddPTM_BT-474_Pertuzumab_2h_R1 1 DAVAHCHEAER 11 0 P49792;O14715;Q99666;J3KQ37;F8W705;Q99666-2;H0YBN8 P49792 RANBP2;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 0 122.55 0.00022467 117420000 137960 156120 134570 154380 163740 160490 163440 68800 176190 147270 FALSE TRUE 132568.3707 151667.6105 158889.7925 162347.5703 169006.8458 163735.2178 165440.2276 67379.25596 156189.6498 137295.2717 0.965571276 1.104681964 1.157285247 1.182470221 1.230973534 1.192577251 1.204995813 0.490761664 1.137618564 1 17.06692242 1.781770569 25 0.822393991 1.153217571 0.336402666 0.170178087 63.88043177 36972.23108 0.074671278 0.041569307 60.50211666 -1.781770569 0.33082358 ATAAVIFLHGLGDTGHGWAEAFAGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATAAVIFLHGLGDTGHGWAEAFAGIR 26 0 B4DP64;E5RGR0;O75608-2;O75608 B4DP64 LYPLA1 Acyl-protein thioesterase 1 0 221.39 1.60E-34 91515000 58588 63206 46646 70102 45169 57712 62802 28707 64828 62459 FALSE TRUE 56298.31619 61403.42677 55075.96983 73719.97262 46621.90191 58878.97618 63570.58966 28114.19042 57468.99722 58228.5963 0.966849963 1.054523562 0.945857763 1.266044131 0.800670201 1.011169424 1.091741751 0.482824457 0.986954879 1 15.82944022 1.781778219 25 0.767958436 1.018801429 0.189662225 0.175068208 85.68019376 49580.54062 0.075889354 0.042249022 60.50318239 -1.781778219 0.250842993 DTHEDHDTST(ph)ENTDESNHDPQFEPIVSLPEQEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.001)HEDHDT(0.29)S(0.29)T(0.358)ENT(0.061)DESNHDPQFEPIVSLPEQEIK 287.53 1.81E-74 821450000 665250 723020 791510 768040 770780 894220 841140 97688 842010 729730 TRUE FALSE 639251.2945 702400.1775 934553.464 807678.6364 795572.8387 912301.7411 851434.1229 95670.70866 746428.5548 680304.7371 0.939654334 1.03247874 1.373727703 1.187230652 1.169435983 1.341019239 1.251548132 0.140629197 1.09719735 1 19.37582161 1.781910217 25 0.655044246 1.191891589 0.342940353 0.269729739 63.28575857 36510.00246 0.118740245 0.066112166 60.52157438 -1.781910217 0.536847343 TDIELEIYGMEGIPEKDMDER ddPTM_BT-474_Pertuzumab_2h_R1 6 TDIELEIYGMEGIPEKDMDER 21 1 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;J3QS27;J3KTL1;J3KRB6;J3KRW6;H0Y3M2 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;;;;; 245.88 2.71E-30 1407028000 1629083 1469803 1391980 1384994 1467616 1355143 1656862 1746156 2068618 1971547 FALSE TRUE 1565416.635 1427885.658 1643541.75 1456473.706 1514823.201 1382544.92 1677139.173 1710097.268 1833797.157 1838012.366 0.851689937 0.77686401 0.894195154 0.792417795 0.824163771 0.752195658 0.912474369 0.930405747 0.997706648 1 20.80971504 1.78191793 1.801428379 0.991408807 0.817487895 0.747867277 0.042056522 0.15811177 1.002860833 0.028178366 0.011806517 60.52264922 -1.78191793 -0.173920912 DWQSYYYHHPQDR ddPTM_BT-474_Pertuzumab_2h_R1 6 DWQSYYYHHPQDR 13 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 171.21 1.47E-05 12420730000 2260730 2611330 2232710 2848520 2423690 2338900 2578710 702158 2546870 2448390 FALSE TRUE 2172378.172 2536857.425 2636210.363 2995532.459 2501650.19 2386194.161 2610269.024 687658.1919 2257759.995 2282558.365 0.951729518 1.111409664 1.154936673 1.312357443 1.095985202 1.04540335 1.143571645 0.301266422 0.989135713 1 21.12222032 1.781985002 25 0.689507513 1.121779879 0.373950482 0.202566367 59.06809377 34018.08955 0.088723478 0.049403011 60.53199702 -1.781985002 0.432272367 LLEAQIATGGIIDPVHSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEAQIATGGIIDPVHSHR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 ; 173.98 3.10E-12 174666000 132819 150281 128218 167147 157899 168800 158779 15396.7 163030 128593 FALSE TRUE 127628.2866 145995.133 151389.8448 175773.4767 162977.9647 172213.2517 160722.1849 15078.75276 144523.5179 119883.2816 1.064604547 1.217810616 1.262810317 1.466205082 1.359472001 1.436507655 1.340655534 0.125778612 1.205535217 1 16.87127095 1.781998401 25 0.68532009 1.314884957 0.413985776 0.28246265 56.63378067 32606.0729 0.123760337 0.068912285 60.53386467 -1.781998401 0.629564866 GSLLFTAGPLEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GSLLFTAGPLEEER 14 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 237.76 6.15E-17 330550000 315370 355370 272980 312510 365070 340380 327920 303300 304610 366600 FALSE TRUE 303044.9917 345235.1955 322313.5584 328638.6786 376812.8081 347262.7168 331933.1831 297036.749 270031.9498 341769.8555 0.886693156 1.010139397 0.943071934 0.961578891 1.102533773 1.016071813 0.971218432 0.869113365 0.790098792 1 18.38266563 1.782004044 4.387899619 0.872161361 0.989860116 0.27921452 0.071155692 0.22698983 8.499447642 0.035400639 0.018790193 60.53465119 -1.782004044 0.117698755 THLMSEEEWR ddPTM_BT-474_Pertuzumab_2h_R1 2 THLMSEEEWR 10 0 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 ; 239.93 2.94E-12 1084790000 451070 510530 445260 486310 468250 452710 481630 116945 469250 455710 FALSE TRUE 433441.6857 495970.1843 525728.3868 511408.5174 483311.6865 461864.1064 487524.332 114530.0449 415982.7073 424844.3558 1.020236423 1.167416202 1.237461154 1.203755 1.13762059 1.087137207 1.147536328 0.269581185 0.979141423 1 18.69657487 1.782015537 25 0.672449631 1.147572445 0.437243538 0.198808513 52.15995192 30018.48581 0.085904184 0.047834658 60.53625317 -1.782015537 0.475122814 VHITHEVSSLDTLHALIAHMFPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHITHEVSSLDTLHALIAHMFPQK 24 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 232.54 8.60E-35 86371000 256310 321720 276190 327370 306880 334820 310570 88747 328880 261600 FALSE TRUE 246293.1218 312544.8606 326103.6768 344265.6049 316751.0739 341590.2898 314370.8486 86914.34344 291546.9212 243881.599 1.009888089 1.281543429 1.337139326 1.411609594 1.298790377 1.400639865 1.289030619 0.356379259 1.195444521 1 17.89582138 1.782048618 24.99999999 0.783475467 1.30060199 0.434914832 0.22532038 54.94868821 31599.36014 0.098246435 0.054708663 60.54086441 -1.782048618 0.517126523 DGNASGTTLLEALDCILPPTRPTDKPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGNASGTTLLEALDCILPPTRPTDKPLR 28 2 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;; 303.19 5.61E-72 41747650000 5850535 5118593 4864975 6021709 6291180 5526203 6333643 7311460 8220240 8801089 FALSE TRUE 5621889.624 4972615.739 5744184.203 6332490.123 6493541.518 5637946.611 6411156.018 7160475.796 7287112.817 8204983.403 0.68517989 0.606048239 0.700084805 0.771785854 0.791414339 0.68713687 0.781373429 0.872698389 0.888132548 1 22.96806898 1.78206593 0.273004428 1.042973455 0.603124327 0.834615385 0.045124312 0.712466148 0.197216715 0.102371417 0.117780722 60.54327786 -1.78206593 -0.439849128 EKEES(ph)PQPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKEESPQPR 9 1 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 EKEES(1)PQPR;EKEES(1)PQPR;EKEES(1)PQPR 153.49 4.72E-05 2785200000 3537207 3090001 2638747 2536034 2657326 3009958 3147221 3417330 4050830 3733960 TRUE FALSE 3398969.04 3001877.197 3115627.282 2666919.019 2742801.304 3070821.413 3185737.632 3346760.941 3590996.761 3481055.563 0.976419071 0.86234682 0.895023715 0.766123657 0.787922299 0.882152369 0.915164258 0.961421293 1.031582718 1 21.73109341 1.782084039 1.605235245 1.013705773 0.855438126 0.556792253 0.055216548 0.282085046 1.402534503 0.043285522 0.017668861 60.54580231 -1.782084039 -0.158267646 LVIGSLPAHLS(ph)PHMFGGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVIGSLPAHLSPHMFGGFK 19 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 LVIGSLPAHLS(1)PHMFGGFK 209.01 4.06E-16 178090000 217250 284440 258610 283160 249400 286430 275710 71134 265030 269620 TRUE FALSE 208759.6298 276328.0497 305346.5797 297773.9215 257422.1775 292221.8108 279084.2215 69665.05804 234944.9055 251358.3972 0.830525784 1.099338843 1.214785673 1.184658737 1.024124041 1.162570314 1.11030395 0.27715429 0.934700842 1 17.93938636 1.782141905 25 0.660662941 1.098630917 0.355164499 0.2097319 60.95276906 34977.06845 0.091637423 0.051032143 60.55387008 -1.782141905 0.437967977 KLS(ph)VPTS(ph)DEEDEVPAPKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 KLS(0.693)VPT(0.37)S(0.937)DEEDEVPAPKPR 90.836 0.0011653 394900000 368760 316650 252800 291290 280150 299140 304530 374900 377320 317140 TRUE FALSE 354348.4515 307619.452 298486.5835 306323.5118 289161.2792 305188.8158 308256.9292 367158.184 334488.2155 295659.8253 1.19850051 1.040450632 1.009560846 1.036067418 0.978020192 1.032229575 1.042606749 1.241826425 1.131327921 1 18.1735787 1.782144831 25 1.150346316 1.042639822 0.140112803 0.07813652 94.38384697 54157.47796 0.034884333 0.019426972 60.55427807 -1.782144831 -0.107706495 VCEIHFHEINNK ddPTM_BT-474_Pertuzumab_2h_R1 2 VCEIHFHEINNK 12 0 H0YHB7;O43347;B4DM51;Q96DH6-3;B4DHE8;Q96DH6-2;Q96DH6 H0YHB7;B4DHE8 MSI1;MSI2 RNA-binding protein Musashi homolog 1;RNA-binding protein Musashi homolog 2 0 ; 160.86 3.87E-05 897210000 988690 1014100 855470 988930 938200 1025310 1041590 29159.32 1174340 673160 FALSE TRUE 950050.9017 985178.8609 1010072.459 1039968.796 968378.0551 1046042.471 1054337.29 28557.16985 1041033.846 627566.2736 1.513865454 1.569840354 1.609507237 1.65714577 1.543068989 1.666823911 1.680041351 0.045504628 1.658842883 1 19.2594083 1.782182342 24.99999995 0.802168019 1.606433561 0.424680894 0.370288876 57.38173016 32897.32934 0.157917254 0.08794687 60.55950858 -1.782182342 0.804265543 GTYVPSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTYVPSSPTR 10 0 Q9Y4P8-4;Q9Y4P8 Q9Y4P8-4 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 1 GTYVPS(0.003)S(0.997)PTR;GTYVPS(0.009)S(0.991)PTR 198.4 3.12E-07 3378200000 2413000 2799500 2440500 2939000 2950600 2347500 2751700 2401700 2422090 2584700 TRUE FALSE 2318697.292 2719661.001 2881552.639 3090682.142 3045508.729 2394968.058 2785376.128 2352104.056 2147144.497 2409635.967 0.96226041 1.128660527 1.195845629 1.282634466 1.26388748 0.993912811 1.155932334 0.976124231 0.891065923 1 21.20038378 1.782310813 1.566323209 0.935399123 1.157066603 0.401949885 0.100930326 0.370507048 1.748375013 0.078617734 0.031953975 60.57742557 -1.782310813 0.22166748 SGTICSSELPGAFEAAGFHLNEHLYNMIIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGTICSSELPGAFEAAGFHLNEHLYNMIIR 30 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;A0A075B7C0 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ; 251.16 3.13E-47 1659900000 802090 879180 673690 882030 918820 681260 967550 203823 948220 951290 FALSE TRUE 770743.436 854106.6472 795440.7692 927551.674 948374.6798 695035.544 979391.1663 199613.9838 840582.0409 886858.281 0.869071702 0.963070048 0.896919819 1.045884888 1.069364407 0.78370531 1.104337849 0.225079912 0.947820028 1 19.75834406 1.782361254 25 0.64086937 0.959846463 0.168966914 0.218994337 87.45474987 49933.51144 0.094141083 0.052438607 60.58446177 -1.782361254 0.318977093 LFFAGEHTIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFFAGEHTIR 10 0 R4GMQ1;O60341;O60341-2;R4GMP9 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 194.54 4.52E-07 707360000 410670 437010 354130 442070 431750 384920 425600 398400 433620 419700 FALSE TRUE 394620.5624 424546.9027 418129.1686 464885.2857 445637.6309 392703.3461 430808.6201 390172.9008 384397.2755 391273.3452 1.008554677 1.085039162 1.068636987 1.188134309 1.138941961 1.003654736 1.101042597 0.99718753 0.98242643 1 18.57781731 1.782376732 1.425285087 0.983972716 1.092519397 0.368816648 0.052909087 0.430457405 1.661398163 0.042486463 0.017052879 60.58662095 -1.782376732 0.108546682 GT(ph)PSQS(ph)PVVGR ddPTM_BT-474_Pertuzumab_2h_R1 5 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 GT(0.999)PS(0.032)QS(0.969)PVVGR;GT(0.999)PS(0.001)QS(0.999)PVVGR;GT(1)PS(0.008)QS(0.993)PVVGR;GT(1)PS(0.093)QS(0.908)PVVGR;GT(0.984)PS(0.017)QS(0.999)PVVGR 211.83 5.66E-05 2802300000 1861910 1874230 1837880 1993590 1725980 1831840 1934040 2261990 2341230 2479210 TRUE FALSE 1789144.499 1820778.795 2170025.799 2096479.419 1781497.714 1868881.06 1957709.36 2215279.116 2075463.386 2311290.898 0.774088844 0.787775696 0.938880433 0.907059955 0.770780396 0.808587556 0.847019889 0.958459672 0.897967187 1 21.14026742 1.782384306 5.067458719 0.946129076 0.834486032 0.478246191 0.056747522 0.195772457 10.14311921 0.0294224 0.016033577 60.58767759 -1.782384306 -0.111643044 DEFEGLFK ddPTM_BT-474_Pertuzumab_2h_R1 6 DEFEGLFK 8 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 163.77 0.00077691 3204903000 5052590 4743120 3993817 4145746 4647760 4524250 4706330 5572190 6269930 5562840 FALSE TRUE 4855129.197 4607850.862 4715588.574 4359708.448 4797259.421 4615733.435 4763927.474 5457122.329 5558193.832 5186063.892 0.936187694 0.888506381 0.909280848 0.840658453 0.925028986 0.890026334 0.918601771 1.052266698 1.071755757 1 22.30620855 1.782417067 4.14165454 1.047276 0.897607117 0.824775984 0.029633906 0.073737789 2.435033574 0.014460736 0.007591321 60.59224828 -1.782417067 -0.149668883 FSDFLGLHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSDFLGLHSK 10 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ; 115.57 0.0012049 3910300000 767510 1432220 1355240 2177200 1706680 1501720 1342480 726100 512175 774640 FALSE TRUE 737514.8607 1391374.488 1600162.015 2289565.553 1761576.912 1532085.807 1358909.672 711105.7813 454035.0412 722172.9428 1.021244105 1.926649983 2.215760132 3.170384014 2.439272933 2.121494335 1.881695632 0.984675192 0.628706802 1 19.46198484 1.782426305 2.431939581 0.790752873 2.198409702 0.564017218 0.504224229 0.206548912 2.402529834 0.33354893 0.15281141 60.59353715 -1.782426305 1.407656829 QVEEAMLAVLHTVLLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 QVEEAMLAVLHTVLLHR 17 0 H3BMZ4;F8VVA0;F8VQD9;Q9BSB4 H3BMZ4 ATG101 Autophagy-related protein 101 0 141.13 3.67E-07 39303000 31773 29817 29364 31333 32139 31506 33012 15555 34054 32800 FALSE TRUE 30531.27603 28966.64835 34670.728 32950.09988 33172.78012 32143.07291 33416.01073 15233.78381 30188.33269 30578.42678 0.998458039 0.947290342 1.133829685 1.077560337 1.084842603 1.0511683 1.092796924 0.498187298 0.987242833 1 14.90022656 1.782801727 25 0.775010272 1.055866628 0.336106899 0.140054638 66.5278214 37606.64805 0.060945462 0.033962671 60.64593933 -1.782801727 0.280856356 HLEDEL ddPTM_BT-474_Pertuzumab_2h_R1 2 HLEDEL 6 0 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 ; 148.62 0.02499 427190000 664750 755900 629720 815360 721810 755470 752760 252400 777290 691370 FALSE TRUE 638770.8351 734342.4721 743524.412 857440.8273 745027.6742 770746.121 761972.5021 247187.8518 689055.2979 644542.8941 0.991044725 1.139322889 1.15356855 1.330308402 1.155900842 1.195802681 1.182190525 0.383508769 1.069060421 1 19.29791685 1.782810261 25 0.752424101 1.169973971 0.400770434 0.189102301 60.49946918 34192.35937 0.082339321 0.045885337 60.64713108 -1.782810261 0.41754987 ERDFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDFLK 6 1 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3;H0YJZ3;E9PNH9;E9PNS4;C9J979;H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;G3V2U3;Q15172;Q15172-2;C9IYS7;A0A087WYI0;Q5TA45-2;Q5TA45-4;Q5TA45-3;Q5TA45;Q5TA45-5 E9PFR3;H0YJ75;Q15172;C9IYS7 PPP2R5D;PPP2R5C;CPSF3L;PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform;Integrator complex subunit 11 0 68.915 0.086532 314930000 547000 729800 536860 667870 609140 705090 662430 412120 780520 561560 FALSE TRUE 525622.6353 708986.8185 633882.5444 702338.8507 628733.5413 719347.4029 670537.0165 403609.578 691918.6418 523525.041 1.004006674 1.354255791 1.210796991 1.34155732 1.200961734 1.374045836 1.280811736 0.77094608 1.321653384 1 18.99789902 1.782868848 25 1.007473634 1.260804931 0.283277262 0.159754571 83.02291816 46859.82433 0.068245745 0.038033587 60.65531298 -1.782868848 0.253331298 MPMILGYWDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 MPMILGYWDIR 11 0 H3BQT3;B9ZVX7;E7EWW9;P09488-2;P09488 H3BQT3 GSTM1 Glutathione S-transferase Mu 1 0 51.927 0.07963 245640000 115320 113280 136140 89840 109660 112380 105920 245320 114160 184350 FALSE TRUE 110813.1669 110049.3653 160743.5264 94476.65317 113187.3135 114652.4006 107216.2806 240254.0563 101201.0354 171863.8103 0.64477313 0.640328904 0.935295954 0.549718134 0.658587246 0.667111944 0.623844429 1.397932793 0.58884436 1 17.39090626 1.782957121 25 1.036897911 0.677308402 0.334558717 0.205191496 76.53852617 43113.97167 0.08870473 0.04944054 60.66764279 -1.782957121 -0.359589508 GLDGIPFTVDATSQIHCIEDFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLDGIPFTVDATSQIHCIEDFHR 23 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 97.57 0.0018828 30002000 23360 29182 16554 27750 24568 29365 25509 11103 24626 26938 FALSE TRUE 22447.06537 28349.75793 19545.67604 29182.18083 25358.25203 29958.78042 25821.18677 10873.71917 21830.55972 25113.46527 0.893825887 1.12886683 0.778294665 1.162013307 1.009747232 1.19293694 1.028180958 0.432983623 0.869277079 1 14.61617349 1.782969475 24.99999999 0.707047751 1.032825376 0.28847548 0.17985011 74.26005893 41818.87175 0.077897652 0.043417819 60.66936852 -1.782969475 0.325777624 KHEDSAIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KHEDSAIPR 9 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 ; 121.83 0.00039136 419630000 701050 698580 612580 675780 668460 668330 719550 474530 741360 782770 FALSE TRUE 673652.1909 678657.1824 723286.8328 710657.0868 689961.623 681844.0905 728356.0681 464730.7897 657203.9208 729752.2907 0.923124462 0.929982942 0.991140202 0.973833307 0.945473734 0.934350052 0.998086717 0.636833615 0.900584937 1 19.47704731 1.78300664 25 0.806663207 0.956259826 0.207785547 0.089834463 80.55617024 45326.5254 0.038693084 0.021567459 60.67456065 -1.78300664 0.149596619 HVIADQEVMETNR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVIADQEVMETNR 13 0 Q9H307 Q9H307 PNN Pinin 0 ; 189.99 4.79E-06 1705340000 873060 927050 862590 1045530 956610 1000450 1025950 658410 1059410 1106480 FALSE TRUE 838939.85 900611.4417 1018479.201 1099489.929 987380.2294 1020679.784 1038505.883 644813.6034 939150.2182 1031537.124 0.813290991 0.873077101 0.987341296 1.065875287 0.957193112 0.989474601 1.006755703 0.625099755 0.910437634 1 19.97636431 1.783052216 25 0.804772727 0.959691794 0.142452525 0.112091121 102.9774019 57882.89398 0.051042351 0.028452696 60.6809283 -1.783052216 0.154919067 HDDYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 HDDYYR 6 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 99.919 0.03825 219940000 103020 100620 87382 104760 107550 91677 111650 50178 110320 119160 FALSE TRUE 98993.86451 97750.41612 103173.8712 110166.6762 111009.4434 93530.77175 113016.4061 49141.80677 97796.9361 111089.1871 0.891120613 0.879927369 0.928748098 0.991695763 0.999282166 0.841943075 1.017348394 0.442363546 0.880346132 1 16.76135887 1.783118192 25 0.714048157 0.934299773 0.172143617 0.145269269 89.53053156 50249.96162 0.062774718 0.034995514 60.6901474 -1.783118192 0.220251615 DHYSNGFCTVYAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DHYSNGFCTVYAK 13 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 116.84 0.00055375 414730000 279730 454480 314710 423680 353060 373690 394380 179910 367630 445850 FALSE TRUE 268797.8423 441518.6754 371585.0977 445546.1756 364416.4955 381246.2678 399206.5404 176194.7956 325898.1836 415652.1824 0.646689356 1.062231101 0.893980865 1.071920693 0.876734229 0.917224266 0.960434126 0.423899604 0.784064652 1 18.66501726 1.783122463 24.99999982 0.674007952 0.927297585 0.160018765 0.174260603 92.559334 51944.92313 0.07460525 0.04159072 60.69074427 -1.783122463 0.253289633 LMSELYHPDDHVL ddPTM_BT-474_Pertuzumab_2h_R1 2 LMSELYHPDDHVL 13 0 P49770 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ; 152.7 4.53E-05 678880000 670850 813200 707190 876430 816000 790820 848500 30991 866570 691490 FALSE TRUE 644632.4403 790008.3322 834994.9644 921662.6573 842247.3811 806810.9222 858884.1968 30351.02502 768200.6066 644654.7664 0.999965367 1.22547505 1.295259118 1.429699593 1.306509197 1.251539528 1.332316523 0.047081053 1.191646516 1 19.29816723 1.783305715 25 0.645324972 1.270414659 0.373451636 0.298127482 65.89854598 36831.18606 0.129258624 0.072073612 60.71635821 -1.783305715 0.625089688 ENIKPNETS(ph)PSFSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ENIKPNETSPSFSK 14 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 ENIKPNET(0.09)S(0.893)PS(0.017)FS(0.001)K;ENIKPNET(0.49)S(0.51)PSFSK;ENIKPNET(0.135)S(0.857)PS(0.008)FS(0.001)K;ENIKPNET(0.176)S(0.816)PS(0.008)FSK 150.76 1.87E-05 798770000 1093130 912420 1207500 1118650 1214080 1293590 1402160 1690030 2123970 2121400 TRUE FALSE 1050409.271 886398.675 1425722.111 1176383.661 1253131.986 1319747.276 1419320.054 1655130.29 1882865.83 1977715.688 0.531122485 0.448193176 0.720893361 0.594819401 0.633625952 0.667308898 0.717656265 0.836889903 0.952040701 1 20.91540361 1.783418507 0.595913653 1.023684783 0.551008403 0.857244063 0.063270936 0.265579611 0.200378403 0.061050578 0.035424086 60.73212921 -1.783418507 -0.472676379 RKPS(ph)PEPEGEVGPPK ddPTM_BT-474_Pertuzumab_2h_R1 6 RKPSPEPEGEVGPPK 15 2 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK 180.08 5.07E-07 15614330000 8519590 7442590 6587250 6203760 7335120 7337150 7577700 8924550 10225900 8997230 TRUE FALSE 8186635.004 7230334.62 7777712.608 6523936.797 7571060.796 7485512.2 7670438.159 8740254.924 9065098.702 8387839.598 0.976012346 0.862002013 0.927260532 0.777785116 0.90262346 0.892424338 0.91447125 1.042015029 1.080742973 1 22.99986784 1.783536287 3.264322451 1.049017182 0.886554115 0.640234869 0.050868043 0.134174 2.741033925 0.027075733 0.013480662 60.7486019 -1.783536287 -0.162463066 FDQLFDDES(ph)DPFEVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FDQLFDDESDPFEVLK 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK 203.89 2.79E-11 224600000 423250 373920 336580 303740 363360 358360 375340 477240 498690 501440 TRUE FALSE 406708.9221 363256.1677 397407.4932 319416.0578 375047.8044 365606.2847 379933.5232 467384.8272 442080.8019 467477.0222 0.87000837 0.777056733 0.850111287 0.683276488 0.802280725 0.782083969 0.812731974 0.999802782 0.945673864 1 18.83453593 1.783557331 4.960317254 0.979536019 0.792046818 0.74983645 0.048964389 0.092668452 4.53593369 0.023237861 0.012638295 60.75154547 -1.783557331 -0.187489201 FTMDCVAPTIHVYEHHENR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTMDCVAPTIHVYEHHENR 19 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 ; 105.89 0.00011291 403000000 70988 84933 67587 83622 70569 97188 81440 19720.3 78576 79455 FALSE TRUE 68213.71048 82510.794 79801.47436 87937.74144 72838.91597 99153.20795 82436.68708 19313.06891 69656.3819 74073.44208 0.920892948 1.113905223 1.077329096 1.187169638 0.983333755 1.338579728 1.112904771 0.260728655 0.940369179 1 16.17666876 1.783705579 24.99999999 0.655102712 1.11164106 0.366700128 0.216124818 67.27351871 37266.50748 0.093496708 0.052159902 60.77228681 -1.783705579 0.456538348 (ac)MELDLSPPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVK 40 1 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLSPPHLS(0.004)S(0.004)S(0.004)PEDLCPAPGT(0.831)PPGT(0.11)PRPPDT(0.046)PLPEEVK 46.489 0.05408 292020000 30737 33229 26936 50041 51572 33409 33372 32401 24341 30915 TRUE FALSE 29535.76406 32281.34145 31803.93439 52623.62201 53230.86022 34084.55287 33780.41652 31731.90803 21577.91173 28821.09951 1.024796575 1.120059332 1.103494833 1.825871424 1.846940648 1.182625002 1.172072443 1.100995748 0.748684543 1 14.81483775 1.783775696 1.589974149 0.896664633 1.369674543 0.307640386 0.27717689 0.501893017 2.443946905 0.228798405 0.093352416 60.78209929 -1.783775696 0.47300991 GGRT(ph)PPQQGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGRTPPQQGGR 11 1 A0A2R8Y4Z8;M0QYB4;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 GGRT(1)PPQQGGR;GGRT(1)PPQQGGR 77.527 0.052338 299915000 94830 111219 87743 104527 112692 103492 101367 92825 100310 95686 TRUE FALSE 91123.93876 108047.143 103600.1119 109921.651 116316.8405 105584.6791 102607.5597 90908.13131 88923.22933 89205.10199 1.021510393 1.211221562 1.161369805 1.232235024 1.303925873 1.183617044 1.150243174 1.019091165 0.996840173 1 16.44483861 1.78387858 2.535440005 0.997532044 1.19261752 0.594652187 0.066844308 0.182432191 2.296632928 0.041281473 0.019176398 60.79650024 -1.78387858 0.195085476 TSAEAPSHHLQQQQQQQR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSAEAPSHHLQQQQQQQR 18 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 0 ;; 243.83 2.39E-24 172233000 171551 219105 171222 218428 190493 203617 202872 87504.9 203986 204489 FALSE TRUE 164846.5973 212856.3399 202165.6242 229701.0953 196620.3803 207734.2752 205354.8082 85697.89324 180830.3645 190638.7779 0.864706536 1.116542722 1.060464332 1.204902265 1.03137663 1.089674816 1.077193268 0.449530228 0.948549747 1 17.54048208 1.783941593 25 0.740727141 1.070674837 0.34344728 0.161184433 70.48839532 38844.24962 0.069548238 0.038812416 60.805322 -1.783941593 0.329947696 TWDHFWLNEGHTVYLER ddPTM_BT-474_Pertuzumab_2h_R1 4 TWDHFWLNEGHTVYLER 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;;; 255.72 2.59E-27 915249000 587488 613952 547438 669577 682032 687658 651017 322628 672736 648932 FALSE TRUE 564528.3195 596442.6901 646372.2243 704133.9492 703970.1787 701562.9159 658984.3408 315965.6191 596369.8296 604979.2576 0.933136653 0.985889487 1.068420473 1.163897671 1.163626967 1.159647884 1.089267661 0.522275128 0.985769053 1 19.20652615 1.784017903 25 0.785230506 1.085890227 0.362706608 0.143772717 72.76785862 40033.05727 0.065042081 0.036300843 60.81600713 -1.784017903 0.300659721 NGSLDSPGKQDT(ph)EEDEEEDEKDKGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 1 NGSLDSPGKQDT(1)EEDEEEDEKDKGK;NGSLDS(0.027)PGKQDT(0.973)EEDEEEDEKDKGK 165.1 8.36E-12 515350000 346674 170974 183256 101389 195038 153030 206536 330687 395658 266840 TRUE FALSE 333125.5968 166097.9889 216374.4357 106621.6984 201311.5744 156124.3714 209063.6493 323858.1979 350744.5626 248766.6891 1.339108536 0.667685812 0.869788622 0.428601188 0.809238468 0.627593558 0.840400498 1.30185516 1.409933797 1 17.92443379 1.78408193 4.729475837 1.266603043 0.771017145 0.409898146 0.240328321 0.174129201 7.622881045 0.114708006 0.061903521 60.82497376 -1.78408193 -0.495585898 RPHPQHSQQPPPPQQER ddPTM_BT-474_Pertuzumab_2h_R1 3 RPHPQHSQQPPPPQQER 17 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 0 ;; 52.522 0.072818 41305000 26216 33476.9 26753.5 35111.5 26450.6 30048.8 31559.3 12138.5 31895.5 31232.7 FALSE TRUE 25191.44974 32522.17159 31588.45258 36923.60872 27301.40757 30656.40732 31945.53215 11887.83573 28274.85656 29117.28141 0.865171765 1.116937091 1.084869571 1.268099456 0.937635873 1.052859534 1.097133063 0.408274233 0.971067874 1 14.82958804 1.784191917 25 0.729915929 1.066481678 0.29058825 0.183395398 80.82543437 44296.27935 0.079825401 0.044563042 60.84037986 -1.784191917 0.336565749 DHYEATAMHR ddPTM_BT-474_Pertuzumab_2h_R1 7 DHYEATAMHR 10 0 O75832;B1AJY5;B1AJY7;O75832-2;B1AJY6 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 ;;;;;; 208.6 6.40E-08 1794088000 2017106 1920822 1727797 2087244 1795391 1616959 2036402 540957 2085395 1892258 FALSE TRUE 1938275.267 1866042.037 2040048.353 2194966.913 1853141.382 1649655.019 2061324.097 529786.0489 1848669.702 1764093.68 1.098737153 1.057790784 1.156428582 1.244246231 1.050477876 0.935128921 1.168489021 0.300316278 1.047943045 1 20.75049574 1.784234873 25 0.70796943 1.099152737 0.315280941 0.206680776 78.73168888 43108.20461 0.090082529 0.050291514 60.84639785 -1.784234873 0.391183307 KPVTVSPTTPTS(ph)PTEGEAS ddPTM_BT-474_Pertuzumab_2h_R1 4 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPTTPT(0.001)S(0.935)PT(0.032)EGEAS(0.032);KPVTVSPTTPT(0.001)S(0.999)PTEGEAS;KPVTVSPTT(0.002)PT(0.012)S(0.864)PT(0.101)EGEAS(0.02);KPVTVSPTTPT(0.016)S(0.956)PT(0.014)EGEAS(0.014) 228.55 1.07E-19 1136100000 800040 928650 827960 1153660 1166870 1151360 955670 871140 857050 926820 TRUE FALSE 768773.5523 902165.8112 977590.7899 1213200.531 1204403.433 1174641.288 967365.7753 853150.6546 759761.277 864045.6559 0.889737188 1.044118219 1.131411035 1.404093085 1.393911797 1.35946669 1.119577153 0.987390711 0.879306865 1 19.72074802 1.784413221 2.975623318 0.942193174 1.21174597 0.33562072 0.155061025 0.301845048 5.156512181 0.098608336 0.047966311 60.87139032 -1.784413221 0.269552796 ERPEIS(ph)PPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 ERPEIS(0.46)PPS(0.46)DFEHT(0.081)IHVGFDAVTGEFTGMPEQWAR 105.48 1.07E-05 81498000 14061 17838 16224 16949 16632 18629 17457 3928.3 17882 15582 TRUE FALSE 13511.48057 17329.27771 19156.0377 17823.73992 17166.98338 19005.69114 17670.64399 3847.179232 15852.11033 14526.61726 0.930118852 1.192932766 1.318685373 1.226971125 1.181760562 1.308335644 1.216432131 0.264836552 1.091245817 1 13.82641117 1.784473797 25 0.707393119 1.205938456 0.388291824 0.230086454 69.75982072 37996.96726 0.099916293 0.055801863 60.87988136 -1.784473797 0.498545336 GDPNKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDPNKPR 7 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 82.305 0.022663 166090000 356080 322040 302680 342310 335170 290020 324000 335730 290550 325580 FALSE TRUE 342163.9999 312855.7345 357381.0091 359976.6601 345951.0474 295884.4031 327965.2089 328797.0582 257567.9821 303528.1766 1.127289083 1.030730451 1.177422844 1.185974443 1.139765841 0.974816923 1.08050993 1.08325053 0.848580138 1 18.21147092 1.78463638 0.88756608 0.952079953 1.123152368 0.428963128 0.074687892 0.593742339 0.87730462 0.067470033 0.029400275 60.90267664 -1.78463638 0.171072415 MDS(ph)DEDEKEGEEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MDSDEDEKEGEEEK 14 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 1 MDS(1)DEDEKEGEEEK;MDS(1)DEDEKEGEEEK 176.94 1.30E-06 982870000 1215600 737220 831780 572640 830870 697310 853460 1291290 1455590 999440 TRUE FALSE 1168093.008 716195.2074 982101.1488 602194.019 857595.6881 711410.086 863904.8988 1264624.41 1290357.526 931747.0386 1.253658944 0.768658421 1.054042683 0.646306341 0.920416865 0.763522777 0.927188242 1.357261529 1.384879664 1 19.8295788 1.784832187 6.566056966 1.27752729 0.889228743 0.411592134 0.186105968 0.165119412 15.69739963 0.081177733 0.046023925 60.93014155 -1.784832187 -0.388298547 EEKDQDELKPGPTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEKDQDELKPGPTNR 15 2 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 ; 83.418 0.0049055 365760000 244630 218990 164727 180081 219160 242190 235700 269330 363960 316440 FALSE TRUE 235069.5891 212744.6196 194496.8332 189375.002 226209.4804 247087.2477 238584.5671 263768.2414 322644.7866 295007.2369 0.796826517 0.721150511 0.659295125 0.641933411 0.766792987 0.837563344 0.808741404 0.894107698 1.093684311 1 18.17039082 1.784847828 0.954442919 1.045366214 0.712405106 0.803955956 0.060037674 0.233613189 0.396127868 0.054475633 0.02303743 60.93233596 -1.784847828 -0.332961108 FHQLDIDDLQSIR ddPTM_BT-474_Pertuzumab_2h_R1 4 FHQLDIDDLQSIR 13 0 O75828;P16152;E9PQ63;A8MTM1;P16152-2 O75828;P16152 CBR3;CBR1 Carbonyl reductase [NADPH] 3;Carbonyl reductase [NADPH] 1 0 ;;; 251.84 9.62E-24 1605600000 1787890 1965870 1655450 2049540 2011400 1910350 1969000 652410 2020660 1853330 FALSE TRUE 1718017.282 1909805.312 1954626.64 2155317.005 2076098.508 1948978.586 1993097.211 638937.5055 1791283.148 1727802.308 0.994336721 1.105337864 1.1312791 1.247432646 1.201583363 1.128010176 1.153544709 0.369797808 1.0367408 1 20.72050673 1.784891381 25 0.735126141 1.142239268 0.400388634 0.182446992 69.93451108 37748.65062 0.079290904 0.044314013 60.93844685 -1.784891381 0.407113127 EGLELPEDEEEKKK ddPTM_BT-474_Pertuzumab_2h_R1 7 EGLELPEDEEEKKK 14 2 P08238;Q58FF7;P07900;P07900-2;Q58FG0 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AA5P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ;;;;;; 192.51 6.73E-07 53364330000 36898350 26811140 25339270 18570915 27637510 25325790 29623460 39894500 48689300 38186600 FALSE TRUE 35456321.69 26046512.54 29918639.76 19529362.15 28526495.61 25837894.83 29986000.76 39070664.63 43162294.79 35600187.57 0.995958845 0.731639756 0.840406801 0.548574698 0.801301835 0.725779739 0.842298954 1.097484797 1.212417623 1 25.08538151 1.784996424 3.192756535 1.12321103 0.767032354 0.619266667 0.115513613 0.140857036 2.749123418 0.061827294 0.030650794 60.95318783 -1.784996424 -0.356178676 VEYHAGGSTQNSIK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEYHAGGSTQNSIK 14 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZH83 P55263-3 ADK Adenosine kinase 0 126.56 8.47E-05 138000000 98825 90928 96949 94333 86197 81038 96518 117060 128910 117290 FALSE TRUE 94962.80974 88334.82247 114469.8409 99201.53743 88969.60479 82676.64388 97699.21616 114642.6701 114276.6772 109345.8438 0.86846291 0.807848011 1.046860465 0.907227325 0.813653283 0.756102299 0.893488154 1.048441039 1.045093926 1 16.73853886 1.785021595 4.966662151 1.034764134 0.868510024 0.500038061 0.073785729 0.175367457 8.535626352 0.038763602 0.021128488 60.9567207 -1.785021595 -0.16625411 FLENGS(ph)QEDLLHGNPGSTYLASNSTSAPNWK ddPTM_BT-474_Pertuzumab_2h_R1 3 FLENGSQEDLLHGNPGSTYLASNSTSAPNWK 31 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK;FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK;FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK 352.27 9.88E-121 4036200000 1640670 1749540 1384280 1649480 1516890 1610790 1600670 1823330 1812060 1827160 TRUE FALSE 1576550.803 1699644.832 1634450.189 1734609.86 1565682.144 1643361.277 1620259.478 1785677.598 1606362.546 1703404.826 0.925529139 0.99779266 0.959519525 1.018319212 0.91914859 0.964750864 0.951188733 1.048299013 0.943030407 1 20.69998991 1.785087375 25 1.002200876 0.964164493 0.153999521 0.036611515 152.1461636 81778.08878 0.015885102 0.008880158 60.96595413 -1.785087375 -0.038036383 RASEDTTS(ph)GSPPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RASEDTTSGSPPKK 14 2 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 RASEDT(0.047)T(0.047)S(0.453)GS(0.453)PPKK 53.169 0.07866 440760000 135560 115200 98928 87874 108480 111450 114690 145840 169210 134490 TRUE FALSE 130262.1653 111914.6088 116806.4902 92409.18767 111969.3577 113703.5954 116093.6105 142828.353 150001.9902 125380.8725 1.038931718 0.892597145 0.931613315 0.737027792 0.893033806 0.906865562 0.925927601 1.139155839 1.196370604 1 16.93595775 1.785489504 4.315715076 1.126391394 0.895370498 0.568494039 0.082818786 0.137813686 4.905230682 0.041643398 0.022118218 61.0224308 -1.785489504 -0.231020896 DSPDS(ph)PEPPNKKPLVEMDETPQVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSPDSPEPPNKKPLVEMDETPQVEK 25 2 Q9NVM9-2;Q9NVM9;H0YH12 Q9NVM9-2 ASUN Protein asunder homolog 1 DS(0.001)PDS(0.999)PEPPNKKPLVEMDETPQVEK;DS(0.006)PDS(0.994)PEPPNKKPLVEMDETPQVEK;DSPDS(1)PEPPNKKPLVEMDETPQVEK;DS(0.173)PDS(0.827)PEPPNKKPLVEMDETPQVEK 256.79 3.45E-45 1543660000 895664 706677 848942 735718 750496 677970 960702 1167404 1429890 1340520 TRUE FALSE 860660.4607 686523.2639 1002364.704 773688.4941 774636.3854 691679.0179 972459.3585 1143296.699 1267574.882 1249725.386 0.688679665 0.549339296 0.80206797 0.619086803 0.619845283 0.553464806 0.778138437 0.914838341 1.014282734 1 20.25317968 1.785529111 2.139273193 0.998241094 0.641046896 0.819996395 0.070941854 0.115540178 1.039915508 0.045179573 0.019954227 61.02799621 -1.785529111 -0.357194198 GGAAPEGPNEAEVTSGKPEQEVPDAEEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGAAPEGPNEAEVTSGKPEQEVPDAEEEK 29 1 P49321;P49321-3;P49321-4;E9PPR5 P49321 NASP Nuclear autoantigenic sperm protein 0 317.19 2.61E-92 402510000 179690 148240 164600 139490 149900 167220 174320 231270 266780 242950 FALSE TRUE 172667.5161 144012.3403 194346.8815 146689.0956 154721.6696 170601.303 176453.3803 226494.1937 236496.2528 226494.7801 0.762346559 0.635830725 0.858063402 0.647648902 0.683113622 0.753223994 0.779061576 0.999997411 1.04415763 1 17.78911828 1.785529191 2.552837983 1.028808915 0.720914303 0.823282348 0.060654135 0.097933822 1.246595336 0.034972236 0.016302308 61.02800745 -1.785529191 -0.307894612 EGLEQALPSGKPSS(ph)PVELDLFGDPSPSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPSGKPS(0.022)S(0.978)PVELDLFGDPSPSSK;EGLEQALPS(0.006)GKPS(0.134)S(0.86)PVELDLFGDPSPSSK 311.82 2.74E-92 5297800000 1406970 1330160 1121750 1086090 1254480 1361730 1312880 1654640 1812060 1659530 TRUE FALSE 1351984.057 1292225.139 1324475.178 1142143.235 1294831.488 1389265.114 1328947.418 1620471.106 1606362.546 1547128.555 0.873866656 0.83524096 0.856086053 0.738234216 0.836925596 0.897963591 0.858976724 1.047405596 1.038286405 1 20.56116165 1.785644316 4.222781717 1.033073168 0.838657469 0.812089398 0.04100089 0.086874664 2.951123146 0.022009158 0.011640173 61.04418729 -1.785644316 -0.194415698 HIISATSLSTS(ph)PTELGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATSLS(0.001)T(0.036)S(0.866)PT(0.097)ELGSR;HIISATSLST(0.013)S(0.983)PT(0.004)ELGSR;HIISATSLST(0.094)S(0.905)PTELGSR 285.59 7.40E-40 7841300000 2094940 2151110 2003860 2338260 2272520 2474910 2268680 1419090 2329230 2425380 TRUE FALSE 2013067.429 2089762.449 2366002.078 2458937.879 2345617.67 2524954.376 2296444.784 1389785.296 2064825.575 2261106.852 0.890301768 0.924221006 1.046391096 1.087493002 1.037375862 1.116689542 1.015628599 0.614648217 0.913192392 1 21.10859774 1.785648796 24.99999998 0.801339925 1.021787523 0.313886534 0.113069969 88.33732652 46914.72401 0.051300998 0.028710664 61.04481699 -1.785648796 0.220447598 DITDTLVAVTISEGAHHLDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DITDTLVAVTISEGAHHLDLR 21 0 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 ;;; 123.43 1.53E-05 103338100 101490.6 117968.4 97167.9 128716.5 110151.9 131371.9 125698.6 32368 116973.8 134163.9 FALSE TRUE 97524.23515 114604.0567 114728.301 135359.574 113695.0359 134028.3298 127236.9371 31699.58949 103695.4246 125076.8596 0.779714453 0.916269062 0.917262405 1.082211166 0.909001364 1.071567757 1.017270001 0.253440881 0.829053631 1 16.93245538 1.785669188 24.99999999 0.613645463 0.9606232 0.239798982 0.198735868 94.72126051 50283.35903 0.086456745 0.048387283 61.04768336 -1.785669188 0.346977737 RKEFEDDLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKEFEDDLVK 10 2 O43148;O43148-2;K7EPP5 O43148 RNMT mRNA cap guanine-N7 methyltransferase 0 ; 118.28 0.00047591 239814000 211260 182225 148219 140688 175684 166597 180723 209544 246600 210442 FALSE TRUE 203003.7256 177028.1214 175005.4704 147948.9245 181335.0354 169965.7055 182934.7421 205216.8432 218607.0018 196188.5759 1.03473775 0.902336543 0.892026815 0.7541159 0.924289473 0.866338444 0.932443397 1.046018313 1.114269783 1 17.58188151 1.785811235 2.985930623 1.064350966 0.891076844 0.507843666 0.069358235 0.188546568 3.234154055 0.039543854 0.019276747 61.06765387 -1.785811235 -0.173274122 HDEES(ph)HSLSPPGENTVMADSFQIK ddPTM_BT-474_Pertuzumab_2h_R1 2 HDEESHSLSPPGENTVMADSFQIK 24 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 HDEES(0.395)HS(0.329)LS(0.275)PPGENT(0.001)VMADSFQIK;HDEES(0.381)HS(0.309)LS(0.309)PPGENT(0.001)VMADSFQIK 169.91 1.44E-11 558080000 273440 283990 267280 312110 240230 306210 303790 24314.8 332180 229575 TRUE FALSE 262753.6625 275890.8833 315583.4416 328218.0345 247957.2161 312401.776 307507.8729 23812.69088 294472.319 214025.6808 1.227673528 1.289055044 1.474512033 1.533545102 1.158539551 1.45964622 1.436780258 0.111260905 1.375873764 1 17.70742439 1.785905401 25 0.734698843 1.371329191 0.370761833 0.31494366 82.38096568 43514.16746 0.135620562 0.075939303 61.08089621 -1.785905401 0.636630348 TKEVYELLDS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 TKEVYELLDS(1)PGK 154.39 2.80E-05 230060000 375840 287910 357990 255180 256440 345080 355870 420390 455050 492790 TRUE FALSE 361151.7573 279699.0887 422686.7564 268349.8704 264688.6255 352057.754 360225.2435 411708.7996 403394.6317 459412.8944 0.786115849 0.608818542 0.920058539 0.584114799 0.576145399 0.766321012 0.784099114 0.896162917 0.878065541 1 18.80943182 1.785938105 1.305811528 0.952952251 0.697819863 0.49377785 0.100770905 0.36332491 1.164066162 0.079934099 0.032022517 61.08549605 -1.785938105 -0.255132388 YKDLDEDELLGNLSETELK ddPTM_BT-474_Pertuzumab_2h_R1 1 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 0 219.06 2.94E-19 456040000 540050 426370 386200 339230 457400 437320 456490 586310 660840 591910 FALSE TRUE 518944.2489 414210.3451 455994.931 356737.701 472112.6864 446162.91 462076.6612 574202.4936 585824.2137 551819.4085 0.940424061 0.750626634 0.82634812 0.646475451 0.855556508 0.808530659 0.837369353 1.040562338 1.061623068 1 19.07383667 1.785995369 3.523233151 1.041634394 0.799716077 0.671516431 0.072129695 0.123031498 2.896701613 0.03744905 0.019036773 61.093551 -1.785995369 -0.241918317 STLINSLFLTDLYS(ph)PEYPGPSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 1 STLINSLFLTDLY(0.005)S(0.995)PEYPGPSHR 114.31 0.00043914 94215000 123760 91696 80004 72657 92024 84299 92899 107870 122760 103260 TRUE FALSE 118923.3224 89080.91986 94462.50248 76406.83648 94984.03553 86003.58354 94035.92575 105642.4468 108824.7995 96266.10823 1.235360238 0.925361184 0.981264375 0.793704429 0.986681993 0.893394208 0.97683315 1.097400204 1.130458076 1 16.55474035 1.786027505 5.105770809 1.085092179 0.959060612 0.157375902 0.109546491 0.312107474 16.08964207 0.052123105 0.02858521 61.09807189 -1.786027505 -0.126031567 IAAPELHKGDS(ph)DS(ph)EEDEPTK ddPTM_BT-474_Pertuzumab_2h_R1 3 IAAPELHKGDSDSEEDEPTK 20 1 Q92733 Q92733 PRCC Proline-rich protein PRCC 2 IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(0.997)EEDEPT(0.003)K;IAAPELHKGDS(1)DS(0.999)EEDEPT(0.001)K 154.86 3.72E-08 1707030000 2399250 1911360 1682400 1454020 1768040 1818370 1935680 2568240 2906860 2429580 TRUE FALSE 2305484.657 1856849.884 1986447.105 1529062.146 1824910.612 1855138.687 1959369.431 2515204.947 2576885.439 2265022.383 1.017863963 0.819793172 0.877009923 0.675075954 0.805692088 0.819037684 0.865055218 1.110454787 1.137686523 1 21.11109388 1.786089932 4.413999574 1.093593793 0.829623093 0.625344123 0.085970103 0.125310559 4.667889843 0.043324703 0.023130442 61.10685498 -1.786089932 -0.2639707 EELMSS(ph)DLEETAGSTSIPK ddPTM_BT-474_Pertuzumab_2h_R1 7 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.197)S(0.803)DLEETAGSTSIPK;EELMS(0.026)S(0.974)DLEETAGSTSIPK;EELMS(0.161)S(0.839)DLEETAGSTSIPK;EELMS(0.076)S(0.924)DLEETAGSTSIPK;EELMS(0.028)S(0.972)DLEETAGSTSIPK;EELMS(0.2)S(0.8)DLEETAGSTSIPK;EELMS(0.024)S(0.976)DLEETAGSTSIPK 372.27 4.97E-108 3941865000 2919210 2507936 2683886 2592328 2597150 2583719 2714610 3326480 3220640 3002990 TRUE FALSE 2805124.046 2436412.121 3168923.903 2726118.359 2680689.688 2635963.568 2747832.209 3257787.026 2855046.449 2799594.813 1.001975012 0.870273123 1.131922337 0.973754611 0.957527738 0.941551812 0.98151068 1.16366376 1.019807022 1 21.41678661 1.786166448 25 1.078662171 0.978868248 0.19230827 0.073831143 129.4798156 68016.89542 0.032776038 0.018363799 61.11762205 -1.786166448 -0.099793923 HECQANGPEDLNR ddPTM_BT-474_Pertuzumab_2h_R1 14 HECQANGPEDLNR 13 0 P60981;P60981-2 P60981 DSTN Destrin 0 ;;;;;;;;;;;;; 322.07 9.05E-51 7312755000 2119875 2105590 1795623 2158644 2118087 2095791 2155484 1449712 2257737 2308176 FALSE TRUE 2037027.941 2045540.635 2120132.02 2270051.876 2186217.192 2138169.33 2181863.458 1419774.941 2001448.161 2151841.184 0.946644184 0.950600189 0.985264171 1.054934673 1.015975161 0.993646439 1.013951901 0.659795412 0.930109609 1 21.03714017 1.786271602 25 0.826646528 0.995518166 0.292960961 0.087976651 90.34960657 47356.83592 0.038423286 0.021531355 61.13242196 -1.786271602 0.168871638 RPDHSGGS(ph)PS(ph)PPTSEPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 2 RPDHS(0.023)GGS(0.977)PS(0.995)PPT(0.003)S(0.003)EPAR;RPDHSGGS(1)PS(0.824)PPT(0.149)S(0.027)EPAR;RPDHS(0.062)GGS(0.938)PS(0.997)PPT(0.001)S(0.001)EPAR;RPDHS(0.008)GGS(0.992)PS(0.997)PPT(0.001)S(0.001)EPAR 170.59 5.38E-11 1783514000 760363 863299 695684 866100 827376 855997 819848 739052 854199 782745 TRUE FALSE 730647.1733 838678.5578 821409.5742 910799.5248 853989.3004 873305.8458 829881.5451 723790.3179 757233.9106 729728.984 1.001258261 1.14930142 1.125636493 1.248133958 1.17028283 1.196753678 1.137246243 0.99186182 1.037691975 1 19.47700123 1.78637126 5.399335419 1.011368933 1.153768769 0.518180534 0.060396485 0.157023628 9.201652576 0.029536978 0.016357158 61.14645174 -1.78637126 0.142399836 SKGQENDHVHEK ddPTM_BT-474_Pertuzumab_2h_R1 6 SKGQENDHVHEK 12 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 ;;;;; 210.41 2.83E-08 1012890000 1092941 1011359 857593 865850 891444 1023204 966250 10778.1 1200908 482400 FALSE TRUE 1050227.657 982516.0315 1012579.132 910536.6223 920118.1058 1043893.886 978075.2565 10555.52847 1064585.958 449726.6183 2.335257943 2.184696194 2.251543695 2.024644718 2.045949847 2.321174339 2.174821807 0.023470989 2.367184674 1 18.77868875 1.786373657 25 1.029507667 2.186241817 0.446439118 0.537862937 78.96124021 41299.23008 0.228365251 0.128001896 61.14678923 -1.786373657 1.15673415 VHTGERPHQCPECGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHTGERPHQCPECGK 15 1 Q9BWE0;Q9BWE0-4;C9JZE3;C9JYJ8 Q9BWE0 REPIN1 Replication initiator 1 0 76.588 0.01833 64146000 68905 56736 58920 67026 64938 60354 64807 8345.3 67036 55255 FALSE TRUE 66212.11642 55117.94483 69568.15467 70485.21989 67026.78975 61574.39923 65600.12745 8172.966639 59426.35432 51512.52963 1.285359443 1.069991034 1.350509384 1.368312145 1.301174495 1.195328586 1.273479053 0.15865978 1.153629122 1 15.65263577 1.786426606 25 0.681185129 1.26222247 0.423721329 0.257008884 76.48796541 39961.36152 0.110697106 0.06205335 61.15424465 -1.786426606 0.581037342 KEEEESQPAKK ddPTM_BT-474_Pertuzumab_2h_R1 3 KEEEESQPAKK 11 2 O75400-3;O75400;O75400-2;F5H578 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;; 146.36 2.01E-05 1662700000 1934560 1603950 1314400 1152100 1478560 1454340 1580090 1774390 2183040 1725590 FALSE TRUE 1858955.256 1558206.916 1551941.319 1211560.019 1526119.225 1483747.751 1599427.614 1737748.226 1935230.451 1608714.252 1.15555342 0.968603911 0.964709125 0.753123196 0.948657739 0.922319019 0.994227292 1.080209381 1.202967182 1 20.61747666 1.78647521 2.729616676 1.110923544 0.945136843 0.276100666 0.101992256 0.309729411 4.475390648 0.06062976 0.028844775 61.16108903 -1.78647521 -0.165786701 NGSLDSPGKQDTEEDEEEDEKDKGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 211.3 6.11E-26 211710000 355590 201800 201490 106130 217430 172800 221720 341260 412470 254900 FALSE TRUE 341693.1497 196044.8616 237903.7251 111607.382 224423.8334 176294.1344 224433.4757 334212.8617 365648.1348 237635.396 1.437888275 0.824981736 1.001129163 0.469658072 0.944404063 0.741868162 0.944444639 1.406410271 1.538693903 1 17.85839022 1.786513174 5.194626459 1.353142054 0.884392147 0.331387507 0.261434135 0.197828893 10.58066583 0.122609756 0.067484268 61.16643571 -1.786513174 -0.468749908 YNPPDHEVVAMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 YNPPDHEVVAMAR 13 0 O60885;O60885-2;O60885-3;M0QZD9;Q15059;Q15059-2 O60885;Q15059 BRD4;BRD3 Bromodomain-containing protein 4;Bromodomain-containing protein 3 0 ; 196.84 1.39E-07 931990000 712140 759180 614350 764220 731260 786730 704070 714560 753910 724890 FALSE TRUE 684308.7815 737528.9297 725376.7111 803661.4858 754781.642 802638.2196 712686.6193 699804.0863 668329.2974 675792.5546 1.012601836 1.091354033 1.07337186 1.189213288 1.116883631 1.187699116 1.054593772 1.035530921 0.98895629 1 19.36622093 1.786666596 2.351252315 1.00212299 1.112542756 0.456108884 0.050379985 0.258877738 2.805871996 0.032276853 0.014690483 61.18804757 -1.786666596 0.110419767 KRPIYEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KRPIYEDK 8 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 146.81 0.00030786 1447770000 1284400 1377780 1170390 1243760 1276290 1252060 1464310 1619710 1845570 1859590 FALSE TRUE 1234204.228 1338487.063 1381905.508 1307950.603 1317343.027 1277377.511 1482230.664 1586262.422 1636068.631 1733638.313 0.711915639 0.77206823 0.797112926 0.75445414 0.759871893 0.736818921 0.854982641 0.914990405 0.943719701 1 20.72537151 1.786744748 1.410979487 0.977225149 0.756535125 0.919566246 0.026464904 0.104443565 0.394217038 0.020791133 0.008363955 61.19905943 -1.786744748 -0.220690024 KRS(ph)YS(ph)PDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRSYSPDGK 9 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 KRS(0.99)Y(0.051)S(0.959)PDGK 91.307 0.05333 890970000 1817300 1482400 1385200 1239000 1457200 1371800 1508700 1867200 2098600 1695300 TRUE FALSE 1746277.907 1440123.403 1635536.454 1302944.938 1504072.161 1399538.736 1527163.922 1828641.667 1860375.726 1580475.821 1.104906436 0.911196099 1.03483801 0.824400425 0.951657812 0.885517334 0.96626845 1.157019705 1.177098505 1 20.59192753 1.787077887 6.082708198 1.124830719 0.947059086 0.414051603 0.085075623 0.166435907 12.87602578 0.038036026 0.021460492 61.24602215 -1.787077887 -0.177771634 NFQETIHQLEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NFQETIHQLEGR 12 0 Q9Y4K3 Q9Y4K3 TRAF6 TNF receptor-associated factor 6 0 82.908 0.013687 183300000 93028 124710 98314 139840 123780 113890 112370 115540 105490 122430 FALSE TRUE 89392.36291 121153.3929 116081.5268 147057.1592 127761.4961 116192.9338 113745.2177 113154.0586 93515.21745 114137.7071 0.783197466 1.061466855 1.017030478 1.288418726 1.119362737 1.018006554 0.996561265 0.991381915 0.819319223 1 16.80041596 1.787088347 1.665705857 0.91803183 1.060419566 0.139984783 0.124648535 0.664599578 3.567212465 0.093126685 0.03845883 61.24749727 -1.787088347 0.142387736 LASDDRPS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 5 LASDDRPSPPR 11 1 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 1 LASDDRPS(1)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR;LAS(0.001)DDRPS(0.999)PPR;LASDDRPS(1)PPR 94.532 0.0051075 11972440000 4880850 5326370 4005150 5102490 5071370 5071650 4848580 4976810 5153170 5281720 TRUE FALSE 4690100.986 5174467.143 4728969.699 5365830.12 5234495.222 5174202.238 4907918.372 4874037.134 4568203.745 4923984.4 0.952501187 1.05086993 0.960394939 1.089733371 1.063060887 1.050816131 0.99673719 0.989856331 0.927745373 1 22.23139476 1.78709671 2.244831692 0.965553429 1.029544711 0.236127384 0.044298867 0.390250155 3.860167422 0.027755919 0.012458875 61.24867664 -1.78709671 0.063991282 DKDGQVDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDGQVDAR 9 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 0 ; 83.869 0.01448 438570000 1779040 1756290 1437670 1587310 1636560 1614460 1673180 1817760 2035570 1786340 FALSE TRUE 1709513.15 1706202.329 1697488.95 1669231.259 1689201.439 1647105.487 1693656.877 1780222.621 1804500.627 1665349.601 1.026519086 1.024531022 1.01929886 1.002330837 1.014322421 0.989044875 1.016997798 1.068978321 1.083556646 1 20.66739364 1.787169721 7.47980059 1.057280997 1.012536106 0.354350574 0.022735244 0.201270621 24.93733259 0.009913166 0.00571875 61.25897429 -1.787169721 -0.044744891 EAMEDGEIDGNK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAMEDGEIDGNK 12 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 247.22 3.01E-16 540843000 999200 859590 871210 997330 992820 866310 1003330 1231580 1357980 1304980 FALSE TRUE 960150.1593 835075.3348 1028657.027 1048802.321 1024754.957 883827.3818 1015609.053 1206147.443 1203827.804 1216592.542 0.789212597 0.686405108 0.845523042 0.862081826 0.842315666 0.726477725 0.834798026 0.991414464 0.989507795 1 20.21441463 1.787212026 3.639045418 0.995377923 0.794241467 0.757050905 0.051146156 0.113229013 2.830580795 0.028780081 0.014757641 61.26494186 -1.787212026 -0.201136456 LLAHVTLELQHYHQLLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLAHVTLELQHYHQLLEK 18 0 P56192;H0YIP0 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 204.05 3.88E-16 495340000 404090 433700 403280 438550 416900 451330 434180 170370 474680 383210 FALSE TRUE 388297.7161 421331.3006 476161.6669 461183.6181 430309.9671 460456.2018 439493.6247 166851.8 420796.3164 357254.8454 1.086892791 1.179357834 1.332834734 1.290909344 1.204490219 1.288873217 1.2301964 0.467038592 1.177860348 1 18.44659405 1.787277841 25 0.82505295 1.236043604 0.430669929 0.180253316 80.77978543 41465.94995 0.077874817 0.043749939 61.27422695 -1.787277841 0.410990654 EDGNEEDKENQGDETQGQQPPQR ddPTM_BT-474_Pertuzumab_2h_R1 6 EDGNEEDKENQGDETQGQQPPQR 23 1 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;; 290.71 1.49E-61 7870171000 2760591 2377967 2350267 2156697 2458816 2254203 2796640 3065000 3620560 3515037 FALSE TRUE 2652704.052 2310149.709 2775012.528 2268004.391 2537906.05 2299784.529 2830866.117 3001706.679 3209569.207 3276960.413 0.809501403 0.704967231 0.846825161 0.69210613 0.774469548 0.701804184 0.863869489 0.916003339 0.979434843 1 21.64392681 1.787406257 1.722742968 0.985108901 0.755092587 0.783504752 0.049816804 0.143553195 0.826993984 0.033009997 0.013741337 61.29234771 -1.787406257 -0.230016314 MCIVLRPSRVHNSEENT(ph)MRALTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.05)RVHNS(0.166)EENT(0.775)MRALT(0.008)LK 53.342 0.070636 457940000 82906 108740 87100 120260 98682 108330 100620 85325 83309 108330 TRUE FALSE 79665.94186 105638.8417 102840.9075 126466.633 101856.1962 110520.5068 101851.4177 83563.00893 73852.11158 100992.7126 0.788828617 1.046004597 1.01830028 1.252235233 1.008549959 1.094341403 1.008502644 0.827416224 0.731261788 1 16.62389167 1.787678658 4.28958677 0.834266186 1.043324757 0.301352102 0.123036585 0.225634001 7.855996402 0.061263147 0.032576544 61.33080396 -1.787678658 0.209058571 SGS(ph)AAQAEGLCK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSAAQAEGLCK 12 0 F8WF93;H7BZZ2;F8WE30;H7C0X4;Q92685 F8WF93 ALG3 "Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase" 1 S(0.007)GS(0.993)AAQAEGLCK 128.06 0.00021339 0 165480 212480 124570 185880 138450 115560 156030 235370 215970 145490 TRUE FALSE 159012.8587 206420.2784 147082.57 195473.2891 142903.37 117896.7024 157939.5418 230509.5272 191453.991 135635.8327 1.172351402 1.521871281 1.084393166 1.441162598 1.053581249 0.869215015 1.164438177 1.699473676 1.411529588 1 17.04937884 1.787707891 25 1.446431574 1.188125364 0.085499895 0.239027204 185.1685708 94218.89174 0.108912227 0.061260999 61.33493236 -1.787707891 -0.25830621 KESYSIYVYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KESYSIYVYK 10 1 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03 Q16778 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C 0 ; 124.12 0.00071174 22932000000 3487500 3818400 2713200 4017700 3204700 3531400 3921400 4247000 4862400 4815600 FALSE TRUE 3351204.644 3709502.971 3203535.595 4225053.978 3307782.086 3602807.328 3969391.266 4159297.966 4310440.737 4489435.123 0.746464656 0.826273878 0.713572088 0.941110376 0.736792491 0.802507939 0.884162742 0.926463542 0.960129865 1 22.0981025 1.787725124 1.167472239 0.989723486 0.793151932 0.621090496 0.059924174 0.297554629 0.754451657 0.046984697 0.018959358 61.33736621 -1.787725124 -0.196571554 KIPDTVLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIPDTVLEK 9 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 112.13 0.0036495 0 556520 565880 435650 492580 590730 505520 546120 629610 705960 630110 FALSE TRUE 534770.5831 549741.6565 514381.646 518002.1128 609731.3669 515741.9608 552803.5799 616608.3335 625822.3804 587432.0885 0.910353033 0.935838657 0.875644447 0.881807656 1.037960607 0.877960144 0.941051044 1.049667435 1.065352732 1 19.16406255 1.787764453 4.448498707 1.043264226 0.921569876 0.560807692 0.046920113 0.146189157 5.495392976 0.023205563 0.012431778 61.34292107 -1.787764453 -0.12169435 VEDQSIWPSMDDDEEESGAKVDSPLPSDKAPT(ph)PPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEDQSIWPSMDDDEEESGAKVDSPLPSDKAPTPPGK 36 2 Q12893 Q12893 TMEM115 Transmembrane protein 115 1 VEDQSIWPSMDDDEEESGAKVDS(0.006)PLPS(0.091)DKAPT(0.903)PPGK;VEDQSIWPSMDDDEEESGAKVDSPLPSDKAPT(1)PPGK 208.35 8.35E-29 272560000 167748 165632 134806 113012 124827 174022 167070 255010 328490 236460 TRUE FALSE 161192.2227 160908.3375 159168.4429 118844.5629 128842.1738 177540.8441 169114.6526 249743.9544 291201.1923 220444.3536 0.731215021 0.729927235 0.722034565 0.539113663 0.584465747 0.805377145 0.767153478 1.13291155 1.320973695 1 17.750055 1.787767422 2.506449627 1.187983951 0.680048011 0.806463202 0.102465307 0.107169348 1.31315678 0.062611645 0.02908363 61.34334046 -1.787767422 -0.50793594 GPS(ph)PEPPPS(ph)PLQVPTYPQLTLEVPQAPEVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPSPEPPPSPLQVPTYPQLTLEVPQAPEVLR 31 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 2 GPS(0.999)PEPPPS(0.981)PLQVPT(0.013)Y(0.007)PQLTLEVPQAPEVLR 66.083 0.0031816 45539000 22487 29301 21916 31615 29713 32005 27701 20718 24682 23679 TRUE FALSE 21608.18318 28465.36417 25876.70872 33246.65394 30668.74563 32652.16303 28040.01312 20290.16606 21880.20284 22075.20024 0.978844266 1.289472524 1.172207203 1.506063527 1.389285048 1.479133266 1.270204248 0.919138483 0.991166676 1 14.4301389 1.787775812 5.476850735 0.967265881 1.313257387 0.519415213 0.144175701 0.157608111 9.451760384 0.071424859 0.039728461 61.34452554 -1.787775812 0.345991506 IQSS(ph)YRRWMIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQSSYRRWMIR 11 2 Q8IZT6 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 IQS(0.008)S(0.989)Y(0.002)RRWMIR;IQS(0.034)S(0.966)YRRWMIR 109.39 0.00047336 0 122550 236470 148831 257940 228190 255750 174589 109425 67796 122348 TRUE FALSE 117760.6105 229726.1071 175728.0724 271252.3143 235529.9386 260921.4402 176725.6724 107165.3355 60100.0823 114061.261 1.032433006 2.014058982 1.540646412 2.378128314 2.06494244 2.287555284 1.549392589 0.939541914 0.526910555 1 16.79944936 1.78781016 2.800830482 0.762429049 1.906361748 0.609139117 0.380152077 0.160534882 2.430985109 0.217943075 0.104568533 61.34937747 -1.78781016 1.143932699 TAST(ph)PT(ph)PPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 2 T(0.004)AS(0.158)T(0.839)PT(0.893)PPQT(0.107)GGGLEPQANGETPQVAVIVRPDDR 119.99 3.72E-06 244200000 104450 90460 73334 76559 86130 80503 88037 102950 108960 110480 TRUE FALSE 100367.9785 87880.16937 86587.08511 80510.21916 88900.44967 82130.82582 89114.42314 100824.0465 96591.3176 102997.0912 0.974473913 0.853229624 0.840675053 0.781674688 0.863135538 0.797409178 0.865213009 0.978901883 0.937806267 1 16.65224407 1.787853802 4.699508235 0.968849111 0.847582099 0.535703266 0.050463491 0.157178471 6.651504854 0.024985801 0.013530745 61.35554276 -1.787853802 -0.121267012 QHFESK ddPTM_BT-474_Pertuzumab_2h_R1 1 QHFESK 6 0 H0YC70;Q9Y5V0 H0YC70 ZNF706 Zinc finger protein 706 0 70.912 0.089617 225220000 419930 408540 396490 411130 414410 364530 423470 255460 472170 403180 FALSE TRUE 403518.6713 396888.8392 468144.5629 432348.4686 427739.874 371901.0464 428652.5525 250184.6617 418571.2411 375872.2595 1.07355268 1.055914155 1.245488463 1.15025373 1.137992664 0.989434674 1.140420826 0.66561087 1.113599715 1 18.51988292 1.787896975 25 0.890636813 1.113779128 0.3127941 0.123576448 108.2991587 54894.32016 0.054319694 0.030569823 61.36164237 -1.787896975 0.223142315 YVLHCQGTEEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 YVLHCQGTEEEK 12 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ;;; 245.69 1.75E-16 3133430000 2706280 2385230 2134830 2262890 2142540 2340510 2556950 2863520 3273910 3182280 FALSE TRUE 2600515.586 2317205.576 2520641.27 2379678.024 2211456.745 2387836.716 2588242.719 2804387.311 2902269.462 2966741.341 0.876556223 0.781060871 0.849632974 0.80211847 0.745416095 0.804868521 0.872419406 0.9452753 0.978268453 1 21.50044772 1.787947341 1.792934655 0.988009489 0.807108455 0.824186115 0.034279397 0.132565873 0.830028745 0.024403029 0.010264792 61.36875905 -1.787947341 -0.180901034 DAQHYGGWEHR ddPTM_BT-474_Pertuzumab_2h_R1 5 DAQHYGGWEHR 11 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;; 154.36 1.85E-05 13136570000 2111950 2600930 2149490 2645330 2452210 2629100 2617550 394764 2693030 2335070 FALSE TRUE 2029412.659 2526754.023 2537950.658 2781855.798 2531087.562 2682262.203 2649584.36 386611.9854 2387328.525 2176913.629 0.932243077 1.160704765 1.165848118 1.277889835 1.162695445 1.232139929 1.21712884 0.177596382 1.096657439 1 21.05385274 1.788053014 25 0.66979612 1.170970502 0.346555027 0.246576748 95.00215665 48002.517 0.105898953 0.059628108 61.38369314 -1.788053014 0.501174381 VELDNMPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VELDNMPLR 9 0 Q15233;Q15233-2;C9JYS8;C9IZL7;C9J4X2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 138.98 0.00028267 474440000 952400 1102380 972703 1249170 1238110 951878 1087930 979690 917410 1034340 FALSE TRUE 915179.1551 1070941.202 1148492.07 1313639.813 1277934.933 971125.6253 1101244.413 959459.0591 813269.4629 964283.2305 0.949077124 1.110608551 1.191031881 1.362296649 1.32526927 1.007095835 1.142034184 0.994997143 0.843392727 1 19.87909743 1.788108378 1.512397134 0.919679199 1.177870826 0.378776975 0.123982844 0.41344999 1.808031388 0.099959933 0.040582685 61.39151882 -1.788108378 0.258191628 DGDKPEETQGK ddPTM_BT-474_Pertuzumab_2h_R1 6 DGDKPEETQGK 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 170.66 1.41E-05 6757470000 6620550 6226180 5343100 4326930 5251260 5294840 6258590 6877560 8966500 7022570 FALSE TRUE 6361811.587 6048615.442 6308717.027 4550243.376 5420171.547 5401905.293 6335184.497 6735535.983 7948660.511 6546925.079 0.971725124 0.923886461 0.963615277 0.695019925 0.827895765 0.825105714 0.96765801 1.028809082 1.214105922 1 22.64238604 1.788120358 2.173471062 1.104552656 0.866776241 0.520889671 0.091556444 0.232433658 2.15444967 0.060678989 0.0269921 61.39321231 -1.788120358 -0.237776415 IHQESELHSYLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHQESELHSYLSR 13 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 238.03 5.32E-17 1090200000 408940 541020 439980 566240 495650 449390 520070 131080 499330 536920 FALSE TRUE 392958.1727 525590.6393 519494.1733 595463.7143 511593.0324 458476.9737 526434.7722 128373.1522 442648.1518 500553.9302 0.785046623 1.050018005 1.037838566 1.189609507 1.022053772 0.915939215 1.051704403 0.25646218 0.884316604 1 18.93316599 1.788212825 24.99999999 0.633306627 1.014311271 0.270635465 0.208743248 108.0203366 54404.58453 0.090556565 0.05101577 61.40628517 -1.788212825 0.381004645 AYQQKPYPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYQQKPYPSPK 11 1 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1 1 AYQQKPYPS(1)PK;AYQQKPYPS(1)PK 121.76 0.00024521 1292270000 1548450 1198520 1163860 925310 1168070 1210110 1350170 1575680 1828260 1773370 TRUE FALSE 1487934.862 1164339.383 1374195.392 973065.36 1205642.032 1234579.253 1366693.784 1543141.657 1620723.589 1653258.07 0.900001572 0.70426959 0.831204406 0.58857439 0.729252168 0.746755316 0.826666937 0.933394299 0.980320991 1 20.65688051 1.788333512 1.714393331 0.991390688 0.742312367 0.629886025 0.07645133 0.216899397 1.236358699 0.053849681 0.022407891 61.42335191 -1.788333512 -0.249078322 DEDEWKELEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 DEDEWKELEQK 11 1 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ;; 178.32 6.92E-06 904830000 2008230 1444580 1429860 1143580 1571270 1646830 1762700 2304490 2874950 2469810 FALSE TRUE 1929746.151 1403381.993 1688267.509 1202600.301 1621811.327 1680130.031 1784272.45 2256901.476 2548597.729 2302527.569 0.838099043 0.609496282 0.733223581 0.522295723 0.704361306 0.729689431 0.774919039 0.980184345 1.106869582 1 21.134787 1.788344917 1.821447181 1.060974403 0.678418102 0.778092769 0.081683728 0.1399498 0.905315521 0.054841247 0.02317195 61.42496485 -1.788344917 -0.382556301 AHTCFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHTCFNR 7 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;K7ERN1;K7EKL1;Q9HCE7-2;Q9HAU4;Q9HCE7;Q76N89-2;Q76N89;Q96PU5-5;Q96PU5-6;Q96PU5-9;P46934-4;H0Y8X6;P46934-3;P46934-2;P46934;A0A2R8YE75;A0A2R8Y6F3;Q9P2P5 Q96PU5-7;Q96PU5-5;P46934-4;A0A2R8YE75 NEDD4L;SMURF1;SMURF2;HECW1;NEDD4;HECW2 E3 ubiquitin-protein ligase NEDD4-like;E3 ubiquitin-protein ligase SMURF1;E3 ubiquitin-protein ligase SMURF2;E3 ubiquitin-protein ligase HECW1;E3 ubiquitin-protein ligase NEDD4;E3 ubiquitin-protein ligase HECW2 0 ; 99.139 0.010748 227640000 197194 330320 368860 400130 372510 293790 313180 145082 128466 176232 FALSE TRUE 189487.4405 320899.597 435521.2072 420780.7573 384492.1225 299730.6351 317012.7905 142086.006 113883.0783 164295.6497 1.153332062 1.953183774 2.65083834 2.561119288 2.340245303 1.824337015 1.929526382 0.86481904 0.693159426 1 17.32593475 1.788348628 2.720972612 0.792578394 2.12794237 0.650352074 0.404855147 0.161058252 2.306865816 0.253062091 0.120480536 61.42548977 -1.788348628 1.335363977 RPLEQQQPHHIPTSAPVYQQPQQQPVAQSYGGYKEPAAPVSIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPLEQQQPHHIPTSAPVYQQPQQQPVAQSYGGYKEPAAPVSIQR 44 2 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 229.34 2.72E-45 9966700000 2032490 2216040 1706340 1872420 1910260 2385860 2040830 322880 2177140 1691820 FALSE TRUE 1953058.044 2152840.709 2014713.595 1969055.821 1971705.248 2434103.724 2065806.288 316212.4152 1930000.195 1577231.524 1.238282404 1.364949074 1.2773734 1.248425352 1.250105148 1.543276105 1.309767308 0.200485731 1.223663213 1 20.58896302 1.788430029 25 0.722831939 1.322333566 0.439471046 0.259047211 85.41531603 42832.10416 0.11104221 0.062601045 61.43700395 -1.788430029 0.599501628 IAQEIASLS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 3 IAQEIASLSK 10 0 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 IAQEIASLS(1)K;IAQEIASLS(1)K;IAQEIAS(0.001)LS(0.999)K 158.11 8.48E-06 230348000 379436 357285 396245 405059 345948 338957 418470 560013 608830 619500 TRUE FALSE 364607.2216 347095.5816 467855.2859 425964.1435 357075.7316 345810.9428 423591.361 548448.5359 539718.1708 577540.7132 0.63130999 0.600988941 0.810081913 0.737548252 0.618269368 0.598764615 0.733439827 0.949627487 0.934511037 1 19.13956313 1.788477143 3.268940564 0.962667183 0.670351417 0.810145834 0.063984391 0.104708842 2.12197985 0.037703679 0.018860998 61.44366932 -1.788477143 -0.292315766 GKS(ph)DSEDGEKENEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKSDSEDGEKENEK 14 2 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 GKS(0.988)DS(0.012)EDGEKENEK 61.102 0.045739 168500000 192360 142900 131380 110000 145010 140820 155100 233450 268610 203870 TRUE FALSE 184842.3585 138824.6319 155123.2885 115677.1132 149674.3783 143667.4769 156998.1602 228629.1759 238118.5189 190061.7033 0.972538683 0.730418751 0.816173305 0.608629257 0.787504141 0.755899134 0.826037847 1.202920799 1.252848495 1 17.53610834 1.788532095 4.555684663 1.171179649 0.772927478 0.720207687 0.104577313 0.096269981 3.794717306 0.050014733 0.026944212 61.45144436 -1.788532095 -0.398252171 KDREDS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 KDREDSPER 9 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 KDREDS(1)PER;KDREDS(1)PER 125.61 0.00039118 785500000 829400 718010 728860 774140 773240 792430 950980 966950 1086760 1161400 TRUE FALSE 796986.131 697533.0578 860581.2154 814093.4582 798111.9668 808453.4775 962618.3777 946982.1446 963395.5609 1082737.344 0.736084458 0.644231089 0.794819926 0.75188453 0.737124263 0.746675528 0.889059922 0.874618531 0.889777716 1 20.04625188 1.788665151 0.500470299 0.998847897 0.703451687 0.821669606 0.041939858 0.33922121 0.198489719 0.042321023 0.029502682 61.47027425 -1.788665151 -0.29539621 SES(ph)LELPQAAPPQIYHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SESLELPQAAPPQIYHEK 18 0 H0YGT9;Q15040;B0QY58;B0QY55;B0QY57;B0QY56 H0YGT9 JOSD1 Josephin-1 1 S(0.029)ES(0.971)LELPQAAPPQIYHEK;S(0.024)ES(0.976)LELPQAAPPQIYHEK 165.13 1.86E-11 789710000 749530 708530 572620 673910 641390 694250 689020 769870 801630 823290 TRUE FALSE 720237.539 688323.4181 676105.1719 708690.5759 662020.8918 708288.2107 697452.4329 753971.9155 710632.3231 767527.835 0.938386214 0.896805805 0.880886844 0.923341856 0.862536656 0.922817621 0.908699856 0.982338205 0.925871728 1 19.54985955 1.788720427 7.195040537 0.965737923 0.90316899 0.544691626 0.026991853 0.163889524 18.29912144 0.011598904 0.006693309 61.47809855 -1.788720427 -0.062568933 TRHS(ph)PTPQQSNR ddPTM_BT-474_Pertuzumab_2h_R1 11 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 TRHS(0.955)PT(0.045)PQQSNR;TRHS(0.999)PTPQQSNR;T(0.027)RHS(0.486)PT(0.486)PQQSNR;TRHS(0.994)PT(0.006)PQQSNR;TRHS(0.999)PTPQQSNR;TRHS(1)PTPQQSNR;TRHS(0.996)PT(0.004)PQQSNR;TRHS(1)PTPQQSNR;TRHS(0.999)PTPQQSNR;T(0.001)RHS(0.999)PTPQQSNR;T(0.008)RHS(0.992)PTPQQSNR 197.17 1.20E-07 1.5681E+11 24106283.9 25411793.4 20333467.6 24457259.9 24159177.7 23474972.3 25112764.6 18199237.3 27808235.2 25577522.5 TRUE FALSE 23164183.67 24687073.93 24008177.51 25719502.01 24936279.59 23949652.32 25420102.13 17823416.69 24651560.92 23845134.12 0.971442792 1.035308663 1.006837596 1.078605886 1.04575967 1.004383209 1.06604987 0.747465567 1.033819344 1 24.50719156 1.788723047 25 0.89981508 1.030617651 0.24978859 0.077310791 118.7986022 59224.26171 0.033054622 0.018653865 61.47846941 -1.788723047 0.130802571 S(ph)PRPDHPGT(ph)PPHK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPRPDHPGTPPHK 13 1 P30291 P30291 WEE1 Wee1-like protein kinase 2 S(1)PRPDHPGT(1)PPHK;S(1)PRPDHPGT(1)PPHK;S(1)PRPDHPGT(1)PPHK 155.49 0.00061073 1309320000 722050 714490 568270 711820 618000 627080 677990 355728 687060 720860 TRUE FALSE 693831.4877 694113.4448 670969.0301 748557.1155 637878.5313 639759.9872 686287.4444 348382.0925 609067.8292 672035.5101 1.032432777 1.032852333 0.99841306 1.11386542 0.949173848 0.951973486 1.021207115 0.518398339 0.906303045 1 19.35817794 1.788820414 25 0.756242291 1.013309045 0.339682981 0.125508846 99.37456964 49444.86642 0.053981246 0.030473938 61.49225429 -1.788820414 0.257066754 DEEPSGWEEPS(ph)PQSISR ddPTM_BT-474_Pertuzumab_2h_R1 3 DEEPSGWEEPSPQSISR 17 0 Q9UPQ9-1;Q9UPQ9;H0Y720 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 DEEPSGWEEPS(1)PQSISR;DEEPSGWEEPS(1)PQSISR;DEEPSGWEEPS(1)PQSISR 387.38 8.92E-122 469280000 354210 337400 335230 351960 332100 332110 352740 407680 423360 421850 TRUE FALSE 340367.0816 327777.6823 395813.5182 370124.6978 342782.2981 338825.4917 357056.9376 399261.2655 375301.9477 393277.7238 0.865462397 0.833450924 1.006447847 0.941128051 0.871603646 0.861542547 0.907900235 1.015214545 0.954292412 1 18.58518895 1.789044573 7.843525799 0.989011034 0.898922076 0.434290539 0.047928866 0.253717948 33.62568393 0.02294901 0.013349862 61.52400133 -1.789044573 -0.090088958 HCGDFEQQLANR ddPTM_BT-474_Pertuzumab_2h_R1 1 HCGDFEQQLANR 12 0 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 0 108.01 0.0017524 317650000 284980 389090 305790 481760 361710 450080 371550 306810 304700 375010 FALSE TRUE 273842.6665 377993.5342 361053.0553 506623.6913 373344.7306 459180.926 376097.14 300474.2663 270111.7334 349610.2387 0.783279882 1.081185538 1.03273021 1.449109995 1.067888435 1.313408119 1.075761229 0.859454996 0.772608189 1 18.41538791 1.789400422 4.233729865 0.861619987 1.13198534 0.282012983 0.173115614 0.252044006 8.47889951 0.087930489 0.046715628 61.57443314 -1.789400422 0.270365352 LREYEAALNSK ddPTM_BT-474_Pertuzumab_2h_R1 3 LREYEAALNSK 11 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ;; 200.21 4.34E-08 1548390000 1140530 1335700 1006070 1373220 1128360 1086670 1297170 1383660 1625790 1486080 FALSE TRUE 1095956.827 1297607.144 1187889.229 1444092.049 1164654.724 1108643.212 1313045.154 1355086.937 1441237.135 1385426.478 0.79106098 0.936612057 0.857417732 1.042344774 0.840647081 0.800218005 0.947755204 0.978100938 1.040284099 1 20.40189872 1.789405112 2.525382913 1.013262281 0.885763298 0.397453701 0.070002063 0.286839505 3.558666331 0.042071677 0.019614649 61.57509808 -1.789405112 -0.127498983 AGPLT(ph)PPKPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGPLTPPKPPR 11 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 AGPLT(1)PPKPPR 82.069 0.03225 446720000 657990 674430 575540 624690 611950 669720 665130 869050 890740 857500 TRUE FALSE 632275.0234 655195.9167 679552.8808 656930.3258 631633.9275 683262.1973 673270.0599 851103.8138 789626.9295 799420.7612 0.790916441 0.819588318 0.850056583 0.8217579 0.790114491 0.854696588 0.842197367 1.064650626 0.98774884 1 19.60859551 1.789427805 6.547414875 1.019679424 0.824056507 0.91188101 0.027541611 0.052065541 4.670571626 0.012405144 0.00709648 61.57831562 -1.789427805 -0.195622917 HGFLEEFITPIVK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGFLEEFITPIVK 13 0 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 ; 152.14 4.51E-05 470050000 1322550 1319930 1059370 1338960 1340590 1242390 1300910 936110 1430960 1326940 FALSE TRUE 1270863.284 1282286.889 1250821.725 1408063.886 1383711.295 1267511.977 1316830.926 916779.0014 1268523.42 1237065.172 1.027321206 1.036555646 1.011120314 1.13822935 1.118543571 1.024612127 1.064479832 0.741091918 1.025429742 1 20.23849008 1.789606488 25 0.894351907 1.061217274 0.360814403 0.081649335 106.95053 52394.62987 0.035844422 0.020296619 61.60365609 -1.789606488 0.166865367 CSNNVVHVHSCADSCALLVNLLQYVMSTGDLHPPPRPPS(ph)PTEIAGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 CSNNVVHVHSCADSCALLVNLLQYVMSTGDLHPPPRPPSPTEIAGQK 47 1 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 CSNNVVHVHSCADSCALLVNLLQYVMS(0.002)T(0.002)GDLHPPPRPPS(0.825)PT(0.17)EIAGQK 129.01 5.72E-11 222960000 85639 73562 81183 74044 89110 103050 86123 17098 99198 63276 TRUE FALSE 82292.1332 71464.08378 95854.57401 77865.41971 91976.30408 105133.7416 87176.99904 16744.92033 87937.45891 58990.26016 1.39501221 1.211455647 1.624922042 1.31997078 1.5591778 1.782222037 1.477820216 0.283859069 1.490711495 1 15.84818915 1.789708321 25 0.84886941 1.484980711 0.393120662 0.312677053 107.2319707 52427.87025 0.13612934 0.077116109 61.61810262 -1.789708321 0.636111301 ATGHSGGGCISQGR ddPTM_BT-474_Pertuzumab_2h_R1 6 ATGHSGGGCISQGR 14 0 Q9HA64;I3L3W5;I3L139;I3L407 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;;;;; 218.6 5.32E-12 1214721000 526403.9 659565.8 504329.2 644281.6 624870.6 627468 591993.9 566637.9 607437 589826 FALSE TRUE 505831.4536 640755.6292 595472.7052 677533.0506 644970.1303 640155.8329 599238.8984 554936.6294 538483.2983 549876.5597 0.919900012 1.165271765 1.082920693 1.232154815 1.172936215 1.164180981 1.089769855 1.009202192 0.979280329 1 19.06874826 1.789809421 2.754199907 0.99082087 1.130097154 0.341038588 0.078457907 0.276026821 4.036922613 0.045291994 0.021665209 61.63244847 -1.789809421 0.139276284 RYEPSDKDRQS(ph)PPPAK ddPTM_BT-474_Pertuzumab_2h_R1 5 RYEPSDKDRQSPPPAK 16 3 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RYEPSDKDRQS(1)PPPAK;RYEPSDKDRQS(1)PPPAK;RYEPS(0.009)DKDRQS(0.991)PPPAK;RYEPSDKDRQS(1)PPPAK;RYEPS(0.004)DKDRQS(0.996)PPPAK 187.47 7.38E-09 4878260000 1834730 1642340 1465850 1473610 1612050 1639730 1688590 1994600 2239170 2042900 TRUE FALSE 1763026.723 1595502.071 1730761.703 1549663.189 1663903.052 1672886.464 1709255.47 1953410.813 1984988.809 1904532.563 0.925700488 0.837739455 0.908759312 0.813671144 0.873654294 0.878371153 0.89746718 1.025664171 1.042244615 1 20.86100552 1.790020063 3.355037187 1.02795228 0.871242058 0.819268836 0.031564678 0.083119027 1.763849036 0.016094932 0.008114655 61.66234871 -1.790020063 -0.156710222 GGGSQHYPEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GGGSQHYPEER 11 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 96.745 0.0067836 432910000 322550 385070 307940 433610 364670 390530 349320 327010 302470 362990 FALSE TRUE 309944.3894 374088.1806 363591.6081 455988.6641 376399.9417 398426.7842 353595.0827 320257.1292 268134.8737 338404.364 0.915899505 1.105447271 1.074429431 1.347466855 1.112278628 1.177368931 1.044889252 0.946374111 0.79235052 1 18.36838865 1.790038389 2.469082705 0.892435002 1.128025397 0.41384296 0.110910974 0.251951742 2.991063751 0.067774288 0.031401765 61.66495079 -1.790038389 0.235590396 SIAVLELICDVHNPGQDLVIHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIAVLELICDVHNPGQDLVIHR 22 0 Q9UKN8;F2Z356 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 0 79.635 0.0042684 199680000 52457 68764 34652 57507 58829 69953 51992 44059 45743 42946 FALSE TRUE 50406.92245 66802.91805 40914.38723 60474.94316 60721.28821 71367.49759 52628.29365 43149.16625 40550.44641 40037.22917 1.259001272 1.668520011 1.021908561 1.510467743 1.516620642 1.782528389 1.314483913 1.077726085 1.012818501 1 15.28905451 1.790136672 3.204842228 1.024016382 1.45888741 0.481784375 0.198229547 0.204248557 3.972827469 0.108611069 0.05413815 61.67890741 -1.790136672 0.434871028 DDKEEEEDGTGS(ph)PQLNNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDKEEEEDGTGSPQLNNR 18 1 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 DDKEEEEDGT(0.112)GS(0.888)PQLNNR;DDKEEEEDGT(0.048)GS(0.952)PQLNNR 254.34 9.50E-31 2910700000 3074840 2338300 2314200 2128640 2459400 2382030 2701660 3302990 3764500 3603610 TRUE FALSE 2954671.853 2271613.973 2732427.419 2238499.365 2538508.835 2430196.279 2734723.723 3234782.102 3337169.742 3359534.285 0.879488525 0.676169308 0.813335179 0.666312404 0.755613314 0.723372966 0.814018698 0.962866227 0.993342963 1 21.67982982 1.7902002 2.422239549 0.995566267 0.747932682 0.760121454 0.058681553 0.117852735 1.348112352 0.033122954 0.015260222 61.68793045 -1.7902002 -0.247633586 LTPYEVDELRR ddPTM_BT-474_Pertuzumab_2h_R1 8 LTPYEVDELRR 11 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 211.63 1.39E-08 10544760000 3766288 4516150 3006101 4185830 3739290 3603350 3676520 3793410 3847308 3625395 FALSE TRUE 3619097.301 4387353.824 3549370.321 4401861.188 3859567.659 3676212.206 3721514.352 3715074.758 3410577.725 3379843.767 1.070788341 1.298093677 1.050158104 1.302385995 1.141936706 1.087687023 1.101090644 1.099185351 1.009093307 1 21.68852513 1.790242279 0.691625644 0.999010014 1.180468899 0.366493692 0.080046089 0.684536934 0.652155483 0.068023668 0.034729789 61.69390766 -1.790242279 0.181458885 SLLNEIESVYDEHQEQHSEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLLNEIESVYDEHQEQHSEGR 21 0 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 0 ; 134.29 4.91E-06 81531000 49623 51838 43931 49190 46306 55654 49911 4698.8 52540 41756 FALSE TRUE 47683.6783 50359.63099 51870.30894 51728.70179 47795.47454 56779.36201 50521.82575 4601.768138 46575.87947 38927.82893 1.224925191 1.293666572 1.332473718 1.328836034 1.227797076 1.458580239 1.297833122 0.118212812 1.196467431 1 15.24851426 1.790283612 25 0.67705591 1.312834533 0.44486235 0.269039431 92.94954647 44939.27568 0.113803722 0.064633286 61.69977945 -1.790283612 0.635778623 ALVS(ph)SESYLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALVSSESYLQR 11 0 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 ALVS(0.975)S(0.025)ESYLQR 133.05 0.00017808 164010000 61943 78873 74279 110470 83338 79313 81242 51110 68920 56196 TRUE FALSE 59522.19908 76623.61926 87702.86763 116171.3699 86018.64246 80916.7632 82236.2639 50054.56064 61096.49054 52389.79487 1.136141098 1.462567652 1.674044876 2.217442734 1.641896913 1.544513839 1.569700055 0.95542578 1.166190681 1 15.67699819 1.79032656 5.300646336 1.046072254 1.629927065 0.506062414 0.255711855 0.174131214 9.504063138 0.131972272 0.073281145 61.70588133 -1.79032656 0.583854811 DQHLNNSS(ph)SSPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNS(0.005)S(0.584)S(0.304)S(0.108)PQR;DQHLNNS(0.019)S(0.433)S(0.274)S(0.274)PQR;DQHLNNS(0.001)S(0.585)S(0.279)S(0.136)PQR;DQHLNNS(0.009)S(0.33)S(0.33)S(0.33)PQR 162.26 2.63E-05 1184566000 508168 576325 484125 566499 469772 520160 586879 255186 613023 592116 TRUE FALSE 488308.2328 559888.7753 571617.1568 595736.0813 484882.643 530677.9916 594061.4008 249916.3199 543435.199 552011.4559 0.884598005 1.01427021 1.035516837 1.079209634 0.878392355 0.961353222 1.076175855 0.452737561 0.984463625 1 19.07433868 1.790337579 25 0.752893717 0.990665067 0.183498641 0.15723097 147.8250423 71395.98838 0.067467933 0.038326565 61.70744703 -1.790337579 0.237771349 GKLPES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 GKLPESPK 8 1 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 1 GKLPES(1)PK;GKLPES(1)PK;GKLPES(1)PK;GKLPES(1)PK 120.77 0.0008853 3833630000 5592100 4341670 4474820 3942670 4506140 4729660 5311000 6232700 8212500 6482000 TRUE FALSE 5373554.55 4217849.823 5283519.516 4146151.671 4651084.085 4825296.966 5375997.607 6103992.567 7280251.43 6042968.366 0.889224339 0.697976486 0.874325198 0.686111762 0.769668779 0.798497803 0.88962862 1.010098382 1.204747566 1 22.52682596 1.790355947 1.891213108 1.102648984 0.780594785 0.732227546 0.07787776 0.147927536 1.033053614 0.049498756 0.021167791 61.71005686 -1.790355947 -0.322054199 EVAEQEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EVAEQEER 8 0 I3L2B2;O95208-3;O95208-2;F6PQP6;O95208;E9PBC1;I3L356;I3L2H1;O95208-5 I3L2B2 EPN2 Epsin-2 0 ; 101.72 0.0177 0 154978 171314 136255 159137 165027 155843 155944 141388 154294 146205 FALSE TRUE 148921.2884 166428.2925 160879.3095 167350.0796 170335.2433 158994.2522 157852.4893 138468.2884 136779.192 136302.4051 1.092580049 1.221022419 1.180311597 1.227785229 1.249686263 1.166481634 1.158104944 1.015890279 1.003498008 1 17.05645149 1.790417721 2.384490173 0.998211414 1.194977798 0.805945317 0.040403861 0.111372719 1.23554338 0.024745009 0.01134814 61.71883519 -1.790417721 0.196766384 MFPMDSKPSLLNPTGSILVS(ph)SPLKPNPLDLPQLQHR ddPTM_BT-474_Pertuzumab_2h_R1 1 MFPMDSKPSLLNPTGSILVSSPLKPNPLDLPQLQHR 36 2 O75376;O75376-2;A0A088AWL3;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 MFPMDSKPSLLNPT(0.002)GS(0.006)ILVS(0.545)S(0.447)PLKPNPLDLPQLQHR 109.01 1.01E-05 181190000 124510 118700 89608 92207 86353 99168 107810 118630 127650 134150 TRUE FALSE 119644.0115 115314.7922 105802.1589 96965.81432 89130.62267 101173.2449 109129.411 116180.249 113159.7072 125063.901 0.956663038 0.92204698 0.845984797 0.77533016 0.712680653 0.808972406 0.872589214 0.928967097 0.904815108 1 16.9323059 1.790533956 2.266775265 0.94550509 0.833148468 0.332134647 0.068251921 0.388828849 3.907499017 0.048528915 0.021914792 61.73535584 -1.790533956 -0.112356622 MKPWFEVGDENSGWSAQK ddPTM_BT-474_Pertuzumab_2h_R1 2 MKPWFEVGDENSGWSAQK 18 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 250.86 3.59E-25 2407000000 2371500 2356600 2002160 1857350 2210400 1993550 2191200 2430500 2666600 2457800 FALSE TRUE 2278819.158 2289392.075 2363994.85 1953208.056 2281499.523 2033860.947 2218016.561 2380309.326 2363898.747 2291331.017 0.99453948 0.999153793 1.031712499 0.852433822 0.995709265 0.887632966 0.968003551 1.038832586 1.031670557 1 21.12775446 1.79053904 6.230461708 1.026267142 0.959485215 0.231553937 0.051845457 0.291324455 23.04070214 0.024165694 0.013764395 61.73607855 -1.79053904 -0.066781927 DLVKPGDENLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLVKPGDENLR 11 1 Q4V328-4;Q4V328;A0A087WT45 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 0 90.434 0.0068935 0 803190 715080 698340 780080 790330 814920 827040 952160 1140900 1071100 FALSE TRUE 771800.4468 694686.6185 824545.5725 820340.0223 815751.6822 831398.2407 837161.5629 932497.5633 1011389.815 998553.443 0.772918518 0.695692978 0.825740053 0.82152841 0.816933423 0.832602648 0.838374319 0.933848428 1.012854968 1 19.92948012 1.790777115 0.748228866 1.023026999 0.773401632 0.845117746 0.037018879 0.241673785 0.262718635 0.035146563 0.016936766 61.7699308 -1.790777115 -0.249625367 S(ph)EAEDEDDEDYVPYVPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SEAEDEDDEDYVPYVPLR 18 0 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 S(1)EAEDEDDEDYVPYVPLR;S(1)EAEDEDDEDYVPYVPLR;S(1)EAEDEDDEDYVPYVPLR 342.58 1.28E-75 882360000 468290 407571 403688 424170 394900 386116 420571 548220 479830 501430 TRUE FALSE 449988.7091 395947.4741 476643.4016 446061.4645 407602.3171 393923.5301 425718.0737 536899.0654 425361.71 467467.6995 0.962609202 0.84700499 1.019628526 0.954208098 0.871936858 0.842675399 0.910689817 1.148526553 0.909927489 1 18.83450716 1.790849953 25 1.035344034 0.913911963 0.280277029 0.075022311 147.8707772 70717.99195 0.033426221 0.019036186 61.78029155 -1.790849953 -0.121432071 KWS(ph)LNTYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KWSLNTYK 8 1 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 1 KWS(1)LNTYK;KWS(0.999)LNT(0.001)YK 155.48 0.00025009 1426140000 2075240 1579660 977900 1033130 1690290 1229750 1225280 2551400 1709640 1344300 TRUE FALSE 1994137.327 1534609.643 1154628.283 1086449.963 1744659.713 1254616.388 1240275.343 2498712.698 1515568.835 1253249.364 1.59117362 1.224504626 0.921307696 0.866906455 1.392108996 1.001090784 0.989647694 1.993787327 1.209311474 1 20.25724207 1.791085741 25 1.509457908 1.129466786 0.093704572 0.319952356 202.5018196 96410.02839 0.141284211 0.080552362 61.81384249 -1.791085741 -0.379991122 AVPIGT(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 4 AVPIGTPPK 9 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 AVPIGT(1)PPK;AVPIGT(1)PPK;AVPIGT(1)PPK;AVPIGT(1)PPK 119.53 0.0090824 4777670000 6572330 6482940 6448150 6409620 6534000 6507320 7695120 8928340 10046300 10389200 TRUE FALSE 6315476.078 6298052.899 7613474.143 6740421.256 6744172.044 6638902.469 7789295.18 8743966.659 8905886.142 9685530.23 0.652052694 0.650253806 0.78606684 0.695926924 0.69631418 0.685445434 0.8042198 0.902786575 0.919504243 1 23.2073996 1.791192345 1.367700765 0.971223105 0.693285034 0.8889004 0.039406448 0.129858302 0.458445472 0.031907305 0.012847861 61.8290174 -1.791192345 -0.277938071 DDAYWPEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDAYWPEAK 9 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 160.56 0.00015168 575270000 1682450 1537880 1258000 1307770 1460910 1468650 1492780 1710460 1889590 1705980 FALSE TRUE 1616697.994 1494021.168 1485348.584 1375264.166 1507901.497 1498347.109 1511049.088 1675138.403 1675091.665 1590432.455 1.016514715 0.939380458 0.933927486 0.864710829 0.948107851 0.942100436 0.95008693 1.053259695 1.053230308 1 20.60098767 1.791301804 5.070227873 1.039810292 0.938202519 0.57052867 0.037014669 0.138534804 6.797072544 0.018248078 0.010066358 61.84460272 -1.791301804 -0.101607773 EKEEPPS(ph)PIEATPPQSLLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEEPPSPIEATPPQSLLEK 20 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 EKEEPPS(1)PIEATPPQSLLEK;EKEEPPS(1)PIEATPPQSLLEK 144.76 9.25E-08 198155000 318800 242740 240370 239440 285900 224940 257840 327810 317640 269710 TRUE FALSE 306340.9435 235817.2929 283810.206 251797.5271 295096.2331 229488.4409 260995.523 321040.6089 281582.8389 251442.3015 1.218334949 0.937858473 1.128728954 1.001412752 1.173614111 0.912688277 1.037993693 1.276796335 1.119870591 1 17.93986786 1.791341977 25 1.162413692 1.053315197 0.063314628 0.111667772 237.6577244 112598.1438 0.046899327 0.026776422 61.85032371 -1.791341977 -0.109098495 WQIGEQEFEALMR ddPTM_BT-474_Pertuzumab_2h_R1 2 WQIGEQEFEALMR 13 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5;A0A0A0MSR2 P35611 ADD1 Alpha-adducin 0 ; 208.95 9.72E-08 58574000 49344 53840 52019 50040 53048 54154 75566 78283 86609 100348 FALSE TRUE 47415.58193 52304.53591 61419.99046 52622.5704 54754.3371 55249.03098 76490.79931 76666.42869 76777.50941 93551.34058 0.506840219 0.559099801 0.656537791 0.562499373 0.585286504 0.590574444 0.817634454 0.819511813 0.82069919 1 16.51347071 1.791370097 0.664406161 0.979181563 0.553253249 0.879628953 0.053199296 0.224540791 0.200345843 0.05071031 0.026764016 61.85432856 -1.791370097 -0.425928314 DSFSHS(ph)PGAVSSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSFSHSPGAVSSLK 14 0 Q9H6R7-3;Q9H6R7 Q9H6R7-3 C2orf44 WD repeat and coiled-coil-containing protein C2orf44 1 DS(0.017)FS(0.014)HS(0.969)PGAVSSLK 110.77 0.00044474 235220000 299950 371950 356030 409600 352720 415840 352050 349260 314230 402760 TRUE FALSE 288227.6224 361342.3502 420372.5408 430739.5051 364065.5591 424248.5697 356358.4932 342047.6589 278559.9278 375480.7065 0.767622989 0.962345985 1.119558299 1.147168144 0.969598578 1.129881143 0.949072714 0.910959346 0.741875476 1 18.51837925 1.791521596 2.770735668 0.865461481 1.022044648 0.186103059 0.120091874 0.381670414 5.631162373 0.070352735 0.03375958 61.87590951 -1.791521596 0.156583167 EKEAEDGIIAYDDCGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEAEDGIIAYDDCGVK 17 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 153.68 1.08E-08 221390000 1159330 969760 836580 797950 910840 971150 1005780 1262610 1443380 1306850 FALSE TRUE 1114022.102 942103.3943 987768.6156 839132.2951 940137.9958 990787.3184 1018089.037 1236536.662 1279533.554 1218335.885 0.914380111 0.77327066 0.810752295 0.688752835 0.771657477 0.813230022 0.835639046 1.014939047 1.050230539 1 20.2164805 1.791528745 2.723247613 1.032108983 0.789948219 0.782033054 0.053655129 0.111780608 1.596267776 0.031718456 0.015145795 61.87692807 -1.791528745 -0.242160765 YSLLPFWYTLLYQAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 YSLLPFWYTLLYQAHR 16 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 134.24 2.93E-05 84313000 200780 212000 174800 116230 167760 160610 197330 238430 312980 226180 FALSE TRUE 192933.2956 205953.9676 206390.2484 122228.6442 173156.1528 163857.6442 199744.9836 233506.3372 277451.8225 210860.6271 0.914980185 0.976730319 0.978799367 0.579665563 0.821187697 0.777089808 0.947284404 1.107396579 1.315806684 1 17.68593021 1.79161091 2.665164042 1.169011934 0.842329737 0.513517866 0.12989798 0.207171198 2.839951975 0.078832053 0.037412252 61.88863587 -1.79161091 -0.326682197 AVAHHTDCTFIR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVAHHTDCTFIR 12 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QRR3 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;;; 147.91 3.82E-05 1601400000 552990 679940 608850 743470 668830 557370 686910 254754 684950 718300 FALSE TRUE 531378.5394 660548.7769 718882.7388 781840.5758 690343.5244 568640.4033 695316.6101 249493.2409 607197.3475 669648.9012 0.793518123 0.986410604 1.073521867 1.167538055 1.030903692 0.849162005 1.038330099 0.37257321 0.906739855 1 19.35304536 1.791623633 25 0.691611811 0.997142025 0.222315142 0.18556672 149.5485414 70477.28129 0.081355265 0.046522711 61.89044899 -1.791623633 0.305530214 AADRLPNLSS(ph)PSAEGPPGPPSGPAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AADRLPNLS(0.055)S(0.94)PS(0.005)AEGPPGPPSGPAPR;AADRLPNLS(0.057)S(0.938)PS(0.006)AEGPPGPPSGPAPR;AADRLPNLS(0.117)S(0.875)PS(0.008)AEGPPGPPSGPAPR;AADRLPNLS(0.101)S(0.885)PS(0.014)AEGPPGPPSGPAPR 216.7 2.36E-34 4509650000 378047 410936 346851 461158 482405 465513 368750 334955 321840 300155 TRUE FALSE 363272.5053 399216.5076 409534.6914 484958.4196 497921.9949 474925.9918 373262.8728 328038.0622 285306.0725 279825.2345 1.2982121 1.426663712 1.463537383 1.733076077 1.779403476 1.6972236 1.333914268 1.172296211 1.019586647 1 18.09416654 1.791677347 2.050815559 1.030693957 1.56979593 0.707787442 0.144917202 0.186424378 1.533884958 0.107659873 0.047198094 61.8981041 -1.791677347 0.539101973 IS(ph)PPIKEEETKGDSVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISPPIKEEETKGDSVEK 17 2 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;A0A087WTC9;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 IS(1)PPIKEEETKGDSVEK;IS(1)PPIKEEETKGDSVEK;IS(1)PPIKEEETKGDSVEK 133.1 1.12E-05 6894870000 2929900 1939690 1821530 1159570 1817470 1707660 1977560 2632790 3067670 2276110 TRUE FALSE 2815396.269 1884371.94 2150720.991 1219415.547 1875930.573 1742190.055 2001761.971 2578421.966 2719440.962 2121947.042 1.326798555 0.888039099 1.013560163 0.574668228 0.884060976 0.821033711 0.943360947 1.21512079 1.281578149 1 21.01695722 1.791822845 4.928594987 1.185667179 0.902966404 0.257424982 0.18769008 0.248831661 11.43210054 0.091068287 0.050006545 61.91884475 -1.791822845 -0.282700775 TPLDLFAHFGPEPGDHSDPLPPS(ph)APSPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 TPLDLFAHFGPEPGDHSDPLPPS(0.769)APS(0.23)PT(0.001)R 181.85 1.68E-17 1075600000 170910 178020 170830 217810 183110 176760 188670 65266 196630 181710 TRUE FALSE 164230.6482 172943.0439 201702.7811 229051.2002 188999.8994 180334.2083 190978.9999 63918.23429 174309.3867 169402.6198 0.969469353 1.020899465 1.190670966 1.352111322 1.115684631 1.064530221 1.127367452 0.3773155 1.028965118 1 17.37009666 1.791851463 25 0.734867962 1.125619311 0.343636668 0.194767796 124.8428923 58582.71624 0.085772134 0.049113565 61.92292511 -1.791851463 0.390751349 QGIAVMTPTVPGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 QGIAVMTPTVPGSPK 15 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;E7EX50;H0Y7S5;Q9UPX8-2 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 QGIAVMTPTVPGS(1)PK;QGIAVMTPTVPGS(1)PK;QGIAVMTPT(0.005)VPGS(0.994)PK;QGIAVMTPT(0.002)VPGS(0.998)PK;QGIAVMTPT(0.007)VPGS(0.993)PK 214.81 2.54E-12 366317000 1297135 1190905 1027513 906979 899562 989574 1085752 1243593 1352560 1286480 TRUE FALSE 1246441.53 1156941.555 1213207.456 953788.2949 928497.2287 1009583.864 1099039.758 1217912.37 1199023.059 1199345.564 1.039268054 0.964644045 1.01155788 0.795257283 0.774169895 0.841778962 0.916366218 1.015480781 0.9997311 1 20.19381597 1.79206633 4.86077405 1.0055541 0.899763853 0.234817752 0.081557615 0.327017819 14.55618427 0.044747674 0.024514195 61.95356897 -1.79206633 -0.105790247 VLDEEGS(ph)EREFDEDS(ph)DEKEEEEDTYEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLDEEGSEREFDEDSDEKEEEEDTYEK 27 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 2 VLDEEGS(1)EREFDEDS(1)DEKEEEEDTYEK 219.92 1.55E-34 263030000 199080 148510 150040 122560 163550 147150 171480 218680 260170 219220 TRUE FALSE 191299.7335 144274.6402 177155.5656 128885.3363 168810.7343 150125.4738 173578.6235 214164.1816 230636.5923 204372.0341 0.936036745 0.705941206 0.866828803 0.630640767 0.825997231 0.734569553 0.849326691 1.047913343 1.128513465 1 17.64083827 1.792069604 3.0048241 1.073054911 0.779123436 0.675466928 0.085375724 0.12555067 2.155376748 0.044307865 0.021752411 61.95403599 -1.792069604 -0.293931475 ELLSDTAHLNETHCAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLSDTAHLNETHCAR 16 0 Q9BV36-2;Q9BV36-5;C9JKV5;C9JI01;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 242.93 3.28E-20 1004000000 292770 345780 284890 396490 356720 347340 350240 96876 344350 358500 FALSE TRUE 281328.2247 335918.693 336375.9603 416952.8964 368194.2228 354363.4528 354526.3419 94875.47675 305260.8316 334218.4757 0.84174947 1.005087143 1.006455312 1.247545922 1.101657298 1.060274876 1.060762249 0.283872627 0.913357142 1 18.35043196 1.792182216 25 0.654806603 1.053523948 0.313187063 0.203240803 127.8061629 59603.18037 0.088005733 0.050491187 61.97010275 -1.792182216 0.398717345 NSDGGS(ph)DPETQKEK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSDGGSDPETQKEK 14 1 O75554-2;O75554 O75554-2 WBP4 WW domain-binding protein 4 1 NSDGGS(0.999)DPET(0.001)QKEK;NSDGGS(1)DPETQKEK 113.86 0.0012121 251120000 1041440 816640 658270 559640 750570 720080 787920 979920 1121950 920790 TRUE FALSE 1000739.373 793350.2268 777234.0321 588523.0875 774712.7657 734640.511 797562.8007 959684.3096 994590.9396 858424.0731 1.165786707 0.924193824 0.90541966 0.685585488 0.902482572 0.855801385 0.929101158 1.117960621 1.15862424 1 19.71133101 1.792212107 4.464071701 1.103795069 0.897128192 0.34009114 0.115694399 0.221937727 8.2340162 0.059062189 0.0318202 61.97436807 -1.792212107 -0.206666877 S(ph)PSKPLPEVTDEYKNDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSKPLPEVTDEYKNDVK 18 2 P05455;E7ERC4;E9PGX9;E9PFL9 P05455 SSB Lupus La protein 1 S(0.973)PS(0.027)KPLPEVTDEYKNDVK;S(0.952)PS(0.048)KPLPEVTDEYKNDVK;S(0.982)PS(0.018)KPLPEVTDEYKNDVK 132.26 7.92E-06 1813480000 1645350 1177330 1116030 820410 1163160 1130490 1210060 1446690 1696760 1297610 TRUE FALSE 1581047.903 1143753.701 1317721.447 862751.4584 1200574.098 1153349.282 1224869.076 1416815.346 1504150.918 1209721.719 1.306951738 0.945468436 1.089276506 0.713181755 0.992438243 0.953400492 1.012521357 1.171191129 1.243385892 1 20.20624378 1.792421797 4.83061762 1.155096135 0.988339397 0.142981275 0.149288702 0.331558621 14.53099597 0.071421871 0.039097268 62.00429833 -1.792421797 -0.166756738 ASGQAFELILS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 26 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR 204.23 8.34E-08 68506532800 6012329.5 7113079.1 7175958.2 10202216.7 11205727.2 9957378.1 7315559.2 6201087 5107386.4 5879275 TRUE FALSE 5777361.016 6910221.049 8472813.475 10728754.33 11566169.59 10158723.11 7405089.202 6073032.386 4527617.308 5481066.468 1.054057828 1.260743888 1.54583301 1.957420949 2.11020422 1.853420893 1.351030725 1.10800196 0.82604678 1 22.3860252 1.792568344 2.357120982 0.937298578 1.64231025 0.483072668 0.301428018 0.268332489 2.904251821 0.212306414 0.097203533 62.02522444 -1.792568344 0.705011672 EQHTEDTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQHTEDTVK 9 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 136.48 0.00019169 1147490000 1247360 1142590 1147020 1248840 1215870 1225310 1493660 1456640 1704760 1802170 FALSE TRUE 1198611.792 1110004.452 1354312.029 1313292.782 1254979.563 1250086.608 1511939.858 1426559.875 1511242.792 1680107.421 0.713413784 0.660674692 0.806086571 0.781671913 0.746963883 0.744051596 0.89990666 0.849088491 0.899491766 1 20.68012205 1.792619204 0.284428549 1.030100686 0.665633681 0.801556539 0.043301693 0.724388516 0.209171684 0.085512573 0.097717497 62.03248854 -1.792619204 -0.364467005 LKTDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKTDLK 6 1 Q8IZT6;Q8IZT6-2;Q5VYL4 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 0 ; 102.72 0.032194 2560500000 2847000 2582100 2265100 2167300 2356200 2484300 2556000 2939700 3208900 3157300 FALSE TRUE 2735736.092 2508461.036 2674453.957 2279154.613 2431989.313 2534534.248 2587281.093 2878994.168 2844639.125 2943453.259 0.929430792 0.852217044 0.908610982 0.774313166 0.82623677 0.861075079 0.878995134 0.978100861 0.966429182 1 21.48907829 1.792640497 2.855528129 0.983103859 0.85563974 0.650238516 0.040488747 0.157225258 2.450830462 0.023739082 0.011499132 62.03552994 -1.792640497 -0.12746412 LEELKESILADK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEELKESILADK 12 1 O75832;B1AJY5;B1AJY7;O75832-2;B1AJY6 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 ; 146.47 5.91E-05 490260000 755000 657070 530050 464900 508380 521530 596710 735210 795060 750180 FALSE TRUE 725493.7653 638331.0069 625841.8259 488893.5447 524732.5044 532075.6939 604012.7155 720027.6566 704808.122 699369.6404 1.037353816 0.912723358 0.89486559 0.699048853 0.750293513 0.760793239 0.863653039 1.029538051 1.007776262 1 19.41569564 1.792684886 4.717082225 1.013890156 0.835885377 0.414027764 0.090816063 0.214207897 8.907366267 0.049186398 0.026809055 62.0418709 -1.792684886 -0.17800478 SKESVPEFPLSPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKESVPEFPLSPPK 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ; 98.694 0.0022584 1060400000 1620810 1462130 1151050 1175390 1336790 1500650 1402160 1582540 1798780 1720540 FALSE TRUE 1557466.953 1420431.484 1359070.34 1236052.019 1379789.064 1530994.171 1419320.054 1549859.996 1594590.036 1604006.293 0.970985563 0.885552314 0.847297386 0.770602973 0.860214246 0.954481399 0.884859405 0.966243089 0.994129538 1 20.61324837 1.792893452 1.049182341 1.003758934 0.867608987 0.470629476 0.05195558 0.460375177 0.93902638 0.046804866 0.019310369 62.07167318 -1.792893452 -0.136149947 AHQLVMEGYNWCHDR ddPTM_BT-474_Pertuzumab_2h_R1 9 AHQLVMEGYNWCHDR 15 0 P67775;P62714;H0YC23 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 0 ;;;;;;;; 248.81 1.11E-18 6868120000 1575310 1623875 1333854 1646159 1536084 1613330 1611410 592483 1645810 1625243 FALSE TRUE 1513745.144 1577563.675 1574911.089 1731117.463 1585493.537 1645952.638 1631130.918 580248.019 1458984.549 1515163.844 0.999063665 1.041183553 1.039432861 1.142528229 1.04641722 1.086319902 1.076537646 0.382960576 0.962921967 1 20.53104238 1.792920258 25 0.715052339 1.063474446 0.362361204 0.162903703 118.1357166 54345.07784 0.068436078 0.03944748 62.07550454 -1.792920258 0.348422107 SRDYNGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRDYNGR 7 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 91.9 0.014651 50931000 37695 42242 28451 32119 34859 35355 34942 47039 38159 44400 FALSE TRUE 36221.83773 41037.29952 33592.72859 33776.66544 35980.27139 36069.90232 35369.63065 46067.62821 33827.3503 41392.74845 0.875076893 0.991412773 0.811560716 0.816004414 0.869240936 0.871406313 0.854488575 1.112939583 0.8172289 1 15.33709043 1.792924684 25 0.988709946 0.870276759 0.261983398 0.081429659 179.7533881 82683.86344 0.035387954 0.020399269 62.07613709 -1.792924684 -0.118433186 KS(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSKSPPKVPIVIQDDSLPAGPPPQIR 26 3 Q7Z422-5;Q7Z422;Q7Z422-4 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 KS(0.5)KS(0.5)PPKVPIVIQDDSLPAGPPPQIR;KS(0.472)KS(0.472)PPKVPIVIQDDS(0.056)LPAGPPPQIR 223.61 1.23E-33 2692400000 1151790 923290 664610 529010 750160 888660 835240 1029380 1215520 938700 TRUE FALSE 1106776.773 896958.6732 784719.8112 556312.2695 774289.5777 906629.3141 845461.917 1008122.943 1077539.265 875121.0129 1.264712831 1.024953875 0.896698628 0.635697534 0.884780009 1.036004508 0.966108578 1.151981187 1.231303156 1 19.739123 1.792929362 3.602990404 1.145323658 0.943385202 0.189397694 0.157378954 0.353070663 8.523830305 0.088904184 0.045719442 62.07680577 -1.792929362 -0.201938456 QKFNDS(ph)EGDDTEETEDYR ddPTM_BT-474_Pertuzumab_2h_R1 6 QKFNDSEGDDTEETEDYR 18 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 QKFNDS(1)EGDDTEETEDYR;QKFNDS(1)EGDDTEETEDYR;QKFNDS(1)EGDDTEETEDYR;QKFNDS(1)EGDDTEETEDYR;QKFNDS(1)EGDDTEETEDYR;QKFNDS(1)EGDDTEETEDYR 317.14 1.36E-61 23991300000 12350700 10954000 9521600 9676900 10277800 10777900 11027500 12435800 13878600 13125400 TRUE FALSE 11868020.99 10641602.65 11242364.93 10176325.97 10608394.77 10995836.52 11162457.84 12178996.38 12303159.51 12236404.97 0.969894427 0.869667412 0.918763718 0.831643444 0.866953554 0.898616591 0.912233444 0.995308378 1.005455405 1 23.54467642 1.793025306 2.575184552 1.004659084 0.889049605 0.66603133 0.034221738 0.152005241 1.948660354 0.020236526 0.009519289 62.0905213 -1.793025306 -0.115609479 ESGCSWHGGPDGLYEYLRPSGTPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESGCSWHGGPDGLYEYLRPSGTPAR 25 1 Q8IZ83;F5H4B6;Q8IZ83-3;M0QY06 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 69.704 0.024038 286730000 142740 147950 99809 130130 122060 152360 138780 54639 144710 137690 FALSE TRUE 137161.563 143730.6109 117846.7065 136846.0249 125986.1708 155440.8236 140478.4312 53510.68556 128283.1275 128364.1337 1.068534949 1.119710053 0.918065687 1.0660768 0.981474865 1.210936569 1.094374473 0.416866332 0.999368934 1 16.96988263 1.793067648 25 0.742135118 1.064376461 0.308135519 0.170939961 136.8998175 62806.638 0.07279891 0.042001877 62.09657519 -1.793067648 0.322241343 LSYLEEAVMHLDHSDPITR ddPTM_BT-474_Pertuzumab_2h_R1 10 LSYLEEAVMHLDHSDPITR 19 0 Q6P2E9;Q6P2E9-2;I3L0V0;I3L3M2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;;;;;;;;; 282.5 5.40E-40 660266000 392163 432152 412153 473922 470572 473889 466478 41085.846 500630 388074 FALSE TRUE 376836.8364 419827.4481 486638.2154 498381.1712 485708.3757 483471.3603 472186.8973 40237.40892 443800.5812 361789.4023 1.041591694 1.160419419 1.345086982 1.37754497 1.342516869 1.336333671 1.305142976 0.111217766 1.226682093 1 18.46479062 1.793167238 25 0.683338325 1.280300753 0.372038382 0.285561573 124.1757914 56865.20444 0.12174243 0.070290533 62.11081644 -1.793167238 0.596962428 QSHSS(ph)S(ph)SPHPK ddPTM_BT-474_Pertuzumab_2h_R1 4 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QS(0.002)HS(0.076)S(0.9)S(0.642)S(0.38)PHPK;QS(0.027)HS(0.16)S(0.786)S(0.552)S(0.475)PHPK;QS(0.071)HS(0.311)S(0.58)S(0.617)S(0.42)PHPK;QS(0.073)HS(0.441)S(0.5)S(0.526)S(0.46)PHPK 107.61 0.0011484 2191330000 3737330 3412070 2711990 3262580 3249650 3231670 3549100 1246850 3757050 3413800 TRUE FALSE 3591271.012 3314761.104 3202106.921 3430962.145 3354177.944 3297016.582 3592534.947 1221102.112 3330565.435 3182580.285 1.128414899 1.041532595 1.006135473 1.078044177 1.053917778 1.035957081 1.128812041 0.38368305 1.046498481 1 21.60176548 1.793347007 24.99999999 0.743064253 1.062847388 0.294708413 0.173377684 139.2609235 63563.99178 0.072502737 0.041911258 62.13653147 -1.793347007 0.319783135 CSKQSPSGAHGT(ph)HFGDDR ddPTM_BT-474_Pertuzumab_2h_R1 6 CSKQSPSGAHGTHFGDDR 18 1 A0A0A0MRP9;Q96C92-3;Q96C92 A0A0A0MRP9 SDCCAG3 Serologically defined colon cancer antigen 3 1 CS(0.006)KQS(0.007)PS(0.007)GAHGT(0.98)HFGDDR;CS(0.012)KQS(0.015)PS(0.015)GAHGT(0.958)HFGDDR;CS(0.014)KQS(0.014)PS(0.014)GAHGT(0.958)HFGDDR;CS(0.011)KQS(0.011)PS(0.011)GAHGT(0.967)HFGDDR;CS(0.015)KQS(0.015)PS(0.015)GAHGT(0.955)HFGDDR;CS(0.015)KQS(0.015)PS(0.015)GAHGT(0.955)HFGDDR 73.464 0.029557 4406930000 574810 1069319 1029895 1791974 1483431 1275354 1048877 655831 417648 723313 TRUE FALSE 552345.7897 1038823.069 1216019.936 1884457.993 1531146.905 1301142.532 1061713.47 642287.8607 370238.35 674322.3662 0.819112367 1.540543694 1.803321375 2.794595118 2.270645291 1.92955565 1.574489478 0.952493782 0.549052454 1 19.36307892 1.793426304 2.404422752 0.763082022 1.89965219 0.471599795 0.485769976 0.253261254 2.845867993 0.324701835 0.149678386 62.14787792 -1.793426304 1.136570167 ELTIGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELTIGSK 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ; 124.83 0.0095567 742260000 1865100 1870640 1460200 1718690 1630050 1661260 1723200 1937280 1969330 1925740 FALSE TRUE 1792209.83 1817291.179 1724090.622 1807391.797 1682482.039 1694851.815 1744289.037 1897274.491 1745779.915 1795307.915 0.998274344 1.012244843 0.960331433 1.006730813 0.937155139 0.944045198 0.971582102 1.056796149 0.972412532 1 20.77579987 1.793470038 25 1.015859129 0.975061482 0.197638064 0.03060609 210.9415628 96065.96181 0.013929351 0.008058033 62.15413665 -1.793470038 -0.040797647 EKFPEFCSS(ph)PSPPVEVK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.158)S(0.78)PS(0.062)PPVEVK;EKFPEFCS(0.005)S(0.99)PS(0.006)PPVEVK;EKFPEFCS(0.044)S(0.609)PS(0.346)PPVEVK 241.13 1.44E-20 4342910000 2189870 1886430 1572020 1515850 1766410 1843220 1877410 2178930 2526370 2200390 TRUE FALSE 2104287.459 1832630.863 1856118.983 1594083.2 1823228.182 1880491.171 1900386.305 2133934.334 2239587.069 2051355.625 1.025803344 0.893375503 0.904825551 0.777087688 0.88879186 0.916706566 0.926405096 1.040255677 1.091759538 1 20.96814619 1.793535014 2.706972152 1.054057217 0.895490978 0.532356027 0.059977111 0.193635964 2.726383313 0.035822351 0.017105311 62.16343631 -1.793535014 -0.158566239 KDVIELTDDSFDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDVIELTDDSFDK 13 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 126.88 0.00014436 0 110820 107990 100390 113950 109070 95260 113590 157160 156300 163120 FALSE TRUE 106489.0319 104910.2309 118532.7062 119830.9732 112578.3356 97186.22247 114980.1484 153914.5911 138557.4793 152071.7371 0.700255247 0.689873299 0.779452569 0.78798977 0.740297558 0.639081425 0.756091504 1.01211832 0.91113235 1 17.21439252 1.793537261 5.597387548 0.970800324 0.726068258 0.847334766 0.048068343 0.075451676 4.545967701 0.023402148 0.013176349 62.16375795 -1.793537261 -0.244732066 DALTAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DALTAEK 7 0 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 82.241 0.058218 108450000 274710 231470 225910 224180 237710 225050 258000 286820 334010 306780 FALSE TRUE 263974.0295 224868.7022 266736.9623 235749.9567 245356.158 229600.6652 261157.4812 280897.0668 296094.5851 286001.5173 0.92298122 0.786250032 0.932641773 0.824296175 0.857884113 0.802795269 0.913133202 0.982152365 1.035290259 1 18.12566328 1.793619978 2.433531342 1.014323718 0.85394823 0.688915636 0.045442523 0.14075213 1.618333544 0.025550136 0.011822967 62.17559905 -1.793619978 -0.160375488 TLDFDPLLSPAS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 3 TLDFDPLLSPASPKR 15 1 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 TLDFDPLLS(0.027)PAS(0.973)PKR;TLDFDPLLS(0.327)PAS(0.673)PKR;TLDFDPLLS(0.007)PAS(0.993)PKR 186.05 2.44E-07 326750000 734550 703490 556070 555030 631560 644690 654070 711860 768970 768310 TRUE FALSE 705842.9739 683427.154 656564.2187 583675.1648 651874.701 657726.0735 662074.7043 697159.8422 681679.7494 716271.6794 0.985440293 0.954145157 0.916641321 0.814879579 0.9100942 0.918263408 0.924334611 0.973317614 0.951705573 1 19.45014737 1.793627138 2.170415626 0.975935153 0.913048912 0.278015492 0.042197565 0.427941234 3.936574374 0.029360525 0.013118185 62.17662411 -1.793627138 -0.062886241 PGPYDRPGTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 PGPYDRPGTAR 11 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 120.77 0.00038807 564790000 386370 350360 341130 350050 358360 298890 366260 433530 473480 442930 FALSE TRUE 371270.2332 340368.0758 402779.7794 368116.1225 369886.9749 304933.7606 370742.3994 424577.454 419732.5354 412929.9566 0.899111889 0.824275571 0.975419131 0.891473521 0.895762027 0.738463644 0.897833624 1.028206957 1.016473929 1 18.65553756 1.793801792 4.8812199 1.016389098 0.871567165 0.556413329 0.057612337 0.154465407 6.868608077 0.028757566 0.015800249 62.20163374 -1.793801792 -0.144821933 ENGSGHEASLQLRPPPEPST(ph)PVSGQDDLIQHQDMR ddPTM_BT-474_Pertuzumab_2h_R1 4 ENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMR 35 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ENGSGHEASLQLRPPPEPS(0.006)T(0.992)PVS(0.002)GQDDLIQHQDMR;ENGSGHEASLQLRPPPEPS(0.154)T(0.813)PVS(0.033)GQDDLIQHQDMR;ENGSGHEASLQLRPPPEPS(0.152)T(0.847)PVS(0.001)GQDDLIQHQDMR;ENGSGHEASLQLRPPPEPS(0.296)T(0.703)PVS(0.001)GQDDLIQHQDMR 207.48 4.67E-28 2601920000 262632 294245 248400 318923 277528 330888 274818 256304 254405 276037 TRUE FALSE 252368.0511 285853.4207 293291.4056 335382.6542 286454.9402 337578.7821 278181.3049 251011.2328 225526.011 257340.7681 0.980676528 1.110797262 1.139700514 1.303262816 1.113134706 1.311796745 1.080984202 0.975404071 0.876371096 1 17.9733205 1.794020731 3.037262553 0.939085197 1.162475234 0.486993366 0.095292584 0.199776854 3.487292158 0.053560157 0.026413903 62.23299908 -1.794020731 0.223390037 RIDIS(ph)PSTLR ddPTM_BT-474_Pertuzumab_2h_R1 9 RIDISPSTLR 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 RIDIS(0.897)PS(0.085)T(0.018)LR;RIDIS(1)PSTLR;RIDIS(0.94)PS(0.054)T(0.006)LR;RIDIS(0.972)PS(0.022)T(0.006)LR;RIDIS(1)PSTLR;RIDIS(0.971)PS(0.028)T(0.001)LR;RIDIS(0.86)PS(0.133)T(0.008)LR;RIDIS(0.984)PS(0.014)T(0.002)LR;RIDIS(0.999)PS(0.001)TLR 141.73 2.27E-05 75697070000 1339234 1356056 1107871 1293976 1341724 1353160 1248788 1257717 1279522 1304852 TRUE FALSE 1286895.255 1317382.611 1308087.934 1360758.256 1384881.771 1380521.822 1264071.041 1231744.704 1134276.027 1216473.212 1.057890336 1.082952422 1.075311747 1.118609307 1.138440006 1.134855917 1.039127725 1.012553908 0.932429926 1 20.21427312 1.794120443 2.094321326 0.970703515 1.100860729 0.74898624 0.031091781 0.151541515 1.298020793 0.021240032 0.009391037 62.24728912 -1.794120443 0.130157213 EAADGYQR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAADGYQR 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 160.52 0.00082099 1999700000 3111200 3636300 3066740 3528950 3545080 3476050 3450360 3437430 3733570 3670740 FALSE TRUE 2989610.864 3532596.284 3620968.137 3711079.532 3659110.718 3546338.113 3492586.538 3366445.869 3309750.786 3422117.51 0.873614321 1.032283746 1.058107481 1.084439538 1.069253381 1.036299339 1.020592229 0.983731815 0.967164563 1 21.70645787 1.794195133 3.234486059 0.98077036 1.03186706 0.098884946 0.055211293 0.499672445 9.807547311 0.031073957 0.015579761 62.25799539 -1.794195133 0.0510967 KTLEEEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 KTLEEEAK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;; 123.75 0.0021395 1445460000 1466060 1289170 1042660 1040600 1202520 1115230 1282790 1451690 1675940 1534490 FALSE TRUE 1408764.754 1252404.134 1231091.856 1094305.491 1241200.148 1137780.715 1298489.168 1421712.094 1485694.317 1430557.626 0.98476617 0.875465701 0.860567819 0.764950304 0.867633799 0.795340708 0.907680435 0.993816725 1.038542098 1 20.44814618 1.794267719 2.77698962 1.017502961 0.855109768 0.60303239 0.055232485 0.171296557 2.527834314 0.03264079 0.015709724 62.26840173 -1.794267719 -0.162393193 EEHGGLIRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 EEHGGLIRSPR 11 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR 141.06 2.32E-05 57799930000 8057410 8438280 5669710 7108140 7931800 8431740 7306090 6774070 7271730 6971500 TRUE FALSE 7742517.509 8197628.516 6694352.719 7474991.957 8186933.55 8602235.56 7395504.115 6634183.087 6446273.696 6499314.095 1.191282248 1.261306716 1.030009109 1.150120128 1.259661163 1.323560522 1.137889938 1.020751265 0.991839077 1 22.63185604 1.794310125 3.257366887 1.000867309 1.199296283 0.585886375 0.074275999 0.180116785 3.581467676 0.043557138 0.021879818 62.27448219 -1.794310125 0.198428974 LPLDINPVVHPHGHIFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPLDINPVVHPHGHIFK 17 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 89.541 0.0013987 433010000 525800 579490 441510 510220 531070 535890 569460 173466 636840 491730 FALSE TRUE 505251.1547 562963.5126 521300.6783 536552.5153 548152.3489 546726.063 576429.2218 169883.8665 564548.5931 458424.6891 1.102146474 1.228039253 1.137156638 1.170426742 1.195730426 1.19261915 1.257413127 0.370581844 1.231496921 1 18.80632522 1.794478268 25 0.79910135 1.183637362 0.314011874 0.206778294 144.0331531 64411.7882 0.085736117 0.049973682 62.29859729 -1.794478268 0.384536011 LSDNPAWEGDKGNTK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSDNPAWEGDKGNTK 15 1 Q9BY42;A2A2L6;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ; 200.94 6.08E-09 771890000 838360 733850 681560 577480 709640 755080 747980 912030 1026950 904490 FALSE TRUE 805595.9643 712921.3165 804733.0532 607283.812 732466.2151 770348.2349 757134.003 893196.2618 910374.9413 843228.0867 0.95537136 0.845466758 0.954348018 0.72018926 0.86864542 0.913570417 0.897899412 1.059258196 1.079630714 1 19.6855634 1.794528912 3.585306465 1.053934166 0.873035915 0.575940789 0.065593993 0.152698558 3.636634684 0.034306373 0.017646816 62.3058625 -1.794528912 -0.180898251 GPS(ph)PAPASS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSPAPASSPK 11 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.021)S(0.979)PK;GPS(1)PAPAS(0.334)S(0.666)PK 152.02 4.85E-05 1173460000 3534200 3143700 2672580 2782430 2869500 2816060 3041100 3461900 3800000 3339600 TRUE FALSE 3396079.557 3054044.754 3155574.657 2926031.546 2961800.074 2873002.663 3078317.891 3390410.555 3368639.931 3113405.917 1.090792414 0.98093369 1.013544247 0.939816915 0.951305468 0.922784481 0.988730019 1.088971578 1.081979035 1 21.57006225 1.794570134 7.380472166 1.064534464 0.979459829 0.30989326 0.049260564 0.255648267 27.7520952 0.022500402 0.013188461 62.31177663 -1.794570134 -0.085074635 STPENHPET(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 STPENHPETPK 11 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 STPENHPET(1)PK;STPENHPET(1)PK 99.566 0.017217 2251700000 3431300 2916500 2484800 2313900 2559500 2556000 2883300 3011700 3376000 3328800 TRUE FALSE 3297201.002 2833324.276 2933858.634 2433320.656 2641828.642 2607684.071 2918586.688 2949507.343 2992770.633 3103337.411 1.062469389 0.912992659 0.945388221 0.784098 0.851286306 0.840283774 0.940467085 0.950430763 0.964371654 1 21.56538913 1.794820288 2.273743954 0.973883714 0.895208049 0.16868039 0.070614816 0.534421634 5.380714671 0.046529299 0.021110517 62.34767862 -1.794820288 -0.078675665 IRYESLTDPSK ddPTM_BT-474_Pertuzumab_2h_R1 5 IRYESLTDPSK 11 1 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ;;;; 125.82 0.00029219 6072560000 6144900 5603060 5312260 5679010 5390590 5740460 6113680 6970880 7909440 7582770 FALSE TRUE 5904750.514 5443266.215 6272303.553 5972104.387 5563983.223 5856536.034 6188501.045 6826928.892 7011593.53 7069182.234 0.835280563 0.769999419 0.887274277 0.844808379 0.787075936 0.828460187 0.875419651 0.965731066 0.991853555 1 22.7531119 1.79507884 1.953846377 0.996578971 0.824536329 0.853512898 0.029879109 0.113431716 0.844215254 0.020456541 0.008866366 62.38480766 -1.79507884 -0.172042642 KQDDS(ph)PPRPIIGPALPPGFIK ddPTM_BT-474_Pertuzumab_2h_R1 3 KQDDSPPRPIIGPALPPGFIK 21 2 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 1 KQDDS(1)PPRPIIGPALPPGFIK;KQDDS(1)PPRPIIGPALPPGFIK;KQDDS(1)PPRPIIGPALPPGFIK 198.68 6.64E-22 3810700000 3616110 3246100 2659320 2639910 2911100 3028010 3126960 3640370 4053540 3686840 TRUE FALSE 3474788.423 3153524.406 3139918.28 2776156.071 3004738.175 3089238.437 3165228.672 3565195.087 3593399.133 3437127.043 1.010957227 0.917488463 0.913529887 0.807696671 0.874200499 0.89878506 0.920893709 1.037260201 1.045465905 1 21.71277175 1.795401883 3.921182174 1.031788079 0.899924119 0.569466001 0.048330038 0.158390778 4.469904584 0.026280694 0.013812913 62.43122883 -1.795401883 -0.13186396 HVAAGTQQPYTDGVR ddPTM_BT-474_Pertuzumab_2h_R1 3 HVAAGTQQPYTDGVR 15 0 P14923 P14923 JUP Junction plakoglobin 0 ;; 164.63 1.47E-06 1296240000 1601090 1793300 1436130 1807010 1410250 1648240 1633790 1502770 1649280 1729340 FALSE TRUE 1538517.633 1742156.84 1695670.638 1900270.003 1455611.972 1681568.542 1653784.811 1471737.274 1462060.649 1612210.261 0.954290932 1.080601508 1.051767675 1.178673805 0.902867329 1.043020617 1.0257873 0.912869313 0.906867227 1 20.62060848 1.795416483 5.701962121 0.932544004 1.037846051 0.257607433 0.072644561 0.254624063 15.73899026 0.033499912 0.018972754 62.43332768 -1.795416483 0.105302046 DHNVGSPPKS(ph)PTHASPQHTQTEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DHNVGSPPKSPTHASPQHTQTEK 23 1 A0A0C4DGH6;A0JNW5;F8W665;A0JNW5-2 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 DHNVGSPPKS(0.978)PT(0.022)HASPQHTQTEK;DHNVGSPPKS(0.955)PT(0.044)HASPQHTQTEK;DHNVGSPPKS(0.995)PT(0.005)HASPQHTQTEK;DHNVGS(0.001)PPKS(0.993)PT(0.006)HASPQHTQTEK 177.85 1.91E-17 588500000 160943 227890 215353 284566 204544 246911 230784 29421.7 226875 226631 TRUE FALSE 154653.1696 221390.8003 254272.0776 299252.4854 211123.3435 251903.7096 233608.4036 28814.13161 201121.1011 211281.0805 0.731978317 1.047849622 1.203477742 1.416371426 0.999253426 1.192268181 1.105675923 0.136378191 0.951912498 1 17.68880406 1.795438313 25 0.602251983 1.113455875 0.290642216 0.276859076 155.7600874 68480.02292 0.118794436 0.069775151 62.43646597 -1.795438313 0.511203893 LKELEVAEGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKELEVAEGGK 11 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 119.69 0.00050383 340010000 788120 784730 664030 708150 741070 758560 777500 931690 1022000 960140 FALSE TRUE 757319.3991 762350.2687 784034.9923 744697.7064 764907.1896 773898.6029 787015.2776 912450.2759 905986.8446 895108.8626 0.846064016 0.851684416 0.875910211 0.831963281 0.854540963 0.864586013 0.879239733 1.019373524 1.012152692 1 19.77170363 1.795744315 3.757580596 1.013189186 0.855149093 0.96926989 0.012507459 0.033605366 0.872480092 0.00663425 0.003454157 62.48047394 -1.795744315 -0.158040093 AEELSPAALS(ph)PLLEPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEELSPAALSPLLEPIR 17 0 A0A5F9ZH52;A5YM69 A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 AEELS(0.003)PAALS(0.997)PLLEPIR 71.692 0.031443 29689000 2760.8 2141.2 3123.7 3696.5 1814.7 4334.5 2786.1 2198 2387.2 2254.2 TRUE FALSE 2652.904884 2080.135072 3688.222076 3887.276808 1873.071474 4422.14656 2820.197125 2152.610532 2116.215064 2101.521026 1.262373705 0.989823583 1.755025065 1.849744428 0.891293235 2.104259964 1.341979019 1.024310728 1.006992096 1 11.03721818 1.795885366 4.159992363 1.011057124 1.473898801 0.255520914 0.352526701 0.30238817 9.568734175 0.177250027 0.094436635 62.50076972 -1.795885366 0.462841677 WFHPNITGVEAENLLLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 WFHPNITGVEAENLLLTR 18 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 202.97 1.23E-15 663990000 443700 501100 426950 498860 470520 474660 477330 445740 506610 487800 FALSE TRUE 426359.7135 486809.1186 504109.3625 524606.2244 485654.7031 484257.9504 483171.7073 436535.3132 449101.7567 454760.8715 0.93754705 1.070472745 1.108515253 1.153586989 1.067934234 1.064862834 1.062474231 0.959922765 0.987555845 1 18.7947486 1.795891929 6.096029279 0.980278674 1.072051723 0.350608956 0.052020156 0.224705107 16.03069874 0.025028831 0.014339942 62.50171427 -1.795891929 0.09177305 RQS(ph)SGSATNVASTPDNR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQSSGSATNVASTPDNR 17 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 RQS(0.474)S(0.474)GS(0.045)ATNVAS(0.005)T(0.001)PDNR;RQS(0.677)S(0.207)GS(0.114)AT(0.001)NVAS(0.001)TPDNR 263.14 2.33E-27 845650000 568800 619040 512380 654940 670800 625410 547660 601770 595510 564840 TRUE FALSE 546570.6672 601385.5853 604978.4638 688741.5319 692376.8912 638056.2187 554362.4269 589343.2392 527910.2014 526582.8837 1.037957526 1.142053044 1.148876051 1.307945156 1.314848835 1.211691907 1.05275436 1.119184192 1.002520624 1 19.0063011 1.795925073 1.415609722 1.016784773 1.196567605 0.42130975 0.083530832 0.437730523 1.660743084 0.070770439 0.028668266 62.50648433 -1.795925073 0.179782832 GGGPGKSPT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.159)PT(0.841)R 80.69 0.03759 929390000 320490 315670 268060 284520 279820 298660 303370 334240 364590 350880 TRUE FALSE 307964.8965 306667.4007 316504.405 299204.1113 288820.6644 304699.1098 307082.7328 327337.8272 323203.2717 327114.5851 0.941458775 0.937492288 0.967564332 0.914676768 0.88293423 0.931475158 0.938761972 1.000682459 0.988042987 1 18.31943656 1.796026088 4.068761453 0.996132192 0.929089843 0.684324589 0.020465488 0.135137912 4.090828373 0.011440513 0.006066527 62.52102486 -1.796026088 -0.067042348 EFLHAQEEVKR ddPTM_BT-474_Pertuzumab_2h_R1 4 EFLHAQEEVKR 11 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 165.7 1.38E-05 4314170000 3016760 2844030 2374520 2797260 2779680 2863790 2921570 3024040 3421380 3336750 FALSE TRUE 2898861.684 2762921.049 2803648.585 2941626.924 2869090.932 2921697.796 2957325.048 2961592.517 3032999.286 3110748.95 0.93188545 0.888185158 0.901277676 0.94563302 0.922315165 0.939226483 0.950679433 0.952051279 0.975006127 1 21.56883054 1.796057272 0.347982553 1.004790686 0.899704264 0.789937923 0.01425673 0.549911334 0.201095816 0.019406038 0.019675336 62.52551419 -1.796057272 -0.105086422 KLENDTISK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLENDTISK 9 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 78.342 0.048174 187620000 258560 263860 212130 215510 229360 222160 242790 285520 308980 289600 FALSE TRUE 248455.1893 256334.9711 250466.6098 226632.4969 236737.5727 226652.2274 245761.3366 279623.9122 273905.8857 269985.1341 0.920255073 0.949441057 0.927705189 0.839425836 0.876854104 0.839498916 0.910277292 1.035701144 1.014522102 1 18.04252045 1.796187425 5.164489654 1.018579758 0.892254488 0.724055507 0.034559979 0.114503426 5.664223815 0.01837043 0.010232528 62.5442552 -1.796187425 -0.12632527 LLDQHDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDQHDQR 8 0 P29084;E5RH41 P29084 GTF2E2 Transcription initiation factor IIE subunit beta 0 ; 109.21 0.0036612 293100000 540990 534480 474330 496240 537180 534990 500870 481920 506390 489320 FALSE TRUE 519847.5127 519237.1537 560051.9824 521851.0059 554458.8826 545807.8644 506999.7969 471968.1836 448906.7302 456177.9206 1.139571841 1.138233856 1.22770515 1.143963753 1.215444364 1.196480232 1.111408014 1.034614264 0.984060626 1 18.79923709 1.796280653 2.045889216 0.994474576 1.177455808 0.863138313 0.030525963 0.103669098 0.845970361 0.02021122 0.008889817 62.55768264 -1.796280653 0.182981231 LIPGPLS(ph)PVAR ddPTM_BT-474_Pertuzumab_2h_R1 11 LIPGPLSPVAR 11 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR 208.79 1.93E-08 17902973000 4927898 5427827 4672764 5744641 5506817 5231953 4735176 4473969 4020789 4312773 TRUE FALSE 4735310.298 5273030.688 5517236.4 6041122.61 5683948.77 5337746.674 4793126.5 4381579.977 3564365.889 4020665.043 1.177743047 1.311482213 1.372219854 1.502518251 1.413683734 1.327578054 1.192122808 1.089764984 0.886511523 1 21.93900272 1.796282378 1.553072246 0.94893999 1.361664456 0.785739185 0.08523077 0.174028194 0.803253291 0.067850476 0.027840559 62.55793114 -1.796282378 0.412724466 DKEEIVICDR ddPTM_BT-474_Pertuzumab_2h_R1 5 DKEEIVICDR 10 1 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ;;;; 145.31 2.80E-05 2414960000 2932700 2651930 2309100 2586750 2464920 2708950 2800070 3061210 3603020 3299020 FALSE TRUE 2818086.842 2576299.553 2726405.736 2720252.477 2544206.39 2763726.825 2834338.094 2997994.944 3194020.275 3075574.437 0.916279836 0.83766451 0.886470411 0.884469725 0.827229658 0.898605084 0.921563809 0.974775609 1.038511777 1 21.55242446 1.796332934 1.546324953 1.019388049 0.871029804 0.829378585 0.026664427 0.135662099 0.620426699 0.018969875 0.007778221 62.56521399 -1.796332934 -0.148358246 FSVCVLGDQQHCDEAK ddPTM_BT-474_Pertuzumab_2h_R1 5 FSVCVLGDQQHCDEAK 16 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;; 274.17 3.17E-35 8338410000 6653640 5823100 4845640 5053610 5870790 5259090 5738110 6499310 7155490 6495380 FALSE TRUE 6393608.393 5657030.889 5721354.939 5314427.418 6059629.292 5365432.403 5808334.707 6365096.977 6343228.773 6055442.127 1.055845017 0.934206086 0.944828605 0.877628306 1.000691471 0.886051306 0.959192506 1.051136621 1.047525291 1 22.52980087 1.796497005 5.545627665 1.036753975 0.946294051 0.354868952 0.050217746 0.201057206 11.58533732 0.022781345 0.012860365 62.58885482 -1.796497005 -0.090459923 SNS(ph)PLPVPPSK ddPTM_BT-474_Pertuzumab_2h_R1 9 SNSPLPVPPSK 11 0 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.009)NS(0.991)PLPVPPSK;S(0.016)NS(0.984)PLPVPPSK;S(0.024)NS(0.976)PLPVPPSK;S(0.002)NS(0.998)PLPVPPSK;S(0.152)NS(0.848)PLPVPPSK;S(0.009)NS(0.991)PLPVPPSK;S(0.002)NS(0.998)PLPVPPSK;S(0.109)NS(0.891)PLPVPPSK;S(0.047)NS(0.953)PLPVPPSK 115.12 0.0012236 24839300000 26093850 23773470 22466220 24483190 24436140 25067740 28519890 29311990 35747490 34174790 TRUE FALSE 25074073.49 23095473.91 26526365.71 25746770.37 25222150.64 25574626.88 28868924.95 28706687.16 31689584.8 31860101.03 0.787005461 0.72490272 0.832588876 0.808119546 0.791653191 0.80271644 0.906115298 0.901023105 0.994647969 1 24.92524751 1.79658312 0.85321356 1.006849383 0.781075964 0.876064518 0.030741444 0.184906771 0.253478864 0.026854214 0.01199528 62.60126661 -1.79658312 -0.225773419 DKSHS(ph)HTPSRR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKSHSHTPSRR 11 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.011)HS(0.883)HT(0.106)PSRR;DKS(0.034)HS(0.895)HT(0.071)PSRR 85.45 0.0072213 882820000 95061 122079 90013 120272 107927 147017 117663 4794.51 129750 92781 TRUE FALSE 91345.91102 118597.4264 106280.3514 126479.2523 111398.57 149989.7845 119102.995 4695.501693 115021.324 86496.86023 1.056060426 1.371118283 1.228719183 1.462240965 1.287891487 1.73404889 1.376963218 0.054285227 1.329774557 1 16.40036014 1.796589615 24.99999769 0.692241538 1.370582981 0.351904266 0.342722812 146.7178165 63224.41565 0.143130353 0.084887455 62.60220282 -1.796589615 0.678341443 FGAQQDTIEVPEKDLVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FGAQQDTIEVPEKDLVDK 18 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 184.83 5.13E-14 566330000 646520 552340 474550 422470 520100 580900 557140 671400 792230 702610 FALSE TRUE 621253.2836 536587.804 560311.7413 444273.7273 536829.4888 592646.196 563958.446 657535.3554 702299.3717 655021.5989 0.94844702 0.819191008 0.855409566 0.678258134 0.819559981 0.904773517 0.86097687 1.00383767 1.072177426 1 19.32118295 1.796636417 1.656982369 1.044272912 0.826249559 0.606463945 0.068242656 0.238173508 1.259794151 0.050629108 0.021048026 62.60894945 -1.796636417 -0.218023353 TKEDEKDDKPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKEDEKDDKPIR 12 3 P35998;C9JLS9 P35998 PSMC2 26S protease regulatory subunit 7 0 98.531 0.0018866 317820000 375080 255000 275420 181380 268420 268280 291230 468180 502240 394990 FALSE TRUE 360421.4589 247727.6497 325194.5207 190741.0435 277053.9731 273704.8054 294794.1599 458511.9194 445227.8208 368236.9755 0.978775851 0.672739747 0.883112078 0.517984494 0.752379559 0.743284416 0.800555565 1.245154479 1.209079616 1 18.49027497 1.796700211 5.538830977 1.16982446 0.751794035 0.652254471 0.129344402 0.111182355 6.378988828 0.058181087 0.032846089 62.61814687 -1.796700211 -0.418030425 AAVLS(ph)DS(ph)EDEEKASAK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAVLSDSEDEEKASAK 16 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 AAVLS(1)DS(1)EDEEKASAK;AAVLS(1)DS(1)EDEEKASAK;AAVLS(1)DS(1)EDEEKASAK 171.68 2.75E-09 575070000 2763700 2071630 1872580 1677750 2021480 1915000 2160560 2793200 3128670 2643970 TRUE FALSE 2655691.549 2012549.141 2210996.861 1764338.879 2086502.74 1953722.612 2187001.58 2735519.444 2773516.498 2464891.557 1.077407053 0.816485875 0.896995592 0.715787627 0.846488656 0.792620108 0.88726077 1.10979302 1.125208324 1 21.23309275 1.796757275 4.613469953 1.087983805 0.850299347 0.531089302 0.09301147 0.147588895 5.734981468 0.044650765 0.024339637 62.62637507 -1.796757275 -0.237684458 S(ph)KSKDQAEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSKDQAEEK 10 2 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 S(0.825)KS(0.175)KDQAEEK;S(0.5)KS(0.5)KDQAEEK 107.37 0.0018056 280820000 352360 219272 190577 139598 214137 199040 221233 253441 278964 254817 TRUE FALSE 338589.3816 213018.5772 225018.5033 146802.6695 221024.9111 203064.7252 223940.5156 248207.3548 247297.1762 237558.0176 1.425291325 0.896701275 0.947214939 0.617965544 0.930403921 0.854800554 0.942677153 1.044828363 1.040996969 1 17.85792037 1.796792843 5.12894048 1.03188943 0.925803472 0.033524459 0.187623184 0.672869616 32.66180382 0.090515781 0.050390616 62.63150428 -1.796792843 -0.106085958 MADGGS(ph)PFLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 MADGGSPFLGR 11 0 O60504-2;O60504;E5RIA0;E5RJP2 O60504-2 SORBS3 Vinexin 1 MADGGS(1)PFLGR 85.522 0.015895 38139000 95413 104800 93120 92778 89280 91215 72823 91294 78946 67928 TRUE FALSE 91684.15448 101811.2066 109948.8554 97566.2837 92151.77228 93059.4298 73714.22966 89408.747 69984.38105 63327.17606 1.447785298 1.607701669 1.736203354 1.540670053 1.455169455 1.469502283 1.164022056 1.411854319 1.105123983 1 15.95053713 1.796977844 0.499265716 1.00318987 1.620445136 0.757785866 0.108777115 0.423551962 0.246381369 0.110005641 0.077201656 62.65818977 -1.796977844 0.617255266 EEASDYLELDTIK ddPTM_BT-474_Pertuzumab_2h_R1 4 EEASDYLELDTIK 13 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;; 320.59 1.21E-50 1090210000 1367660 1412000 1312460 1364570 1341460 1422820 1493980 1636620 1912690 1783080 FALSE TRUE 1314210.335 1371731.142 1549650.718 1434995.621 1384609.279 1451590.395 1512263.774 1602823.225 1695569.45 1662310.403 0.790592619 0.825195547 0.932227046 0.863253709 0.832942678 0.873236666 0.909736094 0.964214157 1.020007723 1 20.66475837 1.796993306 1.413854219 1.012091625 0.852701362 0.774629606 0.034812648 0.198118446 0.749531632 0.028361886 0.011496644 62.6604207 -1.796993306 -0.159390262 HLIEQDFPGMR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLIEQDFPGMR 11 0 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 ;; 147.28 3.54E-05 1729790000 1422720 1508250 1501830 1445800 1408470 1581930 1523570 1022550 1612050 1641140 FALSE TRUE 1367118.529 1465236.187 1773244.089 1520417.911 1453774.717 1613917.708 1542215.905 1001433.985 1429056.842 1529984.126 0.893550793 0.957680646 1.158995089 0.993747507 0.950189412 1.05485912 1.00799471 0.654538807 0.934033771 1 20.54508525 1.797005815 24.99999913 0.825161077 1.006404873 0.240155938 0.10751673 177.600932 75987.58375 0.045795006 0.027258354 62.66222553 -1.797005815 0.181243796 LGSQHSPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGSQHSPGR 9 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 ;; 91.867 0.010463 65311000 265928 310919 254769 268062 284921 337358 260366 238289 220812 251624 FALSE TRUE 255535.2398 302051.8945 300811.4256 281896.7119 294085.7427 344179.6099 263552.437 233368.2489 195746.3475 234581.2824 1.089324933 1.287621465 1.282333452 1.201701641 1.25366244 1.467208323 1.123501561 0.994828942 0.834449985 1 17.83972838 1.797035705 2.757678817 0.92467432 1.262857778 0.674057716 0.099034241 0.142157825 2.062393408 0.056096032 0.027008328 62.66653832 -1.797035705 0.338183458 SPSELFAQHIVTIVHHVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSELFAQHIVTIVHHVK 18 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 147.56 2.63E-08 262040000 279700 260220 236390 273770 286500 332390 294840 94547 310190 285370 FALSE TRUE 268769.0148 252798.7804 279110.9315 287899.3025 295715.5327 339111.1535 298448.3401 92594.57141 274978.5316 266041.6357 1.0102517 0.950222621 1.049125001 1.08215882 1.111538545 1.274654445 1.121810649 0.348045415 1.033592095 1 18.02129252 1.797235069 25 0.722806449 1.087191924 0.302702099 0.194154128 160.2076788 68277.86671 0.082569812 0.0492454 62.69531215 -1.797235069 0.364385475 SQSASVES(ph)IPEVLEECTSPADHSDSASVHDMDYVNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 S(0.009)QS(0.007)AS(0.044)VES(0.923)IPEVLEECT(0.009)S(0.007)PADHSDSASVHDMDYVNPR;SQSASVES(1)IPEVLEECTSPADHSDSASVHDMDYVNPR 345.88 1.11E-144 295130000 66483 91065 81070 113031 88507 113015 99113 27293.2 100147 100255 TRUE FALSE 63884.77086 88467.91536 95721.15239 118864.5435 91353.90804 115300.2407 100325.9745 26729.58588 88778.73241 93464.63955 0.683518079 0.946538881 1.024142958 1.271759502 0.977416791 1.233624195 1.073411025 0.28598608 0.949864385 1 16.51213303 1.79737687 25 0.667341904 1.041720084 0.210014684 0.238427028 193.2818912 82174.90515 0.102006902 0.060912304 62.71578607 -1.79737687 0.374378179 NDKSEEEQSSSSVK ddPTM_BT-474_Pertuzumab_2h_R1 8 NDKSEEEQSSSSVK 14 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;;;;;;; 262.24 1.37E-24 15845730000 6384537 5372624 5719126 4910018 4460443 5742468 6220908 6877593 8800060 7461850 FALSE TRUE 6135022.236 5219402.024 6752699.289 5163424.617 4603917.2 5858584.637 6297041.333 6735568.301 7801114.082 6956452.253 0.881918255 0.750296535 0.970710219 0.742249703 0.661819708 0.842179954 0.905208733 0.968247615 1.121421351 1 22.7299203 1.7976027 1.713461917 1.05473639 0.803959067 0.584040916 0.085068854 0.248335745 1.408397222 0.061629891 0.025840269 62.74840638 -1.7976027 -0.250777323 KRQDCS(ph)SSDTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KRQDCSSSDTEK 12 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 1 KRQDCS(0.598)S(0.201)S(0.201)DTEK;KRQDCS(0.333)S(0.333)S(0.333)DT(0.002)EK 141.55 4.77E-05 75680000 97881 71600 65423 60558 69313 69078 76816 83695 96341 89452 TRUE FALSE 94055.70231 69558.0381 77246.39143 63683.40564 71542.51559 70474.80449 77756.09719 81966.669 85404.77357 83393.33636 1.12785633 0.834095878 0.926289735 0.763651011 0.857892473 0.845089159 0.932401803 0.98289231 1.024119879 1 16.34764449 1.797660913 2.425197445 1.008634255 0.884292485 0.225070705 0.090203325 0.385114844 4.379415314 0.053884137 0.024995096 62.75681764 -1.797660913 -0.124341769 TIQFVDWCPTGFK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIQFVDWCPTGFK 13 0 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ; 221.8 4.31E-11 282990000 578870 569630 477030 489690 492190 485710 541490 578380 639650 627980 FALSE TRUE 556247.1204 553384.7101 563239.9325 514962.9596 508021.7383 495531.389 548116.9166 566436.2509 567039.6136 585446.3553 0.950124833 0.945235554 0.962069244 0.879607423 0.867751133 0.846416387 0.936237644 0.967528871 0.968559474 1 19.15917746 1.797712578 3.08199222 0.977929928 0.90866954 0.423895168 0.036278179 0.273863507 4.880379275 0.022712091 0.01127921 62.76428386 -1.797712578 -0.069260388 ARS(ph)RT(ph)PPSAPSQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSRTPPSAPSQSR 14 2 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ARS(0.994)RT(0.935)PPS(0.05)APS(0.01)QS(0.011)R 68.168 0.055782 137790000 67314 72104 48707 54736 68028 75603 63747 57715 67375 59465 TRUE FALSE 64683.29446 70047.66452 57509.43838 57560.93152 70216.1824 77131.74446 64527.15485 56523.16508 59726.87246 55437.38258 1.166781176 1.263545666 1.037376508 1.038305361 1.266585454 1.391330919 1.163964672 1.019585746 1.077375404 1 15.75857152 1.797752402 5.202908353 1.036928179 1.192759142 0.338412681 0.101127474 0.269353336 13.39405614 0.052939985 0.029587498 62.77003947 -1.797752402 0.155830963 QTDFEHR ddPTM_BT-474_Pertuzumab_2h_R1 3 QTDFEHR 7 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;; 143.73 0.0024017 2654870000 4225870 4631500 3532630 4433830 4306360 4174990 3984940 3792180 4070170 3648070 FALSE TRUE 4060718.328 4499414.155 4171054.824 4662660.498 4444877.98 4259411.158 4033708.888 3713870.158 3608141.365 3400982.97 1.193983729 1.322974621 1.22642626 1.370974374 1.306939206 1.252405906 1.186042072 1.091999046 1.06091133 1 21.69752035 1.797838064 1.271784115 1.01940083 1.288503942 0.827546328 0.047432484 0.163229326 0.493931276 0.037079974 0.014973986 62.78242168 -1.797838064 0.269103113 TFTEMDSHEEK ddPTM_BT-474_Pertuzumab_2h_R1 6 TFTEMDSHEEK 11 0 B0YIW6;P48444;P48444-2;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;;; 206.11 2.75E-08 6733630000 8857840 8646380 7149710 7813420 8559770 8337350 9106900 8873570 10767000 10140580 FALSE TRUE 8511665.82 8399793.708 8441821.641 8216671.543 8835102.776 8505936.929 9218352.966 8690327.679 9544775.299 9453749.484 0.900348146 0.888514522 0.892960159 0.869144201 0.934560704 0.899742155 0.975100195 0.919246664 1.009628541 1 23.1724552 1.797953255 0.608140069 1.004164409 0.887493303 0.711983767 0.025166854 0.3869366 0.299935468 0.022260032 0.0127514 62.79907623 -1.797953255 -0.116671106 DDAT(ph)PVRDEPMDAESITFK ddPTM_BT-474_Pertuzumab_2h_R1 4 DDATPVRDEPMDAESITFK 19 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 DDAT(1)PVRDEPMDAESITFK;DDAT(1)PVRDEPMDAESITFK;DDAT(1)PVRDEPMDAESITFK;DDAT(1)PVRDEPMDAESITFK 302.77 7.36E-50 2211560000 2590790 2272280 2513280 2668150 2641720 2428010 3045990 3263600 3780340 3783630 TRUE FALSE 2489539.063 2207476.799 2967485.604 2805853.541 2726693.323 2477106.026 3083267.737 3196205.52 3351211.652 3527361.37 0.70577942 0.625815324 0.841276323 0.795453952 0.773012186 0.702254679 0.87410033 0.906117969 0.950061902 1 21.75015795 1.797972383 1.108628851 0.989542786 0.739082049 0.724571005 0.059253261 0.268289034 0.611200514 0.051987746 0.021263861 62.80184209 -1.797972383 -0.250460737 WEGGDS(ph)NSDDYDLESDMSNGWDPNEMFK ddPTM_BT-474_Pertuzumab_2h_R1 1 WEGGDSNSDDYDLESDMSNGWDPNEMFK 28 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 WEGGDS(0.352)NS(0.352)DDY(0.296)DLESDMSNGWDPNEMFK 89.297 9.14E-07 0 25942 23705 20326 24061 25596 20532 24231 29472 32945 25581 TRUE FALSE 24928.15796 23028.95661 23999.36035 25302.79109 26419.31859 20947.17111 24527.54623 28863.3929 29205.22172 23848.37608 1.045276956 0.96564045 1.006331008 1.060985914 1.107803671 0.878347902 1.028478675 1.21028756 1.224620981 1 14.54160341 1.798020165 7.409795987 1.164116691 1.011004361 0.350083718 0.081036651 0.230140778 23.99448785 0.035233815 0.020809291 62.80875213 -1.798020165 -0.15311233 AFLQAILEHEEENEEEDEVPDDETLNQMIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFLQAILEHEEENEEEDEVPDDETLNQMIAR 31 0 F6VDE0;P51531-2;P51531;A0A0U1RQZ9 F6VDE0 SMARCA2 Probable global transcription activator SNF2L2 0 168.72 1.01E-12 36248000 15409 15089 14116 16820 15245 17516 15742 13608 16169 14608 FALSE TRUE 14806.79924 14658.67649 16667.07521 17688.08222 15735.36927 17870.18552 15934.6553 13326.99004 14333.56291 13618.58715 1.087249293 1.076372779 1.223847601 1.298819182 1.155433313 1.312190856 1.170066699 0.9785883 1.052499995 1 13.73328942 1.798074326 5.725235852 1.011962105 1.194893844 0.545940874 0.074727813 0.164432743 10.02294733 0.03705538 0.021081245 62.81658544 -1.798074326 0.18293174 YSQKEDKYEEEIK ddPTM_BT-474_Pertuzumab_2h_R1 5 YSQKEDKYEEEIK 13 2 P06753-2;P06753-6;P06753-5;P06753-7;A0A494C034;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;; 190.44 2.48E-06 15207060000 7685970 6195640 4992260 4016000 5705210 6052000 6115600 8037130 9525210 7340470 FALSE TRUE 7385593.795 6018946.413 5894472.434 4223266.241 5888723.261 6174375.587 6190444.542 7871160.457 8443948.094 6843293.429 1.079245523 0.879539432 0.86135024 0.617139435 0.860510122 0.902252059 0.904600191 1.150200636 1.233901218 1 22.70625938 1.798174503 3.522797982 1.146682674 0.858272358 0.496007706 0.117907479 0.181377158 4.140373984 0.064321608 0.033052215 62.83107689 -1.798174503 -0.288410316 KQELVAELDQDEKDQQNTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQELVAELDQDEKDQQNTSR 20 2 O43318;Q9UG54;O43318-2 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 0 ; 164.65 1.00E-11 428840000 304320 263760 243390 220098 268190 270870 289690 316090 384370 349300 FALSE TRUE 292426.838 256237.823 287375.9872 231457.2842 276816.5749 276347.177 293235.3129 309562.631 340737.929 325641.5999 0.898002092 0.786870667 0.882491633 0.710773084 0.850065148 0.848623693 0.900484806 0.950623726 1.046358724 1 18.31292549 1.798197337 1.322919981 1.023102654 0.822019243 0.69587753 0.051275805 0.222311152 0.730760069 0.038628112 0.015607389 62.83438043 -1.798197337 -0.201083412 WCDKSDEDDWSKPLPPSER ddPTM_BT-474_Pertuzumab_2h_R1 3 WCDKSDEDDWSKPLPPSER 19 2 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;; 182.15 1.68E-14 1461620000 945773 829722 682611 645143 767201 805649 839367 1015470 1183600 1064950 FALSE TRUE 908811.1456 806059.1409 805973.9923 678438.9075 791878.7169 821939.7748 849639.4244 994500.1896 1049242.69 992819.9879 0.915383611 0.81188851 0.811802746 0.683345335 0.797605534 0.827883992 0.855783964 1.001692353 1.056830748 1 19.92117264 1.798208815 2.175855053 1.033836728 0.801897491 0.753434765 0.054313456 0.143842961 1.324533861 0.036254323 0.016275593 62.83604108 -1.798208815 -0.231939237 SEDPPT(ph)TPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDPPTTPIR 10 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0;H7C151 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEDPPT(0.714)T(0.286)PIR 94.616 0.089231 636910000 606590 640890 535110 672480 721920 676240 573940 557480 500440 557070 TRUE FALSE 582883.7922 622612.4447 631816.2805 707186.7734 745141.2124 689914.0361 580964.0494 545967.8432 443632.1492 519339.1527 1.122356728 1.198855202 1.216577408 1.361705101 1.434787284 1.328446031 1.118660217 1.051274182 0.854224348 1 18.98631747 1.798239547 1.966743792 0.939573831 1.279231553 0.683632726 0.094549224 0.194931501 1.467225399 0.069378769 0.030210944 62.84048778 -1.798239547 0.339657723 EGSVIDHIHLISVGDMIEAINGQSLLGCR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGSVIDHIHLISVGDMIEAINGQSLLGCR 29 0 O14908;O14908-2;K7ESN1;K7EIT0 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 251.37 2.48E-47 472660000 301730 371820 354180 462300 397730 424410 399650 64451 460980 306400 FALSE TRUE 289938.058 361216.0576 418188.2047 486159.3584 410523.3467 432991.861 404541.0362 63120.06433 408651.483 285647.2551 1.015021334 1.264552875 1.464002182 1.701957046 1.437168883 1.515827137 1.416225884 0.220972067 1.430615823 1 18.12387514 1.798502203 25 0.7994635 1.416453299 0.33979783 0.324271411 160.6746993 67028.95137 0.136809745 0.082497103 62.8785043 -1.798502203 0.6169898 GADS(ph)GEEKEEGINREDK ddPTM_BT-474_Pertuzumab_2h_R1 5 GADSGEEKEEGINREDK 17 2 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK 226.99 9.91E-16 6060820000 3486300 2598490 2537070 2313240 2782620 2583980 2978840 3591590 4250370 3675670 TRUE FALSE 3350051.542 2524383.609 2995574.986 2432626.594 2872125.499 2636229.846 3015295.935 3517422.411 3767885.817 3426713.597 0.977628111 0.736677735 0.874183062 0.709900762 0.838157441 0.76931724 0.879938124 1.026471081 1.099562514 1 21.70839419 1.798554623 2.788371625 1.054168295 0.812939282 0.644089684 0.074477816 0.140423885 2.075286302 0.039555121 0.019128499 62.88609433 -1.798554623 -0.241229013 APAKES(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 3 APAKESPPK 9 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 APAKES(1)PPK;APAKES(1)PPK;APAKES(1)PPK 89.301 0.0073884 1712430000 4063060 3001690 3393090 2837220 3324370 3606610 4184950 4973910 6500310 5740930 TRUE FALSE 3904271.123 2916084.74 4006296.842 2983649.264 3431301.38 3679538.125 4236166.67 4871197.02 5762422.06 5352091.698 0.729485096 0.544849548 0.74854787 0.557473495 0.641114087 0.687495344 0.791497401 0.910148274 1.076667289 1 22.3516714 1.798557424 1.402162741 1.040240361 0.640905459 0.852300853 0.065267393 0.130888118 0.486417605 0.046688829 0.018932809 62.88649988 -1.798557424 -0.399334902 EGS(ph)PAPLEPEPGAAQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGSPAPLEPEPGAAQPK 17 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK 237.51 4.12E-19 0 759193 585354 508286 502431 560249 547159 603666 797906 871408 739070 TRUE FALSE 729522.8982 568660.277 600144.587 528361.5241 578269.9179 558222.9299 611053.8451 781428.9623 772489.4171 689012.1306 1.058795435 0.825326945 0.871021801 0.766839219 0.839273929 0.810178668 0.886854988 1.13412947 1.121155032 1 19.39416986 1.798582865 5.321136183 1.095327649 0.85548583 0.609761994 0.080287922 0.123940939 6.428009934 0.037238086 0.020921958 62.89018391 -1.798582865 -0.239841819 GGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDAR 42 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 255.4 6.06E-67 527040000 139577 154136 135264 171941 169035 176550 164694 64017 168841 169867 FALSE TRUE 134122.1765 149740.1922 159709.2137 180814.8956 174472.1643 180119.962 166709.5744 62695.02658 149674.8775 158361.7568 0.846935392 0.945557786 1.008508727 1.141783845 1.10173168 1.137395578 1.052713596 0.395897519 0.945145347 1 17.27286445 1.798757368 25 0.714349011 1.039956276 0.282935173 0.175292377 165.9678808 68943.53227 0.074300486 0.044902041 62.91545882 -1.798757368 0.325607264 S(ph)AS(ph)PPPATSSSSSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SASPPPATSSSSSSR 15 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 S(0.999)AS(0.974)PPPAT(0.02)S(0.005)S(0.001)SSSSR;S(1)AS(1)PPPATSSSSSSR 92.952 0.0073743 94458000 210903 212943 191661 206995 203434 219635 207286 190437 210447 206048 TRUE FALSE 202660.6776 206870.0741 226298.4062 217678.0368 209977.6394 224076.1702 209822.8281 186504.4094 186557.9388 192092.1854 1.055017814 1.076931233 1.178071902 1.133195691 1.093108701 1.16650331 1.09230278 0.970910966 0.971189632 1 17.5514393 1.798891211 4.187983857 0.97797007 1.118339172 0.738064513 0.036418025 0.107052561 3.39319627 0.018906197 0.010117451 62.93485138 -1.798891211 0.140369103 RKPEEES(ph)PRK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKPEEESPRK 10 3 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 RKPEEES(1)PRK;RKPEEES(1)PRK 101.53 0.018055 242951000 389550 291476 320296 319421 353982 302613 379860 463910 529120 520680 TRUE FALSE 374325.9553 283163.3899 378180.6121 335906.3561 365368.1525 308732.0422 384508.8403 454330.0964 469056.5159 485413.8798 0.771148026 0.583344238 0.779088996 0.6919999 0.752694078 0.636018159 0.792125764 0.93596437 0.966302233 1 18.88885584 1.798946201 2.38009331 0.977401595 0.702056729 0.806599985 0.058072022 0.107549331 1.17818181 0.033086101 0.015277206 62.94282069 -1.798946201 -0.275344866 NGIHDLDNISFPK ddPTM_BT-474_Pertuzumab_2h_R1 4 NGIHDLDNISFPK 13 0 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ;;; 151.44 4.23E-05 2046850000 3624890 3374800 3237720 3298440 3507400 3259590 3775020 4118380 4938660 4413490 FALSE TRUE 3483225.291 3278554.008 3822848.027 3468672.884 3620218.706 3325501.143 3821219.824 4033334.014 4378044.021 4114560.391 0.84656074 0.796817569 0.929102422 0.843023933 0.879855528 0.808227569 0.928706705 0.980258796 1.064036885 1 21.97230687 1.799036877 2.072552666 1.028144746 0.853117266 0.774137902 0.039765241 0.133153014 1.11277424 0.024880183 0.011012676 62.95596378 -1.799036877 -0.17502748 IEQLQNHENEDIYK ddPTM_BT-474_Pertuzumab_2h_R1 4 IEQLQNHENEDIYK 14 0 O00629;H7C4F6 O00629 KPNA4 Importin subunit alpha-3 0 ;;; 266.28 7.52E-25 4972560000 3666130 3415710 3059690 3011530 3319990 3372160 3625170 3825890 4580180 4196490 FALSE TRUE 3522853.586 3318297.295 3612644.045 3166955.424 3426780.493 3440347.386 3669535.915 3746884.035 4060257.168 3912257.994 0.90046556 0.848179568 0.923416618 0.809495547 0.875908618 0.879376409 0.93795857 0.957729281 1.037829605 1 21.89957008 1.799057616 1.356310219 1.016476885 0.86969053 0.767992916 0.031694902 0.183031164 0.634014051 0.023544366 0.009528427 62.95897017 -1.799057616 -0.146786355 SMEMLVEHQAHDILT ddPTM_BT-474_Pertuzumab_2h_R1 4 SMEMLVEHQAHDILT 15 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;; 105.46 0.0013133 2052310000 1258800 1271960 1199950 1387120 1440630 1419590 1390310 264817 1463030 1287730 FALSE TRUE 1209604.704 1235684.946 1416807.658 1458709.429 1486969.172 1448295.082 1407325.03 259348.4364 1296952.968 1200510.9 1.007574945 1.029299231 1.18017059 1.215073873 1.238613637 1.206398944 1.172271763 0.216031721 1.080334188 1 20.19521707 1.799148958 25 0.679951223 1.154529762 0.352485954 0.230138206 146.1690772 60326.51111 0.09493784 0.057565928 62.97221334 -1.799148958 0.474578539 NQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 NQKPSQVNGAPGSPTEPAGQK 21 1 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 NQKPSQVNGAPGS(0.985)PT(0.015)EPAGQK 237.67 4.39E-30 3632300000 1844200 1448800 1405500 1340400 1348900 1463400 1557300 1838600 2054700 1917800 TRUE FALSE 1772126.625 1407481.643 1659505.115 1409578.205 1392288.594 1492990.951 1576358.703 1800632.267 1821459.07 1787905.698 0.99117455 0.787223646 0.928183806 0.788396282 0.778725967 0.835050167 0.881678886 1.007118144 1.018766858 1 20.76983921 1.799328214 3.164632458 1.012827539 0.846395009 0.556043743 0.062892475 0.167605459 3.127494744 0.033512319 0.016780887 62.99821061 -1.799328214 -0.16643253 VVESPDFSKDEDYLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVESPDFSKDEDYLGK 16 1 Q9Y6Y8 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 145.55 1.10E-06 78725000 63705 63805 54892 53971 63092 73105 66613 78284 87008 91939 FALSE TRUE 61215.33817 61985.34387 64812.20547 56756.44978 65121.41148 74583.23319 67428.22982 76667.40804 77131.21661 85711.88964 0.71419891 0.723182561 0.756163535 0.662177091 0.759771039 0.870162045 0.786684672 0.894478098 0.899889349 1 16.38720772 1.799331168 0.493458526 0.999301498 0.701951341 0.844757185 0.039273971 0.323784076 0.185192655 0.040119954 0.028552773 62.9986391 -1.799331168 -0.297350156 HPDGRPTGDAFALFACEELAQAALR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPDGRPTGDAFALFACEELAQAALR 25 1 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 0 115.55 0.00090634 85804000 36825 40952 33663 46152 41899 45597 40259 38017 39420 42152 FALSE TRUE 35385.83829 39784.08906 39746.65293 48533.91025 43246.71939 46519.00258 40751.70168 37231.93566 34945.20686 39297.00749 0.900471576 1.012394877 1.011442231 1.235053592 1.100509228 1.183779772 1.037017938 0.947449642 0.889258727 1 15.26213183 1.799377794 3.645526387 0.937818888 1.078635856 0.279050832 0.091307643 0.291445086 7.072539222 0.050650478 0.026269287 63.00540309 -1.799377794 0.140816969 LTSS(ph)CPDLPSQTDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTSSCPDLPSQTDKK 15 1 P56962 P56962 STX17 Syntaxin-17 1 LT(0.017)S(0.118)S(0.865)CPDLPSQTDKK 144.97 2.54E-06 790280000 613310 494060 300200 352370 426570 441430 456200 577680 643930 581480 TRUE FALSE 589341.1671 479969.8925 354452.8179 370555.8579 440291.0115 450356.017 461783.1121 565750.7061 570833.766 542095.8417 1.087153086 0.885396743 0.653856368 0.683561521 0.812201418 0.830768256 0.85184773 1.043635945 1.053012626 1 19.04818841 1.799379156 3.540830241 1.038636945 0.814943389 0.408186389 0.111631119 0.230980005 5.307640712 0.063451294 0.032679199 63.00560069 -1.799379156 -0.223693556 DGIEPMWEDEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DGIEPMWEDEK 11 0 D6RBW1;P06730;P06730-3;P06730-2;H0Y8J7 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;;; 232.84 8.34E-14 822730000 1289190 1200350 1137190 1089310 1259650 1223240 1302030 1520650 1734110 1638860 FALSE TRUE 1238807.03 1166117.193 1342705.53 1145529.42 1300167.786 1247974.751 1317964.633 1489248.046 1537261.103 1527858.552 0.810812642 0.763236355 0.878815338 0.749761434 0.850973923 0.816813015 0.862622152 0.974729005 1.006154071 1 20.54307956 1.79939916 1.891495237 1.006890594 0.810169847 0.84422383 0.035095599 0.109999583 0.764335778 0.022307316 0.009614496 63.00850278 -1.79939916 -0.196720748 IVDS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 3 IVDSPEK 7 0 E9PQC4;Q9BZD4 E9PQC4 NUF2 Kinetochore protein Nuf2 1 IVDS(1)PEK;IVDS(1)PEK;IVDS(1)PEK 176.38 0.00079089 1737770000 2559560 2323860 2904450 2683730 2783150 2754420 3247950 3739000 4604140 4294880 TRUE FALSE 2459529.565 2257585.788 3429348.724 2822237.627 2872672.547 2810116.26 3287699.384 3661788.343 4081497.329 4003983.952 0.614270585 0.563834874 0.856484133 0.704857377 0.717453562 0.701830051 0.821107033 0.914536219 1.019359063 1 21.93300476 1.799603414 1.285251928 1.017688027 0.690150019 0.763400034 0.072130908 0.21525044 0.665737728 0.059847184 0.024194345 63.03814341 -1.799603414 -0.327538008 KRES(ph)ES(ph)ESDETPPAAPQLIK ddPTM_BT-474_Pertuzumab_2h_R1 4 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.957)ES(0.961)ES(0.082)DETPPAAPQLIK;KRES(0.5)ES(0.5)ES(0.5)DET(0.5)PPAAPQLIK;KRES(0.935)ES(0.962)ES(0.075)DET(0.027)PPAAPQLIK;KRES(0.995)ES(0.947)ES(0.059)DETPPAAPQLIK 213.57 2.99E-22 3752090000 3547940 3072990 2766270 2364260 2641120 2953880 3087020 3914630 4440460 3921370 TRUE FALSE 3409282.582 2985351.334 3266196.524 2486279.742 2726074.023 3013609.477 3124799.874 3833791.523 3936397.597 3655772.117 0.932575246 0.816613082 0.893435482 0.680097025 0.745690359 0.824342815 0.854757839 1.048695433 1.076762301 1 21.80174471 1.799759657 3.300770191 1.05051622 0.811228128 0.688068114 0.068343483 0.132951153 2.67938313 0.03852899 0.019508796 63.06082633 -1.799759657 -0.239288092 S(ph)PYSGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPYSGPK 7 0 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 S(0.996)PYS(0.004)GPK;S(0.999)PYS(0.001)GPK 98.582 0.011703 2039840000 2250900 1972770 1764720 1830890 1730400 1794430 1971760 2566000 2591100 2530500 TRUE FALSE 2162932.339 1916508.531 2083644.16 1925382.452 1786059.888 1830714.604 1995890.989 2513011.203 2296969.191 2359106.981 0.916843686 0.812387292 0.883234282 0.816148851 0.757091519 0.776020172 0.846036659 1.06523834 0.973660461 1 21.16980941 1.799768788 6.590540175 1.015178255 0.824894423 0.747383265 0.048822021 0.105875512 8.556504773 0.022694855 0.013239947 63.0621522 -1.799768788 -0.190283832 VDIEGPDVNIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDIEGPDVNIEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 347.73 9.37E-87 356850000 684230 730830 653290 678420 629060 685250 710720 871160 950570 843390 FALSE TRUE 657489.5351 709987.444 771354.0354 713433.3375 649294.2862 699106.2245 719418.004 853170.2416 842665.2787 786266.4441 0.836217214 0.902985813 0.981033899 0.907368415 0.825794222 0.889146713 0.914979915 1.085090491 1.071729927 1 19.58465876 1.79978493 5.194344431 1.058611031 0.894079567 0.720980279 0.045170952 0.109361292 5.344002406 0.022528395 0.012618363 63.06449618 -1.79978493 -0.164531464 DQVLHEHIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DQVLHEHIQR 10 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ; 151.98 1.09E-05 1360210000 874030 915780 772520 863610 889140 969720 935940 15816.1 1004070 789070 FALSE TRUE 839871.9413 889662.851 912131.5486 908181.0156 917739.9956 989328.4028 947394.3137 15489.49201 890092.183 735625.5861 1.14171116 1.209396285 1.239939945 1.234569641 1.247563996 1.34488036 1.287875696 0.021056217 1.209979914 1 19.48861213 1.799803353 25 0.636892536 1.245929696 0.362420909 0.29384444 142.9625688 58372.51048 0.118517358 0.072254564 63.06717133 -1.799803353 0.60903716 RNPDTQWITKPVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNPDTQWITKPVHK 14 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 190.87 3.32E-07 6286200000 6834900 7590400 6053600 6082800 6586200 7210800 7187100 7610000 8849000 8440800 FALSE TRUE 6567784.552 7373929.224 7147620.182 6396734.037 6798051.104 7356607.317 7275057.88 7452850.841 7844498.618 7869097.098 0.834630005 0.937074372 0.908315159 0.812893011 0.863892137 0.934873115 0.924509863 0.947103683 0.99687404 1 22.90776668 1.800271047 0.932956115 1.001341272 0.876221006 0.63792385 0.035833475 0.377684358 0.611749306 0.032426444 0.013938119 63.1351253 -1.800271047 -0.125120266 SECDS(ph)SPEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.657)S(0.343)PEPK;SECDS(0.657)S(0.343)PEPK 196.11 3.56E-07 399940000 1315910 1151180 955570 966970 974330 989530 1125990 1328550 1486860 1388020 TRUE FALSE 1264482.782 1118349.474 1128262.756 1016875.438 1005670.209 1009538.975 1139770.202 1301114.978 1318077.886 1294008.169 0.977182998 0.864252251 0.871913163 0.785833862 0.777174544 0.780164298 0.880806033 1.00549209 1.0186009 1 20.30341529 1.800300217 3.450406114 1.011200832 0.83902764 0.634479317 0.056040286 0.153140597 3.346363977 0.032176317 0.0164805 63.13936604 -1.800300217 -0.172173192 FRPAGAAPRPPPKPM ddPTM_BT-474_Pertuzumab_2h_R1 2 FRPAGAAPRPPPKPM 15 3 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ; 110.51 0.0011196 1667140000 918350 905360 883660 854370 983870 991380 922350 818700 895540 934500 FALSE TRUE 882459.8667 879540.0192 1043357.019 898464.1381 1015517.072 1011426.383 933637.9952 801793.5589 793882.0536 871205.4826 1.012918174 1.009566671 1.19760153 1.031288434 1.165645869 1.160950434 1.071662213 0.920326576 0.911245475 1 19.73265351 1.800406131 4.75361434 0.937123736 1.098216391 0.519422825 0.065704859 0.159489284 6.463957261 0.032346951 0.017812332 63.15476606 -1.800406131 0.161092654 QIEETLAHFHLTK ddPTM_BT-474_Pertuzumab_2h_R1 3 QIEETLAHFHLTK 13 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;; 268.9 4.27E-25 1174447000 1853683 2027101 1608812 2321873 1826347 1892271 2015748 68446.7 2241110 1601402 FALSE TRUE 1781239.019 1969290.064 1899560.116 2441705.144 1885093.11 1930534.016 2040417.327 67033.25173 1986708.588 1492937.616 1.193110147 1.319070565 1.272364026 1.6355038 1.262673731 1.293110975 1.366713053 0.044900236 1.330737847 1 20.50972245 1.800561901 25 0.687793742 1.338860559 0.358885923 0.323556696 147.6828748 59561.89664 0.130505512 0.080047124 63.17742216 -1.800561901 0.651066817 DKDPVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDPVNK 7 1 P62851;E9PQK3;E9PK60 P62851 RPS25 40S ribosomal protein S25 0 ; 93.143 0.013818 2605800000 8007700 6562400 6146500 5165000 6102200 6488900 6730900 7737700 8783200 8034700 FALSE TRUE 7694750.231 6375246.777 7257309.278 5431566.269 6298482.805 6620110.004 6813274.768 7577913.791 7786167.958 7490502.612 1.027267545 0.851110681 0.968868133 0.725127078 0.840862507 0.883800507 0.909588464 1.011669601 1.03947203 1 22.8366311 1.80068949 2.68570496 1.023658261 0.876761249 0.387573191 0.075485364 0.259639506 3.567524966 0.043984866 0.021082386 63.19598539 -1.80068949 -0.146897012 YKDPQDENK ddPTM_BT-474_Pertuzumab_2h_R1 4 YKDPQDENK 9 1 C9JVE2;Q96GG9;C9J8R4;C9JRU6;C9J0B2;C9JRE2;C9JAV2;H7C216;Q6PH85-2;Q6PH85 C9JVE2 DCUN1D1;DCUN1D2 DCN1-like protein;DCN1-like protein 1;DCN1-like protein 2 0 ;;; 115.18 0.0013849 1958120000 5146680 4453930 3859050 3526970 3960950 3764550 4574120 5464290 6409620 5736330 FALSE TRUE 4945542.056 4326908.277 4556466.179 3708997.344 4088357.554 3840671.78 4630099.449 5351450.502 5682026.809 5347803.26 0.924780104 0.809100123 0.852025768 0.693555309 0.764492887 0.718177463 0.86579465 1.000682008 1.062497353 1 22.35051496 1.800812238 2.822938052 1.030578998 0.791240835 0.717763176 0.063616005 0.13458845 2.028547734 0.037612921 0.018286637 63.21384946 -1.800812238 -0.239338163 DMS(ph)PLSETEMALGK ddPTM_BT-474_Pertuzumab_2h_R1 12 DMSPLSETEMALGK 14 0 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMS(1)PLSETEMALGK;DMS(0.971)PLS(0.029)ETEMALGK;DMS(1)PLSETEMALGK;DMS(0.998)PLS(0.002)ET(0.001)EMALGK;DMS(0.998)PLS(0.002)ET(0.001)EMALGK;DMS(0.993)PLS(0.004)ET(0.003)EMALGK;DMS(1)PLSETEMALGK;DMS(0.997)PLS(0.003)ETEMALGK;DMS(1)PLSETEMALGK;DMS(0.999)PLS(0.001)ETEMALGK;DMS(1)PLSETEMALGK;DMS(0.999)PLS(0.001)ETEMALGK 353.65 5.38E-82 3278638000 5378513 4829673 4745507 4716952 5069215 5023182 5499227 5854889 6799390 6512440 TRUE FALSE 5168314.766 4691935.455 5603125.678 4960394.458 5232270.904 5124754.182 5566528.185 5733983.496 6027551.753 6071346.638 0.851263331 0.772799798 0.922880213 0.817017172 0.861797426 0.84408855 0.916852309 0.944433556 0.992786627 1 22.53358511 1.800883324 1.132965087 1.001731078 0.841060592 0.742340986 0.036192788 0.225164906 0.536020966 0.028362574 0.011580299 63.22419728 -1.800883324 -0.160670486 SEENTKEEKPDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEENTKEEKPDSK 13 2 P50502;Q3KNR6;Q8NFI4;F6VDH7;Q8IZP2 P50502 ST13;ST13P5;ST13P4 Hsc70-interacting protein;Putative protein FAM10A5;Putative protein FAM10A4 0 ; 132.65 6.55E-05 3296700000 4456900 3549000 2992700 2328970 3237300 3200900 3638800 4386500 5507200 4265800 FALSE TRUE 4282719.421 3447785.995 3533547.462 2449168.421 3341430.695 3265624.391 3683332.723 4295917.242 4882045.744 3976873.566 1.076906105 0.866958916 0.888523963 0.615852724 0.84021547 0.821153687 0.926188037 1.080224747 1.22760899 1 21.92320327 1.800978246 2.593187829 1.124116414 0.843842861 0.478221866 0.116862336 0.219068564 2.817778678 0.07012671 0.033279782 63.23801747 -1.800978246 -0.280273553 AEDGENYDIKK ddPTM_BT-474_Pertuzumab_2h_R1 6 AEDGENYDIKK 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;;;; 198.55 8.55E-08 9850790000 9670610 8565880 7327920 7220490 8085770 8568320 8615550 10659470 11693570 10655480 FALSE TRUE 9292671.87 8321589.489 8652238.153 7593140.354 8345856.135 8741577.301 8720989.678 10439348.22 10366164.96 9933774.849 0.9354623 0.837706674 0.870991973 0.764376128 0.840149516 0.879985447 0.87791296 1.050894386 1.043527271 1 23.24391062 1.801167058 4.052618143 1.036189714 0.852020184 0.778064493 0.042449456 0.09539562 2.813782284 0.021918407 0.011668716 63.26551649 -1.801167058 -0.18416953 AQNDLIWNIKDELKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQNDLIWNIKDELKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 244.58 2.72E-18 4667500000 5306400 4121300 3713500 3280000 4006300 4187400 4270000 5128700 5775200 5107500 FALSE TRUE 5099020.021 4003764.559 4384612.056 3449281.193 4135166.278 4272072.097 4322257.537 5022790.553 5119623.508 4761564.476 1.070870729 0.840850645 0.920834335 0.724400816 0.868446978 0.897199254 0.90773895 1.054861397 1.07519777 1 22.18300424 1.801241671 3.572701708 1.050335342 0.879719166 0.420113496 0.082268864 0.205341704 4.77601434 0.042945444 0.022201464 63.27638662 -1.801241671 -0.170616176 ASLEQLLQVLHSTTPHYIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASLEQLLQVLHSTTPHYIR 19 0 Q96H55;Q96H55-3 Q96H55 MYO19 Unconventional myosin-XIX 0 137.69 1.95E-06 51957000 44771 50690 43942 51077 49461 55504 52077 21370 54610 52810 FALSE TRUE 43021.29982 49244.37083 51883.29688 53713.09009 51051.95798 56626.32891 52714.3339 20928.70203 48410.90174 49233.13166 0.87382822 1.000228285 1.053828898 1.090994789 1.036943137 1.150167113 1.070708527 0.425093861 0.983299256 1 15.58734189 1.801355449 25 0.739831922 1.044702489 0.280201426 0.16470748 162.0872596 64544.98737 0.067147152 0.041432075 63.29296616 -1.801355449 0.304870567 VLEENQEHYHIVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLEENQEHYHIVQK 14 0 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 ; 200.16 1.14E-08 654740000 579940 629450 477770 602720 613680 691310 621250 64620 713030 477540 FALSE TRUE 557275.3036 611498.7023 564113.6669 633826.4514 633419.5745 705288.7619 628853.0433 63285.57442 632089.8237 445195.7905 1.251753309 1.373550055 1.267113659 1.423702706 1.422788778 1.584221542 1.412531423 0.14215223 1.419801888 1 18.76408043 1.801388223 25 0.760566654 1.395322092 0.378763824 0.308126358 143.8017468 57233.60913 0.124055202 0.076564836 63.29774277 -1.801388223 0.634755437 LVNACLAEELPHIHAFEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVNACLAEELPHIHAFEQK 19 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 188.84 8.85E-15 454150000 476920 458940 366660 413300 459000 472420 448670 33139 558180 278020 FALSE TRUE 458281.4391 445851.4805 432923.6183 434630.4625 473764.1519 481972.6561 454160.9577 32454.66807 494817.7465 259189.4578 1.768133022 1.720175984 1.670297944 1.676883259 1.827868139 1.859538039 1.752235456 0.125216004 1.909096731 1 17.98364751 1.801478116 24.99999996 0.916729435 1.753083748 0.406550687 0.406093055 141.9744494 56425.58446 0.161439128 0.099701211 63.31084585 -1.801478116 0.836354312 LLQHGINADDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLQHGINADDKR 12 1 Q96P70 Q96P70 IPO9 Importin-9 0 ; 137.16 6.31E-05 967610000 1837870 1106960 1084580 888670 1257380 1152750 1258960 1495560 1729960 1402550 FALSE TRUE 1766044.009 1075390.585 1280587.732 934534.3652 1297824.77 1176059.395 1274367.529 1464676.163 1533582.193 1307554.039 1.350647052 0.822444467 0.979376526 0.714719497 0.992559184 0.899434639 0.974619397 1.120164918 1.172863337 1 20.31843914 1.801488661 4.310615093 1.109829098 0.944605789 0.126056029 0.159569811 0.367720996 12.20436106 0.07613 0.041102825 63.31238311 -1.801488661 -0.165223308 T(ph)AS(ph)PPPPPKR ddPTM_BT-474_Pertuzumab_2h_R1 5 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR 99.732 0.0038907 8869310000 5244150 5127790 4161620 4526450 4591270 4940540 4865560 5137290 5849600 5347710 TRUE FALSE 5039202.82 4981550.45 4913717.309 4760060.627 4738952.369 5040441.104 4925106.179 5031203.166 5185577.932 4985504.838 1.010770821 0.999206823 0.98560075 0.954780064 0.950546138 1.011019198 0.987885147 1.009166239 1.04013096 1 22.24930817 1.801702851 1.655932617 1.020432566 0.982658521 0.309726094 0.021211644 0.44339762 2.337814203 0.016266647 0.006789541 63.34361596 -1.801702851 -0.037774045 SKQPPPAS(ph)SPTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKQPPPASSPTKR 13 2 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 SKQPPPAS(0.504)S(0.493)PT(0.003)KR 87.388 0.004378 366540000 403280 344770 296410 267100 321560 293050 333270 373790 413090 388490 TRUE FALSE 387519.3718 334937.4972 349977.8806 280885.063 331903.2694 298975.6718 337348.658 366071.1059 366197.755 362177.2263 1.06997167 0.924788951 0.966316641 0.7755459 0.916411208 0.825495504 0.931446357 1.01075131 1.011100998 1 18.46633631 1.801779394 4.234994887 1.008233476 0.907941415 0.243339503 0.073893461 0.299835905 9.603883876 0.037610117 0.020232381 63.35478104 -1.801779394 -0.100292061 VWCDGCYDMVHYGHSNQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VWCDGCYDMVHYGHSNQLR 19 0 Q99447-3;Q99447;I3L1L9;I3L1R7;I3L2Q1 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 104.61 0.00020228 88473000 25069 30877 25711 35482 21486 28764 29025 9076.8 26931 33463 FALSE TRUE 24089.27576 29996.41819 30357.54964 37313.23027 22177.1167 29345.62779 29380.21663 8889.360908 23873.90578 31196.5212 0.77217827 0.961530871 0.973106887 1.196070229 0.710884286 0.940669878 0.941778618 0.284947185 0.765274616 1 14.92909754 1.801881075 24.99999996 0.60491362 0.933497166 0.198775326 0.207650481 188.5958749 74477.43872 0.08444471 0.052299948 63.36961586 -1.801881075 0.328583546 VLS(ph)PPKLNEVSSDANR ddPTM_BT-474_Pertuzumab_2h_R1 8 VLSPPKLNEVSSDANR 16 1 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7ESQ0 Q9H6Z4 RANBP3 Ran-binding protein 3 1 VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR 207.37 1.07E-11 9242704000 5497620 4879650 4129761 4075285 4653630 4658032 4848850 5772000 6373750 5822250 TRUE FALSE 5282766.932 4740487.16 4876100.679 4285610.947 4803318.235 4752220.599 4908191.677 5652806.183 5650228.621 5427903.822 0.973260969 0.87335504 0.89833955 0.789551747 0.884930609 0.875516729 0.904251777 1.041434478 1.040959606 1 22.37196373 1.802130719 4.04648901 1.031460484 0.879553057 0.693678403 0.043250501 0.116435492 3.413044553 0.022016279 0.011727191 63.40605295 -1.802130719 -0.151907427 SISS(ph)PSVSSETMDKPVDLSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SISSPSVSSETMDKPVDLSTR 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 SIS(0.023)S(0.976)PSVSSETMDKPVDLSTR;SIS(0.037)S(0.959)PS(0.004)VSSETMDKPVDLSTR;SIS(0.309)S(0.684)PS(0.007)VSSETMDKPVDLSTR;SIS(0.013)S(0.965)PS(0.022)VSSETMDKPVDLSTR 264.44 4.87E-37 1981310000 1544670 1577620 1678550 1744630 1831690 1890720 1636370 1615110 1611760 1695540 TRUE FALSE 1484302.589 1532627.822 1981901.324 1834670.563 1890607.972 1928951.654 1656396.386 1581757.414 1428799.762 1580699.566 0.939016256 0.969588311 1.253812785 1.160669999 1.196057754 1.220315167 1.047888177 1.000669228 0.903903432 1 20.59213176 1.802134085 2.578389458 0.957565332 1.126694558 0.325082476 0.099099528 0.32881974 4.178447718 0.063327819 0.030031989 63.40654438 -1.802134085 0.169129226 SEEAHAEDSVMDHHFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEEAHAEDSVMDHHFR 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 180.97 8.28E-10 4121730000 1691840 2075870 1946650 2551060 2127430 2208070 2215660 395692 2240450 2196710 FALSE TRUE 1625721.022 2016668.22 2298452.958 2682720.512 2195860.718 2252718.688 2242775.91 387520.8219 1986123.509 2047924.875 0.793838213 0.984737402 1.122332653 1.309970178 1.072236948 1.100000647 1.095145597 0.189226093 0.969822445 1 20.96573136 1.802171511 24.99999993 0.630877427 1.077848932 0.28057648 0.24335233 164.1584549 64530.92248 0.100227235 0.062197716 63.41200875 -1.802171511 0.446971504 GSWAQDGDESWMQR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSWAQDGDESWMQR 14 0 I3VM54;Q9Y2K7;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 ;; 340.27 1.61E-68 579210000 719292 742630 664652 720750 742160 796870 740020 692543 776850 774760 FALSE TRUE 691181.2734 721450.9195 784769.4015 757947.9939 766032.2504 812983.2574 749076.5861 678241.745 688665.2448 722284.8151 0.95693729 0.998845475 1.086509622 1.049375507 1.060568123 1.125571576 1.037093084 0.939022572 0.95345386 1 19.46220831 1.802199715 6.239804404 0.959637746 1.049134385 0.397845919 0.045363303 0.211798209 14.89235478 0.021949206 0.012744168 63.41612703 -1.802199715 0.089496639 CHVIGTCSSDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 CHVIGTCSSDEK 12 0 Q8N4Q0-2;Q8N4Q0;J3KTQ8;J3QQQ7 Q8N4Q0-2 ZADH2 Zinc-binding alcohol dehydrogenase domain-containing protein 2 0 147.62 0.00034952 0 83455 84105 66939 77627 62218 68740 78654 23994 91763 64113 FALSE TRUE 80193.48634 81706.40775 79036.36635 81633.33877 64219.29847 70129.9699 79616.59118 23498.51552 81346.44894 59770.5694 1.341688512 1.367000659 1.322329152 1.365778168 1.074430094 1.173319421 1.332036686 0.393145251 1.360978317 1 15.86714767 1.802203284 24.99999999 0.851830176 1.278177421 0.318305958 0.23843951 166.096304 65260.07124 0.096763948 0.060061962 63.41664809 -1.802203284 0.426347245 KDDDS(ph)DDESQSSHTGKK ddPTM_BT-474_Pertuzumab_2h_R1 4 KDDDSDDESQSSHTGKK 17 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.996)DDES(0.003)QSSHTGKK;KDDDS(1)DDESQSSHTGKK;KDDDS(0.998)DDES(0.001)QSSHTGKK;KDDDS(1)DDESQSSHTGKK 163.91 1.39E-09 371942000 244273 228305 152267 147143 168159 199824 209367 233357 310174 235583 TRUE FALSE 234726.5411 221793.9649 179785.0341 154737.0679 173567.987 203864.5782 211929.296 228538.0964 274964.3479 219626.7536 1.068752041 1.009867702 0.818593505 0.704545623 0.790286175 0.928231988 0.964952095 1.040574942 1.251961992 1 17.74469428 1.802209345 1.852296504 1.124413092 0.877124623 0.407113223 0.114903704 0.338070708 2.247193653 0.085248205 0.036615052 63.41753328 -1.802209345 -0.247288469 S(ph)LLDRAEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLDRAEER 9 1 P02549-2;P02549 P02549-2 SPTA1 "Spectrin alpha chain, erythrocytic 1" 1 S(1)LLDRAEER 56.225 0.074691 167410000 70504 111090 83590 137990 104020 100030 95039 74429 58725 89911 TRUE FALSE 67748.62573 107921.822 98696.57245 145111.6804 107365.8978 102052.6751 96202.11571 72892.01514 52058.7842 83821.24789 0.808251218 1.287523447 1.177464843 1.73120401 1.280891188 1.217503649 1.147705601 0.869612622 0.621069067 1 16.35502838 1.802400171 2.324857128 0.790772451 1.270787662 0.407844866 0.22618605 0.266479749 2.780802973 0.141341333 0.064989603 63.44540452 -1.802400171 0.480015211 VTPTEEHVEGPLPS(ph)PVTNGTSPAQLNGGSACSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTPTEEHVEGPLPSPVTNGTSPAQLNGGSACSSR 34 0 H3BN50;Q15599-3;H3BQS0;H3BUQ9;Q15599;Q15599-2 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 VTPTEEHVEGPLPS(1)PVTNGTSPAQLNGGSACSSR 311.65 1.49E-104 775860000 192700 191510 198180 243990 234590 258660 150390 169860 125840 119480 TRUE FALSE 185169.071 186048.3223 233995.5345 256582.3531 242135.8004 263890.2824 152230.5178 166352.3316 111555.1708 111387.5132 1.662386256 1.670279881 2.100733985 2.303510922 2.173814582 2.369119077 1.366674894 1.493455836 1.001505174 1 16.76522799 1.802456091 1.616600999 1.06442319 2.038408265 0.690047116 0.268677794 0.223889267 1.122223805 0.209272824 0.086952839 63.45357432 -1.802456091 0.973985075 DHIIDDALVR ddPTM_BT-474_Pertuzumab_2h_R1 4 DHIIDDALVR 10 0 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG77 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 ;;; 182.28 1.79E-06 847100000 1060570 1151590 923860 1095890 1040110 1037000 1102210 351766 1156160 1086510 FALSE TRUE 1019121.752 1118747.781 1090822.053 1152449.014 1073566.083 1057968.851 1115699.176 344501.9092 1024917.564 1012919.71 1.006122935 1.104478242 1.076908705 1.137749619 1.059872833 1.044474542 1.101468522 0.340107815 1.011844822 1 19.95008839 1.802483584 24.99999999 0.711692773 1.077566061 0.335877113 0.179643592 142.0935834 55584.41588 0.071226625 0.044291287 63.45759137 -1.802483584 0.365873288 GSS(ph)PTPPCS(ph)PVQPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSPTPPCSPVQPSK 15 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 2 GSS(0.562)PT(0.438)PPCS(1)PVQPSK 265.43 9.87E-21 0 309320 335820 274850 352570 345940 362030 314960 302040 310570 312370 TRUE FALSE 297231.4324 326242.7424 324521.509 370766.18 357067.4743 369350.4946 318814.5747 295802.7685 275315.3956 291212.9017 1.020667116 1.120289453 1.114378886 1.2731791 1.226138925 1.268317758 1.094781766 1.015761207 0.945409335 1 18.15171475 1.802596316 2.68805691 0.978597654 1.172774954 0.547978892 0.074121768 0.208465255 2.862007784 0.046576782 0.022365967 63.47406554 -1.802596316 0.1941773 FRRS(ph)ET(ph)PPHWR ddPTM_BT-474_Pertuzumab_2h_R1 4 FRRSETPPHWR 11 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR 81.311 0.041627 7083470000 942860 1015480 589250 736020 832850 884620 747050 683260 727600 628810 TRUE FALSE 906011.9888 986519.5047 695740.5828 774006.0804 859639.3766 902507.6225 756192.6214 669150.4422 645005.8983 586220.1386 1.545514951 1.682848199 1.186824773 1.320333488 1.466410517 1.539537049 1.289946509 1.141466146 1.100279325 1 19.161083 1.802695091 1.974583311 1.059767887 1.449124714 0.629040859 0.12960387 0.226492265 1.713521461 0.092165557 0.0403352 63.48850364 -1.802695091 0.389356828 T(ph)PPFSESEEQLHLHDAGMKPR ddPTM_BT-474_Pertuzumab_2h_R1 7 TPPFSESEEQLHLHDAGMKPR 21 1 Q8IVM0-2 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 1 T(1)PPFSESEEQLHLHDAGMKPR;T(1)PPFSESEEQLHLHDAGMKPR;T(1)PPFSESEEQLHLHDAGMKPR;T(1)PPFSESEEQLHLHDAGMKPR;T(0.999)PPFS(0.001)ESEEQLHLHDAGMKPR;T(0.984)PPFS(0.015)ES(0.001)EEQLHLHDAGMKPR;T(0.985)PPFS(0.013)ES(0.002)EEQLHLHDAGMKPR 240.43 8.52E-30 4332568000 1186023 1169067 1123519 1288207 1247239 1191091 1259124 102334.2 1436520 978819 TRUE FALSE 1139671.91 1135726.354 1326563.876 1354691.518 1287357.575 1215175.676 1274533.536 100220.963 1273452.272 912522.7173 1.248924425 1.244600635 1.453732439 1.484556485 1.4107677 1.331666218 1.396714309 0.109828458 1.395529391 1 19.79950095 1.802957251 25 0.737947872 1.370700926 0.373472157 0.308222815 141.0314032 54763.00341 0.12292303 0.076666239 63.5268398 -1.802957251 0.632753053 KAELLDNEKPAAVVAPITTGYTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAELLDNEKPAAVVAPITTGYTVK 24 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 131.33 3.21E-05 2392500000 2822670 2395330 1967300 2135060 2444980 2568130 2627930 2994030 3710800 3344100 FALSE TRUE 2712356.936 2327017.534 2322834.872 2245250.702 2523625.002 2620059.348 2660091.393 2932202.234 3289565.541 3117601.128 0.870014099 0.746412847 0.745071219 0.720185364 0.809476549 0.840408776 0.853249432 0.940531554 1.055159209 1 21.57200493 1.803047945 1.12797345 1.031878695 0.773321769 0.82503274 0.044440437 0.184404136 0.434944741 0.03724333 0.015235587 63.54010744 -1.803047945 -0.258556925 DQGGFGDRNEYGSR ddPTM_BT-474_Pertuzumab_2h_R1 5 DQGGFGDRNEYGSR 14 1 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;; 231.17 5.84E-13 7540070000 3054111 3268590 2429401 2762160 2934500 3204410 2847622 2783787 2995136 2833670 FALSE TRUE 2934752.966 3175373.013 2868447.802 2904715.409 3028890.858 3269205.366 2882472.05 2726300.826 2655140.718 2641743.007 1.110915391 1.201999212 1.08581637 1.099545036 1.146550156 1.237518319 1.09112508 1.032008344 1.005071542 1 21.3330587 1.803073989 2.87829857 1.009785731 1.145282216 0.645956857 0.044329428 0.162108492 2.524331832 0.025687799 0.012579874 63.54391799 -1.803073989 0.135496485 DGPIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGPISPK 7 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 DGPIS(1)PK;DGPIS(1)PK 99.257 0.011183 1111000000 2678000 2249650 2239000 2582200 1927950 2033280 2426200 2925900 3029200 3227300 TRUE FALSE 2573340.799 2185492.185 2643637.106 2715467.651 1989964.263 2074394.315 2455892.561 2865479.143 2685337.915 3008712.096 0.855296458 0.726387941 0.87866071 0.902534893 0.661400692 0.68946255 0.816260407 0.952393932 0.89252073 1 21.52071463 1.803161812 4.352301113 0.94203359 0.784662379 0.462234425 0.078502661 0.208838233 7.012808982 0.041034048 0.022237213 63.55676907 -1.803161812 -0.157371211 LKDDEVAQLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKDDEVAQLKK 11 2 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ; 139.46 2.20E-05 1540180000 1644010 1539210 1337130 1073720 1396880 1652700 1684640 1779020 2405600 2132300 FALSE TRUE 1579760.272 1495313.238 1578779.135 1129134.818 1441811.914 1686118.726 1705257.128 1742282.615 2132526.373 1987877.422 0.794697024 0.752216018 0.794203464 0.568010283 0.725302223 0.848200552 0.857828108 0.876453747 1.072765529 1 20.92279737 1.803173443 1.01399479 1.028204061 0.729486051 0.704569081 0.072774184 0.297181367 0.565778573 0.064549697 0.027020261 63.5584713 -1.803173443 -0.298718011 LEPTNVQTVTCS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEPTNVQTVTCSPR 14 0 J3KTI7;J3QR52;J3QLN7;Q99741 J3KTI7 CDC6 Cell division control protein 6 homolog 1 LEPTNVQTVT(0.003)CS(0.997)PR;LEPTNVQTVT(0.002)CS(0.998)PR 162.61 4.63E-06 330590000 360670 426440 308910 336510 315940 369750 347750 319040 313580 387330 TRUE FALSE 346574.6177 414278.3487 364736.9087 353877.3214 326102.497 377226.5983 352005.8685 312451.7125 277983.713 361095.7941 0.959785806 1.147281014 1.010083514 0.980009535 0.903091375 1.044671814 0.974826831 0.865287599 0.769833705 1 18.46202209 1.803220085 3.705094313 0.862716514 1.00786284 0.342026389 0.079079688 0.228123516 5.647974368 0.040672858 0.021246505 63.5652976 -1.803220085 0.145146326 DGDSVMVLPTIPEEEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DGDSVMVLPTIPEEEAK 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;; 232.5 2.92E-16 537190000 1496900 1252170 1189460 1136090 1286280 1307260 1361000 1705840 1905940 1723820 FALSE TRUE 1438399.493 1216459.338 1404421.881 1194723.741 1327654.364 1333693.693 1377656.325 1670613.808 1689585.682 1607064.136 0.89504797 0.756945109 0.87390531 0.743420075 0.826136515 0.829894503 0.85725037 1.039543955 1.051349255 1 20.61599608 1.803305342 3.400149802 1.036772912 0.818459532 0.81189507 0.045210933 0.084837637 1.792440722 0.022426563 0.011474082 63.57777747 -1.803305342 -0.21831338 AAKNS(ph)EEEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 AAKNSEEEEEEK 12 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AAKNS(1)EEEEEEK;AAKNS(1)EEEEEEK;AAKNS(1)EEEEEEK;AAKNS(1)EEEEEEK;AAKNS(1)EEEEEEK 235.26 2.92E-16 3047800000 2411680 1632592 2113760 1624017 1834363 1808020 2178796 2919720 3401560 3006620 TRUE FALSE 2317428.879 1586032.075 2495763.452 1707832.712 1893366.952 1844579.403 2205460.757 2859426.762 3015429.169 2802978.949 0.826773558 0.565838026 0.890396788 0.609292022 0.675483828 0.658078222 0.786827442 1.020138507 1.07579444 1 21.41852948 1.803368038 2.936111936 1.044017499 0.701522067 0.717615 0.09192636 0.11952603 1.929762744 0.048078201 0.023679199 63.5869564 -1.803368038 -0.342495432 LEVTEIVKPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 LEVTEIVKPSPK 12 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 LEVTEIVKPS(1)PK;LEVTEIVKPS(1)PK;LEVTEIVKPS(1)PK 107.98 0.0010633 4101830000 4403070 3406310 3304580 2756740 3381820 3278950 3736600 4845340 5528670 4870150 TRUE FALSE 4230993.157 3309165.374 3901791.116 2899015.682 3490599.312 3345252.616 3782329.629 4745282.036 4901078.56 4540290.403 0.931877211 0.728844431 0.859370386 0.638508867 0.768805297 0.736792654 0.833058966 1.045149454 1.079463674 1 22.11435315 1.803452 3.347309757 1.050379915 0.772822923 0.706780762 0.076127262 0.117250836 2.40640161 0.039282185 0.020021904 63.5992508 -1.803452 -0.277556992 KGDYIEAESSYSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGDYIEAESSYSR 13 1 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ; 190.41 7.12E-06 875440000 459810 482950 381210 459290 460530 455800 480830 562490 535270 598190 FALSE TRUE 441840.1169 469176.7389 450103.127 482994.0119 475343.3657 465016.5883 486714.5414 550874.3849 474508.3936 557674.0585 0.792290963 0.841309958 0.80710788 0.866086569 0.85236772 0.833850134 0.872758081 0.987807083 0.85087048 1 19.08906264 1.803484858 0.313572256 1.009430838 0.78966584 0.63526625 0.039877954 0.916647661 0.295158848 0.065412464 0.071751662 63.60406289 -1.803484858 -0.219764998 GQPDEELKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQPDEELKPK 10 1 P54577 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 ; 93.258 0.0069557 0 800530 1095770 735930 898210 959520 1199050 898370 757000 823050 786790 FALSE TRUE 769244.4026 1064519.712 868928.9217 944566.7257 990383.8322 1223295.613 909364.5208 741367.6855 729620.8145 733500.0125 1.048731274 1.451287927 1.18463382 1.287752842 1.350216517 1.667751318 1.239760743 1.010726207 0.994711387 1 19.48443746 1.803487122 3.916809306 1.000896391 1.336906793 0.478535009 0.153070184 0.188545447 5.173851713 0.078354115 0.041476407 63.60439442 -1.803487122 0.336010402 HSSVYPTQEELEAVQNMVSHTER ddPTM_BT-474_Pertuzumab_2h_R1 4 HSSVYPTQEELEAVQNMVSHTER 23 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;K7ERM6;K7ENK6;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;; 225.39 6.72E-33 1975060000 457607 887850 660730 1242420 836850 924720 829030 479313 538455 805920 FALSE TRUE 439723.2125 862529.3873 780138.6089 1306541.445 863768.0403 943418.472 839175.9171 469415.0191 477331.8458 751334.3206 0.585256391 1.147996789 1.038337512 1.738961484 1.149645393 1.255657363 1.116914128 0.624775158 0.635312181 1 19.51909548 1.803499771 5.825776659 0.722502463 1.173115931 0.288962975 0.280693928 0.243528885 14.67996432 0.131069917 0.075347507 63.60624688 -1.803499771 0.450613468 GSTIETEQKEDKGEDSEPVTSK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSTIETEQKEDKGEDSEPVTSK 22 2 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ;; 195.13 6.62E-19 2028050000 1426200 1108320 1002490 791990 1003270 1062470 1172870 1436860 1757300 1429210 FALSE TRUE 1370462.527 1076711.799 1183662.243 832864.6988 1035541.091 1083953.871 1187223.934 1407188.339 1557818.671 1332408.334 1.028560459 0.808094464 0.888362984 0.625082175 0.777194997 0.81352979 0.891036106 1.05612394 1.169175118 1 20.34560485 1.803568015 2.543503049 1.093590715 0.81561191 0.549736809 0.101727384 0.194048364 2.399521135 0.061088341 0.028888612 63.6162426 -1.803568015 -0.277978806 TSTLPPLPLPPLLPGDDDMDS(ph)PKETLPSKPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSTLPPLPLPPLLPGDDDMDSPKETLPSKPVK 32 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 TSTLPPLPLPPLLPGDDDMDS(0.663)PKET(0.151)LPS(0.186)KPVK 104.31 3.08E-06 175630000 89009 62074 69171 63775 77150 64491 81292 111260 132990 107880 TRUE FALSE 85530.42988 60303.7103 81671.7384 67066.43539 79631.59982 65795.05221 82286.87581 108962.4421 117893.5327 100573.1915 0.850429708 0.599600245 0.812062709 0.666842072 0.791777596 0.654200699 0.818179025 1.083414382 1.172216283 1 16.61788627 1.80358063 3.224733609 1.101482466 0.727470837 0.787619235 0.082563665 0.090249316 1.729537954 0.040440354 0.020420302 63.61809052 -1.80358063 -0.374011629 CGHTNNLRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 CGHTNNLRPK 10 1 M0R2S1;P62987 M0R2S1 UBA52 Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40 0 ; 169.76 2.72E-06 2240800000 2633500 2363880 2070120 2054320 2223320 2074350 2300300 1425690 2594700 2236770 FALSE TRUE 2530579.909 2296464.457 2444236.734 2160343.701 2294835.107 2116294.778 2328451.759 1396249.003 2300160.534 2085271.576 1.213549323 1.101278358 1.172143121 1.036001127 1.100496997 1.014877296 1.116617992 0.669576577 1.103050826 1 20.99180385 1.803599713 25 0.888065762 1.103449779 0.329430369 0.116579317 155.8660679 59925.33513 0.046692299 0.029231355 63.62088603 -1.803599713 0.215384017 RRES(ph)EKSLENET(ph)LNK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(0.999)EKS(0.014)LENET(0.987)LNK 177.69 1.41E-06 818160000 562620 451550 545320 483670 509580 443340 550800 740430 798790 758820 TRUE FALSE 540632.1884 438672.2361 643871.4546 508632.2667 525971.1035 452304.6386 557540.8552 725139.8618 708114.708 707424.4455 0.764226048 0.62009765 0.910162857 0.718991646 0.743501454 0.639368121 0.788127776 1.025042132 1.00097574 1 19.43221655 1.803726183 4.11211817 1.010497379 0.734354036 0.733460397 0.074473044 0.106969771 3.214878097 0.036695831 0.019646446 63.63941561 -1.803726183 -0.276143342 RTHEHVSEK ddPTM_BT-474_Pertuzumab_2h_R1 4 RTHEHVSEK 9 1 P20810-6;P20810-10;P20810-7;P20810-9;H0YA91;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 0 ;;; 114.5 0.0010573 86549000 142151 196271 155127 185173 145631 157360 170801 9571.1 169792 167418 FALSE TRUE 136595.5818 190673.5432 183161.8997 194729.8007 150315.3534 160541.927 172891.3137 9373.45344 150517.924 156078.6297 0.875171585 1.221650546 1.173523243 1.247639097 0.963074533 1.028596466 1.107719321 0.06005597 0.964372408 1 17.25191349 1.803754115 25 0.571748556 1.095639262 0.313489622 0.267441775 146.2447176 56093.07426 0.106816244 0.06692754 63.64350878 -1.803754115 0.523890706 SLIIDEGEDDLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLIIDEGEDDLGR 13 0 J3KNF4;O14618;E9PP76 J3KNF4 CCS Copper chaperone for superoxide dismutase;Superoxide dismutase [Cu-Zn] 0 154.66 0.00010773 158070000 182610 206320 177850 185310 191540 193080 188840 160400 180950 179000 FALSE TRUE 175473.3993 200435.9556 209991.4513 194873.8713 197701.0581 196984.2099 191151.0804 157087.6839 160409.3146 166876.1706 1.051518612 1.201105915 1.258366911 1.167775307 1.184717131 1.180421442 1.145466604 0.941342814 0.961247577 1 17.34841843 1.803772719 4.375843656 0.963198969 1.177831378 0.772180517 0.050408601 0.093539542 3.165793323 0.025035007 0.013591076 63.64623517 -1.803772719 0.214632409 LSDEHEPEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSDEHEPEQR 10 0 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 0 120.06 0.00060965 162630000 241500 283660 229510 284590 267340 285510 251010 253310 266470 248600 FALSE TRUE 232061.913 275570.2945 270987.5624 299277.724 275939.2339 291283.2078 254081.9355 248079.06 236221.4427 231762.1006 1.001293622 1.189022251 1.169248819 1.29131434 1.190614139 1.256819847 1.096304939 1.070403916 1.019241033 1 17.82228514 1.803797528 1.989214897 1.019616095 1.186959065 0.463750345 0.073666742 0.28099417 2.156058375 0.04922924 0.021612235 63.64987102 -1.803797528 0.16734297 VPDS(ph)PENELK ddPTM_BT-474_Pertuzumab_2h_R1 2 VPDSPENELK 10 0 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 VPDS(1)PENELK;VPDS(1)PENELK 199.15 2.98E-07 520320000 350690 306150 358330 329110 332100 367610 391460 482640 552740 545240 TRUE FALSE 336984.6471 297418.9018 423088.202 346095.4065 342782.2981 375043.3261 396250.8046 472673.3153 489995.2725 508310.4092 0.662950514 0.585112751 0.832342196 0.680874128 0.674356244 0.737823423 0.779544934 0.92989108 0.963968598 1 18.95535025 1.803835189 1.341487194 0.996688533 0.688786194 0.816234577 0.057780911 0.170842644 0.577807395 0.045699957 0.018546335 63.65539087 -1.803835189 -0.307902339 RRESEKS(ph)LENET(ph)LNK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(0.434)EKS(0.571)LENET(0.995)LNK 148.2 6.77E-06 1397500000 910450 718490 819270 873510 812420 629870 877480 1134400 1190300 1240400 TRUE FALSE 874868.6074 697999.3687 967330.3136 918591.9558 838552.2271 642606.403 888218.8627 1110974.244 1055182.134 1156386.603 0.756553738 0.603603818 0.836511173 0.794364059 0.725148687 0.555702047 0.768098541 0.960729085 0.91248215 1 20.14119237 1.80414738 4.106090477 0.953086785 0.713606923 0.648014949 0.080882228 0.141172818 4.224706044 0.041955295 0.022463463 63.70116567 -1.80414738 -0.239479863 KQEIVAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQEIVAEK 8 1 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0;F8VV53 Q9ULV4 CORO1C Coronin-1C;Coronin 0 82.417 0.037619 0 232820 218500 206370 205810 200050 158330 223820 248880 288740 262280 FALSE TRUE 223721.137 212268.5939 243665.6497 216431.8788 206484.7899 161531.5411 226559.1761 243740.541 255963.4457 244515.542 0.914956715 0.868119025 0.996524179 0.885145693 0.844464889 0.660618707 0.926563499 0.996830463 1.046818716 1 17.89956664 1.804154449 3.550640331 1.017660652 0.86428003 0.411219475 0.080784491 0.243694649 5.56423619 0.04553439 0.023562685 63.7022026 -1.804154449 -0.153380622 ASPHATPSTLHFPT(ph)SPIIQQPGPYFSHPAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPHATPSTLHFPTSPIIQQPGPYFSHPAIR 31 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;B1AKN6 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 ASPHAT(0.003)PS(0.016)T(0.016)LHFPT(0.482)S(0.482)PIIQQPGPYFSHPAIR;AS(0.002)PHAT(0.001)PS(0.007)T(0.007)LHFPT(0.492)S(0.492)PIIQQPGPYFSHPAIR 155.71 6.29E-09 593650000 89823 88456 77946 100249 98781 100640 88313 52837 64123 65272 TRUE FALSE 86312.61786 85933.32149 92032.5761 105422.8629 101958.3806 102675.0098 89393.80091 51745.89749 56844.02587 60851.0693 1.418424012 1.412190821 1.512423317 1.732473465 1.67553967 1.687316442 1.469058834 0.850369568 0.934149991 1 15.89299499 1.80417166 4.509163581 0.919081589 1.574074803 0.876328161 0.108763757 0.073296169 2.624572079 0.059846497 0.032715813 63.70472713 -1.80417166 0.654993214 QEEKHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 QEEKHLK 7 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 0 ; 76.035 0.025147 1086440000 1775310 1280500 1455520 1443590 1566500 1162070 1830920 1876560 2415010 2179350 FALSE TRUE 1705928.922 1243981.394 1718564.842 1518093.853 1616887.895 1185567.852 1853327.347 1837808.38 2140868.189 2031740.683 0.839639102 0.612273704 0.84585836 0.747188785 0.795814106 0.583523213 0.912186955 0.904548693 1.053711336 1 20.95428485 1.804219782 1.981616099 1.006928304 0.74192373 0.598575853 0.091328485 0.205165033 1.561747158 0.05681809 0.024924607 63.71178632 -1.804219782 -0.265004573 KQSFDDNDS(ph)EELEDKDSK ddPTM_BT-474_Pertuzumab_2h_R1 4 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KQSFDDNDS(1)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK;KQS(0.001)FDDNDS(0.999)EELEDKDSK;KQS(0.001)FDDNDS(0.999)EELEDKDSK 222.72 2.89E-19 7531280000 5708540 3584840 3599620 2294880 3317010 3143790 3838950 4980450 5807510 4562180 TRUE FALSE 5485443.946 3482603.873 4250151.407 2413319.032 3423704.639 3207359.588 3885932.218 4877601.967 5148265.812 4253179.485 1.289727829 0.818823632 0.999288044 0.567415281 0.804975349 0.754108685 0.913653476 1.146813104 1.210451106 1 22.02011031 1.804435725 4.16683235 1.134084814 0.85755318 0.266672805 0.181903668 0.264793331 8.139135326 0.09091767 0.048853342 63.74347349 -1.804435725 -0.276531634 VSFELFADKVPKTAENFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSFELFADKVPKTAENFR 18 2 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 113.28 0.00014155 237840000 211120 228270 195490 125050 344070 240340 212650 105060 186000 77725 FALSE TRUE 202869.197 221759.9631 230819.3917 131503.8455 355137.324 245199.8395 215252.4743 102890.4743 164886.0598 72460.61652 2.799716684 3.060420595 3.185446146 1.814831998 4.901108231 3.383904958 2.970613343 1.419950302 2.275526592 1 16.14490946 1.804552401 4.744794493 1.634931791 3.195654554 0.474729684 0.768719617 0.191152626 7.548008551 0.371140606 0.205190655 63.76060092 -1.804552401 1.560722764 S(ph)LS(ph)PKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSPKPR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)LS(1)PKPR;S(1)LS(1)PKPR;S(1)LS(1)PKPR 135.43 0.0017515 2748580000 3108560 2538860 2401670 2260760 2432550 2355150 2730910 3260160 3822570 3263760 TRUE FALSE 2987074.039 2466454.199 2835705.194 2377438.095 2510795.18 2402772.747 2764331.693 3192836.557 3388647.879 3042702.628 0.981717375 0.810612965 0.93196922 0.781357361 0.825185858 0.789683725 0.908511949 1.049342294 1.113696701 1 21.53692191 1.804553528 3.187566075 1.06444346 0.850501182 0.658012028 0.064562582 0.132807361 2.487333377 0.033910529 0.01708571 63.76076626 -1.804553528 -0.213942278 DDANNDPQWSEEQLIAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDANNDPQWSEEQLIAAK 18 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 249.3 2.85E-24 240360000 240091 216253 228612 229322 233627 231724 260900 280980 338650 310980 FALSE TRUE 230707.9783 210085.6762 269927.2738 241157.3359 241141.8246 236409.618 264092.9722 275177.6648 300207.8717 289917.0476 0.795772378 0.724640644 0.931050023 0.831814955 0.831761453 0.81543883 0.910925985 0.94916 1.035495754 1 18.14528064 1.804800745 1.425649791 1.016978236 0.821331715 0.713617468 0.049887766 0.22143629 0.851281745 0.038924152 0.015881539 63.79707167 -1.804800745 -0.195646521 EAFDEVDMAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAFDEVDMAHR 11 0 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 107.18 0.0022324 542400000 596340 612860 524000 599510 638900 648760 585070 575940 610770 590250 FALSE TRUE 573034.3735 595381.8329 618698.4563 630450.7829 659450.7987 661878.3717 592230.2617 564046.6377 541437.9502 550271.8418 1.041365976 1.081977648 1.124350565 1.145707876 1.198409129 1.202820718 1.076250349 1.025032711 0.983946314 1 19.06978498 1.804933638 2.643953572 0.998223775 1.133252083 0.604538359 0.046599411 0.197037431 2.615417098 0.030391323 0.014552595 63.81659647 -1.804933638 0.135028308 DLTPEHLPLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLTPEHLPLLR 11 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 ; 186.74 3.90E-06 234330000 415880 477880 370920 441300 437880 425580 434300 439120 461530 470600 FALSE TRUE 399626.9498 464251.3303 437953.4951 464075.5459 451964.8079 434185.5192 439615.0933 430052.0185 409139.0493 438725.8428 0.910880807 1.058180953 0.998239566 1.057780282 1.030175941 0.989651114 1.002026893 0.980229511 0.932562 1 18.74296016 1.804940644 1.822780263 0.96526503 1.012841186 0.128148379 0.042242664 0.577678738 3.710385798 0.027777269 0.011905773 63.8176259 -1.804940644 0.047576156 ISNLS(ph)PEEEQGLWK ddPTM_BT-474_Pertuzumab_2h_R1 8 ISNLSPEEEQGLWK 14 0 F5GX09;Q5HYJ3-3;Q5HYJ3-2;Q5HYJ3 F5GX09 FAM76B Protein FAM76B 1 ISNLS(1)PEEEQGLWK;ISNLS(1)PEEEQGLWK;ISNLS(1)PEEEQGLWK;ISNLS(1)PEEEQGLWK;ISNLS(1)PEEEQGLWK;ISNLS(1)PEEEQGLWK;ISNLS(1)PEEEQGLWK;ISNLS(1)PEEEQGLWK 381.02 5.55E-98 4029858000 3392504 3148010 2723954 2703882 2891708 2939847 3044608 3391593 3683634 3447175 TRUE FALSE 3259921.193 3058231.837 3216233.082 2843429.674 2984722.414 2999292.721 3081868.823 3321555.419 3265483.311 3213694.767 1.014384199 0.951624861 1.000789843 0.884785233 0.928751058 0.933284876 0.958979943 1.033562818 1.016114954 1 21.61580148 1.805007549 5.789161047 1.018648155 0.95022001 0.404737593 0.035107087 0.204492115 12.00728823 0.016656195 0.009582563 63.82745813 -1.805007549 -0.068428144 HGAVSVS(ph)LFIR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGAVSVSLFIR 11 0 Q9BT04-2 Q9BT04-2 1 HGAVS(0.28)VS(0.72)LFIR 57.348 0.072931 186410000 29089 52409 36457 69012 56293 62373 42977 29568 21079 33107 TRUE FALSE 27952.16972 50914.34663 43045.59088 72573.71759 58103.71547 63634.2248 43502.96538 28957.41047 18686.20029 30864.6334 0.905637509 1.649601535 1.394657449 2.351355244 1.882533796 2.061719767 1.409476173 0.93820685 0.605424339 1 14.91366704 1.805196222 2.806371542 0.803502322 1.727359408 0.507683479 0.376759472 0.207049253 3.068079915 0.221711278 0.108005465 63.855193 -1.805196222 0.923857085 AFVDRT(ph)PPPAAVAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFVDRTPPPAAVAQR 15 1 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 AFVDRT(1)PPPAAVAQR 75.682 0.050286 725920000 325120 386140 315190 396240 388230 365390 323220 287180 263780 273000 TRUE FALSE 312413.951 375127.6653 372151.8444 416689.9939 400717.7705 372778.4361 327175.663 281249.6326 233836.8003 254509.4668 1.227514068 1.473924212 1.462231834 1.637227876 1.574470983 1.464693792 1.285514708 1.105065506 0.918774469 1 17.95735979 1.805199563 1.705328255 0.963151711 1.486279939 0.804837644 0.103540014 0.150177245 0.840673285 0.077138634 0.032509405 63.85568422 -1.805199563 0.523128228 QMEHVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 QMEHVQR 7 0 Q8NI27;A0A0C4DG98;H0Y815 Q8NI27 THOC2 THO complex subunit 2 0 91.783 0.029153 0 28549 40377 35346 47815 43113 42285 37695 30105 30511 32528 FALSE TRUE 27433.27352 39225.48749 41733.80847 50282.73788 44499.7688 43140.03167 38156.32269 29483.32123 27047.51919 30324.84959 0.904646648 1.293509713 1.376224748 1.658136432 1.467435763 1.422596724 1.258252661 0.972249546 0.891925914 1 14.88821287 1.805277313 2.884369606 0.938567603 1.369995725 0.494049362 0.180250859 0.215166989 3.352829436 0.108285191 0.053156615 63.86711703 -1.805277313 0.431428122 LFQECCPHSTDR ddPTM_BT-474_Pertuzumab_2h_R1 9 LFQECCPHSTDR 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;; 245.5 1.80E-16 52221310000 10459900 12314790 8110830 10247860 10276840 11482820 9782920 9326550 9501570 9484130 FALSE TRUE 10051115.54 11963584.25 9576637.405 10776753.28 10607403.89 11715010.49 9902646.301 9133953.483 8422991.607 8841761.428 1.13677751 1.353077025 1.083114206 1.218846875 1.19969352 1.324963423 1.119985693 1.033046815 0.952637286 1 23.07590238 1.805422694 2.504590307 0.984515182 1.218152572 0.627802044 0.076960879 0.165855088 1.988133366 0.043600227 0.02055642 63.88850036 -1.805422694 0.23363739 NTSNIPVILEPETEES(ph)ENEFYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTSNIPVILEPETEESENEFYIK 23 0 Q6P0N0 Q6P0N0 MIS18BP1 Mis18-binding protein 1 1 NTSNIPVILEPET(0.094)EES(0.906)ENEFYIK 140.71 6.35E-10 0 43940 39422 35106 34450 29339 35176 38122 45809 47757 50270 TRUE FALSE 42222.77622 38297.72316 41450.43513 36227.96863 30282.71558 35887.28282 38588.54844 44863.02814 42335.82557 46865.16812 0.900941529 0.817189497 0.884461462 0.77302547 0.646166797 0.765755982 0.823395071 0.95727872 0.903353754 1 15.51622844 1.805447218 3.895623645 0.948760374 0.794733017 0.502490167 0.069436643 0.203361173 5.491080826 0.038563873 0.020423063 63.89210818 -1.805447218 -0.154027358 GLPSPYNMSS(ph)APGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPS(0.001)PYNMS(0.044)S(0.478)APGS(0.478)R;GLPSPYNMS(0.13)S(0.804)APGS(0.066)R 126.91 8.54E-05 5854400000 3513850 3815580 2600250 3287590 3194420 3229210 2177890 3115330 2820860 2207060 TRUE FALSE 3376524.857 3706763.394 3070173.017 3457262.914 3297171.42 3294506.839 2204543.669 3050997.347 2500647.799 2057573.86 1.64102243 1.801521426 1.492132592 1.680261876 1.602455923 1.601160912 1.071428692 1.482813038 1.215338048 1 20.97251279 1.805598989 0.389191289 0.989435735 1.744757566 0.690513175 0.143150167 0.628578844 0.262845128 0.167470808 0.154367385 63.91444007 -1.805598989 0.755321831 VKPET(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKPETPPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKPET(1)PPR;VKPET(1)PPR 101.38 0.008787 6613760000 3534400 3199100 3121900 3110100 3286900 3465700 3424300 4174100 4372200 4208100 TRUE FALSE 3396271.741 3107864.8 3686096.776 3270612.634 3392626.124 3535778.829 3466207.608 4087903.376 3875886.186 3923081.639 0.865715285 0.792199879 0.939592166 0.833684571 0.864786012 0.901275873 0.883542054 1.042013334 0.987969801 1 21.90355593 1.805693516 5.479738644 1.011362892 0.867188829 0.73770742 0.038650288 0.100928788 5.273551468 0.017622062 0.010042921 63.928353 -1.805693516 -0.144174063 LKEEEEDK ddPTM_BT-474_Pertuzumab_2h_R1 6 LKEEEEDK 8 1 P27797 P27797 CALR Calreticulin 0 ;;;;; 140.16 0.0005964 4612720000 5464200 4579760 4987290 4584970 4760640 4329590 5745220 7072090 8625670 7613300 FALSE TRUE 5250653.023 4449149.729 5888604.245 4821600.851 4913770.309 4417137.276 5815531.721 6926048.87 7646520.103 7097644.41 0.739774032 0.626848779 0.829656137 0.679324093 0.692310015 0.622338486 0.819360817 0.975823593 1.077332092 1 22.75890887 1.805799101 2.422053012 1.03458236 0.700514564 0.849002287 0.060201633 0.094735534 1.065487442 0.035259415 0.016463039 63.94389708 -1.805799101 -0.334067797 LLEDS(ph)EESSEETVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEDSEESSEETVSR 15 0 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 LLEDS(1)EESSEETVSR;LLEDS(0.998)EES(0.002)SEETVSR 245.19 5.50E-16 74838000 197020 277680 147087 202264 203346 272642 210507 169281 184918 207011 TRUE FALSE 189320.2406 269760.8383 173668.8928 212702.8693 209886.8088 278155.008 213083.2476 165785.2882 163926.8839 192989.9606 0.980984918 1.397797261 0.899885633 1.102144737 1.08755299 1.441292631 1.104115711 0.859035816 0.849406277 1 17.55816627 1.80602969 5.154166731 0.891782516 1.154959013 0.322320947 0.16104178 0.231618444 10.68026234 0.074808922 0.042138476 63.97785722 -1.80602969 0.263176498 NS(ph)PPFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPPFLK 7 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 NS(1)PPFLK;NS(1)PPFLK 101.97 0.009131 1341690000 3213500 2907600 2580300 2560700 2779300 2911200 2940700 3438100 3693900 3654900 TRUE FALSE 3087912.867 2824678.095 3046617.608 2692858.034 2868698.709 2970066.459 2976689.166 3367102.034 3274583.958 3407350.368 0.906250469 0.828995492 0.894131005 0.790308522 0.841914802 0.871664531 0.873608184 0.988187791 0.961035293 1 21.70021887 1.806202709 3.362554981 0.982846801 0.853421598 0.758694935 0.032335472 0.108100152 2.224602218 0.016826701 0.008605738 64.00335043 -1.806202709 -0.129425204 DDDHNGHIDFITAASNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DDDHNGHIDFITAASNLR 18 0 A0AVT1;A0AVT1-2;H0Y9U5 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ;;; 202.35 7.53E-16 1980080000 1307420 1281040 1447280 1618130 1521350 1488690 1596460 41314.5 1797370 1270650 FALSE TRUE 1256324.581 1244505.993 1708835.691 1701641.883 1570285.604 1518792.332 1615997.955 40461.34114 1593340.093 1184587.744 1.060558483 1.050581521 1.442557294 1.436484458 1.3255967 1.282127339 1.364185949 0.034156475 1.345058736 1 20.17595363 1.806228377 25 0.687120969 1.285524433 0.293552817 0.334395041 152.0631686 56191.56394 0.134033456 0.084935029 64.00713333 -1.806228377 0.598403464 YKEETIEK ddPTM_BT-474_Pertuzumab_2h_R1 6 YKEETIEK 8 1 P61254 P61254 RPL26 60S ribosomal protein L26 0 ;;;;; 125.97 0.0011302 6773740000 13056730 10821260 10955070 8689840 10756730 9260200 11097020 13008060 14033100 13437730 FALSE TRUE 12546458.56 10512648.26 12934894.84 9138323.684 11102729.99 9447447.589 11232828.65 12739439.02 12440121.32 12527580.58 1.001506913 0.839160299 1.032513402 0.729456388 0.886262908 0.754131856 0.896647887 1.016911361 0.993018663 1 23.57860448 1.80623001 4.830751307 1.003324245 0.870252544 0.298937621 0.08869395 0.252173942 10.22085086 0.041501182 0.023071232 64.00737395 -1.80623001 -0.133071701 AVTIANS(ph)PSKPSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVTIANSPSKPSEK 14 1 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVTIANS(0.951)PS(0.049)KPSEK;AVTIANS(0.982)PS(0.018)KPSEK 228.46 1.00E-12 1180810000 1640480 1247980 1321310 1173790 1269850 1284000 1447310 1738450 1849920 1986090 TRUE FALSE 1576368.228 1212388.832 1560100.109 1234369.443 1310695.878 1309963.36 1465022.613 1702550.4 1639924.837 1851570.355 0.851368258 0.654789503 0.842582138 0.666660837 0.707883378 0.707487758 0.791232485 0.91951699 0.885694045 1 20.82031794 1.806329094 2.423640865 0.936881141 0.73451707 0.634860164 0.066741375 0.167708666 1.887541268 0.037794631 0.017658159 64.02197884 -1.806329094 -0.202364071 EELEEVIK ddPTM_BT-474_Pertuzumab_2h_R1 2 EELEEVIK 8 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ; 141.39 0.0014757 160075000 215810 224320 215790 231510 227750 217840 244830 289690 320290 317810 FALSE TRUE 207375.9066 217922.6132 254788.0532 243458.2588 235075.7856 222244.8741 247826.3028 283707.8003 283932.022 296284.4456 0.699921679 0.735518237 0.859944074 0.821704489 0.79341251 0.750106451 0.836447226 0.957552124 0.958308903 1 18.17662336 1.806502618 2.559778885 0.976162126 0.781381998 0.801707805 0.043387305 0.12564075 1.567097657 0.02766286 0.013138668 64.04756418 -1.806502618 -0.194780128 KPEEESPR ddPTM_BT-474_Pertuzumab_2h_R1 3 KPEEESPR 8 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 0 ;; 107.15 0.0065062 1766100000 1118190 1424530 1073200 1755330 1407470 1493510 1330540 1205500 1174250 1371850 FALSE TRUE 1074489.899 1383903.799 1267151.113 1845922.792 1452742.551 1523709.795 1346823.547 1180606.004 1040954.063 1278933.378 0.840145325 1.082076536 0.990787429 1.443329906 1.135901663 1.191391062 1.053083429 0.923117673 0.813923603 1 20.28650968 1.806534406 3.009288956 0.897348823 1.122618189 0.261915745 0.15002006 0.322287088 5.416789596 0.085353605 0.042427774 64.05225239 -1.806534406 0.225269367 RVEIQMPKPAEAPTAPS(ph)PAQTLENSEPAPVSQLQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVEIQMPKPAEAPTAPSPAQTLENSEPAPVSQLQSR 36 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;K7EJ51 Q9UHD8 9-Sep Septin-9 1 RVEIQMPKPAEAPT(0.028)APS(0.82)PAQT(0.151)LENSEPAPVSQLQSR 123.17 1.26E-08 94210000 42709 49301 35819 41389 38403 44463 35029 45135 39960 38906 TRUE FALSE 41039.88506 47894.98375 42292.29009 43525.09125 39638.26737 45362.07232 35457.69538 44202.94648 35423.90833 36270.86197 1.131483589 1.320480991 1.166012821 1.200001568 1.092840512 1.250647761 0.977580721 1.218690268 0.9766492 1 15.14652341 1.806575252 0.361778048 0.986224179 1.234532929 0.362182412 0.090993524 1.306269815 0.498807897 0.110154953 0.108806119 64.05827687 -1.806575252 0.248308751 LLSDATVEKDESHAGK ddPTM_BT-474_Pertuzumab_2h_R1 6 LLSDATVEKDESHAGK 16 1 Q14320 Q14320 FAM50A Protein FAM50A 0 ;;;;; 274.6 1.85E-35 2665810000 3902420 3458820 2902620 2913710 3179100 3595600 3524790 3790370 4439760 4208640 FALSE TRUE 3749909.112 3360177.84 3427188.002 3064086.922 3281358.639 3668305.496 3567927.434 3712097.535 3935777.058 3923585.064 0.955735393 0.856404993 0.873483803 0.780940612 0.836316426 0.934937165 0.909353914 0.946098396 1.003107361 1 21.90374105 1.806647882 1.041821757 1.002840192 0.861291419 0.574325045 0.044765129 0.375642606 0.75436538 0.039345138 0.016383238 64.06899065 -1.806647882 -0.141548773 SGPIS(ph)PGIHSCDLTVEGLATVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGPISPGIHSCDLTVEGLATVTR 23 0 Q9BUB4-2;Q9BUB4 Q9BUB4-2 ADAT1 tRNA-specific adenosine deaminase 1 1 SGPIS(1)PGIHSCDLTVEGLATVTR;S(0.033)GPIS(0.967)PGIHSCDLTVEGLATVTR 332.19 9.06E-87 863230000 537330 563080 533330 743990 751440 693940 603750 521410 508760 577860 TRUE FALSE 516330.5496 547021.5097 629714.5949 782387.4131 775610.75 707971.9423 611138.8731 510642.7013 451007.6977 538721.0275 0.958437713 1.015407756 1.168906656 1.452305318 1.439726149 1.314171725 1.134425504 0.947879654 0.837182279 1 19.03917885 1.806788064 2.940201245 0.912550139 1.232168233 0.421516886 0.154669107 0.264320885 4.25654692 0.098774989 0.048802962 64.08967425 -1.806788064 0.319618094 MVIQLRPGRS(ph)PEPDGPAPAFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 MVIQLRPGRSPEPDGPAPAFLR 22 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 MVIQLRPGRS(1)PEPDGPAPAFLR;MVIQLRPGRS(1)PEPDGPAPAFLR 200.2 8.74E-23 2811000000 508240 614540 434390 502870 541780 575720 481410 477510 475490 465790 TRUE FALSE 488377.4189 597013.9209 512893.936 528823.181 559206.8457 587361.4529 487301.6396 467649.2516 421514.3686 434241.6284 1.124667436 1.374842672 1.181125674 1.21780858 1.287778069 1.352614338 1.122190061 1.076933258 0.970690834 1 18.72813851 1.806799343 2.034933531 0.998694754 1.256626177 0.67184251 0.075392095 0.173940399 1.393768521 0.04722531 0.020927733 64.09133876 -1.806799343 0.257931423 AVPMAPAPASPGS(ph)SNDSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVPMAPAPASPGSSNDSSAR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 AVPMAPAPAS(0.425)PGS(0.527)S(0.048)NDSSAR 272.13 2.13E-44 963400000 323600 313010 291320 342850 310580 327710 302310 280880 294660 280300 TRUE FALSE 310953.3542 304083.2613 343968.0044 360544.5296 320570.0878 334336.5207 306009.7602 275079.7298 261211.4321 261315.0313 1.189955865 1.163665403 1.316296283 1.379731306 1.226757168 1.279438534 1.171037727 1.052674729 0.999603547 1 17.99543059 1.806834521 1.891472968 1.000008312 1.262443613 0.776252104 0.058337184 0.160276609 1.108915796 0.043080071 0.018685877 64.09653034 -1.806834521 0.262435301 GSESFQGHGYHHPHSYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSESFQGHGYHHPHSYR 17 0 F5H2Q3;J3KNH0;Q96MD2 F5H2Q3 C12orf66 UPF0536 protein C12orf66 0 43.791 0.07299 24428000 5965.5 6649.1 4161.7 9350.2 5681.1 6507.5 6215.1 3109.3 5252.2 4347.2 FALSE TRUE 5732.361665 6459.474178 4913.811767 9832.764943 5863.837741 6639.086109 6291.162253 3045.091868 4655.992275 4052.760272 1.414433936 1.593845613 1.212460505 2.426189629 1.446875055 1.638164032 1.552315417 0.751362445 1.148844729 1 11.98468912 1.80687962 6.787258541 0.957553837 1.624801295 0.473362379 0.312011836 0.193844507 15.27533802 0.136675292 0.08095452 64.10318668 -1.80687962 0.667247458 PQS(ph)PSIPSS(ph)HLR ddPTM_BT-474_Pertuzumab_2h_R1 1 PQSPSIPSSHLR 12 0 Q9P2P6;H3BN21 Q9P2P6 STARD9 StAR-related lipid transfer protein 9 2 PQS(0.5)PS(0.5)IPS(0.015)S(0.985)HLR 55.776 0.066017 14488000000 2238300 3749600 3523900 2705200 3328400 3924900 2620900 1708700 1105900 1744400 TRUE FALSE 2150824.761 3642665.079 4160747.119 2844815.696 3435461.009 4004264.167 2652975.358 1673414.748 980362.8683 1626250.234 1.322566919 2.239916713 2.558491326 1.749309938 2.112504544 2.462268157 1.631345104 1.029002003 0.602836419 1 20.63311783 1.806954544 2.552397985 0.814270563 2.08883192 0.701513267 0.348324025 0.141028484 1.748659031 0.20291465 0.096330133 64.11424671 -1.806954544 1.274561357 KEES(ph)PPPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 KEESPPPPK 9 1 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 KEES(1)PPPPK;KEES(1)PPPPK;KEES(1)PPPPK;KEES(1)PPPPK 83.314 0.0099551 4540210000 5331900 4356230 3935010 3521290 4097280 4084910 4523170 5528500 6430500 5396400 TRUE FALSE 5123523.453 4231994.586 4646153.841 3703024.199 4229072.732 4167509.679 4578525.907 5414334.543 5700536.599 5030897.021 1.018411514 0.841200797 0.92352394 0.736056449 0.840620016 0.828383022 0.91008142 1.076216532 1.133105403 1 22.26238423 1.806992252 3.391143941 1.080757823 0.859962799 0.600076835 0.074717593 0.147842711 3.084678426 0.039268692 0.02013891 64.11981372 -1.806992252 -0.220795024 NSEEEEEEKKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSEEEEEEKKK 11 2 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 134.98 7.29E-05 233240000 114540 77273 56909 42216 68615 64160 77204 89341 113700 86409 FALSE TRUE 110063.6502 75069.2497 67193.72223 44394.77282 70822.06379 65457.35916 78148.84565 87496.07713 100793.2527 80556.44146 1.366292356 0.931883886 0.834119792 0.551101464 0.879160778 0.812565178 0.970112932 1.086146254 1.251212825 1 16.29771233 1.807045674 2.665420343 1.133436177 0.879157805 0.189573488 0.197009543 0.408912237 5.495859693 0.11870081 0.057071632 64.12770151 -1.807045674 -0.254278372 SKQEALKNDLVEALKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKQEALKNDLVEALKR 16 3 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 95.409 0.0016482 757940000 1890000 1983800 1364300 1152900 1400000 1697100 1638600 1785800 2134800 1858000 FALSE TRUE 1816136.71 1927223.966 1610859.359 1212401.307 1445032.271 1731416.525 1658653.677 1748922.606 1892466.454 1732156.005 1.048483338 1.1126157 0.929973602 0.69993771 0.834239103 0.999573087 0.957565988 1.009679614 1.09254966 1 20.72413744 1.807241684 1.703465787 1.045425666 0.929441718 0.14059568 0.108888429 0.770088629 4.297549298 0.08752334 0.036938374 64.1566508 -1.807241684 -0.115983948 NEVNGTSEDIKSEGDT(ph)QSN ddPTM_BT-474_Pertuzumab_2h_R1 1 NEVNGTSEDIKSEGDTQSN 19 1 O95232 O95232 LUC7L3 Luc7-like protein 3 1 NEVNGTSEDIKSEGDT(0.5)QS(0.5)N 303.7 2.65E-47 0 392020 318020 309430 321650 347270 328500 376930 420660 515020 444930 TRUE FALSE 376699.425 308950.381 365350.8842 338250.395 358440.2549 335142.4951 381542.9821 411973.224 456557.0887 414794.4948 0.908159172 0.744827583 0.880799743 0.815465006 0.864139374 0.80797238 0.919836176 0.993198389 1.100682614 1 18.66203722 1.80741174 2.001903645 1.048601233 0.835080606 0.756452923 0.049509338 0.133110343 1.031960469 0.029724304 0.013114701 64.18177739 -1.80741174 -0.213520627 SLKES(ph)EQES(ph)EEEILAQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLKESEQESEEEILAQK 17 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 S(0.123)LKES(0.877)EQES(1)EEEILAQK;S(0.013)LKES(0.987)EQES(1)EEEILAQK 179.58 5.17E-10 997450000 1185990 949700 940220 726510 924060 903430 1045870 1265940 1443120 1377790 TRUE FALSE 1139640.2 922615.4859 1110138.669 764005.2682 953783.2291 921697.9736 1058669.67 1239797.897 1279303.068 1284471.056 0.887244749 0.718284372 0.864276905 0.594801467 0.742549413 0.717570061 0.824206715 0.965220579 0.995976563 1 20.29274295 1.807464717 2.447969434 0.995925393 0.749904572 0.649271884 0.076599606 0.164307345 1.882366662 0.045084275 0.021147606 64.18960701 -1.807464717 -0.246020821 SREDEDALEQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SREDEDALEQAR 12 1 O60885 O60885 BRD4 Bromodomain-containing protein 4 0 78.814 0.022541 590030000 68858 58931 63371 53592 62717 64292 66284 85213 93656 84748 FALSE TRUE 66166.95323 57250.34558 74823.54938 56357.88954 64734.34926 65592.02829 67095.20342 83453.32177 83024.56352 79007.94247 0.837472173 0.724615068 0.947038323 0.713319291 0.819339768 0.830195373 0.849220994 1.056264967 1.050838193 1 16.26971007 1.807491365 3.822517393 1.04146313 0.8119346 0.720210817 0.062566681 0.10771946 2.792035655 0.030253454 0.015979021 64.19354577 -1.807491365 -0.22952853 RGSLT(ph)LTISGES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 2 RGS(0.316)LT(0.683)LT(0.002)IS(0.051)GES(0.947)PK 84.107 0.0071538 111100000 141300 109830 102750 84023 124340 116700 119660 157600 158670 172790 TRUE FALSE 135777.8398 106697.7559 121319.2107 88359.4371 128339.509 119059.754 121124.4349 154345.5049 140658.4468 161086.7794 0.842886302 0.662361966 0.753129531 0.548520725 0.796710379 0.739103199 0.751920396 0.958151287 0.873184301 1 17.29747857 1.807595263 3.940590472 0.938173457 0.719443695 0.604302185 0.080082346 0.146315893 4.009186998 0.039283354 0.020898646 64.2089049 -1.807595263 -0.218729762 IEAELQDICNDVLELLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEAELQDICNDVLELLDK 18 0 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ; 309.23 9.66E-61 1259830000 891640 850740 700380 834140 908470 784440 873590 1026660 1086100 1109170 FALSE TRUE 856793.723 826477.7282 826954.2459 877190.0654 937691.7626 800301.9143 884281.2557 1005459.112 962810.4813 1034044.928 0.828584619 0.799266749 0.799727578 0.848309432 0.906819169 0.773952749 0.855167152 0.972355345 0.931110879 1 19.97986744 1.807649672 4.076405328 0.96427701 0.827532469 0.744059225 0.037181717 0.112353735 3.276884315 0.018913692 0.010141651 64.21694959 -1.807649672 -0.136744541 GVPHPEDDHSQVEGPESLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVPHPEDDHSQVEGPESLR 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;; 235.7 2.09E-24 5503090000 1018520 1238500 1059590 1325350 1303500 1288580 1258690 242169 1306390 1224010 FALSE TRUE 978715.1124 1203179.193 1251081.483 1393751.472 1345428.261 1314635.97 1274094.225 237168.1255 1158094.084 1141106.712 0.857689383 1.054396736 1.096375536 1.221403272 1.179055602 1.152071017 1.116542573 0.207840444 1.014886751 1 20.12200228 1.80779517 24.99999998 0.653843126 1.105227616 0.312379466 0.231149873 132.3068472 47784.32908 0.092120484 0.058671478 64.23846722 -1.80779517 0.45138449 GIEGMIMKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GIEGMIMKR 9 1 Q13393-3;Q13393-4;Q13393-2;Q13393 Q13393-3 PLD1 Phospholipase D1 0 58.676 0.065073 190580000 166070 232350 209180 377930 269830 321530 222620 155480 105960 183320 FALSE TRUE 159579.8008 225723.6055 246983.4792 397435.0126 278509.327 328031.5569 225344.4902 152269.2837 93931.86502 170903.5731 0.933741746 1.320765865 1.445162759 2.325492705 1.629628462 1.919395545 1.318547565 0.890966063 0.549619082 1 17.38282303 1.807811912 2.82244744 0.76881558 1.61063696 0.482461295 0.360362322 0.222301865 3.317111973 0.216443791 0.105834393 64.24094374 -1.807811912 0.84182138 KPEDWDEEMDGEWEPPVIQNPEYK ddPTM_BT-474_Pertuzumab_2h_R1 12 KPEDWDEEMDGEWEPPVIQNPEYK 24 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;;;;;;;; 304.31 2.72E-62 22894230000 8363690 7810890 6777420 6622380 6947440 7264870 8098300 9370530 11061310 10001590 FALSE TRUE 8036827.748 7588131.065 8002250.557 6964161.825 7170910.717 7411770.649 8197409.418 9177025.281 9805676.462 9324173.401 0.861934608 0.813812736 0.85822627 0.746893213 0.769066641 0.794898414 0.879156689 0.984218642 1.051640295 1 23.1525444 1.807830681 2.158620323 1.025334195 0.80586126 0.866907081 0.035932085 0.102145865 0.918737343 0.024054758 0.010862348 64.24372007 -1.807830681 -0.219472935 HLGAVNTIVFVDENRR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLGAVNTIVFVDENRR 16 1 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 0 82.651 0.0061012 195710000 194640 313570 210800 367990 307240 328980 239360 165250 122620 169850 FALSE TRUE 187033.2536 304627.2906 248896.2492 386982.008 317122.6536 335632.201 242289.3593 161837.5298 108700.6917 158345.9082 1.181168846 1.923809046 1.571851474 2.443902797 2.002720861 2.119613982 1.530127062 1.022050595 0.686476164 1 17.27272006 1.807994718 2.49753239 0.850290761 1.891819916 0.641020824 0.324426224 0.166988435 1.985614603 0.194939569 0.092030379 64.26799002 -1.807994718 1.041529155 AES(ph)PAEKVPEESVLPLVQK ddPTM_BT-474_Pertuzumab_2h_R1 4 AESPAEKVPEESVLPLVQK 19 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK 288.91 9.91E-42 5266186000 5671800 4502873 4935785 4830840 4809072 5151425 5908989 7244256 8269060 8354936 TRUE FALSE 5450139.785 4374455.471 5827791.145 5080160.231 4963760.168 5255590.343 5981304.975 7094659.582 7330390.976 7789048.743 0.69971828 0.561616138 0.748203194 0.652218313 0.637274246 0.674740975 0.767912125 0.910850582 0.941115047 1 22.89301572 1.80800522 1.506790948 0.979379514 0.65631214 0.890194082 0.045711487 0.10964329 0.473323275 0.032709877 0.013476316 64.26954426 -1.80800522 -0.323067374 RRS(ph)PSPKPT(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSPSPKPTK 10 3 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 2 RRS(0.985)PS(0.102)PKPT(0.913)K 73.887 0.034769 125410000 194370 179720 162130 156130 186950 165080 187940 223610 273850 202510 TRUE FALSE 186773.8055 174594.5616 191430.4976 164187.888 192963.4165 168418.0307 190240.0659 218992.3754 242763.6961 188793.8173 0.989300435 0.924789615 1.013965925 0.869667717 1.022085465 0.892073867 1.007660466 1.159955228 1.28586677 1 17.52645199 1.808046273 3.506261227 1.168346093 0.953073835 0.542515563 0.079949253 0.148382323 3.281798088 0.038576008 0.019965058 64.27561978 -1.808046273 -0.215272258 GEPPHSELHPMK ddPTM_BT-474_Pertuzumab_2h_R1 3 GEPPHSELHPMK 12 0 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;Q5JV98 B4DR80 STK24 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit 0 ;; 98.407 0.0025307 479452000 458800 499780 418350 501620 492020 462640 503130 156382 543270 479380 FALSE TRUE 440869.5888 485526.7637 493955.1511 527508.6683 507846.2701 471994.8978 509287.4554 153152.6571 481600.2672 446911.1656 0.986481482 1.086405534 1.105264735 1.180343453 1.136347241 1.056126886 1.13957201 0.342691499 1.07761968 1 18.76962856 1.808129328 25 0.734489828 1.101389277 0.308277332 0.191349389 130.9793007 47077.60501 0.074928076 0.047764513 64.28791303 -1.808129328 0.366899448 AKPVATAPIPGTPWCVVWTGDER ddPTM_BT-474_Pertuzumab_2h_R1 2 AKPVATAPIPGTPWCVVWTGDER 23 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 182.39 3.61E-17 1013170000 918710 950690 742390 877150 824160 886010 842960 838560 848490 891340 FALSE TRUE 882805.7975 923577.252 876556.3874 922419.8166 850669.8549 903925.7293 853276.3966 821243.443 752172.9724 830968.7479 1.062381467 1.111446435 1.054860835 1.11005356 1.023708602 1.087797503 1.026845352 0.988296425 0.905176006 1 19.66443469 1.80819434 1.932946646 0.952585376 1.075248799 0.688333918 0.033412885 0.164154224 1.185679908 0.020771215 0.009076396 64.29753748 -1.80819434 0.122663423 SEDPPTT(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEDPPTTPIR 10 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0;H7C151 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEDPPT(0.02)T(0.98)PIR;SEDPPT(0.119)T(0.881)PIR 143 0.00038855 2780500000 2170770 2477650 2024230 2671570 2758520 2602160 2109790 2201820 1942910 2077900 TRUE FALSE 2085933.908 2406989.848 2390053.39 2809450.048 2847250.301 2654777.458 2135610.241 2156351.648 1722359.002 1937161.982 1.076798909 1.242534114 1.233791191 1.450291753 1.469804966 1.37044681 1.10244278 1.11314989 0.889114601 1 20.88551316 1.808548043 1.74333243 0.967731042 1.311007953 0.575785327 0.119400198 0.267082682 1.562651653 0.090669869 0.038526996 64.34992471 -1.808548043 0.343276911 DKSEEVQK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKSEEVQK 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 123.63 0.0012217 3146090000 3878600 3413780 2827250 2762830 2888420 3027530 3278780 3602140 4105890 3724840 FALSE TRUE 3727020.024 3316422.337 3338196.967 2905419.987 2981328.652 3088748.731 3318906.69 3527754.55 3639806.58 3472553.269 1.073279439 0.955038578 0.961309074 0.836681186 0.858540797 0.889474831 0.955754004 1.015896453 1.048164362 1 21.72756539 1.80859268 3.073988672 1.025812765 0.924321284 0.300170804 0.062516027 0.310652415 5.409600331 0.037125554 0.018590101 64.35653897 -1.80859268 -0.101491481 SYS(ph)PDGKES(ph)PSDKK ddPTM_BT-474_Pertuzumab_2h_R1 6 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.13)Y(0.085)S(0.786)PDGKES(0.887)PS(0.113)DKK;S(0.065)YS(0.935)PDGKES(1)PSDKK;S(0.108)Y(0.006)S(0.886)PDGKES(0.994)PS(0.006)DKK;S(0.101)Y(0.011)S(0.888)PDGKES(0.939)PS(0.061)DKK;S(0.15)Y(0.013)S(0.837)PDGKES(0.589)PS(0.41)DKK;S(0.441)Y(0.037)S(0.522)PDGKES(0.996)PS(0.004)DKK 145.88 4.54E-06 21098090000 8086330 5115580 5229250 3555770 5122330 5140430 5877130 7859170 9555850 7037340 TRUE FALSE 7770307.284 4969688.667 6174291.799 3739283.716 5287094.396 5244373.017 5949056.075 7696875.393 8471109.969 6560694.694 1.184372638 0.757494274 0.941103357 0.569952405 0.805874171 0.799362455 0.906772278 1.173179938 1.291191004 1 22.64541716 1.808669444 3.445520039 1.176937161 0.830970569 0.428187294 0.160420909 0.198542566 4.248837557 0.082631859 0.04260393 64.36791536 -1.808669444 -0.345966591 S(ph)PS(ph)PEPIYNSEGK ddPTM_BT-474_Pertuzumab_2h_R1 5 SPSPEPIYNSEGK 13 0 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 S(1)PS(1)PEPIYNSEGK;S(1)PS(1)PEPIYNSEGK;S(1)PS(1)PEPIYNSEGK;S(1)PS(1)PEPIYNSEGK;S(1)PS(1)PEPIYNSEGK 233.21 1.82E-16 1430780000 2587900 2112440 2918250 2861080 2502700 2453190 3131420 3673400 4223280 4277330 TRUE FALSE 2486762.007 2052195.279 3445642.691 3008740.682 2583201.618 2502795.183 3169743.255 3597543.006 3743870.96 3987622.629 0.623620196 0.514641296 0.864084446 0.754519914 0.647804935 0.627640932 0.794895493 0.902177398 0.938872935 1 21.92709746 1.808836276 1.882744126 0.964265334 0.676115948 0.662269073 0.088198838 0.215475316 1.475257453 0.063366035 0.027495561 64.39264666 -1.808836276 -0.288149386 LRS(ph)GSAS(ph)PMDLLS(ph)YFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRSGSASPMDLLSYFK 16 1 P11678 P11678 EPX Eosinophil peroxidase;Eosinophil peroxidase light chain;Eosinophil peroxidase heavy chain 3 LRS(0.998)GS(0.133)AS(0.641)PMDLLS(0.645)Y(0.583)FK 57.328 0.020363 0 32456 36241 29591 36489 39021 40068 37534 19864 40802 37913 TRUE FALSE 31187.58364 35207.44216 34938.75195 38372.20166 40276.1459 40878.20241 37993.35232 19453.80146 36170.32802 35345.11874 0.882373147 0.996104792 0.988502888 1.085643592 1.139510839 1.156544492 1.074925016 0.550395702 1.023347192 1 15.10922337 1.80885751 25 0.808437727 1.051427979 0.245611295 0.143387136 151.692728 53957.66187 0.058867999 0.037593342 64.39579513 -1.80885751 0.242990252 EADPEDGKPVMDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EADPEDGKPVMDK 13 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 81.904 0.012588 409990000 856410 800950 639370 591390 726660 752230 784480 952210 1087400 1007500 FALSE TRUE 822940.5504 778107.6902 754918.3817 621911.7088 750033.6788 767440.606 794080.7009 932546.5307 963962.9108 939261.1276 0.87615736 0.828425309 0.803736426 0.662128657 0.798535846 0.817068421 0.845431241 0.992851193 1.026299165 1 19.84116678 1.808896294 2.160594492 1.018495366 0.792639541 0.768289165 0.051408714 0.1449997 1.305411114 0.035111721 0.015874236 64.40154609 -1.808896294 -0.225855825 FGLSVGHHLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 FGLSVGHHLGK 11 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 130.98 0.00012307 5873600000 9266100 13439200 10121100 14024200 11662200 12445800 12391700 4895400 12368900 13563600 FALSE TRUE 8903970.568 13055927.17 11950207.91 14747990.64 12037325.25 12697462.6 12543353.33 4794308.279 10964834.33 12644925.29 0.704153671 1.032503307 0.94505959 1.166316946 0.9519491 1.004154814 0.991967374 0.379148802 0.867133184 1 23.59205518 1.808979699 25 0.680369015 0.980319519 0.205383345 0.185503708 151.8869054 53932.97338 0.073076167 0.046678995 64.4139154 -1.808979699 0.299950503 ILQEAWTEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILQEAWTEGR 10 0 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 0 ; 132.01 0.00054663 273070000 104306 110134 95091 111627 106376 130173 109032 105200 109689 119704 FALSE TRUE 100229.6062 106993.0862 112276.059 117388.0828 109797.6806 132805.1872 110366.3662 103027.5832 97237.56457 111596.3415 0.898144194 0.95875084 1.006090859 1.051899026 0.983882439 1.190049651 0.988978355 0.923216495 0.871332907 1 16.76793021 1.80903983 4.610156228 0.923719727 1.01741007 0.184499971 0.07669454 0.332951929 12.15760031 0.038398807 0.021192018 64.42283461 -1.80903983 0.093690343 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK ddPTM_BT-474_Pertuzumab_2h_R1 12 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK 38 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;; 333.6 9.23E-130 3302621500 905518.8 1632633.8 1150967.8 1774793 1666018.5 1673437.3 1419909.1 522580.12 839126.2 1089756.2 FALSE TRUE 870130.1242 1586072.683 1358973.285 1866390.279 1719607.498 1707275.349 1437286.372 511788.6579 743872.1117 1015946.042 0.856472773 1.561178072 1.337643171 1.837095872 1.692616957 1.68047837 1.414727075 0.503755748 0.732196476 1 19.95439235 1.809172375 6.101924428 0.711152011 1.514324644 0.598566794 0.276070202 0.13754111 8.624988664 0.125926923 0.073507726 64.44249928 -1.809172375 0.803172633 ADS(ph)DSEDKGEESKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADSDSEDKGEESKPK 15 2 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 1 ADS(0.86)DS(0.14)EDKGEESKPK 87.85 0.0082748 0 177200 111510 103750 88398 109720 109510 140300 175930 243330 165450 TRUE FALSE 170274.8281 108329.844 122499.9329 92960.23137 113249.2434 111724.3672 142017.0334 172296.984 215708.1985 154243.9241 1.103932158 0.702328112 0.794196164 0.602683262 0.734221747 0.724335612 0.920730163 1.117042276 1.398487491 1 17.23485414 1.809174054 2.376409274 1.209571231 0.766325385 0.570296142 0.152844241 0.183645988 1.985536553 0.089843545 0.041827569 64.44274835 -1.809174054 -0.443245845 S(ph)PESRPSVVYPSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPESRPSVVYPSTK 14 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 S(0.99)PES(0.01)RPSVVYPSTK 146.78 5.04E-06 0 64232 59743 54457 60932 61210 57389 64682 76779 81523 86406 TRUE FALSE 61721.74243 58039.18813 64298.59129 64076.70782 63178.87524 58549.4449 65473.59766 75193.48682 72268.85081 80553.64466 0.766219116 0.720503565 0.798208344 0.795453863 0.784308091 0.726837937 0.812794976 0.933458531 0.897151844 1 16.29766224 1.809325415 2.868053095 0.941667057 0.766679948 0.846949759 0.033875248 0.093325151 1.431076588 0.018920323 0.009304071 64.465212 -1.809325415 -0.174987109 AFPEHFTYEPNEADAAQGYR ddPTM_BT-474_Pertuzumab_2h_R1 3 AFPEHFTYEPNEADAAQGYR 20 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 0 ;; 286 3.65E-45 768680000 654190 728710 641220 864030 764020 734030 719570 660710 690700 699250 FALSE TRUE 628623.5316 707927.9043 757102.7179 908622.6918 788595.3972 748872.5895 728376.3129 647066.1076 612294.6317 651889.1747 0.964310432 1.085963584 1.161397899 1.393830005 1.209707766 1.148772857 1.117331505 0.9926014 0.939261849 1 19.31426719 1.809328849 2.252593062 0.965366866 1.169919981 0.394209572 0.101714733 0.312439272 3.048732401 0.069405569 0.031793863 64.46572169 -1.809328849 0.204553115 NNKNEFVSLINCSSQPPLISHGIGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NNKNEFVSLINCSSQPPLISHGIGK 25 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 181.38 1.45E-17 390430000 339860 267010 216940 254330 260250 257530 285860 310630 360290 333650 FALSE TRUE 326577.8955 259395.1362 256145.8838 267456.0018 268621.1776 262737.433 289358.4402 304215.3819 319391.3897 311051.5883 1.049915537 0.833929631 0.823483607 0.859844514 0.863590439 0.844674784 0.930258681 0.978022275 1.026811634 1 18.24679435 1.809412025 2.121914206 1.010098944 0.87340938 0.442676902 0.06126441 0.265457288 2.305980387 0.03865098 0.017385804 64.47806929 -1.809412025 -0.136689564 YFDGSGGNNHAVEHYR ddPTM_BT-474_Pertuzumab_2h_R1 4 YFDGSGGNNHAVEHYR 16 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 212.7 2.21E-12 6892900000 2718440 2979940 2596860 3195300 2936620 2527100 2950930 266705 2954260 2943720 FALSE TRUE 2612200.359 2894955.029 3066170.369 3360209.816 3031079.049 2578199.693 2987044.364 261197.4485 2618904.79 2744339.222 0.95185039 1.054882358 1.117270906 1.224414893 1.104484105 0.939461008 1.088438463 0.095176808 0.954293394 1 21.38802739 1.809436748 25 0.583562157 1.072420593 0.316955757 0.246638221 122.0191246 43047.84683 0.097210288 0.062155494 64.48173997 -1.809436748 0.488858436 LNATNIELATVQPGQNFHMFTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNATNIELATVQPGQNFHMFTK 22 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 147.75 1.96E-09 0 153800 162400 140500 139400 171700 154250 152820 150510 167880 151490 FALSE TRUE 147789.326 157768.511 165891.4754 146594.4507 177222.8864 157369.0407 154690.2569 147401.9159 148822.9662 141229.4474 1.046448377 1.117107756 1.174623837 1.037987852 1.254857891 1.114279236 1.095311635 1.043705252 1.053767249 1 17.10768141 1.809502023 1.912747724 1.028587387 1.12783635 0.329441725 0.058882148 0.379370529 2.680716112 0.038640161 0.0168521 64.4914324 -1.809502023 0.099248964 KGDNVPQVNGENTER ddPTM_BT-474_Pertuzumab_2h_R1 1 KGDNVPQVNGENTER 15 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 104.2 0.0022655 181750000 136040 137440 119570 119390 135900 132740 135570 165670 166200 171730 FALSE TRUE 130723.4064 133520.3458 141178.9588 125551.7322 140271.3469 135424.0937 137229.1462 162248.8566 147333.6728 160098.5741 0.816518243 0.833988351 0.88182521 0.78421518 0.876156129 0.845879449 0.857154081 1.013430991 0.920268488 1 17.28860093 1.809671155 6.263983625 0.975799675 0.841927152 0.762856973 0.034696542 0.09825098 6.447145813 0.014712246 0.008632479 64.51655291 -1.809671155 -0.133872523 RRS(ph)PS(ph)PKPTK ddPTM_BT-474_Pertuzumab_2h_R1 4 RRSPSPKPTK 10 3 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 2 RRS(1)PS(0.994)PKPT(0.006)K;RRS(0.997)PS(0.982)PKPT(0.02)K;RRS(1)PS(0.93)PKPT(0.07)K;RRS(1)PS(0.969)PKPT(0.031)K 95.981 0.010123 10888620000 2056700 1625370 1451670 1377180 1587770 1525700 1681940 2051560 2378200 1859650 TRUE FALSE 1976321.89 1579016.039 1714019.061 1448256.425 1638842.064 1556550.699 1702524.085 2009194.569 2108236.706 1733694.249 1.139948345 0.910781148 0.988651293 0.835358614 0.945288978 0.897823074 0.982020957 1.158909404 1.216037203 1 20.72541806 1.809945924 4.473839913 1.140229329 0.946866029 0.418542195 0.09019272 0.178455308 6.133593996 0.042412442 0.023272553 64.55738403 -1.809945924 -0.1933633 GFYDPPRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFYDPPRR 8 1 P31942;P31942-3;P31942-2 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ; 72.138 0.075248 2412900000 3846100 4198700 3316100 4164700 4092700 4241700 3842000 3813200 3937400 3985900 FALSE TRUE 3695790.16 4078957.187 3915393.036 4379640.666 4224345.412 4327470.08 3889019.545 3734456.087 3490442.859 3715931.443 0.994579749 1.097694414 1.053677415 1.178611805 1.136820062 1.164572099 1.046580004 1.004985196 0.939318422 1 21.82529245 1.810121097 2.493703876 0.973770304 1.106111216 0.515845043 0.05298623 0.220271992 2.605831489 0.03257746 0.015400048 64.58342853 -1.810121097 0.132340912 GVTECYECHPKPTQR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVTECYECHPKPTQR 15 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;; 260.96 3.79E-25 6037520000 4707630 4873190 4099780 4644250 4743960 4974840 4749380 4616580 5262130 4974570 FALSE TRUE 4523650.615 4734211.393 4840701.445 4883940.299 4896553.782 5075434.673 4807504.333 4521246.01 4664795.063 4637637.943 0.975421253 1.020823844 1.043785976 1.05310944 1.055829248 1.0944008 1.036627782 0.974902756 1.005855809 1 22.14495876 1.810194387 7.245708814 0.992204508 1.042803227 0.344138734 0.029211248 0.282135011 24.03226525 0.013796372 0.00828753 64.59432836 -1.810194387 0.050598719 IGDKDVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IGDKDVGR 8 1 P45877 P45877 PPIC Peptidyl-prolyl cis-trans isomerase C 0 88.948 0.012999 145330000 225110 239800 146330 212710 176080 206110 221050 236090 271280 264930 FALSE TRUE 216312.4523 232961.1388 172775.0861 223687.9886 181743.7731 210277.6854 223755.276 231214.659 240485.4317 246986.0551 0.875808362 0.943215756 0.699533769 0.905670518 0.735846293 0.851374728 0.905942953 0.936144589 0.973680201 1 17.91407006 1.810211639 1.444560728 0.985412218 0.83251716 0.442894321 0.069124284 0.372246316 1.469737941 0.05134486 0.021064878 64.59689441 -1.810211639 -0.152895058 VGEGDKEDATR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGEGDKEDATR 11 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 82.774 0.016432 687870000 1691500 1580800 1288600 1227400 1392600 1338000 1490600 1694300 1950900 1666000 FALSE TRUE 1625394.31 1535717.132 1521478.685 1290746.261 1437394.244 1365055.277 1508842.409 1659312.113 1729442.011 1553160.336 1.046507738 0.988769219 0.979601815 0.831045083 0.925464172 0.878888834 0.971465968 1.068345666 1.113498697 1 20.56677534 1.810419948 3.820942526 1.068452748 0.93905677 0.422838955 0.061711712 0.211137832 5.424299729 0.033246777 0.017601605 64.6278856 -1.810419948 -0.129395978 SLS(ph)PQLLQQMPSKPEGAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSPQLLQQMPSKPEGAAK 19 1 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.192)LS(0.808)PQLLQQMPSKPEGAAK;S(0.146)LS(0.854)PQLLQQMPSKPEGAAK 240.49 1.53E-24 4094600000 3637900 3543700 3258200 3003300 3000400 3557700 3635100 4232100 4833000 4635000 TRUE FALSE 3495726.846 3442637.146 3847029.218 3158300.673 3096910.591 3629639.132 3679587.441 4144705.656 4284378.102 4321067.322 0.808996154 0.796709907 0.890296062 0.730907537 0.71670038 0.839986712 0.851545965 0.959185624 0.991509223 1 22.04295628 1.810433365 1.642558339 0.999429096 0.793147225 0.772417187 0.04573499 0.176071329 0.909916237 0.034925148 0.014654709 64.62988233 -1.810433365 -0.206281872 DKAPVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_BT-474_Pertuzumab_2h_R1 5 DKAPVQPQQSPAAAPGGTDEKPSGK 25 2 Q13200;C9JPC0;F8WBS8 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK 250.98 4.12E-40 25854700000 11368130 9297170 9101170 7570580 8824540 9373280 10011490 11843240 13946080 12080970 TRUE FALSE 10923850.91 9032023.814 10745953.87 7961298.541 9108389.343 9562814.144 10134013.61 11598672.96 12362979.47 11262715.14 0.969912741 0.801940181 0.954117523 0.70687205 0.808720564 0.849068277 0.899784242 1.029829203 1.09769086 1 23.42505133 1.810453894 2.486973066 1.054934165 0.843497665 0.578521539 0.074079545 0.183189825 2.155444437 0.043236899 0.020428233 64.63293734 -1.810453894 -0.2114365 EGPGEEHFEDMAS(ph)DEDMKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGPGEEHFEDMASDEDMKPK 20 1 Q99856 Q99856 ARID3A AT-rich interactive domain-containing protein 3A 1 EGPGEEHFEDMAS(1)DEDMKPK 193.54 4.22E-18 364420000 264240 193440 147420 119180 190360 174070 191980 228950 277490 214330 TRUE FALSE 253913.2087 187923.2806 174062.0733 125330.8941 196483.1023 177589.8147 194329.5087 224222.1025 245990.4985 199813.2382 1.270752684 0.940494645 0.87112383 0.627240193 0.983333757 0.888779023 0.972555725 1.122158394 1.231102107 1 17.60829264 1.810504571 3.170314831 1.134988491 0.917452091 0.218904342 0.156430393 0.338504994 6.213273098 0.087009597 0.043989599 64.64047968 -1.810504571 -0.217536401 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 37 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 413.45 1.78E-199 7447900000 3149600 2342590 2088020 1536780 1963460 1887410 2336750 2969230 3567750 2676570 FALSE TRUE 3026510.15 2275781.627 2465371.662 1616093.4 2026616.474 1925574.723 2365347.846 2907914.363 3162753.977 2495283.53 1.212892288 0.912033282 0.988012638 0.647659226 0.812178837 0.771685742 0.947927487 1.165364308 1.267492828 1 21.25077232 1.810591593 3.841809274 1.162818836 0.880515608 0.35275351 0.152394492 0.232266402 6.0233629 0.079815613 0.042316784 64.65343341 -1.810591593 -0.282303227 TTAPTEGKS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 3 TTAPTEGKSPLK 12 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 TTAPTEGKS(1)PLK;TTAPTEGKS(1)PLK;TTAPTEGKS(1)PLK 157.68 3.94E-05 1462530000 1334550 993570 1051220 943610 1033260 991520 1216110 1491850 1707010 1654890 TRUE FALSE 1282394.311 965234.3564 1241198.838 992309.8252 1066495.746 1011569.214 1230993.118 1461042.776 1513237.381 1542802.826 0.831210761 0.625636886 0.804509051 0.643186419 0.691271579 0.655669796 0.797894 0.947005509 0.980836537 1 20.55712226 1.810593403 2.398213786 0.985661553 0.705581108 0.781923335 0.063156495 0.115195013 1.265501437 0.035646527 0.016661411 64.65370293 -1.810593403 -0.280080445 VDS(ph)PTVTTTLK ddPTM_BT-474_Pertuzumab_2h_R1 6 VDSPTVTTTLK 11 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0 Q07866-6 KLC1 Kinesin light chain 1 1 VDS(0.859)PT(0.14)VTTTLK;VDS(1)PTVTTTLK;VDS(0.953)PT(0.047)VTTTLK;VDS(0.972)PT(0.028)VTTTLK;VDS(0.998)PT(0.002)VTTTLK;VDS(0.545)PT(0.453)VT(0.002)TTLK 241.31 1.07E-15 1180130000 2519760 2325450 2583030 2349640 2683750 2726610 2988370 3504590 4048230 4099800 TRUE FALSE 2421284.993 2259130.443 3049840.98 2470905.202 2770075.256 2781743.922 3024942.566 3432218.992 3588691.902 3822116.894 0.633493182 0.591067857 0.797945501 0.646475571 0.724748963 0.727801896 0.791431202 0.897989017 0.938927825 1 21.86594047 1.810706244 0.738172251 1.007408454 0.662549437 0.849361177 0.050388166 0.226828659 0.239938952 0.044916342 0.022045216 64.6705037 -1.810706244 -0.344859017 RIDFTPVS(ph)PAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 5 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 2 RIDFT(0.001)PVS(0.999)PAPS(0.869)PT(0.131)R;RIDFT(0.026)PVS(0.974)PAPS(0.961)PT(0.039)R;RIDFT(0.037)PVS(0.963)PAPS(0.5)PT(0.5)R;RIDFT(0.006)PVS(0.994)PAPS(0.988)PT(0.012)R;RIDFT(0.027)PVS(0.973)PAPS(0.646)PT(0.354)R 218.66 1.28E-12 1776226000 2172350 2118760 1602153 1828831 1977750 1925810 1629927 1874140 1579130 1676743 TRUE FALSE 2087452.16 2058335.039 1891697.687 1923217.187 2041366.125 1964751.198 1649874.534 1835438.354 1399873.783 1563175.703 1.335391892 1.31676499 1.210163184 1.230326945 1.305909579 1.256897221 1.055463267 1.174172776 0.895531948 1 20.57604852 1.810761085 0.943229918 0.965678549 1.282603027 0.745534738 0.070782207 0.274390655 0.453258321 0.059974189 0.025807499 64.67867057 -1.810761085 0.316924477 RPS(ph)RHDNSAIGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPSRHDNSAIGR 12 2 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR 175.27 1.47E-05 238917000 90580 140815 85697 136882 110756.7 136535 105344.2 86582.3 77205.5 97732.3 TRUE FALSE 87040.03346 136799.0941 101184.3542 143946.4964 114319.2898 139295.8312 106633.4338 84794.34525 68441.45531 91112.80427 0.955299688 1.50142557 1.110539348 1.579871211 1.254700596 1.528828274 1.170345208 0.930652348 0.751172745 1 16.47536619 1.810807586 2.939300302 0.871050709 1.329608353 0.499104698 0.190475133 0.184027031 2.944756193 0.098112512 0.048629712 64.68559628 -1.810807586 0.458557643 AGAGMITQHSSNAS(ph)PINR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGAGMITQHSSNASPINR 18 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 1 AGAGMITQHSS(0.001)NAS(0.999)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR 298.91 1.22E-49 4025180000 1312060 2433210 1835940 2565790 1891070 2566180 2003490 1607530 1450650 2102500 TRUE FALSE 1260783.245 2363817.233 2167735.198 2698210.729 1951897.984 2618069.918 2028009.31 1574333.944 1285978.294 1960095.802 0.643225317 1.205970254 1.105933289 1.376570842 0.995817644 1.335684672 1.034648055 0.803192345 0.656079306 1 20.90249274 1.810979582 3.829918434 0.796917481 1.125048797 0.278564778 0.206519614 0.253825643 6.538711754 0.10127783 0.053673588 64.71121912 -1.810979582 0.328131316 GDDQLELIKDDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDDQLELIKDDEK 13 1 P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 163.23 3.57E-05 474250000 512780 394210 624650 631690 511710 572340 825490 985960 1180550 1261200 FALSE TRUE 492739.9907 382967.5168 737538.1503 664291.5966 528169.6169 583913.1069 835592.5936 965599.5815 1046538.913 1175777.801 0.419075773 0.325714192 0.627276812 0.564980557 0.4492087 0.496618584 0.710672198 0.821243249 0.890082219 1 20.16518401 1.811002353 1.033526057 0.980749858 0.467969424 0.855236959 0.079756291 0.190631079 0.376603935 0.07184281 0.030046678 64.71461216 -1.811002353 -0.512780434 down ESTSSKS(ph)PPRK ddPTM_BT-474_Pertuzumab_2h_R1 6 ESTSSKSPPRK 11 2 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 EST(0.001)S(0.131)S(0.298)KS(0.57)PPRK;ES(0.007)T(0.006)S(0.026)S(0.119)KS(0.843)PPRK;ES(0.001)T(0.001)S(0.005)S(0.071)KS(0.922)PPRK;ES(0.014)T(0.012)S(0.262)S(0.158)KS(0.555)PPRK;ES(0.001)T(0.005)S(0.019)S(0.02)KS(0.955)PPRK;ES(0.003)T(0.002)S(0.041)S(0.273)KS(0.681)PPRK 80.507 0.019074 51647300000 1305730 1168850 965260 959530 1050530 1185790 1140160 1291160 1529950 1312940 TRUE FALSE 1254700.628 1135515.542 1139703.954 1009051.458 1084321.252 1209767.486 1154113.619 1264497.095 1356276.49 1224013.404 1.025070987 0.927698617 0.931120484 0.824379418 0.885873674 0.988361305 0.942892958 1.033074548 1.108056893 1 20.22318793 1.811068036 1.784944162 1.059730445 0.922065242 0.463503977 0.056505978 0.294855185 1.808785065 0.040466624 0.017336544 64.72440049 -1.811068036 -0.137665202 KKS(ph)PNELVDDLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKSPNELVDDLFK 13 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK 183.88 5.20E-06 5961800000 4885300 3745500 3379000 2552980 3463900 3439200 4087800 4843300 6026500 5041800 TRUE FALSE 4694377.075 3638682.007 3989660.465 2684739.604 3575319.489 3508742.98 4137827.719 4743284.162 5342396.985 4700314.395 0.998736825 0.774135877 0.84880715 0.571182984 0.760655392 0.746491125 0.880329989 1.009141892 1.136604179 1 22.16432583 1.811158359 2.238799109 1.068454207 0.775949819 0.562563069 0.10459409 0.208516192 2.007592926 0.065980995 0.030215326 64.73786298 -1.811158359 -0.292504388 GSS(ph)GSPAHAESYSSGGGGQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 GS(0.067)S(0.526)GS(0.405)PAHAES(0.002)YSSGGGGQQK 263.18 6.29E-37 632820000 417340 437540 372650 451570 360230 446000 424820 376640 479480 450370 TRUE FALSE 401029.8914 425061.7876 439996.1446 474875.5818 371817.1251 455018.4256 430019.0742 368862.2524 425051.4405 419866.0388 0.955137721 1.012374778 1.047944115 1.131016891 0.885561324 1.083722863 1.024181607 0.878523668 1.012350134 1 18.67956957 1.811235265 25 0.95025312 1.022324634 0.106724388 0.07144001 228.4009538 78584.1093 0.028657302 0.018379063 64.74932788 -1.811235265 0.072071514 DVEEEKFPTQLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVEEEKFPTQLSR 13 1 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ; 169.04 2.66E-05 2608600000 2227250 2016190 1780000 2085030 2071410 1935610 2262110 2775400 3043000 3104800 FALSE TRUE 2140206.608 1958690.235 2101685.596 2192638.648 2138038.784 1974749.36 2289794.379 2718087.02 2697571.397 2894509.131 0.739402265 0.676691676 0.72609396 0.757516577 0.738653322 0.68223981 0.791082106 0.939049385 0.931961613 1 21.46488728 1.811340539 2.503867859 0.961592235 0.72075665 0.931463426 0.028746585 0.063603552 0.757230728 0.01711269 0.00810754 64.76502529 -1.811340539 -0.240835585 T(ph)KSPKPAESPQSATK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKSPKPAESPQSATK 15 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 T(0.761)KS(0.219)PKPAES(0.02)PQSATK 179.41 3.20E-05 715930000 465860 343190 303850 298340 295010 291460 347370 462910 499150 407020 TRUE FALSE 447653.6762 333402.5572 358762.4541 313737.3632 304499.2646 297353.5209 351621.218 453350.7467 442488.5846 379452.1729 1.179736758 0.878641845 0.945474765 0.82681662 0.802470736 0.783638999 0.926654907 1.194750694 1.166124788 1 18.53355853 1.811348137 5.950234936 1.135718715 0.893331788 0.416320149 0.115357347 0.191217699 11.19629186 0.053191358 0.030986346 64.76615824 -1.811348137 -0.242386927 DGLAPEKTS(ph)PDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLAPEKTSPDR 12 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.147)S(0.853)PDR;DGLAPEKT(0.133)S(0.867)PDR 145.43 3.87E-05 1652020000 1284870 1174870 1363370 1343780 1209430 1128110 1447320 1715480 1980730 1878070 TRUE FALSE 1234655.86 1141363.858 1609761.287 1413132.647 1248332.414 1150921.157 1465032.735 1680054.739 1755885.834 1750866.646 0.705168416 0.651885088 0.919408277 0.80710467 0.712979722 0.657343699 0.836747184 0.959556082 1.002866688 1 20.73963778 1.811439042 2.678067995 0.994200884 0.747890407 0.683884734 0.074318576 0.163932558 2.211054695 0.045895697 0.022176837 64.77971636 -1.811439042 -0.246310477 TLDS(ph)DEERPRPAPPDWSHMR ddPTM_BT-474_Pertuzumab_2h_R1 10 TLDSDEERPRPAPPDWSHMR 20 2 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 T(0.006)LDS(0.994)DEERPRPAPPDWSHMR;T(0.004)LDS(0.996)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.053)LDS(0.947)DEERPRPAPPDWSHMR;T(0.121)LDS(0.879)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.042)LDS(0.958)DEERPRPAPPDWSHMR;T(0.028)LDS(0.972)DEERPRPAPPDWSHMR;T(0.006)LDS(0.994)DEERPRPAPPDWSHMR 267.71 3.39E-37 16434710000 3741630 3933880 3220281 3335571 3489796 3890205 3584827 3374937 3725337 3648622 TRUE FALSE 3595402.963 3821689.594 3802257.411 3507720.219 3602048.458 3968867.61 3628699.185 3305243.372 3302452.362 3401497.582 1.057005885 1.123531475 1.117818643 1.031228197 1.058959582 1.166800068 1.06679458 0.971702402 0.970881878 1 21.69773863 1.811484787 4.32191542 0.978633809 1.092410861 0.639135883 0.037458898 0.135711208 4.348095667 0.01890954 0.010310226 64.78654012 -1.811484787 0.113777051 SQEPLPDDDEEFELPEFVEPFLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SQEPLPDDDEEFELPEFVEPFLK 23 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 148.29 1.08E-07 422450000 568329 579354 475111 553780 571409 565613 574870 668200 707440 702120 FALSE TRUE 546118.0744 562831.3912 560974.1265 582360.6522 589788.8894 577050.0824 581905.431 654401.4365 627134.377 654564.787 0.834322416 0.859855896 0.857018492 0.889691385 0.901039746 0.881578254 0.888995929 0.999750444 0.958093667 1 19.32017647 1.811660697 4.459775412 0.984374706 0.87281109 0.860490183 0.020853264 0.079511005 2.696936602 0.010860403 0.005964402 64.812787 -1.811660697 -0.111563617 DLKPQNLLIDDKGTIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLKPQNLLIDDKGTIK 16 2 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 140.02 9.79E-07 1603720000 1144370 964560 790080 634030 920140 938340 960570 1130750 1334980 1191060 FALSE TRUE 1099646.755 937051.6932 932865.0312 666752.3643 949737.1387 957313.8777 972325.743 1107399.617 1183438.667 1110388.445 0.990326187 0.843895393 0.840124945 0.600467672 0.855319724 0.862143227 0.875662699 0.997308304 1.065787988 1 20.08263303 1.81214448 1.759577262 1.038397592 0.821322952 0.464721503 0.091119741 0.307835973 1.832899024 0.066162055 0.028264411 64.88502559 -1.81214448 -0.21707464 DGGQTES(ph)NEEGKENR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGGQTESNEEGKENR 15 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 DGGQT(0.022)ES(0.978)NEEGKENR;DGGQT(0.04)ES(0.96)NEEGKENR;DGGQT(0.001)ES(0.999)NEEGKENR;DGGQTES(1)NEEGKENR 167.92 7.77E-07 1137250000 554699 462982 393659 343944 440322 402122 448173 547163 605694 499750 TRUE FALSE 533020.7498 449778.2067 464801.9382 361694.9911 454485.357 410253.1824 453657.8752 535863.8928 536938.1564 465901.4874 1.144063207 0.965393369 0.997639954 0.776333626 0.975496686 0.880557786 0.973720599 1.150165662 1.152471436 1 18.82966541 1.812187416 5.720634169 1.113531697 0.950176079 0.311382832 0.095813404 0.230879481 12.45613483 0.043992479 0.025462634 64.89144058 -1.812187416 -0.163355618 KPS(ph)PEPEGEVGPPK ddPTM_BT-474_Pertuzumab_2h_R1 9 KPSPEPEGEVGPPK 14 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK 172.24 2.19E-06 15051540000 10764820 9159530 8430040 7718830 8527390 8405190 9465580 11410670 12858260 11574010 TRUE FALSE 10344118.93 8898309.173 9953535.753 8117199.741 8801681.244 8575148.701 9581422.6 11175035.68 11398644.23 10790091.99 0.95866828 0.824674079 0.922469962 0.752282719 0.815718833 0.794724337 0.887983402 1.035675663 1.05639917 1 23.36320383 1.812248976 3.511416703 1.036126984 0.841863348 0.673437239 0.057828583 0.1296344 2.848814291 0.03021049 0.015694552 64.90063947 -1.812248976 -0.194263636 REPVSLEEWTK ddPTM_BT-474_Pertuzumab_2h_R1 1 REPVSLEEWTK 11 1 Q8TC07-2;Q8TC07-3;Q8TC07;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 77.22 0.031911 0 127250 138110 124270 136520 140640 133480 137220 121140 154670 145660 FALSE TRUE 122276.9293 134171.238 146728.3534 143565.8136 145163.8133 136179.0571 138899.3394 118638.4167 137112.51 135794.3185 0.900456887 0.988047509 1.08051909 1.057229899 1.068997694 1.002833245 1.022865618 0.873662595 1.009707266 1 17.05106359 1.812506629 25 0.94720716 1.021556931 0.143676672 0.059365199 184.6312693 62432.2231 0.025121288 0.016136053 64.93915443 -1.812506629 0.074349771 SACKEDIPSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SACKEDIPSEK 11 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 120.59 0.0003937 550600000 3117800 2290200 1831500 1680200 2239400 2297400 2318900 2761300 3136500 2741800 FALSE TRUE 2995952.929 2224885.738 2162492.791 1766915.323 2311432.335 2343855.002 2347279.392 2704278.19 2780457.669 2556095.444 1.172081792 0.870423577 0.846014102 0.691255613 0.904282483 0.916966934 0.91830663 1.057972306 1.087775371 1 21.28551028 1.812550031 3.125479026 1.057035958 0.888309425 0.256042524 0.112664447 0.318723774 5.683359345 0.063178049 0.031874873 64.94564443 -1.812550031 -0.168726532 NKKDELQSER ddPTM_BT-474_Pertuzumab_2h_R1 1 NKKDELQSER 10 2 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 72.846 0.026301 313130000 306240 271110 183750 226500 258760 224880 279410 299180 376580 318530 FALSE TRUE 294271.8022 263378.2082 216957.7125 238189.6921 267083.2504 229427.2277 282829.5032 293001.8284 333832.2172 296955.6794 0.990962028 0.886927668 0.730606375 0.802105192 0.899404419 0.772597541 0.952430018 0.986685384 1.124181958 1 18.1798881 1.812824588 2.054784189 1.054741547 0.844839052 0.550083157 0.076873252 0.22888494 1.86189025 0.050450295 0.022538427 64.98671551 -1.812824588 -0.209902494 DLGLSESGEDVNAAILDESGKK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLGLSESGEDVNAAILDESGKK 22 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;; 327.06 1.92E-80 2092380000 1345710 1284600 1213230 1050760 1191050 1262050 1333590 1580990 1843670 1642690 FALSE TRUE 1293118.165 1247964.466 1432487.649 1104989.85 1229361.205 1287569.516 1349910.873 1548342.004 1634384.311 1531429.143 0.844386547 0.814901866 0.935392705 0.72154161 0.802754218 0.840763362 0.881471323 1.011043842 1.067228163 1 20.54644719 1.812849141 2.268457549 1.038466573 0.825259624 0.751061323 0.051463498 0.138174464 1.36249862 0.031940671 0.014706973 64.99038961 -1.812849141 -0.213206949 DS(ph)IARQVAPES(ph)HWPELRVLILVVS(ph)AEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSIARQVAPESHWPELRVLILVVSAEK 27 2 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 3 DS(1)IARQVAPES(1)HWPELRVLILVVS(1)AEK 48.097 0.090587 130600000 31491 55080 45475 74365 57131 59285 49935 23833 23828 36851 TRUE FALSE 30260.2969 53509.17233 53693.34409 78202.98656 58968.6705 60483.78332 50546.11947 23340.84022 21123.14534 34355.04895 0.880810764 1.557534452 1.562895287 2.276317134 1.71644845 1.760550055 1.471286493 0.679400581 0.614848355 1 15.06823452 1.813131634 3.903265214 0.732616136 1.650466504 0.571275867 0.333660192 0.15784057 4.182192052 0.175809395 0.093758172 65.03267729 -1.813131634 0.917850368 IFSNTDPDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IFSNTDPDKK 10 1 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 97.734 0.0093912 723670000 1532700 1324000 1249600 1095500 1184800 1292300 1462500 1702000 1967900 1916300 FALSE TRUE 1472800.39 1286240.816 1475430.517 1152038.886 1222910.168 1318431.191 1480398.512 1666853.105 1744512.242 1786507.294 0.824402114 0.719975127 0.825874331 0.644855406 0.684525707 0.737993735 0.828655174 0.933023397 0.97649321 1 20.76871037 1.813247204 1.778518897 0.987072818 0.735221514 0.794010151 0.052830197 0.15002471 0.91263694 0.037545851 0.016099238 65.04998544 -1.813247204 -0.251851305 RPPEEDFRHS(ph)PEEDFR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPPEEDFRHSPEEDFR 16 2 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR 152.81 2.67E-07 6183960000 2648100 2912110 2385280 2974790 2899050 3133010 2776200 2667500 2920480 2745840 TRUE FALSE 2544609.324 2829059.474 2816353.156 3128319.268 2992300.576 3196361.609 2810175.966 2612415.193 2588959.354 2559861.811 0.994041676 1.105161014 1.10019734 1.222065681 1.168930511 1.248646155 1.097784245 1.020529773 1.011366841 1 21.2876345 1.813381365 3.446392553 1.01064132 1.143187477 0.426061829 0.066512265 0.235847946 5.001324577 0.037325569 0.019318936 65.07008367 -1.813381365 0.132546157 DPS(ph)PESNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DPSPESNKK 9 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(1)PESNKK 102.4 0.0021993 322990000 611250 483900 504140 419570 472710 430740 527080 656840 733780 656010 TRUE FALSE 587361.6742 470099.6458 595249.3125 441224.058 487915.1465 439449.8579 533530.5627 643276.0245 650484.3707 611577.8584 0.960403759 0.768666882 0.973300953 0.721451982 0.797797271 0.718550961 0.872383713 1.05183014 1.063616614 1 19.22217665 1.813389514 3.985267478 1.043603783 0.820413478 0.570614165 0.083296214 0.151010652 4.150023281 0.040953538 0.021951973 65.07130466 -1.813389514 -0.223190306 EDKLECSEELGDLVK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDKLECSEELGDLVK 15 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;; 230.82 2.52E-13 8523300000 10357240 8418390 8274840 8223170 9368390 8536930 10783300 13039500 15632500 14775300 FALSE TRUE 9952467.61 8178305.76 9770287.661 8647568.789 9669732.773 8709552.574 10915269.25 12770229.77 13857964.14 13774555.77 0.722525487 0.593725554 0.709299655 0.627792935 0.70199961 0.63229281 0.792422597 0.92708832 1.006055249 1 23.71550246 1.813605118 1.809087479 1.00207317 0.662081181 0.92318486 0.040601653 0.0738215 0.464901362 0.025108945 0.010818775 65.10361706 -1.813605118 -0.339991988 SSTLSSSSMSLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 9 SSTLSSSSMSLSPK 14 0 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 SSTLSSSSMSLS(1)PK;SSTLSSSSMS(0.001)LS(0.999)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMS(0.007)LS(0.993)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMS(0.002)LS(0.998)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMSLS(1)PK 272.05 5.96E-33 4553760000 5735630 5014880 4011710 4066540 4640650 4680790 4932850 6032950 6683570 5991600 TRUE FALSE 5511475.239 4871860.532 4736715.237 4276414.617 4789920.722 4775438.781 4993219.694 5908367.474 5924879.153 5585783.595 0.986696879 0.872189273 0.847994763 0.765589025 0.857519924 0.854927281 0.893915707 1.057750873 1.060706891 1 22.41332825 1.813632737 3.888349869 1.045086189 0.86007252 0.687501226 0.052960214 0.124931124 3.283026551 0.028014101 0.014932406 65.10775754 -1.813632737 -0.185013669 TSSISGPLS(ph)PAYTGQVPYNYNQLEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 TSSISGPLS(0.999)PAYTGQVPYNYNQLEGR 171.19 4.00E-12 185040000 59206 74625 63776 109420 105790 98063 81749 57168 65458 66320 TRUE FALSE 56892.16406 72496.76807 75301.74189 115067.1793 109192.8314 100045.901 82749.46872 55987.46082 58027.48226 61828.08733 0.920166975 1.172553951 1.217921258 1.861082629 1.766071637 1.618130293 1.33837989 0.905534414 0.938529474 1 15.91597476 1.813736317 4.168979653 0.941250704 1.442206065 0.389931409 0.267325085 0.245502318 7.307477927 0.14974629 0.081135672 65.12328762 -1.813736317 0.500955361 EAAANTNRPSPGGHER ddPTM_BT-474_Pertuzumab_2h_R1 1 EAAANTNRPSPGGHER 16 1 O60356;O60356-2 O60356 NUPR1 Nuclear protein 1 0 59.513 0.060756 103880000 22943 30252 23859 38274 28707 29919 25966 21747 17445 23752 FALSE TRUE 22046.3622 29389.24258 28170.85204 40249.32573 29630.38673 30523.98268 26283.77968 21297.91685 15464.71674 22143.25588 0.995624235 1.327232216 1.272209118 1.817678752 1.338122401 1.37847762 1.18698803 0.961824086 0.698393986 1 14.43457975 1.813778365 2.083119516 0.84557825 1.369763118 0.520996575 0.201076576 0.239373365 1.999085636 0.13225625 0.059378794 65.12959306 -1.813778365 0.524184868 VKLEAEIATYR ddPTM_BT-474_Pertuzumab_2h_R1 6 VKLEAEIATYR 11 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 204.48 3.01E-08 28097950000 17599540 18739310 16042820 16973370 16972830 17603710 18288980 19571490 21958300 20972540 FALSE TRUE 16911730.52 18204883.23 18942114.44 17849367.66 17518776.49 17959669.08 18512806.01 19167331.89 19465685.84 19552051.19 0.864959403 0.931098382 0.968804463 0.91291535 0.89600709 0.918556775 0.946847256 0.980323328 0.995582799 1 24.22081663 1.81383788 1.795132185 0.997450863 0.917365518 0.660089214 0.024741098 0.22387995 1.387666347 0.017876717 0.007688072 65.13851895 -1.81383788 -0.080085345 LQEVPHEGPMCDLLWSDPDDRGGWGISPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQEVPHEGPMCDLLWSDPDDRGGWGISPR 29 1 P67775;P62714;H0YC23;E5RHC1 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform;Serine/threonine-protein phosphatase 0 71.881 0.0043517 77022000 58673 87363 80699 66246 89480 105480 74119 53457 51126 63629 FALSE TRUE 56379.99429 84871.49278 95283.10444 69664.964 92358.20546 107612.8779 75026.09049 52353.09427 45322.39082 59319.35116 0.950448601 1.430755582 1.606273545 1.174405361 1.556965875 1.814127697 1.264782723 0.882563502 0.764040569 1 15.8562152 1.813871483 3.694336769 0.865366206 1.432035117 0.522755933 0.229235631 0.175221536 4.200440518 0.119627303 0.063002797 65.14355925 -1.813871483 0.566668911 KLFIGGLSFETTEESLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLFIGGLSFETTEESLR 17 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 209.73 6.44E-12 11618700000 702880 764770 572820 588520 660170 711240 651480 605970 652860 650770 FALSE TRUE 675410.6725 742959.5084 676341.3163 618893.5877 681404.9676 725621.7601 659453.0071 593456.5077 578750.0698 606692.7683 1.113266398 1.224605842 1.11480036 1.020110376 1.123146679 1.196028366 1.086963685 0.978182927 0.953942589 1 19.21060659 1.813947491 3.441075094 0.973140999 1.130528714 0.634260229 0.052315786 0.156282271 3.301307751 0.029335776 0.015184592 65.15496127 -1.813947491 0.157387715 STLESEKPGS(ph)PEAAET(ph)SPPSNIIDHCEK ddPTM_BT-474_Pertuzumab_2h_R1 1 STLESEKPGSPEAAETSPPSNIIDHCEK 28 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 2 STLES(0.006)EKPGS(0.993)PEAAET(0.526)S(0.474)PPSNIIDHCEK 94.642 0.035495 191790000 286130 257380 215080 183270 233920 231740 261930 273790 335430 299690 TRUE FALSE 274947.7233 250039.7744 253949.7404 192728.5867 241444.2492 236425.9416 265135.5777 268136.1408 297353.3926 279391.7294 0.984093996 0.894943365 0.908937931 0.689814932 0.864178227 0.84621668 0.948974325 0.959713952 1.064288457 1 18.09192979 1.81416297 1.646253271 1.024598838 0.860555219 0.441402849 0.073186772 0.346794961 1.798248689 0.05461685 0.022998099 65.18729644 -1.81416297 -0.16404362 ELAQIAGRPTEDEDEKEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELAQIAGRPTEDEDEKEK 18 2 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;; 181.88 4.01E-14 2289010000 1666450 1130970 1261490 988130 1191510 1170160 1396850 1759050 2131760 1745530 FALSE TRUE 1601323.292 1098715.843 1489469.305 1039127.508 1229836.001 1193821.437 1413945.068 1722725.003 1889771.542 1627303.698 0.984034691 0.675175657 0.915298912 0.638557823 0.755750757 0.733619323 0.868888253 1.058637674 1.161290018 1 20.63405209 1.814562159 2.785529627 1.089751222 0.777736917 0.607003734 0.103908164 0.155199463 2.241362045 0.055345103 0.027110935 65.24724204 -1.814562159 -0.312014305 VPDGKPENEFAFNAEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 VPDGKPENEFAFNAEFK 17 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 170.5 1.68E-09 518680000 634660 543410 561250 584120 555380 524940 658230 752860 895740 824070 FALSE TRUE 609856.7855 527912.4789 662680.3599 614266.5032 573244.3021 535554.6465 666285.6156 737313.1779 794059.3504 768255.0049 0.793820778 0.687157878 0.862578643 0.799560692 0.746164097 0.697105314 0.867271429 0.959724536 1.033588256 1 19.55122573 1.814566392 2.294290982 1.009705308 0.766698473 0.807964185 0.050877935 0.119917676 1.206609046 0.031643813 0.014641937 65.24787804 -1.814566392 -0.243006834 EADKEINK ddPTM_BT-474_Pertuzumab_2h_R1 3 EADKEINK 8 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 0 ;; 130.75 0.00094357 1663260000 1659540 1424030 1280660 1301770 1391500 1352140 1553550 1831490 2110770 1958250 FALSE TRUE 1594683.342 1383418.059 1512103.75 1368954.506 1436258.861 1379481.197 1572562.81 1793669.091 1871164.239 1825615.983 0.873504262 0.757781522 0.828270438 0.749858962 0.786725617 0.755625066 0.861387512 0.98250076 1.024949527 1 20.7999519 1.814598941 2.468586926 1.01137462 0.790140494 0.870105456 0.036364935 0.083449674 0.964295995 0.020467877 0.0096825 65.25276837 -1.814598941 -0.221234127 WDKDDFES(ph)EEEDVK ddPTM_BT-474_Pertuzumab_2h_R1 6 WDKDDFESEEEDVK 14 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 WDKDDFES(1)EEEDVK;WDKDDFES(1)EEEDVK;WDKDDFES(1)EEEDVK;WDKDDFES(1)EEEDVK;WDKDDFES(1)EEEDVK;WDKDDFES(1)EEEDVK 252.25 8.87E-24 3034570000 3757190 2732800 2833790 2312740 3024670 2652440 3187810 4169080 4852160 3977140 TRUE FALSE 3610354.861 2654863.22 3345918.89 2432100.789 3121961.257 2706074.154 3226823.372 4082987.041 4301363.139 3707764.765 0.973728133 0.716027954 0.902408621 0.655947975 0.842006291 0.729839762 0.870288051 1.101199051 1.160096018 1 21.82211829 1.814962109 3.560074059 1.099837457 0.799079507 0.64118613 0.09470159 0.126486389 2.832325558 0.045528219 0.023783732 65.30735707 -1.814962109 -0.30075795 SGPKPFSAPKPQTS(ph)PS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 S(0.001)GPKPFS(0.003)APKPQT(0.127)S(0.872)PS(0.998)PK 95.926 0.0083012 1102100000 2158900 1634400 1356200 1137100 1538600 1752200 1784900 2265700 2938500 2281000 TRUE FALSE 2074527.801 1587788.512 1601295.509 1195785.867 1588090.466 1787630.685 1806744.14 2218912.503 2604933.799 2126505.838 0.975557068 0.746665485 0.753017217 0.562324281 0.74680748 0.840642265 0.849630463 1.043454696 1.22498314 1 21.02005339 1.814992577 1.825996222 1.121567851 0.755780994 0.633886027 0.10890822 0.206782397 1.326232248 0.075867285 0.032810355 65.3119389 -1.814992577 -0.365786857 ATDSDLSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATDSDLSSPR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 1 ATDSDLSS(1)PR;ATDSDLSS(1)PR 168.83 5.05E-06 550690000 900520 928110 760940 876850 916150 958890 823300 862090 866730 854860 TRUE FALSE 865326.6828 901641.2115 898458.785 922104.3336 945618.7968 978279.4128 833375.7917 844287.5402 768342.444 796959.5708 1.085784919 1.131351256 1.127358047 1.157027743 1.186532958 1.22751448 1.045693938 1.059385659 0.964092122 1 19.60414701 1.815185527 1.940739869 0.995654741 1.150328701 0.684899909 0.044192591 0.190858543 1.383993706 0.030307646 0.01333826 65.34096247 -1.815185527 0.15467396 S(ph)PS(ph)PKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPKPR 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)PS(1)PKPR;S(1)PS(1)PKPR 76.465 0.023151 2676400000 2581800 2094120 2081530 2163800 2216400 1995900 2470200 2599600 3025200 2917900 TRUE FALSE 2480900.402 2034397.748 2457708.774 2275473.977 2287692.519 2036258.465 2500431.047 2545917.352 2681791.979 2720268.034 0.912005865 0.747866652 0.903480372 0.836488886 0.840980554 0.748550672 0.919185542 0.9359068 0.985855785 1 21.37531738 1.815300757 2.115769083 0.981422534 0.832517337 0.579432931 0.054221207 0.207517758 1.784694769 0.03269039 0.014765667 65.35830145 -1.815300757 -0.148905197 GKHSLDS(ph)DEEEDDDDGGSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKHSLDSDEEEDDDDGGSSK 20 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GKHS(0.001)LDS(0.999)DEEEDDDDGGSSK 229.56 1.38E-25 487590000 706970 622660 618320 597700 630920 620690 809420 838150 1035800 1013500 TRUE FALSE 679340.8308 604902.3464 730064.1785 628547.3686 651214.1148 633240.7771 819325.9241 820841.9096 918220.3264 944854.7423 0.718989703 0.640206711 0.772673455 0.665231745 0.689221407 0.670199078 0.86714485 0.868749314 0.9718111 1 19.84973303 1.815442622 1.230318066 0.986570151 0.68988379 0.869462218 0.045276037 0.142809758 0.40240423 0.034789241 0.01422404 65.37965463 -1.815442622 -0.296686361 APIDTS(ph)DVEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 APIDTSDVEEK 11 0 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2 D6RIY6 EXOSC9 Exosome complex component RRP45 1 APIDT(0.025)S(0.975)DVEEK;APIDT(0.052)S(0.948)DVEEK 166.62 2.12E-05 2068100000 3457400 3034000 3245200 3363300 3505800 3279000 3983900 4611200 5169000 5329100 TRUE FALSE 3322280.986 2947473.291 3831679.829 3536880.316 3618567.241 3345303.627 4032656.16 4515977.109 4582236.79 4968155.31 0.668715203 0.593273178 0.771247996 0.711910175 0.728352279 0.673349245 0.811700905 0.908984689 0.922321567 1 22.24427884 1.815459389 1.224051883 0.97892255 0.686875284 0.85469851 0.047040839 0.163069302 0.454640409 0.038981957 0.015941957 65.38217888 -1.815459389 -0.292047266 MTDLSDNPIHESMWELEVEDLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 MTDLSDNPIHESMWELEVEDLHR 23 0 Q96E14;Q96E14-2 Q96E14 RMI2 RecQ-mediated genome instability protein 2 0 ; 220.52 1.11E-32 111280000 51916 103309 70117 115089 84507 93262 85628 61102 61756 91670 FALSE TRUE 49887.06532 100362.7285 82788.70164 121028.7571 87225.2444 95147.82154 86675.94108 59840.22235 54745.71778 85461.10925 0.58373997 1.174367257 0.968729547 1.416185188 1.020642549 1.113346438 1.014215025 0.700204138 0.640592174 1 16.38298042 1.81574043 4.995797645 0.753312414 1.06334572 0.233529317 0.213885145 0.262533813 10.7455439 0.097744914 0.055232608 65.42450261 -1.81574043 0.310033306 DQECDKFNQCGTCNEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQECDKFNQCGTCNEFK 17 1 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ; 320.23 1.49E-58 1581640000 816640 762780 640330 602680 671450 780700 783200 862470 1047820 967410 FALSE TRUE 784724.806 741026.2612 756051.8751 633784.387 693047.799 796486.2889 792785.0359 844659.6931 928875.8664 901886.459 0.87009268 0.821640301 0.838300506 0.702731902 0.768442404 0.883133659 0.879029758 0.936547705 1.029925505 1 19.78258629 1.815890675 1.180112677 1.014965378 0.802870665 0.743672559 0.0476841 0.244359424 0.631588482 0.041469029 0.017005211 65.44714032 -1.815890675 -0.212094713 DKGETIQGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DKGETIQGLR 10 1 F5H0D0;Q14232-2;Q14232;H0YGG4 F5H0D0;H0YGG4 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 ;;; 114.86 0.0011849 2739980000 2070540 2014370 1695150 1914850 1896890 1914760 2015980 2214230 2411650 2407990 FALSE TRUE 1989621.008 1956922.14 2001501.313 2013675.638 1957905.19 1953477.759 2040652.166 2168505.377 2137889.602 2244894.692 0.886287011 0.871721131 0.891579155 0.897002271 0.872159035 0.870186814 0.909019106 0.965971983 0.952334027 1 21.09821634 1.816045142 2.3654478 0.973867792 0.881671841 0.899159047 0.013677882 0.081149456 0.864192754 0.008183457 0.003826591 65.47042232 -1.816045142 -0.092195951 TVFPGAVPVLPAS(ph)PPPKDSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVFPGAVPVLPASPPPKDSLR 21 1 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR 198.56 5.14E-22 10924807000 1930530 1976605 1706847 1798537 1757793 2002451 1721165 1917598 1883997 1919987 TRUE FALSE 1855082.753 1920234.161 2015312.222 1891359.71 1814334.008 2042941.931 1742229.132 1877998.931 1670133.559 1789944.57 1.036391173 1.072789735 1.125907615 1.056658257 1.013625806 1.141343685 0.973342505 1.049193904 0.933064401 1 20.77148348 1.816096821 1.416408756 0.979356283 1.071554302 0.369407044 0.048481917 0.4297101 1.625959134 0.035251643 0.014492743 65.47821333 -1.816096821 0.092198019 TYEEGLKHEANNPQLK ddPTM_BT-474_Pertuzumab_2h_R1 4 TYEEGLKHEANNPQLK 16 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 215.48 9.66E-15 10011040000 3560930 3359290 2997800 2692530 3168750 3576530 3503510 3810610 4835240 4246750 FALSE TRUE 3421764.919 3263486.338 3539569.146 2831491.796 3270675.722 3648849.887 3546387.003 3731919.572 4286363.826 3959113.84 0.864275456 0.824297171 0.894030657 0.715183223 0.826113078 0.92163298 0.895752723 0.942614869 1.082657382 1 21.91674612 1.816135749 1.085091834 1.035544321 0.828096809 0.672365654 0.054965649 0.294461354 0.641095898 0.046306184 0.019213748 65.48408283 -1.816135749 -0.207447512 PIPQT(ph)PESAGNK ddPTM_BT-474_Pertuzumab_2h_R1 2 PIPQTPESAGNK 12 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 PIPQT(0.997)PES(0.003)AGNK;PIPQT(1)PESAGNK 145.06 0.00071071 538140000 1507450 1158900 1400010 1258990 1480820 1251030 1427240 1589950 1779890 1656590 TRUE FALSE 1448537.187 1125849.307 1653022.95 1323966.625 1528451.92 1276326.684 1444706.99 1557116.977 1577844.349 1544387.684 0.937936247 0.728993969 1.070341966 0.857276083 0.9896815 0.826428945 0.935456172 1.008242291 1.021663385 1 20.55860352 1.816257769 3.627849472 1.011767811 0.902279951 0.234784718 0.08686904 0.32422994 7.485605434 0.042504028 0.022329283 65.50248394 -1.816257769 -0.10948786 FWEVISDEHGIDPTGTYHGDSDLQLER ddPTM_BT-474_Pertuzumab_2h_R1 12 FWEVISDEHGIDPTGTYHGDSDLQLER 27 0 P68371;M0R2D3;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;P04350;M0QYM7;M0R278 P68371;P04350 TUBB4B;TUBB4A Tubulin beta-4B chain;Tubulin beta-4A chain 0 ;;;;;;;;;;; 334.06 1.43E-95 53439406000 6273738 8169121 7017846 8293516 7386371 8521129 7956514 3119854.5 8238076 8355832 FALSE TRUE 6028553.383 7936145.667 8286126.883 8721545.355 7623960.331 8693432.067 8053888.198 3055428.414 7302924.149 7789884.056 0.773895136 1.018775839 1.063703493 1.119598866 0.978700103 1.115989918 1.033890638 0.392230281 0.93748817 1 22.89317042 1.816278003 25 0.709456884 1.023478661 0.247057966 0.179133888 105.0125182 33785.71507 0.070593156 0.045467818 65.50553571 -1.816278003 0.314021777 GEEGS(ph)DDDETENGPKPK ddPTM_BT-474_Pertuzumab_2h_R1 8 GEEGSDDDETENGPKPK 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK 280.32 3.93E-36 6321430000 5113140 4035839 3862846 3417660 3834824 3952604 4506037 5430939 6460206 5623807 TRUE FALSE 4913312.836 3920740.823 4560948.201 3594045.842 3958174.597 4032528.361 4561183.229 5318788.212 5726870.498 5242901.543 0.937136201 0.747818892 0.869928257 0.685507026 0.754958788 0.769140585 0.869973085 1.014474174 1.092309373 1 22.32193402 1.816439074 2.461770558 1.04924646 0.7893112 0.710753626 0.06885401 0.139351849 1.599106571 0.040043226 0.018956087 65.52983501 -1.816439074 -0.25993526 LEDTENWLYEDGEDQPK ddPTM_BT-474_Pertuzumab_2h_R1 5 LEDTENWLYEDGEDQPK 17 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;;; 357.72 1.25E-87 1151290000 651600 590590 522829 484990 534285 539090 585075 729921 791840 715227 FALSE TRUE 626134.7516 573746.9514 617315.8306 510020.392 551470.7623 549990.7692 592235.3229 714847.8763 701953.6429 666784.0382 0.939036803 0.860468935 0.92581075 0.764895922 0.827060533 0.824840934 0.888196611 1.072083066 1.052745121 1 19.34686004 1.816473325 4.555473011 1.046654252 0.855190059 0.731396771 0.05015475 0.107383537 3.708235222 0.02488998 0.013792396 65.53500317 -1.816473325 -0.191464193 EDVRPEEIADQELAEALQK ddPTM_BT-474_Pertuzumab_2h_R1 6 EDVRPEEIADQELAEALQK 19 1 Q5TDH0;Q5TDH0-3 Q5TDH0 DDI2 Protein DDI1 homolog 2 0 ;;;;; 251.69 7.13E-31 478786000 517137 528518 432461 452483 485846 519475 507156 617462 636368 600147 FALSE TRUE 496926.7143 513445.1841 510616.3227 475835.7019 501473.6778 529979.1404 513362.7268 604711.1939 564130.1725 559498.5091 0.888164501 0.917688208 0.912632142 0.850468221 0.896291357 0.947239594 0.917540831 1.080809303 1.008278241 1 19.09377476 1.816645499 6.722366686 1.034953534 0.903744191 0.777647008 0.030729858 0.102373312 7.095828254 0.013862239 0.008293563 65.56098946 -1.816645499 -0.131209344 AAPEAS(ph)SPPAS(ph)PLQHLLPGK ddPTM_BT-474_Pertuzumab_2h_R1 5 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.5)S(0.5)PPAS(0.999)PLQHLLPGK;AAPEAS(0.5)S(0.5)PPAS(1)PLQHLLPGK;AAPEAS(0.5)S(0.5)PPAS(1)PLQHLLPGK;AAPEAS(0.816)S(0.184)PPAS(1)PLQHLLPGK;AAPEAS(0.501)S(0.501)PPAS(0.999)PLQHLLPGK 178.35 3.28E-17 2846765000 1041947 1209180 1049151 1356520 1432030 1379550 1089113 957150 911994 904885 TRUE FALSE 1001226.559 1174695.37 1238755.924 1426530.16 1478092.545 1407445.446 1102441.891 937384.518 808468.2645 843596.333 1.18685504 1.392485155 1.468422604 1.691010385 1.752132492 1.668387345 1.306835802 1.111176615 0.95835915 1 19.6861933 1.816906855 2.28339216 0.998889448 1.533283497 0.669618559 0.158089676 0.18797393 1.870574487 0.108652278 0.050300745 65.60045549 -1.816906855 0.534394049 AATESVPCS(ph)PSPLAGEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AATESVPCSPSPLAGEIR 18 0 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;J9JIE4 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 1 AATES(0.036)VPCS(0.9)PS(0.064)PLAGEIR 98.507 0.001268 117530000 179510 175380 159920 204250 209980 183890 170530 165220 147390 170730 TRUE FALSE 172494.5507 170378.3341 188821.1014 214791.367 216734.1974 187608.3818 172616.9972 161808.1493 130658.9051 159166.305 1.08373786 1.070442228 1.18631328 1.349477623 1.361683915 1.178694082 1.084507158 1.016598012 0.82089551 1 17.28017543 1.817043482 1.795438571 0.918546023 1.210647906 0.579268604 0.100124307 0.264372267 1.636770134 0.076802618 0.033119966 65.62109639 -1.817043482 0.292101882 KLGAGEGGEASVS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 4 KLGAGEGGEASVSPEK 16 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KLGAGEGGEASVS(1)PEK;KLGAGEGGEAS(0.004)VS(0.996)PEK;KLGAGEGGEAS(0.011)VS(0.989)PEK;KLGAGEGGEAS(0.002)VS(0.998)PEK 267.93 1.28E-27 5314220000 8646040 6897290 6914600 6312120 7035550 7406180 7979870 9520900 11011500 10303600 TRUE FALSE 8308143.198 6700586.042 8164222.034 6637889.27 7261854.855 7555938.034 8077530.036 9324290.088 9761520.684 9605727.995 0.864915517 0.697561501 0.849932669 0.691034482 0.755992139 0.786607536 0.840907638 0.970701033 1.016218728 1 23.19546353 1.817152782 1.883485987 1.011285903 0.768442094 0.782226094 0.052444624 0.13346862 0.91039299 0.032846821 0.014355144 65.63761339 -1.817152782 -0.242843809 SAS(ph)QSS(ph)LDKLDQELK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 S(0.004)AS(0.745)QS(0.256)S(0.995)LDKLDQELK;S(0.068)AS(0.76)QS(0.204)S(0.968)LDKLDQELK 180.39 7.55E-06 502980000 3138900 2281990 2202470 1864690 2421510 2090340 2577060 3506180 3998200 3296390 TRUE FALSE 3016228.318 2216909.88 2600505.323 1960926.874 2499400.068 2132608.107 2608598.831 3433776.158 3544341.098 3073122.569 0.981486501 0.721386743 0.846209438 0.63808938 0.813309594 0.693954783 0.848843081 1.117357372 1.153335416 1 21.55127388 1.817304716 3.879092765 1.102174234 0.777234489 0.673304317 0.095741916 0.117139549 3.035172892 0.045824207 0.02448448 65.66058022 -1.817304716 -0.324939745 ATEDGEEDEEMIESIENLEDLK ddPTM_BT-474_Pertuzumab_2h_R1 4 ATEDGEEDEEMIESIENLEDLK 22 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ;;; 237.39 1.61E-30 161993000 170942 153870 159715 163352 175341 170682 196548 220282 250770 256345 FALSE TRUE 164261.3977 149481.7783 188579.0533 171782.6163 180981.0025 174133.307 198953.4132 215733.0997 222303.6409 238982.5248 0.687336439 0.625492506 0.789091393 0.718808274 0.75729806 0.72864452 0.83250193 0.902714957 0.930208772 1 17.8665456 1.817329488 0.668778361 1.005107679 0.693671959 0.875243581 0.039530245 0.22229755 0.199225312 0.036723383 0.019501136 65.66432559 -1.817329488 -0.311435719 TQT(ph)PPVS(ph)PAPQPTEER ddPTM_BT-474_Pertuzumab_2h_R1 9 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;T(0.086)QT(0.914)PPVS(1)PAPQPTEER;T(0.046)QT(0.954)PPVS(1)PAPQPTEER;T(0.388)QT(0.612)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;T(0.001)QT(0.999)PPVS(1)PAPQPTEER 305.55 1.09E-45 14550850000 3632257 3683025 4294072 5143451 4919231 3920795 4055673 3711427 3628886 3543982 TRUE FALSE 3490304.381 3577988.733 5070106.332 5408905.123 5077462.533 4000076.161 4105307.539 3634784.735 3216950.075 3303944.942 1.056405128 1.082944418 1.534561386 1.637105102 1.536787877 1.210696979 1.242547201 1.100134778 0.973669395 1 21.65575821 1.817347233 1.407523512 0.987692126 1.366658423 0.395334822 0.180666903 0.463898119 1.731878474 0.155789896 0.064065226 65.66700857 -1.817347233 0.378966298 KQEETAVLEEDSADWEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQEETAVLEEDSADWEK 17 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 190.55 4.69E-10 302963000 415730 371080 346060 341230 383420 374710 404750 500100 542240 543720 FALSE TRUE 399482.812 360497.1617 408600.7401 358840.9212 395753.0525 382286.8929 409703.4516 489772.7602 480687.1885 506893.3601 0.788100306 0.711189355 0.806088168 0.707921921 0.78074223 0.75417617 0.808263599 0.966224454 0.948300424 1 18.95132274 1.81736687 2.632184349 0.974971763 0.756892003 0.901296158 0.031630468 0.068435627 0.888245066 0.016768554 0.008101523 65.66997795 -1.81736687 -0.21807976 IGEEEIQKPEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGEEEIQKPEEK 12 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 141.46 5.52E-05 599620000 1133890 896350 926930 689310 974310 906280 1011480 1201070 1426920 1216570 FALSE TRUE 1089576.325 870786.9756 1094446.87 724885.3717 1005649.566 924605.6025 1023858.795 1176267.485 1264942.024 1134170.63 0.960681132 0.767774224 0.964975499 0.639132554 0.886682779 0.815226191 0.902737884 1.037116862 1.11530134 1 20.11320627 1.817490773 2.559158685 1.063983301 0.835022564 0.510005663 0.092643959 0.1991441 2.453734509 0.050860836 0.024375419 65.68871604 -1.817490773 -0.228960738 LEKVPDS(ph)PENELK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEKVPDSPENELK 13 1 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 LEKVPDS(1)PENELK;LEKVPDS(1)PENELK 150.7 2.69E-05 703770000 564820 511860 467820 361240 481330 573420 555520 627410 877300 694090 TRUE FALSE 542746.21 497262.254 552365.4806 379883.6397 496812.4166 585014.9453 562318.6199 614453.7642 777712.5819 647078.6661 0.838763876 0.768472645 0.853629566 0.587074895 0.767777463 0.904086282 0.869011218 0.949581243 1.201882588 1 19.30358159 1.817627382 1.218842862 1.089156096 0.769102476 0.637360057 0.092594824 0.287324785 0.793820943 0.075008582 0.030724401 65.70938196 -1.817627382 -0.320053621 SHFEQWGTLTDCVVMR ddPTM_BT-474_Pertuzumab_2h_R1 6 SHFEQWGTLTDCVVMR 16 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;;;; 239.86 7.67E-20 3818410000 2461080 2485180 2125660 2585710 2443080 2235070 2506000 1311256 2593630 2735580 FALSE TRUE 2364898.273 2414305.1 2509814.047 2719158.803 2521663.887 2280264.647 2536669.178 1284178.105 2299211.996 2550296.73 0.927303182 0.946676154 0.984126285 1.066212716 0.988772741 0.894117386 0.994656484 0.503540663 0.901546855 1 21.28223369 1.818034166 24.99999999 0.746791076 0.97251963 0.237535183 0.128748512 96.90753014 30488.8654 0.05053833 0.032572565 65.77095769 -1.818034166 0.225728553 FNGGHSPT(ph)HSPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.253)PT(0.746)HSPEK;FNGGHS(0.104)PT(0.879)HS(0.017)PEK;FNGGHS(0.095)PT(0.902)HS(0.003)PEK 140.46 7.35E-05 1744340000 1668257 1658440 1445847 1569530 1546180 1389708 1667700 187857 1791000 1532150 TRUE FALSE 1603059.672 1611142.915 1707143.716 1650533.631 1595914.284 1417808.848 1688109.811 183977.6873 1587693.188 1428376.116 1.122295209 1.127954253 1.195164002 1.155531525 1.117292754 0.992601901 1.181838448 0.128801991 1.1115372 1 20.44594448 1.818114003 24.99999988 0.650510861 1.125638434 0.303910542 0.251702276 88.53390207 27826.38957 0.09752263 0.062856203 65.78304959 -1.818114003 0.475127573 VDVDVPDVNIEGPDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDVDVPDVNIEGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 239.61 1.82E-19 1465690000 2043790 1973200 1889810 1921980 1793170 1871470 2006870 2523640 2637160 2345050 FALSE TRUE 1963916.427 1916926.268 2231340.706 2021173.618 1850848.942 1909312.406 2031430.675 2471525.952 2337800.653 2186217.675 0.898316965 0.87682315 1.02063977 0.924507034 0.846598654 0.873340486 0.929198725 1.130503143 1.069335721 1 21.06000562 1.81845314 6.476533956 1.076407813 0.908669782 0.64735824 0.052951344 0.137045646 8.740507508 0.024404218 0.01453643 65.83443911 -1.81845314 -0.167738031 KS(ph)SVNGSSATSSG ddPTM_BT-474_Pertuzumab_2h_R1 4 KSSVNGSSATSSG 13 1 R4GMX3;P35226 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 1 KS(0.4)S(0.372)VNGS(0.212)S(0.016)ATSSG;KS(0.795)S(0.204)VNGS(0.001)SATSSG;KS(0.601)S(0.32)VNGS(0.074)S(0.004)ATSSG;KS(0.464)S(0.464)VNGS(0.053)S(0.013)AT(0.002)S(0.002)S(0.002)G 107.11 0.0013997 1931620000 2462980 2453310 2057550 2326030 2361220 2386130 2206110 2381460 2377820 2372920 TRUE FALSE 2366724.019 2383344.001 2429395.055 2446076.687 2437170.786 2434379.183 2233109.034 2332282.019 2107899.842 2212200.015 1.069850828 1.077363703 1.098180562 1.105721305 1.101695493 1.100433581 1.009451686 1.054281712 0.952852286 1 21.0770504 1.818465416 1.239364704 0.986236742 1.092785528 0.717259202 0.026532165 0.236365655 0.676020883 0.020743506 0.008495776 65.83630004 -1.818465416 0.106548786 HISFGGNLITFS(ph)PLQPGEF ddPTM_BT-474_Pertuzumab_2h_R1 1 HISFGGNLITFSPLQPGEF 19 0 Q15398-1;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 HISFGGNLITFS(1)PLQPGEF 127.53 2.44E-05 48071000 32373 41042 36759 53590 39311 55842 43431 30710 35935 49572 TRUE FALSE 31107.82737 39871.52234 43402.169 56355.78632 40575.47402 56971.1635 43962.52157 30075.82777 31855.80945 46214.44429 0.673119148 0.862750228 0.939147266 1.21944096 0.877982515 1.23275665 0.951272319 0.650788476 0.689304176 1 15.49605621 1.818635005 7.753806796 0.747558385 0.977775433 0.176306693 0.178274447 0.393409682 33.63709824 0.077889714 0.047664371 65.86201369 -1.818635005 0.230217048 KMS(ph)DDEDDDEEEYGKEEHEK ddPTM_BT-474_Pertuzumab_2h_R1 4 KMSDDEDDDEEEYGKEEHEK 20 2 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 KMS(1)DDEDDDEEEYGKEEHEK;KMS(1)DDEDDDEEEYGKEEHEK;KMS(1)DDEDDDEEEYGKEEHEK;KMS(1)DDEDDDEEEYGKEEHEK 204.05 5.22E-22 3190870000 1665790 996233 1085252 773914 1174163 1062893 1330370 1547460 2035010 1592630 TRUE FALSE 1600689.085 967821.4103 1281381.178 813855.7943 1211931.019 1084385.425 1346651.466 1515504.41 1804004.196 1484759.752 1.078079523 0.651837046 0.863022571 0.54813972 0.81624722 0.730344033 0.906982739 1.020706824 1.21501421 1 20.50179808 1.818735036 2.081207458 1.105863851 0.770703208 0.470975805 0.14089458 0.242304952 2.013013127 0.085160556 0.038385166 65.87718551 -1.818735036 -0.335160643 EEEPVKK ddPTM_BT-474_Pertuzumab_2h_R1 7 EEEPVKK 7 1 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4;Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q14103-3;Q14103-2;Q99729-3 HNRNPD;HNRNPAB Heterogeneous nuclear ribonucleoprotein D0;Heterogeneous nuclear ribonucleoprotein A/B 0 ;;;;;; 103.92 0.013257 24321350000 18716070 16417770 17039800 16045210 15907150 15259050 18421330 22207530 24351070 24370860 FALSE TRUE 17984625.29 15949551.27 20119270.91 16873305.21 16418817.93 15567598.45 18646775.75 21748936.74 21586838.62 22720199.94 0.791569851 0.70199872 0.885523497 0.742656546 0.72265288 0.685187564 0.820713541 0.957251116 0.950116578 1 24.4374722 1.818923257 3.039571638 0.969490239 0.75613824 0.757695471 0.054033745 0.121459644 2.041379963 0.030010041 0.015105971 65.90574254 -1.818923257 -0.213351999 GILQVLPDEITFPLS(ph)PLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 GILQVLPDEITFPLSPLRK 19 1 A0A0U1RR07;Q9HCH5-7;Q9HCH5-8;A0A0U1RQP0;A0A0U1RRJ3;Q9HCH5-11 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 GILQVLPDEITFPLS(1)PLRK;GILQVLPDEITFPLS(1)PLRK 215.91 2.42E-19 746550000 527980 654940 513360 569180 644540 594530 528940 493500 440050 507760 TRUE FALSE 507345.9579 636261.7525 606135.5716 598555.448 665272.2145 606551.8039 535413.3259 483309.0525 390097.3688 473368.9629 1.071776981 1.344113793 1.280471723 1.264458583 1.405398889 1.281351021 1.131069774 1.020998609 0.824087339 1 18.85260559 1.819198997 1.889375603 0.918073405 1.282698989 0.718123675 0.092048816 0.162556749 1.114568541 0.060032653 0.026305043 65.94760023 -1.819198997 0.364625584 KLEEEQIILEDQNCK ddPTM_BT-474_Pertuzumab_2h_R1 5 KLEEEQIILEDQNCK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;;; 261.74 9.27E-25 4923870000 5238410 4860090 3842160 3994550 4571560 4769960 4756390 5403650 6246460 5693590 FALSE TRUE 5033687.146 4721484.992 4536523.78 4200709.204 4718608.379 4866411.859 4814600.124 5292062.739 5537388.048 5307958.078 0.948328354 0.889510603 0.854664584 0.791398339 0.88896866 0.916814298 0.907053155 0.997005376 1.043223772 1 22.33972555 1.819234251 1.547593971 1.026779922 0.874056229 0.691057685 0.039716149 0.218925474 0.996609346 0.0310711 0.012971787 65.95295378 -1.819234251 -0.152723693 FDFLCQYHKPASK ddPTM_BT-474_Pertuzumab_2h_R1 2 FDFLCQYHKPASK 13 1 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 169.04 1.75E-05 6268000000 9653500 8835400 7988900 8692900 8783600 9157400 9818700 10583800 12280600 11825100 FALSE TRUE 9276230.547 8583423.043 9432671.942 9141541.611 9066132.471 9342568.902 9938864.188 10365240.83 10886557.77 11024175.44 0.841444387 0.778600004 0.855635144 0.82922679 0.822386447 0.847461921 0.901551707 0.940228218 0.987516738 1 23.39416742 1.819247315 1.045704434 1.001635343 0.821986345 0.925580199 0.019167613 0.116254894 0.234906703 0.015431349 0.00646479 65.95493783 -1.819247315 -0.179648998 QVLEPSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVLEPSFR 8 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 118.32 0.0044398 695440000 1062480 1388450 1737940 1543670 1767650 1772310 1418710 1076950 1050500 1166170 FALSE TRUE 1020957.107 1348852.765 2052024.418 1623338.994 1824508.068 1808147.323 1436072.597 1054710.606 931251.6441 1087184.267 0.939083776 1.240684589 1.887466992 1.493159019 1.678195797 1.663147064 1.320910025 0.97013049 0.856572039 1 20.05216505 1.819295288 2.983053316 0.924378051 1.499834131 0.489678998 0.246094231 0.216315527 3.514109657 0.143539398 0.071913348 65.96222367 -1.819295288 0.57545608 VASPLS(ph)PTSLTHTSRPPAALTPVPLSQGDLSHPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VASPLSPTSLTHTSRPPAALTPVPLSQGDLSHPPR 35 1 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L0Y2;I3L410;I3L1N0;Q9BUL5-3;I3L2W6 I3L4Q4 PHF23 PHD finger protein 23 1 VAS(0.017)PLS(0.94)PT(0.017)S(0.017)LT(0.003)HT(0.005)S(0.001)RPPAALTPVPLSQGDLSHPPR;VAS(0.222)PLS(0.594)PT(0.051)S(0.051)LT(0.024)HT(0.026)S(0.031)RPPAALTPVPLSQGDLSHPPR 250.41 1.35E-48 1518330000 113840 221628 201847 302056 233944 265765 220235 135005 150392 218896 TRUE FALSE 109391.0069 215307.3864 238325.243 317645.1464 241469.0212 271138.9504 222930.3018 132217.0996 133320.1307 204069.9789 0.536046544 1.055066441 1.167860379 1.556550101 1.183265772 1.328656727 1.09242086 0.647900785 0.653305946 1 17.63870444 1.819371439 5.421848899 0.738112295 1.159494667 0.289086781 0.25928086 0.252841979 11.71626796 0.124305583 0.071682446 65.97379082 -1.819371439 0.421382372 GDAAVRDELMAAVR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDAAVRDELMAAVR 14 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;; 188.12 7.93E-07 1397920000 838380 1007650 718730 906790 927970 897110 862860 714370 797660 791760 FALSE TRUE 805615.1827 978912.8086 848620.4991 953589.5406 957818.9978 915250.1789 873419.9388 699618.0099 707112.9809 738133.39 1.091422219 1.326200416 1.149684475 1.291893245 1.297623181 1.239952279 1.183281979 0.947820569 0.957974521 1 19.49352203 1.819583495 3.631307539 0.962976939 1.237328593 0.753475551 0.067684975 0.101189534 2.323573099 0.033067848 0.017421344 66.00601212 -1.819583495 0.274351654 RGS(ph)LPDQK ddPTM_BT-474_Pertuzumab_2h_R1 5 RGSLPDQK 8 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 RGS(1)LPDQK;RGS(1)LPDQK;RGS(1)LPDQK;RGS(1)LPDQK;RGS(1)LPDQK 137.55 0.00045534 2057200000 3522240 3334790 2764833 2672200 3106400 3060370 3284090 3937180 4471140 3931030 TRUE FALSE 3384586.967 3239685.054 3264499.826 2810112.562 3206320.177 3122252.778 3324281.676 3855875.857 3963594.932 3664777.837 0.923544923 0.884005852 0.890777005 0.766789336 0.87490165 0.851962361 0.907089549 1.052144503 1.081537574 1 21.80529431 1.819681422 3.283624336 1.052076493 0.864029063 0.778802897 0.042670536 0.105134299 2.023734139 0.023200634 0.011921718 66.02089722 -1.819681422 -0.18804743 EAEGSSAEYKK ddPTM_BT-474_Pertuzumab_2h_R1 5 EAEGSSAEYKK 11 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;;; 181.66 9.82E-06 6237320000 5417310 5027620 3905420 3908180 4321510 4639820 4756270 5406050 6199860 5534380 FALSE TRUE 5205595.536 4884237.2 4611216.27 4109881.638 4460515.294 4733640.339 4814478.655 5294413.178 5496077.885 5159531.513 1.008927947 0.946643545 0.893727707 0.796561011 0.86451944 0.917455456 0.933123219 1.026142231 1.065228087 1 22.29880864 1.819850073 2.468304035 1.03846307 0.899708934 0.525310911 0.053453529 0.228066796 2.621674959 0.034871978 0.016567671 66.04654037 -1.819850073 -0.138754135 EVEDKES(ph)EGEEEDEDEDLSK ddPTM_BT-474_Pertuzumab_2h_R1 7 EVEDKESEGEEEDEDEDLSK 20 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK 319.31 7.98E-67 12091950000 5857274 4257353 3956239 3061633 4197428 3872134 4528004 5863690 6863910 5262412 TRUE FALSE 5628365.257 4135937.461 4671219.393 3219644.246 4332442.084 3950431.202 4583419.067 5742602.752 6084747.713 4905984.148 1.147244893 0.843039304 0.952147266 0.656268783 0.883093372 0.805227062 0.934250688 1.17053023 1.240270561 1 22.22611114 1.820212817 3.974126342 1.154041269 0.872633941 0.437715722 0.129001154 0.187660876 5.033306616 0.063373956 0.034134622 66.10172872 -1.820212817 -0.281407328 ILDWHVANTDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILDWHVANTDKK 12 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 144.57 3.97E-05 5716900000 16160700 14366900 12541900 11607500 13398100 12861600 15743600 15711100 19181400 18030500 FALSE TRUE 15529121.98 13957170.08 14808500.32 12206564.47 13829062.05 13121670.36 15936274.89 15386660.29 17004007.89 16809278.18 0.923842286 0.830325368 0.880971816 0.726180169 0.822704099 0.780620692 0.948064201 0.915367105 1.011584656 1 24.00275444 1.820217199 1.51871887 0.994080366 0.826723846 0.583935929 0.057204791 0.274635859 1.201694647 0.04229339 0.017611821 66.10239568 -1.820217199 -0.16735652 EATNPPVIQEEKPK ddPTM_BT-474_Pertuzumab_2h_R1 4 EATNPPVIQEEKPK 14 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 261.39 1.52E-24 2806270000 2215950 2122630 1760260 1753170 1872610 1883880 2123630 2433220 2869850 2521150 FALSE TRUE 2129348.224 2062094.671 2078378.139 1843651.314 1932844.201 1921973.344 2149619.619 2382973.157 2544076.659 2350390.265 0.905955175 0.877341394 0.884269379 0.784402208 0.822350326 0.817725198 0.914579868 1.013862758 1.082406057 1 21.16446889 1.820289845 2.503781514 1.042523991 0.84798608 0.814756828 0.039056978 0.113518246 1.339461877 0.024414802 0.011652746 66.11345372 -1.820289845 -0.194537911 LEGGRQDS(ph)EDEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 LEGGRQDSEDEEER 14 1 A0A3B3ISZ4;Q9BYE7-3;Q9BYE7 A0A3B3ISZ4 PCGF6 Polycomb group RING finger protein 6 1 LEGGRQDS(1)EDEEER;LEGGRQDS(1)EDEEER 191.97 2.59E-07 752500000 543190 530560 393660 426990 476400 519980 451510 416980 424030 444250 TRUE FALSE 521961.5343 515428.9483 464803.1189 449027.0051 491723.8387 530494.3519 457035.7144 408369.2173 375895.8921 414160.5518 1.260287905 1.244514829 1.122277621 1.084185838 1.187278307 1.280890586 1.103523048 0.986016692 0.907609115 1 18.65983062 1.820439903 2.805730531 0.954583322 1.189830013 0.737459925 0.061606415 0.139460534 2.026562427 0.037280333 0.018384905 66.13630128 -1.820439903 0.235246691 TATESFASDPILYRPVAVALDTK ddPTM_BT-474_Pertuzumab_2h_R1 4 TATESFASDPILYRPVAVALDTK 23 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 311.37 3.18E-73 12878490000 21381190 17761840 16479000 18022220 18676790 17982560 18971640 21554060 23745870 21054730 FALSE TRUE 20545589.46 17255289.71 19457121.87 18952348.93 19277545.91 18346179.68 19203820.61 21108961.13 21050338.39 19628674.38 1.046713041 0.87908584 0.991260107 0.965544008 0.982111453 0.934662185 0.978355452 1.075414504 1.072427917 1 24.22645941 1.820485136 5.399395762 1.055440777 0.96402659 0.408106828 0.044530907 0.178854009 8.166369948 0.019049862 0.010986657 66.14318997 -1.820485136 -0.091414187 GLPPS(ph)MER ddPTM_BT-474_Pertuzumab_2h_R1 4 GLPPSMER 8 0 P38159;P38159-2;H3BUY5 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER 116.52 0.0023665 2820770000 2334060 2393670 1840130 2026700 2120280 1939520 1680500 2253310 1826350 1649090 TRUE FALSE 2242842.355 2325404.875 2172682.424 2131298.23 2188480.732 1978738.423 1701066.462 2206778.361 1619030.405 1537395.665 1.458858253 1.512561098 1.413222681 1.386304305 1.4234987 1.287071681 1.106459775 1.435400405 1.053099369 1 20.55205708 1.82050388 0.191856205 0.879527058 1.645850751 0.683013017 0.099491659 1.892956964 0.346359577 0.495259791 0.604742575 66.14604469 -1.82050388 0.766323693 DGGQTESNEEGKENR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGGQTESNEEGKENR 15 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ;;; 188.47 2.72E-07 2553100000 1199998 1060998 977709 831373 939894 1059596 1049140 1226335 1346510 1241690 FALSE TRUE 1153100.751 1030739.376 1154402.765 874280.2602 970126.5441 1081021.757 1061979.689 1201010.754 1193659.83 1157589.23 0.996122563 0.89041894 0.997247327 0.755259497 0.838057679 0.933856094 0.917406331 1.037510304 1.031160103 1 20.14269197 1.820734198 3.547724127 1.026719427 0.897699857 0.391741777 0.06770956 0.237277286 5.219912039 0.03629279 0.019028603 66.181133 -1.820734198 -0.12901957 KGEDEYANVDAIVVSVGVDEEIVYAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGEDEYANVDAIVVSVGVDEEIVYAK 26 1 Q9Y5B9;G3V5A4;G3V401 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 157.43 1.75E-08 33816000 89215 78127 70615 73716 78306 78366 86583 85736 104790 95441 FALSE TRUE 85728.37917 75898.89445 83376.70132 77520.49159 80824.78361 79950.61421 87642.62865 83965.52164 92894.67852 88976.69606 0.963492498 0.853019923 0.937062231 0.871244888 0.908381488 0.898556788 0.985006553 0.943679922 1.044033805 1 16.44113991 1.821094176 1.150393433 1.013379531 0.901980092 0.568420437 0.037180398 0.318997316 0.781957808 0.027925318 0.011518005 66.23601192 -1.821094176 -0.11139944 SPSPFHAVAECR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPFHAVAECR 12 0 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EPX3;B9ZVU2;F8WAN0;E5RJ35 E5RIA4 DNPEP Aspartyl aminopeptidase 0 ; 120.57 0.00039486 438950000 417880 621240 427670 536180 477100 488320 478090 474540 393480 538300 FALSE TRUE 401548.7876 603522.8435 504959.4825 563852.3141 492446.3548 498194.165 483941.0084 464740.5832 348813.8 501840.4615 0.800152276 1.202618939 1.006215164 1.123568858 0.981280691 0.992734152 0.964332384 0.926072365 0.695069104 1 18.93686927 1.821800775 1.701923256 0.849785576 1.030199766 0.223892444 0.120451872 0.453464753 2.511500756 0.07927026 0.033850252 66.34386593 -1.821800775 0.18041419 EKEDFEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKEDFEK 7 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 81.594 0.024421 2187200000 4676000 4018300 3955670 3779770 4034000 3797180 4765100 5459900 6460300 6116200 FALSE TRUE 4493256.75 3903702.018 4670547.562 3974844.383 4163757.274 3873961.581 4823416.719 5347151.157 5726953.828 5701944.326 0.788021856 0.68462647 0.819114901 0.697103331 0.730234642 0.679410629 0.845924906 0.937776809 1.004386136 1 22.44302252 1.821891399 2.048326436 0.995021601 0.733360239 0.861037178 0.044608818 0.100236927 0.805493287 0.027274739 0.012267446 66.35771131 -1.821891399 -0.261661363 QEALKNDLVEALKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEALKNDLVEALKR 14 2 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 165.49 2.23E-06 1241120000 2507660 2380140 1952290 1804640 2142020 2179500 2235030 2717010 2873600 2571150 FALSE TRUE 2409657.875 2312260.738 2305112.231 1897777.687 2210920.019 2223570.983 2262382.966 2660902.794 2547400.975 2397003.72 1.005279155 0.964646287 0.961664019 0.791729137 0.922368205 0.927646029 0.943837903 1.110095396 1.062743855 1 21.19280072 1.821968713 6.228467483 1.065935284 0.926769703 0.499662515 0.05789376 0.179629158 10.36466785 0.027094383 0.016079517 66.36952561 -1.821968713 -0.139165581 GQFSTDELVAEVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQFSTDELVAEVEK 14 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 273.5 1.21E-32 262200000 490380 484050 428310 482400 495550 506120 550560 605400 687560 702930 FALSE TRUE 471215.4075 470245.3679 505715.1447 507296.7218 511489.8158 516354.0932 557297.918 592898.2784 609511.0713 655319.925 0.719061621 0.717581368 0.771707261 0.774120704 0.780519249 0.787942001 0.85042114 0.904746302 0.930096962 1 19.32183987 1.822143297 0.533926867 1.005816834 0.726702402 0.972135422 0.014948986 0.130411911 0.082780712 0.016071416 0.010616949 66.39621107 -1.822143297 -0.279114432 DAYRPTTDADKIEDEVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DAYRPTTDADKIEDEVTR 18 2 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5;H0Y4F5;H0Y6T5;H0Y314 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 139.17 2.56E-07 330400000 324220 253010 257470 250610 270590 285870 295760 355190 393230 387330 FALSE TRUE 311549.124 245794.4025 304000.5564 263544.0121 279293.7731 291650.4873 299379.5994 347855.2024 348592.179 361095.7941 0.862788016 0.680690295 0.841883404 0.729845145 0.773461718 0.807681762 0.829086365 0.963332191 0.965373135 1 18.46202209 1.822188313 1.662526334 0.990780837 0.77506127 0.75519228 0.04944428 0.154963121 0.817761012 0.032051517 0.013614771 66.40309357 -1.822188313 -0.215719567 AKGPSESS(ph)KER ddPTM_BT-474_Pertuzumab_2h_R1 1 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPSES(0.01)S(0.99)KER 61.444 0.068733 91855000 114040 103640 79466 70199 88814 90254 94816 126530 130200 113370 TRUE FALSE 109583.1907 100684.2887 93827.27391 73821.9788 91670.78297 92078.99772 95976.38657 123917.1113 115420.2418 105691.3489 1.036822709 0.952625638 0.887747908 0.698467562 0.867344243 0.871206571 0.908081764 1.172443275 1.09205004 1 16.68949777 1.822198049 6.309697878 1.101113313 0.881079064 0.51252545 0.088763541 0.178146468 10.48330174 0.042086123 0.025038365 66.4045822 -1.822198049 -0.220034249 STQKS(ph)PATAPK ddPTM_BT-474_Pertuzumab_2h_R1 2 STQKSPATAPK 11 1 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.272)T(0.272)QKS(0.456)PAT(0.001)APK;S(0.26)T(0.26)QKS(0.48)PATAPK 97.69 0.0056686 50148000 259000 225100 186233 161639 183650 196188 212162 236410 269210 243810 TRUE FALSE 248877.9937 218680.3684 219889.4458 169981.2082 189557.269 200155.0558 214758.502 231528.0509 238650.4094 227296.5315 1.094948489 0.962092853 0.967412236 0.747838988 0.833964635 0.880590014 0.944838448 1.018616735 1.049951831 1 17.79421614 1.82238729 3.004181916 1.02761475 0.908085081 0.236116593 0.086449479 0.375774281 6.157497367 0.051658194 0.025992329 66.43352396 -1.82238729 -0.119529669 S(ph)PSELFAQHIVTIVHHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSELFAQHIVTIVHHVK 18 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.985)PS(0.015)ELFAQHIVTIVHHVK;S(0.986)PS(0.014)ELFAQHIVTIVHHVK 257.2 2.15E-30 2408400000 1666990 1646010 1553460 1387200 1616620 1534280 1627890 422930 1751240 1564260 TRUE FALSE 1601842.188 1599067.406 1834204.779 1458793.558 1668620.05 1565304.193 1647812.605 414196.3477 1552446.577 1458311.277 1.098422685 1.096519949 1.257759442 1.000330712 1.144213912 1.073367681 1.129945733 0.284024648 1.064550896 1 20.47586727 1.822429572 24.99999832 0.70368198 1.114380755 0.329630639 0.207628604 69.48193479 20713.90752 0.080185599 0.051725619 66.43999213 -1.822429572 0.410698775 ADHGVPLPGS(ph)PPPTVALPLPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADHGVPLPGSPPPTVALPLPSR 22 0 A0A1W2PRX0;V9GYJ6;V9GY36;Q9UK80-2;Q9UK80-3;Q9UK80 A0A1W2PRX0 USP21 Ubiquitin carboxyl-terminal hydrolase 21 1 ADHGVPLPGS(0.994)PPPT(0.006)VALPLPSR;ADHGVPLPGS(0.999)PPPT(0.001)VALPLPSR 131.13 8.10E-06 355570000 420920 506600 465170 666480 620380 629560 512570 424210 385960 509550 TRUE FALSE 404469.981 492152.264 549236.5667 700877.1127 640335.0861 642290.1345 518842.985 415449.9153 342147.4389 475037.7246 0.851448127 1.036027748 1.156195683 1.475413586 1.34796681 1.352082374 1.092214277 0.874561943 0.720253195 1 18.85768256 1.822505987 3.166598526 0.84424357 1.212545152 0.417509661 0.177223817 0.244151931 4.390441695 0.104446013 0.053288725 66.45168342 -1.822505987 0.368301582 AHVIVMAATNRPNSIDPALRR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHVIVMAATNRPNSIDPALRR 21 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 184.32 2.40E-17 3798800000 1200280 1075520 891180 832740 1001280 1136120 996740 798880 998330 867790 FALSE TRUE 1153371.731 1044847.223 1052236.05 875717.8112 1033487.081 1159093.125 1008938.402 782382.8488 885003.7637 809013.8104 1.425651473 1.291507276 1.300640405 1.082451004 1.277465313 1.432723533 1.247121359 0.967082192 1.093929118 1 19.6258048 1.822524671 5.294881544 1.022999311 1.293237528 0.634668428 0.095513904 0.14646422 6.38166188 0.046171167 0.026566715 66.45454233 -1.822524671 0.270238217 KVQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_BT-474_Pertuzumab_2h_R1 3 KVQIPVSRPDPEPVSDNEEDSYDEEIHDPR 30 2 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 KVQIPVS(0.036)RPDPEPVS(0.964)DNEEDS(0.508)Y(0.492)DEEIHDPR;KVQIPVSRPDPEPVS(1)DNEEDS(0.502)Y(0.498)DEEIHDPR;KVQIPVSRPDPEPVS(1)DNEEDS(0.798)Y(0.202)DEEIHDPR 210.79 2.94E-26 2417430000 1350420 1460250 1138810 1214060 1294710 1480280 1343170 1323830 1487050 1448960 TRUE FALSE 1297644.093 1418605.1 1344618.3 1276717.782 1336355.523 1510212.276 1359608.116 1296492.448 1318246.318 1350820.649 0.960633889 1.050180201 0.995408459 0.945142335 0.989291602 1.117996144 1.006505281 0.959781337 0.975885525 1 20.36540471 1.822646463 7.812154925 0.975077386 1.011420214 0.082485494 0.046313026 0.678067307 55.78724702 0.020911397 0.012851616 66.47318122 -1.822646463 0.036342828 DVYLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 9 DVYLSPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR 118.21 0.0053053 71725570000 64486090 67507540 58113290 64760220 64416240 59925460 63171360 65243630 64473670 64942880 TRUE FALSE 61965902.31 65582291.06 68615654.23 68102502.72 66488246.86 61137193.86 63944470 63896326.24 57154889.28 60544240.89 1.023481365 1.083212707 1.133314304 1.124838659 1.098176241 1.009793714 1.056161066 1.055365883 0.944018596 1 25.8514864 1.822652692 0.852032231 0.983305537 1.09218935 0.483338748 0.040663709 0.538981677 0.734008986 0.037483742 0.016964435 66.4741345 -1.822652692 0.108883813 EGLELPEDEEEKKKQEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 EGLELPEDEEEKKKQEEK 18 3 P07900;P07900-2;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ;;;; 193.8 1.29E-14 15023650000 6886050 4053200 3327330 1806183 3935140 3379290 4042560 5769810 6618480 4160020 FALSE TRUE 6616935.553 3937606.704 3928652.547 1899400.321 4061717.352 3447621.559 4092034.059 5650661.407 5867177.897 3878258.14 1.706161713 1.015302892 1.012994083 0.489756033 1.047304539 0.888961342 1.055121632 1.457010133 1.512838415 1 21.8869774 1.822785894 5.699611345 1.364456414 1.00093162 0.153408097 0.306320688 0.340670837 16.8015111 0.140650463 0.082156608 66.49452592 -1.822785894 -0.363524795 FTENDKEYQEYLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FTENDKEYQEYLK 13 1 Q9BTL3;A0A3B3IU46 Q9BTL3 FAM103A1 RNMT-activating mini protein 0 ; 186.56 7.02E-06 1237250000 1662600 1435730 1175020 1126710 1362110 1312280 1400190 1713420 1815610 1691040 FALSE TRUE 1597623.754 1394784.386 1387372.252 1184859.638 1405923.505 1338815.201 1417325.944 1678037.278 1609509.564 1576504.355 1.013396347 0.88473234 0.880030714 0.751573971 0.891798047 0.849230259 0.899030783 1.064403833 1.020935692 1 20.58829772 1.822892029 5.108958809 1.032010453 0.874043962 0.544666458 0.061591006 0.158404715 6.478865909 0.029428648 0.01681151 66.5107782 -1.822892029 -0.157966491 LLPSAPQTLPDGPLAS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 11 LLPSAPQTLPDGPLASPAR 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQT(0.001)LPDGPLAS(0.999)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR 334.14 2.34E-75 12391189000 1174162 1357435 1266821 1524472 1496062 1405971 1224474 1131187 1039785 1101286 TRUE FALSE 1128274.451 1318722.283 1495763.735 1603150.183 1544184.193 1434400.697 1239459.479 1107827.593 921752.9659 1026694.918 1.098938381 1.284434411 1.456872639 1.56146695 1.504034125 1.397105091 1.207232506 1.079023158 0.897786625 1 19.96957612 1.822957016 1.79739239 0.958159291 1.395827702 0.666549589 0.124866594 0.216590941 1.34028308 0.093870605 0.040692432 66.52073141 -1.822957016 0.43766841 ACSMPQELPQS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 ACSMPQELPQSPR 13 0 Q8N5J2;Q8N5J2-3 Q8N5J2 FAM63A Protein FAM63A 1 ACSMPQELPQS(1)PR 169.98 2.89E-05 178960000 157860 169020 154060 228060 216070 197940 168600 146250 137720 148370 TRUE FALSE 151690.6567 164199.7151 181902.069 239830.2039 223020.0878 201942.4824 170663.3772 143229.8864 122086.603 138320.7677 1.09665858 1.187093723 1.315074172 1.733869815 1.612339863 1.45995779 1.233823236 1.035490829 0.882633931 1 17.07765826 1.822989936 2.265605184 0.948365028 1.410089768 0.535931778 0.178243978 0.251666427 2.455289928 0.124591307 0.057836837 66.52577394 -1.822989936 0.461724739 VKPAS(ph)PVAQPK ddPTM_BT-474_Pertuzumab_2h_R1 5 VKPASPVAQPK 11 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 VKPAS(1)PVAQPK;VKPAS(1)PVAQPK;VKPAS(1)PVAQPK;VKPAS(1)PVAQPK;VKPAS(1)PVAQPK 151.54 2.19E-05 7452550000 15005800 12175200 10779250 9921710 11263900 11696120 12616700 14546300 16698500 15053000 TRUE FALSE 14419356.75 11827975.22 12727300.26 10433770.64 11626213.57 11932623.56 12771106.95 14245913.82 14802956.29 14033446.9 1.027499291 0.842841769 0.906926171 0.743493079 0.828464571 0.850298836 0.910047762 1.015140038 1.054833954 1 23.74236607 1.823043534 2.623137236 1.030896977 0.860475897 0.510285749 0.068480353 0.210338795 2.69714056 0.039970148 0.01938078 66.53398474 -1.823043534 -0.17042108 AATEALGEKS(ph)PDSATVSGYDIMK ddPTM_BT-474_Pertuzumab_2h_R1 2 AATEALGEKSPDSATVSGYDIMK 23 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AATEALGEKS(0.995)PDS(0.005)ATVSGYDIMK;AATEALGEKS(0.975)PDS(0.025)ATVSGYDIMK 225.17 7.25E-33 587960000 480460 441150 378960 321340 399360 416390 424590 501210 564210 488770 TRUE FALSE 461683.092 428568.8339 447446.5019 337924.3959 412205.7771 424809.6911 429786.2594 490859.8383 500163.2462 455665.1725 1.013206889 0.940534541 0.981963356 0.741606812 0.904624277 0.932284749 0.943206296 1.077237998 1.0976552 1 18.79761458 1.823148385 3.6973909 1.066158043 0.915575957 0.432164242 0.071366173 0.212020749 4.986098623 0.037896762 0.020107999 66.5500498 -1.823148385 -0.150582086 ALSTGEKGFGYKGSCFHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALSTGEKGFGYKGSCFHR 18 2 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 174.19 3.87E-12 2420200000 2374700 2801200 2106400 1424650 3367100 2839100 2320500 1260090 1976590 1242320 FALSE TRUE 2281894.099 2721312.519 2487073.337 1498176.357 3475405.829 2896508.547 2348898.973 1234068.701 1752215.79 1158176.56 1.970247178 2.34965256 2.14740431 1.293564737 3.000756491 2.500921403 2.028100943 1.065527264 1.512909042 1 20.14342377 1.823173907 4.660857701 1.217605991 2.210636316 0.536213996 0.42419005 0.174579667 6.097319395 0.206656801 0.115739386 66.55396092 -1.823173907 0.993030325 GTSYQSPHGIPIDLLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GTSYQSPHGIPIDLLDR 17 0 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ;; 184.83 6.14E-10 1718110000 1187760 1405300 1256970 1459450 1474730 1650870 1394580 1303780 1329910 1547730 FALSE TRUE 1141341.026 1365222.22 1484132.44 1534772.389 1522166.03 1684251.722 1411647.287 1276856.487 1178944.192 1442900.869 0.791004463 0.946164944 1.028575471 1.063671402 1.054934586 1.1672678 0.978339758 0.884923223 0.817065273 1 20.46054076 1.823197233 4.435754418 0.889266589 1.01526435 0.181428675 0.100111228 0.338890243 10.87790399 0.051058904 0.028278438 66.55753557 -1.823197233 0.125997761 TSIFWNDVKDPVSIEER ddPTM_BT-474_Pertuzumab_2h_R1 4 TSIFWNDVKDPVSIEER 17 1 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 287.48 1.05E-36 4119650000 1905800 1857520 1645940 1660080 1799930 1965880 1916140 2270740 2531270 2486480 FALSE TRUE 1831319.229 1804545.348 1943397.972 1745756.928 1857826.383 2005631.441 1939590.295 2223848.425 2243930.842 2318068.495 0.790019464 0.778469382 0.83836952 0.753108431 0.801454481 0.865216643 0.836726912 0.959354062 0.968017488 1 21.14449177 1.823460163 1.011718276 1.002272376 0.791901458 0.891412626 0.027286076 0.146611261 0.277293945 0.022255448 0.009424528 66.5978429 -1.823460163 -0.210370918 DLAGEVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLAGEVEK 8 0 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9;H3BN71;B4DGE1 O43747 AP1G1 AP-1 complex subunit gamma-1 0 112.84 0.0068939 101790000 157950 146500 133540 153120 156080 144970 154790 182220 184710 192240 FALSE TRUE 151777.1394 142321.9634 157673.6486 161022.5415 161100.4549 147901.3927 156684.3663 178457.0933 163742.4952 179219.4136 0.846878898 0.794121354 0.87977996 0.898465955 0.898900692 0.82525319 0.87426001 0.995746442 0.913642623 1 17.4513674 1.823815324 5.785744182 0.966452498 0.858743923 0.64710065 0.037342998 0.14412992 7.234911306 0.017472328 0.010244088 66.65232819 -1.823815324 -0.107708574 DFVAEPMGEKPVGSLAGIGEVLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFVAEPMGEKPVGSLAGIGEVLGK 24 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ; 221.6 8.33E-33 1494130000 2009990 1802450 1528420 1549490 1607710 1780910 1773320 2183720 2248490 2129730 FALSE TRUE 1931437.369 1751045.891 1804639.494 1629459.365 1659423.452 1816921.22 1795022.421 2138625.419 1993250.842 1985481.49 0.972780345 0.881925064 0.908917813 0.82068726 0.835778858 0.91510358 0.904074115 1.077131884 1.003913082 1 20.92105748 1.824000819 6.052553307 1.031532495 0.886673339 0.662633455 0.044340189 0.12857037 6.948111155 0.020463376 0.012101517 66.68080273 -1.824000819 -0.144859156 TLVGICSEHQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLVGICSEHQSR 12 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 122.52 0.00035705 141360000 376920 476980 348070 361180 349830 466900 387830 365600 378110 417560 FALSE TRUE 362189.5497 463376.9974 410973.9918 379820.5431 361082.5997 476341.0379 392576.3796 358050.2322 335188.538 389278.2893 0.93041292 1.190348936 1.055733143 0.975704409 0.927569324 1.223651693 1.00847232 0.919779608 0.8610512 1 18.57044236 1.824012819 4.196904124 0.918773195 1.052449954 0.237632238 0.097616498 0.297908811 8.680299909 0.04757954 0.026033813 66.68264515 -1.824012819 0.133676759 GKNENESEKR ddPTM_BT-474_Pertuzumab_2h_R1 7 GKNENESEKR 10 2 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;;;;;; 157.38 5.22E-06 6241350000 3223800 2750199 2272353 2244159 2451437 2582485 2688400 2935240 3203920 3181130 FALSE TRUE 3097810.332 2671766.017 2683017.735 2359980.315 2530289.697 2634704.616 2721301.443 2874626.268 2840224.434 2965669.232 1.044556925 0.900898181 0.904692171 0.79576653 0.853193495 0.888401373 0.917601132 0.969301039 0.957701015 1 21.49992627 1.824061784 2.318102522 0.976723219 0.891764352 0.252924288 0.059358999 0.413844591 4.213220906 0.037905811 0.017734866 66.69016371 -1.824061784 -0.084958867 KYPS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 6 KYPSPQK 7 1 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK 88.681 0.011288 7228400000 11785800 9637600 8537200 7820900 8903100 8137100 9785300 11368600 12941200 11504400 TRUE FALSE 11325197.91 9362745.084 10080061.95 8224537.586 9189476.297 8301637.737 9905055.429 11133834.44 11472169.23 10725196.74 1.055943138 0.872967211 0.939848675 0.766842584 0.856811909 0.774031278 0.92353135 1.038100718 1.069646507 1 23.35450078 1.824315562 3.657695244 1.040775383 0.872976441 0.44180499 0.078942013 0.206397384 4.753556737 0.040988917 0.021710967 66.7291453 -1.824315562 -0.167798942 KNDMDEPPSGDFGGDEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KNDMDEPPSGDFGGDEEK 18 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;; 172.3 1.78E-11 1125210000 1985700 1635800 1465710 1277640 1649760 1582290 1712290 2059180 2358350 2049620 FALSE TRUE 1908096.649 1589148.586 1730596.402 1343579.154 1702826.029 1614284.988 1733245.517 2016657.213 2090639.995 1910797.412 0.998586578 0.831667751 0.905693294 0.703151022 0.891159899 0.844822679 0.907079686 1.05540085 1.094119126 1 20.8657434 1.824437459 3.119330602 1.058565921 0.8578317 0.56887024 0.072763952 0.16564424 2.893341276 0.038416134 0.019552692 66.74787734 -1.824437459 -0.200734221 PNSS(ph)PSPSPGQASETPHPRPS ddPTM_BT-474_Pertuzumab_2h_R1 1 PNSSPSPSPGQASETPHPRPS 21 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 PNS(0.127)S(0.564)PS(0.309)PSPGQASETPHPRPS 234.73 5.31E-30 352130000 59796 50430 56118 53245 49846 58009 60501 64323 79219 70222 TRUE FALSE 57459.10621 48991.78578 66259.77094 55992.98083 51449.34186 59181.98173 61241.42934 62994.70757 70226.39123 65465.80139 0.877696522 0.748356924 1.012128005 0.855301236 0.785896464 0.904013706 0.935472079 0.962253669 1.072718729 1 15.99845384 1.824514383 1.386544096 1.030920597 0.859769486 0.495303582 0.068767184 0.349108763 1.261362197 0.05231995 0.021596414 66.75970101 -1.824514383 -0.171151111 TFDHMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TFDHMAR 7 0 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 0 ; 185.42 0.0006137 840220000 1002050 1137250 1029120 1158280 1110990 1164180 1104430 950430 1132670 1054060 FALSE TRUE 962888.7782 1104816.743 1215104.877 1218058.97 1146726.002 1187720.517 1117946.345 930803.2884 1004094.05 982667.5773 0.97987234 1.12430365 1.23653706 1.239543257 1.16695211 1.208669691 1.137664832 0.947220922 1.021804396 1 19.90634393 1.824850423 5.352980663 0.988185483 1.165388616 0.528852476 0.07196126 0.170447863 7.45809267 0.034945429 0.020190245 66.81137709 -1.824850423 0.177203133 WLPEEDFR ddPTM_BT-474_Pertuzumab_2h_R1 4 WLPEEDFR 8 0 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 0 ;;; 122.74 0.0032044 489609000 1000650 1149700 952490 1147630 1166570 1133700 1034970 1106280 1047290 1158200 FALSE TRUE 961543.4917 1116911.682 1124626.131 1206859.322 1204093.784 1156624.191 1047636.272 1083434.931 928406.0298 1079754.082 0.890520821 1.03441302 1.041557656 1.117716841 1.115155574 1.071192237 0.970254514 1.00340897 0.859830998 1 20.04227134 1.824897061 1.830805577 0.940996395 1.048920284 0.252904847 0.070508912 0.457609116 2.936536988 0.049183441 0.021463247 66.81855222 -1.824897061 0.107923889 (ac)S(ph)DQEAKPSTEDLGDKK ddPTM_BT-474_Pertuzumab_2h_R1 9 SDQEAKPSTEDLGDKK 16 2 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(1)DQEAKPSTEDLGDKK;S(0.982)DQEAKPS(0.009)T(0.009)EDLGDKK;S(0.997)DQEAKPS(0.002)TEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(0.999)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK 115.8 1.03E-11 28692540000 14361240 10285980 9583239 7573360 10039361 9445871 10869013 14346100 16403320 12321040 TRUE FALSE 13799986.86 9992633.921 11315143.47 7964222.017 10362286.16 9636872.983 11002031.23 14049848.02 14541283.88 11486524.99 1.201406594 0.869944037 0.985079776 0.693353475 0.902125419 0.838972012 0.957820685 1.22315914 1.265942824 1 23.45343907 1.824934193 4.630725099 1.182746187 0.905584663 0.393864976 0.136891713 0.19470879 6.677609192 0.064149562 0.035924384 66.82426541 -1.824934193 -0.277161524 AKGEVDVDVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKGEVDVDVPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 75.479 0.034635 303550000 407880 365230 368860 322530 314200 333600 367120 459520 456060 454190 FALSE TRUE 391939.5987 354813.998 435521.2072 339175.812 324306.5283 340345.6206 371612.9244 450030.7514 404289.9808 423427.3067 0.925636095 0.837957289 1.028561929 0.80102489 0.765908394 0.803787604 0.877630985 1.062828836 0.954803751 1 18.69175479 1.825134339 6.689411009 1.008587456 0.85910073 0.439616724 0.074010726 0.224073921 14.10558586 0.034142472 0.020559779 66.85506857 -1.825134339 -0.149486726 SGPKPFSAPKPQT(ph)SPS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFSAPKPQT(0.797)S(0.214)PS(0.99)PKR 71.091 0.038962 1910500000 441710 322670 254740 189450 274260 372810 331890 399440 554360 422050 TRUE FALSE 424447.4849 313467.7675 300777.1847 199227.5372 283081.822 380348.4736 335951.7691 391191.4244 491431.3769 393464.1776 1.078744925 0.79668693 0.764433465 0.506342251 0.719460215 0.966666079 0.853830636 0.994223735 1.248986324 1 18.58587277 1.825245398 1.352150634 1.117127508 0.776737784 0.40647659 0.153174864 0.4207704 1.442236086 0.123658611 0.050967931 66.8721672 -1.825245398 -0.340389724 RVPS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVPSPGK 7 1 D6RIF6;H0Y9L2 D6RIF6 SLAIN2 1 RVPS(1)PGK 54.157 0.082903 194940000 498840 465450 491760 452130 399980 430200 483560 602380 639150 578290 TRUE FALSE 479344.7813 452175.8217 580631.9711 475464.4835 412845.72 438898.9388 489477.9519 589940.6425 566596.3715 539121.9032 0.889121326 0.83872649 1.076995699 0.881923885 0.765774341 0.814099624 0.90791702 1.094262056 1.050961514 1 19.040252 1.825397539 5.369926229 1.054539309 0.879152353 0.481840476 0.079275206 0.193614649 8.488151815 0.039205522 0.022675889 66.89559786 -1.825397539 -0.175386956 MNEAFGDTK ddPTM_BT-474_Pertuzumab_2h_R1 3 MNEAFGDTK 9 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 139.43 0.00025939 1324540000 1313910 1271590 1041660 1065410 1185340 1192890 1216260 1337640 1456870 1408840 FALSE TRUE 1262560.945 1235325.498 1229911.134 1120395.938 1223467.538 1217011.053 1231144.954 1310017.267 1291492.225 1313418.012 0.961278841 0.940542529 0.936420182 0.853038353 0.931514207 0.926598419 0.937359578 0.997410767 0.983306315 1 20.32489471 1.825556228 3.363165087 0.993538482 0.923538098 0.570372964 0.026707886 0.181397265 3.607574399 0.01483585 0.007704197 66.92004561 -1.825556228 -0.070000384 (ac)TT(ph)SQKHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSQKHR 7 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 T(0.032)T(0.614)S(0.354)QKHR 69.954 0.01223 762840000 575900 686300 340110 425880 495900 645600 497440 351970 420210 439550 TRUE FALSE 553393.1913 666727.396 401575.4427 447859.7178 511851.0739 658654.4743 503527.8195 344701.6965 372509.5225 409778.887 1.350467798 1.627041844 0.979980803 1.092930192 1.249090888 1.607341167 1.228779314 0.841189499 0.909050062 1 18.64448613 1.825596316 5.0101246 0.90761418 1.310741554 0.467308655 0.191180343 0.201083274 7.845002486 0.095189556 0.054266596 66.92622295 -1.825596316 0.403127375 DS(ph)DGVDGFEAEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDGVDGFEAEGK 13 0 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 DS(1)DGVDGFEAEGK;DS(1)DGVDGFEAEGK 305.82 1.86E-41 392880000 676140 541890 617990 583160 600170 531510 643760 810380 859710 840110 TRUE FALSE 649715.7013 526435.8278 729674.5401 613256.9575 619475.0131 542257.4964 651638.5275 793645.3698 762119.325 783208.6014 0.829556392 0.672152766 0.931647761 0.783005902 0.79094511 0.692353857 0.832011454 1.013325656 0.973073232 1 19.57903708 1.825639424 4.19587167 0.994726167 0.783958328 0.660082186 0.068030553 0.130150863 3.772561754 0.032682985 0.017904019 66.9328664 -1.825639424 -0.210767838 EKDRES(ph)EKDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKDRESEKDR 10 3 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 EKDRES(1)EKDR;EKDRES(1)EKDR;EKDRES(1)EKDR 135.04 0.00085462 1611610000 2930380 2033960 1885270 1550450 2065190 1948150 2231830 2751360 3289140 2539620 TRUE FALSE 2815857.51 1975953.452 2225980.227 1630468.91 2131618.712 1987542.928 2259143.803 2694543.455 2915770.616 2367609.275 1.189325257 0.834577509 0.940180565 0.688656244 0.900325376 0.839472521 0.954187765 1.138086205 1.231525255 1 21.17499958 1.825689208 3.425907734 1.139764183 0.888782372 0.372206662 0.12926223 0.224128095 4.601143785 0.065890941 0.034378869 66.9405394 -1.825689208 -0.25098181 TPDTIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPDTIRR 7 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 112.37 0.010213 83750000 270310 311590 195330 202350 233760 307880 240870 218040 234190 235940 FALSE TRUE 259745.9864 302703.7583 230630.4761 212793.3077 241279.1027 314105.5445 243817.8391 213537.3978 207605.733 219959.5736 1.180880568 1.376179055 1.048513017 0.967420077 1.096924761 1.428014882 1.108466593 0.970802926 0.943835858 1 17.74687887 1.825708336 4.089870231 0.969029417 1.177941774 0.337001863 0.131377657 0.280888127 7.796989041 0.06986808 0.038047979 66.94348781 -1.825708336 0.208912357 DESETEKEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DESETEKEK 9 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 163.64 5.73E-05 1977330000 3349750 2430410 2172500 1783220 2538070 2502210 2583870 3024780 3554230 2951620 FALSE TRUE 3218838.067 2361097.086 2565119.077 1875252.198 2619709.327 2552806.401 2615492.174 2962317.236 3150768.711 2751704.148 1.16976168 0.858049034 0.932192903 0.681487579 0.952031609 0.927718339 0.950499048 1.076539147 1.145024516 1 21.39189394 1.825976964 2.706619872 1.086412121 0.909190435 0.254358536 0.116645834 0.332271834 4.497744247 0.065921642 0.032326179 66.98490775 -1.825976964 -0.177221686 RMGESDDSILR ddPTM_BT-474_Pertuzumab_2h_R1 4 RMGESDDSILR 11 1 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;; 184.65 7.72E-06 1856130000 1169010 1273760 927960 1037120 1045240 1067570 1047580 950020 940170 1024380 FALSE TRUE 1123323.797 1237433.612 1095663.014 1090645.887 1078861.094 1089156.997 1060400.597 930401.755 833445.8431 954997.8302 1.176257957 1.295744946 1.147293721 1.142040173 1.129700047 1.140481122 1.110369641 0.974244889 0.872720143 1 19.86513793 1.826021535 1.788897706 0.928241366 1.175924411 0.781002619 0.052990796 0.155408211 0.951191597 0.037951041 0.016472553 66.99178277 -1.826021535 0.247683045 FPPEDFRHS(ph)PEDFR ddPTM_BT-474_Pertuzumab_2h_R1 7 FPPEDFRHSPEDFR 14 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR 200.99 1.12E-08 2939770000 1509051 1605009 1372288 1616719 1622755 1698353 1554612 1429698 1600745 1524387 TRUE FALSE 1450075.619 1559235.715 1620290.968 1700158.061 1674952.388 1732694.861 1573637.807 1400174.237 1419035.138 1421138.911 1.020361632 1.097173333 1.140135532 1.196334889 1.178598641 1.219229766 1.107307523 0.985247977 0.998519658 1 20.43861615 1.826040975 4.019049814 0.993967194 1.14510944 0.610275951 0.052539197 0.159014719 4.282236409 0.028580909 0.015504265 66.99478143 -1.826040975 0.151142246 RKS(ph)LSDS(ph)ESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.994)LS(0.04)DS(0.784)ES(0.164)DDS(0.018)K;RKS(0.997)LS(0.173)DS(0.453)ES(0.26)DDS(0.117)K 105.2 0.0072374 3916300000 7651000 5542200 5487700 4854800 5898900 6387000 6889400 7983400 10606200 8468300 TRUE FALSE 7351990.461 5384141.882 6479449.463 5105356.81 6088643.476 6516149.516 6973714.538 7818540 9402228.641 7894734.498 0.931252402 0.681991508 0.820730509 0.646678721 0.771228403 0.825379184 0.883337437 0.990348694 1.190949315 1 22.91245932 1.826092981 1.550675687 1.093393077 0.76668043 0.683244037 0.086742342 0.19879415 0.907063092 0.060148701 0.025255691 67.00280449 -1.826092981 -0.326712646 GPS(ph)PEPPPSPLQVPTYPQLTLEVPQAPEVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPSPEPPPSPLQVPTYPQLTLEVPQAPEVLR 31 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 1 GPS(0.877)PEPPPS(0.121)PLQVPT(0.001)Y(0.001)PQLTLEVPQAPEVLR 57.543 0.02723 25515000 11548 11981 9802.9 12239 11318 12491 14749 17121 16745 20246 TRUE FALSE 11096.69139 11639.31361 11574.50209 12870.65626 11682.05375 12743.57658 14929.50267 16767.44537 14844.1778 18874.72039 0.587912889 0.616661512 0.613227738 0.681899175 0.618925924 0.675166377 0.790978747 0.888354636 0.786458157 1 14.20416765 1.826125273 0.547953816 0.984908435 0.593490799 0.885618785 0.043972463 0.248437919 0.163549729 0.043812751 0.02821418 67.00778667 -1.826125273 -0.391417636 PVIVEPLEQLDDEDGLPEK ddPTM_BT-474_Pertuzumab_2h_R1 6 PVIVEPLEQLDDEDGLPEK 19 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;; 349.57 2.39E-90 1532923000 1824559 1338554 1570292 1482871 1665541 1512881 1861626 2229589 2722644 2397318 FALSE TRUE 1753253.217 1300379.751 1854078.695 1559402.15 1719114.639 1543472.49 1884409.136 2183547.208 2413580.867 2234945.517 0.784472464 0.581839575 0.829585635 0.697736092 0.76919756 0.690608554 0.843156633 0.977002433 1.07992828 1 21.09180823 1.826247085 2.045578985 1.038942517 0.724071662 0.796146465 0.066542206 0.122251763 0.977135471 0.039847057 0.017980901 67.02658384 -1.826247085 -0.314870854 ERDAEQSGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 ERDAEQSGSPR 11 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5 P08651-3 NFIC Nuclear factor 1 C-type 1 ERDAEQS(0.03)GS(0.97)PR;ERDAEQSGS(1)PR;ERDAEQS(0.005)GS(0.995)PR;ERDAEQS(0.006)GS(0.994)PR;ERDAEQS(0.001)GS(0.999)PR 184.04 1.34E-05 1340065000 1857068 1827358 1385212 1681804 1711610 1769857 1615565 1657698 1719665 1673897 TRUE FALSE 1784491.729 1775243.539 1635550.622 1768602.106 1766665.49 1805644.721 1635336.768 1623465.957 1524455.839 1560522.465 1.143521974 1.137595631 1.04807887 1.133339728 1.132098723 1.157077044 1.04794183 1.040334883 0.976888108 1 20.5735977 1.826277255 1.788889995 0.995378125 1.122296364 0.73913629 0.032090337 0.17866743 1.093420264 0.02235287 0.009704258 67.03124026 -1.826277255 0.12691824 TSGGDHAPDS(ph)PSGENSPAPQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSGGDHAPDSPSGENSPAPQGR 22 0 H0YDE3;E9PRI1;Q96NY9;E9PL60;E9PII7;H0YDU2 H0YDE3 MUS81 Crossover junction endonuclease MUS81 1 TSGGDHAPDS(1)PSGENSPAPQGR;TSGGDHAPDS(0.999)PS(0.001)GENSPAPQGR 201.35 9.90E-23 1600490000 534530 547840 496560 541650 487690 526600 521590 415600 509580 508060 TRUE FALSE 513639.9766 532216.1396 586299.4379 569604.6214 503376.9918 537248.2128 527973.3744 407017.7148 451734.6147 473648.6437 1.084432487 1.123651776 1.237836201 1.202588942 1.062764559 1.134275839 1.114694155 0.859324143 0.953733576 1 18.85345773 1.826393064 6.112671319 0.92809088 1.141598908 0.712574324 0.058060145 0.116332282 6.264613048 0.02700307 0.016026706 67.04911718 -1.826393064 0.213508028 DEFTNTCPSDKEVEIAYSDVAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DEFTNTCPSDKEVEIAYSDVAK 22 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 ;;; 274.97 1.84E-45 1975160000 1385330 1222000 982410 907960 1115070 1175970 1177620 1454370 1607890 1346130 FALSE TRUE 1331189.772 1187149.756 1159953.341 954819.9244 1150937.239 1199748.919 1192032.066 1424336.751 1425369.068 1254955.416 1.060746665 0.945969667 0.924298446 0.760839718 0.917114046 0.956009197 0.949860091 1.134970002 1.135792595 1 20.25920468 1.826469168 4.666738027 1.101584051 0.92276371 0.470128826 0.077350765 0.181962082 6.283062742 0.038540113 0.021645585 67.06086757 -1.826469168 -0.178820341 STGKGDSCDS(ph)SEDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 STGKGDSCDSSEDKK 15 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 1 STGKGDS(0.016)CDS(0.868)S(0.116)EDKK 91.457 0.0029329 42946000 148050 91340 61520 61558 68521 73012 93793 102410 131260 104580 TRUE FALSE 142264.0423 88735.07263 72638.03251 64735.01576 70725.04019 74488.35266 94940.86679 100295.1977 116359.9151 97496.70345 1.459167718 0.910134081 0.745030652 0.663971329 0.725409554 0.764008936 0.973785404 1.028703476 1.193475379 1 16.57306582 1.826595547 2.47495482 1.090916351 0.858265852 0.135520663 0.215681034 0.522551697 6.000578345 0.133049231 0.063612462 67.08038505 -1.826595547 -0.232650499 SFGTRPLSSGFSPEEAQQQDEEFEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 226.67 5.62E-34 1521090000 317752 340493 252079 287438 307980 321904 314936 386001 382421 379771 FALSE TRUE 305333.9005 330782.473 297635.2828 302272.7096 317886.4564 328413.1194 318790.281 378029.9445 339010.1713 354048.7719 0.862406326 0.934285046 0.840661814 0.853760085 0.897860638 0.927592878 0.900413464 1.067734093 0.95752393 1 18.43358859 1.826687214 7.373342834 1.012455111 0.888106426 0.682002783 0.037655589 0.142093104 10.22972724 0.01622705 0.009925083 67.09454535 -1.826687214 -0.124348685 DKLELEITDSKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKLELEITDSKK 12 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 148.72 3.75E-05 2428600000 3792800 3187200 3330000 2757400 3365100 2987000 3607000 4505900 5057100 4650600 FALSE TRUE 3644573.183 3096304.177 3931805.075 2899709.744 3473341.498 3047399.187 3651143.545 4412851.59 4483039.209 4335610.72 0.840613565 0.714156408 0.90686303 0.668812292 0.801119317 0.702876569 0.842129006 1.017815453 1.034004088 1 22.0478038 1.826749085 3.282208068 1.021951054 0.772350995 0.731261514 0.066213185 0.112579829 2.142647361 0.03265272 0.016867655 67.10410447 -1.826749085 -0.249600059 METVSNASSSSNPSS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 11 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.001)S(0.999)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.001)S(0.999)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.005)S(0.995)PGR 473.64 5.84E-215 22083780000 7987759 8615970 6605903 8328316 8037402 8140878 7630501 7685112 7982933 7813703 TRUE FALSE 7675588.547 8370250.972 7799736.62 8758141.387 8295932.335 8305492.131 7723885.354 7526411.752 7076743.913 7284473.936 1.053691538 1.149053596 1.070734371 1.202302522 1.138851262 1.140163614 1.06032164 1.033212805 0.971483181 1 22.79639336 1.826756463 1.72701534 0.990082109 1.128308189 0.652404485 0.040974361 0.207372442 1.18119837 0.027842537 0.011981521 67.10524456 -1.826756463 0.13822608 KREPEDEGEDDD ddPTM_BT-474_Pertuzumab_2h_R1 10 KREPEDEGEDDD 12 2 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;;;;;;; 227.31 5.26E-11 22389892000 10330460 9198915 8067531 8065743 8775679 8621450 9043373 10073172 10995749 9739202 FALSE TRUE 9926734.202 8936570.951 9525513.313 8482016.963 9057956.685 8795781.626 9154048.504 9865157.478 9747557.671 9079557.174 1.093305985 0.984251851 1.049116508 0.934188397 0.997620976 0.968745662 1.008204291 1.086524077 1.073571925 1 23.11419051 1.826983986 7.270273949 1.06128294 1.001265992 0.179518806 0.04603007 0.345469946 24.27240791 0.019364194 0.011823023 67.14040948 -1.826983986 -0.060016948 DKEVS(ph)DDEAEEKEDK ddPTM_BT-474_Pertuzumab_2h_R1 3 DKEVSDDEAEEKEDK 15 2 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEKEDK;DKEVS(1)DDEAEEKEDK;DKEVS(1)DDEAEEKEDK 273.87 9.61E-34 2883450000 2298020 1337760 2001520 1250390 1717090 1360250 2101760 3171360 3815470 3023800 TRUE FALSE 2208210.838 1299608.395 2363239.188 1314922.778 1772321.759 1387755.187 2127481.968 3105870.308 3382353.841 2818995.333 0.783332563 0.461018285 0.838326747 0.466450853 0.62870688 0.492287153 0.754695101 1.10176497 1.199843718 1 21.42674966 1.82706816 3.173175025 1.118755519 0.609800843 0.744974017 0.127500923 0.107579018 1.929726062 0.06323551 0.032392957 67.15342388 -1.82706816 -0.508954676 NS(ph)QEDSEDS(ph)EDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 NS(0.871)QEDS(0.129)EDS(0.999)EDKDVK 168.78 1.48E-05 1956400000 1183900 761120 633450 487470 662410 575540 744360 1076600 1185700 757960 TRUE FALSE 1137631.879 739413.6028 747928.506 512628.3851 683717.0192 587177.8131 753469.7003 1054367.834 1051104.307 706622.6941 1.609956613 1.046405117 1.058455258 0.725462668 0.967584292 0.830963707 1.066297059 1.492122801 1.487504315 1 19.43058056 1.827162857 6.482987501 1.371127164 1.018693574 0.198440055 0.253512547 0.30707229 18.04408946 0.112857143 0.06770889 67.16806814 -1.827162857 -0.35243359 S(ph)RSPNRFDAHDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRSPNRFDAHDPR 13 2 Q96T58;A0A669KB49;F6WRY4 Q96T58 SPEN Msx2-interacting protein 1 S(0.5)RS(0.5)PNRFDAHDPR;S(0.5)RS(0.5)PNRFDAHDPR;S(0.5)RS(0.5)PNRFDAHDPR;S(0.5)RS(0.5)PNRFDAHDPR 59.513 0.051566 5333180000 2513770 2646530 1819200 2326650 2430660 2536920 2320390 2040660 2317360 2198990 TRUE FALSE 2415529.089 2571053.556 2147969.908 2446728.685 2508844.386 2588218.261 2348787.627 1998519.658 2054303.008 2050050.449 1.178277876 1.254141603 1.047764414 1.193496817 1.223796413 1.262514424 1.145721867 0.974863647 1.002074368 1 20.96722798 1.827189984 4.084529232 0.991392692 1.191584868 0.716963037 0.056414268 0.120892475 3.335419215 0.028745005 0.015666128 67.17226362 -1.827189984 0.200192176 TYLLGPDDHLAEALLAPLTQAPEADDPQPGRGDDLGAQDGVS(ph)SPAASPGHVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TYLLGPDDHLAEALLAPLTQAPEADDPQPGRGDDLGAQDGVSSPAASPGHVVR 53 1 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 TYLLGPDDHLAEALLAPLTQAPEADDPQPGRGDDLGAQDGVS(0.453)S(0.453)PAAS(0.095)PGHVVR 68.807 1.77E-05 29760000 18959 31806 22815 29993 30190 33708 26521 21642 21795 25974 TRUE FALSE 18218.06132 30898.92402 26938.17802 31540.94232 31161.08877 34389.59886 26845.57193 21195.08514 19320.92297 24214.75784 0.752353645 1.276036879 1.112469437 1.302550392 1.28686353 1.420191731 1.108645071 0.875296184 0.797898666 1 14.56359896 1.827224527 3.871106386 0.878014619 1.20490099 0.367993274 0.174507374 0.225154634 5.676340027 0.087172042 0.046910211 67.17760658 -1.827224527 0.326886371 TRDELDQFLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TRDELDQFLDK 11 1 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 194.24 5.47E-07 1702850000 1692740 1575420 1528830 1556000 1673410 1556600 1722930 2040600 2176000 2224000 FALSE TRUE 1626585.849 1530490.564 1805123.59 1636305.346 1727236.752 1588075.519 1744015.733 1998460.897 1928989.603 2073366.499 0.784514388 0.738166921 0.87062446 0.789202173 0.833059063 0.76594057 0.841151689 0.963872474 0.930365955 1 20.98354373 1.827439231 3.210169358 0.962682991 0.79887958 0.79941765 0.037536551 0.103234861 1.888692469 0.019559753 0.010052365 67.21082579 -1.827439231 -0.163803411 FHPEPYGLEDDQR ddPTM_BT-474_Pertuzumab_2h_R1 6 FHPEPYGLEDDQR 13 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;;;;; 194.7 7.98E-07 6115360000 4647130 5414670 4112850 5536040 4355410 4998110 4819580 4174380 4770970 4744610 FALSE TRUE 4465515.022 5260248.913 4856133.485 5821755.688 4495505.718 5099175.209 4878563.462 4088177.594 4229389.487 4423253.339 1.009554434 1.189226235 1.097864651 1.316170529 1.016334669 1.152811024 1.102935574 0.924246766 0.95617166 1 22.07667644 1.827489062 4.689380451 0.955266072 1.134024415 0.452305844 0.083970841 0.180747628 6.265795742 0.038179097 0.021482392 67.21853794 -1.827489062 0.178758344 IPSKEEEADMSS(ph)PTQR ddPTM_BT-474_Pertuzumab_2h_R1 7 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.022)S(0.973)PT(0.004)QR;IPSKEEEADMS(0.049)S(0.95)PT(0.001)QR;IPSKEEEADMS(0.057)S(0.941)PT(0.002)QR;IPSKEEEADMS(0.041)S(0.83)PT(0.129)QR;IPSKEEEADMS(0.052)S(0.948)PTQR;IPSKEEEADMS(0.069)S(0.93)PT(0.001)QR;IPSKEEEADMS(0.137)S(0.494)PT(0.368)QR 194.7 1.03E-10 10242260000 5937260 6178530 5507460 6367250 6582610 6940010 5625680 5611920 5596550 5400230 TRUE FALSE 5705225.315 6002324.374 6502780.535 6695864.536 6794345.629 7080341.757 5694528.755 5496031.891 4961253.107 5034467.612 1.133233095 1.1922461 1.291652074 1.330004491 1.349565863 1.406373484 1.13110843 1.091680852 0.985457349 1 22.26340779 1.827649694 2.174725643 1.012682782 1.283301458 0.678677037 0.079460745 0.189249797 1.701545676 0.05398598 0.024847251 67.24340458 -1.827649694 0.270618676 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF ddPTM_BT-474_Pertuzumab_2h_R1 2 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF 41 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 73.303 0.0012092 356440000 78251 116722 88934 128411 99986 122648 110511 9205.7 112551 110213 FALSE TRUE 75192.86441 113393.2028 105006.3521 135038.3071 103202.1405 125128.0266 111863.4667 9015.599078 99774.68233 102748.1753 0.731817029 1.103603081 1.02197778 1.314264771 1.004418231 1.217812639 1.088714873 0.087744615 0.971060381 1 16.64875325 1.827742431 25 0.585252931 1.081151892 0.2629206 0.278097271 61.14179592 17140.30362 0.108625023 0.070095415 67.25776495 -1.827742431 0.495898961 KILDSVGIEADDDRLNK ddPTM_BT-474_Pertuzumab_2h_R1 4 KILDSVGIEADDDRLNK 17 2 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;; 304.19 6.57E-47 8189240000 5260170 4721260 4025240 4058790 4191270 4804190 4710190 5806880 6103950 5932990 FALSE TRUE 5054596.741 4586614.287 4752690.409 4268264.638 4326086.006 4901334.013 4767834.714 5686965.899 5411055.186 5531143.303 0.913843027 0.829234398 0.859260039 0.771678549 0.782132331 0.886133977 0.861998045 1.02817186 0.978288735 1 22.39914629 1.827856264 4.067833537 1.003022761 0.837534346 0.74947055 0.042060886 0.110715591 3.028662442 0.021735674 0.011840441 67.27539624 -1.827856264 -0.165488415 S(ph)IEVENDFLPVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIEVENDFLPVEK 13 0 Q5JPT1;Q5VSN0;Q5JPT2;Q96B97-2;Q96B97 Q5JPT1 SH3KBP1 SH3 domain-containing kinase-binding protein 1 1 S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK 252.36 9.81E-24 83394000 194405 189350 140461 151907 164629 176210 175807 217918 232420 201510 TRUE FALSE 186807.4377 183949.9234 165845.4272 159746.9385 169924.4413 179773.0869 177958.5787 213417.9171 206036.656 187861.5482 0.994388897 0.979178151 0.882806667 0.85034399 0.904519541 0.956944562 0.947285809 1.136038317 1.096747354 1 17.51931028 1.828029852 5.728337433 1.088249432 0.926343022 0.626663754 0.051800793 0.137320664 6.578134247 0.024924608 0.014631701 67.30229163 -1.828029852 -0.16190641 RLDLLHQQLQELHAHVVLPDPAATHDGPQS(ph)PGAGGPTCSATNLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLDLLHQQLQELHAHVVLPDPAATHDGPQSPGAGGPTCSATNLSR 45 1 Q16512;Q16512-2;Q16512-3;K7EM57;K7EKY9 Q16512 PKN1 Serine/threonine-protein kinase N1 1 RLDLLHQQLQELHAHVVLPDPAAT(0.002)HDGPQS(0.998)PGAGGPTCSATNLSR 137.68 5.11E-11 1002900000 62915 68837 65901 85098 96633 119730 76714 16014 51907 34287 TRUE FALSE 60456.21224 66873.83616 77810.77666 89489.91798 99741.2882 122151.0226 77652.84888 15683.3053 46014.73497 31964.71095 1.891342372 2.092114528 2.434271243 2.79964734 3.120356332 3.821433669 2.429330551 0.490644365 1.439547977 1 14.96419243 1.828186244 5.828392363 0.96744972 2.707959259 0.663115421 0.549624568 0.140730839 6.92379341 0.272333237 0.16041954 67.32653187 -1.828186244 1.74050954 RNDDISELEDLS(ph)ELEDLKDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNDDISELEDLSELEDLKDAK 21 2 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 RNDDISELEDLS(1)ELEDLKDAK 189.34 1.15E-17 61935000 80920 65182 64969 47600 60763 63073 68062 84530 94193 82626 TRUE FALSE 77757.55694 63323.07318 76710.34353 50056.6417 62717.49708 64348.37927 68894.96312 82784.42596 83500.60553 77029.66742 1.00944947 0.822060841 0.995854534 0.64983588 0.814199245 0.835371376 0.894395178 1.074708339 1.084005791 1 16.23312658 1.828550556 3.740194488 1.060108526 0.849311384 0.455647618 0.09691347 0.197571725 4.687745416 0.049092458 0.026226687 67.38303312 -1.828550556 -0.210797143 TKMIMVEER ddPTM_BT-474_Pertuzumab_2h_R1 5 TKMIMVEER 9 1 Q5JYW6;H0Y5P0;H0YE38;B1AJZ9-4;B1AJZ9;B1AJZ9-3 Q5JYW6 FHAD1 Forkhead-associated domain-containing protein 1 0 ;;;; 75.378 0.051686 1937110000 287188 536024 349087 593120 527582 532803 414711 208956 200830 281691 FALSE TRUE 275964.3755 520737.1203 412174.7863 623730.9943 544552.1542 543576.6417 419786.3573 204640.9856 178032.6203 262611.8177 1.050845228 1.982915792 1.56952109 2.375106345 2.073601101 2.069886445 1.598505204 0.779252767 0.677930727 1 18.00257231 1.828556006 3.375455514 0.788359157 1.87816813 0.643268229 0.343687682 0.142672714 2.8427121 0.181021832 0.094301692 67.3838787 -1.828556006 1.089808972 GATKESS(ph)EKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GATKESSEKDR 11 2 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 GAT(0.001)KES(0.382)S(0.618)EKDR;GAT(0.011)KES(0.431)S(0.558)EKDR 146 1.88E-05 1308340000 1551080 1143450 1069930 958980 1110200 1081590 1245370 1509280 1713920 1520650 TRUE FALSE 1490462.079 1110839.926 1263290.151 1008473.073 1145910.591 1103460.491 1260611.211 1478112.841 1519362.987 1417655.021 1.051357387 0.78357563 0.891112529 0.711367052 0.808314134 0.778370248 0.889222831 1.042646355 1.071743805 1 20.43507507 1.828599884 3.335235767 1.044565458 0.830445544 0.514990674 0.086762632 0.179631065 3.505787459 0.044696224 0.023214922 67.39068699 -1.828599884 -0.214119914 KGS(ph)SSQAPASK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGSSSQAPASK 11 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 KGS(0.756)S(0.103)S(0.141)QAPASK 58.831 0.063597 220210000 171430 169160 105150 162900 164140 159790 137720 126800 128740 119550 TRUE FALSE 164730.3261 164335.7224 124152.944 171307.2885 169419.7122 163021.0633 139405.4586 124181.5357 114125.9749 111452.772 1.478028075 1.474487529 1.113951154 1.537039281 1.520103171 1.462691868 1.250802973 1.11420769 1.023985073 1 16.76607297 1.828653297 1.874965101 1.02172223 1.427133297 0.696877318 0.114289564 0.195783842 1.315555007 0.079513881 0.035042585 67.39897574 -1.828653297 0.405411068 FQQDDAHIFCAMEQIEDEIK ddPTM_BT-474_Pertuzumab_2h_R1 2 FQQDDAHIFCAMEQIEDEIK 20 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 231.06 1.25E-25 284190000 182647 122156 155080 181733 143560 114332 190162 218052 254252 261180 FALSE TRUE 175508.9533 118672.2305 183106.4057 191112.2619 148177.7378 116643.8714 192489.2594 213549.15 225390.3789 243490.046 0.720805455 0.487380213 0.752007767 0.78488737 0.608557681 0.479049856 0.790542622 0.877034415 0.92566568 1 17.89350327 1.828671847 2.44879265 0.939332968 0.642799781 0.630201639 0.100853579 0.190118226 2.136820187 0.061387261 0.029307556 67.40185462 -1.828671847 -0.296533187 NYS(ph)SPPPCHLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NYS(0.61)S(0.39)PPPCHLSR;NYS(0.621)S(0.379)PPPCHLSR;NY(0.001)S(0.499)S(0.499)PPPCHLSR;NYS(0.548)S(0.452)PPPCHLSR 101.39 0.0017392 1089310000 650500 994850 771750 1047060 800390 871700 876530 784460 838720 1034290 TRUE FALSE 625077.7408 966477.8521 911222.3925 1101098.892 826135.2712 889326.3712 887257.2363 768260.6269 743512.0218 964236.6171 0.648261775 1.002324362 0.945019486 1.141938475 0.856776497 0.922311345 0.920165466 0.796755291 0.771088765 1 19.87902769 1.828673642 7.033705656 0.836071515 0.930443604 0.037454999 0.129582963 0.60596352 39.79526453 0.055326359 0.033655547 67.40213324 -1.828673642 0.094372089 MEIGDTLSTAEESS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 2 MEIGDTLSTAEESSPPK 17 0 Q9BYW2;C9JG86;Q9BYW2-3;Q9BYW2-2 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 MEIGDTLSTAEESS(1)PPK;MEIGDTLSTAEES(0.013)S(0.987)PPK 340.31 5.97E-63 117390000 266290 220630 225020 211870 226430 230010 251750 306290 328310 338820 TRUE FALSE 255883.0924 214337.8484 265686.1195 222804.6361 233713.3266 234660.9598 254830.9918 299965.0045 291041.6252 315871.4196 0.810086246 0.678560437 0.841121111 0.705364975 0.7399002 0.74290026 0.806755458 0.949642753 0.921392716 1 18.26897788 1.828680298 2.508619218 0.959114571 0.750778563 0.787852328 0.04735677 0.112967593 1.327651814 0.025786467 0.012398833 67.40316621 -1.828680298 -0.208336009 QSFDDNDS(ph)EELEDKDSK ddPTM_BT-474_Pertuzumab_2h_R1 6 QSFDDNDSEELEDKDSK 17 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 QSFDDNDS(1)EELEDKDSK;QSFDDNDS(1)EELEDKDSK;QSFDDNDS(1)EELEDKDSK;QSFDDNDS(1)EELEDKDSK;QSFDDNDS(1)EELEDKDSK;QSFDDNDS(1)EELEDKDSK 277.2 5.34E-36 9616600000 8193420 5873250 6080840 4625620 5918150 5767250 6804850 7979130 9565660 8222760 TRUE FALSE 7873212.088 5705750.661 7179783.056 4864348.803 6108512.669 5883867.746 6888129.79 7814358.177 8479806.379 7665825.141 1.027053441 0.744310046 0.936596247 0.634549929 0.796849988 0.767545259 0.89855034 1.019376001 1.106183121 1 22.87000966 1.828682213 2.515473172 1.054464196 0.811188775 0.482217542 0.103442547 0.218637182 2.582483221 0.058316921 0.028062784 67.40346346 -1.828682213 -0.243275421 DDTHKVDVINFAQNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDTHKVDVINFAQNK 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ; 225.55 5.91E-13 1517680000 5368700 4870100 3763500 3659800 4241500 4121600 4729300 5106800 6012700 5438900 FALSE TRUE 5158885.269 4731209.516 4443648.169 3848682.717 4377931.7 4204941.576 4787178.588 5001342.795 5330163.503 5070518.459 1.017427569 0.933082002 0.876369587 0.759031398 0.863409084 0.829292233 0.944120138 0.98635728 1.051206804 1 22.27370184 1.828698251 2.301401901 1.020487125 0.876414245 0.454205189 0.064888602 0.27610947 2.762880087 0.042589885 0.019959483 67.40595264 -1.828698251 -0.14407288 LLPEKHEIENLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPEKHEIENLR 12 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ; 205.72 5.92E-08 520730000 580830 660770 450350 508900 548580 621260 564600 558230 607580 618090 FALSE TRUE 558130.5215 641925.4866 531738.263 535164.39 566225.5739 633822.3029 571509.7437 546702.3554 538610.0656 576226.2138 0.968596201 1.11401646 0.922794296 0.928740098 0.982644594 1.099953955 0.991814898 0.948763424 0.934719825 1 19.13627577 1.828851053 5.528871991 0.956614699 1.003296492 0.081592244 0.061441874 0.549447798 24.73115815 0.029123443 0.016987739 67.42967293 -1.828851053 0.046681794 SHSGT(ph)S(ph)PDNTAPPPPPPRPQPSHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 S(0.143)HS(0.54)GT(0.706)S(0.612)PDNTAPPPPPPRPQPSHSR 126.42 0.002011 559330000 21431 27109 25273 32737 31302 33984 27716 7357.7 23009 15962 TRUE FALSE 20593.45283 26335.87786 29840.39329 34426.56049 32308.85726 34671.17976 28055.1967 7205.760924 20397.11478 14880.87952 1.383886806 1.769779657 2.005284247 2.313476192 2.171165838 2.329914688 1.885318449 0.484229505 1.370692824 1 13.86117218 1.828978702 6.975840492 0.925445388 2.012214599 0.673462317 0.328056711 0.139162908 8.998616445 0.147515016 0.089641749 67.44949486 -1.828978702 1.086769211 IEDVGS(ph)DEEDDSGKDKK ddPTM_BT-474_Pertuzumab_2h_R1 55 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.994)DEEDDS(0.006)GKDKK;IEDVGS(0.999)DEEDDS(0.001)GKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.99)DEEDDS(0.01)GKDKK;IEDVGS(0.998)DEEDDS(0.002)GKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK 266.18 6.63E-28 7.15629E+11 27952721 19257900.2 18386931.2 13782054.8 19296136.9 17283567.5 21451987.6 28747246 34201807 25424352 TRUE FALSE 26860297.76 18708683.74 21709858.68 14493348.3 19916814.67 17633053.08 21714523.44 28153605.32 30319361.26 23702337.99 1.133234104 0.789318073 0.915937436 0.611473362 0.840289033 0.743937289 0.916134242 1.187798661 1.279171754 1 24.49852604 1.829038821 3.717732854 1.175417003 0.830159288 0.498564662 0.14118402 0.17205945 4.037485254 0.069935168 0.037320557 67.45883258 -1.829038821 -0.345257715 EIIDPVLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIIDPVLDR 9 0 P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8 P68366-2 TUBA4A Tubulin alpha-4A chain 0 78.516 0.068746 33948000 122180 144180 114370 139420 145230 156710 127960 128240 124920 135450 FALSE TRUE 117405.0705 140068.1276 135039.2031 146615.4829 149901.4548 159878.7836 129526.0128 125591.7992 110739.6053 126275.8509 0.929750778 1.109223392 1.069398481 1.161073015 1.187095187 1.266107355 1.025738586 0.994582878 0.876965822 1 16.94621924 1.829121611 2.754384219 0.947753008 1.122527817 0.397773526 0.088766835 0.26502029 3.691131683 0.05186626 0.025622237 67.47169348 -1.829121611 0.174774808 KPGDGEVS(ph)PSTEDAPFQHSPLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPGDGEVSPSTEDAPFQHSPLGK 23 1 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 KPGDGEVS(0.853)PS(0.121)T(0.027)EDAPFQHSPLGK 167.22 5.20E-12 520130000 332260 301060 229940 292450 276180 290570 297000 350050 383490 333640 TRUE FALSE 319274.9119 292474.0636 271495.273 307543.3795 285063.5805 296445.5245 300634.7748 342821.3452 339957.8229 311042.2656 1.026467934 0.940303283 0.872856531 0.988751091 0.916478601 0.953071519 0.966539947 1.10216965 1.092963435 1 18.24675111 1.829152981 5.113367764 1.073318992 0.947301574 0.556128639 0.046140733 0.143025154 5.667888678 0.020930469 0.012016101 67.47656736 -1.829152981 -0.126017418 EVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVHDELEDLPSPPPPLSPPPTTSPHK 26 0 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 EVHDELEDLPS(1)PPPPLS(0.985)PPPT(0.005)T(0.005)S(0.005)PHK 80.721 0.0084152 260900000 100420 118070 89764 104310 97806 113100 100060 75201 87369 89503 TRUE FALSE 96495.47538 114702.7592 105986.3516 109693.4516 100952.0188 115386.9595 101284.5642 73648.07307 77451.2374 83440.88209 1.156453203 1.374658996 1.270196922 1.314624784 1.209862795 1.382858817 1.213848196 0.882637758 0.928216906 1 16.34846679 1.829282575 4.406814652 0.929599374 1.286570438 0.830171021 0.070380408 0.074448637 2.31551851 0.031447643 0.017470652 67.49670548 -1.829282575 0.356971063 SMSSLQNDRDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SMSSLQNDRDR 11 1 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 ; 77.597 0.02935 327970000 222120 346390 245850 343520 277620 283540 293260 286810 301950 302310 FALSE TRUE 213439.3048 336511.2964 290280.5639 361249.1084 286549.8994 289273.3731 296849.0036 280887.2733 267673.9019 281834.2744 0.75732203 1.194004161 1.029968993 1.281778482 1.016731907 1.026395294 1.053275029 0.996639865 0.949756386 1 18.10448755 1.829448149 1.406417955 0.973224196 1.068479928 0.049677237 0.128525206 1.12137268 4.170601926 0.093996765 0.038994787 67.52244338 -1.829448149 0.095255732 SERDDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SERDDLR 7 1 Q32MZ4-4 Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 86.833 0.018045 171870000 293790 326920 284080 346190 358250 363420 313190 289380 300840 305420 FALSE TRUE 282308.362 317596.5617 335419.5753 364056.9074 369773.4366 370768.6014 317022.9129 283404.2019 266689.9044 284733.6314 0.991482322 1.115416399 1.178011792 1.27858766 1.298664421 1.302159494 1.113401713 0.995330971 0.93662945 1 18.11925338 1.829454502 2.996797829 0.97093433 1.198563782 0.533642697 0.09001839 0.210217484 3.401276158 0.054516115 0.027562215 67.52343111 -1.829454502 0.227629452 LGHDPYR ddPTM_BT-474_Pertuzumab_2h_R1 6 LGHDPYR 7 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-6 P18583-7 SON Protein SON 0 ;;;;; 117.16 0.0052935 2630690000 1676190 1825710 1561820 1991490 1808470 1710730 1788320 1545840 1872020 1860660 FALSE TRUE 1610682.642 1773642.538 1844075.616 2094271.038 1866641.08 1745322.133 1810205.995 1513917.864 1659516.138 1734635.841 0.928542236 1.022486966 1.063090923 1.20732605 1.076099684 1.006160539 1.043565429 0.872758321 0.956694252 1 20.72620139 1.82945964 7.711511333 0.932357119 1.054995886 0.309882605 0.072061566 0.310369377 23.13558343 0.032977443 0.020322587 67.52422999 -1.82945964 0.122638767 DKFEPGILQLSQWFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKFEPGILQLSQWFK 15 1 G3V3Y1;Q8N8N7;G3V2R9 G3V3Y1 PTGR2 Prostaglandin reductase 2 0 ; 148.33 3.24E-06 733170000 262370 271670 239230 227511 252220 251970 263250 324360 332120 324290 FALSE TRUE 252116.2903 263922.2376 282464.1826 239252.87 260332.8854 257065.006 266471.7322 317661.8527 294419.13 302325.5495 0.833923202 0.872973647 0.934304703 0.791374961 0.861101173 0.850292033 0.881406592 1.050727777 0.973847994 1 18.20574338 1.829467187 5.550031855 1.009823112 0.859634693 0.761170312 0.037957196 0.100451699 4.531723377 0.017086495 0.009978489 67.52540339 -1.829467187 -0.150188419 RSDAEEVDFAGWLCSTIGLNQPST(ph)PTHAAGV ddPTM_BT-474_Pertuzumab_2h_R1 3 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.371)T(0.491)PT(0.137)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.221)T(0.7)PT(0.078)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.138)T(0.741)PT(0.12)HAAGV 171.76 3.67E-13 337370000 189712 203860 168358 202072 202298 198770 161543 154176 141432 134534 TRUE FALSE 182297.8453 198046.1124 198784.0357 212500.9601 208805.0989 202789.2656 163520.0116 150992.2117 125377.2323 125421.8923 1.453477076 1.579039422 1.584922951 1.69428922 1.664821787 1.616857008 1.303759722 1.20387445 0.999643921 1 16.93642967 1.829579486 1.467900768 1.008813234 1.607862812 0.913463817 0.07441252 0.108486571 0.441190587 0.058461227 0.024387787 67.54286619 -1.829579486 0.599049579 DKDFAIDIIK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKDFAIDIIK 10 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 127.37 0.00032632 6836150000 22496710 19458440 17772960 16239320 18884810 17307720 21124490 23413770 27387430 25630180 FALSE TRUE 21617513.7 18903504.34 20984929.23 17077433.25 19492257.06 17657693.96 21383017.83 22930267.47 24278523.76 23894225.08 0.904717087 0.791132765 0.87824272 0.71470965 0.815772723 0.738994209 0.894903172 0.959657298 1.016083329 1 24.51015864 1.830072944 2.302428625 0.999973436 0.80640048 0.68997756 0.055285781 0.157359964 1.5743212 0.03256961 0.015282967 67.61965394 -1.830072944 -0.193572956 KPSLVSDLPWEGAAPQSPSFSGSEDSGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPSLVSDLPWEGAAPQSPSFSGSEDSGSPK 30 1 Q13425;Q13425-2;H7BY41;H0YCS0 Q13425 SNTB2 Beta-2-syntrophin 1 KPSLVSDLPWEGAAPQSPSFSGSEDS(0.001)GS(0.999)PK;KPSLVSDLPWEGAAPQSPSFSGSEDS(0.009)GS(0.991)PK 271.27 1.96E-71 872870000 1040450 810290 824090 811480 750830 790840 999810 1248350 1472270 1355950 TRUE FALSE 999788.0637 787181.3226 973021.3948 853360.58 774981.1288 806831.3266 1012045.974 1222571.136 1305144.082 1264110.299 0.790902554 0.622715694 0.769728239 0.675068134 0.613064485 0.638260227 0.800599421 0.967139606 1.032460603 1 20.26969092 1.830176274 2.37009154 1.012788546 0.682851304 0.860785766 0.056622998 0.094786877 1.001240024 0.033703822 0.015954852 67.63574442 -1.830176274 -0.329937242 KGNS(ph)PNSEPPTPK ddPTM_BT-474_Pertuzumab_2h_R1 5 KGNSPNSEPPTPK 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KGNS(1)PNSEPPTPK;KGNS(0.956)PNS(0.044)EPPTPK;KGNS(0.956)PNS(0.044)EPPTPK;KGNS(0.958)PNS(0.042)EPPTPK;KGNS(0.991)PNS(0.009)EPPTPK 127.97 0.00010461 3899220000 2372990 2060070 1933220 1785370 1873640 2071960 2206420 2647490 3181620 2601820 TRUE FALSE 2280250.927 2001318.821 2282595.858 1877513.16 1933907.332 2113856.451 2233422.828 2592818.406 2820455.836 2425596.414 0.940078454 0.825083187 0.941045198 0.77404186 0.797291471 0.871479047 0.920772646 1.068940567 1.162788591 1 21.2099081 1.830268487 2.494946022 1.09297209 0.854620777 0.708286302 0.062770882 0.139068551 1.615846955 0.03620363 0.017402206 67.65010689 -1.830268487 -0.238351313 NDLSICGTLHSVDQYLNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDLSICGTLHSVDQYLNIK 19 0 Q9Y333 Q9Y333 LSM2 U6 snRNA-associated Sm-like protein LSm2 0 ; 275.23 1.97E-39 520730000 510950 447050 348370 408190 430130 414130 453610 497960 551480 542360 FALSE TRUE 490981.5091 434300.5717 411328.2084 429256.7348 443965.5221 422503.9923 459161.4149 487676.952 488878.3024 505625.4741 0.971037921 0.858937284 0.813503729 0.848961844 0.878052125 0.835606618 0.908105779 0.964502338 0.966878307 1 18.94770962 1.830333582 2.33932033 0.979595219 0.864396803 0.596578992 0.040139744 0.198327466 2.04402257 0.024530471 0.011568409 67.66024746 -1.830333582 -0.115198416 TPRPAS(ph)PGPS(ph)LPARSPS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPRPASPGPSLPARSPSPPR 20 2 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 3 T(0.121)PRPAS(0.883)PGPS(0.517)LPARS(0.518)PS(0.962)PPR 65.775 0.016078 610160000 101390 110410 79543 95994 96427 105380 86676 91834 88249 88637 TRUE FALSE 97427.56671 107261.2149 93918.18952 100948.2618 99528.66203 107510.8558 87736.76682 89937.59581 78231.34349 82633.53704 1.179031785 1.298034899 1.136562622 1.221637914 1.204458451 1.301055959 1.061757368 1.088390973 0.946726309 1 16.3344398 1.830475676 1.649803385 0.989125257 1.220374425 0.71747234 0.060339522 0.18385443 0.952325267 0.040386935 0.017240239 67.68238843 -1.830475676 0.231249168 VKELEEQLENETLHK ddPTM_BT-474_Pertuzumab_2h_R1 4 VKELEEQLENETLHK 15 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ;;; 256.26 5.70E-25 631795000 1038010 906070 795500 766390 874190 954400 937450 1036010 1247150 1108200 FALSE TRUE 997443.4216 880229.7707 939264.5458 805943.4797 902309.1153 973698.6219 948922.7935 1014616.031 1105578.76 1033140.627 0.965447874 0.85199415 0.909135234 0.780090782 0.873365244 0.942464749 0.918483669 0.982069628 1.070114495 1 19.97860521 1.8307864 1.274362913 1.034325481 0.876284531 0.586893503 0.050192399 0.299447928 0.906296676 0.039408173 0.016268215 67.73083043 -1.8307864 -0.15804095 S(ph)GDEEFKGEDELCDSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGDEEFKGEDELCDSGR 17 1 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 S(1)GDEEFKGEDELCDSGR;S(1)GDEEFKGEDELCDSGR;S(1)GDEEFKGEDELCDSGR;S(1)GDEEFKGEDELCDSGR 234.72 2.33E-20 4047500000 2471500 1907820 1919860 1968180 2084950 1957050 2460990 2982220 3612390 3233910 TRUE FALSE 2374911.048 1853410.842 2266821.409 2069758.006 2152014.31 1996622.892 2491108.332 2920636.115 3202326.632 3014874.395 0.78773134 0.614755575 0.75187922 0.686515501 0.713798994 0.662257405 0.826272675 0.96874222 1.062175803 1 21.52366647 1.830883318 2.112999961 1.028556379 0.700739138 0.888761092 0.048723744 0.082335848 0.698855549 0.028109822 0.01285964 67.74594704 -1.830883318 -0.327817241 LS(ph)DVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSDVLK 6 0 Q14669-3;Q14669;Q14669-2;Q14669-4;Q92797;A0A087WUE9;M0R3C7;Q92797-2 Q14669-3;Q92797 TRIP12;SYMPK E3 ubiquitin-protein ligase TRIP12;Symplekin 1 LS(1)DVLK;LS(1)DVLK 88.819 0.053361 56647000 199422 187778 160132 174213 180551 181352 190009 264860 254250 237440 TRUE FALSE 191628.3678 182422.7553 189071.4145 183204.1538 186358.5869 185019.0617 192334.387 259390.5484 225388.6059 221357.9773 0.865694429 0.824107437 0.854143216 0.827637459 0.841887829 0.835836431 0.86888392 1.171814775 1.018208644 1 17.75602184 1.831035128 6.901614533 1.075720672 0.842460421 0.833807563 0.044550281 0.078168432 4.875960432 0.017940763 0.010898044 67.76963205 -1.831035128 -0.233260251 IKQHLENDPGS(ph)NEDTDIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKQHLENDPGSNEDTDIPK 19 1 O43396;K7ER96;K7EML9 O43396 TXNL1 Thioredoxin-like protein 1 1 IKQHLENDPGS(0.987)NEDT(0.013)DIPK 71.651 0.011943 245070000 346650 361070 231800 270600 340140 366070 318810 281520 345090 317820 TRUE FALSE 333102.5348 350772.6371 273691.4164 284565.6984 351080.912 373472.1862 322711.6921 275706.5136 305916.8299 296293.7683 1.124230647 1.183867751 0.923716411 0.960417426 1.184908188 1.260479383 1.089161254 0.930517423 1.03247811 1 18.17666876 1.831163533 7.397960579 0.983331103 1.104180324 0.227340904 0.098245013 0.424141612 29.24552813 0.046847502 0.028741756 67.789672 -1.831163533 0.120849221 FYEQFSK ddPTM_BT-474_Pertuzumab_2h_R1 5 FYEQFSK 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;; 159.04 0.003253 6861170000 5491604 5574217 4888737 4703298 5044746 4689388 5245362 5530361 6035020 5940410 FALSE TRUE 5276986.044 5415245.789 5772240.525 4946035.773 5207014.837 4784210.638 5309556.309 5416157.113 5349949.83 5538060.74 0.952858102 0.977823474 1.042285521 0.893098867 0.940223497 0.863878326 0.95873927 0.97798803 0.966033072 1 22.40094945 1.831167527 4.593009283 0.978558598 0.945818634 0.109778388 0.045381143 0.601561165 19.88692062 0.023170948 0.013011693 67.79029556 -1.831167527 -0.032739964 KPEENPASK ddPTM_BT-474_Pertuzumab_2h_R1 3 KPEENPASK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 137.89 0.00024346 1563680000 2249430 2138580 1756150 1974730 2037770 2129040 2199650 2546470 2879920 2733630 FALSE TRUE 2161519.789 2077589.792 2073525.37 2076646.052 2103316.723 2172090.648 2226569.975 2493884.505 2553003.555 2548478.805 0.848160787 0.815227416 0.813632574 0.814857101 0.825322431 0.852308696 0.873685891 0.978577691 1.001775471 1 21.28120492 1.831310622 1.616125808 1.007141392 0.823550562 0.975385537 0.011797577 0.049640246 0.24637554 0.008573254 0.003645255 67.81263531 -1.831310622 -0.18359083 IKEDEDDKTVLDLAVVLFETATLR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKEDEDDKTVLDLAVVLFETATLR 24 2 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 ; 231.44 6.57E-34 1572590000 1248820 1109910 1030660 878820 1003870 1095610 1215750 1321260 1755710 1366830 FALSE TRUE 1200014.734 1078256.454 1216923.189 924176.0055 1036160.39 1117763.985 1230628.712 1293975.519 1556409.161 1274253.387 0.941739489 0.846186845 0.955008793 0.725268628 0.81315098 0.8771913 0.965764521 1.015477403 1.221428311 1 20.28122076 1.831393742 1.74909988 1.104469457 0.855148911 0.601101209 0.080928235 0.227053861 1.324762204 0.055077862 0.023870289 67.82561528 -1.831393742 -0.249320546 EEKESEDKPEIEDVGS(ph)DEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEKESEDKPEIEDVGSDEEEEK 22 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 EEKESEDKPEIEDVGS(1)DEEEEK;EEKESEDKPEIEDVGS(1)DEEEEK 206.4 4.87E-23 218500000 271203 191914 191028 135697 195515 185403 221216 345670 393680 280160 TRUE FALSE 260604.0869 186440.8006 225551.009 142700.3384 201803.9175 189151.9757 223923.3076 338531.7937 348991.0968 261184.5137 0.997777714 0.71382793 0.863569612 0.546358344 0.772648863 0.724208235 0.857337613 1.296140376 1.336186024 1 17.99470983 1.831416846 4.226266538 1.236630925 0.763840702 0.67355103 0.137074412 0.115551141 3.335963416 0.064483856 0.035534067 67.82922355 -1.831416846 -0.472790223 NWTEDMEGGISS(ph)PVKK ddPTM_BT-474_Pertuzumab_2h_R1 9 NWTEDMEGGISSPVKK 16 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 NWTEDMEGGIS(0.287)S(0.713)PVKK;NWTEDMEGGIS(0.25)S(0.75)PVKK;NWTEDMEGGIS(0.182)S(0.818)PVKK;NWTEDMEGGIS(0.055)S(0.945)PVKK;NWTEDMEGGIS(0.268)S(0.732)PVKK;NWTEDMEGGIS(0.094)S(0.906)PVKK;NWTEDMEGGIS(0.107)S(0.893)PVKK;NWTEDMEGGIS(0.104)S(0.896)PVKK;NWTEDMEGGIS(0.001)S(0.999)PVKK 206.11 1.28E-11 11203260000 9591090 7936790 7364150 6442310 7439200 7650590 8109420 9905390 10410710 10045500 TRUE FALSE 9216259.599 7710440.52 8695015.72 6774798.391 7678488.624 7805290.172 8208665.508 9700840.235 9228929.846 9365109.337 0.984105926 0.82331559 0.92844786 0.72340836 0.819903788 0.833443571 0.876515715 1.035849117 0.985458847 1 23.15886441 1.8314353 4.591741104 1.007971207 0.84772069 0.524949327 0.0661426 0.166750424 5.50506028 0.031424596 0.017648776 67.83210589 -1.8314353 -0.160250517 WPEVDDDSIEDLGEVKK ddPTM_BT-474_Pertuzumab_2h_R1 6 WPEVDDDSIEDLGEVKK 17 1 O43583 O43583 DENR Density-regulated protein 0 ;;;;; 193.9 1.68E-10 4221510000 4222810 3251950 3115010 2680050 3372190 3172170 3503840 4724320 4886620 4396060 FALSE TRUE 4057777.917 3159207.57 3677961.6 2818367.702 3480659.554 3236313.451 3546721.042 4626761.141 4331911.384 4098310.941 0.990109822 0.770855998 0.897433517 0.687690061 0.849291233 0.789670061 0.865410432 1.128943413 1.0569992 1 21.96659802 1.831482533 5.262125375 1.0701246 0.826165155 0.622940504 0.080707952 0.125763415 5.155508551 0.035224517 0.020377617 67.83948356 -1.831482533 -0.243959445 SQVAELNDDDKDDEIVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQVAELNDDDKDDEIVFK 18 1 Q9BYG3;H7BZL0;C9J808 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 ; 254.44 1.42E-30 601550000 657670 437800 499630 340337 517600 464290 505370 638640 684240 568960 FALSE TRUE 631967.5293 425314.3727 589924.2552 357901.8334 534249.0741 473678.2619 511554.8692 625451.8608 606567.9438 530423.8324 1.19143879 0.801838731 1.112175244 0.674746894 1.00721167 0.893018437 0.96442663 1.1791549 1.143553337 1 19.01678607 1.831522271 5.938478102 1.122259659 0.937863933 0.198382243 0.144270855 0.297358141 14.71313968 0.060050118 0.03557711 67.84569122 -1.831522271 -0.184395727 QQEKEDKDEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQEKEDKDEKK 11 3 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 61.641 0.037684 37054000 191880 123960 111450 92055 118110 118620 135290 156290 194070 145230 FALSE TRUE 184381.1175 120424.7822 131591.4942 96805.96958 121909.1154 121018.5777 136945.7195 153062.5569 172039.9872 135393.4427 1.361817188 0.889443238 0.971919256 0.714997474 0.900406349 0.893828942 1.011464933 1.130501993 1.270667055 1 17.04679834 1.831633031 2.960067549 1.152502499 0.940465557 0.1818256 0.165472041 0.375346966 5.928637178 0.090210741 0.045535279 67.86299639 -1.831633031 -0.212036942 YSPTS(ph)PTYSPTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.041)S(0.959)PTYSPT(0.001)S(0.999)PK;YSPT(0.095)S(0.9)PT(0.005)YSPT(0.455)S(0.545)PK 255.64 4.00E-24 462450000 961140 817180 685360 780770 717530 759530 806110 906790 966960 919920 TRUE FALSE 923577.5862 793874.8265 809219.7978 821065.6333 740610.0041 774888.217 815975.4153 888064.4696 857194.7546 857612.999 1.076916496 0.925679563 0.943572216 0.957384781 0.863571337 0.903540662 0.951449449 1.03550724 0.999512316 1 19.70996725 1.831642603 5.925602625 1.013561406 0.940167495 0.24523941 0.052284819 0.29643578 14.60624864 0.023849229 0.014125051 67.86449215 -1.831642603 -0.073393911 GKKPDIDITGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKKPDIDITGPK 12 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 109.22 0.0009119 1756460000 2977300 2813000 2408490 2377510 2260840 2759700 2703200 3219100 3611700 3006600 FALSE TRUE 2860943.824 2732775.994 2843757.72 2500213.576 2333561.972 2815503.025 2736282.57 3152624.46 3201714.957 2802960.304 1.020686529 0.974960648 1.014555117 0.891990362 0.832534791 1.004474812 0.976211674 1.124748166 1.14226197 1 21.41851988 1.831819247 4.245678231 1.100268911 0.954172001 0.452660999 0.065059495 0.192134049 5.582529804 0.033110792 0.018270455 67.89210079 -1.831819247 -0.14609691 DGWPAMCIHGDK ddPTM_BT-474_Pertuzumab_2h_R1 6 DGWPAMCIHGDK 12 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;; 146.5 6.48E-05 5506430000 7681380 7654060 6128480 6457380 7311270 7363240 7344410 8228220 9271670 8342200 FALSE TRUE 7381183.177 7435773.703 7236032.663 6790646.156 7546443.639 7512129.758 7434293.087 8058304.382 8219188.892 7777175.364 0.949082775 0.956102101 0.930419121 0.873150706 0.970332195 0.965920068 0.955911721 1.036147959 1.056834713 1 22.89081484 1.831887988 2.542618232 1.037005084 0.939410124 0.659430762 0.028947398 0.164322197 1.97423399 0.017567356 0.008502007 67.90284763 -1.831887988 -0.09759496 DNEEKDSAFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DNEEKDSAFR 10 1 O14787-2;O14787;Q92973-2;Q92973;Q92973-3;S4R398 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ;;; 150.09 2.02E-05 3450790000 3909950 3552340 2997480 2729760 3436950 3628070 3587710 4020550 4827870 4350720 FALSE TRUE 3757144.831 3451030.741 3539191.315 2870643.241 3547502.618 3701432.061 3631617.468 3937524.237 4279830.438 4056041.859 0.926308199 0.850837063 0.87257268 0.707744974 0.874621797 0.912572451 0.895359958 0.970779981 1.055174129 1 21.95164111 1.832041538 1.2077545 1.028875994 0.845404482 0.600269784 0.05665561 0.315794764 0.854873563 0.04671593 0.019322952 67.92685979 -1.832041538 -0.183471512 ITNDFYPEEDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ITNDFYPEEDGK 12 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 164.13 0.00044612 0 151060 144440 142160 134240 144130 141040 155450 197590 212780 199860 FALSE TRUE 145156.4082 140320.7126 167851.4743 141168.1425 148766.0723 143891.9254 157352.4436 193509.6975 188626.1064 186323.3042 0.779056645 0.753103393 0.900861409 0.757651562 0.798429767 0.772270147 0.844512952 1.038569482 1.012359175 1 17.5074486 1.83204328 3.809662627 1.01968128 0.79599315 0.858105113 0.040610614 0.076613425 1.862363755 0.020130539 0.010829459 67.92713221 -1.83204328 -0.22368813 EIAENALGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIAENALGK 9 0 P31942;P31942-3;P31942-2 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 87.149 0.031771 256380000 156370 227730 191820 247870 203420 217020 207720 185830 206420 205040 FALSE TRUE 150258.8875 221235.3634 226486.141 260662.6004 209963.189 221408.2931 210262.1395 181992.5456 182988.067 191152.4582 0.786068298 1.157376502 1.184845558 1.363637187 1.098406953 1.158281171 1.09997089 0.952080592 0.957288589 1 17.54436423 1.832305183 3.79123976 0.965635397 1.138061187 0.206971275 0.134564828 0.342425124 8.253203697 0.069303038 0.037246065 67.9681083 -1.832305183 0.17242579 SLDSEPSVPSAAKPPS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLDSEPSVPSAAKPPSPEK 19 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK 268.75 3.97E-32 6818400000 4464880 3174100 3178640 2546810 3377290 3121470 3568490 4718290 5236400 4338000 TRUE FALSE 4290387.553 3083577.776 3753090.956 2678251.169 3485923.6 3184588.262 3612162.248 4620855.663 4641985.825 4044183.396 1.060878584 0.76247229 0.928021949 0.662247704 0.861959822 0.787449023 0.893174689 1.142593006 1.147817834 1 21.94741699 1.832407322 4.278219919 1.108489841 0.837060438 0.530610015 0.10623823 0.153270632 4.501794292 0.049023381 0.027110099 67.9840952 -1.832407322 -0.271429403 ADRDQS(ph)PFSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(0.996)PFS(0.004)K;ADRDQS(0.501)PFS(0.499)K;ADRDQS(1)PFSK;ADRDQS(0.838)PFS(0.162)K 152.95 1.04E-05 14639240000 16318850 15798340 13175710 13630760 13879280 14650370 15035110 16675060 18416910 16712190 TRUE FALSE 15681091.3 15347786.81 15556853.89 14334245.16 14325719.65 14946610.52 15219114.17 16330714.18 16326299.59 15580258.49 1.006471832 0.985079087 0.998497804 0.920026145 0.919478946 0.959330074 0.97682039 1.048167089 1.047883744 1 23.89321583 1.832547601 4.562866608 1.035943133 0.963615128 0.500187992 0.030027107 0.184673472 6.013073908 0.01568761 0.008804839 68.00605793 -1.832547601 -0.072328005 VIPEDAS(ph)ESEEKLDQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VIPEDASESEEKLDQK 16 1 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 VIPEDAS(1)ESEEKLDQK 214.55 1.02E-14 646920000 1706900 1363200 1422500 1284800 1387200 1192300 1522700 2015100 2144500 1961800 TRUE FALSE 1640192.461 1324322.871 1679577.393 1351108.682 1431820.548 1216409.123 1541335.258 1973487.481 1901065.35 1828925.539 0.896806582 0.724098845 0.918341047 0.7387445 0.782875255 0.665094941 0.842754517 1.079042005 1.039443821 1 20.80256491 1.832819943 4.548783296 1.043678453 0.786225475 0.699004312 0.073848044 0.113185084 3.664006618 0.034217671 0.019195255 68.04871721 -1.832819943 -0.257452977 S(ph)PS(ph)PKPTK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSPKPTK 8 1 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 2 S(1)PS(0.983)PKPT(0.017)K;S(0.976)PS(0.874)PKPT(0.15)K;S(0.991)PS(0.83)PKPT(0.178)K;S(1)PS(0.996)PKPT(0.004)K 69.721 0.030264 11475450000 6274060 4832170 4530230 4231410 4629420 4582320 5291200 6055710 7120950 6187810 TRUE FALSE 6028862.799 4694361.243 5348943.335 4449793.577 4778329.499 4674977.65 5355955.288 5930657.472 6312609.609 5768704.117 1.045098288 0.813763568 0.927234822 0.771367969 0.828319394 0.810403438 0.928450338 1.028074478 1.094285559 1 22.45981584 1.832846519 2.778759283 1.049589279 0.860801337 0.512432217 0.075786975 0.196123411 2.765367043 0.041359585 0.020541568 68.05288145 -1.832846519 -0.188787942 APLDIPIPDPPPKDDEMETDKQEK ddPTM_BT-474_Pertuzumab_2h_R1 4 APLDIPIPDPPPKDDEMETDKQEK 24 2 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 98.121 0.0031164 1286260000 1982250 1412530 1368740 1026130 1490390 1439110 1662040 2128700 2605450 2094420 FALSE TRUE 1904781.479 1372246.027 1616101.765 1079088.692 1538329.748 1468209.79 1682380.543 2084741.601 2309690.239 1952563.068 0.975528786 0.702792166 0.827682236 0.552652414 0.787851503 0.751939753 0.861626736 1.067694885 1.182901734 1 20.89693772 1.832869697 2.477464193 1.103565406 0.758098556 0.63304307 0.107723356 0.16334033 1.869443712 0.061346464 0.029488998 68.05651358 -1.832869697 -0.345466849 DKDDDEVFEK ddPTM_BT-474_Pertuzumab_2h_R1 7 DKDDDEVFEK 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;;;; 149.41 2.13E-05 4308230000 10693600 7849020 9081180 7413490 8589140 8150450 10226340 12889090 15007860 13917910 FALSE TRUE 10275682.29 7625173.635 10722351.24 7796101.107 8865417.489 8315257.683 10351493.01 12622925.79 13304230.65 12975237.56 0.7919456 0.587671216 0.826370322 0.600844576 0.683256661 0.640855911 0.797788323 0.972847374 1.025355458 1 23.62925762 1.832917791 2.424897076 1.010972401 0.686227746 0.789128903 0.071817815 0.112371389 1.236009337 0.039451569 0.018845449 68.06405064 -1.832917791 -0.324744655 EQEKGEGSDSKES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQEKGEGSDSKESPK 15 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 EQEKGEGSDS(0.047)KES(0.953)PK;EQEKGEGS(0.007)DS(0.287)KES(0.706)PK 98.269 0.0015619 805220000 1064450 611950 718360 488440 709610 633680 890620 1213780 1543480 1209350 TRUE FALSE 1022850.117 594497.7852 848183.6318 513648.4469 732435.2501 646493.4438 901519.674 1188715.019 1368270.621 1127439.647 0.907232702 0.527298988 0.752309566 0.455588419 0.649644752 0.57341734 0.799616792 1.054349137 1.21360875 1 20.10461878 1.833004778 2.509861526 1.114186653 0.636420794 0.709025143 0.12719615 0.133956081 1.570100944 0.069795225 0.033681666 68.07768481 -1.833004778 -0.477765859 LENVSQLSLDKS(ph)PTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LENVSQLSLDKSPTEK 16 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 LENVSQLSLDKS(0.998)PT(0.002)EK;LENVSQLSLDKS(0.999)PT(0.001)EK 246.34 2.08E-20 1414720000 1324540 1041810 1093680 899990 1034200 1162740 1206890 1328290 1632060 1440070 TRUE FALSE 1272775.512 1012098.599 1291332.305 946438.5918 1067465.982 1186251.399 1221660.281 1300860.347 1446795.391 1342532.776 0.948040551 0.753872544 0.961862777 0.70496498 0.795113536 0.883592133 0.90996682 0.968959842 1.077661132 1 20.35652588 1.833174588 1.459459582 1.035817109 0.831978323 0.513884882 0.077392573 0.303514018 1.218678571 0.05537537 0.023143984 68.10430858 -1.833174588 -0.203838785 NSGEPLPPKPGPGS(ph)PSHPGALDLDGVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSGEPLPPKPGPGSPSHPGALDLDGVSR 28 1 A1X283;G3V144;A0A1B0GUF2 A1X283 SH3PXD2B SH3 and PX domain-containing protein 2B 1 NSGEPLPPKPGPGS(0.869)PS(0.131)HPGALDLDGVSR 66.386 0.008478 249070000 76511 83916 70284 79231 78915 83453 82845 93343 108280 99155 TRUE FALSE 73520.86553 81522.79784 82985.88226 83320.12141 81453.37264 85140.47684 83858.88189 91415.43443 95988.50835 92439.14353 0.795343431 0.881907758 0.8977353 0.901351075 0.881156721 0.921043549 0.907179347 0.988925589 1.038396773 1 16.49621627 1.833225106 1.160680662 1.025580037 0.875368162 0.771808613 0.031923233 0.220450647 0.549758405 0.026045947 0.010813371 68.11223107 -1.833225106 -0.150211875 GPLPSNGVMHVDECVEFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPLPSNGVMHVDECVEFHR 19 0 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 88.555 0.0014676 313170000 202610 284190 311190 278620 354410 333110 278190 154610 201740 203550 FALSE TRUE 194691.7772 276085.1795 367428.9554 292999.6116 365809.9195 339845.7124 281594.5724 151417.2495 178839.321 189763.3772 1.025971292 1.45489179 1.936247978 1.544026123 1.927716111 1.790891991 1.483924752 0.797926616 0.942433275 1 17.53384207 1.833322095 4.421874857 0.903524272 1.631490969 0.605440952 0.252858576 0.148446876 4.586246015 0.127023921 0.070825174 68.12744388 -1.833322095 0.727966697 AGGS(ph)VESLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGGSVESLR 9 0 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 AGGS(1)VESLR;AGGS(0.999)VES(0.001)LR;AGGS(0.998)VES(0.002)LR 143.4 0.00010703 828910000 614850 652570 503680 635730 607550 584290 580050 617210 589200 622260 TRUE FALSE 590820.9822 633959.3425 594706.1803 668540.1015 627092.3975 596104.7441 587148.8254 604464.3978 522316.4861 580113.7759 1.01845708 1.092818976 1.025154383 1.152429281 1.080981738 1.027565227 1.012127017 1.041975597 0.900369044 1 19.14597635 1.833444159 1.119676697 0.965304637 1.072946395 0.429276379 0.047537052 0.463591237 1.074057065 0.038370099 0.016000773 68.14659468 -1.833444159 0.107641758 GQPAS(ph)PSAHMVSHSHSPSVVS ddPTM_BT-474_Pertuzumab_2h_R1 1 GQPASPSAHMVSHSHSPSVVS 21 0 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;G5E9M9;Q14135-5 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 GQPAS(0.963)PS(0.037)AHMVSHSHSPSVVS 96.679 0.00080075 194040000 86117 146540 100450 138390 130970 133460 119570 6221.5 103090 67726 TRUE FALSE 82751.45243 142360.8227 118603.5495 145532.3245 135182.769 136158.6526 121033.3334 6093.023851 91387.65539 63138.8577 1.310626379 2.254725978 1.878455738 2.304956564 2.141039194 2.156495344 1.916938916 0.096501965 1.447407488 1 15.94624054 1.833523298 8.290975629 0.779196308 2.028384495 0.623060676 0.407613398 0.166513158 13.10741845 0.162646962 0.101263355 68.15901386 -1.833523298 1.249188187 DPAQPMS(ph)PGEATQSGARPADR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPAQPMSPGEATQSGARPADR 21 1 Q9BQG0;Q9BQG0-2 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 DPAQPMS(1)PGEATQSGARPADR;DPAQPMS(1)PGEATQSGARPADR 173.24 2.76E-12 2028910000 796970 836870 633050 734550 765040 903700 731460 704890 725340 738460 TRUE FALSE 765823.5313 813003.287 747456.2171 772460.2135 789648.2064 921973.4332 740411.8263 690333.7752 643002.4441 688443.4464 1.112398608 1.180929663 1.085719126 1.122038735 1.14700519 1.339214481 1.075486781 1.002745801 0.933994575 1 19.39297862 1.833526656 3.226785931 0.974894177 1.161085106 0.589872923 0.068510009 0.174505719 3.197177182 0.03732138 0.019293551 68.15954087 -1.833526656 0.186190929 RDVKPDEDLASK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDVKPDEDLASK 12 2 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 ; 166.6 2.89E-05 321670000 746680 686600 625670 593500 650160 642080 723860 929230 1013440 951600 FALSE TRUE 717498.9201 667018.8403 738742.487 624130.6061 671072.9869 655063.2975 732718.8152 910041.0758 898398.5399 887147.2844 0.808770914 0.751869337 0.832716844 0.703525353 0.756439205 0.738392947 0.82592691 1.025806077 1.012682511 1 19.75881412 1.833629041 3.409834481 1.016257839 0.765285891 0.909166628 0.034959862 0.061845638 1.245083862 0.01797582 0.009423186 68.17561136 -1.833629041 -0.250971949 EGS(ph)PGSQQHPPSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGSPGSQQHPPSQK 14 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 EGS(0.93)PGS(0.07)QQHPPSQK;EGS(0.882)PGS(0.118)QQHPPSQK 239.48 7.76E-10 0 354650 356070 285400 332420 325930 367500 352450 401720 431800 440460 TRUE FALSE 340789.8859 345915.2322 336978.1287 349576.236 336413.8345 374931.1018 356763.3885 393424.3416 382783.8743 410627.2519 0.829925156 0.842406905 0.820642388 0.851322542 0.819268163 0.913069213 0.868825405 0.958105776 0.93219306 1 18.64746985 1.833712935 0.633805781 0.9952345 0.826933024 0.851602271 0.023199973 0.231307267 0.189520224 0.019716033 0.01105051 68.18878236 -1.833712935 -0.168301475 SESTGTPGHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SESTGTPGHLR 11 0 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;H0YC07 Q8N573-2 OXR1 Oxidation resistance protein 1 0 73.887 0.029631 0 37364 44361 32237 46048 38220 40227 39464 33681 34710 44331 FALSE TRUE 35903.77357 43095.86771 38062.94301 48424.5428 39449.38101 41040.4175 39946.97224 32985.47558 30769.86632 41328.42188 0.868742912 1.042765868 0.92098709 1.171700747 0.954533931 0.993031324 0.966573859 0.798130538 0.744520718 1 15.33484666 1.833842345 4.657834045 0.828734254 0.995988842 0.301911388 0.097071828 0.224104123 7.507003238 0.043846151 0.02474518 68.20910408 -1.833842345 0.167254587 EEMEMDPKPDLDSDSWCLLGTDSCRPS(ph)L ddPTM_BT-474_Pertuzumab_2h_R1 1 EEMEMDPKPDLDSDSWCLLGTDSCRPSL 28 2 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 EEMEMDPKPDLDSDSWCLLGT(0.005)DS(0.208)CRPS(0.787)L 69.625 0.0095589 49768000 52683 53327 47546 44923 48069 57390 53537 58244 66904 65525 TRUE FALSE 50624.09012 51806.16617 56138.61986 47241.48141 49615.18304 58550.46512 54192.20182 57041.24105 59309.3384 61086.93339 0.828722074 0.848072792 0.918995549 0.773348387 0.812206151 0.958477728 0.887132465 0.933771559 0.970900569 1 15.8985762 1.833888582 0.720587855 0.996279162 0.84029487 0.598908639 0.045303845 0.480126573 0.48525355 0.042006316 0.021200752 68.21636636 -1.833888582 -0.155984292 ESEQES(ph)EEEILAQKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESEQESEEEILAQKK 15 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 ESEQES(1)EEEILAQKK 223.51 7.70E-13 466110000 698740 615020 531530 475530 603060 622560 662910 788270 930390 862020 TRUE FALSE 671432.4683 597480.2318 627589.2948 500072.1603 622457.9726 635148.5897 671022.8909 771991.949 824776.0277 803634.6176 0.835494706 0.743472492 0.780938602 0.62226309 0.774553459 0.790344985 0.834985049 0.960625553 1.026307242 1 19.61618019 1.833894713 1.490073157 1.019374546 0.748248178 0.813261029 0.051453639 0.157196269 0.658959257 0.038527138 0.016162074 68.21732926 -1.833894713 -0.271126369 ADGYVLEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADGYVLEGK 9 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 123.35 0.0013029 324180000 319160 367220 275910 315560 303790 331230 331750 385310 400610 403430 FALSE TRUE 306686.8743 356747.2451 325773.0746 331846.0894 313561.6812 337927.6975 335810.0557 377353.2139 355134.4323 376105.3268 0.815428159 0.948530158 0.866175115 0.882322227 0.8337071 0.898492187 0.892861738 1.003317919 0.944241964 1 18.52077721 1.833984011 4.730340721 0.980596511 0.877223539 0.632723126 0.037022817 0.137663705 4.722554464 0.01661332 0.009409137 68.23135737 -1.833984011 -0.103372973 KEKT(ph)PELPEPSVK ddPTM_BT-474_Pertuzumab_2h_R1 4 KEKTPELPEPSVK 13 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KEKT(1)PELPEPSVK;KEKT(1)PELPEPSVK;KEKT(1)PELPEPSVK;KEKT(1)PELPEPSVK 208.2 2.28E-06 3639640000 4289650 2889850 2627180 1930520 2934370 2785610 3118250 4180550 4726190 3695420 TRUE FALSE 4122005.736 2807434.307 3101969.867 2030154.369 3028756.676 2841936.943 3156412.076 4094220.182 4189692.725 3445125.912 1.196474626 0.814900349 0.900393758 0.589283068 0.87914252 0.824915262 0.916196434 1.188409448 1.2161218 1 21.71612528 1.834145071 4.205089631 1.151309555 0.855823063 0.390232786 0.148875571 0.207703356 5.90729651 0.07214378 0.039784775 68.25666596 -1.834145071 -0.295486492 APS(ph)PTAEQPPGGGDSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPTAEQPPGGGDSAR 17 0 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 APS(0.971)PT(0.029)AEQPPGGGDSAR 269.99 1.50E-26 0 60141 54764 39785 53119 54996 66891 51981 49732 53869 50486 TRUE FALSE 57790.62323 53202.18434 46975.03451 55860.47796 56764.99629 68243.58185 52617.15903 48705.01682 47754.01696 47066.53825 1.227849453 1.130361108 0.998055864 1.186840588 1.206058452 1.449938415 1.117931358 1.034811963 1.014606528 1 15.52241413 1.834374241 3.823915432 1.019503954 1.192873234 0.368771669 0.105802867 0.284804693 6.936851788 0.057826609 0.031187972 68.29269334 -1.834374241 0.17336928 WLSTSIPEAQWHSSLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 WLSTSIPEAQWHSSLAR 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 195.27 2.77E-11 5856600000 1437830 3177200 2178490 3312740 2436480 3146050 2646540 1577680 2169560 2941260 FALSE TRUE 1381638.014 3086589.367 2572191.603 3483710.908 2514851.592 3209665.287 2678929.148 1545100.357 1923280.644 2742045.84 0.503871231 1.125651994 0.938055654 1.270478727 0.917144256 1.170536699 0.976981898 0.56348451 0.701403535 1 21.38682126 1.834525486 7.970693599 0.714182383 1.006167058 0.17900148 0.219308102 0.368115696 27.18045555 0.089341525 0.055406576 68.31648067 -1.834525486 0.291984675 RRVEHHDHAVVSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 RRVEHHDHAVVSGR 14 2 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;; 200.44 1.16E-08 769980000 449820 730960 325233 557240 362658 482820 455470 74487.2 350699 238404 FALSE TRUE 432240.5371 710113.7365 384009.8379 585999.2232 374323.2239 492582.9512 461044.1781 72949.01329 310889.1198 222256.6847 1.944780818 3.195016327 1.727776325 2.636587619 1.684193321 2.216279577 2.074377104 0.328219659 1.398784114 1 17.76186729 1.834611751 6.644821057 0.873921336 2.235628775 0.605343291 0.482419071 0.144816718 8.277021361 0.199920636 0.120969786 68.33005191 -1.834611751 1.361707438 LPTEEEWEFAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPTEEEWEFAAR 12 0 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;Q8NBJ7-2;F8WA42 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 82.171 0.036459 20219000 14767 15578 14034 16894 19345 17861 16167 11964 13949 16400 FALSE TRUE 14189.88931 15133.73069 16570.25598 17765.90136 19967.24949 18222.16166 16364.85658 11716.93922 12365.568 15289.21339 0.928098062 0.989830563 1.083787345 1.161989234 1.305969704 1.191831207 1.070353076 0.766353305 0.808777252 1 13.90022656 1.835041492 5.497892371 0.839884899 1.115398689 0.495925756 0.113515645 0.182769365 7.867235056 0.056687923 0.033164553 68.39769905 -1.835041492 0.27551379 EVDEDFDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVDEDFDGK 9 0 Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2;C9JTV4 Q9BUP0 EFHD1;PP1187 EF-hand domain-containing protein D1 0 ;; 154.28 0.00017699 1686510000 1172640 1105090 1054380 1408350 1110750 1002510 1336980 1653480 1861280 1796780 FALSE TRUE 1126811.932 1073573.915 1244929.921 1481035.112 1146478.283 1022781.439 1353342.361 1619335.06 1649995.298 1675082.49 0.672690413 0.640908088 0.743205142 0.884156524 0.68443094 0.610585714 0.8079258 0.966719591 0.985023309 1 20.67580071 1.835208223 2.958904858 0.986648857 0.711613824 0.754128572 0.070674433 0.135091174 2.124758633 0.041930544 0.02122059 68.42396285 -1.835208223 -0.275035033 TSS(ph)PLFNK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSPLFNK 8 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 TS(0.07)S(0.93)PLFNK;TSS(1)PLFNK 140.17 0.00068587 648590000 2286210 2352700 1770300 2000750 2144940 2184640 2308900 2719000 2883300 3017000 TRUE FALSE 2196862.386 2285603.3 2090232.59 2104008.947 2213933.943 2228814.918 2337157.009 2662851.7 2555999.872 2812655.903 0.78106333 0.812613906 0.743152615 0.748050604 0.787132881 0.792423601 0.830943098 0.946739236 0.908749581 1 21.42350164 1.835225575 1.3563356 0.968788179 0.772126774 0.892711837 0.027144382 0.123329092 0.424843079 0.020869059 0.008664839 68.42669677 -1.835225575 -0.196661405 RRES(ph)EKS(ph)LENETLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(1)EKS(0.962)LENET(0.038)LNK 158 2.66E-06 770270000 454300 361930 484410 423700 382870 415410 479270 623470 670310 674850 TRUE FALSE 436545.4537 351608.1108 571953.6626 445567.2078 395185.3613 423809.8748 485135.4496 610595.1266 594219.219 629141.8084 0.693874494 0.558869409 0.909101342 0.708214272 0.628134001 0.673631714 0.771106678 0.970520666 0.944491704 1 19.26302571 1.835305414 2.943662001 0.973122716 0.696965072 0.680389032 0.084615048 0.152082559 2.370141211 0.047343542 0.023928942 68.43927717 -1.835305414 -0.276157644 EDEEEDDDVVAPKPPIEPEEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDEEEDDDVVAPKPPIEPEEEK 22 1 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5;E7EV09;E7EQU2;E7EMU4;E7ESD3 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ;;; 216.46 1.22E-25 1823690000 1571700 1110900 1347990 1053220 1320090 1270410 1536120 2004780 2487870 2008280 FALSE TRUE 1510276.226 1079218.22 1591601.779 1107576.81 1362551.894 1296098.561 1554919.496 1963380.592 2205457.428 1872257.407 0.80666057 0.576426199 0.850097734 0.591572936 0.727758848 0.692265153 0.830505191 1.048670223 1.177966993 1 20.83634737 1.835634208 2.339644647 1.098214795 0.703869873 0.774544088 0.088744407 0.115995417 1.191139336 0.04884258 0.023135258 68.49111048 -1.835634208 -0.394344922 VPS(ph)SQSMEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 VPS(0.77)S(0.089)QS(0.141)MEDR 100.22 0.0043639 396760000 54093 50591 40197 55692 44680 53126 51921 68801 64452 67449 TRUE FALSE 51978.98576 49148.19421 47461.49208 58566.27079 46117.17278 54200.24412 52556.42473 67380.23531 57135.67916 62880.61915 0.826629675 0.781611169 0.754787289 0.931388265 0.733408376 0.861954683 0.835812774 1.071558076 0.90863735 1 15.9403278 1.83566076 6.715983462 0.996124344 0.815771953 0.613792323 0.063874676 0.146389291 8.422277412 0.026514508 0.016078939 68.49529814 -1.83566076 -0.18035239 FDALKDDDSGDHDQNEENSTQK ddPTM_BT-474_Pertuzumab_2h_R1 2 FDALKDDDSGDHDQNEENSTQK 22 1 B9A044;B8ZZ50;O60573-2;O60573;B4E1E4;B9A023;B8ZZL3 B9A044 EIF4E2 Eukaryotic translation initiation factor 4E type 2 0 ; 298.72 7.09E-56 687700000 548560 441640 474360 413890 498420 464890 571600 614660 751900 704950 FALSE TRUE 527121.6687 429044.8596 560087.4041 435250.9125 514452.132 474290.3943 578595.4118 601967.0562 666547.4642 657203.1086 0.802068131 0.652834495 0.852228781 0.662277623 0.782790168 0.721680084 0.880390558 0.915952844 1.014218368 1 19.32597978 1.835687901 1.403221689 1.004536764 0.741682668 0.749224264 0.06081769 0.181679405 0.671788539 0.041830307 0.017428761 68.49957876 -1.835687901 -0.262854096 NGSLDS(ph)PGKQDTEEDEEEDEKDKGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 1 NGSLDS(1)PGKQDTEEDEEEDEKDKGK 215.47 9.53E-33 179490000 174270 85294 104810 50124 107630 75923 108160 150170 176320 118040 TRUE FALSE 167459.3357 82861.49863 123751.4985 52710.90565 111092.0167 77458.21508 109483.6944 147068.937 156304.8928 110045.0457 1.521734438 0.752978002 1.124553111 0.4789939 1.009514022 0.70387735 0.994898896 1.336443055 1.42037192 1 16.74773467 1.835733221 4.692707213 1.28209319 0.911439831 0.202652568 0.280405361 0.292452913 9.849284883 0.126322651 0.071500834 68.50672724 -1.835733221 -0.370653359 RPETWES(ph)PEKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPETWESPEKPK 12 2 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 RPET(0.202)WES(0.798)PEKPK;RPET(0.028)WES(0.972)PEKPK 142.54 4.84E-05 193130000 203242 155610 136059 135041 161317 153598 178091 201417 226590 227933 TRUE FALSE 195299.0779 151172.1552 160647.8879 142010.4822 166505.9078 156703.8568 180270.5309 197257.6686 200868.4531 212494.8949 0.919076564 0.711415468 0.756008223 0.668300677 0.783576038 0.737447631 0.848352291 0.928293683 0.945286019 1 17.69706866 1.835887037 1.652330916 0.972825324 0.755239273 0.659372759 0.063002159 0.209375726 1.086024652 0.043138043 0.018501811 68.53099494 -1.835887037 -0.217586051 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPTSPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVPLFPHPPVPSLSTSESKPPPQPSPPTSPVR 32 1 E9PKC0;Q6IQ23;Q6IQ23-2;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 TVPLFPHPPVPSLSTSESKPPPQPS(0.988)PPT(0.005)S(0.006)PVR;TVPLFPHPPVPSLSTSES(0.001)KPPPQPS(0.974)PPT(0.01)S(0.013)PVR 114.3 1.45E-06 1168580000 685280 629720 512920 471190 495720 602780 702800 883400 1006170 1043970 TRUE FALSE 658498.5 611761.0022 605616.0538 495508.1724 511665.284 614968.6246 711401.0766 865157.4813 891953.7998 973260.982 0.676589848 0.628568301 0.622254529 0.509121584 0.52572259 0.631864049 0.730945851 0.888926503 0.916459014 1 19.89246719 1.835986762 1.517586041 0.964557993 0.590070406 0.906070761 0.048935761 0.116509458 0.507082559 0.039742048 0.01675019 68.54673323 -1.835986762 -0.374487586 KS(ph)PPKADEK ddPTM_BT-474_Pertuzumab_2h_R1 8 KSPPKADEK 9 2 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KS(1)PPKADEK;KS(1)PPKADEK;KS(1)PPKADEK;KS(1)PPKADEK;KS(1)PPKADEK;KS(1)PPKADEK;KS(1)PPKADEK;KS(1)PPKADEK 87.18 0.007115 13443900000 12694870 8677560 8677100 6518940 8834620 8019900 10110560 13017570 15654380 12295020 TRUE FALSE 12198740.45 8430084.485 10245244.99 6855383.275 9118793.576 8182067.873 10234296.06 12748752.63 13877360.41 11462267.34 1.064251956 0.735463956 0.893823594 0.598082654 0.795548848 0.713826299 0.892868379 1.112236545 1.210699419 1 23.45038912 1.836026016 3.171156566 1.123743841 0.792543412 0.545799031 0.124709725 0.17000911 3.014517502 0.06429138 0.033150017 68.55292915 -1.836026016 -0.331200428 S(ph)TTPPPAEPVSLPQEPPKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPKPR;S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPKPR;S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPKPR 140.59 1.22E-07 20705800000 1589191 1511607 1299870 1443546 1456079 1550628 1535697 1815170 1956372 1778914 TRUE FALSE 1527083.659 1468497.448 1534785.424 1518047.582 1502915.103 1581982.761 1554491.319 1777686.105 1734292.852 1658426.57 0.920802697 0.885476315 0.925446717 0.915354113 0.906229513 0.953905822 0.937329 1.071911254 1.04574594 1 20.66138371 1.836089401 4.664403939 1.044374542 0.918340813 0.845144848 0.023298494 0.075928608 2.530309012 0.01115348 0.006306054 68.56293518 -1.836089401 -0.126033729 AKDDDDDDDDDAEM ddPTM_BT-474_Pertuzumab_2h_R1 1 AKDDDDDDDDDAEM 14 1 Q8IYL3 Q8IYL3 C1orf174 UPF0688 protein C1orf174 0 81.565 0.028517 134840000 196860 163490 140250 130450 148250 156020 162600 205630 209850 201960 FALSE TRUE 189166.4936 158827.4253 165596.2948 137182.5401 153018.5959 159174.8313 164589.9474 201383.6686 186028.7078 188281.0693 1.004702673 0.843565558 0.879516435 0.728605062 0.812713654 0.845410704 0.874171514 1.069590636 0.988037238 1 17.52252843 1.836226834 5.346020101 1.02228266 0.847230955 0.55402931 0.067282135 0.159098635 6.525867829 0.031581821 0.018386079 68.58463532 -1.836226834 -0.175051705 S(ph)TTPPPAEPVSLPQEPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPK;S(0.334)T(0.334)T(0.332)PPPAEPVSLPQEPPK 188.47 3.95E-14 1146080000 468910 426760 368820 420520 441110 432420 450000 539900 586960 538070 TRUE FALSE 450584.4788 414589.2226 435473.9784 442223.0876 455298.7038 441163.8287 455507.2346 528750.8763 520330.7615 501626.0396 0.898247785 0.826490632 0.868124746 0.88157921 0.907645672 0.879467559 0.908061382 1.054073821 1.03728818 1 18.93625272 1.836473713 3.988286072 1.034462771 0.877002815 0.889176734 0.024254517 0.06754551 1.755311943 0.012448567 0.006791301 68.62363403 -1.836473713 -0.157459957 ETKPEPMEEDLPENKK ddPTM_BT-474_Pertuzumab_2h_R1 3 ETKPEPMEEDLPENKK 16 2 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 166.57 3.73E-09 4358490000 2466970 1910540 1830780 1425930 1870500 1957580 2106330 2750350 3175340 2668070 FALSE TRUE 2370558.085 1856053.27 2161642.671 1499522.418 1930666.331 1997163.609 2132107.897 2693554.311 2814888.715 2487359.242 0.953042104 0.746194292 0.869051255 0.602857196 0.77619119 0.802925277 0.857177307 1.082897181 1.131677591 1 21.24618346 1.836558426 2.905118212 1.084837596 0.785150886 0.66022124 0.089597933 0.144609804 2.199364945 0.048652831 0.024527693 68.63702103 -1.836558426 -0.29968671 DMES(ph)PTKLDVTLAK ddPTM_BT-474_Pertuzumab_2h_R1 17 DMESPTKLDVTLAK 14 1 E7EVA0;P27816-6;P27816;P27816-2;P27816-5;H7C456 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMES(0.663)PT(0.337)KLDVTLAK;DMES(0.991)PT(0.009)KLDVTLAK;DMES(0.98)PT(0.02)KLDVTLAK;DMES(0.99)PT(0.01)KLDVTLAK;DMES(0.939)PT(0.061)KLDVTLAK;DMES(0.969)PT(0.031)KLDVTLAK;DMES(0.904)PT(0.096)KLDVTLAK;DMES(0.997)PT(0.003)KLDVTLAK;DMES(0.975)PT(0.025)KLDVTLAK;DMES(0.984)PT(0.016)KLDVTLAK;DMES(0.956)PT(0.044)KLDVTLAK;DMES(0.988)PT(0.012)KLDVTLAK;DMES(0.923)PT(0.077)KLDVTLAK;DMES(0.984)PT(0.016)KLDVTLAK;DMES(0.931)PT(0.069)KLDVTLAK;DMES(0.974)PT(0.026)KLDVTLAK;DMES(0.856)PT(0.144)KLDVTLAK 250.27 6.67E-18 17963710000 19445030 15515070 15320280 12605860 15648720 15328920 16956940 20936390 23750390 20535000 TRUE FALSE 18685096.73 15072595.39 18088995.39 13256449.95 16152075.29 15638881.27 17164464.1 20504046.23 21054345.3 19144146.16 0.976021421 0.787321371 0.944883895 0.692454489 0.843708315 0.816901477 0.896590736 1.071034773 1.099779803 1 24.19039998 1.83658174 3.351153169 1.065429007 0.839531896 0.599204807 0.077835793 0.14955532 2.91287063 0.038884142 0.020339306 68.6407057 -1.83658174 -0.225897111 STNS(ph)PTIVSPAIVSPTQDSRPNMSRPLITR ddPTM_BT-474_Pertuzumab_2h_R1 1 STNSPTIVSPAIVSPTQDSRPNMSRPLITR 30 2 A0A2U3U043 A0A2U3U043 1 S(0.095)T(0.409)NS(0.495)PT(0.001)IVSPAIVSPTQDSRPNMSRPLITR 160.77 2.25E-12 89976000 26912 29382 22623 26455 21972 30337 26128 25649 27456 28441 TRUE FALSE 25860.24929 28544.05413 26711.47935 27820.34572 22678.74933 30950.43493 26447.76228 25119.33919 24339.30998 26514.66574 0.975318699 1.076538336 1.007422821 1.04924369 0.855328502 1.167294931 0.997476738 0.947375292 0.917956509 1 14.69450294 1.836629265 4.773181905 0.950515547 1.021865176 0.127951358 0.076647338 0.418952095 14.44202688 0.034712038 0.019733146 68.64821744 -1.836629265 0.071349629 IDFVGELNDK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDFVGELNDK 10 0 E9PLK3;P55786;P55786-2;A6NEC2;E9PP11;E9PJY4;E9PPD4;A6NEC2-3 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 ; 101.95 0.0070054 106018000 164326 164436 128694 129879 137218 143239 154714 173577 192974 186628 FALSE TRUE 157903.9582 159746.4463 151951.8686 136582.0708 141631.7416 146135.3907 156607.4362 169992.5743 171068.4005 173987.5193 0.90755911 0.918148882 0.873349245 0.785010737 0.814033915 0.839918813 0.9001073 0.977038899 0.983222252 1 17.4086243 1.836750871 2.482926196 0.989653039 0.854984801 0.704996714 0.037700444 0.174993682 2.004931625 0.025526603 0.012316934 68.66744223 -1.836750871 -0.134668238 GWDGPQS(ph)PPGVVGETSGPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GWDGPQSPPGVVGETSGPR 19 0 A0A087WTE6 A0A087WTE6 SRCIN1 1 GWDGPQS(1)PPGVVGETSGPR;GWDGPQS(1)PPGVVGETSGPR;GWDGPQS(1)PPGVVGETSGPR;GWDGPQS(1)PPGVVGETSGPR 180.31 3.55E-14 825820000 632300 785040 750080 962580 1075690 1042410 767570 681220 632960 690140 TRUE FALSE 607589.017 762651.4278 885636.1414 1012258.869 1110290.546 1063488.244 776963.7513 667152.5689 561109.0344 643396.2031 0.9443466 1.185352702 1.376501971 1.573305631 1.725671585 1.652929003 1.207597663 1.036923385 0.872104982 1 19.2953479 1.83685815 2.753235725 0.955627368 1.41899163 0.444417909 0.218420408 0.267866064 3.701995117 0.137731229 0.068444554 68.6844066 -1.83685815 0.463364262 SVFGTPT(ph)LETANK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVFGTPTLETANK 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 SVFGT(0.422)PT(0.556)LET(0.021)ANK 96.464 0.047232 220730000 461960 457410 418140 413290 448520 505520 482630 573250 559970 632930 TRUE FALSE 443906.0925 444365.1147 493707.1995 434619.9464 462947.0531 515741.9608 488536.5703 561412.1872 496404.5532 590061.0873 0.752305315 0.753083239 0.836705233 0.736567714 0.784574789 0.874048419 0.827942362 0.951447569 0.841276545 1 19.17050479 1.836947236 0.373796955 1.001432694 0.740020884 0.71410286 0.044148976 0.604895524 0.237741766 0.053851077 0.052606636 68.69849712 -1.836947236 -0.26141181 FEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_BT-474_Pertuzumab_2h_R1 1 FEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 34 2 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 146.5 1.23E-10 768680000 223280 203300 187350 210830 212030 196670 225250 272690 312050 268890 FALSE TRUE 214553.9708 197502.0831 221208.3126 221710.9616 218850.1375 200646.8021 228006.6769 267058.8562 276627.3922 250677.8408 0.85589524 0.787872125 0.882440633 0.884445792 0.873033439 0.800416987 0.909560559 1.065346883 1.103517532 1 17.93547495 1.836970772 3.358984209 1.064464937 0.849322268 0.849870058 0.039116983 0.082259496 1.607797731 0.020366103 0.010662195 68.70222023 -1.836970772 -0.215142669 AEELSPAALS(ph)PSLEPIR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEELSPAALSPSLEPIR 17 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AEELSPAALS(0.993)PS(0.007)LEPIR;AEELSPAALS(0.977)PS(0.023)LEPIR;AEELSPAALS(0.984)PS(0.016)LEPIR;AEELSPAALS(0.994)PS(0.006)LEPIR 296.47 3.89E-46 237221000 319729 396755 339165 492850 417772 430292 327256 292221 239842 269805 TRUE FALSE 307233.6372 385439.9359 400459.6602 518286.0476 431210.0158 438992.7991 331261.0568 286186.5342 212616.1417 251530.867 1.221455008 1.532376286 1.592089531 2.060526621 1.714342342 1.745284005 1.316979744 1.137778984 0.84528847 1 17.94037593 1.837031053 1.884296844 0.945164496 1.657665523 0.667212937 0.206488543 0.205454368 1.388626324 0.145872131 0.064831181 68.71175687 -1.837031053 0.712501026 YFPSSCLDLNSPTS(ph)PTPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFPSSCLDLNSPTSPTPTR 19 0 A0A096LNR9;A0A1B0GUM4;A0A669KBC2;O76039;O76039-1 A0A096LNR9 CDKL5 Cyclin-dependent kinase-like 5 1 YFPSSCLDLNSPTS(0.998)PT(0.001)PTR;YFPSSCLDLNSPT(0.004)S(0.993)PT(0.002)PT(0.001)R 281.9 1.07E-39 185734000 154098 179099 147242 175410 185515 178009 158529 164094 167415 161079 TRUE FALSE 148075.6798 173991.2719 173851.9048 184462.9311 191482.2585 181608.4639 160469.1253 160705.4016 148410.7511 150168.9759 0.986060396 1.158636602 1.157708533 1.228369109 1.275111969 1.209360741 1.068590396 1.070163798 0.988291691 1 17.19622726 1.8371102 1.826837305 1.007837692 1.173761239 0.451206881 0.074517888 0.32529494 2.06688938 0.053171011 0.023426586 68.72428026 -1.8371102 0.165923546 RRGDS(ph)ESEEDEQDS(ph)EEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RRGDS(0.999)ES(0.287)EEDEQDS(0.715)EEVR 132.95 6.74E-05 652720000 477650 509600 372120 468510 451040 463140 440640 445160 483980 446740 TRUE FALSE 458982.9099 495066.707 439370.3618 492689.8572 465548.1112 472505.0081 446032.6841 435967.2904 429040.6194 416481.9019 1.102047671 1.188687203 1.054956673 1.182980233 1.117811144 1.134515104 1.070953341 1.046785679 1.030154294 1 18.66789428 1.837209957 1.223908373 1.011081848 1.133352614 0.624944751 0.036918678 0.273423698 0.760434816 0.027111083 0.011245385 68.74006787 -1.837209957 0.122270766 DYNPYNYSDSIS(ph)PFNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYNPYNYSDSISPFNK 16 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;H7C5M8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 DYNPYNYSDS(0.001)IS(0.999)PFNK;DYNPYNYSDSIS(1)PFNK 331.56 1.52E-71 202542000 280970 311860 319140 314720 365810 343210 293030 271070 264680 270130 TRUE FALSE 269989.3818 302966.0581 376815.6972 330962.7369 377576.6109 350149.9414 296616.1888 265472.3098 234634.636 251833.8545 1.072093275 1.203039435 1.496286899 1.314210663 1.49930839 1.390400596 1.177824917 1.05415656 0.931704105 1 17.94211271 1.837356906 2.1602331 0.976965729 1.336568347 0.596242881 0.12302359 0.21691021 1.913178069 0.081274923 0.037634577 68.76333101 -1.837356906 0.359602618 NGVAAEVS(ph)PAKEENPR ddPTM_BT-474_Pertuzumab_2h_R1 4 NGVAAEVSPAKEENPR 16 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 NGVAAEVS(1)PAKEENPR;NGVAAEVS(1)PAKEENPR;NGVAAEVS(1)PAKEENPR;NGVAAEVS(1)PAKEENPR 182.15 1.33E-09 2530910000 1270180 930990 987580 953330 1037840 903760 1111610 1368130 1529280 1369510 TRUE FALSE 1220539.961 904439.0767 1166057.675 1002531.476 1071223.066 922034.6464 1125214.216 1339877.637 1355682.546 1276751.868 0.955972724 0.708390643 0.913300152 0.785220293 0.839022126 0.722172154 0.881310021 1.049442473 1.06182147 1 20.28404674 1.837457497 3.739196304 1.041725426 0.818039354 0.633176624 0.073360657 0.131026404 3.060708712 0.034123889 0.018345337 68.77925965 -1.837457497 -0.223686071 DKLSGEYEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DKLSGEYEK 9 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;;; 127.87 0.00039522 5039050000 5035700 4721940 3957050 3807600 4382730 4629820 4717410 5374030 6153040 5736500 FALSE TRUE 4838899.277 4587274.894 4672176.959 4004110.692 4523704.491 4723438.133 4775143.075 5263054.403 5454572.695 5347961.745 0.904811872 0.857761351 0.873636945 0.748717153 0.845874504 0.883222124 0.892890283 0.98412342 1.019934875 1 22.35055772 1.837472519 1.579201974 1.01451758 0.845962059 0.750565805 0.038718035 0.186950939 0.883149827 0.029213457 0.012421221 68.78163876 -1.837472519 -0.168555521 LEGPVS(ph)PDVEPGKEETEESK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEGPVSPDVEPGKEETEESK 20 1 O14686;O14686-3;A0A3B3ISC8 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LEGPVS(1)PDVEPGKEETEESK 229.99 1.20E-25 488210000 1209700 1007800 882580 740440 945360 844360 1009600 1328500 1476200 1176500 TRUE FALSE 1162423.587 979058.5307 1042081.839 778654.1971 975768.363 861433.5377 1021955.787 1301066.011 1308627.965 1096814.607 1.059817748 0.892638122 0.950098432 0.709923256 0.889638373 0.785395756 0.931748885 1.186222359 1.193116828 1 20.06488826 1.837737957 4.681048086 1.141528789 0.876549935 0.54193546 0.100498761 0.153552131 5.118793717 0.047286768 0.026785248 68.82369058 -1.837737957 -0.264978854 NFGDQPDIR ddPTM_BT-474_Pertuzumab_2h_R1 3 NFGDQPDIR 9 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;; 172.59 0.0016675 275430000 1570740 1701010 1420940 1624790 1552020 1436180 1629360 1843140 1939440 1962740 FALSE TRUE 1509353.744 1652498.86 1677735.467 1708645.607 1601942.133 1465220.544 1649300.595 1805078.515 1719282.902 1829801.872 0.824872773 0.903102618 0.916894606 0.933787222 0.875472999 0.800753659 0.901354743 0.986488506 0.939600581 1 20.80325601 1.837805345 4.839125295 0.971905873 0.879491005 0.546338301 0.040359098 0.187138533 6.561431951 0.020007312 0.011416568 68.83437054 -1.837805345 -0.092414867 LKPGEIDPNPETKPARPDPIDMDEDELEMLSEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKPGEIDPNPETKPARPDPIDMDEDELEMLSEAR 34 3 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 ; 237.42 2.52E-47 934910000 1097050 938040 858160 786030 883270 992080 994180 1085680 1333370 1158320 FALSE TRUE 1054176.073 911288.0176 1013248.602 826597.1025 911681.1817 1012140.537 1006347.072 1063260.329 1182011.428 1079865.955 0.97621012 0.843889942 0.938309609 0.765462694 0.844254028 0.937283496 0.931918511 0.984622512 1.094590882 1 20.04242081 1.837826993 1.400406758 1.043862656 0.874579079 0.537510256 0.060463721 0.307158224 1.1306239 0.045444808 0.01896037 68.83780173 -1.837826993 -0.169283577 DGLEMEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLEMEK 7 0 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;P13693-2;H0YCX0 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ; 138.9 0.0063773 722220000 767270 670140 647630 652620 732350 673990 811760 830270 976400 952090 FALSE TRUE 737284.2401 651028.2633 764671.1475 686301.7964 755906.7029 687618.5396 821694.5617 813124.6344 865563.1654 887604.0963 0.830645378 0.733466943 0.861500246 0.773207108 0.851625974 0.774690588 0.925744445 0.916089322 0.975168061 1 19.7595568 1.837951761 1.028017603 0.994317806 0.799605254 0.750938996 0.042320136 0.22929062 0.447060836 0.032418278 0.013781203 68.85758085 -1.837951761 -0.194712552 FDEFDEAIDEAIEDDIK ddPTM_BT-474_Pertuzumab_2h_R1 3 FDEFDEAIDEAIEDDIK 17 0 Q96T23-2;Q96T23;Q96T23-3;H0YDG9 Q96T23-2 RSF1 Remodeling and spacing factor 1 0 ;; 226.04 5.12E-15 57087000 88959 80157 83906 92297 95103 82808 109021 124466 147250 143781 FALSE TRUE 85482.38393 77871.00084 99069.68068 97060.45923 98162.07437 84482.4345 110355.2316 121895.7336 130534.7973 134042.5848 0.637725571 0.58094225 0.739091094 0.724101668 0.732320065 0.630265633 0.823284867 0.909380655 0.973830798 1 17.03233189 1.837967155 1.573117394 0.987081318 0.675282973 0.86372416 0.051377726 0.135879181 0.636714621 0.039195109 0.016658663 68.86002165 -1.837967155 -0.311798345 EVLDEDT(ph)DEEKETLK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVLDEDTDEEKETLK 15 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK 285.5 6.92E-34 3179480000 3079610 2392410 2241890 1846340 2447750 2457640 2820200 3611200 4308800 3824500 TRUE FALSE 2959255.437 2324180.809 2647049.394 1941629.829 2526484.102 2507335.165 2854714.451 3536627.458 3819683.088 3565463.208 0.829977836 0.651859428 0.742413885 0.544565941 0.708599123 0.70322845 0.800657386 0.991912481 1.07130066 1 21.76565809 1.838005592 2.034611118 1.041185012 0.689152007 0.813273029 0.06959166 0.120747951 0.948476887 0.043446128 0.019767317 68.86611633 -1.838005592 -0.352033005 YS(ph)PPRDDDKVDNQAK ddPTM_BT-474_Pertuzumab_2h_R1 5 YSPPRDDDKVDNQAK 15 2 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 Y(0.002)S(0.998)PPRDDDKVDNQAK;YS(1)PPRDDDKVDNQAK;YS(1)PPRDDDKVDNQAK;YS(1)PPRDDDKVDNQAK;YS(1)PPRDDDKVDNQAK 142.43 2.39E-06 6011120000 4119780 3076020 2658350 2452700 3101170 2795980 3194610 4191880 4493720 3726270 TRUE FALSE 3958774.443 2988294.921 3138772.98 2579284.141 3200921.949 2852516.631 3233706.593 4105316.213 3983611.745 3473886.414 1.139580853 0.860216647 0.903533566 0.742477972 0.921423895 0.821131232 0.930861349 1.181764665 1.146730569 1 21.72811915 1.83803322 5.294567153 1.123527989 0.889974847 0.446558053 0.105143339 0.178132422 7.141743051 0.047182482 0.027444116 68.87049749 -1.83803322 -0.233553142 DTSSDKDLDDALDKLSDSLGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTSSDKDLDDALDKLSDSLGQR 22 2 E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 E7EVY3 CAST 0 78.916 0.004596 34007000 60539 52131 46024 42050 47244 52465 51996 59538 71336 54039 FALSE TRUE 58173.06895 50644.27492 54341.5606 44220.20554 48763.64617 53525.87825 52632.3426 58308.51949 63238.23634 50378.8904 1.154711199 1.005267772 1.078657354 0.87775267 0.967938074 1.062466399 1.044730088 1.157399836 1.255252663 1 15.62053173 1.838085409 3.081698215 1.155149292 1.018394255 0.232967073 0.089935856 0.309320599 5.209117446 0.047940188 0.024575098 68.87877418 -1.838085409 -0.136755037 GGSGYVNQLSAGYESVDS(ph)PTGSENSLTHQSNDTDSSHDPQEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGSGYVNQLSAGYESVDSPTGSENSLTHQSNDTDSSHDPQEEK 43 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 GGSGYVNQLSAGYES(0.001)VDS(0.936)PT(0.048)GS(0.011)ENS(0.003)LT(0.003)HQSNDTDSSHDPQEEK;GGSGYVNQLS(0.001)AGY(0.022)ES(0.088)VDS(0.188)PT(0.088)GS(0.088)ENS(0.088)LT(0.088)HQS(0.088)NDT(0.088)DS(0.088)S(0.088)HDPQEEK 170.35 5.90E-20 338130000 59218 71936 49480 56195 66143 68149 61480 46173 63301 55986 TRUE FALSE 56903.69509 69884.45571 58422.13668 59095.23068 68270.54966 69527.01947 62232.41063 45219.51141 56115.33586 52194.01835 1.090234032 1.338936106 1.119326285 1.132222284 1.308014823 1.332087884 1.192328405 0.866373444 1.075129634 1 15.67159686 1.83821504 6.882693094 0.972901032 1.223495574 0.558933218 0.095962808 0.168163641 9.805263243 0.041391448 0.025223544 68.89933663 -1.83821504 0.250594542 VGS(ph)PQPSSSGGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGSPQPSSSGGEK 13 0 V9GYB6;O94761 V9GYB6 RECQL4 ATP-dependent DNA helicase Q4 1 VGS(1)PQPSSSGGEK;VGS(0.999)PQPS(0.001)SSGGEK 157.58 1.13E-06 239950000 331740 275850 255400 238620 271860 293550 305300 367220 425890 392230 TRUE FALSE 318775.234 267983.0281 301556.4613 250935.2068 280604.6238 299485.7821 309036.3527 359636.7787 377544.7527 365663.9127 0.871771107 0.732867037 0.82468204 0.686245479 0.767383967 0.819019246 0.845137685 0.983517285 1.032491147 1 18.48015873 1.838359067 1.711238736 1.022719615 0.775239986 0.808658394 0.048451937 0.136872945 0.761897575 0.0324918 0.014083098 68.92218972 -1.838359067 -0.247479629 NDTKEDVFVHQTAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDTKEDVFVHQTAIK 15 1 P67809;P16989;P16989-3;P16989-2;Q9Y2T7 P67809;P16989;P16989-2;Q9Y2T7 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3;Y-box-binding protein 2 0 ; 256.8 5.48E-25 2154540000 2606200 2728040 2261130 2137570 2285700 2652180 2752800 2768960 3447400 3180700 FALSE TRUE 2504346.823 2650238.97 2669766.49 2247890.244 2359221.616 2705808.897 2786489.59 2711780.008 3056065.605 2965268.356 0.844559926 0.893760244 0.900345658 0.758073123 0.795618249 0.912500513 0.939709077 0.914514197 1.030620247 1 21.49973124 1.838409368 1.048484999 1.005938707 0.844487743 0.633914113 0.04808008 0.365778108 0.741783593 0.04344021 0.018386098 68.93017295 -1.838409368 -0.161450964 RECPSDECGAGVFMASHFDR ddPTM_BT-474_Pertuzumab_2h_R1 4 RECPSDECGAGVFMASHFDR 20 1 P62979 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;; 187.86 1.79E-17 2063170000 1539920 1750980 1350620 1681120 1577000 1907090 1626580 1462330 1697650 1623630 FALSE TRUE 1479738.224 1701043.765 1594707.078 1767882.805 1627725.637 1945652.666 1646486.573 1432132.374 1504939.889 1513660.094 0.977589506 1.123795079 1.053543715 1.167952311 1.075357436 1.285396024 1.087751853 0.946138687 0.994238994 1 20.52960984 1.838523192 5.498045611 0.977873154 1.117650533 0.379975489 0.076345231 0.220653452 9.329954402 0.03454093 0.020249619 68.94824112 -1.838523192 0.13977738 RLTAEDLFEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLTAEDLFEAR 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 153.38 5.21E-05 674410000 504040 688840 502460 725410 686470 705050 591470 340730 427300 451020 FALSE TRUE 484341.5596 669194.9576 593265.6992 762848.497 708550.931 719306.5941 598708.5868 333693.8064 378794.6954 420472.0137 1.151899636 1.591532696 1.410951692 1.814266996 1.685132204 1.710712177 1.423896401 0.793617163 0.900879685 1 18.68165025 1.838559767 4.260463309 0.886266553 1.571661483 0.732593277 0.17901925 0.110544414 3.177694092 0.088488347 0.049092633 68.95404805 -1.838559767 0.68539493 KGS(ph)GS(ph)EQEGEDEEGGER ddPTM_BT-474_Pertuzumab_2h_R1 2 KGSGSEQEGEDEEGGER 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 2 KGS(1)GS(1)EQEGEDEEGGER;KGS(1)GS(1)EQEGEDEEGGER 99.441 0.0055305 479670000 881710 718600 629660 586690 669550 637460 734650 852790 1011020 798780 TRUE FALSE 847251.7984 698106.2316 743453.5687 616969.1412 691086.6838 650349.878 743640.8665 835179.5885 896253.2481 744677.9191 1.137742609 0.937460631 0.998355866 0.82850468 0.928034344 0.873330417 0.998607381 1.121531292 1.203544815 1 19.50625705 1.838624885 3.608414263 1.12160546 0.945144181 0.374874008 0.090026628 0.222322151 4.889570817 0.045456046 0.024248439 68.96438778 -1.838624885 -0.176461279 TGGMAFHSYFMEAIAPPLLQELK ddPTM_BT-474_Pertuzumab_2h_R1 3 TGGMAFHSYFMEAIAPPLLQELK 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 148.88 1.01E-07 1415650000 1453340 1345570 1389630 1408350 1453820 1525520 1711240 1712910 2240180 2093990 FALSE TRUE 1396541.866 1307195.661 1640767.053 1481035.112 1500583.441 1556367.06 1732182.667 1677537.81 1985884.158 1952162.192 0.715382088 0.66961427 0.840487056 0.758663967 0.768677647 0.797252946 0.887314934 0.859322968 1.017274162 1 20.89664149 1.838628543 0.587865286 1.018466438 0.729114996 0.80375357 0.047915278 0.327581119 0.238625784 0.045115095 0.027207361 68.96496867 -1.838628543 -0.289351442 NGSTAVAESVAS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 1 NGSTAVAESVASPQK 15 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 NGSTAVAESVAS(1)PQK 191.64 1.75E-07 227920000 247210 200320 176290 190560 192960 200330 210730 263910 274130 257060 TRUE FALSE 237548.7599 194607.0697 208149.5245 200394.8244 199166.7336 204380.8099 213308.9768 258460.1663 243011.9116 239649.0972 0.99123578 0.812050085 0.868559602 0.83620104 0.831076503 0.852833631 0.890088797 1.07849422 1.014032243 1 17.87056398 1.838706651 5.131265091 1.035100894 0.861317491 0.690171359 0.049788108 0.110654359 4.222874593 0.021964927 0.012698674 68.9773732 -1.838706651 -0.173783403 VESGDPSLHPPPSPGTPSAT(ph)PASPPASATPSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPSPGTPS(0.005)AT(0.69)PAS(0.304)PPAS(0.001)ATPSQR 180.44 4.68E-19 402990000 79693 118990 102580 117570 120170 130760 102420 76776 80195 86180 TRUE FALSE 76578.50945 115596.5217 121118.4879 123637.8018 124035.3772 133404.0568 103673.4466 75190.54877 71091.5998 80342.95184 0.953145331 1.438788581 1.50751852 1.53887552 1.543823999 1.660432605 1.290386328 0.935869881 0.884851728 1 16.29388385 1.838760876 3.412463171 0.930491522 1.453800693 0.604990919 0.179757113 0.159204674 3.189407562 0.095873663 0.050454443 68.98598608 -1.838760876 0.52330917 SGSSQELDVKPSAS(ph)PQER ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)GS(0.001)S(0.001)QELDVKPS(0.194)AS(0.802)PQER;SGSSQELDVKPS(0.22)AS(0.78)PQER 56.72 0.055645 681500000 377740 384920 375610 369120 371270 396760 438500 478020 524710 543520 TRUE FALSE 362977.5032 373942.4585 443491.0824 388170.3274 383212.2367 404782.759 443866.4942 468148.72 465147.1206 506706.9063 0.716346074 0.737985715 0.875241835 0.766064805 0.756279877 0.798849895 0.87598272 0.92390436 0.917980621 1 18.95079197 1.839013487 0.874819803 0.984077814 0.767485775 0.783101395 0.041921683 0.270920723 0.38663679 0.038059533 0.01714358 69.02612396 -1.839013487 -0.216592039 EKLEDFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKLEDFFK 8 1 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ; 95.311 0.0088831 862800000 2287880 2218030 1877010 1842200 2001010 1569460 2332740 2472180 2929000 2851600 FALSE TRUE 2198467.12 2154773.956 2216227.461 1937276.163 2065374.304 1601195.557 2361288.77 2421128.619 2596512.199 2658458.592 0.826970609 0.810535083 0.8336513 0.728721586 0.776906705 0.602302237 0.888217246 0.910726474 0.97669838 1 21.34215856 1.83906725 2.546477739 0.965253669 0.767832474 0.625674762 0.068499604 0.188527898 2.258520593 0.040466178 0.019705616 69.03466954 -1.83906725 -0.197421195 GSLDYRPLTTADPIDEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSLDYRPLTTADPIDEHR 18 1 O00139-1;O00139-5;O00139;O00139-4;O00139-2;D6R9M0 O00139-1 KIF2A Kinesin-like protein KIF2A 0 132.59 8.70E-06 535640000 807230 834920 753170 882080 894880 879780 809750 804660 802670 862120 FALSE TRUE 775682.5592 811108.8991 889284.5732 927604.2545 923664.6279 897569.7544 819659.9627 788043.4898 711554.2667 803727.8445 0.965105993 1.009183525 1.106449875 1.154127309 1.149225617 1.116758316 1.019822777 0.98048549 0.885317426 1 19.61634754 1.839404068 2.308672029 0.944795872 1.086419235 0.459058684 0.062094882 0.273737265 2.734543932 0.041085649 0.019443397 69.0882302 -1.839404068 0.141623364 VQMTSPSSTGS(ph)PMFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VQMTSPSSTGSPMFK 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 VQMTSPSS(0.007)T(0.003)GS(0.989)PMFK;VQMTSPS(0.016)S(0.175)T(0.04)GS(0.768)PMFK 166.66 1.42E-06 115824000 192951 174990 152205 150316 164229 157669 172509 216874 206557 225300 TRUE FALSE 185410.2616 169999.4565 179711.8293 158073.8268 169511.5749 160857.1752 174620.2167 212395.4761 183109.5153 210040.2303 0.882736899 0.809366169 0.855606705 0.752588333 0.807043368 0.765839834 0.831365574 1.011213308 0.871783063 1 17.68030616 1.83960386 6.214502208 0.957940026 0.810504353 0.644447928 0.049787422 0.135968384 6.808888816 0.021180418 0.012707869 69.1200208 -1.83960386 -0.147435673 IEDVGSDEEDDSGKDK ddPTM_BT-474_Pertuzumab_2h_R1 3 IEDVGSDEEDDSGKDK 16 1 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 ;; 247.46 2.47E-20 1648190000 1480080 1089270 1138560 939000 1133580 1162170 1332090 1686210 2012300 1726690 FALSE TRUE 1422236.837 1058205.086 1344323.119 987461.9025 1170042.63 1185669.874 1348392.516 1651389.174 1783872.14 1609739.748 0.883519736 0.657376503 0.835118298 0.613429533 0.726852046 0.736559978 0.837646282 1.025873391 1.108174251 1 20.61839603 1.839636981 2.330519581 1.06120684 0.736087314 0.754910299 0.077032746 0.126120718 1.282123943 0.043557008 0.020675095 69.12529229 -1.839636981 -0.325119527 GGSGSHNWGTVKDELTES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSGSHNWGTVKDELTESPK 20 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 GGSGSHNWGTVKDELT(0.005)ES(0.995)PK 179.44 3.52E-17 489610000 558000 607690 435540 403710 517450 524170 410990 433140 406730 380080 TRUE FALSE 536192.7431 590359.2762 514251.7665 424545.5215 534094.2492 534769.0765 416019.8186 424195.5076 360559.7156 354336.8431 1.513228877 1.666096224 1.451307637 1.198141062 1.507306563 1.509211043 1.17408005 1.197153262 1.017562025 1 18.43476196 1.839853371 0.86054815 0.981352938 1.491972229 0.705613314 0.120132376 0.338719661 0.468757468 0.110822332 0.050332185 69.1597431 -1.839853371 0.510619291 ERAVELLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERAVELLR 8 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ;;; 155.84 0.00036705 1091090000 529200 618152 410279 640114 392342 527533 612524 1026750 879430 1190870 FALSE TRUE 508518.2789 600522.9102 484425.5419 673150.3603 404962.0367 538200.0787 620020.2519 1005547.254 779600.7933 1110211.314 0.458037378 0.540908656 0.43633634 0.606326338 0.364761223 0.484772648 0.558470486 0.905726001 0.702209375 1 20.08240287 1.839916237 3.969545115 0.854278386 0.485157439 0.781796382 0.091583962 0.098788995 2.532475937 0.042476132 0.023201308 69.16975492 -1.839916237 -0.369120947 KEESETANKNDSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEESETANKNDSSK 14 2 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 169.09 1.91E-06 178790000 571380 481450 316270 364440 431430 450280 443180 530000 577790 467690 FALSE TRUE 549049.8379 467719.5174 373427.0244 383248.7921 445307.3378 459384.9701 448603.7694 519055.3148 512201.7015 436012.9397 1.259251247 1.07271935 0.856458583 0.878984904 1.021316794 1.053603983 1.028877193 1.190458511 1.17473968 1 18.73401143 1.839971884 6.496207836 1.139222121 1.014351403 0.122556109 0.114703081 0.4167103 22.13844229 0.053410243 0.03228608 69.17861841 -1.839971884 -0.124870718 NFGEEVDDESLKELFSQFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NFGEEVDDESLKELFSQFGK 20 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 B1ANR0 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ; 264.59 1.30E-36 1150350000 1347230 1124630 1017420 887750 1053830 1133990 1167620 1424480 1585450 1457810 FALSE TRUE 1294578.762 1092556.654 1201290.426 933566.8839 1087727.399 1156920.055 1181909.683 1395063.99 1405476.363 1359071.23 0.952546661 0.803899479 0.88390542 0.686915346 0.80034613 0.851257851 0.869645135 1.026483351 1.034144739 1 20.37418964 1.840005259 2.68303817 1.027008483 0.823811619 0.634560025 0.064560544 0.165472169 2.177746391 0.036966939 0.018283893 69.18393479 -1.840005259 -0.203196864 QNGSNDSDRYS(ph)DNEEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 QNGSNDSDRYSDNEEGK 17 1 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 QNGS(0.001)NDS(0.106)DRY(0.002)S(0.892)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK 294.91 2.55E-46 2313540000 2028350 1675780 1678534 1709875 1808540 1823920 1983820 2457910 2780340 2566840 TRUE FALSE 1949079.84 1627988.395 1981882.433 1798121.854 1866713.332 1860800.912 2008098.583 2407153.3 2464727.459 2392985.64 0.81449709 0.680316826 0.8282049 0.751413558 0.780077114 0.777606384 0.839160314 1.005920495 1.029980046 1 21.19038031 1.840054861 2.409713205 1.021450748 0.769719488 0.887058766 0.03827238 0.078712373 0.851292409 0.021225279 0.010178952 69.19183707 -1.840054861 -0.251731261 DSSKGEDSAEET(ph)EAKPAVVAPAPVVEAVSTPSAAFPSDATAEQGPILTK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSKGEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAEQGPILTK 49 2 Q12906;Q12906-5;Q12906-2;Q12906-3 Q12906 ILF3 Interleukin enhancer-binding factor 3 1 DS(0.111)S(0.111)KGEDS(0.358)AEET(0.42)EAKPAVVAPAPVVEAVSTPSAAFPSDATAEQGPILTK 85.647 1.66E-05 772970000 1226500 910770 794230 597470 960490 901190 964550 1230500 1450800 1090400 TRUE FALSE 1178567.024 884795.7313 937765.0286 628305.4983 991385.0331 919412.6793 976354.4514 1205089.745 1286111.266 1016546.237 1.159383589 0.870393986 0.922501107 0.618078623 0.975248343 0.904447477 0.960462413 1.185474602 1.265177342 1 19.95524441 1.840092584 3.498076308 1.169622747 0.898919429 0.3744608 0.138842375 0.227618796 4.746054762 0.071014865 0.037636185 69.19784733 -1.840092584 -0.270703317 NVSES(ph)PNRK ddPTM_BT-474_Pertuzumab_2h_R1 6 NVSESPNRK 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.018)ES(0.982)PNRK;NVS(0.017)ES(0.983)PNRK;NVSES(1)PNRK;NVS(0.006)ES(0.994)PNRK;NVS(0.032)ES(0.968)PNRK;NVS(0.016)ES(0.984)PNRK 146.36 5.82E-05 9763883000 7192390 6649040 5645320 6231160 6371380 6391430 6942250 7328440 8721500 7744610 TRUE FALSE 6911303.447 6459415.889 6665554.903 6552750.914 6576321.224 6520669.094 7027211.332 7177105.153 7731471.884 7220060.667 0.957236202 0.894648423 0.923199293 0.907575603 0.910840162 0.903132175 0.97328979 0.994050533 1.070831983 1 22.78357953 1.840180585 1.825016477 1.031906185 0.914959898 0.786041328 0.024834793 0.135332391 0.857043216 0.015546358 0.006865132 69.2118703 -1.840180585 -0.116946287 KKEPEPNFQLLDNPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKEPEPNFQLLDNPAR 16 2 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 184.01 1.06E-09 1818170000 1488800 1418480 1186780 1278710 1349010 1428530 1460280 1659370 1844390 1817360 FALSE TRUE 1430616.05 1378026.339 1401257.546 1344704.376 1392402.132 1457415.855 1478151.343 1625103.43 1635022.58 1694268.588 0.84438563 0.813345858 0.827057502 0.793678396 0.821830813 0.860203551 0.872442158 0.959176981 0.965031513 1 20.69223117 1.840396326 1.15148523 0.994444002 0.818441307 0.951104661 0.015242077 0.088715327 0.217527094 0.012186846 0.005086317 69.24626071 -1.840396326 -0.176002695 EHPDAWTR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHPDAWTR 8 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;H7BZC5 O14980 XPO1 Exportin-1 0 ;;; 122.52 0.0013871 3898630000 5755300 5897400 5186290 5951100 5824100 5901200 5804100 5242080 6032200 6140300 FALSE TRUE 5530376.513 5729211.926 6123567.971 6258236.984 6011437.466 6020526.307 5875132.312 5133829.216 5347449.945 5724412.012 0.966103855 1.000838499 1.069728727 1.093254114 1.0501406 1.051728334 1.026329394 0.896830837 0.934148334 1 22.44869608 1.840701654 6.161339728 0.935294902 1.040879485 0.519544762 0.040876744 0.170277263 8.36755097 0.019068602 0.011430038 69.2949609 -1.840701654 0.105584583 IVKPNGEKPDEFESGISQALLELEMNSDLK ddPTM_BT-474_Pertuzumab_2h_R1 3 IVKPNGEKPDEFESGISQALLELEMNSDLK 30 2 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;; 220.55 6.22E-34 1174030000 1107290 935420 890150 639045 893060 928910 1012360 1324070 1545330 1314640 FALSE TRUE 1064015.883 908742.7375 1051019.906 672026.189 921786.086 947693.1966 1024749.565 1296727.492 1369910.617 1225598.262 0.868160404 0.74146869 0.857556623 0.548325018 0.752111124 0.773249462 0.836121914 1.058036334 1.117748499 1 20.22505473 1.8408844 2.553769361 1.073540052 0.751520114 0.709422752 0.08625324 0.142579136 1.714716675 0.049855042 0.024332754 69.32412546 -1.8408844 -0.322019938 DRYGVFPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRYGVFPLR 9 1 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 ; 173.37 5.06E-05 959920000 657340 728230 513250 623160 614040 590980 604840 653300 593180 602320 FALSE TRUE 631650.4261 707461.5934 606005.6922 655321.3623 633791.1543 602930.0205 612242.2128 639809.1267 525844.6932 561524.3299 1.124885232 1.259894818 1.079215378 1.167040015 1.128697584 1.073738017 1.090321791 1.13941479 0.936459322 1 19.09898901 1.840914052 0.409028982 0.982294799 1.179531643 0.488954827 0.060243996 0.948116169 0.417002255 0.067136862 0.060021935 69.32885888 -1.840914052 0.197236844 GLEFPMTDLDMLS(ph)PIHTPQR ddPTM_BT-474_Pertuzumab_2h_R1 3 GLEFPMTDLDMLSPIHTPQR 20 0 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;B0QY01 O60784 TOM1 Target of Myb protein 1 1 GLEFPMTDLDMLS(1)PIHTPQR;GLEFPMTDLDMLS(1)PIHTPQR;GLEFPMTDLDMLS(1)PIHTPQR 282.05 5.41E-45 245802000 188063 231933 256045 349437 360554 342658 273933 225558 228346 268393 TRUE FALSE 180713.29 225318.4979 302318.0272 367471.4854 372151.5469 349586.7795 277285.474 220900.1485 202425.1194 250214.5031 0.722233475 0.900501351 1.208235428 1.468625843 1.48733004 1.397148348 1.108191055 0.882843104 0.80900634 1 17.93280589 1.840948175 3.736074327 0.885335635 1.212129322 0.248087587 0.231103283 0.348939496 8.100203467 0.132164852 0.071210219 69.3343064 -1.840948175 0.326793688 MEIVDHALHALTDEVIIPHSGWER ddPTM_BT-474_Pertuzumab_2h_R1 2 MEIVDHALHALTDEVIIPHSGWER 24 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ; 329.43 3.05E-87 938060000 263190 326230 251120 315960 273970 328710 284720 9191.6 268240 149846 FALSE TRUE 252904.2438 316926.2398 296502.9701 332266.7335 282782.4939 335356.7414 288204.4885 9001.790248 237790.5198 139696.797 1.810379689 2.268672201 2.122475079 2.378484981 2.024258967 2.400604371 2.063071558 0.064438058 1.702190207 1 17.09193942 1.841151311 8.488852866 0.850110081 2.173984748 0.660283977 0.403711593 0.155612579 11.64203183 0.157981217 0.098829315 69.36674426 -1.841151311 1.323874667 TSS(ph)KESS(ph)PIPS(ph)PTSDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSKESSPIPSPTSDRK 17 2 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 3 T(0.235)S(0.276)S(0.489)KES(0.416)S(0.584)PIPS(0.88)PT(0.073)S(0.047)DRK 95.195 0.0017355 441630000 793300 533190 454450 393280 498860 508000 554300 793810 826180 626130 TRUE FALSE 762296.959 517983.9432 536579.2242 413577.2279 514906.285 518272.1081 561083.6892 777417.5461 732395.51 583721.6574 1.305925434 0.887381746 0.919238163 0.708517874 0.88210927 0.887875414 0.961217872 1.331829197 1.254699908 1 19.15492107 1.841200692 6.067995836 1.223426604 0.918207661 0.346265909 0.161462477 0.219310019 10.519809 0.071556962 0.042789269 69.37463195 -1.841200692 -0.305218943 EETKEDAEEKQ ddPTM_BT-474_Pertuzumab_2h_R1 4 EETKEDAEEKQ 11 2 P43487;F6WQW2;P43487-2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;; 149.23 0.0001369 6134610000 7702100 5717610 5211750 4714750 5700420 5717760 6558080 8138000 9786000 8148700 FALSE TRUE 7401093.417 5554549.361 6153629.16 4958078.813 5883779.186 5833377.025 6638339.745 7969947.456 8675134.306 7596781.291 0.974240686 0.73117142 0.810031107 0.6526552 0.774509488 0.767874815 0.873835838 1.049121615 1.141948672 1 22.85695686 1.841262205 2.461897523 1.079812659 0.777736298 0.692918701 0.082735327 0.145364447 1.634247302 0.047235378 0.022817738 69.3844587 -1.841262205 -0.30207636 GEAEAPHHGTGHPESAGEHALEPPAPAGASAS(ph)TPPPPAPEAQLPPFPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEAEAPHHGTGHPESAGEHALEPPAPAGASASTPPPPAPEAQLPPFPR 48 0 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 GEAEAPHHGT(0.002)GHPES(0.002)AGEHALEPPAPAGAS(0.078)AS(0.459)T(0.459)PPPPAPEAQLPPFPR 97.043 3.51E-06 630330000 41937 44761 37518 59634 54342 66434 49849 6383.7 44181 36360 TRUE FALSE 40298.05568 43484.46011 44298.33718 62711.71789 56089.95978 67777.341 50459.06697 6251.874364 39165.7581 33897.30481 1.188827722 1.282829427 1.306839509 1.850050269 1.654702641 1.99949056 1.488586401 0.184435736 1.155423958 1 15.04888295 1.84128788 8.819610991 0.708707891 1.556898722 0.514838456 0.335501049 0.237059217 18.57639577 0.145022157 0.091040689 69.38856084 -1.84128788 0.848190832 MDRT(ph)PEKDK ddPTM_BT-474_Pertuzumab_2h_R1 5 MDRTPEKDK 9 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 MDRT(1)PEKDK;MDRT(1)PEKDK;MDRT(1)PEKDK;MDRT(1)PEKDK;MDRT(1)PEKDK 112.43 0.0031576 4121450000 8476150 6511980 5911210 5133760 6423080 6037210 6883320 8362730 9580970 7947250 TRUE FALSE 8144892.687 6326264.706 6979497.141 5398713.969 6629684.201 6159286.523 6967560.129 8190036.703 8493378.452 7408975.679 1.099327767 0.853864958 0.94203267 0.728672114 0.894817919 0.831327675 0.940421515 1.105420919 1.146363387 1 22.82084267 1.841515817 3.722138458 1.094283166 0.885066809 0.448313806 0.094783882 0.193028067 4.450491529 0.046759294 0.025181085 69.42498862 -1.841515817 -0.209216358 NESS(ph)PAPPDSDADKLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NESSPAPPDSDADKLK 16 1 Q8ND04;Q8ND04-2;J3KTD7 Q8ND04 SMG8 Protein SMG8 1 NES(0.203)S(0.797)PAPPDSDADKLK 203.81 1.62E-11 328990000 467270 384580 381110 321830 393060 450980 516170 543650 760460 669250 TRUE FALSE 449008.5718 373612.1549 449985.0547 338439.6849 405703.1319 460099.1246 522487.0429 532423.4375 674135.7689 623921.1014 0.719656012 0.598813142 0.721221087 0.542439876 0.650247493 0.737431582 0.837424863 0.853350586 1.0804824 1 19.25100408 1.841574092 1.042391701 1.033150544 0.642369354 0.841694372 0.064405352 0.182292956 0.3653043 0.052145188 0.022139568 69.43430489 -1.841574092 -0.39078119 AIEALHGHELRPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AIEALHGHELRPGR 14 1 Q96PK6;Q96PK6-2;A0A0A6YYI9;F8WDX3;A0A0A0MSL8;B8ZZ74;Q96PK6-3;Q96PK6-4 Q96PK6 RBM14;RBM14-RBM4 RNA-binding protein 14 0 71.513 0.024759 292420000 213080 285480 221010 337610 295720 315940 276300 169990 227750 291120 FALSE TRUE 204752.598 277338.3899 260951.4233 355034.0926 305232.1024 322328.5233 279681.4421 166479.6471 201896.7748 271402.1831 0.754425022 1.021872362 0.961493457 1.308147519 1.124648663 1.187641601 1.030505499 0.613405704 0.743902545 1 18.0500728 1.841583839 6.874856629 0.752043539 1.070164525 0.356796005 0.163869614 0.232110865 13.16143506 0.072497945 0.04423358 69.43586325 -1.841583839 0.318120986 EAAGEGPALYEDPPDQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAAGEGPALYEDPPDQK 17 0 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5M0;G3V359;G3V5D9;G3V3Y6 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 192.18 4.68E-10 356350000 271590 262070 221520 232830 256090 262260 261030 306110 334220 293320 FALSE TRUE 260975.9625 254596.0202 261553.5917 244846.3842 264327.3674 267563.0769 264224.5632 299788.7215 296280.7468 273453.1751 0.954371667 0.931040644 0.956484018 0.895386876 0.966627531 0.978460304 0.966251583 1.096307334 1.083478905 1 18.06093429 1.841825947 4.767344015 1.067703336 0.947383979 0.713893705 0.031955311 0.10778449 3.649111925 0.014950321 0.008524216 69.47458279 -1.841825947 -0.120319357 DVPLHALYDNVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DVPLHALYDNVEK 13 0 P08243-2;P08243;P08243-3;F8WEJ5 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ;; 231.06 3.05E-12 1166340000 1272680 1266440 1126560 1069930 1237600 1338790 1239820 1366860 1621540 1497150 FALSE TRUE 1222942.259 1230322.371 1330154.452 1125149.216 1277408.528 1365861.251 1254993.288 1338633.863 1437469.577 1395746.697 0.876192121 0.881479694 0.953005624 0.806127084 0.915215154 0.978588202 0.899155478 0.959080803 1.029892874 1 20.41260571 1.841897298 0.732145943 1.014013023 0.885812344 0.519938405 0.044027277 0.544354902 0.564442404 0.03956698 0.019815378 69.48599781 -1.841897298 -0.128200679 IKGDVDVTGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKGDVDVTGPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 117.23 0.00080459 993350000 2738100 2607700 2373500 2385600 2208700 2568500 2588800 3098200 3303300 2993200 FALSE TRUE 2631092.025 2533330.949 2802444.248 2508721.102 2279744.841 2620436.83 2620482.509 3034221.087 2928323.233 2790467.898 0.94288561 0.907851673 1.004291879 0.899032418 0.816975835 0.939067184 0.939083553 1.087352085 1.049402229 1 21.41207562 1.841916292 5.102230042 1.051778093 0.918194537 0.58313837 0.048235717 0.152894803 5.717161152 0.023254767 0.013453618 69.48903675 -1.841916292 -0.133583556 KGNAEGSS(ph)DEEGKLVIDEPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 KGNAEGS(0.103)S(0.897)DEEGKLVIDEPAK 217.68 2.98E-25 1002700000 540390 381650 393840 339130 447490 361600 463640 662190 744610 576790 TRUE FALSE 519270.9614 370765.7157 465015.6489 356632.5399 461883.9223 368911.7998 469314.165 648515.5451 660084.9945 537723.4995 0.965683965 0.689509973 0.864785804 0.663226622 0.858961758 0.686062261 0.872779719 1.206039062 1.227554673 1 19.036505 1.842098026 4.169453426 1.161629153 0.784510847 0.692076578 0.106007677 0.108249652 2.987487162 0.047462824 0.026261657 69.51812116 -1.842098026 -0.377118306 LLDDAMAADKSDEWFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDDAMAADKSDEWFAK 17 1 Q9HC38-2;F6TLX2;Q9HC38;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 239.18 2.58E-20 1483670000 2974100 2634300 2473600 2298500 2632600 2522200 2878300 3268200 3788000 3481200 FALSE TRUE 2857868.884 2559172.343 2920634.545 2417125.86 2717279.97 2573200.612 2913525.496 3200710.528 3358002.121 3245415.223 0.880586516 0.788550052 0.89992631 0.744781698 0.837267278 0.79287254 0.89773582 0.986225277 1.034691061 1 21.62997164 1.842279226 2.275549222 1.015569756 0.822958188 0.778213981 0.0436726 0.121868316 1.182625069 0.024706434 0.011668929 69.54713216 -1.842279226 -0.192611567 IEINFPAEYPFKPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEINFPAEYPFKPPK 15 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 89.541 0.0058003 371280000 104760 116930 77054 101770 102410 111570 107710 142960 139960 136860 FALSE TRUE 100665.8634 113595.2709 90979.37186 107022.3619 105704.1107 113826.0218 109028.1872 140007.826 124072.3276 127590.3503 0.788977091 0.890312399 0.713058406 0.838796677 0.828464773 0.892120929 0.8545175 1.097323001 0.972427204 1 16.9611597 1.84228421 5.746663396 1.028290596 0.828132386 0.713799177 0.056364734 0.113825536 5.032883313 0.024962636 0.014788827 69.54793028 -1.84228421 -0.200158211 ATSEEDVSIKS(ph)PICEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ATSEEDVSIKSPICEK 16 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 ATSEEDVSIKS(1)PICEK;ATSEEDVSIKS(1)PICEK;ATSEEDVS(0.001)IKS(0.999)PICEK 229.68 1.79E-15 1151250000 2091980 1777340 1498920 1602690 1978120 1774170 1909520 2297050 2499470 2375580 TRUE FALSE 2010223.109 1726652.003 1769808.187 1685405.023 2041748.026 1810044.933 1932889.277 2249615.115 2215740.644 2214679.851 0.90768113 0.779639551 0.799125972 0.761015197 0.921915656 0.817294171 0.872762389 1.015774408 1.000478983 1 21.07866673 1.842578918 3.264409524 1.007688518 0.828778425 0.721420762 0.048390001 0.12517854 2.317681576 0.025491001 0.013303981 69.59514085 -1.842578918 -0.178910093 DGQAMLWDLNEGK ddPTM_BT-474_Pertuzumab_2h_R1 5 DGQAMLWDLNEGK 13 0 P63244;J3KPE3;H0YAF8;D6R9L0;H0Y8W2;D6RAC2;D6R9Z1;D6RFX4;D6REE5;H0YAM7;H0Y8R5 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;;; 240.4 1.77E-16 939761000 1550390 1508470 1282111 1314330 1458687 1524833 1513723 1753988 2000940 1840159 FALSE TRUE 1489799.045 1465449.913 1513816.978 1382162.729 1505606.992 1555666.168 1532248.395 1717767.535 1773801.68 1715523.392 0.86842246 0.854229047 0.882422814 0.805679908 0.87763711 0.906817229 0.893166716 1.001308139 1.033971142 1 20.71021737 1.842622797 1.506403031 1.025085132 0.859888547 0.867093739 0.025668243 0.125468446 0.536971359 0.01873538 0.007926776 69.60217271 -1.842622797 -0.165196585 KANEDELK ddPTM_BT-474_Pertuzumab_2h_R1 1 KANEDELK 8 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 125.48 0.0020206 174750000 473050 458000 371400 347680 422760 333140 454730 489800 580730 531380 FALSE TRUE 454562.683 444938.2884 438520.2417 365623.8065 436358.4593 339876.3191 460295.1218 479685.4588 514807.965 495389.1593 0.917587062 0.898159114 0.885203549 0.738053709 0.880839742 0.686079444 0.929158649 0.968300274 1.039199093 1 18.91820277 1.842948408 2.854678673 1.005862449 0.836542805 0.517232181 0.072022922 0.213053032 3.125041033 0.040061786 0.020199958 69.65437629 -1.842948408 -0.169319644 (ac)SDKPDMAEIEKFDK ddPTM_BT-474_Pertuzumab_2h_R1 18 SDKPDMAEIEKFDK 14 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;;;;;;;;;;;;;;;; 102.5 6.94E-06 1.86691E+11 144360310 121342010 92394230 82377540 114706950 116126570 119374270 152867630 176132670 138840860 FALSE TRUE 138718549.5 117881454.7 109091922.7 86629054.71 118396603.2 118474728.8 120835208 149710860 156138827.7 129437044.9 1.07170671 0.910724243 0.842818397 0.669275591 0.914704159 0.915307738 0.933544243 1.156630701 1.20629166 1 26.94767533 1.842966094 3.415516819 1.137140695 0.879991574 0.494621221 0.105152373 0.192730308 3.849923163 0.056750648 0.029961433 69.65721298 -1.842966094 -0.257149122 KWDGS(ph)EEDEDNSKK ddPTM_BT-474_Pertuzumab_2h_R1 4 KWDGSEEDEDNSKK 14 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(0.999)EEDEDNS(0.001)KK;KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK 151.87 3.56E-06 3667620000 4689160 3124730 3064520 2151340 3051850 2887540 3530640 4626400 5466790 4226010 TRUE FALSE 4505902.443 3035615.76 3618346.934 2262370.915 3150015.527 2945928.037 3573849.028 4530863.223 4846222.918 3939778.579 1.143694335 0.770504154 0.918413779 0.574238087 0.79954126 0.747739493 0.90711926 1.150029915 1.230074945 1 21.90968312 1.842984467 3.447138632 1.143240498 0.815392203 0.456750852 0.145851326 0.197503178 4.006385976 0.07423215 0.039280025 69.66015983 -1.842984467 -0.327848295 GVEPSPS(ph)PIKPGDIK ddPTM_BT-474_Pertuzumab_2h_R1 4 GVEPSPSPIKPGDIK 15 1 Q92890;Q92890-1;Q92890-3;C9JNP9 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPS(0.005)PS(0.995)PIKPGDIK;GVEPS(0.002)PS(0.998)PIKPGDIK;GVEPS(0.006)PS(0.994)PIKPGDIK;GVEPS(0.003)PS(0.997)PIKPGDIK 224.4 6.89E-13 6256830000 4826640 3733150 4624090 3949870 4420670 4096890 5211520 6193400 7325700 6922000 TRUE FALSE 4638009.573 3626684.217 5459765.925 4153723.264 4562864.865 4179731.923 5275300.141 6065504.126 6494117.248 6453166.775 0.71871838 0.562000696 0.846059945 0.643672077 0.707073755 0.647702449 0.817474633 0.939926758 1.006345795 1 22.62157588 1.843034103 1.982827358 0.998415922 0.6874649 0.783078532 0.069530919 0.135769202 1.011537695 0.042593489 0.01931139 69.66812192 -1.843034103 -0.310951022 NGDLDEVKDYVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGDLDEVKDYVAK 13 1 P58546;C9JL85 P58546 MTPN Myotrophin 0 ; 176.23 1.54E-05 2507180000 5257400 4243400 3647900 3175500 4080300 4052900 4292500 5320400 5857000 4994100 FALSE TRUE 5051934.996 4122382.387 4307156.677 3339387.936 4211546.555 4134852.415 4345032.899 5210531.881 5192137.915 4655845.159 1.08507367 0.885420852 0.925107372 0.717246348 0.904571869 0.888099212 0.933242569 1.119137708 1.115186983 1 22.15061165 1.843215185 4.30889699 1.087704791 0.894442168 0.442743805 0.088718661 0.192516749 5.578483668 0.043172554 0.024086087 69.69717656 -1.843215185 -0.193262624 YRHDENILESEPIVYR ddPTM_BT-474_Pertuzumab_2h_R1 1 YRHDENILESEPIVYR 16 1 Q96F86;H3BSQ0;H3BPN4 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 114.59 0.00034358 257520000 109540 130250 102070 116880 116530 132120 118010 113670 124430 125630 FALSE TRUE 105259.0557 126535.3975 120516.3195 122912.1908 120278.2933 134791.5569 119454.2417 111322.6748 110305.2281 117120.9682 0.898720847 1.0803821 1.028990124 1.049446506 1.026957812 1.150874681 1.019921911 0.950493123 0.941805978 1 16.83763986 1.843366573 4.825086094 0.9603955 1.043611825 0.231113177 0.060465343 0.288962343 9.915256614 0.027615749 0.015801242 69.72147602 -1.843366573 0.083216325 KDPFS(ph)PDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDPFSPDK 8 1 H0YHD0;Q5PSV4-2;Q5PSV4 H0YHD0 BRMS1L Breast cancer metastasis-suppressor 1-like protein 1 KDPFS(1)PDK;KDPFS(1)PDK 63.727 0.043784 533290000 1325340 1108750 998980 872510 1078220 1003000 1113880 1397100 1446940 1326980 TRUE FALSE 1273544.248 1077129.536 1179517.908 917540.3457 1112901.926 1023281.347 1127511.997 1368249.397 1282689.437 1237102.463 1.02945737 0.870687407 0.953452074 0.741685005 0.899603678 0.827159737 0.91141359 1.106011376 1.036849797 1 20.23853357 1.843535529 5.61439761 1.054512798 0.882551028 0.480235012 0.074916868 0.174405615 7.42240345 0.033116301 0.019545701 69.74860554 -1.843535529 -0.171961771 TAPPAS(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 5 TAPPASPEAR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPPAS(1)PEAR;TAPPAS(1)PEAR;TAPPAS(1)PEAR;TAPPAS(1)PEAR;TAPPAS(1)PEAR 154.94 1.43E-05 5035434000 3103510 3025542 2390506 2883233 2791282 2743555 2614043 2627673 2472114 2560577 TRUE FALSE 2982221.398 2939256.504 2822523.611 3032037.001 2881066.121 2799031.562 2646034.44 2573410.634 2191489.983 2387146.839 1.249282763 1.231284333 1.182383741 1.270151023 1.206907792 1.172542684 1.108450639 1.078027791 0.91803736 1 21.18685588 1.843603097 1.074088419 0.963245411 1.228911359 0.887592854 0.036453938 0.147531505 0.313927395 0.029237917 0.012351021 69.75945797 -1.843603097 0.265665948 LNEDKPK ddPTM_BT-474_Pertuzumab_2h_R1 4 LNEDKPK 7 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;; 93.178 0.013795 5312210000 6818800 5654060 5000070 4664710 5821560 5392700 6007900 7019700 8147500 6975900 FALSE TRUE 6552313.757 5492811.745 5903693.875 4905456.242 6008815.764 5501744.089 6081426.477 6874740.742 7222629.957 6503416.08 1.007518768 0.844604078 0.90778351 0.754289159 0.923947613 0.845977563 0.935112624 1.057096864 1.110590168 1 22.6327663 1.843606538 2.961559481 1.065013891 0.876865077 0.580566372 0.066269099 0.164061672 2.56589908 0.034505275 0.017577757 69.76001062 -1.843606538 -0.188148814 RDSLT(ph)GSSDLYK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSLTGSSDLYK 12 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(0.218)LT(0.734)GS(0.036)S(0.011)DLYK 162.64 0.00012017 856000000 875250 793300 803130 733230 809780 699480 902310 1010100 1147400 1133600 TRUE FALSE 841044.2624 770675.8607 948273.4565 771072.0882 835827.3091 713623.9649 913352.7397 989241.082 1017151.962 1056820.262 0.795825262 0.729240239 0.897289246 0.729615163 0.7908888 0.675255756 0.864246052 0.936054235 0.962464478 1 20.0112986 1.84361389 2.582231908 0.968152477 0.772839221 0.698958445 0.057444168 0.150680195 1.845511696 0.031946976 0.015675651 69.76119163 -1.84361389 -0.195313256 FQFDGDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FQFDGDKK 8 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 71.349 0.078523 4378900000 5343300 4995000 3735400 3797300 5026200 4573600 5141700 6249400 7432100 6387200 FALSE TRUE 5134477.929 4852547.491 4410469.874 3993279.108 5187872.288 4666081.326 5204625.663 6120347.706 6588439.166 5954589.255 0.862272393 0.814925645 0.740684149 0.670622093 0.871239319 0.783610947 0.874052842 1.027837092 1.106447294 1 22.50557056 1.843868417 2.205919763 1.060587973 0.786900167 0.784420549 0.0595508 0.131871703 1.205608337 0.037598205 0.017615248 69.80208843 -1.843868417 -0.273687805 DEDKDEDEKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEDKDEDEKEK 11 2 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG77 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 111.12 0.00095756 153520000 175070 94952 97657 71364 112800 83140 120660 162440 192730 146410 FALSE TRUE 168228.0708 92244.06193 115305.7923 75047.10459 116428.3144 84821.14776 122136.6732 159085.5572 170852.0984 136493.5203 1.232498587 0.675812755 0.844771181 0.549821738 0.852995177 0.621429849 0.89481664 1.165517285 1.251723144 1 17.05847294 1.84390162 3.696121842 1.155748493 0.7829082 0.405671954 0.184013855 0.206622264 4.696514359 0.088885579 0.047864485 69.80742526 -1.84390162 -0.372840293 ENIEKDEDDVDQELANIDPTWIES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENIEKDEDDVDQELANIDPTWIESPK 26 1 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 ENIEKDEDDVDQELANIDPTWIES(1)PK 125.73 6.62E-05 47052000 51558 35134 53255 41179 54307 43164 56294 75389 85973 78903 TRUE FALSE 49543.05636 34132.01272 62879.36315 43304.25312 56053.83398 44036.80565 56982.94281 73832.1908 76213.70547 73558.82953 0.673516105 0.464009731 0.854817342 0.588702314 0.762027269 0.598661044 0.774658096 1.003716227 1.036091873 1 16.1666109 1.84404799 2.761609513 1.022196104 0.659057211 0.721049015 0.09887377 0.131111138 1.811699281 0.052445183 0.026229394 69.83095639 -1.84404799 -0.363138893 HINDSAPEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 HINDSAPEVR 10 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 114.86 0.0012992 269500000 74768 134340 79285 128040 113660 104950 101450 75437 70442 105290 FALSE TRUE 71845.9839 130508.7547 93613.56319 134648.1597 117315.9771 107072.1609 102691.5754 73879.19959 62445.71948 98158.61452 0.731937632 1.329570057 0.953696868 1.37174063 1.19516741 1.090807582 1.04617996 0.752651206 0.636171566 1 16.58282727 1.844060081 3.29881122 0.769432063 1.127585598 0.34943301 0.191154688 0.231906096 4.365025288 0.09452452 0.049515073 69.83290062 -1.844060081 0.358153535 FSHEEIAMATVTALRR ddPTM_BT-474_Pertuzumab_2h_R1 4 FSHEEIAMATVTALRR 16 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;; 233.4 7.72E-20 9362700000 3285940 3543360 2362310 2379800 2732900 2996760 2559140 2169050 2298310 2073650 FALSE TRUE 3157521.832 3442306.842 2789231.966 2502621.763 2820806.21 3057356.54 2590459.521 2124258.36 2037415.484 1933199.838 1.633313726 1.78062649 1.442805814 1.29454892 1.459138447 1.581500515 1.33998538 1.098830197 1.053908367 1 20.88255935 1.844069593 2.007911069 1.028446887 1.527126509 0.756948654 0.122046146 0.174301323 1.330120808 0.087974635 0.040071051 69.8344301 -1.844069593 0.498679622 KTST(ph)SPPPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.09)S(0.063)T(0.502)S(0.346)PPPEK 77.078 0.01997 834700000 852290 705050 855140 829070 795890 814700 1001300 1144200 1381200 1308400 TRUE FALSE 818981.5645 684942.6643 1009682.82 871858.4021 821490.5247 831173.7922 1013554.209 1120571.87 1224411.966 1219780.903 0.671416943 0.561529257 0.827757525 0.714766398 0.673473837 0.681412367 0.830931364 0.918666514 1.003796636 1 20.2181906 1.844140138 1.540033769 1.001021523 0.686905249 0.808914229 0.062851421 0.163352356 0.731489894 0.046820145 0.019912539 69.84577465 -1.844140138 -0.314116275 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAGENPLEFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAGENPLEFLR 42 0 P54725-3 P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLTGIPGS(0.805)PEPEHGS(0.192)VQES(0.002)QVSEQPATEAGENPLEFLR;AVEY(0.003)LLT(0.005)GIPGS(0.453)PEPEHGS(0.453)VQES(0.08)QVS(0.005)EQPATEAGENPLEFLR 157.86 4.41E-15 266565000 14062.3 20263.3 15819.8 20083.2 18901.1 22160.9 18446.3 16143.2 17485.3 19890.3 TRUE FALSE 13512.72977 19685.41052 18678.78977 21119.69636 19509.07105 22609.00858 18672.05134 15809.83728 15500.44205 18543.11226 0.728719622 1.061602294 1.007316868 1.138951005 1.052092592 1.219267201 1.006953475 0.852598909 0.835913725 1 14.17859578 1.844201154 5.19533826 0.883973091 1.045261084 0.19000151 0.125777075 0.316808303 12.0616601 0.057755154 0.033580653 69.8555882 -1.844201154 0.161287993 TLDFDPLLSPAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLDFDPLLSPASPK 14 0 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 TLDFDPLLSPAS(1)PK;TLDFDPLLSPAS(1)PK 212.39 2.62E-09 373910000 1034240 861130 844780 809490 927880 846530 954000 1186940 1191490 1292460 TRUE FALSE 993820.7574 836571.4155 997450.538 851267.8759 957726.1029 863647.4166 965675.3374 1162429.274 1056237.05 1204920.533 0.82480191 0.694295925 0.827814375 0.706492962 0.794845865 0.716767117 0.801443175 0.964735219 0.87660308 1 20.20050657 1.844640373 4.130697216 0.940547173 0.759901376 0.714793454 0.052583925 0.110606716 2.995930623 0.023155954 0.012805635 69.92627171 -1.844640373 -0.180645796 DGLAPEKTS(ph)PDRDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLAPEKTSPDRDK 14 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.049)S(0.951)PDRDK;DGLAPEKT(0.404)S(0.596)PDRDK 143.99 7.07E-06 3301000000 2007240 1448550 1510050 1121480 1356230 1268940 1593150 2026740 2315080 1877870 TRUE FALSE 1928794.842 1407238.772 1782949.626 1179359.717 1399854.37 1294598.836 1612647.446 1984887.111 2052281.824 1750680.192 1.101740255 0.80382401 1.018432512 0.673658 0.799605991 0.73948334 0.921154791 1.133780527 1.172276829 1 20.73948413 1.84473772 3.994756281 1.113766051 0.849161804 0.431122288 0.125539494 0.199693912 5.1332466 0.061191465 0.033580157 69.94194739 -1.84473772 -0.264604246 YSKEEEMDDMDRDLGDEYGWK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSKEEEMDDMDRDLGDEYGWK 21 2 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 185.14 2.08E-17 797440000 202050 290090 211030 201590 211940 284640 228810 290580 348810 296200 FALSE TRUE 194153.6626 281816.9172 249167.8153 211994.0841 218757.2426 290395.6158 231610.2452 284579.4215 309214.5511 276138.1102 0.703103467 1.020565097 0.902330414 0.767710346 0.792202288 1.051631793 0.838747846 1.030569164 1.119782238 1 18.07503048 1.844870384 1.209155055 1.066791572 0.860859815 0.3688127 0.106409087 0.505680621 1.370596893 0.083569002 0.03485409 69.96331579 -1.844870384 -0.205931757 LTWHSCPEDEAQ ddPTM_BT-474_Pertuzumab_2h_R1 6 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;; 178.84 5.00E-05 6608930000 4523000 4856540 3217810 4496900 4175900 4618790 4316480 3655530 4559310 4381410 FALSE TRUE 4346236.16 4718036.234 3799339.847 4728985.548 4310221.616 4712185.098 4369306.373 3580042.028 4041756.243 4084653.198 1.064040433 1.155064091 0.93014992 1.157744689 1.055223395 1.153631623 1.069688456 0.876461686 0.989498018 1 21.96178216 1.844991275 7.329742331 0.945514773 1.085760911 0.408041663 0.070684897 0.221750059 13.32135709 0.028792493 0.017741094 69.98279367 -1.844991275 0.140246138 GPHHLDNSSPGPGSEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPHHLDNSSPGPGSEAR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 0 ;; 173.58 8.44E-10 348257000 273641 326837 298194 378749 336951 362430 344853 56881.9 353359 353024 FALSE TRUE 262946.8072 317515.9288 352084.2891 398296.2813 347789.3349 369758.5829 349073.4142 55707.26889 313247.1677 329113.37 0.798955105 0.964761561 1.069796372 1.210209969 1.056746297 1.123499124 1.060647928 0.169264679 0.951791073 1 18.32822511 1.84506629 24.99996315 0.614618395 1.049191249 0.269664391 0.237139992 26.73767307 6262.043026 0.094013619 0.060675594 69.99488275 -1.84506629 0.434572854 EMEHNTVCAAGTS(ph)PVGEIGEEK ddPTM_BT-474_Pertuzumab_2h_R1 8 EMEHNTVCAAGTSPVGEIGEEK 22 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 EMEHNTVCAAGT(0.002)S(0.998)PVGEIGEEK;EMEHNTVCAAGT(0.006)S(0.994)PVGEIGEEK;EMEHNTVCAAGT(0.001)S(0.999)PVGEIGEEK;EMEHNTVCAAGT(0.008)S(0.992)PVGEIGEEK;EMEHNTVCAAGT(0.007)S(0.993)PVGEIGEEK;EMEHNTVCAAGT(0.023)S(0.977)PVGEIGEEK;EMEHNTVCAAGT(0.249)S(0.751)PVGEIGEEK;EMEHNTVCAAGT(0.002)S(0.998)PVGEIGEEK 252.77 3.36E-37 15131710000 8512160 8861240 7459930 8326970 7931920 8908240 8756380 9396940 10804850 10197820 TRUE FALSE 8179495.377 8608526.111 8808105.296 8756725.92 8187057.41 9088370.716 8863543.198 9202889.905 9578328.726 9507112.568 0.860355373 0.905482716 0.926475334 0.921071025 0.861150781 0.955954887 0.932306537 0.96800052 1.007490829 1 23.18057581 1.845091623 0.905776286 1.007133095 0.898719631 0.723423797 0.025311876 0.300408944 0.457454692 0.021624802 0.009622619 69.99896567 -1.845091623 -0.108413463 HFGAEYR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFGAEYR 7 0 P04818;P04818-2 P04818 TYMS Thymidylate synthase 0 ; 101.69 0.0088735 304440000 48269 59591 41084 60006 55559 69330 51362 43609 40671 54760 FALSE TRUE 46382.59412 57891.52303 48508.79271 63102.91685 57346.10569 70731.9001 51990.58352 42708.45891 36054.19859 51051.05642 0.908553071 1.133992655 0.950201545 1.236074653 1.123308893 1.385512956 1.018403676 0.836583254 0.706238051 1 15.6396532 1.845121301 3.842693483 0.830849691 1.125367375 0.419667129 0.143079894 0.208573875 5.039796328 0.070976916 0.038606792 70.00374939 -1.845121301 0.294517684 TQS(ph)APLPQNAQALQHLVIQQQHQQFLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQSAPLPQNAQALQHLVIQQQHQQFLEK 28 0 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 T(0.024)QS(0.976)APLPQNAQALQHLVIQQQHQQFLEK 397 4.38E-146 656580000 292030 298190 220360 257030 329370 285850 317690 412890 449810 452750 TRUE FALSE 280617.1447 289685.9132 260183.9539 270295.3491 339964.4852 291630.0829 321577.9853 404363.6772 398749.4546 422084.8392 0.664835878 0.686321531 0.616425727 0.640381563 0.805441119 0.690927642 0.761879971 0.958015166 0.944713995 1 18.68717348 1.845211612 1.256036527 0.999403423 0.673382513 0.868074621 0.049311935 0.149852617 0.439418647 0.040079558 0.016706565 70.01830803 -1.845211612 -0.32602091 KS(ph)PEKNER ddPTM_BT-474_Pertuzumab_2h_R1 3 KSPEKNER 8 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 KS(1)PEKNER;KS(1)PEKNER;KS(1)PEKNER 78.705 0.023575 358221000 705910 507013 514328 410027 522886 601580 611800 664310 840030 757830 TRUE FALSE 678322.2568 492553.4857 607278.5108 431188.5426 539705.1031 613744.3598 619287.3914 650591.7664 744673.3161 706501.4991 0.960114391 0.697172598 0.859557286 0.610315113 0.763912184 0.868709211 0.876554957 0.920863957 1.05402935 1 19.4303331 1.845340158 1.135690181 1.021883606 0.774697465 0.50523562 0.09154959 0.379120579 0.903337304 0.072381786 0.030348642 70.0390357 -1.845340158 -0.247186141 DEDGSTLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEDGSTLFR 9 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 141.93 0.00024553 1043420000 1008480 909750 872200 769530 843250 885190 912490 1021220 1082600 1071680 FALSE TRUE 969067.4867 883804.8207 1029825.942 809245.5355 870373.9021 903089.1483 923657.3256 1000131.45 959707.7866 999094.159 0.969946104 0.884606133 1.030759646 0.809979248 0.871163037 0.903907945 0.924494771 1.001038232 0.960577917 1 19.93026112 1.845346909 4.586618981 0.985667781 0.909832728 0.266562303 0.056125356 0.304049204 9.636716154 0.02657887 0.015057669 70.04012436 -1.845346909 -0.075835053 ELLVDCYKPTEAFISGLLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLVDCYKPTEAFISGLLDK 20 1 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 0 ; 226.51 3.98E-25 1075310000 1235510 1019550 941880 1013110 989130 954310 1148750 1306030 1479420 1430510 FALSE TRUE 1187224.903 990473.4322 1112098.668 1065396.729 1020946.265 973606.802 1162808.746 1279060.024 1311482.444 1333620.284 0.890227089 0.742695237 0.833894536 0.798875618 0.765544944 0.730047986 0.871918912 0.95908861 0.983400193 1 20.34691652 1.845433455 2.566833581 0.984111115 0.79229586 0.778009025 0.044606158 0.119668132 1.448042934 0.024834281 0.012182364 70.05408341 -1.845433455 -0.191815255 FFDANYDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FFDANYDGK 9 0 Q15691;C9JB30;Q9UPY8;Q9UPY8-2 Q15691;C9JB30;Q9UPY8-2 MAPRE1;MAPRE3 Microtubule-associated protein RP/EB family member 1;Microtubule-associated protein RP/EB family member 3 0 107.79 0.0063205 103640000 159890 146320 164310 187080 156370 147870 176380 215140 220450 237120 FALSE TRUE 153641.322 142147.0969 194004.4721 196735.2212 161399.7831 150860.0327 178538.5912 210697.2838 195425.4402 221059.6512 0.695022005 0.643025971 0.877611409 0.889964406 0.730118691 0.682440382 0.807648932 0.953124112 0.884039395 1 17.7540762 1.845447435 3.880581459 0.938953377 0.758015596 0.539370062 0.079263407 0.204190399 5.009492903 0.042695728 0.023282384 70.05633841 -1.845447435 -0.180937781 EEDDVVSEDLVQQDVQDLYEAGELK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEDDVVSEDLVQQDVQDLYEAGELK 25 0 P08133;P08133-2 P08133 ANXA6 Annexin A6 0 ;; 146.25 2.63E-07 139851000 86974 96237 45211 138038 63674 69707 95625 120508 139919 118456 FALSE TRUE 83574.95993 93492.41499 53381.63341 145162.1577 65722.13204 71116.5233 96795.28735 118019.4677 124035.9817 110432.8696 0.756794243 0.846599525 0.483385369 1.314483253 0.595131977 0.643979673 0.876507943 1.068698732 1.12317992 1 16.75281012 1.845530075 3.488979173 1.072088436 0.779066815 0.274614559 0.20993095 0.313684762 6.476381665 0.105218943 0.055940038 70.06967054 -1.845530075 -0.293021621 ASEVEEILDGNDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASEVEEILDGNDEK 14 0 Q12824-2;Q12824;A0A0U1RQQ2;A0A0U1RRB8;B5MCL5;A0A2R8YEE8;A0A0G2JSE9;C9JTA6;A0A2R8Y5N5;A0A0G2JRV3;G5E975 Q12824-2 SMARCB1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 0 225.33 6.55E-12 58663000 79543 71689 70027 69044 79691 72793 80338 96079 104150 102060 FALSE TRUE 76434.37162 69644.49991 82682.43664 72607.36911 82254.33339 74264.92433 81321.20048 94094.93507 92327.32863 95147.38529 0.803326033 0.731964412 0.868993261 0.763104198 0.864493892 0.78052512 0.854686655 0.988938737 0.970361175 1 16.53787639 1.845599388 3.010078053 0.987378448 0.803198983 0.808351835 0.040068985 0.099377331 1.596567232 0.020477052 0.010491431 70.08085444 -1.845599388 -0.184179465 VHNNS(ph)PDTSRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHNNSPDTSRR 11 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 VHNNS(0.997)PDT(0.001)S(0.001)RR;VHNNS(0.997)PDT(0.002)S(0.002)RR 95.981 0.0045037 124054000 63272 66448 54665 63834 61033 59097 61684 34021 65244 55949 TRUE FALSE 60799.26029 64552.9681 64544.18152 67128.48039 62996.18187 60291.98183 62438.90724 33318.45446 57837.77465 52159.5244 1.165640619 1.237606532 1.237438076 1.286984135 1.207759898 1.155915099 1.197075855 0.638779875 1.108863152 1 15.67064309 1.845831026 10.01457681 0.881622755 1.215799698 0.570083124 0.117014429 0.239165106 20.82961309 0.046234256 0.029317903 70.11824315 -1.845831026 0.334176943 LVEQANS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEQANSPK 9 0 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 LVEQANS(1)PK;LVEQANS(1)PK 91.123 0.011503 716740000 1424580 1177300 1068210 986710 1101470 1109670 1192990 1456320 1581050 1324440 TRUE FALSE 1368905.839 1143724.557 1261259.309 1037634.221 1136899.783 1132108.288 1207590.168 1426246.483 1401575.832 1234734.499 1.108664121 0.926291893 1.021482197 0.840370316 0.920764572 0.916883985 0.978016059 1.155103777 1.135123246 1 20.23576943 1.845858919 5.43221591 1.10950349 0.950629438 0.397963253 0.077267753 0.194896688 7.851122651 0.034488011 0.020249452 70.12274666 -1.845858919 -0.158874052 SAYQEYDS(ph)DS(ph)DVPEELKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAYQEYDSDSDVPEELKR 18 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 2 SAYQEY(0.001)DS(0.999)DS(1)DVPEELKR 92.518 0.0081185 256360000 304290 287160 234780 236650 258680 241260 276490 335550 363720 325750 TRUE FALSE 292398.0104 278970.478 277209.9687 248863.5349 267000.6771 246138.4425 279873.7673 328620.7752 322432.0304 303686.6624 0.962827963 0.918612875 0.912815751 0.819474695 0.879197904 0.810501326 0.921587287 1.082104735 1.061726017 1 18.21222402 1.845913719 4.614265689 1.053384768 0.882618828 0.70961807 0.046842621 0.117608398 3.756151122 0.023120694 0.013120257 70.13159541 -1.845913719 -0.17076594 LDSS(ph)PSVSSTLAAK ddPTM_BT-474_Pertuzumab_2h_R1 8 LDSSPSVSSTLAAK 14 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LDS(0.055)S(0.92)PS(0.023)VS(0.001)STLAAK;LDS(0.201)S(0.699)PS(0.1)VSSTLAAK;LDS(0.004)S(0.996)PSVSSTLAAK;LDS(0.13)S(0.845)PS(0.025)VSSTLAAK;LDS(0.074)S(0.916)PS(0.01)VSSTLAAK;LDS(0.009)S(0.991)PSVSSTLAAK;LDS(0.011)S(0.983)PS(0.006)VSSTLAAK;LDS(0.013)S(0.986)PS(0.001)VSSTLAAK 369.03 4.80E-97 9144990000 10295450 9343290 9230640 9957690 9733940 10033240 11313910 12403360 13303760 13995820 TRUE FALSE 9893092.432 9076828.517 10898821.98 10471607.57 10047041.02 10236118.99 11452373.01 12147226.28 11793572.94 13047870.65 0.758215091 0.695655925 0.835295067 0.802552988 0.770013843 0.784504941 0.877719693 0.930973843 0.903869548 1 23.63731105 1.84593602 0.642596535 0.994470166 0.755688148 0.814345475 0.037596227 0.297288121 0.248280487 0.03626835 0.020194178 70.13519682 -1.84593602 -0.238782018 VVTVFSVADGYSENNVFYGHHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVTVFSVADGYSENNVFYGHHAK 23 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 218.69 1.27E-32 2152170000 1562820 1828200 1622290 1484510 1729100 1747480 1548010 727260 999500 1270890 FALSE TRUE 1501743.267 1776061.526 1915473.891 1561125.739 1784718.072 1782815.243 1566955.009 712241.8269 886040.9502 1184811.488 1.267495531 1.499024565 1.616690849 1.317615295 1.506330829 1.504724811 1.322535294 0.601143586 0.747832849 1 20.1762261 1.845957923 4.779767268 0.755535453 1.453962299 0.836445391 0.132383515 0.074843029 2.516122587 0.059917371 0.0342646 70.13873408 -1.845957923 0.698426846 LSFASETPLEKEPHS(ph)PADQPEQQAESTLTSAETR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSFASETPLEKEPHSPADQPEQQAESTLTSAETR 34 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 LSFASETPLEKEPHS(1)PADQPEQQAESTLTSAETR 207.52 1.09E-27 145920000 91894 95309 66794 60648 90489 90487 75707 74170 71871 79136 TRUE FALSE 88302.68089 92590.88064 78865.16162 63778.05055 93399.66087 92316.70914 76633.52491 72638.36358 63712.50539 73776.04823 1.196901745 1.255026297 1.068980564 0.864481794 1.265988937 1.25131003 1.038731767 0.984579214 0.86359336 1 16.17086489 1.845990869 2.66084949 0.938876309 1.143058077 0.365677554 0.11781928 0.319222267 4.121127693 0.071062897 0.035230479 70.14405507 -1.845990869 0.204181767 CRDDSFFGETSHNYHK ddPTM_BT-474_Pertuzumab_2h_R1 4 CRDDSFFGETSHNYHK 16 1 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 251.04 2.37E-21 4224180000 2874130 3049590 2708640 3336780 3006050 3055090 3386390 167305 3775470 3073450 FALSE TRUE 2761805.822 2962618.679 3198151.501 3508991.616 3102742.328 3116866.013 3427833.654 163850.0933 3346894.474 2865282.494 0.963886049 1.033970886 1.11617319 1.22465817 1.082874842 1.087804089 1.196333577 0.057184621 1.168085339 1 21.45024595 1.846082655 20.41774655 0.633966218 1.102422504 0.227555552 0.282918385 6.742259691 1271.291616 0.110032225 0.070978529 70.15888118 -1.846082655 0.468456286 RVS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_BT-474_Pertuzumab_2h_R1 6 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.25)S(0.25)S(0.25)S(0.25)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.779)S(0.074)S(0.074)S(0.074)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.845)S(0.12)S(0.01)S(0.025)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.903)S(0.085)S(0.008)S(0.003)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.928)S(0.049)S(0.011)S(0.011)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.676)S(0.139)S(0.139)S(0.046)ELDLPSGDHCEAGLLQLDVPLLR 313.37 1.90E-92 2759452000 434070 569638 445933 640278 586269 619254 512123 532777 519074 548284 TRUE FALSE 417106.0645 553392.482 526523.0128 673322.8243 605126.8748 631775.7402 518390.5145 521774.9688 460150.8957 511148.2363 0.81601781 1.082645782 1.0300789 1.317275061 1.183857894 1.235993192 1.014168645 1.020789923 0.900229841 1 18.96338222 1.84609409 2.473376194 0.965409747 1.117562456 0.177146655 0.130259792 0.486625407 5.500068531 0.079336989 0.03852566 70.16072858 -1.84609409 0.152152709 QDMPNAMPVSELTDKLGLQHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDMPNAMPVSELTDKLGLQHLR 22 1 P84085;C9J1Z8 P84085 ARF5 ADP-ribosylation factor 5 0 ; 82.267 0.0026978 756910000 916250 1056100 671680 629910 908950 1187930 859050 763720 908310 777750 FALSE TRUE 880441.937 1025981.062 793067.5174 662419.7306 938187.2022 1211950.759 869563.3109 747948.9151 805202.4567 725072.2998 1.214281579 1.415005183 1.093777155 0.91359128 1.293922279 1.671489531 1.199278074 1.031550806 1.110513334 1 19.46776533 1.846121337 5.058088241 1.055760676 1.264142612 0.212068365 0.187656987 0.399795885 14.56723236 0.094526091 0.054713899 70.16513042 -1.846121337 0.208381936 LYAYEPADTALLLDNMK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYAYEPADTALLLDNMK 17 0 O95994 O95994 AGR2 Anterior gradient protein 2 homolog 0 160.69 1.27E-08 0 67435 72225 52495 60573 63270 59088 68033 76395 85287 82261 FALSE TRUE 64799.56565 70165.21372 61982.01424 63699.17979 65305.13701 60282.79984 68865.6082 74817.41655 75605.57731 76689.3892 0.844961295 0.914927273 0.808221514 0.830612689 0.851553751 0.786064415 0.897980919 0.9755902 0.985867512 1 16.22673936 1.846142327 2.835669122 0.988325079 0.841482796 0.804890608 0.032405919 0.111889916 1.618174465 0.018157358 0.009161093 70.16852178 -1.846142327 -0.146842283 DFS(ph)PVPWSQYFESMEDVEVENETGKDTFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFSPVPWSQYFESMEDVEVENETGKDTFR 29 1 Q9Y570;Q9Y570-4 Q9Y570 PPME1 Protein phosphatase methylesterase 1 1 DFS(0.989)PVPWS(0.011)QYFESMEDVEVENETGKDTFR 123.09 1.56E-05 14274000 54101 48297 41585 57518 44603 49327 61006 64083 84306 72582 TRUE FALSE 51986.67311 46919.61685 49100.33455 60486.51087 46037.696 50324.42574 61752.60968 62759.66366 74735.93632 67665.95649 0.768284021 0.69340063 0.725628323 0.893898705 0.68036718 0.743718531 0.912609721 0.927492448 1.104483557 1 16.04614256 1.846191201 1.501329706 1.040436743 0.749470205 0.758666673 0.066926983 0.185606908 0.788225318 0.048630829 0.020619924 70.17641866 -1.846191201 -0.290966538 NVS(ph)ES(ph)PNRK ddPTM_BT-474_Pertuzumab_2h_R1 4 NVSESPNRK 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNRK;NVS(1)ES(1)PNRK;NVS(1)ES(1)PNRK;NVS(1)ES(1)PNRK 117.27 0.00078802 2414790000 7414060 6340410 5837050 5801520 5838310 5682890 6466290 7658810 8241980 7539450 TRUE FALSE 7124310.339 6159587.715 6891934.779 6100937.142 6026104.543 5797801.929 6545426.391 7500652.897 7306384.984 7028796.336 1.013588956 0.876336064 0.98052845 0.867991737 0.857345163 0.824864124 0.931230054 1.067131915 1.039493056 1 22.74484622 1.846216701 4.903231561 1.03961691 0.900482489 0.529020264 0.055660721 0.16556327 5.770288421 0.026290704 0.015119293 70.18053928 -1.846216701 -0.13913442 SLFGQLHPPDEGHGD ddPTM_BT-474_Pertuzumab_2h_R1 2 SLFGQLHPPDEGHGD 15 0 Q9NY61;A0A087WTH8 Q9NY61 AATF Protein AATF 0 ; 91.969 0.0054235 353520000 172197 194400 145762 192013 192160 195236 181499 61055 171250 167364 FALSE TRUE 165467.3509 188855.9023 172104.4359 201922.8139 198341.0009 199183.8057 183720.2391 59794.19291 151810.4179 156028.2872 1.060495849 1.21039528 1.103033552 1.294142348 1.271186171 1.276587786 1.17748033 0.383226619 0.972967278 1 17.25144808 1.846289197 9.797883053 0.725713153 1.206401115 0.53533166 0.174000659 0.237246804 20.04827202 0.069171496 0.043805109 70.19225529 -1.846289197 0.480687962 EGLEQALPSGKPS(ph)SPVELDLFGDPSPSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPS(0.102)GKPS(0.449)S(0.449)PVELDLFGDPSPSSK;EGLEQALPS(0.006)GKPS(0.497)S(0.497)PVELDLFGDPSPSSK 121.26 1.74E-05 170680000 321993 275606 224418 255724 272171 272942 292145 341236 388367 355880 TRUE FALSE 309409.1576 267745.9867 264975.3248 268921.9463 280925.6274 278461.0742 295720.3579 334189.3574 344281.2063 331775.9306 0.932584703 0.807008472 0.798657468 0.810552911 0.846732995 0.839304629 0.891325532 1.007274267 1.037691932 1 18.3398497 1.846355127 2.278801883 1.023485926 0.834591771 0.823162669 0.036408495 0.111090661 1.078233664 0.022006037 0.010432717 70.20291198 -1.846355127 -0.188894155 SLVESVSS(ph)SPNKESNEEEQVWHFLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 S(0.002)LVES(0.042)VS(0.283)S(0.336)S(0.336)PNKESNEEEQVWHFLGK;S(0.004)LVES(0.084)VS(0.072)S(0.418)S(0.418)PNKES(0.002)NEEEQVWHFLGK 121.26 8.76E-05 9146830000 388710 359520 297660 303490 341980 346850 354650 385970 444660 397700 TRUE FALSE 373518.7835 349266.8416 351453.7834 319153.1553 352980.0973 353863.5446 358990.3128 377999.5846 394184.061 370763.4248 1.007431582 0.942020756 0.947919239 0.860799998 0.952035918 0.954418697 0.968246296 1.019516919 1.06316868 1 18.50013941 1.846528082 1.970403615 1.034886748 0.940229959 0.512295206 0.036403746 0.252248782 1.853251842 0.023965522 0.01087702 70.23087543 -1.846528082 -0.094656789 DDDKNNDGYIDYAEFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDDKNNDGYIDYAEFAK 17 1 Q8NI22-2;Q8NI22-3;Q8NI22 Q8NI22-2 MCFD2 Multiple coagulation factor deficiency protein 2 0 ; 244.1 1.56E-20 1117660000 2296700 1950570 1650400 1671930 1700130 1528640 2177600 2519100 3071600 2732200 FALSE TRUE 2206942.425 1894941.653 1948663.993 1758218.508 1754816.225 1559550.148 2204250.12 2467079.705 2722924.845 2547145.66 0.866437463 0.74394711 0.765038303 0.690270107 0.688934384 0.612273641 0.865380474 0.968566401 1.06901026 1 21.28045003 1.846773554 2.512763963 1.022854587 0.727536438 0.781660467 0.067093103 0.126243396 1.468143947 0.04007461 0.019559703 70.27058263 -1.846773554 -0.295318149 VPLVAEKPLKEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VPLVAEKPLKEPK 13 2 P41250 P41250 GARS Glycine--tRNA ligase 0 123.02 0.0001284 2266200000 1194100 1047600 1014600 1124500 1264900 1018400 1465400 1650000 2104900 1891600 FALSE TRUE 1147433.252 1017723.474 1197960.79 1182535.58 1305586.657 1038992.746 1483334.004 1615926.923 1865960.576 1763480.247 0.65066408 0.577110787 0.679316251 0.670569223 0.74034663 0.589171751 0.84114013 0.916328338 1.058112547 1 20.74999399 1.846886104 1.64849128 1.02229449 0.652139108 0.887898607 0.054551853 0.107262616 0.551853507 0.037265868 0.016116852 70.28879601 -1.846886104 -0.370155381 DEFEFLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DEFEFLEK 8 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 ;; 163.99 0.00077406 144122000 199593 198617 166642 153756 174178 180026 192745 226793 244116 246189 FALSE TRUE 191792.6849 192952.6376 196757.9163 161691.3656 179780.5936 183666.2491 195103.871 222109.6453 216404.9751 229514.3997 0.835645542 0.840699485 0.85727918 0.704493338 0.783308558 0.800238457 0.850072462 0.967737299 0.942881908 1 17.80822515 1.847000204 2.570592808 0.971286998 0.802389667 0.761769084 0.041631608 0.140280618 1.700245575 0.025600145 0.012578825 70.30726494 -1.847000204 -0.168897331 S(ph)PHPDILIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPHPDILIR 9 0 H0Y4T1;Q5T0A6;Q5T0A3;Q86SQ9-3;Q86SQ9-4;Q86SQ9;Q86SQ9-2 H0Y4T1 DHDDS Dehydrodolichyl diphosphate syntase complex subunit DHDDS 1 S(1)PHPDILIR;S(1)PHPDILIR;S(1)PHPDILIR;S(1)PHPDILIR 76.064 0.023504 729470000 15632 17020 18497 24683.4 21854 16064 11608 11314 4734.6 4306.2 TRUE FALSE 15021.08416 16534.60626 21839.81936 25957.31323 22556.95376 16388.82509 11750.06218 11080.36195 4197.148057 4014.537238 3.741672643 4.118682997 5.44018353 6.465829482 5.618817915 4.082369676 2.926878362 2.760059576 1.045487389 1 11.97101798 1.847034317 1.117797888 1.066774562 5.092004408 0.790080409 0.800117167 0.238441624 0.549960469 0.733524476 0.3084986 70.31278781 -1.847034317 4.025229846 KSLS(ph)DSESDDS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.1)LS(0.899)DS(0.01)ES(0.009)DDS(0.983)K 193.96 1.43E-06 762850000 1965000 1444500 1311300 1125200 1461200 1369400 1659100 2201100 2616800 2069400 TRUE FALSE 1888205.628 1403304.274 1548281.08 1183271.707 1508200.825 1397090.206 1679404.562 2155646.516 2319751.835 1929237.695 0.978731461 0.727387962 0.802535159 0.613336402 0.781759982 0.724166965 0.870501632 1.117356623 1.202418883 1 20.87959947 1.847065466 3.041819249 1.12312576 0.765075262 0.698964323 0.097969417 0.127824533 2.089162334 0.051218391 0.026341663 70.31783103 -1.847065466 -0.358050498 KSLSDS(ph)ESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 8 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KSLS(0.213)DS(0.787)ESDDSK;KSLS(0.02)DS(0.978)ES(0.002)DDSK;KSLSDS(0.995)ES(0.005)DDSK;KS(0.003)LS(0.417)DS(0.576)ES(0.005)DDSK;KSLSDS(1)ESDDSK;KSLS(0.009)DS(0.967)ES(0.024)DDSK;KSLS(0.001)DS(0.952)ES(0.046)DDSK;KS(0.014)LS(0.149)DS(0.836)ES(0.001)DDSK 272.74 1.01E-27 34407660000 7239720 5839720 4663750 4805150 4957160 5173690 5900160 6696710 7897100 6753090 TRUE FALSE 6956783.738 5673176.903 5506593.37 5053144.367 5116611.553 5278305.557 5972367.923 6558420.598 7000654.315 6295697.199 1.105006089 0.901119721 0.874659818 0.802634594 0.812715636 0.838398892 0.948642817 1.041730628 1.111974432 1 22.58593472 1.847137827 2.811450409 1.060115085 0.882093543 0.424328162 0.083757915 0.246827174 3.51344498 0.048421318 0.024392544 70.32954812 -1.847137827 -0.178021542 KDS(ph)DTESSDLFTNLNLGR ddPTM_BT-474_Pertuzumab_2h_R1 3 KDSDTESSDLFTNLNLGR 18 1 Q9Y3S2 Q9Y3S2 ZNF330 Zinc finger protein 330 1 KDS(0.957)DT(0.043)ESSDLFTNLNLGR;KDS(0.997)DT(0.003)ESSDLFTNLNLGR;KDS(1)DTESSDLFTNLNLGR 318.32 1.20E-61 1689880000 656410 558030 701900 755060 640350 574200 907350 1036770 1255140 1267040 TRUE FALSE 630756.7715 542115.5308 828748.9437 794028.7371 660947.4393 585810.7174 918454.4207 1015360.337 1112661.769 1181222.252 0.53398653 0.458944563 0.701602888 0.67220943 0.559545368 0.495936066 0.777545817 0.859584498 0.941958016 1 20.17184901 1.847149507 1.765463025 0.957859557 0.575454365 0.818279584 0.077184604 0.150942307 0.891991209 0.055681862 0.024507309 70.33143962 -1.847149507 -0.382405191 TTAPTEGKS(ph)PLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 TTAPTEGKSPLKK 13 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 TTAPTEGKS(1)PLKK;TTAPT(0.004)EGKS(0.996)PLKK 147.09 2.22E-05 3742100000 7100200 4967000 5393400 4237500 5271800 4875800 6084900 7894700 8885000 8084500 TRUE FALSE 6822716.334 4825346.023 6368107.356 4456197.883 5441372.235 4974392.017 6159368.826 7731671.686 7876412.049 7536929.614 0.905238165 0.640227025 0.844920635 0.591248441 0.721961397 0.660002451 0.817225202 1.025838383 1.045042538 1 22.84554549 1.847266306 3.098593105 1.029601072 0.722637813 0.689883373 0.088559324 0.129075181 2.177811286 0.044476055 0.022986287 70.35035704 -1.847266306 -0.306963259 AGPGDRDPPTR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGPGDRDPPTR 11 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 ;; 84.718 0.014367 799390000 615240 722920 515780 649050 638260 647400 595690 504010 559380 514590 FALSE TRUE 591195.7406 702303.0294 608992.9195 682547.5483 658790.2126 660490.8716 602980.2324 493602.0174 495881.5275 479736.361 1.23233465 1.463935375 1.269432482 1.422755505 1.373233855 1.376778842 1.256899167 1.028902659 1.033654248 1 18.87188227 1.847340302 2.567895839 1.014191689 1.360900165 0.845641357 0.06403207 0.090071897 1.08938142 0.033722014 0.016569065 70.36234447 -1.847340302 0.346708475 IKFSDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IKFSDDR 7 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 73.208 0.04516 570510000 1304600 1554600 1157600 1510700 1385100 1483800 1345300 1197800 1252500 1349200 FALSE TRUE 1253614.79 1510264.33 1366804.071 1588667.408 1429652.999 1513803.453 1361764.184 1173065.011 1110321.451 1257817.482 0.996658742 1.200702289 1.086647379 1.263034924 1.136614032 1.20351599 1.082640529 0.932619421 0.882736539 1 20.26249116 1.847461153 3.195918084 0.929463821 1.15191517 0.617631024 0.073306564 0.146203352 2.600763471 0.03669019 0.019114245 70.38192702 -1.847461153 0.22245135 VLLSLEHGLWAPNLHFHS(ph)PNPEIPALLDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR 30 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 VLLS(0.165)LEHGLWAPNLHFHS(0.835)PNPEIPALLDGR 56.156 0.023892 155450000 17956 20613 26071 28950 23528 29486 24310 7754.4 26015 13231 TRUE FALSE 17254.25967 20025.13742 30782.60965 30444.11297 24284.79949 30082.22712 24607.51305 7594.26893 23061.88626 12334.85259 1.398821717 1.623459809 2.495579857 2.468137561 1.968795275 2.438799079 1.994958017 0.615675694 1.869652361 1 13.59045285 1.847541885 7.886488498 1.143553045 2.087803603 0.45984757 0.443583908 0.23732873 15.31257154 0.191910004 0.119343241 70.39501162 -1.847541885 0.944250558 FKDLEDK ddPTM_BT-474_Pertuzumab_2h_R1 3 FKDLEDK 7 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ;; 127.46 0.0035135 2623470000 6103850 5252100 4665530 4593540 5227130 5188590 5807940 6769440 7910240 7231500 FALSE TRUE 5865304.794 5102315.25 5508695.055 4830613.15 5395265.384 5293506.845 5879019.307 6629648.698 7012302.718 6741704.064 0.870003302 0.756828719 0.817107218 0.716527024 0.800282144 0.785188254 0.872037582 0.983378777 1.04013802 1 22.68468187 1.847581024 1.966731606 1.021329386 0.786783441 0.861981929 0.038888986 0.101769725 0.744602159 0.023921234 0.010860428 70.40135594 -1.847581024 -0.234545946 DLNES(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLNESPVK 8 0 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 DLNES(1)PVK;DLNES(1)PVK;DLNES(1)PVK;DLNES(1)PVK 146.79 0.00057453 3820640000 3876600 3341100 3205280 2979640 3022010 2833910 3384890 4067500 4314360 3990780 TRUE FALSE 3725098.186 3245815.099 3784545.397 3133419.577 3119215.696 2891213.602 3426315.296 3983504.704 3824611.94 3720480.916 1.001241041 0.872418156 1.017219409 0.842208211 0.838390457 0.777107494 0.920933442 1.07069618 1.027988592 1 21.82705769 1.847730953 5.222371871 1.036784017 0.888731204 0.446841245 0.070317763 0.201566896 7.643528372 0.033543048 0.019559294 70.4256645 -1.847730953 -0.148052813 GQKPEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 GQKPEQR 7 1 Q92522 Q92522 H1FX Histone H1x 0 ;;; 80.18 0.027919 474645000 1442740 1180760 1132330 990360 1331470 1061560 1067720 1103470 845810 1023580 FALSE TRUE 1386356.126 1147085.881 1336967.22 1041472.598 1374297.942 1083025.471 1080787.077 1080682.959 749797.1947 954252.0149 1.4528197 1.202078553 1.40106303 1.091402043 1.440183432 1.134947009 1.132601304 1.132492195 0.785743371 1 19.8640108 1.847792306 0.969165521 0.918035907 1.304308586 0.571664123 0.129848727 0.382172625 0.662819598 0.102688182 0.04463426 70.43561425 -1.847792306 0.386272679 SGGSGHAVAEPAS(ph)PEQELDQNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGGSGHAVAEPASPEQELDQNK 22 0 P46013 P46013 MKI67 Antigen KI-67 1 SGGSGHAVAEPAS(1)PEQELDQNK 162.75 1.02E-11 512160000 293930 258320 225650 314430 323150 207620 233280 255190 180540 207700 TRUE FALSE 282442.8906 250952.9665 266429.9746 330657.77 333544.4132 211818.2187 236134.9504 249920.2373 160045.8561 193632.294 1.458655913 1.296028474 1.375958364 1.707658176 1.722566037 1.093919895 1.2195019 1.290695019 0.826545267 1 17.56296006 1.847906416 0.948759619 0.959842895 1.479303166 0.547367123 0.182878887 0.468436519 0.779484402 0.166793225 0.073022873 70.45412344 -1.847906416 0.519460271 NS(ph)RDGDPLPSSLSCK ddPTM_BT-474_Pertuzumab_2h_R1 5 NSRDGDPLPSSLSCK 15 1 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 NS(1)RDGDPLPSSLSCK;NS(0.994)RDGDPLPS(0.005)S(0.001)LSCK;NS(1)RDGDPLPSSLSCK;NS(1)RDGDPLPSSLSCK;NS(0.915)RDGDPLPS(0.028)S(0.056)LSCK 254.24 6.57E-25 4292950000 3854330 3335830 2700240 3064630 3358170 3394250 3411680 3906070 4393370 3909560 TRUE FALSE 3703698.522 3240695.395 3188233.435 3222795.922 3466188.588 3462884.061 3453433.16 3825408.29 3894653.056 3644762.019 1.016170193 0.889137721 0.874743925 0.884226708 0.951005462 0.950098811 0.947505802 1.049563255 1.068561688 1 21.79739319 1.847926673 2.737583724 1.046143801 0.92289334 0.579451176 0.042442067 0.180267408 2.4459225 0.024325364 0.012173046 70.45740969 -1.847926673 -0.123250461 DDEENYLDLFSHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDEENYLDLFSHK 13 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ; 225.32 1.26E-11 1082600000 1023500 878080 810960 826040 961200 892890 963460 1066270 1201370 1136450 FALSE TRUE 983500.4885 853038.0181 957518.5117 868672.0234 992117.8709 910944.8476 975251.1117 1044251.152 1064995.514 1059477.229 0.928288463 0.805149931 0.903765069 0.81990627 0.93642208 0.859805971 0.920502192 0.985628688 1.005208498 1 20.01492115 1.847988898 1.963511183 1.00392402 0.87298258 0.650293493 0.039791826 0.180866094 1.318832573 0.023712703 0.010764179 70.46750554 -1.847988898 -0.13094144 EQLDSSNSTIAILQTEKDKLELEITDSKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQLDSSNSTIAILQTEKDKLELEITDSKK 29 3 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 195.51 2.04E-25 420370000 331140 248290 196313 172197 236540 256180 253130 323630 375370 292750 FALSE TRUE 318198.6827 241209.0123 231791.1261 181084.1078 244148.5239 261360.1351 256227.8807 316946.9274 332759.5713 272921.7817 1.165896986 0.883802717 0.849295079 0.663501853 0.894573245 0.957637509 0.938832654 1.161310487 1.21924886 1 18.05812801 1.848087725 3.087073556 1.144566349 0.890083484 0.381229367 0.126994209 0.245795627 4.118291148 0.070105805 0.036219599 70.48354276 -1.848087725 -0.254482866 S(ph)GTPTQDEMMDKPTSSSVDTMSLLSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SGTPTQDEMMDKPTSSSVDTMSLLSK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.456)GT(0.403)PT(0.118)QDEMMDKPT(0.006)S(0.008)S(0.009)SVDTMSLLSK;S(0.492)GT(0.492)PT(0.017)QDEMMDKPTSSSVDTMSLLSK;S(0.362)GT(0.328)PT(0.298)QDEMMDKPT(0.003)S(0.004)S(0.004)S(0.001)VDTMSLLSK;S(0.345)GT(0.305)PT(0.345)QDEMMDKPT(0.002)S(0.002)S(0.001)SVDTMSLLSK 89.793 0.016529 2247000000 2306030 1649740 1515440 1264870 1560300 1624440 1769590 2415640 2600600 2115070 TRUE FALSE 2215907.798 1602691.03 1789313.719 1330150.092 1610488.467 1657287.29 1791246.772 2365756.19 2305390.791 1971814.425 1.12379125 0.812800135 0.907445293 0.674581784 0.816754582 0.84048847 0.908425635 1.19978643 1.169172292 1 20.91109235 1.848092776 4.691251303 1.138403473 0.853683418 0.498898085 0.116506862 0.166603485 5.426098546 0.054366167 0.031001468 70.48436255 -1.848092776 -0.284720055 AGAEDDEEKGEGT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGAEDDEEKGEGTPR 15 1 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 AGAEDDEEKGEGT(1)PR 79.013 0.034282 527610000 129570 109590 137920 129220 129620 124180 147050 203190 219840 204340 TRUE FALSE 124506.2612 106464.6005 162845.212 135889.0597 133789.345 126691.0047 148849.6419 198994.0555 194884.6848 190499.8698 0.653576621 0.558869676 0.854831094 0.713328885 0.702306753 0.665045099 0.781363484 1.044588932 1.023017418 1 17.53943049 1.848119101 3.36101366 1.027294655 0.695339092 0.815864904 0.070217558 0.099854974 1.933195143 0.037651019 0.019871117 70.48863509 -1.848119101 -0.331955563 KDEDPENKIEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEDPENKIEFK 12 2 Q13123;E7EQZ7;D6REL4 Q13123 IK Protein Red 0 ; 99.011 0.0022703 346360000 869040 660880 572160 447550 597450 583070 664630 792790 941810 720970 FALSE TRUE 835076.956 642032.3495 675562.0396 470648.1091 616667.5218 594860.0749 672763.9408 776418.6095 834899.6772 672138.0597 1.242418792 0.955209038 1.005094162 0.700225352 0.917471512 0.88502662 1.000931179 1.155147515 1.242155038 1 19.35839807 1.848215175 3.614359995 1.148476077 0.940829317 0.25385401 0.137213198 0.297376135 6.490505292 0.070743391 0.038002121 70.50423026 -1.848215175 -0.20764676 VSGEEELHTGPPAPQGPLSVPQGLPTQS(ph)LASPPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSGEEELHTGPPAPQGPLSVPQGLPTQSLASPPAR 35 0 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 VSGEEELHTGPPAPQGPLSVPQGLPT(0.031)QS(0.584)LAS(0.385)PPAR 138.84 1.12E-09 654620000 64950 77049 68061 79776 78549 74919 66232 61563 54909 62883 TRUE FALSE 62411.68219 74851.63796 80361.13671 83893.24892 81075.59992 76433.91351 67042.56703 60291.70254 48675.96052 58623.8784 1.064611962 1.276811429 1.370791884 1.431042285 1.382979123 1.30380172 1.143605112 1.02844957 0.830309455 1 15.8392008 1.848407493 1.787188845 0.921992232 1.316702724 0.704481006 0.102786472 0.190676207 1.15420971 0.072869555 0.032211654 70.53545846 -1.848407493 0.394710493 KSSSISEEKGDS(ph)DDEKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 KSSSISEEKGDSDDEKPR 18 3 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KSSSISEEKGDS(1)DDEKPR;KSSSISEEKGDS(1)DDEKPR;KSSSISEEKGDS(1)DDEKPR 175.47 2.34E-12 4067440000 3429420 2348300 1860880 1392890 2116420 1904000 2206880 2934410 3139620 2135970 TRUE FALSE 3295394.475 2281328.783 2197182.411 1464777.22 2184496.571 1942500.185 2233888.458 2873813.408 2783223.5 1991298.849 1.654896991 1.145648622 1.103391594 0.735588845 1.097020958 0.975494053 1.121824812 1.443185391 1.397692517 1 20.92527832 1.848648441 7.594098095 1.323407516 1.097140085 0.073089255 0.241585662 0.519089387 31.73270359 0.105012319 0.065046468 70.57460256 -1.848648441 -0.226267431 RT(ph)T(ph)RY(ph)DIDMT(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 RTTRYDIDMTK 11 2 O00217;E9PPW7;E9PKH6 O00217 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" 4 RT(1)T(1)RY(1)DIDMT(1)K 42.599 0.06361 458320000 8446 19163 20619 22250 23046 23105 18517 14482 15137 17117 TRUE FALSE 8115.920982 18616.49 24345.31197 23398.32517 23787.29552 23572.19893 18743.61659 14182.94164 13418.71122 15957.65034 0.508591228 1.166618493 1.525620091 1.466276342 1.490651506 1.477172292 1.174584991 0.88878634 0.840895178 1 13.96196062 1.848653391 3.674855851 0.899439516 1.299413879 0.240862831 0.284019712 0.329873106 7.393260242 0.151320965 0.081633338 70.57540698 -1.848653391 0.399974363 S(ph)PAKEEAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPAKEEAAK 9 1 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 S(1)PAKEEAAK;S(1)PAKEEAAK;S(1)PAKEEAAK 94.767 0.007271 459130000 2303840 1929521 1723394 1781958 1888955 2036032 2243298 2384135 2783710 2755990 TRUE FALSE 2213803.386 1874492.95 2034849.632 1873925.066 1949714.953 2077201.962 2270752.152 2334901.779 2467714.911 2569324.343 0.861628619 0.729566493 0.791978498 0.729345468 0.758843452 0.808462337 0.883793499 0.908761008 0.960452859 1 21.29295759 1.848757404 1.047705984 0.987176394 0.768766269 0.826590468 0.037580316 0.188248326 0.380891487 0.030125879 0.012829191 70.59231174 -1.848757404 -0.218410125 IVDDLKDEAEQYR ddPTM_BT-474_Pertuzumab_2h_R1 3 IVDDLKDEAEQYR 13 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 152 3.84E-05 1695610000 1268320 1168710 1093820 1204150 1250060 1154050 1259060 1516850 1603380 1498100 FALSE TRUE 1218752.652 1135379.535 1291497.606 1266296.326 1290269.315 1177385.682 1274468.753 1485526.517 1421371.024 1396632.353 0.872636703 0.812940881 0.924722676 0.906678356 0.92384321 0.84301762 0.91252988 1.063648937 1.017713088 1 20.41352087 1.84911523 4.883267704 1.03049168 0.882541543 0.767776786 0.036023163 0.102121265 3.514183692 0.017196806 0.009896452 70.6504984 -1.84911523 -0.147950137 QQLSAEELDAQLDAYNAR ddPTM_BT-474_Pertuzumab_2h_R1 4 QQLSAEELDAQLDAYNAR 18 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ;;; 425.39 2.08E-168 708820000 618065 624461 578251 561204 599163 587447 524628 616805 554594 556768 FALSE TRUE 593910.3365 606651.9837 682753.8188 590167.8057 618435.622 599325.5808 531048.5544 604067.7612 491638.8142 519057.6074 1.144208905 1.16875656 1.315371953 1.136998663 1.191458546 1.154641743 1.02310138 1.163777878 0.947175818 1 18.98553514 1.849262823 0.689924233 0.989782975 1.202635105 0.553547302 0.067843527 0.525209752 0.492042816 0.060410937 0.031743134 70.67451279 -1.849262823 0.21285213 EKEDPEPSTDGTYVWK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEDPEPSTDGTYVWK 16 1 Q9UHG3;Q9UHG3-2 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 82.007 0.01021 418380000 103860 110650 108850 125710 85705 119460 118020 136210 144260 151940 FALSE TRUE 99801.03638 107494.3703 128521.6164 132197.9082 88461.77916 121875.563 119464.3641 133397.2159 127884.2096 141648.9685 0.704565924 0.758878596 0.90732476 0.933278298 0.624514108 0.860405581 0.843383227 0.941745057 0.902824856 1 17.11196057 1.849359562 1.513313346 0.957471383 0.798012024 0.37166762 0.088384375 0.460791238 1.987932535 0.066283343 0.028213153 70.6902572 -1.849359562 -0.159459359 SGDET(ph)PGSEVPGDK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 SGDET(1)PGSEVPGDK;SGDET(1)PGSEVPGDK;SGDET(1)PGSEVPGDK 272.77 6.08E-32 961170000 1567670 1461870 1296300 1309140 1349360 1320140 1426990 1674820 1820780 1484370 TRUE FALSE 1506403.723 1420178.899 1530570.246 1376704.872 1392763.39 1346834.135 1444453.93 1640234.382 1614092.688 1383832.298 1.088573901 1.026265178 1.106037378 0.994849502 1.006453883 0.973263984 1.043807066 1.185284073 1.166393276 1 20.40023769 1.849701812 7.163562674 1.134856661 1.031028572 0.274296877 0.059982704 0.257753301 14.57782028 0.025325237 0.015579669 70.7459873 -1.849701812 -0.103828089 APTQTPTQTIILNS(ph)DDETLATLHTALQSSHGVLGPER ddPTM_BT-474_Pertuzumab_2h_R1 1 APTQTPTQTIILNSDDETLATLHTALQSSHGVLGPER 37 0 Q9H4Z2-2;Q9H4Z2 Q9H4Z2-2 ZNF335 Zinc finger protein 335 1 APTQTPTQTIILNS(0.964)DDET(0.034)LAT(0.001)LHT(0.001)ALQSSHGVLGPER 72.348 0.0064181 39826000 9970.5 13789 9466.5 12820 11952 11689 11524 8208.1 11492 10239 TRUE FALSE 9580.841837 13395.75122 11177.30713 13481.64174 12336.44693 11925.35959 11665.03416 8038.599867 10187.47634 9545.50341 1.003702102 1.40335723 1.170949991 1.412355238 1.292383063 1.24931699 1.222044942 0.842134723 1.067253962 1 13.22060557 1.849749326 6.139887213 0.961224665 1.263971894 0.530707914 0.120934753 0.156957964 7.323695278 0.050077794 0.030114236 70.75372771 -1.849749326 0.302747229 VSIVNHLEFLRDEELEER ddPTM_BT-474_Pertuzumab_2h_R1 1 VSIVNHLEFLRDEELEER 18 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 125.73 1.75E-05 26236000 20497 24368 13656 19475 19822 21135 18828 12968 16235 16919 FALSE TRUE 19695.95458 23673.0485 16123.94298 20480.10708 20459.59263 21562.36418 19058.4227 12700.20627 14392.07086 15773.06106 1.248708447 1.500853158 1.022245645 1.298423116 1.297122515 1.367037387 1.208289413 0.805183358 0.912446278 1 13.94517505 1.849810662 4.851470644 0.894046692 1.286911273 0.669766729 0.120349647 0.122357244 4.165819033 0.054727942 0.031462956 70.76372111 -1.849810662 0.392864581 LYFHSDTCLPLRPQEMEVDS(ph)EDEKDPEWLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LYFHSDTCLPLRPQEMEVDSEDEKDPEWLR 30 2 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR;LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR;LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR 364.74 7.47E-137 1571660000 1179110 1068150 813010 893220 1056970 1022920 1043040 1167660 1296080 1233030 TRUE FALSE 1133029.078 1037687.408 959938.9923 939319.1912 1090968.4 1043604.143 1055805.036 1143547.413 1148954.432 1149515.78 0.985657698 0.902716975 0.835081179 0.817143364 0.949067789 0.90786413 0.918478071 0.99480793 0.999511666 1 20.13259484 1.849919785 1.515106149 1.006622599 0.892369086 0.474137001 0.046146854 0.345716488 1.494949639 0.035639222 0.015179476 70.78150379 -1.849919785 -0.114253513 HSLYTAELITVPFDSES(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSLYTAELITVPFDSESPIR 20 0 A0A075B754;Q96QE3-2;Q96QE3 A0A075B754 ATAD5 ATPase family AAA domain-containing protein 5 1 HSLYTAELITVPFDS(0.035)ES(0.965)PIR;HSLYTAELITVPFDS(0.205)ES(0.795)PIR 68.129 0.013821 219692000 237010 242040 209170 245160 239080 222390 220500 165538 176601 187143 TRUE FALSE 227747.3872 235137.2562 246971.672 257812.737 246770.2253 226886.8782 223198.545 162119.5825 156553.9949 174467.6379 1.305384711 1.347741386 1.415572968 1.477710939 1.414418331 1.300452513 1.279312012 0.929224379 0.897323978 1 17.41259993 1.85015406 2.424852635 0.923051454 1.383880584 0.91914782 0.057599223 0.074146671 0.806017008 0.036281445 0.01757376 70.81969623 -1.85015406 0.46082913 YS(ph)PSQNSPIHHIPSRR ddPTM_BT-474_Pertuzumab_2h_R1 4 YSPSQNSPIHHIPSRR 16 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 YS(0.982)PS(0.018)QNSPIHHIPSRR;Y(0.005)S(0.994)PS(0.001)QNSPIHHIPSRR;YS(0.82)PS(0.18)QNSPIHHIPSRR;YS(0.5)PS(0.5)QNSPIHHIPSRR 170.38 2.49E-09 2533720000 803650 1179170 736100 1103542 1085028 1164200 936970 474716 677331 722982 TRUE FALSE 772242.4695 1145541.226 869129.6445 1160495.935 1119928.911 1187740.922 948436.9191 464912.9487 600443.2245 674013.7852 1.145736907 1.699581301 1.289483485 1.721768843 1.661581611 1.762190845 1.407147658 0.689767715 0.890847098 1 19.36241857 1.850201403 4.817830756 0.843271026 1.556435894 0.703977353 0.199158833 0.111072231 3.741777346 0.090242227 0.051814102 70.82741679 -1.850201403 0.713164869 TSQVGAASAPAKES(ph)PRK ddPTM_BT-474_Pertuzumab_2h_R1 4 TSQVGAASAPAKESPRK 17 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 TSQVGAASAPAKES(1)PRK;TSQVGAASAPAKES(1)PRK;TSQVGAASAPAKES(1)PRK;TSQVGAASAPAKES(1)PRK 215.42 2.93E-15 4252640000 3937060 3186200 2823700 2399000 3057740 2972040 3306560 3830840 4316480 3995340 TRUE FALSE 3783195.343 3095332.696 3334005.403 2522812.677 3156094.984 3032136.685 3347026.67 3751731.815 3826491.287 3724732.063 1.015695969 0.831021572 0.895099391 0.677313867 0.847334769 0.81405498 0.898595285 1.007248777 1.027319877 1 21.82870522 1.85048417 2.777334962 1.016025747 0.840834075 0.465333406 0.078622066 0.228688555 3.178660758 0.043879679 0.02208815 70.8735473 -1.85048417 -0.175191673 NKPGPNIES(ph)GNEDDDASFK ddPTM_BT-474_Pertuzumab_2h_R1 9 NKPGPNIESGNEDDDASFK 19 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK 292.36 8.54E-50 73492280000 13468882 9993551 9589276 8036142 9642920 9129075 10800897 13579230 15150770 12836900 TRUE FALSE 12942503.2 9708544.71 11322271.49 8450888.252 9953093.279 9313671.151 10933081.61 13298814.16 13430918.11 11967445.33 1.081475858 0.811246214 0.946089259 0.706156412 0.831680698 0.77825057 0.913568544 1.111249209 1.122287818 1 23.51261188 1.850503035 4.04265933 1.086789101 0.852371627 0.485565418 0.100183506 0.178176277 4.633587993 0.048062575 0.026544935 70.876626 -1.850503035 -0.234417474 T(ph)AS(ph)PPPPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 TASPPPPPK 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 T(1)AS(1)PPPPPK;T(1)AS(1)PPPPPK;T(1)AS(1)PPPPPK;T(1)AS(1)PPPPPK 113.67 0.0093511 5259580000 5584670 5086740 4459290 4565410 4615660 4762030 5067530 5614070 6255390 5725370 TRUE FALSE 5366414.922 4941671.156 5265182.899 4801031.357 4764126.896 4858321.509 5129547.948 5498137.493 5545304.352 5337585.59 1.005401193 0.925825183 0.986435311 0.899476229 0.892562155 0.910209575 0.961024018 1.030079499 1.03891624 1 22.34775587 1.850559448 3.611248596 1.025836139 0.934771513 0.544987062 0.03512098 0.176735146 3.844833595 0.018389166 0.00989183 70.8858331 -1.850559448 -0.091064626 DSGRGDS(ph)VSDSGSDALR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 DSGRGDS(0.358)VS(0.261)DS(0.143)GS(0.237)DALR;DSGRGDS(0.704)VS(0.113)DS(0.141)GS(0.041)DALR 121.26 0.00015999 418930000 530570 637240 423340 539320 582190 515230 428930 467570 416570 384170 TRUE FALSE 509834.7378 619066.5391 499846.9551 567154.3698 600916.6701 525648.3036 434179.3736 457914.5161 369282.72 358149.8237 1.423523632 1.728512757 1.395636468 1.583567357 1.677836007 1.467677125 1.212284203 1.278555749 1.031084467 1 18.45020371 1.850604303 1.007459872 1.016580202 1.568718262 0.776567848 0.112455052 0.233097981 0.436183374 0.09183239 0.039523169 70.8931547 -1.850604303 0.55213806 EAHLEKEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAHLEKEEK 9 1 A0A1W2PRI9;E9PNW5 A0A1W2PRI9 C4orf50 0 ;;; 63.397 0.045864 3258620000 4687360 3042900 3082600 2445350 3497980 3196560 3670090 4315330 5159180 4305550 FALSE TRUE 4504172.789 2956119.471 3639694.392 2571554.807 3610495.703 3261196.633 3715005.659 4226216.927 4573531.515 4013931.264 1.122135008 0.736464896 0.906765501 0.64065741 0.899491164 0.812469477 0.925527971 1.05288722 1.139414508 1 21.93658448 1.850621031 2.559748168 1.07703806 0.842933925 0.370971155 0.122056671 0.263399956 3.160966555 0.066309625 0.032635599 70.89588538 -1.850621031 -0.234104135 TT(ph)PLGGLGPGEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPLGGLGPGEAR 13 0 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 T(0.194)T(0.806)PLGGLGPGEAR 108.91 0.013177 187760000 146140 140580 135450 158810 136070 151350 153370 188100 194670 188540 TRUE FALSE 140428.6872 136570.796 159928.8281 167006.2031 140446.8151 154410.4007 155246.9879 184215.6693 172571.8777 175770.0179 0.798934249 0.776985732 0.909875473 0.950140446 0.799037383 0.878479746 0.883239302 1.048049443 0.981804973 1 17.42332948 1.850632273 4.601210752 1.011606909 0.855487138 0.644130692 0.052494885 0.147341932 4.645177138 0.026343508 0.014979782 70.89772063 -1.850632273 -0.156119771 VEVTEFEDIK ddPTM_BT-474_Pertuzumab_2h_R1 8 VEVTEFEDIK 10 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;;;; 208.22 2.74E-07 5262056000 8254550 7330320 6495090 6231060 7196400 6982480 7425030 8868680 9665070 8411480 FALSE TRUE 7931953.06 7121266.451 7668897.245 6552645.753 7427878.742 7123670.53 7515899.738 8685538.659 8567931.773 7841762.967 1.011501252 0.908120595 0.977955758 0.83560875 0.947220513 0.908427169 0.958445157 1.107600255 1.092602749 1 22.9027466 1.850637167 4.790277806 1.075068936 0.929370408 0.580914769 0.051284926 0.13772566 4.59845839 0.022868681 0.013117429 70.89851966 -1.850637167 -0.145698529 S(ph)SPGAGPSDHHSASR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPGAGPSDHHSASR 15 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR 200.71 4.37E-09 1411273900 359732.6 653450.3 483052.3 769187.8 543304.3 669183.4 567327.1 160105.58 399022.9 538682.6 TRUE FALSE 345673.8523 634814.5372 570350.5961 808885.6745 560780.1762 682714.7468 574270.2188 156799.3438 353727.4932 502197.1477 0.68832301 1.264074358 1.135710544 1.610693486 1.116653447 1.359455644 1.143515493 0.312226671 0.704359821 1 18.93789431 1.850790387 7.191467371 0.612679118 1.213279088 0.431264736 0.26884693 0.197938319 11.17619423 0.112108309 0.069020867 70.92353713 -1.850790387 0.60059997 LEYGDNAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEYGDNAEK 9 0 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 114.5 0.0044578 0 75502 69190 79691 70965 74485 73716 79709 93633 96084 104360 FALSE TRUE 72551.29837 67216.76894 94092.93642 74627.51215 76880.87767 75206.58803 80684.50259 91699.44583 85176.94714 97291.60425 0.745709755 0.690879439 0.967122879 0.767049868 0.790210813 0.773001829 0.829305912 0.942521675 0.875480961 1 16.57002769 1.851064524 3.310359883 0.933194677 0.791903789 0.462673127 0.072204415 0.235586229 4.437298069 0.037605629 0.019814022 70.96831991 -1.851064524 -0.141290888 FVHFIDAPSLALIMPIVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FVHFIDAPSLALIMPIVQR 19 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 167.05 1.87E-11 266720000 181663 207731 158100 183125 190917 222800 192543 183152 206800 207508 FALSE TRUE 174563.4091 201806.7153 186672.1869 192576.1032 197058.0187 227305.1687 194899.3988 179369.8472 183324.931 193453.2983 0.902354267 1.043180535 0.964947036 0.995465597 1.018633543 1.1749873 1.007475192 0.927199736 0.94764438 1 17.5616258 1.851187659 6.61765133 0.952288047 1.020511375 0.128480463 0.067112167 0.440740784 22.44336344 0.030256991 0.018419004 70.98844435 -1.851187659 0.068223328 KTVEDEDQDS(ph)EEEKDNDSYIK ddPTM_BT-474_Pertuzumab_2h_R1 4 KTVEDEDQDSEEEKDNDSYIK 21 2 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 KTVEDEDQDS(1)EEEKDNDSYIK;KTVEDEDQDS(1)EEEKDNDSYIK;KTVEDEDQDS(1)EEEKDNDSYIK;KTVEDEDQDS(1)EEEKDNDSYIK 291.08 5.24E-55 1194850000 1647270 1169650 1060690 818170 1206630 1029690 1267280 1816990 1935830 1572190 TRUE FALSE 1582892.867 1136292.727 1252380.278 860395.8517 1245442.35 1050511.037 1282789.352 1779468.522 1716082.694 1465704.171 1.079953853 0.775253799 0.854456379 0.587018765 0.849722867 0.716727876 0.875203453 1.214070722 1.170824733 1 20.48316252 1.851267326 4.717250817 1.143875217 0.802431854 0.550975748 0.128051833 0.150651932 4.916427636 0.058703547 0.033572904 71.00146773 -1.851267326 -0.341443362 SLKNEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLKNEPR 7 1 Q13393-3;Q13393-4;Q13393-2;Q13393;F8WBV7;C9IY79 Q13393-3 PLD1 Phospholipase D1 0 67.032 0.060432 260030000 397620 456010 287520 354510 375030 413060 369740 357810 389340 376760 FALSE TRUE 382080.5708 443005.0413 339481.2598 372806.3036 387093.1805 421412.3562 374264.9887 350421.0985 345143.7554 351241.7096 1.087799542 1.261254086 0.966517502 1.061395311 1.102070654 1.199778798 1.065548249 0.997663685 0.982638867 1 18.42210465 1.851364433 3.529192182 0.99286375 1.111534399 0.339080388 0.074186391 0.28529239 5.974820853 0.038555283 0.020636987 71.0173452 -1.851364433 0.118670648 MSDLTPVHFTPLDSSVDR ddPTM_BT-474_Pertuzumab_2h_R1 4 MSDLTPVHFTPLDSSVDR 18 0 Q9Y314;A0A075B6F9;M0R3B2 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 0 ;;; 210.39 4.17E-16 637030000 380828 485266 399563 442137 418533 439998 434903 414417 437555 504150 FALSE TRUE 365944.8207 471426.6888 471772.9223 464955.7436 431995.494 448895.061 440225.473 405859.1441 387885.5908 470003.4714 0.778600251 1.0030281 1.003764761 0.989260233 0.91913256 0.95508882 0.936643024 0.863523716 0.825282395 1 18.84231189 1.851594946 5.422689139 0.882993471 0.947967026 0.057891361 0.07405962 0.453753242 17.90696549 0.032650319 0.019215409 71.05504945 -1.851594946 0.064973554 TENNDHINLK ddPTM_BT-474_Pertuzumab_2h_R1 8 TENNDHINLK 10 0 P61956;P61956-2 P61956 SUMO2 Small ubiquitin-related modifier 2 0 ;;;;;;; 189.57 9.96E-07 24991530000 36692800 35894500 29915700 31565700 33542700 34119800 34802000 38222500 42288300 38906700 FALSE TRUE 35258804.81 34870824 35322132.46 33194809.56 34621631.41 34809725.73 35227917.29 37433192.02 37487909.47 36271514.55 0.97207975 0.96138318 0.973825684 0.915175723 0.954512979 0.95969871 0.971228186 1.032027267 1.033535818 1 25.11233365 1.851667493 3.609668381 1.024740214 0.955744674 0.736484117 0.017551972 0.115384348 2.506404113 0.009084837 0.004889979 71.06691983 -1.851667493 -0.06899554 GHRPVS(ph)PAPGASGLRPCLWQLETELR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHRPVSPAPGASGLRPCLWQLETELR 26 2 Q13129 Q13129 RLF Zinc finger protein Rlf 1 GHRPVS(1)PAPGASGLRPCLWQLETELR;GHRPVS(1)PAPGASGLRPCLWQLETELR 206.58 1.54E-25 334930000 54105 66190 47516 59576 54741 57903 56005 40207 61437 42738 TRUE FALSE 51990.51678 64302.32601 56103.19819 62650.7245 56501.79398 59073.83833 56690.40594 39376.7114 54462.92932 39843.31719 1.304874203 1.613879831 1.408095564 1.572427421 1.418099645 1.482653617 1.422833487 0.988288982 1.366927584 1 15.28205014 1.851695119 6.219331467 1.127288541 1.470997613 0.608164522 0.125984281 0.141320998 6.648660338 0.050758852 0.030609598 71.07144069 -1.851695119 0.343709073 ERS(ph)PSPSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 ERS(0.998)PS(0.002)PSFR;ERS(0.959)PS(0.041)PSFR 81.565 0.01267 381840000 66690 72120 72889 80573 74701 88318 71833 72641 74585 73827 TRUE FALSE 64083.68107 70063.20821 86061.66371 84731.38219 77103.82551 90103.85047 72712.11374 71140.93797 66118.42349 68826.63153 0.931088441 1.017966544 1.250412257 1.231084252 1.1202615 1.309142238 1.05645318 1.033625159 0.960651742 1 16.07067928 1.851771161 2.960334535 0.996296462 1.146516561 0.265527385 0.106401188 0.367201124 5.707537017 0.061108141 0.031316324 71.08388582 -1.851771161 0.150220098 ESGVVAVS(ph)PEKS(ph)ESPQKEDGLSSQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESGVVAVSPEKSESPQKEDGLSSQLK 26 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 2 ESGVVAVS(0.999)PEKS(0.563)ES(0.437)PQKEDGLSSQLK 93.043 0.0048397 389890000 391740 307090 297770 208820 352390 302810 350630 409720 515190 398810 TRUE FALSE 376430.3677 298332.0939 351583.6629 219597.2252 363724.9444 308933.0257 354921.1148 401259.1388 456707.7911 371798.2435 1.012458704 0.802403183 0.945630242 0.590635456 0.978285806 0.830915775 0.954606755 1.079238931 1.228375333 1 18.50416043 1.851871571 2.267360895 1.123120551 0.854281317 0.43911798 0.122132832 0.250059211 2.396663383 0.070022408 0.033296129 71.10032253 -1.851871571 -0.268839234 AVPAPSPGPTHNS(ph)PELGRPPAAGVLAPDMSDKDK ddPTM_BT-474_Pertuzumab_2h_R1 5 AVPAPSPGPTHNSPELGRPPAAGVLAPDMSDKDK 34 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 AVPAPSPGPTHNS(1)PELGRPPAAGVLAPDMSDKDK;AVPAPSPGPT(0.053)HNS(0.947)PELGRPPAAGVLAPDMSDKDK;AVPAPS(0.001)PGPT(0.07)HNS(0.929)PELGRPPAAGVLAPDMSDKDK;AVPAPS(0.01)PGPT(0.034)HNS(0.948)PELGRPPAAGVLAPDMS(0.008)DKDK;AVPAPS(0.003)PGPT(0.214)HNS(0.783)PELGRPPAAGVLAPDMSDKDK 254.78 8.81E-60 2883840000 1479340 1270810 1173499 1047495 1332199 1369871 1585470 1668209 2104520 2017880 TRUE FALSE 1421525.757 1234567.743 1385576.374 1101556.342 1375050.391 1397570.73 1604873.456 1633759.901 1865623.712 1881207.19 0.755645505 0.656263568 0.736535763 0.585558225 0.730940429 0.742911646 0.853108294 0.868463564 0.991716235 1 20.84322732 1.851922503 0.948406201 1.002297088 0.683828499 0.853346674 0.049088266 0.183995437 0.305841429 0.040109141 0.017600141 71.1086614 -1.851922503 -0.318468589 MIIEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 4 MIIEEAKR 8 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 133.58 0.0014643 1374160000 1163470 1226880 922770 976000 1201160 1057450 1387920 1330890 1605630 1618080 FALSE TRUE 1118000.306 1191890.584 1089535.066 1026371.477 1239796.402 1078832.364 1404905.78 1303406.656 1423365.614 1508486 0.741140657 0.790123729 0.722270585 0.680398411 0.821881278 0.715175589 0.931334981 0.864049554 0.943572306 1 20.52466988 1.851966807 0.828462471 0.98514212 0.737169909 0.753107981 0.051909051 0.281516029 0.362706661 0.0433731 0.020206589 71.11591575 -1.851966807 -0.24797221 ERHPS(ph)WRSEET(ph)QER ddPTM_BT-474_Pertuzumab_2h_R1 1 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(0.999)WRS(0.084)EET(0.917)QER 100.28 0.0034894 411560000 107040 133890 63442 75212 99411 105900 87869 63322 70766 73291 TRUE FALSE 102856.7585 130071.5883 74907.38066 79093.70033 102608.6451 108041.3706 88944.36711 62014.37857 62732.94036 68326.93529 1.505361802 1.903664898 1.096308218 1.157577169 1.501730535 1.581241279 1.301746767 0.907612471 0.918128994 1 16.0601668 1.85204807 3.561978111 0.934058845 1.449651246 0.540982727 0.211697635 0.196048688 4.166454162 0.115144727 0.061797001 71.12922391 -1.85204807 0.515592401 IMEVIDAITTTAQSHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 IMEVIDAITTTAQSHQR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 194.32 8.06E-11 1100660000 602080 769180 651600 865080 834350 824630 720460 575900 631500 659390 FALSE TRUE 578550.048 747243.7395 769358.6148 909726.8825 861187.6255 841304.5836 729277.205 564007.4637 559814.7675 614728.928 0.941146612 1.215566253 1.251541256 1.479882988 1.400922563 1.368578157 1.186339493 0.917489707 0.910669308 1 19.22959085 1.852406193 3.551564909 0.935235097 1.286904926 0.537870851 0.137647212 0.188458237 3.985146959 0.075443211 0.040471006 71.18790179 -1.852406193 0.351669829 DPNNDFRK ddPTM_BT-474_Pertuzumab_2h_R1 1 DPNNDFRK 8 1 Q9BRA2;I3L2R6 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 74.464 0.065595 812320000 955440 940630 736560 866570 908520 852530 920490 1021900 1155600 1018600 FALSE TRUE 918100.3485 913804.1534 869672.7767 911293.7816 937743.3709 869768.7407 931755.232 1000797.408 1024421.133 949609.3147 0.966819022 0.96229485 0.915821658 0.959651266 0.987504394 0.915922714 0.981198497 1.053904371 1.078781681 1 19.85697456 1.852485501 3.715555438 1.049439903 0.952026686 0.687963838 0.027793193 0.121283699 2.758548969 0.013506111 0.0073236 71.20090296 -1.852485501 -0.097413216 YVWLVYEQDRPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 YVWLVYEQDRPLK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 235.73 9.81E-17 13538700000 4507200 4187800 4193900 5379400 4270200 3553000 4755600 5465500 5672600 6166200 FALSE TRUE 4331053.641 4068368.044 4951831.023 5657031.479 4407554.861 3624844.094 4813800.455 5352635.515 5028670.229 5748557.782 0.753415692 0.707719779 0.861404062 0.984078389 0.76672359 0.630565827 0.837392723 0.931126679 0.874770755 1 22.45476862 1.85253052 4.20095075 0.925922895 0.788634334 0.343602631 0.092476262 0.307784843 8.467967604 0.048527165 0.027070526 71.20828393 -1.85253052 -0.137288561 DQSDKHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQSDKHDR 8 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 68.626 0.03366 25621000 28080 29731 22274 29316 24890 29106 25468 19329 22592 21473 FALSE TRUE 26982.60256 28883.10099 26299.40728 30829.00227 25690.60945 29694.54326 25779.685 18929.8494 20027.45087 20018.61458 1.347875621 1.442812182 1.313747621 1.540016775 1.283336034 1.483346569 1.28778567 0.945612361 1.000441404 1 14.28905451 1.852674021 3.652378154 0.979201449 1.400036886 0.861819989 0.075015771 0.071610842 1.58434188 0.034392568 0.018576134 71.23181669 -1.852674021 0.420835437 DFDRVRVNGWAT(ph)LFLRT(ph)S(ph)IPT(ph)INMENK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFDRVRVNGWATLFLRTSIPTINMENK 27 3 P26006;P26006-1 P26006 ITGA3 Integrin alpha-3;Integrin alpha-3 heavy chain;Integrin alpha-3 light chain 4 DFDRVRVNGWAT(1)LFLRT(1)S(1)IPT(1)INMENK;DFDRVRVNGWAT(1)LFLRT(1)S(1)IPT(1)INMENK 77.733 0.0049205 1553310000 1501050 756580 832840 502510 928700 777170 940240 1246390 1455820 980770 TRUE FALSE 1442387.307 735003.0792 983352.7144 528444.6013 958572.4789 792884.9099 951746.9384 1220651.611 1290561.417 914341.5743 1.577514735 0.803860504 1.075476323 0.577950972 1.048374596 0.867164889 1.040909617 1.335006135 1.411465314 1 19.80237369 1.852690626 4.626038419 1.27878083 0.96992111 0.15759047 0.260343883 0.333206321 10.55310731 0.117532868 0.06698619 71.23454023 -1.852690626 -0.30885972 DGDKS(ph)PMSSLQISNEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DGDKSPMSSLQISNEK 16 1 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 DGDKS(0.996)PMS(0.003)SLQISNEK;DGDKS(0.999)PMS(0.001)SLQISNEK;DGDKS(0.982)PMS(0.015)S(0.003)LQISNEK;DGDKS(0.995)PMS(0.004)SLQISNEK;DGDKS(0.659)PMS(0.17)S(0.17)LQISNEK 286.57 1.38E-35 1770365000 2608980 1903580 1979740 1582570 1989350 2000540 2291190 2736420 3282910 2829170 TRUE FALSE 2507018.177 1849291.762 2337523.057 1664246.627 2053339.249 2040992.289 2319230.269 2679911.971 2910247.82 2637547.796 0.950510994 0.701140569 0.886248606 0.630982547 0.778503143 0.773821916 0.879313077 1.016061955 1.1033915 1 21.33076581 1.852713164 2.18969944 1.05497093 0.779913701 0.63017855 0.086594585 0.176825827 1.586295928 0.050133182 0.023606921 71.23823716 -1.852713164 -0.27505723 S(ph)PQLSDFGLER ddPTM_BT-474_Pertuzumab_2h_R1 5 SPQLSDFGLER 11 0 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 S(1)PQLSDFGLER;S(1)PQLSDFGLER;S(1)PQLSDFGLER;S(1)PQLSDFGLER;S(1)PQLSDFGLER 224.75 6.27E-12 3034010000 1501890 1739180 1542620 1678930 1653120 1514510 1484580 1316430 1265547 1265890 TRUE FALSE 1443194.478 1689580.289 1821405.749 1765579.779 1706294.106 1545134.43 1502748.734 1289245.26 1121887.41 1180150.143 1.222890568 1.431665538 1.543367817 1.496063691 1.445827988 1.309269367 1.273353855 1.092441727 0.950631085 1 20.17053899 1.852756436 1.240993949 0.965495348 1.434582566 0.821800881 0.08364831 0.180729237 0.516536422 0.068836463 0.028841291 71.2453355 -1.852756436 0.469087218 SSDRLDEAAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSDRLDEAAQR 11 1 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 105.17 0.0022815 505230000 97547 113010 90424 139180 127050 131810 114410 99243 114700 110280 FALSE TRUE 93734.7554 109787.0654 106765.6283 146363.0965 131136.6786 134475.2885 115810.1838 97193.59737 101679.7369 102810.6374 0.911722345 1.067857065 1.038468694 1.423618219 1.275516639 1.307990029 1.126441648 0.945365186 0.98900016 1 16.64963002 1.852760067 4.591542333 0.976467628 1.179039779 0.277559628 0.138430882 0.309543786 9.698602864 0.071660746 0.040777301 71.2459312 -1.852760067 0.202572151 ARS(ph)PYSPAEEDALFMDLPTGPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ARSPYSPAEEDALFMDLPTGPR 22 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 ARS(0.836)PY(0.004)S(0.161)PAEEDALFMDLPTGPR;ARS(0.967)PY(0.017)S(0.016)PAEEDALFMDLPTGPR;ARS(0.993)PY(0.001)S(0.006)PAEEDALFMDLPTGPR 170.44 4.33E-12 248979000 138791 155944 135910 132950 146260 144109 117915 141072 135784 123889 TRUE FALSE 133366.8943 151496.6298 160471.9603 139811.5654 150964.5857 147022.9827 119358.079 138158.8139 120370.3696 115497.8877 1.154712843 1.311683121 1.389393032 1.210511882 1.307076595 1.272949538 1.033422181 1.196202084 1.042186762 1 16.81750694 1.852769542 0.766510574 1.017176629 1.289801288 0.58420064 0.081383149 0.445172052 0.498918639 0.071120577 0.034705082 71.24748548 -1.852769542 0.272624658 TSES(ph)PSKPGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSESPSKPGEK 11 1 P20810-6;P20810-10;P20810-7;P20810-9;H0YA91;P20810-5;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EN75;D6RGF7;D6RBR1 P20810-6;P20810-5;A0A0C4DGB5 CAST Calpastatin 1 TSES(1)PSKPGEK;TSES(1)PSKPGEK;TSES(1)PSKPGEK 214.45 8.20E-12 3150300000 3667700 2803970 2598390 2014990 2263450 2387920 3051680 3640600 4114700 4072300 TRUE FALSE 3524362.229 2724003.521 3067976.874 2118983.875 2336255.925 2436205.378 3089027.373 3565420.338 3647616.506 3796479.494 0.928323789 0.717507766 0.808111009 0.558144428 0.615374304 0.641701182 0.813655751 0.939138574 0.960789203 1 21.85623078 1.853027499 2.522797479 0.970256573 0.705458104 0.571308827 0.098505191 0.211095753 2.463623249 0.059756145 0.029344324 71.28981691 -1.853027499 -0.264798469 S(ph)PHKDLGHR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPHKDLGHR 9 1 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR 112.08 0.0012199 5203500000 1901820 1948360 1679540 1970920 1852550 1725350 1852870 624649 1912320 1614770 TRUE FALSE 1827494.772 1892794.68 1983070.239 2072639.417 1912138.953 1760237.759 1875545.977 611749.7799 1695241.451 1505400.19 1.21395944 1.25733655 1.317304364 1.376802947 1.27018647 1.169282275 1.245878664 0.406370202 1.12610684 1 20.52171563 1.853062934 10.61276667 0.785260386 1.26808654 0.519961649 0.182489399 0.280727259 24.38379847 0.072143342 0.045920874 71.29563371 -1.853062934 0.482826154 SSSISEEKGDS(ph)DDEKPR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSSISEEKGDSDDEKPR 17 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.097)S(0.097)S(0.097)IS(0.097)EEKGDS(0.612)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(0.999)DDEKPR 285.46 2.09E-36 15077510000 6251780 4093294 3936344 3057644 4129443 3773056 4587483 6143301 6955111 5296722 TRUE FALSE 6007453.526 3976557.263 4647728.924 3215449.373 4262270.284 3849349.777 4643625.989 6016439.688 6165595.957 4937970.301 1.216583568 0.80530198 0.941222535 0.651168228 0.863162398 0.779540893 0.94039164 1.218403376 1.248609364 1 22.23548673 1.853073742 4.279209221 1.173976379 0.864922381 0.40657836 0.149984144 0.198377972 5.607286219 0.070344358 0.039417011 71.29740803 -1.853073742 -0.309053998 DYEYNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYEYNR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 135.5 0.031577 2327350000 1607140 1755830 1443840 1680370 1681430 1643370 1623440 1671350 1778360 1723020 FALSE TRUE 1544331.192 1705755.448 1704774.006 1767094.097 1735514.723 1676600.067 1643308.144 1636836.038 1576488.028 1606318.321 0.961410433 1.061903749 1.061292761 1.100089611 1.080430137 1.043753312 1.023027705 1.018998549 0.981429402 1 20.61532639 1.853183815 1.476535415 0.994189063 1.05608718 0.310684333 0.034900855 0.480021369 1.966856864 0.026431529 0.011236135 71.31548088 -1.853183815 0.061898117 VDVEGPDVNIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDVEGPDVNIEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 176.89 5.14E-12 146440000 291180 283764 263281 288196 273548 268718 291533 359250 353120 357880 FALSE TRUE 279800.3637 275671.3286 310861.7334 303069.8301 282346.9198 274151.6621 295100.8681 351831.362 313035.298 333640.4688 0.838628373 0.826252671 0.931726701 0.90837251 0.846261009 0.821697868 0.884487632 1.054522442 0.938241392 1 18.34793477 1.85343414 6.310564055 0.999609001 0.864396484 0.677523351 0.0419722 0.13577418 6.460836046 0.019004846 0.011493957 71.35659853 -1.85343414 -0.135212517 KGEFETGFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGEFETGFEK 10 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 144.57 5.13E-05 3350300000 4310500 3728200 3414500 3355600 3672900 3750000 4207400 4586800 5373800 5116200 FALSE TRUE 4142040.894 3621875.386 4031576.105 3528782.918 3791042.164 3825827.569 4258891.42 4492080.977 4763788.753 4769675.217 0.868411518 0.759354719 0.845251704 0.73983715 0.794821868 0.802114902 0.892910151 0.94180018 0.998765856 1 22.1854596 1.85358123 1.46326564 0.99821292 0.796519728 0.832701471 0.036331332 0.141471703 0.568917546 0.025267329 0.010729092 71.38077029 -1.85358123 -0.201693192 RRS(ph)PS(ph)PAPPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSPSPAPPPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(1)PS(1)PAPPPR 83.087 0.084419 518700000 99329 98499 95420 116870 112080 103500 98273 101250 100910 100010 TRUE FALSE 95447.11287 95689.90496 112664.5166 122901.6747 115685.155 105592.8409 99475.69437 99159.15212 89455.11985 93236.23362 1.023712661 1.026316714 1.208376961 1.318175026 1.240774648 1.132530099 1.066920987 1.063525931 0.959445876 1 16.50860311 1.853585018 1.47618408 0.990975997 1.165633498 0.390709033 0.086742612 0.467289163 1.913603888 0.072577721 0.030861322 71.38139278 -1.853585018 0.174657501 KIDFLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIDFLTK 7 1 Q99471;H3BPF6;Q99471-3;H3BMQ1 Q99471 PFDN5 Prefoldin subunit 5 0 77.677 0.059965 447900000 1010400 1005800 796190 857110 920420 885800 973290 1090400 1186900 1175800 FALSE TRUE 970912.4509 977115.5688 940079.2442 901345.5498 950026.1452 903711.4829 985201.4142 1067882.859 1052168.088 1096162.019 0.885738088 0.891397031 0.857609759 0.82227402 0.866684057 0.824432399 0.898773537 0.974201661 0.959865485 1 20.06402962 1.85368324 3.00004199 0.9768852 0.858254491 0.841302573 0.023225654 0.099252834 1.577316207 0.01305013 0.00672045 71.39753856 -1.85368324 -0.118630709 FFSDCK ddPTM_BT-474_Pertuzumab_2h_R1 2 FFSDCK 6 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;E7EN40;D6R9T0;D6RFM3;D6RDU3;D6RJ04;D6RIH9;D6RAM1;D6RDL0;D6RF17;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ; 113.25 0.061181 222940000 804030 730220 593410 658870 700760 693800 718820 825450 850860 853010 FALSE TRUE 772607.6187 709394.8406 700652.3873 692874.3597 723300.5818 707829.1114 727617.1342 808404.169 754273.9399 795234.8729 0.971546451 0.892057007 0.881063458 0.871282665 0.909543339 0.890088118 0.914971361 1.01656026 0.948492031 1 19.6010215 1.853714537 5.581344344 0.987653067 0.900360859 0.619837166 0.030192139 0.139874917 5.69997005 0.013366658 0.007916559 71.40268394 -1.853714537 -0.087292208 GTGHVSSGYVER ddPTM_BT-474_Pertuzumab_2h_R1 2 GTGHVSSGYVER 12 0 Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5;Q6IN85-4;G3V4R3;G3V5A2 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 0 ; 99.732 0.0036308 267800000 159238 244720 206854 275480 219996 239960 224180 171868 192736 248390 FALSE TRUE 153014.8029 237740.8252 244237.1192 289697.5558 227072.3711 244812.1556 226923.5819 168318.8657 170857.4173 231566.3241 0.660781759 1.026664072 1.05471778 1.251034912 0.980593236 1.057201027 0.979950702 0.726871087 0.737833612 1 17.82106594 1.8538911 5.56637395 0.797703165 1.018088214 0.217239639 0.153669304 0.287872509 11.68524148 0.069506519 0.04114854 71.43171874 -1.8538911 0.220385049 KNS(ph)STDQGS(ph)DEEGSLQK ddPTM_BT-474_Pertuzumab_2h_R1 4 KNSSTDQGSDEEGSLQK 17 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 2 KNS(0.981)S(0.011)T(0.008)DQGS(1)DEEGSLQK;KNS(0.996)ST(0.004)DQGS(1)DEEGSLQK;KNS(0.73)S(0.063)T(0.207)DQGS(1)DEEGSLQK;KNS(0.995)S(0.003)T(0.002)DQGS(1)DEEGSLQK 273.94 3.93E-35 3020460000 5211590 4000400 4227770 3660030 4356700 3876530 4813900 5571100 6637800 5730800 TRUE FALSE 5007915.301 3886312.509 4991822.085 3848924.587 4496837.212 3954916.093 4872813.948 5456054.838 5884304.772 5342647.812 0.937347075 0.727413194 0.934334858 0.72041518 0.841687001 0.74025394 0.912059735 1.021226746 1.101383617 1 22.34912349 1.853953877 2.686625393 1.050265592 0.8152225 0.6275351 0.076839164 0.154971015 2.025849078 0.039466161 0.019739794 71.44204489 -1.853953877 -0.235043092 TTFDEAMADLHTLSEDSYK ddPTM_BT-474_Pertuzumab_2h_R1 10 TTFDEAMADLHTLSEDSYK 19 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;;;;;;;;; 343.76 2.84E-76 3733949000 4745024 4204392 4204939 4417029 4675930 4748613 5018468 5165642 6434773 6241252 FALSE TRUE 4559583.216 4084486.857 4964865.016 4644992.396 4826335.535 4844633.208 5079885.513 5058969.688 5704324.546 5818526.443 0.783631949 0.701979599 0.853285632 0.798310782 0.829477288 0.832622015 0.873053609 0.869458915 0.980372712 1 22.4722224 1.854109646 0.330868907 1.021504235 0.738801906 0.793000295 0.03808702 0.593583999 0.199439128 0.0536672 0.058807232 71.46767366 -1.854109646 -0.282702329 LELGLHECSLPVS(ph)PLGSIATR ddPTM_BT-474_Pertuzumab_2h_R1 1 LELGLHECSLPVSPLGSIATR 21 0 Q96MT8-3;Q96MT8-2 Q96MT8-3 1 LELGLHECSLPVS(0.988)PLGS(0.01)IAT(0.002)R 79.373 0.0049333 72387000 37313 42022 35281 47106 48361 48558 42245 33067 38916 42297 TRUE FALSE 35854.76671 40823.5737 41657.06152 49537.14631 49916.57549 49539.87603 42762.00695 32384.15489 34498.41883 39432.18652 0.909276656 1.03528557 1.056422816 1.256261716 1.265884038 1.256330942 1.084444225 0.821261963 0.874879683 1 15.26708609 1.854264799 5.218747713 0.885848432 1.136501422 0.44702174 0.114744301 0.206643019 7.703845425 0.057826116 0.033818762 71.49321026 -1.854264799 0.25065299 PST(ph)PGLSVVSGISATSEDIPNKIEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 PSTPGLSVVSGISATSEDIPNKIEDLR 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 PS(0.194)T(0.806)PGLSVVSGISATSEDIPNKIEDLR 122.11 0.00014838 33971000 18812 19347 22223 23011 20633 23697 28108 30046 42288 36149 TRUE FALSE 18076.80624 18795.2425 26239.19045 24198.60047 21296.67918 24176.16958 28451.99411 29425.5396 37487.64353 33700.59603 0.536394259 0.557712466 0.778597222 0.718046661 0.63193776 0.717381068 0.84425789 0.87314597 1.112373309 1 15.04048649 1.854376293 0.999306491 1.053191292 0.642906477 0.801786852 0.078390783 0.236160633 0.434748815 0.068679706 0.029687189 71.51156668 -1.854376293 -0.410284816 TEDEEFLIQHLLQAPS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 8 TEDEEFLIQHLLQAPSPPR 19 0 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR 328.54 2.17E-75 3593249000 1437471 1527316 1231682 1337309 1487902 1510986 1422253 1436916 1595525 1476481 TRUE FALSE 1381293.044 1483758.443 1454274.336 1406327.678 1535761.719 1541539.172 1439658.958 1407243.182 1414407.691 1376477.627 1.003498362 1.077938656 1.056518688 1.021685824 1.115718621 1.119915894 1.045900732 1.02235093 1.027555889 1 20.39254973 1.854463299 3.656645067 1.019003448 1.067163146 0.280872321 0.034728619 0.332463701 7.361417339 0.01824039 0.009866289 71.52589465 -1.854463299 0.048159699 DKLNNLVLFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKLNNLVLFDK 11 1 P62851 P62851 RPS25 40S ribosomal protein S25 0 ; 196.5 5.50E-08 6506200000 20377100 17613400 16841800 15169700 17342900 16908100 18207800 21591600 22865500 21324200 FALSE TRUE 19580740.4 17111083.08 19885487.9 15952610.03 17900750.13 17249993.37 18430632.5 21145725.91 20269904.3 19879892.94 0.984952005 0.8607231 1.000281438 0.802449494 0.900444996 0.867710577 0.927099183 1.063674034 1.019618383 1 24.24480665 1.854482196 4.98447288 1.031367351 0.900538264 0.497004055 0.056282927 0.16750266 5.869197141 0.024709427 0.014319335 71.52900699 -1.854482196 -0.130829087 DKDDDEVFEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDDDEVFEKK 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 144.27 2.07E-05 2669900000 3243700 2345900 2219380 1684370 2455000 2404810 2884800 3738700 4628500 3803600 FALSE TRUE 3116932.618 2278997.229 2620471.336 1771300.538 2533967.305 2453436.906 2920105.045 3661494.538 4103092.084 3545978.784 0.879004869 0.642699059 0.73899803 0.499523727 0.714603064 0.69189272 0.823497608 1.03257655 1.15711129 1 21.75775247 1.854652548 2.127510382 1.086527218 0.685292585 0.749014898 0.095438229 0.141096004 1.197160409 0.057767387 0.027009782 71.55706979 -1.854652548 -0.401234633 KDS(ph)LTQAQEQGNLLN ddPTM_BT-474_Pertuzumab_2h_R1 6 KDSLTQAQEQGNLLN 15 1 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 KDS(0.947)LT(0.053)QAQEQGNLLN;KDS(0.964)LT(0.036)QAQEQGNLLN;KDS(0.999)LT(0.001)QAQEQGNLLN;KDS(1)LTQAQEQGNLLN;KDS(1)LTQAQEQGNLLN;KDS(0.99)LT(0.01)QAQEQGNLLN 205.78 4.48E-09 3930210000 5922520 5271840 4132270 4323180 5674580 5090750 5302780 6956570 6904810 6341200 TRUE FALSE 5691061.371 5121492.285 4879063.111 4546299.838 5857108.019 5193688.453 5367677.008 6812914.398 6121004.916 5911704.876 0.96267684 0.866330846 0.825322511 0.769033626 0.990764617 0.878543256 0.907974454 1.152444945 1.035404345 1 22.49514282 1.854885392 6.170294238 1.073779612 0.880120616 0.578270088 0.069192527 0.151910774 6.997602682 0.030800436 0.018569901 71.59544481 -1.854885392 -0.193658996 RTT(ph)GAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTTGAK 6 1 I3L2A8;Q6NT04-2;Q6NT04 I3L2A8 TIGD7 Tigger transposable element-derived protein 7 1 RT(0.262)T(0.738)GAK 53.71 0.097755 498440000 1839700 1799000 1570400 1775600 1680800 1720300 1694900 711830 1715600 1241300 TRUE FALSE 1767802.49 1747694.281 1854206.213 1867238.929 1734864.458 1755085.645 1715642.693 697130.4617 1520852.28 1157225.645 1.527621253 1.510245032 1.602285795 1.61354783 1.499158324 1.516632173 1.48254811 0.602415324 1.314222759 1 20.14223877 1.855000182 7.700690253 0.943601843 1.54191923 0.711873949 0.164373278 0.123812392 7.403696736 0.06544611 0.040654523 71.61437102 -1.855000182 0.598317387 FEEESKEPVADEEEEDS(ph)DDDVEPITEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 FEEESKEPVADEEEEDSDDDVEPITEFR 28 1 P54105;E9PJF4 P54105 CLNS1A Methylosome subunit pICln 1 FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR 251.9 1.19E-53 5222780000 1835338 1502564 1370768 1462825 1554124 1505581 1748249 2053825 2332950 2242610 TRUE FALSE 1763610.962 1459712.346 1618496.27 1538321.574 1604113.81 1536024.879 1769644.594 2011412.796 2068123.297 2090716.027 0.843544001 0.698187763 0.774134913 0.735786952 0.76725571 0.734688432 0.846429917 0.962068865 0.989193783 1 20.99556569 1.855052988 2.119079986 0.992840254 0.755739279 0.885345415 0.036195751 0.085452276 0.719427406 0.020642441 0.009643247 71.62307913 -1.855052988 -0.237100974 SVTSS(ph)PVEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVTSSPVEKK 10 1 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3;F8VVB8 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 SVT(0.003)S(0.021)S(0.977)PVEKK 122.39 0.00029998 204120000 459990 456950 364440 344960 409050 486740 479300 476380 674540 574050 TRUE FALSE 442013.0823 443918.2334 430302.4149 362763.4269 422207.4647 496582.2163 485165.8168 466542.5865 597969.0471 535169.0822 0.825931648 0.829491554 0.804049466 0.677848252 0.788923499 0.927897804 0.906565482 0.871766703 1.117346026 1 19.02963525 1.855112739 0.873807418 1.034265401 0.787958452 0.641440387 0.069303591 0.396306023 0.563319129 0.063004782 0.028627571 71.63293381 -1.855112739 -0.246306949 MLS(ph)SSDAITQEFMDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 MLSSSDAITQEFMDLR 16 0 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;E9PNZ4;E9PLY5;A0A5F9ZGX0;A0A669KBB0 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 MLS(0.981)S(0.019)SDAITQEFMDLR;MLS(0.968)S(0.027)S(0.005)DAITQEFMDLR;MLS(0.987)S(0.013)SDAITQEFMDLR;MLS(0.498)S(0.498)S(0.005)DAITQEFMDLR;MLS(0.986)S(0.014)SDAITQEFMDLR;MLS(0.986)S(0.014)SDAITQEFMDLR 282.49 1.47E-35 447003000 245752 300371 280990 347773 411294 377904 286433 262111 240943 268444 TRUE FALSE 236147.7401 291804.7132 331771.1436 365721.6062 424523.645 385545.4778 289938.4527 256698.3163 213592.1608 250262.0488 0.943601882 1.165996661 1.325694987 1.46135464 1.696316509 1.540567096 1.158539436 1.025718112 0.853474036 1 17.93308 1.855158967 2.641161472 0.946183688 1.364091322 0.441064317 0.198162746 0.277788735 3.51923177 0.125152356 0.062361128 71.64055916 -1.855158967 0.417907634 DFPLNDLLSATELDKIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFPLNDLLSATELDKIR 17 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 114.99 0.00030715 246960000 229590 271940 186460 238000 246280 294750 221000 215310 221330 209540 FALSE TRUE 220617.369 264184.5375 220157.4698 250283.2085 254201.8199 300710.0469 223704.6641 210863.7733 196205.5463 195347.6692 1.12935757 1.352381314 1.12700331 1.281219323 1.301279001 1.539358254 1.145161675 1.079428151 1.00439154 1 17.57568452 1.855467428 3.05790082 1.029610787 1.286267528 0.508994176 0.113248069 0.213878784 3.510309703 0.060938813 0.031576768 71.69146054 -1.855467428 0.256656741 DYIHVVDLAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DYIHVVDLAK 10 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ;;; 141.93 3.66E-05 1389040000 4158190 4083470 3690800 4070480 4068060 4035840 4502160 4738710 5559460 5219620 FALSE TRUE 3995683.338 3967013.434 4357809.661 4280557.961 4198912.844 4117447.45 4557258.781 4640853.983 4928373.408 4866090.488 0.821128038 0.815236265 0.895546368 0.879670851 0.862892471 0.846151024 0.936533916 0.953713046 1.012799376 1 22.21433172 1.855600533 1.283752978 1.006322468 0.852785123 0.849223064 0.026048814 0.168822842 0.517439424 0.021424194 0.008997282 71.7134362 -1.855600533 -0.153537345 IS(ph)PVPSPESAYTAETTSPHPSHDGSSFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISPVPSPESAYTAETTSPHPSHDGSSFK 28 0 Q9UBU7;B4DXK0;Q9UBU7-2 Q9UBU7 DBF4 Protein DBF4 homolog A 1 IS(0.848)PVPS(0.152)PESAYTAETTSPHPSHDGSSFK 137.62 7.99E-06 281550000 93036 113520 95234 129820 109410 121990 111520 42007 92770 128130 TRUE FALSE 89400.05026 110282.5207 112444.9023 136520.0258 112929.272 124456.7214 112884.8151 41139.54077 82239.13852 119451.641 0.748420445 0.923239897 0.941342466 1.142889496 0.94539741 1.041900474 0.945025235 0.344403312 0.688472237 1 16.86606715 1.855613569 9.973835571 0.610706992 0.964823893 0.319675134 0.177689928 0.331107672 26.3272759 0.071513977 0.045375266 71.71558897 -1.855613569 0.354116901 IGNEGLAADLTDDPDTEEALKEFDFLVTAEDGEGAGEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 IGNEGLAADLTDDPDTEEALKEFDFLVTAEDGEGAGEAR 39 1 Q13033-2;Q13033;G3V340;H0YJZ4;H0YJT2 Q13033-2 STRN3 Striatin-3 0 93.359 0.00018231 8707600 5730.9 3761.8 3635.3 6591.3 5431.1 3789.3 5635.8 7010.3 8226.9 6901.3 FALSE TRUE 5506.930092 3654.517147 4292.279577 6931.477783 5605.796264 3865.922242 5704.772606 6865.534855 7293.016802 6433.868804 0.855928254 0.568012382 0.667138188 1.077342108 0.871294774 0.600870543 0.886678417 1.067092766 1.133535206 1 12.6514708 1.855872838 3.472238165 1.074623778 0.775715061 0.45516807 0.142626229 0.228335601 4.644206797 0.077211033 0.041292326 71.75841504 -1.855872838 -0.298908717 GVTIPYRPKPSSS(ph)PVIFAGGQDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GVTIPYRPKPSSSPVIFAGGQDR 23 2 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 GVTIPYRPKPS(0.003)S(0.006)S(0.991)PVIFAGGQDR;GVTIPYRPKPS(0.005)S(0.03)S(0.965)PVIFAGGQDR;GVT(0.001)IPYRPKPS(0.045)S(0.14)S(0.815)PVIFAGGQDR 251.88 9.75E-44 55155030000 7091670 6976560 5715510 6558860 6616220 7181430 7635600 7788280 8554650 9020450 TRUE FALSE 6814519.696 6777595.34 6748429.798 6897363.551 6829036.725 7326643.435 7729046.757 7627449.296 7583561.996 8409486.887 0.810337157 0.805946359 0.802478188 0.820188395 0.812063425 0.871235491 0.919086605 0.907005314 0.90178653 1 23.00358635 1.855889954 0.409647803 0.997308297 0.786184649 0.915595421 0.018259569 0.294806572 0.129235075 0.022249027 0.020029531 71.76124321 -1.855889954 -0.211123649 QQQQQQQQHSENKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQQQQQQQHSENKR 14 1 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ; 111.39 0.00042486 83619000 58981 60088 45351 58363 57908 52331 61377 60433 76179 62866 FALSE TRUE 56675.95731 58374.34907 53546.93453 61375.12142 59770.66341 53389.16867 62128.15009 59185.03743 67531.47929 58608.02982 0.967033997 0.99601282 0.913645019 1.047213524 1.019837445 0.910953138 1.060062081 1.009845197 1.152256431 1 15.83881072 1.856000777 1.988371435 1.065384635 0.980532127 0.276250229 0.057326832 0.412783747 3.073265479 0.034967725 0.016038968 71.77955758 -1.856000777 -0.084852507 DPALCQHKPLT(ph)PQGDELSEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPALCQHKPLTPQGDELSEPR 21 1 K7EQL6;Q8NFA0 K7EQL6 USP32 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 32 1 DPALCQHKPLT(1)PQGDELSEPR;DPALCQHKPLT(1)PQGDELSEPR 175.21 2.94E-12 699500000 219091 196316 189200 218214 224134 227671 213871 183449 221962 226576 TRUE FALSE 210528.6815 190717.2599 223392.6487 229476.0507 231343.4737 232274.6636 216488.4173 179660.714 196765.8043 211229.8057 0.996680752 0.902889908 1.057581093 1.086381015 1.095221732 1.099630153 1.024895216 0.850546226 0.931524808 1 17.6884539 1.856024168 7.165435533 0.914319408 1.040583151 0.377276199 0.064424685 0.252555357 13.83684618 0.030148523 0.018575332 71.78342375 -1.856024168 0.126263742 VAQGATEKS(ph)PEDK ddPTM_BT-474_Pertuzumab_2h_R1 5 VAQGATEKSPEDK 13 1 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 VAQGATEKS(1)PEDK;VAQGAT(0.001)EKS(0.999)PEDK;VAQGAT(0.001)EKS(0.999)PEDK;VAQGATEKS(1)PEDK;VAQGATEKS(1)PEDK 178.85 2.85E-05 1621170000 2086895 1446606 1454189 1190554 1446713 1305505 1632044 2153077 2415628 1902909 TRUE FALSE 2005336.836 1405350.213 1716993.301 1251998.635 1493247.838 1331903.206 1652017.443 2108615.208 2141416.037 1774023.278 1.130389246 0.79218251 0.967852745 0.705739688 0.841729562 0.750781132 0.931226474 1.188606279 1.207095793 1 20.75859351 1.856071196 4.321926787 1.14704985 0.856932948 0.478630642 0.123954314 0.172603137 4.937329461 0.057261263 0.032211964 71.7911973 -1.856071196 -0.290116902 S(ph)PEIHRR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPEIHRR 7 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4;Q9Y2W1;A0A3B3ITZ9 E9PK91;Q9NYF8;Q9NYF8-4;Q9Y2W1 BCLAF1;THRAP3 Bcl-2-associated transcription factor 1;Thyroid hormone receptor-associated protein 3 1 S(1)PEIHRR;S(1)PEIHRR;S(1)PEIHRR;S(1)PEIHRR 91.867 0.0098547 2792540000 1056446 1126347 848422 981581 1074770 1142230 1039090 858604 1050590 1110714 TRUE FALSE 1015158.922 1094224.686 1001750.728 1032240.513 1109340.953 1165326.673 1051806.694 840873.5274 931331.4276 1035484.351 0.98037109 1.0567274 0.967422373 0.996867323 1.071325657 1.125392838 1.015763003 0.81205817 0.899416226 1 19.98187432 1.856123058 7.247903252 0.887075744 1.03408527 0.468099905 0.06128652 0.193345894 10.72918869 0.026609218 0.016418128 71.79977076 -1.856123058 0.147009526 KAEDS(ph)DS(ph)EPEPEDNVR ddPTM_BT-474_Pertuzumab_2h_R1 3 KAEDSDSEPEPEDNVR 16 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 2 KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR 166.3 4.49E-09 10866640000 2102940 1839580 1536040 1612740 1728480 1764430 1874400 2330460 2501470 2242280 TRUE FALSE 2020754.78 1787116.98 1813636.597 1695973.705 1784078.129 1800107.984 1897339.468 2282335.187 2217513.613 2090408.378 0.96667943 0.854912848 0.867599181 0.811312145 0.853459136 0.861127425 0.907640578 1.091813069 1.060804021 1 20.99535338 1.856158292 4.260243081 1.057182554 0.866422562 0.783201749 0.042724776 0.09416822 2.637131041 0.020548389 0.011523063 71.80559608 -1.856158292 -0.190759992 MESSFGS(ph)PSKQESSESLPK ddPTM_BT-474_Pertuzumab_2h_R1 3 MESSFGSPSKQESSESLPK 19 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 MES(0.029)S(0.026)FGS(0.943)PS(0.003)KQESSESLPK;MESSFGS(0.996)PS(0.004)KQESSESLPK;MESSFGS(0.994)PS(0.006)KQESSESLPK 254.61 3.99E-31 5902420000 2116380 1777700 1542080 1324080 1736820 1808500 1855630 2358140 2721400 2209690 TRUE FALSE 2033669.53 1727001.737 1820768.159 1392415.927 1792686.393 1845069.109 1878339.755 2309443.585 2412478.081 2060025.728 0.987205889 0.838339887 0.883857 0.67592162 0.870225244 0.89565343 0.911804027 1.121075117 1.171091238 1 20.97423092 1.856221482 2.862379507 1.112318507 0.852169926 0.619452781 0.083376115 0.160953666 2.352692657 0.045868694 0.023377653 71.81604457 -1.856221482 -0.260148581 EIAIVHS(ph)DAEKEQEEEEQKQEMEVK ddPTM_BT-474_Pertuzumab_2h_R1 5 EIAIVHSDAEKEQEEEEQKQEMEVK 25 2 Q9H307 Q9H307 PNN Pinin 1 EIAIVHS(1)DAEKEQEEEEQKQEMEVK;EIAIVHS(1)DAEKEQEEEEQKQEMEVK;EIAIVHS(1)DAEKEQEEEEQKQEMEVK;EIAIVHS(1)DAEKEQEEEEQKQEMEVK;EIAIVHS(1)DAEKEQEEEEQKQEMEVK 347.06 3.71E-103 4067660000 2020802 1283880 1874474 1351889 1649037 1471061 2229582 2693022 3611340 2911871 TRUE FALSE 1941826.824 1247264.999 2213233.149 1421660.153 1702079.773 1500806.861 2256868.291 2637410.155 3201395.823 2714647.384 0.715314569 0.459457463 0.815293052 0.523699749 0.626998476 0.552855178 0.831367015 0.97154797 1.179304481 1 21.37233338 1.856222214 1.989551144 1.080444625 0.614055545 0.770391492 0.106556136 0.135266411 1.008148545 0.062981995 0.028898936 71.81616573 -1.856222214 -0.46638908 IGEEFLTDLSQLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGEEFLTDLSQLKK 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 205.61 1.93E-08 911720000 711980 643120 474190 434470 569880 541190 583550 704460 776150 627160 FALSE TRUE 684155.0345 624778.8473 559886.6813 456893.0488 588210.7078 552133.2326 590691.6595 689912.6548 688044.7059 584681.8946 1.170132068 1.068579091 0.95759196 0.781438681 1.006035441 0.94433099 1.010278692 1.179979509 1.176784697 1 19.15729239 1.856237286 5.376647906 1.134484389 0.981624427 0.237169432 0.103854279 0.293390487 11.33094455 0.049573577 0.029185371 71.81865805 -1.856237286 -0.152859962 S(ph)SSQRSPSPGPNHTSNSSNASNATVVPQNSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSQRSPSPGPNHTSNSSNASNATVVPQNSSAR 33 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.243)S(0.243)S(0.243)QRS(0.243)PS(0.027)PGPNHTSNSSNASNATVVPQNSSAR 98.74 5.44E-05 56954000 16433 33509 13666 22762 26866 32506 18353 16584 12358 15633 TRUE FALSE 15790.78019 32553.35613 16135.7502 23936.74955 27730.16929 33163.29359 18577.6095 16241.5346 10955.17165 14574.16299 1.083477673 2.233634697 1.107147643 1.642409898 1.902693782 2.275485297 1.274694782 1.114405995 0.751684447 1 13.83112541 1.856417105 2.7529494 0.936808953 1.70977255 0.425252488 0.388165436 0.250012223 3.40979245 0.209958685 0.105915953 71.84840068 -1.856417105 0.772963597 VKPEEMMDERPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKPEEMMDERPK 12 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 64.65 0.035362 197250000 330460 283940 261540 270980 300830 296900 325620 380820 431380 416100 FALSE TRUE 317545.2579 275842.3092 308806.0959 284965.3103 310506.4702 302903.5214 329605.035 372955.9339 382411.5509 387917.1764 0.818590352 0.711085577 0.79606193 0.734603487 0.800445273 0.780845861 0.849678888 0.961431864 0.985807214 1 18.56538913 1.856505671 1.574088139 0.999135076 0.767743186 0.909293859 0.029621035 0.091314833 0.426453407 0.019314748 0.008331304 71.86305421 -1.856505671 -0.231391891 LIILDEIHLLHDDRGPVLEALVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIILDEIHLLHDDRGPVLEALVAR 24 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 252.75 5.91E-44 745100000 291940 343491 265383 316236 310030 351471 312330 33885.3 304463 257624 FALSE TRUE 280530.662 333694.973 313343.6115 332556.9779 320002.3965 358577.9844 316152.388 33185.55671 269901.6367 240174.897 1.168026574 1.389383225 1.304647636 1.384645032 1.332372369 1.492986939 1.316342348 0.138172462 1.123771218 1 17.87372584 1.85652387 10.36042203 0.668598226 1.350544819 0.51664157 0.256381927 0.25810283 21.25354018 0.100045547 0.063615044 71.86606575 -1.85652387 0.681946593 QIEHCEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 QIEHCEGR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 172.59 0.00028266 1592789000 1314481 1351268 1047232 1348727 1238532 1321259 1253828 1086741 1262674 1260648 FALSE TRUE 1263109.629 1312731.16 1236490.118 1418334.962 1278370.507 1347975.762 1269172.722 1064299.419 1119340.541 1175263.188 1.074746186 1.116967819 1.052096356 1.206823269 1.087731258 1.146956508 1.07990511 0.905583898 0.952416916 1 20.16455244 1.85657157 4.901701791 0.94658636 1.11427789 0.717088955 0.04537447 0.106137215 3.624559355 0.02008844 0.011612963 71.87395934 -1.85657157 0.167691529 SCFES(ph)S(ph)PDPELK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.001)CFES(0.999)S(1)PDPELK 142.91 9.03E-05 275840000 848790 738960 643980 656340 734190 764010 784080 981680 1099100 931680 TRUE FALSE 815618.3484 717885.5843 760361.5113 690213.7861 757805.8881 779458.8057 793675.8056 961407.9649 974334.7758 868576.4837 0.939028817 0.826508198 0.875411119 0.794649405 0.872468806 0.897398007 0.913766168 1.106877728 1.121760483 1 19.72829337 1.856670655 3.288436632 1.086894738 0.864655229 0.791124859 0.047815052 0.097673444 1.813928043 0.02435613 0.012862415 71.89035948 -1.856670655 -0.222239508 ARHDS(ph)PDLAPNVTYSLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ARHDSPDLAPNVTYSLPR 18 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR 191.41 1.38E-14 3117790000 475010 540600 464625 487161 568640 575820 503470 467043 516210 491709 TRUE FALSE 456446.084 525182.6173 548593.073 512303.4376 586930.822 587463.4749 509631.6165 457398.3988 457612.0049 458405.1115 0.995726428 1.145673563 1.196742923 1.117577934 1.280375823 1.281537793 1.111749419 0.99780388 0.998269857 1 18.80626361 1.856813356 3.672509944 0.999220012 1.173763217 0.49007885 0.077397281 0.206956042 4.608987231 0.041069535 0.022271231 71.91398506 -1.856813356 0.174543205 LLPPAS(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 1 LLPPASP 7 0 Q9Y4R8 Q9Y4R8 TELO2 Telomere length regulation protein TEL2 homolog 1 LLPPAS(1)P 75.189 0.046305 14375000 13408 14993 14467 20085 20156 18309 16001 14889 15198 15814 TRUE FALSE 12884.00054 14565.41432 17081.50872 21121.58926 20804.33605 18679.22052 16196.82502 14581.53695 13472.78676 14742.90369 0.873912006 0.98796103 1.158625809 1.432661414 1.411142369 1.266997392 1.098618383 0.989054616 0.913848929 1 13.84773308 1.856896244 2.769114952 0.960170431 1.198356059 0.268554909 0.161744487 0.394978504 5.442198948 0.10228854 0.051701014 71.92771179 -1.856896244 0.238185628 AALAHPFFQDVTKPVPHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AALAHPFFQDVTKPVPHLR 19 1 G3V5T9;P24941;P24941-2;E7ESI2 G3V5T9 CDK2 Cyclin-dependent kinase 2 0 119.23 4.11E-05 354540000 228560 250540 157020 194030 194050 209060 203480 153260 199850 213770 FALSE TRUE 219627.6225 243394.8445 185397.0069 204043.9116 200291.7945 213287.3364 205970.2491 150095.1274 177163.8658 199291.1675 1.102043935 1.221302718 0.930282105 1.023848242 1.00502093 1.07022975 1.033514188 0.753144905 0.888969983 1 17.60451825 1.857046543 7.332019424 0.858662195 1.055560469 0.436208495 0.090129069 0.213940642 11.98457019 0.039029792 0.024119556 71.95260847 -1.857046543 0.196898274 TVSLTPSPTTQVETPDLVDHDNTS(ph)PLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLTPSPTTQVETPDLVDHDNT(0.05)S(0.95)PLFR 291.4 2.31E-71 756340000 121530 136620 132910 169050 149120 141180 136090 119900 126900 124180 TRUE FALSE 116780.4732 132723.7314 156929.7936 177774.6908 153916.5802 144034.7563 137755.5101 117424.0231 112494.844 115769.178 1.008735445 1.146451358 1.355540363 1.535596036 1.329512595 1.244154609 1.189915248 1.01429435 0.971716704 1 16.82089168 1.857065706 1.991453248 0.980548574 1.284359152 0.474631089 0.129158315 0.302705154 2.259426479 0.091772553 0.042150733 71.95578338 -1.857065706 0.303810578 AQSDIEHLFQHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQSDIEHLFQHNR 13 0 A0A087X211;Q8TCG1-2;Q8TCG1 A0A087X211 KIAA1524 Protein CIP2A 0 ; 325.29 5.95E-52 404190000 171315 176482 173805 226620 202748 217636 208250 13454 226520 200321 FALSE TRUE 164619.8204 171448.9062 205215.4298 238315.8854 209269.5736 222036.749 210798.6258 13176.1702 200806.3992 186753.0802 0.88148383 0.91805129 1.098859679 1.276101497 1.120568257 1.188932192 1.128755818 0.070553965 1.075250802 1 17.51077251 1.857413101 22.69752989 0.608756551 1.093894268 0.247462621 0.279390794 8.53496633 1600.349009 0.111357932 0.071857868 72.01336438 -1.857413101 0.485137717 ELEAIFGRPVVDGEEGEPHS(ph)ISPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 ELEAIFGRPVVDGEEGEPHS(0.627)IS(0.373)PR 61.112 0.037672 363860000 140830 176640 180040 220900 191130 200550 170680 160790 140750 183930 TRUE FALSE 135326.2079 171602.4001 212577.233 232300.6755 197277.87 204605.2584 172768.8329 157469.6303 124772.6501 171472.2573 0.789201764 1.000758973 1.239717937 1.354742039 1.15049439 1.193226599 1.007561431 0.918338819 0.727655027 1 17.38761565 1.857526872 2.410943242 0.861225767 1.132043611 0.318532708 0.155331214 0.3399414 3.641654179 0.0968978 0.047133626 72.03223197 -1.857526872 0.270817844 IYEKDEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IYEKDEEK 8 1 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 70.1 0.047611 1856490000 2479700 2084330 1921380 1878970 1879510 1650070 2279800 2719100 3148100 2815100 FALSE TRUE 2382790.583 2024886.949 2268616.107 1975943.867 1939966.146 1683435.546 2307700.874 2662949.635 2790740.886 2624430.77 0.907926629 0.771552815 0.864422157 0.752903788 0.739195017 0.641447877 0.879314822 1.014677036 1.063369977 1 21.32357311 1.857593806 3.252020606 1.029773244 0.779108455 0.709222418 0.070122526 0.134747405 2.454911932 0.037799465 0.01992028 72.04333455 -1.857593806 -0.25066479 EDENDAS(ph)DDEDDDEKRR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDENDASDDEDDDEKRR 17 2 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 EDENDAS(1)DDEDDDEKRR;EDENDAS(1)DDEDDDEKRR 109.68 0.0016489 0 158202 134114 126074 112111 125489 131461 139323 169053 174399 177866 TRUE FALSE 152019.2909 130289.2 148858.3763 117897.0621 129525.4677 134119.2315 141028.0766 165561.9965 154601.9567 165818.9774 0.916778606 0.785731537 0.897716164 0.710998608 0.781125717 0.808829204 0.850494188 0.998450232 0.932353818 1 17.3392496 1.85760883 3.91136439 0.974349867 0.813630544 0.605545954 0.057773204 0.153190491 3.766549617 0.028091963 0.015465318 72.04582686 -1.85760883 -0.160719323 VFQGTDEQLNDLYHNHQR ddPTM_BT-474_Pertuzumab_2h_R1 4 VFQGTDEQLNDLYHNHQR 18 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;A0A494C0Y7;E7ESD9 Q92878-2 RAD50 DNA repair protein RAD50 0 ;;; 230.33 8.07E-20 3316070000 639192 690269 582610 721686 679691 748020 673647 145474 689806 513421 FALSE TRUE 614211.67 670583.204 687900.5871 758932.3009 701553.8783 763145.4769 681891.2935 142469.9111 611502.1148 478646.5384 1.283225973 1.400998754 1.437178653 1.585579838 1.465703441 1.594382108 1.42462389 0.297651606 1.277565104 1 18.86860115 1.857628697 9.635607139 0.792431369 1.466019411 0.554356608 0.243480925 0.219225663 16.56962724 0.096354116 0.061016597 72.04912273 -1.857628697 0.673588042 LKEDILENEDEQNS(ph)PPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEDILENEDEQNSPPKK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LKEDILENEDEQNS(1)PPKK 215.84 4.85E-19 2804500000 1658700 1200200 1142700 970210 1227500 1134000 1351500 1705600 2005400 1542400 TRUE FALSE 1593876.17 1165971.471 1349211.309 1020282.654 1266983.652 1156930.257 1368040.061 1670378.764 1777755.399 1437931.874 1.108450406 0.810866976 0.938299883 0.709548674 0.881115215 0.804579325 0.951394211 1.161653618 1.236327973 1 20.4555639 1.857630721 3.548092201 1.148764952 0.868539886 0.507979868 0.112350743 0.172244406 3.626904876 0.054643522 0.029408483 72.0494585 -1.857630721 -0.280225066 (ac)MERPEEGKQS(ph)PPPQPWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MERPEEGKQSPPPQPWGR 18 2 F5GWH4;Q96EP1-2;Q96EP1-4;Q96EP1;Q96EP1-5;Q96EP1-3 F5GWH4 CHFR E3 ubiquitin-protein ligase CHFR 1 MERPEEGKQS(1)PPPQPWGR;MERPEEGKQS(1)PPPQPWGR 91.725 2.88E-11 895400000 490200 466850 363190 411440 446550 454170 453440 530930 551560 527530 TRUE FALSE 471042.4421 453535.8951 428826.5121 432674.4677 460913.6863 463353.6286 458989.3344 519966.11 488949.2211 491799.9232 0.957792834 0.922195945 0.87195319 0.87977742 0.937197556 0.942158806 0.933284681 1.057271637 0.994203533 1 18.90771198 1.857707412 5.538673648 1.020511969 0.917464152 0.694111691 0.029432832 0.125642402 5.026902806 0.014160704 0.008388138 72.06218263 -1.857707412 -0.103047816 QQFS(ph)PSMTER ddPTM_BT-474_Pertuzumab_2h_R1 4 QQFSPSMTER 10 0 Q8TDB6 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 1 QQFS(0.937)PS(0.063)MTER;QQFS(0.999)PS(0.001)MTER;QQFS(0.935)PS(0.065)MTER;QQFS(0.998)PS(0.002)MTER 193 1.89E-06 1186510000 941510 1145870 874720 1201070 1239320 1085180 928240 873000 759470 842390 TRUE FALSE 904714.7483 1113190.91 1032801.362 1263057.367 1279183.853 1107123.083 939600.0788 854972.2449 673258.1496 785334.175 1.152012452 1.417474172 1.315110681 1.608305619 1.628840173 1.409747746 1.196433453 1.088673169 0.857288745 1 19.58294715 1.857785524 1.743251956 0.946024532 1.43443495 0.681657732 0.136104712 0.210754184 1.209785877 0.098015615 0.043371123 72.07514482 -1.857785524 0.488410418 KELS(ph)EESEDEELQLEEFPMLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KELSEESEDEELQLEEFPMLK 21 1 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 KELS(0.858)EES(0.142)EDEELQLEEFPMLK 188.22 1.59E-17 31731000 69701 47834 66514 75064 63891 71236 99908 114800 129520 146080 TRUE FALSE 66977.00786 46469.82115 78534.5594 78938.06204 65946.11204 72676.44073 101130.704 112429.3399 114817.4326 136185.8715 0.491805847 0.341223511 0.576671857 0.579634739 0.484236076 0.533656244 0.742593214 0.825558031 0.84309357 1 17.05521751 1.857868493 0.733883157 0.987846152 0.466322028 0.877174166 0.067433791 0.212631595 0.220770986 0.062781858 0.031626878 72.0889157 -1.857868493 -0.521524124 down KVELS(ph)ESEEDKGGK ddPTM_BT-474_Pertuzumab_2h_R1 4 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.997)ES(0.003)EEDKGGK;KVELS(0.983)ES(0.017)EEDKGGK;KVELS(0.995)ES(0.005)EEDKGGK;KVELS(0.988)ES(0.012)EEDKGGK 144.01 7.06E-06 3857590000 3473840 2281080 2142620 1619138 2343800 2162320 2566840 3390340 3960520 2886920 TRUE FALSE 3338078.492 2216025.832 2529839.096 1702701.906 2419190.456 2206043.592 2598253.756 3320328.294 3510938.373 2691386.337 1.240282172 0.823377083 0.939976198 0.63264864 0.898864062 0.819668125 0.965396056 1.233686985 1.304509251 1 21.35991807 1.857871263 3.883167048 1.200752976 0.88071152 0.388097871 0.159691777 0.210971544 5.1287168 0.076991987 0.042322596 72.08937544 -1.857871263 -0.320041456 NSTWSGESK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSTWSGESK 9 0 P19338 P19338 NCL Nucleolin 0 ; 144.28 0.00023249 691560000 501120 442630 360560 336610 365580 372740 405650 451570 474960 467370 FALSE TRUE 481535.6764 430006.6258 425721.2126 353982.4824 377339.2127 380277.0582 410614.466 442244.9217 421044.532 435714.6136 1.105163016 0.98689971 0.977064343 0.812418201 0.866023771 0.872766362 0.942393147 1.014987581 0.966330986 1 18.73302398 1.857909256 5.945635115 0.993507398 0.930196912 0.098191336 0.076544059 0.552817206 24.14359978 0.037225294 0.02232878 72.09568223 -1.857909256 -0.063310486 RPAS(ph)PALLLPPCMLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPASPALLLPPCMLK 15 1 Q9HAW0-2;Q9HAW0 Q9HAW0-2 BRF2 Transcription factor IIIB 50 kDa subunit 1 RPAS(1)PALLLPPCMLK 116.29 0.00028185 348640000 456020 449840 394430 431280 453800 441960 478110 565860 603140 620750 TRUE FALSE 438198.2342 437011.0036 465712.275 453538.4125 468396.8891 450896.734 483961.2532 554174.7933 534674.0758 578706.0496 0.757203479 0.755151953 0.804747549 0.7837112 0.809386543 0.779146398 0.836281655 0.957610161 0.923913058 1 19.1424712 1.857984369 2.28892981 0.962650102 0.782121577 0.918010356 0.023886217 0.075988397 0.738975956 0.014240784 0.006824572 72.10815258 -1.857984369 -0.180528525 QEETDHKNDNQILSEIVEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 QEETDHKNDNQILSEIVEAK 20 1 O60502;O60502-3;O60502-2;O60502-4 O60502 MGEA5 Protein O-GlcNAcase 0 ; 94.358 0.0008289 868560000 894920 754350 747370 660370 774470 835370 850610 990780 1240240 993090 FALSE TRUE 859945.537 732836.6766 882436.3842 694451.7748 799381.5309 852261.7538 861020.0196 970320.0468 1099453.155 925827.1297 0.928840287 0.791548069 0.953132994 0.750087951 0.863424181 0.920540916 0.930000852 1.048057478 1.187536117 1 19.82038331 1.858103732 1.704226762 1.099682063 0.859621715 0.63570736 0.071726121 0.205491101 1.127050609 0.04655271 0.020483594 72.1279737 -1.858103732 -0.240060348 LSS(ph)SKENLDASK ddPTM_BT-474_Pertuzumab_2h_R1 6 LSSSKENLDASK 12 1 K7EQL6;Q8NFA0;K7EN13 K7EQL6 USP32 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 32 1 LS(0.01)S(0.562)S(0.428)KENLDASK;LS(0.101)S(0.515)S(0.383)KENLDASK;LSS(0.5)S(0.5)KENLDASK;LSS(0.5)S(0.5)KENLDASK;LSS(0.589)S(0.411)KENLDASK;LSS(0.748)S(0.252)KENLDASK 205.66 6.00E-08 5897810000 4831710 3750430 3463920 3018650 3568290 3438930 4305550 5280630 6375380 5323420 TRUE FALSE 4642881.431 3643471.408 4089927.398 3174442.888 3683067.288 3508467.521 4358242.609 5171583.145 5651673.59 4962860.022 0.935525365 0.734147526 0.824106942 0.639639819 0.742125966 0.706944686 0.878171576 1.042057024 1.138793672 1 22.24274033 1.858180258 2.593281495 1.073987664 0.759179027 0.729892266 0.080403489 0.133140623 1.629326241 0.044861418 0.022292386 72.14068441 -1.858180258 -0.314808638 RGS(ph)SPGSLEIPK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGSSPGSLEIPK 12 1 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 RGS(0.665)S(0.335)PGSLEIPK;RGS(0.996)S(0.004)PGSLEIPK;RGS(0.499)S(0.499)PGS(0.001)LEIPK;RGS(0.763)S(0.232)PGS(0.005)LEIPK 155.96 4.22E-05 1297670000 3071450 2871630 2382860 2240800 2669950 2717400 2842970 3407950 3811790 3383610 TRUE FALSE 2951414.338 2789733.924 2813495.808 2356447.957 2755831.367 2772347.69 2877763.117 3337574.642 3379091.58 3154435.081 0.935639588 0.884384637 0.891917486 0.747026931 0.873637053 0.878872958 0.912291121 1.0580578 1.071219249 1 21.58895023 1.858209237 3.009268868 1.050186594 0.865885362 0.719795108 0.048563529 0.133167068 2.123099067 0.027090479 0.014008299 72.14549827 -1.858209237 -0.184301231 MDPKELGK ddPTM_BT-474_Pertuzumab_2h_R1 1 MDPKELGK 8 1 A0A3B3IU97;A0A2R8Y5X9;Q76EJ3 A0A3B3IU97 SLC35D2 UDP-N-acetylglucosamine/UDP-glucose/GDP-mannose transporter 0 59.8 0.087855 417710000 404050 474370 364820 700290 560060 680040 436880 326110 229300 428790 FALSE TRUE 388259.2793 460841.4321 430751.0894 736432.0508 578074.8385 693790.8747 442226.6681 319375.7145 203270.8253 399747.6714 0.971260891 1.152830811 1.07755747 1.842242253 1.446099327 1.735572023 1.106264526 0.798943277 0.508497835 1 18.6087301 1.858249961 3.191151891 0.74005544 1.374371843 0.473588175 0.281395572 0.220111615 3.88250199 0.155681768 0.081700775 72.15226373 -1.858249961 0.634316403 QYPDSPHPVPHR ddPTM_BT-474_Pertuzumab_2h_R1 3 QYPDSPHPVPHR 12 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 0 ;; 87.363 0.0061244 310419000 202181 232001 207531 219028 243467 229040 220919 58828.8 210329 186249 FALSE TRUE 194279.543 225384.5586 245036.4682 230332.0613 251298.3372 233671.3457 223622.6728 57613.96472 186453.3337 173634.1893 1.118901431 1.298042508 1.411222462 1.326536336 1.447286034 1.345768058 1.287895395 0.331812329 1.073828457 1 17.40569152 1.858255893 8.983700069 0.739725504 1.330727616 0.572128862 0.203065849 0.187762923 13.10765682 0.081051372 0.051081265 72.15324927 -1.858255893 0.591002113 DWHRPCLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DWHRPCLR 8 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ; 113.7 0.0025523 833300000 151385 164181 119127 159243 155429 137392 149685 112570 156369 162313 FALSE TRUE 145468.7068 159498.7186 140655.8989 167461.5503 160428.5149 140170.1604 151516.8898 110245.3902 138618.6467 151319.3959 0.961335498 1.054053366 0.929529873 1.106676043 1.06019796 0.926319852 1.001305146 0.728560866 0.916066614 1 17.2072374 1.858292767 10.78598003 0.853443112 1.00785415 0.29801604 0.084017943 0.414812816 35.24749055 0.033725389 0.021488884 72.1593757 -1.858292767 0.154411039 NFEDVAFDEKK ddPTM_BT-474_Pertuzumab_2h_R1 6 NFEDVAFDEKK 11 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 178.15 1.23E-05 16640800000 16273080 15606090 12318920 11135170 13120730 14402080 15165140 17241780 20983500 17758440 FALSE TRUE 15637110.04 15161019.59 14545222.88 11709857.46 13542770.2 14693299.93 15350735.52 16885731.22 18601541.05 16555645.04 0.94451832 0.915761334 0.878565761 0.707303003 0.818015255 0.887509963 0.927220624 1.019937983 1.123576943 1 23.98081989 1.858324685 1.845559741 1.063911508 0.852354359 0.619806683 0.066656946 0.232083433 1.491948303 0.047717402 0.021457698 72.1646792 -1.858324685 -0.211557148 TKPTQAAGPSS(ph)PQKPPT(ph)PEETK ddPTM_BT-474_Pertuzumab_2h_R1 6 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 2 TKPTQAAGPS(0.004)S(0.996)PQKPPT(1)PEETK;TKPTQAAGPS(0.003)S(0.997)PQKPPT(1)PEETK;TKPTQAAGPS(0.055)S(0.944)PQKPPT(0.999)PEET(0.001)K;TKPTQAAGPS(0.03)S(0.97)PQKPPT(0.595)PEET(0.405)K;TKPTQAAGPS(0.025)S(0.975)PQKPPT(0.932)PEET(0.068)K;TKPTQAAGPS(0.005)S(0.995)PQKPPT(0.986)PEET(0.014)K 176.94 1.24E-16 9613620000 6206210 4029150 4122020 3122190 4195750 3739870 4758810 6201240 7301520 5516600 TRUE FALSE 5963664.452 3914242.587 4866960.708 3283326.6 4330710.109 3815492.734 4817049.74 6073182.227 6472682.06 5142955.768 1.159579184 0.76108813 0.946335323 0.638412374 0.842066373 0.741887138 0.936630599 1.180873898 1.258552932 1 22.29416632 1.858353303 3.659207854 1.163760942 0.838864258 0.45754535 0.14408973 0.188603864 4.173363598 0.069539264 0.037715328 72.16943463 -1.858353303 -0.324896683 TSPT(ph)TPEASATNS(ph)PCTSKPATPAPSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPTTPEASATNSPCTSKPATPAPSEK 27 1 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 2 T(0.01)S(0.041)PT(0.434)T(0.381)PEAS(0.251)AT(0.216)NS(0.663)PCT(0.003)S(0.001)KPATPAPSEK 77.689 0.032922 983060000 426940 343630 340260 333330 342360 360020 388020 427640 531930 411810 TRUE FALSE 410254.7128 333830.0088 401752.551 350533.2012 353372.3203 367299.8511 392768.7048 418809.0846 471547.5364 383917.7419 1.068600557 0.869535248 1.046454767 0.913042465 0.920437588 0.95671497 1.023054321 1.09088234 1.228251485 1 18.55043771 1.858492009 2.336606138 1.122630235 0.958556382 0.412867446 0.076306718 0.245909114 2.484559023 0.042090575 0.020302716 72.19248802 -1.858492009 -0.164073854 RFS(ph)DQAGPAIPTSNSYSK ddPTM_BT-474_Pertuzumab_2h_R1 6 RFSDQAGPAIPTSNSYSK 18 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK 234.73 5.49E-24 7307560000 6814530 7734320 6896350 8530970 9753060 8830370 7149890 7435810 7380570 6848410 TRUE FALSE 6548210.634 7513744.766 8142673.853 8971254.384 10066776.03 9008926.132 7237392.493 7282257.925 6542758.635 6384561.091 1.025632074 1.176861598 1.275369401 1.405148178 1.576737365 1.411048622 1.133577139 1.140604314 1.024778139 1 22.60615601 1.858502349 2.057696265 1.045031747 1.316526812 0.389980839 0.144214935 0.371437 2.951243312 0.101528366 0.047146137 72.19420685 -1.858502349 0.271495064 IGDEYFTFITDCKDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGDEYFTFITDCKDPK 16 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 165.45 6.40E-09 1579130000 2991780 2597760 2464100 2053380 2572410 2570700 2908430 3576480 4176100 3718690 FALSE TRUE 2874857.93 2523674.428 2909417.684 2159355.188 2655153.904 2622681.315 2944024.236 3502624.438 3702046.636 3466819.814 0.829249307 0.727950849 0.839218027 0.622863403 0.765875946 0.756509267 0.849200245 1.010327801 1.067850893 1 21.72518142 1.858885572 2.204009176 1.039466964 0.753139149 0.81125778 0.058030511 0.116342642 1.053374763 0.034199844 0.016217502 72.25793924 -1.858885572 -0.286327816 LGS(ph)PGAPQQEDAMDDKELIEYFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSPGAPQQEDAMDDKELIEYFK 23 1 H0YGG4 H0YGG4 EIF2B1 1 LGS(1)PGAPQQEDAMDDKELIEYFK 221.8 1.04E-32 126170000 113920 74788 75506 60119 70234 81294 90021 121140 142010 114610 TRUE FALSE 109467.8805 72655.11947 89151.61382 63221.74879 72493.14039 82937.82038 91122.70393 118638.4167 125889.6202 106847.3626 1.024525807 0.679989826 0.834382914 0.591701538 0.67847384 0.776227118 0.852830633 1.110354189 1.178219257 1 16.70519177 1.85891002 2.756688173 1.112998397 0.753093481 0.6172961 0.116406015 0.162443688 2.218261764 0.06337653 0.032043623 72.2620071 -1.85891002 -0.359904915 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHS(ph)PHSHL ddPTM_BT-474_Pertuzumab_2h_R1 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHS(0.967)PHS(0.033)HL 201.73 3.65E-38 183550000 25769 34981 26514 39433 30445 37215 30840 2048.9 26313 17566 TRUE FALSE 24761.91899 33983.37613 31305.6696 41468.14186 31424.29107 37967.5128 31217.42915 2006.589499 23326.05855 16376.23917 1.512063834 2.075163642 1.911651953 2.532213985 1.918895464 2.318451288 1.906263631 0.122530544 1.424384335 1 13.99931646 1.85899335 7.187492265 0.786870581 2.058662131 0.654909309 0.391125388 0.133002369 7.23337235 0.159391407 0.098301612 72.27587367 -1.85899335 1.27179155 IYEDGDDDMKR ddPTM_BT-474_Pertuzumab_2h_R1 4 IYEDGDDDMKR 11 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;; 189.57 4.25E-06 8300100000 4094040 3662350 3375030 3506560 3692070 3917670 4012640 4653790 5327960 4978130 FALSE TRUE 3934040.391 3557903.364 3984972.998 3687533.982 3810828.785 3996887.972 4061747.889 4557687.61 4723152.317 4640956.821 0.847678731 0.76663143 0.858653323 0.794563303 0.821129981 0.861220676 0.875196225 0.982057749 1.017710894 1 22.14599084 1.859138807 1.427996648 1.016465764 0.817622252 0.897931194 0.02657891 0.106327071 0.406181258 0.018441372 0.007835593 72.30008484 -1.859138807 -0.198843512 APTAALPQGVVMAASPGSLHS(ph)PQQLAEEATR ddPTM_BT-474_Pertuzumab_2h_R1 1 APTAALPQGVVMAASPGSLHSPQQLAEEATR 31 0 Q03060-6;G5E998;Q03060-26;Q03060-32;Q03060-21;Q03060-31;Q03060;J3KR46;C9K092;C9IYM9;Q03060-12;Q03060-7;Q03060-22;Q03060-20;Q03060-16;Q03060-15;E9PAR2;Q03060-1;Q03060-23;Q03060-9;Q03060-24;Q03060-30;Q03060-8;Q03060-2;Q03060-13;Q03060-14;Q03060-19;Q03060-17;Q03060-29;Q03060-28;Q03060-10;Q03060-27;Q03060-11;E9PB41 Q03060-6 CREM cAMP-responsive element modulator 1 APTAALPQGVVMAAS(0.035)PGS(0.035)LHS(0.929)PQQLAEEAT(0.001)R 103.68 0.00010745 125800000 24937 25869 20923 28145 19349 23446 24401 30599 26660 30749 TRUE FALSE 23962.43447 25131.24145 24704.25153 29597.56682 19971.37816 23920.09418 24699.62674 29967.11996 23633.66857 28666.34284 0.835908319 0.876681117 0.861785951 1.032484924 0.696683852 0.834431316 0.861624619 1.045376458 0.824439612 1 14.80707024 1.859410474 11.16193595 0.960385813 0.857511522 0.196092737 0.092273167 0.746882046 65.35731138 0.037697342 0.024056877 72.34532535 -1.859410474 -0.102874291 APSQAAESS(ph)PAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 APSQAAESSPAKK 13 1 Q8NFH8-3;Q8NFH8-2;Q8NFH8-4;Q8NFH8 Q8NFH8-3 REPS2 RalBP1-associated Eps domain-containing protein 2 1 APSQAAES(0.202)S(0.798)PAKK 114.29 0.00046217 367410000 238170 201040 187760 170850 196990 192180 232580 267710 300390 307070 TRUE FALSE 228862.0531 195306.536 221692.4087 179667.589 203326.3623 196066.0113 235426.3836 262181.6949 266290.9865 286271.8754 0.799456994 0.682241438 0.774412116 0.627611737 0.710256158 0.684894424 0.822387401 0.915848595 0.930203102 1 18.12702642 1.859524472 1.826928204 0.960346397 0.709698665 0.821952405 0.0492336 0.129584907 0.816135749 0.03142309 0.014103947 72.3643178 -1.859524472 -0.250647732 LTRPAAS(ph)PAVGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTRPAASPAVGEK 13 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 LTRPAAS(1)PAVGEK 104.29 0.00093466 1644600000 3025100 2634200 2233000 2335000 2273000 2606100 2603400 3003100 3162900 3093200 TRUE FALSE 2906875.748 2559075.195 2636552.773 2455509.63 2346113.109 2658797.128 2635261.188 2941084.936 2803860.852 2883694.809 1.008038624 0.887429276 0.914296743 0.851515085 0.813578851 0.922010581 0.913848851 1.019901595 0.972315393 1 21.45948706 1.859564605 4.150059341 0.997506519 0.895055748 0.44810775 0.04869183 0.208204531 5.597519599 0.024328112 0.013589468 72.37100524 -1.859564605 -0.102450772 SLVESVSSS(ph)PNKESNEEEQVWHFLGK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 SLVES(0.004)VS(0.091)S(0.452)S(0.453)PNKESNEEEQVWHFLGK;SLVESVS(0.004)S(0.109)S(0.887)PNKES(0.001)NEEEQVWHFLGK;S(0.001)LVES(0.056)VS(0.067)S(0.398)S(0.478)PNKESNEEEQVWHFLGK;SLVESVSSS(0.999)PNKESNEEEQVWHFLGK;SLVES(0.006)VS(0.042)S(0.419)S(0.532)PNKESNEEEQVWHFLGK 246.32 1.28E-45 5193910000 3556900 3049430 2557690 2447500 3179740 2813570 3126240 3419480 4052920 3368950 TRUE FALSE 3417892.416 2962463.242 3019921.479 2573815.768 3282019.225 2870462.313 3164499.86 3348866.543 3592849.513 3140768.016 1.088234597 0.943228926 0.961523253 0.819486111 1.044973461 0.913936432 1.007556064 1.06625721 1.143939793 1 21.58268596 1.859599326 2.894345134 1.079519228 0.958361859 0.286882156 0.075369236 0.298963864 4.449779862 0.039630289 0.02030842 72.37679139 -1.859599326 -0.121157369 AST(ph)PVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASTPVLK 7 0 Q04724;A0A669KBK8;A0A669KAE5;F6T2C8 Q04724 TLE1 Transducin-like enhancer protein 1 1 AS(0.006)T(0.994)PVLK;AS(0.416)T(0.584)PVLK 134.48 0.035442 842220000 3726500 3399200 2867200 2903100 2977400 3397700 3466200 4168900 4589900 4465100 TRUE FALSE 3580864.26 3302258.144 3385366.821 3052929.339 3073170.775 3466403.822 3508620.392 4082810.758 4068873.794 4162674.8 0.860231566 0.793301976 0.813267186 0.733405679 0.738268282 0.832734717 0.84287641 0.980814249 0.97746617 1 21.98907942 1.859627321 1.887817925 0.995217752 0.788785016 0.84572845 0.036515749 0.124069177 0.833520711 0.025059739 0.0113545 72.38145696 -1.859627321 -0.206432736 EGQPSPADEKGNDS(ph)DGEGESDDPEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGQPSPADEKGNDSDGEGESDDPEK 25 1 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEK;EGQPSPADEKGNDS(1)DGEGESDDPEK;EGQPSPADEKGNDS(1)DGEGESDDPEK;EGQPS(0.001)PADEKGNDS(0.991)DGEGES(0.008)DDPEK 270.82 3.89E-53 5897500000 4254750 3101300 3054580 2557730 3239260 2899380 3615450 4678610 5490200 4295200 TRUE FALSE 4088469.666 3012853.96 3606610.555 2689734.752 3343453.74 2958007.45 3659696.959 4581995.069 4866975.513 4004282.278 1.021024339 0.752407985 0.900688389 0.671714571 0.834969542 0.738711021 0.913945797 1.144273742 1.215442662 1 21.93311225 1.859672577 3.422405505 1.134823578 0.814880166 0.625373748 0.103224464 0.139233783 2.761192459 0.050112272 0.026776112 72.38899995 -1.859672577 -0.319943412 IPHGVSGVQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IPHGVSGVQDR 11 0 Q9BPU6 Q9BPU6 DPYSL5 Dihydropyrimidinase-related protein 5 0 ; 148.18 3.49E-05 842170000 172900 177240 141144 181693 172220 167907 173411 152269 184744 202111 FALSE TRUE 166142.8768 172185.2887 166651.8605 191070.1975 177759.6127 171302.1946 175533.2557 149124.5919 163772.6356 188421.8419 0.881760178 0.91382871 0.884461476 1.014055459 0.943412987 0.909141917 0.931597175 0.79144005 0.869180738 1 17.52360669 1.859752488 21.25555514 0.863128304 0.926914912 0.037838901 0.060105145 8.847664431 1514.43985 0.024066638 0.015527156 72.40232091 -1.859752488 0.063786607 VDVGKDQEFTVK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDVGKDQEFTVK 12 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 192.18 4.03E-06 2565000000 4538780 4361140 3814910 3013910 3808010 4341880 4348720 4953400 5768350 5445810 FALSE TRUE 4361399.46 4236764.557 4504349.099 3169458.256 3930498.1 4429675.788 4401940.936 4851110.559 5113551.091 5076960.438 0.859057208 0.83450809 0.887213748 0.624282638 0.774183322 0.872505477 0.867042592 0.955514745 1.007207197 1 22.27553359 1.859799643 1.33102512 1.006309 0.798631102 0.586996812 0.068692697 0.318523829 1.051806854 0.055642829 0.023480162 72.41018266 -1.859799643 -0.207677899 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEK ddPTM_BT-474_Pertuzumab_2h_R1 5 KISENSYSLDDLEIGPGQLSSSTFDSEK 28 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.782)ENS(0.141)YS(0.077)LDDLEIGPGQLSSSTFDSEK;KIS(0.927)ENS(0.07)YS(0.004)LDDLEIGPGQLSSSTFDSEK;KIS(0.428)ENS(0.095)Y(0.049)S(0.428)LDDLEIGPGQLSSSTFDSEK;KIS(0.948)ENS(0.044)YS(0.008)LDDLEIGPGQLSSSTFDSEK;KIS(0.992)ENS(0.006)YS(0.002)LDDLEIGPGQLSSSTFDSEK 264.38 3.89E-54 9365410000 1346457 1163063 1295681 1257291 1299771 1290582 1456530 1756940 1952970 1919070 TRUE FALSE 1293835.972 1129893.582 1529839.379 1322179.939 1341579.315 1316678.452 1474355.45 1720658.575 1731277.033 1789089.68 0.723181172 0.631546643 0.855093736 0.739023848 0.749867002 0.735948828 0.824081356 0.961750881 0.967685999 1 20.77079427 1.860002782 2.050323275 0.985566418 0.738856004 0.811979012 0.051116372 0.130933748 1.032492717 0.032443403 0.015067997 72.44406008 -1.860002782 -0.246710414 KKPS(ph)SEER ddPTM_BT-474_Pertuzumab_2h_R1 3 KKPSSEER 8 2 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 KKPS(0.636)S(0.364)EER;KKPS(0.649)S(0.351)EER;KKPS(0.608)S(0.392)EER 101.95 0.0039836 398149000 638450 480882 500795 489050 509800 495240 581278 650440 738020 714100 TRUE FALSE 613498.6682 467167.7162 591299.7966 514289.9291 526198.18 505254.0921 588391.854 637008.1867 654243.0636 665733.3709 0.921538104 0.701733962 0.888193115 0.772516373 0.790403791 0.758943616 0.883825086 0.956851819 0.982740377 1 19.34458496 1.860026377 2.309519513 0.984287851 0.802680699 0.627073208 0.060030057 0.17460941 1.724979675 0.03293173 0.015849931 72.44799597 -1.860026377 -0.181607152 RELDDLEQWIQER ddPTM_BT-474_Pertuzumab_2h_R1 1 RELDDLEQWIQER 13 1 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 111.81 0.001524 45759000 32948 34525 31243 34264 41905 32966 34559 31736 34620 33534 FALSE TRUE 31660.35573 33540.3808 36889.3051 36032.36915 43252.91238 33632.59511 34981.94338 31080.64051 30690.08274 31262.71231 1.012719415 1.072855754 1.179977755 1.152566955 1.383530384 1.075805412 1.118966999 0.994176071 0.981683305 1 14.93215533 1.86008417 2.055954561 0.984827585 1.155554307 0.356896106 0.092820511 0.357146466 2.831095365 0.061286365 0.028489146 72.45763748 -1.86008417 0.170726722 SNS(ph)EDKLNSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SNSEDKLNSK 10 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 S(0.006)NS(0.994)EDKLNSK;SNS(1)EDKLNSK;SNS(1)EDKLNSK;SNS(0.998)EDKLNS(0.002)K 218.12 1.82E-08 5410280000 4800760 3767680 3269320 2969330 3293990 3281070 3858310 4715590 5361790 4452310 TRUE FALSE 4613140.992 3660229.455 3860158.85 3122577.477 3399944.18 3347415.483 3905529.152 4618211.419 4753142.078 4150751.078 1.111399095 0.881823407 0.929990447 0.752292156 0.819115412 0.806460185 0.940921072 1.112620664 1.145128192 1 21.98494098 1.860125598 3.816613723 1.095746396 0.876470765 0.461472145 0.097085128 0.197993377 4.68137784 0.049349286 0.027057643 72.4645497 -1.860125598 -0.219275631 TQLEELEDELQATEDAK ddPTM_BT-474_Pertuzumab_2h_R1 6 TQLEELEDELQATEDAK 17 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3 P35579;P35580;P35749 MYH9;MYH10;MYH11 Myosin-9;Myosin-10;Myosin-11 0 ;;;;; 425.69 3.46E-160 2884510000 1449597 1318626 1243010 1258989 1395122 1400662 1493418 1730049 2032768 1848442 FALSE TRUE 1392945.147 1281020.078 1467649.558 1323965.573 1439997.366 1428984.345 1511694.896 1694322.884 1802016.699 1723245.377 0.808326641 0.743376477 0.851677641 0.768297766 0.835631063 0.829240202 0.877237169 0.983216265 1.04571103 1 20.71669671 1.860177662 1.477851819 1.029074715 0.800272825 0.896156788 0.031213252 0.107239307 0.439655986 0.021744907 0.009294833 72.47323738 -1.860177662 -0.22880189 AAEEQGDDQDS(ph)EKSKPAGSDGER ddPTM_BT-474_Pertuzumab_2h_R1 4 AAEEQGDDQDSEKSKPAGSDGER 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 AAEEQGDDQDS(1)EKSKPAGSDGER;AAEEQGDDQDS(1)EKSKPAGSDGER;AAEEQGDDQDS(1)EKSKPAGSDGER;AAEEQGDDQDS(1)EKSKPAGSDGER 212.28 1.75E-25 1678860000 1435630 1044400 858689 789695 1037590 932701 1047000 1267990 1429720 1053350 TRUE FALSE 1379523.992 1014614.735 1013873.204 830451.2536 1070965.025 951560.8533 1059813.499 1241805.563 1267424.179 982005.6663 1.404802477 1.033206599 1.03245148 0.845668495 1.090589455 0.968997314 1.079233589 1.264560487 1.29064854 1 19.90537182 1.860383121 5.806042575 1.209577065 1.049491825 0.10670294 0.151727672 0.389996507 16.47249264 0.066957152 0.040033658 72.5075317 -1.860383121 -0.16008524 AGT(ph)PVSELTK ddPTM_BT-474_Pertuzumab_2h_R1 4 AGTPVSELTK 10 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 AGT(1)PVSELTK;AGT(1)PVSELTK;AGT(1)PVSELTK;AGT(1)PVSELTK 167.18 5.95E-05 1720630000 4150290 3243390 3285730 2630260 3004260 3023870 3699930 4746990 5295550 4879180 TRUE FALSE 3988092.078 3150891.693 3879534.502 2766008.034 3100894.751 3085014.723 3745210.85 4648962.998 4694421.365 4548708.793 0.87675256 0.692700244 0.852886979 0.608086417 0.681708787 0.67821768 0.823356917 1.022040146 1.032033832 1 22.11702565 1.860392909 3.047514806 1.02282793 0.728158999 0.73228952 0.077156549 0.126119213 2.053625703 0.04102518 0.021315987 72.50916588 -1.860392909 -0.294668931 RASS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 1 RASSPFR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 RAS(0.133)S(0.867)PFR 57.55 0.070383 228990000 235140 350230 296550 434900 343560 380240 299980 224300 180150 296910 TRUE FALSE 225950.4688 340241.7833 350143.1817 457345.2411 354610.9194 387928.7133 303651.245 219668.1266 159700.1273 276800.0212 0.816294984 1.2291971 1.264968045 1.652258692 1.281108715 1.401476458 1.097005859 0.793598662 0.576951282 1 18.07848453 1.860432897 2.909558834 0.760035064 1.288068603 0.496821423 0.216238 0.207127832 3.110460826 0.119685509 0.061454444 72.51584246 -1.860432897 0.528033539 FQESEERPK ddPTM_BT-474_Pertuzumab_2h_R1 5 FQESEERPK 9 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;;; 166.34 5.55E-05 5579180000 5158480 5034530 4344070 4483660 4707920 4988170 5148790 5792500 6446600 6282910 FALSE TRUE 4956880.899 4890950.134 5129140.082 4715062.23 4859354.522 5089034.215 5211802.432 5672882.851 5714808.994 5857362.909 0.846264945 0.835008896 0.875673944 0.804980382 0.829614726 0.868826858 0.889786498 0.968504588 0.975662441 1 22.48181985 1.860502105 1.417224065 0.993735185 0.838950669 0.923568935 0.017930172 0.100055827 0.376210194 0.013447815 0.00571391 72.52739929 -1.860502105 -0.154784516 GCEHYDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GCEHYDR 7 0 Q96PM5-2;Q96PM5;D6RAF6;H0YAI4;Q96PM5-5;Q96PM5-3;Q96PM5-4;Q96PM5-8;Q96PM5-7 Q96PM5-2 RCHY1 RING finger and CHY zinc finger domain-containing protein 1 0 75.213 0.054001 0 59596 62041 53403 71061 64761 79482 60268 48147 48107 62085 FALSE TRUE 57266.92243 60271.65142 63054.11004 74728.46673 66844.09638 81089.1805 61005.57781 47152.74762 42646.09504 57879.92765 0.989409019 1.041322162 1.089395108 1.291094681 1.154875258 1.400989666 1.054002316 0.814664937 0.736802839 1 15.8207755 1.860842129 4.106847317 0.835037574 1.162329715 0.537897397 0.127734213 0.172754589 4.570322455 0.064407873 0.035920001 72.58420581 -1.860842129 0.327292141 DQS(ph)PFSK ddPTM_BT-474_Pertuzumab_2h_R1 8 DQSPFSK 7 0 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 DQS(0.991)PFS(0.009)K;DQS(0.973)PFS(0.027)K;DQS(1)PFSK;DQS(0.957)PFS(0.043)K;DQS(1)PFSK;DQS(1)PFSK;DQS(0.931)PFS(0.069)K;DQS(1)PFSK 200.71 0.0003651 39789650000 20922000 17655790 15786940 15015870 16792920 16439240 18007970 20400900 23149700 19886500 TRUE FALSE 20104345.11 17152264.16 18639991.24 15790840.85 17333079.52 16771652.7 18228356.92 19979614.29 20521843.11 18539569.64 1.08440193 0.925170567 1.005416609 0.851737185 0.93492351 0.904640885 0.983213595 1.077674114 1.106921223 1 24.14410442 1.860886603 3.842867012 1.068591082 0.946909352 0.37317068 0.063449158 0.222355171 5.313124948 0.030746239 0.016892202 72.59163921 -1.860886603 -0.12168173 SKS(ph)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_BT-474_Pertuzumab_2h_R1 6 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.155)KS(0.845)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.193)KS(0.807)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.159)KS(0.841)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.096)KS(0.904)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.163)KS(0.837)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.109)KS(0.89)PLPPEEEAKDEEEDQT(0.001)LVNLDTYTSDLHFQVSK 252.72 3.51E-62 20280299000 3894694 2954492 2845062 2311669 2690158 2661939 3231193 3914380 4808291 3515802 TRUE FALSE 3742485.053 2870232.781 3359227.991 2430974.514 2776689.375 2715765.23 3270737.306 3833546.685 4262473.964 3277673.599 1.141811391 0.875692071 1.024881792 0.741676815 0.847152497 0.828564879 0.997883776 1.169593789 1.300457118 1 21.64424076 1.860897048 3.246203344 1.176056788 0.903564652 0.435151655 0.124447675 0.210592779 3.82084341 0.063991201 0.033786681 72.593385 -1.860897048 -0.272492135 DINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DINVSVGSQQPDTKDSPVCPHFTTNGNENSSIEK 34 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 DINVSVGSQQPDTKDS(1)PVCPHFTTNGNENSSIEK;DINVSVGS(0.006)QQPDT(0.132)KDS(0.862)PVCPHFTTNGNENSSIEK;DINVSVGSQQPDT(0.056)KDS(0.944)PVCPHFTTNGNENSSIEK 388.9 9.68E-167 1740510000 1061060 985310 873753 744884 870280 963072 1081750 1173330 1440780 1337590 TRUE FALSE 1019592.602 957209.9235 1031659.604 783327.5525 898273.3466 982545.9757 1094988.78 1149100.325 1277228.695 1246993.838 0.817640449 0.767613996 0.827317323 0.628172753 0.720351071 0.787931701 0.8781028 0.921496394 1.024246196 1 20.25002291 1.860932761 1.371571874 1.00704159 0.75094963 0.778614246 0.054742898 0.199164637 0.699760055 0.043553846 0.018441457 72.59935481 -1.860932761 -0.25609196 KRESES(ph)ES(ph)DETPPAAPQLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.603)ES(0.642)ES(0.745)DET(0.009)PPAAPQLIK 85.805 0.012766 719430000 326430 286320 242070 214780 250920 279220 288500 359130 408850 351930 TRUE FALSE 313672.7547 278154.4339 285817.4338 225864.8215 258991.0697 284866.0197 292030.7493 351713.84 362439.062 328093.4676 0.956046937 0.847790223 0.871146371 0.688416088 0.789381976 0.868246545 0.89008401 1.071992815 1.104682348 1 18.32374734 1.860990925 2.646449206 1.07000999 0.830606582 0.673410125 0.068937712 0.158584094 2.010688137 0.040707505 0.020387099 72.60907847 -1.860990925 -0.239403408 VGFGDDFDEDELMAELEELEQEELNKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGFGDDFDEDELMAELEELEQEELNKK 27 1 Q96CF2 Q96CF2 CHMP4C Charged multivesicular body protein 4c 0 ; 245.55 3.17E-45 106677000 61054 58018 48393 40801 58179 54288 61051 73194 90542 73035 FALSE TRUE 58667.94218 56363.38345 57138.6916 42906.7445 60050.38037 55385.74056 61798.1604 71682.51832 80264.05174 68088.2744 0.861645308 0.827798677 0.839185485 0.630163488 0.881948924 0.813440215 0.907618249 1.052788001 1.178823409 1 16.05511875 1.86099502 2.041871161 1.097823034 0.805111847 0.71180022 0.076328545 0.161380145 1.261970985 0.047342403 0.021978474 72.60976318 -1.86099502 -0.292711187 DPS(ph)PESNK ddPTM_BT-474_Pertuzumab_2h_R1 1 DPSPESNK 8 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(1)PESNK 119.22 0.0038156 0 783350 580450 591860 595040 608090 580630 667100 746460 851290 756640 TRUE FALSE 752735.816 563896.1343 698822.2679 625750.0857 627649.7671 592370.7364 675264.1694 731045.3401 754655.1281 705392.0989 1.06711688 0.799408067 0.990686271 0.887095399 0.889788485 0.839775123 0.957289103 1.03636735 1.069837796 1 19.42806589 1.861000451 3.435096756 1.039462915 0.908053118 0.362655228 0.0722995 0.233174451 4.650945569 0.034441583 0.018435694 72.6106711 -1.861000451 -0.131409797 NWTEDMEGGISS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 3 NWTEDMEGGISSPVK 15 0 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 NWTEDMEGGIS(0.003)S(0.997)PVK;NWTEDMEGGISS(1)PVK;NWTEDMEGGIS(0.099)S(0.901)PVK 310.08 4.12E-56 649730000 1717770 1579150 1344030 1464680 1432930 1371940 1561440 1734650 1822360 1904280 TRUE FALSE 1650637.649 1534114.188 1586926.119 1540272.31 1479021.495 1399681.567 1580549.37 1698828.871 1615493.333 1775301.419 0.929778815 0.86414294 0.893891089 0.867611716 0.833110073 0.788419111 0.890299164 0.956924189 0.909982561 1 20.75963256 1.861016919 4.222045071 0.949418265 0.861643956 0.510359457 0.040309101 0.200255278 5.520350044 0.020018678 0.011234185 72.61342452 -1.861016919 -0.08777431 S(ph)WTSPK ddPTM_BT-474_Pertuzumab_2h_R1 6 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.98)WT(0.006)S(0.015)PK;S(0.978)WT(0.019)S(0.003)PK;S(0.997)WT(0.003)SPK;S(0.999)WT(0.001)SPK;S(0.996)WT(0.001)S(0.003)PK;S(0.982)WT(0.009)S(0.009)PK 121.85 0.020428 16045340000 6081850 5766280 5265890 5333450 5423330 5460490 5738070 7041020 7068520 6362510 TRUE FALSE 5844164.578 5601831.34 6217553.462 5608709.994 5597776.335 5570904.849 5808294.217 6895620.476 6266131.243 5931571.531 0.985264116 0.944409304 1.048213518 0.945568972 0.943725673 0.939195426 0.979216753 1.162528419 1.056403216 1 22.49998296 1.861045388 8.096868829 1.088120494 0.96769121 0.482428115 0.04852009 0.197822993 12.1942835 0.01995669 0.01247101 72.61818459 -1.861045388 -0.120429284 DHAVVVGVYRPPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHAVVVGVYRPPPK 14 1 P22087 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 131.26 3.44E-05 1566190000 3278200 3061180 2599260 2791470 2877400 2913000 2987730 1845060 3298600 3114400 FALSE TRUE 3150084.32 2973878.144 3069004.102 2935538.101 2969954.184 2971902.856 3024294.733 1806958.866 2924156.757 2903458.914 1.084941931 1.024253565 1.057016542 1.011048611 1.022902088 1.023573243 1.041617885 0.622346973 1.007128685 1 21.46934119 1.861049632 20.2548287 0.833785237 1.035978404 0.316379273 0.103121629 3.447638609 554.8657002 0.039857602 0.025710502 72.6188943 -1.861049632 0.202193167 ILEDHGS(ph)PAGEIDDEDKDKDETETVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILEDHGSPAGEIDDEDKDKDETETVK 26 2 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;H0YBA1 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 ILEDHGS(1)PAGEIDDEDKDKDETETVK 220.62 1.54E-34 301000000 129880 87301 93095 58096 99983 81546 115760 146000 183910 148560 TRUE FALSE 124804.146 84811.26096 109919.3374 61094.34152 103199.044 83194.91599 117176.7055 142985.049 163033.3078 138497.8989 0.901126638 0.612364965 0.793653465 0.441121071 0.745130755 0.600694427 0.84605403 1.032398687 1.177153655 1 17.07950456 1.861155654 2.403436524 1.08963814 0.676564705 0.6596247 0.12419181 0.158696163 1.687311701 0.068698811 0.033483744 72.63662448 -1.861155654 -0.413073435 YYEVLGAAATTDYNNNHEGREEDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 YYEVLGAAATTDYNNNHEGREEDQR 25 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ; 129.32 6.15E-05 1017760000 172583 183868 129008 130899 161460 185804 145960 132089 136817 138529 FALSE TRUE 165838.2656 178624.2647 152322.6154 137654.7131 166653.5075 189561.0842 147746.3021 129361.316 121286.1077 129146.3074 1.284111554 1.383115539 1.179457767 1.065881912 1.2904241 1.467801039 1.14402266 1.001664845 0.939137248 1 16.97864687 1.861191239 3.262710521 0.977713486 1.271256911 0.618732124 0.103958181 0.178200421 3.260769901 0.058360421 0.030858178 72.64257642 -1.861191239 0.293543425 YS(ph)PPAISPLVSEK ddPTM_BT-474_Pertuzumab_2h_R1 4 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YS(1)PPAISPLVSEK;YS(0.999)PPAIS(0.001)PLVSEK;YS(1)PPAISPLVSEK;Y(0.001)S(0.998)PPAISPLVSEK 216.27 2.91E-11 793220000 916746 820509 984329 1018345 1010830 1039801 1192260 1383541 1634553 1723212 TRUE FALSE 880918.5528 797108.8867 1162219.147 1070901.907 1043344.265 1060826.489 1206851.235 1354970.395 1449005.396 1606497.316 0.548347354 0.496178163 0.723449168 0.66660672 0.649452853 0.660335052 0.751231404 0.843431471 0.90196565 1 20.61548714 1.861351517 0.390177566 1.028278111 0.539547293 0.867504234 0.053807296 0.404445117 0.166251292 0.068315619 0.064920198 72.66939044 -1.861351517 -0.488730817 TKPIVKPQTSPEYGQGINPISR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKPIVKPQTSPEYGQGINPISR 22 2 O95793-2;O95793-3;O95793;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ; 268.13 3.64E-38 2065960000 1373150 1316730 1124490 1301850 1165200 1301900 1318140 1651960 1577400 1642010 FALSE TRUE 1319485.78 1279178.15 1327710.357 1369038.635 1202679.716 1328225.31 1334271.792 1617846.449 1398340.165 1530795.2 0.861961012 0.835629841 0.86733376 0.894331674 0.785656838 0.867670156 0.871620052 1.056866685 0.913473053 1 20.54584985 1.86170433 6.473177145 0.992343478 0.852643023 0.687640324 0.041897012 0.12302406 5.89862645 0.017435452 0.010609889 72.7284497 -1.86170433 -0.139700455 QGDFESDHSGYVRPVPVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGDFESDHSGYVRPVPVPR 19 1 A6NHR9;A6NHR9-2 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 0 124.84 1.71E-05 499200000 108310 122670 88330 123780 105170 104480 99833 100980 99661 94355 FALSE TRUE 104077.1255 119171.5717 104293.1959 130168.3006 108552.8886 106592.6572 101054.7861 98894.72771 88347.90109 87964.25181 1.183175248 1.354772754 1.185631592 1.479786367 1.234056862 1.211772453 1.148816525 1.124260432 1.004361423 1 16.42462972 1.861791518 0.930800321 0.998288639 1.296083141 0.633391272 0.083485312 0.340002797 0.54461107 0.068221486 0.030299056 72.74305197 -1.861791518 0.297794503 VQAMQISSEKEEDDNEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ;;; 280.65 1.58E-39 2144420000 1673400 1245705 1329273 1183495 1321444 1374573 1637510 1906380 2323010 2114600 FALSE TRUE 1608001.678 1210178.713 1569502.201 1244575.319 1363949.446 1402367.808 1657550.337 1867012.587 2059311.644 1971376.259 0.815674669 0.613875057 0.796145431 0.631323074 0.691876774 0.711364866 0.840808714 0.947060501 1.044606089 1 20.91077173 1.861911039 1.673797971 1.020023293 0.702949641 0.817694226 0.061157959 0.131672729 0.695673539 0.039011323 0.017140629 72.76307404 -1.861911039 -0.317073652 KPS(ph)VSEEVQATPNK ddPTM_BT-474_Pertuzumab_2h_R1 4 KPSVSEEVQATPNK 14 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 KPS(0.889)VS(0.111)EEVQATPNK;KPS(0.999)VS(0.001)EEVQATPNK;KPS(0.992)VS(0.008)EEVQATPNK;KPS(0.981)VS(0.019)EEVQATPNK 176.85 1.33E-06 11675380000 11787320 11019660 10155390 9415920 10658310 11605420 11092830 12090450 13390980 13091080 TRUE FALSE 11326658.5 10705390.09 11990694.88 9901876.76 11001144.22 11840089.54 11228587.37 11840777.98 11870892.09 12204409.49 0.928079192 0.87717395 0.982488738 0.811335998 0.901407334 0.970148499 0.920043479 0.970204908 0.972672385 1 23.54089916 1.861917585 0.844533311 0.993985431 0.90163811 0.362453961 0.044012612 0.646142247 0.861378472 0.037511437 0.017387726 72.76417082 -1.861917585 -0.092347321 WIAQDLSSLAGLLDQHGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 WIAQDLSSLAGLLDQHGVR 19 0 A0A2P0CU24;A0A0A0MRV4;J3KPF5;A0A2P0CTB1;A0A0A0MT35;J3KPF6;A0A0G2JRR6;A0A0G2JSF1;J3QKK8;J3KRV9;A0A2P0CTH9;Q8TBF2-2;Q8TBF2;Q8TBF2-7;Q8TBF2-3;Q8TBF2-4;Q8TBF2-6 A0A2P0CU24 FAM213B Prostamide/prostaglandin F synthase 0 ; 193.22 5.77E-15 142251000 182154 185869 173096 176251 197264 189338 181667 161140 186907 175577 FALSE TRUE 175035.2203 180568.1981 204378.2977 185347.3352 203609.1757 193166.5441 183890.2951 157812.4027 165690.1009 163685.0134 1.06934176 1.103144352 1.24860727 1.13234151 1.243908477 1.180111362 1.123440022 0.96412249 1.012249671 1 17.32056271 1.862112585 4.017796028 0.991179115 1.165523256 0.667069098 0.053918828 0.136951629 3.50412841 0.027156585 0.015082135 72.79684967 -1.862112585 0.174344141 TKPTQAAGPSS(ph)PQKPPTPEETK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 1 TKPTQAAGPS(0.029)S(0.971)PQKPPTPEETK;TKPTQAAGPS(0.158)S(0.842)PQKPPT(0.001)PEETK 193.34 3.92E-18 1549800000 2156000 1668560 1544900 1305040 1586570 1553760 1837180 2179900 2534100 2240500 TRUE FALSE 2071741.136 1620974.302 1824097.796 1372393.271 1637603.465 1585178.092 1859663.958 2134884.303 2246439.592 2088748.939 0.991857421 0.776050329 0.873296815 0.657040798 0.784011632 0.758912697 0.89032431 1.022087558 1.075495264 1 20.99420767 1.862236918 2.682511896 1.04058374 0.801098539 0.594801063 0.082942207 0.178987196 2.324220945 0.046041084 0.023166298 72.81769338 -1.862236918 -0.239485201 KGIAFPTSISVNNCVCHFSPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGIAFPTSISVNNCVCHFSPLK 22 1 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7;F8VZ69 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 159.46 1.27E-11 278620000 164720 235900 186440 218720 185100 220430 199120 164210 174320 223290 FALSE TRUE 158282.5603 229172.363 220133.8553 230008.1654 191053.9096 224887.2456 201556.8901 160819.0061 154531.9244 208166.3694 0.760365667 1.100909641 1.057490006 1.10492471 0.917794311 1.08032458 0.968249053 0.772550372 0.742348175 1 17.66737749 1.862239838 4.924979937 0.818327981 1.01195563 0.279590457 0.116917979 0.237485415 8.122392772 0.05160169 0.029936968 72.81818295 -1.862239838 0.19362765 ATIAGGGVIPHIHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATIAGGGVIPHIHK 14 0 Q71UI9;P0C0S5;Q71UI9-4;Q71UI9-3 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z 0 ; 150.21 4.21E-06 8136300000 9597100 9167200 7537000 8041300 7810600 7648200 7864000 91568 7481000 3981100 FALSE TRUE 9222034.722 8905760.432 8899103.56 8456312.457 8061835.042 7802851.844 7960241.984 89677.0888 6631788.243 3711456.551 2.484748129 2.39953245 2.397738849 2.278434986 2.172148571 2.102369174 2.144775744 0.024162236 1.786842484 1 21.82355405 1.862300814 7.691263173 0.864841729 2.289756447 0.6925245 0.411027801 0.131205073 7.620854544 0.165421285 0.102861773 72.8284076 -1.862300814 1.424914718 SSSQRS(ph)PS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSQRSPSPGPNHTSNSSNASNATVVPQNSSAR 33 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 2 S(0.331)S(0.361)S(0.362)QRS(0.526)PS(0.394)PGPNHT(0.01)S(0.01)NS(0.004)S(0.002)NASNATVVPQNSSAR 133.17 6.17E-08 201770000 95704 172640 95621 155600 128170 171070 117130 99687 90492 108590 TRUE FALSE 91963.78187 167716.4762 112901.8418 163630.5346 132292.7045 174529.1526 118563.472 97628.42861 80219.72753 101235.1026 0.908417926 1.656702784 1.11524401 1.616341866 1.306786886 1.723998378 1.171169574 0.964373287 0.792410197 1 16.6273501 1.862351741 3.124740781 0.907717777 1.396548958 0.425284177 0.241649077 0.217994459 3.704228219 0.117924964 0.061744614 72.83694822 -1.862351741 0.488831181 QPSS(ph)PYEDKDKDKK ddPTM_BT-474_Pertuzumab_2h_R1 5 QPSSPYEDKDKDKK 14 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.141)S(0.859)PYEDKDKDKK;QPS(0.03)S(0.97)PYEDKDKDKK;QPS(0.124)S(0.876)PYEDKDKDKK;QPS(0.008)S(0.992)PYEDKDKDKK;QPS(0.002)S(0.998)PYEDKDKDKK 197.09 1.71E-08 9780920000 9263330 5432970 5242990 3209311 5508130 5137130 6138290 8066480 9744680 6388190 TRUE FALSE 8901308.822 5278027.015 6190514.923 3374943.925 5685304.004 5241006.288 6213412.229 7899904.369 8638504.779 5955512.201 1.49463363 0.886242331 1.039459699 0.566692471 0.95462889 0.880026119 1.043304424 1.326486136 1.450505765 1 22.50579416 1.862480627 3.941384697 1.289685626 0.95123391 0.219288495 0.239314206 0.30094537 7.476855344 0.115730331 0.064011014 72.85856732 -1.862480627 -0.338451716 DKENGNNS(ph)PLPK ddPTM_BT-474_Pertuzumab_2h_R1 3 DKENGNNSPLPK 12 1 Q6P1L5 Q6P1L5 FAM117B Protein FAM117B 1 DKENGNNS(1)PLPK;DKENGNNS(1)PLPK;DKENGNNS(1)PLPK 93.754 0.0042358 1694300000 1476890 1350170 1143400 1144970 1232690 1190930 1380580 1643780 1873290 1632450 TRUE FALSE 1419171.506 1311664.474 1350037.815 1204062.039 1272340.593 1215011.421 1397475.951 1609835.369 1660641.973 1521882.707 0.932510435 0.861869622 0.88708401 0.791166121 0.836030653 0.798360751 0.918254701 1.05779201 1.091176057 1 20.53742574 1.862597625 3.265232455 1.05630243 0.850108121 0.799215806 0.044288117 0.102083622 1.869766142 0.023454684 0.012416215 72.87819792 -1.862597625 -0.206194309 KAEFER ddPTM_BT-474_Pertuzumab_2h_R1 3 KAEFER 6 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ;; 100.45 0.060363 1695010000 1808060 1764090 1473820 1716140 1790880 1627650 1751350 1895130 2097220 1896630 FALSE TRUE 1737399.016 1713779.88 1740172.059 1804710.191 1848485.282 1660562.198 1772783.545 1855994.903 1859152.378 1768169.561 0.982597515 0.969239556 0.984165828 1.020665795 1.045423088 0.939141944 1.002609469 1.049670204 1.051455935 1 20.7538252 1.862747552 5.462499433 1.037814374 0.991286968 0.293510332 0.029851499 0.271752249 10.61949218 0.013834869 0.008189636 72.90336115 -1.862747552 -0.046527406 GSLLPTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 GSLLPTSPR 9 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128 BRD8 Bromodomain-containing protein 8 1 GSLLPT(0.004)S(0.996)PR;GSLLPT(0.01)S(0.99)PR;GSLLPT(0.013)S(0.987)PR;GSLLPT(0.001)S(0.999)PR;GSLLPT(0.002)S(0.998)PR;GSLLPT(0.029)S(0.971)PR 127.7 0.00045962 3352170000 6028650 6819820 6013960 7134350 6996230 6670740 6152800 5888230 5505690 6255410 TRUE FALSE 5793043.693 6625325.411 7100816.352 7502554.658 7221270.092 6805626.933 6228099.807 5766635.993 4880707.153 5831725.509 0.993367003 1.136083206 1.217618412 1.286506823 1.238273317 1.16700056 1.067968614 0.988838721 0.836923333 1 22.47549138 1.862771025 1.864705883 0.921770977 1.181870018 0.611212778 0.082963843 0.227595522 1.490721032 0.057530075 0.026041972 72.90730171 -1.862771025 0.260099041 VDVADQAQDKDRDDR ddPTM_BT-474_Pertuzumab_2h_R1 7 VDVADQAQDKDRDDR 15 2 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;;; 232.78 8.01E-15 21524150000 12397200 11033900 10890225 11216100 11265540 11352140 13220800 15105430 17374880 16827590 FALSE TRUE 11912703.72 10719223.98 12858330.91 11794964.27 11627906.33 11581688.05 13382600.11 14793497.59 15402556.46 15687842.34 0.759358965 0.683282235 0.819636673 0.751853825 0.741204945 0.738258825 0.853055494 0.94299122 0.981814843 1 23.90314361 1.862835004 1.747216306 0.989251093 0.747561944 0.905678781 0.032819411 0.095882727 0.552013622 0.02200103 0.009781473 72.91804295 -1.862835004 -0.24168915 SIMEECGGVHIHFPVEGSGSDTVVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIMEECGGVHIHFPVEGSGSDTVVIR 26 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3;H7C2D1 Q00341 HDLBP Vigilin 0 ; 241.65 2.31E-45 260510000 100434 111191 103124 138382 117475 129495 113401 24344 116476 62703 FALSE TRUE 96508.92824 108019.9415 121760.8008 145523.9116 121253.6901 132113.4776 114788.8354 23841.28789 103254.1328 58456.06996 1.650965046 1.847882378 2.082945379 2.489457668 2.074270305 2.260047207 1.963676919 0.407849654 1.766354339 1 15.83506522 1.862929248 7.627424591 1.0197964 2.078844906 0.602435072 0.370455302 0.163554652 9.400321784 0.154497183 0.095992886 72.93386821 -1.862929248 1.059048505 NGALDQQKDELDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGALDQQKDELDVR 14 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 87.566 0.0062856 550800000 1629990 1428690 1184140 1166110 1366030 1430000 1420190 1671910 1841270 1583340 FALSE TRUE 1566288.189 1387945.16 1398140.439 1226293.077 1409969.596 1458915.58 1437570.71 1637384.474 1632256.749 1476098.972 1.061099709 0.9402792 0.947186107 0.830766162 0.955199904 0.988358916 0.973898592 1.109264694 1.105790858 1 20.49335803 1.862977421 4.091214919 1.081015563 0.949449456 0.431170865 0.060292438 0.200272362 5.266023598 0.029957288 0.016713276 72.94195864 -1.862977421 -0.131566106 KAEGEPQEES(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 10 KAEGEPQEESPLK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK 219.23 1.40E-11 54822380000 25817790 18617660 21198010 18070150 19937560 18692540 23915540 30040650 33756510 31880470 TRUE FALSE 24808802.22 18086702.57 25028961.95 19002752.61 20578869.72 19070515.97 24208225.53 29420300.08 29924612.5 29721177.37 0.834718017 0.608545965 0.84212552 0.639367424 0.692397527 0.641647393 0.814510988 0.98987667 1.006844787 1 24.82498793 1.862986024 2.846340712 1.002807836 0.707568322 0.752570732 0.07388848 0.117474038 1.695412859 0.037692964 0.019280138 72.94340362 -1.862986024 -0.295239514 AIPVS(ph)PSAVEEDEDEDGHTVVATAR ddPTM_BT-474_Pertuzumab_2h_R1 3 AIPVSPSAVEEDEDEDGHTVVATAR 25 0 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 AIPVS(0.839)PS(0.161)AVEEDEDEDGHTVVATAR;AIPVS(0.764)PS(0.236)AVEEDEDEDGHTVVATAR;AIPVS(0.819)PS(0.181)AVEEDEDEDGHTVVATAR 277.07 2.72E-53 3464970000 549679 661119 651026 813957 752398 794959 592496 563699 509980 533176 TRUE FALSE 528196.937 642264.5334 768680.8802 855965.4183 776599.565 811033.6156 599747.1433 552058.4187 452089.2084 497063.5146 1.062634696 1.292117636 1.546443981 1.722044353 1.562374912 1.631649863 1.206580499 1.110639591 0.909520001 1 18.92307069 1.863137232 2.168646369 0.985400527 1.478136417 0.563886521 0.182171391 0.241837591 2.119526575 0.121308384 0.057445524 72.9688047 -1.863137232 0.49273589 AQLEQSVEENKER ddPTM_BT-474_Pertuzumab_2h_R1 4 AQLEQSVEENKER 13 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 ;;; 178.68 1.31E-05 2205330000 2048490 2093950 1661730 1774190 1930130 2004580 2064940 2253430 2635220 2431200 FALSE TRUE 1968432.746 2034232.596 1962041.576 1865756.159 1992214.384 2045113.981 2090211.353 2206895.883 2336080.873 2266532.659 0.868477557 0.897508619 0.865657756 0.823176384 0.878970077 0.902309514 0.92220659 0.973688102 1.03068485 1 21.11205552 1.863142574 1.241116445 1.017061147 0.867071249 0.892107165 0.020482406 0.140184304 0.400392723 0.016994084 0.007170454 72.96970224 -1.863142574 -0.149989898 YRTEKPSKS(ph)PPPPPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YRTEKPSKSPPPPPPR 16 3 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 YRT(0.011)EKPS(0.267)KS(0.722)PPPPPPR;YRT(0.001)EKPS(0.116)KS(0.883)PPPPPPR 95.206 0.0030126 3101300000 1903120 1698260 1451440 1486850 1604830 1627200 1706170 1994950 2152730 1972630 TRUE FALSE 1828743.966 1649827.288 1713747.495 1563586.507 1656450.814 1660103.099 1727050.619 1953753.585 1908361.115 1839022.013 0.994411135 0.897122099 0.931879816 0.850227184 0.900723756 0.902709748 0.939113619 1.062387275 1.037704335 1 20.81050732 1.863247588 4.321436396 1.037487567 0.910359105 0.679855609 0.036943239 0.121180674 3.454725968 0.017501981 0.009883973 72.98734865 -1.863247588 -0.127128461 DLKPENILLDEEGHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLKPENILLDEEGHIK 16 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;B7Z3B5;F2Z2J1;Q15349;Q15349-3;Q15349-2;E9PMM7;D6R910;A0A2R8Y7S9;B4DG22;B1AXG1;B7ZB17;P51812 E9PGT3;B4DG22 RPS6KA1;RPS6KA2;RPS6KA3 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-2;Ribosomal protein S6 kinase alpha-3 0 121.19 6.01E-05 73421000 119450 105820 88231 89317 101560 97420 105060 128160 132430 124550 FALSE TRUE 114781.7619 102802.1172 104176.3044 93926.66107 104826.7696 99389.89915 106345.7557 125513.4512 117397.1016 116114.1176 0.988525464 0.885354162 0.89718896 0.808916806 0.902790908 0.855967399 0.915872746 1.080949103 1.011049337 1 16.82518387 1.863255882 5.311558723 1.035344576 0.886936516 0.646176818 0.046691062 0.128022825 4.82801546 0.020951233 0.012340343 72.9887426 -1.863255882 -0.148408061 LSDDFDS(ph)PVKGPLCK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSDDFDSPVKGPLCK 15 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 LSDDFDS(1)PVKGPLCK;LSDDFDS(1)PVKGPLCK;LSDDFDS(1)PVKGPLCK 231.44 1.17E-13 1487370000 2447860 2056640 1619400 1658240 1821230 1729950 2074510 2370440 2661950 2532130 TRUE FALSE 2352194.925 1997986.641 1912061.603 1743821.965 1879811.517 1764930.774 2099898.474 2321489.586 2359776.596 2360626.58 0.996428213 0.846379795 0.809980545 0.738711485 0.796318881 0.747653521 0.889551313 0.98342093 0.999639933 1 21.17073841 1.863292487 2.981792416 0.995299858 0.818028111 0.56259615 0.067304564 0.195488209 3.061752676 0.037993648 0.01967356 72.9948948 -1.863292487 -0.177271747 IMGNLGAADIDHK ddPTM_BT-474_Pertuzumab_2h_R1 1 IMGNLGAADIDHK 13 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 216.88 2.67E-11 441150000 276750 272460 268220 309630 298310 277000 361440 380030 441070 451050 FALSE TRUE 265934.304 264689.7076 316693.3205 325610.0414 307905.4121 282601.1298 365863.4108 372182.2477 391001.5827 420499.9817 0.632424056 0.629464255 0.753135159 0.774340203 0.732236446 0.672059791 0.870067602 0.885094563 0.929849226 1 18.68174621 1.863398275 0.562452012 1.011531325 0.668814058 0.825915603 0.050847618 0.334332174 0.226505856 0.052337054 0.033393162 73.01267755 -1.863398275 -0.342717267 (ac)ASIWVGHR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASIWVGHR 8 0 P12429;D6RFG5;D6RCA8;D6RAZ8 P12429 ANXA3 Annexin A3;Annexin 0 ;; 47.849 0.013803 380280000 78689 113402 134338 115566 125669 136053 87109 82915 62900 67870.2 FALSE TRUE 75613.74688 110167.886 158615.8649 121530.3751 129711.2575 138804.0849 88175.066 81202.77627 55759.8557 63273.2909 1.195034205 1.741143608 2.506837604 1.920721577 2.050015981 2.193723179 1.393559032 1.283365779 0.881254237 1 15.94930901 1.863433581 1.901177413 0.99913563 1.952405984 0.583986983 0.333958451 0.240349527 1.634819114 0.224003314 0.102023556 73.01861332 -1.863433581 0.953270355 KRKPEEES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRKPEEESPR 10 3 P49321;P49321-3;P49321-4;P49321-2;Q5T624 P49321 NASP Nuclear autoantigenic sperm protein 1 KRKPEEES(1)PR 91.62 0.055397 593650000 638220 518450 602070 585990 547450 581830 664380 903880 929200 958110 TRUE FALSE 613277.6568 503664.3136 710877.442 616233.0141 565059.2264 593595.0012 672510.8812 885214.5621 823721.1115 893216.3563 0.686594745 0.563877173 0.795862544 0.689903415 0.632611822 0.664559037 0.752909277 0.991041595 0.922196628 1 19.76865014 1.863516165 3.215525845 0.969816947 0.673046966 0.840523255 0.058109348 0.092070587 1.642682944 0.030346712 0.016015057 73.03249962 -1.863516165 -0.296769981 DEEVLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEEVLKK 7 1 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0G2JJL7;F6QYI9;A0A0D9SEM9;A0A140T9N3;A0A140T9K2;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4;F6R6M7 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 109.86 0.011116 915180000 574370 528540 520320 491810 494790 513100 554290 678070 701120 677830 FALSE TRUE 551922.9854 513466.5567 614353.3985 517192.373 510705.3697 523475.2336 561073.5668 664067.6175 621531.7969 631919.9704 0.873406462 0.812549976 0.972201271 0.818446002 0.808180456 0.828388496 0.887887063 1.050872972 0.983560935 1 19.26938233 1.863751039 4.70283888 1.013041363 0.852806938 0.690480708 0.047710778 0.124380794 3.995006097 0.022489063 0.012933595 73.07200746 -1.863751039 -0.160234426 SYCAEIAHNVSSK ddPTM_BT-474_Pertuzumab_2h_R1 5 SYCAEIAHNVSSK 13 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;;; 175.21 1.86E-05 4779650000 6101750 5284790 4539370 4759680 4709550 5044970 5196550 6255250 6144260 6032100 FALSE TRUE 5863286.864 5134072.964 5359735.137 5005327.655 4861036.953 5146982.75 5260146.933 6126076.902 5446789.364 5623540.494 1.042632639 0.912960966 0.953089098 0.890066971 0.864408633 0.915256635 0.935379933 1.089362993 0.968569422 1 22.42304728 1.863966169 7.995766407 1.026776173 0.925419058 0.369562989 0.052699948 0.259366041 15.65364408 0.022326873 0.013940212 73.10821306 -1.863966169 -0.101357115 VDVEVPDVSLEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDVEVPDVSLEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 266.85 7.09E-27 1380210000 2289910 2176360 1913070 2188020 1930570 2018300 2187760 2707400 2791160 2497130 FALSE TRUE 2200417.786 2114292.344 2258804.305 2300943.974 1992668.537 2059111.409 2214534.461 2651491.244 2474319.218 2327997.161 0.945197796 0.908202286 0.970277947 0.988379201 0.855958319 0.884499107 0.951261668 1.138958109 1.062853194 1 21.15065787 1.863967289 6.074432727 1.078097397 0.925944892 0.632835039 0.048287274 0.136213658 6.047618701 0.021729435 0.013103406 73.10840158 -1.863967289 -0.152152505 IKEEVLS(ph)ESEAENQQAGAAALAPEIVIK ddPTM_BT-474_Pertuzumab_2h_R1 4 IKEEVLSESEAENQQAGAAALAPEIVIK 28 1 Q9UJX5;Q9UJX5-3 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 1 IKEEVLS(0.5)ES(0.5)EAENQQAGAAALAPEIVIK;IKEEVLS(0.609)ES(0.391)EAENQQAGAAALAPEIVIK;IKEEVLS(0.5)ES(0.5)EAENQQAGAAALAPEIVIK;IKEEVLS(0.848)ES(0.152)EAENQQAGAAALAPEIVIK 143.05 6.84E-08 1218934000 658656 580686 479776 464553 539946 580477 585752 702179 791826 720515 TRUE FALSE 632914.9953 564125.4038 566482.1958 488528.636 557313.8535 592214.6427 592920.6082 687678.7583 701941.2321 671713.8773 0.942238975 0.839829908 0.843338533 0.7272868 0.829689355 0.881647176 0.882698167 1.023767383 1.045000343 1 19.35748731 1.864016101 2.043034006 1.032957436 0.836346016 0.7057563 0.051558898 0.171913075 1.344095622 0.033790614 0.015728967 73.11661894 -1.864016101 -0.196611419 DIEIS(ph)TEEEKDTGDLKDSSLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DIEISTEEEKDTGDLKDSSLLK 22 2 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 1 DIEIS(0.88)T(0.12)EEEKDTGDLKDSSLLK;DIEIS(0.528)T(0.472)EEEKDTGDLKDSSLLK 174.53 1.31E-12 609028000 499310 378040 302140 229470 358880 373040 380160 469510 549620 450710 TRUE FALSE 479796.4132 367258.6693 356743.4191 241312.9742 370423.7011 380583.1244 384812.5118 459814.4544 487229.4418 420183.0102 1.141874853 0.874044548 0.849019143 0.574304454 0.881577056 0.905755623 0.915821207 1.094319483 1.159564832 1 18.6806583 1.864089252 2.390072314 1.0999242 0.856927159 0.334608502 0.133515106 0.320402563 3.367233935 0.081249459 0.03962981 73.12893553 -1.864089252 -0.242997041 S(ph)QEDLNEPIKR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQEDLNEPIKR 11 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(1)QEDLNEPIKR;S(1)QEDLNEPIKR;S(1)QEDLNEPIKR;S(1)QEDLNEPIKR 140.84 2.35E-05 3472550000 3599090 3172670 2876600 2900000 3032130 3176260 3460360 4121030 4752960 4220090 TRUE FALSE 3458433.584 3082188.558 3396465.61 3049669.348 3129661.215 3240486.153 3502708.921 4035929.29 4213423.907 3934259.545 0.879055778 0.783422782 0.863304917 0.775157132 0.79548926 0.823658459 0.890309569 1.025842155 1.070957281 1 21.90766071 1.864154572 2.356018317 1.042249918 0.817146424 0.880832132 0.034865396 0.08392607 0.858828646 0.019642993 0.009541443 73.13993538 -1.864154572 -0.225103495 AAKNS(ph)EEEEEEKKK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAKNSEEEEEEKKK 14 3 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AAKNS(1)EEEEEEKKK;AAKNS(1)EEEEEEKKK;AAKNS(1)EEEEEEKKK 167.63 2.00E-05 6141020000 3823770 2129420 1898800 1084940 1967840 1779500 2289800 2938230 3614650 2305590 TRUE FALSE 3674332.841 2068691.027 2241955.399 1140933.883 2031137.361 1815482.709 2317823.257 2877554.524 3204330.086 2149430.336 1.709444954 0.96243688 1.043046319 0.530807565 0.94496543 0.844634357 1.078343047 1.338752169 1.490781084 1 21.03552292 1.864157002 4.041203586 1.308436157 0.980105531 0.134509061 0.298090505 0.391534187 10.10520291 0.145975296 0.081272784 73.14034454 -1.864157002 -0.328330626 KDKEGDRAS(ph)EEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDKEGDRASEEGK 13 3 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 KDKEGDRAS(1)EEGK 116.43 0.0032376 28265000 61110 45987 37743 34766 47365 43429 54204 62266 82135 63368 TRUE FALSE 58721.75364 44675.49579 44563.99969 36560.27743 48888.53824 44307.16414 54867.36477 60980.18534 72811.37914 59076.02892 0.994003062 0.756237286 0.754349954 0.61886823 0.827552886 0.750002411 0.928758513 1.032232302 1.232502937 1 15.85028523 1.864427729 1.959940381 1.114323824 0.774943987 0.632008701 0.104236615 0.196058279 1.414522024 0.065645801 0.030191776 73.18595239 -1.864427729 -0.339379837 ELEAIFGRPVVDGEEGEPHSIS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHS(0.003)IS(0.997)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHS(0.001)IS(0.999)PR 269.59 2.27E-45 6074490000 2683160 3094900 3189910 3985000 3976910 3982870 3188300 2771600 2698550 3098190 TRUE FALSE 2578299.141 3006636.482 3766397.696 4190666.328 4104830.922 4063406.36 3227319.369 2714365.491 2392221.917 2888346.832 0.892655658 1.040954102 1.303997725 1.450887505 1.421169673 1.40682771 1.117358668 0.939764388 0.828232223 1 21.46181256 1.864531288 3.053639778 0.911637792 1.26198628 0.427319105 0.169586952 0.261749278 4.271859955 0.100858959 0.05258897 73.20340587 -1.864531288 0.350348488 KDDS(ph)HSAEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 3 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.5)HS(0.5)AEDS(1)EDEKEDHK;KDDS(0.5)HS(0.5)AEDS(1)EDEKEDHK;KDDS(0.81)HS(0.19)AEDS(1)EDEKEDHK 179.79 4.39E-14 5312980000 986220 602460 680490 451620 694410 533620 811150 904620 1218690 892470 TRUE FALSE 947677.4321 585278.4307 803469.6804 474928.1623 716746.3283 544410.162 821077.0963 885939.2809 1080349.42 832022.212 1.139004967 0.703440872 0.96568297 0.570811879 0.861450954 0.654321669 0.986845164 1.064802439 1.298462234 1 19.66626252 1.86467725 2.538351756 1.142269652 0.809511589 0.393591949 0.168420507 0.256198217 3.006790879 0.0902169 0.044789411 73.22801308 -1.86467725 -0.332758063 ASYHFSPEELDENTS(ph)PLLGDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASYHFSPEELDENTSPLLGDAR 22 0 O75410-3;E7ET87;E7EVI4;O75410-2;O75410;O75410-9;O75410-7;H0YAY0;E5RFM9;R4GMT7;E5RJU4 O75410-3 TACC1 Transforming acidic coiled-coil-containing protein 1 1 ASYHFSPEELDENT(0.155)S(0.845)PLLGDAR;ASYHFSPEELDENT(0.085)S(0.915)PLLGDAR;AS(0.001)YHFS(0.005)PEELDENT(0.25)S(0.745)PLLGDAR 224.41 4.46E-26 578820000 211930 349775 298244 481693 403881 420126 322715 247271 228240 302864 TRUE FALSE 203647.5413 339799.7595 352143.3252 506553.2335 416872.1992 428621.2356 326664.4827 242164.7674 202331.1521 282350.7515 0.721257302 1.203466814 1.247183949 1.794056615 1.476433822 1.518045315 1.156945682 0.857673536 0.716595054 1 18.10712895 1.864682292 3.174082435 0.83947911 1.345342749 0.376961252 0.267105459 0.2666035 4.651298001 0.149303282 0.078607652 73.22886322 -1.864682292 0.505863638 KSGIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 KSGISPK 7 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 1 KS(0.004)GIS(0.996)PK;KS(0.003)GIS(0.997)PK;KSGIS(1)PK;KSGIS(1)PK 80.014 0.019025 6302800000 7026200 5823100 4775370 4596350 5333110 5168750 5804300 6673800 7201000 7093200 TRUE FALSE 6751608.336 5657030.889 5638385.587 4833568.174 5504654.327 5273265.666 5875334.76 6535983.698 6383572.669 6612771.246 1.020995296 0.855470525 0.852650935 0.73094441 0.832427756 0.797436577 0.888482989 0.988387993 0.965340011 1 22.65682356 1.864817119 3.447023016 0.982851173 0.842665708 0.434871393 0.069015259 0.232086563 4.653107089 0.036455489 0.019579859 73.25160072 -1.864817119 -0.140185466 (ac)GDKKS(ph)PTRPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GDKKSPTRPK 10 3 Q8IY57;Q8IY57-5;G3V1X5;A0A0B4J255;F8VRE5;G3V219;G3V212;Q8IY57-4 Q8IY57 YAF2 YY1-associated factor 2 1 GDKKS(0.881)PT(0.119)RPK;GDKKS(0.5)PT(0.5)RPK;GDKKS(0.981)PT(0.019)RPK;GDKKS(0.894)PT(0.106)RPK 58.674 0.00012555 7607160000 11916000 9477700 7630250 6056780 8730540 8420260 9128700 10918000 12189400 10187000 TRUE FALSE 11450309.55 9207405.276 9009205.909 6369371.142 9011365.748 8590523.426 9240419.761 10692539.48 10805710.41 9497025.416 1.205673255 0.969504121 0.948634495 0.670670116 0.948861918 0.904548851 0.972980418 1.125883002 1.137799463 1 23.17904428 1.864827089 4.211138845 1.098391818 0.931485879 0.209897383 0.125796263 0.331242524 9.092466965 0.062763864 0.035276067 73.25328223 -1.864827089 -0.16690594 AAVLS(ph)DS(ph)EDEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAVLSDSEDEEK 12 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 AAVLS(1)DS(1)EDEEK 246.63 1.80E-09 0 446290 403330 430460 397950 380680 416900 461390 618810 625570 640290 TRUE FALSE 428848.4934 391827.4233 508253.6975 418488.2472 392924.9179 425330.0036 467036.6288 606031.3573 554557.9162 596922.588 0.718432343 0.656412458 0.851456634 0.701076246 0.658251046 0.712537961 0.782407364 1.015259549 0.929028198 1 19.18718432 1.864911327 3.714866294 0.979713306 0.717941117 0.821455945 0.055203068 0.094263524 2.134327163 0.027870103 0.015231936 73.26749222 -1.864911327 -0.26177219 KAS(ph)PEPEGEAAGK ddPTM_BT-474_Pertuzumab_2h_R1 8 KASPEPEGEAAGK 13 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK 205.15 4.42E-08 10142230000 13400570 11524840 10152120 9466520 10886460 10543550 11892950 14277280 15782280 14230130 TRUE FALSE 12876860.91 11196162.85 11986833.92 9955088.232 11236632.87 10756747.8 12038499.48 13982449.18 13990741.74 13266310.62 0.970643706 0.843954523 0.903554444 0.750403674 0.847005109 0.810831897 0.907448938 1.053981742 1.054606826 1 23.66126388 1.864930539 3.575536124 1.040579094 0.85138396 0.676761508 0.055972594 0.13230924 2.816911693 0.028167707 0.015259784 73.27073351 -1.864930539 -0.189195134 AVT(ph)PVPTK ddPTM_BT-474_Pertuzumab_2h_R1 4 AVTPVPTK 8 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(0.999)PVPT(0.001)K;AVT(0.999)PVPT(0.001)K;AVT(1)PVPTK;AVT(0.996)PVPT(0.004)K 117.02 0.024134 11757400000 19048100 17541300 16775200 18040400 16614100 17163100 19111300 22670200 23929600 24540000 TRUE FALSE 18303679.19 17041039.3 19806851.8 18971467.21 17148507.62 17510149.64 19345189.81 22202052.45 21213212.13 22877883.94 0.800059972 0.744869558 0.865764153 0.829249211 0.749567034 0.765374529 0.845584751 0.970459178 0.927236635 1 24.44745028 1.864968932 3.227914159 0.962838836 0.793669229 0.802804092 0.038320948 0.110077552 1.976354842 0.020666079 0.010927615 73.27721105 -1.864968932 -0.169169607 S(ph)IVT(ph)AEVS(ph)S(ph)MPACKFQVMIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIVTAEVSSMPACKFQVMIQK 21 1 Q86SZ2-2;Q86SZ2 Q86SZ2-2 TRAPPC6B Trafficking protein particle complex subunit 6B 4 S(1)IVT(1)AEVS(1)S(1)MPACKFQVMIQK 46.66 0.067726 98987000 128120 111430 99564 98155 104980 92031 112580 138740 153210 122960 TRUE FALSE 123112.9288 108252.1255 117557.4296 103220.7913 108356.777 93891.92988 113957.7877 135874.9705 135818.2431 114631.8097 1.073985738 0.944346301 1.025521885 0.900455045 0.945259238 0.819073956 0.994120114 1.185316457 1.184821591 1 16.80664791 1.865018346 5.177537437 1.138447468 0.948775769 0.473655385 0.080417869 0.172268583 6.284473307 0.036217065 0.021243346 73.28554914 -1.865018346 -0.189671699 TDS(ph)IGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TDSIGEK 7 0 A0A286YFF8;Q7Z3U7-2;Q7Z3U7-6;Q7Z3U7-5;Q7Z3U7;Q7Z3U7-3 A0A286YFF8 MON2 Protein MON2 homolog 1 T(0.001)DS(0.999)IGEK;T(0.002)DS(0.998)IGEK;TDS(1)IGEK 90.108 0.018232 1098798000 2201870 1803460 1256680 1395170 1809890 1606740 1766830 2341180 2417030 2045270 TRUE FALSE 2115818.486 1752027.087 1483790.031 1467174.891 1868106.756 1639229.384 1788452.994 2292833.815 2142658.887 1906742.041 1.109651143 0.918859001 0.778180791 0.769466902 0.979737539 0.859701705 0.937962742 1.202487681 1.12372772 1 20.86267825 1.865177558 5.530415375 1.124409149 0.895687164 0.443277579 0.103106148 0.190961799 7.568347329 0.047518112 0.028215315 73.31242033 -1.865177558 -0.228721986 GGS(ph)GYHS(ph)RS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSGYHSRSPAR 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GGS(0.99)GY(0.027)HS(0.984)RS(0.999)PAR 57.328 0.092942 56099000 135980 146600 110780 141340 142310 142160 134920 125920 143190 134230 TRUE FALSE 130665.7513 142419.1115 130800.4103 148634.5743 146887.5304 145034.5726 136571.1913 123319.708 126935.6715 125138.4825 1.044169216 1.138092045 1.045245297 1.187760722 1.173799837 1.158992579 1.091360456 0.985465905 1.014361601 1 16.93316599 1.865246431 3.902676802 1.000205078 1.126728799 0.593740189 0.046023067 0.162719096 3.981282467 0.023325493 0.012894068 73.32404764 -1.865246431 0.126523722 EVSHLNALEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSHLNALEER 11 0 A0A087WYJ2;M0R2B7;P28340;M0R3H8 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ; 179.35 7.14E-06 1059260000 414710 460490 376180 458790 441980 438680 429210 351970 431400 430460 FALSE TRUE 398502.6747 447357.2761 444164.0941 482468.2069 456196.6881 447550.4102 434462.8004 344701.6965 382429.2806 401304.5608 0.993018056 1.114757518 1.106800514 1.202249498 1.13678421 1.115238783 1.082626122 0.858952851 0.952965199 1 18.61433803 1.865417074 5.610391458 0.927233922 1.115120145 0.642617622 0.05817927 0.129454976 5.221495873 0.026328698 0.015674408 73.35286385 -1.865417074 0.187886224 NCNDFQYESK ddPTM_BT-474_Pertuzumab_2h_R1 1 NCNDFQYESK 10 0 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 182.16 0.0067935 0 150970 144790 126360 140280 148250 133570 149030 176540 182280 181780 FALSE TRUE 145069.9255 140660.731 149196.0629 147519.8676 153018.5959 136270.8769 150853.8737 172894.3873 161588.3386 169467.8787 0.85603199 0.830014113 0.880379598 0.870488666 0.902935689 0.80411036 0.890162047 1.020219222 0.953504226 1 17.37065232 1.865578917 4.845779668 0.990009738 0.858990887 0.800895092 0.02983169 0.091212161 3.050618108 0.013411432 0.007766735 73.38020446 -1.865578917 -0.131018851 NVAEALGHS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 NVAEALGHSPK 11 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 NVAEALGHS(1)PK;NVAEALGHS(1)PK 110.97 0.0011097 1240140000 1439620 1240680 1270210 1099950 1117310 1047420 1354530 1714760 1827890 1766820 TRUE FALSE 1383358.059 1205297.021 1499765.203 1156718.551 1153249.291 1068599.55 1371107.143 1679349.607 1620395.59 1647151.708 0.839848602 0.731746211 0.910520382 0.702253803 0.700147585 0.648755998 0.832410966 1.019547622 0.983756131 1 20.65154201 1.865592576 3.861305855 1.000151631 0.755552705 0.702686927 0.071148854 0.131604367 3.167186193 0.036438531 0.020098783 73.3825123 -1.865592576 -0.244598926 IQTQLNLIHPDIFPLLTSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 IQTQLNLIHPDIFPLLTSFR 20 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-2;H7C2I4 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 81.665 0.0048333 64901000 55028 59454 53358 59762 62994 56033 57740 54094 53594 63563 FALSE TRUE 52877.44492 57758.43013 63000.97754 62846.32398 65020.25922 57166.02565 58446.63939 52976.94 47510.2338 59257.82139 0.892328535 0.974697158 1.063167293 1.060557451 1.097243498 0.96470009 0.986310972 0.894007555 0.801754649 1 15.85471797 1.865608769 2.32886357 0.884702362 1.015827014 0.31874141 0.071137001 0.316267432 3.165407144 0.042932307 0.02080768 73.38524854 -1.865608769 0.131124652 LSSESHHGGS(ph)PIHWVLPAGMSAK ddPTM_BT-474_Pertuzumab_2h_R1 9 LSSESHHGGSPIHWVLPAGMSAK 23 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LS(0.002)S(0.002)ES(0.013)HHGGS(0.982)PIHWVLPAGMSAK;LS(0.046)S(0.046)ES(0.303)HHGGS(0.605)PIHWVLPAGMSAK;LSSESHHGGS(1)PIHWVLPAGMSAK;LSSES(0.001)HHGGS(0.998)PIHWVLPAGMSAK;LSSES(0.002)HHGGS(0.998)PIHWVLPAGMSAK;LS(0.001)S(0.001)ES(0.033)HHGGS(0.965)PIHWVLPAGMSAK;LSSES(0.002)HHGGS(0.998)PIHWVLPAGMSAK;LS(0.004)S(0.004)ES(0.025)HHGGS(0.967)PIHWVLPAGMSAK;LS(0.002)S(0.002)ES(0.011)HHGGS(0.986)PIHWVLPAGMSAK 242.05 4.24E-37 18783230000 8250180 12662360 10022280 13695210 11157260 12799960 11720200 2992503 11122630 12358360 TRUE FALSE 7927753.845 12301241.89 11833528.94 14402021.43 11516143.4 13058783.96 11863635.31 2930706.767 9860035.672 11521317.27 0.688094396 1.067694049 1.027098609 1.250032535 0.999550931 1.133445391 1.029711711 0.254372543 0.855808016 1 23.45780234 1.865707503 12.3716927 0.624040673 1.041646463 0.282335275 0.226106834 0.550065869 52.07307507 0.089574219 0.057379608 73.40193395 -1.865707503 0.41760579 RNGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_BT-474_Pertuzumab_2h_R1 4 RNGAAGPHSPDPLLDEQAFGDLTDLPVVPK 30 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK 194.65 2.36E-19 1077030000 590869 679392 625060 745684 888960 871119 645691 549962 566620 543760 TRUE FALSE 567777.1862 660016.4054 738022.2464 784168.8406 917554.2057 888733.623 653593.1596 538605.0925 502299.6731 506930.6509 1.120029308 1.301985596 1.455864318 1.546895693 1.810019189 1.753166082 1.289314739 1.06248279 0.990864672 1 18.95142887 1.865736397 3.049587876 1.017247638 1.504019447 0.559169044 0.189463024 0.212266438 3.455381857 0.113482518 0.059203124 73.40681776 -1.865736397 0.486771809 HAAENPGK ddPTM_BT-474_Pertuzumab_2h_R1 7 HAAENPGK 8 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;; 157.58 0.00087158 1872300000 3611950 3085920 2875060 3041020 3053230 3002530 3114930 2555080 3125050 3446250 FALSE TRUE 3470791.001 2997912.583 3394647.297 3197967.407 3151439.916 3063243.214 3153051.445 2502316.705 2770307.425 3212832.418 1.080290083 0.933105806 1.056590216 0.995373238 0.980891471 0.953440085 0.981393062 0.778850677 0.862263282 1 21.6154143 1.866033658 7.55854465 0.859282612 0.99570388 0.389832769 0.065647329 0.215853623 12.22593913 0.02645908 0.016430669 73.45707948 -1.866033658 0.136421269 GSS(ph)PTPPCSPVQPSK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSSPTPPCSPVQPSK 15 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 GSS(1)PTPPCSPVQPSK;GS(0.001)S(0.999)PT(0.001)PPCSPVQPSK;GS(0.001)S(0.999)PTPPCSPVQPSK;GSS(0.999)PT(0.001)PPCSPVQPSK 335.24 5.29E-69 3007730000 1567330 1615220 1303230 1494420 1310980 1524470 1757890 1859680 2153420 2183910 TRUE FALSE 1506077.011 1569155.507 1538752.651 1571547.195 1353148.862 1555295.828 1779403.584 1821276.958 1908972.789 2035991.83 0.739726451 0.770708155 0.755775455 0.771882859 0.664614092 0.76390082 0.873973833 0.894540406 0.937613187 1 20.95730034 1.866078552 1.263508139 0.968739601 0.741418763 0.872869419 0.035158704 0.154812137 0.458707675 0.028690738 0.012131908 73.46467334 -1.866078552 -0.227320838 WRLS(ph)PGETPER ddPTM_BT-474_Pertuzumab_2h_R1 1 WRLSPGETPER 11 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 WRLS(0.995)PGET(0.005)PER 90.853 0.0067692 267180000 81046 89892 85386 72350 95540 84479 82572 80557 79905 87770 TRUE FALSE 77878.63272 87328.36817 100817.1496 76083.99217 98613.13087 86187.22326 83582.54084 78893.4698 70834.51939 81825.25972 0.95176762 1.067254396 1.23210302 0.929835022 1.205167343 1.053308276 1.021476022 0.964170112 0.865680349 1 16.32025866 1.866088175 2.018904737 0.931358515 1.079303385 0.278324319 0.09379829 0.386161717 2.948499147 0.056806295 0.026393706 73.46630126 -1.866088175 0.14794487 EKDLLPS(ph)PAGPVPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDLLPSPAGPVPSK 15 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 EKDLLPS(1)PAGPVPSK 96.79 0.0021582 127640000 139600 134420 143960 135450 147090 125290 154810 191650 195190 212170 TRUE FALSE 134144.2777 130586.4732 169976.7744 142440.5907 151821.2834 127823.4496 156704.6111 187692.3605 173032.8495 197799.5369 0.678182971 0.660196051 0.859338586 0.720126007 0.767551258 0.646227244 0.792239525 0.948901921 0.874788951 1 17.59367952 1.866353513 3.692711072 0.93369416 0.726733609 0.697274345 0.064290414 0.136546496 3.062518416 0.031861609 0.017405414 73.51120005 -1.866353513 -0.206960551 QHLLGTSPER ddPTM_BT-474_Pertuzumab_2h_R1 1 QHLLGTSPER 10 0 Q8WUY1;H0YAR9 Q8WUY1 THEM6 Protein THEM6 0 87.184 0.014889 0 144060 215250 139760 251680 147070 169550 179600 108930 191970 163450 FALSE TRUE 138429.9759 209111.2808 165017.7409 264669.235 151800.6401 172978.4172 181797.9985 106680.5574 170178.3704 152379.3859 0.908456056 1.372306887 1.082940058 1.73690971 0.996201942 1.135182532 1.19306163 0.700098355 1.116807036 1 17.21730822 1.866371052 8.758942145 0.911883975 1.216884485 0.205323524 0.236158673 0.41500429 27.48310872 0.096136384 0.060510499 73.51416902 -1.866371052 0.30500051 (ac)ATSPQKS(ph)PSVPK ddPTM_BT-474_Pertuzumab_2h_R1 3 ATSPQKSPSVPK 12 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 AT(0.006)S(0.044)PQKS(0.947)PS(0.002)VPK;AT(0.044)S(0.044)PQKS(0.84)PS(0.071)VPK;AT(0.009)S(0.009)PQKS(0.972)PS(0.011)VPK 78.486 0.00020824 1281970000 1982360 1891250 1449850 1276630 1559050 1649600 1845800 2320250 2711650 2283240 TRUE FALSE 1904887.18 1837313.402 1711870.147 1342517.027 1609198.259 1682956.042 1868389.453 2272336.027 2403834.86 2128594.121 0.8949039 0.863158168 0.804225723 0.630705973 0.755991123 0.790642061 0.877757499 1.067529034 1.129306351 1 21.02146945 1.8666978 2.589370779 1.078735479 0.785675834 0.742657688 0.07236008 0.143273328 1.742226333 0.044549784 0.022276011 73.56949932 -1.8666978 -0.293059645 GAQPWGAPWTGPFCPDPEGS(ph)PPFEAAHQTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAQPWGAPWTGPFCPDPEGSPPFEAAHQTDR 31 0 O14924-5;O14924-4;O14924;E9PBG5 O14924-5 RGS12 Regulator of G-protein signaling 12 1 GAQPWGAPWTGPFCPDPEGS(1)PPFEAAHQTDR;GAQPWGAPWTGPFCPDPEGS(1)PPFEAAHQTDR 166.13 8.58E-13 548530000 113676 128503 98442 123864 121456 147806 115483 100079 103922 120110 TRUE FALSE 109233.4162 124838.2203 116232.6592 130256.6359 125362.7425 150794.7386 116896.3155 98012.33368 92125.21024 111974.8427 0.975517479 1.114877389 1.03802476 1.163266969 1.119561676 1.346684085 1.043951594 0.875306732 0.822731321 1 16.77281511 1.866942948 4.239913549 0.889926771 1.127715827 0.505600548 0.099511722 0.179508549 4.978646408 0.048373435 0.027259442 73.61103909 -1.866942948 0.237789056 S(ph)PSVS(ph)PSKQPVSTSSK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSVSPSKQPVSTSSK 16 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 2 S(0.997)PS(0.013)VS(0.978)PS(0.012)KQPVSTSSK;S(0.999)PS(0.114)VS(0.793)PS(0.094)KQPVSTSSK;S(1)PS(0.001)VS(0.906)PS(0.093)KQPVSTSSK 177.4 1.68E-09 1889440000 1709600 1383610 1761890 1574010 1619930 1779830 2186020 2368300 3039940 2881040 TRUE FALSE 1642786.942 1344150.797 2080302.716 1655244.845 1672036.52 1815819.382 2212773.167 2319393.777 2694858.756 2685904.595 0.611632649 0.500446218 0.774525916 0.616270901 0.622522677 0.676055056 0.823846525 0.863542876 1.00333376 1 21.35697663 1.867125827 0.99652803 1.011445018 0.617869229 0.838580572 0.065605926 0.196630542 0.359679167 0.054536934 0.023762676 73.64204281 -1.867125827 -0.393575789 S(ph)KS(ph)PPKS(ph)PEEEGAVSS ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSPPKSPEEEGAVSS 16 2 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 3 S(1)KS(1)PPKS(1)PEEEGAVSS;S(1)KS(1)PPKS(0.996)PEEEGAVS(0.002)S(0.002) 75.358 0.0027328 495660000 1099900 650490 693260 526920 661930 616820 825540 1129520 1357770 960550 TRUE FALSE 1056914.692 631938.6621 818547.5035 554114.4043 683221.5796 629292.523 835643.2055 1106195.017 1203641.642 895491.0929 1.180262652 0.705689501 0.914076656 0.618782709 0.762957426 0.702734542 0.933167523 1.235294272 1.344113472 1 19.77231956 1.867142896 3.519352353 1.216055859 0.803083479 0.506658866 0.165957286 0.174693356 3.624376837 0.080874999 0.043716155 73.64493714 -1.867142896 -0.412972379 FYGDEEKDK ddPTM_BT-474_Pertuzumab_2h_R1 8 FYGDEEKDK 9 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;; 148.96 8.10E-05 28151480000 42241600 36584280 30886760 28843840 33212660 31312600 39711600 47217500 57357100 47913700 FALSE TRUE 40590751.57 35540932.15 36468684.6 30332474.04 34280975.37 31945762.23 40197602.44 46242442.12 50846162.47 44668462.42 0.908711636 0.795660523 0.816430265 0.679057939 0.767453669 0.715174879 0.899910144 1.035236935 1.138301157 1 25.41275326 1.867213402 2.563397597 1.070503809 0.778173375 0.774523902 0.066750627 0.123724098 1.476858416 0.038267867 0.019088974 73.65689404 -1.867213402 -0.292330434 ASEDTT(ph)SGSPPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDT(0.082)T(0.439)S(0.233)GS(0.245)PPKK 142.85 7.84E-05 288120000 309690 263840 228930 201290 234090 252270 267310 307920 365630 300400 TRUE FALSE 297586.9724 256315.5415 270302.7435 211678.601 241619.7174 257371.0722 270581.4197 301561.3444 324125.2152 280053.6404 1.062607049 0.915237314 0.965182038 0.755850203 0.86276228 0.919006344 0.96617712 1.076798516 1.157368334 1 18.09534366 1.867217575 2.494550178 1.090612082 0.906887508 0.450169788 0.080871669 0.246593579 2.800532861 0.047631026 0.023578276 73.65760191 -1.867217575 -0.183724574 LLEAQIATGGVIDPVHSHR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLEAQIATGGVIDPVHSHR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 ;;; 176.69 9.34E-14 1879220000 1055870 1112080 1015760 1253720 1151340 1242710 1148580 65241.3 1210540 919750 FALSE TRUE 1014605.433 1080364.567 1199330.427 1318424.639 1188373.897 1267838.448 1162636.666 63894.04436 1073124.574 857454.5133 1.183276101 1.259967206 1.398710263 1.537603009 1.385932289 1.478607236 1.355916434 0.074515958 1.251523617 1 19.70970061 1.867522476 11.70120825 0.679516458 1.380768601 0.448357584 0.297337598 0.373568404 33.30531082 0.117300707 0.075005631 73.70933218 -1.867522476 0.701252143 DLDDIEDENEQLKQENK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLDDIEDENEQLKQENK 17 1 Q96IZ0;H0YHP5 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 0 ;;; 285.31 2.52E-36 2081620000 2422650 1882260 1752610 1349510 1768650 1803140 2014150 2545370 2935870 2353520 FALSE TRUE 2327970.16 1828579.788 2069345.614 1419158.373 1825540.233 1839600.726 2038799.77 2492807.22 2602602.346 2194113.994 1.061006933 0.833402363 0.94313496 0.64680248 0.832017041 0.838425319 0.929213239 1.136133868 1.186174626 1 21.06520705 1.867585611 3.287538202 1.121333252 0.852111651 0.514716067 0.107185145 0.185240422 3.430047003 0.055368787 0.029460733 73.72004828 -1.867585611 -0.269221601 RVPDPS(ph)PVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVPDPSPVTK 10 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 RVPDPS(0.999)PVT(0.001)K 64.104 0.045483 270700000 476080 415620 378960 417460 362780 433450 459560 521750 550880 595420 TRUE FALSE 457474.2673 403766.9245 447446.5019 439005.1606 374449.1482 442214.656 465184.2327 510975.6802 488346.4119 555091.6731 0.82414183 0.727387825 0.806076768 0.790869656 0.674571726 0.796651576 0.838031366 0.920524852 0.879758129 1 19.08236653 1.867650184 1.447602592 0.945295505 0.76429066 0.70799503 0.04753947 0.217082378 0.851832448 0.034331075 0.014710124 73.73101011 -1.867650184 -0.181004844 ESEDKPEIEDVGS(ph)DEEEEKKDGDK ddPTM_BT-474_Pertuzumab_2h_R1 8 ESEDKPEIEDVGSDEEEEKKDGDK 24 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK 284.48 1.22E-52 13681790000 6409710 3675810 3981877 2622934 4136220 3134750 4519130 6710560 7587150 4990320 TRUE FALSE 6159211.447 3570979.498 4701490.75 2758303.938 4269265.273 3198136.793 4574436.465 6571984.591 6725888.54 4652321.181 1.323900738 0.767569426 1.010568825 0.592887686 0.917663486 0.687428204 0.983258955 1.412624867 1.445705977 1 22.14951927 1.867663652 4.694433611 1.320201867 0.869918147 0.400232035 0.21856097 0.191853468 6.149200805 0.0972176 0.055991036 73.73329673 -1.867663652 -0.45028372 TSVS(ph)PAPDK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSVSPAPDK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 TSVS(1)PAPDK;TSVS(1)PAPDK;TSVS(1)PAPDK 205.52 1.55E-05 2400810000 2304930 2005100 1963890 1878840 1832720 1866130 2154090 2618460 2778370 2711350 TRUE FALSE 2214850.787 1947916.511 2318808.609 1975807.158 1891671.103 1903864.427 2180452.398 2564387.886 2462981.085 2527707.849 0.876228947 0.770625653 0.917356256 0.78165962 0.748374106 0.753197972 0.862620416 1.014511185 0.974393099 1 21.2693983 1.867672865 3.819520945 0.995394847 0.807225295 0.726572417 0.051535012 0.122796823 2.906202252 0.026092646 0.014375108 73.73486077 -1.867672865 -0.188169552 KEQT(ph)PEHGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEQTPEHGK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 KEQT(1)PEHGK 84.169 0.011947 163810000 234540 184030 183250 162970 183340 198230 202200 331030 251720 285910 TRUE FALSE 225373.9175 178781.6446 216367.3514 171380.9012 189237.2976 202238.3464 204674.5841 324194.1148 223145.8009 266545.061 0.845537774 0.670737037 0.811747742 0.642971588 0.709963624 0.7587398 0.76787986 1.216282581 0.837178524 1 18.02401992 1.867774925 7.806541098 1.034520403 0.73705375 0.599275255 0.102519017 0.157570439 9.229392724 0.040755897 0.025398228 73.75219079 -1.867774925 -0.297466653 AEDKEWMPVTK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEDKEWMPVTK 11 1 P15880;E9PQD7;E9PPT0;E9PMM9 P15880 RPS2 40S ribosomal protein S2 0 ;;; 166.48 1.86E-05 6424670000 6943900 6471260 6186180 5420530 6056170 5875170 6540250 7880200 8168400 7908400 FALSE TRUE 6672524.711 6286706.001 7304160.337 5700284.203 6250972.208 5993969.963 6620291.536 7717471.116 7241157.477 7372757.024 0.905024361 0.852694044 0.990695925 0.773155033 0.84784731 0.812988946 0.897939741 1.046755114 0.982150565 1 22.81377278 1.867783376 4.877516153 1.010831465 0.863637707 0.575373933 0.056042655 0.157240488 5.307198273 0.025907134 0.015037065 73.75362586 -1.867783376 -0.147193758 YHIDLDPHFNDILGQHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YHIDLDPHFNDILGQHSR 18 0 P19784;H3BSA1;H3BV19 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ; 94.856 0.00065567 291050000 343020 346610 303660 332120 319610 329180 326180 20193.1 321070 265610 FALSE TRUE 329614.3992 336725.0222 358538.1169 349260.753 329890.5459 335836.2451 330171.8884 19776.10543 284623.4796 247619.9981 1.331129964 1.359845831 1.447936837 1.410470704 1.332245168 1.356256553 1.333381354 0.079864735 1.149436563 1 17.91776831 1.867849926 10.2139509 0.65141956 1.372460369 0.528972698 0.265940736 0.242106512 18.77749065 0.103820427 0.065996396 73.7649286 -1.867849926 0.721040809 VIGQDSSEIHFK ddPTM_BT-474_Pertuzumab_2h_R1 3 VIGQDSSEIHFK 12 0 B8ZZN6;P63165;B8ZZJ0;B9A032;G2XKQ0 B8ZZN6;G2XKQ0 SUMO1 Small ubiquitin-related modifier 1;Small ubiquitin-related modifier 0 ;; 179.67 2.04E-05 2203010000 2369070 2529660 2026070 2354180 2312950 2450310 2330630 2320240 2532660 2462120 FALSE TRUE 2276484.125 2457516.574 2392225.919 2475679.512 2387348.137 2499856.947 2359152.947 2272326.233 2245163.055 2295358.419 0.991777191 1.070646115 1.04220147 1.078559013 1.040076407 1.089092198 1.027792839 0.989965756 0.978131797 1 21.13028802 1.867941511 3.400429628 0.988237679 1.053407921 0.537650013 0.025806816 0.17189391 3.368996346 0.012494271 0.006703137 73.78048591 -1.867941511 0.065170242 VS(ph)SPTKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.835)S(0.165)PTKPK;VS(0.673)S(0.327)PTKPK;VS(0.5)S(0.5)PTKPK 137.98 0.00043912 6245600000 12263200 10568000 8805300 8081400 9688600 9494900 10459300 12132400 13446500 12267100 TRUE FALSE 11783940.59 10266610.99 10396613.58 8498482.022 10000242.62 9686893.383 10587304.04 11881861.7 11920109.69 11436238.39 1.030403546 0.897726214 0.909093815 0.743118649 0.874434607 0.84703493 0.925768044 1.038965899 1.042310355 1 23.44710926 1.86802461 3.454906993 1.030483863 0.878878142 0.47440353 0.067174089 0.209747591 4.221140387 0.0355385 0.019138592 73.79460458 -1.86802461 -0.151605721 NLDDTIDDEKLR ddPTM_BT-474_Pertuzumab_2h_R1 1 NLDDTIDDEKLR 12 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YEU6;P0CB38 B1ANR0;P0CB38 PABPC4;PABPC4L Polyadenylate-binding protein;Polyadenylate-binding protein 4;Polyadenylate-binding protein 4-like 0 131.53 0.00022609 0 179380 163270 133080 133790 154910 152210 159170 197650 193600 194730 FALSE TRUE 172369.6313 158613.6995 157130.5163 140694.9179 159892.8208 155287.7905 161117.9701 193568.4584 171623.3396 181540.7637 0.949481691 0.873708451 0.865538478 0.775004551 0.88075437 0.855387999 0.887502987 1.066253411 0.945370815 1 17.46993401 1.868062056 6.029868978 1.006957334 0.864193913 0.622170537 0.048081244 0.141833699 6.234446863 0.021245304 0.012810532 73.80096759 -1.868062056 -0.142763421 HAPEHHPGHGDRLS(ph)PGER ddPTM_BT-474_Pertuzumab_2h_R1 2 HAPEHHPGHGDRLSPGER 18 1 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 HAPEHHPGHGDRLS(1)PGER;HAPEHHPGHGDRLS(1)PGER 174.5 2.85E-12 646950000 121321 122612 124123 128880 139186 131100 124272 8311.7 123765 74533 TRUE FALSE 116579.6412 119115.2258 146554.7872 135531.5122 143663.0441 133750.9318 125792.8779 8140.06049 109715.7161 69484.81352 1.67777152 1.714262725 2.109162848 1.95051991 2.06754594 1.924894449 1.81036505 0.117148771 1.578988422 1 16.08441008 1.868106774 8.264099338 0.825304619 1.911600985 0.621473872 0.354963191 0.160567012 9.99017548 0.142418591 0.089227003 73.80856709 -1.868106774 1.086296366 QPS(ph)SPYEDKDKDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPSSPYEDKDKDKK 14 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.605)S(0.395)PYEDKDKDKK 104.44 0.0058453 159440000 188630 114500 93312 60308 115320 109780 123370 160460 198430 125900 TRUE FALSE 181258.1311 111234.5721 110175.5541 63420.50311 119029.3725 111999.8268 124879.839 157146.4449 175905.0583 117372.6809 1.54429574 0.94770411 0.938681415 0.540334451 1.014114798 0.954223981 1.063960012 1.338867305 1.498688255 1 16.84073713 1.868510432 3.488426262 1.313142492 0.968246693 0.197213175 0.255511784 0.338578667 6.923912683 0.130611217 0.070519482 73.87720092 -1.868510432 -0.344895799 ET(ph)ERASPIKMDLAPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETERASPIKMDLAPSK 16 2 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.727)ERAS(0.273)PIKMDLAPSK;ET(0.558)ERAS(0.442)PIKMDLAPSK 129.02 9.26E-05 1944390000 2190050 1875620 1564440 1320520 1633090 1850980 1840240 2128000 2463890 2209270 TRUE FALSE 2104460.425 1822129.154 1847169.109 1388672.195 1685619.823 1888408.084 1862761.408 2084056.056 2184199.537 2059634.175 1.02176418 0.884685822 0.896843299 0.67423245 0.818407387 0.916865775 0.904413721 1.011857388 1.060479362 1 20.97395668 1.868554267 1.754014358 1.03567317 0.857615376 0.41152066 0.083216552 0.352875024 2.043808143 0.059480398 0.026596131 73.88465799 -1.868554267 -0.178057794 LLGPAPEDDGGHNDHSQPQASQDQDSHTLS(ph)PQV ddPTM_BT-474_Pertuzumab_2h_R1 1 LLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 33 0 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 LLGPAPEDDGGHNDHSQPQASQDQDS(0.008)HT(0.004)LS(0.989)PQV 193.15 3.28E-20 502840000 408450 459000 359620 544740 500610 660060 492280 189790 509570 447190 TRUE FALSE 392487.3224 445909.7694 424611.3337 572854.0967 516712.5753 673406.8654 498304.6699 185870.7702 451725.7499 416901.423 0.941439153 1.069580829 1.018493366 1.374075657 1.239411877 1.615266411 1.195257781 0.445838656 1.083531322 1 18.66934677 1.868716215 10.28117451 0.787904398 1.219825001 0.320705798 0.238874679 0.402578263 31.42412528 0.102104058 0.064928963 73.91221459 -1.868716215 0.431920603 CPVTVCGDVHGQFHDLMELFR ddPTM_BT-474_Pertuzumab_2h_R1 3 CPVTVCGDVHGQFHDLMELFR 21 0 P67775;P62714;P67775-2;E7ESG8 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform;Serine/threonine-protein phosphatase 0 ;; 207.43 2.12E-22 396339000 228804.6 225261.3 204138.7 214437.3 230740.3 247005.1 228027.6 39792.6 255712.2 185185.3 FALSE TRUE 219862.6633 218837.0683 241031.1041 225504.4348 238162.2713 251999.7124 230818.27 38970.8689 226684.8231 172642.5347 1.273513875 1.267573305 1.396128159 1.306192794 1.379510975 1.459661797 1.336972203 0.225731561 1.313029976 1 17.39742843 1.868815356 13.43671502 0.763755433 1.349530973 0.426601642 0.260108964 0.554717278 56.86179745 0.101113825 0.064914285 73.92908929 -1.868815356 0.58577554 YEPSDKDRQS(ph)PPPAK ddPTM_BT-474_Pertuzumab_2h_R1 7 YEPSDKDRQSPPPAK 15 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK 158.58 9.47E-07 15697060000 14709570 12531060 12006140 12020430 12627870 12564900 14236710 17037640 19232950 17676700 TRUE FALSE 14134703.74 12173686.44 14175916.57 12640805.83 13034056.91 12818970.89 14410943.12 16685806.78 17049706.15 16479441.36 0.857717409 0.738719606 0.860218272 0.767065191 0.790928322 0.777876543 0.874480075 1.012522598 1.034604619 1 23.974164 1.868865655 2.640275321 1.021649944 0.797317836 0.874569493 0.036655854 0.079583145 1.001826122 0.018986057 0.009560722 73.93765199 -1.868865655 -0.224332107 SESSTSAFST(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SESSTSAFSTPTR 13 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 SESSTSAFS(0.02)T(0.979)PT(0.001)R 88.552 0.087818 284630000 352280 401350 311470 474680 302290 394030 396940 401200 353070 470290 TRUE FALSE 338512.5081 389903.891 367759.5576 499178.2917 312013.4324 401997.5566 401797.8705 392915.0798 312990.9738 438436.8394 0.772089564 0.889304584 0.838797119 1.138540941 0.711649671 0.916888182 0.916432732 0.896172594 0.713879277 1 18.7420095 1.868965557 0.008083547 1.775651553 2.26E-05 0.033338961 0.121834559 10289.03835 71.63962714 7818.491731 7909.910738 73.95466203 -1.868965557 -1.775628975 MLDLLEDFLEHEGYKYER ddPTM_BT-474_Pertuzumab_2h_R1 2 MLDLLEDFLEHEGYKYER 18 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 299.79 1.03E-49 515360000 745280 740890 536730 586270 723850 764670 671070 645060 752820 646210 FALSE TRUE 716153.6336 719760.5426 633729.0505 616527.465 747133.2926 780132.1513 679282.7554 631739.2856 667363.0297 602441.6211 1.18875192 1.194739071 1.051934376 1.023381259 1.240175424 1.294950621 1.127549511 1.048631541 1.107763817 1 19.20046192 1.869078783 4.70371361 1.060072328 1.162313497 0.285299209 0.079496535 0.35445592 11.39840949 0.040733913 0.023484563 73.97394546 -1.869078783 0.102241169 QDLPDAMKPHEIQEK ddPTM_BT-474_Pertuzumab_2h_R1 5 QDLPDAMKPHEIQEK 15 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ;;;; 246.69 2.03E-18 3585870000 6357270 5569160 4691250 4553490 5229520 5250640 5492450 6404460 7201990 5790710 FALSE TRUE 6108820.86 5410333.01 5539063.231 4788496.165 5397732.26 5356811.538 5559668.246 6272205.663 6384450.288 5398500.054 1.131577438 1.002191897 1.02603745 0.88700493 0.999857776 0.99227776 1.029854254 1.16184229 1.182634107 1 22.36412719 1.869268793 4.786755059 1.129324821 1.002199598 0.306696944 0.071715364 0.230972776 7.606922158 0.032925878 0.019051603 74.00631725 -1.869268793 -0.127125223 KPATPAEDDEDDDIDLFGS(ph)DNEEEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPATPAEDDEDDDIDLFGSDNEEEDK 26 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 1 KPATPAEDDEDDDIDLFGS(1)DNEEEDK 160.86 1.09E-11 952830000 180050 146940 197410 183850 191240 169880 243380 334610 393450 362730 TRUE FALSE 173013.4469 142749.4151 233086.3784 193338.5205 197391.4083 173315.09 246358.5572 327700.1866 348787.2055 338161.974 0.511628924 0.422133256 0.68927436 0.571733475 0.583718524 0.512520932 0.728522354 0.969062792 1.031420539 1 18.36735491 1.869366188 2.246879345 1.016296266 0.55116644 0.904270237 0.065702541 0.085413204 0.798228396 0.040603331 0.01953113 74.02291572 -1.869366188 -0.465129826 ITFHGEGDQEPGLEPGDIIIVLDQK ddPTM_BT-474_Pertuzumab_2h_R1 3 ITFHGEGDQEPGLEPGDIIIVLDQK 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;; 166.89 1.34E-11 979710000 456700 431870 375090 414860 429000 479470 495430 489360 631180 600280 FALSE TRUE 438851.6591 419553.4904 442877.1068 436270.9743 442799.1746 489165.2119 501493.2205 479254.545 559531.0925 559622.5009 0.784192305 0.749708044 0.791385454 0.779580831 0.791246195 0.874098542 0.896127693 0.856388984 0.999836661 1 19.09409445 1.869457569 0.514090476 1.00783265 0.759228389 0.871295575 0.030837215 0.291960204 0.173268589 0.030752829 0.021663414 74.03849283 -1.869457569 -0.248604261 FAEEDKK ddPTM_BT-474_Pertuzumab_2h_R1 3 FAEEDKK 7 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 105.95 0.012527 4505500000 3395770 3037710 2786230 2590890 2827240 2679670 3352550 3965580 4763900 3994790 FALSE TRUE 3263059.554 2951077.485 3289763.74 2724606.143 2918180.742 2733854.763 3393579.51 3883689.387 4223122.044 3724219.315 0.87617277 0.792401638 0.883343182 0.731591218 0.783568446 0.734074589 0.911219029 1.042819732 1.133961694 1 21.8285066 1.869637073 2.698420999 1.069850462 0.80029689 0.801669718 0.057361884 0.108922567 1.425931961 0.031350544 0.015890212 74.06910099 -1.869637073 -0.269553572 NSQEDS(ph)EDS(ph)EDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 8 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NS(0.012)QEDS(0.988)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK 239.1 4.90E-18 21195908000 25590840 15828610 13995740 10585570 15140250 12669470 16742160 24129150 25882460 17835570 TRUE FALSE 24590721.68 15377193.54 16525081.55 11131892.54 15627249.89 12925655.36 16947055.56 23630874.62 22944391.65 16627550.96 1.478914228 0.92480207 0.993837372 0.669484795 0.939840746 0.77736375 1.019215374 1.421187924 1.37990205 1 23.98707236 1.869667942 5.595144279 1.302846368 0.945679735 0.261679283 0.224564206 0.258482809 10.39837125 0.099746978 0.059434712 74.07436583 -1.869667942 -0.357166633 TET(ph)PPPLASLNVSK ddPTM_BT-474_Pertuzumab_2h_R1 4 TETPPPLASLNVSK 14 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 1 T(0.028)ET(0.972)PPPLASLNVSK;TET(1)PPPLASLNVSK;TET(1)PPPLASLNVSK;T(0.001)ET(0.999)PPPLASLNVSK 162.81 4.90E-05 1212657000 1682740 1285177 1420580 1463870 1417106 1288537 1554711 1987760 2096790 1878820 TRUE FALSE 1616976.66 1248525.01 1677310.407 1539420.506 1462688.501 1314592.101 1573738.018 1946712.061 1858771.19 1751565.848 0.923160646 0.712805066 0.957606252 0.878882463 0.835074801 0.75052394 0.898474939 1.111412433 1.06120543 1 20.74021379 1.869847454 4.715116956 1.064096719 0.842345794 0.632278238 0.072999666 0.132980483 4.292336773 0.033118934 0.019110181 74.10499011 -1.869847454 -0.221750925 FQSSHHPTDITSLDQYVER ddPTM_BT-474_Pertuzumab_2h_R1 6 FQSSHHPTDITSLDQYVER 19 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 232.84 6.28E-22 6997380000 1361582 3242140 2383190 3923890 2450450 3291940 2755930 616368 2179110 2682280 FALSE TRUE 1308369.87 3149677.342 2813885.447 4126402.433 2529270.95 3358505.282 2789657.896 603639.7854 1931746.568 2500606.786 0.523220955 1.259565222 1.125281057 1.650160455 1.011462883 1.343076129 1.115592388 0.241397324 0.772511128 1 21.25384678 1.869866377 8.005342652 0.60088504 1.17599388 0.306714658 0.32154703 0.27137043 16.32924334 0.131926383 0.082429877 74.10821917 -1.869866377 0.575108841 AS(ph)TPVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASTPVLK 7 0 Q04724;A0A669KBK8;A0A669KAE5;F6T2C8 Q04724 TLE1 Transducin-like enhancer protein 1 1 AS(0.594)T(0.406)PVLK 120.15 0.004847 605300000 2027100 1945600 1699700 1659100 1655500 2009600 1948400 2414900 2631800 2532800 TRUE FALSE 1947878.691 1890113.393 2006873.6 1744726.35 1708750.661 2050235.489 1972245.102 2365031.471 2333049.097 2361251.2 0.824934971 0.80047112 0.849919568 0.738899084 0.723663226 0.868283514 0.835254251 1.001600961 0.988056289 1 21.1711201 1.869893344 1.857313626 1.005829766 0.794269335 0.80739763 0.042721552 0.140775115 0.912635712 0.028738739 0.013070848 74.11282087 -1.869893344 -0.211560431 EKEELEEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKEELEEIR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ;;; 118.4 0.00090745 2652810000 8346080 7849160 6753150 7175600 7786190 7881220 8232120 9357000 10460100 10064600 FALSE TRUE 8019905.967 7625309.642 7973594.428 7545933.576 8036639.873 8040583.668 8332867.147 9163774.68 9272713.3 9382915.677 0.85473495 0.812680184 0.84979922 0.804220547 0.856518395 0.856938711 0.888089314 0.97664468 0.988254997 1 23.16160487 1.869998069 1.420824208 1.001620019 0.833667311 0.943038982 0.016476633 0.078906561 0.297845619 0.011460241 0.004905877 74.13069453 -1.869998069 -0.167952707 GLDHLLDENRVPDLAQMYQLFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDHLLDENRVPDLAQMYQLFSR 23 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 281.91 3.13E-52 560970000 230020 272153 193154 251198 227752 272943 241012 222159 259498 247283 FALSE TRUE 221030.5641 264391.4629 228061.2245 264162.3589 235077.8499 278462.0945 243961.577 217571.339 230040.8749 230534.3022 0.958775167 1.146863874 0.989272409 1.145870078 1.019708771 1.207898746 1.058244151 0.943769916 0.997859636 1 17.81462191 1.870071918 5.895585273 0.977641125 1.081719368 0.259951071 0.07345226 0.275694334 11.81180479 0.030372095 0.018257948 74.14330097 -1.870071918 0.104078243 MY(ph)SLDRIFAGFRT(ph)RS(ph)QMLLGHIEEQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 MYSLDRIFAGFRTRSQMLLGHIEEQDK 27 3 Q86VH2-4 Q86VH2-4 3 MY(0.805)S(0.64)LDRIFAGFRT(0.792)RS(0.762)QMLLGHIEEQDK 45.527 0.044958 308480000 607400 322270 305050 215390 406200 319830 389090 470650 580040 389910 TRUE FALSE 583662.1365 313079.1751 360179.3208 226506.3037 419265.7919 326297.1817 393851.7998 460930.913 514196.2909 363501.0484 1.605668372 0.861288232 0.990861849 0.62312421 1.153410131 0.897651281 1.083495637 1.268031867 1.414566184 1 18.4716 1.870109465 3.799026264 1.253734594 1.000463353 0.107405564 0.255651871 0.429212075 10.07910644 0.122468298 0.067489553 74.14971141 -1.870109465 -0.253271241 HIHITQATETTTTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIHITQATETTTTR 14 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 195.87 2.56E-08 302040000 132495 173353 139951 178817 160023 187178 159099 18384.5 158713 109260 FALSE TRUE 127316.9489 168409.1422 165243.2589 188045.7668 165170.2851 190962.8674 161046.1012 18004.85365 140696.5656 101859.7229 1.24992436 1.653343809 1.622262993 1.846124862 1.621546578 1.874763273 1.581057719 0.176761267 1.381277718 1 16.63622417 1.870145724 8.680696406 0.779614607 1.657400632 0.553692521 0.320325858 0.18999568 12.45256767 0.127846667 0.080434602 74.15590243 -1.870145724 0.877786024 AAS(ph)PSPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AASPSPAR 8 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AAS(0.777)PS(0.223)PAR;AAS(0.849)PS(0.151)PAR 88.177 0.015525 556130000 971190 1034760 850580 1014660 835350 1019050 899750 868070 912170 896350 TRUE FALSE 933234.8211 1005249.658 1004298.727 1067026.724 862219.7914 1039655.889 910761.4096 850144.0511 808624.2857 835639.4161 1.11679129 1.20297061 1.201832642 1.276898509 1.031808427 1.244144148 1.089897619 1.017357529 0.967671307 1 19.67252102 1.87024483 2.320614013 0.988009657 1.17928604 0.61265687 0.06533007 0.18834221 1.869143437 0.037099965 0.018029581 74.17282668 -1.87024483 0.191276383 KEESDEEET(ph)ASK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEESDEEETASK 12 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KEES(0.001)DEEET(0.998)AS(0.001)K 233.28 1.05E-15 420850000 305970 257170 223840 213210 248950 243570 282560 365280 411180 359400 TRUE FALSE 294012.3541 249835.7634 264292.8673 224213.7937 256957.7028 248495.1523 286018.0538 357736.8404 364504.5702 335057.5179 0.877498156 0.745650374 0.788798499 0.669180011 0.766906245 0.741649236 0.85363867 1.067687848 1.087886559 1 18.35404925 1.870355801 3.011646314 1.060536564 0.761747299 0.850629947 0.053586865 0.086413738 1.375296497 0.028169888 0.014699471 74.19178176 -1.870355801 -0.298789265 RGAS(ph)SS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGASSSPQR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RGAS(0.73)S(0.54)S(0.73)PQR 69.971 0.035912 173620000 322120 325420 241230 334090 326660 296150 305920 293230 294290 331660 TRUE FALSE 309531.1943 316139.3402 284825.6271 351332.4249 337167.3156 302138.3559 309663.9405 287174.698 260883.433 309196.3728 1.001082877 1.02245488 0.921180364 1.136276023 1.09046336 0.977173028 1.001512203 0.928777707 0.843746745 1 18.23816387 1.870458725 2.023521168 0.912840514 1.028470679 0.320989351 0.065345293 0.363327739 2.781712249 0.041644292 0.01943216 74.20936669 -1.870458725 0.115630166 IDFSSIAVPGTSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGTS(0.01)S(0.99)PR;IDFSSIAVPGTS(0.001)S(0.999)PR 295.22 5.13E-44 1379160000 2140300 2428800 2108650 2501700 2553400 2706600 2276300 2057940 2135300 2301600 TRUE FALSE 2056654.71 2359533.002 2489729.962 2630813.037 2635532.43 2761329.306 2304158.04 2015442.82 1892909.696 2145710.582 0.95849586 1.0996511 1.160328882 1.226080096 1.228279551 1.286906692 1.073843816 0.93928922 0.882183139 1 21.03302406 1.870687185 3.450259881 0.934277389 1.164241057 0.549113813 0.088269576 0.187866987 3.773588396 0.048163776 0.025975702 74.2484146 -1.870687185 0.229963668 GIINDDEDDEDLMMASGRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIINDDEDDEDLMMASGRPR 20 1 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 0 ; 230.29 1.62E-25 316440000 702370 590313 439681 352468 500974 499795 554567 801210 826780 640380 FALSE TRUE 674920.6039 573477.8512 519141.1374 370658.9157 517088.2837 509901.1973 561353.9568 784664.7335 732927.4005 597006.4922 1.130507981 0.96058897 0.869573688 0.620862454 0.86613511 0.85409657 0.94028116 1.314331994 1.227670737 1 19.18738709 1.870731985 5.300634327 1.205853248 0.875757942 0.475814219 0.138905728 0.18102787 6.816097729 0.065595707 0.038725915 74.25607412 -1.870731985 -0.330095305 KDDSHSAEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 6 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHS(0.001)AEDS(0.999)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK 325.81 7.31E-63 16719620000 5417571 3068445 3521221 2534615 3550333 2682812 4048495 4755212 6022586 4465140 TRUE FALSE 5205846.336 2980935.953 4157583.964 2665426.784 3664532.685 2737060.297 4098041.693 4657015.21 5338927.286 4162712.091 1.250590053 0.716104282 0.99876808 0.640310145 0.880323358 0.657518521 0.98446436 1.11874545 1.282559824 1 21.98909235 1.870855098 3.220927622 1.149091025 0.84732479 0.313074475 0.180904779 0.266758641 4.770189845 0.088824015 0.047137455 74.27712717 -1.870855098 -0.301766235 TKEEVEAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKEEVEAAK 9 1 Q92575 Q92575 UBXN4 UBX domain-containing protein 4 0 63.073 0.088745 0 144350 136430 120140 124920 124100 119720 132320 149640 152270 155570 FALSE TRUE 138708.6424 132539.15 141851.9705 131367.1362 128091.7892 122140.8204 133939.3717 146549.8817 134984.948 145033.1053 0.95639297 0.913854459 0.978066147 0.90577345 0.883190006 0.84215821 0.923508956 1.010458139 0.930718181 1 17.14602272 1.871022521 6.736136918 0.979501954 0.912081654 0.365007444 0.039829982 0.275021866 13.73601424 0.018223923 0.011172028 74.30576687 -1.871022521 -0.0674203 LRAETEQGEQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRAETEQGEQQR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 194.83 9.32E-07 1093570000 624090 683090 378560 494570 586050 652210 521150 476420 525380 471800 FALSE TRUE 599699.8728 663608.942 446974.213 520094.817 604900.8305 665398.1331 527527.9896 466581.7605 465741.065 439844.5658 1.363435903 1.508735116 1.01620947 1.182451387 1.375260439 1.512802896 1.199350931 1.060787826 1.058876479 1 18.74663426 1.871154269 3.405309922 1.045939627 1.318341738 0.454242614 0.139436813 0.251659581 4.945832905 0.076259605 0.041015736 74.32831176 -1.871154269 0.272402111 EVEGDDVPESIMLEMK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVEGDDVPESIMLEMK 16 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 243.88 1.17E-19 106090000 236740 234478 206716 211203 221531 233630 233047 276050 282160 269690 FALSE TRUE 227487.9391 227790.917 244074.1796 222103.2121 228656.7458 238354.1587 235899.0989 270349.471 250130.3797 251423.6561 0.904799264 0.906004314 0.970768556 0.883382318 0.909448018 0.948018028 0.938253395 1.075274599 0.994856187 1 17.93976087 1.871216822 6.000777654 1.028599542 0.921771855 0.69329198 0.030708008 0.118798441 5.201557373 0.013318077 0.008030905 74.33901833 -1.871216822 -0.106827687 KKAEPSEVDMNS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 7 KKAEPSEVDMNSPK 14 2 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK 180.81 8.92E-07 3600210000 6307890 4211230 4246078 3001578 4089080 4158650 4528260 5701990 5737840 5521030 TRUE FALSE 6061370.685 4091129.844 5013438.748 3156489.8 4220608.972 4242740.752 4583678.2 5584241.914 5086504.458 5147085.72 1.177631579 0.79484393 0.974034438 0.613257671 0.819999744 0.82429961 0.89053854 1.084932759 0.988229988 1 22.29532438 1.871302207 5.328723352 1.028701396 0.855503884 0.206560295 0.137195957 0.322735018 12.23863429 0.061250332 0.036202309 74.35363528 -1.871302207 -0.173197512 S(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPPKVPIVIQDDSLPAGPPPQIR 23 1 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR 228.55 4.07E-33 1054270000 536001 458616 474761 489051 493223 456395 577830 620550 725950 708750 TRUE FALSE 515053.4883 445536.7207 560560.8737 514290.9807 509087.9657 465623.6196 584901.6564 607735.4256 643543.1994 660745.7312 0.779503316 0.674293756 0.848376081 0.778349305 0.770474846 0.704694102 0.885214431 0.919772004 0.973964975 1 19.33373567 1.871496247 1.845174118 0.97554496 0.761106299 0.780027806 0.049113899 0.153910419 0.984507734 0.03173628 0.014426225 74.38686342 -1.871496247 -0.214438661 RDEQDDDDKGDSK ddPTM_BT-474_Pertuzumab_2h_R1 4 RDEQDDDDKGDSK 13 2 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ;;; 198.16 7.20E-08 5308910000 3466130 2522070 2196210 1927980 2599930 2267500 2698220 3329030 3798850 3010400 FALSE TRUE 3330669.808 2450143.033 2593114.001 2027483.279 2683559.11 2313350.404 2731241.623 3260284.367 3367620.474 2806502.927 1.186768692 0.873023509 0.923966256 0.722423362 0.956193234 0.824282199 0.973183244 1.161689281 1.199934781 1 21.42034213 1.871512828 4.068834625 1.134149884 0.905663434 0.36188127 0.121221346 0.222256449 5.808109006 0.057345647 0.03210896 74.38970348 -1.871512828 -0.22848645 SGPS(ph)PLSS(ph)PNGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGPSPLSSPNGK 12 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 SGPS(1)PLS(0.127)S(0.873)PNGK;SGPS(1)PLS(0.014)S(0.986)PNGK;SGPS(1)PLS(0.065)S(0.935)PNGK 236.22 6.64E-16 1334700000 3440900 3289960 2763490 2788400 2682640 2870610 3121120 3476660 3621040 3835150 TRUE FALSE 3306425.824 3196133.562 3262914.117 2932309.658 2768929.552 2928655.701 3159317.2 3404865.756 3209994.72 3575391.875 0.924772987 0.893925386 0.912603214 0.820136578 0.774440858 0.819114604 0.883628232 0.952305614 0.897802208 1 21.76966994 1.871593271 3.872907805 0.943568812 0.855853396 0.411471203 0.049141884 0.268363359 6.499755774 0.026523908 0.014692533 74.40348384 -1.871593271 -0.087715416 DKEDPQEMPHS(ph)PLGSMPEIR ddPTM_BT-474_Pertuzumab_2h_R1 10 DKEDPQEMPHSPLGSMPEIR 20 1 Q9HB58;Q9HB58-6;G5E9C0;Q9HB58-2;Q9HB58-5;Q9HB58-3;Q9HB58-7 Q9HB58 SP110 Sp110 nuclear body protein 1 DKEDPQEMPHS(1)PLGSMPEIR;DKEDPQEMPHS(0.999)PLGS(0.001)MPEIR;DKEDPQEMPHS(0.998)PLGS(0.002)MPEIR;DKEDPQEMPHS(1)PLGSMPEIR;DKEDPQEMPHS(1)PLGSMPEIR;DKEDPQEMPHS(1)PLGSMPEIR;DKEDPQEMPHS(1)PLGSMPEIR;DKEDPQEMPHS(1)PLGSMPEIR;DKEDPQEMPHS(1)PLGSMPEIR;DKEDPQEMPHS(0.993)PLGS(0.007)MPEIR 287.82 8.78E-46 4032050000 3001356 2731976 2450985 2673670 2812644 2798765 3004758 3004938 3621410 3384795 TRUE FALSE 2884059.689 2654062.719 2893932.511 2811658.429 2903115.249 2855357.946 3041531.127 2942884.98 3210322.719 3155539.82 0.913967135 0.841080408 0.917095862 0.89102296 0.920005899 0.904871467 0.963870305 0.932609046 1.017360864 1 21.5894554 1.871782483 0.616788321 1.00819112 0.885044018 0.70914616 0.026566834 0.380265732 0.296006173 0.023028452 0.013472364 74.43590665 -1.871782483 -0.123147103 STS(ph)PAGQHHS(ph)PISSR ddPTM_BT-474_Pertuzumab_2h_R1 1 STSPAGQHHSPISSR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 S(0.252)T(0.308)S(0.441)PAGQHHS(0.89)PIS(0.088)S(0.022)R 105.06 0.00071012 675160000 360060 448680 337610 413250 406330 460950 406710 142400 396630 403400 TRUE FALSE 345988.4571 435884.0857 398623.6371 434577.882 419399.9735 470270.7248 411687.4386 139459.3902 351606.2252 376077.3587 0.919992786 1.159027726 1.059951172 1.155554494 1.11519602 1.250462741 1.094688178 0.370826339 0.934930586 1 18.52066993 1.871796059 10.43775926 0.70432289 1.116995475 0.421147095 0.177481757 0.297856509 23.67425525 0.069834816 0.044445641 74.43823354 -1.871796059 0.412672585 DYDEEEQGYDS(ph)EK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYDEEEQGYDSEK 13 0 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EK;DYDEEEQGYDS(1)EK 355.95 3.79E-76 1098140000 694620 528800 604940 599280 592180 525130 703300 906580 1020890 923440 TRUE FALSE 667473.4825 513719.1417 714266.1148 630208.9126 611228.0075 535748.4884 711907.1958 887858.8062 905002.8471 860894.5863 0.77532545 0.596727114 0.829678948 0.732039581 0.709991696 0.622316015 0.826938869 1.031321163 1.051235379 1 19.71547707 1.871813746 3.165946002 1.032020127 0.712300161 0.823570538 0.065257423 0.094616409 1.642592371 0.033255549 0.017586853 74.44126526 -1.871813746 -0.319719967 VTAEDKGT(ph)GNK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTAEDKGTGNK 11 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 1 VT(0.001)AEDKGT(0.999)GNK 70.529 0.051406 0 215020 197700 168440 175200 189950 196030 203450 226650 274090 222070 TRUE FALSE 206616.7807 192061.7896 198880.8549 184242.093 196059.9143 199993.8609 205939.882 221969.5983 242976.4523 207029.0011 0.998008876 0.927704759 0.960642489 0.889933739 0.947016665 0.966018576 0.994739292 1.072166687 1.173634858 1 17.65947335 1.871885173 2.102272039 1.095571632 0.944689614 0.615965111 0.047093142 0.182924852 1.505912 0.027632679 0.013057471 74.45350937 -1.871885173 -0.150882019 TPS(ph)SPSKSPASFEIPASAMEANGVDGDGLNKPAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSSPSKSPASFEIPASAMEANGVDGDGLNKPAKK 35 3 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0YA73 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 T(0.1)PS(0.448)S(0.448)PS(0.003)KS(0.001)PASFEIPASAMEANGVDGDGLNKPAKK 127.2 2.86E-08 335450000 292370 213690 154240 130830 162610 217870 201610 264880 285550 224260 TRUE FALSE 280943.8572 207595.7704 182114.5991 137582.152 167840.4983 222275.4807 204077.3635 259410.1354 253135.5611 209070.6704 1.343774603 0.992945447 0.871067179 0.658065293 0.802793132 1.063159554 0.976116655 1.240777269 1.21076553 1 17.67363116 1.871952189 4.405357961 1.17127336 0.938462488 0.188216662 0.179085658 0.343471828 10.09573365 0.090194012 0.051373562 74.4649992 -1.871952189 -0.232810872 QLLNPAQVFDLMNGGPHLGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLLNPAQVFDLMNGGPHLGLR 21 0 Q86XP1-2;Q86XP1;A0A0D9SFR6;Q86XP1-5;Q86XP1-3;Q16760;H7BZR7;Q16760-2 Q86XP1-2 DGKH;DGKD Diacylglycerol kinase eta;Diacylglycerol kinase delta 0 25.186 0.096879 39315000 18234 35982 11717 19011 23244 37654 17156 11500 10307 8427.8 FALSE TRUE 17521.39512 34955.82859 13834.52254 19992.15999 23991.66437 38415.38968 17365.96026 11262.52098 9136.99257 7856.977599 2.230042647 4.449017214 1.760794449 2.544510244 3.053548781 4.88933425 2.210259612 1.433441911 1.162914423 1 12.93975873 1.871970601 3.402310131 1.236863802 3.138699906 0.478962063 0.904089632 0.218739907 4.293164756 0.462399474 0.248784609 74.46815618 -1.871970601 1.901836104 SES(ph)PPPLSDPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SESPPPLSDPK 11 0 Q15059;Q15059-2 Q15059 BRD3 Bromodomain-containing protein 3 1 SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK 208.33 2.09E-08 7906100000 2717280 2537900 2093660 2090090 2295800 2279330 2392740 2844470 2919290 2589640 TRUE FALSE 2611085.693 2465521.577 2472030.935 2197959.795 2369646.492 2325419.614 2422023.068 2785730.7 2587904.438 2414241.376 1.081534647 1.02124071 1.023936943 0.910414268 0.981528407 0.963209245 1.003223245 1.153874144 1.071932767 1 21.20313849 1.871981169 8.361363402 1.090208626 0.993836861 0.284057606 0.054709422 0.303629293 19.17011493 0.023472512 0.014725057 74.46996833 -1.871981169 -0.096371765 DHMVTMHDVLDAQWLYDNHKDESYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DHMVTMHDVLDAQWLYDNHKDESYLR 26 1 O60832;O60832-2;H7C2Q2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 295.04 7.86E-71 85968000 60844 56214 54610 54196 57729 57513 56515 3633.3 61566 39879 FALSE TRUE 58466.14921 54610.83176 64479.24179 56993.06205 59585.90571 58675.95227 57206.64748 3558.271085 54577.28579 37177.95981 1.57260241 1.468903405 1.73434051 1.532979818 1.602721236 1.578245621 1.538724765 0.095709154 1.468001097 1 15.18215998 1.871989457 10.63033909 0.764560206 1.57970103 0.50757607 0.321977465 0.279943628 22.6807435 0.125037019 0.079647651 74.47138952 -1.871989457 0.815140824 KS(ph)SPSTGSLDSGNESK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSSPSTGSLDSGNESK 16 1 Q15057;A0A0U1RQT1;A0A087X1H5 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 KS(0.485)S(0.485)PS(0.026)T(0.005)GSLDSGNESK;KS(0.48)S(0.48)PS(0.024)T(0.016)GSLDSGNESK;KS(0.488)S(0.488)PS(0.021)T(0.003)GSLDSGNESK 118.23 0.0001767 1072930000 439960 457100 391550 341030 387920 426840 440373 494380 558240 531970 TRUE FALSE 422765.8768 444063.9555 462311.795 358630.5992 400397.7991 435470.9973 445762.4165 484170.8802 494870.9355 495939.1981 0.852455056 0.895399995 0.932194504 0.723134208 0.807352596 0.878073358 0.898824731 0.976270644 0.997845981 1 18.91980373 1.872011746 1.68961976 1.000361176 0.845055547 0.606626919 0.052064177 0.26602401 1.428477952 0.038466499 0.017080402 74.47521157 -1.872011746 -0.155305629 NQIGDKEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NQIGDKEK 8 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 138.66 0.00063462 5866600000 6187850 5840990 4777320 4467530 4481750 4279020 5630080 6299660 7479810 6451200 FALSE TRUE 5946021.981 5674410.684 5640687.995 4698099.759 4625909.559 4365544.716 5698982.603 6169569.82 6630733.327 6014254.478 0.98865487 0.943493613 0.937886485 0.781160787 0.769157603 0.725866312 0.947579226 1.025824538 1.102502954 1 22.51995448 1.87221285 3.221109684 1.047316216 0.856942834 0.49277369 0.083336575 0.230617316 4.124651656 0.048386179 0.02570266 74.509706 -1.87221285 -0.190373382 SPPTTMLLPAS(ph)PAKAPETEPIDVAAHLQLLGESLSLIGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPTTMLLPASPAKAPETEPIDVAAHLQLLGESLSLIGHR 40 1 Q9UGU5 Q9UGU5 HMGXB4 HMG domain-containing protein 4 1 SPPT(0.001)TMLLPAS(0.999)PAKAPETEPIDVAAHLQLLGESLSLIGHR 180.11 3.68E-24 146640000 43185 48736 36526 45731 43522 44667 44758 33808 53430 42457 TRUE FALSE 41497.28246 47346.097 43127.06072 48091.18239 44921.92466 45570.19734 45305.76179 33109.85299 47364.8504 39581.34957 1.048404941 1.196171872 1.08958035 1.214996025 1.134926554 1.15130479 1.144623978 0.836501366 1.196645665 1 15.27253318 1.872465211 20.64410634 0.99226043 1.14337279 0.281876893 0.092769114 4.278944826 680.9556016 0.035498677 0.022900499 74.553015 -1.872465211 0.15111236 TDS(ph)REDEIS(ph)PPPPNPVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 TDSREDEISPPPPNPVVK 18 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 2 T(0.156)DS(0.844)REDEIS(1)PPPPNPVVK;T(0.008)DS(0.992)REDEIS(1)PPPPNPVVK 123.64 1.91E-05 319490000 418840 361250 309010 343400 386270 345840 395710 490490 535770 482460 TRUE FALSE 402471.2697 350947.5037 364854.9809 361122.9152 398694.7254 352833.1218 400552.8174 480361.2101 474951.6357 449782.5545 0.894812984 0.780260373 0.811180819 0.80288333 0.886416606 0.784452661 0.890547695 1.067985419 1.055958331 1 18.77886818 1.872558887 3.661647479 1.0461558 0.825923588 0.849363424 0.040294761 0.077620549 1.720037696 0.019160161 0.010487774 74.5690975 -1.872558887 -0.220232212 GQKPALDCSQVS(ph)PPRPATSPENNASLSDTSPMDSSPSGIPK ddPTM_BT-474_Pertuzumab_2h_R1 5 GQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK 41 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 GQKPALDCS(0.073)QVS(0.927)PPRPATSPENNASLSDTSPMDSSPSGIPK;GQKPALDCS(0.017)QVS(0.971)PPRPAT(0.006)S(0.006)PENNASLSDTSPMDSSPSGIPK;GQKPALDCS(0.224)QVS(0.767)PPRPAT(0.005)S(0.005)PENNASLSDTSPMDSSPSGIPK;GQKPALDCS(0.001)QVS(0.882)PPRPAT(0.059)S(0.059)PENNASLSDTSPMDSSPSGIPK;GQKPALDCS(0.079)QVS(0.903)PPRPAT(0.009)S(0.009)PENNASLSDTSPMDSSPSGIPK 222.21 3.67E-44 4759080000 1138280 1087740 857430 970810 997060 1055620 1049710 1194450 1253090 1207100 TRUE FALSE 1093794.759 1056718.72 1012386.674 1020913.62 1029131.34 1076965.36 1062556.665 1169784.19 1110844.477 1125342.042 0.971966494 0.939020032 0.899625746 0.90720295 0.91450537 0.957011575 0.944207739 1.039492125 0.987117192 1 20.10193214 1.872883331 5.121989794 1.010970158 0.930205432 0.67520574 0.024071113 0.129980901 4.694664385 0.011605602 0.006813677 74.62482598 -1.872883331 -0.080764726 EEQEGREGRGSRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEQEGREGRGSRR 13 3 Q13129 Q13129 RLF Zinc finger protein Rlf 0 57.598 0.066472 41927000 68663 99297 75996 118600 100710 104790 82882 64671 54598 81115 FALSE TRUE 65979.57405 96465.14678 89730.16772 124720.9602 103949.4286 106908.9256 83896.33471 63335.52125 48400.26393 75621.0088 0.872503225 1.275639512 1.186577238 1.649289823 1.374610446 1.413746356 1.109431573 0.837538698 0.640037269 1 16.20649947 1.872907859 2.816460566 0.800302322 1.307955075 0.516380248 0.201948703 0.206421496 2.91634723 0.112564912 0.057850357 74.62904075 -1.872907859 0.507652753 VHLENMGSHDIVDGNHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VHLENMGSHDIVDGNHR 17 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3;O15020;O15020-2;A4QPE4 Q01082;Q01082-3;O15020 SPTBN1;SPTB;SPTBN2 "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic;Spectrin beta chain, non-erythrocytic 2" 0 ;;; 302.62 5.85E-47 2182910000 424410 485820 428830 527030 490581 577860 483452 14619.7 489444 345511 FALSE TRUE 407823.588 471964.8893 506329.1203 554230.0815 506360.9834 589544.7251 489368.6302 14317.79809 433884.369 322109.2322 1.266103381 1.465232418 1.571917442 1.720627744 1.572016362 1.830263358 1.519262974 0.044450133 1.347010038 1 18.29719049 1.873030941 9.553865334 0.705844284 1.580783337 0.517185639 0.336110787 0.231496791 16.83472677 0.13429616 0.08506373 74.65019407 -1.873030941 0.874939053 TAS(ph)PPPPPK ddPTM_BT-474_Pertuzumab_2h_R1 6 TASPPPPPK 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 TAS(1)PPPPPK;TAS(1)PPPPPK;TAS(1)PPPPPK;TAS(1)PPPPPK;TAS(1)PPPPPK;T(0.03)AS(0.97)PPPPPK 135.86 0.00021924 13860580000 3676510 3412210 2997540 3178340 3234530 3116530 3423950 3782080 4225260 3763790 TRUE FALSE 3532827.925 3314897.112 3539262.158 3342374.508 3338571.595 3179548.372 3465853.324 3703978.726 3745626.199 3508865.151 1.006829209 0.944720578 1.008662917 0.952551427 0.951467626 0.906147211 0.987741955 1.055605892 1.067475106 1 21.74257307 1.873094345 4.357090157 1.045301986 0.961222955 0.539557933 0.032525887 0.16168602 4.681934237 0.015329525 0.008716472 74.66109321 -1.873094345 -0.084079031 ILEPDDFLDDLDDEDYEEDTPK ddPTM_BT-474_Pertuzumab_2h_R1 3 ILEPDDFLDDLDDEDYEEDTPK 22 0 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 0 ;; 203.63 1.26E-22 207288000 235591 220452 187117 184646 217677 213823 223204 264338 284675 269210 FALSE TRUE 226383.8433 214164.9248 220933.2043 194175.6022 224678.7784 218146.6476 225935.6373 258879.3279 252359.8875 250976.1669 0.902013311 0.853327738 0.880295556 0.77368144 0.895219579 0.869192682 0.90022746 1.031489687 1.005513354 1 17.93719084 1.873180993 3.293904055 1.014735998 0.860968385 0.791194051 0.034405357 0.104016268 1.93310916 0.017675321 0.009445618 74.67599071 -1.873180993 -0.153767613 LNENHSGELWK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNENHSGELWK 11 0 A0A0A0MTH3;Q13418;Q13418-3 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 ; 154.36 3.20E-05 517010000 585940 572390 460340 538820 572330 583130 600850 640670 743900 731530 FALSE TRUE 563040.817 556065.9976 543533.6782 566628.5648 590739.5142 594921.2881 608203.382 627439.9406 659455.5907 681982.8215 0.825593841 0.815366575 0.796990278 0.830854601 0.866208789 0.872340577 0.891816279 0.920023087 0.966968038 1 19.37937587 1.873188512 0.510338853 1.004265216 0.805942621 0.963644065 0.012116025 0.154074755 0.090398589 0.01285814 0.009148293 74.67728354 -1.873188512 -0.198322595 AEGEWEDQEALDYFS(ph)DKESGK ddPTM_BT-474_Pertuzumab_2h_R1 8 AEGEWEDQEALDYFSDKESGK 21 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDY(0.005)FS(0.995)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(0.996)DKES(0.004)GK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK 250.22 4.33E-31 16826775000 4862574 3801804 3791382 3146811 3857583 3689458 4234056 5516862 5905360 5169584 TRUE FALSE 4672539.232 3693380.272 4476569.066 3309218.293 3981665.661 3764061.369 4285873.644 5402936.872 5235008.29 4819443.471 0.969518423 0.766349952 0.928856017 0.686639093 0.826167105 0.781015773 0.889288083 1.121070701 1.086226723 1 22.20043513 1.873345369 4.159090529 1.077173072 0.822732063 0.64354404 0.080550026 0.128089481 3.46412459 0.036769465 0.020706037 74.70426007 -1.873345369 -0.254441009 QNPEQS(ph)ADEDAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QNPEQSADEDAEK 13 0 Q99613-2;Q99613;B5ME19;H3BPE3 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 QNPEQS(1)ADEDAEK 191.91 3.32E-06 508260000 244820 245420 280800 315590 257990 261220 335920 387460 462270 434560 TRUE FALSE 235252.1637 238420.8619 331546.8064 331877.6377 266288.4827 266502.0474 340031.0894 379458.8156 409795.0476 405126.8641 0.580687643 0.588509139 0.818377737 0.819194349 0.657296532 0.657823687 0.839320024 0.936641949 1.011522769 1 18.62801423 1.873366659 1.917355661 0.99791711 0.692746409 0.742040403 0.078395464 0.186664475 1.286304511 0.055391648 0.025499136 74.70792246 -1.873366659 -0.305170702 GLPS(ph)PYNMSS(ph)APGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 GLPS(0.871)PY(0.13)NMS(0.138)S(0.861)APGS(0.001)R 113.8 0.00095935 110500000 115360 117380 104440 109970 113120 109390 83318 102650 84145 80243 TRUE FALSE 110851.6037 114032.4373 123314.6313 115645.5649 116758.6075 111601.9407 84337.67061 100530.2416 74593.21236 74808.07014 1.481813439 1.524333366 1.64841348 1.545896915 1.56077556 1.491843601 1.127387332 1.343842201 0.99712788 1 16.19090629 1.873400236 0.829569379 1.005754512 1.571111262 0.820833997 0.097579486 0.239235588 0.30821218 0.083693058 0.039384187 74.71369861 -1.873400236 0.56535675 EGQPSPADEKGNDS(ph)DGEGESDDPEKK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGQPSPADEKGNDSDGEGESDDPEKK 26 2 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEKK;EGQPSPADEKGNDS(1)DGEGESDDPEKK;EGQPSPADEKGNDS(1)DGEGESDDPEKK 166.28 6.12E-12 2085610000 910025 583161 552549 388670 589324 522556 655862 883870 1001920 749281 TRUE FALSE 874460.2169 566529.8193 652406.8957 408729.3053 608280.1417 533122.4404 663888.6353 865617.7756 888186.242 698531.5305 1.25185504 0.811029702 0.933969144 0.585126494 0.870798404 0.763204547 0.950406111 1.239196425 1.271504869 1 19.41396571 1.873711186 4.153552569 1.189815407 0.856707597 0.377714247 0.171263931 0.215488322 5.817850717 0.080963059 0.045588907 74.767212 -1.873711186 -0.33310781 VGNES(ph)PVQELK ddPTM_BT-474_Pertuzumab_2h_R1 4 VGNESPVQELK 11 0 Q5JSH3-2;Q5JSH3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VGNES(1)PVQELK;VGNES(1)PVQELK;VGNES(1)PVQELK;VGNES(1)PVQELK 289.99 2.12E-35 2963700000 3460140 2974990 2784620 2725730 2816680 3007560 3291640 3782720 4216120 4140850 TRUE FALSE 3324913.903 2890146.198 3287862.778 2866405.252 2907281.07 3068374.924 3331924.075 3704605.51 3737523.733 3860386.541 0.861290409 0.748667567 0.851692633 0.742517678 0.753106208 0.794836188 0.863106334 0.959646261 0.968173444 1 21.88031388 1.873721275 1.924478046 0.98351468 0.78789774 0.820833508 0.03852931 0.125874654 0.8735791 0.023964809 0.011047239 74.76894882 -1.873721275 -0.19561694 VESDLKGPEVDIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VESDLKGPEVDIEGPEGK 18 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 153.36 3.08E-08 214470000 376220 340150 275240 270380 270740 291900 318670 423420 418040 365860 FALSE TRUE 361516.9065 330449.255 324981.9907 284334.3442 279448.598 297802.418 322569.9788 414676.229 370585.8518 341079.9763 1.059918294 0.968832174 0.9528029 0.833629541 0.819305199 0.873116098 0.94573121 1.215774181 1.086507205 1 18.37975054 1.873787051 6.505334405 1.11868498 0.913429566 0.496289455 0.08222816 0.183643298 8.852437393 0.037815368 0.023086535 74.78027388 -1.873787051 -0.205255414 HQAFEAELSANQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQAFEAELSANQSR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 196.47 2.48E-08 642460000 427040 470460 409660 474150 459160 492470 459700 324530 458000 500360 FALSE TRUE 410350.8047 457042.9414 483694.6748 498620.9383 473929.2984 502428.0808 465325.9461 317828.3421 406009.7601 466470.1715 0.879693558 0.979790283 1.036925198 1.068923521 1.015990576 1.07708512 0.997547056 0.681347622 0.870387401 1 18.83142531 1.873799269 8.850626756 0.819072978 1.014437491 0.376710583 0.090066537 0.254962109 17.14974111 0.037006622 0.023321633 74.78237765 -1.873799269 0.195364513 QQSSSSKGDS(ph)PELKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQSSSSKGDSPELKPR 16 2 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 QQS(0.016)S(0.016)S(0.016)S(0.016)KGDS(0.937)PELKPR;QQS(0.004)S(0.002)S(0.01)S(0.038)KGDS(0.946)PELKPR 157.97 8.04E-09 1249020000 1537590 1241760 958780 793070 881990 1056520 1222900 1398280 1690860 1461080 TRUE FALSE 1477499.283 1206346.221 1132052.874 834000.4377 910360.0094 1077883.558 1237866.216 1369405.029 1498920.661 1362119.75 1.084705866 0.885638888 0.831096439 0.61228129 0.668340657 0.791328044 0.908779287 1.005348487 1.100432367 1 20.37742211 1.873848019 2.24357494 1.046918658 0.801761803 0.40029105 0.121811552 0.320197982 2.979141137 0.079868874 0.038542204 74.79077247 -1.873848019 -0.245156855 DEDHIAHIIELLGSIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEDHIAHIIELLGSIPR 17 0 P78362;P78362-2;H7C521;F8WBW4 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 ; 154.6 7.63E-08 168470000 187186 189088 184740 207400 200463 204670 201970 13234.1 237140 167403 FALSE TRUE 179870.5642 183695.3954 218126.6275 218103.9389 206911.0745 208808.5676 204441.7693 12960.81121 210220.8614 156064.6457 1.15253883 1.177046823 1.397668425 1.397523045 1.325803634 1.337962014 1.309981312 0.083047709 1.347011429 1 17.25178423 1.874245884 20.15486036 0.705052762 1.305192119 0.332526846 0.307300771 3.292620581 516.3681291 0.119903274 0.07734324 74.85932106 -1.874245884 0.600139357 VFDGIPPPYDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFDGIPPPYDKK 12 1 P40429;M0QYS1;Q8J015;Q6NVV1 P40429 RPL13A;RPL13a;RPL13AP3 60S ribosomal protein L13a;Putative 60S ribosomal protein L13a protein RPL13AP3 0 124.86 0.00050598 512710000 651000 541650 441910 441960 532110 543780 549160 667440 692930 657750 FALSE TRUE 625558.2003 526202.6723 521772.9672 464769.6086 549225.8014 554775.6042 555880.7844 653657.1308 614271.4914 613200.0066 1.02015361 0.858125679 0.850901764 0.757941297 0.895671552 0.904722111 0.906524427 1.065977044 1.001747366 1 19.22599819 1.87436984 4.430526287 1.026171615 0.875944703 0.500154685 0.063201804 0.182001845 5.405328378 0.030784984 0.017576356 74.88069047 -1.87436984 -0.150226912 TNPPTQKPPS(ph)PPMSGR ddPTM_BT-474_Pertuzumab_2h_R1 12 TNPPTQKPPSPPMSGR 16 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 TNPPTQKPPS(0.961)PPMS(0.039)GR;TNPPTQKPPS(0.996)PPMS(0.004)GR;TNPPTQKPPS(0.862)PPMS(0.138)GR;TNPPTQKPPS(0.987)PPMS(0.013)GR;TNPPTQKPPS(0.986)PPMS(0.014)GR;TNPPTQKPPS(0.999)PPMS(0.001)GR;TNPPTQKPPS(0.999)PPMS(0.001)GR;TNPPTQKPPS(1)PPMSGR;TNPPTQKPPS(0.985)PPMS(0.015)GR;TNPPT(0.001)QKPPS(0.947)PPMS(0.053)GR;TNPPTQKPPS(0.999)PPMS(0.001)GR;TNPPTQKPPS(0.989)PPMS(0.011)GR 171.56 4.92E-09 32155340000 4797550 4143776 3565260 3642388 3671248 3733334 4076650 5002560 5158680 4547330 TRUE FALSE 4610056.442 4025599.566 4209581.791 3830372.081 3789337.026 3808824.571 4126541.262 4899255.388 4573088.273 4239335.289 1.087447944 0.949582727 0.992981565 0.90353129 0.893851693 0.898448533 0.973393464 1.155665937 1.078727669 1 22.01540664 1.874535237 6.431829492 1.091178515 0.94978381 0.42328501 0.064359025 0.199303317 9.496934504 0.028450461 0.017344565 74.90921341 -1.874535237 -0.141394705 AIEDEGGNPDEIEITSEGNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIEDEGGNPDEIEITSEGNKK 21 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7ES42 Q15424 SAFB Scaffold attachment factor B1 0 227.08 3.50E-25 275440000 229500 209660 179350 144240 176600 182110 204520 255680 287370 238000 FALSE TRUE 220530.8863 203680.7021 211762.5346 151684.2437 182280.4994 185792.389 207022.9769 250400.1187 254748.9624 221880.048 0.993919409 0.917976645 0.954400977 0.683631742 0.821527222 0.837355096 0.933040076 1.128538239 1.148138215 1 17.75942042 1.874538964 3.658650217 1.103249576 0.864779299 0.563944096 0.087698846 0.173077489 3.833707174 0.046186982 0.025308582 74.90985628 -1.874538964 -0.238470276 ENASSNHDHDDGASGTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENASSNHDHDDGASGTPK 18 0 A0A0C4DFW2;Q9UK53-3;Q9UK53-4;Q9UK53-5;Q9UK53-2;Q9UK53 A0A0C4DFW2 ING1 Inhibitor of growth protein;Inhibitor of growth protein 1 0 76.713 0.0085453 71536000 63258 84787 71414 97772 76855 95066 83345 6619.9 93639 64658 FALSE TRUE 60785.80742 82368.95778 84320.0984 102818.0246 79327.11087 96988.29965 84365.00104 6483.196752 83009.49329 60278.65607 1.008413448 1.366469712 1.398838393 1.705711961 1.316006627 1.608999038 1.399583311 0.107553771 1.377095952 1 15.87935963 1.87455644 13.20102649 0.733335024 1.41684077 0.35899174 0.34312748 0.617297695 62.9601138 0.135465018 0.086933941 74.91287069 -1.87455644 0.683505745 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEFDLGAALEPTSQKPGVGAGHGGDPK 27 1 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 0 79.382 1.40E-06 170180000 125230 117530 130570 108630 114270 95733 138760 159330 196790 160690 FALSE TRUE 120335.8732 114178.1595 154166.9035 114236.4073 117945.5983 97668.78685 140458.1864 156039.7798 174451.2242 149806.3232 0.803276328 0.76217183 1.029108119 0.762560651 0.787320561 0.651967052 0.937598517 1.041610104 1.164511754 1 17.19273899 1.874631145 2.986998401 1.077750193 0.805673004 0.600096615 0.09780487 0.178877221 2.805297438 0.052810061 0.027587028 74.92575795 -1.874631145 -0.272077189 HMQHENVIGLLDVFTPASSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HMQHENVIGLLDVFTPASSLR 21 0 O15264-2;O15264 O15264-2 MAPK13 Mitogen-activated protein kinase 13 0 115.46 8.85E-05 49145000 184540 214440 179480 214960 198070 203260 203380 86625 223540 192510 FALSE TRUE 177327.9728 208324.3812 211916.0285 226054.1114 204441.1014 207370.0565 205869.0253 84836.16348 198164.6764 179471.1262 0.988058506 1.160768228 1.180780625 1.259556989 1.139130877 1.1554508 1.147087164 0.472700903 1.104159095 1 17.45339223 1.874636519 14.13251039 0.802040189 1.153844506 0.371375563 0.166907865 0.712655629 77.97826907 0.065379273 0.042018296 74.92668514 -1.874636519 0.351804316 SHSAHFFEFLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSAHFFEFLTK 12 0 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ; 91.313 0.004839 961350000 565630 795880 608110 853130 744450 782540 686010 129659 549640 519230 FALSE TRUE 543524.5543 773182.2816 718009.0043 897160.1415 768395.9103 798363.495 694405.5956 126981.4963 487247.1715 484062.0896 1.122840573 1.597279147 1.483299394 1.853398894 1.587391219 1.649299774 1.434538276 0.262324811 1.006579904 1 18.88483259 1.874648901 6.740253961 0.698946532 1.561031778 0.653169395 0.259071229 0.128014075 6.432228332 0.10811107 0.066322159 74.92882125 -1.874648901 0.862085247 KYKPLDLRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYKPLDLRPK 10 3 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 90.685 0.0046708 1811280000 5294900 4538100 4267900 3319400 3997800 3687500 4404000 5204700 5366500 5306400 FALSE TRUE 5087969.454 4408677.831 5039204.469 3490714.632 4126392.868 3762063.777 4457897.469 5097221.126 4757317.418 4946992.802 1.028497444 0.891183393 1.018639944 0.705623552 0.834121462 0.760474884 0.901132799 1.030367605 0.961658448 1 22.23812037 1.874848872 5.286775367 0.996777851 0.868270717 0.253167148 0.095186466 0.31761231 11.97655502 0.044730562 0.026432244 74.96333029 -1.874848872 -0.128507134 FMQDPMEVFVDDETK ddPTM_BT-474_Pertuzumab_2h_R1 1 FMQDPMEVFVDDETK 15 0 O00148;O00148-2 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 160.84 3.92E-06 34255000 62041 51428 53496 61064 60017 61098 67214 74820 93915 83469 FALSE TRUE 59616.36913 49961.32379 63163.91721 64215.52036 61947.50131 62333.44342 68036.58504 73274.94085 83254.16292 77815.57028 0.766123912 0.642047904 0.811713093 0.825227138 0.796081055 0.801040758 0.874331253 0.941648832 1.069890802 1 16.24777124 1.875039243 0.970097204 1.040833864 0.758180291 0.80724898 0.051467768 0.230730969 0.400121495 0.045030645 0.019864142 74.99619735 -1.875039243 -0.282653573 GKQECMDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKQECMDSK 9 1 E9PMQ6;Q00613-2;Q00613;E9PI02;A0A087X1F9 E9PMQ6 HSF1 Heat shock factor protein 1 0 83.438 0.014746 116370000 259490 233550 193160 203950 225960 219940 231010 280540 279250 272490 FALSE TRUE 249348.8439 226889.3827 228068.3088 214475.8839 233228.2086 224387.3375 233837.1695 274746.751 247550.7107 254034.0096 0.981556935 0.893145697 0.897786518 0.844280198 0.918098364 0.883296445 0.920495527 1.081535309 0.974478618 1 17.95466213 1.875055307 6.392956984 1.024085282 0.900607005 0.616406366 0.040970859 0.138750898 6.572671208 0.017352133 0.010570725 74.99897146 -1.875055307 -0.123478277 EFEEDLTGIDDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFEEDLTGIDDRK 13 1 A0A0A0MTB9;H0YAK8;A0A0A0MQT0;P09455;P09455-2;P09455-3 A0A0A0MTB9 RBP1 Retinol-binding protein 1 0 94.122 0.0084985 76228000 43480 42122 37826 37141 39591 41445 42057 58626 52902 49142 FALSE TRUE 41780.75353 40920.7218 44661.99963 39057.85146 40864.48047 42283.0463 42571.70615 57415.35261 46896.78674 45813.56857 0.911973348 0.893200925 0.97486402 0.852538946 0.891973312 0.922937191 0.929237941 1.253239038 1.023644047 1 15.48348732 1.875101876 8.24968781 1.115854938 0.908803132 0.579731563 0.07007358 0.166834018 10.45387506 0.028036553 0.017572192 75.00701395 -1.875101876 -0.207051806 KGQGGAGAGDDEEED ddPTM_BT-474_Pertuzumab_2h_R1 5 KGQGGAGAGDDEEED 15 1 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;; 143.22 9.12E-05 12848070000 8915990 8079530 7424930 6035920 7616530 7687870 8035810 9530220 10366590 9074040 FALSE TRUE 8567543.254 7849109.715 8766780.018 6347434.555 7861522.605 7843323.999 8134154.647 9333417.627 9189818.163 8459447.188 1.012778148 0.927851376 1.036330132 0.750336803 0.929318717 0.927167441 0.961546832 1.103312949 1.086337908 1 23.01213196 1.875102461 4.363203804 1.07122182 0.928164516 0.379877956 0.07549269 0.221926631 6.451935938 0.035755121 0.020356983 75.00711499 -1.875102461 -0.143057304 GCGPCLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GCGPCLR 7 0 O43396;K7ER96;K7EPB7 O43396 TXNL1 Thioredoxin-like protein 1 0 89.775 0.06585 0 194620 205520 136300 155870 186090 195200 173360 165850 182350 177050 FALSE TRUE 187014.0352 199658.7708 160932.442 163914.4694 192075.7539 199147.0777 175481.6315 162425.1395 161650.3925 165058.2458 1.133018434 1.209626153 0.975003952 0.993070468 1.163684692 1.206526077 1.063149743 0.984047412 0.979353632 1 17.33261569 1.875120476 3.951446414 0.987802812 1.109962859 0.360738908 0.074306005 0.287629942 7.203896162 0.039536513 0.022042578 75.0102263 -1.875120476 0.122160047 ILVEDELSS(ph)PVVVFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILVEDELSSPVVVFR 15 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;Q6P474;Q6XYB5;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 1 ILVEDELS(0.016)S(0.984)PVVVFR 212.24 1.02E-09 10119000 27054 32679 24528 34816 33403 29439 25003 23410 20265 20736 TRUE FALSE 25996.69977 31747.02692 28960.75522 36612.85793 34477.43783 30034.27675 25308.99419 22926.57532 17964.60216 19331.53225 1.344782164 1.642240589 1.498109661 1.893944953 1.783481898 1.55364181 1.309207872 1.185967828 0.929290132 1 14.23866837 1.875147929 1.469506548 0.982669247 1.640711489 0.765768741 0.146768219 0.194078172 0.784542571 0.111875747 0.048328007 75.01496807 -1.875147929 0.658042242 THDHQLESSLS(ph)PVEVFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 THDHQLESSLSPVEVFAK 18 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 T(0.235)HDHQLES(0.139)S(0.092)LS(0.534)PVEVFAK;T(0.086)HDHQLES(0.068)S(0.068)LS(0.779)PVEVFAK 104.52 0.00084322 221860000 218631 213931 196140 232870 222225 232991 218100 39207.8 227213 174279 TRUE FALSE 210086.6588 207829.8973 231586.8611 244888.4486 229373.0689 237702.2377 220769.173 38398.14523 201420.7328 162474.9281 1.293040479 1.279150573 1.425369833 1.507238387 1.411744394 1.463008727 1.358789172 0.236332742 1.239703474 1 17.30985758 1.875155803 10.0535449 0.750028674 1.398901077 0.518950667 0.246680243 0.248532102 19.17687526 0.097438741 0.061901236 75.01632817 -1.875155803 0.648872404 HLEINPDHSIIETLR ddPTM_BT-474_Pertuzumab_2h_R1 10 HLEINPDHSIIETLR 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;; 284.44 3.22E-34 74370247000 7729113 7525060 7035832 8550538 8346977 8253517 8166573 2923586.2 8721032 8847741 FALSE TRUE 7427050.719 7310452.657 8307363.354 8991832.291 8615465.096 8420408.769 8266517.963 2863213.123 7731057.009 8248475.621 0.900414945 0.886279234 1.007139226 1.090120491 1.044491794 1.020844233 1.002187355 0.347120275 0.937271002 1 22.97569609 1.87519067 20.48052191 0.685278233 0.996344501 0.234791813 0.176094182 4.084261461 655.2016921 0.069793816 0.045023236 75.02235103 -1.87519067 0.311066268 RPATADS(ph)PKPSAK ddPTM_BT-474_Pertuzumab_2h_R1 7 RPATADSPKPSAK 13 2 Q03111 Q03111 MLLT1 Protein ENL 1 RPAT(0.004)ADS(0.996)PKPSAK;RPAT(0.001)ADS(0.995)PKPS(0.004)AK;RPAT(0.004)ADS(0.984)PKPS(0.012)AK;RPATADS(0.999)PKPS(0.001)AK;RPATADS(0.999)PKPS(0.001)AK;RPATADS(0.999)PKPS(0.001)AK;RPATADS(0.999)PKPSAK 107.51 0.00067278 6517370000 14351910 11569990 9945120 9399150 10698000 10670620 12359180 14543360 16690610 14944040 TRUE FALSE 13791021.49 11240025.21 11742424.41 9884241.258 11042110.89 10886387.25 12510435.34 14243034.53 14795961.93 13931866.86 0.989890417 0.806785288 0.842846442 0.709469977 0.792579415 0.781401901 0.897972646 1.022334959 1.06202292 1 23.73188526 1.87530652 2.710893901 1.034520432 0.815002943 0.646281928 0.068399683 0.164262048 2.1655753 0.03833628 0.019540254 75.04236631 -1.87530652 -0.219517489 FGYVDFESAEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 8 FGYVDFESAEDLEK 14 0 P19338 P19338 NCL Nucleolin 0 ;;;;;;; 352.94 1.28E-81 2697962000 1710556 1546488 1487559 1529441 1599748 1452581 1670754 1887722 2034611 2010607 FALSE TRUE 1643705.58 1502383.676 1756394.002 1608375.633 1651205.347 1481953.183 1691201.187 1848739.881 1803650.489 1874426.797 0.876911055 0.801516324 0.937029925 0.858062655 0.880912154 0.790616729 0.902249792 0.986296122 0.962241093 1 20.83801805 1.875415326 3.782738411 0.979907484 0.858834538 0.661069385 0.039918631 0.141121596 3.30022497 0.019166207 0.010586171 75.06116939 -1.875415326 -0.121072947 CPQVVISFYEER ddPTM_BT-474_Pertuzumab_2h_R1 2 CPQVVISFYEER 12 0 P83916;J3KS05 P83916 CBX1 Chromobox protein homolog 1 0 ; 132.32 0.00042575 126146000 121705 114967 84672 102715 116730 135362 112781 104256 124455 116869 FALSE TRUE 116948.634 111688.2537 99974.11392 108016.1335 120484.7265 138099.1124 114161.2476 102103.0772 110327.3902 108953.3585 1.073382552 1.025101523 0.917586344 0.991397924 1.105837655 1.267506704 1.047799252 0.937126478 1.012611191 1 16.73335114 1.875415568 7.417513543 0.978809706 1.062029984 0.146737867 0.086517088 0.553039717 30.93441351 0.041739333 0.025896585 75.06121121 -1.875415568 0.083220278 ECREPELGLEELLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ECREPELGLEELLR 14 1 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ; 179.79 1.67E-06 125512000 122007 131797 91570 117816 124684 142249 118989 112253 122729 125583 FALSE TRUE 117238.8316 128038.2786 108118.736 123896.4979 128694.5741 145125.3722 120445.223 109934.9363 108797.3184 117077.1516 1.00138097 1.09362311 0.923482802 1.058246603 1.099228777 1.239570406 1.028767965 0.938995653 0.92927883 1 16.83710003 1.875423549 4.880098883 0.952696274 1.069438743 0.296246174 0.077358879 0.291553263 9.913763364 0.037921686 0.022082317 75.06259061 -1.875423549 0.116742468 KWDGS(ph)EEDEDNSK ddPTM_BT-474_Pertuzumab_2h_R1 6 KWDGSEEDEDNSK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK 271.73 2.62E-32 10508900000 8803400 6812090 6242490 5149390 6487920 6270370 7434730 9116270 10382570 9088780 TRUE FALSE 8459353.395 6617815.863 7370646.806 5415150.635 6696609.839 6397161.178 7525718.45 8928015.839 9203984.181 8473188.835 0.998367151 0.78103014 0.869878737 0.639092406 0.790329352 0.754988624 0.888180188 1.053678375 1.086247971 1 23.01447359 1.875599897 3.042154109 1.053687537 0.799677133 0.59796714 0.087949687 0.168000523 2.721111787 0.046424834 0.024379415 75.09307636 -1.875599897 -0.254010404 HSPAPPPDPGFPAPS(ph)PPPADSPSEGFSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSPAPPPDPGFPAPSPPPADSPSEGFSLK 29 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 HSPAPPPDPGFPAPS(1)PPPADSPSEGFSLK 134.78 4.70E-06 332850000 184720 209180 183290 226020 252280 239400 195780 143330 168200 156060 TRUE FALSE 177500.9382 203214.3912 216414.5803 237684.9193 260394.8153 244240.832 198176.0142 140370.1854 149106.6412 145489.9172 1.220022264 1.396759275 1.487488511 1.633686539 1.789779116 1.678747481 1.362128854 0.964810401 1.024858932 1 17.15055965 1.875630664 3.472167186 0.996546185 1.541559876 0.72105418 0.14904195 0.140350909 2.85320098 0.085002964 0.046062406 75.09839646 -1.875630664 0.545013691 QPGYQPPNPHPGPS(ph)SPPAAPASK ddPTM_BT-474_Pertuzumab_2h_R1 3 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.602)S(0.398)PPAAPASK;QPGYQPPNPHPGPS(0.768)S(0.232)PPAAPASK;QPGYQPPNPHPGPS(0.966)S(0.034)PPAAPASK 157.82 1.53E-09 4670970000 1415360 1403200 1182070 1724500 1342940 1391940 1694620 1678000 2085270 2084040 TRUE FALSE 1360046.166 1363182.11 1395696.344 1813501.652 1386136.885 1420085.98 1715359.266 1643348.714 1848558.892 1942886.115 0.700013324 0.701627388 0.718362406 0.933406049 0.71344217 0.730915708 0.882892339 0.845828637 0.951449948 1 20.88976991 1.875640344 0.235668633 1.052741422 0.645596157 0.619135961 0.069038168 1.606498097 0.357945397 0.201524457 0.256748567 75.10007031 -1.875640344 -0.407145265 LDLIHESILHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDLIHESILHK 11 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 ; 162.26 1.47E-05 496730000 338378 692280 560540 822810 588520 780800 667720 128799 629330 839730 FALSE TRUE 325153.8137 672536.8522 661842.0471 865275.3227 607450.2803 796588.311 675891.7571 126139.2556 557891.0968 782854.3391 0.41534395 0.859082997 0.845421701 1.105282655 0.775942918 1.017543457 0.863368475 0.161127363 0.712637165 1 19.57838437 1.875654287 20.95413835 0.526530267 0.855799202 0.089727988 0.261016947 6.530915284 1076.143808 0.103575954 0.066821354 75.10248158 -1.875654287 0.329268935 AGKES(ph)DEKEQEQDKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGKESDEKEQEQDKDR 16 3 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 AGKES(1)DEKEQEQDKDR 118.36 0.0015393 267640000 240330 153580 168980 124580 192650 148220 193180 269740 284010 243980 TRUE FALSE 230937.6379 149200.0488 199518.4449 131009.5887 198846.7622 151217.11 195544.1946 264169.7747 251770.3755 227455.0173 1.01531125 0.65595409 0.877177595 0.57598021 0.874224559 0.664822046 0.859704908 1.161415465 1.106901833 1 17.79522173 1.87579578 4.422790255 1.099411925 0.770899557 0.548996186 0.12613337 0.148314076 4.40072564 0.054819132 0.031308887 75.12695382 -1.87579578 -0.328512368 DKPTYDEIFYTLS(ph)PVNGK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKPTYDEIFYTLSPVNGK 18 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 1 DKPTYDEIFYT(0.003)LS(0.997)PVNGK;DKPTYDEIFYT(0.004)LS(0.996)PVNGK;DKPTYDEIFYTLS(1)PVNGK;DKPTYDEIFYTLS(1)PVNGK 268.13 1.29E-31 3009470000 3646070 3300870 3542330 3550150 3627020 3835430 4347880 4573230 5102060 5586610 TRUE FALSE 3503577.553 3206732.419 4182507.83 3733373.667 3743686.392 3912985.022 4401090.656 4478791.202 4522895.538 5208223.929 0.672701021 0.615705558 0.803058372 0.716822801 0.718802886 0.751308906 0.845027156 0.859945975 0.868414185 1 22.31236005 1.875806939 0.27841234 1.033488526 0.615689146 0.839671514 0.042783212 0.668320163 0.180800677 0.08506673 0.104309428 75.12888417 -1.875806939 -0.41779938 LFPDT(ph)PLALDANK ddPTM_BT-474_Pertuzumab_2h_R1 5 LFPDTPLALDANK 13 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 LFPDT(1)PLALDANK;LFPDT(1)PLALDANK;LFPDT(1)PLALDANK;LFPDT(1)PLALDANK;LFPDT(1)PLALDANK 250.52 8.18E-17 1713631000 2529180 2327702 2503254 2386720 2392775 2705819 2772525 3066971 3408340 3477199 TRUE FALSE 2430336.849 2261318.218 2955647.682 2509898.905 2469740.781 2760532.514 2806455.99 3003636.977 3021439.532 3241685.215 0.749714019 0.697574893 0.911762706 0.774257443 0.761869404 0.851573281 0.865739825 0.926566517 0.932058276 1 21.62831257 1.875871158 0.530602344 1.004131325 0.760990444 0.68926164 0.051656304 0.483305807 0.299632188 0.051024298 0.034836962 75.13999432 -1.875871158 -0.24314088 S(ph)RSPES(ph)QVIGENTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPESQVIGENTK 14 1 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.569)RS(0.44)PES(0.992)QVIGENTK 141.6 0.00011514 533360000 1364800 1206400 1115400 1091300 1154400 1108600 1271800 1556400 1705400 1477600 TRUE FALSE 1311462.107 1171994.653 1316977.592 1147622.124 1191532.324 1131016.652 1287364.669 1524259.796 1511810.142 1377520.836 0.952045205 0.850799946 0.956049127 0.833106908 0.864983159 0.821052301 0.934551867 1.10652395 1.097486225 1 20.39364271 1.875988527 4.195758543 1.075581067 0.878920215 0.735420071 0.050318174 0.105272563 2.891622444 0.023319142 0.013174769 75.16030388 -1.875988527 -0.196660853 LAERLS(ph)PFLAESK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAERLSPFLAESK 13 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 LAERLS(1)PFLAESK;LAERLS(1)PFLAESK 152.89 2.44E-05 382530000 731110 684010 553600 623200 625120 656300 674770 769780 837040 774620 TRUE FALSE 702537.4129 664502.7045 653647.8348 655363.4267 645227.5525 669570.8357 683028.0371 753883.774 742022.7284 722154.2974 0.972835605 0.920167209 0.905135976 0.907511634 0.893476027 0.927185282 0.945820082 1.043937254 1.027512723 1 19.46194759 1.876322614 3.684726052 1.026986612 0.919281385 0.805551854 0.022530106 0.095633144 2.145060206 0.011519303 0.006329235 75.21814421 -1.876322614 -0.107705227 GPPS(ph)PPAPVMHS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 6 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.654)PS(0.346)R;GPPS(1)PPAPVMHS(0.939)PS(0.061)R;GPPS(1)PPAPVMHS(0.807)PS(0.193)R;GPPS(1)PPAPVMHS(0.691)PS(0.309)R;GPPS(1)PPAPVMHS(0.895)PS(0.105)R;GPPS(1)PPAPVMHS(0.992)PS(0.008)R 189.82 1.28E-07 8886320000 1957270 2105730 1834250 2296590 2021120 2089130 2031070 1991420 2079900 2176370 TRUE FALSE 1880777.725 2045676.642 2165739.778 2415117.285 2086131.16 2131373.64 2055926.842 1950296.481 1843798.472 2028962.521 0.926965237 1.008237767 1.067412411 1.19032129 1.028176291 1.050474623 1.013289709 0.961228441 0.908739542 1 20.95231079 1.876362172 2.315333442 0.949287979 1.050438537 0.270159674 0.064567051 0.389156651 3.837439626 0.040286577 0.01966206 75.22499569 -1.876362172 0.101150557 MSSEGPPRMS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 MSSEGPPRMSPK 12 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 MSSEGPPRMS(1)PK;MSSEGPPRMS(1)PK;MSSEGPPRMS(1)PK 150.78 0.00017995 1885770000 3142170 2825850 2377290 2185300 2426570 2440750 2865510 3278800 3705990 3514080 TRUE FALSE 3019370.523 2745259.525 2806919.186 2298083.595 2504622.828 2490103.637 2900578.969 3211091.634 3285301.552 3276068.232 0.921644578 0.837973855 0.856795093 0.701476109 0.76452096 0.760089064 0.885384175 0.980166287 1.002818415 1 21.64353397 1.876494488 2.635215716 0.996984944 0.804390883 0.680900054 0.057156068 0.169493525 2.12206042 0.03445227 0.017443151 75.24791793 -1.876494488 -0.192594061 ESKDPADETEAD ddPTM_BT-474_Pertuzumab_2h_R1 2 ESKDPADETEAD 12 1 P16949 P16949 STMN1 Stathmin 0 ; 141.1 0.00049119 7158900000 6755400 6110800 5844600 6231600 6179100 6391700 6933000 7972400 8987900 8559300 FALSE TRUE 6491391.5 5936525.967 6900849.232 6553213.623 6377856.363 6520944.553 7017848.128 7807767.154 7967631.272 7979570.987 0.813501316 0.743965556 0.864814568 0.821248866 0.79927309 0.817204905 0.879476872 0.97846954 0.998503715 1 22.92787975 1.876568529 1.880109028 1.001569278 0.808135134 0.896791335 0.027731274 0.09745737 0.645706796 0.018167355 0.008337607 75.26074771 -1.876568529 -0.193434145 APVHFVEPLS(ph)PTGVAGHR ddPTM_BT-474_Pertuzumab_2h_R1 3 APVHFVEPLSPTGVAGHR 18 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 APVHFVEPLS(0.982)PT(0.018)GVAGHR;APVHFVEPLS(0.968)PT(0.032)GVAGHR;APVHFVEPLS(0.974)PT(0.026)GVAGHR 142.23 7.35E-08 2618480000 455740 482740 469340 539010 572850 498790 477940 363653 411910 428100 TRUE FALSE 437929.177 468972.7279 554160.1784 566828.3707 591276.2405 508875.8755 483789.1727 356143.4385 365151.7037 399104.4057 1.097279736 1.175062768 1.388509299 1.420250848 1.481507676 1.275044495 1.212187001 0.89235657 0.914927769 1 18.60640668 1.87675901 3.090654029 0.925160496 1.315034595 0.69238401 0.110107345 0.151326802 2.52031884 0.06430516 0.033929039 75.29376431 -1.87675901 0.389874099 SSS(ph)ENDVELLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSENDVELLTK 12 0 Q9C0D6 Q9C0D6 FHDC1 FH2 domain-containing protein 1 1 SS(0.003)S(0.997)ENDVELLTK;S(0.006)S(0.034)S(0.96)ENDVELLTK 309.87 3.08E-46 326330000 1469250 1365180 1197670 1202720 1282540 1289400 1346610 1633290 1581060 1607420 TRUE FALSE 1411830.086 1326246.403 1414115.611 1264792.523 1323794.064 1315472.551 1363090.216 1599561.991 1401584.697 1498548.012 0.942132034 0.885020962 0.943657194 0.844012013 0.883384485 0.877831435 0.909607303 1.067407903 0.935295157 1 20.51513388 1.876789418 7.21826346 1.005424088 0.894767868 0.574500437 0.040661352 0.162656073 8.86425153 0.016693529 0.010328213 75.29903623 -1.876789418 -0.11065622 RTLEGELHDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 RTLEGELHDLR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 158.01 1.97E-05 2665080000 2199560 2284670 1792530 2066010 2152370 2102990 2012070 1946950 2072330 1990360 FALSE TRUE 2113598.763 2219513.449 2116480.046 2172637.024 2221602.936 2145513.899 2036694.315 1906744.802 1837087.786 1855551.144 1.13906791 1.196147816 1.1406207 1.170885012 1.197273889 1.156267724 1.0976223 1.027589462 0.990049664 1 20.82341634 1.876852984 1.701658943 0.995065817 1.169853375 0.936902333 0.018810464 0.076804246 0.417809093 0.012488838 0.005577442 75.31005832 -1.876852984 0.174787558 LHDFLAHSSEESEETSS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 3 LHDFLAHSSEESEETSSPPR 20 0 P46100;P46100-4;A0A096LNL9;P46100-6;A0A096LNW1;A0A087WWG0 P46100 ATRX Transcriptional regulator ATRX 1 LHDFLAHSSEESEET(0.001)S(0.427)S(0.572)PPR;LHDFLAHSSEESEET(0.001)S(0.012)S(0.987)PPR;LHDFLAHSSEESEETS(0.032)S(0.968)PPR 211.75 4.02E-22 725490000 380035 528970 433392 619600 502780 608220 501970 38441.8 443474 422096 TRUE FALSE 365182.812 513884.2935 511715.5752 651577.6303 518952.3753 620518.6251 508113.259 37647.9634 393132.6907 393507.062 0.928020987 1.305908694 1.300397438 1.655821949 1.31878796 1.576893238 1.29124305 0.095672904 0.999048629 1 18.58603 1.87693492 8.63420468 0.613273365 1.362035418 0.484720548 0.299391489 0.213288116 14.11302554 0.121966446 0.076734383 75.324268 -1.87693492 0.748762054 FHGTVK ddPTM_BT-474_Pertuzumab_2h_R1 7 FHGTVK 6 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;; 130.84 0.015589 8960590000 9395340 11668400 9393980 13277870 12271890 11557910 10454160 4783640 8337530 7925880 FALSE TRUE 9028159.726 11335628.66 11091681.15 13963142.46 12666626.49 11791618.86 10582101.14 4684856.162 7391088.548 7389053.088 1.221829051 1.53411114 1.501096422 1.88970661 1.714242182 1.595822728 1.432132238 0.634026594 1.00027547 1 22.81695806 1.876960349 4.996451096 0.85812154 1.585547429 0.738784407 0.185805591 0.109516023 3.851800962 0.088330238 0.051697317 75.32867862 -1.876960349 0.727425889 FHDFLGDSWGILFSHPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FHDFLGDSWGILFSHPR 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ; 299.89 1.49E-46 8610700000 1372110 1466740 1279090 1381180 1277660 1150110 1285760 186200 1198420 1051210 FALSE TRUE 1318486.424 1424910.011 1510250.016 1452462.865 1318757.094 1173366.012 1301495.515 182354.9049 1062380.386 980010.6104 1.345379744 1.453974065 1.54105476 1.482088918 1.345655935 1.197299294 1.32804227 0.186074419 1.084049881 1 19.90243784 1.876992184 8.540448009 0.680772048 1.393115309 0.58160668 0.242066552 0.178950322 11.70639285 0.098753214 0.06207765 75.3342005 -1.876992184 0.712343261 SS(ph)LS(ph)GDEEDELFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 2 S(0.124)S(0.876)LS(1)GDEEDELFK 247.17 4.39E-17 205620000 634840 555330 444770 436870 503890 507260 542420 687920 745020 583360 TRUE FALSE 610029.7509 539492.5321 525149.8329 459416.9131 520098.0795 517517.1448 549058.2982 673714.2116 660448.453 543848.5076 1.121690586 0.991990462 0.965617861 0.84475163 0.956328963 0.951583276 1.009579489 1.238790219 1.21439784 1 19.05284531 1.877060755 5.24552132 1.171529498 0.9672998 0.453428617 0.087100209 0.17682949 6.62670902 0.039614182 0.023393401 75.34609601 -1.877060755 -0.204229697 GHTGGHHS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 5 GHTGGHHSPVK 11 0 H7C280;A0A0A0MQU4;Q96I15-2;Q96I15 H7C280 SCLY Selenocysteine lyase 1 GHTGGHHS(1)PVK;GHTGGHHS(1)PVK;GHTGGHHS(1)PVK;GHTGGHHS(1)PVK;GHT(0.006)GGHHS(0.994)PVK 191.01 3.37E-06 930207000 1151202 1099792 1001448 1037397 988453 936895 995973 54515.5 1063745 542216 TRUE FALSE 1106211.753 1068427.009 1182431.931 1090937.183 1020247.488 955839.6588 1008162.016 53389.73587 942993.1272 505491.2274 2.188389616 2.113641051 2.339173989 2.158172337 2.018328772 1.890912457 1.994420399 0.10561951 1.865498502 1 18.94732653 1.877091587 8.375908634 0.91626573 2.109261575 0.605370435 0.410329622 0.173003084 11.08854776 0.163870027 0.102851239 75.35144526 -1.877091587 1.192995846 YKLDEDEDEDDADLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 YKLDEDEDEDDADLSK 16 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 247.4 2.50E-20 952700000 1355600 967510 1125400 959080 1044800 933160 1240900 1647100 1809200 1602100 FALSE TRUE 1302621.653 939917.5621 1328784.814 1008578.234 1078406.941 952029.1346 1256086.505 1613086.809 1603827.201 1493588.34 0.872142356 0.62930162 0.889659338 0.675271898 0.72202421 0.637410663 0.840985747 1.080007634 1.073808062 1 20.51035114 1.877095263 3.646929866 1.056454093 0.735968512 0.728719758 0.085237067 0.111940369 2.470171932 0.040056433 0.021969165 75.35208312 -1.877095263 -0.320485581 GKNS(ph)DEEAPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GKNSDEEAPK 10 1 Q9UNL4-8;Q9UNL4-3;Q9UNL4-4;Q9UNL4-7;Q9UNL4-5;Q9UNL4-6;Q9UNL4-2;Q9UNL4 Q9UNL4-8 ING4 Inhibitor of growth protein 4 1 GKNS(1)DEEAPK;GKNS(1)DEEAPK;GKNS(1)DEEAPK 112.15 0.0010043 918190000 1289531 1069983 934032 844288 1032009 946218 1061136 1341059 1405121 1127076 TRUE FALSE 1239134.703 1039468.132 1102832.36 887861.8049 1065204.507 965351.1763 1074122.5 1313365.663 1245617.555 1050738.139 1.179299254 0.989274201 1.049578691 0.844988653 1.013767815 0.918736211 1.022255175 1.249945743 1.185469061 1 20.00297174 1.877222644 6.553135116 1.16768982 0.993018984 0.289977025 0.100538233 0.244958848 11.99630082 0.04261635 0.026059131 75.37418753 -1.877222644 -0.174670836 SSSFSDTLEESSPIAAIFDTENLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 119.83 0.00039552 33768000 60058 53537 52084 54406 41424 58518 62039 65994 81280 75006 FALSE TRUE 57710.86696 52010.17718 61496.7374 57213.90018 42756.44058 59701.27405 62798.25184 64631.20084 72053.43515 69925.77681 0.825316065 0.743791196 0.879457336 0.818209004 0.611454638 0.853780634 0.898070135 0.924282915 1.030427382 1 16.09353676 1.877554685 1.400175378 1.005034782 0.782518177 0.621999305 0.070864231 0.283894626 1.038777229 0.054011916 0.023207588 75.43183721 -1.877554685 -0.222516606 APSEEELHGDQTDFGQGSQS(ph)PQKQEEQR ddPTM_BT-474_Pertuzumab_2h_R1 7 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.25)QS(0.75)PQKQEEQR;APSEEELHGDQTDFGQGS(0.017)QS(0.983)PQKQEEQR;APSEEELHGDQTDFGQGS(0.005)QS(0.995)PQKQEEQR;APSEEELHGDQTDFGQGS(0.319)QS(0.681)PQKQEEQR;APSEEELHGDQTDFGQGS(0.006)QS(0.994)PQKQEEQR;APSEEELHGDQTDFGQGS(0.034)QS(0.966)PQKQEEQR;APSEEELHGDQTDFGQGS(0.147)QS(0.853)PQKQEEQR 328.86 4.74E-96 11288300000 2912522 2675583 2587609 2744682 2752988 2759817 3281380 3215613 3963094 3739896 TRUE FALSE 2798697.42 2599277.993 3055247.507 2886335.367 2841540.359 2815622.391 3321538.51 3149209.468 3513220.184 3486589.513 0.802703447 0.745507317 0.876285406 0.82783917 0.814991369 0.807557752 0.952661189 0.90323494 1.007638029 1 21.73338509 1.877703879 0.893514647 1.004668771 0.805878835 0.768302995 0.040958073 0.267688236 0.396016719 0.034693883 0.015794411 75.45775486 -1.877703879 -0.198789937 ELSVQDQPSLS(ph)PTSLQNSSSHTTTAK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELSVQDQPSLSPTSLQNSSSHTTTAK 26 0 O95628-3;O95628-2;O95628;O95628-8;O95628-4;O95628-7;O95628-9;O95628-10;O95628-6 O95628-3 CNOT4 CCR4-NOT transcription complex subunit 4 1 ELSVQDQPSLS(0.988)PT(0.012)SLQNSSSHTTTAK;ELSVQDQPSLS(0.898)PT(0.098)S(0.004)LQNSSSHTTTAK;ELSVQDQPSLS(0.994)PT(0.006)SLQNSSSHTTTAK 263.63 3.85E-53 1985600000 910060 1469730 1203190 1721180 1322500 1540970 1232660 1118430 1059590 1222660 TRUE FALSE 874493.8491 1427814.739 1420633.198 1810010.306 1365039.414 1572129.469 1247745.662 1095334.03 939309.7854 1139848.149 0.767202061 1.252635924 1.246335487 1.587939856 1.197562513 1.379244657 1.09465955 0.960947325 0.82406572 1 20.12041021 1.877729853 2.70478091 0.915659726 1.253027294 0.327411647 0.196982073 0.306763608 4.026186205 0.109731182 0.056001756 75.46226786 -1.877729853 0.337367568 SRTPS(ph)ASNDDQQE ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 S(0.001)RT(0.018)PS(0.965)AS(0.015)NDDQQE 105.53 0.0038034 64467000 51531 66413 49924 68657 69091 71799 55805 47616 47830 50549 TRUE FALSE 49517.11155 64518.96627 58946.37735 72200.396 71313.37476 73250.82497 56487.95828 46632.71296 42400.53892 47125.27121 1.050754941 1.369094853 1.25084431 1.532095077 1.513272453 1.554385218 1.198676566 0.989547896 0.899741006 1 15.5242133 1.878062655 2.981060691 0.956714638 1.385030188 0.621683461 0.144125641 0.173789185 2.716134126 0.080494256 0.042134713 75.52011719 -1.878062655 0.42831555 LREQLQLLEEQHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LREQLQLLEEQHR 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 170.79 1.57E-05 1119270000 823630 1011630 782590 1039760 993830 822180 950640 850360 895970 927060 FALSE TRUE 791441.629 982779.3029 924021.4216 1093422.138 1025797.445 838805.0429 962274.2167 832799.7688 794263.2418 864269.4005 0.915734872 1.137121484 1.069135875 1.265140404 1.18689548 0.970536551 1.113396143 0.963588169 0.91899961 1 19.72112156 1.878087188 1.439648873 0.950354024 1.110136157 0.264379566 0.097151854 0.521099674 2.018763315 0.072120599 0.03112215 75.52438342 -1.878087188 0.159782133 FITHAPPGEFNEVFNDVR ddPTM_BT-474_Pertuzumab_2h_R1 6 FITHAPPGEFNEVFNDVR 18 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;;;;; 222.7 5.55E-19 6397450000 1979070 2107150 1748130 2129880 2104260 2176680 2024360 1994520 2123180 2199840 FALSE TRUE 1901725.756 2047056.145 2064055.978 2239803.362 2171945.434 2220693.961 2049134.723 1953332.465 1882165.507 2050842.877 0.927289836 0.998153573 1.006442766 1.092137963 1.059050139 1.082820135 0.999167097 0.952453494 0.917752173 1 20.96778554 1.878115419 3.742910312 0.95235625 1.030337087 0.296426668 0.048235235 0.291363283 6.711853746 0.025415728 0.01402863 75.52929284 -1.878115419 0.077980836 TFHVDSPDEREEWMR ddPTM_BT-474_Pertuzumab_2h_R1 1 TFHVDSPDEREEWMR 15 1 P31751;P31751-2;M0R0P9;J3QKW1;A8MX96;C9JHS6;J3QLS6;M0QZK3;E7EVP8;A0A1B0GXA2;J3KRI8;A0A5F9ZHJ8;A0A0A0MRF1;C9JIJ1;C9JC83 P31751 AKT2 RAC-beta serine/threonine-protein kinase 0 72.175 0.02495 217340000 36064 44279 41586 52589 49062 46050 43988 41156 42576 45658 FALSE TRUE 34654.57901 43016.20627 49101.51528 55303.12459 50640.12379 46981.16255 44526.3383 40306.11422 37742.95097 42565.54299 0.814146292 1.010587514 1.153550779 1.299246308 1.189697587 1.103736949 1.046065319 0.946918831 0.886701973 1 15.37739841 1.878120183 2.556241452 0.935367179 1.106938257 0.230524264 0.121546112 0.417495565 4.942442543 0.074966939 0.037688149 75.53012141 -1.878120183 0.171571078 VLHEEHVELLMEEFAFLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLHEEHVELLMEEFAFLKK 19 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 174.49 1.79E-12 2151600000 2046090 1947810 1522330 1553270 1791900 1999620 1848170 155217 2171250 1642990 FALSE TRUE 1966126.541 1892260.366 1797448.895 1633434.451 1849538.091 2040053.686 1870788.457 152011.7147 1924778.803 1531708.824 1.283616383 1.235391699 1.173492551 1.066413162 1.207499795 1.331880874 1.221373428 0.099243219 1.256621867 1 20.54671064 1.878436292 19.99325143 0.678848301 1.214519752 0.304736349 0.285592805 3.573277958 574.1478683 0.111403638 0.07185809 75.58511733 -1.878436292 0.53567145 LPEHCIEYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPEHCIEYVR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ; 110.54 0.0018724 1181780000 809210 908170 673910 982860 879100 861700 849330 706760 845010 910970 FALSE TRUE 777585.1786 882269.8808 795700.528 1033585.522 907377.0499 879124.1644 859724.3546 692165.159 749088.0074 849269.1905 0.915593297 1.03885775 0.936923813 1.21702934 1.068421014 1.035153723 1.012310778 0.81501268 0.882038364 1 19.69586239 1.878590074 6.018012025 0.883110299 1.039331254 0.323669834 0.087537562 0.237948766 10.59490926 0.038779426 0.023435269 75.61188661 -1.878590074 0.156220955 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSK 34 2 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 218.19 2.19E-36 12611600000 3982850 3191820 3482860 3422670 3765600 3314820 4402100 4704580 5710570 5409410 FALSE TRUE 3827195.819 3100792.419 4112290.278 3599314.409 3886723.944 3381847.932 4455974.217 4607428.779 5062330.034 5043025.842 0.758908627 0.614867446 0.815441048 0.713721191 0.770712676 0.670598969 0.883591391 0.913623868 1.003827899 1 22.26585819 1.878615062 1.614249093 0.992616021 0.723815718 0.787238166 0.058451105 0.156675243 0.766339896 0.03833451 0.016923332 75.61623709 -1.878615062 -0.268800303 ESTQLS(ph)PADLTEGKPTDPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESTQLSPADLTEGKPTDPSK 20 1 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 ES(0.001)T(0.02)QLS(0.962)PADLT(0.018)EGKPTDPSK;ESTQLS(1)PADLTEGKPTDPSK 195.01 9.99E-19 2369420000 1009850 857240 996760 1062290 1003820 1041950 1299500 1581900 1725720 1858890 TRUE FALSE 970383.9456 832792.3545 1176896.705 1117114.914 1036108.782 1063018.943 1315403.67 1549233.212 1529823.5 1732985.725 0.559949186 0.480553499 0.67911506 0.644618648 0.597874966 0.613403173 0.759038953 0.893967671 0.882767514 1 20.72482834 1.878674885 1.068102278 0.973571136 0.583072727 0.885733456 0.053711925 0.161883969 0.33988734 0.046418194 0.020045527 75.62665381 -1.878674885 -0.390498409 EIIDAS(ph)DKEGMS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIIDASDKEGMSPAK 15 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 EIIDAS(1)DKEGMS(1)PAK 55.588 0.040546 0 342740 237900 254430 172420 263720 234820 275820 409410 402260 338460 TRUE FALSE 329345.3419 231115.3249 300411.1608 181318.6169 272202.7933 239568.2213 279195.5677 400955.5404 356597.1312 315535.8027 1.043765364 0.732453569 0.952066796 0.574637221 0.862668486 0.759242594 0.884830074 1.270713298 1.130132074 1 18.26744419 1.878745181 5.404361177 1.153488755 0.81431176 0.520611974 0.134026008 0.154433579 6.032030177 0.05694291 0.033821303 75.63889596 -1.878745181 -0.339176995 SRS(ph)PESQVIGENT(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPESQVIGENTK 14 1 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.423)RS(0.577)PES(0.375)QVIGENT(0.625)K 205.08 3.20E-07 305900000 1301500 1114800 1026700 1017400 1180300 1146100 1228400 1474600 1678800 1424200 TRUE FALSE 1250635.941 1083006.996 1212247.529 1069908.136 1218265.421 1169274.927 1243433.527 1444148.995 1488229.662 1327737.665 0.941930001 0.815678446 0.913017353 0.805812898 0.917549794 0.880652073 0.936505425 1.087676453 1.120876285 1 20.3405387 1.878903769 2.944540526 1.079484264 0.876807502 0.745756142 0.049485608 0.112849267 1.725541768 0.024655678 0.012874334 75.66652147 -1.878903769 -0.202676762 RGQPAS(ph)PSAHMVSHSHSPSVVS ddPTM_BT-474_Pertuzumab_2h_R1 8 RGQPASPSAHMVSHSHSPSVVS 22 1 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;G5E9M9;Q14135-5 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 RGQPAS(0.991)PS(0.009)AHMVSHSHSPSVVS;RGQPAS(0.751)PS(0.249)AHMVSHSHSPSVVS;RGQPAS(0.963)PS(0.036)AHMVSHSHSPSVVS;RGQPAS(0.942)PS(0.057)AHMVSHSHSPSVVS;RGQPAS(0.953)PS(0.047)AHMVSHSHSPSVVS;RGQPAS(0.947)PS(0.053)AHMVSHSHSPSVVS;RGQPAS(0.994)PS(0.006)AHMVSHSHSPSVVS;RGQPAS(0.874)PS(0.122)AHMVS(0.001)HS(0.002)HS(0.002)PSVVS 208.97 2.94E-23 3809165000 780890 1265955 942579 1315838 1013467 1165419 1015626 52902.6 806357 708901 TRUE FALSE 750371.9555 1229851.203 1112923.993 1383748.557 1046066.086 1188984.571 1028055.535 51810.14282 714822.7339 660886.5038 1.135402147 1.86091136 1.683986564 2.093776388 1.582822588 1.799075278 1.555570478 0.078394917 1.081611941 1 19.33404301 1.878939976 6.935442487 0.646945672 1.709285657 0.620540689 0.34118285 0.137344103 7.208620432 0.139445513 0.085901104 75.67283009 -1.878939976 1.062339984 KSLS(ph)DS(ph)ESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.022)LS(0.937)DS(0.454)ES(0.44)DDS(0.147)K 156.11 4.87E-05 324240000 959260 706930 551940 514430 607270 618960 715520 917540 1014700 833930 TRUE FALSE 921771.0587 686769.0486 651687.8358 540979.7939 626803.3911 631475.7953 724276.7478 898592.4784 899515.51 777447.1783 1.185638181 0.883364256 0.83824066 0.695841221 0.806232769 0.8122427 0.931608948 1.155824477 1.157011737 1 19.56838513 1.878962421 4.030403499 1.116381293 0.859237249 0.407769525 0.125190729 0.21744938 5.636423656 0.062819649 0.03524927 75.67674108 -1.878962421 -0.257144045 HLDRS(ph)PESDRPR ddPTM_BT-474_Pertuzumab_2h_R1 7 HLDRSPESDRPR 12 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 HLDRS(0.999)PES(0.001)DRPR;HLDRS(1)PESDRPR;HLDRS(0.995)PES(0.005)DRPR;HLDRS(0.999)PES(0.001)DRPR;HLDRS(1)PESDRPR;HLDRS(1)PESDRPR;HLDRS(1)PESDRPR 172.91 1.80E-05 24539830000 3591260 3657350 2780660 3537540 3458770 3597610 3379300 2122341 3473450 3119200 TRUE FALSE 3450909.589 3553045.959 3283187.117 3720112.863 3570024.478 3670356.139 3420656.884 2078513.917 3079158.518 2907933.806 1.186722195 1.221845543 1.129044654 1.279297643 1.227684231 1.262186963 1.17631869 0.714773463 1.058881915 1 21.471563 1.879220999 7.461742667 0.900960096 1.217066533 0.672449007 0.091801487 0.130384253 7.431161575 0.036992849 0.022975246 75.7218122 -1.879220999 0.316106436 YNLDAS(ph)EEEDSNKK ddPTM_BT-474_Pertuzumab_2h_R1 4 YNLDASEEEDSNKK 14 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNKK;YNLDAS(0.999)EEEDS(0.001)NKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK 248.1 7.07E-18 1814300000 1783200 1439650 1548890 1348730 1632900 1419300 1831080 2304910 2653920 2366390 TRUE FALSE 1713510.573 1398592.592 1828808.878 1418338.117 1685423.711 1447999.218 1853489.305 2257312.803 2352658.128 2206112.298 0.776710494 0.633962556 0.828973611 0.642912928 0.763979111 0.656357893 0.840160905 1.023208477 1.066427185 1 21.0730748 1.879232465 2.754347383 1.037439863 0.717532654 0.836163663 0.061726767 0.090286486 1.224428517 0.030702702 0.015763067 75.72381133 -1.879232465 -0.319907209 EVTWEVLEGEVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EVTWEVLEGEVEK 13 0 P05455 P05455 SSB Lupus La protein 0 ;;; 265.6 5.71E-24 395925000 614669 549149 634037 678154 606057 557699 683763 807090 849830 894440 FALSE TRUE 590647.0559 533487.8082 748621.59 713153.6092 625551.3738 568976.0559 692131.0961 790423.3095 753360.8612 833858.7821 0.708329838 0.639781963 0.897779823 0.855245066 0.750188626 0.682341025 0.830033947 0.947910277 0.903463365 1 19.66944355 1.879244704 3.394141847 0.944174955 0.760641343 0.569119242 0.075379043 0.203086281 3.979650025 0.041172454 0.022249237 75.72594545 -1.879244704 -0.183533613 WQDEDGKK ddPTM_BT-474_Pertuzumab_2h_R1 6 WQDEDGKK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;;;; 116.52 0.0036163 7070080000 10211780 8706710 7703320 6876350 8424150 8723880 9093040 11131290 12248550 11096190 FALSE TRUE 9812692.348 8458403.156 9095481.283 7231239.248 8695120.435 8900282.831 9204323.344 10901424.97 10858145.95 10344635.17 0.948577904 0.817660847 0.879246212 0.699032796 0.840543943 0.860376677 0.889767807 1.053824016 1.049640299 1 23.30237943 1.87927885 2.813655241 1.041097018 0.835666432 0.669676067 0.060572143 0.150715381 2.124135573 0.033058849 0.01706799 75.73189947 -1.87927885 -0.205430586 GLPS(ph)PYNMSSAPGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 GLPS(0.997)PY(0.003)NMS(0.001)S(0.005)APGS(0.994)R;GLPS(0.999)PY(0.001)NMS(0.002)S(0.001)APGS(0.998)R 153.04 3.98E-06 312540000 214848 250631 280061 326011 313420 327812 259931 232563 241825 235875 TRUE FALSE 206451.5026 243483.2493 330674.2526 342836.4668 323501.4389 334440.5832 263112.1133 227760.4928 214374.0398 219898.9762 0.938847039 1.107250491 1.503755308 1.559063497 1.471136631 1.520882858 1.19651359 1.035750583 0.974875116 1 17.74648136 1.879337183 2.947078406 1.002074493 1.360965166 0.406433922 0.185969409 0.285094475 4.366095307 0.110274097 0.057612386 75.74207232 -1.879337183 0.358890674 GPPS(ph)PPAPVMHSPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 3 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.295)PS(0.705)R;GPPS(1)PPAPVMHS(0.02)PS(0.98)R;GPPS(1)PPAPVMHS(0.345)PS(0.655)R 233.44 1.83E-17 1147640000 777810 887390 705460 821930 850090 852550 799760 793620 821690 869560 TRUE FALSE 747412.3253 862082.506 832952.3149 864349.9058 877433.9169 869789.1451 809547.7021 777231.4697 728415.196 810663.9267 0.921975557 1.063427738 1.027493993 1.066224705 1.082364576 1.072934315 0.998623074 0.958759165 0.898541519 1 19.62874442 1.879365474 2.80701665 0.946195559 1.042536307 0.381967161 0.048802274 0.254228536 3.567774938 0.026136736 0.013486794 75.7470064 -1.879365474 0.096340748 S(ph)KDEYEKS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 SKDEYEKSR 9 2 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)KDEYEKS(1)R 78.326 0.016137 1140500000 1209600 907300 1224800 1008400 1085700 881640 1467400 1952100 2365500 2059300 TRUE FALSE 1162327.495 881424.6923 1446148.606 1060443.645 1120622.527 899467.3649 1485358.48 1911788.453 2096978.357 1919821.777 0.605435103 0.459117978 0.753272321 0.552365671 0.583711749 0.468516076 0.773696026 0.995815589 1.092277618 1 20.87254096 1.879395262 2.569971747 1.041468204 0.574053476 0.861141108 0.082272013 0.091866811 1.098002418 0.044943027 0.022650438 75.75220204 -1.879395262 -0.467414728 NLFEDQNTLTSICEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLFEDQNTLTSICEK 15 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 123.38 0.00023981 46498000 65643 61588 46270 69133 54863 58109 64643 70088 79313 75917 FALSE TRUE 63077.59899 59831.57054 54632.01827 72700.96241 56627.71822 59284.00379 65434.12037 68640.65831 70309.72075 70775.07397 0.891240312 0.845376305 0.771910437 1.027211394 0.800108217 0.837639588 0.924536234 0.969842269 0.9934249 1 16.11095373 1.87946346 2.266423589 0.990688979 0.862447102 0.430710085 0.064619926 0.289691579 2.742002897 0.037707966 0.018334674 75.76409849 -1.87946346 -0.128241877 EAKPEDLMDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAKPEDLMDSK 11 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 109 0.001813 797220000 1137700 1304600 774330 1070600 979650 951270 1097000 1752800 1556600 1202400 FALSE TRUE 1093237.426 1267394.085 914268.6559 1125853.794 1011161.332 970505.3312 1110425.414 1716604.067 1379901.294 1120960.377 0.975268572 1.130632368 0.815611929 1.004365379 0.902049129 0.865780228 0.990601842 1.531369086 1.23099917 1 20.09630385 1.879553049 7.990706219 1.304847699 0.949938682 0.45969482 0.146117629 0.199851129 12.29585589 0.059272044 0.037057692 75.77972915 -1.879553049 -0.354909017 GQYNFDHPDAFDNDLMHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQYNFDHPDAFDNDLMHR 18 0 Q9HA47-3;Q9HA47;Q9HA47-4;G3V170;Q9HA47-2 Q9HA47-3 UCK1 Uridine-cytidine kinase 1 0 ; 294.45 1.65E-49 470450000 404890 448850 399250 452300 460530 494730 443190 183764 424400 449010 FALSE TRUE 389066.4512 436049.2375 471403.3563 475643.2572 475343.3657 504733.7796 448613.8918 179969.2092 376223.8912 418598.1528 0.929450951 1.04168935 1.126147722 1.136276532 1.135560113 1.205771636 1.071705379 0.429933118 0.898771026 1 18.67520642 1.879779417 9.475534881 0.719316911 1.1014729 0.453205189 0.155500786 0.249132384 18.44698484 0.06277917 0.039753845 75.8192382 -1.879779417 0.382155989 IVDKPGDHDPETLEAIAENAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IVDKPGDHDPETLEAIAENAK 21 1 Q96Q11-2;Q96Q11 Q96Q11-2 TRNT1 "CCA tRNA nucleotidyltransferase 1, mitochondrial" 0 ; 88.264 0.0014918 886890000 409750 393560 406760 413530 391000 451870 468180 497540 622290 568000 FALSE TRUE 393736.517 382336.0541 480270.5803 434872.3329 403576.8701 461007.121 473909.7269 487265.6251 551650.2481 529528.8541 0.74356008 0.722030634 0.906977168 0.821243884 0.762143303 0.870598679 0.894964879 0.920187109 1.041775616 1 19.01434977 1.880170606 0.827166239 1.022871695 0.789107788 0.727554665 0.052917224 0.330960924 0.42381948 0.047694902 0.022556567 75.88756301 -1.880170606 -0.233763907 HS(ph)HSHS(ph)PMSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 HS(0.995)HS(0.011)HS(0.993)PMSTR;HS(0.978)HS(0.022)HS(0.996)PMS(0.003)T(0.001)R 120.21 0.00025519 841410000 802570 1009450 941410 1232740 971760 1201800 996210 24291.6 1074350 505640 TRUE FALSE 771204.6771 980661.4744 1111543.729 1296361.859 1003017.543 1226101.219 1008401.916 23789.96997 952394.292 471392.5524 1.636013707 2.080349953 2.358000191 2.750068605 2.12777554 2.601019497 2.13919781 0.050467429 2.020384682 1 18.84656944 1.880279147 8.369534394 0.946913527 2.278651069 0.528889674 0.526086483 0.203158618 13.19085316 0.213554238 0.134052667 75.90653142 -1.880279147 1.331737542 S(ph)QEELREDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SQEELREDK 9 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK 157.86 4.09E-05 4882650000 3847380 3205350 2602460 2588350 2684930 2822250 3149580 3811960 4226140 3527180 TRUE FALSE 3697020.136 3113936.556 3072782.413 2721935.054 2771293.212 2879317.829 3188125.502 3733241.694 3746406.305 3288280.957 1.124301781 0.946980078 0.93446468 0.827768396 0.842778719 0.875630114 0.969541698 1.135317129 1.139320622 1 21.64890214 1.880292623 4.278259506 1.102245767 0.918749968 0.428929037 0.085128109 0.205661923 5.847496612 0.042401799 0.024106917 75.90888687 -1.880292623 -0.183495799 S(ph)PPPETIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPPETIK 8 0 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 S(1)PPPETIK;S(1)PPPETIK 72.325 0.04872 1100210000 876490 814820 787520 796300 783380 832220 898870 991240 1168780 1037220 TRUE FALSE 842235.8018 791582.1314 929842.3823 837397.1384 808578.1291 849048.0586 909870.6399 970770.5476 1036104.994 966968.1655 0.871006753 0.818622742 0.961605992 0.8660028 0.836199327 0.878051718 0.940952011 1.003932272 1.071498557 1 19.88310887 1.8803885 1.929974419 1.035372344 0.871243375 0.757169306 0.039023862 0.156917188 1.092754677 0.024951814 0.011575346 75.92564667 -1.8803885 -0.164128969 VGSLT(ph)PPS(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGSLT(1)PPS(0.931)S(0.069)PK 91.202 0.057918 696050000 1555200 1315000 1114400 1082700 1223300 1249800 1352200 1759900 1858700 1580200 TRUE FALSE 1494421.065 1277497.488 1315796.87 1138578.277 1262648.555 1275071.812 1368748.628 1723557.45 1647708.168 1473171.647 1.014424265 0.867174908 0.893172817 0.772875503 0.857095342 0.865528342 0.929116869 1.169963768 1.118476704 1 20.49049411 1.880404074 4.625171569 1.108752577 0.874439534 0.668396894 0.068395209 0.121409847 3.866561877 0.031834159 0.018384218 75.92836957 -1.880404074 -0.234313043 TVYSHLFDHVVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVYSHLFDHVVNR 13 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 259.48 3.26E-24 2110100000 868530 971680 841070 1048720 989750 980980 975710 130404 990640 998330 FALSE TRUE 834586.8874 943968.6378 993070.0585 1102844.565 1021586.208 1000816.088 987651.0308 127711.1118 878186.7003 930712.2199 0.896718523 1.014243305 1.067000129 1.184946906 1.097639191 1.075322819 1.061177676 0.13721869 0.943564167 1 19.82797562 1.880638384 20.65922257 0.598007359 1.062825591 0.315963475 0.232289647 4.252374059 721.593563 0.090862966 0.058616689 75.96934529 -1.880638384 0.464818232 VELS(ph)PGPPKPAGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VELSPGPPKPAGR 13 1 A0A087WXE2;Q8IZ73-2;Q8IZ73 A0A087WXE2 RPUSD2 RNA pseudouridylate synthase domain-containing protein 2 1 VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR 131.86 7.60E-05 2503810000 3569940 3373910 3137040 3136470 3194520 3458100 3423340 3853370 4041680 4143030 TRUE FALSE 3430422.798 3277689.39 3703972.911 3298343.593 3297274.637 3528025.151 3465235.859 3773796.563 3582885.431 3862418.888 0.888154003 0.848610543 0.958977526 0.853958022 0.853681264 0.913423752 0.897167283 0.977055227 0.927627359 1 21.88107321 1.880685921 1.733883164 0.969843281 0.883239884 0.515372281 0.035500986 0.286245552 1.614935074 0.023157743 0.010425666 75.97766129 -1.880685921 -0.086603397 LVRPEGHQQQHHHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVRPEGHQQQHHHR 14 1 R4GNH4;R4GMZ8;Q9H4M3-2;B7Z1P2 R4GNH4 FBXO44 0 ; 109.84 0.00048026 67030000 35488 38281 33247 38122 39910 35246 35268 3643.8 34382 23732 FALSE TRUE 34101.08973 37189.26336 39255.47248 40089.48099 41193.7414 35958.69827 35699.62033 3568.554257 30479.0995 22124.6105 1.541319325 1.680900252 1.774289878 1.811985842 1.861896796 1.625280511 1.613570568 0.161293427 1.37761067 1 14.43336444 1.880771273 7.999705769 0.774482533 1.718406977 0.638430085 0.294162929 0.150072012 9.29664958 0.117945392 0.073755056 75.99259466 -1.880771273 0.943924444 EEKDKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEKDKDDQEWESPSPPKPTVFISGVIAR 28 3 P51397 P51397 DAP Death-associated protein 1 1 EEKDKDDQEWES(0.004)PS(0.996)PPKPTVFISGVIAR;EEKDKDDQEWES(0.019)PS(0.951)PPKPT(0.023)VFIS(0.007)GVIAR;EEKDKDDQEWES(0.049)PS(0.951)PPKPTVFISGVIAR;EEKDKDDQEWES(0.137)PS(0.863)PPKPTVFISGVIAR 181.38 9.96E-18 8174700000 1661800 1133821 884118 841654 1135276 1039232 1232816 1587350 1805970 1440253 TRUE FALSE 1596855.019 1101485.535 1043897.79 885091.8638 1171793.184 1060245.983 1247903.571 1554570.668 1600963.857 1342703.381 1.189283531 0.820349118 0.777459716 0.659186441 0.872711873 0.789635297 0.929396312 1.157791579 1.192343655 1 20.3567092 1.880814532 3.609182743 1.130386566 0.839659199 0.427771179 0.13609527 0.211838035 4.607262883 0.068504551 0.037574444 76.00016442 -1.880814532 -0.290727367 DEYLLGRPIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DEYLLGRPIDK 11 1 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 0 112.64 0.0013664 124250000 189450 201190 181450 186820 205680 198630 209560 265060 282780 239930 FALSE TRUE 182046.0846 195452.2582 214242.0513 196461.8026 212295.884 202646.4347 212124.658 259586.4184 250679.9999 223679.3274 0.813870851 0.873805642 0.957808904 0.878318997 0.949108201 0.905968545 0.948342703 1.160529323 1.120711524 1 17.7710724 1.880828937 4.589099598 1.106143539 0.901629931 0.725216493 0.054037347 0.108825487 3.430271722 0.024918238 0.014370979 76.00268527 -1.880828937 -0.204513608 RASGQAFELILS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 7 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR 192.25 2.42E-07 4530967000 1530595 1832868 1614640 2269705 2539825 2185198 1577706 1387772 1106696 1321330 TRUE FALSE 1470777.655 1780596.399 1906441.365 2386844.747 2621520.778 2229384.201 1597014.438 1359114.023 981068.5097 1231835.142 1.193972801 1.44548271 1.547643268 1.937633264 2.128142548 1.809807274 1.296451435 1.103324606 0.796428415 1 20.23237776 1.880830902 2.199941582 0.936666294 1.688787736 0.60818153 0.255787263 0.228258587 2.041902406 0.17268243 0.083320218 76.00302928 -1.880830902 0.752121442 KLTS(ph)DEEGEPSGK ddPTM_BT-474_Pertuzumab_2h_R1 5 KLTSDEEGEPSGK 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.287)S(0.713)DEEGEPSGK;KLT(0.073)S(0.927)DEEGEPSGK;KLT(0.296)S(0.704)DEEGEPSGK;KLT(0.298)S(0.702)DEEGEPSGK;KLT(0.162)S(0.838)DEEGEPSGK 177.6 9.38E-06 4939370000 4813200 4011800 3884240 3512740 4186830 4056590 4618760 5540250 6441090 5622410 TRUE FALSE 4625094.823 3897387.392 4586208.572 3694032.932 4321503.189 4138617.029 4675285.767 5425841.901 5709924.466 5241599.163 0.882382395 0.743549301 0.874963619 0.704753038 0.824462736 0.789571446 0.891957897 1.035150101 1.08934779 1 22.3215756 1.880904981 2.416025718 1.05196982 0.800226082 0.7905179 0.05471929 0.112436518 1.198631607 0.029156625 0.01445907 76.01599443 -1.880904981 -0.251743738 HLDGEEDGS(ph)S(ph)DQSQASGTTGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 2 HLDGEEDGS(0.99)S(0.99)DQS(0.02)QASGTTGGR 64.377 0.0043955 0 40659 43986 33369 44646 41529 38314 38156 22504 32569 33229 TRUE FALSE 39070.00133 42731.56235 39399.52059 46950.18541 42864.818 39088.73533 38622.96454 22039.28454 28871.90366 30978.37023 1.261202608 1.37939995 1.271839683 1.515579582 1.383701521 1.261807353 1.246771998 0.711441059 0.932002021 1 14.91897363 1.881024056 4.774216 0.862329483 1.346358176 0.812974117 0.099637588 0.085437659 2.847749135 0.046102386 0.026794551 76.03683929 -1.881024056 0.484028693 SWS(ph)PPPEVSR ddPTM_BT-474_Pertuzumab_2h_R1 13 SWSPPPEVSR 10 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31;C9JXD9 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 SWS(1)PPPEVSR;S(0.026)WS(0.974)PPPEVSR;SWS(1)PPPEVSR;S(0.013)WS(0.987)PPPEVSR;SWS(1)PPPEVSR;SWS(0.999)PPPEVSR;SWS(1)PPPEVSR;S(0.001)WS(0.999)PPPEVSR;S(0.013)WS(0.987)PPPEVSR;S(0.001)WS(0.999)PPPEVSR;S(0.001)WS(0.998)PPPEVSR;S(0.002)WS(0.998)PPPEVSR;S(0.001)WS(0.999)PPPEVSR 194.48 4.81E-07 1.38091E+11 8833967 9059639 7909316 10021456 9483259 10046248 9148123 8822024 9756890 9527140 TRUE FALSE 8488725.803 8801266.966 9338705.343 10538664.55 9788296.638 10249390.02 9260080.466 8639846.121 8649328.751 8881858.322 0.955737583 0.990926296 1.051435973 1.18653824 1.10205503 1.153969096 1.042583672 0.972752076 0.973819716 1 23.08243013 1.881045167 4.2835786 0.98128723 1.07662628 0.280685703 0.064798161 0.320218305 9.132065474 0.034288915 0.019506909 76.04053552 -1.881045167 0.095339051 YHEEFEK ddPTM_BT-474_Pertuzumab_2h_R1 16 YHEEFEK 7 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;;;;;;;;;;; 162.31 0.0012769 1.98045E+11 109354287 107742014 88434638 95376056 95806600 96342364 100866254 40347612.2 114789339 100044441 FALSE TRUE 105080600.6 104669317.3 104416744.3 100298425.7 98888306.3 98290472.61 102100685.4 39514419.91 101758934.5 93268341.9 1.126648104 1.122238426 1.119530402 1.075374812 1.060255863 1.053846038 1.094698193 0.423663797 1.091034025 1 26.47488413 1.881107904 21.64872574 0.770400902 1.091949751 0.303703055 0.167742109 5.856532418 1048.111242 0.06511827 0.042014993 76.05152098 -1.881107904 0.321548849 DQHDTFFLRDPAEALQLPMDYVQR ddPTM_BT-474_Pertuzumab_2h_R1 3 DQHDTFFLRDPAEALQLPMDYVQR 24 1 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ;; 128.77 4.52E-05 478060000 332991 437240 315845 426520 377125 445596 387351 141568 364483 389454 FALSE TRUE 319977.3436 424770.3433 372925.2174 448532.7483 389255.5681 454606.2564 392091.5174 138644.5713 323108.4179 363075.9337 0.881295933 1.169921506 1.027127338 1.235368987 1.072105122 1.252096915 1.07991602 0.381861089 0.889919678 1 18.46991178 1.881260178 9.362918195 0.695779815 1.114297458 0.420770194 0.181454446 0.255442546 18.83311606 0.071507427 0.045249705 76.07819106 -1.881260178 0.418517643 YEAHSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 YEAHSDK 7 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 0 ; 93.195 0.015113 252840000 507250 504680 444570 587460 526700 421830 495990 430930 361670 458140 FALSE TRUE 487426.1092 490287.0205 524913.6884 617778.881 543641.7838 430359.6916 502060.074 422031.1449 320614.7378 427109.7697 1.141219761 1.147918065 1.228990123 1.446417115 1.272838559 1.007609102 1.175482533 0.988109322 0.750661213 1 18.70424737 1.881307241 1.22544425 0.880848515 1.235556095 0.564857958 0.119243387 0.346050509 0.961630865 0.097703174 0.041740833 76.08643586 -1.881307241 0.354707581 LHLNQNGDHNTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHLNQNGDHNTK 12 0 Q86X83-2;Q86X83 Q86X83-2 COMMD2 COMM domain-containing protein 2 0 78.548 0.014707 93111000 112430 130170 102760 133480 119200 121240 118440 64728 123050 104230 FALSE TRUE 108036.1113 126457.679 121331.0179 140368.9188 123034.1763 123691.5559 119889.5041 63391.34418 109081.8799 97170.40926 1.1118211 1.301401116 1.248641627 1.44456445 1.266169168 1.272934392 1.233806722 0.652372926 1.122583312 1 16.56822942 1.881680156 7.831682348 0.895356762 1.279094176 0.579396971 0.133701927 0.16624518 10.10536461 0.054292945 0.033887848 76.15179693 -1.881680156 0.383737414 VLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHR 33 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 264.22 6.52E-60 1310220000 600430 935960 698170 1074630 805050 1039900 852810 447350 761060 899660 FALSE TRUE 576964.5318 909267.3372 824344.8497 1130091.783 830945.1644 1060927.49 863246.9439 438112.0662 674667.6594 838725.2269 0.687906496 1.084106341 0.982854484 1.347392146 0.990723944 1.264928556 1.02923689 0.522354702 0.804396527 1 19.67783872 1.881819256 7.778874337 0.731077656 1.073418818 0.284550915 0.199231296 0.280442155 16.93132174 0.082285968 0.051328209 76.17619152 -1.881819256 0.342341161 IYEDGDDDMK ddPTM_BT-474_Pertuzumab_2h_R1 4 IYEDGDDDMK 10 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;; 172.23 8.79E-06 2528100000 4032320 3406130 3782250 3602560 3921740 3629060 4232410 5099940 5720670 5248980 FALSE TRUE 3874732.476 3308990.507 4465786.711 3788488.553 4047886.329 3702442.08 4284207.5 4994624.457 5071283.525 4893461.909 0.791818256 0.67620645 0.912602733 0.774193939 0.827202991 0.756609972 0.875496239 1.020673002 1.036338612 1 22.22242404 1.88182919 2.827824778 1.023715299 0.791458994 0.764977929 0.056653938 0.12081179 1.718125759 0.029923489 0.015499424 76.17793393 -1.88182919 -0.232256305 KS(ph)LS(ph)DSESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.987)LS(0.746)DS(0.228)ES(0.005)DDS(0.034)K 166.52 3.45E-05 551770000 1746200 1249100 1151300 1015800 1287400 1223900 1428900 1908300 2111700 1710300 TRUE FALSE 1677956.573 1213476.891 1359365.521 1068225.56 1328810.39 1248648.097 1446387.306 1868892.938 1871988.669 1594459.858 1.052366772 0.761058289 0.8525555 0.669960774 0.833392188 0.783116672 0.907133095 1.172116645 1.174058199 1 20.60463635 1.88203401 3.802110458 1.129070783 0.818295043 0.614947708 0.10210627 0.139681627 3.312440256 0.048502486 0.026927867 76.21386913 -1.88203401 -0.31077574 TSGHDHPDVATMLNILALVYR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSGHDHPDVATMLNILALVYR 21 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;E9PQ02;Q9H0B6;Q9H0B6-2;A8MZ87;A8MX29 Q07866-6;Q9H0B6 KLC1;KLC2 Kinesin light chain 1;Kinesin light chain 2 0 ;; 211.13 9.60E-23 693471000 539207 652729 543192 694303 651603 697186 650806 173227 739656 628779 FALSE TRUE 518134.1943 634113.808 641358.8776 730136.061 672562.4023 711283.5786 658770.7585 169649.8019 655693.3518 586191.2383 0.883899589 1.08175245 1.094112016 1.245559492 1.14734298 1.213398516 1.12381543 0.289410334 1.118565596 1 19.16101188 1.882127693 24.03671106 0.719409239 1.121267924 0.263114724 0.224994413 12.92312544 2603.633148 0.088688748 0.057235886 76.2303112 -1.882127693 0.401858685 QHRPLPST(ph)PDSSHHAQATPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QHRPLPSTPDSSHHAQATPR 20 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 QHRPLPS(0.081)T(0.918)PDS(0.001)SHHAQATPR 58.938 0.039139 33204000 17343 27756 20568 33050 23378 27101 23675 6070.6 18584 20706 TRUE FALSE 16665.21639 26964.42606 24285.09513 34755.71446 24129.9746 27649.00079 23964.74173 5945.239989 16474.42223 19303.56418 0.863323282 1.396862559 1.258062755 1.800481722 1.250026906 1.432326203 1.241467198 0.307986646 0.8534394 1 14.23657963 1.882229572 6.756770322 0.66291401 1.348752326 0.502225707 0.272751563 0.171869856 8.86841418 0.114483838 0.070333964 76.24819578 -1.882229572 0.685838316 SRPT(ph)SEGS(ph)DIESTEPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.044)RPT(0.643)S(0.313)EGS(0.844)DIES(0.155)T(0.001)EPQK 255.69 7.01E-21 0 424070 392570 303710 312900 363780 357280 368840 397240 438800 406460 TRUE FALSE 407496.8756 381374.288 358597.153 329048.8065 375481.3141 364504.4464 373353.9743 389036.8552 388989.2636 378930.1022 1.075387976 1.006450229 0.946341161 0.868362805 0.990898617 0.961930563 0.985284548 1.026671814 1.026546219 1 18.53157223 1.882273388 3.904234587 1.019789677 0.971029154 0.127751575 0.049278273 0.471348376 11.66725282 0.025727978 0.014366901 76.25588895 -1.882273388 -0.048760523 YVWDYTDHVWTEVYSPSQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 YVWDYTDHVWTEVYSPSQQR 20 0 Q96IV0-5;Q96IV0;Q96IV0-3 Q96IV0-5 NGLY1 Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase 0 101.64 0.00094457 0 89491 86024 82937 87843 96844 94833 79090 81433 76554 80167 FALSE TRUE 85993.59278 83570.67975 97925.56082 92376.58776 99959.07521 96750.58824 80057.92708 79751.38009 67863.91086 74737.21768 1.150612713 1.118193617 1.310265004 1.236018554 1.337473863 1.294543619 1.071192233 1.067090568 0.908033681 1 16.18953924 1.882320758 1.893673144 0.97532414 1.241056632 0.692655384 0.075254478 0.20049874 1.34487424 0.051227968 0.023671262 76.26420686 -1.882320758 0.265732492 AKGPS(ph)PPGAK ddPTM_BT-474_Pertuzumab_2h_R1 5 AKGPSPPGAK 10 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 AKGPS(1)PPGAK;AKGPS(1)PPGAK;AKGPS(1)PPGAK;AKGPS(1)PPGAK;AKGPS(1)PPGAK 73.877 0.026449 4001020000 8219100 7053000 6241100 5632570 6567990 7023600 7312300 8677100 10080300 8374400 TRUE FALSE 7897888.485 6851855.346 7369005.603 5923267.613 6779255.363 7165622.004 7401790.115 8497914.853 8936026.604 7807194.429 1.011616728 0.877633497 0.943873714 0.758693493 0.868334384 0.917822922 0.948072983 1.088472297 1.144588711 1 22.89637277 1.882362157 2.535776834 1.089842022 0.890321583 0.577535463 0.068960713 0.187703183 2.187663978 0.038971629 0.019614298 76.27147716 -1.882362157 -0.199520439 LSPFFTLDLS(ph)PTEDK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSPFFTLDLSPTEDK 15 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 LSPFFTLDLS(0.999)PT(0.001)EDK;LSPFFTLDLS(1)PTEDK;LSPFFTLDLS(0.982)PT(0.018)EDK 225.7 1.01E-12 312125000 346314 320529 329367 331437 343720 317969 351273 435079 452410 389234 TRUE FALSE 332779.666 311387.8268 388890.9436 348542.5033 354776.066 324398.551 355571.9841 426094.4666 401054.3135 362870.8345 0.917074712 0.858123049 1.071706257 0.960513963 0.977692425 0.893978023 0.979885817 1.174231782 1.10522609 1 18.46909658 1.882385472 6.075072355 1.107646075 0.949332783 0.48840734 0.066676253 0.177787882 8.102371259 0.029161999 0.017662358 76.27557179 -1.882385472 -0.158313292 QDFESTDESEDIESLIPK ddPTM_BT-474_Pertuzumab_2h_R1 3 QDFESTDESEDIESLIPK 18 0 Q8WVV4-1;Q8WVV4 Q8WVV4-1 POF1B Protein POF1B 0 ;; 216.39 2.09E-18 93478000 197325 185873 173482 178151 179459 190253 196801 246599 256269 231596 FALSE TRUE 189613.3208 180572.084 204834.0565 187345.3945 185231.4617 194100.046 199209.5095 241506.6445 227178.4175 215909.7966 0.878206194 0.836331129 0.948702003 0.867702149 0.857911334 0.898986748 0.922651555 1.118553434 1.052191337 1 17.72006918 1.88241956 4.698905526 1.065132696 0.882701508 0.802540415 0.038897239 0.086852284 2.839896304 0.017687876 0.010254986 76.28155894 -1.88241956 -0.182431188 KLPPPPGS(ph)PLGHSPTASPPPTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPPPPGSPLGHSPTASPPPTAR 23 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 KLPPPPGS(0.643)PLGHS(0.356)PT(0.001)ASPPPTAR;KLPPPPGS(0.992)PLGHS(0.008)PTASPPPTAR 156.92 7.56E-09 2358990000 1107230 1016490 891100 1060630 1069570 1160200 1016470 912220 969080 1103970 TRUE FALSE 1063958.227 987500.7004 1052141.592 1115369.241 1103973.69 1183660.039 1028909.864 893382.3382 859074.1011 1029197.129 1.033774967 0.959486451 1.022293556 1.08372751 1.072655238 1.150080977 0.999720885 0.868038118 0.834703165 1 19.97308791 1.882613823 4.393445278 0.890276778 1.05181928 0.554641845 0.060714182 0.164690596 4.889826071 0.029841268 0.017076899 76.31568786 -1.882613823 0.161542503 HQTEDDFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQTEDDFQR 9 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 0 ; 112.85 0.0018965 326230000 121397 150466 125789 170023 145497 164921 127181 96532 92024 114833 FALSE TRUE 116652.671 146174.857 148521.8705 178797.9074 150177.0431 168255.8156 128737.4791 94538.58047 81577.82132 107055.2586 1.089649145 1.36541501 1.387338393 1.670145957 1.402799312 1.57167259 1.202532979 0.88308208 0.762016013 1 16.70799614 1.882794321 3.00425212 0.865270668 1.421466222 0.706693096 0.152799404 0.137736295 2.183856987 0.082629159 0.043487885 76.34741221 -1.882794321 0.556195554 RRPENPKPQDGK ddPTM_BT-474_Pertuzumab_2h_R1 8 RRPENPKPQDGK 12 3 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;;;; 162.32 2.72E-05 10232661000 6830172 6487513 5779230 5160198 5946392 6106839 6821380 7701554 8518260 8614614 FALSE TRUE 6563241.327 6302495.481 6823665.419 5426516.437 6137663.099 6230323.469 6904862.089 7542514.219 7551302.836 8031138.521 0.817224272 0.784757412 0.849651068 0.675684577 0.764233251 0.775770889 0.859761299 0.939158775 0.940253093 1 22.93717309 1.882815559 1.750577111 0.968312871 0.7749471 0.775347199 0.044056425 0.166387858 0.956245631 0.03011187 0.01361501 76.35114587 -1.882815559 -0.193365771 SS(ph)PNVANQPPS(ph)PGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPNVANQPPSPGGK 15 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 2 S(0.378)S(0.622)PNVANQPPS(1)PGGK 226.74 1.20E-12 291120000 505960 481960 446260 449010 411070 434380 512510 576220 658640 616910 TRUE FALSE 486186.5238 468214.9727 526909.109 472183.4599 424292.4399 443163.4612 518782.2507 564320.8556 583873.9484 575126.1362 0.845356337 0.81410832 0.916162692 0.821008523 0.73773806 0.770550029 0.902032125 0.981212329 1.01521025 1 19.13351888 1.882967777 2.634182049 1.00142897 0.818885681 0.76249351 0.045183451 0.144583729 1.80709082 0.027689301 0.014088719 76.37791118 -1.882967777 -0.182543289 S(ph)GDLGDMEPLKGTTPLMQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SGDLGDMEPLKGTTPLMQK 19 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-27;O60716-29;O60716-32;O60716-31 O60716-13 CTNND1 Catenin delta-1 1 S(1)GDLGDMEPLKGTTPLMQK;S(1)GDLGDMEPLKGTTPLMQK;S(1)GDLGDMEPLKGTTPLMQK;S(1)GDLGDMEPLKGTTPLMQK 236.59 2.06E-24 1634330000 1740040 1641550 1415660 1466940 1329980 1622010 1622510 2051690 2109970 1862450 TRUE FALSE 1672037.313 1594734.601 1671501.253 1542648.949 1372760.015 1654808.154 1642366.763 2009321.885 1870455.051 1736304.603 0.962986166 0.918464766 0.96267743 0.888466774 0.790621653 0.953063276 0.945897834 1.15724043 1.077262048 1 20.72758863 1.883148055 5.241891704 1.090483749 0.911638598 0.608010492 0.059306084 0.140299103 5.330335643 0.027459358 0.016246262 76.40962258 -1.883148055 -0.17884515 RFEDLGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RFEDLGSR 8 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ; 135.63 0.0013235 570210000 244550 310360 287750 376690 348490 273300 295530 217640 207360 256500 FALSE TRUE 234992.7156 301508.8367 339752.826 396131.016 359699.4973 278826.3133 299146.7845 213145.6579 183821.3621 239127.0265 0.982710817 1.260873106 1.420804795 1.656571496 1.504219337 1.166017565 1.250995293 0.891349092 0.768718471 1 17.86741767 1.883160963 1.835638054 0.855140732 1.361756652 0.544689399 0.181655388 0.263842093 1.664892692 0.127133873 0.058262286 76.41189365 -1.883160963 0.506615921 NGEELHGGKR ddPTM_BT-474_Pertuzumab_2h_R1 4 NGEELHGGKR 10 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 122.69 0.00031279 428236000 649510 610110 546950 550450 578750 604140 652980 698700 844130 742920 FALSE TRUE 624126.4311 592710.2602 645796.0318 578858.7905 597366.0194 616356.1247 660971.3646 684271.6008 748307.9013 692601.3667 0.901133698 0.855774026 0.932420961 0.835774831 0.86249616 0.889914682 0.954331592 0.987973218 1.080430876 1 19.40166571 1.883181864 1.603327339 1.036135305 0.876830538 0.800677947 0.032463438 0.151003014 0.727881623 0.021769332 0.009630442 76.41557117 -1.883181864 -0.159304768 S(ph)RDDLYDQDDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDDLYDQDDSR 12 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 S(0.731)RDDLY(0.029)DQDDS(0.24)R 86.413 0.029267 158450000 166380 150120 114160 162800 133260 115820 146390 206630 189640 164290 TRUE FALSE 159877.6857 145838.7246 134791.2515 171202.1275 137546.4289 118161.9598 148181.5646 202363.0183 168112.8622 153162.492 1.043843591 0.952183023 0.88005392 1.117781027 0.898042511 0.771481048 0.967479457 1.321230908 1.097611171 1 17.22470351 1.883414508 8.326728169 1.170126556 0.940999701 0.360860405 0.115469598 0.269410305 17.69675753 0.048660437 0.030538041 76.45651664 -1.883414508 -0.229126855 LEEPPELNRQS(ph)PNPR ddPTM_BT-474_Pertuzumab_2h_R1 6 LEEPPELNRQSPNPR 15 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR 212.76 4.31E-10 26649030000 4682620 4881140 3582090 4193810 4172000 4570390 3992280 4280570 4307360 4272910 TRUE FALSE 4499618.033 4741934.666 4229453.346 4410253.037 4306196.169 4662806.417 4041138.717 4192174.734 3818406.551 3983502 1.129563393 1.190393444 1.061742494 1.107129615 1.081007658 1.170529453 1.014468856 1.052384242 0.958555199 1 21.92560587 1.883489125 1.458134628 0.989473818 1.120877798 0.602602624 0.044574674 0.2775479 1.102943663 0.031677853 0.013754329 76.46965404 -1.883489125 0.131403979 VES(ph)EES(ph)GDEEGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VESEESGDEEGKK 13 1 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C003;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 2 VES(1)EES(1)GDEEGKK;VES(1)EES(1)GDEEGKK 131.53 2.33E-06 490330000 1320320 958710 1047450 825090 1101030 936090 1235280 1650580 1922520 1525830 TRUE FALSE 1268720.435 931368.5295 1236747.515 867672.9938 1136445.63 955018.3812 1250397.726 1616494.946 1704283.589 1422484.175 0.89190478 0.654747902 0.869427961 0.609970226 0.798916185 0.671373642 0.879023998 1.136388703 1.198103725 1 20.43998117 1.883498104 3.226740965 1.125326758 0.747138377 0.732929981 0.09730466 0.111634456 2.008673575 0.046108863 0.0246997 76.47123494 -1.883498104 -0.378188381 HTNPSSSS(ph)PGTRT ddPTM_BT-474_Pertuzumab_2h_R1 1 HTNPSSSSPGTRT 13 1 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 1 HTNPS(0.001)S(0.011)S(0.023)S(0.777)PGT(0.142)RT(0.046) 63.374 0.042597 69485000 41780 62583 69092 90220 65520 85920 63221 49046 51668 58635 TRUE FALSE 40147.19141 60798.19412 81578.46134 94876.26501 67627.5103 87657.36127 63994.71751 48033.18296 45802.86525 54663.59922 0.734441054 1.112224496 1.492372667 1.735638823 1.237158022 1.603578295 1.170700766 0.878705092 0.837904307 1 15.73829283 1.883534773 3.845993053 0.898651524 1.336266613 0.325570721 0.263872213 0.279600304 6.766339748 0.13671989 0.076160568 76.47769209 -1.883534773 0.43761509 THS(ph)FENVSCHLPDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 THSFENVSCHLPDSR 15 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 T(0.461)HS(0.535)FENVS(0.003)CHLPDSR 71.1 0.028804 337730000 122930 169700 95437 163040 165110 156620 142930 108780 136320 150230 TRUE FALSE 118125.7597 164860.3222 112684.5889 171454.5139 170420.9131 159786.9637 144679.2201 106533.655 120845.5251 140054.7883 0.843425356 1.177113072 0.804575054 1.224196017 1.216816042 1.140888974 1.033018734 0.760656999 0.862844652 1 17.09563178 1.883552076 6.075088651 0.854654864 1.075502095 0.256354407 0.146340771 0.278587659 12.75200244 0.063702096 0.038591429 76.48073903 -1.883552076 0.220847231 MLPHAPGVQMQAIPEDAIPEES(ph)GDEDEDDPDKR ddPTM_BT-474_Pertuzumab_2h_R1 21 MLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKR 33 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 1 MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR 257.94 9.80E-60 28063320000 5128878 4558987 3922773 3959512 4424176 4437049 4581850 5290163 5730185 5037434 TRUE FALSE 4928435.777 4428969.154 4631705.343 4163862.889 4566483.639 4526769.171 4637924.051 5180919.285 5079718.422 4696244.108 1.049441993 0.943087508 0.986257366 0.886636809 0.972369309 0.963912664 0.987581553 1.103204852 1.081655532 1 22.16307597 1.883577235 4.969896751 1.070044095 0.964237117 0.463554028 0.045265754 0.17152954 6.077455001 0.020089253 0.011775325 76.4851697 -1.883577235 -0.105806978 VSNGS(ph)PSLER ddPTM_BT-474_Pertuzumab_2h_R1 2 VSNGSPSLER 10 0 P46527;E7ES52 P46527 CDKN1B Cyclin-dependent kinase inhibitor 1B 1 VS(0.026)NGS(0.959)PS(0.015)LER;VS(0.001)NGS(0.999)PSLER 154.74 1.46E-05 861560000 362810 416340 351250 354060 374510 363270 359530 333980 352010 344370 TRUE FALSE 348630.9841 404466.3908 414728.6885 372333.079 386556.4543 370615.5683 363930.0357 327083.1963 312051.3005 321045.5132 1.085923864 1.259841282 1.291806524 1.159751698 1.204054997 1.154401956 1.133577704 1.018806315 0.971984618 1 18.29241831 1.883616766 1.329933109 0.977115674 1.206001515 0.730487883 0.053488086 0.212259884 0.698093667 0.040356272 0.017323524 76.49213208 -1.883616766 0.228885841 PKPSSS(ph)PVIFAGGQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 PKPSSSPVIFAGGQDR 16 1 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PKPS(0.027)S(0.147)S(0.826)PVIFAGGQDR;PKPS(0.011)S(0.19)S(0.799)PVIFAGGQDR 146.19 6.95E-07 1447790000 361185 283936 343620 336032 337844 310176 399476 508800 584740 520890 TRUE FALSE 347069.4909 275838.4233 405719.7778 353374.6518 348711.0591 316447.9712 404364.9068 498293.1022 518362.7666 485609.6563 0.714708792 0.568024996 0.8354854 0.727692803 0.718089219 0.651650903 0.832695358 1.026118603 1.067447403 1 18.88943758 1.883784175 2.728490222 1.039042624 0.704795414 0.832572169 0.065724481 0.1021223 1.361062136 0.036063681 0.018534602 76.52162332 -1.883784175 -0.33424721 MTGSEFDFEEMKR ddPTM_BT-474_Pertuzumab_2h_R1 8 MTGSEFDFEEMKR 13 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;;;; 223.22 2.59E-11 9031050000 5446340 5457970 4359430 4761830 5098510 4808480 5401170 5878060 6543570 6355630 FALSE TRUE 5233491.012 5302314.04 5147275.976 5007588.617 5262508.204 4905710.76 5467271.134 5756676.007 5800771.366 5925157.519 0.88326614 0.894881532 0.868715466 0.845140167 0.888163426 0.827946049 0.922721652 0.971565058 0.979007115 1 22.49842208 1.883852451 2.642249589 0.983491237 0.869205782 0.860679334 0.020729594 0.094694507 1.19009542 0.011352631 0.005785165 76.53365447 -1.883852451 -0.114285455 FKAEAPLPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 FKAEAPLPSPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FKAEAPLPS(1)PK;FKAEAPLPS(1)PK;FKAEAPLPS(1)PK;FKAEAPLPS(1)PK;FKAEAPLPS(1)PK;FKAEAPLPS(1)PK 127.66 0.00017074 30924110000 46446260 43047120 38410380 37130820 37657530 38562790 33182440 37742360 32901700 28090970 TRUE FALSE 44631088.81 41819458.29 45351990.1 39047146.07 38868818.65 39342556.04 33588536.63 36962967.08 29166836.95 26188343.58 1.704234889 1.596872981 1.731762452 1.49101244 1.484203021 1.502292648 1.282575835 1.411428217 1.113733553 1 24.64242148 1.883915183 0.312536762 0.945306356 1.76486496 0.879718686 0.078549727 0.467630868 0.144680193 0.118270015 0.137570169 76.54471016 -1.883915183 0.819558604 DTPGHGSGWAET(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 DTPGHGSGWAET(1)PR 157.42 1.95E-05 585870000 318940 416250 311560 414840 355050 377330 315030 334070 290810 320630 TRUE FALSE 306475.4722 404378.9576 367865.8226 436249.9421 366470.5057 384959.8711 318885.4314 327171.3378 257798.468 298913.4445 1.025298386 1.352829607 1.230676737 1.459452394 1.226008774 1.287864023 1.066815285 1.094535371 0.862451899 1 18.18936826 1.883996254 1.39889047 0.951807247 1.276213425 0.546876442 0.116164044 0.29751917 1.085786124 0.082192411 0.035482759 76.5590003 -1.883996254 0.324406178 ELESPLT(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELESPLTPGK 10 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 ELESPLT(1)PGK;ELESPLT(1)PGK 172.13 4.26E-05 1290880000 2753700 2458600 2279100 2270700 2340700 2121900 2469800 3424100 2898700 3115800 TRUE FALSE 2646082.36 2388483.135 2690984.068 2387891.099 2415990.741 2164806.272 2500026.151 3353391.138 2569651.728 2904764.091 0.910945701 0.822264067 0.926403654 0.822060252 0.831733892 0.745260615 0.860664093 1.154445261 0.884633536 1 21.46998957 1.884068216 8.629274073 1.026357849 0.841189334 0.496554936 0.077040294 0.22574969 15.49190251 0.031347895 0.019728572 76.5716871 -1.884068216 -0.185168515 DSPSKS(ph)SAEAQTPEDTPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSPSKSSAEAQTPEDTPNK 19 1 A0A5F9UY30;A0A5H1ZRP2;O43493-4;O43493;O43493-5;O43493-3;O43493-7 A0A5F9UY30 TGOLN2 Trans-Golgi network integral membrane protein 2 1 DS(0.026)PS(0.097)KS(0.515)S(0.362)AEAQTPEDTPNK 125.82 1.61E-05 661910000 490840 547650 383830 437970 418630 366570 494830 667490 706190 594330 TRUE FALSE 471657.4301 532031.5582 453196.6193 460573.6842 432095.6141 373982.2966 500885.8776 653706.0982 626026.2718 554075.4997 0.851251193 0.960214914 0.81793297 0.831247157 0.779849703 0.674966312 0.904002934 1.17981412 1.129857343 1 19.07972305 1.88410609 4.779623116 1.114841381 0.821950997 0.720822567 0.078729128 0.117390865 3.946783557 0.038281855 0.022282252 76.57836505 -1.88410609 -0.292890384 YSPTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 YSPTSPK 7 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YS(0.001)PT(0.166)S(0.833)PK;YSPT(0.039)S(0.961)PK;YS(0.001)PT(0.103)S(0.896)PK;YSPT(0.158)S(0.841)PK;YSPT(0.222)S(0.778)PK 121.5 0.0046487 6421350000 15602850 13665420 11715570 12187160 12294670 13256660 13505730 15364340 16049410 15328230 TRUE FALSE 14993073.37 13275695.6 13832834.11 12816140.79 12690139.23 13524718.75 13671017.16 15047061.01 14227548.26 14290035.33 1.049197782 0.929017689 0.968005592 0.89685858 0.888041137 0.946444039 0.956681831 1.052975774 0.995627228 1 23.76850615 1.884109031 5.855920618 1.019804725 0.942382074 0.335368955 0.044028972 0.242204922 10.62352543 0.019748885 0.011900525 76.57888359 -1.884109031 -0.07742265 ERHPS(ph)WR ddPTM_BT-474_Pertuzumab_2h_R1 11 ERHPSWR 7 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR 120.63 0.0034045 76570580000 10827706 12183213 10539971 12044977 12207558 12099484 11742105 10809334 12235975 12831150 TRUE FALSE 10404547.28 11835759.69 12444778.22 12666619.71 12600225.19 12344143.86 11885808.39 10586117.48 10846998.42 11962084.78 0.869793808 0.989439543 1.040351949 1.058897336 1.053346922 1.031939171 0.993623487 0.884972617 0.906781603 1 23.51196551 1.884118448 5.730785487 0.920617402 1.012397037 0.253028655 0.058022981 0.273912486 11.69737094 0.026716164 0.016045509 76.5805441 -1.884118448 0.091779635 NEGS(ph)ESAPEGQAQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGS(0.999)ES(0.001)APEGQAQQR;NEGS(0.983)ES(0.017)APEGQAQQR 252.33 1.27E-24 108285000 83680 86221 90963 99606 85349 86918 104620 119851 128040 139855 TRUE FALSE 80409.69309 83762.0615 107402.0376 104746.6776 88094.3281 88675.54151 105900.3709 117376.035 113505.436 130382.4963 0.616721534 0.642433332 0.82374583 0.803379906 0.675660695 0.680118452 0.812228435 0.900243808 0.870557316 1 16.99239068 1.884162457 2.028739245 0.926002567 0.712060583 0.668152088 0.068389723 0.217257737 1.664059176 0.04557463 0.021524151 76.58830474 -1.884162457 -0.213941984 LKFNFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKFNFK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 106.29 0.029414 1604720000 1170220 1342790 870480 1135360 1226580 1203680 1387290 1528790 1829310 1763850 FALSE TRUE 1124486.509 1304494.944 1027795.1 1193956.066 1266034.06 1228019.234 1404268.07 1497219.952 1621654.398 1644382.868 0.683834969 0.793303658 0.625033938 0.726081552 0.769914406 0.746796417 0.853978776 0.910505686 0.986178115 1 20.64911482 1.884245857 0.94446106 1.007005925 0.710476046 0.874030499 0.042327314 0.171568227 0.282223474 0.034404064 0.015388571 76.60301386 -1.884245857 -0.296529879 DTS(ph)PSSGSAVSSSK ddPTM_BT-474_Pertuzumab_2h_R1 8 DTSPSSGSAVSSSK 14 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;Q8NEY8-7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 DTS(1)PSSGSAVSSSK;DT(0.062)S(0.938)PS(0.001)SGSAVSSSK;DTS(0.965)PS(0.01)S(0.024)GSAVSSSK;DTS(1)PSSGSAVSSSK;DTS(0.869)PS(0.126)S(0.005)GSAVSSSK;DTS(0.596)PS(0.322)S(0.081)GSAVSSSK;DTS(0.89)PS(0.105)S(0.004)GSAVSSSK;DT(0.139)S(0.723)PS(0.119)S(0.016)GS(0.004)AVSSSK 392.16 4.19E-114 17068900000 15326500 14002170 12400750 13107380 13417550 14370560 14910600 15606270 18278560 17116250 TRUE FALSE 14727523.44 13602841.82 14641841.38 13783853.45 13849137.68 14661142.57 15093080.38 15283995.07 16203654.5 15956951.14 0.922953471 0.852471233 0.917583895 0.863814981 0.867906253 0.918793474 0.945862418 0.957826776 1.015460557 1 23.92768169 1.884248519 1.102302303 1.005905888 0.884025747 0.796547366 0.023725063 0.201403879 0.450587319 0.018343159 0.007909808 76.6034834 -1.884248519 -0.121880141 GGLWDDDDAPRPSQFEEDLALMEEMEAEHR ddPTM_BT-474_Pertuzumab_2h_R1 5 GGLWDDDDAPRPSQFEEDLALMEEMEAEHR 30 1 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6;M0R2J2 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ;;;; 282.95 6.58E-72 455161000 254834 277315 229579 297528 292227 311903 276327 256325 286838 296460 FALSE TRUE 244874.8055 269406.2477 271069.0323 312883.4557 301626.7468 318209.8924 279708.7725 251031.7992 254277.3528 276380.5001 0.886006087 0.974765758 0.980782045 1.132075004 1.091345977 1.151347118 1.012042356 0.908283323 0.920026386 1 18.07629631 1.884350471 5.449034254 0.936065452 1.040847193 0.220464781 0.077639179 0.33571581 13.46207187 0.038057853 0.022673868 76.62146843 -1.884350471 0.104781741 DAALATALGDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAALATALGDKK 12 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 116.19 0.0013928 1953060000 1697480 1629570 1220230 1417790 1443420 1306180 1633450 2000050 2273800 1925380 FALSE TRUE 1631140.605 1583096.259 1440752.705 1490962.312 1489848.915 1332591.855 1653440.65 1958748.269 2015687.757 1794972.298 0.908727453 0.881961388 0.802660134 0.830632492 0.830012205 0.742402463 0.921151068 1.091241503 1.122963156 1 20.77553015 1.884388956 3.598880165 1.078728361 0.833074522 0.809227788 0.051572936 0.095743876 2.078812034 0.02608993 0.014334411 76.62825857 -1.884388956 -0.245653839 TMLAGVILEDYLDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 TMLAGVILEDYLDIK 15 0 P51800-2;P51800-3;P51800 P51800-2 CLCNKA Chloride channel protein ClC-Ka 0 ; 87.498 0.0041334 1190310000 3044000 1617410 1968610 1366060 2327900 1621810 2495500 2770500 3704400 2790300 FALSE TRUE 2925037.115 1571283.05 2324381.618 1436562.52 2402779.018 1654604.109 2526040.675 2713288.207 3283892.042 2601310.496 1.124447512 0.604035179 0.893542552 0.552245694 0.923680207 0.636065595 0.971064654 1.043046653 1.262399105 1 21.31080718 1.884795223 2.429932208 1.120894042 0.781518803 0.391571283 0.173718925 0.261812714 2.818542925 0.091332627 0.045508695 76.69997515 -1.884795223 -0.339375239 VVSETNDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 275.17 8.12E-21 740210000 1072730 1069070 826380 905950 959880 1047190 1006530 1125140 1233390 1205600 FALSE TRUE 1030806.526 1038581.17 975725.2487 952706.1881 990755.4119 1068364.899 1018848.215 1101905.466 1093380.738 1123943.638 0.917133645 0.924050936 0.868126493 0.847645875 0.881499195 0.950550244 0.906494045 0.980392102 0.972807444 1 20.10013826 1.884829518 1.023899586 0.995224783 0.888860634 0.680492505 0.027195108 0.316673934 0.610694852 0.024025285 0.010504086 76.70603215 -1.884829518 -0.106364149 GNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_BT-474_Pertuzumab_2h_R1 7 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK 215.59 6.74E-25 13736337000 22141037 17152492 18320156 17566234 19290526 17335027 22017774 29685850 32537810 28844810 TRUE FALSE 21275740.8 16663319.72 21631015.72 18472829.44 19911023.29 17685553.12 22287234.1 29072826.82 28844254.22 26891125.33 0.791180753 0.619658699 0.804392358 0.686948918 0.740431018 0.657672481 0.828795145 1.081130911 1.072630984 1 24.68062679 1.884840059 3.376509328 1.057548082 0.716757148 0.870352328 0.057542779 0.071977554 1.402442269 0.02696094 0.014608182 76.70789397 -1.884840059 -0.340790934 ECDS(ph)DDNMGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ECDSDDNMGAK 11 0 Q9Y4E5-2;Q9Y4E5 Q9Y4E5-2 ZNF451 Zinc finger protein 451 1 ECDS(1)DDNMGAK;ECDS(1)DDNMGAK 177.21 8.48E-06 364350000 760620 643870 569060 564110 638910 596470 675630 743000 854990 755180 TRUE FALSE 730894.1295 625507.458 671901.8007 593223.7847 659461.1204 608531.0321 683898.562 727656.7904 757935.1196 704030.986 1.038156195 0.888465807 0.954363961 0.842610335 0.936693318 0.864352627 0.971404066 1.033557904 1.076565002 1 19.4252794 1.884935354 3.123749901 1.040976508 0.917915663 0.477916967 0.053806521 0.200035146 3.401429541 0.026699935 0.014208144 76.72472741 -1.884935354 -0.123060845 KNST(ph)DLDSAPEDPT(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNSTDLDSAPEDPTSPK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 KNS(0.455)T(0.545)DLDSAPEDPT(0.631)S(0.369)PK 93.583 0.0018772 246830000 196790 163190 126020 125860 153760 149130 160730 194990 214890 175850 TRUE FALSE 189099.2292 158535.981 148794.6173 132355.6497 158705.83 152145.5108 162697.0618 190963.3884 190496.5881 163939.5229 1.153469438 0.967039419 0.907618948 0.807344363 0.968075466 0.928058763 0.992421223 1.164840455 1.161993062 1 17.32280418 1.884941243 4.54313022 1.122597514 0.948311015 0.357149296 0.091310466 0.224089363 7.021884974 0.043691461 0.02519555 76.72576775 -1.884941243 -0.174286499 MLEDCVQETIHEHNK ddPTM_BT-474_Pertuzumab_2h_R1 2 MLEDCVQETIHEHNK 15 0 Q9NVM9-2;Q9NVM9;F8VRX9;F5H457 Q9NVM9-2 ASUN Protein asunder homolog 0 ; 153.94 1.48E-06 213346000 324190 323030 255310 299400 311210 329450 311050 7151 359630 241740 FALSE TRUE 311520.2964 313817.5007 301450.1963 314852.0699 321220.3523 336111.7047 314856.7229 7003.329351 318806.3101 225366.7345 1.382281627 1.39247481 1.337598457 1.397065413 1.425322832 1.491398921 1.397086059 0.031075258 1.414611215 1 17.78191505 1.885032202 17.04308788 0.708825942 1.404949217 0.396137913 0.324871931 1.657461111 240.0608302 0.125469285 0.080845539 76.74183889 -1.885032202 0.696123275 NSPNNIS(ph)GISNPPGTPR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPNNISGISNPPGTPR 17 0 Q9BWW4-2;Q9BWW4;Q9NW25;A0A087WVT6;Q9BWW4-3 Q9BWW4-2 SSBP3 Single-stranded DNA-binding protein 3 1 NS(0.003)PNNIS(0.997)GISNPPGTPR 316.49 2.75E-58 321270000 92659 91902 82581 84755 90103 76048 91428 108140 115020 102640 TRUE FALSE 89037.78384 89281.04494 97505.2237 89129.21571 93001.24482 77585.74266 92546.92321 105906.8712 101963.4118 95688.10138 0.930500058 0.933042287 1.018990055 0.931455577 0.971920683 0.810819125 0.96717274 1.106792482 1.065580886 1 16.54605192 1.885176147 5.720031853 1.064991483 0.934773377 0.50667307 0.054757284 0.177282719 7.582984685 0.024540543 0.014738432 76.76727901 -1.885176147 -0.130218105 SLTFVQAGQDLEENMDEDISEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLTFVQAGQDLEENMDEDISEK 22 0 Q96RS6-2;Q96RS6;Q96RS6-3 Q96RS6-2 NUDCD1 NudC domain-containing protein 1 0 ;;; 270.35 2.68E-45 130924000 251435 237139 214893 204472 235041 249014 241414 269889 314927 286506 FALSE TRUE 241608.6422 230376.0279 253728.9454 215024.8244 242601.3072 254049.2337 244368.4967 264315.6978 279177.8072 267100.6934 0.904560146 0.862506289 0.949937427 0.80503282 0.908276591 0.951136556 0.914892783 0.989573237 1.045215584 1 18.0270242 1.885181379 1.094577326 1.025218643 0.886560391 0.628623811 0.040419065 0.308758961 0.680959482 0.031843348 0.013752717 76.76820368 -1.885181379 -0.138658252 LEDLLQDAQDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDLLQDAQDEK 12 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 167.3 0.00011537 85424000 218075 180760 185243 223950 181688 158864 239380 278290 314180 325020 FALSE TRUE 209552.3879 175604.9018 218720.5308 235508.0863 187532.1595 162076.3389 242309.604 272543.2142 278515.6036 303006.1059 0.691578103 0.579542453 0.721835391 0.777238748 0.618905546 0.53489463 0.799685549 0.89946443 0.919174888 1 18.20898734 1.885575242 2.6729875 0.936550824 0.658072998 0.760400076 0.071473754 0.14052012 1.803654521 0.041092759 0.021033811 76.83785672 -1.885575242 -0.278477826 DNSGMIDKNELK ddPTM_BT-474_Pertuzumab_2h_R1 4 DNSGMIDKNELK 12 1 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;; 191.49 4.83E-06 5356870000 4536750 4036360 3827030 3760390 3926840 3791500 4444990 5160360 5893860 5260940 FALSE TRUE 4359448.794 3921246.965 4518659.453 3954464.179 4053150.375 3868166.728 4499389.117 5053796.763 5224813.722 4904611.848 0.888846851 0.799501997 0.921308269 0.806274645 0.826395748 0.788679481 0.917379246 1.030417272 1.065285875 1 22.22570754 1.885699905 2.967980445 1.036635125 0.838762812 0.809995592 0.041743242 0.100715755 1.563464 0.021391784 0.01124927 76.85991598 -1.885699905 -0.197872313 SSVKT(ph)PEPVVPTAPEPHPTTSTDQPVTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSVKTPEPVVPTAPEPHPTTSTDQPVTPK 29 1 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.213)S(0.043)VKT(0.745)PEPVVPTAPEPHPTTSTDQPVTPK 158.99 1.09E-11 1055300000 417860 368820 333280 294360 365380 350570 380110 496920 530500 408070 TRUE FALSE 401529.5692 358301.6147 393511.1098 309551.9549 377132.7795 357658.7656 384761.8999 486658.4283 470279.864 380431.0554 1.055459494 0.941830615 1.034382194 0.813687396 0.991330161 0.940140823 1.011384046 1.279228973 1.236176325 1 18.5372755 1.88572798 5.362893771 1.195768289 0.960897102 0.502338093 0.092161085 0.15457944 6.100721685 0.039451995 0.023451759 76.86488472 -1.88572798 -0.234871187 TVTCVTVVEPEAPPS(ph)PDVLQAATHR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVTCVTVVEPEAPPSPDVLQAATHR 25 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR 207.99 1.93E-25 4523300000 1428220 1543500 1214800 1523300 1494580 1544480 1448220 1394740 1492300 1594450 TRUE FALSE 1372403.583 1499480.891 1434341.383 1601917.696 1542654.523 1575710.444 1465943.75 1365938.132 1322900.36 1486456.481 0.923271956 1.008762053 0.964940044 1.077675476 1.037806718 1.060044787 0.986200247 0.918922383 0.889969116 1 20.5034458 1.885777131 4.242119162 0.929307939 1.014542685 0.316331333 0.049180811 0.247937886 7.025681764 0.023686788 0.013481805 76.87358434 -1.885777131 0.085234746 YHRPEETHK ddPTM_BT-474_Pertuzumab_2h_R1 2 YHRPEETHK 9 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 114.5 0.00097861 89876000 130475 166783 137384 141522 142190 154996 135917 42942.9 108900 113333 FALSE TRUE 125375.8928 162026.5121 162212.3449 148825.9674 146763.6705 158130.1253 137580.3929 42056.11411 96538.12855 105656.855 1.186632829 1.533516327 1.53527516 1.408578435 1.389059617 1.496638579 1.302143557 0.39804435 0.913694891 1 16.68902685 1.88600348 6.228504866 0.724406495 1.429498436 0.735941149 0.175312494 0.100982848 4.813850102 0.072637542 0.044181265 76.91366034 -1.88600348 0.70509194 IEDVGS(ph)DEEDDSGKDK ddPTM_BT-474_Pertuzumab_2h_R1 24 IEDVGSDEEDDSGKDK 16 1 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.999)DEEDDS(0.001)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.998)DEEDDS(0.002)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.999)DEEDDS(0.001)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK 315.66 2.14E-57 2.31423E+11 21724037.4 17719334.8 15584201.8 14571767 15791589.7 14513825.4 18729734.5 23864620.3 26857058.5 21892123.6 TRUE FALSE 20875038 17213996.72 18400613.73 15323817.64 16299540.52 14807304.89 18958954.59 23371807.55 23808357.81 20409350.57 1.022817357 0.84343677 0.901577621 0.750823383 0.798631023 0.725515731 0.928934732 1.145151947 1.166541666 1 24.28272694 1.886014329 3.986649214 1.114565509 0.836621852 0.637746157 0.088294912 0.139158035 3.579866092 0.043266965 0.024319894 76.91558174 -1.886014329 -0.277943657 EHAPSIIFMDEIDSIGSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 EHAPSIIFMDEIDSIGSSR 19 0 P62195-2;P62195;J3QSA9;J3QQM1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;;;; 329.41 3.19E-75 1296180000 529925 555848 478258.6 602598 589159 627516 573503 420671.1 624044 596134 FALSE TRUE 509214.9451 539995.7593 564690.5678 633698.155 608109.8343 640204.8035 580521.7013 411984.0948 553205.1413 555757.3132 0.916254151 0.971639502 1.016074021 1.140242584 1.094200328 1.1519503 1.044559716 0.741302157 0.995407758 1 19.0840955 1.886076031 11.27042369 0.885221744 1.053680645 0.283101408 0.095839695 0.546703915 51.19938442 0.041087498 0.026241999 76.92651018 -1.886076031 0.168458901 HPDVEVDGFSELR ddPTM_BT-474_Pertuzumab_2h_R1 4 HPDVEVDGFSELR 13 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 237.41 9.62E-17 10373700000 4880030 5192700 4505570 5428530 5139720 5219300 5121730 2993350 5537870 5060520 FALSE TRUE 4689313.032 5044609.28 5319826.725 5708697.084 5305043.762 5324837.822 5184411.264 2931536.276 4909234.214 4717766.473 0.993968875 1.069279141 1.127615526 1.210042319 1.12448206 1.128677702 1.098912228 0.621382235 1.040584404 1 22.16967258 1.886091997 11.18676592 0.847957297 1.113311187 0.413829537 0.117331368 0.390649837 36.29113311 0.047087793 0.030065684 76.92933829 -1.886091997 0.265353891 ELEQNANHPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEQNANHPHR 11 0 Q9UL15-2;Q9UL15;G3V274 Q9UL15-2 BAG5 BAG family molecular chaperone regulator 5 0 ; 112.83 0.00085171 165038000 51262 56958 47007 61183 56340 59520 54338 11478.8 53923 45787 FALSE TRUE 49258.62437 55333.61361 55502.21057 64340.66196 58152.22727 60723.53518 55003.0047 11241.75877 47801.8871 42685.80571 1.153981366 1.296300086 1.300249805 1.50730813 1.362331724 1.422569732 1.288554914 0.263360585 1.119854394 1 15.38146879 1.886168864 9.131252301 0.723492487 1.345740447 0.534621025 0.227811297 0.214025776 15.87878515 0.090965655 0.057480192 76.9429555 -1.886168864 0.62224796 AEGEPQEES(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEGEPQEESPLK 12 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEPQEES(1)PLK;AEGEPQEES(1)PLK;AEGEPQEES(1)PLK;AEGEPQEES(1)PLK 189.09 8.77E-06 3476590000 4789480 4351930 4070600 4161140 4350820 4203880 4888990 5771160 6190400 6403530 TRUE FALSE 4602301.827 4227817.217 4806247.97 4375896.934 4490768.077 4288885.334 4948822.922 5651983.529 5487691.744 5969813.209 0.77092895 0.708199247 0.805091852 0.733003995 0.752245995 0.718428732 0.8289745 0.946760532 0.919240109 1 22.50925436 1.886175739 2.526182772 0.954576953 0.748256989 0.892224284 0.032161454 0.079774701 0.922745747 0.017054133 0.008600285 76.94417356 -1.886175739 -0.206319964 FTLRDEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 FTLRDEGK 8 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ;;; 131.22 0.00092503 1974720000 1687190 1703680 1215860 1282190 1480410 1498520 1531750 1637600 1869950 1685750 FALSE TRUE 1621252.75 1655092.714 1435592.949 1348363.98 1528028.732 1528821.101 1550496.015 1603782.988 1657681.115 1571572.651 1.03161171 1.053144259 0.913475395 0.85797114 0.972292774 0.972796962 0.986588825 1.020495608 1.054791272 1 20.58377754 1.886264763 2.014296329 1.0300365 0.963314467 0.193542071 0.052915023 0.561142517 4.23689764 0.036569699 0.017264457 76.95994751 -1.886264763 -0.066722033 QSQQPMKPIS(ph)PVKDPVS(ph)PASQK ddPTM_BT-474_Pertuzumab_2h_R1 4 QSQQPMKPISPVKDPVSPASQK 22 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 QS(0.001)QQPMKPIS(0.999)PVKDPVS(0.944)PAS(0.056)QK;QS(0.006)QQPMKPIS(0.994)PVKDPVS(1)PASQK;QSQQPMKPIS(1)PVKDPVS(1)PASQK;QSQQPMKPIS(1)PVKDPVS(0.999)PAS(0.001)QK 201.39 8.22E-23 2169560000 3042390 2195490 2147870 1732740 2392460 2356650 2659910 3422890 4007600 3336710 TRUE FALSE 2923490.035 2132876.775 2536037.888 1822166.919 2469415.649 2404303.078 2692462.774 3352206.125 3552674.049 3110711.66 0.939813893 0.68565557 0.815259711 0.58577172 0.79384267 0.772910942 0.865545595 1.077633189 1.142077582 1 21.56881324 1.886321676 2.401230238 1.088657255 0.756829833 0.690993489 0.091657881 0.149031129 1.568827355 0.050617602 0.02516709 76.97003365 -1.886321676 -0.331827422 DEHCWVGELNGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEHCWVGELNGLR 13 0 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 ; 112.08 0.0004178 0 106934 118954 104342 113828 117100 117872 116263 92170 123123 133702 FALSE TRUE 102754.9011 115561.5484 123198.9205 119702.6767 120866.6278 120255.4526 117685.8614 90266.65729 109146.5932 124646.2445 0.824372218 0.927116167 0.988388547 0.960339216 0.969677252 0.964773974 0.944158903 0.724182728 0.875650877 1 16.92747989 1.886355031 24.97841329 0.835512756 0.944118709 0.122413448 0.076806671 26.0558795 5692.097047 0.0306184 0.019760857 76.97594525 -1.886355031 0.108605953 T(ph)SSDSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.166)S(0.166)S(0.166)DS(0.166)ALHT(0.166)S(0.166)VMNPS(0.004)PQDT(0.001)YPGPTPPSILPSR;T(0.333)S(0.333)S(0.333)DSALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.332)S(0.332)S(0.332)DS(0.003)ALHTSVMNPSPQDTYPGPTPPSILPSR 236.9 4.64E-46 2886160000 250067 354491 242879 329649 270316 291138 283944 273211 261080 312382 TRUE FALSE 240294.1052 344381.2638 286772.6381 346662.2244 279010.9596 297025.0098 287418.9916 267569.0974 231443.2929 291224.0889 0.825117545 1.182530144 0.984714689 1.190362465 0.958062778 1.019919097 0.986934126 0.918773919 0.794725786 1 18.15177017 1.88636065 1.88512792 0.889167507 1.03796363 0.19431406 0.10975188 0.462337266 3.070569287 0.065837421 0.030483388 76.97694117 -1.88636065 0.148796123 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR ddPTM_BT-474_Pertuzumab_2h_R1 3 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR 32 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;; 346.66 9.55E-132 15381541000 2390864.7 2677074.5 2093082.8 2984618.8 2796978.1 2393927.3 2632121.7 1719088.9 2862410.3 3136475.1 FALSE TRUE 2297427.064 2600726.956 2471349.422 3138655.334 2886945.441 2442334.15 2664334.393 1683589.113 2537481.483 2924038.848 0.785703332 0.889429687 0.845183512 1.073397276 0.987314325 0.8352605 0.911182967 0.575775221 0.867800195 1 21.47953105 1.886372316 20.28276351 0.761393011 0.908245241 0.048367932 0.126855971 8.222871676 1449.187513 0.051493301 0.033216494 76.97900903 -1.886372316 0.14685223 KPGPSGPSES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 KPGPSGPSESPK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPSGPSES(1)PK;KPGPSGPS(0.003)ES(0.997)PK;KPGPSGPS(0.015)ES(0.985)PK;KPGPSGPS(0.005)ES(0.995)PK 144.41 3.86E-05 3060790000 4186410 3451590 2798751 2757916 2985283 2936883 3315800 4053450 4075530 3906090 TRUE FALSE 4022800.469 3353154.033 3304547.564 2900252.375 3081307.339 2996268.786 3356379.752 3969744.841 3612892.92 3641527.045 1.104701522 0.920809867 0.907462041 0.79643851 0.846158027 0.822805584 0.921695682 1.090131912 0.992136781 1 21.79611213 1.886511222 6.018691313 1.033031468 0.892327441 0.321938123 0.082712862 0.26081151 11.95067197 0.038110902 0.023071123 77.00363411 -1.886511222 -0.140704027 LNEQAS(ph)EEILKVEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LNEQASEEILKVEQK 15 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 LNEQAS(1)EEILKVEQK;LNEQAS(1)EEILKVEQK;LNEQAS(1)EEILKVEQK;LNEQAS(1)EEILKVEQK 219.22 1.11E-12 915200000 1078739 835772 714485 574120 792430 789577 840448 1041950 1142259 908924 TRUE FALSE 1036580.687 811936.6009 843608.3331 603750.402 817919.2306 805542.7879 850733.654 1020433.368 1012594.547 847361.7679 1.223303584 0.958193574 0.995570446 0.712506069 0.965253876 0.950648021 1.003979276 1.204247592 1.194996736 1 19.69261851 1.886531322 4.725198399 1.150401335 0.958117993 0.250349964 0.126460208 0.276314618 9.199045117 0.059195083 0.034415876 77.00719806 -1.886531322 -0.192283343 SASSGAEGDVSS(ph)EREP ddPTM_BT-474_Pertuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SASSGAEGDVS(0.009)S(0.991)EREP;SASSGAEGDVS(0.079)S(0.921)EREP 221.34 5.37E-13 177100000 751650 783000 583590 686830 666220 734700 634190 737180 722930 689860 TRUE FALSE 722274.687 760669.6066 689057.6949 722277.3786 687649.5713 749556.1374 641951.4069 721956.9754 640866.0172 643135.1677 1.123052701 1.182752312 1.071404161 1.123056886 1.069214694 1.165472167 0.99815939 1.122558696 0.996471736 1 19.29476246 1.886568035 0.242065242 0.976829055 1.168452141 0.419076445 0.050197392 2.125846074 0.48536273 0.12377652 0.158529298 77.01370824 -1.886568035 0.191623086 GTHHSQNPSPGSSS(ph)PRPSVVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTHHSQNPSPGSSSPRPSVVGR 22 1 J3KT00;A0A1W2PQI7;A0A1W2PPP3;Q86VV8-4;Q86VV8-3;Q86VV8;J3KTD2;Q86VV8-2 J3KT00 RTTN Rotatin 1 GTHHSQNPS(0.057)PGS(0.265)S(0.265)S(0.411)PRPS(0.001)VVGR 150.94 3.16E-08 183390000 18870 44225 33340 53170 43203 48397 38440 12312 27012 38971 TRUE FALSE 18132.53954 42963.7463 39365.27964 55914.11007 44592.66373 49375.6205 38910.44022 12057.7529 23945.711 36331.45946 0.499086461 1.18254942 1.083503945 1.538999834 1.227384322 1.359032124 1.070984783 0.331881875 0.659090258 1 15.1489317 1.886667571 6.544404397 0.606064922 1.17165374 0.347670914 0.294522949 0.227706891 11.55763894 0.127371166 0.077990888 77.03136093 -1.886667571 0.565588818 KDDEENYLDLFSHK ddPTM_BT-474_Pertuzumab_2h_R1 5 KDDEENYLDLFSHK 14 1 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;;; 275.18 3.01E-33 14566750000 24010500 19936400 18749100 17728800 20294000 20394800 22113000 24566200 28655400 25792200 FALSE TRUE 23072143.11 19367833.39 22137479.44 18643785.49 20946774.94 20807196.83 22383625.51 24058899.39 25402559.13 24045271.32 0.959529331 0.805473689 0.920658334 0.775361827 0.871139055 0.86533425 0.930895111 1.000566767 1.056447182 1 24.51924987 1.886712676 1.891980662 1.028936926 0.861087638 0.645981689 0.050690398 0.188586514 1.261246957 0.030320323 0.014057492 77.0393617 -1.886712676 -0.167849288 GHPEFSTNR ddPTM_BT-474_Pertuzumab_2h_R1 4 GHPEFSTNR 9 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 139.78 0.00011066 2057280000 96955 153087 144906 208514 201214 202949 145752 68056 86037 116876 FALSE TRUE 93165.89141 148721.1086 171093.7376 219275.4325 207686.231 207052.7678 147535.7566 66650.61982 76270.44046 108959.8844 0.855047634 1.364916175 1.570245219 2.012441861 1.906079766 1.900266038 1.354037381 0.611698702 0.69998643 1 16.73343755 1.886826786 4.144257675 0.74692493 1.622696836 0.563231075 0.325756794 0.172983518 4.737479994 0.169674448 0.096174909 77.05960626 -1.886826786 0.875771906 ELAILLGMLDPAEKDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELAILLGMLDPAEKDEK 17 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ; 112.91 0.00045927 355920000 474000 395460 329130 318040 387270 326010 415550 498520 591220 456460 FALSE TRUE 455475.556 384181.868 388611.1125 334454.0825 399726.8913 332602.1456 420635.6252 488225.3878 524107.1842 425543.5576 1.070338272 0.902802689 0.913211128 0.78594559 0.939332494 0.781593657 0.988466674 1.147298271 1.231618185 1 18.69894728 1.886857945 3.648357318 1.139577419 0.895613104 0.539120526 0.093299634 0.166205966 3.701780826 0.044983123 0.024828094 77.0651353 -1.886857945 -0.243964316 DS(ph)LSPVLHPSDLILTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 DS(0.587)LS(0.413)PVLHPSDLILTR 92.492 0.0030616 88344000 79987 109340 98413 125210 118330 126260 101000 88648 84090 106720 TRUE FALSE 76861.01961 106221.7303 116198.4183 131672.1031 122136.1919 128813.0637 102236.0682 86817.38782 74544.45573 99491.75934 0.772536541 1.067643501 1.167920027 1.323447328 1.227601087 1.294710884 1.027583278 0.872608831 0.749252563 1 16.60228942 1.886894327 3.337835141 0.860725047 1.152708958 0.369043067 0.15531488 0.260644814 4.984997019 0.083372401 0.045119921 77.07159146 -1.886894327 0.29198391 EERLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 EERLSPR 7 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 EERLS(1)PR;EERLS(1)PR;EERLS(1)PR 125.74 0.0024347 631390000 910450 1053500 837980 1002410 1008600 1014090 876110 875240 812630 910370 TRUE FALSE 874868.6074 1023455.211 989421.6268 1054144.5 1041042.535 1034595.595 886832.0963 857165.9881 720383.6492 848709.829 1.030821816 1.205895321 1.165794943 1.242055252 1.226617743 1.219021577 1.044917905 1.009963546 0.848798523 1 19.69491186 1.886993608 1.940902311 0.935854566 1.186179534 0.686190416 0.069730434 0.179766127 1.263268232 0.043439602 0.020295738 77.08921235 -1.886993608 0.250324968 VESEQHGDRLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VESEQHGDRLPR 12 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ; 150.49 4.10E-05 221490000 108157 147487 102506 116913 110855 145369 116540 109098 116674 119262 FALSE TRUE 103930.1049 143280.8152 121031.1144 122946.8939 114420.7518 148308.4608 117966.2514 106845.0882 103429.6567 111184.2785 0.934755401 1.288678733 1.088563204 1.105793873 1.029109091 1.333897767 1.060997589 0.960972987 0.930254331 1 16.76259328 1.887008228 4.225558885 0.96314104 1.134054483 0.309582441 0.110025998 0.260309417 7.349921166 0.049841689 0.028364499 77.0918075 -1.887008228 0.170913442 HS(ph)LS(ph)GSSPGMK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HS(0.968)LS(0.39)GS(0.373)S(0.269)PGMK;HS(0.999)LS(0.628)GS(0.206)S(0.167)PGMK 79.633 0.022908 0 669640 696500 735010 807230 722870 677460 749740 375030 981300 813120 TRUE FALSE 643469.7285 676636.5019 867842.6572 848891.237 746121.77 691158.7054 758915.5424 367285.4994 869906.9379 758046.6581 0.848852404 0.892605349 1.144840687 1.119840353 0.984268926 0.91176275 1.001146215 0.48451569 1.147563845 1 19.53192712 1.887241543 19.89384171 0.800757004 0.990968149 0.020614233 0.183462089 8.47186949 1476.159094 0.074637872 0.048142219 77.13323449 -1.887241543 0.190211145 VS(ph)PATPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPATPK 7 0 J3KNZ9;Q9HAH7;Q9HAH7-1 J3KNZ9 FBRS Probable fibrosin-1 1 VS(1)PATPK;VS(1)PATPK 119.07 0.0051031 439610000 869190 813510 734530 700880 784390 825580 866870 984340 1158190 1036070 TRUE FALSE 835221.0939 790309.4913 867275.9105 737052.5008 809620.6167 842273.7932 877479.0144 964013.035 1026717.127 965896.0561 0.864711155 0.818213809 0.897897766 0.763076416 0.838206774 0.872012871 0.908461122 0.998050493 1.062968546 1 19.88150842 1.887399997 1.606141098 1.034647621 0.836917026 0.830853371 0.036200792 0.136707168 0.660782695 0.024410183 0.010839631 77.16138194 -1.887399997 -0.197730595 S(ph)HHAASTTTAPTPAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHHAASTTTAPTPAAR 16 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(1)HHAASTTTAPTPAAR;S(1)HHAASTTTAPTPAAR 155.79 1.45E-07 423290000 202207 232678 208538 228090 205563 230193 209132 27656.9 205476 147374 TRUE FALSE 194304.5269 226042.2513 246225.4555 239861.7522 212175.1206 234847.6602 211691.42 27085.77535 182151.2259 137392.2277 1.414232305 1.645233177 1.792135258 1.745817476 1.544302208 1.709322748 1.540781626 0.197141977 1.325775329 1 17.06794087 1.88748769 8.053976155 0.771155121 1.646634654 0.62075198 0.280975264 0.157729994 10.25001467 0.112282612 0.070287048 77.176964 -1.88748769 0.875479534 SDKS(ph)PDLAPTPAPQSTPR ddPTM_BT-474_Pertuzumab_2h_R1 8 SDKSPDLAPTPAPQSTPR 18 1 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;Q9BY44-2 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 1 SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(0.992)PDLAPT(0.008)PAPQSTPR;S(0.002)DKS(0.998)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(0.882)PDLAPT(0.118)PAPQSTPR;S(0.008)DKS(0.992)PDLAPTPAPQSTPR 249.51 6.71E-25 28830100000 11063652 9665894 8778253 8456410 9261299 9598098 10299351 11583021 13151395 12222515 TRUE FALSE 10631272.25 9390232.167 10364678.59 8892846.334 9559197.093 9792178.118 10425397.54 11343827.57 11658503.77 11394673.17 0.933003702 0.824089645 0.909607361 0.780438912 0.838918058 0.859364544 0.914936074 0.995537774 1.023153854 1 23.44185621 1.887540077 2.062385172 1.012915298 0.85352374 0.731182173 0.040332523 0.154030204 1.216402056 0.024118514 0.01147866 77.186274 -1.887540077 -0.159391558 EAAAAALKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAAAAALKK 9 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 118.18 0.0016542 574020000 667510 618340 476710 470730 586150 558830 598190 667980 736410 705360 FALSE TRUE 641422.9712 600705.5486 562862.1014 495024.4317 605004.0471 570129.9255 605510.8282 654185.9796 652815.8241 657585.3389 0.975421642 0.91350204 0.855952936 0.752791162 0.920038832 0.867005226 0.920809502 0.994830543 0.992746926 1 19.32681861 1.887563797 2.485761314 0.997958085 0.876933512 0.475121955 0.053861267 0.259113514 2.908337859 0.03233006 0.016248744 77.19048986 -1.887563797 -0.121024573 TPLDLFAHFGPEPGDHS(ph)DPLPPSAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 2 TPLDLFAHFGPEPGDHS(1)DPLPPS(0.017)APS(0.942)PT(0.04)R 92.387 0.00067544 19910000 12094 13195 10491 12225 11153 14191 12217 6550.3 12335 12588 TRUE FALSE 11621.35311 12818.69152 12386.95707 12855.93372 11511.74637 14477.95174 12366.5153 6415.034016 10934.78251 11735.40355 0.990281507 1.092309392 1.055520334 1.095482883 0.980941672 1.23369867 1.053778445 0.546639405 0.93177729 1 13.51857983 1.887636776 9.93221495 0.780158775 1.07719207 0.417626083 0.129696289 0.295424799 24.37694081 0.051153004 0.032484982 77.20346211 -1.887636776 0.297033295 HRMS(ph)PGVAGSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HRMSPGVAGSPR 12 1 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR 136.26 6.85E-05 1107570000 202211 244982 194423 202109 216883 225554 216194 166535 230479 224633 TRUE FALSE 194308.3706 237995.3532 229559.561 212539.8697 223859.2387 230114.8564 218839.8468 163095.9941 204315.9902 209418.4068 0.927847621 1.136458618 1.096176618 1.014905389 1.068956841 1.098828226 1.044988596 0.778804483 0.9756353 1 17.67602873 1.8877348 8.801867547 0.896725625 1.061978681 0.392390986 0.07690266 0.258206114 18.60358538 0.030683062 0.01934105 77.22088944 -1.8877348 0.165253055 NS(ph)PATLFEVPDTW ddPTM_BT-474_Pertuzumab_2h_R1 3 NSPATLFEVPDTW 13 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 NS(0.5)PAT(0.5)LFEVPDTW;NS(0.5)PAT(0.5)LFEVPDTW;NS(0.5)PAT(0.5)LFEVPDTW 76.465 0.029996 54325000 96671 92479 96339 106408 95435 101818 114269 138214 135024 151248 TRUE FALSE 92892.99044 89841.58947 113749.6003 111899.7296 98504.75345 103876.8297 115667.4582 135359.8326 119696.6416 141003.8382 0.658797602 0.637157049 0.806712794 0.793593501 0.698596256 0.73669505 0.820314253 0.959972681 0.848889244 1 17.10537491 1.887911926 0.562895867 0.998326216 0.69180538 0.717303967 0.06040545 0.445934626 0.300690823 0.062157317 0.040104789 77.25239033 -1.887911926 -0.306520836 S(ph)PVGKS(ph)PPSTGSTYGSSQK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(1)PVGKS(0.886)PPS(0.097)T(0.017)GSTYGSSQK;S(1)PVGKS(0.683)PPS(0.29)T(0.026)GS(0.001)TYGSSQK;S(1)PVGKS(0.633)PPS(0.317)T(0.049)GS(0.001)TYGSSQK 153.77 2.41E-08 2965030000 1433410 1118750 1477830 1541220 1454520 1311190 1806430 2306200 2637000 2542010 TRUE FALSE 1377390.752 1086844.345 1744906.755 1620762.549 1501305.957 1337703.16 1828537.631 2258576.164 2337658.815 2369837.399 0.581217409 0.458615577 0.736298092 0.683912976 0.633505893 0.56447044 0.771587803 0.95305111 0.986421607 1 21.17635664 1.887917836 2.288042837 0.98870237 0.612647003 0.844737113 0.070960803 0.116580188 1.120807958 0.04427404 0.021736116 77.25344157 -1.887917836 -0.376055367 SLENYHFVDEHGKDQGINIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLENYHFVDEHGKDQGINIR 20 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 241.68 6.06E-30 1221930000 875800 1026880 688350 776170 846740 957830 879060 409220 1019460 880140 FALSE TRUE 841572.7678 997594.3878 812750.1573 816228.2267 873976.1611 977197.9789 889818.1992 400769.464 903735.1747 820527.3339 1.025648669 1.215796655 0.990521734 0.994760556 1.065139606 1.190938971 1.084446748 0.488429145 1.101407762 1 19.64619187 1.888070628 22.90601931 0.801422058 1.083093343 0.241480747 0.166321658 12.49164762 2539.141295 0.065504406 0.042270111 77.28062539 -1.888070628 0.281671284 S(ph)IDPDSIQSALLASGLGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIDPDSIQSALLASGLGSK 19 0 A3KN83-3;A3KN83-2;A3KN83 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 S(0.672)IDPDS(0.255)IQS(0.073)ALLASGLGSK 67.928 0.02629 80176000 36898 42014 41613 45677 36731 43190 38058 37725 40359 36727 TRUE FALSE 35455.98537 40815.80186 49133.39478 48034.39544 37912.48597 44063.33139 38523.76519 36945.96557 35777.61552 34239.44758 1.035530298 1.192069521 1.434993794 1.402896333 1.107275048 1.286917124 1.125128117 1.079046777 1.044923854 1 15.0633718 1.888160267 1.238181301 1.016197273 1.256682842 0.384218993 0.115184588 0.490713754 1.39242983 0.094179695 0.04042598 77.2965779 -1.888160267 0.240485569 DHGGIFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHGGIFSR 8 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 0 ; 146.69 0.00054923 515600000 76397 89819 80831 85299 101612 92132 87822 46055 83866 94173 FALSE TRUE 73411.32078 87257.45006 95438.95978 89701.29161 104880.4423 93994.97216 88896.79191 45103.94816 74345.88327 87794.57883 0.836171456 0.993881983 1.087071218 1.021717887 1.194611828 1.070623875 1.012554455 0.513744114 0.846816333 1 16.42184424 1.888179222 9.125466946 0.738103255 1.041222646 0.368912649 0.142104585 0.284259647 21.41494071 0.058390013 0.036896928 77.29995156 -1.888179222 0.303119391 EGLELPEDEEEKK ddPTM_BT-474_Pertuzumab_2h_R1 6 EGLELPEDEEEKK 13 1 P08238;Q58FF7;Q58FF6;P07900;P07900-2;Q58FG0 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AA5P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ;;;;; 192.18 4.71E-06 21366800000 11773210 9053440 8901220 7684620 9516760 9288510 10785900 14734120 16203060 13605060 FALSE TRUE 11313099.94 8795244.755 10509868.46 8081224.159 9822875.228 9476330.036 10917901.07 14429855.27 14363756.56 12683577.17 0.891948682 0.693435664 0.828620217 0.637140773 0.77445622 0.747133865 0.860790369 1.137680252 1.13246889 1 23.59645835 1.888189125 3.374718507 1.101627332 0.758455911 0.792380435 0.074780293 0.095368517 1.861030106 0.035883643 0.019485736 77.3017142 -1.888189125 -0.343171421 LSAEERDQLLPNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSAEERDQLLPNLR 14 1 P61457 P61457 PCBD1 Pterin-4-alpha-carbinolamine dehydratase 0 ; 178.67 1.78E-06 372520000 105678 121077 112638 91804 129015 120315 109724 97263 116500 97966 FALSE TRUE 101547.9869 117624.0025 132994.1922 96542.01544 133164.8846 122747.8517 111066.8351 95254.48506 103275.4084 91330.67556 1.111871628 1.287891519 1.456183165 1.057060126 1.458052115 1.343993691 1.216095627 1.042962668 1.130785552 1 16.47881188 1.888354268 3.615283984 1.065516217 1.290800726 0.399842456 0.124311532 0.24130856 5.301573958 0.060187682 0.033187209 77.33111428 -1.888354268 0.225284509 TVSLTPSPT(ph)TQVETPDLVDHDNTSPLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVS(0.001)LT(0.018)PS(0.087)PT(0.425)T(0.425)QVET(0.042)PDLVDHDNT(0.001)SPLFR 86.982 0.013121 692830000 21930 14922 14043 21168 20751 18677 19120 34449 24088 22573 TRUE FALSE 21072.95136 14496.43917 16580.88248 22260.48302 21418.47476 19054.66174 19353.99628 33737.61611 21353.63123 21044.1106 1.00137049 0.688859674 0.787910822 1.057801084 1.017789498 0.905462915 0.919687063 1.603185649 1.014708183 1 14.36112892 1.888426462 12.96095867 1.270804585 0.906507015 0.323454921 0.188443205 0.717346683 80.12341909 0.0766715 0.049183988 77.34397028 -1.888426462 -0.36429757 SHEGETAYIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SHEGETAYIR 10 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 176.43 2.65E-06 6708290000 1803960 1841480 1486800 1645230 1687090 1595550 1711760 1203548 2006220 1801820 FALSE TRUE 1733459.249 1788962.793 1755497.834 1730140.517 1741356.782 1627813.114 1732709.031 1178694.313 1778482.316 1679781.127 1.031955426 1.064997555 1.045075341 1.029979734 1.036656952 0.969062629 1.03150881 0.701695176 1.058758363 1 20.67984183 1.888745758 20.06720911 0.881886245 1.029813188 0.201254934 0.091062023 5.756431554 1027.592634 0.035685332 0.023018299 77.40085491 -1.888745758 0.147926943 RVES(ph)EES(ph)GDEEGKK ddPTM_BT-474_Pertuzumab_2h_R1 6 RVESEESGDEEGKK 14 2 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 2 RVES(1)EES(1)GDEEGKK;RVES(1)EES(1)GDEEGKK;RVES(1)EES(1)GDEEGKK;RVES(1)EES(1)GDEEGKK;RVES(1)EES(1)GDEEGKK;RVES(1)EES(1)GDEEGKK 143.4 4.49E-05 5887370000 14281720 9963300 9930750 8338930 10662840 9622930 12003150 15255790 17834820 13983990 TRUE FALSE 13723574.59 9679156.439 11725457.43 8769303.177 11005819.93 9817512.238 12150048.14 14940752.61 15810286 13036841.9 1.052676307 0.742446408 0.899409345 0.672655482 0.844209051 0.753059085 0.931977869 1.146040791 1.212738953 1 23.63609109 1.888772322 3.32343069 1.133559697 0.82110978 0.586858095 0.108961621 0.153552444 2.918571981 0.052451909 0.028395873 77.40558934 -1.888772322 -0.312449917 EESYS(ph)PSKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESYSPSKDR 10 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 EESYS(0.902)PS(0.098)KDR;EES(0.002)YS(0.996)PS(0.003)KDR 166.24 1.48E-05 1682070000 1988140 1901500 1690150 1653160 1763790 1781810 1958630 2245590 2527320 2297810 TRUE FALSE 1910441.291 1847271.082 1995597.702 1738479.786 1820523.907 1817839.419 1982600.3 2199217.782 2240429.229 2142177.282 0.891822216 0.862333429 0.931574487 0.811548045 0.849847453 0.848594294 0.925507107 1.026627348 1.04586546 1 21.03064645 1.888831701 2.807649122 1.028522382 0.865901492 0.834137608 0.031460371 0.100121374 1.406179946 0.017232682 0.008957651 77.41617352 -1.888831701 -0.16262089 EREEIEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EREEIEK 7 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;; 133.86 0.0029461 7591400000 3796500 3668300 3005020 3065470 3341470 3465760 3548850 3935800 4399400 4022200 FALSE TRUE 3648128.583 3563683.676 3548093.96 3223679.274 3448951.417 3535840.042 3592281.888 3854524.355 3899998.556 3749772.811 0.97289323 0.950373224 0.946215715 0.85969989 0.919776101 0.942947805 0.957999876 1.027935437 1.040062626 1 21.83837176 1.888872212 2.485806572 1.026990452 0.929602617 0.652102141 0.029500257 0.178828488 2.006928715 0.017934306 0.009023083 77.42339513 -1.888872212 -0.097387835 DKEVS(ph)DDEAEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DKEVSDDEAEEK 12 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK 265.43 3.34E-21 5019940000 5186850 3630420 5074350 3736530 4384950 3907290 5565330 7560730 8846590 7419570 TRUE FALSE 4984142.168 3526883.976 5991397.923 3929372.761 4525995.899 3986298.081 5633440.173 7404598.283 7842362.191 6917035.915 0.7205604 0.509883716 0.866179964 0.568071759 0.654325921 0.576301487 0.814429799 1.070487182 1.133774971 1 22.72172252 1.888928144 2.864513068 1.079356801 0.650018696 0.785562899 0.097569989 0.108321673 1.578011382 0.049427189 0.025826006 77.43336709 -1.888928144 -0.429338106 RQVDEGVWPPPNNLLSQS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 RQVDEGVWPPPNNLLSQSPK 20 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RQVDEGVWPPPNNLLS(0.037)QS(0.963)PK;RQVDEGVWPPPNNLLS(0.052)QS(0.948)PK;RQVDEGVWPPPNNLLSQS(1)PK;RQVDEGVWPPPNNLLSQS(1)PK 217.69 6.37E-25 1141510000 932415 911393 774974 840487 864236 900940 885463 1032911 980099 930568 TRUE FALSE 895975.191 885400.964 915029.041 883864.6348 892034.9358 919157.6241 896299.5611 1011581.027 868842.2704 867539.8005 1.032777044 1.020588293 1.054740129 1.018817389 1.028235172 1.059499084 1.033150941 1.166034142 1.001501337 1 19.72657042 1.888934207 22.04799656 1.080618753 1.035577755 0 0.046441582 17.49308535 3448.200048 0.018293059 0.011803401 77.43444797 -1.888934207 -0.045040998 ART(ph)PLTAAQQK ddPTM_BT-474_Pertuzumab_2h_R1 4 ARTPLTAAQQK 11 1 I3L2J0 I3L2J0 CIC 1 ART(1)PLTAAQQK;ART(1)PLTAAQQK;ART(1)PLTAAQQK;ART(1)PLTAAQQK 194.59 7.18E-07 2407950000 2044130 1778710 1431660 1898980 1628330 1759950 1884460 2665630 2463720 2328390 TRUE FALSE 1964243.14 1727982.932 1690392.809 1996986.585 1680706.713 1795537.395 1907522.585 2610583.809 2184048.834 2170686.071 0.904895077 0.796053817 0.778736654 0.919979453 0.774274427 0.827175066 0.878764834 1.20265378 1.006156009 1 21.04971967 1.888983077 6.184135226 1.084806882 0.83243202 0.699340843 0.069266122 0.111794289 5.361172245 0.028845062 0.017537375 77.44316197 -1.888983077 -0.252374862 AGDRNS(ph)EDDGVVMTFSSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGDRNSEDDGVVMTFSSVK 19 1 Q9NY61 Q9NY61 AATF Protein AATF 1 AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK 259.49 1.19E-30 1111150000 1377540 1184350 1285770 1519480 1329820 1184120 1580140 2042260 2294780 2028840 TRUE FALSE 1323704.214 1150573.498 1518137.241 1597900.545 1372594.868 1208063.718 1599478.226 2000086.617 2034286.195 1891424.86 0.699844991 0.608310445 0.80264211 0.844813124 0.725693575 0.638705636 0.845647247 1.057449682 1.075531066 1 20.85104203 1.889007033 3.25324506 1.049492618 0.724904875 0.816574976 0.068483714 0.107135015 1.961521012 0.037873974 0.020407376 77.44743401 -1.889007033 -0.324587744 KADS(ph)DSEDKGEESKPK ddPTM_BT-474_Pertuzumab_2h_R1 7 KADSDSEDKGEESKPK 16 3 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 1 KADS(0.5)DS(0.5)EDKGEESKPK;KADS(0.999)DS(0.001)EDKGEESKPK;KADS(0.819)DS(0.181)EDKGEESKPK;KADS(0.796)DS(0.204)EDKGEESKPK;KADS(1)DSEDKGEESKPK;KADS(1)DSEDKGEESKPK;KADS(0.805)DS(0.195)EDKGEESKPK 200.1 2.60E-11 35934870000 12537880 7117140 6380540 4624790 6648980 5572600 8408500 11507450 14293470 8737640 TRUE FALSE 12047885.79 6914166.136 7533645.512 4863475.966 6862850.48 5685281.79 8511405.738 11269817.14 12670935.21 8145831.86 1.47902461 0.848798042 0.924846675 0.597050866 0.842498421 0.697937533 1.044878643 1.383507213 1.555511509 1 22.9576306 1.889123291 3.823752064 1.347314203 0.880193856 0.341799354 0.253986654 0.236253277 5.707065088 0.122880509 0.06860082 77.46816901 -1.889123291 -0.467120347 DLS(ph)LEEIQKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLSLEEIQKK 10 1 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN2 Stathmin;Stathmin-2 1 DLS(1)LEEIQKK 50.897 0.098085 151600000 130610 134470 127860 128500 129580 128330 143200 153450 179090 161650 TRUE FALSE 125505.6168 130635.0473 150967.1462 135131.9004 133748.0584 130924.9205 144952.5244 150281.2039 158760.454 150701.3015 0.832810437 0.866847505 1.001764051 0.896687016 0.887504335 0.868771001 0.961853169 0.997212382 1.053477657 1 17.20133235 1.889146491 2.227983439 1.0227139 0.89648412 0.617487602 0.043942127 0.214797947 1.963614366 0.027165532 0.013246361 77.47230746 -1.889146491 -0.12622978 RKEEEEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 RKEEEEAK 8 2 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 0 ;; 123.86 0.00074778 1052410000 993100 840360 721089 666918 776710 738850 840150 967590 1066570 960240 FALSE TRUE 954288.5541 816393.7556 851405.8228 701337.7179 801693.5825 753790.0532 850432.007 947608.9284 945497.445 895202.0895 1.066003493 0.911965874 0.951076671 0.783440662 0.895544807 0.842033393 0.949988854 1.058541909 1.056183242 1 19.77185388 1.889149581 4.086081798 1.041785331 0.903602417 0.402142679 0.070359399 0.222682124 5.99086991 0.03441497 0.019476522 77.47285862 -1.889149581 -0.138182913 KLQEDGLLSNVSHVIVDEVHER ddPTM_BT-474_Pertuzumab_2h_R1 1 KLQEDGLLSNVSHVIVDEVHER 22 1 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 99.366 0.00041433 22583000 31853 31089 22718 28740 31268 31766 29146 16709 29871 28596 FALSE TRUE 30608.14954 30202.37216 26823.64796 30223.27484 32273.76362 32408.33028 29502.69747 16363.95331 26480.16931 26659.16745 1.148128485 1.132907553 1.006169754 1.133691624 1.210606583 1.215654253 1.106662371 0.613820868 0.993285682 1 14.70234411 1.889176164 8.759556786 0.832036931 1.139287131 0.529099769 0.11430736 0.212492201 15.4038536 0.047024157 0.029633224 77.47760091 -1.889176164 0.3072502 KRS(ph)PS(ph)PSPTPEAK ddPTM_BT-474_Pertuzumab_2h_R1 6 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.902)PS(0.661)PS(0.437)PTPEAK;KRS(0.894)PS(0.938)PS(0.168)PTPEAK;KRS(1)PS(0.973)PS(0.027)PTPEAK;KRS(0.997)PS(0.994)PS(0.009)PTPEAK;KRS(0.986)PS(0.92)PS(0.095)PTPEAK;KRS(0.996)PS(0.941)PS(0.063)PTPEAK 219.58 1.19E-11 13645840000 7621920 6541260 5337850 5008650 5780000 5719710 6362490 7478890 8392890 6936540 TRUE FALSE 7324046.94 6354709.669 6302518.235 5267147.027 5965918.949 5835366.455 6440356.056 7324448.308 7440164.313 6466721.967 1.132574893 0.982678659 0.974607887 0.814500307 0.922556897 0.902368539 0.995922832 1.13263696 1.150531034 1 22.62460315 1.889187861 4.276636052 1.105271225 0.949109986 0.350805231 0.084012995 0.236271202 6.828101348 0.041303704 0.023588474 77.47968758 -1.889187861 -0.156161238 DHAPSIPTS(ph)PFGDSLESSTELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHAPSIPTSPFGDSLESSTELRR 23 1 J3QL92;Q9Y4B5-2;Q9Y4B5-3;Q9Y4B5 J3QL92 MTCL1 Microtubule cross-linking factor 1 1 DHAPSIPT(0.008)S(0.991)PFGDSLESSTELRR;DHAPSIPT(0.122)S(0.876)PFGDSLESSTELRR 110.83 0.00047877 111596000 69939 89642 75233 87770 96410 94483 74460 43281 51378 58309 TRUE FALSE 67205.70656 87085.49793 88829.27665 92299.82022 99511.11521 96393.511 75371.26375 42387.23223 45545.78483 54359.67949 1.236315357 1.602023756 1.634102288 1.697946365 1.83060526 1.773253851 1.386528847 0.779755006 0.837859701 1 15.73024933 1.889254045 3.578235584 0.858565932 1.638267389 0.816450408 0.159838109 0.096912773 2.094348648 0.083502756 0.045967857 77.49149592 -1.889254045 0.779701457 KAPT(ph)PQEK ddPTM_BT-474_Pertuzumab_2h_R1 6 KAPTPQEK 8 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK 101.89 0.0029742 8956440000 24357500 19664100 18022000 16092100 18220200 18658900 20667000 25080100 27115100 24495800 TRUE FALSE 23405581.97 19103299.12 21278976.3 16922615.21 18806269.28 19036195.74 20919928.93 24562187.17 24037107.52 22836677.65 1.024911869 0.836518316 0.931789493 0.741027897 0.823511615 0.833579912 0.916067094 1.075558693 1.052565872 1 24.44484944 1.889342472 3.849820452 1.047566493 0.860070187 0.543256419 0.072469942 0.169392579 4.139485482 0.035381843 0.019783356 77.50727565 -1.889342472 -0.187496306 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR 32 1 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 304.05 1.72E-90 3257500000 407323 437739 432140 486940 456989 477600 465300 104971 522320 510590 FALSE TRUE 391404.3668 425255.1123 510237.3109 512071.0318 471688.4662 487257.3992 470994.4806 102803.3122 463028.4233 476007.2845 0.822265498 0.893379421 1.07191072 1.075763015 0.990926991 1.023634333 0.98946906 0.21597004 0.972733902 1 18.86062413 1.889364984 23.61051358 0.632506567 0.986898282 0.179534952 0.218325466 17.03453958 3617.268828 0.086122369 0.055578103 77.51129339 -1.889364984 0.354391715 VSELKEELKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSELKEELKK 10 2 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 103.88 0.0015499 3934600000 8611100 6948900 5739500 5313000 7731800 7264600 7623600 10364000 11070000 9188000 FALSE TRUE 8274568.692 6750724.176 6776755.324 5587204.567 7980500.369 7411495.189 7716899.897 10149979.78 9813380.009 8565688.576 0.966013254 0.788112259 0.791151262 0.652277341 0.931682292 0.86525387 0.900908296 1.184957834 1.145661545 1 23.0301378 1.889381894 3.786522899 1.12485584 0.827616766 0.641309924 0.092539472 0.139232208 3.310542126 0.046031984 0.025649945 77.51431156 -1.889381894 -0.297239074 SCDEPLTPPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 SCDEPLTPPPHS(0.893)PT(0.052)S(0.056)MLQLIHDPVS(0.999)PR;SCDEPLT(0.003)PPPHS(0.922)PT(0.031)S(0.044)MLQLIHDPVS(1)PR;SCDEPLT(0.001)PPPHS(0.988)PT(0.161)S(0.029)MLQLIHDPVS(0.821)PR 139.67 1.23E-07 408696000 303228 345254 267210 339917 299671 344970 313803 187537 291698 347845 TRUE FALSE 291377.5145 335407.694 315500.7911 357460.1571 309310.1899 351945.5298 317643.415 183664.2954 258585.6659 324285.1483 0.898522538 1.034298659 0.972911626 1.102301968 0.953821633 1.085296479 0.979518848 0.566366657 0.797402124 1 18.30690343 1.889426995 8.325634903 0.745399289 1.011056376 0.414531691 0.114627985 0.220257716 15.08909703 0.045315652 0.028447878 77.52236176 -1.889426995 0.265657087 TGQAGS(ph)LSGS(ph)PKPFSPQLSAPITTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGQAGSLSGSPKPFSPQLSAPITTK 25 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 2 T(0.001)GQAGS(0.996)LS(0.193)GS(0.81)PKPFSPQLSAPITTK 138.09 7.36E-06 314470000 647120 495540 387970 324490 457070 434100 486550 612200 657140 553070 TRUE FALSE 621829.835 481407.6844 458084.8093 341236.9678 471772.0717 442877.7994 492504.5444 599557.8561 582544.2222 515610.0763 1.206007919 0.933666169 0.888432617 0.661812062 0.914978379 0.85893938 0.955187975 1.162812528 1.129815434 1 18.97592093 1.889503222 4.658904057 1.10980529 0.900017405 0.288778755 0.130059833 0.266958783 8.78226804 0.062442844 0.036254885 77.53596964 -1.889503222 -0.209787884 GFGQEVHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFGQEVHR 8 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 111.74 0.0057498 0 77255 91937 75850 86695 86713 83826 83314 77418 80916 92256 FALSE TRUE 74235.78919 89315.04678 89557.78227 91169.33934 89502.2024 85521.01915 84333.62165 75819.29125 71730.75491 86007.41895 0.863132391 1.038457471 1.041279733 1.060017153 1.040633512 0.994344676 0.98053892 0.881543618 0.834006598 1 16.39217349 1.889512388 3.183847386 0.893375913 1.012519955 0.317445862 0.06509833 0.256109573 4.51448773 0.033093914 0.01774931 77.53760594 -1.889512388 0.119144042 (ac)AT(ph)SPQKSPSVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSPQKSPSVPK 12 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 AT(0.392)S(0.392)PQKS(0.212)PS(0.003)VPK 48.64 0.010482 464690000 683370 644120 504380 478990 499970 551480 618860 804970 900410 698400 TRUE FALSE 656663.1449 625750.3283 595532.6859 503710.7313 516051.9891 562631.3034 626433.7938 788347.0882 798199.2316 651096.7459 1.008549266 0.961071196 0.914660824 0.773634232 0.792588801 0.864128575 0.96212091 1.210798692 1.225930304 1 19.3125124 1.889568364 3.929037857 1.163124103 0.882764433 0.634156339 0.087713576 0.14408487 3.641958682 0.045070344 0.025310311 77.5476005 -1.889568364 -0.28035967 EVEPEPTEDKDLEADEEDTR ddPTM_BT-474_Pertuzumab_2h_R1 3 EVEPEPTEDKDLEADEEDTR 20 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;; 221.92 6.85E-25 5490040000 3016620 2630260 2295370 2320540 2627700 2479910 2678880 3195720 3316290 3049590 FALSE TRUE 2898727.155 2555247.56 2710194.419 2440303.347 2712222.357 2530055.479 2711664.935 3129727.265 2939838.662 2843038.553 1.019587706 0.898773447 0.953273889 0.858343389 0.953987189 0.889912476 0.953791123 1.100838841 1.034048117 1 21.43900223 1.889666327 5.713540813 1.052283349 0.926324073 0.544852359 0.047318171 0.147650756 6.428617607 0.019746339 0.01187035 77.56509472 -1.889666327 -0.125959276 NTPSQHSHSIQHS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 15 NTPSQHSHSIQHSPER 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 NTPSQHSHSIQHS(1)PER;NTPSQHSHS(0.011)IQHS(0.989)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHS(0.004)IQHS(0.996)PER;NTPSQHS(0.003)HS(0.008)IQHS(0.989)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHS(0.001)HS(0.003)IQHS(0.997)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHS(0.001)IQHS(0.999)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER 285.55 1.24E-35 19878329000 3765846.6 5330891.7 3351255.8 4692178.2 4360497.8 5472358.4 4230047.5 62396.73 4105400 2599894.5 TRUE FALSE 3618673.152 5178859.888 3956902.271 4934342.079 4500757.172 5583013.236 4281816.087 61108.21572 3639372.203 2423801.33 1.492974324 2.136668474 1.632519226 2.035786522 1.856900199 2.303412069 1.766570566 0.025211726 1.501514237 1 21.20884002 1.889784913 7.910044592 0.761049718 1.920204119 0.58586669 0.403040702 0.166657283 10.78692811 0.159597684 0.099763422 77.58627704 -1.889784913 1.159154401 QGDETPSTNNGS(ph)DDEKTGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QGDETPSTNNGSDDEKTGLK 20 1 Q9Y3P9;Q9Y3P9-3;Q9Y3P9-4;C9JGR5;B5MCD9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 QGDETPSTNNGS(1)DDEKTGLK 198.99 9.09E-22 799970000 458930 314690 292360 276970 339010 324460 432850 474800 599380 550750 TRUE FALSE 440994.5082 305715.3493 345195.9555 291264.4549 349914.5645 331020.8035 438147.3478 464995.2141 531340.8952 513447.2119 0.858889674 0.595417294 0.672310507 0.567272444 0.681500564 0.644702699 0.853344487 0.905633925 1.034850093 1 18.96985643 1.889794455 1.538641122 1.007300461 0.659810382 0.762016984 0.078607221 0.172579709 0.764517154 0.053127082 0.023414634 77.58798168 -1.889794455 -0.347490079 S(ph)ESDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SESDKDVK 8 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 S(0.996)ES(0.004)DKDVK;S(0.987)ES(0.013)DKDVK;S(0.994)ES(0.006)DKDVK 116.55 0.0013629 1820370000 4208930 2827690 3094620 2673560 2776330 2512620 3245160 3915970 3954770 4151870 TRUE FALSE 4044440.362 2747047.05 3653886.673 2811542.752 2865633.176 2563426.898 3284875.239 3835103.851 3505841.089 3870660.147 1.04489679 0.709710216 0.943995736 0.72637293 0.7403474 0.662271241 0.848660206 0.990813894 0.905747587 1 21.88414821 1.890074122 4.849610222 0.959608182 0.797020879 0.293413367 0.110867839 0.275488388 9.621042852 0.049695309 0.029072703 77.63796121 -1.890074122 -0.162587303 ENS(ph)PAAFPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENSPAAFPDR 10 0 A0A0A0MR03;Q9Y5B0;K7EJD2;A0A0J9YWJ4;A0A0J9YWB6;Q9Y5B0-4 A0A0A0MR03 CTDP1 RNA polymerase II subunit A C-terminal domain phosphatase 1 ENS(1)PAAFPDR;ENS(1)PAAFPDR 124.45 0.0004565 433310000 395920 381860 341080 386610 386250 363180 434050 474670 539350 531590 TRUE FALSE 380447.0087 370969.7267 402720.7433 406562.9884 398674.082 370523.7484 439362.0337 464867.8986 478125.2491 495584.9358 0.767672666 0.748549239 0.812616999 0.820369949 0.804451575 0.747649336 0.886552439 0.938018622 0.964769537 1 18.91877281 1.890141785 1.892794979 0.975027874 0.785507409 0.893564177 0.028561342 0.104727275 0.700375938 0.018962572 0.008817668 77.65005816 -1.890141785 -0.189520465 DYDEEEQGYDS(ph)EKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYDEEEQGYDSEKEK 15 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEK 142.43 2.78E-06 2635600000 262900 185240 196390 149120 189640 172900 219280 297450 325260 261620 TRUE FALSE 252625.5773 179957.1366 231882.0417 156816.1011 195739.9428 176396.1565 221963.6142 291307.5536 288337.8484 243900.2444 1.035774187 0.737830899 0.950724926 0.6429518 0.802540987 0.723230749 0.910059007 1.194371717 1.182195816 1 17.89593168 1.890458184 4.141463324 1.139549424 0.809869621 0.581602408 0.117019829 0.144784039 3.990115874 0.05338472 0.03031566 77.70664958 -1.890458184 -0.329679803 FTDKDQQPS(ph)GS(ph)EGEDDDAEAALKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTDKDQQPSGSEGEDDDAEAALKK 24 2 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 2 FTDKDQQPS(1)GS(1)EGEDDDAEAALKK 108.75 0.011177 329000000 785480 607880 528080 443400 574660 575820 651920 831740 957850 745780 TRUE FALSE 754782.5732 590543.8576 623515.8031 466283.9271 593144.4608 587463.4749 659898.392 814564.2783 849118.8836 695267.6563 1.085600008 0.849376283 0.896799668 0.670653845 0.853116718 0.844945784 0.949128564 1.171583736 1.221283452 1 19.40720895 1.890705886 3.321139598 1.147055943 0.85905622 0.540153419 0.108247584 0.175652684 3.339521788 0.055224506 0.029933266 77.75098257 -1.890705886 -0.287999723 HSVDELQK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSVDELQK 8 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ; 131.03 0.0010225 345300000 540690 564840 487980 469270 515430 493300 524220 335070 620710 565030 FALSE TRUE 519559.237 548731.3162 576168.8411 493489.0809 532009.2741 503274.864 530635.5612 328150.6874 550249.603 526760.0148 0.98633006 1.041710268 1.093797602 0.936838536 1.009965182 0.955415844 1.007357328 0.62296051 1.04459258 1 19.00678631 1.890818998 21.22093801 0.839246586 1.005134842 0.134466032 0.114677625 9.840110901 1900.100746 0.045151989 0.029130762 77.77123546 -1.890818998 0.165888255 FSEGEATLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSEGEATLR 9 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 109.11 0.0062745 0 121570 147530 127250 139330 162770 147520 127410 133590 121070 137520 FALSE TRUE 116818.91 143322.5888 150246.9057 146520.838 168005.6449 150502.9555 128969.2817 130831.3198 107326.6412 128205.6479 0.911183804 1.117911661 1.171921114 1.142857904 1.310438718 1.173918294 1.005956319 1.020480158 0.837144408 1 16.96810029 1.890845357 1.967746224 0.937918642 1.1444042 0.396417034 0.103504445 0.336426786 2.425372822 0.067128602 0.0315913 77.77595582 -1.890845357 0.206485558 SEPVS(ph)PSRER ddPTM_BT-474_Pertuzumab_2h_R1 2 SEPVSPSRER 10 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SEPVS(0.985)PS(0.015)RER;SEPVS(0.994)PS(0.006)RER 89.43 0.0069753 155931000 77105 87216 48022 58075 72681 74295 60465 60971 62247 57110 TRUE FALSE 74091.65136 84728.68507 56700.64364 61072.25771 75018.85037 75797.2958 61204.98876 59711.92754 55180.98152 53241.88883 1.391604486 1.59139142 1.064963037 1.147071583 1.409019327 1.423640248 1.149564565 1.121521585 1.036420434 1 15.70027413 1.890880053 2.043584313 1.044354966 1.330060542 0.447671141 0.142735723 0.337154131 2.614011625 0.09411877 0.044794699 77.78216963 -1.890880053 0.285705576 QVAPEKPVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 QVAPEKPVKK 10 2 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ; 74.76 0.023075 8050500000 10792500 10218200 8727000 8530000 9968600 10409700 10251100 11965100 13892600 11927400 FALSE TRUE 10370717.17 9926786.941 10304163.03 8970234.322 10289249.07 10620191.27 10376556.03 11718016.5 12315570.29 11119546.57 0.93265648 0.892733069 0.926671152 0.806708643 0.925329914 0.955092116 0.933181579 1.053821433 1.107560475 1 23.40659462 1.890964773 1.731672637 1.065936501 0.899666539 0.677497563 0.045276638 0.194548468 1.092231538 0.029977097 0.013604865 77.79734438 -1.890964773 -0.166269963 RSSRS(ph)SPELT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.267)S(0.351)RS(0.414)S(0.359)PELT(0.61)R 74.338 0.045355 494590000 578180 574620 517260 638440 647920 630650 566760 541710 551520 590990 TRUE FALSE 555584.0864 558232.4002 610740.3884 671389.9649 668760.9352 643402.1751 573696.1784 530523.4992 488913.7618 550961.7209 1.008389631 1.013196342 1.108498767 1.218578241 1.213806531 1.167780175 1.041263225 0.962904462 0.88738245 1 19.07159256 1.890985024 2.716279243 0.942767443 1.124113694 0.528512405 0.072262915 0.235389144 3.11208543 0.044774774 0.023113949 77.80097216 -1.890985024 0.181346251 ANLACS(ph)PLGGGEPSPGAGEPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ANLACSPLGGGEPSPGAGEPSK 22 0 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 ANLACS(0.905)PLGGGEPS(0.095)PGAGEPSK;ANLACS(1)PLGGGEPSPGAGEPSK 223.44 8.09E-26 330350000 453620 458570 377040 399140 400590 444190 437090 503160 521670 494190 TRUE FALSE 435892.0289 445492.0326 445179.5152 419739.6632 413475.3412 453171.8261 442439.2382 492769.5702 462452.2086 460718.0711 0.94611446 0.966951506 0.966273179 0.911055349 0.897458483 0.983620688 0.96032534 1.069568574 1.003763988 1 18.81352466 1.890992768 5.808739234 1.029878404 0.945653217 0.581852336 0.030026015 0.155790419 6.974499807 0.013828489 0.008336221 77.80235953 -1.890992768 -0.084225187 WDHESVCK ddPTM_BT-474_Pertuzumab_2h_R1 4 WDHESVCK 8 0 O95232;J3KPP4;C9JL41;O95232-2;H7C5U7 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 153.71 0.00043667 1802150000 4917030 6456920 4979320 6096890 5390170 6210960 5842530 4151600 6192800 6660980 FALSE TRUE 4724867.032 6272774.964 5879193.888 6411551.224 5563549.713 6336549.867 5914032.63 4065868.009 5489819.306 6209825.892 0.760869486 1.010137011 0.946756639 1.032484861 0.895926844 1.020407009 0.952366899 0.654747505 0.88405366 1 22.56612139 1.891076531 23.88885929 0.806813282 0.952433918 0.115145748 0.109859741 24.06213764 5257.951807 0.042592374 0.027487065 77.81736681 -1.891076531 0.145620636 KMS(ph)GGSTMSSGGGNTNNSNSK ddPTM_BT-474_Pertuzumab_2h_R1 13 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.937)GGS(0.025)T(0.032)MS(0.004)S(0.001)GGGNTNNSNSK;KMS(0.728)GGS(0.121)T(0.121)MS(0.026)S(0.005)GGGNTNNSNSK;KMS(0.822)GGS(0.064)T(0.1)MS(0.011)S(0.002)GGGNTNNSNSK;KMS(0.396)GGS(0.266)T(0.266)MS(0.058)S(0.013)GGGNTNNSNSK;KMS(0.562)GGS(0.197)T(0.197)MS(0.038)S(0.007)GGGNTNNSNSK;KMS(0.881)GGS(0.092)T(0.026)MS(0.001)SGGGNTNNSNSK;KMS(0.998)GGS(0.002)TMSSGGGNTNNSNSK;KMS(0.869)GGS(0.062)T(0.062)MS(0.007)SGGGNTNNSNSK;KMS(0.978)GGS(0.019)T(0.002)MSSGGGNTNNSNSK;KMS(0.858)GGS(0.071)T(0.071)MS(0.001)SGGGNTNNSNSK;KMS(0.997)GGS(0.002)TMSSGGGNTNNSNSK;KMS(0.973)GGS(0.023)T(0.004)MSSGGGNTNNSNSK;KMS(0.984)GGS(0.014)T(0.001)MSSGGGNTNNSNSK 244.71 1.54E-30 8364720000 4518241 4098336 3338765 3607167 3901211 3834923 4029469 4711335 4958327 4466805 TRUE FALSE 4341663.147 3981455.47 3942154.106 3793333.321 4026696.995 3912467.771 4078782.847 4614044.286 4395478.506 4164264.319 1.04260028 0.956100565 0.946662797 0.910925203 0.966964795 0.939533966 0.979472611 1.108009466 1.055523418 1 21.98963021 1.891077854 5.916344556 1.063336593 0.957864032 0.521974392 0.040047984 0.158103506 7.250406873 0.017426198 0.010533485 77.81760389 -1.891077854 -0.105472561 S(ph)REDMIDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SREDMIDIK 9 1 P20340-2;P20340;P20340-4;P20340-3;F5H3K7 P20340-2 RAB6A Ras-related protein Rab-6A 1 S(1)REDMIDIK;S(1)REDMIDIK 134.04 0.00015745 443610000 1027860 1091970 864600 1035380 781430 834090 1096010 1688980 1714340 1336180 TRUE FALSE 987690.0948 1060828.085 1020852.453 1088816.086 806565.4056 850955.8713 1109423.298 1654101.973 1519735.31 1245679.338 0.792892733 0.851606069 0.819514639 0.874074131 0.647490394 0.683125942 0.890617083 1.327871405 1.220005232 1 20.24850131 1.891080878 4.924288442 1.206600986 0.782084749 0.761796132 0.100755489 0.099299703 3.556738043 0.04665112 0.027376901 77.81814573 -1.891080878 -0.424516237 FPHHDNELAQSEAYFENDCWVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FPHHDNELAQSEAYFENDCWVR 22 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 150.83 3.07E-08 59112000 53564 61339 47625 68436 54004 62743 55084 33036 50328 50039 FALSE TRUE 51470.65966 59589.67178 56231.89691 71967.99016 55741.08771 64011.70645 55758.13447 32353.79506 44614.97643 46649.81396 1.103341156 1.277382839 1.205404527 1.542728342 1.194883387 1.372174957 1.195248807 0.693546068 0.956380586 1 15.50958371 1.891205981 5.725012195 0.862143365 1.286368008 0.640803883 0.133652162 0.127288522 5.598213104 0.057258472 0.034444055 77.84056522 -1.891205981 0.424224644 CLELFTELAEDKENYK ddPTM_BT-474_Pertuzumab_2h_R1 3 CLELFTELAEDKENYK 16 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 243.69 4.72E-20 3874122000 2825595 2361218 2480535 2562732 2419333 2636624 3251175 3660207 4617271 4139049 FALSE TRUE 2715167.624 2293878.375 2928822.854 2694994.906 2497153.043 2689938.344 3290963.852 3584622.446 4093137.753 3858707.525 0.703646909 0.59446806 0.759016545 0.698419066 0.64714753 0.697108637 0.852866881 0.928969719 1.060753562 1 21.87968627 1.891215252 1.491803886 1.024908832 0.677625016 0.903518146 0.046547215 0.108218415 0.450111984 0.032826334 0.014395992 77.84222698 -1.891215252 -0.347283815 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK ddPTM_BT-474_Pertuzumab_2h_R1 2 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK 31 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 324.62 1.06E-93 4935600000 2029210 2567100 2053580 2407000 2039480 2514280 2334200 1749170 2709600 2389220 FALSE TRUE 1949906.23 2493888.821 2424707.588 2531225.558 2105081.726 2565120.464 2362766.638 1713049.028 2402017.568 2227396.001 0.875419651 1.119643216 1.088583973 1.136405721 0.945086426 1.151623 1.060775289 0.769081487 1.07839718 1 21.08692664 1.891233147 23.0954454 0.921352288 1.060569236 0.145482737 0.109530145 19.97338239 4223.269745 0.042830095 0.027638799 77.84543443 -1.891233147 0.139216948 SYQFGIIGNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYQFGIIGNDR 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 73.499 0.064978 0 107660 162050 84156 90017 103670 137390 92124 92666 78187 91795 FALSE TRUE 103452.5282 157428.4927 99364.86124 94662.78816 107004.6397 140168.1199 93251.44107 90752.41472 69311.53955 85577.64289 1.208873307 1.839598373 1.161107713 1.106162602 1.250380778 1.637905827 1.089670595 1.060468735 0.809925784 1 16.38494632 1.891319832 2.540344125 0.945021288 1.361008229 0.403487464 0.223164062 0.295278409 3.449326085 0.126863111 0.064338432 77.86097403 -1.891319832 0.415986941 HRHPLDHDCSGEGHPTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 HRHPLDHDCSGEGHPTSR 18 1 A0A087X0D9;E9PFU9;Q8WV99;B8ZZ56;E7EV05;B4DEN4;Q8WV99-2 A0A087X0D9 ZFAND2B AN1-type zinc finger protein 2B 0 ;; 172.84 3.29E-12 825930000 146514.5 149472.2 107498.9 190918.3 133242.2 143672.9 130248.2 30389.3 124793.2 56623.8 FALSE TRUE 140788.5514 145209.3992 126926.3425 200771.6163 137528.0564 146578.0645 131842.2164 29761.75034 110627.1991 52788.61959 2.667024682 2.750770911 2.404426248 3.803312492 2.60525957 2.77669819 2.497549992 0.563791032 2.0956638 1 15.68793932 1.891321032 5.58458415 1.218320489 2.828934139 0.679602867 0.497071257 0.123746317 5.270948114 0.213390793 0.127883037 77.86118902 -1.891321032 1.610613649 LLKPECVLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLKPECVLDK 10 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 97.911 0.0054283 0 344690 365360 311120 282260 346320 325990 362290 466230 470910 461750 FALSE TRUE 331219.1337 354940.2905 367346.3048 296827.4724 357459.6973 332581.7412 366723.8134 456602.1876 417454.271 430475.2612 0.76942664 0.824531216 0.853350559 0.689534334 0.830383833 0.772591996 0.851904503 1.060693212 0.969752059 1 18.7155708 1.891474846 4.260386766 1.011613083 0.792801713 0.811706362 0.047340204 0.089145264 2.574966265 0.021820326 0.012467177 77.88877007 -1.891474846 -0.218811369 EKVIET(ph)PENDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKVIETPENDFK 12 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 EKVIET(1)PENDFK;EKVIET(1)PENDFK 162.81 9.97E-05 994170000 2326150 1773310 1630800 1402660 1765820 1717630 1886270 2342700 2378400 2328400 TRUE FALSE 2235241.486 1722736.935 1925521.837 1475051.451 1822619.204 1752361.655 1909354.737 2294322.426 2108414.003 2170695.394 1.029735214 0.793633662 0.887052989 0.679529452 0.839647612 0.807281234 0.879605099 1.056952732 0.971308093 1 21.04972586 1.891496678 4.592646254 1.010950594 0.832960858 0.445808558 0.084548483 0.193595744 6.27321037 0.038450297 0.022285077 77.89268565 -1.891496678 -0.177989736 AMTMPPVS(ph)PVGAEGPVVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AMTMPPVSPVGAEGPVVLR 19 0 O15020;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 AMTMPPVS(1)PVGAEGPVVLR;AMTMPPVS(1)PVGAEGPVVLR 284.5 6.80E-40 162098000 116996 140176 131296 179297 177318 168793 139165 122744 123105 135092 TRUE FALSE 112423.667 136178.3177 155024.1079 188550.5397 183021.5945 172206.1101 140868.1429 120209.2935 109130.6365 125942.0985 0.892661535 1.081277185 1.230915712 1.497120835 1.453220144 1.367343503 1.118515132 0.95448063 0.866514357 1 16.94240109 1.891536679 2.967639756 0.932703335 1.264257493 0.404959951 0.168845271 0.282922704 4.398328309 0.100208289 0.052928037 77.8998604 -1.891536679 0.331554158 HPHVYS(ph)PVIQGNAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HPHVYSPVIQGNAR 14 0 F8VZC1 F8VZC1 ATXN2 1 HPHVY(0.417)S(0.583)PVIQGNAR;HPHVY(0.435)S(0.565)PVIQGNAR 75.294 0.032155 166518000 9960.1 8813.9 4596.4 10729.2 8046.4 7043.6 8319.9 11002.4 9119.6 10553.7 TRUE FALSE 9570.848281 8562.536202 5427.071726 11282.9353 8305.219764 7186.026418 8421.721425 10775.1966 8084.38124 9838.888499 0.972757063 0.870274747 0.551593986 1.146769302 0.844121749 0.730369738 0.855962686 1.095164011 0.821676274 1 13.26427963 1.891553173 11.28978985 0.981464503 0.847826459 0.106921706 0.156794875 1.139016052 112.7080519 0.064139785 0.040969797 77.902819 -1.891553173 -0.133638044 DSDKTDTDWR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSDKTDTDWR 10 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 117.98 0.00080835 7668500000 14579500 13478500 12268200 12338100 13047300 14300200 14613900 16950300 19347100 18287400 FALSE TRUE 14009717.02 13094106.38 14485336.64 12974870.82 13466978.25 14589359.84 14792749.28 16600270.38 17150898.32 17048778.11 0.821743173 0.76803782 0.849640751 0.761044031 0.789908706 0.855742256 0.86767211 0.973692676 1.005989884 1 24.02316501 1.891701899 1.327357633 1.010712561 0.798739437 0.907398062 0.026836824 0.110665949 0.362283868 0.019386386 0.008369689 77.92950168 -1.891701899 -0.211973125 EHDYRDEHLDFIQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 5 EHDYRDEHLDFIQSHLR 17 1 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;;; 218.66 1.54E-15 7024870000 2372098 2680332 2143478 2356212 2627570 2828180 2432134 149697.3 2486759 1854218 FALSE TRUE 2279393.788 2603891.556 2530852.156 2477816.384 2712088.175 2885367.737 2461899.183 146605.9984 2204472.544 1728630.163 1.318612758 1.506332361 1.464079599 1.43339879 1.56892332 1.669164289 1.424190805 0.084810506 1.275271363 1 20.72119781 1.89196537 9.530601598 0.697523731 1.497502741 0.533919284 0.295416795 0.236853153 19.40009088 0.116496467 0.073819351 77.97679302 -1.89196537 0.799979009 YDGHLPIEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 YDGHLPIEIK 10 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 130.94 0.00026331 1046800000 1849600 1866900 1389700 1591900 1778900 1668900 1739500 1946500 2043300 1948500 FALSE TRUE 1777315.587 1813657.84 1640849.704 1674058.15 1836119.934 1702646.301 1760788.521 1906304.095 1811353.15 1816526.359 0.978414422 0.998420876 0.903289784 0.921571075 1.010786287 0.937308888 0.969316251 1.049422754 0.997152142 1 20.79275087 1.89200409 6.583328963 1.019232358 0.957973968 0.365902322 0.033709709 0.2486002 13.11209577 0.014928216 0.009154879 77.98374543 -1.89200409 -0.06125839 IHQDSES(ph)GDELSSSSTEQIR ddPTM_BT-474_Pertuzumab_2h_R1 3 IHQDSESGDELSSSSTEQIR 20 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 IHQDS(0.248)ES(0.752)GDELSSSSTEQIR;IHQDS(0.333)ES(0.667)GDELSSSSTEQIR;IHQDS(0.024)ES(0.976)GDELSSSSTEQIR 221.42 5.06E-25 490480000 480430 577990 415350 538870 519440 468630 484530 242295 480150 428309 TRUE FALSE 461654.2645 561506.2911 490412.9844 566681.1453 536148.2593 478106.0197 490459.8231 237291.5236 425645.385 399299.2499 1.156161111 1.406229266 1.228184086 1.419189105 1.342722931 1.197362679 1.228301388 0.594269896 1.065980928 1 18.60711084 1.89212908 7.111090527 0.852578858 1.294721098 0.624550503 0.140565 0.141165944 8.19080644 0.057442752 0.035541973 78.00619243 -1.89212908 0.442142239 ESVAAT(ph)PPPS(ph)PSLPAKPKPPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESVAATPPPSPSLPAKPKPPSR 22 2 P98164 P98164 LRP2 Low-density lipoprotein receptor-related protein 2 2 ES(0.012)VAAT(0.988)PPPS(0.983)PS(0.015)LPAKPKPPS(0.002)R 62.7 0.071303 564310000 287620 312830 229840 414550 246940 280070 455010 414210 462920 526580 TRUE FALSE 276379.4924 303908.3947 271377.2008 435944.9752 254883.0494 285733.2073 460578.5485 405656.4188 410371.2623 490914.2676 0.562989326 0.619066128 0.55279958 0.888026696 0.519200737 0.582042988 0.938205668 0.826328436 0.835932645 1 18.90511157 1.89213692 0.666365543 0.975376635 0.606383486 0.533047633 0.118276694 0.563728085 0.494831092 0.108422877 0.059818411 78.00760056 -1.89213692 -0.368993149 TSS(ph)SETEEKKPEKPLILQSLGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSSETEEKKPEKPLILQSLGPK 23 3 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 T(0.088)S(0.088)S(0.709)S(0.112)ET(0.002)EEKKPEKPLILQSLGPK 211.19 3.77E-25 3592200000 2413600 1760700 1644200 1223100 1739300 1650300 1916700 2583800 2843000 2120800 TRUE FALSE 2319273.844 1710486.56 1941343.515 1286224.338 1795246.164 1683670.197 1940157.148 2530443.627 2520274.559 1977156.327 1.173035137 0.865124592 0.981886707 0.65054256 0.907994042 0.851561495 0.98128667 1.279839936 1.274696656 1 20.91499551 1.892235702 4.438823351 1.207709113 0.896483112 0.433904362 0.141778371 0.187303471 5.777151044 0.065159873 0.037538262 78.02534574 -1.892235702 -0.311226001 HPNQATPK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPNQATPK 8 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 ; 90.657 0.014703 48817000 124070 130749 111038 127658 115014 116596 121161 89562 124421 130901 FALSE TRUE 119221.2072 127020.1665 131105.0366 134246.4447 118713.5298 118953.651 122643.8046 87712.5134 110297.2497 122034.9587 0.97694307 1.040850654 1.074323604 1.100065474 0.972782972 0.974750615 1.00498911 0.718749073 0.903816832 1 16.89693496 1.892327627 8.630798638 0.846186936 1.024432134 0.421005334 0.076878118 0.246681943 18.0613126 0.031982137 0.020135303 78.04186273 -1.892327627 0.178245198 FDSSLLSS(ph)DDETK ddPTM_BT-474_Pertuzumab_2h_R1 1 FDSSLLSSDDETK 13 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 FDSSLLS(0.108)S(0.892)DDETK 299.56 7.93E-41 168640000 741260 621860 530290 599130 633440 628340 676220 793520 896330 782770 TRUE FALSE 712290.7397 604125.1617 626125.1992 630051.1711 653815.1729 641045.4653 684495.7826 777133.5347 794582.3761 729752.2907 0.976071948 0.827849627 0.857996895 0.863376764 0.895941241 0.878442553 0.93798374 1.064927846 1.088838482 1 19.47704731 1.892384189 2.863808595 1.058785056 0.879686482 0.759683697 0.042045274 0.114185632 1.663912286 0.021671372 0.011352913 78.05202745 -1.892384189 -0.179098574 T(ph)SPINLGLNVNDLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.5)S(0.5)PINLGLNVNDLLK;T(0.5)S(0.5)PINLGLNVNDLLK 159.81 1.95E-05 1078401000 1639362 1550126 1532110 1437296 1490404 1676225 1658717 1967871 2226468 1997921 TRUE FALSE 1575293.921 1505917.924 1808996.359 1511475.019 1538344.198 1710119.418 1679016.875 1927233.776 1973728.687 1862600.031 0.84574997 0.808503113 0.97122105 0.811486628 0.825912258 0.918135611 0.901437156 1.034700818 1.059663188 1 20.82888648 1.892509841 1.864614714 1.041625075 0.859355915 0.699085242 0.04923348 0.180918364 1.174381892 0.031296524 0.014518247 78.07461306 -1.892509841 -0.182269161 ELEKPIQSKPQS(ph)PVIQAAAVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELEKPIQSKPQSPVIQAAAVSPK 23 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 ELEKPIQS(0.019)KPQS(0.981)PVIQAAAVS(1)PK;ELEKPIQS(0.003)KPQS(0.997)PVIQAAAVS(1)PK;ELEKPIQS(0.055)KPQS(0.945)PVIQAAAVS(1)PK;ELEKPIQS(0.002)KPQS(0.998)PVIQAAAVS(1)PK 163.06 8.53E-12 2135160000 1454390 1210380 1204420 941210 1395110 1275380 1417920 1692380 2061150 1677090 TRUE FALSE 1397550.831 1175861.147 1422085.486 989785.9609 1439984.98 1301169.057 1435272.929 1657431.762 1827176.893 1563499.201 0.893860918 0.752070194 0.909553063 0.633058182 0.921001418 0.832216004 0.917987632 1.06007842 1.168645876 1 20.57634705 1.892572555 1.935699424 1.09525535 0.817396831 0.619284435 0.088482345 0.196845622 1.374163965 0.052518582 0.024631373 78.08588833 -1.892572555 -0.277858519 SSFTPSS(ph)PENVIGDFLLQDR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSFTPSSPENVIGDFLLQDR 20 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 SSFTPS(0.137)S(0.863)PENVIGDFLLQDR;SSFTPS(0.118)S(0.882)PENVIGDFLLQDR;SSFTPS(0.002)S(0.998)PENVIGDFLLQDR;SSFTPS(0.021)S(0.979)PENVIGDFLLQDR;SSFTPS(0.152)S(0.848)PENVIGDFLLQDR 326.8 1.07E-79 269036000 264683 260748 236518 306004 268658 289702 257998 240866 247343 271544 TRUE FALSE 254338.8957 253311.7223 279262.0639 321796.9031 277299.6286 295559.9729 261155.4567 235892.0329 219265.6596 253152.083 1.004688141 1.000630606 1.103139506 1.2711604 1.095387505 1.167519419 1.031614884 0.931819443 0.866142032 1 17.94964483 1.892634994 3.077006901 0.924722398 1.10882453 0.491197547 0.078989397 0.223309186 3.708650753 0.044197357 0.02356882 78.09711555 -1.892634994 0.184102133 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGSSPR 40 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.22)S(0.78)PR;VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.029)S(0.971)PR;VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.045)S(0.955)PR;VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.029)S(0.971)PR 202.58 1.54E-31 7228580000 2203070 2196900 1956580 2064420 2112910 2245050 2151740 1407270 2277260 2278710 TRUE FALSE 2116971.589 2134246.563 2310177.53 2170964.964 2180873.669 2290446.449 2178073.638 1378209.383 2018754.992 2124370.942 0.99651692 1.004648727 1.087464286 1.021933091 1.026597392 1.078176322 1.02527934 0.648761172 0.950283659 1 21.01860427 1.892800141 11.59505861 0.829164681 1.037049759 0.397627958 0.09146851 0.445525509 46.02217733 0.035820349 0.022902839 78.12681887 -1.892800141 0.207885079 KEADGEQDEEEKDDGEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEADGEQDEEEKDDGEAK 18 2 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 155.93 8.59E-09 585480000 936450 576508 586738 458744 687745 613958 743744 979640 1148820 876606 FALSE TRUE 899852.4987 560066.5563 692774.6085 482419.8328 709866.9425 626372.6514 752846.1616 959410.0917 1018410.77 817232.6948 1.101097037 0.68532079 0.847707896 0.590309022 0.868622789 0.766455693 0.921213953 1.173974191 1.246169881 1 19.6403874 1.893052011 3.115488467 1.157755386 0.799671043 0.530491525 0.137946171 0.176458498 2.997782629 0.06807136 0.036418392 78.17214181 -1.893052011 -0.358084343 HGS(ph)YDSLASDHSGQEDEEWLSQVEIVTHTGPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 HGSYDSLASDHSGQEDEEWLSQVEIVTHTGPHR 33 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 HGS(0.348)Y(0.302)DS(0.348)LAS(0.001)DHS(0.001)GQEDEEWLSQVEIVTHTGPHR;HGS(0.997)YDS(0.003)LASDHSGQEDEEWLSQVEIVTHTGPHR 274.05 6.84E-74 281550000 92429 123183 96175 121714 105285 108355 103106 31780.1 97095 83427.3 TRUE FALSE 88816.77249 119669.9414 113555.9619 127995.6741 108671.5876 110546.0123 104367.8421 31123.82983 86073.18266 77776.69466 1.141945835 1.53863496 1.460025556 1.645681585 1.397225584 1.421325666 1.341890942 0.400169099 1.106670617 1 16.2470503 1.893120556 7.226941719 0.785318021 1.442357353 0.619132895 0.210207416 0.144283344 8.601212081 0.085787115 0.053175892 78.1844808 -1.893120556 0.657039332 KETTSGTSTEPVKNSS(ph)PAPPQPAPGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KETTSGTSTEPVKNSSPAPPQPAPGK 26 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KETTSGTSTEPVKNS(0.408)S(0.592)PAPPQPAPGK;KETTSGTS(0.001)T(0.002)EPVKNS(0.216)S(0.78)PAPPQPAPGK;KETTSGTSTEPVKNS(0.145)S(0.855)PAPPQPAPGK 228.16 5.94E-35 6396300000 2830110 2521860 1912460 1807680 2220150 2580380 2303620 2679810 3161230 2739890 TRUE FALSE 2719506.172 2449939.022 2258084.064 1900974.581 2291563.141 2632557.052 2331812.391 2624470.987 2802380.423 2554314.81 1.064671497 0.959137461 0.884027316 0.744220945 0.897134187 1.030631401 0.912891544 1.027465752 1.097116304 1 21.28450491 1.893140573 1.303038145 1.051395195 0.912402893 0.256826773 0.085936386 0.614110955 1.935129911 0.069827826 0.030136457 78.1880844 -1.893140573 -0.138992302 (ac)ALYHTEER ddPTM_BT-474_Pertuzumab_2h_R1 2 ALYHTEER 8 0 A0A0C4DGB9 A0A0C4DGB9 PPA2 0 ; 72.485 0.011675 183430000 921140 827620 738240 747800 827000 784490 930110 1018610 1191500 1115470 FALSE TRUE 885140.8304 804017.0879 871656.3901 786394.0476 853601.2061 800352.9253 941492.9644 997575.3475 1056245.915 1039918.223 0.851163881 0.773154148 0.838197053 0.756207584 0.820834934 0.769630638 0.905352886 0.959282495 1.015700938 1 19.98803865 1.893278458 1.918855646 1.001069124 0.800340948 0.875342682 0.03226749 0.097674825 0.670292225 0.018764842 0.008783335 78.21291241 -1.893278458 -0.200728176 SGEIWAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGEIWAR 7 0 Q12996;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 0 ;;; 104.76 0.018793 913833000 2526720 1443410 1459330 1059100 1706490 1351280 1767430 2516400 2783190 1850110 FALSE TRUE 2427972.989 1402245.36 1723063.394 1113760.278 1761380.801 1378603.807 1789060.337 2464435.461 2467253.939 1724800.402 1.407683455 0.812989931 0.998992922 0.645732849 1.021208482 0.799283097 1.037256447 1.428823566 1.430457656 1 20.71799799 1.893318844 4.946153049 1.322332641 0.93236428 0.317650267 0.219185471 0.221287248 8.044585333 0.095402997 0.056078111 78.22018594 -1.893318844 -0.389968361 LLHPS(ph)PDLVSQEATLSEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLHPSPDLVSQEATLSEAR 19 0 A0A087WU05;A0A087WY48;Q8IY22-3;Q8IY22-2;Q8IY22 A0A087WU05 CMIP C-Maf-inducing protein 1 LLHPS(1)PDLVSQEATLSEAR;LLHPS(1)PDLVSQEATLSEAR 243.21 1.23E-24 245990000 202161 253440 206248 269230 220795 257640 230372 196052 225561 240905 TRUE FALSE 194260.3246 246212.1393 243521.6016 283124.9926 227897.0717 262849.6573 233191.3614 192003.4577 199956.2609 224588.2898 0.864961948 1.096282177 1.084302311 1.260640049 1.014732656 1.170362255 1.038305967 0.854913041 0.890323628 1 17.77692318 1.893393324 5.006367367 0.904588043 1.088913279 0.345647206 0.101930324 0.224870036 8.320346034 0.04572361 0.026933387 78.23360154 -1.893393324 0.184325236 DNDFLNEGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DNDFLNEGQK 10 0 P78356;P78356-2 P78356 PIP4K2B Phosphatidylinositol 5-phosphate 4-kinase type-2 beta 0 155.11 3.09E-05 229720000 195530 192290 136750 162230 181980 182810 188470 218170 236170 237910 FALSE TRUE 187888.4714 186806.0775 161463.767 170602.7097 187833.552 186506.5435 190776.5522 213664.7133 209360.9717 221796.1438 0.847122354 0.842242224 0.727982751 0.769186997 0.846874742 0.840891732 0.860143684 0.963338269 0.943934228 1 17.75887476 1.893636137 1.026264398 0.990417887 0.799835488 0.786302251 0.036936826 0.238291871 0.46149674 0.032346491 0.014209307 78.2773541 -1.893636137 -0.1905824 NTETSKS(ph)PEKDVPMVEK ddPTM_BT-474_Pertuzumab_2h_R1 5 NTETSKSPEKDVPMVEK 17 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 NT(0.053)ET(0.154)S(0.154)KS(0.639)PEKDVPMVEK;NTETS(0.002)KS(0.998)PEKDVPMVEK;NTET(0.109)S(0.327)KS(0.564)PEKDVPMVEK;NTET(0.007)S(0.022)KS(0.971)PEKDVPMVEK;NT(0.001)ET(0.181)S(0.113)KS(0.706)PEKDVPMVEK 229.15 9.47E-16 5964730000 5955100 3961880 4529240 3365650 4522610 4144770 5647280 6952350 8652100 7187170 TRUE FALSE 5722368.108 3848891.061 5347774.42 3539351.6 4668083.858 4228580.089 5716393.102 6808781.543 7669949.881 6700376.574 0.854036791 0.574429067 0.798130428 0.528231743 0.696689777 0.631095886 0.853145049 1.016178937 1.144704301 1 22.67581075 1.893701463 2.224331859 1.071130676 0.674631354 0.744539017 0.097786313 0.135580614 1.234400518 0.053626095 0.026233906 78.28912932 -1.893701463 -0.396499322 EQLYQQAMEEAAWHHMPHPSDSER ddPTM_BT-474_Pertuzumab_2h_R1 1 EQLYQQAMEEAAWHHMPHPSDSER 24 0 O75175;H7C3F5;A0A2H2FJL5;B7Z6J7;A0A2R8Y691;H0Y5X7 O75175 CNOT3 CCR4-NOT transcription complex subunit 3 0 81.477 0.0055418 202490000 18442 18114 17472 21715 18895 27817 19752 10404 19108 18065 FALSE TRUE 17721.26625 17597.40646 20629.57906 22835.71375 19502.77484 28379.4788 19993.73088 10189.15376 16938.93995 16841.44146 1.052241656 1.044887191 1.224929535 1.355923946 1.158022897 1.685097969 1.187174562 0.60500485 1.005789201 1 14.039728 1.893795477 7.434821704 0.838244552 1.258389011 0.42340928 0.199958285 0.237150366 14.71210987 0.087489062 0.054390023 78.30607886 -1.893795477 0.420144459 AQYSLPGILHFLQHEWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQYSLPGILHFLQHEWAR 18 0 O43815-2;O43815 O43815-2 STRN Striatin 0 71.697 0.013354 28947000 31767 31885 28814 36596 35895 29980 32113 15906 29809 34752 FALSE TRUE 30525.51052 30975.67102 34021.33076 38484.72395 37049.59527 30586.21614 32506.0085 15577.53554 26425.20729 32398.21609 0.942197263 0.956091871 1.05009889 1.187865525 1.143568991 0.944070996 1.00332711 0.480814607 0.815637726 1 14.98362676 1.893811252 8.603987137 0.713701132 1.039837025 0.409999154 0.143223668 0.253476595 18.74300659 0.060047341 0.037798363 78.30892313 -1.893811252 0.326135893 DGLAPEKT(ph)SPDRDK ddPTM_BT-474_Pertuzumab_2h_R1 4 DGLAPEKTSPDRDK 14 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.943)S(0.057)PDRDK;DGLAPEKT(0.5)S(0.5)PDRDK;DGLAPEKT(0.5)S(0.5)PDRDK;DGLAPEKT(0.627)S(0.373)PDRDK 224.86 4.81E-12 12326280000 6523380 4617660 5190770 3970540 5058340 4735920 5628040 6965800 7778600 6744960 TRUE FALSE 6268439.098 4485968.858 6128857.607 4175460.045 5221046.1 4831683.547 5696917.637 6821953.796 6895605.939 6288117.851 0.996870486 0.713404068 0.974672828 0.664023821 0.830303474 0.768383109 0.905981372 1.084895983 1.09660889 1 22.58419683 1.893829252 3.433392861 1.067270548 0.819793717 0.52390761 0.100084212 0.17257164 3.489052816 0.046779713 0.025600991 78.31216889 -1.893829252 -0.24747683 GVLRPGTALVLLEAQAATGFVIDPVR ddPTM_BT-474_Pertuzumab_2h_R1 3 GVLRPGTALVLLEAQAATGFVIDPVR 26 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 193.53 2.53E-18 242517000 208627.5 203907.8 193080.7 229008 204032.9 231102 211770 172440 219308 225383.7 FALSE TRUE 200474.1067 198092.5492 227974.6775 240827.1303 210595.8035 235775.0408 214361.7046 168879.0537 194413.0753 210118.2612 0.954101302 0.942766935 1.084982696 1.146150405 1.002272731 1.122106377 1.0201955 0.803733349 0.925255492 1 17.68084203 1.8939039 7.407424558 0.891878216 1.044661008 0.369236111 0.076752729 0.249816672 15.44182763 0.033638038 0.020904613 78.32563067 -1.8939039 0.152782793 KAEGS(ph)PSEGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAEGSPSEGKK 11 2 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.991)PS(0.009)EGKK;KAEGS(0.883)PS(0.117)EGKK 105.99 0.0012478 1275430000 1433370 1240100 1004720 924740 1087880 1103660 1272490 1573790 1826170 1478930 TRUE FALSE 1377352.316 1204733.562 1186295.254 972465.9422 1122872.648 1125976.761 1288063.113 1541290.687 1618870.838 1378760.754 0.998978475 0.873779993 0.860406891 0.705318845 0.814407173 0.816658552 0.934218 1.117881171 1.174149201 1 20.39494071 1.894032971 3.043986878 1.10980841 0.840045244 0.666116516 0.079495935 0.149359094 2.434165436 0.043177647 0.022989979 78.34891217 -1.894032971 -0.269763166 THHNDTELIR ddPTM_BT-474_Pertuzumab_2h_R1 3 THHNDTELIR 10 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;; 101.35 0.0033922 1283860000 603889 596967 482818 610384 562570 663422 554662 326659 551674 451028 FALSE TRUE 580288.3502 579942.0857 570073.9528 641885.9914 580665.575 676836.8474 561450.1195 319913.3775 489050.2803 420479.4718 1.380063449 1.37923995 1.355771187 1.526557262 1.380960579 1.609678695 1.335261665 0.760829955 1.16307766 1 18.68167584 1.894098412 6.051113207 0.962596534 1.436430249 0.758811857 0.117158105 0.100132129 4.809382614 0.048959389 0.02970746 78.36071898 -1.894098412 0.473833715 SAS(ph)QS(ph)SLDKLDQELK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 S(0.002)AS(0.998)QS(0.932)S(0.069)LDKLDQELK 168.27 7.19E-07 167390000 716130 530550 533750 474050 599410 484320 654460 874270 972940 809320 TRUE FALSE 688142.8479 515419.2335 630210.4982 498515.7773 618690.567 494113.2822 662469.4773 856216.019 862495.9301 754504.0355 0.91204661 0.68312323 0.835264582 0.660719829 0.819996366 0.654884877 0.878019793 1.134806414 1.143129645 1 19.52516909 1.894225266 3.722988359 1.102004637 0.758926792 0.746664317 0.086024152 0.102183174 2.379065096 0.038827468 0.021625693 78.3836108 -1.894225266 -0.343077844 GADQKPTSADCAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GADQKPTSADCAVR 14 1 M0R3F6;M0R2Z9;Q8IX01-4;Q8IX01-3;Q8IX01 M0R3F6 SUGP2 SURP and G-patch domain-containing protein 2 0 64.04 0.073465 0 138980 150310 118590 139200 135000 148780 132120 128220 126540 147260 FALSE TRUE 133548.5079 146023.306 140021.851 146384.1287 139342.3976 151788.4335 133736.9241 125572.2122 112175.7097 137285.949 0.97277623 1.06364349 1.019928492 1.066271747 1.014979308 1.105637063 0.974148666 0.91467636 0.817095344 1 17.06682445 1.894232913 3.072280955 0.900541966 1.040674631 0.536176277 0.053672439 0.173259157 2.871824806 0.026062032 0.013909544 78.38499109 -1.894232913 0.140132664 ECPDQLGPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ECPDQLGPSPK 11 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 ECPDQLGPS(1)PK 132.24 0.0011344 0 303030 267260 261130 224480 268820 277050 291190 356940 381770 368400 TRUE FALSE 291187.2526 259638.0065 308321.9998 236065.4397 277466.8394 282652.1408 294753.6703 349569.0643 338433.0701 343447.9399 0.847835199 0.755974855 0.897725576 0.687339804 0.807886166 0.822983946 0.858219358 1.017822568 0.985398457 1 18.38973191 1.894281063 2.63039537 1.004404203 0.800343993 0.734241332 0.053042456 0.132105725 1.646223251 0.027994552 0.014366266 78.39368208 -1.894281063 -0.204060209 RIEGLIER ddPTM_BT-474_Pertuzumab_2h_R1 3 RIEGLIER 8 1 Q13618;Q13618-2;Q13618-3;A0A087WTG3;H7C399 Q13618 CUL3 Cullin-3 0 ;; 98.048 0.012505 840060000 364059 399511 406488 426426 397995 397250 396398 203718 413982 365724 FALSE TRUE 349831.1718 388117.3374 479949.4239 448433.897 410796.8706 405282.6672 401249.2373 199511.1521 366988.4989 340953.1877 1.026038718 1.138330279 1.40766956 1.315235971 1.204848306 1.188675401 1.176845537 0.585157022 1.076360369 1 18.37921415 1.894291695 8.591190812 0.848023427 1.219664818 0.476037711 0.153020835 0.238007674 17.64713724 0.064268517 0.040451912 78.39560114 -1.894291695 0.371641391 KKEDDMETK ddPTM_BT-474_Pertuzumab_2h_R1 4 KKEDDMETK 9 2 Q9Y570;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ;;; 160.36 3.68E-05 1299600000 2953610 2347240 2139940 1894870 2527640 2307420 2714190 3141830 3887810 3089510 FALSE TRUE 2838179.656 2280299.013 2526674.761 1992664.468 2608943.836 2354077.613 2747407.069 3076950.113 3446482.108 2880254.736 0.985391889 0.791700465 0.877240033 0.691836192 0.905803158 0.817315769 0.953876418 1.068290965 1.196589338 1 21.45776498 1.894329242 2.236417856 1.105074043 0.839370941 0.619242922 0.085196956 0.179777836 1.653455565 0.04769217 0.023380248 78.40237921 -1.894329242 -0.265703102 NEYLQADEANKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEYLQADEANKR 12 1 Q9UBS8;Q9UBS8-2;E7EP22 Q9UBS8 RNF14 E3 ubiquitin-protein ligase RNF14 0 124.12 0.000527 178310000 89673 84495 60264 66742 73481 79237 79455 96922 99239 95705 FALSE TRUE 86168.48002 82085.28533 71155.04537 70186.56262 75844.5831 80839.22643 80427.39406 94920.52683 87973.80476 89222.8151 0.965767331 0.920003311 0.797498322 0.786643669 0.850058172 0.906037613 0.901421839 1.063859358 0.986001222 1 16.44512505 1.89448048 4.184641121 1.020044188 0.867309627 0.590483677 0.05419354 0.165850078 4.691218642 0.028304112 0.016141593 78.42968658 -1.89448048 -0.152734561 IGELGAPEVWGLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 IGELGAPEVWGLSPK 15 0 Q8N5F7;A0A494C050 Q8N5F7 NKAP NF-kappa-B-activating protein 1 IGELGAPEVWGLS(1)PK;IGELGAPEVWGLS(1)PK;IGELGAPEVWGLS(1)PK;IGELGAPEVWGLS(1)PK;IGELGAPEVWGLS(1)PK 206.13 4.25E-09 3016494000 2932049 2430424 2227004 1850638 2426466 2320829 2596052 3365441 3610480 3040786 TRUE FALSE 2817461.284 2361110.687 2629473.162 1946149.649 2504515.483 2367757.753 2627823.261 3295943.467 3200633.447 2834830.856 0.993872801 0.832892969 0.927559102 0.686513499 0.883479689 0.835237752 0.926977091 1.162659656 1.129038595 1 21.43483123 1.894601635 4.165306894 1.109262927 0.856319825 0.61372196 0.083844153 0.137432372 3.859668867 0.038835837 0.022129328 78.45156929 -1.894601635 -0.252943101 STT(ph)PPPAEPVSLPQEPPKPR ddPTM_BT-474_Pertuzumab_2h_R1 8 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.109)T(0.109)T(0.782)PPPAEPVSLPQEPPKPR;S(0.005)T(0.026)T(0.969)PPPAEPVSLPQEPPKPR;S(0.117)T(0.16)T(0.723)PPPAEPVSLPQEPPKPR;S(0.001)T(0.029)T(0.97)PPPAEPVSLPQEPPKPR;ST(0.001)T(0.999)PPPAEPVSLPQEPPKPR;ST(0.018)T(0.981)PPPAEPVSLPQEPPKPR;ST(0.001)T(0.999)PPPAEPVSLPQEPPKPR;S(0.163)T(0.163)T(0.675)PPPAEPVSLPQEPPKPR 235.99 2.39E-29 1.94191E+11 14829720 14429510 12751400 14078380 13918540 14053310 15013790 17660940 18484370 18260570 TRUE FALSE 14250158.15 14017994.5 15055861.63 14804966.88 14366242.48 14337477.56 15197533.25 17296235.42 16386101.81 17023765.33 0.8370744 0.82343678 0.88440256 0.869664648 0.843893357 0.842203665 0.892724551 1.016005278 0.962542745 1 24.02104683 1.894615185 3.784864578 0.992048332 0.851748817 0.904836992 0.020651569 0.066596151 1.595724141 0.01036578 0.005794598 78.45401704 -1.894615185 -0.140299516 KPPAPPS(ph)PVQS(ph)QSPSTNWS(ph)PAVPVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 KPPAPPS(1)PVQS(0.682)QS(0.318)PSTNWS(1)PAVPVKK 211.59 7.43E-26 5010700000 3826600 3502200 2861600 2657200 3083400 3385400 3406400 3754200 4369800 3935200 TRUE FALSE 3677052.241 3402320.685 3378754.776 2794338.41 3182580.361 3453855.108 3448088.542 3676674.458 3873758.624 3668665.399 1.002286075 0.927400107 0.920976543 0.761677097 0.867503578 0.941447293 0.93987545 1.002183099 1.055904042 1 21.8068239 1.894712906 1.600275703 1.028681606 0.89529912 0.438865586 0.059135597 0.367787201 1.762451525 0.044019752 0.019645674 78.47167197 -1.894712906 -0.133382487 EELMS(ph)SDLEETAGSTSIPK ddPTM_BT-474_Pertuzumab_2h_R1 6 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.564)S(0.436)DLEETAGSTSIPK;EELMS(0.5)S(0.5)DLEETAGSTSIPK;EELMS(0.5)S(0.5)DLEET(0.001)AGSTSIPK;EELMS(0.5)S(0.5)DLEETAGSTSIPK;EELMS(0.573)S(0.427)DLEETAGSTSIPK;EELMS(0.558)S(0.439)DLEET(0.002)AGSTSIPK 165.45 1.40E-11 1159830000 2357946 2207144 2165565 2275254 2244056 2247968 2345158 2797597 2799576 2664598 TRUE FALSE 2265794.863 2144198.414 2556930.768 2392680.132 2316238.099 2293423.453 2373858.745 2739825.644 2481779.869 2484122.404 0.912110796 0.863161336 1.029309491 0.963189305 0.932417056 0.923232869 0.955612631 1.10293504 0.999056997 1 21.24430483 1.894811883 7.25350602 1.04279857 0.939094977 0.448787758 0.047837548 0.223137638 13.54090441 0.020803502 0.012902268 78.48955785 -1.894811883 -0.103703592 LLEQYKEESK ddPTM_BT-474_Pertuzumab_2h_R1 3 LLEQYKEESK 10 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;; 131.37 0.00022979 5595680000 3402980 2757990 2421350 2247130 2874790 2682410 2953670 3690040 3874500 3570400 FALSE TRUE 3269987.779 2679334.826 2858941.808 2363104.649 2967260.231 2736650.168 2989817.897 3613839.384 3434683.003 3328573.628 0.982399113 0.804949845 0.858908988 0.709945134 0.891450983 0.822169035 0.898227959 1.085702102 1.031878332 1 21.66647265 1.894856163 4.102800547 1.044049373 0.840767937 0.62041402 0.067746744 0.13854795 3.799058537 0.031443047 0.017866581 78.49756093 -1.894856163 -0.203281436 IDFYFDENPYFENK ddPTM_BT-474_Pertuzumab_2h_R1 5 IDFYFDENPYFENK 14 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;; 294.49 3.30E-43 6772900000 5540690 5092450 4433840 4633070 5160620 5043900 5260880 6110690 6512950 6107980 FALSE TRUE 5324153.709 4947218.312 5235133.518 4872183.298 5326616.029 5145891.114 5325264.223 5984502.116 5773627.221 5694281.074 0.935000159 0.868804727 0.919366896 0.855627468 0.935432579 0.90369461 0.935195182 1.050967109 1.013934357 1 22.44108228 1.894893039 4.010409209 1.02459454 0.902397842 0.793141089 0.027040704 0.090417984 2.388524449 0.012318971 0.006968675 78.50422656 -1.894893039 -0.122196698 SHELDIDENPASDFDDSGSLLGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHELDIDENPASDFDDSGSLLGFK 24 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 0 169.19 9.53E-12 58073000 30564 36326 29635 31644 29843 41126 34105 13895 42821 32409 FALSE TRUE 29369.52509 35290.01805 34990.70373 33277.15063 30802.9272 41957.5959 34522.38719 13608.06339 37960.1396 30213.90956 0.972053121 1.168005682 1.158099175 1.101385127 1.019494916 1.388684765 1.142599144 0.450390684 1.2563796 1 14.88292525 1.895155515 20.02530196 0.829985665 1.141979168 0.175765634 0.214975469 7.994550475 1519.236607 0.084761755 0.054673858 78.5516868 -1.895155515 0.311993503 EEKESEDKPEIEDVGS(ph)DEEEEKK ddPTM_BT-474_Pertuzumab_2h_R1 4 EEKESEDKPEIEDVGSDEEEEKK 23 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 EEKESEDKPEIEDVGS(1)DEEEEKK;EEKESEDKPEIEDVGS(1)DEEEEKK;EEKESEDKPEIEDVGS(1)DEEEEKK;EEKESEDKPEIEDVGS(1)DEEEEKK 210.21 5.02E-25 2831800000 2380660 1286150 1618980 875346 1591370 1319930 1803860 2639430 3005920 2083890 TRUE FALSE 2287621.175 1249470.261 1911565.7 920522.712 1642557.861 1346619.889 1825936.178 2584924.848 2664700.563 1942746.274 1.17751927 0.643146394 0.983950259 0.473825493 0.845482441 0.693152733 0.939873725 1.330551952 1.371615326 1 20.88966606 1.895343507 3.943432562 1.26084284 0.791767126 0.472708205 0.202246146 0.175917645 4.523315689 0.091877064 0.05181343 78.58569649 -1.895343507 -0.469075713 HGESAWNLENR ddPTM_BT-474_Pertuzumab_2h_R1 9 HGESAWNLENR 11 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;;;;; 224.66 6.04E-12 37830830000 11704250 12040120 9391390 11374260 10797910 10280400 10632750 7350600 11134130 9569500 FALSE TRUE 11246834.97 11696747.57 11088623.08 11961286.92 11145234.58 10488276.73 10762876.78 7198807.541 9870230.24 8921349.241 1.26066525 1.311096253 1.242931174 1.340748647 1.249276794 1.17563795 1.206418052 0.806919149 1.106360705 1 23.08883049 1.895445975 6.140350853 0.957797648 1.261513155 0.729991245 0.079660686 0.110197347 5.440801344 0.034236379 0.020820869 78.60424031 -1.895445975 0.303715507 MDSNFGLAGLPGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 MDSNFGLAGLPGSPK 15 0 O43463;O43463-2 O43463 SUV39H1 Histone-lysine N-methyltransferase SUV39H1 1 MDSNFGLAGLPGS(1)PK;MDSNFGLAGLPGS(1)PK 164.69 1.54E-06 327140000 907100 804750 587680 766110 704380 714730 768120 893690 896510 893800 TRUE FALSE 871649.5291 781799.3179 693886.8489 805649.0289 727037.0224 729182.3303 777520.4823 875234.9892 794741.9433 833262.1299 1.046068815 0.938239349 0.832735371 0.966861447 0.872518979 0.875093568 0.933104307 1.050371735 0.953771826 1 19.66841089 1.895545674 6.935724383 1.004508458 0.917304841 0.265042634 0.05926749 0.313155955 18.0785666 0.025579179 0.015789828 78.6222872 -1.895545674 -0.087203617 HPPGDEIYR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPPGDEIYR 9 0 O95251-4;O95251;O95251-2;E7EUP3;O95251-3;O95251-5 O95251-4 KAT7 Histone acetyltransferase KAT7;Histone acetyltransferase 0 79.986 0.025392 220480000 77134 47078 27937 71557 65200 62298 44470 37509 28631 38739 FALSE TRUE 74119.518 45735.38153 32985.83736 75250.06535 67297.21721 63557.70824 45014.23716 36734.42604 25380.92891 36115.17302 2.052309647 1.266375811 0.91335122 2.083613591 1.863405643 1.759861657 1.246407905 1.017146616 0.702777442 1 15.14031746 1.895554189 2.282947343 0.876721067 1.631130646 0.490341453 0.342908101 0.280129819 2.677999884 0.21189435 0.10461001 78.6238288 -1.895554189 0.754409578 HERGSPS(ph)HSK ddPTM_BT-474_Pertuzumab_2h_R1 3 HERGSPSHSK 10 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HERGS(0.012)PS(0.987)HSK;HERGS(0.124)PS(0.876)HSK;HERGS(0.185)PS(0.813)HS(0.001)K 111.12 0.0010841 2075860000 220635 222361 147990 165979 168858 202769 183087 34978 186826 164171 TRUE FALSE 212012.3403 216019.482 174735.085 174545.1961 174289.4709 206869.1281 185327.6735 34255.69208 165618.2957 153051.5519 1.385234828 1.411416475 1.141674702 1.140434016 1.138763173 1.351630385 1.210883987 0.223817999 1.082107915 1 17.22365815 1.895587952 10.56391816 0.688981726 1.254133778 0.461445607 0.236219726 0.350152366 33.5159525 0.094778606 0.060378234 78.62994134 -1.895587952 0.565152051 TGLVYDQNMMNHCNLWDSHHPEVPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGLVYDQNMMNHCNLWDSHHPEVPQR 26 0 Q9UBN7;A0A2R8YDE6;Q9UBN7-2 Q9UBN7 HDAC6 Histone deacetylase 6 0 67.832 0.011798 80498000 30719 37129 32273 39025 38750 42094 36763 9760.4 38234 33868 FALSE TRUE 29518.46752 36070.11727 38105.44901 41039.08493 39996.42894 42945.16952 37212.91659 9558.844329 33893.83661 31574.09019 0.934895268 1.142396093 1.206858179 1.299770941 1.266748422 1.360139572 1.178590305 0.302743302 1.073469937 1 14.94645354 1.89559502 11.12061945 0.719587751 1.211852497 0.402186135 0.22179292 0.431674288 43.82476676 0.089270213 0.05699109 78.63122106 -1.89559502 0.492264746 VSTLQDLLFHSDCVTLHCGLNEHNHHLINDFTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSTLQDLLFHSDCVTLHCGLNEHNHHLINDFTVK 34 0 Q13363-2;Q13363;H0Y8W7;H0Y9M9 Q13363-2 CTBP1 C-terminal-binding protein 1 0 47.719 0.025769 270160000 241060 237400 193450 180870 225640 233660 212390 73592 265710 117850 FALSE TRUE 231639.1087 230629.5844 228410.7183 190204.7224 232897.9155 238384.7653 214989.2924 72072.29948 235547.7147 109867.9145 2.108341727 2.099153201 2.078957439 1.73121264 2.119799184 2.169739603 1.95679779 0.655990421 2.143917228 1 16.7454106 1.895697101 9.005960725 1.242427144 2.044601966 0.482812461 0.36651002 0.269185912 21.40073173 0.144167116 0.091043559 78.64970545 -1.895697101 0.802174823 SHSSS(ph)PQSVLWNRPQPSEDRLPSQQGLAEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHSSSPQSVLWNRPQPSEDRLPSQQGLAEAR 31 2 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 SHS(0.019)S(0.089)S(0.446)PQS(0.446)VLWNRPQPSEDRLPSQQGLAEAR 88.838 0.00031048 273170000 32437 61851 43602 65530 48243 61445 49426 22794 38847 49030 TRUE FALSE 31169.32618 60087.07004 51481.85132 68912.01115 49794.77991 62687.46 50030.89017 22323.29593 34437.25142 45709.15443 0.681905552 1.314552211 1.12629192 1.50761947 1.08938309 1.371442128 1.094548582 0.488376917 0.753399442 1 15.48019551 1.895712714 6.151624576 0.705425233 1.198671512 0.399844181 0.236624689 0.196074401 9.72106726 0.098814482 0.060111939 78.65253308 -1.895712714 0.49324628 VVSHPTLPVTITAHEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VVSHPTLPVTITAHEDR 17 0 Q13033-2;Q13033 Q13033-2 STRN3 Striatin-3 0 ;; 278.3 4.62E-36 1280470000 397846 452699 389912 474630 439325 491638 440210 375879 451404 470362 FALSE TRUE 382297.7385 439788.4678 460377.7719 499125.7112 453456.2876 501579.2572 445597.4217 368116.9673 400162.5104 438503.9628 0.871822768 1.002929289 1.049882808 1.138246752 1.034098494 1.143842017 1.016176499 0.839483787 0.912563042 1 18.74223035 1.895797656 6.482976229 0.903959776 1.045910205 0.316497353 0.079966037 0.25382096 13.47619419 0.03559262 0.021798912 78.66791787 -1.895797656 0.141950429 VTWDGHSGSMAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTWDGHSGSMAR 12 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 97.957 0.0046293 981580000 1888400 1848000 1507100 1665800 1775700 1720200 1918100 1943100 2295100 2130800 FALSE TRUE 1814599.24 1795296.849 1779466.495 1751772.138 1832817.003 1754983.623 1941574.282 1902974.306 2034569.87 1986479.018 0.913475161 0.903758274 0.895789223 0.881847793 0.922646042 0.883464465 0.97739481 0.957963456 1.024209091 1 20.92178212 1.895892963 1.291408337 1.006285037 0.899166408 0.813601067 0.020753743 0.168602497 0.521484613 0.014686574 0.006347517 78.68518375 -1.895892963 -0.107118629 NSSTETDQQPHS(ph)PDSSSSVHSIR ddPTM_BT-474_Pertuzumab_2h_R1 4 NSSTETDQQPHSPDSSSSVHSIR 23 0 Q92613 Q92613 JADE3 Protein Jade-3 1 NSSTETDQQPHS(1)PDSSSSVHSIR;NSSTETDQQPHS(0.998)PDS(0.001)S(0.001)SSVHSIR;NSSTETDQQPHS(1)PDSSSSVHSIR;NSSTETDQQPHS(1)PDSSSSVHSIR 310.05 2.44E-73 2564280000 808589 1179316 874208 1247754 1032570 1164515 1053597 444228 988842 1150970 TRUE FALSE 776988.4479 1145683.062 1032196.832 1312150.733 1065783.552 1188062.291 1066491.235 435054.5366 876592.8017 1073013.777 0.724117868 1.067724467 0.961960466 1.222864759 0.993261759 1.107219979 0.993921288 0.405451026 0.816944592 1 20.03323717 1.895994762 10.040133 0.679389366 1.024001931 0.292616487 0.184357509 0.396217291 35.91156801 0.07334281 0.046609987 78.70362974 -1.895994762 0.344612565 SEDSTKDDIDLDALAAEIEGAGAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SEDSTKDDIDLDALAAEIEGAGAAK 25 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ;; 229.99 2.61E-34 408705000 437837 354491 388716 351150 359331 422039 461315 585231 678976 631824 FALSE TRUE 420725.846 344381.2638 458965.6281 369272.8936 370889.208 430572.9177 466960.711 573145.7753 601901.491 589029.9977 0.714268964 0.584658277 0.779188887 0.626916957 0.629660984 0.7309864 0.79276219 0.973033254 1.021852017 1 19.16798158 1.896058005 1.641015742 1.019147324 0.668312202 0.885497741 0.051867533 0.106751255 0.537906224 0.033905055 0.015239218 78.71509165 -1.896058005 -0.350835122 IEVLQQHENEDIYK ddPTM_BT-474_Pertuzumab_2h_R1 4 IEVLQQHENEDIYK 14 0 O00505;H0Y4S9 O00505 KPNA3 Importin subunit alpha-4 0 ;;; 246.96 8.85E-18 2704640000 2853090 2634470 2423260 2566080 2690070 2891960 2957260 3059690 3715190 3549880 FALSE TRUE 2741588.089 2559337.495 2861196.987 2698515.696 2776598.545 2950437.413 2993451.832 2996506.332 3293457.207 3309443.466 0.828413634 0.773343773 0.86455533 0.815398639 0.83899259 0.891520717 0.904518196 0.905441161 0.995169502 1 21.6581572 1.896301248 0.537683114 1.007683005 0.807182578 0.861262109 0.026111879 0.279032583 0.175453948 0.024449008 0.01662498 78.75919134 -1.896301248 -0.200500428 DLTQMADELRR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLTQMADELRR 11 1 P41227-2;P41227;C9JN83 P41227-2 NAA10 N-alpha-acetyltransferase 10 0 ;;;;; 254.07 3.20E-20 3679940000 1681982 2003080 1623718 2121620 1990570 2159460 1893880 1720580 1877660 2039910 FALSE TRUE 1616248.284 1945954.12 1917159.962 2231117.062 2054598.492 2203125.761 1917057.87 1685049.422 1664515.909 1901745.079 0.849876412 1.023246565 1.008105652 1.173194603 1.080375343 1.158475857 1.008051968 0.886054309 0.875257114 1 20.85889244 1.896382405 4.752412983 0.912150784 1.055058005 0.285879762 0.089803392 0.26977975 9.360227928 0.042858099 0.025047812 78.77391054 -1.896382405 0.142907221 DQHHLGSPS(ph)RLS(ph)VGEQPDVTHDPYEFLQS(ph)PEPAASAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQHHLGSPSRLSVGEQPDVTHDPYEFLQSPEPAASAK 37 1 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2 Q9H8M2 BRD9 Bromodomain-containing protein 9 3 DQHHLGS(0.414)PS(0.544)RLS(0.64)VGEQPDVT(0.141)HDPY(0.276)EFLQS(0.985)PEPAASAK 72.52 0.0016978 82149000 22184 18246 13321 18213 21614 18420 18677 2393.9 21223 15589 TRUE FALSE 21317.02475 17725.64194 15728.40102 19152.97511 22309.23394 18792.46502 18905.57471 2344.465128 18813.85401 14533.14314 1.466786953 1.219670223 1.082243591 1.317882506 1.535059121 1.293076441 1.30085932 0.161318519 1.29454818 1 13.82705913 1.896390638 16.50392972 0.726604429 1.312195395 0.367494119 0.291934395 2.072812317 326.5428147 0.115373182 0.074316844 78.77540387 -1.896390638 0.585590966 GRPPAEKLS(ph)PNPPNLTK ddPTM_BT-474_Pertuzumab_2h_R1 4 GRPPAEKLSPNPPNLTK 17 2 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28;A0A2R8YF38 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 GRPPAEKLS(1)PNPPNLTK;GRPPAEKLS(1)PNPPNLTK;GRPPAEKLS(1)PNPPNLTK;GRPPAEKLS(1)PNPPNLTK 152.06 1.18E-07 12858980000 4410340 3667820 3646320 3666630 4099300 3848880 4567230 5462370 6335960 5740730 TRUE FALSE 4237979.037 3563217.365 4305291.136 3855865.214 4231157.707 3926706.991 4623125.127 5349570.151 5616728.383 5351905.244 0.791863616 0.665784838 0.804440837 0.720465897 0.790589055 0.733702637 0.863827911 0.999563689 1.049482031 1 22.35162114 1.896395459 2.149618205 1.027227765 0.749122877 0.893837651 0.040882177 0.082545907 0.70400806 0.022642298 0.010989592 78.77627829 -1.896395459 -0.278104887 MQKS(ph)PCY(ph)IPIVS(ph)S(ph)ATLWDR ddPTM_BT-474_Pertuzumab_2h_R1 1 MQKSPCYIPIVSSATLWDR 19 1 F8VX61;F8W1Y6;Q96LP6-3;Q96LP6 F8VX61 C12orf42 Uncharacterized protein C12orf42 4 MQKS(0.977)PCY(0.989)IPIVS(0.992)S(0.992)AT(0.051)LWDR 60.464 0.021306 221930000 36776 51303 37180 68775 55532 61199 44261 42676 35321 47077 TRUE FALSE 35338.75326 49839.88867 43899.25306 72324.48599 57318.23721 62436.48571 44802.67936 41794.72569 31311.50816 43888.43286 0.80519515 1.1356042 1.000246539 1.647916804 1.305998722 1.422618254 1.020831149 0.952294784 0.713434181 1 15.42155314 1.896487497 2.74407602 0.874385548 1.22816118 0.296058013 0.22705717 0.34671703 4.674258978 0.12835364 0.066724228 78.79297467 -1.896487497 0.353775631 LLPDGAADGSFYLHS(ph)PEGPSKPSLASPYLPEGTSKPLSDRPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLPDGAADGSFYLHSPEGPSKPSLASPYLPEGTSKPLSDRPTK 43 3 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 LLPDGAADGSFYLHS(0.999)PEGPS(0.001)KPSLASPYLPEGTSKPLSDRPTK 249.13 1.32E-55 486360000 152860 149300 151870 155490 163220 165590 155510 135960 167690 153180 TRUE FALSE 146886.0622 145042.1102 179316.2873 163514.8575 168470.1195 168938.3433 157413.1779 133152.3785 148654.5342 142804.9822 1.028577995 1.015665616 1.255672489 1.145022079 1.179721582 1.183000346 1.102294721 0.932407094 1.040961821 1 17.12368679 1.896640017 5.594114503 0.988221507 1.137619107 0.448297094 0.071218817 0.209332953 9.19145507 0.033430791 0.020068651 78.82065091 -1.896640017 0.1493976 T(ph)SSSETEEKKPEKPLILQSLGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSSETEEKKPEKPLILQSLGPK 23 3 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 T(0.323)S(0.323)S(0.323)S(0.022)ET(0.01)EEKKPEKPLILQSLGPK 142.46 9.12E-08 3211000000 638760 433080 470920 325460 487950 401430 525470 659910 748400 623810 TRUE FALSE 613796.553 420728.9824 556025.7196 342257.0296 503645.3549 409547.1896 531900.859 646282.6279 663444.7695 581558.7931 1.055433363 0.72345047 0.956095456 0.588516645 0.86602655 0.704223192 0.914612358 1.111293709 1.140804296 1 19.14956552 1.896744841 3.662832389 1.092137364 0.809401176 0.463268082 0.128461587 0.190485699 4.329737985 0.059456239 0.033057974 78.83967778 -1.896744841 -0.282736188 INPPSSGGTSS(ph)SPIK ddPTM_BT-474_Pertuzumab_2h_R1 2 INPPSSGGTSSSPIK 15 0 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 INPPS(0.06)S(0.041)GGT(0.153)S(0.102)S(0.387)S(0.257)PIK;INPPSS(0.002)GGT(0.013)S(0.008)S(0.648)S(0.329)PIK 117.48 0.00038421 307010000 523510 497520 436760 424420 454850 484600 491410 541680 585880 579040 TRUE FALSE 503050.6504 483331.2167 515692.2477 446324.3671 469480.6633 494398.944 497424.0226 530494.1187 519373.3586 539821.105 0.931884 0.895354428 0.955302123 0.826800514 0.869696755 0.915857012 0.921460865 0.982722079 0.962121254 1 19.04212186 1.896783142 1.929923971 0.983339974 0.896129964 0.544508697 0.033721053 0.261847009 1.815626915 0.021833507 0.010266631 78.84663118 -1.896783142 -0.08721001 CLELFSELAEDKENYK ddPTM_BT-474_Pertuzumab_2h_R1 2 CLELFSELAEDKENYK 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 229.68 2.70E-15 3537200000 2900700 2372640 2559290 2591790 2887210 3097800 3337600 3983700 4965100 4682000 FALSE TRUE 2787337.437 2304974.63 3021810.634 2725552.593 2980079.732 3160439.638 3378446.547 3901435.203 4401482.663 4364883.97 0.638582252 0.528072372 0.692300335 0.624427273 0.682739737 0.724060401 0.774006038 0.893823348 1.008384803 1 22.05751187 1.896785042 0.812899599 1.026577326 0.615028837 0.925194906 0.042020552 0.142507162 0.176484727 0.035557757 0.017121788 78.84697612 -1.896785042 -0.411548489 SITST(ph)PLSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 SIT(0.003)S(0.084)T(0.914)PLSGK;SITS(0.017)T(0.983)PLSGK 158.02 9.10E-05 480040000 1188950 1137730 883870 876350 922680 1062910 1167790 1636930 1658190 1672940 TRUE FALSE 1142484.52 1105283.054 1043604.971 921578.5285 952358.8402 1084402.768 1182081.763 1603126.823 1469959.223 1559630.284 0.732535481 0.708682735 0.669136129 0.590895508 0.610631154 0.695294763 0.757924346 1.027889007 0.942504925 1 20.57277264 1.896869205 2.99027306 0.991809879 0.664823169 0.907556492 0.045867436 0.075768 1.196978684 0.026396981 0.01402527 78.86225753 -1.896869205 -0.32698671 VAQGATEKS(ph)PEDKVQIAANEETQER ddPTM_BT-474_Pertuzumab_2h_R1 4 VAQGATEKSPEDKVQIAANEETQER 25 2 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 VAQGAT(0.004)EKS(0.996)PEDKVQIAANEETQER;VAQGAT(0.002)EKS(0.998)PEDKVQIAANEETQER;VAQGATEKS(1)PEDKVQIAANEETQER;VAQGAT(0.004)EKS(0.996)PEDKVQIAANEETQER 200.79 3.39E-25 4605000000 1503090 1148257 1000549 900337 1102061 1074887 1237324 1581270 1772100 1397578 TRUE FALSE 1444347.581 1115509.835 1181370.461 946803.5005 1137509.793 1096621.952 1252466.741 1548616.222 1570938.637 1302918.797 1.108547658 0.856162208 0.906710736 0.726678825 0.873047342 0.841665616 0.961277667 1.188574626 1.205707248 1 20.31331574 1.896955349 3.87157167 1.146839241 0.878345513 0.529120078 0.103032447 0.165668194 4.143704351 0.049415216 0.027792407 78.87790176 -1.896955349 -0.268493728 THINIVVIGHVDSGK ddPTM_BT-474_Pertuzumab_2h_R1 11 THINIVVIGHVDSGK 15 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;;;;;; 235.26 6.51E-18 10029368000 12634611 12068443 11368532 11991159 11851747 13254252 12488916 3151955 15871599 12229574 FALSE TRUE 12140836.43 11724262.82 13423078.62 12610024.15 12232969.21 13522262.06 12641759.09 3086866.028 14069921.62 11401254.06 1.064868511 1.028330985 1.177333524 1.106020801 1.072949444 1.186032868 1.108804262 0.270747938 1.234067897 1 23.44268918 1.897355095 24.70473769 0.737871522 1.10791595 0.18590765 0.235258289 35.1375595 8447.533763 0.091642141 0.059144234 78.95053816 -1.897355095 0.370044428 RIS(ph)LSDMPR ddPTM_BT-474_Pertuzumab_2h_R1 11 RISLSDMPR 9 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(0.999)LS(0.001)DMPR;RIS(1)LSDMPR;RIS(0.996)LS(0.004)DMPR;RIS(1)LSDMPR;RIS(0.976)LS(0.024)DMPR;RIS(0.848)LS(0.152)DMPR 192.6 2.12E-05 8184839000 2855452 3339710 2925278 3767184 4230632 3778850 2934281 2860711 2609813 2725056 TRUE FALSE 2743857.779 3244464.741 3453940.807 3961608.818 4366714.12 3855260.936 2970191.609 2801636.318 2313557.969 2540485.53 1.080052512 1.2771042 1.359559331 1.559390428 1.718850223 1.517529185 1.169143289 1.102795621 0.910675515 1 21.27667282 1.897365307 2.184572631 0.990903078 1.426503206 0.549275154 0.168613949 0.260410216 2.289677835 0.11227285 0.054796986 78.9523947 -1.897365307 0.435600128 ES(ph)SPKKEETVAR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESSPKKEETVAR 12 2 Q68DK7;Q68DK7-2;Q68DK7-3;J3KTC2 Q68DK7 MSL1 Male-specific lethal 1 homolog 1 ES(0.731)S(0.269)PKKEETVAR;ES(0.943)S(0.057)PKKEETVAR;ES(0.58)S(0.419)PKKEET(0.001)VAR;ES(0.631)S(0.368)PKKEET(0.001)VAR 134.25 0.00011718 1404310000 1783930 1294890 1091200 954320 1209900 1158050 1311760 1611640 1751710 1405270 TRUE FALSE 1714212.043 1257961.005 1288404.114 1003572.57 1248817.532 1181466.564 1327813.711 1578359.071 1552863.225 1310089.811 1.308469105 0.960209746 0.983447167 0.766033413 0.953230474 0.901821046 1.013528767 1.204771656 1.185310512 1 20.32123429 1.897522341 5.266934558 1.147139477 0.966673606 0.189181711 0.137262087 0.31663063 12.83922833 0.06229342 0.037056993 78.98094779 -1.897522341 -0.180465871 SVSMLSLNT(ph)PNSNR ddPTM_BT-474_Pertuzumab_2h_R1 7 SVSMLSLNTPNSNR 14 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 SVSMLSLNT(1)PNSNR;SVSMLSLNT(1)PNSNR;SVSMLSLNT(1)PNSNR;SVSMLSLNT(1)PNSNR;SVSMLSLNT(0.997)PNS(0.003)NR;SVSMLSLNT(1)PNSNR;SVSMLS(0.012)LNT(0.988)PNSNR 319.03 5.41E-55 2003490000 2748192 2546046 2304906 2404062 2307299 2185895 2161321 2613180 1780879 2061768 TRUE FALSE 2640789.618 2473435.261 2721453.787 2528135.928 2381515.368 2230095.295 2187771.893 2559216.92 1578721.082 1922122.617 1.373892381 1.286824909 1.415858574 1.315283378 1.239002833 1.160225302 1.138206207 1.331453518 0.821342545 1 20.87426894 1.89761868 0.448195043 0.963675245 1.373355558 0.57647741 0.113575074 0.788033417 0.383596357 0.121594941 0.101424348 78.9984699 -1.89761868 0.409680314 EIPS(ph)LSPTIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIPSLSPTIPR 11 0 Q9ULD5 Q9ULD5 ZNF777 Zinc finger protein 777 1 EIPS(0.67)LS(0.328)PT(0.001)IPR 120.96 0.00044221 141670000 207060 187550 161880 185840 204850 160330 159910 155490 132290 137330 TRUE FALSE 198967.8663 182201.2576 191135.317 195431.2247 211439.1863 163571.9825 161867.0264 152279.0772 117272.9938 128028.5168 1.554090224 1.42313027 1.492912062 1.526466365 1.651500709 1.277621475 1.264304473 1.189415304 0.915991193 1 16.96610566 1.897833391 1.015654315 0.96659643 1.517904465 0.858313685 0.08702509 0.187991529 0.356563771 0.073227568 0.032325964 79.03753575 -1.897833391 0.551308035 DVIATDKEDVAFK ddPTM_BT-474_Pertuzumab_2h_R1 4 DVIATDKEDVAFK 13 1 A0A5K1VW95;P40925;P40925-3;C9JF79;C9JRL4;C9JLV6 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ;;; 175.15 1.71E-05 7201400000 5233550 5093730 3965010 4728280 5110970 5446360 6030230 7005150 8826530 8081190 FALSE TRUE 5029017.08 4948461.808 4681575.508 4972307.097 5275368.992 5556489.131 6104029.759 6860491.205 7824579.318 7533843.803 0.667523407 0.656830953 0.621405969 0.659996043 0.700222772 0.737537076 0.810214536 0.910622968 1.038590595 1 22.84495469 1.897894558 0.991163299 1.029673822 0.652211941 0.972754937 0.02385032 0.076689326 0.138579724 0.02013183 0.008942413 79.04866825 -1.897894558 -0.37746188 RHS(ph)PESPSIAVVESELVAEYITTER ddPTM_BT-474_Pertuzumab_2h_R1 4 RHSPESPSIAVVESELVAEYITTER 25 1 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 RHS(0.333)PES(0.333)PS(0.333)IAVVESELVAEYITTER;RHS(0.333)PES(0.333)PS(0.333)IAVVES(0.001)ELVAEYITTER;RHS(0.333)PES(0.333)PS(0.333)IAVVES(0.001)ELVAEYITTER;RHS(0.333)PES(0.333)PS(0.333)IAVVES(0.001)ELVAEYITTER 148.75 9.73E-08 141055000 74289 76440 67803.1 80494 76179 78963.8 74331 50561.1 74227.8 74735.5 TRUE FALSE 71385.70375 74260.00604 80056.62844 84648.30499 78629.36672 80560.50214 75240.68501 49516.99562 65801.77133 69673.59802 1.024573235 1.065827059 1.149023887 1.214926563 1.128538915 1.156255805 1.07990239 0.710699562 0.944429069 1 16.08832445 1.897939697 7.039614315 0.859780659 1.125427383 0.608570117 0.085087446 0.148126717 8.885275829 0.036239226 0.022412559 79.05688468 -1.897939697 0.265646724 DKENALMPNWLHLPVGYHGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKENALMPNWLHLPVGYHGR 20 1 P16930;P16930-2 P16930 FAH Fumarylacetoacetase 0 ; 156.92 8.31E-09 619920000 655150 624740 511900 554960 600140 633610 607610 340250 742700 656580 FALSE TRUE 629546.0137 606923.0269 604411.7172 583601.5521 619444.0481 646422.0283 615046.1129 333223.7186 658391.8097 612109.2518 1.028486356 0.991527289 0.987424574 0.953427105 1.011982822 1.056056621 1.004797936 0.544386019 1.075611597 1 19.22342965 1.897946626 24.49477549 0.810677067 1.003951054 0.117982555 0.135391339 37.38024426 8962.403569 0.053037849 0.034229378 79.05814616 -1.897946626 0.193273987 LPYDVTPEQALAHEEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPYDVTPEQALAHEEVK 17 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 185.13 5.97E-10 997460000 656880 563370 582640 627270 630840 616070 705370 790980 895060 873110 FALSE TRUE 631208.4034 547303.2392 687936.0088 659643.4799 651131.5415 628527.3575 714002.5291 774645.9866 793456.5412 813973.482 0.775465562 0.672384606 0.845157765 0.810399226 0.799941959 0.772171786 0.87718156 0.95168455 0.974794092 1 19.63462227 1.897995297 1.495699861 0.990892972 0.776362173 0.811596676 0.042609504 0.168956721 0.705877114 0.031564628 0.01392294 79.06700649 -1.897995297 -0.2145308 IKEEEAAKD ddPTM_BT-474_Pertuzumab_2h_R1 1 IKEEEAAKD 9 2 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 81.625 0.082452 385220000 340280 323860 242100 233850 279840 277990 305770 366160 385750 379130 FALSE TRUE 326981.4814 314623.8299 285852.8555 245919.0265 288841.3077 283611.1483 309512.1047 358598.668 341961.2772 353451.1874 0.925110717 0.890147893 0.808747758 0.695765173 0.817202822 0.802405419 0.875685571 1.014563484 0.967492229 1 18.43115146 1.898053866 3.484579297 0.993363551 0.820145086 0.634828543 0.057741478 0.167519769 3.494428419 0.031779773 0.017499926 79.07767031 -1.898053866 -0.173218465 DFPDSFQAGS(ph)PGHLGVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFPDSFQAGSPGHLGVIR 18 0 A1YPR0 A1YPR0 ZBTB7C Zinc finger and BTB domain-containing protein 7C 1 DFPDSFQAGS(1)PGHLGVIR;DFPDSFQAGS(1)PGHLGVIR 247.92 1.26E-24 561930000 152050 183878 157870 204846 175320 175139 154714 153031 135663 152006 TRUE FALSE 146107.7179 178633.9795 186400.6208 215418.1266 180959.327 178680.4306 156607.4362 149870.8564 120263.105 141710.4982 1.031029597 1.260555722 1.315362116 1.520128214 1.276964863 1.260883511 1.105122332 1.057584711 0.848653462 1 17.11258711 1.898278662 1.492534286 0.938261297 1.293614296 0.582299868 0.119151691 0.286711187 1.192650164 0.088627553 0.039085996 79.11861241 -1.898278662 0.355352999 DKS(ph)PVREPIDNLTPEER ddPTM_BT-474_Pertuzumab_2h_R1 12 DKSPVREPIDNLTPEER 17 2 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;H0Y4X3;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 1 DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER 311.27 2.09E-58 73320616000 25365695 21743825 18836616 18665955 20361450 21714975 22884561 25108380 29209678 26620329 TRUE FALSE 24374375.6 21123712.4 22240811.53 19629307.17 21016394.53 22154066.67 23164629.1 24589883.18 25893917.81 24817310.41 0.982152183 0.851168481 0.896181382 0.790952237 0.846844166 0.892686045 0.933406107 0.990835944 1.043381309 1 24.56484344 1.89837893 1.698309621 1.021008522 0.869722653 0.627866929 0.046723192 0.227712505 1.228202323 0.031534743 0.014324732 79.13688111 -1.89837893 -0.151285869 ESTESSNTT(ph)IEDEDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESTESSNTTIEDEDVK 16 0 E9PF82;E9PBG7;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;H0Y9J2 E9PF82;Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 ESTESSNT(0.183)T(0.817)IEDEDVK 386.09 2.98E-120 313030000 552030 476020 425710 472110 425520 471810 518200 621560 685080 629040 TRUE FALSE 530456.0573 462444.3757 502645.2669 496475.6537 439207.2372 481350.3215 524541.8866 608724.5688 607312.5905 586434.5605 0.904544331 0.788569445 0.857120812 0.846600264 0.748945009 0.820808243 0.894459368 1.03800937 1.035601636 1 19.1616106 1.898431583 2.939350153 1.028689673 0.82524584 0.825082784 0.040387925 0.098564368 1.509772016 0.021263284 0.01126406 79.14647605 -1.898431583 -0.203443832 NYSGT(ph)PPPALHEGPPLQLQAGDTVELLK ddPTM_BT-474_Pertuzumab_2h_R1 3 NYSGTPPPALHEGPPLQLQAGDTVELLK 28 0 Q9UKW4-3;Q9UKW4-2;Q9UKW4;Q9UKW4-4;H0YCG7 Q9UKW4-3 VAV3 Guanine nucleotide exchange factor VAV3 1 NY(0.001)S(0.224)GT(0.775)PPPALHEGPPLQLQAGDTVELLK;NYS(0.033)GT(0.967)PPPALHEGPPLQLQAGDTVELLK;NYS(0.192)GT(0.808)PPPALHEGPPLQLQAGDTVELLK 212.36 2.16E-25 265882000 387291 401523 349539 366838 390585 407915 412645 508500 529240 536540 TRUE FALSE 372155.2395 390071.9572 412708.4728 385770.5531 403148.5212 416163.3208 417695.0729 497999.2973 469162.894 500199.6679 0.744013368 0.779832499 0.825087459 0.771233125 0.805975188 0.831994396 0.835056678 0.995601015 0.93795123 1 18.93214457 1.898476049 2.134487808 0.981321627 0.791569321 0.881321585 0.030196274 0.096058404 0.807986666 0.017912462 0.008690606 79.15458003 -1.898476049 -0.189752305 LIVDHNIADYMTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LIVDHNIADYMTAK 14 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 176.32 2.24E-06 785880000 964550 920180 755950 875170 886090 869830 976530 967090 1085530 1072780 FALSE TRUE 926854.3196 893937.3674 892566.981 920337.6286 914591.8896 887418.5586 988481.0663 947119.2535 962305.1853 1000119.655 0.92674343 0.893830416 0.892460194 0.920227519 0.914482467 0.887312387 0.988362804 0.947005939 0.962190054 1 19.93174118 1.898551854 0.772181029 0.989034686 0.902803611 0.649686523 0.022469236 0.383382693 0.432693243 0.019286933 0.009581726 79.16839753 -1.898551854 -0.086231075 S(ph)RS(ph)PPPVSK ddPTM_BT-474_Pertuzumab_2h_R1 9 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 2 S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK 108.71 0.0014605 83540187000 9015545 7815237 8176444 8073058 7613627 7957266 9109503 10785908 12199130 10856345 TRUE FALSE 8663207.534 7592354.093 9654109.315 8489709.491 7858526.227 8118167.37 9220987.823 10563175.23 10814335.91 10121035.08 0.855960627 0.750155891 0.953865809 0.838818305 0.776454796 0.802108411 0.911071619 1.04368527 1.06850098 1 23.27085351 1.8985753 2.935950556 1.042754056 0.830141872 0.746634083 0.053989148 0.128040111 1.957211655 0.02885666 0.015283964 79.17267153 -1.8985753 -0.212612184 (ac)GDREQLLQR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDREQLLQR 9 1 Q04917;F8WEB6;A2IDB1 Q04917 YWHAH 14-3-3 protein eta 0 ;; 85.265 0.0001112 922620000 1296444 905876 823804 785155 930574 826164 975308 1241043 1326647 1008545 FALSE TRUE 1245777.535 880041.3034 972683.7082 825676.9436 960506.7578 842869.6021 987244.1111 1215415.028 1176051.594 940235.3488 1.324963518 0.93597981 1.034510891 0.878159861 1.021559931 0.896445345 1.049996804 1.292671064 1.250805552 1 19.8426624 1.898599722 6.130241002 1.207251605 1.00407257 0.217698775 0.137321726 0.27767898 13.97809548 0.057689625 0.035098037 79.17712393 -1.898599722 -0.203179036 VIHCSGYLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VIHCSGYLK 9 0 H7BZX8;Q14190-2;Q14190;P81133 H7BZX8 SIM2;SIM1 Single-minded homolog 2;Single-minded homolog 1 0 ; 65.06 0.067627 56598000000 3232900 5181200 5732300 4553000 5290800 4948900 3827400 1010760 1250380 2082620 FALSE TRUE 3106554.694 5033437.249 6768254.124 4787980.876 5460983.387 5048970.149 3874240.866 989887.4528 1108442.104 1941562.292 1.600028341 2.592467555 3.485983505 2.46604546 2.812674828 2.600467762 1.995424448 0.509840687 0.570902159 1 20.88878656 1.898648129 2.943328941 0.643168754 2.632078785 0.777468213 0.452638599 0.115571417 1.774876267 0.243771101 0.129200368 79.18594963 -1.898648129 1.988910031 S(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SMDSSDLSDGAVTLQEYLELKK 22 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.998)MDS(0.002)SDLSDGAVTLQEYLELKK 168.06 6.03E-12 146770000 184700 159680 141440 142650 141960 135580 162550 212310 213050 190240 TRUE FALSE 177481.7198 155126.0827 167001.3543 150012.1836 146526.2723 138321.5205 164539.3355 207925.7243 188865.4572 177354.8754 1.000715201 0.874664891 0.941622574 0.845830617 0.82617561 0.779913832 0.927740696 1.172371066 1.064901412 1 17.43627946 1.898677184 5.722093242 1.091388771 0.875324541 0.624306312 0.069519473 0.13661701 6.265162983 0.031257637 0.018836857 79.19124741 -1.898677184 -0.21606423 TPGHPPPPEIPSELGACDFEKPES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPGHPPPPEIPSELGACDFEKPESPR 26 1 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 TPGHPPPPEIPSELGACDFEKPES(1)PR;TPGHPPPPEIPSELGACDFEKPES(1)PR 168.96 5.26E-12 784470000 478920 477140 427550 573900 628330 582070 495030 440020 487000 468030 TRUE FALSE 460203.2769 463532.4344 504817.7958 603519.0478 648540.8051 593839.8542 501088.3252 430933.4332 431717.8017 436329.9112 1.054714025 1.062343934 1.156963533 1.383171385 1.486354221 1.360988186 1.148416169 0.987632115 0.989429765 1 18.73505985 1.898689899 3.494139329 0.99364066 1.254879655 0.438244699 0.130204259 0.265525844 5.57064489 0.075975116 0.041880015 79.19356588 -1.898689899 0.261238995 KGDEVDGVDEVAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KGDEVDGVDEVAK 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 154.6 6.24E-05 4848010000 10680560 9275220 8281190 8180990 8952070 9038440 10202730 12144890 13839420 12380070 FALSE TRUE 10263151.91 9010699.807 9777785.247 8603211.874 9240021.462 9221203.45 10327594.06 11894093.78 12268427.06 11541556.83 0.88923462 0.780717882 0.847180791 0.745411733 0.800587096 0.798956639 0.894818109 1.030545008 1.062978525 1 23.46033451 1.898938888 2.506191291 1.03855596 0.807327865 0.862769263 0.039294937 0.090021869 1.02517842 0.021290887 0.010823474 79.23898219 -1.898938888 -0.231228095 YHTINGHNCEVK ddPTM_BT-474_Pertuzumab_2h_R1 3 YHTINGHNCEVK 12 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 217.91 2.06E-11 4389270000 1945460 1857670 1665220 1726210 1720670 1508080 1726740 119051 1906940 1412130 FALSE TRUE 1869429.272 1804691.07 1966162.297 1815299.905 1776016.913 1538574.411 1747872.361 116592.5552 1690472.166 1316485.177 1.420015436 1.370840403 1.493493683 1.378898856 1.349059559 1.168698621 1.327681003 0.088563515 1.284079908 1 20.32825985 1.898991098 12.90967721 0.693275609 1.359625269 0.427882358 0.294523163 0.686881311 85.56547823 0.115610647 0.074157968 79.24850867 -1.898991098 0.66634966 TTGIVMDSGDGVTHTVPIYEGYALPHAILR ddPTM_BT-474_Pertuzumab_2h_R1 10 TTGIVMDSGDGVTHTVPIYEGYALPHAILR 30 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L3I0;I3L1U9;I3L4N8 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;;;; 326.86 2.23E-105 1.14997E+11 10075959 11241022 8404569 10083288 9610777 10439197 9874670 7323807 10488263 9798131 FALSE TRUE 9682179.383 10920439.06 9923461.577 10603687.7 9919916.37 10650284.72 9995519.165 7172567.826 9297679.355 9134494.86 1.059957834 1.195516471 1.086372233 1.160840075 1.085984121 1.165941289 1.094260747 0.785217786 1.017864644 1 23.12289352 1.899002104 7.621569613 0.915483278 1.127116446 0.594684009 0.07058206 0.15509682 10.38580396 0.027696384 0.01726629 79.25051705 -1.899002104 0.211633168 AEAPLPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 AEAPLPSPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 AEAPLPS(1)PK;AEAPLPS(1)PK;AEAPLPS(1)PK;AEAPLPS(1)PK;AEAPLPS(1)PK;AEAPLPS(1)PK 159.94 6.89E-05 4444670000 6507180 6358800 6292310 6704350 5975720 5935670 5344580 5788760 5288510 4847050 TRUE FALSE 6252872.212 6177453.25 7429470.389 7050362.307 6167934.461 6055693.314 5409988.569 5669220.083 4688180.516 4518754.986 1.383759958 1.36706975 1.64414101 1.560244432 1.364963243 1.340124289 1.197229897 1.254597804 1.037493852 1 22.1074939 1.899074144 0.723921978 1.008078742 1.488212409 0.777430883 0.091089724 0.3276766 0.330285139 0.087381105 0.045352575 79.26366406 -1.899074144 0.480133667 KDDEDSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDDEDSFR 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 123.86 0.0021318 1370470000 1559300 1515490 1277960 1512300 1601610 1582480 1716450 1832100 2103730 2174200 FALSE TRUE 1498360.832 1472269.709 1508915.8 1590349.984 1653127.24 1614478.83 1737456.429 1794266.495 1864923.39 2026939.497 0.739223264 0.726351088 0.744430607 0.784606539 0.81557799 0.796510617 0.857182186 0.885209695 0.920068602 1 20.9508716 1.899078358 0.352567466 1.014005143 0.70546277 0.975186111 0.013217022 0.180120215 0.064202718 0.017823388 0.019103953 79.26443307 -1.899078358 -0.308542372 AEDGATPSPSNET(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 7 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK 363.28 1.20E-82 14811100000 10130110 8741250 7269300 6694250 7247810 6997390 8384090 11874120 11143920 9739190 TRUE FALSE 9734214.102 8491958.109 8583024.215 7039741.045 7480942.391 7138882.02 8486697.001 11628915.27 9878908.921 9079545.987 1.072103618 0.935284443 0.945314251 0.775340645 0.823933532 0.786259801 0.934704997 1.280781582 1.088039968 1 23.11418873 1.899105652 6.743129849 1.146658465 0.884177422 0.4953124 0.104783742 0.18549135 10.63035765 0.04652439 0.028641431 79.2694147 -1.899105652 -0.262481042 EGHGSSS(ph)FDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGHGSSSFDR 10 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 EGHGSS(0.029)S(0.971)FDR;EGHGS(0.016)S(0.013)S(0.971)FDR 133.16 0.00013175 300210000 113553 160248 171479 224415 155611 186421 166199 131141 142517 193269 TRUE FALSE 109115.2232 155677.8839 202469.0698 235997.085 160616.3691 190190.5603 168232.9931 128432.8925 126339.0676 180178.7185 0.605594402 0.864019265 1.123712454 1.309794448 0.89142808 1.055566173 0.933700686 0.712808336 0.701187514 1 17.45906909 1.899276119 5.213146797 0.779265187 0.9886481 0.133384227 0.18895934 0.38966979 15.71342625 0.089194568 0.05300426 79.3005353 -1.899276119 0.209382913 S(ph)SSSQTLTQFDSNIAPADPDTAIVHPVPIR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSSSQTLTQFDSNIAPADPDTAIVHPVPIR 30 0 Q96D71;Q96D71-3;H0YE73 Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.288)S(0.288)S(0.288)S(0.067)QT(0.067)LT(0.001)QFDSNIAPADPDTAIVHPVPIR;S(0.332)S(0.332)S(0.259)S(0.074)QT(0.003)LTQFDSNIAPADPDTAIVHPVPIR;S(0.166)S(0.166)S(0.166)S(0.166)QT(0.166)LT(0.166)QFDS(0.005)NIAPADPDTAIVHPVPIR;S(0.448)S(0.448)S(0.099)S(0.004)QTLTQFDSNIAPADPDTAIVHPVPIR;S(0.291)S(0.291)S(0.291)S(0.093)QT(0.035)LTQFDSNIAPADPDTAIVHPVPIR;S(0.426)S(0.426)S(0.14)S(0.008)QTLTQFDSNIAPADPDTAIVHPVPIR 209.06 5.34E-26 2018770000 65501.9 108036.3 74249.7 118452.2 88995.4 93782.7 75827.5 84551.2 64604.2 79575.5 TRUE FALSE 62942.01333 104955.2105 87668.27247 124565.5322 91858.01786 95679.05045 76755.49963 82805.18817 57270.60206 74185.78051 0.848437705 1.414761829 1.181739571 1.679102537 1.238215966 1.289722232 1.034638971 1.11618679 0.77198894 1 16.17885507 1.899412535 1.381669161 0.922930405 1.297031388 0.321490805 0.209778559 0.478334834 1.699374217 0.150210333 0.065497654 79.32544829 -1.899412535 0.374100983 LSDPPTSPSS(ph)PSQMMPHVQTHF ddPTM_BT-474_Pertuzumab_2h_R1 3 LSDPPTSPSSPSQMMPHVQTHF 22 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 1 LSDPPT(0.004)S(0.004)PS(0.131)S(0.843)PS(0.018)QMMPHVQTHF;LSDPPTS(0.001)PS(0.025)S(0.97)PS(0.004)QMMPHVQTHF;LSDPPTS(0.002)PS(0.039)S(0.957)PS(0.002)QMMPHVQTHF 206.48 5.94E-23 954968000 551259 612826 482162 637637 643622 626878 544672 120804 464724 428220 TRUE FALSE 529715.1888 595348.8025 569299.399 670545.522 664324.6862 639553.9027 551337.8589 118309.3552 411970.4798 399216.278 1.32688775 1.491293906 1.42604255 1.679654761 1.66407214 1.60202361 1.381050546 0.296354036 1.031948101 1 18.60681102 1.899477627 6.626548768 0.720029162 1.533896037 0.714571029 0.2134229 0.113646093 6.385657432 0.089612182 0.055059105 79.33733848 -1.899477627 0.813866875 KADKVEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 KADKVEQR 8 2 Q99832-3;Q99832;Q99832-4 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 109.66 0.0020106 1633410000 3660720 3498960 2834680 2868800 3075330 3131720 3552630 3821850 4426030 4168400 FALSE TRUE 3517655.015 3399173.087 3346969.733 3016859.112 3174250.782 3195045.524 3596108.149 3742927.462 3923605.63 3886070.555 0.90519587 0.874706992 0.861273537 0.776326387 0.816827882 0.82217898 0.925384163 0.963165081 1.009658876 1 21.88988066 1.899538342 1.966501619 0.997162414 0.840974721 0.782624947 0.035165849 0.161213675 1.158514294 0.024157418 0.01144848 79.34843079 -1.899538342 -0.156187693 NWEEGGYFNTDKPHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 NWEEGGYFNTDKPHPR 16 1 O95573 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 138.98 2.19E-06 256810000 105460 129920 110960 168850 102470 108320 132410 168710 172090 153570 FALSE TRUE 101338.5066 126214.8088 131012.9403 177564.3687 105766.0406 110510.3046 134030.4732 165226.0795 152555.0647 143168.5671 0.707826506 0.88158184 0.915095701 1.24024688 0.738751828 0.771889437 0.936172485 1.154066726 1.065562558 1 17.12735526 1.899589254 5.686864163 1.083863446 0.885712481 0.272180714 0.143273981 0.314922964 14.40245032 0.066249409 0.039897769 79.35773314 -1.899589254 -0.198150965 HLHPSCLGS(ph)PPLR ddPTM_BT-474_Pertuzumab_2h_R1 5 HLHPSCLGSPPLR 13 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR 147.83 2.66E-05 8778960000 1332050 2264420 1969180 2828560 2191720 2476790 2017100 212629 1553200 1664250 TRUE FALSE 1279992.013 2199840.959 2325054.63 2974542.321 2262218.664 2526872.391 2041785.873 208238.1368 1376887.248 1551528.865 0.82498756 1.417853711 1.498557122 1.917168534 1.458057736 1.628633825 1.315983169 0.1342148 0.887439015 1 20.56525911 1.899625184 6.802805406 0.601365812 1.477756821 0.524710067 0.332654314 0.171849185 10.00568537 0.142760188 0.087979999 79.36429888 -1.899625184 0.876391009 APKPEDIDEEDDDVPDLVENFDEASKNEAN ddPTM_BT-474_Pertuzumab_2h_R1 1 APKPEDIDEEDDDVPDLVENFDEASKNEAN 30 2 Q96K17;Q96K17-2 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4 0 58.477 0.022705 170720000 115870 96678 67954 68995 91581 84297 90327 108890 119180 90404 FALSE TRUE 111341.6723 93920.8381 80234.79943 72555.84022 94526.78604 86001.5431 91432.44885 106641.3834 105651.186 84280.85656 1.321079031 1.114379254 0.951993166 0.860881619 1.121568882 1.020416102 1.084854291 1.265309678 1.253560896 1 16.36291736 1.89962731 6.303112995 1.198237294 1.055261591 0.10697931 0.132333163 0.412939058 21.73980947 0.059306469 0.036218611 79.36468741 -1.89962731 -0.142975703 NIILEEGK ddPTM_BT-474_Pertuzumab_2h_R1 7 NIILEEGK 8 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;; 131.06 0.0023757 3222161000 4742340 4137690 4270460 4419320 4310360 3602840 4714850 5866910 5991460 5950880 FALSE TRUE 4557004.11 4019687.132 5042227.118 4647401.635 4449006.644 3675691.893 4772551.745 5745756.258 5311334.579 5547821.597 0.821404227 0.724552342 0.908866125 0.837698465 0.801937583 0.662546881 0.860256888 1.035677907 0.957372995 1 22.40348996 1.899696161 4.762958423 0.995556939 0.794898177 0.667154877 0.064505941 0.136408199 4.814417902 0.030420512 0.017811264 79.37727041 -1.899696161 -0.200658762 FKDPLKDGEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKDPLKDGEAK 11 2 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 93.959 0.0049836 3835300000 6452300 5558400 4991300 4013100 5208700 5405400 6164400 7357800 8742300 7722100 FALSE TRUE 6200136.983 5399879.874 5893338.941 4220216.572 5376242.566 5514700.892 6239841.771 7205858.859 7749910.755 7199075.289 0.861240747 0.75007965 0.818624435 0.58621648 0.746796269 0.766029062 0.86675601 1.000942284 1.076514753 1 22.77938018 1.899864821 1.912139904 1.040973988 0.747580981 0.75665513 0.06891741 0.158907322 1.081541186 0.044342497 0.020847385 79.408103 -1.899864821 -0.293393007 SGCSEAQPPES(ph)PETR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGCSEAQPPESPETR 15 0 Q9Y6A5;A0A494BZT8;A0A494C117;H0Y8F2 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 SGCSEAQPPES(0.996)PET(0.004)R;SGCSEAQPPES(1)PETR;SGCSEAQPPES(1)PETR;SGCSEAQPPES(0.999)PET(0.001)R 301.43 2.59E-44 1458350000 607132 634552 642658 718310 681030 745700 632130 584884 590295 666460 TRUE FALSE 583404.6102 616455.1983 758800.5964 755382.0652 702935.9484 760778.5649 639866.196 572805.941 523287.1863 621320.0706 0.938975961 0.992170103 1.221271664 1.215769619 1.131358831 1.224455158 1.029849552 0.921917653 0.842218385 1 19.24497713 1.899874695 3.309491392 0.913740538 1.124519257 0.456159197 0.096713593 0.230123522 4.384854904 0.052598849 0.028677474 79.4099083 -1.899874695 0.210778719 GGAAVDPDSGLEHSAHVLEK ddPTM_BT-474_Pertuzumab_2h_R1 7 GGAAVDPDSGLEHSAHVLEK 20 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;;; 235.37 8.89E-30 8248160000 15652190 17787310 15118150 17501140 17242830 19364540 17560410 358849.3 19895470 14718780 FALSE TRUE 15040485.11 17280033.33 17850336.01 18404375.93 17797461.29 19756104.27 17775319.55 351438.9366 17637019.65 13721863.92 1.096096361 1.259306566 1.30086817 1.341244603 1.297014851 1.439753694 1.295401241 0.025611603 1.285322443 1 23.70997313 1.899918706 24.99963097 0.661651323 1.29735513 0.353368149 0.311794948 33.5874629 8384.307048 0.121088561 0.078149765 79.41795611 -1.899918706 0.635703807 EHNFFHLDPANVVMFEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EHNFFHLDPANVVMFEQR 18 0 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 94.385 0.0011413 112922000 78045 88340 74171 90404 84725 83814 80888 7387.9 84112 63363 FALSE TRUE 74994.91512 85820.62969 87575.34962 95069.76127 87450.25657 85508.77651 81877.93154 7235.337283 74563.95839 59071.36757 1.269564566 1.452829572 1.482534656 1.609405118 1.480416997 1.447550311 1.386084916 0.122484675 1.262269039 1 15.85017139 1.89993955 9.6656604 0.70798339 1.461787221 0.523644545 0.281991781 0.260724257 23.58483467 0.11130617 0.070599281 79.42176793 -1.89993955 0.753803831 LLPEGEETLES(ph)DDEKDEHTSK ddPTM_BT-474_Pertuzumab_2h_R1 5 LLPEGEETLESDDEKDEHTSK 21 1 Q8N6N3 Q8N6N3 C1orf52 UPF0690 protein C1orf52 1 LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEET(0.001)LES(0.999)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK 316.54 6.07E-67 2756250000 2229480 2082750 1852210 1647280 1939430 2201900 2161300 2892260 2936010 2764710 TRUE FALSE 2142349.457 2023352.009 2186945.549 1732296.318 2001813.527 2246423.927 2187750.636 2832533.82 2602726.454 2577453.729 0.831188328 0.785019722 0.848490712 0.672095991 0.776663226 0.871567121 0.848803069 1.098965924 1.009805307 1 21.2975151 1.900089937 3.360756604 1.043077952 0.794894612 0.774848158 0.057375397 0.110148064 2.158616461 0.029722067 0.016262502 79.44927476 -1.900089937 -0.24818334 AHAS(ph)PFSGALTPSAPPGPEMNR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHASPFSGALTPSAPPGPEMNR 22 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 AHAS(0.857)PFS(0.143)GALTPSAPPGPEMNR;AHAS(0.999)PFS(0.001)GALTPSAPPGPEMNR 211.03 2.43E-23 943720000 385300 478820 423200 513540 426350 471300 454650 348910 472130 491410 TRUE FALSE 370242.05 465164.5224 499681.654 540043.8609 440063.935 480830.0089 460214.1427 341704.8866 418535.7817 458126.363 0.808165781 1.015362922 1.09070705 1.178809832 0.960573262 1.049557606 1.004557214 0.74587475 0.913581526 1 18.80538606 1.900157919 8.645693259 0.861311651 1.025330919 0.221263397 0.107318249 0.395356198 31.32824229 0.045426111 0.028612097 79.46171232 -1.900157919 0.164019268 GHDGGHSHGGDMSNRPVCR ddPTM_BT-474_Pertuzumab_2h_R1 7 GHDGGHSHGGDMSNRPVCR 19 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 ;;;;;; 202.96 3.41E-16 763293000 95122.8 110205.7 89885.97 117174.3 106369.6 112396 98178.7 21610.77 100639.1 60631.6 FALSE TRUE 91405.29581 107062.7413 106130.3643 123221.6797 109791.0748 114668.7241 99380.2403 21164.50005 89214.97128 56524.96773 1.617078249 1.89407877 1.87758381 2.179951349 1.942346528 2.028638471 1.758165361 0.374427459 1.578328566 1 15.78660064 1.90031921 7.116870393 0.939699045 1.92898867 0.662069199 0.301072101 0.136338879 8.468715726 0.122454944 0.075840475 79.49122874 -1.90031921 0.989289625 RPYPDPEDEIPDEMIQCVVCEDWFHGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPYPDPEDEIPDEMIQCVVCEDWFHGR 27 1 E9PCJ7;Q8N806;H0YJA0;H0YJM2 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 ;;; 230.75 3.11E-35 438295000 109156 122440 90682 121315 124321 125090 110668 99139 107555 114884 FALSE TRUE 104890.0628 118948.1311 107070.2546 127576.0817 128319.8979 127619.4055 112022.3881 97091.74501 95345.80731 107102.8044 0.979340023 1.110597727 0.999696089 1.191155381 1.198100261 1.191559888 1.045933286 0.906528504 0.890226992 1 16.70863673 1.900374059 3.936438393 0.925813751 1.114586954 0.523890151 0.076121233 0.18408472 4.772865974 0.038621812 0.021840463 79.50126864 -1.900374059 0.188773203 WPPEDEISKPEVPEDVDLDLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 WPPEDEISKPEVPEDVDLDLKK 22 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 65.425 0.012932 189680000 212240 173310 160670 149750 171880 175670 203900 219020 271600 240120 FALSE TRUE 203945.4262 168367.3685 189706.6431 157478.6154 177408.6763 179222.1678 206395.3892 214497.1605 240769.1066 223856.4585 0.911054465 0.752122005 0.84744771 0.703480331 0.792510868 0.800612004 0.921998814 0.958190627 1.075551307 1 17.77221442 1.900426791 1.567743804 1.02954742 0.794236636 0.735632091 0.057226061 0.182623199 0.838954555 0.038103875 0.017003885 79.51092236 -1.900426791 -0.235310785 VGSLT(ph)PPSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGSLT(1)PPS(0.061)S(0.939)PK;VGSLT(1)PPS(0.016)S(0.985)PK 141.34 0.00020251 474300000 1163050 994480 894020 876200 988370 959300 1061600 1353980 1397160 1258550 TRUE FALSE 1117596.72 966118.4041 1055589.301 921420.787 1020161.819 978697.7033 1074592.178 1326019.84 1238560.254 1173307.287 0.952518349 0.823414645 0.899669944 0.78531924 0.869475396 0.834135877 0.915865937 1.130155633 1.055614558 1 20.16214947 1.900558805 4.681862423 1.070470272 0.858819903 0.749803192 0.051837311 0.095834312 3.305582584 0.022583049 0.013188271 79.53509517 -1.900558805 -0.211650369 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.187)T(0.812)PGGT(0.034)LFS(0.556)T(0.337)T(0.072)PGGTR 143.62 3.70E-08 1280800000 331610 369300 289050 400270 341600 344490 342970 342360 366290 354020 TRUE FALSE 318650.3146 358767.9256 341287.7649 420927.9827 352587.8742 351455.8238 347167.3695 335290.1464 324710.2948 330041.9101 0.965484397 1.087037478 1.034074021 1.275377368 1.068312428 1.064882408 1.051888742 1.015901727 0.983845642 1 18.33228971 1.900602002 1.456485854 0.992814684 1.090621999 0.205121152 0.073489453 0.642105025 2.54065665 0.053974971 0.023742199 79.54300651 -1.900602002 0.097807315 RS(ph)SGFISELPSEEGK ddPTM_BT-474_Pertuzumab_2h_R1 6 RSSGFISELPSEEGK 15 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 RS(0.471)S(0.471)GFIS(0.057)ELPSEEGK;RS(0.498)S(0.498)GFIS(0.004)ELPSEEGK;RS(0.489)S(0.489)GFIS(0.023)ELPSEEGK;RS(0.499)S(0.499)GFIS(0.001)ELPSEEGK;RS(0.495)S(0.495)GFIS(0.01)ELPSEEGK;RS(0.498)S(0.498)GFIS(0.004)ELPSEEGK 157.97 1.14E-06 1707580000 2310130 2147790 1658990 1791130 1872330 2175390 2120790 2826780 2730340 2519790 TRUE FALSE 2219847.566 2086537.132 1958806.397 1883570.434 1932555.195 2219377.876 2146744.862 2768406.005 2420403.25 2349122.379 0.944968889 0.888219852 0.833846042 0.801818777 0.822671144 0.944768947 0.913849735 1.178485221 1.030343617 1 21.16369044 1.900652592 5.472445326 1.083757538 0.870792175 0.665989241 0.062248382 0.125290899 5.462782189 0.028749542 0.017221183 79.55227288 -1.900652592 -0.212965363 GDILHVISQEDPNWWQAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDILHVISQEDPNWWQAYR 19 0 Q8N3R9-2;Q8N3R9 Q8N3R9-2 MPP5 MAGUK p55 subfamily member 5 0 143.71 1.42E-07 117640000 59688 87998 55915 86348 74456 90566 71686 56067 72509 61847 FALSE TRUE 57355.32697 85488.3832 66020.08432 90804.43063 76850.94486 92397.30657 72563.31471 54909.19686 64278.0823 57658.0476 0.994749725 1.482679119 1.145028094 1.574878693 1.332874561 1.602504948 1.258511478 0.952324942 1.11481545 1 15.81523437 1.900674991 4.944578874 1.027818922 1.365639483 0.410415299 0.177813532 0.20629039 7.744546743 0.077051627 0.045419148 79.55637597 -1.900674991 0.337820561 EQDDLLVLLADQDQK ddPTM_BT-474_Pertuzumab_2h_R1 6 EQDDLLVLLADQDQK 15 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;;;; 280.23 2.49E-33 355001800 974561 909089 776385 767149 913012 879264 934403 1118702 1209978 1085804 FALSE TRUE 936474.0787 883162.6718 916695.0401 806741.6518 942379.8602 897043.3205 945838.5034 1095600.413 1072626.37 1012261.528 0.925130564 0.872464919 0.905591109 0.796969587 0.930964809 0.886177431 0.934381558 1.082329401 1.059633643 1 19.94915064 1.90085407 3.652174254 1.0534077 0.885452624 0.762280763 0.040087078 0.103801448 2.36375654 0.019202043 0.010699714 79.58918724 -1.90085407 -0.167955076 DCHEEVYAGSHQYPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 DCHEEVYAGSHQYPGR 16 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;; 217.48 8.22E-15 2145010000 305063 330392 297310 341401 328101 343546 308023 77484 316089 221978 FALSE TRUE 293140.8007 320969.5436 351040.5306 359020.7465 338654.6666 350492.7355 311792.6776 75883.92832 280207.9019 206943.2323 1.416527602 1.551002852 1.696313171 1.734875514 1.636461665 1.693666092 1.506658005 0.366689587 1.354032691 1 17.65887554 1.901008781 7.742027725 0.853796764 1.625063654 0.638739493 0.240885146 0.153035433 10.6588349 0.097150667 0.060659859 79.61754484 -1.901008781 0.77126689 LHS(ph)PQTHWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHSPQTHWK 9 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LHS(1)PQTHWK 156 0.00012028 152090000 309910 285510 236390 265650 295870 284810 283980 54307 318370 257090 TRUE FALSE 297798.3746 277367.5343 279110.9315 279360.2283 305386.9273 290569.0533 287455.4322 53185.54147 282229.9723 239677.0653 1.242498418 1.157255218 1.16452916 1.165569296 1.27415999 1.212335661 1.199344759 0.22190501 1.177542674 1 17.87073234 1.901144028 24.99989554 0.71266994 1.20093128 0.365330987 0.234780526 34.72465151 8776.816484 0.090728402 0.058555366 79.64234305 -1.901144028 0.48826134 LLKEGEEPTVYS(ph)DEEEPKDESAR ddPTM_BT-474_Pertuzumab_2h_R1 6 LLKEGEEPTVYSDEEEPKDESAR 23 2 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 LLKEGEEPT(0.001)VYS(0.999)DEEEPKDESAR;LLKEGEEPTVYS(0.999)DEEEPKDES(0.001)AR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPT(0.023)VY(0.006)S(0.97)DEEEPKDESAR 197.35 1.56E-24 12532480000 4572102 6007531 2325039 3424261 3210234 3627513 3863238 6394380 5163054 2609096 TRUE FALSE 4393419.199 5836202.098 2745225.268 3600987.521 3313494.092 3700863.798 3910517.462 6262333.818 4576965.755 2432379.604 1.806222677 2.39937964 1.128617122 1.480438133 1.362243824 1.521499273 1.607692095 2.57457093 1.881682344 1 21.21393697 1.901317806 24.01149783 2.018065943 1.607961888 0 0.484179395 65.18770229 15850.27588 0.197305475 0.12733245 79.67421732 -1.901317806 -0.410104055 NT(ph)PSQHSHSIQHS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 7 NTPSQHSHSIQHSPER 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 NT(1)PSQHSHS(0.227)IQHS(0.773)PER;NT(0.992)PS(0.008)QHSHS(0.002)IQHS(0.998)PER;NT(0.948)PS(0.052)QHSHS(0.002)IQHS(0.998)PER;NT(0.995)PS(0.005)QHSHSIQHS(1)PER;NT(0.979)PS(0.021)QHS(0.002)HS(0.003)IQHS(0.996)PER;NT(0.999)PS(0.001)QHSHSIQHS(1)PER;NT(0.966)PS(0.034)QHSHSIQHS(1)PER 217.1 2.59E-14 799297000 536896 659508 486136 597723 489219 569824 520033 15520.32 519740 343336.8 TRUE FALSE 515913.5108 640699.4776 573991.5892 628571.5557 504955.1734 581346.2317 526397.3194 15199.81997 460741.2941 320082.2927 1.611815219 2.001671108 1.793262552 1.963781096 1.577579219 1.816239901 1.644568698 0.047487225 1.439446369 1 18.28808334 1.901497525 8.074757739 0.744682706 1.795269634 0.61139189 0.344533346 0.167632201 12.37506249 0.136610232 0.08560559 79.7071949 -1.901497525 1.050586928 EGRPSGEAFVELESEDEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGRPSGEAFVELESEDEVK 19 1 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;E7EN40;D6R9T0;D6RFM3;D6RDU3;D6RJ04;D6RIH9;D6RAM1;D6RDL0;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ;;; 306.27 1.23E-50 2494550000 2507220 2313040 1898140 1845230 2119340 2244460 2249400 2579040 2824620 2656120 FALSE TRUE 2409235.071 2247074.364 2241176.122 1940462.541 2187510.496 2289844.519 2276928.83 2525781.923 2503980.979 2476218.627 0.972949256 0.907462023 0.905080068 0.783639425 0.883407657 0.924734389 0.919518497 1.020015719 1.011211592 1 21.23970727 1.901733418 2.113596085 1.014997074 0.890305627 0.557198842 0.04524118 0.237575322 1.960065176 0.028956073 0.014045359 79.75050066 -1.901733418 -0.124691446 LLPQLTYLDGYDRDDK ddPTM_BT-474_Pertuzumab_2h_R1 4 LLPQLTYLDGYDRDDK 16 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;; 176.17 2.98E-09 2457874000 1270719 1219448 1167856 1412649 1151655 1174413 1591854 1745318 2132418 2006170 FALSE TRUE 1221057.897 1184670.537 1378913.558 1485555.984 1188699.029 1198160.436 1611335.585 1709276.573 1890354.848 1870290.319 0.652870779 0.633415318 0.737272467 0.79429165 0.635569257 0.640628048 0.861543028 0.913909758 1.010728029 1 20.8348308 1.90176146 1.851840923 0.989253225 0.685606037 0.85024016 0.055480721 0.13242065 0.846446012 0.037806983 0.017637823 79.75565024 -1.90176146 -0.303647188 TT(ph)PTMSEEPPLDLTGK ddPTM_BT-474_Pertuzumab_2h_R1 4 TTPTMSEEPPLDLTGK 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 T(0.209)T(0.791)PTMSEEPPLDLTGK;T(0.262)T(0.726)PT(0.012)MSEEPPLDLTGK;T(0.205)T(0.795)PT(0.001)MSEEPPLDLTGK;T(0.248)T(0.751)PT(0.001)MSEEPPLDLTGK 260.14 1.00E-25 653311000 787693 724051 585045 601163 711896 678396 734227 877292 939454 876196 TRUE FALSE 756909.0867 703401.7744 690775.6458 632189.0945 734794.7814 692113.6319 743212.6897 859175.6136 832811.1204 816850.4645 0.92661891 0.861114494 0.845657407 0.773934915 0.899546261 0.847295389 0.909851585 1.051815052 1.019539263 1 19.63971247 1.901765735 3.564242384 1.026819709 0.857230951 0.776880808 0.03936337 0.106565135 2.327110466 0.019824609 0.010997844 79.75643522 -1.901765735 -0.169588758 KEPPAPHRHT(ph)PQPPPPQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEPPAPHRHTPQPPPPQPR 19 2 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 KEPPAPHRHT(1)PQPPPPQPR;KEPPAPHRHT(1)PQPPPPQPR 83.606 0.003346 287470000 282870 267850 214200 251540 229960 248020 238280 3029.36 264420 157878 TRUE FALSE 271815.1277 260211.1803 252910.7049 264522.0095 237356.8722 253035.1343 241196.1419 2966.802657 234404.1501 147184.7824 1.846761079 1.767921764 1.718321016 1.797210317 1.612645467 1.719166412 1.638730159 0.020156993 1.59258414 1 17.16726899 1.901904918 9.851094684 0.774748273 1.734877035 0.535841072 0.363601395 0.276647232 26.16915689 0.142050321 0.090195325 79.78199984 -1.901904918 0.960128761 S(ph)PHSTVPEHHPHPISPYEHLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPHSTVPEHHPHPISPYEHLLR 22 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.999)PHST(0.001)VPEHHPHPISPYEHLLR;S(0.997)PHS(0.002)T(0.002)VPEHHPHPISPYEHLLR;S(0.998)PHS(0.001)T(0.001)VPEHHPHPISPYEHLLR 210.43 2.21E-23 1926260000 153773 220167 225634 257850 246216 208693 215666 52853 231982 165484 TRUE FALSE 147763.3812 213888.0527 266411.083 271157.6694 254135.7612 212912.9154 218305.385 51761.56708 205648.3759 154275.6213 0.957788275 1.386402148 1.726851467 1.757618392 1.647283992 1.3800814 1.415034879 0.335513587 1.332993341 1 17.23515058 1.901908651 8.932850153 0.826456904 1.49503053 0.411383664 0.314220525 0.302954824 25.46679979 0.132692369 0.083769605 79.78268565 -1.901908651 0.668573625 TLTPGGHAEHDGQPYCHKPCYGILFGPK ddPTM_BT-474_Pertuzumab_2h_R1 3 TLTPGGHAEHDGQPYCHKPCYGILFGPK 28 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ;; 145.16 6.28E-08 5563950000 4528960 5359580 4373990 5428900 4635210 5335150 5016700 244527 5742870 4010640 FALSE TRUE 4351963.236 5206730.026 5164467.292 5709086.18 4784305.739 5443030.388 5078095.875 239477.432 5090963.474 3738995.78 1.163939061 1.392547714 1.381244482 1.526903617 1.279569708 1.455746598 1.358144318 0.064048596 1.361585777 1 21.83421941 1.902002315 16.30258068 0.705943283 1.374740962 0.379678283 0.318109275 2.109248324 348.3316832 0.123078323 0.079269707 79.79989408 -1.902002315 0.668797678 SQDPQEDKKEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQDPQEDKKEEK 12 2 Q8IWE2;Q8IWE2-2 Q8IWE2 FAM114A1 Protein NOXP20 0 ; 119.87 0.00026503 425620000 1633970 1191800 1017290 848270 1223560 1151000 1321870 1762940 2006220 1467690 FALSE TRUE 1570112.646 1157811.031 1201136.932 892049.3164 1262916.919 1174274.009 1338047.44 1726534.673 1778482.316 1368282.049 1.147506574 0.846178631 0.877843083 0.651948417 0.922994583 0.858210491 0.977903234 1.261826591 1.299792187 1 20.38393422 1.902082876 3.693994046 1.209865965 0.875093198 0.496261725 0.135411698 0.177605486 4.136246127 0.065557086 0.036645616 79.8146982 -1.902082876 -0.334772768 NQAS(ph)DS(ph)ENEELPKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQASDSENEELPKPR 15 1 Q96ST2;Q96ST2-3 Q96ST2 IWS1 Protein IWS1 homolog 2 NQAS(1)DS(1)ENEELPKPR;NQAS(1)DS(1)ENEELPKPR 191 1.99E-10 408920000 895920 742360 792290 830640 762960 730680 899360 1098460 1230900 1060490 TRUE FALSE 860906.4559 721188.6196 935474.4274 873509.4299 787501.3013 745454.8502 910366.6367 1075776.417 1091173.392 988662.0677 0.870779293 0.729459178 0.946202406 0.883526797 0.796532331 0.754003693 0.920806681 1.088113373 1.10368692 1 19.91511796 1.902179703 3.645891579 1.069951557 0.831657696 0.719731037 0.065012382 0.12366223 2.814085093 0.032429479 0.018080369 79.83249513 -1.902179703 -0.23829386 EGEVLYIIEEDKGDGWTR ddPTM_BT-474_Pertuzumab_2h_R1 4 EGEVLYIIEEDKGDGWTR 18 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ;;; 215.81 8.49E-19 454829000 670441 589788 522399 511215 565703 575557 610547 714652 776068 706817 FALSE TRUE 644239.4245 572967.8237 616808.12 537598.8674 583899.3508 587195.1569 618019.0568 699894.1865 687972.0142 658943.655 0.977685147 0.86952476 0.936055936 0.815849524 0.886114232 0.891115883 0.93789363 1.062145725 1.04405287 1 19.32979558 1.902233425 3.553858084 1.039878631 0.893364294 0.682822988 0.042302034 0.127556038 2.773034536 0.0204869 0.01136207 79.84237086 -1.902233425 -0.146514338 ATENTVNPCPDDTLISFLPLAHMFER ddPTM_BT-474_Pertuzumab_2h_R1 2 ATENTVNPCPDDTLISFLPLAHMFER 26 0 E7EPM6;P33121-2;P33121;B7Z3Z9;D6RER0 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ; 180.42 2.16E-17 222324000 200207 237060 176344 221790 229470 249290 215620 175143 216939 226820 FALSE TRUE 192382.6891 230299.2809 208213.2836 233236.6085 236851.1109 254330.8146 218258.8221 171526.2358 192312.9942 211457.2794 0.909794591 1.089105476 0.98465886 1.102996355 1.120089654 1.202752704 1.032165091 0.811162597 0.909464998 1 17.6900067 1.902304614 6.439995386 0.891680308 1.073040803 0.412313295 0.085610079 0.209727004 11.61234497 0.03758326 0.023023866 79.85545967 -1.902304614 0.181360495 VHVGDEDFVHLR ddPTM_BT-474_Pertuzumab_2h_R1 6 VHVGDEDFVHLR 12 0 P04080 P04080 CSTB Cystatin-B 0 ;;;;; 198.81 1.03E-07 6750620000 2092287 2440426 2103993 3200792 2079164 2233657 2433866 649656 3054289 3032900 FALSE TRUE 2010518.111 2370827.44 2484231.338 3365985.259 2146042.198 2278823.075 2463652.38 636240.3766 2707578.917 2827478.982 0.711063857 0.83849516 0.878602937 1.190454564 0.758994925 0.805955797 0.871324737 0.225020374 0.957594711 1 21.43108487 1.902480049 24.43297095 0.618113383 0.870739862 0.006227877 0.236877414 61.82276466 15481.24493 0.094966868 0.061288976 79.88772417 -1.902480049 0.252626479 NAEQYKDQADK ddPTM_BT-474_Pertuzumab_2h_R1 2 NAEQYKDQADK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 187.44 3.27E-06 4994900000 5362300 4577800 3677000 3332800 3881500 4133400 4521400 5254400 6243900 4907500 FALSE TRUE 5152735.388 4447245.626 4341515.694 3504806.207 4006351.973 4216980.18 4576734.246 5145894.804 5535118.649 4575110.654 1.126253719 0.972052036 0.948942227 0.766059331 0.875684169 0.921722008 1.000354875 1.124758545 1.209832738 1 22.12537521 1.902506714 2.852226714 1.125477705 0.927722909 0.394065388 0.096892691 0.260253181 3.776506708 0.054052182 0.0285123 79.89262933 -1.902506714 -0.197754796 SHRPQQNVGVQGAATR ddPTM_BT-474_Pertuzumab_2h_R1 3 SHRPQQNVGVQGAATR 16 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 ;; 133.71 1.94E-05 135097000 107895 112657 90340.8 109523 105293 106532 104896 38002.7 111392 99958 FALSE TRUE 103678.3441 109444.1327 106667.3922 115175.4952 108679.845 108686.15 106179.7486 37217.93096 98747.24715 93187.75563 1.112574752 1.174447565 1.144650297 1.235950951 1.166245976 1.166313635 1.139417383 0.399386494 1.059659034 1 16.50785278 1.902709025 11.70493991 0.756211859 1.167784366 0.450904111 0.169445977 0.482662394 56.25012699 0.065934782 0.042173558 79.92985501 -1.902709025 0.411572507 SCFESS(ph)PDPELK ddPTM_BT-474_Pertuzumab_2h_R1 6 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SCFES(0.007)S(0.993)PDPELK;SCFES(0.037)S(0.963)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.004)S(0.996)PDPELK;SCFES(0.017)S(0.983)PDPELK;SCFES(0.127)S(0.873)PDPELK 264.22 1.66E-21 73693150000 119897330 106354510 90934200 94335410 100417120 103374590 108058520 125088540 135847870 121593220 TRUE FALSE 115211609.8 103321383.5 107368032.8 99204071.82 103647127.9 105464895 109380972.5 122505417.9 120426989.3 113357602.9 1.016355382 0.911464082 0.947162167 0.87514264 0.914337682 0.93037337 0.964919597 1.080698734 1.062363584 1 26.75630592 1.903115922 3.992438339 1.053814573 0.929672627 0.633753306 0.038973789 0.133480267 3.570799479 0.018427054 0.01046697 80.00477755 -1.903115922 -0.124141947 DSLHEKFPDAGEDELLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSLHEKFPDAGEDELLK 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 114.55 0.00021516 951640000 1294160 1377390 993030 1099140 1196950 1214130 1293780 1516390 1659340 1554030 FALSE TRUE 1243582.796 1338108.186 1172492.611 1155866.747 1235450.984 1238680.54 1309613.667 1485076.017 1470978.68 1448774.164 0.858368977 0.923614059 0.809299779 0.797823965 0.852756085 0.85498525 0.903946039 1.025056944 1.015326416 1 20.46640129 1.903130737 2.702419344 1.017030763 0.848937335 0.835286859 0.032468144 0.109467993 1.436326706 0.019085209 0.009934408 80.00750686 -1.903130737 -0.168093429 IFLAQKPAPLLES(ph)PFKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IFLAQKPAPLLESPFKDR 18 2 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 IFLAQKPAPLLES(1)PFKDR 94.201 0.0010476 179290000 187960 162210 174640 152520 185580 199330 214020 228020 305610 273330 TRUE FALSE 180614.3154 157583.9296 206201.3328 160391.5755 191549.3492 203360.5892 216639.2408 223311.3073 270918.434 254817.1156 0.70879978 0.618419721 0.80921304 0.629437999 0.751713042 0.798064874 0.85017539 0.876359136 1.063187743 1 17.95910266 1.903262455 0.805054831 1.030519741 0.691198297 0.808962466 0.060137018 0.244687068 0.297541759 0.049905687 0.024242616 80.0317761 -1.903262455 -0.339321444 ENDFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENDFDR 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 135.6 0.031479 1225900000 1216200 1257700 1002700 1203900 1181900 1172200 1196600 1368700 1339300 1332200 FALSE TRUE 1168669.559 1221831.627 1183910.195 1266033.423 1219916.887 1195902.687 1211244.349 1340435.867 1187268.279 1241968.907 0.940981334 0.983786003 0.953252684 1.019376102 0.982244305 0.962908717 0.975261411 1.07928295 0.955956523 1 20.24419763 1.90329961 24.99999994 1.022235298 0.97517856 0.180984959 0.034669738 60.22110805 15563.1941 0.01369545 0.008839052 80.03862338 -1.90329961 -0.047056737 DQHHLGS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 3 DQHHLGSPSR 10 0 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2 Q9H8M2 BRD9 Bromodomain-containing protein 9 1 DQHHLGS(0.997)PS(0.003)R;DQHHLGS(0.989)PS(0.011)R;DQHHLGS(0.665)PS(0.335)R 141.34 2.43E-05 898015000 711110 823850 713180 815410 845240 715840 762580 65817.7 806430 648976 TRUE FALSE 683319.035 800354.6046 842067.4906 857493.4078 872427.9122 730314.7753 771912.6822 64458.54149 714887.4472 605020.2775 1.129415096 1.322855835 1.391800444 1.417296973 1.441981277 1.207091402 1.275845969 0.106539473 1.181592541 1 19.20662397 1.903367991 11.40670894 0.66888719 1.324474457 0.442527306 0.277044059 0.467311209 53.30242316 0.109230831 0.069804642 80.05122656 -1.903367991 0.655587268 MLVLVLGDLHIPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLVLVLGDLHIPHR 14 0 Q9UBQ0 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 91.858 0.0030007 40743000 53743 56931 46482 63059 52290 51179 51397 29752 50954 44301 FALSE TRUE 51642.66414 55307.38362 54882.33139 66313.48255 53971.95534 52213.87445 52026.01186 29137.6108 45169.91554 41300.45381 1.250413964 1.339147116 1.328855408 1.605635687 1.306812646 1.264244569 1.259695889 0.705503405 1.093690538 1 15.33387001 1.903373183 5.870481388 0.912073012 1.350295363 0.672256743 0.129994567 0.125702835 6.172072587 0.05761493 0.034886307 80.05218366 -1.903373183 0.438222351 THLPGCGARARLCGTGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 THLPGCGARARLCGTGAR 18 2 Q9NYQ6;Q9NYQ6-2 Q9NYQ6 CELSR1 Cadherin EGF LAG seven-pass G-type receptor 1 0 ; 56.407 0.060196 2843500000 462810 1125290 1103490 1945330 1492490 1269400 778650 269063 65626 115374 FALSE TRUE 444722.8735 1093197.831 1302915.19 2045728.714 1540497.296 1295068.138 788179.3516 263506.755 58176.41161 107559.6162 4.134664005 10.1636457 12.11342357 19.01948693 14.32226472 12.04046819 7.327837151 2.449867007 0.540875969 1 16.71477699 1.903417353 1.980290428 0.906555674 12.35478306 0.650692657 3.492504014 0.215322546 1.567189742 2.362522208 1.125550992 80.06032578 -1.903417353 11.44822739 HKSEEHNDKEHSSDK ddPTM_BT-474_Pertuzumab_2h_R1 3 HKSEEHNDKEHSSDK 15 2 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 0 ;; 38.028 0.083834 214931000 53292.1 74200 58332.6 77238 90546 85812 61455 2260.22 40091.4 33637.7 FALSE TRUE 51209.38581 72083.88865 68874.59842 81224.26244 93458.49432 87547.17743 62207.10467 2213.545667 35540.39235 31359.38862 1.63298419 2.298638201 2.196299145 2.590109885 2.980239681 2.791737381 1.983683593 0.070586378 1.133325422 1 14.93660981 1.903573093 5.297436658 0.683935383 2.430574499 0.752090817 0.431126935 0.105246332 4.454381942 0.200196813 0.1194416 80.0890409 -1.903573093 1.746639116 HGSYEDAVHSGALND ddPTM_BT-474_Pertuzumab_2h_R1 1 HGSYEDAVHSGALND 15 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 128.97 0.00051213 0 129760 172610 148760 210750 144240 180810 163870 76901 149360 185910 FALSE TRUE 124688.8357 167687.3318 175644.2411 221626.8328 148879.6106 184466.1021 165875.4901 75312.96748 132405.279 173318.1501 0.719421686 0.967511664 1.013420932 1.278728354 0.858996075 1.064320742 0.957057815 0.434535953 0.763943527 1 17.40306322 1.903887507 9.437778851 0.674888923 0.993560647 0.251282464 0.187636439 0.414742057 38.12383297 0.076594012 0.0485212 80.14704354 -1.903887507 0.318671724 CIIPNHEK ddPTM_BT-474_Pertuzumab_2h_R1 6 CIIPNHEK 8 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3 P35579;P35580;P35749 MYH9;MYH10;MYH11 Myosin-9;Myosin-10;Myosin-11 0 ;;;;; 110.38 0.0034378 4089650000 4597750 4567070 4152220 4630040 4501090 4566370 5109530 5424160 6006680 6008870 FALSE TRUE 4418064.847 4436821.635 4902618.52 4868996.919 4645871.648 4658705.13 5172061.957 5312149.2 5324826.868 5601883.883 0.788674835 0.792023135 0.875173178 0.86917134 0.82934094 0.831631863 0.923271897 0.948279063 0.950542171 1 22.41748065 1.90408068 0.753296889 0.997402964 0.82169926 0.823236911 0.02883278 0.276855019 0.29887988 0.027820917 0.014083297 80.1827007 -1.90408068 -0.175703704 DTHDQLSEPSEVR ddPTM_BT-474_Pertuzumab_2h_R1 5 DTHDQLSEPSEVR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 202.15 9.62E-08 7346630000 4044600 4220770 3680250 4299530 4243280 4379510 4244660 2130860 4591910 4478510 FALSE TRUE 3886532.56 4100397.772 4345353.042 4521429.259 4379768.955 4468066.693 4296607.419 2086856.996 4070655.628 4175176.529 0.930866643 0.982089678 1.040759118 1.082931279 1.049002102 1.070150367 1.029084013 0.499824853 0.974966112 1 21.99340577 1.904170399 24.99999782 0.768127016 1.030064568 0.289153413 0.136216787 43.99622544 11473.97637 0.053464198 0.034505674 80.19926698 -1.904170399 0.261937552 TRAEDEGDLDTNSWPAPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 TRAEDEGDLDTNSWPAPNK 19 1 Q8ND04;Q8ND04-2 Q8ND04 SMG8 Protein SMG8 0 ; 211.33 1.22E-16 491330000 1023670 998050 808080 912580 935790 1061200 966920 1099420 1253370 1195830 FALSE TRUE 983663.8447 969586.5912 954118.0316 959678.3632 965890.5352 1082658.191 978753.4562 1076716.593 1111092.692 1114835.369 0.882340005 0.869712801 0.855837605 0.860825185 0.866397463 0.971137283 0.877935418 0.965807708 0.996642843 1 20.08839925 1.904174232 0.688754469 1.006741005 0.863735739 0.741240284 0.029182228 0.34007479 0.314741499 0.025956634 0.014023869 80.19997485 -1.904174232 -0.143005266 KLDDDS(ph)DSPSFFEEKPEEPVVLALDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLDDDSDSPSFFEEKPEEPVVLALDPK 27 2 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 KLDDDS(0.984)DS(0.016)PSFFEEKPEEPVVLALDPK 244.85 1.15E-45 95425000 169050 112680 100180 79319 116840 110540 126430 180590 187100 140290 TRUE FALSE 162443.3391 109466.4767 118284.7545 83412.6631 120598.2647 112775.1945 127977.2882 176860.7534 165861.1924 130788.0333 1.242035184 0.836976243 0.904400437 0.63776984 0.922089442 0.862274565 0.978509156 1.352270149 1.268167952 1 16.99687102 1.904310114 5.031944928 1.235874977 0.889358535 0.411004561 0.162261933 0.189337671 7.441586573 0.072353058 0.042833555 80.2250717 -1.904310114 -0.346516442 AKIEDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKIEDEK 7 1 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 90.657 0.015484 8313600000 1870270 1722030 1649940 1611180 1793050 1818620 2172830 2447610 2983920 2782240 FALSE TRUE 1797177.781 1672919.39 1948120.861 1694333.193 1850725.082 1855393.742 2199421.744 2397065.998 2645197.911 2593796.407 0.692875422 0.64496943 0.751069304 0.653225206 0.713519796 0.715319729 0.847954657 0.924153489 1.019817093 1 21.30663381 1.904473286 1.279467535 1.012404593 0.686417251 0.946805063 0.030942992 0.083601556 0.253573698 0.021963784 0.009546554 80.25521938 -1.904473286 -0.325987342 MFVSSSGLPPS(ph)PVPSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 MFVSSSGLPPSPVPSPR 17 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 MFVSS(0.001)S(0.001)GLPPS(0.939)PVPS(0.059)PR;MFVSSSGLPPS(0.999)PVPS(0.001)PR 127.3 4.27E-05 129207000 79748 88886 68856 97280 86928 97563 88967 306880 94322 95682 TRUE FALSE 76631.35999 86351.05831 81299.81089 102300.6325 89724.11807 99535.79071 90055.80476 300542.8208 83614.96199 89201.37292 0.859082742 0.968046292 0.91141883 1.146850425 1.005860281 1.115854919 1.009578685 3.369262276 0.937373039 1 16.44477829 1.90452006 24.99905523 2.071462269 1.00728652 0.186513906 0.646717933 51.69392638 13530.59272 0.251137867 0.16208203 80.26386347 -1.90452006 -1.064175748 VPFDAATLHTSTAMAAQHGMDDDGTGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 VPFDAATLHTSTAMAAQHGMDDDGTGQK 28 0 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ; 233.43 3.25E-45 1099800000 323960 467920 357990 570680 470190 530370 429460 279130 344620 468170 FALSE TRUE 311299.285 454575.3797 422686.7564 600132.8632 485314.0884 541094.4448 434715.8599 273365.868 305500.1824 436460.4289 0.713235988 1.041504223 0.968442334 1.374999481 1.111931475 1.23973311 0.996002916 0.626324518 0.699949324 1 18.73549133 1.904631721 5.532928029 0.744886352 1.086489819 0.337815753 0.185574346 0.228169443 10.37411215 0.08368468 0.050269277 80.28450255 -1.904631721 0.341603466 GGSDDSSKDPIDVNYEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 181.94 7.07E-10 11391000000 13093300 11165900 10039900 9948300 10596700 10928100 11934700 14045600 15515800 14125500 FALSE TRUE 12581599.36 10847459.46 11854333.27 10461732.96 10937552.48 11149073.67 12080760.43 13755553.45 13754511.43 13168767.3 0.95541208 0.823726262 0.900185491 0.794435251 0.830567678 0.846630016 0.917379748 1.044558928 1.044479799 1 23.65061697 1.90472967 3.01994093 1.033938155 0.855147061 0.752286239 0.043758285 0.11736949 1.896997245 0.022274013 0.011935324 80.30261164 -1.90472967 -0.178791094 RS(ph)SPPPPPSGSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSPPPPPSGSSSR 14 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RS(0.5)S(0.5)PPPPPSGSSSR 53.188 0.092246 204430000 10814 8656.8 8640.5 10463 7321 11272 9585 7648.2 11079 9252.5 TRUE FALSE 10391.37692 8409.91654 10202.03056 11002.99668 7556.486614 11499.92756 9702.304097 7490.261997 9821.358367 8625.819934 1.204682802 0.974970102 1.182731686 1.275588497 0.87603111 1.333198195 1.124797894 0.868353624 1.138599976 1 13.07444588 1.904762123 10.96833008 0.989518287 1.137819021 0.165519608 0.13989691 0.952136497 105.5629706 0.055624627 0.03549503 80.30861255 -1.904762123 0.148300735 FDSSLLS(ph)SDDETK ddPTM_BT-474_Pertuzumab_2h_R1 1 FDSSLLSSDDETK 13 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 FDSSLLS(0.67)S(0.33)DDETK 296.49 1.09E-40 176360000 875170 720050 570160 656530 666160 700210 775170 868790 1058200 868840 TRUE FALSE 840967.3888 699514.879 673200.5951 690413.592 687587.6414 714368.726 784656.7623 850849.1829 938077.5723 809992.6929 1.03824071 0.863606407 0.831119343 0.852370149 0.848881289 0.881944655 0.968720791 1.050440566 1.158130907 1 19.62754937 1.90491793 2.122503808 1.082745094 0.879030837 0.611323696 0.065393966 0.195912882 1.628562112 0.038953218 0.018968013 80.33742909 -1.90491793 -0.203714257 KSS(ph)PSSPAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSSPSSPAVR 10 1 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 KS(0.17)S(0.826)PS(0.004)SPAVR;KS(0.02)S(0.978)PS(0.002)SPAVR 160.18 4.57E-06 1499150000 618840 593470 508830 606850 530980 637210 696080 766280 793230 884900 TRUE FALSE 594655.0486 576544.8167 600786.8999 638169.6012 548059.4539 650094.8228 704598.8353 750456.0502 703185.8559 824964.9348 0.720824636 0.698871906 0.728257499 0.77357179 0.664342726 0.788027218 0.854095496 0.909682362 0.852382721 1 19.65397327 1.904973161 0.717434128 0.971605926 0.708888578 0.834161333 0.040432697 0.250738652 0.248660818 0.036288091 0.019013754 80.34764672 -1.904973161 -0.262717347 TGTLQDLIQHGS(ph)PINNECHPSLER ddPTM_BT-474_Pertuzumab_2h_R1 4 TGTLQDLIQHGSPINNECHPSLER 24 0 A0A2R8YH03;Q5VWN6 A0A2R8YH03 FAM208B Protein FAM208B 1 TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER 265.38 4.30E-44 1623270000 489503 553311 468374 716980 480774 583630 535820 298403 484622 588628 TRUE FALSE 470372.6816 537531.112 553019.6007 753983.4237 496238.5323 595431.3985 542377.5254 292240.8738 429609.7423 548759.7013 0.85715602 0.97953824 1.007762777 1.373977393 0.904291134 1.085049425 0.988369817 0.532547986 0.782874073 1 19.06581501 1.904986775 7.663860952 0.726964025 1.040035392 0.318349204 0.169014544 0.273976578 19.62345025 0.070787549 0.044172889 80.35016537 -1.904986775 0.313071366 ELSNSVSTYRPFGLGSES(ph)PYK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSNSVSTYRPFGLGSESPYK 21 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ELSNSVSTYRPFGLGS(0.024)ES(0.976)PYK 137.35 2.08E-06 141630000 174910 152530 186060 164130 177440 158610 180750 242210 220160 217430 TRUE FALSE 168074.3238 148179.9937 219685.1809 172600.769 183147.5187 161817.2029 182962.0726 237208.2789 195168.3598 202703.2724 0.829164334 0.731019248 1.08377718 0.851494734 0.90352522 0.798295957 0.902610354 1.17022422 0.962827869 1 17.62900985 1.904989547 7.487984771 1.058557907 0.869373719 0.391340105 0.099177665 0.259248751 18.01234712 0.041696066 0.025964608 80.35067818 -1.904989547 -0.189184188 TEELKPQVEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEELKPQVEEK 11 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 180.09 6.22E-06 2771400000 1879650 1640360 1854820 1623980 1707560 1756840 2242400 2671490 3196600 2966350 FALSE TRUE 1806191.2 1593578.539 2190027.234 1707793.802 1762485.218 1792364.509 2269843.162 2616322.798 2833735.369 2765436.472 0.653130606 0.576248471 0.791928239 0.617549461 0.637326236 0.648130784 0.820790202 0.946079516 1.02469733 1 21.39907577 1.90516116 1.818798868 1.007697298 0.652218904 0.886163927 0.054267683 0.104523972 0.644608692 0.034645784 0.016125301 80.38243535 -1.90516116 -0.355478394 KDDVS(ph)PVMQFSSK ddPTM_BT-474_Pertuzumab_2h_R1 4 KDDVSPVMQFSSK 13 1 Q8IZE3;Q8IZE3-2 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 1 KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK 216.16 1.71E-11 3410470000 3524000 3241650 2685890 2482020 2906250 2896300 3123100 3588500 3878060 3561730 TRUE FALSE 3386278.184 3149201.316 3171290.07 2610117.35 2999732.171 2954865.17 3161321.432 3514396.221 3437838.887 3320490.855 1.019812531 0.948414392 0.955066648 0.786063707 0.903400221 0.889888062 0.95206449 1.058396597 1.035340568 1 21.66296509 1.905213524 4.162123542 1.034775225 0.913969461 0.43888215 0.05747164 0.214182261 6.194885117 0.028850964 0.016538085 80.39212791 -1.905213524 -0.120805764 KRETEDVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KRETEDVPK 9 2 O43148;O43148-2 O43148 RNMT mRNA cap guanine-N7 methyltransferase 0 ; 117.7 0.00062396 371390000 757440 649310 540520 536780 587200 570700 650420 777100 846680 730990 FALSE TRUE 727838.4074 630792.3145 638203.9878 564483.2801 606087.8213 582239.945 658380.0345 761052.6134 750568.436 681479.3962 1.068027018 0.92562199 0.936497848 0.828320391 0.88937072 0.854376447 0.966104094 1.116765404 1.101380966 1 19.37831051 1.905235535 4.505238945 1.080951048 0.912695906 0.518815037 0.066658518 0.168631391 5.57637094 0.031674431 0.018416348 80.39620243 -1.905235535 -0.168255142 NHFAEIETELQAELVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NHFAEIETELQAELVR 16 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 0 ; 173.34 4.26E-09 53672000 35662 37574 33103.8 31423.7 34995.2 37060 35070 19903.1 37932 34950 FALSE TRUE 34268.28961 36502.42631 39086.39305 33045.48092 36120.85239 37809.37859 35499.19715 19492.09403 33626.11838 32582.80537 1.051729255 1.120297221 1.199601833 1.014199991 1.108586323 1.160408938 1.08950708 0.598232528 1.032020356 1 14.9918232 1.9053077 11.50933281 0.834474926 1.11068535 0.420646978 0.120621535 0.507161583 59.77587544 0.047383104 0.030290482 80.40956257 -1.9053077 0.276210424 AELMEISEDKTK ddPTM_BT-474_Pertuzumab_2h_R1 2 AELMEISEDKTK 12 1 P05455;E7ERC4;E9PGX9;E9PFL9 P05455 SSB Lupus La protein 0 ; 125.03 0.00021866 261440000 284450 252240 231630 213900 236190 228210 283270 300570 352420 340720 FALSE TRUE 273333.3795 245046.3622 273490.6936 224939.4046 243787.2659 232824.5626 286736.743 294363.1245 312414.7591 317642.7309 0.860505697 0.771452762 0.861000952 0.708152219 0.767488886 0.732976202 0.902702046 0.926711352 0.983541346 1 18.27704548 1.905485835 2.006830352 0.975714956 0.783051147 0.735682401 0.050372787 0.166641208 1.243949777 0.030837799 0.014775136 80.44255112 -1.905485835 -0.192663809 RIDIS(ph)PSTFR ddPTM_BT-474_Pertuzumab_2h_R1 9 RIDISPSTFR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.992)PS(0.008)TFR;RIDIS(0.989)PS(0.01)T(0.001)FR;RIDIS(0.979)PS(0.02)T(0.001)FR;RIDIS(0.805)PS(0.185)T(0.01)FR;RIDIS(0.472)PS(0.264)T(0.264)FR;RIDIS(0.953)PS(0.036)T(0.011)FR;RIDIS(0.973)PS(0.024)T(0.003)FR;RIDIS(0.968)PS(0.026)T(0.006)FR;RIDIS(0.993)PS(0.007)TFR 160.48 4.51E-06 49599390000 1153609 1134902 884573 1016982 1120164 1081462 957008 963231 961917 947302 TRUE FALSE 1108524.685 1102535.706 1044435.018 1069468.563 1156195.092 1103329.903 968720.1502 943339.9432 852724.2148 883140.3918 1.255207774 1.248426316 1.182637583 1.210983636 1.309186063 1.249325603 1.096903912 1.068165325 0.965559069 1 19.75228327 1.905546389 1.66804636 0.99555514 1.242314135 0.880062751 0.038879607 0.123992221 0.644507094 0.027686029 0.012591443 80.4537681 -1.905546389 0.246758995 GS(ph)PDGSLQTGKPSAPK ddPTM_BT-474_Pertuzumab_2h_R1 8 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 GS(0.826)PDGS(0.172)LQT(0.001)GKPSAPK;GS(1)PDGSLQTGKPSAPK;GS(0.966)PDGS(0.033)LQT(0.001)GKPSAPK;GS(0.994)PDGS(0.005)LQTGKPSAPK;GS(0.996)PDGS(0.004)LQTGKPSAPK;GS(0.967)PDGS(0.033)LQTGKPSAPK;GS(0.983)PDGS(0.017)LQTGKPSAPK;GS(0.767)PDGS(0.233)LQTGKPSAPK 220.87 2.92E-14 6500890000 4464248 4314709 4111313 4246373 4515425 4752959 5155456 5886964 7001678 6644914 TRUE FALSE 4289780.253 4191657.724 4854318.715 4465528.819 4660667.746 4849067.087 5218550.013 5765396.136 6206876.867 6194848.056 0.692475459 0.676636083 0.783605775 0.720845577 0.752345772 0.782758034 0.842401616 0.930675956 1.001941744 1 22.56263747 1.905559793 0.932917913 1.016132574 0.717696452 0.944218478 0.027151904 0.117204364 0.188047543 0.023313394 0.010598764 80.45625118 -1.905559793 -0.298436122 GIGTDEFTLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 GIGTDEFTLNR 11 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 132.88 0.00040341 234380000 194170 193650 126100 155100 186350 177860 174280 240990 207350 179850 FALSE TRUE 186581.6217 188127.2916 148889.0751 163104.7296 192344.117 181456.4511 176412.8908 236013.4723 183812.4973 167668.5993 1.112800026 1.122018627 0.887996176 0.972780415 1.147168389 1.08223276 1.052152231 1.407618798 1.096284564 1 17.355253 1.90557335 25 1.217417021 1.051623334 0.117544219 0.122423004 69.34871365 18355.71466 0.049938921 0.032230147 80.45876271 -1.90557335 -0.165793688 KAVLFCLSEDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAVLFCLSEDKK 12 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 189.3 4.56E-06 14806400000 17519900 14973700 10267700 10726000 12919600 12925500 14061900 16081100 18334200 15654000 FALSE TRUE 16835202.94 14546664.74 12123301.79 11279570.15 13335170.67 13186862.47 14233993.74 15749019.67 16252978.48 14593740.64 1.153590663 0.99677424 0.830719285 0.77290466 0.913759604 0.903597151 0.975349233 1.079162639 1.113695171 1 23.79884638 1.905638295 3.136978758 1.07200537 0.919923407 0.269206215 0.098801571 0.336984407 5.851054418 0.054795524 0.029645061 80.4707955 -1.905638295 -0.152081962 HSCSGSS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCS(0.006)GS(0.42)S(0.574)PPR;HSCS(0.003)GS(0.022)S(0.975)PPR;HSCSGS(0.34)S(0.66)PPR;HSCSGS(0.029)S(0.971)PPR 119.79 0.00041586 6567870000 235557 258992.6 212409.8 260387.7 246524.6 261257.7 243829.5 148761.7 254541.6 245178.8 TRUE FALSE 226351.172 251606.3846 250796.9759 273826.3404 254454.2876 266540.5097 246813.5584 145689.7189 225647.1047 228572.6215 0.990281209 1.100772188 1.097231043 1.197983987 1.113231698 1.166108644 1.079803682 0.637389194 0.987200931 1 17.80229308 1.905795234 9.102929427 0.83910001 1.114607527 0.489894056 0.106809088 0.252040578 22.66555959 0.042863628 0.027096264 80.49988024 -1.905795234 0.275507517 LKNDSDLFGLGLEEAGPKES(ph)SEEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKNDSDLFGLGLEEAGPKESSEEGK 25 2 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 1 LKNDSDLFGLGLEEAGPKES(0.971)S(0.029)EEGK 202.61 2.93E-25 49396000 92003 67493 77195 60413 76065 68848 96833 132370 155070 130030 TRUE FALSE 88407.42105 65568.16572 91145.85369 63530.92217 78511.69981 70240.15373 98018.07122 129636.5132 137467.1037 121222.9523 0.729296056 0.540889035 0.751886107 0.524083278 0.647663651 0.579429493 0.808576836 1.069405676 1.134002275 1 16.88730336 1.906035976 2.663089495 1.080400345 0.626962706 0.867822566 0.076437869 0.082375508 1.052192974 0.038521489 0.020021424 80.54451606 -1.906035976 -0.453437639 KEVQDEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 KEVQDEEK 8 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;; 135.43 0.0013375 6064020000 8865970 8065070 6348220 5912160 7087580 7392460 7712980 8985030 9908190 8824980 FALSE TRUE 8519478.091 7835062.1 7495484.569 6217287.286 7315558.447 7541940.606 7807373.756 8799485.991 8783453.81 8227256.244 1.035518749 0.952329898 0.911055198 0.755693891 0.889185681 0.9167018 0.948964457 1.069552926 1.067604259 1 22.97197995 1.906064467 3.139371035 1.051895843 0.904768293 0.443699745 0.06745977 0.238239347 4.144010796 0.03747223 0.020283213 80.54980019 -1.906064467 -0.14712755 MESSFGS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 3 MESSFGSPSK 10 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 MESSFGS(1)PSK;MESSFGS(1)PSK;MESSFGS(0.999)PS(0.001)K 189.24 1.08E-06 1193930000 1750580 1560630 1809710 1940610 1747510 1706400 2097720 2452990 2719020 2740640 TRUE FALSE 1682165.398 1516122.36 2136764.854 2040765.115 1803720.246 1740904.577 2123392.525 2402334.899 2410368.249 2555014.012 0.65837815 0.593391016 0.836302597 0.79872952 0.705953172 0.681367918 0.831068838 0.940243337 0.943387487 1 21.28489977 1.906088312 2.245216179 0.964068972 0.715974207 0.738158623 0.066356603 0.171179709 1.5835685 0.042026314 0.020826608 80.55422279 -1.906088312 -0.248094765 (ac)VDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_BT-474_Pertuzumab_2h_R1 14 VDYSVWDHIEVSDDEDETHPNIDTASLFR 29 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.003)S(0.003)VWDHIEVS(0.994)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.007)S(0.007)VWDHIEVS(0.967)DDEDET(0.018)HPNIDTASLFR;VDY(0.001)S(0.002)VWDHIEVS(0.997)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.003)S(0.005)VWDHIEVS(0.991)DDEDET(0.001)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.999)DDEDET(0.001)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.019)S(0.02)VWDHIEVS(0.959)DDEDET(0.002)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.015)S(0.016)VWDHIEVS(0.966)DDEDET(0.002)HPNIDTASLFR 208.37 5.09E-107 14047471000 152609.59 140543.3 124890.14 140328.3 144803.34 143140.3 149057.9 203152.5 182442 175436.9 TRUE FALSE 146645.4385 136535.1427 147460.5665 147570.6604 149461.0709 146034.6949 150882.1152 198957.3299 161731.949 163554.4025 0.89661566 0.834799557 0.901599494 0.902272627 0.913830925 0.892881468 0.922519436 1.216459642 0.988857203 1 17.31941107 1.906273768 7.897170463 1.0884354 0.891412135 0.622658829 0.061730532 0.160229207 12.1020106 0.024899687 0.015579508 80.58862917 -1.906273768 -0.197023265 VHNNS(ph)PDTSR ddPTM_BT-474_Pertuzumab_2h_R1 5 VHNNSPDTSR 10 0 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 VHNNS(0.936)PDT(0.052)S(0.012)R;VHNNS(0.999)PDT(0.001)SR;VHNNS(0.954)PDT(0.037)S(0.009)R;VHNNS(1)PDTSR;VHNNS(0.953)PDT(0.039)S(0.008)R 161.25 7.48E-06 376175000 281711 294152 252538 329708 299295 309616 290536 113784 295241 285430 TRUE FALSE 270701.4227 285763.073 298177.2343 346724.2694 308922.0955 315876.6477 294091.6665 111434.3206 261726.4794 266097.5719 1.017301363 1.073903347 1.120556013 1.302996743 1.160935417 1.187070763 1.105202368 0.418772407 0.983573347 1 18.02159582 1.906373 10.11224917 0.741214761 1.147407666 0.451850491 0.166944644 0.342357889 35.19528594 0.067206072 0.042732638 80.60704486 -1.906373 0.406192905 LLVDSQGLSGCS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLVDSQGLSGCSPR 14 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 LLVDSQGLS(0.001)GCS(0.999)PR 133.78 1.87E-05 0 231850 255210 197830 256720 209980 225220 217820 224130 211670 218350 TRUE FALSE 222789.0457 247931.6607 233582.2817 269969.35 216734.1974 229774.1027 220485.7463 219501.6372 187642.109 203560.96 1.094458612 1.217972546 1.147480743 1.326233429 1.064713968 1.128772937 1.083143577 1.078309108 0.921798114 1 17.63510137 1.906406501 0.867431025 0.971123322 1.183068407 0.536859638 0.071884382 0.444344022 0.620274714 0.05968218 0.027954178 80.61326318 -1.906406501 0.211945085 S(ph)SDEDAAGEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSDEDAAGEPK 11 0 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 1 S(0.993)S(0.007)DEDAAGEPK;S(0.993)S(0.007)DEDAAGEPK 203.39 0.00087435 0 587300 478000 404170 401690 443860 439720 487240 558720 630390 529910 TRUE FALSE 564347.6667 464367.908 477212.5097 422421.269 458137.16 448611.4397 493202.9889 547182.2368 558830.77 494018.7237 1.142360886 0.939980381 0.965980613 0.855071374 0.927368009 0.908085905 0.998348777 1.107614369 1.131193502 1 18.9142062 1.906431222 4.010457629 1.088336085 0.9502273 0.334927199 0.076716089 0.239510599 6.518011444 0.036776364 0.020951567 80.61785194 -1.906431222 -0.138108785 VKLDHDGAILDVDEDDVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKLDHDGAILDVDEDDVEK 19 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;H0YEV9 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 203.63 2.98E-16 533830000 857140 734350 684850 597160 755430 734050 863460 986400 1175970 1073860 FALSE TRUE 823642.0212 713407.057 808617.6294 627979.4992 779729.092 748892.9939 874027.2818 966030.4953 1042478.816 1001126.506 0.822715228 0.712604304 0.807707742 0.627272873 0.778851711 0.748050311 0.873043793 0.964943481 1.041305779 1 19.93319286 1.90644525 1.666625972 1.019252101 0.743258125 0.821445378 0.053079218 0.135891194 0.705065382 0.033906238 0.015428284 80.62045594 -1.90644525 -0.275993975 TVYGNHER ddPTM_BT-474_Pertuzumab_2h_R1 4 TVYGNHER 8 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;;; 156.35 0.0003944 2813340000 2196490 2275670 2125700 2506950 2242970 2346840 2282740 2092880 2436750 2395970 FALSE TRUE 2110648.742 2210770.12 2509861.276 2636333.99 2315117.167 2394294.713 2310676.855 2049661.297 2160140.356 2233688.818 0.944916197 0.98973953 1.12363963 1.180260191 1.036454652 1.071901643 1.034466769 0.917612731 0.967073094 1 21.09099678 1.906735389 5.193686212 0.955507535 1.061702753 0.308893787 0.064071369 0.26898598 11.26507736 0.031300386 0.018639293 80.67433395 -1.906735389 0.106195218 DYLDFLDDEEDQGIYQSK ddPTM_BT-474_Pertuzumab_2h_R1 4 DYLDFLDDEEDQGIYQSK 18 0 P25205;P25205-2 P25205 MCM3 DNA replication licensing factor MCM3 0 ;;; 216.93 8.69E-19 233344000 510942 493185 446921 437920 459588 497271 518163 576527 633213 633567 FALSE TRUE 490973.8218 479119.8467 527689.5664 460521.1037 474371.0654 507326.1603 524504.4338 564621.516 561333.3149 590654.9428 0.831236287 0.811167082 0.89339736 0.779678744 0.803127225 0.858921383 0.888004816 0.955924475 0.950357432 1 19.17195604 1.906746404 1.341019478 0.980340242 0.824584905 0.819652797 0.029670267 0.172978132 0.577740536 0.022206168 0.009703011 80.67638018 -1.906746404 -0.155755338 TTS(ph)PS(ph)SDTDLLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSPSSDTDLLDR 13 0 K7ENU0;K7ERZ4;K7EJ43;Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3 K7ENU0;Q96QT6 PHF12 PHD finger protein 12 2 T(0.006)T(0.033)S(0.961)PS(0.98)S(0.02)DTDLLDR 147.7 2.83E-06 0 78941 86172 66573 81761 75020 88968 78978 68028 86185 78837 TRUE FALSE 75855.89845 83714.45893 78604.22201 85980.69501 77433.08643 90766.99392 79944.55639 66623.19803 76401.64012 73497.29977 1.032090957 1.139014075 1.069484488 1.169848352 1.053550085 1.234970457 1.087721 0.90647137 1.039516286 1 16.16540363 1.906751174 6.873985829 0.976018894 1.118598136 0.474034512 0.063404784 0.193505275 12.20067933 0.025699895 0.015871461 80.67726638 -1.906751174 0.142579241 SLS(ph)VEHLETK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSVEHLETK 10 0 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.395)LS(0.605)VEHLETK;S(0.203)LS(0.797)VEHLETK 155.99 7.56E-06 715820000 1771120 1792290 1466470 1536310 1568720 1658250 1813460 2112750 2304600 2275980 TRUE FALSE 1701902.672 1741175.644 1731493.75 1615599.143 1619179.303 1691780.951 1835653.666 2069120.974 2042991.47 2121825.847 0.802093477 0.820602523 0.816039522 0.761419296 0.763106598 0.797323189 0.865129279 0.975160604 0.962845972 1 21.01687482 1.906972237 2.217948817 0.982332728 0.792313529 0.943999306 0.020247528 0.071231087 0.643763822 0.013342429 0.006593167 80.71834283 -1.906972237 -0.190019199 YKELGEK ddPTM_BT-474_Pertuzumab_2h_R1 6 YKELGEK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 99.802 0.0093578 11688610000 14257710 14709820 12021510 12689830 13014240 13947010 14360970 15861480 17894970 16743420 FALSE TRUE 13700502.93 14290310.34 14194064.27 13344753.65 13432854.85 14229028.1 14536723.85 15533934.9 15863608.03 15609373.25 0.877709996 0.91549546 0.909329545 0.854919248 0.86056337 0.91156947 0.931281712 0.995167112 1.016287315 1 23.89590928 1.906988447 1.725139474 1.010435554 0.886164359 0.881868317 0.01903985 0.121176139 0.673232748 0.013776431 0.006328387 80.72135562 -1.906988447 -0.124271195 QRELAEQELEK ddPTM_BT-474_Pertuzumab_2h_R1 3 QRELAEQELEK 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 175.74 8.63E-06 852310000 746560 711140 552890 602030 629380 656040 696670 787130 862090 832440 FALSE TRUE 717383.6098 690858.9835 652809.522 633100.8404 649624.5793 669305.5783 705196.0559 770875.4904 764229.1574 776058.0973 0.924394207 0.890215547 0.841186406 0.815790522 0.837082406 0.862442619 0.908689772 0.993321883 0.984757662 1 19.56580513 1.90725041 2.393151348 0.994610756 0.858817253 0.806886133 0.028561904 0.132837954 1.386874979 0.018120163 0.009155119 80.77006092 -1.90725041 -0.135793503 LSMEDSKS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 7 LSMEDSKSPPPK 12 1 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LSMEDS(0.004)KS(0.996)PPPK;LSMEDS(0.047)KS(0.953)PPPK;LSMEDS(0.018)KS(0.982)PPPK;LSMEDSKS(1)PPPK;LSMEDS(0.004)KS(0.996)PPPK;LSMEDSKS(1)PPPK;LSMEDS(0.002)KS(0.998)PPPK 173.36 2.02E-05 9748330000 5530140 4619750 4245420 3790840 4602750 4455740 5000950 5922260 6690660 5791660 TRUE FALSE 5314016.015 4487999.253 5012661.833 3986485.707 4750801.634 4545838.116 5062153.122 5799963.261 5931164.326 5399385.71 0.984188999 0.831205529 0.92837632 0.738322084 0.879878173 0.841917648 0.937542416 1.074189468 1.098488725 1 22.36436385 1.907278522 3.072601516 1.064772503 0.863644445 0.630108354 0.064887213 0.151091339 2.527100787 0.032315896 0.017421777 80.77528934 -1.907278522 -0.201128058 ELLHSVHPES(ph)PNLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELLHSVHPESPNLK 14 0 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK 250.19 4.49E-18 1851440000 642006 836655 746667 884216 794872 941512 824801 133387 847577 823604 TRUE FALSE 616915.6957 812794.4186 881606.3364 929850.4937 820439.7798 960550.0177 834895.1614 130632.5118 751363.6123 767820.5675 0.803463364 1.058573387 1.148193177 1.21102577 1.068530611 1.25100845 1.087357121 0.170134166 0.978566665 1 19.55040968 1.907280086 16.20888873 0.625058349 1.101955631 0.307805233 0.245123085 2.588618539 450.3455033 0.096755896 0.062312618 80.77558016 -1.907280086 0.476897282 NHFTVAQSEAFDR ddPTM_BT-474_Pertuzumab_2h_R1 4 NHFTVAQSEAFDR 13 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ;;; 230.69 3.66E-12 2352970000 1610750 1674370 1444470 1774510 1610610 1672260 1614120 764776 1652610 1630670 FALSE TRUE 1547800.109 1626618.607 1705517.861 1866092.674 1662416.733 1706074.243 1633874.083 748983.1083 1465012.641 1520223.268 1.018139994 1.069986653 1.121886434 1.227512243 1.093534593 1.122252421 1.074759292 0.492679677 0.963682553 1 20.53585179 1.907511637 10.11937857 0.766564409 1.111214495 0.45904979 0.138854396 0.336104514 35.05669368 0.05530857 0.035169571 80.81865845 -1.907511637 0.344650086 AAIAPFQSAGS(ph)PPELQGLPELHEECEGNHPSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAIAPFQSAGSPPELQGLPELHEECEGNHPSAR 33 0 Q7Z628-2;Q7Z628 Q7Z628-2 NET1 Neuroepithelial cell-transforming gene 1 protein 1 AAIAPFQSAGS(1)PPELQGLPELHEECEGNHPSAR;AAIAPFQS(0.005)AGS(0.995)PPELQGLPELHEECEGNHPSAR 169.75 3.97E-14 90525000 35318 51437 43486 47496 41844 44852 42619 20282.6 37149 45744 TRUE FALSE 33937.73351 49970.06712 51344.88754 49947.27425 43189.95026 45758.93817 43140.58407 19863.75722 32932.00126 42645.71814 0.795806355 1.171748755 1.203986937 1.171214284 1.012761706 1.073001937 1.011604118 0.465785502 0.772222927 1 15.38011327 1.907545559 7.280316381 0.695488474 1.080484138 0.433251233 0.16401479 0.202188921 13.90011388 0.068110138 0.04231148 80.82497125 -1.907545559 0.384995665 SHLDSPEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHLDSPEAR 9 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7ER08 K7EP90 RBM42 RNA-binding protein 42 0 ; 154.56 7.54E-05 249840000 390440 437680 328550 433410 397240 387380 379010 154582 368710 354790 FALSE TRUE 375181.1731 425197.7949 387926.2936 455778.342 410017.5854 395213.089 383648.4378 151389.8277 326855.5866 330759.7573 1.13430115 1.285518524 1.172834013 1.377973989 1.239623553 1.194864491 1.15990059 0.457703286 0.988196355 1 18.33542419 1.907553394 7.865451936 0.764488055 1.235314217 0.592707634 0.154396058 0.166742911 12.70822306 0.062043019 0.038810373 80.82642947 -1.907553394 0.470826161 LAEAHQQECCQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAEAHQQECCQK 12 0 Q9Y5X3;A0A087WUY5 Q9Y5X3 SNX5 Sorting nexin-5 0 200.93 1.54E-07 339780000 293520 298180 247360 282910 290200 329570 333550 325880 388000 414350 FALSE TRUE 282048.9139 289676.1983 292063.4545 297511.019 299534.5466 336234.1312 337632.0847 319150.4641 343955.8666 386285.7054 0.730156229 0.749901418 0.756081445 0.770183869 0.775422291 0.870428614 0.874047577 0.826203143 0.890418314 1 18.55930877 1.907656347 0.06317493 1.395260249 0.297023766 0.911450322 0.023846342 8.109974306 0.429949816 3.443194437 3.811410296 80.84559229 -1.907656347 -1.098236484 WDHSLAWDVPAAEDFPNGSGS(ph)PSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR 48 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WDHSLAWDVPAAEDFPNGS(0.082)GS(0.389)PS(0.274)AAIY(0.251)NIDT(0.002)S(0.001)S(0.001)ESPDHYLVDHTLDGR 88.344 8.92E-06 870920000 13403 18704 13424 11972 14972 15735 14285 5027.6 13802 14103 TRUE FALSE 12879.19594 18170.58023 15850.01542 12589.87635 15453.58798 16053.17248 14459.8241 4923.778303 12235.25482 13147.79125 0.97957107 1.382025307 1.205526854 0.957565884 1.175375216 1.220978655 1.099791123 0.374494712 0.930593937 1 13.68253284 1.907720443 9.11667037 0.706114141 1.158446737 0.435647105 0.193783553 0.28348639 26.12919337 0.077973725 0.049298878 80.8575248 -1.907720443 0.452332596 QEPGGSHGS(ph)ETEDTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEPGGSHGSETEDTGR 16 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 QEPGGS(0.034)HGS(0.919)ET(0.047)EDTGR;QEPGGS(0.012)HGS(0.952)ET(0.036)EDTGR 164.01 7.90E-09 150918000 97882 97769 87403 100258 95914 106484 91120 89477 90375 95518 TRUE FALSE 94056.66323 94980.72385 103198.6664 105432.3274 98999.16092 108637.1794 92235.15382 87629.26868 80116.00888 89048.48078 1.056241077 1.066618128 1.15890429 1.183987941 1.111744524 1.21997791 1.035785821 0.984062478 0.899689789 1 16.44230338 1.907849828 2.837896195 0.956836991 1.132268938 0.669640619 0.053846511 0.160195342 2.308049794 0.029361585 0.015534757 80.88161747 -1.907849828 0.175431946 LQPFHSTELEDDAIYSVHVPAGLYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQPFHSTELEDDAIYSVHVPAGLYR 25 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 170.55 4.85E-12 24831000 10631 22883 15447 19836 16122 14996 17499 11787 17764 11862 FALSE TRUE 10215.52877 22230.39924 18238.61652 20859.73834 16640.57877 15299.22939 17713.158 11543.59433 15747.50519 11058.57617 0.923765285 2.01024064 1.64927349 1.886295126 1.504766844 1.3834719 1.601757561 1.043859006 1.424008384 1 13.43287803 1.907858952 0.928030755 1.101010771 1.63599618 0.256073534 0.301127931 0.678008165 1.076707129 0.240745727 0.109795267 80.88331683 -1.907858952 0.534985408 DIEDVFYK ddPTM_BT-474_Pertuzumab_2h_R1 6 DIEDVFYK 8 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 174.17 0.00063626 2694467000 3391254 3085691 2998972 3192103 3291585 3036020 3428895 3930450 4139800 4181470 FALSE TRUE 3258720.044 2997690.114 3540952.952 3356847.818 3397461.821 3097410.405 3470858.843 3849284.834 3669867.259 3898255.312 0.835943206 0.7689825 0.908343007 0.861115435 0.871533942 0.794563249 0.890362114 0.987437847 0.941412751 1 21.89439715 1.907990516 3.844448812 0.972367248 0.842126402 0.704420038 0.039303587 0.132803577 3.365716057 0.019134642 0.010824611 80.90782299 -1.907990516 -0.130240846 LGPQNFIDETS(ph)DIENLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGPQNFIDETSDIENLLK 18 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 1 LGPQNFIDET(0.031)S(0.969)DIENLLK;LGPQNFIDET(0.163)S(0.837)DIENLLK 180.88 8.01E-14 45322000 133783 119548 124834 112780 114882 109507 131796 189307 169034 168678 TRUE FALSE 128554.6125 116138.6081 147394.2807 118600.5893 118577.2839 111721.3066 133408.9589 185397.7443 149845.969 157253.2888 0.817500311 0.738544859 0.937304916 0.75420101 0.754052807 0.710454499 0.848369912 1.178975306 0.952895613 1 17.26273066 1.908033723 6.207036397 1.055942991 0.786674578 0.679796224 0.079337069 0.12422125 6.864941489 0.033844621 0.020663394 80.91587281 -1.908033723 -0.269268413 GPPPPPTASEPTRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPPPPPTASEPTRR 14 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 ; 177.36 3.38E-06 254550000 58564 58853 42463 54495 52918 55479 51114 43303 50215 50374 FALSE TRUE 56275.25413 57174.57006 50137.00868 57307.49348 54620.15553 56600.82339 51739.54842 42408.77792 44514.80372 46962.12411 1.198311516 1.21746133 1.067605217 1.220291768 1.16306825 1.205244108 1.101729306 0.903042158 0.947887357 1 15.51921004 1.90803679 3.905490153 0.944545117 1.17565401 0.823055654 0.047200457 0.086355908 2.25184295 0.022120829 0.012552239 80.91644428 -1.90803679 0.231108894 HRADHPPAEVTSHAASGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 HRADHPPAEVTSHAASGAK 19 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 188.04 1.10E-14 482026000 695820 751510 585172 765180 632365 763070 689220 87592.45 750220 580906 FALSE TRUE 668626.5851 730077.6706 690925.5975 804671.0315 652705.5945 778499.7982 697654.8805 85783.6353 665058.1708 541560.7192 1.234629029 1.348099382 1.275804491 1.485837142 1.205230681 1.437511567 1.288230213 0.158400771 1.228039899 1 19.04676357 1.908149278 12.1531628 0.706368991 1.333381168 0.439581322 0.268779724 0.612740472 79.35536494 0.104055302 0.066637444 80.93740535 -1.908149278 0.627012177 YPS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 1 YPSPQK 6 0 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 YPS(1)PQK 77.318 0.076298 645710000 1259900 1096300 957100 1001100 1040500 1084400 1120700 1319600 1400000 1215400 TRUE FALSE 1210661.715 1065034.597 1130069.261 1052766.891 1073968.627 1106327.311 1134415.462 1292349.799 1241077.869 1133079.875 1.068469877 0.939946618 0.997342981 0.92911975 0.94783135 0.976389516 1.001178722 1.140563721 1.095313663 1 20.11181814 1.908233982 5.588000057 1.090944693 0.973533522 0.457681448 0.049138922 0.166219548 7.87242013 0.020889579 0.012579866 80.95319282 -1.908233982 -0.117411171 AIEMER ddPTM_BT-474_Pertuzumab_2h_R1 3 AIEMER 6 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 120.9 0.046264 2368220000 2231430 2199210 1783620 2002200 2132220 2002450 2057770 1869050 2227830 2193140 FALSE TRUE 2144223.249 2136490.684 2105959.81 2105533.782 2200804.793 2042940.911 2082953.605 1830453.464 1974936.078 2044596.674 1.048726761 1.04494481 1.030012343 1.029803975 1.076400456 0.999190176 1.018760145 0.895263837 0.965929419 1 20.96338485 1.90829102 6.129851721 0.944283249 1.037135212 0.602044534 0.030460126 0.136557282 7.427581683 0.012935012 0.007885547 80.96382555 -1.90829102 0.092851963 HQEHILR ddPTM_BT-474_Pertuzumab_2h_R1 3 HQEHILR 7 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 117.04 0.015174 66200000 180245 216603 170744 223947 199414 192312 189500 84804 185646 176312 FALSE TRUE 173200.8261 210425.6945 201601.239 235504.9315 205828.3324 196200.6804 191819.1577 83052.76776 164572.2444 164370.2312 1.053723809 1.280193457 1.226506999 1.432771189 1.252223903 1.193650937 1.166994512 0.505278645 1.001229013 1 17.32658951 1.908468814 7.539274318 0.790103076 1.244691812 0.568404267 0.156842061 0.170004233 12.37467164 0.06462068 0.040277973 80.99697778 -1.908468814 0.454588736 STAQQELDGKPAS(ph)PTPVIVASHTANKEEK ddPTM_BT-474_Pertuzumab_2h_R1 8 STAQQELDGKPASPTPVIVASHTANKEEK 29 2 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.95)PT(0.05)PVIVASHTANKEEK;STAQQELDGKPAS(0.991)PT(0.009)PVIVASHTANKEEK;STAQQELDGKPAS(0.961)PT(0.039)PVIVASHTANKEEK;STAQQELDGKPAS(0.967)PT(0.033)PVIVASHTANKEEK;STAQQELDGKPAS(0.992)PT(0.008)PVIVASHTANKEEK;STAQQELDGKPAS(0.966)PT(0.034)PVIVASHTANKEEK;STAQQELDGKPAS(0.999)PT(0.001)PVIVASHTANKEEK;STAQQELDGKPAS(0.972)PT(0.028)PVIVASHTANKEEK 308.15 2.69E-92 38231860000 3212430 2529280 2260140 1770168 2542150 2446830 2793100 3218760 3992890 3124820 TRUE FALSE 3086884.684 2457147.411 2668597.575 1861526.583 2623920.563 2496306.579 2827282.793 3152291.481 3539633.867 2913173.158 1.05962966 0.843460817 0.916044955 0.639003067 0.900708753 0.856902918 0.97051656 1.08208174 1.215044103 1 21.47416003 1.908500551 2.183146119 1.116124141 0.860595335 0.470937935 0.108600792 0.253198925 2.220070254 0.063436005 0.031240822 81.00289699 -1.908500551 -0.255528806 DMHSAYK ddPTM_BT-474_Pertuzumab_2h_R1 9 DMHSAYK 7 0 P08621;P08621-2 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;;;;; 151.29 0.0018911 5160670000 8827850 9687370 7789640 9425470 8759340 8242660 8508160 4037580 8594930 8075450 FALSE TRUE 8482847.862 9411095.693 9197401.228 9911919.636 9041092.126 8409332.233 8612285.407 3954202.562 7619269.579 7528492.579 1.126765787 1.250063754 1.221678992 1.316587555 1.200916655 1.1170008 1.143958809 0.525231648 1.012057792 1 22.84392959 1.908535992 8.102996109 0.800356665 1.206320071 0.574822738 0.137507262 0.183322401 14.69032015 0.056012875 0.035125116 81.00950752 -1.908535992 0.405963406 EADGEQDEEEKDDGEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EADGEQDEEEKDDGEAK 17 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 160.97 2.76E-09 338640000 673930 468770 453810 345590 478930 457800 542070 680820 773980 633720 FALSE TRUE 647592.0705 455401.1386 535823.5619 363425.9413 494335.2184 467057.0297 548704.0148 666760.8291 686121.0352 590797.5799 1.096131894 0.770824313 0.906949487 0.615144601 0.836725192 0.79055339 0.928751291 1.128577455 1.161347065 1 19.17230439 1.908565654 3.278204957 1.107932453 0.827102074 0.481899978 0.120052334 0.196095461 3.708143568 0.059296195 0.032473265 81.01504064 -1.908565654 -0.280830379 ASSTST(ph)PEPTR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 ASSTS(0.002)T(0.998)PEPTR;ASST(0.01)S(0.178)T(0.812)PEPTR;AS(0.003)S(0.002)T(0.023)S(0.127)T(0.844)PEPTR;ASSTS(0.111)T(0.888)PEPTR;ASST(0.002)S(0.116)T(0.882)PEPTR 272.25 5.18E-26 4272230000 4472480 4952250 4165780 4460780 4075500 4630970 4647110 5241340 5382720 5395750 TRUE FALSE 4297690.537 4811016.679 4918629.113 4691001.39 4206592.159 4724611.386 4703982.722 5133104.497 4771696.192 5030291.046 0.854362202 0.956409209 0.977802093 0.932550691 0.836252241 0.939232212 0.935131323 1.020438867 0.948592467 1 22.26221044 1.908570426 5.23920792 0.99011624 0.91921232 0.358820218 0.04387254 0.26168131 11.24271287 0.020297624 0.012111467 81.01593082 -1.908570426 -0.07090392 ANDHQGFYLLNSIIEHMPPESVDQYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ANDHQGFYLLNSIIEHMPPESVDQYR 26 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 150.18 8.16E-08 187770000 78850 69108 105030 93185 117330 116860 94208 65589 88548 96496 FALSE TRUE 75768.45483 67137.1075 124011.2574 97994.28902 121104.026 119222.9893 95360.94568 64234.56423 78496.40226 89960.23997 0.842243805 0.746297559 1.378511856 1.089306665 1.346195008 1.325285363 1.060034363 0.714032824 0.872567729 1 16.45699989 1.908660098 6.365020606 0.839776966 1.129990602 0.239503301 0.205214718 0.331319071 19.09627954 0.095555312 0.058524155 81.03266053 -1.908660098 0.290213636 EETDKEEPASK ddPTM_BT-474_Pertuzumab_2h_R1 1 EETDKEEPASK 11 1 P05455 P05455 SSB Lupus La protein 0 76.073 0.033152 476240000 312250 291920 254550 264280 262940 258000 308230 319300 402230 323400 FALSE TRUE 300046.9248 283594.7274 300552.8474 277919.5225 271397.7039 263216.9368 312002.2109 312706.3434 356570.5367 301495.8299 0.995194278 0.940625704 0.99687232 0.92180221 0.900170672 0.873036741 1.034847517 1.03718298 1.182671537 1 18.20177852 1.908708928 2.450779342 1.083171076 0.939284004 0.525466069 0.057774963 0.220831372 2.411939621 0.032064825 0.016329054 81.04177189 -1.908708928 -0.143887072 RGS(ph)LSNAGDPEIVK ddPTM_BT-474_Pertuzumab_2h_R1 5 RGSLSNAGDPEIVK 14 1 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 RGS(1)LSNAGDPEIVK;RGS(0.989)LS(0.011)NAGDPEIVK;RGS(1)LSNAGDPEIVK;RGS(0.998)LS(0.002)NAGDPEIVK;RGS(0.991)LS(0.009)NAGDPEIVK 205.36 7.56E-09 19985300000 15762800 13775700 12382300 12447700 13759600 13707500 15449100 17215600 19159900 19155800 TRUE FALSE 15146772.35 13382830.52 14620057.05 13090127.29 14202190.03 13984675.04 15638170.71 16860091.84 16984948.48 17858360.6 0.848161412 0.749387406 0.818667367 0.732997142 0.795268409 0.783088401 0.875677844 0.944100761 0.951092256 1 24.09009631 1.90906441 1.611435881 0.975221109 0.783203211 0.85510177 0.032856523 0.121986287 0.591537049 0.020875129 0.009440001 81.10813408 -1.90906441 -0.192017897 TKS(ph)PTDDEVTPSAVVR ddPTM_BT-474_Pertuzumab_2h_R1 5 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.103)KS(0.87)PT(0.027)DDEVTPSAVVR;T(0.029)KS(0.964)PT(0.007)DDEVTPSAVVR;T(0.002)KS(0.98)PT(0.018)DDEVTPSAVVR;T(0.045)KS(0.822)PT(0.133)DDEVTPSAVVR;T(0.351)KS(0.633)PT(0.016)DDEVTPSAVVR 225.74 3.99E-15 9274020000 1329890 1224970 1076399 1124344 1225004 1230814 1237393 1352990 1484670 1318530 TRUE FALSE 1277916.429 1190035.055 1270928.244 1182371.529 1264407.366 1255701.902 1252536.586 1325050.284 1316136.486 1229224.789 1.039611664 0.968118334 1.03392663 0.961883896 1.028621761 1.021539684 1.018964633 1.077956039 1.070704478 1 20.22931734 1.909182903 5.285527304 1.056929049 1.007920205 0.240438814 0.03143535 0.247904031 10.84447692 0.013261734 0.007925342 81.13026665 -1.909182903 -0.049008844 ENQPENSQT(ph)PTKK ddPTM_BT-474_Pertuzumab_2h_R1 6 ENQPENSQTPTKK 13 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 ENQPENS(0.002)QT(0.987)PT(0.011)KK;ENQPENSQT(0.991)PT(0.009)KK;ENQPENSQT(0.999)PT(0.001)KK;ENQPENSQT(0.996)PT(0.004)KK;ENQPENSQT(0.995)PT(0.005)KK;ENQPENS(0.007)QT(0.982)PT(0.011)KK 205.78 3.94E-08 10661150000 3610560 2951990 3175640 2521860 2685240 2972200 3192050 3860360 3942890 3814380 TRUE FALSE 3469455.324 2867802.136 3749548.79 2652013.497 2771613.183 3032299.92 3231115.263 3780642.217 3495309.657 3556028.645 0.975654493 0.806462046 1.0544203 0.745779565 0.779412502 0.852720893 0.908630269 1.063164163 0.982925057 1 21.76183551 1.909186988 4.67603445 1.018164131 0.865887901 0.356639113 0.087715528 0.237294774 8.503074261 0.040292278 0.023622836 81.13102976 -1.909186988 -0.15227623 AKS(ph)PTPDGS(ph)ER ddPTM_BT-474_Pertuzumab_2h_R1 2 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.853)PT(0.418)PDGS(0.729)ER;AKS(0.752)PT(0.249)PDGS(1)ER 109.1 0.023597 1246180000 1867540 1626520 1347650 1364240 1503670 1475750 1607010 1907670 2006890 1790440 TRUE FALSE 1794554.472 1580133.242 1591200.333 1434648.59 1552036.911 1505590.676 1626677.069 1868275.948 1779076.261 1669171.904 1.07511663 0.946656985 0.953287273 0.859497207 0.929824488 0.901998573 0.974541367 1.119283127 1.065843642 1 20.67070111 1.909242961 5.526505186 1.070934637 0.940187072 0.444435222 0.058274781 0.186367415 8.744303868 0.026204781 0.015761326 81.14148672 -1.909242961 -0.130747565 PCSEETPAIS(ph)PSKR ddPTM_BT-474_Pertuzumab_2h_R1 11 PCSEETPAISPSKR 14 1 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(0.667)PS(0.333)KR;PCSEETPAIS(0.811)PS(0.189)KR;PCSEETPAIS(0.997)PS(0.003)KR;PCSEETPAIS(0.979)PS(0.021)KR;PCSEETPAIS(0.997)PS(0.003)KR;PCSEETPAIS(0.949)PS(0.051)KR;PCSEETPAIS(0.854)PS(0.146)KR;PCSEET(0.001)PAIS(0.956)PS(0.042)KR;PCSEETPAIS(0.952)PS(0.048)KR;PCSEETPAIS(0.976)PS(0.024)KR;PCSEET(0.017)PAIS(0.892)PS(0.09)KR 230.5 9.43E-13 95441975300 8305054 5776887 5352195 4946580 5865424 5292400 6485598 7116661 8130820 7540477 TRUE FALSE 7980483.308 5612135.839 6319455.695 5201873.587 6054090.69 5399415.954 6564970.688 6969699.463 7207843.401 7029753.776 1.135243646 0.798340314 0.898958327 0.739979486 0.861209494 0.76808038 0.933883447 0.991457124 1.025333693 1 22.74504273 1.909327042 3.260833543 1.004404908 0.858814224 0.261865204 0.102769739 0.322979513 6.052496641 0.050555461 0.027670283 81.15719752 -1.909327042 -0.145590684 KELS(ph)PAGSISK ddPTM_BT-474_Pertuzumab_2h_R1 2 KELSPAGSISK 11 1 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 KELS(1)PAGSISK;KELS(1)PAGSISK 164.01 1.43E-05 684230000 1743700 1605190 1441350 1336970 1490000 1673900 1713080 2024300 2363400 2119900 TRUE FALSE 1675554.276 1559411.553 1701834.008 1405971.182 1537927.203 1707747.405 1734045.185 1982497.498 2095116.74 1976317.285 0.847816436 0.78904919 0.86111376 0.711409647 0.778178289 0.864105889 0.877412346 1.003127136 1.06011153 1 20.91438315 1.90932917 1.567498306 1.036524643 0.799560109 0.82752478 0.043697276 0.14583357 0.668974858 0.030464284 0.013691243 81.15759523 -1.90932917 -0.236964534 LTPVSLSNS(ph)PIKGADCQEVPQDK ddPTM_BT-474_Pertuzumab_2h_R1 4 LTPVSLSNSPIKGADCQEVPQDK 23 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 LTPVSLS(0.02)NS(0.979)PIKGADCQEVPQDK;LTPVSLS(0.001)NS(0.999)PIKGADCQEVPQDK;LTPVSLS(0.002)NS(0.998)PIKGADCQEVPQDK;LTPVSLS(0.003)NS(0.997)PIKGADCQEVPQDK 285.26 1.67E-52 1865460000 2154810 1740740 1771810 1717150 1848990 1700870 2165780 2324210 2661640 2682000 TRUE FALSE 2070597.643 1691095.8 2092015.481 1805772.317 1908464.443 1735262.757 2192285.463 2276214.251 2359501.786 2500345.751 0.828124527 0.676344781 0.836690478 0.722209045 0.763280215 0.694009121 0.876792925 0.910359797 0.943670204 1 21.25369618 1.909368971 2.032056013 0.955140196 0.753122305 0.730461891 0.054067306 0.157643598 1.204701675 0.030602539 0.014764399 81.16503329 -1.909368971 -0.202017892 GDDTPLHLAASHGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDDTPLHLAASHGHR 15 0 A0A0A0MTH3;Q13418;Q13418-2;A0A087WWY6 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 145.86 2.31E-06 270380000 135480 167710 149870 192530 170710 185200 168940 58266 188240 152450 FALSE TRUE 130185.2918 162927.075 176954.8428 202466.4964 176201.0422 188944.8709 171007.5383 57062.78674 166871.7844 142124.4257 0.9159952 1.146369276 1.245069888 1.424572134 1.23976608 1.329432784 1.203224128 0.401498803 1.174124599 1 17.11679499 1.909374458 13.32780697 0.794228988 1.228819204 0.339048476 0.222347274 1.108244686 160.9294003 0.08980089 0.057647594 81.16605882 -1.909374458 0.434590216 EEPLDPEEAEGPLSLVTTANHS(ph)PDFDHDRDYEDEPVNEDME ddPTM_BT-474_Pertuzumab_2h_R1 3 EEPLDPEEAEGPLSLVTTANHSPDFDHDRDYEDEPVNEDME 41 1 A0A3B3IUB6;Q9H334-8;C9J0F0;Q9H334-3;Q9H334-7;Q9H334-6;Q9H334;Q9H334-4;A0A3B3IRS5;A0A3B3IST0;H0Y882;A0A0B4J2F3;A0A3B3IRW5;A0A3B3IT66 A0A3B3IUB6 FOXP1 Forkhead box protein P1 1 EEPLDPEEAEGPLS(0.001)LVT(0.17)T(0.17)ANHS(0.658)PDFDHDRDYEDEPVNEDME;EEPLDPEEAEGPLSLVT(0.067)T(0.067)ANHS(0.866)PDFDHDRDYEDEPVNEDME;EEPLDPEEAEGPLSLVT(0.005)T(0.125)ANHS(0.87)PDFDHDRDYEDEPVNEDME 277.87 6.14E-81 521730000 236569 262313 207500 233321 237874 276474 238825 130822 260872 218628 TRUE FALSE 227323.6219 254832.0901 244999.8658 245362.7248 245525.4332 282064.4937 241747.8118 128120.48 231258.9042 203820.1308 1.115314866 1.250279298 1.202039587 1.203819877 1.204618171 1.383889278 1.186084077 0.628595809 1.134622489 1 17.63693702 1.909393814 9.497235972 0.885217282 1.229513902 0.507682086 0.134383417 0.28217098 27.90527853 0.053365893 0.033823493 81.16967638 -1.909393814 0.344296619 ESTQLS(ph)PADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK 47 2 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 ES(0.004)T(0.025)QLS(0.965)PADLT(0.004)EGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK;ES(0.003)T(0.011)QLS(0.959)PADLT(0.023)EGKPT(0.001)DPS(0.003)KLESPSFTGTGDTEIAHATEDLENNGSK 161.59 2.44E-21 1847300000 1467170 1159610 1075880 1056310 1256890 1348190 1424750 1511830 1992790 1744170 TRUE FALSE 1409831.374 1126539.058 1270315.449 1110826.286 1297319.008 1375451.326 1442186.517 1480610.182 1766576.834 1626035.812 0.867035869 0.69281319 0.781234607 0.683149951 0.797841596 0.845892394 0.886934043 0.910564313 1.086431689 1 20.6329276 1.9094365 0.957990556 1.034494757 0.755500365 0.754216125 0.059381435 0.25224817 0.426120124 0.047690979 0.021539403 81.17765473 -1.9094365 -0.278994393 ECINAAPDS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ECINAAPDSPSK 12 0 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.942)PS(0.058)K;ECINAAPDS(0.547)PS(0.453)K;ECINAAPDS(0.975)PS(0.025)K;ECINAAPDS(0.974)PS(0.026)K 266.63 1.01E-21 4181310000 5379100 4791370 4444160 4771700 5021400 4837780 5428500 6136800 7008700 6401100 TRUE FALSE 5168878.825 4654724.819 5247318.572 5017968.009 5182917.891 4935603.226 5494935.607 6010072.935 6213101.759 5967547.795 0.866164629 0.78000629 0.879309015 0.840876048 0.868517198 0.827073933 0.920802949 1.007126066 1.041148219 1 22.50870679 1.909459988 2.286889931 1.022122267 0.843035611 0.880795903 0.028368435 0.088328004 0.845995595 0.015683121 0.007835468 81.18204511 -1.909459988 -0.179086656 TTPPTQKPPS(ph)PPMSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPPTQKPPSPPMSGK 16 1 H7C3Q7;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;H0Y6B5;E9PEZ7 H7C3Q7 ABI2 Abl interactor 2 1 TTPPTQKPPS(1)PPMSGK 108.71 0.0006232 100870000 198050 163450 145010 135880 155060 155750 171780 215460 230100 193090 TRUE FALSE 190309.987 158788.566 171216.5327 142892.7831 160047.6457 158899.3717 173882.295 211010.6757 203980.0127 180011.8423 1.057208151 0.882100666 0.951140383 0.793796571 0.889095093 0.882716213 0.9659492 1.172204412 1.133147742 1 17.45773229 1.90978452 4.538724311 1.115140486 0.904954219 0.566172138 0.074879762 0.144918794 4.951495181 0.034021843 0.019854034 81.24273205 -1.90978452 -0.210186267 LLPS(ph)PVTCTPK ddPTM_BT-474_Pertuzumab_2h_R1 3 LLPSPVTCTPK 11 0 H0YCH4;Q9BU19-2;Q9BU19;Q9BU19-5 H0YCH4 ZNF692 Zinc finger protein 692 1 LLPS(0.944)PVT(0.054)CT(0.002)PK;LLPS(1)PVTCTPK;LLPS(0.981)PVT(0.019)CTPK 128.85 0.00026989 515860000 925900 808440 679900 757940 784460 830260 823860 960600 956620 951210 TRUE FALSE 889714.8044 785384.0827 802773.0543 797057.3742 809692.8683 847048.4261 833942.6451 940763.2743 848028.5081 886783.6995 1.003305321 0.885654623 0.905263657 0.898818252 0.913066928 0.955191696 0.940412691 1.060871185 0.956296906 1 19.75822273 1.909836396 6.769410975 1.01060935 0.924152912 0.446566116 0.03928214 0.203232415 12.94055656 0.016561554 0.010215867 81.25243701 -1.909836396 -0.086456438 FKEMELPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKEMELPAK 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 104.52 0.0029607 557260000 805530 725890 633410 605150 714060 597220 748100 888190 929780 930290 FALSE TRUE 774048.997 705188.3279 747881.2771 636381.864 737028.3884 609296.1976 757255.4716 869848.5661 824235.2724 867280.6297 0.892501193 0.813102823 0.862329045 0.733766952 0.849815346 0.702536384 0.873137766 1.002960906 0.950367441 1 19.72613936 1.909973868 4.345392361 0.980054756 0.808460004 0.665030752 0.055459722 0.13056729 4.141059014 0.025027833 0.014498612 81.27816091 -1.909973868 -0.171594752 ASDPHLGTPS(ph)PEDCELETYDMFPDTIHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASDPHLGTPSPEDCELETYDMFPDTIHSR 29 0 Q12851;Q12851-2;C9JCU6 Q12851 MAP4K2 Mitogen-activated protein kinase kinase kinase kinase 2 1 ASDPHLGT(0.048)PS(0.952)PEDCELETYDMFPDTIHSR 109.71 0.00062047 132930000 13987 15048 10550 13720 13362 16571 13756 11982 14796 14193 TRUE FALSE 13440.37258 14618.84577 12456.61968 14428.09084 13791.80087 16906.07697 13924.35004 11734.56751 13116.42011 13231.69547 1.015771003 1.104835416 0.941422791 1.090418902 1.042330584 1.277695441 1.052348135 0.886852901 0.991287937 1 13.69171032 1.909991163 7.449075127 0.951130946 1.079977948 0.280885332 0.085279781 0.339763591 24.74998032 0.037062489 0.023079335 81.28139762 -1.909991163 0.128847003 VIHDNFGIVEGLMTTVHAITATQK ddPTM_BT-474_Pertuzumab_2h_R1 14 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;; 374.82 3.66E-119 99290889000 7504138 7993739 6151386 7068972 7283392 7580029 7205779 5926440 7842347 7282447 FALSE TRUE 7210867.991 7765765.39 7263078.287 7433802.492 7517668.918 7733302.38 7293965.479 5804056.943 6952116.646 6789200.378 1.062108583 1.143840947 1.069798781 1.094945219 1.107298135 1.139059381 1.07434824 0.854895513 1.023996385 1 22.69481024 1.909999524 7.419936417 0.94723038 1.103322024 0.639379773 0.048011354 0.14459636 10.47797899 0.019204578 0.011954693 81.28296255 -1.909999524 0.156091644 HLQELVGQETLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLQELVGQETLPR 13 0 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 ; 205.88 6.63E-08 713970000 455920 481210 412230 478850 457470 485360 466770 377850 488080 527410 FALSE TRUE 438102.1424 467486.362 486729.131 503563.5059 472184.938 495174.3117 472482.4709 370047.2655 432675.2046 491688.0509 0.891016451 0.950778367 0.9899145 1.024152417 0.960334377 1.007090392 0.960939502 0.752605773 0.879979092 1 18.90738377 1.910117154 10.60108557 0.851398356 0.973446062 0.261464033 0.066418858 0.533554922 60.65800124 0.026691198 0.017009175 81.30498117 -1.910117154 0.122047706 VCYYYDGDIGNYYYGQGHPMKPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VCYYYDGDIGNYYYGQGHPMKPHR 24 1 Q92769;H3BM24 Q92769 HDAC2 Histone deacetylase 2 0 188.26 1.09E-17 930000000 352000 378110 336440 352450 352080 327950 357700 51081 384900 363710 FALSE TRUE 338243.4508 367326.673 397242.1921 370639.9867 363404.973 334581.3737 362077.6396 50026.1595 341207.7656 339075.5977 0.997545837 1.083317925 1.171544619 1.093089533 1.071752068 0.986745658 1.067837503 0.147536891 1.006288179 1 18.37124744 1.910133855 24.99999754 0.619335815 1.070270339 0.29600659 0.232475041 57.08930757 15879.79101 0.090384428 0.058333241 81.30810795 -1.910133855 0.450934525 MRPLTEEETR ddPTM_BT-474_Pertuzumab_2h_R1 2 MRPLTEEETR 10 1 Q9Y221;J3QLW7;Q9Y221-2 Q9Y221 NIP7 60S ribosome subunit biogenesis protein NIP7 homolog 0 ; 177.44 2.12E-06 830640000 655040 740540 659450 711800 674030 717760 697990 708890 738130 793440 FALSE TRUE 629440.3126 719420.5243 778627.2844 748536.0833 695710.7871 732273.599 706532.2104 694251.1738 654340.5769 739699.6021 0.85094045 0.972584712 1.052626339 1.01194604 0.940531515 0.989960785 0.955160998 0.938558263 0.884603121 1 19.49657997 1.910138487 3.092454031 0.934416936 0.974229746 0.042491599 0.055676152 0.690833584 11.72423406 0.029231766 0.015818475 81.30897521 -1.910138487 0.03981281 S(ph)KSPLPPEEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSPLPPEEEAK 12 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.5)KS(0.5)PLPPEEEAK 96.993 0.0017587 0 152060 133290 179980 153910 164600 145370 183810 243110 265860 222600 TRUE FALSE 146117.3271 129488.6997 212506.3896 161853.3135 169894.5085 148309.481 186059.5218 238089.6935 235680.6874 207523.1037 0.704101493 0.623972451 1.024013162 0.779929129 0.818677561 0.714664914 0.896572567 1.147292467 1.135684091 1 17.66291244 1.910188379 3.776609345 1.104311119 0.78436479 0.643095407 0.105123485 0.146583369 3.616152379 0.05172847 0.029206855 81.31831653 -1.910188379 -0.319946328 FDDTNPEKEEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 FDDTNPEKEEAK 12 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;A0A0U1RR66 P47897 QARS Glutamine--tRNA ligase 0 ;; 109.22 0.0014787 1358150000 1412190 1060810 1119020 910610 1105420 1183580 1309820 1545010 1887910 1577670 FALSE TRUE 1357000.054 1030556.737 1321251.806 957606.6912 1140976.838 1207512.799 1325849.969 1513105.004 1673602.372 1470813.006 0.92261902 0.700671488 0.898313927 0.651073038 0.775745682 0.820983221 0.901440199 1.028754164 1.137875695 1 20.48818241 1.910215329 1.828406498 1.073411497 0.785252006 0.669378044 0.082209924 0.185685833 1.15605002 0.04978803 0.02330483 81.32336276 -1.910215329 -0.288159491 HSCSGS(ph)SPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.771)S(0.229)PPR;HSCSGS(0.625)S(0.375)PPR;HSCSGS(0.624)S(0.375)PPR;HSCS(0.001)GS(0.503)S(0.497)PPR 104.94 0.0016848 1363750000 24708.2 28013.9 17693.9 26543.7 25540.7 25504.8 19251.3 13537.7 11412 14788.9 TRUE FALSE 23742.57623 27214.971 20891.58133 27913.62354 26362.23981 26020.52453 19486.90317 13258.14176 10116.5576 13787.23463 1.722069499 1.973925282 1.515284384 2.024599152 1.912075954 1.887291051 1.413401867 0.961624439 0.733762634 1 13.7510455 1.91023764 2.228921845 0.862638507 1.843643692 0.88658433 0.150667614 0.088881289 0.810653214 0.085829361 0.042588914 81.32754075 -1.91023764 0.981005185 GNIETTSEDGQVFS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK 285.06 8.90E-36 2853240000 3135600 2772530 2203090 2362190 2538970 2544050 2680750 3181370 3151910 3096100 TRUE FALSE 3013057.285 2693460.159 2601237.37 2484102.909 2620638.276 2595492.434 2713557.82 3115673.598 2794118.391 2886398.389 1.043881294 0.933156064 0.901205246 0.860623716 0.907926739 0.899214898 0.940118949 1.079432974 0.968029362 1 21.46083901 1.910362383 7.098566218 1.02208625 0.920021875 0.384838006 0.051657345 0.247016967 16.90771397 0.022609778 0.014015859 81.35090393 -1.910362383 -0.102064374 QTDPSTPQQES(ph)SKPLGGIQPSSQTIQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTDPSTPQQESSKPLGGIQPSSQTIQPK 28 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 QTDPS(0.028)T(0.171)PQQES(0.692)S(0.109)KPLGGIQPSSQTIQPK 187.89 4.54E-18 701170000 618770 620510 520740 508390 531900 585170 600810 709860 781960 671150 TRUE FALSE 594587.7843 602813.6623 614849.3018 534628.0688 549009.0466 597002.5383 608162.8925 695201.1429 693195.179 625692.4127 0.950287669 0.963434509 0.982670222 0.85445829 0.877442391 0.954147 0.971983806 1.111090895 1.107884905 1 19.25509408 1.910454786 3.423266653 1.082608236 0.929624608 0.646583263 0.046826841 0.147768131 3.038526655 0.024521424 0.013574854 81.36821453 -1.910454786 -0.152983628 AIIGLYNYAHEMTHGASDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AIIGLYNYAHEMTHGASDR 19 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 265.07 1.27E-31 504190000 152540 167700 142000 181070 167580 175310 160000 57508 163840 147680 FALSE TRUE 146578.5682 162917.3602 167662.5588 190415.0444 172970.3629 178854.8883 161958.1279 56320.4397 145241.5701 137677.5021 1.064651566 1.183325945 1.217791987 1.383051272 1.25634443 1.299085803 1.176358704 0.409075113 1.05494048 1 17.0709333 1.910495361 9.312593924 0.762815735 1.238643267 0.50802145 0.180373818 0.267665737 26.19473161 0.072618758 0.04597594 81.37581683 -1.910495361 0.475827533 LS(ph)PIMTEQDDLGEGDVHSMVYPPSAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPIMTEQDDLGEGDVHSMVYPPSAAK 27 0 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 LS(1)PIMTEQDDLGEGDVHSMVYPPSAAK 135.45 1.34E-05 31372000 30681 31262 34141 34364 35689 28585 39751 45945 52050 51040 TRUE FALSE 29481.9526 30370.43837 40311.03816 36137.53016 36836.9691 29163.00829 40237.48463 44996.21969 46141.50221 47583.01534 0.619589835 0.638262165 0.847172838 0.759462802 0.774162142 0.612886932 0.845627044 0.945636156 0.969705301 1 15.53815908 1.910496115 2.812048064 0.969327933 0.717046607 0.724995716 0.072347539 0.153696782 2.1791059 0.040346388 0.021343293 81.37595818 -1.910496115 -0.252281326 GEGERPAQNEK ddPTM_BT-474_Pertuzumab_2h_R1 8 GEGERPAQNEK 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;; 222.25 7.12E-12 17141070000 10095784 9489152 7741150 8273742 8452798 8360637 8924425 10286817 10353021 9894044 FALSE TRUE 9701229.6 9218530.676 9140148.006 8700750.816 8724689.924 8529694.808 9033644.783 10074390.63 9177789.459 9223911.587 1.051747895 0.999416635 0.990918866 0.943282113 0.945877445 0.924737269 0.979372438 1.092203729 0.994999721 1 23.13694725 1.910540361 10.98678088 1.038580304 0.972994134 0.239569312 0.041751392 0.753799945 89.75226233 0.018126428 0.011568234 81.38424918 -1.910540361 -0.06558617 EKEVDGLLTSEPMGS(ph)PVSSK ddPTM_BT-474_Pertuzumab_2h_R1 10 EKEVDGLLTSEPMGSPVSSK 20 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 EKEVDGLLTSEPMGS(0.971)PVS(0.022)S(0.007)K;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(0.99)PVS(0.008)S(0.002)K;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(0.998)PVS(0.001)SK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK 233.22 1.05E-29 13362435000 8672160 7655245 7547950 6866945 7734960 8010120 8454250 9688770 10557600 10463090 TRUE FALSE 8333242.4 7436924.908 8912032.468 7221348.854 7983762.013 8172090.115 8557715.64 9488693.514 9359145.509 9754415.595 0.854304629 0.762416245 0.913640841 0.740315889 0.818476713 0.837783672 0.877317104 0.97275879 0.95947783 1 23.21762401 1.910652169 1.725845715 0.984157443 0.816550334 0.704211587 0.045379822 0.184151965 1.023377992 0.028167313 0.012979374 81.40520406 -1.910652169 -0.167607109 FEKPLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 FEKPLEEK 8 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 111.65 0.0029114 641680000 808690 684400 641910 711330 747040 710740 814550 1011320 1090070 1032710 FALSE TRUE 777085.5007 664881.5821 757917.4162 748041.8265 771069.22 725111.6498 824518.7066 990435.8886 966329.8235 962763.6319 0.807140481 0.690596903 0.787231041 0.776973498 0.800891511 0.753156461 0.856408239 1.028742524 1.00370412 1 19.87682212 1.910687997 2.947646021 1.013486537 0.768744897 0.917180978 0.032357603 0.064824275 1.005043681 0.016680664 0.008928621 81.41191993 -1.910687997 -0.244741641 GLGHPPSS(ph)PLLK ddPTM_BT-474_Pertuzumab_2h_R1 6 GLGHPPSSPLLK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 GLGHPPS(0.017)S(0.983)PLLK;GLGHPPS(0.011)S(0.989)PLLK;GLGHPPS(0.15)S(0.85)PLLK;GLGHPPS(0.101)S(0.899)PLLK;GLGHPPS(0.034)S(0.966)PLLK;GLGHPPS(0.088)S(0.912)PLLK 124.81 0.00020378 5273970000 5746740 5797020 5157660 5793450 6088870 5641170 5579180 5490480 5461180 6083410 TRUE FALSE 5522151.047 5631694.665 6089763.894 6092450.649 6284724.033 5755238.322 5647459.674 5377099.669 4841249.742 5671375.222 0.973688185 0.993003362 1.073771996 1.074245736 1.108148163 1.014787084 0.995783113 0.948112135 0.853628891 1 22.43526718 1.910713053 1.95383138 0.923604362 1.044124751 0.472750877 0.050108348 0.282209651 1.9989257 0.032283143 0.015412165 81.41661697 -1.910713053 0.120520388 SHGLEPAAPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHGLEPAAPSPR 12 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 SHGLEPAAPS(1)PR 87.647 0.0067186 98124000 106090 110210 109730 117440 87111 113820 98161 29164 81900 86790 TRUE FALSE 101943.8855 107066.9187 129560.6519 123501.0925 89913.00443 116121.5184 99362.32368 28561.75321 72603.05535 80911.636 1.259940975 1.323257371 1.601261059 1.526369983 1.111249369 1.435164633 1.228035034 0.352999329 0.897312908 1 16.30405957 1.910730127 6.446599517 0.696288631 1.375149869 0.652366377 0.203590107 0.130067314 7.79009219 0.086829912 0.053280373 81.41981792 -1.910730127 0.678861238 RMEEEQHHWDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RMEEEQHHWDDR 12 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 164.68 2.30E-05 785820000 269060 304530 251630 303760 308830 322150 293300 51638 304030 282620 FALSE TRUE 258544.8377 295845.1026 297105.1385 319437.09 318763.7974 328664.0937 296889.4931 50571.65725 269517.789 263477.8957 0.981277147 1.122846005 1.127628326 1.212386676 1.209831271 1.247406705 1.126809869 0.191938899 1.022923719 1 18.00732241 1.910731749 13.57182501 0.650824352 1.156278968 0.387704623 0.227561537 1.048202653 157.6781358 0.089285138 0.05733944 81.4201221 -1.910731749 0.505454616 S(ph)SPYGTLKPEEMSGPGLAEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPYGTLKPEEMSGPGLAEPK 21 1 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 S(0.5)S(0.5)PYGTLKPEEMSGPGLAEPK;S(0.5)S(0.5)PYGTLKPEEMSGPGLAEPK 225.27 1.74E-25 980850000 299140 261400 273520 244791 272220 304770 323130 417530 462210 452650 TRUE FALSE 287449.2781 253945.1279 322951.1484 257424.6928 280976.2035 310932.6582 327084.5616 408907.8596 409741.8585 421991.6123 0.681172966 0.601777667 0.765302293 0.610023245 0.665833622 0.736821892 0.775097305 0.96899523 0.97097157 1 18.6868548 1.910799831 1.485288254 1.000796082 0.665863403 0.900030118 0.045390538 0.106310209 0.437300453 0.030676503 0.013649483 81.43288687 -1.910799831 -0.334932679 QNS(ph)PAGNKENIKPNET(ph)SPSFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QNSPAGNKENIKPNETSPSFSK 22 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 2 QNS(1)PAGNKENIKPNET(0.652)S(0.202)PS(0.114)FS(0.032)K 80.212 0.012755 409220000 364360 294040 320340 203770 278470 364280 414390 456270 635100 553920 TRUE FALSE 350120.4084 285654.2671 378232.5639 214286.5941 287427.2405 371645.9912 419461.4288 446847.8651 563006.1106 516402.505 0.677999051 0.553162048 0.732437508 0.414960408 0.556595364 0.719682782 0.812276131 0.865309251 1.090246668 1 18.97813647 1.911065877 1.154995279 1.032914186 0.586903464 0.789555092 0.090554715 0.211213858 0.51926765 0.071605241 0.031277188 81.4827873 -1.911065877 -0.446010722 ALKEDDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALKEDDPK 8 1 P61201;P61201-2;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 ; 81.338 0.021086 1150540000 2206780 1720630 1529520 1277640 1720300 1709580 1877570 2210580 2519800 2268810 FALSE TRUE 2120536.598 1671559.317 1805938.288 1343579.154 1775635.012 1744148.879 1900548.263 2164930.75 2233762.868 2115141.478 1.002550714 0.79028251 0.853814417 0.63521952 0.839487585 0.824601521 0.898544274 1.023539453 1.056082012 1 21.01232274 1.911113542 2.189390367 1.035150697 0.815248215 0.529534838 0.084895221 0.232503081 2.049276703 0.050059883 0.024727618 81.49173082 -1.911113542 -0.219902482 RS(ph)PPAPGLQPMR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSPPAPGLQPMR 12 1 P15408;P15408-3;P15408-2;C9JCN8 P15408 FOSL2 Fos-related antigen 2 1 RS(1)PPAPGLQPMR;RS(1)PPAPGLQPMR 90.367 0.0054517 1213210000 1236060 1475550 1141050 1218900 1149770 1271370 1149430 1099050 1049850 1142370 TRUE FALSE 1187753.409 1433468.759 1347263.118 1281807.575 1186753.396 1297077.972 1163497.068 1076354.233 930675.4293 1064996.262 1.115265331 1.345984779 1.265040231 1.203579412 1.114326349 1.217917863 1.092489344 1.010664799 0.873876709 1 20.02241694 1.911181343 1.30026189 0.933362321 1.223256989 0.712267997 0.07121659 0.22796706 0.714518517 0.053523161 0.02340071 81.50445405 -1.911181343 0.289894668 LEPGS(ph)DVEVK ddPTM_BT-474_Pertuzumab_2h_R1 3 LEPGSDVEVK 10 0 Q9ULI0-2;Q9ULI0;H7BYF1 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 LEPGS(1)DVEVK;LEPGS(1)DVEVK;LEPGS(1)DVEVK 186.17 1.44E-06 851450000 1314490 1204630 1279860 1374030 1316850 1192790 1493120 1921920 2051190 1874190 TRUE FALSE 1263118.278 1170275.132 1511159.172 1444943.853 1359207.676 1216909.031 1511393.249 1882231.68 1818347.51 1747249.442 0.722918118 0.669781374 0.864878898 0.826982009 0.777912783 0.696471266 0.865012867 1.077254132 1.040691424 1 20.73665416 1.911524795 3.742389737 1.04259495 0.764737308 0.822790086 0.057827652 0.097759342 2.379191927 0.029909055 0.016873362 81.56893558 -1.911524795 -0.277857642 ERHPS(ph)WRS(ph)EETQER ddPTM_BT-474_Pertuzumab_2h_R1 1 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(0.999)WRS(0.549)EET(0.452)QER 97.69 0.0015417 315100000 124480 154640 108410 115720 150430 132210 117310 95479 100890 104360 TRUE FALSE 119615.184 150229.8186 128002.0986 121692.3231 155268.7176 134883.3768 118745.6749 93507.32528 89437.39017 97291.60425 1.229450217 1.544119041 1.315654106 1.25079984 1.595910755 1.386382492 1.220513073 0.961103746 0.919271409 1 16.57002769 1.911544127 2.485939062 0.949133908 1.393755757 0.749357446 0.11026818 0.135064685 1.515971051 0.060668008 0.031090341 81.57256653 -1.911544127 0.44462185 EDSSGMHHENQTYPPYS(ph)PQAQPQPIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDSSGMHHENQTYPPYSPQAQPQPIHR 27 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 EDSSGMHHENQTYPPYS(1)PQAQPQPIHR;EDSSGMHHENQTYPPYS(1)PQAQPQPIHR 246.89 2.57E-45 1264960000 277840 384620 432900 544700 496090 458350 410060 106190 355900 381260 TRUE FALSE 266981.7056 373651.0142 511134.6598 572812.0323 512047.1854 467618.151 415078.4369 103997.1394 315499.7241 355436.9206 0.751136672 1.051244236 1.43804605 1.611571559 1.440613385 1.315615019 1.167797752 0.29258958 0.887639144 1 18.43923402 1.911558273 7.294002083 0.662347128 1.285503282 0.420088457 0.282274598 0.233920978 16.84995282 0.126373274 0.078555379 81.57522368 -1.911558273 0.623156154 HDDFFPYADGPHQFWTGYFSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 HDDFFPYADGPHQFWTGYFSSR 22 0 O00754;O00754-2 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 109.05 0.00023263 130190000 100800 103510 84346 93375 98700 93786 97573 45061 108340 123510 FALSE TRUE 96860.62456 100557.9961 99589.19847 98194.09494 101874.7751 95682.41718 98767.12756 44130.4746 96041.6974 115144.5577 0.841208881 0.873319575 0.864905823 0.852789719 0.884755452 0.830976462 0.857766355 0.383261489 0.834096716 1 16.8130867 1.911589925 24.99999999 0.658072167 0.85870632 0.04226484 0.150153564 88.41685292 24999.43041 0.058218624 0.037573892 81.58116909 -1.911589925 0.200634153 TVIIHDRPDITHPR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVIIHDRPDITHPR 14 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;;; 148.7 4.96E-06 2127230000 941880 977020 869410 1033030 985990 1017250 947180 513007 969890 921010 FALSE TRUE 905070.2883 949156.3462 1026531.727 1086344.802 1017705.264 1037819.492 958771.8722 502413.2262 859792.1533 858629.1723 1.054087512 1.105432213 1.195547228 1.265208354 1.185267513 1.208693491 1.116630908 0.585134121 1.001354462 1 19.71167566 1.911635961 8.386288268 0.822533796 1.171621481 0.555023383 0.122047681 0.204202632 17.7555314 0.049989006 0.031434945 81.58981731 -1.911635961 0.349087685 TLNMTTS(ph)PEEK ddPTM_BT-474_Pertuzumab_2h_R1 6 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.001)T(0.19)S(0.809)PEEK;TLNMTT(0.253)S(0.747)PEEK;TLNMTT(0.052)S(0.947)PEEK;TLNMT(0.003)T(0.245)S(0.752)PEEK;TLNMT(0.075)T(0.15)S(0.775)PEEK;TLNMTT(0.248)S(0.752)PEEK 286.65 6.88E-28 4552220000 8994010 7890290 7072620 6837440 7681440 7866680 8169130 9395780 10540430 8910920 TRUE FALSE 8642514.146 7665266.655 8350799.764 7190321.098 7928520.494 8025749.659 8269106.257 9201753.86 9343924.575 8307375.451 1.040342307 0.922706178 1.0052272 0.865534625 0.954395349 0.966099306 0.995393347 1.107660766 1.124774561 1 22.98596133 1.911662871 3.385536512 1.087235081 0.955847111 0.490665 0.053448636 0.180496932 3.641692795 0.025654094 0.014181663 81.59487313 -1.911662871 -0.131387969 TYSHLNIAGLVGSIDNDFCGTDMTIGTDSALHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TYSHLNIAGLVGSIDNDFCGTDMTIGTDSALHR 33 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 173.81 5.76E-15 373900000 116300 126210 106170 135210 134390 122040 122780 93590 123100 137270 FALSE TRUE 111754.8674 122610.6144 125357.2807 142188.2043 138712.7764 124507.7324 124282.6184 91657.33379 109126.2041 127972.5806 0.873271969 0.958100663 0.979563592 1.111083356 1.083925757 0.972925073 0.971165993 0.716226346 0.852731136 1 16.96547521 1.911712608 7.770083543 0.828108535 1.000615473 0.314525308 0.090035531 0.28466775 22.39705357 0.039044818 0.024407447 81.6042181 -1.911712608 0.172506938 AREETDKEEPASK ddPTM_BT-474_Pertuzumab_2h_R1 6 AREETDKEEPASK 13 2 P05455 P05455 SSB Lupus La protein 0 ;;;;; 251.68 5.46E-24 10204250000 10793270 9708330 7992610 7338390 9172420 9560520 10138820 11928440 14013640 12375960 FALSE TRUE 10371457.08 9431457.934 9437052.422 7717125.187 9467459.219 9753840.265 10262901.91 11682113.55 12422870.34 11537725.21 0.898916978 0.817445187 0.817930073 0.6688602 0.820565497 0.845386772 0.889508263 1.012514455 1.076717474 1 23.45985547 1.91186614 1.68227529 1.044822919 0.802113759 0.749407193 0.056625288 0.179306714 0.947054461 0.039328177 0.018017919 81.6330719 -1.91186614 -0.24270916 QQTEKPES(ph)EDEWER ddPTM_BT-474_Pertuzumab_2h_R1 2 QQTEKPESEDEWER 14 1 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 QQTEKPES(1)EDEWER;QQT(0.459)EKPES(0.541)EDEWER 186.85 2.67E-06 1069160000 1076010 917760 830190 847620 934200 968520 1023910 1158270 1353520 1226120 TRUE FALSE 1033958.34 891586.3834 980223.8005 891365.7698 964249.3914 988104.138 1036440.917 1134351.32 1199874.084 1143073.8 0.904542068 0.779990219 0.857533258 0.779797218 0.8435583 0.864427247 0.906713912 0.992369276 1.049690828 1 20.12448712 1.911878404 1.491824869 1.028504339 0.829821019 0.82464379 0.03652187 0.140894943 0.584689083 0.024146468 0.010762072 81.6353772 -1.911878404 -0.19868332 KEES(ph)EES(ph)DDDMGFGLFD ddPTM_BT-474_Pertuzumab_2h_R1 40 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 2 KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD 212.78 8.44E-13 30408080300 41326143 36412233 30126195 30163259 34505326 34890320 38330037 47735933 51759945 46769357 TRUE FALSE 39711071.64 35373791.77 35570668.59 31719988.41 35615221.15 35595826.18 38799131.46 46750169.3 45884373.04 43601626.79 0.910770413 0.811295228 0.815810583 0.727495526 0.816832393 0.816387571 0.889855134 1.072211583 1.052354612 1 25.37787863 1.911929885 3.087668651 1.047547032 0.812912333 0.831134851 0.045193761 0.09584841 1.624527763 0.023865878 0.012928611 81.6450549 -1.911929885 -0.234634699 ENPEDVLS(ph)PTSVATYLSSK ddPTM_BT-474_Pertuzumab_2h_R1 3 ENPEDVLSPTSVATYLSSK 19 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 ENPEDVLS(0.996)PT(0.002)S(0.002)VATYLSSK;ENPEDVLS(0.95)PT(0.034)S(0.012)VAT(0.004)YLSSK;ENPEDVLS(0.878)PT(0.025)S(0.031)VAT(0.062)Y(0.002)LS(0.002)S(0.002)K 165.06 2.37E-11 115433000 163359 184398 172592 205315 212507 200357 167621 162918 150383 168698 TRUE FALSE 156974.7497 179139.1496 203783.2137 215911.3318 219342.4806 204408.3558 169672.3959 159553.6864 133312.1523 157271.9342 0.998110378 1.139040799 1.29573795 1.372853541 1.394670205 1.299712863 1.078847264 1.014508324 0.847653798 1 17.26290171 1.912005257 2.154010279 0.940170486 1.257874542 0.564602309 0.116805671 0.246186642 2.103206701 0.076198426 0.037486158 81.65922558 -1.912005257 0.317704056 EHHFGSSGMTLHER ddPTM_BT-474_Pertuzumab_2h_R1 4 EHHFGSSGMTLHER 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 156.6 1.92E-06 977490000 328776 452174 379425 453578 382553 331231 357138 17980.2 338925 259610 FALSE TRUE 315927.0704 439278.4402 447995.5378 476987.2149 394858.1647 337928.7178 361508.7617 17608.90259 300451.6549 242026.3835 1.30534145 1.81500229 1.851019428 1.970806687 1.631467442 1.396247438 1.493675014 0.072756128 1.241400423 1 17.8848048 1.912042728 7.370332201 0.687745088 1.670186369 0.581269827 0.337146423 0.16923081 12.43587249 0.142134501 0.088442962 81.66627147 -1.912042728 0.982441281 EIIDASDKEGMS(ph)PAKR ddPTM_BT-474_Pertuzumab_2h_R1 8 EIIDASDKEGMSPAKR 16 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 EIIDAS(0.001)DKEGMS(0.999)PAKR;EIIDASDKEGMS(1)PAKR;EIIDAS(0.006)DKEGMS(0.994)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR 147.08 5.54E-07 11085390000 5052680 4545320 3800210 3702770 4388270 4343450 5121630 5551540 6852360 6115380 TRUE FALSE 4855215.68 4415691.924 4486992.482 3893870.403 4529422.69 4431277.535 5184310.04 5436898.759 6074508.82 5701179.866 0.851615945 0.774522472 0.787028753 0.682993783 0.794471109 0.777256224 0.909339849 0.953644489 1.065482753 1 22.44282909 1.912113476 1.518639577 1.025994352 0.771536354 0.841109381 0.045132681 0.142516557 0.613123057 0.031508784 0.014095916 81.67957627 -1.912113476 -0.254457997 SKS(ph)PLPPEEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSPLPPEEEAK 12 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.137)KS(0.863)PLPPEEEAK 140.46 3.62E-05 312010000 331640 238110 408090 309760 283320 277380 398740 518080 574490 546880 TRUE FALSE 318679.1422 231319.3359 481840.9409 325746.7507 292433.2451 282988.8136 403619.8994 507381.467 509276.3037 509839.3305 0.62505798 0.453710261 0.945083896 0.638920403 0.573579219 0.55505489 0.791660971 0.995179141 0.998895678 1 18.95968315 1.912151299 2.954419084 0.998265337 0.636288603 0.65342492 0.119003857 0.167339959 2.608393415 0.063652588 0.034130377 81.68669012 -1.912151299 -0.361976733 DFTNEAPPAPLPDASASPLS(ph)PHR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFTNEAPPAPLPDASASPLSPHR 23 0 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDASAS(0.021)PLS(0.978)PHR;DFTNEAPPAPLPDAS(0.014)AS(0.051)PLS(0.935)PHR;DFTNEAPPAPLPDAS(0.001)AS(0.203)PLS(0.796)PHR;DFTNEAPPAPLPDAS(0.001)AS(0.037)PLS(0.963)PHR 178.44 3.32E-17 990470000 974730 995600 895480 1035300 1001620 929130 955250 1005930 940960 1032030 TRUE FALSE 936636.474 967206.4628 1057313.156 1088731.957 1033838.017 947917.6452 966940.6352 985157.194 834146.1656 962129.6889 0.973503349 1.0052766 1.098929976 1.13158545 1.074530834 0.985228557 1.00500031 1.023933889 0.866978927 1 19.87587185 1.912211309 1.146560199 0.952307721 1.054805327 0.315050618 0.058037015 0.626842566 1.51817134 0.048610447 0.021259677 81.69797812 -1.912211309 0.102497606 GPGQVPTATSALSLELQEVEPLGLPQAS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 6 GPGQVPTATSALSLELQEVEPLGLPQASPSR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GPGQVPTATSALSLELQEVEPLGLPQAS(0.846)PS(0.154)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.96)PS(0.04)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.821)PS(0.179)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.967)PS(0.033)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.969)PS(0.031)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.968)PS(0.032)R 239.68 4.69E-46 5066920000 1526145 1785688 1582887 1920190 1819458 1952351 1698180 1578907 1702373 1753739 TRUE FALSE 1466501.566 1734761.927 1868949.892 2019291.236 1877982.519 1991828.875 1718962.835 1546302.019 1509126.754 1634956.695 0.896966611 1.061044572 1.143118896 1.235073223 1.148643584 1.218276227 1.051381263 0.94577552 0.923037753 1 20.64082099 1.912402007 3.848382134 0.953729839 1.123497295 0.385193182 0.090247805 0.247210798 6.35048719 0.046389838 0.026328652 81.73385956 -1.912402007 0.169767456 QHHPPYHQQHHQGPPPGGPGGR ddPTM_BT-474_Pertuzumab_2h_R1 7 QHHPPYHQQHHQGPPPGGPGGR 22 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;;; 169.51 2.85E-12 15174810400 3567944.3 3673897.9 2791815.2 3700032.5 3245406.6 3528592.32 2969866.2 25344.95 3075855.2 1099387.9 FALSE TRUE 3428505.092 3569121.929 3296358.31 3890991.621 3349798.051 3599942.874 3006212.311 24821.56793 2726697.013 1024925.378 3.345126548 3.482323694 3.216193471 3.796365768 3.268333599 3.512395098 2.933103594 0.024217927 2.660385888 1 19.96708744 1.912402846 6.467186712 1.177681987 3.420922385 0.720716749 0.615839755 0.112529181 6.885896248 0.247471208 0.151957758 81.73401748 -1.912402846 2.243240398 VDIDVPDVNIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDIDVPDVNIEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 180.48 5.72E-09 288660000 700680 636420 627590 655230 557920 614360 681730 833000 854760 801220 FALSE TRUE 673296.651 618269.9247 741009.4737 689046.4988 575866.0035 626782.7801 690073.2157 815798.2589 757731.2282 746952.6557 0.901391334 0.827723042 0.992043429 0.922476804 0.77095382 0.839119823 0.923851345 1.09216863 1.014430061 1 19.51065728 1.912487205 4.994915241 1.040881178 0.876362266 0.584933251 0.060119794 0.157464262 6.421914033 0.028692358 0.0170255 81.74989527 -1.912487205 -0.164518912 KLEGDSTDLSDQIAELQAQIAELK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLEGDSTDLSDQIAELQAQIAELK 24 1 P35579 P35579 MYH9 Myosin-9 0 ; 207.55 1.18E-24 481960000 557580 466640 510960 543310 494320 446380 676820 737350 912570 859660 FALSE TRUE 535789.1572 453331.8841 603301.8382 571350.2942 510220.2517 455406.1094 685103.1256 722123.4648 808978.8794 801434.4625 0.668537706 0.565650599 0.752777509 0.712909565 0.636633781 0.56823874 0.854846101 0.901038698 1.009413642 1 19.61222502 1.912533556 2.049195987 0.980032117 0.654536789 0.833576732 0.064322038 0.127066735 0.986448915 0.03973657 0.019269689 81.75862077 -1.912533556 -0.325495328 SEPTQALELTEDDIKEDGIVPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEPTQALELTEDDIKEDGIVPLR 23 1 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 ;;; 248.18 8.28E-38 691289000 622588 547470 512884 535592 582504 589435 611919 773590 803600 709334 FALSE TRUE 598256.5727 531856.6916 605573.5478 563233.9673 601240.7702 601353.7796 619407.8478 757615.0962 712378.697 661290.1764 0.904680871 0.804271272 0.915745568 0.851719846 0.909193561 0.909364453 0.936665733 1.145662106 1.077255829 1 19.33492394 1.912615035 4.253565786 1.085462112 0.882577016 0.772872422 0.046301432 0.093702194 2.892162792 0.021225101 0.012269623 81.77396101 -1.912615035 -0.202885097 SSS(ph)PTSSLTQPIEMPTLSSS(ph)PTEERPTVGPGQQDNPLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPTSSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLK 39 1 Q7LBC6;Q7LBC6-2 Q7LBC6 KDM3B Lysine-specific demethylase 3B 2 S(0.247)S(0.303)S(0.372)PT(0.018)S(0.027)S(0.033)LTQPIEMPTLSS(0.191)S(0.697)PT(0.111)EERPTVGPGQQDNPLLK;S(0.127)S(0.132)S(0.467)PT(0.091)S(0.091)S(0.091)LT(0.001)QPIEMPTLS(0.001)S(0.019)S(0.492)PT(0.488)EERPTVGPGQQDNPLLK 272.38 1.91E-76 645510000 524930 521880 438420 473600 454900 541350 501090 580330 648770 597760 TRUE FALSE 504415.1553 506996.4934 517652.2466 498042.5528 469532.2716 552296.4679 507222.4893 568345.9827 575124.3495 557273.1828 0.905148805 0.909780892 0.92890213 0.893713475 0.842553143 0.991069524 0.910186431 1.019869608 1.032033063 1 19.0880252 1.912651735 1.381952254 1.024528655 0.903668404 0.63162442 0.036276951 0.256118499 0.909445395 0.025799789 0.011363022 81.78087159 -1.912651735 -0.120860251 ELAEDGYSGVEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELAEDGYSGVEVR 13 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82 P23396 RPS3 40S ribosomal protein S3 0 ; 128.08 0.00034943 372300000 484440 426270 355990 297200 342000 382330 415880 466420 578450 430930 FALSE TRUE 465507.5492 414113.197 420325.312 312538.5276 353000.7406 390060.9746 420969.6638 456788.264 512786.7811 401742.7273 1.158720538 1.030792019 1.046254937 0.777956902 0.87867363 0.970922304 1.047858829 1.137016884 1.276405884 1 18.61591238 1.912725009 2.558733574 1.154769096 0.969941123 0.280870759 0.11379724 0.350695942 4.158934524 0.065871627 0.03405818 81.79467077 -1.912725009 -0.184827973 S(ph)EVLAEESIVCLQK ddPTM_BT-474_Pertuzumab_2h_R1 3 SEVLAEESIVCLQK 14 0 O43663-2;O43663-4;O43663;O43663-3;H0YLA0;H0YM42 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 S(1)EVLAEESIVCLQK;S(1)EVLAEESIVCLQK;S(1)EVLAEESIVCLQK 352.62 5.92E-82 172847000 238089 206637 214368 204373 205258 230971 228308 275959 277922 260842 TRUE FALSE 228784.2187 200743.9151 253109.0662 214920.715 211860.31 235641.3919 231102.1016 270260.3502 246373.4597 243174.939 0.940821532 0.825512349 1.040851772 0.883811119 0.87122592 0.969020051 0.950353283 1.111382412 1.013153167 1 17.89163503 1.913086936 5.456162692 1.05077601 0.921795723 0.429310857 0.061460435 0.190766056 9.034472392 0.026632628 0.016011185 81.8628642 -1.913086936 -0.128980286 SHHAASTTTAPTPAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SHHAASTTTAPTPAAR 16 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ;; 73.834 0.019641 99846000 32823.1 51937 38167.2 55063 42886.4 47693 40662 8606.5 34259.8 33208.4 FALSE TRUE 31540.33696 50455.80761 45064.86206 57904.80803 44265.88 48657.38514 41159.63372 8428.772767 30370.77113 30959.16549 1.018772194 1.629753477 1.455622636 1.870360751 1.429815026 1.57166333 1.329481369 0.272254521 0.980994502 1 14.91807896 1.913213294 6.492525956 0.691499599 1.509341509 0.593855939 0.274660589 0.142534361 8.846006444 0.113883721 0.069971345 81.88668575 -1.913213294 0.81784191 S(ph)ESNEDLFGLVPFDEITGSQQQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SESNEDLFGLVPFDEITGSQQQK 23 0 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK 197.4 1.91E-24 448601000 597955 554099 488125 505986 541787 566197 579607 656804 725405 700206 TRUE FALSE 574586.2575 538296.639 576340.0458 532099.9981 559214.0709 577645.8913 586700.4038 643240.7679 643060.0655 652780.4239 0.880213677 0.824621296 0.882900321 0.815128608 0.856664891 0.884900757 0.898771443 0.985386118 0.985109299 1 19.31623827 1.913309073 1.424466318 0.999950731 0.85105994 0.88505059 0.021494307 0.115522727 0.436367958 0.014530009 0.006430838 81.90474697 -1.913309073 -0.148890791 AEKDEPGAWEETFK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEKDEPGAWEETFK 14 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 215.79 5.81E-12 4229990000 2499020 2465370 2197090 1965840 2180140 2329970 2542330 2816100 3394400 2887220 FALSE TRUE 2401355.536 2395060.061 2594153.037 2067297.238 2250266.183 2377083.59 2573443.795 2757946.551 3009081.942 2691666.018 0.892144687 0.88980581 0.963772258 0.768036311 0.836012406 0.883127243 0.956078421 1.024624353 1.117925449 1 21.36006798 1.913319487 1.956775381 1.05909807 0.870065938 0.683156064 0.053755908 0.191661284 1.361027829 0.034333903 0.016434038 81.90671094 -1.913319487 -0.189032131 MAGNEALS(ph)PTSPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALS(0.981)PT(0.018)S(0.001)PFR 156.72 5.76E-06 165450000 132740 171260 154020 185420 203690 192170 149140 133850 138120 125690 TRUE FALSE 127552.374 166375.8325 181854.8402 194989.5484 210241.8738 196055.8091 150965.2199 131085.9507 122441.1966 117176.9043 1.088545347 1.419868816 1.551968292 1.664061271 1.794226217 1.673160852 1.288353031 1.118701262 1.044926023 1 16.83832872 1.913364639 2.56760223 1.055780335 1.54396899 0.578428361 0.181943319 0.22057136 2.633397788 0.109463784 0.056679963 81.91522695 -1.913364639 0.488188655 YGDSEFTVQSTTGHCVHMR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGDSEFTVQSTTGHCVHMR 19 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 178 2.25E-14 920970000 407470 521840 360730 529200 463600 553920 462890 128161 480830 425570 FALSE TRUE 391545.6219 506957.6341 425921.9354 556512.0754 478512.115 565120.6419 468554.9863 125514.4306 426248.1942 396745.7648 0.98689301 1.277789655 1.073538707 1.402691912 1.20609256 1.424389854 1.180995559 0.31635985 1.074361044 1 18.5978553 1.913413525 10.65220711 0.726649193 1.236589629 0.413712262 0.227682418 0.450496022 53.65498796 0.089650476 0.057144897 81.92444817 -1.913413525 0.509940436 QES(ph)DPEDDDVKKPALQSSVVATSK ddPTM_BT-474_Pertuzumab_2h_R1 7 QESDPEDDDVKKPALQSSVVATSK 24 2 Q9H307 Q9H307 PNN Pinin 1 QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK 217.29 6.59E-33 32919100000 6369030 4679142 4657619 3750503 4844630 4894560 5498390 7341990 8050900 6374010 TRUE FALSE 6120121.266 4545697.452 5499354.361 3944066.909 5000461.924 4993531.357 5565680.942 7190375.341 7136995.584 5942292.625 1.029925931 0.764973679 0.925460038 0.663728153 0.841503817 0.840337505 0.936621821 1.21003387 1.201050846 1 22.50258822 1.913448547 3.618761448 1.154251875 0.837973193 0.60540875 0.105027832 0.142493335 3.270827068 0.04932093 0.027679904 81.93105498 -1.913448547 -0.316278682 VALENDDRS(ph)EEEKYTAVQR ddPTM_BT-474_Pertuzumab_2h_R1 3 VALENDDRSEEEKYTAVQR 19 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;A0A5F9ZH85;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 1 VALENDDRS(1)EEEKYTAVQR;VALENDDRS(1)EEEKYTAVQR;VALENDDRS(1)EEEKYTAVQR 268.75 3.42E-32 480080000 481100 417030 349281 323980 416160 447810 420320 481210 528960 530210 TRUE FALSE 462298.0801 405136.7127 412403.8464 340700.6466 429546.1643 456865.025 425464.0019 471272.8453 468914.6784 494298.4044 0.935261122 0.819619706 0.834321622 0.689261069 0.869001721 0.924269674 0.860743223 0.953417695 0.948646959 1 18.91502272 1.913555197 0.864719996 0.987259552 0.824740588 0.45978692 0.062367108 0.534726854 0.741739994 0.054849922 0.025827872 81.95117739 -1.913555197 -0.162518964 IS(ph)DS(ph)ESEDPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ISDSESEDPPR 11 0 Q96ST2;Q96ST2-3;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 IS(1)DS(1)ESEDPPR 198.74 7.69E-08 286230000 371770 321730 277690 326970 338350 337240 347950 426480 424610 407170 TRUE FALSE 357240.8174 312554.5754 327874.7602 343844.9609 349233.335 344059.2239 352208.3162 417673.039 376410.0529 379592.0132 0.941117845 0.823396079 0.863755687 0.905827702 0.920022874 0.906392158 0.927860186 1.100320935 0.99161742 1 18.53409011 1.913563338 5.478190938 1.037919262 0.892531595 0.692879586 0.040793023 0.116183322 5.559148357 0.018261528 0.010986581 81.95271347 -1.913563338 -0.145387667 RPMEEDGEEKS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 13 RPMEEDGEEKSPSK 14 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 RPMEEDGEEKS(0.59)PS(0.41)K;RPMEEDGEEKS(0.975)PS(0.025)K;RPMEEDGEEKS(0.76)PS(0.24)K;RPMEEDGEEKS(0.996)PS(0.004)K;RPMEEDGEEKS(0.972)PS(0.028)K;RPMEEDGEEKS(0.953)PS(0.047)K;RPMEEDGEEKS(0.975)PS(0.025)K;RPMEEDGEEKS(1)PSK;RPMEEDGEEKS(0.884)PS(0.116)K;RPMEEDGEEKS(0.694)PS(0.306)K;RPMEEDGEEKS(0.994)PS(0.006)K;RPMEEDGEEKS(0.884)PS(0.116)K;RPMEEDGEEKS(0.914)PS(0.086)K 191.64 2.43E-07 72776781000 13741086 10179751 9924373 8510376 10299148 9195031 11555541 14147923 15851008 13283667 TRUE FALSE 13204069.17 9889434.468 11717927.97 8949597.525 10630429.45 9380960.827 11696961.17 13855763.45 14051668.02 12383952.4 1.066224154 0.798568514 0.94621875 0.722676996 0.85840361 0.757509438 0.944525688 1.118848248 1.134667477 1 23.5619685 1.913740678 3.952414362 1.092234444 0.852896444 0.515868528 0.097508895 0.168433792 4.563935379 0.044707353 0.025524761 81.98618502 -1.913740678 -0.239338 FSGEEGEIEDDES(ph)GTENREEK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSGEEGEIEDDESGTENREEK 21 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(1)GTENREEK;FSGEEGEIEDDES(0.996)GT(0.004)ENREEK 344.07 2.02E-81 1868270000 1219840 1074340 1109450 1129100 1367620 1137360 1340360 1565320 1783090 1596850 TRUE FALSE 1172167.304 1043700.875 1309952.295 1187372.986 1411610.739 1160358.198 1356763.727 1532995.595 1580681.099 1488693.927 0.787379651 0.701084928 0.879933928 0.79759376 0.948220929 0.779447123 0.911378559 1.029758748 1.06179052 1 20.50561574 1.913760129 2.612981356 1.036599269 0.818244765 0.696755989 0.063285119 0.157797725 1.948043162 0.035160526 0.018297883 81.98985702 -1.913760129 -0.218354504 DKEQWK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKEQWK 6 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 86.472 0.048827 2640800000 2602900 2218700 2453500 2478000 2168140 2114400 2477400 2972200 3204200 2561800 FALSE TRUE 2501175.79 2155424.848 2896902.028 2605889.877 2237880.192 2157154.617 2507719.162 2910823.031 2840472.649 2388287.004 1.04726768 0.902498253 1.212962271 1.091112531 0.937023142 0.903222524 1.050007456 1.218791136 1.189334717 1 21.18754479 1.913849955 6.661712493 1.155784432 1.015996331 0.2066603 0.103278707 0.34412103 22.33503295 0.045917684 0.028294872 82.00681681 -1.913849955 -0.139788101 DAGNFDQNKLEEEMR ddPTM_BT-474_Pertuzumab_2h_R1 4 DAGNFDQNKLEEEMR 15 1 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;;; 221.85 1.35E-12 2014420000 2075000 1890920 1567260 1721749 1755352 1764699 1929198 2357767 2453650 2237060 FALSE TRUE 1993906.706 1836992.813 1850498.746 1810608.672 1811814.491 1800382.423 1952808.102 2309078.288 2175121.939 2085541.934 0.956061671 0.880822765 0.887298747 0.868171789 0.86874997 0.863268388 0.936355233 1.107183821 1.042952867 1 20.99199089 1.913893216 4.701962225 1.057143728 0.886161326 0.811597686 0.034943895 0.082414316 3.056607476 0.015732725 0.009254641 82.01498624 -1.913893216 -0.170982402 HHEDNLLR ddPTM_BT-474_Pertuzumab_2h_R1 4 HHEDNLLR 8 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 171.53 0.00028884 747720000 591720 678560 589330 691650 549700 597860 585430 311707 597480 501393 FALSE TRUE 568594.9282 659208.1332 695835.0406 727346.1394 567381.5997 609949.1388 592594.6675 305270.1415 529656.5752 467433.2055 1.216419633 1.410272367 1.488629888 1.55604294 1.213823907 1.304890478 1.267763309 0.653077569 1.133117136 1 18.8344007 1.914006585 6.438886882 0.901324061 1.367690034 0.625229524 0.150948595 0.143540801 8.871586217 0.065845498 0.040425379 82.03639832 -1.914006585 0.466365972 QEEMNSQQEEEEMETDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEEMNSQQEEEEMETDAR 18 0 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 0 364.3 5.02E-77 0 37999 39039 26997 36127 35171 36511 34919 32034 33636 42355 FALSE TRUE 36513.95707 37925.64594 31875.95845 37991.5188 36302.30716 37249.27744 35346.34917 31372.48671 29817.78229 39486.25812 0.924725684 0.960477081 0.807267134 0.962145329 0.919365594 0.943347868 0.895155703 0.794516579 0.755143275 1 15.26906304 1.914007905 5.755289035 0.829771002 0.918341064 0.138764375 0.072466264 0.322994095 16.78847417 0.030284708 0.018343032 82.03664766 -1.914007905 0.088570062 HHISIAEIYETELVDIEK ddPTM_BT-474_Pertuzumab_2h_R1 4 HHISIAEIYETELVDIEK 18 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R0I4;M0R027 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;; 190.57 1.56E-14 361517000 341896 472175 374798 457160 368522 428525 373045 19254.8 363586 256834 FALSE TRUE 328534.3263 458709.0313 442532.3359 480754.0824 380375.8448 437190.0691 377610.4363 18857.18165 322313.2416 239438.4044 1.372103724 1.915770498 1.848209509 2.007840319 1.588616687 1.825897855 1.577067126 0.078755878 1.34612174 1 17.86929504 1.914104185 7.652166559 0.727757109 1.768410444 0.609667637 0.340062236 0.162309611 12.8704332 0.136543167 0.085264449 82.0548366 -1.914104185 1.040653335 TVDLKPDWGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVDLKPDWGK 10 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 172.17 3.46E-06 19047900000 20932100 18100900 17150100 15626800 17091000 17140500 19391000 22192900 25058400 22291300 FALSE TRUE 20114050.39 17584680.05 20249504.57 16433301.02 17640747.54 17487092.65 19628312.86 21734608.86 22213875.49 20781490.4 0.967882958 0.846170304 0.974400978 0.79076624 0.848868257 0.841474424 0.944509392 1.045863817 1.068926004 1 24.30879579 1.914264965 3.13613519 1.042392748 0.876196584 0.620315108 0.055795013 0.15902191 2.782911626 0.028098914 0.015304975 82.08521974 -1.914264965 -0.166196164 VLSTS(ph)TDLEAAVADALK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLST(0.002)S(0.996)T(0.001)DLEAAVADALK;VLS(0.002)T(0.2)S(0.796)T(0.001)DLEAAVADALK 254.53 5.09E-27 426090000 501170 441040 395110 439160 518040 439600 513420 647250 690480 623940 TRUE FALSE 481583.7223 428461.971 466515.1662 461825.1002 534703.2271 448489.0132 519703.3875 633884.0613 612099.6051 581679.9881 0.82791867 0.736593969 0.802013437 0.793950471 0.91923951 0.771023625 0.893452411 1.089747068 1.052296138 1 19.14986615 1.914335226 3.731733637 1.052565786 0.809948991 0.823942676 0.049236717 0.090297863 2.200967048 0.024093392 0.013612752 82.09850072 -1.914335226 -0.242616795 HYGEHVCTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 HYGEHVCTAK 10 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 ; 93.058 0.0052304 441420000 290529 287402 236879 251481 271837 261659 270771 68168 300078 269594 FALSE TRUE 279174.8055 279205.5764 279688.3046 264459.9645 280580.884 266949.9243 274084.7765 66760.30698 266014.4035 251334.1583 1.110771442 1.110893873 1.112814536 1.052224522 1.116365901 1.062131491 1.090519404 0.265623692 1.058409272 1 17.93924723 1.914403205 24.99995106 0.689325549 1.09336173 0.315382746 0.204071152 67.65935027 19759.73795 0.078818448 0.05086879 82.11135237 -1.914403205 0.404036181 KFGFEIIETK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFGFEIIETK 10 1 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;B0AZT5 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ; 114.82 0.0020929 876510000 1201580 1109730 996480 1001850 1244180 1135200 1190620 1396380 1540120 1481560 FALSE TRUE 1154620.925 1078081.587 1176566.103 1053555.599 1284200.18 1158154.522 1205191.164 1367544.265 1365292.034 1381212.622 0.835947274 0.780532678 0.851835615 0.762775826 0.929762847 0.838505603 0.872560202 0.990104089 0.988473471 1 20.39750399 1.914405157 0.957834496 1.01414955 0.819872522 0.731187631 0.042960276 0.262952144 0.443993502 0.034563041 0.015656298 82.11172137 -1.914405157 -0.194277028 ELLLPNWQGSGSHGLTIAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLLPNWQGSGSHGLTIAQR 20 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 266.14 1.04E-36 573810000 390700 529410 418260 589920 439750 522650 455630 405950 433570 463050 FALSE TRUE 375431.0121 514311.7451 493848.8861 620365.8419 453894.9581 533218.3411 461206.1362 397566.9906 384352.9513 431687.2111 0.869682961 1.191399078 1.143997027 1.437072552 1.05144407 1.235196057 1.068380356 0.92096078 0.890350563 1 18.71962683 1.914546279 3.369999325 0.930971656 1.164069024 0.332533117 0.136934559 0.268542765 5.394791611 0.06755432 0.037391663 82.13840761 -1.914546279 0.233097369 GPTEQLVSPEPEVHDIER ddPTM_BT-474_Pertuzumab_2h_R1 3 GPTEQLVSPEPEVHDIER 18 0 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 ;; 154.26 2.73E-08 1289090000 611450 651130 649640 740570 757540 721750 661160 645110 671800 686320 FALSE TRUE 587553.858 632560.4099 767044.3992 778790.9065 781906.9621 736344.2795 669251.4739 631788.2531 595540.0804 639834.9351 0.918289743 0.988630622 1.198816065 1.217174718 1.222044811 1.150834753 1.045975199 0.987423816 0.930771435 1 19.28734024 1.914652462 2.592354316 0.968501475 1.122716813 0.315068342 0.09402097 0.367580142 4.470827861 0.057697137 0.029984594 82.15849251 -1.914652462 0.154215338 HFHPLFEYFDYESR ddPTM_BT-474_Pertuzumab_2h_R1 3 HFHPLFEYFDYESR 14 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 196.38 1.44E-08 2496215000 1944893 2110421 2108781 2211103 2041871 2064032 2018070 62664.08 2232298 1515393 FALSE TRUE 1868884.431 2050233.859 2489884.636 2325218.291 2107549.635 2105768.141 2042767.744 61370.04485 1978896.89 1412754.082 1.322866063 1.451231948 1.762433156 1.645876179 1.491802191 1.490541183 1.445947154 0.043440005 1.400736982 1 20.43007893 1.914716167 10.88900504 0.715792016 1.532576089 0.473395352 0.334917286 0.452044389 56.12647093 0.132707303 0.084667903 82.17054485 -1.914716167 0.816784073 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 37 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 DREGPTDHLESACPLNLPLQNNHTAADMYLS(0.032)PVRS(0.967)PK;DREGPTDHLESACPLNLPLQNNHTAADMYLS(0.002)PVRS(0.998)PK 302.88 7.17E-93 452490000 206234 199988 140773 152743 171283 196666 196101 153968 237523 189580 TRUE FALSE 198174.1473 194284.538 166213.8126 160626.0845 176792.4733 200642.7213 198500.9427 150788.507 210560.3848 176739.5777 1.1212777 1.099270127 0.940444776 0.908829174 1.000299285 1.135244996 1.123126723 0.853167745 1.191359556 1 17.43126562 1.914862419 0.003885431 2.16E-08 2.046956823 0 0.10725928 79975.77011 256.6834691 67389.34271 67823.26427 82.19822119 -1.914862419 2.046956801 QSNASS(ph)DVEVEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 QSNASSDVEVEEK 13 0 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QSNASS(1)DVEVEEK;QSNAS(0.001)S(0.999)DVEVEEK;QSNAS(0.006)S(0.994)DVEVEEK;QSNAS(0.076)S(0.924)DVEVEEK 366.1 4.27E-91 2062380000 3831230 3406230 3491230 3215130 3373570 3286920 3610020 4396100 4417340 4009250 TRUE FALSE 3681501.296 3309087.655 4122172.923 3381063.245 3482083.943 3353383.774 3654200.505 4305318.999 3915902.082 3737699.926 0.984964381 0.885327266 1.102863527 0.904583918 0.931611422 0.897178436 0.977660213 1.1518632 1.047676956 1 21.83371932 1.914866846 7.250499665 1.080030979 0.950836086 0.360040494 0.068252898 0.252497131 18.73969163 0.028346359 0.01761799 82.19905905 -1.914866846 -0.129194894 PAS(ph)PDRFAVSAEAENK ddPTM_BT-474_Pertuzumab_2h_R1 4 PASPDRFAVSAEAENK 16 1 O15037;G3V331 O15037 KHNYN Protein KHNYN 1 PAS(1)PDRFAVSAEAENK;PAS(1)PDRFAVSAEAENK;PAS(1)PDRFAVSAEAENK;PAS(1)PDRFAVSAEAENK 312.27 6.49E-58 1761190000 3146180 2261170 2138120 2022290 2469370 2231590 2567390 3025590 3589870 2555970 TRUE FALSE 3023223.807 2196683.646 2524525.846 2126660.629 2548799.529 2276714.279 2598810.487 2963110.509 3182363.008 2382851.875 1.268741813 0.921871673 1.059455635 0.89248545 1.069642455 0.955457745 1.090630313 1.243514354 1.335526996 1 21.18425784 1.914892164 4.105625669 1.215006653 1.020175985 0.248848198 0.125665449 0.256535249 7.487534251 0.055661673 0.032023844 82.20385104 -1.914892164 -0.194830668 RQS(ph)GLYDSQNPPTVNNCAQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQSGLYDSQNPPTVNNCAQDR 21 1 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 1 RQS(0.998)GLY(0.002)DSQNPPTVNNCAQDR;RQS(0.999)GLYDS(0.001)QNPPTVNNCAQDR 171 4.58E-12 1170540000 197591 197085 161502 181317 178750 200292 155540 184194 161557 175204 TRUE FALSE 189868.9253 191464.3288 190689.004 190674.7921 184499.6561 204342.0415 157443.545 180390.3295 143217.7267 163337.277 1.162434741 1.172202281 1.16745551 1.1673685 1.129562458 1.251043517 0.963916798 1.104403923 0.876822054 1 17.31749456 1.914976698 1.386124871 0.969140957 1.170757826 0.600104689 0.069339967 0.279352305 0.997941189 0.046949028 0.020722657 82.21985338 -1.914976698 0.201616869 LKEFLEDYDDDRDDPK ddPTM_BT-474_Pertuzumab_2h_R1 6 LKEFLEDYDDDRDDPK 16 2 P49756 P49756 RBM25 RNA-binding protein 25 0 ;;;;; 178.66 1.55E-09 1954114000 2889850 2382250 2080248 1835789 2316390 2353930 2539570 3031630 3517070 2907020 FALSE TRUE 2776911.467 2314310.562 2456195.088 1930534.29 2390898.788 2401528.077 2570650.017 2969025.781 3117826.958 2710124.946 1.024643337 0.853949766 0.906303265 0.712341434 0.882209801 0.886131867 0.948535609 1.095530959 1.150436611 1 21.36992794 1.915043828 2.507644087 1.094219792 0.870322004 0.566764261 0.079411408 0.194492792 2.220531225 0.043960182 0.022647622 82.23256322 -1.915043828 -0.223897789 VKEDPDGEHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKEDPDGEHAR 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 165.7 1.28E-05 14771400000 14026400 13806000 12447900 12689600 13078900 13434400 13636700 15206900 15666600 15215500 FALSE TRUE 13478232.78 13412266.4 14697512.43 13344511.78 13499594.7 13706052.77 13803590.01 14892872.2 13888193.25 14184940.63 0.950179005 0.945528553 1.036134927 0.940752036 0.951684963 0.966239699 0.973115811 1.049907263 0.979080111 1 23.75785678 1.915087242 9.096418563 1.014497585 0.966041301 0.300995616 0.030248928 0.44397865 44.71637132 0.012559352 0.007941792 82.24078405 -1.915087242 -0.048456284 DVEDMELS(ph)DVEDDGSK ddPTM_BT-474_Pertuzumab_2h_R1 7 DVEDMELSDVEDDGSK 16 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK 380.5 4.75E-105 3220530000 4654220 3953580 3884160 3878950 4276610 3917610 4723550 5628410 6340420 5773130 TRUE FALSE 4472327.937 3840827.769 4586114.115 4079143.074 4414171.045 3996826.758 4781358.218 5512181.367 5620682.103 5382110.763 0.830961705 0.713628526 0.852103258 0.757907679 0.820156113 0.742613249 0.888379751 1.02416721 1.044326724 1 22.35974065 1.915110761 2.833961432 1.026576303 0.786410735 0.865207589 0.041683282 0.081097955 1.169684554 0.020232284 0.010764273 82.24523784 -1.915110761 -0.240165568 GGSSVEAPCPSDVT(ph)PEDDRSFQTVWATVFEHHVER ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSSVEAPCPSDVTPEDDRSFQTVWATVFEHHVER 35 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 GGS(0.001)S(0.001)VEAPCPS(0.074)DVT(0.883)PEDDRS(0.021)FQT(0.021)VWATVFEHHVER 64.273 0.010519 85144000 22255 24315 15515 19140 21863 23689 20023 4545 18920 19557 TRUE FALSE 21385.25 23621.56001 18318.90563 20127.81769 22566.24325 24168.00781 20268.04746 4451.144162 16772.28092 18232.38697 1.172926509 1.295582419 1.004745328 1.103959549 1.237700982 1.325553689 1.111650795 0.244133923 0.919916901 1 14.15421583 1.915187447 9.437336367 0.645408032 1.187455091 0.49506807 0.208806113 0.288961439 30.49718122 0.08377544 0.05308795 82.25976178 -1.915187447 0.542047059 ARSPT(ph)DDKVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSPTDDKVK 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.432)PT(0.568)DDKVK 114.7 0.0021226 4293700000 2028100 1672000 1378600 1152000 1471900 1373100 1659700 1918900 2231300 1819200 TRUE FALSE 1948839.61 1624316.197 1627743.687 1211454.858 1519245 1400865.023 1680011.905 1879274.044 1978012.178 1695983.964 1.149090824 0.957742663 0.959763607 0.714307968 0.89578972 0.825989545 0.990582424 1.108073003 1.166291793 1 20.6936911 1.91521076 3.688751064 1.099955017 0.910305603 0.327830503 0.110730811 0.269079237 6.430118771 0.056000561 0.031589609 82.26417757 -1.91521076 -0.189649414 KQS(ph)FDDNDSEELEDKDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KQS(0.95)FDDNDS(0.05)EELEDKDSK;KQS(0.749)FDDNDS(0.251)EELEDKDSK 91.166 0.0020246 769304000 305090 277420 213911 202703 241320 225899 262880 340930 339550 304840 TRUE FALSE 293166.7455 269508.2532 252569.4761 213164.5261 249082.277 230466.8326 266097.2041 333889.6764 301005.7075 284192.9153 1.031576544 0.948328543 0.888725449 0.750069811 0.876454913 0.810952069 0.936325959 1.17486981 1.059159787 1 18.11651106 1.91527568 5.78533581 1.090990975 0.8803694 0.530581885 0.081136789 0.168102743 8.91067657 0.037407711 0.022681548 82.27647566 -1.91527568 -0.210621575 LAS(ph)PMKPVPGT(ph)PPSSK ddPTM_BT-474_Pertuzumab_2h_R1 5 LASPMKPVPGTPPSSK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 LAS(1)PMKPVPGT(0.835)PPS(0.077)S(0.088)K;LAS(1)PMKPVPGT(0.995)PPS(0.003)S(0.002)K;LAS(1)PMKPVPGT(0.991)PPS(0.004)S(0.005)K;LAS(1)PMKPVPGT(0.999)PPS(0.001)SK;LAS(1)PMKPVPGT(0.978)PPS(0.019)S(0.003)K 129.85 2.71E-05 1593170000 3009160 2457030 2288150 2020880 2228210 2222370 2579130 3017230 3051090 3345110 TRUE FALSE 2891558.7 2386957.91 2701669.605 2125177.859 2299882.398 2267307.844 2610694.164 2954923.146 2704743.054 3118542.72 0.927214715 0.765408117 0.866324385 0.681465046 0.737486257 0.727040816 0.837151964 0.947533323 0.867309926 1 21.57244059 1.915314101 3.853693061 0.929453322 0.780086522 0.468732303 0.072887165 0.212370965 5.514399247 0.035052213 0.019940619 82.28375483 -1.915314101 -0.1493668 GPSQEEEDNHS(ph)DEEDRAS(ph)EPKS(ph)QDQDSEVNELSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSQEEEDNHSDEEDRASEPKSQDQDSEVNELSR 34 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 3 GPS(0.088)QEEEDNHS(0.913)DEEDRAS(0.997)EPKS(0.984)QDQDS(0.013)EVNELS(0.005)R;GPSQEEEDNHS(1)DEEDRAS(1)EPKS(0.996)QDQDS(0.004)EVNELSR 152.96 6.67E-11 515230000 125853 115223 106386 111456 114924 116831 131663 149583 178729 154181 TRUE FALSE 120934.5256 111936.9529 125612.3167 117208.2575 118620.6348 119193.4029 133274.3312 146494.0588 158440.4332 143738.1835 0.841352817 0.778755861 0.873896648 0.815428821 0.825254862 0.829239663 0.927201999 1.019172882 1.102284927 1 17.13308383 1.915317893 1.95670491 1.05308211 0.825295747 0.894644099 0.032847793 0.089202566 0.633241486 0.019225633 0.009217616 82.28447325 -1.915317893 -0.227786363 IQPGSQQADFLDALIVSMDVIQHETIGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQPGSQQADFLDALIVSMDVIQHETIGK 28 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 226.9 1.24E-34 458780000 92054 106590 79450 84769 93423 100250 92246 88868 99105 98694 FALSE TRUE 88456.42791 103550.1576 93808.38236 89143.93825 96428.03564 102277.1237 93374.93414 87032.84474 87855.01588 92009.36747 0.961385023 1.125430599 1.019552519 0.968857201 1.048024112 1.111594683 1.014841605 0.945912869 0.954848602 1 16.48949313 1.915356723 5.309853475 0.963788012 1.041144948 0.284561585 0.050930786 0.268761312 12.38877816 0.022736918 0.013629437 82.29183052 -1.915356723 0.077356936 DASDDLDDLNFFNQK ddPTM_BT-474_Pertuzumab_2h_R1 4 DASDDLDDLNFFNQK 15 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;; 318.84 4.24E-56 790020000 1385822 1171772 1173655 1228736 1299297 1204012 1320913 1543816 1586051 1555229 FALSE TRUE 1331662.544 1138354.21 1385760.566 1292151.212 1341090.068 1228357.948 1337078.728 1511935.66 1406009.14 1449891.955 0.918456399 0.785130372 0.95576816 0.891205174 0.924958625 0.847206541 0.922191977 1.042791951 0.969733735 1 20.46751396 1.915441729 5.173988854 1.005285713 0.887226337 0.555178783 0.046805542 0.155412943 6.862370926 0.020207556 0.012069237 82.30793946 -1.915441729 -0.118059377 KQDEDKDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQDEDKDKR 9 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 76.228 0.015782 209360000 699100 516670 400010 369440 461920 435580 512030 575250 615920 622670 FALSE TRUE 671778.3991 501935.0775 472300.7052 388506.8427 476778.0763 444387.726 518296.3763 563370.8865 546003.3437 580496.0063 1.157248959 0.864665858 0.81361577 0.669267038 0.821328779 0.765531065 0.892850891 0.97049916 0.940580707 1 19.14692662 1.915521134 3.813217831 0.964634261 0.837669336 0.169496657 0.118111506 0.423100825 10.77560495 0.059264171 0.033652434 82.32298963 -1.915521134 -0.126964925 TPES(ph)FLGPSASSLVNLDSLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPESFLGPSASSLVNLDSLVK 21 0 Q9H201 Q9H201 EPN3 Epsin-3 1 T(0.366)PES(0.418)FLGPS(0.066)AS(0.075)S(0.075)LVNLDSLVK 68.567 0.01302 16132000 16264 14773 16885 16997 12658 12557 17099 26079 22976 21541 TRUE FALSE 15628.3849 14351.6885 19936.4951 17874.21721 13065.15607 12810.91114 17308.26268 25540.45954 20367.8608 20082.00888 0.778228164 0.714654026 0.992754023 0.890061214 0.650590095 0.637929762 0.861879047 1.271807999 1.014234229 1 14.29361597 1.915545856 6.452882189 1.115630511 0.780997716 0.577900409 0.121195735 0.167877135 10.57975488 0.055148025 0.033877125 82.32767593 -1.915545856 -0.334632795 FSS(ph)PIVK ddPTM_BT-474_Pertuzumab_2h_R1 4 FSSPIVK 7 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 FS(0.001)S(0.999)PIVK;FS(0.009)S(0.991)PIVK;FSS(1)PIVK;FS(0.003)S(0.997)PIVK 165.26 0.0012242 1506080000 5061700 4726500 4595920 4327770 4305880 4888200 4831700 5555400 5309300 5933000 TRUE FALSE 4863883.168 4591704.848 5426504.98 4551126.728 4444382.541 4987042.753 4890831.79 5440679.049 4706610.522 5531152.625 0.87936159 0.830153344 0.981080319 0.822817058 0.803518334 0.901628122 0.884233743 0.983642907 0.850927617 1 22.39914872 1.91559363 6.607939417 0.941631163 0.869829198 0.244359486 0.05921776 0.363960149 23.78633863 0.025119117 0.015470447 82.33673277 -1.91559363 -0.071801966 AQVTELEDELTAAEDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQVTELEDELTAAEDAK 17 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 ; 346.63 3.50E-87 61997000 70403 71005 55749 64082 62618 66869 68758 78496 85125 79102 FALSE TRUE 67651.57293 68980.00692 65824.08443 67389.2797 64632.16484 68221.137 69599.48097 76875.03017 75461.96687 73744.35108 0.917379731 0.935393775 0.892598327 0.91382294 0.876435468 0.925103225 0.943794066 1.042453138 1.02329149 1 16.17024492 1.915649517 3.094624555 1.025294371 0.909643393 0.876573264 0.018683598 0.079041468 1.350241393 0.00968212 0.0052635 82.34732894 -1.915649517 -0.115650978 KQS(ph)FDDNDS(ph)EELEDKDSK ddPTM_BT-474_Pertuzumab_2h_R1 3 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 2 KQS(1)FDDNDS(1)EELEDKDSK;KQS(1)FDDNDS(1)EELEDKDSK;KQS(1)FDDNDS(1)EELEDKDSK 188.22 2.09E-14 1863290000 1439320 1017860 931020 657660 1287610 1072600 1364340 2128080 2343870 1782370 TRUE FALSE 1383069.783 988831.6294 1099276.024 691601.9114 1329027.145 1094288.707 1381037.201 2084134.404 2077803.704 1661648.492 0.83234799 0.595090739 0.661557501 0.416214328 0.799824482 0.658556074 0.831124758 1.254257091 1.2504472 1 20.66418379 1.915856971 3.17241029 1.190317106 0.65468857 0.760998173 0.126614157 0.110646155 1.983000631 0.06310597 0.034506671 82.38667413 -1.915856971 -0.535628536 HLDHVAALFPGDVDR ddPTM_BT-474_Pertuzumab_2h_R1 8 HLDHVAALFPGDVDR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;;;;; 130.24 3.53E-05 4306391000 2863640 3095820 2625640 3034200 2845930 2959250 2842200 253361.2 2979030 2543610 FALSE TRUE 2751725.783 3007530.245 3100151.555 3190795.426 2937471.923 3019088.063 2876983.694 248129.2027 2640863.004 2371329.029 1.160415003 1.268288883 1.307347701 1.345572625 1.238744977 1.273162866 1.213236821 0.104637189 1.113663676 1 21.17726442 1.91591076 12.14025793 0.643942491 1.267778493 0.450604581 0.256570683 0.661070458 94.00952742 0.099901485 0.063978104 82.39687869 -1.91591076 0.623836002 HLLMS(ph)ISK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLLMSISK 8 0 Q8TD26 Q8TD26 CHD6 Chromodomain-helicase-DNA-binding protein 6 1 HLLMS(0.5)IS(0.5)K 60.788 0.09449 26870000 36004 50207 48336 67821 52507 53790 46056 27574 34686 39902 TRUE FALSE 34596.92388 48775.14552 57071.39043 71321.24994 54195.93534 54877.67065 46619.6471 27004.58726 30748.5907 37199.402 0.930039786 1.311180903 1.534201825 1.917268722 1.456903402 1.475229915 1.253236466 0.725941435 0.826588306 1 15.18299181 1.91595894 3.604967987 0.832014148 1.455604731 0.548817038 0.236684688 0.182302355 4.176930644 0.124219397 0.069794168 82.40602011 -1.91595894 0.623590583 NREELDK ddPTM_BT-474_Pertuzumab_2h_R1 6 NREELDK 7 1 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 137.84 0.0025933 14266980000 6238880 5271655 6090377 6109687 5534356 5245844 6763526 8400351 9030715 8676736 FALSE TRUE 5995057.672 5121312.561 7191043.604 6425008.678 5712373.587 5351918.56 6846300.054 8226880.816 8005586.093 8089052.942 0.741132209 0.63311646 0.888984614 0.794284414 0.706185709 0.661624865 0.846366083 1.017038815 0.989681505 1 22.94753937 1.916085665 3.481940793 1.000588403 0.740959754 0.754446117 0.067344962 0.123905518 2.656874717 0.034919037 0.019484105 82.43006925 -1.916085665 -0.259628649 DEALEDEDNKKDDGISFSNQTGPAWAGSER ddPTM_BT-474_Pertuzumab_2h_R1 1 DEALEDEDNKKDDGISFSNQTGPAWAGSER 30 2 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 161.32 2.34E-12 139860000 150670 99281 121880 107720 121180 107410 138370 207450 198960 175890 FALSE TRUE 144781.6498 96449.60309 143906.4272 113279.4421 125077.8648 109581.9038 140063.4135 203166.085 176374.8949 163976.8136 0.882939768 0.588190494 0.87760229 0.690825975 0.762777749 0.668276821 0.854165966 1.238992761 1.075608746 1 17.32313231 1.916143844 4.958323089 1.120363248 0.743304108 0.716970135 0.100821413 0.100213528 4.133051137 0.041987725 0.024930223 82.44111249 -1.916143844 -0.37705914 LQPQEIS(ph)PPPTANLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQPQEISPPPTANLDR 16 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 1 LQPQEIS(1)PPPTANLDR;LQPQEIS(0.996)PPPT(0.004)ANLDR;LQPQEIS(1)PPPTANLDR;LQPQEIS(0.989)PPPT(0.011)ANLDR 210.57 9.79E-12 4887690000 676890 762160 721330 854390 833810 803410 645380 690596 615270 631405 TRUE FALSE 650436.3905 740423.943 851690.3769 898485.1703 860630.2559 819655.5007 653278.3535 676334.9513 545427.129 588639.377 1.104982806 1.25785663 1.44687972 1.526376259 1.462067081 1.392457815 1.109810827 1.148980136 0.926589607 1 19.16702453 1.916231995 1.5810834 0.998240118 1.375430816 0.612948427 0.123946746 0.278644176 1.299583634 0.092552515 0.041908068 82.45784768 -1.916231995 0.377190698 ENDKQETWMLMELQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENDKQETWMLMELQK 15 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 169.61 1.08E-06 615172000 628140 551040 492200 485440 509150 530220 580370 679800 756660 669420 FALSE TRUE 603591.5944 535324.8787 581151.4889 510493.6166 525527.2721 540941.4117 587472.7417 665761.8924 670767.129 624079.5871 0.967170865 0.857783029 0.931213744 0.817994415 0.842083739 0.866782735 0.941342665 1.066790048 1.074810237 1 19.2513705 1.916260324 3.151073935 1.052968419 0.877775914 0.733562149 0.044745162 0.12217334 2.162314517 0.022751879 0.012425972 82.46322659 -1.916260324 -0.175192504 DVAIKEPLVDVVDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVAIKEPLVDVVDPK 15 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 158.64 1.65E-06 966310000 1424100 1170810 1057170 892940 1107840 1232680 1275740 1469480 1726110 1577330 FALSE TRUE 1368444.598 1137419.645 1248224.136 939024.7404 1143474.68 1257605.634 1291352.888 1439134.724 1530169.229 1470496.034 0.930600672 0.773493854 0.848845632 0.63857686 0.777611536 0.855225451 0.878175022 0.978672972 1.040580317 1 20.48787146 1.916417757 1.469050993 1.022248121 0.790946809 0.628027511 0.070487352 0.257261592 1.034398891 0.050855936 0.022681684 82.49312522 -1.916417757 -0.231301312 DPEEIEKEEQAAAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DPEEIEKEEQAAAEK 15 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 214.22 2.28E-12 2719200000 1524580 1271110 1408290 1367110 1513190 1476760 1949330 2356600 2787250 2727250 FALSE TRUE 1464997.728 1234859.187 1662799.33 1437666.711 1561863.131 1506621.099 1973186.484 2307935.386 2470853.065 2542530.928 0.57619662 0.485681088 0.653993748 0.565447089 0.614294644 0.592567462 0.776071772 0.907731489 0.97180846 1 21.27783389 1.916455942 1.369264581 0.993736929 0.571880243 0.944736328 0.041465179 0.084840311 0.295566231 0.029641373 0.013077158 82.50037876 -1.916455942 -0.421856686 AIFTGHSAVVEDVAWHLLHESLFGSVADDQK ddPTM_BT-474_Pertuzumab_2h_R1 4 AIFTGHSAVVEDVAWHLLHESLFGSVADDQK 31 0 Q16576;E9PC52;Q16576-2;Q5JP01;Q5JP02 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;; 296.74 1.28E-81 1528140000 695738 768224 616524 712923 836700 777330 661810 140602 626580 474532 FALSE TRUE 668547.7898 746315.0037 727943.6013 749717.0415 863613.2154 793048.1452 669909.4287 137698.5196 555453.2652 442391.525 1.511212923 1.687001133 1.645473659 1.694691239 1.952146835 1.792638648 1.514290828 0.311259398 1.255569408 1 18.75496422 1.91647355 6.739786935 0.801628062 1.714379047 0.711297077 0.244277235 0.11780591 8.008459109 0.101367191 0.062570305 82.50372358 -1.91647355 0.912750985 QEPES(ph)EEEEEEKQEK ddPTM_BT-474_Pertuzumab_2h_R1 6 QEPESEEEEEEKQEK 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK 311.65 2.15E-56 10482180000 4676200 3340620 3393650 2897920 3586860 3415140 4161690 5316580 6123220 4943800 TRUE FALSE 4493448.934 3245348.788 4006958.046 3047481.998 3702234.609 3484196.471 4212622.007 5206790.765 5428137.736 4608952.023 0.974939403 0.704140285 0.869385931 0.661209313 0.803270373 0.755962842 0.914008648 1.129712512 1.177737956 1 22.13600732 1.916652608 3.02999068 1.115061558 0.789143032 0.689618174 0.091904689 0.129757033 2.130371872 0.044553599 0.024121836 82.53774673 -1.916652608 -0.325918526 EAHAQSIGMNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAHAQSIGMNR 11 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 136.53 9.73E-05 214380000 230920 259220 196980 229240 228280 250720 223440 199210 223200 231420 FALSE TRUE 221895.3911 251827.2994 232578.6678 241071.1039 235622.8335 255789.7302 226174.5256 195096.2439 197863.2717 215745.7173 1.028504268 1.167241244 1.078022177 1.11738535 1.092132147 1.185607452 1.048338426 0.904287911 0.917113323 1 17.7189724 1.916686387 4.322510499 0.934756048 1.11244422 0.717570449 0.047812712 0.105052834 3.396697749 0.020873542 0.012130867 82.54416661 -1.916686387 0.177688172 LGGSLADSYLDEGFLLDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGGSLADSYLDEGFLLDKK 19 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 223.5 3.51E-19 1156570000 1133510 979580 880900 768860 896790 1071760 1043870 1192430 1395760 1315700 FALSE TRUE 1089211.176 951643.3375 1040098.226 808540.9567 925636.0648 1093431.722 1056645.193 1167805.904 1237319.176 1226586.467 0.888001951 0.775846924 0.847961602 0.659179747 0.754643957 0.891442838 0.86145186 0.952077929 1.008750063 1 20.22621751 1.916730843 1.181767442 1.00625738 0.786492136 0.654438737 0.061788096 0.293092 0.755049633 0.04947554 0.021671107 82.55261656 -1.916730843 -0.219765244 FNIDEVLQEWEAEHGKEETNGPSNQKPVKS(ph)PDNSIK ddPTM_BT-474_Pertuzumab_2h_R1 1 FNIDEVLQEWEAEHGKEETNGPSNQKPVKSPDNSIK 36 3 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 FNIDEVLQEWEAEHGKEET(0.013)NGPS(0.195)NQKPVKS(0.789)PDNS(0.003)IK 85.697 0.00040178 693460000 971830 621280 577370 421820 672590 570360 722180 901800 1073400 761430 TRUE FALSE 933849.8092 603561.7027 681713.6025 443590.1808 694224.4682 581893.07 731018.2549 883177.5149 951552.1321 709857.6679 1.315545146 0.850257354 0.960352523 0.624900175 0.977976994 0.819732034 1.02980962 1.244161407 1.340482994 1 19.43717026 1.916791058 3.721314134 1.215868211 0.911931961 0.302619213 0.181238909 0.256322495 6.252932805 0.085585377 0.048418285 82.56406329 -1.916791058 -0.303936251 NEGNLENEGKPEDEVEPDDEGKS(ph)DEEEKPDVEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 NEGNLENEGKPEDEVEPDDEGKSDEEEKPDVEGK 34 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 NEGNLENEGKPEDEVEPDDEGKS(1)DEEEKPDVEGK;NEGNLENEGKPEDEVEPDDEGKS(1)DEEEKPDVEGK;NEGNLENEGKPEDEVEPDDEGKS(1)DEEEKPDVEGK 365.23 2.30E-148 1224750000 1542020 737171 816944 493984 1005969 587451 965540 1608200 1567950 927074 TRUE FALSE 1481756.154 716147.6048 964583.9536 519478.5734 1038326.906 599329.6617 977356.5673 1574990.108 1389962.889 864282.4522 1.714435078 0.828603662 1.116051762 0.601051858 1.201374509 0.693441895 1.130830048 1.822309482 1.608227595 1 19.72114334 1.916802754 6.811474558 1.551934788 1.001901954 0.240062192 0.350396041 0.278101608 19.27849204 0.142618016 0.088133298 82.5662868 -1.916802754 -0.550032833 IMAT(ph)PEQVGK ddPTM_BT-474_Pertuzumab_2h_R1 4 IMATPEQVGK 10 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 IMAT(1)PEQVGK;IMAT(1)PEQVGK;IMAT(1)PEQVGK;IMAT(1)PEQVGK 174.9 3.31E-05 1243000000 2357200 2133720 1941060 2134820 2099520 2183620 2295210 2498330 2824300 2633630 TRUE FALSE 2265078.018 2072868.395 2291852.721 2244998.316 2167052.968 2227774.293 2323299.467 2446738.612 2503697.304 2455251.894 0.922544047 0.844258953 0.93344912 0.914365781 0.882619406 0.907350605 0.946257071 0.996532624 1.01973134 1 21.22743961 1.916831563 1.860874695 1.01075495 0.898579306 0.800186246 0.023489521 0.139276459 0.896615926 0.014545638 0.006880668 82.57176411 -1.916831563 -0.112175645 PAAPPRPLDRES(ph)PGVENK ddPTM_BT-474_Pertuzumab_2h_R1 3 PAAPPRPLDRESPGVENK 18 2 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 PAAPPRPLDRES(1)PGVENK;PAAPPRPLDRES(1)PGVENK;PAAPPRPLDRES(1)PGVENK 192.27 9.57E-15 913080000 693500 503134 560349 493645 560593 522147 637240 756140 868790 750160 TRUE FALSE 666397.2533 488785.1109 661616.5292 519122.0776 578624.983 532705.1701 645038.7337 740525.4448 770168.6015 699350.995 0.952879538 0.698912441 0.946043595 0.742291183 0.827374218 0.761713609 0.922339052 1.058875229 1.101261894 1 19.41565718 1.916952886 3.047743527 1.059231717 0.81863372 0.625432884 0.079997967 0.148817016 2.471648663 0.037763355 0.020478556 82.5948342 -1.916952886 -0.240597998 QHEAPSNRPLNELLTPQGPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 QHEAPSNRPLNELLT(0.037)PQGPS(0.963)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR 215.37 1.82E-32 4065590000 937938 1114846 975767 1213375 1027089 1190679 959181 396165 785705 799369 TRUE FALSE 901282.346 1083051.684 1152109.803 1275997.429 1060126.25 1214755.345 970919.744 387984.0543 696515.0623 745227.0256 1.209406416 1.453317776 1.545984999 1.712226456 1.422554757 1.630047359 1.302850958 0.520625314 0.934634733 1 19.50732047 1.917165409 5.370909931 0.786100752 1.500327188 0.754592295 0.172308137 0.09701271 4.624178245 0.075602428 0.045424461 82.63526207 -1.917165409 0.714226437 ETQS(ph)PEQVK ddPTM_BT-474_Pertuzumab_2h_R1 9 ETQSPEQVK 9 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 ETQS(1)PEQVK;ETQS(1)PEQVK;ET(0.001)QS(0.999)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ET(0.004)QS(0.996)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK 243.77 1.71E-10 27920821000 24779310 23387911 22258047 23842481 23690389 24973910 27166640 29627140 33822470 33054390 TRUE FALSE 23810907.17 22720910.68 26280571.22 25072994.3 24452411.88 25478899.57 27499113.47 29015329.21 29983085 30815586.72 0.772690372 0.737318776 0.852833712 0.813646501 0.793507912 0.826818577 0.892376761 0.941579645 0.972984395 1 24.87715692 1.917243133 0.908424519 1.00091876 0.788032291 0.893669367 0.027372284 0.175126788 0.26678412 0.024323943 0.011241154 82.65005232 -1.917243133 -0.212886469 IDNDGDGFVTTEELK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDNDGDGFVTTEELK 15 0 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ; 290.26 1.59E-43 302840000 569470 579510 518910 546480 530290 526320 597910 699350 752620 708910 FALSE TRUE 547214.4828 562982.9422 612688.5801 574683.8983 547347.2594 536962.551 605227.4014 684908.1781 667185.7328 660894.8943 0.827990181 0.851849435 0.927059031 0.86955415 0.828191085 0.812477984 0.915769522 1.036334497 1.009518667 1 19.33406132 1.917285201 3.799474703 1.016034201 0.855967104 0.843697922 0.031177522 0.092613313 2.35399237 0.016340125 0.009284313 82.65805864 -1.917285201 -0.160067097 LFEES(ph)DDKEDEDADGKEVEDADEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFEESDDKEDEDADGKEVEDADEK 24 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEES(1)DDKEDEDADGKEVEDADEK 162.07 9.65E-12 205730000 483060 258560 291300 201850 295710 256350 375680 569400 624270 465240 TRUE FALSE 464181.4811 251186.122 343944.3899 212267.5027 305221.7807 261533.5726 380277.6842 557641.691 553405.4868 433728.8804 1.070211144 0.57913165 0.792993977 0.489401357 0.703715603 0.602988605 0.876763576 1.28569186 1.275924919 1 18.72643398 1.917340966 3.808409523 1.208006244 0.69600518 0.628088845 0.164645386 0.134023568 3.422403251 0.075664291 0.043012618 82.66867284 -1.917340966 -0.512001064 DVPGGGPSSSAPAGAEADGPKAS(ph)PEARPQIPTKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVPGGGPSSSAPAGAEADGPKASPEARPQIPTKPR 35 3 Q8N3F8;B0QY86 Q8N3F8 MICALL1 MICAL-like protein 1 1 DVPGGGPS(0.001)S(0.006)S(0.006)APAGAEADGPKAS(0.868)PEARPQIPT(0.118)KPR 54.841 0.035282 78934000 62394 50226 58085 51950 56391 63313 71083 82153 96979 95437 TRUE FALSE 59955.5735 48793.60366 68582.25159 54631.14573 58204.86773 64593.23224 71952.93502 80456.51184 85970.35049 88972.96698 0.673862809 0.548409313 0.770821227 0.614019601 0.654185981 0.725987167 0.808705582 0.904280419 0.966252485 1 16.44107944 1.917403673 1.025593931 0.998547355 0.645718255 0.868742751 0.052358463 0.163836559 0.316699624 0.04082825 0.018199293 82.68061008 -1.917403673 -0.3528291 AEMDMVAWGVDLASVEQHINSHR ddPTM_BT-474_Pertuzumab_2h_R1 9 AEMDMVAWGVDLASVEQHINSHR 23 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;;;;;; 139.83 1.16E-07 1698803000 1382800 1706438 1525465 1687680 1779668 1948835 1605595.4 213211.3 1672159 1317512 FALSE TRUE 1328758.647 1657772.059 1801150.459 1774781.367 1836912.637 1988241.779 1625245.157 208808.4121 1482342.521 1228275.739 1.081808103 1.349674187 1.466405631 1.444937249 1.495521388 1.618725923 1.323192428 0.170001251 1.206848327 1 20.22820304 1.917467794 9.858972828 0.709518177 1.419493258 0.488186933 0.281080503 0.338403292 38.78650455 0.112756599 0.071623705 82.69281838 -1.917467794 0.709975081 EEDEEPES(ph)PPEKK ddPTM_BT-474_Pertuzumab_2h_R1 11 EEDEEPESPPEKK 13 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK 185.02 2.54E-06 62733500000 24005420 17627300 22161970 18029320 19358060 17955330 24722550 31932170 36585840 31096470 TRUE FALSE 23067261.65 17124586.66 26167130.97 18959815.37 19980729.58 18318399.07 25025111.96 31272759.53 32432768.82 28990278.39 0.795689553 0.590701008 0.902617444 0.654005978 0.689221722 0.631880758 0.863224272 1.07873264 1.118746374 1 24.78906585 1.917567787 3.100620179 1.072795257 0.711016144 0.763315908 0.08823578 0.113138439 1.943714344 0.043318991 0.023596984 82.71185998 -1.917567787 -0.361779113 QDKPLS(ph)PAGSSQEAADTPDTR ddPTM_BT-474_Pertuzumab_2h_R1 4 QDKPLSPAGSSQEAADTPDTR 21 1 P13994 P13994 CCDC130 Coiled-coil domain-containing protein 130 1 QDKPLS(1)PAGSSQEAADTPDTR;QDKPLS(1)PAGSSQEAADTPDTR;QDKPLS(1)PAGSSQEAADTPDTR;QDKPLS(0.999)PAGS(0.001)SQEAADTPDTR 246.9 1.48E-30 3224820000 2425480 2210930 2013820 2036610 2219410 2342560 2533910 2776260 3296330 3104060 TRUE FALSE 2330689.56 2147876.441 2377762.071 2141719.686 2290799.338 2389928.168 2564920.749 2718929.261 2922144.438 2893819.251 0.805402604 0.742228956 0.821669173 0.740101402 0.791617976 0.825873339 0.88634449 0.939564301 1.009788167 1 21.46454338 1.917596772 1.089426062 1.008878307 0.77606066 0.927023683 0.025263282 0.110767846 0.24177853 0.018897734 0.008337268 82.71738034 -1.917596772 -0.232817648 EKDRQS(ph)PLHGNHITISHTQATGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDRQSPLHGNHITISHTQATGSR 24 2 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 EKDRQS(1)PLHGNHITISHTQATGSR 155.15 3.02E-08 524900000 225060 241310 173730 182440 198160 230540 211160 30933 263550 189140 TRUE FALSE 216264.4064 234428.0751 205126.8756 191855.7503 204533.9964 235201.6768 213744.2392 30294.22274 233632.9089 176329.3793 1.226479712 1.329489595 1.163316495 1.088053227 1.159954156 1.333876848 1.212187328 0.171804738 1.324980045 1 17.42791335 1.917667856 24.99999347 0.728176627 1.216277662 0.259947719 0.280852503 90.55861793 27496.7842 0.109797283 0.070862804 82.73092048 -1.917667856 0.488101035 ENFMTVDQDGSGTVEHHELR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENFMTVDQDGSGTVEHHELR 20 0 H7C2Z6;H7BXD5;P28676;C9JIZ3 H7C2Z6 GCA Grancalcin 0 207.56 3.78E-22 544250000 100570 112330 81087 109220 116960 106080 104520 25681 107670 106390 FALSE TRUE 96639.61321 109126.4584 95741.22467 114856.8573 120722.1246 108225.0103 105799.147 25150.67838 95447.75299 99184.11054 0.974345716 1.100241337 0.965287929 1.158016709 1.21715186 1.091152703 1.066694518 0.253575681 0.962329071 1 16.5978214 1.917995954 15.61578294 0.656693243 1.088212157 0.349356476 0.20579213 2.549658039 484.2107197 0.080763885 0.051990332 82.79344512 -1.917995954 0.431518914 KQGGLGPMNIPLVSDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQGGLGPMNIPLVSDPK 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 148.56 5.74E-07 1499720000 3265200 2848700 2520840 2444580 2629700 2821400 2954500 3327100 3642000 3547900 FALSE TRUE 3137592.374 2767457.865 2976411.864 2570745.067 2714286.689 2878450.641 2990658.055 3258394.222 3228575.429 3307597.573 0.948601607 0.836697272 0.89987122 0.777224257 0.820621804 0.870254188 0.904178332 0.985124142 0.9761089 1 21.65735229 1.918144803 2.068967207 0.989909615 0.853540346 0.634672792 0.043438721 0.201934566 1.596015855 0.026409293 0.012903576 82.82182628 -1.918144803 -0.136369269 ENHGQADHS(ph)PSMTATHFPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ENHGQADHSPSMTATHFPR 19 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 ENHGQADHS(0.988)PS(0.012)MTATHFPR;ENHGQADHS(0.815)PS(0.185)MTATHFPR;ENHGQADHS(0.995)PS(0.005)MTATHFPR 280.45 2.05E-39 2665270000 435320 437140 409460 459630 442830 555670 454508 207483 491940 436275 TRUE FALSE 418307.2131 424673.1952 483458.5304 483351.5594 457074.0291 566906.0281 460070.4049 203198.4035 436097.0336 406725.7057 1.028474983 1.044126765 1.188659885 1.188396879 1.123789381 1.393828864 1.131156449 0.499595675 1.072214093 1 18.63369665 1.918196289 12.04430714 0.804665175 1.165460379 0.383171251 0.170659494 0.791765792 114.9218505 0.069005765 0.04418241 82.83164546 -1.918196289 0.360795204 GKS(ph)EEELEASK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKSEEELEASK 11 1 Q7RTP6;J3QR21;A0A5F9ZHV5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 GKS(1)EEELEASK 149.97 2.07E-05 463480000 608330 488310 341390 330540 409360 408180 472590 630640 644570 553100 TRUE FALSE 584555.7911 474383.8769 403086.7672 347599.209 422527.4362 416433.6793 478373.6978 617617.0636 571401.1159 515638.0443 1.133655279 0.919993942 0.781724257 0.674114745 0.819426419 0.807608523 0.92773158 1.197772489 1.108143827 1 18.97599919 1.918401054 4.776731006 1.116283925 0.846861548 0.45245702 0.120251098 0.193314571 7.570786214 0.058214591 0.034412236 82.87070885 -1.918401054 -0.269422377 S(ph)PQTLAPVGEDAMK ddPTM_BT-474_Pertuzumab_2h_R1 5 SPQTLAPVGEDAMK 14 0 Q92797 Q92797 SYMPK Symplekin 1 S(0.957)PQT(0.043)LAPVGEDAMK;S(1)PQTLAPVGEDAMK;S(1)PQTLAPVGEDAMK;S(0.895)PQT(0.105)LAPVGEDAMK;S(1)PQTLAPVGEDAMK 257.46 2.52E-24 2229610000 2701790 2404690 2347170 2480760 2506500 2369770 2661780 3086220 3308790 3075540 TRUE FALSE 2596201.06 2336110.596 2771355.832 2608792.321 2587123.849 2417688.373 2694355.66 3022488.479 2933190.031 2867230.936 0.905473301 0.814761924 0.966561778 0.909864737 0.902307455 0.843213688 0.939706539 1.054148949 1.023004458 1 21.45122668 1.918463827 4.347006232 1.027975104 0.891600553 0.692685989 0.040217103 0.122358453 4.030419925 0.018673691 0.010875124 82.88268787 -1.918463827 -0.136374551 TAS(ph)NPKVENEDEPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TASNPKVENEDEPVR 15 1 Q9UBF8-2 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 T(0.171)AS(0.829)NPKVENEDEPVR;T(0.046)AS(0.954)NPKVENEDEPVR 127.17 4.83E-05 920330000 639720 514240 432430 411430 483440 527590 528780 630560 711740 604050 TRUE FALSE 614719.0352 499574.3787 510579.7204 432663.9516 498990.2866 538258.2313 535251.3678 617538.7156 630946.2591 563137.1555 1.091597365 0.887127361 0.906670276 0.768310078 0.88609015 0.955820844 0.950481357 1.096604459 1.120413123 1 19.10312682 1.918558644 2.389723175 1.083181339 0.905418384 0.420020936 0.081092362 0.26339625 2.744144237 0.046586243 0.023749138 82.90078516 -1.918558644 -0.177762955 THNDIIHNENMR ddPTM_BT-474_Pertuzumab_2h_R1 4 THNDIIHNENMR 12 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 236.28 2.62E-16 7168100000 1619020 1890100 1527950 1914356 1611218 1891310 1612740 882311 1514447 1427953 FALSE TRUE 1555746.908 1836196.199 1804084.554 2013156.143 1663044.29 1929553.584 1632477.195 864090.9695 1342533.326 1331236.471 1.168648052 1.379316326 1.355194658 1.512245334 1.249247843 1.449444652 1.226286411 0.649089015 1.008485986 1 20.34433543 1.918560491 5.856200817 0.860991293 1.355104503 0.722188531 0.129132974 0.103477896 5.769491396 0.053777712 0.032691524 82.90113775 -1.918560491 0.49411321 HLS(ph)QDHTVPGRPAASELHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLSQDHTVPGRPAASELHSR 20 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 HLS(1)QDHTVPGRPAASELHSR;HLS(0.999)QDHT(0.001)VPGRPAASELHSR 158.67 1.34E-11 803040000 176027 199893 135662 186358 200476 192897 169794 38971 172461 139761 TRUE FALSE 169147.6702 194192.2474 160179.1412 195975.9587 206924.4926 196797.5095 171871.9898 38166.23523 152883.9503 130294.863 1.298191397 1.490406014 1.229358837 1.504095819 1.588124719 1.510401139 1.319100276 0.292922026 1.173368979 1 16.99142068 1.918884477 8.445408877 0.755440708 1.437655394 0.578167495 0.233770562 0.20546491 19.7736858 0.09408549 0.059222519 82.96300559 -1.918884477 0.682214686 VDSDKEDDITELK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDSDKEDDITELK 13 1 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3;H0Y8M2 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 110.98 0.00092601 417190000 271780 233600 209830 202560 239470 244030 282060 302560 380880 342540 FALSE TRUE 261158.5371 226937.9567 247750.9486 213014.1459 247172.77 248964.4538 285511.9347 296312.0303 337644.0992 319339.4607 0.817808537 0.710648024 0.775823157 0.667046113 0.774012612 0.779623205 0.894070323 0.927890432 1.057320315 1 18.28473131 1.919015401 1.214671724 1.023759859 0.742204393 0.862063447 0.044370876 0.147940852 0.403150423 0.032444035 0.014227897 82.98801955 -1.919015401 -0.281555466 THYDPPRK ddPTM_BT-474_Pertuzumab_2h_R1 10 THYDPPRK 8 1 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;H0YBD7;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;;;;;; 123.98 0.00085965 3755948600 2824075 2781185 2338963 2806935 2612222 2715844 2604121 1612966 2707501 2602586 FALSE TRUE 2713707.027 2701868.327 2761665.644 2951801.252 2696246.493 2770760.226 2635991.012 1579657.688 2400156.837 2426310.532 1.118450005 1.113570704 1.138216072 1.216580159 1.111253674 1.14196439 1.086419474 0.651053386 0.989220797 1 21.21033278 1.91902453 8.222235196 0.846437468 1.138716756 0.59568597 0.094889954 0.183920863 17.11403377 0.037991555 0.023869054 82.98976402 -1.91902453 0.292279287 ELGNDAYK ddPTM_BT-474_Pertuzumab_2h_R1 5 ELGNDAYK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 140.14 0.0015223 3049720000 2991580 2967920 2615630 2750180 2847620 2937310 3041100 3490570 3792060 3545090 FALSE TRUE 2874665.746 2883277.827 3088332.525 2892117.119 2939216.283 2996704.421 3078317.891 3418488.51 3361601.246 3304977.897 0.869798781 0.872404572 0.934448768 0.875079111 0.889330088 0.906724497 0.931418602 1.034345347 1.017132747 1 21.65620919 1.91908621 2.778205928 1.020469395 0.891691493 0.886188135 0.020089575 0.081230547 1.130125615 0.01078484 0.005728107 83.00155148 -1.91908621 -0.128777902 DTDFEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTDFEHR 7 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;; 192.11 0.00051611 3156230000 5459370 5880450 4727940 5713700 5905410 5949220 5588330 5502160 6107440 5907930 FALSE TRUE 5246011.785 5712745.324 5582383.93 6008584.742 6095362.876 6069517.305 5656721.654 5388538.473 5414149.016 5507780.639 0.952472898 1.037213662 1.013545073 1.090926661 1.106682215 1.101989658 1.027041929 0.978350233 0.983000118 1 22.39303967 1.919187205 4.551839471 0.986862561 1.053433354 0.294149607 0.043562936 0.292139231 10.52225461 0.021793103 0.012792549 83.0208556 -1.919187205 0.066570793 LHDAFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHDAFFK 7 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 94.262 0.01433 1767270000 3923500 3992300 3226600 3774400 4030300 3672400 3841800 2631600 4444400 4300400 FALSE TRUE 3770165.282 3878443.513 3809718.395 3969197.236 4159938.26 3746658.444 3888817.098 2577256.54 3939890.344 4009130.078 0.940394851 0.967402763 0.950260611 0.990039525 1.037616186 0.934531525 0.969990253 0.642846825 0.982729487 1 21.9348578 1.919278807 24.99972944 0.828235446 0.971279755 0.114075687 0.097598162 115.7013178 35832.03073 0.03822546 0.024670228 83.03836841 -1.919278807 0.143044309 KGNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_BT-474_Pertuzumab_2h_R1 5 KGNAEGSSDEEGKLVIDEPAK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 KGNAEGS(1)S(1)DEEGKLVIDEPAK;KGNAEGS(1)S(1)DEEGKLVIDEPAK;KGNAEGS(1)S(1)DEEGKLVIDEPAK;KGNAEGS(1)S(1)DEEGKLVIDEPAK;KGNAEGS(1)S(1)DEEGKLVIDEPAK 125.82 1.21E-05 1303040000 1901090 1179840 1334930 1031700 1360040 1117980 1663650 2241150 2614280 2018610 TRUE FALSE 1826793.301 1146192.118 1576181.546 1084946.161 1403786.922 1140586.322 1684010.246 2194869.469 2317517.894 1881887.747 0.970723841 0.609065084 0.837553435 0.576520126 0.745946151 0.606086268 0.894851592 1.166312642 1.231485724 1 20.84374914 1.919343702 3.364880776 1.145742782 0.718994476 0.680883906 0.124544067 0.126232232 2.547883199 0.057981442 0.032205954 83.05077744 -1.919343702 -0.426748307 SLAKPETDKEQDSEMEK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLAKPETDKEQDSEMEK 17 2 P49321;P49321-3;P49321-4;E9PPR5;E9PNB5 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;;; 202.97 5.68E-12 4024210000 2893320 2371130 2146120 1722830 2422970 2258390 2687330 3424770 3918910 3224590 FALSE TRUE 2780245.856 2303507.694 2533971.624 1811745.463 2500907.031 2304056.193 2720218.348 3354047.303 3474051.766 3006185.647 0.924841704 0.766255968 0.842919208 0.602672514 0.831920355 0.766438425 0.904873706 1.115715294 1.155634473 1 21.51950268 1.919422675 2.8761901 1.102536316 0.784516597 0.709673365 0.085832893 0.133329781 1.983786076 0.044058636 0.023610945 83.06588085 -1.919422675 -0.318019719 KRNEDEDSPNK ddPTM_BT-474_Pertuzumab_2h_R1 3 KRNEDEDSPNK 11 2 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 ;; 190.15 1.35E-06 5995400000 6542000 5212400 5189100 4458300 5302000 5357800 5700600 6791800 7186300 6524900 FALSE TRUE 6286331.407 5063747.455 6126885.801 4688393.397 5472543.645 5466138.387 5770365.648 6651546.957 6370541.351 6082962.711 1.033432507 0.832447558 1.007220674 0.770741762 0.899651026 0.898598043 0.948611051 1.093471598 1.047276081 1 22.53634273 1.919476247 4.261104606 1.053483028 0.902739496 0.413182859 0.074196893 0.194557086 6.20052098 0.032788197 0.019044455 83.07612805 -1.919476247 -0.150743532 LKEELIDAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKEELIDAIR 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 151.1 1.86E-05 719200000 2333300 2434700 1969990 2289000 2123500 2257200 2333400 2598000 2693400 2730000 FALSE TRUE 2242112.056 2365264.74 2326011.015 2407135.564 2191804.306 2302842.131 2361956.847 2544350.392 2387656.524 2545094.668 0.880954286 0.929342538 0.913919252 0.945794117 0.861187732 0.904815903 0.928042826 0.999707564 0.938140555 1 21.27928789 1.919519327 4.68886213 0.977392381 0.907721955 0.590182387 0.027244635 0.156323386 5.958590904 0.012196565 0.007193923 83.08436924 -1.919519327 -0.069670427 HIPTALPVSGTLSS(ph)SNPDLLQSHHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIPTALPVSGTLSSSNPDLLQSHHR 25 0 A0A2R8Y661;A0A2R8YGD3;Q9Y4G8 A0A2R8Y661 RAPGEF2 Rap guanine nucleotide exchange factor 2 1 HIPTALPVSGTLS(0.022)S(0.521)S(0.454)NPDLLQS(0.002)HHR 205.59 6.96E-25 664180000 161440 213310 157600 211170 187540 194660 181050 28045 178630 173310 TRUE FALSE 155130.7463 207226.6077 186081.8258 222068.509 193572.3944 198596.1586 183265.7441 27465.86095 158352.6713 161571.5593 0.960136468 1.282568594 1.151699139 1.37442821 1.198059827 1.229152949 1.134269823 0.169991928 0.980077632 1 17.30181374 1.919692483 10.536598 0.630139016 1.206592536 0.442236242 0.238595492 0.428835597 54.70798538 0.093507511 0.05958289 83.11750202 -1.919692483 0.57645352 S(ph)PEDQLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPEDQLGK 8 0 Q9UK61-3;Q9UK61;Q9UK61-2 Q9UK61-3 FAM208A Protein FAM208A 1 S(1)PEDQLGK;S(1)PEDQLGK 141.1 0.0006703 915150000 932950 803640 682560 740790 719830 813730 823210 921480 1045620 935550 TRUE FALSE 896489.2826 780720.974 805913.7755 779022.2607 742983.9857 830184.1781 833284.6902 902451.116 926925.6012 872184.3652 1.02786672 0.895132962 0.924017682 0.893185308 0.851865747 0.951844829 0.955399711 1.03470224 1.062763377 1 19.7342736 1.919859973 2.097626209 1.038738661 0.917345359 0.528774904 0.045582562 0.231988968 1.882518499 0.027072091 0.013300638 83.14956339 -1.919859973 -0.121393302 EPGHFNPESR ddPTM_BT-474_Pertuzumab_2h_R1 1 EPGHFNPESR 10 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 67.153 0.072619 0 59632 80947 66795 101580 94281 73943 73565 67869 55366 76719 FALSE TRUE 57301.51551 78638.47082 78866.34235 106822.556 97313.63399 75438.17812 74465.31048 66467.48143 49081.08379 71522.7538 0.801164839 1.099488857 1.102674857 1.493546463 1.360596857 1.054743758 1.041141546 0.929319383 0.686230342 1 16.12611466 1.919890304 1.749014508 0.847130982 1.174862488 0.313828128 0.186952371 0.434805053 2.477806999 0.129775271 0.060474943 83.15537072 -1.919890304 0.327731506 VLGDHLLLDPTHELPPYTPPPMLS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 3 VLGDHLLLDPTHELPPYTPPPMLSPVR 27 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 VLGDHLLLDPTHELPPYTPPPMLS(1)PVR;VLGDHLLLDPTHELPPYTPPPMLS(1)PVR;VLGDHLLLDPTHELPPYT(0.001)PPPMLS(0.999)PVR 88.544 0.012349 553356000 323650 326417 278775 335305 337241 354553 310822 163393 306470 302988 TRUE FALSE 311001.4002 317107.9068 329155.8438 352610.1312 348088.663 361722.3046 314625.9326 160018.8775 271680.8104 282466.3529 1.101021049 1.122639576 1.165292221 1.248326137 1.232319034 1.28058546 1.113852781 0.566505978 0.961816541 1 18.1077195 1.920038233 7.67819008 0.803068629 1.192226995 0.621010843 0.12102671 0.161683263 13.87844198 0.049941958 0.031215937 83.18369976 -1.920038233 0.389158367 IES(ph)DEEEDFENVGK ddPTM_BT-474_Pertuzumab_2h_R1 3 IESDEEEDFENVGK 14 0 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK 366.02 5.86E-97 2186140000 1996900 1750430 1375530 1367830 1645480 1566040 1741510 2035130 2287350 1912260 TRUE FALSE 1918858.94 1700509.45 1624118.869 1438423.87 1698408.359 1597706.402 1762823.12 1993103.854 2027699.617 1782740.927 1.076353222 0.953873569 0.911023495 0.806860856 0.952694995 0.896207844 0.988827425 1.117999718 1.137405658 1 20.76566563 1.920128319 3.76524585 1.094707892 0.928399489 0.473425017 0.071319877 0.192517447 4.846500393 0.035219776 0.020020571 83.20095643 -1.920128319 -0.166308404 DWLSTLEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DWLSTLEPR 9 0 Q9UID3;Q9UID3-2;H0YEE1 Q9UID3 VPS51 Vacuolar protein sorting-associated protein 51 homolog 0 88.181 0.030146 22586000 53496 71445 51698 79391 70638 73710 58767 49099 47203 58740 FALSE TRUE 51405.31718 69407.45855 61040.97862 83488.37902 72910.13542 75200.4667 59486.20813 48085.08849 41844.71333 54761.48748 0.938712945 1.267450205 1.114669842 1.524582017 1.331412618 1.373236378 1.086278165 0.87808222 0.764126675 1 15.74087401 1.920158279 3.051407745 0.868385705 1.266942139 0.536895408 0.156257888 0.194735997 3.251762212 0.081710689 0.044440557 83.20669626 -1.920158279 0.398556434 KYQEDS(ph)DPERS(ph)DYEEQQLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KYQEDSDPERSDYEEQQLQK 20 2 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 2 KYQEDS(1)DPERS(1)DYEEQQLQK 219.93 4.76E-25 140030000 188410 131700 144340 154320 168350 141740 165690 192550 200110 197920 TRUE FALSE 181046.7289 127944.0449 170425.4488 162284.4737 173765.1306 144606.0799 167717.7638 188573.7752 177394.3517 184514.7021 0.981204895 0.693408403 0.923641568 0.879520558 0.941741382 0.78371034 0.908966938 1.021998643 0.96141039 1 17.49337625 1.92018525 4.98217766 0.992595338 0.864342245 0.344854282 0.078199129 0.234717654 10.0367898 0.033520328 0.019957608 83.21186387 -1.92018525 -0.128253093 LNSHMNALHLGSQANR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNSHMNALHLGSQANR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 211.06 4.66E-12 3060000000 825490 1010750 862700 1169720 961320 961930 993620 447990 1039030 1168390 FALSE TRUE 793228.9382 981924.3996 1018609.081 1230089.389 992241.7308 981380.8837 1005780.219 438738.8499 921083.6704 1089253.905 0.728231439 0.901465118 0.935143841 1.129295368 0.910937043 0.900966138 0.923366182 0.402788411 0.845609703 1 20.05490885 1.920231919 24.99942018 0.678100181 0.925807384 0.132853857 0.170128495 124.0924233 38889.53131 0.068011552 0.043894332 83.22080621 -1.920231919 0.247707203 DFYLATSPPDSFLDDHHLTRPHPER ddPTM_BT-474_Pertuzumab_2h_R1 2 DFYLATSPPDSFLDDHHLTRPHPER 25 1 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 0 ; 204.82 1.52E-25 496300000 155714 185014 155241 187081 194542 195458 175821 15903.1 183394 160617 FALSE TRUE 149628.5247 179737.5819 183296.502 196736.2728 200799.6201 199410.2947 177972.75 15574.69543 162575.882 149738.2675 0.999267103 1.200345008 1.224112614 1.313867698 1.341004029 1.33172567 1.188558896 0.104012793 1.085733692 1 17.19208344 1.920289667 12.68003815 0.633823927 1.242929462 0.413465859 0.265157175 0.902194732 142.1547229 0.104632284 0.067090553 83.23187278 -1.920289667 0.609105535 AKS(ph)VDEIAK ddPTM_BT-474_Pertuzumab_2h_R1 4 AKSVDEIAK 9 1 A6ND36;A6ND36-2 A6ND36 FAM83G Protein FAM83G 1 AKS(1)VDEIAK;AKS(1)VDEIAK;AKS(1)VDEIAK;AKS(1)VDEIAK 171.29 3.46E-05 1662780000 3821190 2978040 2180770 2094440 2895530 2540500 2881930 4453650 3831580 3018220 TRUE FALSE 3671853.67 2893109.215 2574883.65 2202534.299 2988667.352 2591870.651 2917199.921 4361680.571 3396635.102 2813793.271 1.304947918 1.028188263 0.9150934 0.782763369 1.062148873 0.921130446 1.03674991 1.550106973 1.207137403 1 21.42408491 1.920308555 9.843502399 1.309430323 0.991224216 0.265312314 0.179757497 0.504795341 59.97616771 0.073999922 0.047005954 83.23549284 -1.920308555 -0.318206108 SLHLS(ph)PQEQSASYQDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLHLSPQEQSASYQDRR 17 1 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 SLHLS(1)PQEQSASYQDRR;SLHLS(0.984)PQEQS(0.016)ASYQDRR 164.94 1.55E-09 891100000 188883 255508 176283 231936 220961 251344 213110 189633 202128 236863 TRUE FALSE 181501.2435 248221.162 208141.2595 243906.2448 228068.4112 256426.3479 215718.1039 185717.0123 179183.2768 220820.058 0.821941834 1.12408793 0.942583121 1.104547508 1.032824705 1.161245723 0.976895423 0.841033255 0.81144475 1 17.7525117 1.920331968 4.943298968 0.872359266 1.037323436 0.289064779 0.102020396 0.237121541 10.00700493 0.043612539 0.025939102 83.23998007 -1.920331968 0.164964169 DHFGRPPVDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHFGRPPVDIR 11 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 ; 142.97 2.25E-05 357290000 253210 262670 243520 282180 261400 273710 269080 113572 298840 270010 FALSE TRUE 243314.2733 255178.9088 287529.4811 296743.3436 269808.1684 279244.6037 272373.0815 111226.6985 264916.936 251721.9822 0.966599226 1.013733114 1.142250186 1.178853515 1.071849848 1.109337378 1.082039316 0.441863271 1.052418759 1 17.94147168 1.920433503 24.99762602 0.767545487 1.085248553 0.301750184 0.165293612 93.36664086 29332.39024 0.065085686 0.042006176 83.2594434 -1.920433503 0.317703066 S(ph)RSPAPPADK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSPAPPADK 10 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.5)RS(0.5)PAPPADK;S(0.5)RS(0.5)PAPPADK;S(0.5)RS(0.5)PAPPADK 73.022 0.028 1659340000 1672010 1546750 1752810 1785220 1674570 1576570 1867660 2208050 2312820 2327820 TRUE FALSE 1606666.001 1502638.204 2069581.758 1877355.418 1728434.065 1608449.326 1890516.982 2162452.996 2050278.37 2170154.678 0.740346307 0.692410647 0.953656336 0.865079083 0.796456622 0.741168057 0.871143887 0.996451091 0.944761399 1 21.04936644 1.920481782 3.86101999 0.976316571 0.803227327 0.573865469 0.069969402 0.187603887 4.964603551 0.035869552 0.02049121 83.26869955 -1.920481782 -0.173089244 LKDEVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDEVLK 7 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;E7EWF7 E7EX90 DCTN1 Dynactin subunit 1 0 101.64 0.020769 0 425000 393570 346610 360310 364620 460320 436650 469730 578130 552150 FALSE TRUE 408390.5301 382345.7689 409250.1373 378905.6423 376348.3334 469627.9858 441993.8533 460029.9114 512503.1061 514752.3887 0.793372773 0.742776095 0.795042716 0.736093024 0.731124987 0.912337652 0.858653331 0.89369165 0.99563036 1 18.97351909 1.920538744 0.728061828 1.002546975 0.756907923 0.816127329 0.041626582 0.275646497 0.27985387 0.037599491 0.019647188 83.27962182 -1.920538744 -0.245639052 HLEINPDHPIVETLR ddPTM_BT-474_Pertuzumab_2h_R1 12 HLEINPDHPIVETLR 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;;; 239.58 4.78E-18 99241719500 12233327 13025915 10960408.8 14506742.2 12718783 13788049.9 13162641 4677563.4 14508605.8 14343798 FALSE TRUE 11755235.06 12654428.66 12941198.48 15255436.9 13127894.21 14066853.72 13323729.34 4580970.081 12861649.69 13372279.79 0.879074866 0.94631797 0.967763066 1.140825435 0.981724464 1.051941325 0.996369322 0.342572108 0.961814283 1 23.67274211 1.92059605 24.99999692 0.688677343 0.999499499 0.210822496 0.18239822 105.9172678 33346.63153 0.071642577 0.046237271 83.29061141 -1.92059605 0.310822155 NINDHHSEADEEFYLSVGS(ph)PSVLLDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 NINDHHSEADEEFYLSVGSPSVLLDAK 27 0 Q03188;H0Y8J2;Q03188-2 Q03188 CENPC Centromere protein C 1 NINDHHSEADEEFYLS(0.001)VGS(0.977)PS(0.021)VLLDAK;NINDHHSEADEEFYLSVGS(0.997)PS(0.003)VLLDAK;NINDHHSEADEEFYLSVGS(0.975)PS(0.024)VLLDAK;NINDHHSEADEEFYLS(0.001)VGS(0.974)PS(0.025)VLLDAK 150.07 1.68E-07 221061000 298107 362240 276415 334321 304456 310387 300153 98756 288389 302714 TRUE FALSE 286456.6489 351909.2699 326369.3393 351575.3469 314249.1037 316663.2378 303826.3622 96716.65409 255652.2897 282210.9112 1.015044555 1.246972587 1.156473143 1.245789348 1.113525705 1.122080066 1.076593251 0.342710541 0.905890877 1 18.10641424 1.920818917 9.030499942 0.682904181 1.15260448 0.50451098 0.174648529 0.256573929 27.62435246 0.069194248 0.043747935 83.33336464 -1.920818917 0.469700299 PSGEAFVELESEDEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 PSGEAFVELESEDEVK 16 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;E7EN40;D6R9T0;D6RFM3;D6RDU3;D6RJ04;D6RIH9;D6RAM1;D6RDL0;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 184.21 4.33E-09 15527000 35078 26599 28734 31285 30036 31860 34166 44344 45670 42907 FALSE TRUE 33707.11298 25840.42256 33926.87298 32899.6226 31002.13522 32504.23103 34584.13373 43428.2809 40485.73306 40000.87067 0.842659482 0.645996503 0.848153363 0.822472662 0.77503651 0.812588088 0.864584524 1.085683391 1.012121296 1 15.28774378 1.920945322 3.388480332 1.037989373 0.789284186 0.773735842 0.05818269 0.106427185 2.18357086 0.028510679 0.015880401 83.35762296 -1.920945322 -0.248705187 EDLAAFVEELDKVESQER ddPTM_BT-474_Pertuzumab_2h_R1 6 EDLAAFVEELDKVESQER 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ;;;;; 291.18 3.24E-49 1563184000 874280 768749 776482.7 908118 911045 782303.3 916103 1210900 1154812 1096394 FALSE TRUE 840112.171 746825.0312 916810.3967 954986.0788 940349.5898 798122.0087 927314.5426 1185894.492 1023722.583 1022134.258 0.821919591 0.730652579 0.896956921 0.934305911 0.919986374 0.780838723 0.9072336 1.160214016 1.00155393 1 19.96315328 1.920982647 6.151894151 1.065439331 0.85097386 0.622041524 0.071768092 0.148707424 9.215100982 0.03255954 0.019922945 83.36478746 -1.920982647 -0.21446547 CSENKLPAELQELPGLSHQYWSAPSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 CSENKLPAELQELPGLSHQYWSAPSDK 27 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 128.27 3.55E-05 1066700000 876980 787260 707090 812370 878830 777710 1026300 1027800 1277400 1202900 FALSE TRUE 842706.652 764808.1156 834876.8921 854296.5131 907098.3651 793435.8291 1038860.166 1006575.571 1132394.907 1121426.512 0.751459541 0.681995751 0.744477577 0.761794468 0.808879009 0.707523695 0.926373824 0.89758496 1.009780753 1 20.09690365 1.921248676 0.986255898 1.008386798 0.733829808 0.839508817 0.045774012 0.19104117 0.341634158 0.036092717 0.016278034 83.41586856 -1.921248676 -0.274556991 (ac)AAGSDLLDEVFFNSEVDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGSDLLDEVFFNSEVDEK 19 0 O00268 O00268 TAF4 Transcription initiation factor TFIID subunit 4 0 54.524 3.35E-05 10373000 32204 29724 22805 24825 25047 30563 29071 35815 38655 37948 FALSE TRUE 30945.43208 28876.30062 26926.37079 26106.22123 25852.6595 31181.0048 29426.77959 35075.40773 34267.04645 35377.74816 0.874714579 0.816227774 0.761110364 0.737927725 0.73076046 0.881373361 0.831787808 0.991453938 0.968604511 1 15.1105546 1.921249825 1.460384015 0.997636331 0.7870243 0.747764494 0.048547891 0.200557859 0.796505921 0.035907155 0.016057973 83.41608919 -1.921249825 -0.21061203 S(ph)DEEDFVKVEDLPLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDEEDFVKVEDLPLK 15 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;H0YBA1 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 S(1)DEEDFVKVEDLPLK;S(1)DEEDFVKVEDLPLK;S(1)DEEDFVKVEDLPLK;S(1)DEEDFVKVEDLPLK 190.57 1.28E-07 333817000 740879 529670 707709 752928 677949 643990 1069600 1286080 1652840 1491140 TRUE FALSE 711924.6296 514564.3302 835607.7592 791786.7043 699755.8453 657011.919 1082690.085 1259521.999 1465216.532 1390143.76 0.512123027 0.370151883 0.601094494 0.569571815 0.503369411 0.472621565 0.77883318 0.906037228 1.054003604 1 20.40680265 1.9213057 1.747400403 1.013803816 0.502575403 0.9118632 0.067688871 0.096733364 0.550161666 0.044978025 0.020978803 83.42682197 -1.9213057 -0.511228414 ELLDT(ph)SFEDLSKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLDTSFEDLSKPK 14 1 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 ELLDT(0.567)S(0.433)FEDLSKPK 149.09 1.23E-05 424950000 249830 186170 211410 182220 245400 204760 231990 355720 270910 309340 TRUE FALSE 240066.3674 180860.6139 249616.4898 191624.396 253293.5139 208900.3875 234829.163 348374.2577 240157.4325 288388.1263 0.832441926 0.627143067 0.865557445 0.66446701 0.878307707 0.72437236 0.814281663 1.208004859 0.832757699 1 18.13765224 1.92131506 8.264004344 1.031817719 0.764614174 0.486683369 0.114001753 0.239139676 23.10027232 0.044370551 0.027892708 83.42861994 -1.92131506 -0.267203545 TTSSYQNLVWSDHSQELHS(ph)PTLK ddPTM_BT-474_Pertuzumab_2h_R1 4 TTSSYQNLVWSDHSQELHSPTLK 23 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 TTSSYQNLVWSDHSQELHS(0.987)PT(0.013)LK;TTSSYQNLVWSDHSQELHS(1)PTLK;TTSSYQNLVWSDHSQELHS(1)PTLK;TTSSYQNLVWSDHSQELHS(0.976)PT(0.024)LK 413.35 2.30E-157 8449400000 2181550 3087480 2748360 3453410 3091840 3082920 2610320 269650 2292920 1892480 TRUE FALSE 2096292.614 2999428.093 3245049.789 3631640.904 3191291.842 3145258.755 2642265.877 264081.6333 2032637.334 1764300.644 1.188171994 1.700066314 1.839283911 2.058402527 1.808814077 1.78272267 1.497627905 0.149680631 1.152092384 1 20.75066499 1.921325008 6.543033224 0.697945749 1.743316326 0.642756827 0.319985807 0.134811324 9.260460795 0.136699346 0.084211246 83.43053106 -1.921325008 1.045370577 RHES(ph)EEGDSHR ddPTM_BT-474_Pertuzumab_2h_R1 5 RHESEEGDSHR 11 1 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR 158.93 1.38E-05 551661600 265391.7 276140.1 223107.8 288221.5 283994.7 276515.1 254749.8 129721.6 251494.8 244563.8 TRUE FALSE 255019.899 268264.8547 263428.3425 303096.6462 293129.6474 282106.4248 257867.5043 127042.8036 222946.1647 227999.276 1.118511881 1.176603976 1.155391136 1.329375476 1.285660431 1.23731281 1.131001417 0.557207048 0.977837161 1 17.79866972 1.921390782 7.376308203 0.804464577 1.217812678 0.627152346 0.127445391 0.152355962 12.56652504 0.052997013 0.033020743 83.44316763 -1.921390782 0.413348101 DANQVHSTTR ddPTM_BT-474_Pertuzumab_2h_R1 6 DANQVHSTTR 10 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;;;; 125.72 0.00040159 492088600 312897.7 380473 330545.9 382415 344727.8 354200.6 349214.7 303867 367768.4 368328.3 FALSE TRUE 300669.312 369622.2826 390282.8971 402151.484 355816.2828 361362.7788 353488.494 297592.0403 326020.873 343381.0962 0.875614049 1.076420009 1.136588186 1.171152077 1.036213952 1.052366548 1.029434928 0.866652368 0.949443277 1 18.38945109 1.92139504 5.520894694 0.927365412 1.064818216 0.307274221 0.079291642 0.242740333 12.57863968 0.036177816 0.021854411 83.44398567 -1.92139504 0.137452804 KEEQEVQATLESEEVDLNAGLHGNWTLENAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEEQEVQATLESEEVDLNAGLHGNWTLENAK 31 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 138.61 2.36E-07 1022200000 31692 24187 22448 22876 22105 22418 26061 27990 33381 27485 FALSE TRUE 30453.4416 23497.21044 26504.85295 24056.6331 22816.0274 22871.30732 26379.94231 27411.99672 29591.72882 25623.41647 1.188500434 0.917020978 1.034399647 0.938853456 0.890436583 0.892593981 1.029524784 1.069802567 1.15487054 1 14.64517523 1.92147297 3.535394544 1.081015697 0.970644685 0.187481021 0.089807367 0.362831992 8.100140627 0.043511094 0.024458216 83.45896024 -1.92147297 -0.110371012 HAPSLHGS(ph)TELLPLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 HAPSLHGSTELLPLSR 16 0 Q9H5N1;B4DHR0;Q9H5N1-2;H3BU67;H3BNR2;H3BT64 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 1 HAPSLHGS(0.945)T(0.055)ELLPLSR;HAPSLHGS(0.83)T(0.17)ELLPLSR;HAPSLHGS(0.957)T(0.043)ELLPLSR 230.06 1.68E-15 1765400000 1324510 1285960 1193750 1289620 1276030 1264580 1297050 481605 1449190 1239160 TRUE FALSE 1272746.685 1249285.68 1409487.18 1356177.443 1317074.664 1290150.674 1312923.686 471659.6885 1284684.027 1155230.589 1.101725228 1.081416724 1.220091636 1.173945232 1.14009677 1.116790609 1.136503567 0.408281855 1.112058526 1 20.13974942 1.921488918 24.98509623 0.773871802 1.140460479 0.357890565 0.176683208 88.94409081 28304.49432 0.068553057 0.044243579 83.46202511 -1.921488918 0.366588676 GRAS(ph)PGGVSTSSSDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GRASPGGVSTSSSDGK 16 1 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGK;GRAS(0.999)PGGVSTSSSDGK 162.44 4.89E-09 1035240000 1302240 1283850 1213070 1324190 1246920 1240610 1345670 1520150 1564400 1607980 TRUE FALSE 1251347.021 1247235.855 1432298.734 1392531.605 1287028.314 1265695.984 1362138.712 1488758.371 1386815.87 1499070.082 0.834748846 0.832006368 0.955458154 0.928930289 0.858551131 0.844320755 0.908655791 0.993121262 0.925117436 1 20.5156364 1.921563648 4.845052108 0.96922483 0.878683533 0.514730753 0.041990399 0.200495155 8.224109383 0.020307698 0.012051261 83.47638773 -1.921563648 -0.090541297 YMTISGFQIEETIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 YMTISGFQIEETIDR 15 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 211.38 3.28E-09 208857000 101205 91745 70967 103968 81509 65870 88711 112665 103598 103091 FALSE TRUE 97249.79671 89128.52243 83792.31555 109333.8009 84130.81101 67201.93653 89796.67175 110338.4284 91837.98936 96108.55475 1.01187451 0.927373455 0.87185075 1.137607378 0.875372762 0.699229498 0.934325482 1.148060427 0.95556519 1 16.55237723 1.921583811 10.86292586 1.04879137 0.917370306 0.165960891 0.113966564 1.116413658 151.2231594 0.049272587 0.031436912 83.4802635 -1.921583811 -0.131421065 KPEEES(ph)PRKDDAK ddPTM_BT-474_Pertuzumab_2h_R1 7 KPEEESPRKDDAK 13 3 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK 163.66 0.000212 3999070000 2986240 2107359 1968215 1618571 2088300 1903517 2352609 2975420 3257980 2668040 TRUE FALSE 2869534.439 2047259.185 2323915.233 1702105.643 2155472.066 1942007.418 2381400.933 2913976.537 2888147.769 2487331.274 1.153659936 0.823074596 0.934300653 0.684309992 0.866580213 0.780759458 0.957412049 1.171527318 1.161143189 1 21.24616723 1.921715051 4.303220557 1.122837785 0.865120297 0.426588452 0.122131632 0.193306576 6.341310777 0.055772723 0.032497359 83.50549418 -1.921715051 -0.257717487 AEDGATPSPSNET(ph)PKK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPS(0.002)NET(0.998)PKK;AEDGATPSPS(0.006)NET(0.994)PKK 243.9 9.74E-20 3263120000 1187070 1001410 898990 730408 873353 862545 1023010 1414060 1342170 1240270 TRUE FALSE 1140677.992 972850.7673 1061457.491 768104.4444 901445.1924 879986.2509 1035529.902 1384859.167 1189812.488 1156265.408 0.986519171 0.841373235 0.918005056 0.664297694 0.779617885 0.761059048 0.895581495 1.197700076 1.029013304 1 20.14104116 1.921766903 5.675985892 1.089706448 0.821130982 0.578934305 0.09522483 0.148701956 8.11305662 0.042802513 0.02595022 83.5154648 -1.921766903 -0.268575466 APAGPSLEETSVSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 APAGPSLEETSVSSPK 16 0 K7EIX2;Q6AI08;A0A087WXZ7 K7EIX2 HEATR6 HEAT repeat-containing protein 6 1 APAGPSLEETSVS(0.021)S(0.979)PK;APAGPSLEETSVS(0.002)S(0.998)PK 210.67 9.53E-12 1936480000 2198640 1916540 1752150 1640720 1849180 1954600 2183140 2569400 2978300 2728900 TRUE FALSE 2112714.718 1861882.156 2068802.481 1725397.756 1908660.554 1994123.351 2209857.92 2516340.992 2640215.87 2544069.172 0.830447042 0.731852017 0.813186412 0.678203948 0.750239252 0.783832206 0.868631224 0.989100854 1.037792486 1 21.27870647 1.921819426 1.796430814 1.021770886 0.757981286 0.879646603 0.040602228 0.105373275 0.632787 0.025500507 0.011991229 83.52556567 -1.921819426 -0.2637896 HPGAHQGNLASGLHSNAIASPGS(ph)PSLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPGAHQGNLASGLHSNAIASPGSPSLGR 28 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 HPGAHQGNLASGLHSNAIAS(0.016)PGS(0.983)PS(0.001)LGR 204.75 5.10E-25 621480000 75470 101000 77791 110770 80768 112280 95548 9760.9 110710 101180 TRUE FALSE 72520.54896 98119.57889 91849.56415 116486.853 83365.97607 114550.3785 96717.34501 9559.334004 98142.66493 94326.98848 0.768820781 1.040206843 0.973735785 1.234926025 0.883797706 1.214396647 1.025341173 0.101342512 1.040451588 1 16.52538299 1.922010342 24.99999022 0.601394341 1.030009657 0.170422497 0.277590913 123.5088671 39590.40179 0.108119076 0.069779002 83.56229176 -1.922010342 0.428615317 IYEFPETDDEEENKLVK ddPTM_BT-474_Pertuzumab_2h_R1 5 IYEFPETDDEEENKLVK 17 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;;; 238.49 2.72E-20 2601820000 2292130 1890170 1709250 1514450 1834760 1851920 2005970 2409020 2663560 2265740 FALSE TRUE 2202551.026 1836264.202 2018149.497 1592610.946 1893776.722 1889367.091 2030519.661 2359272.895 2361203.835 2112279.412 1.042736587 0.869328268 0.955436807 0.753977403 0.896555972 0.894468355 0.961293118 1.116932202 1.117846352 1 21.01036926 1.922063767 3.444107042 1.087940263 0.89696093 0.523640366 0.074652032 0.176018751 3.736513023 0.036317472 0.020316005 83.5725718 -1.922063767 -0.190979333 ASVSQTSPQS(ph)ASSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQT(0.009)S(0.13)PQS(0.604)AS(0.193)S(0.064)PR;ASVSQT(0.004)S(0.008)PQS(0.964)AS(0.025)SPR 283.47 7.08E-34 625730000 577410 651240 543820 683410 663690 706520 611940 577790 625030 628870 TRUE FALSE 554844.1788 632667.2728 642100.3712 718680.872 685038.1916 720806.3185 619429.1048 565858.4346 554079.2147 586276.0748 0.94638721 1.079128588 1.095218445 1.225840356 1.168456673 1.229465689 1.056548496 0.965174018 0.945082425 1 19.16122066 1.922064501 3.922803485 0.969942597 1.128471982 0.438242673 0.077554625 0.226116414 6.203560194 0.039692867 0.022768447 83.57271295 -1.922064501 0.158529385 DHPDVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHPDVAK 7 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;G5E9S8 Q07866-6 KLC1 Kinesin light chain 1 0 ; 142.64 0.0024759 630080000 2048110 2059000 1776160 1834100 1936940 2136270 2182020 2019660 2698880 2411480 FALSE TRUE 1968067.597 2000279.336 2097151.622 1928758.121 1999243.434 2179466.843 2208724.213 1977953.315 2392514.457 2248148.312 0.875417154 0.889745274 0.932835085 0.857931886 0.889284494 0.969449761 0.982463747 0.879814425 1.064215579 1 21.10030578 1.922092612 0.525380198 1.009880419 0.883712136 0.471722124 0.04655729 0.85801339 0.518307789 0.046133925 0.032592976 83.57812273 -1.922092612 -0.126168282 (ac)S(ph)DKPDMAEIEKFDK ddPTM_BT-474_Pertuzumab_2h_R1 5 SDKPDMAEIEKFDK 14 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 S(1)DKPDMAEIEKFDK;S(1)DKPDMAEIEKFDK;S(1)DKPDMAEIEKFDK;S(1)DKPDMAEIEKFDK;S(1)DKPDMAEIEKFDK 110.84 5.28E-06 4643770000 10517030 8017670 6260900 5033890 7248940 6899810 8035680 10931530 11434810 8583120 TRUE FALSE 10106012.84 7789013.902 7392383.903 5293689.666 7482108.738 7039328.886 8134023.056 10705790.09 10136778.31 8001777.637 1.262970967 0.973410441 0.923842706 0.661564206 0.935055819 0.879720633 1.016527005 1.337926467 1.266815796 1 22.93188911 1.922099214 5.218471121 1.230362724 0.928647872 0.345468873 0.159338974 0.218564424 10.31035964 0.072863927 0.043705751 83.57939316 -1.922099214 -0.301714851 RPAS(ph)PSSPEHLPATPAESPAQR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 1 RPAS(0.333)PS(0.333)S(0.333)PEHLPATPAESPAQR;RPAS(0.956)PS(0.022)S(0.022)PEHLPATPAESPAQR;RPAS(0.333)PS(0.333)S(0.333)PEHLPATPAESPAQR;RPAS(0.655)PS(0.173)S(0.173)PEHLPATPAESPAQR 156.27 7.96E-09 3240130000 240547 257800 216396 300131 253767 290669 254734 224107 265522 262450 TRUE FALSE 231146.1573 250447.7964 255503.5709 315620.7969 261929.646 296546.5263 257851.5109 219479.1121 235381.0557 244674.0277 0.94471064 1.0235978 1.044261106 1.289964447 1.070524928 1.212006559 1.053857303 0.897026604 0.962018968 1 17.90050144 1.922108091 5.734360623 0.947088715 1.101847892 0.319451352 0.093958637 0.261172135 14.55091533 0.043116554 0.026176852 83.58110155 -1.922108091 0.154759176 SLIGVEYKPVSATGAEDKDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLIGVEYKPVSATGAEDKDKK 21 3 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 157.73 1.26E-09 744910000 544550 389310 290210 213880 359500 359400 423860 470540 586370 509920 FALSE TRUE 523268.384 378207.26 342657.4027 224918.3724 371063.644 366667.3142 429047.3255 460823.1846 519807.7359 475382.6642 1.100730892 0.79558488 0.72080332 0.473131204 0.780557795 0.771309814 0.902530441 0.969373137 1.093451182 1 18.85872977 1.922127144 1.686015471 1.038447571 0.75648233 0.371582969 0.144699617 0.398381496 2.110889548 0.100873873 0.046631233 83.58476841 -1.922127144 -0.281965241 VQPTHVIHLAAMVGGLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQPTHVIHLAAMVGGLFR 18 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 103.88 0.00030234 156194000 89725 98385 91563 99244 112893 108137 100586 63799 109750 102344 FALSE TRUE 86218.4478 95579.15613 108110.4709 104365.9947 116524.3059 110323.6042 101817.0016 62481.52836 97291.64011 95412.14972 0.903642231 1.001750368 1.133089142 1.093843866 1.221273247 1.156284651 1.067128263 0.654859245 1.019698648 1 16.54188537 1.922154821 12.05026772 0.85487472 1.091784425 0.319572709 0.124248331 0.960753898 146.9454606 0.051897085 0.03323 83.59009533 -1.922154821 0.236909705 EETEELKR ddPTM_BT-474_Pertuzumab_2h_R1 4 EETEELKR 8 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 180.03 0.0003868 6325300000 4205950 4060570 3896670 3957820 4121520 4162670 4564540 5116070 5938510 5369950 FALSE TRUE 4041576.824 3944766.519 4600884.95 4162083.565 4254092.434 4246842.039 4620402.206 5010421.367 5264395.241 5006238.503 0.807308086 0.787970153 0.919030315 0.8313794 0.849758243 0.848309971 0.922928902 1.00083553 1.051567007 1 22.25529559 1.922218935 1.802120396 1.027756665 0.839853756 0.842878565 0.034336952 0.129587304 0.783006438 0.022354673 0.010524837 83.60243655 -1.922218935 -0.187902909 HLDSSSNERPDISSIQR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLDSSSNERPDISSIQR 17 1 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;; 220.64 2.37E-15 2677620000 1117257 962784 927455 879549 1003044 996808 1099442 1199919 1327433 1333397 FALSE TRUE 1073593.361 935326.343 1095066.75 924942.6293 1035307.821 1016964.141 1112897.3 1175140.253 1176748.371 1243084.834 0.86365253 0.752423582 0.880926804 0.7440704 0.832853715 0.818097135 0.895270596 0.94534196 0.946635611 1 20.24549332 1.922221352 1.308766465 0.977668729 0.809164615 0.722904958 0.041768621 0.209165395 0.66415002 0.028479849 0.012559433 83.6029019 -1.922221352 -0.168504114 RKPFTFK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKPFTFK 7 2 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 117.1 0.0029852 879110000 1008480 1122280 829680 969280 1081450 752170 1126760 1326300 1442210 1452460 FALSE TRUE 969067.4867 1090273.673 979621.6321 1019304.657 1116235.821 767379.3928 1140549.626 1298911.442 1278496.367 1354083.59 0.715662972 0.80517457 0.723457281 0.752763466 0.824347795 0.566714934 0.842303706 0.95925499 0.944178318 1 20.36888537 1.922332799 3.949371437 0.958098697 0.737237961 0.708026843 0.067573789 0.12755599 3.549425543 0.031227931 0.017938207 83.62435854 -1.922332799 -0.220860736 KHGGPKDEER ddPTM_BT-474_Pertuzumab_2h_R1 11 KHGGPKDEER 10 2 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;;;;; 168.3 2.99E-06 28106820000 16519380 15527700 11779728 11314946 12903090 13496900 13674600 4774834 16124880 13267980 FALSE TRUE 15873784.37 15084865.2 13908586.89 11898911.72 13318129.61 13769816.57 13841953.85 4676232.009 14294451.22 12369327.9 1.283318261 1.219537983 1.124441603 0.96196914 1.076706004 1.113222697 1.119054646 0.378050614 1.155636858 1 23.56026378 1.922378465 24.99996167 0.768729583 1.123025382 0.265757497 0.204695991 114.5482676 36892.26 0.081537055 0.052623314 83.63315199 -1.922378465 0.354295799 VHLVGIDIFTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHLVGIDIFTGK 12 0 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ; 193.28 3.00E-06 12062000000 16069300 16193500 13809200 14863300 15766300 16221500 15785300 9149000 19026100 17480900 FALSE TRUE 15441293.99 15731677.24 16304829.62 15630396.69 16273437.36 16549509.84 15978485.22 8960069.953 16866336.89 16296903.07 0.94749867 0.965316979 1.000486384 0.959102268 0.998560112 1.015500293 0.98046145 0.549802003 1.034941229 1 23.9580945 1.922424111 24.99998721 0.799951766 0.982457306 0.102932229 0.127103027 135.6189728 43704.19276 0.049628902 0.032030181 83.64194273 -1.922424111 0.18250554 FAS(ph)DDEHDEHDENGATGPVKR ddPTM_BT-474_Pertuzumab_2h_R1 8 FASDDEHDEHDENGATGPVKR 21 1 P05455 P05455 SSB Lupus La protein 1 FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR 241.29 2.52E-30 26808136300 10341486 9219901 7442640 6941528 8246739 8411183.7 8483816 1888214.6 10667182 7617733 TRUE FALSE 9937329.294 8956958.451 8787690.609 7299781.092 8512002.849 8581263.597 8587643.478 1849222.309 9456288.22 7101777.159 1.3992736 1.261227753 1.237393178 1.027880899 1.198573633 1.208326227 1.209224577 0.26038867 1.331538291 1 22.75974866 1.922447127 24.99993682 0.770047546 1.214200316 0.255257701 0.26455574 116.6727963 37609.7299 0.103793732 0.066988163 83.64637543 -1.922447127 0.44415277 HSSDINHLVTQGRES(ph)PEGSYTDDANQEVR ddPTM_BT-474_Pertuzumab_2h_R1 3 HSSDINHLVTQGRESPEGSYTDDANQEVR 29 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 HSSDINHLVT(0.158)QGRES(0.836)PEGS(0.003)Y(0.002)T(0.001)DDANQEVR;HSSDINHLVTQGRES(1)PEGSYTDDANQEVR;HSSDINHLVTQGRES(1)PEGSYTDDANQEVR 222.25 1.03E-34 2927270000 407948 793370 491234 851620 601083 755280 575517 116995 426145 529095 TRUE FALSE 392004.9411 770743.8644 580010.9112 895572.2103 620417.3806 770552.2791 582560.3492 114579.0124 377770.8061 493258.9244 0.794724478 1.562554322 1.175875149 1.815622923 1.25779251 1.562165915 1.181043708 0.232289791 0.765867149 1 18.91198563 1.922518311 6.350278352 0.601959399 1.377837751 0.493968592 0.312718605 0.165170625 10.96556192 0.1277413 0.078471502 83.66008676 -1.922518311 0.775878352 TQLS(ph)PSIK ddPTM_BT-474_Pertuzumab_2h_R1 4 TQLSPSIK 8 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 TQLS(0.989)PS(0.011)IK;TQLS(0.987)PS(0.013)IK;TQLS(0.992)PS(0.008)IK;TQLS(0.988)PS(0.012)IK 131.12 0.0010687 1332670000 1466340 1251810 1415270 1456340 1422870 1319620 1533930 1841240 1847430 1953860 TRUE FALSE 1409033.812 1216109.604 1671040.772 1531501.882 1468637.906 1346303.621 1552702.694 1803217.751 1637717.491 1821523.322 0.773546951 0.667633288 0.917386427 0.840780825 0.806269065 0.739108637 0.852419882 0.989950405 0.899092244 1 20.79671404 1.922680836 4.316942275 0.957493221 0.793762365 0.57556736 0.06593235 0.172201481 5.70966461 0.031582403 0.018424212 83.69140063 -1.922680836 -0.163730856 NRPDYVS(ph)EEEEDDEDFETAVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NRPDYVSEEEEDDEDFETAVKK 22 2 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NRPDYVS(1)EEEEDDEDFETAVKK;NRPDYVS(1)EEEEDDEDFETAVKK 196.15 1.13E-22 174579000 167969 149749 126184 108479 129635 135636 149518 167920 195692 169169 TRUE FALSE 161404.5858 145478.3051 148988.2557 114077.6142 133804.8275 138378.6529 151347.846 164452.3933 173477.8646 157711.0329 1.023419749 0.922435815 0.944691395 0.723333124 0.848417673 0.877418975 0.959652874 1.042745014 1.099972915 1 17.26692406 1.922686417 2.468174008 1.054896374 0.884649972 0.46421116 0.075537147 0.262130696 2.907321112 0.044607273 0.023026791 83.69247606 -1.922686417 -0.170246402 SHHAPMS(ph)PGSSGGGGQPLAR ddPTM_BT-474_Pertuzumab_2h_R1 6 SHHAPMSPGSSGGGGQPLAR 20 0 O14497;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(0.999)PGS(0.001)SGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(0.999)PGS(0.001)SGGGGQPLAR;SHHAPMS(0.988)PGS(0.012)SGGGGQPLAR 187.79 1.79E-17 5882190000 1641010 2114700 1738460 2310300 1982570 2264240 1800340 323420 1691920 1306140 TRUE FALSE 1576877.515 2054390.827 2052638.394 2429534.86 2046341.165 2310024.484 1822373.099 316741.264 1499860.335 1217673.974 1.294991556 1.687143578 1.685704414 1.995226071 1.680532891 1.897079623 1.496601831 0.260119926 1.23174213 1 20.21569648 1.922717578 6.92984029 0.771398368 1.715427365 0.651709668 0.285902822 0.137007515 10.46884585 0.118017953 0.073138967 83.69848133 -1.922717578 0.944028997 LNS(ph)CETK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNSCETK 7 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 LNS(1)CETK;LNS(1)CETK 141.91 0.0026485 559700000 659800 513810 340600 412450 563200 485110 528520 704690 643090 654960 TRUE FALSE 634014.2866 499156.6419 402153.9966 433736.5939 581315.8395 494919.2566 534988.1859 690137.9052 570089.1193 610598.9758 1.0383481 0.817486864 0.658622128 0.710346088 0.95204195 0.810547145 0.876169478 1.130263778 0.933655545 1 19.21986564 1.922756841 6.167371942 1.030523681 0.824254451 0.368755685 0.110971806 0.237776846 15.08588165 0.050042417 0.030646041 83.70604846 -1.922756841 -0.20626923 VGNTGGPPHTHGASR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGNTGGPPHTHGASR 15 0 Q14781 Q14781 CBX2 Chromobox protein homolog 2 0 ; 80.632 0.0094813 89754000 21989.8 28785 23001.4 23721.9 23683.6 28384 22996.3 9484.2 21540.6 20343.3 FALSE TRUE 21130.4143 27964.07998 27158.26464 24946.1901 24445.4045 28957.94393 23277.7356 9288.347956 19095.40139 18965.43017 1.114154233 1.474476441 1.431987801 1.315350608 1.288945428 1.526880417 1.227377148 0.489751504 1.00685306 1 14.21108447 1.922825255 6.870712837 0.790289489 1.363390825 0.650760735 0.171843553 0.132049043 9.971045783 0.069748354 0.04319101 83.7192358 -1.922825255 0.573101337 REDFCPR ddPTM_BT-474_Pertuzumab_2h_R1 2 REDFCPR 7 1 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 0 ; 108.7 0.011536 210336000 303000 428990 473940 305390 389970 475760 331790 231910 226940 304030 FALSE TRUE 291158.425 416755.6252 559591.5007 321151.2145 402513.7392 485380.1932 335850.5453 227120.9775 201178.7226 283437.7773 1.027239304 1.470360194 1.974301048 1.133057201 1.420113236 1.712475302 1.184918074 0.801308067 0.709780907 1 18.11267253 1.922954725 3.528251167 0.825020834 1.46461722 0.529582472 0.260155957 0.184167386 4.107993996 0.127865377 0.071932515 83.74419741 -1.922954725 0.639596386 SKS(ph)PTISDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKSPTISDK 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.154)KS(0.829)PT(0.016)ISDK;S(0.127)KS(0.674)PT(0.199)ISDK;S(0.027)KS(0.677)PT(0.296)ISDK;S(0.033)KS(0.95)PT(0.017)ISDK 131.13 0.00020696 4825820000 3625550 3077680 2775840 2497060 2939830 2884120 3308990 4051210 4451800 3872800 TRUE FALSE 3483859.498 2989907.58 3277496.036 2625933.566 3034392.302 2942438.882 3349486.409 3967551.098 3946450.327 3610491.806 0.964926576 0.828116428 0.907769969 0.727306336 0.840437388 0.814968996 0.927709185 1.098894918 1.093050626 1 21.78376394 1.923069486 3.491455779 1.071127942 0.844110469 0.698291037 0.063467791 0.125324649 2.738601839 0.030814461 0.01730011 83.76632962 -1.923069486 -0.227017473 ADHGDELPFVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADHGDELPFVFR 12 0 O00748;O00748-4 O00748 CES2 Cocaine esterase 0 ; 112.84 0.0012298 117133000 110476 136538 110914 129579 126948 129826 125757 97543 137378 134383 FALSE TRUE 106158.4758 132644.0699 130958.6271 136266.5877 131031.3977 132451.1707 127296.0518 95528.70296 121783.4254 125281.1197 0.847362125 1.058771427 1.04531814 1.087686541 1.045898999 1.057231696 1.016083286 0.76251476 0.972081233 1 16.93480949 1.923121724 12.35854369 0.886052802 1.030738745 0.241644008 0.086282532 1.174816317 187.0052015 0.03450605 0.02211071 83.7764057 -1.923121724 0.144685943 HLQTGENHTSVDPR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLQTGENHTSVDPR 14 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ;; 80.96 0.0085818 771420000 273930 501170 387550 565360 375780 520800 415690 125947 333520 473150 FALSE TRUE 263224.5128 486877.1223 457588.906 594538.2974 387867.305 531330.9328 420777.3386 123346.1504 295660.2078 441103.1291 0.596741432 1.103771636 1.037373974 1.347844207 0.879312069 1.20455036 0.953920548 0.279631094 0.670274565 1 18.75075647 1.923157773 8.321694542 0.579135683 1.043083413 0.30375321 0.249781718 0.3190807 31.90574717 0.100743307 0.063372536 83.78335996 -1.923157773 0.46394773 ETNPHHPPAWIASAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETNPHHPPAWIASAR 15 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 134.85 1.88E-05 964270000 319520 358300 289580 380090 336400 371590 349960 72839 381370 388530 FALSE TRUE 307032.8052 348081.6348 341913.5477 399706.4905 347220.6115 379103.8044 354242.9152 71334.8492 338078.4764 362214.517 0.84765461 0.960982011 0.943953187 1.10350765 0.958604902 1.046627859 0.977992042 0.19694089 0.933365342 1 18.46648484 1.923160073 24.99918812 0.612520292 0.982323369 0.206268183 0.215693063 117.0397465 38077.00182 0.083999717 0.054212697 83.78380373 -1.923160073 0.369803077 (ac)ASHLRPPS(ph)PLLVR ddPTM_BT-474_Pertuzumab_2h_R1 8 ASHLRPPSPLLVR 13 1 Q8TDB6;Q8TDB6-2 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 1 ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR 103.04 8.05E-06 10739980000 81057.3 111285.8 103732 166670.8 135826.6 138508.4 91403.1 81516.6 62670.2 74340.9 TRUE FALSE 77889.4911 108112.0379 122478.6799 175272.7 140195.5859 141309.1347 92521.71848 79833.25372 55556.14163 69305.72463 1.123853643 1.559929407 1.767223134 2.52897868 2.022857227 2.038924425 1.334979455 1.151899849 0.801609707 1 16.0806869 1.923315032 2.191542232 0.960094537 1.8611624 0.544392348 0.351664404 0.256588885 2.264857369 0.224224727 0.111922874 83.8137036 -1.923315032 0.901067863 RSAS(ph)ASHQADIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSASASHQADIK 12 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 RS(0.217)AS(0.665)AS(0.118)HQADIK 116.99 0.00047928 445060000 562250 698780 365220 598330 429360 407880 517730 858450 653960 414320 TRUE FALSE 540276.6484 678851.4786 431223.3783 629209.883 443170.7543 416127.6131 524066.1346 840722.7075 579725.2024 386257.7374 1.398746475 1.757509075 1.116413567 1.628989719 1.147344665 1.077331462 1.356778348 2.176584768 1.500876607 1 18.55920431 1.923327996 24.99962369 1.709085422 1.352630862 0.016903938 0.343637414 199.4507031 65031.36965 0.136925767 0.088370194 83.81620549 -1.923327996 -0.35645456 FIVS(ph)PVPESR ddPTM_BT-474_Pertuzumab_2h_R1 2 FIVSPVPESR 10 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4;H0YH68 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 FIVS(1)PVPESR;FIVS(1)PVPESR 134.75 0.00017023 135452000 232127 246915 229922 234159 230043 254507 206548 212356 193664 214908 TRUE FALSE 223055.2202 239873.226 271474.02 246243.9741 237442.542 259653.3059 209075.7962 207970.7744 171680.0746 200352.0897 1.113316165 1.197258418 1.354984719 1.22905618 1.185126356 1.295985014 1.043541879 1.03802648 0.856891859 1 17.61217803 1.923331525 1.839264227 0.946997013 1.231637771 0.705568373 0.077353514 0.185082802 1.16377881 0.048636173 0.023053545 83.81688671 -1.923331525 0.284640758 RGES(ph)PGLHHFHHVDD ddPTM_BT-474_Pertuzumab_2h_R1 1 RGESPGLHHFHHVDD 15 1 Q5VT52-5 Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 RGES(1)PGLHHFHHVDD 112.55 0.000355 352000000 81662 94835 73956 83060 93871 78820 82239 35594 96143 67189 TRUE FALSE 78470.55876 92130.39865 87321.49434 87346.73655 96890.44597 80413.7944 83245.46548 34858.97146 85229.2497 62638.22918 1.252758256 1.470833385 1.394060711 1.394463696 1.546826071 1.283781414 1.328988169 0.556512723 1.360658671 1 15.93475581 1.923346192 10.31954508 0.927022517 1.39367862 0.470822531 0.197988819 0.42744514 55.94754383 0.0778114 0.049541711 83.81971731 -1.923346192 0.466656103 SLSS(ph)PTVTLSAPLEGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 SLS(0.311)S(0.689)PTVTLSAPLEGAK 401.79 3.67E-140 4190900000 6481100 6298200 5042200 5787500 4633600 4646200 5577600 8979900 6866300 5970300 TRUE FALSE 6227811.447 6118581.503 5953437.703 6086193.569 4782643.952 4740149.347 5645860.337 8794461.927 6086866.41 5565926.263 1.118917347 1.099292591 1.069622094 1.093473625 0.859271885 0.851637108 1.014361325 1.580053618 1.093594511 1 22.40819037 1.923381074 24.99766069 1.291052769 1.011011562 0.216053991 0.168914327 128.7974339 42020.49272 0.069360545 0.044765349 83.82644993 -1.923381074 -0.280041207 ELNEDKLEK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELNEDKLEK 9 1 O00567;A0A494C128;Q5JXT2 O00567 NOP56 Nucleolar protein 56 0 ;;; 140.07 0.00010029 2416010000 5692690 5113750 4228150 3825220 4711280 4510360 4978590 6039940 6341500 5489130 FALSE TRUE 5470213.381 4967910.857 4992270.76 4022640.063 4862822.6 4601562.569 5039519.474 5915213.128 5621639.506 5117346.336 1.068955084 0.970798248 0.975558509 0.786079307 0.950262554 0.899208744 0.984791559 1.155914167 1.098545835 1 22.28696445 1.923509967 5.429238882 1.097398906 0.938138369 0.412509915 0.075739607 0.197053976 10.10386815 0.034316322 0.020705075 83.85133216 -1.923509967 -0.159260537 KSES(ph)DKDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSESDKDVK 9 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KS(0.392)ES(0.608)DKDVK;KS(0.074)ES(0.926)DKDVK 86.772 0.010956 656710000 1269510 818090 808910 563610 792390 761740 928900 1123940 1215300 1133020 TRUE FALSE 1219896.146 794758.8742 955098.0311 592697.9796 817877.944 777142.9047 940268.1561 1100730.246 1077344.239 1056279.546 1.154898956 0.75241339 0.904209529 0.561118486 0.774300655 0.735736016 0.890169803 1.042082326 1.019942347 1 20.01056027 1.92351295 3.670840641 1.021201583 0.801934932 0.293883716 0.142193325 0.285983261 6.910186552 0.068607005 0.038915206 83.85190819 -1.92351295 -0.219266651 LLVQTSVQAKPGHVS(ph)PLQLTNIQVPQQALPTQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLVQTSVQAKPGHVSPLQLTNIQVPQQALPTQR 33 1 P22670 P22670 RFX1 MHC class II regulatory factor RFX1 1 LLVQTSVQAKPGHVS(0.999)PLQLTNIQVPQQALPTQR;LLVQT(0.011)S(0.011)VQAKPGHVS(0.977)PLQLTNIQVPQQALPTQR 194.36 5.64E-21 1707760000 812280 908780 671880 827940 763260 835590 740470 565054 745900 612820 TRUE FALSE 780535.1996 882862.4842 793303.6619 870670.0826 787810.9511 852486.2023 749532.0934 553385.4374 661228.5591 571313.1556 1.366212544 1.545321468 1.388561867 1.523980455 1.378947681 1.492152236 1.311946147 0.968620155 1.157383744 1 19.12392223 1.923583662 3.821402796 1.046971649 1.449364806 0.858865135 0.073642212 0.072587723 1.900203795 0.032198747 0.018403527 83.86556202 -1.923583662 0.402393158 AQFSVAGVHTVPGS(ph)PQAR ddPTM_BT-474_Pertuzumab_2h_R1 6 AQFSVAGVHTVPGSPQAR 18 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 AQFSVAGVHT(0.008)VPGS(0.992)PQAR;AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHT(0.044)VPGS(0.956)PQAR;AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHT(0.002)VPGS(0.998)PQAR;AQFSVAGVHT(0.001)VPGS(0.999)PQAR 121.47 2.46E-05 3688480000 2282400 2502060 2076060 2505730 2350320 2586280 2382610 2279650 2565640 2556710 TRUE FALSE 2193201.285 2430703.699 2451250.224 2635051.026 2425920.177 2638576.354 2411769.094 2232574.431 2274399.303 2383541.754 0.920143849 1.019786498 1.028406664 1.105519138 1.017779602 1.106998167 1.011842603 0.936662606 0.954209969 1 21.18467547 1.923656297 5.812683656 0.959564532 1.036761705 0.265947857 0.051188522 0.278388649 16.12641993 0.022798217 0.013872038 83.87958967 -1.923656297 0.077197173 KPPAPPS(ph)PVQSQS(ph)PSTNWS(ph)PAVPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 KPPAPPS(0.995)PVQS(0.041)QS(0.961)PS(0.106)T(0.017)NWS(0.879)PAVPVK;KPPAPPS(0.992)PVQS(0.194)QS(0.809)PS(0.01)T(0.009)NWS(0.985)PAVPVK 103.41 0.0019024 488530000 368430 292330 324420 311210 317280 316200 361680 408400 442160 452570 TRUE FALSE 354031.3483 283993.0346 383049.9107 327271.5854 327485.5993 322593.7806 366106.348 399966.3973 391967.8505 421917.0308 0.83910182 0.673101615 0.907879708 0.775677589 0.776184831 0.764590564 0.86772119 0.947974052 0.929016422 1 18.6865998 1.923702271 2.404585784 0.957465666 0.788233624 0.627100987 0.058460577 0.18621752 1.964575576 0.031274869 0.016040499 83.88846959 -1.923702271 -0.169232041 GDQVLNFS(ph)DAEDLIDDSK ddPTM_BT-474_Pertuzumab_2h_R1 6 GDQVLNFSDAEDLIDDSK 18 0 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK 237.18 8.04E-24 350100000 560621 467496 448521 437893 496465 479358 506040 591788 606015 577882 TRUE FALSE 538711.3115 454163.4718 529578.722 460492.7102 512434.2476 489050.9472 512233.0689 579567.371 537222.7178 538741.5374 0.999943895 0.843008085 0.982992187 0.854756276 0.951168997 0.907765437 0.950795573 1.07578 0.997180801 1 19.03923378 1.923796654 5.693898883 1.029757134 0.921075898 0.44114804 0.050719926 0.173927835 9.732034278 0.02027066 0.01230448 83.90670262 -1.923796654 -0.108681236 IHYFDPQYFEFEFEA ddPTM_BT-474_Pertuzumab_2h_R1 2 IHYFDPQYFEFEFEA 15 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 116.87 0.000964 281980000 330580 362400 275980 313650 340580 327650 323630 217147 342190 348500 FALSE TRUE 317660.5681 352064.7068 325855.7251 329837.5141 351535.065 334275.3075 327590.6807 212662.8386 303346.0258 324895.7846 0.977730655 1.083623499 1.002954611 1.015210199 1.081993309 1.028869328 1.008294648 0.654557088 0.933671781 1 18.3096175 1.923849981 11.41341789 0.825851986 1.033005897 0.401313421 0.089749254 0.615170713 90.77308526 0.035011727 0.022379804 83.91700612 -1.923849981 0.207153911 SS(ph)PVKVGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPVKVGEK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 S(0.073)S(0.927)PVKVGEK;S(0.157)S(0.843)PVKVGEK 122.42 0.00035502 1145500000 3575200 3031880 2264950 2004690 2552530 2676790 2896700 3151000 3755160 3196050 TRUE FALSE 3435477.231 2945413.751 2674276.849 2108152.291 2634634.446 2730916.528 2932150.681 3085930.749 3328889.98 2979578.687 1.153007721 0.988533635 0.897535232 0.707533686 0.884230531 0.916544524 0.984082311 1.035693658 1.117235129 1 21.50667692 1.923947325 2.173216881 1.059519504 0.91457306 0.216865639 0.106656238 0.482637078 4.191910243 0.067663225 0.033708796 83.93581752 -1.923947325 -0.144946444 GILLEDGSES(ph)PAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GILLEDGSESPAKR 14 1 Q08999;Q08999-2 Q08999 RBL2 Retinoblastoma-like protein 2 1 GILLEDGS(0.01)ES(0.99)PAKR 94.569 0.0025192 355020000 166120 155750 119720 123550 121260 117330 138680 167590 168660 152220 TRUE FALSE 159627.8467 151308.1625 141356.0672 129926.4303 125160.438 119702.493 140377.2073 164129.2079 149514.4239 141910.0038 1.12485267 1.066226189 0.996096564 0.915555118 0.881970507 0.843509899 0.989198813 1.1565725 1.053586216 1 17.11461677 1.924062128 8.536634575 1.084410258 0.965803185 0.20298941 0.086079071 0.525617995 55.05675662 0.040075348 0.025254795 83.95800833 -1.924062128 -0.118607073 TEAQGEEDDAEGQDQDKKS(ph)PKPK ddPTM_BT-474_Pertuzumab_2h_R1 5 TEAQGEEDDAEGQDQDKKSPKPK 23 3 O14617-5;O14617-2;A0A2R8Y611 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 TEAQGEEDDAEGQDQDKKS(1)PKPK;TEAQGEEDDAEGQDQDKKS(1)PKPK;TEAQGEEDDAEGQDQDKKS(1)PKPK;TEAQGEEDDAEGQDQDKKS(1)PKPK;TEAQGEEDDAEGQDQDKKS(1)PKPK 280.32 4.56E-52 4015580000 2507917 1426632 1702909 1134987 1768175 1330563 2113093 2989650 3482970 2482008 TRUE FALSE 2409904.831 1385945.852 2010662.537 1193563.815 1825049.955 1357467.896 2138953.664 2927912.683 3087597.847 2313899.387 1.04149076 0.598965478 0.868949855 0.515823558 0.788733497 0.586658133 0.924393548 1.265358684 1.334369966 1 21.1418947 1.924121351 3.643776425 1.219906435 0.726517726 0.614795985 0.164436994 0.138306519 3.29803122 0.074539218 0.042240617 83.96945819 -1.924121351 -0.49338871 TQLS(ph)PSIKR ddPTM_BT-474_Pertuzumab_2h_R1 4 TQLSPSIKR 9 1 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 TQLS(0.89)PS(0.11)IKR;TQLS(0.944)PS(0.056)IKR;TQLS(0.827)PS(0.173)IKR;TQLS(0.972)PS(0.028)IKR 139.46 6.82E-05 2850000000 3306940 3136820 2648100 2913790 2816150 2937470 3087450 3399630 3532870 3647120 TRUE FALSE 3177701.129 3047360.965 3126670.577 3064171.051 2906734.022 2996867.656 3125235.137 3329426.452 3131833.409 3400097.314 0.934591229 0.896256984 0.919582673 0.901200986 0.854897303 0.881406436 0.919160497 0.979215047 0.92110111 1 21.69714461 1.924246076 4.517036502 0.962664272 0.897186069 0.559693169 0.027166027 0.171245111 6.250478076 0.012597977 0.007410206 83.99357692 -1.924246076 -0.065478203 HS(ph)DENDGGQPHKR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSDENDGGQPHKR 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 HS(1)DENDGGQPHKR 87.932 0.0038279 71443000 68537 57431 59796 60647 75430 59101 57451 20614 59277 40771 TRUE FALSE 65858.49827 55793.12411 70602.46735 63776.99894 77856.27445 60296.06271 58154.10252 20188.3137 52548.12347 38009.54385 1.732683205 1.467871446 1.85749315 1.677920661 2.04833488 1.586340077 1.529986857 0.531138016 1.382498134 1 15.21407409 1.924413208 6.097618884 0.936340523 1.721610242 0.664232261 0.240505553 0.125382226 7.949442493 0.101437598 0.062076789 84.0259068 -1.924413208 0.785269718 EDLHILFSNHGEIK ddPTM_BT-474_Pertuzumab_2h_R1 3 EDLHILFSNHGEIK 14 0 P05455 P05455 SSB Lupus La protein 0 ;; 223.7 1.98E-12 702300000 1062320 1413460 1097080 1323760 1196770 1394390 1281410 508669 1487950 1518540 FALSE TRUE 1020803.36 1373149.505 1295346.76 1392079.412 1235265.194 1422585.521 1297092.279 498164.8074 1319044.154 1415687.933 0.72106524 0.969952115 0.914994562 0.98332364 0.872554724 1.004872252 0.916227545 0.351888856 0.931733699 1 20.43307185 1.924455717 24.99999493 0.675410324 0.919264864 0.070706833 0.181991975 158.6107165 52488.28935 0.07085159 0.045726463 84.03413177 -1.924455717 0.24385454 HAT(ph)RHSPQQEEENTIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 HATRHSPQQEEENTIFK 17 1 O14896;A0A2R8YHF3;B1AJU4 O14896 IRF6 Interferon regulatory factor 6 1 HAT(0.5)RHS(0.5)PQQEEENTIFK 82.586 0.010059 196680000 214040 267450 195330 187120 191270 199160 201130 63344 210540 190550 TRUE FALSE 205675.0802 259822.5879 230630.4761 196777.2856 197422.3733 203187.1517 203591.4891 62035.92426 186640.3819 177643.8788 1.157794356 1.462603663 1.298274265 1.107706536 1.111337889 1.143789209 1.146065322 0.349215096 1.050643474 1 17.43862845 1.92452591 10.46612634 0.731697899 1.213130333 0.442652314 0.204657157 0.472566725 63.90075817 0.083919664 0.053465446 84.04771493 -1.92452591 0.481432434 TTHLAGALS(ph)PGEAWPFESV ddPTM_BT-474_Pertuzumab_2h_R1 4 TTHLAGALSPGEAWPFESV 19 0 Q9Y3X0 Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV 183.76 2.77E-14 490343000 238453 247325 245407 264305 268506 281191 255860 167453 266469 271104 TRUE FALSE 229133.9931 240271.5332 289757.5039 277945.8127 277142.7393 286876.8747 258991.2912 163995.037 236220.5562 252741.8846 0.90659288 0.950659735 1.146456213 1.099722008 1.096544563 1.135058699 1.024726438 0.64886371 0.934631617 1 17.94730524 1.924536203 9.946610228 0.825216515 1.060743713 0.367715881 0.111882022 0.460317347 58.68968046 0.046870298 0.029792901 84.04970693 -1.924536203 0.235527198 KNSSTDQGS(ph)DEEGSLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KNSSTDQGSDEEGSLQK 17 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 KNSSTDQGS(1)DEEGSLQK;KNSSTDQGS(1)DEEGSLQK 190.19 1.92E-10 911250000 745940 659240 529530 536510 601050 626150 761130 959410 1178220 927790 TRUE FALSE 716787.8401 640439.1207 625227.8503 564199.3454 620383.3191 638811.182 770444.9366 939597.8482 1044473.405 864949.9569 0.828704406 0.740434884 0.722848583 0.652291316 0.717247644 0.738552765 0.89073932 1.086303133 1.207553566 1 19.72225714 1.924602094 2.202476646 1.117140895 0.727465058 0.872116001 0.062441833 0.095942465 0.855023401 0.036267639 0.018149285 84.06245984 -1.924602094 -0.389675837 EHNSMWASLSS(ph)PDAEAVEPDFSSIER ddPTM_BT-474_Pertuzumab_2h_R1 4 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNSMWASLS(0.015)S(0.985)PDAEAVEPDFSSIER;EHNSMWASLS(0.104)S(0.896)PDAEAVEPDFSSIER;EHNSMWASLS(0.287)S(0.713)PDAEAVEPDFSSIER;EHNSMWASLS(0.046)S(0.954)PDAEAVEPDFSSIER 208.06 1.53E-25 834740000 191914 394143 302548 486615 365202 433355 331958 162639 262430 331946 TRUE FALSE 184413.7887 382902.4275 357225.1537 511729.2585 376949.054 442117.735 336020.6013 159280.4478 232640.0466 309463.0018 0.595915465 1.237312459 1.154338812 1.653604003 1.218074703 1.428661044 1.085818335 0.514699486 0.751753991 1 18.23940741 1.924758603 5.819863478 0.717521027 1.235161648 0.355728404 0.2740196 0.219013148 12.85969199 0.120331024 0.073260402 84.09275923 -1.924758603 0.51764062 HRHS(ph)PTGPPGFPR ddPTM_BT-474_Pertuzumab_2h_R1 7 HRHSPTGPPGFPR 13 1 P98175-5;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 HRHS(0.905)PT(0.095)GPPGFPR;HRHS(0.931)PT(0.069)GPPGFPR;HRHS(0.965)PT(0.035)GPPGFPR;HRHS(0.754)PT(0.246)GPPGFPR;HRHS(0.997)PT(0.003)GPPGFPR;HRHS(0.997)PT(0.003)GPPGFPR;HRHS(0.976)PT(0.024)GPPGFPR 163.8 2.30E-05 12789280000 2679168 2920649 2459836 2988495 2944466 2944926 2561169 88566 2756076 1644815 TRUE FALSE 2574463.153 2837354.95 2904383.084 3142731.585 3039177.423 3004474.421 2592513.352 86737.08115 2443217.807 1533410.215 1.678913527 1.850356103 1.894067912 2.049504793 1.981972856 1.959341598 1.690684806 0.056564825 1.593323028 1 20.54831227 1.924854377 8.344935255 0.796676346 1.903045944 0.612664478 0.361662458 0.193415938 19.87805044 0.143973208 0.090599615 84.1113061 -1.924854377 1.106369598 HSPTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSPTSEPTPPGDALPPVSSPHTHR 24 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 HSPTSEPTPPGDALPPVS(0.482)S(0.482)PHT(0.036)HR;HSPTSEPTPPGDALPPVS(0.429)S(0.429)PHT(0.142)HR 137.9 1.74E-05 2482200000 359560 428470 347120 503680 419620 371170 339110 11119.5 273090 194412 TRUE FALSE 345507.9977 416250.4551 409852.3056 529674.9852 433117.4584 378675.3117 343260.1296 10889.87844 242089.9681 181244.3021 1.90631095 2.296626434 2.261325189 2.922436618 2.389688688 2.08930878 1.893908529 0.060083977 1.33571078 1 17.46757612 1.924904866 5.1945051 0.73264285 2.31635931 0.753165216 0.386481503 0.098831154 4.730381169 0.173644839 0.104242688 84.121085 -1.924904866 1.583716461 IPDEINDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IPDEINDR 8 0 C9J363;Q9BUL8;C9J6F3;C9J5C3;H7C5M9;C9JSA3;C9JND6 C9J363 PDCD10 Programmed cell death protein 10 0 79.474 0.057313 0 46763 45982 39321 42756 46409 50711 54557 107640 68714 82716 FALSE TRUE 44935.45026 44670.63838 46427.17939 44962.64228 47901.78763 51736.41116 55224.68489 105417.1964 60913.87479 77113.57164 0.582717793 0.579283743 0.602062366 0.583070416 0.621184917 0.670911878 0.716147414 1.367038177 0.789924179 1 16.23469717 1.925033704 7.144400523 1.084218422 0.611681332 0.686889476 0.134258635 0.131621337 10.85832159 0.054558765 0.033921866 84.14604413 -1.925033704 -0.47253709 SNSEDKLNS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSEDKLNSK 10 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 SNS(0.16)EDKLNS(0.839)K 180.24 5.31E-06 847660000 1306100 1034300 951590 877980 956360 905250 1112100 1419600 1453600 1330100 TRUE FALSE 1255056.168 1004802.777 1123563.481 923292.653 987122.1879 923554.7752 1125710.212 1390284.764 1288593.422 1240011.142 1.012132976 0.810317539 0.90609144 0.744584159 0.796059127 0.744795546 0.907822659 1.121187316 1.039178906 1 20.24192165 1.92506714 4.904716837 1.059799048 0.831131473 0.599194592 0.079422304 0.139792873 6.01172534 0.035820617 0.021338117 84.15252284 -1.92506714 -0.228667575 DKGEYTLVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKGEYTLVVK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 126.1 0.00035705 1888910000 3831000 3710500 3045300 3609800 3191800 3556300 4002400 4598600 5009400 5144900 FALSE TRUE 3681280.285 3604680.173 3595653.452 3796102.211 3294467.146 3628210.823 4051382.568 4503637.303 4440753.913 4796431.34 0.767504009 0.751533779 0.749651813 0.791443042 0.686857981 0.756439645 0.84466602 0.938955858 0.925845404 1 22.19352997 1.925120843 1.92236988 0.958980683 0.748428195 0.903980007 0.029934247 0.094030809 0.644345406 0.018497591 0.008894739 84.16292944 -1.925120843 -0.210552489 KKS(ph)PIINESR ddPTM_BT-474_Pertuzumab_2h_R1 7 KKSPIINESR 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KKS(1)PIINESR;KKS(1)PIINESR;KKS(0.977)PIINES(0.023)R;KKS(0.998)PIINES(0.002)R;KKS(0.992)PIINES(0.008)R;KKS(1)PIINESR;KKS(0.833)PIINES(0.167)R 146.59 1.48E-05 38445720000 18164740 16120830 14172420 14267340 14925740 15506290 17362800 20331360 22144020 21589700 TRUE FALSE 17454841.88 15661079.71 16733691.56 15003679.13 15405839.98 15819837.81 17575291.14 19911510.31 19630323.68 20127410.39 0.867217468 0.778097103 0.831388203 0.745435147 0.765415902 0.785984759 0.873201808 0.989273331 0.975302998 1 24.26265823 1.925159296 2.527255338 0.989368106 0.792723298 0.871069843 0.033084253 0.092846516 1.078464056 0.018319413 0.009538424 84.17038161 -1.925159296 -0.196644808 TKPVTGNLRPEEALQALTIYEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKPVTGNLRPEEALQALTIYEGK 23 2 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 130.87 1.85E-05 901920000 1459030 1450300 1319790 1233020 1374640 1633450 1483300 1673100 2065790 1858160 FALSE TRUE 1402009.495 1408938.864 1558305.412 1296656.31 1418856.544 1666479.478 1501453.069 1638549.9 1831290.18 1732305.168 0.809331705 0.81333179 0.899555944 0.748514946 0.819056925 0.962001101 0.866737049 0.945878319 1.057140632 1 20.72426167 1.925293528 0.828192066 1.024961848 0.819713761 0.673039101 0.053139391 0.368700109 0.471501825 0.046185104 0.022352797 84.19640103 -1.925293528 -0.205248087 KTSDDGGDS(ph)PEHDTDIPEVDLFQLQVNTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSDDGGDSPEHDTDIPEVDLFQLQVNTLR 30 1 Q9HAJ7 Q9HAJ7 SAP30L Histone deacetylase complex subunit SAP30L 1 KT(0.012)S(0.012)DDGGDS(0.788)PEHDT(0.189)DIPEVDLFQLQVNTLR 84.822 0.00065203 37505000 47831 45781 30996 37312 40914 42626 44924 48683 64442 47122 TRUE FALSE 45961.71164 44475.3707 36597.6667 39237.67679 42230.03597 43487.92693 45473.79335 47677.67904 57126.81432 43930.38497 1.046239674 1.012405667 0.833083223 0.893178533 0.961294466 0.9899282 1.035133049 1.085300734 1.30039412 1 15.42293152 1.925407398 1.633532262 1.149215132 0.947058854 0.436077992 0.088677702 0.333429552 1.658542129 0.059723037 0.027459112 84.21847978 -1.925407398 -0.202156278 EREEATYLLEQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EREEATYLLEQQR 13 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 0 ; 181.58 1.09E-05 622300000 510060 391330 404440 330770 434490 365310 470260 616150 690630 517840 FALSE TRUE 490126.2913 380169.6516 477531.3047 347841.0793 448465.7654 372696.8185 476015.1826 603426.2872 612232.5778 482766.2356 1.015245589 0.787481857 0.989156386 0.720516585 0.928950147 0.772002661 0.986015896 1.249934736 1.26817605 1 18.88096525 1.925449704 4.177196496 1.191819707 0.866791045 0.594674529 0.111596789 0.133078508 4.188046173 0.048337806 0.02810291 84.22668419 -1.925449704 -0.325028662 HKHEIESGR ddPTM_BT-474_Pertuzumab_2h_R1 6 HKHEIESGR 9 1 O00178;F5H716 O00178 GTPBP1 GTP-binding protein 1 0 ;;;;; 145.34 5.85E-05 241359000 330796 355993 283338 332460 330048 331685 294609 12869.48 315467 189988 FALSE TRUE 317868.1266 345840.4282 334543.4794 349618.3004 340664.2937 338391.898 298214.5131 12603.72074 279656.5087 177119.9435 1.794648983 1.952577566 1.888796218 1.973907023 1.923353671 1.910523971 1.683686812 0.071159241 1.578910331 1 17.43436714 1.925538419 8.145561562 0.798479702 1.902979692 0.63516584 0.346256387 0.175701803 17.64491885 0.136860462 0.085986732 84.24389133 -1.925538419 1.10449999 WSLEDDDDDEDDPAEAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 WSLEDDDDDEDDPAEAEK 18 0 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 351.06 5.02E-90 256400000 438390 369940 467360 503630 448700 442430 581470 686190 770930 793530 FALSE TRUE 421257.2341 359389.6734 551822.3484 529622.4047 463132.843 451376.2377 588586.2038 672019.9367 683417.2584 739783.5063 0.569433125 0.485803847 0.745924103 0.7159154 0.626038346 0.610146393 0.795619528 0.90840081 0.923807104 1 19.49674361 1.925553034 1.71921726 0.958061027 0.625751614 0.802133337 0.071306901 0.168487659 0.927592585 0.050496694 0.023530983 84.24672624 -1.925553034 -0.332309413 HIDSSPYSPAYLS(ph)PPPESSWR ddPTM_BT-474_Pertuzumab_2h_R1 3 HIDSSPYSPAYLSPPPESSWR 21 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR 203.25 3.83E-22 1776250000 499880 628910 590340 741380 736350 687980 575110 416500 479670 497160 TRUE FALSE 480344.137 610974.1026 697027.57 779642.7106 760035.3665 701891.427 582148.3682 407899.1295 425219.8725 463486.9104 1.036370448 1.318212206 1.503877573 1.68212455 1.639820563 1.514371628 1.256019005 0.880066126 0.917436637 1 18.82216907 1.92570261 3.19371482 0.924959144 1.46323569 0.640210054 0.172510821 0.168258652 3.093030404 0.096038097 0.053024337 84.27574691 -1.92570261 0.538276547 ATS(ph)LPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.471)S(0.516)LPS(0.014)IPNPFPELCS(0.06)PPS(0.157)QS(0.772)PILGGPS(0.006)S(0.005)AR;AT(0.452)S(0.512)LPS(0.036)IPNPFPELCS(0.012)PPS(0.187)QS(0.8)PILGGPSSAR 117.93 1.79E-05 162298000 102226 110493 83665 105600 106112 102209 104125 141085 115435 126457 TRUE FALSE 98230.8949 107341.8478 98785.12662 111050.0287 109525.1888 104275.736 105399.3129 138171.5454 102331.3027 117891.9548 0.833228146 0.910510374 0.83792933 0.941964436 0.929030222 0.884502562 0.894033126 1.172018445 0.868009212 1 16.84710574 1.925753734 24.86754613 1.032598739 0.892060981 0.345381866 0.076312759 116.0145168 38856.42637 0.029697731 0.019166738 84.28566824 -1.925753734 -0.140537758 GS(ph)PS(ph)PEKPDVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPSPEKPDVEK 12 1 Q7Z3Z5;Q93074-3;Q93074;Q93074-2 Q7Z3Z5 TNRC11;MED12 Mediator of RNA polymerase II transcription subunit 12 2 GS(1)PS(1)PEKPDVEK 105.31 0.0011627 272490000 476140 406910 466450 425890 466110 395800 564660 738940 833140 735520 TRUE FALSE 457531.9224 395305.3252 550747.8911 447870.2339 481102.8515 403803.3472 571570.478 723680.6308 738565.44 685702.5753 0.667245449 0.576496778 0.803187725 0.653155246 0.701620307 0.588889938 0.833554516 1.05538561 1.077092994 1 19.38722341 1.925846934 3.040509424 1.048698711 0.668963335 0.87791636 0.063119275 0.079577601 1.327072462 0.031672926 0.017294532 84.30375796 -1.925846934 -0.379735376 EGEDGDQPTT(ph)PPKPLK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGEDGDQPTTPPKPLK 16 1 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 EGEDGDQPT(0.155)T(0.845)PPKPLK;EGEDGDQPT(0.214)T(0.786)PPKPLK;EGEDGDQPT(0.331)T(0.669)PPKPLK;EGEDGDQPT(0.161)T(0.839)PPKPLK 143.04 2.34E-06 7392710000 3516080 2245340 2350700 2219370 2413460 2203580 2834500 4021710 3828780 3564140 TRUE FALSE 3378667.706 2181305.102 2775523.781 2333911.952 2491091.133 2248137.897 2869189.459 3938660.283 3394152.946 3322737.623 1.016832531 0.656478287 0.835312353 0.702406334 0.749710454 0.676592061 0.863501662 1.185366023 1.021492917 1 21.66394095 1.925871435 5.236758552 1.080060154 0.76614998 0.605981971 0.106462874 0.128191976 6.280015916 0.044603984 0.026819035 84.30851411 -1.925871435 -0.313910174 LHNGNAS(ph)PPRVPSPPPAPEPPWHCGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHNGNASPPRVPSPPPAPEPPWHCGDR 27 1 O15037 O15037 KHNYN Protein KHNYN 1 LHNGNAS(0.889)PPRVPS(0.111)PPPAPEPPWHCGDR 57.417 0.040978 117410000 45210 49773 30431 48815 42097 50125 39328 20627 37342 30165 TRUE FALSE 43443.14322 48353.52277 35930.55863 51334.348 43451.08824 51138.56184 39809.30783 20201.04524 33103.09271 28121.89768 1.544815493 1.719426026 1.277671907 1.825422615 1.545098013 1.818460561 1.415598203 0.718338622 1.177128695 1 14.77940633 1.925928148 5.416161074 0.953952562 1.616989527 0.723344919 0.181407243 0.103978266 5.425958791 0.075661759 0.045690444 84.3195244 -1.925928148 0.663036965 RTGGPAYGPSSDVSTAS(ph)ETESEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTGGPAYGPSSDVSTASETESEKR 24 2 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 RTGGPAYGPSSDVS(0.006)T(0.178)AS(0.815)ET(0.001)ESEKR 165.34 7.50E-12 552760000 183000 149560 143040 144570 155430 155900 165630 211850 194490 203900 TRUE FALSE 175848.1577 145294.6952 168890.5099 152031.275 160429.5471 159052.4048 167657.0295 207475.2235 172412.3106 190089.6714 0.925080024 0.764348185 0.888478099 0.799787142 0.843967723 0.836723025 0.881989159 1.091459741 0.907005148 1 17.53632062 1.926027496 6.464359692 1.005822571 0.841096539 0.58929681 0.058387213 0.143411692 10.2205935 0.023231706 0.014312436 84.33881527 -1.926027496 -0.164726033 GGHSGQLGPSSVAPSFRPEDELEHLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGHSGQLGPSSVAPSFRPEDELEHLTK 27 1 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 ; 289.23 1.21E-70 619220000 620750 694290 556400 724650 609060 683370 662960 486230 719170 739330 FALSE TRUE 596490.4037 674489.529 656953.8571 762049.2733 628650.968 697188.2096 671073.5028 476189.1806 637532.8366 689254.5206 0.865413843 0.978578317 0.953136813 1.105613747 0.912073768 1.011510536 0.9736222 0.690875673 0.924959964 1 19.3946773 1.926064986 24.99987054 0.836260334 0.975563675 0.156629512 0.095234556 157.1257049 53128.49283 0.037341033 0.024099465 84.34609607 -1.926064986 0.139303342 TGTITTFEHAHNMR ddPTM_BT-474_Pertuzumab_2h_R1 11 TGTITTFEHAHNMR 14 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;; 164.33 2.39E-06 13138310000 5245250 5674540 4636040 4731170 5039610 5637090 5225150 698833 5633930 4907750 FALSE TRUE 5040259.831 5512707.675 5473875.556 4975346.251 5201713.633 5751075.822 5289096.949 684401.8543 4994389.886 4575343.721 1.101613373 1.204872904 1.196385647 1.087425679 1.136901171 1.256971317 1.155999914 0.149584795 1.091587909 1 22.1254487 1.926126987 22.86492186 0.652618971 1.166294475 0.363780909 0.242547862 46.6895566 14450.52435 0.093834816 0.060551508 84.35813845 -1.926126987 0.513675504 ARS(ph)PTDDKVK ddPTM_BT-474_Pertuzumab_2h_R1 7 ARSPTDDKVK 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.822)PT(0.178)DDKVK;ARS(0.999)PT(0.001)DDKVK;ARS(0.814)PT(0.186)DDKVK;ARS(0.5)PT(0.5)DDKVK;ARS(0.977)PT(0.023)DDKVK;ARS(0.832)PT(0.168)DDKVK;ARS(0.979)PT(0.021)DDKVK 164.53 3.20E-06 20996940000 21031730 17746760 15083370 12914670 15591020 14338940 17775310 19810130 22846490 20160240 TRUE FALSE 20209786.74 17240639.78 17809270.49 13581197.67 16092519.32 14628883.19 17992849.56 19401043.89 20253052.24 18794768.99 1.07528785 0.917310545 0.947565277 0.722605193 0.85622331 0.778348657 0.957332839 1.032257641 1.077589847 1 24.16382785 1.926161661 3.637899601 1.037362963 0.878117297 0.358326421 0.091509401 0.26755962 6.391973113 0.04650305 0.026388901 84.36487375 -1.926161661 -0.159245666 VFS(ph)LSEADSHGGHWV ddPTM_BT-474_Pertuzumab_2h_R1 4 VFSLSEADSHGGHWV 15 0 H7BXG1 H7BXG1 CLEC16A 1 VFS(0.989)LS(0.011)EADSHGGHWV;VFS(1)LSEADSHGGHWV;VFS(0.999)LS(0.001)EADSHGGHWV;VFS(0.993)LS(0.007)EADSHGGHWV 288.12 7.08E-35 748770000 823100 857690 726190 803200 812490 650280 726510 41447.9 774720 592780 TRUE FALSE 790932.342 833229.521 857428.687 844653.2483 838624.4787 663429.1071 735401.2467 40591.98638 686777.0335 552630.4826 1.431213744 1.507751648 1.551540702 1.528423196 1.517513972 1.200493147 1.330728705 0.073452312 1.242741859 1 19.07595562 1.926203598 9.847308519 0.675457482 1.45212731 0.511397758 0.296043229 0.347562948 44.84136043 0.118729118 0.075439431 84.37302079 -1.926203598 0.776669828 VDDKWEK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDDKWEK 7 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 122.52 0.0039519 3597420000 4817460 4242240 3984190 3534540 4103280 4155990 4721680 5275780 6204320 5563260 FALSE TRUE 4629188.337 4121255.469 4704221.761 3716958.033 4235265.728 4240026.965 4779465.332 5166833.299 5500031.604 5186455.445 0.89255338 0.79461889 0.907020567 0.716666338 0.816601198 0.817519211 0.921528274 0.996216656 1.060460591 1 22.30631747 1.926224392 1.986699686 1.027974516 0.820497538 0.740468494 0.051817638 0.157211764 1.148260234 0.030738044 0.01493907 84.37706052 -1.926224392 -0.207476977 VFDDES(ph)DEKEDEEYADEK ddPTM_BT-474_Pertuzumab_2h_R1 4 VFDDESDEKEDEEYADEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK 283.57 1.11E-39 3647780000 5201900 3479030 3967350 3306650 4061690 3413430 4900600 6753100 7391000 6271320 TRUE FALSE 4998603.997 3379811.471 4684338.398 3477306.603 4192337.948 3482451.893 4960575.009 6613646.125 6552004.666 5846557.91 0.854965276 0.578085691 0.801213033 0.594761338 0.717060878 0.595641392 0.848460767 1.131203389 1.120660184 1 22.47915607 1.926522774 3.534041626 1.091587802 0.687783209 0.786433218 0.091502427 0.093998262 2.119916182 0.041167958 0.023235983 84.43505172 -1.926522774 -0.403804593 ELEELRK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEELRK 7 1 P61129 P61129 ZC3H6 Zinc finger CCCH domain-containing protein 6 0 112.17 0.010285 331390000 495800 511580 456650 499150 465410 468810 503770 642640 578170 588670 FALSE TRUE 476423.5879 496990.2393 539176.8131 524911.1913 480380.3353 478289.6594 509935.288 629369.2594 512538.5655 548798.8566 0.868120591 0.905596346 0.982467085 0.956472822 0.875330423 0.871520875 0.929184312 1.146812264 0.933927903 1 19.06591795 1.926866301 11.39128018 1.042081368 0.912467401 0.426222992 0.060285036 0.718578953 110.347687 0.024876973 0.015901552 84.50186642 -1.926866301 -0.129613968 TDEEEKEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDEEEKEDR 9 1 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;H3BN59;H3BTB3;H3BMQ5 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ; 166.97 5.50E-05 455670000 1463030 1116970 1244680 1166600 1228050 1173370 1489740 1741860 2002250 1874330 FALSE TRUE 1405853.17 1085115.109 1469621.364 1226808.366 1267551.344 1197096.345 1507971.884 1705889.982 1774962.974 1747379.96 0.804549212 0.62099551 0.841042817 0.702084489 0.725401099 0.685080734 0.862990259 0.976255893 1.015785356 1 20.73676192 1.926892691 2.408461783 1.001251286 0.728546664 0.805016549 0.058949031 0.11426468 1.209876159 0.030858927 0.015877005 84.50700124 -1.926892691 -0.272704623 GFGFVDFNSEEDAK ddPTM_BT-474_Pertuzumab_2h_R1 5 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;; 366.75 1.24E-96 2123680000 2452680 2220780 2004000 2040420 2236410 2259590 2337970 2754460 2859130 2705750 FALSE TRUE 2356826.554 2157445.529 2366167.379 2145726.321 2308346.159 2305280.458 2366582.776 2697579.438 2534573.549 2522487.142 0.934326488 0.855285045 0.93802951 0.850639151 0.915107205 0.913891857 0.938194188 1.069412562 1.004791464 1 21.26641549 1.926961349 4.216948516 1.029381317 0.900473609 0.739466712 0.03268688 0.099789182 3.222182202 0.014398156 0.00839358 84.52036219 -1.926961349 -0.128907709 KS(ph)KSPT(ph)LR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSKSPTLR 8 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 KS(0.663)KS(0.424)PT(0.913)LR;KS(0.668)KS(0.594)PT(0.738)LR 64.827 0.072676 2367800000 4101700 3009200 2633800 2170030 2831500 2678200 3248600 3982400 4554600 3580000 TRUE FALSE 3941401.029 2923380.562 3109786.249 2282025.508 2922577.769 2732355.039 3288357.339 3900162.048 4037580.902 3337523.411 1.180935845 0.875913125 0.931764625 0.683748165 0.87567259 0.818677415 0.985268696 1.168579683 1.209753582 1 21.67034653 1.926975564 3.75260126 1.139340115 0.885223843 0.396591832 0.126810542 0.219254608 5.589715414 0.061185739 0.034949623 84.52312867 -1.926975564 -0.254116273 QAHDLS(ph)PAAESSSTFSFSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 QAHDLSPAAESSSTFSFSGR 20 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR 241.65 6.07E-30 7980400000 2091220 2246590 1976310 2123210 2029460 2332950 2068150 1910540 2124090 2159850 TRUE FALSE 2009492.81 2182519.453 2333473.18 2232789.123 2094739.424 2380123.847 2093460.638 1871086.681 1882972.208 2013561.436 0.997979389 1.083910038 1.158878561 1.108875589 1.040315625 1.182046798 1.039680539 0.92924241 0.935145149 1 20.94131806 1.927063567 4.51912888 0.951556138 1.097000334 0.585732985 0.052695784 0.147230863 5.465386184 0.024101544 0.014205255 84.54025757 -1.927063567 0.145444195 IDDMLNVSGHLLSTAEVESALVEHEAVAEAAVVGHPHPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDDMLNVSGHLLSTAEVESALVEHEAVAEAAVVGHPHPVK 40 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 271.63 1.39E-77 1028850000 314740 312730 316170 316240 340960 348600 319410 37225 382100 231962 FALSE TRUE 302439.6128 303811.2466 373308.9522 332561.1843 351927.2881 355648.9308 323319.0351 36456.29074 338725.6099 216251.0071 1.39855817 1.404900956 1.726276132 1.537848025 1.627401845 1.644611674 1.495109962 0.168583218 1.566353907 1 17.72234733 1.927064447 13.88031122 0.822107249 1.560619073 0.429167109 0.332058802 1.561706368 296.1092445 0.129448405 0.083175398 84.5404289 -1.927064447 0.738511824 VYVPALIFGQLLTSSNYDDDEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VYVPALIFGQLLTSSNYDDDEKK 23 1 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 180.05 7.49E-17 96663000 64699 47186 33115 29509 48044 41194 46221 66758 59851 50269 FALSE TRUE 62170.49155 45840.30148 39099.61714 31031.96303 49589.37889 42026.9709 46786.66642 65379.42397 53056.9654 46864.23586 1.326608456 0.978151049 0.834316754 0.662167268 1.058149738 0.896781312 0.998344805 1.395081404 1.132141908 1 15.51619974 1.927222501 8.531619053 1.215114101 0.945668411 0.207378014 0.184267786 0.45871306 50.22583275 0.078629434 0.049565119 84.57120152 -1.927222501 -0.269445691 RVES(ph)EES(ph)GDEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVESEESGDEEGK 13 1 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 2 RVES(1)EES(1)GDEEGK;RVES(1)EES(1)GDEEGK 146.3 2.82E-05 389460000 1230510 1028130 987730 1014100 1068180 1059170 1196440 1378390 1594850 1383810 TRUE FALSE 1182420.309 998808.739 1166234.783 1066437.823 1102538.98 1080587.143 1211082.391 1349925.765 1413809.314 1290083.316 0.916545694 0.774220336 0.903999585 0.826642597 0.854626183 0.837610354 0.938762928 1.046386499 1.095905432 1 20.29903281 1.927249793 2.483155085 1.055244447 0.849919887 0.800327366 0.043544717 0.108023714 1.213430661 0.022123994 0.011483973 84.57651643 -1.927249793 -0.20532456 EHMDAINHDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHMDAINHDTK 11 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 174.42 6.38E-06 965640000 1579800 1643470 1324260 1539060 1539890 1590190 1557780 189738 1769120 1418970 FALSE TRUE 1518059.669 1596599.845 1563583.24 1618491.071 1589421.96 1622344.731 1576844.578 185819.844 1568296.914 1322861.898 1.14755718 1.20692859 1.181970123 1.223476973 1.201502563 1.226390097 1.191994856 0.14046806 1.185533363 1 20.33523103 1.927284355 24.99905423 0.676428955 1.199823595 0.344337084 0.256029039 116.6595322 40106.01044 0.0987652 0.063742563 84.58324747 -1.927284355 0.523394639 NTSHETAANHK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTSHETAANHK 11 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 124.12 0.00020568 27001000 17048 23518 23670 26373 23885 20214 21726 7826.4 21321 22450 FALSE TRUE 16381.74531 22847.28967 27947.69554 27734.11369 24653.28272 20622.74093 21991.88929 7664.782105 18900.72946 20929.4415 0.78271297 1.091633987 1.335329255 1.325124404 1.177923583 0.985345974 1.050763313 0.366220097 0.903068984 1 14.35324619 1.927306022 9.110933973 0.690186133 1.127666496 0.344503197 0.21713273 0.388963678 46.39584189 0.092297361 0.058411524 84.58746729 -1.927306022 0.437480363 NS(ph)SPAPPQPAPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSPAPPQPAPGK 13 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 NS(0.5)S(0.5)PAPPQPAPGK 79.466 0.021432 35558000 86585 75834 56499 63738 72751 69658 75669 90745 91716 91683 TRUE FALSE 83201.16248 73671.28857 66709.62611 67027.52582 75091.10199 71066.53249 76595.05986 88871.08404 81304.78418 85473.22875 0.973417802 0.861922378 0.780473923 0.784193212 0.878533584 0.831447852 0.896129244 1.039753445 0.951230992 1 16.383185 1.927367906 4.468587299 0.997482632 0.847850096 0.584791216 0.054626116 0.155164562 5.641454804 0.026123733 0.015374117 84.59952146 -1.927367906 -0.149632536 S(ph)SEDLAGPLPSSVSSSSTTSSKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSEDLAGPLPSSVSSSSTTSSKPK 24 1 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 S(0.847)S(0.153)EDLAGPLPSSVSSSSTTSSKPK;S(0.877)S(0.123)EDLAGPLPSSVSSSSTTSSKPK 260.97 2.95E-44 1872810000 1195570 1101620 919810 986780 970360 997260 1085940 1384120 1321050 1230460 TRUE FALSE 1148845.803 1070202.876 1086040.128 1037707.834 1001572.511 1017425.28 1099230.059 1355537.438 1171089.942 1147119.848 1.001504598 0.932947745 0.946753846 0.904620241 0.873119328 0.886938956 0.958252148 1.18168772 1.020895893 1 20.1295847 1.92743007 7.690566625 1.084345849 0.922491875 0.560650851 0.05620462 0.186522678 17.74465796 0.023598713 0.014768275 84.61163171 -1.92743007 -0.161853974 KQEYLENR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQEYLENR 8 1 Q96CF2 Q96CF2 CHMP4C Charged multivesicular body protein 4c 0 78.098 0.045502 0 487070 374690 421290 392850 453520 395700 502180 567360 664820 606570 FALSE TRUE 468034.7659 364004.2081 497426.4745 413125.0356 468107.8827 403701.3251 508325.8291 555643.8177 589352.4208 565486.4736 0.827667482 0.643700999 0.879643453 0.730565725 0.827796781 0.71390094 0.898917751 0.982594357 1.042204276 1 19.10913299 1.92750168 2.368121214 1.013361526 0.770469687 0.725842861 0.065484174 0.142272041 1.458260107 0.034063611 0.017451025 84.62558422 -1.92750168 -0.242891839 THTTALAGRS(ph)PSPAS(ph)GR ddPTM_BT-474_Pertuzumab_2h_R1 1 THTTALAGRSPSPASGR 17 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(0.991)PS(0.119)PAS(0.889)GR 129.43 1.91E-05 4482800000 2102300 2931500 1725900 2281400 2322900 2670500 2020100 321230 1830100 1410400 TRUE FALSE 2020139.792 2847896.49 2037808.522 2399143.327 2397618.188 2724499.34 2044822.588 314596.4882 1622354.72 1314872.352 1.536377116 2.165911 1.549814718 1.824620713 1.823460798 2.072063753 1.555149126 0.239260098 1.233849596 1 20.32649132 1.927581767 6.549409196 0.767277235 1.829969088 0.693454859 0.298047142 0.116157666 8.625271304 0.120011019 0.074066848 84.6411913 -1.927581767 1.062691853 EGLGQGQS(ph)LEQLEALVQTK ddPTM_BT-474_Pertuzumab_2h_R1 6 EGLGQGQSLEQLEALVQTK 19 0 Q9NSC5-2;Q9NSC5;M0QYF9;Q9NSC5-5 Q9NSC5-2 HOMER3 Homer protein homolog 3 1 EGLGQGQS(1)LEQLEALVQTK;EGLGQGQS(1)LEQLEALVQTK;EGLGQGQS(1)LEQLEALVQTK;EGLGQGQS(1)LEQLEALVQTK;EGLGQGQS(1)LEQLEALVQTK;EGLGQGQS(1)LEQLEALVQTK 379.88 1.30E-108 1741242000 830440 813943 679634 785601 785029 779920 844226 1014968 1035593 1021593 TRUE FALSE 797985.4867 790730.1426 802458.9822 826145.9618 810280.1707 795690.5168 854557.8903 994008.5561 918036.8242 952399.5962 0.837868359 0.830250397 0.842565437 0.867436279 0.850777524 0.835458688 0.89726822 1.043688553 0.963919796 1 19.86120748 1.927592561 4.16068942 1.003543863 0.845678161 0.920934273 0.02072361 0.053951735 1.700132637 0.009518966 0.005539638 84.64329503 -1.927592561 -0.157865702 FHTVSGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHTVSGSK 8 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 136.8 0.00077559 3464500000 7963700 8163000 6372100 6391900 6607600 7169600 7198000 3823900 8126200 7641500 FALSE TRUE 7652469.8 7930199.232 7523680.217 6721786.725 6820139.455 7314574.224 7286091.277 3744935.129 7203747.844 7123934.399 1.074191503 1.113176903 1.056113068 0.943549779 0.957355735 1.026760469 1.022762264 0.525683551 1.011203563 1 22.7642428 1.927630862 24.99958436 0.788250479 1.026383124 0.243283619 0.136314448 143.1764309 49458.92132 0.054305117 0.03504813 84.65076008 -1.927630862 0.238132645 TEPATGFIDGDLIESFLDISRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEPATGFIDGDLIESFLDISRPK 23 1 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 201.38 2.07E-24 222622000 154645 145811 124873 116531 136891 138946 139842 156023 165013 149229 FALSE TRUE 148601.3024 141652.613 147440.3289 122545.1789 141294.2233 141755.5833 141553.4282 152801.0705 146281.416 139121.5869 1.068139789 1.018192907 1.059794761 0.88084949 1.015616817 1.018933053 1.017479971 1.098327542 1.051464545 1 17.08598677 1.927727648 9.064562791 1.0602938 1.008128856 0.09211259 0.052825172 0.780611397 93.08989 0.022332999 0.014130152 84.66962719 -1.927727648 -0.052164944 S(ph)ATPVNCEQPDILVSSTPINEGQTVLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SATPVNCEQPDILVSSTPINEGQTVLDK 28 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.5)AT(0.5)PVNCEQPDILVSSTPINEGQTVLDK 141.78 7.92E-08 133210000 140620 156420 113060 125130 134610 138910 146320 157060 183760 166780 TRUE FALSE 135124.4149 151959.0548 133492.457 131587.9743 138939.8529 141718.8554 148110.7079 153816.6561 162900.3352 155483.842 0.869057602 0.977330202 0.858561605 0.846312855 0.893596731 0.911469986 0.952579419 0.989277433 1.047699446 1 17.24640514 1.9277888 1.478946441 1.022221499 0.890442463 0.702074317 0.035497946 0.228618096 0.931120001 0.025647341 0.011555948 84.6815503 -1.9277888 -0.131779036 SHPLDLS(ph)PNVQSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SHPLDLSPNVQSR 13 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2;H0YBM4 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 SHPLDLS(1)PNVQSR;SHPLDLS(1)PNVQSR;SHPLDLS(1)PNVQSR 99.813 0.0017315 741520000 1252520 1207210 1033200 1102810 1152320 1175790 1202180 1242160 1444300 1294960 TRUE FALSE 1203570.134 1172781.553 1219922.223 1159726.156 1189385.419 1199565.279 1216892.638 1216508.962 1280349.119 1207251.206 0.996950865 0.971447821 1.010495759 0.96063367 0.985201268 0.993633532 1.007986269 1.007668459 1.06054905 1 20.20329447 1.927836299 1.479764519 1.027205954 0.984882111 0.429651343 0.019298273 0.355835785 1.450873533 0.012823523 0.005778735 84.69081249 -1.927836299 -0.042323843 YFLHQSHEER ddPTM_BT-474_Pertuzumab_2h_R1 1 YFLHQSHEER 10 0 G3V192;P02794;E9PRK8;E9PKY7 G3V192;E9PKY7 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 0 145.55 1.75E-05 167620000 35330 58775 46061 77348 48895 54709 48938 18402 40406 48693 FALSE TRUE 33949.26454 57098.79455 54385.24732 81339.93955 50467.75208 55815.25346 49536.91788 18021.99227 35819.28028 45394.97974 0.747863855 1.257821787 1.198045415 1.791826762 1.11174743 1.229546831 1.091242207 0.397004082 0.789058184 1 15.47024514 1.927857435 6.112563667 0.674903373 1.238012149 0.385988448 0.275945965 0.206732394 13.68949355 0.12018291 0.073660871 84.69493419 -1.927857435 0.563108776 FGHVDQENS(ph)PSFMFQGSSNTEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FGHVDQENSPSFMFQGSSNTEFK 23 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 FGHVDQENS(0.791)PS(0.209)FMFQGSSNTEFK 150.48 5.38E-08 90828000 61341 71070 74294 77320 92550 96880 69187 42775 59103 56636 TRUE FALSE 58943.7259 69043.15318 87720.57846 81310.49447 95526.9548 98838.97998 70033.7312 41891.6813 52393.87522 52799.99327 1.116358587 1.307635644 1.661374804 1.539971682 1.809222859 1.871950617 1.326396593 0.793403156 0.992308369 1 15.68825013 1.927887433 4.713077699 0.925908529 1.559971912 0.625629464 0.214838317 0.149483416 6.064258623 0.106772683 0.063358537 84.70078447 -1.927887433 0.634063383 NHETDGGS(ph)AHGDDDDDGPHFEPVVPLPDK ddPTM_BT-474_Pertuzumab_2h_R1 1 NHETDGGSAHGDDDDDGPHFEPVVPLPDK 29 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.22)DGGS(0.78)AHGDDDDDGPHFEPVVPLPDK 139.96 1.47E-07 92974000 185910 143080 182040 174930 163350 154770 158230 16283 186500 109230 TRUE FALSE 178644.4317 138999.4985 214938.6775 183958.1583 168604.3011 157899.5554 160166.4661 15946.75036 165329.3019 101831.7548 1.754309665 1.364991684 2.110723495 1.806491095 1.655714383 1.550592502 1.572853835 0.156598994 1.623553499 1 16.63582799 1.927888356 10.54375612 0.839438368 1.699655556 0.458779862 0.377681749 0.501517213 71.7362554 0.150542512 0.095952632 84.70096447 -1.927888356 0.860217187 RDNYVPEVSALDQEIIEVDPDTK ddPTM_BT-474_Pertuzumab_2h_R1 4 RDNYVPEVSALDQEIIEVDPDTK 23 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 210.4 1.07E-24 1468260000 849317 783059 775351 738784 729744 762959 821296 967310 1002131 924041 FALSE TRUE 816124.7527 760726.924 915474.1733 776912.7308 753216.8785 778386.5537 831347.2661 947334.7105 888373.2902 861454.88 0.947379569 0.883072279 1.062707049 0.901861199 0.874354416 0.903572052 0.965050272 1.099691618 1.031247615 1 19.71641571 1.927991905 5.622252467 1.051239484 0.929416846 0.464863149 0.054872367 0.185672958 10.59037638 0.024529305 0.014895056 84.72116223 -1.927991905 -0.121822638 DDFTEFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDFTEFGK 8 0 O75822;O75822-3;H0YGJ7;H0YLP3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 105.57 0.01015 414870000 1213060 1155790 1074440 1158710 1125380 1101660 1268770 1429440 1520880 1592320 FALSE TRUE 1165652.274 1122828.001 1268615.209 1218511.162 1161578.87 1123936.32 1284297.587 1399921.564 1348236.078 1484470.748 0.785230881 0.756382706 0.854590911 0.820838783 0.78248687 0.757129315 0.8651552 0.943044224 0.908226774 1 20.50151723 1.928007952 2.872298004 0.94482156 0.794876562 0.801400609 0.035010366 0.120092566 1.793079686 0.018593327 0.010033434 84.72429267 -1.928007952 -0.149944998 GTEDELDKYSEALKDAQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GTEDELDKYSEALKDAQEK 19 2 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;D6RGJ6;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;H0YKP3;A0A087WTJ7 J3KN67;P09493-3 TPM3;TPM1 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain 0 ; 189.51 7.79E-15 555400000 1160760 910520 893720 752470 941230 899920 1115160 1564000 1683260 1361420 FALSE TRUE 1115396.216 884552.8611 1055235.085 791305.0669 971505.5178 918116.999 1128807.662 1531702.853 1492183.382 1269209.811 0.87881153 0.696931944 0.831411068 0.623462772 0.765441229 0.723376853 0.889378298 1.206816115 1.175679048 1 20.27549915 1.928058999 3.585401691 1.142896884 0.750598539 0.798656863 0.083713177 0.090756805 2.114988307 0.038719643 0.021945018 84.73425183 -1.928058999 -0.392298345 ESS(ph)PLS(ph)SRK ddPTM_BT-474_Pertuzumab_2h_R1 3 ESSPLSSRK 9 1 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 2 ESS(0.999)PLS(0.628)S(0.372)RK;ESS(1)PLS(0.622)S(0.378)RK;ES(0.006)S(0.984)PLS(0.579)S(0.431)RK 94.409 0.0058424 4822400000 1796757 2105760 1608956 2082297 1878288 2007884 1721095 1596464 1579066 1716733 TRUE FALSE 1726537.75 2045705.787 1899730.14 2189764.598 1938704.839 2048484.79 1742158.275 1563496.461 1399817.048 1600457.145 1.07877787 1.278200915 1.186992196 1.368211954 1.211344425 1.279937296 1.08853791 0.976906171 0.874635758 1 20.61005262 1.928113732 2.302057885 0.939546069 1.239026939 0.729735296 0.077241624 0.143991467 1.397597206 0.04218831 0.021449577 84.74493138 -1.928113732 0.29948087 TQS(ph)GNFYTDTLGMAEFR ddPTM_BT-474_Pertuzumab_2h_R1 6 TQSGNFYTDTLGMAEFR 17 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.032)QS(0.968)GNFYTDTLGMAEFR;T(0.011)QS(0.989)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;T(0.001)QS(0.999)GNFYTDTLGMAEFR;T(0.001)QS(0.999)GNFYTDTLGMAEFR;TQS(0.999)GNFYT(0.001)DTLGMAEFR 385.42 1.02E-121 1491793000 1423197 1245340 784820 1104395 1325215 971585 1151357 1768560 1211445 1016478 TRUE FALSE 1367576.888 1209824.123 926654.4322 1161392.958 1367841.744 991231.1144 1165447.651 1732038.618 1073926.842 947631.0397 1.443153327 1.276682666 0.977864162 1.225575049 1.44343282 1.046009547 1.229853817 1.827756316 1.133275291 1 19.85396593 1.92823982 24.99998224 1.441438977 1.226557232 0 0.250994511 301.7909214 105137.2412 0.100570244 0.064905959 84.76953869 -1.92823982 -0.214881745 KFPGYYVTGDGCQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFPGYYVTGDGCQR 14 1 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 143.38 1.47E-05 1348130000 1178200 1108630 860980 966170 1047130 1140420 1029410 886090 1172890 972720 FALSE TRUE 1132154.641 1077012.958 1016578.238 1016034.149 1080811.887 1163480.074 1042008.228 867791.9319 1039748.444 906836.808 1.24846569 1.187659068 1.121015633 1.120415648 1.191848277 1.283009317 1.149058153 0.956943878 1.146566213 1 19.79048342 1.928240384 7.149774409 1.034185068 1.187844153 0.544176354 0.064458797 0.207495723 17.89706022 0.027918731 0.017372004 84.76964876 -1.928240384 0.153659085 VLETLVTVAEEHHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLETLVTVAEEHHR 14 0 H7C5W6;F5H619;Q86XA9-2;Q86XA9 H7C5W6 HEATR5A HEAT repeat-containing protein 5A 0 59.607 0.057567 24982000 10396 7657.8 8012 12131 10505 9397.8 9828.6 1824.2 10893 10235 FALSE TRUE 9989.712827 7439.407042 9459.946626 12757.08236 10842.90287 9587.829955 9948.885347 1786.529633 9656.472307 9541.774334 1.046944989 0.77966705 0.991424267 1.336971712 1.136361277 1.004826736 1.042666175 0.187232434 1.012020613 1 13.22004185 1.928267904 24.99994073 0.635818839 1.049189696 0.218946367 0.253723322 160.8435447 56056.15555 0.102993821 0.066471475 84.77502066 -1.928267904 0.413370857 KEREEEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEREEEFK 8 2 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 137.05 0.00043023 865410000 744690 787900 522040 502210 715280 760740 676450 789660 945990 855960 FALSE TRUE 715586.6915 765429.8634 616384.2407 528129.1183 738287.6308 776122.684 684728.5974 773353.245 838605.1811 797985.0668 0.896741958 0.959203242 0.772425784 0.661828323 0.925189783 0.972603018 0.858071944 0.969132478 1.050903351 1 19.60600222 1.928271961 0.91093958 1.023065911 0.841650878 0.371624801 0.087303165 0.674167962 1.032118079 0.079697226 0.037024762 84.7758125 -1.928271961 -0.181415033 LDNNFEVNFDKDPMEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDNNFEVNFDKDPMEMR 17 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 64.65 0.040963 64941000 80930 74530 72969 84497 77653 77294 82282 105830 97863 93471 FALSE TRUE 77767.16613 72404.47737 86156.12149 88857.9003 80150.77927 78856.93764 83288.99173 103644.5735 86754.00252 87140.12591 0.892438074 0.830897094 0.988707792 1.019712783 0.919791869 0.904944041 0.955805272 1.189401237 0.995568937 1 16.41104958 1.928329745 9.314608128 1.080641524 0.928717034 0.422618268 0.06998577 0.386305532 48.07429857 0.029847733 0.018914035 84.78709284 -1.928329745 -0.15192449 CHEFLIFEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 CHEFLIFEDR 10 0 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 ; 189.72 9.80E-07 491140000 304630 317140 271320 367730 330950 341780 311470 72234 327450 289820 FALSE TRUE 292724.7228 308095.4777 320353.5595 386708.5894 341595.3073 348691.0258 315281.863 70742.34266 290279.2488 270190.2333 1.08340231 1.14029095 1.185659288 1.431245625 1.264277036 1.290538972 1.166888452 0.261824204 1.074351376 1 18.043616 1.928339227 11.58429794 0.700531148 1.236048178 0.445131119 0.223330963 0.67695789 108.1145804 0.089195167 0.057048186 84.78894408 -1.928339227 0.53551703 SEETQER ddPTM_BT-474_Pertuzumab_2h_R1 2 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 142.36 0.005803 79599000 49463 56740 42006 57408 51233 51108 54843 52002 52725 64015 FALSE TRUE 47529.93128 55121.83075 49597.41862 60370.83376 52880.95597 52141.43878 55514.18504 50928.14053 46739.87904 59679.20703 0.79642364 0.923635442 0.831066984 1.011589074 0.886086773 0.873695234 0.93020983 0.8533649 0.783185323 1 15.86494075 1.928412015 0.006903551 1.785162463 3.35E-06 0.083560287 0.070920244 10346.35822 58.14165519 7470.213324 7558.932416 84.80315604 -1.928412015 -1.785159114 THVDSHGHNVFK ddPTM_BT-474_Pertuzumab_2h_R1 4 THVDSHGHNVFK 12 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ;;; 75.739 0.011471 876420000 1292930 1352900 1238550 1370040 1205810 1375320 1200020 93143 1341490 803540 FALSE TRUE 1242400.866 1314316.617 1462383.536 1440747.929 1244595.974 1403129.913 1214706.204 91219.5645 1189209.679 749115.5201 1.658490357 1.754491239 1.952146895 1.923265358 1.661420623 1.873048782 1.621520541 0.12176969 1.587485037 1 19.51482869 1.928486705 9.07808065 0.818722861 1.802374522 0.574608675 0.345632245 0.254693879 30.77124733 0.136364843 0.086291562 84.81774172 -1.928486705 0.983651661 GTSSSHCRPQENISSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTSSSHCRPQENISSR 16 1 E7EWN3;Q9C0A6;Q9C0A6-2;Q9C0A6-3;H0Y3R4 E7EWN3 SETD5 SET domain-containing protein 5 0 ; 102.64 0.00090214 20236400 9073 15734 12152.1 17707.6 12044.7 14705.6 14309.1 40215.5 10932.4 19636.7 FALSE TRUE 8718.417129 15285.28173 14348.25479 18621.49136 12432.12871 15002.95731 14484.21905 39385.03587 9691.399784 18306.68882 0.476242166 0.834956112 0.783771163 1.017196039 0.679103077 0.819534185 0.791198189 2.151401396 0.52939119 1 14.16008325 1.928583086 24.99996454 1.38397447 0.78158237 0.181125449 0.403761737 171.0910267 59890.74591 0.157475776 0.101632019 84.83656693 -1.928583086 -0.6023921 HLPS(ph)PPLTQEVDLHSIAGPPVPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLPSPPLTQEVDLHSIAGPPVPPR 24 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR 262.98 6.39E-44 1023530000 329456 413977 333877 373428 389743 410181 353691 229097 345716 340935 TRUE FALSE 316580.4953 402170.7813 394216.001 392700.6638 402279.4376 418475.1409 358019.5763 224366.0669 306471.769 317843.1688 0.996027369 1.265312018 1.240284642 1.23551708 1.265653873 1.316608888 1.126403244 0.705901806 0.964223237 1 18.27795556 1.928624248 6.154368437 0.867268735 1.225550653 0.647026424 0.108520981 0.123639718 8.360790781 0.045545296 0.027943392 84.84460805 -1.928624248 0.358281919 FWEVISDEHGIDPTGTYHGDSDLQLDR ddPTM_BT-474_Pertuzumab_2h_R1 35 FWEVISDEHGIDPTGTYHGDSDLQLDR 27 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 321.25 1.02E-82 2.11114E+11 3127688.1 3780756.9 3165416.4 4276303.84 3758561.08 3989853.5 3782179 1863005.6 4028089.1 4051712.8 FALSE TRUE 3005454.591 3672933.415 3737477.558 4497004.394 3879458.611 4070531.071 3828466.438 1824533.883 3570837.312 3777286.683 0.795664942 0.972373485 0.98946092 1.190538281 1.027049026 1.077633607 1.013549344 0.483027643 0.945344532 1 21.84891885 1.928625562 24.98969282 0.751083364 1.017865494 0.221761057 0.160397209 157.8307157 55259.12158 0.064476019 0.041612673 84.84486485 -1.928625562 0.26678213 GKEDALVTK ddPTM_BT-474_Pertuzumab_2h_R1 4 GKEDALVTK 9 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;; 101.93 0.0033445 2207660000 4212900 4258530 3264210 3426840 3806270 3900610 4008630 4492860 4850540 4697450 FALSE TRUE 4048255.21 4137080.894 3854125.359 3603699.623 3928702.131 3979483.007 4057688.813 4400080.871 4299927.034 4379287.527 0.92440955 0.944692685 0.880080455 0.822896327 0.897109885 0.908705579 0.92656369 1.004748111 0.981878218 1 22.06226474 1.928677004 2.348326051 0.997031759 0.893942783 0.674856896 0.030668771 0.189757958 1.914054369 0.019224993 0.009835277 84.85491526 -1.928677004 -0.103088976 IPNYQLS(ph)PTKLPSINK ddPTM_BT-474_Pertuzumab_2h_R1 1 IPNYQLSPTKLPSINK 16 1 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 IPNYQLS(0.5)PT(0.5)KLPSINK 254.55 8.41E-27 5028400000 8013200 5886300 5752200 5329600 5545300 6286300 6400400 7598100 7230400 7884000 TRUE FALSE 7700035.285 5718428.487 6791750.497 5604661.295 5723669.611 6413413.293 6478730.01 7441196.58 6409635.304 7350009.658 1.047622472 0.778016459 0.924046472 0.76253795 0.778729536 0.872572091 0.881458707 1.012406368 0.872058079 1 22.80931471 1.928754514 5.65384207 0.960542025 0.853336918 0.212481216 0.086434778 0.315987117 18.35399991 0.036682708 0.022297861 84.8700609 -1.928754514 -0.107205107 YESLTDPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 YESLTDPSK 9 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ; 189.7 8.82E-05 840440000 1946830 1842620 1820010 1891910 1878780 1861140 2129500 2486100 2709900 2647100 FALSE TRUE 1870745.731 1790070.282 2148926.293 1989551.702 1939212.665 1898773.526 2155561.458 2434761.166 2402283.513 2467809.559 0.758059196 0.72536808 0.870782871 0.806201473 0.785803207 0.769416554 0.873471557 0.986608208 0.973447689 1 21.23479964 1.9288303 2.601875289 0.987172106 0.787931916 0.859152689 0.036320805 0.103227641 1.270251939 0.02072414 0.010909817 84.88487246 -1.9288303 -0.19924019 LIVENLSS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 3 LIVENLSSR 9 0 Q08170;A0A0D9SEM4;Q13243;Q13243-3;B4DJK0;B4DUA4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q08170;Q13243;Q13247 SRSF4;SRSF5;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 5;Serine/arginine-rich splicing factor 6 1 LIVENLS(0.121)S(0.879)R;LIVENLS(0.042)S(0.958)R;LIVENLS(0.149)S(0.851)R 88.596 0.013298 203843000 694760 717310 648500 619530 811260 665530 558650 624720 515280 550830 TRUE FALSE 667608.0111 696853.0211 765698.3758 651504.0175 837354.9147 678987.4726 565486.9258 611819.3137 456787.5746 513521.7935 1.300057796 1.357007687 1.491072795 1.268697893 1.630612226 1.322217443 1.101193626 1.1914184 0.889519355 1 18.97006598 1.928869465 1.288179121 0.984472562 1.406632823 0.682659153 0.118199537 0.258804343 0.79538254 0.087310014 0.038644999 84.89252771 -1.928869465 0.422160261 HSES(ph)PGATELNMCHSNCQNKPTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSESPGATELNMCHSNCQNKPTLR 24 1 Q6P0N0 Q6P0N0 MIS18BP1 Mis18-binding protein 1 1 HS(0.162)ES(0.837)PGAT(0.001)ELNMCHSNCQNKPTLR;HS(0.003)ES(0.996)PGAT(0.001)ELNMCHSNCQNKPTLR;HSES(1)PGATELNMCHSNCQNKPTLR;HSES(1)PGATELNMCHSNCQNKPTLR 318.74 5.53E-74 1341440000 933540 881810 841380 895559 925540 1041560 937860 431997 1066630 1027900 TRUE FALSE 897056.2247 856661.6422 993436.0824 941778.9073 955310.8347 1062621.057 949337.8112 423076.111 945550.6341 958279.4174 0.936111335 0.893958095 1.03668728 0.982781108 0.996902174 1.108884358 0.990669103 0.441495563 0.986717044 1 19.87008686 1.928875893 24.9999969 0.739531093 0.994829349 0.18405799 0.156940443 160.7036416 56486.30248 0.061893079 0.039945321 84.89378417 -1.928875893 0.255298256 VLS(ph)TSTDLEAAVADALK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.25)T(0.25)S(0.25)T(0.25)DLEAAVADALK 115.98 0.00018582 38166000 47091 42300 38281 44747 52174 43211 51300 61684 69254 61115 TRUE FALSE 45250.63166 41093.64542 45199.22826 47056.39803 53852.22409 44084.75603 51927.82475 60410.20384 61392.57626 56975.62661 0.794210338 0.721249556 0.793308138 0.825904002 0.945180023 0.773747629 0.911404189 1.060281517 1.077523494 1 15.79805727 1.928884518 2.917230198 1.051992737 0.811232721 0.774794581 0.057023573 0.126958804 1.956059191 0.031660534 0.017162838 84.89547012 -1.928884518 -0.240760017 HFIEITDDQFDFHTYCMR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFIEITDDQFDFHTYCMR 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 167.05 1.40E-11 170527000 84677 100852 77976 121414 110079 115606 101873 44346 103415 110246 FALSE TRUE 81367.72922 97975.7997 92067.99777 127680.1911 113619.791 117943.6325 103119.7522 43430.2396 91675.76275 102778.9402 0.79167706 0.953267269 0.895786603 1.242279701 1.105477355 1.147546689 1.003315971 0.422559714 0.891970306 1 16.64918516 1.928940822 14.36179336 0.708645431 1.031487275 0.25375225 0.185946321 2.608030116 525.7369693 0.076698178 0.049312641 84.90647709 -1.928940822 0.322841845 EFVSPS(ph)LTPPPAIAHPALPTIPER ddPTM_BT-474_Pertuzumab_2h_R1 1 EFVSPSLTPPPAIAHPALPTIPER 24 0 O94763-3;O94763;O94763-2 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 EFVS(0.016)PS(0.574)LT(0.41)PPPAIAHPALPTIPER 122.04 7.92E-05 39497000 35085 39257 42004 56501 55504 53865 45642 38138 47239 44080 TRUE FALSE 33713.83941 38137.4288 49595.05717 59417.02338 57289.33657 54954.18721 46200.58045 37350.43697 41876.62676 41094.42234 0.8203994 0.92804392 1.206856171 1.445865886 1.394090324 1.337266327 1.124254286 0.908893101 1.019034321 1 15.32665497 1.928946433 5.397369813 0.973836462 1.201264359 0.206906766 0.185061533 0.373247056 19.90148951 0.093646378 0.056615574 84.90757415 -1.928946433 0.227427897 EEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 EEPLS(1)EEEPCTSTAIAS(1)PEKK;EEPLS(1)EEEPCTSTAIAS(1)PEKK;EEPLS(0.999)EEEPCT(0.002)S(0.001)T(0.003)AIAS(0.995)PEKK 171.15 2.55E-11 1489250000 2576000 1963620 2009680 1765600 2085310 1743650 2373630 3009030 3147570 3073130 TRUE FALSE 2475327.072 1907619.48 2372873.881 1856722.828 2152385.89 1778907.798 2402679.194 2946892.479 2790271.049 2864984.168 0.863993281 0.665839449 0.828232808 0.648074376 0.751273223 0.620913657 0.838636116 1.028589446 0.973921979 1 21.45009574 1.928992317 3.952776122 0.997553315 0.728079339 0.732823898 0.073025665 0.108204542 3.087569851 0.032334981 0.018675149 84.91654517 -1.928992317 -0.269473976 GMKDDKEEEEDGTGS(ph)PQLNNR ddPTM_BT-474_Pertuzumab_2h_R1 12 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGT(0.006)GS(0.994)PQLNNR;GMKDDKEEEEDGT(0.083)GS(0.917)PQLNNR;GMKDDKEEEEDGT(0.053)GS(0.947)PQLNNR;GMKDDKEEEEDGT(0.014)GS(0.986)PQLNNR;GMKDDKEEEEDGT(0.149)GS(0.851)PQLNNR;GMKDDKEEEEDGT(0.002)GS(0.998)PQLNNR;GMKDDKEEEEDGT(0.003)GS(0.997)PQLNNR;GMKDDKEEEEDGT(0.228)GS(0.772)PQLNNR;GMKDDKEEEEDGT(0.017)GS(0.983)PQLNNR;GMKDDKEEEEDGT(0.005)GS(0.995)PQLNNR;GMKDDKEEEEDGT(0.276)GS(0.724)PQLNNR;GMKDDKEEEEDGT(0.067)GS(0.933)PQLNNR 249.25 6.38E-31 18603480000 7775250 6143141 5694787 5253507 6156957 6093812 7070870 8148040 9340630 8540720 TRUE FALSE 7471384.634 5967944.633 6723961.691 5524641.126 6355001.114 6217033.054 7157405.422 7979780.127 8280320.842 7962249.427 0.93835099 0.749529977 0.844480163 0.693854315 0.798141426 0.780813652 0.898917509 1.002201727 1.039947432 1 22.92474464 1.928994943 2.28354633 1.020037112 0.795137948 0.710583664 0.060832302 0.152397645 1.456460211 0.033440347 0.016974809 84.9170588 -1.928994943 -0.224899165 VYIGEEEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VYIGEEEKK 9 1 Q8TBX8;Q8TBX8-3;Q8TBX8-2;H0YIJ6 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 113.12 0.0029705 310700000 553450 500600 453310 396550 486880 495450 544340 640430 710200 686460 FALSE TRUE 531820.5621 486323.3781 535233.2008 417015.993 502540.9374 505468.3385 551001.7958 627204.8967 629581.0734 639965.4528 0.831014487 0.759921299 0.836347022 0.651622664 0.785262603 0.789836914 0.860986782 0.980060555 0.983773531 1 19.2876345 1.929007312 1.844723597 0.996155816 0.769933041 0.799058265 0.047695949 0.143032731 0.904155325 0.029775281 0.014192441 84.91947728 -1.929007312 -0.226222776 LVEVNGENVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVEVNGENVEK 11 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 129.89 0.0005481 111580000 207850 210650 181420 190640 208780 208970 217750 260030 274440 262920 FALSE TRUE 199726.9922 204642.4682 214206.6297 200478.9532 215495.5983 213195.5166 220414.8896 254660.2896 243286.7217 245112.1942 0.814839069 0.834893053 0.873912578 0.817906893 0.879171267 0.869787475 0.899240816 1.03895398 0.992552502 1 17.90308273 1.929049905 2.884898724 1.013421405 0.849133661 0.896464703 0.024523638 0.075976799 1.145170597 0.012892674 0.006970968 84.92780609 -1.929049905 -0.164287745 KEEELQGALAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEEELQGALAR 11 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;;; 188.91 4.72E-06 1097210000 1724980 1810870 1504240 1657480 1717900 1751330 1793980 1928640 2164580 2080240 FALSE TRUE 1657565.875 1759225.761 1776089.63 1743022.741 1773157.814 1786743.093 1815935.264 1888812.91 1918865.953 1939343.492 0.854704637 0.907124379 0.915820038 0.89876948 0.914308281 0.921313372 0.936365977 0.973944491 0.989440994 1 20.88713692 1.929062558 0.680992637 1.005645577 0.892141924 0.876145887 0.014964961 0.225666432 0.204213203 0.013480583 0.007441859 84.93028051 -1.929062558 -0.113503653 QISSLRDEVEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 QISSLRDEVEAK 12 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 216.88 3.47E-11 2978410000 3202700 3362630 2787200 2755230 3321700 3173670 3256090 3515870 3958050 3769800 FALSE TRUE 3077534.943 3266731.085 3290909.041 2897427.75 3428545.497 3237843.782 3295939.003 3443266.056 3508748.757 3514468.088 0.875675882 0.929509389 0.936388938 0.824428527 0.975551751 0.921289851 0.937820154 0.97974031 0.998372633 1 21.74487492 1.929065308 0.819173724 1.005948617 0.902836755 0.515551684 0.036683669 0.493083082 0.617795931 0.030758396 0.015003042 84.93081811 -1.929065308 -0.103111862 VTEGLTDVILYHQPDDK ddPTM_BT-474_Pertuzumab_2h_R1 8 VTEGLTDVILYHQPDDK 17 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;;; 288.16 6.45E-37 11673000000 10146120 8967960 7834230 8333990 9057730 9121090 9369650 10128650 11588580 10557470 FALSE TRUE 9749598.413 8712202.561 9250049.633 8764108.223 9349080.111 9305524.689 9484318.579 9919489.838 10273092.98 9842403.153 0.990570927 0.88517026 0.93981617 0.890443938 0.949877786 0.945452502 0.963618177 1.0078321 1.043758605 1 23.23057918 1.92908621 1.479470702 1.02443942 0.927865614 0.611840009 0.029868009 0.239930429 0.977824855 0.019713288 0.008891952 84.93490583 -1.92908621 -0.096573806 LLEPPVLTLDPNDENLILEIPDEKEEATS(ph)NSPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEPPVLTLDPNDENLILEIPDEKEEATSNSPSK 34 1 P21675-10;P21675-11;P21675-8;P21675-6;P21675-7;P21675-3;P21675-5;P21675-9;P21675;P21675-2;P21675-12;P21675-4 P21675-10 TAF1 Transcription initiation factor TFIID subunit 1 1 LLEPPVLTLDPNDENLILEIPDEKEEAT(0.105)S(0.566)NS(0.276)PS(0.052)K;LLEPPVLTLDPNDENLILEIPDEKEEAT(0.077)S(0.423)NS(0.423)PS(0.077)K 171.15 7.40E-15 86472000 132681 102211 102857 95793 118152 104356 127999 164645 173541 164766 TRUE FALSE 127495.6798 99296.04236 121445.5479 100736.8882 121952.4664 106466.1498 129565.4901 161245.0232 153841.3532 153606.2521 0.830016214 0.646432297 0.790628938 0.655812422 0.793929054 0.693110784 0.843490993 1.049729559 1.001530544 1 17.22887741 1.929163145 3.342159353 1.018668097 0.733223369 0.822994062 0.058359272 0.085981595 1.740835363 0.026256897 0.014684079 84.9499534 -1.929163145 -0.285444728 AADAVEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AADAVEDLR 9 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 103.56 0.0079146 303500000 1444100 1085500 999440 863400 1272400 1042100 1122800 610400 1448200 1001100 FALSE TRUE 1387662.975 1054542.603 1180061.04 907960.1775 1313327.902 1063171.976 1136541.162 597795.0267 1283806.407 933294.6053 1.486843455 1.129913959 1.26440358 0.972854844 1.407195428 1.1391601 1.217773205 0.640521249 1.375563943 1 19.83197303 1.929207878 24.99853294 0.956350943 1.222186307 0.177250252 0.214713989 210.2104579 74229.81947 0.083133817 0.053654086 84.95870375 -1.929207878 0.265835365 YTFDFS(ph)EEEDDDADDDDDDNNDLEELK ddPTM_BT-474_Pertuzumab_2h_R1 2 YTFDFSEEEDDDADDDDDDNNDLEELK 27 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 YTFDFS(1)EEEDDDADDDDDDNNDLEELK;YT(0.003)FDFS(0.997)EEEDDDADDDDDDNNDLEELK 368.39 5.62E-127 183259000 114856 97643 77977 152606 94029 75887 143672 199667 221130 202206 TRUE FALSE 110367.3005 94858.31724 92069.17849 160482.0139 97053.52818 77421.48713 145430.3009 195543.8067 196028.2495 188510.4075 0.585470595 0.503199364 0.488403689 0.851316466 0.514844403 0.410701394 0.771470938 1.037310402 1.039880249 1 17.52428465 1.929278815 3.37463108 1.024073684 0.564695468 0.778682147 0.111107936 0.11564524 2.388358334 0.056960802 0.031923226 84.97258204 -1.929278815 -0.459378216 EPLIPAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 EPLIPASPK 9 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK 99.5 0.0055543 2159760000 2900420 2686430 2463470 2526650 2759440 2639080 2507270 2608090 2736690 2576240 TRUE FALSE 2787068.38 2609815.647 2908673.829 2657050.709 2848199.894 2692444.006 2537954.72 2554232.03 2426032.424 2401748.97 1.160432841 1.086631317 1.21106488 1.106298261 1.185885756 1.121034729 1.056711068 1.063488342 1.010110738 1 21.19565394 1.929294413 1.096841571 1.007576846 1.149413389 0.712535183 0.036090839 0.261810365 0.579347284 0.02720047 0.012081901 84.97563399 -1.929294413 0.141836543 GVPEKS(ph)PVLEK ddPTM_BT-474_Pertuzumab_2h_R1 6 GVPEKSPVLEK 11 1 O00515;E9PDI4;A0A0J9YYF6 O00515 LAD1 Ladinin-1 1 GVPEKS(1)PVLEK;GVPEKS(1)PVLEK;GVPEKS(1)PVLEK;GVPEKS(1)PVLEK;GVPEKS(1)PVLEK;GVPEKS(1)PVLEK 188.59 1.87E-06 5896960000 8614330 7986890 7352470 6922290 7830170 7638850 8260410 9364520 10163950 9416190 TRUE FALSE 8277672.46 7759111.717 8681224.884 7279550.216 8082034.529 7793312.781 8361503.369 9171139.39 9010181.007 8778423.064 0.942956656 0.883884459 0.988927604 0.829254886 0.920670429 0.887780496 0.952506311 1.044736546 1.026400863 1 23.06553037 1.929464926 3.772323216 1.026163313 0.90865431 0.616911098 0.0403563 0.142229161 3.691933395 0.018368021 0.010524012 85.00900369 -1.929464926 -0.117509003 HHGPQTLYLPVTLSSIPVFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 HHGPQTLYLPVTLSSIPVFQR 21 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 130.05 8.96E-06 468500000 281440 350400 242790 268880 221570 240600 237690 18981 242430 177460 FALSE TRUE 270441.0137 340406.9351 286667.5538 282756.929 228697.0003 245465.0968 240598.9213 18589.03572 214910.3627 165440.4761 1.634672602 2.057579518 1.732753438 1.709115784 1.382352164 1.483706422 1.45429297 0.112360869 1.299019247 1 17.33595272 1.929593169 7.669348966 0.718983588 1.659907672 0.581738312 0.325328306 0.186865148 18.26470408 0.137763255 0.086230131 85.03410972 -1.929593169 0.940924083 IDENS(ph)DKEMEVEES(ph)PEKIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDENSDKEMEVEESPEKIK 19 2 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 2 IDENS(1)DKEMEVEES(1)PEKIK 207.07 1.80E-16 218260000 386390 209030 196720 130100 248950 194820 266050 325370 395270 292260 TRUE FALSE 371289.4516 203068.6691 232271.68 136814.4766 256957.7028 198759.3939 269305.9995 318650.9958 350400.6067 272464.9699 1.362705275 0.745301934 0.852482725 0.502136024 0.943085282 0.729486047 0.988405958 1.169511794 1.286039108 1 18.05571123 1.929652883 3.310199214 1.166675901 0.838683091 0.270162594 0.21535425 0.299399488 5.949644892 0.104797008 0.05851261 85.0458024 -1.929652883 -0.327992811 HSSSPLS(ph)PGGPTHLTKPTTTSSSER ddPTM_BT-474_Pertuzumab_2h_R1 2 HSSSPLSPGGPTHLTKPTTTSSSER 25 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 HSSS(0.001)PLS(0.999)PGGPTHLTKPTTTSSSER;HSSSPLS(1)PGGPTHLTKPTTTSSSER 160.52 1.33E-11 1335200000 283510 594120 394390 704260 453500 547490 450110 248840 359690 444730 TRUE FALSE 272430.1158 577176.2793 465665.0462 740606.943 468087.2394 558560.6229 455618.5808 243701.367 318859.4991 414608.041 0.657078708 1.392101026 1.123145236 1.78628215 1.128987364 1.347201616 1.098914 0.587787363 0.769062506 1 18.66138857 1.929665876 4.989787557 0.754177579 1.25873087 0.338792625 0.281171811 0.216307311 9.956875568 0.122648358 0.073442001 85.04834671 -1.929665876 0.504553292 HGPSSSHMHNTGADS(ph)PSCSNGVASTK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGPSSSHMHNTGADSPSCSNGVASTK 26 0 A0A0D9SEU5;Q6VN20;R4GMX8;Q6VN20-2;Q6VN20-3 A0A0D9SEU5 RANBP10 Ran-binding protein 10 1 HGPS(0.006)S(0.006)S(0.006)HMHNT(0.03)GADS(0.799)PS(0.151)CS(0.001)NGVASTK;HGPS(0.135)S(0.135)S(0.029)HMHNT(0.135)GADS(0.494)PS(0.071)CSNGVASTK 83.944 0.023847 176134000 120012 209970 158283 203502 135529 182338 150109 5415.8 149162 103567 TRUE FALSE 115321.7984 203981.8612 186888.2591 214004.7626 139888.4134 186024.9993 151946.0788 5303.961837 132229.7551 96552.31484 1.194397033 2.112656351 1.935616556 2.216464338 1.448835417 1.926675705 1.573717617 0.054933554 1.369514085 1 16.55902323 1.929666393 7.635748232 0.723911057 1.821978217 0.532041961 0.416913944 0.194277146 18.88724936 0.168424251 0.105388343 85.048448 -1.929666393 1.09806716 EPVS(ph)PMELTGPEDGAASSGAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EPVSPMELTGPEDGAASSGAGR 22 0 A0A0C4DFL8;F5GX28;O94953;K7EQ54 A0A0C4DFL8 KDM4B Lysine-specific demethylase 4B 1 EPVS(1)PMELTGPEDGAASSGAGR 205.21 1.13E-22 321430000 43726 57244 38941 68448 58484 45900 48210 39220 40963 38365 TRUE FALSE 42017.13958 55611.45717 45978.50494 71980.60948 60365.19097 46828.12945 48800.0084 38410.09329 36313.05197 35766.50438 1.174762262 1.554847423 1.285518553 2.012514523 1.687757639 1.309273306 1.364405307 1.073912421 1.01528099 1 15.1263215 1.929670499 1.457459935 0.99959034 1.540986351 0.490991088 0.219019942 0.350320943 1.38497907 0.160299993 0.072136358 85.04925203 -1.929670499 0.541396012 TNS(ph)PGFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNSPGFQK 8 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6;Q5T8P6-5;Q5T8P6-4 A0A087X0H9 RBM26 RNA-binding protein 26 1 TNS(1)PGFQK;T(0.002)NS(0.998)PGFQK 91.313 0.013191 684400000 1118290 1009390 898240 897990 939150 967220 1049050 1141340 1265710 1225180 TRUE FALSE 1074585.99 980603.1855 1060571.949 944335.3715 969358.6127 986777.8511 1061888.588 1117770.93 1122031.907 1142197.467 0.94080579 0.858523341 0.928536422 0.826770675 0.848678657 0.863929294 0.929689146 0.978614436 0.982344944 1 20.12338066 1.929783932 2.389463467 0.987270613 0.875720867 0.683882742 0.033189783 0.16947527 1.768152494 0.018643369 0.009594054 85.07146891 -1.929783932 -0.111549745 ADAPDAGAQS(ph)DSELPSYHQNDVSLDR ddPTM_BT-474_Pertuzumab_2h_R1 6 ADAPDAGAQSDSELPSYHQNDVSLDR 26 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 ADAPDAGAQS(0.988)DS(0.012)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(0.999)DS(0.001)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(0.946)DS(0.053)ELPSYHQNDVSLDR 300.3 8.81E-71 7627020000 799026 1125042 1013804 1198663 1101879 1176261 1056321 926402 1095327 1098430 TRUE FALSE 767799.1806 1092956.904 1197020.935 1260526.141 1137321.939 1200045.803 1069248.572 907271.475 970990.0709 1024032.358 0.749780195 1.067307 1.168928819 1.230943663 1.110630861 1.171882699 1.044155064 0.885979303 0.948202529 1 19.96582987 1.929875848 5.501361344 0.937311919 1.095508599 0.191851952 0.125261884 0.330864591 18.46127491 0.05743455 0.034820377 85.08947578 -1.929875848 0.15819668 GEGSDSKES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEGSDSKESPK 11 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 GEGS(0.002)DS(0.051)KES(0.946)PK 50.843 0.093535 391990000 968680 683290 793030 771700 851490 823120 1083900 1142400 1359900 1372100 TRUE FALSE 930822.9147 663803.2382 936348.1619 811527.5295 878878.9492 839764.0504 1097165.092 1118809.041 1205529.853 1279166.445 0.727679278 0.518934218 0.73199869 0.634419026 0.68707161 0.656493183 0.857718788 0.874639141 0.942433925 1 20.28677257 1.929880967 1.032865928 0.982271277 0.644612369 0.811849076 0.062138659 0.195721342 0.383683314 0.046682482 0.020940826 85.09047879 -1.929880967 -0.337658907 FLKS(ph)PPLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLKSPPLHK 9 1 Q9NYF8-4;E9PJA7 Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 FLKS(1)PPLHK 95.401 0.0048736 941300000 745480 748630 633190 624310 735820 768230 835140 904500 994170 1051600 TRUE FALSE 716345.8174 727279.8054 747621.5182 656530.7139 759488.3186 783764.137 845360.6931 885821.7589 881315.9895 980374.1953 0.730686121 0.741838993 0.76258792 0.669673597 0.774692278 0.799454066 0.862283705 0.903554748 0.898958779 1 19.90297299 1.929987934 0.699063524 0.981779671 0.72322204 0.903581445 0.029382898 0.191775414 0.181371757 0.026631525 0.014409219 85.11143909 -1.929987934 -0.258557631 LTWHAYPEDAENKEK ddPTM_BT-474_Pertuzumab_2h_R1 4 LTWHAYPEDAENKEK 15 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 ;;; 160.47 1.03E-06 2368750000 3525720 3148220 2056340 2352890 2641340 2861060 2958700 3204630 3904540 3281420 FALSE TRUE 3387930.965 3058435.848 2427966.381 2474322.935 2726301.1 2918912.593 2994909.456 3138453.271 3461312.988 3059166.501 1.10746864 0.99976116 0.79366925 0.808822578 0.891190819 0.954152902 0.978995244 1.025917769 1.131456228 1 21.5447072 1.929991208 1.659449662 1.063921119 0.914306305 0.285729371 0.090032596 0.488088037 2.50418969 0.064867419 0.030056045 85.11208071 -1.929991208 -0.149614814 AAQSPFSIPNSSSGPYGS(ph)QDSVHSSPEDGGGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAQSPFSIPNSSSGPYGSQDSVHSSPEDGGGGR 33 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AAQSPFSIPNSSSGPYGS(0.977)QDS(0.018)VHS(0.003)S(0.003)PEDGGGGR;AAQSPFSIPNSS(0.001)S(0.002)GPY(0.009)GS(0.925)QDS(0.056)VHS(0.004)S(0.003)PEDGGGGR 120.98 8.86E-08 1657580000 276145 496160 349270 507990 387110 436070 376370 305150 332970 365300 TRUE FALSE 265352.9481 482010.0026 412390.8585 534207.4248 399561.7447 444887.6342 380976.1286 298848.5459 295172.6415 340557.9056 0.779171306 1.415354025 1.21092728 1.568624354 1.173256407 1.306349454 1.118682381 0.877526379 0.866732607 1 18.3775406 1.930065443 3.181053398 0.905021702 1.2597097 0.359927429 0.193748388 0.250672128 4.598432924 0.093964824 0.052029198 85.12663036 -1.930065443 0.354687998 ILEMDKEENRR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILEMDKEENRR 11 2 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 0 159.99 1.58E-05 272170000 275510 287360 238300 272560 251190 274510 277100 306390 334210 296690 FALSE TRUE 264742.7646 279164.7742 281366.111 286626.8543 259269.7545 280060.7803 280491.2327 300062.9394 296271.8819 276594.922 0.957149765 1.009291031 1.017249734 1.036269401 0.937362669 1.012530448 1.014086703 1.084846161 1.07113999 1 18.07741514 1.930101764 4.637422322 1.059956129 0.996932263 0.345564833 0.03443238 0.21721996 8.652617519 0.015453503 0.009162904 85.13375 -1.930101764 -0.063023866 DKEVS(ph)DDEAEEKEDKEEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DKEVSDDEAEEKEDKEEEK 19 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEKEDKEEEK;DKEVS(1)DDEAEEKEDKEEEK;DKEVS(1)DDEAEEKEDKEEEK;DKEVS(1)DDEAEEKEDKEEEK;DKEVS(1)DDEAEEKEDKEEEK 249.78 4.92E-25 16816690000 14286010 6280130 10116630 5300470 9081810 6066640 11742110 17671340 20843130 13517670 TRUE FALSE 13727696.94 6101026.841 11944930.08 5574027.892 9373934.667 6189311.617 11885813.45 17306420.65 18477105.26 12602106.17 1.08931767 0.484127554 0.947851885 0.442309231 0.743838731 0.491133112 0.943160873 1.373295894 1.466191842 1 23.58716153 1.930103528 3.820719713 1.307228772 0.691575665 0.571329278 0.223811216 0.146271851 3.905799622 0.099221198 0.057012648 85.13409592 -1.930103528 -0.615653107 ERSDYDRS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 3 ERSDYDRSR 9 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A087X0F4 C9JUL9;Q9BXP5-4;REV__Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 1 ERSDYDRS(1)R;ERSDYDRS(1)R;ERSDY(0.001)DRS(0.999)R 100.69 0.0035373 697439000 253965 272580 151702 195116 209975 249410 191662 172419 172917 185462 TRUE FALSE 244039.767 264806.2853 179117.926 205185.9601 216729.0366 254453.2411 194007.6169 168858.4874 153288.1871 172900.4935 1.41144633 1.531553091 1.035959599 1.186728597 1.253489982 1.471674464 1.12207671 0.976622356 0.886568823 1 17.39958246 1.930126639 3.204221606 0.95383122 1.303939591 0.576381831 0.138231396 0.198995737 3.704717345 0.07375686 0.040907959 85.13862644 -1.930126639 0.350108371 HS(ph)SPHQS(ph)EDEEDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 2 HS(0.817)S(0.183)PHQS(1)EDEEDPR 95.5 0.0019774 454430000 653310 785950 566910 642980 609080 658840 636570 419890 750850 547340 TRUE FALSE 627777.9229 763535.4755 669363.2478 676164.2749 628671.6114 672162.1962 644360.5341 411219.1248 665616.6558 510268.1743 1.230290178 1.496341559 1.311787177 1.325115516 1.232041587 1.317272427 1.262788013 0.805888248 1.304444779 1 18.96089614 1.930258529 8.990254824 1.018981043 1.320218759 0.477752625 0.132005506 0.315770417 38.6955975 0.052670397 0.033317407 85.16448582 -1.930258529 0.301237716 STSESFIQHIVSLVHHVK ddPTM_BT-474_Pertuzumab_2h_R1 1 STSESFIQHIVSLVHHVK 18 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 170.11 5.76E-12 467830000 123100 160360 136310 166690 149850 165420 154270 40214 168670 150870 FALSE TRUE 118289.1159 155786.6898 160944.2492 175292.8909 154670.0613 168764.9057 156158.0024 39383.56685 149523.2887 140651.4405 0.841008919 1.107608207 1.14427729 1.246292894 1.09966923 1.199880393 1.110248156 0.280008272 1.063076839 1 17.1017648 1.930273608 24.98972219 0.69955292 1.117674811 0.288477121 0.223475594 147.2082025 52758.36077 0.087747583 0.056631763 85.16744286 -1.930273608 0.418121892 NS(ph)QKHSPTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 2 NS(0.249)QKHS(0.249)PT(0.249)S(0.249)EPT(0.003)PPGDALPPVS(0.423)S(0.423)PHT(0.154)HR 69.248 0.0062086 391940000 101590 133600 129710 139220 132760 131310 119150 23171 111510 114990 TRUE FALSE 97619.75049 129789.8588 153151.4824 146405.1609 137030.346 133965.1782 120608.1933 22692.51075 98851.85229 107201.6249 0.910618198 1.210707944 1.428630234 1.365699084 1.278248778 1.249656228 1.125059377 0.21168066 0.922111511 1 16.70996725 1.930394823 8.560249065 0.632330247 1.249685881 0.493434414 0.23642144 0.251901035 29.03409892 0.097142652 0.061271977 85.19121703 -1.930394823 0.617355633 HSHS(ph)HS(ph)PMSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 HS(0.442)HS(0.558)HS(0.99)PMS(0.008)T(0.002)R 67.234 0.031971 24606000 28314 32898 30632 40227 32827 35999 29731 4166.5 31633 17802 TRUE FALSE 27207.45758 31959.78125 36167.88381 42303.12029 33882.91027 36726.92444 30094.85687 4080.460319 28042.15446 16596.25468 1.639373346 1.925722511 2.179279873 2.54895584 2.041599801 2.21296462 1.813352316 0.245866335 1.689667638 1 14.01857008 1.930524954 7.158829386 0.919150184 2.099223277 0.619141842 0.389996292 0.157698093 14.07107054 0.16269713 0.101304928 85.21674741 -1.930524954 1.180073093 NSSS(ph)PVSPASVPGQR ddPTM_BT-474_Pertuzumab_2h_R1 3 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 NSS(0.051)S(0.949)PVSPASVPGQR;NSS(0.007)S(0.993)PVSPASVPGQR;NSS(0.001)S(0.999)PVSPASVPGQR 236.67 1.08E-17 2696750000 2428860 2363660 2038400 2262610 2173080 2395740 2502380 2726440 3057650 2993180 TRUE FALSE 2333937.466 2296250.731 2406784.224 2379383.573 2242979.092 2444183.504 2533004.875 2670138.061 2710558.391 2790449.253 0.836402047 0.822896431 0.862507792 0.852688352 0.803805728 0.875910394 0.907740885 0.956884652 0.971369893 1 21.41206598 1.930748075 1.200098593 0.989992062 0.836428208 0.927177761 0.017205585 0.114170266 0.303494656 0.013497684 0.005968401 85.26053926 -1.930748075 -0.153563854 VKDSS(ph)PGEK ddPTM_BT-474_Pertuzumab_2h_R1 5 VKDSSPGEK 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 VKDS(0.037)S(0.963)PGEK;VKDS(0.121)S(0.879)PGEK;VKDS(0.152)S(0.848)PGEK;VKDS(0.093)S(0.907)PGEK;VKDS(0.064)S(0.936)PGEK 152.38 0.00021206 5076070000 12867100 9525330 8777240 7735660 8839860 9066600 10304520 12129990 13117880 12134000 TRUE FALSE 12364239.51 9253676.915 10363482.52 8134898.34 9124202.125 9249932.864 10430629.8 11879501.47 11628793.26 11312153.37 1.093004939 0.818029654 0.916137023 0.71912907 0.806584019 0.817698679 0.922072876 1.050153855 1.027991124 1 23.43137025 1.930761122 3.664855108 1.028134966 0.853673101 0.383318046 0.092565327 0.234889072 5.764850151 0.044752021 0.025530659 85.26310063 -1.930761122 -0.174461865 IDKVNEIVETNRPDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDKVNEIVETNRPDSK 16 2 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 165.71 3.90E-09 2709100000 3220500 2641300 2343700 2389400 2764400 2800700 2961300 3435700 3877900 3640800 FALSE TRUE 3094639.3 2565972.71 2767258.725 2512717.22 2853319.437 2857332.073 2997541.275 3364751.594 3437697.049 3394205.373 0.911741913 0.755986285 0.815289124 0.740296165 0.840644311 0.841826513 0.883134915 0.991322335 1.012813508 1 21.69464243 1.930813676 1.494344706 1.01439385 0.807062784 0.774467447 0.044431908 0.16833054 0.699976279 0.029783189 0.01347894 85.27341899 -1.930813676 -0.207331066 DVVICPDASLEDAKK ddPTM_BT-474_Pertuzumab_2h_R1 4 DVVICPDASLEDAKK 15 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 228.73 8.93E-13 4906400000 3072060 2553300 2198250 1994600 2457110 2448640 2656640 3015700 3439680 3001830 FALSE TRUE 2952000.499 2480482.384 2595522.675 2097541.545 2536145.175 2498153.178 2689152.755 2953424.741 3049221.947 2798513.38 1.054845948 0.886357164 0.927464808 0.749519927 0.906247293 0.892671515 0.960921886 1.055354876 1.089586338 1 21.41622921 1.930930455 2.616798213 1.055115373 0.896412522 0.444223271 0.072315672 0.245984277 3.063535551 0.039329095 0.020773046 85.29635156 -1.930930455 -0.158702851 S(ph)CSVTDAVAEQGHLPPPSAPAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCSVTDAVAEQGHLPPPSAPAGR 23 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-4 Q96PU5-7 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.547)CS(0.436)VT(0.018)DAVAEQGHLPPPSAPAGR 151.12 4.92E-08 700600000 202870 235590 151110 199750 190210 199300 154670 201890 171170 171900 TRUE FALSE 194941.6161 228871.2039 178418.9384 210059.1214 196328.2774 203329.9826 156562.8977 197720.9009 151739.4992 160257.0599 1.216430754 1.428150523 1.113329663 1.310763604 1.225083485 1.268773948 0.976948522 1.233773421 0.946850637 1 17.29002839 1.930988922 0.607089806 0.989166503 1.286002335 0.464923638 0.109627028 0.669719795 0.502677395 0.095359199 0.058306884 85.30783538 -1.930988922 0.296835832 DGVSEGQFQQVLHHELLAIR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGVSEGQFQQVLHHELLAIR 20 0 Q9UKV8-2;Q9UKV8 Q9UKV8-2 AGO2 Protein argonaute-2 0 ;; 244.74 3.76E-30 282189000 192060 198118 165599 201022 198479 202952 196498 90767 222273 198495 FALSE TRUE 184554.0829 192467.8686 195526.423 211396.7695 204863.2573 207055.8285 198902.8013 88892.62973 197041.5009 185050.7568 0.997316012 1.040081499 1.056609691 1.142371818 1.107065222 1.118913708 1.074855379 0.480368907 1.064797055 1 17.49756151 1.931085315 24.99656544 0.787391235 1.080291146 0.297992052 0.152165781 147.976607 53673.08831 0.059501977 0.038402202 85.32677173 -1.931085315 0.292899911 TFNTSTGGLLLPSDTKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TFNTSTGGLLLPSDTKR 17 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 209.54 6.71E-12 1786860000 1850470 1758030 1270610 1402190 1607590 1602660 1623710 1769560 1929780 1764810 FALSE TRUE 1778151.587 1707892.706 1500237.492 1474557.194 1659299.592 1635066.883 1643581.449 1733017.968 1710719.465 1645277.847 1.080760669 1.038057316 0.911844461 0.896235974 1.008522418 0.993793776 0.998968929 1.053328452 1.03977542 1 20.64989981 1.93110364 4.244272226 1.035760178 0.984383765 0.112936902 0.052441072 0.462265881 15.41993884 0.026646266 0.01560054 85.33037212 -1.93110364 -0.051376414 THEDIEAQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 THEDIEAQIR 10 0 O75533;B4DGZ4;A0A494C1M2;O75533-2;F8WC19 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 159.09 7.79E-06 2217600000 661640 638640 533520 682450 607310 638810 628310 225050 666950 638720 FALSE TRUE 635782.3773 620426.6125 629938.9321 717671.3263 626844.6777 651727.1759 635999.4457 220402.6389 591240.6321 595458.9255 1.067718276 1.041930158 1.057904929 1.20524069 1.052708509 1.094495603 1.068082816 0.370139114 0.992915895 1 19.18364247 1.931106399 18.49867077 0.718036353 1.086681508 0.366135452 0.171626523 9.99579702 2683.251081 0.066643004 0.042968886 85.33091432 -1.931106399 0.368645155 SIVIRPLEPQPAPHLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIVIRPLEPQPAPHLAR 17 1 Q15029;Q15029-3;Q15029-2;K7EP67 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 152.68 1.22E-07 1443920000 1569830 1711170 1439560 1816350 1627150 1747810 1620630 1592560 1696930 1750830 FALSE TRUE 1508479.308 1662369.107 1699720.515 1910092.041 1679488.757 1783151.916 1640463.755 1559673.079 1504301.621 1632244.725 0.924174718 1.0184558 1.041339261 1.170224055 1.028944209 1.092453778 1.005035415 0.955538747 0.921615244 1 20.63842595 1.931121588 3.527739051 0.955706498 1.049507601 0.287600636 0.060757547 0.302247722 6.86168974 0.030692878 0.017386009 85.33389874 -1.931121588 0.093801103 IEELDQENEAALENGIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEELDQENEAALENGIK 17 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9;Q68E03 P43243;A8MXP9 MATR3;DKFZp686L22104 Matrin-3 0 218.28 1.09E-14 57214000 76154 68940 79056 110150 91633 68450 103350 142250 139140 145960 FALSE TRUE 73177.81749 66973.8987 93343.17779 115834.8547 94580.45866 69834.1059 104614.8282 139312.4878 123345.4105 136073.9992 0.537779575 0.492187333 0.685973649 0.85126369 0.695066355 0.513206831 0.76880836 1.023799467 0.906458333 1 17.0540319 1.931464837 4.173717538 0.970536763 0.638143457 0.691983749 0.103410627 0.142474709 4.596696649 0.053016767 0.030965054 85.4013699 -1.931464837 -0.332393306 HPDSHQLFIGNLPHEVDKSELKDFFQSYGNVVELR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPDSHQLFIGNLPHEVDKSELKDFFQSYGNVVELR 35 2 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 33.813 0.073655 267820000 100270 104940 57665 52470 92072 100040 75314 9360 77774 56595 FALSE TRUE 96351.33755 101947.2139 68086.34825 55177.98299 95033.5795 102062.8773 76235.71526 9166.712729 68945.42158 52761.77024 1.826158165 1.932217465 1.290448519 1.045794763 1.801182543 1.934409647 1.444904424 0.173737778 1.306730636 1 15.68720535 1.931465816 8.791314174 0.750349693 1.622432901 0.479649658 0.376027134 0.316866973 38.43400328 0.161235429 0.101875282 85.40156237 -1.931465816 0.872083208 RHS(ph)HS(ph)HS(ph)PMSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 3 RHS(0.999)HS(0.998)HS(0.99)PMS(0.009)T(0.003)R 65.298 0.02874 89900000 51372 52762 31185 46446 48318 53371 42856 11456 49347 27517 TRUE FALSE 49364.32545 51257.27942 36820.82321 48843.08363 49872.19235 54450.19819 43380.48455 11219.4296 43745.33544 25653.24908 1.924291355 1.998081384 1.435327864 1.903972611 1.944088727 2.122545882 1.691032758 0.437349264 1.705255163 1 14.64685394 1.931522035 8.400032433 1.000928158 1.878357647 0.564063467 0.330332126 0.23374421 26.72312809 0.133391158 0.084049712 85.41261825 -1.931522035 0.877429489 VDIDAPDVDVHGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 7 VDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;;; 280.15 1.72E-39 28572275000 15881414 16471594 13591212 15301639 13610337 15693951 15269867 1887477 17661942 14117287 FALSE TRUE 15260750.78 16001840.27 16047446.34 16091358.42 14048125.85 16011293.44 15456744.2 1848499.94 15657032.39 13161110.58 1.159533665 1.215842704 1.219307919 1.222644421 1.067396689 1.216560969 1.174425525 0.140451669 1.189643708 1 23.6497779 1.93164475 24.99986387 0.675253292 1.184169367 0.317864841 0.259823198 147.5959085 53980.34737 0.100532814 0.06488337 85.43675592 -1.93164475 0.508916075 ISQSALPPLPGS(ph)PAIQINGEWETHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISQSALPPLPGSPAIQINGEWETHK 25 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 ISQSALPPLPGS(1)PAIQINGEWETHK 95.302 0.0064512 462440000 265060 261520 252040 275980 305900 296770 259140 236580 253620 262540 TRUE FALSE 254701.1622 254061.7057 297589.2346 290223.3609 315739.5513 302770.8927 262311.4328 231694.5403 224830.1209 244757.932 1.040624752 1.038012144 1.215851238 1.185756713 1.290007432 1.23702178 1.071717802 0.9466273 0.918581551 1 17.90099609 1.931660782 3.381463844 0.952184054 1.170227621 0.601702147 0.077280714 0.182777702 3.807030186 0.042708635 0.023995781 85.43991002 -1.931660782 0.218043567 FNVLHWHIVDDQSFPYQSITFPELSNK ddPTM_BT-474_Pertuzumab_2h_R1 1 FNVLHWHIVDDQSFPYQSITFPELSNK 27 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 118.67 0.0002025 294830000 89387 94473 69233 70334 81415 84515 77610 54301 82752 73814 FALSE TRUE 85893.65722 91778.72254 81744.94318 73963.94617 84033.78741 86223.95121 78559.8144 53179.66537 73358.33988 68814.51203 1.248191038 1.333711739 1.187902679 1.074830642 1.221163748 1.25299081 1.141616965 0.772797246 1.066030082 1 16.07042522 1.931826858 6.832760893 0.927472255 1.21555286 0.634718825 0.092457544 0.149575421 12.60714352 0.04011642 0.024889295 85.47258888 -1.931826858 0.288080605 ISELDAFLKEPALNEANLSNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISELDAFLKEPALNEANLSNLK 22 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 99.603 0.00089617 247040000 193521 224107 186569 250350 248100 208203 208713 206460 205126 210786 FALSE TRUE 185957.9854 217715.6878 220286.1685 263270.5935 256080.3618 212413.0073 211267.2921 202196.5289 181840.9564 196509.2765 0.946306397 1.107915574 1.120996283 1.339736211 1.303146429 1.080931196 1.07510086 1.028941394 0.925355585 1 17.58423789 1.931921397 1.584470638 0.97357506 1.1639286 0.337780699 0.105755012 0.471753821 2.206818563 0.078346217 0.035945702 85.49119689 -1.931921397 0.190353541 LNECIS(ph)PVANEMNHLPAHSHDLQR ddPTM_BT-474_Pertuzumab_2h_R1 4 LNECISPVANEMNHLPAHSHDLQR 24 0 P23497;P23497-2;P23497-3;P23497-4;P23497-5 P23497 SP100 Nuclear autoantigen Sp-100 1 LNECIS(1)PVANEMNHLPAHSHDLQR;LNECIS(1)PVANEMNHLPAHSHDLQR;LNECIS(1)PVANEMNHLPAHSHDLQR;LNECIS(1)PVANEMNHLPAHSHDLQR 203.83 5.23E-25 1600130000 196214 209552 185968 220913 217320 218834 194644 37209.2 217902 147801 TRUE FALSE 188545.74 203575.7821 219576.5544 232314.3464 224310.2952 223258.9734 197026.1115 36440.81702 193166.6785 137790.3066 1.368352713 1.47743181 1.593555888 1.685999198 1.62791056 1.620280692 1.429898201 0.264465752 1.401888734 1 17.07211487 1.932001628 9.695097655 0.815324861 1.564879989 0.544894219 0.273942488 0.327670053 45.22566219 0.108896739 0.069167544 85.50699185 -1.932001628 0.749555129 NDLVEALKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NDLVEALKR 9 1 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 90.05 0.018748 482600000 1014600 932650 1178100 700640 992360 996550 1014200 1115600 1168000 1151700 FALSE TRUE 974948.3103 906051.7352 1391008.877 736800.1144 1024280.161 1016700.924 1026612.083 1092562.47 1035413.537 1073694.333 0.908031532 0.843863758 1.295535269 0.686228931 0.95397743 0.946918403 0.956149298 1.017573099 0.964346653 1 20.0341519 1.932032215 5.151515959 0.994680481 0.940878892 0.028699692 0.142411763 1.025104863 51.29159374 0.061859438 0.0372513 85.51301425 -1.932032215 -0.053801589 TTCHAPGHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTCHAPGHEK 10 0 Q5T200 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 0 68.536 0.034514 24330000 19622 20779 17432 19423 16876 17553 17997 5476.4 20408 15556 FALSE TRUE 18855.15055 20186.40326 20582.35017 20425.42336 17418.83187 17907.93369 18217.25267 5363.310426 18091.3694 14502.37826 1.300141963 1.391937439 1.419239645 1.40841888 1.201101747 1.234827375 1.256156221 0.36982282 1.247476039 1 13.82400189 1.932059775 12.08869167 0.804652292 1.324131497 0.463120516 0.216279057 0.839314681 148.1531385 0.086041897 0.055108228 85.5184409 -1.932059775 0.519479204 GNAEGSS(ph)DEEGKLVIDEPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.216)S(0.784)DEEGKLVIDEPAK 156.78 8.77E-09 3155400000 1229700 947520 1035600 930710 923610 881120 1146500 1532500 1589800 1357700 TRUE FALSE 1181641.964 920497.6573 1222755.957 978744.0546 953318.7545 898936.8501 1160531.21 1500853.339 1409332.569 1265741.77 0.933556901 0.727239694 0.966039034 0.773257293 0.75317002 0.710205566 0.916878338 1.185750028 1.113443992 1 20.27155167 1.932080322 4.684956512 1.111277398 0.809341555 0.676472453 0.089183263 0.116242008 4.78990331 0.039694651 0.023604716 85.52248698 -1.932080322 -0.301935843 DLYDDKDGLRK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLYDDKDGLRK 11 2 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 83.314 0.0094489 1374770000 1893330 1672630 1355150 1281050 1509540 1564430 1650930 1848060 2147320 1803770 FALSE TRUE 1819336.57 1624928.23 1600055.75 1347165.144 1558095.725 1596063.846 1671134.575 1809896.915 1903565.236 1681599.051 1.081908657 0.966299445 0.951508476 0.801121494 0.926556021 0.949134602 0.993777068 1.076295157 1.131997092 1 20.68140233 1.932108414 2.481600963 1.078624239 0.939692552 0.375984036 0.070451217 0.293848672 3.301128603 0.04056386 0.021139217 85.52801926 -1.932108414 -0.138931687 NRVPS(ph)AGDVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 1 NRVPS(1)AGDVEK;NRVPS(1)AGDVEK;NRVPS(1)AGDVEK;NRVPS(1)AGDVEK 127.05 0.0001785 3294160000 6008530 5325030 4422710 4528520 4395290 4708030 5124510 5750240 5979100 6010120 TRUE FALSE 5773710.005 5173165.358 5221992.08 4762237.46 4536668.495 4803229.592 5187225.286 5631495.535 5300377.634 5603049.219 1.030458556 0.923276801 0.931991113 0.849936753 0.809678501 0.857252793 0.925786136 1.005076935 0.945980916 1 22.41778074 1.932199503 5.117794006 0.981453497 0.896035443 0.29086455 0.05778564 0.292325145 14.45463202 0.028047129 0.01687765 85.54595978 -1.932199503 -0.085418054 GSGEKPVSAPGDDT(ph)ESLHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVSAPGDDT(0.785)ES(0.214)LHS(1)QGEEEFDMPQPPHGHVLHR;GS(0.002)GEKPVS(0.003)APGDDT(0.5)ES(0.5)LHS(0.995)QGEEEFDMPQPPHGHVLHR 220.89 3.97E-39 713370000 376429 353313 272456 295670 339489 361224 316384 194398 350111 280903 TRUE FALSE 361717.7385 343236.8592 321694.86 310929.5641 350408.972 368528.1968 320256.002 190383.6134 310367.8671 261877.1896 1.381249505 1.310678718 1.228418788 1.187310604 1.338066032 1.407255811 1.222924389 0.726995786 1.185165717 1 17.99853088 1.932293577 8.142650296 0.947278073 1.302247501 0.610219331 0.120504485 0.200753631 22.25453387 0.049541518 0.031157252 85.56449224 -1.932293577 0.354969427 RLEEALMADMLAHVEELAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEEALMADMLAHVEELAR 19 1 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 ; 169.98 8.49E-12 138444000 131125 134624 105462 131003 137755 138961 127416 113835 130035 141066 FALSE TRUE 126000.49 130784.6553 124521.3294 137764.0805 142186.0147 141770.8866 128975.3551 111484.2675 115273.972 131511.4742 0.958095032 0.994473343 0.946847643 1.047544189 1.081168131 1.078011539 0.980715606 0.847715138 0.876531669 1 17.00482915 1.932335552 5.988125045 0.895139763 1.018624448 0.428598217 0.055950208 0.196457077 13.21257404 0.0255829 0.015676331 85.57276252 -1.932335552 0.123484685 THAPSALS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 THAPSALSPPR 11 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 THAPSALS(1)PPR;THAPSALS(1)PPR 127.32 0.00018618 576290000 248740 240080 218065 246670 234280 224098 220950 113898 224110 215916 TRUE FALSE 239018.9658 233233.1535 257474.1963 259400.6683 241815.829 228629.4151 223654.0522 111545.9665 198669.9723 201291.817 1.187425149 1.158681743 1.279109107 1.28867965 1.201319719 1.135810777 1.111093613 0.554150527 0.986974907 1 17.618929 1.932483603 7.32091468 0.803565794 1.205738586 0.62398775 0.124197745 0.151664187 14.41706049 0.051585601 0.03219532 85.60193909 -1.932483603 0.402172792 SVEDVRPHHT(ph)DANNQSACFEAPDQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEDVRPHHTDANNQSACFEAPDQK 25 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.022)VEDVRPHHT(0.978)DANNQSACFEAPDQK 230.32 4.11E-34 414350000 153050 151100 138240 143670 129250 151920 146480 10859 189200 155590 TRUE FALSE 147068.6368 146790.7759 163223.0431 151084.8259 133407.4436 154991.9265 148272.6661 10634.75786 167722.8092 145051.7507 1.013904597 1.011988999 1.125274547 1.041592571 0.919723085 1.068528478 1.022205284 0.073316991 1.156296345 1 17.14620818 1.932594138 24.99998274 0.617119392 1.030518534 0.140760165 0.275040268 202.0658192 74942.92641 0.107340877 0.069276924 85.62372902 -1.932594138 0.413399142 HLCEPGADGSETFADGVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLCEPGADGSETFADGVPR 19 0 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 0 ; 237.86 3.12E-24 863630000 314470 383580 292570 354710 332120 338760 323510 231940 329970 333610 FALSE TRUE 302180.1647 372640.674 345443.9072 373016.6256 342802.9414 345609.9593 327469.2122 227150.3579 292513.1889 311014.2976 0.971595734 1.198146442 1.110701051 1.199355234 1.10220959 1.111234956 1.052907261 0.730353427 0.94051364 1 18.24662138 1.932612532 6.481414642 0.865559798 1.119284938 0.564279126 0.087705976 0.143325202 11.15975656 0.035935839 0.022195572 85.62735566 -1.932612532 0.25372514 RPAS(ph)VSSSAAVEHEQR ddPTM_BT-474_Pertuzumab_2h_R1 5 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RPAS(0.972)VS(0.028)SSAAVEHEQR;RPAS(0.991)VS(0.008)S(0.001)SAAVEHEQR;RPAS(0.999)VS(0.001)SSAAVEHEQR;RPAS(0.973)VS(0.007)S(0.015)S(0.005)AAVEHEQR;RPAS(0.997)VS(0.003)SSAAVEHEQR 222.62 5.80E-15 5255740000 1239403 1241703 1001354 1026317 1158246 1094130 804998 898731 872189 683790 TRUE FALSE 1190965.761 1206290.846 1182320.943 1079285.343 1195502.034 1116254.058 814849.8063 880171.8908 773181.7612 637476.2942 1.868251057 1.892291301 1.854690054 1.693059574 1.875367045 1.751051872 1.278243307 1.380713132 1.212879237 1 19.28201217 1.932739115 0.736695201 1.038505198 1.877562979 0.905903635 0.096385233 0.183152069 0.189565295 0.085880426 0.044787872 85.65231679 -1.932739115 0.839057781 S(ph)VS(ph)PPPKR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)VS(1)PPPKR;S(1)VS(1)PPPKR;S(1)VS(1)PPPKR;S(1)VS(1)PPPKR 89.548 0.04839 13713000000 8679370 8107210 6911640 7076220 7142090 7852520 8166810 9081460 10351380 9257280 TRUE FALSE 8340170.625 7876000.309 8160727.097 7441424.562 7371821.811 8011303.335 8266757.864 8893924.677 9176334.739 8630276.18 0.966385137 0.91260119 0.945592809 0.862246399 0.854181449 0.928278906 0.957878716 1.030549254 1.063272432 1 23.0409753 1.932795934 2.187008394 1.037128751 0.907880579 0.700888731 0.034966852 0.171950846 1.512237156 0.021382753 0.010752322 85.66352356 -1.932795934 -0.129248171 DTAAWTVGR ddPTM_BT-474_Pertuzumab_2h_R1 5 DTAAWTVGR 9 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 164.96 0.00014393 1812880000 1295747 1207787 1051659 1115081 1162191 1073469 1118914 794687 1282820 1049933 FALSE TRUE 1245107.775 1173342.097 1241717.175 1172630.464 1199573.929 1095175.279 1132607.604 778276.4357 1137199.652 978820.1027 1.272049656 1.198731099 1.26858569 1.198004067 1.22553054 1.118872892 1.157115185 0.795116931 1.161806596 1 19.90068421 1.932872187 8.178173559 0.965111811 1.209034157 0.547701719 0.092178024 0.223623572 25.16273 0.037533061 0.023614301 85.67856558 -1.932872187 0.243922346 ADAHEEDELR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADAHEEDELR 10 0 F8W9X7;Q567U6 F8W9X7 CCDC93 Coiled-coil domain-containing protein 93 0 ; 116.23 0.0011174 172120000 196864 217340 180614 223350 225290 234180 220930 452900 242450 281930 FALSE TRUE 189170.3372 211141.676 213254.9675 234877.1203 232536.6575 238915.28 223633.8074 443547.4567 214928.0924 262834.63 0.719731404 0.803325178 0.811365563 0.893630799 0.884726101 0.908994679 0.850853662 1.687553336 0.817731257 1 18.00379585 1.932972169 24.9999733 1.250918988 0.842424706 0.307383516 0.216252544 163.4157257 60950.06341 0.084406832 0.054475217 85.69829246 -1.932972169 -0.408494283 LHQEDQACATCLILACSTAACDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHQEDQACATCLILACSTAACDR 23 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 171.29 6.33E-12 230630000 59232 56698 45166 49293 74203 64987 59181 38793 61645 68151 FALSE TRUE 56917.14796 55081.02855 53328.50091 51837.01764 76589.80688 66301.08167 59905.27478 37991.91099 54647.31804 63535.07207 0.895838253 0.866938948 0.839355323 0.815880363 1.205472889 1.043535161 0.942869392 0.597967544 0.860112632 1 15.95526558 1.93297549 24.95466297 0.77362157 0.946463315 0.115095011 0.142654193 273.8058839 101942.8005 0.060953938 0.03933975 85.69894776 -1.93297549 0.172841745 YDSSREAGTVK ddPTM_BT-474_Pertuzumab_2h_R1 3 YDSSREAGTVK 11 1 Q96J01;D6REC9 Q96J01 THOC3 THO complex subunit 3 0 ;; 74.962 0.023668 1032307000 567124 710406 551459 827830 685161 836460 660268 299082 571494 755571 FALSE TRUE 544960.1671 690145.9164 651119.9084 870554.4055 707199.8258 853373.7943 668348.5573 292905.8522 506620.397 704395.5032 0.773656511 0.979770475 0.92436693 1.235888647 1.003981176 1.211498072 0.948825701 0.415825841 0.719227188 1 19.42602617 1.932996353 8.669035101 0.654210796 1.028768998 0.352138507 0.183285964 0.333952282 40.72566388 0.075194588 0.047482205 85.70306474 -1.932996353 0.374558202 VMEIVDADEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VMEIVDADEK 10 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 167.97 1.18E-05 175349000 357150 327100 321970 338730 373800 341220 381320 455600 481200 463590 FALSE TRUE 343192.1831 317771.4283 380157.1412 356211.8959 385823.6165 348119.7022 385986.7082 446191.7008 426576.1934 432190.6364 0.794075934 0.73525755 0.879605223 0.824200864 0.892716278 0.805477197 0.893093639 1.032395576 0.987009337 1 18.72130829 1.933016788 3.379901506 1.007283908 0.824374185 0.786464786 0.042907328 0.112494816 2.346799761 0.022035667 0.0123944 85.70709746 -1.933016788 -0.182909724 DKFQETSDEFEAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DKFQETSDEFEAAR 14 1 G8JLG1;Q14683;V9GY57 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ;;; 276.64 3.78E-33 2721650000 1740480 1668970 1317060 1508360 1561180 1564210 1641470 1998130 1894180 1948090 FALSE TRUE 1672460.117 1621372.61 1555082.04 1586206.64 1611396.773 1595839.398 1661558.801 1956867.917 1679160.627 1816144.129 0.920885127 0.892755472 0.856254751 0.873392488 0.887262606 0.878696449 0.914882676 1.077484923 0.924574543 1 20.79244727 1.933076716 7.156955059 1.006933857 0.884536866 0.653791537 0.03764647 0.143339694 13.2627335 0.015361278 0.009571541 85.71892494 -1.933076716 -0.122396991 KHLEINPDHPIVETLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KHLEINPDHPIVETLR 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;; 239.58 3.20E-20 8934960000 2504450 2744210 1754420 1989210 2151710 2423580 2155110 350279 2351340 1886230 FALSE TRUE 2406573.325 2665947.818 2071482.721 2091873.366 2220921.706 2472586.448 2181484.881 343045.6162 2084425.741 1758473.962 1.368557839 1.516057602 1.178000224 1.189595872 1.262982424 1.406097845 1.240555691 0.195081431 1.185360594 1 20.74589254 1.933132421 12.81042811 0.707153168 1.314881273 0.448259379 0.257965092 1.119791874 213.4433497 0.102079323 0.065481111 85.72992058 -1.933132421 0.607728105 KAS(ph)PEPPDSAEGALK ddPTM_BT-474_Pertuzumab_2h_R1 8 KASPEPPDSAEGALK 15 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(0.586)PEPPDS(0.414)AEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK 204.81 3.12E-09 21138120000 9222850 7744620 6801860 6327550 7484570 7335580 8152620 9608630 10616200 9199260 TRUE FALSE 8862410.826 7523751.02 8031107.409 6654115.614 7725317.991 7483910.454 8252394.202 9410208.433 9411093.483 8576185.926 1.033374381 0.877284038 0.936442782 0.775882854 0.90078714 0.87263855 0.962245254 1.09724865 1.097351849 1 23.03190475 1.933178272 3.57508833 1.072232127 0.895133813 0.559470117 0.065337994 0.162825595 3.818545064 0.03129673 0.017807035 85.7389719 -1.933178272 -0.177098314 HETWSGHVISS(ph) ddPTM_BT-474_Pertuzumab_2h_R1 1 HETWSGHVISS 11 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 HETWSGHVIS(0.071)S(0.929) 198.97 0.00047766 0 62414 76096 67515 84051 75104 73611 66144 22791 62663 57880 TRUE FALSE 59974.79188 73925.81659 79716.46236 88388.88218 77519.78837 75099.46485 66953.49006 22320.35789 55549.75894 53959.73605 1.11147304 1.370018128 1.477332326 1.638052531 1.436622824 1.391768573 1.240804625 0.413648389 1.02946684 1 15.71959567 1.933225657 6.540020285 0.762340162 1.410481531 0.633371122 0.19955898 0.134839426 10.75339881 0.085656609 0.052962219 85.7483273 -1.933225657 0.64814137 PAT(ph)PGASSVEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 PATPGASSVEQLRK 14 1 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 PAT(0.845)PGAS(0.11)S(0.045)VEQLRK;PAT(0.951)PGAS(0.038)S(0.011)VEQLRK 82.121 0.0067968 1593670000 1596080 1320850 1181900 1127890 1254230 1343000 1609680 1757520 2226160 1942760 TRUE FALSE 1533703.429 1283180.651 1395495.621 1186100.538 1294573.447 1370156.38 1629379.745 1721226.598 1973455.65 1811175.135 0.846800179 0.708479609 0.770491817 0.654878987 0.714769887 0.75650132 0.899625726 0.950336919 1.089599571 1 20.78849463 1.933229484 1.544500405 1.034372805 0.732897462 0.836366553 0.054680342 0.142131619 0.631607776 0.036992757 0.016891391 85.74908297 -1.933229484 -0.301475343 FHDLLSQLDDQYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 FHDLLSQLDDQYSR 14 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75;D2KFR9;A0A669KB17;E7ENM1 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ;;; 183.06 1.45E-06 1200019000 605173 692433 682878 738255 681970 740368 708330 277232 792993 708646 FALSE TRUE 581522.1701 672685.4888 806289.2451 776356.429 703906.1844 755338.7482 716998.7544 271507.0623 702975.7591 660648.7752 0.880228938 1.018219535 1.220450677 1.175142463 1.065477165 1.143328765 1.085294912 0.410970356 1.064068815 1 19.33352396 1.933293174 24.99918285 0.75670643 1.092352799 0.265239744 0.187155857 177.8318442 66644.01986 0.07447335 0.048064783 85.76165911 -1.933293174 0.335646369 THQPERPRS(ph)PAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 THQPERPRSPAAR 13 2 Q9P2Y4;G3V2Q8 Q9P2Y4 ZNF219 Zinc finger protein 219 1 THQPERPRS(1)PAAR;THQPERPRS(1)PAAR;THQPERPRS(1)PAAR 83.792 0.005239 442824000 162766 165385 128384 142700 149231 167310 139196 55081.5 147171 110975 TRUE FALSE 156404.9248 160668.3817 151585.8447 150064.7641 154031.1506 170693.1228 140899.5223 53944.04778 130464.7651 103458.5644 1.511763919 1.552973238 1.465184111 1.450481794 1.488819718 1.649869431 1.361893267 0.521407271 1.261033978 1 16.65869355 1.933420992 7.55519695 0.887176215 1.513767759 0.690028736 0.177064897 0.140348371 14.19895187 0.070591057 0.044173804 85.78690355 -1.933420992 0.626591544 CLLADLPLPPELPGGDDLS(ph)KSPEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 CLLADLPLPPELPGGDDLSKSPEEK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0;Q9BVE2;A0A087X209 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 CLLADLPLPPELPGGDDLS(0.587)KS(0.413)PEEK;CLLADLPLPPELPGGDDLS(0.604)KS(0.396)PEEK 209.07 1.50E-25 636790000 638020 464310 445530 384070 461630 437130 540960 647190 755600 609530 TRUE FALSE 613085.473 451068.3334 526047.1818 403891.8987 476478.7482 445969.0681 547580.4303 633825.3003 669827.4557 568245.9902 1.078908578 0.793790614 0.925738484 0.710769466 0.838507893 0.78481692 0.963632722 1.115406552 1.178763189 1 19.11615607 1.933437875 3.264073909 1.107700767 0.848894699 0.531549666 0.101455637 0.178026189 3.458829659 0.048913931 0.027319293 85.79023847 -1.933437875 -0.258806067 VPHSLDLSSPNMANTVNAALKPLETLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPHSLDLSSPNMANTVNAALKPLETLSR 28 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 166.91 3.54E-12 191650000 76003 85095 59285 60596 91864 90827 77037 62154 84616 80055 FALSE TRUE 73032.71873 82668.17392 69999.11829 63723.36682 94818.88899 92663.58417 77979.80185 60870.49818 75010.74642 74632.80354 0.978560569 1.107665396 0.937913558 0.853825179 1.270472024 1.241593237 1.044846209 0.81559978 1.005064032 1 16.18752226 1.933440974 11.1271917 0.922171826 1.067736422 0.153968319 0.129527245 1.45328827 239.7311284 0.057635974 0.036820232 85.79085067 -1.933440974 0.145564596 SVWGSLAVQNS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVWGSLAVQNSPK 13 0 P18615;P18615-3;P18615-4 P18615 NELFE Negative elongation factor E 1 SVWGSLAVQNS(1)PK;SVWGSLAVQNS(1)PK 281.65 1.91E-32 993440000 948670 853560 727700 658540 762430 637500 873600 1004320 1044990 1168570 TRUE FALSE 911594.9276 829217.3045 859211.5776 692527.3283 786954.2534 650390.6868 884291.3781 983580.441 926367.1162 1089421.713 0.83676956 0.761153642 0.788685931 0.635683427 0.722359619 0.597005438 0.811707136 0.902846372 0.850329221 1 20.0551311 1.933468742 3.889115497 0.902662363 0.722811208 0.572482507 0.074434754 0.180634571 5.061890716 0.035924745 0.020768151 85.79633606 -1.933468742 -0.179851155 FEPES(ph)PGFESR ddPTM_BT-474_Pertuzumab_2h_R1 6 FEPESPGFESR 11 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR 265.75 5.88E-21 3476870000 2801010 2940610 2426660 2649190 2657180 2488600 2382760 2673710 2264770 2375870 TRUE FALSE 2691543.433 2856746.682 2865211.443 2785915.013 2742650.608 2538921.197 2411920.93 2618496.954 2007682.804 2214950.209 1.215171078 1.289756614 1.293578263 1.257777715 1.238244813 1.146265585 1.088927832 1.182192242 0.906423448 1 21.07884284 1.933484631 0.664263956 0.97623558 1.275338407 0.755137444 0.060403702 0.354289155 0.307409742 0.054635806 0.030852919 85.79947504 -1.933484631 0.299102827 S(ph)RSPAPPADKEAEKPVFFPAFAAEAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPAPPADKEAEKPVFFPAFAAEAQK 27 3 C9J0Q5;C9JE98 C9J0Q5 NCOR2 1 S(0.601)RS(0.399)PAPPADKEAEKPVFFPAFAAEAQK 235.94 2.83E-44 1238800000 1218400 1079000 938260 762210 972420 994530 1105600 1356100 1518300 1247600 TRUE FALSE 1170783.581 1048227.976 1107824.453 801547.7494 1003698.772 1014640.078 1119130.664 1328096.061 1345948.949 1163098.941 1.006607039 0.901237152 0.952476539 0.689148379 0.862952185 0.872359214 0.962197303 1.141859918 1.157209333 1 20.1495424 1.933637613 3.257620906 1.111859004 0.876357441 0.55925793 0.086412097 0.177011319 3.426226004 0.044229811 0.024696906 85.82970368 -1.933637613 -0.235501564 PCSEETPAIS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 6 PCSEETPAISPSK 13 0 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(0.991)PS(0.009)K;PCSEETPAIS(1)PSK;PCSEETPAIS(1)PSK;PCSEETPAIS(0.999)PS(0.001)K;PCSEETPAIS(1)PSK;PCSEETPAIS(0.997)PS(0.003)K 349.01 7.11E-76 3211690000 3053410 2125960 2213470 2063300 2314520 2094260 2639430 3005920 3267800 3345970 TRUE FALSE 2934079.361 2065329.702 2613493.267 2169787.16 2388968.638 2136607.372 2671732.134 2943846.702 2896853.044 3119344.472 0.940607678 0.66210376 0.837834132 0.69559075 0.765855987 0.684953968 0.856504358 0.943738894 0.928673659 1 21.57281145 1.933747335 3.118315881 0.950599599 0.760119447 0.543168788 0.078808525 0.184410682 3.264613216 0.036867673 0.020388544 85.85139085 -1.933747335 -0.190480151 YSPNCK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSPNCK 6 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2 P00338 LDHA L-lactate dehydrogenase A chain 0 113.08 0.061517 250260000 360280 351330 282240 327960 308270 317140 299740 300920 335570 283350 FALSE TRUE 346199.8593 341310.4124 333247.0464 344886.0549 318185.7845 323552.7881 303408.3078 294705.8968 297477.5004 264158.4521 1.310576499 1.292066976 1.261542244 1.305602952 1.20452623 1.224843595 1.148584516 1.115640611 1.126132812 1 18.01104405 1.934131103 0.382917053 0.994473696 1.328187894 0.941250957 0.023183437 0.240643928 0.093956772 0.026594671 0.026912186 85.92728763 -1.934131103 0.333714198 SILKPSTPIPPQEGEEVGESS(ph)EEQDNAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SILKPSTPIPPQEGEEVGESSEEQDNAPK 29 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;A0A3B3ISZ5;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SILKPSTPIPPQEGEEVGES(0.431)S(0.569)EEQDNAPK 79.884 2.45E-06 0 102870 92876 88284 77818 92409 90566 100550 122860 136350 110670 TRUE FALSE 98849.72667 90227.26742 104238.8827 81834.19631 95381.41941 92397.30657 101780.561 120322.8981 120872.1196 103174.2223 0.958085503 0.874513666 1.010319054 0.793165138 0.924469478 0.895546431 0.986492156 1.166210855 1.171534099 1 16.65472304 1.934142859 3.688037378 1.126389505 0.908817836 0.631098486 0.069094728 0.132525107 3.326123427 0.031514755 0.018053999 85.92961363 -1.934142859 -0.217571669 HHGDVMDLQFFDQER ddPTM_BT-474_Pertuzumab_2h_R1 3 HHGDVMDLQFFDQER 15 0 Q8NFH3;B4E301;F5H0E3;B4DVD1;Q8NFH3-2 Q8NFH3 NUP43 Nucleoporin Nup43 0 ;; 228.48 3.42E-13 325871000 255972 286325 261086 288686 269736 317487 242780 7976.1 247053 150440 FALSE TRUE 245968.3312 278159.2913 308270.048 303585.1191 278412.3034 323906.8047 245751.2143 7811.390748 219008.5792 140250.5648 1.75377783 1.983302468 2.197995056 2.164591062 1.985106469 2.309486633 1.752229765 0.055695966 1.561552208 1 17.09764706 1.934227749 7.470801646 0.79337701 2.066080241 0.673371578 0.370815601 0.142730212 14.36949204 0.148673798 0.092978087 85.9464116 -1.934227749 1.272703231 ADIDISGPNVDVDVPDVNIEGPDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADIDISGPNVDVDVPDVNIEGPDAK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 118.37 0.00077571 64780000 51455 51347 44889 47206 39915 49525 48419 57138 55992 53099 FALSE TRUE 49444.08171 49882.63383 53001.44085 49642.30732 41198.90222 50526.42943 49011.56621 55958.08033 49636.0229 49502.55743 0.998818733 1.007677914 1.070680862 1.002823084 0.832258056 1.020683214 0.990081498 1.130407866 1.002696133 1 15.59521544 1.934230913 24.77359227 1.059204654 0.988459533 0.114567651 0.066819822 304.6953393 114770.1335 0.02835344 0.018301586 85.94703785 -1.934230913 -0.070745121 ENKEPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENKEPSPK 8 1 H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BV44 H3BRD5 MYO9A Unconventional myosin-IXa 1 ENKEPS(1)PK 55.401 0.075196 394790000 344050 238160 254060 218770 262480 215030 302880 375050 427290 356700 TRUE FALSE 330604.1456 231367.91 299974.2935 230060.7459 270922.9076 219378.0539 306586.736 367305.0864 378785.8305 332540.3913 0.994177412 0.695758819 0.902068745 0.691827976 0.814706768 0.659703482 0.921953375 1.104542775 1.139067134 1 18.34317006 1.934290653 3.78471913 1.086126678 0.789367604 0.617262295 0.101247177 0.138434147 3.671680613 0.045164058 0.026001141 85.95886118 -1.934290653 -0.296759074 TNS(ph)MGSATGPLPGTK ddPTM_BT-474_Pertuzumab_2h_R1 7 TNSMGSATGPLPGTK 15 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 T(0.233)NS(0.765)MGS(0.002)ATGPLPGTK;T(0.001)NS(0.999)MGSATGPLPGTK;T(0.061)NS(0.939)MGSATGPLPGTK;TNS(1)MGSATGPLPGTK;TNS(0.997)MGS(0.003)ATGPLPGTK;TNS(1)MGSATGPLPGTK;T(0.001)NS(0.998)MGS(0.001)ATGPLPGTK 326.11 8.47E-58 4171858000 4536020 3916260 3474980 3320380 3813990 3532160 3829170 5140250 4661920 4006090 TRUE FALSE 4358747.324 3804572.099 4102986.187 3491745.21 3936670.452 3603582.695 3876032.528 5034102.041 4132718.386 3734753.956 1.167077504 1.018694175 1.098596115 0.934933131 1.054064203 0.964878206 1.03782808 1.347907279 1.106557068 1 21.83258177 1.934297149 24.95584737 1.19082561 1.034321732 0.169927538 0.102606055 210.4552167 79936.28905 0.040102151 0.025880045 85.96014681 -1.934297149 -0.156503879 SASQSS(ph)LDKLDQELKEQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 SASQS(0.154)S(0.846)LDKLDQELKEQQK 168.56 8.26E-12 472040000 495910 357260 267660 199940 284520 353920 374820 413100 532490 445550 TRUE FALSE 476529.2889 347071.2946 316032.1161 210258.9274 293671.8442 361076.5049 379407.1593 404569.3406 472043.9676 415372.5016 1.147233596 0.835566373 0.760840245 0.506193661 0.707008391 0.869283603 0.913414243 0.973991632 1.136435286 1 18.66404618 1.934300661 1.537893448 1.055417967 0.782031372 0.321884739 0.153445407 0.479467887 2.112265006 0.112902179 0.051548355 85.96084197 -1.934300661 -0.273386595 TPTGNAPSSES(ph)DIDISSPNVSHDESIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPTGNAPSSESDIDISSPNVSHDESIAK 28 0 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 1 TPTGNAPS(0.037)S(0.17)ES(0.792)DIDISSPNVSHDESIAK 129.63 1.71E-05 136850000 38283 39146 29785 31053 36028 35179 41885 46947 55700 51487 TRUE FALSE 36786.85804 38029.59441 35167.81206 32655.64905 37186.87334 35890.34348 42397.60116 45977.52804 49377.16951 47999.73963 0.766397033 0.792287514 0.732666726 0.680329712 0.77473073 0.747719545 0.883288149 0.957870363 1.028696612 1 15.55073896 1.934434059 1.623497888 1.011099614 0.744916122 0.926016091 0.031524847 0.094077511 0.46194049 0.022007284 0.01017757 85.98724981 -1.934434059 -0.266183493 VSS(ph)PTKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.114)S(0.886)PTKPK;VS(0.019)S(0.981)PTKPK;VS(0.022)S(0.976)PT(0.002)KPK 145.99 0.00033947 5673600000 9201100 7922600 6668800 6236300 7373400 7113800 8036700 9676100 10202300 9241600 TRUE FALSE 8841510.84 7696655.205 7874000.507 6558156.19 7610572.107 7257645.91 8135055.539 9476285.154 9044177.676 8615658.2 1.026214206 0.893333397 0.913917466 0.761190386 0.883341926 0.842378579 0.944217534 1.099891028 1.049737288 1 23.03852959 1.934452243 4.524077198 1.056094072 0.8827826 0.549248264 0.065853113 0.156454412 6.080353291 0.0306904 0.018192837 85.99085025 -1.934452243 -0.173311471 VEIKNVT(ph)PDT(ph)AY(ph)RDFCLAFIGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEIKNVTPDTAYRDFCLAFIGK 22 2 A0A0G2JM25;A0A0G2JNK1;K7ERG0;A0A0G2JMB6;A0A0G2JPH3;A0A0G2JNK3;Q8WX94;Q8WX94-2;Q8WX94-3 A0A0G2JM25 NLRP7 "NACHT, LRR and PYD domains-containing protein 7" 3 VEIKNVT(1)PDT(1)AY(1)RDFCLAFIGK 46.66 0.072276 303370000 55733 91274 81078 107470 95361 111400 86446 63016 77823 93373 TRUE FALSE 53554.89274 88670.95489 95730.59817 113016.5396 98428.37317 113652.5843 87503.95201 61714.69758 68988.8593 87048.76354 0.615228644 1.018635432 1.099735301 1.29831298 1.130726838 1.305619743 1.00522912 0.708966964 0.79253118 1 16.40953619 1.934485762 6.283011131 0.811784437 1.094020183 0.239180511 0.19219904 0.299157326 22.5823881 0.086165191 0.053106117 85.99748731 -1.934485762 0.282235747 KVEEDLKADEPSS(ph)EES(ph)DLEIDK ddPTM_BT-474_Pertuzumab_2h_R1 4 KVEEDLKADEPSSEESDLEIDK 22 2 P50502;Q3KNR6;F6VDH7 P50502 ST13 Hsc70-interacting protein 2 KVEEDLKADEPS(0.111)S(0.895)EES(0.994)DLEIDK;KVEEDLKADEPS(0.001)S(0.999)EES(1)DLEIDK;KVEEDLKADEPS(0.187)S(0.836)EES(0.977)DLEIDK;KVEEDLKADEPS(0.47)S(0.53)EES(0.999)DLEIDK 306.76 6.84E-57 720750000 1228650 813652 1081999 887998 988012 879815 1406640 1821190 2222180 1865670 TRUE FALSE 1180633 790447.4416 1277540.288 933827.6832 1019792.303 897605.4621 1423854.881 1783581.79 1969927.443 1739306.509 0.678795252 0.454461268 0.734511302 0.536896561 0.586321214 0.516070892 0.818633676 1.025455709 1.132593613 1 20.73008076 1.934490193 2.460797299 1.064033977 0.583379795 0.863938147 0.083221324 0.090428167 1.000031289 0.043019297 0.022412054 85.99836467 -1.934490193 -0.480654181 PAPPKPEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 PAPPKPEPK 9 1 Q15651;A0A087WZE9;Q15651-2;P05204 Q15651;P05204 HMGN3;HMGN2 High mobility group nucleosome-binding domain-containing protein 3;Non-histone chromosomal protein HMG-17 0 ; 78.655 0.026591 993070000 2519600 1628030 1969620 1778270 2280320 1600180 2172570 2900100 2869300 2494020 FALSE TRUE 2421131.246 1581600.178 2325574.148 1870046.728 2353668.564 1632536.736 2199158.562 2840211.922 2543589.093 2325097.804 1.041302969 0.680229527 1.000204871 0.80428734 1.012287982 0.702136802 0.945834862 1.22154514 1.093970795 1 21.14885997 1.934496181 6.4288077 1.121204434 0.869594323 0.398470431 0.126769899 0.199471076 15.69846494 0.050152048 0.030976897 85.99955045 -1.934496181 -0.251610111 NHSGNDERDEEDEER ddPTM_BT-474_Pertuzumab_2h_R1 2 NHSGNDERDEEDEER 15 1 A0A0D9SGE8;Q8IWS0-3;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 0 ; 181.51 3.51E-07 218060000 54625 56357 50114 63102 51093 55599 51068 24949.7 50728 48267 FALSE TRUE 52490.19461 54749.75354 59170.71458 66358.70178 52736.45275 56723.24987 51692.98546 24434.47998 44969.57011 44997.8331 1.16650494 1.216719779 1.314968089 1.47470883 1.171977607 1.260577365 1.148788328 0.543014592 0.999371903 1 15.45756791 1.934718543 6.925774534 0.805283392 1.267317374 0.621714851 0.145491284 0.144308654 12.96154064 0.061212135 0.038059178 86.04359406 -1.934718543 0.462033982 HAPHCLS(ph)EEEGEQDRPR ddPTM_BT-474_Pertuzumab_2h_R1 3 HAPHCLSEEEGEQDRPR 17 1 E9PH18;A0A0J9YX62;O75190-3;O75190;O75190-4 E9PH18 DNAJB6 DnaJ homolog subfamily B member 6 1 HAPHCLS(1)EEEGEQDRPR;HAPHCLS(1)EEEGEQDRPR;HAPHCLS(1)EEEGEQDRPR 206.8 4.02E-12 2248060000 445552 439143 344793 423420 392564 445442 404976 100110 435990 383000 TRUE FALSE 428139.3353 426619.0716 407104.765 445272.7569 405191.1776 454449.1424 409932.2174 98042.69352 386498.243 357059.0689 1.19907145 1.194813712 1.140160832 1.247056288 1.13480153 1.272756197 1.148079557 0.274583961 1.082449031 1 18.44580324 1.934721461 14.78086365 0.706535232 1.19598464 0.433266215 0.20721667 2.338608904 528.6947799 0.080024933 0.051478091 86.04417231 -1.934721461 0.489449409 NFYES(ph)DDDQKEK ddPTM_BT-474_Pertuzumab_2h_R1 6 NFYESDDDQKEK 12 1 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK 207.4 2.08E-07 2832570000 2545800 1897830 2127580 1821720 2173260 1927280 2547150 3267690 3663140 3159380 TRUE FALSE 2446307.321 1843705.747 2512081.034 1915739.188 2243164.882 1966250.922 2578322.784 3200211.06 3247315.704 2945392.379 0.830553966 0.625962693 0.852885019 0.650419007 0.761584398 0.667568415 0.875374976 1.086514341 1.102506996 1 21.49002841 1.934735496 3.166895433 1.069214356 0.730468963 0.799082324 0.074215021 0.095783874 1.752341462 0.034166574 0.018977719 86.04695295 -1.934735496 -0.338745393 FLSAQSHST(ph)SPQGLDSPLPLEGSGAHQVLHNESK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESK 34 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLSAQS(0.02)HS(0.122)T(0.429)S(0.429)PQGLDSPLPLEGSGAHQVLHNESK 151.96 2.02E-10 223350000 51464 55355 62132 69141 66058 77291 65535 18802 79069 90231 TRUE FALSE 49452.72998 53776.3296 73360.63452 72709.3753 68182.81556 78853.87698 66337.03693 18413.73213 70093.4186 84119.574 0.58788612 0.639284379 0.872099454 0.864357388 0.810546372 0.937402239 0.788604052 0.218899493 0.833259315 1 16.36015392 1.934905959 24.99946754 0.57388578 0.793628994 0 0.217516132 342.9777092 131719.9901 0.087812489 0.056672948 86.08073352 -1.934905959 0.219743214 VMEGLDAFDDLMQHTHIQPWYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMEGLDAFDDLMQHTHIQPWYLR 23 0 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 271.62 7.38E-52 1139900000 390310 462730 356210 456550 296390 385890 346640 27709 352410 267960 FALSE TRUE 375056.2537 449533.3935 420585.0708 480112.6002 305923.6535 393692.9602 350882.284 27136.79947 312405.8942 249810.8305 1.501361061 1.799495212 1.683614237 1.921904664 1.224621258 1.575964338 1.40459196 0.108629395 1.250569855 1 17.9304765 1.934908787 7.99043582 0.700267388 1.614271662 0.566676658 0.322915704 0.200519106 22.54032277 0.132110358 0.083026559 86.08129405 -1.934908787 0.914004275 DIEIS(ph)T(ph)EEEKDTGDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIEISTEEEKDTGDLK 16 1 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 2 DIEIS(1)T(1)EEEKDTGDLK 128.98 0.00013264 132160000 576500 449230 488290 397240 552330 510570 565630 772920 787090 665010 TRUE FALSE 553969.7426 436418.4002 576534.865 417741.604 570096.1961 520894.0752 572552.3491 756958.9319 697742.843 619968.2804 0.893545299 0.703936659 0.92994252 0.673811253 0.919557039 0.840194719 0.923518779 1.220963968 1.125449261 1 19.24183488 1.934963838 4.090005043 1.13282947 0.825779366 0.650451763 0.094145306 0.12059542 3.784447088 0.04136173 0.024149294 86.09220641 -1.934963838 -0.307050104 AVVVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 AVVVSPK 7 0 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 AVVVS(1)PK;AVVVS(1)PK;AVVVS(1)PK;AVVVS(1)PK;AVVVS(1)PK 121.73 0.0046253 6145540000 11049950 9558250 9699950 9802630 9702940 9345350 10987640 13866370 14315740 12760970 TRUE FALSE 10618105.74 9285658.069 11452946.74 10308544.91 10015043.88 9534319.38 11122110.03 13580024.61 12690677.21 11896658.14 0.892528441 0.780526595 0.962702854 0.866507618 0.841836738 0.801428374 0.93489364 1.141499105 1.066743035 1 23.50405303 1.935027689 4.824643353 1.078678974 0.858854587 0.734726164 0.056770336 0.100464863 4.495487325 0.025050568 0.014989737 86.10486467 -1.935027689 -0.219824386 RLVPDSDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLVPDSDVR 9 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 86.898 0.02217 492230000 716710 818020 594600 684650 717640 738370 664310 282610 697560 605730 FALSE TRUE 688700.1808 794690.8705 702057.4468 719984.8685 740723.5423 753300.3473 672440.0245 276774.0047 618375.9132 564703.3676 1.219578668 1.40727135 1.243232265 1.274978883 1.311703781 1.333975306 1.190784513 0.490122816 1.095045556 1 19.10713371 1.935047208 8.475553174 0.812028019 1.297382412 0.607774168 0.155629249 0.200373996 24.49387376 0.061444111 0.038760707 86.10873471 -1.935047208 0.485354393 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA ddPTM_BT-474_Pertuzumab_2h_R1 1 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA 33 2 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 151.99 5.36E-11 502670000 128700 125080 87972 146080 147080 128040 112880 12252 113920 90733 FALSE TRUE 123670.2617 121512.8409 103870.4973 153619.2063 151810.9618 130629.0565 114261.4592 11998.99192 100988.2792 84587.57309 1.462038184 1.436533009 1.227964032 1.816096628 1.79471944 1.544305526 1.350806685 0.141852893 1.193890255 1 16.36815811 1.935147581 8.174066194 0.695252881 1.542656042 0.562890431 0.30050509 0.21570106 25.13247003 0.125484648 0.078983563 86.12863834 -1.935147581 0.847403161 QDDIDLQKDDEDTR ddPTM_BT-474_Pertuzumab_2h_R1 3 QDDIDLQKDDEDTR 14 1 Q9NYB0 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 0 ;; 182.18 1.42E-06 2272980000 3038580 2495250 2325369 2444911 2758460 2624626 2932590 3556160 3884570 3540280 FALSE TRUE 2919828.934 2424087.913 2745614.906 2571093.15 2847188.371 2677697.736 2968479.914 3482724.053 3443609.899 3300493.682 0.8846643 0.734462219 0.831880067 0.779002597 0.862655301 0.811302185 0.899404816 1.055213065 1.043362064 1 21.65425041 1.935242102 2.815028531 1.038149281 0.814596209 0.840103627 0.041912689 0.090713041 1.308302549 0.020733344 0.011202496 86.14738558 -1.935242102 -0.223553072 TLVLSDKHS(ph)PQKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLVLSDKHSPQKK 13 2 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 TLVLSDKHS(1)PQKK 121.82 0.00012641 593510000 714090 563570 523390 525270 590750 584450 693850 739090 909400 815020 TRUE FALSE 686182.5733 547497.5354 617978.2157 552379.2476 609752.0103 596267.9794 702341.5439 723827.5332 806168.7245 759817.9695 0.903088109 0.720564079 0.813324034 0.726988923 0.802497486 0.78475109 0.924355006 0.952632818 1.061002447 1 19.53529431 1.93529514 1.517105024 1.021887733 0.784162338 0.767731391 0.05324694 0.168131275 0.720639598 0.034222757 0.015591991 86.15790704 -1.93529514 -0.237725395 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK ddPTM_BT-474_Pertuzumab_2h_R1 3 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK 35 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 220.62 8.22E-37 4743220000 861460 1461040 868200 1343490 1068240 1178790 1011050 136704 988100 837739 FALSE TRUE 827793.1908 1419372.57 1025103.053 1412827.68 1102600.91 1202625.941 1023423.532 133881.0146 875935.0305 780998.1913 1.059916911 1.817382659 1.312554964 1.809002499 1.411784204 1.539857524 1.310404485 0.171422951 1.121558334 1 19.57495968 1.935318559 7.886334921 0.685267108 1.502554059 0.513213098 0.314378222 0.204071996 22.65568742 0.123449506 0.077522951 86.16255299 -1.935318559 0.81728695 KGDSSAEELK ddPTM_BT-474_Pertuzumab_2h_R1 5 KGDSSAEELK 10 1 P26373;P26373-2 P26373 RPL13 60S ribosomal protein L13 0 ;;;; 142.89 5.60E-05 15436060000 13257720 11641990 10712990 9331370 10870210 10889230 12258130 14459200 15891760 14182280 FALSE TRUE 12739593.65 11309971.84 12649065.6 9812963.124 11219860.18 11109417.69 12408148.66 14160612.47 14087794.03 13221701.54 0.963536622 0.855409707 0.956689694 0.742186102 0.848594271 0.840241149 0.938468367 1.071012866 1.065505373 1 23.65640452 1.93534021 3.411125171 1.050338629 0.865224145 0.624624653 0.061433913 0.152330501 3.253588099 0.030238501 0.017076385 86.16684866 -1.93534021 -0.185114483 GHEGPVWQVAWAHPMYGNILASCSYDRK ddPTM_BT-474_Pertuzumab_2h_R1 2 GHEGPVWQVAWAHPMYGNILASCSYDRK 28 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6;E7ERC8 P55735 SEC13 Protein SEC13 homolog 0 ; 163.94 3.12E-12 716160000 316400 316640 212251 189324 277010 300800 250042 111825 258880 235214 FALSE TRUE 304034.7382 307609.7372 250609.4772 199095.0343 285920.2782 306882.3821 253102.0888 109515.7747 229493.0277 219282.7463 1.3864964 1.402799547 1.14285999 0.907937527 1.303888624 1.399482574 1.154227102 0.499427231 1.046562174 1 17.74243278 1.935602625 9.102017024 0.800169911 1.247559834 0.458111937 0.196740957 0.359239444 48.59171182 0.084238979 0.053358679 86.21892932 -1.935602625 0.447389923 HEEEEAKAER ddPTM_BT-474_Pertuzumab_2h_R1 1 HEEEEAKAER 10 1 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 189.58 5.98E-07 59260000 105140 104320 57494 67415 88966 106130 80138 46970 80391 71102 FALSE TRUE 101031.0126 101344.8957 67884.44475 70894.29623 91827.67219 108276.0213 81118.75282 46000.05309 71265.35071 66286.19821 1.524163631 1.528898903 1.024111302 1.069518213 1.385321148 1.633462534 1.223765354 0.693961252 1.075115976 1 16.01642089 1.935628351 7.036786814 0.902723477 1.348189005 0.480510659 0.202990065 0.231942312 21.67867909 0.092923481 0.057869901 86.22403664 -1.935628351 0.445465529 FY(ph)SFIHMT(ph)FQEFFAAMYYLLEEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYSFIHMTFQEFFAAMYYLLEEEK 24 0 A0A2R8YEG7;Q96P20-3;Q96P20-2;Q96P20-5;Q96P20-4;Q96P20-6;Q96P20 A0A2R8YEG7 NLRP3 "NACHT, LRR and PYD domains-containing protein 3" 2 FY(0.28)S(0.696)FIHMT(0.467)FQEFFAAMY(0.278)Y(0.278)LLEEEK 64.16 0.044569 254210000 288930 136780 179400 107990 211380 146980 235980 268280 374070 248210 TRUE FALSE 277638.2962 132879.1683 211821.5707 113563.3768 218179.2297 149952.0363 238867.9938 262739.9242 331607.1418 231398.5156 1.199827473 0.574243823 0.915397275 0.490769686 0.942872209 0.648025057 1.032279715 1.13544343 1.433056478 1 17.82002008 1.935707127 2.506134137 1.21340391 0.784043266 0.397564845 0.217090747 0.257322863 2.950169428 0.109743142 0.05752439 86.23967821 -1.935707127 -0.429360645 AGQDMGLEHGFEKPLDSAMS(ph)AEEDTDVR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGQDMGLEHGFEKPLDSAMSAEEDTDVR 28 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 AGQDMGLEHGFEKPLDS(0.001)AMS(0.999)AEEDTDVR;AGQDMGLEHGFEKPLDS(0.017)AMS(0.983)AEEDTDVR;AGQDMGLEHGFEKPLDS(0.003)AMS(0.997)AEEDTDVR 193.4 1.23E-18 291491000 273494 252410 210543 271391 246243 241818 246647 242460 275144 244979 TRUE FALSE 262805.5521 245211.5139 248592.8036 285397.522 254163.6297 246707.7256 249665.5398 237453.1163 243910.8066 228386.3541 1.150706018 1.073669725 1.088474855 1.249625982 1.112866969 1.080220955 1.093171879 1.039699229 1.067974519 1 17.80111693 1.935725884 0.941195125 1.022734422 1.133399029 0.441260525 0.047781051 0.561741338 0.916148446 0.041310853 0.019055121 86.24340286 -1.935725884 0.110664606 SKPPPTYES(ph)EEEDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKPPPTYESEEEDK 14 1 O60885;O60885-2;O60885-3 O60885 BRD4 Bromodomain-containing protein 4 1 SKPPPTYES(1)EEEDK;SKPPPTYES(1)EEEDK;SKPPPTYES(1)EEEDK;SKPPPTYES(1)EEEDK 204.51 8.20E-09 3588060000 2703300 1966600 2522170 2136150 2288890 2168040 2841780 3597280 4044490 3594150 TRUE FALSE 2597652.047 1910514.494 2977982.224 2246396.957 2362514.226 2211879.254 2876558.554 3522994.911 3585376.451 3350715.019 0.775253053 0.570181135 0.888760222 0.670423162 0.705077636 0.660121569 0.85849096 1.051415859 1.070033241 1 21.67603756 1.935748242 2.933243559 1.04508206 0.711579533 0.770958913 0.08008002 0.114301943 1.791223392 0.039358852 0.021493212 86.24784285 -1.935748242 -0.333502527 DSFPWEVPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSFPWEVPKK 10 1 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 97.452 0.0096995 440920000 582850 527290 516360 434620 541120 592170 608190 701400 812550 788330 FALSE TRUE 560071.5776 512252.2055 609677.7384 457050.7903 558525.6162 604144.0831 615633.2112 686915.8449 720312.7305 734935.7069 0.762068807 0.697002745 0.829566087 0.621892209 0.759965274 0.822036645 0.83766948 0.934661139 0.980103054 1 19.48725852 1.935794658 1.009112143 1.001039871 0.730374238 0.800869658 0.051408938 0.21558408 0.403422187 0.040546425 0.018346328 86.25706127 -1.935794658 -0.270665633 SGSPSDNS(ph)GAEEMEVSLAKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 SGSPSDNS(1)GAEEMEVSLAKPK;SGS(0.001)PS(0.045)DNS(0.954)GAEEMEVSLAKPK 198.93 5.02E-22 8914400000 1055620 996130 756640 774600 843330 885390 970980 1263550 1270750 1101960 TRUE FALSE 1014365.203 967721.3477 893381.6794 814577.1988 870456.4753 903293.1924 982863.1437 1237457.251 1126499.787 1027323.268 0.987386576 0.941983286 0.869620798 0.792912245 0.847305325 0.879268698 0.956722362 1.204545142 1.096538765 1 19.9704588 1.935900898 4.995159243 1.117206224 0.884265456 0.663215579 0.067771822 0.120470291 5.843288319 0.03179923 0.019126499 86.27816472 -1.935900898 -0.232940768 S(ph)GDETPGSEVPGDK ddPTM_BT-474_Pertuzumab_2h_R1 5 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(1)GDETPGSEVPGDK;S(0.998)GDET(0.002)PGSEVPGDK;S(0.999)GDET(0.001)PGSEVPGDK;S(0.998)GDET(0.002)PGSEVPGDK;S(0.997)GDET(0.003)PGSEVPGDK 297.45 1.15E-43 3404650000 3582480 3192220 3196880 3257990 3141320 3010170 3775860 4743680 5113040 4604970 TRUE FALSE 3442472.721 3101181.011 3774627.33 3426135.254 3242363.411 3071037.7 3822070.104 4645721.35 4532629.135 4293071.28 0.801867124 0.722368861 0.879237051 0.798061581 0.755254968 0.715347475 0.890288061 1.082144005 1.055801043 1 22.0335787 1.935904532 3.705880171 1.049466198 0.780963948 0.860010609 0.048150853 0.080176178 2.043076136 0.023549752 0.013524726 86.27888661 -1.935904532 -0.268502251 AEEKEGEKDAAAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEEKEGEKDAAAAK 14 2 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 0 94.551 0.0023172 125350000 170120 173800 126940 129790 153170 169070 166110 234590 219770 165350 FALSE TRUE 163471.5223 168843.3942 149880.8818 136488.4775 158096.8522 172488.7112 168142.9039 229745.6345 194822.631 154150.6972 1.060465669 1.095313853 0.972301031 0.885422382 1.025599332 1.118961603 1.090769662 1.490396337 1.263845279 1 17.23398189 1.935977733 7.858305805 1.303393499 1.027333189 0.359893379 0.128800624 0.261846893 29.2219502 0.053872009 0.033827686 86.29343027 -1.935977733 -0.27606031 VESESYRK ddPTM_BT-474_Pertuzumab_2h_R1 1 VESESYRK 8 1 Q9UHY7;A0A0C4DGY8;D6RA00;Q9UHY7-2 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 104.44 0.0073445 88258000 64713 67991 45465 67905 56882 61508 63688 78147 70771 78005 FALSE TRUE 62183.94442 66051.96325 53681.53686 71409.58519 58711.66119 62751.7339 64467.4328 76533.23714 62737.37278 72721.65187 0.855095323 0.908284693 0.738178183 0.981957689 0.807347739 0.862903032 0.886495715 1.052413348 0.862705551 1 16.15009735 1.936022706 8.244892107 0.975996421 0.860219519 0.319863923 0.073557389 0.371914799 44.47340163 0.028964563 0.018244516 86.30236668 -1.936022706 -0.115776902 LYKDDQLLDDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 LYKDDQLLDDGK 12 1 B8ZZU8;Q15370;Q15370-2 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;; 182.33 1.55E-05 6221430000 9190900 8111000 7718270 6912140 7909890 8100830 8975000 10883700 12043500 10665400 FALSE TRUE 8831709.467 7879682.221 9113133.081 7268876.374 8164318.795 8264634.333 9084838.735 10658947.79 10676372.37 9943022.958 0.888231829 0.792483559 0.916535456 0.731052961 0.821110323 0.831199361 0.913689808 1.072002734 1.073755176 1 23.24525311 1.936024881 2.807144887 1.055560632 0.827634876 0.78216206 0.051398653 0.111602581 1.601485834 0.025974769 0.014034249 86.30279902 -1.936024881 -0.227925756 YLAEVAAGDDKK ddPTM_BT-474_Pertuzumab_2h_R1 7 YLAEVAAGDDKK 12 1 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;; 187.44 1.68E-05 37081940000 13794130 11306580 11017960 9463480 11067160 11194430 12451390 13783410 16235480 13773400 FALSE TRUE 13255040.15 10984127.41 13009150.47 9951891.337 11423145.25 11420789.04 12603773.84 13498777.77 14392496.38 12840515.35 1.032282567 0.855427303 1.013133049 0.775038312 0.889617351 0.889433853 0.981562927 1.051264486 1.120865945 1 23.61419977 1.936129418 2.49853179 1.065076345 0.904607216 0.440819417 0.074550721 0.246759877 2.812683363 0.039289811 0.020584874 86.32357511 -1.936129418 -0.160469129 DSDQVAQS(ph)DGEESPAAEEQLLGEHIK ddPTM_BT-474_Pertuzumab_2h_R1 6 DSDQVAQSDGEESPAAEEQLLGEHIK 26 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 1 DSDQVAQS(1)DGEESPAAEEQLLGEHIK;DSDQVAQS(1)DGEESPAAEEQLLGEHIK;DSDQVAQS(1)DGEESPAAEEQLLGEHIK;DSDQVAQS(1)DGEESPAAEEQLLGEHIK;DSDQVAQS(1)DGEESPAAEEQLLGEHIK;DSDQVAQS(1)DGEESPAAEEQLLGEHIK 278.9 6.20E-61 3000100000 2014517 1900656 1910417 2016948 2040696 2026138 2402792 2669410 3134010 2965320 TRUE FALSE 1935787.448 1846451.152 2255671.849 2121042.928 2106336.84 2067107.899 2432198.087 2614285.751 2778250.324 2764476.235 0.700236603 0.66792079 0.815949083 0.767249471 0.761929805 0.747739435 0.879804303 0.945671269 1.004982531 1 21.39857474 1.936133552 1.362476096 1.004926019 0.739378404 0.887449176 0.038837562 0.138124012 0.476005421 0.02999 0.013421902 86.32439668 -1.936133552 -0.265547615 YTDHGSDHHYR ddPTM_BT-474_Pertuzumab_2h_R1 2 YTDHGSDHHYR 11 0 J3KPD3;Q9Y580;G3V1T9 J3KPD3 RBM7 RNA-binding protein 7 0 ; 109.42 0.0011168 47604000 85154 137386 109186 176662 138638 147577 124256 30177 124592 113881 FALSE TRUE 81826.08754 133467.8858 128918.339 185779.547 143097.4172 150561.1081 125776.6821 29553.8344 110448.8385 106167.7384 0.770724598 1.257141649 1.214289208 1.749868178 1.347842756 1.418143687 1.184697762 0.278369256 1.040323926 1 16.69598591 1.936142143 9.213483333 0.700764605 1.31030519 0.371366904 0.298787341 0.404533228 56.03890062 0.124594482 0.078976625 86.3261044 -1.936142143 0.609540585 SHTPSPTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 SHTPSPTSPK 10 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 SHTPSPT(0.001)S(0.999)PK;SHTPSPT(0.011)S(0.989)PK;SHTPSPT(0.01)S(0.99)PK;SHTPSPT(0.015)S(0.985)PK;SHTPS(0.002)PT(0.041)S(0.957)PK 136.24 7.91E-05 4176910000 6467350 5454530 5546500 5326240 5704820 6535950 5926190 2394020 8360830 7517370 TRUE FALSE 6214598.812 5298972.145 6548875.931 5601127.885 5888320.716 6668111.387 5998716.486 2344582.65 7411743.63 7008211.834 0.886759556 0.756109015 0.934457474 0.799223542 0.840203015 0.951471152 0.85595536 0.334547914 1.057579851 1 22.74061495 1.936202734 24.99993317 0.691390562 0.86009074 0 0.196513514 417.9018676 163759.9113 0.077753957 0.050183507 86.33814901 -1.936202734 0.168700178 HGLLVPNNTTDQELQHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 HGLLVPNNTTDQELQHIR 18 0 P56537;B7ZBH1 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ; 153.86 1.75E-08 6231300000 1762360 1781120 1429110 1964100 1651060 1869220 1691790 1050200 1797740 1721730 FALSE TRUE 1693485.023 1730324.201 1687381.967 2065467.436 1704167.844 1907016.909 1712494.632 1028513.003 1593668.092 1605115.694 1.055054804 1.078005909 1.051252551 1.286802842 1.061710287 1.188086888 1.066897943 0.640771882 0.992868052 1 20.61424586 1.936249689 9.820175901 0.841360981 1.120651975 0.45811147 0.11615771 0.399307267 59.82622483 0.046338323 0.029462596 86.34748429 -1.936249689 0.279290994 HCFTSPDYQQQCHEMAER ddPTM_BT-474_Pertuzumab_2h_R1 1 HCFTSPDYQQQCHEMAER 18 0 Q6IQ49-3;Q6IQ49-2;Q6IQ49 Q6IQ49-3 SDE2 Protein SDE2 homolog 0 145.62 5.19E-08 191160000 67432 100150 58324 104240 99630 93577 75927 38847 59717 69835 FALSE TRUE 64796.68289 97293.82006 68864.44421 109619.8389 102834.6894 95469.19105 76856.21734 38044.79587 52938.17651 65105.01325 0.995264107 1.494413643 1.057744109 1.683738831 1.57952029 1.466387706 1.180496148 0.584360466 0.813119818 1 15.99048102 1.936270607 4.61985641 0.769652825 1.389643352 0.573800087 0.222808978 0.143509193 5.901449671 0.101010709 0.060145516 86.35164342 -1.936270607 0.619990527 TSNRYS(ph)PESQAQSVHHQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSNRYSPESQAQSVHHQR 18 1 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.004)S(0.004)NRYS(0.985)PES(0.008)QAQSVHHQR;TS(0.002)NRYS(0.982)PES(0.016)QAQSVHHQR;T(0.041)S(0.041)NRY(0.004)S(0.913)PESQAQSVHHQR;T(0.05)S(0.05)NRYS(0.898)PES(0.003)QAQSVHHQR 225.17 2.54E-19 476600000 214852 219957 220448 250433 215757 214371 227794 129549 232856 267481 TRUE FALSE 206455.3463 213684.0417 260287.8574 263357.8771 222697.0199 218705.7285 230581.8111 126873.7679 206423.1631 249364.2736 0.827926725 0.856915221 1.043805729 1.056117115 0.893059044 0.877053177 0.924678615 0.508788874 0.827797664 1 17.92789526 1.936295114 24.99949158 0.722395438 0.929844381 0.163116889 0.135122027 240.2061165 94262.51503 0.054770421 0.03534734 86.35651617 -1.936295114 0.207448943 RSGPLEES(ph)ERDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSGPLEESERDR 12 2 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 RS(0.037)GPLEES(0.963)ERDR 55.724 0.06541 1046300000 234930 330950 259720 422000 353230 359810 235800 216630 163970 188900 TRUE FALSE 225748.6759 321511.63 306657.1814 443779.4706 364591.9637 367085.6047 238685.7909 212156.5148 145356.813 176105.6347 1.281893542 1.82567486 1.74132521 2.51996179 2.070302658 2.084462574 1.355355786 1.204711678 0.825395583 1 17.42608155 1.936341049 2.040561149 0.980892394 1.940901842 0.636693594 0.310260701 0.216267654 1.663265308 0.195595203 0.096640171 86.36565058 -1.936341049 0.960009449 NDKSEEEQSSSS(ph)VKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVKK 15 2 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKSEEEQSSS(0.138)S(0.862)VKK 132.13 2.57E-05 327690000 234210 171730 231450 144800 146660 164130 232810 339300 349660 303970 TRUE FALSE 225056.8143 166832.4285 273278.1636 152273.1454 151377.4521 167448.8211 235659.1984 332293.3364 309968.0627 283381.8412 0.794182201 0.588719545 0.964346066 0.537342635 0.534181906 0.590894675 0.831595975 1.172599257 1.093817661 1 18.11238779 1.936419488 3.881399365 1.097947964 0.66744748 0.677258144 0.129554301 0.131293214 3.701139319 0.062485908 0.036205575 86.3812508 -1.936419488 -0.430500484 RRT(ph)PEPLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRTPEPLSR 9 2 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 RRT(0.884)PEPLS(0.116)R 67.08 0.077308 0 67778 89772 73300 107170 73376 92481 71495 68986 54329 80384 TRUE FALSE 65129.16083 87211.79046 86546.94055 112701.0565 75736.20568 94351.02918 72369.9772 67561.41499 48161.79969 74939.52008 0.869089644 1.163762329 1.15489051 1.503893492 1.010631047 1.259029002 0.965711778 0.901545872 0.642675582 1 16.19343912 1.93642612 2.265391118 0.825674315 1.168931646 0.387343905 0.175966329 0.296593204 2.793545222 0.098561641 0.050231174 86.38256985 -1.93642612 0.343257331 TAFDEAIAELDTLSEESYK ddPTM_BT-474_Pertuzumab_2h_R1 4 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 462.04 3.11E-214 4527680000 6752690 6284870 6117260 6725170 7102250 6734540 7738740 9151960 10091880 9908630 FALSE TRUE 6488787.409 6105631.661 7222784.96 7072256.83 7330700.321 6870717.013 7833449.015 8962968.828 8946292.091 9237509.664 0.702439039 0.660960787 0.781897418 0.765602103 0.793579719 0.743784555 0.848004419 0.970279778 0.96847445 1 23.13907254 1.936635894 1.58549149 0.993351364 0.737992098 0.893165909 0.036939237 0.122742904 0.574765734 0.027269877 0.012561473 86.42430464 -1.936635894 -0.255359266 FATVEVTDKPVDEALR ddPTM_BT-474_Pertuzumab_2h_R1 4 FATVEVTDKPVDEALR 16 1 Q9NRV9;A0A3B3IRV5;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ;;; 268.93 1.11E-27 3005260000 2534300 2592140 2014570 2433240 2283440 2463850 2604140 3094990 3311690 3150130 FALSE TRUE 2435256.754 2518214.705 2378647.613 2558819.808 2356888.921 2513670.735 2636010.244 3031077.375 2935760.835 2936768.889 0.829229962 0.857477997 0.809953967 0.871304452 0.802544909 0.855930729 0.897588589 1.032113009 0.999656747 1 21.48579831 1.936637942 2.705466006 1.013533332 0.837305409 0.92191076 0.022422459 0.0627326 0.836710473 0.011181855 0.005987837 86.42471229 -1.936637942 -0.176227924 TQIAICPNNHEVHIYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQIAICPNNHEVHIYEK 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 151.23 1.49E-07 1054900000 982630 907510 810620 883350 882220 1007870 919490 41335 1118770 934340 FALSE TRUE 944227.7332 881628.7033 957117.0661 928939.7994 910597.4075 1028249.822 930742.9937 40481.41781 991771.9199 871056.3196 1.08400308 1.012137428 1.098800439 1.066452052 1.04539441 1.180463076 1.068522176 0.046473938 1.138585299 1 19.73240648 1.936661808 24.99932115 0.606178122 1.080565132 0.217976084 0.277175811 209.640991 82743.81242 0.107635214 0.069467365 86.42946166 -1.936661808 0.474387011 SLSS(ph)PGGPSKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSSPGGPSKPK 12 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 SLS(0.011)S(0.989)PGGPSKPK;SLS(0.009)S(0.99)PGGPSKPK;S(0.028)LS(0.237)S(0.735)PGGPSKPK 140.27 3.61E-05 3036960000 3398400 3275600 3142230 3059730 3325750 3427500 3607400 3886300 4201200 4291200 TRUE FALSE 3265586.771 3182183.095 3710100.86 3217643.032 3432725.769 3496806.398 3651548.44 3806046.547 3724297.389 4000553.202 0.8162838 0.795435765 0.927396955 0.804299523 0.858062772 0.874080714 0.912760875 0.95138006 0.930945597 1 21.93176808 1.936800632 0.519301755 0.998497595 0.823825365 0.705721606 0.035310425 0.462595734 0.27377806 0.033982901 0.024503859 86.45709358 -1.936800632 -0.17467223 VLS(ph)PPHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSPPHIK 8 0 A0A0D9SG79;Q9NZ09-2;Q9NZ09;Q9NZ09-3;Q9NZ09-4 A0A0D9SG79 UBAP1 Ubiquitin-associated protein 1 1 VLS(1)PPHIK;VLS(1)PPHIK 88.496 0.0093875 241150000 622470 693050 662040 844470 903440 818370 633660 520730 516700 544760 TRUE FALSE 598143.1842 673284.8926 781685.355 888053.1979 932499.9681 834918.0021 641414.9206 509976.7435 458046.3822 507862.92 1.177765024 1.325721698 1.539166031 1.748608065 1.836125323 1.643982991 1.262968599 1.004162193 0.90190948 1 18.95407962 1.936802187 2.647147299 0.963399823 1.555898937 0.666649863 0.182375884 0.186898856 2.387599187 0.111393434 0.059318076 86.45740321 -1.936802187 0.592499115 GALHTVS(ph)HEDIR ddPTM_BT-474_Pertuzumab_2h_R1 5 GALHTVSHEDIR 12 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2;H0YD72 Q13136-2 PPFIA1 Liprin-alpha-1 1 GALHT(0.007)VS(0.993)HEDIR;GALHT(0.086)VS(0.914)HEDIR;GALHTVS(1)HEDIR;GALHT(0.034)VS(0.966)HEDIR;GALHT(0.062)VS(0.938)HEDIR 187.16 6.98E-06 9985160000 7411010 8146550 6348440 7924010 7392170 7814630 7068650 1343100 7337370 6611770 TRUE FALSE 7121379.536 7914218.37 7495744.328 8332969.106 7629945.861 7972647.173 7155158.253 1315364.516 6504462.518 6163948.929 1.155327472 1.283952619 1.216062043 1.351888084 1.237834049 1.293431738 1.160807517 0.213396401 1.055242766 1 22.55542348 1.936855083 11.19521649 0.672776064 1.256665739 0.498067369 0.220867871 0.57200874 100.239575 0.086036732 0.054986222 86.46793422 -1.936855083 0.583889675 MESTAGITTTTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 MESTAGITTTTSPR 14 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 MESTAGITTTT(0.076)S(0.924)PR;MESTAGITTTT(0.019)S(0.981)PR 140.3 1.05E-05 622000000 592290 722070 742730 972130 820180 834670 708520 644660 648800 696780 TRUE FALSE 569142.652 701477.2706 876957.8329 1022301.746 846561.8346 851547.5993 717191.0797 631347.5457 575150.944 649586.47 0.876161494 1.079882822 1.350024783 1.573773151 1.303231939 1.310907229 1.104073303 0.971922253 0.885410905 1 19.30916206 1.93694233 2.556203053 0.945125727 1.262655401 0.367870963 0.173280131 0.327480382 3.904920202 0.103694722 0.054708165 86.48530666 -1.93694233 0.317529674 DHENVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DHENVK 6 0 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 70.716 0.090136 108960000 232130 206990 182610 185430 174940 215260 185420 72106 179180 191560 FALSE TRUE 223058.103 201086.8479 215611.6891 195000.0645 180567.104 219612.7047 187689.2254 70616.9859 158840.2376 178585.4706 1.249027159 1.125997805 1.20733052 1.091914498 1.011096274 1.229734446 1.050977019 0.395424027 0.88943539 1 17.44625518 1.936972609 9.163536593 0.700418431 1.144305032 0.529760063 0.161733532 0.282637731 39.42060155 0.064195315 0.040685395 86.49133675 -1.936972609 0.443886601 TLDGIFSEQVAMGYSHSLVIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLDGIFSEQVAMGYSHSLVIAR 22 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 252.75 5.22E-37 384710000 257010 292790 219861 275580 236553 264990 255790 225529 287800 259082 FALSE TRUE 246965.7651 284439.9159 259594.7735 289802.7168 244161.9421 270348.2794 258920.4345 220871.7473 255130.1506 241534.1454 1.022487999 1.17763853 1.074774637 1.199841606 1.010879608 1.119296317 1.071982738 0.914453511 1.056290199 1 17.88186763 1.93709507 7.306149631 0.983070602 1.102948836 0.37038885 0.064297832 0.250711949 25.47215726 0.025575474 0.015982191 86.51572869 -1.93709507 0.119878234 HEEQPAPGYDTHGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HEEQPAPGYDTHGR 14 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 ; 133.47 2.57E-05 906300000 244220 303490 247940 316890 305160 287570 268650 146384 268220 272730 FALSE TRUE 234675.6124 294834.7623 292748.2734 333244.7309 314975.7485 293384.8624 271937.8191 143361.1192 237772.7901 254257.7542 0.922983109 1.159590052 1.151383856 1.310657101 1.238804887 1.153887571 1.069535991 0.56384168 0.93516436 1 17.95593225 1.937200466 7.45977973 0.790366102 1.162612197 0.502378386 0.142002082 0.19538053 20.54844867 0.0597657 0.037406019 86.5367272 -1.937200466 0.372246094 QEPSPKPNNK ddPTM_BT-474_Pertuzumab_2h_R1 2 QEPSPKPNNK 10 1 Q8N684-2;Q8N684;Q8N684-3;F5H669;F5H6M0;F5H047;J3QT54;F5H5B7;F5H1W4;F5H2K8;F5H6P5;F5H6A8;F5GXA3;C9JM38;C9J286;C9J323 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ; 74.944 0.036913 162183000 346560 376010 274800 304960 373700 410600 372190 422780 503260 509760 FALSE TRUE 333016.0521 365286.563 324462.4729 320699.0221 385720.3999 418902.6133 376744.9726 414049.4453 446132.0346 475233.5012 0.700741954 0.768646491 0.682743266 0.674824105 0.811643958 0.881466926 0.792757606 0.87125475 0.938763857 1 18.85827702 1.937376669 0.428075641 1.004993225 0.689823228 0.813929913 0.045221065 0.465831182 0.21046142 0.05266928 0.047308085 86.57184415 -1.937376669 -0.315169997 KPIETGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 7 KPIETGSPK 9 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KPIET(0.015)GS(0.985)PK;KPIET(0.353)GS(0.647)PK;KPIET(0.191)GS(0.809)PK;KPIET(0.001)GS(0.999)PK;KPIET(0.235)GS(0.765)PK;KPIET(0.006)GS(0.994)PK;KPIET(0.004)GS(0.996)PK 101.38 0.0024637 48690500000 36321000 28249900 24939400 23473300 27634400 26696000 30592300 37002800 40514000 34219800 TRUE FALSE 34901535.17 27444240.51 29446504.35 24684759.83 28523285.57 27235811.41 30966697.72 36238679.25 35915020.57 31902062.47 1.094021278 0.860265399 0.923028233 0.773766895 0.894089077 0.853731994 0.970680117 1.135935311 1.125789927 1 24.92714636 1.937402604 4.032501644 1.097224293 0.893676733 0.497256476 0.083790621 0.169705888 5.21691981 0.038505138 0.022477432 86.57701412 -1.937402604 -0.20354756 AVS(ph)PLDPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVSPLDPSK 9 0 Q14865;Q14865-2 Q14865 ARID5B AT-rich interactive domain-containing protein 5B 1 AVS(0.999)PLDPS(0.001)K;AVS(0.999)PLDPS(0.001)K 90.653 0.011837 646630000 1516570 1477100 1415340 1591360 1491200 1436500 1629420 1882060 1978950 1952770 TRUE FALSE 1457300.768 1434974.554 1671123.422 1673490.28 1539165.802 1465547.014 1649361.329 1843194.803 1754307.892 1820507.149 0.800491648 0.788227915 0.917943895 0.919244004 0.845459906 0.805021291 0.905990032 1.012462272 0.963636915 1 20.79590898 1.937488088 4.091562709 0.989797574 0.849999074 0.688156732 0.043844237 0.143275364 4.548404297 0.022392445 0.013104146 86.59405722 -1.937488088 -0.1397985 S(ph)SPVPPVPERR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPVPPVPERR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.5)S(0.5)PVPPVPERR 70.438 0.031707 4546500000 714410 790420 741640 764990 789000 894480 880140 1309200 1063500 1080700 TRUE FALSE 686490.0674 767877.9955 875670.8457 804471.2256 814378.9016 912566.9985 890911.4166 1282164.562 942775.9386 1007503.226 0.681377537 0.762159341 0.869149421 0.798480049 0.808313939 0.905770795 0.88427649 1.272615838 0.935754759 1 19.94235303 1.937502659 6.841123993 1.096528759 0.812104224 0.584773635 0.099030974 0.158147207 14.49122174 0.042148365 0.026208129 86.59696246 -1.937502659 -0.284424535 FRQDLMNIAGTTLSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 FRQDLMNIAGTTLSSK 16 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 107.57 0.0010192 558240000 339840 331480 237350 269640 280720 292030 301650 352420 376750 300940 FALSE TRUE 326558.6771 322026.515 280244.4248 283556.1527 289749.6137 297935.0467 305341.6829 345142.4038 333982.9195 280557.0658 1.163965257 1.147811102 0.998885642 1.010689757 1.032765341 1.061940985 1.088340734 1.230203926 1.19042776 1 18.09793472 1.937550882 8.550514575 1.164508878 1.066162358 0.126131753 0.075512111 0.533164456 68.67614179 0.032267468 0.020376043 86.60657859 -1.937550882 -0.098346519 KNEIMVAPDKDYFLIVIQNPTE ddPTM_BT-474_Pertuzumab_2h_R1 2 KNEIMVAPDKDYFLIVIQNPTE 22 2 Q9NP97;B1AKR6 Q9NP97 DYNLRB1 Dynein light chain roadblock-type 1 0 ; 125.58 8.34E-05 730200000 1528660 1398150 1184400 1344550 1346370 1503300 1464220 1612780 1841800 1769480 FALSE TRUE 1468918.277 1358276.131 1398447.427 1413942.387 1389677.214 1533697.756 1482139.562 1579475.529 1632726.585 1649631.544 0.890452346 0.823381522 0.8477332 0.857126182 0.842416732 0.929721405 0.898467035 0.957471707 0.989752282 1 20.65371239 1.937561692 0.792314106 1.003283167 0.847818544 0.853248022 0.022971571 0.207679011 0.244668191 0.019027569 0.009498486 86.6087343 -1.937561692 -0.155464623 KAPAGPSLEETSVSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 KAPAGPSLEETSVSSPK 17 1 K7EIX2;Q6AI08;A0A087WXZ7 K7EIX2 HEATR6 HEAT repeat-containing protein 6 1 KAPAGPSLEETS(0.01)VS(0.249)S(0.741)PK;KAPAGPSLEETSVS(0.024)S(0.976)PK;KAPAGPSLEETSVS(0.002)S(0.998)PK;KAPAGPSLEETSVS(0.035)S(0.965)PK;KAPAGPSLEETSVS(0.009)S(0.991)PK;KAPAGPSLEETSVS(0.031)S(0.969)PK 255.35 2.81E-27 8273840000 6203830 5174330 4607260 3998740 4690730 5086040 5702320 6896070 7850760 7016550 TRUE FALSE 5961377.465 5026763.175 5439894.37 4205115.451 4841611.59 5188883.214 5772106.698 6753663.745 6959574.638 6541312.819 0.911342666 0.768463963 0.831621193 0.642854969 0.740159005 0.793247985 0.88240799 1.032463044 1.063941571 1 22.64114878 1.937587204 2.232238774 1.040771202 0.773783913 0.743971295 0.065737297 0.150915617 1.381546683 0.038827376 0.019722421 86.61382211 -1.937587204 -0.266987289 TPAAEHAFEHWQEDAFFASQFLNGLNPVLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPAAEHAFEHWQEDAFFASQFLNGLNPVLIR 31 0 O15296-4;O15296;I3L1D5;O15296-3;O15296-2 O15296-4 ALOX15B Arachidonate 15-lipoxygenase B 0 ; 290.66 1.99E-81 870030000 419070 458040 340000 447210 495370 439470 403750 78055 438690 345440 FALSE TRUE 402692.2811 444977.1477 401445.5633 470290.5617 511304.0259 448356.3845 408691.2133 76443.13697 388891.7503 322043.0411 1.250430004 1.381731914 1.246558727 1.460334495 1.587688478 1.392225036 1.269057738 0.237369318 1.207576941 1 18.29689399 1.937711275 10.49776532 0.735069559 1.387324974 0.50539249 0.250050598 0.467516369 77.41840002 0.099764724 0.063617665 86.63856994 -1.937711275 0.652255415 GHPHSASSPS(ph)ER ddPTM_BT-474_Pertuzumab_2h_R1 3 GHPHSASSPSER 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 GHPHS(0.004)AS(0.213)S(0.131)PS(0.653)ER;GHPHSAS(0.044)S(0.184)PS(0.771)ER;GHPHSAS(0.036)S(0.036)PS(0.928)ER 136.83 6.64E-05 817311000 79089 108429 82224 92771 99791 115863 81026 5951.8 62445 69244 TRUE FALSE 75998.11444 105336.7111 97083.70586 97558.92243 103000.8681 118205.8292 82017.62043 5828.89325 55356.50539 64554.0422 1.177278941 1.631760111 1.50391366 1.51127519 1.595575809 1.831114291 1.270526486 0.090294783 0.857521907 1 15.97821982 1.937782582 6.733517822 0.57257146 1.546155229 0.684084989 0.269712124 0.118264318 10.58438098 0.11010657 0.068384102 86.65279634 -1.937782582 0.973583769 S(ph)PSLDVTVPEAELNLETPEISVGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSLDVTVPEAELNLETPEISVGGK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.499)PS(0.499)LDVT(0.002)VPEAELNLETPEISVGGK;S(0.494)PS(0.494)LDVT(0.012)VPEAELNLETPEISVGGK 148.28 1.40E-07 159135000 360350 338970 158307 312420 421400 211080 350340 578500 472570 449900 TRUE FALSE 346267.1236 329302.9075 186916.5964 328544.0336 434954.7137 215348.1822 354627.5657 566553.7728 418925.8348 419427.8723 0.825570131 0.785124045 0.445646579 0.783314737 1.037019098 0.51343317 0.845503099 1.350777596 0.998803042 1 18.67806321 1.937811685 7.25298129 1.144124573 0.732590873 0.477451236 0.179372556 0.213949065 21.72392862 0.075876791 0.047401994 86.65860325 -1.937811685 -0.411533699 SHLGNVHDQDN ddPTM_BT-474_Pertuzumab_2h_R1 2 SHLGNVHDQDN 11 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ; 154.94 3.18E-05 417240000 488080 512420 458840 486680 425440 592840 420890 71218 414280 263030 FALSE TRUE 469005.294 497806.2833 541762.5948 511797.6131 439124.664 604827.631 426040.9777 69747.32341 367252.6712 245214.7438 1.912630891 2.030083002 2.209339399 2.08714046 1.790775943 2.466522288 1.737419908 0.284433645 1.497677772 1 17.9036862 1.937929896 6.804186532 0.878277702 2.075871692 0.72045443 0.321408465 0.113903193 10.40513409 0.128811883 0.080075472 86.68219418 -1.937929896 1.197593989 TAPAAPAEDAVAAAAAAPSEPSEPSRPS(ph)PQPKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.012)EPS(0.048)EPS(0.189)RPS(0.751)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.009)EPS(0.214)RPS(0.778)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.008)EPS(0.039)RPS(0.953)PQPKPR 176.71 4.60E-17 4058300000 3194550 3230760 2301990 2697180 2775000 2985090 2977260 3389530 3608090 3560600 TRUE FALSE 3069703.454 3138621.888 2718010.8 2836381.783 2864260.395 3045450.565 3013696.598 3319535.021 3198514.75 3319437.391 0.924766186 0.945528268 0.818816709 0.854476663 0.862875258 0.91745986 0.907893792 1.000029412 0.963571345 1 21.66250731 1.938023255 1.883610116 0.990117621 0.882400286 0.598902136 0.036559296 0.244289369 1.607728969 0.024206293 0.011696108 86.70083005 -1.938023255 -0.107717335 AALDGGVASAAS(ph)PESKPSPGTK ddPTM_BT-474_Pertuzumab_2h_R1 4 AALDGGVASAASPESKPSPGTK 22 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 AALDGGVASAAS(1)PESKPSPGTK;AALDGGVASAAS(0.996)PES(0.004)KPSPGTK;AALDGGVASAAS(0.999)PESKPSPGTK;AALDGGVASAAS(0.992)PES(0.008)KPSPGTK 208.28 4.28E-23 3393650000 2343760 1977200 2106510 2022180 2154120 2370970 2717260 2878350 3158010 3438080 TRUE FALSE 2252163.268 1920812.192 2487203.216 2126544.952 2223409.226 2418912.638 2750514.641 2818911.067 2799525.944 3205215.779 0.702655741 0.59927703 0.775986201 0.663463897 0.693684725 0.754680123 0.858137121 0.879476223 0.87342823 1 21.61199005 1.938087372 0.611732405 0.984508019 0.664653353 0.837937431 0.046506993 0.271068132 0.205669951 0.041788912 0.025458993 86.71363091 -1.938087372 -0.319854667 NTPSQHS(ph)HSIQHS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 NTPSQHSHSIQHSPER 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 NT(0.007)PS(0.094)QHS(0.772)HS(0.13)IQHS(0.998)PER;NT(0.214)PS(0.273)QHS(0.398)HS(0.116)IQHS(1)PER 81.48 0.0059894 466037000 75238 96703 64095 86038 98801 88384 90689 384859.9 82553 98051 TRUE FALSE 72297.61578 93945.12512 75678.39229 90478.43149 101979.0239 90171.18504 91798.87911 376912.4086 73181.92953 91409.91844 0.790916533 1.027734481 0.827901322 0.989809783 1.11562318 0.986448589 1.004255126 4.123320697 0.800590688 1 16.48006309 1.938090076 24.99999549 2.382203343 0.965289242 0.180044262 0.867196879 233.107389 94131.00781 0.336842756 0.217402195 86.71417099 -1.938090076 -1.416914101 VDISAPDVDVHGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDISAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 250.95 2.00E-25 3076760000 2908910 3127390 2527340 2985650 2584970 2857480 2857170 395390 3279940 2547280 FALSE TRUE 2795226.581 3038199.899 2984086.558 3139739.754 2668117.908 2915260.203 2892136.901 387225.0583 2907614.962 2374750.457 1.177061183 1.279376488 1.256589529 1.322134604 1.123536117 1.227606966 1.217869816 0.163059263 1.224387579 1 21.17934449 1.938259072 24.96978773 0.699731903 1.232751475 0.350661226 0.260620296 184.4119852 74580.94917 0.100800592 0.065055516 86.74792029 -1.938259072 0.533019572 GGQS(ph)DDDEDEGVPASYHTVSLQLLDLMHTLHTR ddPTM_BT-474_Pertuzumab_2h_R1 3 GGQSDDDEDEGVPASYHTVSLQLLDLMHTLHTR 33 0 Q92538-3;Q92538-2 Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR 160.73 9.09E-14 305746000 41903 52247 41038 53017 56479.64 59680.3 44874.53 4361.9 45950.36 32208 TRUE FALSE 40265.38443 50756.96672 48454.47949 55753.21372 58296.35891 60887.07656 45423.71792 4271.825241 40734.26777 30026.52347 1.340993887 1.690404377 1.613722599 1.856798832 1.941495457 2.027776429 1.512786452 0.142268393 1.356609526 1 14.87394983 1.938259129 8.20297959 0.755854865 1.752489629 0.597467678 0.333475438 0.202383046 24.921106 0.136963251 0.086291163 86.74793175 -1.938259129 0.996634765 FHDIISDAEIEIVK ddPTM_BT-474_Pertuzumab_2h_R1 3 FHDIISDAEIEIVK 14 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;; 133.16 4.62E-05 318447000 844426 905416 681898 838307 761954 768063 730974 312879 831002 557163 FALSE TRUE 811424.8984 879594.4222 805132.1373 881572.1247 786462.9424 783593.7601 739919.8785 306417.9393 736670.1368 519425.8537 1.562157318 1.693397462 1.550042478 1.69720494 1.514100495 1.508576738 1.424495668 0.589916611 1.418239257 1 18.9865583 1.938469331 7.234138776 0.965763842 1.582540753 0.639016024 0.196075365 0.148750895 15.19568779 0.079465981 0.049646913 86.78992863 -1.938469331 0.616776911 EIKEEEEGS(ph)EDDSNVKPDFMVTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIKEEEEGSEDDSNVKPDFMVTLK 24 2 E9PGM7;O94988-6;O94988-5;O94988-1;O94988 E9PGM7 FAM13A Protein FAM13A 1 EIKEEEEGS(1)EDDSNVKPDFMVTLK 99.319 0.0025546 151940000 277530 212520 181930 157180 191280 193810 228420 299180 331270 240830 TRUE FALSE 266683.8208 206459.1377 214808.798 165292.0786 197432.6949 197728.971 231215.4723 293001.8284 293665.6184 224518.3696 1.187804015 0.919564569 0.956753777 0.736207371 0.879360986 0.880680594 1.029828752 1.305023856 1.307980362 1 17.77647396 1.938471964 4.208027628 1.230134881 0.918508696 0.46274653 0.132472042 0.175308329 5.946419281 0.061421176 0.036138556 86.7904548 -1.938471964 -0.311626185 LLPPYLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPPYLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 89.08 0.042192 300520000 300200 375930 280220 366540 354080 357620 328820 308540 330180 356010 FALSE TRUE 288467.8521 365208.8445 330861.9875 385457.1733 365469.3048 364851.3214 332844.1975 302168.5412 292699.3506 331897.1256 0.869148389 1.100367603 0.996881148 1.161375449 1.101152365 1.099290392 1.00285351 0.910428316 0.881897817 1 18.34037661 1.938481861 3.719960636 0.923892525 1.060925323 0.322014642 0.079744223 0.250246022 6.476912781 0.03753609 0.021623628 86.79243265 -1.938481861 0.137032798 VSDQNS(ph)PVLPK ddPTM_BT-474_Pertuzumab_2h_R1 8 VSDQNSPVLPK 11 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK 203.96 3.65E-08 11768460000 9271450 8840530 7733970 7719740 8526170 9085690 9438460 9849300 11231250 11101940 TRUE FALSE 8909111.484 8588406.74 9131670.42 8118156.707 8800422.001 9269408.877 9553970.697 9645908.513 9956325.585 10349995.72 0.860784075 0.829798096 0.882287362 0.784363292 0.850282671 0.895595431 0.923089338 0.931972223 0.961964223 1 23.30312683 1.938482798 0.796941174 0.989256342 0.837665325 0.815303907 0.026282408 0.256395164 0.305262802 0.022998066 0.01144773 86.79261986 -1.938482798 -0.151591017 SSPVNNHHS(ph)PGQTPTLGQPEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPVNNHHSPGQTPTLGQPEAR 22 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;E7EWM2;E7EMW0;Q96L14 Q5SW79 CEP170;CEP170P1 Centrosomal protein of 170 kDa;Cep170-like protein 1 SSPVNNHHS(1)PGQTPTLGQPEAR 120.31 2.46E-05 496910000 72242 66705 65730 63739 61615 67588 64824 38062 72525 62793 TRUE FALSE 69418.70277 64802.63871 77608.87316 67028.57743 63596.90243 68954.67567 65617.3355 37276.0064 64292.26605 58539.97418 1.185834188 1.106980992 1.3257415 1.145005244 1.08638419 1.177907518 1.120897924 0.636761579 1.098262631 1 15.83713449 1.938498428 11.63356584 0.872953755 1.168613413 0.452762922 0.126048364 0.781050342 146.4937311 0.049977037 0.031982674 86.79574346 -1.938498428 0.295659658 TRDELEVIHLIEEHR ddPTM_BT-474_Pertuzumab_2h_R1 8 TRDELEVIHLIEEHR 15 1 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;;;;;; 220.59 1.06E-12 3200660000 1134499 1205311 1026987 1228517 1215560 1204844 1159561 165855.2 1247781 1087005 FALSE TRUE 1090161.525 1170936.71 1212586.396 1291920.91 1254659.591 1229206.771 1173752.054 162430.2322 1106138.132 1013381.183 1.075766496 1.155475087 1.196574809 1.274861751 1.23809245 1.212975721 1.158253255 0.160285424 1.091532141 1 19.95074552 1.9385053 18.30163254 0.657775983 1.195728111 0.394351807 0.240234199 10.83855136 3225.046424 0.093403193 0.060219637 86.79711693 -1.9385053 0.537952128 S(ph)RS(ph)PTIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPTIK 7 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 2 S(0.997)RS(0.98)PT(0.023)IK 52.716 0.081956 859320000 313180 306150 245730 292580 282280 305330 308360 1164200 391770 428950 TRUE FALSE 300940.5794 297418.9018 290138.8772 307680.0889 291359.7926 311503.9818 312133.8019 1140158.863 347297.912 399896.8344 0.75254554 0.743739075 0.725534318 0.769398661 0.728587394 0.778960859 0.780535816 2.851132505 0.86846877 1 18.60926834 1.938704906 24.99681609 1.788121522 0.750959756 0.328384124 0.509824945 190.6497919 77748.57371 0.196798119 0.127009871 86.83701901 -1.938704906 -1.037161766 LPSNSLGFTATHNTS(ph)PAAPPTEVTICQSSEVSKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSNSLGFTATHNTSPAAPPTEVTICQSSEVSKPK 35 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 LPS(0.001)NSLGFT(0.001)AT(0.001)HNT(0.197)S(0.794)PAAPPT(0.003)EVT(0.001)ICQS(0.001)S(0.001)EVSKPK 60.959 0.013301 562920000 385290 339600 315660 331230 360830 395490 365320 409720 477600 464320 TRUE FALSE 370232.4408 329914.9405 372706.7838 348324.82 372436.4246 403487.0788 369790.8954 401259.1388 423384.8503 432871.1928 0.855294709 0.762154992 0.861010827 0.804684686 0.860386255 0.932118111 0.85427467 0.926971223 0.978085068 1 18.72357827 1.938738027 0.454645192 1.006970103 0.804378339 0.735546265 0.036507517 0.481507373 0.236003562 0.036704014 0.030804431 86.84364176 -1.938738027 -0.202591764 EIAVHIGDRDNAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIAVHIGDRDNAVR 14 1 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 143.38 5.49E-06 472430000 271310 343610 205717 300910 295840 342490 275680 243870 278260 270920 FALSE TRUE 260706.9053 333810.5792 242894.638 316440.0012 305355.9623 349415.3825 279053.8543 238833.9993 246673.0914 252570.3471 1.032215018 1.32165388 0.961691033 1.252878672 1.208993715 1.383437868 1.104855964 0.945613775 0.976651037 1 17.94632574 1.938749085 5.040746353 0.977010712 1.196062778 0.409548315 0.117539573 0.20535023 10.40298336 0.051158675 0.030872957 86.84585298 -1.938749085 0.219052067 GHEGPVWQVAWAHPMYGNILASCSYDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHEGPVWQVAWAHPMYGNILASCSYDR 27 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6;E7ERC8 P55735 SEC13 Protein SEC13 homolog 0 196.55 3.62E-25 1386600000 232540 267440 232170 368720 288420 321450 291820 103980 309550 324920 FALSE TRUE 223452.0797 259812.8731 274128.2836 387749.6834 297697.2912 327949.9392 295391.3805 101832.7767 274411.1817 302912.879 0.737677713 0.857714845 0.904974013 1.280069981 0.982781888 1.082654327 0.975169433 0.336178432 0.905907938 1 18.20854339 1.93881781 24.99832512 0.669121139 0.984207994 0.163601156 0.213701522 280.0839172 114438.2379 0.087369559 0.056386429 86.85959701 -1.93881781 0.315086855 NSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 43 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 NS(0.044)PMAQT(0.956)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 143.82 8.74E-14 351810000 101550 106450 82555 70041 101610 89034 110650 110400 152970 114430 TRUE FALSE 97581.31373 103414.1502 97474.52493 73655.8244 104878.3779 90834.32848 112004.1678 108120.2014 135605.4869 106679.5542 0.9147143 0.969390536 0.913713276 0.690439935 0.983116013 0.851468955 1.049912222 1.013504436 1.271147859 1 16.70292418 1.938819076 1.632422483 1.11729039 0.886102431 0.457661732 0.103701033 0.331488073 1.645169628 0.067287032 0.031272601 86.85985027 -1.938819076 -0.231187959 LSSLIILMPHHVEPLER ddPTM_BT-474_Pertuzumab_2h_R1 3 LSSLIILMPHHVEPLER 17 0 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 ;; 141.97 4.23E-07 1689510000 1833920 2240660 1769980 1942220 1847540 2135690 1865940 238697 2034840 1612320 FALSE TRUE 1762248.379 2176758.571 2089854.759 2042458.207 1906967.802 2178875.115 1888775.932 233767.8235 1803853.494 1503116.13 1.172396692 1.448163935 1.390348169 1.358815973 1.268676294 1.44957204 1.256573523 0.155522131 1.200075934 1 20.51952505 1.938976897 12.6613529 0.694711105 1.35150683 0.46898857 0.264345133 1.063151534 219.6028713 0.10247307 0.065727907 86.89142039 -1.938976897 0.656795725 TESALSYYEFLLHIQQQVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 TESALSYYEFLLHIQQQVNK 20 0 O95486 O95486 SEC24A Protein transport protein Sec24A 0 ; 244.86 6.39E-30 236560000 277370 256700 227370 213480 270480 278880 275290 274100 352240 324120 FALSE TRUE 266530.0738 249379.1673 268460.8168 224497.7284 279180.2348 284519.1447 278659.0814 268439.7392 312255.1919 302167.0637 0.882061964 0.825302282 0.888451619 0.742958963 0.923926756 0.941595491 0.922202036 0.888381864 1.033385929 1 18.20498689 1.938986549 0.55545409 1.006002445 0.839092945 0.517086595 0.054357736 0.704623465 0.460495608 0.052315739 0.035119381 86.89335165 -1.938986549 -0.166909499 IEFYELDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEFYELDKK 9 1 O15305;H3BV55;H3BPH4 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 90.827 0.017905 686610000 409130 469510 287370 450860 608240 576740 722200 2012400 1041300 1172300 FALSE TRUE 393140.7473 456120.0345 339304.1515 474128.9386 627804.592 588402.078 731038.4996 1970843.237 923095.9895 1092899.077 0.359722829 0.417348723 0.310462474 0.433826827 0.574439676 0.538386472 0.668898451 1.803316773 0.844630588 1 20.05972875 1.938991276 7.215869551 1.293298256 0.450967372 0.664500345 0.244998846 0.137748513 14.1291707 0.100985382 0.063092351 86.89429733 -1.938991276 -0.842330884 LEQLESGEEELVLAEYES(ph)DEEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEQLESGEEELVLAEYESDEEKK 23 1 Q96FC9-5;F5GXJ8;F6WZM0;F5H235;C9K0E8;B4DMS8;Q96FC9-4;Q96FC9-3;Q96FC9-2;A8MPP1;Q96FC9 Q96FC9-5 DDX11;DDX11L8 Probable ATP-dependent RNA helicase DDX11;Putative ATP-dependent RNA helicase DDX11-like protein 8 1 LEQLESGEEELVLAEYES(1)DEEKK;LEQLESGEEELVLAEY(0.018)ES(0.982)DEEKK 263.01 4.53E-44 115352000 142567 98615 111971 90884 115953 112427 141327 169674 198482 184573 TRUE FALSE 136995.324 95802.59675 132206.6505 95574.53413 119682.7336 114700.351 143056.6021 166170.1726 175951.1555 172071.7063 0.796152528 0.55675973 0.768323005 0.555434337 0.695539878 0.666584608 0.831377832 0.965703056 1.022545538 1 17.39265037 1.939010887 1.848077684 1.010018058 0.664715255 0.795769698 0.073521471 0.133010455 0.843345441 0.041981323 0.020189146 86.89822133 -1.939010887 -0.345302803 SGS(ph)PSDNSGAEEMEVSLAKPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.03)GS(0.92)PS(0.051)DNSGAEEMEVSLAKPK;S(0.105)GS(0.598)PS(0.293)DNS(0.004)GAEEMEVSLAKPK;S(0.134)GS(0.85)PS(0.016)DNSGAEEMEVSLAKPK;S(0.004)GS(0.673)PS(0.238)DNS(0.084)GAEEMEVSLAKPK 187.72 1.68E-17 3494410000 2138830 1997390 1617380 1641610 1785290 1939870 2109900 2582490 2814890 2726180 TRUE FALSE 2055242.159 1940426.393 1909676.544 1726333.689 1842715.474 1979095.501 2135721.587 2529160.679 2495355.488 2541533.4 0.808662266 0.763486481 0.751387546 0.679248869 0.725040825 0.778701354 0.840327964 0.995131789 0.981830688 1 21.27726776 1.939026994 1.996403679 0.999203546 0.744783718 0.917980027 0.032237045 0.088729363 0.654019786 0.021097393 0.010379639 86.90144427 -1.939026994 -0.254419828 RS(ph)STSGDTEEEEEEEVVPFSSDEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSTSGDTEEEEEEEVVPFSSDEQK 25 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;O15231-2;H7BZT5;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 RS(0.476)S(0.476)T(0.034)S(0.013)GDT(0.002)EEEEEEEVVPFSSDEQK;RS(0.439)S(0.308)T(0.083)S(0.168)GDT(0.002)EEEEEEEVVPFSSDEQK 182.92 1.31E-17 998490000 973530 829150 756760 843980 872750 829980 914040 1126840 1096760 1078560 TRUE FALSE 935483.3713 805503.4538 893523.366 887537.9089 900822.7964 846762.7643 925226.2949 1103570.36 972260.4028 1005508.171 0.930358796 0.801090908 0.888628648 0.882675979 0.895888092 0.842124201 0.920157908 1.097525005 0.966934363 1 19.93949337 1.939035388 6.019313437 1.02835333 0.872836723 0.689222938 0.044361572 0.109192348 8.055165668 0.018104409 0.011139663 86.90312385 -1.939035388 -0.155516608 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR 39 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 ; 221.47 7.96E-40 876840000 107135 95164 65318 98771 107736 102743 90140 46934 93356 88985 FALSE TRUE 102948.0458 92450.0159 77122.41559 103868.5831 111201.4263 104820.5339 91243.16028 45964.7965 82758.61826 82957.96669 1.240966358 1.114419984 0.929656532 1.252062789 1.340455061 1.263537886 1.099872187 0.554073326 0.997596995 1 16.34009291 1.939118504 8.933369528 0.806393239 1.184348756 0.477899324 0.15681587 0.324245098 45.39220556 0.066958718 0.042397883 86.91975711 -1.939118504 0.377955518 LCLTLHNNEGSYLAHTQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LCLTLHNNEGSYLAHTQGK 19 0 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 205.88 2.26E-16 1044600000 555930 566870 457950 534210 558160 535050 543650 397980 629030 640720 FALSE TRUE 534203.641 550703.4226 540711.752 561780.6421 576113.7233 545869.0776 550303.3513 389761.5739 557625.1515 597323.4637 0.894328908 0.921951767 0.905224363 0.940496525 0.964492035 0.913858421 0.921281993 0.652513416 0.933539674 1 19.18815287 1.939263366 24.99957925 0.814280397 0.924515781 0.012541877 0.088396916 322.9437516 132924.7917 0.034591668 0.02232618 86.94875461 -1.939263366 0.110235384 RAGDLLEDS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 7 RAGDLLEDSPK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK 174.59 6.63E-06 56839580000 29627120 23603430 24609030 22482590 24959310 22356070 27749010 35173540 36547450 32569860 TRUE FALSE 28469259.4 22930283.29 29056429.15 23642919.16 25762148.87 22808125.05 28088610.69 34447194.11 32398736.7 30363874.37 0.93760299 0.755183051 0.956940764 0.778652911 0.848447354 0.751159907 0.925066753 1.134479536 1.067015899 1 24.85585255 1.939276669 4.794589942 1.074751406 0.837059604 0.669451677 0.071873359 0.11139559 5.074892213 0.030203738 0.018120125 86.951418 -1.939276669 -0.237691802 KNS(ph)STDQGSDEEGSLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNSSTDQGSDEEGSLQK 17 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 KNS(0.875)S(0.063)T(0.063)DQGSDEEGSLQK 140.95 3.93E-07 251180000 147560 119710 121150 108920 133270 129590 147670 175500 220130 161580 TRUE FALSE 141793.1921 116295.988 143044.5 114541.3743 137556.7506 132210.3986 149477.2296 171875.8637 195141.7653 150636.0427 0.941296582 0.772032947 0.949603411 0.760384913 0.913172891 0.87768104 0.992307199 1.141000923 1.295452017 1 17.20070748 1.939344451 2.160500501 1.167082762 0.863589425 0.655853718 0.089422407 0.166496752 1.430781028 0.04822091 0.024295347 86.96498987 -1.939344451 -0.303493337 GMGGHGYGGAGDASSGFHGGHFVHMR ddPTM_BT-474_Pertuzumab_2h_R1 1 GMGGHGYGGAGDASSGFHGGHFVHMR 26 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 51.645 0.043322 54671000 16847 16412 12445 18759 15431 16372 15324 7910.4 15276 16749 FALSE TRUE 16188.60061 15943.94583 14694.08834 19727.15424 15927.35213 16703.05306 15511.5397 7747.047476 13541.93252 15614.57531 1.036762146 1.021093786 0.941049503 1.263380774 1.020031081 1.069709084 0.993401318 0.496142055 0.867262302 1 13.93060571 1.939413469 10.0604634 0.734519749 1.056899944 0.404610536 0.142896608 0.469599613 76.24515495 0.057015382 0.03630321 86.97881156 -1.939413469 0.322380195 NQDPAHPDKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 NQDPAHPDKPK 11 1 Q8ND04;Q8ND04-2;Q8ND04-3 Q8ND04 SMG8 Protein SMG8 0 ;; 91.961 0.0062193 336446000 1030540 877840 808280 742810 842740 873600 1020510 1064660 1337240 1170010 FALSE TRUE 990265.3575 852804.8627 954354.1761 781146.5131 869847.4975 891264.7906 1032999.307 1042674.399 1185442.121 1090764.181 0.90786384 0.781841646 0.874940884 0.716146099 0.797466137 0.817101264 0.947041831 0.955911844 1.086799642 1 20.0569078 1.93949864 1.55882102 1.030002193 0.809735482 0.718265033 0.056859199 0.19842025 0.897967034 0.037716844 0.017345435 86.99587096 -1.93949864 -0.220266712 KLQIQCVVEDDKVGTDLLEEEITK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLQIQCVVEDDKVGTDLLEEEITK 24 2 P29692;P29692-2;E9PRY8;P29692-4;E9PQZ1;H0YE72;H0YE58;P29692-3 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ; 290.41 4.82E-62 363520000 534820 414850 445510 471890 461810 470720 587540 729390 819180 790930 FALSE TRUE 513918.6431 403018.8842 526023.5673 496244.2995 476664.5381 480238.2809 594730.4903 714327.8416 726190.1207 737359.6066 0.696971516 0.546570331 0.713388098 0.673001742 0.646447858 0.651294533 0.806567765 0.968764542 0.984852051 1 19.49200886 1.939511489 2.050735244 0.993107309 0.65074929 0.922857433 0.042768738 0.077195345 0.599495819 0.02487185 0.012340056 86.99844481 -1.939511489 -0.342358019 IGLIHGHQVIPWGDMASLALLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGLIHGHQVIPWGDMASLALLQR 23 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 201.31 1.32E-24 1157410000 398660 448230 367060 390030 382420 365020 366490 184639 373900 371890 FALSE TRUE 383079.9265 435446.9193 433395.9072 410159.495 394720.8866 372400.9545 370975.2142 180826.1401 331456.4395 346701.5591 1.104927037 1.255970468 1.250054682 1.183033316 1.13850335 1.074125411 1.070013112 0.52156137 0.956028119 1 18.4033348 1.939545956 7.622562759 0.776511733 1.166734972 0.563456509 0.132515671 0.178595328 20.16896269 0.055181641 0.03461647 87.0053496 -1.939545956 0.390223239 IKELEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKELEQK 7 1 O60925 O60925 PFDN1 Prefoldin subunit 1 0 ; 93.178 0.013795 862690000 1211800 1062920 926650 984500 1016430 1092170 1149090 1301770 1489210 1360060 FALSE TRUE 1164441.516 1032606.562 1094116.268 1035310.163 1049124.394 1114254.426 1163152.907 1274887.995 1320161.124 1267941.925 0.918371334 0.814395787 0.862907241 0.816528062 0.827423065 0.878789796 0.917355034 1.005478224 1.04118422 1 20.27405724 1.939547401 1.731632098 1.024656457 0.846318365 0.853203301 0.030267288 0.117790392 0.657133126 0.018807383 0.008883517 87.005639 -1.939547401 -0.178338092 APLATGEDDDDEVPDLVENFDEASK ddPTM_BT-474_Pertuzumab_2h_R1 5 APLATGEDDDDEVPDLVENFDEASK 25 0 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 ;;;; 198.6 7.55E-25 656484000 495275 481833 545677 581693 530772 553095 686375 742052 869710 888680 FALSE TRUE 475919.1054 468091.5946 644292.9724 611714.2454 547844.7634 564278.9599 694775.0626 726728.3669 770984.1669 828488.912 0.574442335 0.564994399 0.777672414 0.738349345 0.66125781 0.68109416 0.838605143 0.877173317 0.930590809 1 19.66012286 1.939672985 0.491881925 1.019624444 0.61554042 0.808794105 0.061160194 0.411688198 0.225196484 0.066796573 0.051260849 87.03080194 -1.939672985 -0.404084023 DWYDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DWYDVK 6 0 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 112.75 0.062188 4075800000 5644200 5224400 4818800 4314300 5100300 4973700 5211600 6091300 5995500 5926000 FALSE TRUE 5423618.424 5075405.227 5689664.354 4536961.54 5264355.781 5074271.622 5275381.12 5965512.526 5314915.975 5524626.742 0.981716716 0.918687445 1.029873079 0.82122499 0.952888951 0.918482254 0.954884622 1.079803723 0.962040736 1 22.39744556 1.939704938 9.147408075 1.021670801 0.936018521 0.264900168 0.056896827 0.520870647 75.87652567 0.022746601 0.014421984 87.03720534 -1.939704938 -0.08565228 AHLLAEVIENLECDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHLLAEVIENLECDPR 16 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 ; 155.92 2.13E-07 120981000 94954 88922 67691 77606 93009 81721 80044 51952 82631 85723 FALSE TRUE 91243.0927 86386.03162 79924.26948 81611.25496 96000.71895 83373.45461 81023.60242 50879.17305 73251.0753 79916.90486 1.141724556 1.080948165 1.000092153 1.021201398 1.201256719 1.043251797 1.013848103 0.636650946 0.916590494 1 16.28621309 1.939827914 8.256986135 0.813348863 1.076240131 0.488350005 0.103242347 0.240800192 30.71972126 0.042300855 0.026672667 87.06185458 -1.939827914 0.262891268 DVHHEPVYPQPPFSYSDLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVHHEPVYPQPPFSYSDLSR 20 0 A0A3B3ITS5;Q14181;H0YDR7;Q14181-2 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 0 ; 167.16 8.17E-12 1229330000 684880 782720 655390 748890 719340 779710 738770 156680 792630 803620 FALSE TRUE 658114.1324 760397.592 773833.5521 787540.3026 742478.2244 795476.2704 747811.2883 153444.5032 702653.9654 749190.1016 0.8784341 1.014959475 1.032893454 1.051188878 0.991041156 1.061781608 0.998159595 0.204813842 0.937884742 1 19.51497231 1.939880947 24.99910508 0.619780267 1.010038794 0.253409839 0.209893435 219.9727413 91469.96534 0.081352398 0.052502878 87.07248666 -1.939880947 0.390258527 GAPSS(ph)PATGVLPSPQGK ddPTM_BT-474_Pertuzumab_2h_R1 4 GAPSSPATGVLPSPQGK 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 1 GAPS(0.013)S(0.986)PATGVLPSPQGK;GAPS(0.033)S(0.967)PATGVLPSPQGK;GAPS(0.011)S(0.989)PATGVLPSPQGK;GAPS(0.023)S(0.977)PATGVLPSPQGK 240.24 2.72E-20 1562270000 1940480 2020970 1752800 2166690 2119310 2090480 1911630 1928090 1945060 2050300 TRUE FALSE 1864643.896 1963333.914 2069569.951 2278513.131 2187479.531 2132750.938 1935025.1 1888274.268 1724264.943 1911431.355 0.975522292 1.027153766 1.082733076 1.192045492 1.144419613 1.115787356 1.012343496 0.98788495 0.902080495 1 20.86622196 1.93990042 2.302428163 0.957667483 1.093066316 0.461807293 0.06131575 0.29127684 2.832942221 0.038235798 0.019637015 87.07639088 -1.93990042 0.135398832 KAEQGS(ph)EEEGEGEEEEEEGGESK ddPTM_BT-474_Pertuzumab_2h_R1 6 KAEQGSEEEGEGEEEEEEGGESK 23 1 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK 294.75 7.66E-62 11375970000 5964880 4292190 4440340 3857370 4554710 4126010 5164430 6661400 6994000 6028330 TRUE FALSE 5731765.895 4169780.944 5242808.213 4056449.328 4701216.384 4209440.749 5227633.839 6523839.762 6200070.441 5620025.84 1.019882481 0.741950493 0.932879734 0.721784818 0.836511525 0.749007366 0.93017968 1.160820243 1.103210309 1 22.42214533 1.939936915 4.538201825 1.098029732 0.829195988 0.597006136 0.093170152 0.129735118 5.250468057 0.039686294 0.02364584 87.08370846 -1.939936915 -0.268833744 AST(ph)PDWVSEGPQPGLR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AS(0.001)T(0.999)PDWVSEGPQPGLR;AST(1)PDWVSEGPQPGLR;AS(0.061)T(0.939)PDWVSEGPQPGLR;AS(0.003)T(0.997)PDWVSEGPQPGLR;AS(0.089)T(0.911)PDWVSEGPQPGLR 340.47 5.58E-71 2519790000 1261282 1402021 1142023 1358066 1159995 1299461 1369335 1687379 1567384 1700417 TRUE FALSE 1211989.705 1362036.734 1348411.96 1428155.949 1197307.293 1325736.992 1386093.331 1652534.034 1389461.139 1585246.242 0.764543497 0.859195687 0.850600951 0.9009048 0.755281584 0.836297199 0.874370993 1.042446271 0.876495463 1 20.59627553 1.93996429 5.760573229 0.974712334 0.832002868 0.573695737 0.055862928 0.151114733 10.31282129 0.023661171 0.014504915 87.0891977 -1.93996429 -0.142709466 RHS(ph)LSSTK ddPTM_BT-474_Pertuzumab_2h_R1 2 RHSLSSTK 8 1 P42858;A0A3B3IU44 P42858 HTT Huntingtin 1 RHS(0.998)LS(0.002)STK;RHS(1)LSSTK 101.35 0.0033429 383200000 161310 162104 110225 142202 141244 149957 146082 119429 186399 155495 TRUE FALSE 155005.8269 157480.9526 130145.1094 149541.0623 145787.2415 152989.2333 147869.7952 116962.7494 165239.767 144963.1851 1.069277187 1.086351355 0.897780421 1.031579584 1.005684591 1.055366113 1.020050677 0.806844505 1.139874009 1 17.14532703 1.940013413 24.99990177 0.948945234 1.022289633 0.003376587 0.090842372 528.290761 220168.1096 0.036502722 0.023558352 87.09904894 -1.940013413 0.0733444 WKDTDEADLVLAK ddPTM_BT-474_Pertuzumab_2h_R1 3 WKDTDEADLVLAK 13 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 ;; 164.65 3.34E-05 3600770000 6449890 5950690 4457650 5173980 5084550 5732200 6258050 7077800 8113900 7767300 FALSE TRUE 6197821.168 5780982.148 5263246.515 5441009.728 5248099.168 5848109.011 6334637.888 6931640.957 7192844.088 7241213.853 0.855909146 0.798344347 0.726845888 0.751394702 0.724754064 0.807614459 0.874803316 0.95724848 0.993320213 1 22.78780013 1.940188479 1.568465316 0.995517119 0.769074289 0.869045365 0.036228312 0.135413692 0.62043444 0.026511664 0.012216509 87.13416602 -1.940188479 -0.22644283 EDLPAENGETKTEES(ph)PAS(ph)DEAGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDLPAENGETKTEESPASDEAGEK 24 1 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 2 EDLPAENGETKT(0.001)EES(0.999)PAS(1)DEAGEK;EDLPAENGETKTEES(1)PAS(1)DEAGEK 236.6 1.16E-37 738960000 2053750 1366660 1446940 1113720 1512070 1122360 1530460 2172460 2046390 1566950 TRUE FALSE 1973487.179 1327684.195 1708434.245 1171199.223 1560707.105 1145054.888 1549190.227 2127597.942 1814092.386 1460819.081 1.350945648 0.908862851 1.169504333 0.80174146 1.068378094 0.783844422 1.060494244 1.45644178 1.241832346 1 20.47834608 1.940259447 9.73413109 1.277796053 1.001835661 0.198629154 0.190001105 0.647559039 102.6609568 0.074926557 0.047647359 87.14840574 -1.940259447 -0.275960392 SHMMDVQGSTQDSAIKDFVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHMMDVQGSTQDSAIKDFVLK 21 1 P13667 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 249.28 7.25E-31 1686130000 656890 765270 575770 539780 604970 691580 647110 294580 871610 661690 FALSE TRUE 631218.0126 743445.2489 679824.4469 567638.1105 624429.4095 705564.2214 655029.5258 288496.8201 772668.4869 616873.1469 1.023254158 1.205183355 1.10204902 0.920186125 1.012249297 1.143775223 1.061854498 0.467676088 1.252556528 1 19.23461432 1.940294544 24.99990012 0.826888976 1.06939267 0.081309357 0.198214334 349.3449519 146277.0323 0.078885289 0.050912244 87.15544892 -1.940294544 0.242503693 MSLQTDEDEHSIEMHLPYTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 MSLQTDEDEHSIEMHLPYTAK 21 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 96.131 0.00076557 85846000 69896 82343 62916 78193 76689 82577 76242 8214.6 86702 70933 FALSE TRUE 67164.38705 79994.65826 74286.32076 82228.5501 79155.77133 84246.76352 77175.0724 8044.965639 76859.95244 66128.64473 1.015662537 1.209682409 1.123360702 1.24346341 1.196996727 1.273982914 1.167044519 0.121656291 1.162279263 1 16.01298771 1.940339497 24.96767295 0.658875426 1.183499388 0.318886069 0.265107968 207.6067973 86882.02341 0.102659191 0.066255099 87.16447061 -1.940339497 0.524623961 ASPDSRHS(ph)PATISSSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPDSRHSPATISSSTR 17 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 AS(0.001)PDS(0.09)RHS(0.858)PAT(0.018)IS(0.022)S(0.004)S(0.004)T(0.004)R;ASPDS(0.038)RHS(0.953)PAT(0.003)IS(0.004)S(0.001)S(0.001)T(0.001)R;ASPDS(0.035)RHS(0.962)PAT(0.001)IS(0.001)SSTR;ASPDS(0.025)RHS(0.975)PATISSSTR 121.33 3.67E-05 1079410000 633760 876380 513745 636460 646970 824390 642283 537240 615660 652460 TRUE FALSE 608991.9585 851386.5005 606590.1497 669307.7769 667780.3776 841059.7306 650143.4515 526145.8063 545772.8579 608268.303 1.001189698 1.399689078 0.997241097 1.100349588 1.097838527 1.382711751 1.06884322 0.864989682 0.897256778 1 19.2143483 1.940444975 5.487360947 0.916327516 1.165559628 0.398703259 0.132906344 0.203251488 12.58468674 0.056790396 0.034651091 87.18564306 -1.940444975 0.249232113 AFS(ph)HSGVHSLDGGEVDSQALQELTQMVSGPASYSGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AFSHSGVHSLDGGEVDSQALQELTQMVSGPASYSGPK 37 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 AFS(0.333)HS(0.333)GVHS(0.333)LDGGEVDS(0.001)QALQELTQMVSGPASYSGPK 129.25 2.26E-08 14382000 10528 11866 9588.9 9338.5 9040.1 9820.6 8765.9 3566.6 8125.4 7276 TRUE FALSE 10116.55412 11527.5933 11321.82753 9820.461104 9330.883027 10019.17926 8873.179706 3492.948464 7203.038656 6783.190039 1.491415405 1.699435403 1.669100743 1.447764407 1.37558921 1.477060086 1.308113094 0.514941855 1.061895453 1 12.7277482 1.940510305 5.259031911 0.820281845 1.521830592 0.767227376 0.163909874 0.093209931 5.265424029 0.074149032 0.045033598 87.19875921 -1.940510305 0.701548747 LLGLNELDDLLGKESPS(ph)KDSEPSCWGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLGLNELDDLLGKESPSKDSEPSCWGK 27 2 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 LLGLNELDDLLGKES(0.131)PS(0.869)KDSEPSCWGK 180.96 9.14E-18 194740000 335320 260860 199840 211690 194420 192570 261390 370510 389380 253300 TRUE FALSE 322215.3237 253420.5282 235955.5334 222615.3463 200673.6959 196463.8973 264588.969 362858.839 345179.2148 236143.7654 1.364487956 1.073162054 0.999202892 0.942711089 0.849794597 0.831967327 1.120457144 1.536601394 1.46173334 1 17.84930592 1.940574847 6.234452748 1.380784131 0.999950761 0.35221176 0.19193073 0.211379121 17.05722645 0.083892495 0.05183477 87.21171905 -1.940574847 -0.38083337 LQCPQVDLFYLHAPDHGTPVEETLHACQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LQCPQVDLFYLHAPDHGTPVEETLHACQR 29 0 O43488;H3BLU7;H7C5H7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ;; 344.37 7.46E-107 902320000 257353 309712 253912 300968 304120 338428 293492 29329 306072 285303 FALSE TRUE 247295.3602 300879.317 299799.5466 316500.9945 313902.296 345271.246 297083.8429 28723.3459 271327.9897 265979.1737 0.9297546 1.13121382 1.127154215 1.189946529 1.180176221 1.298113838 1.116944003 0.107990958 1.020109905 1 18.02095376 1.940587955 19.83004728 0.610799111 1.150525915 0.35716825 0.254106904 22.74835825 7592.118269 0.099265331 0.064027608 87.21435135 -1.940587955 0.539726803 ENEVQSSHHGEPPSEEHLS(ph)PQSFAMK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENEVQSSHHGEPPSEEHLSPQSFAMK 26 0 Q8IZH2-2;H7C5E4;H7C583 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 1 ENEVQSSHHGEPPSEEHLS(0.998)PQS(0.002)FAMK 116.82 0.001528 59855000 37384 56163 44313 63289 51031 56571 47616 14460 43836 49674 TRUE FALSE 35922.99195 54561.28623 52321.34484 66555.35287 52672.45846 57714.90438 48198.73885 14161.39595 38859.92106 46309.53573 0.775714794 1.178186854 1.129817952 1.437184628 1.137399838 1.246285532 1.040795121 0.305798703 0.839134326 1 15.49902167 1.940668533 8.690080712 0.645069753 1.161914298 0.416185365 0.226431994 0.303691177 42.12129362 0.092194763 0.058313129 87.23053431 -1.940668533 0.516844546 TGSNISGASS(ph)DISLDEQYK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGSNISGASSDISLDEQYK 19 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 TGSNISGAS(0.017)S(0.983)DISLDEQYK;TGSNISGAS(0.002)S(0.998)DISLDEQYK 325.98 4.74E-58 200390000 519340 473620 465570 482770 522290 489510 544820 680770 682130 651610 TRUE FALSE 499043.6186 460112.8213 549708.8555 507685.8176 539089.9322 499408.2276 551487.6701 666711.8616 604697.4621 607475.8743 0.821503602 0.75741744 0.904906481 0.835730008 0.887426077 0.822103805 0.907834687 1.097511671 0.9954263 1 19.21246759 1.940707702 4.580559154 1.036790711 0.840886035 0.779437922 0.04576557 0.09271937 3.850622728 0.020704607 0.012360749 87.23840212 -1.940707702 -0.195904676 THSQGGYGSQGYK ddPTM_BT-474_Pertuzumab_2h_R1 2 THSQGGYGSQGYK 13 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 225.36 1.26E-11 498670000 422290 415930 380530 451420 394600 415730 419520 182896 505920 425250 FALSE TRUE 405786.4399 404068.0836 449300.2358 474717.8403 407292.6674 424136.3454 424654.2113 179119.1337 448490.0826 396447.4387 1.02355672 1.019222334 1.133316026 1.197429455 1.027356032 1.069842567 1.071148833 0.451810546 1.131272494 1 18.59677008 1.940804249 24.99964317 0.79045789 1.08043751 0.216896237 0.173533969 257.7991128 108873.4491 0.06819035 0.044008892 87.25779798 -1.940804249 0.28997962 EALSEEIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EALSEEIKK 9 1 B1ANH0;B1ANG9;Q16774;Q16774-2;B1ANH5 B1ANH0 GUK1 Guanylate kinase 0 100.48 0.0074299 311730000 363640 328530 263190 293660 322650 314450 344900 423300 457840 383140 FALSE TRUE 349428.5468 319160.6461 310754.2876 308815.8278 333028.3303 320808.3944 349120.9894 414558.7071 405867.9226 357189.5865 0.978271932 0.893532897 0.869998173 0.864571195 0.932357333 0.898145989 0.977410884 1.160612523 1.13628151 1 18.4463305 1.940815834 3.887903719 1.112037081 0.904479993 0.746000244 0.050028188 0.100754904 2.894631543 0.023135645 0.013464149 87.26012562 -1.940815834 -0.207557088 QPSS(ph)PYEDKDKDK ddPTM_BT-474_Pertuzumab_2h_R1 4 QPSSPYEDKDKDK 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.011)S(0.989)PYEDKDKDK;QPS(0.003)S(0.997)PYEDKDKDK;QPS(0.05)S(0.95)PYEDKDKDK;QPS(0.01)S(0.99)PYEDKDKDK 205.31 3.70E-08 3457550000 4136480 2515080 3020030 2401670 3239610 2848100 3797300 4894650 5876960 4434360 TRUE FALSE 3974821.788 2443352.381 3565816.601 2525620.477 3343814.998 2905690.533 3843772.493 4793573.767 5209832.139 4134016.847 0.961491434 0.591035903 0.862554927 0.610936184 0.808853742 0.702873414 0.929791202 1.159543839 1.260234859 1 21.97911284 1.940837788 2.813453173 1.156777443 0.749734477 0.668705027 0.120476462 0.138796479 2.007842734 0.057532541 0.031236084 87.26453676 -1.940837788 -0.407042966 DRDAS(ph)PSKEER ddPTM_BT-474_Pertuzumab_2h_R1 6 DRDASPSKEER 11 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DRDAS(0.978)PS(0.022)KEER;DRDAS(0.996)PS(0.004)KEER;DRDAS(0.86)PS(0.14)KEER;DRDAS(0.994)PS(0.006)KEER;DRDAS(0.981)PS(0.019)KEER;DRDAS(0.998)PS(0.002)KEER 186.75 3.06E-06 5496280000 3319910 2829250 2352760 2326270 2552840 2670350 2839610 3284440 3548020 3167380 TRUE FALSE 3190164.247 2748562.56 2777956.069 2446329.073 2634954.417 2724346.307 2874361.997 3216615.166 3145263.644 2952850.531 1.080367669 0.930816691 0.940770973 0.828463563 0.892342633 0.922615716 0.973419401 1.089325427 1.065161819 1 21.4936769 1.940891812 3.928767206 1.058365278 0.927116721 0.415202745 0.062609539 0.209600274 6.165112954 0.030510158 0.017789455 87.27539274 -1.940891812 -0.131248557 DGVSSSFSSSS(ph)WK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGVSSSFSSSSWK 13 0 K7EIX2;Q6AI08;A0A087WXZ7;K7ELR8 K7EIX2 HEATR6 HEAT repeat-containing protein 6 1 DGVSSSFS(0.001)S(0.035)S(0.202)S(0.762)WK 96.746 0.0015602 0 133850 114840 123250 121770 123370 123080 137020 157260 168780 167570 TRUE FALSE 128618.994 111564.8756 145524.0167 128054.5643 127338.3081 125568.7619 138696.8917 154012.526 149620.802 156220.3346 0.823317875 0.714150792 0.931530566 0.819704839 0.815119929 0.803792683 0.887828669 0.985867342 0.95775497 1 17.25322273 1.940894424 2.767596858 0.979822088 0.818403132 0.678689969 0.050180885 0.159909624 2.237932226 0.026176932 0.014153482 87.27591766 -1.940894424 -0.161418955 HSTPSNSSNPSGPPS(ph)PNS(ph)PHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSTPSNSSNPSGPPSPNSPHR 21 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 2 HSTPSNSSNPSGPPS(1)PNS(1)PHR 153.12 2.44E-08 165710000 37386 63891 50172 69605 53770 61120 48199 24132 40442 37469 TRUE FALSE 35924.91379 62068.89124 59239.19647 73197.32239 55499.56088 62355.88828 48788.87378 23633.66577 35851.19371 34931.19126 1.028448 1.776890195 1.695882515 2.09547169 1.588825313 1.785106263 1.396713711 0.676577721 1.026337563 1 15.09222822 1.94089859 4.313199216 0.885363347 1.681119959 0.619361239 0.265920685 0.134670477 4.886179333 0.121175933 0.071728562 87.27675497 -1.94089859 0.795756612 HS(ph)LSPVPWEEDSFLQVK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSLSPVPWEEDSFLQVK 17 0 P10073 P10073 ZSCAN22 Zinc finger and SCAN domain-containing protein 22 1 HS(0.517)LS(0.483)PVPWEEDSFLQVK;HS(0.562)LS(0.438)PVPWEEDSFLQVK 191.59 1.51E-10 170989000 251334 240938 206071 207520 209309 247694 230095 162012 276148 249229 TRUE FALSE 241511.5894 234066.6841 243312.6137 218230.1321 216041.6141 252702.5424 232910.9714 158666.3956 244800.8367 232348.4978 1.039436844 1.007394867 1.047188237 0.939236251 0.929817133 1.087601361 1.002420819 0.682881091 1.05359337 1 17.82593079 1.940999085 24.99999014 0.868354653 1.006904002 0.112334239 0.102839264 325.8755232 138079.8388 0.040855122 0.026366935 87.29695287 -1.940999085 0.138549349 KTDVKEEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTDVKEEDK 9 2 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 ; 100.56 0.0025748 398790000 519070 361750 477160 399650 453300 413810 553490 730990 789380 736970 FALSE TRUE 498784.1705 351433.2442 563393.4264 420275.9844 467880.8062 422177.5217 560263.7762 715894.8011 699772.8918 687054.3655 0.725974822 0.511507185 0.820012876 0.611707029 0.680995318 0.614474695 0.815457705 1.041976934 1.018511674 1 19.39006474 1.9410668 2.99624612 1.022457121 0.660423032 0.812456095 0.077122161 0.098429304 1.619271269 0.036866359 0.020332592 87.31056519 -1.9410668 -0.362034089 SHVEDGDIAGAPASS(ph)PEAPPAEQDPVQLK ddPTM_BT-474_Pertuzumab_2h_R1 3 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 SHVEDGDIAGAPAS(0.218)S(0.782)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.017)S(0.983)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.243)S(0.757)PEAPPAEQDPVQLK 228.8 4.24E-35 2239170000 1193980 1299220 1164060 1363020 1351900 1431380 1325730 580230 1638500 1319540 TRUE FALSE 1147317.942 1262167.518 1374431.536 1433365.626 1395385.091 1460323.484 1341954.68 568248.0477 1452504.349 1230166.38 0.932652656 1.026013666 1.117272881 1.165180295 1.134305988 1.187094289 1.090872504 0.461927798 1.180738128 1 20.23042202 1.941130905 24.9986438 0.809926852 1.100346514 0.188672093 0.184809927 280.6280881 119167.4941 0.073395877 0.047370131 87.32345392 -1.941130905 0.290419662 AKEEASAMEEEMALAEEQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 AKEEASAMEEEMALAEEQLR 20 1 Q92620;H3BMS7;Q92620-2 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 ;;; 171.85 6.58E-12 69296000 148126 159142 128584 139707 143929 160846 153063 168331 183326 184665 FALSE TRUE 142337.0722 154603.426 151821.9891 146917.295 148558.607 164098.4163 154936.2308 164854.906 162515.601 172157.4751 0.826784153 0.898034929 0.881878577 0.853388997 0.86292278 0.953187866 0.899968071 0.957582039 0.943993869 1 17.3933693 1.941204997 0.437027279 1.000138137 0.852623664 0.739398236 0.026385974 0.517979145 0.240357832 0.027826513 0.024466841 87.33835281 -1.941204997 -0.147514473 TPVLPAGPPTTDPWALNS(ph)PHHK ddPTM_BT-474_Pertuzumab_2h_R1 4 TPVLPAGPPTTDPWALNSPHHK 22 0 Q9H201 Q9H201 EPN3 Epsin-3 1 TPVLPAGPPTTDPWALNS(1)PHHK;TPVLPAGPPTTDPWALNS(1)PHHK;TPVLPAGPPTTDPWALNS(1)PHHK;TPVLPAGPPTTDPWALNS(1)PHHK 236.79 1.08E-30 4152910000 2282070 2326080 2422070 3273300 3305140 3165310 2547680 539963 2445400 2393570 TRUE FALSE 2192884.181 2259742.476 2859791.928 3442235.405 3411452.83 3229314.737 2578859.27 528812.5754 2167808.444 2231451.372 0.982716544 1.012678342 1.2815838 1.542599336 1.528804469 1.447181318 1.155686968 0.236981447 0.971479133 1 21.08955094 1.941212796 8.826087764 0.660703651 1.306560121 0.466245681 0.266089856 0.319425364 45.63815853 0.116085299 0.073493661 87.33992123 -1.941212796 0.64585647 DFTPVCTTELGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;; 145.46 0.00014868 2366180000 1107364 989097 842706 862742 1007647 1004313 1018750 1231771 1187859 1161101 FALSE TRUE 1064086.991 960888.922 995001.7201 907268.218 1040058.881 1024620.897 1031217.767 1206334.498 1053018.226 1082458.595 0.983027892 0.887691156 0.919205339 0.838155124 0.960830175 0.946568212 0.952662552 1.114439392 0.972802314 1 20.04588041 1.941285191 7.098792284 1.040479734 0.921133797 0.463984555 0.050754667 0.199343648 20.63438347 0.021334439 0.013326209 87.3544817 -1.941285191 -0.119345936 RPMEEDGEEKSPS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 2 RPMEEDGEEKSPSK 14 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 RPMEEDGEEKS(0.103)PS(0.897)K;RPMEEDGEEKS(0.417)PS(0.583)K 106.34 0.00049443 2424600000 1103870 808880 764220 637250 748030 751350 926050 1025590 1244590 1044250 TRUE FALSE 1060729.54 785811.5344 902331.554 670138.5489 772091.0643 766542.8118 937383.2769 1004411.208 1103309.361 973522.0174 1.089579405 0.807184142 0.926873289 0.688365067 0.793090501 0.787391346 0.962878353 1.031729319 1.133317317 1 19.89285408 1.941496469 2.622200333 1.061318181 0.841189447 0.435761322 0.104910285 0.254731762 3.201138833 0.056082462 0.029912111 87.39698863 -1.941496469 -0.220128734 LSEIPLTLHSVSELVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSEIPLTLHSVSELVR 16 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 0 103.39 0.0028735 0 31159 37496 26629 43414 36092 34170 30900 20609 23878 27961 FALSE TRUE 29941.27183 36426.65079 31441.45266 45654.60174 37252.93196 34860.94081 31278.16344 20183.41695 21167.46954 26067.17656 1.148619673 1.397414511 1.206170242 1.75142105 1.429112657 1.337350086 1.199906072 0.774284737 0.812035377 1 14.66994671 1.941542445 2.856344531 0.842055896 1.389976946 0.66878765 0.161605385 0.152014833 2.268811494 0.085103574 0.046410902 87.4062414 -1.941542445 0.54792105 PGS(ph)LPLNAEACWPK ddPTM_BT-474_Pertuzumab_2h_R1 2 PGSLPLNAEACWPK 14 0 Q01581;D6RIW1 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 PGS(1)LPLNAEACWPK;PGS(1)LPLNAEACWPK 230.22 1.04E-12 453130000 619750 430660 397580 400820 521210 459030 562210 683540 830810 641560 TRUE FALSE 595529.4848 418377.9985 469431.5501 421506.3682 537975.193 468311.9011 569090.4942 669424.6601 736499.9318 598106.5698 0.995691261 0.699504101 0.784862722 0.704734557 0.899463775 0.782990732 0.95148678 1.119239771 1.231385792 1 19.19004304 1.94175484 2.421266467 1.133911434 0.80327033 0.659062515 0.098070152 0.159349464 1.710843565 0.051654337 0.026957053 87.44899845 -1.94175484 -0.330641104 EKEIS(ph)DDEAEEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EKEISDDEAEEEK 13 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 EKEIS(1)DDEAEEEK;EKEIS(1)DDEAEEEK;EKEIS(1)DDEAEEEK;EKEIS(1)DDEAEEEK 254.71 2.14E-23 3345680000 3082300 2278190 3236520 2578730 2758920 2714540 3856120 5338500 6006100 5351710 TRUE FALSE 2961840.308 2213218.252 3821431.16 2711818.564 2847663.167 2769429.859 3903312.35 5228258.109 5324312.708 4989233.915 0.593646311 0.443598815 0.765935457 0.54353406 0.570761607 0.555081182 0.782347033 1.047907995 1.067160369 1 22.25038688 1.941793839 2.575971623 1.046689174 0.578897738 0.875096647 0.077633148 0.088122723 1.069108013 0.041039035 0.021789348 87.4568517 -1.941793839 -0.467791436 AS(ph)PITNDGEDEFVPSDGLDKDEYTFSPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 AS(0.941)PIT(0.059)NDGEDEFVPSDGLDKDEYTFSPGK 124.35 2.75E-11 0 216550 190380 137600 157960 174170 163920 180300 226380 230180 179100 TRUE FALSE 208086.9866 184950.5488 162467.3809 166112.3345 179772.3362 167234.5747 182506.5653 221705.1739 204050.9314 166969.3975 1.246258235 1.107691299 0.973036876 0.994866946 1.076678355 1.001588179 1.093053985 1.327819213 1.22208581 1 17.34922418 1.941844045 10.05014358 1.217661825 1.060304611 0.173786305 0.105815633 0.743663086 125.7586658 0.043690386 0.027827863 87.46696257 -1.941844045 -0.157357214 IHGSGHVEEPAS(ph)PLAAYQK ddPTM_BT-474_Pertuzumab_2h_R1 5 IHGSGHVEEPASPLAAYQK 19 0 Q12955;A0A087WY90;H0Y951;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IHGS(0.35)GHVEEPAS(0.65)PLAAYQK;IHGSGHVEEPAS(1)PLAAYQK;IHGSGHVEEPAS(1)PLAAYQK;IHGS(0.001)GHVEEPAS(0.999)PLAAYQK;IHGSGHVEEPAS(1)PLAAYQK 187.19 1.22E-14 3903240000 1414027 2485750 2122190 3013700 2356200 2838680 1941790 142823 1523193 1367891 TRUE FALSE 1358765.262 2414858.844 2505716.941 3169237.418 2431989.313 2896080.055 1965554.207 139873.6551 1350286.516 1275242.524 1.065495571 1.893646736 1.964894436 2.485203683 1.907079843 2.271003358 1.541317961 0.109683964 1.05884684 1 20.28234021 1.94193371 5.940709343 0.658279161 1.952675505 0.622628437 0.419401976 0.12937566 9.643524414 0.181533088 0.111768108 87.48502303 -1.94193371 1.294396344 ARS(ph)DPTHQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ARSDPTHQHR 10 1 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 1 ARS(0.98)DPT(0.02)HQHR;ARS(0.992)DPT(0.008)HQHR 64.65 0.043076 1154810000 27576 26842.7 24201 26007 29762 31141 23148.8 11505.1 19511.3 17842.7 TRUE FALSE 26498.29943 26077.17248 28574.65905 27349.22439 30719.32176 31770.69236 23432.10194 11267.51566 17296.45902 16634.19804 1.59300132 1.567684383 1.71782607 1.644156474 1.846757006 1.909962373 1.408670372 0.677370537 1.03981322 1 14.02186469 1.942025442 4.630327804 0.893036041 1.708097833 0.878212951 0.134310966 0.067406628 2.89405661 0.062781604 0.037581472 87.50350345 -1.942025442 0.815061793 RPMEEDGEEKS(ph)PSKK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPMEEDGEEKSPSKK 15 3 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 RPMEEDGEEKS(0.95)PS(0.05)KK;RPMEEDGEEKS(0.997)PS(0.003)KK;RPMEEDGEEKS(0.999)PS(0.001)KK;RPMEEDGEEKS(0.853)PS(0.147)KK 129.46 0.00036321 5765180000 4508520 3128360 2915660 2187950 3136180 2808130 3649900 4606890 5214790 4214580 TRUE FALSE 4332322.054 3039142.236 3442584.621 2300870.362 3237058.078 2864912.313 3694568.568 4511756.112 4622828.901 3929122.743 1.102618151 0.773491294 0.87617131 0.585593913 0.823862803 0.729148082 0.940303678 1.148285866 1.176554973 1 21.90577581 1.94217779 3.583687229 1.118515367 0.806486654 0.503335163 0.129715726 0.182425454 4.396156944 0.061681882 0.035405692 87.53420459 -1.94217779 -0.312028713 NDKS(ph)EEEQSSS(ph)SVKKDETNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVKKDETNVK 21 3 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 2 NDKS(0.999)EEEQS(0.092)S(0.082)S(0.439)S(0.387)VKKDETNVK 101.49 0.00076626 369790000 465460 255300 293420 171880 251850 266520 341040 478050 542000 366250 TRUE FALSE 447269.3086 248019.094 346447.5211 180750.7474 259950.984 271909.217 345213.7495 468178.1004 480474.4322 341443.5613 1.30993628 0.726383866 1.014655306 0.529372253 0.76132929 0.796351866 1.011041908 1.371172731 1.407185511 1 18.3812876 1.942204796 3.749019799 1.290507246 0.840477083 0.401865395 0.217958215 0.204918012 5.454761097 0.101108708 0.058536972 87.539648 -1.942204796 -0.450030164 EHLLVSIPLLINHLQAESIVVHTYAAHALER ddPTM_BT-474_Pertuzumab_2h_R1 3 EHLLVSIPLLINHLQAESIVVHTYAAHALER 31 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 239.26 2.32E-46 13972650000 217876 273210 199507 211705 263134 246367 211245 42023.2 215519 184543 FALSE TRUE 209361.165 265418.3183 235562.3529 222631.1204 271597.9441 251348.7095 213830.2795 41155.40623 191054.1866 172043.7382 1.216906626 1.542737452 1.369200387 1.294037916 1.578656375 1.460958197 1.242883244 0.239214787 1.110497764 1 17.39241586 1.942208149 8.641134422 0.707112818 1.411717962 0.575496777 0.238445591 0.225839436 31.93567547 0.09473397 0.059926125 87.54032395 -1.942208149 0.704605144 IEKEEQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEKEEQEK 8 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 93.058 0.011046 0 347300 310650 218890 207160 255930 280680 286240 304840 367820 316060 FALSE TRUE 333727.132 301790.5662 258448.2922 217851.5524 264162.2209 286355.5419 289743.0907 298544.9475 326066.6156 294652.9747 1.132610768 1.024223721 0.877127721 0.739349578 0.896519783 0.971839983 0.983336724 1.013208666 1.106612333 1 18.16865731 1.942237955 1.642175891 1.04841538 0.928633776 0.171046246 0.098909328 0.687909154 3.454307628 0.072335535 0.033764502 87.54633207 -1.942237955 -0.119781604 HLCEPGADGAETFADGVPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLCEPGADGAETFADGVPR 19 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38;K7EMY3 Q14839-2 CHD4;CHD5 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 326.49 3.77E-75 2334860000 1273950 1349670 1047390 1359310 1348700 1384320 1281330 985600 1351810 1414820 FALSE TRUE 1224162.626 1311178.733 1236676.672 1429464.152 1392082.16 1412311.899 1297011.3 965247.0156 1198358.196 1318992.981 0.928103973 0.994075595 0.937591549 1.083754176 1.055412864 1.070750125 0.983334497 0.731806029 0.908540237 1 20.33100546 1.942261245 11.00553973 0.851964665 1.013914708 0.339691151 0.079351057 0.76279028 143.7365271 0.032620083 0.020846217 87.55102707 -1.942261245 0.161950043 GVHPHIVEMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVHPHIVEMDR 11 0 O76041-2;O76041 O76041-2 NEBL Nebulette 0 ; 152.07 1.92E-05 805630000 162837 195612 143337 180864 172599 159156 145925 12923.1 140644 126150 FALSE TRUE 156473.15 190033.3373 169241.1844 190198.4127 178150.8036 162374.2434 147710.8738 12656.23347 124678.6827 117605.7481 1.330488964 1.615850758 1.439055379 1.617254392 1.514813743 1.380665877 1.255983454 0.107615773 1.060141062 1 16.84359905 1.942474274 7.37663264 0.633398366 1.480859832 0.629884702 0.258009121 0.146169854 16.449769 0.104609518 0.065555099 87.59398296 -1.942474274 0.847461466 HHHHDSDSNS(ph)PCCK ddPTM_BT-474_Pertuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 HHHHDS(0.017)DS(0.119)NS(0.864)PCCK 138.91 2.12E-05 50442000 17209 33778 25780 27930 16531 24911 19495 1241.6 18458 6517.4 TRUE FALSE 16536.45325 32814.68451 30439.01947 29371.47065 17062.73463 25414.71749 19733.58564 1215.960526 16362.72522 6075.970693 2.721615046 5.400731203 5.009737705 4.834037577 2.808231884 4.182824239 3.247807904 0.200126134 2.693022407 1 12.5688992 1.942514095 4.751939215 1.276636277 4.196155588 0.622448102 0.995229433 0.134115404 6.132087741 0.448544521 0.269547708 87.60201478 -1.942514095 2.91951931 YGPADVEDTTGSGATDSKDDDDIDLFGS(ph)DDEEESEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 9 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR 39 2 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(0.994)DDEEES(0.006)EEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR 459.67 3.64E-269 45329017000 8437714 5671108 5600724 4662747 6054029 5237751 7085998 8781452 10074128 8330568 TRUE FALSE 8107958.808 5509373.552 6612899.414 4903391.931 6248762.341 5343661.914 7172718.563 8600111.947 8930555.224 7766331.209 1.043988286 0.709392042 0.851483054 0.631365287 0.804596427 0.688054858 0.923565886 1.10735838 1.149906562 1 22.8888018 1.942575175 3.440674996 1.092431191 0.781324778 0.586103229 0.111578899 0.155860586 3.440508169 0.05197455 0.02960243 87.61433621 -1.942575175 -0.311106413 LHPGT(ph)SCPRLSPPLHMAPGAGEHHLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHPGTSCPRLSPPLHMAPGAGEHHLAR 27 1 Q6ZN04 Q6ZN04 MEX3B RNA-binding protein MEX3B 1 LHPGT(0.333)S(0.333)CPRLS(0.333)PPLHMAPGAGEHHLAR 75.88 0.0066466 141860000 36197 39776 28332 36945 30989 37095 35204 16045 41644 37630 TRUE FALSE 34782.38122 38641.62742 33452.22264 38851.73588 31985.78933 37845.08632 35634.83708 15713.66514 36916.74771 35081.28658 0.991479635 1.10148832 0.953563164 1.107477509 0.911762151 1.078782736 1.015779082 0.447921575 1.052320234 1 15.09841404 1.942622985 24.9992343 0.762016234 1.025105278 0.17995549 0.165579161 286.8593336 124984.3078 0.063982358 0.041295653 87.62398183 -1.942622985 0.263089044 (ac)ADLEEQLSDEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADLEEQLSDEEK 12 0 P47755;F8W9N7;C9JUG7;P47755-2;F8WED3 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ; 105.4 1.96E-15 335890000 406870 398130 359030 369960 402360 373830 423880 513940 534760 490690 FALSE TRUE 390969.0706 386775.7222 423914.7076 389053.6799 415302.2748 381389.0987 429067.5702 503326.9594 474056.2867 457455.1292 0.854661027 0.845494339 0.926680412 0.85047397 0.907853576 0.833719144 0.937944604 1.10027613 1.036290242 1 18.80327071 1.942639483 4.602607409 1.051685175 0.872655992 0.829086331 0.035602716 0.074906205 3.184902293 0.015326417 0.009172223 87.62731071 -1.942639483 -0.179029183 KADGYNQPDSK ddPTM_BT-474_Pertuzumab_2h_R1 5 KADGYNQPDSK 11 1 O60506-2;O60506;O43390;O43390-3;B4DT28;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;;;; 161.87 4.14E-05 6469380000 5673200 4874050 4191636 4284013 4628060 4516340 4820922 5702720 5773870 5106630 FALSE TRUE 5451485.072 4735046.866 4949157.868 4505111.424 4776925.753 4607663.489 4879921.886 5584956.839 5118444.484 4760753.402 1.145088731 0.994600322 1.039574506 0.946302201 1.003397015 0.967843343 1.025031434 1.173124581 1.075133293 1 22.18275847 1.94273819 12.9375993 1.101297076 1.011133553 0.159881443 0.06424023 2.26178904 509.3137961 0.025714383 0.01650509 87.64722887 -1.94273819 -0.090163523 SLS(ph)SPTVTLSAPLEGAK ddPTM_BT-474_Pertuzumab_2h_R1 7 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 SLS(0.994)S(0.006)PTVTLSAPLEGAK;SLS(0.897)S(0.103)PTVTLSAPLEGAK;S(0.028)LS(0.772)S(0.199)PTVTLSAPLEGAK;S(0.045)LS(0.903)S(0.052)PTVTLSAPLEGAK;S(0.006)LS(0.497)S(0.497)PTVTLSAPLEGAK;SLS(0.967)S(0.033)PTVTLSAPLEGAK;SLS(0.966)S(0.034)PTVTLSAPLEGAK 488.65 8.15E-232 11154660000 11038850 10024850 7806760 9094090 7889090 8309010 9194190 13927890 10471270 9323590 TRUE FALSE 10607439.54 9738951.093 9217615.192 9563437.075 8142849.745 8477023.875 9306711.248 13640274.2 9282615.329 8692094.945 1.220354771 1.120437726 1.060459561 1.100245353 0.936810953 0.975256705 1.070709801 1.569273494 1.067937636 1 23.0512725 1.942798908 24.99988417 1.286740355 1.062691719 0.090801901 0.162178291 345.2434674 150888.7056 0.065096194 0.042008976 87.65948363 -1.942798908 -0.224048636 SAS(ph)ASHQADIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 SAS(0.629)AS(0.371)HQADIK 225.1 6.00E-12 380540000 396140 472630 265400 421690 295440 265420 359860 544920 467940 307080 TRUE FALSE 380658.4108 459151.0552 313363.6838 443453.4714 304943.0959 270786.9743 364264.0743 533667.2116 414821.413 286281.1981 1.329666123 1.603846352 1.094600993 1.549013608 1.065187298 0.945877606 1.272399573 1.864136434 1.44899985 1 18.1270734 1.942902769 24.99692624 1.542362733 1.262312105 0.03625352 0.278730736 482.8016328 211367.3245 0.113462451 0.073224905 87.68044977 -1.942902769 -0.280050628 FYCDYCDTYLTHDSPSVR ddPTM_BT-474_Pertuzumab_2h_R1 5 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 0 ;;;; 346.09 2.99E-90 4932469000 945870 2051477 1381322 2387271 1665349 2050384 1557468 1293072 1176100 1749221 FALSE TRUE 908904.3547 1992970.885 1630957.613 2510478.342 1718916.463 2091844.169 1576528.759 1266369.611 1042594.059 1630744.704 0.557355393 1.222123169 1.000130559 1.539467421 1.054068402 1.282753925 0.966753874 0.776559083 0.639336161 1 20.63709951 1.942914184 3.759466785 0.788587551 1.127223105 0.22665352 0.248752773 0.309585353 8.309911124 0.115019983 0.066670982 87.68275449 -1.942914184 0.338635554 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_BT-474_Pertuzumab_2h_R1 12 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLR 32 2 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 1 KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR 437.2 6.43E-209 2.60298E+11 3549263 3125137 2728484 2632814 2987241 2819956 3470296 4085266 4602359 4218506 TRUE FALSE 3410553.878 3036011.153 3221581.754 2768693.846 3083328.32 2876977.442 3512766.521 4000903.829 4079918.501 3932782.831 0.867211342 0.771975286 0.819160857 0.704003746 0.784006759 0.731537328 0.893201245 1.017321322 1.03741261 1 21.90711909 1.942965055 2.862809324 1.020026904 0.778129009 0.856241556 0.043716657 0.090646373 1.360749615 0.02239573 0.012236091 87.69302575 -1.942965055 -0.241897894 EIVEHLLDHGAEVNHEDVDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIVEHLLDHGAEVNHEDVDGR 21 0 Q9ULJ7-2;Q9ULJ7 Q9ULJ7-2 ANKRD50 Ankyrin repeat domain-containing protein 50 0 245.82 1.04E-30 59225000 29962 33041 33277 31199 31643 32327 28982 7472 33490 20895 FALSE TRUE 28791.05192 32098.70303 39290.89414 32809.18413 32660.82583 32980.67409 29336.69039 7317.700589 29688.3556 19479.76304 1.477998057 1.647797407 2.017010888 1.684270187 1.676654165 1.69307368 1.506008586 0.375656551 1.524061435 1 14.24968851 1.943057087 8.482232999 0.905537849 1.700982424 0.56334751 0.287354194 0.233118843 32.640188 0.115858412 0.073235714 87.71161075 -1.943057087 0.795444575 AFAAVPTSHPPEDAPAQPPT(ph)PGPAAS(ph)PEQLSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 2 AFAAVPTSHPPEDAPAQPPT(0.998)PGPAAS(0.875)PEQLS(0.126)FR 71.204 0.0064302 99717000 47751 58776 39855 63262 55933 36293 39684 36645 25421 24490 TRUE FALSE 45884.83813 57099.76603 47057.68507 66526.9594 57732.13574 37026.86933 40169.66466 35888.26794 22535.31465 22831.27049 2.009736521 2.500945625 2.061106722 2.913852711 2.528643151 1.621761231 1.759414339 1.571890971 0.98703726 1 14.47872352 1.943195155 0.897708098 1.006708648 2.402750764 0.749808002 0.303033458 0.292706255 0.435528098 0.262555054 0.12372327 87.73950004 -1.943195155 1.396042117 up NTPS(ph)QHSHSIQHS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 NTPSQHSHSIQHSPER 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 NT(0.172)PS(0.813)QHS(0.015)HSIQHS(1)PER 115.77 0.00022677 317790000 134720 150380 109690 130920 153820 150910 115600 0 123960 64158 TRUE FALSE 129454.9935 146091.3096 129513.423 137676.7969 158767.76 153961.5036 117014.7474 0 109888.5805 59812.52151 2.16434603 2.442487057 2.165322908 2.301805599 2.654423455 2.5740681 1.956358709 0 1.837216986 1 15.86815992 1.943229126 7.302320029 0.861552405 2.376136189 0.680714609 0.43935343 0.135860503 15.22768646 0.177144344 0.110973101 87.74636329 -1.943229126 1.514583784 EFLEDYDDDRDDPK ddPTM_BT-474_Pertuzumab_2h_R1 4 EFLEDYDDDRDDPK 14 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ;;; 143.93 8.20E-06 2446580000 2689690 2369320 2072750 2101080 2372550 2270200 2616000 3040360 3314570 3227590 FALSE TRUE 2584573.941 2301749.313 2447342.033 2209516.991 2448865.225 2316104.999 2648015.391 2977575.504 2938313.909 3008982.454 0.858952812 0.764959367 0.813345398 0.734307037 0.813851613 0.769730311 0.880036833 0.989562269 0.976514139 1 21.52084426 1.943232904 2.61760486 0.988920253 0.790414472 0.87665214 0.03288089 0.083437537 1.045795291 0.01653737 0.008829757 87.74712669 -1.943232904 -0.198505781 ASS(ph)LGEIDESSELR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASSLGEIDESSELR 14 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR 389.36 5.48E-114 2605330000 2087240 2525380 2055020 2636910 2658240 2591400 1973780 1825460 1769230 1667720 TRUE FALSE 2005668.353 2453358.635 2426407.828 2773001.241 2743744.704 2643799.884 1997935.71 1787763.613 1568394.428 1554763.839 1.290014794 1.577962243 1.560627902 1.783551413 1.764734061 1.700451102 1.285041278 1.149861843 1.008766983 1 20.56826403 1.943348963 2.141158911 1.044671097 1.622953339 0.768503301 0.138395234 0.156951098 1.325867233 0.086149033 0.043437284 87.77057895 -1.943348963 0.578282242 ENYSHHTQDDR ddPTM_BT-474_Pertuzumab_2h_R1 6 ENYSHHTQDDR 11 0 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;;;; 232.42 2.01E-13 1376932000 630370 863224.5 848962.8 1100324.8 920323.6 881609 897911.9 222916.9 939923 1020624 FALSE TRUE 605734.4435 838606.1824 1002389.263 1157112.695 949926.6444 899435.738 908900.8144 218313.5881 833226.8815 951496.2274 0.636612554 0.881355236 1.053487375 1.216098037 0.998350405 0.945285659 0.95523323 0.229442411 0.875701719 1 19.85983841 1.943351988 24.99383216 0.610156948 0.968474379 0.163787112 0.235612433 324.3144327 143090.9599 0.095905935 0.061896809 87.77119024 -1.943351988 0.358317432 HVDAHATLNDGVVVQVMGLLSNNNQALR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVDAHATLNDGVVVQVMGLLSNNNQALR 28 0 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 175 6.07E-13 341350000 322380 312190 281420 297300 328670 327530 316400 198774 386520 331850 FALSE TRUE 309781.0332 303286.6469 332278.8542 312643.6886 339241.969 334152.881 320272.1978 194669.2474 342643.87 309373.5039 1.001317273 0.980325215 1.074037854 1.010570345 1.096545001 1.080095344 1.035228272 0.629236974 1.107541097 1 18.23899012 1.943363755 24.99943141 0.861355603 1.041895283 0.153291805 0.120667438 319.3812594 140975.235 0.047467418 0.030635076 87.77356852 -1.943363755 0.180539681 SDEAVKPFGLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDEAVKPFGLK 11 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 152.85 2.99E-05 16348520000 20381140 19969790 18688370 19768970 20559610 21917550 24047320 25577800 31096200 29969300 FALSE TRUE 19584622.52 19400271.14 22065774.18 20789248.91 21220928.53 22360737.88 24341618.3 25049609.49 27566289.74 27939452.62 0.700966579 0.694368333 0.78977117 0.744082184 0.759532723 0.800328417 0.871227459 0.896567654 0.986643873 1 24.73580042 1.943409861 0.661142257 1.011367616 0.719514662 0.940091737 0.025570359 0.157411087 0.135340353 0.023549841 0.01341939 87.78288721 -1.943409861 -0.291852954 YKVPDGKPENEFAFNAEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 YKVPDGKPENEFAFNAEFK 19 2 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 224.4 1.11E-19 6556100000 5075800 3890100 3726100 3098700 4068100 4083900 4547100 5362700 6232300 5454100 FALSE TRUE 4877432.124 3779158.157 4399489.157 3258624.278 4198954.131 4166479.256 4602748.77 5251958.371 5524835.432 5084688.949 0.959239036 0.743242742 0.865242535 0.640869935 0.825803539 0.819416743 0.905217372 1.032896687 1.086563109 1 22.27772809 1.943456713 1.989701516 1.051176716 0.799375978 0.628012329 0.079394801 0.196897426 1.441967822 0.046139526 0.022762513 87.79235775 -1.943456713 -0.251800738 S(ph)PVGKS(ph)PPSTGSTYGSSQKEESAASGGAAYTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPVGKSPPSTGSTYGSSQKEESAASGGAAYTK 32 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(0.983)PVGKS(0.976)PPS(0.013)T(0.012)GS(0.003)T(0.003)Y(0.006)GS(0.003)S(0.001)QKEESAASGGAAYTK 89.51 7.82E-05 793580000 252580 203030 203670 170180 198930 203150 243310 290280 341690 288410 TRUE FALSE 242708.8944 197239.7832 240477.6996 178963.0102 205328.7641 207257.8322 246287.7006 284285.6166 302902.7837 268875.7338 0.902680547 0.733572273 0.894382309 0.665597478 0.763656732 0.770831303 0.915990808 1.057312285 1.126553071 1 18.03658003 1.943513406 2.44713143 1.071059378 0.783861462 0.739604198 0.072420594 0.136082915 1.492714158 0.038367115 0.020113707 87.80381901 -1.943513406 -0.287197915 IS(ph)DAELEAELEK ddPTM_BT-474_Pertuzumab_2h_R1 4 ISDAELEAELEK 12 0 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK 277.24 7.22E-28 348339000 649185 543926 554959 487200 538701 598929 635315 730851 893932 732672 TRUE FALSE 623814.1325 528413.763 655252.4363 512344.4504 556028.8069 611039.7547 643090.175 715758.6714 792456.587 683047.4728 0.913280785 0.773612061 0.959307314 0.750086152 0.814041233 0.89457875 0.941501434 1.047890081 1.160177906 1 19.38162633 1.94357345 1.741400394 1.085160412 0.842519383 0.670564452 0.06896437 0.194729956 1.098331989 0.042262644 0.020060494 87.81595925 -1.94357345 -0.242641028 EEVVLLTHGDSVDK ddPTM_BT-474_Pertuzumab_2h_R1 6 EEVVLLTHGDSVDK 14 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;; 247.32 8.16E-18 2879800000 4137284 3844026 3845978 4026999 3895203 3964055 4384695 4943396 5334260 5349155 FALSE TRUE 3975594.367 3734398.142 4541031.778 4234832.901 4020495.742 4044210.908 4438356.209 4841313.145 4728737.168 4986851.967 0.797215236 0.748848806 0.910600878 0.849199641 0.806219188 0.810974726 0.890011622 0.970815492 0.948240934 1 22.24969795 1.943767268 2.495134471 0.971688054 0.821861598 0.737715611 0.040678954 0.157350674 1.793625873 0.023251234 0.012258481 87.85515874 -1.943767268 -0.149826456 HSLS(ph)LDDIR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSLSLDDIR 9 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 HS(0.005)LS(0.995)LDDIR;HS(0.01)LS(0.99)LDDIR;HSLS(1)LDDIR;HSLS(1)LDDIR 161.93 4.13E-05 1610060000 2662390 2758530 2168570 2575560 2432140 2480330 2323640 1459010 2385410 2212130 TRUE FALSE 2558340.855 2679859.425 2560478.839 2708484.96 2510371.992 2530483.972 2352077.401 1428880.934 2114628.257 2062300.465 1.240527702 1.299451497 1.2415644 1.313331887 1.21726782 1.227020027 1.140511502 0.692857786 1.025373506 1 20.97582311 1.943813563 5.838592875 0.878828503 1.25343068 0.754568721 0.088913076 0.090272227 6.643322624 0.03724207 0.022923449 87.8645244 -1.943813563 0.374602177 KHGLAHDEMKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 9 KHGLAHDEMKSPR 13 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR 147.64 1.89E-05 6738153000 11903518 10878111 9977507 9074693 10732274 10596653 9302357 385520.9 10641454 6490886 TRUE FALSE 11438315.36 10567877.93 11780664.46 9543038.993 11077487.34 10810924.58 9416202.028 377559.7587 9433480.755 6051252.51 1.890239308 1.746395132 1.946814225 1.577035329 1.830610658 1.786559818 1.556074881 0.062393655 1.558930278 1 22.52880236 1.943816802 9.495123183 0.777544496 1.782570525 0.571790307 0.354399657 0.307764618 50.44065347 0.138984171 0.088350866 87.86517977 -1.943816802 1.005026029 HDIAFVEFENDGQAGAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 HDIAFVEFENDGQAGAAR 18 0 P08579 P08579 SNRPB2 U2 small nuclear ribonucleoprotein B 0 ;; 302.44 1.14E-49 645010000 404320 412460 401460 506420 407390 400230 431340 255922 511230 529050 FALSE TRUE 388518.7274 400697.0446 474012.7524 532556.3969 420494.0693 408322.9248 436618.8679 250637.1213 453197.3137 493216.9723 0.787723759 0.812415361 0.961063343 1.07976089 0.852553933 0.827876873 0.885247046 0.508168079 0.918859932 1 18.91186292 1.943821108 24.99982567 0.739947823 0.89096318 0 0.147037555 493.8430355 219760.9468 0.060247872 0.038882174 87.86605095 -1.943821108 0.151015357 ILDSVGIEADDDRLNK ddPTM_BT-474_Pertuzumab_2h_R1 8 ILDSVGIEADDDRLNK 16 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;;;;;; 314.84 7.99E-58 47415120000 22696800 20500800 19230040 18703110 19491650 20266170 22697420 26782130 29079550 27887260 FALSE TRUE 21809783.96 19916137.26 22705336 19668379.75 20118616.62 20675965.84 22975197.82 26229069.66 25778561.4 25998431.04 0.838888467 0.766051506 0.873334855 0.756521796 0.773839644 0.795277446 0.883714782 1.008871251 0.991542965 1 24.63192123 1.943847924 2.644118644 1.001654183 0.799136032 0.876241038 0.03348953 0.086497934 1.106564947 0.017526709 0.009388442 87.87147646 -1.943847924 -0.202518151 NDKSEEEQSSSS(ph)VKKDETNVK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDKSEEEQSSSSVKKDETNVK 21 3 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKSEEEQSS(0.014)S(0.155)S(0.831)VKKDETNVK;NDKSEEEQS(0.004)S(0.23)S(0.23)S(0.536)VKKDETNVK 238.23 3.84E-29 1018220000 1109530 732120 729400 440430 582300 671480 825790 1093580 1245730 881360 TRUE FALSE 1066168.341 711240.6544 861218.8054 463160.6451 601030.2083 685057.7857 835896.265 1070997.191 1104319.953 821664.7022 1.297571063 0.865609357 1.048138983 0.563685703 0.731478676 0.83374372 1.017320402 1.303447973 1.344003156 1 19.64819027 1.943880986 3.755218793 1.241135362 0.87566938 0.341499172 0.200381191 0.242341263 6.507566518 0.097137197 0.056347062 87.87816626 -1.943880986 -0.365465981 GTCSGFEPHSWR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTCSGFEPHSWR 12 0 Q9NZU5;F8WB09;C9IYS1;H7C3D2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ; 203.51 1.24E-07 556700000 631880 663560 588740 609850 590090 631340 632290 551590 665090 804780 FALSE TRUE 607185.431 644635.9185 695138.4145 641324.4316 609070.7808 644106.1274 640028.1542 540199.4737 589591.7715 750271.5338 0.809287576 0.859203488 0.926515779 0.85478977 0.811800466 0.858497355 0.853062025 0.720005291 0.785837853 1 19.5170533 1.943924688 24.99498259 0.799761275 0.855173221 0 0.074668812 655.4194348 292144.8506 0.029283936 0.018897681 87.88700974 -1.943924688 0.055411947 NHAVVCQGCHNAIDPEVQR ddPTM_BT-474_Pertuzumab_2h_R1 4 NHAVVCQGCHNAIDPEVQR 19 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;;; 229.6 4.43E-20 3218340000 660101 689141 529786 615668 536540 574686 526861 128001.2 560556 421100 FALSE TRUE 634303.5231 669487.3734 625530.1152 647442.6993 553798.2964 586306.5447 533308.8825 125357.9305 496924.0329 392578.5219 1.615736694 1.705359147 1.593388533 1.649205606 1.410668861 1.493475858 1.358476974 0.319319381 1.265795262 1 18.58262172 1.943935303 7.344511784 0.795101078 1.568127259 0.648402285 0.234282041 0.145974874 16.7172215 0.096357673 0.060408013 87.88915773 -1.943935303 0.773026181 VADYCENNYIQATDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 VADYCENNYIQATDKR 16 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 176.28 5.17E-09 396600000 225570 215870 216920 202400 207240 251120 236500 279480 314520 304570 FALSE TRUE 216754.475 209713.599 256122.2694 212845.8883 213906.0628 256197.8185 239394.3577 273708.6403 278817.0082 283941.2026 0.763378027 0.738581076 0.902025726 0.749612548 0.75334633 0.902291799 0.843112432 0.96396239 0.981953326 1 18.11523269 1.943975951 0.949397347 1.005031454 0.784042446 0.721906341 0.051873036 0.289213203 0.479723539 0.04260793 0.01969597 87.8973842 -1.943975951 -0.220989008 KLSVEEFFMDLHNFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSVEEFFMDLHNFR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 101.39 0.0011627 62950000 205730 233380 163920 162000 197560 215230 184550 168050 182670 193290 FALSE TRUE 197689.8442 226724.2309 193543.9904 170360.8394 203914.6968 219582.0981 186808.5781 164579.7088 161934.0674 180198.2961 1.097068332 1.258192978 1.074061157 0.945407604 1.131612791 1.218558126 1.036683377 0.913325555 0.898643721 1 17.45922584 1.944002128 4.327893631 0.933625235 1.11845565 0.495105209 0.082826884 0.192827646 7.167051496 0.040412197 0.024004912 87.90268236 -1.944002128 0.184830414 IWDPTPSHTPAGAAT(ph)PGRGDTPGHATPGHGGATSSAR ddPTM_BT-474_Pertuzumab_2h_R1 6 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHT(0.001)PAGAAT(0.999)PGRGDTPGHATPGHGGATSSAR;IWDPTPSHTPAGAAT(1)PGRGDTPGHATPGHGGATSSAR;IWDPTPSHTPAGAAT(1)PGRGDTPGHATPGHGGATSSAR;IWDPTPSHTPAGAAT(1)PGRGDTPGHATPGHGGATSSAR;IWDPT(0.001)PS(0.004)HT(0.034)PAGAAT(0.957)PGRGDT(0.003)PGHATPGHGGATSSAR;IWDPTPSHT(0.002)PAGAAT(0.998)PGRGDTPGHATPGHGGATSSAR 204.03 1.29E-30 8565490000 2471201 3578229 2483500 3573814 3049876 3285190 2781218 806080 2714438 2649720 TRUE FALSE 2374623.733 3476181.412 2932323.695 3758258.969 3147978.031 3351618.793 2815255.378 789434.1663 2406306.378 2470252.104 0.961288011 1.407217266 1.187054427 1.521407051 1.274354964 1.356792202 1.139663184 0.319576356 0.974113684 1 21.23622685 1.944188972 8.250310393 0.696972156 1.292352363 0.512479694 0.224043483 0.223066227 30.66988481 0.088990695 0.056189965 87.9405083 -1.944188972 0.595380207 S(ph)VIAQIGPGGT(ph)IS(ph)SELK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVIAQIGPGGTISSELK 17 0 Q8NAT2;Q8NAT2-1 Q8NAT2 TDRD5 Tudor domain-containing protein 5 3 S(0.908)VIAQIGPGGT(0.706)IS(0.706)S(0.68)ELK 49.224 0.084864 0 16229 13053 12964 13993 13993 12876 16179 19482 20179 21442 TRUE FALSE 15594.75274 12680.74122 15306.88318 14715.18041 14443.09755 13136.36154 16377.00344 19079.68989 17888.36452 19989.71424 0.780138853 0.634363306 0.765737969 0.736137607 0.722526464 0.657156045 0.819271514 0.95447537 0.894878451 1 14.28697023 1.944203429 3.29016066 0.941990879 0.715997198 0.820867293 0.048737057 0.095252458 1.915293199 0.022784272 0.012874891 87.94343591 -1.944203429 -0.225993681 DHQPCIIFMDEIDAIGGR ddPTM_BT-474_Pertuzumab_2h_R1 5 DHQPCIIFMDEIDAIGGR 18 0 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ;;;; 204.78 1.04E-15 1138864300 252212.6 286845.1 243357.5 300477 282532.5 310465.8 284141.1 120348.3 325372.4 320922.8 FALSE TRUE 242355.8528 278664.5586 287337.6137 315984.654 291620.4145 316743.6312 287618.5038 117863.0655 288437.4892 299186.4129 0.810049662 0.9314078 0.9603966 1.056146404 0.974711424 1.058683207 0.961335446 0.393945248 0.964072821 1 18.19068513 1.944235662 24.99949068 0.708409801 0.971536552 0.14312659 0.170836839 322.3603069 144515.3697 0.067448283 0.043530085 87.94996328 -1.944235662 0.263126751 TSSKDDKGS(ph)TSSTSGSSGSSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSKDDKGSTSSTSGSSGSSTK 22 2 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 T(0.001)S(0.001)S(0.001)KDDKGS(0.888)T(0.048)S(0.048)S(0.012)T(0.001)SGSSGSSTK 132.78 5.26E-06 100920000 131380 111990 95436 68371 97780 97408 106410 126560 141840 103470 TRUE FALSE 126245.5244 108796.1548 112683.4082 71899.6355 100925.1825 99377.6565 107712.2774 123946.4918 125738.9178 96461.88474 1.308760706 1.127866775 1.16816511 0.745368346 1.046270066 1.03022719 1.116630446 1.28492712 1.303508823 1 16.55767138 1.944318915 5.489585287 1.22346054 1.062771694 0.107090304 0.154311213 0.382162158 24.70157499 0.069517917 0.042548506 87.96682456 -1.944318915 -0.160688847 YSHDFNFHINYGDLGFLGPEDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSHDFNFHINYGDLGFLGPEDLR 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 107.47 0.00077711 638920000 469980 626880 613280 650170 593720 717050 626770 169539 733360 668340 FALSE TRUE 451612.662 609001.9962 724113.3383 683725.3516 612817.543 731549.2423 634440.5987 166037.9604 650112.0473 623072.7365 0.724815315 0.977417179 1.162165018 1.097344357 0.983540937 1.174099266 1.01824484 0.266482468 1.043396716 1 19.24904107 1.944376383 24.99983362 0.67693391 1.032123748 0.159551732 0.234147422 331.4985347 148990.1431 0.093072264 0.060069815 87.97846547 -1.944376383 0.355189838 DGLLENQTPEFFQDVCKPK ddPTM_BT-474_Pertuzumab_2h_R1 4 DGLLENQTPEFFQDVCKPK 19 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 252.77 6.72E-31 8872620000 5222600 4374910 4218140 4061820 4515940 4970290 5178550 6254830 7219800 6621130 FALSE TRUE 5018495.018 4250141.85 4980451.73 4271451.017 4661199.311 5070792.669 5241926.644 6125665.575 6400238.572 6172674.968 0.813017864 0.688541333 0.806854687 0.69199351 0.755134417 0.821490309 0.849214752 0.992384275 1.036866287 1 22.5574644 1.944405731 1.400748595 1.028415295 0.749431986 0.875404178 0.041999037 0.122095909 0.4451363 0.028070045 0.012692977 87.98441104 -1.944405731 -0.278983309 DDKLTPK ddPTM_BT-474_Pertuzumab_2h_R1 4 DDKLTPK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 112.84 0.0057124 1683390000 2075740 1785610 1771890 1696760 1597200 1675230 1949470 2296780 2470190 2258160 FALSE TRUE 1994617.786 1734686.151 2092109.938 1784329.987 1648575.389 1709104.298 1973328.197 2249350.69 2189784.387 2105212.812 0.947466106 0.823995627 0.993775986 0.847577013 0.783092037 0.811843956 0.93735331 1.06846713 1.040172459 1 21.00553465 1.944485019 4.209089571 1.039006644 0.866952738 0.600860314 0.061251864 0.150907307 5.270614771 0.029284091 0.017329395 88.00047557 -1.944485019 -0.172053906 S(ph)QTPPGVAT(ph)PPIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQTPPGVATPPIPK 14 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 S(0.627)QT(0.373)PPGVAT(1)PPIPK;S(0.5)QT(0.5)PPGVAT(1)PPIPK 110.56 0.0037275 307200000 567480 535050 476450 448250 445130 560580 545660 762040 605200 677660 TRUE FALSE 545302.2542 519790.8979 562555.1136 471384.2362 459448.0107 571915.3117 552337.9503 746303.6077 536500.2332 631761.4846 0.863145772 0.822764462 0.890454906 0.746142726 0.727249163 0.905270938 0.874282405 1.181305961 0.849213265 1 19.26902046 1.944498437 8.9194862 1.030167439 0.826172607 0.442011103 0.091902518 0.341882628 52.50149615 0.037945381 0.024057671 88.00319447 -1.944498437 -0.203994832 VYMGHGGKPWVSDFSHPHYLAGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VYMGHGGKPWVSDFSHPHYLAGR 23 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 227.8 2.65E-33 4420590000 2953070 3726210 2944630 3100420 2662440 2740010 2739090 287687 2911700 2477460 FALSE TRUE 2837660.76 3619942.139 3476790.144 3260433.048 2748079.801 2795414.88 2772611.803 281746.1629 2581176.023 2309659.428 1.228605709 1.567305593 1.505325895 1.411651003 1.189820355 1.210314753 1.200441836 0.121986021 1.117556984 1 21.1392487 1.944514926 10.02812301 0.651013978 1.351164392 0.484327747 0.274658553 0.430736309 76.22283979 0.112202821 0.071495644 88.00653576 -1.944514926 0.700150414 LDDIKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDDIKDR 7 1 Q16513-3;Q16513-2;Q16513;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 0 92.439 0.01429 249910000 643050 613050 495960 593540 608420 570100 626160 718240 729720 751170 FALSE TRUE 617918.8951 595566.4142 585591.0046 624172.6705 627990.3819 581627.8126 633823.1334 703408.093 646885.2448 700292.5868 0.882372464 0.85045369 0.836209058 0.891302696 0.896754291 0.830549721 0.905083311 1.004448864 0.923735674 1 19.41759829 1.944534121 4.961323084 0.973332487 0.865325663 0.746221807 0.029026355 0.101309727 5.200303639 0.012585623 0.00761824 88.0104255 -1.944534121 -0.108006823 HSPTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSPTSEPTPPGDALPPVSSPHTHR 24 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 HSPTSEPTPPGDALPPVS(0.244)S(0.244)PHT(0.513)HR 111.49 0.0033193 220160000 74939 99811 73284 108160 101080 93450 76523 7473.1 75574 48511 TRUE FALSE 72010.30103 96964.48801 86528.04899 113742.1506 104331.33 95339.62303 77459.51136 7318.777873 66995.15635 45225.30676 1.592256774 2.144031626 1.91326616 2.515011145 2.306923656 2.108103402 1.712747064 0.161829259 1.481364332 1 15.46484267 1.944576945 6.125288053 0.81227119 2.104365447 0.674419883 0.376633343 0.11518168 9.477116479 0.159282075 0.098523795 88.01910427 -1.944576945 1.292094258 S(ph)HDRLPYQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHDRLPYQR 9 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 S(1)HDRLPYQR 106.67 0.0017554 325660000 66546 68598 64758 71090 58879 78105 69262 40448 86483 72558 TRUE FALSE 63945.30875 66641.6522 76461.21113 74758.96342 60772.89651 79684.33661 70109.64907 39612.73467 76665.81241 67643.58203 0.945327063 0.985188102 1.13035426 1.105189305 0.898428124 1.178002912 1.036456778 0.585609654 1.133378956 1 16.04566544 1.944588772 24.99937722 0.847972786 1.044212563 0.102793392 0.153934114 396.2384793 178766.5144 0.060945245 0.039333684 88.02150135 -1.944588772 0.196239776 HPTPGSSDPLIQPSSPAVCPEPPS(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPTPGSSDPLIQPSSPAVCPEPPSSPK 27 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9 A0A0G2JQJ7 MAPT Microtubule-associated protein tau 1 HPTPGSSDPLIQPSSPAVCPEPPS(0.694)S(0.306)PK;HPTPGSSDPLIQPSSPAVCPEPPS(0.597)S(0.403)PK 182.74 9.89E-18 2115550000 1120260 1188380 969910 1111350 1029030 1142200 1110630 790410 1295160 1191230 TRUE FALSE 1076479.001 1154488.566 1145194.313 1168706.907 1062129.684 1165296.067 1124222.222 774087.7573 1148138.867 1110546.931 0.969323286 1.039567562 1.031198485 1.05237057 0.956402341 1.049299254 1.012314015 0.697032908 1.03384993 1 20.08283893 1.944665631 24.99823101 0.871141685 1.018151769 0.185556798 0.090752114 306.9152346 138653.5212 0.035287687 0.022775526 88.03708024 -1.944665631 0.147010084 S(ph)TPDSTYSESFK ddPTM_BT-474_Pertuzumab_2h_R1 1 STPDSTYSESFK 12 0 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 S(0.693)T(0.307)PDSTYSESFK 263.29 1.92E-21 603440000 1227500 1095800 1062500 1036000 1058400 1216400 1315800 1503600 1767800 1668900 TRUE FALSE 1179527.943 1064548.857 1254517.385 1089468.084 1092444.397 1240996.441 1331903.154 1472550.135 1567126.755 1555863.916 0.75811768 0.684217203 0.806315624 0.700233531 0.702146496 0.797625312 0.856053759 0.946451755 1.007238961 1 20.56928445 1.94475225 1.290146442 1.0063024 0.730050341 0.911459064 0.034649257 0.114656194 0.353439192 0.025133139 0.01125742 88.05464079 -1.94475225 -0.276252059 LDVTILS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDVTILSPSR 10 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 LDVT(0.001)ILS(0.976)PS(0.024)R;LDVT(0.001)ILS(0.972)PS(0.027)R;LDVT(0.006)ILS(0.964)PS(0.031)R;LDVT(0.001)ILS(0.987)PS(0.012)R 78.884 0.03007 563442000 380373 406012 359385 403872 397468 410520 375493 350378 374061 396809 TRUE FALSE 365507.6026 394432.9353 424333.864 424715.8823 410252.9192 418820.9957 380088.3957 343142.5719 331599.1635 369932.773 0.988037907 1.066228688 1.147056695 1.148089365 1.108993172 1.132154343 1.027452617 0.927580893 0.896376822 1 18.49690359 1.944882852 3.198698278 0.935392879 1.101574006 0.658231205 0.050504307 0.150835182 2.858765489 0.026322286 0.014791445 88.08112487 -1.944882852 0.166181127 KEPEKPIDR ddPTM_BT-474_Pertuzumab_2h_R1 6 KEPEKPIDR 9 2 O00422;O00422-2;U3KQ12 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ;;;;; 129.16 0.00022339 6261290000 9874480 9247590 8016730 7949620 8653160 9242000 9674930 11198350 12542480 11639570 FALSE TRUE 9488574.405 8983857.788 9465531.442 8359900.841 8931496.75 9428879.572 9793334.687 10967100.16 11118710.25 10851211.56 0.874425345 0.827912878 0.872301806 0.770411746 0.823087515 0.868924131 0.902510714 1.010679785 1.024651505 1 23.3713528 1.94494989 1.826481739 1.019558737 0.833943673 0.874880961 0.029173679 0.110217012 0.68281612 0.018554593 0.008937202 88.09472215 -1.94494989 -0.185615064 EAIHDMNFSNEDMIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAIHDMNFSNEDMIR 15 0 Q96EI5;Q96EI5-2;A2RQR6;Q9H3H9 Q96EI5 TCEAL4;TCEAL2 Transcription elongation factor A protein-like 4;Transcription elongation factor A protein-like 2 0 ; 172.82 1.00E-06 342200000 180721 221157 198811 279980 237850 244930 216227 198538 205583 234783 FALSE TRUE 173658.2235 214849.8189 234740.5702 294429.8014 245500.6613 249882.6524 218873.2507 194438.1209 182246.0797 218880.9383 0.79339126 0.98158305 1.072457803 1.345159627 1.121617365 1.141637341 0.999964878 0.88832825 0.832626546 1 17.73978679 1.945000083 3.536894758 0.898309704 1.085612772 0.234249495 0.135459124 0.348465527 8.213797779 0.070428872 0.040432933 88.10490417 -1.945000083 0.187303068 LEQMPSKEDAIEHFMK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEQMPSKEDAIEHFMK 16 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 164.01 4.52E-09 3083430000 3312910 2990980 2921620 2984930 3249050 3089520 3552760 3605560 4441970 3960640 FALSE TRUE 3183437.815 2905680.179 3449621.725 3138982.595 3353558.644 3151992.211 3596239.74 3531103.926 3937736.188 3692382.325 0.862163648 0.786939142 0.934253666 0.850123936 0.908237108 0.853647302 0.973961909 0.956321316 1.066448661 1 21.81612051 1.94507332 1.126628742 1.027177651 0.861362938 0.683700181 0.044550602 0.271183289 0.633746516 0.033241 0.014883272 88.11976286 -1.94507332 -0.165814713 TMHHLLLEVEVIEGTLQCPESGR ddPTM_BT-474_Pertuzumab_2h_R1 4 TMHHLLLEVEVIEGTLQCPESGR 23 0 F5GYQ2;Q9UI30;Q9UI30-2 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;; 258.91 6.68E-44 680699000 189082.7 197372.6 165328.8 182871 202549.4 210315.9 182140.2 50978.3 187827.6 182258.2 FALSE TRUE 181693.139 191743.7267 195207.3919 192308.9942 209064.5854 214568.6316 184369.2863 49925.58029 166506.1983 169913.6898 1.069326075 1.128477211 1.148862061 1.131804003 1.23041637 1.262809559 1.085076114 0.293829063 0.979945751 1 17.37444257 1.945159138 13.06484286 0.681794115 1.162607883 0.460036947 0.191392047 1.337890738 317.8114651 0.075004913 0.048160899 88.13717734 -1.945159138 0.480813768 LKQEFHYIEEDLYR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKQEFHYIEEDLYR 14 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ;; 129.93 3.91E-05 146359000 277105 374216 257172 304378 289270 271776 312786 354912 376851 348336 FALSE TRUE 266275.4302 363543.7261 303648.7012 320086.9851 298574.6323 277271.4969 316613.9686 347582.9432 334072.4544 324742.8925 0.819957685 1.119481702 0.935043409 0.985662789 0.919418528 0.853818523 0.974968124 1.070332719 1.028729072 1 18.30893842 1.945244095 7.061207584 1.037016972 0.945456304 0.226750002 0.077070245 0.384258116 42.05379118 0.032161051 0.020122664 88.15442058 -1.945244095 -0.091560667 FTDEYQLFEELGK ddPTM_BT-474_Pertuzumab_2h_R1 2 FTDEYQLFEELGK 13 0 E9PF82;E9PBG7;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5 E9PF82;Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 0 ; 213.59 1.09E-08 83966000 114306 97535 84502 93138 89863 110974 107027 124816 137975 138353 FALSE TRUE 109838.7951 94753.3973 99773.39114 97944.86334 92753.52501 113217.9703 108336.8284 122238.506 122312.6564 128982.2281 0.851580848 0.734623666 0.773543709 0.759367122 0.719118644 0.877779614 0.839936091 0.947715882 0.94829077 1 16.97681277 1.945367661 1.028479585 0.986888839 0.767140667 0.792170785 0.042486635 0.213690645 0.415387667 0.032907273 0.014919717 88.17950588 -1.945367661 -0.219748171 AITSLLGGGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 AITSLLGGGSPK 12 0 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AITSLLGGGS(1)PK;AITSLLGGGS(1)PK 225.09 1.94E-11 6321400000 2948020 2533350 2098160 2120960 2584110 2405970 2584300 3117940 3240990 2692640 TRUE FALSE 2832808.119 2461101.338 2477344.185 2230423 2667230.245 2454620.362 2615927.436 3053553.449 2873086.403 2510265.094 1.128489627 0.980414915 0.986885485 0.8885209 1.062529312 0.977833125 1.042092105 1.216426686 1.144535057 1 21.2594083 1.945389 6.895755902 1.141585331 1.000383309 0.300293172 0.077166168 0.238678465 25.08870851 0.031903645 0.019930103 88.1838386 -1.945389 -0.141202022 S(ph)LSVEHLETK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSVEHLETK 10 0 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.615)LS(0.385)VEHLETK;S(0.584)LS(0.416)VEHLETK 151.26 1.30E-05 119150000 690520 663820 518400 567840 582480 593930 661490 793140 821790 796560 TRUE FALSE 663533.715 644888.5035 612086.4117 597146.2905 601215.9982 605939.6715 669585.5125 776761.3818 728503.8444 742608.2817 0.893517796 0.868410061 0.824238602 0.80412016 0.809600449 0.815961371 0.901667176 1.045990734 0.981006895 1 19.50224188 1.945550821 3.843440058 1.010185076 0.835033217 0.867424701 0.030196366 0.079879296 2.272626346 0.015438924 0.009008472 88.21670277 -1.945550821 -0.175151858 ASAPYNHHGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASAPYNHHGSR 11 0 Q8N684-2;Q8N684;Q8N684-3;F5H669 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ; 82.171 0.019669 25802000 11454.4 18035.1 12965.1 18620.3 12098.2 14547.4 13932.1 10906.1 11919.3 15350 FALSE TRUE 11006.74938 17520.75661 15308.18198 19581.29591 12487.34959 14841.5584 14102.60521 10680.88522 10566.27103 14310.33083 0.769147095 1.224343226 1.069729426 1.36833286 0.872610825 1.037121963 0.98548422 0.746375842 0.73836665 1 13.8047694 1.945590519 3.252669495 0.804931614 1.069904139 0.257672109 0.170409884 0.293794586 5.777177333 0.082089065 0.046332215 88.22476677 -1.945590519 0.264972525 S(ph)LPGSLSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPGSLSEK 9 0 Q5VWQ8;Q5VWQ8-5;F8WA47;A0A3B3ITC7 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 S(1)LPGSLSEK 104.43 0.0034204 62063000 107660 114310 93316 100450 110000 99340 106620 120430 124040 112560 TRUE FALSE 103452.5282 111049.9907 110180.277 105634.2365 113538.2499 101348.7229 107924.8475 117943.0784 109959.4992 104936.2109 0.985861098 1.058261869 1.049973846 1.006651904 1.081973981 0.965812678 1.028480507 1.12395023 1.047869922 1 16.67915308 1.945841051 24.96492818 1.072338107 1.026531655 0.071870872 0.043429935 491.2320564 226436.0167 0.017049683 0.011005434 88.27567576 -1.945841051 -0.045806453 TLPLTGSTFHDQIAMLSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLPLTGSTFHDQIAMLSHR 19 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 151.63 3.69E-08 1231400000 165890 188480 157020 202400 190460 193380 170540 98806 165290 180610 FALSE TRUE 159406.8354 183104.7349 185397.0069 212845.8883 196586.3189 197290.2761 172627.1195 96765.62157 146526.9722 168377.1238 0.946725017 1.087468005 1.101081921 1.264102174 1.167535793 1.17171663 1.025240933 0.574695774 0.870230877 1 17.36133662 1.946088205 7.254546822 0.773752748 1.126656203 0.539964326 0.125434411 0.170391749 19.83170843 0.052781293 0.033100403 88.32592712 -1.946088205 0.352903456 KGVNLPGAAVDLPAVSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGVNLPGAAVDLPAVSEK 18 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 215.57 1.51E-18 6764000000 10216700 9237400 8466700 8876700 8997200 9500700 9671500 10999200 11485400 11013600 FALSE TRUE 9817420.069 8973958.396 9996821.031 9334827.551 9286603.109 9692810.663 9789862.71 10772062.68 10181625.54 10267639.06 0.956151654 0.874004077 0.973624118 0.909150341 0.9044536 0.944015523 0.95346775 1.049127517 0.991622853 1 23.29160115 1.946157031 3.977227252 1.017162451 0.925808022 0.622464543 0.03004584 0.131070668 4.042825055 0.01333265 0.007830709 88.33992604 -1.946157031 -0.09135443 S(ph)PESCSKPEK ddPTM_BT-474_Pertuzumab_2h_R1 5 SPESCSKPEK 10 1 Q03111 Q03111 MLLT1 Protein ENL 1 S(0.997)PES(0.003)CSKPEK;S(1)PESCSKPEK;S(0.999)PES(0.001)CSKPEK;S(1)PESCSKPEK;S(0.997)PES(0.002)CS(0.001)KPEK 146.5 7.51E-05 6927060000 5964390 5318990 4510290 4631080 5013070 5386390 5737440 6528110 7615290 6850120 TRUE FALSE 5731295.045 5167297.613 5325399.734 4870090.594 5174319.949 5495306.496 5807656.507 6393302.247 6750834.205 6386155.271 0.897456263 0.809140617 0.833897628 0.762601344 0.810240235 0.860503114 0.909413608 1.001119136 1.057104614 1 22.6065162 1.946157344 1.623467977 1.03146976 0.820659438 0.85899155 0.034778817 0.126905576 0.622793474 0.023331905 0.010894307 88.33998965 -1.946157344 -0.210810322 ELSDDCFQQWGVRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSDDCFQQWGVRPR 15 1 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 96.673 0.0032914 187700000 63218 72113 56073 72066 65154 63115 62739 55052 55437 64827 FALSE TRUE 60747.37067 70056.40785 66206.63844 75785.3349 67249.73758 64391.22854 63506.81865 53915.15696 49144.02417 60436.20955 1.005148588 1.159179379 1.095479662 1.253972337 1.112739169 1.065441215 1.05080744 0.892100239 0.813155301 1 15.88312556 1.946222713 1.924007374 0.88567242 1.126218766 0.62074542 0.074166192 0.200758961 1.37709928 0.044430647 0.021752695 88.35328734 -1.946222713 0.240546346 SHS(ph)SPASLQLGTGAGAAGSPAQQHAHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSSPASLQLGTGAGAAGSPAQQHAHLR 28 0 C9JR84;C9J038;Q9GZV5 C9JR84 WWTR1 WW domain-containing transcription regulator protein 1 1 S(0.124)HS(0.752)S(0.124)PASLQLGTGAGAAGSPAQQHAHLR;S(0.159)HS(0.818)S(0.023)PASLQLGTGAGAAGSPAQQHAHLR 267.05 5.83E-54 952520000 114895 162000 99378 136638 122592 133957 107872 7934.7 97615 93283 TRUE FALSE 110404.7764 157379.9186 117337.8153 143689.9036 126535.283 136665.7023 109192.1698 7770.845672 86534.15444 86964.85932 1.269533203 1.809695546 1.349255506 1.652275467 1.455016245 1.571504897 1.255589564 0.089356158 0.995047369 1 16.40814494 1.946238025 7.123925913 0.607863632 1.518230528 0.632718894 0.278055734 0.133946722 15.14338988 0.110321808 0.069108471 88.35640247 -1.946238025 0.910366897 ESVNS(ph)PVFGK ddPTM_BT-474_Pertuzumab_2h_R1 3 ESVNSPVFGK 10 0 Q9UPS8-2;E7ESJ3;Q9UPS8 Q9UPS8-2 ANKRD26 Ankyrin repeat domain-containing protein 26 1 ESVNS(1)PVFGK;ES(0.001)VNS(0.999)PVFGK;ESVNS(1)PVFGK 152.16 1.94E-05 467930000 808330 869860 708530 751320 793150 884250 874660 953640 1038300 1068330 TRUE FALSE 776739.5699 845052.4445 836577.1322 790095.7152 818662.3901 902130.1408 885364.3507 933947.0007 920436.5369 995971.0575 0.779881668 0.848470885 0.839961288 0.793291842 0.821974076 0.905779474 0.888945862 0.937725041 0.924159924 1 19.92574429 1.946244652 0.537974825 0.993458692 0.806055366 0.847386025 0.025787994 0.312922924 0.194653207 0.025353023 0.017675622 88.35775068 -1.946244652 -0.187403326 AAGGAPS(ph)PPPPVR ddPTM_BT-474_Pertuzumab_2h_R1 6 AAGGAPSPPPPVR 13 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR 145.52 4.39E-05 3656900000 1163837 1191980 1108285 1241110 1196440 1158090 1313660 1475110 1624360 1559510 TRUE FALSE 1118352.963 1157985.897 1308576.753 1305163.836 1234924.579 1181507.373 1329736.964 1444648.463 1439969.463 1453882.999 0.769217994 0.796478051 0.900056438 0.897708988 0.849397496 0.812656434 0.914610712 0.993648364 0.990430086 1 20.47147974 1.946316597 2.855909984 0.993936835 0.841946291 0.764350333 0.039017252 0.143761216 2.153547291 0.022254187 0.0121887 88.37238919 -1.946316597 -0.151990543 RPASPS(ph)SPEHLPATPAESPAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 1 RPAS(0.013)PS(0.493)S(0.493)PEHLPATPAESPAQR 184.03 2.48E-17 294620000 63834 71329 81843 76528 83778 74846 73944 65503 73376 74072 TRUE FALSE 61339.29671 69294.76676 96633.85069 80477.61925 86472.79546 76359.4374 74848.94879 64150.34016 65046.6641 69055.03746 0.888266794 1.003471569 1.399374387 1.165412723 1.252230085 1.105776497 1.083902805 0.928974084 0.941953932 1 16.07545904 1.946355935 2.563899171 0.950048989 1.148554244 0.270817762 0.129624101 0.375232996 4.51943253 0.073820374 0.039302315 88.3803944 -1.946355935 0.198505255 LGAGEGGEASVS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 5 LGAGEGGEASVSPEK 15 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LGAGEGGEAS(0.002)VS(0.998)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEAS(0.003)VS(0.997)PEK 345.71 3.42E-82 4723457000 4283870 3489730 3772300 3817020 3731510 3533240 4341130 5239710 5515360 5444660 TRUE FALSE 4116451.624 3390206.317 4454038.524 4014016.86 3851537.408 3604684.534 4394258.048 5131508.157 4889279.455 5075888.329 0.810981518 0.667904039 0.877489463 0.790800861 0.758790808 0.710158361 0.86571212 1.010957654 0.963236214 1 22.2752289 1.946433921 3.661010843 0.988103398 0.770398168 0.768165196 0.054495851 0.108425882 2.770080558 0.025705569 0.014878288 88.3962661 -1.946433921 -0.21770523 EFDRHS(ph)GSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EFDRHSGSDR 10 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 EFDRHS(0.998)GS(0.002)DR;EFDRHS(0.967)GS(0.033)DR;EFDRHS(0.971)GS(0.029)DR 114.56 0.00081085 1038706000 913008 969155 858762 905859 882438 985794 910288 835461 935200 1034695 TRUE FALSE 877326.638 941515.6483 1013959.396 952610.4915 910822.4197 1005727.43 921428.3768 818208.4384 829040.0167 964614.186 0.909510404 0.976054118 1.051155385 0.987555963 0.944234942 1.042621438 0.955229967 0.848223518 0.859452441 1 19.8795925 1.946440133 6.660268664 0.888842763 0.987087994 0.302997942 0.054815552 0.234249395 23.45817855 0.022872013 0.014261676 88.39753062 -1.946440133 0.098245231 KS(ph)SPSVKPAVDPAAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSSPSVKPAVDPAAAK 16 2 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7 Q6FI81-3 CIAPIN1 Anamorsin 1 KS(0.591)S(0.409)PSVKPAVDPAAAK;KS(0.494)S(0.494)PS(0.012)VKPAVDPAAAK 133.26 1.81E-05 3135690000 4600190 3530580 3221640 3057690 3274810 3863750 4195060 5219090 5596550 5765320 TRUE FALSE 4420409.489 3429891.315 3803862.013 3215497.747 3380147.238 3941877.672 4246400.399 5111313.968 4961253.107 5374829.741 0.822427817 0.638139528 0.707717676 0.598251089 0.628884523 0.733395821 0.790053007 0.950972257 0.923053072 1 22.35778762 1.946452327 1.68042741 0.967980806 0.675191812 0.800048338 0.060553635 0.151421 0.795840555 0.039117846 0.018433163 88.40001269 -1.946452327 -0.292788994 YSKEEEMDDMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSKEEEMDDMDR 12 1 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ; 175.15 2.60E-05 1669040000 1338530 1673190 1597770 1906680 1529580 1787520 1882570 2331200 2620900 2320270 FALSE TRUE 1286218.768 1625472.259 1886522.581 2005083.983 1578780.33 1823664.879 1905609.455 2283059.905 2323386.42 2163116.046 0.594613853 0.751449402 0.872131934 0.926942402 0.729863907 0.843073067 0.88095572 1.055449572 1.07409236 1 21.04467963 1.946467614 2.027744678 1.054305652 0.789713892 0.637559258 0.086509411 0.219603375 1.668942129 0.054234027 0.026976537 88.40312425 -1.946467614 -0.26459176 HVIRPPPIS(ph)PPPDSLPLDDGAAHVMHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HVIRPPPISPPPDSLPLDDGAAHVMHR 27 1 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;A0A0C4DGG3 Q8NHM5-4 KDM2B Lysine-specific demethylase 2B 1 HVIRPPPIS(1)PPPDSLPLDDGAAHVMHR 123.73 4.17E-05 277400000 95672 103660 103350 120850 113390 114500 93674 3641.3 85370 87478 TRUE FALSE 91933.03247 100703.7183 122027.644 127087.083 117037.2923 116815.2685 94820.41043 3566.105883 75679.1555 81553.03714 1.127279077 1.234824868 1.496297971 1.558336604 1.435106483 1.432384036 1.162683988 0.043727444 0.927974704 1 16.31545099 1.946475526 8.073256981 0.560975914 1.382623966 0.582301344 0.270406132 0.191116489 26.55309024 0.111189199 0.070189912 88.40473481 -1.946475526 0.821648052 HLDSVLSDHTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLDSVLSDHTR 11 0 Q2M389;A0A087X256;F8W1W1 Q2M389 KIAA1033 WASH complex subunit 7 0 186.46 2.32E-06 126830000 34326 68909 41826 62129 51507 48397 47366 37273 35927 43154 FALSE TRUE 32984.50197 66943.78279 49384.88861 65335.48514 53163.76943 49375.6205 47945.67928 36503.29952 31848.71758 40231.14114 0.819874879 1.663979218 1.227528905 1.624002782 1.321458152 1.227298533 1.191755389 0.907339401 0.791643405 1 15.29602504 1.946680356 1.687330733 0.87164461 1.350473625 0.40154996 0.224637376 0.324593924 1.719921815 0.137304145 0.064783525 88.44643986 -1.946680356 0.478829015 YHEDFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YHEDFEK 7 0 O76041-2;O76041;H0Y3P5;H7BZD5;H0Y786;A0A087X1N7;P20929-4;P20929;P20929-3;P20929-2 O76041-2;A0A087X1N7 NEBL;NEB Nebulette;Nebulin 0 155.51 0.0016062 426430000 631310 609870 509160 505630 543800 552370 549030 214980 622380 508950 FALSE TRUE 606637.7072 592477.1047 601176.5382 531725.6249 561291.8209 563539.2999 555749.1934 210540.5879 551730.0316 474478.3632 1.278536082 1.248691512 1.267026244 1.12065305 1.182966104 1.187702841 1.171284586 0.44373064 1.162813891 1 18.85598277 1.946701961 18.30576891 0.807146857 1.20979417 0.42432887 0.17732191 13.14165453 4512.994435 0.069143844 0.044582573 88.45083983 -1.946701961 0.402647312 YRLEVGIQAMEHLIHVLQTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YRLEVGIQAMEHLIHVLQTDR 21 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 266.46 3.40E-37 971870000 380180 423500 357880 404630 426310 470490 398560 70342 446320 345630 FALSE TRUE 365322.1453 411422.1946 422556.877 425513.0028 440022.6483 480003.6302 403437.6965 68889.41312 395655.6247 322220.1722 1.133765595 1.276835624 1.311391754 1.320565996 1.365596217 1.489675916 1.252055989 0.213796091 1.227904578 1 18.29768729 1.946767925 16.52087766 0.728103175 1.321233479 0.428738227 0.256084889 6.095260292 1890.998601 0.100145411 0.064522559 88.46427557 -1.946767925 0.593130304 NMVDLVNTHHLHSS(ph)SDDEDDRLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHS(0.007)S(0.883)S(0.11)DDEDDRLK 230.36 1.97E-33 1394300000 366690 500200 456860 421950 474640 472300 458530 131900 610950 532120 TRUE FALSE 352359.3494 485934.7857 539424.7648 443726.8901 489907.2267 481850.2296 464141.6273 129176.2189 541597.5173 496079.0384 0.710288728 0.979551136 1.087376654 0.89446813 0.987558814 0.971317456 0.935620317 0.260394431 1.091756505 1 18.92021047 1.94688481 24.99939551 0.675905666 0.947816502 0.025937975 0.230759616 466.6902951 219653.2784 0.090954789 0.058703354 88.48808781 -1.94688481 0.271910836 SKHDSSAPDPAPDS(ph)ADEVMPEAVPEVASEPGLESASHPNVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKHDSSAPDPAPDSADEVMPEAVPEVASEPGLESASHPNVDR 42 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.071)KHDS(0.071)S(0.071)APDPAPDS(0.788)ADEVMPEAVPEVASEPGLESASHPNVDR;SKHDSSAPDPAPDS(1)ADEVMPEAVPEVASEPGLESASHPNVDR 233.98 1.12E-54 756690000 124608 250931 157611 243190 185607 223666 189886 143253 177186 214983 TRUE FALSE 119738.1816 243774.6936 186094.8137 255741.065 191577.2177 228188.6798 192209.8817 140294.7755 157072.5881 200422.0099 0.5974303 1.216307 0.928514856 1.276012875 0.955869157 1.138541021 0.959025816 0.699996849 0.783709275 1 17.61268143 1.947006283 6.614936532 0.801299257 1.033916051 0.161221118 0.189910377 0.32506443 32.41275849 0.075922472 0.047335584 88.5128416 -1.947006283 0.232616794 AHALSDETWGLVECHPHLALER ddPTM_BT-474_Pertuzumab_2h_R1 4 AHALSDETWGLVECHPHLALER 22 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;; 238.63 5.09E-31 1992020000 452450 495824 370664 506969 501061 523653 417247 14067.4 459962 302787 FALSE TRUE 434767.7538 481683.585 437651.2302 533133.7308 517178.0821 534241.6224 422353.3936 13776.90327 407749.0421 282278.9668 1.540205984 1.706409764 1.550420972 1.888676783 1.832152385 1.892601594 1.496226936 0.048805986 1.444489636 1 18.10676211 1.947034022 9.558253235 0.735390551 1.73339168 0.578140782 0.342786654 0.311688536 54.67038697 0.135834392 0.086447495 88.51849502 -1.947034022 0.99800113 LTPEEEEILNK ddPTM_BT-474_Pertuzumab_2h_R1 4 LTPEEEEILNK 11 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;; 158.85 6.83E-05 490142000 715709 683175 596318 610533 670372 671385 686299 779870 798610 760922 FALSE TRUE 687738.301 663691.5179 704085.9276 642042.6813 691935.1242 684960.8647 694698.1325 763765.412 707955.1408 709384.0752 0.969486524 0.935588408 0.992531341 0.905070615 0.975402675 0.965571245 0.979297614 1.076659935 0.997985669 1 19.43620742 1.947086674 6.858091542 1.032525635 0.957558719 0.493726808 0.030313327 0.170711646 18.26889213 0.012283998 0.007679131 88.52922738 -1.947086674 -0.074966916 HEIEGTGLPQAQLLWR ddPTM_BT-474_Pertuzumab_2h_R1 2 HEIEGTGLPQAQLLWR 16 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 234.21 1.14E-19 568660000 401800 445210 362260 427790 452800 421390 418990 248610 451540 444290 FALSE TRUE 386097.2118 432513.0467 427728.4404 449868.2932 467364.7232 429910.7945 424117.725 243476.1166 400283.0722 414197.8426 0.932156501 1.044218492 1.032666993 1.086119354 1.128361076 1.037935861 1.023949624 0.587825651 0.966405498 1 18.65996051 1.94730682 18.38069861 0.805676069 1.047401302 0.342959023 0.115198223 15.04853498 5248.599388 0.045397553 0.029272444 88.57411463 -1.94730682 0.241725233 S(ph)VSHGSNHTQKPDEQR ddPTM_BT-474_Pertuzumab_2h_R1 7 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.974)VS(0.026)HGSNHTQKPDEQR;S(0.745)VS(0.255)HGSNHTQKPDEQR;S(0.971)VS(0.029)HGSNHTQKPDEQR;S(0.674)VS(0.326)HGSNHTQKPDEQR;S(0.545)VS(0.454)HGS(0.001)NHTQKPDEQR;S(0.667)VS(0.333)HGSNHTQKPDEQR;S(0.973)VS(0.027)HGSNHTQKPDEQR 270.49 2.39E-35 4042724000 1094373 1662408 1322418 1740516 1412082 1594627 1332017 84900.1 1275850 1318758 TRUE FALSE 1051603.693 1614997.752 1561408.35 1830344.239 1457502.9 1626871.451 1348318.622 83146.88327 1131020.857 1229437.346 0.855353627 1.313607201 1.270018643 1.488765772 1.185504007 1.323265033 1.096695677 0.067630029 0.919949976 1 20.22956678 1.947369705 10.29241349 0.563892937 1.249547466 0.446805754 0.281056191 0.48582721 93.41705985 0.111421868 0.071111412 88.58694099 -1.947369705 0.685654529 DSDSGLEQMSIGHHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDSGLEQMSIGHHIR 16 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 0 ; 240.2 4.31E-20 761680000 465590 588110 447140 641660 555600 606610 554160 224631 551990 624620 FALSE TRUE 447394.2281 571337.6786 527948.1446 674776.1495 573471.3786 618876.0698 560941.9758 219992.2914 489330.4093 582313.931 0.768304181 0.981150627 0.906638355 1.158784143 0.984814802 1.062787677 0.963298224 0.377789848 0.84032063 1 19.15143761 1.947428814 21.42341964 0.670311024 0.98520471 0.246348082 0.176791052 65.89161428 26850.90968 0.069658745 0.044944603 88.59899868 -1.947428814 0.314893686 FAHGNAELHEWEER ddPTM_BT-474_Pertuzumab_2h_R1 1 FAHGNAELHEWEER 14 0 Q8IWR0;Q8IWR0-2 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 0 145.86 4.90E-06 127780000 43567 45837 35603 42817 41909 41718 38914 21428 41726 37496 FALSE TRUE 41864.35347 44529.77364 42037.25408 45026.7905 43257.04105 42561.56654 39390.24117 20985.50431 36989.43941 34956.36252 1.197617557 1.273867486 1.202563741 1.288085695 1.237458303 1.217562798 1.12684039 0.600334325 1.058160425 1 15.09326745 1.947457555 7.783378963 0.8456226 1.233565331 0.637792377 0.116763633 0.156285985 20.9210192 0.046716772 0.029445149 88.60486238 -1.947457555 0.38794273 (ac)S(ph)GFSPELIDYLEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGFSPELIDYLEGK 14 0 A0A494C1S7;Q9Y5Q9;Q9Y5Q9-2;F8WC64 A0A494C1S7 GTF3C3 General transcription factor 3C polypeptide 3 1 S(0.5)GFS(0.5)PELIDYLEGK 57.836 0.00010186 4654700 45911 46083 39808 41411 38102 44067 43691 48033 48494 50032 TRUE FALSE 44116.74736 44768.75796 47002.19112 43548.22667 39327.58543 44958.06493 44225.70353 47041.10176 42989.16442 46643.28808 0.945832706 0.959811364 1.007694634 0.933644013 0.843156369 0.963869975 0.948168651 1.008528852 0.921658103 1 15.50938187 1.947481637 13.55707935 0.977853012 0.942430475 0.108934903 0.044220638 5.79806457 1493.732417 0.019131532 0.012295357 88.6097757 -1.947481637 -0.035422537 VFNFNSSSTSHSSLKS(ph)PSHMEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFNFNSSSTSHSSLKSPSHMEK 22 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 VFNFNSSSTSHS(0.002)S(0.003)LKS(0.765)PS(0.231)HMEK 121.26 1.66E-05 230500000 66570 104290 105110 139110 111170 127360 95147 52178 75784 90219 TRUE FALSE 63968.3708 101315.7513 124105.7152 146289.4838 114745.884 129935.3065 96311.43745 51100.50607 67181.31803 84108.38677 0.760546876 1.204585597 1.475545067 1.739297226 1.364262096 1.54485553 1.145087204 0.607555418 0.798746957 1 16.35996204 1.947484293 4.941843112 0.776087369 1.365617818 0.473894308 0.256227753 0.176459638 9.196853446 0.120323847 0.073006188 88.61031754 -1.947484293 0.589530449 HQVLNDRDEEVELCSSVECK ddPTM_BT-474_Pertuzumab_2h_R1 2 HQVLNDRDEEVELCSSVECK 20 1 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 119.54 2.97E-05 515620000 275221 289214 224110 240211 265141 298854 268218 155552 321885 313683 FALSE TRUE 264465.059 280965.8999 264611.6623 252608.3185 273669.5011 304897.0326 271500.5321 152339.7968 285345.9643 292436.971 0.90434892 0.96077421 0.904850236 0.863804319 0.935823881 1.042607683 0.928407004 0.520932071 0.975752017 1 18.15776619 1.947567944 24.99824738 0.765415994 0.936371049 0.045805297 0.133495405 443.0964298 211256.0337 0.052893281 0.034138743 88.62738668 -1.947567944 0.170955055 THFGGGK ddPTM_BT-474_Pertuzumab_2h_R1 7 THFGGGK 7 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ;;;;;; 117.93 0.0051196 5068730000 23097300 22276740 20207420 19517920 21363980 22598000 21640370 9066960 24631120 22159300 FALSE TRUE 22194631.98 21641429.19 23859350.31 20525242.19 22051171.82 23054947.04 21905211.32 8879724.107 21835098.52 20658430.87 1.074361945 1.047583397 1.154944945 0.993552817 1.067417557 1.116006689 1.060352137 0.429835362 1.056958229 1 24.30022734 1.94762435 24.99874481 0.760457835 1.075060974 0.292547657 0.164353175 290.4927086 138650.751 0.063669414 0.041089186 88.63889842 -1.94762435 0.314603138 NDDDSSEAMNDILAQVATNTETSK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDDDSSEAMNDILAQVATNTETSK 24 0 O43747;O43747-2 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ; 242.53 1.24E-37 76030000 117932 104655 90705 92430 93321 103816 109441 125028 140350 128315 FALSE TRUE 113323.0871 101670.3419 107097.4112 97200.32338 96322.75472 105915.2306 110780.3717 122446.1281 124418.0564 119624.1108 0.947326474 0.849915132 0.89528282 0.812547928 0.805211877 0.885400359 0.926070597 1.023590707 1.040075079 1 16.86814867 1.947632547 2.181027242 1.026578398 0.860550665 0.755112416 0.039512617 0.148304989 1.299386615 0.023407784 0.011910992 88.64057139 -1.947632547 -0.166027733 NSPLDCGSAS(ph)PNK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPLDCGSASPNK 13 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 NSPLDCGSAS(1)PNK;NSPLDCGSAS(1)PNK 278.08 2.84E-32 328900000 637820 513870 523130 557770 550260 500560 662900 768530 836480 872880 TRUE FALSE 612893.2893 499214.9307 617671.228 586556.5765 567959.6126 510681.6662 671012.7685 752659.5869 741526.2972 813759.0601 0.753163091 0.613467739 0.759034533 0.720798828 0.69794567 0.627558808 0.824584083 0.924916998 0.911235688 1 19.63424218 1.947711155 2.79456665 0.938453421 0.696010831 0.829368111 0.050738343 0.103815773 1.489131775 0.0254684 0.013890149 88.65661704 -1.947711155 -0.24244259 TAS(ph)PPGPPPYGK ddPTM_BT-474_Pertuzumab_2h_R1 4 TASPPGPPPYGK 12 0 P54259 P54259 ATN1 Atrophin-1 1 TAS(1)PPGPPPYGK;TAS(1)PPGPPPYGK;TAS(1)PPGPPPYGK;T(0.005)AS(0.995)PPGPPPYGK 182.25 1.80E-05 2287510000 1181680 1107340 979040 1000420 1053870 1079210 1127360 1267590 1351940 1280930 TRUE FALSE 1135498.639 1075759.747 1155974.307 1052051.796 1087768.686 1101032.366 1141156.969 1241413.824 1198473.439 1194171.47 0.950867331 0.900841943 0.968013669 0.880988888 0.910898236 0.922005251 0.955605621 1.039560779 1.003602472 1 20.18757858 1.947911474 3.747100184 1.016768133 0.921556311 0.729235229 0.025029814 0.10988477 2.971979384 0.011465431 0.00667524 88.69751937 -1.947911474 -0.095211822 S(ph)VSENSLVAMDFSGQTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSENSLVAMDFSGQTGR 18 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 S(0.454)VS(0.454)ENS(0.091)LVAMDFSGQTGR 63.918 0.041479 10649000 13044 11378 11633 11743 11153 11502 12174 13745 14191 13361 TRUE FALSE 12534.22606 11053.51058 13735.34187 12349.05764 11511.74637 11734.57832 12322.98905 13461.16095 12580.09717 12456.04757 1.006276348 0.887401121 1.102704674 0.991410603 0.924189339 0.942078798 0.989317758 1.080692802 1.009958986 1 13.60455874 1.94794512 10.32624952 1.038219301 0.974972762 0.149043893 0.05740974 1.148417763 224.1154458 0.02394568 0.015286508 88.70439135 -1.94794512 -0.063246539 RHS(ph)DENDGGQPHK ddPTM_BT-474_Pertuzumab_2h_R1 8 RHSDENDGGQPHK 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK 204.78 3.53E-08 1773989400 502406.8 515298.3 415997.1 534527 594577.4 484463.5 443567.1 117664.9 446881 395687.4 TRUE FALSE 482772.1868 500602.497 491177.0298 562114.0025 613702.5221 494259.6839 448995.6069 115235.0787 396152.9424 368887.14 1.308725988 1.357061396 1.331510309 1.523810243 1.663659303 1.339866941 1.217162536 0.312385731 1.07391367 1 18.49281997 1.947950935 6.96527827 0.72633968 1.418061883 0.621082412 0.216376322 0.139535432 15.5966823 0.090961 0.056956492 88.7055789 -1.947950935 0.691722203 KPPT(ph)PGPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPTPGPEK 9 1 Q6ZRI6;Q6ZRI6-3 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 1 KPPT(1)PGPEK 69.03 0.073816 0 461900 374210 308020 292050 324990 311220 372310 455590 482730 401640 TRUE FALSE 443848.4373 363537.8972 363686.0659 307122.7355 335443.5985 317513.0816 376866.4412 446181.9073 427932.5142 374436.5651 1.185376854 0.970893153 0.971288864 0.820226346 0.89586229 0.847975629 1.00648942 1.191608804 1.142870526 1 18.5143618 1.948067811 5.969315193 1.126615443 0.941083181 0.326099028 0.103634611 0.226020233 18.45446767 0.046265245 0.02863264 88.72945442 -1.948067811 -0.185532262 DSNPDEIEIDFETLKPTTLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSNPDEIEIDFETLKPTTLR 20 1 Q15059 Q15059 BRD3 Bromodomain-containing protein 3 0 ;; 167.53 1.24E-11 224072000 224078 203669 188280 184040 209847 205308 214431 246335 263579 232357 FALSE TRUE 215320.784 197860.5595 222306.3843 193538.3265 216596.9193 209459.4684 217055.2707 241248.0962 233658.6169 216619.2534 0.994005753 0.913402463 1.026254041 0.893449328 0.999896897 0.966947606 1.002012828 1.113696462 1.078660429 1 17.72480195 1.948068835 4.650093734 1.074267457 0.965364004 0.478360079 0.045550009 0.152192911 6.875202358 0.019095982 0.011505176 88.72966353 -1.948068835 -0.108903453 DHRDNLEFFLAGIGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DHRDNLEFFLAGIGR 15 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 147.35 2.24E-06 1651875000 1636952 1977922 1089909 1242459 1442088 1845810 1450006 789200 1576177 1340322 FALSE TRUE 1572978.106 1921513.601 1286879.801 1306582.458 1488474.07 1883133.543 1467751.607 772902.7442 1397255.995 1249540.797 1.258844937 1.537775802 1.029882181 1.045650099 1.191216864 1.507060472 1.174632802 0.618549427 1.118215586 1 20.25296658 1.948097603 10.75526977 0.876153134 1.258202029 0.386790409 0.195494857 0.770973349 157.8374722 0.082577431 0.052786484 88.73554128 -1.948097603 0.382048894 QEDKDDLDVTELTNEDLLDQLVK ddPTM_BT-474_Pertuzumab_2h_R1 4 QEDKDDLDVTELTNEDLLDQLVK 23 1 P42166;P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 ;;; 277.5 7.71E-52 1250570000 918965 842716 650298 717794 689830 682472 839095 1138250 1116650 922929 FALSE TRUE 883050.8318 818682.5648 767821.3144 754839.4344 712019.0084 696272.0514 849364.0956 1114744.74 989892.5734 860418.1968 1.026304226 0.951493783 0.892381539 0.877293666 0.827526674 0.809225158 0.987152641 1.295584803 1.150478427 1 19.71467851 1.948101577 6.263122228 1.174221962 0.89547121 0.613164829 0.08854411 0.129714501 11.76293237 0.038519207 0.023934764 88.73635332 -1.948101577 -0.278750752 KNDMDEPPPLDYGS(ph)GEDDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KNDMDEPPPLDYGSGEDDGK 20 1 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5;H7C2H0 Q12873-3;H7C2H0 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 KNDMDEPPPLDYGS(1)GEDDGK;KNDMDEPPPLDYGS(1)GEDDGK;KNDMDEPPPLDYGS(1)GEDDGK 202.98 6.78E-22 1359700000 2714020 2100800 2184300 1882810 2318990 2159050 2575070 3048230 3460600 3042190 TRUE FALSE 2607953.098 2040887.241 2579051.599 1979982.05 2393582.419 2202707.47 2606584.477 2985282.985 3067767.196 2836139.762 0.919543223 0.719600377 0.909352788 0.698125698 0.843957851 0.776656884 0.919060659 1.052586697 1.081669965 1 21.4354972 1.948201716 2.803438623 1.050201467 0.807976391 0.688701573 0.070163132 0.135802406 1.961370464 0.033301608 0.018185247 88.75681642 -1.948201716 -0.242225076 RGEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_BT-474_Pertuzumab_2h_R1 3 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFSEPGTTSTQRPS(0.287)S(0.712)PETATK;RGEGDAPFSEPGTT(0.001)S(0.005)T(0.024)QRPS(0.21)S(0.76)PETATK;RGEGDAPFSEPGTTSTQRPS(0.322)S(0.677)PETATK 235.16 2.80E-45 28832700000 6198300 6050010 5506240 5627010 5743730 6007670 6243790 6731900 7738030 6907880 TRUE FALSE 5956063.583 5877469.638 6501340.054 5917420.66 5928482.292 6129149.204 6320203.37 6592883.912 6859641.275 6440003.135 0.924854144 0.912650121 1.009524362 0.918853693 0.920571336 0.95173078 0.981397561 1.02373924 1.06516117 1 22.61862996 1.948219852 1.970680762 1.035178609 0.939100116 0.648027482 0.029810698 0.202508605 1.455774491 0.017995713 0.008888515 88.7605229 -1.948219852 -0.096078493 HS(ph)PVQMNR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSPVQMNR 8 0 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 HS(1)PVQMNR;HS(1)PVQMNR;HS(1)PVQMNR;HS(1)PVQMNR 93.096 0.010603 975804000 529132 527686 486445 563735 532513 542803 531112 416158 557117 608878 TRUE FALSE 508452.9365 512636.9119 574356.4324 592829.4309 549641.7643 553778.8486 537611.9075 407564.1919 493875.4138 567638.1507 0.895734256 0.903105105 1.011835501 1.044379117 0.968296024 0.975584266 0.947103197 0.717999999 0.870053243 1 19.11461203 1.948279956 14.10219406 0.831625754 0.968630746 0.238949592 0.077458257 3.129010802 851.9743316 0.031648375 0.020353982 88.77280774 -1.948279956 0.137004992 ENALVQMADGNQAQLAMSHLNGHK ddPTM_BT-474_Pertuzumab_2h_R1 5 ENALVQMADGNQAQLAMSHLNGHK 24 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;; 234.39 1.36E-37 4737568000 1942958 2233225 1853755 1956414 2019410 2049614 1988466 196680 2125928 1881009 FALSE TRUE 1867025.053 2169535.61 2188769.765 2057384.761 2084366.157 2091058.599 2012801.442 192618.4893 1884601.566 1753606.585 1.06467726 1.237184913 1.248153254 1.173230517 1.188616748 1.192433136 1.147806731 0.109841336 1.074700325 1 20.74189369 1.948294087 21.57277384 0.629158895 1.187513107 0.388339768 0.250436339 56.53741213 23587.98508 0.096741939 0.062420973 88.7756962 -1.948294087 0.558354212 HVLVILTDMSSYAEALR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVLVILTDMSSYAEALR 17 0 P21281;P15313;C9JL73;C9JNS9 P21281;P15313 ATP6V1B2;ATP6V1B1 "V-type proton ATPase subunit B, brain isoform;V-type proton ATPase subunit B, kidney isoform" 0 ; 270.75 1.36E-35 443260000 227664 230029 222044 283610 257356 262243 251800 134386 309570 279200 FALSE TRUE 218766.6392 223468.7981 262172.2901 298247.1461 265634.0895 267545.7331 254881.6037 131610.8821 274428.9114 260289.5353 0.840474201 0.85853931 1.00723331 1.145828417 1.020533112 1.027877409 0.9792234 0.505632629 1.054321723 1 17.98975779 1.948371093 24.99752785 0.784398201 0.989195909 0.073078988 0.162351394 479.5858561 232203.486 0.066510944 0.042924834 88.79143874 -1.948371093 0.204797708 AVSDWIDEQEK ddPTM_BT-474_Pertuzumab_2h_R1 6 AVSDWIDEQEK 11 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;K7ERM6;K7ENK6;K7EQ75;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 215.89 2.90E-11 1599020000 1566398 1480611 1454378 1559574 1547400 1554070 1714924 2089347 2122980 2189212 FALSE TRUE 1505181.434 1438385.424 1717216.457 1640063.801 1597173.526 1585494.36 1735911.753 2046201.254 1881988.211 2040934.721 0.737496118 0.704767972 0.841387252 0.803584644 0.782569628 0.776847169 0.850547416 1.002580451 0.922120728 1 20.96079861 1.948542592 3.092069904 0.972909568 0.776406978 0.830576302 0.040381708 0.103624371 1.836557666 0.021147473 0.011832895 88.82650867 -1.948542592 -0.196502591 TIVLVPS(ph)PLGQQQDMIFEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 TIVLVPSPLGQQQDMIFEAR 20 0 Q96R06;F5GZT2 Q96R06 SPAG5 Sperm-associated antigen 5 1 TIVLVPS(1)PLGQQQDMIFEAR;TIVLVPS(1)PLGQQQDMIFEAR;TIVLVPS(1)PLGQQQDMIFEAR;TIVLVPS(1)PLGQQQDMIFEAR 204.78 9.75E-22 519164000 300204 328984 335763 404952 409625 402665 296579 246371 228998 266368 TRUE FALSE 288471.6958 319601.6984 396442.8431 425851.6212 422800.9601 410807.1622 300208.6225 241283.3528 203003.1071 248326.6581 1.161662215 1.2870213 1.596457046 1.71488484 1.702599968 1.654301497 1.208926278 0.971636934 0.81748415 1 17.92187962 1.948589638 2.71739284 0.923056346 1.528294204 0.694907035 0.175066432 0.169932771 2.303680127 0.103268749 0.055957984 88.83613134 -1.948589638 0.605237858 FATLAELVQYYMEHHGQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FATLAELVQYYMEHHGQLK 19 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 201.67 3.40E-16 517770000 160970 157240 138380 156810 174130 162190 160600 105210 199000 172370 FALSE TRUE 154679.1144 152755.6692 163388.3442 164902.9829 179731.0496 165469.5929 162565.4708 103037.3767 176410.3543 160695.2264 0.962561975 0.950592451 1.016759165 1.026184701 1.118459171 1.029710693 1.011638457 0.641197496 1.097794616 1 17.29396755 1.948593122 24.99929082 0.861452234 1.019423201 0.09326407 0.118955032 449.4306885 218558.4606 0.047635855 0.030741685 88.83684403 -1.948593122 0.157970967 S(ph)IGSAVDQGNESIVAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SIGSAVDQGNESIVAK 16 0 Q9H0H5;F8VRD2;F8W1E5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 S(1)IGSAVDQGNESIVAK;S(1)IGSAVDQGNESIVAK;S(1)IGSAVDQGNESIVAK 365.1 1.17E-72 633130000 1768950 1586890 1401750 1549810 1393380 1335620 1542670 2165250 1801950 1552400 TRUE FALSE 1699817.478 1541633.451 1655077.407 1629795.88 1438199.333 1362627.152 1561549.657 2120536.831 1597400.19 1447254.565 1.17451174 1.06521236 1.143597986 1.126129376 0.993743166 0.941525551 1.07897373 1.465213434 1.103745138 1 20.46488728 1.948627289 24.99893145 1.249030947 1.070139073 0.090303266 0.131029032 441.0109929 214603.4393 0.052903258 0.034141841 88.84383348 -1.948627289 -0.178891873 YLEYER ddPTM_BT-474_Pertuzumab_2h_R1 2 YLEYER 6 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 0 ; 128.75 0.038361 596180000 596490 638100 666870 605760 640550 616440 561250 593910 511870 582140 FALSE TRUE 573178.5113 619902.0128 787388.2434 637023.3462 661153.8725 628904.8392 568118.7454 581645.551 453764.6635 542711.1393 1.056139205 1.142231968 1.450842237 1.173779751 1.218242679 1.158820584 1.046816076 1.07174058 0.836107149 1 19.049825 1.948635308 1.162956216 0.939606372 1.217503838 0.504963716 0.106833079 0.401924823 1.002107106 0.083900563 0.037592113 88.84547381 -1.948635308 0.277897465 SMESS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SMESSPR 7 0 Q1ED39;H3BPL4 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 SMES(0.313)S(0.687)PR;SMES(0.015)S(0.985)PR 103.8 0.0086999 173466000 413080 418290 351680 381480 381690 411350 344790 391450 355040 386040 TRUE FALSE 396936.3769 406360.7787 415236.3991 401168.2285 393967.4055 419667.7788 349009.6432 383366.4207 314737.3476 359893.167 1.10292835 1.129115015 1.153776835 1.114686983 1.094678759 1.166089877 0.969759015 1.065222838 0.874529934 1 18.45720919 1.948677155 1.325494221 0.960476013 1.127076401 0.622802213 0.053728298 0.274569962 0.894470873 0.036691107 0.016524891 88.854035 -1.948677155 0.166600388 KGGHS(ph)SPASSDKNSNSNHR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGGHSSPASSDKNSNSNHR 19 2 Q13029-5;Q13029-3;Q13029-2;Q13029 Q13029-5 PRDM2 PR domain zinc finger protein 2 1 KGGHS(0.5)S(0.5)PASSDKNSNSNHR 76.733 0.0059637 18502000 32084 36172 21403 23899 27668 30273 24504 18499 25125 16958 TRUE FALSE 30830.12181 35140.40998 25270.99821 25132.43025 28557.96635 30885.1408 24803.88728 18116.98919 22272.91533 15809.41956 1.950110926 2.222751433 1.598477295 1.589712397 1.806389301 1.953591066 1.568930927 1.145961692 1.408838272 1 13.94849678 1.948681939 3.282047225 1.209352728 1.843522964 0.697384678 0.196488044 0.152666666 3.07638481 0.102195316 0.057968908 88.85501378 -1.948681939 0.634170236 WTGPEISPNTSGSS(ph)PVIHFTPSDLEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 WTGPEISPNTSGSSPVIHFTPSDLEVR 27 0 A0AVK6 A0AVK6 E2F8 Transcription factor E2F8 1 WTGPEISPNTSGS(0.09)S(0.909)PVIHFTPSDLEVR 131.94 2.54E-05 298260000 94512 140080 71873 105990 100440 105250 87610 92803 79344 92790 TRUE FALSE 90818.36655 136085.0556 84862.04991 111460.1566 103670.7438 107378.2271 88682.19739 90886.58562 70337.20176 86505.25065 1.049859585 1.573142145 0.981004613 1.288478512 1.198432963 1.24129144 1.025165487 1.050648197 0.813097485 1 16.40050008 1.948759688 1.416552288 0.92648469 1.233444638 0.375709681 0.158255692 0.411695912 1.53550299 0.104390226 0.047450823 88.87092239 -1.948759688 0.306959948 RLEEFEGER ddPTM_BT-474_Pertuzumab_2h_R1 1 RLEEFEGER 9 1 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 75.509 0.061027 385760000 170910 160270 138520 208720 203100 200500 166000 118480 166160 156330 FALSE TRUE 164230.6482 155699.2565 163553.6454 219492.0642 209632.896 204554.2474 168031.5577 116033.3466 147298.2134 145741.6299 1.126861614 1.068323832 1.122216387 1.506035471 1.438387207 1.403540276 1.152941392 0.796157877 1.010680432 1 17.1530535 1.948898143 5.649913827 0.923501175 1.279111904 0.520803582 0.146478104 0.178168945 12.96838378 0.072032833 0.044392529 88.89925936 -1.948898143 0.355610729 GSTAPVGGGAFPTIVEREPWDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSTAPVGGGAFPTIVEREPWDGR 23 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ; 120.52 7.42E-05 360120000 165544 222538 117191 154519 157610 191898 156650 136143 163505 146579 FALSE TRUE 159074.3575 216191.4341 138370.0206 162493.7441 162679.6688 195778.309 158567.1296 133331.5995 144944.5979 136651.0738 1.164091529 1.582069048 1.012579095 1.189114287 1.190474866 1.432687674 1.160379682 0.975708392 1.060691247 1 17.06013727 1.948899053 5.151720033 1.019156991 1.261548599 0.362989116 0.147737456 0.229952037 13.42192774 0.064607799 0.039444022 88.89944573 -1.948899053 0.242391608 ALEEGLTPQEICDKYHIIHADIYR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALEEGLTPQEICDKYHIIHADIYR 24 1 P56192;P56192-2;H0YHV5 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;; 130.71 3.96E-05 1298250000 662840 677820 537360 553520 670070 749800 639870 74630 757100 628840 FALSE TRUE 636935.48 658489.2373 634472.9055 582087.2335 691623.4101 764961.4697 647700.9205 73088.86442 671157.182 586248.1067 1.086460617 1.123226207 1.08226005 0.992902539 1.179745234 1.304842542 1.104823901 0.12467224 1.144834711 1 19.16115183 1.948952443 24.99798794 0.648119398 1.129004958 0.263167494 0.264686378 326.2503016 159764.1703 0.103903445 0.06705878 88.91037516 -1.948952443 0.48088556 DVVHLDSEKDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVVHLDSEKDFR 12 1 Q14554;Q14554-2 Q14554 PDIA5 Protein disulfide-isomerase A5 0 ; 121.04 0.00023031 564170000 880630 1006620 762820 900150 855520 913740 905130 873960 1082630 950330 FALSE TRUE 846214.006 977912.1832 900678.5428 946606.8494 883038.5778 932216.4489 916207.2517 855912.4206 959734.3812 885963.3026 0.955134376 1.103784074 1.016609311 1.068449276 0.996698819 1.052206616 1.034136797 0.966081121 1.083266517 1 19.75688742 1.948962071 24.99863665 1.00953757 1.035438929 0.015003085 0.046649175 1041.689094 510222.5793 0.017764376 0.011466475 88.91234625 -1.948962071 0.025901358 SDPMVQCIIEESGEHIIAGAGELHLEICLK ddPTM_BT-474_Pertuzumab_2h_R1 9 SDPMVQCIIEESGEHIIAGAGELHLEICLK 30 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;; 299.95 2.00E-81 1873273700 1077061.7 1108190.1 880110.9 971735.1 1171487.8 1259548.4 1089670.6 626750.8 1314118.9 1198100.3 FALSE TRUE 1034968.938 1076585.603 1039166.518 1021886.465 1209169.769 1285017.332 1103006.315 613808.177 1164945.632 1116951.9 0.926601171 0.963860309 0.930359238 0.914888515 1.082562078 1.150467923 0.987514606 0.549538594 1.042968486 1 20.09113563 1.949012206 24.99971757 0.802719857 0.997328222 0.102837417 0.14451981 459.0328107 225066.5803 0.058989335 0.038070048 88.92261095 -1.949012206 0.194608366 AES(ph)PESSAIESTQSTPQK ddPTM_BT-474_Pertuzumab_2h_R1 4 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(0.709)PES(0.253)S(0.037)AIESTQSTPQK;AES(0.998)PES(0.001)SAIESTQSTPQK;AES(0.981)PES(0.009)S(0.009)AIESTQSTPQK;AES(0.997)PES(0.003)SAIESTQSTPQK 498.44 1.05E-266 6069820000 2302965 2280627 1758888 2032529 2255768 2164711 2252155 2463790 2888790 2383477 TRUE FALSE 2212962.582 2215585.751 2076758.188 2137428.065 2328326.826 2208482.94 2279717.547 2412911.876 2560866.67 2222041.98 0.995913939 0.997094461 0.93461699 0.96192065 1.047832061 0.993897937 1.02595611 1.08589842 1.152483478 1 21.08345464 1.949043107 2.173034155 1.089823958 0.986921044 0.455484349 0.043998579 0.257803457 2.243081034 0.025169291 0.012808939 88.92893815 -1.949043107 -0.102902915 ERPGFPPR ddPTM_BT-474_Pertuzumab_2h_R1 8 ERPGFPPR 8 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;;;;;;; 110.87 0.0030483 693242000 636632 751032 646749 728486 749875 731418 672216 655120 649063 737217 FALSE TRUE 611751.7176 729613.3027 763630.9312 766083.2498 773995.4104 746207.7731 680442.7805 641591.5431 575384.0893 687284.6359 0.89009951 1.061588263 1.111083954 1.114652081 1.126164285 1.085733238 0.990045092 0.933516493 0.837184566 1 19.39054818 1.949172028 2.486670202 0.914447773 1.071571855 0.425929447 0.073224281 0.263315341 2.987605272 0.040607874 0.021491119 88.95534092 -1.949172028 0.157124081 SKS(ph)PS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 S(0.413)KS(0.587)PS(1)PPR;S(0.417)KS(0.583)PS(1)PPR 68.551 0.031986 2765300000 821910 728930 655890 682150 662910 695880 745680 828890 904300 817130 TRUE FALSE 789788.8485 708141.6301 774423.9132 717355.8432 684233.1022 709951.1704 754805.8549 811773.1318 801647.6551 761785.0573 1.036760752 0.929581938 1.016591105 0.941677493 0.898197064 0.931957333 0.990838357 1.065619658 1.052327881 1 19.53902446 1.949242825 4.656480415 1.044027689 0.956945027 0.421348942 0.041835762 0.189060537 8.638069195 0.019003244 0.011465475 88.9698431 -1.949242825 -0.087082662 EELSSGDSLS(ph)PDPWKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EELSSGDSLSPDPWKR 16 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 EELSSGDS(0.001)LS(0.999)PDPWKR;EELSSGDSLS(1)PDPWKR 166.57 4.06E-09 597980000 501130 486830 448420 505440 477280 470280 502770 593360 594430 546060 TRUE FALSE 481545.2856 472946.0851 529459.469 531525.819 492632.1447 479789.3838 508923.0497 581106.9086 526952.7985 509074.8698 0.945922327 0.929030508 1.040042439 1.044101468 0.967700772 0.942473126 0.999701772 1.141495963 1.035118466 1 18.95751832 1.949265981 11.55704875 1.073655723 0.980453044 0.334671263 0.049554412 1.108858705 250.8658099 0.021112941 0.013526544 88.97458703 -1.949265981 -0.093202679 DLYEPSHGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLYEPSHGAK 10 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 165.11 5.95E-06 1568660000 1371840 1377570 1212670 1573460 1520240 1468640 1755240 4255040 2144480 2423190 FALSE TRUE 1318226.976 1338283.052 1431826.445 1654666.459 1569139.9 1498336.907 1776721.152 4167171.937 1901047.621 2259065.183 0.583527641 0.592405683 0.633813692 0.732456271 0.694597001 0.663255278 0.78648512 1.844644399 0.841519596 1 21.10729447 1.949348572 12.23919336 1.321112649 0.658437055 0.508671933 0.249919383 0.94796804 228.0664401 0.097807854 0.062748331 88.99150917 -1.949348572 -0.662675594 HFS(ph)QSEETGNEVFGALNEEQPLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HFSQSEETGNEVFGALNEEQPLPR 24 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 HFS(0.653)QS(0.211)EET(0.136)GNEVFGALNEEQPLPR;HFS(0.885)QS(0.041)EET(0.073)GNEVFGALNEEQPLPR;HFS(0.855)QS(0.111)EET(0.033)GNEVFGALNEEQPLPR;HFS(0.664)QS(0.328)EET(0.009)GNEVFGALNEEQPLPR 263.49 2.29E-44 1780730000 1065690 1212960 908080 1123790 1082090 1144090 1093510 409295 1194270 1101310 TRUE FALSE 1024041.657 1178367.568 1072190.256 1181788.937 1116896.408 1167224.284 1106892.702 400842.9152 1058701.476 1026717.293 0.997393989 1.147704024 1.044289663 1.151036361 1.087832469 1.13685071 1.078089081 0.390412159 1.031151889 1 19.96960756 1.949462238 24.57949413 0.738154302 1.097546876 0.345828461 0.171819181 235.2437314 114412.3544 0.066172767 0.042708594 89.01480355 -1.949462238 0.359392574 RHSS(ph)DINHLVTQGRES(ph)PEGSYTDDANQEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHSSDINHLVTQGRESPEGSYTDDANQEVR 30 2 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 2 RHS(0.372)S(0.628)DINHLVT(0.003)QGRES(0.997)PEGSYTDDANQEVR 170.6 8.89E-13 434340000 49466 57869 33772 46170 39024 50276 39947 14924 33669 42740 TRUE FALSE 47532.81403 56218.63278 39875.35165 48552.83923 40279.2424 51292.61517 40435.88334 14615.81418 29847.03627 39845.18173 1.192937564 1.41092675 1.000757179 1.218537277 1.01089368 1.28729781 1.014824919 0.366815097 0.74907517 1 15.28211766 1.949485265 6.932450809 0.645427799 1.179948949 0.570044924 0.184795669 0.14682251 16.70273079 0.074967435 0.046978167 89.01952343 -1.949485265 0.534521149 FHCPHCDTVIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 FHCPHCDTVIAR 12 0 A0A2R8Y595;A0A2R8YFL0;P49711-2;P49711 A0A2R8Y595 CTCF Transcriptional repressor CTCF 0 130.01 0.00012962 153260000 107170 89147 77631 110280 85154 83451 75622 5322.6 70858 61597 FALSE TRUE 102981.6779 86604.61484 91660.64859 115971.564 87893.05574 85138.4364 76547.48466 5212.68645 62814.4969 57424.98033 1.793325437 1.508134863 1.596180757 2.019531628 1.530571804 1.482602796 1.332999754 0.090773848 1.093853172 1 15.80939084 1.949559999 6.060541647 0.639409017 1.638944476 0.662043247 0.293815216 0.113307109 9.768902053 0.124474747 0.077234678 89.03484337 -1.949559999 0.999535459 ISHLPLVEELR ddPTM_BT-474_Pertuzumab_2h_R1 3 ISHLPLVEELR 11 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ;; 118.48 0.0009544 564730000 501840 532950 433830 476940 462240 483360 472830 429150 489540 519560 FALSE TRUE 482227.538 517750.7878 512232.7315 501554.9306 477108.3694 493133.8704 478616.635 420287.9025 433969.4715 484369.7384 0.995577345 1.068916463 1.057524223 1.035479492 0.985008624 1.018093888 0.988122496 0.867700579 0.895946706 1 18.88574921 1.949563086 4.338512021 0.90911233 1.027370405 0.57847651 0.039807132 0.134676094 5.185321435 0.018145207 0.010844003 89.03547613 -1.949563086 0.118258074 HRDTHPGS(ph)PGSPGPALRPLPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDT(0.002)HPGS(0.499)PGS(0.499)PGPALRPLPAR 78.991 0.0038413 137230000 96400 93100 95432 91819 77184 86008 90625 35141 95679 105510 TRUE FALSE 92632.58142 90444.87915 112678.6853 96557.78959 79666.69346 87747.14069 91734.09586 34415.32607 84817.92104 98363.71372 0.9417353 0.919494351 1.14553102 0.981640342 0.809919537 0.892068196 0.93260098 0.349878271 0.862288722 1 16.58583858 1.949645906 24.7999012 0.659174601 0.948017694 0.188305304 0.177842068 349.9766688 172366.3283 0.071227423 0.045971428 89.05245697 -1.949645906 0.288843093 S(ph)REDLTAVVSVSTK ddPTM_BT-474_Pertuzumab_2h_R1 4 SREDLTAVVSVSTK 14 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(0.701)REDLT(0.299)AVVSVSTK;S(0.975)REDLT(0.025)AVVSVSTK;S(0.915)REDLT(0.085)AVVSVSTK;S(1)REDLTAVVSVSTK 224.36 8.36E-12 3008640000 4557830 4089910 3420390 3489980 3449270 3254900 3931540 5161840 4827480 4343580 TRUE FALSE 4379704.965 3973269.771 4038530.559 3670098.286 3560218.902 3320716.308 3979655.363 5055246.2 4279484.709 4049385.458 1.08157275 0.981203151 0.997319371 0.906334634 0.879199804 0.820054387 0.98278008 1.248398369 1.056823252 1 21.94927155 1.949693484 10.58368504 1.126106584 0.940177161 0.374728469 0.089382989 0.689555996 143.1491965 0.038140198 0.024378621 89.06221347 -1.949693484 -0.185929423 ANT(ph)PELKK ddPTM_BT-474_Pertuzumab_2h_R1 6 ANTPELKK 8 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 ANT(1)PELKK;ANT(1)PELKK;ANT(1)PELKK;ANT(1)PELKK;ANT(1)PELKK;ANT(1)PELKK 97.214 0.0049168 7871720000 4372190 3435980 3001560 2386720 3285050 3240350 3595120 4359050 4607080 4191740 TRUE FALSE 4201319.981 3337989.215 3544008.661 2509898.905 3390716.617 3305872.097 3639118.154 4269034.094 4084103.593 3907829.716 1.075103136 0.854179802 0.906899461 0.642274379 0.867672561 0.845961144 0.931237648 1.092430941 1.04510787 1 21.89793617 1.949707509 3.720088337 1.051959769 0.857619707 0.389090659 0.100536814 0.228242411 6.103167297 0.048503564 0.028253575 89.06508965 -1.949707509 -0.194340061 VTDHLEALIDPFDLDVFTPHLNSNLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTDHLEALIDPFDLDVFTPHLNSNLHR 27 0 A0A087WVI0;E9PBL8;Q8WTW3;J3QKY9;J3QLT5 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 ; 106.45 0.00066914 143053000 92437 125964 89707 108133 109884 122676 108214 29971 116983 105683 FALSE TRUE 88824.45985 122371.6301 105919.0504 113713.7571 113418.5187 125156.5928 109538.3553 29352.08838 103703.5803 98524.99628 0.901542382 1.242036383 1.075047495 1.154161496 1.151164912 1.270302943 1.111782385 0.297915143 1.052561118 1 16.58820217 1.949880907 22.77158752 0.705323075 1.14113594 0.335003958 0.21501116 110.8247475 50352.544 0.083135642 0.053649694 89.10065722 -1.949880907 0.435812865 CLLADLPLPPELPGGDDLSKS(ph)PEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 CLLADLPLPPELPGGDDLSKSPEEK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0;Q9BVE2;A0A087X209 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 CLLADLPLPPELPGGDDLS(0.133)KS(0.867)PEEK 118.75 0.00040993 40691000 156500 117560 105650 90524 121480 114560 135880 177220 192030 155360 TRUE FALSE 150383.807 114207.3039 124743.3052 95195.95449 125387.5145 116876.4817 137542.9401 173560.3451 170231.5595 144837.3288 1.038294535 0.788521197 0.861264884 0.657261186 0.865712697 0.806949994 0.94963737 1.198312248 1.175329322 1 17.14407395 1.949994127 3.651198947 1.139999077 0.829818521 0.615267871 0.101432699 0.139848279 3.585084048 0.047176988 0.027391516 89.12388866 -1.949994127 -0.310180556 NKPQER ddPTM_BT-474_Pertuzumab_2h_R1 1 NKPQER 6 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-3;Q8IXQ4-2 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 0 72.823 0.077138 13926000 22529 20557 17938 18525 17922 26300 25035 56653 27565 36011 FALSE TRUE 21648.54177 19970.73449 21179.79563 19481.07747 18498.47741 26831.80402 25341.38582 55483.09575 24435.93676 33571.94289 0.644840301 0.594863829 0.630877864 0.580278524 0.551010034 0.799232982 0.754838226 1.652662639 0.727867816 1 15.03496841 1.950007985 11.57689904 1.200782967 0.638034218 0.482058777 0.225169927 0.785336076 180.6533283 0.089192816 0.057155119 89.12673246 -1.950007985 -0.562748749 FAEVEHVVNAILFLLSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FAEVEHVVNAILFLLSDR 18 0 Q7Z4W1 Q7Z4W1 DCXR L-xylulose reductase 0 ; 146.64 8.24E-08 1186770000 161237 177817 148350 188741 205228 168789 178347 146965 198758 193200 FALSE TRUE 154935.6798 172745.8333 175160.145 198481.9456 211829.345 172202.0292 180529.6639 143930.1214 176195.8251 180114.3919 0.860207106 0.959089562 0.972493887 1.101977158 1.176082282 0.956070347 1.002305602 0.799103946 0.978244011 1 17.45855394 1.950015433 21.97113961 0.902771464 1.010240909 0.108074008 0.095551681 157.3771259 69175.11323 0.041294222 0.026645357 89.12826109 -1.950015433 0.107469446 HDLINQLQHNHALVTLVAENLATYMESMR ddPTM_BT-474_Pertuzumab_2h_R1 2 HDLINQLQHNHALVTLVAENLATYMESMR 29 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 218.76 7.91E-35 431660000 141877 151638 136311 151278 132099 166384 130444 17125.1 161133 75578 FALSE TRUE 136332.29 147313.4327 160945.4299 159085.4757 136348.0843 169748.3985 132040.4127 16771.4607 142841.8574 70459.03474 1.934915664 2.090767114 2.284241198 2.25784353 1.935139827 2.409178597 1.874002577 0.238031372 2.027303637 1 16.10449709 1.95011113 9.912136288 1.015226866 2.149588529 0.552800461 0.426775591 0.382546655 74.39214648 0.166029094 0.105913043 89.14790252 -1.95011113 1.134361663 KTS(ph)TSPPPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.053)S(0.374)T(0.374)S(0.199)PPPEK 109.24 0.0021667 112100000 219960 202100 219290 215460 191540 206470 263230 289490 339570 331340 TRUE FALSE 211363.72 196336.3059 258920.5811 226579.9164 197701.0581 210644.9649 266451.4875 283511.9303 301023.4372 308898.0467 0.68425075 0.63560229 0.838207246 0.733510357 0.640020422 0.681923914 0.862587156 0.917817168 0.974507416 1 18.23677122 1.950185722 1.943147952 0.969968804 0.703557735 0.807401558 0.057888294 0.151516406 1.059752908 0.037135163 0.018295823 89.16321547 -1.950185722 -0.26641107 WDHSLAWDVPAAEDFPNGS(ph)GSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR 48 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WDHSLAWDVPAAEDFPNGS(0.468)GS(0.468)PS(0.063)AAIYNIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.331)GS(0.331)PS(0.331)AAIY(0.005)NIDT(0.001)SSESPDHYLVDHTLDGR 116.89 1.27E-08 899524000 28323 43248 36348 46083 43846 36723 39775 8283 47484 40747 TRUE FALSE 27216.10585 42014.60938 42916.89216 48461.34915 45256.34641 37465.56422 40261.77835 8111.953155 42093.81539 37987.1694 0.716455221 1.106021061 1.129773364 1.275729409 1.191358744 0.986268912 1.059878348 0.213544554 1.108106133 1 15.21322459 1.950196849 24.96315967 0.674052295 1.081910716 0.174862682 0.264921459 403.5132373 202254.8421 0.105644946 0.068187085 89.16549992 -1.950196849 0.407858421 IPTNDELLYDPEKDNR ddPTM_BT-474_Pertuzumab_2h_R1 4 IPTNDELLYDPEKDNR 16 1 G3V2W9;A0A087X060;Q56P03 G3V2W9 EAPP E2F-associated phosphoprotein 0 ;;; 137.45 1.09E-05 1266940000 695020 630760 630840 715240 673430 682260 751910 890950 981970 878210 FALSE TRUE 667857.85 612771.3424 744846.821 752153.6221 695091.4875 696055.7647 761112.0995 872551.5712 870500.8824 818728.0545 0.815726109 0.748443075 0.90976096 0.918685537 0.848989458 0.850167233 0.929627482 1.065740408 1.063235683 1 19.64302481 1.950263148 2.842867255 1.048890963 0.85018125 0.765203232 0.048050417 0.133390821 1.986034533 0.026893923 0.014766722 89.17911289 -1.950263148 -0.198709713 HHLGAATPENPEIELLR ddPTM_BT-474_Pertuzumab_2h_R1 3 HHLGAATPENPEIELLR 17 0 A0A087WV05;Q99417 A0A087WV05 MYCBP C-Myc-binding protein 0 ;; 127.75 2.27E-05 411179000 358590 405710 335573 380610 325104 370492 311090 94111 333104 219139 FALSE TRUE 344575.9064 394139.548 396218.5059 400253.3277 335561.2654 377983.6021 314897.2125 92167.57496 295291.4304 204296.5203 1.686645988 1.92925238 1.939428558 1.95917839 1.642520709 1.850171513 1.541373353 0.451146083 1.445406069 1 17.64030511 1.950339834 6.24748392 0.919626819 1.830401811 0.715345826 0.244548964 0.102533941 9.562381637 0.100665886 0.062657462 89.19486113 -1.950339834 0.910774992 DLGDEYGWK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGDEYGWK 9 0 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ; 149.94 0.00020109 528070000 543170 666530 671450 833120 600720 666860 828620 1056950 1141280 1084200 FALSE TRUE 521942.3159 647521.217 792795.9513 876117.423 620042.7044 680344.3661 838760.8994 1035123.613 1011726.679 1010766.168 0.516382851 0.64062415 0.784351491 0.866785465 0.613438324 0.673097683 0.829826844 1.024098002 1.00095028 1 19.94701785 1.950387523 2.800305081 1.010112496 0.690763479 0.725023741 0.08971222 0.155559205 2.245368394 0.050203804 0.027462628 89.20465612 -1.950387523 -0.319349017 ATDSSDPLKPYQDFIIDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ATDSSDPLKPYQDFIIDSR 19 1 Q96Q11-2;Q96Q11 Q96Q11-2 TRNT1 "CCA tRNA nucleotidyltransferase 1, mitochondrial" 0 ;; 168.27 1.49E-11 502900000 1139680 1123740 940600 1098450 1054140 1120380 1132550 1294380 1330700 1275250 FALSE TRUE 1095140.046 1091692.035 1110587.344 1155141.136 1088047.37 1143034.851 1146410.486 1267650.601 1179644.515 1188876.182 0.921155678 0.918255452 0.934148872 0.971624425 0.915189813 0.96144146 0.964280809 1.066259565 0.992234964 1 20.18116704 1.950413178 4.696028425 1.025457481 0.938071174 0.678426698 0.025242519 0.111084796 5.224626252 0.011237188 0.006795868 89.20992569 -1.950413178 -0.087386307 LHLGIPEAVFVEDVDSFMK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHLGIPEAVFVEDVDSFMK 19 0 P61758 P61758 VBP1 Prefoldin subunit 3 0 ; 235.16 3.73E-24 529270000 348390 357120 316160 359980 347880 373440 355120 189576 435260 427890 FALSE TRUE 334774.5336 346935.2873 373297.1449 378558.6109 359069.8761 380991.2127 359466.0648 185661.1894 385851.1096 398908.6292 0.839226101 0.869711162 0.935796114 0.948985766 0.900130631 0.955083908 0.901123813 0.465422846 0.967266891 1 18.60569881 1.95044515 24.99992106 0.734442611 0.910735059 0.009158455 0.144245085 514.783252 259702.0458 0.056769683 0.036640503 89.21649357 -1.95044515 0.176292448 AMLDSGIYPPGS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 7 AMLDSGIYPPGSPGK 15 0 O95295 O95295 SNAPIN SNARE-associated protein Snapin 1 AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK 289.98 7.28E-44 2162852000 4800380 4467800 3905120 3971700 4395200 4517790 4627490 5430330 5616800 5760050 TRUE FALSE 4612775.842 4340382.718 4610862.053 4176679.913 4536575.6 4609142.809 4684122.607 5318191.788 4979204.412 5369916.683 0.859003242 0.808277479 0.858646852 0.777792312 0.844813033 0.858326689 0.872289624 0.990367654 0.927240534 1 22.35646827 1.950522964 2.026395191 0.97381111 0.83020226 0.799191127 0.030743014 0.129459625 0.98285719 0.017297932 0.008632277 89.23248023 -1.950522964 -0.14360885 QESCSPHHPQVLAQQGSGSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 QESCSPHHPQVLAQQGSGSSPK 22 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 QESCSPHHPQVLAQQGSGS(0.001)S(0.999)PK;QESCSPHHPQVLAQQGSGS(0.003)S(0.997)PK 198.09 3.22E-22 876860000 256340 327770 260130 309350 255220 285030 284640 86553 321530 303740 TRUE FALSE 246321.9494 318422.3205 307141.2776 325315.5906 263429.3831 290793.5019 288123.5095 84765.6503 285031.2624 283167.4193 0.86988097 1.124501969 1.084663195 1.148845412 0.930295525 1.026931356 1.017502332 0.299348175 1.006582124 1 18.11129576 1.950595582 24.99073483 0.682700983 1.037004144 0.224638575 0.203565985 359.2062016 181700.2562 0.079470271 0.051292091 89.24740194 -1.950595582 0.354303161 HTDEEFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HTDEEFLK 8 0 Q9H0C8;E9PC05;F8SNU7;H7C2I8 Q9H0C8 ILKAP;ILKAP3 Integrin-linked kinase-associated serine/threonine phosphatase 2C 0 105.57 0.0075337 0 130770 129620 113780 115750 121110 134470 126330 98172 157560 153800 FALSE TRUE 125659.3638 125923.3645 134342.577 121723.8714 125005.6131 137189.0755 127876.0643 96144.71389 139674.4493 143382.989 0.876389624 0.878230851 0.936949201 0.848942209 0.871830152 0.956801616 0.89184962 0.670544774 0.974135428 1 17.12951435 1.950596738 24.99979747 0.829014775 0.895501784 0 0.091801934 883.2449786 446951.3043 0.036542118 0.023587712 89.24763934 -1.950596738 0.06648701 HQWAHAEEKPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HQWAHAEEKPHR 12 1 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 0 103.85 0.0014201 66016000 27795 28728 23662 25551 24901 25387 22121 5682 21876 18481 FALSE TRUE 26708.74067 27908.70557 27938.24976 26869.69017 25701.96328 25900.34253 22391.72342 5564.664714 19392.72819 17229.26541 1.550196136 1.619843035 1.621557803 1.559537771 1.491761992 1.503276078 1.299633088 0.322977479 1.125569067 1 14.07257357 1.950709404 6.26262385 0.751991542 1.549164495 0.729987649 0.20043466 0.096631595 9.110491888 0.083011696 0.051695697 89.27079534 -1.950709404 0.797172953 SEPVKEESSELEQPFAQDTSSVGPDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SEPVKEESSELEQPFAQDTSSVGPDR 26 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;; 256.01 1.17E-52 1265260000 1043940 970820 874270 909860 983260 932940 1032270 1185930 1253330 1206860 FALSE TRUE 1003141.671 943133.1641 1032270.037 956817.9836 1014887.451 951804.686 1044903.229 1161440.131 1111057.233 1125118.297 0.891587732 0.838252445 0.917476891 0.850415451 0.902027328 0.845959655 0.928705214 1.03228268 0.98750259 1 20.10164527 1.95080401 4.040572904 1.006893119 0.875102533 0.836681004 0.026121678 0.075120338 2.449013681 0.011084095 0.006559325 89.29024403 -1.95080401 -0.131790587 KDPFS(ph)PDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDPFSPDKK 9 2 H0YHD0;Q5PSV4-2;Q5PSV4 H0YHD0 BRMS1L Breast cancer metastasis-suppressor 1-like protein 1 KDPFS(1)PDKK;KDPFS(1)PDKK 80.469 0.018921 634280000 1492050 1045700 1033010 809610 1067020 912880 1212750 1471920 1602280 1447450 TRUE FALSE 1433739.036 1015877.66 1219697.886 851394.0691 1101341.667 931339.0591 1227591.997 1441524.338 1420395.892 1349412.922 1.062490964 0.752829355 0.903872985 0.63093665 0.816163569 0.690180925 0.909723019 1.068260363 1.052602853 1 20.36390045 1.950882361 4.248455386 1.040532085 0.80255152 0.45747449 0.11217629 0.184789641 6.80528134 0.049898517 0.029769068 89.30635443 -1.950882361 -0.237980565 LHTDDELNWLDHGR ddPTM_BT-474_Pertuzumab_2h_R1 6 LHTDDELNWLDHGR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;;; 278.82 1.97E-33 1996697000 671599 712361 649699 766882 722357 735690 712294 167960.7 777194 722159 FALSE TRUE 645352.1686 692045.1618 767114.0618 806460.8719 745592.2689 750566.1559 721011.267 164492.2529 688970.1954 673246.5277 0.958567393 1.027922363 1.139425203 1.197868595 1.107458024 1.114845937 1.070946878 0.244326923 1.023354993 1 19.36077536 1.951104815 24.77226401 0.668356583 1.095697152 0.316207162 0.212618558 288.2254201 146025.9971 0.083284168 0.05375293 89.35211057 -1.951104815 0.427340569 HVVRPPPRS(ph)PEPDTLPLAAGSDHPLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVVRPPPRSPEPDTLPLAAGSDHPLPR 27 2 H3BVB1;H3BME1;H7C112;H3BPZ0;Q6PCT2-2;Q6PCT2-3;Q6PCT2 H3BVB1 FBXL19 F-box/LRR-repeat protein 19 1 HVVRPPPRS(1)PEPDTLPLAAGSDHPLPR;HVVRPPPRS(1)PEPDTLPLAAGSDHPLPR 153.63 2.65E-08 1239470000 120882 161483 116583 139974 118329 152875 124638 67496 119877 130886 TRUE FALSE 116157.7978 156877.6629 137652.1415 147198.0749 122135.1597 155966.2372 126163.3571 66102.18401 106269.0655 122020.9746 0.951949434 1.285661448 1.128102295 1.206334201 1.000935783 1.27819203 1.033948118 0.541728045 0.870908185 1 16.89676963 1.951107941 8.106534165 0.760546971 1.145369614 0.505883795 0.147323174 0.210628598 32.18311981 0.057578307 0.036444393 89.35275373 -1.951107941 0.384822643 DNHLLGTFDLTGIPPAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNHLLGTFDLTGIPPAPR 18 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 141.07 1.23E-07 737610000 558810 650090 494890 693210 585230 670620 557440 93669 597010 498120 FALSE TRUE 536971.0874 631550.0697 584327.6318 728986.6512 604054.4544 684180.3959 564262.1175 91734.70242 529239.9277 464381.8887 1.156313587 1.359979976 1.258291174 1.569799919 1.300770915 1.473314125 1.215082093 0.197541516 1.139665307 1 18.82495218 1.951114233 11.65444849 0.693627074 1.355551124 0.495633612 0.255120302 0.773838484 183.3423728 0.09962375 0.063865714 89.35404819 -1.951114233 0.66192405 NDSDPTYGQQGHPNTWK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDSDPTYGQQGHPNTWK 17 0 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 ; 219.68 4.25E-15 1399790000 1715690 1576460 1365450 1439660 1467240 1567440 1638950 1743570 2006190 1860890 FALSE TRUE 1648638.938 1531500.904 1612217.189 1513961.025 1514435.107 1599134.711 1659007.96 1707564.67 1778455.722 1734850.263 0.950306187 0.882785643 0.929312013 0.87267533 0.872948599 0.921771028 0.956283084 0.984272076 1.025134999 1 20.72637972 1.951143514 1.566374251 1.009487714 0.90060655 0.771317704 0.024349077 0.174709847 0.798111159 0.016326292 0.007588164 89.3600728 -1.951143514 -0.108881165 RS(ph)SLSSHSHQSQIYR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSLSSHSHQSQIYR 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 RS(0.499)S(0.499)LS(0.002)SHSHQSQIYR 211.4 6.58E-10 327740000 27672 76989 39486 50373 42873 48268 38947 4764.5 28932 35704 TRUE FALSE 26590.54765 74793.3491 46621.99856 52972.75657 44252.04898 49244.01203 39423.64504 4666.11141 25647.76065 33285.73628 0.798857127 2.247009003 1.400659976 1.591455154 1.329459821 1.47943286 1.18440057 0.140183512 0.770533073 1 15.02261646 1.951264853 5.385349238 0.559292428 1.494164006 0.477073394 0.388953903 0.148220482 9.876397984 0.160833729 0.098891098 89.38504302 -1.951264853 0.934871577 LEHEISHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEHEISHLK 9 0 P12270 P12270 TPR Nucleoprotein TPR 0 136.57 0.00010937 97920000 143060 130140 130950 147080 153900 141110 140850 16402 164780 134610 FALSE TRUE 137469.057 126428.5346 154615.578 154670.8164 158850.3333 143963.3409 142573.7644 16063.29297 146074.8652 125492.7448 1.0954343 1.007456924 1.232067863 1.232508036 1.265812884 1.147184573 1.136111611 0.128001766 1.164010441 1 16.93724443 1.951268975 24.97085231 0.658350338 1.165105839 0.296068145 0.265119519 333.6843867 170986.6245 0.103940809 0.067082848 89.38589132 -1.951268975 0.506755501 DKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKDDQEWESPSPPKPTVFISGVIAR 25 2 P51397 P51397 DAP Death-associated protein 1 1 DKDDQEWES(0.098)PS(0.902)PPKPTVFISGVIAR;DKDDQEWES(0.026)PS(0.973)PPKPT(0.001)VFISGVIAR;DKDDQEWES(0.066)PS(0.934)PPKPTVFISGVIAR 202.61 2.93E-25 6478010000 4852190 3857930 3375980 2810890 3805400 3824410 4289310 5315020 6042450 5046890 TRUE FALSE 4662561.05 3747905.614 3986094.684 2955960.37 3927804.147 3901742.191 4341803.859 5205262.98 5356536.408 4705059.645 0.99096747 0.796569203 0.847193231 0.628251413 0.834804326 0.829265192 0.922794648 1.106311795 1.138463019 1 22.16578158 1.95127737 2.517162143 1.093620133 0.812374942 0.627747655 0.089236098 0.175096952 2.037352626 0.048407574 0.025754546 89.38761911 -1.95127737 -0.281245191 DSDAGSS(ph)TPTTSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSDAGSSTPTTSTR 14 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 DSDAGS(0.31)S(0.527)T(0.163)PTTSTR 170.98 3.24E-06 43274000 113880 118990 98538 110490 111230 115620 116920 132640 139930 127290 TRUE FALSE 109429.4437 115596.5217 116346.0086 116192.4021 114807.814 117957.9156 118350.9019 129900.9376 124045.733 118668.5349 0.922143715 0.974112656 0.980428457 0.979134041 0.967466347 0.994011729 0.99732336 1.094653589 1.045312754 1 16.85657793 1.951382779 4.668313341 1.055813291 0.972002179 0.593349823 0.028129315 0.127466229 5.946874788 0.012373554 0.007485303 89.40931742 -1.951382779 -0.083811111 EVAWVIFDEIHYMR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVAWVIFDEIHYMR 14 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 189.3 7.34E-07 209570000 201175 196114 171140 195054 226640 211409 196491 168662 209382 213115 FALSE TRUE 193312.8586 190521.0207 202068.805 205120.7603 233930.0814 215683.8348 198895.7156 165179.0708 185613.8332 198680.5312 0.972983399 0.958931505 1.017053879 1.032414998 1.17741824 1.085581126 1.001083067 0.831380255 0.93423262 1 17.60009098 1.95146289 7.707423826 0.905815482 1.041951175 0.364739738 0.06916582 0.289969569 41.240194 0.031527748 0.019909148 89.4258116 -1.95146289 0.136135694 HSLPQEPVMPMDQSSMHSDHAQTVIPY(ph)NPSSHES(ph)LDQVGEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSLPQEPVMPMDQSSMHSDHAQTVIPYNPSSHESLDQVGEEK 42 0 P41743 P41743 PRKCI Protein kinase C iota type 2 HSLPQEPVMPMDQS(0.002)S(0.002)MHS(0.002)DHAQT(0.004)VIPY(0.451)NPS(0.393)S(0.411)HES(0.736)LDQVGEEK 66.261 0.0011147 77608000 43704 53874 40048 41843 41881 50881 42665 18990 46807 39412 TRUE FALSE 41995.99936 52337.56627 47285.56446 44002.52224 43228.1404 51909.84868 43187.14703 18597.84986 41493.66559 36742.59014 1.14297874 1.424438671 1.286941511 1.197589013 1.176513148 1.41279775 1.175397458 0.506166 1.129307037 1 15.16516571 1.951516529 11.23311071 0.827589875 1.274904061 0.505548763 0.172816722 0.660513078 151.7781148 0.067820475 0.043443482 89.43685696 -1.951516529 0.447314186 CDVTDNQSEVADKTEDYLWLK ddPTM_BT-474_Pertuzumab_2h_R1 1 CDVTDNQSEVADKTEDYLWLK 21 1 H3BVG0;Q8N1F7;Q8N1F7-2;H3BPA9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 173.77 3.53E-12 111290000 190940 160210 144640 130320 141970 154250 164870 192420 204850 188390 FALSE TRUE 183477.8537 155640.9677 170779.6655 137045.8308 146536.594 157369.0407 166887.7284 188446.4598 181596.2868 175630.1775 1.04468296 0.88618579 0.972382241 0.780309129 0.834347468 0.896025062 0.950222398 1.072973121 1.033969728 1 17.42218123 1.95152609 3.713006812 1.040681015 0.896985061 0.4221571 0.069342113 0.215206234 5.758875613 0.033790986 0.019714123 89.43882608 -1.95152609 -0.143695954 QDVEALWENMAVIDCFASDHAPHTLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QDVEALWENMAVIDCFASDHAPHTLEEK 28 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 306.76 1.24E-72 78271000 111573 131487 114385 130099 123333 147466 127478 13593.6 178188 157451 FALSE TRUE 107212.6038 127737.1195 135056.914 136813.425 127300.118 150447.8636 129038.1139 13312.88741 157960.8453 146786.7035 0.730397245 0.870222687 0.920089564 0.932055981 0.867245567 1.024942041 0.879085849 0.090695459 1.076125027 1 17.16336176 1.951545134 24.99927128 0.58715233 0.897021533 0.00508251 0.265235474 561.6879039 289790.0923 0.10453506 0.06746357 89.44274795 -1.951545134 0.309869203 TPLDLFAHFGPEPGDHSDPLPPSAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 7 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 TPLDLFAHFGPEPGDHSDPLPPS(0.011)APS(0.985)PT(0.003)R;TPLDLFAHFGPEPGDHSDPLPPS(0.118)APS(0.856)PT(0.025)R;TPLDLFAHFGPEPGDHSDPLPPS(0.118)APS(0.678)PT(0.204)R;TPLDLFAHFGPEPGDHSDPLPPS(0.044)APS(0.918)PT(0.038)R;TPLDLFAHFGPEPGDHSDPLPPS(0.401)APS(0.597)PT(0.002)R;TPLDLFAHFGPEPGDHSDPLPPS(0.031)APS(0.964)PT(0.005)R;TPLDLFAHFGPEPGDHSDPLPPSAPS(0.964)PT(0.035)R 229.5 9.13E-35 2995036000 872604 838214 807551 961829 916179 912626 877365 354171 967367 856324 TRUE FALSE 838501.671 814308.9574 953493.4296 1011469.11 945648.7296 931079.923 888102.4553 346857.2451 857555.5537 798324.4127 1.050326982 1.020022618 1.194368372 1.266990078 1.184541916 1.166292685 1.112458095 0.434481571 1.074194325 1 19.6066156 1.951569193 19.8105388 0.773406125 1.149679344 0.381820312 0.173384041 30.30072288 12393.77688 0.069110442 0.044582182 89.44770315 -1.951569193 0.376273219 SSS(ph)FPYTTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSFPYTTK 9 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 SS(0.016)S(0.984)FPYTTK;SS(0.004)S(0.995)FPYTTK 123.51 0.00058281 347820000 727260 674920 426820 590330 771820 601730 687220 899740 842990 785510 TRUE FALSE 698837.8752 655671.9424 503955.8686 620797.002 796646.2912 613897.3929 695630.4039 881160.0546 747297.3093 732306.708 0.9542967 0.895351545 0.688175956 0.847728138 1.087858793 0.83830639 0.949916744 1.203266398 1.020470386 1 19.48208849 1.95158463 7.122302615 1.093215332 0.884940394 0.381446853 0.106997719 0.243358899 30.23682735 0.046946708 0.029516474 89.45088255 -1.95158463 -0.208274939 SYEALVQHVIEDHER ddPTM_BT-474_Pertuzumab_2h_R1 6 SYEALVQHVIEDHER 15 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ;;;;; 292.8 3.37E-44 1969318000 1003470 1114893 890099 1158900 1141619 1194980 1086876 336120 1164043 1123436 FALSE TRUE 964253.283 1083097.343 1050959.689 1218710.968 1178340.212 1219143.314 1100177.514 329179.0045 1031905.719 1047344.679 0.920664708 1.034136483 1.003451596 1.163619764 1.125073947 1.164032566 1.050444553 0.314298636 0.98525895 1 19.99830488 1.95162716 24.56956278 0.688340153 1.073904049 0.312503658 0.193395297 271.9107796 138108.4908 0.076184773 0.049168556 89.45964287 -1.95162716 0.385563896 (ac)MLSLQYPDVYRDETAVQDYHGHK ddPTM_BT-474_Pertuzumab_2h_R1 1 MLSLQYPDVYRDETAVQDYHGHK 23 1 P48147 P48147 PREP Prolyl endopeptidase 0 83.905 0.00040834 104770000 132930 142090 101620 102860 131790 138560 111170 16458 120960 92267 FALSE TRUE 127734.9486 138037.7323 119984.9945 108168.6169 136029.145 141361.7781 112530.5317 16118.13655 107229.1279 86017.67391 1.48498492 1.604760116 1.394887691 1.257516183 1.581409248 1.643403869 1.308225701 0.187381684 1.246594136 1 16.3923455 1.951654464 10.58854184 0.726988375 1.487183748 0.551052816 0.272779627 0.482688274 104.3554274 0.1083676 0.069309818 89.46526728 -1.951654464 0.760195372 PVTVEPMDQLDDEEGLPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 PVTVEPMDQLDDEEGLPEK 19 0 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 156.73 1.30E-08 33885000 129060 97593 121060 125430 132950 114640 155910 188400 209510 209770 FALSE TRUE 124016.1925 94809.74319 142938.235 131903.4573 137226.4575 116958.0993 157818.0732 184509.4742 185727.3031 195562.0911 0.634152518 0.484806348 0.730909729 0.674483775 0.701702752 0.598061203 0.806997268 0.943482825 0.949710152 1 17.57726721 1.951667027 2.209776045 0.967723226 0.637980232 0.833800243 0.065513278 0.122958025 1.106003708 0.038557483 0.019764957 89.46785532 -1.951667027 -0.329742995 ESEDKPEIEDVGS(ph)DEEEEKK ddPTM_BT-474_Pertuzumab_2h_R1 8 ESEDKPEIEDVGSDEEEEKK 20 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK 285.95 1.93E-45 57066390000 7625220 4361950 6381970 4387351 5854800 4703223 7772030 10634580 12510330 9657230 TRUE FALSE 7327217.972 4237551.457 7535333.945 4613782.711 6043124.959 4798325.391 7867146.428 10414972.21 11090209.79 9003137.21 0.813851639 0.470674983 0.836967578 0.512463889 0.671224354 0.532961487 0.873822785 1.156815892 1.231816147 1 23.10199638 1.951676318 3.139296492 1.141276633 0.63737895 0.751325654 0.126037337 0.110200908 2.02575889 0.057809546 0.032560085 89.46976937 -1.951676318 -0.503897683 SNLTLYLDES(ph)KT(ph)LYDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNLTLYLDESKTLYDK 16 1 A0A0G2JPZ2;Q7RTR8 A0A0G2JPZ2 TAS2R42 Taste receptor type 2 member 42 2 S(0.187)NLT(0.187)LY(0.163)LDES(0.731)KT(0.731)LYDK 92.935 0.010547 23652000 7031.7 10749 10360 19684 14107 14408 17513 160630 13575 34653 TRUE FALSE 6756.89339 10442.44904 12232.28246 20699.8936 14560.76447 14699.33963 17727.32933 157312.9344 12034.02291 32305.92144 0.209153402 0.323236378 0.378639021 0.640746113 0.450715034 0.4550045 0.548733128 4.869476781 0.372502079 1 14.979511 1.951734196 24.99808226 2.560228781 0.423730597 0.285188727 1.125169585 341.9678312 177113.2075 0.436032877 0.281426074 89.48169376 -1.951734196 -2.136498184 NHDDWSHDYDNRR ddPTM_BT-474_Pertuzumab_2h_R1 2 NHDDWSHDYDNRR 13 1 J3KPD3;Q9Y580;G3V1T9 J3KPD3 RBM7 RNA-binding protein 7 0 ; 169.04 1.19E-05 583410000 357610 369280 309890 346080 336980 378760 289490 8378 326920 166746 FALSE TRUE 343634.2058 358748.496 365894.0165 363941.2303 347819.2677 386418.7867 293032.8652 8204.991372 289809.4122 155452.1449 2.210546571 2.3077745 2.353740546 2.34117857 2.237468437 2.485773271 1.885035844 0.052781461 1.864299861 1 17.246111 1.951908379 7.605739955 0.88645069 2.310239839 0.678922798 0.413960438 0.139352002 19.55929849 0.163260213 0.103055099 89.5175894 -1.951908379 1.423789149 SCDEPLTPPPHSPTSMLQLIHDPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 SCDEPLT(0.004)PPPHS(0.022)PT(0.272)S(0.082)MLQLIHDPVS(0.62)PR;SCDEPLT(0.002)PPPHS(0.178)PT(0.178)S(0.178)MLQLIHDPVS(0.466)PR 105.66 0.0033868 412950000 124490 142783 101917 133348 121900 131307 127366 91820 135068 145753 TRUE FALSE 119624.7932 138710.9686 120335.669 140230.1063 125821.0242 133962.1175 128924.7432 89923.88491 119735.6469 135881.0195 0.88036426 1.02082667 0.885595865 1.03200658 0.925964676 0.985878072 0.948806122 0.661784002 0.881180075 1 17.05198442 1.951922046 24.63456309 0.808879988 0.957957791 0.183610329 0.092675356 339.3141955 173859.7528 0.035329025 0.02280212 89.52040658 -1.951922046 0.149077803 LS(ph)ESPASLPSCPPVETALINQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSESPASLPSCPPVETALINQR 22 0 Q2TAZ0 Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 LS(0.779)ES(0.182)PAS(0.039)LPSCPPVETALINQR 97.94 0.00079595 114040000 40585 39265 35749 42376 37671 43445 40591 34466 38734 57674 TRUE FALSE 38998.89333 38145.20064 42209.63953 44563.03044 38882.72193 44323.48767 41087.7648 33754.26506 34337.07871 53767.68861 0.72532211 0.70944468 0.785037271 0.828806884 0.723161492 0.82435174 0.764172049 0.62777973 0.638619208 1 15.71445183 1.951932787 24.90060964 0.70957533 0.767639539 0 0.105113216 1130.640939 585712.4085 0.04067469 0.026255584 89.52262073 -1.951932787 0.058064208 DCQIDQHHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCQIDQHHR 9 0 P10588 P10588 NR2F6 Nuclear receptor subfamily 2 group F member 6 0 ; 85.533 0.00853 106765000 119801 132352 108273 129438 128832 131167 125187 40889 136450 126104 FALSE TRUE 115119.0445 128577.4505 127840.3396 136118.3107 132975.9983 133819.2866 126719.076 40044.62786 120960.768 117562.8638 0.979212659 1.093691038 1.087421108 1.157834254 1.13110547 1.138278554 1.077883542 0.340623106 1.028902871 1 16.84307288 1.951944069 24.49398744 0.714746381 1.102035182 0.344394252 0.18457327 249.0348277 126931.8787 0.071696395 0.046272047 89.52494619 -1.951944069 0.3872888 NDKSEEEQSS(ph)SSVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVKK 15 2 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKS(0.051)EEEQS(0.085)S(0.36)S(0.36)S(0.144)VKK 94.45 0.0035176 437590000 407570 304990 308780 216690 223400 299250 348020 422480 520830 387660 TRUE FALSE 391641.7138 296291.9838 364583.4148 227873.3969 230585.8639 305301.04 352279.1729 413755.6404 461707.5619 361403.4429 1.083669017 0.819837192 1.008798953 0.630523592 0.638028963 0.844765168 0.974753229 1.144858048 1.277540574 1 18.46325072 1.951968638 2.500480433 1.158157592 0.826471002 0.461936599 0.146062619 0.251940095 2.893617259 0.081965675 0.043554694 89.53001107 -1.951968638 -0.33168659 ATGEPGTFVCTSHLPAAASAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 ATGEPGTFVCTSHLPAAASASPK 23 0 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAAS(0.002)AS(0.998)PK;ATGEPGTFVCTSHLPAAASAS(1)PK 268.28 1.33E-44 4970470000 6210250 5151180 4457110 4535450 4659460 4634350 5292580 6537160 6598790 5776060 TRUE FALSE 5967546.564 5004273.39 5262608.925 4769525.118 4809335.763 4728059.732 5357352.177 6402165.362 5849723.024 5384842.311 1.108211944 0.929325893 0.977300471 0.885731623 0.893124716 0.878031233 0.994894905 1.188923462 1.086331351 1 22.36047267 1.952138915 6.975059791 1.108619294 0.940479278 0.421415591 0.075839741 0.198599278 23.95939733 0.032036882 0.020125561 89.56512058 -1.952138915 -0.168140015 HGYEKPTPIQTQAIPAIMSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGYEKPTPIQTQAIPAIMSGR 21 1 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 89.028 0.0014241 399100000 359180 357400 312520 338540 319870 370870 348880 314540 402010 365310 FALSE TRUE 345142.8485 347207.3019 368999.316 356012.09 330158.909 378369.2455 353149.6978 308044.6391 356375.5102 340567.2283 1.013435292 1.019497101 1.083484508 1.045350405 0.969438283 1.110997225 1.036945626 0.904504642 1.046417507 1 18.37758009 1.952156321 24.36776085 0.972453808 1.041346743 0.207719721 0.048904605 363.2851092 185027.5499 0.019537741 0.012608535 89.56871038 -1.952156321 0.068892936 ELHDLFNLPHDRPYFK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELHDLFNLPHDRPYFK 16 1 H0YA18;D6RGX2;Q9NUQ7 H0YA18 UFSP2 Ufm1-specific protease 2 0 ; 184.99 1.12E-09 590310000 335090 461490 401660 516760 346390 402430 396810 184805 435380 399070 FALSE TRUE 321994.3123 448328.757 474248.8969 543430.0455 357531.9489 410567.4103 401666.2795 180988.7122 385957.4877 372040.6334 0.865481572 1.205053203 1.274723388 1.460673907 0.96100242 1.103555293 1.079630135 0.486475659 1.037406812 1 18.50510067 1.952247872 12.52791056 0.783812434 1.154024295 0.287878744 0.208260478 1.70961266 447.0039558 0.085792777 0.055096432 89.58759372 -1.952247872 0.370211861 VS(ph)PSPSQESLSSSK ddPTM_BT-474_Pertuzumab_2h_R1 4 VSPSPSQESLSSSK 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VS(0.913)PS(0.086)PS(0.001)QESLSSSK;VS(0.994)PS(0.006)PSQESLSSSK;VS(0.639)PS(0.361)PSQESLSSSK;VS(0.996)PS(0.004)PSQESLSSSK 290.37 1.95E-43 1518330000 991000 853725 999104 1054502 944420 943620 1156700 1326590 1479880 1456670 TRUE FALSE 952270.6244 829377.5989 1179664.318 1108924.975 974798.127 962700.6429 1170856.041 1299195.453 1311890.227 1358008.443 0.70122585 0.610730812 0.8686723 0.816581797 0.717814482 0.708906228 0.862186127 0.956691734 0.966039816 1 20.37306102 1.952280232 2.396331794 0.974109114 0.740121038 0.719092939 0.066462364 0.173144736 1.827384503 0.039307716 0.02064274 89.59426932 -1.952280232 -0.233988076 HETWSGHVISS ddPTM_BT-474_Pertuzumab_2h_R1 4 HETWSGHVISS 11 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ;;; 207.34 2.33E-08 1914130000 1362050 1840330 1388060 1875690 1605960 1634660 1457250 438674 1466100 1470090 FALSE TRUE 1308819.58 1787845.59 1638913.319 1972494.586 1657617.162 1667713.945 1475084.261 429615.2286 1299674.474 1370519.495 0.954980637 1.304502123 1.195833642 1.439231323 1.209480907 1.216848028 1.076295716 0.313468893 0.948307908 1 20.38629142 1.952284872 8.731054509 0.68069679 1.225461987 0.490499001 0.208511406 0.26266828 45.6607415 0.083508432 0.053069959 89.59522661 -1.952284872 0.544765197 HNTPSLLEAALTQEAST(ph)PDSQVWPTAPDITR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNTPSLLEAALTQEAS(0.293)T(0.701)PDS(0.005)QVWPTAPDITR;HNTPSLLEAALTQEAS(0.14)T(0.827)PDS(0.033)QVWPTAPDITR 97.593 0.0011741 337980000 88378 135433 120154 148426 129722 141430 130618 72823 142915 149168 TRUE FALSE 84924.09005 131570.5834 141868.5006 156086.2836 133894.6259 144289.8115 132216.5422 71319.1796 126691.8883 139064.7185 0.610680343 0.94611045 1.020161707 1.122400314 0.962822399 1.037573103 0.950755473 0.51284884 0.911028259 1 17.08539692 1.952311612 24.74351111 0.748323732 0.964127964 0.091258785 0.174384 500.7688721 259827.0574 0.07083697 0.045721439 89.60074321 -1.952311612 0.215804233 LHELNQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LHELNQK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 102.3 0.0086325 431240000 472400 529450 446100 490600 519190 587940 538990 1142120 574420 687770 FALSE TRUE 453938.0857 514350.6044 526720.1934 515919.9248 535890.2179 599828.5496 545586.3209 1118534.823 509214.2498 641186.7253 0.707965508 0.802185361 0.821477072 0.804632885 0.835778716 0.935497455 0.850900836 1.744475952 0.79417466 1 19.29038503 1.952326955 24.99770333 1.27112471 0.823878304 0.305754638 0.234932825 350.4755654 183773.788 0.091569675 0.059102731 89.60390877 -1.952326955 -0.447246405 MHDLNTDQENLVGTHDAPIR ddPTM_BT-474_Pertuzumab_2h_R1 9 MHDLNTDQENLVGTHDAPIR 20 0 O43684;O43684-2;J3QT28;J3QSX4 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ;;;;;;;; 362.14 3.22E-96 7942260000 1244424 1369360 1169243 1474387 1388838 1442927 1273434 440666 1379984 1217483 FALSE TRUE 1195790.534 1330307.194 1380551.22 1550480.29 1433511.236 1472103.973 1289018.666 431566.0931 1223334.002 1135021.792 1.053539714 1.172054319 1.216321334 1.366035701 1.262981245 1.296983003 1.13567746 0.380227143 1.07780662 1 20.11428857 1.952406696 12.66034799 0.752188699 1.231419304 0.469060298 0.190945766 1.23528621 327.5832527 0.075904131 0.048756908 89.62036238 -1.952406696 0.479230606 GLEYLYLSVHDEDRDDHTR ddPTM_BT-474_Pertuzumab_2h_R1 7 GLEYLYLSVHDEDRDDHTR 19 1 O43237 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;;;;; 188.49 1.04E-14 4334557000 1390273 1946037 1583923 1942785 1885349 2180129 1708191 503495 1775877 1621665 FALSE TRUE 1335939.594 1890537.93 1870173.12 2043052.367 1945992.963 2224212.702 1729096.352 493097.6523 1574286.888 1511828.185 0.883658346 1.250497873 1.237027553 1.351378673 1.28717865 1.471207326 1.143712208 0.326159849 1.041313361 1 20.52786276 1.952552071 12.06374997 0.719198177 1.257660174 0.432350101 0.23080277 1.046608627 264.8853297 0.09218161 0.059160066 89.65036678 -1.952552071 0.538461997 QQADKESEVS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQADKESEVSPSR 13 1 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 QQADKES(0.008)EVS(0.496)PS(0.496)R 142.55 0.00010625 99783000 137240 157790 121590 135100 133650 139810 143800 160930 165550 161300 TRUE FALSE 131876.5091 153289.9837 143564.0178 142072.5272 137948.9736 142637.054 145559.8674 157606.7393 146757.458 150375.0073 0.876984224 1.019384713 0.954706638 0.944788165 0.917366363 0.948542291 0.967979121 1.048091316 0.975943148 1 17.19820528 1.952603377 6.472625723 1.01249589 0.947287168 0.370318857 0.037232391 0.223641184 23.33950557 0.015388833 0.009623457 89.66095848 -1.952603377 -0.065208722 VQGGHS(ph)PDDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQGGHSPDDHR 11 0 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 1 VQGGHS(1)PDDHR 86.641 0.0092228 122160000 129520 135340 113030 125770 135590 136310 116320 17487 129040 98377 TRUE FALSE 124458.2152 131480.2357 133457.0353 132261.0048 139951.3755 139066.2816 117743.559 17125.88734 114391.9202 91713.83816 1.35702766 1.43359212 1.455146115 1.44210522 1.525957023 1.51630642 1.28381454 0.18673177 1.247270014 1 16.48485181 1.952785702 11.04113643 0.72401129 1.45203305 0.551092011 0.256459257 0.558016282 129.2904733 0.10017762 0.064167619 89.69860764 -1.952785702 0.72802176 YVATLGVEVHPLVFHTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 YVATLGVEVHPLVFHTNR 18 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 321.57 6.80E-62 27684000000 10084900 10554300 10046600 12489400 10644300 11020000 10883700 3904000 12034000 11570500 FALSE TRUE 9690770.959 10253301.7 11862244.11 13133979.43 10986683.58 11242831.95 11016897.98 3823381.036 10667950.77 10786819.73 0.898389998 0.950539821 1.099698002 1.217595154 1.018528524 1.042274946 1.021329572 0.354449331 0.988980166 1 23.36276624 1.952786362 24.70370246 0.70403359 1.042960333 0.249728935 0.188349627 337.7174488 176704.0465 0.075123246 0.04848692 89.6987441 -1.952786362 0.338926743 SGSPS(ph)DNS(ph)GAEEMEVSLAKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 2 S(0.006)GS(0.311)PS(0.684)DNS(1)GAEEMEVSLAKPK 215.34 3.75E-25 544030000 714680 667510 512060 519600 538360 588500 680510 774110 885330 824790 TRUE FALSE 686749.5155 648473.2684 604600.6327 546416.6183 555676.8383 600399.8732 688838.2849 758124.358 784831.05 768926.2387 0.89312795 0.843349122 0.786292108 0.710622932 0.722665986 0.780828957 0.895844426 0.985951994 1.020684444 1 19.55248568 1.952820296 2.244617933 1.005951813 0.784886117 0.78162053 0.050474551 0.153996622 1.428720459 0.032476543 0.016741715 89.70575297 -1.952820296 -0.221065696 KETKPEPMEEDLPENK ddPTM_BT-474_Pertuzumab_2h_R1 1 KETKPEPMEEDLPENK 16 2 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 97.836 0.0016525 1040000000 734660 583800 521470 496540 647390 670790 723720 711660 991160 860250 FALSE TRUE 705948.675 567150.5956 615711.229 522166.4889 668213.8873 684353.8334 732577.1018 696963.9723 878647.6721 801984.5013 0.880252267 0.707183985 0.767734574 0.651092993 0.8332005 0.85332551 0.913455435 0.869049179 1.095591836 1 19.61321483 1.952861137 0.827995758 1.026883268 0.754080536 0.650648649 0.073500531 0.375517798 0.47938471 0.062084412 0.030510329 89.71418934 -1.952861137 -0.272802732 AGLESGAEPGDGDS(ph)DTTKK ddPTM_BT-474_Pertuzumab_2h_R1 4 AGLESGAEPGDGDSDTTKK 19 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.998)DT(0.001)T(0.001)KK;AGLESGAEPGDGDS(0.999)DTT(0.001)KK;AGLESGAEPGDGDS(0.991)DT(0.005)T(0.004)KK;AGLESGAEPGDGDS(0.999)DT(0.001)TKK 211.64 7.33E-17 6594500000 5939900 4270910 4209680 3484510 4143160 4311920 4899500 6033700 6558600 5552200 TRUE FALSE 5707762.141 4149107.828 4970462.82 3664345.979 4276428.504 4399109.977 4959461.547 5909101.986 5814095.224 5176144.549 1.102705322 0.801582682 0.960263527 0.707929608 0.826180271 0.849881593 0.958138147 1.141602969 1.123248234 1 22.30344648 1.953018863 3.632349509 1.099080015 0.866555738 0.453495215 0.10418497 0.191745597 4.895434204 0.048391105 0.028157895 89.74677738 -1.953018863 -0.232524277 SQRPEESEPLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQRPEESEPLEK 12 1 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 184.11 1.34E-05 1351870000 1411470 1403890 1222530 1311950 1315110 1420050 1465190 1654910 1759080 1804050 FALSE TRUE 1356308.192 1363852.432 1443468.366 1379659.897 1357411.708 1448764.384 1483121.434 1620735.53 1559396.613 1681860.087 0.806433426 0.810919079 0.858257103 0.820317878 0.807089554 0.861406008 0.881834015 0.963656575 0.927185695 1 20.68162626 1.953056126 1.164965098 0.976378644 0.820691374 0.886980998 0.022073996 0.143165402 0.358244847 0.016727008 0.007517514 89.75447804 -1.953056126 -0.15568727 SDNKDDDIDIDAI ddPTM_BT-474_Pertuzumab_2h_R1 2 SDNKDDDIDIDAI 13 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 142.89 0.00033077 2712200000 5682800 5064500 4847400 4640300 5033000 5426700 5818600 6866600 7683900 7327000 FALSE TRUE 5460709.893 4920065.419 5723433.01 4879786.439 5194891.016 5536431.592 5889809.767 6724802.31 6811655.886 6830735.764 0.799432167 0.720283376 0.837894073 0.71438665 0.760517051 0.810517605 0.86225115 0.984491648 0.997206761 1 22.70360955 1.953059149 1.596165786 1.005558711 0.766082125 0.892265541 0.034405893 0.105198567 0.499021996 0.021743142 0.010167443 89.75510283 -1.953059149 -0.239476586 CRDDSFFGETSHNYHKFDSEYER ddPTM_BT-474_Pertuzumab_2h_R1 2 CRDDSFFGETSHNYHKFDSEYER 23 2 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 232.59 1.46E-34 1925930000 615300 667610 375346 415570 472610 640850 460940 70603 487617 366800 FALSE TRUE 591253.3957 648570.4165 443179.3717 437017.6175 487811.9299 653808.4261 466581.1216 69145.02338 432264.7624 341956.3093 1.729031984 1.896647024 1.296011682 1.277992555 1.426532913 1.911964799 1.364446594 0.202204263 1.264093543 1 18.38345248 1.95319701 10.10324209 0.744888734 1.57452896 0.522968332 0.325281824 0.456633908 96.79391076 0.134597738 0.086019324 89.78359893 -1.95319701 0.829640226 VDEFVTHNLSFDEINK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDEFVTHNLSFDEINK 16 0 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 ;;; 273.49 3.32E-35 2514270000 2290920 2026520 1898890 1939810 2114180 2155010 2206590 2352870 2861250 2448430 FALSE TRUE 2201388.314 1968725.634 2242061.664 2039923.827 2182184.52 2198585.779 2233594.908 2304282.412 2536452.895 2282595.655 0.964423247 0.862494253 0.98224215 0.89368602 0.956010108 0.963195463 0.978532884 1.009500919 1.111214283 1 21.12224389 1.953212875 1.210752145 1.051700121 0.929100561 0.553273836 0.042395017 0.320868142 0.868708855 0.030123158 0.013535533 89.78687882 -1.953212875 -0.12259956 DNSEEFLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNSEEFLKR 9 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;A0A5F9ZH85;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 0 85.963 0.023185 436290000 711870 760260 529610 687390 652250 672410 681440 770040 744480 711140 FALSE TRUE 684049.3334 738578.1292 625322.3081 722866.2803 673230.2136 686006.5909 689779.6666 754138.4049 659969.7515 662973.8544 1.031789306 1.114038094 0.943208098 1.090339047 1.015470232 1.034741546 1.040432684 1.137508515 0.995468746 1 19.33859245 1.953341197 24.98467466 1.066945994 1.038624405 0 0.057125864 1395.229658 747109.5037 0.022368671 0.01441521 89.8134124 -1.953341197 -0.028321589 SS(ph)TPGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTPGLK 7 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 S(0.138)S(0.431)T(0.431)PGLK;S(0.018)S(0.491)T(0.491)PGLK 96.668 0.013178 6088200000 9295000 8377100 7118500 7023200 7146300 7487700 8447900 11127800 10367600 9534000 TRUE FALSE 8931741.124 8138193.31 8404971.3 7385668.194 7376167.23 7639106.424 8551287.927 10898007.04 9190713.513 8888253.688 1.004892686 0.915612177 0.945626846 0.830947051 0.829878117 0.85946089 0.962088643 1.22611341 1.034029162 1 23.08346856 1.953355442 7.302851817 1.108458986 0.895774034 0.556257993 0.074708754 0.167261673 22.49715596 0.031886935 0.020105938 89.81635822 -1.953355442 -0.212684952 S(ph)SPSIICMPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPSIICMPK 10 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 S(0.525)S(0.475)PSIICMPK 164.33 6.49E-06 517210000 1111800 1158000 1065600 1044100 993470 961500 1255800 1418900 1591400 1567200 TRUE FALSE 1068349.627 1124974.974 1258177.624 1097986.126 1025425.865 980942.1888 1271168.856 1389599.219 1410750.944 1461052.148 0.731219367 0.769975921 0.861144912 0.751503721 0.701840702 0.671394372 0.870036609 0.951094881 0.965571931 1 20.47857624 1.953362517 3.089857361 0.965562555 0.752317877 0.80399611 0.049606868 0.123529951 2.199268187 0.027277953 0.015332148 89.81782137 -1.953362517 -0.213244679 GPSLDIDTPDVNIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 GPSLDIDTPDVNIEGPEGK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 345.38 3.09E-90 313360000 690325 752006 613614 713482 601475 713054 707454 834236 830470 756844 FALSE TRUE 663346.3358 730559.5252 724507.6996 750304.8915 620821.9896 727472.4404 716112.0337 817008.7351 736198.5272 705582.2818 0.940140297 1.035399477 1.026822411 1.063383975 0.879871853 1.031024247 1.014923493 1.157921275 1.04339146 1 19.42845481 1.953435144 13.94272977 1.085107719 0.999220184 0.187857794 0.062625202 3.947015036 1180.249164 0.025215849 0.016224711 89.83284301 -1.953435144 -0.085887535 ERHPGSFDVVHVK ddPTM_BT-474_Pertuzumab_2h_R1 6 ERHPGSFDVVHVK 13 1 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;;;;; 206.2 4.12E-08 3763620000 3173850 3628547 2867244 3077495 3057426 3370278 3219278 1931654 3492294 3468703 FALSE TRUE 3049812.433 3525064.392 3385418.772 3236324.886 3155770.884 3438427.33 3258676.487 1891764.67 3095863.426 3233764.656 0.943115148 1.090080685 1.046897079 1.000791718 0.975881432 1.063289292 1.007703662 0.585003818 0.957355824 1 21.62478326 1.953468924 24.52630057 0.800095138 1.022700438 0.30117225 0.11257709 282.5324386 148920.8137 0.043679856 0.028190982 89.83983048 -1.953468924 0.222605299 SCDEPLT(ph)PPPHSPTSMLQLIHDPVSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 SCDEPLT(1)PPPHSPTSMLQLIHDPVSPR 153.86 9.87E-08 375310000 250030 294160 241560 361110 320550 350510 293610 190520 305310 308450 TRUE FALSE 240258.5512 285770.8448 285215.2655 379746.9304 330860.7819 357597.5524 297203.287 186585.6954 270652.4888 287558.4068 0.83551218 0.993783656 0.991851599 1.320590605 1.150586365 1.243564938 1.033540596 0.648861904 0.941208751 1 18.13349549 1.953528155 10.95579182 0.828336395 1.097560116 0.291660412 0.154565608 0.970336966 226.5393777 0.066511452 0.042605974 89.8520842 -1.953528155 0.269223721 IADPEHDHTGFLTEY(ph)VATR ddPTM_BT-474_Pertuzumab_2h_R1 5 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 1 IADPEHDHTGFLT(0.054)EY(0.945)VAT(0.001)R;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLT(0.038)EY(0.962)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR 302.44 3.69E-50 10657100000 3290310 4213350 3873720 5212730 4892880 4843850 3379160 121222 2558010 2205650 TRUE FALSE 3161721.048 4093189.383 4573787.374 5481759.62 5050263.929 4941795.966 3420515.171 118718.7233 2267635.429 2056259.361 1.537608099 1.990599757 2.224324159 2.665889199 2.456044225 2.403294088 1.663464851 0.057735287 1.102796404 1 20.97159082 1.953551209 5.13079665 0.652307404 2.224077527 0.748296329 0.386305933 0.095480223 5.762173845 0.17604559 0.107967996 89.85685397 -1.953551209 1.571770123 VDDKPSS(ph)PGDSSK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDDKPSSPGDSSK 13 1 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.027)S(0.972)PGDS(0.001)SK;VDDKPS(0.117)S(0.883)PGDSSK;VDDKPS(0.001)S(0.999)PGDSSK;VDDKPS(0.251)S(0.749)PGDSSK 197.38 8.13E-08 2631300000 4565580 3400230 2913980 2475710 3229720 2826620 3425140 4264330 4413670 3565660 TRUE FALSE 4387152.086 3303258.77 3440601.007 2603481.69 3333606.877 2883776.193 3467057.888 4176270.095 3912648.685 3324154.672 1.319779769 0.99371392 1.03503036 0.783201128 1.002843491 0.867521664 1.04298934 1.256340486 1.177035689 1 21.66455608 1.953655787 8.24170608 1.167749405 0.988844228 0.160313824 0.143165138 0.486342175 80.23545721 0.059911741 0.038013397 89.87849407 -1.953655787 -0.178905176 NQEQMKPLEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NQEQMKPLEEK 11 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 122.46 0.00035599 439750000 346480 292930 282630 269970 301230 313740 352020 454560 497280 434880 FALSE TRUE 332939.1785 284575.9232 333707.5281 283903.1841 310919.3365 320084.0378 356328.1261 445173.1772 440830.8592 405425.1902 0.821209897 0.701919688 0.823105066 0.700260346 0.766896937 0.789502097 0.878899818 1.09804025 1.087329721 1 18.6290762 1.953674933 2.579220696 1.071932618 0.76296048 0.884599403 0.047420205 0.078224216 0.956918931 0.023862901 0.012809336 89.88245653 -1.953674933 -0.308972138 GAHNGQGLGNAFLSHISACDGIFHLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAHNGQGLGNAFLSHISACDGIFHLTR 27 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 394.97 6.19E-146 1944160000 143144 213647 162452 224190 136927 198478 167943 71095 172269 170699 FALSE TRUE 137549.7742 207553.9967 191810.6901 235760.4728 141331.3813 202491.3611 169998.3367 69626.86341 152713.7453 159137.4047 0.864345969 1.304243947 1.205314932 1.481489994 0.888109125 1.272430963 1.068248769 0.437526699 0.95963451 1 17.27991345 1.953689496 10.28654557 0.74016814 1.177860468 0.342075688 0.225251363 0.61498901 134.4554914 0.0891099 0.05699076 89.88547043 -1.953689496 0.437692327 TAESQTPTPSATSFFSGKS(ph)PVTTLLECMHK ddPTM_BT-474_Pertuzumab_2h_R1 1 TAESQTPTPSATSFFSGKSPVTTLLECMHK 30 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAESQTPTPSATSFFS(0.045)GKS(0.949)PVT(0.003)T(0.003)LLECMHK 126.68 7.81E-06 780790000 315370 292470 241750 188330 270690 299160 359230 530490 642270 455510 TRUE FALSE 303044.9917 284129.042 285439.6027 198049.7339 279396.9897 305209.2202 363626.3642 519535.1961 569362.2022 424657.902 0.713621459 0.669077487 0.672163644 0.466374776 0.657934277 0.718717864 0.856280697 1.223420531 1.340754993 1 18.69594157 1.953711088 2.198346052 1.218517511 0.639170872 0.842736295 0.10369799 0.10703954 0.953432923 0.058806234 0.030151822 89.88993952 -1.953711088 -0.579346639 HTPSPGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPAT(ph)SPRPLIEVGELLDLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HTPSPGLPAEGAPEAPRPS(0.471)S(0.499)PPPEVLEPHS(0.033)LDQPPAT(0.509)S(0.481)PRPLIEVGELLDLT(0.008)R;HTPSPGLPAEGAPEAPRPS(0.435)S(0.565)PPPEVLEPHS(0.068)LDQPPAT(0.486)S(0.446)PRPLIEVGELLDLTR 136.94 2.91E-13 1148790000 82893 86987 81119 76258 79181 85770 67174 31553 55986 46534 TRUE FALSE 79653.44992 84506.21593 95779.00778 80193.68452 81727.92878 87504.32817 67996.09551 30901.41952 49630.70399 43382.21073 1.836085542 1.947946278 2.207794535 1.848538449 1.883904195 2.017055532 1.567372763 0.712306243 1.144033537 1 15.40481595 1.953837664 3.79052659 0.941858305 1.95469974 0.907836358 0.14293557 0.059847647 1.692605759 0.066637784 0.039125239 89.91614191 -1.953837664 1.012841435 LDFLPEMMVDHCSLNSS(ph)PVSK ddPTM_BT-474_Pertuzumab_2h_R1 5 LDFLPEMMVDHCSLNSSPVSK 21 0 Q92879-4;G5EA30;F5H0D8;E9PKU1;F5H3J7 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 LDFLPEMMVDHCSLNS(0.005)S(0.994)PVS(0.001)K;LDFLPEMMVDHCSLNS(0.214)S(0.785)PVSK;LDFLPEMMVDHCS(0.001)LNS(0.173)S(0.826)PVSK;LDFLPEMMVDHCSLNS(0.01)S(0.99)PVSK;LDFLPEMMVDHCS(0.088)LNS(0.197)S(0.713)PVS(0.003)K 224.08 2.13E-25 1180133000 1023463 1518839 1415381 1729616 1450836 1688841 1438431 1264468 1368897 1649733 TRUE FALSE 983464.9345 1475523.199 1671171.832 1818881.689 1497503.458 1722990.522 1456034.949 1238356.294 1213505.551 1537995.114 0.639446072 0.95938094 1.086591118 1.182631643 0.973672441 1.120283482 0.946709736 0.805175701 0.789017819 1 20.55261949 1.953858552 6.10486188 0.849498416 1.006406387 0.126961323 0.14722187 0.371444314 34.64612072 0.065013659 0.040531235 89.9204667 -1.953858552 0.156907971 QLSSTS(ph)PLAPYPTSQMVSSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 QLSSTSPLAPYPTSQMVSSDR 21 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 QLSS(0.003)T(0.025)S(0.972)PLAPYPTSQMVSSDR;QLSSTS(1)PLAPYPTSQMVSSDR;QLSST(0.003)S(0.997)PLAPYPTSQMVSSDR 298.1 6.09E-55 709750000 486970 606410 500370 593780 563800 574790 456440 433930 390340 426540 TRUE FALSE 467938.674 589115.7805 590797.9897 624425.057 581935.139 586412.6476 462026.0493 424969.1939 346030.2396 397650.0659 1.176759956 1.481492979 1.485723354 1.570287825 1.463435289 1.474695211 1.161891042 1.06870143 0.870187809 1 18.60113988 1.953901386 1.808810765 0.956623365 1.455610986 0.790441603 0.107759743 0.150938013 0.917417599 0.067681779 0.032755139 89.92933594 -1.953901386 0.498987621 ELHEVCHLLEQER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELHEVCHLLEQER 13 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ; 228.8 3.94E-12 443890000 145078 161375 119866 158431 150511 145809 145776 20366.2 159882 163105 FALSE TRUE 139408.1914 156772.743 141528.4526 166607.6429 155352.323 148757.3579 147560.0503 19945.63085 141732.8656 152057.7531 0.916810807 1.031007889 0.930754597 1.095686603 1.02166657 0.978295121 0.970421089 0.131171416 0.932098908 1 17.21425985 1.953927927 24.9750338 0.581114018 0.997937522 0.234996258 0.228866056 382.0760766 207117.5446 0.088716952 0.057261368 89.9348319 -1.953927927 0.416823504 SS(ph)PSARPPDVPGQQPQAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.198)S(0.802)PSARPPDVPGQQPQAAK;S(0.408)S(0.591)PSARPPDVPGQQPQAAK;S(0.135)S(0.862)PS(0.003)ARPPDVPGQQPQAAK;S(0.047)S(0.953)PSARPPDVPGQQPQAAK 261.54 2.23E-31 7292700000 2847280 2622290 2653100 2821530 2622380 2698400 2955980 3288360 3519380 3534610 TRUE FALSE 2736005.15 2547504.857 3132574.188 2967149.501 2706731.234 2752963.497 2992156.167 3220454.217 3119874.737 3295207.716 0.830298235 0.773093861 0.95064544 0.900443844 0.82141445 0.835444601 0.908032642 0.97731448 0.946791524 1 21.65193798 1.953936089 3.05662954 0.971232777 0.853830331 0.581550178 0.046549883 0.204105321 3.552865086 0.0247318 0.01387313 89.93652207 -1.953936089 -0.117402446 TAT(ph)PPGYKPGS(ph)PPSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 2 T(0.007)AT(0.992)PPGY(0.001)KPGS(0.981)PPS(0.019)FR;T(0.115)AT(0.885)PPGYKPGS(0.592)PPS(0.408)FR 104.52 0.0031057 1116630000 1434050 1171900 1060120 1023830 1121710 1064350 1272130 1574790 1660390 1418660 TRUE FALSE 1378005.741 1138478.559 1251707.266 1076669.989 1157790.821 1085871.886 1287698.707 1542270.036 1471909.488 1322572.895 1.041912885 0.860805906 0.946418357 0.814072323 0.875407946 0.821029896 0.973631558 1.166113446 1.112913696 1 20.33491581 1.953992096 5.001313091 1.105007622 0.889887422 0.599858125 0.072713117 0.123716929 7.018201998 0.031227197 0.019106682 89.94812102 -1.953992096 -0.2151202 HTTENKPHS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 HTTENKPHSPK 11 1 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 HTTENKPHS(1)PK;HTTENKPHS(1)PK;HTTENKPHS(1)PK;HTTENKPHS(1)PK 125.28 0.00020026 561801000 440202 395851 343623 325013 345284 370781 368444 114402 531699 417388 TRUE FALSE 422998.4192 384561.7171 405723.32 341786.9599 356390.3734 378278.4459 372953.1279 112039.5587 471342.7586 389117.939 1.087069952 0.988290897 1.042674416 0.87836341 0.915892941 0.972143425 0.958457811 0.287932134 1.211310791 1 18.56984797 1.954141555 24.99942355 0.721270453 0.975380809 0.012136502 0.231461232 659.5975219 359574.1173 0.091636502 0.059146888 89.97908129 -1.954141555 0.254110356 YHTLS(ph)LGR ddPTM_BT-474_Pertuzumab_2h_R1 4 YHTLSLGR 8 0 V9GZ20;V9GXZ5;Q70EL4-2;Q70EL4-3;Q70EL4-4;Q70EL4 V9GZ20 USP43 Ubiquitin carboxyl-terminal hydrolase 43 1 YHTLS(1)LGR;YHTLS(1)LGR;YHTLS(1)LGR;YHTLS(1)LGR 70.525 0.032918 1033220000 643670 671250 513870 716390 693550 806370 614630 250598 652250 543140 TRUE FALSE 618514.6648 652106.6072 606737.74 753362.9738 715858.6656 822675.3539 622152.0258 245423.0637 578209.3145 506352.644 1.221509697 1.2878507 1.198251351 1.487822731 1.413755165 1.624708321 1.228693151 0.484688026 1.141910329 1 18.94978296 1.954158463 9.819445538 0.827098997 1.372624443 0.558348432 0.196263609 0.372447309 78.01246858 0.080453295 0.051395339 89.98258443 -1.954158463 0.545525446 DFYLATS(ph)PPDSFLDDHHLTRPHPER ddPTM_BT-474_Pertuzumab_2h_R1 7 DFYLATSPPDSFLDDHHLTRPHPER 25 1 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 DFY(0.002)LAT(0.133)S(0.848)PPDS(0.017)FLDDHHLTRPHPER;DFYLAT(0.003)S(0.996)PPDSFLDDHHLTRPHPER;DFYLAT(0.026)S(0.974)PPDSFLDDHHLTRPHPER;DFYLAT(0.027)S(0.973)PPDSFLDDHHLTRPHPER;DFYLAT(0.021)S(0.979)PPDSFLDDHHLTRPHPER;DFYLAT(0.198)S(0.802)PPDSFLDDHHLTRPHPER;DFYLAT(0.023)S(0.977)PPDSFLDDHHLTRPHPER 168.96 5.29E-12 7224062000 1480345 1859405 1509021 1927714 1745745 1996814 1750522 268076.7 1943663 1683176 TRUE FALSE 1422491.481 1806376.59 1781734.663 2027203.551 1801898.473 2037190.947 1771945.412 262540.8225 1723026.525 1569172.99 0.906523047 1.151164723 1.135460955 1.291892967 1.148310916 1.298257719 1.129222478 0.167311586 1.098047529 1 20.58157298 1.954240383 24.56717371 0.659015432 1.164547592 0.316585846 0.255490313 297.5945889 159770.3485 0.099812832 0.064417872 89.99955941 -1.954240383 0.50553216 SS(ph)PLPAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPLPAK 7 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 S(0.407)S(0.593)PLPAK;S(0.342)S(0.658)PLPAK;S(0.259)S(0.741)PLPAK;S(0.042)S(0.958)PLPAK 113.26 0.0064726 4898120000 8756500 8083000 8073100 9049700 8726200 8808400 10502800 11596900 13367400 13038600 TRUE FALSE 8414286.299 7852480.754 9532088.755 9516756.102 9006886.148 8986511.883 10631336.41 11357419.96 11849988.79 12155484.01 0.692221412 0.646003133 0.784180107 0.78291873 0.740973057 0.73929692 0.874612348 0.93434535 0.974867705 1 23.535104 1.954293632 1.134000336 0.997940516 0.722570667 0.883850298 0.03950522 0.164382528 0.38936856 0.033459377 0.015069453 90.01059498 -1.954293632 -0.275369849 VDINAPDVDVHGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDINAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 279.53 1.84E-39 2778990000 4505300 4838760 3936240 4531720 4056200 4673660 4386070 587240 5271600 4182600 FALSE TRUE 4329227.895 4700763.302 4647606.129 4765602.612 4186671.357 4768164.607 4439748.037 575113.2888 4673190.068 3899308.777 1.110255213 1.205537589 1.191905129 1.222166001 1.073695774 1.222823039 1.138598734 0.147491087 1.198466276 1 21.89478697 1.954350119 24.92971107 0.676207863 1.172244937 0.29080171 0.260237674 362.5326808 197980.956 0.10071962 0.065006615 90.02230307 -1.954350119 0.496037074 THTGEKPYR ddPTM_BT-474_Pertuzumab_2h_R1 2 THTGEKPYR 9 1 Q9HCG1;Q8N8E2-2;M0QZI7;Q8N8E2;Q9UJW8-3;G5E9B8;Q9NX65-3;Q8WXB4;Q9NX65;Q9UJW8;Q9UJW8-4;A0A0A0MP75;A0A1W2PQ54;Q9BSK1-2;O94892;Q86UD4;Q86TJ5;Q9BSK1;Q9NX65-2;Q9UJW8-2;E7EN86;P52747-2;P52747-3;P52747;Q99612;Q499Z4 Q9HCG1;E7EN86;Q99612;Q499Z4 ZNF160;ZNF513;ZNF180;ZSCAN32;ZNF606;ZNF577;ZNF432;ZNF329;ZNF554;ZNF143;KLF6;ZNF672 Zinc finger protein 160;Zinc finger protein 513;Zinc finger protein 180;Zinc finger and SCAN domain-containing protein 32;Zinc finger protein 606;Zinc finger protein 577;Zinc finger protein 432;Zinc finger protein 329;Zinc finger protein 554;Zinc finger protein 143;Krueppel-like factor 6;Zinc finger protein 672 0 ; 90.906 0.0066774 162125000 244660 220450 182816 209971 216540 201791 192036 74994 216800 176928 FALSE TRUE 235098.4167 214162.9818 215854.9179 220807.6285 223505.2058 205871.3523 194386.194 73445.34769 192189.7729 164944.509 1.425318237 1.298394128 1.308651735 1.338678261 1.355032715 1.248124921 1.178494484 0.445273069 1.165178363 1 17.33162123 1.954489115 9.028340391 0.808431933 1.319011152 0.565433714 0.177317638 0.260735469 49.64370505 0.070567037 0.044962249 90.05111916 -1.954489115 0.51057922 LHYTPPLQS(ph)PIIDNDPLLGQSPWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHYTPPLQSPIIDNDPLLGQSPWR 24 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 LHYTPPLQS(1)PIIDNDPLLGQSPWR;LHYTPPLQS(1)PIIDNDPLLGQSPWR 250.24 1.19E-38 113706000 67557 77004 63716 78208 95990 94359 74945 47786 71346 82160 TRUE FALSE 64916.79775 74807.92131 75230.89855 82244.32425 99077.60553 96267.00363 75862.19933 46799.2024 63247.10119 76595.23002 0.847530554 0.976665535 0.982187775 1.073752559 1.293521875 1.256827659 0.990429813 0.610993692 0.825731592 1 16.22496693 1.954532079 8.831479546 0.776198384 1.077685846 0.361322223 0.15193206 0.395302625 73.19596698 0.067709037 0.043107431 90.06002822 -1.954532079 0.301487462 LS(ph)PIPEEVPK ddPTM_BT-474_Pertuzumab_2h_R1 6 LSPIPEEVPK 10 0 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK 184.55 1.62E-06 3760400000 5652080 5087170 4938740 5045510 5358180 5130430 5945070 6926640 7680300 7113010 TRUE FALSE 5431190.465 4942088.892 5831280.18 5305909.376 5530530.726 5234170.81 6017827.545 6783602.463 6808464.542 6631239.497 0.819030962 0.745273775 0.879365039 0.800138402 0.834011609 0.789320128 0.907496637 1.022976544 1.02672578 1 22.66084713 1.95465064 2.754990177 1.018957276 0.811832287 0.882852018 0.033474526 0.081186099 1.136761915 0.016873461 0.009227629 90.08461778 -1.95465064 -0.207124989 MDIDAPDVDVHGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 9 MDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;;;;; 223.06 3.10E-19 5275740000 7088300 7532700 6339150 7323170 6564970 7460880 6983580 1034562 7979300 6574360 FALSE TRUE 6811281.399 7317874.771 7484775.419 7701119.681 6776138.222 7611744.105 7069047.141 1013197.933 7073523.316 6129072.741 1.111306993 1.193961155 1.221192134 1.256490175 1.105573144 1.241907941 1.153363231 0.16531015 1.15409355 1 22.5472374 1.954669029 24.57123074 0.675127218 1.190157692 0.345745273 0.248252328 285.4964456 154750.1133 0.0959577 0.061930206 90.08843221 -1.954669029 0.515030474 HDDGTQS(ph)DSENAGAHRR ddPTM_BT-474_Pertuzumab_2h_R1 1 HDDGTQSDSENAGAHRR 17 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 HDDGTQS(1)DSENAGAHRR 132.01 1.18E-05 181370000 28954 24166 25136 20198 22625 29108 24889 6997.8 31724 26751 TRUE FALSE 27822.44567 23476.80934 29678.63435 21240.4212 23352.75367 29696.5837 25193.59903 6853.292985 28122.82452 24939.13094 1.115614082 0.941364372 1.190042845 0.851690512 0.936390034 1.190762572 1.010203567 0.274800794 1.127658561 1 14.60612357 1.95488752 24.99972813 0.700806979 1.033252216 0.130988126 0.236678391 525.7231005 291336.1834 0.092982724 0.060012817 90.13376659 -1.95488752 0.332445237 HPAPEDPDWIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPAPEDPDWIKR 12 1 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 0 66.498 0.037583 386110000 268480 318630 236760 275880 285620 334650 290200 190950 340880 330780 FALSE TRUE 257987.5048 309542.9844 279547.7987 290118.1999 294807.2267 341416.8523 293751.5544 187006.8158 302184.7315 308375.976 0.836600529 1.003784369 0.906516138 0.940793779 0.955999331 1.107144781 0.952576002 0.606424723 0.979923065 1 18.23433085 1.954888701 24.99234373 0.808664037 0.96330559 0.065691928 0.122068615 587.2123822 325323.6769 0.048481977 0.031296165 90.13401158 -1.954888701 0.154641553 ALDIDS(ph)DEESEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDIDSDEESEPK 13 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 ALDIDS(1)DEESEPK 287.54 1.29E-23 0 268240 240880 225930 228610 245370 243500 259060 341410 313390 278630 TRUE FALSE 257756.8842 234010.3382 266760.5768 240408.5895 253262.5489 248423.7368 262230.4538 334359.7642 277815.281 259758.1419 0.992295688 0.90087778 1.026957518 0.925509352 0.974993688 0.956365544 1.009517745 1.287196473 1.0695152 1 17.98680944 1.954931894 10.74572949 1.15034862 0.963527409 0.439935915 0.076335178 0.574355135 135.4228662 0.029634237 0.01898479 90.14297636 -1.954931894 -0.186821211 FHFPPLDT(ph)HSPTNDVQPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FHFPPLDTHSPTNDVQPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 FHFPPLDT(0.576)HS(0.42)PT(0.004)NDVQPGR;FHFPPLDT(0.675)HS(0.323)PT(0.002)NDVQPGR 166.91 3.55E-11 441850000 326183 388690 263435 381633 355971 312759 270176 44511 200628 181360 TRUE FALSE 313435.4077 377604.9418 311043.5646 401329.1249 367421.1305 319083.2013 273482.4947 43591.8323 177853.5505 169076.3257 1.853810145 2.233340122 1.839663616 2.373656532 2.173108086 1.887213955 1.617509096 0.257823395 1.051912796 1 17.36731514 1.954979973 3.964631397 0.714565682 2.064664763 0.827855351 0.261958536 0.07877044 2.491818933 0.118539138 0.070248604 90.15295644 -1.954979973 1.350099081 THVEKEDGEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 THVEKEDGEAR 11 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 ;; 184.03 3.06E-06 965550000 1224010 1267700 834160 948790 1058310 1093660 960420 401534 1087970 832971 FALSE TRUE 1176174.336 1231546.437 984911.2678 997757.1656 1092351.502 1115774.555 972173.9073 393242.1826 964468.2067 776553.1322 1.514608965 1.58591394 1.2683115 1.284853701 1.406666791 1.436829636 1.251909067 0.506394432 1.241986114 1 19.56672511 1.955118156 8.840186369 0.864623976 1.405477287 0.5718984 0.19180686 0.254842632 47.86069326 0.07825261 0.049841191 90.1816456 -1.955118156 0.540853311 TLTPGGHAEHDGKPFCHKPCYATLFGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTPGGHAEHDGKPFCHKPCYATLFGPK 28 2 P52943;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ; 124.45 1.31E-05 4076600000 3057500 3554800 2740500 3028300 2839700 3265900 3041000 39714.8 3839600 2699420 FALSE TRUE 2938009.52 3453420.585 3235769.312 3184590.926 2931041.529 3331938.736 3078216.668 38894.6755 3403744.705 2516585.879 1.167458478 1.372264151 1.285777425 1.26544099 1.164689651 1.323991668 1.223171716 0.015455334 1.352524757 1 21.2630364 1.955195215 24.98229331 0.664777692 1.265591985 0.284921676 0.322799932 392.1611736 218660.9448 0.125037785 0.080704283 90.19764845 -1.955195215 0.600814293 IHIDPEIQDGS(ph)PTTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHIDPEIQDGSPTTSR 16 0 C9J542;P50479-2;P50479 C9J542 PDLIM4 PDZ and LIM domain protein 4 1 IHIDPEIQDGS(0.981)PT(0.014)T(0.004)S(0.001)R;IHIDPEIQDGS(0.917)PT(0.034)T(0.018)S(0.032)R 191.41 7.35E-10 1467140000 968030 1150030 791400 1032780 996490 1006140 987270 350020 1100520 1044600 TRUE FALSE 930198.3174 1117232.27 934423.5846 1086081.9 1028543.006 1026484.84 999352.5056 342791.9647 975593.5834 973848.3116 0.95517783 1.147234387 0.959516563 1.115247505 1.056163464 1.054050028 1.026189083 0.351997288 1.001792139 1 19.89333755 1.955311582 24.88929851 0.706720222 1.050857182 0.273738441 0.181625852 368.6645905 205327.8138 0.069987612 0.045171981 90.22181974 -1.955311582 0.344136961 TIDDLEDKLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIDDLEDKLK 10 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 159.94 6.87E-06 1284040000 2917800 2618000 2063130 1724700 2242730 2051190 2561600 3035600 3452100 2829600 FALSE TRUE 2803769.15 2543337.203 2435983.485 1813711.974 2314869.447 2092666.467 2592949.627 2972913.799 3060232.08 2637948.672 1.06285963 0.964134454 0.923438546 0.687546347 0.877526342 0.793293095 0.982941653 1.126979395 1.160080222 1 21.33098506 1.955391285 4.04277503 1.103433768 0.880659159 0.465204902 0.101002029 0.197487332 6.564472815 0.049336847 0.02934917 90.23837886 -1.955391285 -0.222774609 DEDHIAHIIELLGS(ph)IPR ddPTM_BT-474_Pertuzumab_2h_R1 4 DEDHIAHIIELLGSIPR 17 0 P78362;P78362-2;H7C521;F8WBW4 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 DEDHIAHIIELLGS(1)IPR;DEDHIAHIIELLGS(1)IPR;DEDHIAHIIELLGS(1)IPR;DEDHIAHIIELLGS(1)IPR 189.07 2.42E-10 106334000 126448 121824 120348 128653 127032 130316 124819 11553 155437 114884 TRUE FALSE 121506.2724 118349.6988 142097.5607 135292.7967 131118.0996 132951.0788 126346.5723 11314.42651 137792.4434 107102.8044 1.134482641 1.10501027 1.32673987 1.263204989 1.224226578 1.241340781 1.179675668 0.105640805 1.286543749 1 16.70863673 1.955406555 24.99805796 0.684180482 1.217717407 0.278728624 0.288353603 402.6062728 225691.1459 0.112328295 0.072496255 90.24155191 -1.955406555 0.533536926 IEDVGS(ph)DEEDDSGK ddPTM_BT-474_Pertuzumab_2h_R1 22 IEDVGSDEEDDSGK 14 0 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK 393.63 3.52E-114 1.94874E+11 10739620 9108339 9915013 10079700.7 9840803 9076945 11748581 14078860 15568341 14514983 TRUE FALSE 10319903.78 8848578.09 11706876.41 10599915.26 10157341.37 9260487.047 11892363.65 13788126.62 13801088.2 13531870.27 0.762636913 0.653906512 0.865133656 0.783329654 0.750623614 0.684346425 0.878841092 1.018937245 1.019895101 1 23.68985792 1.955429762 3.248213887 1.011623442 0.752722748 0.824056508 0.054389332 0.100591338 2.003019647 0.027322252 0.015567575 90.24637418 -1.955429762 -0.258900694 CNEIINWLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 CNEIINWLDK 10 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 126.03 0.00091546 1041130000 989740 897440 917460 1114450 992600 884560 1164200 1297350 1421040 1510050 FALSE TRUE 951059.8666 871845.8899 1083265.431 1171966.898 1024527.88 902446.4093 1178447.828 1270559.269 1259729.497 1407772.968 0.675577588 0.619308588 0.769488728 0.832497089 0.72776499 0.641045417 0.837100764 0.902531372 0.894838532 1 20.42498326 1.955482547 2.775610353 0.923419307 0.715944978 0.700336305 0.064883937 0.173129361 2.463310774 0.036093026 0.019792248 90.25734351 -1.955482547 -0.207474329 TNHSNIMDDPFIR ddPTM_BT-474_Pertuzumab_2h_R1 4 TNHSNIMDDPFIR 13 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ;;; 158.93 4.03E-05 995860000 791880 857970 732350 808890 866730 850150 794620 365300 870830 791820 FALSE TRUE 760932.4541 833501.5356 864701.936 850636.9098 894609.1576 867340.6155 804344.7973 357756.4273 771977.0292 738189.3261 1.030809343 1.129116212 1.171382334 1.152328921 1.211896631 1.174956864 1.089618569 0.484640477 1.045771053 1 19.49363135 1.955494751 16.15314786 0.786419725 1.147533232 0.437798331 0.149465882 5.776619636 2095.887655 0.058393389 0.037638091 90.25987982 -1.955494751 0.361113508 DLTVLCHLEQLLLVTHLDLSHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLTVLCHLEQLLLVTHLDLSHNR 23 0 Q92696;H0YKZ8;H0YMG5;H0YLG7 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ; 256.53 4.86E-44 449290000 161996 183664 175789 195293 219964 209938 192193 56295 214743 205466 FALSE TRUE 155665.0172 178426.0825 207557.9827 205372.0951 227039.3418 214183.0902 194545.1154 55132.48858 190366.2749 191549.6048 0.812661646 0.931487605 1.083573014 1.072161414 1.185277005 1.118159917 1.015638302 0.287823557 0.993822332 1 17.54735852 1.955542365 24.89877416 0.673995956 1.042344223 0.225292439 0.212486852 425.3190256 238201.8104 0.085356104 0.055092028 90.2697761 -1.955542365 0.368348267 ANAS(ph)PQKPLDLK ddPTM_BT-474_Pertuzumab_2h_R1 4 ANASPQKPLDLK 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK 156.49 3.94E-05 5277400000 14093100 11554900 10333300 9780000 11040000 10889900 12541800 14754300 15401100 15526200 TRUE FALSE 13542326.07 11225365.57 12200757.17 10284746.97 11395111.63 11110101.24 12695290.3 14449618.55 13652831.69 14474596.64 0.935592639 0.775521822 0.842908267 0.710537725 0.787248993 0.767558607 0.877073856 0.998274349 0.943227092 1 23.78701981 1.955571769 3.471182943 0.97711178 0.799241145 0.657598461 0.057067697 0.142103892 3.286827521 0.027042344 0.015634252 90.27588806 -1.955571769 -0.177870635 THTGERPNACADCGK ddPTM_BT-474_Pertuzumab_2h_R1 2 THTGERPNACADCGK 15 1 Q6DD87 Q6DD87 ZNF787 Zinc finger protein 787 0 ; 103.83 0.00086603 114055000 164627 160499 138870 132060 137244 130645 130065 48477 150491 119280 FALSE TRUE 158193.1948 155921.7257 163966.8981 138875.6324 141658.5779 133286.7314 131656.7744 47475.93301 133407.8926 111201.0594 1.422587121 1.402160434 1.474508418 1.248869689 1.273895939 1.198610267 1.183952519 0.426937776 1.199699835 1 16.76281101 1.955577488 9.126166408 0.80943033 1.327126531 0.50919756 0.199220789 0.307517373 60.81106158 0.081795261 0.052172203 90.27707676 -1.955577488 0.517696201 TISINS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 TISINSPK 8 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 TISINS(1)PK;TISINS(1)PK 170.02 0.00031219 671950000 2043500 1624600 1434140 1339900 1595940 1378360 1712620 1947420 2167500 1949160 TRUE FALSE 1963637.761 1578267.999 1693321 1409052.4 1647274.859 1406231.384 1733579.556 1907205.096 1921454.487 1817141.657 1.080618978 0.868544284 0.931859656 0.77542243 0.906519782 0.773869983 0.954014537 1.049563246 1.057404897 1 20.79323946 1.955646521 4.836801381 1.03486749 0.884272008 0.385349403 0.082351631 0.203951544 10.74664692 0.036032066 0.022002824 90.29142794 -1.955646521 -0.150595483 YGDGGSTFQSTTGHCVHMR ddPTM_BT-474_Pertuzumab_2h_R1 7 YGDGGSTFQSTTGHCVHMR 19 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;D6RIT2;H0YBG7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ;;;;;; 176.94 2.38E-14 6104600000 1177521 1521763 1025381 1402041 1297997 1426800 1198254 454137 1142605 1332921 FALSE TRUE 1131502.178 1478363.809 1210690.156 1474400.504 1339748.252 1455650.874 1212918.591 444758.9122 1012901.271 1242641.073 0.910562351 1.18969495 0.974287895 1.186505529 1.078145798 1.171416996 0.976081201 0.357914221 0.815119742 1 20.24497822 1.955746584 10.31545435 0.656067911 1.087880589 0.447647751 0.174355059 0.477512524 109.6186994 0.067517085 0.043226453 90.31223365 -1.955746584 0.431812678 IKGDVDVSVPEVEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKGDVDVSVPEVEGK 15 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 137.19 1.66E-05 242110000 483490 455050 344730 376390 402940 411520 438950 543660 539300 462870 FALSE TRUE 464594.6763 442072.4195 407030.3795 395815.533 415900.931 419841.2164 444322.0014 532433.231 478080.9249 431519.4026 1.076648404 1.024455486 0.943249312 0.917260106 0.963805865 0.972937054 1.029668652 1.233856989 1.107901341 1 18.7190659 1.955770879 7.650098447 1.138461807 0.980956879 0.412856994 0.067896948 0.219581255 33.6479843 0.028741052 0.018203701 90.31728598 -1.955770879 -0.157504928 NHETDGGS(ph)AHGDDDDDGPHFEPVVPLPDKIEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 NHETDGGSAHGDDDDDGPHFEPVVPLPDKIEVK 33 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.173)DGGS(0.827)AHGDDDDDGPHFEPVVPLPDKIEVK;NHETDGGS(1)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.059)DGGS(0.941)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.257)DGGS(0.743)AHGDDDDDGPHFEPVVPLPDKIEVK 289.28 9.43E-90 2236740000 2009513 1764283 1525517 1385297 1450254 1647158 1388688 136955 1738702 850398 TRUE FALSE 1930979.01 1713967.376 1801211.857 1456792.344 1496902.737 1680464.663 1405683.179 134126.8314 1541331.838 792799.786 2.435645221 2.161917052 2.271963097 1.83752868 1.888122025 2.119658321 1.773062006 0.169181215 1.944162783 1 19.59659705 1.955777004 9.200839937 0.949956102 2.09194255 0.553672029 0.431637775 0.30160131 60.52998441 0.172354602 0.109978887 90.31855975 -1.955777004 1.141986448 EIFDDDLEDDALDADEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EIFDDDLEDDALDADEK 17 0 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 0 ;; 386.83 2.06E-121 376389000 843761 785165 907956 996944 951751 871747 1194657 1379281 1513844 1622905 FALSE TRUE 810785.8873 762772.863 1072043.847 1048396.399 982364.9353 889374.3216 1209277.57 1350798.365 1341998.776 1512984.199 0.535885231 0.504151242 0.708562487 0.692932815 0.64928962 0.587827898 0.79926649 0.892804014 0.886987965 1 20.52896549 1.955791483 1.636703054 0.939880736 0.613729266 0.816073946 0.067253817 0.168290091 0.839251054 0.047705455 0.022499166 90.32157093 -1.955791483 -0.32615147 NWRDPDQTDGLGLSYLSSHIANVER ddPTM_BT-474_Pertuzumab_2h_R1 4 NWRDPDQTDGLGLSYLSSHIANVER 25 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;;; 285.95 6.53E-54 4238780000 1503060 1708960 1110580 1378020 1321690 1470420 1325370 1276780 1403180 1313190 FALSE TRUE 1444318.753 1660222.134 1311286.511 1449139.777 1364203.359 1500152.9 1341590.275 1250414.047 1243896.889 1224246.472 1.179761418 1.356117557 1.071096827 1.18369937 1.114320842 1.225368367 1.095849819 1.021374434 1.01605103 1 20.22346261 1.955793864 2.560721851 1.012751561 1.187362783 0.554973113 0.070605075 0.219910671 2.654214696 0.037786154 0.020281913 90.32206631 -1.955793864 0.174611222 DLEIQALHAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLEIQALHAR 10 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 129.89 0.00029116 209630000 220700 304650 290950 263810 308340 318410 241200 184580 197620 217830 FALSE TRUE 212074.8 295961.6803 343531.1371 277425.2657 318258.0361 324848.4684 244151.8778 180768.3585 175187.0061 203076.1801 1.044311548 1.457392394 1.691636789 1.366114261 1.567185457 1.599638462 1.202267433 0.890150477 0.862666444 1 17.6316615 1.955851802 3.314759726 0.913969959 1.465478772 0.670882206 0.168013848 0.142535058 2.971379968 0.082943405 0.047494171 90.33411664 -1.955851802 0.551508813 TLAYLLPAIVHINHQPYLER ddPTM_BT-474_Pertuzumab_2h_R1 2 TLAYLLPAIVHINHQPYLER 20 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 170.14 5.64E-12 1773130000 790390 867060 633690 695970 667120 697090 626100 138125 680030 558680 FALSE TRUE 759500.685 842332.2977 748211.8794 731889.0951 688578.5207 711185.6374 633762.3991 135272.6705 602835.8453 520840.106 1.458222353 1.617256982 1.436548128 1.40520879 1.322053568 1.365458668 1.216807984 0.25972015 1.157429772 1 18.99048102 1.955860271 8.150011885 0.725232105 1.424657386 0.591388961 0.230622255 0.187472026 31.88171129 0.094024033 0.059727274 90.33587817 -1.955860271 0.699425281 THTTALAGRS(ph)PS(ph)PASGR ddPTM_BT-474_Pertuzumab_2h_R1 6 THTTALAGRSPSPASGR 17 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(0.996)PS(0.998)PAS(0.005)GR;THTTALAGRS(1)PS(0.999)PAS(0.001)GR;THTTALAGRS(0.999)PS(0.994)PAS(0.006)GR;T(0.001)HT(0.001)T(0.001)ALAGRS(0.996)PS(0.999)PAS(0.001)GR;THTTALAGRS(0.996)PS(0.988)PAS(0.016)GR;THTTALAGRS(1)PS(1)PASGR 120.23 4.63E-05 15015680000 6065236 7799730 4871125 6374000 6204440 7495460 5269480 858749 4900040 4100240 TRUE FALSE 5828199.872 7577289.337 5751445.645 6702962.904 6404011.447 7647023.337 5333969.473 841015.5331 4343808.002 3822527.093 1.52469812 1.982272239 1.504618674 1.753542288 1.675334482 2.000515144 1.395403968 0.220015585 1.136370756 1 21.8660953 1.955915811 6.824511971 0.719604985 1.735770613 0.711052064 0.271184129 0.104611101 12.94121111 0.107575323 0.067724599 90.34743155 -1.955915811 1.016165627 EILSDDKHDWDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EILSDDKHDWDQR 13 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;C9J668;D6RBU8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 0 ; 155.43 2.39E-05 640910000 625700 650020 538460 581690 604650 660700 688470 659790 821520 781500 FALSE TRUE 601246.9523 631482.066 635771.7 611711.0906 624099.1164 674059.8067 696895.7018 646165.1059 728264.4937 728568.3089 0.825244448 0.866743802 0.87263156 0.839607053 0.856610298 0.925184088 0.956527608 0.88689708 0.999582997 1 19.47470472 1.955934307 0.444475408 1.003995724 0.836672084 0.757427865 0.029880419 0.529811643 0.250433087 0.032571519 0.028323046 90.35127946 -1.955934307 -0.16732364 TIDDLEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIDDLEDK 8 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 179.21 0.00057125 364890000 550150 489330 555320 550410 556030 521250 618880 743720 768570 784930 FALSE TRUE 528649.5298 475374.7875 655678.677 578816.7261 573915.2099 531790.0321 626454.0386 728361.9221 681325.1557 731765.992 0.72242976 0.649626783 0.896022341 0.790986097 0.784287896 0.726721436 0.856085204 0.995348144 0.931069718 1 19.48102284 1.955935078 3.459084859 0.971328846 0.765457316 0.704067245 0.061930194 0.14056284 3.227687545 0.030923509 0.017871949 90.35143979 -1.955935078 -0.20587153 HGTDLWIDNMSSAVPNHS(ph)PEKK ddPTM_BT-474_Pertuzumab_2h_R1 7 HGTDLWIDNMSSAVPNHSPEKK 22 1 Q8N6H7;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSS(0.001)AVPNHS(0.999)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK 309.25 1.78E-67 9703550000 8513900 7604230 7018390 6238590 7011880 7368900 7242370 2434089 9658530 7330150 TRUE FALSE 8181167.375 7387364.806 8286769.196 6560564.378 7237423.488 7517904.207 7331004.29 2383824.212 8562134.166 6833672.411 1.1971846 1.081024135 1.212637759 0.960034954 1.059082592 1.100126514 1.072776664 0.348835014 1.252933072 1 22.70422966 1.955987562 24.99994869 0.773879616 1.096498342 0.145143403 0.224763532 533.6142134 303102.7718 0.088092744 0.056856642 90.36235947 -1.955987562 0.322618726 VAVEEVDEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAVEEVDEEGK 11 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 226.9 1.02E-11 850910000 630380 522580 539810 608640 606730 553500 689800 822270 892940 880630 FALSE TRUE 605744.0527 507676.5301 637365.675 640051.9833 626246.0215 564692.1492 698241.9787 805289.8372 791577.1947 820984.1457 0.737826736 0.618375559 0.776343463 0.779615522 0.762799166 0.687823452 0.850493864 0.980883542 0.964180854 1 19.64699484 1.956043721 2.766048226 0.97983792 0.728434487 0.856827414 0.046575095 0.100317796 1.417771218 0.025309406 0.013873639 90.37404504 -1.956043721 -0.251403432 S(ph)SS(ph)PVTELASR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.999)S(0.038)S(0.963)PVTELASR;S(1)S(0.008)S(0.992)PVTELASR 164.68 3.29E-05 1711550000 777580 746510 695310 789360 718100 745850 803860 863440 970860 906370 TRUE FALSE 747191.3139 725220.2657 820967.9841 830098.9642 741198.3387 760931.598 813697.8791 845609.6623 860652.043 844980.7526 0.884270218 0.858268385 0.971581875 0.982388015 0.877177778 0.900531279 0.962978005 1.000744289 1.018546328 1 19.68855895 1.956050803 2.633680657 1.007158331 0.914352093 0.561705045 0.03730559 0.233924717 2.989355507 0.021512474 0.011638981 90.3755188 -1.956050803 -0.092806238 RDEGSQDQTGSLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDEGSQDQTGSLSR 14 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 0 81.619 0.020844 110710000 69049 54691 58494 52578 53410 59324 56729 44367 65817 55824 FALSE TRUE 66350.48874 53131.26623 69065.16699 55291.55688 55127.98116 60523.57193 57423.26647 43450.80595 58345.73009 52042.99076 1.274916906 1.020911086 1.327079132 1.062420819 1.059277731 1.162953378 1.103381371 0.834902171 1.121106401 1 15.66741625 1.956112038 11.91204622 0.967452953 1.144121314 0.305812842 0.110556936 1.4276031 385.6250516 0.043207394 0.02775343 90.38826248 -1.956112038 0.176668361 S(ph)REDLSALTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SREDLSALTR 10 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)REDLSALTR;S(1)REDLSALTR;S(1)REDLSALTR 176.42 1.51E-06 3829700000 553450 534690 405960 437960 437242 449631 490560 596800 573520 549764 TRUE FALSE 531820.5621 519441.1647 479326.0025 460563.1681 451306.286 458722.8469 496563.62 584475.8714 508416.414 512527.9946 1.037641978 1.013488376 0.935219164 0.898610755 0.880549532 0.89502008 0.968851702 1.140378433 0.991977842 1 18.96727128 1.956130183 11.44655966 1.058509415 0.940553642 0.348561321 0.060629612 1.090867414 282.7431719 0.026714559 0.017146895 90.39203895 -1.956130183 -0.117955773 NRHS(ph)PDHPGMGSSQASSSSSLR ddPTM_BT-474_Pertuzumab_2h_R1 11 NRHSPDHPGMGSSQASSSSSLR 22 1 J3KR33;A0JLT2 J3KR33 MED19 Mediator of RNA polymerase II transcription subunit 19 1 NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(0.999)PDHPGMGS(0.001)SQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR 283.73 4.59E-46 8046654000 917751.4 1036328.2 888907.7 1086935.8 913718 1001163.9 969469.1 237857.86 1067928.9 999499.3 TRUE FALSE 881884.6607 1006773.134 1049553.095 1143032.687 943108.5693 1021408.12 981333.7528 232946.0121 946702.0884 931802.3221 0.946428915 1.080457851 1.126368834 1.226690103 1.01213374 1.096163956 1.053156586 0.249995097 1.015990265 1 19.8296644 1.95629028 24.54350642 0.666889602 1.085820964 0.300714761 0.212865867 317.0867966 178047.2274 0.083060111 0.05360685 90.4253669 -1.95629028 0.418931362 EFDEDS(ph)DEKEEEEDTYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFDEDSDEKEEEEDTYEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 EFDEDS(1)DEKEEEEDTYEK;EFDEDS(1)DEKEEEEDTYEK 284.28 9.62E-40 3041100000 2662800 1797590 2337500 1962350 2160140 2004920 3032500 3865100 4443100 4165000 TRUE FALSE 2558734.832 1746324.493 2759938.247 2063627.119 2229622.865 2045460.856 3069612.642 3785284.334 3938737.915 3882900.84 0.658975065 0.449747383 0.710792874 0.531465315 0.574215762 0.526786787 0.790546236 0.974859902 1.014380247 1 21.88870343 1.956412947 2.417398591 1.000331436 0.573227449 0.878927121 0.070099316 0.086787968 0.933395677 0.035934116 0.018987995 90.4509114 -1.956412947 -0.427103987 SVVLYVILAPFDNEQSDLVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVVLYVILAPFDNEQSDLVHR 21 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 146.64 1.07E-07 293640000 424900 446720 380320 415570 388800 465870 424940 313540 466530 468950 FALSE TRUE 408294.4382 433979.983 449052.2842 437017.6175 401306.1051 475290.2106 430140.5428 307065.2894 413571.4703 437187.5988 0.933911299 0.992663068 1.027138659 0.999611194 0.917926552 1.087153917 0.983880934 0.702365049 0.945981705 1 18.73789295 1.956469299 24.83470875 0.848064436 0.995149532 0.226125524 0.085515045 418.7546701 238903.0813 0.033465187 0.021599093 90.46264852 -1.956469299 0.147085097 FHWEQDQIAHMK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHWEQDQIAHMK 12 0 Q9UG63;Q9UG63-2 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ; 117.79 0.00040209 353294000 384703 366677 333007 348820 379271 352008 357985 90544 423928 381019 FALSE TRUE 369668.3814 356219.731 393188.7726 366822.642 391470.5962 359125.8429 362366.1275 88674.23476 375805.4707 355212.2438 1.040697183 1.002836296 1.106912218 1.032685805 1.102075176 1.011017636 1.020139744 0.249637326 1.057974429 1 18.43832179 1.956485982 24.99013137 0.673094674 1.048514308 0.230311555 0.210807698 431.3289373 247711.8974 0.081841029 0.052823261 90.46612368 -1.956485982 0.375419634 HCQLEPDHEGVPEETDDFGEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 HCQLEPDHEGVPEETDDFGEFR 22 0 E9PFH4;C9J7E5;Q9Y5L0-5;Q9Y5L0-3;Q9Y5L0;Q9Y5L0-1 E9PFH4 TNPO3 Transportin-3 0 ; 186.55 1.82E-17 364640000 271230 254846 230116 257916 260796 276598 257557 85503 308720 278587 FALSE TRUE 260630.0317 247578.0416 271703.0801 271227.0757 269184.7402 282191.0011 260709.0596 83737.33317 273675.3999 259718.0544 1.003511413 0.953256955 1.046146294 1.04431352 1.036449857 1.086528242 1.003815696 0.322416296 1.053740375 1 17.98658678 1.956501085 24.99918342 0.703352715 1.02838054 0.198586383 0.191353457 456.314011 262246.6791 0.074619711 0.048161172 90.4692697 -1.956501085 0.325027825 KQNS(ph)PVAPTAQPK ddPTM_BT-474_Pertuzumab_2h_R1 4 KQNSPVAPTAQPK 13 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 KQNS(1)PVAPTAQPK;KQNS(1)PVAPTAQPK;KQNS(1)PVAPTAQPK;KQNS(1)PVAPTAQPK 159.81 2.53E-05 5453200000 7583900 6523300 6560900 6379600 6776900 7180100 7428900 8388500 9036400 9102800 TRUE FALSE 7287512.804 6337261.871 7746600.576 6708851.921 6994885.143 7325286.541 7519817.1 8215274.544 8010625.756 8486259.248 0.858742656 0.746767414 0.912840434 0.790554675 0.824260129 0.86319382 0.886116825 0.968067826 0.943952514 1 23.01669732 1.956510229 1.215661756 0.982618477 0.82415109 0.683773089 0.042437675 0.247617926 0.676017292 0.030064895 0.013542662 90.47117473 -1.956510229 -0.158467387 HQAS(ph)DS(ph)ENEEPPKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HQASDSENEEPPKPR 15 1 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 HQAS(1)DS(1)ENEEPPKPR 72.916 0.022376 284860000 602350 519600 526050 587330 533810 521570 551340 301280 739160 545690 TRUE FALSE 578809.4961 504781.5167 621118.9369 617642.1717 550980.4834 532116.5028 558087.4638 295058.4627 655253.6556 508729.9302 1.137753967 0.992238684 1.220920768 1.214086561 1.083051047 1.045970506 1.097021092 0.579990374 1.288018685 1 18.95654045 1.956667231 24.9991898 0.891627831 1.113973251 0.113822294 0.175617189 627.4140265 361961.6413 0.069759684 0.0450268 90.5038868 -1.956667231 0.222345419 SEPVKEES(ph)SELEQPFAQDTSSVGPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEPVKEESSELEQPFAQDTSSVGPDR 26 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 S(0.03)EPVKEES(0.733)S(0.237)ELEQPFAQDTSSVGPDR;SEPVKEES(0.794)S(0.206)ELEQPFAQDTSSVGPDR 226.64 9.10E-35 809330000 496448 403357 395007 405320 471020 480046 522510 544453 648349 655020 TRUE FALSE 477046.2633 391853.6533 466393.5518 426238.6138 486170.7861 489752.859 528904.6337 533209.8553 574751.1396 610654.912 0.781204333 0.641694099 0.763759601 0.698002432 0.796146525 0.802012478 0.86612688 0.873177051 0.941204481 1 19.2199978 1.956746467 0.531712329 0.999751644 0.703276363 0.848304805 0.039747749 0.276824734 0.16884585 0.035047791 0.024883447 90.52040052 -1.956746467 -0.296475281 QYTS(ph)PEEIDAQLQAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QYTSPEEIDAQLQAEK 16 0 Q13442;F8WBW6 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 QYTS(1)PEEIDAQLQAEK;QYT(0.034)S(0.966)PEEIDAQLQAEK 285.34 8.26E-36 214620000 615980 519170 486210 440280 546250 533060 546670 612480 653680 603990 TRUE FALSE 591906.8206 504363.7799 574078.9627 463002.9036 563820.6273 543838.8384 553360.311 599832.074 579476.9869 563081.2193 1.051192617 0.89572119 1.019531362 0.822266642 1.001313146 0.965826633 0.982736223 1.065267413 1.029117944 1 19.10298351 1.957014138 3.973547234 1.037102551 0.955576667 0.206257881 0.062523975 0.300505994 9.628903711 0.027338237 0.016245397 90.57620857 -1.957014138 -0.081525884 HDDPALTLVAGLTSNKPTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 HDDPALTLVAGLTSNKPTDK 20 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;Q6XYB5;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 163.18 1.20E-11 1223790000 368270 362810 295750 321050 349370 332940 341830 241030 434870 435880 FALSE TRUE 353877.6013 352463.014 349198.6039 337619.429 360607.8033 339672.2749 346013.4178 236052.6463 385505.3807 406357.4594 0.870852972 0.867371832 0.859338486 0.830843439 0.887415243 0.835895262 0.851500101 0.580899011 0.94868538 1 18.63238985 1.957020992 24.99977243 0.776520931 0.857813379 0 0.109635396 1079.228866 627757.7667 0.043340188 0.027977793 90.57763803 -1.957020992 0.081292449 DLDELDKDHLQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDELDKDHLQLR 13 1 Q8WXH0;Q8WXH0-2;G3V5X4;A0A0A0MRE3;A0A669KB61;A0A669KBG2 Q8WXH0 SYNE2 Nesprin-2 0 ; 224.42 8.50E-12 266399000 469240 471710 384070 411740 421100 399780 447160 535870 552670 462480 FALSE TRUE 450901.582 458257.2927 453479.9926 432989.9507 434645.0639 407863.8255 452632.4778 524804.0972 489933.2186 431155.8177 1.045797282 1.062857728 1.051777511 1.004253991 1.008092773 0.945977785 1.04981183 1.217202867 1.136325195 1 18.71784982 1.957086601 11.25915403 1.139937614 1.019963698 0.337073501 0.059115692 0.89559441 233.212978 0.024058581 0.015443791 90.59132286 -1.957086601 -0.119973916 FLQEHGSDS(ph)FLAEHK ddPTM_BT-474_Pertuzumab_2h_R1 4 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 FLQEHGS(0.015)DS(0.985)FLAEHK;FLQEHGS(0.002)DS(0.998)FLAEHK;FLQEHGS(0.001)DS(0.999)FLAEHK;FLQEHGSDS(1)FLAEHK 249.06 2.92E-18 1503720000 1440830 1449980 1264010 1303550 1481050 1542830 1427240 881450 1848030 1609360 TRUE FALSE 1384520.771 1408627.99 1492444.725 1370826.372 1528689.318 1574027.08 1444706.99 863247.7495 1638249.382 1500356.614 0.92279446 0.938862119 0.994726661 0.91366703 1.01888398 1.04910197 0.962909069 0.575361712 1.091906662 1 20.51687402 1.957086625 24.9990233 0.823714396 0.974677665 0.008432492 0.134266458 716.8583154 417602.011 0.053333451 0.034422322 90.59132769 -1.957086625 0.150963268 RAHT(ph)PTPGIYMGR ddPTM_BT-474_Pertuzumab_2h_R1 5 RAHTPTPGIYMGR 13 1 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RAHT(0.999)PT(0.001)PGIYMGR;RAHT(0.991)PT(0.009)PGIYMGR;RAHT(0.999)PT(0.001)PGIYMGR;RAHT(0.999)PT(0.001)PGIYMGR;RAHT(0.996)PT(0.004)PGIYMGR 138.66 2.73E-05 2949200000 609250 698210 453011 530330 574380 662790 519401 426838 493282 483531 TRUE FALSE 585439.8364 678297.7344 534880.1649 557700.3949 592855.4543 676192.0679 525757.5848 418023.6461 437286.6954 450781.0147 1.298723365 1.50471673 1.186563204 1.237186964 1.315173965 1.500045578 1.166325927 0.927331969 0.970064579 1 18.78206723 1.957125103 4.210209057 0.968965392 1.335914294 0.750084522 0.096766912 0.1091186 4.045272221 0.045495614 0.027298949 90.59935435 -1.957125103 0.366948902 NKPSDLGTK ddPTM_BT-474_Pertuzumab_2h_R1 4 NKPSDLGTK 9 1 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 114.86 0.0014312 4621830000 4306430 4356480 3512100 3671850 4022630 4399090 4707110 5468720 6634530 5813760 FALSE TRUE 4138129.955 4232237.456 4146814.596 3861354.619 4152021.547 4488042.614 4764717.02 5355789.021 5881405.969 5419988.857 0.763494181 0.780857225 0.765096517 0.712428516 0.766057211 0.828053845 0.879100889 0.988154987 1.085132483 1 22.36985845 1.957218313 1.347267769 1.045816449 0.757826116 0.940261834 0.029246037 0.092757715 0.312418001 0.021491146 0.009761326 90.61880119 -1.957218313 -0.287990333 DKLDETGNSLK ddPTM_BT-474_Pertuzumab_2h_R1 3 DKLDETGNSLK 11 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ;; 167.98 1.70E-05 795020000 1120220 955640 802235 810810 913380 1003700 1068630 1131740 1336990 1293640 FALSE TRUE 1076440.564 928386.0829 947216.7101 852656.0013 942759.6972 1023995.502 1081708.214 1108369.174 1185220.5 1206020.611 0.892555695 0.769792883 0.785406735 0.706999527 0.781711099 0.849069653 0.896923489 0.919030043 0.982753106 1 20.20182313 1.957244973 1.060876385 0.989425916 0.78230721 0.756717286 0.045181828 0.252207157 0.521922509 0.037134002 0.016876054 90.62436437 -1.957244973 -0.207118706 ELSNSVSTYRPFGLGSES(ph)PYKQPSDGMER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSNSVSTYRPFGLGSESPYKQPSDGMER 29 2 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ELSNS(0.001)VS(0.006)T(0.006)YRPFGLGS(0.035)ES(0.951)PYKQPSDGMER 89.577 0.00087036 190260000 56448 52385 51637 55423 52898 50264 55172 72510 65376 60154 TRUE FALSE 54241.94975 50891.03109 60968.95456 58283.38767 54599.51221 51280.37252 55847.21144 71012.64316 57954.79056 56079.716 0.967229395 0.907476619 1.087183725 1.039295343 0.973605362 0.914419262 0.995854035 1.266280363 1.033435878 1 15.77519142 1.957346646 23.65411893 1.129886048 0.982727641 0.2712751 0.08339039 253.0795063 140348.5944 0.033916732 0.021890727 90.64558283 -1.957346646 -0.147158408 DLIALANTAGEVLLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLIALANTAGEVLLHR 16 0 Q9UJX5;Q9UJX5-3;D6RFM7;D6RAP6;Q9UJX5-2 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 0 97.904 0.002915 42526000 116510 127000 132640 94692 123550 128410 114150 72002 117680 123290 FALSE TRUE 111956.6604 123378.0843 156610.9986 99579.06547 127524.098 131006.5382 115547.0018 70515.13354 104321.4598 114939.4585 0.974048963 1.073418006 1.362552083 0.866361011 1.109489288 1.139787327 1.005285768 0.613498049 0.907620943 1 16.81051463 1.957376246 9.110498281 0.799904297 1.088992809 0.340488082 0.150747478 0.404663744 83.19117072 0.060918585 0.038903118 90.6517611 -1.957376246 0.289088512 HGTDLWIDNMSSAVPNHS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGTDLWIDNMSSAVPNHSPEK 21 0 Q8N6H7;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 HGTDLWIDNMSSAVPNHS(1)PEK;HGTDLWIDNMSSAVPNHS(1)PEK 180.09 9.22E-17 625850000 326610 323410 351750 423890 336020 370600 357200 108167 443340 386900 TRUE FALSE 313845.7201 314186.6635 415319.0496 445767.0137 346828.3885 378093.7859 361571.5205 105933.3137 393013.9018 360694.9184 0.870114061 0.871059301 1.151441366 1.235856096 0.961556071 1.048237074 1.002430314 0.293692282 1.089601993 1 18.46041957 1.957400087 24.9989948 0.698979791 1.028557342 0.132964456 0.228104463 571.2677659 335237.4736 0.091881426 0.0593032 90.65673768 -1.957400087 0.329577551 SS(ph)TPPLHVHVDENTPVHVHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTPPLHVHVDENTPVHVHIK 21 0 Q5BJF6-9;Q5BJF6-3;Q5BJF6-4 Q5BJF6-9 ODF2 Outer dense fiber protein 2 1 S(0.26)S(0.37)T(0.37)PPLHVHVDENTPVHVHIK 248.45 7.42E-31 992750000 594220 565590 490950 507920 603720 548510 477490 14473 689940 183530 TRUE FALSE 570997.2255 549459.927 579675.5861 534133.8121 623139.2021 559601.248 483333.6655 14174.12749 611620.9037 171099.3496 3.33722616 3.211350179 3.387947338 3.121775818 3.641972944 3.270621713 2.824871436 0.082841504 3.574653586 1 17.38447475 1.957422272 10.615833 1.449962698 3.30744108 0.481998709 0.821595028 0.588818681 145.0453011 0.318230105 0.204065076 90.66136886 -1.957422272 1.857478382 PIS(ph)PSPSAILER ddPTM_BT-474_Pertuzumab_2h_R1 2 PISPSPSAILER 12 0 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P2-8;Q5T5P2-6;Q5T5P1;Q5T5P2-4;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 PIS(0.987)PS(0.013)PSAILER;PIS(0.993)PS(0.007)PSAILER 184.96 1.43E-05 955520000 390700 371370 396130 409930 396290 369830 427950 478360 546990 461180 TRUE FALSE 375431.0121 360778.8912 467719.5029 431086.5364 409037.0278 377308.216 433187.3801 468481.6988 484897.9884 429943.8678 0.873209366 0.839130217 1.087861784 1.002657716 0.951373094 0.877575526 1.007544037 1.089634564 1.127816966 1 18.71378879 1.957444999 4.211780403 1.078104937 0.943928643 0.400938895 0.073186899 0.231707504 8.610452568 0.035335573 0.021211956 90.66611337 -1.957444999 -0.134176294 SST(ph)PGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTPGLK 7 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 SS(0.056)T(0.944)PGLK 109.71 0.07787 956730000 4338600 3943600 3429600 3371600 3567700 3505200 4090900 4851900 5027000 4933500 TRUE FALSE 4169042.715 3831132.389 4049405.011 3545608.68 3682458.311 3576077.546 4140965.658 4751706.569 4456356.035 4599349.651 0.906441787 0.832972633 0.880429913 0.770893485 0.800647611 0.777518088 0.900337216 1.033125753 0.968910036 1 22.13299845 1.957447585 4.271753675 0.999571921 0.827121915 0.769817183 0.042174418 0.100893555 3.887666892 0.019860083 0.011948348 90.66665318 -1.957447585 -0.172450006 THVADFAPEVAWVTR ddPTM_BT-474_Pertuzumab_2h_R1 4 THVADFAPEVAWVTR 15 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;;; 180.62 6.22E-07 1411620000 1369940 1405580 1210610 1414030 1319100 1408760 1347620 480414 1504180 1416530 FALSE TRUE 1316401.23 1365494.235 1429394.157 1487008.258 1361530.049 1437246.092 1364112.577 470493.283 1333431.792 1320587.161 0.99683025 1.034005384 1.082392892 1.126020532 1.031003548 1.088338683 1.032959139 0.356275827 1.009726455 1 20.33274809 1.957517901 24.83681697 0.71151107 1.06127065 0.30014821 0.175935724 372.510281 217784.5205 0.068267375 0.044066305 90.68133417 -1.957517901 0.34975958 HEDGDSNGTFFVYHAIYLEELTAVELTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEDGDSNGTFFVYHAIYLEELTAVELTEK 29 0 F8VX55;Q12800-2;Q12800-3;Q12800-4;Q12800;F8VWL0 F8VX55 TFCP2 Alpha-globin transcription factor CP2 0 121.35 1.65E-05 11481000 13507 11190 10758 10330 11527 11631 11362 4667 13720 10334 FALSE TRUE 12979.13151 10870.87216 12702.20991 10863.13254 11897.77642 11866.18679 11501.05155 4570.624819 12162.56312 9634.068975 1.347211811 1.12837807 1.318467819 1.127574711 1.234968989 1.231690039 1.193789621 0.474423095 1.262453398 1 13.23392954 1.957578789 24.59742494 0.848947402 1.224989379 0.341780356 0.194091975 339.5395526 196877.2353 0.074623004 0.048163526 90.69404849 -1.957578789 0.376041976 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGS(ph)QPDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLR 48 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGS(0.001)EGLGS(0.001)AAHGS(0.998)QPDLR;FQPQLNPDVVAPLPT(0.005)HT(0.004)AHEDFT(0.006)FGES(0.004)RPELGS(0.05)EGLGS(0.116)AAHGS(0.816)QPDLR 242.46 2.79E-61 9987900000 532912 703380 608940 832350 689290 694540 673750 71716 748700 669550 TRUE FALSE 512085.2099 683320.2911 718989.0038 875307.6832 711461.6388 708584.0747 681995.554 70235.03954 663710.7148 624200.7821 0.820385402 1.094712328 1.151855339 1.402285464 1.139796135 1.135186137 1.092590034 0.112519948 1.063296833 1 19.25165064 1.957627694 24.60460701 0.620635949 1.135378739 0.275977715 0.277570243 368.391313 213915.5321 0.11027512 0.071175008 90.70426199 -1.957627694 0.51474279 GHPHSAS(ph)SPSER ddPTM_BT-474_Pertuzumab_2h_R1 1 GHPHSASSPSER 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 GHPHSAS(0.599)S(0.395)PS(0.006)ER 171.21 2.52E-05 1192100000 519750 644370 591250 732480 640750 696680 535010 42784 491360 518580 TRUE FALSE 499437.5954 625993.1985 698102.0273 770283.3806 661360.3057 710767.3469 541557.6124 41900.49545 435582.8727 483456.1147 1.033056735 1.294829416 1.443982207 1.59328501 1.367984157 1.470179661 1.120179466 0.086668664 0.900977068 1 18.88302541 1.957676009 7.917853541 0.569064995 1.371415369 0.57543107 0.267081699 0.174616688 29.52594856 0.109202122 0.069393857 90.71435329 -1.957676009 0.802350374 HEAMITDLEER ddPTM_BT-474_Pertuzumab_2h_R1 2 HEAMITDLEER 11 0 P35579 P35579 MYH9 Myosin-9 0 ; 172.13 1.37E-05 2242660000 1842990 1964110 1798950 2266300 2002410 2065710 2027400 1566170 2296700 2323100 FALSE TRUE 1770963.913 1908095.506 2124060.282 2383264.015 2066819.336 2107480.072 2052211.928 1533828.042 2035988.245 2165754.368 0.817712267 0.881030432 0.98074847 1.100431355 0.954318443 0.973092841 0.947573722 0.708218838 0.940082714 1 21.0464382 1.957773794 24.98466082 0.844734319 0.956633251 0.050087816 0.099189599 764.5932579 452398.1048 0.041523085 0.026798276 90.73478068 -1.957773794 0.111898932 KMEEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KMEEVK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 105.95 0.052177 973370000 1695690 1628680 1348090 1399940 1535690 1247630 1653810 1899250 2049960 2025940 FALSE TRUE 1629420.56 1582231.641 1591719.851 1472191.071 1585086.864 1272857.933 1674049.821 1860029.824 1817257.135 1888721.279 0.862710966 0.83772638 0.842749996 0.779464438 0.839238103 0.673925765 0.886340319 0.984809058 0.962162684 1 20.84897839 1.957783057 4.869298372 0.973261915 0.807111002 0.702937957 0.051178703 0.116911898 6.373885835 0.022910667 0.014038489 90.73671604 -1.957783057 -0.166150913 AAAAAAGSGT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAAAAGSGTPR 12 0 Q9NR33 Q9NR33 POLE4 DNA polymerase epsilon subunit 4 1 AAAAAAGS(0.056)GT(0.944)PR 100.69 0.034545 112370000 89696 87714 77800 70246 75815 90223 60145 73622 68329 63631 TRUE FALSE 86190.58116 85212.4826 91860.19065 73871.40448 78253.65833 92047.37088 60881.0725 72101.67997 60572.57838 59321.21569 1.452946979 1.436458805 1.548521715 1.245277994 1.319151292 1.551677082 1.026295092 1.215445084 1.021094691 1 15.85626054 1.957796826 0.779384906 0.994483248 1.441277918 0.635312277 0.123315325 0.402770029 0.460006806 0.104291276 0.053149808 90.7395928 -1.957796826 0.446794671 HGAGAEISTVNPEQYSK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGAGAEISTVNPEQYSK 17 0 P78356;P48426-2;P48426;H7BXS3 P78356 PIP4K2B;PIP4K2A Phosphatidylinositol 5-phosphate 4-kinase type-2 beta;Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha 0 ; 216.71 1.07E-17 928510000 800670 847380 754690 768480 804070 842250 816050 654340 970970 902080 FALSE TRUE 769378.9312 823213.5521 891079.271 808141.3449 829933.6418 859280.8721 826037.064 640827.6503 860749.5562 840981.3181 0.914858529 0.978872579 1.059570827 0.960950413 0.986863351 1.021759763 0.982229981 0.761999864 1.023506156 1 19.68171423 1.957801239 24.99922228 0.894571865 0.989953125 0.058183324 0.076016739 657.0118537 389223.3729 0.030117263 0.019442324 90.74051481 -1.957801239 0.09538126 ALEHAFQLEHIMDLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEHAFQLEHIMDLTR 16 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 212.9 1.91E-12 1215800000 491630 595170 502620 516390 578750 559180 543080 239610 630990 585390 FALSE TRUE 472416.5561 578196.3343 593454.6147 543040.9498 597366.0194 570487.0027 549726.3755 234661.9698 559362.6605 545741.0139 0.865642391 1.059470188 1.087429018 0.995052481 1.094596162 1.045343832 1.007302661 0.429987785 1.02495991 1 19.05785694 1.957802996 24.93076848 0.745897083 1.030491616 0.204033039 0.167058626 460.614088 272138.6288 0.065115203 0.042030972 90.74088194 -1.957802996 0.284594533 PASTPPIMASAIKDEDDEDRIIAELEVFER ddPTM_BT-474_Pertuzumab_2h_R1 3 PASTPPIMASAIKDEDDEDRIIAELEVFER 30 2 A0A087WTE6 A0A087WTE6 SRCIN1 0 ;; 166.35 1.58E-12 65319000 62856 57565.2 48202.5 51721.6 61331 56697 64796.9 70041.8 87064 73016 FALSE TRUE 60399.51803 55923.49686 56913.76401 54390.95797 63303.76731 57843.45219 65589.90385 68595.41235 77180.85972 68070.56128 0.887307478 0.821551869 0.836099526 0.799037895 0.929972754 0.849757239 0.963557559 1.007710397 1.1338361 1 16.05474339 1.957928263 1.438361808 1.065460755 0.847257221 0.7732703 0.047401047 0.175845713 0.676496196 0.031733228 0.014567996 90.7670589 -1.957928263 -0.218203534 THEAQIQEMR ddPTM_BT-474_Pertuzumab_2h_R1 7 THEAQIQEMR 10 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;; 186.74 1.31E-06 5449870000 1889132 2094591 1603992 1986305 1845354 1845095 1863183 916340 2043691 1905117 FALSE TRUE 1815302.633 2034855.315 1893869.035 2088818.439 1904711.487 1882404.085 1885985.191 897417.2588 1811699.766 1776081.729 1.022082826 1.145699144 1.06631863 1.176082387 1.072423333 1.059863437 1.061879732 0.505279258 1.020054278 1 20.76026654 1.957933434 22.84088961 0.786001041 1.092069872 0.373336038 0.140107083 136.0788255 73886.09639 0.054255381 0.035016932 90.76813967 -1.957933434 0.306068831 RGDGDLEDQEEDIDQIVAEIK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDGDLEDQEEDIDQIVAEIK 21 1 Q99767;Q99767-2;H0YMS0 Q99767 APBA2 Amyloid beta A4 precursor protein-binding family A member 2 0 ; 172 9.90E-12 66320000 109731 105690 94765 97470 103500 101333 110079 133002 134568 120171 FALSE TRUE 105442.5912 102675.8247 111891.1435 102500.4384 106829.1715 103382.0227 111426.1797 130255.4622 119292.4048 112031.7111 0.941185225 0.916488944 0.998745287 0.914923439 0.953561902 0.922792499 0.994595 1.162666007 1.064809272 1 16.77354763 1.957998965 6.242325278 1.091256348 0.943217017 0.64809879 0.043907353 0.106587472 11.16997873 0.017732833 0.011124575 90.78183677 -1.957998965 -0.148039331 HEDVCTALLITAFNSLAWK ddPTM_BT-474_Pertuzumab_2h_R1 2 HEDVCTALLITAFNSLAWK 19 0 Q9HAV4;H0Y3W3 Q9HAV4 XPO5 Exportin-5 0 ; 209.31 2.29E-16 170245000 321250 292990 250250 231854 310530 301100 284670 184430 330620 304560 FALSE TRUE 308695.1948 284634.2121 295475.7418 243820.0127 320518.4795 307188.4483 288153.8766 180621.456 293089.4037 283931.8799 1.08721569 1.002473594 1.040657153 0.858727145 1.128856962 1.081908972 1.014869752 0.636143627 1.032252538 1 18.11518532 1.958123209 24.99314386 0.843154268 1.030292225 0.193025854 0.122126003 542.5845619 323827.5744 0.048489151 0.031291802 90.80781154 -1.958123209 0.187137957 S(ph)LPTTVPESPNYR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 S(1)LPTTVPESPNYR;S(0.994)LPT(0.005)T(0.001)VPESPNYR;S(0.994)LPT(0.005)T(0.001)VPESPNYR 237.41 1.01E-16 1258490000 496132 521447 359609 472858 428854 427088 381998 462002 393047 376619 TRUE FALSE 476742.6129 506575.8421 424598.3458 497262.258 442648.4784 435724.012 386673.0058 452461.4973 348429.9523 351110.2597 1.357814532 1.442782796 1.209302019 1.416256701 1.260710749 1.240989119 1.101286548 1.288659288 0.992366195 1 18.42156463 1.95821395 0.346520639 0.974823869 1.41500498 0.655026338 0.088524443 0.833166435 0.283263309 0.112926671 0.12768345 90.82678667 -1.95821395 0.440181111 NESEDNKFS(ph)DDS(ph)DDDFVQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NESEDNKFSDDSDDDFVQPR 20 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 2 NESEDNKFS(1)DDS(1)DDDFVQPR;NESEDNKFS(1)DDS(1)DDDFVQPR 263.25 1.00E-36 584630000 1375120 1206290 984790 953410 1088000 1081000 1253610 1604170 1651960 1413800 TRUE FALSE 1321378.79 1171887.79 1162763.46 1002615.604 1122996.508 1102858.561 1268952.054 1571043.329 1464436.426 1318042.067 1.002531576 0.889112586 0.882189946 0.760685588 0.852018715 0.836740032 0.962755352 1.191952342 1.111069566 1 20.32996499 1.958258682 4.55110907 1.116222733 0.867530802 0.673434368 0.071482263 0.112877896 5.154360428 0.032647818 0.019843596 90.83614231 -1.958258682 -0.248691931 TVSS(ph)PPTS(ph)PRPGSAATVSASTSNIIPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.065)VS(0.432)S(0.502)PPT(0.187)S(0.813)PRPGSAATVSASTSNIIPPR;T(0.018)VS(0.164)S(0.814)PPT(0.091)S(0.912)PRPGSAATVSASTSNIIPPR 108.9 0.00042162 6212800000 631130 682040 586910 766650 704660 765300 735540 1392850 735750 961940 TRUE FALSE 606464.7418 662588.887 692977.6927 806216.8984 727326.0289 780774.8903 744541.7585 1364087.161 652230.7445 896786.947 0.676264016 0.738847604 0.77273392 0.899006058 0.811035476 0.870635877 0.8302326 1.521082756 0.727297322 1 19.77440575 1.958264147 24.9352868 1.149433164 0.801169094 0.294199678 0.193246272 447.0490053 267090.9216 0.076015014 0.049063666 90.83728542 -1.958264147 -0.34826407 S(ph)ESELIDELSEDFDR ddPTM_BT-474_Pertuzumab_2h_R1 6 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 S(0.999)ES(0.001)ELIDELSEDFDR;S(0.922)ES(0.078)ELIDELSEDFDR;S(0.986)ES(0.014)ELIDELSEDFDR;S(0.999)ES(0.001)ELIDELSEDFDR;S(1)ESELIDELSEDFDR;S(0.886)ES(0.114)ELIDELSEDFDR 363.83 8.37E-85 439577000 207552 223072 200611 224077 244491 217368 214102 217875 223482 228114 TRUE FALSE 199440.6384 216710.205 236865.8703 235641.6408 252355.2751 221763.3299 216722.2443 213375.8051 198113.2603 212663.6356 0.937822011 1.019028027 1.113805233 1.108048587 1.186640463 1.042789141 1.019084639 1.003348807 0.931580332 1 17.69821384 1.958385852 1.823230248 0.973401403 1.075122405 0.289582607 0.06389182 0.470543869 2.905424048 0.042980518 0.020927773 90.86274487 -1.958385852 0.101721002 HLVDETMDPFVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLVDETMDPFVDR 13 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 0 ; 202.32 9.48E-08 587950000 143425 163890 141418 150216 152926 156235 152606 93840 166517 167157 FALSE TRUE 137819.7924 159216.0177 166975.3784 157968.6658 157845.0037 159394.1787 154473.6379 91902.17121 147614.6883 155835.3075 0.884393881 1.021694122 1.071486181 1.013689826 1.012896283 1.022837387 0.991262124 0.589739082 0.947248031 1 17.24966262 1.958423437 24.99275321 0.797683415 1.00895248 0.261969318 0.112410349 439.8992886 264434.2686 0.043914448 0.0283453 90.8706086 -1.958423437 0.211269065 EGDNVNYDWIHWDPEHSYEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGDNVNYDWIHWDPEHSYEFK 21 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ; 296.69 3.85E-55 663270000 565440 613470 459130 474630 468190 493420 455580 70135 540140 375000 FALSE TRUE 543341.9797 595974.4362 542105.0043 499125.7112 483249.7565 503397.2905 461155.5243 68686.68774 478825.5717 349600.916 1.554177792 1.704727903 1.550639542 1.427701383 1.382289732 1.439919827 1.319091293 0.196471704 1.369634774 1 18.41534944 1.958427439 11.66181182 0.763688295 1.500186246 0.505131885 0.285453136 0.817822668 228.1411628 0.113961342 0.073248583 90.871446 -1.958427439 0.736497951 HDELADSLPCAEGEFIFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HDELADSLPCAEGEFIFLR 19 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 174.23 4.89E-12 484670000 201827 186512 167440 210660 205250 199552 194692 95016 210347 210240 FALSE TRUE 193939.3777 181192.8604 197700.1327 221532.1878 211852.0527 203587.0782 197074.6989 93053.8864 186469.2904 196000.2575 0.989485321 0.924452155 1.008672821 1.130264779 1.080876399 1.038708218 1.005481837 0.474764103 0.951372681 1 17.58049602 1.95843367 24.83207448 0.747795127 1.029409831 0.299663704 0.14336811 397.703709 237590.9018 0.057050364 0.036826044 90.87274976 -1.95843367 0.281614705 RS(ph)PRPDHPGT(ph)PPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPRPDHPGTPPHK 14 2 P30291 P30291 WEE1 Wee1-like protein kinase 2 RS(1)PRPDHPGT(1)PPHK 134.9 6.81E-05 64379000 73891 73921 59705 59547 63457 71772 66795 37635 74024 72603 TRUE FALSE 71003.25803 71812.84546 70495.02163 62620.22781 65498.15204 73223.27901 67612.45719 36857.8241 65621.10585 67685.53414 1.049016735 1.060977746 1.041507946 0.925164123 0.967683167 1.081815782 0.998920346 0.544545073 0.969499712 1 16.04655991 1.95847576 24.8489166 0.783489676 1.01894027 0.274343885 0.125350152 415.7733626 248806.2415 0.04940495 0.03189017 90.88155721 -1.95847576 0.235450594 EEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 6 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 2 EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK 182.95 1.60E-14 2206511000 3795550 3176680 3110010 3263130 3108200 3007550 3527020 4197920 4069970 4408000 TRUE FALSE 3647215.71 3086084.197 3672057.989 3431540.53 3208178.076 3068364.722 3570184.726 4111231.485 3607964.068 4109442.234 0.887520861 0.750973982 0.893566032 0.835038026 0.780684554 0.746662089 0.868775985 1.0004354 0.877969287 1 21.97051116 1.958515627 5.887269813 0.954868213 0.814842615 0.564118242 0.056439178 0.144536766 13.17856575 0.023589066 0.01474253 90.88990019 -1.958515627 -0.140025598 RS(ph)SLLSLMTGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSLLSLMTGK 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RS(0.5)S(0.5)LLSLMTGK 189.32 1.69E-06 606120000 712690 920540 776280 770730 714890 639410 828440 1104100 1068700 875290 TRUE FALSE 684837.2869 894287.1005 916571.0643 810507.4677 737885.0861 652339.3083 838578.6965 1081299.949 947385.6564 816005.8287 0.839255386 1.095932246 1.12324083 0.993261861 0.90426448 0.799429717 1.027662631 1.325113021 1.161003541 1 19.63821993 1.95853406 10.65239082 1.192922358 0.967097197 0.351537436 0.120739799 0.797290855 202.4385144 0.051697361 0.033175103 90.89375816 -1.95853406 -0.225825162 HLNRPTLDDS(ph)SEEEHAIEITTQEITQLFHR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLNRPTLDDSSEEEHAIEITTQEITQLFHR 30 1 H3BU86;O14662;F8W9Z6;B7ZBM8;O14662-6;O14662-2;O14662-5;B7ZBM4;B7ZBM5;Q96NX8;O14662-4 H3BU86;Q96NX8 STX16-NPEPL1;STX16 Syntaxin-16 1 HLNRPTLDDS(0.5)S(0.5)EEEHAIEITTQEITQLFHR;HLNRPT(0.003)LDDS(0.499)S(0.499)EEEHAIEITTQEITQLFHR;HLNRPT(0.008)LDDS(0.495)S(0.495)EEEHAIEIT(0.001)T(0.001)QEITQLFHR 209.18 4.05E-26 76100000 15897.6 27426.7 15886.3 27045 22297.6 23087.2 20223.5 11461.6 24259.6 15868.5 TRUE FALSE 15276.30422 26644.51737 18757.3078 28440.79569 23014.82255 23554.039 20471.00124 11224.91395 21505.75191 14793.71236 1.032621417 1.801070395 1.267924328 1.922492137 1.555716509 1.592165538 1.383763638 0.758762485 1.45370894 1 13.85269651 1.958640378 7.523581469 1.048924019 1.543777586 0.342321827 0.282843083 0.2560669 40.49345305 0.111302144 0.070635262 90.9160122 -1.958640378 0.494853567 THFELEPS(ph)PPSGLGFTR ddPTM_BT-474_Pertuzumab_2h_R1 1 THFELEPSPPSGLGFTR 17 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 THFELEPS(1)PPSGLGFTR 110.67 0.00035244 61940000 42932 47954 43755 52674 48476 55673 48772 19652 57809 51620 TRUE FALSE 41254.16998 46586.39887 51662.50182 55392.51145 50035.27456 56798.7462 49368.88633 19246.17933 51246.76468 48123.73142 0.857252103 0.968054585 1.07353483 1.151043567 1.039721424 1.180264799 1.025874031 0.399931152 1.064895908 1 15.55446089 1.958701964 24.99455674 0.744426549 1.052004553 0.190502019 0.18935296 524.4948763 317436.0898 0.075457301 0.048702357 90.92890554 -1.958701964 0.307578003 LKSEDEPTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LKSEDEPTR 9 1 O14787-2;O14787;A0A075B780;K7ENW1;K7ESC1;E7EW37;Q92973-2;Q92973 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ;;; 152.69 7.28E-05 4186690000 4976200 4869100 4187160 4288690 4768300 4851600 5145700 5219900 6212700 5849600 FALSE TRUE 4781724.603 4730238.035 4943872.955 4510029.805 4921676.7 4949702.676 5208674.616 5112107.241 5507460.342 5453401.382 0.876833423 0.867392239 0.906566858 0.827012261 0.902496691 0.907635864 0.955124014 0.937416281 1.009912889 1 22.37872491 1.958785733 0.789330373 1.003347773 0.870655364 0.804750536 0.024173766 0.2612516 0.30531633 0.020272135 0.010259629 90.94644621 -1.958785733 -0.132692408 SNS(ph)LNNGQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSLNNGQPK 10 0 O60333-3 O60333-3 KIF1B Kinesin-like protein KIF1B 1 SNS(1)LNNGQPK;SNS(1)LNNGQPK 146.58 0.0029943 289800000 676540 587900 525630 523120 568980 582010 630920 801720 773000 706730 TRUE FALSE 650100.0688 571133.6676 620623.0336 550118.2859 587281.7584 593778.641 638641.3877 785164.2018 685252.2807 658862.5476 0.986700597 0.866847979 0.941961318 0.83495152 0.891357022 0.901217778 0.969308986 1.191696515 1.040053473 1 19.32961799 1.958880116 5.8527904 1.095785484 0.902504811 0.620362161 0.060130567 0.109403185 9.873541106 0.024750889 0.0154684 90.9662132 -1.958880116 -0.193280674 GETITGLLQEFDVQEQDIETLHGSVHVTLCGTPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GETITGLLQEFDVQEQDIETLHGSVHVTLCGTPK 34 0 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1 Q92597 NDRG1 Protein NDRG1 0 ;;; 319.96 5.86E-105 657820000 529091.6 874688.9 572683.4 791806.7 715790.1 820352.6 570140.9 254736.9 458530.3 396738.9 FALSE TRUE 508414.1153 849743.629 676180.0297 832671.9387 738814.1386 836940.6916 577118.4549 249476.494 406479.8627 369867.4209 1.374584747 2.297427621 1.828168666 2.251271379 1.997510721 2.262812684 1.560338711 0.674502484 1.098988015 1 18.4966487 1.958915781 4.253904859 0.917215313 2.01558916 0.755647326 0.273799768 0.092928734 3.566628021 0.116474613 0.070154369 90.97368382 -1.958915781 1.098373847 HPPEQTNGVHT(ph)PPHVASALAGAVS(ph)PGALR ddPTM_BT-474_Pertuzumab_2h_R1 2 HPPEQTNGVHTPPHVASALAGAVSPGALR 29 0 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 2 HPPEQT(0.33)NGVHT(0.637)PPHVAS(0.032)ALAGAVS(1)PGALR;HPPEQT(0.003)NGVHT(0.997)PPHVASALAGAVS(1)PGALR 145.62 1.28E-07 1098730000 147682 164530 126298 172181 133409 149909 146520 27471.7 167095 138507 TRUE FALSE 141910.4242 159837.7655 149122.8581 181067.282 137700.2216 152940.2627 148313.1556 26904.39979 148127.0761 129125.7975 1.099009082 1.23784533 1.154864953 1.402254898 1.066403649 1.184428407 1.148594304 0.208358053 1.147153233 1 16.97841773 1.958955807 24.67778483 0.692526419 1.192867159 0.338534025 0.246541791 354.9774584 213429.2649 0.095592399 0.061701964 90.98206872 -1.958955807 0.50034074 SLS(ph)DSESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 SLS(0.999)DS(0.001)ESDDSK;SLS(1)DSESDDSK;SLS(0.999)DS(0.001)ESDDSK;SLS(0.922)DS(0.078)ESDDSK;S(0.05)LS(0.95)DSESDDSK 368.51 9.15E-86 4125008000 2579890 2239960 1954150 2081700 2056060 2053180 2330940 2599070 2866620 2634200 TRUE FALSE 2479065.047 2176078.534 2307308.375 2189136.786 2122195.037 2094696.706 2359466.741 2545398.296 2541213.315 2455783.288 1.00948038 0.88610365 0.93954071 0.891420997 0.864162179 0.852964802 0.960779704 1.036491416 1.034787283 1 21.22775182 1.959005227 4.168214835 1.024152806 0.904883189 0.600287049 0.042492377 0.145591334 5.304092844 0.019688823 0.011821936 90.99242248 -1.959005227 -0.119269616 TLHEWLQQHGIPGLQGVDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLHEWLQQHGIPGLQGVDTR 20 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 192.81 5.57E-18 1169760000 152000 152297 157094 175520 141902 162716 159752 117091 182589 196061 FALSE TRUE 146059.672 147953.6387 185484.3803 184578.6082 146466.4067 166006.229 161707.0928 114673.0299 161862.2622 182781.6138 0.799093896 0.809455807 1.014786862 1.009831374 0.801319146 0.908221705 0.884701089 0.62737727 0.885550022 1 17.47976143 1.95902953 24.99670859 0.786189702 0.894018516 0 0.11565585 949.6543919 579397.2904 0.04741509 0.030600669 90.99751436 -1.95902953 0.107828814 DEELEKDTMDNWDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DEELEKDTMDNWDEK 15 1 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 ; 222.45 1.28E-12 653040000 1203050 903530 808360 670070 930430 838900 987880 1180410 1307490 1081610 FALSE TRUE 1156033.476 877762.209 954448.6339 704652.393 960358.1259 855863.1328 999969.9709 1156034.121 1159069.217 1008351.591 1.146458721 0.870492214 0.946543489 0.698816166 0.952404037 0.848774515 0.9916878 1.146459361 1.149469319 1 19.94356733 1.959081581 4.126346825 1.109339037 0.903036682 0.359735672 0.111620009 0.214827763 7.629044582 0.050090256 0.030029508 91.00842124 -1.959081581 -0.206302354 MMDYLQGSGETPQTDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MMDYLQGSGETPQTDVR 17 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 128.31 8.69E-05 67196000 37132 44334 37618 39324 41322 39955 41338 53198 42452 39287 FALSE TRUE 35680.84039 43069.63773 44416.40941 41353.51635 42651.15966 40762.91748 41843.90681 52099.44271 37633.02693 36626.0565 0.974192796 1.175928884 1.212699746 1.129073679 1.164503191 1.112948577 1.142462793 1.422469348 1.02749328 1 15.16058275 1.959164718 24.99831568 1.218312926 1.135235552 0 0.126781389 1323.94887 810486.0081 0.050524246 0.032616851 91.02584482 -1.959164718 -0.083077374 EGEETEGS(ph)EEDDKENDKTEEMPNDSVLENK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGEETEGSEEDDKENDKTEEMPNDSVLENK 30 2 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 EGEETEGS(1)EEDDKENDKTEEMPNDSVLENK 311.88 1.51E-92 1428800000 1206300 647250 788490 574740 878890 703270 1112000 1645700 1840600 1353200 TRUE FALSE 1159156.462 628791.0637 930987.6829 604402.4003 907160.295 717490.6012 1125608.989 1611715.72 1631662.804 1261546.559 0.91883764 0.498428742 0.737973305 0.479096389 0.719085862 0.568738899 0.892245301 1.277571334 1.293382946 1 20.26676202 1.959181863 3.401963897 1.210798603 0.646901399 0.738750994 0.142482325 0.106686932 2.372914885 0.06388602 0.036919611 91.02943826 -1.959181863 -0.563897204 IAEFTTNLTEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 IAEFTTNLTEEEEK 14 0 P35579 P35579 MYH9 Myosin-9 0 ;;; 300.78 1.73E-43 911410000 588107 487969 397068 463078 501311 504491 578323 941690 700850 689364 FALSE TRUE 565123.1283 474052.6019 468827.0203 486977.5111 517436.1236 514692.1537 585400.6899 922243.7724 621292.4462 642672.7623 0.879332627 0.73762672 0.729495706 0.757737903 0.80513156 0.800861938 0.91088455 1.435013006 0.966732189 1 19.2937248 1.959202127 7.829248626 1.181128349 0.78593994 0.598418471 0.126056149 0.158518214 27.21937035 0.050729207 0.032269798 91.03368574 -1.959202127 -0.395188409 ASIANSDGPTAGSQT(ph)PPFK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASIANSDGPTAGSQTPPFK 19 0 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASIANSDGPT(0.001)AGS(0.023)QT(0.977)PPFK;ASIANSDGPTAGS(0.002)QT(0.998)PPFK 253.58 7.85E-30 207787000 253110 254430 206887 237840 248010 228210 248780 333220 291000 281550 TRUE FALSE 243218.1814 247173.9055 244276.0831 250114.9509 255987.4669 232824.5626 251824.6441 326338.8906 257966.9 262480.3677 0.926614754 0.941685306 0.930645157 0.952890127 0.97526329 0.887017054 0.959403731 1.243288759 0.982804551 1 18.00184999 1.959229642 19.74895621 1.102135167 0.937052161 0.432492814 0.069986873 31.38334231 15201.25237 0.027094876 0.017486113 91.03945341 -1.959229642 -0.165083006 DQHFDQNLNFMYIEVDKVTER ddPTM_BT-474_Pertuzumab_2h_R1 2 DQHFDQNLNFMYIEVDKVTER 21 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ; 165.66 8.66E-12 135607000 129976 113484 104045 104985 120126 135068 117252 54563 144634 123144 FALSE TRUE 124896.3942 110247.5474 122848.246 110403.2884 123989.9619 137799.1675 118686.9651 53436.25498 128215.7547 114803.3472 1.087915965 0.96031649 1.070075472 0.961673079 1.080020443 1.200306183 1.033828437 0.465459033 1.116829411 1 16.80880518 1.959371424 24.86356689 0.788437864 1.05779773 0.1796716 0.172487035 519.7744726 318086.7558 0.068131657 0.043979515 91.06917961 -1.959371424 0.269359866 GLCTSPAEHQYFMTEY(ph)VATR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLCTSPAEHQYFMTEYVATR 20 0 Q13164-2;Q13164;Q13164-4;Q13164-3;I3L0J8;C9JUK9 Q13164-2 MAPK7 Mitogen-activated protein kinase 7 1 GLCTSPAEHQYFMTEY(0.998)VAT(0.001)R;GLCTSPAEHQYFMT(0.004)EY(0.995)VAT(0.001)R 235.7 8.74E-29 645510000 308130 348940 303690 405880 409160 405270 322100 244450 294360 302840 TRUE FALSE 296087.9389 338988.5728 358573.5385 426827.5154 422321.003 413464.8371 326041.9562 239402.0221 260945.4869 282328.3771 1.048736022 1.200688986 1.270058441 1.511812308 1.495850355 1.464482038 1.154832396 0.847955932 0.924262342 1 18.10701462 1.959411426 4.185997983 0.918955077 1.338307684 0.634538372 0.138363031 0.148321364 5.472576431 0.070635549 0.042462558 91.07756811 -1.959411426 0.419352607 RCDELTR ddPTM_BT-474_Pertuzumab_2h_R1 3 RCDELTR 7 1 P17844;P17844-2;J3KTA4;J3QSF1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 112.41 0.010198 1485430000 961510 910480 871020 1055910 965440 991280 957650 892560 1044350 1058630 FALSE TRUE 923933.1262 884514.0019 1028432.69 1110405.642 996494.2544 1011324.361 969370.0072 874128.3241 925799.7663 986928.0472 0.936170705 0.896229471 1.042054375 1.125113067 1.009692913 1.024719445 0.982209402 0.885706234 0.938062069 1 19.91258538 1.959479729 7.743013764 0.929630383 1.00763348 0.165249843 0.063050805 0.445018829 75.44685435 0.028891138 0.018374939 91.09189339 -1.959479729 0.078003097 APGTPHSHTKPYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 APGTPHSHTKPYVR 14 1 J3QQ67;Q07020;F8VYV2;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 192.18 2.60E-07 3957500000 1994460 2421400 2003770 2401500 2163660 2082310 2137910 594730 2286320 2171430 FALSE TRUE 1916514.298 2352344.043 2365895.813 2525441.703 2233256.089 2124415.735 2164074.382 582448.6177 2026786.539 2024357.112 0.946727377 1.162020292 1.16871465 1.247527765 1.10319275 1.049427358 1.069018094 0.287720291 1.001200098 1 20.94903238 1.959491354 22.14028588 0.682464844 1.118030576 0.357366898 0.203418003 106.1919267 58039.23324 0.079841497 0.051533184 91.09433169 -1.959491354 0.435565732 VAPYRPDQQVEEDDDFMDENQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAPYRPDQQVEEDDDFMDENQGK 23 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 242.34 2.24E-37 991080000 442980 418630 393570 372580 407160 437000 438460 482120 555310 506850 FALSE TRUE 425667.8519 406691.0823 464696.8539 391808.8985 420256.6712 445836.4394 443826.0046 472164.0535 492273.5368 472520.598 0.900845071 0.860684347 0.983442533 0.829189034 0.889393336 0.943528052 0.939273349 0.999245441 1.041803339 1 18.85001769 1.959567262 1.31601534 1.022773347 0.894538383 0.625594429 0.03966542 0.276452987 0.887637724 0.028184617 0.012789743 91.11025492 -1.959567262 -0.128234965 APPQTHLPSGASSGTGSASATHGGGSPPGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 APPQTHLPSGASSGTGSASATHGGGSPPGTR 31 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ; 181.9 1.75E-18 192040000 27637 46607 30975 53946 38326 43007 37704 34124 34528 41921 FALSE TRUE 26556.91549 45277.81399 36572.87154 56730.15952 39558.7906 43876.63101 38165.43283 33419.32748 30608.52619 39081.65333 0.679523849 1.158543975 0.935806662 1.451580337 1.012208728 1.12269127 0.97655625 0.855115499 0.783194251 1 15.25420388 1.959687725 3.386183052 0.867200401 1.074199785 0.151277974 0.188706435 0.404248409 8.904032246 0.088716235 0.051245098 91.13553037 -1.959687725 0.206999385 VFYELQHSDKPVGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFYELQHSDKPVGTK 15 1 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 231.23 1.34E-13 1358630000 2793500 2720100 2324300 2367000 2449500 2384700 2787800 2958000 3346500 3271100 FALSE TRUE 2684326.932 2642525.411 2744352.714 2489161.154 2528290.392 2432920.268 2821917.93 2896916.266 2966619.35 3049545.483 0.880238365 0.866530906 0.899921883 0.816240049 0.829071219 0.797797666 0.925356892 0.949950175 0.972807051 1 21.5401628 1.959697374 2.830708807 0.969521912 0.849410986 0.759276964 0.03181801 0.143585186 2.135620072 0.017370612 0.009612727 91.13755512 -1.959697374 -0.120110926 FHDEVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHDEVGK 7 0 B0QYR6;Q9UJY5-4;Q9UJY5-3;Q9UJY5;Q9UJY5-6;B0QYR8;B0QYR9;B0QYS0;B0QYS1;B0QYS2;B0QYS3;B0QYR5;B0QYS5 B0QYR6 GGA1 ADP-ribosylation factor-binding protein GGA1 0 ; 77.741 0.037226 370890000 645640 596540 523340 589970 572790 610180 594080 439000 719180 668900 FALSE TRUE 620407.675 579527.2633 617919.1796 620418.4224 591214.3105 622518.2577 601350.5287 429934.4966 637541.7014 623594.8072 0.994889098 0.929333049 0.990898533 0.994906332 0.948074461 0.998273639 0.964328955 0.68944528 1.022365315 1 19.25024939 1.959833704 24.99095675 0.858794845 0.97478926 0.052469436 0.089315812 666.7686576 414854.0034 0.034971085 0.022570386 91.16616881 -1.959833704 0.115994416 HKS(ph)ESPCESPYPNEK ddPTM_BT-474_Pertuzumab_2h_R1 4 HKSESPCESPYPNEK 15 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H0Y594;B7ZBA0;B7ZB98 Q8NI27 THOC2 THO complex subunit 2 1 HKS(0.499)ES(0.499)PCES(0.002)PYPNEK;HKS(0.653)ES(0.343)PCES(0.004)PYPNEK;HKS(0.494)ES(0.494)PCES(0.012)PYPNEK;HKS(0.495)ES(0.495)PCES(0.01)PYPNEK 157.38 1.18E-06 637750000 716290 802900 713430 823480 767700 782120 783100 531863 1030540 1057710 TRUE FALSE 688296.5949 780002.0781 842362.6712 865979.9015 792393.7677 797935.0023 792683.8121 520879.8432 913557.4196 986070.3596 0.698019759 0.791020712 0.854262237 0.878213094 0.803587452 0.809206964 0.803881594 0.528238009 0.926462712 1 19.91133107 1.959853641 24.99409241 0.740876677 0.810129473 0 0.12898168 1658.114143 1032296.871 0.051813923 0.033450302 91.17035402 -1.959853641 0.069252796 EVIKS(ph)PTASR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVIKSPTASR 10 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EVIKS(0.998)PT(0.002)ASR;EVIKS(0.995)PT(0.005)ASR;EVIKS(0.965)PT(0.035)ASR;EVIKS(0.464)PT(0.464)AS(0.071)R 171.36 2.45E-06 1956240000 1485920 1455570 1157160 1306160 1395260 1374570 1406900 1568570 1619770 1538350 TRUE FALSE 1427848.604 1414058.569 1366284.553 1373571.074 1440139.805 1402364.747 1424118.063 1536178.481 1435900.5 1434156.184 0.995601887 0.985986453 0.952674868 0.95775557 1.004172224 0.977832653 0.993000678 1.071137508 1.001216266 1 20.45177072 1.959859399 10.96595304 1.032066357 0.978888536 0.408950855 0.02368631 0.72293388 195.6939085 0.009728302 0.006251557 91.17156284 -1.959859399 -0.053177822 RDS(ph)SSHEETPGSHPLYGHGECK ddPTM_BT-474_Pertuzumab_2h_R1 3 RDSSSHEETPGSHPLYGHGECK 22 1 B7ZBM3;Q8IVH2-3;Q8IVH2-2;Q8IVH2 B7ZBM3 FOXP4 Forkhead box protein P4 1 RDS(0.333)S(0.333)S(0.333)HEETPGSHPLYGHGECK;RDS(0.834)S(0.112)S(0.054)HEETPGSHPLYGHGECK;RDS(0.648)S(0.176)S(0.176)HEETPGSHPLYGHGECK 269.89 4.70E-39 2492310000 1984000 2196280 1837050 2167970 2138270 2199020 1769220 226914 1812210 1641820 TRUE FALSE 1906463.087 2133644.245 2169045.8 2279859.192 2207049.396 2243485.691 1790872.244 222228.1466 1606495.518 1530618.069 1.245551144 1.393975602 1.41710453 1.489502337 1.441933452 1.465738408 1.17003208 0.145188503 1.049573078 1 20.54568291 1.959993023 8.616229936 0.640263006 1.40622335 0.606194186 0.240819792 0.197343819 40.04766915 0.09551175 0.061022139 91.19961879 -1.959993023 0.765960344 HQHMHDRDDLYAEQMER ddPTM_BT-474_Pertuzumab_2h_R1 14 HQHMHDRDDLYAEQMER 17 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;;;;;;;;;; 286.68 1.05E-36 5738805000 4648385 4827598 4055362 3884158 4116364 4690720 3500123 1016253.72 3605524 1908168 FALSE TRUE 4466720.975 4689919.632 4788256.124 4084619.86 4248770.586 4785569.572 3542958.552 995267.7255 3196240.031 1778926.082 2.5109087 2.636376902 2.691655473 2.296115562 2.388390743 2.690145263 1.991627752 0.559476718 1.796724475 1 20.76257513 1.960004887 5.119167756 1.100861238 2.519770261 0.811177322 0.305544991 0.075181515 4.784405024 0.127365969 0.078716744 91.20211028 -1.960004887 1.418909023 HLAEVLER ddPTM_BT-474_Pertuzumab_2h_R1 3 HLAEVLER 8 0 Q5VTR2 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 ;; 135.79 0.001701 0 141230 153849 120880 144395 154506 150836 142344 135260 153384 153192 FALSE TRUE 135710.5755 149461.3772 142725.705 151847.2433 159475.8258 153886.0073 144086.0485 132466.8337 135972.4914 142816.1694 0.950246573 1.0465298 0.999366567 1.063235654 1.116651052 1.077511096 1.008891704 0.927533866 0.95208051 1 17.1237998 1.960026569 5.300507296 0.954587316 1.044890366 0.397286942 0.045177708 0.191661744 13.42819349 0.020706998 0.012844717 91.2066635 -1.960026569 0.09030305 KGNAEGS(ph)SDEEGKLVIDEPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 KGNAEGS(0.5)S(0.5)DEEGKLVIDEPAK 106.63 0.00018903 1047800000 366570 244890 277350 243890 290810 245900 341980 435680 517650 363870 TRUE FALSE 352244.0391 237905.977 327473.3146 256477.1921 300164.1678 250872.2665 346165.2535 426683.0557 458888.5422 339224.7608 1.038379505 0.701322558 0.965357935 0.756068606 0.884853355 0.739545857 1.020459865 1.257818134 1.352756624 1 18.37188195 1.960099853 3.67714313 1.223284939 0.844333095 0.608400112 0.127599364 0.134469597 3.59829582 0.055452817 0.032598715 91.22205539 -1.960099853 -0.378951844 FYCDYCDTYLTHDS(ph)PSVR ddPTM_BT-474_Pertuzumab_2h_R1 4 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 1 FYCDYCDTYLTHDS(0.945)PS(0.055)VR;FYCDYCDTYLTHDS(0.994)PS(0.006)VR;FYCDYCDTYLTHDS(1)PSVR;FYCDYCDTYLTHDS(0.998)PS(0.002)VR 277.25 2.54E-39 2228990000 2307960 2427910 1974810 2024540 2060800 2274640 2011860 2017220 1956760 2212920 TRUE FALSE 2217762.372 2358668.384 2331702.096 2129026.752 2127087.504 2320634.779 2036481.744 1975563.702 1734636.808 2063036.957 1.074998857 1.143299142 1.130227982 1.031986724 1.031046727 1.124863406 0.987128096 0.957599763 0.840817127 1 20.97633824 1.96014415 2.169655381 0.922583681 1.088823673 0.643403293 0.052615291 0.19351192 1.68180252 0.03025955 0.01554133 91.2313603 -1.96014415 0.166239991 THETLSHAGQK ddPTM_BT-474_Pertuzumab_2h_R1 4 THETLSHAGQK 11 0 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6;E9PNQ9;Q16890-4;Q16890-3;Q16890-2 Q16890-5 TPD52L1 Tumor protein D53 0 ;;; 236.69 8.51E-16 887240000 1034009 1060295 980761 1003831 908156 1062761 987602 102898 1140366 984313 FALSE TRUE 993598.7851 1030056.425 1158006.33 1055638.838 937367.6625 1084250.756 999688.5687 100773.1203 1010916.432 917644.6038 1.082770804 1.122500389 1.261933351 1.150378735 1.021493134 1.181558472 1.089407124 0.109817156 1.101642649 1 19.80757599 1.960306226 24.82831606 0.628585851 1.137049075 0.304109545 0.257898814 410.7509531 256922.653 0.100292921 0.064741547 91.26541348 -1.960306226 0.508463224 LLTETEDWLYEEGEDQAK ddPTM_BT-474_Pertuzumab_2h_R1 3 LLTETEDWLYEEGEDQAK 18 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;; 125.89 2.87E-05 45621000 55052 58991 51069 54377 53588 61009 63270 63755 77037 74104 FALSE TRUE 52900.50698 57308.63444 60298.30432 57183.40349 55311.70669 62242.64378 64044.31719 62438.43697 68292.08273 69084.87008 0.765732163 0.829539585 0.872814905 0.827726873 0.800634157 0.90095912 0.927038252 0.903793217 0.988524443 1 16.07608217 1.960311277 0.537326655 1.005369271 0.80796324 0.807127119 0.032288588 0.378311859 0.234198623 0.032150392 0.022609716 91.2664749 -1.960311277 -0.197406031 HPHDIIDDINSGAVECPAS ddPTM_BT-474_Pertuzumab_2h_R1 4 HPHDIIDDINSGAVECPAS 19 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;; 265.87 1.86E-31 8140600000 3126280 3239920 2557410 3128270 2630510 3147960 2373950 61390.7 2696750 1426780 FALSE TRUE 3004101.521 3147520.654 3019590.876 3289720.39 2715122.743 3211613.908 2403003.11 60122.96059 2390626.246 1330142.92 2.258480256 2.366302603 2.270125136 2.47320821 2.041226324 2.414487842 1.806575124 0.045200376 1.797270211 1 20.34314984 1.960341386 7.137092443 0.856023201 2.287012519 0.68455519 0.410343902 0.115799588 17.14102944 0.162442857 0.10302393 91.27280258 -1.960341386 1.430989318 DLFAEGLLEFLRPAVQQLDSHVHAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLFAEGLLEFLRPAVQQLDSHVHAVR 26 1 O95295 O95295 SNAPIN SNARE-associated protein Snapin 0 157.31 8.40E-09 110350000 41348 44989 35320 48496 48781 42430 37917 5192.4 46813 28448 FALSE TRUE 39732.07445 43705.95777 41703.10969 50998.88437 50350.08517 43287.96367 38381.03959 5085.175125 41498.9845 26521.19162 1.498125537 1.647963575 1.572444794 1.922948452 1.898485026 1.632202817 1.447183827 0.19174007 1.564748111 1 14.69485798 1.960416019 10.02656291 0.825815038 1.693484334 0.510458435 0.336415656 0.417853489 103.8502055 0.134836024 0.086531196 91.28848895 -1.960416019 0.867669296 EKTHGEVER ddPTM_BT-474_Pertuzumab_2h_R1 3 EKTHGEVER 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 129.16 0.00023865 299133000 311868 278328 215561 287199 259008 283594 314269 320047 355283 366118 FALSE TRUE 299679.8538 270390.358 254517.6678 302021.3748 267339.2275 289328.465 318115.118 313437.9176 314952.7633 341320.5018 0.878001328 0.792189032 0.745685262 0.884861511 0.783249838 0.847673853 0.932012922 0.918309671 0.922747862 1 18.38076755 1.960533256 0.756403789 0.97896775 0.807590247 0.650073918 0.044139427 0.391063054 0.423166435 0.03796897 0.019743919 91.31313561 -1.960533256 -0.171377503 FDDDKVSIVTPEDILR ddPTM_BT-474_Pertuzumab_2h_R1 6 FDDDKVSIVTPEDILR 16 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ;;;;; 248.06 2.11E-20 3470780000 3942170 3552200 3646210 3644930 3940340 3751940 4366020 5069900 5495120 5514350 FALSE TRUE 3788105.638 3450894.734 4305161.257 3833045.274 4067084.615 3827806.797 4419452.659 4965204.793 4871337.015 5140858.163 0.736862508 0.671268225 0.837440194 0.745604168 0.791129513 0.744585179 0.859672163 0.965831897 0.947572732 1 22.29357778 1.960720517 2.13829278 0.97328487 0.754280553 0.843154158 0.041895672 0.117480581 0.992274727 0.024100216 0.012330262 91.35251693 -1.960720517 -0.219004318 SQECLIPVHVDGDGHCLVHAVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQECLIPVHVDGDGHCLVHAVSR 23 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 0 101.5 0.00069875 176650000 42485 45819 37885 42362 35082 46037 39474 22205 43563 38453 FALSE TRUE 40824.63923 44512.28698 44731.66225 44548.3079 36210.44439 46967.89968 39957.09462 21746.45899 38617.91087 35848.54406 1.13880885 1.241676284 1.247795787 1.242681093 1.010095259 1.310175934 1.114608575 0.606620424 1.077251863 1 15.12962691 1.960740562 12.70777673 0.853249706 1.197535601 0.48586694 0.137957212 1.296857516 418.6832033 0.053872381 0.034706532 91.35673328 -1.960740562 0.344285895 TEKPSKS(ph)PPPPPPR ddPTM_BT-474_Pertuzumab_2h_R1 5 TEKPSKSPPPPPPR 14 2 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 TEKPS(0.046)KS(0.954)PPPPPPR;TEKPSKS(1)PPPPPPR;TEKPS(0.005)KS(0.995)PPPPPPR;TEKPS(0.003)KS(0.997)PPPPPPR;TEKPS(0.009)KS(0.991)PPPPPPR 143.39 4.77E-06 3818320000 4038450 3679930 3663050 3763740 3812180 3567540 4375600 5176710 5615640 5361510 TRUE FALSE 3880622.909 3574981.999 4325044.619 3957987.072 3934802.232 3639678.103 4429149.902 5069809.129 4978176.09 4998370.152 0.776377657 0.715229543 0.865290982 0.791855535 0.787217055 0.728172983 0.886118828 1.014292454 0.995959871 1 22.25302631 1.960770196 3.30795235 1.001605667 0.7799497 0.869876464 0.03913775 0.08308598 1.738188285 0.019376905 0.011147836 91.36296721 -1.960770196 -0.221655967 VIEPPAASCPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIEPPAASCPSSPR 14 0 A0A0A0MRX4;Q3MIN7;Q3MIN7-2 A0A0A0MRX4 RGL3 Ral guanine nucleotide dissociation stimulator-like 3 1 VIEPPAAS(0.001)CPS(0.581)S(0.418)PR 118.51 0.00025319 183340000 129330 150340 105160 171030 173420 146740 137590 139680 133600 151580 TRUE FALSE 124275.6406 146052.4504 124164.7513 179856.8788 178998.2118 149707.1833 139273.8676 136795.5592 118434.2881 141313.3516 0.879433112 1.033536101 0.878648407 1.272752198 1.266675865 1.059398717 0.985567648 0.968029968 0.838096944 1 17.10853826 1.961015141 2.223735384 0.928032521 1.072697346 0.168415579 0.130103665 0.579897771 5.291670107 0.079359304 0.041090601 91.41451117 -1.961015141 0.144664825 HFPNIDR ddPTM_BT-474_Pertuzumab_2h_R1 5 HFPNIDR 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 133.12 0.0033029 2081160000 1587254 1807760 1561577 1866080 1782820 1711142 1740550 1176410 2019980 2018745 FALSE TRUE 1525222.359 1756204.455 1843788.701 1962388.612 1840166.024 1745742.464 1761851.372 1152116.722 1790680.339 1882013.603 0.810420475 0.933151839 0.979689359 1.042706923 0.977764465 0.927592904 0.936152304 0.612172367 0.951470455 1 20.84384563 1.961119406 24.98843181 0.80213228 0.950459887 0.061817501 0.113172972 707.145911 454479.3663 0.045464431 0.029345686 91.43646054 -1.961119406 0.148327606 ISEEDELDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISEEDELDTK 10 0 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 156.83 2.39E-05 570510000 394400 367270 343050 324070 348940 345710 400530 522280 495990 478200 FALSE TRUE 378986.412 356795.8192 405046.7661 340795.2915 360163.972 352700.4931 405431.806 511494.7355 439687.2946 445811.0881 0.850105397 0.800329621 0.908561444 0.764438796 0.807884733 0.791143385 0.909425128 1.147335159 0.986263703 1 18.76607297 1.961129021 5.255625151 1.055847691 0.82200234 0.771142024 0.054501863 0.081641378 5.648092386 0.02292042 0.014226541 91.43848491 -1.961129021 -0.233845351 KDEESGGGSNPFQHLEK ddPTM_BT-474_Pertuzumab_2h_R1 4 KDEESGGGSNPFQHLEK 17 1 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;; 259.18 2.22E-27 1122070000 1720260 1689970 1478870 1532810 1645450 1729560 1896040 2054600 2405810 2303160 FALSE TRUE 1653030.337 1641773.71 1746134.706 1611918.508 1698377.394 1764532.888 1919244.305 2012171.792 2132712.535 2147164.922 0.769866497 0.764623944 0.813228033 0.750719468 0.790986 0.821796626 0.893850437 0.937129594 0.993269084 1 21.03400158 1.961148949 1.038063678 1.001789871 0.773729887 0.966044134 0.016646938 0.081555638 0.161563369 0.013035021 0.005960194 91.4426806 -1.961148949 -0.228059984 TEWEALELTDHQWALDDVEEELMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TEWEALELTDHQWALDDVEEELMAK 25 0 Q9P0I2 Q9P0I2 EMC3 ER membrane protein complex subunit 3 0 201.82 5.99E-25 35225000 25256 35998 29175 44013 25408 30939 35711 42775 46041 38905 FALSE TRUE 24268.9676 34971.37229 34447.57149 46284.5162 26225.27139 31564.60778 36148.0419 41891.6813 40814.6187 36269.9297 0.669120889 0.96419741 0.949755673 1.276112653 0.723058236 0.87026934 0.996639426 1.154997588 1.125301842 1 15.14648633 1.961194715 4.843230028 1.105319024 0.921763284 0.213166719 0.157550425 0.324234004 17.87136391 0.070614983 0.043433538 91.45231735 -1.961194715 -0.18355574 DFGNSPLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFGNSPLHR 9 0 Q9UKA9;Q9UKA9-2;Q9UKA9-4;Q9UKA9-3 Q9UKA9 PTBP2 Polypyrimidine tract-binding protein 2 0 ; 104.05 0.0033234 605150000 352310 500150 381600 472170 405250 483980 421580 382860 444680 434940 FALSE TRUE 338541.3357 485886.2117 450563.6086 496538.7503 418285.2343 493766.4072 426739.4221 374953.8072 394201.7907 405481.1264 0.834912684 1.198295506 1.11118269 1.224566861 1.031577568 1.217729692 1.052427337 0.924713341 0.972182834 1 18.62927524 1.961197506 6.135696217 0.963537977 1.112088863 0.240522666 0.108409091 0.255268886 26.93754535 0.043988358 0.027673947 91.4529051 -1.961197506 0.148550886 RPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_BT-474_Pertuzumab_2h_R1 3 RPSPPEPWDEEDGASCSTFFGSEER 25 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 RPS(1)PPEPWDEEDGASCSTFFGSEER;RPS(1)PPEPWDEEDGASCSTFFGSEER;RPS(1)PPEPWDEEDGASCSTFFGSEER 163.89 1.07E-11 546828000 98851 109841 81364.8 111586 103434 106823 99442 90171 109591 101410 TRUE FALSE 94987.79363 106708.4422 96069.22931 117344.9668 106761.0485 108983.0343 100659.0009 88308.93734 97150.68912 94541.41037 1.004721563 1.128695265 1.016160315 1.24120178 1.129251702 1.152754479 1.064708053 0.934076792 1.027599321 1 16.52865877 1.961232874 5.678485234 0.983301023 1.114910483 0.412122851 0.066610879 0.18094548 15.53140305 0.028457323 0.017795015 91.46035307 -1.961232874 0.131609459 ESEDKPEIEDVGS(ph)DEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 ESEDKPEIEDVGSDEEEEK 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK 316.22 6.39E-62 28906600000 11317420 7729830 11330660 9265560 9450440 8868780 13709730 18203530 20776410 18321950 TRUE FALSE 10875122.71 7509382.817 13378362.31 9743756.662 9754421.985 9048112.808 13877513.78 17827620.74 18417959.04 17080988.01 0.636679957 0.439633984 0.783231175 0.570444558 0.571068956 0.529718351 0.81245381 1.043711332 1.078272465 1 24.02588809 1.961266743 2.767280401 1.044975485 0.589215464 0.849327962 0.085339982 0.094747868 1.345552086 0.043187843 0.023794066 91.467486 -1.961266743 -0.455760022 HACVEVQDEIAFIPNDVYFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HACVEVQDEIAFIPNDVYFEK 21 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 76.186 0.011361 74104000 111680 105340 105170 121500 115000 113310 113810 85511 140690 134970 FALSE TRUE 107315.4221 102335.8063 124176.5585 127770.6296 118699.0794 115601.2058 115202.8408 83745.16797 124719.461 125828.3617 0.852871489 0.813296819 0.986872569 1.015435851 0.943341214 0.918721378 0.915555438 0.665550809 0.991187196 1 16.94109762 1.961327581 24.99209947 0.833952018 0.924368479 0 0.105211414 1117.793344 722373.8382 0.043471566 0.028066083 91.48030022 -1.961327581 0.090416461 EKELGNDAYK ddPTM_BT-474_Pertuzumab_2h_R1 5 EKELGNDAYK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 146.16 2.66E-05 8456520000 6378800 6138530 5272100 4963640 5595440 5903100 6709020 7574750 8786960 8226420 FALSE TRUE 6129509.444 5963465.135 6224885.747 5219814.055 5775422.409 6022464.727 6791126.994 7418328.765 7789501.139 7669237.246 0.799233255 0.77758256 0.811669472 0.680617105 0.75306347 0.78527558 0.88550227 0.967283776 1.015681337 1 22.87065167 1.961397731 1.684274151 1.005136945 0.762450738 0.901570366 0.033859468 0.108921894 0.575061738 0.023111043 0.011033592 91.49507781 -1.961397731 -0.242686207 S(ph)KDEYEK ddPTM_BT-474_Pertuzumab_2h_R1 5 SKDEYEK 7 1 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK 122.69 0.0030257 6901520000 7948920 5352690 8963930 7596390 6370000 5948020 10257160 13359270 14798060 14562500 TRUE FALSE 7638267.418 5200036.522 10583911.55 7988440.598 6574896.835 6068293.04 10382690.19 13083396.41 13118246.27 13576168.9 0.562623187 0.383026799 0.779594864 0.588416412 0.484296924 0.446981257 0.764773204 0.963703126 0.966270113 1 23.69457308 1.96144505 2.967268768 0.970353109 0.544701646 0.789807702 0.100753122 0.120794044 1.989194185 0.052396959 0.029396266 91.50504735 -1.96144505 -0.425651463 GHTEVIVPHLTESYNSHRDPPEEEIPFCTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHTEVIVPHLTESYNSHRDPPEEEIPFCTLK 31 1 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 44.05 0.041196 192210000 14087 18203 11397 19224 13814 15896 15288 7121.9 16120 17092 FALSE TRUE 13536.46447 17683.86826 13456.69142 20216.15294 14258.33986 16217.42801 15475.09912 6974.830276 14290.12518 15934.34362 0.849515034 1.10979584 0.844508676 1.268715765 0.894818149 1.017765677 0.971178951 0.4377231 0.896812917 1 13.95985197 1.961555048 23.79952471 0.712890132 1.002589227 0.203064744 0.18290961 322.7154196 199777.5972 0.070182027 0.045306011 91.52822673 -1.961555048 0.289699095 EVGSIIGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVGSIIGK 8 0 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;H3BSP4;C9JZY3;C9J0A4;C9K0A2;C9J5V4;C9JTY5;C9JSA6;C9J7A9;C9IZV9;F8WC71;P57723-2;P57723;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;Q15365 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15365 PCBP2;PCBP3;PCBP4;PCBP1 Poly(rC)-binding protein 3;Poly(rC)-binding protein 4;Poly(rC)-binding protein 2;Poly(rC)-binding protein 1 0 105.14 0.010343 159480000 407580 445780 353190 416030 445510 430700 415300 229130 468910 435210 FALSE TRUE 391651.323 433066.7909 417019.2897 437501.3582 459840.2338 439409.0491 420382.5656 224398.3854 415681.3026 405732.8391 0.965293625 1.067369336 1.027817444 1.078299107 1.133357198 1.083000947 1.03610683 0.55306932 1.02451974 1 18.63017055 1.961555987 24.62697264 0.805799936 1.062140191 0.306009437 0.128754642 386.4974129 247586.8947 0.05033596 0.032495255 91.52842444 -1.961555987 0.256340255 EETNGPSNQKPVKS(ph)PDNSIK ddPTM_BT-474_Pertuzumab_2h_R1 3 EETNGPSNQKPVKSPDNSIK 20 2 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 EETNGPSNQKPVKS(1)PDNSIK;EETNGPSNQKPVKS(1)PDNSIK;EETNGPSNQKPVKS(0.999)PDNSIK 144.18 8.32E-08 3505880000 2092160 1567760 1642420 1463440 1752850 1603340 2146800 2795650 3205750 2579300 TRUE FALSE 2010396.074 1523049.02 1939241.829 1538968.314 1809232.012 1635760.633 2173073.181 2737918.851 2841846.7 2404601.714 0.836061982 0.63338931 0.806471117 0.640009655 0.752404027 0.680262608 0.903714394 1.13861636 1.181836761 1 21.19736652 1.961636476 2.959700312 1.118549961 0.722151186 0.834618106 0.076049973 0.087716543 1.436849625 0.035404717 0.019854179 91.54538933 -1.961636476 -0.396398776 GPS(ph)LDIDTPDVNIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPSLDIDTPDVNIEGPEGK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPS(1)LDIDTPDVNIEGPEGK 254.62 6.91E-31 110310000 139280 105810 59699 113980 145970 103360 129850 194270 174130 140080 TRUE FALSE 133836.7836 102792.4024 70487.9373 119862.5215 150665.2576 105450.01 131439.1431 190258.2566 154363.4924 130592.2568 1.02484471 0.787124787 0.539755871 0.91783789 1.153707435 0.80747521 1.006484966 1.45688773 1.182026379 1 16.99470983 1.961702557 6.716591214 1.257961566 0.870439018 0.401376927 0.184003845 0.192567568 25.63318093 0.080467265 0.050953962 91.55931963 -1.961702557 -0.387522548 QESCS(ph)PHHPQVLAQQGSGSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 QESCSPHHPQVLAQQGSGSSPK 22 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 2 QES(0.417)CS(0.583)PHHPQVLAQQGSGS(0.014)S(0.986)PK;QES(0.41)CS(0.59)PHHPQVLAQQGSGS(0.012)S(0.988)PK 132.6 4.89E-06 445900000 273300 245230 222980 232840 235890 225070 237050 104110 306040 258010 TRUE FALSE 262619.1339 238236.2805 263277.4462 244856.9003 243477.6161 229621.0696 239951.0888 101960.0921 271299.6222 240534.7529 1.091813681 0.990444323 1.09455055 1.01796891 1.012234669 0.954627416 0.997573473 0.423889234 1.127901972 1 17.87588583 1.96172886 24.98195491 0.76762135 1.023013373 0.117321099 0.178236862 640.8509833 418322.4561 0.069919175 0.045142958 91.56486521 -1.96172886 0.255392023 VHDRS(ph)EEEEEEEEEEEEEQPRR ddPTM_BT-474_Pertuzumab_2h_R1 1 VHDRSEEEEEEEEEEEEEQPRR 22 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 VHDRS(1)EEEEEEEEEEEEEQPRR 384.97 5.80E-132 577680000 65898 63462 48789 52117 57389 69203 51761 20696 55289 43326 TRUE FALSE 63322.63331 61652.1259 57606.25761 54806.76462 59234.9693 70602.33207 52394.4666 20268.62037 49012.82451 40391.49143 1.567722089 1.526364185 1.426197834 1.356888856 1.466520973 1.74795061 1.297165931 0.501804208 1.213444287 1 15.3017638 1.961729337 8.576017697 0.860679476 1.504160356 0.668622265 0.191269771 0.183252923 38.55514388 0.076679157 0.049070364 91.5649656 -1.961729337 0.64348088 LHNGNAS(ph)PPRVPS(ph)PPPAPEPPWHCGDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LHNGNASPPRVPSPPPAPEPPWHCGDR 27 1 O15037 O15037 KHNYN Protein KHNYN 2 LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR;LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR;LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR;LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR 93.759 0.0072787 3431030000 1058062 1137429 910119 1032672 1078250 1119151 953111 438053 1003557 961917 TRUE FALSE 1016711.767 1104990.639 1074597.749 1085968.326 1112932.89 1141781 964775.4575 429007.0525 889637.4166 896765.5048 1.133754322 1.232195744 1.198304064 1.210983607 1.241052298 1.273221365 1.075839171 0.478393794 0.992051335 1 19.77437126 1.961748643 9.131050285 0.767729864 1.212662278 0.598562377 0.141168884 0.234239182 53.7360858 0.055400916 0.035517567 91.56903614 -1.961748643 0.444932414 KPNVS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPNVSPEK 8 1 A0A0U1RR07;Q9HCH5-13;Q9HCH5;Q9HCH5-14;Q9HCH5-15;Q9HCH5-6 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 KPNVS(1)PEK;KPNVS(1)PEK 62.14 0.049933 745180000 369930 329470 298790 337370 348720 339120 442630 491930 573840 570620 TRUE FALSE 355472.7266 320073.8382 352787.9995 354781.7061 359936.8955 345977.2387 448047.0383 481771.4736 508700.0889 531971.3991 0.668217741 0.6016749 0.66317099 0.66691876 0.676609487 0.65036812 0.842238961 0.905634164 0.956254584 1 19.02098916 1.961752366 1.366333646 0.978077362 0.646981984 0.957556338 0.028731706 0.074610452 0.258613827 0.019949873 0.009110311 91.56982121 -1.961752366 -0.331095378 NAS(ph)ASFQELEDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NASASFQELEDKK 13 1 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 NAS(0.969)AS(0.031)FQELEDKK;NAS(0.959)AS(0.041)FQELEDKK 200.67 6.62E-08 1438800000 665820 445740 575690 482240 492720 397360 605390 1066920 780590 715330 TRUE FALSE 639799.0183 433027.9316 679729.9892 507128.4642 508568.7863 405394.8915 612798.9439 1044887.729 691980.6957 666880.062 0.959391433 0.64933405 1.019268723 0.760449282 0.762609074 0.607897753 0.918904281 1.566830063 1.037638903 1 19.34706779 1.961805483 11.20453558 1.259337012 0.791456094 0.482664654 0.186211151 0.677816889 197.3346267 0.072961879 0.046966348 91.58102137 -1.961805483 -0.467880918 VPHLIDHQISSGENTR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPHLIDHQISSGENTR 16 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 172.91 2.55E-09 159690000 103420 123770 109940 126420 114550 121440 110140 76298 114310 119730 FALSE TRUE 99378.23206 120240.2008 129808.6036 132944.5514 118234.6048 123895.6 111487.9263 74722.41964 101334.008 111620.5805 0.890321764 1.0772225 1.162945069 1.191039778 1.059254524 1.109970935 0.998811562 0.66943228 0.907843407 1 16.76824353 1.961909054 7.532559549 0.82437215 1.086590215 0.446252465 0.108850246 0.191756814 32.6751623 0.045369477 0.028901984 91.60286445 -1.961909054 0.262218065 ERS(ph)KDAS(ph)PINR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSKDASPINR 11 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 ERS(1)KDAS(1)PINR 91.401 0.052971 577380000 1189000 921990 949190 989500 1035900 981100 1213100 1461700 1640500 1486900 TRUE FALSE 1142532.565 895695.7479 1120729.748 1040568.214 1069220.664 1000938.514 1227946.281 1431515.384 1454277.318 1386190.939 0.824224523 0.646156112 0.808495941 0.750667303 0.771337219 0.722078385 0.885842092 1.032697116 1.049117605 1 20.40269456 1.961920804 2.707505244 1.030919101 0.752010628 0.865580873 0.048245218 0.085044123 1.154618918 0.023576352 0.01292181 91.60534274 -1.961920804 -0.278908473 AHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_BT-474_Pertuzumab_2h_R1 18 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.999)PT(0.001)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.954)PT(0.046)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.929)PT(0.071)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.997)PT(0.003)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.204)PT(0.204)PGIY(0.186)MGRPT(0.204)HS(0.204)GGGGGGGGGGGGGGGGR;AHT(0.946)PT(0.054)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.991)PT(0.009)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.999)PT(0.001)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.919)PT(0.081)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.837)PT(0.163)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.76)PT(0.24)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.499)PT(0.499)PGIY(0.001)MGRPT(0.001)HSGGGGGGGGGGGGGGGGR;AHT(0.99)PT(0.01)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.411)PT(0.411)PGIY(0.113)MGRPT(0.033)HS(0.033)GGGGGGGGGGGGGGGGR;AHT(0.725)PT(0.275)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.756)PT(0.244)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.365)PT(0.287)PGIY(0.261)MGRPT(0.08)HS(0.007)GGGGGGGGGGGGGGGGR;AHT(0.911)PT(0.089)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 306.02 2.57E-90 60292064000 4900349.3 4650149.9 3406777.1 3902347.7 4313180.8 4464022.2 3908475.4 1912653.1 4421343.4 3671187.8 TRUE FALSE 4708838.232 4517532.178 4022457.505 4103748.332 4451918.178 4554287.787 3956308.491 1873156.145 3919451.033 3422534.98 1.375833486 1.319937474 1.175286017 1.19903766 1.300766304 1.330676768 1.155958526 0.547300804 1.145189474 1 21.70663386 1.961944315 10.86534128 0.848037889 1.274478288 0.554159425 0.152825076 0.53598504 151.5300489 0.060684112 0.039049689 91.61030204 -1.961944315 0.426440399 KTESASVQGR ddPTM_BT-474_Pertuzumab_2h_R1 3 KTESASVQGR 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 147.62 4.26E-05 405014000 621120 644970 450200 568680 541760 535510 571620 665410 670400 546120 FALSE TRUE 596845.9437 626576.0871 531561.1546 598029.643 559186.2024 546338.3791 578615.6566 651669.051 594299.0025 509130.806 1.17228409 1.23067801 1.044056161 1.174609032 1.098315395 1.073080577 1.136477404 1.279963898 1.167281562 1 18.95767684 1.961952166 24.75217027 1.187196857 1.130678554 0 0.083411117 1241.067637 807379.0609 0.033226421 0.021452106 91.61195808 -1.961952166 -0.056518303 KQAEEIGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KQAEEIGEK 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 137.89 0.00024346 1648860000 2498670 2465720 2064660 2270120 2421050 2467960 2609450 3023590 3311610 3218720 FALSE TRUE 2401019.214 2395400.08 2437789.99 2387281.165 2498925.272 2517863.842 2641385.23 2961151.81 2935689.916 3000713.227 0.800149508 0.798276909 0.812403521 0.795571247 0.832777104 0.83908846 0.88025247 0.986815995 0.978330715 1 21.51687402 1.961984967 1.38519432 1.000385919 0.80616673 0.975278309 0.012534402 0.056187269 0.200264203 0.008864088 0.004056762 91.6188775 -1.961984967 -0.194219189 MEIGDTLSTAEES(ph)SPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEIGDTLSTAEESSPPK 17 0 Q9BYW2;C9JG86;Q9BYW2-3;Q9BYW2-2 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 MEIGDTLSTAEES(0.581)S(0.419)PPK 164.65 2.69E-09 94003000 185950 152310 156150 136760 164770 163940 182480 218790 235720 229750 TRUE FALSE 178682.8684 147966.2679 184369.7785 143818.2 170069.9767 167254.9791 184713.2448 214271.91 208962.0538 214188.8279 0.834230572 0.690821596 0.860781491 0.671455189 0.794018896 0.780876299 0.862385058 1.000387892 0.975597354 1 17.70852371 1.961998603 2.166303235 0.995983013 0.766944998 0.76354582 0.054680728 0.133751978 1.15933003 0.028765142 0.014790948 91.62175421 -1.961998603 -0.229038015 RASEDTTSGS(ph)PPKK ddPTM_BT-474_Pertuzumab_2h_R1 3 RASEDTTSGSPPKK 14 2 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 RASEDTT(0.001)S(0.005)GS(0.995)PPKK;RASEDTTS(0.001)GS(0.999)PPKK;RASEDT(0.004)T(0.011)S(0.042)GS(0.943)PPKK 180.88 8.88E-07 4060620000 5099040 4316220 3483549 3184472 3819780 3925380 4498830 5285620 6007690 5211120 TRUE FALSE 4899763.88 4193125.632 4113103.795 3348822.982 3942646.693 4004753.873 4553888.027 5176470.1 5325722.217 4858166.201 1.008562424 0.863108724 0.846637111 0.689318324 0.811550394 0.824334473 0.93736769 1.065519352 1.096241256 1 22.21198042 1.96208661 2.710219884 1.060554706 0.833743596 0.60774145 0.0765013 0.186757897 2.541122245 0.042109346 0.023089284 91.64032266 -1.96208661 -0.226811111 HS(ph)LSGS(ph)SPGMK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HS(0.999)LS(0.331)GS(0.377)S(0.293)PGMK 70.438 0.060464 0 249600 232610 273110 296030 241750 257350 258440 137090 288200 267530 TRUE FALSE 239845.3561 225976.1905 322467.0523 311308.1438 249526.1083 262553.7933 261602.866 134259.0436 255484.7442 249409.9548 0.961651095 0.906043188 1.292919733 1.248178502 1.000465713 1.052699735 1.048887027 0.538306675 1.024356644 1 17.92815952 1.962151236 23.60228283 0.800590368 1.080627866 0.245865204 0.168407413 307.7748191 191925.7503 0.069842106 0.045089097 91.65396051 -1.962151236 0.280037498 VDINTPDVDVHGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 3 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 288.55 9.24E-41 2926620000 2410130 2473770 2062460 2338740 2102630 2445240 2245380 295481 2707310 2183260 FALSE TRUE 2315939.455 2403220.502 2435192.401 2459442.652 2170263.004 2494684.428 2272859.632 289379.2141 2399987.519 2035385.856 1.137838041 1.18071986 1.196427888 1.208342214 1.066266132 1.225656758 1.116672608 0.14217413 1.179131471 1 20.95687089 1.962152606 24.85122149 0.666196558 1.168326671 0.298617201 0.258128578 443.9358746 291494.9174 0.099960147 0.064531641 91.65424951 -1.962152606 0.502130113 NHSDSSTSESEVSSVS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 4 NHSDSSTSESEVSSVSPLK 19 0 Q9NY27-2;Q9NY27;Q9NY27-3;H7C559;C9IZ04 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 NHSDSSTSESEVSSVS(1)PLK;NHSDSSTSESEVSS(0.004)VS(0.996)PLK;NHSDSSTSESEVSSVS(1)PLK;NHSDSSTSESEVS(0.001)S(0.02)VS(0.98)PLK 225.17 1.16E-19 5502300000 6743300 6490000 5597400 5846700 5486900 5287410 5329710 2138450 5922000 5702600 TRUE FALSE 6479764.381 6304911.554 6608974.693 6148448.888 5663391.122 5394325.053 5394936.585 2094290.26 5249759.387 5316357.823 1.218835262 1.185945673 1.243139554 1.156515248 1.065276513 1.014665535 1.014780563 0.393933277 0.987472921 1 22.34200678 1.962153653 9.580294076 0.720513439 1.139114184 0.440665222 0.17223743 0.376122681 92.62370716 0.070637207 0.045356483 91.65447054 -1.962153653 0.418600745 NNASTDYDLSDK ddPTM_BT-474_Pertuzumab_2h_R1 3 NNASTDYDLSDK 12 0 P39023;G5E9G0;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;; 307.55 1.03E-37 1015370000 1706500 1563180 1419690 1310180 1341010 1467890 1620360 1897330 2033400 1907390 FALSE TRUE 1639808.093 1518599.637 1676259.564 1377798.547 1384144.805 1497571.742 1640190.45 1858149.472 1802576.957 1778200.776 0.922172634 0.854009096 0.942671708 0.774827323 0.778396244 0.842183718 0.922387658 1.044960444 1.01370834 1 20.7619868 1.962174581 3.273050026 1.021719578 0.850242573 0.681766747 0.051009154 0.147842882 3.026061992 0.026570319 0.01527251 91.65888743 -1.962174581 -0.171477004 S(ph)NLT(ph)LYLDESKTLYDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNLTLYLDESKTLYDK 16 1 A0A0G2JPZ2;Q7RTR8 A0A0G2JPZ2 TAS2R42 Taste receptor type 2 member 42 2 S(0.412)NLT(0.412)LY(0.353)LDES(0.412)KT(0.412)LYDK 73.887 0.077494 20582000 7004.2 7261.2 8104.8 13354 12032 10084 13542 80209 10021 21029 TRUE FALSE 6730.46812 7054.117685 9569.51765 14043.20154 12419.02021 10287.90539 13707.73105 78552.65612 8883.458091 19604.6871 0.343309132 0.359817918 0.488123968 0.716318576 0.633471993 0.52476764 0.699206826 4.006830393 0.453129297 1 14.258911 1.962242626 24.85149958 2.203814394 0.525796932 0.27845818 0.88741747 459.7648575 302611.6403 0.345060381 0.222756793 91.6732496 -1.962242626 -1.678017462 VNFPENGFLS(ph)PDKLSLLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNFPENGFLSPDKLSLLEK 19 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 VNFPENGFLS(1)PDKLSLLEK;VNFPENGFLS(1)PDKLSLLEK 179.44 2.17E-14 1019560000 857280 676600 770000 604860 752970 863010 950780 1092320 1392930 1240380 TRUE FALSE 823776.5498 657304.0305 909156.1286 636076.8971 777189.9639 880460.6535 962415.9301 1069763.21 1234810.426 1156367.958 0.712382719 0.568421173 0.786216984 0.550064443 0.672095728 0.761401808 0.832274817 0.925106237 1.067835214 1 20.14116911 1.962249428 1.129291303 1.033270942 0.653095319 0.826043095 0.068368151 0.179786594 0.422366636 0.050245032 0.022760739 91.67468538 -1.962249428 -0.380175623 IESDVQEPTEPEDDLDIMLGNK ddPTM_BT-474_Pertuzumab_2h_R1 2 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 186.01 3.35E-17 99922000 277640 255272 256550 249857 245138 263810 275970 324240 322530 314520 FALSE TRUE 266789.5219 247991.8925 302914.2919 262752.1497 253023.0864 269144.419 279347.4034 317544.3307 285917.7466 293217.2803 0.90986971 0.84576152 1.033071078 0.896100494 0.862920105 0.917900946 0.952697614 1.082965951 0.975105377 1 18.1616106 1.962263189 5.435971895 1.027082379 0.912199438 0.451223435 0.053243028 0.166372075 12.80076556 0.0230555 0.014380792 91.67759017 -1.962263189 -0.114882941 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR 31 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;; 154.63 3.18E-09 251581000 60500 70881 61738 72286 67794 78180 65781 51823.3 69847 66153 FALSE TRUE 58135.59311 68859.54328 72895.42995 76016.68912 69974.65558 79760.85317 66586.04756 50753.13075 61918.26138 61672.39839 0.942651731 1.116537464 1.181978192 1.232588502 1.134618685 1.293299032 1.079673392 0.822947251 1.003986597 1 15.91233733 1.962365255 8.232761473 0.929122227 1.155995957 0.474909818 0.097383896 0.245041993 49.24185578 0.040862937 0.026134317 91.69913832 -1.962365255 0.226873731 FFMPAWNLEIIGTYAQTEMGHGTHLR ddPTM_BT-474_Pertuzumab_2h_R1 3 FFMPAWNLEIIGTYAQTEMGHGTHLR 26 0 Q15067-2;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;; 142.45 1.62E-07 158694000 88120 113089 81832 92747 99363 95453 91114 52237 103177 91368 FALSE TRUE 84676.17298 109863.8124 96620.86274 97533.68378 102559.1011 97383.12506 92229.08039 51158.2877 91464.77951 85179.56398 0.994090237 1.289790735 1.134319762 1.145036194 1.204034117 1.143268649 1.082760654 0.600593444 1.073787834 1 16.37821972 1.962366674 13.62561117 0.845686512 1.155460481 0.414175718 0.135300453 2.104865399 761.0372342 0.052368917 0.033785669 91.69943798 -1.962366674 0.30977397 ELLSAEENKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLSAEENKR 10 1 Q9NWH9;H7BXE3;H0YL55;H0YKU6 Q9NWH9 SLTM SAFB-like transcription modulator 0 103.21 0.0045605 535300000 270880 215710 212420 243220 277240 250510 278530 460600 310710 350160 FALSE TRUE 260293.7101 209558.162 250809.0193 255772.6133 286157.6764 255575.4838 281938.7335 451088.449 275439.5034 326443.3513 0.797362572 0.641943422 0.768307941 0.783513012 0.876592141 0.782909141 0.863668175 1.38182765 0.843758962 1 18.31647313 1.962387454 12.5631246 1.118986822 0.777848568 0.481618258 0.137019604 1.246641155 415.2203737 0.054550359 0.035173414 91.7038257 -1.962387454 -0.341138255 DHLYGTLDPNTR ddPTM_BT-474_Pertuzumab_2h_R1 5 DHLYGTLDPNTR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 172.76 3.49E-05 3896670000 3498438 3926151 3354876 3593530 3858717 4129188 3688176 1384519 4193164 3747146 FALSE TRUE 3361715.175 3814181.018 3961176.722 3778992.514 3982836.137 4212683.01 3733313.001 1355928.199 3717173.602 3493348.464 0.962318878 1.091840982 1.133919723 1.081767981 1.14011991 1.205915486 1.068691841 0.388145704 1.064071804 1 21.73617913 1.962407892 24.6603886 0.744171047 1.107079403 0.313669279 0.181093382 400.023634 262414.4634 0.070690718 0.045635599 91.7081415 -1.962407892 0.362908355 SETIQDTDTQSLVGS(ph)PSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SETIQDTDTQSLVGSPSTR 19 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 SETIQDTDTQSLVGS(0.997)PS(0.001)T(0.001)R 305.83 4.59E-48 0 55522 86260 86975 125910 94220 97748 86970 75283 84101 90975 TRUE FALSE 53352.13886 83799.94926 102693.3172 132408.2302 97250.67187 99724.53153 88034.36488 73728.37974 74554.20706 84813.18222 0.629054794 0.988053355 1.210817877 1.561175123 1.146645714 1.175814053 1.037979741 0.869303307 0.879040323 1 16.37200089 1.962509976 3.756159161 0.906920885 1.137506965 0.142070973 0.218775513 0.436967984 12.39248028 0.110394631 0.065349701 91.7297006 -1.962509976 0.23058608 DHHYFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DHHYFK 6 0 Q92905 Q92905 COPS5 COP9 signalosome complex subunit 5 0 124.12 0.018491 69593000 228890 231180 227070 227790 225890 253060 180320 37287 165930 104340 FALSE TRUE 219944.7257 224586.9727 268106.6001 239546.2692 233155.957 258177.0466 182526.8101 36517.01042 147094.322 97272.95886 2.26110862 2.308832541 2.756229514 2.462619334 2.396924692 2.654150235 1.876439375 0.375407625 1.512181019 1 16.56975118 1.962595454 4.925207034 0.927384111 2.464507944 0.842533958 0.291919284 0.067039687 3.913588282 0.123091348 0.076009155 91.74775661 -1.962595454 1.537123833 S(ph)RS(ph)RS(ph)PPPVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSRSPPPVSK 11 2 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 3 S(1)RS(1)RS(1)PPPVSK;S(1)RS(1)RS(1)PPPVSK 57.973 0.072156 2149300000 1316550 1063000 883990 951120 993930 1045680 1128820 1322260 1479900 1218270 TRUE FALSE 1265097.77 1032684.281 1043746.657 1000207.417 1025900.661 1066824.366 1142634.837 1294954.869 1311907.956 1135755.488 1.113882155 0.90924877 0.918988874 0.880653827 0.903275989 0.939308132 1.006057069 1.140170471 1.155097176 1 20.11522085 1.962718485 3.326101469 1.110706463 0.9374153 0.47240159 0.072154562 0.189312519 4.023022829 0.034544304 0.019940055 91.77375147 -1.962718485 -0.173291163 HFIDVGAGVIDEDYR ddPTM_BT-474_Pertuzumab_2h_R1 8 HFIDVGAGVIDEDYR 15 0 P33316-2;H0YNJ9;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMM5;H0YKI0;H0YMP1 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;;;;;; 220.85 1.61E-12 16090240000 6823806 6735392 5977666 7430123 6807146 7215013 6816802 3944871 7360908 7796193 FALSE TRUE 6557124.117 6543305.215 7057963.219 7813592.538 7026104.033 7360905.506 6900228.062 3863408.035 6525328.583 7268149.904 0.902172383 0.900271087 0.97108113 1.075045595 0.966697733 1.012761928 0.949378886 0.531553158 0.897797744 1 22.79315674 1.962762021 24.52559295 0.753416893 0.973305278 0.221362113 0.123783272 433.9419458 285801.0818 0.049035221 0.031657951 91.78295195 -1.962762021 0.219888385 LNIQS(ph)PLTSQENSHNHGDGAEDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNIQSPLTSQENSHNHGDGAEDFK 24 0 O75182-2;O75182;O75182-3 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 1 LNIQS(0.984)PLT(0.016)SQENSHNHGDGAEDFK 118.35 0.00090496 110360000 54341 53849 50538 56822 55017 54583 53075 11053 71762 41229 TRUE FALSE 52217.29364 52313.27924 59671.34081 59754.59023 56786.67177 55686.70566 53724.54773 10824.75169 63615.87861 38436.52311 1.358533224 1.361030473 1.552464583 1.554630476 1.477414375 1.448796643 1.397747335 0.281626714 1.655089313 1 15.23019022 1.962784575 24.54024438 0.884236072 1.460445664 0.304912234 0.317613833 420.4917286 277275.9518 0.12359867 0.07979574 91.78771851 -1.962784575 0.576209592 GWSQEGPVKS(ph)PAECR ddPTM_BT-474_Pertuzumab_2h_R1 8 GWSQEGPVKSPAECR 15 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR 231.62 1.03E-13 9611980000 5524630 6133770 5722540 7100200 6892220 6460880 5108500 4826000 4842230 4152990 TRUE FALSE 5308721.352 5958840.885 6756730.275 7466642.173 7113914.516 6591523.42 5171019.351 4726341.414 4292560.351 3871704.288 1.371158786 1.539074382 1.745156596 1.928515614 1.837411637 1.702486277 1.335592537 1.220739256 1.108700467 1 21.88453734 1.96283605 1.800801959 1.094897065 1.703811669 0.745596535 0.153018427 0.196283706 1.182998839 0.106601268 0.051915831 91.79859836 -1.96283605 0.608914604 TGS(ph)QEGTSMEGSRPAAPAEPGTLK ddPTM_BT-474_Pertuzumab_2h_R1 4 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.192)GS(0.799)QEGT(0.004)S(0.004)MEGSRPAAPAEPGTLK;T(0.002)GS(0.998)QEGTSMEGSRPAAPAEPGTLK;T(0.007)GS(0.993)QEGTSMEGSRPAAPAEPGTLK;T(0.027)GS(0.904)QEGT(0.027)S(0.041)MEGSRPAAPAEPGTLK 197.35 1.14E-24 5191300000 2708080 2120820 1593500 1599470 2384110 2059810 2403430 3214530 3346710 2753790 TRUE FALSE 2602245.24 2060336.29 1881480.897 1682018.838 2460797.063 2101460.769 2432843.895 3148148.832 2966805.511 2567273.35 1.013622191 0.802538728 0.732871276 0.655177151 0.958525536 0.818557466 0.947637265 1.226261641 1.155625096 1 21.29180548 1.962846148 3.755078998 1.145692171 0.824085273 0.59241815 0.109603497 0.14788041 4.194713956 0.052100861 0.030852463 91.80073281 -1.962846148 -0.321606898 S(ph)GSPAPETTNESVPFAQHSSLDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSPAPETTNESVPFAQHSSLDSR 24 0 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 1 S(0.545)GS(0.455)PAPETTNESVPFAQHSSLDSR 150.62 8.01E-08 295410000 41144 63800 55104 79380 54460 67672 56928 49135 49504 67605 TRUE FALSE 39536.04699 61980.48647 65062.51858 83476.81131 56211.75536 69040.37421 57624.70189 48120.34508 43884.51346 63026.05313 0.627296888 0.983410564 1.032311486 1.324481023 0.891881255 1.095425951 0.914299707 0.763499262 0.696291633 1 15.9436607 1.962931266 4.706455381 0.800622134 1.004930613 0.152805913 0.178665362 0.33023246 17.00921849 0.079729682 0.048977811 91.81872666 -1.962931266 0.204308478 ADEESDSQMS(ph)PSHSSTDDHSNWFIIGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ADEESDSQMSPSHSSTDDHSNWFIIGSK 28 0 B4E2D5;R4GND2;F6S7C4;Q8NEM7-2;Q8NEM7;Q8NEM7-3 B4E2D5 SUPT20H Transcription factor SPT20 homolog 1 ADEES(0.005)DS(0.03)QMS(0.843)PS(0.03)HS(0.03)S(0.03)T(0.03)DDHSNWFIIGSK;ADEES(0.031)DS(0.07)QMS(0.861)PS(0.02)HS(0.006)S(0.006)T(0.006)DDHSNWFIIGSK;ADEES(0.123)DS(0.123)QMS(0.721)PS(0.021)HS(0.004)S(0.004)T(0.004)DDHSNWFIIGSK;ADEES(0.105)DS(0.128)QMS(0.728)PS(0.024)HS(0.005)S(0.005)T(0.005)DDHSNWFIIGSK 223.86 3.12E-34 526668000 311321 411035 352172 436559 423650 414225 395240 241356 433700 448708 TRUE FALSE 299154.2311 399312.6842 415817.3144 459089.8623 437277.087 422600.9133 400077.0653 236371.9143 384468.1942 418316.6075 0.715138309 0.954570479 0.994025355 1.097469845 1.045325668 1.010241778 0.956397758 0.565055056 0.919084223 1 18.67423575 1.96298123 24.17005822 0.774970902 0.979514423 0.134743289 0.143313529 471.923036 308123.9756 0.058352634 0.037670669 91.82929071 -1.96298123 0.204543521 DNQESS(ph)DAELSSSEYIK ddPTM_BT-474_Pertuzumab_2h_R1 3 DNQESSDAELSSSEYIK 17 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 DNQES(0.002)S(0.998)DAELSSSEYIK;DNQES(0.005)S(0.995)DAELSSSEYIK;DNQES(0.203)S(0.797)DAELSSSEYIK 295.16 4.34E-46 1048690000 1793060 1618590 1356310 1418940 1531780 1582570 1615080 1816190 1899820 1768100 TRUE FALSE 1722985.233 1572429.398 1601425.388 1492171.663 1581051.095 1614570.65 1634845.832 1778685.042 1684160.398 1648345.012 1.045281916 0.953944342 0.971535313 0.905254454 0.959174859 0.979510138 0.991810465 1.07907327 1.021728088 1 20.65258681 1.96298924 5.01020773 1.041554081 0.966379343 0.366244475 0.037320915 0.182226411 11.20074946 0.016436476 0.010175441 91.8309845 -1.96298924 -0.075174738 DISTTLNADEAVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DISTTLNADEAVAR 14 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;O95757;E9PDE8;D6RJ96 Q92598-2;O95757 HSPH1;HSPA4L Heat shock protein 105 kDa;Heat shock 70 kDa protein 4L 0 104.26 0.005378 0 108700 115700 101960 113760 91015 107260 109770 135910 111260 117060 FALSE TRUE 104451.8838 112400.3493 120386.4401 119631.1672 93942.58013 109428.8707 111113.3981 133103.411 98630.23124 109131.4219 0.957120158 1.029954043 1.1031327 1.096211935 0.860820637 1.002725601 1.01816137 1.219661658 0.90377482 1 16.73570703 1.96317126 24.99620053 1.078892129 1.010870827 0 0.099164593 1487.083221 1009302.739 0.041190986 0.026564379 91.86948029 -1.96317126 -0.068021302 TLEPVRPPVVPNDYVPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLEPVRPPVVPNDYVPSPTR 20 1 H7C3Q7;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;H0Y6B5 H7C3Q7 ABI2 Abl interactor 2 1 TLEPVRPPVVPNDYVPS(0.954)PT(0.046)R;TLEPVRPPVVPNDYVPS(0.86)PT(0.14)R 119.45 3.07E-05 662420000 123175 144683 118857 154935 130508 146179 148075 299480 141546 182207 TRUE FALSE 118361.1848 140556.7825 140337.1039 162931.2139 134705.9083 149134.8395 149887.1861 293295.6333 125478.2915 169865.9576 0.696791673 0.82745704 0.826163793 0.9591752 0.793012975 0.877956017 0.882385077 1.726629853 0.738690043 1 17.37403723 1.963173534 24.98139893 1.253009451 0.837825742 0.238281497 0.243173386 559.6988627 379673.5242 0.09491847 0.061265423 91.8699614 -1.963173534 -0.415183709 NSS(ph)PAPPQPAPGK ddPTM_BT-474_Pertuzumab_2h_R1 7 NSSPAPPQPAPGK 13 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 NSS(1)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NS(0.001)S(0.999)PAPPQPAPGK;NS(0.01)S(0.99)PAPPQPAPGK;NS(0.006)S(0.994)PAPPQPAPGK;NS(0.013)S(0.987)PAPPQPAPGK;NSS(1)PAPPQPAPGK 257.55 6.98E-24 16744760000 10782040 9374470 9499140 10149130 9712980 9464780 11017360 12839570 13763050 13009290 TRUE FALSE 10360665.96 9107119.294 11215845.91 10672927.82 10025406.82 9656164.336 11152193.75 12574428.39 12200726.26 12128159.2 0.854265333 0.750906971 0.924777266 0.88001218 0.826622297 0.796177241 0.919528971 1.036796119 1.005983353 1 23.53185726 1.963197446 3.794128394 1.014196871 0.84033729 0.75382731 0.044880184 0.112546931 3.278528353 0.021511678 0.012769239 91.87501993 -1.963197446 -0.173859581 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK 41 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 371.48 1.65E-176 1737400000 1189100 1359100 937630 1083100 1109200 1382500 1137600 68763 1447800 1064600 FALSE TRUE 1142628.657 1320339.799 1107080.598 1138998.921 1144878.425 1410455.097 1151522.289 67343.02002 1283451.814 992493.6938 1.151270446 1.33032563 1.115453534 1.147613257 1.153537229 1.421122478 1.160231341 0.06785234 1.293158659 1 19.92069841 1.96328882 24.93738754 0.666084055 1.220260556 0.263995027 0.306681792 518.5125506 352217.6008 0.119533667 0.077174258 91.89435205 -1.96328882 0.5541765 GKTPATPTSQFVFSFPVSVGVHSAPSSLPYLHS(ph)PITTSPSC ddPTM_BT-474_Pertuzumab_2h_R1 1 GKTPATPTSQFVFSFPVSVGVHSAPSSLPYLHSPITTSPSC 41 1 Q13115-2;Q13115 Q13115-2 DUSP4 Dual specificity protein phosphatase 4 1 GKTPATPTSQFVFSFPVS(0.002)VGVHS(0.002)APS(0.011)S(0.05)LPY(0.18)LHS(0.657)PIT(0.042)T(0.046)S(0.009)PS(0.002)C 93.972 0.00010038 154500000 57475 88194 61468 89455 78080 87992 64779 31746 55307 58888 TRUE FALSE 55228.81346 85678.79347 72576.63495 94071.78327 80591.51411 89771.25853 65571.78478 31090.43401 49028.78123 54899.46331 1.005999151 1.560649017 1.321991702 1.713528286 1.467983642 1.635193736 1.194397556 0.56631581 0.893064855 1 15.74450443 1.963329358 5.210523421 0.789311685 1.460827387 0.64508916 0.208969904 0.108072529 7.45122602 0.08769775 0.054552251 91.90293019 -1.963329358 0.671515702 ILENEKDLEEAEEYK ddPTM_BT-474_Pertuzumab_2h_R1 5 ILENEKDLEEAEEYK 15 1 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;;; 258.16 7.48E-25 3006320000 3524260 2646910 3005450 2471530 3020350 2816170 3590860 4479140 5021670 4434740 FALSE TRUE 3386528.023 2571422.718 3548601.671 2599085.959 3117502.301 2873114.887 3634806.019 4386644.194 4451631.074 4134371.11 0.819115636 0.62196224 0.85831716 0.62865328 0.754045106 0.69493396 0.879167816 1.06101849 1.076737176 1 21.97923646 1.963337466 2.806822688 1.051313701 0.727073642 0.791037666 0.072772659 0.105391406 1.5444218 0.034258456 0.018982985 91.90464586 -1.963337466 -0.32424006 VADPDHDHTGFLTEY(ph)VATR ddPTM_BT-474_Pertuzumab_2h_R1 6 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHTGFLT(0.253)EY(0.747)VATR;VADPDHDHTGFLT(0.36)EY(0.639)VATR;VADPDHDHTGFLT(0.003)EY(0.997)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLTEY(1)VATR 277.44 9.62E-39 12782500000 5258830 6710460 5476130 8402400 7569190 7158160 5032380 166684.4 3718650 3100170 TRUE FALSE 5053309.11 6519084.251 6465788.507 8836048.871 7812659.871 7302902.9 5093967.772 163242.3089 3296524.442 2890192.725 1.748433268 2.255588077 2.237147873 3.057252479 2.703162251 2.526787518 1.762501071 0.056481461 1.140589835 1 21.46273427 1.963345977 4.558954794 0.665348104 2.433421132 0.766086686 0.416559202 0.09295866 4.393495656 0.192497819 0.117809881 91.90644706 -1.963345977 1.768073027 AES(ph)PTPGMAQGMEPGAGQEGAMFVHAR ddPTM_BT-474_Pertuzumab_2h_R1 3 AESPTPGMAQGMEPGAGQEGAMFVHAR 27 0 A0A0A0MSQ9;Q86VX9-5;Q86VX9 A0A0A0MSQ9 MON1A Vacuolar fusion protein MON1 homolog A 1 AES(0.936)PT(0.064)PGMAQGMEPGAGQEGAMFVHAR;AES(0.944)PT(0.056)PGMAQGMEPGAGQEGAMFVHAR;AES(0.964)PT(0.036)PGMAQGMEPGAGQEGAMFVHAR 131.08 2.84E-05 904960000 177915 166584 132616 151960 153512 161574 158288 140633 164899 192121 TRUE FALSE 170961.8851 161833.1874 156582.6612 159802.6738 158449.8529 164841.137 160225.1759 137728.8794 146180.3568 179108.4735 0.954515896 0.903548471 0.874233687 0.89221169 0.884658608 0.920342481 0.894570607 0.768969087 0.81615545 1 17.45047407 1.96336749 24.031681 0.83497098 0.902420761 0.041496177 0.06016265 540.0889366 354308.2582 0.023292673 0.015036138 91.9109997 -1.96336749 0.06744978 LGAGGGS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 7 LGAGGGSPEK 10 0 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK 187.85 1.24E-06 3281940000 4923480 4050390 4933681 4922920 4580000 4359180 5869600 6786440 7411290 7880380 TRUE FALSE 4731064.958 3934876.843 5825306.906 5176992.491 4727319.859 4447325.606 5941433.921 6646297.642 6569991.43 7346634.843 0.643977149 0.535602616 0.792921798 0.704675352 0.643467378 0.605355472 0.808728628 0.904672382 0.894285829 1 22.80865214 1.963395322 2.467284529 0.927254705 0.657033677 0.76745571 0.068867973 0.146174543 1.642505061 0.038295902 0.020483033 91.91689019 -1.963395322 -0.270221028 EHGVPILISEIHPGQPADR ddPTM_BT-474_Pertuzumab_2h_R1 3 EHGVPILISEIHPGQPADR 19 0 Q9HD26-2;Q9HD26;A0A0J9YVX5 Q9HD26-2 GOPC Golgi-associated PDZ and coiled-coil motif-containing protein 0 ;; 106.67 0.00017901 580070000 388299 471773 395211 468189 417364 485581 437925 257699 488923 457316 FALSE TRUE 373123.8458 458318.496 466634.4191 492352.2904 430788.8921 495399.7805 443284.4571 252377.4256 433422.5108 426341.58 0.875175829 1.075003043 1.09450835 1.154830571 1.010431336 1.161978573 1.039740147 0.591960619 1.016608586 1 18.70165024 1.96340348 23.87481628 0.82210145 1.068844813 0.275910832 0.134212339 310.2905677 202426.3419 0.052675065 0.034009772 91.91861678 -1.96340348 0.246743363 HMCDGDIVIFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 HMCDGDIVIFNR 12 0 P24928;P24928-2 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 0 ; 191.29 5.55E-06 563220000 773820 790730 671110 823230 761410 861000 781880 552980 862980 835460 FALSE TRUE 743578.2589 768179.1546 792394.5058 865716.999 785901.4441 878410.0099 791448.8813 541560.7698 765018.1283 778873.55 0.954684183 0.986269407 1.017359629 1.111498778 1.009023152 1.127795404 1.016145536 0.695312827 0.982210948 1 19.5710296 1.963505577 24.11491218 0.857922532 1.036999317 0.302235605 0.09294478 337.8544598 223247.807 0.037003293 0.023891773 91.9402281 -1.963505577 0.179076785 RHS(ph)SDINHLVTQGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RHSSDINHLVTQGR 14 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 RHS(0.825)S(0.175)DINHLVTQGR;RHS(0.911)S(0.089)DINHLVTQGR;RHS(0.912)S(0.088)DINHLVTQGR;RHS(0.92)S(0.08)DINHLVTQGR 154.31 2.89E-06 5202320000 1567690 2426720 2102010 3191140 2386560 2724620 2089440 311425 1940340 2264630 TRUE FALSE 1506422.942 2357512.322 2481889.966 3355835.118 2463325.87 2779713.683 2115011.192 304993.9649 1720080.738 2111244.593 0.713523647 1.116645759 1.175557761 1.589505607 1.166764797 1.316623234 1.001784066 0.144461691 0.814723573 1 21.0096623 1.963531977 9.979490986 0.561167008 1.191898996 0.38636623 0.289753212 0.487016844 130.6231658 0.118727927 0.076404221 91.94581727 -1.963531977 0.630731989 TCS(ph)LPDLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TCSLPDLSK 9 0 Q96PY6-4;Q96PY6-2;Q96PY6-6;Q96PY6;Q96PY6-3 Q96PY6-4 NEK1 Serine/threonine-protein kinase Nek1 1 T(0.005)CS(0.995)LPDLSK 104.43 0.0034204 232950000 945510 653300 455150 511270 570590 538390 616530 853670 687310 568190 TRUE FALSE 908558.4239 634668.5236 537405.7298 537656.706 588943.5455 549276.6147 624075.2786 836041.4162 609289.4502 529705.9852 1.715212683 1.198152449 1.014535884 1.015009686 1.111831019 1.036946212 1.178154101 1.578312195 1.150240827 1 19.01483228 1.963557466 24.62256532 1.324889243 1.15957044 0 0.238695149 1241.128825 838572.1685 0.098563679 0.063646695 91.95121374 -1.963557466 -0.165318803 NSSYVHGGVDASGKPQEAVYGQNDIHHK ddPTM_BT-474_Pertuzumab_2h_R1 3 NSSYVHGGVDASGKPQEAVYGQNDIHHK 28 1 Q9UN86-2;Q9UN86;D6RB17;D6RAC7;D6RE13;D6RBW8;D6RGJ4;D6RBM9;D6REX8;D6RBR0 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;; 150.48 1.92E-08 1947390000 968940 982670 848240 861420 908120 951560 908070 215493 1234860 1191890 FALSE TRUE 931072.7536 954645.2137 1001535.837 905877.9894 937330.5045 970801.1952 919183.2323 211042.9942 1094683.87 1111162.229 0.837926929 0.859141167 0.901340786 0.815252684 0.843558645 0.873680881 0.827226852 0.189929957 0.985170159 1 20.08363803 1.963563838 24.99890251 0.603413774 0.854704503 0 0.218747419 854.6607509 586382.8769 0.085919264 0.055471131 91.95256281 -1.963563838 0.251290729 MPTQSEEEKLS(ph)PSPTTEDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 MPTQSEEEKLSPSPTTEDPR 20 1 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 MPT(0.001)QS(0.005)EEEKLS(0.945)PS(0.043)PT(0.003)T(0.003)EDPR;MPTQS(0.001)EEEKLS(0.964)PS(0.035)PTTEDPR;MPTQSEEEKLS(0.837)PS(0.158)PT(0.004)TEDPR;MPTQSEEEKLS(0.915)PS(0.066)PT(0.016)T(0.003)EDPR 130.01 1.02E-05 4079850000 5338620 4786820 4254810 4454750 4910060 4819480 5179180 6048200 6444710 6017490 TRUE FALSE 5129980.828 4650304.58 5023748.815 4684660.181 5067996.539 4916933.188 5242564.354 5923302.556 5713133.539 5609920.042 0.914448119 0.828943112 0.895511661 0.835067193 0.903399068 0.876471171 0.934516769 1.055862207 1.01839839 1 22.41954878 1.963617892 3.174667598 1.02859383 0.874168703 0.839314281 0.029090458 0.083698102 1.602628791 0.013412798 0.007666819 91.96400822 -1.963617892 -0.154425128 KEVS(ph)PEVVR ddPTM_BT-474_Pertuzumab_2h_R1 5 KEVSPEVVR 9 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KEVS(1)PEVVR;KEVS(1)PEVVR;KEVS(1)PEVVR;KEVS(1)PEVVR;KEVS(1)PEVVR 166.7 3.71E-05 7018030000 11047540 10548260 8424570 9219050 9573720 9989390 10230930 11219730 12278830 11442340 TRUE FALSE 10615789.92 10247433.95 9947077.203 9694846.275 9881667.398 10191382.31 10356139.18 10988038.65 10884988.7 10667340.12 0.995167474 0.960636282 0.932479614 0.908834458 0.926347832 0.955381772 0.970826754 1.03006359 1.020403266 1 23.34669715 1.963630281 2.701214375 1.019441233 0.94378034 0.649037281 0.022973485 0.173312445 2.344401142 0.013010672 0.007138017 91.96663185 -1.963630281 -0.075660893 ASS(ph)LSESSPPK ddPTM_BT-474_Pertuzumab_2h_R1 6 ASSLSESSPPK 11 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 AS(0.016)S(0.983)LS(0.001)ESSPPK;ASS(0.736)LS(0.264)ESSPPK;ASS(0.996)LS(0.004)ESSPPK;ASS(0.999)LS(0.001)ESSPPK;ASS(0.856)LS(0.143)ESSPPK;ASS(0.998)LS(0.002)ESSPPK 253.16 2.21E-20 7809620000 11935090 10131730 4803460 7775460 12234740 8016400 9422720 14046100 11153450 10471710 TRUE FALSE 11468653.49 9842782.98 5671552.074 8176752.422 12628281.52 8178497.1 9538038.066 13756043.13 9887357.115 9762451.754 1.174771848 1.008228591 0.580955708 0.837571609 1.293556357 0.837750322 0.977012569 1.409076682 1.012794466 1 23.21881208 1.963631041 23.36967007 1.187818876 0.947232422 0.12304623 0.211771088 424.6179149 272846.0875 0.088845169 0.057370105 91.9667928 -1.963631041 -0.240586454 SS(ph)GPTSLFAVTVAPPGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSGPTSLFAVTVAPPGAR 18 0 Q00839;A0A1X7SBS1;A0A1W2PP22;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.189)S(0.81)GPTSLFAVTVAPPGAR 109.36 0.00038249 45269000 41685 41570 42633 40709 44958 40092 31430 42148 30595 33980 TRUE FALSE 40055.90411 40384.4643 50337.73147 42809.99637 46404.1149 40902.68771 31814.64974 41277.62907 27121.98386 31678.50433 1.26445061 1.274822317 1.589018564 1.351389444 1.464845512 1.291181152 1.004297722 1.303016981 0.856163649 1 14.9512166 1.963831165 0.930864193 0.987943625 1.395331002 0.566156665 0.14029223 0.436650945 0.696943167 0.116382173 0.054794121 92.009181 -1.963831165 0.407387377 VSISEGDDKIEYR ddPTM_BT-474_Pertuzumab_2h_R1 6 VSISEGDDKIEYR 13 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;;;; 222.29 1.61E-11 12332640000 6784240 6246280 5208590 5340640 5740010 5758160 6184620 6946350 7319690 7014380 FALSE TRUE 6519104.4 6068142.21 6149898.077 5616271.07 5924642.635 5874593.94 6260309.23 6802905.445 6488789.478 6539289.795 0.996913213 0.927951261 0.940453516 0.85885031 0.906007047 0.89835351 0.957337788 1.040312581 0.9922774 1 22.64070253 1.963920672 4.777711017 1.012883386 0.919371094 0.566817396 0.034921685 0.143963268 7.785828513 0.016003591 0.00986361 92.02814586 -1.963920672 -0.093512292 EFETAETLLNSEVHMLLEHR ddPTM_BT-474_Pertuzumab_2h_R1 6 EFETAETLLNSEVHMLLEHR 20 0 O15514;E9PHV4 O15514 POLR2D DNA-directed RNA polymerase II subunit RPB4 0 ;;;;; 257.83 1.80E-36 293225700 102889.7 110042.3 84216 112511 102799.2 108474.3 101171.4 30308.06 113468.9 105153.2 FALSE TRUE 98868.65677 106904.0013 99435.70457 118317.7062 106105.8296 110667.7247 102409.5659 29682.18797 100588.3862 98031.0801 1.008543991 1.090511308 1.014328359 1.206940759 1.08236928 1.128904471 1.044664261 0.302783443 1.026086687 1 16.5809516 1.963979164 24.68567765 0.692546956 1.090104749 0.31511908 0.196291114 416.5136823 285443.1062 0.076142089 0.04916166 92.0405412 -1.963979164 0.397557792 (ac)S(ph)DQEAKPSTEDLGDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDQEAKPSTEDLGDK 15 1 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.998)DQEAKPS(0.001)TEDLGDK;S(1)DQEAKPSTEDLGDK;S(1)DQEAKPSTEDLGDK;S(0.984)DQEAKPS(0.007)T(0.009)EDLGDK 138.45 1.19E-18 1757720000 2967370 2219990 2356440 2132180 2453600 2235770 2761120 3408360 3667330 3194800 TRUE FALSE 2851401.9 2156678.059 2782301.127 2242222.065 2532522.272 2280978.801 2794911.413 3337976.175 3251030.073 2978413.35 0.957356003 0.724103006 0.934155471 0.75282434 0.850292412 0.765836885 0.938389365 1.120722943 1.091530856 1 21.50611256 1.96398704 4.048935495 1.077632828 0.828469063 0.667359486 0.075766494 0.113245559 3.902114682 0.031741109 0.019084531 92.04221051 -1.96398704 -0.249163764 (ac)TECFLPPTSS(ph)PSEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.007)S(0.27)S(0.573)PS(0.149)EHR;TECFLPPT(0.002)S(0.123)S(0.751)PS(0.123)EHR 89.466 2.18E-06 589360000 34347.4 32712 23839 40798 22535.6 35143 27060 23905 28572.2 21021 TRUE FALSE 33005.06563 31779.08579 28147.2376 42903.58967 23260.47804 35853.61554 27391.16837 23411.3534 25328.80364 19597.22895 1.684170029 1.621611192 1.436286613 2.189268176 1.186926892 1.829524758 1.397706199 1.194625702 1.29246863 1 14.25836205 1.964148964 3.120517517 1.187211076 1.649572902 0.434865456 0.252531641 0.245566217 4.52823269 0.117193244 0.066750612 92.07653412 -1.964148964 0.462361826 TKHEIHHTGER ddPTM_BT-474_Pertuzumab_2h_R1 1 TKHEIHHTGER 11 1 Q86T24 Q86T24 ZBTB33 Transcriptional regulator Kaiso 0 77.593 0.020768 12036000 23596 26005 23906 25813 26161 26391 21557 4039.8 26450 15328 FALSE TRUE 22673.84223 25263.36286 28226.34599 27145.21202 27002.49232 26924.6441 21820.82101 3956.376718 23447.50689 14289.82091 1.586712834 1.767927186 1.975276399 1.899618771 1.889631263 1.884183453 1.527018509 0.276866781 1.640853797 1 13.80270021 1.964183776 8.662112596 0.892962814 1.831956121 0.583456194 0.323400054 0.211188665 48.03795819 0.128220871 0.082313743 92.08391521 -1.964183776 0.938993307 HSPEEDFRQS(ph)PQEHFR ddPTM_BT-474_Pertuzumab_2h_R1 3 HSPEEDFRQSPQEHFR 16 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 HSPEEDFRQS(1)PQEHFR;HSPEEDFRQS(1)PQEHFR;HSPEEDFRQS(1)PQEHFR 269.39 4.91E-28 1654390000 702476 722409 593296 672290 642338 658572 634986 352542 722640 634760 TRUE FALSE 675022.4613 701806.6026 700517.785 706986.9675 662999.3851 671888.7771 642757.1486 345261.8845 640608.9368 591767.1398 1.140689328 1.185950614 1.1837727 1.194704673 1.120372086 1.13539386 1.086165664 0.583442137 1.0825355 1 19.17467006 1.964190396 14.92575448 0.84046072 1.157880183 0.475527996 0.12455279 3.44787518 1436.249395 0.048660007 0.03143389 92.08531872 -1.964190396 0.317419463 SS(ph)AIGIENIQEVQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSAIGIENIQEVQEK 15 0 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 S(0.191)S(0.809)AIGIENIQEVQEK;S(0.246)S(0.754)AIGIENIQEVQEK 221.13 1.65E-12 191763000 232254 233355 203155 197354 195332 210955 231218 292290 280806 250104 TRUE FALSE 223177.2569 226699.9439 239869.6277 207539.4636 201615.0312 215220.6546 234047.715 286254.1094 248930.0801 233164.2333 0.957167631 0.97227581 1.028758246 0.890099912 0.864691073 0.923043177 1.003789096 1.227693053 1.067616918 1 17.83098697 1.964221887 7.381349045 1.122401945 0.941064596 0.511631669 0.068381836 0.167346939 28.89460704 0.029171283 0.018623599 92.09199623 -1.964221887 -0.181337349 HHYEQQQEDLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HHYEQQQEDLAR 12 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y7I0;A0A2R8Y5M9;A0A2R8YE38;K7EMY3;Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q14839-2;Q12873-3 CHD4;CHD5;CHD3 Chromodomain-helicase-DNA-binding protein 4;Chromodomain-helicase-DNA-binding protein 3 0 ; 169.23 2.57E-05 679200000 255200 257790 192717 265630 232900 226980 201659 40616 237010 172762 FALSE TRUE 245226.5019 250438.0816 227545.2489 279339.1961 240391.44 231569.6911 204126.9632 39777.26541 210105.6184 161060.6759 1.522572165 1.55493003 1.41279209 1.734372432 1.492552038 1.437779209 1.267391696 0.246970685 1.304512211 1 17.29724477 1.964230509 8.07804082 0.762726697 1.516004504 0.565784502 0.261253201 0.176100271 35.96328093 0.104590503 0.067005382 92.09382456 -1.964230509 0.753277806 ELDKAESEIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDKAESEIKK 11 2 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 74.46 0.022927 82140000 406090 354380 328030 271150 361380 389990 407450 477280 552060 531530 FALSE TRUE 390219.5538 344273.4294 387312.318 285144.084 373004.1159 397875.865 412436.495 467424.0012 489392.4632 495528.9997 0.787480761 0.694759398 0.781613827 0.575433696 0.752739226 0.802931544 0.832315556 0.943282838 0.987616191 1 18.91860996 1.964239894 1.126292202 1.002057094 0.713352491 0.794186168 0.057117894 0.207498599 0.484873151 0.043937764 0.019934658 92.09581476 -1.964239894 -0.288704603 DHAEQQHIAAQQK ddPTM_BT-474_Pertuzumab_2h_R1 3 DHAEQQHIAAQQK 13 0 X6R8P6;Q9NRY2 X6R8P6 INIP SOSS complex subunit C 0 ;; 144.51 2.39E-05 458990000 479688 490800 420492 476813 452470 449313 447054 163026 488301 457268 FALSE TRUE 460941.2626 476802.8645 496484.2582 501421.3761 467024.1085 458398.4167 452525.1806 159659.4561 432871.1176 426296.8311 1.08126833 1.118476211 1.164644497 1.176225905 1.095537368 1.075303364 1.061526025 0.374526491 1.015421852 1 18.70149881 1.96430768 21.77476474 0.7248701 1.11775347 0.399198874 0.170910057 92.76935488 56594.94485 0.066564539 0.042987231 92.11019036 -1.96430768 0.39288337 YGDGGSSFQSTTGHCVHMR ddPTM_BT-474_Pertuzumab_2h_R1 5 YGDGGSSFQSTTGHCVHMR 19 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 ;;;; 183.74 1.53E-14 1338115000 514746 642255 428742 607003 556273 623655 494067 195895 473831 530959 FALSE TRUE 494629.1572 623938.5162 506225.2167 638330.4976 574166.0262 636265.7314 500113.5397 191849.6998 420043.6913 494996.674 0.999257537 1.26049032 1.022684077 1.289565226 1.15993916 1.285393953 1.010337172 0.387577755 0.848578816 1 18.91705931 1.9643641 8.738593812 0.681824908 1.170206774 0.535042733 0.173896811 0.219735441 50.86427852 0.067639069 0.043442224 92.12215742 -1.9643641 0.488381866 AEGPLDS(ph)PSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_BT-474_Pertuzumab_2h_R1 2 AEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK 42 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;F8W1U7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 AEGPLDS(0.348)PS(0.115)EGHS(0.187)Y(0.092)QNS(0.187)GLDHFQNS(0.065)NIDQS(0.004)FWET(0.002)FGSAEPTK;AEGPLDS(0.826)PS(0.052)EGHS(0.119)YQNS(0.003)GLDHFQNSNIDQSFWETFGSAEPTK 208.73 1.53E-35 2065890000 160452 201195 183110 204053 214546 225977 173622 85739 165286 169114 TRUE FALSE 154181.3585 195457.1156 216202.0503 214584.1998 221447.0669 230546.4098 175746.838 83968.45969 146523.4262 157659.7581 0.977937302 1.239740045 1.371320449 1.361058791 1.404588397 1.46230346 1.114722235 0.532592849 0.929364779 1 17.26645494 1.964404778 6.714639988 0.779330101 1.309170212 0.616727891 0.169094322 0.122638262 17.18537053 0.071806841 0.045640511 92.13078629 -1.964404778 0.529840111 IHS(ph)PIIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHSPIIR 7 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 IHS(1)PIIR;IHS(1)PIIR 106.2 0.0049957 1246720000 415190 453010 351310 408530 423320 424880 410910 246440 480940 432600 TRUE FALSE 398963.9158 440090.5983 414799.5318 429614.2823 436936.4722 433471.3647 415938.8395 241350.9279 426345.7075 403299.6167 0.98924943 1.091224936 1.02851457 1.065248427 1.083404135 1.074812241 1.031339536 0.598440757 1.057143845 1 18.62149251 1.964440202 24.82700041 0.834155343 1.057162746 0.2666686 0.118510907 486.6043646 339734.8622 0.045938445 0.029660755 92.13830138 -1.964440202 0.223007403 HLMLPDFDLLEDIESK ddPTM_BT-474_Pertuzumab_2h_R1 11 HLMLPDFDLLEDIESK 16 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;;;;; 238.17 8.78E-20 7752903000 5434840 5094664 4624327 4566073 4923508 5230469 5003721 3532576 6364127 5755498 FALSE TRUE 5222440.444 4949369.171 5460045.756 4801728.575 5081877.106 5336232.667 5064958.034 3459627.071 5641697.984 5365672.994 0.973305762 0.922413493 1.017588243 0.894897729 0.947108986 0.994513209 0.94395578 0.64477039 1.051442753 1 22.3553277 1.964567026 24.99880796 0.843041586 0.957081724 0 0.108568882 964.7451196 680649.5291 0.042790206 0.027633403 92.16521202 -1.964567026 0.114040139 THKPDPGT(ph)PQHTSSRPPEPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 THKPDPGTPQHTSSRPPEPQK 21 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 THKPDPGT(1)PQHTSSRPPEPQK 145.14 1.22E-07 166120000 186500 253790 238460 283230 195920 268270 211730 44193 203520 230030 TRUE FALSE 179211.3738 246552.1577 281555.0265 297847.5342 202221.9447 273694.6032 214321.2151 43280.39911 180417.2628 214449.8632 0.83567959 1.149696036 1.312917725 1.38889123 0.942980059 1.276263827 0.999400102 0.201820596 0.841302765 1 17.71028087 1.964573935 11.49521786 0.594176897 1.157932623 0.402786915 0.249237303 0.859256405 277.129568 0.099458112 0.06418984 92.16667823 -1.964573935 0.563755725 AHQGTGAGIS(ph)PVILNSGEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHQGTGAGISPVILNSGEGK 20 0 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 AHQGT(0.072)GAGIS(0.928)PVILNSGEGK 105.17 0.00016743 468030000 297560 322370 323190 310510 319660 303400 313660 190670 352640 345670 TRUE FALSE 285931.0262 313176.3232 381597.6223 326535.4583 329942.1542 309534.9559 317498.6649 186732.5979 312609.7856 322257.463 0.887275111 0.971820234 1.184138976 1.013275085 1.023846434 0.960520675 0.985232931 0.579451585 0.970062206 1 18.29785424 1.964608749 24.39232299 0.79791822 1.010894369 0.200050165 0.129511159 470.0064785 323936.5349 0.052001654 0.03357961 92.17406665 -1.964608749 0.212976148 RQS(ph)SS(ph)RFNLS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 RQSSSRFNLSK 11 2 E9PFR3;Q14738;H0Y8C4 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 3 RQS(0.998)S(0.02)S(0.991)RFNLS(0.991)K 54.436 0.081388 209290000 190100 228030 287410 242770 278520 252880 433410 962410 455720 917120 TRUE FALSE 182670.6818 221526.8077 339351.3804 255299.3888 287478.8487 257993.4069 438714.2012 942535.8972 403988.5761 855002.6455 0.213649259 0.25909488 0.396900971 0.298594852 0.336231531 0.301745741 0.513114437 1.102377755 0.472499797 1 19.70556936 1.964611248 5.175462 0.86084637 0.310787213 0.712679902 0.158105586 0.097374369 6.661770001 0.064931487 0.040436708 92.17459718 -1.964611248 -0.550059157 GKDS(ph)TEMR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKDSTEMR 8 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 GKDS(0.982)T(0.018)EMR;GKDS(0.883)T(0.117)EMR 104.79 0.0027323 1060390000 2129250 1928800 1949810 1927350 1917110 1955420 2246140 2611200 2767200 2820800 TRUE FALSE 2046036.556 1873792.512 2302184.04 2026820.764 1978775.584 1994959.932 2273628.933 2557277.808 2453079.057 2629744.703 0.778036192 0.712537803 0.875440128 0.770729098 0.752459196 0.758613537 0.864581619 0.972443372 0.932820229 1 21.32649132 1.964661974 2.774135852 0.965016743 0.775268555 0.810401046 0.041936561 0.114070335 1.632576722 0.021612409 0.011953954 92.18536378 -1.964661974 -0.189748188 FQMQVLPQCGHAVHEDAPDKVAEAVATFLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 FQMQVLPQCGHAVHEDAPDKVAEAVATFLIR 31 1 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 133.95 1.64E-06 248590000 271120 234600 198080 194720 235580 245110 220570 25562 280290 206890 FALSE TRUE 260524.3307 227909.4377 233877.4623 204769.5225 243157.6446 250066.2921 223269.4016 25034.13577 248472.6543 192877.156 1.350726732 1.18163002 1.212572121 1.061657724 1.260686593 1.296505492 1.15757307 0.129793161 1.288243042 1 17.55732276 1.9647514 24.88075838 0.692912429 1.219248459 0.281860005 0.285848122 516.6677445 364697.0624 0.111333698 0.07188876 92.20434765 -1.9647514 0.52633603 S(ph)PSAIPEQNHSLNDQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSAIPEQNHSLNDQAK 17 0 Q13129 Q13129 RLF Zinc finger protein Rlf 1 S(0.837)PS(0.163)AIPEQNHSLNDQAK;S(0.862)PS(0.138)AIPEQNHSLNDQAK 265.05 1.04E-27 2076700000 816170 743520 521470 728150 708110 651820 708150 827110 828860 728830 TRUE FALSE 784273.1741 722315.5376 615711.229 765729.9088 730887.0012 665000.247 716816.5515 810029.8895 734771.2877 679465.6949 1.154249847 1.063064027 0.906169706 1.126958895 1.075679032 0.978710554 1.054970923 1.192157155 1.08139571 1 19.37404119 1.964817919 24.47928784 1.115292346 1.04666871 0.022843656 0.07989894 954.7264203 664285.7117 0.032484505 0.020958375 92.21847147 -1.964817919 -0.068623636 DLPDGHAAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLPDGHAASPR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR 158.89 1.89E-05 5066730000 4074330 4461050 3964700 4557710 4323410 4560870 3830960 3286690 3603120 3554060 TRUE FALSE 3915100.679 4333825.222 4681209.484 4792933.959 4462476.409 4653093.916 3877844.434 3218818.703 3194108.923 3313340.351 1.181617421 1.30799277 1.412836892 1.446556481 1.346821014 1.404351326 1.170373105 0.9714724 0.964014736 1 21.65985498 1.964861551 2.816166573 0.976598879 1.355026836 0.848432306 0.07028788 0.101230328 1.495735125 0.03840082 0.021328492 92.22773669 -1.964861551 0.378427957 AAEEPSKVEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAEEPSKVEEK 11 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 0 ;;; 138.89 4.38E-05 5602500000 7059570 6305600 5427350 5009600 5660890 5765810 6727030 8804300 9169200 7298690 FALSE TRUE 6783674.2 6125770.462 6408192.876 5268146.056 5842977.668 5882398.629 6809357.405 8622488.128 8128350.856 6804343.225 0.996962378 0.900273584 0.941779781 0.774232851 0.858712954 0.864506453 1.000736909 1.267203585 1.194582723 1 22.69802448 1.96490227 4.424407974 1.177028625 0.887607618 0.665488632 0.083384727 0.110344462 4.840998416 0.037097028 0.022653674 92.23638433 -1.96490227 -0.289421007 DLEEAEEYKEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEEAEEYKEAR 12 1 E5RJD8;O75347;E5RIW3;E5RHG6;E5RIX8 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 150.49 6.22E-05 843890000 731650 726250 682110 607470 709270 763200 756790 898840 1025970 905310 FALSE TRUE 703056.3091 705538.0611 805382.4505 638821.5995 732084.3137 778632.4269 766051.8224 880278.6399 909506.1868 843992.5473 0.833012461 0.835952952 0.954253036 0.756904313 0.867406135 0.922558415 0.907652354 1.04299338 1.077623481 1 19.68687073 1.964904433 1.515017102 1.051978299 0.853717906 0.696475211 0.052757662 0.211171563 0.902266135 0.035193671 0.016417659 92.2368437 -1.964904433 -0.198260393 HLLVSNVGGDGEEIER ddPTM_BT-474_Pertuzumab_2h_R1 4 HLLVSNVGGDGEEIER 16 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;;; 200.94 3.42E-11 1605270000 923070 1063350 855910 945400 1053690 1082510 940640 645850 1005860 985800 FALSE TRUE 886995.4039 1033024.299 1010591.977 994192.2073 1087582.896 1104399.094 952151.8337 632512.9718 891678.9897 919030.8879 0.965142103 1.12403654 1.099627869 1.081783235 1.183401897 1.201699647 1.036038991 0.688239079 0.970238325 1 19.80975382 1.964905394 10.79797672 0.854007397 1.112254187 0.495323511 0.099113265 0.553683063 168.5886177 0.039698716 0.025613202 92.23704772 -1.964905394 0.258246791 ARHT(ph)S(ph)KDS(ph)KAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ARHTSKDSKAAK 12 3 A0A087WYV3;A0A0D9SEW3;A0A087WXF8;Q9NP64-2;Q9NP64-3;Q9NP64 A0A087WYV3 ZCCHC17 Nucleolar protein of 40 kDa 3 ARHT(1)S(1)KDS(1)KAAK 57.175 0.09091 99073000 46080 82313 74715 108100 87362 78769 69663 60439 53873 66479 TRUE FALSE 44279.14266 79965.51383 88217.66253 113679.054 90172.07807 80361.76315 70515.55663 59190.91353 47757.56289 61976.31812 0.714452617 1.290259187 1.423409218 1.834233743 1.454944095 1.296652747 1.137782282 0.955056953 0.770577607 1 15.91942943 1.964907364 1.90011978 0.886585933 1.36975042 0.345227553 0.263098442 0.38870563 2.604362833 0.16989913 0.084203074 92.23746612 -1.964907364 0.483164487 SYENQKPPFDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SYENQKPPFDAK 12 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 97.273 0.0045732 381040000 321270 425240 240120 387040 282080 357360 396600 607710 523460 398030 FALSE TRUE 308714.4132 413112.5716 283515.0254 407015.1808 291153.3594 364586.064 401453.7094 595160.5761 464039.0153 371071.0736 0.831954941 1.113297697 0.764045073 1.096865829 0.784629631 0.982523538 1.081878212 1.603899141 1.250539447 1 18.50133602 1.96492089 6.587145556 1.351675117 0.938214934 0.428321793 0.179087167 0.151341728 20.4204906 0.070842786 0.045012636 92.24033896 -1.96492089 -0.413460183 FIPHENGVHTIDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 FIPHENGVHTIDVK 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ; 209.39 3.88E-09 455360000 726580 713610 638630 679880 650190 742440 672480 78604 885280 728130 FALSE TRUE 698184.4503 693258.5415 754044.6472 714968.6883 671103.9518 757452.6455 680710.0114 76980.79993 784786.7258 678813.1065 1.02853708 1.02128043 1.110828061 1.05326294 0.988643185 1.115848587 1.002794443 0.113404999 1.156116048 1 19.3726549 1.964952375 24.99322283 0.633022182 1.051994214 0.160592986 0.262935214 634.2471318 452294.6113 0.102504037 0.066184496 92.24702626 -1.964952375 0.418972032 FVIKPIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 FVIKPIDK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 99.802 0.0085761 0 2215700 2416400 1911500 2237100 2054100 2233500 2359200 2845800 2756500 2777900 FALSE TRUE 2129107.994 2347486.638 2256950.571 2352556.999 2120171.992 2278662.9 2388072.595 2787033.236 2443593.676 2589750.359 0.822128661 0.906452867 0.871493487 0.908410724 0.818678134 0.879877434 0.922124632 1.076178337 0.943563409 1 21.3043816 1.965145729 4.92822774 1.012945824 0.871109674 0.693105538 0.041164833 0.101526185 6.05291992 0.01730473 0.010725332 92.28810517 -1.965145729 -0.14183615 DLILQCLDDKDESIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLILQCLDDKDESIR 15 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ; 223.06 1.20E-12 643000000 434681 433175 386897 407090 438182 454707 438194 504700 565600 546240 FALSE TRUE 417693.186 420821.2731 456817.8944 428099.9637 452276.522 463901.4871 443556.7493 494277.7686 501395.4592 509242.6783 0.820224235 0.82636686 0.897053436 0.840660027 0.888135542 0.910963489 0.871012522 0.970613402 0.984590414 1 18.95799381 1.965233877 0.527189821 1.011698258 0.836120712 0.816600622 0.026589455 0.347316447 0.208793186 0.025801736 0.018573917 92.30683856 -1.965233877 -0.175577546 KDPEDTGAEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KDPEDTGAEK 10 1 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ;; 106.26 0.0039131 1858500000 1049590 913460 827634 874060 984030 881860 1045450 1420280 1273150 1219780 FALSE TRUE 1008570.862 887409.0152 977205.8744 919170.3413 1015682.219 899691.8134 1058244.53 1390950.722 1128627.349 1137163.214 0.886918298 0.780370842 0.859336516 0.808301157 0.893171891 0.791172105 0.930600389 1.223175974 0.992493721 1 20.1170079 1.965239855 6.759871445 1.093095151 0.837975879 0.695237398 0.069310347 0.096589935 13.98765467 0.027250225 0.017348245 92.30810916 -1.965239855 -0.255119272 SENQEFYQDTFGQQWK ddPTM_BT-474_Pertuzumab_2h_R1 2 SENQEFYQDTFGQQWK 16 0 O60506-2;O60506 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 372.75 4.96E-104 389420000 1093130 1083740 911030 1009400 1056570 1032350 1058140 1202890 1190500 1151280 FALSE TRUE 1050409.271 1052832.796 1075673.387 1061495.255 1090555.534 1053224.824 1071089.834 1178049.901 1055359.431 1073302.78 0.978670037 0.980928044 1.002208703 0.988998887 1.016074451 0.981293297 0.99793819 1.097593263 0.983282118 1 20.03362569 1.965249648 24.90559963 1.040293061 0.992165065 0.179129032 0.030440485 621.3190447 445299.0346 0.011936138 0.007708939 92.3101907 -1.965249648 -0.048127996 GVSSESSGDREK ddPTM_BT-474_Pertuzumab_2h_R1 1 GVSSESSGDREK 12 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 0 63.555 0.063701 845240000 577360 905910 520250 865940 738730 718500 593890 510610 474550 517960 FALSE TRUE 554796.1329 880074.3338 614270.7479 910631.2672 762491.9213 733028.5623 601158.2035 500065.7251 420681.0735 482878.1078 1.148936189 1.82256002 1.272103121 1.885840862 1.57905672 1.518040579 1.244948143 1.035594112 0.871195166 1 18.88129953 1.965255167 1.805713974 0.943199734 1.562798915 0.598466971 0.209952786 0.221130833 1.340105462 0.122099856 0.059633018 92.3113638 -1.965255167 0.619599181 LHDVLHSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHDVLHSDK 9 0 Q00535;Q00535-2 Q00535 CDK5 Cyclin-dependent-like kinase 5 0 157.66 3.93E-05 87179000 77976 68094 67650 73689 75870 64610 69399 18445 88009 63335 FALSE TRUE 74928.61171 66152.02579 79875.85987 77492.09812 78310.42745 65916.45847 70248.32572 18064.1043 78018.58728 59045.26404 1.269002907 1.120361249 1.35279029 1.312418521 1.326277877 1.116371644 1.189736838 0.305936549 1.321335226 1 15.84953373 1.965386546 24.67594036 0.785938338 1.246234409 0.29518983 0.248644763 477.1875208 340186.3674 0.097443229 0.062925573 92.33929317 -1.965386546 0.460296071 SVASLFDAFHAGFHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVASLFDAFHAGFHK 15 0 Q5GLZ8-6;Q5GLZ8-3;Q5GLZ8-2;Q5GLZ8 Q5GLZ8-6 HERC4 Probable E3 ubiquitin-protein ligase HERC4 0 106.52 0.00071097 116900000 109520 129410 100340 114970 123430 125040 115750 55615 129220 125310 FALSE TRUE 105239.8373 125719.3535 118473.6701 120903.6155 127400.238 127568.3945 117166.5831 54466.53082 114551.4873 116822.6421 0.900851371 1.076155711 1.014132774 1.034933069 1.090544057 1.091983473 1.00294413 0.466232657 0.980558951 1 16.83396039 1.96550863 24.4786012 0.750864272 1.039020639 0.276318969 0.149133836 413.5993016 293531.5622 0.05798249 0.037442164 92.36525426 -1.96550863 0.288156367 YSYLTEPGMSPQS(ph)PCER ddPTM_BT-474_Pertuzumab_2h_R1 7 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLT(0.002)EPGMS(0.087)PQS(0.911)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMS(0.012)PQS(0.988)PCER;YSYLTEPGMS(0.002)PQS(0.998)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMSPQS(1)PCER 318.32 2.25E-58 2823990000 1899040 2506200 2155640 2692060 2503050 2809730 2145610 1952510 2007030 2052340 TRUE FALSE 1824823.417 2434725.63 2545212.1 2830997.539 2583562.876 2866544.666 2171868.617 1912189.986 1779200.369 1913333.184 0.953740537 1.272504784 1.33025033 1.479615554 1.350294292 1.498194193 1.135123059 0.99940251 0.929895736 1 20.86765669 1.965531705 3.65230843 0.984746023 1.322760806 0.530639918 0.1420161 0.189954728 5.066228862 0.06964106 0.041144046 92.37016196 -1.965531705 0.338014784 DKRPLS(ph)GPDVGTPQPAGLASGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKRPLSGPDVGTPQPAGLASGAK 23 2 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 DKRPLS(0.997)GPDVGT(0.003)PQPAGLASGAK;DKRPLS(0.999)GPDVGT(0.001)PQPAGLASGAK;DKRPLS(0.997)GPDVGT(0.003)PQPAGLASGAK;DKRPLS(1)GPDVGTPQPAGLASGAK 220.78 1.48E-32 3772020000 2160140 1881480 1549570 1544660 1708840 1838940 1904310 2559530 2295450 1973170 TRUE FALSE 2075719.341 1827822.033 1829611.769 1624380.088 1763806.391 1876124.627 1927615.515 2506674.811 2034880.139 1839525.438 1.128399367 0.993637812 0.994610746 0.883043014 0.958837727 1.019895995 1.047887393 1.36267472 1.106198423 1 20.8109022 1.96556248 12.72148142 1.19880126 0.993035378 0.298486566 0.103569947 1.68962568 622.6237097 0.041740302 0.026980221 92.37670765 -1.96556248 -0.205765882 RVPGS(ph)SGHLHK ddPTM_BT-474_Pertuzumab_2h_R1 3 RVPGSSGHLHK 11 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 RVPGS(0.5)S(0.5)GHLHK;RVPGS(0.5)S(0.5)GHLHK;RVPGS(0.5)S(0.5)GHLHK 85.837 0.0070148 991691000 1201050 1343240 966860 982200 1040920 1002880 883960 135133 984890 649023 TRUE FALSE 1154111.638 1304932.11 1141593.11 1032891.46 1074402.137 1023158.921 894778.1669 132342.4563 873089.4162 605064.0941 1.907420469 2.156684099 1.886730878 1.707077762 1.775683184 1.690992625 1.47881551 0.21872469 1.442970133 1 19.20672845 1.965727 5.741062325 0.804744175 1.840910895 0.662087372 0.307073392 0.103220958 9.669671292 0.130579939 0.082266778 92.41170858 -1.965727 1.03616672 ERS(ph)PALK ddPTM_BT-474_Pertuzumab_2h_R1 8 ERSPALK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK 86.18 0.012273 92071200000 36056900 31235400 29394970 30159400 31683200 31554200 35040400 39642600 43414000 41360000 TRUE FALSE 34647756.48 30344596.97 34707294.97 31715930.25 32702318.9 32192247.54 35469234.9 38823966.46 38485824.73 38558650.36 0.898572854 0.786972487 0.900116955 0.822537354 0.848118868 0.834890414 0.9198775 1.006880845 0.998111302 1 25.20055122 1.965820391 2.717145743 1.002227357 0.84682977 0.821729878 0.031912507 0.098464801 1.35038411 0.01518262 0.008360308 92.43158301 -1.965820391 -0.155397587 VMTNKKMVTPYANGWK ddPTM_BT-474_Pertuzumab_2h_R1 1 VMTNKKMVTPYANGWK 16 2 O43251-10;O43251-7;A0A0G2JRA5;B0QYV1;A0A0G2JRD1;S4R469;B0QYY4;O43251-9;O43251-8;O43251-6;S4R3K7;O43251-4;O43251;O43251-2;O43251-5;O43251-3 O43251-10 RBFOX2 RNA binding protein fox-1 homolog 2;RNA binding protein fox-1 homolog 0 64.394 0.097622 516580000 235170 411070 302980 452770 390500 453160 327490 270840 240570 376150 FALSE TRUE 225979.2964 399346.6861 357735.2258 476137.514 403060.7871 462323.2057 331497.9206 265247.0594 213261.5022 350673.0255 0.644415966 1.138800698 1.020138989 1.357781977 1.149392049 1.318388277 0.945319134 0.756394248 0.608149149 1 18.41976693 1.965823688 4.373291042 0.774033248 1.117900821 0.325631568 0.203371534 0.228530459 9.753166917 0.090982904 0.055532133 92.43228467 -1.965823688 0.343867573 IYEFPETDDEEENK ddPTM_BT-474_Pertuzumab_2h_R1 4 IYEFPETDDEEENK 14 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;; 229.29 3.11E-12 785290000 582611 511804 557064 583958 610596 537622 695380 818180 929900 858020 FALSE TRUE 559841.918 497207.851 657737.8566 614096.1424 630236.3749 548493.0852 703890.2685 801284.2971 824341.6505 799905.5412 0.699885035 0.621583206 0.822269409 0.767710824 0.787888497 0.685697319 0.879966736 1.001723648 1.030548744 1 19.60947012 1.965847468 2.63539856 1.012415839 0.734130151 0.839474073 0.054936551 0.110718754 1.425112081 0.030328649 0.016562157 92.43734611 -1.965847468 -0.278285689 THYDPPR ddPTM_BT-474_Pertuzumab_2h_R1 6 THYDPPR 7 0 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;H0YBD7;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;; 105.39 0.0079373 5520420000 3471260 3757150 3234390 3744450 3669050 3839370 3439270 1883400 3799190 3484170 FALSE TRUE 3335599.322 3649999.761 3818916.222 3937701.513 3787068.325 3917004.692 3481360.815 1844507.132 3367921.879 3248184.063 1.02691204 1.123704719 1.175708072 1.212277826 1.165903241 1.205906013 1.071786804 0.567857947 1.036863002 1 21.63120196 1.965902903 14.3078694 0.820093125 1.153609604 0.48006301 0.129128306 2.596867809 1088.772609 0.050779621 0.032838607 92.44914589 -1.965902903 0.333516479 FVSEDDRNS(ph)FTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 1 FVSEDDRNS(0.999)FT(0.001)LK;FVSEDDRNS(0.994)FT(0.006)LK 156.17 1.51E-06 723140000 617220 595270 497705 518920 563206 559300 590920 670570 697380 661300 TRUE FALSE 593098.36 578293.4824 587651.3649 545701.5234 581322.0325 570609.4292 598151.8557 656722.4952 618216.3461 616509.562 0.962026214 0.938012187 0.953190998 0.885146893 0.942924601 0.925548385 0.970223161 1.065226779 1.002768463 1 19.23376375 1.965905612 5.109719473 1.028087798 0.934380789 0.702762635 0.025582723 0.096230415 6.413998172 0.010949333 0.006822395 92.44972244 -1.965905612 -0.09370701 IMYTVFEHTFHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 IMYTVFEHTFHVR 13 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 202.18 5.55E-08 1171820000 407440 455520 307490 443280 395150 428960 394130 94539 461850 440360 FALSE TRUE 391516.7944 442529.0156 363060.2831 466157.7339 407860.3586 437633.8651 398953.4808 92586.73661 409422.7242 410534.025 0.953676847 1.077935052 0.884361005 1.135491106 0.993487345 1.066011191 0.971791512 0.225527559 0.997293036 1 18.64714227 1.965928951 24.75566349 0.640830552 1.019248603 0.210966833 0.216989836 527.4272714 383222.305 0.08399832 0.054251253 92.45469091 -1.965928951 0.37841805 SDHLIQTDTVNLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDHLIQTDTVNLHR 14 0 P51151 P51151 RAB9A Ras-related protein Rab-9A 0 202.25 9.66E-09 151600000 32998 50819 41626 70296 51251 48070 49908 33316 56888 54602 FALSE TRUE 31708.40168 49369.69188 49148.74417 73923.98498 52899.53496 49042.00834 50518.78903 32628.01296 50430.31273 50903.75791 0.622908857 0.969863403 0.965522904 1.452230405 1.039206871 0.963426088 0.992437319 0.640974543 0.99069921 1 15.63548454 1.966003756 23.65477483 0.832176032 1.017590163 0.052697405 0.210458508 672.3996554 467857.5502 0.089108352 0.057559967 92.47061712 -1.966003756 0.185414131 HSHGPLQADVFVELLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSHGPLQADVFVELLSPR 18 0 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 HSHGPLQADVFVELLS(1)PR 83.606 0.0066408 34416000 36049 39257 32099 41357 40821 38287 29818 3444.2 28106 22146 TRUE FALSE 34640.16523 38137.4288 37900.00334 43491.43973 42134.04454 39061.18937 30182.9216 3373.076066 24915.52471 20646.03169 1.677812266 1.847203829 1.835704018 2.1065278 2.040781743 1.891946595 1.46192363 0.163376484 1.206794849 1 14.33357689 1.966034762 5.328017474 0.713404532 1.896636283 0.764978326 0.274127555 0.080309798 6.062904883 0.116220934 0.072751967 92.47721911 -1.966034762 1.183231751 EEEKLELQK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEEKLELQK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 125.75 0.00044953 1305430000 2446300 2105510 1898360 1701230 2030250 2035410 2278410 2683120 2977940 2627180 FALSE TRUE 2350695.891 2045462.916 2241435.881 1789030.684 2095554.835 2076567.385 2306293.863 2627712.634 2639896.736 2449238.759 0.95976592 0.835142311 0.915156137 0.730443562 0.855594347 0.847841958 0.941637011 1.072869121 1.077843769 1 21.22390199 1.966054517 2.881720836 1.056445492 0.8532206 0.679414137 0.059143745 0.144655444 2.246968686 0.029630758 0.016576097 92.48142586 -1.966054517 -0.203224892 VLPGMHHPIQMKPADSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLPGMHHPIQMKPADSEK 18 1 Q92879-4;G5EA30;Q92879-6;Q92879;Q92879-5;Q92879-3;Q92879-2 Q92879-4 CELF1 CUGBP Elav-like family member 1 0 186.94 2.93E-14 546800000 400200 384020 322160 306420 340290 309190 337210 114830 467360 411200 FALSE TRUE 384559.7416 373068.1256 380381.4784 322234.3729 351235.7369 315442.0336 341336.8769 112458.7204 414307.2521 383349.0577 1.003158176 0.973181277 0.992258806 0.840576927 0.916229556 0.822858508 0.890407502 0.293358541 1.080757194 1 18.54829911 1.966070012 24.94058683 0.682612887 0.920012722 7.47E-05 0.210117889 917.995912 674781.2523 0.083585645 0.053979359 92.48472555 -1.966070012 0.237399835 AAGDGDCGTTHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AAGDGDCGTTHSR 13 0 H0YCY6;Q3LXA3-2;Q3LXA3;I3L252 H0YCY6 TKFC;DAK Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing);ATP-dependent dihydroxyacetone kinase;FAD-AMP lyase (cyclizing) 0 ;; 212.59 1.27E-08 916000000 430480 486568 358517 458132 473009 469735 440070 416972 473671 478181 FALSE TRUE 413656.3657 472691.557 423308.9971 481776.2474 488223.7641 479233.3635 445455.7083 408361.3825 419901.8539 445793.375 0.927910527 1.060337779 0.94956323 1.080716481 1.095179497 1.075012305 0.999242549 0.916032865 0.941920355 1 18.76601565 1.966072415 6.101596339 0.946104217 1.034523224 0.286317771 0.0552655 0.223528767 25.04963594 0.023779716 0.015060796 92.48523715 -1.966072415 0.088419008 EGDQIVGATIYFDNLQSGEVTQLLNTMGHHTVGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGDQIVGATIYFDNLQSGEVTQLLNTMGHHTVGLK 35 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 323.12 1.40E-105 762950000 322580 369220 307930 334450 297920 359180 325560 113284 386690 343140 FALSE TRUE 309973.217 358690.2071 363579.8009 351711.0046 307502.8674 366442.8657 329544.3007 110944.6458 342794.5723 319898.8222 0.968972674 1.121261418 1.136546232 1.099444512 0.961250389 1.145496139 1.030151654 0.346811673 1.071571849 1 18.28725616 1.966094312 24.75737714 0.722283828 1.074711068 0.2456666 0.193849028 511.4412827 373445.328 0.075451912 0.048731545 92.4899005 -1.966094312 0.35242724 TKEELEAEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKEELEAEKR 10 2 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 113.65 0.00082126 1406990000 2670300 2220100 2039000 1839470 2193600 2045140 2373700 2784000 2981800 2664300 FALSE TRUE 2565941.724 2156784.922 2407492.657 1934405.267 2264159.136 2086494.132 2402750.051 2726509.427 2643318.565 2483844.588 1.033052445 0.868325229 0.969260585 0.778794807 0.911554268 0.84002604 0.967351203 1.097697272 1.064204491 1 21.24414348 1.966139714 4.770505368 1.059822196 0.896882683 0.500341321 0.068675027 0.150023426 8.198424674 0.029165122 0.01802927 92.49957002 -1.966139714 -0.162939513 SDPDGGDS(ph)PLPASGGPLTCK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDPDGGDSPLPASGGPLTCK 20 0 Q8N1G0 Q8N1G0 ZNF687 Zinc finger protein 687 1 SDPDGGDS(1)PLPASGGPLTCK;SDPDGGDS(1)PLPASGGPLTCK 433.57 5.25E-174 455810000 519540 440700 414290 425360 419430 417000 466780 539170 558650 519920 TRUE FALSE 499235.8024 428131.6675 489161.4188 447312.8806 432921.3469 425432.0257 472492.5933 528035.9511 495234.3941 484705.3553 1.029977897 0.883282313 1.009193345 0.922855247 0.893163944 0.877712658 0.97480374 1.089395744 1.021722555 1 18.8867485 1.966199319 7.187827279 1.043795163 0.933683423 0.429524286 0.051863205 0.187038458 31.92808149 0.021192003 0.013552809 92.51226601 -1.966199319 -0.11011174 HIVDCIR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIVDCIR 7 0 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 78.178 0.049554 0 58703 67046 65032 69669 72049 65009 67476 52606 82556 74077 FALSE TRUE 56408.82186 65133.91372 76784.72903 73264.62544 74366.52152 66323.52652 68301.79147 51519.66772 73184.58898 69059.69881 0.816812451 0.943153747 1.111860178 1.060888285 1.076843989 0.960379609 0.989025331 0.746016397 1.059729339 1 16.07555642 1.966209225 24.99428524 0.897151336 1.002165286 0.021519579 0.109769564 1173.560207 868054.8036 0.045837168 0.029606939 92.51437618 -1.966209225 0.10501395 AVEEEDKMTPEQLAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEEEDKMTPEQLAIK 16 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 ; 200.71 3.18E-11 362020000 307225 290663 270407 261078 282969 278598 345650 473430 469540 443900 FALSE TRUE 295218.3073 282373.5758 319275.5601 274552.2669 292070.9549 284231.4424 349880.1681 463653.5051 416239.7877 413834.2576 0.713373294 0.682334946 0.771505873 0.663435329 0.705767948 0.686824344 0.845459654 1.120384542 1.005812786 1 18.65869355 1.966274335 3.621550509 1.048507773 0.705657137 0.928697512 0.041861919 0.051448901 1.346317718 0.019072953 0.011258751 92.52824722 -1.966274335 -0.342850637 RHT(ph)PLSK ddPTM_BT-474_Pertuzumab_2h_R1 5 RHTPLSK 7 1 P61956;P61956-2;A8MUA9;A8MU27;P55854;P55854-2 P61956;A8MUA9 SUMO2;SUMO3 Small ubiquitin-related modifier 2;Small ubiquitin-related modifier 3 1 RHT(1)PLSK;RHT(1)PLSK;RHT(1)PLSK;RHT(1)PLSK;RHT(1)PLSK 91.584 0.00955 2463950000 2660040 2515520 2368160 2463160 2588690 2880750 2571040 1370740 3399030 2912220 TRUE FALSE 2556082.696 2443779.833 2796139.191 2590283.983 2671957.565 2939000.739 2602505.157 1342433.74 3013186.364 2714972.745 0.941476374 0.900112105 1.02989586 0.95407366 0.984156312 1.082515743 0.958575058 0.494455697 1.109840373 1 21.37250628 1.966323257 24.99967033 0.790574151 0.982750861 0.030862843 0.159690022 889.5860143 660376.2292 0.063227435 0.040841023 92.53867085 -1.966323257 0.19217671 QFDVDILISGHTHKFEAFEHENK ddPTM_BT-474_Pertuzumab_2h_R1 1 QFDVDILISGHTHKFEAFEHENK 23 1 Q9UBQ0;F8VXU5;Q9UBQ0-2;Q05DG7 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 135.68 4.81E-06 271320000 712090 743040 505370 526080 675460 761920 617960 10153 855110 417780 FALSE TRUE 684260.7355 721849.2267 596701.6009 553231.0518 697186.7843 777326.5444 625522.7793 9943.337002 758041.4977 389483.3885 1.756841898 1.853350484 1.532033505 1.420422714 1.790029575 1.995788697 1.606031985 0.025529553 1.94627427 1 18.57120227 1.96633543 24.31467059 0.86568992 1.718460818 0.330539511 0.460092838 411.0467196 296883.0092 0.180623565 0.116670338 92.54126466 -1.96633543 0.852770898 EQHGVAASCLEDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQHGVAASCLEDLR 14 0 O00273;O00273-2;K7ERT1 O00273 DFFA DNA fragmentation factor subunit alpha 0 ; 173.03 2.76E-06 534920000 188098 197687 149371 176518 188406 203441 179048 157490 191455 189024 FALSE TRUE 180746.9222 192049.1603 176365.6624 185628.1151 194466.2501 207554.7164 181239.243 154237.7765 169721.831 176221.2361 1.025681843 1.089818484 1.000819574 1.053381075 1.103534707 1.17780763 1.028475608 0.875250792 0.963117924 1 17.42702827 1.966355905 9.044481513 0.936898428 1.075279935 0.537257375 0.053364177 0.28551593 73.28995529 0.022759246 0.014667929 92.54562762 -1.966355905 0.138381507 AIVDALPPPCESACTVPTDVDKWFHHQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIVDALPPPCESACTVPTDVDKWFHHQK 28 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 122.78 2.92E-05 1832300000 539090 531930 378450 459370 528180 573240 486530 152930 617130 474840 FALSE TRUE 518021.7668 516759.8772 446844.3336 483078.1408 545169.3894 584831.3056 492484.2997 149771.9421 547075.9896 442678.6639 1.17019818 1.167347603 1.009410143 1.091261405 1.231523979 1.321119253 1.112509682 0.338331061 1.235830941 1 18.75590031 1.966389076 24.81332978 0.769756407 1.162739797 0.245365479 0.226908953 566.5218748 418235.1124 0.089996938 0.058122535 92.55269641 -1.966389076 0.392983391 KDKS(ph)PVREPIDNLTPEER ddPTM_BT-474_Pertuzumab_2h_R1 7 KDKSPVREPIDNLTPEER 18 3 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;H0Y4X3;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 1 KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER 227.38 2.14E-19 67750690000 4883670 4107150 3635770 3197240 3666540 3964650 4252690 4873890 5460120 4821070 TRUE FALSE 4692810.777 3990018.103 4292834.516 3362249.94 3784477.589 4044817.939 4304735.692 4773242.468 4840310.068 4494534.635 1.044114944 0.887748883 0.955123247 0.74807521 0.842017672 0.899941433 0.957771169 1.062010387 1.076932422 1 22.09974032 1.966449016 2.656683258 1.052322971 0.889229849 0.451420383 0.07363842 0.247498899 3.240358619 0.039799594 0.021794707 92.56547122 -1.966449016 -0.163093122 DGQDAIAQS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 6 DGQDAIAQSPEK 12 0 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK 291.13 4.20E-36 6796930000 7139330 5563280 6048800 5880090 6034930 5392380 6976950 8694080 9020180 8361420 TRUE FALSE 6860317.091 5404620.701 7141952.715 6183562.15 6229049.004 5501417.618 7062336.001 8514544.21 7996246.982 7795093.576 0.880081429 0.693336218 0.916211287 0.793263364 0.799098682 0.705753891 0.905997591 1.092295317 1.02580513 1 22.89413491 1.96647763 4.691466393 1.041902955 0.798244874 0.721438358 0.067171416 0.097938353 5.111573494 0.028335875 0.017486706 92.57157017 -1.96647763 -0.243658081 RFEKPLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RFEKPLEEK 9 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 213.34 1.15E-06 6974800000 8068900 7601600 6512300 6404200 7733600 7359200 8189500 10005600 10366400 10047000 FALSE TRUE 7753558.467 7384809.811 7689217.475 6734721.529 7982358.267 7508008.066 8289725.551 9798980.863 9189649.731 9366507.741 0.827796088 0.788427236 0.820926827 0.719021616 0.852223528 0.801580298 0.885039097 1.046172291 0.981118042 1 23.15907982 1.966479355 3.086127963 1.011399538 0.800730954 0.864553173 0.036636283 0.081186489 1.464834948 0.01757307 0.010006574 92.57193783 -1.966479355 -0.210668584 HEHPPNPPVS(ph)PGKTVNDVNSNNNMSYR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEHPPNPPVSPGKTVNDVNSNNNMSYR 27 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 HEHPPNPPVS(0.993)PGKT(0.007)VNDVNSNNNMSYR 133.94 1.74E-05 149720000 205430 199450 123300 109210 157080 203800 150610 7555.3 178600 106500 TRUE FALSE 197401.5685 193761.8813 145583.0528 114846.3412 162132.6209 207920.9756 152453.2102 7399.280415 158326.0768 99286.66014 1.988198296 1.951539925 1.46629016 1.156714719 1.632974869 2.09414815 1.535485331 0.074524417 1.594635941 1 16.59931227 1.966534673 19.89468896 0.791413786 1.696114511 0.418689419 0.431201606 45.53486445 27068.95356 0.176571096 0.11412435 92.58372997 -1.966534673 0.904700725 T(ph)KFASDDEHDEHDENGATGPVK ddPTM_BT-474_Pertuzumab_2h_R1 3 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.646)KFAS(0.354)DDEHDEHDENGATGPVK;T(0.505)KFAS(0.495)DDEHDEHDENGATGPVK;T(0.635)KFAS(0.365)DDEHDEHDENGATGPVK 219.09 1.65E-25 4382880000 2044780 1689630 1431650 1322600 1563290 1613170 1558860 481550 2214400 1537230 TRUE FALSE 1964867.737 1641443.407 1690381.002 1390859.545 1613574.643 1645789.403 1577937.795 471605.8242 1963030.596 1433112.043 1.371049631 1.145369907 1.179517687 0.970516961 1.125923581 1.148402465 1.101056824 0.329078125 1.369767706 1 20.45071998 1.966563779 24.9387408 0.797568113 1.145547111 0.130950075 0.259018941 776.3340462 579035.6399 0.102208456 0.066023767 92.589935 -1.966563779 0.347978998 LEKEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEKEEAK 7 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6;K7EQK3 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 76.827 0.036211 970870000 533190 464900 370600 350220 422470 416640 481480 554780 594430 600480 FALSE TRUE 512352.3453 451641.5072 437575.664 368294.8962 436059.1312 425064.7463 487372.4963 543323.5991 526952.7985 559808.9547 0.915227134 0.806777925 0.781651776 0.657893899 0.778942758 0.759303228 0.870605038 0.970551819 0.94130827 1 19.09457504 1.966566029 2.676527026 0.967737035 0.778322287 0.656223582 0.060575306 0.178188838 2.36942605 0.03334066 0.018297029 92.59041462 -1.966566029 -0.189414748 KHPDASVNFSEFSK ddPTM_BT-474_Pertuzumab_2h_R1 3 KHPDASVNFSEFSK 14 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;; 152.74 4.27E-06 1023510000 1300680 1196930 1011380 1094420 1172960 1115060 1170790 1276960 1316250 1260500 FALSE TRUE 1249847.988 1162794.728 1194158.864 1150903.147 1210689.324 1137607.277 1185118.478 1250590.33 1166834.818 1175125.212 1.063587075 0.989507089 1.016197127 0.979387673 1.030264104 0.968073245 1.008504001 1.064218789 0.992945097 1 20.16438306 1.966597062 24.97374272 1.028732888 1.005540917 0 0.031312367 1420.906158 1062339.926 0.012201168 0.007881428 92.59703111 -1.966597062 -0.023191971 YGPLS(ph)EPGSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGPLSEPGSAR 11 0 Q9H1Z4 Q9H1Z4 WDR13 WD repeat-containing protein 13 1 YGPLS(0.999)EPGS(0.001)AR 135.5 0.0012449 0 228960 195730 150750 203830 191330 182840 197280 267540 202670 183880 TRUE FALSE 220011.9901 190147.972 177993.8784 214349.6907 197484.3032 186537.1501 199694.3717 262015.2055 179663.7513 171425.6438 1.283425193 1.109215446 1.038315356 1.25039455 1.152011442 1.088151959 1.164903729 1.528448135 1.048056447 1 17.38722341 1.966630255 24.87379754 1.27483246 1.148647174 0 0.154012258 1242.579407 926216.5326 0.061177854 0.039520986 92.60410855 -1.966630255 -0.126185286 KAGTQIENIDEDFRDGLK ddPTM_BT-474_Pertuzumab_2h_R1 3 KAGTQIENIDEDFRDGLK 18 2 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;; 227.95 1.51E-19 1544830000 1675920 1511290 1319080 1360680 1443770 1407530 1605850 1858150 2031300 1823040 FALSE TRUE 1610423.194 1468189.489 1557467.099 1430904.858 1490210.173 1435991.221 1625502.873 1819778.553 1800715.34 1699563.877 0.947550848 0.863862494 0.916392211 0.84192473 0.876819161 0.844917476 0.956423524 1.070732661 1.059516129 1 20.69673315 1.966638783 3.765020793 1.047344771 0.881003256 0.812658946 0.034696486 0.085784728 2.473883363 0.015640483 0.009309204 92.6059268 -1.966638783 -0.166341515 KETQS(ph)PEQVK ddPTM_BT-474_Pertuzumab_2h_R1 10 KETQSPEQVK 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 KETQS(1)PEQVK;KET(0.436)QS(0.564)PEQVK;KET(0.002)QS(0.998)PEQVK;KETQS(1)PEQVK;KET(0.003)QS(0.997)PEQVK;KET(0.001)QS(0.999)PEQVK;KET(0.278)QS(0.722)PEQVK;KETQS(1)PEQVK;KET(0.021)QS(0.979)PEQVK;KET(0.035)QS(0.965)PEQVK 217.46 4.44E-09 54430990000 13274400 10820380 10843730 9762320 10356430 10067860 12512860 14211650 16255020 14555990 TRUE FALSE 12755621.77 10511793.36 12803433.23 10266154.51 10689553.98 10271439.03 12665996.12 13918174.46 14409818.28 13570099.83 0.939979951 0.774629036 0.943503245 0.756527559 0.78772847 0.756916983 0.933375309 1.025650116 1.061880049 1 23.693928 1.966659977 3.322097948 1.028641787 0.824776761 0.655333264 0.065883864 0.146177738 3.117424789 0.031310793 0.018146809 92.61044635 -1.966659977 -0.203865026 HIANYISGIQTIGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIANYISGIQTIGHR 15 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 208.39 1.69E-09 2792600000 734940 801020 788460 831140 875170 911100 789560 434830 792090 895490 FALSE TRUE 706217.7323 778175.6939 930952.2612 874035.235 903320.6379 929523.0662 799222.8715 425850.6085 702175.2639 834837.6647 0.8459342 0.932128157 1.115129684 1.046952326 1.082031485 1.11341774 0.957339259 0.510099899 0.841091979 1 19.67113617 1.966682013 15.35149656 0.730386868 1.027242059 0.35262581 0.139259926 5.22681596 2407.228307 0.056205901 0.036364779 92.61514538 -1.966682013 0.296855192 DHLLSVSLSGYINYLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHLLSVSLSGYINYLDR 17 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 219.97 4.16E-15 727290000 683510 722300 637800 662680 707480 618500 627430 281730 686310 701240 FALSE TRUE 656797.6735 701700.7112 753064.6478 696880.9942 730236.7367 631006.4938 635108.676 275912.177 608402.966 653744.3902 1.004670454 1.073356379 1.151925216 1.065983899 1.117006505 0.96521898 0.971493883 0.422049017 0.930643498 1 19.31836714 1.966733827 13.65690522 0.714165454 1.061661064 0.37174839 0.154211354 2.223941951 911.8282935 0.06098454 0.039465037 92.6261956 -1.966733827 0.347495609 SHKEPPS(ph)PADVPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHKEPPSPADVPEK 14 1 F8VW41;Q86VP3-4;Q86VP3;Q86VP3-3;Q86VP3-2 F8VW41 PACS2 Phosphofurin acidic cluster sorting protein 2 1 S(0.008)HKEPPS(0.992)PADVPEK 90.223 0.0035253 327120000 420210 370450 306040 281720 339680 340770 292380 91088 332730 268720 TRUE FALSE 403787.7286 359885.1287 361348.2358 296259.603 350606.1157 347660.6029 295958.2339 89207.00097 294959.8853 250519.355 1.611802523 1.436556184 1.44239648 1.182581693 1.399517078 1.387759452 1.181378716 0.356088259 1.1773936 1 17.93456254 1.966747946 8.282811289 0.770668552 1.392707877 0.561495476 0.220584681 0.187655094 42.71075681 0.088880534 0.057187571 92.62920692 -1.966747946 0.622039324 IHVYGYSMAYGPAQHAISTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHVYGYSMAYGPAQHAISTEK 21 0 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ; 270 2.97E-38 1732000000 762530 746320 686900 841030 811920 807860 770130 364040 905400 962170 FALSE TRUE 732729.4846 725035.6843 811038.11 884435.6591 838036.1442 824195.4827 779555.0813 356522.4468 802622.7877 897001.3689 0.816865514 0.80828827 0.904165967 0.985991426 0.934264064 0.918834142 0.869067884 0.397460315 0.894784351 1 19.77475066 1.966781487 24.9619938 0.681165515 0.896910057 0.051848113 0.158714256 786.5184559 591027.0108 0.063111436 0.040760182 92.63636119 -1.966781487 0.215744541 HLPSTEPDPHVVR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLPSTEPDPHVVR 13 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;M0R3F1;M0QYZ0;M0QYI8;M0QYM5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ;;; 135.6 4.75E-05 2300190000 1697040 2053800 1733230 2244160 1476780 1841180 1821090 937530 1921900 2099520 FALSE TRUE 1630717.801 1995227.635 2046463.216 2359981.367 1524281.97 1878409.921 1843377.044 918169.6779 1703733.969 1957317.64 0.833139071 1.019368341 1.045544767 1.205722218 0.778760656 0.959685788 0.941787376 0.469095899 0.870443271 1 20.90044647 1.966834093 23.82375751 0.717003051 0.978230523 0.184134752 0.168596795 401.3007436 288261.6201 0.067662446 0.04370939 92.64758288 -1.966834093 0.261227472 DHTLEDEDVIQIVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DHTLEDEDVIQIVK 14 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 ;;; 165.7 3.92E-06 980260000 1257150 1277620 1108160 1131720 1236260 1315070 1189540 332381 1497250 1230540 FALSE TRUE 1208019.188 1241183.529 1308429.163 1190128.205 1276025.426 1341661.616 1204097.946 325517.2162 1327288.457 1147194.43 1.053020444 1.081929529 1.140546998 1.037425021 1.112300925 1.169515456 1.04960233 0.283750695 1.15698649 1 20.12967849 1.966868601 24.99632127 0.717165893 1.0989807 0.224167904 0.217797739 607.8107236 458568.3395 0.084754599 0.05474476 92.65494472 -1.966868601 0.381814808 LSFSDTYQDYEEYWR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSFSDTYQDYEEYWR 15 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 0 88.021 0.01616 22755000 19796 20901 17891 18480 24090 22962 22885 38787 24694 29443 FALSE TRUE 19022.35043 20304.92394 21124.30168 19433.75501 24864.87673 23426.30737 23165.07348 37986.0349 21890.84065 27448.79938 0.693012112 0.739738145 0.769589277 0.708000184 0.90586391 0.853454719 0.843937585 1.383886937 0.797515415 1 14.74445543 1.966881562 19.45615308 1.105820997 0.784564478 0.411647857 0.148158052 34.9583841 20536.19489 0.059014664 0.038152563 92.65770987 -1.966881562 -0.321256519 THKHS(ph)PEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 THKHSPEKR 9 2 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 THKHS(1)PEKR;THKHS(1)PEKR;T(0.003)HKHS(0.997)PEKR;T(0.001)HKHS(0.999)PEKR 126.5 0.00022403 1316273000 1000236 777196 665297 575563 727863 631965 680920 78370 877674 523059 TRUE FALSE 961145.6713 755031.131 785530.9674 605267.8754 751275.3744 644743.7653 689253.3026 76751.63211 778044.127 487631.748 1.971048184 1.548363358 1.610910222 1.241239681 1.540661324 1.322193987 1.413470935 0.157396709 1.59555675 1 18.89543253 1.966930209 23.20267496 0.814379352 1.515837231 0.345579001 0.375120106 242.5873502 170205.0765 0.148059518 0.095656475 92.66808951 -1.966930209 0.70145788 LHGSAFRPSLPAPES(ph)PGLPAHPSNPQLPEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHGSAFRPSLPAPESPGLPAHPSNPQLPEAR 31 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 LHGSAFRPSLPAPES(1)PGLPAHPSNPQLPEAR 86.944 0.00032831 83282000 37839 69628 59407 87467 61917 93422 60889 29338 46953 67658 TRUE FALSE 36360.21005 67642.27761 70143.1664 91981.18235 63908.61654 95311.05685 61634.1778 28732.16005 41623.09228 63075.4634 0.576455694 1.072402389 1.112051543 1.458272003 1.013208831 1.511063918 0.977149821 0.455520396 0.659893563 1 15.94479128 1.96698183 9.063178027 0.66165643 1.1405584 0.318418931 0.271127688 0.402794991 105.5838537 0.111229441 0.071751611 92.67910466 -1.96698183 0.47890197 QGS(ph)FTIEKPSPNIPIELIPHINK ddPTM_BT-474_Pertuzumab_2h_R1 3 QGSFTIEKPSPNIPIELIPHINK 23 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 QGS(0.978)FT(0.022)IEKPSPNIPIELIPHINK;QGS(0.95)FT(0.05)IEKPSPNIPIELIPHINK;QGS(0.949)FT(0.051)IEKPSPNIPIELIPHINK 226.07 6.40E-33 3870870000 3500690 2474460 2199310 1994470 2615690 2585480 2757080 3364050 3613350 2860870 TRUE FALSE 3363879.165 2403890.824 2596774.24 2097404.836 2699826.044 2637760.177 2790821.97 3294581.192 3203177.656 2667100.727 1.26124939 0.90131235 0.97363186 0.786398809 1.012269997 0.988999085 1.046387915 1.235266879 1.200996132 1 21.34684088 1.966987356 4.173800348 1.167838429 0.976508328 0.230679709 0.125876417 0.256569992 9.688133103 0.055900246 0.033917928 92.68028395 -1.966987356 -0.191330101 AGAAS(ph)MIHYMVLISAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGAASMIHYMVLISAR 16 0 C9IYN1;Q9NV64 C9IYN1 TMEM39A Transmembrane protein 39A 1 AGAAS(0.972)MIHY(0.027)MVLIS(0.001)AR;AGAAS(0.99)MIHY(0.009)MVLIS(0.001)AR 41.967 0.085681 551040000 864610 615620 560250 535440 699130 652890 633040 218740 895930 641640 TRUE FALSE 830820.0853 598063.1204 661499.6377 563074.1226 721618.1514 666091.8831 640787.3329 214222.9426 794227.7824 598181.1513 1.388910506 0.999802684 1.105851691 0.941310373 1.206353878 1.113528706 1.071226219 0.358123859 1.327737895 1 19.19022293 1.967011526 24.87643747 0.796644474 1.112722898 0.10648015 0.253562905 815.5464356 614998.2481 0.099404596 0.064218597 92.68544217 -1.967011526 0.316078425 YYIEYMESTR ddPTM_BT-474_Pertuzumab_2h_R1 1 YYIEYMESTR 10 0 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 89.047 0.025819 0 28219 33137 26233 32697 41119 33339 36836 91505 35328 37417 FALSE TRUE 27116.17028 32191.9652 30973.88665 34384.49609 42441.62998 34013.13742 37286.80999 89615.38977 31317.71355 34882.71326 0.77735267 0.922862994 0.887943734 0.985717362 1.216695205 0.975071439 1.06891943 2.569048718 0.897800389 1 15.09022464 1.967146343 24.96163739 1.702212507 0.973089033 0.17512086 0.447121767 652.7165647 495921.9043 0.175474816 0.113332151 92.71421867 -1.967146343 -0.729123474 VHELNEEIGK ddPTM_BT-474_Pertuzumab_2h_R1 6 VHELNEEIGK 10 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;B8ZZ09;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;;;; 155 1.35E-05 10760790000 17458500 15583660 13415900 13702770 14611060 15663450 14923040 8976370 18769900 16916300 FALSE TRUE 16776202.52 15139229.27 15840451.57 14409971.6 15081038.01 15980175.69 15105672.63 8791004.823 16639219.64 15770543.93 1.063768161 0.959968745 1.004432798 0.913726988 0.956278875 1.013292614 0.95784094 0.557431935 1.055082165 1 23.91072908 1.967158595 24.99310987 0.805656939 0.980831116 0.070981399 0.132524782 818.224323 622687.62 0.05205482 0.03362999 92.71683437 -1.967158595 0.175174177 AASSS(ph)SPGSPVASSPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AASSSSPGSPVASSPSR 17 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 AASS(0.027)S(0.486)S(0.486)PGS(0.001)PVASSPSR;AAS(0.002)S(0.044)S(0.948)S(0.006)PGSPVASSPSR;AASSS(0.998)S(0.001)PGS(0.001)PVASSPSR 274.81 1.11E-35 369377000 520130 595440 483006 595440 587870 549890 484383 498903 461335 484919 TRUE FALSE 499802.7446 578458.6342 570295.9286 626170.7298 606779.3724 561009.1526 490311.024 488600.4787 408966.1849 452075.0042 1.105574827 1.279563411 1.261507324 1.385103631 1.342209516 1.240964768 1.084578929 1.080795165 0.904642329 1 18.78620263 1.967225727 1.492954913 0.975053637 1.281645847 0.724915365 0.077800131 0.215602691 0.894426641 0.055181896 0.025709808 92.73116738 -1.967225727 0.306592211 IATS(ph)LDGFDVASVQQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 IATSLDGFDVASVQQQR 17 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 1 IAT(0.222)S(0.778)LDGFDVASVQQQR 64.588 0.042185 0 44321 35866 30780 30053 36847 36311 36427 43817 41157 37747 TRUE FALSE 42588.88632 34843.1368 36342.6307 31604.03893 38032.21722 37045.2333 36872.80452 42912.16364 36485.0299 35190.36207 1.210242914 0.990132944 1.03274387 0.898087916 1.080756633 1.052709638 1.047809751 1.219429444 1.03679041 1 15.10289274 1.967233838 24.79129376 1.115745663 1.037344246 0.005507921 0.091672456 1173.897212 888183.6092 0.03673636 0.023733198 92.73289931 -1.967233838 -0.078401417 EQAPDIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 EQAPDISPK 9 0 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 EQAPDIS(1)PK;EQAPDIS(1)PK;EQAPDIS(1)PK 110.8 0.0023371 1179000000 2226750 2054560 1675770 1809510 2082420 1921830 2104060 2497610 2516250 2337870 TRUE FALSE 2139726.148 1995965.96 1978618.916 1902899.028 2149402.931 1960690.719 2129810.116 2446033.481 2230615.849 2179523.983 0.981740126 0.915780683 0.907821585 0.873080105 0.986179986 0.899595845 0.977190493 1.122278764 1.023441755 1 21.05558165 1.967245385 6.333602368 1.059935552 0.926915947 0.598652216 0.044135787 0.113584641 14.39807271 0.018000973 0.011451453 92.73536478 -1.967245385 -0.133019605 S(ph)SPVNNHHSPGQTPTLGQPEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPVNNHHSPGQTPTLGQPEAR 22 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;E7EWM2;E7EMW0;Q96L14 Q5SW79 CEP170;CEP170P1 Centrosomal protein of 170 kDa;Cep170-like protein 1 S(0.333)S(0.333)PVNNHHS(0.333)PGQTPTLGQPEAR;S(0.383)S(0.383)PVNNHHS(0.234)PGQTPTLGQPEAR;S(0.373)S(0.373)PVNNHHS(0.255)PGQTPTLGQPEAR 175.32 2.70E-12 1945640000 597430 676190 595750 714080 714430 748710 657800 190576 733070 715980 TRUE FALSE 574081.7751 656905.7233 703415.2774 750933.7544 737410.2898 763849.4292 665850.3532 186640.539 649854.9669 667486.0369 0.860065594 0.984149011 1.053827704 1.125017922 1.104757626 1.144367653 0.997549486 0.279617144 0.973585859 1 19.34837813 1.967284635 24.32657601 0.662914524 1.051092788 0.268020083 0.203736486 415.070708 308638.5739 0.080589758 0.052062043 92.74374623 -1.967284635 0.388178265 NLAPHHAS(ph)PDPPAPPASASDPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLAPHHASPDPPAPPASASDPHR 23 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 NLAPHHAS(1)PDPPAPPASASDPHR;NLAPHHAS(1)PDPPAPPASASDPHR 118.97 0.00038632 3124900000 835250 808210 688590 845870 707400 768070 733020 117291.8 820580 693390 TRUE FALSE 802607.5066 785160.6421 813033.5306 889525.4521 730154.1634 783600.9016 741990.918 114869.6833 727431.1986 646426.0777 1.241607562 1.214617834 1.257736281 1.376066781 1.12952461 1.212204966 1.147835682 0.177699643 1.125312273 1 19.30212587 1.967300915 22.55826435 0.67291925 1.234719277 0.416380709 0.242779108 142.4870263 98297.42598 0.094322806 0.06095021 92.74722309 -1.967300915 0.561800027 HRDLLHNEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HRDLLHNEDR 10 1 Q8N684-2;Q8N684;Q8N684-3;F5H669 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ; 101.71 0.0018897 88482000 143828 183471 125773 137498 136270 157263 132086 24029 142704 128207 FALSE TRUE 138207.0427 178238.5867 148502.9789 144594.2883 140653.2483 160442.9656 133702.508 23532.79275 126504.8402 119523.4257 1.156317617 1.491243961 1.242459192 1.209756894 1.176783944 1.342355816 1.118630153 0.19688854 1.058410428 1 16.86693388 1.967313774 14.84034187 0.661298743 1.268256303 0.474240813 0.238388857 3.333284342 1512.485991 0.092739501 0.06003662 92.74996909 -1.967313774 0.60695756 NHSGS(ph)RT(ph)PPVALNSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 NHS(0.198)GS(0.803)RT(0.999)PPVALNSSR 84.108 0.017417 563690000 381020 343460 255330 301550 282980 347820 266030 23022 318240 197570 TRUE FALSE 366129.3172 333664.8571 301473.8108 317113.0316 292082.3087 354853.1587 269285.7547 22546.58765 282114.7294 184188.4079 1.987797828 1.811541024 1.636768645 1.721677467 1.585780082 1.926577045 1.4620125 0.12241046 1.531663868 1 17.49082274 1.967315573 10.9699433 0.787941209 1.756564402 0.572226457 0.342222297 0.522810277 173.8583324 0.13320726 0.086194315 92.7503533 -1.967315573 0.968623193 HDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HDSIPAADTFEDLSDVEGGGSEPTQR 26 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDSIPAADTFEDLS(1)DVEGGGSEPTQR 261.92 4.84E-53 664260000 140332 251450 165774 251240 187368 214360 181250 139220 142483 206568 TRUE FALSE 134847.6703 244278.8922 195733.0494 264206.5265 193394.8619 218694.5061 183468.1917 136345.0583 126308.9272 192576.9654 0.700227413 1.268474097 1.016388689 1.371952902 1.004247115 1.135621312 0.952700607 0.708002944 0.655888034 1 17.55507562 1.967628066 3.596994422 0.762767919 1.096729676 0.32731185 0.187281352 0.231219404 5.968193163 0.083268283 0.049162829 92.81711515 -1.967628066 0.333961756 EKEIS(ph)DDEAEEEKGEK ddPTM_BT-474_Pertuzumab_2h_R1 8 EKEISDDEAEEEKGEK 16 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK 233.28 9.43E-20 51952440000 6107470 4116074 5782470 4488060 5072860 4705820 7358340 10057770 11621860 9658810 TRUE FALSE 5868783.32 3998687.6 6827490.959 4719689.314 5236033.149 4800974.905 7448393.566 9850073.535 10302595.18 9004610.196 0.651753179 0.444071149 0.758221712 0.524141436 0.5814836 0.533168544 0.827175569 1.093892275 1.144146715 1 23.10223239 1.967928734 2.73618253 1.08855776 0.581218359 0.868591559 0.086658 0.084332866 1.175366757 0.04247175 0.023478865 92.8813959 -1.967928734 -0.507339401 YDYNSGEELESYK ddPTM_BT-474_Pertuzumab_2h_R1 2 YDYNSGEELESYK 13 0 Q9Y3F4;Q9Y3F4-2;H0YH33 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 274 8.63E-32 831280000 556210 566150 489030 528420 569910 558690 598390 696480 743290 718960 FALSE TRUE 534472.6983 550003.9563 577408.5994 555691.8195 588241.6727 569987.0946 605713.2758 682097.4446 658914.8353 670264.1988 0.797406007 0.820577852 0.861464181 0.829063853 0.877626574 0.850391675 0.903693315 1.017654599 0.983067329 1 19.35437035 1.967972431 2.394914003 1.002764768 0.839773984 0.907510491 0.022904076 0.082583679 0.875556525 0.012909778 0.006874527 92.89074177 -1.967972431 -0.162990784 AGDLLEDS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 AGDLLEDSPK 10 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK 193.81 5.58E-07 1.07095E+11 85731100 66131800 65817000 62905200 65669400 60558700 77909900 94594900 102874300 89459900 TRUE FALSE 82380633.83 64245785.81 77711595.99 66151744.91 67781715.89 61783238.41 78863384.66 92641482.26 91196440.75 83400701.29 0.987769078 0.770326686 0.931785882 0.79317972 0.812723572 0.740799987 0.945596181 1.110799799 1.093473308 1 26.31355618 1.967990555 4.507747526 1.072704854 0.836874375 0.653656795 0.074527747 0.115294099 5.412869026 0.031898258 0.01961788 92.89461845 -1.967990555 -0.23583048 TGSSS(ph)PPGGPPKPGSQLDSMLGSLQSDLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 TGS(0.003)S(0.027)S(0.97)PPGGPPKPGSQLDSMLGSLQSDLNK 322.43 4.82E-93 3418100000 1182500 1002200 1022700 851710 1036600 971370 1146100 1358700 1505600 1286700 TRUE FALSE 1136286.593 973618.2373 1207524.64 895666.8552 1069943.18 991011.7669 1160126.315 1330642.37 1334690.6 1199550.663 0.947260193 0.811652452 1.00664747 0.746668634 0.891953307 0.82615249 0.96713407 1.109284011 1.112658799 1 20.19406266 1.968166921 3.710730511 1.081240193 0.870843408 0.600501483 0.073813326 0.140871364 3.931945249 0.03231019 0.019211553 92.93235026 -1.968166921 -0.210396786 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_BT-474_Pertuzumab_2h_R1 1 NKDSGSDTASAIIPSTTPSVDSDDESVVKDK 31 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPSTTPS(0.005)VDS(0.989)DDES(0.006)VVKDK 212.36 7.27E-27 1024500000 1192000 1124400 736860 660810 762450 870130 1042400 1334400 1587200 1034000 TRUE FALSE 1145415.322 1092333.213 870026.9934 694914.4833 786974.8967 887724.6248 1055157.203 1306844.174 1407027.71 963966.259 1.188231758 1.133165401 0.902549218 0.720890878 0.816392575 0.9209084 1.094599726 1.355694934 1.459623402 1 19.87862312 1.968172631 3.392521126 1.303807014 0.93865041 0.421717251 0.168709788 0.222592901 4.997715939 0.08592051 0.050119332 92.93357229 -1.968172631 -0.365156604 HTQWGIDFLER ddPTM_BT-474_Pertuzumab_2h_R1 2 HTQWGIDFLER 11 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ; 135.58 0.0011357 0 184074 192445 168127 187802 200721 184163 184595 162151 204170 210160 FALSE TRUE 176880.1846 186956.657 198511.2889 197494.4837 207177.3733 187886.902 186854.1288 158802.5252 180993.4776 195925.676 0.902792264 0.95422234 1.013196907 1.008007157 1.057428396 0.958970288 0.953699039 0.810524319 0.923786413 1 17.57994695 1.968193805 9.942361853 0.88825191 0.984601162 0.195930881 0.058935696 0.616129812 188.3991287 0.024450636 0.015824435 92.9381033 -1.968193805 0.096349251 VDVDIPDVNIEGPDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDVDIPDVNIEGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 178.58 6.43E-09 379360000 210940 193210 200230 193980 181060 192780 215640 275220 251770 248320 FALSE TRUE 202696.2316 187699.84 236416.0151 203991.331 186883.9593 196678.1437 218279.0668 269536.6108 223190.1251 231501.0652 0.875573645 0.810794714 1.021230787 0.881168002 0.807270408 0.849577705 0.942885799 1.164299657 0.964099776 1 17.82065931 1.968205869 7.484957396 1.059783536 0.876868492 0.507009502 0.073809708 0.171212847 33.49941425 0.030828555 0.019813065 92.94068489 -1.968205869 -0.182915044 NHVQPYIPSILEALMVPTSQGFTEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NHVQPYIPSILEALMVPTSQGFTEVR 26 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 123.79 0.00012474 183728000 126318 140128 110717 116815 125889 114213 104239 39653 104859 86688 FALSE TRUE 121381.3529 136131.6866 130726.0248 122843.8361 129938.334 116522.4651 105514.7081 38834.15169 92955.84592 80816.54455 1.501936931 1.684453195 1.617565135 1.520033266 1.607818483 1.441814492 1.305607765 0.480522298 1.150208122 1 16.30236305 1.968222494 4.674009107 0.827795244 1.560254534 0.756722434 0.172779997 0.085366455 4.453617507 0.074353158 0.045979569 92.94424279 -1.968222494 0.732459291 HIPTALPVSGTLSSSNPDLLQS(ph)HHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIPTALPVSGTLSSSNPDLLQSHHR 25 0 A0A2R8Y661;A0A2R8YGD3;Q9Y4G8 A0A2R8Y661 RAPGEF2 Rap guanine nucleotide exchange factor 2 1 HIPTALPVSGTLS(0.041)S(0.258)S(0.258)NPDLLQS(0.442)HHR 111.79 0.0041612 666480000 187460 266770 206380 296020 250830 246890 212670 31586 223540 229700 TRUE FALSE 180133.856 259161.9808 243677.4569 311297.6277 258898.1747 251882.285 215272.7191 30933.73806 198164.6764 214142.2144 0.841187976 1.210233029 1.137923494 1.453695753 1.209001109 1.17623835 1.005279224 0.14445418 0.925388191 1 17.7082097 1.968297674 11.95675246 0.589721047 1.17827236 0.391820948 0.259296463 1.021034052 383.4432134 0.103115376 0.066832863 92.96033379 -1.968297674 0.588551313 NHSVNEEEQEEQGEGS(ph)EDEWEQVGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NHSVNEEEQEEQGEGSEDEWEQVGPR 26 0 Q14694;Q14694-3;Q14694-2;H3BNA1 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 NHSVNEEEQEEQGEGS(1)EDEWEQVGPR;NHSVNEEEQEEQGEGS(1)EDEWEQVGPR 254.29 9.25E-53 6490400000 2862800 2674600 2216580 2507100 2509800 2981100 2563000 1476870 2839400 2592100 TRUE FALSE 2750918.611 2598323.027 2617165.314 2636491.731 2590529.996 3041379.885 2594366.761 1446372.118 2517083.216 2416534.758 1.138373285 1.075226838 1.083024072 1.091021647 1.07200196 1.258570718 1.073589673 0.598531477 1.041608529 1 21.20450832 1.968303544 23.31249261 0.835594227 1.117003764 0.420053655 0.123194124 214.0312164 157417.5311 0.048197837 0.031147136 92.96159017 -1.968303544 0.281409537 GLQSIFQEQGMAESVHTWQDHGYLATYTNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLQSIFQEQGMAESVHTWQDHGYLATYTNK 30 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 295.01 3.26E-81 1096000000 259390 294450 247690 337460 316170 317600 283310 33910 321740 278110 FALSE TRUE 249252.752 286052.5743 292453.0928 354876.351 326339.8952 324022.0896 286777.2325 33209.74665 285217.424 259273.362 0.961351178 1.103285629 1.127972001 1.368734329 1.258671129 1.249731508 1.106080587 0.12808777 1.100064511 1 17.98411446 1.968310033 24.49607379 0.638649567 1.184321392 0.3319621 0.26597434 429.7137891 332164.3676 0.105315086 0.068051636 92.96297913 -1.968310033 0.545671825 LVES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVESPK 6 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PK;LVES(1)PK 86.794 0.055776 466890000 1859440 1598770 1506020 1639350 1733330 1690330 1972730 2371500 2565000 2525900 TRUE FALSE 1786771.029 1553174.645 1778191.315 1723957.05 1789084.134 1724509.631 1996872.86 2322527.696 2273831.953 2354818.543 0.758772277 0.659572963 0.755128806 0.73209762 0.759754563 0.732332279 0.847994367 0.986287331 0.96560814 1 21.16718446 1.968360851 2.167384067 0.987591963 0.72989398 0.937578895 0.029004533 0.067009209 0.582205286 0.016142076 0.008348028 92.97385759 -1.968360851 -0.257697983 GDS(ph)PELKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDSPELKPR 9 1 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 GDS(1)PELKPR;GDS(1)PELKPR;GDS(1)PELKPR 146.16 5.78E-05 1197110000 905850 838420 917010 901550 857950 835730 1121770 1236780 1420550 1439350 TRUE FALSE 870448.3805 814509.0825 1082734.106 948079.1035 885546.7409 852629.0332 1135498.557 1211240.061 1259295.119 1341861.542 0.64868718 0.606999349 0.806889587 0.706540186 0.659938982 0.635407608 0.846211417 0.902656513 0.938468746 1 20.35580439 1.968414388 2.146640128 0.946789043 0.680415856 0.818030557 0.057441309 0.137586226 1.172882592 0.034173222 0.017622789 92.98531961 -1.968414388 -0.266373188 DGDSVMVLPTIPEEEAKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGDSVMVLPTIPEEEAKK 18 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ; 153.86 4.84E-08 708520000 1044040 776170 808480 646130 811350 805300 933870 1103720 1272190 1051370 FALSE TRUE 1003237.763 754034.3915 954590.3205 679476.8467 837447.8096 821583.7178 945298.9804 1080927.796 1127776.325 980159.7734 1.02354513 0.769297427 0.973912975 0.693230701 0.854399285 0.838214075 0.964433561 1.102807752 1.15060458 1 19.90265741 1.968429384 2.806531375 1.09419274 0.85230234 0.532084322 0.094492771 0.1889293 2.779292323 0.045660314 0.025426307 92.98853032 -1.968429384 -0.241890399 RKPVLPALTINPTIAEGPS(ph)PTSEGASEANLVDLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKPVLPALTINPTIAEGPSPTSEGASEANLVDLQK 35 2 P36507 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 RKPVLPALTINPTIAEGPS(0.97)PT(0.026)S(0.004)EGASEANLVDLQK;RKPVLPALTINPTIAEGPS(0.967)PT(0.028)S(0.005)EGASEANLVDLQK 338.2 3.13E-118 1682410000 727520 701230 619700 589310 700340 713290 683350 604400 824810 774050 TRUE FALSE 699087.7141 681231.607 731693.5752 619724.3597 722867.0721 727713.2125 691713.0417 591918.9288 731181.0267 721622.904 0.968771515 0.944027141 1.013955587 0.85879253 1.001724125 1.008439738 0.95855195 0.820260728 1.013245315 1 19.4608856 1.968467823 24.9887245 0.915749826 0.965525981 0 0.065638187 1499.628428 1188429.001 0.026246268 0.016959876 92.99676096 -1.968467823 0.049776156 AQGPRPHQENNHQESYPLSVSPMENNHCPAS(ph)SESHPKPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQGPRPHQENNHQESYPLSVSPMENNHCPASSESHPKPSSPR 42 2 P41212 P41212 ETV6 Transcription factor ETV6 2 AQGPRPHQENNHQESYPLS(0.005)VS(0.14)PMENNHCPAS(0.666)S(0.186)ES(0.077)HPKPS(0.481)S(0.446)PR 109.03 2.83E-06 1198700000 17074 18750 16450 17824 15953 20393 16895 3166.2 17703 17311 TRUE FALSE 16406.7292 18215.26836 19422.88093 18743.89878 16466.14273 20805.36043 17101.76606 3100.816864 15693.42966 16138.51055 1.01661979 1.128683363 1.203511369 1.1614392 1.020301265 1.289174758 1.059686767 0.192137735 0.972421191 1 13.97821982 1.96849503 23.38357964 0.630295591 1.1384161 0.39149564 0.224073514 221.5328867 164425.1479 0.086671812 0.056018289 93.00258716 -1.96849503 0.508120509 HEDEQALLDQNSQT(ph)PPPSPFSVQAFNK ddPTM_BT-474_Pertuzumab_2h_R1 3 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 HEDEQALLDQNS(0.022)QT(0.978)PPPSPFSVQAFNK;HEDEQALLDQNS(0.002)QT(0.998)PPPSPFSVQAFNK;HEDEQALLDQNS(0.07)QT(0.93)PPPSPFSVQAFNK 179.8 6.96E-17 663150000 469700 469370 336264 413000 386934 432240 412280 262410 502080 440700 TRUE FALSE 451343.6047 455984.0272 397034.385 434314.9795 399380.0835 440980.189 417325.606 256991.1418 445085.9833 410850.9965 1.098557892 1.109852553 0.966370748 1.057110688 0.972080114 1.073333624 1.015759021 0.625509355 1.083327014 1 18.64825574 1.968570878 24.97364273 0.851160049 1.042767683 0.184721179 0.121061644 702.7634923 558416.4156 0.04756897 0.030732438 93.01883118 -1.968570878 0.191607633 KKS(ph)EPDDELLFDFLNSSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKSEPDDELLFDFLNSSQK 19 2 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 KKS(1)EPDDELLFDFLNSSQK;KKS(1)EPDDELLFDFLNSSQK 242.43 1.09E-24 3118600000 1053500 995230 1024060 1034770 1134030 973360 1156110 1481210 1514310 1152470 TRUE FALSE 1012328.055 966847.0148 1209130.422 1088174.604 1170507.105 993042.0061 1170258.82 1450622.496 1342411.877 1074412.18 0.942215729 0.899884637 1.125387858 1.012809258 1.089439534 0.924265402 1.089208445 1.350154552 1.249438439 1 20.03511613 1.968722756 7.69635445 1.234741952 1.004978524 0.408687377 0.105756868 0.197630991 41.51798044 0.042592365 0.027425949 93.05136658 -1.968722756 -0.229763427 MNLASEPQEVLHIGSAHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 MNLASEPQEVLHIGSAHNR 19 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 0 ; 125.23 1.60E-05 1089310000 502130 736630 535660 733920 628200 733330 592480 157596 582880 644400 FALSE TRUE 482506.2045 715622.0336 632465.6777 771797.6992 648406.6235 748158.435 599730.9475 154341.5875 516713.906 600754.214 0.803167407 1.191206016 1.052786086 1.284714582 1.079320974 1.245365272 0.998296697 0.256913034 0.860108667 1 19.19641534 1.968739001 15.88150538 0.624214261 1.11755905 0.386551558 0.220447354 6.137746972 3117.184976 0.085243495 0.055234387 93.05484741 -1.968739001 0.49334479 EEDKEPLIELFVK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEDKEPLIELFVK 13 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 ;; 133.77 9.43E-05 177748000 412711 356101 401480 361677 396611 386054 463136 573681 604795 599201 FALSE TRUE 396581.7978 345945.3481 474036.3669 380343.1933 409368.353 393860.2764 468803.9969 561834.2869 536141.2071 558616.5826 0.709935598 0.619289436 0.848589859 0.680866278 0.732825279 0.705063703 0.839223202 1.00576013 0.959766007 1 19.09149888 1.968774523 2.726348087 0.988346849 0.716633281 0.828508899 0.055439039 0.103682218 1.435018736 0.027922598 0.015433518 93.06245883 -1.968774523 -0.271713568 SHVSSEPYEPIS(ph)PPQVPVVHEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SHVSSEPYEPISPPQVPVVHEK 22 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK 211.72 4.93E-23 3032080000 1061290 1421710 1143540 1503100 1214210 1472530 1262100 322391 1336310 1365020 TRUE FALSE 1019813.613 1381164.223 1350203.116 1580675.171 1253266.167 1502305.566 1277545.957 315733.5132 1184617.691 1272565.98 0.801383685 1.085338006 1.061008339 1.242116477 0.98483394 1.180532554 1.003913336 0.248107775 0.930889015 1 20.27930903 1.968794069 24.3012227 0.638593981 1.067640923 0.290826172 0.221319567 411.6508546 320567.0754 0.086231358 0.055727605 93.0666474 -1.968794069 0.429046943 QHLEETTQK ddPTM_BT-474_Pertuzumab_2h_R1 2 QHLEETTQK 9 0 P12270 P12270 TPR Nucleoprotein TPR 0 ; 154.84 7.47E-05 287500000 333430 337460 294000 326560 341670 345700 324460 174775 380300 326760 FALSE TRUE 320399.187 327835.9712 347132.34 343413.8007 352660.1258 352690.2909 328430.8385 171165.8352 337129.9383 304628.2542 1.051771077 1.076183731 1.13952772 1.12732091 1.157673725 1.157772748 1.078136496 0.561884306 1.106692941 1 18.21669023 1.968795012 24.62284643 0.835637183 1.119473568 0.344088116 0.136115562 448.7088389 354060.9415 0.053122268 0.03432328 93.0668493 -1.968795012 0.283836385 SYHEEFNPPKEPMKDDITGEPLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYHEEFNPPKEPMKDDITGEPLIR 24 2 F8W1A4;P54819-2;P54819;P54819-6;P54819-3;P54819-5;F8VY04;A0A5K1VW67;P54819-4 F8W1A4 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 0 ; 193.4 2.91E-18 339400000 342460 432640 331730 412070 336550 398900 364450 308650 419540 354050 FALSE TRUE 329076.2846 420301.5308 391680.9903 433336.9821 347375.4364 406966.0313 368910.2481 302276.2696 371915.5781 330069.8781 0.996989748 1.273371364 1.186660814 1.312864368 1.052429983 1.232969314 1.117673173 0.915794775 1.126778306 1 18.33241196 1.968916068 7.753185084 1.007284122 1.181032926 0.338177845 0.100873567 0.246212386 52.76360426 0.039611028 0.025521196 93.09279464 -1.968916068 0.173748804 QGGS(ph)PDEPDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 QGGSPDEPDSK 11 0 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 QGGS(1)PDEPDSK;QGGS(1)PDEPDSK 162.16 2.68E-05 358270000 1150320 985790 857830 906240 969410 1027060 1050420 1200480 1397430 1156880 TRUE FALSE 1105364.223 957676.2344 1012858.963 953011.155 1000591.953 1047827.857 1063275.354 1175689.668 1238799.605 1078523.487 1.024886556 0.887951209 0.939116278 0.883625778 0.927742386 0.97153921 0.98586203 1.090091855 1.148606979 1 20.04062616 1.968961359 1.990341019 1.090852705 0.931493487 0.598011926 0.051069345 0.198473259 1.457593395 0.02889834 0.014573451 93.10250356 -1.968961359 -0.159359218 LHDPEGMGIIPR ddPTM_BT-474_Pertuzumab_2h_R1 5 LHDPEGMGIIPR 12 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;;; 205.56 1.00E-07 1687140000 2000040 2146300 1920800 2157430 2095710 2140730 2037350 1489320 2179320 2290390 FALSE TRUE 1921876.226 2085089.625 2267931.288 2268775.221 2163120.415 2184017.027 2062283.699 1458565.022 1931932.73 2135259.845 0.900066673 0.976503928 1.062133629 1.062528865 1.013047859 1.022834309 0.965823295 0.683085492 0.904776407 1 21.02598022 1.96896405 16.39781036 0.826664634 1.008926667 0.330735584 0.086935542 8.65186727 4570.160419 0.034782174 0.022537235 93.10308027 -1.96896405 0.182262034 DLS(ph)MSTRSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLSMSTRSLK 10 1 Q9Y3S2 Q9Y3S2 ZNF330 Zinc finger protein 330 1 DLS(0.25)MS(0.25)T(0.25)RS(0.25)LK 54.157 0.05669 0 42631 45620 34368 42490 41651 41712 45402 59539 51649 52022 TRUE FALSE 40964.93339 44318.96227 40579.06211 44682.91399 42990.74224 42555.44522 45957.64326 58309.49884 45786.02205 48498.5036 0.844663863 0.913821231 0.836707508 0.921325622 0.886434406 0.877458933 0.94760951 1.202294803 0.94407082 1 15.56565261 1.969060368 9.301567818 1.072392728 0.88427117 0.552793645 0.066866959 0.255899132 73.9656167 0.026065316 0.01687532 93.12373111 -1.969060368 -0.188121558 DSASFNPELLTHILDGS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSASFNPELLTHILDGSPEK 20 0 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 1 DSASFNPELLTHILDGS(1)PEK;DSASFNPELLTHILDGS(1)PEK;DSASFNPELLTHILDGS(1)PEK;DSASFNPELLTHILDGS(1)PEK 229.71 1.40E-25 177695000 204995 213650 216633 224712 216441 257094 284577 312814 393214 375573 TRUE FALSE 196983.5688 207556.9112 255783.4021 236309.4132 223403.0213 262292.6168 288059.7385 306354.2816 348577.9952 350135.1062 0.562593026 0.592790918 0.730527724 0.674909225 0.638048049 0.749118304 0.822710243 0.874960197 0.995552828 1 18.41755219 1.969238551 0.707612045 1.019010799 0.621819576 0.911207345 0.044206946 0.193213049 0.185844889 0.041262357 0.022580027 93.16194591 -1.969238551 -0.397191223 DHS(ph)PTPSVFNSDEER ddPTM_BT-474_Pertuzumab_2h_R1 7 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 DHS(0.975)PT(0.025)PSVFNSDEER;DHS(0.992)PT(0.006)PS(0.003)VFNSDEER;DHS(0.836)PT(0.164)PSVFNSDEER;DHS(0.849)PT(0.151)PSVFNSDEER;DHS(0.968)PT(0.032)PSVFNSDEER;DHS(0.841)PT(0.159)PSVFNSDEER;DHS(0.671)PT(0.329)PSVFNSDEER 271.47 2.24E-33 11126980000 2172560 2053650 1696720 1999320 2056260 2021310 1897280 660253 2211220 1727099 TRUE FALSE 2087653.953 1995081.913 2003355.047 2102505.145 2122401.47 2062182.273 1920499.48 646618.5448 1960211.576 1610121.046 1.296581992 1.239088153 1.244226359 1.305805641 1.318162678 1.280762262 1.192767143 0.401596232 1.217431186 1 20.61873772 1.969350008 21.75693192 0.804184576 1.276445677 0.459558447 0.194075734 94.87503732 67346.41191 0.075037526 0.048537746 93.185858 -1.969350008 0.472261102 RHS(ph)DPWGR ddPTM_BT-474_Pertuzumab_2h_R1 3 RHSDPWGR 8 1 Q92576-2;Q92576 Q92576-2 PHF3 PHD finger protein 3 1 RHS(1)DPWGR;RHS(1)DPWGR;RHS(1)DPWGR 102.05 0.0030872 1025370000 284443 351150 342308 387752 346488 325668 308017 217855 253075 263506 TRUE FALSE 273326.6531 341135.5458 404170.6702 407763.9272 357633.1012 332253.2301 311786.6042 213356.2181 224346.987 245658.5039 1.112628502 1.388657589 1.645254138 1.659881179 1.455814049 1.352500422 1.2691871 0.868507358 0.913247388 1 17.90629466 1.969388106 2.130043305 0.908674733 1.460522503 0.694564668 0.149755426 0.17978535 1.509584596 0.092260999 0.047507678 93.19403293 -1.969388106 0.55184777 RSS(ph)DPALIGLSTSVSDSNFSSEEPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSDPALIGLSTSVSDSNFSSEEPSR 26 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 RS(0.128)S(0.872)DPALIGLSTSVSDSNFSSEEPSR 321.92 1.70E-82 2201300000 370860 447390 358220 459330 423310 432350 419680 384450 478450 442070 TRUE FALSE 356366.3812 434630.8752 422958.3226 483036.0763 436926.1506 441092.4132 424816.1694 376510.9732 424138.3618 412128.2051 0.86469787 1.054601141 1.026278515 1.172052944 1.060170464 1.070279606 1.03078645 0.913577301 1.029141797 1 18.65273368 1.969406291 17.33170589 0.971522048 1.048267215 0.106009751 0.075933582 28.87647981 16356.71835 0.031326966 0.020297917 93.19793524 -1.969406291 0.076745167 RGEDVETSKK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGEDVETSKK 10 2 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;; 131.17 0.00014464 1705370000 2054630 1689410 1459610 1333250 1613930 1713400 1737210 2076070 2201390 1873730 FALSE TRUE 1974332.788 1641229.681 1723393.996 1402059.192 1665843.524 1748046.122 1758470.496 2033198.429 1951497.436 1746820.598 1.130243592 0.939552512 0.986589005 0.802634909 0.953643165 1.000701574 1.006669201 1.163942325 1.11717107 1 20.73630002 1.969427756 3.541514061 1.109130344 0.961242602 0.291651941 0.084803619 0.254249797 6.341532399 0.040305993 0.023769661 93.20254179 -1.969427756 -0.147887742 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADS(ph)TESLSDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADSTESLSDHR 43 0 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 1 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADS(0.903)T(0.096)ES(0.001)LSDHR;NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADS(0.788)T(0.205)ES(0.003)LS(0.004)DHR 199.15 8.14E-36 1339540000 165730 261020 186106 276840 224750 248620 210132 20584.8 217708 212460 TRUE FALSE 159253.0884 253575.9652 219739.4941 291127.7456 231979.2879 253647.2667 212703.6583 20159.71669 192994.7005 198069.895 0.804024703 1.280234764 1.1094038 1.469823295 1.171199126 1.280594746 1.073881815 0.101780822 0.97437675 1 17.59565009 1.969469265 19.42028366 0.591142375 1.197124528 0.363193175 0.283662053 35.11316231 22334.21048 0.110408694 0.071477669 93.21145021 -1.969469265 0.605982153 QALPCVAESPTVHVEVHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QALPCVAESPTVHVEVHQR 19 0 Q15645;Q15645-2 Q15645 TRIP13 Pachytene checkpoint protein 2 homolog 0 ; 102.33 0.00022811 722140000 394030 448270 393450 454250 403940 489780 418760 132433 469790 482390 FALSE TRUE 378630.872 435485.7785 464555.1672 477693.8969 416933.0969 499683.6872 423884.9101 129698.2123 416461.4087 449717.2956 0.841930866 0.968354526 1.032993776 1.062209307 0.927100427 1.111106226 0.942558612 0.288399431 0.926051572 1 18.77865884 1.969500642 24.61713119 0.648182365 0.994808712 0.215919799 0.194579708 531.5190271 429007.3606 0.075871106 0.049036368 93.21818481 -1.969500642 0.346626347 EEALGLYQWIYHTHEDAQEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEALGLYQWIYHTHEDAQEAR 21 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 ;;; 234.04 5.28E-30 275611000 231132 245389 236001 233828 231765 275501 230810 17553.7 289178 205615 FALSE TRUE 222099.1059 238390.746 278651.6305 245895.8911 239219.9317 281071.819 233634.7218 17191.20996 256351.7258 191688.5129 1.158645881 1.243636055 1.453668904 1.282788871 1.247961748 1.466294535 1.218824844 0.089683047 1.337334835 1 17.54840436 1.96950211 24.70390512 0.694458037 1.311340168 0.329014412 0.308123186 492.0410718 398562.4827 0.11975449 0.077405728 93.21850003 -1.96950211 0.616882131 S(ph)SEREESQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSEREESQSR 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(0.971)S(0.029)EREESQSR;S(0.865)S(0.135)EREESQSR 117.63 0.00056454 126479000 28919.8 27774.6 29174 24309.5 29411.2 29103.5 28128 20549 32288 30198 TRUE FALSE 27789.58224 26982.4956 34446.39077 25564.11621 30357.23796 29691.99271 28472.23888 20124.65597 28622.8016 28152.66256 0.987103162 0.958434945 1.223557122 0.908053231 1.078307883 1.05467796 1.011351549 0.714840237 1.01669963 1 14.78098375 1.969506801 24.35336877 0.874895573 1.036032751 0.182040777 0.11111783 575.5759252 459682.0466 0.043443812 0.028079006 93.21950684 -1.969506801 0.161137178 S(ph)PSMAQDSGASELLPNGDLEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSMAQDSGASELLPNGDLEKR 22 1 F8WE91;Q9Y6K1;Q9Y6K1-3 F8WE91 DNMT3A DNA (cytosine-5)-methyltransferase 3A 1 S(0.962)PS(0.038)MAQDSGASELLPNGDLEKR;S(0.968)PS(0.032)MAQDSGASELLPNGDLEKR 156.52 6.85E-09 331740000 155223 152933 136752 138701 156482 149527 158875 173503 196978 173538 TRUE FALSE 149156.7136 148571.5006 161466.1284 145859.3752 161515.3856 152550.5384 160819.3598 169920.1024 174617.8832 161784.1167 0.921949055 0.918331809 0.99803449 0.901567955 0.998338953 0.942926546 0.994036764 1.05028915 1.079326493 1 17.30371045 1.969608267 2.509978999 1.048911354 0.947759134 0.602952176 0.034948232 0.181508183 2.118015748 0.017799685 0.009621952 93.24128869 -1.969608267 -0.10115222 DRPGS(ph)PES(ph)PLLDAPFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 2 DRPGS(1)PES(1)PLLDAPFSR;DRPGS(1)PES(1)PLLDAPFSR 162.61 1.61E-09 301230000 190491 212640 189518 232340 236920 250320 182753 177707 168245 170274 TRUE FALSE 183046.4011 206575.7154 223768.1184 244331.0952 244540.747 255381.6419 184989.5859 174037.2883 149146.5329 158741.1903 1.153112187 1.301336565 1.409641177 1.539178929 1.540499643 1.608792535 1.1653534 1.096358721 0.939557859 1 17.276317 1.969627002 2.936707978 1.022986796 1.428538759 0.667236832 0.131221373 0.176450199 2.864390663 0.072343732 0.040815369 93.24531095 -1.969627002 0.405551963 SKESVPEFPLS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 5 SKESVPEFPLSPPK 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK 171.35 1.83E-06 42562500000 20693050 16427180 17049190 14843160 17548960 17010170 18410530 21520250 21655120 20604980 TRUE FALSE 19884342.73 15958692.91 20130357.89 15609217.27 18113438.24 17354127.29 18635843.57 21075849.32 19196921.56 19209386.35 1.035136801 0.830775779 1.047943829 0.812582817 0.94294726 0.90341914 0.970142577 1.097164112 0.999351109 1 24.1953081 1.969817788 6.450583252 1.041315436 0.925866094 0.273264589 0.074908509 0.207760443 29.00517747 0.028934018 0.018508467 93.28628284 -1.969817788 -0.115449342 VKEEPPS(ph)PPQSPR ddPTM_BT-474_Pertuzumab_2h_R1 6 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VKEEPPS(0.999)PPQS(0.001)PR;VKEEPPS(1)PPQSPR;VKEEPPS(0.977)PPQS(0.023)PR;VKEEPPS(0.997)PPQS(0.003)PR;VKEEPPS(1)PPQSPR;VKEEPPS(1)PPQSPR 143.22 2.47E-05 6455870000 4727000 4209170 3592420 3870570 3989230 4326960 4630550 5408760 6298480 5416830 TRUE FALSE 4542263.614 4089128.593 4241650.207 4070330.582 4117547.206 4414454.096 4687220.056 5297067.216 5583502.956 5049943.279 0.899468244 0.809737529 0.839940168 0.806015109 0.81536504 0.874159144 0.928172812 1.048935983 1.105656568 1 22.26783575 1.969827798 1.877256334 1.062998744 0.833425593 0.874269395 0.03582269 0.10217426 0.668748315 0.021074505 0.010451284 93.28843288 -1.969827798 -0.22957315 S(ph)LPSS(ph)PLLTHQSISVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(0.991)LPS(0.18)S(0.828)PLLT(0.001)HQSISVR 53.779 0.078495 85910000 46781 72592 61271 71457 58574 51490 54243 53288 33850 47993 TRUE FALSE 44952.7468 70521.74724 72344.03267 75144.90433 60458.08591 52531.16308 54906.84206 52187.58418 30007.48991 44742.39136 1.00470148 1.576172956 1.616901343 1.679501297 1.351248426 1.174080363 1.227177189 1.166401316 0.670672465 1 15.44935475 1.969901284 0.942152738 0.884748415 1.47123969 0.514258688 0.209918178 0.456447231 0.745992641 0.176189275 0.08293961 93.3042194 -1.969901284 0.586491276 GRPAPGFHHGDGPGNAVQEIMIPASK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRPAPGFHHGDGPGNAVQEIMIPASK 26 1 Q96AE4;E9PEB5;Q96AE4-2;C9JSZ1 Q96AE4;C9JSZ1 FUBP1 Far upstream element-binding protein 1 0 82.486 0.010051 424740000 611020 623880 519550 548320 524250 527160 543780 215090 667660 625340 FALSE TRUE 587140.6629 606087.5532 613444.2423 576618.8609 541112.9774 537819.5364 550434.9423 210648.3163 591870.0359 582985.1648 1.007127965 1.039627747 1.052246745 0.989079818 0.928176238 0.922526968 0.944166294 0.361327061 1.015240304 1 19.15309965 1.969914872 24.82159714 0.704105715 0.987174234 0.148230388 0.178017691 674.5480689 556531.9125 0.07035794 0.045489724 93.30713868 -1.969914872 0.283068519 SRDHDKPHQQSDK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRDHDKPHQQSDK 13 2 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 0 ;; 122.64 0.00013975 118212000 89245 93730 77986 80263 86900 97216 84568 23040.6 103299 96400 FALSE TRUE 85757.20673 91056.91217 92079.80499 84405.38305 89695.21742 99181.77413 85602.96848 22564.80356 91572.93058 89870.74214 0.954228314 1.013198623 1.024580445 0.939186448 0.99804692 1.103604708 0.952512091 0.251080641 1.018940407 1 16.4555639 1.969956081 24.94047856 0.655544343 1.005402782 0.178793382 0.207708209 666.7409088 553483.532 0.080967489 0.052330183 93.31599288 -1.969956081 0.349858438 AHIVFDFHQAADGIQEQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHIVFDFHQAADGIQEQQR 19 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 141.22 9.67E-08 353190000 130730 165485 150877 159415 153695 164392 154200 96590 183090 163972 FALSE TRUE 125620.9271 160765.5298 178143.8301 167642.4273 158638.7393 167716.1189 156087.1457 94595.38275 162306.3908 152866.0304 0.821771369 1.051675964 1.165359169 1.096662397 1.037763189 1.097144463 1.021071492 0.618812319 1.061755776 1 17.22190832 1.970049814 24.72566974 0.843361812 1.053366956 0.1667594 0.138877642 686.2855636 566568.9456 0.055559761 0.035914616 93.3361353 -1.970049814 0.210005144 SQSASVESIPEVLEECTSPADHS(ph)DSASVHDMDYVNPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 S(0.003)QS(0.002)AS(0.002)VES(0.086)IPEVLEECT(0.049)S(0.23)PADHS(0.457)DS(0.086)AS(0.086)VHDMDYVNPR 125.44 3.12E-08 55293000 10659 16529 10965 15174 14305 17389 14080 5817.7 16795 20287 TRUE FALSE 10242.4345 16057.6091 12946.61942 15957.13196 14765.13332 17740.61749 14252.31525 5697.562462 14888.50201 18912.94342 0.541556873 0.849027502 0.684537522 0.843714889 0.78068934 0.938014623 0.753574678 0.301252023 0.787212317 1 14.20708629 1.970053006 24.98402388 0.595740415 0.781757583 0 0.19665711 1221.256902 1018862.513 0.077036914 0.049807534 93.33682131 -1.970053006 0.186017167 FTLTQSEADADILFNFSHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTLTQSEADADILFNFSHFK 20 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 223.46 6.45E-25 381720000 459780 467160 381810 433010 470660 497690 452590 507920 642570 575870 FALSE TRUE 441811.2893 453837.0542 450811.5603 455357.698 485799.2063 507753.6328 458128.9318 497431.2745 569628.1475 536865.812 0.822945472 0.845345418 0.839709943 0.848177865 0.904880131 0.945773826 0.853339739 0.926546752 1.061025185 1 19.03420201 1.970053251 0.474397007 1.022153206 0.828009517 0.692750835 0.041460454 0.585472725 0.301808385 0.043906415 0.035697514 93.33687394 -1.970053251 -0.194143689 VVELRPPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 VVELRPPSR 9 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 VVELRPPS(1)R 96.64 0.0043791 284510000 504700 395150 324840 513260 395940 349670 433000 652090 441370 452800 TRUE FALSE 484975.766 383880.7089 383545.814 539749.4101 408675.7697 356740.567 438299.1835 638624.1136 391267.528 422131.4527 1.1488738 0.909386653 0.90859331 1.278628746 0.968124424 0.845093548 1.038300228 1.51285603 0.926885513 1 18.6873328 1.97021756 24.94508261 1.221567947 1.005176143 0.054112976 0.190186046 1025.523518 858953.6229 0.076535495 0.049459527 93.37219322 -1.97021756 -0.216391804 ENPPGPPIAASAPGPSQSLGLNVHNMTPAT(ph)SPIGASGVAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENPPGPPIAASAPGPSQSLGLNVHNMTPATSPIGASGVAHR 41 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 ENPPGPPIAAS(0.001)APGPS(0.021)QS(0.021)LGLNVHNMT(0.113)PAT(0.347)S(0.347)PIGAS(0.15)GVAHR;ENPPGPPIAASAPGPS(0.11)QS(0.11)LGLNVHNMT(0.11)PAT(0.362)S(0.286)PIGAS(0.022)GVAHR 102.26 1.99E-05 393020000 48976 82760 81677 84608 74963 89980 78497 54112 80395 101161 TRUE FALSE 47061.96377 80399.76583 96437.8508 88974.62902 77374.25297 91799.45725 79457.66977 52994.56829 71268.89664 94309.27537 0.49901734 0.852511755 1.02257016 0.943434553 0.820430999 0.973387367 0.842522323 0.561923184 0.755693397 1 16.52511205 1.970298202 24.2144581 0.718453387 0.866204751 0.009935198 0.168573142 940.5099666 766750.9272 0.068574108 0.044339593 93.38953274 -1.970298202 0.147751363 TVLPTVPES(ph)PEEEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 TVLPTVPESPEEEVK 15 0 O75152;E9PBY7;E9PQ61;A0A1W2PPR9 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 TVLPTVPES(1)PEEEVK;TVLPTVPES(1)PEEEVK;TVLPTVPES(1)PEEEVK;TVLPTVPES(1)PEEEVK 334.25 5.81E-69 1020020000 2328300 1995280 2042300 1878790 2173370 2323620 2387110 2699250 3042620 3020560 TRUE FALSE 2237307.462 1938376.568 2411389.041 1975754.577 2243278.42 2370605.188 2416324.166 2643509.544 2697234.533 2815974.781 0.794505504 0.688350116 0.8563248 0.701623676 0.796625891 0.841841768 0.858077346 0.938754694 0.957833341 1 21.42520298 1.970315409 0.812990759 0.99753033 0.75728525 0.78358993 0.045536171 0.253223695 0.312309761 0.036237091 0.018156106 93.39323277 -1.970315409 -0.24024508 DHQTITIQEMPEKAPAGQLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DHQTITIQEMPEKAPAGQLPR 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 216.49 3.71E-25 339030000 144860 152380 103700 136120 135150 149140 133000 60806 156930 152820 FALSE TRUE 139198.711 148034.2716 122440.8968 143145.1695 139497.2225 152155.713 134627.6938 59550.33485 139115.9643 142469.3653 0.977043105 1.039060371 0.859419122 1.004743506 0.979138373 1.067988986 0.944958894 0.417986946 0.976462301 1 17.12029221 1.970327433 24.67058657 0.720479397 0.986562105 0.172040304 0.161613343 602.4187968 500866.6843 0.063079324 0.040785263 93.3958186 -1.970327433 0.266082708 DGIDDESYGQIFKPIISK ddPTM_BT-474_Pertuzumab_2h_R1 3 DGIDDESYGQIFKPIISK 18 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 ;; 219.95 6.43E-19 4213991000 4349260 3928788 3447461 3473955 3888947 3839284 4183577 4849450 5291890 4750590 FALSE TRUE 4179286.111 3816742.813 4070493.891 3653246.234 4014038.512 3916916.953 4234776.867 4749307.163 4691176.833 4428828.308 0.94365503 0.861795163 0.91909047 0.824878722 0.906343221 0.884413818 0.956184474 1.072361996 1.059236553 1 22.07849364 1.970390558 3.133024102 1.049466379 0.888127884 0.79122395 0.035263729 0.098818196 1.852761435 0.016417881 0.009422349 93.40939478 -1.970390558 -0.161338495 RAVVVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 RAVVVSPK 8 1 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 RAVVVS(1)PK;RAVVVS(1)PK;RAVVVS(1)PK;RAVVVS(1)PK;RAVVVS(1)PK;RAVVVS(1)PK 105.2 0.0027152 2808870000 4249850 3739590 3551050 3836770 3839100 3692700 4332850 5272070 5419590 5201450 TRUE FALSE 4083761.164 3632940.555 4192803.728 4034786.159 3962588.138 3767368.924 4385876.714 5163199.912 4804380.864 4849151.159 0.842160005 0.749191031 0.864646943 0.832060298 0.817171503 0.776913072 0.904462775 1.064763655 0.990767396 1 22.2093008 1.970448987 4.073793954 1.020673006 0.814787261 0.867277606 0.035858075 0.0682938 2.44507638 0.015879934 0.009640037 93.4219626 -1.970448987 -0.205885746 NHLEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NHLEGK 6 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 124.37 0.018383 191021000 906930 806570 705730 785640 720490 830880 748450 162454 862170 733050 FALSE TRUE 871486.1729 783567.4133 833271.1099 826186.9746 743665.2152 847680.9629 757609.755 159099.2681 764300.0761 683399.8706 1.275221449 1.146572376 1.219302411 1.208936393 1.088184601 1.240387948 1.108589257 0.232805529 1.118379018 1 19.38237045 1.970458706 24.10944764 0.69153742 1.18949123 0.382876555 0.226072973 338.3129263 276105.6266 0.087298293 0.056458556 93.42405334 -1.970458706 0.49795381 HSLEEEDENEEEILTVQDLVDFSPVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSLEEEDENEEEILTVQDLVDFSPVYR 27 0 Q8TAG9-2;Q8TAG9 Q8TAG9-2 EXOC6 Exocyst complex component 6 0 ; 109.97 0.0014712 48702000 39808 47198 36069 43773 44663 45938 41542 15943.9 47538 42389 FALSE TRUE 38252.25935 45851.95925 42587.47065 46032.12978 46099.62596 46866.89783 42050.40342 15614.65289 42141.68554 39517.95527 0.967971624 1.160281673 1.077673942 1.164840879 1.166548867 1.185964646 1.064083481 0.395128057 1.066393371 1 15.27022068 1.970522826 24.39597789 0.747375681 1.124551626 0.337688618 0.180227557 413.1271163 341912.6688 0.069937101 0.045229163 93.43784775 -1.970522826 0.377175945 QDEEKPLHALLHGR ddPTM_BT-474_Pertuzumab_2h_R1 3 QDEEKPLHALLHGR 14 1 P24593;C9JXX4 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 0 ;; 185.12 7.83E-07 912040000 772550 772280 631862 666279 593528 592089 625756 118348 738830 587002 FALSE TRUE 742357.8919 750255.3305 746053.5191 700665.739 612619.3671 604061.4453 633414.1891 115904.0724 654961.1158 547243.8317 1.356539533 1.370970831 1.363292697 1.280353836 1.119463266 1.103825042 1.157462455 0.211796033 1.196835995 1 19.06182426 1.970525301 22.15784161 0.707631062 1.257446193 0.383404078 0.254504963 137.3415399 103246.7362 0.102065768 0.06605122 93.43838007 -1.970525301 0.54981513 (ac)ATS(ph)PQKS(ph)PSVPKS(ph)PTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSPQKSPSVPKSPTPK 17 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 3 AT(0.495)S(0.556)PQKS(0.924)PS(0.198)VPKS(0.691)PT(0.135)PK 53.964 1.84E-05 243390000 791320 569750 616000 526700 751570 560760 663180 889680 788010 692020 TRUE FALSE 760394.3395 553501.2878 727324.9028 553883.0501 775744.9316 572098.9514 671296.1952 871307.7971 698558.4084 645148.869 1.178633919 0.857943514 1.127375305 0.858535257 1.202427794 0.886770448 1.040529136 1.350553088 1.08278638 1 19.29927258 1.970570369 24.5345742 1.186432954 1.012860003 0.110948574 0.145835452 753.8857605 628490.2681 0.054793571 0.035439414 93.44807706 -1.970570369 -0.173572951 HLNEIDLFHCIDPNDSK ddPTM_BT-474_Pertuzumab_2h_R1 8 HLNEIDLFHCIDPNDSK 17 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;;;;; 260.65 1.72E-27 22524830000 17805620 16692180 13338770 14190850 15926340 16870250 15269860 5822791 19360790 16819930 FALSE TRUE 17109756.69 16216135.37 15749382.46 14923241.47 16438625.19 17211378.01 15456737.11 5702548.331 17163034.29 15680701.16 1.09113467 1.034146063 1.004379989 0.951694782 1.04833483 1.097615332 0.985717217 0.363666667 1.094532324 1 23.90248673 1.970684532 24.84084202 0.730194905 1.033491932 0.168330489 0.18843381 677.7317677 574284.0037 0.073805028 0.047732845 93.47264506 -1.970684532 0.303297027 VDLHLLNHDGNIIDAASIAAIVALCHFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDLHLLNHDGNIIDAASIAAIVALCHFR 28 0 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2;D6RA17 D6RIY6 EXOSC9 Exosome complex component RRP45 0 ; 203.99 1.15E-25 235867000 172549 151869 150354 156877 169823 168978 154061 45531 181640 144847 FALSE TRUE 165805.5943 147537.8448 177526.3124 164973.4408 175285.511 172394.8509 155946.4446 44590.76894 161020.9887 135036.3837 1.227858669 1.092578465 1.31465541 1.221696229 1.298061354 1.276654826 1.154847607 0.330212997 1.192426695 1 17.04298865 1.970687828 23.5066114 0.760476665 1.235542086 0.39312415 0.214854894 252.9599582 202858.0364 0.083439877 0.053980324 93.47335436 -1.970687828 0.475065421 GRFPESSAVQSSSFER ddPTM_BT-474_Pertuzumab_2h_R1 2 GRFPESSAVQSSSFER 16 1 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 113.88 0.00057143 663400000 141404 117132 106841 117760 128391 121440 126596 141896 142698 143188 FALSE TRUE 135877.7753 113791.51 126149.5454 123837.6077 132520.8131 123895.6 128145.3197 138965.798 126499.5213 133489.7492 1.01788921 0.852436316 0.945012977 0.927693763 0.992741494 0.928128195 0.959963746 1.041022242 0.947634721 1 17.02636943 1.970719095 11.78473707 1.000724144 0.94156593 0.201772924 0.046060958 1.596845129 639.5012087 0.017958487 0.011678814 93.48008417 -1.970719095 -0.059158215 CQSLTEDLEFRK ddPTM_BT-474_Pertuzumab_2h_R1 4 CQSLTEDLEFRK 12 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;;; 153.32 0.00011312 2033020000 1176460 1315750 833750 1207580 1053850 1176640 1238390 1307400 1604530 1364520 FALSE TRUE 1130482.643 1278226.098 984427.1717 1269903.349 1087748.042 1200432.467 1253545.787 1280401.733 1422390.481 1272099.845 0.88867446 1.004815859 0.773859989 0.99827333 0.855080713 0.943662144 0.985414621 1.006526129 1.118143742 1 20.27878048 1.970720598 1.480250326 1.052900679 0.907400489 0.432268885 0.068991096 0.365121084 1.488968267 0.044113427 0.020574782 93.48040782 -1.970720598 -0.145500191 SCDEPLTPPPHS(ph)PTSMLQLIHDPVSPR ddPTM_BT-474_Pertuzumab_2h_R1 7 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 SCDEPLTPPPHS(0.732)PT(0.134)S(0.134)MLQLIHDPVSPR;SCDEPLT(0.009)PPPHS(0.834)PT(0.079)S(0.079)MLQLIHDPVSPR;SCDEPLTPPPHS(0.989)PT(0.005)S(0.005)MLQLIHDPVSPR;SCDEPLT(0.009)PPPHS(0.971)PT(0.01)S(0.01)MLQLIHDPVSPR;SCDEPLT(0.001)PPPHS(0.914)PT(0.043)S(0.043)MLQLIHDPVSPR;SCDEPLTPPPHS(0.993)PT(0.006)S(0.001)MLQLIHDPVSPR;SCDEPLT(0.017)PPPHS(0.848)PT(0.067)S(0.067)MLQLIHDPVS(0.001)PR 168.26 1.86E-11 4074210000 1153606 1336898 1114524 1360137 1281288 1497640 1279621 729742 1429594 1545527 TRUE FALSE 1108521.802 1298770.978 1315943.279 1430333.834 1322501.792 1527923.307 1295281.385 714672.5727 1267312.482 1440847.08 0.769354235 0.901394045 0.913312244 0.992703427 0.917864089 1.060434052 0.898972141 0.496008621 0.879560711 1 20.4584858 1.970827708 24.97133422 0.72626561 0.931244446 0.103800777 0.141249931 813.5178077 696366.1668 0.055934681 0.036166726 93.50346554 -1.970827708 0.204978837 KQEVPHDGPMCDLLWSDPEDTTGWGVSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQEVPHDGPMCDLLWSDPEDTTGWGVSPR 29 1 P60510;H3BTA2;H3BV22 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit;Serine/threonine-protein phosphatase 0 ; 237.28 1.75E-45 400040000 351830 365500 272070 310520 319500 344450 330400 305340 376140 382070 FALSE TRUE 338080.0946 355076.2979 321239.1012 326545.9744 329777.0077 351415.015 334443.534 299034.6223 333442.1641 356192.0586 0.949151129 0.996867531 0.901870475 0.916769385 0.925840427 0.986588574 0.938941579 0.839531975 0.936130259 1 18.44229583 1.970861338 24.84442272 0.902852414 0.945755865 0 0.046913276 1233.95869 1052105.596 0.01896679 0.012251755 93.51070638 -1.970861338 0.042903451 EEPLDPEEAEGPLSLVT(ph)TANHSPDFDHDRDYEDEPVNEDME ddPTM_BT-474_Pertuzumab_2h_R1 1 EEPLDPEEAEGPLSLVTTANHSPDFDHDRDYEDEPVNEDME 41 1 A0A3B3IUB6;Q9H334-8;C9J0F0;Q9H334-3;Q9H334-7;Q9H334-6;Q9H334;Q9H334-4;A0A3B3IRS5;A0A3B3IST0;H0Y882;A0A0B4J2F3;A0A3B3IRW5;A0A3B3IT66 A0A3B3IUB6 FOXP1 Forkhead box protein P1 1 EEPLDPEEAEGPLS(0.017)LVT(0.328)T(0.328)ANHS(0.328)PDFDHDRDYEDEPVNEDME 93.589 0.00025466 261710000 60065 74312 50343 66319 79557 68471 64652 34632 71206 68291 TRUE FALSE 57717.59339 72192.69452 59441.09997 69741.73154 82116.02316 69855.53053 65443.23052 33916.8371 63122.9934 63665.58974 0.906574393 1.133935848 0.933645635 1.095438396 1.289802285 1.097225845 1.027921532 0.532734201 0.9914774 1 15.95822621 1.970869282 22.49464499 0.787195776 1.081159915 0.289150385 0.158362498 189.869885 146615.9137 0.06360191 0.041160874 93.51241705 -1.970869282 0.293964139 LFIGGLNTETNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFIGGLNTETNEK 13 0 P38159;P38159-2;H3BT71;H0Y6E7;H3BR27;P38159-3;H3BNC1;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 173.64 4.96E-05 300230000 436150 429640 291380 337140 376020 387420 387290 478920 439060 416520 FALSE TRUE 419104.7758 417387.0879 344038.8477 354539.8358 388115.0248 395253.8978 392029.7709 469030.1346 389219.7495 388308.7294 1.079308149 1.074884638 0.885993081 0.913035966 0.999501158 1.017885687 1.009582688 1.20787945 1.002346123 1 18.56684461 1.970871738 24.08893331 1.09706248 0.992196198 0.125662996 0.079597325 618.1616838 511215.4534 0.033668857 0.021783266 93.51294567 -1.970871738 -0.104866283 YHNVGLSK ddPTM_BT-474_Pertuzumab_2h_R1 3 YHNVGLSK 8 0 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;; 107.57 0.0039768 3972260000 7690550 7626710 6183890 7149950 6839320 6281410 6734830 3088640 7920510 7036340 FALSE TRUE 7389994.804 7409203.698 7301456.483 7518959.776 7059312.939 6408424.414 6817252.864 3024858.505 7021406.91 6559762.424 1.126564398 1.129492689 1.113067213 1.146224404 1.076153751 0.976929346 1.039253013 0.461123179 1.070375184 1 22.64521213 1.970976937 24.34047462 0.775515119 1.091100707 0.305623365 0.159902936 438.1212609 367433.8854 0.063223939 0.040891753 93.53560009 -1.970976937 0.315585588 HLAGYESSSTLMTSELESTSLGDS(ph)DEEDTMSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLAGYESSSTLMTSELESTSLGDSDEEDTMSR 32 0 I3L0M7;I3L2W9;I3L2N2;O14641 I3L0M7 DVL2 Segment polarity protein dishevelled homolog DVL-2 1 HLAGYESSSTLMTSELEST(0.012)S(0.056)LGDS(0.926)DEEDT(0.003)MS(0.003)R;HLAGYESSSTLMTSELESTS(0.005)LGDS(0.995)DEEDTMSR 164.62 3.62E-14 116763000 54392 62391 53208 68304 58059 65768 59258 32892 68700 58195 TRUE FALSE 52266.30051 60611.66977 62823.86921 71829.17763 59926.52046 67097.87402 59983.21713 32212.76871 60901.46401 54253.40082 0.963373719 1.117195768 1.157971081 1.323957145 1.104567079 1.236749642 1.105612113 0.593746534 1.122537262 1 15.72742595 1.97097983 23.68209265 0.857636178 1.156562357 0.326392794 0.15365737 322.0884648 262841.4392 0.060956438 0.03943253 93.53622311 -1.97097983 0.298926179 NKFGS(ph)ADNIAHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NKFGSADNIAHLK 13 1 G3V207;Q9ULS5;A0A0C4DFR1;O75069-3;O75069-5;O75069-2;O75069 G3V207 TMCC3;TMCC2 Transmembrane and coiled-coil domains protein 3;Transmembrane and coiled-coil domains protein 2 1 NKFGS(1)ADNIAHLK;NKFGS(1)ADNIAHLK 123.97 0.0001312 682980000 1320400 1877350 884380 1390360 984470 1031210 1318850 2069300 1645650 1030630 TRUE FALSE 1268797.308 1823809.816 1044207.139 1462116.646 1016136.372 1052061.773 1334990.481 2026568.232 1458842.711 960824.5121 1.320529704 1.898171615 1.086782368 1.521731209 1.057567078 1.094957258 1.389421756 2.109197056 1.518323786 1 19.87391343 1.971006209 24.84252017 1.686640708 1.332826998 0.022393214 0.350242555 1113.636016 954186.4766 0.140492039 0.090875694 93.54190485 -1.971006209 -0.35381371 YLSEVASGDNK ddPTM_BT-474_Pertuzumab_2h_R1 7 YLSEVASGDNK 11 0 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;;; 230.06 4.83E-12 8008500000 4909780 4756890 4293420 4441580 4681630 4603160 5074730 6021000 6196910 5885920 FALSE TRUE 4717900.37 4621228.155 5069336.501 4670810.476 4832218.881 4696239.049 5136836.064 5896664.246 5493462.756 5487261.396 0.859791439 0.842173868 0.923837254 0.851209764 0.880624875 0.855843874 0.936138393 1.074609686 1.001130138 1 22.38765487 1.971015342 4.180068006 1.030009624 0.870815095 0.853925681 0.028900137 0.069259374 2.665303947 0.012583944 0.007679813 93.54387184 -1.971015342 -0.159194529 TS(ph)PADGKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPADGKPR 9 1 Q12955;A0A087WY90;H0Y951;A0A087WX55;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 T(0.01)S(0.99)PADGKPR;T(0.069)S(0.931)PADGKPR 132.17 0.00018927 1477060000 1483720 1290260 1380620 1286140 1375820 1629060 1659240 1766130 2029220 2116530 TRUE FALSE 1425734.582 1253463.048 1630128.746 1352517.84 1420074.5 1662000.709 1679546.275 1729658.798 1798871.453 1973175.538 0.722558411 0.635251666 0.826144818 0.685452365 0.719689897 0.842297443 0.851189488 0.876586378 0.911663163 1 20.91208788 1.971055 0.479363181 0.998950906 0.687713802 0.79291699 0.048934795 0.397478169 0.207890597 0.048196874 0.038740758 93.5524144 -1.971055 -0.311237104 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR 31 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 257.8 1.01E-58 1359700000 386953 400219 320564 397161 420731 410132 366846 236037 393408 402101 FALSE TRUE 371830.449 388805.146 378497.0457 417658.5268 434264.1947 418425.15 371335.5711 231162.7535 348749.9731 374866.3411 0.991901401 1.037183399 1.009685331 1.114153182 1.158450752 1.11619824 0.990581256 0.616653799 0.930331521 1 18.51601677 1.971083941 12.44792278 0.8056504 1.071221249 0.454768534 0.105711353 1.13543506 487.3293984 0.042535541 0.027675066 93.55864885 -1.971083941 0.26557085 NPDDITQEEYGEFYK ddPTM_BT-474_Pertuzumab_2h_R1 7 NPDDITQEEYGEFYK 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;; 303.7 3.67E-44 16613500000 9134449 9399599 7735787 8727422 8878189 9386835 9523813 10676519 12008603 11368847 FALSE TRUE 8777464.634 9131531.64 9133815.793 9177845.295 9163764.012 9576643.235 9640368.272 10456045.15 10645436.73 10598824.87 0.828154512 0.861560763 0.861776273 0.86593046 0.86460189 0.903557079 0.909569541 0.986528722 1.004397833 1 23.33740098 1.97111081 1.041722532 1.011502985 0.855061671 0.953844644 0.013289355 0.094698995 0.18899478 0.010367407 0.004768781 93.56443718 -1.97111081 -0.156441314 S(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSPPKVPIVIQDDSLPAGPPPQIR 25 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 S(0.5)KS(0.5)PPKVPIVIQDDSLPAGPPPQIR;S(0.5)KS(0.5)PPKVPIVIQDDSLPAGPPPQIR 154.02 4.67E-08 6306800000 1757190 1403740 1430670 1220830 1350770 1516180 1612360 1870770 2116990 1916340 TRUE FALSE 1688517.072 1363706.71 1689223.894 1283837.183 1394218.744 1546838.198 1632092.544 1832137.946 1876678.17 1786544.585 0.945130106 0.763320838 0.945525742 0.71861469 0.780399636 0.86582681 0.913547055 1.025520416 1.05045135 1 20.76874049 1.97114007 2.011466894 1.032255805 0.828246435 0.597128185 0.069452247 0.212151823 1.591336808 0.039596211 0.020070112 93.57074117 -1.97114007 -0.20400937 DHS(ph)PTPSVFNS(ph)DEERYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DHSPTPSVFNSDEERYR 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 DHS(0.992)PT(0.008)PS(0.034)VFNS(0.962)DEERY(0.004)R 74.062 0.033113 161200000 81506 90940 61852 65079 68056 83276 63472 27295 67311 56308 TRUE FALSE 78320.65541 88346.48024 73030.03229 68437.73499 70245.08305 84959.89778 64248.78932 26731.34871 59670.13747 52494.20901 1.491986581 1.68297574 1.39120169 1.303719711 1.338149186 1.618462291 1.223921468 0.509224717 1.13669943 1 15.67987066 1.97120734 7.342816407 0.835018266 1.460584965 0.666805083 0.185550087 0.114414484 23.13686545 0.07616623 0.049172366 93.58523593 -1.97120734 0.625566699 QRGEKEDEDEDVKK ddPTM_BT-474_Pertuzumab_2h_R1 3 QRGEKEDEDEDVKK 14 3 O43823 O43823 AKAP8 A-kinase anchor protein 8 0 ;; 169.25 1.47E-06 546790000 812820 620220 497100 438340 632810 644780 675110 894790 928970 817320 FALSE TRUE 781054.0958 602531.9329 586937.0279 460962.7799 653164.9084 657817.8934 683372.1981 876312.2738 823517.2202 761962.1884 1.02505624 0.79076356 0.77029679 0.604968051 0.857214332 0.863320915 0.896858412 1.150073176 1.08078489 1 19.53935988 1.971288342 2.698534427 1.089936287 0.806212773 0.543243292 0.104632548 0.199251429 2.703708198 0.055784385 0.030822206 93.60269258 -1.971288342 -0.283723514 HSHEGDYLESIVFIYSMPGYTCSIR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSHEGDYLESIVFIYSMPGYTCSIR 25 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 123.14 9.56E-05 129340000 135020 143760 112580 104010 138170 145050 99316 27154 100160 52769 FALSE TRUE 129743.2691 139660.1056 132925.7103 109377.9686 142614.3635 147983.0104 100531.4589 26593.26041 88790.2567 49194.90863 2.637331235 2.838913811 2.702021694 2.223359523 2.89896592 3.008096051 2.043533807 0.540569363 1.804866788 1 15.58622139 1.971363745 5.074035416 1.099915104 2.700304213 0.809238143 0.348283711 0.074169819 5.05608761 0.146120367 0.091759358 93.61894547 -1.971363745 1.600389109 KSCVEEPEPEPEAAEGDGDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSCVEEPEPEPEAAEGDGDKK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 111.83 0.00013445 498160000 177700 135270 132270 109530 143140 130100 158160 202510 209480 176080 FALSE TRUE 170755.2875 131412.232 156174.1313 115182.8564 147744.2281 132730.7111 160095.6094 198328.0977 185700.7086 164153.9448 1.040214341 0.800542638 0.951388232 0.701675836 0.900034588 0.808574606 0.97527726 1.208183562 1.131259495 1 17.32468989 1.971375033 4.706189111 1.129650084 0.86299317 0.554564334 0.098375351 0.127777518 6.925977429 0.040817535 0.025386927 93.62137883 -1.971375033 -0.266656914 YYHSPTNTVHMYPPEMAPSSAPPSTPPT(ph)HK ddPTM_BT-474_Pertuzumab_2h_R1 1 YYHSPTNTVHMYPPEMAPSSAPPSTPPTHK 30 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 YYHSPTNTVHMYPPEMAPSSAPPS(0.307)T(0.307)PPT(0.386)HK 86.48 0.0010394 322620000 102570 128830 115500 129300 126170 155210 122910 49637 132720 132170 TRUE FALSE 98561.451 125155.8945 136373.4193 135973.1885 130228.3726 158348.4525 124414.2093 48611.9786 117654.182 123218.0082 0.799894857 1.015727298 1.106765328 1.103517177 1.056893993 1.285108036 1.009708006 0.394520081 0.954845674 1 16.91085359 1.971514584 24.31009879 0.712413168 1.07006 0.277147869 0.191667064 465.20322 397014.1031 0.076454199 0.049470733 93.65146682 -1.971514584 0.357646832 GEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_BT-474_Pertuzumab_2h_R1 2 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GEGDAPFSEPGTTSTQRPS(1)S(0.997)PET(0.003)ATK;GEGDAPFSEPGTTSTQRPS(1)S(0.999)PET(0.001)ATK 173.9 1.81E-12 1570090000 1161670 1076600 1037700 1139340 1191810 1185030 1300570 1441150 1657380 1659620 TRUE FALSE 1116270.652 1045896.422 1225235.474 1198141.474 1230145.651 1208992.119 1316486.765 1411389.749 1469241.171 1547212.459 0.721472119 0.67598759 0.79189866 0.774387168 0.795072224 0.781400196 0.850876528 0.91221457 0.949605312 1 20.56123989 1.971516699 0.476024245 1.013308781 0.709993986 0.916448007 0.027995451 0.252484958 0.130736401 0.029655799 0.024035692 93.65192288 -1.971516699 -0.303314796 HYNGEAYEDDEHHPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HYNGEAYEDDEHHPR 15 0 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;;; 155.06 8.23E-07 5208130000 2008241 2232540 1860984 2189970 1995277 2259230 1729474 26956.913 2109713 1345801 FALSE TRUE 1929756.721 2168870.145 2197305.206 2302994.614 2059456.897 2304913.179 1750639.82 26400.24333 1870227.225 1254648.7 1.5380853 1.728667272 1.751331035 1.835569283 1.64146099 1.837098448 1.395322707 0.021041941 1.490638157 1 20.25885204 1.971517381 11.22088494 0.723009052 1.716217925 0.554660413 0.350186516 0.55000751 214.9708614 0.135401074 0.088165646 93.65206995 -1.971517381 0.993208874 S(ph)HSSPASLQLGTGAGAAGSPAQQHAHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSSPASLQLGTGAGAAGSPAQQHAHLR 28 0 C9JR84;C9J038;Q9GZV5 C9JR84 WWTR1 WW domain-containing transcription regulator protein 1 1 S(0.499)HS(0.403)S(0.098)PASLQLGTGAGAAGSPAQQHAHLR;S(0.427)HS(0.325)S(0.248)PASLQLGTGAGAAGSPAQQHAHLR 201.28 6.98E-25 934300000 72148 95665 76647 91436 85061 97256 73185 19820.9 82666 61773 TRUE FALSE 69328.3764 92936.72787 90498.8179 96155.02292 87797.06432 99222.58296 74080.65992 19411.59149 73282.10224 57589.05969 1.203846299 1.613791376 1.57145851 1.669675168 1.524544155 1.722941536 1.286366895 0.337070819 1.272500413 1 15.81350715 1.971537561 8.997260733 0.799057397 1.554801079 0.585448037 0.254421014 0.206339599 61.69149538 0.09927077 0.064508976 93.6564217 -1.971537561 0.755743682 SNS(ph)ELEDEILCLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSELEDEILCLEK 14 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5;Q86UF2;A4D2H0;A0A5F9ZHA4;G3V5K6;A0A2R8YE69;Q8IX94;P0CG41;A4FU28 Q96PC5 MIA2;CTAGE6;CTAGE15;CTAGE5;CTAGE4;CTAGE8;CTAGE9 Melanoma inhibitory activity protein 2;cTAGE family member 6;cTAGE family member 15;cTAGE family member 4;cTAGE family member 8;cTAGE family member 9 1 S(0.003)NS(0.997)ELEDEILCLEK 185.33 1.25E-06 9580900 22214 25159 15642 28561 20864 19111 23410 34146 27708 26176 TRUE FALSE 21345.85232 24441.48995 18468.85735 30035.03663 21535.10951 19497.43751 23696.49858 33440.87317 24562.704 24403.0762 0.874719734 1.001574135 0.756824967 1.230788954 0.882475198 0.798974578 0.971045551 1.370354823 1.006541298 1 14.5747754 1.971547547 23.27845271 1.167762126 0.928239835 0.238323496 0.155931184 336.6779804 275452.8557 0.061750667 0.039969802 93.65857519 -1.971547547 -0.23952229 NGLEGSSEETS(ph)FHDESLQDDREEIENNSYHMHPAGIILTK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGLEGSSEETSFHDESLQDDREEIENNSYHMHPAGIILTK 40 1 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 NGLEGS(0.001)S(0.003)EET(0.068)S(0.928)FHDES(0.001)LQDDREEIENNSYHMHPAGIILTK;NGLEGS(0.068)S(0.058)EET(0.225)S(0.647)FHDES(0.002)LQDDREEIENNSYHMHPAGIILTK 159.1 1.02E-18 215007000 70059 78864 72414 84881 83815 93794 78120 26555 88264 84423 TRUE FALSE 67321.01683 76614.87594 85500.82064 89261.71858 86510.98559 95690.57894 79076.05593 26006.62997 78244.64075 78704.95501 0.85535932 0.973444123 1.086346096 1.134130863 1.099180929 1.215813908 1.00471509 0.330431927 0.994151394 1 16.26416685 1.97169041 24.75736569 0.692241778 1.066935717 0.265636809 0.19959273 579.7370253 506992.1544 0.079586505 0.05148489 93.68938965 -1.97169041 0.374693939 LPLPDDEHDLS(ph)DRELELEDSAALSDLHWHDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LPLPDDEHDLSDRELELEDSAALSDLHWHDR 31 1 Q8NF91;Q8NF91-4;A0A0C4DG40;E7ENN3;H0Y325;Q8NF91-2;Q8NF91-8;Q8NF91-11;Q8NF91-3;Q8NF91-9;A0A5F9ZH87;A0A5F9ZHE1;Q5JV20;F8WAI0;H0Y326;A0A5F9ZHB2 Q8NF91 SYNE1 Nesprin-1 1 LPLPDDEHDLS(1)DRELELEDSAALSDLHWHDR;LPLPDDEHDLS(1)DRELELEDSAALSDLHWHDR;LPLPDDEHDLS(1)DRELELEDSAALSDLHWHDR;LPLPDDEHDLS(1)DRELELEDSAALSDLHWHDR 325.44 4.57E-94 237004000 80574 87766 55080.4 68424.6 78815 80728 62596 21581.9 71839 50128.5 TRUE FALSE 77425.079 85262.99961 65034.65354 71956.00181 81350.15605 82360.37547 63362.06857 21136.22622 63684.13789 46733.25205 1.656744943 1.824461082 1.391614123 1.53971741 1.740733899 1.762350615 1.355824082 0.452273816 1.362715735 1 15.51216181 1.971704549 7.399847945 0.881723719 1.641014352 0.643552563 0.236853547 0.118547727 24.72845556 0.095315177 0.061612066 93.69243988 -1.971704549 0.759290633 LLEDGEDFNLGDALDSSNSMQTIQK ddPTM_BT-474_Pertuzumab_2h_R1 7 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 402.32 1.76E-158 3239387000 2208093 2119068 1793852 2130412 2090368 2168592 2206288 2456928 2672248 2656047 FALSE TRUE 2121798.284 2058634.255 2118040.96 2240362.819 2157606.585 2212442.416 2233289.213 2406191.578 2368905.61 2476150.571 0.856893886 0.831384924 0.85537648 0.904776489 0.871355163 0.89350076 0.901919794 0.971746875 0.956688837 1 21.23966761 1.97176054 0.526808766 1.004254667 0.845751624 0.883997621 0.017898856 0.269546956 0.161640193 0.018038036 0.013040505 93.70451987 -1.97176054 -0.158503043 AQT(ph)PENKPGHMEQDEDSCTAQPELAK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQTPENKPGHMEQDEDSCTAQPELAK 26 1 F5H527;Q76I76;A0A3B3IS79 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 AQT(1)PENKPGHMEQDEDSCTAQPELAK 95.319 0.011305 151510000 172310 130180 104180 88015 108360 125000 154950 172000 202170 202950 TRUE FALSE 165575.9347 126467.3939 123007.6435 92557.4647 111845.4978 127527.5856 156846.3245 168448.1399 179220.5092 189204.0157 0.875118501 0.668418127 0.650132308 0.489193976 0.591137019 0.674021559 0.828979892 0.890298968 0.947234172 1 17.52958318 1.971784848 1.625117516 0.957393784 0.644038176 0.66671355 0.092608258 0.239707382 1.179013814 0.064463424 0.030753981 93.70976474 -1.971784848 -0.313355608 DFTNEAPPAPLPDAS(ph)ASPLSPHRR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDAS(0.333)AS(0.333)PLS(0.333)PHRR 69.133 0.015529 600780000 208930 229120 178880 261420 220920 236530 206740 180140 194040 227250 TRUE FALSE 200764.7846 222585.7219 211207.5952 274911.9175 228026.0924 241312.7987 209270.146 176420.046 172013.3927 211858.1551 0.947637746 1.05063561 0.996929267 1.297622541 1.076314916 1.13903002 0.987784236 0.832727189 0.811927172 1 17.69273914 1.971827103 3.981314804 0.868687976 1.087915227 0.455918125 0.099118936 0.186743849 6.31264806 0.045824937 0.027753729 93.71888276 -1.971827103 0.219227251 SKSEEAHAEDSVMDHHFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 172.84 3.29E-12 5427990000 7347200 8868000 6195720 6542200 6991400 8613100 6807900 766086 7395900 6307160 FALSE TRUE 7060063.301 8615093.323 7315424.427 6879843.726 7216284.73 8787262.783 6891217.117 750266.0564 6556348.438 5879970.435 1.200697075 1.465159292 1.244126056 1.170047333 1.227265479 1.49443996 1.171981593 0.12759691 1.115030851 1 22.48737747 1.971917059 21.8317263 0.650403131 1.299092776 0.451389082 0.26677271 102.5996594 79760.36991 0.103616503 0.067126544 93.73829696 -1.971917059 0.648689646 VKPLQDQNELFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKPLQDQNELFGK 13 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 119.87 0.00028716 1382800000 690330 703490 592300 558820 588050 578020 680020 798800 843140 767330 FALSE TRUE 663351.1404 683427.154 699341.7856 587660.7672 606965.1623 589707.9604 688342.2882 782304.5009 747430.2819 715358.0556 0.927299462 0.955363749 0.977610834 0.821491787 0.848477427 0.824353561 0.962234622 1.093584527 1.044833809 1 19.448306 1.97203087 5.458078243 1.051316757 0.893568615 0.623849307 0.05345811 0.12712665 10.96260333 0.025227856 0.015986351 93.76286515 -1.97203087 -0.157748143 HTDSWLHTSELNDGYDWGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTDSWLHTSELNDGYDWGR 19 0 Q9H089;F8WFC6 Q9H089 LSG1 Large subunit GTPase 1 homolog 0 128.69 1.21E-05 148420000 51716 68611 54518 79727 57531 67293 57890 22081 57674 67892 FALSE TRUE 49694.88154 66654.28146 64370.61535 83841.72002 59381.53686 68653.71057 58598.47514 21625.01963 51127.08931 63293.61437 0.785148424 1.053096464 1.01701595 1.324647373 0.938191593 1.084686208 0.925819701 0.341661949 0.807776421 1 15.94977233 1.972075643 14.25771299 0.640903842 1.039667142 0.3122584 0.201333848 3.248217886 1657.106771 0.079284756 0.051620384 93.77253205 -1.972075643 0.398763301 AHLDHIPDYTPPLLTTIS(ph)PEQESDER ddPTM_BT-474_Pertuzumab_2h_R1 2 AHLDHIPDYTPPLLTTISPEQESDER 26 0 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;K7EM61 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 AHLDHIPDYTPPLLTT(0.003)IS(0.996)PEQESDER;AHLDHIPDYTPPLLTT(0.002)IS(0.998)PEQESDER 211.73 1.59E-25 493400000 180540 217990 188872 221040 204656 217970 193910 18825.1 245440 170599 TRUE FALSE 173484.2972 211773.1386 223005.3718 232447.9009 211238.9461 222377.5027 196283.1286 18436.35511 217578.6802 159044.1778 1.090793135 1.331536568 1.402159922 1.461530401 1.3281778 1.398212156 1.234142182 0.115919711 1.368039266 1 17.27906803 1.972214385 24.61912 0.716073966 1.341374589 0.336201456 0.308266551 494.0767836 437770.2347 0.120080661 0.0777223 93.80249387 -1.972214385 0.625300622 SNS(ph)VEKPVSSILSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SNSVEKPVSSILSR 14 1 H0YJN0;Q9UI08-5;Q9UI08;Q9UI08-2;Q9UI08-4;Q9UI08-3 H0YJN0 EVL Ena/VASP-like protein 1 S(0.006)NS(0.994)VEKPVSSILSR;S(0.006)NS(0.994)VEKPVSSILSR;SNS(0.989)VEKPVS(0.005)S(0.005)ILS(0.001)R 159.69 3.05E-07 1675170000 940230 841060 551010 697850 951910 779100 916520 1280280 1156460 1026020 TRUE FALSE 903484.7721 817073.7923 650589.7642 733866.1221 982529.0497 794853.9358 927736.6459 1253841.771 1025183.509 956526.7515 0.944547312 0.854209034 0.680158462 0.767219653 1.027184078 0.830979306 0.969901411 1.310827709 1.071777143 1 19.86744579 1.972215781 5.791699157 1.158944519 0.850645198 0.532192055 0.115119201 0.127772055 13.33557111 0.049936146 0.031827974 93.80279542 -1.972215781 -0.308299321 HEQVENCLLTSPFEDIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEQVENCLLTSPFEDIFK 18 0 A0A3B3ITS5;Q14181;H0YDR7;Q14181-2 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 0 123.55 3.37E-05 84998000 137740 142610 129880 124000 133240 135290 134220 85620 191010 161710 FALSE TRUE 132356.9685 138542.9024 153352.2052 130399.6549 137525.7856 138025.6565 135862.6245 83851.91708 169327.3456 150757.2377 0.87794769 0.918980107 1.017212888 0.864964475 0.912233388 0.915549121 0.901201339 0.556204918 1.123178882 1 17.20186774 1.972377889 24.98784568 0.81503883 0.918783568 0 0.145072988 1734.089286 1568710.704 0.05797731 0.037505693 93.8378155 -1.972377889 0.103744738 HCECAEEGTR ddPTM_BT-474_Pertuzumab_2h_R1 6 HCECAEEGTR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;;;; 179.37 2.38E-06 1325953600 595113.2 575952.7 591397.5 615826.6 623320.1 625849.4 603288.2 404628.5 732963 678213.6 FALSE TRUE 571855.5182 559527.0929 698276.1838 647609.4846 643369.7571 638504.5037 610671.4215 396272.7801 649760.1131 632277.5888 0.904437431 0.884938993 1.10438231 1.024248678 1.017543194 1.009848388 0.965828035 0.626738615 1.027650077 1 19.27019856 1.972464064 24.93376181 0.831562869 0.9934578 0.089824415 0.119405308 898.1810643 813300.8931 0.048128281 0.031142699 93.85643708 -1.972464064 0.161894931 ESENSGDSGYPS(ph)EK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESENSGDSGYPSEK 14 0 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 ESENSGDSGYPS(1)EK 185.33 7.90E-08 0 294270 208100 90301 154460 224830 180400 227060 395880 313930 191660 TRUE FALSE 282769.6031 202165.1918 106620.3994 162431.6991 232061.8611 184047.8116 229838.8282 387704.9397 278293.9825 178678.6975 1.582559125 1.131445408 0.596715786 0.90907143 1.298766246 1.030048988 1.286324735 2.169844224 1.557510696 1 17.44700812 1.972495476 11.27244623 1.711566619 1.07900212 0.240319975 0.3617416 0.944987424 384.3189517 0.147056131 0.095921383 93.86322596 -1.972495476 -0.632564499 NENTFLDLTVQQIEHLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 NENTFLDLTVQQIEHLNK 18 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 208.34 6.43E-16 1347350000 851900 806410 715000 728340 746070 781950 852110 905710 1094520 921300 FALSE TRUE 818606.8062 783411.9764 844216.4051 765929.7147 770068.0191 797761.5648 862538.3771 887006.772 970274.6782 858899.5304 0.953087966 0.912111311 0.982904723 0.891757054 0.896575201 0.928818257 1.004236638 1.032724714 1.129671916 1 19.71212986 1.972521819 2.005326207 1.062398006 0.925811191 0.679981813 0.039361086 0.181272412 1.351831148 0.022610866 0.011463983 93.86891963 -1.972521819 -0.136586815 HKGFAFVEYEVPEAAQLALEQMNSVMLGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HKGFAFVEYEVPEAAQLALEQMNSVMLGGR 30 1 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5;A0A0J9YVR6;E9PQ56;A0A0J9YWM1;H0YEM1;H0YCP8;E9PN18;E9PMU7 A0A0J9YVP6;E9PN18 PUF60 Poly(U)-binding-splicing factor PUF60 0 ; 204.92 9.01E-26 139334000 132860 149514 118130 110664 131098 156807 124320 89212 133900 117108 FALSE TRUE 127667.6843 145250.0071 139478.7188 116375.3823 135314.8862 159977.745 125841.4653 87369.74102 118700.2334 109176.1709 1.169373164 1.330418588 1.277556427 1.065941234 1.23941777 1.46531742 1.152645897 0.800263834 1.087235726 1 16.73629848 1.972702556 10.73193298 0.949143178 1.257306521 0.558762937 0.117268634 0.495826913 192.5580223 0.048063835 0.031359826 93.90799243 -1.972702556 0.308163342 GSEEELADIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSEEELADIK 10 0 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 90.15 0.023057 0 89116 85905 77168 83234 102030 86429 91977 103680 129100 118190 FALSE TRUE 85633.2482 83455.07351 91113.97419 87529.71671 105311.8876 88176.6536 93102.64204 101538.9718 114445.1092 110184.886 0.777177808 0.757409446 0.826918986 0.794389502 0.955774348 0.800260878 0.844967449 0.921532666 1.038664316 1 16.74956682 1.972757494 0.423415664 1.027165122 0.769613325 0.657916204 0.055389943 0.679609322 0.29905837 0.061485633 0.057053965 93.91987238 -1.972757494 -0.257551797 SRSES(ph)ETSTMAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.191)RS(0.191)ES(0.617)ETSTMAAK;SRSES(0.973)ET(0.001)S(0.016)T(0.01)MAAK 206.43 1.63E-07 2709500000 2882880 2676060 2033300 2448520 2735850 2538040 2629520 3203660 2878840 2823560 TRUE FALSE 2770213.862 2599741.389 2400762.541 2574888.411 2823851.1 2589360.908 2661700.852 3137503.301 2552046.152 2632317.766 1.052385809 0.987624451 0.912033711 0.97818297 1.072762239 0.983680975 1.011162439 1.191916623 0.969505348 1 21.32790223 1.972775153 24.59470749 1.081733439 0.996060703 0.075859391 0.069336897 847.4021376 765535.1206 0.028202559 0.018263053 93.92369137 -1.972775153 -0.085672736 TEES(ph)PAS(ph)DEAGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 2 TEES(1)PAS(1)DEAGEK;TEES(1)PAS(1)DEAGEK 344.61 1.13E-63 1408580000 2829300 2165100 2815500 2562900 2550500 2005630 2877400 3753200 3710800 3380700 TRUE FALSE 2718727.828 2103353.468 3324323.48 2695171.576 2632539.149 2046185.213 2912614.482 3675695.108 3289565.541 3151722.178 0.862616587 0.667366395 1.054764124 0.855142498 0.835270052 0.649227659 0.924134273 1.16624972 1.043735886 1 21.58770894 1.972833881 7.673464508 1.078602706 0.823264613 0.49669698 0.112249642 0.180232531 42.12694288 0.046491675 0.03016026 93.93639316 -1.972833881 -0.255338093 GVAGAHGLLCLLSDHVDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVAGAHGLLCLLSDHVDKR 19 1 U3KQ56;Q9UBQ7 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 158.64 1.42E-11 478620000 290080 319740 247950 311680 331070 350800 302270 186570 321740 342180 FALSE TRUE 278743.3529 310621.3283 292760.0806 327765.8422 341719.1672 357893.4164 305969.2707 182717.2643 285217.424 319003.8438 0.873793085 0.973722838 0.917732141 1.027466748 1.071207052 1.121909417 0.959139762 0.572774491 0.894087735 1 18.28321428 1.97283746 23.81729655 0.772602619 1.001194664 0.26537758 0.122684697 378.5202933 331902.121 0.04964588 0.032152464 93.93716733 -1.97283746 0.228592045 DT(ph)LSNPQSPQPSPYNSPKPQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DTLSNPQSPQPSPYNSPKPQHK 22 1 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 DT(0.59)LS(0.41)NPQSPQPSPYNSPKPQHK;DT(0.545)LS(0.454)NPQSPQPSPYNSPKPQHK 128.17 2.50E-05 545520000 389996 414804 367766 432817 359837 393831 433478 519060 528810 491922 TRUE FALSE 374754.5252 402974.1961 434229.4971 455154.7372 371411.4839 401794.5327 438783.0334 508341.2296 468781.7058 458603.6848 0.817164226 0.878698121 0.946851304 0.99247946 0.809874618 0.876125827 0.956780436 1.108454307 1.0221935 1 18.80688842 1.972857042 4.707045829 1.052316415 0.891686552 0.598692717 0.057248157 0.135587968 7.413556545 0.026151482 0.016303707 93.94140308 -1.972857042 -0.160629864 EVS(ph)PLLPK ddPTM_BT-474_Pertuzumab_2h_R1 6 EVSPLLPK 8 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 EVS(1)PLLPK;EVS(1)PLLPK;EVS(1)PLLPK;EVS(1)PLLPK;EVS(1)PLLPK;EVS(1)PLLPK 148.73 0.00054192 2838152000 5298380 4920470 4160460 4676230 4881200 4645180 4923220 5807660 5655590 5378590 TRUE FALSE 5091313.452 4780143.013 4912347.671 4917570.791 5038208.231 4739108.722 4983471.839 5687729.791 5013591.133 5014293.309 1.015360119 0.953303431 0.979668992 0.980710638 1.004769351 0.945119966 0.993853278 1.134303369 0.999859965 1 22.25761496 1.972921458 24.05699517 1.06075239 0.978925961 0.316780992 0.040751579 378.3073085 336093.223 0.015735443 0.010182921 93.95533763 -1.972921458 -0.081826429 TNLEFLQEQFNSIAAHVLHCTDSGFGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TNLEFLQEQFNSIAAHVLHCTDSGFGAR 28 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ; 211.78 4.47E-26 702430000 247050 290130 231501 318060 289510 318930 267692 59003 304240 269470 FALSE TRUE 237395.0129 281855.7765 273338.3804 334475.1147 298822.3521 325378.9831 270968.0948 57784.56743 269703.9507 251218.5569 0.944974033 1.121954445 1.088050118 1.331410859 1.189491556 1.295202819 1.078614964 0.230017114 1.073582915 1 17.93858351 1.973049357 24.38572209 0.675313635 1.167415703 0.337014256 0.237462811 441.1172435 399134.8695 0.093439019 0.060514044 93.98301152 -1.973049357 0.492102068 ENLQLNQETEAIKEELLYFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENLQLNQETEAIKEELLYFK 20 1 Q96BW5-2;Q96BW5 Q96BW5-2 PTER Phosphotriesterase-related protein 0 145.75 1.29E-07 45938000 47108 47879 43406 43879 38786 44506 47356 57017 56550 49106 FALSE TRUE 45266.96728 46513.5378 51250.42976 46143.60045 40033.58691 45405.94181 47935.55689 55839.57903 50130.68108 45780.00688 0.98879337 1.016022953 1.11949371 1.007942191 0.874477521 0.991829074 1.047084965 1.219737235 1.095034372 1 15.48243006 1.973080643 9.794945514 1.130453668 1.002143816 0.262869966 0.075382525 0.522635229 184.8256536 0.031910061 0.020822548 93.9897822 -1.973080643 -0.128309853 RGT(ph)FSDQELDAQSLDDEDDNMHHAVYPAVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGTFSDQELDAQSLDDEDDNMHHAVYPAVNR 31 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RGT(0.891)FS(0.109)DQELDAQSLDDEDDNMHHAVYPAVNR 167.5 8.84E-13 423360000 121790 133230 113460 129720 128510 141360 120840 30986 141400 111100 TRUE FALSE 117030.3122 129430.4108 133964.7459 136414.8647 132643.6409 144218.3961 122318.8761 30346.12827 125348.8648 103575.098 1.12990781 1.249628659 1.293406894 1.317062376 1.280651849 1.392404147 1.180967997 0.29298672 1.210222024 1 16.66031766 1.973096986 23.81057322 0.751128538 1.279304497 0.418011153 0.228082368 291.8234564 258278.291 0.088386042 0.057263438 93.99331924 -1.973096986 0.528175959 S(ph)VS(ph)RS(ph)PVPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVSRSPVPEK 10 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 3 S(1)VS(1)RS(1)PVPEK;S(1)VS(1)RS(1)PVPEK 94.551 0.0065443 316690000 942380 835780 913300 1052220 889260 913960 1146130 1463870 1566980 1445000 TRUE FALSE 905550.7477 811944.3727 1078353.626 1106525.2 917863.8555 932440.8974 1160156.682 1433640.573 1389103 1347128.863 0.672207962 0.602722126 0.800482905 0.821395214 0.681348222 0.692169044 0.861206907 1.064219328 1.031158219 1 20.36145643 1.973104943 3.034645042 1.035054316 0.714845727 0.84386047 0.06162951 0.102028378 1.786422252 0.033270842 0.01899775 93.99504132 -1.973104943 -0.320208589 IEHTYTGGVDSDLGEAMSDCDPDGPLMCHTTK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEHTYTGGVDSDLGEAMSDCDPDGPLMCHTTK 32 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 293.8 1.12E-89 350320000 450800 425970 344940 411300 409290 432930 408760 311250 463420 457280 FALSE TRUE 433182.2376 413821.7527 407278.3311 432527.2423 422455.1846 441684.1412 413762.5272 304822.5787 410814.5044 426308.0183 1.016125006 0.970710695 0.955361649 1.014588569 0.990962324 1.036068106 0.970571768 0.715028959 0.963656527 1 18.70153667 1.973108226 24.60487072 0.856623846 0.995404685 0.239718843 0.07532972 549.0608203 502367.3469 0.029345167 0.019008887 93.99575193 -1.973108226 0.138780839 NGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_BT-474_Pertuzumab_2h_R1 4 NGAAGPHSPDPLLDEQAFGDLTDLPVVPK 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;NGAAGPHS(0.834)PDPLLDEQAFGDLT(0.166)DLPVVPK;NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK 276.45 2.28E-71 1506450000 525276 549607 606556 687082 811581 727925 571085 491188 560520 489418 TRUE FALSE 504747.6332 533932.7465 716174.162 722542.3844 837686.2399 742644.1422 578074.1091 481044.7962 496892.1195 456269.2829 1.106249428 1.170214096 1.569630455 1.583587612 1.835947041 1.627644398 1.266958199 1.0543002 1.089032591 1 18.79952601 1.973155555 3.528603054 1.063225528 1.491998627 0.478269622 0.202870957 0.237035787 5.900632274 0.10866469 0.064319329 94.00599597 -1.973155555 0.428773099 IYPHGLVLLDLQSYDGDAQGKEEIDSILNK ddPTM_BT-474_Pertuzumab_2h_R1 2 IYPHGLVLLDLQSYDGDAQGKEEIDSILNK 30 1 P52788;H7C2R7 P52788 SMS Spermine synthase 0 ; 325.56 1.06E-93 969140000 591900 491990 394930 464780 420760 443710 527500 583000 666450 613110 FALSE TRUE 568767.8936 477958.9269 466302.6362 488767.3515 434294.1275 452682.1202 533955.7028 570960.8463 590797.39 571583.5136 0.995074001 0.836201387 0.815808408 0.855111003 0.759808702 0.791978966 0.934169181 0.998910628 1.033615169 1 19.12460478 1.973176965 3.034434601 1.009157511 0.838056924 0.618094789 0.059370241 0.173720691 3.041447477 0.030268089 0.017284182 94.01063032 -1.973176965 -0.171100588 GTPKPPGPPAQPPGPPNAS(ph)SNPDLRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTPKPPGPPAQPPGPPNASSNPDLRR 26 2 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 GTPKPPGPPAQPPGPPNAS(0.59)S(0.41)NPDLRR;GTPKPPGPPAQPPGPPNAS(0.599)S(0.401)NPDLRR 166.74 5.85E-12 1114160000 166464 190542 129124 175997 132603 162415 165483 204010 182853 177950 TRUE FALSE 159958.4028 185107.9287 152459.5791 185080.2263 136868.2959 165699.1426 167508.2305 199797.1222 162096.294 165897.288 0.964201433 1.115798401 0.918999828 1.115631416 0.825018284 0.998805614 1.009710481 1.204342305 0.977088269 1 17.33993078 1.973400707 24.17258442 1.089142786 0.991638686 0.071094893 0.099199971 836.9571576 760598.5379 0.03885322 0.025177223 94.05907581 -1.973400707 -0.097504101 QSHS(ph)GSISPYPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QS(0.089)HS(0.455)GS(0.455)ISPYPK 102.65 0.00061632 0 262160 260740 241440 264540 254540 264680 262420 237040 324100 295240 TRUE FALSE 251914.4974 253303.9505 285073.5788 278192.9411 262727.5103 270032.0109 265631.5745 232145.0412 287309.5267 275243.1318 0.915243536 0.92029163 1.035715503 1.010717104 0.954528851 0.981067208 0.965079756 0.843418107 1.043839041 1 18.07034704 1.973500459 24.9737135 0.934828036 0.971670498 0 0.060265151 2124.035493 2001731.939 0.02496933 0.016143128 94.08068252 -1.973500459 0.036842462 YHQIGSGK ddPTM_BT-474_Pertuzumab_2h_R1 4 YHQIGSGK 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;; 135.83 0.00081697 3327110000 7694800 7930600 6080980 6855530 6927300 7345800 6860190 2784910 8327900 7637800 FALSE TRUE 7394078.709 7704427.053 7179948.357 7209344.725 7150122.896 7494337.109 6944147.057 2727400.635 7382551.705 7120485.003 1.038423465 1.082008747 1.008351026 1.012479448 1.004162342 1.052503742 0.975235122 0.383035795 1.036804614 1 22.76354408 1.973551206 24.95091441 0.723330236 1.030355312 0.217159305 0.17185057 677.5980669 639222.7786 0.066846667 0.043303758 94.09167641 -1.973551206 0.307025076 HGLAHDEMKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 14 HGLAHDEMKSPR 12 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR 189.1 1.05E-05 9807605000 14653820 13660760 11624765 11744052 12745120 12726539 11824252 1479993 14140830 10606748 TRUE FALSE 14081132.51 13271168.5 13725618.63 12350163.93 13155078.36 12983878.34 11968960.73 1449430.627 12535622.26 9888343.51 1.424013284 1.342102293 1.388060459 1.248961863 1.330362193 1.313048877 1.210411099 0.14657972 1.26771711 1 23.23729743 1.973557932 23.46880822 0.702079412 1.332191484 0.425490794 0.271335651 246.4326639 218721.9665 0.105005801 0.068068806 94.09313346 -1.973557932 0.630112072 AYRPPS(ph)GEK ddPTM_BT-474_Pertuzumab_2h_R1 6 AYRPPSGEK 9 1 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 AYRPPS(1)GEK;AYRPPS(1)GEK;AYRPPS(1)GEK;AYRPPS(1)GEK;AYRPPS(1)GEK;AYRPPS(1)GEK 93.623 0.0056163 5925340000 4359320 3749210 3311160 3478070 3509210 3469940 3942390 4685590 4734700 4427930 TRUE FALSE 4188952.955 3642286.202 3909560.268 3657573.61 3622086.927 3540104.564 3990638.148 4588830.929 4197236.705 4128022.357 1.014760239 0.882331995 0.947078269 0.88603532 0.877438786 0.857578825 0.966719122 1.111629379 1.016766951 1 21.97701935 1.973576449 6.566645587 1.052020076 0.908665545 0.580387979 0.05004117 0.114565946 18.06588923 0.020399226 0.013154996 94.09714555 -1.973576449 -0.143354531 QWTEILHFTEHSGLTTGVAFGHHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 QWTEILHFTEHSGLTTGVAFGHHAK 25 0 Q9UMS4;H0YGZ5 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 165.85 4.54E-12 611690000 450780 452010 437730 522270 497630 570280 452620 64222 520470 391160 FALSE TRUE 433163.0192 439119.1174 516837.5483 549224.4173 513636.7209 581811.4523 458159.299 62895.79326 461388.4276 364666.3848 1.187833695 1.204166701 1.417288705 1.506101029 1.408511292 1.595462254 1.256379305 0.172474886 1.265234326 1 18.47621769 1.973591173 22.95517258 0.71907321 1.389416716 0.44040735 0.284279137 191.8004159 166716.6266 0.112322109 0.072831519 94.10033574 -1.973591173 0.670343507 HLPHFKPWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_BT-474_Pertuzumab_2h_R1 6 HLPHFKPWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 44 1 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 HLPHFKPWLHPEQSPLPSLALSELS(0.001)VQHADS(0.999)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;HLPHFKPWLHPEQSPLPS(0.001)LALS(0.001)ELS(0.029)VQHADS(0.968)LENIDES(0.001)AVAESR;HLPHFKPWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;HLPHFKPWLHPEQS(0.001)PLPS(0.001)LALS(0.011)ELS(0.046)VQHADS(0.94)LENIDESAVAESR;HLPHFKPWLHPEQS(0.116)PLPS(0.116)LALS(0.116)ELS(0.116)VQHADS(0.537)LENIDESAVAESR 369.63 9.13E-177 65687162000 2595131 2843579 2451798 2750871 2559755 2936483 2509137 368180.4 3085890 2130101 TRUE FALSE 2493710.411 2762482.911 2894892.439 2892843.782 2642091.844 2995860.698 2539844.569 360577.3461 2735592.704 1985827.362 1.255753878 1.391099228 1.457776489 1.45674485 1.330474086 1.508620918 1.278985584 0.181575374 1.377558169 1 20.92130878 1.973609701 24.00287814 0.754151228 1.401046275 0.410844881 0.286531526 330.5908841 300682.9872 0.110553058 0.071649092 94.10435044 -1.973609701 0.646895046 GIDDNLDEIPDGEMPQVDHLVFVVHGIGPVCDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIDDNLDEIPDGEMPQVDHLVFVVHGIGPVCDLR 34 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8;A0A0C4DH82 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 132.57 2.11E-08 171186000 68821 80204 65313 84278 88480 88463 78503 50944 90059 88285 FALSE TRUE 66131.39923 77916.66045 77116.51198 88627.59768 91326.03956 90251.78247 79463.7432 49891.9886 79835.87988 82305.37831 0.803488187 0.94667763 0.936955926 1.076814171 1.1095999 1.096547812 0.965474491 0.60618139 0.969995904 1 16.32869909 1.973707936 24.27702071 0.807683044 1.001763383 0.142159185 0.132938751 631.5577144 583153.4558 0.055152763 0.035735411 94.1256386 -1.973707936 0.194080339 HGYIGEFEIIDDHR ddPTM_BT-474_Pertuzumab_2h_R1 7 HGYIGEFEIIDDHR 14 0 P62244;I3L3P7;I3L246;H3BN98 P62244 RPS15A 40S ribosomal protein S15a 0 ;;;;;; 226.59 1.36E-12 28330110000 8789940 8972760 8115310 9252820 9198040 9076290 8256910 1822732 9160300 8241320 FALSE TRUE 8446419.427 8716865.67 9581927.041 9730359.149 9493903.31 9259818.802 8357960.535 1785091.947 8120461.147 7683128.056 1.099346434 1.134546451 1.247138792 1.266458021 1.235682035 1.205214691 1.087833038 0.232339216 1.056921229 1 22.87326237 1.973726974 21.96389874 0.673364356 1.197584817 0.430207107 0.216943135 112.6649673 94185.61417 0.0845206 0.054844759 94.12976483 -1.973726974 0.524220461 GLDT(ph)PGKR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLDTPGKR 8 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 GLDT(1)PGKR;GLDT(1)PGKR;GLDT(1)PGKR;GLDT(1)PGKR 116.52 0.0013221 2443500000 3824160 3511510 3091170 2822830 2949740 3282990 3370930 4208800 3578490 3945370 TRUE FALSE 3674707.599 3411365.173 3649813.182 2968516.595 3044621.066 3349374.307 3412184.45 4121886.809 3172274.817 3678146.576 0.999065025 0.927468523 0.992296828 0.807068596 0.82775958 0.910614691 0.927691265 1.120642346 0.862465579 1 21.81054754 1.97373031 23.79791016 1.011872242 0.907738281 0.164467193 0.081678328 568.8681513 515340.5026 0.033880592 0.021966294 94.13048792 -1.97373031 -0.104133961 HVTENRDDVFLDGTGWEGGDEWIR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVTENRDDVFLDGTGWEGGDEWIR 24 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 ; 123.12 6.93E-05 233940000 81400 109471 89406 102497 108204 107961 92200 70003 95046 92273 FALSE TRUE 78218.79801 106348.9943 105563.653 107786.8825 111684.4799 110144.0454 93328.37118 68557.41359 84256.77655 86023.26752 0.9092749 1.236281733 1.227152328 1.252996841 1.298305483 1.280398299 1.08492009 0.796963607 0.979464963 1 16.39243931 1.973744772 5.510378014 0.909409547 1.209034406 0.533259928 0.114837457 0.128704037 11.63921481 0.048985413 0.031165253 94.1336226 -1.973744772 0.299624858 IADPEHDHTGFLT(ph)EYVATR ddPTM_BT-474_Pertuzumab_2h_R1 1 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 1 IADPEHDHTGFLT(0.54)EY(0.46)VATR 229.15 3.20E-19 888380000 360730 409070 385940 444310 435050 468620 312540 52848 258650 222550 TRUE FALSE 346632.2728 397403.7241 455687.9432 467240.8923 449043.7784 478095.8175 316364.958 51756.67033 229289.1363 207476.4903 1.670706268 1.915415687 2.196335318 2.25201849 2.164311618 2.30433731 1.524823162 0.249458 1.105133097 1 17.66258834 1.973764467 4.984080262 0.729944512 2.084457671 0.818886268 0.27315272 0.071209595 4.669292848 0.118706673 0.074681355 94.1378915 -1.973764467 1.354513159 NETLDATHLAEFHQIEGVVADHGLTLGHLMGVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 NETLDATHLAEFHQIEGVVADHGLTLGHLMGVLR 34 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 276.07 2.59E-74 445010000 231977 251035 225696 240148 252565 257774 227093 28334 284370 199913 FALSE TRUE 222911.0824 243875.7276 266484.2878 252542.0671 260688.9826 262986.3669 229872.2321 27748.893 252089.5098 186372.7144 1.196049985 1.308537724 1.42984604 1.355037768 1.398750796 1.411077623 1.233400676 0.148889246 1.35260953 1 17.50783113 1.973789711 24.12241568 0.727234849 1.351439659 0.374316605 0.289468482 370.4782055 340965.6854 0.112283115 0.072770642 94.14336362 -1.973789711 0.62420481 DQDMSS(ph)PTTMK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDMSSPTTMK 11 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 DQDMS(0.013)S(0.903)PT(0.07)T(0.014)MK 157.86 0.0013097 0 379600 372950 315890 358940 365950 370210 408920 451010 504120 492360 TRUE FALSE 364764.8123 362313.8312 372978.3499 377464.9364 377721.1141 377695.8999 413924.4853 441696.4859 446894.411 459012.0187 0.794673772 0.789334084 0.812567721 0.822342163 0.82290027 0.822845338 0.901772652 0.962276516 0.973600675 1 18.8081724 1.973794738 1.268528695 0.993165411 0.804947823 0.979660479 0.010987015 0.059437884 0.177129489 0.008682007 0.003969442 94.14445334 -1.973794738 -0.188217588 S(ph)VDIHDSIQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVDIHDSIQPR 11 0 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR 197.43 5.99E-08 4352070000 1216950 2015520 1525230 1929420 1543710 1709830 1516620 1502640 1355840 1648820 TRUE FALSE 1169390.249 1958039.343 1800872.99 2028997.597 1593364.834 1744403.934 1535180.849 1471609.959 1201930.727 1537143.953 0.760755196 1.273816509 1.171570812 1.319978909 1.036574897 1.134834464 0.998722889 0.957366391 0.781924637 1 20.55182085 1.973849302 1.658674962 0.89463596 1.135458276 0.262408266 0.152175863 0.458341173 2.348368327 0.095247905 0.045762975 94.15628221 -1.973849302 0.240822316 NDKS(ph)EEEQSSSSVK ddPTM_BT-474_Pertuzumab_2h_R1 6 NDKSEEEQSSSSVK 14 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(0.997)EEEQS(0.003)SSSVK 297.36 6.73E-44 22153600000 12359697 9615290 10905461 8468539 8484822 10294848 12615451 14320594 17841552 15013883 TRUE FALSE 11876666.38 9341071.344 12876320.39 8905601.313 8757744.005 10503016.88 12769842.66 14024868.73 15816253.81 13996979.33 0.84851639 0.667363373 0.919935658 0.636251658 0.625688143 0.750377394 0.912328465 1.00199253 1.129976221 1 23.73861218 1.973851938 2.023867359 1.054947153 0.734911635 0.688844759 0.092004587 0.184866916 1.404238464 0.054112035 0.027543943 94.15685381 -1.973851938 -0.320035518 VHVQFFDDS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 6 VHVQFFDDSPTR 12 0 P52701;P52701-2;A0A087WWJ1;A0A494C0M1;F8WAX8;C9J7Y7;C9J8Y8;C9JH55 P52701 MSH6 DNA mismatch repair protein Msh6 1 VHVQFFDDS(0.951)PT(0.049)R;VHVQFFDDS(0.997)PT(0.003)R;VHVQFFDDS(0.935)PT(0.065)R;VHVQFFDDS(0.989)PT(0.011)R;VHVQFFDDS(0.987)PT(0.013)R;VHVQFFDDS(0.987)PT(0.013)R 225.31 1.16E-11 3798110000 2458650 2570060 2307730 2535170 2511610 3012810 2496730 1231266 2966010 2708780 TRUE FALSE 2362563.24 2496764.405 2724788.146 2666010.428 2592398.217 3073731.082 2527285.729 1205839.927 2629320.979 2525311.918 0.935553039 0.988695451 1.078990729 1.055715299 1.02656555 1.217168881 1.000781611 0.47750138 1.04118662 1 21.26803016 1.973890345 24.59883579 0.770915765 1.053166033 0.225644558 0.160588022 587.2920378 553307.9563 0.063332084 0.041041484 94.16518087 -1.973890345 0.282250268 HDS(ph)PEDVKR ddPTM_BT-474_Pertuzumab_2h_R1 5 HDSPEDVKR 9 1 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 1 HDS(1)PEDVKR;HDS(1)PEDVKR;HDS(1)PEDVKR;HDS(1)PEDVKR;HDS(1)PEDVKR 158.34 4.10E-05 3937392000 4733110 4024890 4183340 3502370 3888900 4606680 4096700 1690861 6812900 4864440 TRUE FALSE 4548134.828 3910104.078 4939362.596 3683127.735 4013990 4699830.226 4146836.64 1655944.129 6039528.154 4534967.146 1.002903589 0.862212217 1.089172741 0.812161944 0.885119974 1.036353754 0.914413822 0.365150193 1.331768888 1 22.11266067 1.973892428 24.85156162 0.78127116 0.944300373 0 0.241794174 1756.500339 1671994.626 0.09625948 0.062378298 94.16563253 -1.973892428 0.163029212 HTGPNS(ph)PDTANDGFVR ddPTM_BT-474_Pertuzumab_2h_R1 6 HTGPNSPDTANDGFVR 16 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;E5RGH4;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 1 HTGPNS(0.997)PDT(0.003)ANDGFVR;HTGPNS(0.998)PDT(0.002)ANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR 376.52 1.38E-104 17952330000 3644526 3755037 3177807 3542226 3807585 3749973 3125581 1363532 3662755 2801017 TRUE FALSE 3502093.895 3647947.021 3752107.415 3725040.708 3930059.429 3825800.023 3163832.795 1335374.588 3246974.408 2611301.624 1.341129597 1.396984166 1.43687247 1.426507254 1.505019334 1.465093112 1.211592244 0.511382743 1.24343139 1 21.31633768 1.973900568 7.658791653 0.862025298 1.423927808 0.628293508 0.174234895 0.118497507 28.43506768 0.068880863 0.044778206 94.1673974 -1.973900568 0.56190251 KSESEVEEAAAIIAQRPDNPR ddPTM_BT-474_Pertuzumab_2h_R1 5 KSESEVEEAAAIIAQRPDNPR 21 2 Q16643;Q16643-3;Q16643-2;D6R9W4;D6R9Q9 Q16643 DBN1 Drebrin 0 ;;;; 221.6 2.39E-25 7685770000 4752350 4640910 4053060 4491840 4496490 4909750 4981290 5660570 6083780 6195440 FALSE TRUE 4566622.908 4508555.791 4785538.102 4723664.401 4641123.684 5009028.509 5042252.517 5543677.251 5393174.8 5775817.33 0.790645314 0.780591825 0.828547343 0.817834798 0.803544056 0.867241504 0.872993765 0.959808272 0.933750929 1 22.46159368 1.973949519 0.720425534 0.994452459 0.794927752 0.930445903 0.019016148 0.151312175 0.150098964 0.016440049 0.008901821 94.1780121 -1.973949519 -0.199524708 HAEELER ddPTM_BT-474_Pertuzumab_2h_R1 2 HAEELER 7 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 161.11 0.0013213 239900000 168384 188304 161545 191423 186563 212920 183247 127653 197692 209920 FALSE TRUE 161803.3671 182933.7543 190739.775 201302.364 192563.9683 217225.3883 185489.6316 125016.9209 175250.833 195701.9314 0.826784723 0.93475702 0.974644316 1.028617155 0.9839656 1.10998081 0.947817072 0.638812913 0.89549874 1 17.57829847 1.974046417 24.54166827 0.801807693 0.981501287 0.196346686 0.109328737 626.7056547 592610.8978 0.044085151 0.028578655 94.19902703 -1.974046417 0.179693594 VEGFPTIYFAPSGDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEGFPTIYFAPSGDKK 16 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 100.68 0.0031617 218950000 268980 248680 234880 249750 245520 258070 272980 328310 335630 302780 FALSE TRUE 258467.9642 241587.8899 277328.0409 262639.6274 253417.3738 263288.3522 276320.8109 321530.2838 297530.6895 282272.4409 0.915668435 0.855867789 0.982483589 0.930447289 0.897775826 0.932745511 0.978915299 1.139077845 1.054055042 1 18.10672876 1.974067926 4.296050296 1.077287574 0.920264958 0.682372235 0.043987712 0.106696335 4.483033986 0.019369065 0.01192844 94.20369246 -1.974067926 -0.157022617 S(ph)PLELEPEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLELEPEAK 10 0 Q92466-4;Q92466;A0A087WTQ7;A0A087WV56;A0A087WW71;A0A087X0X5;Q92466-3;Q92466-2;Q92466-5 Q92466-4 DDB2 DNA damage-binding protein 2 1 S(1)PLELEPEAK 196.11 3.56E-07 142860000 219450 190410 187240 195780 188000 183020 204400 273920 218780 240180 TRUE FALSE 210873.6514 184979.6932 221078.4331 205884.2293 194047.1907 186720.7898 206901.5083 268263.4563 193945.0116 223912.3947 0.941768551 0.826125296 0.987343436 0.91948563 0.866621033 0.833901089 0.924028831 1.198073276 0.866164698 1 17.77257487 1.974187751 24.48083958 1.047828398 0.895135008 0.273872938 0.088576404 565.6796294 536500.7301 0.034827129 0.022581137 94.22968752 -1.974187751 -0.15269339 HS(ph)PS(ph)PRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSPSPRPR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 HS(1)PS(1)PRPR;HS(1)PS(1)PRPR 85.958 0.0093168 270650000 143249 147061 105701 133396 128714 140767 119709 62393 138305 115944 TRUE FALSE 137650.6707 142866.9643 124803.522 140280.5835 132854.2027 143613.4052 121174.0346 61104.56275 122605.1962 108091.0096 1.273470118 1.321728466 1.154615194 1.297800659 1.22909577 1.328634136 1.121037124 0.565306615 1.134277464 1 16.72188701 1.9741881 11.0718969 0.849306249 1.261265328 0.559988576 0.143757173 0.483477761 205.4275261 0.055384036 0.036245181 94.22976327 -1.9741881 0.41195908 HKGYS(ph)PPESR ddPTM_BT-474_Pertuzumab_2h_R1 1 HKGYSPPESR 10 1 Q14669-3;G5E9G6;C9JLD7 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 HKGYS(0.961)PPES(0.039)R 85.45 0.0086186 93581000 238240 209110 175170 199030 209390 214280 198100 128420 230130 194230 TRUE FALSE 228929.3174 203146.3875 206827.1156 209301.9622 216125.2195 218612.8884 200524.4071 125768.0821 204006.6072 181074.6291 1.264281576 1.121893158 1.142220292 1.155887841 1.193569859 1.207308221 1.107413049 0.694564903 1.126643794 1 17.46622489 1.974214511 18.63296447 0.90509477 1.17432438 0.490340005 0.107742298 20.76458783 15003.93799 0.041645037 0.027107216 94.23549382 -1.974214511 0.26922961 DAQRLS(ph)PIPEEVPK ddPTM_BT-474_Pertuzumab_2h_R1 4 DAQRLSPIPEEVPK 14 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK 195.77 1.56E-08 3728410000 5012190 4407670 4181130 4491520 4764890 4758490 5122840 5935120 6534140 6227010 TRUE FALSE 4816308.074 4281967.567 4936753.2 4723327.885 4918157.014 4854709.928 5185534.848 5812557.698 5792411.821 5805249.066 0.829647104 0.737602731 0.850394728 0.813630532 0.847191388 0.836262126 0.893249332 1.00125897 0.997788683 1 22.46892653 1.97422981 1.600559824 1.009131416 0.813111815 0.879880895 0.029860753 0.117412782 0.560261397 0.019619718 0.009343085 94.23881349 -1.97422981 -0.196019601 KQFS(ph)LENVQEGEILHDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQFSLENVQEGEILHDAK 18 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 KQFS(1)LENVQEGEILHDAK 224.21 2.22E-19 307270000 194130 168380 105340 133790 202680 153340 202190 243330 282310 261440 TRUE FALSE 186543.185 163577.9673 124377.2813 140694.9179 209199.3863 156440.6399 204664.4617 238305.1505 250263.3523 243732.4359 0.765360524 0.671137457 0.510302541 0.577251515 0.858315741 0.641854004 0.839709581 0.977732609 1.026795434 1 17.89493873 1.974278029 1.330286975 1.030044617 0.654970053 0.725267588 0.091182299 0.229151606 0.752482983 0.068152255 0.031317411 94.24927745 -1.974278029 -0.375074564 CLTTDEYDGHSTYPSHQYQ ddPTM_BT-474_Pertuzumab_2h_R1 4 CLTTDEYDGHSTYPSHQYQ 19 0 P30043;M0R192;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;; 208.49 2.68E-16 9148800000 3477790 4394510 3081640 4395800 3807370 4323530 3781290 1673950 4391200 4188260 FALSE TRUE 3341874.122 4269182.877 3638560.899 4622667.765 3929837.514 4410954.739 3827566.558 1639382.348 3892729.385 3904585.42 0.855884495 1.09337674 0.93186869 1.183907449 1.006467292 1.129685809 0.980274766 0.419860797 0.996963561 1 21.89673794 1.974317655 24.5372337 0.730878037 1.038714698 0.215582616 0.178378061 572.027213 546521.132 0.068932009 0.044688312 94.25787734 -1.974317655 0.307836661 LLHEVQELTTEVEK ddPTM_BT-474_Pertuzumab_2h_R1 6 LLHEVQELTTEVEK 14 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;;;; 237.21 2.75E-17 861139000 1110897 1103975 964844 1051925 1085530 1146246 1245575 1263349 1464205 1472417 FALSE TRUE 1067481.917 1072490.714 1139212.774 1106214.975 1120447.058 1169423.879 1260818.719 1237260.402 1297994.587 1372688.885 0.77765758 0.781306475 0.829913308 0.805874505 0.816242537 0.851922014 0.918502898 0.90134073 0.945585413 1 20.38857325 1.974391309 0.455210451 1.00241126 0.775217462 0.946387446 0.016497211 0.206976956 0.100565974 0.017520474 0.014975387 94.27386427 -1.974391309 -0.227193798 DQETLHSHGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DQETLHSHGVR 11 0 B4DML5;G3XAG9;Q9BYM8-4;Q9BYM8-3;Q9BYM8;H0Y4S7 B4DML5 RBCK1 RanBP-type and C3HC4-type zinc finger-containing protein 1 0 ; 116.03 0.00060389 117819000 86197 92605 84913 88652 87152 86964 79473 27273 85559 91126 FALSE TRUE 82828.32594 89963.99607 100258.668 93227.34034 89955.32323 88722.47166 80445.61435 26709.80302 75846.70101 84953.95485 0.974979047 1.058973608 1.180153039 1.097386702 1.058871519 1.044359522 0.946931953 0.314403291 0.892797765 1 16.37439349 1.974408817 15.08450229 0.652317752 1.067959449 0.389608419 0.177684774 3.963193437 2334.954046 0.069464864 0.045375676 94.27766487 -1.974408817 0.415641697 CGHEGMAYHTR ddPTM_BT-474_Pertuzumab_2h_R1 1 CGHEGMAYHTR 11 0 Q9P1U0 Q9P1U0 ZNRD1 DNA-directed RNA polymerase I subunit RPA12 0 87.184 0.0080459 25713000 23719 24328 17435 20311 21057 22345 20991 18193 24603 20894 FALSE TRUE 22792.03526 23634.18926 20585.89234 21359.25314 21734.31753 22796.83121 21247.89414 17817.30819 21810.17058 19478.83077 1.170092575 1.213326895 1.056834087 1.096536717 1.115791691 1.170338789 1.090819792 0.914701113 1.119685819 1 14.24961946 1.974491492 12.29964098 1.002150918 1.133857371 0.451066363 0.061707088 1.196705317 575.0315747 0.025043249 0.016395049 94.29561383 -1.974491492 0.131706452 RSS(ph)LSSHSHQSQIYR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSLSSHSHQSQIYR 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 RS(0.209)S(0.79)LS(0.002)SHSHQSQIYR 254.71 4.95E-25 305180000 28585 61908 31860 51308 34653 39909 33095 7284 22615 32345 TRUE FALSE 27467.8666 60142.44445 37617.81072 53956.01203 35767.64522 40715.98732 33500.02651 7133.582855 20047.84001 30154.24434 0.910912119 1.994493504 1.247512964 1.789333913 1.186156244 1.350257259 1.110955597 0.236569777 0.664843058 1 14.88007346 1.974508629 4.08404722 0.563556181 1.431112824 0.512793593 0.336473585 0.145649253 5.317489033 0.142973172 0.087324976 94.29933467 -1.974508629 0.867556643 SFAHLLPS(ph)PEPSPEGSYVGQHSQGLGGHYADSYLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFAHLLPSPEPSPEGSYVGQHSQGLGGHYADSYLK 35 0 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 SFAHLLPS(0.997)PEPS(0.003)PEGSYVGQHSQGLGGHYADSYLK;S(0.002)FAHLLPS(0.757)PEPS(0.233)PEGS(0.005)Y(0.002)VGQHSQGLGGHYADSYLK 118.86 4.20E-06 468960000 314770 472850 378850 467850 424090 470040 408030 184058 436500 455360 TRUE FALSE 302468.4404 459364.781 447316.6225 491995.7946 437731.24 479544.5308 413023.5932 180257.138 386950.35 424518.0616 0.712498402 1.082085363 1.053704572 1.158951383 1.031125127 1.129621032 0.972923488 0.424615945 0.911505033 1 18.69546641 1.97455379 23.55913117 0.710773865 1.038848716 0.246755977 0.183616357 343.8853821 318382.0182 0.072042728 0.046744522 94.30914122 -1.97455379 0.328074851 LSGEHSESS(ph)TPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSGEHSESSTPRPR 14 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 LSGEHS(0.01)ES(0.057)S(0.466)T(0.466)PRPR 61.641 0.050351 429130000 98458 112870 93706 113880 107670 110870 103080 97139 96680 125800 TRUE FALSE 94610.15251 109651.0581 110640.7587 119757.3604 111133.3033 113111.8674 104341.5239 95133.0457 85705.29172 117279.4539 0.806706966 0.934955394 0.943394217 1.021128223 0.94759397 0.964464478 0.889682893 0.81116549 0.7307784 1 16.83959077 1.97456037 4.010330261 0.829392686 0.940651365 0.188557182 0.080210109 0.284066926 9.868557017 0.03548889 0.021604051 94.31057013 -1.97456037 0.111258679 HNS(ph)WDTVNTVLPEDPEVADLFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNSWDTVNTVLPEDPEVADLFSR 23 0 Q8N961 Q8N961 ABTB2 Ankyrin repeat and BTB/POZ domain-containing protein 2 1 HNS(0.49)WDT(0.49)VNT(0.02)VLPEDPEVADLFSR;HNS(0.471)WDT(0.471)VNT(0.057)VLPEDPEVADLFSR 90.884 0.0034638 102813000 134275 129118 116676 129536 129912 147703 128101 59104 168239 156794 TRUE FALSE 129027.3846 125435.6811 137761.9486 136221.3685 134090.7375 150689.6559 129668.7384 57883.48175 149141.214 146174.2027 0.882696003 0.858124612 0.942450488 0.931911144 0.917335172 1.030890903 0.887083603 0.395989721 1.020297777 1 17.1573292 1.974562175 24.85532462 0.71412184 0.927417574 0.01558203 0.171619979 954.7182214 932855.0299 0.06765016 0.043867204 94.31096206 -1.974562175 0.213295735 HEALLYTWLAEHKPLVLCGPPGSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 HEALLYTWLAEHKPLVLCGPPGSGK 25 1 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 101.47 0.0034754 741480000 644250 690350 688920 569370 701840 802490 681620 391940 953420 832420 FALSE TRUE 619071.9977 670661.8939 813423.1689 598755.2539 724415.321 818716.8976 689961.8695 383846.302 845191.7587 776039.452 0.797732636 0.864211081 1.048172444 0.771552596 0.93347744 1.054993912 0.889080919 0.49462215 1.089109267 1 19.56577047 1.974603351 24.74733322 0.776780932 0.915496237 0 0.173664454 1433.386567 1396737.267 0.06956962 0.045102637 94.3199041 -1.974603351 0.138715306 QGLYELSASNFELHVAQGDHFIK ddPTM_BT-474_Pertuzumab_2h_R1 1 QGLYELSASNFELHVAQGDHFIK 23 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 290.36 9.67E-62 532730000 529660 559200 392490 480650 435860 458340 451190 156210 540500 505560 FALSE TRUE 508960.3016 543252.1635 463421.6739 505456.4041 449879.8327 467607.9488 456711.7982 152984.2089 479144.706 471317.9709 1.079866105 1.152623488 0.983246349 1.072431851 0.95451449 0.99212841 0.969009939 0.324588109 1.016606061 1 18.84634117 1.974636579 24.76872599 0.690713917 1.034516148 0.231761709 0.190835222 628.4497443 613713.736 0.07494232 0.048585945 94.32712099 -1.974636579 0.343802231 HGDLPDIQIK ddPTM_BT-474_Pertuzumab_2h_R1 4 HGDLPDIQIK 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 137.98 7.69E-05 1809700000 4357170 4269390 3342190 3755340 4072980 3949110 3916620 2810650 4922390 4324710 FALSE TRUE 4186886.979 4147631.177 3946198.08 3949153.547 4203991.101 4028963.71 3964552.767 2752609.095 4363620.924 4031793.54 1.038467605 1.028731044 0.97876988 0.979502921 1.042709915 0.999298121 0.983322367 0.682725707 1.082302673 1 21.94299033 1.974638094 24.98537306 0.87307357 1.008948886 0.081691267 0.100196265 934.5891891 920712.9612 0.039438438 0.0255732 94.32745005 -1.974638094 0.135875316 LLTEIHGGAGGPSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLTEIHGGAGGPSGR 15 0 K7EPJ1;Q16763 K7EPJ1 UBE2S Ubiquitin-conjugating enzyme E2 S 0 105.46 0.0013133 113870000 87252 92635 81163 92505 85984 96218 86332 79663 89985 93214 FALSE TRUE 83842.09538 89993.1405 95830.95956 97279.19414 88749.75345 98163.59388 87388.55684 78017.93121 79770.28005 86900.53275 0.964805309 1.035587903 1.102766077 1.119431505 1.021279739 1.129608655 1.005615893 0.897784268 0.917949264 1 16.4070774 1.974740364 5.67110709 0.931906972 1.064161213 0.527568589 0.052344742 0.131459751 13.19691354 0.022322096 0.014267078 94.34966536 -1.974740364 0.132254241 DHASIQMNVAEVDKVTGR ddPTM_BT-474_Pertuzumab_2h_R1 5 DHASIQMNVAEVDKVTGR 18 1 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;;; 282.5 1.31E-39 2334960000 1577980 2434390 1632700 2338470 1943960 2546170 2014730 1173361 1981050 2307940 FALSE TRUE 1516310.797 2364963.581 1927765.209 2459158.717 2006489.239 2597655.302 2039386.868 1149130.685 1756169.509 2151621.168 0.704729448 1.099154264 0.895959399 1.142932944 0.932547638 1.207301425 0.947837332 0.534076678 0.816207581 1 21.03699266 1.974810818 22.08627143 0.733983075 1.007233648 0.221897379 0.171419954 180.548728 158306.7717 0.065843104 0.042776743 94.3649726 -1.974810818 0.273250573 LKGDVDVSGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKGDVDVSGPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 127.37 0.00026265 861200000 2327570 2153010 1885280 2084850 1927350 2006410 2232900 2558300 2772200 2420200 FALSE TRUE 2236605.991 2091608.263 2225992.034 2192449.358 1989344.963 2046980.985 2260226.898 2505470.211 2457511.478 2256277.698 0.991281345 0.927017213 0.986577156 0.971710778 0.881693315 0.907238052 1.001750316 1.110444079 1.089188392 1 21.10551321 1.974909145 4.859874729 1.07518678 0.944127309 0.630504927 0.041835765 0.115581284 7.052360481 0.018497048 0.011621307 94.38633972 -1.974909145 -0.131059472 NNFEHIQHIIIDDAQNFR ddPTM_BT-474_Pertuzumab_2h_R1 2 NNFEHIQHIIIDDAQNFR 18 0 Q08AF3 Q08AF3 SLFN5 Schlafen family member 5 0 ; 156.83 5.05E-09 316250000 169136 175403 124111 159984 150815 159778 144437 20766.4 171693 144680 FALSE TRUE 162525.9781 170400.6782 146540.6185 168240.7934 155666.1014 163008.8206 146204.6632 20337.56658 152203.1304 134880.6947 1.20496101 1.263343717 1.086446202 1.247330419 1.154102162 1.208540785 1.083955443 0.150781894 1.128427836 1 17.04132435 1.97491046 24.40658886 0.653376296 1.189078863 0.357196074 0.248941649 433.102662 421312.654 0.096199977 0.06240802 94.38662564 -1.97491046 0.535702567 DVDDGSGSPHS(ph)PHQLSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 DVDDGSGSPHS(1)PHQLSSK 155.87 1.01E-08 628490000 119370 146180 129900 140840 120330 151240 129460 47202 162080 130320 TRUE FALSE 114704.8884 142011.0895 153375.8196 148108.7693 124200.5237 154298.1764 131044.3702 46227.2622 143681.3579 121493.3103 0.944125138 1.168879909 1.262421933 1.219069337 1.022282819 1.270013765 1.078613875 0.380492243 1.182627731 1 16.89051735 1.974979123 24.5152835 0.771542536 1.153402545 0.246501203 0.215668421 563.3058052 551922.3345 0.08429227 0.054686119 94.40154949 -1.974979123 0.381860009 RPS(ph)PPPQPS(ph)SVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSPPPQPSSVK 12 1 H0YAU4;H3BLZ3;Q8IX03-2 H0YAU4 WWC1 Protein KIBRA 2 RPS(0.994)PPPQPS(0.997)S(0.009)VK 54.982 0.0873 444060000 849970 832690 664250 643350 728840 751280 791420 892720 976140 858900 TRUE FALSE 816752.2327 808942.4965 784294.7512 676553.3706 752283.8005 766471.3963 801105.6347 874285.02 865332.6795 800725.938 1.020014707 1.010261387 0.979479637 0.844925009 0.939502225 0.957220642 1.000474191 1.091865492 1.080685211 1 19.61094901 1.975050075 3.636479247 1.065475684 0.95639592 0.430838921 0.050520617 0.215741632 5.808611991 0.02542124 0.01518173 94.41697355 -1.975050075 -0.109079764 DKS(ph)HS(ph)HT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 DKS(1)HS(0.959)HT(0.617)PS(0.424)R 61.444 0.076632 45427000 155550 126620 120430 113060 135640 124610 123920 37777 197790 126900 TRUE FALSE 149470.934 123008.9216 142194.38 118895.0401 140002.9838 127129.6996 125436.57 36996.89175 175337.7084 118304.95 1.263437701 1.03976141 1.201930942 1.004987874 1.183407658 1.074593241 1.060281671 0.312724799 1.482082605 1 16.85215091 1.975082665 24.89048352 0.813054728 1.119555047 0.042135638 0.280349115 1107.750727 1106555.708 0.109934728 0.071312876 94.42405886 -1.975082665 0.306500319 HSS(ph)IS(ph)PVRLPLNSSLGAELSR ddPTM_BT-474_Pertuzumab_2h_R1 11 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.557)S(0.65)IS(0.793)PVRLPLNSSLGAELSR;HS(0.449)S(0.563)IS(0.988)PVRLPLNSSLGAELSR;HS(0.547)S(0.612)IS(0.841)PVRLPLNS(0.001)SLGAELSR;HS(0.553)S(0.657)IS(0.789)PVRLPLNSSLGAELSR;HS(0.482)S(0.521)IS(0.998)PVRLPLNSSLGAELSR;HS(0.486)S(0.526)IS(0.987)PVRLPLNSSLGAELSR;HS(0.498)S(0.59)IS(0.912)PVRLPLNSSLGAELSR;HS(0.535)S(0.594)IS(0.869)PVRLPLNS(0.001)S(0.001)LGAELSR;HS(0.512)S(0.597)IS(0.89)PVRLPLNS(0.001)S(0.001)LGAELSR;HS(0.487)S(0.519)IS(0.992)PVRLPLNS(0.001)S(0.001)LGAELS(0.001)R;HS(0.141)S(0.859)IS(1)PVRLPLNSSLGAELSR 203.99 7.36E-22 2413944000 965002.8 974652.8 831532.9 998769.7 954218.6 1045866.8 938678.3 536056.3 1150703.2 986313.2 TRUE FALSE 927289.4237 946856.6564 981809.3924 1050316.324 984911.9079 1067014.943 950166.1258 524986.5501 1020080.197 919509.3284 1.008461138 1.029741219 1.067753596 1.142257388 1.071127695 1.160417747 1.033340388 0.57094206 1.109374495 1 19.81050469 1.975093264 24.87667715 0.834859579 1.080996451 0.237986388 0.138023236 675.291859 674476.0247 0.054141551 0.035116103 94.42636341 -1.975093264 0.246136872 DQHHLGS(ph)PS(ph)RLSVGEQPDVTHDPYEFLQS(ph)PEPAASAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQHHLGSPSRLSVGEQPDVTHDPYEFLQSPEPAASAK 37 1 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2 Q9H8M2 BRD9 Bromodomain-containing protein 9 3 DQHHLGS(0.405)PS(0.405)RLS(0.405)VGEQPDVT(0.405)HDPY(0.383)EFLQS(0.995)PEPAASAK 53.728 0.020654 56459000 9371.1 10986 9132.3 8074.7 10227 8189.8 8901.7 3335.9 11576 8670.6 TRUE FALSE 9004.867052 10672.69004 10782.70976 8491.436235 10555.96074 8355.403367 9010.641667 3267.012499 10261.94101 8083.332539 1.114004281 1.320332918 1.333943606 1.05048706 1.305892179 1.03365825 1.114718666 0.404166534 1.2695186 1 12.98073448 1.975095996 23.7592731 0.808629043 1.193082909 0.240056197 0.226582305 404.6297027 386029.5814 0.089234467 0.057927732 94.42695735 -1.975095996 0.384453866 HLPNLLDETQIFSYFSQFGTVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLPNLLDETQIFSYFSQFGTVTR 23 0 Q9BYG3 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 ; 204.04 1.80E-24 222650000 176417 177376 162028 164471 177256 194453 162101 133202 159898 171508 FALSE TRUE 169522.4286 172317.4101 191310.0639 172959.368 182957.6002 198384.9729 164084.8405 130451.3322 141747.0494 159891.6104 1.060233418 1.077713895 1.196498449 1.081728851 1.144260163 1.240746606 1.026225454 0.815873527 0.886519618 1 17.28673472 1.975116197 5.775748803 0.888133067 1.13255854 0.708598926 0.066799451 0.088833524 9.513360886 0.02801519 0.017948424 94.4313496 -1.975116197 0.244425472 TSNRYS(ph)PESQAQSVHHQRPGSR ddPTM_BT-474_Pertuzumab_2h_R1 6 TSNRYSPESQAQSVHHQRPGSR 22 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.001)S(0.004)NRYS(0.995)PESQAQSVHHQRPGSR;T(0.013)S(0.013)NRYS(0.973)PESQAQSVHHQRPGSR;T(0.187)S(0.187)NRYS(0.619)PES(0.006)QAQSVHHQRPGSR;T(0.004)S(0.004)NRYS(0.979)PES(0.014)QAQSVHHQRPGSR;T(0.011)S(0.011)NRYS(0.976)PES(0.002)QAQSVHHQRPGSR;T(0.004)S(0.004)NRYS(0.989)PES(0.004)QAQSVHHQRPGSR 207.17 3.99E-23 3631310000 257818 376731 285499 378930 294974 391423 314803 131951 321946 335617 TRUE FALSE 247742.1875 365987.0007 337095.0202 398486.6227 304462.1066 399337.8412 318655.6533 129226.1657 285400.0398 312885.3617 0.791798588 1.169715959 1.077375491 1.27358666 0.973078782 1.276307204 1.018442191 0.413014419 0.912155296 1 18.25527464 1.975185661 22.5554308 0.71130873 1.103087269 0.328536224 0.19764615 184.6766422 167864.1522 0.07610618 0.049454747 94.44645497 -1.975185661 0.391778539 VPGGGEQPAQPNGWQYHS(ph)PSRPGSTAFPSQDGETGGHRR ddPTM_BT-474_Pertuzumab_2h_R1 3 VPGGGEQPAQPNGWQYHSPSRPGSTAFPSQDGETGGHRR 39 2 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 VPGGGEQPAQPNGWQYHS(0.853)PS(0.143)RPGS(0.001)T(0.001)AFPSQDGETGGHRR;VPGGGEQPAQPNGWQYHS(0.985)PS(0.015)RPGSTAFPSQDGETGGHRR;VPGGGEQPAQPNGWQYHS(0.962)PS(0.038)RPGSTAFPSQDGETGGHRR 258.57 6.63E-63 2580390000 10870 21303.9 7941.4 25899 26943 23462 17196.5 7750.3 17352 16978.7 TRUE FALSE 10445.18838 20696.33363 9376.587635 27235.65049 27809.64606 23936.41772 17406.95591 7590.253597 15382.27371 15828.71753 0.659888482 1.307518035 0.592378228 1.720647958 1.756910882 1.512214598 1.099707281 0.479524231 0.971795326 1 13.95025675 1.97531585 11.18095646 0.766643675 1.276616601 0.200732639 0.388821927 1.195948195 536.9159082 0.165414385 0.108516566 94.47477154 -1.97531585 0.509972926 S(ph)ASQLSQTEAGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASQLSQTEAGGK 13 0 A0A590UJL1;F8W6W8;D6RA03 A0A590UJL1;D6RA03 RIMS2 1 S(0.997)AS(0.003)QLSQTEAGGK;S(0.969)AS(0.03)QLSQTEAGGK 263.21 3.88E-24 663080000 494310 450990 411900 430930 462810 428030 462910 606570 458790 435630 TRUE FALSE 474991.8187 438128.2068 486339.4927 453170.3489 477696.704 436685.0599 468575.2311 594044.1175 406710.0826 406124.3921 1.169572249 1.078802986 1.197513624 1.115841249 1.176232488 1.075249525 1.153772687 1.462714698 1.001442146 1 18.63156215 1.97534402 24.94659892 1.231659676 1.134877005 0 0.131890945 1709.082799 1729225.889 0.052139388 0.033788711 94.48089961 -1.97534402 -0.09678267 VWS(ph)PLVTEEGKR ddPTM_BT-474_Pertuzumab_2h_R1 5 VWSPLVTEEGKR 12 1 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(1)PLVTEEGKR;VWS(1)PLVTEEGKR;VWS(0.999)PLVT(0.001)EEGKR;VWS(0.999)PLVT(0.001)EEGKR;VWS(1)PLVTEEGKR 222.56 1.50E-11 1571382000 1519510 1309710 1437804 1280111 1358625 1379641 1432785 1636790 1579380 1640600 TRUE FALSE 1460125.869 1272358.353 1697647.167 1346177.682 1402326.407 1407538.286 1450319.851 1602989.715 1400095.404 1529480.701 0.954654654 0.831889119 1.109950041 0.880153428 0.916864401 0.920272015 0.948243316 1.04806142 0.915405734 1 20.54461047 1.975379674 22.51682859 0.994410037 0.93536346 0.089462245 0.07370826 458.9439176 419730.4518 0.028988098 0.018840265 94.48865654 -1.975379674 -0.059046577 LSYAGGRPPS(ph)YAGS(ph)PVHHAAER ddPTM_BT-474_Pertuzumab_2h_R1 1 LSYAGGRPPSYAGSPVHHAAER 22 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 LS(0.006)Y(0.001)AGGRPPS(0.98)Y(0.013)AGS(0.999)PVHHAAER 101.74 0.00087268 341170000 118800 128790 87467 133820 90213 106870 104310 39884 112710 121680 TRUE FALSE 114157.1647 125117.0353 103274.2326 140726.4662 93114.78307 109030.9846 105586.577 39060.38146 99915.63332 113438.5052 1.006335234 1.102950317 0.910398391 1.240552897 0.820839299 0.961146168 0.930782513 0.34433089 0.880791166 1 16.7915509 1.975485314 23.12832426 0.661030443 1.003889095 0.245273154 0.19323491 279.6062086 263792.8126 0.075378732 0.048981709 94.51164314 -1.975485314 0.342858652 S(ph)RAS(ph)PATHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRASPATHR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RAS(0.999)PAT(0.001)HR 113.54 0.0010151 114330000 13934 13776 9160 16280 10978 10814 12909 17110 13490 10986 TRUE FALSE 13389.44388 13383.12197 10815.41576 17120.21275 11331.11734 11032.66649 13066.9842 16756.67252 11958.67175 10241.90843 1.307319233 1.306701974 1.055996139 1.671584242 1.106348237 1.077208077 1.275834898 1.636088882 1.167621428 1 13.32219695 1.975535909 24.66225524 1.367925436 1.252881102 0 0.227963057 2191.742801 2209492.94 0.091367338 0.059329481 94.52265436 -1.975535909 -0.115044334 (ac)SKPHSEAGTAFIQTQQLHAAMADTFLEHMCR ddPTM_BT-474_Pertuzumab_2h_R1 9 SKPHSEAGTAFIQTQQLHAAMADTFLEHMCR 31 1 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BR70;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;; 131.95 1.12E-219 38255050000 2267855 2346055 1914088 2071373 2197972 2353489 2129139 1393146 2408394 2159771 FALSE TRUE 2179224.719 2279147.808 2260006.28 2178276.809 2268671.766 2401078.16 2155196.04 1364377.048 2135003.21 2013487.786 1.082313354 1.13194022 1.122433568 1.081842574 1.126737287 1.192497008 1.070379495 0.677618736 1.060350713 1 20.94126529 1.975580123 23.40964168 0.876126922 1.122463437 0.46632722 0.098469947 226.800567 217417.2141 0.038056124 0.024728254 94.53227793 -1.975580123 0.246336516 HHYDS(ph)DEKSETR ddPTM_BT-474_Pertuzumab_2h_R1 1 HHYDSDEKSETR 12 1 Q9BQ39 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 1 HHYDS(0.937)DEKS(0.063)ETR 242.93 1.55E-16 1091300000 838720 831110 765900 748370 712270 818260 684830 31668 903030 474670 TRUE FALSE 805941.8951 807407.5565 904315.1674 786993.4654 735180.8114 834805.7778 693211.1544 31014.04473 800521.8202 442520.1781 1.821254566 1.824566645 2.043556909 1.778435209 1.661349805 1.886480706 1.566507447 0.070085041 1.809006368 1 18.75538372 1.975604112 18.19863222 0.846846986 1.825328656 0.478300534 0.404108157 17.17146944 12808.51691 0.155877434 0.101740913 94.5374998 -1.975604112 0.97848167 MFFDALYDEDVVKEDAFYSWESSKDPAEQQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 MFFDALYDEDVVKEDAFYSWESSKDPAEQQGK 32 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 261.86 1.20E-59 645590000 596730 502410 482690 363720 520210 536410 596380 588920 791140 680570 FALSE TRUE 573409.1319 488081.7587 569922.8204 382491.6328 536943.0271 547256.5777 603678.6768 576758.5962 701333.1039 634474.3877 0.903754577 0.769269443 0.898259774 0.602848027 0.846280067 0.862535334 0.951462641 0.909033694 1.105376541 1 19.2752024 1.975669731 1.087585721 1.029590654 0.798138059 0.511279571 0.089066975 0.412304202 0.897831786 0.068339327 0.031346652 94.55178469 -1.975669731 -0.231452594 HNGPNDASDGTVR ddPTM_BT-474_Pertuzumab_2h_R1 3 HNGPNDASDGTVR 13 0 P31942;P31942-2 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;; 212.09 3.88E-08 530990000 436340 463640 389970 440850 439520 453620 425770 287091 483230 440080 FALSE TRUE 419287.3504 450417.4412 460446.2538 463602.3213 453657.56 462792.5072 430980.7006 281162.4705 428375.7563 410272.9896 1.021971616 1.097848146 1.122292389 1.129984993 1.105745617 1.128011151 1.050473006 0.685305827 1.044123711 1 18.64622465 1.975670956 22.00837292 0.873105008 1.102163262 0.437605895 0.094301519 115.6307813 104600.3215 0.03658995 0.023801406 94.55205139 -1.975670956 0.229058253 VMFAYEQCLLVLGHHPDIWYEAAQYLEQSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VMFAYEQCLLVLGHHPDIWYEAAQYLEQSSK 31 0 Q12996;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 0 121.5 4.85E-06 113900000 101170 90847 79445 74239 100120 107040 86822 41198 101770 76377 FALSE TRUE 97216.16455 88256.13251 93802.47874 78070.48369 103340.4507 109204.4221 87884.55361 40347.2469 90217.49625 71203.91776 1.365320443 1.239484221 1.317378056 1.096435226 1.451330966 1.533685583 1.234265703 0.566643637 1.267029949 1 16.119669 1.975687635 22.75789043 0.897418739 1.328478473 0.440827761 0.194163544 189.9940457 177845.4034 0.077549478 0.050418812 94.55568269 -1.975687635 0.431059734 YLMEEDEDAYKK ddPTM_BT-474_Pertuzumab_2h_R1 10 YLMEEDEDAYKK 12 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;;;; 224.24 3.29E-11 30033370000 21657350 19225820 16412290 15457030 19719360 19163360 21798720 26855980 29785790 27022940 FALSE TRUE 20810956.82 18677518.44 19378355.89 16254769.17 20353651.12 19550856.27 22065499.26 26301394.63 26404631.99 25192652.2 0.826072485 0.74138754 0.769206661 0.645218655 0.807920141 0.776053911 0.875870435 1.044010548 1.048108463 1 24.58649968 1.975702205 2.115072872 1.039843415 0.754394654 0.864522417 0.047709484 0.102900774 0.853227253 0.02714193 0.01402435 94.55885496 -1.975702205 -0.285448761 NDKS(ph)EEEQSSSSVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDKSEEEQSSSSVKK 15 2 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKS(1)EEEQSSSSVKK;NDKS(1)EEEQSSSSVKK 274.17 1.42E-33 1156650000 681629 513765 537914 317503 427596 560447 597572 751390 893120 727070 TRUE FALSE 654990.1851 499112.9252 635127.0256 333889.3679 441350.0137 571779.6223 604885.2649 735873.5339 791736.7619 677824.9013 0.966311777 0.736344924 0.937007514 0.49258941 0.651126881 0.84355063 0.892391625 1.085639569 1.168054995 1 19.37055311 1.975715385 1.968182755 1.099878955 0.755146828 0.525160057 0.133419433 0.259135917 1.863384933 0.080988338 0.040944715 94.56172467 -1.975715385 -0.344732127 YPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR ddPTM_BT-474_Pertuzumab_2h_R1 3 YPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR 35 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;; 393.03 3.21E-167 1167875000 450260 524111 407091 398536 486443 523527 453159 274325 525808 486855 FALSE TRUE 432663.3414 509163.8674 480661.3994 419104.4907 502089.8809 534113.0746 458704.8954 268660.0929 466120.4802 453879.8772 0.953255174 1.121803131 1.059005749 0.92338196 1.106217539 1.176771876 1.010630606 0.591918934 1.026968816 1 18.791951 1.97578528 24.4511398 0.821033824 1.059129893 0.252473826 0.13287345 549.6209395 554986.2786 0.052531495 0.034115908 94.57694471 -1.97578528 0.238096069 AGGGDLLLPPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 AGGGDLLLPPSPK 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK 146 4.15E-05 1895830000 6716580 6469600 5814130 5681730 6268120 6426220 6973190 8107900 8900600 8389400 TRUE FALSE 6454088.628 6285093.342 6864872.626 5974964.766 6469739.772 6556162.571 7058529.985 7940469.032 7890241.202 7821178.465 0.825206669 0.803599275 0.877728677 0.763946865 0.827207792 0.838257636 0.902489314 1.01525225 1.008830221 1 22.89895457 1.975795108 2.111392002 1.012796166 0.81999456 0.903048311 0.027188849 0.084907145 0.701614269 0.015119028 0.007808585 94.57908494 -1.975795108 -0.192801606 QELSHALYQHDAACR ddPTM_BT-474_Pertuzumab_2h_R1 5 QELSHALYQHDAACR 15 0 Q9UMS4;F5GY56;F5H2I0 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;;;; 238.83 5.08E-18 7193800000 2009580 2187690 1690650 2093290 1983780 2264780 1931260 636404 2240570 2213550 FALSE TRUE 1931043.392 2125299.223 1996188.063 2201324.948 2047590.085 2310575.403 1954895.338 623262.035 1986229.887 2063624.287 0.935753375 1.029886708 0.967321463 1.066727583 0.992230077 1.119668642 0.947311655 0.302023018 0.962495886 1 20.9767489 1.975870144 24.70487841 0.664131751 1.019079595 0.24378459 0.188626539 582.3113999 596187.2894 0.072921491 0.047369611 94.59542737 -1.975870144 0.354947844 GNDS(ph)DGEGESDDPEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNDSDGEGESDDPEKK 16 1 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 GNDS(1)DGEGESDDPEKK 149.85 4.87E-07 340150000 410250 322020 307100 293100 356760 286850 404920 453130 548190 472660 TRUE FALSE 394216.9764 312836.3049 362599.8014 308226.9261 368235.5094 292650.3035 409875.5321 443772.7072 485961.7694 440646.3172 0.894633544 0.709948756 0.822881725 0.699488261 0.835671365 0.664138771 0.930168972 1.00709501 1.102838604 1 18.74926162 1.975890517 3.088691275 1.03488625 0.770532899 0.733729195 0.071963981 0.120826677 2.207544761 0.032645587 0.018780345 94.59986515 -1.975890517 -0.264353351 NHDEESLECLCR ddPTM_BT-474_Pertuzumab_2h_R1 2 NHDEESLECLCR 12 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 Q04637-9;A0A0A0MSA7 EIF4G1;EIF4G3 Eukaryotic translation initiation factor 4 gamma 1;Eukaryotic translation initiation factor 4 gamma 3 0 ; 215.02 4.24E-11 2619900000 1586710 1520260 1194030 1603020 1535760 1398120 1338960 340880 1564530 1358930 FALSE TRUE 1524699.619 1476903.673 1409817.782 1685752.054 1585159.115 1426390.944 1355346.593 333840.7089 1386931.113 1266888.461 1.203499492 1.165772457 1.112819183 1.330623892 1.251222317 1.125900968 1.069823142 0.263512313 1.094753924 1 20.27285808 1.97599966 20.18038597 0.694858405 1.192737092 0.399455652 0.217535611 49.38069198 41520.2146 0.085063977 0.055455357 94.62364205 -1.97599966 0.497878687 DSGS(ph)ISLQETR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSGSISLQETR 11 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 DS(0.006)GS(0.981)IS(0.013)LQETR 68.42 0.060092 191660000 313670 321530 223640 282580 294750 292870 267820 267670 265240 290960 TRUE FALSE 301411.4296 312360.2792 264056.7228 297163.9877 304230.9014 298792.0321 271097.6613 262142.521 235131.0672 271253.02 1.111181839 1.151545812 0.973470167 1.095523241 1.121576089 1.101525181 0.999427255 0.966413281 0.866832993 1 18.04927967 1.976008727 2.17672237 0.936711582 1.091400456 0.607015317 0.053959719 0.212675455 1.867251838 0.030619204 0.015963594 94.62561765 -1.976008727 0.154688874 SKESDEPHHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKESDEPHHSK 11 1 Q8IVM0-2;Q8IVM0 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 0 80.979 0.014792 16736000 28689 40674 28832 40210 31707 40193 32652 4978.1 37959 35146 FALSE TRUE 27567.80216 39514.01734 34042.58376 42285.24292 32726.88445 41005.73 33051.60494 4875.300495 33650.05346 32765.53012 0.841365974 1.205963011 1.038975522 1.290540479 0.998820539 1.2514899 1.008730969 0.148793579 1.026995545 1 14.99989125 1.976013067 24.19386243 0.617703861 1.111499483 0.270117309 0.261734906 446.0713293 449918.6352 0.100524079 0.065315589 94.62656327 -1.976013067 0.493795622 DPETLVGYSMVGCQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPETLVGYSMVGCQR 15 0 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 165.7 5.81E-09 0 60712 75540 49648 61743 69652 65856 62798 61837 66215 69580 FALSE TRUE 58339.30792 73385.67316 58620.49801 64929.56363 71892.41984 67187.65344 63566.54071 60560.04434 58698.5508 64867.28462 0.899364113 1.131320258 0.903698966 1.000960099 1.108300128 1.035771018 0.979947613 0.933599189 0.904902234 1 15.98520343 1.976018518 3.810657713 0.940879333 1.017168232 0.141913688 0.073213705 0.387556546 11.79151816 0.032512684 0.01963336 94.62775089 -1.976018518 0.076288898 EPDCFKDIVNMLMHHDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EPDCFKDIVNMLMHHDR 17 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 173.87 9.19E-10 1316246000 2009970 2147348 1329027 1324803 1723849 2163335 1641160 600959 1836317 1463517 FALSE TRUE 1931418.15 2086107.738 1569211.743 1393176.242 1779298.169 2207079.116 1661245.007 588548.9866 1627865.993 1364391.69 1.415589207 1.528965438 1.150118221 1.021096985 1.30409631 1.617628671 1.217571918 0.431363655 1.193107525 1 20.37982644 1.976059325 22.93093211 0.814848054 1.331331739 0.420034013 0.241323807 222.6936832 213300.2437 0.099537516 0.064748209 94.63664276 -1.976059325 0.516483684 DLIHDVSFDFHGR ddPTM_BT-474_Pertuzumab_2h_R1 7 DLIHDVSFDFHGR 13 0 K7ELV2;Q96EE3;Q96EE3-1;K7EP88;K7ENI5 K7ELV2 SEH1L Nucleoporin SEH1 0 ;;;;;; 248.77 1.11E-17 2268670000 1179245.8 1358193 1191059.4 1490414.9 1414209.1 1387690.5 1300164 637329.7 1536217 1502209 FALSE TRUE 1133159.57 1319458.665 1406310.329 1567335.392 1459698.42 1415750.553 1316075.796 624168.619 1361832.087 1400463.046 0.809132075 0.942158859 1.004175249 1.119155122 1.042296992 1.010916037 0.939743322 0.445687318 0.972415581 1 20.41747249 1.976076724 24.6114758 0.731511792 0.993414554 0.156393922 0.163409192 677.0398062 696515.2171 0.065396498 0.042484759 94.64043408 -1.976076724 0.261902763 HKSDS(ph)PES(ph)DAER ddPTM_BT-474_Pertuzumab_2h_R1 2 HKSDSPESDAER 12 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 2 HKS(0.011)DS(0.989)PES(1)DAER;HKS(0.017)DS(0.983)PES(1)DAER 64.454 0.025232 106080000 643390 701700 722240 822200 644120 685290 682550 306120 854130 728800 TRUE FALSE 618245.6075 681688.203 852764.8341 864633.8405 664838.7048 699147.0333 690903.2511 299798.515 757172.7432 679437.7269 0.909937119 1.003312263 1.255103743 1.272572609 0.978513083 1.02900826 1.016875019 0.441245022 1.114410804 1 19.3739818 1.976089734 24.65966624 0.774616003 1.079196966 0.17190606 0.198190699 737.1098127 760211.5032 0.080786182 0.052475535 94.64326926 -1.976089734 0.304580963 HSPES(ph)PSIAVVESELVAEYITTVSHR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSPESPSIAVVESELVAEYITTVSHR 26 0 Q7Z589-4;E9PMC9 Q7Z589-4 EMSY;C11orf30 Protein EMSY 1 HS(0.25)PES(0.743)PS(0.008)IAVVESELVAEYITTVSHR;HS(0.039)PES(0.961)PSIAVVESELVAEYITTVSHR;HS(0.007)PES(0.992)PS(0.002)IAVVESELVAEYITTVSHR;HS(0.002)PES(0.996)PS(0.002)IAVVESELVAEYITTVSHR 176.78 4.48E-17 70189000 28986.8 24761.9 23013 28347.5 30657.2 30194.7 26787.6 15181.7 28940.6 32592.3 TRUE FALSE 27853.96381 24055.71486 27171.96102 29810.51787 31643.31668 30805.25752 27115.43466 14868.19259 25655.38442 30384.79449 0.916707329 0.791702404 0.8942618 0.981099868 1.041419473 1.013837942 0.89240145 0.489330036 0.844349447 1 14.89106191 1.976112745 24.51696111 0.713580434 0.938825408 0.173070335 0.138378032 645.5251871 662541.2226 0.05623717 0.036533355 94.64828401 -1.976112745 0.225244973 HAQFVVEQVESYDEAGDSDEQPIFLTPCMR ddPTM_BT-474_Pertuzumab_2h_R1 1 HAQFVVEQVESYDEAGDSDEQPIFLTPCMR 30 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 169.7 1.90E-12 198010000 60073 62237 47512 62883 63165 57660 55771 40352 64791 61248 FALSE TRUE 57725.28075 60462.0617 56098.4753 66128.39917 65196.75959 58825.92471 56453.54218 39518.7171 57436.19731 57099.61841 1.010957382 1.058887316 0.982466729 1.158123312 1.141807273 1.030233237 0.988685104 0.692101247 1.005894591 1 15.80119348 1.976141416 9.728586773 0.858831639 1.062929074 0.342822478 0.097417393 0.366263555 144.322868 0.039358532 0.025851761 94.6545328 -1.976141416 0.204097435 GSEPEEEAPVREDESEVDGDCSLTGPPALVGS(ph)YGTSPEGIGGYIHSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSEPEEEAPVREDESEVDGDCSLTGPPALVGSYGTSPEGIGGYIHSHR 48 1 Q8TBX8;Q8TBX8-3;Q8TBX8-2 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 1 GSEPEEEAPVREDESEVDGDCSLTGPPALVGS(0.236)Y(0.214)GT(0.236)S(0.236)PEGIGGY(0.059)IHS(0.018)HR 88.649 9.65E-06 108670000 10628 15753 11575 16077 17758 15278 13988 4579 17380 16585 TRUE FALSE 10212.64601 15303.73986 13666.85998 16906.7359 18329.2022 15586.93163 14159.18933 4484.44205 15407.09526 15461.68318 0.660513211 0.989784856 0.883917994 1.093460246 1.185459693 1.00810057 0.915759893 0.290035826 0.996469471 1 13.91640976 1.976198396 24.74255446 0.663187071 0.980841413 0.09643706 0.230464955 846.738526 880211.5791 0.092524136 0.060110406 94.66695236 -1.976198396 0.317654342 HRS(ph)HS(ph)AEGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HRSHSAEGGK 10 1 P21127-2;P21127;P21127-9;A0A087X1I0;A0A087WYI9 P21127-2 CDK11B Cyclin-dependent kinase 11B 2 HRS(1)HS(1)AEGGK 60.657 0.055004 43072000 163650 153530 121930 141380 148530 145590 135870 43007 172910 123950 TRUE FALSE 157254.3771 149151.4747 143965.4633 148676.6387 153307.6023 148533.9296 137532.8177 42118.89042 153281.9817 115554.7561 1.360864601 1.290742846 1.24586359 1.28663366 1.326709584 1.285398668 1.19019608 0.36449292 1.326487865 1 16.81821712 1.976203185 23.80151113 0.814122256 1.292257701 0.374266131 0.225247157 327.7423204 327806.2004 0.087124049 0.056647009 94.66799626 -1.976203185 0.478135445 GFGSSAPEGLEPDSMAS(ph)AASALHLLSPRPR ddPTM_BT-474_Pertuzumab_2h_R1 6 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.006)MAS(0.362)AAS(0.362)ALHLLS(0.269)PRPR;GFGSSAPEGLEPDS(0.029)MAS(0.324)AAS(0.324)ALHLLS(0.324)PRPR;GFGSSAPEGLEPDS(0.014)MAS(0.474)AAS(0.145)ALHLLS(0.367)PRPR;GFGSSAPEGLEPDS(0.065)MAS(0.312)AAS(0.312)ALHLLS(0.312)PRPR;GFGSSAPEGLEPDS(0.051)MAS(0.316)AAS(0.316)ALHLLS(0.316)PRPR;GFGSSAPEGLEPDS(0.064)MAS(0.312)AAS(0.312)ALHLLS(0.312)PRPR 120.34 1.49E-05 2906420000 1439520 1767720 1531970 1726660 1673880 1761470 1296060 1207617 1098439 1147676 TRUE FALSE 1383261.967 1717306.356 1808831.057 1815773.13 1727721.87 1797088.13 1311921.57 1182679.287 973748.8098 1069942.882 1.292837206 1.605044891 1.690586561 1.697074825 1.614779535 1.679611276 1.226160379 1.10536675 0.910094198 1 20.02910235 1.97620719 2.061689739 0.992233632 1.60837856 0.827017366 0.12227994 0.127381997 1.004133036 0.07201641 0.036940235 94.66886939 -1.97620719 0.616144928 FYSHMVRPGDLTGHSDFHLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 FYSHMVRPGDLTGHSDFHLFK 21 1 B9A044;B8ZZ50;O60573-2;O60573;B4E1E4;B9A023;B8ZZL3;C9JEL3 B9A044 EIF4E2 Eukaryotic translation initiation factor 4E type 2 0 ; 200.99 2.41E-22 294170000 301480 347830 286630 299290 309690 330180 293230 96476 332130 301570 FALSE TRUE 289697.8283 337910.229 338430.417 314736.3928 319651.4601 336856.4658 296818.6365 94483.73689 294427.9948 281144.3953 1.03042363 1.201909889 1.203760141 1.119483077 1.136965436 1.198161768 1.055751569 0.336068364 1.047248317 1 18.10095176 1.976208247 23.5832483 0.714478866 1.149506034 0.392760518 0.189406613 270.4844149 268113.1926 0.07308425 0.047525692 94.66909963 -1.976208247 0.435027169 QETVADFT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 QETVADFTPK 10 0 O75400-3;O75400;O75400-2;F5H578 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 QETVADFT(1)PK;QETVADFT(1)PK;QETVADFT(1)PK;QETVADFT(1)PK 203.74 2.23E-06 4692630000 8043790 6328520 7177840 7109630 6903800 6691250 8304280 10074830 10329130 10667790 TRUE FALSE 7729429.794 6148036.806 8475035.358 7476558.856 7125866.997 6826551.66 8405910.263 9866781.24 9156610.466 9945251.081 0.777198055 0.618188194 0.852169069 0.751771755 0.716509512 0.686413204 0.845218506 0.992109818 0.920701789 1 23.24557636 1.976291088 3.573869302 0.965240594 0.734370296 0.754657744 0.06055208 0.112126857 2.89684662 0.027772763 0.016549067 94.68715932 -1.976291088 -0.230870297 SKPNLPS(ph)ESR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 SKPNLPS(0.999)ES(0.001)R;SKPNLPS(0.995)ES(0.005)R;SKPNLPS(1)ESR;SKPNLPS(1)ESR 141.07 2.31E-05 1835350000 2248770 2008900 2168200 2493370 2153890 2046480 2403720 2805150 2910290 2746330 TRUE FALSE 2160885.582 1951608.139 2560041.971 2622053.125 2223171.828 2087861.228 2433137.444 2747222.672 2579926.08 2560318.623 0.843990886 0.762252058 0.999891946 1.024112039 0.868318423 0.815469297 0.950326035 1.073000308 1.00765821 1 21.28789193 1.97637414 6.402068396 1.030138592 0.88996389 0.408957395 0.076025484 0.190382386 29.16135878 0.034582069 0.022391182 94.7052686 -1.97637414 -0.140174702 VGQQAIVLCIS(ph)PSKPNPVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGQQAIVLCISPSKPNPVFK 20 1 Q16656-2;Q16656;Q16656-4;C9JP85 Q16656-2 NRF1 Nuclear respiratory factor 1 1 VGQQAIVLCIS(0.998)PS(0.002)KPNPVFK;VGQQAIVLCIS(0.999)PS(0.001)KPNPVFK 241.48 5.81E-30 1091980000 1180680 980990 922390 919670 1071030 1085480 1188660 1345960 1601350 1454710 TRUE FALSE 1134537.72 953013.1257 1089086.391 967134.2789 1105480.653 1107429.149 1203207.177 1318165.456 1419571.461 1356181.196 0.836567948 0.702718139 0.803053747 0.713130577 0.815142295 0.816579048 0.887202374 0.971968539 1.046741737 1 20.37111852 1.97645584 1.201716577 1.028096525 0.766270039 0.861940802 0.040997141 0.14417806 0.384736073 0.028498571 0.013022847 94.72308629 -1.97645584 -0.261826486 TTHS(ph)PYEER ddPTM_BT-474_Pertuzumab_2h_R1 3 TTHSPYEER 9 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 T(0.001)THS(0.999)PYEER;TTHS(1)PYEER;TTHS(1)PYEER 165.39 5.51E-05 924370000 471360 489000 400792 464120 469820 473590 450640 298995 505190 500110 TRUE FALSE 452938.7301 475054.1988 473224.03 488073.2888 484932.187 483166.3143 456155.0671 292820.6488 447842.9491 466237.1042 0.971477229 1.018911182 1.014985778 1.046834935 1.040097801 1.036310302 0.97837573 0.628050934 0.960547638 1 18.8307043 1.97650783 24.30516149 0.816957173 1.02172366 0.32009944 0.096730261 426.1223933 440868.3874 0.037476437 0.024365072 94.73442634 -1.97650783 0.204766486 HQAS(ph)DS(ph)ENEELPKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 HQASDSENEELPKPR 15 1 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 HQAS(1)DS(1)ENEELPKPR;HQAS(1)DS(1)ENEELPKPR;HQAS(1)DS(1)ENEELPKPR 96.591 0.0020716 4238980000 2637310 2247830 2332520 2389490 2251120 2235870 2276650 1117690 3233620 2263610 TRUE FALSE 2534241.009 2183724.089 2754058.251 2512811.865 2323529.319 2281080.823 2304512.324 1094609.311 2866553.014 2110293.678 1.200894944 1.034796299 1.305059234 1.190740365 1.101045481 1.080930511 1.092033942 0.51869999 1.358366868 1 21.00901235 1.976548059 24.71842722 0.880500105 1.147708649 0.117185843 0.205514447 873.2747492 920433.5424 0.081065744 0.052705765 94.74320224 -1.976548059 0.267208544 VQS(ph)LPSVPLSCAAYR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQSLPSVPLSCAAYR 15 0 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 VQS(0.986)LPS(0.014)VPLSCAAYR;VQS(0.995)LPS(0.005)VPLSCAAYR;VQS(0.999)LPS(0.001)VPLSCAAYR;VQS(0.999)LPS(0.001)VPLSCAAYR 220.93 1.68E-12 1176010000 563850 508100 402483 575600 533022 430145 534920 760010 582210 604110 TRUE FALSE 541814.1186 493609.4855 475220.6313 605306.785 550167.1367 438842.8266 541466.511 744315.5279 516119.9616 563193.0916 0.96203971 0.876448047 0.843796983 1.074776651 0.976871245 0.779204918 0.961422502 1.32159918 0.916417423 1 19.10327011 1.976743859 24.74572336 1.121681826 0.918830536 0.231628523 0.123848076 714.8436876 760629.3082 0.049651286 0.032264618 94.78592647 -1.976743859 -0.20285129 QILEDAAALIIHHVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QILEDAAALIIHHVK 15 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 179.17 3.94E-07 96744000 205930 212190 169290 190840 199040 203490 187650 75699 229590 216720 FALSE TRUE 197882.0279 206138.549 199884.4688 200689.2753 205442.3024 207604.7072 189946.5168 74135.7892 203527.9057 202041.3614 0.979413456 1.020278955 0.9893245 0.993307875 1.016832895 1.027535678 0.94013679 0.366933724 1.007357624 1 17.62429114 1.976744617 24.75501416 0.704201091 1.002812398 0.187175605 0.171779749 655.0663346 697307.687 0.066650089 0.043348878 94.78609192 -1.976744617 0.298611307 ITPPAAKPGS(ph)PQAK ddPTM_BT-474_Pertuzumab_2h_R1 5 ITPPAAKPGSPQAK 14 1 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 ITPPAAKPGS(1)PQAK;ITPPAAKPGS(1)PQAK;ITPPAAKPGS(1)PQAK;ITPPAAKPGS(1)PQAK;ITPPAAKPGS(1)PQAK 173.87 1.59E-06 7602630000 5521690 4877190 4610570 4048850 4375930 4713410 4965410 5377020 5904170 5615480 TRUE FALSE 5305896.25 4738097.316 5443802.561 4257811.634 4516685.763 4808718.38 5026178.173 5265982.658 5233953.374 5235138.538 1.01351592 0.905056721 1.039858357 0.813314032 0.862763369 0.918546538 0.960085036 1.005891749 0.999773614 1 22.31979629 1.976752002 2.97005091 1.0016447 0.922044 0.234122537 0.061620934 0.391318127 6.555879 0.031451307 0.017928331 94.78770367 -1.976752002 -0.0796007 DDRDLQIESLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDRDLQIESLKR 12 2 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 102.97 0.0012917 235660000 158510 159100 133180 149150 156720 155830 171910 228320 197920 201460 FALSE TRUE 152315.254 154562.6238 157248.5886 156847.6494 161761.0411 158980.9894 174013.886 223605.1122 175452.9513 187814.9348 0.810985847 0.822951721 0.837252846 0.835118089 0.861278904 0.846476823 0.926517831 1.19056087 0.934179977 1 17.51895226 1.976794652 5.97145173 1.062903735 0.839598731 0.684494895 0.062102931 0.086120072 10.52472423 0.025178526 0.016230869 94.79701278 -1.976794652 -0.223305004 LEDTHFVQCPSVPSHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDTHFVQCPSVPSHK 16 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3;Q9H1B7 Q7Z5L9;Q9H1B7 IRF2BP2;IRF2BPL Interferon regulatory factor 2-binding protein 2;Interferon regulatory factor 2-binding protein-like 0 ; 202.34 1.77E-11 1355360000 1538280 1638970 1262300 1654750 1419440 1629160 1529270 1305090 1765650 1793570 FALSE TRUE 1478162.317 1592228.18 1490425.69 1740151.846 1465097.577 1662102.731 1547985.664 1278139.435 1565220.814 1672089.906 0.884020836 0.952238378 0.891354995 1.040704713 0.876207416 0.99402713 0.925778965 0.764396358 0.936086516 1 20.67322099 1.976938015 24.91203443 0.866758993 0.941498841 0 0.074722848 1228.479137 1327027.256 0.028788664 0.018701916 94.82831087 -1.976938015 0.074739848 YRS(ph)PYSGPK ddPTM_BT-474_Pertuzumab_2h_R1 7 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.5)PYS(0.5)GPK;Y(0.171)RS(0.826)PY(0.002)S(0.002)GPK;Y(0.017)RS(0.982)PY(0.001)S(0.001)GPK;YRS(0.823)PY(0.001)S(0.176)GPK;YRS(0.843)PYS(0.157)GPK;Y(0.016)RS(0.979)PY(0.001)S(0.003)GPK;Y(0.046)RS(0.949)PY(0.003)S(0.002)GPK 145.23 0.00025695 24940780000 16242040 14745790 11731290 12199050 13562440 12853810 14252700 16451540 16490270 16216530 TRUE FALSE 15607283.12 14325254.51 13851395.06 12828644.43 13998688.2 13113722.85 14427128.81 16111809.95 14618363.68 15118169.98 1.032352668 0.947552153 0.916208449 0.848558023 0.925951237 0.867414698 0.954290686 1.065724884 0.966940027 1 23.84978018 1.977033689 11.11374362 1.016188271 0.919748866 0.366481042 0.051431541 0.760709946 364.4592226 0.021425029 0.014112533 94.84920373 -1.977033689 -0.096439405 EKDLEDLFYK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKDLEDLFYK 10 1 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;; 106.01 0.002256 6630990000 4520790 4092130 3254160 3591840 3889580 3843820 4210770 6467400 4871790 4681670 FALSE TRUE 4344112.529 3975426.459 3842259.1 3777215.293 4014691.873 3921544.674 4262302.663 6333845.93 4318764.823 4364576.321 0.995311391 0.910839029 0.880328082 0.865425419 0.919835415 0.898493779 0.976567334 1.451193762 0.989503793 1 22.05741018 1.977120194 23.3553441 1.201244121 0.910924478 0.391896268 0.125765407 242.024712 247054.2357 0.048765109 0.031765379 94.86809815 -1.977120194 -0.290319643 GS(ph)LTLTISGESPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSLTLTISGESPK 13 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(1)LTLTISGESPK;GS(0.988)LT(0.012)LTISGESPK;GS(0.664)LT(0.336)LTISGESPK;GS(1)LTLTISGESPK 415.95 7.93E-127 2615850000 4697720 4470160 4078870 4070740 4450110 4692300 4665740 5203290 5900790 5523840 TRUE FALSE 4514127.909 4342675.414 4816012.543 4280831.379 4593251.83 4787181.521 4722840.722 5095840.243 5230957.057 5149705.397 0.876579835 0.843286184 0.935201564 0.831276947 0.891944582 0.929602987 0.917108914 0.989540149 1.015777924 1 22.29605847 1.977132799 1.03023856 1.014114463 0.874074788 0.773149991 0.029002047 0.228839911 0.446750474 0.022232669 0.010287171 94.8708515 -1.977132799 -0.140039674 CLQLS(ph)PPSQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 CLQLSPPSQSK 11 0 Q9HBH9 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 CLQLS(0.973)PPS(0.024)QS(0.002)K 118.51 0.00085769 0 265850 252000 219300 255080 264760 240050 263940 356060 307580 252510 TRUE FALSE 255460.2881 244813.2067 258932.3883 268244.7094 273276.2458 244903.9755 267170.1767 348707.2366 272664.8079 235407.2728 1.085184349 1.039956004 1.099933682 1.139492022 1.160865774 1.040341586 1.134927454 1.481293388 1.158268411 1 17.84479937 1.977147573 24.78706791 1.277025859 1.096368183 0.099456711 0.12043695 778.8377591 844771.7587 0.046946095 0.030553663 94.87407905 -1.977147573 -0.180657676 TAMPS(ph)PGVSQNK ddPTM_BT-474_Pertuzumab_2h_R1 5 TAMPSPGVSQNK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 TAMPS(1)PGVSQNK;TAMPS(1)PGVSQNK;TAMPS(1)PGVSQNK;TAMPS(1)PGVSQNK;TAMPS(1)PGVSQNK 252.14 4.96E-21 1737230000 2080520 1946570 1689170 1866890 1971180 1912830 2011660 2443700 2367850 2137120 TRUE FALSE 1999210.978 1891055.729 1994440.594 1963240.417 2034584.795 1951508.733 2036279.297 2393236.741 2099061.595 1992370.959 1.003433105 0.949148411 1.00103878 0.985378957 1.021187739 0.979490654 1.022038234 1.201200374 1.053549584 1 20.92605486 1.977192797 19.30134686 1.108359445 0.990721335 0.382586332 0.051424261 31.15229965 26362.71868 0.019812393 0.012959494 94.88395898 -1.977192797 -0.11763811 LIT(ph)EMYT(ph)VAWFVRDMRLMFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LITEMYTVAWFVRDMRLMFR 20 2 Q9HB58;Q9HB58-6 Q9HB58 SP110 Sp110 nuclear body protein 2 LIT(0.994)EMY(0.203)T(0.802)VAWFVRDMRLMFR 60.278 0.069273 779430000 67601 140810 129090 220320 176840 176710 105050 13603 52021 70859 TRUE FALSE 64959.07818 136794.2367 152419.4346 231690.7416 182528.2192 180283.1973 106335.6333 13322.0933 46115.79417 66059.65682 0.983339625 2.0707682 2.307299825 3.507295568 2.763081554 2.729096789 1.609690974 0.201667613 0.698093154 1 16.01148185 1.977196273 3.983495537 0.588438894 2.435173416 0.609974369 0.62908168 0.147977698 5.083239369 0.306019741 0.186741189 94.8847184 -1.977196273 1.846734521 Y(ph)PVPENWLHKEAHQLFLEPEVLDPES(ph)VELK ddPTM_BT-474_Pertuzumab_2h_R1 1 YPVPENWLHKEAHQLFLEPEVLDPESVELK 30 1 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 2 Y(1)PVPENWLHKEAHQLFLEPEVLDPES(1)VELK 44.301 0.049268 275560000 216950 156310 292460 175130 220360 206020 298920 356060 373880 438680 TRUE FALSE 208471.3541 151852.1918 345314.0277 184168.4803 227448.0795 210185.8656 302578.2724 348707.2366 331438.7098 408967.8129 0.509750028 0.371305973 0.844355025 0.450325122 0.556151541 0.513942318 0.739858402 0.852652032 0.810427372 1 18.64162778 1.977358252 1.990776753 0.886425658 0.541540759 0.615015793 0.123701075 0.227346014 1.67254931 0.071221926 0.036183561 94.92011427 -1.977358252 -0.344884898 KLLVLDVDYTLFDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLLVLDVDYTLFDHR 15 1 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 156.5 1.37E-06 105810000 189320 215220 157800 173790 196570 209770 179640 156270 196160 173470 FALSE TRUE 181921.1651 209082.1363 186317.9702 182759.3227 202892.8526 214011.6931 181838.4881 153042.9699 173892.7392 161720.7224 1.124909427 1.292859278 1.152097069 1.130092174 1.254587845 1.323341189 1.124398193 0.946341122 1.075265659 1 17.30314503 1.977414344 6.45244148 1.008402165 1.213159804 0.643567209 0.068608782 0.106992046 17.11867928 0.028650866 0.018601402 94.93237465 -1.977414344 0.20475764 HDS(ph)PDLAPNVTYSLPR ddPTM_BT-474_Pertuzumab_2h_R1 5 HDSPDLAPNVTYSLPR 16 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR 232.01 8.53E-16 1251430000 832286 788606 734745 786337 738720 774743 744535 362091 917106 812480 TRUE FALSE 799759.343 766115.729 867529.7658 826919.9468 762481.5997 790408.8343 753646.842 354613.6943 812999.9717 757450.0059 1.055857597 1.011440654 1.145329407 1.091715546 1.006642806 1.043512876 0.99497899 0.468167789 1.073338128 1 19.53079114 1.977424846 24.58847128 0.773950436 1.056546572 0.229138729 0.157495699 590.0974015 642723.1352 0.061571459 0.040084218 94.93467029 -1.977424846 0.282596137 LKDLFDYS(ph)PPLHK ddPTM_BT-474_Pertuzumab_2h_R1 5 LKDLFDYSPPLHK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 LKDLFDYS(1)PPLHK;LKDLFDY(0.013)S(0.987)PPLHK;LKDLFDYS(1)PPLHK;LKDLFDYS(1)PPLHK;LKDLFDYS(1)PPLHK 118.24 0.0002677 81343797600 14445124 12702820 11478277 11798417 12756799 13933552 14013438 15347818 17686359 16962897 TRUE FALSE 13880592.58 12340548.01 13552656.99 12407334.72 13167133.03 14215297.97 14184938.65 15030880.19 15678677.67 15813984.88 0.877741612 0.780356634 0.85700455 0.784579903 0.832625877 0.898906764 0.896986987 0.950480243 0.991443826 1 23.91469761 1.977460531 0.896816745 1.001495313 0.821283098 0.827926672 0.030413044 0.20946588 0.311052353 0.024005567 0.011547909 94.94247107 -1.977460531 -0.180212215 GFGFVTFSSMAEVDAAMAARPHS(ph)IDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR 214.62 2.47E-34 69442000 38176 39841 28572 37902 39819 40769 34652 28555 38986 30854 TRUE FALSE 36684.03971 38704.77369 33735.59598 39858.12676 41099.8143 41593.37711 35076.08154 27965.32927 34560.47272 28764.2311 1.275335315 1.345586939 1.172831489 1.38568372 1.428851484 1.446010393 1.219434005 0.972225858 1.201508659 1 14.81198829 1.977494033 5.751684515 1.062529558 1.340694513 0.656608542 0.092137511 0.109468174 11.87141301 0.039821886 0.02562142 94.9497954 -1.977494033 0.278164955 GYFNEELSEILSDPSDDTK ddPTM_BT-474_Pertuzumab_2h_R1 3 GYFNEELSEILSDPSDDTK 19 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 142.58 1.54E-07 72307000 278961 246080 229484 227526 240419 260586 258254 287644 325907 292219 FALSE TRUE 268058.8957 239062.0393 270956.8636 239268.6441 248152.2955 265855.2275 261414.5897 281704.0509 288911.4037 272426.7468 0.983966878 0.877527784 0.994604483 0.87828617 0.910895492 0.975877848 0.959577548 1.034054307 1.06051042 1 18.05550883 1.977668301 1.628712897 1.037579042 0.929946976 0.517349978 0.040826023 0.272295229 1.34562688 0.025077345 0.012029801 94.9879031 -1.977668301 -0.107632066 AS(ph)GVAVSDGVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIK 154.47 7.50E-05 262220000 678080 651810 503400 619070 669850 624770 703580 824940 857230 886090 TRUE FALSE 651579.8839 633221.017 594375.5781 651020.2769 691396.3336 637403.2775 712190.6225 807904.7007 759920.8442 826074.3351 0.788766648 0.766542416 0.719518272 0.788089218 0.836966244 0.77160523 0.862138663 0.978004843 0.919918235 1 19.65591208 1.977669441 2.504135753 0.964289791 0.777564321 0.862352833 0.033461029 0.102307602 1.192961338 0.0184049 0.010017844 94.9881526 -1.977669441 -0.186725471 FDEISFVNFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDEISFVNFAR 11 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 166.33 4.78E-05 999150000 756030 839920 653920 699560 802420 706660 778430 1001610 787200 856650 FALSE TRUE 726483.5118 815966.304 772097.8904 735664.3754 828230.568 720949.1494 787956.6592 980926.4035 697840.3562 798628.3325 0.909664086 1.021709687 0.966779989 0.921159876 1.037066348 0.902734251 0.986637497 1.228263967 0.873798647 1 19.60716473 1.977736009 24.95931537 1.071400338 0.963059586 0.072857209 0.092696884 1094.521434 1227025.147 0.036100485 0.023520869 95.00271329 -1.977736009 -0.108340752 SHTGDRPYQCEHAGCGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHTGDRPYQCEHAGCGK 17 1 E7EN86;P52747-2;P52747-3;P52747 E7EN86 ZNF143 Zinc finger protein 143 0 ; 148.03 2.44E-07 167139000 170160 165763 153688 159587 161131 172364 151422 30513 186852 155059 FALSE TRUE 163509.9591 161035.6015 181462.8404 167823.3042 166313.925 175849.3182 153275.1477 29882.89589 165641.3443 144556.7158 1.131112852 1.113995989 1.2553055 1.16095128 1.150509847 1.216472837 1.060311497 0.20672091 1.145857136 1 17.14127611 1.977778641 24.5581048 0.680416888 1.168441368 0.324372963 0.236165964 499.939679 552511.4696 0.091320505 0.059499853 95.01203949 -1.977778641 0.48802448 HGEPEEDIVGLQAFQER ddPTM_BT-474_Pertuzumab_2h_R1 1 HGEPEEDIVGLQAFQER 17 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 190.24 3.10E-10 165600000 172490 181860 140200 169820 170950 182190 164430 98166 196200 182440 FALSE TRUE 165748.9001 176673.5309 165537.2587 178584.4306 176448.762 185874.0066 166442.3435 96138.8378 173928.1985 170083.1763 0.974516726 1.038747833 0.973272386 1.049982923 1.03742631 1.092841812 0.97859381 0.565246016 1.022606717 1 17.37588092 1.977779653 24.71765496 0.803713632 1.027967894 0.222907025 0.124119662 622.9183171 692926.2846 0.048191054 0.031401121 95.01226096 -1.977779653 0.224254262 GDTPGHAT(ph)PGHGGATSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDT(0.396)PGHAT(0.604)PGHGGATSSAR 100.94 0.0020442 714100000 201540 211480 188280 277000 235330 240640 215250 87333 248480 254530 TRUE FALSE 193663.594 205448.7975 222306.3843 291296.0032 242899.6032 245505.9057 217884.2939 85529.54303 220273.5921 237290.4564 0.816145735 0.865811464 0.936853457 1.227592578 1.023638316 1.034621912 0.918217686 0.360442406 0.928286773 1 17.85629455 1.977819738 24.04288919 0.678718279 0.988363614 0.169605365 0.193585088 520.3324699 564027.2257 0.07850881 0.051183156 95.02103101 -1.977819738 0.309645335 SEEEKDQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEEEKDQEK 9 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 97.734 0.0059196 187300000 154630 140070 118460 123980 128220 128620 147030 201590 149350 191400 FALSE TRUE 148586.8886 136075.3407 139868.3571 130378.6227 132344.3127 131220.7845 148829.3971 197427.0961 132396.4141 178436.3075 0.832716675 0.76259895 0.783855926 0.730673171 0.741689371 0.735392849 0.834075751 1.106428948 0.74198136 1 17.44504967 1.977820746 12.12554231 0.963571617 0.764527002 0.464162936 0.08853313 0.917497456 499.4589624 0.03398046 0.022422422 95.02125145 -1.977820746 -0.199044615 VSENDFEDLLSNQGFSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSENDFEDLLSNQGFSSR 18 0 O14976-2;O14976;A0A087X1U9;H0Y8H5 O14976-2 GAK Cyclin-G-associated kinase 0 115.78 0.00041731 45713000 28487 30485 24020 31479 29919 29719 32174 42674 35466 36165 FALSE TRUE 27373.69655 29615.59765 28360.94832 33103.63496 30881.37181 30319.93854 32567.75504 41792.76699 31440.04837 33715.51234 0.811902138 0.878396785 0.841183964 0.981851755 0.915939568 0.899287492 0.96595759 1.239570871 0.93250988 1 15.0411249 1.977888021 10.36034084 1.088752782 0.894447878 0.42729492 0.08548038 0.415869581 190.8772968 0.034024104 0.022455395 95.03597205 -1.977888021 -0.194304904 VHGEPTS(ph)DLS(ph)DID ddPTM_BT-474_Pertuzumab_2h_R1 2 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 2 VHGEPT(0.095)S(0.905)DLS(1)DID;VHGEPT(0.054)S(0.946)DLS(1)DID 147.39 5.90E-05 907380000 1176290 1105170 906150 977800 1043590 1028790 897110 465400 961640 847480 TRUE FALSE 1130319.286 1073651.634 1069911.462 1028264.375 1077158.02 1049592.839 908089.1005 455789.3274 852478.6587 790079.4247 1.430640074 1.358916079 1.35418216 1.301469628 1.363354096 1.328464969 1.14936432 0.576890516 1.078978432 1 19.59163817 1.978002762 5.382601122 0.840597361 1.347274556 0.729442604 0.127500477 0.080301692 6.979500414 0.052243701 0.033420528 95.06108393 -1.978002762 0.506677195 IAILTCPFEPPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IAILTCPFEPPKPK 14 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 123.64 9.28E-05 178230000 185500 178970 159350 144580 164830 182260 185380 218450 230570 237060 FALSE TRUE 178250.4549 173865.9508 188148.0897 152041.7911 170131.9066 185945.4221 187648.7359 213938.9312 204396.6602 221003.715 0.806549586 0.786710535 0.851334511 0.687960341 0.769814691 0.841367857 0.84907503 0.968033189 0.924856219 1 17.7537111 1.978036943 1.429634859 0.972241569 0.781645536 0.760271842 0.043976534 0.198077597 0.75310928 0.030795375 0.014351016 95.06856594 -1.978036943 -0.190596033 HCAPS(ph)PDRS(ph)PELSSSR ddPTM_BT-474_Pertuzumab_2h_R1 7 HCAPSPDRSPELSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 2 HCAPS(1)PDRS(0.999)PELS(0.001)SSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(0.986)PELS(0.013)S(0.001)SR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR 189.11 6.09E-10 14510150000 7171092 7693030 6094630 7343300 7011390 7421970 6738785 3365639 7584290 7020151 TRUE FALSE 6890837.797 7473632.317 7196065.215 7722288.593 7236917.727 7572047.319 6821256.267 3296137.379 6723353.195 6544669.92 1.052893099 1.141941826 1.099530657 1.179935533 1.105772761 1.156979254 1.042261313 0.503636917 1.027302107 1 22.641889 1.978065804 23.12335857 0.784608296 1.122399243 0.42775746 0.139555515 203.2542308 214272.8687 0.053597474 0.034991157 95.074884 -1.978065804 0.337790947 AEDNADTLALVFEAPNQEK ddPTM_BT-474_Pertuzumab_2h_R1 6 AEDNADTLALVFEAPNQEK 19 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;;;; 393.38 8.99E-127 1252219000 2062030 2077190 1802880 1883750 2001190 2089490 2214030 2405570 2662670 2655850 FALSE TRUE 1981443.588 2017950.575 2128700.521 1980970.563 2065560.094 2131740.919 2241125.961 2355894.139 2360414.864 2475966.914 0.800270624 0.815015162 0.85974514 0.800079578 0.834243819 0.860973104 0.905151821 0.951504693 0.953330536 1 21.23956061 1.978092185 0.883593675 0.990715042 0.817149624 0.93513278 0.017145252 0.131300262 0.189482294 0.014347486 0.006944857 95.08065944 -1.978092185 -0.173565418 DKLELEITDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKLELEITDSK 11 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 127.76 0.00025537 179570000 523470 407130 500100 481810 531310 473310 648800 737270 849490 840740 FALSE TRUE 503012.2137 395519.051 590479.1947 506676.2718 548400.0687 482880.6525 656740.2085 722045.1169 753059.4566 783795.9309 0.641764258 0.504619934 0.753358331 0.646439018 0.699672003 0.61607956 0.837896935 0.9212157 0.960785106 1 19.58011856 1.97811546 1.738633718 0.972381754 0.641191124 0.835122018 0.063742554 0.1377713 0.775365748 0.039853876 0.01946724 95.08575527 -1.97811546 -0.331190629 SAS(ph)EPSLHR ddPTM_BT-474_Pertuzumab_2h_R1 6 SASEPSLHR 9 0 Q96II5;P10398;P04049;P04049-2;H7C155 Q96II5;P04049 ARAF;RAF1 Serine/threonine-protein kinase A-Raf;RAF proto-oncogene serine/threonine-protein kinase 1 S(0.037)AS(0.963)EPSLHR;S(0.006)AS(0.992)EPS(0.001)LHR;S(0.101)AS(0.899)EPSLHR;S(0.106)AS(0.891)EPS(0.003)LHR;S(0.13)AS(0.87)EPSLHR;S(0.117)AS(0.883)EPSLHR 113.44 0.0011589 5912700000 3301170 3861960 3130330 3818160 3536050 3540080 3500860 3562860 3529790 3951460 TRUE FALSE 3172156.627 3751820.682 3696050.265 4015215.695 3649790.26 3611662.843 3543704.572 3489285.696 3129103.037 3683824.095 0.861104262 1.018458153 1.00331888 1.089958584 0.990761276 0.98041132 0.961963569 0.947191181 0.849417061 1 21.81277274 1.978135054 1.736912102 0.924142219 0.998210203 0.144904626 0.062901274 0.607485757 3.412170557 0.039288267 0.019185925 95.09004516 -1.978135054 0.074067984 NAS(ph)ASFQELEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 NASASFQELEDK 12 0 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 NAS(0.999)AS(0.001)FQELEDK;NAS(0.795)AS(0.205)FQELEDK 311.65 2.75E-46 1643500000 1163510 878290 939250 986490 954420 905450 1189240 1899750 1411730 1322170 TRUE FALSE 1118038.743 853242.0291 1108993.369 1037402.867 985119.7861 923758.8194 1203794.275 1860519.499 1251476.329 1232618.248 0.907043802 0.692219209 0.89970546 0.841625433 0.799209153 0.749428155 0.976615653 1.509404474 1.015299206 1 20.23329462 1.978153061 9.402639856 1.234725401 0.817585875 0.537976098 0.146534482 0.211819638 86.57148789 0.056474331 0.037260485 95.09398798 -1.978153061 -0.417139526 NHAAPFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 NHAAPFSK 8 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;P34932;A0A087WYC1;A0A087WTS8 Q92598-2;P34932 HSPH1;HSPA4 Heat shock protein 105 kDa;Heat shock 70 kDa protein 4 0 ; 109.71 0.0035651 1403550000 2402300 2238100 1978200 1983910 1944500 1892480 1951640 813890 2402100 2092200 FALSE TRUE 2308415.46 2174271.579 2335704.745 2086299.833 2007046.608 1930747.242 1975524.754 797082.8871 2129423.678 1950493.43 1.183503325 1.114728994 1.19749429 1.06962669 1.028994293 0.989876311 1.012833329 0.408657048 1.091735889 1 20.89540771 1.978162372 24.03886865 0.753505887 1.09025946 0.266890999 0.181418852 438.3807706 482568.806 0.072024745 0.04698253 95.09602683 -1.978162372 0.336753574 EIFDDDLEDDALDADEKGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIFDDDLEDDALDADEKGK 19 1 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 0 ; 227.04 1.24E-19 195047000 269870 215653 227122 197049 224549 222541 288750 345320 409150 352390 FALSE TRUE 259323.182 209502.7876 268167.9977 207218.7225 231771.8225 227040.9315 292283.8089 338189.0213 362705.0073 328522.3114 0.789362466 0.637712509 0.816285495 0.630759968 0.705497966 0.691097449 0.889692416 1.02942482 1.104049846 1 18.32563183 1.978162516 2.316832806 1.052681033 0.708134337 0.858738194 0.060678028 0.096051462 0.956234224 0.031247074 0.016631322 95.09605834 -1.978162516 -0.344546696 SCMLTGT(ph)PESVQSAK ddPTM_BT-474_Pertuzumab_2h_R1 5 SCMLTGTPESVQSAK 15 0 Q96AE4;E9PEB5;Q96AE4-2;C9JSZ1 Q96AE4;C9JSZ1 FUBP1 Far upstream element-binding protein 1 1 SCMLTGT(1)PESVQSAK;SCMLTGT(0.999)PES(0.001)VQSAK;SCMLTGT(0.998)PES(0.002)VQSAK;SCMLTGT(0.998)PES(0.001)VQSAK;SCMLTGT(0.985)PES(0.015)VQSAK 349.2 2.95E-81 895960000 1710360 1656270 1441110 1446760 1544670 1758970 1639810 1789130 2091960 1933200 TRUE FALSE 1643517.24 1609034.801 1701550.634 1521427.457 1594355.713 1794537.579 1659878.485 1752183.84 1854489.471 1802262.642 0.91191883 0.89278597 0.944119128 0.844176327 0.884641159 0.995713686 0.920996999 0.972213372 1.028978478 1 20.78137784 1.978165656 0.869595268 1.011182447 0.898102003 0.57997993 0.036257976 0.438670773 0.613996212 0.030895958 0.015055358 95.09674579 -1.978165656 -0.113080444 S(ph)VEDDAEGHLIYHVGDWLQER ddPTM_BT-474_Pertuzumab_2h_R1 5 SVEDDAEGHLIYHVGDWLQER 21 0 B1AVT0;P49760-3;P49760 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER;S(0.992)VEDDAEGHLIY(0.008)HVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER 273.88 1.67E-44 252136000 94501.3 101036.1 87496.9 104044.7 94321 103427.9 91149 29996.8 112685.3 86698.3 TRUE FALSE 90808.08472 98154.64935 103309.5362 109414.4594 97354.92063 105519.283 92264.50873 29377.3556 99893.73716 80826.14692 1.12349887 1.214392286 1.278169752 1.353701291 1.204497855 1.305509257 1.141518088 0.363463517 1.235908688 1 16.30253445 1.978223309 24.21999197 0.784920945 1.247379059 0.368862224 0.214751051 404.3354268 449700.3208 0.083196625 0.05428505 95.10937097 -1.978223309 0.462458114 RMEEEQHHWDDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 RMEEEQHHWDDRR 13 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ; 116.84 0.00033257 1072370000 801570 873000 496670 533290 646200 794710 544320 114281 585570 471520 FALSE TRUE 770243.7582 848102.8948 586429.3174 560813.1608 666985.6099 810779.5807 550981.551 111921.0574 519098.5485 439583.5304 1.752212503 1.929332734 1.334056617 1.275782922 1.517312555 1.844426655 1.253417184 0.254607031 1.180887164 1 18.74577781 1.978241971 8.64758664 0.734015744 1.588532865 0.589209042 0.296039674 0.167003773 59.70796623 0.121703641 0.080186402 95.11345781 -1.978241971 0.854517121 DLYDDKDGLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLYDDKDGLR 10 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;;;;; 177.57 2.11E-06 3914580000 9714520 8643520 7588070 7528390 8626440 8720870 9116160 10685750 11388520 10432940 FALSE TRUE 9334865.818 8397015.272 8959403.045 7916931.11 8903917.277 8897211.967 9227726.293 10465085.53 10095742.95 9726307.681 0.95975432 0.863330212 0.921151514 0.813970868 0.915446804 0.914757404 0.948738884 1.07595666 1.037983095 1 23.2134608 1.978242359 2.887019829 1.044281789 0.89437214 0.698208413 0.040832829 0.132262664 2.084731635 0.019838347 0.011241489 95.1135429 -1.978242359 -0.149909649 VMQEQGTHPK ddPTM_BT-474_Pertuzumab_2h_R1 8 VMQEQGTHPK 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 139.64 4.07E-05 5239750000 11948580 12050710 9688280 10412810 11095880 11334630 11476700 12422260 13724330 12430630 FALSE TRUE 11481616.28 11707035.55 11439167.71 10950216.37 11452789.06 11563823.98 11617155.29 12165735.99 12166401.6 11588692.36 0.990760297 1.010211954 0.987097367 0.944905261 0.988272767 0.997854083 1.002456095 1.049793679 1.049851115 1 23.46621445 1.978242419 2.802173092 1.037822631 0.985712285 0.499940258 0.020567364 0.208405994 3.079201227 0.010775751 0.006057104 95.11355598 -1.978242419 -0.052110345 DSS(ph)PGSSSTSLLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSPGSSSTSLLIK 14 0 A0A0A0MTP3;Q99550-2;Q99550;U3KQJ0;H0YG46;J3KNE4 A0A0A0MTP3 MPHOSPH9 M-phase phosphoprotein 9 1 DS(0.002)S(0.996)PGS(0.002)SSTSLLIK 209.19 7.33E-09 60471000 100510 104970 108800 93646 101870 110800 118230 143690 148130 156190 TRUE FALSE 96581.95808 101976.3584 128462.5802 98479.08128 105146.7411 113040.4519 119676.9341 140722.7513 131314.9034 145611.1122 0.663287002 0.700333627 0.882230609 0.6763157 0.722106572 0.776317482 0.821894238 0.966428655 0.901819246 1 17.15176093 1.978243182 1.751882132 0.960473225 0.734030118 0.718132248 0.061601965 0.195595015 1.117510477 0.03877212 0.018981632 95.11372319 -1.978243182 -0.226443107 QHQNTMEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 QHQNTMEDK 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 114.5 0.0016287 123670000 167590 164750 152770 158840 169240 153390 155900 81479 198840 180760 FALSE TRUE 161040.3975 160051.4913 180378.9374 167037.7514 174683.7583 156491.6509 157807.9508 79796.43018 176268.5168 168516.9642 0.955633151 0.949764862 1.07039038 0.991222173 1.0365945 0.92864034 0.936451422 0.473521645 1.045998649 1 17.36253431 1.97828091 24.38335983 0.762253492 0.987908374 0.100306652 0.153490949 653.5868498 733760.972 0.060257628 0.039316354 95.12198627 -1.97828091 0.225654882 FPDEDEILEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FPDEDEILEK 10 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 125.48 0.0072777 0 42764 39537 46699 53551 43083 44941 55940 66726 70616 74685 FALSE TRUE 41092.7356 38409.44347 55138.54811 56314.77353 44468.80382 45849.73781 56624.61045 65348.08478 62599.96773 69626.51843 0.590187999 0.551649635 0.791918788 0.808812142 0.638676252 0.658509701 0.813262127 0.938551665 0.899082263 1 16.08734926 1.978300456 2.484338134 0.941408853 0.6773011 0.70749746 0.078655124 0.180130308 2.067063555 0.045720574 0.024843455 95.12626741 -1.978300456 -0.264107752 ASSSS(ph)GTIVQEAYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSSSGTIVQEAYGK 15 0 Q8WXH0;Q8WXH0-2;G3V5X4;A0A0A0MRE3;A0A0C4DGK3;Q8WXH0-7 Q8WXH0 SYNE2 Nesprin-2 1 ASSS(0.079)S(0.918)GT(0.003)IVQEAYGK;ASS(0.002)S(0.043)S(0.949)GT(0.006)IVQEAYGK 237.34 2.73E-13 191910000 418770 562130 385070 610030 455720 424670 512460 713650 580380 527210 TRUE FALSE 402404.0054 546098.6028 454660.7148 641513.7214 470378.6477 433257.1184 518731.6388 698912.8781 514497.6956 491501.5971 0.818723699 1.111082051 0.925044227 1.305211876 0.95702364 0.881496868 1.055401736 1.421995131 1.046787434 1 18.90683658 1.978318454 24.6404287 1.21203654 1.009625303 0.123712061 0.166371715 909.9951683 1034181.077 0.065852945 0.04296829 95.13020962 -1.978318454 -0.202411237 WKGYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 WKGYDSEDDTWEPEQHLVNCEEYIHDFNR 29 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 WKGYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;WKGYDS(1)EDDTWEPEQHLVNCEEYIHDFNR 225.73 6.96E-35 267570000 74383 81274 58290 63129 65289 71184 63981 44163 77451 61497 TRUE FALSE 71476.03013 78956.1451 68824.29965 66387.09526 67389.07998 72623.38925 64764.01862 43251.01862 68659.08718 57331.75341 1.246709299 1.377180016 1.200456912 1.157946361 1.175423321 1.266721929 1.129636105 0.75439902 1.19757522 1 15.80704678 1.978339635 10.7019389 0.952923782 1.232589704 0.485097388 0.115596797 0.45019576 219.0472695 0.046119453 0.030478686 95.13484937 -1.978339635 0.279665922 PSSS(ph)PVIFAGGQDR ddPTM_BT-474_Pertuzumab_2h_R1 6 PSSSPVIFAGGQDR 14 0 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PSS(0.014)S(0.986)PVIFAGGQDR;PSSS(1)PVIFAGGQDR;PSS(0.002)S(0.998)PVIFAGGQDR;PSS(0.031)S(0.969)PVIFAGGQDR;PSS(0.024)S(0.976)PVIFAGGQDR;PSS(0.001)S(0.999)PVIFAGGQDR 264.97 1.05E-24 3490890000 4085790 3448540 3802900 4118550 3894000 3493800 4764790 5339880 5940740 6205790 TRUE FALSE 3926112.81 3350191.016 4490168.625 4331108.859 4019254.046 3564447.03 4823102.925 5229609.612 5266372.101 5785466.316 0.678616484 0.579070179 0.776111791 0.748618801 0.694715659 0.61610367 0.833658458 0.903921884 0.910276167 1 22.46400182 1.978356337 2.695450391 0.929110646 0.685586652 0.782275203 0.060667806 0.135375997 1.841289211 0.03236529 0.018000889 95.13850814 -1.978356337 -0.243523993 RKEEWER ddPTM_BT-474_Pertuzumab_2h_R1 4 RKEEWER 7 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 0 ;;; 141.52 0.001435 1386560000 1370420 1392500 1124410 1251410 1300010 1307520 1365570 1530180 1603610 1540250 FALSE TRUE 1316862.471 1352787.263 1327615.899 1315995.42 1341826.002 1333958.95 1382282.254 1498581.248 1421574.916 1435927.496 0.917081451 0.942099979 0.924570289 0.916477624 0.934466403 0.928987678 0.962640703 1.04363295 0.990004663 1 20.45355147 1.978412237 4.105420334 1.014503606 0.928295469 0.862924369 0.014932555 0.066105809 2.476204214 0.006466509 0.003975818 95.15075469 -1.978412237 -0.086208137 QKS(ph)DAEEDGGTVSQEEEDRKPK ddPTM_BT-474_Pertuzumab_2h_R1 6 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKS(0.976)DAEEDGGT(0.023)VS(0.001)QEEEDRKPK;QKS(0.812)DAEEDGGT(0.186)VS(0.002)QEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK 172.05 3.80E-12 20316200000 3637021 4489413 2085162 2899444 2781203 2689987 3930204 6540210 5947600 2886190 TRUE FALSE 3494882.198 4361379.337 2461997.158 3049084.652 2870662.92 2744380.38 3978303.012 6405152.378 5272453.382 2690705.781 1.298871926 1.620905328 0.915000509 1.133191401 1.066881017 1.019948149 1.478535127 2.380472969 1.959505725 1 21.35955322 1.978433662 8.382347721 1.933580155 1.182727777 0.324413529 0.373036282 0.209158344 70.91449464 0.147093473 0.096883298 95.15544877 -1.978433662 -0.750852379 S(ph)PLIESTANMDNNQSQK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPLIESTANMDNNQSQK 17 0 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 S(0.994)PLIES(0.006)TANMDNNQSQK;S(0.998)PLIES(0.002)TANMDNNQSQK;S(0.716)PLIES(0.048)T(0.237)ANMDNNQSQK 329.6 6.06E-72 969030000 479300 465650 458190 547470 472180 435450 501300 590540 589520 552030 TRUE FALSE 460568.4261 452370.1179 540995.1254 575724.9923 487368.0985 444255.0974 507435.0594 578345.1426 522600.1611 514640.5164 0.89493231 0.879002145 1.051209744 1.118693484 0.947006858 0.863233817 0.985999048 1.123784708 1.015466417 1 18.97320552 1.978465329 23.08359722 1.058851196 0.96280752 0.188386976 0.079669579 461.8445104 495061.9734 0.035310787 0.023061924 95.16238735 -1.978465329 -0.096043676 NKEFER ddPTM_BT-474_Pertuzumab_2h_R1 5 NKEFER 6 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;;; 91.9 0.043199 1382340000 2223890 2168060 1766160 1874900 1961930 2046260 2129600 2376050 2608940 2370410 FALSE TRUE 2136977.92 2106229.052 2085344.4 1971663.814 2025037.26 2087636.779 2155662.682 2326983.737 2312784.069 2209860.019 0.967019586 0.953105189 0.943654522 0.892212084 0.916364495 0.944691863 0.975474764 1.053000514 1.046574918 1 21.07552356 1.978543977 2.83788855 1.037747778 0.934366981 0.770231419 0.023596651 0.123542543 1.87639091 0.012714834 0.007173917 95.1796222 -1.978543977 -0.103380797 ERLEDTHFVQCPSVPGHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERLEDTHFVQCPSVPGHK 18 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 0 60.564 0.042991 146380000 97362 126420 75522 87448 101230 98236 96811 76688 116000 110880 FALSE TRUE 93556.9854 122814.6254 89170.50538 91961.20176 104486.1549 100222.3992 97995.80198 75104.366 102832.1663 103369.9988 0.905069038 1.18810706 0.862634288 0.889631448 1.010797679 0.969550163 0.948010091 0.726558642 0.994797015 1 16.65745801 1.978588969 24.0872454 0.866873217 0.972754179 0.025500964 0.111904831 886.5866577 997401.2741 0.044688855 0.029171584 95.1894832 -1.978588969 0.105880962 GSAFSTS(ph)ISK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSAFSTSISK 10 0 K7ER00;Q9Y285;K7EPH2;K7ER16 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 1 GSAFS(0.016)T(0.074)S(0.91)ISK 136.61 0.00011867 377130000 1038600 841040 510950 709930 896700 594100 803400 1329100 690690 593150 TRUE FALSE 998010.3638 817054.3627 603290.031 746569.5724 925543.1699 606113.109 813232.2495 1301653.621 612285.7668 552975.4222 1.804800582 1.477559996 1.09098887 1.350095397 1.673751007 1.096094121 1.470648092 2.353908634 1.107256746 1 19.07685583 1.978624261 24.93649626 1.70618662 1.401625253 0 0.413742524 1760.043309 2053228.206 0.164838626 0.107592553 95.19721891 -1.978624261 -0.304561367 VEYSEEELK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEYSEEELK 9 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 185.72 9.89E-05 619250000 640100 557400 577700 501570 612350 524080 647380 758720 781680 805400 FALSE TRUE 615084.1843 541503.4978 682103.2409 527456.0878 632046.7939 534677.2567 655302.8301 743052.1669 692946.9635 750849.5406 0.819184339 0.721187759 0.908441977 0.702479071 0.841775562 0.712096402 0.872748526 0.989615265 0.922883915 1 19.51816432 1.978638605 4.474489696 0.963853078 0.785689037 0.637366395 0.063048507 0.120881812 5.821137027 0.025437281 0.01588396 95.20036313 -1.978638605 -0.178164041 VQS(ph)PQQIVHPFLQMEGHVIQSNGDHSQQQLHPQNSEVMK ddPTM_BT-474_Pertuzumab_2h_R1 1 VQSPQQIVHPFLQMEGHVIQSNGDHSQQQLHPQNSEVMK 39 0 A0A3B3IRW6;Q2KHR3-2;Q2KHR3 A0A3B3IRW6 QSER1 Glutamine and serine-rich protein 1 1 VQS(1)PQQIVHPFLQMEGHVIQSNGDHSQQQLHPQNSEVMK 55.336 0.013385 70380000 13051 13419 11645 12294 11517 19921 12933 3395.6 18246 15785 TRUE FALSE 12540.95249 13036.30326 13749.51054 12928.49481 11887.45476 20323.81627 13091.27792 3325.479673 16174.79057 14715.86789 0.852206107 0.885867103 0.93433229 0.878541103 0.807798416 1.381081729 0.889602844 0.225979174 1.099139425 1 13.84508501 1.978664399 24.92403875 0.656225653 0.958196 0.03159286 0.269127651 1150.816334 1344371.02 0.107576255 0.070193755 95.20601744 -1.978664399 0.301970347 YVSGDVTHPQAGAEDALIVHCVDDSGHWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YVSGDVTHPQAGAEDALIVHCVDDSGHWGR 30 0 A0A494C179;A0A0A0MRH8;A0A494C1P7;A0A0A0MSH9;A0A494C1F7;Q86WJ1-5;Q86WJ1-3;Q86WJ1-4;Q86WJ1-2;Q86WJ1 A0A494C179 CHD1L Chromodomain-helicase-DNA-binding protein 1-like 0 ; 206.95 4.07E-26 232163000 74125 89763 61931 79538 72140 94816 72320 22319.8 79417 71631 FALSE TRUE 71228.11305 87203.04713 73123.30935 83642.96571 74460.44862 96733.24448 73205.07379 21858.88833 70401.9151 66779.36857 1.066618547 1.30583815 1.094998514 1.252527053 1.115021753 1.448549852 1.096222911 0.327329964 1.054246493 1 16.02711483 1.978689533 23.61475272 0.717282213 1.215159174 0.423983145 0.213578482 270.1802825 299393.9299 0.081604093 0.053329705 95.21152764 -1.978689533 0.497876961 TAHNSEADLEESFNEHELEPSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 TAHNSEADLEESFNEHELEPSSPK 24 0 Q8IWS0-5;Q8IWS0 Q8IWS0-5 PHF6 PHD finger protein 6 1 TAHNSEADLEESFNEHELEPS(0.037)S(0.963)PK 246.35 1.20E-37 507250000 113480 176240 134400 176530 137880 155660 142880 82511 158340 155700 TRUE FALSE 109045.0761 171213.8078 158689.0697 185640.7345 142315.0354 158807.5519 144628.6082 80807.11902 140365.907 145154.3003 0.751235588 1.179529696 1.093244013 1.278919977 0.980439678 1.094060262 0.996378391 0.556698071 0.967011702 1 17.14722779 1.978836123 20.48477578 0.788119677 1.073119358 0.230930388 0.172386441 78.29254913 75779.03252 0.067273717 0.04412237 95.24367041 -1.978836123 0.284999681 FHDPDSAVVAQHLTNTVFVDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FHDPDSAVVAQHLTNTVFVDR 21 0 Q05519-2;Q05519;B4DWT1;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 0 ;;; 358.25 5.71E-96 2327440000 674402 841488 712212 944320 857896 959302 768415 234200 819758 798667 FALSE TRUE 648045.6242 817489.5861 840924.5515 993056.4684 885491.004 978699.7437 777819.0926 229363.6882 726702.5085 744572.5727 0.870359248 1.097931372 1.129405759 1.333726899 1.189260841 1.314445065 1.044651819 0.308047458 0.975999567 1 19.50605295 1.978881932 22.9833976 0.682436221 1.163117095 0.383230608 0.21702011 213.3145012 232155.403 0.08610804 0.056335321 95.25371698 -1.978881932 0.480680874 HELSTEYIPDPER ddPTM_BT-474_Pertuzumab_2h_R1 1 HELSTEYIPDPER 13 0 A0A3B3IUD7;Q14690 A0A3B3IUD7 PDCD11 Protein RRP5 homolog 0 120.53 0.00026286 202150000 107550 118020 107260 123570 114420 123600 112890 67155 130980 135010 FALSE TRUE 103346.8271 114654.1852 126644.268 129947.4625 118100.4232 126099.2767 114271.5816 65768.22578 116111.6995 125865.6524 0.821088399 0.910925125 1.006186084 1.032429896 0.938305415 1.00185614 0.907885347 0.522527191 0.922505046 1 16.94152511 1.97897505 24.76184201 0.750270204 0.955415068 0.124076326 0.132241519 757.9713138 892689.2151 0.052190177 0.034083469 95.2741427 -1.97897505 0.205144864 VDKLDASESLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDKLDASESLRK 12 2 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 96.745 0.0029875 495100000 488100 487070 419770 367810 460310 468670 446960 363940 546260 507180 FALSE TRUE 469024.5124 473179.2405 495631.7767 386792.7182 475116.2892 478146.8285 452430.0302 356424.5118 484250.8549 472828.2469 0.991955357 1.000742328 1.048227935 0.818040633 1.004839056 1.011248443 0.956859141 0.753813915 1.024158049 1 18.8509567 1.978978994 24.73446005 0.887811614 0.977713295 0.01545787 0.09066048 1182.523566 1391420.268 0.036269184 0.023677269 95.27500807 -1.978978994 0.089901682 CYQSEFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 CYQSEFGR 8 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ; 160.63 0.00081944 897770000 449770 397760 190690 872630 418640 370640 596330 557200 840610 854550 FALSE TRUE 432192.4912 386416.2742 225151.9249 917666.5389 432105.9358 378134.5947 603628.0649 545693.6253 745187.4769 796670.5673 0.542498379 0.485038974 0.282616095 1.151877045 0.542389732 0.474643611 0.757688422 0.684967724 0.93537719 1 19.60362375 1.978996897 0.092516552 1.43690382 1.11E-08 0.310625938 0.215227869 18.16811449 1.335603279 8.898603875 10.61813428 95.27893561 -1.978996897 -1.436903809 QAIEEEGGDPDNIELTVSTDT(ph)PNKKPTK ddPTM_BT-474_Pertuzumab_2h_R1 3 QAIEEEGGDPDNIELTVSTDTPNKKPTK 28 2 Q9NWH9;H7BXE3;H0YL55;H0YKU6;H0YNF3;H0YMR6;H0YLE6;H0YMW8 Q9NWH9 SLTM SAFB-like transcription modulator 1 QAIEEEGGDPDNIELT(0.009)VS(0.007)T(0.041)DT(0.935)PNKKPT(0.008)K;QAIEEEGGDPDNIELTVS(0.02)T(0.02)DT(0.955)PNKKPT(0.004)K;QAIEEEGGDPDNIELTVSTDT(0.987)PNKKPT(0.012)K 173.6 9.00E-11 1186460000 977033 705554 777320 621422 674102 615894 832158 1056950 1001409 1047580 TRUE FALSE 938849.4702 685432.2907 917799.0154 653493.6639 695785.103 628347.7987 842342.1985 1035123.613 887733.2486 976626.4735 0.961318883 0.701836689 0.939764629 0.669133678 0.712437275 0.643385998 0.86250191 1.059897147 0.9089793 1 19.89744736 1.979133935 6.911955123 0.988623409 0.76703088 0.461778574 0.105488833 0.148550255 30.79350979 0.042711373 0.027955152 95.30900492 -1.979133935 -0.221592528 IHIPEPDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 IHIPEPDLR 9 0 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 0 ;;; 108.98 0.0025238 641140000 565324 594350 495122 601940 558165 609880 548144 371628 596726 591950 FALSE TRUE 543230.5131 577399.7199 584601.5593 633006.1955 576118.8841 622212.1915 554852.3502 363953.7519 528988.1662 551856.6992 0.984368793 1.046285604 1.059335802 1.147048131 1.043964647 1.127488698 1.005428313 0.659507717 0.95856074 1 19.07393417 1.979254509 20.74720051 0.834259375 1.068959517 0.440467776 0.095587384 59.54926378 59553.32412 0.037032729 0.024311076 95.33546939 -1.979254509 0.234700142 (ac)MLTAVCGSLGSQHT(ph)EAPHASPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLTAVCGSLGSQHTEAPHASPPR 23 0 Q3SY56 Q3SY56 SP6 Transcription factor Sp6 1 MLTAVCGSLGS(0.048)QHT(0.508)EAPHAS(0.444)PPR 87.739 4.90E-05 95743000 19220 14538 15697 13008 16517 17399 18797 35519 19059 22964 TRUE FALSE 18468.86115 14123.39047 18533.79708 13679.34444 17048.28431 17750.8197 19027.04331 34785.52024 16895.50222 21408.62783 0.862683087 0.659705544 0.865716254 0.638964092 0.796327744 0.829143271 0.888755854 1.624836515 0.789191272 1 14.38590471 1.979257906 22.64206293 1.219775899 0.776509561 0.35114168 0.211869626 184.0207068 200876.0376 0.081828117 0.053607937 95.33621514 -1.979257906 -0.443266338 MFS(ph)PMEEK ddPTM_BT-474_Pertuzumab_2h_R1 7 MFSPMEEK 8 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 MFS(1)PMEEK;MFS(1)PMEEK;MFS(1)PMEEK;MFS(1)PMEEK;MFS(1)PMEEK;MFS(1)PMEEK;MFS(1)PMEEK 172.27 0.00029845 1760719000 3731310 3312100 3050497 3096170 3519990 3461450 3682840 4313860 4720710 4269350 TRUE FALSE 3585486.28 3217642.151 3601789.666 3255963.705 3633213.675 3531442.891 3727911.698 4224777.283 4184834.792 3980183.122 0.900834502 0.808415606 0.904930642 0.818043694 0.912825758 0.887256386 0.936618136 1.061452992 1.051417652 1 21.92440338 1.97930117 2.348999743 1.044407694 0.868607918 0.800554416 0.036786616 0.11404841 1.167995012 0.018981764 0.010155238 95.34571286 -1.97930117 -0.175799775 SLGGQQGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLGGQQGSPK 10 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK 147.02 2.90E-05 1113320000 2022430 1828740 1574820 1488700 1591130 1607970 1877230 2133190 2356230 2154900 TRUE FALSE 1943391.2 1776586.126 1859425.006 1565531.985 1642310.141 1640484.255 1900204.102 2089138.881 2088760.649 2008946.704 0.967368221 0.884337112 0.925572093 0.779279999 0.817498114 0.816589237 0.945870838 1.039917524 1.03972925 1 20.93800786 1.979315213 3.710101311 1.026891257 0.862929294 0.652489979 0.052827756 0.147072501 4.201783725 0.026216238 0.01581144 95.34879601 -1.979315213 -0.163961963 HTGCCGDNDPIDVCEIGSK ddPTM_BT-474_Pertuzumab_2h_R1 6 HTGCCGDNDPIDVCEIGSK 19 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 288.57 6.45E-41 12577280000 8915490 8423300 6643180 7721070 7793380 8209340 7802460 5416970 9863640 9208050 FALSE TRUE 8567062.794 8183075.731 7843750.403 8119555.348 8044061.145 8375338.479 7897948.839 5305107.677 8743960.939 8584380.572 0.997982641 0.953251742 0.913723516 0.945852211 0.937057843 0.975648553 0.920037127 0.617995397 1.018589619 1 23.03328261 1.979353989 24.9840813 0.8195666 0.950671705 0.006162967 0.108277367 1080.770946 1307857.602 0.04241658 0.027727287 95.35730956 -1.979353989 0.131105105 FDDPGLMLMGFKPLVLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FDDPGLMLMGFKPLVLLK 18 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 95.57 0.0018405 152756000 258760 285910 221700 225867 242677 219197 253119 298110 292640 285268 FALSE TRUE 248647.3731 277756.1267 261766.1217 237524.0229 250482.9261 223629.3135 256216.746 291953.9243 259420.734 265946.5443 0.93495245 1.04440585 0.984280967 0.893126939 0.941854412 0.84088069 0.963414459 1.097791758 0.975461948 1 18.02077677 1.97940881 24.32509966 1.034113541 0.941102808 0.294395456 0.057947458 629.9604918 744193.6025 0.024755835 0.016197865 95.36934719 -1.97940881 -0.093010733 SSTSPSIINEDVIINGHS(ph)HEDDNPFAEYMWMENEEEFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.162)S(0.162)T(0.162)S(0.162)PS(0.162)IINEDVIINGHS(0.191)HEDDNPFAEYMWMENEEEFNR;S(0.153)S(0.153)T(0.153)S(0.153)PS(0.153)IINEDVIINGHS(0.235)HEDDNPFAEYMWMENEEEFNR 111.05 1.06E-05 80497000 20502 19542.8 15709.5 18709.4 18648.4 23502 17893.8 7529.5 18588.8 17945.1 TRUE FALSE 19700.75917 18985.45848 18548.55611 19674.99438 19248.24272 23977.22654 18112.78968 7374.013194 16478.67735 16729.66239 1.177594545 1.134838112 1.108722679 1.176054478 1.150545795 1.433216402 1.082675146 0.440774776 0.984997603 1 14.03012071 1.9794383 23.31870287 0.75027204 1.192873693 0.50660616 0.168454988 209.9429174 238092.2651 0.06584485 0.043128692 95.3758233 -1.9794383 0.442601652 SEEHNDKEHSSDKGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEHNDKEHSSDKGR 15 2 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 0 ; 101.36 0.00057978 57891000 43161 74359 36186 43374 47757 67172 39614 2747.209 36748 33935 FALSE TRUE 41474.2204 72238.35413 42725.61515 45612.53734 49293.14728 68530.26386 40098.80798 2690.478174 32576.5211 31636.55222 1.310958922 2.28338264 1.350514268 1.441767011 1.558107436 2.166173589 1.267483501 0.085043343 1.029711483 1 14.94930476 1.979607128 9.510525133 0.620463435 1.683582486 0.557382795 0.389217442 0.221920706 98.3519497 0.151479323 0.100340551 95.41290694 -1.979607128 1.063119051 LVLVLGDLHIPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVLVLGDLHIPHR 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 125.28 0.00011679 397430000 210050 236420 206240 255900 254190 277150 224940 90649 259260 225530 FALSE TRUE 201841.0138 229677.5331 243512.1558 269107.0297 262366.2522 282754.1629 227692.883 88777.06647 229829.8917 210254.6522 0.95998358 1.092377889 1.158177254 1.279909989 1.247849926 1.344817629 1.08293862 0.42223592 1.093102527 1 17.6817782 1.97977522 24.00445519 0.76883432 1.185642525 0.367946782 0.194212594 373.4676939 443261.8349 0.0775571 0.050808609 95.44984345 -1.97977522 0.416808206 RAPS(ph)PLPK ddPTM_BT-474_Pertuzumab_2h_R1 4 RAPSPLPK 8 1 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 RAPS(1)PLPK;RAPS(1)PLPK;RAPS(1)PLPK;RAPS(1)PLPK 66.663 0.037424 4212770000 6124100 6212300 5378280 5661380 5700160 5954780 6184300 6919100 7300500 6988100 TRUE FALSE 5884763.401 6035131.286 6350254.835 5953564.5 5883510.823 6075189.732 6259985.313 6776218.167 6471777.846 6514789.763 0.90329291 0.926373913 0.9747444 0.913853665 0.903100643 0.93252276 0.960888308 1.040128448 0.993397804 1 22.63528719 1.979788293 3.681021429 1.014030284 0.92687128 0.744104364 0.022369902 0.112959503 3.165032825 0.010668903 0.006427589 95.45271662 -1.979788293 -0.087159004 SGLTVPTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 7 SGLTVPTSPK 10 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 SGLTVPT(0.155)S(0.845)PK;SGLTVPT(0.046)S(0.954)PK;SGLTVPT(0.107)S(0.893)PK;SGLTVPT(0.093)S(0.907)PK;SGLTVPT(0.194)S(0.806)PK;SGLTVPTS(1)PK;SGLTVPT(0.031)S(0.969)PK 219.74 6.47E-09 12548180000 13354500 11862140 8862920 9721320 11761440 9431450 11208990 14484300 12855490 9290580 TRUE FALSE 12832591.38 11523843.38 10464646.8 10223038.49 12139757.4 9622160.381 11346168.97 14185194.14 11396188.67 8661320.741 1.481597525 1.330494936 1.208204512 1.180309423 1.401605801 1.110934541 1.309981389 1.637763404 1.315756454 1 23.0461556 1.979791529 24.75508332 1.409995012 1.278373773 0 0.181833478 1603.429522 1964176.127 0.07137573 0.046726928 95.45342788 -1.979791529 -0.131621239 VDDLLIIEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDDLLIIEEK 10 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 174.73 7.02E-06 62143000 174444 159545 170228 159068 175540 180839 198348 226580 262250 245500 FALSE TRUE 167626.5356 154994.9328 200991.9863 167277.5185 181186.4035 184495.6885 200775.4422 221901.0438 232480.4794 228872.0663 0.732402771 0.677212101 0.878184872 0.730877827 0.791649267 0.806108371 0.877238736 0.969541838 1.01576607 1 17.80418187 1.979805309 1.165807971 1.017393772 0.75823546 0.818517378 0.048378982 0.189752293 0.476018024 0.036500735 0.016720315 95.45645652 -1.979805309 -0.259158312 IDGDKDGFVTVDELK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDGDKDGFVTVDELK 15 1 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ; 238.81 8.03E-18 1183230000 2038650 1791600 2152900 2034700 2019150 1929200 2648900 3213500 3666100 3416200 FALSE TRUE 1958977.304 1740505.322 2541976.921 2139711.111 2084097.793 1968209.746 2681318.031 3147140.102 3249939.698 3184817.731 0.615098718 0.546500764 0.7981546 0.671847274 0.654385265 0.61799761 0.841906274 0.988169612 1.020447627 1 21.60277938 1.979809085 2.464271084 1.004875971 0.653162447 0.868303497 0.061686601 0.101797686 1.149718588 0.034301086 0.018620826 95.45728651 -1.979809085 -0.351713523 YQQPFEDFRIS(ph)QEHLADHFDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YQQPFEDFRISQEHLADHFDSR 22 1 P19174-2;P19174;V9GY71;V9GYH5 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 YQQPFEDFRIS(1)QEHLADHFDSR 160.41 1.12E-11 636390000 152740 179410 115640 132060 174240 162740 129590 10935 154370 120180 TRUE FALSE 146770.7519 174293.4025 136538.7204 138875.6324 179844.5878 166030.7143 131175.9612 10709.18843 136846.5648 112040.1016 1.309984103 1.555634099 1.218659377 1.239517195 1.605180514 1.481886503 1.170794737 0.09558353 1.221407004 1 16.77365567 1.979813244 17.52287373 0.662170545 1.396013648 0.459991704 0.297967344 11.46510527 9951.171947 0.115763813 0.076420158 95.45820064 -1.979813244 0.733843102 HADNSSDT(ph)EMEDMIAEETLEEMDSELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.3)S(0.3)DT(0.4)EMEDMIAEETLEEMDSELLK 174.33 5.33E-12 11251000 6978 5148.5 5875 7217.2 6795.7 7163.3 6108.4 2338 8319 5277.5 TRUE FALSE 6705.292045 5001.669821 6936.743189 7589.680557 7014.289862 7308.146834 6183.156426 2289.719483 7374.661996 4920.050224 1.362850325 1.01658918 1.40989276 1.542602252 1.425654118 1.485380535 1.256726282 0.465385388 1.498899739 1 12.26445733 1.9798363 24.09689483 0.911783939 1.369406403 0.278816748 0.269171215 494.9947128 591548.9836 0.107440652 0.07039183 95.4632686 -1.9798363 0.457622464 GRAEGEWEDQEALDYFS(ph)DK ddPTM_BT-474_Pertuzumab_2h_R1 2 GRAEGEWEDQEALDYFSDK 19 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 GRAEGEWEDQEALDYFS(1)DK;GRAEGEWEDQEALDYFS(1)DK 127.41 1.42E-05 135241000 224990 198626 208919 229890 217970 220760 263860 331820 337870 356920 TRUE FALSE 216197.1421 192961.381 246675.3107 241754.6505 224981.203 225223.9185 267089.1976 324967.801 299516.4141 332745.4905 0.649737256 0.579906825 0.741333294 0.726545235 0.676135994 0.676865427 0.802683147 0.97662571 0.900136659 1 18.34405959 1.979840133 2.546845076 0.95666659 0.675273116 0.874918829 0.048013139 0.097366134 1.177057107 0.026471946 0.014509144 95.46411102 -1.979840133 -0.281393474 NTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_BT-474_Pertuzumab_2h_R1 4 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK;NTFT(0.003)AWS(0.987)DEES(0.01)DYEIDDRDVNK 218.98 6.88E-26 3662620000 573578 575130 465859 519391 573955 589997 635192 698794 836333 786270 TRUE FALSE 551161.9376 558727.8555 550050.0843 546196.8318 592416.7838 601927.1436 642965.6697 684363.6597 741395.984 733015.2326 0.75191062 0.762232258 0.750393798 0.745137082 0.808191641 0.821165941 0.877151853 0.933628156 1.011433257 1 19.48348365 1.979866697 0.849548139 1.014751883 0.752298495 0.975423481 0.015437015 0.081216218 0.108749589 0.013060881 0.006437363 95.46995032 -1.979866697 -0.262453388 IVSRPEELREDDVGTGAGLLEIK ddPTM_BT-474_Pertuzumab_2h_R1 5 IVSRPEELREDDVGTGAGLLEIK 23 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;; 221.83 9.64E-33 3653022000 2304159 2210544 1886746 2008268 2251369 2371474 2362629 2602597 3071130 2929610 FALSE TRUE 2214109.919 2147501.449 2227722.973 2111914.952 2323786.329 2419426.829 2391543.56 2548852.462 2722508.198 2731184.905 0.810677415 0.786289293 0.815661718 0.773259602 0.850834495 0.885852446 0.875643226 0.933240535 0.996823098 1 21.38109556 1.979934947 0.661542054 1.008797224 0.792872129 0.924713547 0.021322981 0.17627597 0.151068839 0.019373576 0.011247054 95.48495485 -1.979934947 -0.215925094 EIS(ph)DDEAEEEKGEK ddPTM_BT-474_Pertuzumab_2h_R1 6 EISDDEAEEEKGEK 14 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 1 EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK 258.96 5.57E-24 13216020000 4726960 3309777 5054790 3941740 3859930 3576641 6078780 7858260 9072350 8131560 TRUE FALSE 4542225.177 3215385.401 5968302.996 4145173.674 3984088.154 3648963.132 6153173.928 7695984.185 8042494.862 7580802.198 0.599174739 0.424148437 0.787291746 0.546798817 0.525549678 0.481342612 0.81167847 1.015193905 1.060902877 1 22.85391909 1.979983177 2.863726869 1.024533527 0.563005122 0.836161113 0.092417982 0.101214959 1.569673813 0.046579295 0.026384336 95.49555931 -1.979983177 -0.461528404 HSLS(ph)PVPWEEDSFLQVK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSLSPVPWEEDSFLQVK 17 0 P10073 P10073 ZSCAN22 Zinc finger and SCAN domain-containing protein 22 1 HS(0.088)LS(0.912)PVPWEEDSFLQVK;HS(0.124)LS(0.876)PVPWEEDSFLQVK 229.96 6.07E-16 256520000 444180 427000 379960 390080 399110 439210 399340 260310 472650 424940 TRUE FALSE 426820.9545 414822.3781 448627.2242 410212.0755 411947.7356 448091.1271 404227.2424 254934.5075 418996.7535 396158.4353 1.077399637 1.047112319 1.132443952 1.035474797 1.039856025 1.131090713 1.020367627 0.643516545 1.057649456 1 18.595718 1.980008005 24.3049518 0.853570029 1.074853257 0.323008051 0.108279023 441.8225565 537138.074 0.041704847 0.027340305 95.50101889 -1.980008005 0.221283229 HGKNPVMELNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGKNPVMELNEK 12 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 102.62 0.0014026 407080000 349220 370720 285650 280160 316610 333200 316270 263210 360030 334290 FALSE TRUE 335572.0963 360147.4286 337273.3092 294619.0912 326794.0482 339937.5323 320140.6069 257774.6215 319160.9038 311648.2405 1.076765573 1.155621569 1.082224333 0.945357788 1.048599047 1.090773148 1.027249845 0.827133248 1.024106227 1 18.24955904 1.980012872 20.80832692 0.930201996 1.064493817 0.347926181 0.069439763 82.80752574 86208.62404 0.028830614 0.018967902 95.50208914 -1.980012872 0.134291821 S(ph)HNNFVAILDLPEGEHQYK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHNNFVAILDLPEGEHQYK 19 0 Q9Y478 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 S(1)HNNFVAILDLPEGEHQYK;S(1)HNNFVAILDLPEGEHQYK 160.67 5.19E-11 303250000 747030 641660 527770 599110 630350 640690 571850 147741 713110 552130 TRUE FALSE 717835.2417 623360.4851 623149.7792 630030.1389 650625.7802 653645.1908 578848.4714 144690.0967 632160.7424 514733.7433 1.394575839 1.211034818 1.210625469 1.223992301 1.264004524 1.26987049 1.124559015 0.281096972 1.228131535 1 18.97346684 1.98002354 23.98853422 0.743105431 1.25109993 0.383651916 0.232331525 350.560653 420966.5398 0.089510044 0.058692437 95.504435 -1.98002354 0.507994499 SVS(ph)HGSNHTQKPDEQR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.45)VS(0.549)HGS(0.001)NHTQKPDEQR;S(0.427)VS(0.572)HGS(0.001)NHTQKPDEQR;S(0.496)VS(0.503)HGSNHTQKPDEQR 211.49 4.20E-12 519475000 126553 159164 134231 176294 151583 168657 133512 21701.5 149155 132965 TRUE FALSE 121607.1688 154624.7986 158489.5277 185392.5545 156458.8049 172067.3601 135145.9598 21253.35644 132223.5497 123959.1621 0.981026064 1.247384993 1.278562431 1.495593801 1.262180239 1.388097154 1.090245832 0.171454502 1.066670244 1 16.91950538 1.980051719 18.40662463 0.64819483 1.280026267 0.4406403 0.259827975 18.1159585 16714.95707 0.101197903 0.066784358 95.51063214 -1.980051719 0.631831437 ETAAVIFLHGLGDTGHSWADALSTIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETAAVIFLHGLGDTGHSWADALSTIR 26 0 O95372;Q5QPQ3;Q5QPQ2;Q5QPN5;Q5QPN9 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ; 297.99 1.04E-70 1223050000 441120 544280 412530 539920 497330 487380 456180 195903 542170 474020 FALSE TRUE 423880.5427 528757.6673 487083.3477 567785.3359 513327.0711 497235.1575 461762.8673 191857.5346 480625.1346 441914.2032 0.959191942 1.196516572 1.102212475 1.284831607 1.161598943 1.12518483 1.044915198 0.434151094 1.087598296 1 18.75340677 1.980119079 22.92045389 0.768166418 1.141827952 0.330939695 0.180660966 214.4698908 247258.631 0.070099563 0.046030761 95.52544719 -1.980119079 0.373661534 HS(ph)CSGSS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HS(1)CS(0.355)GS(0.123)S(0.522)PPR 67.519 0.091708 43214000 101070 102350 107340 121380 111180 109090 102710 45258 123090 107690 TRUE FALSE 97120.07266 99431.07821 126738.7258 127644.4363 114756.2057 111295.8745 103966.9957 44323.40648 109117.3392 100396.0604 0.96736936 0.990388247 1.262387441 1.271408817 1.143034948 1.108568146 1.035568481 0.441485516 1.086868736 1 16.61534313 1.980127466 23.35870252 0.770177337 1.126701191 0.291787096 0.185759177 301.0022561 353805.0993 0.074871327 0.049138244 95.52729192 -1.980127466 0.356523854 VKPTTQSEVSPLFAGTDVIPAHQFPDELAAYHPT(ph)PPLS(ph)PELPGSCR ddPTM_BT-474_Pertuzumab_2h_R1 1 VKPTTQSEVSPLFAGTDVIPAHQFPDELAAYHPTPPLSPELPGSCR 46 1 H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BV44 H3BRD5 MYO9A Unconventional myosin-IXa 2 VKPTTQSEVSPLFAGTDVIPAHQFPDELAAY(0.018)HPT(0.983)PPLS(0.998)PELPGSCR 102.28 3.57E-07 35816000 8847.7 10072 8685.6 12147 10705 12636 10134 6052.4 10771 11496 TRUE FALSE 8501.922102 9784.756422 10255.28113 12773.90813 11049.33605 12891.50858 10258.02292 5927.415825 9548.321236 10717.36568 0.793284689 0.912981484 0.956884503 1.191888801 1.030974997 1.202861688 0.95714033 0.553066491 0.890920542 1 13.38766272 1.98020985 24.23467174 0.762528094 1.021640012 0.225256799 0.157102159 561.6372375 687770.1761 0.064602902 0.042370278 95.54541476 -1.98020985 0.259111919 S(ph)SPVKVGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPVKVGEK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 S(0.894)S(0.106)PVKVGEK;S(0.987)S(0.013)PVKVGEK 168.85 0.00015499 523580000 1302120 1112220 828220 709130 919160 917870 1023710 1144110 1254050 1124800 TRUE FALSE 1251231.711 1080500.575 977897.7777 745728.2843 948725.6162 936429.9603 1036238.469 1120483.729 1111695.501 1048616.294 1.193221694 1.030406051 0.932560159 0.711154584 0.904740487 0.893014886 0.98819604 1.068535493 1.060154708 1 20.00005544 1.980240161 4.746916186 1.046899758 0.935192481 0.126248361 0.11465846 0.397916881 23.16251603 0.054137679 0.034211663 95.55208342 -1.980240161 -0.111707277 ACDELVEEMEHYGK ddPTM_BT-474_Pertuzumab_2h_R1 3 ACDELVEEMEHYGK 14 0 E7ETU9;O00469-3;O00469;O00469-2 E7ETU9 PLOD2 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2" 0 ;; 167.98 3.56E-06 151513000 201611 224300 182121 217436 206310 211829 201401 191990 229011 190314 FALSE TRUE 193731.8192 217903.1836 215034.316 228657.898 212946.1485 216112.3275 203865.8057 188025.3394 203014.6314 177423.8633 1.091915234 1.228150372 1.211980801 1.288766313 1.200211429 1.218056712 1.149032616 1.059752256 1.14423521 1 17.43684054 1.980245512 2.848170483 1.075350682 1.211296849 0.54559724 0.05622223 0.204266591 3.131148214 0.027642205 0.015638762 95.55326082 -1.980245512 0.135946167 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 ; 179.08 2.69E-20 113682000 37886.9 43484.9 42544.6 57483 42790 52944 42868 14522.6 51381 39701 FALSE TRUE 36406.23806 42244.75323 50233.35562 60449.70452 44166.37921 54014.56395 43392.63141 14222.70323 45548.44429 37012.01591 0.983632941 1.141379419 1.357217498 1.633245394 1.193298396 1.45937914 1.172393082 0.384272591 1.230639379 1 15.1757061 1.98026543 23.30810908 0.797000407 1.302557183 0.335366753 0.260030737 287.8606151 339985.4949 0.104276494 0.06847085 95.55764314 -1.98026543 0.505556777 VHDAES(ph)S(ph)DEDGYDWGPATDL ddPTM_BT-474_Pertuzumab_2h_R1 2 VHDAESSDEDGYDWGPATDL 20 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 VHDAES(1)S(1)DEDGYDWGPATDL;VHDAES(1)S(1)DEDGYDWGPATDL 195.6 2.68E-21 104599000 108986 110176 84479 97554 97065 125550 100296 66690 119096 101605 TRUE FALSE 104726.7066 107033.8884 99746.23453 102588.7736 100187.1839 128088.707 101523.4524 65312.82819 105576.7214 94723.20285 1.105607744 1.129964836 1.053028524 1.083037424 1.05768366 1.352242145 1.071790748 0.689512456 1.114581414 1 16.53143024 1.980274708 24.85884657 0.895312372 1.128851678 0.303720343 0.128354907 680.4972582 857597.6752 0.050926164 0.033390814 95.5596846 -1.980274708 0.233539306 YHIEVNR ddPTM_BT-474_Pertuzumab_2h_R1 4 YHIEVNR 7 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 170.06 0.00098884 2027410000 2139740 2278120 2129500 2478880 2198320 2278380 2026480 1049360 2275650 2372100 FALSE TRUE 2056116.595 2213150.248 2514348.02 2606815.294 2269030.959 2324450.405 2051280.668 1027690.349 2017327.752 2211435.554 0.92976555 1.000775376 1.136975489 1.178788723 1.026044352 1.051104745 0.927578769 0.464716391 0.912225431 1 21.07655177 1.980277682 10.24104888 0.723539545 1.053938903 0.359994457 0.148505437 0.370719576 187.492339 0.059001118 0.039189784 95.56033898 -1.980277682 0.330399358 EGNTTEDDFPSS(ph)PGNGNK ddPTM_BT-474_Pertuzumab_2h_R1 5 EGNTTEDDFPSSPGNGNK 18 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 EGNTTEDDFPS(0.02)S(0.98)PGNGNK;EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPS(0.002)S(0.998)PGNGNK;EGNTTEDDFPS(0.001)S(0.999)PGNGNK;EGNTTEDDFPS(0.238)S(0.762)PGNGNK 414.06 1.50E-147 2473070000 3940480 3612130 3005170 3211960 3408470 3545180 3703200 4284590 4612390 4179580 TRUE FALSE 3786481.685 3509115.589 3548271.069 3377729.641 3518106.533 3616865.969 3748520.869 4196111.719 4088810.824 3896493.324 0.971766501 0.900582985 0.910631887 0.866863962 0.90289043 0.928236152 0.962024199 1.076894369 1.049356558 1 21.89374491 1.980438826 2.940704517 1.048522057 0.910197138 0.77276676 0.030969885 0.110893362 1.823597235 0.015407305 0.008793845 95.59580307 -1.980438826 -0.13832492 DINELNLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DINELNLPK 9 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 97.965 0.011482 0 50769 56037 51099 48981 56362 51565 58123 82227 58903 76474 FALSE TRUE 48784.89135 54438.87963 60333.72599 51508.91528 58174.93492 52607.67963 58834.32666 80528.98372 52216.57838 71294.34786 0.684274319 0.763579179 0.846262401 0.722482452 0.815982426 0.737894114 0.82523129 1.129528302 0.732408388 1 16.12150009 1.980560011 20.67913632 0.970623447 0.767618903 0.418460293 0.100631745 67.65414391 71965.54295 0.038395558 0.025312672 95.62248184 -1.980560011 -0.203004544 HNYECLVYVQLPFMEDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNYECLVYVQLPFMEDLR 18 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 166.25 2.61E-11 2114400000 601290 582070 470800 515190 542440 569290 495780 336770 543270 530970 FALSE TRUE 577790.922 565469.9335 555884.0329 541779.0176 559888.0752 580801.4339 501847.5039 329815.5818 481600.2672 495006.929 1.167238049 1.142347512 1.122982327 1.094487745 1.131071188 1.173319806 1.01381915 0.666284778 0.972916214 1 18.91708919 1.980606512 7.497420885 0.841347671 1.132608638 0.627230779 0.088122854 0.095595981 26.47037099 0.034420716 0.02270197 95.6327209 -1.980606512 0.291260967 AAAYNLVQHGITNLCVIGGDGSLTGANIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAYNLVQHGITNLCVIGGDGSLTGANIFR 30 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 264.99 1.46E-58 328360000 71507 67229 58972 77895 59147 72993 71752 92568 77503 73918 FALSE TRUE 68712.42738 65311.69474 69629.55223 81915.17028 61049.51697 74468.96847 72630.12244 90656.43845 68705.18436 68911.46802 0.997111647 0.947762348 1.010420388 1.188701571 0.885912298 1.080646961 1.05396278 1.315549372 0.997006541 1 16.07245647 1.980646932 24.00107051 1.150623786 1.020794631 0.059907021 0.113779058 687.1036173 852122.8984 0.044896455 0.029495733 95.64162176 -1.980646932 -0.129829155 YPESNRT(ph)PVKPSSVEEEDSFFR ddPTM_BT-474_Pertuzumab_2h_R1 3 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 YPES(0.173)NRT(0.827)PVKPSSVEEEDSFFR;YPES(0.298)NRT(0.702)PVKPSSVEEEDSFFR;YPES(0.117)NRT(0.835)PVKPS(0.042)S(0.006)VEEEDSFFR 246.76 2.60E-29 3827110000 1703650 1506240 1310720 1525370 1415420 1449180 1538330 1797510 1770760 1598080 TRUE FALSE 1637069.475 1463283.51 1547596.261 1604094.529 1460948.27 1478483.413 1557156.543 1760390.79 1569750.748 1489840.618 1.098821884 0.982174531 1.038766323 1.07668868 0.980607088 0.992376899 1.045183306 1.181596722 1.053636697 1 20.50672657 1.98068222 24.52916096 1.102288928 1.026004288 0.092632009 0.056803807 767.2438427 974222.5977 0.022182907 0.014568781 95.64939339 -1.98068222 -0.07628464 KIPEPS(ph)PVTR ddPTM_BT-474_Pertuzumab_2h_R1 8 KIPEPSPVTR 10 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 KIPEPS(1)PVTR;KIPEPS(0.999)PVT(0.001)R;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(0.995)PVT(0.005)R;KIPEPS(0.999)PVT(0.001)R;KIPEPS(1)PVTR;KIPEPS(1)PVTR 152.99 1.04E-05 10838470000 4739620 5164620 4416280 4822420 4861630 4986680 5089320 6131360 5584200 5724800 TRUE FALSE 4554390.41 5017330.094 5214400.036 5071305.674 5018008.744 5087514.086 5151604.621 6004745.273 4950305.027 5337054.197 0.85335285 0.940093525 0.977018378 0.950206891 0.940220683 0.953243849 0.965252446 1.125104796 0.927535087 1 22.34761223 1.980778453 23.23157001 1.034880051 0.940351823 0.291630203 0.05482402 305.2134445 368886.4291 0.021627483 0.0142282 95.67059023 -1.980778453 -0.094528228 MIMDTAGNDPYCFVEFHEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 MIMDTAGNDPYCFVEFHEHR 20 0 C9JTN7;P31483-2;H7BY49;F8W8I6;P31483-3;P31483;E5RGV5;E5RG67 C9JTN7 TIA1 Nucleolysin TIA-1 isoform p40 0 ;;; 193.18 4.79E-18 802107000 157089.4 196505 103642 204661 155988.8 173313 133814.3 12249.4 167825 127401.5 FALSE TRUE 150950.1726 190900.8698 122372.4149 215223.5787 161006.3214 176817.5076 135451.9594 11996.44561 148774.2096 118772.4829 1.270918725 1.607281965 1.030309478 1.812066006 1.355586054 1.488707681 1.140432162 0.101003577 1.252598295 1 16.85784111 1.980797197 11.55392225 0.668510225 1.422155142 0.40862749 0.338332527 0.636172169 379.7458528 0.128924427 0.08581124 95.67471945 -1.980797197 0.753644917 SQEPIPDDQKVS(ph)DDDKEKGEGALPTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQEPIPDDQKVSDDDKEKGEGALPTGK 27 3 E5RJU9;Q86UE4;H0YBJ8 E5RJU9 MTDH Protein LYRIC 1 SQEPIPDDQKVS(1)DDDKEKGEGALPTGK;SQEPIPDDQKVS(1)DDDKEKGEGALPTGK 253.21 4.67E-52 3265580000 2206950 1619200 1110960 940060 1244800 933410 1565080 2973180 2450660 1055700 TRUE FALSE 2120699.954 1573022.001 1311735.185 988576.6093 1284840.122 952284.1897 1584233.917 2911782.794 2172471.351 984196.4987 2.154752589 1.598280428 1.332798061 1.004450443 1.305471137 0.967575267 1.609672377 2.958538054 2.207355293 1 19.90858686 1.98088432 23.33249666 2.275711477 1.371176268 0.191422143 0.553814434 340.3514648 415430.0724 0.219252916 0.144246824 95.6939145 -1.98088432 -0.904535209 ASEDTTSGS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASEDTTSGSPPK 12 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTTSGS(1)PPK;ASEDTTS(0.002)GS(0.998)PPK;ASEDTTS(0.001)GS(0.999)PPK 228.93 9.86E-12 1473840000 1614030 1364360 1244970 1178140 1291760 1352500 1468720 1628380 1864440 1645800 TRUE FALSE 1550951.923 1325449.789 1469963.773 1238943.947 1333310.634 1379848.477 1486694.635 1594753.384 1652796.588 1534328.5 1.010834331 0.863863109 0.958050231 0.807482848 0.868986422 0.899317504 0.968954585 1.039381973 1.077211684 1 20.54917597 1.980928658 2.407444902 1.043972854 0.896188967 0.55958783 0.05458618 0.205405489 2.212868196 0.028886019 0.015590429 95.70368453 -1.980928658 -0.147783887 AQAVS(ph)EEEEEEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQAVSEEEEEEEGK 14 0 G3V529;Q9GZR7;Q9GZR7-2 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 AQAVS(1)EEEEEEEGK;AQAVS(1)EEEEEEEGK 255.19 2.96E-24 1805990000 850230 713480 765070 772120 752210 644670 789160 936560 976800 825770 TRUE FALSE 817002.0716 693132.249 903335.1679 811969.2057 776405.5178 657705.6691 798817.9761 917219.7087 865917.7591 769839.8624 1.061262363 0.900359 1.17340659 1.054724814 1.008528599 0.854340885 1.037641742 1.191442212 1.124802445 1 19.55419885 1.980934754 24.10159888 1.123650212 1.007786197 0.168202251 0.093523326 690.523765 872934.1143 0.038331327 0.025185108 95.70502787 -1.980934754 -0.115864015 TQS(ph)VEITK ddPTM_BT-474_Pertuzumab_2h_R1 4 TQSVEITK 8 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 TQS(1)VEITK;T(0.001)QS(0.999)VEITK;T(0.004)QS(0.996)VEITK;TQS(1)VEITK 118.97 0.001872 1783030000 2790310 2203690 1508850 1927410 2214750 1799440 2218550 3241460 2503220 2343200 TRUE FALSE 2681261.6 2140842.919 1781532.759 2026883.861 2285989.445 1835825.91 2245701.279 3174522.718 2219064.96 2184492.977 1.22740683 0.98001822 0.815536043 0.92785094 1.046462254 0.840389934 1.028019455 1.453208022 1.01582609 1 21.05886704 1.98095347 24.6888686 1.215179331 0.96463622 0.179835565 0.16053136 721.6011245 935367.2709 0.063579898 0.041790459 95.70915227 -1.98095347 -0.250543112 LHHQNQQQIQQQQQQLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHHQNQQQIQQQQQQLQR 18 0 H7C308;G3V1P5;Q96RN5-3;Q96RN5-2;Q96RN5 H7C308 MED15 Mediator of RNA polymerase II transcription subunit 15 0 211.13 1.95E-16 90392000 34261 33844 27562 37759 34292 34195 29701 2656.3 38599 26593 FALSE TRUE 32922.04224 32878.80226 32543.06651 39707.74652 35395.03332 34886.44633 30064.48972 2601.446477 34217.40334 24791.83242 1.327939044 1.326194922 1.31265273 1.601646294 1.427689278 1.407174981 1.212677192 0.104931593 1.380188554 1 14.59757729 1.980953506 22.96755198 0.71139186 1.395747112 0.390359336 0.309558269 203.3776013 245245.636 0.119942745 0.078968018 95.70916039 -1.980953506 0.684355252 QAAPCVLFFDELDSIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAAPCVLFFDELDSIAK 17 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 226.88 4.49E-15 192761000 123888 123092 112494 117271 122151 117435 130159 157760 144896 152532 FALSE TRUE 119046.32 119581.5367 132824.1682 123323.3704 126080.0978 119809.6162 131751.9248 154502.2009 128448.0135 142200.8718 0.837170114 0.840933921 0.934060154 0.867247639 0.88663379 0.842537846 0.926519811 1.086506707 0.903285697 1 17.11757078 1.980986942 8.223578099 1.006497745 0.871703167 0.575748352 0.049213801 0.134899848 48.38431777 0.019287388 0.01277925 95.71652907 -1.980986942 -0.134794579 KVEEVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEEVTK 7 1 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 93.551 0.040698 0 216320 226770 179030 185970 182300 201380 214300 230130 270140 230400 FALSE TRUE 207865.9752 220302.7416 211384.7035 195567.934 188163.8451 205452.0416 216922.6675 225377.7351 239474.8397 214794.8028 0.967742108 1.025642794 0.984123921 0.910487272 0.87601675 0.956503784 1.0099065 1.049269964 1.114900531 1 17.71259956 1.981052655 2.444056621 1.060565597 0.952761827 0.498337449 0.045816128 0.260735151 2.897161183 0.02684847 0.014556955 95.73101314 -1.981052655 -0.10780377 FDVHDVTLHADAIHR ddPTM_BT-474_Pertuzumab_2h_R1 1 FDVHDVTLHADAIHR 15 0 P13639 P13639 EEF2 Elongation factor 2 0 128.06 2.58E-05 80688000 54746 61151 47753 55876 57301 58498 49883 2110.3 65502 51784 FALSE TRUE 52606.4658 59407.03335 56383.02936 58759.76706 59144.1387 59680.86964 50493.48308 2066.721568 58066.48757 48276.62356 1.089688175 1.230554852 1.167915757 1.217147404 1.225109263 1.236227086 1.045919937 0.042809986 1.202786842 1 15.55903716 1.981070741 24.57661714 0.617724541 1.192616799 0.293121052 0.288991743 518.312943 672945.832 0.11130153 0.073185494 95.73499991 -1.981070741 0.574892258 LFIGGLS(ph)FETTDDSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 LFIGGLS(1)FETTDDSLR;LFIGGLS(1)FETTDDSLR;LFIGGLS(1)FETTDDSLR;LFIGGLS(1)FETTDDSLR 199.58 3.96E-11 191605000 105872 93053 63295 113708 99823 70576 93692 147802 61581 48577 TRUE FALSE 101734.4052 90399.21955 74733.81449 119576.4835 103033.8975 72003.09508 94838.63072 144749.837 54590.58305 45286.83652 2.246445391 1.99614781 1.650232611 2.640424739 2.275140093 1.589934308 2.094176542 3.196289433 1.205440416 1 15.46680414 1.981147848 24.89354608 2.194764671 2.060042877 0 0.649627729 6162.51035 8137349.827 0.261100275 0.17172615 95.7519986 -1.981147848 -0.134721794 NFQAATESVPNSGNIHNGSLEQTEEPETSSHS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFQAATESVPNSGNIHNGSLEQTEEPETSSHSPSR 35 0 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312 E7EUR8 FAM193A Protein FAM193A 1 NFQAATESVPNSGNIHNGSLEQTEEPET(0.006)S(0.091)S(0.263)HS(0.542)PS(0.098)R;NFQAATESVPNSGNIHNGSLEQTEEPET(0.002)S(0.001)S(0.01)HS(0.94)PS(0.047)R 226.34 1.27E-36 609740000 87611 106963 87535 122582 100275 100615 100202 82044 108733 121310 TRUE FALSE 84187.06526 103912.52 103354.5217 128908.4717 103500.4364 102649.5042 101428.302 80349.76273 96390.08569 113093.5656 0.744401901 0.918819027 0.913885075 1.139839132 0.915175287 0.907651144 0.896852986 0.710471566 0.852303888 1 16.78715733 1.981177017 20.38253093 0.817481954 0.929647554 0.040092411 0.1120411 123.2933695 133506.4529 0.045568891 0.030120542 95.75842999 -1.981177017 0.1121656 SEDDSAKFDS(ph)NEEDSASVFSPSFGLK ddPTM_BT-474_Pertuzumab_2h_R1 11 SEDDSAKFDSNEEDSASVFSPSFGLK 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 SEDDSAKFDS(1)NEEDSASVFSPSFGLK;SEDDS(0.022)AKFDS(0.975)NEEDS(0.003)ASVFSPSFGLK;SEDDS(0.007)AKFDS(0.993)NEEDSASVFSPSFGLK;S(0.025)EDDS(0.025)AKFDS(0.899)NEEDS(0.048)AS(0.002)VFSPSFGLK;SEDDS(0.001)AKFDS(0.999)NEEDSASVFSPSFGLK;SEDDS(0.004)AKFDS(0.996)NEEDSASVFSPSFGLK;S(0.001)EDDS(0.15)AKFDS(0.82)NEEDS(0.024)AS(0.005)VFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;S(0.027)EDDS(0.021)AKFDS(0.939)NEEDS(0.013)ASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;SEDDS(0.037)AKFDS(0.963)NEEDSASVFSPSFGLK 382.8 5.71E-145 14485710000 3986683 3280146 2480183 2611213 3142411 3001834 3243599 4101283 3972779 3220207 TRUE FALSE 3830879.021 3186599.448 2928407.239 2745978.016 3243489.504 3062533.14 3283295.135 4016590.073 3521805.783 3002099.512 1.276066635 1.061456969 0.975453088 0.914685874 1.080407059 1.020130455 1.093666323 1.337927026 1.173114272 1 21.51754037 1.981196968 21.11092872 1.209870247 1.047099922 0.13517805 0.117868744 128.8670181 144682.7098 0.047481392 0.031356129 95.76282904 -1.981196968 -0.162770325 LHVGEESKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHVGEESKK 9 1 P78356;P78356-2 P78356 PIP4K2B Phosphatidylinositol 5-phosphate 4-kinase type-2 beta 0 90.906 0.0072143 109010000 340890 327630 261990 260810 283590 362700 299210 209700 387200 331440 FALSE TRUE 327567.6419 318286.3132 309337.4209 274270.4354 292711.9299 370034.0425 302871.8215 205369.6217 343246.6793 308991.2736 1.060119395 1.030081884 1.00112025 0.887631654 0.947314552 1.197554993 0.980195389 0.664645378 1.110862049 1 18.23720657 1.981299498 24.94835422 0.871535729 1.017306958 0.05255534 0.131546897 1180.378253 1574742.521 0.053048421 0.034896929 95.78543999 -1.981299498 0.145771229 RPLEDGDGSWTS(ph)PSSTTHWEGMPSPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPLEDGDGSWTSPSSTTHWEGMPSPFK 27 1 C9JSZ1 C9JSZ1 FUBP1 1 RPLEDGDGS(0.007)WT(0.197)S(0.771)PS(0.008)S(0.008)T(0.008)T(0.002)HWEGMPSPFK 116.82 0.00027665 40926000 45197 54428 40681 57827 53817 50150 47388 46222 45407 50768 TRUE FALSE 43430.65127 52875.76673 48032.96164 60811.4584 55548.07268 51164.06736 47967.94852 45267.49955 40252.58772 47329.43814 0.917624484 1.1171856 1.014864396 1.284854855 1.173647414 1.081019961 1.013490766 0.956434332 0.850476771 1 15.53045018 1.98138757 2.002582632 0.926204142 1.108206411 0.366028534 0.096293369 0.349868759 2.606158916 0.057769772 0.029506213 95.80486649 -1.98138757 0.182002269 KLS(ph)PQDPSEDVSSVDPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSPQDPSEDVSSVDPLK 18 1 Q53T59;H7BZZ1;H7C0Y9;F8WDN8 Q53T59 HS1BP3 HCLS1-binding protein 3 1 KLS(0.994)PQDPS(0.006)EDVSSVDPLK 121.5 2.33E-05 348490000 302530 240080 262160 248670 262320 255030 303650 377310 372160 384110 TRUE FALSE 290706.7931 233233.1535 309538.1437 261503.8885 270757.761 260186.8813 307366.1595 369518.4166 329913.957 358093.8876 0.811817245 0.651318443 0.864404991 0.730266273 0.756108301 0.726588446 0.858339587 1.031903725 0.921305748 1 18.44997837 1.981412487 3.865906674 0.983012086 0.756485826 0.751889361 0.058530483 0.099556934 3.183388152 0.024922125 0.015206468 95.81036334 -1.981412487 -0.22652626 EES(ph)DGEYDEFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESDGEYDEFGR 12 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EES(1)DGEYDEFGR;EES(1)DGEYDEFGR 304.26 8.80E-37 8205600000 2451570 2211440 2484720 2592800 2435550 2217960 2769400 3432100 3388900 3313500 TRUE FALSE 2355759.934 2148371.896 2933764.176 2726614.719 2513891.678 2262808.671 2803292.746 3361225.936 3004206.279 3089073.694 0.762610468 0.695474472 0.949722948 0.882664186 0.813801135 0.732520132 0.907486523 1.08810157 0.972526582 1 21.55874286 1.981416068 5.544608562 1.024050817 0.811570593 0.631722544 0.073289711 0.116426226 11.52633991 0.032595398 0.021060454 95.81115338 -1.981416068 -0.212480224 GFGSSAPEGLEPDSMASAAS(ph)ALHLLSPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMAS(0.086)AAS(0.457)ALHLLS(0.457)PRPR 125.82 8.35E-06 1694400000 69952 91373 90922 91384 85847 87253 68213 53722 52314 53706 TRUE FALSE 67218.1985 88767.1315 107353.6279 96100.33919 88608.34672 89017.31544 69047.8111 52612.62193 46375.53404 50068.44478 1.342526192 1.772915693 2.144137458 1.919379354 1.769744339 1.777912532 1.379068421 1.050813984 0.926242751 1 15.61161402 1.981424899 1.830939023 0.962644912 1.819114362 0.783272575 0.188240295 0.160031753 0.998237311 0.121300514 0.060313184 95.81310157 -1.981424899 0.85646945 IAEGEHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IAEGEHPK 8 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 ; 92.439 0.011777 543720000 710740 1012130 590620 982350 665320 526710 808990 1151780 975120 691450 FALSE TRUE 682963.495 983265.0434 697358.1723 1033049.201 686720.622 537360.4371 818890.6616 1127995.341 864428.4656 644617.4756 1.059486472 1.525346551 1.081817044 1.602577095 1.065314932 0.833611339 1.270351321 1.749867764 1.340994463 1 19.29808377 1.981520116 24.8314227 1.462731947 1.203478282 0.034643706 0.276711521 1300.16862 1747035.403 0.110758327 0.072942887 95.83411035 -1.981520116 -0.259253665 IDS(ph)PGFKPASQQK ddPTM_BT-474_Pertuzumab_2h_R1 3 IDSPGFKPASQQK 13 1 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 IDS(1)PGFKPASQQK;IDS(1)PGFKPASQQK;IDS(1)PGFKPASQQK 138.55 2.90E-05 2384370000 3589900 3118240 2799430 2480890 2823640 2815750 3619920 4307740 4836370 4520640 TRUE FALSE 3449602.739 3029310.848 3305349.274 2608929.03 2914464.945 2872686.394 3664221.664 4218783.664 4287365.553 4214453.026 0.818517306 0.718790986 0.78428903 0.619043329 0.691540498 0.681627337 0.869441809 1.001027568 1.017300591 1 22.00691397 1.981544928 2.705768717 1.005926869 0.716169129 0.856113922 0.052846663 0.098921478 1.35931398 0.028107868 0.015699243 95.83958585 -1.981544928 -0.28975774 EGLELPEDEEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGLELPEDEEEK 12 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;Q58FG0 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AA5P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ;;; 300.5 4.06E-36 9360600000 7980300 6530040 7735000 7595000 7714500 7027700 9121300 11252600 11925400 11504000 FALSE TRUE 7668421.053 6343809.653 9132886.564 7986978.86 7962643.899 7169804.909 9232929.198 11020229.88 10571678.59 10724823.83 0.715016039 0.591507119 0.851565182 0.744718886 0.742449855 0.668524259 0.86089332 1.02754414 0.985720488 1 23.35445061 1.981567563 3.378650048 1.002328533 0.721910136 0.805361679 0.062927672 0.103232207 2.341930391 0.030365835 0.017976865 95.84458104 -1.981567563 -0.280418396 TQTPPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 5 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPTEERLPS(0.191)S(0.809)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.265)S(0.735)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.181)S(0.712)PVY(0.106)EDAASFK;TQTPPVSPAPQPTEERLPS(0.076)S(0.924)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.29)S(0.71)PVYEDAASFK 310.89 1.87E-92 16915400000 4012590 3998930 2925950 2946360 3051920 3603650 3791930 4198890 4894870 4415470 TRUE FALSE 3855773.547 3884884.432 3454734.252 3098421.993 3150087.778 3676518.272 3838336.774 4112181.454 4339224.879 4116406.284 0.936684399 0.943756316 0.839259785 0.752700725 0.765251912 0.893137853 0.932448478 0.998973661 1.054129398 1 21.97295395 1.981579817 1.815699682 1.02404175 0.847839643 0.601897533 0.059891409 0.270418112 1.659127661 0.042062587 0.020865958 95.84728542 -1.981579817 -0.176202106 KYVATLGVEVHPLVFHTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYVATLGVEVHPLVFHTNR 19 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 150.13 3.20E-08 3820400000 2858600 2971300 1995370 2194000 2367000 2679100 2286900 960680 2603900 2360300 FALSE TRUE 2746882.752 2886561.433 2355977.746 2307232.603 2443136.705 2733273.238 2314887.766 940841.6223 2308316.188 2200434.779 1.248336364 1.311814129 1.070687379 1.048534874 1.11029726 1.242151444 1.052013806 0.427570783 1.049027315 1 21.06935718 1.981588703 22.94102781 0.756395003 1.163790197 0.41846568 0.176950692 194.1391343 241902.3389 0.069804658 0.046078629 95.84924638 -1.981588703 0.407395194 THTDSSEKELEPEAAEEALENGPK ddPTM_BT-474_Pertuzumab_2h_R1 4 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;;; 133.53 2.49E-05 611648000 1113930 996880 667920 653830 851820 854830 775420 247875 1079530 711410 FALSE TRUE 1070396.384 968449.9584 788628.0018 687574.2447 879219.5639 872115.2483 784909.8219 242756.2946 956986.2802 663225.567 1.613925092 1.46021204 1.189079615 1.036712514 1.325672 1.314960236 1.183473408 0.366023728 1.442927305 1 19.3391401 1.981614076 24.23202134 0.843093485 1.305491488 0.249555646 0.285897941 550.5453587 725599.071 0.114485019 0.075463716 95.85484647 -1.981614076 0.462398004 DDSFFGETSHNYHKFDSEYER ddPTM_BT-474_Pertuzumab_2h_R1 1 DDSFFGETSHNYHKFDSEYER 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 106.49 0.00023587 461980000 218100 229480 158770 164940 185470 224000 171960 8134.4 215570 163580 FALSE TRUE 209576.4109 222935.4551 187463.2708 173452.5732 191435.811 228529.4335 174064.4979 7966.421797 191099.3973 152500.5809 1.374266312 1.461866268 1.229262667 1.13738959 1.255312012 1.498547954 1.141402196 0.052238632 1.253106029 1 17.21845521 1.981626574 24.56918109 0.646561057 1.316404835 0.378518968 0.307748384 472.7007208 632100.88 0.119510358 0.078750903 95.857605 -1.981626574 0.669843778 HIEPELAGRDS(ph)PIRAEMPGNLQHYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 HIEPELAGRDSPIRAEMPGNLQHYGR 26 2 P86791;P86790 P86791 CCZ1;CCZ1B Vacuolar fusion protein CCZ1 homolog;Vacuolar fusion protein CCZ1 homolog B 1 HIEPELAGRDS(1)PIRAEMPGNLQHYGR;HIEPELAGRDS(1)PIRAEMPGNLQHYGR;HIEPELAGRDS(1)PIRAEMPGNLQHYGR;HIEPELAGRDS(1)PIRAEMPGNLQHYGR 243.92 1.46E-45 4542070000 849717 1016586 613260 727973 901683 981326 794959 398751 941370 849942 TRUE FALSE 816509.1202 987593.9626 724089.7239 765543.7738 930686.4526 1001169.084 804687.946 390516.6525 834509.6241 792374.6713 1.03045838 1.246372453 0.9138224 0.966138623 1.174553511 1.263504653 1.015539713 0.492843432 1.053175542 1 19.59582324 1.981643261 24.39996235 0.782789541 1.098520072 0.262762035 0.177620245 544.5219512 723783.3348 0.070771255 0.046636502 95.86128826 -1.981643261 0.315730531 KEES(ph)DEEETASK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEESDEEETASK 12 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KEES(1)DEEETASK;KEES(1)DEEETASK 234.04 3.18E-16 625110000 959190 757670 664820 638380 696700 730220 871180 1115910 1194070 1001810 TRUE FALSE 921703.7944 736061.9934 784967.7628 671326.8683 719109.9882 744985.5487 881841.7614 1092866.069 1058524.18 933956.5164 0.986880843 0.788111631 0.840475706 0.718798848 0.769960887 0.797666204 0.94420002 1.170146628 1.133376299 1 19.83299586 1.981800376 3.454132475 1.114134001 0.811176416 0.728029899 0.07752512 0.113501975 2.71837511 0.036349932 0.021639561 95.89597429 -1.981800376 -0.302957585 VNPQISDEKDEDEKEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNPQISDEKDEDEKEEK 17 2 P26358;P26358-2 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 119.38 6.92E-05 449990000 629320 359692 421744 308911 440095 349488 524048 676910 731740 632250 FALSE TRUE 604725.4786 349433.9363 497962.5224 324853.9337 454251.0554 356554.8868 530461.4562 662931.5719 648675.9429 589427.1444 1.025954581 0.592836519 0.844824551 0.551135008 0.770665314 0.604917656 0.899961024 1.124704857 1.100519291 1 19.16895398 1.981814478 4.161208309 1.078451774 0.724370137 0.56931011 0.13385234 0.137454723 5.397917441 0.055589955 0.034441161 95.89908816 -1.981814478 -0.354081638 DFDWNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFDWNLK 7 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739;Q9Y5A9;Q9Y5A9-2 A0A024R7W5;Q9Y5A9 YTHDF3;YTHDF2 YTH domain-containing family protein 3;YTH domain-containing family protein 2 0 ; 127.12 0.0090405 1021930000 1119260 1218040 970560 960910 960830 979430 1104170 1218670 1287200 1291760 FALSE TRUE 1075518.082 1183302.692 1145961.782 1010502.68 991735.9696 999234.7457 1117683.163 1193504.039 1141082.452 1204267.945 0.893088691 0.982590874 0.951583729 0.839101202 0.823517701 0.829744535 0.92810173 0.991061868 0.947532032 1 20.19972499 1.981889068 6.319361544 0.974465247 0.888006395 0.412137323 0.049626286 0.198362084 31.69608579 0.023563172 0.015426589 95.91556035 -1.981889068 -0.086458852 VQENSPGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQENSPGHR 9 0 Q9H8Y8;F8WEG2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ; 117.53 0.0011373 576730000 585180 550630 488840 514160 567060 536450 535350 485510 625420 587720 FALSE TRUE 562310.5186 534926.5715 577184.2622 540695.8592 585299.9999 547297.3866 541901.7734 475484.0488 554424.9436 547913.2009 1.02627664 0.976298017 1.053422807 0.986827582 1.068234894 0.998876073 0.989028504 0.867809076 1.011884625 1 19.06358784 1.981910188 13.05087772 0.941008582 1.016778022 0.218906494 0.045605472 1.691735979 1217.7319 0.017515014 0.011695404 95.92022482 -1.981910188 0.07576944 DEDDADYKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DEDDADYKPK 10 1 P11387 P11387 TOP1 DNA topoisomerase 1 0 ; 91.936 0.0089464 781200000 2724670 2072970 1507820 1686420 1759990 1745890 2072040 2879680 2638770 2046410 FALSE TRUE 2618186.884 2013850.925 1780316.615 1773456.338 1816601.677 1781193.092 2097398.245 2820213.602 2339227.892 1907804.828 1.372355728 1.055585401 0.933175443 0.929579542 0.952194716 0.933634859 1.099377785 1.478250584 1.226135849 1 20.86348216 1.981950321 20.25555832 1.288154885 1.018046729 0.213493629 0.166268284 69.16404284 77615.32827 0.066916679 0.044370849 95.92908921 -1.981950321 -0.270108157 AAGNESFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGNESFR 8 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 132.08 0.0039202 0 125060 115510 123430 134850 117280 107750 127530 148070 145260 152860 FALSE TRUE 120172.5169 112215.7679 145736.5467 141809.6247 121052.4177 109928.7788 129090.7503 145012.3028 128770.6938 142506.656 0.84327652 0.787442292 1.022664841 0.99510878 0.849450974 0.771393996 0.90585769 1.017582664 0.903611785 1 17.12066978 1.98199192 23.50771608 0.972193919 0.880830463 0.222046669 0.079878665 576.2860148 752281.0305 0.034885405 0.023047811 95.93827831 -1.98199192 -0.091363455 HLCICSVDPPGCTDIDDALHCR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLCICSVDPPGCTDIDDALHCR 22 0 Q9Y2L1;G3V1J5;Q9Y2L1-2;F2Z2C0 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 ; 117.66 7.17E-05 424660000 132537 142297 86739 138117 123657 157636 119317 43172 143086 126612 FALSE TRUE 127357.3075 138238.8289 102414.6668 145245.2349 127634.5397 160823.5079 120777.2371 42280.48311 126843.4771 118036.4565 1.078965866 1.171153667 0.867652841 1.230511651 1.081314566 1.362490139 1.023219781 0.358198512 1.074612717 1 16.84887299 1.982043908 24.71532734 0.727396585 1.129692047 0.282318397 0.216987456 594.468243 818243.8475 0.084079446 0.055471472 95.94976329 -1.982043908 0.402295462 MHEFHS(ph)QENLVVHIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 MHEFHSQENLVVHIPK 16 0 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 MHEFHS(1)QENLVVHIPK 144.27 2.23E-06 325490000 747120 717350 631700 622780 573710 695130 567570 0 765700 442080 TRUE FALSE 717921.7244 696891.8804 745862.2421 654921.7504 592163.9032 709186.0049 574516.0914 0 678780.9461 412137.5278 1.741946986 1.690920708 1.809741146 1.589085454 1.436811412 1.720750859 1.393991211 0 1.646976798 1 18.65276631 1.982051839 22.18397558 0.752659288 1.650378217 0.436057 0.389515367 126.3289774 156142.119 0.14979 0.09913338 95.95151563 -1.982051839 0.897718929 LWHLDPDTEYEIR ddPTM_BT-474_Pertuzumab_2h_R1 3 LWHLDPDTEYEIR 13 0 Q5TG12;E9PGC5;Q15262;Q15262-2;Q15262-3;Q15262-4;H0YDP9 Q5TG12 PTPRK Protein-tyrosine-phosphatase;Receptor-type tyrosine-protein phosphatase kappa 0 ;; 152.47 4.41E-05 595580000 397018 444608 387337 466487 384471 448642 407905 380417 443615 418381 FALSE TRUE 381502.0976 431928.2152 457337.4122 490562.45 396837.8589 457713.8486 412897.0634 372561.256 393257.685 390043.6822 0.978100954 1.107384211 1.172528701 1.257711565 1.017419015 1.173493815 1.058591851 0.955178286 1.00824011 1 18.57327618 1.982089569 5.052238035 0.986991519 1.12160519 0.371857179 0.075610247 0.192759847 13.88619568 0.032734944 0.020940582 95.95985194 -1.982089569 0.134613671 VWDLSDIDKDGHLDRDEFAVAMHLVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 VWDLSDIDKDGHLDRDEFAVAMHLVYR 27 2 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 0 ; 222.47 7.49E-35 601540000 454110 431550 383160 411800 429650 465620 422410 246990 587540 581100 FALSE TRUE 436362.8792 419242.6165 452405.5353 433053.0474 443470.0824 475035.1554 427579.5799 241889.5702 520844.9224 541741.5794 0.805481609 0.773879341 0.835094725 0.799371995 0.818600786 0.876866708 0.78926853 0.446503609 0.961426891 1 19.0472453 1.982095025 24.90538681 0.710329459 0.817540336 0 0.149256057 1714.436641 2384738.132 0.058608537 0.038689164 95.96105749 -1.982095025 0.107210877 LKPVELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKPVELR 7 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 94.302 0.013042 2598100000 5044500 5401500 4225200 5277900 4950900 4576100 5074200 5483000 5781600 5794600 FALSE TRUE 4847355.363 5247454.509 4988787.629 5550293.052 5110150.195 4668631.877 5136299.577 5369774.134 5125297.006 5402126.581 0.897305032 0.971368299 0.923485882 1.027427434 0.945951584 0.864221119 0.950792156 0.994011165 0.948755445 1 22.36509601 1.982095363 23.8899812 0.978293013 0.940521866 0.165350929 0.042548804 856.1277577 1142321.614 0.017621228 0.01163788 95.96113215 -1.982095363 -0.037771147 SWPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 SWPSPK 6 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.001)WPS(0.999)PK;SWPS(1)PK;S(0.002)WPS(0.998)PK;S(0.045)WPS(0.955)PK 103.56 0.036271 4730320000 13928900 11803000 10441000 10231300 11401700 11852300 13184600 15694000 16554600 16652400 TRUE FALSE 13384543.19 11466390 12327920.96 10759338.62 11768446.04 12091961.63 13345957.08 15369913.42 14675391.21 15524518.12 0.862155146 0.738598771 0.794093631 0.693054595 0.75805548 0.77889449 0.859669652 0.990041256 0.945304138 1 23.88804515 1.982113863 2.32275022 0.978961953 0.765009277 0.824005559 0.042879258 0.113611498 1.138590598 0.022901679 0.012243056 95.96521986 -1.982113863 -0.213952676 ERS(ph)ESLDPDSSMDTTLILK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSESLDPDSSMDTTLILK 19 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 ERS(0.585)ES(0.415)LDPDSSMDTTLILK 105.16 0.00020525 86370000 34765 31807 21148 24165 35247 22454 30307 45190 33171 27093 TRUE FALSE 33406.34537 30899.8955 24969.91403 25412.15855 36380.75177 22908.03526 30677.90613 44256.81071 29405.56714 25257.96698 1.322606265 1.223372235 0.988595561 1.006104671 1.440367382 0.906962753 1.214583349 1.75219212 1.164209581 1 14.6244509 1.982132784 24.90485367 1.41263005 1.143500513 0.025849412 0.239309478 1092.656219 1523036.409 0.093520442 0.061742382 95.96940092 -1.982132784 -0.269129537 ITKPGS(ph)IDSNNQLFAPGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 ITKPGS(1)IDSNNQLFAPGGR;ITKPGS(1)IDSNNQLFAPGGR;IT(0.001)KPGS(0.999)IDSNNQLFAPGGR 296.78 6.09E-50 2164380000 1315810 1092869 620295 1004428 1195296 984930 1199706 1599407 1385368 1586936 TRUE FALSE 1264386.69 1061701.446 732396.1049 1056266.649 1233743.781 1004845.959 1214388.361 1566378.687 1228106.833 1479451.411 0.854632116 0.717631845 0.495045731 0.713958324 0.833919771 0.679201731 0.820836934 1.058756425 0.830109609 1 20.49663089 1.982206927 4.873142628 0.965131773 0.712788341 0.522520383 0.105749086 0.149767364 9.57317031 0.046785935 0.029784496 95.98578643 -1.982206927 -0.252343432 S(ph)ASPYPS(ph)HSLSS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASPYPSHSLSSPQR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 3 S(1)AS(0.084)PY(0.026)PS(0.89)HSLS(0.115)S(0.885)PQR 304.49 8.49E-45 157830000 184500 186450 142720 156910 171960 172250 168980 161970 191840 183510 TRUE FALSE 177289.536 181132.6286 168512.6788 165008.1439 177491.2496 175733.013 171048.0278 158625.2629 170063.1275 171080.7042 1.03629183 1.058755453 0.984989392 0.964504703 1.037470885 1.02719365 0.999809 0.927195522 0.994052066 1 17.38431753 1.982223691 17.60582659 0.96512003 1.016681051 0.273131521 0.031490071 18.15236893 17976.67208 0.013185263 0.008779334 95.9894914 -1.982223691 0.051561021 HLEGLSEEAIMELNLPTGIPIVYELDK ddPTM_BT-474_Pertuzumab_2h_R1 3 HLEGLSEEAIMELNLPTGIPIVYELDK 27 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;; 215.07 3.02E-34 4381160000 4664200 4481400 3578600 4030300 4096700 4185200 4004300 2669930 5075600 3930700 FALSE TRUE 4481917.907 4353594.86 4225332.626 4238304.266 4228474.076 4269827.612 4053305.821 2614795.012 4499439.167 3664470.188 1.223073917 1.188055745 1.153054169 1.156594009 1.153911441 1.165196438 1.106109646 0.713553359 1.227855307 1 21.8051732 1.982268672 24.16275672 0.938939457 1.168440806 0.327284378 0.119150282 423.6149561 577265.9758 0.045885551 0.030335269 95.99943396 -1.982268672 0.229501348 ASTSKS(ph)ES(ph)SQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 AST(0.001)S(0.01)KS(0.99)ES(0.988)S(0.012)QK 133.16 0.0020026 98686000 393660 341840 285450 226260 344860 312550 346480 520000 413420 314340 TRUE FALSE 378275.332 332091.0579 337037.1648 237937.3057 355952.7351 318869.9751 350720.3259 509261.8183 366490.2948 293049.4718 1.290824138 1.13322524 1.150103301 0.811935624 1.214650663 1.088109708 1.196795625 1.737801522 1.250608959 1 18.16078471 1.982390442 24.1384162 1.425410767 1.110890218 0.126885019 0.210758094 545.6618443 747968.438 0.08215803 0.05432557 96.0263545 -1.982390442 -0.314520549 GNYDEGFGHRPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNYDEGFGHRPHK 13 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 146.77 2.55E-05 405410000 256810 280030 233560 278690 259080 292280 243600 54791 315210 276600 FALSE TRUE 246773.5813 272043.8186 275769.4875 293073.2243 267413.5435 298190.1019 246581.2497 53659.5467 279428.6823 257865.6356 0.956985139 1.054982832 1.069430934 1.136534628 1.037026678 1.156377821 0.95623928 0.208091111 1.083621249 1 17.97626 1.982437404 24.60922055 0.652476942 1.068525298 0.218813265 0.230238437 568.2196713 796205.3033 0.088627797 0.058595426 96.03673892 -1.982437404 0.416048356 QVDFLNWEVTDHNLHELR ddPTM_BT-474_Pertuzumab_2h_R1 1 QVDFLNWEVTDHNLHELR 18 0 Q9NV31 Q9NV31 IMP3 U3 small nucleolar ribonucleoprotein protein IMP3 0 142.78 6.37E-08 49658000 35729 39423 35796 48071 33646 43636 35607 6270.4 45677 37082 FALSE TRUE 34332.67118 38298.69464 42265.13348 50551.95007 34728.25415 44518.34982 36042.76912 6140.914049 40491.93845 34570.40311 0.993123253 1.107846342 1.222581448 1.462289864 1.004566074 1.28775906 1.042590363 0.177635014 1.171289161 1 15.07724981 1.982477931 24.32724791 0.671228731 1.181755515 0.26583974 0.276736257 484.7629041 673033.2256 0.107446877 0.071084695 96.04570113 -1.982477931 0.510526784 SHDDGNIDLESDSFLKFDSEPSAVALELPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHDDGNIDLESDSFLKFDSEPSAVALELPTR 31 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 0 136.45 8.27E-07 64833000 99529 102190 68007 68370 93314 103890 80428 34900 87134 77087 FALSE TRUE 95639.29664 99275.64125 80297.37771 71898.58389 96315.52956 105990.727 81412.30192 34179.3028 77242.91362 71865.82883 1.330803502 1.381402579 1.117323476 1.000455781 1.34021316 1.474841781 1.132837445 0.475598812 1.074821162 1 16.13301833 1.982507219 23.13081617 0.794959236 1.265924819 0.47843652 0.195351241 206.9808755 273691.3541 0.079313526 0.052545264 96.05217852 -1.982507219 0.470965582 HFFHHADEDDEEEDDS(ph)PPER ddPTM_BT-474_Pertuzumab_2h_R1 1 HFFHHADEDDEEEDDSPPER 20 0 A0A087WZV0;O43314-2;O43314;D6RFG4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 HFFHHADEDDEEEDDS(1)PPER 138.66 2.34E-06 556970000 67348 58810 56051 57237 47300 60452 44364 9453.7 52706 24111 TRUE FALSE 64715.9657 57132.79638 66180.66255 60191.00843 48821.44746 61674.38086 44906.9399 9258.477791 46723.03584 22477.94049 2.879087865 2.541727361 2.944249388 2.677781287 2.171971559 2.743773651 1.997822706 0.41189173 2.078617294 1 14.45622224 1.982703832 5.304484041 1.1122246 2.631169509 0.709201936 0.428665071 0.08837391 7.553222739 0.17396356 0.112117711 96.09567294 -1.982703832 1.518944909 KVFANPEDCVAFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVFANPEDCVAFGK 14 1 P10620;F5H7F6;F5H6X2;P10620-2 P10620 MGST1 Microsomal glutathione S-transferase 1 0 ; 168.5 5.58E-06 1967620000 2067630 3337200 1772890 3218900 2041330 2180400 2650900 3715500 3213000 2303900 FALSE TRUE 1986824.734 3242026.323 2093290.661 3385027.815 2106991.233 2224489.182 2683342.507 3638773.627 2848273.71 2147854.801 0.925027489 1.509425275 0.974595983 1.576004027 0.980974707 1.035679498 1.249312806 1.69414321 1.32610161 1 21.03446504 1.982740408 24.39123539 1.4308385 1.180463037 0.047282251 0.264381591 952.1615831 1345591.978 0.100651237 0.066628182 96.10376641 -1.982740408 -0.250375463 VEEAEPEEFVVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEEAEPEEFVVEK 13 0 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ; 231.92 3.77E-12 279280000 364850 344890 289370 305110 314030 337810 361990 417310 445590 448800 FALSE TRUE 350591.2586 335054.0749 341665.596 320856.7637 324131.0601 344640.7497 366420.1419 408692.4027 395008.4913 418402.3763 0.83792846 0.80079391 0.816595735 0.766861715 0.774687427 0.823706483 0.875760184 0.976792738 0.944087591 1 18.67453152 1.98282706 1.958332636 0.975547627 0.798831956 0.914399676 0.023346825 0.088375768 0.629955641 0.014069716 0.007146669 96.12294327 -1.98282706 -0.176715671 DHGDMTNRK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHGDMTNRK 9 1 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 102.07 0.002366 138099000 171413 178650 120501 149125 134769 145578 140061 79780 174300 142322 FALSE TRUE 164713.9905 173555.0769 142278.2112 156821.3591 139103.9673 148521.6869 141775.1084 78132.51512 154514.1947 132682.4042 1.24141548 1.308048931 1.072321625 1.18193034 1.048398001 1.119377417 1.068529842 0.588868702 1.164541717 1 17.01761753 1.982833454 22.19880561 0.861266362 1.154711861 0.31626645 0.153796417 155.0443402 200493.5413 0.060811643 0.040384829 96.12435841 -1.982833454 0.293445499 SSEDEELRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSEDEELRK 9 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 108.43 0.0041884 521430000 553820 555750 487890 513620 507790 556500 564510 605050 710510 626430 FALSE TRUE 532176.1021 539900.5541 576062.5761 540127.9898 524123.5265 567752.8113 571418.6422 592555.5061 629855.8835 584001.3381 0.911258361 0.924485132 0.98640626 0.924874576 0.897469736 0.972177244 0.978454337 1.014647514 1.078517877 1 19.15561215 1.982885422 1.501858754 1.038133028 0.932972821 0.678419138 0.029910676 0.233492303 0.980960732 0.020355462 0.009618308 96.13586145 -1.982885422 -0.105160207 DRQS(ph)PLHGNHITISHTQATGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRQSPLHGNHITISHTQATGSR 22 1 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 DRQS(1)PLHGNHITISHTQATGSR 181.92 2.41E-17 496080000 68296 62003 66037 90367 67192 84735 66156 14320 85048 65369 TRUE FALSE 65626.91681 60234.73515 77971.35489 95030.8517 69353.2917 86448.39976 66965.63692 14024.287 75393.70759 60941.49941 1.076883855 0.988402578 1.279445955 1.559378299 1.138030609 1.418547305 1.098851153 0.230127042 1.237148878 1 15.89513738 1.982955606 24.46297117 0.718785105 1.244363439 0.28160108 0.286748449 528.1995893 758097.9307 0.113445836 0.07518912 96.15139875 -1.982955606 0.525578333 HSS(ph)YPAGTEDDEGMGEEPSPFR ddPTM_BT-474_Pertuzumab_2h_R1 8 HSSYPAGTEDDEGMGEEPSPFR 22 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 1 HS(0.146)S(0.854)YPAGTEDDEGMGEEPSPFR;HS(0.412)S(0.588)YPAGTEDDEGMGEEPSPFR;HS(0.141)S(0.859)YPAGTEDDEGMGEEPSPFR;HS(0.127)S(0.873)YPAGTEDDEGMGEEPSPFR;HS(0.136)S(0.864)YPAGTEDDEGMGEEPSPFR;HS(0.129)S(0.871)YPAGTEDDEGMGEEPSPFR;HS(0.152)S(0.843)Y(0.005)PAGTEDDEGMGEEPSPFR;HS(0.121)S(0.879)YPAGTEDDEGMGEEPSPFR 332.17 5.53E-81 8134810000 2146050 2214910 1938340 2312200 2207370 2324260 1901620 981900 2088610 2022490 TRUE FALSE 2062179.993 2151742.935 2288641.156 2431532.919 2278372.061 2371258.13 1924892.594 961623.4219 1851519.749 1885504.951 1.093701712 1.141202485 1.213808086 1.289592434 1.208361749 1.257624982 1.020889706 0.510008431 0.981975544 1 20.84651951 1.983087353 7.618952335 0.772713275 1.198294175 0.582697121 0.138172606 0.099560112 31.23259841 0.054584642 0.036256365 96.18057139 -1.983087353 0.4255809 RPTETNPVTSNS(ph)DEECNETVK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPTETNPVTSNSDEECNETVK 21 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 RPTETNPVTSNS(1)DEECNETVK;RPTETNPVTSNS(1)DEECNETVK;RPTETNPVTSNS(1)DEECNETVK;RPTETNPVTSNS(1)DEECNETVK 384.32 3.26E-131 6308400000 1727050 1567250 1425200 1586740 1563600 1609390 1641870 1830920 1913440 1685600 TRUE FALSE 1659554.977 1522553.564 1682765.343 1668631.842 1613894.614 1641932.968 1661963.696 1793110.862 1696234.313 1571432.811 1.056077591 0.968895109 1.070847784 1.061853762 1.027021075 1.044863616 1.057610408 1.14106747 1.079418924 1 20.58364916 1.983109773 14.61087085 1.091713197 1.03832178 0.079128909 0.042327099 4.62822314 4000.882433 0.016396658 0.010986261 96.18553673 -1.983109773 -0.053391418 GWMDPQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GWMDPQSK 8 0 J3KN30;F5H8E7;Q99572-7;Q99572-5;Q99572-2;Q99572-8;Q99572 J3KN30 P2RX7 P2X purinoceptor 7 0 ; 77.674 0.075846 159783000 461690 388480 219600 342160 432710 281020 385060 590120 420700 391480 FALSE TRUE 443646.6444 377400.9308 259286.605 359818.9186 446628.5101 286702.4169 389772.4795 577933.8158 372943.8997 364964.7109 1.215587785 1.03407513 0.710442948 0.985900576 1.22375807 0.785562024 1.067973061 1.583533417 1.021862905 1 18.47739745 1.983113292 24.73684783 1.281415203 0.986403799 0.128044096 0.215746216 816.3501708 1195846.612 0.08542937 0.05666061 96.18631627 -1.983113292 -0.295011404 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK 39 0 Q01081-2 Q01081-2 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;; 332.42 9.84E-130 216483000 159667 153752 127845 123750 141928 145953 137892 91176.4 179446 160038 FALSE TRUE 153427.0371 149367.1435 150949.4354 130136.7523 146493.243 148904.2697 139579.5635 89293.57548 159076.0424 149198.4837 1.028341799 1.001130439 1.01173572 0.872239108 0.981868176 0.998028036 0.93552937 0.598488492 1.066204149 1 17.18687335 1.983134317 24.53656655 0.824466101 0.978356718 0.034596122 0.124942731 804.7287926 1170736.212 0.048900297 0.032443163 96.19097286 -1.983134317 0.153890618 FQDADPLEQDELHTFTDTMLPGCFHLLDELPDTVYR ddPTM_BT-474_Pertuzumab_2h_R1 7 FQDADPLEQDELHTFTDTMLPGCFHLLDELPDTVYR 36 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ;;;;;; 373.56 1.78E-161 642093000 225900.4 235519 210340.9 252700.1 248094.2 269264 232109.2 152378.7 264799.6 267710.8 FALSE TRUE 217071.9626 228802.2287 248354.1796 265741.9824 256074.3753 274708.7026 234949.8218 149232.0266 234740.6595 249578.5091 0.869754225 0.91675453 0.995094412 1.064763082 1.026027346 1.100690535 0.941386431 0.597936205 0.940548369 1 17.92913419 1.98321664 24.61355134 0.793531133 0.998498706 0.204168634 0.118895602 610.7563727 895700.8564 0.047476574 0.031516445 96.2092081 -1.98321664 0.204967573 SDKVPDNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDKVPDNK 8 1 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 86.275 0.014728 865250000 1757190 1706240 1441110 1392890 1594830 1662660 1805770 2081030 2328000 2204220 FALSE TRUE 1688517.072 1657579.706 1701550.634 1464777.22 1646129.155 1696280.124 1827869.553 2038056.003 2063735.2 2054926.216 0.821692311 0.806637091 0.828034905 0.712812562 0.801064847 0.825470088 0.889506173 0.991790356 1.004286764 1 20.97065516 1.983260811 1.697754488 1.006941155 0.793066129 0.899364103 0.030038961 0.107365039 0.576584857 0.019842464 0.009670588 96.2189938 -1.983260811 -0.213875026 HLPS(ph)PPTLDSIITEYLR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLPSPPTLDSIITEYLR 17 0 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 HLPS(0.998)PPT(0.002)LDSIITEYLR;HLPS(0.999)PPT(0.001)LDSIITEYLR;HLPS(0.959)PPT(0.041)LDSIITEYLR;HLPS(0.861)PPT(0.139)LDSIITEYLR 282.72 3.03E-36 1135776400 246485 256743 204722 243789 240124 256275 233316 164985.6 265147 263962 TRUE FALSE 236852.0937 249420.941 241719.8194 256370.9795 247847.8065 261457.0561 236171.391 161578.5897 235048.6241 246083.6186 0.962486227 1.013561741 0.982267006 1.04180433 1.007169059 1.062472413 0.959720083 0.656600348 0.955157541 1 17.9087891 1.983261078 24.53895519 0.826362866 1.011511553 0.291844 0.09074893 472.5299895 692719.8086 0.03463785 0.023002741 96.21905294 -1.983261078 0.185148687 KGAGDGS(ph)DEEVDGK ddPTM_BT-474_Pertuzumab_2h_R1 16 KGAGDGSDEEVDGK 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK 191.61 3.85E-08 58925960000 19569190 15215330 16792090 14801890 16203610 15057230 21072310 26238580 29679790 26021940 TRUE FALSE 18804404.42 14781403.69 19826794.2 15565817.32 16724813.83 15361697.51 21330199.23 25696744.15 26310664.67 24259450.83 0.775137267 0.609304959 0.817281246 0.641639311 0.689414363 0.633225279 0.879253178 1.059246738 1.084553185 1 24.53204356 1.983296693 3.049078565 1.050201128 0.69384413 0.859402339 0.064215039 0.082597378 1.476747754 0.02983059 0.017242864 96.22694387 -1.983296693 -0.356356998 DHAPDRPFVCPDCGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHAPDRPFVCPDCGK 15 1 Q9BWE0;Q9BWE0-4 Q9BWE0 REPIN1 Replication initiator 1 0 ; 102.64 0.0009227 515600000 1119910 1006750 889560 901830 928900 965670 922890 632630 1074180 1022870 FALSE TRUE 1076142.679 978038.4757 1050323.28 948373.5544 958778.9121 985196.509 934184.6039 619565.9694 952243.5897 953590.1038 1.128517038 1.02563824 1.101441045 0.994529568 1.00544134 1.033144645 0.979650062 0.649719378 0.998587953 1 19.86300974 1.983547856 21.96363395 0.836557865 1.041915951 0.319146785 0.101408309 123.4174069 164761.4525 0.039110065 0.026071579 96.28261038 -1.983547856 0.205358085 RHQYS(ph)DYDYHSSSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RHQYSDYDYHSSSEK 15 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RHQY(0.001)S(0.999)DYDYHSSSEK 100.21 0.0010557 124550000 74448 106400 75617 98649 75334 100650 81186 32253 85149 93838 TRUE FALSE 71538.48985 103365.5762 89282.67399 103740.2867 77757.18653 102685.212 82179.57855 31586.96428 75483.24249 87482.26868 0.817748453 1.181560306 1.020580231 1.18584358 0.888833677 1.173783139 0.939385544 0.361067045 0.862840478 1 16.41670301 1.983553601 24.01155639 0.665288965 1.049793136 0.307419433 0.19376815 359.5843572 524988.4098 0.072740824 0.048377882 96.2838841 -1.983553601 0.384504171 EAPSPLMIHSPQMSQFQS(ph)LTHQSPPQQNVQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 EAPSPLMIHS(0.004)PQMS(0.169)QFQS(0.577)LT(0.144)HQS(0.105)PPQQNVQPK 55.492 0.083348 1960200000 486810 520450 381910 477830 473730 516830 473480 427060 533540 513170 TRUE FALSE 467784.927 505607.2756 450929.6325 502490.8636 488967.9557 527280.6567 479274.5899 418241.0618 472974.776 478412.5388 0.977785675 1.056843696 0.942553959 1.050329627 1.02206342 1.102146399 1.001801899 0.874226798 0.988633737 1 18.86789568 1.983575943 24.59306435 0.939737607 1.026287804 0.259348641 0.05192486 602.868097 902722.0585 0.020221549 0.013446605 96.28883729 -1.983575943 0.086550197 YS(ph)PSQNS(ph)PIHHIPSRR ddPTM_BT-474_Pertuzumab_2h_R1 4 YSPSQNSPIHHIPSRR 16 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 YS(1)PSQNS(1)PIHHIPSRR;YS(0.997)PS(0.003)QNS(1)PIHHIPSRR;YS(0.926)PS(0.074)QNS(1)PIHHIPSRR;Y(0.001)S(0.869)PS(0.131)QNS(1)PIHHIPSRR 213.72 1.21E-12 8350400000 2704790 2920290 1675350 1917870 2123430 3019530 2128760 820380 2284830 2023750 TRUE FALSE 2599083.816 2837006.188 1978123.013 2016851.501 2191732.054 3080586.965 2154812.402 803438.8663 2025465.677 1886679.61 1.377596812 1.503703211 1.048467902 1.068995228 1.161687466 1.632808745 1.142118879 0.425848068 1.073561015 1 20.84741802 1.983580211 24.36123579 0.773002043 1.289064981 0.431291327 0.236006263 423.3939401 628168.1154 0.095674093 0.063622125 96.28978357 -1.983580211 0.516062937 GDMEIPFEEVLER ddPTM_BT-474_Pertuzumab_2h_R1 1 GDMEIPFEEVLER 13 0 A0A669KBF0;O76024;A0A669KB26;A0A669KAX3 A0A669KBF0 WFS1 Wolframin 0 124.1 0.00030498 0 7029.5 11973 6871 14289 8463.8 9533 10881 17706 11687 7788.9 FALSE TRUE 6754.779368 11631.54176 8112.742545 15026.457 8736.045814 9725.763792 11014.16493 17340.36491 10360.34076 7261.350865 0.930237292 1.601842684 1.117249765 2.06937487 1.203088237 1.339387667 1.516820374 2.388035675 1.426778701 1 12.82602225 1.983627274 24.47342121 1.807480238 1.401304319 0 0.443424281 1014.301086 1516142.891 0.170246401 0.113180512 96.30021876 -1.983627274 -0.406175918 HQAFEAELHANADR ddPTM_BT-474_Pertuzumab_2h_R1 3 HQAFEAELHANADR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 192.78 1.93E-07 1208890000 282087 348608 282690 332814 332436 359359 306515 161262 369972 344712 FALSE TRUE 271062.7282 338666.0412 333778.3714 349990.5704 343129.1059 366625.4852 310266.2223 157931.8833 327974.3296 321364.3492 0.843474794 1.053838243 1.038629121 1.089077153 1.067726108 1.140840563 0.965465594 0.491441828 1.020568493 1 18.29385037 1.983634217 24.49817783 0.767736131 1.044013966 0.212769149 0.157009257 538.56818 806189.8384 0.060717153 0.040379131 96.30175848 -1.983634217 0.276277836 GPFVEAEVPDVDLECPDAK ddPTM_BT-474_Pertuzumab_2h_R1 5 GPFVEAEVPDVDLECPDAK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;; 286.53 8.30E-40 453884000 1264750 1259910 1073010 1280670 1192561 1270810 1295670 1498440 1490030 1428320 FALSE TRUE 1215322.172 1223978.6 1266926.776 1346765.532 1230920.808 1296506.649 1311526.797 1467496.69 1320888.041 1331578.614 0.912692768 0.919193645 0.951447224 1.011405198 0.924407162 0.973661363 0.984941319 1.102072889 0.991971504 1 20.34470617 1.983694826 5.070315893 1.04343386 0.951017148 0.460552205 0.039244356 0.143761266 10.567927 0.016847376 0.010815456 96.31519889 -1.983694826 -0.092416712 HRPS(ph)PPAT(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 7 HRPSPPATPPPK 12 1 A9Z1X7;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK 104.2 0.0049595 39501750000 6274250 5945980 5179760 5613080 5735830 6074410 5726450 4378020 7371890 6473750 TRUE FALSE 6029045.373 5776406.472 6115857.855 5902771.731 5920328.181 6197238.732 5796532.008 4287612.357 6535063.953 6035277.146 0.998967442 0.957107078 1.013351617 0.97804485 0.980953822 1.026835816 0.960441727 0.710425098 1.082810912 1 22.52498859 1.983764576 24.9151312 0.883036116 0.990938211 0.008439309 0.093086531 1020.853623 1566617.041 0.036106258 0.024028164 96.33066891 -1.983764576 0.107902095 S(ph)PSGHPHVR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPSGHPHVR 9 0 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;Q8WX93-7 Q8WX93-8 PALLD Palladin 1 S(0.976)PS(0.024)GHPHVR;S(0.999)PS(0.001)GHPHVR;S(0.998)PS(0.002)GHPHVR;S(0.999)PS(0.001)GHPHVR;S(0.997)PS(0.003)GHPHVR;S(0.981)PS(0.019)GHPHVR 155 4.79E-05 2289524300 453181 467821.1 447633.3 583489 451532.7 528056.3 371319.3 14799.5 410621.6 353280.1 TRUE FALSE 435470.1855 454479.3003 528530.5949 613602.9372 466056.6594 538733.9602 375863.6167 14493.88515 364009.5574 329352.1242 1.32220245 1.379919141 1.604758421 1.863060512 1.41507106 1.635738532 1.141221171 0.044007262 1.105229117 1 18.32927133 1.983768867 7.069940896 0.603439712 1.53114838 0.587003775 0.304802717 0.094468839 23.48487759 0.121648762 0.080622094 96.33162066 -1.983768867 0.927708667 THPEVCGR ddPTM_BT-474_Pertuzumab_2h_R1 2 THPEVCGR 8 0 O14545;F8VNX8 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 0 ; 136.8 0.00077559 243510000 463660 509580 451830 535920 482300 479690 475870 368400 530640 580510 FALSE TRUE 445539.6546 495047.2773 533485.7319 563578.8954 497813.6175 489389.6605 481693.8394 360792.4113 470403.9718 541191.5406 0.823256871 0.914735801 0.985761402 1.041366786 0.919847374 0.9042818 0.890061657 0.666663065 0.869200526 1 19.04577976 1.98377312 18.77192593 0.800778173 0.934325718 0.09096455 0.095022918 34.64302841 40074.82963 0.037878873 0.025359121 96.33256408 -1.98377312 0.133547546 FHDTS(ph)SPLMVTPPSAEAHWAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 FHDTSSPLMVTPPSAEAHWAVR 22 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 FHDTS(0.699)S(0.301)PLMVTPPSAEAHWAVR;FHDT(0.074)S(0.463)S(0.463)PLMVTPPSAEAHWAVR 214.17 3.27E-25 948870000 139679 185380 122590 160340 129693 134645 134080 40654 183954 161913 TRUE FALSE 134220.1903 180093.1439 144744.74 168615.1666 133864.6931 137367.6142 135720.9111 39814.48069 163072.3131 150946.4883 0.889190545 1.193092638 0.958914259 1.117052596 0.886835425 0.910041802 0.899132618 0.263765531 1.080331944 1 17.20367767 1.983843881 24.00206807 0.670033752 0.992935538 0.090414949 0.229737499 519.4805817 771756.6506 0.089402018 0.059574268 96.34826111 -1.983843881 0.322901786 SRSESDVS(ph)SVEQDSFIEPYATTSQLRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSESDVSSVEQDSFIEPYATTSQLRPR 28 2 K7EQI2;A0A0C4DGP8;K7EJF0;Q96ST8-3;Q96ST8 K7EQI2 CEP89 Centrosomal protein of 89 kDa 1 S(0.002)RS(0.052)ES(0.052)DVS(0.445)S(0.445)VEQDS(0.004)FIEPYATTSQLRPR 77.31 0.0060071 88136000 16633 16426 14699 20680 17445 18002 16759 15843 16185 19906 TRUE FALSE 15982.96397 15957.54656 17355.43628 21747.29728 18006.13427 18366.01277 16964.10166 15515.83651 14347.74665 18557.74889 0.861255536 0.859885898 0.935212368 1.171871513 0.970275779 0.989668137 0.91412497 0.836083978 0.773140468 1 14.1797341 1.983867698 3.919181236 0.854500995 0.967894558 0.156270893 0.09717392 0.36760533 12.25820869 0.046315473 0.028440097 96.353545 -1.983867698 0.113393562 ITHEVDELTQIIADVSQDPTLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ITHEVDELTQIIADVSQDPTLPR 23 0 P36954;K7EKS1 P36954 POLR2I DNA-directed RNA polymerase II subunit RPB9 0 ;;; 193.87 4.81E-18 228622000 239009 262519 207918 243789 240741 278909 245712 227008 271291 271476 FALSE TRUE 229668.264 255032.2152 245493.4077 256370.9795 248484.6529 284548.7311 248719.097 222320.2055 240495.183 253088.6887 0.907461591 1.007679231 0.969989647 1.012968935 0.981808607 1.124304419 0.982734939 0.878428059 0.950240741 1 17.9492835 1.983924165 24.90411282 0.929681568 1.003838455 0.154026412 0.057899918 938.7216307 1454233.611 0.023148301 0.015410903 96.36607376 -1.983924165 0.074156887 GDLSGHFEHLMVALVTPPAVFDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDLSGHFEHLMVALVTPPAVFDAK 24 0 P12429;D6RA82;D6RFG5;D6RCA8;D6RAZ8 P12429 ANXA3 Annexin A3;Annexin 0 ; 144.88 1.28E-07 339100000 149839 143421 133772 139828 132233 131068 125635 25995 167370 161052 FALSE TRUE 143983.1262 139330.7735 157947.5761 147044.5398 136486.3945 133718.2848 127172.5587 25458.19417 148370.8593 150143.8046 0.958968148 0.927982169 1.051975315 0.979358024 0.909037805 0.890601415 0.847005037 0.169558739 0.988191685 1 17.19598542 1.983953834 24.41249796 0.597304622 0.948322073 0.11241839 0.226943166 581.7855705 885122.6994 0.087977842 0.058621967 96.37265728 -1.983953834 0.351017451 LHVGNIS(ph)PTCTNK ddPTM_BT-474_Pertuzumab_2h_R1 5 LHVGNISPTCTNK 13 0 Q9BWF3;E9PB51;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2 Q9BWF3 RBM4 RNA-binding protein 4 1 LHVGNIS(0.999)PT(0.001)CTNK;LHVGNIS(1)PTCTNK;LHVGNIS(0.999)PT(0.001)CTNK;LHVGNIS(0.995)PT(0.005)CTNK;LHVGNIS(0.938)PT(0.062)CTNK 270.21 5.32E-26 3949920000 3632270 3564570 3292460 3566220 3652200 3922540 3376820 1576870 4260430 3775810 TRUE FALSE 3490316.873 3462911.954 3887480.762 3750273.042 3769676.33 4001856.446 3418146.533 1544307.083 3776803.848 3520071.026 0.991547286 0.983761955 1.10437566 1.06539698 1.070909167 1.136868096 0.971044763 0.438714751 1.072933989 1 21.74717311 1.983992525 24.40697962 0.757358325 1.057955614 0.221502483 0.166888179 495.3818746 755319.8729 0.064331187 0.042889485 96.38124342 -1.983992525 0.300597288 ADEGS(ph)PVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADEGSPVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK 41 0 O15040-2;O15040 O15040-2 TECPR2 Tectonin beta-propeller repeat-containing protein 2 1 ADEGS(0.999)PVEPS(0.001)QEQDILTSMEASGHLSTNLWHAVTDDDTGQK 107.28 1.30E-05 40441000 25431 42099 26406 32474 30744 41919 30972 14804 32286 37840 TRUE FALSE 24437.1284 40898.37774 31178.1516 34149.98703 31732.90868 42766.6309 31351.0446 14498.29223 28621.02863 35277.0631 0.692720036 1.15934758 0.883808029 0.96805074 0.899533745 1.212307011 0.888709032 0.410983539 0.811321185 1 15.10644284 1.98400878 24.62371183 0.668953005 0.977460734 0.188799331 0.19510354 619.9337003 954589.79 0.073668201 0.049085711 96.38485088 -1.98400878 0.308507729 S(ph)RSPAPPADKEAFAAEAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPAPPADKEAFAAEAQK 19 2 Q9Y618;Q9Y618-4;Q9Y618-5 Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.623)RS(0.377)PAPPADKEAFAAEAQK 162.61 1.42E-11 536840000 475290 400830 348870 380170 384920 399120 430600 517770 534380 436330 TRUE FALSE 456715.1413 389398.7209 411918.5696 399790.6193 397301.3014 407190.4799 435869.8116 507077.8686 473719.4227 406776.9805 1.122765454 0.957278164 1.012639823 0.982825082 0.976705469 1.001016526 1.071520348 1.246574641 1.164567922 1 18.63387851 1.984058764 5.598607661 1.164069297 1.005954949 0.376081118 0.071602819 0.134346306 14.05728055 0.028431432 0.018490625 96.39594475 -1.984058764 -0.158114347 SHLEVPLEENVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHLEVPLEENVNR 13 0 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ; 140.82 3.95E-05 479480000 198962 218010 227440 270770 241230 246140 216570 90289 252900 242740 FALSE TRUE 191186.3451 211792.5683 268543.4674 284744.4721 248989.382 251117.1194 219220.4484 88424.5006 224191.8522 226299.0036 0.844839535 0.935897043 1.18667543 1.258266575 1.100267249 1.109669576 0.968720343 0.390741891 0.990688641 1 17.78787071 1.984060238 23.05961541 0.714518808 1.077764345 0.26283157 0.195690593 245.6839348 355423.2789 0.078723044 0.052559615 96.39627201 -1.984060238 0.363245537 HFKDEDEDEDVAS(ph)PDGLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFKDEDEDEDVASPDGLGR 19 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR 149.73 5.01E-08 1117510000 833020 738100 654840 702440 599810 718710 620300 241270 729790 707700 TRUE FALSE 800464.6574 717050.1107 773184.1548 738693.0126 619103.4334 733242.8086 627891.417 236287.6902 646947.2987 659766.8486 1.213253832 1.086823492 1.17190513 1.119627356 0.938366992 1.111366553 0.951686824 0.358138168 0.980569576 1 19.33159676 1.984080196 15.70315644 0.694910375 1.09599831 0.36786192 0.182574207 4.388905518 4327.812466 0.070383171 0.047310279 96.40070185 -1.984080196 0.401087934 S(ph)PSAQCPFPGGTVLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSAQCPFPGGTVLSR 16 0 P78411-3;P78411-2;P78411;H0YML8 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 S(1)PSAQCPFPGGTVLSR;S(1)PSAQCPFPGGTVLSR;S(0.978)PS(0.022)AQCPFPGGTVLSR 282.47 1.47E-35 793800000 143593 145605 137954 169348 134544 124332 159375 232741 167639 194167 TRUE FALSE 137981.2268 141452.488 162885.3566 178088.0706 138871.7299 126846.0782 161325.4789 227934.817 148609.3235 181015.8961 0.762260275 0.781436829 0.89984007 0.983825589 0.76717975 0.70074552 0.891222718 1.259197794 0.820973885 1 17.46575687 1.984268254 24.38039779 1.060445335 0.821254764 0.354186823 0.124747777 473.4581838 733744.8823 0.050032106 0.03340212 96.44245422 -1.984268254 -0.239190571 KHLEINPDHSIIETLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KHLEINPDHSIIETLR 16 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 248.97 6.99E-21 5119900000 2468199 2585402 1764508 1868499 2061267 2544976 1883430 362044 2195243 1643733 FALSE TRUE 2371739.054 2511668.866 2083393.847 1964932.457 2127569.525 2596437.158 1906479.98 354567.6649 1946048.218 1532401.5 1.547726921 1.639040987 1.359561347 1.28225694 1.388389091 1.694358273 1.244112578 0.231380395 1.269933642 1 20.54736291 1.984345622 21.63899217 0.745712938 1.472571864 0.526291818 0.272513224 77.03974417 106491.0731 0.105334256 0.07052591 96.45963673 -1.984345622 0.726858927 RHS(ph)PESPSIAVVESELVAEYITTVSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 RHSPESPSIAVVESELVAEYITTVSHR 27 1 Q7Z589-4;E9PMC9 Q7Z589-4 EMSY;C11orf30 Protein EMSY 1 RHS(0.906)PES(0.081)PS(0.013)IAVVESELVAEYITTVSHR;RHS(1)PESPSIAVVESELVAEYITTVSHR 230.51 2.50E-35 74479000 25797.4 27841 22942.7 28877 24634.6 29842 23599.3 16239.9 22512.5 26227 TRUE FALSE 24789.20909 27047.00194 27088.95625 30367.34543 25426.99428 30445.42569 23888.11529 15904.54039 19956.97538 24450.62193 1.013847793 1.10618871 1.107904589 1.241986626 1.039932414 1.245180011 0.976994179 0.650475903 0.81621545 1 14.57758354 1.984404384 6.684341412 0.789491682 1.124875097 0.618790118 0.106207436 0.086718839 17.758066 0.041242454 0.027275859 96.47268899 -1.984404384 0.335383415 SQT(ph)PPGVATPPIPK ddPTM_BT-474_Pertuzumab_2h_R1 6 SQTPPGVATPPIPK 14 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SQT(1)PPGVATPPIPK;S(0.059)QT(0.941)PPGVATPPIPK;S(0.001)QT(0.999)PPGVATPPIPK;SQT(1)PPGVATPPIPK;S(0.002)QT(0.998)PPGVATPPIPK;SQT(1)PPGVATPPIPK 208.38 9.08E-08 16551440000 4382680 3925560 3383990 3555640 3738230 3954360 4100260 4559220 5118950 4698200 TRUE FALSE 4211400.02 3813606.872 3995552.269 3739147.007 3858473.563 4034319.869 4150440.208 4465070.514 4537868.256 4379986.729 0.961509767 0.870689139 0.912229309 0.853689118 0.880932706 0.921080386 0.94759196 1.01942558 1.03604612 1 22.06249507 1.984422838 1.859113742 1.023717079 0.89425543 0.770487959 0.028952984 0.148955206 0.95806446 0.017106242 0.008566326 96.47678832 -1.984422838 -0.12946165 DLVMGSS(ph)PQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLVMGSSPQLK 11 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.325)S(0.675)PQLK;DLVMGS(0.31)S(0.69)PQLK 189.99 2.59E-06 1134900000 3622400 3500550 3476380 3555730 3526530 3464880 4228500 4865800 5247700 5413000 TRUE FALSE 3480832.603 3400717.741 4104639.198 3739241.651 3639964.04 3534942.248 4280249.648 4765319.53 4652003.096 5046372.689 0.68976923 0.673893498 0.813384078 0.740976119 0.721303056 0.700491713 0.84818342 0.944305905 0.921850878 1 22.26681533 1.984478341 2.502295773 0.951208137 0.725506071 0.866384353 0.040951622 0.103523824 1.209518555 0.022400355 0.012269115 96.48911904 -1.984478341 -0.225702066 KIIDSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIIDSVR 7 1 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 103.56 0.013385 282770000 887680 1140450 857910 965470 942130 998420 979020 947440 1104790 1097910 FALSE TRUE 852988.4842 1107925.483 1012953.421 1015298.022 972434.4671 1018608.736 991001.5396 927875.0329 979378.8709 1023547.578 0.833364763 1.08243672 0.989649571 0.991940233 0.95006279 0.995174781 0.968202711 0.906528483 0.956847432 1 19.96514673 1.984499528 23.40920573 0.942396079 0.979389728 0.003156908 0.061747492 847.5100846 1279928.913 0.023288151 0.015574839 96.49382629 -1.984499528 0.036993649 VVVHPLVLLSVVDHFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVVHPLVLLSVVDHFNR 17 0 P51665;H3BNT7;H3BTM8;H3BQV2 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 238.67 1.70E-20 1302250000 261340 292919 234870 264924 278019 293990 263640 211311 284233 289012 FALSE TRUE 251126.5439 284565.2369 277316.2337 278596.7594 286961.7336 299934.6792 266866.5052 206947.354 251968.0614 269436.9598 0.932041929 1.056147743 1.029243478 1.033996077 1.065042204 1.113190556 0.990459903 0.768073371 0.935165174 1 18.03958824 1.984502759 22.99495743 0.876299012 1.040711092 0.424238465 0.069677184 176.1229236 261332.296 0.026860443 0.017979721 96.4945443 -1.984502759 0.16441208 HLSDAIVEVEEALIQIHDPELR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLSDAIVEVEEALIQIHDPELR 22 0 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 ;;; 220.63 5.79E-26 133089000 24617.9 42180.4 33606.4 52371.6 45850.5 51558.4 36802 19402 33717.6 40463.7 FALSE TRUE 23655.80525 40977.45629 39679.82405 55074.50455 47325.32297 52600.94617 37252.39388 19001.34192 29890.1194 37723.05756 0.627091407 1.08627081 1.051871895 1.459969263 1.254546318 1.394397739 0.987523183 0.503706305 0.792356753 1 15.20315899 1.984518735 12.35311313 0.718980317 1.160726289 0.32525999 0.242034989 1.032390213 819.8449479 0.09910241 0.066800986 96.49809383 -1.984518735 0.441745972 QQQLEEEAAKPPEPEKPVS(ph)PPPIESK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQQLEEEAAKPPEPEKPVSPPPIESK 26 2 C9J0Q5;C9JE98;C9J330;H7C1Y3;H0YGK8;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 QQQLEEEAAKPPEPEKPVS(1)PPPIESK 156.9 1.07E-08 1442500000 952020 726970 659950 502960 730620 600550 853860 1096500 1193000 976670 TRUE FALSE 914814.0059 706237.5274 779217.6455 528917.8259 754121.0558 612693.5325 864309.7941 1073856.892 1057575.641 910519.271 1.004716797 0.775642592 0.855794787 0.580896904 0.828231845 0.672905618 0.949249315 1.179389526 1.161508246 1 19.79633003 1.98456036 4.31922485 1.123477751 0.782028983 0.623228668 0.114143133 0.124159652 5.476393499 0.04933524 0.030913419 96.50734318 -1.98456036 -0.341448768 SSQCHTGS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSQCHTGSSPR 11 0 O15226;O15226-2 O15226 NKRF NF-kappa-B-repressing factor 1 SSQCHT(0.007)GS(0.6)S(0.393)PR;SSQCHTGS(0.5)S(0.5)PR;SSQCHT(0.011)GS(0.494)S(0.494)PR;SSQCHT(0.001)GS(0.5)S(0.5)PR 96.464 0.0045042 117453000 176828 189634 156437 196394 180470 207238 181029 151262 191291 203930 TRUE FALSE 169917.3663 184225.824 184708.6458 206529.9179 186274.9814 211428.4943 183244.4871 148138.3868 169576.4476 190117.6395 0.893748559 0.969009633 0.971549228 1.086326963 0.979787999 1.112092991 0.963847897 0.779193279 0.89195536 1 17.53653287 1.984561106 23.99246973 0.867266714 1.005006699 0.281434762 0.077132737 403.5675891 627154.5718 0.030486558 0.020389376 96.50750899 -1.984561106 0.137739985 SS(ph)GFISELPSEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.226)S(0.774)GFISELPSEEGK;S(0.246)S(0.754)GFISELPSEEGK 188.63 7.24E-08 0 367810 344640 287180 273460 292080 348510 347830 440380 461020 434640 TRUE FALSE 353435.5786 334811.2046 339079.8143 287573.3034 301475.0185 355557.111 352086.8476 431285.9991 408686.9424 405201.4457 0.872246588 0.826283342 0.836817879 0.709704534 0.744012692 0.877482336 0.868918044 1.064374285 1.008601886 1 18.6282798 1.984590138 2.117115056 1.030922879 0.802143237 0.762347573 0.052811314 0.150303741 1.2514324 0.031584254 0.016454297 96.51396069 -1.984590138 -0.228779642 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(ph)KGSPTSAYPER ddPTM_BT-474_Pertuzumab_2h_R1 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESKGSPTSAYPER 44 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(0.499)KGS(0.499)PT(0.002)SAYPER 432.14 1.04E-235 914030000 152930 177790 105390 122940 138870 201920 127680 11097 137770 130600 TRUE FALSE 146953.3265 172719.6033 124436.3174 129284.9481 143336.8797 206002.9607 129242.586 10867.84307 122130.9272 121754.3457 1.206965761 1.418590871 1.022027729 1.06185079 1.177262946 1.691955713 1.061502859 0.089260412 1.003092962 1 16.89361374 1.984605543 24.76732638 0.591038698 1.257048022 0.40068217 0.301043301 485.6522187 781339.6437 0.11785297 0.078804038 96.51738419 -1.984605543 0.666009324 IKS(ph)FENLANADRPVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKSFENLANADRPVAK 16 2 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 IKS(1)FENLANADRPVAK 92.792 0.0024269 231460000 251950 232530 184940 199100 224670 203750 228680 296970 233520 255920 TRUE FALSE 242103.5155 225898.4721 218362.772 209375.5749 231896.7146 207869.9646 231478.6542 290837.4657 207011.7886 238586.3105 1.014741856 0.946820761 0.915235965 0.877567428 0.971961527 0.871256881 0.970209287 1.219003157 0.86765996 1 17.86415174 1.984633021 24.57168365 1.063567606 0.931075203 0.152693066 0.090660231 653.5558123 1045030.072 0.034981913 0.023400111 96.52349098 -1.984633021 -0.132492404 VYEDSGIPLPAES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 VYEDSGIPLPAESPK 15 0 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK 369.39 1.67E-97 7325020000 9344770 7568280 6539380 6533330 7255130 6647120 7685810 9425900 8860030 8456880 TRUE FALSE 8979566.057 7352440.065 7721191.434 6870515.944 7488497.845 6781529.321 7779871.242 9231251.871 7854276.539 7884087.985 1.138947977 0.932566973 0.979338568 0.8714408 0.949824236 0.860153937 0.986781383 1.170871239 0.996218783 1 22.91051245 1.984653901 24.25661558 1.075718376 0.949038472 0.205417459 0.085020602 548.847332 867527.624 0.033248771 0.022258457 96.52813173 -1.984653901 -0.126679903 DIAANEENRK ddPTM_BT-474_Pertuzumab_2h_R1 6 DIAANEENRK 10 1 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 ;;;;; 134.98 0.00025074 4685490000 2465110 2335200 2113230 2529290 2435590 2355640 2861720 3041960 3240020 3444220 FALSE TRUE 2368770.776 2268602.382 2495137.67 2659826.96 2513932.964 2403272.655 2896742.585 2979142.463 2872226.513 3210939.912 0.737718812 0.706522839 0.777073922 0.828363979 0.78292744 0.748463914 0.902147865 0.927810095 0.894512695 1 21.61456424 1.984693928 0.478715947 1.002091526 0.727793018 0.816751807 0.039060799 0.397708445 0.206878609 0.042291927 0.03430239 96.53702877 -1.984693928 -0.274298507 HGS(ph)GADSDYENTQSGDPLLGLEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.94)GADS(0.06)DYENTQSGDPLLGLEGK 215.27 9.18E-33 436700000 398870 454900 381410 409090 463790 416850 389310 173380 500330 412400 TRUE FALSE 383281.7194 441926.6974 450339.2714 430203.1839 478708.2266 425278.9926 394074.4922 169799.6424 443534.636 384467.7807 0.996915057 1.149450538 1.171331628 1.118957701 1.245119229 1.106149888 1.024987039 0.441648562 1.153632783 1 18.55250318 1.98471236 22.73827835 0.785620424 1.132490459 0.269593634 0.182605452 189.2580536 281494.6869 0.070264178 0.047088186 96.54112595 -1.98471236 0.346870035 RFPGYDSESK ddPTM_BT-474_Pertuzumab_2h_R1 6 RFPGYDSESK 10 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 222.18 8.06E-09 12552900000 16250000 16208700 13693000 13427900 14930400 14544400 15865700 17747700 18554300 18103100 FALSE TRUE 15614932.03 15746443.75 16167629.7 14120915.53 15410649.88 14838497.73 16059869.18 17381203.79 16448093.65 16876960.91 0.925221793 0.933014174 0.957970442 0.836697768 0.91311759 0.879216217 0.951585375 1.029877588 0.974588597 1 24.0085518 1.984716103 5.15014286 1.002387511 0.908250927 0.619246422 0.033049604 0.118475934 9.236835635 0.014296318 0.009215461 96.54195812 -1.984716103 -0.094136585 SKS(ph)LDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSLDSR 7 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 S(0.113)KS(0.887)LDSR 102.06 0.0052598 291820000 1179700 1084100 751690 1013500 982170 954610 1033900 1261000 1114400 1096300 TRUE FALSE 1133596.02 1053182.529 887537.1043 1065806.856 1013762.39 973912.8683 1046553.177 1234959.909 987897.9839 1022046.625 1.109143157 1.030464271 0.868391992 1.042816278 0.991894465 0.95290454 1.023977921 1.208320521 0.966587982 1 19.96302958 1.984894561 24.45289799 1.090124479 0.995720557 0.051325098 0.084678347 813.2723289 1316534.788 0.033397114 0.022386473 96.58163665 -1.984894561 -0.094403922 LALEAEVSELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LALEAEVSELR 11 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 138.98 0.00010784 32899000 47463 48735 41580 41447 44463 43554 42067 33269 44106 43289 FALSE TRUE 45608.09349 47345.12552 49094.43094 43586.08464 45893.19278 44434.69172 42581.82853 32581.98352 39099.27179 40356.99747 1.130116122 1.173157779 1.216503556 1.080013068 1.137180555 1.101040575 1.055128756 0.807344093 0.968835004 1 15.30053122 1.984906583 3.963821796 0.907000287 1.139739272 0.718059267 0.059494813 0.102682628 3.53958337 0.026683169 0.016448553 96.58431032 -1.984906583 0.232738984 HAVSDPSILDSLDLNEDEREVLINNINRR ddPTM_BT-474_Pertuzumab_2h_R1 1 HAVSDPSILDSLDLNEDEREVLINNINRR 29 2 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 120.08 2.79E-05 85986000 19421 20914 14580 11410 16285 20051 14544 8944.8 13876 14926 FALSE TRUE 18662.00585 20317.5532 17214.93033 11998.87147 16808.82181 20456.44496 14721.99382 8760.086754 12300.85465 13915.04873 1.341138376 1.460113694 1.237144811 0.862294607 1.207959968 1.470095101 1.057990821 0.629540502 0.88399652 1 13.76435834 1.984909293 7.901589369 0.807399451 1.251613908 0.52479031 0.180982032 0.134813709 50.38968803 0.077570686 0.051863932 96.58491292 -1.984909293 0.444214457 CSDIVFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 CSDIVFAR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 121.62 0.0077663 0 81213 100850 69255 107090 95595 104850 111000 182090 100650 122350 FALSE TRUE 78039.10617 97973.85674 81770.91907 112616.9277 98669.89999 106970.1388 112358.4512 178329.7779 89224.63396 114063.1255 0.684174713 0.858944171 0.716891797 0.987321075 0.865046434 0.937815252 0.985054992 1.563430575 0.782239076 1 16.79947295 1.984921975 14.49395722 1.20193554 0.854219953 0.234298553 0.204992635 2.979582832 2861.894441 0.079636981 0.053755292 96.58773351 -1.984921975 -0.347715587 S(ph)TELLLGVK ddPTM_BT-474_Pertuzumab_2h_R1 3 STELLLGVK 9 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 S(0.983)T(0.017)ELLLGVK;S(0.997)T(0.003)ELLLGVK;S(0.997)T(0.003)ELLLGVK 192.1 3.69E-05 346293000 419793 448372 436940 540633 417283 374630 572134 700712 730082 789747 TRUE FALSE 403387.0255 435584.8696 515904.7777 568535.1339 430705.2867 382205.2753 579135.947 686242.0523 647206.1521 736256.7323 0.547889082 0.591620899 0.700713155 0.772196856 0.584993342 0.519119566 0.786595112 0.932068968 0.879049554 1 19.4898494 1.984936952 3.750678577 0.921637613 0.627342422 0.780442075 0.075493503 0.115527452 3.42933013 0.037058315 0.022574722 96.59106441 -1.984936952 -0.294295191 HTLGDS(ph)DNES ddPTM_BT-474_Pertuzumab_2h_R1 2 HTLGDSDNES 10 0 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 HTLGDS(0.9)DNES(0.1);HTLGDS(1)DNES 89.189 0.012255 258967000 506380 593170 496110 608270 513580 635380 544490 419790 600580 590470 TRUE FALSE 486590.1098 576253.3724 585768.1129 639662.8876 530099.7671 648227.8189 551153.6315 411121.1898 532404.6762 550476.941 0.883942766 1.046825633 1.064110173 1.162015772 0.962982693 1.177574882 1.00122928 0.746845434 0.967169806 1 19.07032261 1.984957568 24.71767569 0.87591691 1.054462259 0.273262928 0.102325185 580.4066893 953721.9147 0.03938339 0.026404204 96.59564978 -1.984957568 0.178545349 ATSLPS(ph)IPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.319)S(0.319)LPS(0.362)IPNPFPELCS(0.021)PPS(0.178)QS(0.801)PILGGPSSAR 167.58 6.07E-13 281240000 84581 77697 63904 73564 74060 73412 78234 101700 82633 71829 TRUE FALSE 81275.48101 75481.15763 75452.87434 77360.64686 76442.20716 74896.44094 79191.45109 99599.85946 73252.84827 66963.95785 1.213719792 1.127190806 1.12676844 1.155257983 1.141542549 1.118458994 1.182598126 1.487365184 1.093914557 1 16.03109718 1.984963188 24.92467303 1.269679108 1.145859675 0 0.125372639 1149.707081 1905727.018 0.04825396 0.032303218 96.59689976 -1.984963188 -0.123819433 ES(ph)KGSPVFLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESKGSPVFLPR 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ES(0.622)KGS(0.378)PVFLPR;ES(0.75)KGS(0.25)PVFLPR 106.32 0.0014213 2989690000 2508000 2445800 1786560 1853040 2058600 2159500 2239600 2476700 2637600 2567600 TRUE FALSE 2409984.587 2376048.179 2109431.134 1948675.616 2124816.739 2203166.57 2267008.895 2425555.28 2338190.706 2393694.165 1.006805557 0.992628137 0.88124505 0.814087131 0.887672606 0.92040437 0.947075415 1.013310437 0.976812635 1 21.1908074 1.984964601 3.020962303 0.996979567 0.913025696 0.313076373 0.052340008 0.342640661 6.00835771 0.029041144 0.01677616 96.59721404 -1.984964601 -0.083953871 IRS(ph)SVEKENQK ddPTM_BT-474_Pertuzumab_2h_R1 1 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.683)S(0.317)VEKENQK 57.414 0.088843 300810000 128070 109340 101020 79720 98997 90571 106630 132520 133600 94854 TRUE FALSE 123064.8828 106221.7303 119276.5612 83834.35875 102181.3284 92402.40768 107934.9698 129783.4157 118434.2881 88429.45409 1.39167299 1.201203053 1.348832947 0.948036597 1.155512374 1.044927944 1.220577136 1.467649179 1.339308145 1 16.43223936 1.985058905 24.30041316 1.326738405 1.174568657 0.018003002 0.16536934 898.3484826 1461085.852 0.065040292 0.043651357 96.61819171 -1.985058905 -0.152169748 LNEQAS(ph)EEILK ddPTM_BT-474_Pertuzumab_2h_R1 4 LNEQASEEILK 11 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 LNEQAS(1)EEILK;LNEQAS(1)EEILK;LNEQAS(1)EEILK;LNEQAS(1)EEILK 191.06 2.10E-06 1229800000 1312220 1136750 1403650 1610040 1345640 1186270 1637310 1987730 2036140 2157680 TRUE FALSE 1260936.992 1104331.003 1657320.779 1693134.357 1388923.733 1210257.192 1657347.89 1946682.681 1805005.923 2011538.412 0.626852057 0.548998218 0.8239071 0.841711174 0.690478355 0.60165751 0.823920577 0.967758144 0.897326103 1 20.93986786 1.985067785 4.130667559 0.94381665 0.695725614 0.641446628 0.089151614 0.153027253 5.928245688 0.043214637 0.026869774 96.62016738 -1.985067785 -0.248091036 QHHHLLQSPVSHHEPES(ph)PQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QHHHLLQSPVSHHEPESPQLR 21 0 Q9Y6D6 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 QHHHLLQSPVSHHEPES(1)PQLR;QHHHLLQSPVSHHEPES(1)PQLR 196.55 4.34E-22 889050000 272315 279831 239811 253853 248767 269955 226677 139503 274677 160550 TRUE FALSE 261672.6287 271850.4939 283150.1823 266954.3838 256768.8165 275413.6751 229451.1409 136622.2143 243496.8185 149675.8055 1.748262706 1.816262107 1.891756529 1.783550674 1.715499814 1.8400681 1.532987514 0.912787567 1.626828182 1 17.19148151 1.985074732 5.001228438 1.17727357 1.794201511 0.702476981 0.180435379 0.092983884 6.563946457 0.07235942 0.046485632 96.62171281 -1.985074732 0.61692794 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_BT-474_Pertuzumab_2h_R1 4 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 49 1 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ;;; 267.59 3.60E-74 3581380000 2768409 2721531 1726302 1765901 2118270 2772207 1998590 308888.1 2651173 1911452 FALSE TRUE 2660216.516 2643915.601 2038283.173 1857039.362 2186406.078 2828262.925 2023049.342 302509.4528 2350222.956 1781987.653 1.492836671 1.483689068 1.143825643 1.042116851 1.226947939 1.587139462 1.135276857 0.169759567 1.318877239 1 20.76505591 1.985108061 24.77392893 0.716101993 1.31452764 0.317878861 0.31435172 558.8082556 929621.6198 0.123814589 0.083020217 96.62912809 -1.985108061 0.598425647 QKS(ph)DAEEDGGTVS(ph)QEEEDRKPK ddPTM_BT-474_Pertuzumab_2h_R1 6 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.067)VS(0.933)QEEEDRKPK;QKS(1)DAEEDGGT(0.32)VS(0.68)QEEEDRKPK;QKS(1)DAEEDGGT(0.046)VS(0.954)QEEEDRKPK;QKS(1)DAEEDGGTVS(1)QEEEDRKPK;QKS(0.988)DAEEDGGT(0.027)VS(0.985)QEEEDRKPK;QKS(1)DAEEDGGT(0.01)VS(0.99)QEEEDRKPK 185 5.32E-17 14425860000 4948160 5425610 2862800 3893960 3428770 3271050 5124860 8599240 7520270 3718200 TRUE FALSE 4754780.437 5270876.915 3380171.643 4094927.742 3539059.501 3337192.872 5187579.57 8421662.689 6666600.477 3466363.002 1.371691434 1.52057846 0.97513493 1.181332636 1.020971981 0.962736121 1.496548275 2.429538592 1.923226296 1 21.72499131 1.985166939 9.989449273 1.94847878 1.177033372 0.32762399 0.373985895 0.277967621 177.9965257 0.14444889 0.097363015 96.64222923 -1.985166939 -0.771445408 KGDSNANSDVCAAALR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGDSNANSDVCAAALR 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 ;;; 198.85 6.36E-11 781790000 240222 260540 211187 249995 234660 215483 244594 270125 275463 278692 FALSE TRUE 230833.8587 253109.6543 249353.1887 262897.2719 242208.052 219840.2139 247587.4145 264546.8244 244193.5951 259815.9426 0.88845148 0.974188311 0.959730131 1.011859662 0.932229368 0.846138277 0.952933881 1.018208589 0.939871482 1 17.98713043 1.985184139 24.77497465 0.987430218 0.938119645 0.190585092 0.046405697 1065.044293 1780958.606 0.019488668 0.013087462 96.64605665 -1.985184139 -0.049310573 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR ddPTM_BT-474_Pertuzumab_2h_R1 6 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;; 407.59 4.70E-199 5760150000 1759777.3 1824818.5 1636454 1681781.2 1650638.9 1859497 1713556.6 1293103.8 2136662 2062674.9 FALSE TRUE 1691003.258 1772776.463 1932197.641 1768578.129 1703733.199 1897097.303 1734527.618 1266400.755 1894117.087 1922968.092 0.87937146 0.921895933 1.004799637 0.919712676 0.885991404 0.986546429 0.902005408 0.658565662 0.984996629 1 20.87490339 1.985242887 24.87500754 0.827509098 0.933996014 0 0.098239874 1013.352933 1708135.016 0.038065235 0.025537068 96.65913112 -1.985242887 0.106486917 RRS(ph)PPADAIPK ddPTM_BT-474_Pertuzumab_2h_R1 5 RRSPPADAIPK 11 2 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4;M0R1Q8 P18754-2 RCC1 Regulator of chromosome condensation 1 RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK 106.3 0.0018507 30638620700 6617132 6355710 5503821 5714793 6018368 6024099 6361368 6845573 7531055 7033191 TRUE FALSE 6358527.166 6174451.374 6498483.887 6009734.152 6211954.272 6145910.409 6439220.324 6704209.525 6676161.209 6556826.709 0.969756781 0.941682867 0.991101973 0.916561382 0.947402539 0.937330005 0.982063521 1.022477766 1.018200039 1 22.64456634 1.985307355 3.672391334 1.014568934 0.950526947 0.679220693 0.019400207 0.126393925 3.552246773 0.00874557 0.005304952 96.67348054 -1.985307355 -0.064041988 S(ph)TPPYLFPEYPEASK ddPTM_BT-474_Pertuzumab_2h_R1 4 STPPYLFPEYPEASK 15 0 Q8TE76-2;Q8TE76-3;Q8TE76 Q8TE76-2 MORC4 MORC family CW-type zinc finger protein 4 1 S(0.5)T(0.5)PPYLFPEYPEASK;S(0.5)T(0.5)PPYLFPEYPEASK;S(0.5)T(0.5)PPYLFPEYPEASK;S(0.5)T(0.5)PPYLFPEYPEASK 139.66 5.32E-06 600829000 400854 382366 337851 349860 361394 360543 416845 520921 510458 496924 TRUE FALSE 385188.1825 371461.2961 398908.1912 367916.3165 373018.5662 367833.4265 421946.4738 510163.7993 452512.9479 463266.8949 0.831460626 0.801830004 0.861076402 0.794177872 0.805191501 0.793998947 0.910806445 1.101230856 0.976786714 1 18.82148407 1.985370866 4.358838632 1.033024013 0.816115945 0.875404962 0.035694018 0.059550797 2.705251352 0.015105425 0.009493518 96.68761906 -1.985370866 -0.216908068 EQPGEEYS(ph)EEEESVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQPGEEYSEEEESVLK 16 0 Q96PY6-4;Q96PY6-2;Q96PY6-6;Q96PY6;Q96PY6-3 Q96PY6-4 NEK1 Serine/threonine-protein kinase Nek1 1 EQPGEEYS(1)EEEESVLK 171.04 5.31E-09 52838000 47431 42260 34875 43407 42121 42989 45487 54001 53008 53057 TRUE FALSE 45577.34408 41054.78618 41177.68829 45647.24047 43475.86022 43858.26703 46043.68351 52885.86048 46990.75407 49463.40213 0.92143569 0.830003283 0.832487991 0.922848783 0.878950059 0.886681165 0.930863659 1.06919173 0.950010554 1 15.59407385 1.985384006 4.309095606 1.012451436 0.877707345 0.672259412 0.039741232 0.111082409 4.875178926 0.017400195 0.010912779 96.6905446 -1.985384006 -0.134744091 FLSPQDTFEALKR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLSPQDTFEALKR 13 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 188.4 9.85E-06 536570000 716360 702680 603540 605770 620460 546910 665950 787580 771170 739160 FALSE TRUE 688363.8592 682640.2544 712613.1037 637033.8623 640417.6594 557968.8949 674100.0953 771316.1978 683630.0146 689096.0348 0.998937484 0.990631523 1.034127419 0.924448597 0.929359084 0.809711371 0.978238244 1.119315972 0.99206784 1 19.39434553 1.985503907 24.91633307 1.049983242 0.947006784 0.266319713 0.065207216 769.9890759 1323480.907 0.027666151 0.018594402 96.71724286 -1.985503907 -0.102976458 DT(ph)TLIRHSPQPSPSSSFNEGLLTGGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTTLIRHSPQPSPSSSFNEGLLTGGHR 27 1 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 DT(0.395)T(0.395)LIRHS(0.21)PQPSPSSSFNEGLLTGGHR 243.69 3.79E-45 448920000 62449 74813 50413 77275 70646 72380 60553 36420 67122 66981 TRUE FALSE 60008.42404 72679.40649 59523.75053 81263.17201 72918.39275 73843.57319 61294.06573 35667.91427 59502.59196 62444.31721 0.960990955 1.163907458 0.953229264 1.301370175 1.167734648 1.182550735 0.981579565 0.571195521 0.952890425 1 15.93028266 1.985507533 8.671102537 0.789064749 1.122752875 0.414668605 0.145915193 0.153709232 76.3759377 0.056814102 0.038190567 96.71805024 -1.985507533 0.333688126 VGMVETNSQDRPVDDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 VGMVETNSQDRPVDDVK 17 1 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 ;; 222.3 3.11E-15 1110780000 848670 789600 606540 711720 683540 738920 815730 940070 981640 1028890 FALSE TRUE 815503.0381 767081.3811 716155.2704 748451.9545 705526.6849 753861.4687 825713.1478 920657.226 870208.3426 959202.3639 0.850188729 0.799707559 0.746615414 0.780285769 0.735534765 0.785925366 0.860833103 0.959815427 0.907220807 1 19.87147569 1.985580019 2.41736104 0.952336412 0.779259013 0.820679577 0.036103976 0.119304524 1.298849992 0.019605948 0.010640942 96.73419445 -1.985580019 -0.173077399 TNSGISSASGGSTEPT(ph)TPDSERPAQALLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 TNSGISSASGGST(0.001)EPT(0.499)T(0.499)PDSERPAQALLR 204.51 3.90E-25 1007200000 86242 91012 85054 125450 116760 100640 100310 92546 108250 105000 TRUE FALSE 82871.56729 88416.42687 100425.1498 131924.4895 120515.6914 102675.0098 101537.6238 90634.89276 95961.91382 97888.25648 0.846593558 0.903238346 1.025916217 1.347704968 1.231155767 1.048900179 1.037280951 0.925901595 0.980321004 1 16.57884817 1.985634443 3.351612983 0.962693534 1.077395917 0.089762773 0.136773218 0.614093682 13.73264753 0.073520765 0.043654477 96.74631738 -1.985634443 0.114702383 SAS(ph)PSTQQEKHPTHHER ddPTM_BT-474_Pertuzumab_2h_R1 1 SASPSTQQEKHPTHHER 17 1 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 1 S(0.133)AS(0.823)PS(0.044)TQQEKHPTHHER 126.26 2.22E-05 258880000 126680 156760 63247 72461 96938 155580 88953 0 92899 55652 TRUE FALSE 121729.2055 152289.3583 74677.13982 76200.72089 100056.0988 158725.9342 90041.63342 0 82353.49498 51882.64047 2.346241526 2.935266149 1.439347326 1.468713238 1.928508224 3.059326448 1.735486718 0 1.587303465 1 15.66296428 1.985636405 23.75747901 0.780427992 2.170785712 0.481903236 0.616413313 279.4428511 462199.6393 0.252144087 0.169811399 96.74675441 -1.985636405 1.39035772 CELLYEGPPDDEAAMGIK ddPTM_BT-474_Pertuzumab_2h_R1 1 CELLYEGPPDDEAAMGIK 18 0 P13639 P13639 EEF2 Elongation factor 2 0 265.13 1.18E-30 102480000 266670 265790 215900 209490 238970 269840 258670 296310 320880 323260 FALSE TRUE 256248.2416 258209.9294 254917.9327 220301.804 246656.6871 275296.3497 261835.6808 290191.095 284455.0476 301365.3123 0.850291096 0.856800431 0.845876822 0.731012479 0.818464093 0.913497136 0.868831515 0.962921355 0.94388782 1 18.20115384 1.985751454 1.025067228 0.982156096 0.821748121 0.692301863 0.041200275 0.31418989 0.607448941 0.034755425 0.016188623 96.77238713 -1.985751454 -0.160407975 PCIQAQYGTPAPS(ph)PGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 PCIQAQYGTPAPSPGPR 17 0 P22736;F8VVX9;P22736-3 P22736 NR4A1 Nuclear receptor subfamily 4 group A member 1 1 PCIQAQYGTPAPS(1)PGPR;PCIQAQYGT(0.17)PAPS(0.83)PGPR 195.46 1.80E-11 244930000 209574 195593 164525 157539 196619 168045 189421 218993 213406 207947 TRUE FALSE 201383.6164 190014.8791 194258.3273 165669.6067 202943.4287 171442.985 191739.1909 214470.718 189181.0456 193862.5645 1.038795793 0.98015251 1.002041461 0.85457245 1.046841763 0.88435323 0.989047016 1.106302904 0.975851352 1 17.56467472 1.985774109 24.62982212 1.041315888 0.965720004 0.13221026 0.065298244 800.5130511 1385958.202 0.024853071 0.016737153 96.77743542 -1.985774109 -0.075595885 SHLLNCCPHDVLSGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHLLNCCPHDVLSGTR 16 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 188.04 7.19E-10 4120600000 2528500 2547100 2059000 2106300 2093200 2271700 2149300 1338590 2855800 2158000 FALSE TRUE 2429683.425 2474459.202 2431107.102 2215006.395 2160529.679 2317635.33 2175603.776 1310947.649 2531621.556 2011836.738 1.207694133 1.229950301 1.208401784 1.10098715 1.07390905 1.151999706 1.081401754 0.651617313 1.25836332 1 20.9400818 1.985780198 24.12110273 0.915090634 1.156894877 0.231797507 0.146652935 438.688681 744148.5253 0.05717456 0.038532009 96.77879214 -1.985780198 0.241804243 QAALGIMQMVEDTLIEHAHTKPLLPSQLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QAALGIMQMVEDTLIEHAHTKPLLPSQLVR 30 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 120.6 1.25E-05 99321000 223040 234110 164010 189260 196470 213660 175630 15353 234260 196890 FALSE TRUE 214323.3502 227433.412 193650.2554 199027.7313 202789.636 217980.3516 177779.4125 15035.95518 207667.7869 183554.4649 1.167628095 1.239051374 1.055001607 1.084297957 1.104792717 1.187551344 0.968537663 0.081915497 1.131368757 1 17.48584868 1.985790435 24.27323497 0.608120618 1.131425143 0.272839719 0.270012022 395.6411177 675846.2745 0.103038975 0.069426287 96.7810736 -1.985790435 0.523304525 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.471)S(0.529)RPS(0.527)T(0.47)PGLS(0.003)VVSGISATSEDIPNK;EVS(0.46)S(0.54)RPS(0.54)T(0.46)PGLSVVSGISATSEDIPNK;EVS(0.117)S(0.883)RPS(0.558)T(0.442)PGLSVVSGISATSEDIPNK 225.72 9.11E-35 847210000 615482 614736 623646 671458 605346 608015 729928 878389 877257 946460 TRUE FALSE 591428.283 597204.3312 736352.7051 706112.0278 624817.5039 620309.4799 738861.0772 860249.9602 777674.4631 882355.4212 0.670283503 0.676829673 0.83453072 0.800258049 0.708124514 0.703015435 0.837373534 0.974947215 0.881361914 1 19.75100038 1.98593318 3.572205775 0.945069629 0.736846803 0.751856783 0.056557578 0.124496869 3.261843156 0.027695767 0.016706519 96.81288892 -1.98593318 -0.208222826 GS(ph)PHYFS(ph)PFRPY ddPTM_BT-474_Pertuzumab_2h_R1 33 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 2 GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.008)FS(0.992)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.006)FS(0.994)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.001)FS(0.999)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.001)FS(0.999)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY 186.85 6.39E-06 10615229800 2344418.4 2474241.2 2061198.7 2417986.3 2312945.3 2301983.9 2212658.2 2151993 2163886.8 2351567.5 TRUE FALSE 2252795.937 2403678.264 2433703.156 2542778.863 2387343.286 2348531.592 2239737.373 2107553.593 1918251.442 2192293.739 1.02759767 1.096421625 1.110117277 1.159871425 1.088970535 1.071266843 1.021641094 0.961346354 0.874997455 1 21.06400968 1.98594019 1.683939582 0.934698029 1.099441987 0.716157178 0.041723966 0.187849256 0.992767216 0.026627282 0.01297781 96.81445171 -1.98594019 0.164743958 ESLKEEDES(ph)DDDNM ddPTM_BT-474_Pertuzumab_2h_R1 20 ESLKEEDESDDDNM 14 1 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 1 ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM 247.44 2.81E-17 65656450000 33540650 28646870 24991390 24454820 27104970 26191960 30524250 36921250 37903130 33570040 TRUE FALSE 32229844.32 27829889.32 29507890.1 25716936.19 27976825.98 26721579.38 30897814.9 36158813.29 33600525.59 31296311.29 1.029828852 0.889238641 0.942855208 0.821724195 0.893933656 0.853825204 0.987266985 1.155369812 1.073625747 1 24.89948929 1.9859565 5.388415797 1.089756264 0.902702568 0.595583692 0.062996862 0.10503615 9.677561024 0.025926011 0.016852169 96.81808768 -1.9859565 -0.187053696 NPDGGPLESSSDLAALS(ph)PLTSSGHQEQDTELGSTHTAGATSSLTPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPDGGPLESSSDLAALSPLTSSGHQEQDTELGSTHTAGATSSLTPSR 47 0 Q7Z434;Q7Z434-4 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 1 NPDGGPLES(0.001)S(0.001)S(0.001)DLAALS(0.664)PLT(0.077)S(0.063)S(0.063)GHQEQDT(0.022)ELGS(0.022)T(0.022)HT(0.026)AGAT(0.008)S(0.008)S(0.008)LT(0.008)PS(0.008)R 48.233 0.032021 115110000 4312.9 5579.6 7178.9 7401.9 3983.4 6478.9 5359.3 3429.7 6718.7 4683.9 TRUE FALSE 4144.3471 5420.475271 8476.286924 7783.912946 4111.529679 6609.907797 5424.888717 3358.875496 5956.021343 4366.655281 0.949089597 1.241333451 1.941139471 1.782580132 0.941574137 1.51372329 1.242344167 0.769210135 1.36397791 1 12.09231293 1.986201463 9.853532349 1.01530027 1.407264641 0.184772429 0.327706682 0.459402283 307.5286024 0.136214474 0.092096083 96.87271303 -1.986201463 0.391964371 AAESETPGKS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 5 AAESETPGKSPEK 13 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AAES(0.006)ET(0.033)PGKS(0.962)PEK;AAESET(0.009)PGKS(0.99)PEK;AAESETPGKS(1)PEK;AAESET(0.005)PGKS(0.995)PEK;AAESET(0.001)PGKS(0.999)PEK 253.06 2.36E-23 2442380000 3857670 2844270 3007410 2749540 3010830 2437050 3187250 3979750 3667350 3728030 TRUE FALSE 3706907.992 2763154.204 3550915.886 2891444.089 3107676.081 2486328.821 3226256.519 3897566.772 3251047.803 3475527.208 1.066574298 0.795031671 1.021691293 0.831944024 0.894159618 0.715381774 0.928278309 1.121431811 0.935411409 1 21.72880041 1.986221755 24.78954812 1.03054391 0.881701453 0.236302731 0.104796828 691.7186046 1244525.991 0.039890876 0.026944944 96.87723955 -1.986221755 -0.148842457 IQHSITAQDHQPTPDSCIISMVVGQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IQHSITAQDHQPTPDSCIISMVVGQLK 27 0 P61970;H3BRV9 P61970 NUTF2 Nuclear transport factor 2 0 ; 129.78 2.95E-05 1013800000 1169720 1185990 917410 999600 1105780 1064040 958850 555450 1136730 1095450 FALSE TRUE 1124006.049 1152166.726 1083206.395 1051189.476 1141348.418 1085555.618 970584.6931 543979.7634 1007693.176 1021254.196 1.100613397 1.128187998 1.060662859 1.029312271 1.117594838 1.06296319 0.950385024 0.532658535 0.98672121 1 19.96191057 1.986233276 8.369282561 0.776079968 1.077345888 0.40214296 0.127013566 0.132563978 62.0843158 0.049362281 0.033208746 96.87980937 -1.986233276 0.30126592 QNGSNDS(ph)DRYS(ph)DNEEDSKIELK ddPTM_BT-474_Pertuzumab_2h_R1 4 QNGSNDSDRYSDNEEDSKIELK 22 2 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 2 QNGSNDS(0.998)DRY(0.004)S(0.997)DNEEDSKIELK;QNGS(0.179)NDS(0.821)DRYS(1)DNEEDSKIELK;QNGS(0.233)NDS(0.767)DRY(0.001)S(0.999)DNEEDSKIELK;QNGS(0.411)NDS(0.589)DRY(0.097)S(0.903)DNEEDSKIELK 153.06 1.97E-08 901387000 1144808 1230593 715926 1014090 880741 761029 1108632 1781634 1476249 963370 TRUE FALSE 1100067.638 1195497.693 845309.7539 1066427.306 909070.8341 776417.5278 1122199.77 1744842.635 1308671.402 898120.0918 1.224855838 1.331111177 0.941199024 1.187399454 1.01219296 0.864491881 1.24949857 1.942772076 1.457122955 1 19.77654884 1.986363854 23.89476284 1.577572018 1.094568474 0.272739369 0.254215752 322.6549263 565391.1114 0.097642026 0.066060979 96.9089425 -1.986363854 -0.483003544 KNPDDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KNPDDFK 7 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 99.442 0.016877 504610000 756010 685160 602500 604600 649500 686840 709730 804240 886550 807120 FALSE TRUE 726464.2934 665619.9076 711385.1525 635803.4785 670391.7574 700728.3754 718415.888 787632.163 785912.5607 752453.0435 0.9654613 0.884599927 0.945421324 0.844974293 0.890941652 0.93125861 0.954765077 1.046752578 1.04446725 1 19.52124203 1.986400229 2.263692056 1.035474133 0.905855135 0.708648058 0.034226318 0.152845969 1.456373643 0.018488372 0.009846107 96.9170595 -1.986400229 -0.129618998 RHSS(ph)DINHLVTQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHSSDINHLVTQGR 14 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 RHS(0.405)S(0.595)DINHLVTQGR 123.41 4.85E-05 1397800000 232680 413500 365710 501030 379780 458800 332130 38765 367380 346550 TRUE FALSE 223586.6084 401707.3849 431801.9322 526888.2183 391995.9686 468077.2503 336194.7063 37964.4892 325676.5626 323077.8598 0.692051781 1.243376396 1.336525915 1.630839757 1.213317337 1.448806336 1.040599645 0.117508793 1.00804358 1 18.30152236 1.986439239 19.97381701 0.602609604 1.27534307 0.351581726 0.326025637 37.87733781 55789.05287 0.127131671 0.086236983 96.92576539 -1.986439239 0.672733465 RPENPKPQDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 RPENPKPQDGK 11 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;; 153.75 1.82E-05 1316390000 2234370 2147850 1993980 2112440 2302180 2449820 2674820 3055490 3596950 3525500 FALSE TRUE 2147048.35 2086595.421 2354336.542 2221463.282 2376231.71 2499357.039 2707555.247 2992393.064 3188639.316 3286714.745 0.653250591 0.634857474 0.716319098 0.67589172 0.722980817 0.760442336 0.82378772 0.910451103 0.970160042 1 21.64821482 1.986593173 0.738622688 1.010520992 0.660796702 0.976736317 0.019213871 0.086691396 0.089791367 0.016776166 0.00898912 96.96012641 -1.986593173 -0.34972429 EHRPGPIGNER ddPTM_BT-474_Pertuzumab_2h_R1 1 EHRPGPIGNER 11 1 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 0 120.87 0.0002544 95588000 39849 38024 30107 47818 55372 41624 40914 35864 46900 38744 FALSE TRUE 38291.65702 36939.59275 35548.00463 50285.89271 57153.09067 42465.6658 41414.71777 35123.39587 41576.10862 36119.83437 1.060128256 1.022695519 0.984168539 1.392196105 1.582318736 1.175688276 1.146592128 0.972412982 1.151060334 1 15.14050366 1.986677944 3.906792439 1.040532826 1.2088643 0.146829526 0.173305 0.472659772 15.70415158 0.088218361 0.054355306 96.97905419 -1.986677944 0.168331474 KS(ph)PGDEDDKDCK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPGDEDDKDCK 12 2 Q9Y3E1;H3BPM9 Q9Y3E1 HDGFRP3 Hepatoma-derived growth factor-related protein 3 1 KS(1)PGDEDDKDCK 49.595 0.088079 160070000 112440 83139 79501 76141 99070 76004 107380 133800 152160 118190 TRUE FALSE 108045.7205 80767.95712 93868.59919 80070.64613 102256.6765 77540.85295 108694.1486 131036.9832 134887.4347 110184.886 0.980585672 0.733022105 0.851919012 0.726693551 0.928046307 0.703734022 0.986470581 1.189246438 1.224191807 1 16.74956682 1.986728303 4.196428997 1.148760935 0.818901882 0.672660963 0.099390124 0.107650346 4.381213855 0.040733374 0.025472072 96.99030004 -1.986728303 -0.329859053 LEEAEK ddPTM_BT-474_Pertuzumab_2h_R1 6 LEEAEK 6 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2;Q8ND24;E9PN76;Q8ND24-2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2;Q8ND24 TPM3;TPM1;TPM4;RNF214 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain;RING finger protein 214 0 ;;;;; 124.89 0.042251 4064030000 5097270 4722630 4191170 4230690 4436230 4605420 4897640 5654880 5792900 5683870 FALSE TRUE 4898063.053 4587945.216 4948607.651 4449036.418 4578925.367 4698544.748 4957578.783 5538104.752 5135314.278 5298896.422 0.924355312 0.865830326 0.933894014 0.83961566 0.864128113 0.886702508 0.935587033 1.045143047 0.969129016 1 22.3372605 1.986759319 3.818361284 1.007578701 0.884675273 0.740316519 0.031471659 0.103434435 3.229709812 0.013953183 0.008555358 96.99722704 -1.986759319 -0.122903427 SRPTS(ph)EGSDIES(ph)TEPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.011)RPT(0.39)S(0.594)EGS(0.066)DIES(0.935)T(0.004)EPQK 224.38 3.27E-14 278100000 876340 776650 689030 728520 775560 730350 781980 845680 905880 813280 TRUE FALSE 842091.664 754500.7024 813553.0484 766119.0045 800506.5917 745118.1774 791550.1052 828216.4125 803048.3002 758195.8212 1.110651946 0.995126432 1.073011781 1.010450049 1.055804542 0.982751628 1.043991648 1.092351592 1.059156853 1 19.53221098 1.986800714 24.65587266 1.062615985 1.035188553 0 0.041633966 1314.639401 2455707.208 0.015498521 0.010427218 97.00647279 -1.986800714 -0.027427432 NSDDAPWS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSDDAPWSPK 10 0 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9;Q9UPP1-5;H0Y589 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 NSDDAPWS(1)PK;NSDDAPWS(1)PK 203.74 2.10E-07 1570970000 3707800 2895800 2654700 2804700 3018800 2693400 3113600 3718500 3629500 3374500 TRUE FALSE 3562895.077 2813214.619 3134463.343 2949450.903 3115902.444 2747862.393 3151705.168 3641711.676 3217494.376 3145942.109 1.132536758 0.894235978 0.996351247 0.937541379 0.990451297 0.873462479 1.001831902 1.157590175 1.022744305 1 21.58506069 1.98686724 24.37580262 1.078143912 0.965317154 0.199868393 0.077010285 506.9818696 941011.7862 0.028633373 0.019433446 97.02133365 -1.98686724 -0.112826758 GATKES(ph)SEKDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GATKESSEKDR 11 2 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 GAT(0.007)KES(0.497)S(0.497)EKDR;GATKES(0.5)S(0.5)EKDR;GAT(0.002)KES(0.83)S(0.169)EKDR 158.93 1.53E-05 1233900000 3444840 2617670 2306960 2053690 2452620 2320270 2769200 3204840 3493230 3030550 TRUE FALSE 3310211.844 2543016.615 2723878.99 2159681.187 2531510.75 2367187.449 2803090.298 3138658.934 3096693.175 2825288.149 1.171636898 0.900091063 0.964106614 0.764410946 0.896018606 0.837856999 0.992143155 1.110916398 1.096062777 1 21.42996658 1.986917459 5.519434377 1.075552736 0.914474312 0.289678791 0.102466014 0.198985159 20.13101866 0.043019767 0.028102069 97.03255327 -1.986917459 -0.161078423 HLLQAPVDDAQEILHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLLQAPVDDAQEILHSR 17 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;; 202.03 6.34E-12 2465220000 773460 780090 659920 885100 837590 825410 748220 452880 893990 863200 FALSE TRUE 743232.3281 757842.597 779182.2238 930780.1171 864531.843 842100.3557 757376.9402 443527.8697 792508.0031 804734.6951 0.923574356 0.941729742 0.968247335 1.156629785 1.074306661 1.046432272 0.941151096 0.55114794 0.984806555 1 19.61815371 1.987004773 23.56577607 0.783121637 1.0192191 0.211201083 0.134882303 290.9681351 527646.143 0.053150803 0.036120128 97.05206335 -1.987004773 0.236097463 SNS(ph)PDKFK ddPTM_BT-474_Pertuzumab_2h_R1 6 SNSPDKFK 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 S(0.003)NS(0.997)PDKFK;S(0.04)NS(0.96)PDKFK;S(0.086)NS(0.914)PDKFK;S(0.094)NS(0.906)PDKFK;S(0.001)NS(0.999)PDKFK;S(0.004)NS(0.996)PDKFK 125.54 0.00076157 9823020000 14045920 10492330 10814650 9165250 10591770 9436230 12713350 15404560 17009650 14515880 TRUE FALSE 13496989.92 10193099.02 12769097.83 9638269.651 10932463.9 9627037.036 12868939.78 15086450.45 15078785.84 13532706.52 0.99736072 0.753219543 0.943573099 0.7122204 0.807854947 0.711390365 0.950950925 1.114813983 1.114247606 1 23.68994707 1.987088024 4.516626522 1.080170679 0.817776291 0.610053241 0.091728271 0.122178022 6.219403716 0.038232133 0.024252756 97.0706693 -1.987088024 -0.262394388 VTS(ph)PEKAEEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTSPEKAEEAK 11 1 P56211;H3BMD8;P56211-2;H3BTD3 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 VT(0.182)S(0.818)PEKAEEAK;VT(0.294)S(0.706)PEKAEEAK 123.76 0.00022 513540000 1101570 886360 970120 870330 970510 851820 1131440 1374570 1362730 1521710 TRUE FALSE 1058519.427 861081.8806 1145442.264 915247.8356 1001727.336 869044.384 1145286.901 1346184.649 1208038.603 1418643.226 0.746149142 0.60697564 0.807420952 0.64515716 0.706116462 0.6125884 0.807311437 0.948924031 0.85154504 1 20.43608038 1.987154369 4.044104439 0.921275829 0.688354234 0.731939003 0.066675428 0.105617057 3.86726074 0.027712973 0.017212452 97.08549943 -1.987154369 -0.232921595 EDS(ph)GTFSLGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.845)GT(0.155)FSLGK;EDS(0.87)GT(0.13)FSLGK;EDS(0.999)GT(0.001)FSLGK;EDS(0.948)GT(0.052)FS(0.001)LGK 223.08 1.21E-07 4509110000 8296670 6432030 4330170 5903140 7693180 5639060 7521820 10368840 9322160 8379770 TRUE FALSE 7972426.964 6248594.802 5112728.043 6207801.763 7940638.121 5753085.657 7613874.283 10154719.83 8263947.478 7812200.714 1.020509746 0.799850776 0.654454261 0.794629067 1.016440618 0.736423175 0.974613244 1.299853934 1.057825801 1 22.89729759 1.98717013 7.076849665 1.149678355 0.834634349 0.487847292 0.128826488 0.112189207 30.17099336 0.052179728 0.034887834 97.08902285 -1.98717013 -0.315044006 HIPGAAFFDIDQCSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 HIPGAAFFDIDQCSDR 16 0 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;;; 238.22 8.75E-20 1366550000 999577 1109260 812164 1197100 1041461 1025451 1006864 826406 1165630 1181960 FALSE TRUE 960512.4257 1077624.991 958940.1013 1258882.474 1074960.539 1046186.322 1019186.303 809340.4273 1033312.569 1101904.796 0.871683678 0.977965605 0.870256763 1.142460291 0.975547563 0.949434402 0.924931361 0.734492154 0.937751222 1 20.07156815 1.987178851 18.16981686 0.853362921 0.96677729 0.06921099 0.096166768 24.6295673 34902.45296 0.037450941 0.025527236 97.09097239 -1.987178851 0.113414369 ERPLCPLQPQNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPLCPLQPQNR 12 1 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 152.23 6.35E-05 1087080000 606630 689110 601490 659100 595620 664930 639970 579780 710870 788080 FALSE TRUE 582922.2289 669457.2575 710192.6231 693116.23 614778.6582 678375.3402 647802.1443 567807.3404 630175.0178 734702.6397 0.79341246 0.911194845 0.966639542 0.943396951 0.836772083 0.923333201 0.881720181 0.772839663 0.857727989 1 19.48680093 1.987280697 24.31995239 0.845531865 0.899471008 0 0.071847638 973.2404457 1860884.03 0.027829761 0.018938938 97.11374376 -1.987280697 0.053939143 QHLASIYEKEEDWR ddPTM_BT-474_Pertuzumab_2h_R1 2 QHLASIYEKEEDWR 14 1 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ; 153.24 3.87E-06 390920000 558920 561500 417250 437420 521610 572180 456980 175084 589740 466310 FALSE TRUE 537076.7885 545486.5698 492656.3567 459995.2986 538388.0594 583749.8716 462572.6579 171468.4542 522795.1876 434726.4084 1.235436307 1.254781304 1.133256106 1.058125961 1.23845262 1.342798276 1.064054654 0.394428429 1.202584378 1 18.72974821 1.987377174 24.38612506 0.781099249 1.203334228 0.337681504 0.206261685 364.588453 704350.6332 0.078834058 0.053716239 97.13531973 -1.987377174 0.422234979 SQT(ph)PERPAKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQTPERPAKK 10 2 A8CG34-2;A8CG34;A6NF01;C9JFL1;Q96HA1-2;Q96HA1-3;Q96HA1 A8CG34-2;Q96HA1-2 POM121C;POM121B;POM121 Nuclear envelope pore membrane protein POM 121C;Putative nuclear envelope pore membrane protein POM 121B;Nuclear envelope pore membrane protein POM 121 1 S(0.202)QT(0.798)PERPAKK;S(0.008)QT(0.992)PERPAKK 82.069 0.030741 470250000 475020 484890 315580 401700 330750 334640 424840 576880 504500 434390 TRUE FALSE 456455.6932 471061.412 372612.326 422431.7851 341388.8741 341406.6501 430039.319 564967.2264 447231.275 404968.3784 1.127139099 1.163205418 0.920102274 1.04312289 0.843001312 0.843045206 1.061908391 1.395089732 1.10436098 1 18.62744974 1.987395763 24.70676356 1.214911612 0.987218082 0.225210775 0.138071071 572.685362 1122574.879 0.056069784 0.038215252 97.13947739 -1.987395763 -0.22769353 TLT(ph)PPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLTPPLR 7 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.001)LT(0.999)PPLR 103.8 0.092722 137230000 38507 35899 36506 43783 38218 37178 41620 52314 47088 45663 TRUE FALSE 37002.10387 34875.19567 43103.44627 46042.64588 39447.31668 37929.76463 42129.35801 51233.69762 41742.76765 42570.20434 0.869201932 0.819239565 1.012526177 1.081569764 0.926641469 0.890993248 0.989644252 1.203510728 0.980563009 1 15.37755639 1.987407359 22.16088077 1.087122095 0.938380415 0.278277371 0.089362043 148.5662593 261450.1448 0.036980812 0.025224396 97.14207118 -1.987407359 -0.14874168 LRDEYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRDEYR 6 1 P18074;E7EVE9;A8MX75;K7EIT8;P18074-2 P18074 ERCC2 TFIIH basal transcription factor complex helicase XPD subunit 0 ; 134.12 0.012921 350720000 138536 140841 117020 137610 134863 138187 132609 110846 153337 155907 FALSE TRUE 133121.86 136824.3526 138168.1171 144712.0686 139200.9909 140981.2358 134231.9086 108556.9914 135930.8266 145347.28 0.915888209 0.941361631 0.95060683 0.995629699 0.957713078 0.969961294 0.923525425 0.746880102 0.935214106 1 17.14914455 1.987415063 24.62459935 0.858230915 0.955511685 0.081903131 0.064839249 561.8859069 1099426.508 0.024682662 0.016825442 97.14379441 -1.987415063 0.09728077 KDGS(ph)SPPLLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDGSSPPLLEK 11 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;Q6W2J9-3 H7BYY2 BCOR BCL-6 corepressor 1 KDGS(0.741)S(0.259)PPLLEK;KDGS(0.616)S(0.384)PPLLEK 95.57 0.0046917 996560000 2171310 1947270 1664930 1550120 1810610 1833470 1999850 2346400 2446100 2306740 TRUE FALSE 2086452.805 1891735.766 1965819.887 1630121.879 1868849.915 1870544.02 2024324.763 2297946.02 2168428.983 2150502.445 0.97021643 0.879671525 0.914121205 0.758019077 0.86902943 0.869817202 0.941326417 1.068562384 1.008335976 1 21.03624234 1.987506313 3.626844197 1.030253731 0.873543783 0.615977244 0.052451278 0.147139844 4.016425927 0.024764633 0.015022953 97.16420755 -1.987506313 -0.156709948 VHCEELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHCEELEK 8 0 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 127.56 0.0026642 0 155300 176170 119180 171400 187220 195930 163050 136300 172840 184900 FALSE TRUE 149230.7043 171145.8041 140718.4771 180245.9745 193242.1013 199891.8388 165045.4547 133485.3574 153219.9278 172376.5583 0.865725049 0.992860084 0.816343466 1.045652473 1.121046291 1.1596231 0.957470414 0.77438231 0.888867543 1 17.39520407 1.98763557 24.66794728 0.863492559 1.004031129 0.16205782 0.110151067 736.0288884 1468431.528 0.046266345 0.031588518 97.1931304 -1.98763557 0.14053857 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 44 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.978)PMAQT(0.022)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 52.451 0.013082 249030000 89944 81913 82875 91159 82264 86821 82089 64850 99714 88462 TRUE FALSE 86428.88904 79576.92144 97852.35604 95863.72691 84910.09627 88576.58011 83093.62974 63510.82484 88394.88476 82470.38995 1.047999035 0.964915062 1.186515016 1.162401766 1.029582815 1.074041 1.007557134 0.770104578 1.071837842 1 16.33158861 1.987679167 10.75125692 0.913512756 1.075944528 0.261139008 0.093848511 0.407341954 344.4799982 0.037516064 0.025541177 97.20288758 -1.987679167 0.162431771 IHVSDQELQSANASVDDSRLEELK ddPTM_BT-474_Pertuzumab_2h_R1 4 IHVSDQELQSANASVDDSRLEELK 24 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 269.25 3.32E-45 1955246000 1054232 1625190 1056308 1234696 1130938 1549340 1193064 829809 1206641 1227802 FALSE TRUE 1013031.448 1578841.172 1247206.353 1298418.809 1167315.648 1580668.716 1207665.074 812673.1542 1069668.172 1144641.877 0.885020432 1.379332003 1.089603987 1.134345016 1.019808616 1.38092861 1.055059315 0.709980275 0.934500296 1 20.12646486 1.987681963 23.92021929 0.857581708 1.155258062 0.363794363 0.156602903 291.3066222 565683.6805 0.057986913 0.039598951 97.20351347 -1.987681963 0.297676353 IAHIMGPPDR ddPTM_BT-474_Pertuzumab_2h_R1 6 IAHIMGPPDR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;; 103.7 0.0021085 3577700000 1659100 1823600 1361070 1769900 1705160 1731520 1622440 1598450 1721920 1735850 FALSE TRUE 1594260.538 1771592.713 1607045.626 1861244.751 1760008.02 1766532.521 1642295.906 1565441.449 1526454.86 1618279.333 0.985157818 1.094738515 0.99305824 1.150138121 1.087579866 1.091611618 1.014840808 0.967349342 0.943257959 1 20.62602922 1.987691266 3.229937548 0.968355575 1.06947238 0.454007492 0.047666118 0.214893476 4.408973967 0.022369455 0.013191177 97.20559568 -1.987691266 0.101116806 HIEDTGS(ph)TPSIGENDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HIEDTGSTPSIGENDLK 17 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 HIEDT(0.046)GS(0.527)T(0.427)PSIGENDLK 162.42 1.83E-09 187300000 313430 299800 247800 253350 296900 295050 270070 164460 355780 316920 TRUE FALSE 301180.8091 291249.9975 292582.9723 266425.4239 306450.0581 301016.1132 273375.1974 161063.8435 315393.346 295454.7261 1.019380577 0.98576862 0.990280224 0.901747037 1.037214947 1.018823145 0.925269333 0.545138829 1.067484518 1 18.17257755 1.987739056 24.60585743 0.799051758 0.988281146 0.071379679 0.137368513 594.8859175 1193845.23 0.052442346 0.035822538 97.21629282 -1.987739056 0.189229388 KSSTPEEVKK ddPTM_BT-474_Pertuzumab_2h_R1 5 KSSTPEEVKK 10 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;; 113.77 0.00081242 18820150000 10030760 8880450 7121630 6928790 8413370 8873160 9047600 9765960 12006940 10192100 FALSE TRUE 9638746.81 8627188.261 8408666.961 7286385.682 8683993.687 9052581.375 9158327.235 9564289.513 10643962.51 9501779.989 1.014414859 0.907954959 0.884957026 0.766844285 0.913933357 0.952724793 0.963853851 1.006578717 1.120207216 1 23.17976637 1.987761056 1.325029351 1.054076297 0.893798544 0.48318776 0.06420613 0.379908492 1.238378855 0.047867364 0.022218196 97.22121754 -1.987761056 -0.160277753 QPSS(ph)PYEDKDK ddPTM_BT-474_Pertuzumab_2h_R1 6 QPSSPYEDKDK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.077)S(0.923)PYEDKDK;QPS(0.035)S(0.965)PYEDKDK;QPS(0.031)S(0.969)PYEDKDK;QPS(0.05)S(0.95)PYEDKDK;QPS(0.004)S(0.996)PYEDKDK;QPS(0.126)S(0.874)PYEDKDK 204.94 8.28E-08 6543800000 5729790 3968810 4914370 4521370 5019600 4357270 6077530 7354300 8454380 7332100 TRUE FALSE 5505863.472 3855623.425 5802505.979 4754718.448 5181059.993 4445376.985 6151908.63 7202431.135 7494674.226 6835490.336 0.80548186 0.564059524 0.84887926 0.695592886 0.757964643 0.650337688 0.89999522 1.053681708 1.096435494 1 22.7046134 1.987775169 3.072421126 1.051795795 0.719990512 0.780183185 0.078664374 0.106690251 1.949042964 0.035860663 0.020873816 97.22437697 -1.987775169 -0.331805283 EMLPGALHGELHPSEGPWGAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EMLPGALHGELHPSEGPWGAPR 22 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 0 ; 215.98 7.98E-26 163558000 87471 100211 85011 110482 98509 111149 87774 33414 96427 100405 FALSE TRUE 84052.53662 97353.0804 100374.3788 116183.9893 101677.6314 113396.5089 88848.20447 32723.98922 85481.01121 93604.47992 0.897954208 1.040047234 1.072324517 1.241222529 1.086247491 1.211443181 0.949187523 0.349598537 0.913214958 1 16.51428996 1.987804532 22.9606195 0.673851402 1.093674659 0.376343001 0.18604863 150.3441143 283054.9712 0.071019624 0.048550221 97.23095069 -1.987804532 0.419823257 MHSVGICGSDVHYWEYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 MHSVGICGSDVHYWEYGR 18 0 Q00796;A0A6I8PIS1;H0YKB3;Q00796-2 Q00796 SORD Sorbitol dehydrogenase 0 132.59 1.01E-05 390880000 35528 35823 35909 39758 41008 43011 33656 7442.4 37172 44116 FALSE TRUE 34139.52648 34801.36311 42398.55509 41809.91514 42327.05956 43880.71189 34067.8922 7288.711839 32952.3904 41127.98403 0.830080231 0.846172355 1.030893103 1.016580709 1.029154736 1.066930775 0.82833849 0.177220256 0.801215795 1 15.32783274 1.987884895 24.01233883 0.55173883 0.969896129 0.258417568 0.213804686 301.8737684 598318.4084 0.081618252 0.055803019 97.24894429 -1.987884895 0.418157299 HIDDS(ph)SPEDLIAAFTETR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIDDSSPEDLIAAFTETR 18 0 O95197-7;O95197-2;O95197 O95197-7 RTN3 Reticulon-3 1 HIDDS(0.5)S(0.5)PEDLIAAFTETR;HIDDS(0.5)S(0.5)PEDLIAAFTETR 99.569 0.00065179 20355500 35769 36917 32896 40104 33358 35511 34686 24102.1 48794 34788 TRUE FALSE 34371.10794 35864.16331 38841.03897 42173.77225 34430.99036 36229.05675 35110.49764 23604.38321 43255.10968 32431.77777 1.05979722 1.105834024 1.197622876 1.300384226 1.061643633 1.117085132 1.08259553 0.727816507 1.333726137 1 14.98512049 1.98793302 23.72431984 0.969005218 1.141344498 0.082111177 0.153449212 456.732883 897959.884 0.059607903 0.040784384 97.25972105 -1.98793302 0.172339279 KSEGDGDKEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSEGDGDKEEK 11 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 103.85 0.0015065 191790000 691990 517270 404320 384470 535410 508680 617480 726120 819670 789290 FALSE TRUE 664946.2658 502517.9661 477389.618 404312.5428 552631.9489 518965.8581 625036.9049 711125.3683 726624.4979 735830.6853 0.903667486 0.682926081 0.648776448 0.549464097 0.751031399 0.705278902 0.849430334 0.966425269 0.987488715 1 19.48901431 1.987972498 1.774941747 0.994361455 0.693496752 0.687719476 0.084112233 0.203357269 1.193630368 0.053424664 0.026473553 97.26856252 -1.987972498 -0.300864703 AEDEALLS(ph)EEDDPIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEDEALLSEEDDPIDR 16 0 Q04721 Q04721 NOTCH2 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain 1 AEDEALLS(1)EEDDPIDR 143.97 1.43E-06 59316000 102020 102290 89846 97609 97002 102750 104510 121140 122280 117040 TRUE FALSE 98032.94561 99372.78935 106083.1708 102646.6122 100122.1574 104827.6754 105789.0246 118638.4167 108399.287 109112.7766 0.898455238 0.910734677 0.97223418 0.940738706 0.917602508 0.960727778 0.96953838 1.087300868 0.99346099 1 16.73546052 1.987991077 4.038095978 1.03583364 0.934891427 0.624809602 0.031999357 0.12551744 4.583341486 0.014260596 0.008865758 97.2727238 -1.987991077 -0.100942214 RRPGAQPLPPPPPSQS(ph)PEPTEPHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRPGAQPLPPPPPSQSPEPTEPHPR 25 2 K7EPZ6;A0A0A0MS90;Q9UIS9-4;Q9UIS9-11;Q9UIS9-7;Q9UIS9-10;Q9UIS9-6;Q9UIS9-5;Q9UIS9;Q9UIS9-9;Q9UIS9-12 K7EPZ6;Q9UIS9-6 MBD1 Methyl-CpG-binding domain protein 1 1 RRPGAQPLPPPPPS(0.001)QS(0.999)PEPTEPHPR 173.03 2.63E-12 301960000 77622 68757 62852 105750 59134 82857 73438 58611 77535 86327 TRUE FALSE 74588.44642 66796.11768 74210.75454 111207.7702 61036.09881 84532.42531 74336.75621 57400.66237 68733.55185 80479.9954 0.926794864 0.829971689 0.922101873 1.381806368 0.758400874 1.050353257 0.923667501 0.713228947 0.854045176 1 16.2963426 1.98800611 22.42536381 0.822532936 0.978107873 0.085144982 0.169885845 281.7047339 526710.9795 0.066448443 0.045496204 97.27609087 -1.98800611 0.155574937 AVLFCLS(ph)EDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVLFCLSEDKK 11 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 AVLFCLS(1)EDKK;AVLFCLS(1)EDKK 106.58 0.0014166 916270000 690770 499760 290580 394290 490420 355440 483980 749750 476890 348790 TRUE FALSE 663773.9447 485507.3341 343094.2699 414639.3542 506194.8047 362627.2403 489903.092 734267.4005 422755.4465 325166.1426 2.04133782 1.493105433 1.055135283 1.275161524 1.556726665 1.115206022 1.506623931 2.258129935 1.300121357 1 18.31081752 1.988032642 24.48554871 1.715001206 1.400499027 0 0.404768565 988.2869485 2022062.401 0.157652015 0.107943124 97.28203399 -1.988032642 -0.314502179 DRYDSFIELQEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DRYDSFIELQEK 12 1 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ;;; 308.74 2.86E-46 2807450000 2710200 2490740 2254730 2353410 2480160 2409890 2734370 3113130 3410900 3142950 FALSE TRUE 2604282.388 2419706.534 2662209.867 2474869.772 2559936.599 2458619.627 2767834.038 3048842.778 3023708.932 2930075.197 0.888810769 0.825817213 0.908580732 0.844643774 0.873676075 0.839097792 0.944629012 1.04053397 1.031956086 1 21.48250626 1.988083252 3.285241257 1.025819417 0.863655319 0.890476738 0.0252932 0.066984017 1.431478437 0.011243986 0.006662545 97.29337124 -1.988083252 -0.162164097 DHIKDEWEGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHIKDEWEGLR 11 1 O60306;H0YH15 O60306 AQR Intron-binding protein aquarius 0 ; 198.55 3.20E-08 703780000 411720 406030 335030 328800 392630 407430 344950 116618 503610 396230 FALSE TRUE 395629.5272 394450.4219 395577.3737 345769.4074 405259.3005 415668.5138 349171.6013 114209.7975 446442.3041 369392.9892 1.071026086 1.067834078 1.070884898 0.936047563 1.097095268 1.125274507 0.945257792 0.309182364 1.208583588 1 18.49479696 1.988170945 24.58601061 0.728678365 1.056120091 0.112272363 0.22391013 535.3579923 1112710.375 0.085168834 0.058350642 97.3130187 -1.988170945 0.327441726 ALGVISNFQSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALGVISNFQSSPK 13 0 Q6N039;E9PC87;O94876-2;O94876 Q6N039 DKFZp686H13261;TMCC1 Transmembrane and coiled-coil domains protein 1 1 ALGVISNFQS(0.043)S(0.957)PK 146.59 4.44E-05 341380000 1098600 1256400 828430 1565700 1122100 1177500 1390600 1888600 1918900 1318400 TRUE FALSE 1055665.497 1220568.702 978145.7293 1646505.965 1158193.366 1201309.857 1407618.579 1849599.75 1701074.517 1229103.594 0.858890579 0.993056003 0.795820413 1.339599016 0.942307362 0.977386986 1.145239983 1.504836337 1.383996048 1 20.22917509 1.988279188 4.94176985 1.348869209 0.993948736 0.364367886 0.181042618 0.167229825 11.46897227 0.074662176 0.04817466 97.33727595 -1.988279188 -0.354920473 LNNDLVGS(ph)TENLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNNDLVGSTENLLK 14 0 Q8N5G2;A0A3B3ITD2 Q8N5G2 TMEM57 Macoilin 1 LNNDLVGS(0.701)T(0.299)ENLLK 173.87 2.76E-06 67953000 122900 145490 94401 178260 94516 80583 151630 271580 201230 148070 TRUE FALSE 118096.9321 141340.7676 111461.3606 187460.02 97556.19298 82212.44347 153485.6933 265971.7781 178387.214 138041.087 0.855520155 1.023903612 0.807450615 1.358001621 0.706718522 0.595565025 1.111884125 1.926758068 1.292276219 1 17.07473821 1.988315509 23.94020145 1.511818792 0.901875056 0.370319227 0.291247505 264.5924018 542119.5041 0.111985537 0.076811305 97.34541688 -1.988315509 -0.609943736 ATS(ph)PEAGGGGGALK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSPEAGGGGGALK 14 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 AT(0.024)S(0.976)PEAGGGGGALK 152.88 6.87E-06 350330000 501150 511250 458820 504450 456770 581980 546950 582430 696380 677220 TRUE FALSE 481564.5039 496669.6506 541738.9804 530484.725 471462.4219 593748.0343 553643.7377 570402.617 617329.8619 631351.2862 0.762752076 0.786677182 0.858062686 0.840237023 0.746751345 0.940440049 0.876918682 0.903463142 0.977791406 1 19.26808342 1.988397115 0.428094901 1.009649322 0.777896983 0.714886649 0.04445263 0.58656508 0.260697099 0.047911927 0.044301791 97.36371026 -1.988397115 -0.231752339 HADNS(ph)SDTEMEDMIAEETLEEMDSELLK ddPTM_BT-474_Pertuzumab_2h_R1 6 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.412)S(0.412)DT(0.175)EMEDMIAEETLEEMDSELLK;HADNS(0.653)S(0.345)DT(0.002)EMEDMIAEETLEEMDSELLK;HADNS(0.347)S(0.347)DT(0.307)EMEDMIAEETLEEMDSELLK;HADNS(0.461)S(0.461)DT(0.078)EMEDMIAEETLEEMDSELLK;HADNS(0.32)S(0.32)DT(0.32)EMEDMIAEET(0.04)LEEMDSELLK;HADNS(0.361)S(0.361)DT(0.279)EMEDMIAEETLEEMDSELLK 382.33 2.23E-129 640380000 435945 377605 330545.5 333053.4 352292.5 367960 331721.4 146772.5 468036 336731.8 TRUE FALSE 418907.7874 366836.0751 390282.4248 350242.3259 363624.3082 375400.4033 335781.1057 143741.5966 414906.5154 313924.6553 1.33442143 1.16854815 1.243235975 1.115689131 1.158317138 1.195829627 1.069623236 0.457885656 1.321675467 1 18.26005882 1.988484492 23.73495264 0.840652681 1.191640393 0.232205476 0.208269885 286.0571103 589600.3931 0.078785967 0.054125349 97.38330103 -1.988484492 0.350987712 LIDVLENR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIDVLENR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 138.54 0.0016302 229520000 120161 130516 109417 130276 124287 118149 124405 121056 121035 138562 FALSE TRUE 115464.9753 126793.8115 129191.0859 136999.56 128284.8042 120538.0537 125927.5056 118556.1513 107295.6142 129177.0723 0.893850381 0.981550435 1.000108483 1.060556316 0.993092674 0.933122663 0.974844091 0.917780138 0.830608809 1 16.9789905 1.988526239 1.593728708 0.908174962 0.985872775 0.182741827 0.056240084 0.563905327 2.67031721 0.036966883 0.017797024 97.39266249 -1.988526239 0.077697813 SLTWPPS(ph)GSPSHAGTTPPENGLSEHPCETEQINAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLTWPPSGSPSHAGTTPPENGLSEHPCETEQINAK 35 0 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5 P23497 SP100 Nuclear autoantigen Sp-100 1 SLTWPPS(0.491)GS(0.491)PS(0.018)HAGTTPPENGLSEHPCETEQINAK;SLTWPPS(0.554)GS(0.434)PS(0.012)HAGTTPPENGLSEHPCETEQINAK 274.99 7.12E-74 518170000 236745 290730 216438 275570 256910 283070 251570 196453 283290 281600 TRUE FALSE 227492.7437 282438.6651 255553.1612 289792.2007 265173.7435 288793.8693 254648.7889 192396.1769 251132.1068 262526.9812 0.866549955 1.075846238 0.973435797 1.103856828 1.010081868 1.100054052 0.969990923 0.732862489 0.956595416 1 18.00210618 1.988533955 24.56461672 0.862959677 1.025947506 0.243148475 0.09324231 419.2782074 898252.7821 0.03460034 0.023771439 97.39439286 -1.988533955 0.162987829 HGQALGELAEQLEQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGQALGELAEQLEQAR 16 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 133.86 3.14E-05 454210000 148560 159370 145690 139190 131760 161910 142510 110540 162550 155080 FALSE TRUE 142754.111 154824.9236 172019.4239 146373.6126 135998.1801 165183.9311 144254.08 108257.3104 144098.0055 144576.2935 0.987396395 1.070887349 1.189817637 1.012431631 0.94066722 1.142538152 0.997771326 0.748790191 0.996691795 1 17.14147148 1.988570648 24.42529974 0.883756515 1.057722029 0.294533256 0.094867237 389.2334819 831818.0578 0.036823242 0.025308901 97.40262211 -1.988570648 0.173965514 AES(ph)PESSAIESTQS(ph)TPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 AES(1)PESSAIESTQS(0.628)T(0.371)PQK 252.9 2.50E-30 261970000 628280 588130 478930 497990 531990 527520 571500 664830 639830 651960 TRUE FALSE 603726.123 571357.1082 565483.3047 523691.3236 549101.9415 538186.8158 578494.188 651101.0282 567199.1808 607802.1685 0.993293796 0.940037956 0.930373951 0.861614767 0.903422149 0.885463797 0.951780395 1.071238409 0.933197034 1 19.2132423 1.988575531 19.8652412 1.009922901 0.917304587 0.394877876 0.045293269 31.78160408 55262.0063 0.018039955 0.012397763 97.40371707 -1.988575531 -0.092618314 EAASSSSGTQPAPPAPAS(ph)PWDSKK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAASSSSGTQPAPPAPASPWDSKK 24 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 EAASSSSGTQPAPPAPAS(0.999)PWDS(0.001)KK;EAASSSSGTQPAPPAPAS(0.995)PWDS(0.005)KK;EAASSSSGTQPAPPAPAS(0.994)PWDS(0.006)KK 218.69 7.04E-33 7175160000 5744240 4778380 4371030 3500300 4084670 3903610 4621300 5449320 5338660 5166590 TRUE FALSE 5519748.75 4642105.281 5160972.354 3680950.902 4216057.12 3982543.669 4677856.852 5336789.638 4732637.698 4816652.257 1.145972027 0.963761765 1.071485355 0.764213546 0.875308595 0.826828149 0.971184259 1.107987322 0.982557479 1 22.19959934 1.988644759 24.36134864 1.041531609 0.933978752 0.113423439 0.108673406 729.2054687 1564425.051 0.044596078 0.030665611 97.41924486 -1.988644759 -0.107552857 DIDLICSNALEYNPDRDPGDR ddPTM_BT-474_Pertuzumab_2h_R1 3 DIDLICSNALEYNPDRDPGDR 21 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ;; 152.06 5.12E-08 1000143000 1191763 1304840 757116 1151546 1062182 997334 997618 1012063 894906 978500 FALSE TRUE 1145187.584 1267627.241 893943.7032 1210977.427 1096348.049 1017500.777 1009827.148 991163.5454 793320.0226 912225.3234 1.255377981 1.389598828 0.979959315 1.327498148 1.201839086 1.115405099 1.10699311 1.086533688 0.869653585 1 19.79903069 1.988650486 0.79336217 0.949486016 1.240014202 0.491404943 0.109787898 0.54232739 0.63912972 0.091821325 0.047115904 97.42052947 -1.988650486 0.290528186 SSHYGGS(ph)LPNVNQIGSGLAEFQSPLHSPLDSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSHYGGSLPNVNQIGSGLAEFQSPLHSPLDSSR 33 0 Q53ET0 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 S(0.001)S(0.001)HYGGS(0.998)LPNVNQIGSGLAEFQSPLHSPLDSSR;S(0.002)S(0.002)HYGGS(0.997)LPNVNQIGSGLAEFQSPLHSPLDSSR;S(0.013)S(0.013)HYGGS(0.974)LPNVNQIGSGLAEFQSPLHSPLDSSR;S(0.001)S(0.001)HYGGS(0.998)LPNVNQIGSGLAEFQSPLHSPLDSSR 221.47 7.35E-36 3158370000 440023 493848 389102 508241 447565 480385 421963 224150 491984 498241 TRUE FALSE 422826.4147 479763.9386 459421.3869 534471.3789 461961.3347 490098.7138 427127.1094 219521.2242 436136.0389 464494.6933 0.910293316 1.032872809 0.989077795 1.150651206 0.99454599 1.05512231 0.919552183 0.472602222 0.938947302 1 18.82530259 1.988667713 22.79743427 0.732956814 1.022479776 0.27489239 0.146154683 144.8014067 291299.908 0.054977228 0.037814569 97.42439388 -1.988667713 0.289522962 GLGS(ph)SPDLELLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLGSSPDLELLLR 13 0 Q9NQQ7-2;Q9NQQ7;Q9NQQ7-3 Q9NQQ7-2 SLC35C2 Solute carrier family 35 member C2 1 GLGS(0.5)S(0.5)PDLELLLR 205.87 6.97E-08 118070000 101350 153430 71575 155980 124210 101000 135600 216360 150820 110470 TRUE FALSE 97389.12995 149054.3266 84510.19468 164030.1465 128205.3275 103042.2892 137259.5134 211892.0904 133699.5459 102987.7685 0.94563783 1.447301255 0.820584773 1.592714833 1.244859747 1.00052939 1.332774905 2.057449088 1.298208009 1 16.65211348 1.988695309 24.57515021 1.60081305 1.191401986 0.073147634 0.335379568 600.6064418 1305651.914 0.125093783 0.086039012 97.43058477 -1.988695309 -0.409411063 HEAPSS(ph)PISGQPCGDDQNASPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 HEAPSSPISGQPCGDDQNASPSK 23 0 O75376;O75376-2;A0A088AWL3;E7EVU5;E7EW50;J3KS51;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 HEAPS(0.035)S(0.965)PISGQPCGDDQNASPSK;HEAPS(0.025)S(0.975)PISGQPCGDDQNASPSK 261.21 5.95E-44 1016490000 859080 792570 592820 665670 701020 737180 655710 416040 794620 735900 TRUE FALSE 825506.2038 769966.6796 699955.7612 700025.3085 723568.945 752086.2847 663734.7751 407448.6286 704418.0689 686056.8375 1.203262119 1.12230742 1.020259143 1.020360516 1.054677842 1.096244864 0.967463246 0.593899232 1.026763426 1 19.38796858 1.988738149 12.42466809 0.816478067 1.076390949 0.349605327 0.123613165 0.657799295 720.8782776 0.047810557 0.032762785 97.44019614 -1.988738149 0.259912881 EYIDHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EYIDHLK 7 0 M0R3F6;M0R2Z9;Q8IX01-4;Q8IX01-3;Q8IX01 M0R3F6 SUGP2 SURP and G-patch domain-containing protein 2 0 66.799 0.066894 230500000 530820 620950 459430 525110 584980 649340 545430 408480 667250 624600 FALSE TRUE 510074.9675 603241.114 542459.221 552210.99 603796.413 662470.0997 552105.1355 400044.7453 591506.5773 582295.2857 0.875973033 1.035971145 0.931587863 0.948334983 1.036924783 1.137687555 0.948153195 0.68701354 1.015818936 1 19.15139141 1.988745245 24.98251405 0.854021749 0.997420735 0.084362487 0.1093591 717.9821085 1593725.878 0.042382155 0.029170542 97.44178812 -1.988745245 0.143398987 LSNNNKTAER ddPTM_BT-474_Pertuzumab_2h_R1 1 LSNNNKTAER 10 1 I3L100;I3L2W2;Q96JN8-2;Q96JN8;K7EPS7;I3L2Z9 I3L100 NEURL4 Neuralized-like protein 4 0 51.276 0.094734 1020600000 1271800 845650 794520 761210 1002000 801030 958390 1132400 1192300 990370 FALSE TRUE 1222096.65 821532.89 938107.438 800496.1393 1034230.24 817227.3754 970119.0635 1109015.544 1056955.103 923291.3578 1.323630552 0.889787263 1.016047026 0.867002743 1.120155876 0.885124039 1.050718232 1.201154473 1.14476876 1 19.81642646 1.988784232 24.05470249 1.134727798 1.005586575 0.086495318 0.135712418 574.6701996 1232507.151 0.050139942 0.034505844 97.45053604 -1.988784232 -0.129141222 RDS(ph)FSGVK ddPTM_BT-474_Pertuzumab_2h_R1 4 RDSFSGVK 8 1 Q14865;Q14865-2;Q14865-3 Q14865 ARID5B AT-rich interactive domain-containing protein 5B 1 RDS(1)FSGVK;RDS(1)FSGVK;RDS(0.999)FS(0.001)GVK;RDS(0.982)FS(0.018)GVK 140.09 0.0004013 1687820000 2101380 1977430 1683150 1750320 1891350 1616040 1952780 2411780 2187820 2063240 TRUE FALSE 2019255.746 1921035.633 1987332.646 1840654.225 1952186.99 1648717.436 1976678.706 2361975.9 1939467.846 1923494.917 1.04978481 0.99872145 1.033188406 0.956932201 1.014916636 0.85714676 1.02764956 1.227960562 1.008304118 1 20.87529859 1.988876779 24.96431953 1.110014159 0.984192742 0.194095014 0.078167228 562.9445986 1263439.799 0.029864566 0.02057006 97.47130457 -1.988876779 -0.125821417 S(ph)RS(ph)HTSEGAHLDITPNSGAAGNSAGPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSHTSEGAHLDITPNSGAAGNSAGPK 27 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 S(0.541)RS(0.456)HT(0.456)S(0.456)EGAHLDIT(0.091)PNSGAAGNSAGPK;S(0.355)RS(0.355)HT(0.369)S(0.362)EGAHLDIT(0.304)PNS(0.256)GAAGNSAGPK;S(0.471)RS(0.382)HT(0.382)S(0.382)EGAHLDIT(0.382)PNS(0.001)GAAGNSAGPK 94.542 0.0068994 3080150000 820654 921842 678602 690213 705077 707915 617941 222035 610631 448116 TRUE FALSE 788581.9344 895551.9687 801240.4768 725834.9756 727756.442 722229.5263 625503.5468 217449.8997 541314.7289 417764.7042 1.887622211 2.143675518 1.917922861 1.737425322 1.742024721 1.728794987 1.497262791 0.520508069 1.295740697 1 18.67233108 1.989066009 3.783852375 0.898803569 1.857583707 0.786513753 0.213516842 0.094016578 2.874754637 0.098466183 0.060448808 97.51378391 -1.989066009 0.958780138 HLLTDLPLPPELPGGDLS(ph)PPDS(ph)PEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HLLTDLPLPPELPGGDLS(1)PPDS(1)PEPK;HLLTDLPLPPELPGGDLS(1)PPDS(1)PEPK;HLLTDLPLPPELPGGDLS(1)PPDS(1)PEPK 137.21 9.12E-06 716180000 367000 334510 323110 299792 332390 349420 326460 242154 427600 379700 TRUE FALSE 352657.2343 324970.1023 381503.1645 315264.301 343081.6262 356485.5118 330455.3151 237153.4353 379060.6406 353982.5808 0.996255899 0.918039813 1.077745588 0.890620946 0.969204828 1.007070775 0.933535527 0.669957925 1.070845463 1 18.43331884 1.989075606 24.86461508 0.858134026 0.973876305 0 0.111015717 807.7186677 1838418.859 0.042008557 0.028996309 97.51593882 -1.989075606 0.115742279 VLADPSDDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLADPSDDTK 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 101.65 0.0074206 161390000 366760 350800 302950 319820 312740 337160 370500 387100 466360 408480 FALSE TRUE 352426.6137 340795.5275 357699.8041 336325.9485 322799.5661 343977.6062 375034.2898 379106.2497 413420.7679 380813.2858 0.925457769 0.894915015 0.939304949 0.883178085 0.847658362 0.903271023 0.984824595 0.995517394 1.085625905 1 18.53872429 1.98911577 1.864731661 1.03322021 0.896991016 0.764442875 0.03251816 0.166491888 1.078043349 0.020073117 0.010102322 97.52495752 -1.98911577 -0.136229194 HPSSPCS(ph)VKHSPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HPSSPCSVKHSPTR 14 1 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 HPSSPCS(0.685)VKHS(0.275)PT(0.04)R;HPSSPCS(0.611)VKHS(0.378)PT(0.01)R 121.27 6.98E-05 87583000 48076 72336 42240 56142 53766 65613 46350 22297 47758 45186 TRUE FALSE 46197.13677 70273.0481 49873.70762 59039.49535 55495.43222 66939.73981 46917.24516 21836.55916 42336.71206 42125.51197 1.096654607 1.668182648 1.183931192 1.401514013 1.317382973 1.589054629 1.11374896 0.518368992 1.005013591 1 15.3624066 1.989146888 7.545388884 0.793378603 1.377526766 0.580647091 0.203222567 0.085174695 30.98752269 0.075719828 0.051102515 97.53194566 -1.989146888 0.584148163 IIDKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 IIDKPR 6 1 P49903;P49903-2;P49903-3;Q99611 P49903 SEPHS1;SEPHS2 "Selenide, water dikinase 1;Selenide, water dikinase 2" 0 110.36 0.026236 519750000 1723900 1875200 1448200 1701400 1602600 1447400 1707200 1884500 1996600 1919000 FALSE TRUE 1656528.082 1821721.132 1709921.955 1789209.458 1654149.084 1476667.42 1728093.224 1845584.416 1769954.338 1789024.421 0.925939335 1.01827628 0.95578458 1.000103429 0.924609561 0.825403724 0.965941663 1.031614994 0.989340513 1 20.77074165 1.989347699 24.92094161 1.007568053 0.943352923 0.257751679 0.049520712 725.7624682 1697913.482 0.020905506 0.014454678 97.57705326 -1.989347699 -0.06421513 EGEDGDQPT(ph)TPPKPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGEDGDQPTTPPKPLK 16 1 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 EGEDGDQPT(0.5)T(0.5)PPKPLK;EGEDGDQPT(0.587)T(0.413)PPKPLK 147.9 1.59E-06 3413800000 1052870 814950 895770 826040 917120 849350 1109010 1254190 1421510 1393550 TRUE FALSE 1011722.676 791708.4239 1057655.565 868672.0234 946619.9977 866524.4389 1122582.396 1228290.538 1260146.144 1299163.617 0.778749238 0.60939855 0.814104976 0.668639432 0.728638014 0.666986381 0.864080845 0.945447149 0.969967237 1 20.30915171 1.989499344 2.445673254 0.969239652 0.709683851 0.806901015 0.05745601 0.114431074 1.278347899 0.028208346 0.015420044 97.61113077 -1.989499344 -0.259555801 VKQELLEEVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKQELLEEVKK 11 2 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 108.17 0.0011805 482720000 693620 646380 537950 516660 601420 592430 666600 785360 853880 740080 FALSE TRUE 666512.5636 627945.8753 635169.5316 543324.8845 620765.2205 604409.3405 674758.0502 769142.0416 756951.1222 689953.7224 0.966025027 0.910127527 0.920597297 0.787480184 0.899720083 0.876014319 0.97797581 1.114773378 1.097104193 1 19.39614007 1.989530557 3.555480061 1.079538435 0.891413369 0.706709197 0.051076669 0.119673261 3.11260058 0.023966994 0.014509453 97.61814641 -1.989530557 -0.188125067 QNGSNDSDRYS(ph)DNEEDSKIELK ddPTM_BT-474_Pertuzumab_2h_R1 6 QNGSNDSDRYSDNEEDSKIELK 22 2 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK 273 1.20E-45 13310630000 5967940 6187600 3734610 5349280 4245900 3894410 5533530 8309490 6945010 4436900 TRUE FALSE 5734706.307 6011135.706 4409537.103 5625356.982 4382473.23 3973157.638 5601250.995 8137896.128 6156641.581 4136384.811 1.386405417 1.45323416 1.06603648 1.359969451 1.059493599 0.960538688 1.35414166 1.967393388 1.488411224 1 21.97993898 1.989537735 24.6346916 1.609759183 1.212935293 0.122799295 0.270687264 491.5819389 1157490.274 0.10339222 0.071613242 97.61975991 -1.989537735 -0.39682389 MKEYGEQIDPSTHR ddPTM_BT-474_Pertuzumab_2h_R1 3 MKEYGEQIDPSTHR 14 1 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;; 134.9 2.16E-05 1943090000 2132240 2578410 1792650 2155380 2076460 2715800 2242140 2177220 2509800 2348000 FALSE TRUE 2048909.703 2504876.271 2116621.732 2266619.42 2143251.222 2770715.337 2269579.98 2132259.646 2224898.026 2188967.869 0.936016345 1.144318428 0.966949658 1.035474048 0.979114976 1.265763366 1.036826539 0.974093625 1.0164142 1 21.06181935 1.989596054 24.98749979 0.9968331 1.058806546 0.074639473 0.090257528 1272.659775 3056586.73 0.034920337 0.024205929 97.6328695 -1.989596054 0.061973446 LSS(ph)TDDGYIDLQFK ddPTM_BT-474_Pertuzumab_2h_R1 4 LSSTDDGYIDLQFK 14 0 Q96A57;Q96A57-2;Q5JWB9;A0A087WTT2 Q96A57 TMEM230 Transmembrane protein 230 1 LS(0.317)S(0.643)T(0.04)DDGYIDLQFK;LS(0.02)S(0.979)T(0.001)DDGYIDLQFK;LS(0.021)S(0.958)T(0.021)DDGYIDLQFK;LS(0.021)S(0.959)T(0.021)DDGYIDLQFK 271.08 6.30E-33 469096000 617081 763302 421936 808344 799282 653237 896114 1469230 1167883 834559 TRUE FALSE 592964.7923 741533.3743 498189.2211 850062.7307 824991.6314 666445.8997 907080.9112 1438889.887 1035309.818 778033.5756 0.762132652 0.953086599 0.640318409 1.092578466 1.060354794 0.8565773 1.165863453 1.84939305 1.330674987 1 19.56947289 1.989608418 6.567482126 1.494309947 0.90922272 0.462736621 0.235093458 0.105542408 21.73127453 0.09264573 0.061981623 97.63564913 -1.989608418 -0.585087227 DDTDDEIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDTDDEIAK 9 0 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 124.23 0.0034087 0 206550 237180 176600 274690 178390 128760 245260 388590 336120 252050 FALSE TRUE 198477.7976 230415.8586 208515.5484 288866.7838 184128.0764 131363.6154 248261.5652 380565.4807 297965.0667 234978.429 0.844663906 0.980583025 0.88738166 1.229333199 0.783595657 0.559045424 1.056529173 1.619576241 1.268052851 1 17.8421688 1.989638549 24.78179322 1.35805186 0.889594858 0.425393104 0.212348627 359.2704368 859277.8926 0.08333245 0.057748424 97.64242331 -1.989638549 -0.468457002 EKQS(ph)S(ph)EEEEKETR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQSSEEEEKETR 13 2 Q92504;A2AAT0 Q92504 SLC39A7 Zinc transporter SLC39A7 2 EKQS(1)S(1)EEEEKETR 90.385 0.034504 1597700000 2979300 3690800 1868400 2851900 2178100 1906600 3316900 6145300 4640200 2437600 TRUE FALSE 2862865.662 3585541.998 2206061.442 2999086.901 2248160.565 1945152.758 3357493.214 6018397.407 4113463.949 2272499.181 1.259787324 1.577796827 0.970764461 1.319730685 0.989289934 0.855953117 1.477445291 2.64836065 1.810105801 1 21.11584834 1.989651053 23.83363021 2.017705867 1.171289386 0.290163221 0.429468798 231.1650352 532372.9795 0.161211441 0.111672899 97.64523462 -1.989651053 -0.846416481 S(ph)DDELLDDFFHDQSTATSQAGTLSSIPTALTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDDELLDDFFHDQSTATSQAGTLSSIPTALTR 32 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(1)DDELLDDFFHDQSTATSQAGTLSSIPTALTR;S(1)DDELLDDFFHDQSTATSQAGTLSSIPTALTR;S(1)DDELLDDFFHDQSTATSQAGTLSSIPTALTR;S(1)DDELLDDFFHDQSTATSQAGTLSSIPTALTR 332.65 3.17E-117 666340000 96958 98068 82744 88223 92526 91085 100416 116548 125851 107830 TRUE FALSE 93168.77417 95271.19666 97697.68143 92776.1996 95502.18282 92926.80111 101644.921 114141.2431 111564.9221 100526.5781 0.926807377 0.947721473 0.971859217 0.922902196 0.950019235 0.924400322 1.011124849 1.135433487 1.10980523 1 16.61721746 1.989661825 4.213762298 1.093616715 0.94276527 0.755841955 0.035824539 0.086402122 3.579132709 0.014979968 0.009419285 97.64765652 -1.989661825 -0.150851445 VNTLIRPDGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNTLIRPDGEK 11 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ; 113.76 0.0012302 773950000 694400 715890 713780 698620 819270 743780 844650 1018090 1060940 1042700 FALSE TRUE 667262.0803 695473.5181 842775.924 734675.8619 845622.5636 758819.7412 854987.0794 997066.0857 940506.539 972077.0003 0.686429244 0.715451058 0.866984739 0.755779492 0.869913148 0.780616907 0.879546661 1.025706899 0.967522674 1 19.89071107 1.989704666 2.702314799 0.999343115 0.782587058 0.751601507 0.056180278 0.139765283 1.925686536 0.029533758 0.016625422 97.65728952 -1.989704666 -0.216756056 DHS(ph)DSKDQSDKHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHSDSKDQSDKHDR 14 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 DHS(1)DSKDQSDKHDR;DHS(1)DSKDQSDKHDR 197.38 1.12E-08 485830000 305902 235687 219688 160213 226026 239504 197768 41547 294940 203414 TRUE FALSE 293947.0116 228965.4375 259390.5085 168481.6121 233296.3316 244346.935 200188.3439 40689.03993 261459.6477 189636.5886 1.550054311 1.207390616 1.367829439 0.888444648 1.230228477 1.288501005 1.05564198 0.214563235 1.378740514 1 17.53287782 1.989729646 23.72341327 0.7416485 1.234807666 0.209253135 0.314825162 275.3199809 635959.2332 0.119440789 0.082798578 97.66290678 -1.989729646 0.493159166 GFIYVHKPPVHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFIYVHKPPVHIR 13 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 143.17 2.59E-05 4075700000 3053000 3187500 2723100 3242900 3091700 3332300 3003700 2434300 3391700 3301400 FALSE TRUE 2933685.385 3096595.621 3215224.745 3410266.458 3191147.338 3399681.389 3040460.179 2384030.854 3006688.435 3077793.237 0.953178189 1.006109047 1.044652612 1.108023247 1.036829667 1.104584073 0.987870186 0.774590972 0.976897473 1 21.55346489 1.9897562 24.07798803 0.88939565 1.043674986 0.365277712 0.071112098 242.2827877 569483.9652 0.02734712 0.018960637 97.66887824 -1.9897562 0.154279336 KVNVTVDYIRPASPATETVPAFSER ddPTM_BT-474_Pertuzumab_2h_R1 2 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 198.67 4.23E-25 1111400000 273110 231708 220406 248709 271636 245689 226663 228250 224760 234155 FALSE TRUE 262436.5593 225099.9147 260238.2671 261544.9013 280373.4186 250656.9999 229436.9696 223536.5577 199246.1871 218295.4733 1.202207977 1.031170786 1.192137717 1.198123339 1.284375779 1.148246439 1.051038604 1.02400913 0.912736229 1 17.73592269 1.989764497 1.804949399 0.971054937 1.177317404 0.665429796 0.064063601 0.229785135 1.39476379 0.041540271 0.020717275 97.67074423 -1.989764497 0.206262467 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK ddPTM_BT-474_Pertuzumab_2h_R1 3 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK 32 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;; 254.13 2.37E-59 1304800000 319528 423409 274657 388786 368533 397341 316415 140119 349848 377179 FALSE TRUE 307040.4925 411333.7899 324293.6296 408851.2921 380387.1986 405375.5073 320287.3814 137225.4937 310134.7217 351632.3304 0.873186183 1.169783761 0.922252027 1.162723836 1.081775382 1.152839123 0.91085874 0.390252778 0.881985799 1 18.4237082 1.989766189 17.99406407 0.679884894 1.061997881 0.349032767 0.17685892 9.435713862 16589.78007 0.06536187 0.045200023 97.67112466 -1.989766189 0.382112987 FSVIILDEAHER ddPTM_BT-474_Pertuzumab_2h_R1 1 FSVIILDEAHER 12 0 Q8IX18-4;Q8IX18-3;Q8IX18-2;Q8IX18;J3KTK0;J3KSW6 Q8IX18-4 DHX40 Probable ATP-dependent RNA helicase DHX40 0 147.87 6.59E-05 136030000 82093 91703 78498 95955 84927 89210 86872 82912 97245 96691 FALSE TRUE 78884.7148 89087.72023 92684.33478 100907.249 87658.75408 91013.88732 87935.16552 81199.83823 86206.15528 90142.03245 0.875115777 0.988303878 1.028203295 1.119425049 0.972451494 1.009672013 0.975517893 0.90079884 0.956336938 1 16.45991236 1.989789796 6.943389085 0.940424482 1.003200006 0.093568636 0.060929398 0.26409125 68.94283958 0.025467232 0.017121645 97.67643399 -1.989789796 0.062775525 HEISPGHDGT(ph)WNDNQLQEMAQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEISPGHDGTWNDNQLQEMAQLR 23 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;C9J1B2 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 HEIS(0.097)PGHDGT(0.903)WNDNQLQEMAQLR 130.9 6.13E-05 166860000 70890 83455 77604 105230 90737 92584 74977 26399 96060 83265 TRUE FALSE 68119.54043 81074.94511 91628.76909 110660.9329 93655.63801 94456.11191 75894.59095 25853.85142 85155.67152 77625.38739 0.877542035 1.044438525 1.180396932 1.425576562 1.206507834 1.216819846 0.977703217 0.333059226 1.097008007 1 16.24424094 1.989790434 14.74271107 0.715775746 1.162733543 0.288606221 0.232843573 2.12180028 3061.27942 0.091698722 0.063275991 97.6765775 -1.989790434 0.446957797 EDKYEEEIK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDKYEEEIK 9 1 P06753-2;P06753-6;P06753-5;P06753-7;A0A494C034;A0A2R8Y6A3;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;P06753;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;P67936;P67936-2 TPM3;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-4 chain 0 ;;; 138.71 0.00011753 8421200000 8068900 5800700 6878400 5803900 6740400 5817800 8477100 10513300 11916500 10315400 FALSE TRUE 7753558.467 5635269.715 8121479.889 6103439.975 6957211.087 5935439.902 8580845.286 10296196.68 10563788.88 9616728.77 0.806257372 0.585986134 0.844515852 0.634669036 0.723448821 0.61719947 0.892283176 1.070654786 1.098480484 1 23.1971148 1.989791383 3.340956576 1.057411619 0.701615085 0.798450421 0.080034545 0.094789186 2.113182219 0.035079688 0.020918741 97.67679098 -1.989791383 -0.355796534 AFGSGIDIKPGT(ph)PPIAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFGSGIDIKPGTPPIAGR 18 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 AFGSGIDIKPGT(1)PPIAGR;AFGSGIDIKPGT(1)PPIAGR 93.729 0.0033873 4722530000 2849470 2627570 2266200 2259020 2058940 2440720 2743780 3180030 3427660 3348800 TRUE FALSE 2738109.562 2552634.276 2675752.751 2375608.293 2125167.675 2490073.031 2777359.2 3114361.269 3038566.407 3121982.793 0.877041849 0.817632398 0.857068385 0.760929336 0.680710887 0.797593451 0.889613872 0.997558755 0.973280959 1 21.57403116 1.989816775 2.72589326 0.988815266 0.795077766 0.739275502 0.051039651 0.15180423 2.131075001 0.028736973 0.016218943 97.68250198 -1.989816775 -0.1937375 QKDFDIAEQNES(ph)S(ph)DEESLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKDFDIAEQNESSDEESLRK 20 2 Q96KC8 Q96KC8 DNAJC1 DnaJ homolog subfamily C member 1 2 QKDFDIAEQNES(0.874)S(0.874)DEES(0.251)LRK 46.027 0.09376 68863000 55462 76586 38250 56706 48185 42659 60828 90496 77254 53674 TRUE FALSE 53294.48372 74401.84227 45162.62587 59632.60346 49734.91429 43521.59421 61572.43126 88627.22598 68484.4498 50038.61217 1.065067183 1.486888605 0.902555525 1.191731762 0.993930729 0.869760218 1.230498381 1.77117674 1.368632079 1 15.61075416 1.989982888 24.50250024 1.474426362 1.091881953 0.202683489 0.242039225 402.7381858 985123.546 0.091723571 0.063718483 97.71987159 -1.989982888 -0.382544409 KTDAPQPDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTDAPQPDVK 10 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 78.908 0.045849 200660000 251550 313680 268170 374780 243440 262050 345200 487660 421340 352310 FALSE TRUE 241719.1479 304734.1535 316634.2844 394122.4407 251270.4687 267348.8305 349424.6609 477589.6506 373511.2496 328447.7299 0.735944036 0.927801065 0.964032495 1.199954833 0.765024221 0.813976795 1.063866878 1.454081143 1.137201495 1 18.32530427 1.989994335 9.358197831 1.250619298 0.914618175 0.389203423 0.16295366 0.165705919 130.0303696 0.064717404 0.044234636 97.72244732 -1.989994335 -0.336001122 GPDPSS(ph)PDKAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPDPSSPDKAK 11 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 GPDPS(0.075)S(0.925)PDKAK 69.108 0.052295 0 515700 433420 366840 356380 430640 390960 453630 542120 542220 496930 TRUE FALSE 495545.8739 421059.286 433136.1483 374772.8145 444491.9267 398865.4791 459181.6596 530925.0326 480669.4588 463272.4885 1.069663937 0.908880403 0.934948997 0.808968423 0.95946109 0.860973809 0.991169713 1.146031862 1.037552349 1 18.82150148 1.990009192 7.52747657 1.075580751 0.920362523 0.417696885 0.072269525 0.116779408 43.04658011 0.028189342 0.019067427 97.72579041 -1.990009192 -0.155218228 EKPDQDAEGKAEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKPDQDAEGKAEEK 14 2 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 0 ;; 138.91 7.14E-06 1293530000 2557470 2370350 1663170 1461200 1797710 1718980 2257930 3181470 2999700 1946960 FALSE TRUE 2457521.245 2302749.939 1963741.816 1536612.707 1855534.975 1753738.953 2285563.223 3115771.533 2659186.632 1815090.665 1.353938562 1.268669375 1.08189737 0.846576282 1.022282253 0.966199093 1.259200583 1.716592781 1.465043418 1 20.79161018 1.99003985 9.705371065 1.477303228 1.085820328 0.264856641 0.215905749 0.212025969 181.9049272 0.086434233 0.059162868 97.73268951 -1.99003985 -0.391482899 GPEVDIRDPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GPEVDIRDPK 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 90.05 0.010119 2529900000 6334900 6214200 5499900 6478500 5677000 6033200 6539100 7623600 7871600 6907800 FALSE TRUE 6087325.104 6036977.1 6493854.275 6812856.161 5859605.861 6155195.438 6619127.462 7466169.996 6978048.968 6439928.553 0.945247304 0.937429204 1.008373652 1.057908656 0.909886781 0.955786293 1.027826226 1.159356029 1.083559998 1 22.61861325 1.990056595 5.695225504 1.098122287 0.971978349 0.463238183 0.053253314 0.12756082 14.78672285 0.022252931 0.014690664 97.73645769 -1.990056595 -0.126143937 GEGPGEAGGPLT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEGPGEAGGPLTPR 14 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 GEGPGEAGGPLT(1)PR 103.79 0.012244 432630000 246600 282380 238280 269580 261440 272130 191010 197050 171370 164410 TRUE FALSE 236962.5994 274326.7989 281342.4965 283493.0561 269849.455 277632.6551 193347.6375 192980.8486 151916.796 153274.3643 1.54600282 1.789776133 1.835548285 1.84957907 1.76056483 1.811344359 1.261447982 1.259054961 0.991142888 1 17.2257569 1.990062095 1.545958697 1.044939546 1.781974896 0.883962547 0.11341509 0.120656755 0.537573556 0.074178752 0.035493084 97.73769543 -1.990062095 0.737035351 VLST(ph)STDLEAAVADALK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.041)T(0.477)S(0.477)T(0.005)DLEAAVADALK 130.98 0.00031827 17405000 43810 30416 29989 29845 37506 34681 38404 46921 50282 43039 TRUE FALSE 42097.85677 29548.56546 35408.6794 31385.30403 38712.41455 35382.27358 38873.99964 45952.06495 44574.19816 40123.93019 1.049195743 0.736432481 0.882482828 0.782209117 0.964821102 0.881824722 0.968848252 1.145253337 1.110913062 1 15.29217531 1.990107512 3.181619824 1.097849874 0.875531129 0.506376985 0.08883012 0.178131715 3.535800534 0.040506798 0.023860706 97.74791721 -1.990107512 -0.222318745 IVAERPGTNSTGPAPMAPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 IVAERPGTNSTGPAPMAPPR 20 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 189.34 2.03E-17 952110000 205960 185431 157679 157275 182903 164045 190425 246010 210911 207875 FALSE TRUE 197910.8555 180142.6894 186175.1029 165391.9816 188786.2411 167362.1023 192755.4781 240929.8075 186969.2675 193795.4411 1.021235868 0.929550708 0.960678444 0.853435874 0.974152127 0.863601854 0.994633708 1.243217107 0.964776397 1 17.56417511 1.990157851 24.25282696 1.101997836 0.932667375 0.323565273 0.084014009 266.0080139 655491.6939 0.031159281 0.021663277 97.75924775 -1.990157851 -0.169330462 AIPELDAYEAEGLALDDEDVEELTAS(ph)QR ddPTM_BT-474_Pertuzumab_2h_R1 6 AIPELDAYEAEGLALDDEDVEELTASQR 28 0 P49736;F8WDM3;C9J013;C9JZ21;H7C4N9 P49736 MCM2 DNA replication licensing factor MCM2 1 AIPELDAYEAEGLALDDEDVEELT(0.009)AS(0.991)QR;AIPELDAYEAEGLALDDEDVEELT(0.01)AS(0.99)QR;AIPELDAYEAEGLALDDEDVEELTAS(1)QR;AIPELDAYEAEGLALDDEDVEELT(0.002)AS(0.998)QR;AIPELDAYEAEGLALDDEDVEELT(0.003)AS(0.997)QR;AIPELDAYEAEGLALDDEDVEELT(0.112)AS(0.888)QR 171.48 2.04E-12 483005000 171681 180591.8 146295.5 181709.7 170471.6 165117.6 162608.9 168971.6 159607.7 176864.1 TRUE FALSE 164971.5167 175441.4987 172734.3512 191087.7594 175954.9738 168456.391 164598.9564 165482.2774 141489.703 164884.937 1.000525092 1.064023809 1.047605405 1.158915805 1.067137951 1.021660281 0.998265575 1.003622771 0.858111757 1 17.33110008 1.990290574 1.282811622 0.942966502 1.068743472 0.476775292 0.052116177 0.390921682 1.193004884 0.038050568 0.017634516 97.78912801 -1.990290574 0.12577697 GVTIPYRPKPSSSPVIFAGGQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVTIPYRPKPSSSPVIFAGGQDR 23 2 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 0 65.207 0.016633 5218900000 1103900 1125800 869600 1102100 1024900 1066500 905740 914450 872600 916320 FALSE TRUE 1060758.368 1093693.286 1026756.064 1158979.513 1057866.839 1088065.361 916824.7171 895566.2879 773546.1062 854256.8302 1.241732381 1.280286265 1.201929008 1.356710853 1.238347534 1.273698169 1.073242478 1.048357188 0.905519369 1 19.70431035 1.990417526 1.613824041 0.967921596 1.270125668 0.864096117 0.050945956 0.122070975 0.592839277 0.031219346 0.015102123 97.81771776 -1.990417526 0.302204072 SRSHT(ph)SEGAHLDITPNSGAAGNSAGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSHTSEGAHLDITPNSGAAGNSAGPK 27 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.211)RS(0.211)HT(0.288)S(0.288)EGAHLDIT(0.002)PNSGAAGNSAGPK 111.58 0.001853 519320000 228620 328350 199590 283160 240870 284250 202100 69322 214640 146030 TRUE FALSE 219685.2776 318985.7795 235660.3529 297773.9215 248617.8023 289997.7298 204573.3603 67890.47648 190274.967 136139.258 1.613680586 2.343084457 1.731024219 2.187274456 1.826202125 2.130155063 1.502677209 0.498684049 1.397649508 1 17.05472363 1.990433173 5.140237626 0.923160127 1.973320097 0.709663957 0.288394353 0.082167883 6.509740805 0.111578166 0.072727403 97.82124209 -1.990433173 1.05015997 HDDGTQS(ph)DSENAGAHR ddPTM_BT-474_Pertuzumab_2h_R1 3 HDDGTQSDSENAGAHR 16 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 HDDGT(0.001)QS(0.999)DSENAGAHR;HDDGTQS(1)DSENAGAHR;HDDGTQS(1)DSENAGAHR 231.93 5.70E-16 348377000 240436 228847 225382 206663 209737 216625 183931 44855 275270 188548 TRUE FALSE 231039.4953 222320.5076 266113.541 217328.9022 216483.3811 221005.3059 186182.0026 43928.72858 244022.5036 175777.476 1.314386237 1.26478382 1.51392287 1.236386522 1.231576343 1.257301623 1.059191466 0.249911021 1.388246715 1 17.42339069 1.990438352 10.06862868 0.760622883 1.292718357 0.297023889 0.277560818 0.212848021 203.7234836 0.106751715 0.073256764 97.82240855 -1.990438352 0.532095473 HPQGEQMYR ddPTM_BT-474_Pertuzumab_2h_R1 5 HPQGEQMYR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 155.06 7.42E-05 1937160000 45467.8 78093.9 61852.5 80883 94416.5 81717.6 102858.7 236623.2 65118.4 82515 FALSE TRUE 43690.86811 75866.73843 73030.62265 85057.38132 97453.49247 83369.98586 104117.5155 231736.8482 57726.43223 76926.18555 0.567958333 0.986227744 0.949359729 1.105701273 1.266844206 1.083766019 1.353473005 3.012457287 0.750413293 1 16.23118715 1.990462284 23.66696853 1.904163667 1.026039084 0.103558825 0.605139225 267.2730169 663213.2744 0.229476221 0.159901283 97.82779926 -1.990462284 -0.878124583 HAASYS(ph)SDSENQGSYSGVIPPPPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HAASYSSDSENQGSYSGVIPPPPGR 25 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;F2Z3L2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 HAAS(0.059)Y(0.04)S(0.318)S(0.265)DS(0.318)ENQGSYSGVIPPPPGR 116.24 0.00085706 456140000 158910 184550 124700 173390 164630 182270 152840 101230 169470 174700 TRUE FALSE 152699.6215 179286.8147 147236.0639 182338.6787 169925.4735 185955.6243 154710.5016 99139.56512 150232.4761 162867.4134 0.937570127 1.100814527 0.904024082 1.119552861 1.043336232 1.141760776 0.949916858 0.608713327 0.922421944 1 17.31333845 1.990463718 23.84146043 0.795005334 1.041690907 0.33421635 0.119302381 200.0179248 500060.6144 0.043995634 0.030669304 97.82812232 -1.990463718 0.246685573 ALEHFTDLYDIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEHFTDLYDIKR 13 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 201.04 6.82E-08 7050800000 12131600 15002800 10287400 10746800 12202400 14347400 12487400 11922800 14123800 14148600 FALSE TRUE 11657483.66 14574934.83 12146562.02 11301443.64 12594901.28 14637514.26 12640224.54 11676590.01 12520525.44 13190302.72 0.883791973 1.10497349 0.920870603 0.856799414 0.954860669 1.109717841 0.958296773 0.885240488 0.949221993 1 23.65297434 1.990466966 24.98623861 0.929494479 0.974940023 0.010416197 0.082452553 1494.531437 3917189.304 0.032846014 0.022904159 97.82885407 -1.990466966 0.045445543 EQYVPPRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 8 EQYVPPRSPK 10 1 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK 96.591 0.0057574 6982980000 6237527 5527452 4749091 4923739 5315909 5492841 5674827 6355791 6793990 6507733 TRUE FALSE 5993757.549 5369814.481 5607357.387 5177853.76 5486900.041 5603910.008 5744277.23 6224541.695 6022764.738 6066958.447 0.987934498 0.885091686 0.924245227 0.853451331 0.904390575 0.923677005 0.946813346 1.025974011 0.992715673 1 22.532542 1.990519189 2.638541587 1.008135414 0.9088576 0.605286422 0.033367001 0.175098265 2.293925773 0.01682862 0.009416095 97.84061846 -1.990519189 -0.099277814 HHHHDS(ph)DSNSPCCK ddPTM_BT-474_Pertuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 HHHHDS(0.902)DS(0.085)NS(0.014)PCCK 90.731 0.0025548 86828000 159700 177690 151480 148180 137670 178830 112080 0 154450 32075 TRUE FALSE 153458.7474 172622.4552 178855.8057 155827.5876 142098.2806 182446.0651 113451.6686 0 136917.4835 29902.53168 5.131965048 5.772837465 5.981293075 5.211183763 4.752048492 6.101358476 3.794048938 0 4.578792357 1 14.86798001 1.990623318 5.911927683 1.766783182 5.450134561 0.669592854 1.144372681 0.084816626 11.42657078 0.443772849 0.294591536 97.86407995 -1.990623318 3.683351379 YREYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_BT-474_Pertuzumab_2h_R1 3 YREYSPPYAPSHQQYPPSHATPLPK 25 1 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 Y(0.216)REY(0.216)S(0.519)PPY(0.009)APS(0.036)HQQY(0.003)PPSHATPLPK;YREYS(1)PPYAPSHQQYPPSHATPLPK;Y(0.003)REY(0.002)S(0.772)PPYAPS(0.223)HQQYPPSHATPLPK 168.69 6.60E-12 1061320000 890700 924021 695818 777702 801532 923450 807620 689918 946890 806433 TRUE FALSE 855890.4593 897668.8258 821567.791 817839.2934 827314.0047 942122.7917 817503.8951 675670.9522 839403.0169 751812.5746 1.138435946 1.194006134 1.092782721 1.087823377 1.100425868 1.253135188 1.087377257 0.898722601 1.116505689 1 19.52001352 1.990671551 24.88617848 0.993629757 1.142307429 0.454197273 0.068038411 335.5899616 895277.6651 0.026003906 0.018166241 97.87494941 -1.990671551 0.148677673 RVDALNDEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVDALNDEIR 10 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 155.99 1.88E-05 495050000 565290 644190 506700 452090 610690 566590 707260 1270430 620760 732990 FALSE TRUE 543197.8418 625818.3319 598271.9615 475422.4191 630333.3985 578046.838 715915.6594 1244195.177 550293.9272 683343.9344 0.794911339 0.915817497 0.875506361 0.695729332 0.922424809 0.845909079 1.0476652 1.820745182 0.805295693 1 19.38225236 1.990718101 17.77339957 1.33345779 0.852244843 0.25554398 0.257862461 9.002487543 17237.16013 0.097118808 0.067507365 97.88544078 -1.990718101 -0.481212947 SKDEEEDEES(ph)DDADDTPILKPVSLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKDEEEDEESDDADDTPILKPVSLLR 26 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ITI3 A0A3B3IS53 KAT6A Histone acetyltransferase KAT6A 1 SKDEEEDEES(1)DDADDTPILKPVSLLR;SKDEEEDEES(1)DDADDTPILKPVSLLR 238.36 2.77E-45 572320000 568260 460790 435410 420790 506500 452010 556520 670110 745800 627270 TRUE FALSE 546051.771 447648.7204 514098.2726 442507.0223 522792.0325 461149.9519 563330.8582 656271.9943 661139.9106 584784.4442 0.933765897 0.76549355 0.879124398 0.756701083 0.893991004 0.788581086 0.963313686 1.122245985 1.130570276 1 19.15754541 1.990735526 3.507127778 1.092394602 0.834515957 0.75603345 0.063205961 0.098902206 2.488236659 0.026991035 0.016311418 97.8893683 -1.990735526 -0.257878645 TSS(ph)EDNLYLAVLR ddPTM_BT-474_Pertuzumab_2h_R1 7 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 1 T(0.006)S(0.043)S(0.951)EDNLYLAVLR;TSS(1)EDNLYLAVLR;T(0.001)S(0.001)S(0.998)EDNLYLAVLR;T(0.001)S(0.001)S(0.997)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TS(0.001)S(0.999)EDNLYLAVLR;T(0.001)S(0.002)S(0.997)EDNLYLAVLR 367.69 3.86E-91 15374810000 7019250 6999770 6073410 6322050 6352420 6036190 6709320 7282610 7614150 7546880 TRUE FALSE 6744929.95 6800143.413 7171010.289 6648331.758 6556751.358 6158245.898 6791430.665 7132221.559 6749823.613 7035723.096 0.958669046 0.966516635 1.019228613 0.944939371 0.931922884 0.875282585 0.965278277 1.0137155 0.959364591 1 22.74626727 1.990747506 24.95766389 0.99178721 0.949701911 0.214580634 0.035600062 716.8019764 1933500.748 0.015094261 0.010551902 97.8920686 -1.990747506 -0.042085298 LKTEGSDLCDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKTEGSDLCDR 11 1 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;; 97.273 0.0058274 1539800000 1866970 2960290 1384270 2628030 1719300 2005910 2237170 2849330 2525680 1950150 FALSE TRUE 1794006.748 2875865.428 1634438.382 2763662.943 1774602.846 2046470.875 2264549.156 2790490.34 2238975.395 1818064.603 0.986767327 1.581827963 0.898999067 1.520112618 0.976094492 1.125631548 1.245582336 1.534868637 1.231515861 1 20.79397203 1.990767268 23.72041211 1.333724875 1.192356106 0 0.245140123 637.8677239 1638787.067 0.088870896 0.062043363 97.89652329 -1.990767268 -0.141368769 S(ph)PGAFDMSGVR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPGAFDMSGVR 11 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR 225.17 5.94E-12 5185270000 1092454 1272530 1280020 1485230 1327360 1144700 1049844 947330 813026 857124 TRUE FALSE 1049759.69 1236238.69 1511348.088 1561882.898 1370055.74 1167846.618 1062692.305 927767.3044 720734.697 799070.228 1.313726445 1.547096422 1.891383304 1.954625318 1.714562365 1.461506858 1.329911024 1.16105853 0.90196665 1 19.60796278 1.990794024 1.243350156 0.967947573 1.697383705 0.731909892 0.175074602 0.255360749 0.731142703 0.142041199 0.065695611 97.90255446 -1.990794024 0.729436132 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 SCDEPLT(1)PPPHS(0.876)PT(0.103)S(0.021)MLQLIHDPVSPR 152.02 1.35E-07 328390000 211710 241730 211090 293070 285340 328180 229440 117490 224070 224220 TRUE FALSE 203436.1391 234836.0971 249238.6587 308195.3778 294518.2202 334816.0245 232247.9554 115063.7904 198634.513 209033.3797 0.973223221 1.123438263 1.192339037 1.474383557 1.408953061 1.601734732 1.111056788 0.550456538 0.950252602 1 17.67337381 1.990804329 23.88293628 0.795404393 1.301421735 0.508753569 0.202186763 180.9878804 470060.5862 0.082929522 0.057940157 97.90487762 -1.990804329 0.506017342 NHLS(ph)PQQGGATPQVPSPCCR ddPTM_BT-474_Pertuzumab_2h_R1 4 NHLSPQQGGATPQVPSPCCR 20 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR 239.87 1.17E-29 1786960000 580057 607766 401019 495353 549323 617390 429338 137642.7 511110 399165 TRUE FALSE 557387.7312 590433.1087 473492.0539 520918.2277 566992.4732 629874.0488 434592.3669 134800.3301 453090.9355 372129.199 1.497833905 1.586634723 1.272386191 1.399831642 1.523644139 1.692621946 1.167853445 0.362240669 1.217563515 1 18.50544407 1.990812215 9.155476551 0.782576457 1.482142422 0.605794552 0.228288317 0.096203804 75.35357419 0.087610989 0.059989497 97.90665546 -1.990812215 0.699565965 GHVQDPNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHVQDPNDR 9 0 Q14CX7;Q14CX7-2;F8VSB9;F8W0N5 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 90.629 0.011301 33889000 145520 127420 122560 74811 125390 126770 98158 11481 160740 72018 FALSE TRUE 139832.9175 123786.1064 144709.3183 78672.00468 129423.2832 129333.3763 99359.28697 11243.91334 142493.4691 67140.15671 2.082701685 1.843697013 2.155331852 1.171757835 1.927658343 1.926319249 1.479878687 0.167469275 2.122328515 1 16.03488828 1.990824635 19.32591383 0.958989469 1.826128687 0.29527369 0.510353262 21.89975299 46126.16308 0.191749141 0.13353398 97.90945546 -1.990824635 0.867139218 SEDMPFS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 SEDMPFSPK 9 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEDMPFS(1)PK;SEDMPFS(1)PK;SEDMPFS(1)PK 209.8 8.22E-06 3613330000 7407800 6273400 5538900 5420700 6469900 6278300 6754700 7867000 8394500 7481400 TRUE FALSE 7118294.986 6094488.774 6539902.442 5700462.977 6678010.209 6405251.528 6837366.039 7704543.701 7441591.553 6974678.114 1.020591183 0.873802156 0.937663694 0.817308395 0.957465004 0.918358012 0.980312772 1.104645057 1.066944084 1 22.73369521 1.990841133 3.531087027 1.06609886 0.916985414 0.544962715 0.055412587 0.155595369 3.982882682 0.024616367 0.014903287 97.91317485 -1.990841133 -0.149113446 HVIECAK ddPTM_BT-474_Pertuzumab_2h_R1 2 HVIECAK 7 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y713 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 ; 81.297 0.027584 686280000 644270 676580 580530 638370 667850 676480 642150 536270 784070 775910 FALSE TRUE 619091.2161 657284.6008 685444.6848 671316.3522 689332.0018 690158.8891 650008.8238 525195.8371 695065.6607 723356.9246 0.85585856 0.908658753 0.947588475 0.928056855 0.95296247 0.954105595 0.898600403 0.726053514 0.960888929 1 19.46434816 1.990869829 24.72169961 0.85198848 0.92631937 0 0.075392493 659.8429598 1786652.304 0.028620353 0.020019184 97.91964477 -1.990869829 0.074330889 AKKDDTDDEIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKKDDTDDEIAK 12 2 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 ; 151.44 3.68E-05 1153720000 2346000 2669500 1499070 1846840 1596610 1355900 2302500 3757900 3337900 1721260 FALSE TRUE 2254315.726 2593368.474 1769985.296 1942155.634 1647966.411 1383317.227 2330678.684 3680298.052 2958995.586 1604677.527 1.404840342 1.616130612 1.103016192 1.210308988 1.026976687 0.862053094 1.45242807 2.293481394 1.843981445 1 20.61385197 1.990936043 24.12771758 1.860394597 1.205870433 0.260704863 0.360114829 260.98816 694734.9843 0.137924966 0.096462919 97.934575 -1.990936043 -0.654524164 TAS(ph)PLPLRPDAPVEKS(ph)PEETATQVPSLESLTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TASPLPLRPDAPVEKSPEETATQVPSLESLTLK 33 2 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 2 T(0.238)AS(0.762)PLPLRPDAPVEKS(1)PEETATQVPSLESLTLK;T(0.458)AS(0.542)PLPLRPDAPVEKS(0.717)PEET(0.152)AT(0.13)QVPS(0.002)LESLTLK 294.34 7.33E-90 650950000 138800 116825 117533 99754 111881 115220 146999 164583 209543 164655 TRUE FALSE 133375.5425 113493.2654 138773.8276 104902.3159 115479.754 117549.8273 148798.0177 161184.3035 185756.5571 153502.7702 0.868880362 0.739356464 0.904047708 0.683390376 0.752297524 0.765783101 0.9693507 1.050041659 1.210118598 1 17.22790517 1.99099047 2.194041163 1.098905852 0.781794218 0.752231655 0.07818447 0.143907537 1.289476488 0.04211351 0.02230902 97.94684921 -1.99099047 -0.317111634 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSGSVGNGSSRYSPSQNSPIHHIPSR 27 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 S(0.004)GS(0.005)GS(0.001)VGNGS(0.029)S(0.033)RY(0.005)S(0.909)PS(0.015)QNS(0.998)PIHHIPSR;S(0.001)GS(0.002)GS(0.001)VGNGS(0.06)S(0.067)RY(0.013)S(0.848)PS(0.02)QNS(0.988)PIHHIPSR;SGSGSVGNGS(0.006)S(0.007)RYS(0.984)PS(0.004)QNS(1)PIHHIPSR;S(0.001)GS(0.001)GS(0.001)VGNGS(0.035)S(0.04)RY(0.021)S(0.889)PS(0.125)QNS(0.887)PIHHIPSR 179.2 2.61E-17 3272790000 555649 644142 367139 460120 472336 642465 465987 242361 543773 507971 TRUE FALSE 533933.6228 625771.7008 433489.1843 483866.8483 487529.1164 655456.0825 471689.8883 237356.1607 482046.1687 473565.6717 1.127475353 1.32140427 0.915372904 1.021752372 1.029485762 1.384086984 0.996039022 0.501210655 1.017907753 1 18.85320498 1.991020924 24.9466005 0.775370005 1.127786435 0.313032638 0.188055904 387.599874 1076870.537 0.071926116 0.050382604 97.95371784 -1.991020924 0.35241643 S(ph)PVLQEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPVLQEK 7 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 S(1)PVLQEK;S(1)PVLQEK;S(1)PVLQEK;S(1)PVLQEK 84.054 0.022896 705830000 1075630 1067460 1054820 1192830 1099620 962330 1157660 1432020 1218770 1277470 TRUE FALSE 1033593.19 1037017.086 1245449.438 1254392.099 1134990.276 981788.9719 1171827.789 1402448.287 1080420.339 1190945.819 0.867875913 0.870750851 1.045764986 1.053273859 0.953015878 0.824377529 0.983947188 1.177592015 0.907195207 1 20.18367635 1.991025744 24.80677926 1.056188548 0.940679472 0.145013026 0.093639805 574.8483614 1589005.896 0.037724267 0.026423777 97.95480482 -1.991025744 -0.115509075 HDS(ph)PEDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 HDSPEDVK 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 1 HDS(1)PEDVK;HDS(1)PEDVK;HDS(1)PEDVK 180.07 0.00025284 3959870000 5374800 4314920 4515210 3549130 4242370 4843080 4281050 1845410 7540860 5575270 TRUE FALSE 5164746.874 4191862.706 5331208.887 3732301.025 4378829.684 4941010.396 4333442.771 1807301.639 6684853.187 5197651.997 0.993669233 0.806491606 1.02569562 0.718074436 0.842463036 0.950623551 0.833730841 0.347715014 1.286129427 1 22.30942861 1.991039676 24.81476668 0.751784792 0.882838834 0 0.241308927 1237.399788 3426863.098 0.091768328 0.064311992 97.95794724 -1.991039676 0.131054042 VQDLFCSVGLNVNNPHFLIMQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQDLFCSVGLNVNNPHFLIMQGR 23 0 O95347-2;O95347 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 150.53 8.30E-08 186450000 55937 66913 72036 40007 58816 59815 63650 84862 61331 58506 FALSE TRUE 53750.9202 65004.70675 85054.50763 42071.76606 60707.87006 61024.50028 64428.96774 83109.57004 54368.962 54543.33651 0.985471804 1.191799236 1.559393192 0.771345663 1.113020837 1.11882595 1.18124361 1.523734618 0.99680301 1 15.73511533 1.991134537 23.64140321 1.261901208 1.131466566 0 0.233599834 646.4187861 1723794.559 0.09046519 0.063342517 97.97934627 -1.991134537 -0.130434642 ESGLQAAHPNSIFLIDHAWTCR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESGLQAAHPNSIFLIDHAWTCR 22 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 233.5 1.18E-30 1658350000 492970 652980 458060 591310 566960 650260 537680 351720 653000 637620 FALSE TRUE 473704.1874 634357.6497 540841.6315 621827.58 585196.7833 663408.7027 544260.2887 344456.8591 578874.1776 594433.4295 0.796900315 1.067163484 0.909843903 1.046084472 0.984461429 1.11603532 0.915595022 0.579470874 0.973825073 1 19.18115573 1.991162476 24.55723634 0.790163119 0.991693778 0.120324672 0.138190266 383.6902164 1066178.017 0.050962362 0.035717372 97.98564958 -1.991162476 0.201530659 YSPSQNS(ph)PIHHIPSRR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSPSQNSPIHHIPSRR 16 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 YSPSQNS(1)PIHHIPSRR;YSPSQNS(1)PIHHIPSRR 233.31 5.62E-20 2014400000 926080 1162340 661070 818440 852010 978600 757040 310930 901950 856530 TRUE FALSE 889887.7698 1129191.201 780540.0544 860679.7865 879415.6754 998387.9625 766304.882 304509.1868 799564.4173 798516.4602 1.114426332 1.414111365 0.977487746 1.077848522 1.101311894 1.250303547 0.959660721 0.381343657 1.00131238 1 19.60696262 1.991170028 13.04736091 0.711710574 1.149497226 0.384157452 0.19863977 0.65970785 969.7858889 0.075431814 0.052257614 97.98735339 -1.991170028 0.437786652 EGHSINTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGHSINTR 8 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;A0A5F9ZH85;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 0 68.016 0.057598 77288000 56047 36815 36467 35959 42290 37384 34968 16717 43369 21083 FALSE TRUE 53856.62128 35765.07225 43057.3981 37814.8483 43650.29626 38139.93009 35395.94884 16371.78811 38445.93294 19655.02963 2.740093619 1.819639701 2.190655466 1.923927311 2.220820679 1.94046668 1.800859602 0.832956674 1.956035359 1 14.26261092 1.991197904 4.00366838 1.251329897 2.112634168 0.536933214 0.36202916 0.156626441 5.610163332 0.151087604 0.094218657 97.99364326 -1.991197904 0.861304271 IKS(ph)VPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKSVPK 6 1 Q9Y2C9 Q9Y2C9 TLR6 Toll-like receptor 6 1 IKS(1)VPK 72.547 0.051664 2421600000 3210100 2614000 2757800 2262400 2874100 2772500 3323500 3975600 4269800 4300500 TRUE FALSE 3084645.743 2539451.279 3256195.807 2379162.735 2966548.037 2828561.85 3364173.987 3893502.471 3785110.204 4009223.305 0.769387362 0.633402304 0.812176215 0.593422355 0.739930857 0.705513671 0.839108658 0.971136346 0.944100619 1 21.93489134 1.991270838 2.164122803 0.973470978 0.704247965 0.791821999 0.060466066 0.126150421 1.099667234 0.03122602 0.016476343 98.01010118 -1.991270838 -0.269223013 DDTDDEIAKYDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDTDDEIAKYDGK 13 1 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 84.297 0.0085061 0 55806 65697 42598 67034 52081 50397 63391 87520 85019 52763 FALSE TRUE 53625.03982 63823.38588 50296.40619 70493.63277 53756.23266 51416.06187 64166.79802 85712.68142 75367.99955 49189.31501 1.090176592 1.297505075 1.022506741 1.433108649 1.092843693 1.045268914 1.304486513 1.742506099 1.532202665 1 15.58605734 1.9914523 22.82101634 1.511426842 1.172497794 0.205044479 0.212305811 132.9040125 354832.6444 0.077590625 0.054407592 98.05106146 -1.9914523 -0.338929048 RPNEDS(ph)DEDEEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RPNEDSDEDEEK 12 1 Q12996;E9PLP8;H0YE74 Q12996 CSTF3 Cleavage stimulation factor subunit 3 1 RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK 212.95 8.73E-09 4021936000 2916320 2384790 2839560 2722590 2810420 2604790 3197250 3759660 4077950 3825120 TRUE FALSE 2802346.99 2316778.124 3352731.658 2863103.196 2900819.712 2657460.638 3236378.902 3682021.707 3615038.212 3566041.215 0.785842569 0.649677888 0.940183092 0.802880007 0.813456586 0.745213103 0.907555103 1.032523598 1.013739885 1 21.76589195 1.991566155 3.443670332 1.01451061 0.792085515 0.690212061 0.067985895 0.136874235 3.292840903 0.031982659 0.019261074 98.07677015 -1.991566155 -0.222425095 RSNS(ph)PDKFK ddPTM_BT-474_Pertuzumab_2h_R1 5 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.016)NS(0.984)PDKFK;RS(0.345)NS(0.655)PDKFK;RS(0.494)NS(0.506)PDKFK;RS(0.316)NS(0.684)PDKFK;RS(0.031)NS(0.969)PDKFK 127.02 0.00036009 16712300000 13853400 11396800 10201870 8903560 10947200 10252770 12654200 14821200 16421400 14664000 TRUE FALSE 13311993.81 11071774.42 12045574.85 9363073.799 11299326.63 10460088.03 12809065.88 14515137.04 14557311.52 13670794.22 0.973754238 0.809885238 0.881117414 0.684896111 0.826530372 0.76514121 0.936965745 1.061762529 1.064847534 1 23.70459372 1.991578978 3.596483136 1.04382084 0.819770418 0.648897735 0.072201571 0.138191516 3.7099776 0.033075235 0.020133907 98.07966599 -1.991578978 -0.224050422 VGELKDDDFER ddPTM_BT-474_Pertuzumab_2h_R1 3 VGELKDDDFER 11 1 P36507;A0A1B0GUL7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ;; 176.87 7.51E-06 1967060000 3136210 2711800 2444710 2354140 2687310 2589720 3010360 3545700 3914100 3352010 FALSE TRUE 3013643.446 2634462.119 2886523.479 2475637.448 2773749.767 2642085.913 3047201.686 3472480.056 3469787.777 3124975.377 0.964373501 0.843034521 0.923694791 0.792210225 0.887606919 0.845474154 0.975112223 1.111202373 1.110340837 1 21.57541339 1.991584349 3.520301788 1.081827942 0.873964912 0.736566025 0.053007898 0.105878407 2.691563598 0.023313492 0.014117631 98.080879 -1.991584349 -0.207863031 KCS(ph)LPAEEDSVLEK ddPTM_BT-474_Pertuzumab_2h_R1 5 KCSLPAEEDSVLEK 14 1 E7EVA0;P27816-6;P27816 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 KCS(1)LPAEEDSVLEK;KCS(1)LPAEEDSVLEK;KCS(1)LPAEEDSVLEK;KCS(0.992)LPAEEDS(0.008)VLEK;KCS(1)LPAEEDSVLEK 235.56 1.88E-17 7090630000 6712640 5663170 5680570 5071130 5790870 6667280 6642460 7942030 8626280 8752240 TRUE FALSE 6450302.608 5501661.936 6707175.363 5332851.627 5977138.593 6802096.97 6723752.412 7778024.305 7647060.859 8159442.989 0.790532223 0.674269303 0.822013877 0.653580353 0.732542479 0.833647221 0.824045517 0.953254323 0.937203786 1 22.96003924 1.991596571 1.070345146 0.984369232 0.731564447 0.780797909 0.051608441 0.214318984 0.452225685 0.03822217 0.017757905 98.08363912 -1.991596571 -0.252804785 ALEAFETFKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALEAFETFKK 10 1 Q00796 Q00796 SORD Sorbitol dehydrogenase 0 117.25 0.0015753 431530000 515660 464450 431620 387360 443300 422120 461320 510170 515700 518520 FALSE TRUE 495507.4371 451204.3407 509623.3353 407351.696 457559.1471 430655.5556 466965.7722 499634.8112 457159.898 483400.1786 1.025046037 0.933397133 1.054247305 0.842680069 0.94654319 0.890888284 0.966002482 1.03358425 0.945717272 1 18.88285848 1.991619108 24.53646148 0.997572416 0.946340189 0.09669176 0.059848271 625.4973648 1831250.454 0.022710831 0.015968129 98.08872925 -1.991619108 -0.051232227 SLS(ph)PSHLTEDR ddPTM_BT-474_Pertuzumab_2h_R1 5 SLSPSHLTEDR 11 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SLS(1)PSHLTEDR;S(0.419)LS(0.563)PS(0.018)HLTEDR;S(0.004)LS(0.996)PSHLTEDR;S(0.035)LS(0.965)PS(0.001)HLTEDR;S(0.027)LS(0.971)PS(0.002)HLTEDR 233 1.93E-15 6978620000 2864130 3282340 2494890 3322280 2972880 2952700 2934580 2718280 3084320 3008610 TRUE FALSE 2752196.633 3188730.877 2945772.122 3493743.269 3068505.385 3012405.617 2970494.268 2662146.568 2734200.924 2804834.165 0.981233282 1.136869665 1.050248232 1.245614915 1.094005993 1.074004893 1.059062352 0.949127974 0.97481732 1 21.41948404 1.991626019 2.271468288 0.969723768 1.104815645 0.41079425 0.064697417 0.27816869 2.674077206 0.034971078 0.018733495 98.09029008 -1.991626019 0.135091877 VFIDQNLS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFIDQNLSPGK 11 0 F5H452;Q5JSB6;Q5JSB5;Q14186 F5H452 TFDP1 Transcription factor Dp-1 1 VFIDQNLS(1)PGK;VFIDQNLS(1)PGK 185.87 4.49E-06 390570000 790890 687070 690240 698990 679460 591910 743840 866910 866410 909840 TRUE FALSE 759981.1444 667475.4363 814981.7223 735064.9577 701315.448 603878.8257 752943.3364 849008.0056 768058.7691 848215.7264 0.895976248 0.786917073 0.960818925 0.866601426 0.826812597 0.711940143 0.887679057 1.000934054 0.905499327 1 19.69407171 1.991654906 24.91974903 0.962762839 0.841165356 0.423763692 0.066286496 371.775186 1110178.57 0.02618691 0.018425718 98.09681483 -1.991654906 -0.121597483 AGAAS(ph)PLNSPLSSAVPSLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGAASPLNSPLSSAVPSLGK 20 0 O75962-5;O75962;E7EPJ7;O75962-4 O75962-5 TRIO Triple functional domain protein 1 AGAAS(1)PLNSPLSSAVPSLGK;AGAAS(1)PLNSPLSSAVPSLGK 199.97 1.47E-21 355670000 675980 640940 564210 674080 596090 593860 693580 844760 812310 770670 TRUE FALSE 649561.9543 622661.0187 666175.2978 708869.3496 615263.7762 605868.2561 702068.2395 827315.4108 720099.9743 718471.8345 0.904088265 0.866646386 0.927211431 0.986634849 0.856350586 0.843273497 0.977168771 1.151493171 1.002266115 1 19.45457208 1.99170419 7.735538594 1.067453043 0.900214166 0.608705807 0.055112587 0.08167763 35.36195486 0.022114995 0.01505508 98.10794751 -1.99170419 -0.167238877 AIGSTSKPQES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 AIGSTSKPQESPK 13 1 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGSTSKPQES(1)PK;AIGSTSKPQES(1)PK;AIGST(0.002)S(0.002)KPQES(0.996)PK;AIGSTSKPQES(0.999)PK 135.55 5.01E-05 6976170000 7232150 5272910 4845120 4251200 4638700 4220470 5466300 6657240 6555260 6315450 TRUE FALSE 6949509.582 5122531.77 5720740.963 4470604.941 4787907.998 4305810.795 5533198.215 6519765.668 5811134.367 5887698.946 1.180343908 0.870039691 0.971642914 0.759312761 0.813205302 0.731323193 0.939789596 1.107353777 0.98699584 1 22.48927247 1.991717557 24.20369393 1.038426504 0.877621534 0.214291615 0.122049432 349.9887214 1022768.747 0.048158864 0.033869162 98.11096723 -1.991717557 -0.160804971 ISTCAPSTLHITQNTEQELHS(ph)PTVK ddPTM_BT-474_Pertuzumab_2h_R1 6 ISTCAPSTLHITQNTEQELHSPTVK 25 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 ISTCAPSTLHITQNTEQELHS(1)PTVK;ISTCAPSTLHITQNTEQELHS(0.983)PT(0.017)VK;ISTCAPSTLHITQNTEQELHS(0.998)PT(0.002)VK;ISTCAPSTLHITQNTEQELHS(0.987)PT(0.013)VK;ISTCAPSTLHITQNTEQELHS(0.662)PT(0.338)VK;ISTCAPSTLHITQNTEQELHS(0.986)PT(0.014)VK 357.27 5.13E-103 20413160000 6410550 7890180 6281970 7980510 7685820 7752990 5972040 3854230 4896170 5343790 TRUE FALSE 6160018.619 7665159.792 7417261.721 8392385.077 7933041.38 7909760.77 6045127.612 3774638.804 4340377.308 4981850.344 1.236492105 1.538617032 1.488856792 1.684591969 1.592388537 1.587715452 1.213430191 0.75767808 0.871237996 1 22.24825025 1.991881928 3.417196342 0.862225904 1.52963412 0.844706238 0.123878283 0.08439753 1.992607457 0.058994823 0.035473989 98.14810703 -1.991881928 0.667408215 AVLHTDSSLPFS(ph)FPDELPNSCLLAALSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVLHTDSSLPFSFPDELPNSCLLAALSDR 29 0 Q8NCE2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 AVLHTDSSLPFS(1)FPDELPNSCLLAALSDR;AVLHT(0.001)DS(0.031)S(0.027)LPFS(0.941)FPDELPNSCLLAALSDR 199.7 2.33E-25 328160000 155982 155169 122862 132142 128171 143911 130242 97543 163044 135416 TRUE FALSE 149886.051 150743.732 145065.8965 138961.8645 132293.7366 146820.979 131835.9406 95528.70296 144535.9287 126244.1537 1.187271225 1.194065053 1.149090015 1.100739008 1.047919707 1.162992303 1.044293432 0.756698034 1.144892056 1 16.94585705 1.991891254 12.39980873 0.930235601 1.134413418 0.369883226 0.09851872 0.476803411 720.8045401 0.037973031 0.026352579 98.15021479 -1.991891254 0.204177818 SQSS(ph)DTEQQS(ph)PTSGGGK ddPTM_BT-474_Pertuzumab_2h_R1 9 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 SQS(0.004)S(0.996)DTEQQS(0.999)PT(0.001)SGGGK;S(0.005)QS(0.23)S(0.765)DTEQQS(0.993)PT(0.006)S(0.001)GGGK;SQS(0.004)S(0.996)DTEQQS(0.998)PT(0.002)SGGGK;SQS(0.155)S(0.845)DTEQQS(0.756)PT(0.23)S(0.014)GGGK;S(0.058)QS(0.43)S(0.512)DT(0.05)EQQS(0.938)PT(0.006)S(0.006)GGGK;S(0.076)QS(0.423)S(0.501)DT(0.401)EQQS(0.598)PT(0.001)SGGGK;S(0.253)QS(0.344)S(0.403)DT(0.084)EQQS(0.866)PT(0.027)S(0.024)GGGK;S(0.003)QS(0.047)S(0.951)DTEQQS(0.998)PT(0.002)SGGGK;SQS(0.001)S(0.999)DTEQQS(0.969)PT(0.031)SGGGK 341.28 2.11E-72 2253842000 3660040 3375748 3383652 3224592 3526336 4141693 4077700 4470770 5781096 5196268 TRUE FALSE 3517001.59 3279474.972 3995153.185 3391013.58 3639763.8 4225440.87 4127604.112 4378447.037 5124850.218 4844320.14 0.726005196 0.676973213 0.824708745 0.699997829 0.751346669 0.872246414 0.852050235 0.903831066 1.057909071 1 22.20786278 1.991893749 0.73874869 1.027389227 0.724628328 0.82784313 0.050046768 0.258333864 0.26758838 0.043232799 0.023230735 98.15077869 -1.991893749 -0.302760899 KNPLPPSVGVVDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNPLPPSVGVVDKK 14 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 88.311 0.00371 1677400000 2164000 1826100 1781300 1537500 1897500 1819800 2104500 2212400 2544600 2454800 FALSE TRUE 2079428.488 1774021.416 2103220.535 1616850.559 1958534.811 1856597.603 2130255.501 2166713.167 2255747.676 2288534.209 0.908628973 0.775178019 0.919025167 0.706500498 0.855803161 0.811260586 0.930838391 0.946768966 0.985673566 1 21.12599243 1.992086613 1.749801141 0.982035598 0.825279908 0.558777 0.059854078 0.255676939 1.459495227 0.034754613 0.017212503 98.19437561 -1.992086613 -0.15675569 LTFSCLGGSDNFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTFSCLGGSDNFK 13 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 313.3 2.72E-50 446100000 481130 476080 405880 436660 468320 458670 493580 556260 604020 558780 FALSE TRUE 462326.9077 462502.6645 479231.5448 459196.0749 483383.9381 467944.6217 499620.5797 544773.0366 535454.1819 520933.3329 0.887497264 0.887834652 0.919947937 0.881487219 0.927919002 0.898281204 0.959087369 1.045763445 1.027874678 1 18.99073923 1.992097031 3.01760563 1.027897227 0.901183901 0.908321064 0.017638327 0.06558227 1.154222423 0.008348517 0.004859395 98.19673119 -1.992097031 -0.126713326 DLKPQNLLIDDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLKPQNLLIDDK 12 1 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 173.68 2.96E-05 1695920000 1729410 1461430 1582280 1504210 1679010 1699040 1977270 2234660 2510100 2522600 FALSE TRUE 1661822.745 1419751.447 1868233.194 1581842.458 1733016.881 1733395.753 2001468.422 2188513.49 2225163.971 2351742.055 0.706634787 0.603702028 0.794403957 0.672625833 0.736907722 0.737068825 0.851057801 0.930592488 0.946176885 1 21.1652984 1.992107066 1.011127276 0.990915288 0.69195296 0.864600699 0.045430373 0.169909889 0.319710338 0.034671229 0.016260224 98.19900027 -1.992107066 -0.298962328 ESESEAKVDGETAS(ph)DSESR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESESEAKVDGETASDSESR 19 1 O95674 O95674 CDS2 Phosphatidate cytidylyltransferase 2 1 ESESEAKVDGET(0.011)AS(0.975)DS(0.011)ES(0.003)R 130.15 4.07E-06 0 195090 270670 161020 312830 182070 209720 275060 426030 340300 218290 TRUE FALSE 187465.6671 262950.7566 190119.8959 328975.1938 187926.4469 213960.6821 278426.2666 417232.3316 301670.5707 203505.0239 0.921184468 1.292109411 0.934227039 1.616545811 0.923448686 1.051377888 1.368154266 2.050231113 1.482374071 1 17.63470488 1.992187085 11.41833171 1.648023419 1.14167065 0.201934187 0.316970875 0.363302237 513.1586236 0.117874637 0.081709821 98.21709517 -1.992187085 -0.506352769 HSVGVVIGR ddPTM_BT-474_Pertuzumab_2h_R1 6 HSVGVVIGR 9 0 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;; 172.23 5.63E-05 2211060000 1798700 1786080 1505763 1770560 1840280 1893880 1676760 1258929 1950610 1907240 FALSE TRUE 1728404.815 1735142.747 1777887.87 1861938.814 1899474.277 1932175.551 1697280.69 1232931.676 1729184.93 1778060.936 0.97207288 0.975862363 0.999902666 1.047173793 1.068284129 1.086675666 0.954568348 0.693413623 0.972511625 1 20.76187334 1.992225393 24.27738167 0.846930181 1.024265913 0.303078411 0.086479094 209.5361689 654308.744 0.032833546 0.023178775 98.22575893 -1.992225393 0.177335731 FGS(ph)ADNIAHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FGSADNIAHLK 11 0 G3V207;Q9ULS5;A0A0C4DFR1;O75069-3;O75069-5;O75069-2;O75069 G3V207 TMCC3;TMCC2 Transmembrane and coiled-coil domains protein 3;Transmembrane and coiled-coil domains protein 2 1 FGS(1)ADNIAHLK;FGS(1)ADNIAHLK 136.17 6.75E-05 312580000 442880 547890 360670 566920 390980 306360 509430 746980 641950 458000 TRUE FALSE 425571.76 532264.7136 425851.0921 596178.8091 403556.2268 312554.8091 515664.5567 731554.602 569078.5273 426979.2521 0.996703605 1.246582149 0.997357811 1.396271145 0.945142474 0.732014044 1.207704014 1.713325878 1.332801359 1 18.70380644 1.992248593 24.85500819 1.436104402 1.061136884 0.218673592 0.23545938 367.9055107 1179695.249 0.089719554 0.063380821 98.23100624 -1.992248593 -0.374967518 IDSLS(ph)AQLSQLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDSLSAQLSQLQK 13 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 IDS(0.333)LS(0.667)AQLSQLQK 288.06 2.51E-33 291000000 487590 415710 350730 419290 398760 340400 442260 553900 552490 475570 TRUE FALSE 468534.4437 403854.3578 414114.7129 440929.6071 411586.4775 347283.1212 447672.5102 542461.7714 489773.6514 443359.2203 1.056782903 0.910896491 0.934038797 0.99451999 0.928336344 0.783299648 1.009728657 1.223526537 1.104688093 1 18.75811655 1.992250111 24.88299986 1.12983779 0.932685099 0.467894575 0.082645786 249.0004317 799479.671 0.031322691 0.02213455 98.23134961 -1.992250111 -0.197152691 ESVSTEDLSPPS(ph)PPLPK ddPTM_BT-474_Pertuzumab_2h_R1 4 ESVSTEDLSPPSPPLPK 17 0 Q13127-4;Q13127 Q13127-4 REST RE1-silencing transcription factor 1 ESVSTEDLSPPS(1)PPLPK;ESVSTEDLSPPS(1)PPLPK;ESVSTEDLSPPS(1)PPLPK;ESVSTEDLS(0.001)PPS(0.999)PPLPK 308.78 4.88E-58 897480000 1295520 1162640 998090 1080570 1160920 1082730 1170570 1378590 1235280 1149270 TRUE FALSE 1244889.646 1129482.646 1178467.065 1136338.347 1198262.046 1104623.542 1184895.786 1350121.635 1095056.193 1071428.919 1.161896626 1.05418346 1.099902237 1.060582113 1.118377547 1.030981638 1.105902374 1.260113117 1.022052115 1 20.03110471 1.992271707 24.91685037 1.137969332 1.085320841 0 0.076873237 873.8142895 2817273.657 0.028575787 0.020201403 98.23623443 -1.992271707 -0.052648491 SPVAEEPGGGGSSSSEAKLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPVAEEPGGGGSSSSEAKLSPR 22 1 Q7L8J4 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 SPVAEEPGGGGSSSSEAKLS(1)PR 106.28 0.00029783 423570000 162440 134170 139020 123490 115800 158730 194080 240340 290150 265640 TRUE FALSE 156091.6652 130343.603 164144.0065 129863.3337 119524.8122 161939.6294 196455.2091 235376.895 257213.3884 247647.9662 0.630296576 0.52632616 0.662811849 0.524386837 0.482639991 0.653910597 0.793284161 0.950449538 1.038625079 1 17.91793125 1.992273439 1.602014734 1.01581948 0.565935829 0.92792742 0.052731346 0.092046152 0.440570296 0.034918736 0.016886388 98.23662633 -1.992273439 -0.449883651 AEELS(ph)PAALSPLLEPIR ddPTM_BT-474_Pertuzumab_2h_R1 6 AEELSPAALSPLLEPIR 17 0 A0A5F9ZH52;A5YM69 A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 AEELS(0.999)PAALS(0.001)PLLEPIR;AEELS(1)PAALSPLLEPIR;AEELS(1)PAALSPLLEPIR;AEELS(1)PAALSPLLEPIR;AEELS(1)PAALSPLLEPIR;AEELS(1)PAALSPLLEPIR 202.34 1.12E-11 333590000 209996 233077 215882 269363 250331 252279 203893 194568 189575 197602 TRUE FALSE 201789.1242 226429.8722 254896.6797 283264.8567 258383.124 257380.2542 206388.3035 190550.1028 168055.2408 184218.2405 1.095380803 1.229139262 1.383666888 1.537659115 1.402592508 1.397148586 1.120346731 1.034371527 0.912261675 1 17.49105639 1.992273948 2.359184942 0.979790989 1.349643727 0.664210442 0.115132567 0.197136764 2.047750905 0.068479655 0.037129882 98.23674147 -1.992273948 0.369852738 GSSGS(ph)PAHAESYSSGGGGQQK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 GS(0.022)S(0.137)GS(0.841)PAHAESYSSGGGGQQK;GS(0.025)S(0.171)GS(0.804)PAHAESYSSGGGGQQK;GSS(0.002)GS(0.998)PAHAESYSSGGGGQQK 371.19 2.17E-112 1208120000 874430 949830 758270 974520 733320 1007380 875480 767640 1057000 994660 TRUE FALSE 840256.3089 922741.7784 895306.2566 1024815.094 756907.9038 1027749.914 886194.3861 751787.9657 937013.7913 927290.7922 0.906141111 0.995094296 0.965507545 1.105171218 0.816257327 1.108336158 0.95568121 0.810735933 1.010485383 1 19.8226623 1.992285352 24.90322411 0.910335463 0.984815441 0.01064519 0.096339307 740.4663763 2390258.451 0.035161866 0.02484497 98.23932097 -1.992285352 0.074479979 SHELDIDENPAS(ph)DFDDSGSLLGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHELDIDENPASDFDDSGSLLGFK 24 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 SHELDIDENPAS(1)DFDDSGSLLGFK 207.9 4.51E-25 22260000 17424 20283 16063 14708 17241 20113 15949 5142.6 25482 19377 TRUE FALSE 16743.05082 19704.5487 18965.94142 15467.08164 17795.57242 20519.69864 16144.18863 5036.403513 22589.39019 18064.57853 0.926844254 1.090783749 1.049896702 0.85621049 0.985108642 1.135907965 0.893693069 0.278799946 1.25047978 1 14.14087597 1.99230032 24.95046967 0.718781559 1.006077358 0.01736837 0.247082896 518.2104569 1679239.077 0.092829029 0.065605128 98.24270696 -1.99230032 0.287295799 VHTIVISVQHDEEVCLDEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 VHTIVISVQHDEEVCLDEMR 20 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 208.47 3.26E-22 322160000 22499 33134 28191 36751 34893 38725 27366 8260.7 34218 24626 FALSE TRUE 21619.71421 32189.05076 33285.74081 38647.72351 36015.36503 39508.04603 27700.91329 8090.113658 30333.71609 22958.05909 0.94170479 1.402080666 1.449849949 1.683405525 1.568746073 1.720879186 1.206587769 0.352386656 1.321266575 1 14.48671306 1.992355933 22.88207322 0.809317187 1.472147963 0.410072852 0.301635937 92.52655871 276973.0399 0.115458536 0.08145114 98.25528804 -1.992355933 0.662830776 VGVSSKPDSS(ph)PVLSPGNK ddPTM_BT-474_Pertuzumab_2h_R1 3 VGVSSKPDSSPVLSPGNK 18 1 Q8N4C8;Q8N4C8-4;Q8N4C8-2;Q8N4C8-3;Q8N4C8-5 Q8N4C8 MINK1 Misshapen-like kinase 1 1 VGVS(0.002)S(0.002)KPDS(0.298)S(0.698)PVLSPGNK;VGVSSKPDS(0.483)S(0.517)PVLSPGNK;VGVSSKPDS(0.149)S(0.851)PVLSPGNK 250.81 2.54E-25 2985880000 4458900 4372900 3395500 3646300 3578300 3809800 4423700 5290400 5554600 5270400 TRUE FALSE 4284641.258 4248189.174 4009142.382 3834485.98 3693399.269 3886836.766 4477838.564 5181151.391 4924065.095 4913431.114 0.872026321 0.864607456 0.815955753 0.780409024 0.751694525 0.791063653 0.911346564 1.054487439 1.002164268 1 22.2282994 1.992359941 3.504329177 1.020724415 0.811550594 0.860980158 0.037145962 0.088302832 2.220998924 0.019523557 0.011821279 98.25619472 -1.992359941 -0.209173821 QKDEEDKAR ddPTM_BT-474_Pertuzumab_2h_R1 5 QKDEEDKAR 9 2 O00170 O00170 AIP AH receptor-interacting protein 0 ;;;; 106.4 0.0016547 2010690000 2352510 2063486 1594316 1482709 1820041 1833977 2047602 2128419 2519410 2278142 FALSE TRUE 2260571.308 2004637.4 1882444.367 1559231.789 1878584.272 1871061.271 2072661.166 2084466.404 2233417.139 2123841.413 1.06437858 0.943873392 0.88633942 0.734156411 0.884521914 0.880979747 0.975902039 0.981460476 1.051593177 1 21.01824461 1.992389731 2.03392458 1.014065204 0.892214287 0.296806575 0.07792678 0.439667067 3.385957525 0.048434186 0.025099403 98.26293489 -1.992389731 -0.121850917 VLLALFCHEPCRPLHQLATDSTFSLDQPGGTLDLTLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLLALFCHEPCRPLHQLATDSTFSLDQPGGTLDLTLIR 38 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 233.05 5.79E-50 2890300000 588320 598170 495230 587400 721010 667450 563130 372590 642940 641570 FALSE TRUE 565327.804 581110.7773 584729.0773 617715.7844 744201.9415 680946.2963 570021.7534 364895.8863 569956.1466 598115.8924 0.945181045 0.971568863 0.977618359 1.032769388 1.244243717 1.138485543 0.953028937 0.610075557 0.952919248 1 19.19006553 1.992406213 23.55677297 0.803643031 1.051971521 0.299288054 0.12904534 155.8256327 483388.6567 0.051355721 0.036269248 98.26666397 -1.992406213 0.248328489 KLS(ph)GDQITLPTTVDYSSVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSGDQITLPTTVDYSSVPK 20 1 O00559-2;E9PND3;E9PN10;O00559;E9PJ38 O00559-2 EBAG9 Receptor-binding cancer antigen expressed on SiSo cells 1 KLS(1)GDQITLPTTVDYSSVPK;KLS(1)GDQITLPTTVDYSSVPK 281.85 5.29E-45 18092900000 4143900 4624200 3509300 4040900 3769100 4021700 4679900 5981100 6164000 5157200 TRUE FALSE 3981951.807 4492322.344 4143508.574 4249451.333 3890336.525 4103021.529 4737174.016 5857588.195 5464288.562 4807898.25 0.828210498 0.934363023 0.861812867 0.883848017 0.809155336 0.853391922 0.985289989 1.218326156 1.136523337 1 22.19697493 1.992454555 4.013171871 1.137422367 0.865298613 0.785421763 0.059848344 0.084565288 3.054477856 0.025791644 0.016122994 98.27760291 -1.992454555 -0.272123753 TEES(ph)PASDEAGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEES(1)PASDEAGEK;TEES(1)PASDEAGEK;TEES(1)PASDEAGEK 327.79 2.55E-62 1590060000 2699820 2101830 2485860 2358390 2413620 1919310 2622100 3349230 3299940 2877040 TRUE FALSE 2594308.05 2041887.866 2935110.2 2480106.791 2491256.279 1958119.763 2654190.044 3280067.23 2925344.646 2682175.518 0.967240224 0.76128048 1.094302062 0.924662377 0.92881926 0.730049078 0.989566129 1.22291297 1.090661154 1 21.35497222 1.992502527 24.62014641 1.123529529 0.901989157 0.410161203 0.108653187 241.8425633 794161.2634 0.04099593 0.029000767 98.2884592 -1.992502527 -0.221540372 NQGGYDRYS(ph)GGNYR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQGGYDRYSGGNYR 14 1 P98179 P98179 RBM3 RNA-binding protein 3 1 NQGGYDRYS(1)GGNYR;NQGGYDRYS(1)GGNYR 246.12 6.33E-18 862270000 676230 598450 521850 634370 589190 582810 626440 740990 599360 726080 TRUE FALSE 649802.184 581382.7919 616159.9035 667109.9117 608141.8314 594594.8175 634106.5601 725688.2976 531323.1655 676901.9549 0.959964998 0.858887743 0.910264624 0.98553403 0.898419375 0.878406117 0.936777558 1.072072982 0.784933714 1 19.36858736 1.992509851 24.93535253 0.971364071 0.91428 0.029288065 0.075832549 770.5439194 2565210.784 0.028408856 0.020101674 98.29011683 -1.992509851 -0.057084071 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLASPK 38 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLS(0.252)LAS(0.748)PK 248.72 2.33E-50 344070000 80962 94557 74783 97112 98707 99259 70213 35062 58167 57151 TRUE FALSE 77797.91553 91860.32694 88297.95164 102123.962 101882.0003 101266.085 71072.2877 34337.95745 51564.12602 53280.11187 1.460168022 1.724101616 1.657240358 1.916737003 1.912195691 1.900635743 1.333936533 0.64447983 0.967793126 1 15.70130949 1.992552425 4.019113885 0.851672964 1.765493402 0.862745831 0.159350962 0.071937913 2.609622614 0.073728706 0.046111476 98.29975266 -1.992552425 0.913820438 KLELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLELEK 6 1 Q96EX2-3;Q96EX2-5 REV__A0A087WZP0 0 100.19 0.060842 1398700000 2212900 1849200 1608700 1553900 1769500 1602800 1856200 2183500 2107100 1949300 FALSE TRUE 2126417.422 1796462.627 1899427.875 1634096.965 1826417.575 1635209.714 1878916.731 2138409.962 1867910.842 1817272.175 1.170114995 0.98854902 1.045208253 0.899203206 1.005032488 0.899815524 1.033921477 1.176714194 1.027865208 1 20.79334308 1.992657609 24.86797817 1.092200499 0.995645851 0.090759694 0.084440245 482.6250366 1634605.499 0.031919388 0.022618034 98.32356319 -1.992657609 -0.096554649 YQQELEEEIKELYENFCK ddPTM_BT-474_Pertuzumab_2h_R1 2 YQQELEEEIKELYENFCK 18 1 Q6DD88;F5H6I7 Q6DD88 ATL3 Atlastin-3 0 ; 202.07 1.22E-15 229720000 325610 390100 232250 347490 296500 329180 359410 475930 430370 329400 FALSE TRUE 312884.8012 378974.7299 274222.7414 365424.0005 306037.1918 335836.2451 363808.5671 466101.8792 381516.2019 307089.4446 1.018871885 1.234085823 0.892973517 1.189959495 0.996573465 1.093610513 1.18469903 1.51780495 1.242361822 1 18.2282994 1.99266034 7.072694413 1.321204589 1.077210682 0.193122569 0.151509515 0.145682844 43.0260576 0.057210879 0.038808288 98.32418154 -1.99266034 -0.243993907 DIVVQETMEDIDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DIVVQETMEDIDK 13 0 O43852;O43852-3;O43852-15;O43852-6;H0Y875;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 227.31 2.17E-11 124542000 114473 113906 131093 145813 122711 121698 165840 183089 209476 214772 FALSE TRUE 109999.2686 110657.5124 154784.4212 153338.4264 126658.1108 124158.8169 167869.5995 179308.1482 185697.1627 200225.3011 0.549377466 0.552664982 0.77305126 0.765829421 0.632577951 0.620095544 0.838403531 0.895531919 0.927441046 1 17.61126476 1.992664652 2.042347378 0.941242331 0.653678092 0.751409033 0.076157469 0.183847569 1.42767004 0.047838857 0.024828463 98.32515768 -1.992664652 -0.287564239 S(ph)PNSHDSEPWTLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPNSHDSEPWTLLR 14 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.986)PNS(0.014)HDSEPWTLLR;S(0.996)PNS(0.004)HDSEPWTLLR 151.96 4.38E-06 280040000 59655 87656 87469 131166 86989 100487 82025 73799 68413 91520 TRUE FALSE 57323.61665 85156.1367 103276.594 137935.493 89787.08019 102518.916 83028.84649 72275.02486 60647.04305 85321.26888 0.67185612 0.998064584 1.210443719 1.616660122 1.052341126 1.201563424 0.973131876 0.84709271 0.71080803 1 16.3806178 1.992724961 2.947982177 0.83906887 1.142176542 0.21878718 0.229700548 0.395521073 6.607297495 0.119546707 0.069186194 98.33881287 -1.992724961 0.303107672 DLANDIMTLMSHTKPYIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLANDIMTLMSHTKPYIR 18 1 O14617-5;O14617-2;O14617;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ; 112.56 0.00016362 165398000 303590 374710 302900 297710 323260 364600 318480 284490 337000 343520 FALSE TRUE 291725.3672 364023.6377 357640.768 313074.8488 333657.9515 371972.4618 322377.6535 278615.1821 298745.1728 320253.0844 0.910921335 1.136674884 1.116744179 0.977585741 1.041857105 1.161495329 1.006634032 0.869984383 0.932840892 1 18.28885294 1.992746076 24.15356416 0.924448961 1.061534461 0.343361552 0.075861746 205.2798733 683526.3726 0.02859878 0.020244064 98.34359398 -1.992746076 0.1370855 RHAS(ph)APSHVQPSDSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RHASAPSHVQPSDSEK 16 1 O60343-2;O60343-3;O60343;A0A3B3IRT3 O60343-2 TBC1D4 TBC1 domain family member 4 1 RHAS(0.991)APS(0.009)HVQPSDSEK 117.31 0.00016914 254940000 314650 292330 214010 281640 285980 257110 224850 107010 192830 164750 TRUE FALSE 302353.1301 283993.0346 252686.3676 296175.4742 295178.8064 262308.9404 227601.7816 104800.2061 170940.7468 153591.3358 1.9685559 1.849017285 1.645186341 1.928334516 1.921845428 1.707836833 1.481866021 0.682331497 1.112958267 1 17.22873731 1.992806312 2.979560727 0.910337597 1.836842455 0.889417699 0.142134436 0.073933639 1.265103383 0.068520406 0.039775963 98.35723513 -1.992806312 0.926504858 SLVEIIEHGLVDEQQK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLVEIIEHGLVDEQQK 16 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;;; 256.37 1.23E-26 753208000 948780 838170 741810 768240 868010 898910 914870 919700 1130460 1047510 FALSE TRUE 911700.6287 814266.2123 875871.5685 807888.9585 895930.33 917086.5761 926066.4527 900707.8736 1002134.92 976561.2147 0.933582673 0.833809699 0.896893667 0.827279382 0.917433865 0.93909789 0.948293296 0.922326077 1.026187509 1 19.89735096 1.992822538 0.650791441 1.005016055 0.871655142 0.607342832 0.037280503 0.491932928 0.409697219 0.032871289 0.019485214 98.36091001 -1.992822538 -0.133360913 TNPFPLLEDEDDLFTDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNPFPLLEDEDDLFTDQK 18 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;Q5SRD0 Q641Q2;A0A0A0MR88 FAM21A;FAM21C;FAM21D WASH complex subunit FAM21A;WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 0 ; 169.92 3.96E-11 77258000 60712 54720 49283 53101 54423 61701 61395 72420 83452 77141 FALSE TRUE 58339.30792 53159.43918 58189.53439 55841.54897 56173.56522 62948.63649 62146.37038 70924.50169 73978.87882 71916.17136 0.81121265 0.739186169 0.809130037 0.776481116 0.781097828 0.875305725 0.864150151 0.986210756 1.028682109 1 16.1340286 1.992897446 1.097666463 1.024494707 0.780888245 0.916749131 0.028342122 0.119619388 0.265656026 0.020835243 0.009663625 98.37787704 -1.992897446 -0.243606462 IHDENLR ddPTM_BT-474_Pertuzumab_2h_R1 4 IHDENLR 7 0 O95232;J3KPP4;D6RDI2 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 210.67 1.66E-08 2196140000 950634 1079343 873669 1129612 1035092 1167742 979206 739560 1068373 1096797 FALSE TRUE 913482.1723 1048561.194 1031560.423 1187911.411 1068386.674 1191354.543 991189.8159 724287.8276 947095.776 1022509.962 0.893372393 1.025477729 1.00885122 1.161760232 1.044866763 1.165127566 0.969369348 0.708343052 0.926246013 1 19.96368347 1.992915324 24.73454868 0.844056553 1.053075868 0.353697323 0.101069066 239.1646484 834989.763 0.038239741 0.027120896 98.38192678 -1.992915324 0.209019316 KS(ph)PPPAKDEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 KSPPPAKDEAR 11 2 Q8IXJ6-5;Q8IXJ6-2;Q8IXJ6-3;Q8IXJ6 Q8IXJ6-5 SIRT2 NAD-dependent protein deacetylase sirtuin-2 1 KS(1)PPPAKDEAR;KS(1)PPPAKDEAR;KS(1)PPPAKDEAR 86.214 0.011527 331610000 304250 262933 257356 240859 266239 300602 314563 357497 445230 377202 TRUE FALSE 292359.5736 255434.4083 303865.9541 253289.7619 274802.8192 306680.3784 318412.7161 350114.562 394689.357 351653.7726 0.831384721 0.726380401 0.864105486 0.720281657 0.78145847 0.872108882 0.905472203 0.995622937 1.122380557 1 18.42379617 1.992983744 1.282178391 1.059543395 0.783774755 0.813375048 0.052666356 0.170807012 0.520833854 0.03639583 0.016902062 98.39742751 -1.992983744 -0.27576864 KGQSEEIQK ddPTM_BT-474_Pertuzumab_2h_R1 5 KGQSEEIQK 9 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;;; 175.65 8.62E-05 2313950000 2758744 2571153 2290273 1932907 2641772 2188034 2658492 3021964 3169531 3209712 FALSE TRUE 2650929.235 2497826.234 2704176.278 2032664.562 2726746.996 2232277.547 2691027.42 2959559.387 2809739.129 2992315.347 0.885912388 0.834746992 0.903706984 0.679294902 0.911249878 0.746003441 0.899312776 0.989053306 0.938984967 1 21.51283079 1.9929883 5.639367606 0.968561391 0.827083135 0.486409887 0.068735127 0.136582225 15.42169021 0.026755544 0.017756637 98.39845972 -1.9929883 -0.141478256 GQSQT(ph)SPDHRS(ph)DTS(ph)S(ph)PEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 4 GQS(0.143)QT(0.463)S(0.395)PDHRS(0.938)DT(0.238)S(0.861)S(0.964)PEVR 62.831 0.085452 599630000 383850 418680 341050 429720 419170 474650 401300 367420 442720 403380 TRUE FALSE 368848.7176 406739.6563 402685.3216 451897.9007 432652.9837 484247.7482 406211.2294 359832.6486 392464.2816 376058.7133 0.980827473 1.081585513 1.070804391 1.201668475 1.150493177 1.287691871 1.080180342 0.95685231 1.043625019 1 18.5205984 1.992990408 24.981526 1.001152756 1.132984849 0.346266199 0.078984913 358.8710964 1278984.716 0.0322311 0.022854043 98.39893738 -1.992990408 0.131832094 KLSPT(ph)EPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSPTEPK 8 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 KLS(0.499)PT(0.501)EPK 107.11 0.0023824 1759500000 2272500 2478600 1777400 2200000 2106000 2089100 2511000 3129400 3312700 2766600 TRUE FALSE 2183688.188 2407912.755 2098615.718 2313542.264 2173741.403 2131343.033 2541730.369 3064776.796 2936656.184 2579215.718 0.846648139 0.933583313 0.813664287 0.896994481 0.842791624 0.82635315 0.985466377 1.188259197 1.138584944 1 21.29850101 1.992991209 4.111821674 1.124113401 0.863315212 0.80144599 0.055501665 0.078973616 3.060130144 0.023359514 0.014691768 98.39911881 -1.992991209 -0.260798189 S(ph)PEPEVLSTQEDLFDQSNK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPEPEVLSTQEDLFDQSNK 19 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(1)PEPEVLSTQEDLFDQSNK;S(1)PEPEVLSTQEDLFDQSNK;S(1)PEPEVLSTQEDLFDQSNK 331.34 1.80E-75 569934000 990840 862323 966777 1036817 964660 931854 1175410 1427920 1535670 1457640 TRUE FALSE 952116.8774 837730.3923 1141495.11 1090327.25 995689.165 950696.7263 1189795.019 1398432.953 1361347.18 1358912.744 0.700646073 0.616471069 0.840006185 0.802352656 0.732710153 0.699601008 0.875549239 1.029082227 1.001791458 1 20.37402139 1.993024069 3.111725155 1.009609956 0.735144058 0.823007077 0.05795682 0.108328294 2.04717961 0.030138993 0.017708479 98.40656412 -1.993024069 -0.274465898 DDKHGSYEDAVHSGALND ddPTM_BT-474_Pertuzumab_2h_R1 2 DDKHGSYEDAVHSGALND 18 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 263.52 4.01E-31 2096900000 2501500 3333900 1904410 2204900 2306500 3221700 2288900 1293620 2691000 2352200 FALSE TRUE 2403738.614 3238820.436 2248579.25 2318695.153 2380690.667 3286844.981 2316912.243 1266906.295 2385528.962 2192883.399 1.096154322 1.476968834 1.025398456 1.057372752 1.085643983 1.498869016 1.056559708 0.577735367 1.087850345 1 21.06439767 1.99307445 24.93868515 0.835494562 1.205084791 0.329940904 0.199412478 288.375612 1038432.298 0.075300659 0.053489802 98.41798069 -1.99307445 0.369590229 RQQELK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQQELK 6 1 P35221-2;P35221;G3XAM7;P26232;P26232-5;P26232-2;P26232-3;E5RIB1;E5RJ41 P35221-2;REV__E7EW15 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 0 ; 138.85 0.019443 551150000 372950 471320 321510 470840 302860 368660 405920 445710 467280 469850 FALSE TRUE 358374.7017 457878.4151 379614.009 495140.1088 312601.767 376114.5578 410887.7704 436505.9327 414236.3334 438026.641 0.818157318 1.045320928 0.866645938 1.130388115 0.713659257 0.858656809 0.938042877 0.996528275 0.945687533 1 18.74065909 1.993186226 22.16144367 0.977086078 0.910466624 0.085109013 0.109680772 199.0585659 647427.921 0.041530767 0.029423044 98.44331409 -1.993186226 -0.066619455 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK 40 1 P68363;P68363-2;F8VVB9;F8VS66;F8W0F6;Q9BQE3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1C;TUBA1A Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ; 253.88 3.77E-63 1285270000 526020 665750 390260 478920 483110 653990 488760 325090 570250 540670 FALSE TRUE 505462.5569 646763.4618 460788.6633 503637.1186 498649.6719 667214.1259 494741.5911 318376.7779 505517.6107 504049.9393 1.002802535 1.283133696 0.914172639 0.999180992 0.989286245 1.323706391 0.981532885 0.63163737 1.002911758 1 18.94320715 1.993230658 24.96802857 0.829586658 1.084494183 0.244347321 0.157153492 324.8020452 1198000.217 0.059047394 0.042004165 98.45338633 -1.993230658 0.254907525 HYQEEGQGTEVVQGVLLGLVVEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 HYQEEGQGTEVVQGVLLGLVVEDR 24 0 A0A087WZK9;B3KS98;O15372;E5RGU4;E5RFH0;E5RFW7 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;; 222.69 8.25E-33 633416000 444769 483498 431408 452381 501454 597083 448461 294418 507284 521970 FALSE TRUE 427386.9358 469709.1104 509373.0222 475728.4376 517583.7233 609156.4274 453949.3999 288338.1654 449699.247 486616.507 0.878282856 0.965255193 1.046764783 0.977624949 1.063637825 1.251820312 0.932868888 0.592536754 0.924134797 1 18.89242573 1.993301706 24.99023606 0.785888304 1.032838741 0.265264241 0.13525524 292.8913271 1092730.343 0.051765146 0.036812686 98.46949386 -1.993301706 0.246950437 SCFES(ph)SPDPELK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SCFES(0.747)S(0.253)PDPELK 123.95 0.00034793 130580000 651510 608590 499580 526760 556800 595460 621960 749620 788340 687540 TRUE FALSE 626048.2689 591233.6091 589865.2191 553946.1467 574709.9777 607500.6092 629571.7325 734140.085 698850.9482 640972.3034 0.976716569 0.92240118 0.920266314 0.864227898 0.89662217 0.947779812 0.982213629 1.145353834 1.090298199 1 19.28990249 1.993319024 3.249476185 1.091643017 0.918084784 0.711955517 0.044227699 0.117479871 2.45843216 0.020960908 0.012463256 98.47342071 -1.993319024 -0.173558233 TYS(ph)LPEDDDFIK ddPTM_BT-474_Pertuzumab_2h_R1 2 TYSLPEDDDFIK 12 0 F8W9X7;Q567U6 F8W9X7 CCDC93 Coiled-coil domain-containing protein 93 1 TYS(1)LPEDDDFIK;TYS(1)LPEDDDFIK 262.11 2.24E-21 68386000 310120 241380 171610 208700 242940 161363 255800 412070 252060 212660 TRUE FALSE 298000.1675 234496.0787 202623.7444 219471.032 250754.3857 164625.8704 258930.5569 403560.6105 223447.2055 198256.3488 1.503105295 1.18279228 1.022029033 1.107006325 1.264798768 0.830368719 1.306039169 2.035549494 1.127062043 1 17.59700754 1.993319055 24.94351369 1.544647269 1.1434723 0.041395107 0.31172379 393.2523789 1468221.234 0.115943625 0.082498112 98.47342767 -1.993319055 -0.401174969 CDENILWLDYK ddPTM_BT-474_Pertuzumab_2h_R1 5 CDENILWLDYK 11 0 P14618;P14618-3;B4DNK4;H3BUW1;H3BTJ2;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;; 186.72 9.08E-06 5253044000 3675950 3222910 3014450 3135410 3357620 3201330 3425510 3880940 3964530 3542210 FALSE TRUE 3532289.81 3130995.762 3559228.171 3297228.886 3465620.897 3266063.086 3467432.416 3800797.233 3514493.175 3302292.962 1.069647621 0.948127801 1.077805093 0.998466497 1.049458948 0.989028873 1.050007512 1.15095701 1.064258446 1 21.65503668 1.993346655 23.98199553 1.091504186 1.021270793 0.130049022 0.050882685 209.0340144 753464.744 0.018099036 0.012856453 98.47968599 -1.993346655 -0.070233393 ASPSCSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPSCSSPTR 10 0 Q8N5I9;J3KN91;A0A087WT30 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 ASPS(0.002)CS(0.13)S(0.862)PT(0.007)R;ASPSCS(0.045)S(0.954)PT(0.001)R 119.55 0.0007107 365940000 619390 647210 527160 605470 587810 615060 581520 510760 655810 670800 TRUE FALSE 595183.554 628752.2045 622429.5386 636718.3793 606717.4425 627496.9346 588636.8157 500212.6275 581365.1982 625366.1185 0.951736169 1.005414566 0.995304223 1.018152983 0.970179587 1.00340731 0.94126752 0.799871648 0.929639744 1 19.25434153 1.99337525 8.939522837 0.883300637 0.990357481 0.306610805 0.050813851 0.110783156 94.75566574 0.019081336 0.013157121 98.48617023 -1.99337525 0.107056844 YVDEASKK ddPTM_BT-474_Pertuzumab_2h_R1 5 YVDEASKK 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;;; 122.13 0.0022503 6266320000 4756850 4155950 3569600 3489880 3880000 3665060 4273500 4886630 5311010 4619700 FALSE TRUE 4570947.043 4037426.375 4214706.125 3669993.125 4004803.724 3739170.024 4325800.371 4785719.383 4708126.41 4306803.604 1.061331666 0.937453097 0.978615816 0.852138491 0.929878418 0.868200728 1.004410874 1.111199818 1.093183447 1 22.03818611 1.993415489 5.982460041 1.075813427 0.935242275 0.482803701 0.060458524 0.121222849 17.37605101 0.024667525 0.016502765 98.49529588 -1.993415489 -0.140571152 STAQQELDGKPAS(ph)PTPVIVASHTANK ddPTM_BT-474_Pertuzumab_2h_R1 6 STAQQELDGKPASPTPVIVASHTANK 26 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.971)PT(0.029)PVIVASHTANK;STAQQELDGKPAS(0.997)PT(0.003)PVIVASHTANK;STAQQELDGKPAS(0.971)PT(0.029)PVIVASHTANK;STAQQELDGKPAS(0.947)PT(0.053)PVIVASHTANK;STAQQELDGKPAS(0.976)PT(0.024)PVIVASHTANK;STAQQELDGKPAS(0.981)PT(0.019)PVIVASHTANK 268.49 9.88E-54 14702540000 2716780 2213760 2559420 2485800 2589810 2449570 3151640 3837660 4164560 4035520 TRUE FALSE 2610605.234 2150625.732 3021964.128 2614092.436 2673113.591 2499101.984 3190210.713 3758410.98 3691816.608 3762190.636 0.693905622 0.571641881 0.80324588 0.694832529 0.710520505 0.66426777 0.847966257 0.998995358 0.981294401 1 21.84314152 1.993433326 2.683997578 0.992583362 0.690265126 0.863182946 0.05430686 0.094395404 1.284816513 0.027698821 0.015620939 98.49934134 -1.993433326 -0.302318236 LQEALRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQEALRR 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 109.36 0.011298 175090000 357660 408210 343840 391990 372520 389430 369030 328030 420220 421370 FALSE TRUE 343682.2518 396568.2505 405979.5367 412220.6509 384502.4441 397304.5414 373546.2995 321256.0659 372518.3873 392830.2346 0.874887474 1.009515601 1.033473244 1.049360804 0.978800536 1.011389925 0.950910258 0.817798727 0.948293574 1 18.58354645 1.993442803 10.31127678 0.897410918 0.996111361 0.178078854 0.062523026 0.208969999 284.8588099 0.024124082 0.016739715 98.50149069 -1.993442803 0.098700444 LGIYDADGDGDFDVDDAK ddPTM_BT-474_Pertuzumab_2h_R1 5 LGIYDADGDGDFDVDDAK 18 0 Q12797;Q12797-10;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;E5RHK2;G3XAN5;E5RG29;Q12797-4;Q12797-3;Q12797-9;Q12797-5;Q12797-8 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 0 ;;;; 346.46 6.82E-90 3877200000 5173100 7557650 3980240 6693060 4335910 3643750 5977790 8715040 7324740 4379530 FALSE TRUE 4970929.533 7342113.222 4699557.908 7038489.629 4475378.483 3717429.122 6050947.982 8535071.378 6493266.223 4082900.532 1.217499543 1.798259145 1.151034141 1.723894465 1.096127238 0.91048731 1.482021895 2.090443133 1.590356212 1 21.96116299 1.993449994 24.9814768 1.707628249 1.327238739 0.043547953 0.361997061 485.5248522 1851775.038 0.136058564 0.096867583 98.50312166 -1.993449994 -0.380389509 T(ph)TPTMSEEPPLDLTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPTMSEEPPLDLTGK 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 T(0.751)T(0.248)PTMSEEPPLDLTGK;T(0.499)T(0.499)PT(0.001)MSEEPPLDLTGK 229.9 3.09E-14 473202000 602650 569720 494771 497070 538610 560320 639400 712990 821700 772240 TRUE FALSE 579097.7717 553472.1434 584187.1258 522723.8423 555934.8798 571650.0543 647225.1685 698266.5073 728424.0608 719935.497 0.804374523 0.768780183 0.811443703 0.726070383 0.772200957 0.794029544 0.899004385 0.969901485 1.011790728 1 19.45750813 1.993536376 1.681784934 1.00280861 0.774100409 0.947562104 0.022879983 0.074413896 0.392572457 0.01456675 0.007143384 98.52271611 -1.993536376 -0.2287082 TEESPASDEAGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 0 ; 259.55 1.30E-23 396300000 469680 378630 403070 410250 439460 314190 441130 550770 493200 499390 FALSE TRUE 451324.3863 367831.8431 475913.7152 431423.0517 453595.63 320543.1371 446528.6809 539396.407 437214.0037 465565.8705 0.969410378 0.790074759 1.022226382 0.926663828 0.974288836 0.688502224 0.959109568 1.158582364 0.939102351 1 18.82862578 1.993551525 24.98009911 1.052347884 0.894765207 0.251816971 0.10464937 332.1665209 1286748.038 0.039236078 0.02794052 98.52615285 -1.993551525 -0.157582677 SS(ph)PEQPRPSTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPEQPRPSTSK 12 1 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BRN3;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 1 S(0.037)S(0.963)PEQPRPSTSK;S(0.026)S(0.974)PEQPRPSTSK;S(0.013)S(0.987)PEQPRPSTSK;S(0.17)S(0.829)PEQPRPS(0.001)TSK 188.12 5.82E-06 6334560000 4874470 4763080 3782590 4103850 4157810 4289310 4477940 4950780 5146420 4607670 TRUE FALSE 4683970.323 4627241.622 4466188.156 4315650.19 4291549.735 4376042.787 4532742.369 4848544.663 4562219.977 4295588.407 1.090414137 1.077207866 1.039715106 1.004670323 0.999059809 1.018729537 1.055208726 1.128726545 1.062071024 1 22.03442433 1.993571444 23.98569917 1.081418515 1.036832565 0.022419437 0.040669053 285.680271 1065906.826 0.016246715 0.011569004 98.53067192 -1.993571444 -0.04458595 EVLLFPAMKPEDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVLLFPAMKPEDKK 14 2 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ; 154.07 3.50E-06 1079600000 1949130 1735660 1536450 1295610 1566920 1843020 1909390 2079520 2599900 2291600 FALSE TRUE 1872955.845 1686160.676 1814120.693 1362476.587 1617321.405 1880287.127 1932757.686 2036577.185 2304770.252 2136387.891 0.876692783 0.789257739 0.849153237 0.637747758 0.757035467 0.880124408 0.904684816 0.953280626 1.07881638 1 21.02674218 1.993618313 1.261538842 1.028176575 0.78219152 0.685421469 0.066923803 0.270292107 0.797354447 0.050978082 0.023652701 98.54130583 -1.993618313 -0.245985055 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(ph)PHTLR ddPTM_BT-474_Pertuzumab_2h_R1 7 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHTLR 38 0 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 NNSQIASGQNQPQAAAGS(0.116)HQLS(0.116)MGQPHNAAGPS(0.759)PHT(0.008)LR;NNSQIASGQNQPQAAAGSHQLS(0.004)MGQPHNAAGPS(0.995)PHT(0.001)LR;NNSQIASGQNQPQAAAGSHQLS(0.007)MGQPHNAAGPS(0.96)PHT(0.032)LR;NNSQIASGQNQPQAAAGSHQLS(0.007)MGQPHNAAGPS(0.838)PHT(0.154)LR;NNSQIASGQNQPQAAAGS(0.319)HQLS(0.319)MGQPHNAAGPS(0.335)PHT(0.028)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(1)PHTLR;NNSQIASGQNQPQAAAGSHQLS(0.043)MGQPHNAAGPS(0.835)PHT(0.121)LR 265.29 1.72E-62 5057040000 629188 730297 674368 705262 554527 668913 562775 253602 617046 661094 TRUE FALSE 604598.6374 709469.6446 796241.2988 741660.6563 572363.8646 682438.8792 569662.4088 248365.0301 547001.5249 616317.5145 0.98098565 1.151143084 1.29193359 1.203374298 0.928683432 1.107284578 0.924300211 0.402982268 0.887532014 1 19.23331426 1.993676834 6.229817334 0.68783905 1.110007515 0.422106855 0.176606188 0.113431665 19.28958834 0.071503795 0.048076314 98.55458516 -1.993676834 0.422168465 EDEIS(ph)PPPPNPVVK ddPTM_BT-474_Pertuzumab_2h_R1 5 EDEISPPPPNPVVK 14 0 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK 210.07 6.03E-09 7431370000 4288010 3969470 4566230 4787360 4157790 4112980 5249090 6068020 6552700 6680460 TRUE FALSE 4120429.829 3856264.602 5391449.336 5034436.223 4291529.091 4196147.274 5313329.934 5942713.266 5808864.967 6227986.494 0.661599031 0.619183199 0.865680962 0.808356959 0.689071676 0.673756643 0.853137678 0.954194951 0.932703527 1 22.57033439 1.993827179 3.123095022 0.954096876 0.72462952 0.706192585 0.070330196 0.157463165 3.003031708 0.036650559 0.021575616 98.58870891 -1.993827179 -0.229467356 EQSTCNFQAIVISLKEEFYTK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQSTCNFQAIVISLKEEFYTK 21 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 225.05 2.69E-25 121950000 97526 93887 75955 72325 90283 105670 88487 80999 108810 95032 FALSE TRUE 93714.5761 91209.43468 89681.75811 76057.70192 93187.03469 107806.7198 89569.93038 79326.34234 96458.34497 88595.39799 1.057781535 1.029505333 1.012262038 0.858483664 1.051827034 1.216843338 1.010999808 0.895377685 1.08875119 1 16.43494414 1.993844535 24.98806858 0.975610872 1.035834572 0.031011902 0.092403244 790.4029104 3208641.303 0.037600679 0.026863923 98.59264893 -1.993844535 0.0602237 HSETFTR ddPTM_BT-474_Pertuzumab_2h_R1 3 HSETFTR 7 0 Q9UNS2-2;Q9UNS2 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ;; 134.81 0.0045528 579570000 164551 204158 201857 242780 199847 228053 188696 149869 185528 204178 FALSE TRUE 158120.165 198335.6137 238337.0502 255309.9049 206275.2603 232664.3879 191005.3181 146774.1528 164467.6392 190348.8422 0.830686245 1.041958603 1.252106645 1.341273747 1.083669635 1.222305243 1.003448804 0.771079829 0.86403278 1 17.53828627 1.993911119 5.365131747 0.859068149 1.137056392 0.389888959 0.139927592 0.163905579 15.32763325 0.060947971 0.040259572 98.60776584 -1.993911119 0.277988242 VEHILK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEHILK 6 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4;F8WA47;F6R503 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 0 94.669 0.044219 227310000 471070 506710 462270 469040 540360 547900 488090 443420 527360 527620 FALSE TRUE 452660.0636 492259.1269 545812.4721 493247.2106 557741.1701 558978.9134 494063.3914 434263.222 467496.3037 491883.8274 0.920258074 1.000762984 1.109636954 1.002771758 1.133888002 1.136404334 1.004431054 0.882857288 0.950420155 1 18.9079581 1.993954035 24.56844071 0.934468496 1.054127563 0.322458213 0.06843338 225.8115068 917612.2234 0.02719351 0.019416547 98.61751055 -1.993954035 0.119659067 VSVIQFLEAPIGDEDAEEAAAEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSVIQFLEAPIGDEDAEEAAAEKR 24 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3 A0A0G2JNZ2 SCRIB Protein scribble homolog 0 119.52 1.10E-06 0 24608 26253 20925 32250 22242 21827 26537 33773 30467 21420 FALSE TRUE 23646.29215 25504.29014 24706.61297 33914.42636 22957.43413 22268.35689 26861.76774 33075.57575 27008.51389 19969.20432 1.184137924 1.27718109 1.237235724 1.698336389 1.149641907 1.115134912 1.345159642 1.656329176 1.352508265 1 14.28548923 1.993970731 24.919776 1.432089562 1.283653896 0 0.21765509 667.9940016 2760913.687 0.082812049 0.059096401 98.62130171 -1.993970731 -0.148435666 SHILEQHPHTLDLS(ph)PSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHILEQHPHTLDLSPSEK 18 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 SHILEQHPHTLDLS(1)PSEK;SHILEQHPHT(0.004)LDLS(0.98)PS(0.015)EK 157.73 3.76E-09 371610000 317350 272420 224500 223910 238260 252570 201482 59557 258020 145989 TRUE FALSE 304947.6112 264650.8483 265072.144 235466.0219 245923.8493 257677.1384 203947.797 58327.12714 228730.6513 136101.035 2.240597297 1.944517529 1.947612992 1.730082522 1.806921228 1.893278317 1.49850291 0.428557558 1.680594503 1 17.05431851 1.993985605 5.418728225 0.966139481 1.902218668 0.621738181 0.310075374 0.098857969 9.598911944 0.124686863 0.082490626 98.62467964 -1.993985605 0.936079187 APS(ph)PSGLMSPSR ddPTM_BT-474_Pertuzumab_2h_R1 10 APSPSGLMSPSR 12 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 APS(0.919)PS(0.081)GLMSPSR;APS(0.878)PS(0.122)GLMSPSR;APS(0.95)PS(0.05)GLMSPSR;APS(0.992)PS(0.008)GLMSPSR;APS(0.98)PS(0.02)GLMSPSR;APS(0.947)PS(0.053)GLMSPSR;APS(0.944)PS(0.056)GLMSPSR;APS(0.956)PS(0.044)GLMSPSR;APS(0.92)PS(0.08)GLMSPSR;APS(0.966)PS(0.034)GLMSPSR 136.24 0.00014132 7501770000 2435260 3038750 2373120 3077280 2754980 2393310 2664380 2290520 2139080 2621580 TRUE FALSE 2340087.347 2952087.825 2801995.574 3236098.79 2843596.434 2441704.368 2696987.479 2243219.962 1896260.606 2444018.052 0.957475476 1.207882987 1.146470899 1.324089561 1.163492402 0.999053328 1.103505548 0.917840996 0.775878314 1 21.22082351 1.994026271 1.320525177 0.880365096 1.161396397 0.485579544 0.108880201 0.353080059 1.143442213 0.077640236 0.036200437 98.63391479 -1.994026271 0.281031301 FEHLLED ddPTM_BT-474_Pertuzumab_2h_R1 3 FEHLLED 7 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 ;; 103.29 0.019566 210330000 477420 522920 434660 544810 494990 540090 490390 426250 557980 548800 FALSE TRUE 458761.8986 508006.8336 513212.731 572927.7094 510911.8029 551010.9898 496391.5395 417447.7885 494640.4496 511629.2872 0.896668565 0.992919769 1.003094904 1.119810229 0.998597648 1.07697312 0.97021721 0.815918477 0.966794634 1 18.96473933 1.994069942 24.72267016 0.903605105 1.017741907 0.211443346 0.071243278 251.0794992 1046762.553 0.027129996 0.019375094 98.64383369 -1.994069942 0.114136802 RGHDDLGDHYLDCGDLSNALK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGHDDLGDHYLDCGDLSNALK 21 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6;J3KSA5;J3KRJ4;J3QLT0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 54.271 0.042907 201160000 156940 114350 86385 100360 135730 120930 100200 23555 161760 109330 FALSE TRUE 150806.6113 111088.85 101996.6911 105539.5916 140095.8787 123375.2875 101426.2776 23068.58102 143397.683 101924.9817 1.479584384 1.08990797 1.000703551 1.035463434 1.374499915 1.210451897 0.995107145 0.226329018 1.40689437 1 16.63714817 1.994073374 22.38607138 0.746512826 1.178248877 0.142689534 0.310003139 83.13742624 314027.6338 0.116747054 0.083153985 98.64461318 -1.994073374 0.431736051 KEELSEEGYLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEELSEEGYLAK 12 1 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 128.96 0.00038911 166020000 531320 452880 372270 393100 400790 353370 453740 554690 516590 534280 FALSE TRUE 510555.427 439964.3058 439547.4701 413387.9381 413681.7743 360515.3835 459293.0058 543235.4577 457948.8689 498092.7397 1.025020817 0.88329797 0.882461106 0.829941706 0.830531629 0.723791685 0.922103394 1.09063115 0.919404826 1 18.92605486 1.994125715 24.9681924 1.011653423 0.858219258 0.383257198 0.079724183 241.5658897 1026757.92 0.031145264 0.022262718 98.65650241 -1.994125715 -0.153434165 APS(ph)LTDLVK ddPTM_BT-474_Pertuzumab_2h_R1 4 APSLTDLVK 9 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 APS(1)LTDLVK;APS(0.999)LT(0.001)DLVK;APS(1)LTDLVK;APS(1)LTDLVK 160.36 6.86E-05 892050000 2159290 2045490 1706980 1912390 1970640 1942420 2088740 2473180 2389700 2104780 TRUE FALSE 2074902.56 1987154.628 2015469.258 2011088.677 2034027.425 1981697.063 2114302.625 2422107.969 2118431.274 1962221.376 1.057425317 1.012706646 1.027136531 1.024904071 1.036594265 1.009925326 1.077504634 1.234370392 1.079608703 1 20.90405638 1.994151463 15.03145428 1.137010807 1.028948915 0.215601721 0.057498316 1.322302485 3394.134521 0.021132102 0.014881191 98.6623517 -1.994151463 -0.108061891 QKSDAEEDGGT(ph)VS(ph)QEEEDRKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(0.057)DAEEDGGT(0.952)VS(0.992)QEEEDRKPK 63.488 0.0045079 0 1151400 1364300 606850 824780 776460 840610 1174500 1886300 1533900 844450 TRUE FALSE 1106402.015 1325391.5 716521.2943 867346.9946 801435.5411 857607.7101 1188873.882 1847347.246 1359778.103 787254.6493 1.405392799 1.683561349 0.910151874 1.101736262 1.018013094 1.089365062 1.510151618 2.346568861 1.727240485 1 19.58647085 1.994168829 8.95705235 1.863047011 1.205184282 0.22516804 0.375798822 0.131726279 119.2110307 0.146211752 0.101073022 98.66629693 -1.994168829 -0.657862729 EAEALKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAEALKR 7 1 Q9BUQ8;F8VVA2;H0YIL9 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 94.662 0.022505 217200000 237850 239510 195670 243220 222180 198030 237250 275510 270640 258390 FALSE TRUE 228554.559 232679.4093 231031.9217 255772.6133 229326.6215 202034.3023 240153.5365 269820.6222 239918.0818 240889.0152 0.948796104 0.965919551 0.959080353 1.061786122 0.952001158 0.838702845 0.996946815 1.120103472 0.995969375 1 17.87800908 1.994174783 24.9910594 1.05365813 0.956387304 0.27713802 0.059796066 288.3639114 1237126.063 0.023560266 0.016857739 98.66764953 -1.994174783 -0.097270826 FAAFFGNVPIFHIPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FAAFFGNVPIFHIPGR 16 0 Q92620;J3KTG2 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 ; 143.25 1.43E-06 251990000 127867 147520 105940 142108 141412 131772 130341 106140 152629 172884 FALSE TRUE 122869.8163 143312.874 125085.7146 149442.2109 145960.6454 134436.5201 131936.1521 103948.1719 135303.1958 161174.4127 0.76234071 0.88917882 0.77608916 0.927208038 0.905606808 0.834105848 0.818592418 0.644942148 0.839483101 1 17.2982632 1.994195155 22.10069399 0.774460022 0.851432125 0 0.097921858 121.6841156 463287.0861 0.036231649 0.025815043 98.67227811 -1.994195155 0.076972103 LTVENS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 LTVENSPK 8 0 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LTVENS(1)PK;LTVENS(1)PK;LTVENS(1)PK;LTVENS(1)PK;LTVENS(1)PK 141.08 0.00067049 4971670000 8690880 6904100 9075070 7793580 8492370 8467450 10310900 12333150 13693900 13203900 TRUE FALSE 8351230.801 6707201.828 10715137.02 8195807.598 8765534.794 8638667.641 10437087.88 12078466.14 12139425.88 12309588.09 0.678433002 0.54487622 0.870470802 0.665806811 0.712090017 0.701783648 0.847882789 0.981224234 0.98617645 1 23.55327915 1.99419682 1.998356208 0.995203941 0.69291277 0.759500999 0.074373775 0.157845504 1.174060435 0.042884243 0.02213914 98.67265639 -1.99419682 -0.302291171 EVLAGRPLFPHVLCHNCAVEFNFGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLAGRPLFPHVLCHNCAVEFNFGQK 26 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 128.17 5.78E-05 1408200000 881190 801460 509510 591640 622810 794580 578300 234570 708230 566640 FALSE TRUE 846752.1206 778603.1455 601589.791 622174.6113 642843.2493 810646.952 585377.4084 229726.0475 627834.6995 528260.9681 1.60290495 1.473898684 1.138811738 1.17777888 1.216904689 1.53455773 1.108121636 0.434872272 1.188493448 1 19.01089129 1.994241027 22.04685221 0.801621566 1.336860345 0.461515063 0.230454316 41.07953882 157263.5623 0.088218002 0.06285664 98.68270091 -1.994241027 0.535238779 LTPAEEENNSFQRLS(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 1 LTPAEEENNSFQRLSP 16 1 Q5HYI7-5;Q5HYI7 Q5HYI7-5 MTX3 Metaxin-3 1 LTPAEEENNS(0.001)FQRLS(0.999)P 138.05 3.29E-05 0 186120 204010 188100 263700 171170 218460 189460 171680 192470 189940 TRUE FALSE 178846.2246 198191.8345 222093.8543 277309.5886 176675.8385 222877.4109 191778.6682 168134.748 170621.6125 177075.1946 1.01000157 1.119252389 1.254234704 1.566055535 0.997744709 1.258659697 1.083035196 0.949510452 0.963554567 1 17.4340026 1.994260759 3.324765134 0.969543274 1.207004357 0.319452769 0.150441507 0.296298086 6.556798093 0.072863814 0.043635573 98.68718448 -1.994260759 0.237461083 FKIPGSPPESMGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FKIPGSPPESMGR 13 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 154.65 4.22E-05 5509800000 3753100 4166800 2969300 3495200 3711100 3457200 3744200 4084700 4360500 4068100 FALSE TRUE 3606424.703 4047966.944 3505918.562 3675587.691 3830470.902 3527106.953 3790022.64 4000349.518 3865514.321 3792563.964 0.950919942 1.067343091 0.924419099 0.969156414 1.009995069 0.930005924 0.999329919 1.05478762 1.019235103 1 21.85474208 1.994307722 24.91623 1.029836014 0.977323672 0.225101778 0.040740385 319.1785681 1397109.131 0.015024065 0.010749101 98.69785667 -1.994307722 -0.052512342 TAQEVETYRR ddPTM_BT-474_Pertuzumab_2h_R1 1 TAQEVETYRR 10 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 127.17 0.00058218 905250000 793310 807860 664970 679090 756460 763230 751510 759280 833940 840780 FALSE TRUE 762306.5681 784820.6238 785144.8712 714137.9163 780792.2229 778663.0335 760707.2042 743600.6027 739274.6274 783833.2217 0.972536692 1.001259709 1.001673378 0.911084012 0.99612035 0.993403969 0.970496252 0.948671965 0.943152965 1 19.5801872 1.994341995 23.60261388 0.958574919 0.979261335 0.046491068 0.028663181 294.5759423 1228834.569 0.010998375 0.007849244 98.70564599 -1.994341995 0.020686415 PAGAT(ph)LERPK ddPTM_BT-474_Pertuzumab_2h_R1 1 PAGATLERPK 10 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 PAGAT(1)LERPK 120.87 0.00085688 1600800000 1392600 2001200 944080 1807100 947890 786070 1666500 2903000 1960400 1208100 TRUE FALSE 1338175.652 1944127.735 1114696.257 1900364.648 978379.7427 801964.874 1686895.126 2843052.036 1737863.611 1126274.311 1.188143634 1.726158287 0.989720041 1.687301778 0.868686903 0.712051111 1.497765783 2.52429804 1.543019843 1 20.10312682 1.994348878 24.61869509 1.896612327 1.208244516 0.143780104 0.472263217 242.7605326 1057569.944 0.17681236 0.126501531 98.70721041 -1.994348878 -0.688367811 ASQEPS(ph)PKPGTEVIPAAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASQEPSPKPGTEVIPAAPR 19 1 I3L4I0;I3L1Y9;Q96CP2 I3L4I0 FLYWCH2 FLYWCH family member 2 1 ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR 245.48 8.42E-25 3293200000 2105491 2047028 1658629 1702510 1892463 1840538 1994132 2408681 2162458 2087966 TRUE FALSE 2023206.084 1988648.766 1958380.156 1790376.745 1953335.791 1877754.939 2018536.784 2358940.896 1916984.834 1946546.203 1.039382513 1.021629367 1.006079462 0.919770999 1.003488018 0.964659835 1.036983751 1.211859699 0.984813425 1 20.89248516 1.994364578 24.0873906 1.097928687 0.992401733 0.149882456 0.066919083 168.8528542 721726.7585 0.025128878 0.017959432 98.71077871 -1.994364578 -0.105526954 VKLNFDMTAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKLNFDMTASPK 12 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 VKLNFDMT(0.001)AS(0.999)PK 104.45 0.0012937 905050000 1040900 993690 694200 618050 886720 842400 900360 1039000 1046300 1029000 TRUE FALSE 1000220.477 965350.9341 819657.3824 649947.6346 915242.1541 859433.9052 911378.875 1017544.287 927528.4104 959304.9135 1.04265126 1.006302502 0.854428421 0.677519343 0.954068035 0.895892321 0.95004087 1.060709971 0.966875492 1 19.87162992 1.99440488 4.49052227 1.01463528 0.900216485 0.190798909 0.095319879 0.326242068 16.53221139 0.044415383 0.028506734 98.71993938 -1.99440488 -0.114418795 HPSS(ph)PSALR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPSSPSALR 9 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 HPS(0.01)S(0.99)PSALR 85.729 0.0094158 306900000 24171 41806 41729 51165 31807 63828 38838 24643 44599 37777 TRUE FALSE 23226.3706 40613.73381 49270.35856 53805.63178 32830.10104 65118.64589 39313.31106 24134.11344 39536.30849 35218.33014 0.659496646 1.153198736 1.398997578 1.527773508 0.932187895 1.848998679 1.116274136 0.685271373 1.122605993 1 15.10403889 1.994418479 24.98313146 0.900935099 1.272474546 0.160978676 0.32012373 368.1058101 1647659.992 0.121236525 0.08681442 98.7230306 -1.994418479 0.371539447 QSQEGAGLPSHHGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSQEGAGLPSHHGR 14 0 Q92754;A2A2R7 Q92754 TFAP2C Transcription factor AP-2 gamma 0 ; 84.759 0.0046295 135284000 28089.4 37140 28759 42219 31139 35413 29479 13371.6 37385 36705 FALSE TRUE 26991.63519 36080.80356 33956.39104 44397.92765 32140.61421 36129.07512 29839.77282 13095.47179 33141.21153 34218.93766 0.788792319 1.054410395 0.992327447 1.297466569 0.93926394 1.055821063 0.872025108 0.38269662 0.96850498 1 15.06250735 1.994429932 11.59549116 0.693187638 1.024887085 0.185616204 0.201643041 0.282394038 557.9993873 0.076367595 0.053400844 98.72563415 -1.994429932 0.331699447 QIDNPDYK ddPTM_BT-474_Pertuzumab_2h_R1 4 QIDNPDYK 8 0 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;; 168.27 0.00071615 2100160000 4176360 4479390 3645890 4173910 3996280 4238140 4407010 4558580 5297800 4838840 FALSE TRUE 4013143.234 4351642.183 4304783.425 4389325.995 4124823.976 4323838.095 4460944.307 4464443.73 4696415.954 4511101.057 0.889615015 0.964651895 0.954264463 0.973005468 0.914371885 0.958488413 0.988881484 0.98965722 1.041079749 1 22.10504817 1.994502092 1.413874923 1.015605642 0.942644567 0.600258302 0.025761211 0.297250046 1.106169103 0.017453309 0.008225946 98.7420393 -1.994502092 -0.072961075 FLPLFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLPLFDR 7 0 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 180.49 0.0015951 1352200000 904020 1406820 958850 1463950 722530 541050 1284960 1026990 872430 776290 FALSE TRUE 868689.899 1366698.871 1132135.525 1539504.635 745770.8336 551990.4017 1300685.725 1005782.298 773395.4039 723711.1869 1.200326753 1.888458954 1.564347139 2.1272362 1.030481285 0.762721942 1.797244189 1.389756461 1.068651995 1 19.46505455 1.994523075 0.295460913 0.980100575 1.716274588 0.175614967 0.385405284 3.258966958 0.889315469 0.674402599 0.877063332 98.74681003 -1.994523075 0.736174013 KIPDPDSDDVSEVDAR ddPTM_BT-474_Pertuzumab_2h_R1 6 KIPDPDSDDVSEVDAR 16 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0;A0A2R8Y583 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ;;;;; 150.45 1.18E-06 5286340000 1780240 1807780 1485330 1743360 1702580 1649440 1799400 1952610 2093570 2048540 FALSE TRUE 1710666.253 1756223.884 1753762.172 1833335.019 1757345.032 1682792.807 1821421.595 1912287.921 1855916.711 1909790.561 0.895735002 0.919589781 0.918300785 0.95996653 0.920176834 0.881139975 0.953728452 1.001307662 0.971790702 1 20.864983 1.994584305 5.727090276 0.988386803 0.918068673 0.729975247 0.020532944 0.08799689 10.6087395 0.008695208 0.005802408 98.76073319 -1.994584305 -0.07031813 EHSAFGDRPEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHSAFGDRPEKR 12 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 182.71 9.92E-06 1213990000 866299 943957 588307 720674 818435 890438 767308 637152 926828 802328 FALSE TRUE 832443.0773 917036.2706 694627.1617 757868.0715 844760.7051 908443.2664 776698.5448 623994.5885 821618.371 747985.6099 1.112913225 1.226007905 0.928663804 1.013212101 1.129380958 1.214519711 1.038387015 0.834233413 1.098441414 1 19.51265099 1.994647738 24.74518763 0.953432368 1.10101103 0.227619169 0.102113531 256.5869243 1186282.391 0.040010053 0.028669325 98.77515915 -1.994647738 0.147578663 EYINECDSDYHEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EYINECDSDYHEER 14 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 249.13 4.71E-18 255270000 95370 107120 99330 135260 109200 118910 108690 97603 116090 125950 FALSE TRUE 91642.83496 104065.0425 117281.1406 142240.7848 112712.5172 121314.4417 110020.1807 95587.46394 102911.9499 117419.2943 0.780475096 0.886268676 0.998823415 1.211391924 0.959914789 1.033172975 0.936985539 0.814069481 0.876448377 1 16.84130997 1.994716893 19.84449071 0.876017003 0.984862532 0.086885548 0.111879935 29.93367502 112436.9766 0.045450621 0.032355792 98.79088887 -1.994716893 0.108845528 QRELEIEER ddPTM_BT-474_Pertuzumab_2h_R1 2 QRELEIEER 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 141.88 9.64E-05 445110000 268800 297790 203929 273930 262580 294780 266060 265110 285570 292530 FALSE TRUE 258294.9988 289297.3208 240783.5067 288067.5601 271026.1242 300740.6536 269316.1219 259635.3859 253153.2908 272716.6825 0.94711844 1.060798034 0.882907142 1.056288737 0.993801045 1.102758551 0.987530793 0.952033383 0.928264778 1 18.05704343 1.994728874 24.93791255 0.958522834 1.008962499 0.108898914 0.06028841 449.6075936 2127114.949 0.022273539 0.015982169 98.79361428 -1.994728874 0.050439665 S(ph)VDEVFDEVVQIFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVDEVFDEVVQIFDK 15 0 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 1 S(1)VDEVFDEVVQIFDK;S(1)VDEVFDEVVQIFDK 314.17 3.09E-56 513580000 151618 128935 105082 138965 128966 100198 143587 236584 114451 110458 TRUE FALSE 145692.6009 125257.9 124072.6549 146137.0003 133114.3085 102224.0722 145344.2607 231698.4577 101459.0023 102976.5813 1.414812952 1.216372679 1.204862828 1.41912849 1.292665836 0.992692425 1.411430238 2.250011166 0.985262873 1 16.65195675 1.994766544 24.99717203 1.620666273 1.256614901 0 0.362177974 390.768382 1866475.488 0.134637956 0.096590666 98.80218378 -1.994766544 -0.364051373 LNLTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 LNLTSPK 7 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;H0Y785;H0Y472;H0Y4P6;H0Y7Y3;A0A0A0MQZ8 Q8IWZ3-6;A0A0A0MQZ8 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 LNLT(0.066)S(0.934)PK;LNLT(0.029)S(0.971)PK;LNLT(0.052)S(0.948)PK;LNLT(0.162)S(0.838)PK 120.76 0.0047241 2205190000 8919900 7686400 6915000 6850200 7042400 7208300 8116300 9100600 9894600 9181200 TRUE FALSE 8571300.447 7467191.398 8164694.323 7203739.643 7268925.192 7354056.765 8215629.707 8912669.43 8771406.49 8559349.146 1.001396286 0.872401776 0.953891959 0.841622362 0.849238075 0.859184108 0.959842807 1.041278873 1.024774938 1 23.02906967 1.994768888 4.061507081 1.023025988 0.893502458 0.585120746 0.047514161 0.145532061 5.453696042 0.021233252 0.013356105 98.80271718 -1.994768888 -0.12952353 QVQEEIS(ph)RMSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QVQEEISRMSSK 12 1 Q5JRG1;H7BYF2;Q9BVL2-2;Q9BVL2-3;Q9BVL2 Q5JRG1 NUPL1 Nucleoporin p58/p45 1 QVQEEIS(0.999)RMS(0.001)SK 64.04 0.040222 152970000 221480 143050 185190 159580 166550 211900 153270 30801 239540 182220 TRUE FALSE 212824.3167 138970.3541 218657.9525 167815.9429 171907.232 216184.7632 155145.7641 30164.94859 212348.4234 169878.0771 1.25280625 0.818059378 1.287146383 0.987861093 1.011944772 1.272587769 0.913277138 0.177568225 1.250004869 1 17.37414016 1.994856765 24.89740169 0.67471296 1.090920597 0.127393398 0.295457526 254.6635267 1232778.55 0.107939579 0.077448268 98.82271137 -1.994856765 0.416207637 SEEITTGSAWFSFLESHNKLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEEITTGSAWFSFLESHNKLDK 22 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 145.02 5.76E-08 200560000 156380 156450 125950 128860 133790 149530 148150 167130 180790 172060 FALSE TRUE 150268.4967 151988.1992 148711.9667 135510.48 138093.4769 152553.5991 149963.104 163678.7071 160267.4771 160406.2229 0.93679967 0.947520591 0.927095994 0.844795654 0.860898501 0.951045391 0.934895799 1.020401229 0.999135035 1 17.29137059 1.994895233 1.909268116 1.009021867 0.906454415 0.614569447 0.033555056 0.24115593 1.638176129 0.021948753 0.011181596 98.83146494 -1.994895233 -0.102567452 EENPES(ph)DGEPVVEDGTSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EENPESDGEPVVEDGTSVK 19 0 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0;E7EVX2;A0A087WTW2 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 EENPES(1)DGEPVVEDGTSVK 256.06 6.27E-31 297020000 236830 229810 214530 242530 252300 227680 271780 331370 350210 305920 TRUE FALSE 227574.4218 223256.0438 253300.3432 255047.0024 260415.4586 232283.8456 275106.1249 324527.0937 310455.629 285199.7659 0.797947435 0.782805845 0.8881506 0.894274936 0.91309843 0.814460155 0.964608523 1.137893969 1.088554992 1 18.12161327 1.994938057 4.05082165 1.085583852 0.853160145 0.796640326 0.051454438 0.090908133 3.381697447 0.023767921 0.014945718 98.84121084 -1.994938057 -0.232423707 ELGPLPDDDDMAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELGPLPDDDDMASPK 15 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 1 ELGPLPDDDDMAS(1)PK;ELGPLPDDDDMAS(1)PK;ELGPLPDDDDMAS(1)PK 164.01 3.97E-09 66034000 183890 145040 133038 145118 147158 137052 157661 181581 178038 181498 TRUE FALSE 176703.3755 140903.6012 157080.926 152607.5574 151891.4707 139823.2853 159590.5025 177831.2889 157827.8726 169204.9788 1.044315461 0.832739097 0.92834695 0.901909379 0.897677313 0.826354439 0.943178526 1.05098142 0.932761398 1 17.36841249 1.9949776 24.95398088 0.999454158 0.901009731 0.290936364 0.062155726 222.4284661 1105146.214 0.022319294 0.016029311 98.85021088 -1.9949776 -0.098444427 NMSVIAHVDHGK ddPTM_BT-474_Pertuzumab_2h_R1 4 NMSVIAHVDHGK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 184.21 8.45E-06 9260990000 9567350 9749090 8155580 8400160 7494870 8124710 7086690 527784 11642770 10008500 FALSE TRUE 9193447.385 9471055.499 9629474.726 8833693.264 7735949.3 8288997.203 7173419.032 516885.076 10321131.56 9330615.38 0.985299148 1.015051539 1.032029972 0.946742836 0.82909315 0.888365543 0.768804494 0.055396676 1.106157648 1 23.1535408 1.994995522 14.85427136 0.564701851 0.940426617 0.050677313 0.278059284 1.475245005 4370.209224 0.10551703 0.074542576 98.85429022 -1.994995522 0.375724766 KT(ph)S(ph)LS(ph)LT(ph)PDVP ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSLSLTPDVP 11 1 C9JHQ1 C9JHQ1 SMARCAL1 4 KT(1)S(1)LS(1)LT(1)PDVP 43.544 0.067053 558470000 27081 10963 22591 13949 20260 26319 17685 8876.3 24265 17267 TRUE FALSE 26022.64458 10650.34597 26673.69623 14668.90956 20911.6813 26851.18821 17901.43432 8693.001303 21510.53893 16097.49071 1.61656528 0.661615289 1.657009575 0.91125442 1.29906466 1.66803564 1.112063653 0.540022135 1.336266584 1 13.9745482 1.995059633 24.99617678 0.887251389 1.281236581 0.150523209 0.354865387 321.5846537 1627085.453 0.128318731 0.092211009 98.86888413 -1.995059633 0.393985192 EKDS(ph)PFKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDSPFKPK 9 2 Q15291 Q15291 RBBP5 Retinoblastoma-binding protein 5 1 EKDS(1)PFKPK 79.82 0.013493 408370000 980190 684520 581550 463450 637030 509160 732150 951990 946910 827310 TRUE FALSE 941883.0911 664998.1598 686649.0215 487368.71 657520.6485 519455.5641 741110.2707 932331.0738 839420.7466 771275.5568 1.221201791 0.862205672 0.890277172 0.631899592 0.852510679 0.673501914 0.960889094 1.20881709 1.088353882 1 19.55688686 1.995115461 23.68264697 1.112907496 0.844419754 0.32857158 0.155363048 108.7816198 527428.2813 0.05982682 0.042918454 98.88159454 -1.995115461 -0.268487743 HKSDSPES(ph)DAER ddPTM_BT-474_Pertuzumab_2h_R1 3 HKSDSPESDAER 12 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 HKSDSPES(1)DAER;HKSDS(0.009)PES(0.991)DAER;HKSDSPES(1)DAER 143.14 3.74E-05 434336000 376029 438442 390251 461002 409078 495756 387791 206292 488254 473290 TRUE FALSE 361333.371 425938.0634 460778.0368 484794.3685 422236.3654 505780.526 392536.9023 202031.9981 432829.4528 441233.6467 0.818916177 0.965334504 1.044294877 1.098724841 0.956945075 1.146287301 0.889635016 0.457879855 0.980952962 1 18.75118328 1.995130809 24.98029427 0.732970876 1.008030433 0.170426777 0.166531421 216.091409 1108610.752 0.061616774 0.044275802 98.88508902 -1.995130809 0.275059557 VKGDMDVSVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKGDMDVSVPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 134.98 0.00011823 811180000 2195100 2213200 1972500 1857500 1715500 1891100 2184200 2607000 2567400 2434600 FALSE TRUE 2109313.065 2150081.703 2328974.628 1953365.798 1770680.615 1929339.338 2210930.893 2553164.539 2275959.515 2269702.373 0.929334652 0.947296759 1.026114549 0.860626407 0.7801378 0.850040675 0.974106085 1.124889575 1.002756812 1 21.1140717 1.995136723 6.765572789 1.05518329 0.900456407 0.462721031 0.069347895 0.123948909 30.59972057 0.030709529 0.020887712 98.88643569 -1.995136723 -0.154726883 ENPPVEDS(ph)S(ph)DEDDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENPPVEDSSDEDDKR 15 1 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 2 ENPPVEDS(1)S(1)DEDDKR 76.817 0.097046 384660000 335420 460210 253140 481300 302630 236300 441770 728530 554780 362510 TRUE FALSE 322311.4156 447085.2614 298888.0291 506139.9507 312364.3688 241078.1479 447176.5134 713485.6009 491803.7002 337956.8748 0.953705752 1.322906248 0.884396949 1.497646559 0.924272865 0.713339973 1.323176259 2.111173508 1.455226205 1 18.36647964 1.995201925 24.92309697 1.663491478 1.064772628 0.261024271 0.335580646 188.8496096 980961.2919 0.123091576 0.088489939 98.90128294 -1.995201925 -0.598718849 QDHPSSMGVYGQESGGFSGPGENR ddPTM_BT-474_Pertuzumab_2h_R1 3 QDHPSSMGVYGQESGGFSGPGENR 24 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;Q01844-4 B0QYK0 EWSR1 RNA-binding protein EWS 0 ;; 367.19 1.25E-118 2154780000 489390 743880 560470 865500 683330 829450 655740 545000 599740 771710 FALSE TRUE 470264.0978 722665.2707 661759.3966 910168.5587 705309.93 846222.0473 663765.1423 533745.5595 531660.0295 719441.3943 0.65365171 1.004481083 0.91982391 1.265104518 0.980357727 1.17622096 0.922611831 0.741888865 0.738990047 1 19.45651764 1.995254394 24.59360622 0.806773024 1.011146658 0.174700213 0.165837312 234.403219 1214772.452 0.062751749 0.045095934 98.91323233 -1.995254394 0.204373634 EEEDKDDEEKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEEDKDDEEKPK 12 2 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;; 123.64 0.00018964 2556080000 2163260 1427770 2082400 1453210 1885950 1524830 2723330 3491840 4263580 3397500 FALSE TRUE 2078717.408 1387051.398 2458736.003 1528210.342 1946613.295 1555663.107 2756658.927 3419732.284 3779596.273 3167384.299 0.656288348 0.43791699 0.77626703 0.482483399 0.614580711 0.491150729 0.870326638 1.079670782 1.193286294 1 21.59486049 1.995270437 2.7981998 1.096926163 0.576701862 0.833202988 0.103714569 0.095418968 1.422944795 0.048676737 0.027835771 98.91688623 -1.995270437 -0.520224301 S(ph)RSHTSEGAHLDITPNSGAAGNSAGPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSHTSEGAHLDITPNSGAAGNSAGPK 27 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.331)RS(0.22)HT(0.22)S(0.22)EGAHLDIT(0.009)PNSGAAGNSAGPK;S(0.24)RS(0.24)HT(0.24)S(0.24)EGAHLDIT(0.042)PNSGAAGNSAGPK;S(0.313)RS(0.228)HT(0.228)S(0.228)EGAHLDIT(0.001)PNSGAAGNSAGPK 133.62 1.85E-05 1511990000 364431 583260 371750 519740 411537 506930 350199 128625 337491 261108 TRUE FALSE 350188.6336 566625.9959 438933.4945 546563.8437 424774.4614 517180.4719 354484.8401 125968.8488 299180.4366 243422.9226 1.438601714 2.327742966 1.803172396 2.245326109 1.745006004 2.124616969 1.456250859 0.517489674 1.229056136 1 17.8931055 1.995271246 4.670008709 0.880264875 1.956183193 0.71347564 0.293109241 0.087698854 5.047009088 0.114970891 0.074452225 98.91707046 -1.995271246 1.075918318 SALSSS(ph)LRDLSEAGVHH ddPTM_BT-474_Pertuzumab_2h_R1 3 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALS(0.031)S(0.343)S(0.626)LRDLSEAGVHH;SALS(0.001)S(0.376)S(0.623)LRDLSEAGVHH;SALS(0.003)S(0.333)S(0.664)LRDLSEAGVHH 203.71 5.70E-12 901310000 878550 1054510 580390 791540 810930 871340 611220 138637 581070 482791 TRUE FALSE 844215.2947 1024436.407 685279.3837 832391.4743 837014.2999 888959.0918 618700.2932 135774.0975 515109.3696 450091.1355 1.875654124 2.276064393 1.522534726 1.849384288 1.859655154 1.975064652 1.374611149 0.301659124 1.144455709 1 18.77985763 1.99530466 4.70529208 0.751118348 1.88130674 0.763511207 0.268390442 0.080269836 4.735668934 0.111064865 0.072025993 98.92468143 -1.99530466 1.130188392 DINTFVGT(ph)PVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DINTFVGTPVEK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 DINTFVGT(1)PVEK;DINTFVGT(1)PVEK;DINTFVGT(1)PVEK;DINTFVGT(1)PVEK 203.99 1.33E-06 562940000 1448810 1250620 1535420 1253990 1276020 1393430 1510690 1862190 1641170 1836220 TRUE FALSE 1392188.903 1214953.542 1812904.549 1318708.574 1317064.342 1421606.109 1529178.276 1823735.126 1454871.262 1711851.184 0.813265146 0.709730819 1.05903163 0.770340662 0.769380163 0.830449587 0.893289259 1.065358451 0.849881856 1 20.70712586 1.995342418 5.246765874 0.979876096 0.827623738 0.301888512 0.099530554 0.203786434 17.58598974 0.040896909 0.027007211 98.93328237 -1.995342418 -0.152252358 TNT(ph)PVKEDWNVR ddPTM_BT-474_Pertuzumab_2h_R1 6 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 T(0.015)NT(0.985)PVKEDWNVR;T(0.037)NT(0.963)PVKEDWNVR;T(0.001)NT(0.999)PVKEDWNVR;T(0.004)NT(0.996)PVKEDWNVR;T(0.001)NT(0.999)PVKEDWNVR;T(0.009)NT(0.991)PVKEDWNVR 131.72 0.00031322 7088870000 7580880 5465020 4925610 4396810 4678450 4278580 5503000 6475800 6211550 6056570 TRUE FALSE 7284610.828 5309162.98 5815777.297 4623729.891 4828936.593 4365095.819 5570347.36 6342072.467 5506440.885 5646353.119 1.290144395 0.940281783 1.030005948 0.818887837 0.855231065 0.773082329 0.986538965 1.123215699 0.975220779 1 22.42888793 1.995494635 24.92561161 1.048596441 0.938622008 0.056663578 0.139258432 424.3084973 2347460.197 0.054553252 0.039273178 98.96796376 -1.995494635 -0.109974433 LLS(ph)NELK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLSNELK 7 0 P06753-3;P06753-4 P06753-3 TPM3 Tropomyosin alpha-3 chain 1 LLS(1)NELK;LLS(1)NELK 85.533 0.021756 127423000 314820 286290 237540 249963 304140 272590 303350 377270 348110 295250 TRUE FALSE 302516.4863 278125.2895 280468.762 262863.6204 313922.9393 278101.9566 307062.488 369479.2427 308594.0122 275252.4545 1.099051003 1.010437091 1.018950994 0.954991013 1.140490972 1.010352322 1.115566757 1.342328603 1.121130828 1 18.0703959 1.995630271 12.02732322 1.201635559 1.039707918 0.191363942 0.094835485 0.256613811 670.612487 0.035246131 0.024784434 98.99887764 -1.995630271 -0.161927641 QS(ph)GDGQESTEPVENK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSGDGQESTEPVENK 15 0 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 QS(0.991)GDGQES(0.002)T(0.006)EPVENK 258.9 8.09E-25 307070000 301070 268640 266870 293210 272170 276310 339430 408660 427420 440620 TRUE FALSE 289303.8515 260978.6502 315099.3455 308342.6032 280924.5952 281897.1775 343584.0459 400221.0282 378901.0735 410776.4149 0.704285448 0.635330172 0.767082369 0.750633659 0.683886866 0.686254535 0.836425932 0.974303815 0.922402211 1 18.64799382 1.995651783 2.810858997 0.961022172 0.705306805 0.897735198 0.039523876 0.081358269 1.225621746 0.020421866 0.011698028 99.00378147 -1.995651783 -0.255715367 ESNVLHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESNVLHEK 8 0 Q9NX62;H0YBS3 Q9NX62 IMPAD1 Inositol monophosphatase 3 0 ; 76.465 0.035731 393820000 376030 563450 424750 542000 403660 312760 508840 625900 648830 628620 FALSE TRUE 361334.3319 547380.9577 501511.7735 569972.685 416644.0905 319084.2215 515067.3361 612974.9463 575177.5385 586043.0075 0.616566237 0.934028648 0.855759334 0.972578254 0.710944564 0.544472364 0.878889995 1.045955567 0.981459605 1 19.16064702 1.995698966 24.98510146 1.001289149 0.783321728 0.417243231 0.125005057 193.7961938 1125782.256 0.050329735 0.036277332 99.01453803 -1.995698966 -0.217967421 SFEEEFGTASDKER ddPTM_BT-474_Pertuzumab_2h_R1 2 SFEEEFGTASDKER 14 1 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ; 136.83 2.26E-05 476980000 167815 176583 142963 151520 167588 167377 177127 192532 213330 208027 FALSE TRUE 161256.6043 171547.0257 168799.5943 159339.9654 172978.6202 170761.4776 179294.7332 188556.1469 189113.6728 193937.146 0.831489004 0.884549604 0.870382997 0.82160622 0.891931349 0.880499075 0.924499184 0.972253902 0.975128678 1 17.56522963 1.995699546 1.065739966 0.995436247 0.857020423 0.884271205 0.019716847 0.154755894 0.323790694 0.015051613 0.007016513 99.01467044 -1.995699546 -0.138415824 FSLAHSMLAISGHLDS(ph)DDDSGSGSLVGIDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 FSLAHSMLAISGHLDSDDDSGSGSLVGIDNK 31 0 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 FSLAHSMLAIS(0.075)GHLDS(0.909)DDDS(0.005)GS(0.005)GS(0.005)LVGIDNK 107.19 0.00022408 101450000 111370 124720 93673 78561 94795 128930 95975 64710 116710 103950 TRUE FALSE 107017.5373 121163.1077 110601.7948 82615.54262 97844.16727 131537.0529 97149.57076 63373.71589 103461.5701 96909.37391 1.104305321 1.25027232 1.141290985 0.85250311 1.009646057 1.357320222 1.002478572 0.653948254 1.067611583 1 16.5643486 1.995725132 24.98745096 0.858605649 1.114980224 0.243199018 0.162292591 204.0733558 1192851.843 0.063004433 0.045406777 99.02050388 -1.995725132 0.256374575 IEEVPELPLVVEDK ddPTM_BT-474_Pertuzumab_2h_R1 4 IEEVPELPLVVEDK 14 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;; 213.73 1.45E-09 324911000 477480 460638 512926 498839 485158 475518 599170 734488 748178 793815 FALSE TRUE 458819.5537 447501.0553 605623.1382 524584.1406 500763.5477 485133.2998 606502.8217 719320.5661 663247.9701 740049.203 0.619985201 0.60469095 0.818355233 0.708850355 0.676662505 0.655541953 0.819543916 0.971990191 0.89622145 1 19.49726167 1.995792744 3.075506552 0.949542824 0.684791117 0.8058465 0.060623173 0.114389164 2.10886938 0.030530575 0.01793833 99.0359209 -1.995792744 -0.264751707 EVDDFFEQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVDDFFEQEK 10 0 Q9Y5X3;Q5QPE5;A0A087WUY5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 ; 167.67 1.20E-05 331480000 361810 306720 318170 297510 342760 329750 373940 428150 458370 464090 FALSE TRUE 347670.0652 297972.6459 375670.3967 312864.5268 353785.1867 336417.7709 378516.3896 419308.5529 406337.7592 432656.7709 0.803570147 0.688704456 0.86828734 0.723124074 0.817704033 0.777562709 0.874865286 0.969148251 0.939168844 1 18.72286345 1.995827834 2.007694322 0.971256065 0.776611304 0.754815547 0.048519819 0.148888224 1.118222352 0.026049268 0.013486909 99.04392308 -1.995827834 -0.194644761 VQT(ph)TPSKPGGDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.497)T(0.497)PS(0.006)KPGGDR;VQT(0.498)T(0.498)PS(0.005)KPGGDR;VQT(0.477)T(0.477)PS(0.046)KPGGDR;VQT(0.794)T(0.206)PSKPGGDR 143.31 0.0003955 4196230000 4637340 3989260 3907080 3769000 3706250 3849240 4201450 5054640 4224570 4557760 TRUE FALSE 4456107.626 3875490.211 4613176.269 3963518.542 3825464.897 3927074.27 4252868.602 4950259.918 3745014.524 4249058.856 1.048728148 0.912082026 1.085693662 0.932799162 0.900308757 0.92422214 1.000896609 1.165025029 0.881375065 1 22.0187119 1.995833517 24.91984496 1.046092312 0.965312662 0.027082711 0.086403449 312.510325 1869135.039 0.032350628 0.023329058 99.04521918 -1.995833517 -0.08077965 IS(ph)PTAGNQNGLLNK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISPTAGNQNGLLNK 14 0 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 IS(1)PTAGNQNGLLNK;IS(0.998)PT(0.002)AGNQNGLLNK;IS(0.844)PT(0.156)AGNQNGLLNK 334.74 1.55E-68 468120000 704480 700250 559810 651350 626770 610910 676660 768750 783810 701330 TRUE FALSE 676948.1428 680279.5556 660980.1199 684966.2516 646930.6263 623263.0188 684941.1675 752875.0439 694835.1748 653828.2944 1.035360734 1.040455975 1.010938385 1.047624059 0.989450337 0.953251831 1.047585694 1.151487402 1.062718118 1 19.31855229 1.995844607 24.98587103 1.091059472 1.013356257 0.234007576 0.043965156 170.6618796 1026171.614 0.01654147 0.011927621 99.04774838 -1.995844607 -0.077703214 PGPTPSGTNVGSSGRS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 6 PGPTPSGTNVGSSGRSPSK 19 1 P60468 P60468 SEC61B Protein transport protein Sec61 subunit beta 1 PGPTPSGTNVGSSGRS(0.981)PS(0.019)K;PGPTPSGTNVGSS(0.005)GRS(0.995)PSK;PGPTPSGTNVGS(0.001)S(0.003)GRS(0.99)PS(0.006)K;PGPTPSGTNVGSS(0.005)GRS(0.994)PS(0.001)K;PGPTPSGT(0.001)NVGS(0.053)S(0.072)GRS(0.865)PS(0.009)K;PGPTPSGTNVGSS(0.001)GRS(0.999)PSK 259.67 2.71E-31 11934350000 2432950 2894220 1230629 2069890 1631970 1544170 2266230 3294150 2920550 1584250 TRUE FALSE 2337867.624 2811679.679 1453031.035 2176717.271 1684463.797 1575394.175 2293964.801 3226124.651 2589021.408 1476947.336 1.582905204 1.90371018 0.983806937 1.473794777 1.140503629 1.066655619 1.553179822 2.184319354 1.752954451 1 20.49418695 1.995886384 24.50106257 1.800199154 1.357324138 0.066957443 0.377372949 197.653158 1177243.645 0.141857029 0.102255882 99.05727677 -1.995886384 -0.442875016 HLGGSGSVVPGS(ph)PCLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLGGSGSVVPGSPCLDR 17 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 HLGGSGSVVPGS(1)PCLDR;HLGGSGSVVPGS(1)PCLDR;HLGGSGSVVPGS(1)PCLDR 90.316 0.0024686 882300000 770190 878600 777980 821930 697560 869190 780110 579570 918600 1112250 TRUE FALSE 740090.1233 853543.1882 918578.2921 864349.9058 719997.6509 886765.6173 789657.2195 567601.677 814324.3791 1036916.317 0.713741419 0.823155325 0.885875048 0.833577302 0.694364279 0.855194969 0.761543826 0.54739391 0.785332785 1 19.98386804 1.995890117 24.93869374 0.709081721 0.802976499 0 0.121364189 369.4903714 2242065.641 0.044623327 0.032165397 99.05812805 -1.995890117 0.093894778 LS(ph)STSSEETQLFHIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.417)S(0.357)T(0.069)S(0.069)S(0.084)EET(0.005)QLFHIPR 76.027 0.0039173 0 44126 50786 41834 44840 45445 41061 52910 74858 51010 64885 TRUE FALSE 42401.50714 49337.633 49394.33439 47154.19777 46906.7797 41891.28155 53557.52841 73312.15614 45219.55865 60490.28116 0.700963962 0.815629091 0.816566454 0.779533454 0.775443241 0.692529126 0.885390634 1.211965869 0.74755081 1 15.88441575 1.996005903 17.56988561 1.019713318 0.771127256 0.435941304 0.112542023 2.721224945 11969.00636 0.04127104 0.029437818 99.08454119 -1.996005903 -0.248586062 HKSDSPES(ph)DAEREK ddPTM_BT-474_Pertuzumab_2h_R1 1 HKSDSPESDAEREK 14 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 HKSDS(0.003)PES(0.997)DAEREK 106.75 0.00048198 341750000 532080 695890 395460 434920 434980 591700 445320 222210 574670 480180 TRUE FALSE 511285.7254 676043.8985 466928.419 457366.2733 448971.5267 603664.5794 450769.9594 217621.2858 509435.8708 447656.9809 1.142137277 1.510182857 1.043049564 1.021689134 1.002936502 1.34849808 1.006953937 0.486134016 1.138004974 1 18.77203416 1.996038829 24.58683173 0.79984856 1.172449632 0.268561786 0.216104282 135.8687732 843334.4619 0.081848119 0.059050626 99.09205358 -1.996038829 0.372601071 YKYEDKDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 YKYEDKDGK 9 2 A0A499FJT0;Q8NHP1;O43488;H3BLU7 A0A499FJT0;O43488 AKR7L;AKR7A2 Aflatoxin B1 aldehyde reductase member 4;Aflatoxin B1 aldehyde reductase member 2 0 ; 96.113 0.0042676 1356030000 1572590 1247550 1156860 1171250 1259600 1194370 1507280 1757890 2086230 1633610 FALSE TRUE 1511131.444 1211971.095 1365930.336 1231698.353 1300116.178 1218520.98 1525726.544 1721588.957 1849409.917 1522964.14 0.992230483 0.795797527 0.896889362 0.808750726 0.853674846 0.800098274 1.001813834 1.130419891 1.214348958 1 20.53845054 1.99614993 3.241781684 1.124357171 0.854822947 0.712171832 0.073501112 0.118851389 2.479221508 0.032847016 0.019585102 99.11740662 -1.99614993 -0.269534224 TPITSVPLGPLASS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPITSVPLGPLASSPTK 17 0 Q15911 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 TPITSVPLGPLAS(0.193)S(0.804)PT(0.003)K;TPITSVPLGPLAS(0.397)S(0.6)PT(0.002)K 154.47 1.43E-07 678180000 1222550 1085620 962070 971150 1079690 1028800 1133490 1307870 1331930 1183660 TRUE FALSE 1174771.394 1054659.181 1135937.45 1021271.168 1114419.209 1049603.041 1147361.99 1280862.027 1180734.89 1103489.654 1.064596655 0.955749043 1.029404713 0.925492291 1.009904538 0.951167088 1.039757813 1.160737686 1.070000871 1 20.07364167 1.996151708 9.478359967 1.096193795 0.988295095 0.339064625 0.053353998 0.096985754 129.3536113 0.019438988 0.013557373 99.1178123 -1.996151708 -0.1078987 HAVSDPSILDSLDLNEDEREVLINNINR ddPTM_BT-474_Pertuzumab_2h_R1 4 HAVSDPSILDSLDLNEDEREVLINNINR 28 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;; 433.74 1.72E-188 2248780000 835361 841432 587678 807640 817699 828087 689783 423794 822378 772766 FALSE TRUE 802714.1686 817435.1832 693884.4874 849322.3972 844001.031 844831.4865 698224.7707 415042.5058 729025.0971 720425.8705 1.114221742 1.13465551 0.963158759 1.178917127 1.171530709 1.172683438 0.969183367 0.576107165 1.01193631 1 19.45849046 1.996166662 8.5510724 0.804688067 1.116821047 0.434936273 0.129332427 0.084559879 67.31518794 0.049598229 0.034404464 99.12122538 -1.996166662 0.31213298 SSLSSLS(ph)PPSSPLDTPFLPASR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLSSLSPPSSPLDTPFLPASR 22 0 Q9ULE0;Q9ULE0-2 Q9ULE0 WWC3 Protein WWC3 1 SSLSS(0.001)LS(0.999)PPSSPLDTPFLPASR 186.56 3.20E-19 0 82541 87803 72786 78008 69808 61141 88272 119820 92988 112990 TRUE FALSE 79315.20647 85298.94441 85940.04932 82034.00223 72053.43772 62377.31291 89352.29914 117345.6751 82432.39208 105337.0867 0.752965636 0.809771251 0.815857473 0.778776069 0.68402725 0.592168579 0.848251095 1.114001525 0.782558116 1 16.68465394 1.996254274 24.96886502 0.978921632 0.742897925 0.5214062 0.097271956 112.0824055 747139.0023 0.037270445 0.02692941 99.14122341 -1.996254274 -0.236023706 DLADELALVDVIEDK ddPTM_BT-474_Pertuzumab_2h_R1 12 DLADELALVDVIEDK 15 0 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;;;;;;;; 308.37 1.01E-55 9830705300 2880281 2326119 2345497 2222820 2467889 2166545 2522650 2929359 3063067 2187757 FALSE TRUE 2767716.434 2259780.364 2769380.483 2337540.007 2547270.891 2210354.024 2553522.945 2868866.713 2715360.476 2039578.27 1.357004276 1.107964522 1.357820155 1.146089876 1.248920391 1.083730915 1.251985758 1.406597999 1.331334284 1 20.95983944 1.996323117 24.91642683 1.300689213 1.212545923 0 0.133346427 360.6996279 2444291.295 0.047202295 0.034116224 99.15694016 -1.996323117 -0.08814329 ISEKEEVTTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISEKEEVTTR 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 136.53 0.00010509 1348720000 1979590 2059600 1528780 1994320 2099980 2152590 2227400 2529800 2877900 2967200 FALSE TRUE 1902225.434 2000862.225 1805064.554 2097247.094 2167527.764 2196116.845 2254659.587 2477558.746 2551212.857 2766228.901 0.687660169 0.723317663 0.652536221 0.758161081 0.783567753 0.793902791 0.815066167 0.895644878 0.922271059 1 21.39948911 1.996337148 0.442535068 1.007854162 0.672629049 0.943329779 0.024569959 0.215661968 0.100101253 0.026122257 0.023355006 99.16014393 -1.996337148 -0.335225113 LVPS(ph)QEETK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVPSQEETK 9 0 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 LVPS(1)QEETK;LVPS(1)QEETK 132.17 0.00032784 540090000 1199280 1079450 979860 1196930 1064830 967150 1186250 1400380 1375350 1402660 TRUE FALSE 1152410.812 1048665.143 1156942.499 1258703.701 1099081.224 986706.4356 1200767.682 1371461.664 1219226.034 1307656.589 0.881279398 0.801942308 0.884744901 0.962564416 0.840496835 0.754560826 0.918259192 1.048793449 0.932374787 1 20.31855229 1.996360421 24.95477513 0.995239773 0.8558056 0.541785214 0.057543567 110.3288662 756471.6198 0.022589004 0.016321205 99.16545783 -1.996360421 -0.139434173 TEWLDGK ddPTM_BT-474_Pertuzumab_2h_R1 12 TEWLDGK 7 0 P62937;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37;P62937-2 P62937;P62937-2 PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D" 0 ;;;;;;;;;;; 170.06 0.0023005 80057005000 37721691 34261329 30492089 32684432 32356039 30034682 35422717 40187780 43006600 39353530 FALSE TRUE 36247485.61 33284229.44 36002687.78 34371279.45 33396800.38 30642003.85 35856230.81 39357888.3 38124671.07 36688080.36 0.987990793 0.907221886 0.981318385 0.9368514 0.91029021 0.835203247 0.977326436 1.072770445 1.039156879 1 25.12880808 1.99643227 24.99349087 1.040308157 0.926034969 0.571301042 0.043062605 98.93117675 693057.6011 0.016665332 0.01203984 99.181865 -1.99643227 -0.114273188 QKSDAEEDGGTVS(ph)QEEEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.089)VS(0.911)QEEEDR 136.25 5.25E-07 0 511110 680880 543600 751670 499110 524260 792410 1406600 764470 705790 TRUE FALSE 491135.2561 661461.9691 641840.6123 790463.7788 515164.3264 534860.8964 802107.7506 1377553.218 677690.5705 657986.2146 0.746421802 1.005282412 0.975462096 1.201337902 0.782940911 0.812875535 1.219034279 2.093589786 1.029946457 1 19.32769783 1.996512237 16.02853438 1.536096709 0.940402702 0.258360483 0.317269286 1.286612105 5906.90712 0.118118981 0.084165664 99.20012896 -1.996512237 -0.595694007 DLLHNEDRHDDYFQER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLHNEDRHDDYFQER 16 1 Q8N684-2;Q8N684;Q8N684-3 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ; 132.59 2.47E-05 891660000 538780 681460 412490 520450 555330 572920 428630 164571 416670 397950 FALSE TRUE 517723.8819 662025.428 487036.1188 547310.4869 573192.6938 584504.8349 433875.7022 161172.5513 369371.3684 370996.492 1.395495357 1.784451989 1.312778232 1.475244372 1.545008392 1.575499627 1.169487344 0.43443147 0.995619571 1 18.50104602 1.996626454 4.858975816 0.754134805 1.511093895 0.734945119 0.189146457 0.08073284 5.313227358 0.076398499 0.049952759 99.2262215 -1.996626454 0.75695909 KFMQDPMEIFVDDETK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFMQDPMEIFVDDETK 16 1 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 169.98 8.71E-09 110280000 411680 369070 388920 300460 379570 380590 399040 456360 489000 434090 FALSE TRUE 395591.0905 358544.485 459206.4955 315966.7766 391779.2138 388285.7906 403923.5709 446936.0065 433490.7701 404688.6977 0.977519493 0.885976028 1.134715395 0.780765014 0.968100211 0.95946784 0.998109345 1.104394586 1.071170934 1 18.62645303 1.996638468 3.503080266 1.06810609 0.949973663 0.234439583 0.086134712 0.304851891 7.692081834 0.037966029 0.023115201 99.22896659 -1.996638468 -0.118132427 GGAGT(ph)GGTGSPQASLEILAPEDSQVLQQATR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGAGTGGTGSPQASLEILAPEDSQVLQQATR 31 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3;D6RCL7;D6RJA4;D6RF61;D6RIC7;D6RBK2 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 GGAGT(0.363)GGT(0.331)GS(0.302)PQAS(0.003)LEILAPEDSQVLQQATR 86.944 0.002409 59523000 29053 31273 29058 30722 27930 36027 29418 25744 31677 32167 TRUE FALSE 27917.57664 30381.12466 34309.42699 32307.5661 28828.39382 36755.49062 29778.02628 25212.3774 28081.15976 29988.30044 0.930948944 1.013099249 1.144093746 1.077339017 0.961321362 1.225661011 0.992988127 0.840740457 0.936403843 1 14.87211214 1.996674096 24.99472158 0.910230503 1.061328853 0.312757945 0.087755568 136.6221806 1026742.361 0.032833859 0.023766649 99.2371072 -1.996674096 0.15109835 FQPQLNPDVVAPLPTHTAHEDFTFGES(ph)RPELGSEGLGSAAHGSQPDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLR 48 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPT(0.058)HT(0.058)AHEDFT(0.058)FGES(0.206)RPELGS(0.206)EGLGS(0.206)AAHGS(0.206)QPDLR 95.786 3.20E-06 2040000000 30809 34099 28528 48393 46300 43373 31551 7961.4 42922 37449 TRUE FALSE 29604.95022 33126.52991 33683.6442 50890.56853 47789.28155 44250.03178 31937.13058 7796.994308 38049.6745 34912.54587 0.847974545 0.948843147 0.964800571 1.457658479 1.368828321 1.267453595 0.914775184 0.223329296 1.089856771 1 15.09145794 1.996811743 15.70482937 0.6558351 1.145386103 0.231599142 0.285643205 1.159820933 5703.424809 0.113160613 0.080669221 99.26856479 -1.996811743 0.489551003 DQGSTYSGDLESEAVSTPHS(ph)WEEELNHYALK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQGSTYSGDLESEAVSTPHSWEEELNHYALK 31 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5;H7C1I7;Q5VZL5-3 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 DQGSTYSGDLESEAVS(0.002)T(0.063)PHS(0.93)WEEELNHY(0.004)ALK 135.84 2.78E-06 49084000 52810 50610 37227 49312 45023 56569 44527 31079 54671 49965 TRUE FALSE 50746.12682 49166.65235 43954.74701 51856.99823 46471.20568 57712.86394 45071.93475 30437.20779 48464.97728 46580.82605 1.08942093 1.055512676 0.943623176 1.113269185 0.997646663 1.238983265 0.96760703 0.653427824 1.040449073 1 15.5074486 1.996844545 24.99923629 0.847217555 1.068000413 0.269168197 0.1227004 120.3328052 953346.1128 0.044757175 0.032415142 99.27606277 -1.996844545 0.220782858 EREQQDLEFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EREQQDLEFAK 11 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 155.88 2.86E-05 302670000 308180 316160 254840 274450 294070 290190 328230 354930 402010 383890 FALSE TRUE 296135.9849 307143.4264 300895.2569 288614.3974 303529.0286 296057.8406 332246.9769 347600.5715 356375.5102 357888.7884 0.827452534 0.858209132 0.840750721 0.806435985 0.848109911 0.827234186 0.928352571 0.971253034 0.995771652 1 18.44915182 1.996849367 1.930479038 0.992223385 0.834007166 0.950695921 0.015916933 0.066353066 0.460948531 0.009331452 0.004778054 99.27716509 -1.996849367 -0.158216219 SKLS(ph)PSPSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SKLS(0.706)PS(0.292)PS(0.002)LR;S(0.001)KLS(0.998)PS(0.001)PSLR;S(0.016)KLS(0.977)PS(0.007)PSLR;S(0.002)KLS(0.992)PS(0.006)PSLR 160.27 4.50E-06 4190160000 5641900 5696700 4539420 4951100 5461100 5173400 5553600 6394000 6290600 5777700 TRUE FALSE 5421408.311 5534235.694 5359794.173 5206626.864 5636761.241 5278009.693 5621566.618 6261961.666 5576517.46 5386371.233 1.006504765 1.027451591 0.995065869 0.966629785 1.046485843 0.979882274 1.043664904 1.162556644 1.03530136 1 22.36088223 1.99685281 22.08227229 1.088788583 1.005218315 0.240030919 0.045408222 25.57734438 179465.7529 0.016514199 0.011911366 99.27795217 -1.99685281 -0.083570267 RAEHQDKVDEVPGLSGQSDDVPAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RAEHQDKVDEVPGLSGQSDDVPAGK 25 2 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 78.067 0.01624 948650000 960690 913590 729110 778370 857730 813950 910870 1106980 1018190 949440 FALSE TRUE 923145.1727 887535.3077 860876.396 818541.769 885319.6644 830408.6267 922017.4995 1084120.476 902609.3398 885133.5831 1.042944467 1.002713404 0.972594886 0.924766368 1.00021023 0.938173223 1.041670452 1.224810014 1.019743638 1 19.75553568 1.996930887 21.363358 1.11318267 0.980180581 0.293799186 0.066138453 15.96500481 111130.3091 0.02444234 0.017617165 99.29580175 -1.996930887 -0.133002089 TPLEQEIFNLLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPLEQEIFNLLHK 13 0 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;Q5TAP6;X6RJY0 Q9BVJ6-3 UTP14A;UTP14C U3 small nucleolar RNA-associated protein 14 homolog A;U3 small nucleolar RNA-associated protein 14 homolog C 0 81.619 0.014577 85144000 68982 95689 82766 84247 93525 111030 80358 62605 80841 71066 FALSE TRUE 66286.10718 92960.04341 97723.65732 88594.99777 96533.31656 113275.1027 81341.44524 61312.18487 71664.26859 66252.63652 1.000505197 1.403114627 1.475015372 1.337229768 1.45704868 1.709744829 1.22774654 0.925430113 1.081681762 1 16.01569025 1.996940721 24.84515163 1.014710847 1.406578147 0.525610972 0.167788546 86.98209277 706405.6471 0.064458349 0.046689314 99.29805012 -1.996940721 0.3918673 ELPPS(ph)PEKK ddPTM_BT-474_Pertuzumab_2h_R1 7 ELPPSPEKK 9 1 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-3;P27816-6;P27816;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ELPPS(1)PEKK;ELPPS(1)PEKK;ELPPS(1)PEKK;ELPPS(1)PEKK;ELPPS(1)PEKK;ELPPS(1)PEKK;ELPPS(1)PEKK 107.09 0.0017336 2804980000 6913070 5428310 5226610 4486070 5206080 5016160 6007820 7249530 7290010 6654380 TRUE FALSE 6642899.582 5273499.914 6171174.692 4717596.61 5373538.291 5117590.192 6081345.498 7099824.672 6462478.627 6203672.915 1.070801068 0.850060921 0.994761454 0.760452183 0.86618659 0.82492908 0.980281453 1.14445503 1.041718143 1 22.56469119 1.99694495 6.210017085 1.075058647 0.890242004 0.417766719 0.088561826 0.125312593 21.24674025 0.034874014 0.023622256 99.29901727 -1.99694495 -0.184816643 LDFLRPYTVPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDFLRPYTVPNK 12 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ; 132.79 0.00015933 752640000 1010070 985750 837420 1111260 1036580 959950 1155360 1266010 1399930 1424730 FALSE TRUE 970595.3477 957637.3752 988760.4223 1168612.262 1069922.537 979360.8467 1169499.641 1239866.451 1241015.815 1328231.768 0.730742459 0.720986652 0.744418592 0.879825562 0.805523978 0.737341833 0.880493653 0.933471462 0.934336797 1 20.34107548 1.996952967 0.433989249 1.015131522 0.725059421 0.765975317 0.04673208 0.524695757 0.236997524 0.054091879 0.049479584 99.30085027 -1.996952967 -0.290072101 QS(ph)PSFK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSPSFK 6 0 Q6IN85-2;Q6IN85;Q6IN85-4 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 QS(0.988)PS(0.012)FK 82.645 0.061571 1290900000 1335300 1313300 1081600 1179100 1282000 1308400 1405300 1623800 1810600 1709400 TRUE FALSE 1283115 1275845.97 1277069.18 1239953.492 1323236.694 1334856.744 1422498.482 1590267.963 1605068.279 1593620.815 0.805157028 0.800595698 0.801363265 0.778073103 0.830333465 0.837625068 0.89262042 0.997896079 1.007183304 1 20.60387697 1.996980273 1.46182493 1.01310371 0.801188879 0.977422174 0.013196701 0.052636047 0.209607498 0.009080226 0.004315953 99.30709394 -1.996980273 -0.211914831 LS(ph)PENNQVLTK ddPTM_BT-474_Pertuzumab_2h_R1 6 LSPENNQVLTK 11 0 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK 239.98 1.20E-15 4586370000 3459050 3208890 3455630 3535790 3517090 3286940 3866990 4545400 4658290 4535230 TRUE FALSE 3323866.502 3117375.599 4080139.211 3718272.546 3630220.394 3353404.179 3914315.38 4451535.902 4129500.448 4228054.833 0.786145552 0.737307278 0.96501568 0.879428648 0.85860296 0.793131667 0.925795794 1.05285671 0.976690372 1 22.01156266 1.996991078 4.719794319 1.011407403 0.841373049 0.624663767 0.06035922 0.129259 7.716010086 0.026957975 0.017546781 99.30956455 -1.996991078 -0.170034354 EDSGT(ph)FSLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.318)GT(0.682)FSLGK 211.63 6.18E-07 1499200000 2022800 1692400 1089100 1498900 1928900 1359400 1897400 2634000 2303300 1918500 TRUE FALSE 1943746.74 1644134.409 1285924.597 1576258.409 1990944.82 1386887.999 1920620.949 2579606.98 2041839.04 1788558.286 1.086767345 0.919251233 0.718972709 0.881301113 1.113156242 0.775422311 1.073837494 1.442282871 1.141611686 1 20.7703657 1.997073568 13.28679455 1.247363072 0.915254044 0.387900296 0.154335925 0.247944414 1093.761563 0.058296035 0.041352143 99.32842922 -1.997073568 -0.332109028 DGPVRPQNAEEEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGPVRPQNAEEEKR 14 2 Q92504 Q92504 SLC39A7 Zinc transporter SLC39A7 0 ; 153.24 3.63E-06 415720000 137757 204924 112871 204557 129673 149247 194926 289851 239232 173813 FALSE TRUE 132373.3041 199079.7682 133269.3005 215114.2113 133844.0498 152264.8766 197311.5627 283865.4756 212075.3863 162040.4907 0.81691498 1.228580383 0.822444439 1.327533695 0.825991388 0.939671782 1.217668262 1.751818168 1.308780203 1 17.30599483 1.997177277 7.535390294 1.449421536 1.00937312 0.295013032 0.239382153 0.114372838 48.13285614 0.0891492 0.061497878 99.35215161 -1.997177277 -0.440048416 GIGIENIHYLNDGLWHMK ddPTM_BT-474_Pertuzumab_2h_R1 2 GIGIENIHYLNDGLWHMK 18 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ; 154.26 1.58E-08 1600310000 1218930 1354340 959440 993970 1284140 1365820 973450 375200 1191110 1090680 FALSE TRUE 1171292.868 1315715.549 1132832.151 1045268.911 1325445.529 1393437.816 985363.3723 367451.9889 1055900.186 1016807.272 1.151932033 1.293967486 1.11410705 1.027991183 1.303536634 1.370405046 0.969075851 0.361378207 1.03844673 1 19.95561482 1.997214764 14.15693269 0.713033354 1.202723844 0.447563596 0.199868698 0.310994786 1561.48681 0.075009533 0.053356844 99.36072775 -1.997214764 0.48969049 S(ph)SPPSAGNSPSSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPPSAGNSPSSLK 14 0 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 1 S(0.618)S(0.382)PPSAGNSPSSLK 182.37 1.61E-06 289610000 493830 437060 372100 444810 460320 414110 468790 540520 563910 486400 TRUE FALSE 474530.5776 424595.4767 439346.7473 467766.6974 475126.6109 422483.5879 474527.1923 529358.0731 499897.3009 453455.6948 1.046476168 0.936354933 0.96888572 1.03155987 1.047790592 0.931697612 1.046468702 1.167386537 1.102417076 1 18.79060207 1.997243251 24.81958074 1.108131694 0.99379383 0.37236977 0.054890063 81.8372676 736802.2944 0.020138325 0.014604005 99.36724546 -1.997243251 -0.114337865 DSDEADLVLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDEADLVLAK 11 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ; 207.83 5.03E-08 177828000 421020 380500 385760 455450 394580 391540 477260 534310 566920 614800 FALSE TRUE 404566.0729 369648.5125 455475.4132 478955.8291 407272.024 399457.2071 483100.8506 523276.3118 502565.6183 573159.0484 0.705853068 0.644931828 0.79467543 0.835642097 0.710574186 0.696939546 0.842873984 0.912968771 0.876834484 1 19.12857601 1.997261077 2.835007868 0.919654167 0.734276774 0.701073248 0.058192775 0.168107131 2.583307036 0.030631141 0.017619167 99.37132405 -1.997261077 -0.185377393 GKPYLTLEQLMDFINQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKPYLTLEQLMDFINQK 17 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ; 149.57 2.92E-07 283800000 413550 427460 391390 402620 380500 343510 428670 479450 518650 510100 FALSE TRUE 397388.0088 415269.2593 462122.8794 423399.2665 392739.1281 350456.0076 433916.1917 469549.19 459775.0264 475550.4727 0.835637922 0.873239084 0.971764105 0.890335077 0.825862134 0.73694808 0.912450343 0.987380345 0.966826978 1 18.85923894 1.997329381 24.99986266 0.974979044 0.858831585 0.514582425 0.055929077 99.48395143 931281.3554 0.023482683 0.017036731 99.38695414 -1.997329381 -0.11614746 S(ph)SPLPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPLPAK 7 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 S(0.558)S(0.442)PLPAK;S(0.691)S(0.309)PLPAK 110.41 0.0071437 2834510000 4472300 4281100 4211100 4864300 4622300 4589900 5797200 6166000 7126300 7081600 TRUE FALSE 4297517.572 4159007.22 4972139.445 5115347.106 4770980.477 4682710.923 5868147.868 6038669.945 6317352.3 6601956.924 0.650946018 0.629965822 0.753131155 0.774822854 0.722661558 0.709291347 0.888849766 0.914678786 0.956890869 1 22.65446229 1.997345098 0.809482825 1.003960606 0.687892752 0.869494904 0.04480561 0.221858254 0.27134007 0.041363987 0.021097102 99.39055089 -1.997345098 -0.316067854 SQT(ph)PERPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQTPERPAK 9 1 A8CG34-2;A8CG34;A6NF01;C9JFL1;Q96HA1-2;Q96HA1-3;Q96HA1 A8CG34-2;Q96HA1-2 POM121C;POM121B;POM121 Nuclear envelope pore membrane protein POM 121C;Putative nuclear envelope pore membrane protein POM 121B;Nuclear envelope pore membrane protein POM 121 1 S(0.141)QT(0.859)PERPAK;S(0.053)QT(0.947)PERPAK 120.53 0.0010513 565770000 946330 909340 781790 1053910 798640 793150 1011060 1336260 1146430 1078730 TRUE FALSE 909346.3774 883406.5135 923076.8438 1108302.421 824328.9809 809188.0364 1023433.655 1308665.764 1016292.073 1005666.656 0.90422246 0.87842876 0.917875559 1.102057441 0.819684113 0.804628483 1.017666886 1.301291791 1.010565545 1 19.93972075 1.997375766 23.85551215 1.142941837 0.909209617 0.389943832 0.10964502 47.34228682 430367.0071 0.041518744 0.030080095 99.39756973 -1.997375766 -0.23373222 RQDLEDSLQAQQYFADANEAESWMR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQDLEDSLQAQQYFADANEAESWMR 25 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 264.97 4.18E-45 878250000 315330 350620 256780 323680 318970 380940 311260 291060 331120 315770 FALSE TRUE 303006.555 340620.6609 303185.858 340385.1636 329229.9597 388642.8678 315069.293 285049.5093 293532.6458 294382.6166 1.029294999 1.157067849 1.02990408 1.156267878 1.118374323 1.32019639 1.070271392 0.968295997 0.9971127 1 18.16733296 1.997543112 24.99937961 0.993531077 1.136891599 0.424950405 0.076446647 91.63489783 932410.3856 0.02923866 0.021230655 99.43587784 -1.997543112 0.143360521 QPPVS(ph)PLTLS(ph)PGPEAHQGFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPPVSPLTLSPGPEAHQGFSR 21 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 2 QPPVS(0.999)PLT(0.014)LS(0.987)PGPEAHQGFSR;QPPVS(1)PLT(0.005)LS(0.995)PGPEAHQGFSR 144.4 6.76E-08 226030000 235430 294700 243350 285320 290170 262030 207500 200881 178490 175284 TRUE FALSE 226229.1353 286295.4445 287328.7583 300045.3994 299503.5816 267328.4261 210039.4471 196732.7372 158228.5635 163411.8586 1.38441076 1.751986955 1.758310326 1.836129899 1.832814241 1.635918155 1.285337851 1.203907347 0.96828079 1 17.31815316 1.997559482 1.497048405 1.021384062 1.729325915 0.836714292 0.130346643 0.154742056 0.646611994 0.089936723 0.042985681 99.43962591 -1.997559482 0.707941853 ALNHSVEDIEPDLLT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALNHSVEDIEPDLLTPR 17 0 Q8IWR0;I3L2K5 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 1 ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR 218.44 1.71E-14 228700000 199242 215957 205975 238220 225630 250310 210621 192998 210007 228500 TRUE FALSE 191455.4024 209798.1178 243199.2644 250514.5627 232887.5939 255371.4397 213198.6428 189012.5239 186167.8858 213023.4915 0.898752532 0.98485907 1.141654672 1.175995009 1.093248412 1.198794734 1.000822216 0.887284884 0.873931248 1 17.70065301 1.997564147 7.353672148 0.916334567 1.086608879 0.401025633 0.088855587 0.126996847 47.3745316 0.037654455 0.025952715 99.44069416 -1.997564147 0.170274311 DREPHGYS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 4 DREPHGYSPER 11 1 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 DREPHGYS(1)PER;DREPHGYS(1)PER;DREPHGYS(1)PER;DREPHGYS(1)PER 137.39 4.80E-05 1150998000 756775 820131 664915 706138 787000 823737 761625 750927 850567 848580 TRUE FALSE 727199.3963 796741.6669 785079.9315 742581.8668 812314.5697 840393.5265 770945.9946 735420.095 754014.2 791104.9208 0.919219913 1.007125156 0.992384083 0.938664199 1.026810159 1.0623035 0.974518012 0.929611327 0.953115295 1 19.59350952 1.997584092 24.99960622 0.952832094 0.993388586 0.086116789 0.041612276 172.8120073 1788248.109 0.016071497 0.011662768 99.44526105 -1.997584092 0.040556492 SLSS(ph)SLDDTEVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSSLDDTEVKK 13 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 SLS(0.001)S(0.5)S(0.5)LDDTEVKK 240.11 8.25E-17 279650000 384030 559280 269110 530730 392140 384430 539780 858030 680390 375470 TRUE FALSE 369021.683 543329.882 317744.1633 558121.0389 404753.5392 392203.438 546385.9891 840311.3807 603154.9796 350039.0825 1.054229946 1.552197767 0.907739105 1.594453496 1.156309565 1.120456137 1.560928526 2.400621596 1.723107532 1 18.41715648 1.997604993 9.780865203 1.892962608 1.25165278 0.203124561 0.384104374 0.105925042 185.2362497 0.140302226 0.098434003 99.45004696 -1.997604993 -0.641309828 KYTLENKEEGS(ph)LSDTEADAVSGQLPDPTTNPSAGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KYTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 35 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KYT(0.002)LENKEEGS(0.455)LS(0.455)DT(0.087)EADAVSGQLPDPTTNPSAGK;KY(0.116)T(0.123)LENKEEGS(0.231)LS(0.231)DT(0.231)EADAVS(0.065)GQLPDPT(0.002)T(0.001)NPSAGK;KYT(0.015)LENKEEGS(0.444)LS(0.444)DT(0.098)EADAVSGQLPDPTTNPSAGK 231.33 9.38E-38 3752200000 1810830 1448920 1181420 1007136 1451600 1453770 1524400 1687540 2030690 1749340 TRUE FALSE 1740060.762 1407598.22 1394928.875 1059114.41 1498292.032 1483166.225 1543056.063 1652691.709 1800174.585 1630855.644 1.066961854 0.863104117 0.85533559 0.649422537 0.9187153 0.909440533 0.946163487 1.013389331 1.103822151 1 20.63719766 1.997624769 1.440077342 1.051073468 0.86089434 0.354708073 0.09849588 0.451014862 1.742456819 0.0694025 0.032906776 99.45457583 -1.997624769 -0.190179128 GKHQPWQS(ph)PERPLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GKHQPWQSPERPLSR 15 2 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-2;V9GYS7;J3QRS2;V9GYU5;J3QL08 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 1 GKHQPWQS(1)PERPLSR;GKHQPWQS(1)PERPLSR;GKHQPWQS(1)PERPLSR 219.95 9.05E-13 2042600000 1221380 1337640 919280 1033250 1042050 1395250 1115590 1042260 1243230 1137820 TRUE FALSE 1173647.119 1299491.817 1085414.345 1086576.156 1075568.485 1423462.911 1129242.924 1020736.967 1102103.742 1060754.438 1.106426782 1.225063757 1.023247517 1.024342786 1.013965576 1.341934438 1.064565826 0.962274519 1.038981034 1 20.01665928 1.997723853 24.96636183 1.00052512 1.12075259 0.243934895 0.09651697 126.8594176 1391486.199 0.037751834 0.027423685 99.47726873 -1.997723853 0.12022747 VGSGQGGS(ph)PCWK ddPTM_BT-474_Pertuzumab_2h_R1 4 VGSGQGGSPCWK 12 0 A0A669KBI7;Q9UMN6;Q9UMN6-2 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 VGSGQGGS(1)PCWK;VGSGQGGS(1)PCWK;VGSGQGGS(1)PCWK;VGSGQGGS(1)PCWK 178.14 2.35E-05 947510000 1015580 945030 786191 830790 839252 859370 912030 999990 1003800 1016720 TRUE FALSE 975890.0108 918078.6697 928273.2024 873667.1715 866247.3028 876747.0502 923191.696 979339.857 889852.8323 947856.6488 1.029575529 0.968583879 0.979339232 0.921729222 0.913901173 0.924978531 0.973978182 1.033215158 0.938805286 1 19.85430936 1.9977404 24.82592488 0.99667221 0.954034702 0.132353153 0.038408413 134.9536189 1482727.11 0.015227693 0.011052085 99.48105909 -1.9977404 -0.042637508 QPT(ph)PPSEAAASK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPTPPSEAAASK 12 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 QPT(0.94)PPS(0.06)EAAASK 92.939 0.083312 471520000 438340 579130 338930 704080 445680 417580 579830 835860 711340 442800 TRUE FALSE 421209.1882 562613.7794 400182.1905 740417.6532 460015.702 426023.7537 586926.133 818599.1989 630591.6654 412808.7616 1.020349439 1.36289205 0.969413025 1.793609347 1.114355471 1.032012383 1.421787005 1.982998606 1.527563666 1 18.65511407 1.997939014 24.85820692 1.63515533 1.232165149 0.106324245 0.321892395 100.0678815 1206960.182 0.116817591 0.084911872 99.52656468 -1.997939014 -0.402990181 HLSPNDNENDTSYVIES(ph)DEDLEMEMLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLSPNDNENDTSYVIESDEDLEMEMLK 27 0 Q14191 Q14191 WRN Werner syndrome ATP-dependent helicase 1 HLSPNDNENDTSYVIES(1)DEDLEMEMLK 168.87 4.34E-12 31294000 22691 29779 22231 28573 29490 31971 24676 12894 31125 33803 TRUE FALSE 21804.21063 28929.73208 26248.63623 30047.65595 30438.57263 32617.47553 24977.99227 12627.73439 27591.82049 31513.4927 0.691900794 0.918010972 0.832933261 0.953485424 0.965890164 1.035032068 0.792612628 0.400708817 0.875555774 1 14.94368204 1.998047828 24.96101983 0.668290396 0.903738459 0.057586115 0.172701472 92.66076633 1184795.46 0.063608454 0.0462575 99.55150453 -1.998047828 0.235448064 KHS(ph)PSPPPPTPTESR ddPTM_BT-474_Pertuzumab_2h_R1 4 KHSPSPPPPTPTESR 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 KHS(0.976)PS(0.024)PPPPTPTESR;KHS(0.764)PS(0.236)PPPPTPTESR;KHS(0.854)PS(0.146)PPPPTPTESR;KHS(0.749)PS(0.251)PPPPTPTESR 150.98 1.89E-06 803620000 296737 297698 250299 248715 271106 304722 268759 204201 356793 329379 TRUE FALSE 285140.19 289207.9445 295533.5972 261551.211 279826.3707 310883.6876 272048.153 199984.178 316291.3544 307069.8669 0.92858408 0.94183108 0.962431124 0.851764498 0.911279161 1.012420042 0.885948712 0.651266046 1.030030584 1 18.22820742 1.998063733 24.99873749 0.833414842 0.932941863 0 0.106737993 137.7463478 1778427.371 0.039612853 0.028810666 99.55515038 -1.998063733 0.099527021 FEDRFDK ddPTM_BT-474_Pertuzumab_2h_R1 4 FEDRFDK 7 1 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ;;; 98.392 0.010302 3830280000 2688630 3445690 2962350 3100240 2576200 1756810 3264840 4189770 4059270 3702830 FALSE TRUE 2583555.367 3347422.295 3497712.542 3260243.758 2659065.813 1792333.902 3304796.089 4103249.785 3598478.687 3452034.026 0.748415383 0.969695626 1.013232348 0.944441374 0.770289572 0.51921096 0.957347484 1.18864697 1.042422717 1 21.71901525 1.998190123 24.99891164 1.091737341 0.836253054 0.392902534 0.1391599 71.97473286 994157.8741 0.057144145 0.041575292 99.58412762 -1.998190123 -0.255484287 LLSLLEKDEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLSLLEKDEFK 11 1 P35270 P35270 SPR Sepiapterin reductase 0 ; 165.7 1.94E-05 589020000 669460 651960 504220 495330 544810 494910 604260 684970 729520 683830 FALSE TRUE 643296.7631 633366.7391 595343.7703 520894.0407 562334.3084 504917.4193 611655.1146 670825.1301 646707.948 637513.585 1.009071459 0.993495282 0.933852681 0.81707128 0.882074236 0.792010447 0.959438558 1.052252291 1.014422223 1 19.28209656 1.998219635 24.97458969 1.022484355 0.902527858 0.398860872 0.064807257 70.11796211 983608.9686 0.027053236 0.019677832 99.59089493 -1.998219635 -0.119956498 GSSGPTQINQVVSHPNQPLTITAHDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSGPTQINQVVSHPNQPLTITAHDDR 27 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317 F5GYK2 STRN4 Striatin-4 0 334.49 1.37E-95 843440000 91260 101910 74764 90968 88920 100510 84725 67797 89352 100570 FALSE TRUE 87693.45831 99003.62658 88275.51792 95662.86938 91780.19256 102542.3811 85761.88989 66396.96826 79209.13555 93758.30432 0.935314039 1.055945149 0.941522125 1.020313561 0.97890201 1.09368852 0.914712467 0.708171599 0.844822612 1 16.51665886 1.998248017 24.49017127 0.816790015 1.003422522 0.4028753 0.081494325 36.85502799 515184.7562 0.028788686 0.020937636 99.59740364 -1.998248017 0.186632507 AS(ph)WESLDEEWRAPQAGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASWESLDEEWRAPQAGSR 18 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 AS(1)WESLDEEWRAPQAGSR;AS(0.999)WES(0.001)LDEEWRAPQAGSR 190.57 1.63E-14 335260000 124240 148769 67310 100439 113603 150708 104062 88189 104819 88956 TRUE FALSE 119384.5634 144526.2538 79474.4143 105622.6688 117257.1437 153755.419 105335.5419 86367.86633 92920.38656 82930.93089 1.439566181 1.742730393 0.958320538 1.27362213 1.41391327 1.854017764 1.270159888 1.041443348 1.120455125 1 16.33962267 1.998298502 24.99804997 1.082878585 1.439969779 0.366102691 0.230961922 77.0682853 1132280.855 0.09140243 0.066527632 99.60898213 -1.998298502 0.357091193 AEPEKTEGAAEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEPEKTEGAAEAK 13 1 P80723 P80723 BASP1 Brain acid soluble protein 1 0 137.46 4.97E-06 0 141920 145010 113390 121780 128570 101550 147940 202110 193470 124940 FALSE TRUE 136373.6095 140874.4568 133882.0953 128065.0804 132705.5708 103603.4106 149750.534 197936.3579 171508.0967 116477.7025 1.17081301 1.209454288 1.149422529 1.099481511 1.139321672 0.889469901 1.285658377 1.699349778 1.472454324 1 16.82969428 1.998310334 24.99360749 1.474356213 1.114445686 0.295420732 0.184532835 55.10251765 815086.8322 0.066410601 0.04833793 99.61169592 -1.998310334 -0.359910527 DKLDGNELDLSLSDLNEVPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKLDGNELDLSLSDLNEVPVK 21 1 Q96AG4;I3L223 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 161.58 1.80E-11 160950000 33719 43623 23720 51986 29855 26599 44408 68795 54352 37291 FALSE TRUE 32401.2242 42378.91475 28006.73165 54669.00369 30815.31319 27136.85 44951.47839 67374.35921 48182.18882 34765.24735 0.932000393 1.21900225 0.805595639 1.572518761 0.886382682 0.780574052 1.29300039 1.937980148 1.3859297 1 15.08535823 1.998321735 24.85221728 1.56301506 1.047720587 0.238722498 0.310339713 60.24130506 892077.7339 0.112834636 0.082115707 99.61431083 -1.998321735 -0.515294473 YDGKWEVEEMK ddPTM_BT-474_Pertuzumab_2h_R1 2 YDGKWEVEEMK 11 1 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85 P27824 CANX Calnexin 0 ; 139.46 3.56E-05 1758040000 1409870 1958860 1082740 1583760 1121870 954630 1682440 2485000 2248300 1323770 FALSE TRUE 1354770.722 1902995.231 1278415.203 1665498.043 1157955.967 973933.2727 1703030.204 2433683.882 1993082.41 1234109.879 1.097771556 1.541998215 1.035900632 1.349554097 0.938292438 0.789178735 1.37996643 1.972015558 1.614995912 1 20.23503942 1.998360132 24.99411431 1.646751944 1.13720737 0.246299837 0.301089525 63.23511339 963809.526 0.111550861 0.081205784 99.62311839 -1.998360132 -0.509544574 QQS(ph)VESLAEEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQSVESLAEEVK 12 0 Q8WXH0;Q8WXH0-2;G3V5X4;A0A0A0MRE3 Q8WXH0 SYNE2 Nesprin-2 1 QQS(0.991)VES(0.009)LAEEVK 218.2 3.66E-11 249150000 301450 278830 217150 247280 245650 241630 283220 383420 292380 258880 TRUE FALSE 289669.0007 270878.0414 256393.8355 260042.1504 253551.5553 246515.9242 286686.1311 375502.243 259190.2482 241345.827 1.20022378 1.122364719 1.062350398 1.077466943 1.050573604 1.021421945 1.187864462 1.555867974 1.073937144 1 17.88074236 1.998380873 24.65675948 1.296740159 1.088551897 0.041259349 0.150071724 63.40489975 965567.9447 0.055181691 0.040154277 99.62787634 -1.998380873 -0.208188261 HTWMEDADSCVAHNALECAR ddPTM_BT-474_Pertuzumab_2h_R1 4 HTWMEDADSCVAHNALECAR 20 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ;;; 263.09 1.04E-36 1017880000 132271 144304 112617 157529 127208 148617 117246 62668 142568 130657 FALSE TRUE 127101.7031 140188.5912 132969.3971 165659.0906 131299.7608 151622.1376 118680.8916 61373.8839 126384.2783 121807.485 1.043463816 1.150902928 1.091635683 1.360007479 1.07792851 1.244768641 0.974331681 0.503859709 1.037573991 1 16.89424326 1.998405364 8.806743939 0.778629398 1.158924978 0.418048128 0.162437166 0.078324758 77.66588643 0.060839007 0.042543966 99.63349487 -1.998405364 0.380295581 APKPEDIDEEDDDVPDLVENFDEASK ddPTM_BT-474_Pertuzumab_2h_R1 5 APKPEDIDEEDDDVPDLVENFDEASK 26 1 Q96K17;Q96K17-2 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4 0 ;;;; 242.94 3.16E-45 1604619000 548571 426295 493150 476632 522389 463580 629448 787839 831355 820999 FALSE TRUE 527132.2388 414137.484 582273.1751 501231.0346 539192.1166 472953.9052 637151.3729 771569.8493 736983.0657 765392.0065 0.688708837 0.541078925 0.760751576 0.654868395 0.704465309 0.617923758 0.832451041 1.008071476 0.962883149 1 19.54583931 1.998412093 3.065110231 0.98697976 0.662166503 0.873635933 0.056200378 0.080303043 1.471929086 0.026222055 0.015438649 99.63503852 -1.998412093 -0.324813257 ESHRLPVDIAYK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESHRLPVDIAYK 12 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 75.78 0.019761 515000000 458290 435810 385650 429910 424710 449850 428190 397330 527750 462440 FALSE TRUE 440379.5201 423381.1255 455345.5337 452097.7066 438371.1829 458946.2752 433430.3173 389124.9967 467842.0325 431118.5269 1.021481316 0.982052728 1.056195699 1.048662209 1.016822882 1.06454779 1.005362308 0.902594002 1.085181924 1 18.71772504 1.998412909 24.99380167 0.977321354 1.030955483 0.070035705 0.047426164 92.42277623 1455509.594 0.017585968 0.012804743 99.63522561 -1.998412909 0.053634128 SGSGSVGNGSSRYS(ph)PSQNSPIHHIPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SGSGSVGNGSSRYSPSQNSPIHHIPSR 27 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.001)GS(0.001)GSVGNGS(0.023)S(0.017)RYS(0.624)PS(0.334)QNSPIHHIPSR;SGSGSVGNGS(0.041)S(0.041)RYS(0.91)PS(0.007)QNSPIHHIPSR;SGSGSVGNGS(0.008)S(0.006)RYS(0.968)PS(0.018)QNSPIHHIPSR 210.36 8.19E-26 1888020000 102455 168406 102317 123152 145378 168055 109790 54318 119421 100186 TRUE FALSE 98450.94533 163603.2258 120807.9579 129507.8895 150054.2154 171453.1872 111133.6429 53196.31432 105864.8287 93400.31298 1.054075112 1.751634663 1.293442753 1.386589459 1.606570798 1.835681078 1.189863709 0.569551778 1.133452612 1 16.51113976 1.998539125 24.63963427 0.859807299 1.493656888 0.52796765 0.248967452 30.37044293 512244.6823 0.090565445 0.065931509 99.66418619 -1.998539125 0.633849589 LLKPGEEPSEYT(ph)DEEDTKDHNKQD ddPTM_BT-474_Pertuzumab_2h_R1 6 LLKPGEEPSEYTDEEDTKDHNKQD 24 3 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPS(0.003)EYT(0.997)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPS(0.002)EYT(0.997)DEEDT(0.001)KDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD 289.41 4.80E-62 7083740000 2063280 2335400 1368808 1896410 1414879 1392829 2112070 2930940 3025460 1626610 TRUE FALSE 1982644.737 2268796.679 1616182.055 1994283.947 1460389.868 1420992.957 2137918.144 2870415.065 2682022.465 1516438.256 1.307435188 1.496135217 1.065775048 1.315110549 0.963039453 0.937059555 1.40982868 1.892866428 1.768632817 1 20.53225533 1.998624941 24.29219471 1.652617274 1.185025517 0.256385286 0.274001763 36.20136739 639553.3873 0.10160419 0.073964993 99.68388175 -1.998624941 -0.467591757 NTADHDESPPRT(ph)PT(ph)GNAPSSESDIDISSPNVSHDESIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NTADHDESPPRTPTGNAPSSESDIDISSPNVSHDESIAK 39 1 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 2 NT(0.001)ADHDES(0.422)PPRT(0.624)PT(0.71)GNAPS(0.087)S(0.082)ES(0.074)DIDIS(0.001)SPNVSHDESIAK;NT(0.079)ADHDES(0.554)PPRT(0.68)PT(0.68)GNAPS(0.003)S(0.003)ES(0.001)DIDISSPNVSHDESIAK 99.197 0.00012071 1393620000 256236 231745 209440 210519 233942 245770 219762 188814 264340 225666 TRUE FALSE 246222.0138 225135.8595 247290.467 221383.9108 241466.9569 250739.6378 222451.5131 184914.9249 234333.2314 210381.4408 1.170359956 1.07013175 1.175438603 1.052297722 1.147757882 1.191833447 1.057372324 0.878950749 1.113849351 1 17.68264791 1.998653277 20.07910724 0.980152866 1.129928956 0.448673989 0.067800201 3.05925892 45613.40901 0.024499932 0.017729096 99.69038595 -1.998653277 0.14977609 KEETPGT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 KEETPGTPK 9 1 Q99442 Q99442 SEC62 Translocation protein SEC62 1 KEET(0.02)PGT(0.98)PK;KEET(0.001)PGT(0.999)PK;KEET(0.245)PGT(0.755)PK 116.51 0.00076296 2144620000 4978410 6748750 3645730 7067650 4374760 3831510 6882320 11088000 9271100 5088250 TRUE FALSE 4783848.233 6556282.258 4304594.51 7432412.263 4515478.128 3908985.757 6966547.891 10859028.93 8218683.596 4743618.295 1.008480855 1.38212686 0.907449597 1.566823425 0.951905876 0.824051497 1.46861477 2.289186914 1.732576924 1 22.17755649 1.998686046 19.96796922 1.832598988 1.125977554 0.30423761 0.368059208 3.238327533 49213.08641 0.132887172 0.09615532 99.69790812 -1.998686046 -0.706621434 LKEEEEDKKR ddPTM_BT-474_Pertuzumab_2h_R1 6 LKEEEEDKKR 10 3 P27797 P27797 CALR Calreticulin 0 ;;;;; 191.53 3.43E-07 15940590000 8273160 6986470 5787540 4848390 5922360 6011150 7249180 8461410 10079510 7386170 FALSE TRUE 7949835.761 6787222.716 6833477.221 5098615.989 6112858.088 6132699.572 7337897.633 8286678.927 8935326.282 6885898.127 1.154509639 0.985669929 0.992387209 0.740443134 0.887735772 0.890617238 1.065641329 1.203427465 1.297626848 1 22.71521341 1.998720653 3.488428926 1.183806777 0.935151182 0.413913755 0.119974313 0.218062726 5.453716789 0.056997851 0.034760187 99.70585298 -1.998720653 -0.248655595 LQLELS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 LQLELSK 7 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 LQLELS(1)K 94.692 0.0147 34967000 98316 74886 87128 74120 83137 61983 93737 115210 118240 115630 TRUE FALSE 94473.70203 72750.3246 102873.9678 77945.34208 85811.17711 63236.33873 94884.18145 112830.8732 104817.8909 107798.2771 0.876393432 0.674874651 0.95431922 0.723066678 0.796034774 0.586617341 0.88020128 1.046685311 0.972352191 1 16.71797459 1.998822558 24.99809394 0.999510665 0.768709667 0.548372502 0.09685171 31.12197896 660753.6431 0.035218801 0.025673774 99.72925115 -1.998822558 -0.230800998 LRLEEALSEAAPDPSLPPLAQS(ph)PPKHER ddPTM_BT-474_Pertuzumab_2h_R1 2 LRLEEALSEAAPDPSLPPLAQSPPKHER 28 2 A0A1B0GW72;Q96PX9 A0A1B0GW72 PLEKHG4B Pleckstrin homology domain-containing family G member 4B 1 LRLEEALSEAAPDPSLPPLAQS(1)PPKHER;LRLEEALSEAAPDPSLPPLAQS(1)PPKHER 67.586 0.0063321 527790000 738490 829570 673980 513850 659080 862190 613620 429910 641970 583410 TRUE FALSE 709628.9944 805911.4758 795783.1786 540369.8601 680279.9068 879624.0725 621129.6651 421032.2083 569096.257 543895.1211 1.304716602 1.481740587 1.463118803 0.993518491 1.25075567 1.617267812 1.142002642 0.774105507 1.04633455 1 19.05296896 1.998910854 24.98834803 0.925798959 1.345073271 0.547064983 0.168482442 29.14963328 668790.8451 0.065542357 0.047787356 99.749529 -1.998910854 0.419274312 KIPLKPS(ph)PSKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIPLKPSPSKK 11 3 A2A3N6;A6PW57;Q99755-4;Q99755-3;Q99755 A2A3N6 PIPSL;PIP5K1A Putative PIP5K1A and PSMD4-like protein;Phosphatidylinositol 4-phosphate 5-kinase type-1 alpha 1 KIPLKPS(0.5)PS(0.5)KK 84.468 0.088079 560760000 1005200 778770 797530 614000 702550 776850 907190 986060 1164200 1056100 TRUE FALSE 965915.6727 756560.2421 941661.412 645688.6136 725148.1588 792558.4393 918292.4626 965697.5164 1032044.897 984569.4063 0.981053917 0.768417378 0.956419533 0.655808122 0.736512991 0.804979755 0.932684336 0.980832342 1.048219547 1 19.90913339 1.998946033 2.245539148 1.01142551 0.81008469 0.471881568 0.091980781 0.273294034 2.573758529 0.050800254 0.027302422 99.75760937 -1.998946033 -0.20134082 SLS(ph)SSLDDTEVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSSLDDTEVKK 13 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 S(0.004)LS(0.903)S(0.089)S(0.004)LDDTEVKK 117.4 0.00031201 459260000 295150 358700 168700 335860 222850 194640 328040 516740 396850 229170 TRUE FALSE 283615.2117 348470.2272 199187.8427 353193.7748 230018.1726 198575.7542 332054.6516 506069.1384 351801.2517 213648.1118 1.327487565 1.63104754 0.932317356 1.653156548 1.076621603 0.929452418 1.554212901 2.368704007 1.646638713 1 17.70487704 1.998962365 24.99676947 1.858258978 1.267794015 0.140334486 0.398689475 43.52027006 1048424.235 0.144364778 0.105270087 99.761361 -1.998962365 -0.590464964 IETMLGDVAVAVHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IETMLGDVAVAVHPK 15 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ; 103.21 0.0014902 290160000 1026730 878780 884400 843790 954740 1036330 965200 1115540 1319700 1187880 FALSE TRUE 986604.2565 853718.0548 1044230.753 887338.103 985450.0792 1057285.303 977012.4063 1092503.709 1169893.189 1107423.83 0.890900331 0.770904537 0.942936864 0.801263328 0.889858113 0.954725079 0.882238923 0.986527181 1.056409622 1 20.07877604 1.999001973 0.818269662 1.030428681 0.852024498 0.585168377 0.054123594 0.413095749 0.515495897 0.043785084 0.022227543 99.77045957 -1.999001973 -0.178404183 MISTPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 8 MISTPSPK 8 0 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 MIS(0.002)T(0.015)PS(0.983)PK;MIS(0.008)T(0.045)PS(0.947)PK;MIS(0.012)T(0.008)PS(0.98)PK;MIST(0.007)PS(0.993)PK;MISTPS(1)PK;MISTPS(1)PK;MIST(0.001)PS(0.999)PK;MISTPS(1)PK 153.7 0.00045825 3748300000 7621570 6383200 5472670 5474480 5944450 5619810 6543010 7473630 7519670 7594440 TRUE FALSE 7323710.618 6201157.386 6461703.208 5757018.569 6135658.633 5733446.409 6623085.314 7319296.929 6666068.587 7080061.814 1.034413372 0.87586204 0.912661976 0.813131117 0.866610885 0.809801745 0.93545586 1.033789975 0.941526891 1 22.75533053 1.999007039 24.94606816 0.992800786 0.881290286 0.369257767 0.062284068 34.88779514 876496.775 0.02348348 0.017126934 99.7716235 -1.999007039 -0.1115105 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGR ddPTM_BT-474_Pertuzumab_2h_R1 6 ASEDNRVPSPPPTGDDGGGGGR 22 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 ASEDNRVPS(0.833)PPPT(0.167)GDDGGGGGR;AS(0.037)EDNRVPS(0.962)PPPT(0.001)GDDGGGGGR;AS(0.011)EDNRVPS(0.978)PPPT(0.011)GDDGGGGGR;ASEDNRVPS(0.882)PPPT(0.118)GDDGGGGGR;AS(0.001)EDNRVPS(0.989)PPPT(0.01)GDDGGGGGR;AS(0.011)EDNRVPS(0.97)PPPT(0.019)GDDGGGGGR 142.26 1.78E-39 3825600000 30182 46101 31203.2 33892.6 38344.4 42649 32159.5 20795.1 31334.8 40282.6 TRUE FALSE 29002.45407 44786.24462 36842.31235 35641.80115 39577.78245 43511.392 32553.07758 20365.67392 27777.80487 37554.22362 0.772282084 1.192575436 0.98104311 0.949075702 1.053883655 1.158628453 0.866828666 0.542300491 0.739671925 1 15.19668755 1.999203791 10.316821 0.70839383 1.021950855 0.355659389 0.152227751 0.07493631 200.9804724 0.055562724 0.039267413 99.816834 -1.999203791 0.313557025 TPSRHS(ph)CSGS(ph)SPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPSRHSCSGSSPPR 14 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 TPSRHS(0.999)CS(0.452)GS(0.507)S(0.041)PPR;T(0.002)PSRHS(0.995)CS(0.007)GS(0.818)S(0.178)PPR 111.45 0.00037049 738010000 643970 910980 682680 869260 774490 977310 739960 642920 719410 707370 TRUE FALSE 618802.9405 884999.7423 806055.4621 914122.6128 799402.1742 997071.8778 749015.8518 629643.4773 637745.5928 659459.1998 0.938349091 1.342008334 1.222297698 1.386170081 1.212208692 1.511953853 1.135803173 0.954787616 0.967073616 1 19.33092388 1.999214726 24.98090348 0.988021425 1.277058555 0.471641686 0.139611869 23.26008338 739957.1274 0.050821439 0.037077403 99.81934725 -1.999214726 0.28903713 EGEEPTVYS(ph)DEEEPKDESAR ddPTM_BT-474_Pertuzumab_2h_R1 6 EGEEPTVYSDEEEPKDESAR 20 1 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR 326.89 6.14E-80 33004600000 5187190 6746260 3890480 6772030 4441220 3973030 6834120 10675200 8885870 5570010 TRUE FALSE 4984468.88 6553863.27 4593576.279 7121535.28 4584075.875 4053367.389 6917758.005 10454753.39 7877183.29 5192748.261 0.959890337 1.262118427 0.884613705 1.371438576 0.882784153 0.780582301 1.332195912 2.013337228 1.516958438 1 22.30806686 1.99922008 18.47818058 1.6352114 1.039081876 0.345405785 0.290180191 0.835116332 19766.96967 0.105329927 0.076145769 99.82057785 -1.99922008 -0.596129524 SISLLEPSLELEST(ph)SETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 SISLLEPS(0.013)LELES(0.06)T(0.463)S(0.463)ET(0.001)SDMPEVFSSHESSHEEPLQPFPQLAR 254.41 1.48E-66 270800000 100370 141310 68653 127800 89229 94880 80535 10576 67049 82993 TRUE FALSE 96447.42944 137279.9772 81060.12428 134395.7733 92099.13182 96798.53861 81520.61142 10357.6019 59437.87861 77371.81019 1.246544823 1.774289329 1.047669999 1.737012136 1.190344799 1.25108277 1.053621613 0.133867902 0.768211038 1 16.23952041 1.999235222 4.094648846 0.542839503 1.378235323 0.54159004 0.300296602 0.132675986 5.108123358 0.12510945 0.079394794 99.82405824 -1.999235222 0.83539582 RPPEEDFRHS(ph)PEEDFRQS(ph)PQEHFR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPPEEDFRHSPEEDFRQSPQEHFR 24 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 2 RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR 146.58 9.22E-08 2581560000 281686 266083 226174 266093 248159 296502 250835 222055 292646 251651 TRUE FALSE 270677.3997 258494.5734 267048.673 279826.0916 256141.2596 302497.4736 253904.7938 217469.4867 259426.053 234606.4536 1.153750869 1.101822091 1.138283576 1.192746778 1.091791192 1.289382576 1.082258352 0.926954409 1.105792483 1 17.83988317 1.999339306 25 1.003251173 1.158317332 0.516959077 0.06538319 16.91707798 640134.4376 0.023485035 0.017143677 99.84798513 -1.999339306 0.155066159 HGS(ph)PTAPICLGSPEFTDQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGSPTAPICLGSPEFTDQGR 20 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 HGS(0.958)PT(0.042)APICLGSPEFTDQGR 165.74 1.05E-11 261490000 226650 201930 157610 187050 196960 200610 183880 116590 267530 240750 TRUE FALSE 217792.2674 196171.1541 186093.633 196703.6729 203295.3973 204666.4716 186130.3784 114182.3758 237161.116 224443.7881 0.970364425 0.874032451 0.829132473 0.876405066 0.905774221 0.911882986 0.829296191 0.508734845 1.056661528 1 17.77599464 1.999365593 24.95835386 0.767664226 0.88872078 0 0.146954061 47.25650027 1859175.086 0.054442863 0.039741257 99.85402892 -1.999365593 0.121056554 KDDTDDEIAK ddPTM_BT-474_Pertuzumab_2h_R1 5 KDDTDDEIAK 10 1 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 ;;;; 199.8 4.36E-07 4753000000 5703520 7113250 4681020 6793900 4754730 3698020 7388920 11371450 10239630 6490410 FALSE TRUE 5480620.133 6910387.075 5526984.443 7144533.993 4907670.209 3772796.498 7479347.813 11136625.58 9077270.13 6050808.75 0.905766545 1.142060072 0.913429043 1.180756869 0.811076736 0.623519376 1.236090599 1.840518523 1.500174688 1 22.52869655 1.999369058 24.94437182 1.539792687 0.943198227 0.465991439 0.24521417 15.65536451 618953.4389 0.090127139 0.065792517 99.85482575 -1.999369058 -0.59659446 EAYPT(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAYPTPTK 8 0 Q9BZF1-3;Q9BZF1-2;Q9BZF1;F8VZB8;F8VVD3;F8VVE7;F8VZ43;F8VQX7 Q9BZF1-3 OSBPL8 Oxysterol-binding protein-related protein 8;Oxysterol-binding protein 1 EAYPT(0.958)PT(0.042)K;EAY(0.002)PT(0.997)PTK 99.568 0.024838 184820000 578710 767330 543030 725620 591940 612860 729340 962870 786000 738960 TRUE FALSE 556093.3734 745446.4997 641167.6006 763069.3352 610980.2877 625252.4491 738265.8811 942986.398 696776.5752 688909.581 0.80720807 1.082067256 0.930699207 1.107648023 0.88688023 0.907597261 1.07164409 1.368810108 1.011419487 1 19.39395512 1.999392124 12.96280469 1.180852272 0.964681069 0.244035109 0.128928787 0.089264242 1103.072853 0.047336409 0.033802044 99.8601293 -1.999392124 -0.216171203 AGHDDVPPLS(ph)PLLPPMQNNQIQR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGHDDVPPLSPLLPPMQNNQIQR 23 0 O14544 O14544 SOCS6 Suppressor of cytokine signaling 6 1 AGHDDVPPLS(1)PLLPPMQNNQIQR 106.63 0.00091754 170500000 87945 112800 78989 93433 111390 112370 82775 71926 72793 78514 TRUE FALSE 84508.01217 109583.0544 93264.0694 98255.08833 114972.9605 114642.1984 83788.02521 70440.70297 64529.84381 73196.17685 1.154541341 1.497114455 1.274165857 1.342352737 1.570750898 1.566232054 1.14470494 0.962354948 0.881601288 1 16.15948068 1.999488939 3.717700171 0.957032364 1.404123416 0.725994104 0.125311809 0.120518445 3.55385324 0.058102027 0.0360486 99.88239309 -1.999488939 0.447091053 DRFVGQSEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRFVGQSEGK 10 1 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 133.32 0.00018262 356070000 384400 351070 325280 378380 369620 325420 397160 472580 453120 468420 FALSE TRUE 369377.223 341057.8273 384065.3318 397908.2371 381509.163 332000.2154 402020.5629 462821.0579 401683.7172 436693.4962 0.845850067 0.781000474 0.879484891 0.911184253 0.873631429 0.760259125 0.920601214 1.059830435 0.91982986 1 18.73626152 1.999710677 24.9857004 0.997454909 0.845016326 0.627114452 0.052526603 6.24046259 538945.9789 0.019947676 0.014571854 99.93340312 -1.999710677 -0.152438583 EGTAPS(ph)ENGETK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGTAPSENGETK 12 0 Q15651;A0A087WZE9 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 EGTAPS(1)ENGETK;EGTAPS(1)ENGETK;EGTAPS(1)ENGETK;EGTAPS(1)ENGETK 242.92 2.69E-16 935529000 1809390 1446955 1372147 1580564 1575705 1289385 1742080 2252480 2017740 1853260 TRUE FALSE 1738677.038 1405689.26 1620124.486 1662137.097 1626388.982 1315457.248 1763400.096 2205965.501 1788694.614 1727737.049 1.006331976 0.813601387 0.937714733 0.962031287 0.941340572 0.76137584 1.020641478 1.276794696 1.035281737 1 20.72045223 1.999805315 24.99999904 1.138264867 0.904328844 0.457110668 0.096849853 4.807409951 617372.8243 0.034894836 0.025493314 99.95518211 -1.999805315 -0.233936023 LIDLES(ph)PTPESQK ddPTM_BT-474_Pertuzumab_2h_R1 6 LIDLESPTPESQK 13 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LIDLES(0.65)PT(0.35)PESQK;LIDLES(0.701)PT(0.299)PESQK;LIDLES(1)PTPESQK;LIDLES(0.975)PT(0.025)PESQK;LIDLES(0.969)PT(0.031)PESQK;LIDLES(0.981)PT(0.019)PESQK 327.94 2.53E-62 3799000000 4339660 4210420 3538930 3933880 3956950 3883790 4236520 4833240 4793050 4514830 TRUE FALSE 4170061.289 4090342.944 4178493.374 4136908.018 4084228.89 3962322.895 4288367.799 4733431.905 4248963.058 4209036.543 0.990740101 0.971800293 0.99274343 0.982863412 0.970347691 0.941384769 1.018847842 1.12458798 1.009485904 1 22.0050586 1.999852374 19.53007252 1.061830349 0.976150932 0.428331598 0.035065592 0.225180661 29501.28692 0.012793273 0.009282488 99.96601357 -1.999852374 -0.085679417 EGQEKEESKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGQEKEESKK 10 2 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 54.143 0.078193 266622000 802202 655736 483515 477389 670190 673374 742506 847456 962361 965512 FALSE TRUE 770851.059 637035.0513 570896.9162 502027.1035 691747.27 686990.0836 751593.0105 829955.7375 853117.8138 900117.0123 0.856389834 0.70772471 0.634247446 0.55773538 0.768508161 0.763223086 0.834994784 0.922053162 0.947785457 1 19.77975303 1.999891475 1.089095677 0.98182238 0.69138676 0.695538526 0.073650089 0.292322712 0.639255362 0.060280822 0.028116972 99.97501431 -1.999891475 -0.29043562 NHSGS(ph)RTPPVALNSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.034)GS(0.778)RT(0.187)PPVALNSSR 129.32 3.38E-05 157000000 98805 108050 49551 55935 88446 93048 56414 20389 53788 27114 TRUE FALSE 94943.59137 104968.5198 58505.96796 58821.81205 91290.94591 94929.49431 57104.41141 19967.96002 47682.21174 25277.54463 3.756044852 4.152639085 2.314543157 2.327038204 3.611543259 3.755487161 2.259096453 0.789948562 1.886346654 1 14.62556871 2.000109577 4.417440379 1.251101057 3.272904675 0.695639953 0.622238058 0.120018561 5.800964523 0.285452306 0.184427023 100.0252342 -2.000109577 2.021803618 LRLDTGS(ph)PEPETR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRLDTGSPEPETR 13 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LRLDT(0.411)GS(0.588)PEPETR 61.87 0.087357 0 127720 154110 101060 121120 122650 160680 122470 110620 122230 134500 TRUE FALSE 122728.5612 149714.9337 119323.7901 127371.0177 126595.1486 163929.0597 123968.8245 108335.6583 108354.9628 125390.1952 0.978773189 1.193992349 0.951619781 1.015797268 1.00960963 1.307351499 0.988664419 0.863988274 0.864142229 1 16.93606502 2.00030955 24.99999676 0.902279877 1.07660275 0.333264995 0.106241236 11.34782177 916418.844 0.039649068 0.029005166 100.071302 -2.00030955 0.174322873 DAVFDGSSCIS(ph)PTIVQQFGYQR ddPTM_BT-474_Pertuzumab_2h_R1 3 DAVFDGSSCISPTIVQQFGYQR 22 0 P04049;P04049-2;A0A0B4J1W9 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 DAVFDGSSCIS(1)PTIVQQFGYQR;DAVFDGSSCIS(0.999)PTIVQQFGYQR;DAVFDGSSCIS(0.982)PT(0.017)IVQQFGYQR 209.16 3.88E-23 230729000 168465 172410 159362 212206 214145 229538 171060 138008 165350 173179 TRUE FALSE 161881.2016 167493.0356 188162.2584 223157.9771 221033.1684 234179.4156 173153.4834 135158.0866 146580.1612 161449.4321 1.002674333 1.037433415 1.165456304 1.382215931 1.3690551 1.450481508 1.072493605 0.837154302 0.907901374 1 17.30072284 2.000413385 24.9604162 0.911399404 1.237461922 0.511809032 0.140479142 11.95357088 721725.5976 0.059785782 0.043738213 100.0952306 -2.000413385 0.326062519 HKEDKDDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 HKEDKDDRR 9 3 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 40.496 0.096813 159660000 297190 258580 208180 222280 267020 258390 237340 169900 325900 289900 FALSE TRUE 285575.4862 251205.5516 245802.7569 233751.8974 275608.9408 263614.8228 240244.6379 166391.5056 288905.1983 270264.8148 1.056650628 0.929479303 0.909488559 0.864899479 1.019773665 0.975394533 0.888923103 0.615660998 1.068970811 1 18.04401418 2.00046803 24.43702872 0.827202745 0.952292411 0 0.12610662 21.06127656 1099590.96 0.04685723 0.034271166 100.107826 -2.00046803 0.125089666 SS(ph)VEKENQK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSVEKENQK 9 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(0.009)S(0.991)VEKENQK;S(0.388)S(0.612)VEKENQK;S(0.128)S(0.872)VEKENQK 168.02 3.61E-05 3335370000 3457730 2639710 2477430 2268490 2592780 2615030 3064230 3433650 3690720 3830870 TRUE FALSE 3322598.089 2564428.055 2925156.711 2385567.041 2676179.123 2667907.698 3101730.963 3362743.928 3271764.938 3571401.763 0.930334448 0.718045245 0.819050027 0.667963785 0.749335779 0.747019763 0.868491189 0.941575368 0.916101059 1 21.76805901 2.000491448 2.575204536 0.946792216 0.765684912 0.583252639 0.068404215 0.197394868 2.470409723 0.034152316 0.019163079 100.1132242 -2.000491448 -0.181107304 FPQS(ph)PHSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 FPQSPHSGR 9 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 FPQS(1)PHSGR;FPQS(1)PHSGR;FPQS(1)PHSGR 94.191 0.0057255 131090000 184053 249499 212729 351070 289362 366387 255212 228130 230059 277533 TRUE FALSE 176860.0053 242383.5328 251173.8624 369188.7648 298669.5915 373795.5962 258335.3608 223419.0358 203943.6668 258735.4427 0.683555385 0.936800657 0.970774857 1.42689676 1.154343558 1.444701941 0.998453703 0.863503792 0.78823243 1 17.98111817 2.000504224 24.99842634 0.884304018 1.115966278 0.169370016 0.216662346 30.43413069 1508803.214 0.087313062 0.063889162 100.1161693 -2.000504224 0.23166226 SGLTVPT(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGLTVPTSPK 10 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 SGLTVPT(0.669)S(0.331)PK 105.46 0.028462 5518500000 4909100 4367100 3218300 3577700 4474300 3570000 4364300 5499500 4994200 3738200 TRUE FALSE 4717246.945 4242554.584 3799918.401 3762345.526 4618219.923 3642187.846 4417711.609 5385933.403 4427279.353 3485008.384 1.353582667 1.217372848 1.090361337 1.07958005 1.325167521 1.045101602 1.267632993 1.545457804 1.270378394 1 21.7327307 2.000533707 24.99998405 1.351050221 1.181613091 0 0.160116111 29.16565569 1366132.711 0.058141637 0.042542301 100.1229662 -2.000533707 -0.16943713 EIEELKQELIQAEIQNGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIEELKQELIQAEIQNGVK 19 1 Q12904;Q12904-2;A0A5F9ZHC5;D6R937 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 209.85 1.86E-16 437990000 759350 766190 621380 593440 692870 722870 759970 899850 950110 916440 FALSE TRUE 729673.7625 744339.0114 733677.1885 624067.5095 715156.7928 737486.9267 769270.7402 881267.783 842257.496 854368.7025 0.854050201 0.871215213 0.858736031 0.730442849 0.837058744 0.863195157 0.900396676 1.03148416 0.985824379 1 19.70449927 2.000592529 2.232429751 1.009271083 0.831724726 0.787358564 0.03937354 0.140092746 1.304526534 0.022903015 0.01230581 100.1365279 -2.000592529 -0.177546357 S(ph)NGDLSPK ddPTM_BT-474_Pertuzumab_2h_R1 6 SNGDLSPK 8 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 S(1)NGDLSPK;S(1)NGDLSPK;S(1)NGDLSPK;S(1)NGDLSPK;S(1)NGDLSPK;S(1)NGDLSPK 157.03 0.00040228 13840060000 12345420 11147610 10570260 10537200 10631050 9958760 12113490 14871700 13571290 13022140 TRUE FALSE 11862947.34 10829691.08 12480541.12 11081026.15 10973007.38 10160132.95 12261738.51 14564594.2 12030734.05 12140138.86 0.977167352 0.892056607 1.028039404 0.912759424 0.903861768 0.836904179 1.010016332 1.199705734 0.990988175 1 23.53328159 2.000636161 24.98778689 1.090530886 0.926500148 0.415113612 0.072674772 16.36982751 642967.6127 0.026723641 0.019560186 100.1465887 -2.000636161 -0.164030738 GHQLLEEVTQGDMSAADTFLSDLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHQLLEEVTQGDMSAADTFLSDLPR 25 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 ; 218.93 1.38E-33 112334000 46709 52768 43703 48543 48410 56742 46597 40800 51282 49628 FALSE TRUE 44883.56064 51263.10831 51601.10427 51048.31005 49967.15161 57889.36212 47167.26802 39957.46574 45460.68235 46266.65136 0.970106099 1.107992621 1.115298012 1.103350006 1.079982021 1.251211411 1.019465785 0.863634272 0.982579915 1 15.49768506 2.000682173 24.99249287 0.935577228 1.106713356 0.486089532 0.072026228 16.6240654 609028.1434 0.026468214 0.019377935 100.1571996 -2.000682173 0.171136128 ESVS(ph)PEDSEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ESVSPEDSEK 10 0 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 ESVS(1)PEDSEK;ESVS(1)PEDSEK;ESVS(1)PEDSEK 267.07 8.87E-18 2222250000 3420530 2791170 2697270 2654780 2949480 2840500 3042870 3553460 3355100 2924680 TRUE FALSE 3286851.906 2711568.564 3184726.689 2791793.514 3044352.703 2897936.856 3080109.553 3480079.809 2974243.114 2726588.819 1.205481327 0.994491192 1.168026021 1.023914385 1.116542649 1.062843373 1.129656783 1.276349329 1.090829352 1 21.37866572 2.000798036 24.90049731 1.16557454 1.092057125 0 0.089176609 50.89226264 1587894.935 0.031361976 0.022960193 100.1839235 -2.000798036 -0.073517415 LKFS(ph)DDEEEEEVVK ddPTM_BT-474_Pertuzumab_2h_R1 6 LKFSDDEEEEEVVK 14 1 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK 224.89 1.80E-12 1529100000 2104490 1616653 1723399 1563083 1790711 1680350 2242960 2871880 3062980 2818780 TRUE FALSE 2022244.204 1570547.639 2034855.536 1643753.901 1848310.846 1714327.828 2270410.015 2812574.674 2715283.351 2627861.52 0.769539867 0.59765236 0.774338952 0.625510092 0.703351692 0.652366122 0.863976278 1.070290292 1.03326729 1 21.32545782 2.000801026 3.095390271 1.037147458 0.685197249 0.884760479 0.056280559 0.070047505 1.315679828 0.024821778 0.014694739 100.1846134 -2.000801026 -0.351950209 SSDQPLTVPVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 8 SSDQPLTVPVSPK 13 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK 296.95 1.05E-40 11773700000 11243070 9829030 8989350 8703310 9635860 9105860 10090570 11962160 10157630 10598500 TRUE FALSE 10803678.39 9548715.688 10613925.51 9152488.872 9945806.188 9289986.728 10214061.41 11715137.22 9004578.427 9880654.155 1.093417321 0.966405214 1.074212835 0.92630394 1.006593899 0.940219806 1.03374344 1.18566413 0.911334238 1 23.23617513 2.000829461 24.99792209 1.067147548 0.998705753 0 0.082019838 56.90899002 1715058.521 0.029854682 0.021845948 100.1911729 -2.000829461 -0.068441795 QNVAYEYLCHLEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 QNVAYEYLCHLEEAK 15 0 P46940;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 154.82 2.41E-06 40204000 71301 64644 62297 73533 67630 59805 75395 88914 84177 97166 FALSE TRUE 68514.47809 62800.41641 73555.45369 77328.04694 69805.38037 61014.29808 76317.70656 87077.89483 74621.57986 90584.86027 0.756356834 0.693277179 0.81200604 0.853653102 0.770607585 0.673559554 0.842499578 0.961285303 0.823775404 1 16.46698233 2.000839924 8.086642605 0.918794654 0.763376983 0.581551309 0.064055483 0.084757193 51.98029752 0.025274677 0.017692426 100.1935869 -2.000839924 -0.15541767 IQYQLVDISQDNALRDEMR ddPTM_BT-474_Pertuzumab_2h_R1 6 IQYQLVDISQDNALRDEMR 19 1 Q5T123;Q9H299 Q5T123 SH3BGRL3 SH3 domain-binding glutamic acid-rich-like protein 3 0 ;;;;; 250.94 1.35E-25 7288470000 1692000 1916250 1435470 1812170 2005220 2049110 1781800 1756990 1946450 1824900 FALSE TRUE 1625874.769 1861600.426 1694891.361 1905696.311 2069719.722 2090544.408 1803606.201 1720707.543 1725497.156 1701297.898 0.955667301 1.094223668 0.996234324 1.120142636 1.216553389 1.228793859 1.060135444 1.011408728 1.014223998 1 20.69820435 2.000895708 24.99903609 1.016301915 1.106288699 0.216062448 0.079117695 51.10550641 1426323.302 0.032620172 0.023874382 100.2064571 -2.000895708 0.089986783 DKYVGVSSDSVGGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKYVGVSSDSVGGFR 15 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 171.26 9.97E-07 1035370000 679620 717370 575060 609000 639630 709740 658030 668680 721580 728550 FALSE TRUE 653059.699 696911.31 678986.1341 640430.563 660204.2798 724091.4291 666083.168 654871.5243 639669.2635 679204.6596 0.961506506 1.026069683 0.999678263 0.942912499 0.972025546 1.066087252 0.980681093 0.964174075 0.94179163 1 19.37348683 2.000917021 24.99997692 0.966612821 0.995512227 0.101209247 0.034847432 66.619582 1816151.858 0.01342525 0.00983427 100.211375 -2.000917021 0.028899407 S(ph)DSELEVKPAESLLR ddPTM_BT-474_Pertuzumab_2h_R1 6 SDSELEVKPAESLLR 15 1 Q92539 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 S(0.996)DS(0.004)ELEVKPAESLLR;S(0.967)DS(0.033)ELEVKPAESLLR;S(0.983)DS(0.017)ELEVKPAESLLR;S(0.999)DS(0.001)ELEVKPAESLLR;S(0.987)DS(0.013)ELEVKPAESLLR;S(0.997)DS(0.003)ELEVKPAESLLR 256.33 5.72E-25 3272620000 2433260 2230670 2066960 2242840 2350620 2146970 2582480 3244370 3136330 2792440 TRUE FALSE 2338165.509 2167053.476 2440505.651 2358593.241 2426229.827 2190383.204 2614085.163 3177372.626 2780306.967 2603305.552 0.898152546 0.832423791 0.93746416 0.90599939 0.93198043 0.84138537 1.00414074 1.220514674 1.067991026 1 21.31191322 2.000934045 5.8632628 1.119606101 0.89470616 0.692304226 0.061092254 0.072988686 9.705032376 0.023632885 0.016041801 100.2153031 -2.000934045 -0.224899941 EAPPMEKPEVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAPPMEKPEVVK 12 1 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 ; 112.15 0.0011897 614550000 678790 627760 542930 537910 575740 655950 681050 752940 917820 798270 FALSE TRUE 652262.1364 609856.8994 641049.5284 565671.5996 594259.2 669213.7584 689384.8936 737391.5259 813632.9214 744202.4619 0.876457913 0.819477132 0.861391303 0.760104445 0.798518186 0.899236152 0.926340517 0.990848007 1.093295122 1 19.50533564 2.00100312 1.351092177 1.042314241 0.823791434 0.824079221 0.040804008 0.169515973 0.575486988 0.029163857 0.013715504 100.231244 -2.00100312 -0.218522807 (ac)S(ph)DNGELEDKPPAPPVR ddPTM_BT-474_Pertuzumab_2h_R1 5 SDNGELEDKPPAPPVR 16 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR 87.001 5.96E-09 1661390000 1766020 1771360 1429890 1572700 1634990 1705320 1807090 2179990 2205680 2109030 TRUE FALSE 1697001.986 1720842.547 1688302.931 1653867.235 1687580.938 1739802.739 1829205.708 2134972.445 1955300.453 1966183.52 0.8630944 0.875219698 0.858670065 0.841156087 0.85830286 0.884862843 0.93033315 1.085845967 0.994464878 1 20.90696656 2.001080861 3.25195326 1.03359837 0.862932885 0.882360821 0.026526034 0.070048448 1.47777363 0.012231904 0.007343314 100.2491873 -2.001080861 -0.170665485 EQEPMPTVDSHEPR ddPTM_BT-474_Pertuzumab_2h_R1 6 EQEPMPTVDSHEPR 14 0 A6NGP5;Q9H910;Q9H910-3;Q9H910-2;H3BU16 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ;;;;; 216.54 6.09E-12 3229860000 1523907 1587719 1329971 1570169 1555530 1588771 1508427 1451189 1738048 1601784 FALSE TRUE 1464351.03 1542438.809 1570326.345 1651205.61 1605565.035 1620897.038 1526887.581 1421221.44 1540752.078 1493293.743 0.980618205 1.032910515 1.051585699 1.105747358 1.075183662 1.085450901 1.02249647 0.951736018 1.031780977 1 20.51006655 2.001123188 9.429196603 0.988603309 1.057031547 0.357132142 0.036488979 0.098991108 147.0480003 0.014855359 0.010505795 100.2589584 -2.001123188 0.068428238 RRS(ph)QSIEQESQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 RRS(0.943)QS(0.057)IEQESQEK 102.03 0.001356 258260000 124030 124290 71295 105930 112050 118040 97972 83529 116250 79189 TRUE FALSE 119182.7705 120745.3709 84179.59245 111397.06 115654.19 120426.8497 99171.01064 81804.09696 103053.7874 73825.4585 1.614385781 1.635551927 1.140251536 1.50892473 1.566589526 1.63123741 1.343317233 1.10807435 1.395911241 1 16.17183079 2.001162864 5.493191658 1.18881527 1.506098104 0.476648224 0.163396366 0.155692978 15.98327588 0.067480458 0.045414272 100.2681182 -2.001162864 0.317282834 QPLSEASNQQPLS(ph)GGEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPLSEASNQQPLSGGEEK 18 0 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 QPLSEASNQQPLS(1)GGEEK 322.15 1.09E-61 170970000 120980 117720 94536 100530 101910 103550 115000 131600 129730 133490 TRUE FALSE 116251.9678 114362.7409 111620.7581 105718.3653 105188.0277 105643.8519 116407.4044 128882.414 115003.5943 124448.6034 0.93413638 0.918955599 0.896922545 0.849494188 0.845232689 0.84889544 0.935385382 1.035627645 0.924105142 1 16.92519051 2.001225397 6.23302663 0.989698524 0.881978594 0.605539832 0.037872236 0.098087273 16.85760693 0.016014491 0.010959554 100.2825565 -2.001225397 -0.10771993 GCLTTPNS(ph)PSMHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GCLTTPNSPSMHSR 14 0 O75128-3;O75128;O75128-7;A0A0J9YWK3;A0A3B3IU00;O75128-5;O75128-4 O75128-3 COBL Protein cordon-bleu 1 GCLTTPNS(0.985)PS(0.015)MHSR;GCLTT(0.001)PNS(0.824)PS(0.175)MHSR 228.51 1.71E-12 650970000 291218 412560 298365 389360 308440 362787 315309 322786 329224 330499 TRUE FALSE 279836.8786 400794.1927 352286.1926 409454.9163 318361.2527 370122.8017 319167.8459 316120.3563 291851.8717 308114.0084 0.908225108 1.300798347 1.143363116 1.328907174 1.033257963 1.201252756 1.035875803 1.025985018 0.947220392 1 18.23310475 2.001236434 1.623437319 0.980378124 1.164415991 0.279820303 0.11649819 0.453781028 2.232659608 0.070340317 0.034394207 100.2851051 -2.001236434 0.184037866 APQVDVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 APQVDVDK 8 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 99.802 0.018836 0 275330 255510 222210 300920 248580 243300 281340 322380 327240 317140 FALSE TRUE 264569.7992 248223.105 262368.29 316450.5173 256575.8015 248219.6927 284783.1231 315722.7403 290093.0871 295659.8253 0.89484528 0.839556422 0.887399192 1.070319638 0.867807458 0.83954488 0.963212106 1.067858103 0.981171814 1 18.1735787 2.001241713 9.700094259 1.021863911 0.902715009 0.396735984 0.064680472 0.09826735 172.7672542 0.026133443 0.018515773 100.286324 -2.001241713 -0.119148902 TGENVEDAFLEAAKK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGENVEDAFLEAAKK 15 1 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 ; 146.76 6.14E-06 205280000 443720 511190 334940 374680 362250 429320 483440 593280 718360 505510 FALSE TRUE 426378.9318 496611.3617 395471.1087 394017.2797 373902.1002 438001.1446 489356.4833 581028.5607 636814.7844 471271.3574 0.904741876 1.053769455 0.839157955 0.836073047 0.79339025 0.929403278 1.038375186 1.232895977 1.351269867 1 18.84619848 2.001368924 2.499643236 1.217728438 0.889303186 0.625503342 0.104471475 0.175791378 2.067276231 0.054693281 0.030442033 100.3157038 -2.001368924 -0.328425252 VKGDMDVSLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKGDMDVSLPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 124.86 0.00031045 1837290000 4609000 4429700 3821000 4102000 3685700 3728100 4364600 5002000 5053200 4555800 FALSE TRUE 4428875.184 4303369.293 4511539.698 4313704.712 3804253.888 3803484.736 4418015.28 4898706.952 4479581.921 4247231.608 1.042767523 1.013217477 1.062230675 1.015650925 0.89570201 0.895520915 1.040210586 1.153388231 1.054706297 1 22.01809135 2.001370968 24.99911953 1.089005844 0.987408377 0.24172537 0.06342217 52.95520579 965609.9972 0.025626699 0.01878025 100.3161758 -2.001370968 -0.101597467 SELVAMLEEEELRK ddPTM_BT-474_Pertuzumab_2h_R1 6 SELVAMLEEEELRK 14 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;;;;; 304.42 5.69E-44 1954854000 997400 993305 776092 880574 966650 938109 1008032 1199588 1210987 1096194 FALSE TRUE 958420.5053 964976.9139 916349.0885 926020.5297 997743.1751 957078.2067 1020368.597 1174816.089 1073520.833 1021947.804 0.937837042 0.944252642 0.896669169 0.906132902 0.9763152 0.936523571 0.998454709 1.149585218 1.050465423 1 19.96289008 2.001431245 4.450045212 1.082387 0.933886457 0.679688414 0.040742659 0.09787835 4.841101507 0.017161043 0.011129827 100.3301 -2.001431245 -0.148500544 GHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.177)GS(0.823)DDETGKLQGSGVSLASK;GHYEVT(0.179)GS(0.821)DDET(0.001)GKLQGSGVSLASK;GHYEVT(0.179)GS(0.821)DDETGKLQGSGVSLASK;GHYEVT(0.098)GS(0.902)DDETGKLQGSGVSLASK 269.74 1.69E-46 11317960000 3769130 3334670 3330150 3023210 3043160 3332890 3629560 3829120 4552260 3931330 TRUE FALSE 3621828.233 3239568.477 3931982.184 3179238.23 3141046.005 3400283.319 3673979.641 3750047.334 4035506.529 3665057.517 0.988205019 0.883906586 1.072829598 0.867445658 0.857025024 0.927757151 1.002434375 1.023189218 1.101075907 1 21.80540441 2.001455586 2.354102075 1.045218797 0.930738183 0.372048086 0.064029282 0.323514118 3.359050916 0.034546097 0.01888227 100.3357234 -2.001455586 -0.114480614 KLTATPTPLGGMTGFHMQTEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLTATPTPLGGMTGFHMQTEDR 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 263.83 1.25E-37 1350790000 962320 1110130 804530 825450 885570 1092730 914950 868160 1033810 944400 FALSE TRUE 924711.4705 1078470.179 949926.4677 868051.5734 914055.1633 1114825.749 926147.4318 850232.1926 916456.2229 880434.9468 1.050289376 1.224928864 1.078928626 0.985934937 1.038185918 1.266221603 1.051920344 0.965695644 1.040913047 1 19.74785689 2.001513985 24.99849347 1.000995457 1.107482839 0.255783791 0.080928633 67.78609029 1119247.482 0.031439057 0.023047601 100.3492162 -2.001513985 0.106487382 THTTALAGRS(ph)PS(ph)PASGRR ddPTM_BT-474_Pertuzumab_2h_R1 6 THTTALAGRSPSPASGRR 18 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(1)PS(0.995)PAS(0.005)GRR;THTTALAGRS(0.999)PS(0.946)PAS(0.055)GRR;THTTALAGRS(1)PS(0.967)PAS(0.034)GRR;THTTALAGRS(0.982)PS(0.639)PAS(0.379)GRR;THTTALAGRS(0.997)PS(0.903)PAS(0.1)GRR;THTTALAGRS(0.999)PS(0.974)PAS(0.026)GRR 127.92 1.31E-05 2625006000 672222 936828 447666 570105 597164 831658 489120 156258.2 524547 395311 TRUE FALSE 645950.8211 910110.5827 528569.2045 599528.1874 616372.3224 848474.6946 495105.9969 153031.4136 465002.6236 368536.2339 1.752747116 2.469528093 1.434239448 1.626782206 1.672487712 2.302282969 1.343439129 0.415241161 1.26175551 1 18.49144694 2.001534256 7.528960725 0.838392603 1.860740697 0.614099239 0.351293124 0.074239808 31.02882987 0.136038516 0.094883199 100.3539002 -2.001534256 1.022348094 PDYLGADQR ddPTM_BT-474_Pertuzumab_2h_R1 1 PDYLGADQR 9 0 P35998;C9JLS9 P35998 PSMC2 26S protease regulatory subunit 7 0 75.378 0.057859 0 331080 273180 248070 255600 279590 238260 309320 351360 388770 366820 FALSE TRUE 318141.0276 265389.1739 292901.7673 268791.5466 288583.2663 243077.7804 313105.5507 344104.2932 344638.4595 341974.9547 0.930305051 0.776048568 0.856500639 0.785997755 0.843872519 0.710805798 0.915580356 1.006226592 1.007788596 1 18.38353114 2.001571705 5.282712588 0.996470319 0.8161274 0.706672369 0.054288563 0.08893501 7.877242466 0.021259166 0.014233681 100.3625542 -2.001571705 -0.180342919 SVPGTTSSPLVGDIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVPGTTSSPLVGDISPK 17 0 Q9UQR0;H0Y6S1;B4DRC2;Q9UQR0-2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 SVPGTTSSPLVGDIS(1)PK;SVPGTTSSPLVGDIS(1)PK;SVPGTTSSPLVGDIS(1)PK;SVPGTTSSPLVGDIS(1)PK 268.26 6.61E-28 756403000 452933 401593 329072 322401 368523 358041 388370 433803 428792 418196 TRUE FALSE 435231.8776 390139.9608 388542.6306 339040.1542 380376.877 365280.8343 393122.9882 424844.8165 380117.3298 389871.2124 1.116347819 1.000689326 0.996592255 0.869620899 0.975647508 0.93692692 1.008340641 1.089705531 0.974981783 1 18.57263811 2.001604574 24.76731183 1.035903063 0.97813715 0.055699085 0.064285905 92.78408889 1432137.869 0.024882618 0.018237704 100.3701501 -2.001604574 -0.057765912 AKADS(ph)PVNGLPK ddPTM_BT-474_Pertuzumab_2h_R1 3 AKADSPVNGLPK 12 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 AKADS(1)PVNGLPK;AKADS(1)PVNGLPK;AKADS(1)PVNGLPK 161.08 4.02E-05 1169620000 2607130 2165510 1812610 1582090 1984140 2097570 2276950 2751830 2943750 2668920 TRUE FALSE 2505240.477 2103751.775 2140188.948 1663741.854 2047961.665 2139984.303 2304815.995 2695003.749 2609587.841 2488151.671 1.006868073 0.845507852 0.860152125 0.668665771 0.823085541 0.860069877 0.926316519 1.083134835 1.048805775 1 21.246643 2.001655624 2.654815663 1.050928557 0.835136333 0.557105162 0.079268881 0.202283188 2.702936329 0.042007237 0.023813134 100.3819492 -2.001655624 -0.215792224 QLS(ph)LPLTQSK ddPTM_BT-474_Pertuzumab_2h_R1 4 QLSLPLTQSK 10 0 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 1 QLS(0.999)LPLT(0.001)QSK;QLS(0.995)LPLT(0.005)QSK;QLS(0.988)LPLT(0.012)QSK;QLS(0.991)LPLT(0.009)QSK 157.22 1.00E-05 1236460000 2884580 2498290 1450860 2160670 2863870 1943930 2672570 3777140 2743600 2478150 TRUE FALSE 2771847.425 2427041.215 1713062.676 2272182.438 2955988.979 1983237.596 2705277.711 3699140.739 2432158.03 2310302.693 1.199776736 1.050529536 0.741488412 0.983499887 1.279481251 0.858431929 1.170962454 1.601149819 1.052744317 1 21.13965045 2.001692068 24.90014426 1.310083388 1.017667332 0.117766706 0.212763527 65.68558055 966604.3898 0.079171812 0.058053075 100.3903729 -2.001692068 -0.292416056 THTTALAGRS(ph)PSPASGR ddPTM_BT-474_Pertuzumab_2h_R1 1 THTTALAGRSPSPASGR 17 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 THT(0.001)T(0.001)ALAGRS(0.963)PS(0.034)PAS(0.001)GR 60.747 0.045804 48899000 20778 25214 18656 22218 19841 29536 20507 15517 23415 22992 TRUE FALSE 19965.97279 24494.92141 22027.5542 23364.67364 20479.20378 30133.23816 20757.9708 15196.56853 20757.02736 21434.73136 0.931477631 1.142767828 1.027657115 1.09003809 0.955421528 1.405813661 0.968426917 0.708969395 0.968382902 1 14.38766272 2.001693753 24.99999191 0.854760034 1.093735526 0.27690574 0.143141558 55.20705166 814851.7293 0.051656048 0.037881246 100.3907625 -2.001693753 0.238975492 EALGLGPPAAQLT(ph)PPPAPVGLR ddPTM_BT-474_Pertuzumab_2h_R1 5 EALGLGPPAAQLTPPPAPVGLR 22 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR 242.22 1.18E-29 2340313000 609160 695084 599135 833593 818167 747998 602994 600941 551438 593639 TRUE FALSE 585353.3537 675260.8849 707412.0222 876614.8346 844484.0846 763123.0321 610373.6209 588531.3583 488841.0701 553431.3018 1.057680243 1.22013497 1.27822915 1.583963234 1.525905893 1.378893875 1.102889589 1.063422608 0.883291329 1 19.07804472 2.001737754 2.240115269 0.980345914 1.351507438 0.551709143 0.146678162 0.262329257 2.46097513 0.089663018 0.048278654 100.4009343 -2.001737754 0.371161524 SESAPT(ph)LHPYSPLSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 S(0.001)ES(0.404)APT(0.556)LHPYS(0.04)PLSPK 225.09 8.05E-14 334780000 157310 120960 83585 107590 89758 72532 128620 171570 149850 158930 TRUE FALSE 151162.1513 117510.3392 98690.66884 113142.7328 92645.14759 73998.64674 130194.09 168027.0195 132839.6562 148165.5295 1.020224824 0.79310174 0.666083867 0.763623855 0.625281385 0.49943227 0.878707014 1.13404933 0.896562491 1 17.17685032 2.001742272 24.97390051 1.020418299 0.722061395 0.464501262 0.136531447 46.00751289 659467.4831 0.053036688 0.038894561 100.4019787 -2.001742272 -0.298356904 EELDFQK ddPTM_BT-474_Pertuzumab_2h_R1 4 EELDFQK 7 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 126.67 0.0091423 752831000 1512410 1428290 1448090 1559240 1458720 1246250 1637360 1882840 2011450 1921870 FALSE TRUE 1453303.345 1387556.568 1709792.076 1639712.563 1505641.054 1271450.029 1657398.501 1843958.696 1783118.629 1791700.033 0.811130947 0.774435755 0.954284782 0.915171364 0.840342148 0.709633312 0.925042402 1.029167083 0.995210468 1 20.77289769 2.00177668 24.99109234 1.00280118 0.838912686 0.596033665 0.064444575 42.20924977 593715.6601 0.026011715 0.01907673 100.4099336 -2.00177668 -0.163888493 EYGS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 8 EYGSPLK 7 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK 152.38 0.0019065 16035250000 12368820 11414300 10599750 11042830 11728650 11106210 12960610 13791800 16005500 14776870 TRUE FALSE 11885432.84 11088775.34 12515360.62 11612751.78 12105912.68 11330785.18 13119225.82 13506994.51 14188622.74 13776019.43 0.862762491 0.804933195 0.908488891 0.842968597 0.878767102 0.822500667 0.952323411 0.980471505 1.029950837 1 23.71565575 2.001789656 2.405028297 1.003716638 0.85421622 0.831116639 0.030647075 0.110644258 1.200912362 0.015510367 0.008536033 100.4129338 -2.001789656 -0.149500418 DKEIS(ph)PSVTKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKEISPSVTKK 11 2 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 DKEIS(0.946)PS(0.025)VT(0.029)KK;DKEIS(0.902)PS(0.093)VT(0.005)KK 128.06 0.00014277 532680000 833880 658330 649950 493050 679340 832460 800350 956350 1252830 1030080 TRUE FALSE 801291.0477 639555.073 767410.4231 518496.3696 701191.5881 849292.9116 810144.9227 936601.0383 1110613.991 960311.7641 0.834407197 0.665986919 0.799126338 0.539925042 0.730170778 0.884392906 0.84362699 0.975309346 1.156513991 1 19.87314333 2.001890277 1.126357719 1.071168779 0.711356344 0.695960074 0.092279204 0.268958579 0.629886405 0.069904732 0.032574701 100.436201 -2.001890277 -0.359812435 SRS(ph)ESETSTMAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.007)RS(0.88)ES(0.098)ET(0.005)S(0.009)T(0.002)MAAK;S(0.012)RS(0.482)ES(0.482)ET(0.022)S(0.002)TMAAK;S(0.15)RS(0.574)ES(0.276)ETSTMAAK;S(0.41)RS(0.585)ES(0.004)ETSTMAAK 171.04 1.56E-05 2467240000 2166660 1983720 1595540 1774230 1920680 1882580 1998650 2373570 2151750 1956890 TRUE FALSE 2081984.532 1927146.248 1883889.571 1865798.223 1982460.417 1920647.057 2023110.077 2324554.95 1907492.361 1824348.097 1.141221094 1.056347882 1.032637123 1.022720514 1.086667846 1.052785409 1.108949591 1.274183887 1.04557478 1 20.7989496 2.001974775 16.27875421 1.150679281 1.06405026 0 0.076388899 1.212264193 9964.110295 0.028287148 0.020514703 100.455744 -2.001974775 -0.086629021 MMNGGHYTYSENRVEK ddPTM_BT-474_Pertuzumab_2h_R1 5 MMNGGHYTYSENRVEK 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;; 138.05 5.23E-06 1829780000 2119960 2470990 1605930 1925630 2064180 2459170 2037770 1942720 2252550 2189430 FALSE TRUE 2037109.619 2400519.785 1896157.275 2025011.995 2130576.224 2508896.102 2062708.839 1902602.153 1996849.967 2041137.956 0.998026426 1.176069348 0.92897066 0.992099524 1.043817846 1.229165376 1.010568067 0.932128153 0.978302305 1 20.96094226 2.00198199 24.99963601 0.964788636 1.061880757 0.193718821 0.083934798 97.85929028 1234319.088 0.032227051 0.023644418 100.457413 -2.00198199 0.097092121 NATDLQNSS(ph)MSEEELTK ddPTM_BT-474_Pertuzumab_2h_R1 3 NATDLQNSSMSEEELTK 17 0 Q5QNY5;P40855;P40855-5;H0YJ60 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 1 NATDLQNS(0.007)S(0.979)MS(0.014)EEELTK;NATDLQNS(0.002)S(0.772)MS(0.226)EEELTK;NATDLQNSS(0.747)MS(0.253)EEELTK 437.58 1.37E-161 1142310000 1866820 1746900 1678790 1477690 1719790 1738610 1846600 2120920 2190940 2150080 TRUE FALSE 1793862.611 1697080.122 1982184.697 1553953.758 1775108.607 1773765.885 1869199.243 2077122.261 1942233.676 2004453.167 0.89493865 0.846654914 0.988890502 0.775250719 0.88558248 0.884912611 0.932523281 1.036253825 0.968959369 1 20.93477728 2.001997334 3.298875557 1.003777564 0.878658467 0.527954737 0.0516759 0.181117305 3.957101561 0.023287647 0.014051135 100.4609623 -2.001997334 -0.125119097 ARGDS(ph)EALDEES ddPTM_BT-474_Pertuzumab_2h_R1 5 ARGDSEALDEES 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 ARGDS(1)EALDEES;ARGDS(1)EALDEES;ARGDS(1)EALDEES;ARGDS(1)EALDEES;ARGDS(1)EALDEES 218.07 9.25E-11 10145970000 3976840 4539190 3508130 4195070 3947310 4057020 3829690 3616690 3797110 4054140 TRUE FALSE 3821420.696 4409736.746 4142127.129 4411578.065 4074278.811 4139055.724 3876558.892 3542004.088 3366077.992 3779549.487 1.01107836 1.166736078 1.095931445 1.167223258 1.077980015 1.095118807 1.025666923 0.937149811 0.890602968 1 21.84978285 2.002038888 2.082763836 0.933622543 1.108866436 0.681479283 0.048857122 0.164814046 1.334552904 0.026100877 0.013744358 100.4705751 -2.002038888 0.175243893 RDS(ph)LTGSSDLYK ddPTM_BT-474_Pertuzumab_2h_R1 6 RDSLTGSSDLYK 12 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(1)LTGSSDLYK;RDS(1)LTGSSDLYK;RDS(0.77)LT(0.186)GS(0.011)S(0.033)DLYK;RDS(0.995)LT(0.005)GSSDLYK;RDS(0.94)LT(0.056)GS(0.002)S(0.002)DLYK;RDS(0.841)LT(0.157)GS(0.001)S(0.002)DLYK 233.12 3.34E-16 4148310000 4387160 4551530 3927590 3925980 4160560 3332610 4464240 5077910 5409050 4912840 TRUE FALSE 4215704.937 4421724.821 4637392.882 4128600.298 4294388.191 3399997.658 4518874.705 4973049.384 4795037.321 4580088.971 0.920441713 0.965423346 1.012511528 0.901423602 0.937621129 0.742343146 0.986634699 1.08579755 1.046931042 1 22.12694419 2.002042857 24.9999378 1.049385995 0.91605212 0.429794024 0.068107292 60.37530269 738848.7603 0.026612086 0.019526188 100.4714933 -2.002042857 -0.133333874 IRS(ph)SVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IRSSVEK 7 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.5)S(0.5)VEK;IRS(0.647)S(0.353)VEK 93.096 0.0091971 7658600000 3816400 3361000 3356700 3542400 3384300 3074200 3829500 4390200 4631000 4405300 TRUE FALSE 3667250.869 3265147.571 3963330.359 3725223.689 3493159.083 3136362.43 3876366.567 4299540.836 4105308.295 4106925.107 0.892943205 0.795034603 0.965035947 0.907059075 0.850553393 0.763676558 0.943861031 1.046900229 0.99960632 1 21.96962721 2.002055204 24.94652833 1.014380159 0.864505361 0.618678407 0.054217921 41.46378484 503290.829 0.020989163 0.015397611 100.4743498 -2.002055204 -0.149874799 IYHLPDAES(ph)DEDEDFK ddPTM_BT-474_Pertuzumab_2h_R1 6 IYHLPDAESDEDEDFK 16 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0 Q15019-2 2-Sep Septin-2 1 IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK 334.03 7.63E-72 4017020000 3340810 2746090 3393590 3557990 3352410 3141590 4162210 4434410 5222500 5082100 TRUE FALSE 3210247.452 2667774.202 4006887.203 3741618.29 3460243.312 3205115.102 4213148.371 4342837.884 4629663.695 4737884.84 0.677569751 0.563072825 0.84571224 0.78972335 0.73033504 0.676486494 0.889246681 0.916619553 0.977158342 1 22.1758117 2.002058049 1.995591787 0.966920078 0.716097397 0.699922527 0.07469764 0.204484816 1.519681304 0.045834313 0.023819189 100.4750079 -2.002058049 -0.250822681 S(ph)FDASDTLALPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFDASDTLALPR 12 0 Q5JXC2 Q5JXC2 MIIP Migration and invasion-inhibitory protein 1 S(0.999)FDAS(0.001)DTLALPR;S(0.929)FDAS(0.071)DT(0.001)LALPR 174.29 3.23E-05 124587000 105948 83082 81085 91376 80564 74907 96584 119961 101260 110658 TRUE FALSE 101807.435 80712.58271 95738.86323 96091.92631 83155.41423 76421.67086 97766.02388 117483.7634 89765.38932 103163.0351 0.986859634 0.782378908 0.928034573 0.931456953 0.806058237 0.740785406 0.947684641 1.13881647 0.870131334 1 16.6545666 2.002082977 24.96876025 1.024617637 0.860963315 0.312580442 0.092986029 63.54314234 761686.9306 0.034309105 0.025171622 100.4807752 -2.002082977 -0.163654322 LAIRES(ph)IESEIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAIRESIESEIRR 13 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 LAIRES(1)IESEIRR;LAIRES(1)IESEIRR 198.85 6.40E-08 592070000 347760 346170 275420 325100 362710 402110 327510 317800 333370 347440 TRUE FALSE 334169.1547 336297.5705 325194.5207 341878.45 374376.8966 410240.9397 331518.1653 311237.3189 295527.2352 323907.5793 1.031680566 1.038251625 1.003973175 1.055481476 1.155813943 1.266537018 1.023496165 0.9608831 0.912381352 1 18.3052227 2.002091325 24.99971627 0.963103757 1.09161528 0.402543095 0.073542334 74.7774048 893879.3151 0.030902876 0.022675379 100.4827068 -2.002091325 0.128511523 IEGDNENKLPR ddPTM_BT-474_Pertuzumab_2h_R1 3 IEGDNENKLPR 11 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ;; 167.18 1.78E-05 1298630000 2934060 2804930 2148920 2118040 2402790 2707580 2582100 3038670 3312740 2966010 FALSE TRUE 2819393.691 2724936.143 2537277.646 2227352.298 2480077.923 2762329.123 2613700.512 2975920.403 2936691.643 2765119.501 1.019628154 0.985467768 0.917601444 0.805517554 0.896915277 0.998990865 0.945239622 1.076235729 1.062048726 1 21.3989104 2.002129479 1.841934332 1.05235618 0.927218816 0.376791242 0.06112413 0.364734712 2.309767054 0.039907233 0.020240492 100.4915348 -2.002129479 -0.125137364 IVDDWANDGWGLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 IVDDWANDGWGLKK 14 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 177.88 3.28E-06 1217710000 916200 1168630 709530 1073020 738560 765230 1044700 1381810 1242190 926800 FALSE TRUE 880393.8911 1135301.817 837757.8544 1128398.691 762316.4531 780703.4749 1057485.351 1353275.141 1101181.799 864027.0105 1.018942557 1.313965655 0.969596835 1.305976176 0.882283128 0.903563737 1.223903117 1.566241708 1.274476128 1 19.72071689 2.002157307 24.89997723 1.356134381 1.074261343 0.180223797 0.19204242 75.3143152 869280.6103 0.070275795 0.051566117 100.497974 -2.002157307 -0.281873037 GDLS(ph)DVEEEEEEEMDVDEATGAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDLSDVEEEEEEEMDVDEATGAVK 24 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 GDLS(1)DVEEEEEEEMDVDEATGAVK;GDLS(1)DVEEEEEEEMDVDEATGAVK 142.31 1.70E-07 277970000 157262 173113 151947 146575 155145 148849 167163 182206 196516 189720 TRUE FALSE 151116.0272 168175.9867 179407.2029 154139.7533 160135.3798 151858.8288 169208.7908 178443.3824 174208.3275 176870.0954 0.854389923 0.950844666 1.014344469 0.871485668 0.905384143 0.858589624 0.956684002 1.008895156 0.984950718 1 17.43233062 2.002189843 24.52303734 0.994900136 0.913435329 0.440396702 0.044968856 54.86486758 614398.1877 0.017653913 0.012952689 100.5055034 -2.002189843 -0.081464807 VLHTLEVLDSHSFER ddPTM_BT-474_Pertuzumab_2h_R1 1 VLHTLEVLDSHSFER 15 0 Q7Z3Z5;Q93074-3;Q93074;Q93074-2 Q7Z3Z5 TNRC11;MED12 Mediator of RNA polymerase II transcription subunit 12 0 105.46 0.00075946 27876000 15984 16462 13108 15631 17381 18936 13998 9533.5 16010 15067 FALSE TRUE 15359.32761 15992.51988 15476.90719 16437.71778 17940.07565 19318.89889 14169.31171 9336.629893 14192.61192 14046.49867 1.093463074 1.138541373 1.101833813 1.170235955 1.277191994 1.375353342 1.008743321 0.664694463 1.010402112 1 13.77792294 2.002278223 24.48735672 0.850011722 1.189239979 0.557522321 0.120283974 34.82076768 374264.252 0.045898772 0.03367107 100.5259585 -2.002278223 0.339228257 EEDEEPES(ph)PPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEDEEPESPPEK 12 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EEDEEPES(1)PPEK;EEDEEPES(1)PPEK;EEDEEPES(1)PPEK 270.79 1.12E-27 2030430000 692310 573670 635950 696020 625160 612850 810640 962240 1067370 1019400 TRUE FALSE 665253.7598 557309.4933 750880.3116 731941.6756 645268.8392 625242.2469 820560.8548 942369.4077 946206.6324 950355.13 0.700005439 0.586422355 0.79010497 0.770177013 0.678976541 0.657903795 0.863425502 0.991597118 0.995634792 1 19.8581072 2.002280793 2.855109687 0.992522227 0.698967064 0.858675667 0.054520093 0.09927994 1.554808706 0.028607281 0.016577696 100.5265535 -2.002280793 -0.293555163 VEGDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEGDLK 6 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 98.133 0.093712 362240000 900500 728920 764870 805630 786950 737870 886810 1090900 1049700 909430 FALSE TRUE 865307.4644 708131.9153 903099.0234 847208.6608 812262.9614 752790.237 897663.0461 1068372.534 930542.4567 847833.4961 1.020610142 0.835225216 1.065184411 0.999263021 0.958045377 0.887898674 1.058772802 1.260120694 1.097553306 1 19.69342144 2.002290127 9.507920651 1.151031059 0.962522881 0.395464577 0.086388127 0.080859645 119.2343111 0.032076615 0.022763256 100.528714 -2.002290127 -0.188508178 SAAEMYGSVTEHPSPS(ph)PLLSSSFDLDYDFQR ddPTM_BT-474_Pertuzumab_2h_R1 5 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGSVTEHPS(0.001)PS(0.999)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPSPS(1)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.001)PS(0.999)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.013)PS(0.985)PLLS(0.001)S(0.001)SFDLDYDFQR;SAAEMYGSVTEHPS(0.005)PS(0.981)PLLS(0.006)S(0.007)S(0.001)FDLDYDFQR 390.86 1.50E-155 794821000 240612 346393 355443 525476 420460 502302 360120 313859 314838 384809 TRUE FALSE 231208.617 336514.2108 419679.4569 552595.8793 433984.4778 512458.8906 364527.2563 307377.702 279098.9101 358745.5437 0.644491956 0.938030358 1.169852739 1.54035608 1.209727857 1.428474582 1.016116472 0.8568126 0.77798572 1 18.45260139 2.00231969 24.9631419 0.880883396 1.170639962 0.215214431 0.236852746 110.3019234 1186993.147 0.096253765 0.070641414 100.5355573 -2.00231969 0.289756566 VTEELLFELFHQAGPVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTEELLFELFHQAGPVIK 18 0 J3KPD3;Q9Y580;I3L521;F5GXV8;F5GY08;F5H606 J3KPD3 RBM7 RNA-binding protein 7 0 77.562 0.013371 33638000 58838 75494 55753 54124 73401 96212 62799 54401 67798 60214 FALSE TRUE 56538.54591 73340.98504 65828.80732 56917.34613 75762.00983 98157.47256 63567.55295 53277.60034 60101.85527 56135.65215 1.007177146 1.306495645 1.172673779 1.013925089 1.349623758 1.748576329 1.132391814 0.949086691 1.070653907 1 15.77662971 2.002364866 24.99978079 1.010877131 1.271629211 0.260500779 0.197085132 103.7866734 1097152.135 0.078448009 0.05758741 100.5460159 -2.002364866 0.26075208 LEDVEDELIREEVILS(ph)PVPSVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDVEDELIREEVILSPVPSVLK 23 1 Q4G0A6 Q4G0A6 FAM188B Protein FAM188B 1 LEDVEDELIREEVILS(1)PVPSVLK;LEDVEDELIREEVILS(0.995)PVPS(0.005)VLK 181.64 2.54E-17 40631000 76860 88715 66127 79881 92566 104887 74550 63267 69956 74968 TRUE FALSE 73856.22623 86184.93506 78077.61989 84003.66798 95543.46946 107007.887 75462.3652 61960.51434 62014.88816 69890.35059 1.056744252 1.233144981 1.117144488 1.201935135 1.367048078 1.531082418 1.079725092 0.886538897 0.887316885 1 16.09280566 2.002427238 24.99826457 0.929791818 1.252140777 0.576975471 0.126056138 55.68999318 573549.0548 0.051021897 0.037450822 100.560457 -2.002427238 0.322348958 VAVEYLDPS(ph)PEVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VAVEYLDPSPEVQK 14 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 1 VAVEYLDPS(1)PEVQK 180.74 1.80E-06 29244000 91312 85936 73507 82687 85207 76630 88984 104480 95825 95482 TRUE FALSE 87743.42609 83485.18942 86791.35005 86954.48598 87947.76054 78179.5111 90073.01281 102322.4515 84947.34773 89014.91909 0.985715956 0.937878619 0.975020266 0.976852946 0.988011464 0.878274248 1.011886701 1.149497776 0.954304611 1 16.44175953 2.002473272 24.99124216 1.058581809 0.958049357 0.259381472 0.056255628 72.58215656 733402.7047 0.020388164 0.01496697 100.5711166 -2.002473272 -0.100532451 PFSAPKPQT(ph)SPSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 PFSAPKPQTSPSPK 14 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 PFSAPKPQT(0.844)S(0.156)PSPK;PFSAPKPQT(0.831)S(0.166)PS(0.003)PK 143.67 1.47E-05 1421320000 910580 647860 719210 636450 735050 678010 928890 1005610 1303470 1031500 TRUE FALSE 874993.5269 629383.6671 849187.2457 669297.2608 758693.5508 691719.8267 940258.0337 984843.8021 1155505.55 961635.5862 0.909901359 0.654492904 0.883065537 0.695998849 0.7889616 0.719315962 0.977769591 1.024134107 1.201604399 1 19.87513076 2.002488863 2.311027561 1.083752027 0.771332507 0.69224119 0.090746693 0.155637303 1.556510495 0.045110147 0.024541122 100.5747272 -2.002488863 -0.31241952 SKWDEEWDKNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKWDEEWDKNK 11 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 136.99 4.94E-05 1937980000 3113500 2869800 1829730 1611130 2097940 1910180 2396060 2635130 3039300 2586110 FALSE TRUE 2991820.978 2787956.114 2160402.913 1694280.612 2165422.145 1948805.148 2425383.699 2580713.645 2694291.406 2410950.466 1.24093009 1.156372208 0.896079344 0.70274385 0.898161192 0.808314055 1.005986532 1.070413383 1.117522506 1 21.20117058 2.002556269 24.95328684 1.062401762 0.940644141 0.101027635 0.148864144 184.1462979 1797550.327 0.062218245 0.045680151 100.5903383 -2.002556269 -0.121757621 VEQVLSLEPQHELK ddPTM_BT-474_Pertuzumab_2h_R1 3 VEQVLSLEPQHELK 14 0 O95292;E5RK64;O95292-2 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ;; 199.58 2.05E-08 1401550000 1203780 1570810 907736 1384600 1149702 1050614 1403702 1862950 1612860 1234440 FALSE TRUE 1156734.947 1526012.037 1071784.088 1456059.372 1186683.209 1071858.135 1420880.925 1824479.431 1429774.894 1150830.279 1.005130789 1.326009633 0.931313771 1.265225115 1.031153968 0.931378114 1.23465723 1.585359253 1.242385537 1 20.13424365 2.002603794 24.82019903 1.358218201 1.091265472 0.152991216 0.184628928 84.59437019 806372.5972 0.065980137 0.04843634 100.6013466 -2.002603794 -0.266952728 LGASNS(ph)PGQPNSVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGASNSPGQPNSVKR 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 LGAS(0.278)NS(0.721)PGQPNS(0.001)VKR 58.427 0.069827 2334300000 776060 822930 535090 761450 830810 835340 734120 722960 772810 783240 TRUE FALSE 745730.7172 799460.8421 631792.666 800748.5258 857533.7582 852231.1471 743104.3802 708030.6234 685083.8487 730190.4572 1.021282475 1.094866188 0.865243663 1.096629678 1.174397378 1.167135422 1.017685691 0.969651981 0.938226242 1 19.47791329 2.002614221 24.94130361 0.97285775 1.069775937 0.232146806 0.082405428 125.9326424 1201464.73 0.033451156 0.024562225 100.603762 -2.002614221 0.096918187 ENPPVEDS(ph)SDEDDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENPPVEDSSDEDDKR 15 1 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 1 ENPPVEDS(0.977)S(0.023)DEDDKR;ENPPVEDS(0.901)S(0.099)DEDDKR 202.22 3.69E-09 1025810000 252980 363600 204465 391450 227790 170376 344930 519780 422750 239730 TRUE FALSE 243093.2619 353230.484 241416.3738 411652.7814 235117.0722 173821.1195 349151.3565 509046.3614 374761.1923 223492.8736 1.087700283 1.580499988 1.080197189 1.841905627 1.052011496 0.777747928 1.562248276 2.27768498 1.676837325 1 17.7698693 2.002629614 24.99579166 1.825096015 1.256449884 0.143735818 0.410592231 99.3954723 944794.4258 0.149928745 0.110094253 100.6073278 -2.002629614 -0.568646131 FHS(ph)PSTTWSPNKDTPQEK ddPTM_BT-474_Pertuzumab_2h_R1 4 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.831)PS(0.141)T(0.024)T(0.004)WSPNKDTPQEK;FHS(0.654)PS(0.155)T(0.155)T(0.033)WS(0.002)PNKDTPQEK;FHS(0.835)PS(0.138)T(0.023)T(0.003)WSPNKDTPQEK;FHS(0.888)PS(0.11)T(0.002)T(0.001)WSPNKDTPQEK 184.38 3.53E-14 2174250000 1727710 1666270 1249659 1188338 1432630 1794420 1241862 597235 1821230 1215623 TRUE FALSE 1660189.183 1618749.611 1475500.18 1249668.267 1478711.845 1830704.402 1257060.279 584901.8885 1614491.606 1133287.771 1.464931701 1.428365903 1.301964264 1.102692801 1.304798201 1.615392355 1.109215426 0.51611065 1.424608688 1 20.11208282 2.002630982 24.94778987 0.898021473 1.354869408 0.335738733 0.242453369 72.48796862 687346.873 0.089854969 0.06597643 100.6076448 -2.002630982 0.456847934 QKHLPHFKPWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKHLPHFKPWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 46 2 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 QKHLPHFKPWLHPEQSPLPSLALS(0.001)ELS(0.012)VQHADS(0.987)LENIDESAVAESR 101.92 1.42E-07 725530000 367890 494930 242700 278760 320270 498330 251620 31778 323590 235520 TRUE FALSE 353512.4521 480815.081 286561.2888 293146.837 330571.7754 508406.574 254699.4008 31121.77319 286857.4198 219568.0206 1.610036157 2.189822906 1.30511396 1.335107163 1.505555201 2.315485527 1.160002263 0.14174092 1.306462658 1 17.74430842 2.002631754 24.98880417 0.703247156 1.691435498 0.484030781 0.415022944 58.76485068 557974.0852 0.15439725 0.113369088 100.6078236 -2.002631754 0.988188342 MQAHIQDLEEQLDEEEGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 MQAHIQDLEEQLDEEEGAR 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 193.54 5.07E-15 205770000 109277 122420 101098 107186 130961 130061 112797 105187 127624 119262 FALSE TRUE 105006.334 118928.7015 119368.6575 112717.8823 135173.4795 132690.9225 114177.4434 103014.8517 113136.6586 111184.2785 0.94443509 1.069653939 1.073610938 1.013793351 1.215760729 1.19343242 1.026920757 0.926523543 1.017559857 1 16.76259328 2.002674979 24.97499769 0.974078338 1.088551319 0.269996555 0.076775569 100.8275336 941372.3634 0.030495133 0.022393597 100.6178375 -2.002674979 0.11447298 THS(ph)TSSSLGSGESPFSR ddPTM_BT-474_Pertuzumab_2h_R1 4 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.091)HS(0.771)T(0.137)S(0.001)SSLGSGESPFSR;T(0.122)HS(0.661)T(0.178)S(0.02)S(0.007)S(0.012)LGSGESPFSR;T(0.066)HS(0.74)T(0.159)S(0.034)S(0.001)SLGSGESPFSR;THS(0.236)T(0.236)S(0.236)S(0.236)S(0.058)LGSGESPFSR 298.75 3.10E-46 2382850000 827590 1020880 665180 940350 837330 888400 697720 300198 760310 643309 TRUE FALSE 795246.8679 991765.5019 785392.8228 988881.5762 864263.4799 906364.0567 706258.9061 293998.8064 674002.7963 599737.1084 1.325992433 1.653667062 1.309561826 1.648858412 1.441070542 1.511268928 1.177614152 0.490212799 1.123830403 1 19.19397072 2.002716884 4.935429055 0.815206598 1.481020946 0.678695347 0.187463586 0.087385273 6.065687961 0.07337334 0.048669315 100.6275466 -2.002716884 0.665814348 KTTHFVEGGDAGNREDQINR ddPTM_BT-474_Pertuzumab_2h_R1 4 KTTHFVEGGDAGNREDQINR 20 2 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;;; 143.95 9.74E-08 1464820000 865809 878786 674934 780236 816308 978210 816009 793789 951557 830725 FALSE TRUE 831972.2271 853723.8837 796909.5876 820504.0735 842565.2882 997990.0764 825995.5622 777396.9798 843540.2386 774459.2558 1.074262101 1.102348351 1.028988396 1.059454151 1.08794011 1.288628251 1.066544891 1.003793258 1.089198989 1 19.56282982 2.002757509 24.99919817 1.032356414 1.106615329 0.19678601 0.069199995 145.6697838 1320613.545 0.027375246 0.020113416 100.63696 -2.002757509 0.074258915 SGGQRHS(ph)PLSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGGQRHSPLSQR 12 1 A7MCY6 A7MCY6 TBKBP1 TANK-binding kinase 1-binding protein 1 1 S(0.03)GGQRHS(0.917)PLS(0.052)QR 54.315 0.081967 41113000 21947 30543 19345 23965 25483 29926 22801 19410 23999 23546 TRUE FALSE 21089.28698 29671.94354 22841.07183 25201.83652 26302.68384 30531.12422 23080.04546 19009.17672 21274.73413 21951.20845 0.960734669 1.351722554 1.040538241 1.148084242 1.198233979 1.390863027 1.051424823 0.865974043 0.969182821 1 14.42201274 2.00279588 24.98904198 0.937295222 1.18547489 0.427311118 0.123666344 71.08149368 635307.3405 0.044524738 0.032698254 100.6458519 -2.00279588 0.248179668 GFGSSAPEGLEPDSMASAASALHLLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 16 GFGSSAPEGLEPDSMASAASALHLLSPR 28 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR 289.33 2.60E-71 7229873000 1567025 1976163 2076787 2450193 1968131 2239117 1727230 1447537 1504758 1666485 TRUE FALSE 1505783.931 1919804.766 2452108.609 2576647.754 2031437.721 2284393.48 1748368.357 1417644.855 1333944.18 1553612.487 0.969214617 1.235703744 1.578327047 1.658488057 1.30755754 1.470375335 1.125356788 0.912482918 0.858608045 1 20.56719527 2.002803588 3.107931937 0.920929762 1.383284561 0.545835586 0.182827748 0.201523081 3.826074127 0.093807077 0.055727523 100.6476381 -2.002803588 0.462354799 TSPTT(ph)PEASATNS(ph)PCTSKPATPAPSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPTTPEASATNSPCTSKPATPAPSEK 27 1 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 2 T(0.003)S(0.003)PT(0.12)T(0.874)PEAS(0.002)AT(0.001)NS(0.99)PCT(0.007)S(0.001)KPATPAPSEK 173.01 7.33E-12 758560000 750820 645380 642210 612340 730560 643960 790280 839680 1033200 860770 TRUE FALSE 721477.1243 626974.3943 758271.6329 643942.9408 754059.1259 656981.3124 799951.683 822340.3146 915915.4675 802469.2812 0.89907133 0.781306411 0.944922941 0.802451827 0.93967351 0.818699641 0.996862686 1.02476236 1.141371376 1 19.61408664 2.00289047 2.34016617 1.061753368 0.864439138 0.654974565 0.062942752 0.168920877 1.733694051 0.03101204 0.016942938 100.667775 -2.00289047 -0.197314231 SSEGPKPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSEGPKPEK 9 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 79.974 0.021304 0 137440 141320 119600 117770 132300 140600 141370 172790 180610 166800 FALSE TRUE 132068.6929 137289.692 141214.3805 123848.1238 136555.5497 143443.0283 143100.1283 169221.8261 160107.91 155502.4874 0.849302767 0.882877787 0.908116538 0.796438217 0.87815669 0.922448449 0.92024334 1.088225847 1.029616392 1 17.24657813 2.002997006 2.246562172 1.046939829 0.869091868 0.774945561 0.039602684 0.131014091 1.236887103 0.021454246 0.01157582 100.6924728 -2.002997006 -0.177847961 GQDTPKPAGQHGSLS(ph)PAAAHTASPEPPTQSGPLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GQDTPKPAGQHGS(0.052)LS(0.948)PAAAHTASPEPPTQSGPLTR 204.16 6.32E-28 239210000 111020 165170 146350 182150 168140 160320 145870 107910 157340 179250 TRUE FALSE 106681.2157 160459.5133 172798.7005 191550.7833 173548.3758 163561.7802 147655.2007 105681.6208 139479.4228 167109.2378 0.63839209 0.960207319 1.034046369 1.146260888 1.038532507 0.978771625 0.883584909 0.632410405 0.834660158 1 17.35043196 2.00303748 6.02211654 0.775359265 0.977312275 0.133986075 0.150071459 0.207025361 30.55858965 0.061423248 0.042027849 100.7018572 -2.00303748 0.201953011 KGTVLLADNVICPGAPDFLAHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGTVLLADNVICPGAPDFLAHVR 23 1 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ; 88.239 0.0040357 1725000000 1400020 1540180 951390 1143600 1332860 1416730 1228560 1184220 1341850 1214660 FALSE TRUE 1345305.671 1496255.574 1123327.337 1202621.333 1375732.652 1445377.251 1243595.485 1159765.443 1189528.813 1132389.996 1.188023274 1.32132532 0.991996874 1.06202045 1.214892976 1.276395284 1.098204231 1.024174928 1.050458603 1 20.11093948 2.003108775 23.86317477 1.035970328 1.172033252 0.3597565 0.090239134 65.46389557 502498.4862 0.036210302 0.026581286 100.7183901 -2.003108775 0.136062924 EIVVIHQDPEALK ddPTM_BT-474_Pertuzumab_2h_R1 4 EIVVIHQDPEALK 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 153.81 4.48E-05 2721730000 3678230 3522840 3312770 3526300 3521300 3956590 4084970 4292710 4915360 5042710 FALSE TRUE 3534480.705 3422372.052 3911461.231 3708292.766 3634565.812 4036594.961 4134963.085 4204064.038 4357388.94 4701162.76 0.751831171 0.727984166 0.832019956 0.788803314 0.773120608 0.858637568 0.87956178 0.894260474 0.926874725 1 22.1645862 2.003190347 0.356296132 1.010899783 0.728543683 0.899280202 0.02566006 0.385539777 0.133252239 0.033257338 0.037733012 100.7373094 -2.003190347 -0.2823561 VRVELSTGMPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VRVELSTGMPR 11 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ; 168.02 1.69E-05 2214670000 783690 906080 650870 770250 729270 697770 840040 767020 804520 765730 FALSE TRUE 753062.5284 880239.4855 768496.6875 810002.6948 752727.6319 711879.3875 850320.6608 751180.769 713194.2624 713866.4251 1.054906775 1.233059092 1.076527289 1.13466983 1.054437645 0.997216513 1.191148135 1.052270765 0.99905842 1 19.44529462 2.003245358 0.226874901 0.976555086 1.16647533 0.241588933 0.067812611 3.827201048 0.750292968 0.199034137 0.280051093 100.7500703 -2.003245358 0.189920244 GHEGDFLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHEGDFLIR 9 0 P16333-2;P16333;C9JAB9 P16333-2 NCK1 Cytoplasmic protein NCK1 0 ; 171.56 5.69E-05 261210000 47195 56532 45514 67209 59599 65608 52334 47476 47593 60099 FALSE TRUE 45350.56722 54919.76271 53739.39225 70677.66454 61516.05596 66934.63871 52974.47915 46495.60401 42190.44217 56028.4412 0.80942047 0.98021222 0.959144875 1.261460484 1.097943377 1.194654666 0.945492646 0.829857176 0.753018311 1 15.77387173 2.003320773 24.07740552 0.853458999 1.056142379 0.298992409 0.130863956 73.34209428 531763.832 0.051444345 0.037783099 100.767567 -2.003320773 0.202683381 THPVEIFYTPEPERDYLEAAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 THPVEIFYTPEPERDYLEAAIR 22 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 185.87 2.04E-17 969280000 71014 67620 83168 76795 65112 103829 71928 53793 88889 83371 FALSE TRUE 68238.69437 65691.54381 98198.30766 80758.39915 67206.38661 105928.4935 72808.27638 52682.15575 78798.69337 77724.20791 0.877959341 0.845187691 1.263419857 1.039037918 0.864677665 1.362876462 0.936751603 0.677808847 1.013824335 1 16.24607639 2.003368628 24.99939048 0.847879058 1.044642822 0.102735916 0.181307236 160.3037667 1189643.38 0.067809534 0.049827751 100.7786714 -2.003368628 0.196763765 KEDIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEDIQK 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 89.123 0.081013 1598700000 1970800 1693900 1596000 1565900 1486800 1433500 1734700 1887900 2047000 1956900 FALSE TRUE 1893778.957 1645591.631 1884432.703 1646716.287 1534624.272 1462486.352 1755929.778 1848914.205 1814633.142 1824357.42 1.038052597 0.902011641 1.032929558 0.902628108 0.841186193 0.801644643 0.962492195 1.013460512 0.994669752 1 20.79895697 2.003438953 24.99483311 1.000148378 0.916593775 0.225196027 0.069138119 156.0921204 1134492.972 0.027632879 0.020314332 100.7949916 -2.003438953 -0.083554603 YGNPWEK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGNPWEK 7 0 P11216;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 139.68 0.0062246 1248560000 1004620 1096140 886590 948480 1056620 989880 1061200 1171840 1269690 1112430 FALSE TRUE 965358.3397 1064879.16 1046816.535 997431.1665 1090607.142 1009896.052 1074187.283 1147641.094 1125560.114 1037084.125 0.93083899 1.026801138 1.009384398 0.961764954 1.051609137 0.97378412 1.035776421 1.106603666 1.085312258 1 19.9841015 2.003446804 5.831233242 1.075046372 0.996411828 0.374647848 0.041103642 0.138713238 17.91845403 0.015596777 0.010636368 100.7968137 -2.003446804 -0.078634543 MTNNEDSLSPT(ph)SSTLSNLELDAAEKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 MTNNEDS(0.021)LS(0.476)PT(0.483)S(0.019)S(0.001)TLSNLELDAAEKDR 149 1.85E-07 150040000 133650 124770 121650 122940 134130 151870 127390 124150 141160 128920 TRUE FALSE 128426.8102 121211.6818 143634.8611 129284.9481 138444.4133 154940.9155 128949.0369 121586.2591 125136.1086 120188.1336 1.068548171 1.008516217 1.195083548 1.075688126 1.151897522 1.289153187 1.072893247 1.011632809 1.041168582 1 16.87493494 2.003459217 24.99886433 1.024735485 1.131662169 0.332339108 0.072505261 126.9562736 917472.0304 0.028606082 0.021018741 100.7996948 -2.003459217 0.106926684 FHFPPLDTHS(ph)PTNDVQPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 FHFPPLDTHSPTNDVQPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 FHFPPLDT(0.127)HS(0.853)PT(0.02)NDVQPGR 153.83 2.70E-08 276310000 302340 328190 256100 322600 319800 321430 259480 165920 264130 228960 TRUE FALSE 290524.2185 318830.3425 302382.9669 339249.4247 330086.6574 327929.5348 262655.5939 162493.694 234147.0697 213452.3353 1.361073039 1.493684021 1.416629931 1.589345107 1.546418581 1.536312706 1.23051169 0.761264541 1.096952486 1 17.70355442 2.003477714 4.151215199 0.935358495 1.491282936 0.853043192 0.1000624 0.06798943 2.727432427 0.042861301 0.02747003 100.8039881 -2.003477714 0.555924441 NGS(ph)PPPGAPSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 NGSPPPGAPSSR 12 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(0.999)PPPGAPSSR 113.69 0.0011938 1075060000 544990 500060 440618 512940 485991 487450 514420 572760 581200 498760 TRUE FALSE 523691.1883 485798.7784 520247.4741 539412.8949 501623.3419 497306.573 520715.6258 560932.3058 515224.6126 464978.541 1.126269585 1.044776771 1.118863406 1.160081267 1.07880966 1.069525858 1.119870231 1.206361706 1.108061055 1 18.82680461 2.003490671 24.90625003 1.13658149 1.099454448 0 0.057810158 260.0057498 1855156.211 0.021170556 0.015552848 100.8069954 -2.003490671 -0.037127041 SAS(ph)WGSTDQLK ddPTM_BT-474_Pertuzumab_2h_R1 5 SASWGSTDQLK 11 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 SAS(0.995)WGS(0.005)TDQLK;SAS(0.997)WGS(0.002)T(0.001)DQLK;SAS(1)WGSTDQLK;SAS(0.999)WGS(0.001)TDQLK;S(0.012)AS(0.986)WGS(0.001)T(0.001)DQLK 237.27 1.48E-15 1524964000 3124140 3230210 2642350 2885290 2987900 2592450 3129980 3576670 3553200 3270060 TRUE FALSE 3002045.155 3138087.574 3119881.424 3034200.163 3084008.517 2644871.115 3168285.632 3502810.515 3149855.632 3048575.924 0.984736884 1.029361791 1.023389773 0.995284434 1.011622671 0.867575938 1.039267419 1.148998943 1.033221974 1 21.53970405 2.003500839 24.99596646 1.081505115 0.987600688 0.254616284 0.05621819 107.5191202 767681.0087 0.021037881 0.015458396 100.8093556 -2.003500839 -0.093904427 VDDSSEDKTEFTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDDSSEDKTEFTVK 14 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 206.63 9.64E-09 5527900000 5236700 4100000 4086600 3883000 4325600 4362000 5397500 5894700 6935900 6612300 FALSE TRUE 5032043.975 3983072.014 4825139.526 4083402.095 4464736.852 4450202.629 5463556.22 5772972.385 6148565.71 6164443.031 0.816301481 0.64613656 0.782737305 0.662412172 0.724272547 0.721914795 0.886301681 0.936495374 0.99742437 1 22.55553912 2.003544907 1.699384256 0.98708281 0.718227798 0.839940761 0.050133593 0.126002357 0.679562971 0.028904295 0.014338456 100.8195854 -2.003544907 -0.268855012 LYSSGSS(ph)TPTGLAGGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LYSSGSSTPTGLAGGSR 17 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 LYSSGS(0.003)S(0.628)T(0.369)PTGLAGGSR;LYSSGS(0.06)S(0.903)T(0.036)PTGLAGGSR 322.68 1.04E-58 668280000 517970 601440 600750 634970 537390 585810 661560 817940 751990 786160 TRUE FALSE 497727.1598 584287.5201 709318.8886 667740.8778 554675.6374 597655.4796 669656.3692 801049.2532 666627.2478 732912.683 0.6791084 0.797213002 0.967808178 0.91107835 0.756809986 0.8154525 0.913691883 1.092966832 0.909558892 1 19.4832818 2.003590433 4.923480037 1.010477163 0.829570339 0.472240443 0.08496983 0.162638069 11.18496402 0.037018259 0.024584208 100.8301545 -2.003590433 -0.180906823 LYSSGSST(ph)PTGLAGGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LYSSGSSTPTGLAGGSR 17 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 LYSSGSS(0.002)T(0.996)PT(0.002)GLAGGSR;LYSSGSS(0.048)T(0.952)PTGLAGGSR 486.25 1.20E-230 492110000 660910 749700 774060 774870 689280 698960 813170 958060 903200 962450 TRUE FALSE 635080.9065 728319.29 913949.8609 814861.1336 711451.3172 713093.4501 823121.8177 938275.7262 800672.5225 897262.4042 0.707798414 0.811712701 1.01859819 0.908163687 0.792913326 0.794743485 0.91737023 1.045709395 0.892350464 1 19.77517044 2.003805118 7.275981409 0.983970829 0.847471865 0.356043299 0.0848427 0.150351046 51.72906914 0.03524118 0.024640903 100.8800102 -2.003805118 -0.136498965 WTKPSSFS(ph)DSER ddPTM_BT-474_Pertuzumab_2h_R1 4 WTKPSSFSDSER 12 1 Q8NC56;H0Y9B7;Q8NC56-2 Q8NC56 LEMD2 LEM domain-containing protein 2 1 WT(0.002)KPS(0.127)S(0.127)FS(0.735)DS(0.009)ER;WTKPS(0.016)S(0.041)FS(0.938)DS(0.004)ER;WTKPSS(0.002)FS(0.923)DS(0.075)ER;WTKPS(0.001)S(0.004)FS(0.994)DSER 136.36 6.74E-05 4134570000 3560350 5119770 2880890 5300370 3108210 3219220 4251120 5536140 4498300 3315240 TRUE FALSE 3421207.586 4973759.172 3401530.908 5573922.731 3208188.397 3284314.834 4303146.478 5421816.774 3987671.842 3090695.842 1.106937648 1.609268406 1.100571225 1.803452367 1.03801492 1.062645761 1.392290506 1.754238221 1.290218141 1 21.55950025 2.003849142 24.9881842 1.46728338 1.298704761 0 0.297150371 330.2864665 2144166.438 0.108236144 0.079578432 100.890237 -2.003849142 -0.16857862 LLELER ddPTM_BT-474_Pertuzumab_2h_R1 1 LLELER 6 0 Q08379;Q08379-2;A0A1W2PRP4;Q8IXS0 Q08379 GOLGA2;FAM217A Golgin subfamily A member 2;Protein FAM217A 0 101.72 0.08422 126520000 234490 339370 280900 451330 372280 351070 280340 252960 212870 292780 FALSE TRUE 225325.8716 329691.4999 331664.8786 474623.1954 384254.7243 358168.8759 283770.8848 247736.2876 188705.89 272949.7498 0.825521444 1.207883503 1.215113327 1.738866571 1.407785589 1.31221544 1.039645154 0.907625993 0.691357622 1 18.05827585 2.003852548 2.322127979 0.85169764 1.305128487 0.415417674 0.223410792 0.303519386 3.067231415 0.127715526 0.06967326 100.8910281 -2.003852548 0.453430847 LVVDSHVQYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVVDSHVQYR 10 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 73.841 0.04378 349170000 216340 246830 196330 218330 226900 208270 238380 268150 283820 251810 FALSE TRUE 207885.1936 239790.6501 231811.1983 229598.0375 234198.4446 212481.3621 241297.3657 262612.6088 251601.9435 234754.6844 0.885542259 1.021452035 0.987461438 0.978033891 0.997630548 0.905120861 1.027870291 1.118668236 1.07176538 1 17.84079442 2.003876572 24.00000128 1.075814749 0.968470487 0.477001245 0.047539909 50.00587464 309584.993 0.016988059 0.012481375 100.8966095 -2.003876572 -0.107344261 ALAAGADS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALAAGADSPK 10 0 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 ALAAGADS(1)PK;ALAAGADS(1)PK;ALAAGADS(1)PK 142.97 3.65E-05 1327310000 1502420 1291790 1268420 1372430 1356990 1365570 1542270 1913080 1911360 1698480 TRUE FALSE 1443703.765 1254949.414 1497651.71 1443261.277 1400638.816 1393182.761 1561144.762 1873574.229 1694390.426 1583440.437 0.91175123 0.792546019 0.945821311 0.911471782 0.884554154 0.879845385 0.985919473 1.183230001 1.070068938 1 20.59463117 2.003888896 4.314754709 1.102245414 0.888430442 0.706319232 0.056614565 0.095456332 4.29343474 0.023632449 0.015289087 100.8994725 -2.003888896 -0.213814972 RAFS(ph)TEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RAFSTEK 7 1 Q9NZ32;H0YJD9 Q9NZ32 ACTR10 Actin-related protein 10 1 RAFS(0.622)T(0.378)EK;RAFS(0.846)T(0.154)EK 101.48 0.0055293 1004140000 943810 1005070 602120 768660 1047520 690280 1014140 1313420 1237340 1033320 TRUE FALSE 906924.8618 976406.3877 710936.4781 808330.6347 1081214.432 704237.9345 1026551.349 1286297.418 1096882.351 963332.316 0.941445487 1.013571715 0.737997123 0.839098431 1.122369108 0.731043611 1.065625363 1.335258245 1.1386334 1 19.87767404 2.003915323 24.23151428 1.196521569 0.902761694 0.426753476 0.135613355 59.9186717 370826.7236 0.049236283 0.036185928 100.9056125 -2.003915323 -0.293759875 KAPGFGGFGSSAVSGGSTAAMITETIIETDKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAPGFGGFGSSAVSGGSTAAMITETIIETDKPK 33 2 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 247.09 1.59E-47 650310000 705090 574530 568710 518120 603290 621650 667920 760000 862430 781330 FALSE TRUE 677534.3033 558144.9669 671488.5479 544860.2353 622695.3707 634220.1889 676094.2048 744305.7344 764530.562 728409.8232 0.930155363 0.76625129 0.921855426 0.7480133 0.85486954 0.870691428 0.928178318 1.021822758 1.049588484 1 19.47439085 2.003917878 1.781630725 1.031682759 0.840338137 0.669150092 0.055304708 0.189136739 1.121132851 0.031307772 0.015747858 100.9062061 -2.003917878 -0.191344622 KVSQPIEGHAASFAQFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVSQPIEGHAASFAQFK 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 198.51 9.17E-12 2191430000 3623800 4102400 2794800 2657100 3596500 4008300 3342700 3211100 3700700 3614000 FALSE TRUE 3482177.89 3985403.569 3299882.53 2794233.249 3712184.689 4089350.572 3383608.963 3144789.663 3280612.051 3369220.561 1.033526249 1.182885922 0.979420157 0.829341148 1.101793314 1.213737866 1.004270543 0.933387888 0.973700591 1 21.68398344 2.00396071 24.98430154 0.963428394 1.055565114 0.132699455 0.10157398 234.5009067 1479231.824 0.041108354 0.030224988 100.9161585 -2.00396071 0.09213672 LHLETPQPS(ph)PQEGGSVDIWR ddPTM_BT-474_Pertuzumab_2h_R1 3 LHLETPQPSPQEGGSVDIWR 20 0 O14613 O14613 CDC42EP2 Cdc42 effector protein 2 1 LHLETPQPS(1)PQEGGSVDIWR;LHLETPQPS(1)PQEGGSVDIWR;LHLET(0.013)PQPS(0.986)PQEGGS(0.001)VDIWR 238.2 8.18E-30 791789000 324713 444623 444151 574248 606285 590459 383289 207930 337747 321184 TRUE FALSE 312022.857 431942.7874 524418.9658 603885.0081 625786.7076 602398.4855 387979.8054 203636.1728 299407.3765 299429.9216 1.042056369 1.442550514 1.75139132 2.016782441 2.0899271 2.011817932 1.29572824 0.680079572 0.999924707 1 18.19185887 2.004016365 4.88205985 0.880446064 1.74147789 0.603478944 0.303464208 0.129768826 8.666429529 0.139722469 0.092720284 100.9290918 -2.004016365 0.861031826 EHGGPEGMDPDGVIESNWNEIVDNFDDMNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHGGPEGMDPDGVIESNWNEIVDNFDDMNLK 31 0 Q14240;Q14240-2;E7EQG2;E9PBH4;F8WE11;E7EMV8;C9JUF0 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 98.565 0.00016681 10860000 7588.4 6112.2 5031.2 7962 7873.6 7219.7 6294.9 4170.4 9056.6 6404.8 FALSE TRUE 7291.836939 5937.88604 5940.449758 8372.919774 8126.861495 7365.687281 6371.938869 4084.279783 8028.532736 5970.997191 1.221209239 0.99445467 0.994884032 1.402264899 1.36105599 1.233577415 1.067148194 0.684019713 1.344588262 1 12.54375617 2.004089956 10.72910938 0.949741044 1.19492528 0.149154986 0.195452936 0.204868146 427.2960868 0.077381354 0.055491986 100.9461955 -2.004089956 0.245184237 YRT(ph)EKPSKSPPPPPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 YRTEKPSKSPPPPPPR 16 3 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 Y(0.001)RT(0.737)EKPS(0.226)KS(0.037)PPPPPPR 92.492 0.0048887 2705400000 1196100 1019700 931850 837040 904060 1080900 1043900 1205500 1333400 1234700 TRUE FALSE 1149355.09 990619.1544 1100256.024 880239.7347 933139.9109 1102756.539 1056675.56 1180606.004 1182038.022 1151072.669 0.998507844 0.860605226 0.955852791 0.764712566 0.810669852 0.958025126 0.917992051 1.025657228 1.026901301 1 20.13454749 2.004109818 1.679045717 1.021982808 0.879690762 0.41781801 0.06654856 0.352924436 1.85826593 0.042674276 0.021108829 100.9508122 -2.004109818 -0.142292046 DNTFFRES(ph)PVGR ddPTM_BT-474_Pertuzumab_2h_R1 6 DNTFFRESPVGR 12 1 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 DNTFFRES(1)PVGR;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR 176.49 1.50E-05 14057570000 5725370 6050280 4720620 5247890 5097850 5943210 5475170 5548890 6085640 6030980 TRUE FALSE 5501616.211 5877731.938 5573741.044 5518734.232 5261826.975 6063385.778 5542176.768 5434303.482 5394823.66 5622496.353 0.978500628 1.04539542 0.99132853 0.981545187 0.935852448 1.078415244 0.985714604 0.966528592 0.959506831 1 22.42277939 2.004109984 24.99985182 0.972749961 1.002140152 0.091906888 0.037602512 258.6949312 1573555.565 0.014049765 0.010333112 100.950851 -2.004109984 0.029390191 EQTLHT(ph)PVMMQTPQLTSTIMR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQTLHTPVMMQTPQLTSTIMR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 EQT(0.015)LHT(0.985)PVMMQTPQLTSTIMR;EQT(0.003)LHT(0.997)PVMMQTPQLTSTIMR 160.33 7.85E-11 350970000 166223 170902 156295 169528 168931 182133 161469 144711 181443 183202 TRUE FALSE 159726.8214 166028.0423 184540.9833 178277.3604 174364.819 185815.854 163445.1059 141722.6673 160846.3513 170793.5654 0.935203976 0.97209776 1.080491428 1.043817781 1.020909767 1.087955823 0.956974612 0.829789266 0.941758848 1 17.3818941 2.0042224 20.94950643 0.90204826 1.024319992 0.358753325 0.05887122 13.43044058 66632.19729 0.022233099 0.016302948 100.9769852 -2.0042224 0.122271733 ATTPPNQGRPDS(ph)PVYANLQELK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 ATTPPNQGRPDS(1)PVYANLQELK;ATTPPNQGRPDS(1)PVYANLQELK 302.39 4.24E-56 2160300000 862480 852240 735460 799970 830070 773940 872810 1026280 960770 871530 TRUE FALSE 828773.3281 827934.9496 868373.9822 841256.5476 856769.9554 789589.5971 883491.7099 1005086.959 851707.4175 812500.4968 1.020028088 1.018996238 1.068767325 1.035392041 1.054485454 0.971801987 1.087373747 1.237029347 1.048254642 1 19.63200917 2.004227277 24.78373041 1.13162383 1.031051245 0.129259792 0.06415091 116.0175939 680184.607 0.023180901 0.017051495 100.9781192 -2.004227277 -0.100572585 GEGQLGPAER ddPTM_BT-474_Pertuzumab_2h_R1 2 GEGQLGPAER 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 111.27 0.0041324 1520890000 2277200 1884200 1831730 1527070 1812430 1618730 2176300 2575800 2950900 2379300 FALSE TRUE 2188204.506 1830464.461 2162764.358 1605882.266 1870728.457 1651461.83 2202934.21 2522608.83 2615926.203 2218147.892 0.986500726 0.82522201 0.975031631 0.723974389 0.843374089 0.744522868 0.993141268 1.13725908 1.179329031 1 21.08092413 2.004285842 4.493315397 1.111463473 0.848433058 0.624089128 0.089562125 0.11940027 6.082042194 0.037225887 0.024311481 100.991737 -2.004285842 -0.263030415 IHVSDQELQSANAS(ph)VDDSRLEELK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHVSDQELQSANASVDDSRLEELK 24 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 IHVSDQELQSANAS(1)VDDSRLEELK;IHVSDQELQSANAS(1)VDDSRLEELK 246.31 4.36E-38 403210000 264010 453980 324170 385840 342030 457370 315140 201481 336070 397970 TRUE FALSE 253692.1973 441032.9349 382754.7301 405753.2486 353031.7056 466618.3348 318996.7776 197320.3469 297920.7425 371015.1374 0.683778562 1.188719517 1.031641816 1.093629903 0.951529116 1.257680045 0.859794508 0.531839073 0.802988106 1 18.50111852 2.004435206 24.90916857 0.718647567 1.041830524 0.279594119 0.181240134 109.1490701 613002.9795 0.063726088 0.046879402 101.0264765 -2.004435206 0.323182957 TAFDEAIAELDTLNEDSYK ddPTM_BT-474_Pertuzumab_2h_R1 6 TAFDEAIAELDTLNEDSYK 19 0 P27348 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 282.85 8.83E-40 609984000 856910 812707 798601 851620 888445 860638 995371 1155189 1283195 1200415 FALSE TRUE 823421.0098 789529.3921 942925.9655 895572.2103 917022.6403 878040.69 1007552.648 1131333.943 1137532.083 1119109.823 0.735782131 0.705497688 0.842567857 0.800254088 0.819421492 0.784588494 0.900316151 1.010923075 1.01646153 1 20.09392019 2.004439023 2.084465216 1.014636062 0.78078355 0.882597388 0.037372401 0.108295361 0.878981648 0.022853518 0.012063764 101.0273643 -2.004439023 -0.233852512 ELLDTS(ph)FEDLSKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLDTSFEDLSKPK 14 1 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 ELLDT(0.039)S(0.961)FEDLSKPK 166.9 2.26E-06 123270000 175540 122610 142100 115030 167130 139290 167360 215310 190770 206300 TRUE FALSE 168679.7027 119113.2828 167780.631 120966.7121 172505.8882 142106.5392 169408.2017 210863.7733 169114.5894 192327.1172 0.877045864 0.619326513 0.872371163 0.628963371 0.896940019 0.73887937 0.880833676 1.096380876 0.879307046 1 17.55320266 2.004541749 4.936845409 1.000861031 0.770677701 0.478743385 0.102829416 0.135317244 9.380860045 0.039230465 0.026112794 101.0512636 -2.004541749 -0.23018333 TQDQISNIK ddPTM_BT-474_Pertuzumab_2h_R1 3 TQDQISNIK 9 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;; 213.53 4.03E-06 1243520000 1178610 1178687 934016 1040697 1106045 1016307 1157156 1304571 1280789 1302000 FALSE TRUE 1132548.618 1145072.001 1102813.468 1094407.497 1141621.942 1036857.424 1171317.621 1277631.153 1135399.202 1213814.38 0.933049267 0.943366646 0.908551988 0.901626735 0.940524318 0.854214154 0.964989079 1.052575397 0.935397719 1 20.21111639 2.004551208 24.93553926 1.003570126 0.914886334 0.52188033 0.035717111 82.74283602 453335.7178 0.012834306 0.009443299 101.0534647 -2.004551208 -0.088683791 LNFDMTAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 LNFDMTASPK 10 0 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 LNFDMT(0.001)AS(0.999)PK;LNFDMT(0.001)AS(0.999)PK;LNFDMT(0.008)AS(0.992)PK;LNFDMTAS(1)PK;LNFDMTAS(1)PK 151.66 2.04E-05 852171000 1868130 1595780 1477420 1541520 1780860 1462630 1809400 2096960 2076960 2068590 TRUE FALSE 1795121.414 1550269.917 1744422.659 1621078.032 1838142.979 1492205.381 1831543.978 2053657.043 1841192.208 1928482.557 0.930846591 0.803880705 0.904557136 0.840597716 0.953155097 0.77377178 0.949733236 1.06490828 0.954736252 1 20.87903467 2.00456748 24.94946937 1.012150354 0.868588433 0.548847731 0.057017123 78.68778182 429822.6878 0.019548697 0.014382859 101.057251 -2.00456748 -0.143561921 DKDDKEDEKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKDDKEDEKEK 11 3 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 70.412 0.022709 194090000 116890 82816 89816 68214 100010 81226 108080 134440 145230 118030 FALSE TRUE 112321.8096 80454.16877 106047.7491 71734.53271 103226.9125 82868.44537 109402.7154 131663.767 128744.0993 110035.723 1.020775858 0.731164086 0.963757462 0.651920402 0.938121818 0.753104929 0.994247254 1.19655475 1.170020933 1 16.74761244 2.004575568 4.553241896 1.136113781 0.839914302 0.53637585 0.116721907 0.12790309 6.791551318 0.045259612 0.029654996 101.059133 -2.004575568 -0.296199479 NADDDRGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NADDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 100.48 0.004226 410390000 614490 752710 516110 672400 621240 708540 624190 609320 678500 648010 FALSE TRUE 590475.0514 731243.4478 609382.5578 707102.6446 641222.7488 722867.1643 631829.0239 596737.3291 601479.5245 604119.7055 0.977413989 1.210428068 1.008711605 1.17046777 1.061416708 1.196562797 1.045867265 0.987779944 0.995629706 1 19.20447492 2.004642723 24.96297372 0.999039964 1.10701905 0.321648864 0.071706336 132.8254599 714170.9961 0.024339835 0.017910587 101.0747609 -2.004642723 0.107979086 YGLIYHASLVGQTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 YGLIYHASLVGQTSPK 16 0 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 YGLIYHASLVGQT(0.048)S(0.952)PK 92.474 0.0020191 0 160350 243640 193670 247430 215470 262230 203700 184380 202510 220840 TRUE FALSE 154083.3447 236691.6257 228670.4772 260199.892 222400.7882 267532.4703 206192.9415 180572.4886 179521.9138 205882.3101 0.748404973 1.149645279 1.110685406 1.26382831 1.080232625 1.299443697 1.001508782 0.877066556 0.871963763 1 17.65146035 2.004731872 24.99463415 0.911835022 1.119252721 0.268692988 0.142825153 154.1418202 814201.002 0.052693681 0.038775155 101.095511 -2.004731872 0.207417699 HGSGPNIILTGDSS(ph)PGFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGSGPNIILTGDSSPGFSK 19 0 Q53ET0;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HGSGPNIILTGDS(0.021)S(0.979)PGFSK 177.6 2.56E-14 352810000 150110 269480 237620 276620 219570 266500 193040 143540 158420 183400 TRUE FALSE 144243.5352 261794.6942 280563.2198 290896.3914 226632.6685 271888.8126 195402.4813 140575.8488 140436.8258 170978.1546 0.843637221 1.531158731 1.640930214 1.701365838 1.325506577 1.590196205 1.142850569 0.822186022 0.821372918 1 17.38345248 2.004762827 3.610593156 0.875114707 1.458001981 0.538812844 0.231519667 0.170353403 4.668018796 0.105399326 0.065385603 101.1027171 -2.004762827 0.582887274 IIIEELSLVAASPTLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 IIIEELSLVAASPTLSPR 18 0 Q16513-3;Q16513-2;Q16513;Q16513-4;B1AL79;H0Y5V5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 IIIEELSLVAASPT(0.047)LS(0.953)PR 160.55 4.23E-11 221490000 80041 81086 70058 86782 96189 94878 71455 56885 72544 59128 TRUE FALSE 76912.90923 78773.50667 82719.03903 91260.82942 99283.00654 96796.49817 72329.48766 55710.30487 64309.10925 55123.20789 1.39529088 1.429044311 1.500620922 1.655579073 1.801110827 1.756002632 1.312142207 1.010650632 1.166643084 1 15.75037223 2.004766138 4.308043683 1.076082497 1.589985532 0.771327926 0.12987533 0.106644386 4.773033675 0.063361816 0.041037605 101.1034879 -2.004766138 0.513903035 ELQGDGPPSS(ph)PTNDPTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELQGDGPPSSPTNDPTVK 18 0 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 ELQGDGPPS(0.114)S(0.87)PT(0.016)NDPTVK;ELQGDGPPS(0.033)S(0.964)PT(0.003)NDPTVK 316.38 2.55E-61 1740900000 1971590 1853010 1510050 1714530 1761130 1741890 1820080 1966900 2061360 1909990 TRUE FALSE 1894538.083 1800163.969 1782949.626 1803017.099 1817778.346 1777112.209 1842354.683 1926282.828 1827363.055 1780624.676 1.063973845 1.01097328 1.001305693 1.012575599 1.020865526 0.998027396 1.034667613 1.081801715 1.026248304 1 20.76395202 2.004772393 24.37692871 1.04838798 1.016732458 0.040345777 0.026144182 136.7805179 698655.2346 0.009526119 0.007008648 101.1049441 -2.004772393 -0.031655522 KEIMDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEIMDLK 7 1 A0A087X0P0;Q02224-3;Q02224 A0A087X0P0 CENPE Kinesin-like protein;Centromere-associated protein E 0 93.178 0.024253 1069700000 1715700 1626700 1411800 1329800 1424900 1001300 1626800 1866300 1975900 1955100 FALSE TRUE 1648648.547 1580308.109 1666943.665 1398431.137 1470733.203 1021546.972 1646709.265 1827760.253 1751604.116 1822679.336 0.904519251 0.867024757 0.914556737 0.767239256 0.806907268 0.56046445 0.903455278 1.002787609 0.961005088 1 20.79762934 2.004774688 24.99777567 0.979460869 0.803407624 0.439384509 0.093953828 129.6732357 678897.5163 0.037290648 0.027440668 101.1054784 -2.004774688 -0.176053244 KDEEKEDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEEKEDPK 9 2 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 79.974 0.0143 1316430000 2851700 1950580 2183450 1676380 2229880 1964230 2923800 3630100 4220000 3579500 FALSE TRUE 2740252.411 1894951.368 2578047.986 1762898.173 2301606.115 2003948.076 2959582.339 3555137.166 3740963.292 3337057.277 0.821158339 0.567851017 0.772551314 0.528279267 0.689711301 0.600513539 0.88688389 1.065350958 1.121036584 1 21.67014502 2.004807685 2.889884133 1.065388945 0.65899973 0.802805952 0.088993271 0.101623382 1.637542109 0.040610539 0.023681492 101.1131603 -2.004807685 -0.406389215 DNS(ph)PPPAFKPEPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DNSPPPAFKPEPPK 14 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 DNS(1)PPPAFKPEPPK;DNS(1)PPPAFKPEPPK 174.02 1.58E-06 6060730000 1739450 1328640 1569180 1299300 1623290 1506120 2021110 2194100 2753630 2421350 TRUE FALSE 1671470.371 1290748.488 1852765.732 1366357.029 1675504.597 1536574.778 2045844.949 2148791.068 2441049.467 2257349.808 0.740456958 0.57179817 0.820770324 0.605292553 0.742244109 0.680698567 0.906303906 0.951908765 1.081378463 1 21.10619857 2.004865395 1.631647862 1.028142593 0.686793336 0.794838865 0.073604394 0.150193893 0.746815361 0.043155447 0.021195582 101.1265974 -2.004865395 -0.341349257 FEDENFILK ddPTM_BT-474_Pertuzumab_2h_R1 11 FEDENFILK 9 0 P62937;F8WE65;C9J5S7;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;;;;;;;;; 230.7 1.87E-07 14550543000 7567699 7031944 7350333 8501053 7377697 6516247 8631391 10025588 10281603 10997852 FALSE TRUE 7271944.957 6831399.842 8678701.68 8939793.364 7615007.324 6648009.979 8737024.545 9818556.104 9114478.531 10252957.69 0.709253386 0.666285773 0.846458353 0.871923365 0.74271323 0.648399241 0.852146747 0.957631583 0.888960904 1 23.28953681 2.004938587 5.959100758 0.93568393 0.75302229 0.618806025 0.070884952 0.11516133 16.1410966 0.030526514 0.020943263 101.1436418 -2.004938587 -0.18266164 RHS(ph)VVAGGGGGEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHSVVAGGGGGEGR 14 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 RHS(1)VVAGGGGGEGR 52.784 0.094213 73610000 39004 40691 26625 38886 36561 38313 27985 26459 22524 26665 TRUE FALSE 37479.68056 39530.53252 31436.72977 40892.91112 37737.01777 39087.71511 28327.4888 25912.6124 19967.16995 24858.9558 1.507693278 1.5901928 1.264603792 1.644997137 1.518045169 1.572379605 1.139528508 1.042385393 0.80321837 1 14.60147808 2.004975171 2.121885775 0.936370762 1.516322967 0.835151446 0.1146645 0.119178081 1.002819003 0.062635558 0.033263255 101.1521623 -2.004975171 0.579952205 IDS(ph)LSAQLSQLQK ddPTM_BT-474_Pertuzumab_2h_R1 3 IDSLSAQLSQLQK 13 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 IDS(1)LSAQLSQLQK;IDS(0.872)LS(0.128)AQLSQLQK;IDS(0.991)LS(0.009)AQLSQLQK 309.29 1.60E-50 520110000 859340 766040 638411 714526 796939 539084 867540 1128820 1020440 877170 TRUE FALSE 825756.0427 744193.2892 753786.0691 751402.7725 822573.2667 549984.6478 878157.214 1105509.473 904603.9292 817758.4946 1.009779841 0.910040427 0.921771005 0.918856579 1.005887768 0.672551434 1.073858871 1.3518777 1.106199367 1 19.64131532 2.005044872 24.99553492 1.1970595 0.909151112 0.453589723 0.121150511 95.46823971 473008.0803 0.043191523 0.031790059 101.1683978 -2.005044872 -0.287908388 DSDAGSST(ph)PTTSTR ddPTM_BT-474_Pertuzumab_2h_R1 5 DSDAGSSTPTTSTR 14 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 DSDAGS(0.21)S(0.182)T(0.606)PT(0.002)TSTR;DSDAGS(0.006)S(0.061)T(0.657)PT(0.276)T(0.001)STR;DSDAGS(0.25)S(0.156)T(0.56)PT(0.031)T(0.003)STR;DSDAGS(0.019)S(0.257)T(0.723)PT(0.001)TSTR;DSDAGS(0.011)S(0.278)T(0.71)PT(0.001)TSTR 222.07 4.50E-11 1009499000 2083450 2035240 1502867 1803972 1796537 1827516 1935739 2141780 2205970 2136150 TRUE FALSE 2002026.471 1977196.948 1774468.498 1897075.211 1854324.244 1864469.626 1959429.153 2097551.495 1955557.534 1991466.658 1.005302531 0.992834573 0.891036007 0.952602045 0.931134969 0.936229396 0.983912608 1.053269703 0.981968504 1 20.92539989 2.005072784 6.0642192 1.018101706 0.950345915 0.380772369 0.03434324 0.142010734 21.36998236 0.014156842 0.00973713 101.1749 -2.005072784 -0.067755791 IWEDLDDDDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IWEDLDDDDPK 11 0 O75717;C9JYB3 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 0 ; 197.06 1.36E-07 186135000 433290 370680 339240 341480 383910 380090 416390 487930 523290 477930 FALSE TRUE 416356.5478 360108.5693 400548.2144 359103.8237 396258.8138 387775.6802 421485.9054 477854.075 463888.313 445559.3754 0.934458056 0.808216793 0.89897831 0.805961772 0.889351309 0.87031202 0.945970231 1.072481248 1.041136914 1 18.76525817 2.005188858 2.900497164 1.043574746 0.864472307 0.778157488 0.040547578 0.104608851 1.699901296 0.018438497 0.010768152 101.2019447 -2.005188858 -0.179102438 AEVDMDTDAPQVSHKPGGEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 AEVDMDTDAPQVSHKPGGEPK 21 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 230.71 4.92E-26 1062490000 743590 699320 750160 720260 750800 824730 999830 1099160 1319090 1286820 FALSE TRUE 714529.6807 679376.0783 885730.5992 757432.7049 774950.1639 841406.6057 1012066.219 1076461.962 1169352.433 1199662.535 0.595608898 0.566305989 0.738316463 0.631371475 0.645973464 0.701369411 0.843625761 0.897303975 0.974734477 1 20.1941972 2.005215893 0.983310758 0.998963387 0.62649199 0.919352751 0.042838444 0.141408026 0.251848658 0.035200602 0.016753103 101.2082447 -2.005215893 -0.372471397 IVPQSQVPNPES(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IVPQSQVPNPESPGK 15 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 IVPQSQVPNPES(1)PGK 168.05 1.34E-06 146010000 130320 119510 106170 121250 117280 108710 134030 166690 146040 158630 TRUE FALSE 125226.9503 116101.6918 125357.2807 127507.727 121052.4177 110908.1907 135670.2992 163247.7932 129462.1514 147885.8488 0.846781158 0.785076414 0.847662449 0.862203707 0.818553085 0.749958103 0.917398793 1.103877041 0.87541947 1 17.17412448 2.005239088 8.047972885 1.006318484 0.821075515 0.631818542 0.060098385 0.067326158 36.78218322 0.0224128 0.01584862 101.2136503 -2.005239088 -0.185242969 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSR 44 2 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 VGDPPQPLPEEPMEVQGAERAS(0.976)PEPQRENAS(0.006)PAPGT(0.008)T(0.008)AEEAMS(0.002)R 66.137 0.00093474 144040000 2761.8 3151.6 2482.5 3360.5 2740.5 4411.5 2841.6 2531.3 2774.3 3100.8 TRUE FALSE 2653.865803 3061.719454 2931.142973 3533.935808 2828.650671 4500.703553 2876.376351 2479.02777 2459.373095 2890.780054 0.918044871 1.05913262 1.013962639 1.222485191 0.978507745 1.556916634 0.995017365 0.857563607 0.850764516 1 11.49724313 2.00526772 24.99981195 0.896784891 1.128048782 0.257890999 0.17069993 181.7104855 862365.8406 0.063756676 0.046933661 101.2203232 -2.00526772 0.231263891 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_BT-474_Pertuzumab_2h_R1 5 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 40 1 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR 300.48 1.66E-93 9079540000 1164249 1290960 1096321 1254433 1282580 1328530 1200683 1143981 1309345 1298848 TRUE FALSE 1118748.862 1254143.085 1294450.592 1319174.437 1323835.351 1355393.787 1215377.318 1120357.393 1160713.645 1210875.868 0.923917052 1.035732165 1.069020059 1.089438209 1.093287417 1.119349904 1.003717515 0.925245454 0.958573604 1 20.20761955 2.005335492 10.59019828 0.955811025 1.058474554 0.393204423 0.052445532 0.150597343 251.5563495 0.020956629 0.015060674 101.23612 -2.005335492 0.102663529 PGGPPNPPGPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 PGGPPNPPGPSPK 13 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 PGGPPNPPGPS(1)PK 111.74 0.00040179 0 161750 101880 134340 114190 106170 98777 135450 150140 162580 171620 TRUE FALSE 155428.6312 98974.48215 158618.2264 120083.3596 109585.0545 100774.3386 137107.6776 147039.5565 144124.6 159996.0245 0.971453082 0.618605884 0.991388548 0.750539646 0.684923608 0.629855266 0.856944277 0.919020063 0.900801132 1 17.28767653 2.005597518 24.95079627 0.920202533 0.769689797 0.269763848 0.121052174 197.0190092 878202.501 0.044327862 0.032641166 101.2972179 -2.005597518 -0.150512736 KDSLSVNEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDSLSVNEFK 10 1 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 176.62 3.92E-06 3435100000 5247800 5247000 4677500 4558200 4723300 4438400 5321100 6005400 6355100 5752300 FALSE TRUE 5042710.174 5097360.697 5522828.3 4793449.248 4875229.234 4528147.489 5386221.214 5881386.391 5633695.691 5362691.597 0.940331936 0.950522812 1.029861255 0.893851373 0.909101175 0.844379619 1.00438765 1.096722846 1.050535088 1 22.35452586 2.005725433 24.84054867 1.057513541 0.930677002 0.552489057 0.049484692 98.33169898 426623.0556 0.019359135 0.014255231 101.327058 -2.005725433 -0.126836539 IEGCIIGFDEYMNLVLDDAEEIHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEGCIIGFDEYMNLVLDDAEEIHSK 25 0 A6NHK2;P62304 A6NHK2 SNRPE Small nuclear ribonucleoprotein E 0 ; 84.327 0.018248 218435000 45730.3 33559.2 35858 26972.8 34004 23068.6 36964 43975 41107 40651 FALSE TRUE 43943.10932 32602.12447 42338.33826 28364.86944 35097.76954 23535.0629 37416.37649 43066.90088 36440.70569 37897.67156 1.159520031 0.860267218 1.117175185 0.748459424 0.926119418 0.621016066 0.987300141 1.136399655 0.961555267 1 15.20982159 2.005733121 24.99950256 1.051317881 0.898250409 0.120945681 0.153504156 258.5822983 1127552.537 0.056683743 0.041742791 101.3288517 -2.005733121 -0.153067472 RTS(ph)FSTSDVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.007)S(0.966)FS(0.015)T(0.006)S(0.006)DVSK 142.29 4.00E-05 147790000 685330 763790 627150 636260 621090 556210 726270 799030 908920 823140 TRUE FALSE 658546.5459 742007.457 740489.9559 669097.4548 641067.9239 567456.9473 735158.3095 782529.7513 805743.2121 767387.9946 0.858166339 0.966926069 0.96494858 0.871915458 0.835389566 0.7394655 0.958000796 1.019731553 1.049981519 1 19.54959667 2.0057384 24.93885625 1.016289127 0.87696168 0.54657111 0.061854522 125.7482234 546493.7735 0.025820932 0.019014736 101.3300833 -2.0057384 -0.139327446 ELHINLIPNKQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELHINLIPNKQDR 13 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 150.34 2.48E-05 69953660000 31919340 36482170 28129510 30644290 30680130 34799780 32246910 32570130 36307130 35350090 FALSE TRUE 30671896.9 35441734.23 33213138.19 32225845.48 31666984.24 35503455.39 32641557.33 31897545.43 32185696.81 32955796.92 0.93069808 1.075432475 1.00780868 0.977850591 0.960892687 1.077305322 0.990464816 0.967888761 0.976632333 1 24.97402892 2.005765931 24.99085874 0.978248523 1.007488247 0.053496174 0.04361224 380.5559967 1649405.304 0.015932603 0.011736637 101.3365071 -2.005765931 0.029239724 SSSAS(ph)SPPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSASSPPKK 10 1 P51608;P51608-2 P51608 MECP2 Methyl-CpG-binding protein 2 1 S(0.001)S(0.001)S(0.001)AS(0.499)S(0.499)PPKK 62.408 0.039585 0 128240 81491 77720 82641 87210 68279 94765 109970 107360 101330 TRUE FALSE 123228.239 79166.95647 91765.73287 86906.11191 90015.18885 69659.64816 95924.76242 107699.0811 95172.94289 94466.82884 1.304460418 0.838039738 0.971406937 0.91996432 0.952876157 0.737397974 1.015433286 1.140073001 1.00747473 1 16.52752021 2.005812427 24.99852343 1.067997996 0.941981467 0.078581222 0.141067426 284.8917508 1225276.896 0.050941584 0.037516548 101.347357 -2.005812427 -0.126016529 EY(ph)FTFPASK ddPTM_BT-474_Pertuzumab_2h_R1 2 EYFTFPASK 9 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 EY(0.995)FT(0.005)FPASK;EY(0.998)FT(0.002)FPASK 134.25 0.0026204 482050000 449860 518740 274340 446700 413440 357370 503320 627600 677730 565140 TRUE FALSE 432278.9739 503946.0431 323919.3407 469754.2405 426738.6731 364596.2663 509479.7807 614639.8407 600796.9317 526862.5644 0.820477679 0.956503796 0.61480804 0.891606791 0.809962032 0.692013992 0.967006986 1.166603745 1.140329513 1 19.00706715 2.005813353 4.769677102 1.111356101 0.801801349 0.662611365 0.098103825 0.104578735 6.444665749 0.039791663 0.026375356 101.3475731 -2.005813353 -0.309554752 ERFS(ph)PPRHELS(ph)PPQK ddPTM_BT-474_Pertuzumab_2h_R1 4 ERFSPPRHELSPPQK 15 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 ERFS(1)PPRHELS(1)PPQK;ERFS(1)PPRHELS(1)PPQK;ERFS(1)PPRHELS(1)PPQK;ERFS(1)PPRHELS(1)PPQK 131.18 2.96E-05 1415560000 1453340 1453200 1119540 1242430 1337710 1486120 1343780 1366800 1510290 1433430 TRUE FALSE 1396541.866 1411756.159 1321865.782 1306551.961 1380738.657 1516170.365 1360225.582 1338575.102 1338848.211 1336342.509 1.04504785 1.056432875 0.989166904 0.977707401 1.033222132 1.134567189 1.017871969 1.001670674 1.001875044 1 20.34985839 2.006008363 24.98954697 1.003468466 1.038225054 0.158039148 0.039713727 336.926762 1401310.406 0.016304527 0.012003454 101.3930911 -2.006008363 0.034756587 EQDFFFELDAMDHLQSFIADCDRR ddPTM_BT-474_Pertuzumab_2h_R1 6 EQDFFFELDAMDHLQSFIADCDRR 24 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;;; 263.08 2.45E-44 1493465000 973847 1124499 732852 888122 978874 1105352 888933 828391 949421 897528 FALSE TRUE 935787.9826 1092429.39 865294.6586 933958.0829 1010360.371 1127702.975 899812.028 811284.4364 841646.7084 836737.6291 1.118376836 1.305581764 1.034129013 1.116189891 1.207499622 1.347737852 1.075381334 0.969580437 1.005866928 1 19.67441579 2.006046206 24.99537516 0.99694708 1.186461032 0.515776932 0.086173625 125.6382739 519393.4893 0.033037541 0.024333654 101.4019264 -2.006046206 0.189513952 AVLSAEQLRDEEVHAGLGELLR ddPTM_BT-474_Pertuzumab_2h_R1 6 AVLSAEQLRDEEVHAGLGELLR 22 1 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 ;;;;; 220.52 6.07E-26 1662453000 1092081 1478907 841064 1077596 1187457 1404213 1050040 955474 1120697 948322 FALSE TRUE 1049401.267 1436730.02 993062.9742 1133210.859 1225652.633 1432607.149 1062890.704 935743.128 993480.1749 884091.3063 1.186982905 1.625092352 1.123258386 1.281780344 1.386341687 1.620428952 1.202240873 1.058423628 1.123730284 1 19.75383585 2.006062585 24.99471804 1.082990146 1.371283209 0.448215769 0.15471385 143.0328508 589690.2679 0.057064618 0.04202923 101.4057508 -2.006062585 0.288293063 SRVPVRPPQQYS(ph)DDEDDYEDDEEDDVQNTNSALR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALR 34 2 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.024)RVPVRPPQQYS(0.976)DDEDDYEDDEEDDVQNTNSALR 274.25 5.01E-74 361610000 33403 36291 28959 32054 31771 32061 36762 41578 42932 46363 TRUE FALSE 32097.57383 35256.01621 34192.53549 33708.31078 32792.94307 32709.29539 37211.90435 40719.39977 38058.53935 43222.79271 0.742607588 0.815681126 0.791076498 0.779873503 0.75869561 0.756760342 0.860932439 0.942081648 0.880520137 1 15.39950467 2.006066809 3.034795487 0.932600612 0.776426414 0.83174409 0.033628143 0.100019401 1.801374903 0.015574279 0.009224444 101.4067371 -2.006066809 -0.156174199 SKENMAQESSIQEQGVTSNTS(ph)DSESSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKENMAQESSIQEQGVTSNTSDSESSSK 28 1 Q92796-2;Q92796-3 Q92796-2 DLG3 Disks large homolog 3 1 SKENMAQESSIQEQGVTS(0.258)NT(0.191)S(0.502)DS(0.048)ES(0.001)SSK;SKENMAQESSIQEQGVTS(0.001)NT(0.061)S(0.938)DSESSSK 290.39 2.31E-71 1555940000 688620 597030 629270 610520 659800 690660 715370 818360 915990 881830 TRUE FALSE 661707.9691 580003.289 742993.087 642029.0104 681023.0662 704625.6184 724124.9121 801460.58 812010.6553 822102.8686 0.804896801 0.705511817 0.903771432 0.780959458 0.828391546 0.85710152 0.88082032 0.974890869 0.987723905 1 19.6489594 2.006117216 0.900641531 1.010484561 0.795962504 0.749720458 0.045873558 0.270479631 0.405290729 0.036699807 0.017939378 101.4185077 -2.006117216 -0.214522057 HS(ph)SIS(ph)PVRLPLNSSLGAELSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.542)S(0.542)IS(0.879)PVRLPLNS(0.034)S(0.004)LGAELSR;HS(0.501)S(0.501)IS(0.998)PVRLPLNSSLGAELSR 75.224 0.016564 1693280000 575560 610087 554609 600642 595664 637210 542474 375054 692735 652645 TRUE FALSE 553066.4789 592687.9161 654839.1835 631641.2056 614824.0735 650094.8228 549112.9591 367309.0038 614098.627 608440.7728 0.908989837 0.974109466 1.076257892 1.038130963 1.010491244 1.06846032 0.902492048 0.603689003 1.00929894 1 19.21475731 2.00617693 11.61802555 0.808500677 1.012518632 0.187326982 0.117892234 0.256686928 459.5816883 0.043871078 0.031711073 101.4324534 -2.00617693 0.204017956 LKQSAEEQAQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKQSAEEQAQAR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 156.81 5.86E-05 567170000 682570 722370 498210 529910 587820 702420 573370 555630 613110 544180 FALSE TRUE 655894.4098 701768.7149 588247.6296 557258.7186 606727.7641 716623.4137 580387.0736 544156.0463 543512.3232 507322.2039 1.292855713 1.383280112 1.159514851 1.098431558 1.195941671 1.412560712 1.144020642 1.072604436 1.071335571 1 18.95254278 2.00619498 24.91546306 1.069113484 1.250895988 0.507978397 0.092103935 144.2766227 580260.579 0.037201005 0.027399136 101.4366691 -2.00619498 0.181782505 GLAAEDS(ph)GGDSKDLSEVSETTESTDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLAAEDSGGDSKDLSEVSETTESTDVK 27 1 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GLAAEDS(1)GGDSKDLSEVSETTESTDVK 214 3.75E-27 180320000 152160 142410 128990 108510 121880 154860 147150 201000 208250 185860 TRUE FALSE 146213.419 138348.6062 152301.3624 114110.2141 125800.3809 157991.3753 148950.8657 196849.2798 184610.3331 173271.5367 0.843839801 0.798449699 0.878975078 0.658562949 0.726030272 0.911813783 0.859638395 1.136073954 1.065439464 1 17.40267516 2.006299599 1.999356865 1.07906456 0.790054145 0.69393708 0.077425886 0.174749429 1.30506056 0.045026398 0.023502663 101.4611077 -2.006299599 -0.289010415 KPEDWDERPK ddPTM_BT-474_Pertuzumab_2h_R1 3 KPEDWDERPK 10 2 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ;; 117.23 0.00055392 3694660000 5295500 7129200 4534850 7163900 5004700 3664250 7407700 10614300 9515000 5946700 FALSE TRUE 5088546.006 6925882.196 5354398.272 7533629.738 5165680.721 3738343.646 7498357.648 10395111 8434897.09 5543924.712 0.917859868 1.249274216 0.96581367 1.358898277 0.931773245 0.674313567 1.352535981 1.875045484 1.521466746 1 22.40247623 2.006321652 24.41419036 1.575496228 1.034433559 0.35082863 0.270887869 101.3915403 391570.9521 0.098472854 0.072523552 101.4662599 -2.006321652 -0.54106267 SDGEAKPEPSPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDGEAKPEPSPSPR 14 1 P26358;K7EJL0;K7ENQ6;K7ERQ1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 SDGEAKPEPS(0.214)PS(0.786)PR 72.421 0.023421 187140000 137010 134750 116720 139260 127890 118470 150330 196990 142920 180940 TRUE FALSE 131655.4977 130907.0619 137813.9004 146447.2253 132003.698 120865.5446 152169.7835 192922.0877 126696.3208 168684.7726 0.780482409 0.776045519 0.816990759 0.868170985 0.782546616 0.716517221 0.902095555 1.143684072 0.75108333 1 17.36397022 2.006324256 12.55170477 0.991391465 0.795167981 0.39594407 0.096823272 0.330078989 643.373228 0.035566586 0.02579281 101.4668681 -2.006324256 -0.196223485 ARS(ph)VDALDDLTPPSTAESGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSVDALDDLTPPSTAESGSR 21 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 ARS(1)VDALDDLTPPSTAESGSR 162.02 1.16E-11 362340000 167940 283870 103370 287300 131630 140570 222950 340160 203360 144950 TRUE FALSE 161376.7191 275774.3055 122051.2585 302127.5874 135863.9985 143412.4217 225678.5288 333135.5771 180275.4254 135132.4074 1.194211827 2.040771055 0.903197544 2.235789277 1.005413883 1.061273343 1.670054824 2.465253033 1.334065076 1 17.04401418 2.006485256 24.52473934 1.83884744 1.426602904 0 0.549696643 287.7631498 1088202.466 0.198004807 0.14585258 101.5044906 -2.006485256 -0.412244536 KNPDSQYGELIEK ddPTM_BT-474_Pertuzumab_2h_R1 5 KNPDSQYGELIEK 13 1 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ;;;; 220.85 3.22E-11 4686990000 7854080 7381290 6158375 6234760 7235980 7371960 7493388 8468460 9418450 8831360 FALSE TRUE 7547133.87 7170782.836 7271330.355 6556536.711 7468731.868 7521026.082 7585094.324 8293583.342 8349307.041 8233204.121 0.916670322 0.870958952 0.883171393 0.796352989 0.907147662 0.913499286 0.921280975 1.007333624 1.014101791 1 22.97302256 2.00649107 1.322509884 1.015424493 0.871870494 0.759000525 0.031837509 0.204940631 0.666395284 0.022889574 0.010780407 101.5058496 -2.00649107 -0.143553999 S(ph)PQMVSAIVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPQMVSAIVR 10 0 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y7Z0 A0A2R8Y804 CTNNB1 Catenin beta-1 1 S(1)PQMVSAIVR;S(1)PQMVSAIVR;S(1)PQMVSAIVR 83.087 0.016854 745670000 231178 271524 185134 226668 200420 187762 240636 285863 273040 240804 TRUE FALSE 222143.3082 263780.4014 218591.8321 238366.3626 206866.6913 191558.6763 243580.9754 279959.8292 242045.6439 224494.1306 0.989528357 1.1749991 0.973708451 1.061793295 0.921479287 0.853290355 1.085021576 1.247069705 1.078182504 1 17.7763182 2.006575291 24.98748444 1.143413619 0.999778684 0.195936666 0.09924188 201.0418722 763997.0139 0.038024436 0.028014875 101.525536 -2.006575291 -0.143634935 VLGTEDLYDYIDKYNIELDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLGTEDLYDYIDKYNIELDPR 21 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ; 193.85 5.29E-18 2276390000 2721500 2819670 2391960 2672210 2631430 2548060 2871360 3176040 3319320 3405280 FALSE TRUE 2615140.771 2739255.772 2824240.381 2810123.078 2716072.336 2599583.519 2906500.563 3110453.664 2942524.709 3174637.352 0.823760474 0.862856279 0.889626142 0.88517924 0.855553575 0.818859993 0.915537821 0.979782356 0.926885305 1 21.59816037 2.006627595 4.83429433 0.963237526 0.859212208 0.773782626 0.02741834 0.089515767 5.760636501 0.011538423 0.007679391 101.5377638 -2.006627595 -0.104025317 S(ph)PVS(ph)PLAAQGIPLPAQLTK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 2 S(1)PVS(1)PLAAQGIPLPAQLTK;S(1)PVS(1)PLAAQGIPLPAQLTK;S(1)PVS(1)PLAAQGIPLPAQLTK;S(1)PVS(1)PLAAQGIPLPAQLTK 229.98 9.91E-20 1302670000 1232300 1200270 1023060 1056840 1149340 1173780 1215920 1382340 1447450 1425360 TRUE FALSE 1184140.354 1166039.475 1207949.7 1111383.639 1186309.565 1197514.636 1230800.793 1353794.196 1283141.544 1328819.098 0.891122317 0.877500539 0.90903999 0.836369406 0.892754753 0.901187105 0.926236532 1.018794957 0.965625454 1 20.34171328 2.006637865 2.477609193 0.996040405 0.882693434 0.825878557 0.022508636 0.106584045 1.233665165 0.011377264 0.006348387 101.540165 -2.006637865 -0.113346971 SSS(ph)QRS(ph)PSPGPNHTSNSSNASNATVVPQNSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSQRSPSPGPNHTSNSSNASNATVVPQNSSAR 33 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 2 S(0.099)S(0.117)S(0.724)QRS(0.803)PS(0.257)PGPNHTSNSSNASNATVVPQNSSAR 228.1 2.45E-36 185600000 114890 218540 110060 176870 147010 213470 130680 110910 103200 116200 TRUE FALSE 110399.9718 212307.4532 129950.2903 185998.2819 151738.7102 217786.5097 132279.3009 108619.6697 91485.16865 108329.6705 1.01911112 1.959827369 1.1995817 1.716965269 1.400712376 2.010404986 1.221080987 1.002677007 0.844507033 1 16.72506891 2.006648781 24.91901856 0.989988782 1.559515935 0.461640225 0.292673063 131.5323819 492968.5532 0.101298444 0.074635754 101.5427174 -2.006648781 0.569527153 ADILEDKDGK ddPTM_BT-474_Pertuzumab_2h_R1 6 ADILEDKDGK 10 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;; 149.31 2.15E-05 19728000000 21437480 17376400 15816670 13128620 16879570 15914180 19123350 23009410 24689880 20439120 FALSE TRUE 20599679.58 16880842.09 18675094.11 13806189.65 17422516.7 16235975.62 19357387.28 22534257.64 21887188.33 19054760.2 1.081077871 0.885912072 0.980075 0.724553314 0.914339331 0.852069271 1.015881967 1.182605155 1.148646748 1 24.18364812 2.006670279 4.499843149 1.125793173 0.901768719 0.475334054 0.096136897 0.150584264 7.690974701 0.039942169 0.026200556 101.5477438 -2.006670279 -0.224024453 VKLDENSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKLDENSEK 9 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 ; 92.866 0.008925 322810000 741700 610770 534990 457230 590430 501630 643090 738220 802800 736620 FALSE TRUE 712713.544 593351.4376 631674.5938 480827.6951 609421.7172 511773.3023 650960.3278 722975.499 711669.5096 686728.0713 1.037839538 0.86402677 0.919832202 0.700171895 0.887427998 0.745234284 0.947915711 1.052782796 1.036319235 1 19.38937941 2.0066794 7.742397478 1.027170578 0.855175955 0.436224015 0.087331705 0.114141854 49.87274898 0.033738384 0.023861811 101.5498767 -2.0066794 -0.171994623 EAKPDELMDSK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAKPDELMDSK 11 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ;;; 136.27 9.37E-05 2816410000 3962200 5079620 3016040 4734640 3189420 3358080 4906470 6812100 6484100 4518200 FALSE TRUE 3807352.844 4934754.211 3561105.519 4978995.338 3292010.591 3425982.678 4966516.848 6671427.754 5748052.152 4212178.29 0.903891664 1.171544477 0.845430861 1.182047624 0.781545881 0.813351773 1.179085145 1.583842681 1.364626983 1 22.00613507 2.006681916 6.960712111 1.381972295 0.96009891 0.430610862 0.187286174 0.103149756 27.75421526 0.0705874 0.049464829 101.5504649 -2.006681916 -0.421873385 S(ph)HSANDSEEFFREDDGGADLHNATNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSANDSEEFFREDDGGADLHNATNLR 27 1 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 S(0.452)HS(0.418)ANDS(0.13)EEFFREDDGGADLHNATNLR;S(0.53)HS(0.466)ANDS(0.004)EEFFREDDGGADLHNATNLR 97.243 0.0025433 1276260000 228692 255354 196503 236063 208538 222767 189909 100812 195971 184700 TRUE FALSE 219754.4638 248071.5539 232015.4633 248246.2397 215245.8142 227271.5014 192233.1632 98730.19697 173725.1937 172190.1045 1.276231665 1.440684148 1.347437845 1.441698642 1.250047526 1.319887122 1.116400758 0.573379041 1.008915084 1 17.39364271 2.006698713 4.252228367 0.816211073 1.346002238 0.737478982 0.128792373 0.088163311 3.792317601 0.053529349 0.034676903 101.5543925 -2.006698713 0.529791165 KPNEGADGQWK ddPTM_BT-474_Pertuzumab_2h_R1 6 KPNEGADGQWK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;;; 142.51 6.03E-05 7239870000 6714640 5906730 5511090 5851290 6276600 5963780 6793160 7709330 8311440 7992080 FALSE TRUE 6452224.445 5738275.844 6507066.557 6153275.778 6478492.539 6084371.718 6876296.724 7550129.641 7367960.176 7450769.303 0.865980972 0.77015884 0.873341569 0.825857778 0.869506527 0.816609865 0.922897548 1.013335581 0.988885829 1 22.82895796 2.006721506 3.092024485 0.999912886 0.836539524 0.859142076 0.029811095 0.082077623 1.5437567 0.013442225 0.008010507 101.5597225 -2.006721506 -0.163373362 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_BT-474_Pertuzumab_2h_R1 3 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.153)PS(0.846)PGLPAEGAPEAPRPS(0.511)S(0.49)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HT(0.126)PS(0.874)PGLPAEGAPEAPRPS(0.531)S(0.469)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HT(0.135)PS(0.865)PGLPAEGAPEAPRPS(0.521)S(0.479)PPPEVLEPHS(0.001)LDQPPATSPRPLIEVGELLDLTR 187.06 2.55E-32 557887000 4778.6 6251.3 6005 3890.2 5866.1 9323.7 4416 2861.7 4196.6 3279.2 TRUE FALSE 4591.847029 6073.019045 7090.237081 4090.973688 6054.788434 9512.231602 4470.044329 2802.604895 3720.219562 3057.096863 1.502028635 1.986531444 2.319271321 1.338189096 1.98056807 3.111524439 1.462186031 0.916753711 1.216912557 1 11.57794655 2.006843601 24.99950913 1.073846699 2.038025431 0.496001586 0.454435385 140.6981975 513964.6004 0.173018491 0.127494735 101.5882784 -2.006843601 0.964178731 LS(ph)SPVKR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSSPVKR 7 1 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.5)S(0.5)PVKR;LS(0.5)S(0.5)PVKR;LS(0.5)S(0.5)PVKR 109.71 0.0042668 487190000 467610 397988 444740 442630 424110 385680 490850 570400 565170 625910 TRUE FALSE 449335.2842 386637.7719 525114.4112 465474.1873 437751.8833 393478.7139 496857.1691 558621.0407 501014.271 583516.5582 0.770047187 0.662599487 0.899913471 0.797705191 0.750196164 0.674323133 0.851487695 0.957335371 0.858611918 1 19.15441407 2.006853171 6.195524184 0.927477436 0.762116117 0.569850854 0.070008529 0.113757667 18.48320324 0.027983035 0.019369404 101.5905171 -2.006853171 -0.165361319 SSS(ph)KESLVR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSSKESLVR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.004)S(0.033)S(0.963)KESLVR;S(0.008)S(0.068)S(0.872)KES(0.051)LVR;S(0.016)S(0.173)S(0.81)KESLVR;S(0.007)S(0.056)S(0.884)KES(0.053)LVR;S(0.019)S(0.204)S(0.777)KESLVR 142.97 6.24E-05 10200500000 5848930 4974170 4150170 4087350 4739150 4570830 5271940 6134140 6624930 5793100 TRUE FALSE 5620347.349 4832311.542 4900198.039 4298298.623 4891589.064 4663255.314 5336459.579 6007467.865 5872895.72 5400728.177 1.040664734 0.894751853 0.907321731 0.795873905 0.905727691 0.863449365 0.988100012 1.112344052 1.087426645 1 22.36472251 2.006876058 4.113068619 1.074987165 0.897315753 0.581621118 0.06290424 0.136720978 5.337892706 0.027344771 0.017581932 101.5958711 -2.006876058 -0.177671412 LISPESTVMLLEAQAATGGIIDPHRNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LISPESTVMLLEAQAATGGIIDPHRNEK 28 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 221.6 1.40E-34 485990000 467190 480330 371460 373270 434490 521490 407420 385570 460020 377910 FALSE TRUE 448931.6983 466631.4587 438591.0851 392534.5094 448465.7654 532034.8851 412406.1278 377607.8448 407800.4582 352313.8191 1.274238119 1.32447674 1.244887544 1.114161546 1.272915626 1.510116425 1.170564722 1.071794021 1.157492088 1 18.42650154 2.007017138 24.98636437 1.093599173 1.285812947 0.489100844 0.098267453 157.5433736 560972.1548 0.038343964 0.028257641 101.6288796 -2.007017138 0.192213775 KRS(ph)PSPS(ph)PTPEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.825)PS(0.251)PS(0.918)PT(0.005)PEAK 163.11 0.00019328 6330800000 2157700 1877900 1538000 1441400 1696900 1565300 1891900 2192800 2299800 1926500 TRUE FALSE 2073374.699 1824344.131 1815950.813 1515790.827 1751482.33 1596951.438 1915053.638 2147517.914 2038736.346 1796016.439 1.154429689 1.015772512 1.011099216 0.843973804 0.975203952 0.889163041 1.066278457 1.195711725 1.135143477 1 20.77636912 2.007041156 18.44978955 1.131772167 0.977933408 0.290901368 0.089988358 7.213020472 18897.7038 0.03433846 0.025198151 101.6345003 -2.007041156 -0.153838759 YSSSS(ph)IPEPFGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 YSSSSIPEPFGSR 13 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 YSSS(0.001)S(0.999)IPEPFGSR;YSSS(0.007)S(0.993)IPEPFGSR;YSSSS(1)IPEPFGSR;YSSS(0.001)S(0.999)IPEPFGSR 317.99 7.88E-51 638690000 1383940 1265000 801220 1276500 908950 737340 1251480 1617800 1302350 1365710 TRUE FALSE 1329854.095 1228923.439 946018.277 1342380.318 938187.2022 752249.52 1266795.987 1584391.865 1154512.688 1273209.245 1.04448982 0.965217181 0.743018699 1.054328126 0.736868041 0.590829451 0.994962919 1.244408074 0.906773723 1 20.28003811 2.007236605 24.99636132 1.088084193 0.853728256 0.234724682 0.157847467 207.8668394 718001.0762 0.060228006 0.044388755 101.6802499 -2.007236605 -0.234355937 T(ph)RNSGIWESPELDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRNSGIWESPELDR 14 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 T(0.739)RNS(0.261)GIWESPELDR 144.72 1.42E-05 211530000 138180 145140 126730 143910 100730 130380 125010 143440 107020 120280 TRUE FALSE 132779.7728 141000.7493 149632.9301 151337.2123 103970.0719 133016.3729 126539.9098 140477.9139 94871.53826 112133.3285 1.184124066 1.257438366 1.334419767 1.34961848 0.927200444 1.186234055 1.128477247 1.252775743 0.846060128 1 16.77485562 2.007253165 0.388489451 0.973973612 1.282904201 0.326605718 0.133158465 1.589070077 0.615076074 0.15905062 0.165695075 101.6841271 -2.007253165 0.308930589 DKDTDKFK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKDTDKFK 8 2 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 120.68 0.00082431 14444970000 25128400 19477570 17223060 13431200 16883580 14725670 21199170 24368000 29225100 23582170 FALSE TRUE 24146354.35 18922088.77 20335650.07 14124385.84 17426655.68 15023433.14 21458611.78 23864792.28 25907589.17 21984928.62 1.098313975 0.860684567 0.924981401 0.642457662 0.792663737 0.683351463 0.976060107 1.085506926 1.178424985 1 24.39001151 2.007289428 4.969851541 1.084575181 0.827674105 0.456195703 0.125173196 0.165018143 11.64149151 0.053477507 0.035821701 101.692618 -2.007289428 -0.256901076 KIEEIKDFLLTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIEEIKDFLLTAR 13 2 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 ; 179.79 7.56E-06 7011300000 6534000 5653200 5099500 4801400 5542600 5199900 6017800 7101800 6869400 6604000 FALSE TRUE 6278644.056 5491976.271 6021093.088 5049200.829 5720882.763 5305045.541 6091447.637 6955145.348 6089614.511 6156705.198 1.019805863 0.892031711 0.977973266 0.820114114 0.929211742 0.861669573 0.989400571 1.129686273 0.989102826 1 22.55372706 2.007378163 7.890131188 1.055526509 0.915328074 0.427688468 0.063655513 0.098630985 45.98510187 0.023523372 0.016685417 101.713398 -2.007378163 -0.140198434 LS(ph)TPQKK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSTPQKK 7 1 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 1 LS(0.5)T(0.5)PQKK;LS(0.5)T(0.5)PQKK;LS(0.5)T(0.5)PQKK 101.65 0.0054552 14972700000 4914300 3801210 3454850 3161140 3267430 3007410 3887100 4376000 4445500 4255200 TRUE FALSE 4722243.723 3692803.213 4079218.248 3324286.814 3372529.853 3068221.891 3934671.493 4285634.071 3940865.477 3966991.514 1.190384125 0.930882559 1.028290137 0.837986873 0.850147988 0.773437977 0.991852763 1.080323478 0.993414144 1 21.91961388 2.007447314 24.99848588 1.034150081 0.926916138 0.115575493 0.110463902 329.6113919 1106405.29 0.042925808 0.031641363 101.7295947 -2.007447314 -0.107233943 RKT(ph)SQSEEEEAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RKTSQSEEEEAPR 13 2 Q7RTP6;A0A5F9ZHV5;Q7RTP6-2;Q7RTP6-4;Q7RTP6-3;J3KSK6;Q7RTP6-5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 RKT(0.965)S(0.035)QSEEEEAPR 157.84 7.70E-05 292700000 189800 198520 155450 152790 196750 218450 165910 156140 170220 158590 TRUE FALSE 182382.4062 192858.404 183543.273 160675.5102 203078.6424 222867.2087 167940.4562 152915.6544 150897.3392 147848.558 1.23357582 1.304432093 1.241427549 1.086757371 1.373558492 1.507401977 1.135895124 1.034272207 1.020620973 1 17.17376065 2.007536562 24.97190387 1.0378502 1.287122209 0.594837936 0.101556689 134.2007086 444663.1055 0.040823593 0.030090948 101.7505024 -2.007536562 0.249272009 TGLWVGDCFIYTSSVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGLWVGDCFIYTSSVNR 17 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 90.731 0.0072817 0 33800 42207 29557 45276 30944 31507 40553 50256 43216 41103 FALSE TRUE 32479.05863 41003.29768 34898.60739 47612.69979 31939.34186 32144.09313 41049.29974 49218.19604 38310.30086 38319.0572 0.847595453 1.070049753 0.910737631 1.242533175 0.833510639 0.838853967 1.071250254 1.284431289 0.999771489 1 15.22577445 2.007570759 24.79591471 1.139213501 0.966532365 0.152188606 0.140733994 227.0524892 743643.697 0.052033846 0.038353397 101.7585146 -2.007570759 -0.172681137 ELEELKR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELEELKR 7 1 Q8TE76-2;Q8TE76-3;Q8TE76 Q8TE76-2 MORC4 MORC family CW-type zinc finger protein 4 0 ;; 116.11 0.0088642 7336700000 3688250 3638270 3073690 3427490 3188590 3205830 3584230 3857500 4153900 3967360 FALSE TRUE 3544109.112 3534510.102 3629174.157 3604383.17 3291153.893 3270654.079 3628094.879 3777841.277 3682366.687 3698647.173 0.95821768 0.955622404 0.981216641 0.974513924 0.889826398 0.884283882 0.980924838 1.02141164 0.995598259 1 21.81856625 2.007613895 24.98176682 1.006328845 0.941559614 0.480727656 0.030778962 164.4245246 539486.9011 0.012903654 0.009511329 101.7686223 -2.007613895 -0.064769231 SSQKS(ph)PELGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSQKSPELGK 10 1 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 S(0.018)S(0.093)QKS(0.888)PELGK;S(0.01)S(0.037)QKS(0.952)PELGK 121.45 0.0013541 104335000 183882 167721 141523 127558 147719 148501 167113 200675 194207 167759 TRUE FALSE 176695.6881 162937.7613 167099.3543 134141.2837 152470.5158 151503.792 169158.1789 196530.9911 172161.4355 156396.5335 1.129792868 1.041824634 1.068433875 0.857699852 0.974897029 0.968715793 1.081598007 1.256619867 1.100800841 1 17.25484901 2.007629518 7.536319464 1.15309669 1.004571162 0.219105483 0.090435259 0.143693165 54.22034575 0.035699255 0.02524376 101.7722834 -2.007629518 -0.148525527 TPS(ph)PAPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPSPAPK 7 0 Q96P11-2;Q63ZY6;Q63ZY6-6;Q3KNT7-3 Q96P11-2 NSUN5;NSUN5P2 Probable 28S rRNA (cytosine-C(5))-methyltransferase;Putative methyltransferase NSUN5C 1 T(0.117)PS(0.883)PAPK;T(0.101)PS(0.899)PAPK 93.267 0.015798 6473400000 5319300 4850000 4087300 4189100 4250500 4458500 4849300 5397900 5760400 5381500 TRUE FALSE 5111415.875 4711682.749 4825966.031 4405299.953 4387221.193 4548653.925 4908647.184 5286431.479 5106503.542 5017006.212 1.018817928 0.939142299 0.961921478 0.87807345 0.874469954 0.906647059 0.978401656 1.053702399 1.017838792 1 22.25839529 2.007641601 4.489849604 1.027673883 0.927306264 0.512229904 0.041171616 0.157126588 7.961562605 0.018630617 0.012235356 101.7751149 -2.007641601 -0.100367619 GNEFFCEVDEDYIQDK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNEFFCEVDEDYIQDK 16 0 P67870;Q5SRQ3;Q5SRQ6;N0E472;A0A0G2JM12;N0E644;A0A0G2JM58 P67870 CSNK2B;CSNK2B-LY6G5B-1181;CSNK2B-LY6G5B--991;CSNK2B-LY6G5B-562 Casein kinase II subunit beta 0 ; 261.27 1.85E-26 274930000 378820 282220 246350 353200 272480 171066 355270 403100 454540 489590 FALSE TRUE 364015.2956 274171.3619 290870.925 371428.6943 281244.5667 174525.0717 359617.9005 394775.8441 402942.5248 456429.6332 0.797527744 0.600687032 0.63727441 0.813769894 0.616183846 0.38237016 0.787893411 0.86492159 0.88281412 1 18.80003293 2.007695442 24.99989588 0.882279307 0.640900738 0.52171527 0.117326373 156.8806284 509649.8361 0.045011407 0.033182312 101.787733 -2.007695442 -0.241378569 TTNSS(ph)LEEIMDK ddPTM_BT-474_Pertuzumab_2h_R1 3 TTNSSLEEIMDK 12 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 1 TTNSS(1)LEEIMDK;TTNS(0.008)S(0.992)LEEIMDK;TTNS(0.013)S(0.987)LEEIMDK 289.22 4.68E-36 388000000 952260 905370 731970 768990 810770 554690 890840 969300 1112620 1063990 TRUE FALSE 915044.6264 879549.734 864253.2616 808677.6661 836849.1534 565906.2118 901742.3664 949283.6163 986320.0421 991925.0096 0.922493755 0.886709908 0.871288911 0.81526089 0.843661714 0.5705131 0.909083205 0.957011475 0.994349404 1 19.91987153 2.007755104 24.99995856 0.96751972 0.817762615 0.40108472 0.090709412 201.111438 648315.4467 0.035704759 0.026323155 101.8017173 -2.007755104 -0.149757106 GFGSSAPEGLEPDS(ph)MASAASALHLLSPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.25)MAS(0.25)AAS(0.25)ALHLLS(0.25)PRPR 66.886 0.0095657 106440000 48869 63505 56528 69585 52549 56025 46989 44391 41027 39216 TRUE FALSE 46959.14545 61693.89958 66743.86706 73176.29019 54239.28631 57157.86389 47564.06544 43474.31034 36369.78696 36559.86539 1.28444525 1.687476114 1.825604836 2.001547035 1.483574563 1.563404659 1.300991263 1.189126652 0.994800899 1 15.15797314 2.007759447 1.113396381 1.000259319 1.692983032 0.688873716 0.17989662 0.288254047 0.659655288 0.14302133 0.066972031 101.8027353 -2.007759447 0.692723712 QEPS(ph)PKPNNK ddPTM_BT-474_Pertuzumab_2h_R1 7 QEPSPKPNNK 10 1 Q8N684-2;Q8N684;Q8N684-3;F5H669;F5H6M0;F5H047;J3QT54;F5H5B7;F5H1W4;F5H2K8;F5H6P5;F5H6A8;F5GXA3;C9JM38;C9J286;C9J323 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 QEPS(1)PKPNNK;QEPS(1)PKPNNK;QEPS(1)PKPNNK;QEPS(1)PKPNNK;QEPS(1)PKPNNK;QEPS(1)PKPNNK;QEPS(1)PKPNNK 143.42 8.94E-05 7111550000 14226670 10816340 10687670 9234660 10675950 10939570 12369180 13997480 15784090 13693610 TRUE FALSE 13670676.01 10507868.57 12619169.71 9711261.909 11019351.63 11160775.6 12520557.72 13708427.15 13992346.28 12766129.6 1.07085518 0.823105272 0.988488298 0.760705258 0.863170904 0.874248966 0.980763796 1.073812313 1.096052344 1 23.60581786 2.00776146 3.114642278 1.061901003 0.89007508 0.422611467 0.083691503 0.221876186 4.246834209 0.038279301 0.022886995 101.8032071 -2.00776146 -0.171825924 GEFKDEEETVTTK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEFKDEEETVTTK 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 171.76 3.41E-06 2312580000 1757590 1569360 1384980 1265660 1571840 1535870 1724100 2019000 2228740 2005390 FALSE TRUE 1688901.44 1524603.389 1635276.695 1330980.864 1622399.661 1566926.344 1745200.052 1977306.944 1975742.779 1869563.149 0.903366886 0.815486436 0.874683851 0.711920785 0.867796128 0.83812432 0.93348013 1.057630466 1.056793818 1 20.83426977 2.007762359 2.45593865 1.044114638 0.830714815 0.762991834 0.05064847 0.129192823 1.468925045 0.025884987 0.014420715 101.8034178 -2.007762359 -0.213399823 AVQPHISPLTINIPDTMAHLISPLPSPTGT(ph)ISAANSCPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVQPHISPLTINIPDTMAHLISPLPSPTGTISAANSCPSSPR 42 0 Q01167;Q01167-2;E9PPI7;Q01167-3 Q01167 FOXK2 Forkhead box protein K2 2 AVQPHISPLTINIPDT(0.001)MAHLIS(0.021)PLPS(0.249)PT(0.284)GT(0.322)IS(0.17)AANS(0.167)CPS(0.393)S(0.393)PR 55.919 0.03942 68257000 8179.3 19444 13489 15785 18049 22430 13974 11476 10967 18980 TRUE FALSE 7859.643913 18889.47616 15926.76236 16599.66574 18629.56248 22883.54997 14145.01799 11239.01659 9722.072137 17694.46769 0.444186513 1.067535711 0.900098417 0.938127443 1.052846731 1.293260151 0.79940342 0.635171218 0.549441345 1 14.11101074 2.00795268 24.94514506 0.695072522 0.964143206 0.159210749 0.227988416 259.1104625 812746.9861 0.083661524 0.061679742 101.8480409 -2.00795268 0.269070684 LST(ph)PQKK ddPTM_BT-474_Pertuzumab_2h_R1 4 LSTPQKK 7 1 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 1 LS(0.024)T(0.976)PQKK;LS(0.375)T(0.625)PQKK;LS(0.148)T(0.852)PQKK;LS(0.088)T(0.912)PQKK 101.9 0.010628 7220800000 4219610 3304790 2849152 2539000 2854770 2600820 3282500 3664140 3827430 3494380 TRUE FALSE 4054702.976 3210540.625 3364057.145 2670038.094 2946596.27 2653410.362 3322672.217 3588474.229 3392956.192 3257702.53 1.244651081 0.985522955 1.032647123 0.819607705 0.90450133 0.814503577 1.019943407 1.101535268 1.041518113 1 21.63542344 2.007960851 24.99223256 1.059409473 0.957542809 0.085119094 0.116952379 381.5284784 1197763.414 0.045546014 0.033576525 101.8499573 -2.007960851 -0.101866664 ESSYGPEIDSHDFVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESSYGPEIDSHDFVLR 16 0 E5RGL4;E5RHV6;Q11201 E5RGL4 ST3GAL1 "CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1" 0 ; 235.71 1.04E-19 573400000 227220 359330 295950 344730 259810 208622 320850 367310 370490 348910 FALSE TRUE 218339.9912 349082.2602 349434.7484 362521.5566 268167.0246 212840.4798 324776.6583 359724.9201 328433.5284 325278.0149 0.671241157 1.07318123 1.074264882 1.114497568 0.824424069 0.654334047 0.998458683 1.105899888 1.009700974 1 18.31131379 2.007984258 24.99971459 1.050770072 0.91562457 0.14033032 0.152695255 387.9245178 1214634.851 0.061064604 0.045019706 101.8554468 -2.007984258 -0.135145502 AQS(ph)SPAAPASLSAPEPASQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQSSPAAPASLSAPEPASQAR 21 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;H0YI15;Q8WUI4-10 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 AQS(0.939)S(0.061)PAAPASLSAPEPASQAR 342.34 9.01E-81 215940000 89670 84682 62150 85621 89560 74400 96899 138160 95409 91665 TRUE FALSE 86165.59726 82266.95227 73381.88752 90039.91007 92440.77874 75904.41898 98084.87895 135306.9477 84578.57031 85456.4479 1.008298372 0.962676946 0.858705099 1.053635065 1.081729712 0.888223427 1.147776222 1.583343926 0.989727193 1 16.38290173 2.008030152 11.57421356 1.283256705 0.981279701 0.204471606 0.172201201 0.304845625 424.8591888 0.063609151 0.046125498 101.866211 -2.008030152 -0.301977005 (ac)AADDDNGDGTSLFDVFSAS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AADDDNGDGTSLFDVFSASPLK 22 0 Q9UKL3;A0A087WTW5;A0A096LP21 Q9UKL3 CASP8AP2 CASP8-associated protein 2 1 AADDDNGDGTSLFDVFS(0.013)AS(0.987)PLK 61.767 0.0002582 5846500 8420.3 8623 5704.3 8155.5 8281.4 5487.5 8853.3 11513 8773.9 9823.4 TRUE FALSE 8091.225367 8377.080483 6735.193901 8576.406332 8547.778752 5598.46101 8961.649334 11275.25253 7777.923655 9158.052368 0.883509402 0.914722929 0.735439549 0.93648802 0.933362074 0.61131568 0.978554061 1.231184544 0.849298884 1 13.1608251 2.008104103 24.99744446 1.065603584 0.839766454 0.306764844 0.129317279 180.1440555 555659.4247 0.047110546 0.034734528 101.883558 -2.008104103 -0.225837131 VKAPVHFVEPLS(ph)PTGVAGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKAPVHFVEPLSPTGVAGHR 20 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 VKAPVHFVEPLS(0.999)PT(0.001)GVAGHR;VKAPVHFVEPLS(1)PTGVAGHR 188.3 1.57E-17 1774800000 2437040 2570470 2200870 2468780 2555600 2890320 2109610 1624390 1988270 2033780 TRUE FALSE 2341797.783 2497162.712 2598616.167 2596194.032 2637803.195 2948764.251 2135428.038 1590845.779 1762569.925 1896030.269 1.235105695 1.317047915 1.370556267 1.369278789 1.3912242 1.555230578 1.12626263 0.839040286 0.929610647 1 20.85455057 2.008113201 5.144426625 0.919782888 1.370744401 0.855677225 0.083447507 0.060617297 4.807782472 0.035278132 0.023814852 101.8856924 -2.008113201 0.450961513 SSS(ph)PAELDLKDDLQQTQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPAELDLKDDLQQTQGK 19 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 SS(0.093)S(0.906)PAELDLKDDLQQTQGK;S(0.019)S(0.019)S(0.963)PAELDLKDDLQQTQGK 267.24 7.82E-32 1289950000 1471190 1240360 1157510 1072320 1283980 1266340 1521030 1816010 2115280 1768580 TRUE FALSE 1413694.268 1204986.147 1366697.806 1127662.564 1325280.383 1291946.262 1539644.82 1778508.759 1875162.282 1648792.501 0.857411874 0.730829468 0.82890831 0.68393237 0.803788458 0.783571166 0.933801445 1.078673488 1.137294281 1 20.65297842 2.0081318 2.276342521 1.082654073 0.775655027 0.845764129 0.055781552 0.100512765 0.976810879 0.028407655 0.015464859 101.8900558 -2.0081318 -0.306999046 SHFEQWGTLTDCVVMRDPNTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHFEQWGTLTDCVVMRDPNTK 21 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 246.73 1.52E-30 1762710000 474120 477670 341450 353350 401380 451850 363640 235163 501840 385250 FALSE TRUE 455590.8662 464047.3193 403157.6105 371586.4358 414290.7522 460986.7166 368090.3351 230306.8019 444873.2271 359156.6744 1.26850174 1.292047044 1.122511815 1.034608187 1.153509824 1.283525407 1.024873993 0.641243274 1.238660615 1 18.4542538 2.008235159 11.82604539 0.898346694 1.182358674 0.294094006 0.157537454 0.344637865 482.6956702 0.05954201 0.04322642 101.9143077 -2.008235159 0.28401198 SALS(ph)PSKS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SALSPSKSPAK 11 1 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 2 S(0.003)ALS(0.984)PS(0.014)KS(0.999)PAK;SALS(0.998)PS(0.003)KS(0.999)PAK;SALS(0.999)PS(0.15)KS(0.85)PAK 182.85 6.70E-05 817000000 2382090 1693010 1845470 1444820 1748610 1692140 2138980 2544290 2695000 2618270 TRUE FALSE 2288995.289 1644727.012 2178987.481 1519387.333 1804855.629 1726356.23 2165157.477 2491749.522 2389074.898 2440932.241 0.937754539 0.673811008 0.892686591 0.622461905 0.739412426 0.707252828 0.887020721 1.020818801 0.978755108 1 21.21900082 2.008300534 3.644456811 0.996527815 0.757260051 0.586204381 0.089692339 0.150542831 4.230681368 0.03828472 0.023925124 101.9296502 -2.008300534 -0.239267764 KLLYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLLYEK 6 1 H7C4X7;P05408-2;P05408 REV__J3KTF2 SCG5 Neuroendocrine protein 7B2;N-terminal peptide;C-terminal peptide 0 ; 105.12 0.053316 2131870000 1629980 1645220 1429010 1364950 1478340 1269420 1609860 1764020 1823190 1914760 FALSE TRUE 1566278.58 1598299.936 1687263.895 1435395.233 1525892.149 1295088.542 1629561.948 1727592.371 1616229.115 1785071.6 0.877431796 0.895370212 0.945207966 0.804110733 0.854807252 0.725510698 0.912883241 0.967800043 0.905414167 1 20.76755051 2.008302991 24.99984786 0.950705653 0.851883585 0.406869752 0.058555621 201.661527 607189.2518 0.022725686 0.016757082 101.9302269 -2.008302991 -0.098822068 GGS(ph)PQMDDIK ddPTM_BT-474_Pertuzumab_2h_R1 9 GGSPQMDDIK 10 0 Q13144;A0A3B3IUB1;A0A3B3ITG6 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 1 GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK 148.68 2.59E-05 11913520000 15286640 14359030 14558420 15653420 15715190 16287100 19200400 20234990 23514810 24226690 TRUE FALSE 14689221.21 13949524.52 17189450.34 16461294.88 16220683.36 16616436.32 19435380.24 19817130.39 20845507.35 22585794.71 0.650374335 0.617623808 0.761073523 0.72883399 0.718180767 0.735702973 0.860513455 0.877415678 0.922947703 1 24.42891234 2.008336139 0.465297532 1.010754801 0.646467835 0.90525004 0.035924388 0.28140571 0.139703547 0.038517496 0.032711672 101.9380071 -2.008336139 -0.364286966 FLESLPEEEQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLESLPEEEQQR 12 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 ; 153.12 0.00016373 28744000 117236 123190 100118 116578 110622 104995 118752 136123 125839 120707 FALSE TRUE 112654.2875 119676.7418 118211.5497 122594.6046 114180.2571 107118.0708 120205.3225 133312.0125 111554.2843 112531.4074 1.001091963 1.063496357 1.050476062 1.089425676 1.014652351 0.951894883 1.068193541 1.184664936 0.991316885 1 16.77996819 2.008362322 24.99588039 1.090991518 1.031302114 0 0.062663412 345.7387638 1033446.436 0.02360555 0.017407328 101.9441529 -2.008362322 -0.059689404 GTQEVAPPTPLT(ph)PTSHTANTSPRPVSGMER ddPTM_BT-474_Pertuzumab_2h_R1 4 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.941)PT(0.011)S(0.043)HT(0.003)ANT(0.001)S(0.001)PRPVS(0.001)GMER;GTQEVAPPTPLT(0.996)PT(0.003)S(0.001)HTANTSPRPVSGMER;GTQEVAPPTPLT(0.985)PT(0.013)S(0.002)HTANTSPRPVSGMER;GTQEVAPPT(0.005)PLT(0.815)PT(0.105)S(0.074)HT(0.001)ANTSPRPVSGMER 191.82 2.80E-18 1904280000 125941 176997 177508 198217 205540 250949 160330 145964 138693 151858 TRUE FALSE 121019.0865 171949.2189 209587.6442 208447.0031 212151.3808 256023.3607 162292.1665 142949.7924 122949.1521 141572.5224 0.854820444 1.214566329 1.480426008 1.47236907 1.498535006 1.808425508 1.14635357 1.009728371 0.868453497 1 17.11118176 2.008415494 24.99237794 0.989866346 1.400337637 0.410651773 0.231326472 198.2007502 588614.7472 0.092474611 0.068189223 101.9566352 -2.008415494 0.41047129 ANSTSDSVFTETPS(ph)PVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ANSTSDSVFTETPSPVLK 18 0 C9JEZ4;Q9UKI2 C9JEZ4 CDC42EP3 Cdc42 effector protein 3 1 ANSTSDSVFTET(0.003)PS(0.997)PVLK 194.51 7.26E-15 144200000 123250 163580 150550 176600 176370 178120 143840 112830 147420 147310 TRUE FALSE 118433.2537 158914.8586 177757.734 185714.3472 182043.1012 181721.7084 145600.3569 110500.0211 130685.4996 137332.5625 0.862382902 1.157153523 1.294359697 1.352296526 1.325564003 1.323223751 1.060202725 0.80461632 0.951598785 1 17.06731421 2.008423143 5.162838367 0.903238372 1.229321086 0.477509256 0.141091307 0.144637281 11.60454513 0.060988381 0.041220313 101.9584308 -2.008423143 0.326082714 RPDADLK ddPTM_BT-474_Pertuzumab_2h_R1 5 RPDADLK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ;;;; 111.74 0.01044 10948060000 7896180 11614440 6160140 11980830 7235960 6410590 10398090 14154390 11836850 7877510 FALSE TRUE 7587588.556 11283207.54 7273414.33 12599162.07 7468711.225 6540216.522 10525344.94 13862096.9 10493180.41 7343959.231 1.033174112 1.536392998 0.990394159 1.715581701 1.016987022 0.890557302 1.433197626 1.887550906 1.428817901 1 22.80812662 2.008458643 24.93875532 1.568148371 1.21384883 0.077878292 0.320287601 280.8532445 828040.3775 0.115849103 0.085426944 101.9667654 -2.008458643 -0.354299541 VKAS(ph)PITNDGEDEFVPSDGLDKDEYTFSPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKASPITNDGEDEFVPSDGLDKDEYTFSPGK 31 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VKAS(0.999)PIT(0.001)NDGEDEFVPSDGLDKDEYTFSPGK 308.03 8.67E-93 3103100000 303240 224890 206700 173950 220470 204890 250310 305270 320530 238490 TRUE FALSE 291389.0456 218476.3574 244055.288 182927.5803 227561.6178 209033.0162 253373.3687 298966.0678 284144.7782 222336.8599 1.31057462 0.982636696 1.097682535 0.82274968 1.023499288 0.940163571 1.139592278 1.344653639 1.277992225 1 17.76238762 2.008541346 6.793137312 1.24542355 1.021846831 0.226597759 0.144271945 0.155969831 36.70095283 0.054768511 0.038432653 101.9861848 -2.008541346 -0.223576719 RPLRPQVVTDDDGQAPEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPLRPQVVTDDDGQAPEAK 19 2 Q9HDC9;Q9HDC9-2 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 ; 106.67 0.0001741 2533100000 978480 1590360 850760 1617340 876100 898260 1412810 1898440 1649580 1173370 FALSE TRUE 940239.9198 1545004.49 1004511.257 1700811.111 904280.5522 916423.4326 1430100.391 1859236.551 1462326.594 1093896.605 0.859532716 1.412386219 0.918287206 1.554818896 0.826659986 0.83776056 1.307345123 1.699645599 1.336805131 1 20.06104495 2.008591671 24.43212435 1.443290338 1.086899718 0.14968837 0.284319228 195.1286325 554883.7991 0.102834795 0.075819994 101.9980035 -2.008591671 -0.35639062 VSHPQEPMLTAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSHPQEPMLTASPR 14 0 O75052-3;O75052;E9PSG0 O75052-3 NOS1AP Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein 1 VSHPQEPMLTAS(1)PR;VSHPQEPMLT(0.005)AS(0.995)PR 200.45 1.24E-08 397950000 603790 730380 677650 838740 563730 779380 646100 552860 657820 740790 TRUE FALSE 580193.2193 709550.2775 800116.4292 882027.4719 581862.8874 795139.5976 654007.1651 541443.2478 583147.0314 690615.6335 0.840110173 1.027417051 1.158555339 1.277161172 0.842527825 1.151348969 0.946991544 0.784000856 0.844387244 1 19.39752347 2.008653248 7.624463481 0.855130561 1.054263621 0.243752107 0.136958035 0.161914438 62.56177467 0.053072356 0.037641074 102.0124664 -2.008653248 0.199133061 YISKPENLK ddPTM_BT-474_Pertuzumab_2h_R1 2 YISKPENLK 9 1 Q9H9S4;Q5TAW7;B7ZBJ4;Q9Y376;A0A087X0K1 Q9H9S4;Q9Y376 CAB39L;CAB39 Calcium-binding protein 39-like;Calcium-binding protein 39 0 ; 91.855 0.0095495 1204300000 1623770 1565720 1457570 1257330 1464980 1226080 1597690 1720970 1884780 1968400 FALSE TRUE 1560311.273 1521067.199 1720985.322 1322220.952 1512102.412 1250872.178 1617243.008 1685431.368 1670827.676 1835078.515 0.85026949 0.828883989 0.937826534 0.720525548 0.823998755 0.681645045 0.881293631 0.918451911 0.910493836 1 20.80741036 2.008707078 24.99023864 0.925408976 0.808484226 0.429214362 0.069851186 201.0638859 577072.1947 0.026267086 0.019371154 102.0251116 -2.008707078 -0.116924749 DQDGYYWITGR ddPTM_BT-474_Pertuzumab_2h_R1 6 DQDGYYWITGR 11 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;;;;; 172.61 3.06E-05 11741600000 4749850 4551820 4075010 4824200 4822810 4911910 4596870 4619600 5179450 4838220 FALSE TRUE 4564220.611 4422006.55 4811454.955 5073177.54 4977940.064 5011232.186 4653127.87 4524203.646 4591500.55 4510523.05 1.011904952 0.980375558 1.06671774 1.124742626 1.103628118 1.111009107 1.031616027 1.00303304 1.017953018 1 22.10486331 2.008786761 24.27452826 1.009830394 1.067217655 0.294012047 0.041668511 198.0366175 547097.6065 0.017978348 0.013256024 102.0438324 -2.008786761 0.057387261 NEDEDSPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 NEDEDSPNK 9 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 159.4 0.0025325 0 231420 206730 201390 208780 215330 193810 231920 261090 262090 286890 FALSE TRUE 222375.8506 200834.2628 237785.6529 219555.1608 222256.285 197728.971 234758.3063 255698.4003 232338.642 267458.6848 0.831440006 0.750898267 0.889055643 0.820893743 0.830992963 0.739287906 0.877736711 0.956029528 0.86868984 1 18.02895653 2.008873686 8.23230104 0.931922759 0.812252739 0.580531779 0.049998064 0.09505882 50.16408736 0.018439037 0.013157926 102.0642587 -2.008873686 -0.11967002 HMEMENISSEEVVEIEYVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HMEMENISSEEVVEIEYVEK 20 0 Q9GZL7 Q9GZL7 WDR12 Ribosome biogenesis protein WDR12 0 ; 76.061 0.011716 134097000 78946 80224 64917 70446 71753 75800 72522 67203 87402 83072 FALSE TRUE 75860.70304 77936.09007 76648.94597 74081.7265 74061.00041 77332.72793 73409.54593 65815.23457 77480.49138 77445.45945 0.97953713 1.006335176 0.989715169 0.956566428 0.956298806 0.998544375 0.947887022 0.849826898 1.000452343 1 16.24089304 2.008913065 15.82238089 0.924770148 0.979848872 0.023823236 0.043873661 3.232401071 5734.760907 0.016285216 0.011935604 102.0735137 -2.008913065 0.055078724 DLEEDHACIPIKK ddPTM_BT-474_Pertuzumab_2h_R1 6 DLEEDHACIPIKK 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 191.26 2.41E-06 30949350000 44556550 40280390 33845340 35153020 38493330 43191760 44634790 46716710 56522730 53438790 FALSE TRUE 42815230.77 39131632.72 39961945.82 36967271.57 39731502.92 44065126.98 45181043.91 45751993.61 50106506.65 49819333.15 0.859409953 0.785470825 0.802137309 0.742026624 0.797511737 0.884498531 0.906897806 0.91835821 1.005764298 1 25.57020238 2.009193269 0.916759556 0.998365352 0.792818528 0.841859007 0.033915421 0.221321359 0.343334322 0.029076573 0.014152607 102.1393921 -2.009193269 -0.205546824 EQQIEEHRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQQIEEHRR 9 1 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 62.823 0.051995 91677000 32149 36384 33309 36407 32089 40778 34104 34315 36658 35206 FALSE TRUE 30892.58154 35346.36394 39328.67725 38285.96963 33121.17183 41602.5591 34521.37495 33606.38326 32496.73752 32821.46626 0.941231001 1.076928241 1.198260825 1.16649175 1.009131389 1.26754115 1.051792588 1.023914745 0.990106209 1 15.00235207 2.009256466 24.99389092 1.01496152 1.114537456 0.224628037 0.08752188 304.4002736 821924.7388 0.032862599 0.024238513 102.1542563 -2.009256466 0.099575935 TPDVFS(ph)SSPLHLQPPPLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPDVFSSSPLHLQPPPLGK 19 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 T(0.004)PDVFS(0.374)S(0.311)S(0.311)PLHLQPPPLGK;T(0.009)PDVFS(0.357)S(0.357)S(0.277)PLHLQPPPLGK 140.2 1.14E-07 306750000 256070 305220 257350 334500 341820 378350 263410 203880 249510 255030 TRUE FALSE 246062.5013 296515.4244 303858.8697 351763.5851 352814.9507 386000.4962 266633.6904 199669.8068 221186.6708 237756.5909 1.034934511 1.24713861 1.278025011 1.479511393 1.483933418 1.623511233 1.121456567 0.839807662 0.93030721 1 17.85912581 2.009312573 7.588579542 0.923313197 1.361985788 0.61863781 0.15403463 0.090916085 33.79563678 0.064746694 0.045962312 102.1674545 -2.009312573 0.438672591 VRS(ph)PGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VRSPGPK 7 1 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 VRS(1)PGPK 51.995 0.089857 92768000 290730 262560 276540 259920 265120 232740 301040 330550 360170 358290 TRUE FALSE 279367.9502 255072.0459 326516.9296 273334.5023 273647.8256 237446.1623 304724.2176 323724.027 319285.0116 334022.6992 0.836374147 0.763636862 0.977529163 0.81831116 0.81924919 0.710868342 0.912285956 0.969167748 0.955878185 1 18.34958662 2.009352873 24.8653628 0.963873856 0.824157785 0.537880524 0.064517153 153.0544669 406905.6026 0.024540759 0.0181006 102.1769355 -2.009352873 -0.139716071 IVRS(ph)SSSTGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 IVRSSSSTGQK 11 1 A0A1B0GW14;A0A0G2JH35;A0A0D9SG49;A0A0D9SEV1;Q4VXP6;O43526-4;O43526-5;O43526-3;O43526-2;O43526 A0A1B0GW14 KCNQ2 Potassium voltage-gated channel subfamily KQT member 2 1 IVRS(0.998)S(0.001)SSTGQK 77.744 0.019033 0 595570 544500 582080 567020 590030 400530 590420 643160 683450 643250 TRUE FALSE 572294.466 528971.3931 687274.8043 596283.9702 609008.8508 408628.991 597645.7366 629878.5212 605867.6213 599682.1046 0.954329738 0.882086341 1.146065222 0.99433344 1.015552817 0.681409347 0.996604254 1.05035404 1.010314659 1 19.1938384 2.009410346 24.99970793 1.025233193 0.947390954 0.086590343 0.110846962 517.853386 1375732.821 0.043277694 0.031921407 102.1904581 -2.009410346 -0.077842238 SGITS(ph)PVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGITSPVEK 9 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 SGIT(0.023)S(0.977)PVEK;SGIT(0.002)S(0.998)PVEK 145.23 0.00010246 798100000 2080000 1924500 1870400 1950910 2120000 1898870 2153600 2446800 2442900 2424900 TRUE FALSE 1998711.3 1869615.144 2208422.887 2051596.699 2188191.725 1937266.452 2179956.401 2396272.725 2165592.233 2260659.363 0.884127584 0.827022052 0.976893256 0.907521377 0.967944026 0.856947528 0.96430114 1.05998841 0.957947167 1 21.10831219 2.00944547 8.407905542 1.012608316 0.906638429 0.478655488 0.048376505 0.110719123 61.76746984 0.018392953 0.013157761 102.1987232 -2.00944547 -0.105969886 TS(ph)SPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSPPR 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.098)S(0.451)S(0.451)PPR 94.662 0.046392 71487000 327860 299590 257980 300920 288420 299840 283020 270960 282810 320490 TRUE FALSE 315046.8687 291045.9865 304602.7247 316450.5173 297697.2912 305902.9702 286483.6834 265364.5813 250706.5944 298782.9268 1.054433973 0.974105146 1.019478348 1.059131861 0.996366474 1.023830155 0.958835521 0.888151757 0.839092772 1 18.18873819 2.00945332 2.935184888 0.898547516 1.019698337 0.563993696 0.044149538 0.170456071 2.852064863 0.020335179 0.011973662 102.2005706 -2.00945332 0.121150821 EASDGEVRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EASDGEVRR 9 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 110.76 0.0035842 61004000 87014 93605 73723 94581 93821 108070 84784 84742 79412 91726 FALSE TRUE 83613.39668 90935.47705 87046.38606 99462.33674 96838.83767 110255.2494 85821.61195 82992.04809 70397.48268 85513.31632 0.977782178 1.063407209 1.017927848 1.163121032 1.132441611 1.289334272 1.003605235 0.970516075 0.823234155 1 16.38386148 2.009470611 24.92484931 0.942745695 1.108411662 0.436433651 0.090505572 193.6463485 509638.1939 0.035526943 0.026206578 102.2046395 -2.009470611 0.165665967 (ac)AADVSVTHRPPLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 AADVSVTHRPPLSPK 15 1 A0A087WZ13;Q8IY67-2;Q8IY67;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 AADVSVT(0.002)HRPPLS(0.998)PK;AADVSVT(0.001)HRPPLS(0.999)PK;AADVSVTHRPPLS(1)PK;AADVSVT(0.001)HRPPLS(0.999)PK;AADVSVTHRPPLS(1)PK;AADVSVT(0.001)HRPPLS(0.999)PK 110.77 1.44E-08 42199300000 5036130 5130720 4297520 4322550 4468740 4023110 4933720 5247230 5895450 5648010 TRUE FALSE 4839312.472 4984396.889 5074177.462 4545637.324 4612481.081 4104460.041 4994100.341 5138872.867 5226223.232 5265465.252 0.919066453 0.946620413 0.963671246 0.863292626 0.875987374 0.779505674 0.948463261 0.975957987 0.992547283 1 22.32812958 2.009570378 24.99779469 0.980675493 0.892582163 0.458138882 0.048095109 211.094578 551375.8972 0.019776448 0.014588115 102.228121 -2.009570378 -0.08809333 RAQS(ph)IER ddPTM_BT-474_Pertuzumab_2h_R1 1 RAQSIER 7 1 O14681-3;O14681;E9PLB8;E9PL33;E9PM05;E9PS58;E9PK61 O14681-3 EI24 Etoposide-induced protein 2.4 homolog 1 RAQS(1)IER 65.933 0.073348 219590000 260770 422490 239110 441980 298900 310040 364020 457240 357850 338360 TRUE FALSE 250578.8201 410440.9989 282322.496 464790.6408 308514.39 316309.2212 368474.9857 447797.8342 317228.3682 315442.5758 0.794372223 1.301159166 0.895004408 1.473455635 0.978036618 1.002747395 1.168120647 1.419585904 1.005661228 1 18.26701787 2.009651619 23.39489934 1.214740582 1.08970205 0 0.216547312 267.1443002 647534.8438 0.077153752 0.056888239 102.2472459 -2.009651619 -0.125038532 SLSFPILNPALSQPSQPSS(ph)PLPGSHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSFPILNPALSQPSQPSSPLPGSHGR 27 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 SLSFPILNPALSQPSQPS(0.132)S(0.863)PLPGS(0.004)HGR 140.52 1.43E-07 369380000 89493 122020 114460 136720 141910 135600 113320 100210 114360 116530 TRUE FALSE 85995.51462 118540.1091 135145.4681 143776.1356 146474.664 138341.9249 114706.8441 98140.62848 101378.3322 108637.3193 0.791583548 1.091154585 1.244005918 1.323450694 1.348290486 1.273429111 1.055869611 0.903378591 0.93318146 1 16.72916026 2.009675403 4.58800024 0.942439427 1.19141153 0.324903829 0.150587443 0.230140782 12.43781126 0.068433836 0.045307808 102.2528457 -2.009675403 0.248972103 RAETFAGYDCTNS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 2 RAETFAGYDCTNSPTK 16 1 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 RAETFAGYDCT(0.056)NS(0.849)PT(0.095)K;RAETFAGYDCT(0.043)NS(0.953)PT(0.004)K 141.1 1.00E-06 1085790000 409400 342220 280850 350560 326890 334420 369700 414920 420380 451110 TRUE FALSE 393400.1954 332460.2207 331605.8425 368652.4436 337404.7137 341182.2015 374224.4992 406351.757 372660.2248 420555.9179 0.935428985 0.790525603 0.788494058 0.876583655 0.802282644 0.811264774 0.889832917 0.966225274 0.886113377 1 18.68193811 2.009691042 3.913612091 0.944546055 0.830901566 0.523930893 0.049713298 0.168073774 5.706370524 0.020931111 0.013351627 102.2565278 -2.009691042 -0.11364449 NDVDVQIDQESYLPEDIAGGVEIYNGDRK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDVDVQIDQESYLPEDIAGGVEIYNGDRK 29 1 P36543;C9J8H1;P36543-3;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 ; 260.76 6.35E-58 330520000 222070 199691 158773 175418 191862 202262 208750 235380 268630 246930 FALSE TRUE 213391.2589 193996.0082 187466.813 184471.344 198033.4155 206351.8762 211304.7449 230519.3207 238136.2486 230205.2112 0.926961027 0.842709021 0.814346522 0.801334353 0.860247318 0.896382298 0.917897314 1.001364476 1.034452033 1 17.81256097 2.009720944 1.347561735 1.022443941 0.845105997 0.812204669 0.033687667 0.177944525 0.601353907 0.024705046 0.011695773 102.2635686 -2.009720944 -0.177337944 TRWS(ph)GAQPLEQPSGSVLWMAAEVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRWSGAQPLEQPSGSVLWMAAEVIR 25 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 T(0.256)RWS(0.744)GAQPLEQPSGSVLWMAAEVIR 131.84 4.64E-05 147300000 56570 58484 52264 56886 73148 78273 57625 54280 61011 60823 TRUE FALSE 54359.18186 56816.09358 61709.26741 59821.89328 75500.87185 79855.73369 58330.23199 53159.09903 54085.28706 56703.40403 0.958658176 1.001987351 1.088281532 1.054996509 1.331505103 1.408305816 1.028690129 0.937493964 0.953827869 1 15.79114773 2.009817635 24.97959589 0.963394583 1.143540409 0.273594583 0.131394841 288.4575975 733936.7123 0.055240785 0.040749978 102.2863391 -2.009817635 0.180145826 DLISLDSS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLISLDSSPAK 11 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.006)S(0.994)PAK;DLISLDS(0.005)S(0.995)PAK;DLISLDS(0.029)S(0.971)PAK 243.37 8.53E-16 502108000 2644250 2182410 2220590 2239810 2205270 1940400 2621090 3183920 2917840 3290360 TRUE FALSE 2540909.787 2120169.804 2621900.01 2355406.863 2276204.512 1979636.217 2653167.683 3118170.939 2586619.036 3067500.986 0.828332182 0.691171678 0.854734855 0.767858551 0.742038722 0.645357973 0.864928062 1.016518317 0.843233318 1 21.54863238 2.009850615 9.81281178 0.951583417 0.756352859 0.616204105 0.070758401 0.115906776 100.4711594 0.025976047 0.018758967 102.2941069 -2.009850615 -0.195230558 TQTPPVS(ph)PAPQPTEERLPSSPVY(ph)EDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.011)QT(0.041)PPVS(0.819)PAPQPT(0.13)EERLPS(0.15)S(0.419)PVY(0.431)EDAASFK 80.923 0.0053889 137160000 127330 145740 113870 143010 154000 176260 121990 108010 122890 118710 TRUE FALSE 122353.8028 141583.6379 134448.842 150390.7632 158953.5499 179824.098 123482.9501 105779.5558 108940.0424 110669.666 1.105576689 1.279335549 1.21486625 1.35891585 1.436288331 1.62487251 1.11577955 0.955813455 0.984371295 1 16.75590031 2.009859824 24.99321822 0.990313068 1.337067691 0.612899675 0.128967955 142.4746986 361151.1512 0.051957734 0.038329961 102.2962761 -2.009859824 0.346754623 GQSQT(ph)SPDHRSDT(ph)S(ph)S(ph)PEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 4 GQS(0.224)QT(0.415)S(0.361)PDHRS(0.604)DT(0.699)S(0.699)S(0.998)PEVR 71.678 0.013007 606420000 268770 280730 247450 288040 260290 295890 265190 256510 316760 264230 TRUE FALSE 258266.1713 272723.8553 292169.7195 302905.7789 268662.4642 301873.0985 268435.4745 251212.9789 280802.7328 246333.4667 1.048441264 1.107132778 1.186073997 1.229657435 1.090645408 1.22546523 1.089723934 1.019808563 1.139929286 1 17.91025312 2.009877332 24.32432257 1.055276728 1.149622813 0.313949461 0.063629638 172.2022443 424069.9322 0.023643984 0.017440049 102.3003999 -2.009877332 0.094346085 S(ph)PGYEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGYEPR 7 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 S(0.995)PGY(0.005)EPR;S(1)PGYEPR 102.07 0.0091091 575300000 740860 670720 604830 638290 673680 677960 602720 489460 671100 524520 TRUE FALSE 711906.3721 651591.7223 714136.2354 671232.2234 695349.529 691668.8157 610096.2677 479352.48 594919.5415 488993.7932 1.455859731 1.332515323 1.460419836 1.372680457 1.422000726 1.41447361 1.247656465 0.980283363 1.216619822 1 18.89945663 2.009941137 3.585393327 1.068936963 1.406243616 0.832216079 0.069189096 0.081301973 2.191880312 0.028918057 0.018032998 102.3154307 -2.009941137 0.337306654 DENWDKEIEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DENWDKEIEK 10 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ;;; 176.29 2.32E-06 2628580000 4700630 4420180 3594360 3513610 4439650 4822950 5179810 6249740 7481580 6867030 FALSE TRUE 4516924.183 4294120.794 4243940.808 3694947.833 4582455.374 4920473.353 5243202.064 6120680.685 6632302.404 6401919.942 0.705557743 0.670755154 0.662916882 0.577162455 0.715793921 0.76859339 0.819004629 0.956069545 1.035986464 1 22.6100732 2.009970458 1.108320789 1.027192178 0.658752302 0.934401013 0.038142573 0.115794997 0.262586176 0.030457015 0.014288907 102.3223387 -2.009970458 -0.368439876 EIQNGNLHES(ph)DSESVPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIQNGNLHESDSESVPR 17 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 EIQNGNLHES(0.952)DS(0.048)ESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(0.996)DS(0.004)ESVPR 348 3.01E-63 1942380000 768261 1317670 637929 1549750 839691 866604 1112440 1474830 1165730 726083 TRUE FALSE 738236.5108 1280091.342 753216.961 1629732.783 866700.4236 884127.3266 1126054.373 1444374.245 1033401.218 676904.7517 1.090606188 1.891095222 1.112736997 2.407624971 1.28038756 1.306132546 1.66353445 2.133792445 1.526656764 1 19.36859332 2.009982969 24.7353412 1.734260891 1.538635918 0 0.460880038 709.9229208 1759006.558 0.165095582 0.121784141 102.3252864 -2.009982969 -0.195624973 S(ph)SSPVTELASRS(ph)PIRQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.348)S(0.303)S(0.348)PVT(0.002)ELAS(0.258)RS(0.74)PIRQDR 96.903 0.0074101 690860000 531150 644070 334740 366990 441540 601000 398990 370270 387320 328660 TRUE FALSE 510392.0708 625701.7542 395234.9643 385930.3979 455742.5351 613152.6318 403872.959 362623.7951 343353.0574 306399.5655 1.665772828 2.042110449 1.289933175 1.259565748 1.487412472 2.001153725 1.318125104 1.183499704 1.120605562 1 18.22505473 2.009995774 24.99419884 1.154021009 1.609839463 0.475988327 0.246747185 206.9033609 517354.8045 0.098600564 0.072742196 102.3283036 -2.009995774 0.455818455 NPSDSAVHS(ph)PFTKR ddPTM_BT-474_Pertuzumab_2h_R1 4 NPSDSAVHSPFTKR 14 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(0.999)PFT(0.001)KR;NPSDSAVHS(1)PFTKR;NPSDSAVHS(0.999)PFT(0.001)KR;NPSDSAVHS(0.998)PFT(0.002)KR 183.74 6.46E-07 3957460000 2651160 2951190 2174500 2403920 2331510 3013810 2242160 2016930 2235300 2357630 TRUE FALSE 2547549.736 2867024.951 2567480.521 2527986.599 2406505.137 3074751.303 2269600.225 1975279.691 1981558.115 2197945.62 1.159059493 1.30441123 1.168127409 1.150158847 1.094888388 1.398920553 1.032600718 0.898693613 0.90155011 1 21.06772426 2.009997743 24.42784568 0.933030501 1.207325259 0.691319484 0.085185385 82.51783637 201617.5989 0.031171583 0.022993214 102.3287675 -2.009997743 0.274294758 WEAERDDWLHNR ddPTM_BT-474_Pertuzumab_2h_R1 3 WEAERDDWLHNR 12 1 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 ;; 170.95 2.39E-05 317357000 348203 395957 249729 300711 346172 382239 299898 276699 322857 294730 FALSE TRUE 334594.8418 384664.694 294860.5855 316230.7307 357306.9368 389968.1345 303568.2414 270985.069 286207.6269 274767.6746 1.217737284 1.399963422 1.07312691 1.150902235 1.300396553 1.419264967 1.104817886 0.98623344 1.041635001 1 18.06785276 2.010013387 23.51997801 1.017201279 1.255526995 0.572717095 0.098580614 75.69749577 177800.7191 0.038569837 0.028443948 102.3324536 -2.010013387 0.238325716 KKDVDDDGEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKDVDDDGEEK 11 2 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 148.89 1.95E-05 163580000 427030 278060 306870 240170 305250 260510 369090 471790 497300 379880 FALSE TRUE 410341.1955 270130.001 362328.2353 252565.2025 315068.6435 265777.6907 373607.0338 462047.3716 440848.5889 354150.3892 1.158663686 0.762755059 1.02309145 0.713158054 0.88964647 0.750465618 1.054938933 1.304664306 1.244806168 1 18.4340026 2.010027196 5.702688714 1.209694704 0.877247133 0.463337598 0.145324384 0.118625211 13.57056453 0.054541189 0.037568646 102.3357074 -2.010027196 -0.332447571 S(ph)RSPGRPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPGRPPK 9 2 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.768)RS(0.232)PGRPPK 86.911 0.010882 284220000 266370 344900 165940 344650 236270 210780 290940 361750 341060 216520 TRUE FALSE 255959.9659 335063.7897 195929.0493 362437.4278 243869.8391 215042.116 294500.6107 354279.7361 302344.2986 201854.9075 1.268039351 1.659923921 0.970642982 1.795534388 1.208144217 1.065330136 1.458971765 1.755120747 1.497829814 1 17.62295914 2.010075335 24.97405964 1.527925974 1.335891349 0 0.295809207 522.4589356 1295030.251 0.105817493 0.078063329 102.3470513 -2.010075335 -0.192034625 S(ph)SSETILSSLAGSDIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.293)S(0.293)S(0.293)ET(0.12)ILS(0.001)S(0.001)LAGSDIVK 78.69 0.015869 20029000 71957 65430 58619 73002 64358 62732 71627 79606 77955 83310 TRUE FALSE 69144.84089 63564.00046 69212.75727 76769.64197 66428.13352 64000.48402 72503.59265 77962.10828 69105.87521 77667.3395 0.890269209 0.818413517 0.891143661 0.988441763 0.855290447 0.824033428 0.933514565 1.003795273 0.889767509 1 16.24502043 2.010126038 21.78962856 0.965870716 0.879733821 0.358698725 0.05283329 48.01941292 103328.1147 0.020293182 0.014957022 102.3590008 -2.010126038 -0.086136895 SECEAEVGWNLTYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SECEAEVGWNLTYSR 15 0 Q9Y365;F5H0V7;F5H8G1;F5H1Z6;F5H3G8;F5H5A8 Q9Y365 STARD10 PCTP-like protein 0 102.73 0.0035553 70905000 95996 99144 83009 96406 89272 84840 99657 110010 118400 103210 FALSE TRUE 92244.37019 96316.51019 98010.57283 101381.5252 92143.51495 86555.52293 100876.6322 107738.2551 104959.7284 96219.49477 0.958686911 1.001008272 1.018614503 1.053648488 0.957638732 0.899563266 1.048401183 1.119713373 1.090836411 1 16.5540416 2.010150083 24.96587016 1.08362789 0.985264778 0.413379909 0.048164793 179.2887334 440989.4343 0.018565098 0.013696703 102.3646683 -2.010150083 -0.098363111 SCTPSPDQISHRAS(ph)LEDAPVDDLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCTPSPDQISHRASLEDAPVDDLTR 25 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 SCTPSPDQIS(0.003)HRAS(0.997)LEDAPVDDLTR 227.11 3.45E-34 329610000 37772 48242 30450 33427 42879 42320 34825 30118 34828 35323 TRUE FALSE 36295.82848 46866.18539 35952.99236 35152.17148 44258.24198 43175.7394 35251.19877 29496.05278 30874.47145 32930.54175 1.102193482 1.423182945 1.091782596 1.067464111 1.343987667 1.311115369 1.070471268 0.895705057 0.937563423 1 15.00713863 2.010233673 4.475548029 0.941141748 1.224128447 0.559466036 0.111605758 0.143202307 7.160013047 0.047655638 0.031411773 102.3843725 -2.010233673 0.282986699 PTS(ph)SPAKGPPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 PTSSPAKGPPQK 12 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 PT(0.004)S(0.498)S(0.498)PAKGPPQK 136.17 6.95E-05 603060000 844970 571310 626770 526830 627020 570670 737360 856970 945790 860920 TRUE FALSE 811947.6382 555016.7982 740041.2814 554019.7594 647188.6677 582209.3384 746384.0322 839273.27 838427.8843 802609.1216 1.011635199 0.691515687 0.922044444 0.69027344 0.806355984 0.725395865 0.929947109 1.045681201 1.044627904 1 19.61433803 2.010257173 4.168485106 1.0279042 0.802627877 0.524467876 0.095287029 0.149564785 6.057022683 0.038084178 0.024696245 102.3899129 -2.010257173 -0.225276324 KDPEQEVEK ddPTM_BT-474_Pertuzumab_2h_R1 5 KDPEQEVEK 9 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;; 132.25 0.0004976 3529220000 1732100 1530460 1252340 1264020 1410500 1318670 1576540 1794860 1898410 1821190 FALSE TRUE 1664407.617 1486812.779 1478665.696 1329256.224 1455870.013 1345334.411 1595834.168 1757795.514 1682910.456 1697839.179 0.980309347 0.875708841 0.87091034 0.782910561 0.857484049 0.792380355 0.939920687 1.035313318 0.991207222 1 20.69526838 2.010267863 5.388437025 1.007770179 0.857608119 0.62906716 0.051541072 0.107679499 9.981612239 0.021467896 0.01466488 102.3924331 -2.010267863 -0.15016206 AADKS(ph)PESQNLIDGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 AADKSPESQNLIDGTK 16 1 Q9HCE3 Q9HCE3 ZNF532 Zinc finger protein 532 1 AADKS(1)PESQNLIDGTK;AADKS(0.927)PES(0.073)QNLIDGTK 226.71 3.45E-15 757090000 613180 506140 461710 415540 558200 537630 597760 773830 804000 697390 TRUE FALSE 589216.2477 491705.3828 545151.2677 436986.0692 576155.0099 548501.247 605075.5657 757850.1401 712733.2906 650155.1541 0.906270209 0.756289294 0.838494111 0.672125825 0.886180793 0.843646695 0.930663338 1.165645055 1.096251081 1 19.31042452 2.010335207 2.784030123 1.101759994 0.810731248 0.724908965 0.073965738 0.125866729 1.873838226 0.035503605 0.020599435 102.4083118 -2.010335207 -0.291028747 KFGYVDFESAEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 6 KFGYVDFESAEDLEK 15 1 P19338 P19338 NCL Nucleolin 0 ;;;;; 274.17 2.89E-33 12405260000 17399560 14657630 12570840 11723380 13964110 15182580 14509910 16521380 18510140 16529920 FALSE TRUE 16719565.96 14239608.74 14842670.42 12328425.05 14413278.28 15489582.17 14687486.62 16180207.73 16408946.51 15410333.8 1.084958067 0.924029871 0.96316346 0.800010254 0.935299551 1.005142548 0.953093347 1.049958291 1.064801498 1 23.87739478 2.010377684 1.551108596 1.043181914 0.939226783 0.226336686 0.069609367 0.539802677 2.426113891 0.046298156 0.022553298 102.4183285 -2.010377684 -0.103955131 AVLS(ph)PGSVFS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 3 AVLSPGSVFSPGR 13 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 2 AVLS(0.993)PGS(0.016)VFS(0.991)PGR;AVLS(0.999)PGS(0.09)VFS(0.911)PGR;AVLS(0.975)PGS(0.025)VFS(1)PGR 178.85 2.08E-05 135896000 432204 601522 601198 845135 896579 773129 516681 452283 369945 458042 TRUE FALSE 415312.9899 584367.1815 709847.8522 888752.5186 925418.2778 788762.1981 523004.2966 442943.198 327950.3945 427018.4074 0.972588026 1.368482415 1.662335487 2.08129791 2.167162497 1.847138635 1.22478162 1.037292984 0.768000603 1 18.70393874 2.010407284 2.860198712 0.946354022 1.706149144 0.511726121 0.329618157 0.245096782 3.872841501 0.181874131 0.106385891 102.4253094 -2.010407284 0.759795122 TGSGS(ph)PFAGNSPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGS(0.001)GS(0.999)PFAGNSPAR;T(0.033)GS(0.012)GS(0.956)PFAGNSPAR;TGS(0.002)GS(0.997)PFAGNSPAR 165.57 3.22E-07 765140000 812610 796350 639720 772570 731040 706850 782210 830450 878380 895250 TRUE FALSE 780852.3028 773638.8777 755331.6345 812442.4303 754554.5655 721142.9913 791782.92 813300.9173 778669.9849 834613.9201 0.935585046 0.926942217 0.905007233 0.973435035 0.904076181 0.86404381 0.948681661 0.974463638 0.932970283 1 19.67074946 2.01042151 24.99654259 0.965123622 0.918727277 0.369063074 0.030125104 238.6954164 572520.9816 0.011344112 0.008370438 102.4286644 -2.01042151 -0.046396345 VLPYIFEDPDWR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLPYIFEDPDWR 12 0 Q8IV36-2;Q8IV36;J3KSF1;E9PIM7 Q8IV36-2 HID1 Protein HID1 0 ; 127.76 0.00061402 456690000 425400 569970 328610 432460 431160 536090 403040 393690 362050 438400 FALSE TRUE 408774.8977 553715.0137 387997.1369 454779.3124 445028.653 546930.1071 407972.5241 385560.1639 320951.6018 408706.7775 1.000166673 1.354797728 0.949328854 1.112727602 1.088870255 1.338196813 0.998203471 0.943366211 0.785285734 1 18.64070664 2.010488595 24.88750747 0.920139682 1.140599545 0.393935816 0.130302304 197.2186483 467961.4596 0.046936993 0.034630185 102.4444878 -2.010488595 0.220459863 TNAVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 TNAVSPK 7 0 Q6XZF7 Q6XZF7 DNMBP Dynamin-binding protein 1 TNAVS(1)PK;TNAVS(1)PK;TNAVS(1)PK 82.954 0.024222 599680000 1111220 953260 764000 846490 840870 903630 983570 1107550 1170080 1166840 TRUE FALSE 1067792.294 926073.9581 902071.7951 890177.4503 867917.3472 921902.0177 995607.2239 1084678.705 1037257.424 1087808.887 0.981599163 0.851320456 0.829255769 0.818321546 0.797858298 0.847485278 0.915240936 0.997122489 0.953529095 1 20.05299369 2.010613129 3.00575539 0.98139536 0.84891655 0.590966183 0.048038627 0.181978298 3.214981623 0.023890965 0.014184402 102.4738679 -2.010613129 -0.132478809 MDSFDEDLARPSGLLAQER ddPTM_BT-474_Pertuzumab_2h_R1 2 MDSFDEDLARPSGLLAQER 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 139.17 4.38E-07 1143250000 695020 730330 528440 679570 683340 733880 638750 637080 684730 653860 FALSE TRUE 667857.85 709501.7035 623940.8631 714642.6891 705320.2517 748719.5564 646567.2136 623924.0754 607002.321 609573.4798 1.095615003 1.163931383 1.023569568 1.172365125 1.157071748 1.22826793 1.060687899 1.023542027 0.995782036 1 19.21744061 2.010623208 23.99399838 1.017321575 1.138681526 0.583429 0.051033553 97.41782973 220030.3019 0.019549366 0.014421549 102.4762462 -2.010623208 0.121359951 GDKENASQCFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDKENASQCFEK 12 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 ; 94.673 0.004569 138100000 427130 320130 317740 305580 316810 288000 368690 417720 422120 414630 FALSE TRUE 410437.2874 311000.2058 375162.6861 321351.0204 327000.4814 293823.5573 373202.1385 409093.936 374202.7073 386546.7408 1.061805065 0.804560414 0.970549345 0.831338067 0.845953275 0.760124265 0.96547739 1.058329803 0.968065871 1 18.56028335 2.010702776 24.90066954 1.014435647 0.8750414 0.33680652 0.083196931 202.0334608 470041.3793 0.029930426 0.022084686 102.4950228 -2.010702776 -0.139394247 SASQSS(ph)LDKLDQELK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 SASQS(0.017)S(0.983)LDKLDQELK;SASQS(0.313)S(0.687)LDKLDQELK 264.92 2.20E-25 1055400000 1195030 900230 967050 843560 918140 940910 1399910 1512450 1958590 1727220 TRUE FALSE 1148326.906 874556.3218 1141817.447 887096.2327 947672.8069 959935.8449 1417042.517 1481217.379 1736259.074 1610233.851 0.713142942 0.543123796 0.709100387 0.55091143 0.588531167 0.596146854 0.880022809 0.919877183 1.078265168 1 20.61883879 2.010825111 1.862523752 1.01007361 0.610461012 0.869925302 0.067531298 0.109936503 0.713101288 0.038311624 0.019647227 102.5238982 -2.010825111 -0.399612599 VKEEASS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKEEASSPLK 10 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 VKEEAS(0.023)S(0.977)PLK;VKEEAS(0.093)S(0.907)PLK 131.35 0.00015285 1737280000 2342810 1961050 1729390 1638240 1799940 1713580 2198080 2612000 2784960 2591790 TRUE FALSE 2251250.395 1905122.774 2041929.243 1722789.763 1857836.705 1748229.762 2224980.761 2558061.287 2468823.016 2416245.755 0.931714165 0.788463992 0.845083427 0.713002707 0.768893934 0.723531436 0.920842077 1.058692512 1.021759898 1 21.20433577 2.010870354 4.260306281 1.026548016 0.792667816 0.751770237 0.059995235 0.097585654 4.2071468 0.02608452 0.017019099 102.5345793 -2.010870354 -0.2338802 FKVETR ddPTM_BT-474_Pertuzumab_2h_R1 1 FKVETR 6 1 Q53GQ0;E9PI21;A0A1B0GVY6 Q53GQ0 HSD17B12 Very-long-chain 3-oxoacyl-CoA reductase 0 83.843 0.051552 513220000 875270 1300000 748160 1442700 850200 946500 1192800 1545600 1377100 941120 FALSE TRUE 841063.4807 1262925.273 883369.1547 1517157.92 877547.4551 965638.8785 1207397.843 1513682.82 1220777.381 877377.1041 0.958611157 1.439432676 1.006829504 1.729197072 1.000194159 1.100597308 1.37614469 1.72523629 1.391394163 1 19.74283753 2.010882246 16.5242014 1.47726599 1.223203206 0.039746319 0.279467854 6.827019164 10363.20367 0.099829734 0.073356942 102.537387 -2.010882246 -0.254062784 RAPS(ph)PGAYK ddPTM_BT-474_Pertuzumab_2h_R1 4 RAPSPGAYK 9 1 P54259 P54259 ATN1 Atrophin-1 1 RAPS(1)PGAYK;RAPS(1)PGAYK;RAPS(1)PGAYK;RAPS(1)PGAYK 104.24 0.0020161 3968780000 3263450 2988410 2477570 2732600 2700960 2824750 2998960 3325220 3520320 3282840 TRUE FALSE 3135910.766 2903183.473 2925322.012 2873629.813 2787838.831 2881868.38 3035662.17 3256553.045 3120708.032 3060490.323 1.024643255 0.948600769 0.955834426 0.938944257 0.91091248 0.941636168 0.991887524 1.06406252 1.019675837 1 21.54533138 2.010897674 4.561640893 1.03405797 0.951272701 0.536005893 0.030971868 0.134321782 7.113980658 0.013215418 0.008756784 102.5410296 -2.010897674 -0.082785269 S(ph)QDVELWEGEVVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SQDVELWEGEVVK 13 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK 254.89 8.43E-24 897450000 748700 656020 406732 599050 801460 597730 772700 999970 984250 919920 TRUE FALSE 719439.9763 637310.9519 480237.5201 629967.0423 827239.6888 609816.5101 782156.5337 979320.2701 872522.0663 857612.999 0.838886511 0.743121842 0.559969964 0.734558645 0.964583897 0.711062578 0.912015716 1.141913977 1.017384377 1 19.70996725 2.010954716 4.090933729 1.063188043 0.758345756 0.626411756 0.102180649 0.136386263 5.233112622 0.046510413 0.03005577 102.5544988 -2.010954716 -0.304842287 QIDDILSVASVRPAVLQVECHPYLAQNELIAHCQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QIDDILSVASVRPAVLQVECHPYLAQNELIAHCQAR 36 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 282.1 1.24E-76 560240000 100320 98174 79012 70280 79643 107830 75954 50944 103440 90334 FALSE TRUE 96399.38349 95374.17364 93291.22601 73907.15922 82204.78942 110010.3965 76883.54777 49891.9886 91697.92486 84215.59772 1.144673743 1.13250011 1.107766596 0.877594664 0.976123089 1.306294789 0.91293715 0.592431687 1.088847284 1 16.36179984 2.011180628 24.99016215 0.824526803 1.08116984 0.218391899 0.162806065 237.6228225 531115.781 0.060994707 0.045010657 102.6078594 -2.011180628 0.256643037 IIFDDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 IIFDDFR 7 0 P46977;P46977-2 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 107.66 0.017281 65087000 178420 306360 168680 327300 204960 168210 248350 323400 242330 187970 FALSE TRUE 171447.1491 297622.9128 199164.2283 344191.9922 211552.7245 171611.3214 251389.3816 316721.677 214821.7143 175238.6245 0.978363929 1.698386492 1.136531566 1.964133154 1.207226576 0.979300779 1.434554639 1.807373677 1.225881081 1 17.41896127 2.011222947 24.96183069 1.480835958 1.346331739 0 0.352410502 947.0852462 2106476.482 0.129381214 0.095475314 102.6178583 -2.011222947 -0.13450422 RLDLFQEHMFEVLER ddPTM_BT-474_Pertuzumab_2h_R1 1 RLDLFQEHMFEVLER 15 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 0 123.36 6.70E-05 125790000 61531 68934 50797 59421 66376 74698 59100 57806 63727 59600 FALSE TRUE 59126.30049 66968.06981 59977.14787 62487.72493 68511.04432 76208.44474 59823.28348 56612.2859 56492.97813 55563.23891 1.06412624 1.205258569 1.079439375 1.124623513 1.233028269 1.371562318 1.076670199 1.018880235 1.016732992 1 15.76184308 2.011226598 24.99814496 1.022420428 1.18019572 0.462773694 0.082036815 206.811388 460502.7977 0.032428289 0.023930489 102.618721 -2.011226598 0.157775292 THS(ph)AGTSPTITHQK ddPTM_BT-474_Pertuzumab_2h_R1 1 THSAGTSPTITHQK 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 T(0.009)HS(0.984)AGT(0.006)S(0.001)PTITHQK 135.23 2.20E-05 82790000 50474 49666 41800 32774 36662 49333 33168 10958 43354 38085 TRUE FALSE 48501.42028 48249.57431 49354.18984 34465.47007 37841.26653 50330.54706 33573.91991 10731.71347 38432.63567 35505.46903 1.366026745 1.358933585 1.390044722 0.970708767 1.065786978 1.417543506 0.945598547 0.302255223 1.082442698 1 15.11575364 2.011229516 8.168285891 0.693872258 1.244835585 0.421929209 0.241653514 0.11127637 51.56382639 0.092569402 0.066304288 102.6194107 -2.011229516 0.550963327 ENARS(ph)PSSVTGNALWK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENARSPSSVTGNALWK 16 1 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 ENARS(0.988)PS(0.01)S(0.002)VTGNALWK;ENARS(0.998)PS(0.002)SVTGNALWK 181.26 1.41E-09 513690000 288070 339920 195560 185468 267310 354500 241170 213797 288210 235090 TRUE FALSE 276811.9059 330225.8144 230902.0422 195040.0257 275908.2689 361668.2329 244121.5106 209382.0172 255493.6091 219167.1449 1.263017347 1.506730466 1.053543141 0.889914525 1.258894297 1.650193659 1.113859975 0.955353127 1.165747764 1 17.74167202 2.011251071 24.99767549 1.035206202 1.264167336 0.210600542 0.20419773 360.1821717 800250.9847 0.082086272 0.060573977 102.6245041 -2.011251071 0.228961134 S(ph)FEDLTDHPVTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SFEDLTDHPVTR 12 0 P78536 P78536 ADAM17 Disintegrin and metalloproteinase domain-containing protein 17 1 S(1)FEDLTDHPVTR;S(0.999)FEDLT(0.001)DHPVTR;S(1)FEDLTDHPVTR 140.6 3.85E-05 790580000 594130 795260 447930 834900 574250 477040 706500 945410 712060 518790 TRUE FALSE 570910.7428 772579.9634 528880.9151 877989.2891 592721.2728 486686.0756 715146.3583 925886.9531 631229.934 483651.8912 1.180416645 1.597388488 1.093515656 1.815333104 1.225512158 1.006273488 1.478638606 1.914366448 1.305132773 1 18.88360951 2.011313042 24.90353951 1.5551977 1.332165843 0 0.316407232 497.8527068 1095924.732 0.115312582 0.085092022 102.6391489 -2.011313042 -0.223031857 GQES(ph)PLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GQESPLKK 8 1 A0A3B3ITL0;A0A3B3IRJ9;Q9Y2H2-4;Q9Y2H2 A0A3B3ITL0 INPP5F Phosphatidylinositide phosphatase SAC2 1 GQES(1)PLKK 54.143 0.080925 149210000 298050 278650 264480 256910 255220 298270 306770 324390 375620 361130 TRUE FALSE 286401.8765 270703.1748 312277.4193 270169.1559 263429.3831 304301.2238 310524.343 317691.2331 332981.1923 336670.3434 0.850689353 0.804060055 0.927546561 0.802473877 0.782454969 0.90385515 0.922339461 0.943627021 0.989042245 1 18.36097712 2.011530052 1.177628643 0.988919299 0.836593192 0.702024067 0.040674758 0.276469316 0.709578199 0.030990941 0.014531901 102.6904487 -2.011530052 -0.152326107 VAHSDKPGSTSTASFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VAHSDKPGSTSTASFR 16 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ; 237.06 5.71E-20 894290000 443063 758000 450627 857610 499833 516150 702380 874040 841630 616750 FALSE TRUE 425747.6081 736382.5822 532065.323 901871.3549 515910.5824 526586.9066 710975.9365 855990.7686 746091.6908 574976.9732 0.740460276 1.280716649 0.925368055 1.568534736 0.897271728 0.915839992 1.236529409 1.488739217 1.297602731 1 19.13314465 2.011599468 21.21450074 1.327972355 1.075367795 0.118101494 0.247294611 58.29747413 106618.6934 0.089193288 0.065761397 102.7068638 -2.011599468 -0.25260456 YEDFKEEGSENAVK ddPTM_BT-474_Pertuzumab_2h_R1 5 YEDFKEEGSENAVK 14 1 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;; 230.16 9.26E-13 7368000000 6684830 5568800 4888842 4582820 5473570 5731100 6369270 7953070 8659690 7500160 FALSE TRUE 6423579.453 5409983.276 5772364.501 4819339.889 5649632.35 5846986.769 6447219.032 7788836.325 7676678.296 6992167.483 0.91868215 0.773720494 0.825547231 0.689248348 0.807994426 0.836219496 0.922063015 1.113937323 1.097896799 1 22.73730831 2.01162674 2.420772727 1.081497895 0.800138256 0.783925127 0.061349092 0.121285137 1.340602533 0.031836722 0.01772493 102.7133136 -2.01162674 -0.281359639 YKEEFEK ddPTM_BT-474_Pertuzumab_2h_R1 10 YKEEFEK 7 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;;;;; 122.52 0.0039519 1.94769E+11 92460240 80719440 72649190 68586150 76224260 76735110 88099710 107430670 105521500 100863700 FALSE TRUE 88846791.6 78417400.6 85778514.71 72125889.42 78676082.55 78286746.5 89177900.6 105212189.1 93543141.7 94032111.76 0.944855858 0.833942779 0.912225761 0.767034666 0.836693775 0.832553316 0.948377091 1.118896377 0.994799967 1 26.48665018 2.011697637 4.426577701 1.048771122 0.852666851 0.686498408 0.055546592 0.100290808 4.838474251 0.022943335 0.015122292 102.7300824 -2.011697637 -0.19610427 HS(ph)PGPTPQPDCSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSPGPTPQPDCSLR 14 0 Q4ZG55;Q4ZG55-4 Q4ZG55 GREB1 Protein GREB1 1 HS(1)PGPTPQPDCSLR;HS(1)PGPTPQPDCSLR;HS(1)PGPTPQPDCSLR;HS(1)PGPTPQPDCSLR 143.43 5.88E-06 2634920000 2130130 2013150 1762620 1764970 1496670 2008470 1576730 766887 2170700 2151500 TRUE FALSE 2046882.165 1955736.933 2081164.643 1856060.313 1544811.75 2049082.64 1596026.493 751050.5155 1924291.236 2005776.989 1.020493393 0.975052034 1.037585262 0.925357267 0.770181211 1.021590462 0.795714829 0.374443679 0.95937447 1 20.93572978 2.011734598 10.41290493 0.677645393 0.949157105 0.118438098 0.180732414 0.299174053 249.8773343 0.067203231 0.048801802 102.7388258 -2.011734598 0.271511713 KADGVHTVEPTEAGDYK ddPTM_BT-474_Pertuzumab_2h_R1 1 KADGVHTVEPTEAGDYK 17 1 Q13445 Q13445 TMED1 Transmembrane emp24 domain-containing protein 1 0 165.8 1.57E-09 266710000 911180 1066700 842250 919360 865920 712100 1046500 1128100 1368600 1198200 FALSE TRUE 875570.0782 1036278.76 994463.3108 966808.2798 893773.1032 726499.1499 1059307.38 1104804.341 1213242.266 1117044.847 0.78382715 0.927696648 0.890262655 0.86550534 0.800122847 0.650375992 0.948312311 0.989042064 1.086117777 1 20.09125568 2.011808831 24.99971808 1.010046123 0.8264853 0.608884832 0.074627092 166.6145014 352727.4544 0.029915252 0.022078485 102.7563882 -2.011808831 -0.183560824 EIIDASDKEGMS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIIDASDKEGMSPAK 15 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 EIIDAS(0.001)DKEGMS(0.999)PAK;EIIDASDKEGMS(1)PAK 168.05 7.73E-07 1011980000 986910 847140 835610 790790 940380 894700 1057740 1201320 1361890 1284550 TRUE FALSE 948340.4661 822980.3966 986623.315 831602.7667 970628.1767 912791.447 1070684.939 1176512.322 1207293.957 1197546.284 0.791902976 0.687222204 0.823870716 0.694422234 0.810514123 0.762218095 0.894065601 0.982435784 1.008139704 1 20.19164999 2.01180964 1.740538367 1.0057514 0.75592295 0.863050022 0.042325219 0.111145937 0.629662265 0.023737569 0.011941599 102.7565797 -2.01180964 -0.249828451 ECPFLHIDPESK ddPTM_BT-474_Pertuzumab_2h_R1 2 ECPFLHIDPESK 12 0 O95639;C9K0K2;B7Z7B0;H7C016;O95639-3;O95639-2 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 0 ; 135.6 0.00012484 465380000 900650 885790 810100 859630 882590 897280 964840 1083100 1146960 1171140 FALSE TRUE 865451.6023 860528.1365 956503.0906 903995.6073 910979.3089 915423.6164 976648.0005 1060733.607 1016761.909 1091817.645 0.792670467 0.788161046 0.876064877 0.82797307 0.834369469 0.838440028 0.894515678 0.971530009 0.931256162 1 20.05830049 2.011913891 1.740558317 0.970015499 0.824378656 0.841810273 0.027557163 0.138576064 0.785091484 0.01725174 0.008679612 102.7812489 -2.011913891 -0.145636844 FIHQQPQSSS(ph)PVYGSSAK ddPTM_BT-474_Pertuzumab_2h_R1 4 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQSS(0.006)S(0.994)PVYGSSAK;FIHQQPQSS(0.009)S(0.991)PVYGSSAK;FIHQQPQSSS(1)PVYGSSAK;FIHQQPQSS(0.002)S(0.998)PVYGSSAK 277.8 2.42E-39 8800300000 6410800 6745000 6196100 6566000 6571400 6845200 6382900 6232200 6891800 6840000 TRUE FALSE 6160258.848 6552639.204 7315873.101 6904872.047 6782775.049 6983614.634 6461015.84 6103502.892 6109471.757 6376720.708 0.966054361 1.027587612 1.14727827 1.082824913 1.063677611 1.095173359 1.013219198 0.957153868 0.958089908 1 22.60438326 2.011951568 4.227749735 0.969811145 1.066577535 0.455366645 0.04529392 0.185418073 7.808278966 0.020399127 0.013308222 102.7901661 -2.011951568 0.096766389 STQPGVIASQVLDLRDDEFSVSSVLASDVIHATR ddPTM_BT-474_Pertuzumab_2h_R1 1 STQPGVIASQVLDLRDDEFSVSSVLASDVIHATR 34 1 Q9Y5S2;H0YLY0 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 150.23 8.35E-11 97121000 27318 32466 25379 30289 25531 31938 28410 28722 29854 32855 FALSE TRUE 26250.38236 31540.10147 29965.54985 31852.21892 26352.2278 32583.80824 28757.69008 28128.88066 26465.09908 30629.70159 0.857023771 1.02972278 0.978316742 1.039912806 0.860348826 1.06379777 0.938882476 0.918353076 0.864033853 1 14.90264369 2.0121276 24.99864336 0.920947244 0.974931226 0.071450328 0.07187485 479.8321214 989074.6557 0.025200613 0.018598623 102.8318384 -2.0121276 0.053983982 MEELHNQEMQK ddPTM_BT-474_Pertuzumab_2h_R1 6 MEELHNQEMQK 11 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;; 216.06 1.24E-11 5779930000 6507620 6556410 6126240 6460260 6253170 5853650 6868630 7272540 7971600 8089560 FALSE TRUE 6253295.016 6369427.606 7233387.845 6793674.793 6454308.892 5972014.814 6952690.349 7122359.508 7066697.388 7541646.896 0.829168364 0.844567201 0.959125765 0.900821119 0.855822207 0.791871443 0.921906109 0.944403736 0.937023105 1 22.84644817 2.012297173 24.65243083 0.949012433 0.867426744 0.484530952 0.044853252 191.7755732 384454.9875 0.017867555 0.013186417 102.8719976 -2.012297173 -0.081585689 QGRPTLQEGPGLQQKPRPEAEPPS(ph)PPSGDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QGRPTLQEGPGLQQKPRPEAEPPSPPSGDLR 31 3 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1;B0QYI1;Q8WUA7-2 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 QGRPTLQEGPGLQQKPRPEAEPPS(0.826)PPS(0.174)GDLR;QGRPTLQEGPGLQQKPRPEAEPPS(0.999)PPS(0.001)GDLR 145.6 1.28E-08 1587950000 636480 637900 580813 620766 642570 654940 628583 637590 709010 681630 TRUE FALSE 611605.6579 619707.7166 685778.8292 652803.8077 663238.8476 668183.3355 636275.7868 624423.5437 628526.1572 635462.593 0.962457373 0.975207232 1.079180485 1.02728912 1.043710291 1.051491217 1.001279688 0.982628326 0.989084431 1 19.27744768 2.012427789 24.10351352 0.989469047 1.024840223 0.174200883 0.032462462 246.9209939 478896.105 0.012979039 0.00957841 102.9029415 -2.012427789 0.035371177 IPSIVSS(ph)PLNSPLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.163)S(0.836)PLNSPLDR 97.797 0.0033308 44363000 39721 49419 48317 56392 58428 49772 47119 41609 40170 53906 TRUE FALSE 38168.65941 48009.61851 57048.95671 59302.39788 60307.38968 50778.42394 47695.65642 40749.75961 35610.07001 50254.89861 0.759501272 0.955322164 1.135191957 1.180032186 1.200030074 1.010417399 0.949074772 0.810861443 0.708589033 1 15.61697661 2.012713934 2.499172625 0.8218153 1.054984505 0.296094456 0.13669757 0.342309133 4.047248768 0.075024401 0.042228019 102.9707638 -2.012713934 0.233169205 S(ph)VDALDDLTPPSTAESGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVDALDDLTPPSTAESGSR 19 0 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 S(1)VDALDDLTPPSTAESGSR;S(1)VDALDDLTPPSTAESGSR 237.3 3.41E-24 534060000 389620 538920 323500 608500 323610 330750 552830 838320 528900 429510 TRUE FALSE 374393.2197 523550.5293 381963.6462 639904.7579 334019.2095 337437.9916 559595.6989 821008.399 468861.4893 400418.9051 0.935003854 1.30750702 0.953910121 1.598088276 0.834174424 0.842712438 1.397525671 2.050373717 1.170927455 1 18.61115056 2.012715573 18.12136569 1.573843296 1.097834125 0.12438004 0.345653991 10.61951407 15132.39529 0.12638192 0.093086002 102.9711524 -2.012715573 -0.47600917 LLQGRPPLDFYPPGVHPSGLVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLQGRPPLDFYPPGVHPSGLVPR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 0 100.64 0.0013712 181720000 86061 110610 76713 114350 83928 90913 95131 87535 85005 101020 FALSE TRUE 82697.64097 107455.5111 90576.74557 120251.6172 86627.62034 92751.32315 96295.24163 85727.37166 75355.58877 94177.82542 0.878100982 1.140985265 0.961762975 1.276857017 0.919830331 0.984853098 1.022483172 0.910271301 0.800141524 1 16.52309979 2.012722444 1.281053114 0.892666141 1.045855543 0.173760305 0.117433508 0.688083823 2.097777911 0.080633478 0.038024982 102.9727814 -2.012722444 0.153189401 QAEREEKR ddPTM_BT-474_Pertuzumab_2h_R1 3 QAEREEKR 8 2 P14678-2;P14678;P14678-3 P14678-2 SNRPB Small nuclear ribonucleoprotein-associated proteins B and B 0 ;; 138.98 0.00038376 174347000 230273.2 251454.6 159056.3 155556 263843 391929 164783.4 123656.2 174579.6 89377.3 FALSE TRUE 221273.8688 244283.361 187801.3116 163584.2638 272329.7497 399854.0729 166800.0685 121102.6563 154762.0557 83323.69586 2.655593544 2.931739387 2.253876399 1.963238213 3.268334978 4.798803855 2.001832334 1.45339996 1.857359471 1 16.34643921 2.012807535 24.98589985 1.54737681 2.95135773 0.472841888 0.739513066 219.3800078 427981.1987 0.295717018 0.218274338 102.9929588 -2.012807535 1.40398092 DLELTNHR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLELTNHR 8 0 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 0 101.54 0.005321 117850000 105050 106250 82559 109290 103390 120690 101380 102570 105320 115400 FALSE TRUE 100944.5299 103219.854 97479.24782 114930.47 106715.6332 123130.4345 102620.7188 100451.8937 93364.51514 107583.8552 0.938286973 0.959436282 0.906076917 1.068287335 0.991929812 1.14450662 0.953867275 0.933707883 0.867830168 1 16.71510207 2.012808672 24.99806391 0.930807024 1.002069827 0.165787849 0.069741305 395.8230561 772505.3163 0.026887488 0.019846243 102.9932286 -2.012808672 0.071262803 AEEDEILNRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 12 AEEDEILNRSPR 12 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR 220.48 7.75E-11 1.44502E+11 34574280 60476220 26769840 59249590 33530920 38167810 47515910 62988670 48196180 33653190 TRUE FALSE 33223078.91 58751497.42 31607745.58 62307468.44 34609472.49 38939589.27 48097423.92 61687931.95 42725151.7 31373829.47 1.05894242 1.87262755 1.007455772 1.985969501 1.103131912 1.241148751 1.533042817 1.966222581 1.361808629 1 24.9030583 2.012846707 23.74608029 1.599934514 1.397966775 0 0.387401369 389.333128 719644.8967 0.136803916 0.100960719 103.0022489 -2.012846707 -0.201967739 T(ph)SPQPESGIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPQPESGIKR 11 1 A0A1B0GVV3;Q5EBL4-2;Q5EBL4;Q5EBL4-3 A0A1B0GVV3 RILPL1 RILP-like protein 1 1 T(0.5)S(0.5)PQPESGIKR 48.823 0.098009 127710000 374980 284130 244430 219130 283630 291080 312840 341450 394700 364540 TRUE FALSE 360325.367 276026.8906 288603.9383 230439.3256 292753.2165 296965.837 316668.6295 334398.9382 349895.3107 339849.3811 1.060250179 0.812203599 0.849211311 0.678063102 0.861420479 0.87381603 0.931791103 0.983962181 1.029559947 1 18.37453597 2.012849129 1.577844826 1.011696026 0.841871142 0.369618855 0.087552264 0.406984618 1.893810162 0.057268127 0.028074867 103.0028234 -2.012849129 -0.169824885 EMPQDLRS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EMPQDLRSPAR 11 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 EMPQDLRS(1)PAR;EMPQDLRS(1)PAR;EMPQDLRS(1)PAR;EMPQDLRS(1)PAR 92.38 0.0060793 1769830000 1552860 1746690 1255930 1499840 1616120 1592900 1377570 1287180 1353950 1385460 TRUE FALSE 1492172.514 1696876.111 1482904.489 1577246.922 1668103.968 1625109.529 1394429.114 1260599.283 1200255.272 1291621.56 1.155270677 1.313756416 1.148095181 1.221137035 1.29148043 1.258193251 1.079595724 0.975981915 0.929262339 1 20.300752 2.012900559 2.716520797 0.967321634 1.233662028 0.835517189 0.052641631 0.101175402 1.429779351 0.025895071 0.014954487 103.0150219 -2.012900559 0.266340394 (ac)SLYPS(ph)LEDLKVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLYPSLEDLKVDK 13 1 B4DHN5;E9PBU7;O00560-2;O00560 B4DHN5 SDCBP Syntenin-1 1 S(0.284)LY(0.247)PS(0.469)LEDLKVDK;S(0.24)LY(0.212)PS(0.547)LEDLKVDK 48.14 0.023791 296150000 469810 366100 292680 281370 320910 332250 388550 452280 495450 438720 TRUE FALSE 451449.3058 355659.1864 345573.7866 295891.5394 331232.3616 338968.3226 393305.1911 442940.2599 439208.5931 409005.1036 1.10377426 0.869571512 0.844913141 0.723442169 0.809848969 0.828763063 0.961614385 1.082970007 1.073846241 1 18.64175932 2.012935502 3.500257035 1.057137006 0.854525294 0.451401165 0.093228268 0.209337732 5.315477656 0.044203547 0.027493182 103.0233107 -2.012935502 -0.202611712 SESGGLGVSMVEYVLSS(ph)SPGDSCLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 SESGGLGVSMVEYVLSSSPGDSCLRK 26 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLS(0.086)S(0.453)S(0.453)PGDS(0.008)CLRK;SESGGLGVSMVEYVLS(0.011)S(0.56)S(0.428)PGDSCLRK 116.35 0.0006178 602710000 134139 133734 102724 113527 117649 145793 109975 98345 123907 116809 TRUE FALSE 128896.6996 129920.0373 121288.5119 119386.1421 121433.2869 148741.0344 111320.9069 96314.14138 109841.5968 108897.4224 1.183652439 1.193049701 1.113786803 1.096317428 1.115116265 1.365882048 1.022254747 0.884448312 1.00867031 1 16.73261028 2.013061579 24.98931196 0.951988206 1.171242575 0.615111592 0.07788377 139.4368993 266768.4569 0.029144927 0.021512846 103.053223 -2.013061579 0.219254369 RQGSFS(ph)EDVISHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQGSFSEDVISHK 13 1 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5;E9PNZ4 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 RQGS(0.269)FS(0.731)EDVISHK 67.252 0.032864 475090000 395830 453590 336400 317730 391230 358710 386910 358910 352480 353710 TRUE FALSE 380360.526 440654.0573 397194.9632 334128.0834 403814.2683 365963.362 391645.1203 351498.3831 312467.9481 329752.9066 1.153471337 1.336315915 1.204523009 1.013268046 1.224596539 1.109810875 1.187692701 1.06594476 0.947582089 1 18.33102585 2.013075636 0.425313644 0.968827666 1.23206192 0.456998034 0.0836743 1.00302565 0.438361711 0.091748282 0.086698058 103.0565586 -2.013075636 0.263234254 VIEASDVVLEVLDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIEASDVVLEVLDAR 15 0 Q9BVP2-2;Q9BVP2 Q9BVP2-2 GNL3 Guanine nucleotide-binding protein-like 3 0 ; 132.59 0.00010824 14932500 23290.1 25015.5 20184.2 27612.3 29927.4 24831.4 24628.4 23188.2 26780.8 24869.4 FALSE TRUE 22379.89714 24302.08243 23831.93394 29037.37411 30890.042 25333.50792 24929.80973 22709.35557 23740.75586 23184.97339 0.965275947 1.04818246 1.027904304 1.252422145 1.332330276 1.092669269 1.075257207 0.979485945 1.023971667 1 14.50090245 2.01311774 2.772114713 1.00107777 1.127904339 0.213074296 0.101187393 0.457247139 6.754192336 0.056031993 0.032565065 103.0665503 -2.01311774 0.126826569 VS(ph)PPASPTLEVELGSAELPLQGAVGPELPPGGGHGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPPASPTLEVELGSAELPLQGAVGPELPPGGGHGR 36 0 Q7Z6J0 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 1 VS(1)PPASPTLEVELGSAELPLQGAVGPELPPGGGHGR;VS(0.998)PPAS(0.002)PTLEVELGSAELPLQGAVGPELPPGGGHGR 209.8 8.48E-31 172944000 9700.4 7232.3 4780.7 6794.3 13298.5 4636.9 10435.3 13043.8 15033.6 8214.1 TRUE FALSE 9321.297644 7026.041885 5644.678836 7144.954637 13726.25833 4730.661295 10563.01032 12774.44097 13327.04875 7657.751691 1.217236863 0.917507144 0.737119596 0.93303556 1.792465842 0.617761124 1.379387939 1.668171219 1.740334408 1 12.90270516 2.013120943 24.76568373 1.538752292 1.042610566 0.242270988 0.352405341 244.8157588 462085.8171 0.128878255 0.095128411 103.0673105 -2.013120943 -0.496141726 RGT(ph)SLMEDDEEPIVEDVMMSSEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGTSLMEDDEEPIVEDVMMSSEGR 24 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 RGT(0.5)S(0.5)LMEDDEEPIVEDVMMSSEGR 76.476 0.013398 14941000 6287.4 5884.1 5306.4 5196.9 5993.5 4638.1 6350.4 6924.1 9029.9 5375.3 TRUE FALSE 6041.681457 5716.291229 6265.38452 5465.112632 6186.286371 4731.88556 6428.118095 6781.114915 8004.863608 5011.226143 1.205629378 1.14069712 1.250269763 1.090573939 1.234485572 0.944257039 1.282743566 1.353184774 1.597386224 1 12.29094793 2.01318374 24.7300041 1.346565899 1.147531868 0.201102376 0.157849766 258.0767072 484096.8858 0.055291369 0.040811925 103.0822145 -2.01318374 -0.19903403 TAFDEAIAELDTLNEESYK ddPTM_BT-474_Pertuzumab_2h_R1 5 TAFDEAIAELDTLNEESYK 19 0 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;; 300.12 6.98E-50 876012000 1413613 1249723 1294912 1370134 1488232 1407322 1661203 1995055 2152645 2102316 FALSE TRUE 1358367.441 1214082.124 1528931.404 1440846.78 1536102.334 1435779.015 1681533.299 1953856.417 1908285.764 1959924.265 0.693071393 0.619453591 0.780097186 0.735154315 0.783755965 0.732568621 0.857958305 0.99690404 0.973652808 1 20.90236648 2.013184967 1.852165221 0.997840055 0.720152221 0.878768599 0.04441875 0.116433352 0.747244337 0.028108971 0.014421034 103.0825058 -2.013184967 -0.277687834 VLESEEQVLVMYHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLESEEQVLVMYHR 14 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 ; 130.24 6.32E-05 174998000 174404 208431 157073 206768 204024 241520 189903 184897 205775 213375 FALSE TRUE 167588.0989 202486.752 185459.5852 217439.3213 210586.6172 246403.6999 192227.0897 181078.8123 182416.2847 198922.9212 0.842477568 1.017915637 0.93231883 1.093083291 1.058634249 1.23868933 0.966339568 0.910296366 0.917019937 1 17.60185 2.013222129 24.98431658 0.933933205 1.035680721 0.141382002 0.099282794 395.9905929 748254.1584 0.038494451 0.028414681 103.0913267 -2.013222129 0.101747516 S(ph)PILLPK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPILLPK 7 0 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 S(1)PILLPK;S(1)PILLPK;S(1)PILLPK;S(1)PILLPK;S(1)PILLPK;S(1)PILLPK 99.442 0.011041 1821648000 2227590 2104710 2266460 2290690 2026430 1756810 2485280 2716060 2877940 3140810 TRUE FALSE 2140533.32 2044685.732 2676059.739 2408912.785 2091611.961 1792333.902 2515695.6 2659972.412 2551248.317 2928080.141 0.731036453 0.698302517 0.913929814 0.822693598 0.714328796 0.612119141 0.85916214 0.908435659 0.871304129 1 21.48152361 2.013242688 24.96018063 0.908254332 0.754073602 0.496211861 0.080880883 215.8919903 406917.4718 0.032090408 0.023688089 103.096207 -2.013242688 -0.15418073 ARQPLSEASNQQPLS(ph)GGEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARQPLSEASNQQPLSGGEEK 20 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 ARQPLSEASNQQPLS(1)GGEEK;ARQPLSEASNQQPLS(1)GGEEK 286.42 1.90E-45 1043240000 1174520 1082110 791350 895240 939070 933060 1039630 1210080 1082950 1163240 TRUE FALSE 1128618.46 1051249.282 934364.5485 941443.4437 969276.0394 951927.1125 1052353.303 1185091.425 960018.0561 1084452.719 1.040726295 0.969382311 0.861600079 0.868127699 0.893792807 0.877794943 0.970400355 1.092801378 0.885255797 1 20.04853572 2.013248194 10.84809696 1.010144005 0.915603985 0.181535268 0.069394321 0.44650711 353.5916601 0.027051156 0.019713415 103.0975142 -2.013248194 -0.09454002 ASWPETEPQPER ddPTM_BT-474_Pertuzumab_2h_R1 1 ASWPETEPQPER 12 0 Q5VY09 Q5VY09 IER5 Immediate early response gene 5 protein 0 52.693 0.084918 889190000 449720 440780 347550 403470 463640 474780 412470 390770 477940 466590 FALSE TRUE 432144.4452 428209.386 410360.0162 424293.1351 478553.4017 484380.3769 417517.9312 382700.4629 423686.2549 434987.4437 0.993464183 0.984417808 0.94338359 0.975414673 1.100154518 1.11355025 0.959839042 0.879796575 0.974019506 1 18.73061423 2.013389326 24.99620963 0.933391503 1.016996463 0.213504144 0.058275789 301.8971892 563602.1952 0.023844317 0.017601226 103.1310231 -2.013389326 0.083604961 TYFTDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 TYFTDKK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 105.57 0.012663 2636400000 2587500 3564900 2007260 3209200 2162260 1407170 3165900 4208200 3621400 2550500 FALSE TRUE 2486377.639 3463232.542 2370016.533 3374827.197 2231811.057 1435623.942 3204645.231 4121299.199 3210313.854 2377752.363 1.045684016 1.456515235 0.996746579 1.419335019 0.938622159 0.603773532 1.3477624 1.733275199 1.350146426 1 21.18116704 2.013423843 24.99536002 1.467091471 1.089366003 0.159760033 0.285550819 301.0168566 560494.8544 0.10735052 0.079243724 103.13922 -2.013423843 -0.377725468 KDPLEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 KDPLEGR 7 1 Q14165;F5GX14 Q14165 MLEC Malectin 0 ;; 87.696 0.030709 564750000 552520 852570 483390 843060 523610 431120 718660 953830 737660 546010 FALSE TRUE 530926.9076 828255.5384 570749.326 886570.4276 540452.3912 439837.5418 727455.1761 934133.0772 653923.9293 509028.2564 1.043020502 1.627130769 1.121252738 1.741691972 1.061733577 0.86407294 1.429105687 1.835130104 1.284651532 1 18.95738622 2.01343397 24.96918109 1.507569151 1.259237305 0 0.323059598 502.6450709 934242.5484 0.119413888 0.088148632 103.1416251 -2.01343397 -0.248331846 APS(ph)PSGLMS(ph)PSRLPGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 APSPSGLMSPSRLPGSR 17 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 APS(0.986)PS(0.014)GLMS(0.972)PS(0.028)RLPGSR;APS(0.991)PS(0.009)GLMS(0.914)PS(0.085)RLPGSR;APS(0.989)PS(0.152)GLMS(0.844)PS(0.014)RLPGSR;APS(0.888)PS(0.112)GLMS(0.975)PS(0.025)RLPGSR 128.95 2.00E-05 1202610000 855450 980810 891540 1028760 951360 1167590 886360 865340 897330 921950 TRUE FALSE 822018.0683 952838.2591 1052661.11 1081854.427 981961.3584 1191199.47 897207.5388 847470.4266 795468.8603 859505.5053 0.956384878 1.108588896 1.224728758 1.258694005 1.142472448 1.385912554 1.043864796 0.985997671 0.925495946 1 19.71314735 2.013667277 24.98719421 0.980439315 1.183108611 0.451002996 0.105173787 211.0819142 385908.8873 0.040441246 0.029853885 103.1970488 -2.013667277 0.202669295 EIILVDDASVDEYLHDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIILVDDASVDEYLHDK 17 0 Q14435;C9J2C3;H7BZS4 Q14435 GALNT3 Polypeptide N-acetylgalactosaminyltransferase 3 0 170.91 1.79E-09 40471000 64812 70676 79107 81409 68056 55388 84260 90556 106280 101210 FALSE TRUE 62279.07539 68660.38968 93403.39463 85610.52825 70245.08305 56507.98331 85291.19909 88685.98695 94215.53996 94354.95655 0.660050915 0.727681854 0.989915083 0.907324123 0.744476873 0.59888728 0.903939784 0.939918688 0.998522424 1 16.52581069 2.013672607 24.75117472 0.960085851 0.781551368 0.43449917 0.10729232 233.2081156 422168.8862 0.043987726 0.032470884 103.1983152 -2.013672607 -0.178534483 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.481)S(0.481)PPPEVLEPHS(0.031)LDQPPAT(0.002)S(0.002)PRPLIEVGELLDLT(0.002)R;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 191.49 1.06E-32 1620260000 202722 248380 146599.5 171998 205108 227228 170138 116911.5 225357 160154 TRUE FALSE 194799.4001 241296.4456 173093.2907 180874.8374 211705.4851 231822.7058 172220.1997 114497.2367 199775.4181 149306.6269 1.304693597 1.616113434 1.159314187 1.211432078 1.417924237 1.552661865 1.153466549 0.76685971 1.338021106 1 17.18791867 2.013744229 10.52677822 0.996796811 1.370874441 0.4145236 0.184195498 0.260396844 190.9395363 0.069122667 0.05034696 103.2153355 -2.013744229 0.37407763 REEQT(ph)DT(ph)SDGESVTHHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 REEQT(1)DT(0.642)S(0.358)DGESVTHHIR;REEQT(1)DT(0.685)S(0.315)DGESVTHHIR 154.1 1.26E-08 620480000 259310 350480 268010 257980 290080 320630 237239 141615 244279 234708 TRUE FALSE 249175.8785 340484.6536 316445.3689 271294.3787 299410.6866 327113.3583 240142.4018 138690.6008 216549.472 218811.0181 1.138772081 1.556067224 1.446203996 1.239857029 1.368352879 1.494958349 1.097487704 0.633837372 0.989664387 1 17.73932586 2.013860191 5.150938065 0.838443292 1.376024228 0.698218162 0.147737478 0.084288083 6.556581897 0.057851856 0.039466553 103.2428992 -2.013860191 0.537580936 RQELVTK ddPTM_BT-474_Pertuzumab_2h_R1 4 RQELVTK 7 1 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;;; 150.24 0.0031459 1394310000 1162940 1784060 936320 1749410 1110520 1128420 1520390 1915650 1690350 1228630 FALSE TRUE 1117491.019 1733180.356 1105533.852 1839697.26 1146240.884 1151237.426 1538996.988 1876091.158 1498468.555 1145413.796 0.975622106 1.513147792 0.965182938 1.606142048 1.000722087 1.005084302 1.343616598 1.637915629 1.308233374 1 20.12743745 2.013863415 24.55800669 1.412388434 1.192983274 0.030490204 0.260074943 365.3720179 647225.9728 0.092610479 0.068362411 103.2436654 -2.013863415 -0.21940516 VASPSQGQVGSSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 VASPSQGQVGSSSPK 15 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.001)S(0.145)S(0.854)PK;VASPSQGQVGS(0.007)S(0.037)S(0.956)PK 103.79 0.0027067 65709000 118970 107056 93800 114525 91097 100068 123716 156864 156436 135428 TRUE FALSE 114320.5209 104002.8677 110751.7466 120435.649 94027.21774 102091.4435 125230.0734 153624.7036 138678.0411 126255.3409 0.905470771 0.823750242 0.877204447 0.95390538 0.744738536 0.808610889 0.991879413 1.21677786 1.098393463 1 16.94598489 2.013968159 4.644547138 1.12545829 0.853429501 0.707542325 0.072992312 0.092784781 5.159725861 0.030196858 0.020189402 103.268569 -2.013968159 -0.272028789 KRS(ph)VSHGSNHTQKPDEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KRSVSHGSNHTQKPDEQR 18 3 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 KRS(0.994)VS(0.006)HGSNHTQKPDEQR;KRS(0.683)VS(0.317)HGSNHTQKPDEQR 127.74 1.01E-05 125779000 96037 155847 67322 76172 83893 127834 66405 12309.6 70513 61891 TRUE FALSE 92283.76787 151402.3962 79488.58297 80103.24605 86591.49453 130418.8911 67217.68425 12055.40246 62508.65985 57699.06744 1.59939791 2.624000748 1.377640688 1.3882936 1.500743398 2.260329271 1.164970029 0.208935828 1.083356502 1 15.81626038 2.013972326 7.427892893 0.677343429 1.77576017 0.537525565 0.431109295 0.102238847 30.56212267 0.166601309 0.119032565 103.2695598 -2.013972326 1.098416742 GSYGS(ph)DAEEEEYRQQLSEHSK ddPTM_BT-474_Pertuzumab_2h_R1 5 GSYGSDAEEEEYRQQLSEHSK 21 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 GSYGS(1)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.022)YGS(0.978)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.007)YGS(0.993)DAEEEEYRQQLSEHSK 324.55 1.16E-67 7596950000 2713340 3004910 1976300 2289870 2432970 2844450 2342020 2303200 2559220 2374300 TRUE FALSE 2607299.673 2919212.909 2333461.373 2408050.465 2511228.69 2901966.728 2370682.341 2255638.115 2268708.075 2213486.546 1.177915302 1.318830202 1.054201742 1.0878993 1.134512741 1.311038792 1.071017281 1.019043065 1.024947759 1 21.07788917 2.013983864 24.92545818 1.023842152 1.176278953 0.474835127 0.079708643 210.7480399 375645.0849 0.031108852 0.022965138 103.2723036 -2.013983864 0.152436802 LESTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 LESTSPK 7 0 Q03111 Q03111 MLLT1 Protein ENL 1 LES(0.175)T(0.288)S(0.536)PK;LES(0.002)T(0.032)S(0.966)PK;LES(0.005)T(0.079)S(0.916)PK;LES(0.137)T(0.188)S(0.675)PK;LES(0.008)T(0.007)S(0.985)PK 112.8 0.0065797 5504420000 12897700 10517400 9028270 8957960 10091100 9609840 11186900 12542600 13640100 12507800 TRUE FALSE 12393643.62 10217454.05 10659879.22 9420281.389 10415689.4 9804157.549 11323808.63 12283590.93 12091733.03 11660635.57 1.062861759 0.876234747 0.914176518 0.80787032 0.893235136 0.84079101 0.971114187 1.053423791 1.036970323 1 23.47514309 2.014047452 4.983100522 1.031594148 0.89457481 0.458679731 0.064069194 0.151843753 10.56852731 0.025994544 0.017630778 103.2874254 -2.014047452 -0.137019338 SGTPT(ph)QDEMMDKPTSSSVDTMSLLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGTPTQDEMMDKPTSSSVDTMSLLSK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.191)GT(0.162)PT(0.646)QDEMMDKPTSSSVDTMSLLSK 111.9 0.0030808 934380000 1290500 999680 921030 766440 946790 986440 1111900 1229900 1416500 1271000 TRUE FALSE 1240065.833 971170.1052 1087480.609 805996.0603 977244.3602 1006386.493 1125507.765 1204502.135 1255704.858 1184914.038 1.046544976 0.819612288 0.917771732 0.680214796 0.824738613 0.849332914 0.949864487 1.016531239 1.059743423 1 20.17635097 2.014059995 2.312348649 1.028649267 0.847250889 0.431487033 0.087175059 0.280610285 2.823554563 0.046859506 0.025780321 103.2904085 -2.014059995 -0.181398378 SQSS(ph)DTEQQSPTSGGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.005)QS(0.028)S(0.967)DTEQQSPTSGGGK;SQS(0.09)S(0.91)DTEQQSPTSGGGK;SQS(0.035)S(0.965)DTEQQSPTSGGGK 375.69 5.47E-105 2529410000 3886920 3876760 2971590 3395170 3588280 3800080 3917110 4507400 5114580 4611860 TRUE FALSE 3735014.869 3766198.601 3508622.416 3570395.131 3703700.285 3876920.221 3965048.764 4414320.615 4533994.32 4299494.614 0.86871021 0.875963093 0.816054613 0.83042205 0.861426893 0.901715334 0.922212753 1.02670686 1.054541226 1 22.03573566 2.01409372 1.47585782 1.037193916 0.850181403 0.908562442 0.023977928 0.109852757 0.446752391 0.016620756 0.008029448 103.2984297 -2.01409372 -0.187012513 VAIEHLDK ddPTM_BT-474_Pertuzumab_2h_R1 6 VAIEHLDK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 160.63 0.00035223 10634700000 18938500 18288500 15559400 16959000 17654400 18438500 19108800 20193900 22678300 22083900 FALSE TRUE 18198362.48 17766929.89 18371329.7 17834256.02 18222269.81 18811339.1 19342659.21 19776888.91 20103954.46 20588137.78 0.88392465 0.862969253 0.892325954 0.866239395 0.885085868 0.913697941 0.93950504 0.960596297 0.976482413 1 24.29531001 2.014104158 0.808892313 0.995717149 0.873058813 0.961917955 0.008953514 0.101521629 0.124006801 0.007311224 0.003767324 103.3009124 -2.014104158 -0.122658336 YEMACAIADAFNLPSSHLRPITDS(ph)PVLGAQRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YEMACAIADAFNLPSSHLRPITDSPVLGAQRPR 33 2 Q9NZL9;Q9NZL9-2 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 1 YEMACAIADAFNLPS(0.039)S(0.158)HLRPIT(0.158)DS(0.644)PVLGAQRPR;YEMACAIADAFNLPS(0.071)S(0.071)HLRPIT(0.071)DS(0.787)PVLGAQRPR 156.72 1.89E-11 843440000 147201 179876 122279 159271 150437 180735 140607 135505 142453 152708 TRUE FALSE 141448.2222 174746.1126 144377.5354 167490.9954 155275.9427 184389.5855 142327.7905 132706.7744 126282.3327 142364.9511 0.993560712 1.227451779 1.014136796 1.17649038 1.090689397 1.295189469 0.999738976 0.932159027 0.887032459 1 17.11923449 2.014240413 24.83319651 0.940631685 1.133177218 0.499841454 0.088853564 159.9098137 278858.0704 0.031011545 0.022893618 103.3333271 -2.014240413 0.192545533 FDQLFDDESDPFEVLK ddPTM_BT-474_Pertuzumab_2h_R1 5 FDQLFDDESDPFEVLK 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;; 284.79 2.11E-35 1375928000 1455543 1353139 1274913 1286136 1378875 1377463 1507494 1778355 1796027 1794012 FALSE TRUE 1398658.77 1314548.801 1505318.139 1352513.633 1423227.767 1405316.246 1525943.163 1741631.348 1592149.545 1672501.969 0.836267338 0.785977431 0.900039681 0.808676855 0.850957304 0.840247887 0.912371519 1.041332913 0.951956753 1 20.67357648 2.0143114 3.334336808 0.999857791 0.837168373 0.812857533 0.034522723 0.091031731 2.053212743 0.015144845 0.009307578 103.3502186 -2.0143114 -0.162689418 HQPST(ph)PDPFLKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQPSTPDPFLKPR 13 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 HQPS(0.001)T(0.999)PDPFLKPR;HQPS(0.004)T(0.996)PDPFLKPR 133.71 0.00015245 2326700000 1338280 1289100 1051020 1243290 1198130 1258250 1108490 759140 1429870 1251150 TRUE FALSE 1285978.538 1252336.13 1240962.694 1307456.346 1236668.94 1283692.677 1122056.032 743463.4937 1267557.152 1166408.496 1.102511292 1.07366856 1.063917742 1.120924916 1.060236567 1.100551549 0.961975188 0.637395472 1.086718038 1 20.1536417 2.014388134 6.868976517 0.850927249 1.082007581 0.313500562 0.112545608 0.123841536 27.42242246 0.042318574 0.030046626 103.368481 -2.014388134 0.231080333 EKLGCQDAFPEVYDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKLGCQDAFPEVYDK 15 1 A0A0A0MTI1;Q15392-2;Q15392 A0A0A0MTI1 DHCR24 Delta(24)-sterol reductase 0 ; 92.211 0.0048611 1167510000 1217440 1783910 1017300 1901030 1177570 1109480 1829630 2641400 2240800 1710230 FALSE TRUE 1169861.099 1733034.633 1201148.74 1999142.386 1215447.608 1131914.446 1852021.559 2586854.167 1986433.778 1594394.599 0.733733732 1.086954656 0.753357256 1.253856723 0.762325468 0.709933693 1.161582936 1.622467969 1.245885918 1 20.6045773 2.014416274 7.922899189 1.367282128 0.900425374 0.406449079 0.218927628 0.121751554 44.81659191 0.08044158 0.057792825 103.3751787 -2.014416274 -0.466856754 RAPS(ph)PVVSPTEMNK ddPTM_BT-474_Pertuzumab_2h_R1 9 RAPSPVVSPTEMNK 14 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(0.999)PVVS(0.001)PTEMNK;RAPS(1)PVVSPTEMNK 203.17 9.44E-09 6034170000 5137229 5098800 4503460 4806201 4825504 5010718 5416049 6442769 6389420 6361478 TRUE FALSE 4936460.411 4953387.216 5317335.401 5054249.61 4980720.719 5112038.151 5482332.228 6309723.569 5664119.828 5930609.429 0.832369838 0.835223981 0.896591736 0.852231068 0.839832867 0.861975184 0.924412962 1.063924989 0.955065394 1 22.49974893 2.014563859 3.6117678 1.011292046 0.854176588 0.834990682 0.030465739 0.080726641 2.218006062 0.013365953 0.008404058 103.4103144 -2.014563859 -0.157115458 HENEALWR ddPTM_BT-474_Pertuzumab_2h_R1 2 HENEALWR 8 0 E9PMQ6;Q00613-2;Q00613;E9PI02 E9PMQ6 HSF1 Heat shock factor protein 1 0 ; 113.71 0.0027969 604730000 70761 81953 68917 70615 73829 82893 68953 57436 86365 79466 FALSE TRUE 67995.58189 79615.78068 81371.83495 74259.44861 76203.77683 84569.15325 69796.86744 56249.92653 76561.20727 74083.69704 0.917821121 1.074673428 1.098377082 1.002372338 1.02861736 1.141535272 0.942135318 0.759275371 1.033442044 1 16.17686848 2.014579599 20.67409753 0.890795341 1.044912844 0.231767684 0.089932639 29.70252973 42117.3109 0.032769577 0.024175574 103.4140623 -2.014579599 0.154117503 TPMAGVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPMAGVSPK 9 0 A0A087WWD1;B7Z6K7;Q9H707 A0A087WWD1 ZNF814;ZNF552 Putative uncharacterized zinc finger protein 814;Zinc finger protein 552 1 TPMAGVS(1)PK;TPMAGVS(1)PK 109.72 0.0025209 380680000 868270 703920 611640 606770 700710 666020 766960 857720 880750 953840 TRUE FALSE 834337.0485 683844.8908 722176.9539 638085.4724 723248.9735 679487.3807 776346.2859 840007.7823 780770.9524 889235.5672 0.938263245 0.769025572 0.812132331 0.717566296 0.813337883 0.764125284 0.873049071 0.944640333 0.87802488 1 19.76220613 2.014628622 3.814367464 0.93137548 0.798213268 0.51216959 0.060407361 0.17803623 5.632834787 0.025567633 0.016317156 103.4257364 -2.014628622 -0.133162212 AADEEAFEDNSEEYIRR ddPTM_BT-474_Pertuzumab_2h_R1 6 AADEEAFEDNSEEYIRR 17 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;;;; 370.7 1.44E-104 6899540000 1777630 2135770 1404117 1414028 1633480 2134560 1605880 1588440 1762180 1581510 FALSE TRUE 1708158.254 2074859.931 1657872.176 1487006.155 1686022.368 2177722.266 1625533.24 1555638.159 1562144.714 1474392.919 1.158550229 1.407263901 1.124443935 1.008554867 1.143536669 1.477029791 1.102510205 1.055104198 1.059517239 1 20.49168962 2.014630689 24.99807388 1.052949099 1.217561562 0.289507656 0.129413618 332.7249193 568493.1444 0.050744178 0.037462781 103.4262286 -2.014630689 0.164612463 AVASS(ph)PAATNSEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVASSPAATNSEVK 14 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AVASS(1)PAATNSEVK;AVASS(1)PAATNSEVK 339.77 8.02E-69 831970000 1593180 1590090 1541300 1614910 1759260 1858120 1587260 1580050 1705500 1733450 TRUE FALSE 1530916.764 1544742.19 1819847.196 1698255.699 1815848.196 1895692.459 1606685.363 1547421.415 1511898.79 1616041.888 0.947324928 0.955880044 1.126113877 1.050873564 1.123639313 1.173046611 0.994210221 0.957537937 0.935556684 1 20.62403316 2.014644029 24.86562323 0.963703646 1.064766622 0.304086761 0.068515388 278.0190251 472075.4669 0.027731535 0.020473194 103.4294057 -2.014644029 0.101062976 TQS(ph)PEFEAQSSK ddPTM_BT-474_Pertuzumab_2h_R1 4 TQSPEFEAQSSK 12 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK 308.96 3.25E-46 2298630000 2890900 2531180 2396820 2398240 2556290 2379250 2675080 3018840 2852490 2740430 TRUE FALSE 2777920.432 2458993.225 2829978.691 2522013.454 2638515.389 2427360.065 2707818.429 2956499.899 2528687.294 2554818.235 1.087326055 0.962492435 1.107702557 0.987159642 1.032760512 0.95011067 1.05988692 1.157225144 0.989771898 1 21.28478922 2.014681222 24.96218907 1.076990378 1.020115344 0 0.064519789 429.2246769 729798.8414 0.023078737 0.017037898 103.4382637 -2.014681222 -0.056875034 DSPSKSS(ph)AEAQTPEDTPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSPSKSSAEAQTPEDTPNK 19 1 A0A5F9UY30;A0A5H1ZRP2;O43493-4;O43493;O43493-5;O43493-3;O43493-7 A0A5F9UY30 TGOLN2 Trans-Golgi network integral membrane protein 2 1 DSPS(0.065)KS(0.183)S(0.751)AEAQTPEDTPNK 258.83 2.92E-31 562500000 683370 835890 598750 845630 597830 476150 911370 1178600 1249400 1063200 TRUE FALSE 656663.1449 812051.2356 706957.4441 889273.0656 617059.7449 485778.0792 922523.6187 1154261.498 1107573.35 991188.517 0.662500759 0.819270221 0.713242165 0.897178539 0.622545292 0.490096557 0.930724683 1.16452267 1.117419473 1 19.91879995 2.01469709 7.10601768 1.097218983 0.711276906 0.725681272 0.109497063 0.077283553 19.28063284 0.044012337 0.031363733 103.4420432 -2.01469709 -0.385942077 AGVLT(ph)PPDLGPHPPPPAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGVLTPPDLGPHPPPPAPR 19 0 I3L2J0 I3L2J0 CIC 1 AGVLT(1)PPDLGPHPPPPAPR 88.945 0.0091081 187570000 171650 183800 151570 159310 151500 184760 155340 153190 164280 166290 TRUE FALSE 164941.7282 178558.204 178962.0707 167532.0082 156373.1351 188495.9738 157241.0974 150026.573 145631.6231 155027.0302 1.063954641 1.151787554 1.154392692 1.080663211 1.008683034 1.21589102 1.014281814 0.967744611 0.939395039 1 17.24216026 2.014725563 24.14319347 0.971850251 1.110492365 0.591271252 0.054794791 105.100975 172316.5466 0.020285128 0.014974805 103.4488251 -2.014725563 0.138642114 TGSGS(ph)PFAGNS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 6 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 TGS(0.001)GS(0.999)PFAGNS(1)PAR;TGSGS(1)PFAGNS(1)PAR;TGSGS(1)PFAGNS(1)PAR;TGS(0.008)GS(0.992)PFAGNS(1)PAR;TGS(0.001)GS(0.999)PFAGNS(1)PAR;TGSGS(1)PFAGNS(1)PAR 243.86 2.16E-17 2334320000 2650170 2505750 2250510 2593840 2382120 2485170 2645220 2959250 3021790 2948100 TRUE FALSE 2546598.426 2434288.463 2657227.219 2727708.393 2458743.053 2535421.84 2677592.994 2898140.453 2678769.068 2748422.561 0.926567284 0.885703857 0.966819024 0.992463252 0.894601539 0.922500738 0.974229011 1.054474117 0.97465692 1 21.3901724 2.01474069 5.032040135 1.015830889 0.932749555 0.506875037 0.034657276 0.139934137 10.02700677 0.014593986 0.009928308 103.4524284 -2.01474069 -0.083081334 S(ph)LESVLSLGPRPTGGGSS(ph)PPEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(1)LESVLSLGPRPT(0.002)GGGS(0.248)S(0.749)PPEIR;S(0.997)LES(0.004)VLS(0.002)LGPRPT(0.099)GGGS(0.151)S(0.747)PPEIR 145.07 8.16E-08 398141000 487914 548188 378321 497513 444962 451740 503585 591207 500011 532143 TRUE FALSE 468845.7815 532554.215 446692.0204 523189.7056 459274.6068 460874.4923 509748.0239 578998.3688 443251.8475 496100.4806 0.945062139 1.073480546 0.900406345 1.054604311 0.925769325 0.928994247 1.027509635 1.167098988 0.893471917 1 18.92027283 2.014745711 20.93385456 1.053393661 0.974821311 0.039539023 0.082694095 60.44673833 85811.25171 0.030001487 0.02213573 103.4536244 -2.014745711 -0.078572351 EGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPK 34 0 Q16576;E9PC52;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 181.9 4.29E-20 295770000 41911 34055 41938 58038 50492 54493 40189 29184 45134 42147 FALSE TRUE 40273.07178 33083.78474 49517.12951 61033.34814 52116.12104 55594.8858 40680.845 28581.3402 40010.57754 39292.34615 1.024959712 0.841990565 1.260223284 1.553313918 1.326368266 1.414903696 1.035337642 0.72740223 1.018279168 1 15.26196069 2.014762629 8.690333269 0.883835102 1.23774703 0.348020385 0.199319551 0.194446432 92.36017141 0.084404283 0.061020425 103.4576548 -2.014762629 0.353911927 YIGTGHADTTKWEWLVNQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIGTGHADTTKWEWLVNQHR 20 1 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 257.02 2.14E-36 1057560000 1636560 1965560 991800 1097290 1401560 1877060 1162930 903710 1401830 1094640 FALSE TRUE 1572601.426 1909504.153 1171040.322 1153921.268 1446642.45 1915015.439 1177162.285 885048.0727 1242700.135 1020499.058 1.541012129 1.871147395 1.147517299 1.13074212 1.417583328 1.876547974 1.153516288 0.867269858 1.217737661 1 19.96084342 2.014835229 24.75055282 1.012789253 1.481279474 0.433504599 0.247684539 200.4600776 334438.708 0.097765582 0.072175848 103.4749509 -2.014835229 0.468490221 SKSDGEAKPEPS(ph)PSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSDGEAKPEPSPSPR 16 2 P26358;K7EJL0;K7ENQ6;K7ERQ1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 SKSDGEAKPEPS(0.608)PS(0.392)PR;SKSDGEAKPEPS(0.915)PS(0.085)PR 176.1 2.59E-09 777080000 782080 697940 605930 509910 582700 573800 697180 779120 818510 852460 TRUE FALSE 751515.449 678035.4346 715435.0298 536226.5162 601443.0747 585402.6291 705712.2974 763030.8997 725596.1763 794722.1249 0.945632977 0.853172969 0.900232934 0.674734601 0.756796691 0.736612976 0.887998805 0.960122885 0.913018719 1 19.60009098 2.01484474 5.543059475 0.947159374 0.808260359 0.42194114 0.076913141 0.177704916 17.69984144 0.032929701 0.022781225 103.477217 -2.01484474 -0.138899015 EKYIDQEELNK ddPTM_BT-474_Pertuzumab_2h_R1 8 EKYIDQEELNK 11 1 P08238;P07900;P07900-2;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ;;;;;;; 200.93 4.12E-08 26423450000 28570220 25339640 21925100 20750610 24199700 25054070 27332730 31789640 35451110 31594660 FALSE TRUE 27453664.22 24616978.28 25887453.29 21821551.47 24978105.33 25560680.46 27667236.13 31133172.82 31426848.62 29454725.54 0.932063148 0.835756498 0.878889646 0.740850613 0.84801691 0.867795574 0.939314002 1.056983973 1.066954387 1 24.81199577 2.014889268 2.220698503 1.048162956 0.844038652 0.760063342 0.047982605 0.141315775 1.309021339 0.026268983 0.014281516 103.4878271 -2.014889268 -0.204124304 EMDRETLIDVAR ddPTM_BT-474_Pertuzumab_2h_R1 6 EMDRETLIDVAR 12 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;; 221.86 2.39E-11 8115140000 4091640 4633360 3069430 3473920 3947360 4634820 3681560 3667410 4000230 3733320 FALSE TRUE 3931734.185 4501221.109 3624144.28 3653209.428 4074330.419 4728539.236 3726616.033 3591676.702 3546140.661 3480458.911 1.129659705 1.293283795 1.041283455 1.049634408 1.170630231 1.358596483 1.070725478 1.031954921 1.018871577 1 21.73084611 2.014972021 24.99825137 1.028204535 1.171392427 0.377628397 0.091812358 271.8235091 453852.1188 0.036035365 0.026605364 103.5075481 -2.014972021 0.143187893 NDWLDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 NDWLDLR 7 0 E9PS41;Q6RFH5-2;Q6RFH5 E9PS41 WDR74 WD repeat-containing protein 74 0 82.279 0.057977 66907000 273580 287060 240010 278810 238470 259290 276590 294670 318690 308520 FALSE TRUE 262888.1911 278873.3299 283385.146 293199.4175 246140.6041 264533.0215 279974.9912 288584.9615 282513.6473 287623.6656 0.914000559 0.969577136 0.985263662 1.019385581 0.855773128 0.919719248 0.973407354 1.0033422 0.982233665 1 18.13382286 2.015120301 7.180921717 0.99389104 0.946341663 0.232926917 0.041966147 0.248385916 63.7064517 0.017295599 0.012344681 103.5428943 -2.015120301 -0.047549377 DDWEEKR ddPTM_BT-474_Pertuzumab_2h_R1 6 DDWEEKR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 148.04 0.0033842 11650270000 6262170 5385860 4658320 4497560 5053030 5075090 5600300 6325540 6854150 6080560 FALSE TRUE 6017437.473 5232260.546 5500182.048 4729679.611 5215565.299 5177711.797 5668838.147 6194915.389 6076095.627 5668718.255 1.061516414 0.923005927 0.97026908 0.834347272 0.920060773 0.913383161 1.00002115 1.092824711 1.071864106 1 22.43459114 2.015128712 4.074986141 1.062553733 0.933041349 0.455280014 0.057731621 0.172776076 6.533329326 0.024882127 0.016165796 103.5448997 -2.015128712 -0.129512385 EIS(ph)DDEAEEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EISDDEAEEEK 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 1 EIS(1)DDEAEEEK;EIS(1)DDEAEEEK 252.75 2.26E-20 3673800000 1631000 1307150 1986670 1658460 1551950 1402760 2191390 2657320 2921040 2872490 TRUE FALSE 1567258.717 1269871.362 2345705.462 1744053.319 1601869.881 1431124.768 2218208.886 2602445.413 2589455.785 2677933.694 0.585249262 0.474198209 0.875938589 0.651268298 0.59817384 0.534413818 0.828328532 0.971810997 0.966960381 1 21.35268881 2.015317615 3.513512437 0.967993054 0.625827087 0.724655204 0.100007451 0.131942396 3.382767995 0.047032052 0.029375413 103.5899481 -2.015317615 -0.342165966 QKSDAEEDGGTVS(ph)QEEEDRKPK ddPTM_BT-474_Pertuzumab_2h_R1 6 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.004)VS(0.996)QEEEDRKPK;QKSDAEEDGGTVS(1)QEEEDRKPK;QKSDAEEDGGT(0.025)VS(0.975)QEEEDRKPK;QKSDAEEDGGT(0.009)VS(0.991)QEEEDRKPK;QKSDAEEDGGT(0.098)VS(0.902)QEEEDRKPK;QKSDAEEDGGT(0.011)VS(0.989)QEEEDRKPK 311.97 2.27E-67 9115890000 3655670 4203400 2092480 3002600 2406820 2548410 3953280 5908400 5469520 2879530 TRUE FALSE 3512802.375 4083523.148 2470637.683 3157564.546 2484237.551 2599940.596 4001661.423 5786389.475 4848643.02 2684496.868 1.308551489 1.521150274 0.920335469 1.176222101 0.925401546 0.968502004 1.490656022 2.155483787 1.806164528 1 21.35622029 2.015340892 6.38534862 1.793489211 1.141684349 0.322812435 0.325612294 0.133103916 22.05614938 0.124445259 0.087818301 103.5955003 -2.015340892 -0.651804862 RTPAPPEPGS(ph)PAPGEGPSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RTPAPPEPGSPAPGEGPSGR 20 1 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR 150.11 5.59E-08 661180000 271270 316850 201377 252720 243153 288910 243595 241356 265235 251871 TRUE FALSE 260668.4685 307813.7482 237770.3035 265762.9095 250974.2371 294751.9581 246576.1885 236371.9143 235126.6348 234811.5528 1.110117732 1.310896949 1.012600533 1.131813602 1.068832577 1.255270257 1.050102457 1.006645165 1.00134185 1 17.84114387 2.015351328 24.34118527 1.009643952 1.145754674 0.407680646 0.080341731 171.3457717 271685.6462 0.029301104 0.021632018 103.5979897 -2.015351328 0.136110722 AVEES(ph)S(ph)DEERQR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEESSDEERQR 12 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 AVEES(1)S(1)DEERQR;AVEES(1)S(1)DEERQR 126.16 0.0034961 744040000 1217590 1314640 794330 996160 1093470 1249670 989550 966770 1064220 970340 TRUE FALSE 1170005.237 1277147.754 937883.1008 1047571.937 1128642.456 1274939.184 1001660.409 946805.8617 943414.2072 904618.0075 1.293369386 1.4118089 1.03677253 1.158026845 1.247645356 1.40936746 1.107274452 1.046636098 1.042886831 1 19.78694919 2.015365378 24.01528495 1.045505868 1.251744526 0.500575374 0.104541814 136.4980344 213337.9902 0.041326398 0.030508887 103.6013412 -2.015365378 0.206238658 DYQASEDKVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYQASEDKVR 10 1 Q96ME1-4;Q96ME1-2;Q96ME1;Q96ME1-3 Q96ME1-4 FBXL18 F-box/LRR-repeat protein 18 0 ; 93.162 0.0081839 497030000 596540 621740 503070 529430 514110 553160 596270 646710 687870 705270 FALSE TRUE 573226.5573 604008.5839 593985.9397 556753.9457 530646.8151 564345.2742 603567.3306 633355.2125 609785.8814 657501.4347 0.871825561 0.91864223 0.903398698 0.846772214 0.807065638 0.858317936 0.917971123 0.963275788 0.927428975 1 19.32663452 2.015382907 3.187969448 0.957951995 0.868094286 0.628942278 0.03303892 0.189222501 3.838123231 0.017109603 0.01039282 103.6055229 -2.015382907 -0.089857708 TLVVHEK ddPTM_BT-474_Pertuzumab_2h_R1 9 TLVVHEK 7 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;;; 108.46 0.0072477 28219760000 35560500 34477630 29394820 31423410 32243660 32021410 33848920 36059290 38411270 35846300 FALSE TRUE 34170756.35 33494361.75 34707117.86 33045175.96 33280806.61 32668904.85 34263173.21 35314653.06 34050983.66 33418398.17 1.022513293 1.002273106 1.038563179 0.988831834 0.99588276 0.977572434 1.025278741 1.056742842 1.018929258 1 24.99413925 2.015396168 24.96808458 1.033899296 1.00438799 0.157653054 0.021046239 286.2904193 464278.3297 0.007885078 0.005821495 103.6086865 -2.015396168 -0.029511307 LDS(ph)ELTARKELEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDSELTARKELEQK 14 2 Q8IUG5-2;Q8IUG5;Q8IUG5-3 Q8IUG5-2 MYO18B Unconventional myosin-XVIIIb 1 LDS(0.5)ELT(0.5)ARKELEQK 101.39 0.00073469 250180000 565380 941370 375710 479950 577930 912220 409970 322810 300840 342480 TRUE FALSE 543284.3245 914523.0493 443609.1546 504720.277 596519.6433 930665.7134 414987.3355 316143.8607 266689.9044 319283.5246 1.701573313 2.864297651 1.389389431 1.580790233 1.868306998 2.914856677 1.299745535 0.990166533 0.835276123 1 18.28447858 2.015404075 24.59047011 0.991780077 2.036459794 0.535629169 0.474153918 153.4004122 244881.3281 0.179085924 0.132217102 103.6105728 -2.015404075 1.044679717 DRS(ph)PHRS(ph)SPSDTRPK ddPTM_BT-474_Pertuzumab_2h_R1 6 DRSPHRSSPSDTRPK 15 3 A0A0D9SGE8;Q8IWS0-3;Q5JRC6;Q8IWS0-2;Q8IWS0-4;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 2 DRS(0.956)PHRS(0.56)S(0.479)PS(0.005)DTRPK;DRS(0.961)PHRS(0.701)S(0.158)PS(0.161)DT(0.018)RPK;DRS(0.89)PHRS(0.583)S(0.517)PS(0.009)DT(0.001)RPK;DRS(0.995)PHRS(0.872)S(0.125)PS(0.007)DTRPK;DRS(0.936)PHRS(0.512)S(0.469)PS(0.08)DT(0.003)RPK;DRS(0.879)PHRS(0.564)S(0.503)PS(0.053)DTRPK 129.32 9.56E-05 2133561000 922261 1220052 1007949 1129139 1021183 1168684 1052950 1044141 1153652 1184577 TRUE FALSE 886218.0205 1185257.312 1190107.806 1187413.999 1054030.279 1192315.591 1065836.317 1022579.123 1022694.261 1104344.545 0.802483269 1.073267684 1.077659877 1.075220596 0.954439702 1.079659058 0.965130241 0.925960225 0.926064484 1 20.07475892 2.015480824 24.30212215 0.943222493 1.017232007 0.09686761 0.08241802 317.8655413 498989.3516 0.03010262 0.022223773 103.6288848 -2.015480824 0.074009514 SNS(ph)FSDER ddPTM_BT-474_Pertuzumab_2h_R1 8 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.104)NS(0.846)FS(0.049)DER;S(0.056)NS(0.942)FS(0.002)DER;S(0.018)NS(0.978)FS(0.003)DER;S(0.002)NS(0.738)FS(0.26)DER;S(0.106)NS(0.885)FS(0.009)DER;S(0.06)NS(0.881)FS(0.06)DER;SNS(1)FSDER;SNS(0.994)FS(0.006)DER 190.66 0.00019433 12108360000 9539830 9551670 8128380 9813740 7604380 8241580 10446560 13134410 12701440 11465780 TRUE FALSE 9167002.897 9279265.724 9597359.081 10320228.3 7848981.789 8408230.394 10574408.13 12863179.84 11259625.78 10689192.51 0.857595454 0.868097914 0.897856323 0.965482499 0.734291368 0.786610437 0.989261641 1.203381811 1.053365422 1 23.34964954 2.015483053 5.535359913 1.106394437 0.855731755 0.660070828 0.075633878 0.092949441 9.167410547 0.030982413 0.021452615 103.6294165 -2.015483053 -0.250662681 TITGFQTHTTPVLLAHGER ddPTM_BT-474_Pertuzumab_2h_R1 2 TITGFQTHTTPVLLAHGER 19 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 191.8 5.13E-15 1592170000 683530 873950 659780 865730 752080 777980 712400 628360 710580 718310 FALSE TRUE 656816.8919 849025.8017 779016.9227 910410.429 776271.3362 793711.2886 721118.5643 615384.1464 629917.9374 669658.2239 0.980824051 1.267849436 1.163305243 1.359515043 1.159205261 1.185248326 1.076845678 0.918952571 0.940655867 1 19.35306544 2.015527332 2.60864354 0.946144113 1.196560631 0.559099216 0.092230733 0.190735814 2.473589787 0.045317828 0.025920101 103.6399827 -2.015527332 0.250416519 GFGSSAPEGLEPDSMASAASALHLLS(ph)PRPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMAS(0.001)AAS(0.002)ALHLLS(0.997)PRPR;GFGSSAPEGLEPDS(0.023)MAS(0.012)AAS(0.012)ALHLLS(0.953)PRPR;GFGSSAPEGLEPDSMAS(0.009)AAS(0.003)ALHLLS(0.988)PRPR;GFGSSAPEGLEPDSMASAASALHLLS(1)PRPR 171.69 8.26E-13 1459070000 498873 639349 597105 592608 569121 701331 492761 396186 450881 448674 TRUE FALSE 479376.4916 621115.3925 705015.156 623192.5699 587427.2938 715512.3933 498791.5565 388004.6207 399698.8791 418284.9103 1.146052558 1.484909872 1.685490293 1.489875811 1.40437123 1.710586195 1.192468445 0.927608458 0.955566097 1 18.67412643 2.015634918 4.730647613 0.972621769 1.492059285 0.72129031 0.147527165 0.097981159 5.739589628 0.061397729 0.041322336 103.6656603 -2.015634918 0.519437517 AAPAQVRPPS(ph)PGNIRPVK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAPAQVRPPSPGNIRPVK 18 2 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AAPAQVRPPS(1)PGNIRPVK;AAPAQVRPPS(1)PGNIRPVK;AAPAQVRPPS(1)PGNIRPVK 135.21 4.64E-06 11838640000 1063950 1024180 1036330 1099750 1015630 992620 1149850 1293250 1275430 1406750 TRUE FALSE 1022369.658 994971.3892 1223617.884 1156508.229 1048298.661 1012691.456 1163922.208 1266543.936 1130648.533 1311469.569 0.779560336 0.758669063 0.933012792 0.881841452 0.799331289 0.772180674 0.887494636 0.965744052 0.862123346 1 20.3227529 2.01572915 6.497454222 0.936155292 0.824944498 0.460293721 0.059375639 0.150607271 26.44961834 0.024086876 0.017041412 103.6881557 -2.01572915 -0.111210794 QAAECHPPVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 QAAECHPPVGR 11 0 Q8N3U4;Q8N3U4-2;B1AMT4 Q8N3U4 STAG2 Cohesin subunit SA-2 0 84.289 0.016073 151050000 101410 108110 77477 114990 112110 115610 96710 86778 95009 116730 FALSE TRUE 97446.78509 105026.8087 91478.81737 120924.6477 115716.12 117947.7134 97893.56591 84986.00397 84223.97663 108823.7731 0.895454939 0.965109053 0.840614277 1.111196977 1.063334937 1.083841426 0.899560483 0.78095072 0.773948322 1 16.73163423 2.01577115 8.30097712 0.830363399 0.993615122 0.299716028 0.09751421 0.181631402 72.90430099 0.038178025 0.027565327 103.6981837 -2.01577115 0.163251723 VDGPRS(ph)PSYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDGPRSPSYGR 11 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VDGPRS(0.994)PS(0.006)YGR;VDGPRS(0.922)PS(0.074)Y(0.004)GR 84.753 0.0095241 725160000 1104960 1396930 437330 613550 1010940 1331970 655690 514610 649570 488540 TRUE FALSE 1061776.942 1357090.924 516365.2594 645215.389 1043457.803 1358903.346 663714.5304 503983.1237 575833.5368 455450.7507 2.331266202 2.979665578 1.133745545 1.416652378 2.291044206 2.98364498 1.457269594 1.106558992 1.264315705 1 18.79693553 2.015773024 24.55064789 1.172077024 2.152920182 0.438932948 0.552061183 199.1103687 309912.9514 0.221695312 0.163678642 103.6986313 -2.015773024 0.980843158 EAFSLFDKDGDGTITTK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAFSLFDKDGDGTITTK 17 1 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479 P0DP25 CALM2;CALM3;CALM1 0 ;; 260.31 2.80E-27 50677720000 23763640 20760220 17718010 19734970 19695860 20461830 22822420 26648380 29822560 24334120 FALSE TRUE 22834930.68 20168158.85 20920048.54 20753494.17 20329395.22 20875582.22 23101727.6 26098081.64 26437228.02 22685948.38 1.006567162 0.889015461 0.922158871 0.914817129 0.896122784 0.920198789 1.01832761 1.150407345 1.165356968 1 24.43529564 2.015959702 3.189525983 1.118383287 0.921514726 0.710029191 0.051584475 0.115660928 2.349226775 0.022906707 0.013925786 103.7432148 -2.015959702 -0.196868561 TDDYLDQPCYETINR ddPTM_BT-474_Pertuzumab_2h_R1 6 TDDYLDQPCYETINR 15 0 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;; 332.41 1.51E-68 3658000000 2139470 2116320 1729320 2060940 2043970 1815120 2138260 2315360 2392790 2376720 FALSE TRUE 2055857.147 2055964.626 2041846.593 2167305.36 2109716.151 1851822.97 2164428.666 2267547.007 2121170.511 2215742.637 0.927841128 0.927889634 0.921517941 0.978139484 0.952148555 0.835757248 0.976841186 1.023380138 0.95731809 1 21.07935889 2.015972492 24.9904117 0.997150591 0.925923995 0.429822367 0.037220849 213.6598498 334288.8323 0.01400448 0.010340025 103.7462702 -2.015972492 -0.071226596 KPSQTAS(ph)YER ddPTM_BT-474_Pertuzumab_2h_R1 6 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 KPSQT(0.103)AS(0.897)YER;KPSQT(0.071)AS(0.929)YER;KPS(0.013)QT(0.071)AS(0.916)YER;KPSQT(0.011)AS(0.989)YER;KPS(0.003)QT(0.024)AS(0.973)Y(0.001)ER;KPSQT(0.025)AS(0.974)YER 117.21 0.00092654 3249100000 2615050 2457440 1435630 2284240 1782690 1332893 2382060 2879170 2698240 2392560 TRUE FALSE 2512850.955 2387356.217 1695080.276 2402129.9 1840031.843 1359845.01 2411212.363 2819714.133 2391947.107 2230509.78 1.126581456 1.07031865 0.759951959 1.076942106 0.824937805 0.6096566 1.081014028 1.264156812 1.072376875 1 21.08894204 2.016008274 24.98746314 1.149292922 0.909499434 0.247154178 0.161815785 280.417212 437704.0386 0.062025473 0.045796083 103.7548183 -2.016008274 -0.239793488 RPNEDS(ph)DEDEEKGAVVPPVHDIYR ddPTM_BT-474_Pertuzumab_2h_R1 9 RPNEDSDEDEEKGAVVPPVHDIYR 24 2 Q12996;E9PLP8;H0YE74 Q12996 CSTF3 Cleavage stimulation factor subunit 3 1 RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR 240.52 7.89E-38 59630440000 8836840 8151630 5972760 6260910 7225990 7427510 7568050 8040470 9201020 8151510 TRUE FALSE 8491486.523 7919153.494 7052170.595 6584036.315 7458420.531 7577699.341 7660670.06 7874431.485 8156558.783 7599400.967 1.117388931 1.042076017 0.927990328 0.866388857 0.98144848 0.997144298 1.008062358 1.036191079 1.073316018 1 22.85745427 2.016209466 1.977246429 1.04072494 0.981646683 0.095119874 0.064123244 0.774592237 5.672443685 0.040410792 0.021210619 103.802895 -2.016209466 -0.059078257 RS(ph)PESCSKPEK ddPTM_BT-474_Pertuzumab_2h_R1 5 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(0.584)PES(0.327)CS(0.09)KPEK;RS(1)PESCSKPEK;RS(1)PESCSKPEK;RS(0.577)PES(0.422)CS(0.001)KPEK;RS(1)PESCSKPEK 169.98 8.48E-06 7401010000 6828710 5867940 5038840 4871480 5757040 5706220 6309620 7204480 7869270 7247850 TRUE FALSE 6561836.464 5700592.097 5949470.476 5122897.667 5942220.42 5821603.678 6386839.017 7055704.97 6975983.46 6756946.664 0.971124502 0.843663918 0.880496883 0.758167545 0.879423905 0.861573129 0.945225608 1.044214987 1.032416535 1 22.68794004 2.016291375 2.69804161 1.029010785 0.860587831 0.671034727 0.050109093 0.154496538 2.155182682 0.02490036 0.014401493 103.8224744 -2.016291375 -0.168422954 NDEELNK ddPTM_BT-474_Pertuzumab_2h_R1 5 NDEELNK 7 0 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;H0YFX9;Q8IUE6;P16104 A0A0U1RR32;Q7L7L0;Q99878;P16104 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;HIST2H2AB;H2AFX Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A;Histone H2A type 2-B;Histone H2AX 0 ;;;; 141.52 0.0059356 25960434000 10473660 9074610 6768080 7694040 7910980 7838450 9059340 10702220 10432360 9123960 FALSE TRUE 10064337.79 8815811.008 7991222.611 8091130.326 8165443.856 7996948.83 9170210.913 10481215.42 9248122.229 8505986.062 1.183206475 1.036424342 0.939482213 0.95122779 0.959964406 0.940155412 1.078089106 1.232216387 1.087248693 1 23.02004706 2.016301887 8.636556085 1.138030188 0.997191212 0.209836138 0.087594464 0.204208747 88.76329166 0.03392527 0.024567549 103.8249875 -2.016301887 -0.140838976 (ac)S(ph)DKPDMAEIEK ddPTM_BT-474_Pertuzumab_2h_R1 5 SDKPDMAEIEK 11 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 S(1)DKPDMAEIEK;S(1)DKPDMAEIEK;S(1)DKPDMAEIEK;S(1)DKPDMAEIEK;S(1)DKPDMAEIEK 128.86 1.01E-05 4927480000 8574860 6999980 7044090 6959340 7831340 6447010 9107090 11688130 11715090 10069500 TRUE FALSE 8239744.991 6800347.424 8317113.758 7318512.371 8083242.163 6577372.959 9218545.292 11446766.03 10385242.1 9387483.796 0.877737333 0.72440577 0.885979027 0.779603196 0.861065898 0.700653455 0.982003857 1.219364665 1.106286021 1 23.16230708 2.016351994 5.364112861 1.126942034 0.807446616 0.763043567 0.076452407 0.068336214 6.009174997 0.028395914 0.019590586 103.8369669 -2.016351994 -0.319495418 VSDYEMK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSDYEMK 7 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 126.67 0.0091423 1446500000 1542480 1451980 1201120 1304920 1430950 1510520 1553160 1637950 1845260 1848810 FALSE TRUE 1482198.176 1410570.952 1418189.103 1372267.078 1476977.806 1541063.749 1572168.037 1604125.76 1635793.821 1723588.452 0.859949006 0.818391972 0.822811908 0.796168642 0.856920226 0.894101923 0.912148161 0.93068955 0.94906288 1 20.71698391 2.016380693 0.657420578 0.989193096 0.819651292 0.898808175 0.019567556 0.216551561 0.18306332 0.018453657 0.010984802 103.8438289 -2.016380693 -0.169541804 DDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_BT-474_Pertuzumab_2h_R1 9 DDEKEAEEGEDDRDSANGEDDS 22 2 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 DDEKEAEEGEDDRDS(0.874)ANGEDDS(0.126);DDEKEAEEGEDDRDS(0.948)ANGEDDS(0.052);DDEKEAEEGEDDRDS(1)ANGEDDS;DDEKEAEEGEDDRDS(1)ANGEDDS;DDEKEAEEGEDDRDS(1)ANGEDDS;DDEKEAEEGEDDRDS(1)ANGEDDS;DDEKEAEEGEDDRDS(0.826)ANGEDDS(0.174);DDEKEAEEGEDDRDS(1)ANGEDDS;DDEKEAEEGEDDRDS(1)ANGEDDS 245.55 5.38E-31 15466850000 4297980 3472263 4613444 4583018 3489617 4309476 6010080 6379500 8144390 7531420 TRUE FALSE 4130010.19 3373237.459 5447195.956 4819548.108 3601863.7 4396616.557 6083633.157 6247761.096 7219872.991 7021310.215 0.588210756 0.480428489 0.775809043 0.686417201 0.512990252 0.626181784 0.866452695 0.88982838 1.028280018 1 22.74330884 2.016473407 1.686554577 0.984942996 0.608129182 0.791907809 0.085086006 0.174778579 0.930305244 0.055609951 0.027839187 103.866 -2.016473407 -0.376813814 DKYAENLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKYAENLK 8 1 Q08379;Q08379-2;B7ZC06 Q08379 GOLGA2 Golgin subfamily A member 2 0 ; 102.06 0.0045943 834520000 973530 844520 879600 847940 905840 662960 1009510 1107390 1187650 1198910 FALSE TRUE 935483.3713 820435.1165 1038563.287 891702.285 934977.1663 676365.5054 1021864.685 1084522.01 1052832.951 1117706.758 0.836966731 0.734034317 0.929191203 0.797796272 0.836513835 0.605136813 0.914251147 0.970309969 0.941958115 1 20.0921103 2.016477998 24.99228272 0.961163037 0.793160025 0.521261184 0.079456868 189.7406823 287779.756 0.029245904 0.021594087 103.867098 -2.016477998 -0.168003012 RPVS(ph)FPETPYTVSPAGADR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPVSFPETPYTVSPAGADR 19 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 RPVS(0.982)FPET(0.018)PYTVSPAGADR 64.68 0.018177 156390000 47078 59782 32266 43211 44679 51764 42303 39573 40723 47381 TRUE FALSE 45238.13971 58077.07589 38097.18395 45441.12489 46116.14061 52810.70355 42820.71677 38755.80372 36100.29576 44171.84267 1.024139746 1.314798577 0.862476674 1.028735098 1.044016682 1.19557393 0.969412055 0.877387072 0.817269409 1 15.4308394 2.016562607 8.580263078 0.894070636 1.076165228 0.322986247 0.118431667 0.206450612 87.27163229 0.044568497 0.03227403 103.8873354 -2.016562607 0.182094592 HQPVPQLQAHS(ph)TPHPDDFANDDIDSYMIAMETTIGNEGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQPVPQLQAHSTPHPDDFANDDIDSYMIAMETTIGNEGSR 40 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 HQPVPQLQAHS(0.484)T(0.484)PHPDDFANDDIDS(0.017)Y(0.016)MIAMETTIGNEGSR;HQPVPQLQAHS(0.5)T(0.5)PHPDDFANDDIDSYMIAMETTIGNEGSR 170.75 3.13E-19 179455000 36720 34880 30063 34557 33341 31900 27096 8720 29457 25746 TRUE FALSE 35284.9418 33885.25655 35496.05285 36340.49091 34413.44354 32545.03986 27427.60895 8539.928953 26113.16485 24002.20049 1.470071122 1.41175625 1.478866609 1.514048303 1.433762024 1.355919007 1.142712268 0.355797751 1.087948785 1 14.55087906 2.016635696 4.202212608 0.740621152 1.440760676 0.683109752 0.189678869 0.098833583 4.064704304 0.07802255 0.051196198 103.9048205 -2.016635696 0.700139524 VAVAGCCHGELDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAVAGCCHGELDK 13 0 Q9UK59;F8WAY1 Q9UK59 DBR1 Lariat debranching enzyme 0 ; 138.42 4.93E-05 560560000 450820 398050 426860 426720 428830 441410 497020 599640 622610 604100 FALSE TRUE 433201.456 386698.0037 504003.0974 448743.0703 442623.7064 450335.6126 503102.6794 587257.2245 551933.923 563183.7689 0.769200889 0.68662846 0.894917654 0.796796881 0.78593122 0.79962463 0.893318855 1.042745294 0.980024556 1 19.10324623 2.016651104 2.76192004 1.010012455 0.7885776 0.794515094 0.049846454 0.11772731 1.728353919 0.025101347 0.014627461 103.9085067 -2.016651104 -0.221434854 YALTGDEVKK ddPTM_BT-474_Pertuzumab_2h_R1 5 YALTGDEVKK 10 1 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 ;;;; 111.86 0.0027227 2090713000 2857980 2612560 2428040 2252160 2529240 2727490 2804180 3318230 3628820 3282070 FALSE TRUE 2746286.982 2538052.347 2866840.839 2368394.247 2610595.302 2782641.717 2838498.394 3249707.391 3216891.567 3059772.476 0.897546142 0.829490548 0.936945757 0.774042602 0.853199159 0.909427658 0.927682831 1.062074849 1.051349926 1 21.54499295 2.016913336 1.957818261 1.045135321 0.859881899 0.738811078 0.045304734 0.155509141 1.116622467 0.025362042 0.01327961 103.9712669 -2.016913336 -0.185253421 KGDVVHCWYTGTLQDGTVFDTNIQTS(ph)AK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGDVVHCWYTGTLQDGTVFDTNIQTSAK 28 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 KGDVVHCWYTGTLQDGTVFDTNIQT(0.014)S(0.986)AK 325.38 3.70E-84 888440000 413810 308860 380160 294300 368880 314090 372770 412790 444970 342670 TRUE FALSE 397637.8477 300051.6152 448863.3686 309488.8583 380745.3602 320441.115 377332.0708 404265.7422 394458.8711 319460.6557 1.244716182 0.939244348 1.405066197 0.968785523 1.191838035 1.003069108 1.181153497 1.265463321 1.234765108 1 18.28527874 2.017078823 24.97288492 1.203006195 1.122804786 0.004607778 0.147368083 684.4333356 1000783.598 0.050822996 0.037528043 104.0108926 -2.017078823 -0.080201409 RS(ph)NSPDKFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.531)NS(0.469)PDKFK 73.881 0.033602 1177700000 965230 775720 660860 567220 720640 684670 849880 951150 1101900 967700 TRUE FALSE 927507.7445 753597.2251 780292.1028 596494.2922 743820.0401 698514.4965 860281.0857 931508.4201 976816.9315 902156.8171 1.028100356 0.835328416 0.86491848 0.661186925 0.824490849 0.774271705 0.953582647 1.032534924 1.082757358 1 19.78301871 2.017101904 3.275193214 1.037583148 0.825291742 0.531762103 0.087596746 0.193006841 4.174371065 0.041553474 0.025493937 104.0164205 -2.017101904 -0.212291407 EVS(ph)RSPTTSSITSGYFSHSASNATLSDMVVPSSDSSDQLAIQTK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSRSPTTSSITSGYFSHSASNATLSDMVVPSSDSSDQLAIQTK 44 1 A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9;H0Y9Z7 A0A1B0GUA8 KIF13A Kinesin-like protein KIF13A 1 EVS(0.072)RS(0.072)PT(0.072)T(0.072)S(0.072)S(0.072)IT(0.072)S(0.072)GY(0.067)FS(0.072)HS(0.072)AS(0.072)NAT(0.072)LS(0.072)DMVVPSSDSSDQLAIQTK 54.913 0.010328 54809000 30663 38151 27923 29450 29572 36961 28973 27170 31929 32068 TRUE FALSE 29464.65606 37062.97083 32969.30724 30969.91803 30523.21024 37708.37674 29327.58024 26608.93001 28304.55378 29896.0058 0.98557166 1.239729852 1.102799734 1.035921596 1.02097954 1.261318218 0.980986572 0.890049667 0.946767069 1 14.86766513 2.01719948 24.97308276 0.933921164 1.107529089 0.43110184 0.086659515 195.5950136 283996.4761 0.031434211 0.023210792 104.0397931 -2.01719948 0.173607925 DNLGEVPLT(ph)PTEEASLPLAVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 DNLGEVPLTPTEEASLPLAVTK 22 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 DNLGEVPLT(0.454)PT(0.454)EEAS(0.093)LPLAVTK;DNLGEVPLT(0.846)PT(0.14)EEAS(0.015)LPLAVTK 94.384 0.0065385 79234000 183183 201915 174888 220004 256341 235231 167726 158564 155491 137215 TRUE FALSE 176024.0058 196156.5819 206494.152 231358.4328 264586.4411 239987.532 169778.681 155289.598 137840.3136 127921.3058 1.376033529 1.533416037 1.614227987 1.80859968 2.068353191 1.876055989 1.327211912 1.213946316 1.077539919 1 16.96489705 2.017207517 3.031689086 1.129673965 1.719202559 0.683691411 0.18891308 0.174744734 3.158694612 0.10188442 0.061104425 104.0417186 -2.017207517 0.589528594 IKELEQEREDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKELEQEREDQK 12 2 O75940 O75940 SMNDC1 Survival of motor neuron-related-splicing factor 30 0 ; 111.83 0.00075331 610840000 284720 271770 226646 252790 263957 255340 291800 282747 345140 311750 FALSE TRUE 273592.8276 264019.3857 267605.9739 265836.5222 272447.4166 260503.1497 295371.1357 276908.1756 305961.1541 290634.8948 0.941362625 0.908422871 0.9207634 0.914675171 0.93742156 0.896324407 1.016296188 0.952769886 1.052733721 1 18.1488484 2.017270374 1.37230421 1.01027813 0.919415287 0.624661914 0.030160742 0.272322198 0.955770292 0.019438661 0.009285405 104.0567779 -2.017270374 -0.090862843 TRPAS(ph)QPTPFALHHAASCEVDPSSGDSISLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRPASQPTPFALHHAASCEVDPSSGDSISLAR 32 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 T(0.245)RPAS(0.649)QPT(0.106)PFALHHAASCEVDPSSGDSISLAR 71.081 0.0019729 207410000 31456 38074 24825 36075 33003 40261 28888 20308 39964 35473 TRUE FALSE 30226.66474 36988.1668 29311.42973 37936.83507 34064.57147 41075.105 29241.53999 19888.6327 35427.45426 33070.38211 0.914010145 1.11846808 0.886334776 1.147154422 1.030062832 1.242051116 0.884221413 0.601403172 1.071274415 1 15.01325209 2.017439152 24.6263603 0.820656057 1.055105762 0.179108688 0.154758105 219.3054399 309686.4329 0.055923068 0.041292448 104.097225 -2.017439152 0.234449705 GEDS(ph)AEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 41 1 Q12906-7;Q12906-4;Q12906-6 Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 GEDS(0.5)AEET(0.5)EAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 130.24 4.19E-09 177020000 302440 283160 352690 365060 304400 337680 425520 519300 547740 577470 TRUE FALSE 290620.3104 275084.554 416428.9285 383900.7903 314191.3024 344508.121 430727.641 508576.2735 485562.8515 538357.4425 0.539827794 0.510970096 0.773517547 0.713096467 0.583610957 0.639924507 0.800077434 0.94468142 0.901933944 1 19.03820484 2.017479405 2.198457606 0.947119675 0.627757845 0.786439919 0.07567637 0.153683219 1.395982843 0.04450409 0.024177941 104.1068736 -2.017479405 -0.31936183 YDDAERR ddPTM_BT-474_Pertuzumab_2h_R1 4 YDDAERR 7 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;; 136.11 0.0048289 1753231000 2935680 3262420 2294120 2636120 2800740 3190380 2767250 2792230 3097040 2975340 FALSE TRUE 2820950.38 3169378.976 2708718.516 2772170.469 2890828.346 3254891.67 2801116.433 2734569.475 2745477.003 2773817.572 1.016992036 1.142605414 0.976530881 0.999406197 1.042184019 1.173433936 1.009841621 0.985850513 0.989782829 1 21.40344148 2.017517681 24.99950741 0.992190681 1.058227477 0.225948464 0.057088682 362.4349782 517229.544 0.021866605 0.016146437 104.1160494 -2.017517681 0.066036796 FYVEACDDGADDVLTIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FYVEACDDGADDVLTIDR 18 0 F8WCQ2;A0A5F9ZHN7;Q9NTJ5 F8WCQ2 SACM1L Phosphatidylinositide phosphatase SAC1 0 180.84 1.78E-13 44395000 45972 95056 47616 98992 53135 49593 75411 98413 73174 59834 FALSE TRUE 44175.36342 92345.09595 56221.27041 104100.989 54844.13553 50595.80444 76333.90238 96380.73716 64867.59429 55781.38989 0.791937302 1.655482162 1.007885794 1.866231537 0.983197723 0.907037357 1.368447479 1.727829611 1.16288953 1 15.76749626 2.017562074 24.95959868 1.420367014 1.225983244 0 0.364493785 731.1490643 1039120.576 0.132296355 0.097687662 104.1266926 -2.017562074 -0.19438377 RS(ph)YSPDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSYSPDGK 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.565)Y(0.004)S(0.431)PDGK 99.283 0.0042406 1137700000 246090 197680 161150 159060 189610 140430 201510 229270 219440 215050 TRUE FALSE 236472.5307 192042.3599 190273.3898 167269.1057 195708.9778 143269.5908 203976.1397 224535.4944 194530.0912 200484.472 1.179505467 0.957891442 0.949067965 0.834324494 0.97618023 0.714616895 1.01741615 1.119964515 0.97030004 1 17.61313097 2.017591 24.98102619 1.049735854 0.928510702 0.1226095 0.116143857 389.6879217 553394.3959 0.043499077 0.032119927 104.1336281 -2.017591 -0.121225153 EAYPEEAYIADLDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAYPEEAYIADLDAK 15 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;; 229.97 9.11E-13 337460000 355267 345857 279978 310048 345105 354670 367298 430680 489550 450525 FALSE TRUE 341382.7729 335993.497 330576.2527 326049.6144 356205.6157 361841.6704 371793.1028 421786.3075 433978.3364 420010.5405 0.812795728 0.79996444 0.787066563 0.776289124 0.848087325 0.861506166 0.885199458 1.004227911 1.033255822 1 18.68006601 2.017659939 1.152473255 1.029304117 0.799491948 0.942514109 0.022106932 0.102509981 0.25189008 0.017105899 0.008058303 104.1501594 -2.017659939 -0.229812169 MEITIRNS(ph)PYRR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEITIRNSPYRR 12 2 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;Q9UQ88-9;A0A087X1I0;A0A087WYI9 P21127-2 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 MEITIRNS(1)PYRR;MEITIRNS(1)PYRR;MEITIRNS(1)PYRR 199.84 8.71E-08 856030000 465050 515840 314955 365150 426520 508450 369000 353265 399640 353312 TRUE FALSE 446875.3319 501128.7483 371874.3746 383995.4353 440239.4032 518731.2074 373515.9324 345969.9543 354274.5426 329381.8635 1.356708979 1.521421802 1.129006833 1.16580625 1.336562367 1.574862689 1.133990586 1.050361275 1.075573921 1 18.32940159 2.017672767 24.51718078 1.058724514 1.338114963 0.540139044 0.129312779 160.3913974 222507.601 0.051311946 0.037888368 104.1532357 -2.017672767 0.279390449 TKDEPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TKDEPQR 7 1 A6NNI4;A0A2R8Y478;G8JLH6;P21926;A0A087WU13 A6NNI4 CD9 Tetraspanin;CD9 antigen 0 ;;; 83.005 0.020932 1488320000 1665770 2267550 1368150 2009560 1243890 1363030 1985790 2568430 2107550 1592150 FALSE TRUE 1600669.867 2202881.694 1615405.139 2113273.632 1283900.852 1390591.4 2010092.692 2515391.023 1868309.76 1484312.262 1.078391594 1.484109341 1.088318934 1.423739254 0.86498029 0.936859066 1.354224945 1.69465084 1.258703985 1 20.5013632 2.017692674 24.28806833 1.427335769 1.157559384 0.065854448 0.246042561 266.9970583 366524.905 0.091797393 0.067781341 104.1580101 -2.017692674 -0.269776385 SLDDDLDGVPLDATEDSK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLDDDLDGVPLDATEDSK 18 0 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ;; 354.94 3.50E-90 527060000 1113890 1035760 910910 940270 995240 1083360 1100850 1295900 1424020 1314290 FALSE TRUE 1070357.947 1006221.139 1075531.7 988797.4474 1027252.798 1105266.281 1114322.532 1269139.212 1262371.22 1225271.968 0.873567645 0.821222688 0.877790179 0.807002424 0.838387579 0.902057919 0.909449135 1.035802047 1.030278381 1 20.22467058 2.017740117 1.64343492 1.029634337 0.844772969 0.882944337 0.02746411 0.107551973 0.54357368 0.016641762 0.008280914 104.169389 -2.017740117 -0.184861368 RSAS(ph)PHDVDLCLVSPCEFEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 RSASPHDVDLCLVSPCEFEHR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.044)AS(0.956)PHDVDLCLVSPCEFEHR;RS(0.2)AS(0.8)PHDVDLCLVSPCEFEHR;RS(0.169)AS(0.831)PHDVDLCLVSPCEFEHR;RS(0.224)AS(0.776)PHDVDLCLVSPCEFEHR 167.74 5.51E-12 915230000 251232 296100 160558 189977 207480 274978 188012 164039 204503 204607 TRUE FALSE 241413.5757 287655.5179 189574.4022 199781.7357 214153.7826 280538.2436 190312.9471 160651.5373 181288.6768 190748.7856 1.265610027 1.508033285 0.993843298 1.047355217 1.122700634 1.470720994 0.997715118 0.842215256 0.950405405 1 17.54131435 2.017779133 24.53374364 0.914997706 1.223548378 0.442557172 0.158603357 176.8910177 244093.847 0.062041844 0.045811381 104.1787478 -2.017779133 0.308550672 VFDKDGNGYISAAELR ddPTM_BT-474_Pertuzumab_2h_R1 7 VFDKDGNGYISAAELR 16 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;;;;; 264.38 4.77E-27 56038960000 15961849 16095758 11158466 21912840 16070296 12508769 18891919 20862440 22645790 21823060 FALSE TRUE 15338042.29 15636722.74 13175049.02 23043764.3 16587211.67 12761704.88 19123123.96 20431623.32 20075134.86 20344964.71 0.753898693 0.768579497 0.647582791 1.132651967 0.815298129 0.627266012 0.939943825 1.004259463 0.986737266 1 24.27816844 2.017792872 24.78675488 0.991129578 0.798631352 0.350720236 0.129307307 255.8786654 356455.8332 0.04972987 0.036720883 104.1820436 -2.017792872 -0.192498226 DETEFYLGK ddPTM_BT-474_Pertuzumab_2h_R1 7 DETEFYLGK 9 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;;; 215.39 1.49E-06 3035450000 2951799 2574607 2428549 2397252 2809786 2487862 2884174 3317646 3360449 3187262 FALSE TRUE 2836439.432 2501181.729 2867441.827 2520974.463 2900165.318 2538168.274 2919471.384 3249135.451 2978984.918 2971385.906 0.954584669 0.841755938 0.965018317 0.848417049 0.976031189 0.854203511 0.982528516 1.093474747 1.002557396 1 21.50270456 2.017816708 6.463469565 1.041641968 0.907376997 0.545093694 0.051810307 0.096548007 16.06302075 0.018253367 0.012948847 104.1877617 -2.017816708 -0.134264971 FSPGDFWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSPGDFWGR 9 0 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 0 ; 152.63 0.00018614 724840000 753340 770830 660870 816640 770960 624290 822090 936000 881770 885420 FALSE TRUE 723898.6399 748846.6831 780303.91 858786.8883 795758.6286 636913.5715 832150.9833 916671.2729 781675.1663 825449.7147 0.87697485 0.907198427 0.945307626 1.04038668 0.964030412 0.771595847 1.008118324 1.110511345 0.946968849 1 19.65482081 2.017939677 24.99929992 1.038408084 0.923046609 0.283171153 0.075026807 274.3566064 382320.0544 0.028918005 0.021353491 104.2172662 -2.017939677 -0.115361475 DDEAAAVALSSLIHALDDLDMVAIVR ddPTM_BT-474_Pertuzumab_2h_R1 4 DDEAAAVALSSLIHALDDLDMVAIVR 26 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;; 220.52 2.97E-34 10077580000 1128560 968780 977270 909630 1179150 1191260 1024590 1005830 1201160 1094220 FALSE TRUE 1084454.628 941151.3429 1153884.428 956576.1133 1217078.431 1215348.093 1037129.239 985059.259 1064809.352 1020107.505 1.063078766 0.922600156 1.131140025 0.937720886 1.1930884 1.19139217 1.016686216 0.965642596 1.043820722 1 19.96028977 2.017967079 24.99866359 0.997293766 1.071237043 0.123039747 0.087197075 496.6014557 690948.2576 0.033620076 0.024825976 104.2238422 -2.017967079 0.073943277 GKPIFPVYPLVGS(ph)SSPTRK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKPIFPVYPLVGSSSPTRK 19 2 A6NEL2 A6NEL2 SOWAHB Ankyrin repeat domain-containing protein SOWAHB 1 GKPIFPVYPLVGS(0.315)S(0.315)S(0.315)PT(0.055)RK;GKPIFPVYPLVGS(0.303)S(0.303)S(0.303)PT(0.092)RK 74.444 0.008249 502700000 544550 521580 394680 454800 476540 454920 504090 568460 535910 521050 TRUE FALSE 523268.384 506705.0491 466007.4556 478272.2825 491868.3419 464118.7941 510259.2042 556721.1023 475075.7435 485758.8194 1.077218494 1.043120637 0.959339156 0.984587955 1.012577275 0.955451091 1.050437344 1.146085424 0.978007448 1 18.88988066 2.018046027 23.58901515 1.067762349 1.004266522 0.04617291 0.055201036 185.6042923 242612.2413 0.020825192 0.015376256 104.2427902 -2.018046027 -0.063495828 TPELNLDQFHDK ddPTM_BT-474_Pertuzumab_2h_R1 5 TPELNLDQFHDK 12 0 P27824;P27824-2;P27824-3;H0Y9Q7;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ;;;; 203.74 1.22E-07 9216700000 3333550 4943150 3308700 5548630 3508820 2690990 4865860 6227520 5518500 3774600 FALSE TRUE 3203271.181 4802176.202 3906655.692 5834995.459 3621684.382 2745403.662 4925409.85 6098919.536 4892063.015 3518942.98 0.910293574 1.364664398 1.110178742 1.658167095 1.029196666 0.780178502 1.399684473 1.733168048 1.390208095 1 21.74671071 2.018113036 24.92657664 1.483548048 1.162504411 0.107502072 0.286650257 351.0111029 483048.1847 0.106587703 0.078706618 104.2588753 -2.018113036 -0.321043638 DLDIFDR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLDIFDR 7 0 Q14165;F5H1S8;H0YG07 Q14165 MLEC Malectin 0 ;;;;; 143.94 0.0055544 1266843000 1729640 2801540 1454359 2754000 1713880 1308878 2260680 2978660 2251440 1624180 FALSE TRUE 1662043.757 2721642.822 1717194.023 2896134.27 1769008.507 1335344.41 2288346.878 2917149.63 1995865.97 1514172.842 1.097657883 1.797445276 1.134080586 1.912684067 1.168300248 0.881896949 1.511285115 1.92656317 1.318122948 1 20.53009847 2.018209693 24.98715303 1.568116384 1.349245341 0 0.373206537 683.1144273 937358.7478 0.137528048 0.101554595 104.282082 -2.018209693 -0.218871043 ECSEAMEVETSVISIDS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ECSEAMEVETSVISIDSPQK 20 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVETSVIS(0.006)IDS(0.994)PQK;ECSEAMEVETSVISIDS(1)PQK 196.4 1.13E-21 127378000 221415 208740 184464 190177 204556 224668 222845 259520 286420 277550 TRUE FALSE 212761.857 202786.9396 217800.7482 199992.0578 211135.7295 229210.9409 225572.2438 254160.8213 253906.8024 258751.2913 0.822263943 0.78371373 0.841737821 0.772912308 0.815979424 0.885834964 0.871772437 0.982259142 0.981277431 1 17.98120654 2.018232341 1.040933703 1.003559871 0.804493335 0.904745499 0.024819987 0.135481953 0.270737782 0.018547092 0.008810448 104.2875202 -2.018232341 -0.199066535 CGETGHVAINCSK ddPTM_BT-474_Pertuzumab_2h_R1 4 CGETGHVAINCSK 13 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ;;; 137.84 5.22E-06 1916620000 2435920 2194240 2812460 2504780 2325770 2288350 2840030 3321260 3445690 3306230 FALSE TRUE 2340721.553 2131662.424 3320734.085 2634051.996 2400580.504 2334622.005 2874787.137 3252674.82 3054549.717 3082296.097 0.759408402 0.691582624 1.077357262 0.854574614 0.778828649 0.757429504 0.932677149 1.055276559 0.990998146 1 21.55557403 2.018239669 5.079227846 1.016361705 0.8258974 0.448789785 0.097977074 0.174523761 12.66031645 0.041608638 0.028519252 104.2892798 -2.018239669 -0.190464305 SPS(ph)PPLPLSCSNSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPPLPLSCSNSTR 15 0 Q96HJ3-2;Q96HJ3 Q96HJ3-2 CCDC34 Coiled-coil domain-containing protein 34 1 S(0.018)PS(0.981)PPLPLSCSNSTR 63.29 0.066967 0 33480 28605 22224 22018 25972 26016 28420 31522 37701 27170 TRUE FALSE 32171.56459 27789.21341 26240.37117 23154.35162 26807.41297 26542.06134 28767.81246 30871.05968 33421.34054 25329.7517 1.270109749 1.097097742 1.035950588 0.914116802 1.058336982 1.047861095 1.135732115 1.218766771 1.319449986 1 14.62854531 2.018364018 3.537873693 1.200460589 1.062885544 0.156051201 0.110487188 0.348595548 9.091073346 0.049971805 0.031398179 104.3191447 -2.018364018 -0.137575045 FTFPALEEDVIYDDVPCES(ph)PDAHQPGAER ddPTM_BT-474_Pertuzumab_2h_R1 2 FTFPALEEDVIYDDVPCESPDAHQPGAER 29 0 Q9HCE6-5;Q9HCE6-3;Q9HCE6-2;Q9HCE6 Q9HCE6-5 ARHGEF10L Rho guanine nucleotide exchange factor 10-like protein 1 FTFPALEEDVIYDDVPCES(1)PDAHQPGAER;FTFPALEEDVIYDDVPCES(1)PDAHQPGAER 90.03 0.0010496 102482000 20319 16300.4 10048.1 19192.5 15894 17317.2 12882.7 11934.2 9683.2 13981.8 TRUE FALSE 19524.91102 15835.52855 11864.01519 20183.02723 16405.24494 17667.36565 13040.36234 11687.7546 8584.003731 13034.80023 1.497906425 1.214865458 0.910180055 1.548395592 1.258572794 1.355399802 1.000426712 0.896657746 0.658545093 1 13.67008085 2.018468363 2.576791159 0.840160695 1.286254736 0.551938794 0.182520543 0.21967279 2.779340897 0.09248952 0.052859399 104.3442117 -2.018468363 0.446094041 RYNEDLELEDAIHTAILTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RYNEDLELEDAIHTAILTLK 20 1 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ; 107.45 0.00014703 202489000 108663 111476 77980 81719 95554 104717 90682 86544 102881 103984 FALSE TRUE 104416.3298 108296.8136 92072.72066 85936.52738 98627.58119 106834.4495 91791.79344 84756.83616 91202.38019 96941.07106 1.07711137 1.117140676 0.949780311 0.886482132 1.017397271 1.102055592 0.946882394 0.874312974 0.940802275 1 16.5648204 2.018485739 24.21665333 0.920954302 1.019568385 0.239821179 0.071442497 222.0316316 290863.832 0.028841989 0.021297151 104.3483866 -2.018485739 0.098614083 KLS(ph)FTESLTSGASLLTLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSFTESLTSGASLLTLNK 19 1 P19838;P19838-2;P19838-3 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 1 KLS(0.762)FT(0.155)ES(0.083)LTSGASLLTLNK;KLS(0.416)FT(0.324)ES(0.259)LT(0.001)SGASLLTLNK 224.53 1.19E-19 550650000 1216400 1123940 1060440 1069800 1204480 1258290 1275710 1361630 1563240 1579530 TRUE FALSE 1168861.743 1091886.332 1252085.097 1125012.506 1243223.193 1283733.486 1291322.521 1333511.865 1385787.549 1472547.026 0.793768703 0.741495051 0.850285305 0.763990885 0.844267226 0.871777582 0.876931261 0.905581853 0.941082033 1 20.48988228 2.018576317 0.377062441 1.007410115 0.756590056 0.859233774 0.028240319 0.398261181 0.147457081 0.031488556 0.034091804 104.3701521 -2.018576317 -0.250820059 KAEEKDS(ph)LSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAEEKDSLSR 10 2 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 KAEEKDS(0.981)LS(0.019)R;KAEEKDS(0.972)LS(0.028)R 76.588 0.018548 526670000 637100 504010 569900 527570 581250 540090 670050 765080 865270 780730 TRUE FALSE 612201.4276 489636.1283 672893.6074 554797.9509 599946.4341 551010.9898 678250.2723 749280.8306 767048.1771 727850.4617 0.841108799 0.672715282 0.924494306 0.762241669 0.824271558 0.757038731 0.931853874 1.029443368 1.053854078 1 19.47328255 2.018609222 3.073114406 1.027505039 0.796849483 0.732781912 0.062929448 0.122754375 2.290130769 0.028092424 0.016944236 104.3780603 -2.018609222 -0.230655557 QKSDAEEDGGT(ph)VSQEEEDRKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.621)VS(0.379)QEEEDRKPK 223.12 8.20E-26 306620000 210280 233450 107510 140770 150840 161670 226990 352050 336290 196990 TRUE FALSE 202062.0251 226792.2346 126939.4485 148035.1566 155691.9056 164939.0782 229767.9715 344780.0445 298115.769 183647.6918 1.100269887 1.234931037 0.691211783 0.806082315 0.847774911 0.898127695 1.251134546 1.87739928 1.623302564 1 17.48658124 2.018615343 4.421489156 1.594440276 0.928216761 0.498454312 0.25299688 0.136651475 6.474402901 0.105180254 0.070072167 104.3795314 -2.018615343 -0.666223515 KGAAPT(ph)PPGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KGAAPTPPGK 10 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KGAAPT(1)PPGK;KGAAPT(1)PPGK;KGAAPT(1)PPGK 59.898 0.05954 1446990000 4494900 4165700 3719700 3689100 3766800 4121600 4384100 4954700 5235900 5309800 TRUE FALSE 4319234.339 4046898.315 4391932.534 3879494.893 3887962.543 4204941.576 4437753.927 4852383.714 4641542.583 4950162.517 0.872543947 0.817528374 0.887229969 0.783710612 0.785421192 0.849455258 0.896486512 0.980247355 0.937654586 1 22.23904446 2.018653629 2.250872666 0.971111447 0.828909163 0.769996475 0.034314822 0.144622575 1.379339197 0.018745039 0.010271033 104.3887337 -2.018653629 -0.142202284 SAAVETASLS(ph)PSLVPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAAVETASLSPSLVPAR 17 0 Q2KHT3;Q2KHT3-3 Q2KHT3 CLEC16A Protein CLEC16A 1 SAAVETAS(0.001)LS(0.999)PSLVPAR;SAAVETAS(0.003)LS(0.978)PS(0.019)LVPAR 218.12 4.98E-15 190906000 175031 206833 204310 224703 247768 232475 189528 182903 187295 181965 TRUE FALSE 168190.595 200934.3254 241233.3619 236299.9488 255737.6827 237175.8038 191847.5004 179125.9891 166034.0568 169640.3485 0.991453958 1.184472486 1.422028215 1.392946613 1.507528634 1.398109624 1.130907252 1.055916182 0.978741545 1 17.37211983 2.018685452 3.085401505 1.023049737 1.326419497 0.497438401 0.137862219 0.237772429 4.476817044 0.071653987 0.043274318 104.3963829 -2.018685452 0.30336976 ELLTTMGDRFTDEEVDELYR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;; 194.92 1.80E-18 93653000 284015 354027 165137 142065 259985 338525 184604 178889 172493 130324 FALSE TRUE 272915.3798 343930.4966 194980.9294 149396.9917 268347.6536 345370.2074 186863.239 175194.8796 152912.3178 121497.0394 2.246271853 2.830772653 1.604820416 1.229634832 2.208676483 2.842622414 1.538006522 1.441968302 1.258568263 1 16.89056163 2.01884183 24.64458142 1.334461537 2.130955595 0.442223046 0.472644825 221.9728977 290332.911 0.191148053 0.141148941 104.4339801 -2.01884183 0.796494057 RTNS(ph)TGGSSGSSVGGGSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTNSTGGSSGSSVGGGSGK 19 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 RT(0.133)NS(0.584)T(0.279)GGS(0.003)S(0.002)GSSVGGGSGK;RT(0.151)NS(0.506)T(0.329)GGS(0.013)S(0.002)GSSVGGGSGK 194.81 1.41E-15 392490000 404820 432140 310440 360490 394040 420930 364070 363110 399260 392050 TRUE FALSE 388999.1868 419815.7903 366543.4137 379094.9321 406714.6545 429441.493 368525.5976 355611.6516 353937.6786 365496.1043 1.064304605 1.148619056 1.002865446 1.037206492 1.112774253 1.174955049 1.008288716 0.972956066 0.968376063 1 18.4794965 2.018880418 24.3729668 0.980734956 1.087786857 0.531219404 0.047779756 142.2433178 183622.6473 0.018691638 0.013802369 104.4432596 -2.018880418 0.107051901 LLASQGSQGAPLLS(ph)TPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLASQGSQGAPLLSTPK 17 0 H3BRB3;Q14807-2;Q14807 H3BRB3 KIF22 Kinesin-like protein;Kinesin-like protein KIF22 1 LLASQGSQGAPLLS(0.67)T(0.33)PK 66.022 0.037361 0 217910 199420 189960 193780 142800 168770 205150 225970 227330 227260 TRUE FALSE 209393.8363 193732.7369 224289.9976 203781.009 147393.2917 172182.645 207660.6871 221303.6405 201524.4514 211867.4778 0.988324581 0.914405264 1.058633444 0.961832421 0.695686253 0.812690305 0.980144236 1.044538043 0.951181623 1 17.69280262 2.018931576 24.74112756 1.005726723 0.904921172 0.173064102 0.095243108 377.9038726 493869.3743 0.039420917 0.029110213 104.4555634 -2.018931576 -0.10080555 KRQDCSSS(ph)DTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRQDCSSSDTEK 12 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 1 KRQDCSS(0.001)S(0.999)DTEK 185.12 7.01E-06 77465000 70359 53645 44728 46485 48266 45093 57705 64761 69099 56665 TRUE FALSE 67609.29249 52115.09712 52811.34457 48884.09642 49818.51972 46004.81136 58411.21105 63423.66272 61255.17121 52827.02908 1.279823864 0.986523339 0.999703097 0.925361454 0.94304981 0.870857441 1.105706909 1.200591133 1.159542232 1 15.68898866 2.018992574 23.94388219 1.145036544 0.993631565 0.189245197 0.113410122 187.2489612 236062.6069 0.042489564 0.031374432 104.4702355 -2.018992574 -0.151404979 AGWGS(ph)PCHLSGESVILLGPTVGTESK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGWGSPCHLSGESVILLGPTVGTESK 26 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 AGWGS(0.992)PCHLS(0.008)GESVILLGPTVGTESK 175.86 6.37E-13 191150000 160510 217720 167040 218680 200010 239700 188870 189740 192800 215290 TRUE FALSE 154237.0917 211510.8388 197227.8438 229966.101 206443.5033 244546.8982 191181.4476 185821.8027 170914.1523 200708.2165 0.768464263 1.053822521 0.98265954 1.145773227 1.028575246 1.218419965 0.952534235 0.925830571 0.851555334 1 17.61474015 2.019000956 24.94632279 0.922961213 1.040622046 0.156477903 0.114655906 383.3331034 503275.32 0.042412185 0.031318914 104.4722518 -2.019000956 0.117660833 WQS(ph)PVTK ddPTM_BT-474_Pertuzumab_2h_R1 8 WQSPVTK 7 0 A9Z1X7 A9Z1X7 SRRM1 1 WQS(1)PVTK;WQS(0.997)PVT(0.003)K;WQS(1)PVTK;WQS(1)PVTK;WQS(1)PVTK;WQS(0.989)PVT(0.011)K;WQS(1)PVTK;WQS(0.999)PVT(0.001)K 160.75 0.0013999 57075160000 39492700 36646900 29884380 33279370 32586740 32848740 35945600 39024900 39372600 38791100 TRUE FALSE 37949281.62 35601766.29 35285152.24 34996922.27 33634922.09 33512964.03 36385513.01 38219022.18 34903187.51 36163744.25 1.049373687 0.984460183 0.97570517 0.967735034 0.930073 0.926700615 1.006132351 1.056832554 0.96514308 1 25.10804072 2.01902791 24.87551394 1.018100574 0.970539548 0.14693219 0.038255511 323.7065729 423185.527 0.014927176 0.011022463 104.478736 -2.01902791 -0.047561026 NSSSPVS(ph)PASVPGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 NSSSPVS(1)PASVPGQR 237.73 1.00E-17 301820000 143140 123130 103800 127180 123830 119000 128610 137140 143590 139390 TRUE FALSE 137545.9306 119618.453 122558.969 133743.775 127813.1044 121406.2615 130183.9677 134308.0111 127290.2652 129948.9911 1.058460934 0.920503129 0.943131362 1.029202104 0.983563653 0.934260901 1.001808221 1.033544084 0.979540234 1 16.98758591 2.019078187 24.96402628 1.010485472 0.97582648 0.076484152 0.041465489 471.9414838 617538.2999 0.0152772 0.011281146 104.490832 -2.019078187 -0.034658992 KES(ph)PTSSSFGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KESPTSSSFGK 11 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 KES(0.876)PT(0.106)S(0.014)S(0.003)SFGK;KES(0.468)PT(0.468)S(0.056)S(0.007)SFGK;KES(0.994)PT(0.006)SSSFGK 121.21 0.00044108 127910000 349872 311140 296451 306085 336287 338560 363480 372133 417540 428730 TRUE FALSE 336198.6154 302266.5918 350026.2902 321882.0835 347103.9768 345405.9152 367928.377 364448.3235 370142.6097 399691.7352 0.841144777 0.756249292 0.875740626 0.805325843 0.868429207 0.864180779 0.92053036 0.911823516 0.926070211 1 18.60852822 2.019194372 0.32810327 1.007359759 0.78361737 0.774079742 0.030762306 0.615425115 0.189602244 0.039719274 0.04894942 104.5187897 -2.019194372 -0.223742388 APS(ph)PGDYK ddPTM_BT-474_Pertuzumab_2h_R1 6 APSPGDYK 8 0 P55198 P55198 MLLT6 Protein AF-17 1 APS(1)PGDYK;APS(1)PGDYK;APS(1)PGDYK;APS(1)PGDYK;APS(1)PGDYK;APS(0.998)PGDY(0.002)K 110.53 0.0054773 7016590000 4080220 3641650 3033060 3425590 3493690 3251600 3832480 4321270 4606570 4012860 TRUE FALSE 3920760.491 3537793.708 3581201.412 3602385.11 3606067.712 3317349.58 3879383.037 4232034.264 4083651.486 3741065.418 1.048033128 0.945664754 0.957267787 0.962930264 0.963914636 0.88673926 1.036972788 1.131237707 1.091574466 1 21.83501776 2.019217167 9.341917896 1.08772226 0.960202922 0.536287217 0.047913418 0.154710483 68.92181027 0.01737204 0.01266734 104.5242758 -2.019217167 -0.127519338 MNTS(ph)RFADHHDLLT(ph)ET(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 MNTSRFADHHDLLTETK 17 1 C9J4A2;C9JYK8;A2RUB1-1;A2RUB1-2 C9J4A2 C17orf104 3 MNT(0.524)S(0.566)RFADHHDLLT(0.91)ET(1)K 46.178 0.078826 356350000 131170 178110 91175 139790 162710 180920 114520 93451 94579 98547 TRUE FALSE 126043.7314 173030.4772 107652.3507 147004.5787 167943.7149 184578.3264 115921.53 91521.20419 83842.78843 91872.32391 1.371944521 1.88337978 1.171760396 1.600096442 1.828012047 2.009074316 1.261767691 0.996178177 0.91260115 1 16.4873427 2.019242871 5.707450918 1.003910743 1.641688352 0.634727717 0.230960631 0.110851813 11.74263933 0.094056005 0.065824756 104.5304623 -2.019242871 0.637777609 YLSVPPSPNISTSESRS(ph)PPEGDTTLFLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 YLSVPPS(0.012)PNIS(0.001)T(0.001)S(0.001)ES(0.051)RS(0.935)PPEGDTTLFLSR;YLSVPPSPNISTSES(0.014)RS(0.986)PPEGDTTLFLSR;YLSVPPS(0.001)PNIS(0.004)T(0.004)S(0.004)ES(0.161)RS(0.827)PPEGDTTLFLSR;YLSVPPSPNIS(0.002)T(0.002)S(0.002)ES(0.226)RS(0.766)PPEGDTTLFLSR 150.79 2.14E-08 1381890000 336585 362720 240398 287524 333837 406522 280915 277091 305926 256617 TRUE FALSE 323430.8861 352375.5807 283843.2662 302363.1481 344575.1703 414742.1534 284352.9218 271368.974 271198.563 239236.102 1.351931767 1.472919755 1.186456659 1.26386923 1.440314264 1.733610228 1.188587004 1.134314477 1.133602164 1 17.86807559 2.019301102 24.99963529 1.11853461 1.401377658 0.515803635 0.141097059 214.2111819 277454.614 0.055660195 0.041102573 104.5444788 -2.019301102 0.282843048 SPQPVCS(ph)PAGSEGTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQPVCSPAGSEGTPK 16 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 SPQPVCS(1)PAGSEGTPK;SPQPVCS(1)PAGSEGTPK 302.9 4.79E-46 693360000 593190 512430 420328 422060 494680 496480 543500 627640 698000 604810 TRUE FALSE 570007.479 497815.9981 496290.6197 443842.5672 510591.8315 506519.1658 550151.5156 614679.0147 618765.9663 563845.68 1.010928166 0.882894054 0.880188742 0.78717029 0.90555244 0.898329425 0.975712921 1.090154694 1.097403045 1 19.10494084 2.019313571 2.621056618 1.070757468 0.887812903 0.637330746 0.056717474 0.167220683 2.195109904 0.028987484 0.016669022 104.5474805 -2.019313571 -0.182944565 GESQNTDLS(ph)PKPLISEQTVILGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GESQNTDLSPKPLISEQTVILGK 23 1 P15622-2;P15622-3;P15622;E9PPG5;E9PL28 P15622-2 ZNF250 Zinc finger protein 250 1 GESQNTDLS(1)PKPLISEQTVILGK;GES(0.002)QNT(0.034)DLS(0.964)PKPLISEQTVILGK 263.19 4.38E-44 333660000 531560 427640 414300 377730 444950 416450 481830 559440 562780 532700 TRUE FALSE 510786.0475 415444.1259 489173.2261 397224.6906 459262.2208 424870.9043 487726.7797 547887.3685 498895.5738 496619.7545 1.028525432 0.836543698 0.985005573 0.799856806 0.924776384 0.855525582 0.98209299 1.103233135 1.004582619 1 18.92178212 2.019497124 5.841851468 1.046733262 0.902390214 0.42323532 0.068904213 0.129503686 14.8059344 0.025106023 0.017635044 104.5916763 -2.019497124 -0.144343048 MDPSAKPSASQS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 5 MDPSAKPSASQSPEK 15 1 P35716 P35716 SOX11 Transcription factor SOX-11 1 MDPSAKPS(0.028)AS(0.201)QS(0.771)PEK;MDPSAKPSAS(0.003)QS(0.997)PEK;MDPSAKPSAS(0.001)QS(0.999)PEK;MDPSAKPSAS(0.001)QS(0.999)PEK;MDPSAKPSAS(0.003)QS(0.997)PEK 167.63 7.87E-07 3761210000 4119940 3301650 3139030 2684490 3164580 2980190 3805080 4445240 4715860 4579790 TRUE FALSE 3958928.19 3207490.175 3706322.548 2823036.851 3266371.59 3040451.484 3851647.707 4353444.241 4180535.343 4269596.744 0.927237027 0.751239606 0.868073209 0.661195195 0.765030467 0.71211678 0.902110419 1.019638271 0.979140559 1 22.02566839 2.019525775 4.224928426 0.995270918 0.777732373 0.658067852 0.071103909 0.121122898 5.031518166 0.029687006 0.019590596 104.5985767 -2.019525775 -0.217538545 VASPSQGQVGSSS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 4 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGSS(0.095)S(0.904)PKR;VASPS(0.008)QGQVGS(0.023)S(0.134)S(0.836)PKR;VASPSQGQVGS(0.001)S(0.035)S(0.964)PKR;VASPSQGQVGS(0.002)S(0.093)S(0.904)PKR 227.88 2.83E-15 1737860000 494215 512128 369439 455035 356037 400554 475820 540366 580783 479277 TRUE FALSE 474900.5314 497522.6109 436204.8454 478519.4109 367489.2534 408653.4763 481643.2275 529207.2533 514854.9487 446815.1419 1.062856844 1.113486461 0.976253498 1.07095612 0.822463742 0.914591826 1.077947416 1.184398655 1.152277308 1 18.76931855 2.019556377 9.651411954 1.132373767 0.993973532 0.260958335 0.090339424 0.330218563 152.7651422 0.035908779 0.026224739 104.6059473 -2.019556377 -0.138400235 S(ph)WGQQAQEYQEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SWGQQAQEYQEQK 13 0 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(1)WGQQAQEYQEQK;S(1)WGQQAQEYQEQK;S(1)WGQQAQEYQEQK;S(1)WGQQAQEYQEQK 324.38 1.92E-51 940820000 557763 484347 410948 447602 411689 464945 526546 668201 613100 599833 TRUE FALSE 535965.0053 470533.8978 485215.4451 470702.7929 424931.3506 474346.5065 532990.0275 654402.4158 543503.4583 559205.7766 0.958439679 0.84143247 0.867686754 0.841734497 0.759883693 0.848250369 0.953119674 1.170235436 0.971920322 1 19.09301974 2.019587089 4.473488825 1.066441643 0.850090806 0.626181447 0.067001993 0.110431013 5.398493441 0.027737255 0.018556333 104.6133451 -2.019587089 -0.216350837 QKS(ph)DAEEDGGTVS(ph)QEEEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.001)VS(0.999)QEEEDR;QKS(1)DAEEDGGT(0.134)VS(0.866)QEEEDR 184 1.47E-14 5121700000 1866640 2981830 1919160 3966900 2299780 2110640 3469640 5225800 4109500 2771680 TRUE FALSE 1793689.645 2896791.128 2265994.903 4171632.184 2373754.512 2153318.587 3512102.492 5117885.404 3643006.788 2583951.645 0.69416533 1.121070177 0.876949423 1.614438952 0.918652838 0.833343221 1.359198226 1.980642871 1.409858732 1 21.30114764 2.019625815 7.797487035 1.596909078 1.036331166 0.265411335 0.32826638 0.170787955 49.87488669 0.122078785 0.088223975 104.6226738 -2.019625815 -0.560577912 QFKEEDGLR ddPTM_BT-474_Pertuzumab_2h_R1 3 QFKEEDGLR 9 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ;; 132.25 0.00028303 3577720000 4407940 7435670 2995930 5916130 3740070 4196090 5597700 7276400 6147140 3980560 FALSE TRUE 4235672.832 7223611.972 3537361.195 6221462.178 3860372.748 4280937.815 5666206.327 7126139.797 5449342.438 3710953.126 1.141397557 1.946565135 0.95322174 1.676513275 1.040264487 1.153595227 1.526887065 1.92029906 1.4684482 1 21.82335835 2.01964872 19.95911343 1.604776364 1.334653964 0.002211083 0.357419008 50.53628341 51332.31206 0.127473507 0.094097034 104.6281919 -2.01964872 -0.270122399 VKPYIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKPYIR 6 1 P48200 P48200 IREB2 Iron-responsive element-binding protein 2 0 ; 91.584 0.043527 1272070000 2060160 2175700 2420600 2021380 2357700 1769200 2563300 2815000 2831000 3165300 FALSE TRUE 1979646.67 2113651.166 2858056.266 2125703.664 2433537.562 1804974.436 2594670.432 2756869.266 2509636.749 2950911.412 0.670859404 0.716270627 0.968533401 0.720354957 0.824673202 0.611666765 0.879277643 0.934243317 0.850461569 1 21.49272918 2.019802507 24.88598767 0.917386651 0.760743783 0.413836324 0.096313993 233.8689922 293904.0116 0.035575415 0.026270819 104.6652479 -2.019802507 -0.156642868 SFGEKS(ph)YLNVHR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFGEKSYLNVHR 12 1 Q6ZN11-3;Q6ZN11-2;Q6ZN11 Q6ZN11-3 ZNF793 Zinc finger protein 793 1 S(0.001)FGEKS(0.593)Y(0.407)LNVHR;SFGEKS(0.554)Y(0.446)LNVHR;SFGEKS(0.554)Y(0.446)LNVHR;S(0.002)FGEKS(0.546)Y(0.451)LNVHR 61.435 0.051258 25865600000 19269900 11327000 11996800 9570510 14315000 12192700 14768600 17103300 19627300 14783500 TRUE FALSE 18516811 11003965.05 14164888.63 10064445.17 14775454.98 12439244.75 14949342.54 16750110.88 17399291.19 13782200.38 1.343530822 0.798418594 1.027766847 0.730249517 1.072067926 0.902558692 1.084684748 1.215343735 1.262446541 1 23.7163029 2.019816587 4.557491692 1.177519718 0.96655038 0.184355116 0.169006898 0.26565034 13.70367147 0.065704193 0.044157163 104.6686413 -2.019816587 -0.210969338 S(ph)LSPNHNTLQTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.605)LS(0.395)PNHNTLQTLK 202.18 6.18E-08 733030000 1336700 1649100 1341200 1477200 1340800 1237300 1576400 1647400 1849700 1870900 TRUE FALSE 1284460.286 1602069.283 1583584.675 1553438.469 1383928.05 1262319.054 1595692.455 1613380.614 1639729.811 1744182.277 0.736425489 0.918521707 0.907923843 0.890639981 0.793453797 0.723731155 0.914865651 0.925006885 0.94011379 1 20.73411939 2.019904651 24.96845411 0.940014844 0.835884317 0.432095041 0.065658983 265.5796293 333142.5912 0.025872815 0.019106009 104.6898678 -2.019904651 -0.104130527 SQEDEISS(ph)PVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQEDEISSPVNK 12 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 SQEDEIS(0.029)S(0.971)PVNK;SQEDEIS(0.003)S(0.997)PVNK 301.31 1.62E-36 1270020000 3581500 3072700 2594900 2673100 2816900 2798300 3153900 3583500 3454200 3581300 TRUE FALSE 3441531.02 2985069.604 3063856.153 2811059.011 2907508.147 2854883.543 3192498.372 3509499.473 3062093.697 3338735.361 1.030788801 0.894071941 0.917669663 0.841953227 0.870841152 0.855079314 0.956199886 1.051146345 0.917141782 1 21.67087031 2.019905734 7.957119306 0.997302945 0.898454341 0.321914623 0.057508377 0.17977666 54.93079023 0.021942714 0.015883096 104.6901288 -2.019905734 -0.098848605 SPQLSLS(ph)PRPAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPQLSLSPRPASPK 14 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 2 SPQLS(0.004)LS(0.995)PRPAS(1)PK;S(0.006)PQLS(0.251)LS(0.743)PRPAS(1)PK;S(0.006)PQLS(0.186)LS(0.808)PRPAS(1)PK;S(0.01)PQLS(0.02)LS(0.971)PRPAS(1)PK 112.56 0.00033371 1863720000 3208330 2698320 2407420 2530590 2814560 2564450 2928830 3286850 3254430 3274580 TRUE FALSE 3082944.917 2621366.556 2842494.347 2661194.053 2905092.879 2616304.936 2964673.898 3218975.399 2885000.75 3052789.78 1.009877895 0.858679026 0.931113687 0.871725289 0.95161904 0.857020995 0.971135948 1.054437295 0.945037477 1 21.54169682 2.019962157 10.68677009 1.00761208 0.91168615 0.381318345 0.050174564 0.343231403 179.3058491 0.017396272 0.01274948 104.703731 -2.019962157 -0.09592593 RPELLTHSTTEVTQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPELLTHSTTEVTQPR 16 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 231.23 9.95E-16 3888010000 1277720 1573410 1250600 1670720 1467230 1608640 1389760 1307020 1378210 1604800 FALSE TRUE 1227785.29 1528537.887 1476611.239 1756946.059 1514424.785 1641167.803 1406768.299 1280029.58 1221761.379 1496105.467 0.820654237 1.021677897 0.986970018 1.174346394 1.012244671 1.096959967 0.940286851 0.855574429 0.816627842 1 20.51278045 2.019963813 6.118285705 0.879787768 1.024292906 0.270830784 0.09480312 0.187146305 24.89592731 0.036858981 0.026064622 104.7041301 -2.019963813 0.144505138 VS(ph)VS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSVSPGR 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 VS(1)VS(1)PGR;VS(1)VS(1)PGR 72.23 0.076267 1322310000 2119700 2083500 1975800 2206300 2013900 1925920 2233100 2389700 2563500 2423700 TRUE FALSE 2036859.781 2024080.62 2332871.011 2320167.407 2078678.922 1964863.422 2260429.346 2340351.86 2272502.227 2259540.64 0.901448615 0.89579297 1.032453663 1.026831457 0.919956422 0.869585343 1.000393313 1.035764446 1.005736381 1 21.10759807 2.020001611 24.98834783 1.017875317 0.945134093 0.309748359 0.050764717 308.6651072 385619.0402 0.02080866 0.015366659 104.7132433 -2.020001611 -0.072741224 KYSDVEVPASVTGYSFASDGDSGTCS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYSDVEVPASVTGYSFASDGDSGTCSPLR 29 1 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5 P35611 ADD1 Alpha-adducin 1 KYSDVEVPASVTGYSFASDGDSGTCS(1)PLR;KYSDVEVPASVTGYSFASDGDSGT(0.004)CS(0.996)PLR 298.51 3.91E-81 363560000 291150 308040 257226 287080 252810 328750 272610 258552 314240 316660 TRUE FALSE 279771.5361 299255.0008 303712.4602 301896.2332 260941.8632 335397.5502 275946.2827 253212.8108 278568.7926 295212.3361 0.947695953 1.013694091 1.028793255 1.022640982 0.883912463 1.136123086 0.934738319 0.857731131 0.943621788 1 18.17139348 2.0200052 24.99420951 0.912541116 1.004936743 0.185951256 0.069073659 287.2156499 358841.5673 0.024563203 0.018139011 104.7141087 -2.0200052 0.092395627 ESEDSETQPFDTHLEAYGPCLS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 6 ESEDSETQPFDTHLEAYGPCLSPPR 25 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR 280.88 1.85E-53 4211960000 1635549 1518476 1347870 1641928 1563799 1745240 1536253 1530655 1754668 1688691 TRUE FALSE 1571629.937 1475170.551 1591460.092 1726668.101 1614100.015 1780529.949 1555054.124 1499046.439 1555485.445 1574314.454 0.998294802 0.937024079 1.01089086 1.096774597 1.025271673 1.130987487 0.987765894 0.952189974 0.988039867 1 20.5862923 2.020039668 24.99969425 0.973567726 1.032768544 0.192792253 0.050989342 375.7724888 468778.1598 0.020518678 0.015152325 104.7224196 -2.020039668 0.059200819 S(ph)RSVSPCSNVES(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSVSPCSNVESR 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.4)RS(0.595)VS(0.235)PCS(0.251)NVES(0.519)R 124.99 0.0024558 260600000 320680 340910 241700 313810 320120 408630 296670 296890 318930 311630 TRUE FALSE 308147.4711 331187.5806 285380.5666 330005.7717 330416.9505 416892.7786 300300.7362 290759.1178 282726.4035 290523.0225 1.06066455 1.139970174 0.982299317 1.135902308 1.137317613 1.434973294 1.033655555 1.000812656 0.973163507 1 18.14829297 2.020087662 24.9994724 0.997870124 1.147395819 0.308412278 0.108808269 309.1975065 384800.5451 0.042610881 0.031466733 104.7339933 -2.020087662 0.149525695 LAPVPS(ph)PEPQKPAPVS(ph)PESVK ddPTM_BT-474_Pertuzumab_2h_R1 5 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 LAPVPS(1)PEPQKPAPVS(0.99)PES(0.01)VK;LAPVPS(1)PEPQKPAPVS(0.98)PES(0.02)VK;LAPVPS(1)PEPQKPAPVS(1)PESVK;LAPVPS(1)PEPQKPAPVS(0.984)PES(0.016)VK;LAPVPS(1)PEPQKPAPVS(1)PESVK 204.29 3.06E-22 12294513000 6447540 5394110 4982190 4989350 5416530 5454690 6152120 7089290 7457590 7421140 TRUE FALSE 6195563.009 5240275.264 5882582.561 5246850.951 5590757.607 5564987.569 6227411.485 6942893.684 6611035.648 6918499.578 0.895506741 0.75742944 0.850268544 0.75837989 0.808088162 0.80436336 0.90011012 1.003525924 0.95555916 1 22.72202776 2.020172564 2.87493524 0.984811698 0.808656484 0.789877884 0.040264896 0.105816493 1.700005954 0.018108729 0.010723466 104.7544701 -2.020172564 -0.176155214 MDPVNNINVDKDKPYLYCFR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDPVNNINVDKDKPYLYCFR 20 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 162.09 1.22E-11 944550000 839530 823200 616280 629790 813220 764390 800600 933330 997400 829170 FALSE TRUE 806720.2395 799723.142 727655.5051 662293.5374 839377.9598 779846.4895 810397.9823 914056.4093 884179.3334 773009.5774 1.043609631 1.03455787 0.94132793 0.856772745 1.085857128 1.008844537 1.048367324 1.182464534 1.143814203 1 19.56012676 2.020223327 3.485711713 1.12751766 0.992627809 0.31123254 0.073705307 0.242755677 6.102307457 0.033875946 0.021246166 104.7667152 -2.020223327 -0.13488985 KMPLDLS(ph)PLATPIIR ddPTM_BT-474_Pertuzumab_2h_R1 2 KMPLDLSPLATPIIR 15 1 B8ZZU6;E9PBF9;P15336-5;P15336;E9PEK8;H7C2N6;P15336-3;P15336-7;P15336-4;C9JCI8 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 KMPLDLS(1)PLATPIIR;KMPLDLS(1)PLATPIIR 221.86 9.06E-13 952090000 2271600 2402100 1647950 1777900 1922590 2336200 1819000 1746400 2060990 1846790 TRUE FALSE 2182823.361 2333594.46 1945771.223 1869657.632 1984431.853 2383439.565 1841261.466 1710336.23 1827035.056 1721705.268 1.267826382 1.355397177 1.130141877 1.085933619 1.152596725 1.384348186 1.069440571 0.993396641 1.061177595 1 20.71540676 2.020250492 24.4543973 1.020947911 1.22110799 0.542561858 0.089955883 150.3322864 181539.5675 0.03578585 0.026426486 104.7732684 -2.020250492 0.200160079 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 3 SCDEPLT(1)PPPHS(0.915)PT(0.042)S(0.042)MLQLIHDPVS(1)PR;S(0.004)CDEPLT(0.99)PPPHS(0.722)PT(0.142)S(0.142)MLQLIHDPVS(1)PR 130.89 6.07E-05 229520000 69969 87361 67389 99443 97355 93582 71632 45207 67890 86605 TRUE FALSE 67234.53413 84869.54982 79567.69136 104575.2651 100486.512 95474.29216 72508.65384 44273.45965 60183.41182 80739.16621 0.832737533 1.051157125 0.985490625 1.295223496 1.244581988 1.182502825 0.898060474 0.548351707 0.745405417 1 16.30098107 2.020306142 5.214038326 0.714845602 1.104225485 0.457394845 0.162323188 0.136277746 10.61405752 0.067020096 0.046304346 104.7866948 -2.020306142 0.389379883 YKAEDEK ddPTM_BT-474_Pertuzumab_2h_R1 10 YKAEDEK 7 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;; 114.89 0.0052918 55294350000 30651770 25410650 23877060 23072670 25916500 25031840 32947980 37717490 44260350 39924140 FALSE TRUE 29453864.94 24685963.14 28192175.88 24263453.26 26750127.76 25538000.96 33351207.24 36938610.65 39236100.62 37220042.44 0.791344206 0.66324382 0.757446097 0.651892144 0.718702237 0.686135729 0.896055057 0.992438703 1.054165929 1 25.14957636 2.020308527 2.340939859 1.017837318 0.7076488 0.907843478 0.043833228 0.076390113 0.790624224 0.021789513 0.012107013 104.7872704 -2.020308527 -0.310188518 EKYQEEFEHFQQELDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKYQEEFEHFQQELDK 16 1 P49257 P49257 LMAN1 Protein ERGIC-53 0 ; 178.12 1.71E-09 538200000 602870 695770 490410 544180 490390 375240 634650 688790 820420 637370 FALSE TRUE 579309.1739 675927.3208 579037.9961 572265.195 506163.8397 382827.6099 642417.0365 674566.2458 727289.3611 594200.3622 0.974939113 1.137541078 0.974482738 0.963084561 0.851840342 0.644273606 1.081145481 1.135250479 1.223980003 1 19.18058996 2.020439183 24.99696723 1.12812812 0.928785492 0.341041373 0.127081239 277.2656444 339092.3815 0.051221944 0.037826324 104.8187998 -2.020439183 -0.199342628 GLSDHVS(ph)LDGQELGTR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLSDHVSLDGQELGTR 16 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 GLSDHVS(1)LDGQELGTR;GLSDHVS(1)LDGQELGTR;GLS(0.001)DHVS(0.999)LDGQELGTR;GLSDHVS(1)LDGQELGTR 282.3 1.51E-35 4732350000 1690490 1873780 1553590 1915330 1786800 2032990 1747410 1769900 1918190 1901820 TRUE FALSE 1624423.782 1820341.629 1834358.272 2014180.411 1844274.045 2074098.451 1768795.326 1733350.946 1700445.113 1773008.037 0.916196513 1.026696772 1.034602345 1.136024411 1.040194971 1.169818978 0.997623975 0.977632876 0.95907355 1 20.75776765 2.020465267 24.96793378 0.979219732 1.057315147 0.225901103 0.064306603 335.6998332 409557.1393 0.024574037 0.018147426 104.8250956 -2.020465267 0.078095415 KLS(ph)SSDAPAQDTGSSAAAVETDASR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSSSDAPAQDTGSSAAAVETDASR 25 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YIM6 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 KLS(0.75)S(0.198)S(0.052)DAPAQDTGSSAAAVETDASR;KLS(0.647)S(0.138)S(0.215)DAPAQDTGSSAAAVETDASR 261.24 2.71E-45 2786300000 604310 708760 622330 755010 981780 956660 631110 610120 614540 624400 TRUE FALSE 580692.8971 688546.8587 734798.8747 793976.1566 1013359.845 976004.3207 638833.713 597520.8088 544779.9956 582108.8318 0.997567577 1.182849016 1.262304975 1.363965144 1.740842588 1.676669838 1.097447209 1.026476109 0.935873098 1 19.15092938 2.020543686 23.99461212 1.008284002 1.374861672 0.424211259 0.205591964 160.8100158 187821.6388 0.086852621 0.064136183 104.8440252 -2.020543686 0.366577671 RKEEEVQQQK ddPTM_BT-474_Pertuzumab_2h_R1 4 RKEEEVQQQK 10 2 Q96CS3 Q96CS3 FAF2 FAS-associated factor 2 0 ;;; 155.15 7.44E-06 609910000 644120 936540 526070 942130 555850 665830 875610 1172390 1085750 842930 FALSE TRUE 618947.0783 909830.7962 621142.5514 990753.4422 573729.4201 679293.5388 886325.9771 1148179.737 962500.2118 785837.6003 0.787627212 1.157784758 0.790421012 1.260761055 0.730086496 0.864419746 1.127874228 1.461090353 1.224808041 1 19.58387167 2.02059477 5.831684749 1.284236188 0.94411702 0.324795496 0.19028461 0.156239901 17.53305524 0.070874355 0.049853108 104.8563582 -2.02059477 -0.340119168 EYLSEEVQAVHK ddPTM_BT-474_Pertuzumab_2h_R1 3 EYLSEEVQAVHK 12 0 Q53GS9;B9A018;A0A087X1B2;Q53GS9-2 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 ;; 198.81 1.79E-07 1089490000 1280360 1313000 1091050 1113980 1223980 1281260 1192840 1196740 1376670 1281500 FALSE TRUE 1230322.116 1275554.526 1288227.005 1171472.641 1263350.428 1307167.955 1207438.333 1172026.901 1220396.193 1194702.864 1.029814319 1.067675122 1.078282345 0.980555649 1.057459948 1.094136454 1.010659947 0.981019579 1.021506042 1 20.18822042 2.020657339 24.12959716 0.998009638 1.050522563 0.377928899 0.030305148 157.6639343 184164.435 0.011489828 0.008484785 104.871466 -2.020657339 0.052512925 KPPLS(ph)PAQTNPVVQR ddPTM_BT-474_Pertuzumab_2h_R1 5 KPPLSPAQTNPVVQR 15 1 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR 195.46 5.77E-09 3017740000 2426870 2636730 2201260 2529320 2593630 2543230 2193840 1977990 2112610 2158480 TRUE FALSE 2332025.237 2561533.042 2599076.649 2659858.508 2677056.464 2594655.853 2220688.87 1937143.815 1872795.37 2012284.227 1.158894557 1.27294793 1.291605139 1.321810544 1.330357028 1.289408235 1.103566206 0.962659146 0.930681334 1 20.94040266 2.020772443 2.559215819 0.961285631 1.283273791 0.897077967 0.047796077 0.084846679 1.05920159 0.025698132 0.014690263 104.8992644 -2.020772443 0.321988159 SATREPPYR ddPTM_BT-474_Pertuzumab_2h_R1 4 SATREPPYR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 103.7 0.0030824 158315000 232099 254092 161022 192335 206396 257154 188574 188266 195632 192578 FALSE TRUE 223028.3145 246845.5449 190122.2573 202261.4324 213034.9148 262353.8301 190881.825 184378.2413 173424.6755 179534.5205 1.242258669 1.374919677 1.058973265 1.126587978 1.186595838 1.461300196 1.063204026 1.026979328 0.965968411 1 17.45390174 2.02088235 24.9929664 1.011758069 1.234312041 0.516953502 0.108834235 203.7868506 243900.6008 0.042309512 0.031244902 104.9258148 -2.02088235 0.222553972 S(ph)RESLNVDVVK ddPTM_BT-474_Pertuzumab_2h_R1 6 SRESLNVDVVK 11 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0;H0YGB8 Q07866-6 KLC1 Kinesin light chain 1 1 S(0.947)RES(0.053)LNVDVVK;S(0.998)RES(0.002)LNVDVVK;S(0.999)RES(0.001)LNVDVVK;S(0.979)RES(0.021)LNVDVVK;S(0.965)RES(0.035)LNVDVVK;S(0.935)RES(0.065)LNVDVVK 168.69 1.08E-05 12274580000 12430150 11600470 9871350 9803240 10493370 11241840 12234950 14191690 15079610 14802750 TRUE FALSE 11944366 11269635.95 11655322.53 10309186.39 10830898.78 11469157.71 12384684.98 13898626.64 13367835.89 13800146.56 0.865524576 0.816631614 0.84457962 0.747034559 0.784839402 0.831089558 0.89743141 1.007136162 0.968673473 1 23.71818025 2.020883536 2.342791646 0.992710293 0.810507126 0.859972718 0.032015698 0.105924967 1.098388655 0.017744267 0.009867313 104.9261013 -2.020883536 -0.182203167 EKEAELK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEAELK 7 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;H0Y9G8;B1AMS2;Q14141-2;Q14141-4;Q14141 REV__Q8TE73;D6RGI3;B1AMS2 SEPT11;SEPT6 Septin-11;Septin-6 0 59.8 0.092434 521130000 392010 381460 300620 343750 341990 342280 395490 452210 491780 445620 FALSE TRUE 376689.8158 370581.1343 354948.7213 361490.9787 352990.4189 349201.1361 400330.1249 442871.7055 435955.1961 415437.7605 0.906729844 0.89202564 0.854396868 0.870144732 0.849683039 0.840561859 0.963634419 1.066036234 1.049387508 1 18.66427283 2.020888317 3.70392332 1.041860408 0.868935498 0.906425248 0.02457065 0.061616676 1.801237906 0.011283171 0.00720577 104.9272563 -2.020888317 -0.17292491 ESEDAELLWR ddPTM_BT-474_Pertuzumab_2h_R1 3 ESEDAELLWR 10 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YB83;E5RGC8 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ;; 103.55 0.0065141 1350370000 825920 947610 738170 1117600 726000 773880 978450 1284950 829060 889640 FALSE TRUE 793642.1333 920585.0906 871573.7395 1175279.47 749352.4493 789528.3838 990424.5638 1258415.333 734948.5845 829383.8904 0.956905653 1.109962589 1.050868904 1.41705124 0.903504949 0.951945647 1.19416904 1.517289337 0.886138003 1 19.6616805 2.020891802 23.37789805 1.232896564 1.0749257 0 0.208003763 251.5578209 281490.432 0.077909545 0.05753132 104.9280983 -2.020891802 -0.157970864 NS(ph)LESIS(ph)SIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLESISSIDR 11 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 2 NS(0.999)LES(0.015)IS(0.518)S(0.468)IDR 94.01 0.012898 61553000 159230 192260 167820 265770 169660 132990 222590 290570 219910 181770 TRUE FALSE 153007.1156 186776.933 198148.8071 279486.4215 175117.268 135679.1489 225314.123 284569.628 194946.7387 169458.556 0.902917617 1.102198304 1.169305415 1.649290707 1.033392896 0.800662723 1.329611961 1.679287459 1.150409536 1 17.37057296 2.020953989 24.99737361 1.390144087 1.127406838 0.050997807 0.270931437 425.7910007 507951.5676 0.104219038 0.076964576 104.9431241 -2.020953989 -0.262737248 KTEAPAAPAAQETK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTEAPAAPAAQETK 14 1 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 0 ; 153.74 1.01E-05 283920000 432560 492160 368850 415490 376110 398890 477020 620920 537080 424410 FALSE TRUE 415655.077 478124.0787 435509.4 436933.4887 388207.9197 406955.8291 482857.9135 608097.785 476112.93 395664.3327 1.050524504 1.208408338 1.100704218 1.104303453 0.9811547 1.02853807 1.220372608 1.536903215 1.203325371 1 18.59391749 2.020997053 7.390968872 1.324305444 1.08532177 0.185131614 0.140033388 0.167228637 40.18776573 0.05235476 0.037756051 104.9535307 -2.020997053 -0.238983674 S(ph)KTPPPPPQTAQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKTPPPPPQTAQTK 14 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 S(0.5)KT(0.5)PPPPPQTAQTK;S(0.5)KT(0.5)PPPPPQTAQTK 102.89 0.00069482 498520000 528910 483040 405230 395700 421610 439250 507940 575530 644700 576680 TRUE FALSE 508239.6125 469264.1721 478464.0753 416122.1244 435171.4685 448131.936 514156.3217 563645.1044 571516.3588 537620.9499 0.945349344 0.87285321 0.889965459 0.774006527 0.809439194 0.833546267 0.956354699 1.048406139 1.063047039 1 19.03622983 2.021011963 3.066379477 1.039414215 0.851123611 0.75986412 0.046345866 0.126561682 2.351557086 0.023586832 0.01425703 104.9571339 -2.021011963 -0.188290605 LADAMAES(ph)PSRDVVGSGTELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LADAMAESPSRDVVGSGTELQR 22 1 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6 K7ESE9 BCAS3 Breast carcinoma-amplified sequence 3 1 LADAMAES(0.903)PS(0.097)RDVVGSGTELQR;LADAMAES(0.8)PS(0.2)RDVVGSGTELQR 269.57 1.33E-38 808940000 585710 605520 476930 572690 601630 656280 551440 551130 607020 603960 TRUE FALSE 562819.8057 588251.1625 563121.8603 602246.5995 620981.9753 669550.4313 558188.6877 539748.9729 538113.6344 563053.2512 0.999585393 1.04475227 1.000121852 1.0696086 1.102883207 1.189142288 0.991360385 0.95861088 0.955706469 1 19.10291185 2.021152531 24.99999928 0.968876603 1.067339574 0.429036016 0.051933554 227.558687 268948.5875 0.020906665 0.015439209 104.991111 -2.021152531 0.098462971 GVPAGNSDT(ph)EGGQPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVPAGNSDTEGGQPGR 16 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 GVPAGNS(0.392)DT(0.608)EGGQPGR 184.22 2.08E-08 339510000 82485 101690 74842 102870 115390 158070 92740 92804 92083 98954 TRUE FALSE 79261.39501 98789.90076 88367.61425 108179.133 119101.6241 161266.2837 93874.97986 90887.56497 81630.12388 92251.75744 0.859185746 1.070872832 0.957896269 1.172651189 1.291049921 1.748110694 1.017595572 0.985212287 0.884862534 1 16.49328878 2.021162896 24.99751957 0.966636967 1.189894782 0.177373676 0.225308211 439.4671057 519094.4424 0.091604943 0.067648991 104.9936166 -2.021162896 0.223257815 ALYETELADARR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALYETELADARR 12 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 135.5 0.00020294 559590000 276380 340870 166545 305760 248940 304040 246690 231355 303870 237532 FALSE TRUE 265578.764 331148.7213 196643.3863 321540.3102 256947.3812 310187.8971 249709.066 226577.4384 269375.9515 221443.7461 1.199305777 1.495407873 0.88800605 1.452018022 1.16032801 1.400752573 1.127641085 1.023182828 1.216453191 1 17.75658073 2.021202743 21.67450502 1.080693864 1.262983964 0.203048352 0.170934533 76.32446097 78021.14364 0.059427965 0.043880401 105.0032504 -2.021202743 0.1822901 KHS(ph)QTDLVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 KHSQTDLVSR 10 1 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 1 KHS(1)QTDLVSR;KHS(1)QTDLVSR;KHS(1)QTDLVSR 167.32 3.23E-06 5786500000 6382200 6276300 3073370 6171200 6122400 3653000 5854900 6549600 7771800 4384700 TRUE FALSE 6132776.568 6097306.069 3628796.326 6489696.372 6319332.556 3726866.163 5926554.018 6414348.471 6889577.846 4087720.364 1.500292589 1.491615259 0.887731059 1.587607711 1.545930737 0.911722386 1.449843309 1.569174968 1.685432768 1 21.96286508 2.021235744 24.99897308 1.488460756 1.318714616 0.015007084 0.286721472 661.3137117 778503.2126 0.104763739 0.077366594 105.0112297 -2.021235744 -0.16974614 S(ph)PGSSWQEYGPSDTCGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGSSWQEYGPSDTCGSR 18 0 Q5JSZ5;A0A494C0D3 Q5JSZ5 PRRC2B Protein PRRC2B 1 S(0.995)PGS(0.004)S(0.001)WQEYGPSDTCGSR 152.32 4.34E-08 95567000 31566 31888 28909 31755 30807 35393 29294 29544 25611 38773 TRUE FALSE 30332.36582 30978.58546 34133.49938 33393.87936 31797.93513 36108.67071 29652.50873 28933.90608 22703.74665 36146.87017 0.839142246 0.857019856 0.944300273 0.92383875 0.879687093 0.998943215 0.820334059 0.800453979 0.628097164 1 15.14158311 2.021254762 23.50854214 0.793107433 0.906371632 0.191845732 0.093844301 159.1610144 176036.4282 0.033344219 0.024623198 105.0158282 -2.021254762 0.113264199 EMEADERDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EMEADERDR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 108.57 0.002718 88249000 84805 103879 54263 72756 83366 95703 71230 68653 79416 71540 FALSE TRUE 81490.72684 100916.4726 64069.53117 76510.94588 86047.5431 97638.18023 72101.73405 67235.29156 70401.02862 66694.53208 1.221850192 1.513114636 0.960641438 1.147184687 1.290173878 1.463960795 1.081074142 1.008108003 1.055574219 1 16.02528087 2.02127464 24.74241723 1.027743955 1.260288673 0.378482404 0.145699946 229.5577822 266974.6456 0.056052801 0.041393843 105.0206349 -2.02127464 0.232544719 KAFEEAEK ddPTM_BT-474_Pertuzumab_2h_R1 6 KAFEEAEK 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 123.88 0.0021302 20957000000 25493900 22609000 18211900 16645000 18147700 13242800 22367100 23968800 26515500 26290900 FALSE TRUE 24497570.2 21964213.46 21503195.45 17504050.44 18731437.25 13510578.49 22640835.26 23473835.9 23505571.6 24510193.93 0.99948496 0.89612565 0.877316414 0.714153894 0.764230479 0.551222831 0.92373138 0.957717266 0.959012061 1 24.54687856 2.021300387 24.99844243 0.960839983 0.797265965 0.329611768 0.112763743 296.4232619 347885.2064 0.045314921 0.033464443 105.0268613 -2.021300387 -0.163574018 LLKPGEEPSEYT(ph)DEEDTKDHNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLKPGEEPSEYTDEEDTKDHNK 22 2 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPSEYT(1)DEEDTKDHNK;LLKPGEEPSEYT(1)DEEDTKDHNK 337.38 5.17E-81 2242300000 732700 818830 662660 965570 707290 608910 1140830 1746860 1653890 1064130 TRUE FALSE 704065.274 795477.7701 782417.4028 1015403.183 730040.6252 621222.5774 1154791.819 1710786.731 1466147.341 992055.5273 0.709703494 0.80184803 0.788683074 1.023534626 0.735886858 0.626197385 1.164039499 1.724486869 1.477888385 1 19.92006135 2.021339477 5.183816055 1.475754212 0.795008077 0.670572588 0.195324756 0.088578691 6.723628149 0.075667804 0.052307367 105.036315 -2.021339477 -0.680746135 ASASRPQPAPADGADPPPAEEPEARPDGEGS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASASRPQPAPADGADPPPAEEPEARPDGEGSPGK 34 2 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 ASASRPQPAPADGADPPPAEEPEARPDGEGS(1)PGK;ASASRPQPAPADGADPPPAEEPEARPDGEGS(1)PGK 83.058 0.00038938 1175400000 595770 532120 419640 502130 532160 497740 577560 687530 668050 674120 TRUE FALSE 572486.6497 516944.4586 495478.2828 528044.9895 549277.4097 507804.6438 584628.352 673332.2652 592215.7647 628461.252 0.910933885 0.822555817 0.788399096 0.840218849 0.874003621 0.808012654 0.930253616 1.071398218 0.942326616 1 19.26146427 2.021399505 4.746948063 1.010853463 0.839931002 0.743526643 0.043374118 0.085021559 4.919629996 0.017371765 0.011806691 105.050834 -2.021399505 -0.170922461 LVNLQHLDLLNNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVNLQHLDLLNNK 13 0 Q96AG4 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 ; 255.23 7.86E-24 1703910000 2085560 3323200 1588440 3507800 1952500 1708140 3038000 4099000 3122000 2172060 FALSE TRUE 2004054.009 3228425.59 1875506.443 3688837.978 2015303.936 1742679.761 3075179.953 4014354.218 2767603.648 2024944.442 0.989683454 1.594327984 0.926201433 1.821698365 0.995239126 0.86060621 1.51864905 1.982451536 1.36675535 1 20.94945089 2.021403961 24.75573129 1.606810325 1.219999552 0.067386468 0.372579975 332.9692033 385108.9958 0.134713963 0.099484534 105.051912 -2.021403961 -0.386810773 RFS(ph)SSDFSDLSNGEELQETCSSSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RFSSSDFSDLSNGEELQETCSSSLR 25 1 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;H7C4B4;H7C1G8 P23497 SP100 Nuclear autoantigen Sp-100 1 RFS(0.749)S(0.198)S(0.053)DFSDLSNGEELQETCSSSLR 243.34 6.46E-39 294630000 112680 99668 95872 117470 97004 104070 126020 158830 149250 163930 TRUE FALSE 108276.341 96825.56623 113198.2031 123532.6408 100124.2218 106174.3667 127562.2705 155550.105 132307.7657 152826.8751 0.708490185 0.633563738 0.74069566 0.808317521 0.655148001 0.694736228 0.834684805 1.017819051 0.86573625 1 17.22153874 2.021452137 3.599215858 0.958890677 0.708034061 0.792805044 0.058385877 0.099580065 2.708219161 0.02613573 0.016569292 105.063566 -2.021452137 -0.250856616 YFQFQEEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 YFQFQEEGK 9 0 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 124.23 0.0012458 321928000 405079 419360 392731 430371 420981 366275 474893 555020 570099 545529 FALSE TRUE 389248.0648 407400.2634 463706.228 452582.4989 434522.2362 373681.3315 480704.8826 543558.643 505383.7516 508579.8349 0.765362757 0.801054693 0.911766838 0.889894699 0.854383533 0.734754518 0.945190606 1.068777418 0.99371567 1 18.95611474 2.021524983 6.864489109 1.023597886 0.833205029 0.731237985 0.05355893 0.084151239 15.92659701 0.021642309 0.015523941 105.0811902 -2.021524983 -0.190392858 ENEVLEAWK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENEVLEAWK 9 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 102.52 0.0093521 0 72240 72460 59335 54543 57171 52097 70957 76542 82578 81405 FALSE TRUE 69416.78093 70393.51175 70058.1544 57357.97077 59009.95714 53150.43703 71825.39299 74961.38095 73204.09164 75891.36684 0.914686134 0.927556251 0.923137338 0.755790456 0.777558233 0.700348923 0.946423763 0.987745828 0.964590502 1 16.21164816 2.021606031 24.91081921 0.978834129 0.834501919 0.489622251 0.071491435 212.8734645 245432.7919 0.029981549 0.022141092 105.1008022 -2.021606031 -0.144332211 AHAASVFLTLLHFDSPPIPHVPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHAASVFLTLLHFDSPPIPHVPHR 24 0 Q9BTW9-4;Q9BTW9;J3KR97;A0A0J9YVR1;A0A0J9YWI5;A0A0J9YXU4;I3L120 Q9BTW9-4 TBCD Tubulin-specific chaperone D 0 146.89 5.76E-08 97719000 8609.9 9673.9 8425.7 8390.7 9587.8 8519.4 7894.9 4594.1 9393.7 7237.1 FALSE TRUE 8273.415589 9398.009844 9948.411419 8823.745033 9896.200294 8691.668105 7991.520148 4499.23023 8327.366558 6746.924771 1.226249865 1.39293236 1.4745105 1.307817314 1.466771993 1.288241443 1.184468542 0.666856439 1.234246244 1 12.72001436 2.021663162 4.083386379 0.927174178 1.364998285 0.574040849 0.149348547 0.126701087 4.775067464 0.061299969 0.040231736 105.114629 -2.021663162 0.437824107 DICNDVLSLLEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DICNDVLSLLEK 12 0 P63104;E7EX29;B0AZS6;E7ESK7 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;; 184.03 3.45E-05 1851361000 588930 564833 543850 524696 575793 533377 611626 680022 725916 684702 FALSE TRUE 565913.9645 548724.5159 642135.7929 551775.6234 594313.9048 544162.2484 619111.2619 665979.3081 643513.059 638326.5237 0.886558749 0.859629822 1.005967587 0.864409676 0.931049992 0.85248259 0.969897441 1.043320751 1.008125207 1 19.28393507 2.021742452 5.734306405 1.018768619 0.902958057 0.601531172 0.043222672 0.107651946 11.27629533 0.016408375 0.011533733 105.1338219 -2.021742452 -0.115810562 TGQLEGAPAPGPAAS(ph)PQTLDHSGATATGGASELK ddPTM_BT-474_Pertuzumab_2h_R1 6 TGQLEGAPAPGPAASPQTLDHSGATATGGASELK 34 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 TGQLEGAPAPGPAAS(0.918)PQT(0.082)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.988)PQT(0.012)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(1)PQTLDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.999)PQT(0.001)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.996)PQT(0.003)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.819)PQT(0.137)LDHS(0.044)GATATGGASELK 346.16 5.17E-132 46208350000 6158140 5502740 5210460 4949830 5331280 5219160 6030150 6872520 7479070 6516500 TRUE FALSE 5917473.081 5345807.243 6152106.028 5205291.319 5502765.463 5324694.991 6103948.78 6730600.06 6630077.328 6075131.651 0.974048534 0.879949201 1.012670405 0.856819509 0.905785385 0.876474009 1.004743458 1.107893696 1.091347103 1 22.53448424 2.021954301 4.524787764 1.074709429 0.917472981 0.632308036 0.051260906 0.111310562 5.582000375 0.02036439 0.013708144 105.1851187 -2.021954301 -0.157236447 LVS(ph)SESK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVSSESK 7 0 A0A669KBF0;O76024;H0Y9G5 A0A669KBF0 WFS1 Wolframin 1 LVS(0.953)S(0.045)ES(0.002)K 68.371 0.065699 48735000 104660 144420 53918 143210 140590 89588 179260 321860 203660 127970 TRUE FALSE 100569.7715 140301.283 63662.182 150601.0853 145112.205 91399.53074 181453.8375 315213.4785 180541.3706 119302.4779 0.842981414 1.176013151 0.533619947 1.262346666 1.216338567 0.766115946 1.52095615 2.642136895 1.513307802 1 16.86426448 2.022003391 6.653806064 1.946013372 0.990586315 0.34429854 0.448152739 0.128487582 21.80452505 0.165914032 0.11873595 105.1970088 -2.022003391 -0.955427057 FLPRPPGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLPRPPGEK 9 1 Q9NY12-2;Q9NY12 Q9NY12-2 GAR1 H/ACA ribonucleoprotein complex subunit 1 0 62.823 0.073049 321800000 351380 265730 271460 237010 268940 237190 309090 334890 374960 320240 FALSE TRUE 337647.6811 258151.6406 320518.8606 249242.1145 277590.6993 241986.1443 312872.7359 327974.4045 332396.1128 298549.8596 1.130959102 0.864685185 1.073585702 0.834842511 0.929796784 0.810538463 1.047974822 1.098558227 1.113368846 1 18.18761236 2.022009916 24.77585783 1.079511609 0.937276902 0.279274332 0.097880035 234.845777 264357.1045 0.034825391 0.025718226 105.1985894 -2.022009916 -0.142234707 RPLEDGDQPDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPLEDGDQPDAK 12 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;;; 170 6.78E-05 5561390000 9614710 8895690 7700570 8716340 9127500 9045260 9541100 10673600 11531100 11083600 FALSE TRUE 9238956.504 8641993.631 9092234.297 9166191.352 9421094.327 9228161.355 9657866.836 10453186.43 10222137.87 10332897.9 0.894130242 0.836357207 0.879930721 0.887088157 0.911757226 0.893085507 0.93467166 1.011641316 0.989280836 1 23.30074158 2.0220606 1.813151776 1.004239258 0.88005348 0.879858496 0.019241213 0.113212875 0.697590507 0.012081349 0.006207579 105.2108672 -2.0220606 -0.124185778 LELTELEAIREDFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LELTELEAIREDFLR 15 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 0 111.74 0.00074663 16618000 18433 19440 15364 17393 21419 22043 18048 17625 20415 20400 FALSE TRUE 17712.61798 18885.59023 18140.61657 18290.65481 22107.96159 22488.72456 18268.87682 17261.03759 18097.57479 19018.28983 0.931346516 0.993022527 0.953851095 0.96174025 1.162457917 1.182478801 0.960595142 0.907601984 0.951587916 1 14.2150999 2.02213957 24.99920874 0.940622188 1.032034877 0.166309228 0.081910926 393.9432157 444824.5976 0.033939288 0.025064189 105.2299998 -2.02213957 0.09141269 IAQEIASLS(ph)KEDVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IAQEIASLSKEDVSK 15 1 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 IAQEIAS(0.022)LS(0.978)KEDVSK;IAQEIAS(0.001)LS(0.999)KEDVSK 184.7 2.75E-07 653810000 558490 377070 449830 392060 393420 394050 574310 744950 758410 741510 TRUE FALSE 536663.5934 366316.3328 531124.2874 412294.2636 406074.7116 402017.961 581338.5776 729566.5222 672318.4763 691286.8672 0.776325457 0.52990495 0.768312422 0.596415588 0.587418525 0.581550121 0.840951283 1.055374486 0.972560753 1 19.39892499 2.022202783 3.588123671 1.007419521 0.637278226 0.821133744 0.077646368 0.085326473 2.302248895 0.03298202 0.020911938 105.2453176 -2.022202783 -0.370141295 KGPGQPS(ph)SPQR ddPTM_BT-474_Pertuzumab_2h_R1 3 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.71)S(0.29)PQR;KGPGQPS(0.821)S(0.179)PQR;KGPGQPS(0.5)S(0.5)PQR 103.83 0.0016422 4818950000 2993210 3023240 2898350 3181590 3041270 2537510 3375600 3718860 3688560 3851820 TRUE FALSE 2876232.044 2937020.155 3422146.318 3345792.241 3139095.212 2588820.191 3416911.603 3642064.241 3269850.133 3590932.801 0.800970724 0.817898947 0.95299648 0.93173346 0.874172641 0.720932508 0.951538721 1.014239041 0.910585164 1 21.77592722 2.022222563 24.99327305 0.978114906 0.856057768 0.435070663 0.066742613 226.7800757 255053.9894 0.026191735 0.019342554 105.2501111 -2.022222563 -0.122057138 RVPGSS(ph)GHLHK ddPTM_BT-474_Pertuzumab_2h_R1 3 RVPGSSGHLHK 11 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 RVPGS(0.384)S(0.616)GHLHK;RVPGS(0.202)S(0.798)GHLHK;RVPGS(0.291)S(0.709)GHLHK 83.929 0.007684 1156960000 1557060 1472360 1094433 1057860 1155530 1181270 994000 283105 1220690 885371 TRUE FALSE 1496208.374 1430369.734 1292221.389 1112456.281 1192698.672 1205156.089 1006164.869 277258.7828 1082122.389 825404.0336 1.812698161 1.732932814 1.565562241 1.347771802 1.444987695 1.460080203 1.218996792 0.335906746 1.311021445 1 19.65474096 2.022225921 4.372945879 0.798818499 1.546635426 0.566431392 0.262609993 0.129179114 5.87241437 0.11036177 0.073732696 105.2509249 -2.022225921 0.747816927 SEDLLDYGPFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEDLLDYGPFR 11 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;;; 179.37 1.66E-05 370310000 626790 1103100 617330 1132840 639070 488113 903570 1194300 890020 627330 FALSE TRUE 602294.3538 1071640.668 728895.2634 1191306.008 659626.2669 497982.9793 914628.1599 1169637.288 788988.6609 584840.3803 1.029843995 1.832364358 1.246314871 2.036976324 1.127874013 0.851485287 1.563893655 1.999925667 1.349066664 1 19.1576834 2.022252977 24.96818857 1.616053046 1.376395264 0 0.414336628 672.36 754395.0866 0.154337056 0.113977586 105.2574822 -2.022252977 -0.239657782 TAFDEAIAELDTLS(ph)EESYK ddPTM_BT-474_Pertuzumab_2h_R1 4 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 1 TAFDEAIAELDTLS(1)EESYK;TAFDEAIAELDTLS(0.976)EES(0.024)YK;TAFDEAIAELDTLS(1)EESYK;TAFDEAIAELDTLS(1)EESYK 281.58 6.86E-40 196341000 263334 219912 256210 284121 270439 242051 321499 389515 410273 395639 TRUE FALSE 253042.6161 213640.3251 302512.8464 298784.5189 279137.916 246945.4371 325433.6009 381471.3791 363700.529 368842.0181 0.686046068 0.579219055 0.820169155 0.810060959 0.756795328 0.66951547 0.882311626 1.03424057 0.986060457 1 18.49264349 2.022324818 3.652372283 1.004104789 0.724690991 0.786802323 0.067285902 0.109845737 3.09742761 0.032274479 0.020570125 105.2748954 -2.022324818 -0.279413797 LLEEALLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLEEALLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 181.81 0.00053946 247320000 368848 405638 314173 390914 398046 314684 422698 495430 411743 476360 FALSE TRUE 354433.0124 394069.6014 370951.0498 411089.1184 410849.5111 321047.1261 427871.1046 485199.1974 365003.6608 444095.7129 0.798100504 0.887352861 0.835295273 0.925676845 0.925137305 0.722923273 0.963465965 1.092555463 0.82190314 1 18.76051112 2.022369745 24.86500552 0.993330317 0.8559712 0.316945854 0.084488632 222.7964209 247647.382 0.030766098 0.022720777 105.2857862 -2.022369745 -0.137359117 IYPSREEYEAHQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IYPSREEYEAHQDR 14 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 0 130.06 3.86E-05 255410000 232090 294910 169090 176310 206430 267160 186730 168720 175520 172170 FALSE TRUE 223019.6662 286499.4555 199648.3244 185409.3802 213070.0084 272562.1582 189015.2576 165235.873 155595.7054 160508.7725 1.389454686 1.784945776 1.243846808 1.155135494 1.327466437 1.698113779 1.177600792 1.02945073 0.969390663 1 17.29229262 2.022434913 9.374085602 1.027744836 1.424597371 0.5418839 0.180223176 0.226800257 88.20103236 0.072088791 0.052713152 105.3015863 -2.022434913 0.396852535 STGEPLGHVPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 STGEPLGHVPAR 12 0 Q93052;C9JUT4;C9JE51;C9J2R5;C9JIY7;C9JT42;C9J3U9;C9J1K7;C9J5C8;C9J4E3 Q93052 LPP Lipoma-preferred partner 0 97.911 0.0046552 432690000 262980 273530 250300 288670 275060 286810 270980 274500 306240 296810 FALSE TRUE 252702.4509 265729.1922 295534.7779 303568.2933 283907.5547 292609.4947 274296.3343 268831.4791 271476.9191 276706.7943 0.913249895 0.960327674 1.068043084 1.097075675 1.02602307 1.057471304 0.991288757 0.971539133 0.981099578 1 18.07799854 2.022483529 22.37958562 0.981141415 1.023616785 0.099613197 0.050155794 155.2304494 154510.6384 0.020569478 0.015189387 105.3133745 -2.022483529 0.04247537 KS(ph)VMLY(ph)AAEMIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSVMLYAAEMIPK 13 1 A0A087WYR0;P09132 A0A087WYR0 SRP19 Signal recognition particle 19 kDa protein 2 KS(1)VMLY(1)AAEMIPK;KS(1)VMLY(1)AAEMIPK 51.875 0.051734 3331896000 2643582 3635408 4258403 2469646 3045298 3404179 2667058 1942193 2135583 2637200 TRUE FALSE 2540267.893 3531729.723 5027991.15 2597104.726 3143252.776 3473013.832 2699698.254 1902086.036 1893160.571 2458580.095 1.0332256 1.436491628 2.045079255 1.056343347 1.278482968 1.412609595 1.098072119 0.773652255 0.770021922 1 21.22939393 2.022570823 2.855039713 0.829401996 1.392364896 0.438072468 0.268821659 0.245561431 3.889300743 0.13380927 0.079278633 105.3345449 -2.022570823 0.5629629 RAS(ph)LTLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RASLTLEEK 9 1 Q6P3W7;A0A0U1RQQ9 Q6P3W7 SCYL2 SCY1-like protein 2 1 RAS(0.999)LT(0.001)LEEK;RAS(1)LTLEEK 170 3.55E-05 547740000 552630 519060 471550 445220 502440 551180 582980 603160 705900 692780 TRUE FALSE 531032.6086 504256.917 556769.5746 468197.8576 518601.4389 562325.2372 590114.6836 590704.5352 625769.1914 645857.3935 0.822213408 0.780755817 0.862062709 0.724924515 0.802965862 0.870664705 0.913691923 0.914605207 0.968896846 1 19.30085612 2.022636722 0.892293085 0.984898256 0.795031332 0.799718623 0.036433672 0.254866351 0.375342438 0.030278682 0.015006572 105.3505293 -2.022636722 -0.189866925 VSNTQYHEVMNLEPENTLDQHSFSLPTCR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSNTQYHEVMNLEPENTLDQHSFSLPTCR 29 0 O43264;O43264-2 O43264 ZW10 Centromere/kinetochore protein zw10 homolog 0 243.55 8.75E-46 119290000 31662 31756 31386 38139 32297 39833 30585 25725 40759 34062 FALSE TRUE 30424.61404 30850.34997 37058.14838 40107.35836 33335.86234 40638.45055 30959.30838 25193.76976 36132.2092 31754.9504 0.958106174 0.97151309 1.167003819 1.263026957 1.04978474 1.279751662 0.974944315 0.793380857 1.137844926 1 14.9546939 2.022709725 24.86472385 0.9366288 1.11556605 0.19788061 0.128935386 272.3660128 298210.3438 0.049263622 0.036381281 105.3682397 -2.022709725 0.17893725 EVEGERR ddPTM_BT-474_Pertuzumab_2h_R1 5 EVEGERR 7 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;Q5VU61;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;;;; 120.62 0.0072434 1037000000 1766823 2056921 1241247 1471827 1543779 1988267 1518985 1546117 1623519 1569066 FALSE TRUE 1697773.604 1998259.627 1465567.944 1547788.168 1593436.054 2028471.121 1537574.793 1514189.144 1439223.929 1462791.762 1.160639298 1.366058846 1.001897866 1.058105609 1.089311613 1.386712158 1.051123497 1.035136499 0.983888457 1 20.48029298 2.022814102 24.99979141 1.01846666 1.172557756 0.31586249 0.115937654 306.0788199 335401.1054 0.044776994 0.03306783 105.3935668 -2.022814102 0.154091096 SRIPS(ph)PLQPEMQGTPDDEPSEPEPSPSTLIYR ddPTM_BT-474_Pertuzumab_2h_R1 5 SRIPSPLQPEMQGTPDDEPSEPEPSPSTLIYR 32 1 Q96GY3;K7EMY4 Q96GY3 LIN37 Protein lin-37 homolog 1 S(0.079)RIPS(0.877)PLQPEMQGT(0.043)PDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR 247.42 2.17E-47 1697308000 531886 525099 439551 520362.4 502727.9 572941 485346 504873 478293 557318 TRUE FALSE 511099.3071 510123.6906 518987.6435 547218.3658 518898.5995 584526.2596 491285.8095 494447.1961 423999.1838 519570.3555 0.983696051 0.981818314 0.998878473 1.053213218 0.998707093 1.125018495 0.945561663 0.95164628 0.816057305 1 18.98695959 2.022852696 24.98832505 0.925047375 1.021966364 0.394630838 0.058267373 230.6139716 252164.2503 0.021389024 0.015795898 105.4029329 -2.022852696 0.096918989 NACDHLSGFNVCNR ddPTM_BT-474_Pertuzumab_2h_R1 3 NACDHLSGFNVCNR 14 0 Q9Y3B4 Q9Y3B4 SF3B6 Splicing factor 3B subunit 6 0 ;; 157.35 5.32E-06 805870000 520584 802249 610331 867129 675469 795747 668432 634392 680853 829935 FALSE TRUE 500239.0017 779369.644 720631.3884 911881.6316 697196.0738 811837.5495 676612.4708 621291.5835 603565.4218 773722.7632 0.6465352 1.007298326 0.931381914 1.178563789 0.901092881 1.049261555 0.87448955 0.802989925 0.780079701 1 19.56145719 2.022951701 17.05394881 0.839034556 0.961855791 0.080316907 0.138347308 12.16522636 9037.318559 0.050267433 0.037098804 105.4269642 -2.022951701 0.122821236 EELKPDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EELKPDQK 8 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 116.3 0.0020949 1457640000 2913700 2470600 2193900 1961370 2338000 2516000 2766700 3185100 3720700 3209700 FALSE TRUE 2799829.383 2400140.907 2590386.533 2062596.541 2413203.893 2566875.244 2800559.702 3119326.572 3298341.734 2992304.16 0.935676734 0.802104592 0.865682897 0.689300429 0.806470119 0.857825644 0.9359208 1.042449699 1.102274889 1 21.5128254 2.023049858 1.867025161 1.057866135 0.815765418 0.719021327 0.062564479 0.177035219 1.157249366 0.037105496 0.01925263 105.4507949 -2.023049858 -0.242100717 KYMEENDQLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KYMEENDQLKK 11 2 P51572;P51572-2;C9JSP1;C9JQ75;C9J0M4;A0A2R8Y5M6;C9JMD7 P51572 BCAP31 B-cell receptor-associated protein 31 0 102.87 0.0015805 320060000 486920 691030 395880 584430 472730 580640 661630 939000 948660 699990 FALSE TRUE 467890.6281 671322.501 467424.3223 614592.5023 487935.7898 592380.9386 669727.2259 919609.3219 840972.0939 652579.0538 0.716986893 1.02872211 0.716272334 0.941790115 0.747703726 0.907753528 1.02627754 1.409192214 1.288689989 1 19.31579316 2.023070985 3.233392901 1.271390176 0.846426904 0.616279527 0.136244552 0.136629138 2.870863335 0.058365438 0.035933466 105.4559249 -2.023070985 -0.424963272 DFFLANASR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFFLANASR 9 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 186.67 9.64E-05 1677860000 1576660 1756850 1510390 1401560 1264880 684466 1848480 2541620 1480130 1837950 FALSE TRUE 1515042.384 1706746.358 1783351.071 1473894.68 1305566.014 698306.3715 1871102.251 2489134.659 1312111.848 1713464.009 0.884198545 0.996079491 1.040787003 0.860184207 0.761945396 0.407540729 1.091999739 1.452691533 0.765765631 1 20.70848446 2.023086661 24.98210128 1.16042521 0.833780898 0.197878485 0.229387116 282.766126 305980.2238 0.088872648 0.065633183 105.4597313 -2.023086661 -0.326644312 APKPPTDGSTSPT(ph)STPSEDQEALGK ddPTM_BT-474_Pertuzumab_2h_R1 1 APKPPTDGSTSPTSTPSEDQEALGK 25 1 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;S4R3G4;F6SRV7;Q8NHM5-5;F8WBN2 Q8NHM5-4;F8WBN2 KDM2B Lysine-specific demethylase 2B 1 APKPPTDGS(0.002)T(0.01)S(0.382)PT(0.551)S(0.05)T(0.005)PSEDQEALGK 157.16 3.14E-08 550430000 530420 436960 336970 387530 434700 403340 466810 560870 539460 480210 TRUE FALSE 509690.6 424498.3286 397867.9749 407530.4697 448682.5203 411495.8111 472522.9604 549287.8385 478222.7624 447684.949 1.138502872 0.948207729 0.888723143 0.91030639 1.002228289 0.919163827 1.055481006 1.226951765 1.068212732 1 18.77212429 2.023126549 6.339119987 1.128138908 0.96364764 0.312741095 0.085183133 0.148277125 21.11094204 0.032641706 0.023277155 105.4694178 -2.023126549 -0.164491268 APSHMSSSHS(ph)FPQLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSHMSSSHSFPQLAR 16 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3;D6RCL7 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 APSHMSS(0.001)S(0.032)HS(0.966)FPQLAR 199.09 2.51E-11 188300000 46976 69614 45497 68436 55584 64108 47922 35606 38819 54617 TRUE FALSE 45140.12599 67628.67688 53719.31998 71967.99016 57371.90984 65404.30768 48508.48377 34870.72366 34412.42986 50917.74194 0.886530397 1.328194737 1.055021647 1.413416766 1.126756758 1.284509194 0.952683326 0.684844267 0.675843597 1 15.63588082 2.023152502 4.152140057 0.762084289 1.189899228 0.546577594 0.162384658 0.134802198 5.299967455 0.064122223 0.042354466 105.4757209 -2.023152502 0.42781494 TFEGIDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TFEGIDPK 8 0 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 102 0.011746 993800000 1990360 1834310 1596990 1628510 1839810 1610700 1985980 2260600 2418900 2235900 FALSE TRUE 1912574.531 1781997.275 1885601.618 1712557.596 1898989.16 1643269.458 2010285.017 2213917.82 2144316.613 2084460.501 0.917539349 0.854896158 0.904599351 0.821583136 0.911021897 0.788342814 0.964415021 1.062105911 1.028715397 1 20.9912426 2.023204838 6.038147398 1.031976227 0.867643261 0.772544241 0.040379498 0.066910022 8.139048957 0.014592809 0.010348818 105.4884323 -2.023204838 -0.164332965 LAWVGDVFTATPAEPRPLT(ph)SPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAWVGDVFTATPAEPRPLTSPLR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 LAWVGDVFTATPAEPRPLT(0.751)S(0.249)PLR 192.3 1.55E-17 1748500000 228300 253850 168130 169430 197870 238130 168550 131960 161890 156320 TRUE FALSE 219377.7836 246610.4465 198514.831 178174.3026 204234.6683 242945.1518 170612.7653 129234.9799 143512.9259 145732.3072 1.505347633 1.692215346 1.362188213 1.222613613 1.401437143 1.667064472 1.170727127 0.886797049 0.984770836 1 17.15296122 2.023237001 5.095137799 0.961057934 1.464331917 0.757344264 0.132779362 0.09275098 6.585002393 0.057702688 0.039876088 105.4962449 -2.023237001 0.503273983 NPFVHELR ddPTM_BT-474_Pertuzumab_2h_R1 3 NPFVHELR 8 0 Q8NF37 Q8NF37 LPCAT1 Lysophosphatidylcholine acyltransferase 1 0 ;; 145.72 0.00056479 944020000 309415 514220 280292 628710 318937 335886 472640 571720 532330 387490 FALSE TRUE 297322.7197 499554.9491 330946.9995 661157.7984 329195.8983 342677.8451 478424.3097 559913.7822 471902.1301 361244.9572 0.82305016 1.382870374 0.91612905 1.830220147 0.911281643 0.948602432 1.324376438 1.549955982 1.30632171 1 18.46261792 2.023363858 24.57685717 1.369190704 1.156247492 0.039187793 0.308274149 451.2275708 474651.8229 0.111631556 0.082440552 105.5270648 -2.023363858 -0.212943212 SIVEEIEDLVAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SIVEEIEDLVAR 12 0 P04844-2;P04844;F2Z3K5;Q5JYR4;Q5JYR7 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 ;; 210.08 1.11E-07 308581000 150849 208140 122925 210984 144891 120917 178576 223409 182190 137194 FALSE TRUE 144953.6543 202204.051 145140.282 221872.9095 149551.5506 123362.0246 180761.4665 218795.5261 161508.555 127901.7282 1.13332053 1.580932907 1.134779678 1.73471393 1.169269194 0.964506315 1.413284004 1.710653399 1.262755064 1 16.96467623 2.02352808 24.99449244 1.443065703 1.297918941 0 0.274359414 723.5520825 768644.8914 0.101159968 0.074707933 105.5669756 -2.02352808 -0.145146762 AYFETEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYFETEKK 8 1 P15170-2;P15170-3;P15170;H3BR35;H3BSV8 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 93.649 0.017508 1257540000 1585390 1499700 1298290 1163350 1398790 1274100 1504980 1637630 1793210 1745380 FALSE TRUE 1523431.206 1456930.024 1532919.883 1223390.633 1443783.351 1299863.175 1523398.395 1603812.368 1589652.319 1627163.858 0.936249412 0.89538003 0.942080833 0.751854601 0.887300528 0.798852045 0.936229248 0.985648962 0.976946674 1 20.63392811 2.023553346 7.180303662 0.980006894 0.86839713 0.489923982 0.054761906 0.147591719 30.47164501 0.021202275 0.015300881 105.5731174 -2.023553346 -0.111609764 GLS(ph)GEEEDDEPDCCNDER ddPTM_BT-474_Pertuzumab_2h_R1 2 GLSGEEEDDEPDCCNDER 18 0 Q6P158-2;Q6P158;A0A087WW12;A0A087WZ11;Q6P158-3 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 1 GLS(1)GEEEDDEPDCCNDER;GLS(1)GEEEDDEPDCCNDER 329.65 7.70E-75 494910000 479920 538040 382420 489620 463850 542580 453280 452880 493460 508400 TRUE FALSE 461164.1958 522695.626 451531.8009 514889.3469 478770.1565 553551.3394 458827.3762 443527.8697 437444.4896 473965.6152 0.972990827 1.102813388 0.952667844 1.08634325 1.010136899 1.167914553 0.96806047 0.935780689 0.922945622 1 18.85442287 2.023560247 24.9997352 0.947310059 1.048605715 0.346807236 0.062049585 222.5122448 236106.3117 0.021670814 0.016004145 105.574795 -2.023560247 0.101295657 NEGSES(ph)APEGQAQQR ddPTM_BT-474_Pertuzumab_2h_R1 3 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGS(0.007)ES(0.993)APEGQAQQR;NEGSES(1)APEGQAQQR;NEGSES(1)APEGQAQQR 311.43 3.78E-56 1288190000 373137 370273 353310 473515 399398 363678 473474 600980 566783 526716 TRUE FALSE 358554.3935 359713.1766 417160.9763 497953.1659 412244.9994 371031.8183 479268.5164 588569.553 502444.17 491041.0562 0.73019229 0.73255214 0.849543986 1.01407644 0.839532651 0.755602436 0.976025345 1.198615769 1.023222323 1 18.90548413 2.023663438 5.431699693 1.094948068 0.828755654 0.608890713 0.09183826 0.114041536 9.843758949 0.038666654 0.027032031 105.5998832 -2.023663438 -0.266192414 S(ph)PGLCSDSLEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPGLCSDSLEK 11 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 S(1)PGLCSDSLEK;S(1)PGLCSDSLEK;S(1)PGLCSDSLEK;S(1)PGLCSDSLEK 262.35 1.03E-20 3971500000 2755690 2414750 2484710 2709690 2576600 2544750 3003470 3412730 3587620 3736910 TRUE FALSE 2647994.588 2345883.694 2933752.369 2849537.426 2659478.679 2596206.589 3040227.364 3342255.933 3180368.418 3483805.757 0.760086748 0.673368109 0.84211135 0.81793809 0.763383169 0.745221396 0.872674189 0.959369197 0.912900615 1 21.73223276 2.023663846 3.055475041 0.950394517 0.768336759 0.769636584 0.046890923 0.127916588 2.359766115 0.022980584 0.013918279 105.5999824 -2.023663846 -0.182057758 VKS(ph)ST(ph)PPRQSPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 VKSSTPPRQSPSR 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 VKS(0.987)S(0.045)T(0.964)PPRQS(0.4)PS(0.604)R 94.281 0.0083665 600490000 465710 392140 374920 364620 383600 394120 468480 446420 604670 483490 TRUE FALSE 447509.5383 380956.5511 442676.3841 383438.0819 395938.8424 402089.3764 474213.3984 437201.271 536030.3966 450742.7917 0.992826833 0.845175027 0.982104189 0.850680452 0.878414142 0.892059471 1.052070953 0.969957322 1.189215682 1 18.78194489 2.023812829 1.647784901 1.0641086 0.903282877 0.471114636 0.072874988 0.32242679 1.639910579 0.043277704 0.021664852 105.6362144 -2.023812829 -0.160825723 EPPKPEQVESR ddPTM_BT-474_Pertuzumab_2h_R1 1 EPPKPEQVESR 11 1 O60664-4;O60664;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 90.697 0.0103 286400000 520080 419550 475580 456570 440810 465600 554890 634660 705420 671480 FALSE TRUE 499754.6986 407584.8448 561527.8852 480133.6324 454989.054 475014.751 561680.9098 621554.0492 625343.679 626000.0615 0.798330111 0.651093937 0.897009313 0.766986558 0.726819504 0.758809432 0.897253761 0.992897745 0.998951466 1 19.25580327 2.02384787 2.517003094 0.996409572 0.764682572 0.763349026 0.057999709 0.135558437 1.636064686 0.029358668 0.016747953 105.6447379 -2.02384787 -0.231727 RHS(ph)HSHS(ph)PMSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 RHS(0.996)HS(0.018)HS(0.984)PMS(0.001)T(0.001)R 99.813 0.0036554 1932800000 193370 275890 239760 268110 245440 248260 184010 66028 191290 96839 TRUE FALSE 185812.8866 268021.8873 283089.9654 281947.1892 253334.8005 253279.9873 186261.9694 64664.49873 169575.5612 90280.00827 2.0581842 2.968784479 3.135688297 3.123030166 2.806100767 2.805493621 2.063158533 0.716265981 1.878329039 1 16.46211893 2.023923512 3.406421914 1.189869255 2.848294953 0.769486922 0.396074679 0.103640716 2.463345254 0.175789146 0.110031875 105.6631398 -2.023923512 1.658425698 EILVGDVGVTITDPFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EILVGDVGVTITDPFK 16 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 201.95 7.36E-11 125997000 166850 160977 146790 182891 159925 176502 187703 222838 234313 236644 FALSE TRUE 160329.3175 156386.0936 173318.2183 192330.0264 165069.1329 180070.9914 190000.1655 218236.3174 207714.7706 220615.8911 0.726735127 0.708861419 0.785610762 0.871786821 0.748219596 0.816219496 0.861226109 0.989213952 0.941522252 1 17.75117719 2.0241227 1.517628518 0.984933789 0.770098995 0.803161079 0.044667676 0.178463732 0.768927429 0.031146372 0.015271037 105.7116131 -2.0241227 -0.214834794 QLDDLKVELSQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 QLDDLKVELSQLR 13 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ;; 225.32 1.15E-11 4405975000 7245660 6816530 5564272 5016924 6422350 5837533 6614399 7192070 7489370 7071760 FALSE TRUE 6962491.597 6622129.238 6569859.727 5275848.049 6628930.72 5955571.917 6695347.994 7043551.241 6639208.116 6592783.396 1.056077711 1.004451207 0.996522915 0.800245925 1.005482862 0.903347123 1.015557101 1.068372919 1.007041748 1 22.65245625 2.024122953 19.07547244 1.035042679 0.959332421 0.160730671 0.068171963 24.84156801 19642.30514 0.025951509 0.019160592 105.7116747 -2.024122953 -0.075710258 LDGQTPHDER ddPTM_BT-474_Pertuzumab_2h_R1 4 LDGQTPHDER 10 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ;;; 175.74 2.71E-06 3451570000 2099480 2264030 1812570 2355490 2044230 2158370 1949370 1937600 1932400 2077850 FALSE TRUE 2017430.001 2199462.081 2140141.719 2477057.121 2109984.514 2202013.72 1973226.973 1897587.883 1713042.053 1937115.369 1.041460944 1.135431641 1.1048086 1.278734948 1.089240501 1.136748877 1.018641948 0.979594666 0.884326293 1 20.88547845 2.024323063 1.847530361 0.945571503 1.137459191 0.612685453 0.063708485 0.225319121 1.442558682 0.037292658 0.019309975 105.7603947 -2.024323063 0.191887688 QDLPNAMNAAEITDKLGLHSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDLPNAMNAAEITDKLGLHSLR 22 1 P61204;P61204-2;H0YGG7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 278.26 9.30E-46 3374260000 2994660 3249950 2071900 2012850 2695100 3524670 2512160 2559800 2878010 2389070 FALSE TRUE 2877625.376 3157264.608 2446338.419 2116733.43 2781790.339 3595941.242 2542904.566 2506939.235 2551310.37 2227256.161 1.292004677 1.417557919 1.098364195 0.95037718 1.248976381 1.61451624 1.141720746 1.125572927 1.145494809 1 21.08683606 2.024369439 24.99751927 1.111642699 1.264037561 0.190154576 0.169424736 461.1185 473000.9686 0.068501104 0.05058938 105.771689 -2.024369439 0.152394861 TAENFR ddPTM_BT-474_Pertuzumab_2h_R1 7 TAENFR 6 0 C9JQD4;O43447;A6NM32;R4GN99;H0Y548;P30405-2;P30405;P49792;P62937;F8WE65;C9J5S7;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37;Q08752 C9JQD4;P30405;P49792;P62937;Q08752 PPIH;PPIF;RANBP2;PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D;PPID "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase H;Peptidyl-prolyl cis-trans isomerase F, mitochondrial;E3 SUMO-protein ligase RanBP2;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D;Peptidyl-prolyl cis-trans isomerase D" 0 ;;;;;; 168.82 0.014504 61232430000 23126700 23616020 18711790 23800570 21549100 20664200 23088610 24801290 25452230 24801070 FALSE TRUE 22222883 22942514.23 22093426.69 25028920.27 22242246.37 21082044.28 23371175.32 24289134.69 22562999.55 23121271.44 0.961144505 0.992268712 0.955545492 1.082506225 0.961981975 0.911802984 1.010808397 1.050510339 0.97585462 1 24.4627174 2.024420968 24.97959007 1.018465333 0.979610979 0.096728555 0.044452264 444.2397891 454399.6388 0.016996516 0.012552288 105.7842394 -2.024420968 -0.038854354 TEDGKVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 TEDGKVEK 8 1 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ;;; 96.331 0.0082232 2832270000 3216010 2811190 2189070 2233410 2580730 2761350 3161000 3698200 4200240 3918390 FALSE TRUE 3090324.774 2731017.614 2584683.645 2348676.558 2663741.524 2817186.389 3199685.264 3621830.878 3723446.364 3652993.955 0.845970404 0.747610767 0.707552127 0.642945646 0.729194068 0.771199302 0.875907626 0.991469168 1.01928621 1 21.80064794 2.024446208 1.749152164 1.012216181 0.72921378 0.862939641 0.047332359 0.128773801 0.738586662 0.030950703 0.01576764 105.7903876 -2.024446208 -0.283002401 AASIFGGAKPVDTAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AASIFGGAKPVDTAAR 16 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 137.81 9.10E-06 1828340000 1773830 1738900 1471300 1718200 1595630 1549160 1772250 1928690 1907450 1962120 FALSE TRUE 1704506.763 1689308.275 1737196.639 1806876.508 1646954.888 1580485.077 1793939.326 1888861.878 1690924.273 1829223.865 0.931819662 0.923510953 0.949690561 0.987783148 0.900357206 0.864019493 0.98071065 1.032602905 0.924394387 1 20.80280022 2.024483198 24.86185062 0.993630446 0.928233941 0.341749666 0.039109234 222.2800838 225716.7615 0.015087739 0.011142527 105.7993983 -2.024483198 -0.065396505 LSPPYSS(ph)PQEFAQDVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPPYSSPQEFAQDVGR 17 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LSPPYS(0.009)S(0.991)PQEFAQDVGR 178.1 8.01E-14 0 134640 149900 138180 147150 146810 168300 136870 135400 156630 142920 TRUE FALSE 129378.1199 145624.9988 163152.1998 154744.4291 151532.277 171703.1413 138545.056 132603.9427 138850.019 133239.9011 0.971016331 1.092953369 1.224499556 1.161397058 1.137289023 1.288676589 1.039816563 0.995226967 1.04210539 1 17.02366666 2.024575267 24.99448539 1.013315728 1.148838702 0.387660955 0.078516004 227.2470859 231122.6365 0.0301473 0.022264322 105.8218298 -2.024575267 0.135522973 KKEPAITSQNS(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 10 KKEPAITSQNSPEAR 15 2 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITS(0.003)QNS(0.997)PEAR;KKEPAIT(0.002)S(0.012)QNS(0.987)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR 285.96 1.95E-34 77634844000 19444992 18264609 15544331 15744604 16609146 17751125 17783029 19592068 21179297 19036292 TRUE FALSE 18685060.22 17743720.23 18353537.39 16557184.9 17143394.27 18110064.91 18000663.03 19187484.95 18775112 17746946.99 1.052860542 0.99981818 1.034179986 0.932959619 0.96599118 1.020460867 1.01429632 1.08117103 1.057934754 1 24.08106752 2.02459866 3.005327805 1.054274316 0.997702925 0.209090216 0.037343676 0.325772932 5.79077658 0.018082471 0.01090821 105.82753 -2.02459866 -0.056571391 GSKPS(ph)PLSVK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSKPSPLSVK 10 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 GSKPS(0.999)PLSVK;GSKPS(1)PLSVK;GSKPS(0.999)PLSVK 103.83 0.0016726 3882100000 7237480 6619870 5536610 5752300 6031750 6664450 7161990 8514190 8941700 9058180 TRUE FALSE 6954631.28 6431077.789 6537198.588 6049176.892 6225766.717 6799209.745 7249640.576 8338369.001 7926675.703 8444661.4 0.823553598 0.761555435 0.774122049 0.716331491 0.737242907 0.805148889 0.858488012 0.987413066 0.938661164 1 23.00960815 2.024655353 1.893667694 0.977796553 0.761775375 0.894784992 0.031654999 0.099908559 0.67225931 0.018736911 0.009778495 105.8413458 -2.024655353 -0.216021179 AAEWQLDQPSWSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAEWQLDQPSWSGR 14 0 Q9NVZ3;Q9NVZ3-2;D6RAN6;F6SKB8;Q9NVZ3-3;H0Y970 Q9NVZ3 NECAP2 Adaptin ear-binding coat-associated protein 2 0 133.05 4.44E-05 0 124300 174600 127020 146490 132910 134930 147880 168720 145150 154440 FALSE TRUE 119442.2186 169620.579 149975.3395 154050.3665 137185.1709 137658.377 149689.7997 165235.873 128673.1805 143979.6412 0.829577137 1.178087245 1.041642681 1.069945481 0.952809506 0.956096125 1.039659485 1.147633593 0.893690104 1 17.1355053 2.024676658 24.85061019 1.046045411 1.013446463 0 0.103691881 1122.264331 1130168.941 0.038139012 0.028166193 105.846538 -2.024676658 -0.032598948 ASEDS(ph)EEEPSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASEDSEEEPSGK 12 0 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 ASEDS(1)EEEPSGK 237.41 4.40E-16 214030000 125730 122080 101030 102800 108970 100170 127430 149920 155160 139370 TRUE FALSE 120816.3326 118598.3979 119288.3684 108105.5203 112475.119 102195.506 128989.5265 146824.0996 137546.8873 129930.3458 0.929854622 0.91278444 0.918094751 0.832026727 0.865657044 0.786540707 0.992759049 1.130021618 1.05862019 1 16.98737889 2.024921029 6.353750016 1.073942176 0.87604725 0.746609781 0.049971931 0.075780263 10.53911939 0.019763435 0.014127977 105.906113 -2.024921029 -0.197894925 LYEEGSNKR ddPTM_BT-474_Pertuzumab_2h_R1 4 LYEEGSNKR 9 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;; 162.49 0.00010219 10073400000 6431700 5630600 4816620 5140500 5393790 5338850 5796720 6228360 6768650 6521800 FALSE TRUE 6180342.053 5470020.801 5687090.379 5405801.821 5567286.154 5446805.205 5867661.993 6099742.189 6000301.228 6080072.677 1.016491477 0.89966372 0.935365526 0.889101514 0.915661119 0.895845411 0.96506445 1.003235079 0.986879853 1 22.53565714 2.025126639 4.762894189 0.994662329 0.922675011 0.471208367 0.034034246 0.157362237 9.033141673 0.013455166 0.009201389 105.9562646 -2.025126639 -0.071987318 DPLSEITEQEKDFLWSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPLSEITEQEKDFLWSHR 18 1 A0A2R8Y2F6;P42336 A0A2R8Y2F6 PIK3CA "Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform" 0 160.55 2.42E-11 17719000 22584 22948 22908 24183 23060 24987 22670 21542 24929 25521 FALSE TRUE 21701.39231 22293.54551 27047.98519 25431.08753 23801.74584 25492.25426 22947.44224 21097.15017 22099.16443 23792.43994 0.912112939 0.937001231 1.13683108 1.068872616 1.000391129 1.071443464 0.964484614 0.886716546 0.928831364 1 14.53821561 2.02513731 7.51923191 0.925748031 1.023505346 0.237001493 0.066839525 0.226537447 50.78912424 0.026715591 0.019372569 105.9588679 -2.02513731 0.097757315 GLAGPPAS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 6 GLAGPPASPGK 11 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK 173.76 1.24E-05 6753900000 6355330 6180590 5013310 6009400 5024450 4980280 6151790 7389790 6121710 5674070 TRUE FALSE 6106956.677 6004325.625 5919326.637 6319545.854 5186065.997 5080984.674 6227077.446 7237188.254 5426799.145 5289760.185 1.154486492 1.135084657 1.119016067 1.194675303 0.980397186 0.960532141 1.177194661 1.36815054 1.02590646 1 22.33477089 2.025250412 24.85335297 1.197361689 1.091644792 0 0.120118481 410.7092895 404249.0173 0.045784129 0.033812553 105.9864661 -2.025250412 -0.105716897 KCLEELQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KCLEELQK 8 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 160.59 0.00056519 1487650000 2034850 1881630 1808870 1551540 1756880 1179890 1944280 2064410 2245700 2226100 FALSE TRUE 1955325.812 1827967.755 2135773.047 1631615.165 1813391.641 1203748.184 1968074.68 2021779.212 1990777.551 2075324.264 0.942178457 0.88081067 1.029127392 0.786197701 0.873787134 0.580028965 0.948321529 0.974199188 0.959260962 1 20.98490534 2.025263376 24.99956817 0.971530345 0.848944374 0.231308344 0.109549971 349.1751088 345527.3774 0.042321846 0.031255653 105.9896299 -2.025263376 -0.122585971 ES(ph)EELLK ddPTM_BT-474_Pertuzumab_2h_R1 4 ESEELLK 7 0 O43303-2;O43303 O43303-2 CCP110 Centriolar coiled-coil protein of 110 kDa 1 ES(1)EELLK;ES(1)EELLK;ES(1)EELLK;ES(1)EELLK 146.81 0.0023013 2000320000 2329590 2139940 1542320 1720930 2451950 1938060 2425960 3143040 3076130 2552820 TRUE FALSE 2238547.047 2078911.006 1821051.533 1809747.404 2530819.199 1977248.901 2455649.624 3078135.126 2726940.619 2379915.228 0.940599489 0.873523133 0.765174957 0.760425154 1.063407288 0.830806441 1.031822309 1.293380155 1.145814182 1 21.18247876 2.02528429 4.557804065 1.177074003 0.872850141 0.571080426 0.106482694 0.123968107 6.268524414 0.043782687 0.029663958 105.9947342 -2.02528429 -0.304223861 QEEEAAQQGPVVVS(ph)PASDYKDK ddPTM_BT-474_Pertuzumab_2h_R1 2 QEEEAAQQGPVVVSPASDYKDK 22 1 I3L0X5;O75391;I3L4C3 I3L0X5 SPAG7 Sperm-associated antigen 7 1 QEEEAAQQGPVVVS(0.999)PAS(0.001)DYKDK;QEEEAAQQGPVVVS(0.997)PAS(0.003)DYKDK 162.91 9.50E-12 714970000 676700 544310 570550 520090 584360 600430 652370 760530 811170 772340 TRUE FALSE 650253.8159 528786.8117 673661.0768 546931.9072 603156.4701 612571.106 660353.8992 744824.7897 719089.3823 720028.7239 0.903094272 0.734396829 0.935603059 0.759597345 0.837683901 0.850759262 0.917121605 1.034437606 0.998695411 1 19.45769494 2.025313772 2.391909221 1.01422167 0.831662478 0.654787637 0.056584223 0.161587859 1.753133792 0.027184251 0.015282465 106.0019297 -2.025313772 -0.182559193 VPS(ph)WGLEDNVVCSQPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPSWGLEDNVVCSQPAR 17 0 B8ZZD4;Q86VP1-2;Q86VP1;Q86VP1-4;Q86VP1-3;H7C3L5 B8ZZD4 TAX1BP1 Tax1-binding protein 1 1 VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR 138.91 2.19E-06 442990000 30288 38091 25033 29179 34862 44904 28979 28533 21564.3 43995 TRUE FALSE 29104.31147 37004.68197 29557.01996 30684.93169 35983.36789 45811.98965 29333.65367 27943.78358 19116.41107 41015.17946 0.70959854 0.90221919 0.720636124 0.748135985 0.877318309 1.116952071 0.715190182 0.681303458 0.466081371 1 15.32387032 2.025394399 24.9945431 0.684849627 0.846043023 0.123323191 0.163904629 375.6261031 369709.8373 0.060124005 0.044403111 106.0216111 -2.025394399 0.161193396 VLS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLSPPK 6 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7ESQ0;K7EL01;Q5XUX1;Q5XUX1-2 Q9H6Z4 RANBP3;FBXW9 Ran-binding protein 3;F-box/WD repeat-containing protein 9 1 VLS(1)PPK;VLS(1)PPK;VLS(1)PPK 84.743 0.058221 618410000 1280360 1134560 1207110 1171480 1195260 1173120 1381590 1611210 1664390 1654310 TRUE FALSE 1230322.116 1102203.46 1425261.629 1231940.223 1233706.623 1196841.29 1398498.312 1577937.95 1475455.425 1542262.11 0.797738664 0.714666756 0.924137097 0.798787842 0.799933173 0.776029757 0.90678381 1.023132151 0.956682664 1 20.55661654 2.025493469 3.711641332 0.991909559 0.803717327 0.741860653 0.050885554 0.112029804 3.28182386 0.022247933 0.014304533 106.045799 -2.025493469 -0.188192232 S(ph)PGRPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGRPPK 7 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(1)PGRPPK;S(1)PGRPPK 58.433 0.066366 879050000 825110 1183480 816700 1446730 921000 972580 1245410 1699040 1339200 1099070 TRUE FALSE 792863.789 1149728.309 964295.8574 1521395.909 950624.8014 992246.234 1260651.7 1663954.23 1187179.63 1024629.01 0.77380572 1.122092287 0.941117076 1.484826112 0.927774631 0.968395609 1.230349412 1.623957758 1.158643391 1 19.96667021 2.025567391 7.488926057 1.354203424 1.054498371 0.136271355 0.232683223 0.239931677 52.61070141 0.08658321 0.062793528 106.0638508 -2.025567391 -0.299705054 IKDDLEDLIVNWDESK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKDDLEDLIVNWDESK 16 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 0 163.51 7.03E-09 132520000 253740 226370 246180 199470 255090 229950 274080 334470 334710 303280 FALSE TRUE 243823.5603 219914.1492 290670.2022 209764.6706 263295.2015 234599.7466 277434.273 327563.0776 296715.124 282738.5755 0.86236397 0.777800301 1.028052864 0.741903259 0.931231973 0.829740852 0.981239552 1.158536917 1.049432761 1 18.10910921 2.025597224 4.485728591 1.084549474 0.864419269 0.558091065 0.083146514 0.126714742 6.11936311 0.032103647 0.021682097 106.0711371 -2.025597224 -0.220130204 RSLSGS(ph)SPCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSLSGSSPCPK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.002)LS(0.07)GS(0.464)S(0.464)PCPK 65.295 0.030786 0 82262 78732 62670 65183 62617 76332 79795 97179 102760 96417 TRUE FALSE 79047.11009 76486.64045 73995.86309 68547.10244 64631.13267 77875.48534 80771.55508 95172.21969 91095.11561 89886.59071 0.87940937 0.850923812 0.823213591 0.762595421 0.719029748 0.866374892 0.898594044 1.058803309 1.013444996 1 16.45581829 2.025691384 2.279834195 1.028982714 0.809560787 0.79217851 0.047365173 0.136394716 1.339564599 0.027238216 0.015086933 106.0941368 -2.025691384 -0.219421928 LYSILQGDS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 4 LYSILQGDSPTK 12 0 O15042-2;O15042;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 LYSILQGDS(0.988)PT(0.012)K;LYSILQGDS(0.992)PT(0.008)K;LYSILQGDS(0.996)PT(0.004)K;LYSILQGDS(0.999)PT(0.001)K 186.62 1.21E-05 1069434000 1498825 1345846 1493666 1448173 1608502 1432706 1730554 2027691 2170241 1979340 TRUE FALSE 1440249.262 1307463.79 1763604.673 1522913.382 1660240.928 1461676.297 1751733.038 1985818.472 1923884.34 1845277.539 0.780505497 0.708545876 0.955739522 0.825303159 0.899724238 0.792117319 0.949305999 1.076162491 1.042598904 1 20.81540639 2.02571846 3.793725684 1.043350077 0.831159344 0.683039609 0.065405953 0.128174182 3.965856634 0.028952818 0.018735718 106.1007515 -2.02571846 -0.212190733 EIEDPEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIEDPEDR 8 0 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ; 97.431 0.019163 3809400000 5539900 8412400 5225500 9497400 6302200 5208200 8145900 10258600 8326300 6693200 FALSE TRUE 5323394.583 8172486.589 6169864.091 9987561.952 6504915.987 5313513.372 8245591.961 10046756.33 7381133.331 6239863.602 0.853126754 1.309721992 0.988781884 1.600605813 1.042477272 0.851543192 1.321437853 1.610092298 1.182899788 1 22.57308306 2.025762389 24.99389444 1.365530455 1.127222388 0.056378999 0.25722556 396.8883104 385047.3362 0.094571161 0.069843496 106.1114842 -2.025762389 -0.238308067 LELSSSAS(ph)PQEER ddPTM_BT-474_Pertuzumab_2h_R1 1 LELSSSASPQEER 13 0 A0A075B6T1;Q9C0C7-6;Q9C0C7-4;Q9C0C7-2;Q9C0C7-3;Q9C0C7;Q9C0C7-5 A0A075B6T1 AMBRA1 Activating molecule in BECN1-regulated autophagy protein 1 1 LELSS(0.001)S(0.005)AS(0.994)PQEER 163.2 4.11E-05 134360000 102040 100640 73359 97664 91790 91106 89929 92652 84122 105490 TRUE FALSE 98052.16399 97769.84574 86616.60316 102704.4507 94742.50871 92948.22574 91029.578 90738.70382 74572.82323 98345.06834 0.997021667 0.994150977 0.880741705 1.044327412 0.963368172 0.945123404 0.92561406 0.922656371 0.758277202 1 16.58556509 2.02576915 1.53314392 0.88275668 0.973476457 0.21746951 0.067477035 0.567943467 2.498476243 0.041961619 0.020652817 106.1131362 -2.02576915 0.090719777 GEWIKPGAIVIDCGINYVPDDKKPNGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEWIKPGAIVIDCGINYVPDDKKPNGR 27 3 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 250.95 9.34E-47 1080300000 531830 475330 401380 402210 446740 565030 507390 589940 713910 661420 FALSE TRUE 511045.4956 461774.0538 473918.2946 422968.1063 461109.7978 576455.2937 513599.5906 577757.5328 632869.9298 616621.4343 0.828783216 0.74887772 0.768572528 0.68594454 0.747800469 0.93486094 0.832925296 0.936972834 1.026350844 1 19.23402551 2.02578433 0.875664419 1.011794957 0.753833437 0.756031521 0.054848605 0.293213178 0.416455173 0.046711392 0.023365685 106.1168451 -2.02578433 -0.25796152 DTDPDSKPFSLQETYEAK ddPTM_BT-474_Pertuzumab_2h_R1 6 DTDPDSKPFSLQETYEAK 18 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141 D6RGI3;B1AMS2 SEPT11;SEPT6 Septin-11;Septin-6 0 ;;;;; 215.57 8.61E-19 6964520000 2667730 2167330 2256920 2270830 2467210 2392340 2740370 3211840 3507310 3150150 FALSE TRUE 2563472.162 2105519.87 2664795.649 2388027.808 2546570.05 2440714.754 2773907.468 3145514.382 3109174.873 2936787.535 0.872883085 0.716946611 0.907384555 0.813142858 0.867127778 0.83108319 0.944538015 1.071073186 1.058699288 1 21.48580747 2.025817043 2.764636609 1.04890768 0.832481966 0.773947067 0.050635099 0.114094842 1.686357725 0.023632988 0.013912103 106.1248385 -2.025817043 -0.216425714 LTVAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 LTVASPK 7 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 LTVAS(1)PK;LTVAS(1)PK;LTVAS(1)PK;LTVAS(1)PK;LTVAS(1)PK;LTVAS(1)PK 125.57 0.0042341 4548730000 6927250 5930480 5307540 5162260 5277790 5016140 6493620 7283790 7965360 7847200 TRUE FALSE 6656525.412 5761348.517 6266730.544 5428684.857 5447554.909 5117569.788 6573090.864 7133377.191 7061165.726 7315702.154 0.909895629 0.787531859 0.85661368 0.742059305 0.744638695 0.699532277 0.89849077 0.975077585 0.965206836 1 22.80256491 2.025877555 5.252172871 0.968927357 0.788613315 0.69302103 0.057062411 0.105902095 8.084316337 0.02374825 0.016561205 106.1396265 -2.025877555 -0.180314042 ES(ph)PSPAPKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESPSPAPKPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 ES(0.996)PS(0.004)PAPKPR;ES(0.997)PS(0.003)PAPKPR 133.05 0.00012562 1237010000 999600 1061680 859110 918450 923770 954010 1032350 1168470 1239800 1093500 TRUE FALSE 960534.5269 1031401.926 1014370.288 965851.3146 953483.901 973300.7358 1044984.208 1144340.686 1099063.102 1019436.271 0.942221259 1.011737521 0.995030603 0.947436679 0.935305058 0.954744071 1.025060848 1.122523024 1.078108689 1 19.95934016 2.02590491 4.455156463 1.079670971 0.96655683 0.61415317 0.036338663 0.116559564 5.516594056 0.015114354 0.010196208 106.1463122 -2.02590491 -0.113114141 ISTCAPSTLHITQNT(ph)EQELHSPTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISTCAPSTLHITQNTEQELHSPTVK 25 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 ISTCAPSTLHIT(0.028)QNT(0.89)EQELHS(0.082)PTVK 128.43 0.00041008 258480000 24395 31784 30361 28592 35493 36359 24115 14459 25943 20266 TRUE FALSE 23441.61643 30877.55144 35847.90808 30067.63655 36634.66458 37094.20389 24410.12658 14160.4166 22998.0594 18893.36577 1.240732685 1.634306551 1.897380727 1.591438863 1.939022672 1.963345459 1.291994602 0.749491476 1.217255818 1 14.20559211 2.025956383 5.375112608 0.972029078 1.717960082 0.679400849 0.224557398 0.096419868 7.889453099 0.090334695 0.06324522 106.1588934 -2.025956383 0.745931004 RYEEIVK ddPTM_BT-474_Pertuzumab_2h_R1 6 RYEEIVK 7 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;; 164.72 0.0019034 5330670000 3423440 3478660 3134540 3119070 3424880 3446880 3621050 4034070 4558300 3999630 FALSE TRUE 3289648.18 3379452.023 3701021.105 3280045.576 3535044.376 3516578.275 3665365.493 3950765.045 4040860.894 3728731.498 0.882243246 0.906327534 0.992568413 0.879667946 0.948055492 0.943103111 0.983006016 1.059546671 1.083709271 1 21.83025348 2.025966046 2.015495601 1.055004475 0.92427574 0.690403882 0.036740074 0.175876459 1.342752481 0.020274757 0.010802044 106.1612554 -2.025966046 -0.130728735 AHSSPAS(ph)LQLGAVSPGTLTPTGVVSGPAATPTAQHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 AHS(0.072)S(0.35)PAS(0.5)LQLGAVS(0.079)PGTLTPTGVVSGPAATPTAQHLR;AHS(0.008)S(0.019)PAS(0.618)LQLGAVS(0.355)PGT(0.001)LTPTGVVSGPAATPTAQHLR 168.13 1.25E-17 8961500000 374243 442402 316220 429348 347214 419358 310162 188218 298235 328818 TRUE FALSE 359617.1698 429785.1281 373367.9883 451506.7017 358382.4536 427837.7061 313957.8553 184331.2325 264380.6131 306546.864 1.173122977 1.402020959 1.217980127 1.472879859 1.169095156 1.395668188 1.024175721 0.601315016 0.862447619 1 18.22574812 2.026184272 4.623002646 0.781980642 1.304224164 0.727877981 0.133243941 0.082942091 4.349243087 0.050559149 0.034407043 106.2146133 -2.026184272 0.522243522 LGFEEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGFEEFK 7 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;K7EIV0;A0A075B7C0;U3KPR7;Q96L46 A0A0C4DGQ5 CAPNS1;CAPNS2 Calpain small subunit 1;Calpain small subunit 2 0 ; 121.52 0.010306 826030000 925510 860190 740650 715120 887390 643990 946950 1060120 1063040 1010930 FALSE TRUE 889340.046 835658.2234 874501.9307 752027.4289 915933.7053 657011.919 958539.0574 1038228.152 942368.1558 942458.8107 0.943638105 0.886678775 0.927894058 0.797941958 0.971855422 0.69712534 1.017062015 1.101616474 0.99990381 1 19.84607004 2.026232108 24.99982434 1.048682985 0.873914883 0.491401966 0.078808736 156.4271032 149078.1165 0.027514206 0.020320093 106.226313 -2.026232108 -0.174768102 QKS(ph)DAEEDGGTVSQEEEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKS(1)DAEEDGGTVSQEEEDR 293.13 8.11E-50 2864500000 333600 460390 328420 633520 351590 320420 573360 843660 718140 471460 TRUE FALSE 320562.5432 447260.128 387772.7997 666216.0431 362899.2117 326899.1119 580376.9512 826238.1262 636619.7579 439527.5943 0.729334284 1.017592829 0.882249044 1.51575476 0.825657402 0.743751055 1.320456232 1.879832204 1.448418179 1 18.74559422 2.026238738 7.160876161 1.555729104 0.975317477 0.355467547 0.294056748 0.15276551 29.27455016 0.110321569 0.079814671 106.2279347 -2.026238738 -0.580411627 CLPNS(ph)KLKGLTFHVFPT(ph)DENIK ddPTM_BT-474_Pertuzumab_2h_R1 1 CLPNSKLKGLTFHVFPTDENIK 22 2 D6RC19;Q8TBB0-3;Q8TBB0-2;Q8TBB0 D6RC19 THAP6 THAP domain-containing protein 6 2 CLPNS(1)KLKGLT(0.017)FHVFPT(0.983)DENIK 67.995 0.038125 603110000 441210 390250 429550 475190 436680 341010 487710 510580 587670 546510 TRUE FALSE 423967.0254 379120.4521 507179.2403 499714.6128 450726.2088 347905.4558 493678.7409 500036.3446 520960.1653 509494.3909 0.832132861 0.74411114 0.995455984 0.980804935 0.884653917 0.682844526 0.968958147 0.981436407 1.022504221 1 18.95870674 2.026247478 24.98621581 0.993237638 0.859034923 0.371541754 0.089504614 262.7272785 250101.3618 0.035706487 0.026370313 106.2300726 -2.026247478 -0.134202715 S(ph)SSQRSPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSQRSPSPGPNHTSNSSNASNATVVPQNSSAR 33 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 2 S(0.3)S(0.3)S(0.3)QRS(0.3)PS(0.439)PGPNHT(0.149)S(0.149)NS(0.032)S(0.032)NASNATVVPQNSSAR 77.276 0.002687 54326000 13846 15837 10658 14479 11970 17291 10888 9046.5 9401.1 9393.7 TRUE FALSE 13304.88301 15385.34427 12584.13769 15226.26293 12355.02592 17640.63587 11021.2506 8859.686614 8333.926541 8757.456332 1.519263415 1.756827974 1.436962653 1.738662729 1.410800745 2.014356132 1.258499064 1.011673513 0.951637807 1 13.09629617 2.026286218 6.803041544 1.023333084 1.636804629 0.761187991 0.16687205 0.076258608 12.6607499 0.059981573 0.043222465 106.2395488 -2.026286218 0.613471545 CPQIVIAFYEER ddPTM_BT-474_Pertuzumab_2h_R1 4 CPQIVIAFYEER 12 0 Q13185;P45973 Q13185;P45973 CBX3;CBX5 Chromobox protein homolog 3;Chromobox protein homolog 5 0 ;;; 155.26 0.00015423 1055000000 642166 667283 524263 677026 606710 539630 686131 709126 829382 768004 FALSE TRUE 617069.4428 648252.7422 619008.9863 711967.393 626225.3781 550541.6883 694528.0764 694482.3003 735234.0324 715986.405 0.861845195 0.905398116 0.864554106 0.994386748 0.874633057 0.768927572 0.970029698 0.969965764 1.026882672 1 19.44957267 2.026314751 24.99862332 0.989208741 0.882798455 0.52028823 0.053548023 192.0489372 182442.8028 0.020617513 0.015226654 106.2465289 -2.026314751 -0.106410286 S(ph)PSVSPS(ph)KQPVSTSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSVSPSKQPVSTSSK 16 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 2 S(0.999)PS(0.022)VS(0.14)PS(0.839)KQPVSTSSK 118.37 0.00015797 351590000 309550 255710 333720 300850 314380 334090 419340 434550 552980 513200 TRUE FALSE 297452.4438 248417.4012 394030.6276 316376.9046 324492.3182 340845.5287 424472.0084 425576.3906 490208.0287 478440.5069 0.6217125 0.519223179 0.823572883 0.66126697 0.678229192 0.71240943 0.887199144 0.88950744 1.02459558 1 18.86798001 2.026446744 0.881249251 1.019060068 0.645482484 0.785682505 0.074021974 0.265386988 0.381600101 0.061469962 0.030683928 106.2788248 -2.026446744 -0.373577584 AGAPVGGS(ph)PGLAK ddPTM_BT-474_Pertuzumab_2h_R1 4 AGAPVGGSPGLAK 13 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK 198.29 1.33E-07 1214710000 2125880 2091130 1756300 1873990 1934560 1865590 2094220 2319320 2213210 2472390 TRUE FALSE 2042798.259 2031493.02 2073702.479 1970706.848 1996786.879 1903313.508 2119849.691 2271425.232 1961975.679 2304932.823 0.886272363 0.881367561 0.899680224 0.854995351 0.866310228 0.825756607 0.91970129 0.98546266 0.851207315 1 21.13629327 2.02645526 10.32356589 0.946107124 0.870413369 0.419899622 0.041153702 0.369490535 140.294557 0.014823485 0.010893313 106.280909 -2.02645526 -0.075693755 DAAEAIKK ddPTM_BT-474_Pertuzumab_2h_R1 4 DAAEAIKK 8 1 O75874;C9J4N6;C9JLU6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;; 118.26 0.0030786 3551110000 4387060 4155040 3407400 3685550 4050590 4096300 4574550 5383800 5880720 5501000 FALSE TRUE 4215608.845 4036542.327 4023192.977 3875761.677 4180880.906 4179129.993 4630534.711 5272622.649 5213165.32 5128412.37 0.822010506 0.787093946 0.784490928 0.755742986 0.815238831 0.814897417 0.90291778 1.028119868 1.016526157 1 22.29008084 2.026572834 2.046279865 1.020605902 0.791308325 0.961529098 0.0196101 0.055236131 0.434960811 0.011208004 0.006003462 106.3096857 -2.026572834 -0.229297577 LIHPDEDISLEERR ddPTM_BT-474_Pertuzumab_2h_R1 3 LIHPDEDISLEERR 14 1 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;; 162.72 2.85E-06 282705000 185464 218144 105641 152019 165444 224267 137960 131808 148213 141667 FALSE TRUE 178215.8618 211922.7467 124732.6787 159864.7188 170765.6565 228801.8324 139648.3957 129086.1187 131388.4816 132071.7679 1.349386509 1.604602937 0.944431052 1.210438244 1.29297623 1.732405313 1.057367505 0.977393737 0.994826401 1 17.01096258 2.026611308 24.99922444 0.995516129 1.343539353 0.423667877 0.199828449 217.9702473 204764.8958 0.076953871 0.056832802 106.319104 -2.026611308 0.348023225 ALANECSQGDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALANECSQGDKR 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 75.89 0.05226 192360000 357530 269560 209290 193810 226830 205330 281390 318780 311230 299120 FALSE TRUE 343557.3323 261872.4127 247113.3586 203812.5573 234126.193 209481.9133 284833.735 312197.0816 275900.4752 278860.336 1.232005015 0.939080891 0.886154561 0.730876826 0.839582267 0.751207276 1.021420755 1.119546387 0.989385867 1 18.08918322 2.026720748 22.54682597 1.054816175 0.8877099 0.194884078 0.133492438 102.9640492 86879.35755 0.052189936 0.038542535 106.3458992 -2.026720748 -0.167106275 RYS(ph)PSPPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RYSPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RY(0.081)S(0.902)PS(0.017)PPPK 74.76 0.02461 230880000 464980 488900 405030 455350 450990 533760 449710 453650 509520 489520 TRUE FALSE 446808.0675 474957.0507 478227.9308 478850.6681 465496.5029 544552.9929 455213.6855 444281.969 451681.4257 456364.3744 0.979059919 1.040740858 1.047908114 1.049272675 1.020010608 1.19324168 0.997478574 0.973524652 0.989738575 1 18.79982665 2.02676495 24.99994684 0.984984773 1.055806412 0.274687927 0.051740942 269.3252896 251563.6464 0.01935064 0.014291045 106.3567235 -2.02676495 0.070821639 GRKDDDS(ph)DDESQSSHTGK ddPTM_BT-474_Pertuzumab_2h_R1 7 GRKDDDSDDESQSSHTGK 18 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.97)DDES(0.03)QSSHTGK;GRKDDDS(0.99)DDES(0.01)QSSHTGK;GRKDDDS(0.97)DDES(0.03)QSSHTGK;GRKDDDS(0.999)DDESQSSHTGK;GRKDDDS(0.977)DDES(0.021)QS(0.002)SHTGK;GRKDDDS(0.916)DDES(0.084)QSSHTGK;GRKDDDS(0.995)DDES(0.002)QS(0.002)SHTGK 301.19 7.33E-50 2265023000 1739857 1897702 1337674 1371108 1356929 1652172 1732720 1971304 2260777 1973066 TRUE FALSE 1671861.465 1843581.397 1579421.448 1441871.048 1400575.854 1685580.05 1753925.546 1930595.884 2004143.073 1839428.482 0.908902673 1.00225772 0.858647924 0.783869045 0.761419032 0.916360742 0.953516575 1.049562895 1.089546613 1 20.81082615 2.02686894 2.101678418 1.052242486 0.866294476 0.584847451 0.066294157 0.248854729 2.069260883 0.041222407 0.022274317 106.3821932 -2.02686894 -0.18594801 KVEPPFKPLLQSEEDVSQFDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEPPFKPLLQSEEDVSQFDSK 22 2 P23443-5;P23443;P23443-3;P23443-2;P23443-4 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 0 196.55 1.19E-22 400690000 285540 253640 237080 197370 217350 237560 268550 324980 323420 298110 FALSE TRUE 274380.7811 246406.4355 279925.6298 207556.2894 224341.2601 242363.626 271836.5952 318269.0494 286706.7175 277918.7442 0.987269793 0.88661323 1.007221124 0.746823644 0.80721889 0.872066498 0.97811537 1.145187419 1.031620657 1 18.08430361 2.026935117 4.182670322 1.07343829 0.881547089 0.490199528 0.079613448 0.162772254 6.471006475 0.034673291 0.02306766 106.3984048 -2.026935117 -0.191891201 AYTDDLGAVGGACLEDEASALRLDEDSEHPPMILR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYTDDLGAVGGACLEDEASALRLDEDSEHPPMILR 35 1 Q9Y4P8-2;Q9Y4P8-6;Q9Y4P8-3;Q9Y4P8-5 Q9Y4P8-2 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 0 138.84 1.04E-09 30869000 12199 14988 11514 12328 15486 16059 11541 9223.2 12811 10493 FALSE TRUE 11722.24959 14560.55691 13594.83593 12964.24956 15984.12125 16383.72398 11682.24221 9032.737697 11356.74899 9782.299764 1.198312245 1.48845949 1.389738227 1.325276251 1.633983996 1.674833565 1.194222472 0.92337568 1.160948781 1 13.25595796 2.026989411 7.029011062 1.028535528 1.452725612 0.652082808 0.140694178 0.104244733 18.66080695 0.05525129 0.039945963 106.4117072 -2.026989411 0.424190084 RVESEES(ph)GDEEGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVESEESGDEEGKK 14 2 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 1 RVES(0.339)EES(0.661)GDEEGKK 176.11 1.79E-06 230350000 58531 49809 40278 43729 48948 42953 62923 81928 79756 81954 TRUE FALSE 56243.54381 48388.49609 47557.13058 45985.85893 50522.45687 43821.53909 63693.0705 80236.15817 70702.43324 76403.18258 0.736141374 0.633330896 0.622449602 0.601884076 0.661261156 0.573556462 0.833644206 1.050167748 0.92538597 1 16.22134511 2.027069636 3.898939108 0.989699657 0.637548845 0.910852448 0.049914517 0.055073216 1.823417726 0.020856472 0.013623414 106.4313659 -2.027069636 -0.352150812 SGGGLHSVAEGVRLS(ph)PEPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGGGLHSVAEGVRLSPEPGR 20 1 Q9NWK9-2;Q9NWK9 Q9NWK9-2 ZNHIT6 Box C/D snoRNA protein 1 1 SGGGLHSVAEGVRLS(1)PEPGR;SGGGLHSVAEGVRLS(1)PEPGR;SGGGLHSVAEGVRLS(1)PEPGR;SGGGLHSVAEGVRLS(1)PEPGR 213.72 2.77E-23 824930000 505558 583857 374828 415226 468610 548574 446992 443271 504032 491370 TRUE FALSE 485800.2344 567205.97 442567.7576 436655.8636 483683.2662 559666.5421 452462.4218 434117.2989 446816.4004 458089.0722 1.060492956 1.238200176 0.966117256 0.953211701 1.055871654 1.221741744 0.987717126 0.947670061 0.975391965 1 18.80526862 2.027085696 24.94026722 0.968327968 1.079573613 0.256154294 0.087532544 293.9102835 270628.6077 0.034368941 0.025382636 106.4353019 -2.027085696 0.111245645 LADFGVLHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LADFGVLHR 9 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;; 191.78 3.55E-05 1310450000 1673030 1742410 1782180 2585110 1548271 1347379 2290730 2476350 2570370 2838630 FALSE TRUE 1607646.138 1692718.173 2104259.57 2718527.837 1598072.543 1374623.927 2318764.639 2425212.507 2278592.373 2646367.062 0.607491743 0.639638468 0.795150303 1.027267863 0.603874106 0.519438118 0.876206734 0.916430885 0.861026577 1 21.33558175 2.027119086 24.82299939 0.911480033 0.710006476 0.379702909 0.134666778 242.1468637 221643.944 0.054103042 0.039956865 106.4434851 -2.027119086 -0.201473557 SEDES(ph)ETEDEEEKSQEDQEQKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 SEDES(0.993)ET(0.007)EDEEEKSQEDQEQKR;SEDES(0.988)ET(0.012)EDEEEKSQEDQEQKR 258.48 1.84E-37 2176740000 1287520 781120 665460 658170 708420 839340 1057280 1373370 1563680 1229370 TRUE FALSE 1237202.295 758843.2224 785723.4251 692138.2326 731206.9727 856312.0299 1070219.309 1345009.43 1386177.602 1146103.675 1.079485497 0.662106962 0.685560515 0.60390543 0.637993742 0.747150584 0.933789266 1.17354953 1.209469642 1 20.12830612 2.027140138 2.5984944 1.142883414 0.718176402 0.628419603 0.134809434 0.169674629 2.195055879 0.067763433 0.039177759 106.448645 -2.027140138 -0.424707013 QQFHDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 QQFHDAK 7 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 94.302 0.0143 3210760000 4217870 3998370 3846420 4943060 3421510 3003580 5023440 5223350 6113100 6317600 FALSE TRUE 4053030.977 3884340.402 4541553.657 5198171.919 3531565.976 3064314.446 5084918.361 5115485.997 5419166.516 5889703.325 0.688155371 0.659513763 0.771100581 0.882586377 0.599616956 0.520283328 0.8633573 0.868547313 0.920108572 1 22.48976353 2.027403361 23.11729171 0.902697697 0.694175922 0.571090175 0.096317586 77.77031892 65605.82362 0.038606335 0.028511514 106.5131824 -2.027403361 -0.208521776 KLEDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 KLEDVK 6 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ;; 86.472 0.085844 3849840000 4208100 4285800 3568500 4048800 4058000 4008000 4332400 4847000 5152800 4480500 FALSE TRUE 4043642.8 4163573.18 4213407.331 4257759.053 4188529.255 4089044.506 4385421.207 4746907.756 4567875.746 4177031.744 0.968066093 0.99677796 1.008708477 1.019326477 1.002752555 0.978935463 1.049889365 1.136430855 1.093569795 1 21.99404668 2.027403578 5.303840157 1.092442243 0.998444245 0.510761669 0.035191447 0.114398333 8.875636214 0.013354047 0.009346839 106.5132358 -2.027403578 -0.093997999 LYTDFDEIRQEIENETER ddPTM_BT-474_Pertuzumab_2h_R1 1 LYTDFDEIRQEIENETER 18 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;F8VZ52;B4DDQ3;B4DPZ9;F8VUJ9;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 241.32 4.98E-24 38581000 58111 74018 45154 51480 56793 67803 51233 52401 52507 53834 FALSE TRUE 55839.95787 71907.07911 53314.33225 54136.88897 58619.79842 69174.02312 51860.00478 51318.90104 46546.62549 50187.77523 1.112620705 1.432760842 1.062297183 1.078686766 1.168009503 1.378304234 1.03331946 1.022537875 0.927449469 1 15.61504837 2.0274219 24.05561055 0.996357126 1.202142457 0.444081942 0.115603629 135.148652 118557.0816 0.043661563 0.032245274 106.5177294 -2.0274219 0.205785331 SS(ph)PQLDPLRK ddPTM_BT-474_Pertuzumab_2h_R1 8 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.112)S(0.888)PQLDPLRK;S(0.098)S(0.902)PQLDPLRK;S(0.163)S(0.837)PQLDPLRK;S(0.392)S(0.608)PQLDPLRK;S(0.496)S(0.504)PQLDPLRK;S(0.117)S(0.883)PQLDPLRK;S(0.156)S(0.844)PQLDPLRK;S(0.149)S(0.851)PQLDPLRK 136.93 6.41E-05 53605933000 10822132 10184312 9864736 10374484 10023368 9507072 11651779 13549049 13733281 13395801 TRUE FALSE 10399191.12 9893865.393 11647513.24 10909912.36 10345778.73 9699311.51 11794376.96 13269256.4 12174336.52 12488491.47 0.832701944 0.792238632 0.932659742 0.873597295 0.828425015 0.776659978 0.944419667 1.062518755 0.974844444 1 23.57409588 2.027422161 5.623984504 1.016244388 0.843069865 0.750903237 0.045248917 0.083585662 7.726621233 0.018368675 0.012973606 106.5177933 -2.027422161 -0.173174523 SDAEEDGGTVS(ph)QEEEDRKPK ddPTM_BT-474_Pertuzumab_2h_R1 5 SDAEEDGGTVSQEEEDRKPK 20 2 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 SDAEEDGGTVS(1)QEEEDRKPK;SDAEEDGGT(0.003)VS(0.997)QEEEDRKPK;SDAEEDGGTVS(1)QEEEDRKPK;SDAEEDGGTVS(1)QEEEDRKPK;SDAEEDGGTVS(1)QEEEDRKPK 339.22 1.72E-80 7267320000 2508720 3133980 1755442 3114670 2002370 1902500 3391020 4846360 4694530 2939060 TRUE FALSE 2410676.449 3044601.959 2072689.419 3275418.492 2066778.05 1940969.854 3432520.317 4746280.972 4161626.635 2739994.848 0.879810577 1.111170687 0.756457415 1.195410456 0.754299976 0.70838449 1.252746997 1.73222259 1.518844693 1 21.38574175 2.027508332 5.990448552 1.498392069 0.913496756 0.511536196 0.227143123 0.112303323 12.53712716 0.084552607 0.060223341 106.5389302 -2.027508332 -0.584895313 FTDDTFDPELAATIGVDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTDDTFDPELAATIGVDFK 19 0 H0Y6T8;Q9NP72;Q9NP72-2;Q9NP72-3 H0Y6T8 RAB18 Ras-related protein Rab-18 0 130.07 9.40E-06 0 19606 25620 16233 28943 21169 19802 25711 30202 30959 28153 FALSE TRUE 18839.77584 24889.34268 19166.6642 30436.7517 21849.92011 20202.41001 26025.65891 29578.31815 27444.66411 26246.17223 0.717810417 0.948303717 0.730265123 1.159664405 0.832499304 0.769727861 0.991598267 1.126957405 1.045663492 1 14.67981941 2.027574435 7.080793534 1.068897002 0.87058549 0.346402049 0.12367148 0.187803127 33.82025088 0.045976269 0.033276343 106.5551476 -2.027574435 -0.198311512 ARDDLITDLLNEAK ddPTM_BT-474_Pertuzumab_2h_R1 6 ARDDLITDLLNEAK 14 1 P36543;C9J8H1;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 ;;;;; 302.35 5.26E-44 1999630000 3818090 3721020 3121550 3476610 3558030 3674360 4035140 4608130 4929400 4932530 FALSE TRUE 3668874.822 3614900.153 3685683.524 3656038.259 3672477.266 3748658.077 4084523.25 4512970.505 4369835.178 4598445.35 0.797851131 0.78611354 0.801506432 0.79505963 0.798634536 0.81520118 0.888240033 0.98141223 0.950285335 1 22.13271476 2.027653833 1.904896545 0.979474204 0.795388062 0.975597159 0.012691133 0.043222912 0.29456321 0.006905264 0.003620202 106.5746299 -2.027653833 -0.184086142 SEMEVQDAELK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEMEVQDAELK 11 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 160.18 6.46E-05 136410000 244390 209520 214720 201140 221970 250420 227130 303020 295880 299400 FALSE TRUE 234838.9686 203544.6947 253524.6804 211520.8595 229109.8666 255483.664 229909.6849 296762.5311 262292.9428 279121.3713 0.841350727 0.729233644 0.908295482 0.757809617 0.82082524 0.915313875 0.823690726 1.063202469 0.93970928 1 18.09053307 2.027677156 1.429367992 1.006639524 0.813795488 0.563276736 0.065887532 0.274060691 1.04626657 0.041940729 0.020357996 106.5803533 -2.027677156 -0.192844036 TIADHCPDSACK ddPTM_BT-474_Pertuzumab_2h_R1 4 TIADHCPDSACK 12 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 ;;; 160.52 6.56E-05 2389880000 3285170 3714990 3124690 3815500 2866670 3520640 3617390 4076490 4138750 4206740 FALSE TRUE 3156781.924 3609042.123 3689390.991 4012418.412 2958879.044 3591829.753 3661660.701 3992309.057 3668936.451 3921813.753 0.804929077 0.920248219 0.9407359 1.023102744 0.754466997 0.915859339 0.933665118 1.017975179 0.935520318 1 21.90308959 2.027712886 3.344711159 0.98522045 0.896543301 0.24355565 0.071683702 0.364742424 8.298428877 0.032767088 0.020494924 106.5891222 -2.027712886 -0.088677149 VVSS(ph)TSEEEEAFTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVSSTSEEEEAFTEK 15 0 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573 Q8N573-2 OXR1 Oxidation resistance protein 1 1 VVS(0.001)S(0.95)T(0.046)S(0.002)EEEEAFTEK;VVSS(0.875)T(0.118)S(0.007)EEEEAFTEK 410.58 4.34E-133 280610000 721080 732580 638390 765320 850680 778220 587690 550000 532560 509340 TRUE FALSE 692899.3964 711687.5357 753761.2739 804818.2569 878042.8948 793956.1416 594882.326 538642.3078 472106.0215 474841.9481 1.459221114 1.498788257 1.587394031 1.694918193 1.849126637 1.672042971 1.252800702 1.134361254 0.994238237 1 18.85708786 2.027751471 2.403608632 1.052775813 1.633169911 0.85093326 0.11095779 0.12315908 1.35144039 0.065845222 0.037163913 106.5985926 -2.027751471 0.580394098 GDDQLELIKDDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_BT-474_Pertuzumab_2h_R1 2 GDDQLELIKDDEKEAEEGEDDRDSANGEDDS 31 3 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 GDDQLELIKDDEKEAEEGEDDRDS(0.876)ANGEDDS(0.124);GDDQLELIKDDEKEAEEGEDDRDS(1)ANGEDDS 171.8 3.43E-12 854430000 512691 420869 557449 504874 436406 554059 635653 797400 934300 766040 TRUE FALSE 492654.4689 408866.2282 658192.4347 530930.6076 450443.3953 565262.4526 643432.3116 780933.4113 828242.1809 714155.4285 0.689842084 0.572517147 0.921637515 0.743438454 0.6307358 0.791511805 0.900969573 1.093506232 1.159750592 1 19.44587857 2.02794686 1.992112525 1.098582203 0.718119799 0.748814118 0.09389278 0.162324115 1.211098079 0.054223797 0.028836237 106.6465621 -2.02794686 -0.380462404 TDYYAR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDYYAR 6 0 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 ;;; 166.66 0.016052 6880550000 2733910 2789920 2404160 2755350 2590480 2331020 2807950 3020510 3011810 3171090 FALSE TRUE 2627065.775 2710354.213 2838645.192 2897553.944 2673805.142 2378154.822 2842314.532 2958135.413 2669921.955 2956309.25 0.888630232 0.916803346 0.960199002 0.980125453 0.904440272 0.804433711 0.961440192 1.000617717 0.903126747 1 21.49536576 2.028054494 24.9998393 0.971244965 0.912139087 0.234099628 0.050493311 321.9601537 286902.9545 0.019886468 0.014686847 106.6729962 -2.028054494 -0.059105878 VMEKPSPLLVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VMEKPSPLLVGR 12 1 Q9UN86-2;Q9UN86;D6RB17;D6RAC7;D6RE13;D6RBW8;D6RGJ4;D6RBM9;D6REX8;D6RBR0;D6R9X5;D6R9A4;Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8;E5RI46;E5RH00 Q9UN86-2;Q13283 G3BP2;G3BP1 Ras GTPase-activating protein-binding protein 2;Ras GTPase-activating protein-binding protein 1 0 ; 73.877 0.034671 1203120000 3012300 3190300 2519880 2306990 2672380 2352490 2921800 3118060 3190270 3347400 FALSE TRUE 2894575.986 3099315.768 2975278.37 2426054.03 2758339.53 2400058.96 2957557.862 3053670.971 2828123.924 3120677.616 0.927547264 0.99315474 0.953407797 0.777412578 0.883891215 0.769082634 0.94772938 0.978528175 0.906253151 1 21.5734279 2.028100642 24.99844812 0.960188332 0.884923619 0.216762323 0.069303665 352.7823637 313835.2021 0.027771017 0.020509955 106.6843319 -2.028100642 -0.075264713 TVSLTPS(ph)PTTQVETPDLVDHDNTS(ph)PLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TVSLT(0.005)PS(0.898)PT(0.045)T(0.052)QVETPDLVDHDNT(0.378)S(0.622)PLFR 103.75 0.00055128 49429000 32826 31317 32665 44726 44915 45742 35159 36227 37121 36929 TRUE FALSE 31543.12363 30423.86982 38568.29213 47034.31422 46359.73177 46666.93458 35589.28636 35478.89979 32907.1797 34427.76594 0.916211749 0.883701541 1.12026706 1.36617387 1.34657973 1.355502842 1.033737897 1.030531573 0.955832562 1 15.07128495 2.028467349 24.89843531 1.007168876 1.169636438 0.194288548 0.160042185 386.3835076 337941.4449 0.069298149 0.051179222 106.7744516 -2.028467349 0.162467562 LLGLNELDDLLGKES(ph)PSKDSEPSCWGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLGLNELDDLLGKESPSKDSEPSCWGK 27 2 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 LLGLNELDDLLGKES(0.85)PS(0.149)KDSEPSCWGK 212.64 2.84E-26 213920000 437720 351360 239160 276370 271480 287280 387310 506320 538080 386290 TRUE FALSE 420613.4185 341339.5568 282381.5321 290633.4888 280212.4008 293088.9984 392050.0156 495864.3151 476999.4142 360126.2342 1.167961061 0.947833077 0.784118193 0.80703226 0.77809494 0.813850729 1.088646087 1.376918058 1.324533924 1 18.45814317 2.028499547 4.27830348 1.269227983 0.875146236 0.546782457 0.143305013 0.138181253 5.808614083 0.060953414 0.040869059 106.7823678 -2.028499547 -0.394081747 AKS(ph)PT(ph)PDGSER ddPTM_BT-474_Pertuzumab_2h_R1 3 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.996)PT(0.989)PDGS(0.015)ER;AKS(0.977)PT(0.667)PDGS(0.356)ER;AKS(0.669)PT(0.981)PDGS(0.35)ER 135.13 0.0031688 1602960000 3438320 3066400 2384670 2433340 2658600 2667670 3016260 3345100 3690650 3224830 TRUE FALSE 3303946.653 2978949.274 2815632.916 2558924.969 2744116.283 2721612.115 3053173.892 3276022.516 3271702.884 3006409.392 1.098967646 0.990866142 0.936543414 0.851156524 0.912755359 0.905269962 1.015554934 1.089679445 1.088242637 1 21.51961005 2.028687858 4.883837087 1.066175261 0.94482234 0.365660907 0.065427803 0.195188885 11.80047626 0.028233104 0.019501009 106.8286791 -2.028687858 -0.121352921 KYES(ph)DEDSLGSSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KYESDEDSLGSSGR 14 1 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 KY(0.006)ES(0.989)DEDS(0.004)LGS(0.002)SGR 53.21 0.092138 655060000 264260 279040 273890 283610 249560 301980 286760 328180 358440 334390 TRUE FALSE 253932.427 271082.0524 323388.0157 298247.1461 257587.324 308086.2425 290269.4547 321402.9683 317751.3939 311741.4675 0.814560954 0.869573287 1.037359637 0.956713101 0.826285082 0.98827482 0.931122372 1.03099203 1.01927856 1 18.24999055 2.028984322 1.530640996 1.020291899 0.912503745 0.327114879 0.065319511 0.50435902 2.212509176 0.044167794 0.021790171 106.9016288 -2.028984322 -0.107788154 KDVLETFTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDVLETFTVK 10 1 A6NNI4;A0A2R8Y478;G8JLH6;P21926 A6NNI4 CD9 Tetraspanin;CD9 antigen 0 ; 147.71 4.24E-05 1135570000 1514090 2061800 1271550 1825720 1228490 1188760 1920220 2458300 1963400 1552960 FALSE TRUE 1454917.689 2002999.483 1501347.37 1919945.628 1268005.497 1212797.542 1943720.227 2407535.246 1740523.063 1447776.636 1.004932427 1.38350035 1.037002071 1.326133866 0.875829506 0.837696584 1.342555321 1.662918979 1.202204138 1 20.46540761 2.029140422 22.71706352 1.397208317 1.091582982 0.140507307 0.229810435 95.95381384 74801.91857 0.085825628 0.063384408 106.9400596 -2.029140422 -0.305625335 LKETAEEEKDDLEER ddPTM_BT-474_Pertuzumab_2h_R1 1 LKETAEEEKDDLEER 15 2 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 96.666 0.0020314 288010000 263210 252370 198300 220640 228460 245470 269040 336250 357420 299140 FALSE TRUE 252923.4622 245172.6547 234137.2212 232027.2568 235808.6234 250433.5716 272332.592 329306.32 316847.18 278878.9814 0.906929095 0.879136368 0.839565678 0.8319998 0.845558967 0.898000883 0.976526057 1.180821582 1.136145788 1 18.08927968 2.029209076 2.821785035 1.121751675 0.8626484 0.82082141 0.049678676 0.094644529 1.465170041 0.023548291 0.014002462 106.9569662 -2.029209076 -0.259103274 RNS(ph)SEASS(ph)GDFLDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSSEASSGDFLDLK 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 2 RNS(0.96)S(0.04)EAS(0.016)S(0.984)GDFLDLK 156.05 7.68E-06 45742000 86587 78420 82978 94959 84877 72527 107220 141040 122240 123720 TRUE FALSE 83203.08431 76183.53838 97973.97044 99859.84537 87607.14579 73993.54563 108532.1904 138127.4747 108363.8277 115340.3342 0.721370238 0.660510817 0.849433731 0.865784255 0.759553424 0.641523593 0.940973435 1.19756437 0.939513731 1 16.81553758 2.029231518 6.188226419 1.068676692 0.75738323 0.686679346 0.090837185 0.090275185 10.80240702 0.035809298 0.025648552 106.9624935 -2.029231518 -0.311293462 GQLGHGDTKR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQLGHGDTKR 10 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 123.67 0.00029594 363960000 419820 426950 329550 352310 415620 489820 387490 392610 434820 424710 FALSE TRUE 403412.9703 414773.804 389107.0158 370492.7613 428988.7948 499724.496 392232.2185 384502.4663 385461.0565 395944.0134 1.018863669 1.0475567 0.982732413 0.935720073 1.083458217 1.262108983 0.990625455 0.971103119 0.973524143 1 18.59493692 2.02937306 24.99998465 0.978964427 1.053896709 0.158140319 0.08065836 408.411906 347605.713 0.032889996 0.024290559 106.9973594 -2.02937306 0.074932283 AQPAAGQQGPEVEPPPPT(ph)PGGPQGEAGVAPTGHVTSIEPAPQGHPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQPAAGQQGPEVEPPPPTPGGPQGEAGVAPTGHVTSIEPAPQGHPR 46 0 A0A494C1T9 A0A494C1T9 1 AQPAAGQQGPEVEPPPPT(0.318)PGGPQGEAGVAPT(0.227)GHVT(0.227)S(0.227)IEPAPQGHPR;AQPAAGQQGPEVEPPPPT(0.25)PGGPQGEAGVAPT(0.25)GHVT(0.25)S(0.25)IEPAPQGHPR 67.333 0.0017684 387920000 45212 46158 40315 48482 45876 52769 40272 32433 45328 43711 TRUE FALSE 43445.06506 44841.61903 47600.8173 50984.16183 47351.6432 53836.02533 40764.86078 31763.24722 40182.55547 40750.41504 1.066125707 1.100396622 1.168106319 1.251132333 1.161991679 1.321116001 1.000354493 0.779458251 0.986064938 1 15.31452713 2.02938921 7.807893398 0.895290007 1.175980176 0.63879522 0.087978504 0.110416923 24.01251342 0.03344971 0.024390594 107.0013383 -2.02938921 0.280690169 VASEAPLEHKPQVEASS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.401)S(0.599)PR;VASEAPLEHKPQVEAS(0.183)S(0.817)PR;VASEAPLEHKPQVEAS(0.161)S(0.839)PR;VASEAPLEHKPQVEAS(0.198)S(0.802)PR 212.82 3.87E-17 5149690000 3329460 3639230 3347700 3745270 3811270 4015120 3413740 3205080 3659580 3769870 TRUE FALSE 3199341.022 3535442.724 3952703.859 3938563.834 3933862.961 4096308.477 3455518.371 3138893.978 3244159.821 3514533.347 0.910317447 1.005949403 1.124673881 1.12065058 1.119313027 1.165534104 0.983208304 0.89311828 0.923069865 1 21.74490171 2.029480079 8.273099412 0.929557861 1.077669074 0.420115959 0.072800493 0.20422567 49.82462843 0.029390293 0.021488562 107.023729 -2.029480079 0.148111213 LGFVDVQNCIS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 4 LGFVDVQNCISR 12 0 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 LGFVDVQNCIS(1)R;LGFVDVQNCIS(1)R;LGFVDVQNCIS(1)R;LGFVDVQNCIS(1)R 141.85 6.38E-05 1917900000 1163510 2083050 1002790 2406760 1281440 1344620 1806170 2350280 1726430 1298540 TRUE FALSE 1118038.743 2023643.454 1184016.46 2530973.172 1322658.681 1371809.138 1828274.449 2301745.897 1530452.904 1210588.729 0.923549605 1.671619275 0.978050127 2.090696131 1.092574753 1.13317521 1.510235809 1.901344231 1.264222 1 20.20727739 2.02954345 24.29213993 1.54295122 1.339389336 0 0.397831698 474.8229121 390421.1609 0.142750538 0.105426542 107.0393468 -2.02954345 -0.203561885 SEDES(ph)ETEDEEEKSQEDQEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDESETEDEEEKSQEDQEQK 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 SEDES(0.619)ET(0.381)EDEEEKSQEDQEQK 272.1 6.78E-45 899930000 1277500 769950 705910 725500 876590 833160 1223200 1637700 1809500 1486600 TRUE FALSE 1227573.888 747991.7799 833483.6399 762943.1419 904786.3134 850007.066 1238169.888 1603880.923 1604093.146 1385911.258 0.885752158 0.539711165 0.601397554 0.550499274 0.652845778 0.613319981 0.893397669 1.15727534 1.157428469 1 20.40240345 2.029673975 2.881552553 1.116114758 0.629810434 0.812110296 0.1004622 0.099525899 1.613802742 0.04673767 0.027988629 107.0715216 -2.029673975 -0.486304324 HGGPGPGGPEPELS(ph)PITEGSEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGGPGPGGPEPELSPITEGSEAR 23 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 HGGPGPGGPEPELS(1)PITEGSEAR 167.27 7.09E-12 133630000 84074 84557 79208 90621 100620 98314 71445 41454 80616 67769 TRUE FALSE 80788.29513 82145.51715 93522.64757 95297.96067 103856.5337 100301.9764 72319.36528 40597.96041 71464.80965 63178.94527 1.278721808 1.300203997 1.480281875 1.508381634 1.643847222 1.587585485 1.144675097 0.642586866 1.131149141 1 15.94715623 2.029675952 5.09840305 0.884708836 1.465865281 0.709558337 0.156581784 0.092462625 6.274590552 0.065105599 0.045392231 107.0720092 -2.029675952 0.581156445 GHYTIGKEIIDLVLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHYTIGKEIIDLVLDR 16 1 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 264.16 3.25E-27 89894000 111380 128520 74460 80309 93314 134380 85779 73742 106000 103140 FALSE TRUE 107027.1465 124854.7354 87916.57835 84453.75711 96315.52956 137097.2557 86828.78906 72219.20193 93967.32439 96154.23593 1.113077811 1.298483985 0.914328708 0.878315514 1.001677447 1.425805679 0.903015746 0.751076655 0.977256212 1 16.55306279 2.029747539 24.99879901 0.868100777 1.096528978 0.237656597 0.168018053 263.4776123 221416.3345 0.065423492 0.048317876 107.0896598 -2.029747539 0.228428201 EYSSMDAFWQEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYSSMDAFWQEGR 13 0 O95470;H0Y3V8;H7BXL7 O95470 SGPL1 Sphingosine-1-phosphate lyase 1 0 75.739 0.071118 63094000 50032 66881 49523 92535 51564 37122 72711 96836 73143 44875 FALSE TRUE 48076.69413 64973.61936 58472.90773 97310.74244 53222.60289 37872.63227 73600.85897 94836.30276 64840.11328 41835.57628 1.149182069 1.553070978 1.397683812 2.326028493 1.272185246 0.90527335 1.759288756 2.266881712 1.549879769 1 15.35244269 2.029872246 24.99500109 1.813035867 1.459325065 0 0.462406809 451.4655814 377752.8285 0.174393584 0.128796678 107.120415 -2.029872246 -0.353710801 DTSPDKGELVS(ph)DEEEDT ddPTM_BT-474_Pertuzumab_2h_R1 2 DTSPDKGELVSDEEEDT 17 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 DTSPDKGELVS(0.934)DEEEDT(0.066);DTSPDKGELVS(0.924)DEEEDT(0.076) 187.56 1.21E-09 680020000 1735240 1774800 1409830 1468430 1608880 1493320 1752630 1964610 2049920 1956740 TRUE FALSE 1667424.902 1724184.442 1664617.642 1544215.848 1660631.086 1523515.954 1774079.21 1924040.117 1817221.676 1824208.257 0.914054026 0.945168642 0.912515134 0.846512915 0.910329772 0.835165584 0.972520108 1.054726131 0.996170075 1 20.79883901 2.030022071 6.626272547 1.020981904 0.895958856 0.730770301 0.034034295 0.085242616 12.1848901 0.013308526 0.009602862 107.1573762 -2.030022071 -0.125023048 RDSFDDRGPSLNPVLDYDHGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 164.42 8.39E-12 601260000 215827 282090 211218 243591 223133 300050 210156 205235 209456 259290 FALSE TRUE 207392.2422 274045.0694 249389.7911 256162.7607 230310.2756 306117.2166 212727.952 200996.8255 185679.433 241728.0573 0.857956848 1.133691605 1.031695674 1.059714638 0.952766005 1.266370234 0.88003004 0.831499776 0.768133559 1 17.88302541 2.030132104 24.99989132 0.849807746 1.051285629 0.373039002 0.114084464 180.179867 149490.2119 0.039822846 0.029410811 107.1845291 -2.030132104 0.201477884 ELSNSVSTYRPFGLGS(ph)ESPYKQPSDGMERPSSLMDSSQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSNSVSTYRPFGLGSESPYKQPSDGMERPSSLMDSSQEK 40 3 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ELSNSVS(0.004)T(0.004)YRPFGLGS(0.495)ES(0.495)PYKQPS(0.001)DGMERPSSLMDSSQEK 114.72 3.16E-06 1078100000 934140 715100 609970 541380 675950 667210 735040 833760 879490 706790 TRUE FALSE 897632.7761 694706.0482 720205.1477 569320.6867 697692.5456 680701.4433 744035.6394 816542.5646 779653.9823 658918.4838 1.362281979 1.054312582 1.093010995 0.864022942 1.058845006 1.033058656 1.129177065 1.239216359 1.18323283 1 19.32974047 2.03017448 6.716963758 1.171598878 1.067451801 0.031539224 0.128280834 0.380855609 56.30124699 0.049174829 0.03552789 107.1949879 -2.03017448 -0.104147077 GVGVALDDPYENYRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVGVALDDPYENYRR 15 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 144.27 6.84E-06 1169140000 632750 722190 520430 655280 628330 759200 611800 625580 665860 669750 FALSE TRUE 608021.4305 701593.8483 614483.2779 689099.0793 648540.8051 774551.5442 619287.3914 612661.5544 590274.3643 624387.2359 0.973789013 1.123651811 0.984138116 1.103640561 1.038683637 1.240498683 0.991832241 0.981220498 0.945365841 1 19.25208152 2.030260887 24.99984832 0.976712992 1.078152114 0.308378611 0.072048308 231.7188236 191432.1654 0.02584902 0.019090551 107.2163175 -2.030260887 0.101439122 FQEHLQLQNLGINPANIGFSTLTMESDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FQEHLQLQNLGINPANIGFSTLTMESDK 28 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 252.67 1.89E-53 973380000 543490 493720 549460 550930 617480 513910 728020 746900 865770 861400 FALSE TRUE 522249.8099 479639.589 648759.6447 579363.5633 637341.805 524301.6123 736929.7265 731476.254 767491.4192 803056.6107 0.650327515 0.597267469 0.807862903 0.721447972 0.793644927 0.652882506 0.917656012 0.910865117 0.955712722 1 19.61514217 2.030267189 0.677346721 1.01215553 0.678717684 0.732968468 0.069673877 0.363141013 0.322693523 0.062124427 0.036362835 107.2178735 -2.030267189 -0.333437846 KIEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KIEDLEK 7 1 Q96IZ0;H0YHP5;Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q96IZ0;Q9ULJ8 PAWR;PPP1R9A PRKC apoptosis WT1 regulator protein;Neurabin-1 0 ; 95.358 0.021686 521500000 1020490 948200 778390 732480 910140 887770 982050 1060410 1234280 1099350 FALSE TRUE 980608.1226 921158.2644 919062.3882 770283.3806 939415.4797 905721.3177 994068.6217 1038512.163 1094169.709 1024890.045 0.956793489 0.898787405 0.896742429 0.751576605 0.916601233 0.883725354 0.969927092 1.013291297 1.067597167 1 19.96703771 2.030271107 1.869923363 1.033067787 0.87847463 0.607470293 0.052048698 0.234179904 1.538475834 0.031209381 0.016307402 107.2188408 -2.030271107 -0.154593157 DSKPSSTPR ddPTM_BT-474_Pertuzumab_2h_R1 9 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;;;;;;; 138.23 0.00012983 80520530000 9214050 9202620 7673680 8340930 8464970 7290330 9138440 9701110 10311910 10032600 FALSE TRUE 8853954.739 8940170.288 9060484.676 8771406.397 8737253.448 7437745.468 9250278.962 9500778.688 9141345.208 9353083.066 0.946634888 0.955852763 0.96871637 0.937809098 0.934157581 0.795218584 0.989008533 1.015791116 0.977361705 1 23.15701057 2.030330443 24.99996843 1.000204283 0.924830447 0.373449897 0.046025257 216.1360607 178150.0133 0.017950992 0.013257569 107.2334905 -2.030330443 -0.075373836 S(ph)STPLHSPS(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.995)S(0.115)T(0.085)PLHS(0.249)PS(0.555)PIR;S(0.996)S(0.192)T(0.138)PLHS(0.241)PS(0.433)PIR 100.22 0.0049043 351050000 490920 713110 533090 757890 629360 434310 517480 496100 289730 414230 TRUE FALSE 471734.3037 692772.801 629431.2215 797004.7937 649603.936 443092.0458 523813.075 485855.3616 256841.065 386173.8331 1.221559472 1.793940297 1.629916808 2.063849814 1.682154202 1.147390133 1.356417836 1.258126056 0.665091839 1 18.55889089 2.030442101 0.938479261 0.904804619 1.688826062 0.57654739 0.255600556 0.418007976 0.679827556 0.211187553 0.103455278 107.2610641 -2.030442101 0.784021443 SYS(ph)PDGK ddPTM_BT-474_Pertuzumab_2h_R1 6 SYSPDGK 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK 143.7 0.0025214 85252000000 20958140 18441160 16561940 17518900 17767430 16945340 19712670 21659390 22674240 21456090 TRUE FALSE 20139072.72 17915236.17 19555050.98 18423052.53 18338935.52 17287986.38 19953919.55 21212116.03 20100355.33 20002849.91 1.00681017 0.895634185 0.977613243 0.921021385 0.916816134 0.864276164 0.997553831 1.060454691 1.004874576 1 24.25370223 2.030503447 11.0757744 1.028630209 0.929935139 0.521485324 0.04039698 0.388245044 139.0319721 0.014617904 0.010768683 107.2762162 -2.030503447 -0.09869507 SWTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 SWT(0.024)S(0.976)PK;SWT(0.006)S(0.994)PK;SWTS(1)PK 125.49 0.018776 1385732000 6471350 5815470 4978130 5233150 5908970 5745470 6284350 7329350 7815110 6777430 TRUE FALSE 6218442.488 5649618.49 5877788.829 5503233.499 6099037.386 5861647.34 6361259.755 7177996.361 6927971.476 6318388.629 0.984181704 0.894154953 0.930267062 0.870986864 0.965283673 0.927712378 1.006785136 1.136048569 1.09647758 1 22.59112525 2.030544316 3.457358839 1.090215133 0.926545568 0.692784884 0.044243142 0.112749996 2.771855014 0.018867858 0.011960668 107.286312 -2.030544316 -0.163669565 RTNST(ph)GGSSGSSVGGGSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTNSTGGSSGSSVGGGSGK 19 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 RT(0.293)NS(0.293)T(0.389)GGS(0.011)S(0.011)GS(0.002)SVGGGSGK 71.678 0.016605 0 102500 109940 84308 91555 111780 113670 96771 96419 110620 107100 TRUE FALSE 98494.18668 106804.6188 99544.33102 96280.16452 115375.5052 115968.4853 97955.31245 94427.91396 98062.88136 99846.02161 0.986460803 1.069693285 0.996978442 0.964286438 1.155534325 1.161473271 0.981063751 0.945735368 0.982141099 1 16.60741732 2.03064804 24.98503194 0.968296855 1.055512912 0.269548834 0.062972601 259.5526519 211592.5368 0.025301323 0.01868608 107.3119385 -2.03064804 0.087216057 SCLLLQFTDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCLLLQFTDKR 11 1 P61019;E9PKL7;A0A3B3ITL1;Q8WUD1;E9PE37;H0YD31;H0YDL5 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 207.95 3.40E-08 1663810000 1003150 1336560 968250 1208030 975590 633260 1345260 1532850 1459780 1477690 FALSE TRUE 963945.789 1298442.617 1143234.314 1270376.573 1006970.738 646064.9511 1361723.694 1501196.112 1294071.894 1377604.74 0.699725953 0.942536404 0.829871066 0.922163329 0.730957661 0.468977009 0.988471987 1.089714682 0.939363706 1 20.39373058 2.030677554 24.99638228 1.024519461 0.777736247 0.44882217 0.129013777 183.2122668 149282.4608 0.050337401 0.037176271 107.3192314 -2.030677554 -0.246783213 AVQCTSDYPEHVCEVLLTMER ddPTM_BT-474_Pertuzumab_2h_R1 2 AVQCTSDYPEHVCEVLLTMER 21 0 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 119.06 6.78E-05 250030000 269970 273730 242510 313220 276830 286770 271930 262410 301160 302160 FALSE TRUE 259419.2739 265923.4884 286336.9516 329385.3217 285734.4884 292568.6859 275257.9607 256991.1418 266973.5794 281694.4341 0.920924387 0.944013996 1.016480686 1.169300071 1.014341974 1.038603006 0.977150868 0.912304649 0.947741762 1 18.10377153 2.030713563 5.219892433 0.943598937 1.020232269 0.160645463 0.065177212 0.299772988 21.56833104 0.028000026 0.019626983 107.3281301 -2.030713563 0.076633333 ASEKPVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASEKPVSPK 9 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E7EUY6;E7EU80 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 ASEKPVS(1)PK;ASEKPVS(1)PK;ASEKPVS(1)PK 132.86 0.00017753 3360430000 3632993 3062460 2902316 2371810 2756163 2962093 3350262 3830046 4426080 3573538 TRUE FALSE 3491011.617 2975121.639 3426829.063 2494219.398 2844817.486 3021988.55 3391263.509 3750954.212 3923649.954 3331499.088 1.047880106 0.893027901 1.028614738 0.748677797 0.853915133 0.907095716 1.017939198 1.12590582 1.177743067 1 21.66774007 2.030897969 2.901314038 1.111895296 0.907193901 0.471327466 0.089491581 0.217684593 3.585133483 0.043076822 0.025886607 107.3737124 -2.030897969 -0.204701395 EKPGVESMR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKPGVESMR 9 1 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 129.82 0.00034527 1301880000 1129500 1259530 957950 1156710 1026000 998530 1205140 1310600 1397960 1189000 FALSE TRUE 1085357.891 1223609.438 1131072.874 1216407.942 1059002.222 1018720.961 1219888.864 1283535.652 1239269.442 1108467.971 0.979151333 1.103874419 1.020392924 1.097377618 0.95537467 0.919035089 1.100517918 1.157936617 1.11800203 1 20.08013565 2.030993744 24.99125664 1.114452913 1.01759124 0.246535654 0.066244429 229.4754934 185032.6194 0.02502562 0.018482504 107.397394 -2.030993744 -0.096861673 GQICWYQKPGVGLDAINDANLLEACIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQICWYQKPGVGLDAINDANLLEACIYR 28 1 P14324-2;P14324;A0A087WVN4;A0A087X090 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ; 272.27 1.73E-61 343940000 319420 300431 218196 273520 318373 380580 266836 252912 333057 273880 FALSE TRUE 306936.7133 291863.002 257628.8709 287636.4 328613.7567 388275.5884 270101.6188 247689.2788 295249.7656 255329.8637 1.202118346 1.143082121 1.009004067 1.126528624 1.287016536 1.520682237 1.057853613 0.970075632 1.156346388 1 17.96200276 2.031049952 24.99995321 1.032602441 1.208727625 0.280071183 0.132185139 272.6012067 219484.4382 0.053852347 0.039772296 107.4112948 -2.031049952 0.176125184 KAES(ph)EELEVQKPQVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAESEELEVQKPQVK 15 2 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 KAES(1)EELEVQKPQVK;KAES(1)EELEVQKPQVK 240.07 4.14E-18 1554980000 1249120 1014060 816230 773170 964400 928560 1221680 1595910 1631170 1448620 TRUE FALSE 1200303.009 985140.0017 963740.9179 813073.3964 995420.8018 947336.1194 1236631.285 1562953.901 1446006.42 1350503.677 0.888781741 0.729461177 0.713615916 0.602051968 0.737073744 0.701468745 0.915681539 1.157311844 1.070716389 1 20.36506614 2.031074006 3.437116998 1.087064605 0.723257217 0.81052548 0.075503185 0.092611212 2.24496141 0.034361359 0.021758339 107.417244 -2.031074006 -0.363807388 DRYLPDTLLLEECGLLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRYLPDTLLLEECGLLR 17 1 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 192.62 1.61E-10 316991000 251226 279771 194961 245877 260442 272723 238591 248127 259292 255472 FALSE TRUE 241407.8102 271792.205 230194.7896 258566.7414 268819.3535 278237.6459 241510.948 243003.0907 229858.2592 238168.6539 1.013600263 1.141175384 0.966520093 1.085645559 1.128693256 1.168237891 1.014033308 1.020298376 0.965107101 1 17.86162402 2.031134025 24.94716359 1.002334312 1.083996821 0.342363603 0.057303503 231.0539393 185138.5883 0.021723007 0.016043335 107.4320902 -2.031134025 0.08166251 RADS(ph)GEEENTK ddPTM_BT-474_Pertuzumab_2h_R1 4 RADSGEEENTK 11 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 RADS(1)GEEENTK;RADS(1)GEEENTK;RADS(1)GEEENTK;RADS(1)GEEENTK 245.93 5.93E-16 788985000 1889740 1713506 1471352 1609369 1663984 1682521 1837630 2004300 2240720 2080750 TRUE FALSE 1815886.872 1664638.487 1737258.036 1692428.727 1717507.557 1716542.727 1860119.466 1962910.505 1986362.859 1939818.949 0.936111523 0.858141162 0.895577413 0.872467365 0.885395803 0.884898422 0.958913958 1.011903975 1.023993946 1 20.88749058 2.031162823 2.427007947 1.013430682 0.886110807 0.885178888 0.020024927 0.082795392 0.928647009 0.009712226 0.00551738 107.4392142 -2.031162823 -0.127319875 TVSPGSVS(ph)PIHGQGQVVENLK ddPTM_BT-474_Pertuzumab_2h_R1 3 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 TVSPGS(0.045)VS(0.955)PIHGQGQVVENLK;TVSPGS(0.479)VS(0.521)PIHGQGQVVENLK;TVSPGS(0.017)VS(0.983)PIHGQGQVVENLK 338.6 1.29E-80 3571270000 2820250 2856050 2428870 2604590 2680920 2914180 2985020 2977870 3444990 3392690 TRUE FALSE 2710031.512 2774598.25 2867820.839 2739013.202 2767154.227 2973106.716 3021551.568 2916375.944 3053929.178 3162900.084 0.856818565 0.877232343 0.906706112 0.865981577 0.874878799 0.939993878 0.95531047 0.922057563 0.965547155 1 21.59281655 2.031215236 0.347762411 1.004032879 0.854231985 0.811602028 0.019867437 0.622634433 0.205887222 0.027629743 0.032648476 107.4521812 -2.031215236 -0.149800894 TDCNHIFLNFVPTVIMDPSKIEESVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDCNHIFLNFVPTVIMDPSKIEESVR 26 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 143.67 1.55E-07 408130000 477180 500020 435040 362130 480700 533220 493580 522530 714680 576550 FALSE TRUE 458531.278 485759.9192 513661.4054 380819.5727 496162.1521 544002.0737 499620.5797 511739.5729 633552.5226 537499.755 0.853081836 0.903739797 0.955649562 0.708501854 0.923092797 1.012097343 0.929527084 0.952074058 1.178702905 1 19.03590457 2.031237641 0.876767258 1.058692901 0.869879382 0.424036327 0.086196106 0.62070959 0.883997082 0.072326573 0.036285228 107.4577248 -2.031237641 -0.188813519 IEDVTPIPSDSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 IEDVTPIPSDSTR 13 0 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 0 ; 171.74 5.72E-05 414680000 354500 366650 304600 378010 373710 395790 353950 361550 399780 385550 FALSE TRUE 340645.7481 356193.501 359647.9958 397519.1414 385730.7215 403793.145 358281.746 354083.8662 354398.6504 359436.3551 0.947722019 0.990977946 1.000588813 1.105951404 1.073154443 1.12340652 0.996787723 0.98510866 0.985984432 1 18.45537681 2.031295158 24.99937916 0.989269257 1.042344603 0.182956136 0.050044848 344.1894265 274945.9909 0.020642922 0.01524567 107.4719573 -2.031295158 0.053075346 SKHEEEEWT(ph)DDDLVESL ddPTM_BT-474_Pertuzumab_2h_R1 3 SKHEEEEWTDDDLVESL 17 1 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 S(0.012)KHEEEEWT(0.988)DDDLVESL;S(0.031)KHEEEEWT(0.969)DDDLVESL;S(0.001)KHEEEEWT(0.999)DDDLVESL 172.3 2.62E-09 1474140000 1477220 1576460 1243730 1330170 1365100 1506490 1295240 1036320 1543620 1576070 TRUE FALSE 1419488.609 1531500.904 1468499.678 1398820.233 1409009.681 1536952.26 1311091.535 1014919.63 1368394.729 1469321.375 0.966084502 1.042318536 0.999440764 0.952017889 0.958952687 1.046028654 0.892310938 0.690740397 0.931310707 1 20.48671855 2.031325148 7.262695724 0.827750024 0.991611614 0.27489477 0.082506797 0.160223242 28.13018304 0.030368227 0.022083769 107.4793789 -2.031325148 0.16386159 QKPITPETAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKPITPETAEK 11 1 A0A590UJK8;P60953-1;P60953 A0A590UJK8 CDC42 Cell division control protein 42 homolog 0 112.51 0.0013833 150520000 215180 270520 168280 261520 228930 208470 289970 412610 341540 265760 FALSE TRUE 206770.5277 262805.0345 198691.9394 275017.0785 236293.7414 212685.4062 293518.7396 404089.4593 302769.8111 247759.8385 0.83456031 1.060724918 0.801953781 1.110014764 0.953720921 0.858433746 1.184690551 1.630972404 1.222029417 1 17.91858282 2.031418973 5.81645734 1.367892815 0.948368946 0.433244252 0.175414952 0.123279195 11.97226606 0.064743593 0.046144762 107.5026013 -2.031418973 -0.419523869 VKDS(ph)SPGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKDSSPGEK 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 VKDS(0.771)S(0.229)PGEK 87.184 0.035863 133840000 508510 374120 360530 315250 365380 375970 422240 485120 507870 472350 TRUE FALSE 488636.867 363450.4639 425685.7909 331520.0903 377132.7795 383572.371 427407.4994 475102.1025 450218.7268 440357.3138 1.109637224 0.825353531 0.966682686 0.752843384 0.856424471 0.871048031 0.970592485 1.078901355 1.022394117 1 18.7483151 2.031443961 4.024302705 1.040011827 0.889114259 0.312710862 0.090712374 0.228389089 8.130784878 0.037373563 0.024765506 107.5087868 -2.031443961 -0.150897568 LREENK ddPTM_BT-474_Pertuzumab_2h_R1 4 LREENK 6 1 O95292;Q9HCK0;Q8NHV4-2;Q8NHV4;Q8NHV4-3 O95292;Q8NHV4-2 VAPB;ZBTB26;NEDD1 Vesicle-associated membrane protein-associated protein B/C;Zinc finger and BTB domain-containing protein 26;Protein NEDD1 0 ;;; 115.46 0.022264 3060440000 2256340 3619930 1907760 3715450 2103980 2102710 3115210 3913590 3180290 2355860 FALSE TRUE 2168159.738 3516693.141 2252534.67 3907204.82 2171656.427 2145228.237 3153334.872 3832772.999 2819276.812 2196295.504 0.987189444 1.60119307 1.025606375 1.778997777 0.988781529 0.976748454 1.43575164 1.745108066 1.283650951 1 21.06664075 2.031487876 24.99022869 1.46688982 1.245109457 0.005114298 0.315154919 451.6099124 358416.6039 0.114138624 0.084296283 107.5196585 -2.031487876 -0.221780363 RLQSIGTENTEENRR ddPTM_BT-474_Pertuzumab_2h_R1 5 RLQSIGTENTEENRR 15 2 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;; 259.96 3.93E-25 5794980000 807940 908652 443987 377679 656528 1005088 375751 371701 333108 246181 FALSE TRUE 776364.8116 882738.1346 524225.3273 397171.0585 677645.8194 1025411.568 380349.5531 364025.2445 295294.9763 229506.9416 3.382750893 3.846237192 2.284137132 1.730540504 2.952615789 4.467889123 1.657246402 1.586118668 1.286649433 1 17.80817826 2.031489923 24.44186286 1.422455631 3.038800214 0.574375698 0.72970795 125.2644108 97227.16288 0.293091211 0.216459996 107.5201651 -2.031489923 1.616344583 RNS(ph)RTEEPTVASESVENGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSRTEEPTVASESVENGHR 20 2 Q14686;A0A0D9SFT8;F6M2K2 Q14686 NCOA6 Nuclear receptor coactivator 6 1 RNS(0.497)RT(0.497)EEPT(0.006)VASESVENGHR 217.94 5.34E-25 488250000 163690 176100 73896 101750 154880 164620 103320 88501 83827 86912 TRUE FALSE 157292.8138 171077.8004 87250.65101 107001.3297 159861.8559 167948.7292 104584.4611 86673.42342 74311.31039 81025.37283 1.941278495 2.111410222 1.076831219 1.320590402 1.972985131 2.07279181 1.290761862 1.069707184 0.917136297 1 16.30608613 2.031604844 5.05792983 1.039753614 1.726356329 0.541836379 0.313500871 0.166344196 10.87453081 0.137070734 0.095658521 107.5486204 -2.031604844 0.686602715 EWAMNVGDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EWAMNVGDKK 10 1 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 105.17 0.0041443 4688800000 1744670 1558390 1269450 1276530 1380700 1435480 1625180 1854820 2013270 1860900 FALSE TRUE 1676486.368 1513946.243 1498867.854 1342411.866 1425111.469 1464506.389 1645069.439 1816517.319 1784732.03 1734859.585 0.966352771 0.87266212 0.863970702 0.773787042 0.821456377 0.84416422 0.948243566 1.047068785 1.028747251 1 20.72638747 2.031811617 3.138901009 1.027496411 0.852744419 0.720949976 0.047078615 0.135187888 2.656534253 0.023365658 0.01440469 107.599838 -2.031811617 -0.174751991 EGIREETVSLR ddPTM_BT-474_Pertuzumab_2h_R1 5 EGIREETVSLR 11 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;; 219.43 9.01E-12 8971170000 2386120 2487490 1888220 2148670 2436650 2617690 2266280 2321330 2565480 2446860 FALSE TRUE 2292867.792 2416549.221 2229463.357 2259563.116 2515027.06 2670621.485 2294015.413 2273393.724 2274257.466 2281131.993 1.005144726 1.059364047 0.977349563 0.990544661 1.102534649 1.170743952 1.005647819 0.996607707 0.996986353 1 21.1213185 2.031835672 24.99660102 0.998397498 1.050967879 0.182806046 0.053154568 362.8182799 284874.6993 0.021836587 0.016127294 107.6057979 -2.031835672 0.052570381 RDS(ph)PTYDPYKR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDSPTYDPYKR 11 2 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 RDS(0.999)PT(0.001)YDPYKR;RDS(0.987)PT(0.011)Y(0.002)DPYKR;RDS(0.972)PT(0.028)YDPYKR;RDS(0.988)PT(0.012)YDPYKR 107.14 0.0011673 5264410000 1360970 1183120 1332740 1361100 1315460 1280080 1519780 1724250 1783200 1900630 TRUE FALSE 1307781.788 1149378.576 1573595.765 1431346.534 1357772.966 1305964.095 1538379.522 1688643.635 1580778.612 1771898.637 0.738068059 0.648670613 0.888084528 0.807803846 0.766281398 0.737042214 0.868209665 0.953013677 0.892138285 1 20.75686465 2.031877479 3.445359661 0.939557615 0.766980461 0.640700162 0.062077354 0.163040285 3.973353293 0.028699671 0.018204308 107.6161569 -2.031877479 -0.172577155 GNAEGS(ph)SDEEGKLVIDEPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.582)S(0.418)DEEGKLVIDEPAK;GNAEGS(0.63)S(0.37)DEEGKLVIDEPAK 237.2 8.26E-30 2471000000 1674610 1299590 1352530 1298460 1356630 1328150 1688440 1981210 2180750 1991590 TRUE FALSE 1609164.39 1262526.966 1596962.258 1365473.676 1400267.236 1355006.103 1709103.634 1940297.321 1933200.402 1856697.835 0.866680813 0.679985155 0.86010886 0.735431286 0.75417077 0.729793549 0.920507151 1.045025897 1.041203563 1 20.82430762 2.032009787 3.348410149 1.028314473 0.768855468 0.814987209 0.055475752 0.08959557 2.042371176 0.023475985 0.014765667 107.6489471 -2.032009787 -0.259459005 (ac)GS(ph)ASPGLSSVSPSHLLLPPDTVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 1 GS(0.5)AS(0.5)PGLSSVSPSHLLLPPDTVSR;GS(0.462)AS(0.462)PGLS(0.031)S(0.04)VS(0.004)PSHLLLPPDTVSR;GS(0.497)AS(0.497)PGLS(0.003)S(0.004)VSPSHLLLPPDTVSR 118.71 6.85E-44 877290000 0 8453 5104.7 6313.2 5430.3 10709.9 3236.1 1573.6 2770.4 6801.9 TRUE FALSE 0 8211.928716 6027.232843 6639.025009 5604.970531 10926.46152 3275.70436 1541.10461 2455.915806 6341.201254 0 1.295011526 0.95048755 1.046966457 0.883897278 1.723090165 0.516574735 0.243030389 0.387295042 1 12.63054045 2.032054416 24.99982011 0.439450358 1.004766291 0.182759505 0.445492988 243.7428902 190098.5191 0.158663819 0.11718017 107.6600099 -2.032054416 0.565315933 DCSPSS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DCSPSSPLK 9 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCSPS(0.042)S(0.958)PLK;DCSPS(0.314)S(0.686)PLK 152.69 8.38E-05 802160000 1316590 1183300 1226410 1166680 1290970 1180400 1361740 1502130 1559430 1623230 TRUE FALSE 1265136.207 1149553.443 1448049.568 1226892.495 1332495.222 1204268.497 1378405.381 1471110.491 1382410.044 1513287.186 0.836018582 0.759639976 0.956890127 0.810746635 0.880530302 0.795796401 0.910868336 0.972129087 0.91351467 1 20.52925437 2.032083212 5.263523717 0.955279243 0.842320345 0.513904821 0.053577326 0.147334034 10.72027727 0.020244355 0.014233173 107.6671486 -2.032083212 -0.112958897 EVDDLGPEVGDIK ddPTM_BT-474_Pertuzumab_2h_R1 4 EVDDLGPEVGDIK 13 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;; 251.43 2.65E-18 1484310000 2962680 2848400 2354760 2423050 2708750 2850200 2886150 3455630 3658000 3365520 FALSE TRUE 2846895.19 2767166.421 2780317.513 2548103.901 2795879.404 2907832.997 2921471.567 3384270.033 3242759.176 3137570.333 0.907356613 0.881945623 0.886137112 0.812126464 0.891096966 0.926778586 0.931125443 1.078627624 1.033525573 1 21.58121637 2.032162447 2.029254159 1.044608227 0.877618204 0.794491607 0.034415957 0.132260944 1.025903498 0.019431216 0.010434812 107.6867938 -2.032162447 -0.166990023 DADDAVYELNGK ddPTM_BT-474_Pertuzumab_2h_R1 6 DADDAVYELNGK 12 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 ;;;;; 322.47 1.64E-46 2800600000 4204370 3788380 3938500 3841710 3935890 3882800 4619650 5199030 5723430 5495080 FALSE TRUE 4040058.572 3680339.112 4650274.561 4039981.113 4062491.476 3961312.876 4676186.659 5091668.214 5073730.221 5122893.337 0.788628282 0.718410256 0.90774378 0.788613162 0.793007234 0.77325695 0.912801878 0.993904788 0.990403252 1 22.28852742 2.032299253 2.937483845 0.991609913 0.796093054 0.804392657 0.044537624 0.112646239 1.90776421 0.021345787 0.012897539 107.7207214 -2.032299253 -0.195516859 TPTSS(ph)PASSPLVAK ddPTM_BT-474_Pertuzumab_2h_R1 4 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 TPTS(0.002)S(0.998)PASSPLVAK;TPTS(0.037)S(0.957)PAS(0.004)S(0.001)PLVAK;TPTS(0.023)S(0.976)PAS(0.001)SPLVAK;TPTS(0.003)S(0.994)PAS(0.002)S(0.001)PLVAK 181.76 1.68E-06 1737370000 3623430 4030450 3147290 3550180 3685660 3467080 3412040 3473030 3510190 3521130 TRUE FALSE 3481822.35 3915505.512 3716075.314 3733405.215 3804212.601 3537186.733 3453797.566 3401310.717 3111727.947 3282640.729 1.060677253 1.192791364 1.132038386 1.137317643 1.158887894 1.077543059 1.052139985 1.036150769 0.947934363 1 21.64642543 2.032339473 1.096144627 0.98128874 1.139851401 0.738085132 0.036853617 0.23928624 0.53165418 0.026690892 0.012737061 107.7306978 -2.032339473 0.158562661 AGGGPTLQCPPPSS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGGGPTLQCPPPSSPEK 17 0 Q96N66-3;Q96N66-2;Q96N66 Q96N66-3 MBOAT7 Lysophospholipid acyltransferase 7 1 AGGGPTLQCPPPS(0.02)S(0.98)PEK 155.26 1.13E-07 75307000 96270 131780 65322 131450 85303 80185 125970 163200 163730 104310 TRUE FALSE 92507.66197 128021.7634 77127.13848 138234.1503 88046.84847 81806.39564 127511.6585 159829.863 145144.0568 97244.99079 0.951284598 1.316486972 0.793121968 1.421504071 0.905412688 0.841240201 1.311241407 1.643579393 1.492560754 1 16.56933632 2.032391922 7.945332742 1.457187147 1.052341123 0.283332008 0.243861736 0.213554764 44.36175464 0.087381516 0.063884765 107.743709 -2.032391922 -0.404846024 RFVNVVPTFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFVNVVPTFGK 11 1 P62861;E9PR30 P62861 FAU 40S ribosomal protein S30 0 111.63 0.0026207 331680000 958180 955200 850540 846710 844210 740870 955760 1015300 1051300 1085100 FALSE TRUE 920733.2663 927958.6312 1004251.498 890408.8046 871364.7813 755850.899 967456.8768 994333.7002 931960.8314 1011605.21 0.910170546 0.917313021 0.99273065 0.880193968 0.86136842 0.747179721 0.956358139 0.98292663 0.921269307 1 19.94821494 2.032561149 24.99998039 0.967037069 0.886750534 0.299917843 0.060262194 258.5902156 198540.7485 0.024215044 0.017883887 107.7857007 -2.032561149 -0.080286535 VNDAEPGS(ph)PEAPQGK ddPTM_BT-474_Pertuzumab_2h_R1 4 VNDAEPGSPEAPQGK 15 0 Q8N8A6 Q8N8A6 DDX51 ATP-dependent RNA helicase DDX51 1 VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK 356.83 1.33E-82 3561060000 4583630 4379070 3925040 4097600 4104300 4290080 4741770 5332850 5735910 5593220 TRUE FALSE 4404496.672 4254183.211 4634382.04 4309077.627 4236318.537 4376828.357 4799801.2 5222724.784 5084793.544 5214386.227 0.844681709 0.815855026 0.888768464 0.826382519 0.81242899 0.839375559 0.920492075 1.001599144 0.975147088 1 22.31406602 2.032584135 2.66102906 0.991271121 0.83702152 0.914154237 0.021300723 0.073853026 1.008047457 0.010740198 0.006292019 107.7914056 -2.032584135 -0.154249601 DILLRPELEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 DILLRPELEELR 12 1 P00387-2;P00387;P00387-3 P00387-2 CYB5R3 NADH-cytochrome b5 reductase 3;NADH-cytochrome b5 reductase 3 membrane-bound form;NADH-cytochrome b5 reductase 3 soluble form 0 ; 177.38 2.13E-05 1908790000 1873120 3005900 1781480 3614100 2048550 2029870 2908200 3660400 2852700 2415400 FALSE TRUE 1799916.4 2920174.675 2103433.065 3800624.134 2114443.471 2070915.362 2943791.422 3584811.461 2528873.455 2251802.807 0.799322389 1.29681634 0.934110686 1.687813925 0.939000282 0.919669945 1.307304269 1.591973973 1.123043922 1 21.10264906 2.032644813 23.21084691 1.340495467 1.117287878 0.037299492 0.28101414 181.5163815 129058.844 0.102768802 0.075900999 107.8064667 -2.032644813 -0.223207589 DRGDAYYDTDYRHS(ph)YEYQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRGDAYYDTDYRHSYEYQR 19 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 DRGDAYYDT(0.004)DYRHS(0.996)YEYQR 136.44 3.04E-06 514390000 90954 104440 83033 81624 89491 108230 82163 78667 104470 79750 TRUE FALSE 87399.41713 101461.4735 98038.91016 85836.62442 92369.55929 110418.4848 83168.53537 77042.49896 92611.00357 74348.46147 1.17553767 1.364674823 1.318640739 1.15451783 1.242386964 1.485148214 1.118631559 1.036235282 1.245634432 1 16.18201527 2.032701051 24.97968065 1.092845278 1.287780051 0.434350881 0.10649251 169.3992474 129400.012 0.039021936 0.028819431 107.8204279 -2.032701051 0.194934773 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHK 35 0 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 170.37 3.76E-15 345190000 552270 566700 473160 558270 506780 484140 590730 644810 706010 699430 FALSE TRUE 530686.6778 550538.2709 558670.5374 587082.3816 523081.0389 493929.6425 597959.5304 631494.4482 625866.7046 652056.9831 0.813865493 0.84431006 0.856781772 0.900354412 0.802201422 0.757494598 0.917035698 0.968465126 0.959834372 1 19.31463852 2.032709101 6.262503157 0.965754448 0.8329737 0.765616938 0.036740104 0.092238591 10.78166749 0.015199519 0.010936627 107.8224265 -2.032709101 -0.132780748 LAENFCVCHLATGDMLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LAENFCVCHLATGDMLR 17 0 F8W1A4;P54819-2;P54819;P54819-3;P54819-5;F8VZG5;A0A5F9ZHP2;G3V213 F8W1A4 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 0 ;; 204.29 8.92E-12 2180632000 676506 797202 667230 782194 647406 693993 687872 623589 649422 659610 FALSE TRUE 650067.3976 774466.5795 787813.3035 822563.1261 668230.4019 708026.014 696290.3833 610711.6692 575702.3372 614934.0272 1.05713356 1.259430354 1.281134672 1.337644511 1.086670069 1.151385324 1.13230095 0.993133641 0.93620179 1 19.23007211 2.032729353 1.05400467 0.956610574 1.222768126 0.593068039 0.081475117 0.351264178 0.720796466 0.064394609 0.030853118 107.8274545 -2.032729353 0.266157552 DFDDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFDDEK 6 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ; 97.068 0.09653 1319420000 2464100 1970110 2022560 1751900 1969850 1808130 2372700 2599100 2949400 2918400 FALSE TRUE 2367800.248 1913924.392 2388081.584 1842315.769 2033212.014 1844691.627 2401737.812 2545427.677 2614596.477 2720734.169 0.870279895 0.703458799 0.877734257 0.677139204 0.747302709 0.678012446 0.882753574 0.935566475 0.960989319 1 21.37556457 2.032774944 4.148083866 0.950081908 0.75771003 0.651350637 0.068119885 0.130694681 5.007850203 0.027575095 0.018450007 107.8387744 -2.032774944 -0.192371878 KSS(ph)PSVKPAVDPAAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSPSVKPAVDPAAAK 16 2 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7 Q6FI81-3 CIAPIN1 Anamorsin 1 KS(0.227)S(0.736)PS(0.037)VKPAVDPAAAK 162.83 6.25E-09 879750000 2187300 1602000 1745200 1388600 1706200 1981300 2389600 2632100 3102200 3159700 TRUE FALSE 2101817.898 1556312.529 2060596.462 1460265.812 1761081.473 2021363.243 2418844.64 2577746.215 2750051.261 2945690.705 0.713522942 0.52833535 0.699529132 0.495729511 0.597850097 0.68621028 0.821146849 0.875090589 0.933584526 1 21.49017453 2.032912238 1.199507107 0.961987154 0.599106888 0.831599036 0.066115947 0.173370246 0.463016193 0.046268311 0.022062852 107.8728711 -2.032912238 -0.362880265 SKPIPIMPAS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKPIPIMPASPQK 13 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 1 SKPIPIMPAS(1)PQK;SKPIPIMPAS(1)PQK;SKPIPIMPAS(1)PQK;SKPIPIMPAS(1)PQK 230.96 8.48E-12 2686040000 2899990 2563940 2673020 2479240 2520950 2222390 3049310 3539170 3419910 3680060 TRUE FALSE 2786655.185 2490818.942 3156094.175 2607193.874 2602038.646 2267328.248 3086628.368 3466084.903 3031696.154 3430806.258 0.812244987 0.726015623 0.919927835 0.759936201 0.758433572 0.660873299 0.899680173 1.010282902 0.883668714 1 21.71011623 2.032937904 8.734251443 0.963190435 0.77630161 0.614732767 0.069470987 0.168856531 40.93131272 0.025991306 0.019072147 107.8792463 -2.032937904 -0.186888825 RVVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_BT-474_Pertuzumab_2h_R1 5 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.004)S(0.113)T(0.126)T(0.756)PGGT(0.004)LFS(0.016)T(0.248)T(0.728)PGGT(0.005)R;RVVLGDGVQLPPGDYS(0.016)T(0.274)T(0.709)PGGT(0.001)LFS(0.037)T(0.096)T(0.788)PGGT(0.078)R;RVVLGDGVQLPPGDYS(0.008)T(0.049)T(0.94)PGGT(0.004)LFS(0.021)T(0.285)T(0.694)PGGTR;RVVLGDGVQLPPGDY(0.012)S(0.024)T(0.075)T(0.878)PGGT(0.012)LFS(0.031)T(0.075)T(0.886)PGGT(0.006)R;RVVLGDGVQLPPGDY(0.004)S(0.109)T(0.122)T(0.764)PGGT(0.002)LFS(0.05)T(0.044)T(0.9)PGGT(0.005)R 171.45 1.52E-14 5211170000 3004388 3082297 2241929 2448581 2654630 3216110 2398430 2455181 2672750 2371849 TRUE FALSE 2886973.195 2994392.907 2647095.442 2574952.559 2740018.585 3281141.948 2427782.704 2404480.654 2369350.625 2211201.555 1.305612864 1.354192657 1.197129875 1.164503776 1.239153699 1.483872848 1.097947267 1.087409083 1.07152178 1 21.0763991 2.032971893 24.92159045 1.070186272 1.282091674 0.623161343 0.086360322 129.4847997 97869.70813 0.033496229 0.02473846 107.8876896 -2.032971893 0.211905402 PLPS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 5 PLPSPPK 7 0 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 1 PLPS(1)PPK;PLPS(1)PPK;PLPS(1)PPK;PLPS(1)PPK;PLPS(1)PPK 71.223 0.057587 1911000000 3324010 2538100 2916820 2700840 3027390 2689860 3585370 4262400 4618020 4302950 TRUE FALSE 3194104.014 2465715.873 3443954.258 2840230.676 3124768.749 2744250.812 3629248.831 4174379.95 4093801.73 4011507.364 0.796235361 0.614660687 0.858518743 0.708020806 0.778951268 0.684094671 0.904709502 1.040601343 1.020514574 1 21.93571301 2.032977461 3.627482921 1.018201659 0.740517074 0.799219936 0.063542445 0.090447644 2.489188229 0.026076278 0.016817449 107.8890728 -2.032977461 -0.277684585 KNGSTAVAESVAS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 3 KNGSTAVAESVASPQK 16 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK 195.09 6.65E-11 3863970000 2830570 2477230 2277370 2304220 2385530 2458680 2746820 3132900 3274360 3254880 TRUE FALSE 2719948.195 2406581.826 2688941.419 2423141.07 2462262.739 2508396.194 2780436.405 3068204.52 2902668.38 3034424.078 0.896363898 0.793093438 0.886145558 0.798550568 0.811443185 0.82664655 0.916297898 1.011132406 0.956579669 1 21.53299129 2.03300056 3.201372245 0.987940189 0.833063972 0.799121072 0.034685257 0.097992222 2.014133804 0.015090184 0.009372786 107.8948113 -2.03300056 -0.154876216 YIDQEELNK ddPTM_BT-474_Pertuzumab_2h_R1 6 YIDQEELNK 9 0 P08238;P07900;P07900-2;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ;;;;; 222.42 8.93E-07 16554440000 13876600 13130000 11770300 11978400 12802800 12871400 13820700 15650600 16503900 15207900 FALSE TRUE 13334287.13 12755545.26 13897455.04 12596606.66 13214613.69 13131668.53 13989841.86 15327409.64 14630446.46 14177855.39 0.940500997 0.899680869 0.980222654 0.888470528 0.932060127 0.926209795 0.98673893 1.081080969 1.031922393 1 23.75713598 2.033069503 3.672276053 1.045131206 0.927703881 0.730927546 0.029873816 0.100488546 2.84791994 0.012307184 0.007966607 107.9119407 -2.033069503 -0.117427325 LALFNPDVCWDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LALFNPDVCWDR 12 0 O00483 O00483 NDUFA4 Cytochrome c oxidase subunit NDUFA4 0 87.298 0.024723 150630000 335990 342910 276700 318060 324970 296310 356420 400220 435490 388630 FALSE TRUE 322859.1393 333130.5425 326705.8452 334475.1147 335422.9552 302301.5912 360781.9746 391955.3171 386055.0009 362307.7439 0.891118517 0.919468458 0.90173575 0.923179591 0.92579571 0.834377946 0.995788748 1.081829808 1.065544437 1 18.46685612 2.033122446 5.832687028 1.054050958 0.90286511 0.824526573 0.031508532 0.063076253 6.035837864 0.011828277 0.008447867 107.9250967 -2.033122446 -0.151185848 YWGPAS(ph)PTHKLPPSFPGNKDELMQHMDEVNDELIR ddPTM_BT-474_Pertuzumab_2h_R1 1 YWGPASPTHKLPPSFPGNKDELMQHMDEVNDELIR 35 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.899)PT(0.101)HKLPPSFPGNKDELMQHMDEVNDELIR 261.89 2.23E-60 529510000 253270 268410 183390 185340 217500 276590 176910 137080 180790 147010 TRUE FALSE 243371.9284 260755.2096 216532.6525 194905.4196 224496.085 282182.8393 179075.0775 134249.2501 160267.4771 137052.8818 1.775751996 1.902588302 1.579920464 1.422118361 1.63802528 2.058934009 1.306613004 0.979543432 1.169384219 1 17.06437314 2.033409537 6.591891194 1.06937654 1.712247317 0.766519498 0.170618576 0.088308907 11.66738294 0.069006409 0.04991221 107.9964642 -2.033409537 0.642870777 TEESPAS(ph)DEAGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEESPAS(1)DEAGEK;TEESPAS(1)DEAGEK 315.43 1.03E-50 328781000 709580 516890 651700 633410 661850 513220 769550 942580 897080 878180 TRUE FALSE 681848.8291 502148.8033 769476.687 666100.366 683139.0063 523597.66 778967.9831 923115.3936 795247.2393 818700.0864 0.832843236 0.613348907 0.939876152 0.813607299 0.834419121 0.639547581 0.951469282 1.127537921 0.971353555 1 19.64297552 2.033410011 7.635755833 1.04547433 0.78328005 0.589237547 0.097148874 0.128108694 23.90386098 0.035736571 0.026093999 107.9965821 -2.033410011 -0.26219428 NSSNTS(ph)VGSPSNTIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSNTSVGSPSNTIGR 16 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 NSSNT(0.023)S(0.818)VGS(0.158)PS(0.001)NTIGR 99.451 0.0029391 0 72088 75325 67469 68014 71660 82418 79243 91149 105880 99373 TRUE FALSE 69270.72126 73176.80475 79662.14914 71524.21069 73965.00898 84084.54843 80212.79954 89266.7413 93860.94629 92642.3782 0.747721751 0.789884782 0.859888862 0.772046358 0.798392814 0.907625107 0.86583269 0.963562713 1.013153463 1 16.49938467 2.033555476 0.813151419 1.016216864 0.78959815 0.849626601 0.035486069 0.226520707 0.279541292 0.03010217 0.015650308 108.0327612 -2.033555476 -0.226618715 SSLFPFEDAFLDDSHGDQALSSGLSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALSSGLS(0.062)S(0.933)PT(0.005)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.307)S(0.614)PT(0.079)R 318.18 1.65E-92 450900000 170182 192161 155143 201048 190434 184000 163081 143973 160575 160762 TRUE FALSE 163531.0993 186680.7564 183180.7912 211424.1114 196559.4826 187720.6061 165076.8341 140999.9072 142347.1992 149873.4465 1.091127902 1.245589267 1.222236463 1.410684256 1.311503052 1.252527452 1.101441502 0.940793119 0.94978265 1 17.19338527 2.033580667 2.615129872 0.959444604 1.264433743 0.746553258 0.076518665 0.141395489 1.860067086 0.040442618 0.023586653 108.0390278 -2.033580667 0.304989139 NKEDFEK ddPTM_BT-474_Pertuzumab_2h_R1 4 NKEDFEK 7 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ;;; 93.467 0.013601 1471880000 3581300 3123280 2767870 2578570 3041470 3284260 3397290 3978380 4493740 4044100 FALSE TRUE 3441338.837 3034207.112 3268085.68 2711650.307 3139301.645 3350669.987 3438867.051 3896225.063 3983629.474 3770189.505 0.91277609 0.804789019 0.866822656 0.719234485 0.832664151 0.888727207 0.912120477 1.033429502 1.056612531 1 21.84620561 2.033956063 1.583637815 1.039292838 0.825053561 0.748457453 0.050171676 0.181063031 0.851557627 0.031777901 0.015880325 108.132455 -2.033956063 -0.214239277 EVVNKDVLDVYIEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVVNKDVLDVYIEHR 15 1 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ;;; 143.02 2.69E-06 852800000 1875220 1976420 1427900 1551080 1740400 1957940 1686940 1660920 1994560 1887480 FALSE TRUE 1801934.329 1920054.437 1685953.293 1631131.425 1796381.547 1997530.888 1707585.276 1626621.422 1768145.911 1759639.298 1.024036194 1.091163648 0.95812437 0.926969195 1.020880557 1.135193383 0.970417788 0.924406168 1.004834293 1 20.7468483 2.033971267 24.99999728 0.962863362 1.023827124 0.139664468 0.059382937 319.4365192 235077.1398 0.023628736 0.017450889 108.1362407 -2.033971267 0.060963761 ENEVEEVKEEGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENEVEEVKEEGPK 13 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 86.497 0.0069719 527300000 384340 291920 334180 331240 339880 304720 426090 496750 550520 530960 FALSE TRUE 369319.5679 283594.7274 394573.7598 348335.3361 350812.5489 310881.6472 431304.6169 486491.9389 488027.2776 494997.6063 0.746103745 0.572921412 0.797122561 0.703711153 0.708715647 0.628046769 0.871326672 0.982816751 0.98591846 1 18.91706202 2.033979681 3.449601482 0.980709019 0.693617095 0.839494992 0.058706296 0.087133753 2.127678487 0.025479611 0.016209526 108.1383356 -2.033979681 -0.287091924 QEKPAEKPAETPVATSPTATDSTSGDSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;;; 334.06 1.70E-105 13166990000 6660550 5408490 5143030 4878600 5275840 5523210 6627180 7614430 8459660 8112520 FALSE TRUE 6400248.342 5254245.161 6072489.927 5130385.131 5445542.185 5634893.09 6708285.411 7457189.36 7499354.863 7563051.795 0.846252084 0.694725529 0.80291529 0.678348538 0.720019158 0.745055467 0.886981287 0.986002683 0.99157788 1 22.85053707 2.034036832 2.339813202 0.992279888 0.742031073 0.847786108 0.046805878 0.103302681 1.074688189 0.023551791 0.013261392 108.152567 -2.034036832 -0.250248815 NLS(ph)FEIK ddPTM_BT-474_Pertuzumab_2h_R1 6 NLSFEIK 7 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 NLS(1)FEIK;NLS(1)FEIK;NLS(1)FEIK;NLS(1)FEIK;NLS(1)FEIK;NLS(1)FEIK 112.85 0.0065693 2797610000 3403690 2922940 1726880 2339860 3950370 2659240 3613670 4947470 4718860 3719030 TRUE FALSE 3270670.032 2839580.613 2038965.63 2460620.455 4077437.239 2713011.655 3657895.174 4845303.016 4183194.796 3467136.786 0.943334582 0.818998727 0.588083412 0.709698119 1.176024337 0.782493401 1.055018997 1.397494046 1.206527188 1 21.72531332 2.034067387 4.418328439 1.243448244 0.836074279 0.477538766 0.171279532 0.157983626 7.085001949 0.072418031 0.049292518 108.1601764 -2.034067387 -0.407373965 YQEEFEHFQQELDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 YQEEFEHFQQELDKK 15 1 P49257 P49257 LMAN1 Protein ERGIC-53 0 180.64 4.03E-07 108380000 135260 177960 121150 134750 136580 88786 168780 172510 211660 191350 FALSE TRUE 129973.8897 172884.755 143044.5 141704.4636 140973.2197 90581.31375 170845.5801 168947.6082 187633.2442 178389.6941 0.728595283 0.969140936 0.801865269 0.79435342 0.790254283 0.507772123 0.957709923 0.947070452 1.051816615 1 17.44467274 2.034083609 24.99972176 0.983408909 0.774876586 0.502854512 0.109016037 164.7019402 120805.291 0.041816147 0.030883126 108.1642167 -2.034083609 -0.208532323 (ac)S(ph)TGGDFGNPLRK ddPTM_BT-474_Pertuzumab_2h_R1 4 STGGDFGNPLRK 12 1 P20340-2;P20340;P20340-3;F5H3K7;F5GX61 P20340-2;F5GX61 RAB6A Ras-related protein Rab-6A 1 S(0.5)T(0.5)GGDFGNPLRK;S(0.986)T(0.014)GGDFGNPLRK;S(0.957)T(0.043)GGDFGNPLRK;S(0.5)T(0.5)GGDFGNPLRK 124.92 6.59E-05 984620000 1285560 1528230 982750 1306910 1345550 1324090 1484430 1838190 1848330 1645210 TRUE FALSE 1235318.894 1484646.377 1160354.786 1374359.782 1388830.838 1350864.007 1502596.898 1800230.734 1638515.327 1533778.461 0.805408946 0.967966635 0.756533499 0.896061469 0.905496376 0.880742585 0.9796701 1.17372279 1.068286828 1 20.54865868 2.034119949 3.522361064 1.097327488 0.871482439 0.663112515 0.067521619 0.122384977 3.138249409 0.028358194 0.018156995 108.1732677 -2.034119949 -0.225845049 KLFIGGLSFETTDDSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLFIGGLSFETTDDSLR 17 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 263.09 3.56E-27 1713410000 1462270 1491190 983360 1156100 1330170 1468980 1186120 1189680 1347430 1275460 FALSE TRUE 1405122.872 1448662.721 1161075.027 1215766.46 1372956.126 1498683.782 1200636.091 1165112.692 1194475.395 1189071.958 1.181697089 1.218313754 0.976454805 1.022449862 1.154645114 1.260381066 1.009725343 0.979850449 1.004544247 1 20.18140459 2.034247446 24.94601073 0.993116455 1.12849154 0.413905548 0.079807072 191.1368309 139224.2902 0.032377212 0.02391205 108.2050291 -2.034247446 0.135375085 DKDVTLS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKDVTLSPVK 10 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 DKDVTLS(1)PVK;DKDVT(0.002)LS(0.998)PVK;DKDVT(0.001)LS(0.999)PVK;DKDVT(0.013)LS(0.987)PVK 129.93 0.00017567 2321490000 4048140 3321590 3613660 2696990 3116130 2074720 3700240 3750780 4343950 4501160 TRUE FALSE 3889934.213 3226861.505 4266728.747 2836181.977 3216363.151 2116672.26 3745524.644 3673325.082 3850843.007 4196292.424 0.926993122 0.76897918 1.016785371 0.675878059 0.766477363 0.504414861 0.892579512 0.875373952 0.917677468 1 22.00068379 2.034303902 24.99998706 0.908872258 0.775154112 0.222860184 0.131989991 307.7001808 224244.4276 0.050374013 0.037203497 108.219096 -2.034303902 -0.133718146 RTHS(ph)DAS(ph)DDEAFTTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTHSDASDDEAFTTSK 16 1 Q13017-2;Q13017;H0YK04 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 RT(0.321)HS(0.684)DAS(0.996)DDEAFTTSK 89.201 0.020545 505680000 361730 361680 245250 309520 317010 350740 294970 263580 352340 302190 TRUE FALSE 347593.1917 351365.2405 289572.1306 325494.3643 327206.9146 357832.2031 298579.9311 258136.9809 312343.8403 281722.4021 1.233814525 1.247203765 1.027863345 1.155372671 1.161451528 1.270158853 1.059837375 0.916281343 1.108693657 1 18.10391476 2.034394461 7.830535395 0.996202797 1.175796756 0.519796772 0.076776291 0.161277748 30.90200748 0.029357602 0.021472211 108.2416642 -2.034394461 0.179593959 AHATGAGPAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHATGAGPAGR 11 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ; 76.228 0.035927 31665000 19775.1 23470 17010.5 29683 19969.9 21548 20790 16349.9 19510.7 27338 FALSE TRUE 19002.26723 22800.65858 20084.67575 31214.94319 20612.24997 21983.71532 21044.43424 16012.26885 17295.92713 25486.37291 0.745585388 0.894621556 0.788055476 1.224769931 0.808755724 0.862567436 0.825713189 0.628267855 0.678634311 1 14.63743845 2.034511755 3.792122029 0.727032326 0.894163578 0.084977961 0.154383706 0.369469292 11.29460646 0.065109847 0.04261339 108.2709021 -2.034511755 0.167131252 YDLIQNSESPAS(ph)PPVAVPHSWSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDLIQNSESPASPPVAVPHSWSR 23 0 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 YDLIQNSESPAS(1)PPVAVPHSWSR;YDLIQNSES(0.001)PAS(0.999)PPVAVPHSWSR 202.14 1.37E-24 584380000 226420 284080 225820 281740 285300 292070 235120 207798 230960 252890 TRUE FALSE 217571.2561 275978.3165 266630.6973 296280.6352 294476.9336 297975.8555 237997.4689 203506.8987 204742.3891 235761.535 0.922844585 1.170582455 1.130933837 1.256696242 1.249045709 1.263886645 1.009483879 0.863189573 0.868429997 1 17.84696883 2.034602873 4.845342308 0.903148953 1.171526954 0.577822807 0.098930834 0.130214034 7.415392331 0.040858116 0.028386439 108.2936203 -2.034602873 0.268378001 TFLEFYEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TFLEFYEEK 9 0 O43148;O43148-2;K7EP06 O43148 RNMT mRNA cap guanine-N7 methyltransferase 0 ; 116.3 0.0031067 39488000 91929 91467 80498 79917 92562 71976 93099 102407 98430 100114 FALSE TRUE 88336.31305 88858.45072 95045.77927 84041.52595 95539.34079 73431.40403 94238.37341 100292.2597 87256.63905 93333.18961 0.946461954 0.952056295 1.018349203 0.900446307 1.023637371 0.786766255 1.009698413 1.07456158 0.934894001 1 16.51010258 2.034628091 24.9999974 1.019110272 0.940587758 0.168992471 0.069939213 259.6822829 187478.3874 0.025192003 0.018605477 108.2999088 -2.034628091 -0.078522514 SSDITSDLGNVLTST(ph)PNAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSDITSDLGNVLTSTPNAK 19 0 B7Z2R7;Q5T8D3-4;Q5T8D3-2;Q5T8D3-3 B7Z2R7 ACBD5 Acyl-CoA-binding domain-containing protein 5 1 SSDITSDLGNVLTS(0.096)T(0.903)PNAK;SSDITSDLGNVLTS(0.016)T(0.984)PNAK;SSDITSDLGNVLTS(0.004)T(0.996)PNAK 322.43 4.63E-61 767710000 517576 758200 490898 831450 436643 610838 762460 1073530 841180 864240 TRUE FALSE 497348.5577 736576.8784 579614.1886 874361.2341 450688.0186 623189.5629 771791.2136 1051361.23 745692.7729 805704.255 0.617284264 0.914202542 0.719388268 1.085213624 0.559371526 0.773471853 0.957908822 1.304897205 0.925516737 1 19.61989085 2.0346612 4.773295758 1.116312435 0.788490916 0.390884803 0.166477519 0.169035181 9.24857342 0.064380438 0.044598917 108.3081655 -2.0346612 -0.32782152 IDCDNLEQYFIQQGGGPDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDCDNLEQYFIQQGGGPDKK 20 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 206.34 1.24E-21 249960000 136240 109230 92160 79237 103520 81146 122740 145140 140460 149180 FALSE TRUE 130915.5902 106114.8673 108815.3621 83326.43107 106849.8148 82786.82772 124242.1288 142142.8083 124515.5697 139075.9057 0.941324736 0.76299965 0.782417066 0.599143544 0.768284156 0.595263624 0.893340426 1.022052005 0.895306552 1 17.08551298 2.034766804 8.561046231 0.97074535 0.739231117 0.543697071 0.096776846 0.184889894 41.2193124 0.036294985 0.026636117 108.3345052 -2.034766804 -0.231514233 PLEGSSSEDSPPEGQAPPSHS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 PLEGSSSEDSPPEGQAPPSHSPR 23 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 PLEGSSSEDSPPEGQAPPS(0.117)HS(0.883)PR 164.2 9.39E-12 553070000 248550 229000 235030 243720 242120 227960 262690 279940 315810 301950 TRUE FALSE 238836.3912 222469.1442 277505.1492 256298.4184 249908.0097 232569.5074 265904.8788 274159.1412 279960.5728 281498.6576 0.848445933 0.790302683 0.985813402 0.910478297 0.887776915 0.826183362 0.944604429 0.973926993 0.994536085 1 18.10276852 2.034947964 4.983044241 0.980988675 0.878173258 0.520400913 0.049712231 0.172232004 10.54113955 0.020912229 0.014611997 108.379705 -2.034947964 -0.102815417 QHEAPSNRPLNELLT(ph)PQGPSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 QHEAPSNRPLNELLT(1)PQGPSPR;QHEAPSNRPLNELLT(1)PQGPSPR 116.94 0.00021565 283680000 138451 162408 132649 141846 149176 158999 120051 82527 114963 128867 TRUE FALSE 133040.1819 157776.2829 156621.6251 149166.6891 153974.3815 162214.0687 121520.22 80822.78861 101912.8822 120138.7233 1.107388011 1.313284164 1.303673127 1.241620395 1.281638237 1.350223011 1.011499179 0.672745526 0.848293368 1 16.87434171 2.035004962 4.461120518 0.809774729 1.267600319 0.796409882 0.097269251 0.073940234 3.385818811 0.038184004 0.026079104 108.3939299 -2.035004962 0.45782559 WEVEEMK ddPTM_BT-474_Pertuzumab_2h_R1 2 WEVEEMK 7 0 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85 P27824 CANX Calnexin 0 ; 117.02 0.012389 231140000 178765 225470 178587 268340 191169 149504 269220 356520 310830 239150 FALSE TRUE 171778.6662 219039.8164 210861.6435 282189.0596 197318.1245 152527.0733 272514.7949 349157.7374 275545.8815 222952.1575 0.770473218 0.982452105 0.945770814 1.265693334 0.885024513 0.68412468 1.222301672 1.566065749 1.235896905 1 17.76637463 2.035008774 10.25830746 1.346212772 0.940792882 0.391557652 0.196390668 0.364815655 104.125619 0.07348634 0.054135451 108.3948814 -2.035008774 -0.40541989 GNDS(ph)DGEGESDDPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNDSDGEGESDDPEK 15 0 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 GNDS(1)DGEGESDDPEK;GNDS(1)DGEGESDDPEK 360.81 5.77E-83 1344970000 1428570 1197230 1543350 1745670 1558600 1330770 1930570 2172950 2504200 2424500 TRUE FALSE 1372739.905 1163086.173 1822267.677 1835764.238 1608733.784 1357679.081 1954196.893 2128077.823 2219933.714 2260286.455 0.607330058 0.514574677 0.806210944 0.812182117 0.711738895 0.600666822 0.864579305 0.941508019 0.982147068 1 21.10807419 2.03501745 3.428875612 0.960680237 0.682202588 0.70231808 0.08816882 0.153188552 3.686699844 0.043320905 0.027544455 108.3970467 -2.03501745 -0.27847765 IINEPTAAAIAYGLDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 IINEPTAAAIAYGLDKK 17 1 P11142;E9PKE3;P11142-2;E9PN89;E9PI65;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ; 221.41 5.92E-15 2986000000 3207500 2968100 2451400 2402900 2609700 2116150 3140400 3190200 3909200 3507100 FALSE TRUE 3082147.354 2883452.694 2894422.511 2526913.957 2693643.371 2158940.003 3178833.155 3124321.255 3465444.005 3269560.993 0.942679265 0.881908213 0.885263348 0.77286032 0.823854755 0.66031495 0.972250758 0.955578214 1.059911105 1 21.64066551 2.035180677 24.9996433 0.991149272 0.829045528 0.548887481 0.075228378 143.8094551 102191.4519 0.029281863 0.021626031 108.4377947 -2.035180677 -0.162103743 S(ph)LVGTPYWMAPEVISR ddPTM_BT-474_Pertuzumab_2h_R1 5 SLVGTPYWMAPEVISR 16 0 Q9NQU5-2;Q9NQU5 Q9NQU5-2 PAK6 Serine/threonine-protein kinase PAK 6 1 S(1)LVGTPYWMAPEVISR;S(1)LVGTPYWMAPEVISR;S(1)LVGTPYWMAPEVISR;S(1)LVGTPYWMAPEVISR;S(1)LVGTPYWMAPEVISR 345.69 4.76E-87 520136000 379165 331416 241467 324863 266154 302329 370697 441761 505617 403102 TRUE FALSE 364346.8126 321964.3402 285105.4583 341629.2184 274715.0851 308442.2995 375233.7008 432638.481 448221.4779 375799.5425 0.969524364 0.856744897 0.758663665 0.909073002 0.731014954 0.820762839 0.998494299 1.151248025 1.192714272 1 18.51960378 2.035184978 3.167845813 1.125831575 0.836271864 0.708964667 0.079108854 0.125478731 2.518282374 0.035945598 0.022310709 108.4388687 -2.035184978 -0.289559711 EKEEEEQRR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEEEEQRR 9 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 88.496 0.0071683 294250000 490050 460210 368820 385750 453170 448750 471760 507600 572950 549240 FALSE TRUE 470898.3042 447085.2614 435473.9784 405658.6037 467746.6246 457824.0325 477533.54 497117.8826 507911.118 512039.4856 0.919652327 0.873146064 0.850469526 0.792240863 0.913497177 0.894118609 0.932610772 0.970858492 0.991937404 1 18.96589554 2.035247257 1.07843333 0.998650739 0.863172071 0.72187361 0.032512773 0.274638424 0.590503257 0.025921122 0.012412072 108.4544203 -2.035247257 -0.135478669 RHS(ph)ASNLHALAHPAPSPGSCSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RHSASNLHALAHPAPSPGSCSPK 23 1 P47974 P47974 ZFP36L2 "Zinc finger protein 36, C3H1 type-like 2" 1 RHS(0.5)AS(0.5)NLHALAHPAPSPGSCSPK 95.794 0.0014422 651340000 386690 457200 319500 365030 361820 406520 269700 16454 399940 264660 TRUE FALSE 371577.7273 444161.1036 377240.7572 383869.242 373458.2689 414740.1129 273000.6693 16114.21915 354540.4879 246734.3425 1.505983008 1.800159229 1.528934941 1.555799806 1.513604734 1.680917657 1.106455901 0.065309997 1.436932064 1 17.91259901 2.035345312 5.345763887 0.694970891 1.589150367 0.508021784 0.33404133 0.117428487 8.641692631 0.126742896 0.089647999 108.4789098 -2.035345312 0.894179476 VVTSTDVAK ddPTM_BT-474_Pertuzumab_2h_R1 3 VVTSTDVAK 9 0 Q5T5Q6;P51801-2;P51801 Q5T5Q6 CLCNKB Chloride channel protein ClC-Kb 0 ;; 92.47 0.02339 1675930000 1008790 1030640 906180 964620 959620 865470 1076120 1135460 1240530 1164710 FALSE TRUE 969365.3715 1001247.156 1069946.884 1014404.154 990487.0488 882970.3964 1089289.878 1112012.354 1099710.235 1085823.154 0.892747007 0.922108865 0.985378585 0.934225937 0.912199233 0.813180667 1.003192715 1.024119213 1.01278945 1 20.05035772 2.035535276 24.99969285 1.014651161 0.914575226 0.59163286 0.04065312 125.8544089 88540.26998 0.015985585 0.011806105 108.5263698 -2.035535276 -0.100075935 EAFSLFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAFSLFDK 8 0 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479;P27482 P0DP25 CALM2;CALM3;CALM1;CALML3 Calmodulin-like protein 3 0 ; 122.52 0.0032269 990650000 666620 614640 615980 797400 662050 589880 790660 911100 921360 990140 FALSE TRUE 640567.7534 597111.069 727301.2884 838553.9096 683345.4395 601807.7778 800336.3336 892285.4666 816771.0755 923076.9359 0.69394839 0.646870316 0.787909718 0.908433389 0.740290883 0.651958417 0.867031016 0.966642575 0.884835319 1 19.81609137 2.035630872 5.805165674 0.940259212 0.744420711 0.619248234 0.075409829 0.131675742 12.03409713 0.0315406 0.022567111 108.5502609 -2.035630872 -0.195838501 LVPLLDTGDIIIDGGNSEYRDTTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVPLLDTGDIIIDGGNSEYRDTTR 24 1 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 205.02 9.31E-25 398184000 127966 152887 68263 102037 120229 147188 95201 97797 106729 87538 FALSE TRUE 122964.9472 148526.8125 80599.6426 107303.1418 124096.275 150164.2422 96366.09832 95777.45777 94613.57136 81608.97329 1.50675768 1.819981388 0.987632111 1.314844894 1.520620466 1.840045722 1.180827235 1.173614296 1.159352551 1 16.31644017 2.035753754 24.99695859 1.142014466 1.484733479 0.378807266 0.231915946 206.0481822 144056.1355 0.090301681 0.066691996 108.5809792 -2.035753754 0.342719013 CALSSPSLAFT(ph)PPIK ddPTM_BT-474_Pertuzumab_2h_R1 2 CALSSPSLAFTPPIK 15 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 CALSSPSLAFT(1)PPIK;CALSSPSLAFT(1)PPIK 167.55 1.46E-05 342560000 519760 530220 425610 498440 484620 504660 529150 611970 572480 620270 TRUE FALSE 499447.2046 515098.6447 502527.1946 524164.5481 500208.2424 514864.571 535625.896 599332.6056 507494.4704 578258.5604 0.863709141 0.89077565 0.869035461 0.90645359 0.865025227 0.890370859 0.926274045 1.036443983 0.877625521 1 19.14135519 2.035828038 4.291688433 0.976975792 0.881998014 0.510675508 0.039537297 0.146898648 6.076034857 0.015455395 0.010470005 108.5995531 -2.035828038 -0.094977778 VTGPPPGT(ph)PQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTGPPPGTPQPR 12 0 F5GYK2;Q9NRL3;Q9NRL3-3;R4GN16;M0QZM0 F5GYK2 STRN4 Striatin-4 1 VTGPPPGT(1)PQPR;VTGPPPGT(1)PQPR 156.08 0.00081472 680750000 304700 373620 313320 369890 366210 370920 267860 233800 214950 249300 TRUE FALSE 292791.9871 362964.7234 369943.8938 388980.0672 377989.4772 378420.2565 271138.1508 228971.9483 190549.7771 232414.6889 1.259782626 1.561711633 1.591740589 1.673646657 1.626357951 1.628211445 1.16661366 0.985187078 0.819869768 1 17.82634173 2.035955982 2.606355176 0.93543965 1.568406382 0.848280531 0.119211413 0.103679001 1.355615173 0.061391188 0.035854278 108.6315514 -2.035955982 0.632966733 NYTDEAIETDDLTIK ddPTM_BT-474_Pertuzumab_2h_R1 3 NYTDEAIETDDLTIK 15 0 O14818;H0Y586;O14818-2 O14818 PSMA7 Proteasome subunit alpha type-7 0 ;; 408.28 1.20E-132 653721000 1089970 965620 837877 891943 959407 996710 1074040 1239070 1381350 1251430 FALSE TRUE 1047372.767 938081.463 989300.0124 937976.2851 990267.1975 1016864.159 1087184.423 1213482.771 1224544.939 1166669.531 0.897745882 0.804067851 0.847969357 0.803977699 0.848798371 0.87159571 0.931870074 1.040125536 1.04960737 1 20.15396453 2.03617097 1.881498284 1.03715934 0.838250965 0.892173081 0.028754463 0.093073845 0.620143543 0.015926028 0.008382512 108.6853405 -2.03617097 -0.198908374 AFGFSHLEALLDDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AFGFSHLEALLDDSK 15 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 237.21 9.91E-18 6654600000 9611200 8351100 8353300 8339100 9311100 7136400 9841300 10212000 11409100 11220200 FALSE TRUE 9235583.678 8112934.805 9862927.128 8769481.95 9610599.988 7280702.898 9961740.773 10001118.63 10113986.8 10460245.86 0.882922237 0.775596952 0.942896301 0.83836289 0.918773814 0.696035542 0.95234289 0.956107415 0.966897617 1 23.31841343 2.036212245 24.99999626 0.96565008 0.845323762 0.461768053 0.066931865 152.1346337 105029.2037 0.023699715 0.017503351 108.6956704 -2.036212245 -0.120326318 QDLPNAMNAAEITDK ddPTM_BT-474_Pertuzumab_2h_R1 1 QDLPNAMNAAEITDK 15 0 P61204;P61204-2;H0YGG7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 206.63 8.84E-09 250000000 111440 113290 124480 110580 143600 107770 151620 195810 169190 185070 FALSE TRUE 107084.8016 110059.0801 146976.305 116287.0471 148219.0244 109949.1832 153475.5709 191766.4551 149984.2605 172535.0441 0.62065537 0.637894062 0.851863492 0.673990885 0.859066199 0.637257108 0.889532742 1.111463796 0.869297373 1 17.3965299 2.036242073 5.406601779 1.005530305 0.722546506 0.636025567 0.096251347 0.107094743 8.048611941 0.036555103 0.025923694 108.7031359 -2.036242073 -0.282983798 EIPSLS(ph)PTIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIPSLSPTIPR 11 0 Q9ULD5 Q9ULD5 ZNF777 Zinc finger protein 777 1 EIPS(0.342)LS(0.646)PT(0.012)IPR;EIPS(0.053)LS(0.946)PT(0.001)IPR 167.83 1.97E-05 196987000 313367 273771 256014 272453 267806 248668 221677 230474 185462 202391 TRUE FALSE 301120.2712 265963.3191 302281.4248 286514.332 276420.2232 253696.2373 224389.9494 225714.6314 164409.1313 188682.8773 1.595906717 1.409578457 1.602060712 1.518496729 1.464998982 1.344564175 1.189243839 1.196264518 0.871351623 1 17.52560398 2.036245682 0.849908704 0.951658129 1.536423602 0.890938073 0.078207727 0.178534952 0.239580528 0.063037014 0.032140776 108.7040393 -2.036245682 0.584765473 KAASLT(ph)EDRDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAASLTEDRDR 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 KAAS(0.098)LT(0.902)EDRDR;KAAS(0.098)LT(0.902)EDRDR 131.96 0.00030952 3821700000 2328300 1987250 1326860 1718320 2052140 1802050 2125110 2641700 2454300 2237700 TRUE FALSE 2237307.462 1930575.576 1566653.118 1807002.701 2118148.947 1838488.686 2151117.732 2587147.972 2175698.153 2086138.586 1.072463487 0.925430165 0.750982283 0.866194947 1.015344312 0.881287896 1.031148049 1.240161123 1.042930785 1 20.99240357 2.036314851 5.155334772 1.124967575 0.914913932 0.376824197 0.100635465 0.162431869 10.75866574 0.040597824 0.028578967 108.7213537 -2.036314851 -0.210053643 TPHDILEDINAS(ph)PEMR ddPTM_BT-474_Pertuzumab_2h_R1 4 TPHDILEDINASPEMR 16 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR 295.35 7.52E-46 1924630000 779620 836946 705041 802169 842460 910730 774380 798400 824730 887000 TRUE FALSE 749151.5885 813077.1195 832457.5923 843569.0382 869558.491 929145.5846 783857.0941 781912.761 731110.108 826922.6999 0.905951171 0.9832565 1.006693361 1.020130465 1.051559585 1.123618428 0.947920639 0.945569351 0.884133557 1 19.65739295 2.03670218 24.99893225 0.939575851 1.01695034 0.266997408 0.057365615 220.057467 149886.7193 0.022371799 0.016522631 108.8183608 -2.03670218 0.07737449 KMS(ph)QPGS(ph)PSPK ddPTM_BT-474_Pertuzumab_2h_R1 5 KMSQPGSPSPK 11 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 KMS(0.999)QPGS(0.5)PS(0.5)PK;KMS(1)QPGS(0.999)PS(0.001)PK;KMS(1)QPGS(0.966)PS(0.035)PK;KMS(1)QPGS(1)PSPK;KMS(1)QPGS(0.933)PS(0.068)PK 137.17 0.0002941 1534240000 3685400 2923170 2715300 2613680 3083490 2677180 3543780 4259420 4628890 3613070 TRUE FALSE 3541370.494 2839804.054 3206015.112 2748572.338 3182673.256 2731314.414 3587149.84 4171461.489 4103437.813 3368353.551 1.051365434 0.843083724 0.95180481 0.815998765 0.944875058 0.810875216 1.06495645 1.238427447 1.218232514 1 21.68361214 2.036760347 5.122197036 1.173588508 0.901396239 0.608385906 0.090809796 0.103632573 6.723172836 0.033444519 0.023528996 108.8329365 -2.036760347 -0.272192269 MPNS(ph)PAPHFAMPPIHEDHLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MPNSPAPHFAMPPIHEDHLEK 21 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPNS(1)PAPHFAMPPIHEDHLEK 135.35 1.13E-05 330350000 83313 134690 120790 135850 143160 123750 87340 10339 79558 71346 TRUE FALSE 80057.03585 130848.7731 142619.44 142861.2348 147764.8714 126252.3098 88408.89305 10125.49604 70526.90937 66513.67187 1.203617747 1.967246273 2.144212399 2.147847664 2.221571404 1.898140732 1.329183769 0.152231801 1.060337031 1 16.0213633 2.036781509 3.710237954 0.654258358 1.960278573 0.689895347 0.356895836 0.113550695 3.284245336 0.154684135 0.100893402 108.8382396 -2.036781509 1.306020215 (ac)SDKPDMAEIEK ddPTM_BT-474_Pertuzumab_2h_R1 7 SDKPDMAEIEK 11 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;;;;; 114.5 3.10E-05 12045930000 9771090 8299980 8602080 8738460 9107020 8244130 10748120 12948980 13357250 12535360 FALSE TRUE 9389225 8063272.697 10156667.21 9189452.968 9399955.569 8410831.957 10879658.71 12681579.04 11840990.98 11686328.9 0.803436655 0.689974821 0.869106739 0.786342148 0.80435487 0.719715492 0.930973174 1.085163625 1.013234445 1 23.47831846 2.036913732 4.348244308 1.036590799 0.781214312 0.838071142 0.050607397 0.071254579 3.033322556 0.020231744 0.013767344 108.871381 -2.036913732 -0.255376486 KEDS(ph)EKEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEDSEKEAK 9 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 KEDS(1)EKEAK 56.951 0.061869 78862000 183500 99398 101740 82100 109220 117760 125650 153100 152260 148100 TRUE FALSE 176328.6171 96563.26636 120126.6812 86337.19084 112733.1605 120141.1879 127187.7423 149938.4315 134976.0831 138069.0551 1.27710454 0.699383843 0.870047826 0.625318909 0.816498385 0.870152894 0.921189344 1.085966956 0.977598369 1 17.07503048 2.037046688 2.966146033 1.02805537 0.839778314 0.155275794 0.163294615 0.410406822 7.111629202 0.074843914 0.04560182 108.9047164 -2.037046688 -0.188277055 LHGELQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LHGELQDR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;; 154.49 0.0004242 3313840000 1010460 994420 834183 923640 968800 864440 887871 658257 812530 944990 FALSE TRUE 970970.1061 966060.1152 984938.4244 971309.1711 999962.3318 881919.5691 898737.0309 644663.7629 720295.0008 880984.9856 1.102141492 1.096568195 1.117996834 1.102526362 1.135050368 1.001060839 1.020150225 0.731753405 0.817601903 1 19.74875791 2.037095536 2.427304598 0.826222766 1.100110516 0.674320656 0.073639263 0.142917368 1.607812523 0.035922357 0.020529562 108.9169661 -2.037095536 0.27388775 IPDPEAVKPDDWDEDAPAK ddPTM_BT-474_Pertuzumab_2h_R1 4 IPDPEAVKPDDWDEDAPAK 19 1 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ;;; 149.94 7.34E-08 2080490000 2324780 2958760 2135250 3311110 2212270 1694410 3618300 5101110 4697190 2989650 FALSE TRUE 2233925.027 2874379.062 2521137.173 3481996.784 2283429.674 1728672.131 3662581.838 4995770.296 4163984.683 2787158.343 0.80150632 1.03129378 0.904554698 1.249299952 0.819268012 0.620227457 1.314091769 1.792424284 1.493989279 1 21.41036354 2.037284182 7.420038848 1.526262887 0.923992465 0.492927081 0.241874384 0.139240778 22.33139879 0.08937181 0.065298075 108.9642871 -2.037284182 -0.602270422 RPAGGRPS(ph)PSAMGK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPAGGRPSPSAMGK 14 2 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 RPAGGRPS(0.999)PS(0.001)AMGK;RPAGGRPS(0.995)PS(0.005)AMGK;RPAGGRPS(0.959)PS(0.041)AMGK;RPAGGRPS(0.967)PS(0.033)AMGK 81.346 0.0095077 1254570000 1066740 1054820 979268 993230 964670 1055360 1121000 1205850 1298670 1341880 TRUE FALSE 1025050.621 1024737.566 1156243.511 1044490.719 995699.4866 1076700.102 1134719.133 1180948.776 1151250.426 1250993.272 0.819389396 0.81913915 0.924260375 0.834929126 0.795927131 0.860676173 0.907054545 0.944008895 0.920269079 1 20.2546426 2.037284956 1.778090517 0.953454145 0.841035618 0.662774111 0.036540825 0.236658955 1.407089907 0.022518646 0.011661275 108.9644814 -2.037284956 -0.112418528 GLLDDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLDDLR 7 0 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 ; 98.133 0.026723 151327000 295450 502570 293130 643710 369150 269050 487660 627430 464480 362000 FALSE TRUE 283903.4874 488237.1957 346105.1116 676931.9502 381024.045 274490.3753 493628.129 614473.3512 411754.1777 337481.4176 0.841241836 1.446708382 1.025553093 2.005834736 1.129022296 0.813349598 1.462682398 1.820762031 1.220079555 1 18.36444854 2.037363286 24.99782551 1.489039113 1.236178315 0.007715719 0.380635896 417.6594895 279432.5472 0.141735911 0.104678678 108.9841361 -2.037363286 -0.252860798 TPTGEGLLDS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 TPTGEGLLDSPSK 13 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425;A0A0J9YWY6 O95425-2 SVIL Supervillin 1 TPTGEGLLDS(1)PSK;TPTGEGLLDS(0.995)PS(0.005)K;TPTGEGLLDS(1)PSK;TPTGEGLLDS(0.999)PS(0.001)K 290.69 1.65E-40 1082520000 1651790 1436010 1430590 1238060 1297250 1418390 1619720 1914540 1865890 2044840 TRUE FALSE 1587236.221 1395056.401 1689129.436 1301956.425 1338977.224 1447070.818 1639542.618 1875004.08 1654081.99 1906341.165 0.83260869 0.731797868 0.886058313 0.682960872 0.702380691 0.759082815 0.860046799 0.983561659 0.867673646 1 20.8623749 2.037371581 3.387803406 0.945637503 0.763364623 0.621449708 0.064684432 0.156113736 3.650212164 0.028719305 0.018245279 108.9862177 -2.037371581 -0.182272879 LEELTNR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEELTNR 7 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 171.08 0.0022125 1290430000 2546810 2455940 2565900 1723950 2372080 2445500 2142000 2191930 2162550 2164500 FALSE TRUE 2447277.85 2385898.996 3029615.208 1812923.266 2448380.107 2494949.686 2168214.437 2146665.88 1917066.39 2017896.487 1.212786615 1.182369369 1.501372953 0.898422331 1.213332856 1.236411135 1.074492399 1.063813676 0.950032077 1 20.94442074 2.037514078 0.637501931 0.964909501 1.235996555 0.306136234 0.138398625 0.925508389 0.741934112 0.122491411 0.075771784 109.0219832 -2.037514078 0.271087054 RVTGGLLDRLDDS(ph)PDQCR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVTGGLLDRLDDSPDQCR 18 2 Q12955;A0A087WY90;A0A087WVC2;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 RVTGGLLDRLDDS(1)PDQCR 76.186 0.0081661 59670000 50364 50584 37806 43702 41182 54192 42790 43950 49725 42969 TRUE FALSE 48395.7192 49141.39385 44638.38519 45957.46546 42506.65643 55287.79937 43313.67682 43042.41714 44080.42646 40058.67136 1.208120928 1.22673549 1.114325156 1.147253863 1.061109992 1.380170572 1.081255952 1.074484392 1.100396618 1 15.28982695 2.037552863 24.99998548 1.069394193 1.184333306 0.356802777 0.08244917 195.1039456 129885.3576 0.03027079 0.022356401 109.0317199 -2.037552863 0.114939113 TMIQSPSGVILQEAADVHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TMIQSPSGVILQEAADVHAR 20 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 226.71 4.23E-25 1016050000 281191 302994 293203 310557 297411 361396 292377 291293 342242 319358 FALSE TRUE 270201.7448 294352.9078 346191.3044 326584.884 306977.4949 368703.6747 295955.1972 285277.6978 303392.123 297727.5982 0.907546853 0.988665174 1.162778682 1.096925129 1.031068321 1.238392668 0.994046904 0.958183586 1.019025864 1 18.18363343 2.037660443 24.99917644 0.98484589 1.074500307 0.162034356 0.086251324 273.6626235 181657.364 0.033219158 0.024533923 109.0587319 -2.037660443 0.089654417 CDILVQEELLAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 CDILVQEELLASPK 14 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK 203.89 1.51E-08 2110390000 1571933 1281056 1178093 1233076 1260444 1121900 1481748 1700450 1708770 1662090 TRUE FALSE 1510500.12 1244521.537 1391000.612 1296715.2 1300987.326 1144585.587 1499882.075 1665335.113 1514797.593 1549515.164 0.974821128 0.80316835 0.897700548 0.836852217 0.83960929 0.738673369 0.967968633 1.074745928 0.977594559 1 20.56338544 2.038029096 8.579138144 1.024733592 0.84790337 0.613996846 0.06168725 0.153655612 31.56208677 0.022302045 0.016385927 109.1513461 -2.038029096 -0.176830222 LDRAS(ph)PDLWPEQLPGVAEFAASFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDRASPDLWPEQLPGVAEFAASFK 24 1 Q52LA3 Q52LA3 LIN52 Protein lin-52 homolog 1 LDRAS(1)PDLWPEQLPGVAEFAASFK;LDRAS(1)PDLWPEQLPGVAEFAASFK 213.41 5.18E-26 1408350000 661110 657220 573960 620100 615870 675190 666260 760510 846590 753590 TRUE FALSE 635273.0903 638476.7291 677687.3397 652103.4353 635680.0179 688842.8044 674413.8892 744805.2027 750488.6524 702548.6781 0.904240674 0.908800698 0.964612647 0.928196801 0.90481989 0.980491211 0.959953253 1.060147469 1.068237228 1 19.42223866 2.038261259 1.649064473 1.049211997 0.92660081 0.740072979 0.029261207 0.175391357 0.895904885 0.017795351 0.009024306 109.2097114 -2.038261259 -0.122611188 SASQS(ph)SLDKLDQELK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 SASQS(0.5)S(0.5)LDKLDQELK;SASQS(0.509)S(0.491)LDKLDQELK 250.94 2.73E-19 1533380000 1015870 743150 792990 657600 811760 782840 1141940 1292160 1589690 1409380 TRUE FALSE 976168.6773 721956.0896 936300.933 691538.8148 837870.9976 798669.5612 1155915.403 1265476.444 1409235.056 1313921.437 0.742942957 0.54946671 0.712600393 0.526316715 0.637687288 0.607851838 0.879744687 0.96312946 1.072541338 1 20.32544759 2.038316337 2.108254209 1.016436243 0.6222886 0.865779812 0.068501634 0.100627474 0.845668171 0.035095363 0.0191889 109.2235624 -2.038316337 -0.394147642 NDKSEEEQS(ph)SSSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVK 14 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKS(0.006)EEEQS(0.669)S(0.239)S(0.085)S(0.001)VK 222.25 1.04E-11 3443900000 1471900 1263800 1215000 960890 985500 1181800 1482100 1634900 2003900 1718200 TRUE FALSE 1414376.521 1227757.661 1434577.528 1010481.648 1017199.503 1205696.806 1500238.383 1601138.744 1776425.673 1601824.784 0.882978298 0.766474382 0.895589544 0.630831573 0.635025449 0.752702055 0.936580829 0.999571714 1.109001241 1 20.61128492 2.038536563 2.399699165 1.037013772 0.754754797 0.676581217 0.086645026 0.185499883 2.038682243 0.047864864 0.02729338 109.2789625 -2.038536563 -0.282258974 AKPVGS(ph)PLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKPVGSPLFK 10 1 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 AKPVGS(1)PLFK 64.374 0.043904 1832800000 3349200 3005400 2795700 2799200 2740100 2481300 3356100 3657500 4054300 3961500 TRUE FALSE 3218309.561 2919688.935 3300945.18 2943667.047 2828237.805 2531473.586 3397172.956 3581971.347 3594072.861 3693184.076 0.871418671 0.790561443 0.893793841 0.797053975 0.765799307 0.685444736 0.919849346 0.969887033 0.973163749 1 21.81643374 2.038592022 9.569119597 0.969545622 0.802535153 0.698503621 0.054082755 0.208361702 49.41876351 0.02130468 0.015690108 109.2929181 -2.038592022 -0.16701047 EEAEKPER ddPTM_BT-474_Pertuzumab_2h_R1 6 EEAEKPER 8 1 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 133.57 0.00083321 9996191000 8782630 8786190 8828730 9683070 8989840 9361210 10714730 11601310 13071470 14026060 FALSE TRUE 8439395.11 8535616.464 10424277.91 10182814.4 9279006.368 9550500.08 10845860.07 11361738.89 11587651.53 13076062.46 0.645407984 0.652766572 0.797203129 0.778737057 0.709617776 0.730380427 0.829443887 0.86889604 0.886172849 1 23.64042484 2.038608695 0.176303813 1.09682626 0.538146104 0.83610541 0.042664694 1.793577942 0.253859663 0.277247953 0.390403133 109.297114 -2.038608695 -0.558680157 S(ph)ASPSTQQEKHPTHHER ddPTM_BT-474_Pertuzumab_2h_R1 1 SASPSTQQEKHPTHHER 17 1 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 1 S(0.467)AS(0.427)PS(0.102)T(0.004)QQEKHPTHHER 62.663 0.0301 219810000 30349 47422 23138 26154 35038 43726 20718 4592.3 27134 14035 TRUE FALSE 29162.92753 46069.57099 27319.5513 27503.81107 36165.02909 44610.16968 20971.55308 4497.4674 24053.86208 13084.39695 2.228832375 3.520954857 2.08794883 2.102031235 2.763981346 3.409417328 1.602790955 0.343727527 1.8383623 1 13.67555981 2.038687519 6.491346281 0.981851333 2.666997875 0.627092869 0.572864985 0.108995726 12.59892919 0.216210968 0.156776235 109.3169532 -2.038687519 1.685146541 LLAETHYQLGLAYGYNSQYDEAVAQFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLAETHYQLGLAYGYNSQYDEAVAQFSK 28 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 230.12 5.73E-35 347120000 189102 167028 167701 171618 185406 203013 168772 167330 200057 182571 FALSE TRUE 181711.6848 162264.525 198008.3012 180475.2255 191369.7524 207118.062 170837.4822 163874.577 177347.3681 170205.3036 1.067602954 0.95334588 1.163349773 1.060338437 1.124346588 1.216871964 1.003714213 0.962805351 1.041961469 1 17.37691647 2.038749197 24.99849914 0.993906855 1.094980626 0.321698647 0.067615008 183.9614615 118679.4482 0.026048631 0.019238152 109.3324794 -2.038749197 0.101073772 TVSSEDVAEMHNILK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSSEDVAEMHNILK 15 0 P78356;P78356-2 P78356 PIP4K2B Phosphatidylinositol 5-phosphate 4-kinase type-2 beta 0 ; 270.06 1.67E-26 612910000 911120 854790 814570 909400 928630 350140 1005620 1040070 1104890 1281950 FALSE TRUE 875512.4231 830412.2261 961780.919 956334.243 958500.2273 357220.0707 1017927.078 1018592.191 979467.5193 1195122.385 0.732571354 0.694834468 0.804755171 0.80019775 0.802010103 0.298898318 0.851734593 0.852291116 0.819554158 1 20.18872693 2.038779939 24.99999921 0.868657326 0.693843059 0.292693847 0.145850955 225.9494572 145660.3881 0.055356136 0.040883148 109.340219 -2.038779939 -0.174814267 KS(ph)STTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.591)S(0.394)T(0.008)T(0.008)LR 53.683 0.084654 266110000 61913 71483 60598 62825 67795 65800 69880 81691 71794 74079 TRUE FALSE 59493.37151 69444.37483 71549.4066 66067.40578 69975.68774 67130.52108 70735.21234 80004.0523 63644.24611 69061.56335 0.861454167 1.005543047 1.036023558 0.956645094 1.01323637 0.972038828 1.02423416 1.158445428 0.921558143 1 16.07559537 2.038849123 6.638825821 1.055704306 0.980496399 0.066838467 0.071606255 0.30643469 37.23387221 0.026791627 0.019461607 109.3576385 -2.038849123 -0.075207907 TGGLEIDSDFGGFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGGLEIDSDFGGFR 14 0 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 84.884 0.018509 238200000 151270 150580 114120 192610 124850 118640 158530 184350 151530 164060 FALSE TRUE 145358.2012 146285.6058 134744.0226 202550.6252 128865.9136 121038.9821 160470.1376 180543.1081 134328.9497 152948.0701 0.950376171 0.956439697 0.8809789 1.324309781 0.842546843 0.791373059 1.049180532 1.180420962 0.878265084 1 17.22268238 2.039046615 24.99993789 1.058407451 0.961787583 0.031517568 0.152355069 424.9695098 272088.7152 0.058057929 0.042878535 109.4073792 -2.039046615 -0.096619869 EAPSPLMIHS(ph)PQMSQFQSLTHQS(ph)PPQQNVQPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 2 EAPS(0.02)PLMIHS(0.968)PQMS(0.02)QFQS(0.059)LT(0.146)HQS(0.788)PPQQNVQPK;EAPSPLMIHS(1)PQMS(0.003)QFQS(0.173)LT(0.173)HQS(0.652)PPQQNVQPK;EAPSPLMIHS(1)PQMS(0.001)QFQS(0.002)LT(0.038)HQS(0.96)PPQQNVQPK 231.35 3.81E-37 918070000 244855 294870 220328 273660 279033 305384 240814 213171 289320 261387 TRUE FALSE 235285.7959 286460.5963 260146.1708 287783.6254 288008.3499 311559.0737 243761.1538 208768.9444 256477.6065 243683.0257 0.965540358 1.17554596 1.067559671 1.180975263 1.181897463 1.278542372 1.000320614 0.856723376 1.052505015 1 17.89464623 2.039424028 10.99917752 0.94749574 1.143233939 0.439489767 0.090331299 0.452133103 124.2353252 0.033407302 0.024643554 109.5024984 -2.039424028 0.195738198 KEDQYMK ddPTM_BT-474_Pertuzumab_2h_R1 5 KEDQYMK 7 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ;;;; 114.89 0.0093038 2225360000 4224680 4123390 3546080 3421270 3743680 3174710 4311060 4357230 5129170 5020500 FALSE TRUE 4059574.835 4005794.954 4186935.538 3597842.155 3864098.867 3238904.811 4363820.042 4267251.678 4546928.125 4680457.063 0.867345813 0.855855507 0.894556981 0.768694618 0.825581522 0.692006094 0.932349124 0.911716873 0.971470962 1 22.15821799 2.039438128 24.99888423 0.943948418 0.820048467 0.573344993 0.057507848 123.9302961 78555.94403 0.021993033 0.016242919 109.5060537 -2.039438128 -0.123899952 PTSS(ph)PAKGPPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 PTSSPAKGPPQK 12 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 PT(0.001)S(0.031)S(0.968)PAKGPPQK 122.63 0.00021506 687020000 1003200 689370 797320 629550 709450 697150 899930 1027000 1168400 1006800 TRUE FALSE 963993.8349 669709.8426 941413.4603 662041.1509 732270.1036 711246.8507 910943.6125 1005792.091 1035768.13 938608.5392 1.027045669 0.713513477 1.002988382 0.7053432 0.78016561 0.757767292 0.970525597 1.071577819 1.103514497 1 19.84016406 2.039478943 4.168326574 1.058692788 0.826078602 0.48698456 0.105773319 0.165467705 6.291039088 0.041882023 0.028291845 109.5163453 -2.039478943 -0.232614186 EEQT(ph)DTS(ph)DGESVTHHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 EEQT(1)DT(0.185)S(0.815)DGESVTHHIR 106.43 0.0013365 320590000 183280 146530 158180 155280 132210 173530 134600 95561 144770 182170 TRUE FALSE 176117.215 142351.1079 186766.6447 163294.0194 136462.6547 177038.8955 136247.2751 93587.63196 128336.3165 169831.4636 1.037011701 0.838190432 1.099717571 0.961506283 0.803518098 1.042438731 0.802249902 0.551061799 0.755668672 1 17.37374424 2.039617774 6.518076059 0.708511545 0.955172801 0.283465482 0.135655331 0.17135975 19.67830722 0.04935681 0.035821059 109.5513601 -2.039617774 0.246661256 LKEDKAPQVDVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKEDKAPQVDVDK 13 2 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 156.17 2.65E-05 1243480000 1786440 1589170 1243750 1138180 1530340 1703270 1722310 1987670 2477400 2138820 FALSE TRUE 1716623.95 1543848.428 1468523.292 1196921.606 1579564.776 1737711.286 1743388.145 1946623.92 2196175.938 1993955.816 0.860913735 0.774264111 0.736487379 0.600274889 0.792176418 0.871489364 0.874336397 0.976262314 1.101416551 1 20.92720201 2.039796847 1.145547346 1.046153292 0.746946701 0.735629063 0.070196015 0.25815943 0.628027839 0.055398722 0.026538 109.5965408 -2.039796847 -0.299206591 TRDDGDEEGLLTHSEEELEHSQDT(ph)DADDGALQ ddPTM_BT-474_Pertuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLT(0.002)HS(0.007)EEELEHS(0.313)QDT(0.678)DADDGALQ;TRDDGDEEGLLTHSEEELEHS(0.067)QDT(0.933)DADDGALQ 71.903 0.0044852 791820000 167490 177201 159184 169265 131900 175415 140072 102857 160609 146066 TRUE FALSE 160944.3056 172147.401 187952.0898 178000.7869 136142.6833 178962.0115 141786.243 100732.967 142377.3396 136172.8197 1.181912117 1.264183273 1.380246735 1.307168254 0.99977869 1.314227111 1.041222788 0.739743564 1.045563571 1 17.05507924 2.039797042 5.150990502 0.896461737 1.238547822 0.572540477 0.122272319 0.12046467 7.723173137 0.048451196 0.03422311 109.5965901 -2.039797042 0.342086085 KS(ph)QEKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSQEKPR 7 2 P14868;H7C278 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 1 KS(1)QEKPR 59.067 0.083295 31606000 70167 56674 54342 46173 54649 48983 62604 71975 64518 61738 TRUE FALSE 67424.79607 55057.71301 64162.80823 48555.99406 56406.83472 49973.46982 63370.16648 70488.6911 57194.18712 57556.43027 1.171455487 0.956586653 1.114780884 0.843624141 0.980026636 0.868251724 1.101009326 1.224688376 0.993706296 1 15.8126895 2.039829212 23.72986994 1.114034956 0.986185467 0.10785408 0.112131628 130.8278311 77945.15808 0.041155263 0.030395105 109.6047087 -2.039829212 -0.127849489 S(ph)SLPNGEGLQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLPNGEGLQLK 12 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 S(0.776)S(0.224)LPNGEGLQLK 139.77 6.20E-05 113000000 347450 362460 342510 389780 375110 323260 431690 489470 536310 510970 TRUE FALSE 333871.2699 352122.9957 404409.1761 409896.5925 387175.7538 329796.5387 436973.1514 479362.2735 475430.3372 476361.5468 0.700877878 0.739192737 0.848954284 0.860473721 0.812777094 0.692324015 0.917314074 1.006299263 0.998045162 1 18.86169743 2.04012433 5.130511263 0.993814344 0.78323966 0.786026451 0.053480731 0.092793958 5.873184633 0.022923831 0.016186672 109.6792141 -2.04012433 -0.210574683 YPIEHGIVTNWDDMEK ddPTM_BT-474_Pertuzumab_2h_R1 3 YPIEHGIVTNWDDMEK 16 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;; 251.02 3.79E-21 1443210000 2032040 1828630 1653410 1755740 1894320 1032060 2169070 2242460 2545570 2529090 FALSE TRUE 1952625.63 1776479.263 1952217.967 1846353.952 1955252.523 1052928.96 2195615.728 2196152.417 2256607.566 2357792.482 0.828158392 0.75345022 0.827985492 0.783085859 0.829272524 0.44657406 0.931216697 0.931444321 0.957084893 1 21.16900532 2.040164425 24.9999895 0.949253071 0.749048453 0.480878235 0.107026987 134.9327652 83987.14237 0.039597327 0.029244532 109.6893404 -2.040164425 -0.200204618 S(ph)NSLDKHQQSSTLGNSVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSLDKHQQSSTLGNSVVR 19 1 A0A0A0MSY4;Q9BZ29-5;X6RGR3;Q6ZSL5;A0A088AWN3;Q9BZ29-3;Q9BZ29;Q9BZ29-4 A0A0A0MSY4 DOCK9 Dedicator of cytokinesis protein 9 1 S(0.5)NS(0.5)LDKHQQSSTLGNSVVR 168.26 9.90E-12 260980000 186070 172120 146600 148770 156240 167940 176520 198620 215230 201580 TRUE FALSE 178798.1787 167211.3061 173093.8811 156448.0375 161265.6015 171335.8619 178680.3046 194518.4276 190797.9927 187926.8071 0.951424555 0.889768249 0.921070729 0.832494523 0.858129843 0.91171592 0.95079732 1.035075467 1.015278212 1 17.51981135 2.040206016 2.398860583 1.019642569 0.889564607 0.747266242 0.031944952 0.144284328 1.585757536 0.017136731 0.009786901 109.6998456 -2.040206016 -0.130077962 REMDELRSYS(ph)SLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 REMDELRSYSSLMK 14 2 Q86WR0;Q86WR0-2 Q86WR0 CCDC25 Coiled-coil domain-containing protein 25 1 REMDELRS(0.002)Y(0.001)S(0.498)S(0.498)LMK 56.851 0.083921 83870000 70135 64433 54062 56220 59499 68573 68697 74838 90933 80782 TRUE FALSE 67394.04666 62595.43393 63832.206 59121.52094 61412.83937 69959.59304 69537.73444 73292.56915 80610.66706 75310.56319 0.894881725 0.831164066 0.847586358 0.785036234 0.815461162 0.928947947 0.923346361 0.973204369 1.070376633 1 16.20056461 2.040269225 1.144826731 1.027898332 0.834495294 0.804015368 0.037864646 0.208957279 0.507707475 0.028969454 0.013882498 109.7158129 -2.040269225 -0.193403038 EKVGEVTYVELLMDAEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKVGEVTYVELLMDAEGK 18 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 172.84 8.93E-12 136960000 438780 374210 321180 304850 352200 393390 391290 460280 526290 448730 FALSE TRUE 421631.9925 363537.8972 379224.3706 320583.345 363528.8329 401344.6153 396078.7241 450775.0572 466547.7656 418337.1174 1.007876124 0.869007033 0.90650424 0.766327757 0.868985365 0.959380841 0.946793167 1.07754019 1.115243535 1 18.67430648 2.040308336 1.661732198 1.073821897 0.882259419 0.570503382 0.064956477 0.255584816 1.326436297 0.040558364 0.020649277 109.7256938 -2.040308336 -0.191562478 HAPEHHPGHGDRLS(ph)PGERR ddPTM_BT-474_Pertuzumab_2h_R1 1 HAPEHHPGHGDRLSPGERR 19 2 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 HAPEHHPGHGDRLS(1)PGERR 71.651 0.012318 78837000 24295 25532 16766 18290 18908 21465 15710 7416.3 20614 8317.6 TRUE FALSE 23345.52454 24803.85236 19795.98916 19233.94909 19516.19299 21899.03701 15902.26368 7263.150813 18273.98514 7754.241543 3.010678015 3.198746418 2.552923977 2.480442347 2.516840994 2.824136556 2.050782606 0.936668115 2.356643785 1 12.92076996 2.04032455 4.062453325 1.431153808 2.744393782 0.673225184 0.417907159 0.12206399 4.351822551 0.172436418 0.115828366 109.7297904 -2.04032455 1.313239974 ANPFGGASHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ANPFGGASHAK 11 0 D6RD47;P62266;D6RDJ2;D6RIX0;D6R9I7 D6RD47 RPS23 40S ribosomal protein S23 0 ; 133.32 0.00016411 2085080000 2686100 2686200 2248200 2282100 2358100 2082700 2568600 2630400 2969900 2889700 FALSE TRUE 2581124.242 2609592.206 2654499.751 2399879.454 2433950.428 2124813.621 2600035.295 2576081.321 2632769.403 2693978.045 0.958108863 0.968676122 0.985345725 0.890831111 0.903478197 0.788727148 0.965128613 0.956236939 0.977279458 1 21.36130666 2.040418477 24.99999784 0.969903618 0.916153711 0.230377013 0.052433556 268.6707881 166179.5592 0.021328583 0.01575219 109.7535249 -2.040418477 -0.053749907 EENGTWEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EENGTWEK 8 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ;; 143.04 0.0014141 1114840000 819070 786340 666680 699620 831860 747130 835180 952480 1009770 863190 FALSE TRUE 787059.8389 763914.3531 787163.9062 735727.472 858617.5324 762237.4805 845401.1827 932810.9552 895145.1429 804725.3725 0.978047749 0.94928578 0.978177069 0.914259072 1.066969629 0.947201998 1.050546201 1.159166825 1.112361028 1 19.618137 2.04043987 4.779530314 1.107957343 0.973902009 0.502403197 0.052897909 0.131270413 6.947421334 0.020160391 0.014060221 109.7589314 -2.04043987 -0.134055333 IKDIAWTEDSKR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKDIAWTEDSKR 12 2 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 198.23 1.04E-07 4717300000 6068400 5832600 4305900 4525800 5299000 5621900 5266200 6177500 6814000 5872100 FALSE TRUE 5831240.219 5666259.959 5084071.914 4759377.08 5469447.147 5735578.67 5330649.331 6049932.466 6040503.287 5474377.437 1.065187829 1.035051022 0.928703213 0.869391476 0.999099388 1.047713413 0.973745306 1.105136161 1.103413741 1 22.38426348 2.040513076 1.601539512 1.076008586 0.979515738 0.215179081 0.063086127 0.535794025 2.580926818 0.042340105 0.021343536 109.7774343 -2.040513076 -0.096492848 QEYVDYSESAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 QEYVDYSESAKK 12 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 115.82 0.0014573 217760000 424360 366710 267300 282840 320130 409530 344120 417220 483510 442350 FALSE TRUE 407775.542 356251.7898 315607.0561 297437.4063 330427.2722 417810.9772 348331.4435 408604.2612 428623.9718 412389.2405 0.988812272 0.863872659 0.765313507 0.721254041 0.801250954 1.013147134 0.844666663 0.990821828 1.039367495 1 18.65364717 2.040565796 1.041501476 1.018214262 0.829706662 0.406133904 0.085289112 0.543562382 1.089636981 0.069912948 0.033736905 109.7907612 -2.040565796 -0.1885076 LYSLLGIDLTAPSNNSS(ph)PRDS(ph)PCKENK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPRDSPCKENK 27 2 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 2 LYSLLGIDLTAPS(0.277)NNS(0.37)S(0.409)PRDS(0.945)PCKENK 70.632 0.011163 454170000 317260 331740 219890 198770 278490 350180 542820 679490 865850 798380 TRUE FALSE 304861.1285 322279.1 259629.0144 209028.5435 287447.8838 357260.8795 549463.1935 665458.294 767562.3379 744305.0115 0.409591664 0.432993323 0.348820726 0.280837211 0.386196357 0.479992576 0.738223155 0.894066658 1.031247037 1 19.50553442 2.040567795 1.388901094 1.009418149 0.36442776 0.974575291 0.043398018 0.064904522 0.23412799 0.032636683 0.015926709 109.7912666 -2.040567795 -0.644990389 down SKSDGEAKPEPSPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSDGEAKPEPSPSPR 16 2 P26358;K7EJL0;K7ENQ6;K7ERQ1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 SKSDGEAKPEPS(0.002)PS(0.998)PR;SKSDGEAKPEPS(0.088)PS(0.912)PR 145.9 9.26E-07 374038000 588900 495627 417086 377662 417228 411503 510155 570080 603070 589530 TRUE FALSE 565885.1369 481492.2032 492462.7182 397153.1811 430648.5175 419823.8726 516398.4295 558307.6488 534612.0219 549600.608 1.029629751 0.876076548 0.896037433 0.722621437 0.783566305 0.76387083 0.939588534 1.015842488 0.972728221 1 19.06802407 2.040673535 6.258901705 0.993377351 0.840840079 0.423379981 0.080081949 0.182355839 18.70502926 0.032785492 0.023731853 109.8180013 -2.040673535 -0.152537272 GYKIPVIENLGATLDQFDAIDFSDNEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GYKIPVIENLGATLDQFDAIDFSDNEIR 28 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 68.269 0.011795 41332000 145070 131630 140970 148410 147750 159350 174350 191130 220220 231720 FALSE TRUE 139400.504 127876.0413 166446.4149 156069.4579 152502.5129 162572.1662 176483.7475 187183.0987 195221.5488 216025.398 0.645296828 0.591949106 0.770494657 0.722458837 0.705947145 0.752560429 0.816958326 0.866486536 0.903697207 1 17.72084141 2.040692769 0.328091217 1.025446936 0.600953738 0.889287384 0.038751091 0.46650349 0.142222521 0.0563482 0.070453117 109.822865 -2.040692769 -0.424493198 RPS(ph)PTSGDSRPAAGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPSPTSGDSRPAAGR 15 2 Q8N1G1 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 RPS(0.894)PT(0.057)S(0.043)GDS(0.006)RPAAGR;RPS(0.836)PT(0.134)S(0.025)GDS(0.005)RPAAGR;RPS(0.987)PT(0.012)S(0.001)GDSRPAAGR;RPS(0.69)PT(0.285)S(0.025)GDSRPAAGR 145.17 3.23E-06 1370242000 314946 354719 265470 348735 326730 319208 312797 300772 337552 318703 TRUE FALSE 302637.5621 344602.7614 313446.3343 366733.2551 337239.5672 325662.6045 316625.1033 294560.9531 299234.5121 297116.9619 1.018580562 1.159821907 1.054959408 1.234306021 1.135039767 1.096075439 1.065658121 0.991397297 1.007126992 1 18.18067144 2.040744114 1.984267996 0.997580246 1.123970958 0.476336845 0.054872443 0.275193929 2.045347608 0.030254837 0.016261621 109.8358497 -2.040744114 0.126390713 IKEDVGDNWR ddPTM_BT-474_Pertuzumab_2h_R1 1 IKEDVGDNWR 10 1 Q9UJC3;Q9UJC3-2;B1AK95 Q9UJC3 HOOK1 Protein Hook homolog 1 0 106.49 0.0021974 535930000 994680 978470 855530 916880 891150 992830 964500 1086600 1118600 1149300 FALSE TRUE 955806.8059 950564.9936 1010143.302 964200.2867 919814.6491 1012905.703 976303.8395 1064161.33 991621.2176 1071456.887 0.892062777 0.887170548 0.9427755 0.899896485 0.858470985 0.945353672 0.911192836 0.993190993 0.925488677 1 20.03114237 2.040837972 1.579807018 0.97229429 0.900127989 0.494873377 0.030787675 0.320756902 1.503053608 0.018871525 0.00948161 109.8595894 -2.040837972 -0.0721663 ESQLAHIKDEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 ES(0.212)QLAHIKDEPPPLS(0.788)PAPLT(0.001)PATPSSLDPFFSR;ES(0.002)QLAHIKDEPPPLS(0.998)PAPLTPATPSSLDPFFSR;ES(0.001)QLAHIKDEPPPLS(0.999)PAPLTPATPSSLDPFFSR 220.32 2.92E-36 2038847000 754053 896775 521667 571051 726026 888036 542847 454820 520534 431446 TRUE FALSE 724583.7751 871199.855 615943.8313 600523.0105 749379.2857 905992.6964 549490.524 445427.8081 461445.1626 402223.7781 1.801444406 2.165958112 1.531346143 1.493007234 1.863090465 2.252459316 1.366131377 1.107412919 1.147234917 1 18.61763885 2.040847409 6.881288824 1.129961666 1.835442504 0.702864378 0.22652282 0.115579184 14.6651029 0.091259558 0.066521102 109.8619767 -2.040847409 0.705480838 EPS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 6 EPSPEK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK 102.51 0.037212 13323170000 12701900 9731190 10396100 10406100 10351900 9414930 12340600 14034500 14750600 14433100 TRUE FALSE 12205495.71 9453665.989 12274906.53 10943160.07 10684878.26 9605306.335 12491627.95 13744682.67 13076173.73 13455533.28 0.907098623 0.702585753 0.912257156 0.813283267 0.794088056 0.713855492 0.928363647 1.021489255 0.971806427 1 23.68169623 2.041041395 6.170788907 0.994480596 0.807171162 0.641335623 0.064986609 0.107689049 10.62055717 0.023817693 0.017223035 109.9110596 -2.041041395 -0.187309434 TLEKEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLEKEPR 7 1 Q9BRX8-2;Q9BRX8 Q9BRX8-2 FAM213A Redox-regulatory protein FAM213A 0 79.597 0.02936 209160000 301740 463080 299290 512320 293550 332990 447720 553210 532740 439510 FALSE TRUE 289947.6672 449873.4118 353378.3607 538760.8966 302992.3023 339723.2859 453199.3313 541786.0202 472265.5886 409741.5962 0.707635422 1.097944207 0.862441997 1.314879674 0.73947167 0.829115933 1.106061321 1.322262678 1.152593715 1 18.64435483 2.041172082 6.672574874 1.199246562 0.940708096 0.249800669 0.183092311 0.229778558 27.07941796 0.067796869 0.049330051 109.9441389 -2.041172082 -0.258538466 S(ph)PPADAIPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPPADAIPK 9 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4;M0R1Q8 P18754-2 RCC1 Regulator of chromosome condensation 1 S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK 104.82 0.0033541 1991190000 1448530 1457690 1272710 1468370 1323250 1426600 1597610 1884060 1898110 1923860 TRUE FALSE 1391919.846 1416118.108 1502717.008 1544152.752 1365813.538 1455446.829 1617162.029 1845153.503 1682644.51 1793555.249 0.776067449 0.789559234 0.837842609 0.860945183 0.761511829 0.811487034 0.901651639 1.028768701 0.938161516 1 20.77439076 2.041228222 3.207442519 0.989432344 0.807379894 0.850833369 0.034405179 0.088247456 1.820842994 0.015880191 0.009964225 109.9583519 -2.041228222 -0.18205245 WAELLS(ph)PLDESR ddPTM_BT-474_Pertuzumab_2h_R1 6 WAELLSPLDESR 12 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 WAELLS(1)PLDESR;WAELLS(1)PLDESR;WAELLS(1)PLDESR;WAELLS(1)PLDESR;WAELLS(1)PLDESR;WAELLS(1)PLDESR 221.63 2.80E-11 184389300 286485 344705 316158 414730 447438 445992 324719 319520 320018 303235 TRUE FALSE 275288.8495 334874.3509 373294.7835 436134.265 461830.2496 455010.2638 328693.0083 312921.8003 283690.8983 282696.6234 0.97379603 1.184571457 1.320478395 1.542764324 1.633660297 1.609535545 1.162705816 1.106917361 1.003517109 1 18.10889513 2.041309018 9.045420037 1.069983652 1.385739924 0.396691917 0.190086328 0.360471406 73.95882133 0.080510765 0.059269044 109.9788105 -2.041309018 0.315756273 IRSS(ph)VEK ddPTM_BT-474_Pertuzumab_2h_R1 6 IRSSVEK 7 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.321)S(0.679)VEK;IRS(0.001)S(0.999)VEK;IRS(0.002)S(0.998)VEK;IRS(0.025)S(0.975)VEK;IRS(0.156)S(0.844)VEK;IRS(0.305)S(0.695)VEK 117.28 0.0031891 18588140000 10064220 8949140 8801930 9511350 9044050 8648230 10553260 12077400 12555660 11905880 TRUE FALSE 9670899.156 8693919.289 10392634.55 10002231.91 9334960.082 8823103.136 10682413.95 11827997.47 11130394.11 11099484.14 0.871292668 0.783272374 0.936316897 0.901143854 0.84102648 0.794911099 0.962424363 1.065634882 1.002784812 1 23.40398929 2.041316348 5.346218482 1.026904948 0.857183455 0.737485421 0.045731174 0.091720927 6.359653738 0.018365512 0.013064608 109.9806668 -2.041316348 -0.169721493 VSDGDWICPDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSDGDWICPDKK 12 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 ; 146.07 0.00010331 1592270000 898660 820200 675710 716570 755170 853160 842680 953770 1062840 1014870 FALSE TRUE 863539.3737 796808.6991 797825.8281 753552.2636 779460.7289 870411.4797 852992.9699 934074.3162 942190.859 946131.9509 0.912705012 0.842175025 0.843250064 0.796455783 0.823839347 0.919968382 0.901558148 0.987255863 0.995834522 1 19.85168188 2.041432366 1.254331096 1.002107636 0.843102094 0.789455453 0.0325731 0.202286991 0.592585048 0.024043912 0.011576795 110.010051 -2.041432366 -0.159005542 YQEEFEHFQQELDK ddPTM_BT-474_Pertuzumab_2h_R1 4 YQEEFEHFQQELDK 14 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 ;;; 272.97 5.37E-33 1115053000 1042920 1346730 932771 1162810 1010180 671355 1207700 1231890 1491030 1289210 FALSE TRUE 1002161.533 1308322.579 1101343.469 1222822.763 1042673.357 684930.2581 1222480.194 1206451.041 1321774.525 1201890.658 0.833820886 1.088553746 0.916342482 1.017415981 0.867527632 0.569877346 1.017130956 1.003794341 1.099746068 1 20.19687422 2.041450829 24.99999632 1.028819024 0.889894327 0.236315053 0.129988318 240.6572508 145145.2411 0.051136443 0.037766738 110.0147278 -2.041450829 -0.138924697 AGTFIAPPVYSNIT(ph)PYQSHLRSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AGTFIAPPVYS(0.002)NIT(0.817)PY(0.018)QS(0.082)HLRS(0.082)PVR 101.6 0.007756 505210000 422740 496310 294320 458500 568350 549410 387940 375330 357690 378870 TRUE FALSE 406218.8534 482155.7247 347510.1711 482163.2399 586631.4939 560519.4466 392687.7258 367579.3043 317086.5308 353208.7974 1.150081358 1.365072807 0.983866126 1.365094084 1.660863201 1.586935124 1.111772211 1.040685586 0.897731124 1 18.43016175 2.041553322 8.31809793 1.006638025 1.350992831 0.457824673 0.184482764 0.259489152 46.57026413 0.076552833 0.056255188 110.0406942 -2.041553322 0.344354805 IACDEEFS(ph)DS(ph)EDEGEGGRR ddPTM_BT-474_Pertuzumab_2h_R1 5 IACDEEFSDSEDEGEGGRR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR 183.01 9.81E-14 11451200000 2002093 2126400 1525249 1932746 1983953 2144934 1840376 1894796 2059748 1994656 TRUE FALSE 1923848.992 2065757.154 1800895.423 2032495.253 2047768.65 2188306.035 1862899.072 1855667.8 1825934.042 1859556.172 1.034574282 1.110887202 0.968454435 1.093000192 1.101213655 1.176789423 1.001797687 0.997908978 0.981919272 1 20.8265269 2.041671295 24.99984336 0.994745926 1.079454237 0.40613262 0.050652181 148.1655341 88888.23852 0.019344702 0.014286998 110.0705902 -2.041671295 0.084708312 KSEIEYYAMLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSEIEYYAMLAK 12 1 E5RI99;P62888 E5RI99 RPL30 60S ribosomal protein L30 0 ; 140.08 9.52E-05 6792700000 8575900 8272000 7480100 7534000 7934600 7393900 8802100 9630200 10365900 10125700 FALSE TRUE 8240744.347 8036090.659 8831920.464 7922830.643 8189823.615 7543409.724 8909822.733 9431333.005 9189206.489 9439877.32 0.872971551 0.851291853 0.935596954 0.839293814 0.867577336 0.799100398 0.94384942 0.99909487 0.973445541 1 23.17033668 2.041910114 6.275807097 0.986344168 0.863358591 0.765477806 0.03275508 0.086853511 8.792055328 0.012490602 0.009050356 110.1311348 -2.041910114 -0.122985577 TLPQQES(ph)LEIELAEEKPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLPQQESLEIELAEEKPVK 19 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TLPQQES(1)LEIELAEEKPVK;TLPQQES(1)LEIELAEEKPVK 215.34 2.47E-19 404830000 285530 255950 218861 290920 374190 244329 385830 531050 454180 465090 TRUE FALSE 274371.1719 248650.5566 258414.0512 305934.4161 386226.1612 249269.4998 390551.903 520083.6319 402623.3905 433589.04 0.632790838 0.573470576 0.59598843 0.705586138 0.890765507 0.574898064 0.900742101 1.19948519 0.928582951 1 18.72596876 2.042060881 4.887684247 1.06297192 0.669436297 0.718770815 0.108031006 0.097414641 5.386686009 0.044067871 0.030914891 110.1693738 -2.042060881 -0.393535623 KSDLFQDDLYPDTAGPEAALEAEEWFEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSDLFQDDLYPDTAGPEAALEAEEWFEGK 29 1 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0;H0YHL7 Q9ULV4 CORO1C Coronin-1C;Coronin 0 44.743 0.080436 10407000 42610 38501 32148 29454 29284 30215 37290 39925 41643 39630 FALSE TRUE 40944.75409 37402.98918 37957.85873 30974.12447 30225.94646 30825.968 37746.36617 39100.5348 36915.86122 36945.8248 1.108237651 1.012373912 1.027392376 0.83836603 0.818115352 0.83435593 1.021667979 1.058320798 0.999188986 1 15.17312372 2.042120605 24.9930069 1.0292363 0.936199728 0.157355859 0.089558179 257.3604355 152708.3335 0.037557398 0.027737952 110.1845253 -2.042120605 -0.093036573 VKPAPDETSFSEALLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKPAPDETSFSEALLK 16 1 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 166.9 5.94E-09 835370000 1419460 1272460 1227070 1170490 1275880 1242120 1429410 1630390 1672370 1664070 FALSE TRUE 1363985.934 1236170.687 1448828.845 1230899.129 1316919.839 1267236.517 1446903.547 1596721.877 1482529.569 1551361.057 0.879218882 0.796829778 0.933908221 0.793431757 0.8488803 0.816854666 0.932667183 1.02923937 0.955631548 1 20.56510306 2.042225551 4.202690957 0.995508744 0.845083205 0.721835914 0.042178476 0.099953593 3.840618239 0.0163442 0.011098926 110.2111543 -2.042225551 -0.150425539 ILLENY(ph)VRSIENER ddPTM_BT-474_Pertuzumab_2h_R1 6 ILLENYVRSIENER 14 1 H0Y9S3;A0A494C037;E7EUS2;Q8TBZ0-2;Q8TBZ0 H0Y9S3 CCDC110 Coiled-coil domain-containing protein 110 1 ILLENY(1)VRSIENER;ILLENY(1)VRSIENER;ILLENY(1)VRSIENER;ILLENY(0.999)VRS(0.001)IENER;ILLENY(0.989)VRS(0.011)IENER;ILLENY(1)VRSIENER 101.53 0.0016164 4506530000 8527930 4963810 4677230 4104980 6370780 5281480 6016650 6547180 7607220 5655960 TRUE FALSE 8194649.067 4822246.999 5522509.505 4316838.51 6575701.924 5388275.144 6090283.562 6411978.445 6743680.278 5272876.791 1.554113512 0.914538152 1.047342793 0.818687536 1.247080519 1.021885274 1.155021026 1.216030395 1.278937579 1 22.33015886 2.04261343 7.841033116 1.188198569 1.083724588 0.014752936 0.199097837 0.729283301 115.535638 0.072171409 0.052958392 110.3096306 -2.04261343 -0.10447398 DGQVINETSQHHDDLE ddPTM_BT-474_Pertuzumab_2h_R1 2 DGQVINETSQHHDDLE 16 0 P08670 P08670 VIM Vimentin 0 ; 171.78 4.80E-09 477790000 370290 477500 325490 392530 325570 390910 289240 120495 316350 265250 FALSE TRUE 355818.6574 463882.1675 384313.2835 412788.5203 336042.2547 398814.468 292779.8056 118006.7361 280439.2742 247284.3812 1.438904696 1.875905648 1.554134885 1.669286666 1.358930366 1.612776618 1.183980178 0.477210633 1.134075969 1 17.91581159 2.042659984 4.114971817 0.812579615 1.586713515 0.708069512 0.205875678 0.099309106 3.625433853 0.082836976 0.055981032 110.3214559 -2.042659984 0.7741339 NS(ph)SEASSGDFLDLK ddPTM_BT-474_Pertuzumab_2h_R1 4 NSSEASSGDFLDLK 14 0 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 NS(0.985)S(0.015)EASSGDFLDLK;NS(0.773)S(0.227)EASSGDFLDLK;NS(0.997)S(0.003)EASSGDFLDLK;NS(0.754)S(0.195)EAS(0.051)SGDFLDLK 243.99 1.52E-17 1200410000 1233820 1102000 1244880 1376130 1361900 1265340 1671510 2010980 2187630 2108290 TRUE FALSE 1185600.95 1070572.039 1469857.508 1447152.234 1405706.75 1290926.042 1691966.439 1969452.56 1939299.414 1965493.64 0.603207727 0.544683543 0.747831221 0.736279276 0.715192724 0.65679482 0.860835367 1.002014211 0.986672953 1 20.90646027 2.042753479 2.505064442 0.996166098 0.668827005 0.865586852 0.058614817 0.108837553 1.312047741 0.032835999 0.019066984 110.3452085 -2.042753479 -0.327339092 RS(ph)ASPHDVDLCLVSPCEFEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSASPHDVDLCLVSPCEFEHR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHR;RS(0.856)AS(0.144)PHDVDLCLVSPCEFEHR 129.22 7.93E-06 1611810000 122448 169154 104213 127737 122530 139333 110434 87764 120240 99581 TRUE FALSE 117662.5968 164329.8935 123046.6073 134329.5219 126471.2887 142150.4087 111785.5243 85951.64273 106590.8593 92836.29017 1.267420279 1.770104053 1.325414954 1.446950558 1.362304423 1.531194412 1.204114513 0.925840989 1.148159401 1 16.50240125 2.042916938 4.144289514 1.023822673 1.453836563 0.657998395 0.13886508 0.117038617 4.341086256 0.054356317 0.036811298 110.3867477 -2.042916938 0.43001389 ALQAPHS(ph)PSKTDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALQAPHSPSKTDGK 14 1 F2Z2Z8;Q5T173;Q96AQ6-3;Q96AQ6-2;Q96AQ6 F2Z2Z8 PBXIP1 Pre-B-cell leukemia transcription factor-interacting protein 1 1 ALQAPHS(0.652)PS(0.135)KT(0.214)DGK;ALQAPHS(0.819)PS(0.075)KT(0.106)DGK;ALQAPHS(0.457)PS(0.457)KT(0.086)DGK 129.05 4.24E-05 795080000 1500887 1944820 1314926 1787760 1589687 1472300 1832400 2247160 1990400 1511897 TRUE FALSE 1442230.677 1889355.638 1552562.379 1880026.508 1640820.726 1502070.915 1854825.459 2200755.361 1764458.136 1409494.87 1.023225205 1.340448751 1.101502682 1.333829976 1.164119687 1.0656803 1.315950487 1.561378766 1.251837218 1 20.4267468 2.042986661 11.29132538 1.359719133 1.183566381 0.023155647 0.166016239 0.985250916 255.4558993 0.059249275 0.043725947 110.404471 -2.042986661 -0.176152752 KLS(ph)PTEPK ddPTM_BT-474_Pertuzumab_2h_R1 5 KLSPTEPK 8 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 KLS(0.994)PT(0.006)EPK;KLS(0.843)PT(0.157)EPK;KLS(0.823)PT(0.177)EPK;KLS(0.86)PT(0.14)EPK;KLS(0.949)PT(0.051)EPK 137.17 0.00046533 5744850000 4496940 4784550 3468710 3926160 3764880 3861830 4814400 5756960 6145690 5120580 TRUE FALSE 4321194.613 4648099.319 4095583.058 4128789.588 3885980.784 3939918.849 4873320.067 5638076.764 5448057.036 4773758.556 0.905197563 0.973677086 0.857936783 0.864892839 0.814029604 0.825328471 1.020856001 1.181056121 1.141251065 1 22.18669417 2.043153298 4.363789795 1.123174578 0.875227547 0.755016482 0.060436136 0.093664808 3.920357799 0.025572991 0.017542197 110.4468409 -2.043153298 -0.247947031 KPS(ph)SETDIENWASK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSSETDIENWASK 14 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 KPS(0.497)S(0.497)ET(0.006)DIENWASK 171.37 1.85E-06 892580000 447870 443230 340350 390070 381940 401390 454640 549220 537290 510110 TRUE FALSE 430366.7453 430589.5144 401858.816 410201.5594 394225.447 409506.3808 460204.0203 537878.4151 476299.0917 475559.7953 0.904968733 0.905437168 0.845022687 0.862565683 0.828971353 0.861103871 0.967710107 1.131042658 1.001554581 1 18.85926723 2.043502688 4.030253176 1.057775 0.867502465 0.785004457 0.041421913 0.085364292 2.961225156 0.017342388 0.011667893 110.535731 -2.043502688 -0.190272535 YEHANDDK ddPTM_BT-474_Pertuzumab_2h_R1 3 YEHANDDK 8 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;; 145.72 0.00056479 2006590000 2129000 1829800 1757700 1860170 1987220 1895610 2245420 2208230 2495110 2504220 FALSE TRUE 2045796.326 1777615.896 2075355.49 1956173.597 2051140.736 1933940.533 2272900.122 2162629.279 2211875.573 2334606.949 0.876291543 0.761419774 0.888952845 0.837902756 0.878580755 0.828379498 0.973568644 0.926335493 0.947429534 1 21.15474825 2.043660187 0.607769928 0.992705358 0.82865025 0.623541982 0.042077126 0.469349392 0.347592668 0.036105844 0.023418299 110.5758246 -2.043660187 -0.164055108 S(ph)PPSTGSTYGSSQKEESAASGGAAYTK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.991)PPS(0.007)T(0.002)GSTYGSSQKEESAASGGAAYTK;S(0.375)PPS(0.375)T(0.056)GS(0.056)T(0.063)YGS(0.063)S(0.01)QKEESAASGGAAYTK;S(0.996)PPS(0.004)T(0.001)GSTYGSSQKEESAASGGAAYTK 189.72 4.20E-18 8603400000 753640 665920 694030 720450 692620 774130 815960 983860 1052900 1003980 TRUE FALSE 724186.9156 646928.6136 819456.6596 757632.5108 714898.7513 789783.439 825945.9626 963542.9472 933379.2061 935979.5403 0.773720882 0.691178157 0.875507022 0.809454137 0.763797413 0.84380417 0.882440189 1.029448728 0.997221804 1 19.83611747 2.043670329 1.753876788 1.015704652 0.785618905 0.814220416 0.046314377 0.146472984 0.848425324 0.028302243 0.014680837 110.578407 -2.043670329 -0.230085747 EFTMAEIEHFVDPSEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EFTMAEIEHFVDPSEK 16 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;; 166.9 6.51E-09 146658000 323393 310511 356709 399913 368465 192468 445336 448918 516023 561006 FALSE TRUE 310754.444 301655.5303 421174.2512 420552.5579 380317.0114 196359.8348 450786.1552 439647.6864 457446.2324 523008.5639 0.594167028 0.576769772 0.805291309 0.804102623 0.727171671 0.375442867 0.861909701 0.840612787 0.874643866 1 18.99647504 2.043707391 24.99999473 0.878348309 0.658313336 0.484104551 0.124344337 132.6583649 75878.11035 0.048209478 0.035605039 110.587844 -2.043707391 -0.220034974 WSEPWVPVEALPPS(ph)PLELSR ddPTM_BT-474_Pertuzumab_2h_R1 3 WSEPWVPVEALPPSPLELSR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 WSEPWVPVEALPPS(0.963)PLELS(0.037)R;WSEPWVPVEALPPS(0.979)PLELS(0.021)R;WSEPWVPVEALPPS(0.979)PLELS(0.021)R 100.97 0.00089783 0 79079 86773 86559 106170 98784 105827 81506 76444 76323 84435 TRUE FALSE 75988.50525 84298.319 102202.1368 111649.4464 101961.4771 107966.8944 82503.49481 74865.40469 67659.13301 78716.14224 0.965348442 1.070915274 1.29836313 1.418380566 1.295305819 1.371597888 1.048114052 0.951080713 0.859533141 1 16.2643719 2.043809035 4.893896379 0.945319876 1.242540966 0.520872031 0.130699518 0.169080253 9.26035853 0.057519726 0.040429061 110.6137294 -2.043809035 0.297221089 QHEAPSNRPLNELLT(ph)PQGPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 QHEAPSNRPLNELLT(1)PQGPS(1)PR 180.65 8.00E-16 176800000 65631 85014 79809 106440 101640 98468 61140 26286 49580 51961 TRUE FALSE 63066.06796 82589.48396 94232.26164 111933.3812 104909.3429 100459.0904 61888.24961 25743.18491 43951.88626 48441.63519 1.301898 1.704927665 1.945274169 2.310685441 2.165685417 2.07381708 1.277583826 0.531426836 0.907316322 1 15.56395994 2.044000486 3.882098988 0.781464991 1.934375821 0.755462017 0.283781164 0.107412788 3.412669191 0.13030223 0.086833802 110.6625022 -2.044000486 1.15291083 ALWEETSFQLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALWEETSFQLDR 12 0 O15067;H0YGH1 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 157.38 0.0001721 41556000 24990 29823 24535 27564 23412 26049 23971 17263 27908 27495 FALSE TRUE 24013.36317 28972.47724 28969.02028 28986.58134 24165.06824 26575.72863 24264.36427 16906.51302 24740.00084 25632.73916 0.93682392 1.130291892 1.130157027 1.13084213 0.94274233 1.036788478 0.946616127 0.659567162 0.96517195 1 14.64570004 2.044010429 4.486034115 0.829279652 1.055223024 0.318573122 0.110180813 0.176910084 7.872875992 0.044398886 0.030675183 110.6650357 -2.044010429 0.225943372 QSHAASAAPQASS(ph)PPDYTMAWAEYYR ddPTM_BT-474_Pertuzumab_2h_R1 3 QSHAASAAPQASSPPDYTMAWAEYYR 26 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 1 QSHAASAAPQAS(0.25)S(0.75)PPDYTMAWAEYYR;QSHAASAAPQAS(0.006)S(0.994)PPDYTMAWAEYYR;QSHAASAAPQAS(0.008)S(0.992)PPDYTMAWAEYYR 240.94 2.75E-45 1694240000 447486 500080 439563 490390 412961 466640 428578 357302 450342 494170 TRUE FALSE 429997.7524 485818.208 519001.8121 515699.0867 426244.2656 476075.7805 433823.0658 349923.5888 399221.0641 460699.4257 0.93335856 1.054523147 1.126551897 1.11938296 0.925211194 1.03337611 0.941661833 0.759548567 0.866554291 1 18.81346627 2.044582417 3.990953736 0.848264522 1.035710345 0.404720839 0.083691986 0.177920596 6.016432178 0.035426759 0.023802338 110.8108832 -2.044582417 0.187445822 HEDEQALLDQNS(ph)QTPPPS(ph)PFSVQAFNK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 2 HEDEQALLDQNS(0.5)QT(0.502)PPPS(0.98)PFS(0.019)VQAFNK 148.95 6.07E-08 106060000 105310 118850 110890 121670 119180 126650 90748 70579 80172 81502 TRUE FALSE 101194.3688 115460.5144 130930.2897 127949.4033 123013.5329 129210.9498 91858.60117 69121.51899 71071.21067 75981.79695 1.331823843 1.519581255 1.723179696 1.683948109 1.618986887 1.700551382 1.208955366 0.909711559 0.935371543 1 16.21336621 2.044598084 3.415544377 0.952613326 1.602972795 0.876682862 0.110018039 0.079710035 1.891579462 0.052131842 0.033484876 110.8148809 -2.044598084 0.650359469 (ac)SKS(ph)ES(ph)PKEPEQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSESPKEPEQLR 13 2 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 2 S(0.044)KS(0.956)ES(1)PKEPEQLR 71.354 5.12E-05 439360000 620020 455540 344700 382170 444150 460620 533550 689480 716090 578420 TRUE FALSE 595788.9329 442548.4452 406994.9578 401893.8395 458436.4881 469934.052 540079.7445 675241.9971 634802.4653 539243.0982 1.10486149 0.820684487 0.75475228 0.745292505 0.850148087 0.871469757 1.00155152 1.252203319 1.177210181 1 19.04057628 2.045101383 3.10767158 1.166469491 0.845478863 0.566140885 0.111074314 0.163895908 3.151680564 0.051350207 0.032041405 110.9433775 -2.045101383 -0.320990628 S(ph)GSESSVDQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSESSVDQK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.988)GS(0.012)ESSVDQK 140.78 4.06E-05 88328000 127490 127400 112150 128040 124250 115860 132900 135290 157970 144920 TRUE FALSE 122507.5499 123766.6767 132417.9998 134648.1597 128246.6141 118202.7686 134526.47 132496.2142 140037.9079 135104.4393 0.906761839 0.916081495 0.980115831 0.996622764 0.949240563 0.87489922 0.995722055 0.980694749 1.036515962 1 17.04371555 2.045339497 24.99770792 0.999746201 0.94099357 0.450929669 0.035452919 137.7768937 75961.96675 0.014170785 0.010465814 111.0042219 -2.045339497 -0.058752631 VKEVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKEVHDELEDLPSPPPPLSPPPTTSPHK 28 1 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 VKEVHDELEDLPS(1)PPPPLS(0.904)PPPT(0.037)T(0.031)S(0.029)PHK 63.625 0.010022 168310000 404040 447040 328070 334150 364660 378940 330440 292420 328020 323980 TRUE FALSE 388249.6701 434290.8569 387359.5469 351395.5215 376389.6201 386602.4264 334484.0236 286381.4248 290784.5448 302036.546 1.285439379 1.437875193 1.282492308 1.16342054 1.246172442 1.27998559 1.107428978 0.948168123 0.962746226 1 18.2043636 2.045414714 2.432550212 0.965054497 1.285062979 0.825100777 0.064875077 0.125469651 1.423338146 0.03666435 0.021144808 111.0234487 -2.045414714 0.320008481 KILGVGGEDDDGEVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 KILGVGGEDDDGEVHR 16 1 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 0 ; 185.67 1.05E-09 674120000 504950 865630 398600 856400 548380 583270 716230 907800 766700 537000 FALSE TRUE 485215.9957 840943.0799 470635.8868 900598.9066 566019.1407 595064.119 724995.437 889053.6128 679667.4303 500628.5117 0.969213667 1.679774644 0.940090058 1.798936508 1.130617069 1.188634097 1.44817049 1.775874909 1.35762829 1 18.93338093 2.045602115 9.880188307 1.500914611 1.304268973 0 0.319557385 1.045800641 218.4843663 0.112114087 0.082680496 111.0713665 -2.045602115 -0.196645638 IREHLEK ddPTM_BT-474_Pertuzumab_2h_R1 6 IREHLEK 7 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 160.88 0.0012129 7580500000 4777380 4865160 3946810 4447390 4647940 5128830 5114530 6539140 5854010 7011710 FALSE TRUE 4590674.708 4726410.4 4660086.363 4676920.331 4797445.211 5232538.457 5177123.148 6404104.474 5189487.327 6536800.636 0.702281584 0.723046436 0.712900182 0.715475443 0.733913344 0.800473924 0.791996488 0.979700136 0.793887961 1 22.64015327 2.045864537 0.707828064 0.96199519 0.702695703 0.728693952 0.053815813 0.329677425 0.316116386 0.045215383 0.025817116 111.1385016 -2.045864537 -0.259299487 ADEVAPAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADEVAPAKK 9 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 110.14 0.0037456 263450000 322430 284140 237940 294250 299570 301370 349190 363180 442680 411630 FALSE TRUE 309829.0791 276036.6054 280941.0509 309436.2778 309205.9411 307463.9079 353463.4917 355680.2061 392428.8223 383749.9335 0.807372333 0.719313754 0.732094071 0.806348746 0.80574852 0.801209019 0.921077662 0.926854118 1.022616001 1 18.54980697 2.045899447 0.859977386 1.014965855 0.75756976 0.897196103 0.032400357 0.168653334 0.231607693 0.026346472 0.013446808 111.1474355 -2.045899447 -0.257396095 (ac)MFCVT(ph)PPELETK ddPTM_BT-474_Pertuzumab_2h_R1 1 MFCVTPPELETK 12 0 O60256;O60256-2;O60256-3;E7EPA1;C9K0K7;C9JJS3;C9JDU5;I3L1T1;I3L275;E7EW35;I3L164;I3L331;I3L2J4;I3L3B8;C9JDH0 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 MFCVT(0.999)PPELET(0.001)K 49.3 0.058071 18250000 49083 53165 36684 41468 48888 45014 51238 59666 61359 55291 TRUE FALSE 47164.7821 51648.78625 43313.61483 43608.16845 50460.52692 45924.21392 51865.06597 58433.87625 54393.78356 51546.09132 0.915002106 1.001992293 0.840289025 0.846003399 0.978939928 0.890934943 1.006188144 1.133623806 1.055245551 1 15.65357541 2.046099524 4.341160167 1.076849965 0.913743617 0.58893259 0.056887956 0.130899391 5.345338187 0.023342961 0.016043559 111.1986523 -2.046099524 -0.163106348 DDLALFCLQELR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDLALFCLQELR 12 0 Q15006;E5RGJ2;H0YAS9 Q15006 EMC2 ER membrane protein complex subunit 2 0 134.2 0.00034841 21768000 13449 13064 11976 16818 13443 10790 16420 17322 18295 18703 FALSE TRUE 12923.39821 12691.42751 14140.3296 17685.979 13875.4063 11008.18119 16620.95287 16964.29465 16218.2283 17436.22915 0.741180797 0.727876848 0.810974063 1.014323616 0.795780222 0.631339557 0.953242397 0.972933683 0.930145398 1 14.08980045 2.046197638 24.98153934 0.964286389 0.795748207 0.468300744 0.092269827 120.3271207 65066.80465 0.036838346 0.027206909 111.2237767 -2.046197638 -0.168538182 LYYGLS(ph)EGEAAGRPAGPDPLDPTDLNGAHFDPEVYLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYYGLSEGEAAGRPAGPDPLDPTDLNGAHFDPEVYLDK 38 1 Q9UID3;E9PKX7;E9PRV0;E9PKE5;A0A1W2PQZ2;E9PQD5;E9PQN6 Q9UID3 VPS51 Vacuolar protein sorting-associated protein 51 homolog 1 LYYGLS(0.999)EGEAAGRPAGPDPLDPT(0.001)DLNGAHFDPEVYLDK 82.722 0.00055181 21588000 32766 29001 16426 25652 30791 26794 31110 41837 31702 35432 TRUE FALSE 31485.4685 28173.91987 19394.54359 26975.90279 31781.42048 27335.79304 31490.73349 40973.05133 28103.32187 33032.15908 0.953176219 0.852923958 0.587141263 0.816655754 0.96213573 0.827550902 0.953335609 1.240398826 0.850786707 1 15.01158365 2.046282515 4.777107641 1.066419921 0.830095328 0.302751714 0.132007203 0.201902967 10.27093262 0.053872301 0.037784839 111.245516 -2.046282515 -0.236324593 ILYLTPEQEKDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILYLTPEQEKDK 12 1 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 120.87 0.00035232 1307090000 532600 511000 416010 354720 450210 471400 491760 525260 597990 559220 FALSE TRUE 511785.4032 496426.7803 491192.2611 373027.1417 464691.4135 480932.031 497778.306 514413.1974 530108.6822 521343.5313 0.981666353 0.952206656 0.942166214 0.715511212 0.891334381 0.922485851 0.954799045 0.986706781 1.01681262 1 18.9918748 2.046319759 1.701254054 1.003479673 0.89399134 0.313250451 0.06769496 0.489672188 2.668571705 0.044559531 0.022962328 111.2550567 -2.046319759 -0.109488334 DKS(ph)PGRPLER ddPTM_BT-474_Pertuzumab_2h_R1 3 DKSPGRPLER 10 2 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 1 DKS(1)PGRPLER;DKS(1)PGRPLER;DKS(1)PGRPLER 73.219 0.035948 5429890000 6119500 5814600 4705100 5011820 5175530 5758100 5804700 6479700 7530200 6406300 TRUE FALSE 5880343.175 5648773.301 5555416.234 5270480.631 5342005.623 5874532.727 5875739.655 6345891.931 6675403.265 5972395.595 0.984587019 0.945813654 0.930182227 0.882473464 0.894449394 0.983614135 0.983816219 1.062537106 1.117709495 1 22.5098783 2.046514389 1.719160587 1.067758487 0.928752907 0.65892526 0.03990323 0.212452519 1.18265248 0.02461653 0.012726382 111.304927 -2.046514389 -0.139005581 KPEEES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 KPEEESPR 8 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR 121.61 0.00087338 21969120000 31519800 28259000 31602600 37436300 29637500 28705600 37388100 41627700 43722800 47754100 TRUE FALSE 30287971.37 27453080.99 37313892.82 39368391.93 30590817.1 29286046.9 37845666.75 40768073.45 38759571.04 44519672.27 0.680327815 0.616650563 0.838143924 0.884292043 0.68713033 0.657822608 0.85008862 0.915731661 0.87061672 1 25.40793964 2.046664925 5.008686168 0.911877769 0.732974308 0.549690883 0.082280202 0.171013508 9.676048919 0.034967225 0.024738826 111.3435144 -2.046664925 -0.178903461 AEHDQLLLNYAK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEHDQLLLNYAK 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ;;; 170.04 4.22E-05 1586250000 1940290 2148900 1849810 2760950 1868860 1565480 2529170 2589080 2925550 2955940 FALSE TRUE 1864461.322 2087615.476 2184111.816 2903442.96 1928973.579 1597135.078 2560122.739 2535614.593 2593453.829 2755731.551 0.676575816 0.757554006 0.792570603 1.053601523 0.699986027 0.579568455 0.929017465 0.920123948 0.941112652 1 21.39400392 2.046693768 24.99991753 0.939796126 0.770494293 0.382507225 0.116216403 148.0219501 79250.51476 0.046006286 0.033977882 111.3509092 -2.046693768 -0.169301833 HEEEEWT(ph)DDDLVESL ddPTM_BT-474_Pertuzumab_2h_R1 2 HEEEEWTDDDLVESL 15 0 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 HEEEEWT(1)DDDLVESL;HEEEEWT(1)DDDLVESL 216.34 2.48E-11 189123000 274340 277300 233637 254480 264830 313570 201377 91980 268810 243390 TRUE FALSE 263618.4895 269391.6755 275860.4031 267613.7433 273348.4975 319910.6002 203841.512 90080.58086 238295.8157 226904.9785 1.161801258 1.187244446 1.215752977 1.179408866 1.204682679 1.409887973 0.898356278 0.396996934 1.050200914 1 17.79172874 2.046707224 6.620869622 0.723824096 1.218024167 0.508421235 0.182392178 0.122351451 12.88296845 0.067174536 0.048980147 111.3543594 -2.046707224 0.49420007 FGDES(ph)PLLTMR ddPTM_BT-474_Pertuzumab_2h_R1 2 FGDESPLLTMR 11 0 H0YJ41;Q9P203-5;Q9P203 H0YJ41 BTBD7 BTB/POZ domain-containing protein 7 1 FGDES(1)PLLTMR;FGDES(1)PLLTMR 166.62 2.12E-05 81372000 61064 64998 59339 58801 67123 57241 69392 81123 67719 77137 TRUE FALSE 58677.55137 63144.32068 70062.87729 61835.72666 69282.07225 58398.45224 70241.24005 79447.7817 60031.82302 71912.44228 0.815958261 0.878072259 0.97428032 0.859875213 0.963422602 0.812077165 0.976760597 1.104784919 0.834790491 1 16.13395379 2.046844031 10.84799149 1.003800569 0.890564909 0.236020611 0.079948765 0.639676683 145.350774 0.029000625 0.021402973 111.3894428 -2.046844031 -0.113235659 VKGEYDMTVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKGEYDMTVPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 102.66 0.0025887 389170000 787220 757720 663140 627290 634560 652780 797550 944060 946650 864830 FALSE TRUE 756454.5721 736110.5675 782984.1495 659664.5121 654971.1987 665979.6589 807310.6555 924564.8311 839190.2607 806254.2938 0.938233232 0.913000493 0.971137959 0.818184185 0.812363052 0.826016883 1.001310209 1.14674097 1.040850594 1 19.62087541 2.047133625 5.140368617 1.078277584 0.88058485 0.6544176 0.060420011 0.111276623 6.655802435 0.02525567 0.017948456 111.4637435 -2.047133625 -0.197692733 KYDYDSSSVR ddPTM_BT-474_Pertuzumab_2h_R1 3 KYDYDSSSVR 10 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;; 106.49 0.0041737 1840990000 4584890 4274310 3683090 4012160 3785090 3529660 4576100 4915470 5366860 5019860 FALSE TRUE 4405707.43 4152410.864 4348706.293 4219228.058 3906840.857 3601032.144 4632103.681 4813963.827 4757636.553 4679860.411 0.941418556 0.887293744 0.929238462 0.901571348 0.834819955 0.769474264 0.989795266 1.028655431 1.016619329 1 22.15803407 2.047217059 13.22906355 1.016015741 0.879285048 0.662427415 0.046226594 0.772891068 215.6937657 0.018538311 0.013689365 111.4851593 -2.047217059 -0.136730693 SQPPGEDS(ph)DTDVDDDSRPPGRPAEVHLER ddPTM_BT-474_Pertuzumab_2h_R1 3 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.003)QPPGEDS(0.958)DT(0.027)DVDDDS(0.012)RPPGRPAEVHLER;SQPPGEDS(0.999)DT(0.001)DVDDDSRPPGRPAEVHLER;SQPPGEDS(0.981)DT(0.019)DVDDDSRPPGRPAEVHLER 254.41 3.44E-58 1490280000 384379 293086.3 302784.4 345441 322629 339790 387066 443907.9 494615.8 452348 TRUE FALSE 369357.0437 284727.7657 357504.2765 363269.2514 333006.6548 346660.7866 391803.0295 434741.0467 438469.088 421710.0671 0.87585541 0.67517422 0.847748974 0.861419444 0.789657826 0.822035834 0.929081519 1.030900329 1.039740623 1 18.68589194 2.04728695 2.264895402 1.027567974 0.806508072 0.763422524 0.053161991 0.139310891 1.362300871 0.027585084 0.015571363 111.5031022 -2.04728695 -0.221059902 LDEGT(ph)PPEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDEGTPPEPK 10 0 Q9Y4G6;H0YMT1;A0A1B0GVU7;H0YN01 Q9Y4G6 TLN2 Talin-2 1 LDEGT(1)PPEPK;LDEGT(1)PPEPK 128.68 0.0036141 1155840000 1414050 1257770 1133010 1194160 1211720 1196050 1400610 1594280 1730420 1504610 TRUE FALSE 1358787.363 1221899.631 1337770.111 1255790.741 1250696.074 1220234.95 1417751.084 1561357.561 1533989.976 1402701.425 0.968693222 0.871104577 0.953709811 0.895265891 0.891633852 0.869917809 1.010729054 1.113107561 1.093596933 1 20.41977652 2.047318244 4.384556344 1.078137379 0.907994407 0.760044764 0.040984317 0.085243125 3.542186257 0.015879137 0.010952316 111.511137 -2.047318244 -0.170142973 T(ph)QSAPLPQNAQALQHLVIQQQHQQFLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQSAPLPQNAQALQHLVIQQQHQQFLEK 28 0 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 T(0.577)QS(0.423)APLPQNAQALQHLVIQQQHQQFLEK 141.69 2.31E-07 338820000 218650 197000 117530 146100 215600 172430 233130 261850 347590 243250 TRUE FALSE 210104.9163 191381.7529 138770.2854 153640.2385 222534.9698 175916.6527 235983.1147 256442.706 308133.0404 226774.4608 0.926492849 0.843929921 0.611930836 0.677502387 0.981305254 0.77573397 1.040607103 1.1308271 1.358764295 1 17.79089865 2.047485412 1.813890339 1.189556236 0.790994839 0.606952929 0.131485422 0.230957065 1.433528301 0.077846046 0.040935235 111.5540678 -2.047485412 -0.398561397 NSNS(ph)DGGEGGEGTKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSNSDGGEGGEGTKK 15 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 NS(0.009)NS(0.991)DGGEGGEGTKK;NS(0.031)NS(0.969)DGGEGGEGTKK 114.87 0.00035054 562910000 390780 356500 294870 278670 348000 316370 380200 429060 468980 428810 TRUE FALSE 375507.8856 346332.9691 348159.5683 293052.1921 359193.736 322767.2182 384853.0013 420199.7611 415743.3565 399766.3168 0.939318471 0.866338545 0.870907712 0.733058739 0.898509257 0.807389729 0.962694918 1.051113472 1.039965948 1 18.60879739 2.047489989 4.077915843 1.031303213 0.8511038 0.697579162 0.053165251 0.114743479 4.04289743 0.022050353 0.014946996 111.5552435 -2.047489989 -0.180199413 KSNSTAAQEDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSNSTAAQEDAK 12 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;H7C1R1;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 78.763 0.039849 34039000 70490 64937 58647 63330 70660 62987 73753 86731 85717 76906 FALSE TRUE 67735.17287 63085.06034 69245.8175 66598.46889 72932.84307 64260.6403 74655.61128 84939.97454 75986.76551 71697.08812 0.944740918 0.879883158 0.965810737 0.928886662 1.017235776 0.89627964 1.041264202 1.184706057 1.059830566 1 16.12962691 2.047505136 5.48055475 1.104908662 0.941435222 0.566543754 0.056443575 0.1111916 7.663562832 0.021029759 0.015081603 111.5591344 -2.047505136 -0.16347344 IADDKYNDTFWK ddPTM_BT-474_Pertuzumab_2h_R1 2 IADDKYNDTFWK 12 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 175.28 2.56E-05 11666600000 8298000 8286800 7335800 7391100 7208400 7807400 9060500 9377900 11605100 9982300 FALSE TRUE 7973704.986 8050468.578 8661542.244 7772555.557 7440264.733 7965270.977 9171385.109 9184243.088 10287737.7 9306189.93 0.856817349 0.865066009 0.93072915 0.835202765 0.799496334 0.85591107 0.985514499 0.986896158 1.10547257 1 23.1497592 2.047630235 2.076239518 1.033799353 0.856468073 0.774419334 0.043131091 0.159018856 1.299701324 0.024705446 0.013561276 111.5912737 -2.047630235 -0.17733128 DYFEEYGK ddPTM_BT-474_Pertuzumab_2h_R1 14 DYFEEYGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;;; 157.33 0.0008809 1.07309E+11 24166618 22294460 22423669 23316440 23388416 21524025 25885875 29334914 29358248 28516550 FALSE TRUE 23222159.85 21658643.83 26476124.8 24519804.26 24140725.64 21959255.53 26202674.08 28729137.77 26025622.77 26585098.67 0.873502865 0.814691121 0.995900942 0.922313833 0.908054769 0.825998647 0.985615077 1.080648153 0.978955282 1 24.66411449 2.047639714 6.903386681 1.029995759 0.894180106 0.553457 0.053683471 0.142194334 16.03727877 0.020723214 0.015151101 111.5937095 -2.047639714 -0.135815653 RGS(ph)PAPANPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGSPAPANPGR 11 1 E9PJN1;O75676-2;O75676 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 RGS(1)PAPANPGR;RGS(1)PAPANPGR 63.257 0.04642 264130000 119186 140775 137983 154845 138018 142555 115193 88465 115911 94745 TRUE FALSE 114528.0794 136760.2348 162919.5975 162836.569 142457.4743 145437.5598 116602.7664 86638.16684 102753.2692 88327.83676 1.296624978 1.548325419 1.844487576 1.843547572 1.612826483 1.646565399 1.320113462 0.980870471 1.163316945 1 16.43058056 2.047829008 2.808304203 1.052249612 1.648871025 0.745627695 0.153356763 0.138572942 2.137511682 0.078259422 0.047410855 111.6423598 -2.047829008 0.596621413 KVTSVVFHPSQDLVFSASPDATIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVTSVVFHPSQDLVFSASPDATIR 24 1 Q9UMS4 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 240.71 9.65E-38 278040000 514620 754370 527100 654490 565510 731380 536220 526530 505530 551300 FALSE TRUE 494508.0815 732856.1062 622358.6953 688268.3073 583700.1427 746169.0047 542782.4208 515656.9715 448144.3538 513959.96 0.96215293 1.425901166 1.210908911 1.339147718 1.13569186 1.451803765 1.056079195 1.003301836 0.871944098 1 18.97129645 2.047925634 8.219533541 0.97619207 1.258779466 0.491396357 0.137579036 0.199471115 30.57262886 0.047973097 0.035291635 111.6672018 -2.047925634 0.282587396 AES(ph)EELEVQKPQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 AESEELEVQKPQVK 14 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 AES(1)EELEVQKPQVK 111.33 0.0014737 0 113170 99166 91391 95771 112640 109940 128720 171200 161470 174340 TRUE FALSE 108747.1913 96337.88277 107907.3867 100713.7528 116263.1679 112163.0621 130295.3139 167664.6602 143140.6025 162531.7965 0.669082565 0.592732529 0.663915548 0.619655692 0.71532568 0.690099196 0.801660455 1.031580674 0.88069292 1 17.31036246 2.048027217 2.336350973 0.973215658 0.652493569 0.889654673 0.049191565 0.085548993 0.892792947 0.024757464 0.014128097 111.6933243 -2.048027217 -0.320722089 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHAT(ph)PGHGGATSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 3 IWDPT(0.029)PS(0.03)HT(0.129)PAGAAT(0.813)PGRGDT(0.999)PGHAT(0.973)PGHGGAT(0.01)S(0.009)S(0.009)AR 62.024 0.0065173 485750000 103910 127650 88031 116520 115320 108060 101750 83091 101630 111250 TRUE FALSE 99849.08232 124009.547 103940.1599 122533.6112 119029.3725 110245.0472 102995.2469 81375.14181 90093.38847 103714.9384 0.96272614 1.195676813 1.002171544 1.181446116 1.147658904 1.062962086 0.99306087 0.784603868 0.868663568 1 16.66226418 2.048279878 3.098590353 0.863820487 1.099778436 0.53416491 0.085820767 0.161357244 3.082833053 0.037040489 0.023173039 111.7583233 -2.048279878 0.235957949 ERDVYEELLTQAEIQGNINK ddPTM_BT-474_Pertuzumab_2h_R1 4 ERDVYEELLTQAEIQGNINK 20 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 254.44 3.61E-36 587230000 514448 532509 457911 565017 533895 515168 587640 682309 682423 660119 FALSE TRUE 494342.8034 517322.3647 540665.7039 594177.5951 551068.2175 525585.0499 594831.7141 668219.0807 604957.202 615408.5522 0.80327581 0.840616145 0.878547596 0.965501037 0.895451023 0.854042486 0.966563939 1.085813771 0.983017217 1 19.23118497 2.048568401 4.436713354 1.031744665 0.877635809 0.677438955 0.046892827 0.119087979 5.053374385 0.020129581 0.013937919 111.8325947 -2.048568401 -0.154108856 AAAT(ph)PESQEPQAK ddPTM_BT-474_Pertuzumab_2h_R1 5 AAATPESQEPQAK 13 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 AAAT(1)PESQEPQAK;AAAT(1)PESQEPQAK;AAAT(1)PESQEPQAK;AAAT(0.996)PES(0.004)QEPQAK;AAAT(1)PESQEPQAK 309.98 1.64E-49 3032450000 3689890 3734770 2990223 3502200 3312400 3457110 3750480 4425040 4105740 3948230 TRUE FALSE 3545685.019 3628258.016 3530622.813 3682948.962 3418946.354 3527015.133 3796379.496 4333661.378 3639673.608 3680812.865 0.963288586 0.985721945 0.959196499 1.000580333 0.928856337 0.958216367 1.031397041 1.177365309 0.988823323 1 21.81159297 2.048725377 5.273187342 1.08199779 0.967558678 0.349042913 0.052653213 0.152154261 9.501207045 0.01997993 0.014268851 111.873024 -2.048725377 -0.114439112 GVLTGPEYEALDALPDAER ddPTM_BT-474_Pertuzumab_2h_R1 1 GVLTGPEYEALDALPDAER 19 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;O60936-1;H3BQJ5 H3BM67 NOL3 Nucleolar protein 3 0 178.58 8.76E-14 30937000 16793 19658 16562 20341 20762 21123 17952 17426 20647 18014 FALSE TRUE 16136.71099 19097.37309 19555.12182 21390.80145 21429.82859 21550.12153 18171.70195 17066.14701 18303.23912 16793.89573 0.960867642 1.137161585 1.164418437 1.273724798 1.276048686 1.283211583 1.082042084 1.016211323 1.089874524 1 14.03564932 2.048729651 8.225718161 1.040064675 1.187954695 0.352437777 0.091409585 0.294661475 44.48187823 0.036936046 0.027176417 111.874125 -2.048729651 0.147890021 DKFS(ph)PFPVQDRPESSLVFK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKFSPFPVQDRPESSLVFK 19 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKFS(1)PFPVQDRPESSLVFK;DKFS(1)PFPVQDRPESSLVFK;DKFS(1)PFPVQDRPESSLVFK;DKFS(1)PFPVQDRPESSLVFK 158.2 1.87E-11 6996023000 2808980 2239510 2396830 2203960 2202840 2349180 2561780 2774460 3095110 2775480 TRUE FALSE 2699201.956 2175641.368 2829990.498 2317706.64 2273696.349 2396682.029 2593131.83 2717166.431 2743766.089 2587494.267 1.043172149 0.840829444 1.093718558 0.895734019 0.878725174 0.926255976 1.002178773 1.050114957 1.060395041 1 21.30312424 2.04879851 3.897048555 1.039851213 0.94320736 0.243753459 0.072131832 0.288373196 9.145910546 0.029192919 0.019579952 111.8918642 -2.04879851 -0.096643852 GRNS(ph)ATSADEQPHIGNYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GRNSATSADEQPHIGNYR 18 1 E9PC69;Q7KZI7-14;E7ETY4;F5H4J8;F5H6N2;F5H4F6;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 GRNS(0.987)AT(0.013)SADEQPHIGNYR 257.37 7.70E-31 454850000 49980 55324 30937 57087 55878 62653 37907 31519 37671 25685 TRUE FALSE 48026.72634 53746.21369 36528.00409 60033.26691 57675.36662 63919.88659 38370.91721 30868.12164 33394.74601 23945.33207 2.005682201 2.244538248 1.525474943 2.507096863 2.408626719 2.669409069 1.602438299 1.289108104 1.394624468 1 14.54745682 2.048834397 5.722093223 1.301632627 2.21577764 0.68301052 0.308587271 0.117515236 8.778977022 0.123703327 0.089225627 111.9011106 -2.048834397 0.914145013 EHAKS(ph)ESSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EHAKSESSQR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 EHAKS(0.99)ES(0.01)SQR;EHAKS(0.848)ES(0.13)S(0.021)QR 119.73 0.0003958 373250000 519250 526190 378330 413940 478560 527470 391480 287810 455380 449700 TRUE FALSE 498957.1359 511183.5764 446702.6469 435303.493 493953.317 538135.8048 396271.0493 281866.6229 403687.1715 419241.4184 1.190142753 1.219305999 1.065502184 1.038312232 1.178207341 1.283594085 0.945209686 0.672325325 0.962899069 1 18.67742173 2.048930394 6.347935427 0.833650724 1.154142841 0.59453986 0.107134805 0.114133756 10.62880335 0.041093891 0.029908777 111.9258481 -2.048930394 0.320492117 EHDYRDEHLDFIQSHLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EHDYRDEHLDFIQSHLRR 18 2 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 72.421 0.0070431 170880000 34560 61116 21739 24447 30709 49987 20394 7163.6 18861 21285 FALSE TRUE 33209.35699 59373.03152 25667.72088 25708.7126 31696.78287 50997.77139 20643.58787 7015.669157 16719.97835 19843.34799 1.673576304 2.992087401 1.293517651 1.295583417 1.597350552 2.570018497 1.040327866 0.353552695 0.842598656 1 14.27636784 2.049042572 7.317304353 0.668395466 1.88148346 0.514854368 0.525469665 0.166162651 20.4133585 0.20295087 0.148825215 111.9547622 -2.049042572 1.213087993 SNNWS(ph)LEDVTASDK ddPTM_BT-474_Pertuzumab_2h_R1 3 SNNWSLEDVTASDK 14 0 Q14680-3;Q14680-4;Q14680-5;Q14680-2;Q14680-8;Q14680-6;Q14680 Q14680-3 MELK Maternal embryonic leucine zipper kinase 1 SNNWS(1)LEDVTASDK;SNNWS(1)LEDVTASDK;SNNWS(1)LEDVTASDK 366.78 5.60E-97 817630000 999310 908610 843450 920050 973420 946230 1095750 1272250 1374320 1297780 TRUE FALSE 960255.8604 882697.3324 995880.1774 967533.8908 1004730.938 965363.4189 1109160.116 1245977.593 1218312.955 1209880.205 0.793678462 0.729574159 0.823122962 0.799693959 0.830438364 0.797900003 0.916752016 1.029835506 1.006969905 1 20.20643278 2.049047972 2.464710543 1.014979929 0.793991231 0.928902242 0.027030151 0.070210333 0.820153832 0.014181471 0.008244101 111.9561542 -2.049047972 -0.220988698 DVKPSNILVNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVKPSNILVNSR 12 1 P36507;G5E9C7;Q02750;Q02750-2 P36507;Q02750 MAP2K2;MAP2K1 Dual specificity mitogen-activated protein kinase kinase 2;Dual specificity mitogen-activated protein kinase kinase 1 0 133.66 0.00014525 1099200000 1235900 1306700 1010300 1045200 1078100 1240100 1292000 1355400 1619100 1489200 FALSE TRUE 1187599.662 1269434.195 1192883.684 1099142.897 1112778.066 1265175.672 1307811.882 1327410.516 1435306.556 1388335.158 0.855412798 0.914357163 0.859218811 0.791698526 0.801519762 0.911289803 0.942000118 0.956116763 1.033832895 1 20.40492446 2.049102621 1.341512579 1.004333559 0.847989107 0.760576991 0.037203006 0.238042637 0.800926152 0.028499985 0.013925341 111.970243 -2.049102621 -0.156344452 QLTSNTVQQHPS(ph)TPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLTSNTVQQHPSTPKR 16 1 O94916-2;O94916;O94916-4;O94916-5 O94916-2 NFAT5 Nuclear factor of activated T-cells 5 1 QLTSNTVQQHPS(0.5)T(0.5)PKR 152.04 2.75E-07 55861000 84248 76262 63034 78346 65824 77901 71465 70112 79610 81191 TRUE FALSE 80955.49502 74087.08243 74425.64598 82389.44645 67941.28874 79476.21159 72339.61005 68664.1627 70573.00655 75691.86125 1.069540287 0.978798529 0.983271448 1.088484879 0.897603621 1.049996793 0.955711867 0.907153841 0.932372456 1 16.20785056 2.049237464 8.099113355 0.934989861 1.006719702 0.22456026 0.055453499 0.314801453 45.88858404 0.019644324 0.014449905 112.0050139 -2.049237464 0.071729841 LKATVT(ph)PS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 LKAT(0.293)VT(0.707)PS(1)PVK;LKAT(0.001)VT(0.999)PS(1)PVK 143.38 8.53E-05 1554230000 3459870 2821330 3066730 2440030 2711110 2542270 3446610 4106120 3911300 4068200 TRUE FALSE 3324654.455 2740868.431 3620956.33 2565960.241 2798315.315 2593676.441 3488790.644 4021327.187 3467305.622 3792657.19 0.876602943 0.722677609 0.954728083 0.676560024 0.737824479 0.683867882 0.919880303 1.06029282 0.914215403 1 21.85477754 2.049389398 5.90328521 0.996652801 0.77572412 0.563899629 0.087025735 0.129671628 10.29174383 0.032804942 0.023741601 112.0442045 -2.049389398 -0.220928681 DSTEEKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 DSTEEKSPR 9 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 DSTEEKS(1)PR;DSTEEKS(1)PR;DSTEEKS(1)PR;DSTEEKS(1)PR 155.99 4.36E-05 912190000 1642410 1401680 1343590 1318520 1450850 1595000 1731240 1825360 2096400 2111970 TRUE FALSE 1578222.801 1361705.459 1586406.601 1386568.975 1497517.908 1627251.993 1752427.433 1787665.678 1858425.461 1968924.391 0.801565976 0.691598654 0.805722459 0.704226623 0.760576645 0.826467487 0.890043031 0.907940237 0.943878531 1 20.90897628 2.049433796 0.855109091 0.980613115 0.743226509 0.85116852 0.037133759 0.202710526 0.275419957 0.029068376 0.014905281 112.0556596 -2.049433796 -0.237386606 GQKPALDCSQVS(ph)PPRPATSPENNASLSDTSPMDSS(ph)PSGIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK 41 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 2 GQKPALDCS(0.031)QVS(0.811)PPRPAT(0.073)S(0.083)PENNAS(0.003)LSDTSPMDS(0.165)S(0.781)PS(0.053)GIPK;GQKPALDCS(0.098)QVS(0.823)PPRPAT(0.037)S(0.039)PENNAS(0.008)LS(0.02)DT(0.016)S(0.013)PMDS(0.241)S(0.683)PS(0.021)GIPK 107.45 4.10E-06 2302500000 335830 305550 250310 266200 280060 275230 306060 323610 350620 358670 TRUE FALSE 322705.3923 296836.0132 295546.5851 279938.6139 289068.3842 280795.3392 309805.6538 316927.3404 310819.0875 334376.9614 0.965094578 0.887728664 0.883872453 0.837194682 0.864498508 0.839756836 0.926516147 0.947814524 0.929546959 1 18.35111592 2.049439128 5.90360973 0.949639029 0.877665342 0.47536624 0.037407026 0.178205039 14.1363295 0.014684015 0.01062745 112.0570352 -2.049439128 -0.071973687 SAKS(ph)EESLTSLHAVDGDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SAKSEESLTSLHAVDGDSK 19 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.095)AKS(0.426)EES(0.333)LT(0.073)S(0.073)LHAVDGDSK;S(0.251)AKS(0.462)EES(0.195)LT(0.082)S(0.01)LHAVDGDSK 215.51 2.45E-19 652500000 1091320 1085190 825790 861460 993230 945590 1122110 1375560 1379320 1132800 TRUE FALSE 1048670.008 1054241.444 975028.6226 905920.0538 1025178.145 964710.4777 1135842.718 1347154.205 1222745.376 1056074.447 0.992988715 0.998264324 0.92325747 0.857818363 0.970744201 0.913487189 1.07553281 1.275624279 1.157821193 1 20.01028011 2.049734493 4.532658257 1.175976656 0.943053603 0.591352886 0.075187586 0.115422616 5.10760805 0.029631149 0.020633748 112.1332714 -2.049734493 -0.232923053 TTGYSDRPTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTGYSDRPTAR 11 1 Q9NP61;Q9NP61-2 Q9NP61 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 0 ; 107.09 0.0020462 547970000 225040 300540 198886 303099 254750 290745 236064 227303 233120 259160 FALSE TRUE 216245.188 291968.8935 234829.1244 318741.9757 262944.2651 296624.0631 238953.0218 222609.1136 206657.1949 241606.8624 0.895029164 1.208446195 0.971947246 1.319258785 1.088314556 1.227713734 0.989015873 0.921369167 0.855344889 1 17.88230191 2.049968947 6.091588914 0.925646991 1.123460079 0.352205635 0.119749028 0.192264268 16.18413861 0.043152961 0.031324569 112.1938231 -2.049968947 0.197813089 DGEAVWFGCDVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGEAVWFGCDVGK 13 0 Q13867;K7ESE8;J3KSD8 Q13867 BLMH Bleomycin hydrolase 0 ; 142.07 8.09E-06 0 233358 223876 191938 196940 212329 90836 238247 249539 264400 275149 FALSE TRUE 224238.1114 217491.2757 226625.4662 207104.097 219158.7551 92672.76616 241162.7381 244385.9324 234386.4205 256512.9132 0.874178647 0.847876518 0.883485605 0.807382734 0.854377085 0.361279146 0.940158275 0.952723703 0.913741213 1 17.96867193 2.050274683 24.99999984 0.949294082 0.774179236 0.271470287 0.144653575 151.0841217 75128.58908 0.055441297 0.040946102 112.2728335 -2.050274683 -0.175114846 ALVHERDEAAYGELR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALVHERDEAAYGELR 15 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 116.43 0.00026995 422610000 365140 425200 192020 225230 311840 381840 234650 209310 216430 202760 FALSE TRUE 350869.9251 413073.7123 226722.2855 236854.1473 321870.6168 389561.0664 237521.7169 204987.6754 191861.7737 189026.8846 1.856190594 2.185264351 1.199418199 1.253018309 1.702776922 2.060876511 1.256549921 1.084436618 1.01499728 1 17.52823191 2.050375268 7.05665534 1.073223602 1.686860735 0.527964806 0.291956009 0.18841123 21.12954655 0.120157157 0.088014546 112.2988393 -2.050375268 0.613637132 RDS(ph)FDDRGPSLNPVLDYDHGSR ddPTM_BT-474_Pertuzumab_2h_R1 10 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.999)FDDRGPS(0.001)LNPVLDYDHGSR;RDS(0.889)FDDRGPS(0.111)LNPVLDYDHGSR;RDS(0.717)FDDRGPS(0.283)LNPVLDYDHGSR;RDS(0.982)FDDRGPS(0.018)LNPVLDYDHGSR;RDS(0.875)FDDRGPS(0.125)LNPVLDYDHGSR;RDS(0.997)FDDRGPS(0.003)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR 265.75 7.07E-38 51272354500 4178599.2 5634848.4 4179315.4 5864167.4 5762554.1 5352919.4 4323198.3 4431492.6 3852078.2 4552415.4 TRUE FALSE 4015294.924 5474148.041 4934610.661 6166817.782 5947911.886 5461159.098 4376106.894 4339980.729 3414806.432 4244076.25 0.946093964 1.289832632 1.162705468 1.453041232 1.40146207 1.286772145 1.031109395 1.022597256 0.804605344 1 22.01701915 2.05038043 2.33200984 0.942071174 1.269867012 0.507365776 0.141458502 0.25513627 2.655045688 0.075312054 0.043052179 112.3001742 -2.05038043 0.327795839 TTHLAGALS(ph)PGGGQSAPAFPESGPSLR ddPTM_BT-474_Pertuzumab_2h_R1 6 TTHLAGALSPGGGQSAPAFPESGPSLR 27 0 A0A2R8Y4Z8 A0A2R8Y4Z8 1 TTHLAGALS(1)PGGGQSAPAFPESGPSLR;T(0.013)T(0.013)HLAGALS(0.974)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;T(0.038)T(0.038)HLAGALS(0.924)PGGGQSAPAFPESGPSLR 287.54 5.01E-62 4208890000 1454244 1655892 1465005 1886957 1898265 1847221 1366934 1028023 1368773 1273149 TRUE FALSE 1397410.537 1608667.581 1729763.992 1984343.077 1959324.418 1884573.074 1383662.947 1006793.966 1213395.627 1186917.484 1.177344302 1.355332281 1.457358254 1.671845856 1.650767171 1.587787777 1.165761703 0.848242594 1.022308327 1 20.17878821 2.050526168 4.121205908 0.950795757 1.49081888 0.734462756 0.143529591 0.114159668 4.079316539 0.065704363 0.044800417 112.3378657 -2.050526168 0.540023123 NS(ph)RFAQDFLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSRFAQDFLIR 11 1 A0A087WVD4;Q9HBK9-2;Q9HBK9 A0A087WVD4 AS3MT Arsenite methyltransferase 1 NS(1)RFAQDFLIR;NS(1)RFAQDFLIR 62.408 0.049155 1597550000 127893 161858 119831 127501 156049 159629 99564 59118 80449 99072 TRUE FALSE 122894.8002 157241.9683 141487.1273 134081.3419 161068.4578 162856.8078 100782.494 57897.19264 71316.76679 92361.7652 1.330580895 1.702457375 1.531879853 1.451697481 1.743886742 1.763249191 1.091171155 0.626852383 0.772145992 1 16.49500813 2.050731002 4.281445688 0.775320119 1.588283262 0.845763337 0.152946457 0.07059202 2.741417798 0.061953037 0.042642597 112.3908619 -2.050731002 0.812963143 VIS(ph)DSESDIGGS(ph)DVEFKPDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 VISDSESDIGGSDVEFKPDTK 21 1 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1 P52701 MSH6 DNA mismatch repair protein Msh6 2 VIS(0.999)DS(0.001)ES(0.003)DIGGS(0.997)DVEFKPDTK 187.48 1.63E-17 91489000 165220 158680 164510 199250 192090 212180 325710 285760 418190 416110 TRUE FALSE 158763.0197 154154.6018 194240.6165 209533.3164 198268.7493 216470.425 329696.1364 279858.9561 370718.8244 387926.4991 0.409260569 0.397380953 0.500714999 0.540136642 0.511098751 0.558019175 0.84989331 0.721422632 0.95564192 1 18.5654238 2.050805005 0.544230603 1.013379193 0.40753275 0.902996205 0.065667315 0.235313632 0.146111889 0.060762216 0.044270985 112.4100147 -2.050805005 -0.605846443 down S(ph)PHLWK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPHLWK 6 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 S(1)PHLWK;S(1)PHLWK;S(1)PHLWK 96.253 0.027323 437150000 769160 816290 831710 904530 765890 760070 1011420 1138240 1288210 1210260 TRUE FALSE 739100.3768 793010.2084 982018.4983 951212.9017 790525.5474 775439.1362 1023798.061 1114734.946 1141977.801 1128288.012 0.655063573 0.702843777 0.870361546 0.843058591 0.700641626 0.687270562 0.90739071 0.987987938 1.01213324 1 20.10570395 2.050827886 3.830517715 0.990776911 0.75018953 0.763559392 0.0649201 0.12156096 3.695076732 0.03037818 0.020323291 112.4159372 -2.050827886 -0.240587381 VRTELADK ddPTM_BT-474_Pertuzumab_2h_R1 4 VRTELADK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 157.59 0.00034151 3961430000 3462270 3426090 3184020 3240730 2931950 2949540 3748390 4181820 4426400 4474780 FALSE TRUE 3326960.661 3328381.268 3759443.242 3407984.464 3026258.834 3009181.72 3794263.918 4095463.956 3923933.629 4171699.165 0.79750733 0.797847864 0.901177936 0.816929584 0.725425951 0.721332388 0.909524817 0.981725622 0.940608005 1 21.99220369 2.050866889 5.562546774 0.966293175 0.796812526 0.736577867 0.049233973 0.108600159 7.456005922 0.021053429 0.015157182 112.4260337 -2.050866889 -0.169480649 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 LIRPEYAWIVQPVSGAVYDRPGASPK 26 2 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PK;LIRPEYAWIVQPVSGAVYDRPGAS(1)PK;LIRPEYAWIVQPVSGAVYDRPGAS(1)PK;LIRPEYAWIVQPVSGAVYDRPGAS(1)PK 168.52 4.80E-12 3278480000 1927380 1675890 1683830 1795420 1852660 1821720 2079200 2246270 2550030 2415960 TRUE FALSE 1852055.859 1628095.258 1988135.538 1888081.841 1912252.491 1858556.427 2104645.872 2199883.74 2260561.285 2252324.877 0.822286286 0.722850986 0.882703715 0.838281307 0.849012729 0.825172445 0.934432636 0.976716886 1.003656847 1 21.10298351 2.050875691 1.439325256 1.003583297 0.817972531 0.797485306 0.039088017 0.181260412 0.704268841 0.026428842 0.013102163 112.4283121 -2.050875691 -0.185610766 VEQHVVDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 VEQHVVDGK 9 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;; 104.43 0.0032608 4798600000 7808500 7550300 6756300 7103200 7449200 7361700 7952300 8479100 9399000 8955100 FALSE TRUE 7503335.187 7334972.837 7977313.703 7469797.003 7688810.283 7510558.618 8049622.626 8304003.622 8332064.924 8348563.101 0.898757678 0.878591052 0.955531342 0.894740438 0.920974087 0.899622908 0.964192584 0.994662617 0.99802383 1 22.99309648 2.050880332 2.758206734 0.996240315 0.908592473 0.813222216 0.01946787 0.111760503 1.660048055 0.009207976 0.005563915 112.4295136 -2.050880332 -0.087647843 MPIEDSS(ph)PEKGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MPIEDSSPEKGR 12 1 O75376;O75376-2;A0A088AWL3 O75376 NCOR1 Nuclear receptor corepressor 1 1 MPIEDS(0.425)S(0.575)PEKGR;MPIEDS(0.235)S(0.765)PEKGR 122.63 0.00021506 1106090000 1085790 980700 930880 1029690 1050140 980950 1207220 1395390 1405170 1536190 TRUE FALSE 1043356.126 952731.3962 1099110.723 1082832.424 1083918.707 1000785.481 1221994.319 1366574.709 1245660.993 1432142.483 0.728528159 0.665249029 0.76745906 0.756092663 0.756851165 0.698803012 0.853263089 0.954217004 0.869788451 1 20.4497436 2.05097771 3.583924997 0.932037185 0.730445406 0.840850956 0.041763208 0.086683135 2.276209727 0.017746776 0.011649701 112.4547256 -2.05097771 -0.201591779 GTWIHPEIDNPEYSPDPSIYAYDNFGVLGLDLWQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTWIHPEIDNPEYSPDPSIYAYDNFGVLGLDLWQVK 36 0 P27797;K7EL50 P27797 CALR Calreticulin 0 264.5 1.29E-62 59390000 30590 42359 32618 37798 37242 36429 35275 32724 36433 39877 FALSE TRUE 29394.50898 41150.96279 38512.79818 39748.75931 38439.92275 37165.61934 35706.706 32048.23796 32297.27858 37176.09527 0.790683066 1.106919984 1.035955979 1.069202105 1.033995703 0.999718208 0.96047489 0.862065737 0.868764682 1 15.18208763 2.051281459 3.03371925 0.896863276 1.016483668 0.184377022 0.087039007 0.333647655 6.087531913 0.03850442 0.024005588 112.5334047 -2.051281459 0.119620392 QAVDFLSNEGHIYSTVDDDHFK ddPTM_BT-474_Pertuzumab_2h_R1 4 QAVDFLSNEGHIYSTVDDDHFK 22 0 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 ;;; 333.28 4.54E-81 2123600000 957110 1077800 859810 1007690 1027100 978930 874960 612303 959500 943100 FALSE TRUE 919705.0831 1047062.199 1015196.793 1059697.002 1060137.604 998724.6353 885668.0222 599658.7291 850581.5826 879222.997 1.046043025 1.190894918 1.154652229 1.205265337 1.205766464 1.135917326 1.007330365 0.68203258 0.967424175 1 19.7458696 2.051283716 3.884466201 0.846215592 1.161085561 0.630113803 0.092675989 0.114551177 3.587012375 0.037624674 0.025280551 112.5339897 -2.051283716 0.31486997 AQT(ph)PPGPSLSGSK ddPTM_BT-474_Pertuzumab_2h_R1 7 AQTPPGPSLSGSK 13 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQT(0.994)PPGPS(0.005)LS(0.001)GSK;AQT(0.919)PPGPS(0.077)LS(0.003)GSK;AQT(0.967)PPGPS(0.033)LSGSK;AQT(1)PPGPSLSGSK;AQT(1)PPGPSLSGSK;AQT(0.995)PPGPS(0.005)LSGSK;AQT(1)PPGPSLSGSK 189.04 6.26E-05 10755100000 2731390 2452970 2703850 2970480 2679750 2646240 3280560 3709690 4055140 3970250 TRUE FALSE 2624644.259 2383013.697 3192495.842 3123786.829 2765946.592 2699748.786 3320708.475 3633083.605 3594817.508 3701341.431 0.709106228 0.643824338 0.862524007 0.843960733 0.747282207 0.729397392 0.897163511 0.981558625 0.971220185 1 21.81961679 2.051358803 3.18212417 0.978007145 0.759355019 0.748373644 0.060001487 0.138933291 2.812287257 0.02971571 0.018812653 112.5534478 -2.051358803 -0.218652126 LIDWGLAEFYHPAQEYNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIDWGLAEFYHPAQEYNVR 19 0 P19784;H3BSA1 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ; 195.97 8.57E-16 604180000 255500 262360 195839 233537 245184 238975 236220 223309 282160 252730 FALSE TRUE 245514.7775 254877.7497 231231.4637 245589.8726 253070.566 243807.2382 239110.931 218697.5911 250130.3797 235612.372 1.042028377 1.081767258 0.981406289 1.0423471 1.074097102 1.034781137 1.014848792 0.928209284 1.061618189 1 17.84605577 2.051360909 4.692327463 0.984817236 1.042528059 0.198211325 0.039687774 0.243674712 11.52851774 0.015610649 0.010961197 112.5539937 -2.051360909 0.057710823 AVGMPSPVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVGMPSPVSPK 11 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 AVGMPSPVS(1)PK;AVGMPSPVS(1)PK;AVGMPSPVS(1)PK 201.38 4.58E-08 1090400000 1834810 1630500 1379620 1414970 1516940 1464390 1727370 1920480 2069450 1915200 TRUE FALSE 1763103.597 1583999.736 1628948.023 1487996.771 1565733.753 1494000.969 1748510.071 1880821.417 1834534.712 1785481.798 0.987466575 0.887155354 0.912329672 0.833386693 0.876925071 0.836749482 0.979293137 1.053397138 1.027473209 1 20.767882 2.052027235 5.106325157 1.029541068 0.887343217 0.690608593 0.042166398 0.103959146 5.875734004 0.016711957 0.011908218 112.7268145 -2.052027235 -0.142197851 LQDYEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQDYEEK 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 113.26 0.014355 597190000 478180 531340 465050 536320 450470 490240 530640 600380 589370 541900 FALSE TRUE 459492.1969 516186.7034 549094.88 563999.5395 464959.7767 500152.9887 537134.1311 587981.9432 522467.1884 505196.6303 0.909531397 1.021754051 1.086893394 1.116396083 0.920354074 0.990016478 1.063217961 1.163867508 1.034185814 1 18.94648549 2.052057242 6.407417705 1.091339604 1.013388585 0.099899985 0.072775122 0.332332841 30.09699789 0.02859378 0.020849681 112.7346037 -2.052057242 -0.077951018 SEPDDSDPFSFDGPEIMGCTGCQIDWK ddPTM_BT-474_Pertuzumab_2h_R1 3 SEPDDSDPFSFDGPEIMGCTGCQIDWK 27 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8VUX1;P55209-3;B7Z4K9 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ;; 207.55 2.36E-25 462530000 461438 456489 347100 382551 422197 455185 436519 504851 529463 540083 FALSE TRUE 443404.4928 443470.3807 409828.6912 402294.503 435777.3499 464389.1526 441861.2501 494425.6504 469360.5799 503502.6974 0.880639757 0.880770616 0.813955304 0.798991753 0.86549159 0.92231711 0.877574743 0.981972198 0.932190795 1 18.94163998 2.052349175 0.932989113 0.981833451 0.844801692 0.685399795 0.034614793 0.331764376 0.534296614 0.028992547 0.014436406 112.8104093 -2.052349175 -0.137031759 S(ph)TELVLSPDMPR ddPTM_BT-474_Pertuzumab_2h_R1 6 STELVLSPDMPR 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 S(0.981)T(0.019)ELVLSPDMPR;S(0.982)T(0.018)ELVLSPDMPR;S(0.966)T(0.034)ELVLSPDMPR;S(0.863)T(0.137)ELVLSPDMPR;S(0.992)T(0.008)ELVLSPDMPR;S(0.993)T(0.007)ELVLSPDMPR 330.31 4.04E-58 2833300000 1473722 1438425 1090745 1286574 1316298 1207077 1395069 1485621 1561869 1455326 TRUE FALSE 1416127.315 1397402.527 1287866.885 1352974.238 1358637.921 1231484.924 1412142.272 1454942.407 1384572.179 1356755.474 1.043760163 1.029959012 0.949225494 0.997213031 1.001387462 0.907669029 1.040822977 1.072368924 1.020502372 1 20.3717293 2.052402594 24.99991849 1.043398603 0.988079933 0.216578009 0.040419285 121.5539665 57989.61897 0.01527915 0.011284398 112.824286 -2.052402594 -0.05531867 LRRY(ph)CVFS(ph)HEELICK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRRYCVFSHEELICK 15 2 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 2 LRRY(1)CVFS(1)HEELICK;LRRY(1)CVFS(1)HEELICK 87.429 0.016964 709210000 455300 782750 623640 1174830 1206580 963410 528580 352820 281940 356130 TRUE FALSE 437506.3726 760426.7364 736345.6208 1235463.117 1245390.741 982890.8103 535048.9202 345534.1437 249935.3532 332008.9979 1.317754565 2.290379903 2.217848388 3.721173598 3.75107527 2.960434255 1.611549457 1.040737287 0.752796927 1 18.34086282 2.052422674 3.130863416 0.974844597 2.759913368 0.582890267 0.68138182 0.199300018 3.893642846 0.34606241 0.218214789 112.8295027 -2.052422674 1.785068771 DATLLIHEATLEDGLEEEAVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DATLLIHEATLEDGLEEEAVEK 22 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 ;;; 315.01 2.52E-67 328845000 223022 176767 173222 181956 197705 220284 224699 227030 304700 270127 FALSE TRUE 214306.0537 171725.7782 204527.0687 191346.771 204064.3609 224738.2934 227448.9336 222341.7512 270111.7334 251831.0577 0.850991358 0.681908657 0.812159829 0.759821972 0.810322455 0.892416906 0.903180631 0.882900438 1.072591029 1 17.94209669 2.052426509 0.667983694 1.021439689 0.763792223 0.7205925 0.056533244 0.37132513 0.32187452 0.04832491 0.028969372 112.8304991 -2.052426509 -0.257647465 SPGS(ph)PPGPELPIETALDDRER ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGSPPGPELPIETALDDRER 21 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.012)PGS(0.988)PPGPELPIETALDDRER 123.44 1.60E-05 36948000 28379 35311 21058 22092 28706 31704 21791 19969 21637 16619 TRUE FALSE 27269.91731 34303.96485 24863.64903 23232.17077 29629.35456 32345.0766 22057.68478 19556.63317 19180.85847 15493.38033 1.7601012 2.214104613 1.604791757 1.499490123 1.912387996 2.087670729 1.423684458 1.262257349 1.238003461 1 13.91936432 2.052466648 4.657061546 1.225212602 1.838552654 0.681986182 0.209830098 0.12951709 5.988315689 0.087785109 0.061608482 112.8409278 -2.052466648 0.613340052 SQLPTLEQDGGTQNPVSS(ph)PGMSQELR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQLPTLEQDGGTQNPVSSPGMSQELR 26 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8;P46937-4;H0YCI3 P46937-6 YAP1 Transcriptional coactivator YAP1 1 SQLPTLEQDGGTQNPVS(0.029)S(0.971)PGMSQELR;SQLPTLEQDGGTQNPVS(0.018)S(0.982)PGMSQELR;SQLPTLEQDGGTQNPVS(0.101)S(0.899)PGMS(0.001)QELR;SQLPTLEQDGGTQNPVS(0.098)S(0.902)PGMSQELR 211.33 7.12E-26 1556940000 429663 480499 426467 494508 484581 533836 425222 403867 447925 454983 TRUE FALSE 412871.2949 466795.639 503539.0736 520029.6171 500167.988 544630.5297 430425.994 395527.0053 397078.4319 424166.5962 0.973370602 1.100500707 1.187125715 1.22600323 1.179178164 1.284001462 1.014756933 0.932480325 0.936137912 1 18.69427149 2.052522485 7.266592637 0.954666668 1.160832275 0.582921023 0.078842082 0.152501676 17.3787728 0.031457843 0.023081739 112.8554365 -2.052522485 0.206165607 EDIQSVMTEIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDIQSVMTEIRR 12 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 182.07 2.78E-05 177600000 171550 210300 120580 129430 159380 186560 139720 141720 137900 143720 FALSE TRUE 164845.6363 204302.4499 142371.4883 136109.8978 164506.6024 190332.371 141429.9352 138793.4325 122246.1701 133985.7164 1.230322461 1.524807684 1.062587059 1.01585379 1.227792088 1.42054225 1.055559794 1.035882303 0.912382106 1 17.03171968 2.052533506 10.06526416 1.001414081 1.239960804 0.419345451 0.143106674 0.460394481 85.15702883 0.057063469 0.042108588 112.8583004 -2.052533506 0.238546723 S(ph)FEMTEFNQALEEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SFEMTEFNQALEEIK 15 0 Q9BVS4-2;Q9BVS4;H0Y919 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 S(0.998)FEMT(0.002)EFNQALEEIK 109.83 0.0010169 16161000 10575 7728.5 8241.9 10990 7731 8556.1 11193 13906 13430 13324 TRUE FALSE 10161.71731 7508.090747 9731.39467 11557.19522 7979.674636 8729.110204 11329.98328 13618.83624 11905.4827 12421.55361 0.818071364 0.604440554 0.783428142 0.930414631 0.642405522 0.702739003 0.912122882 1.09638751 0.958453594 1 13.60055801 2.052539717 4.231775973 1.025089361 0.746754946 0.643300515 0.091664893 0.127470074 4.792048052 0.038040754 0.02615801 112.8599146 -2.052539717 -0.278334415 TLKPEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLKPEEQR 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 105.4 0.0040091 1177250000 2053070 2027450 1855330 1903520 1930390 1799190 2162800 2353800 2468100 2450300 FALSE TRUE 1972833.755 1969629.111 2190629.403 2001760.895 1992482.747 1835570.855 2189268.993 2305193.207 2187931.635 2284338.998 0.863634406 0.862231531 0.958977369 0.87629765 0.872236016 0.803545733 0.958381832 1.009129209 0.957796385 1 21.12334533 2.052566282 8.276237894 0.988483296 0.876500908 0.673162888 0.037440457 0.155682349 22.00417341 0.01446896 0.010653154 112.8668181 -2.052566282 -0.111982388 KLSS(ph)IGIQVDCIQPVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSSIGIQVDCIQPVPK 17 1 Q9Y2H0-3;Q9Y2H0 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 KLS(0.254)S(0.746)IGIQVDCIQPVPK 114.78 0.00021235 619930000 918640 1086000 883700 917490 761330 892800 1092600 1253700 1429500 1187600 TRUE FALSE 882738.5332 1055028.343 1043404.248 964841.7689 785818.8709 910853.0277 1105971.566 1227810.657 1267229.153 1107162.794 0.797297866 0.952911667 0.942412673 0.871454292 0.709759102 0.822691146 0.998924071 1.108970301 1.144573463 1 20.07843594 2.052796794 3.60348747 1.090568577 0.853526804 0.675487034 0.074104112 0.143628807 3.808142574 0.034575685 0.022778762 112.9267408 -2.052796794 -0.237041773 KVMDSDEDDDY(ph) ddPTM_BT-474_Pertuzumab_2h_R1 2 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(0.083)DEDDDY(0.917);KVMDS(0.087)DEDDDY(0.913) 138.66 5.56E-05 12477000000 9432300 8618900 7649600 7869000 8216100 8773500 9085600 10048400 11246800 10258100 TRUE FALSE 9063675.288 8373097.411 9032052.884 8275120.033 8480378.318 8950906.181 9196792.291 9840897.029 9970110.414 9563309.75 0.947755069 0.875543889 0.944448431 0.865298756 0.886761858 0.935963219 0.961674622 1.029026277 1.042537644 1 23.18907857 2.052914094 1.844535928 1.028274079 0.903624627 0.774411655 0.02785014 0.146849882 0.94449287 0.015497977 0.008232966 112.9572456 -2.052914094 -0.124649452 QLHSS(ph)PGNSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLHSSPGNSSR 11 0 A0A0J9YWL0;A0A494C1M5 A0A0J9YWL0 1 QLHS(0.112)S(0.888)PGNSSR 74.789 0.025676 361630000 55873 63354 53260 65377 63159 65747 56931 47439 62596 81125 TRUE FALSE 53689.42139 61547.20595 62885.26676 68751.1148 65190.56659 67076.44939 57627.73861 46459.36807 55490.3645 75630.33149 0.709892715 0.81378998 0.831482099 0.909041564 0.861963253 0.886898789 0.761965966 0.614295444 0.73370516 1 16.20667732 2.052927502 7.367621985 0.727096388 0.838142954 0 0.105980086 0.355210681 41.18413666 0.038810556 0.028492725 112.960733 -2.052927502 0.111046566 AHS(ph)SPASLQLGAVSPGT(ph)LTPTGVVSGPAATPTAQHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 2 AHS(0.795)S(0.204)PASLQLGAVSPGT(0.576)LT(0.419)PT(0.004)GVVSGPAATPTAQHLR 169.79 1.28E-17 313920000 82612 109060 68867 113410 73267 99705 68070 38811 51683 93883 TRUE FALSE 79383.43171 105949.7156 81312.79884 119263.1037 75623.69959 101721.1034 68903.06102 38009.53929 45816.16251 87524.22079 0.906988157 1.21051881 0.929031965 1.362629711 0.864031681 1.162205187 0.787245638 0.434274524 0.523468385 1 16.41739469 2.052986409 4.501090719 0.592519968 1.073997456 0.472877355 0.200090129 0.141500476 6.063507361 0.074455887 0.051924604 112.9760558 -2.052986409 0.481477489 QAS(ph)PAWK ddPTM_BT-474_Pertuzumab_2h_R1 3 QASPAWK 7 0 A0A2R8Y7W8;A0A2R8Y6W5;Q16626 A0A2R8Y7W8 MEA1 Male-enhanced antigen 1 1 QAS(1)PAWK;QAS(1)PAWK;QAS(1)PAWK 98.254 0.011956 658277000 1131490 1145370 1152020 1136190 1265460 1354910 1148600 1190290 1262660 1283310 TRUE FALSE 1087270.12 1112705.169 1360215.641 1194828.902 1306164.67 1382307.209 1162656.91 1165710.096 1119328.13 1196390.271 0.908792178 0.930052004 1.136933051 0.998694934 1.091754674 1.155398236 0.97180405 0.974356048 0.935587791 1 20.19025665 2.053030105 24.999998 0.968617024 1.039563049 0.153032725 0.076482236 182.4429099 86008.11331 0.030122805 0.022247163 112.9874233 -2.053030105 0.070946025 KRDSS(ph)LR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRDSSLR 7 2 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 KRDS(0.292)S(0.708)LR 86.014 0.016056 171120000 219310 207540 160020 173140 186570 182790 199650 218770 217240 218450 TRUE FALSE 210739.1227 201621.1624 188939.1736 182075.7761 192571.1935 186486.139 202093.3764 214252.323 192579.8259 203654.1869 1.034789051 0.990017271 0.927745098 0.894043864 0.945579349 0.9157 0.992335976 1.052039864 0.945621737 1 17.63576195 2.053144128 8.020374264 1.009263416 0.949368312 0.197695287 0.044264314 0.335063876 44.59652225 0.017554484 0.012917772 113.0170919 -2.053144128 -0.059895104 KDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 6 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.01)HS(0.99)AEDS(1)EDEKEDHK;KDDS(0.014)HS(0.986)AEDS(1)EDEKEDHK;KDDS(0.057)HS(0.943)AEDS(1)EDEKEDHK;KDDS(0.014)HS(0.986)AEDS(1)EDEKEDHK;KDDS(0.025)HS(0.975)AEDS(1)EDEKEDHK;KDDS(0.443)HS(0.557)AEDS(1)EDEKEDHK 171.78 6.67E-12 6626089000 2872284 1713210 1987715 1358950 1840319 1476879 2318719 2449326 3328040 2351232 TRUE FALSE 2760031.966 1664350.928 2346939.317 1429085.572 1899514.532 1506742.505 2347096.177 2398746.562 2950254.851 2191980.962 1.259149606 0.759290777 1.070693294 0.651960759 0.866574375 0.6873885 1.070764855 1.094328191 1.345930874 1 21.06380384 2.053194652 8.474255219 1.138815619 0.874100722 0.298127215 0.186689276 0.32021589 46.35052422 0.06723224 0.049525628 113.0302406 -2.053194652 -0.264714897 VDIDVPDVNIEGPDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDIDVPDVNIEGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 346.65 1.00E-86 1338590000 2629650 2568410 2357730 2576750 2269060 2429910 2760540 3226710 3132300 2901630 FALSE TRUE 2526880.371 2495161.462 2783824.258 2709736.376 2342046.376 2479044.445 2794324.314 3160077.311 2776734.436 2705100.016 0.93411717 0.922391574 1.029102156 1.001713933 0.865789199 0.916433563 1.032983734 1.168192412 1.026481246 1 21.36725051 2.053422466 5.354471222 1.0877425 0.947654415 0.446685647 0.060077457 0.151165352 9.32666279 0.02398657 0.017217437 113.0895473 -2.053422466 -0.140088084 EQS(ph)DDETEESVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQSDDETEESVK 12 0 O94885;A0A1B0GWB9;A0A1B0GVI0 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EQS(0.999)DDET(0.001)EESVK 299.27 2.14E-36 613150000 253730 221550 237290 230780 227060 205750 284040 340680 342100 308790 TRUE FALSE 243813.9511 215231.6109 280173.5815 242690.5835 234363.5911 209910.406 287516.1665 333644.8389 303266.2422 287875.3783 0.846942703 0.747655504 0.973246073 0.843040433 0.814114748 0.729171099 0.998752197 1.158990536 1.053463634 1 18.13508488 2.053552378 5.701623138 1.086669295 0.830073265 0.707824569 0.072285254 0.095532787 6.70191332 0.027755003 0.020062978 113.1233814 -2.053552378 -0.25659603 DIDIEDLEELDPDFIMAK ddPTM_BT-474_Pertuzumab_2h_R1 12 DIDIEDLEELDPDFIMAK 18 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;;;;;;;; 336.5 9.53E-75 1351301000 2469054 2394921 2178776 2240954 2401843 2575068 2719312 3006372 3310332 3350508 FALSE TRUE 2372560.64 2326620.198 2572529.29 2356609.904 2479100.461 2627137.639 2752591.754 2944289.368 2934556.989 3123575.109 0.75956574 0.744858093 0.823584899 0.754459177 0.793674035 0.841067542 0.881231172 0.942602391 0.93948661 1 21.57476679 2.053569263 0.756566688 0.991724942 0.763711524 0.934923495 0.021695871 0.144296988 0.155915517 0.018248368 0.010004971 113.1277795 -2.053569263 -0.228013419 ES(ph)MT(ph)KQLPESK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESMTKQLPESK 11 1 Q92539 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 2 ES(1)MT(1)KQLPESK 91.784 0.016255 710450000 582970 653810 432770 554860 617860 633590 531850 533660 537430 589060 TRUE FALSE 560186.8879 635163.9789 510981.1659 583496.3911 637734.028 646401.6239 538358.9394 522639.7345 476423.1995 549162.4415 1.020075019 1.156604915 0.930473622 1.062520571 1.161284858 1.177068159 0.980327311 0.951703349 0.867545126 1 19.06687343 2.053712438 7.830018151 0.942115861 1.083414014 0.439825271 0.075529774 0.2287007 28.97833349 0.029293757 0.021546279 113.1650809 -2.053712438 0.141298152 ATVT(ph)PS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 ATVT(1)PS(1)PVK;ATVT(1)PS(1)PVK;ATVT(1)PS(1)PVK;ATVT(1)PS(1)PVK 196.11 0.00016005 4312070000 6895000 5498400 7384400 7376200 6295400 5423100 8065700 9146600 8324800 10287500 TRUE FALSE 6625535.777 5341591.015 8718925.345 7756886.566 6497897.258 5532758.798 8164410.449 8957719.514 7379803.604 9590718.462 0.690827888 0.556954209 0.909100333 0.808790978 0.677519342 0.576886791 0.851282465 0.933998798 0.76947349 1 23.19320746 2.054035379 9.72769562 0.893549002 0.709787159 0.41079332 0.109688239 0.400592096 68.96942663 0.042311219 0.031217864 113.2492616 -2.054035379 -0.183761843 ERPSSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPSSFR 7 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 0 ; 115.49 0.014723 0 77220 84880 75375 83690 86644 73988 81143 77610 78065 83877 FALSE TRUE 74202.15703 82459.30551 88996.93921 88009.25093 89430.98295 75484.08805 82136.05231 76007.32638 69203.38848 78195.93608 0.948926002 1.054521624 1.138127423 1.125496482 1.143678143 0.965319834 1.050387737 0.972011209 0.884999809 1 16.25480601 2.054071748 1.294830954 0.946854988 1.079909059 0.364117475 0.067082021 0.483637876 1.514617022 0.048458856 0.023655421 113.2587458 -2.054071748 0.13305407 RDYDDMSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;; 201.84 3.34E-05 1761640000 591480 679860 610400 631260 635480 686910 619350 627160 697070 672960 FALSE TRUE 568364.3077 660471.0585 720712.8583 663839.4043 655920.7913 700799.7908 626929.7906 614208.9268 617941.536 627379.8198 0.905933359 1.052745144 1.148766402 1.058114054 1.045492333 1.117026351 0.999282685 0.979006508 0.984956029 1 19.2589796 2.0540844 12.33879722 0.986525392 1.058600822 0.217079426 0.059411867 1.232310605 278.6751382 0.022605537 0.016692857 113.2620452 -2.0540844 0.07207543 LNDADPDDKFHCLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LNDADPDDKFHCLR 14 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ;;; 126.16 5.23E-05 2232010000 2923020 2822960 2595710 2829540 3005280 3054120 3247070 3355410 4009100 4089510 FALSE TRUE 2808785.147 2742451.945 3064812.538 2975572.898 3101947.561 3115876.399 3286808.614 3286119.611 3554003.776 3812523.845 0.736725922 0.719327159 0.803880228 0.780473256 0.813620501 0.817273944 0.862108343 0.861927622 0.932191881 1 21.86231493 2.054164376 0.205227971 1.054563159 0.650981181 0.940540872 0.019784568 0.679736536 0.113760504 0.072231126 0.105223099 113.2829046 -2.054164376 -0.403581978 APYS(ph)PTTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 APYSPTTSK 9 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 APYS(0.971)PT(0.028)T(0.001)SK;APY(0.001)S(0.99)PT(0.008)T(0.002)SK;APYS(0.782)PT(0.203)T(0.013)S(0.002)K;APYS(0.987)PT(0.01)T(0.003)SK 96.113 0.0079591 2722470000 3195630 3071540 2682230 3031390 3042740 3254390 3301510 3492050 3945200 3960170 TRUE FALSE 3070741.247 2983942.687 3166968.627 3187840.401 3140612.495 3320195.996 3341914.867 3419937.947 3497357.436 3691944.159 0.831740978 0.80823072 0.857805127 0.863458456 0.850666305 0.899308292 0.905191066 0.926324397 0.94729424 1 21.8159493 2.054187222 0.319667698 1.010628829 0.800180691 0.951983821 0.012077393 0.292129228 0.085490095 0.01710114 0.022020015 113.2888641 -2.054187222 -0.210448139 NS(ph)PGVPTGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPGVPTGAK 10 0 Q08379;B7ZC06;R4GND7 Q08379 GOLGA2 Golgin subfamily A member 2 1 NS(1)PGVPTGAK;NS(1)PGVPTGAK 166.77 5.71E-06 778650000 2364490 1954230 1987060 1843180 1883390 2074930 2381120 2878250 2881770 2960660 TRUE FALSE 2272083.117 1898497.274 2346165.944 1938306.741 1943970.95 2116886.506 2410260.859 2818813.132 2554643.551 2760131.861 0.823179193 0.68782847 0.850019514 0.7022515 0.704303652 0.766951223 0.8732412 1.021260314 0.925551271 1 21.39630576 2.054220659 2.857428361 0.981691918 0.751361873 0.780031476 0.054075798 0.111774343 1.792919527 0.024375686 0.01495286 113.2975866 -2.054220659 -0.230330045 (ac)SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR 33 1 K7EM18;P41567 K7EM18 EIF1 Eukaryotic translation initiation factor 1 0 ; 89.577 5.57E-73 580140000 276017 333639 224070 200494 250632 299303 226618 167222 318828 273321 FALSE TRUE 265229.9505 324123.9424 264564.4334 210841.5194 258693.8059 305355.1117 229391.4189 163768.8073 282635.9821 254808.7252 1.040898228 1.272028429 1.038286398 0.827450156 1.015247047 1.19836992 0.900249466 0.642712714 1.109208414 1 17.95905515 2.054277996 9.658336194 0.851173127 1.059827144 0.144009712 0.159130674 0.501068834 85.08922451 0.06130011 0.045226396 113.3125455 -2.054277996 0.208654017 KVNIDFEPFKPINTSLYLCDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVNIDFEPFKPINTSLYLCDNK 22 2 B7Z7P8;P62495-2;P62495;I3L492;D6RJE8 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 152.13 2.45E-08 304190000 221890 171860 178950 145130 187610 196400 204260 238630 263300 247890 FALSE TRUE 213218.2935 166958.7211 211290.2457 152620.1767 193644.646 200371.3426 206759.795 233702.2071 233411.2878 231100.1895 0.922622755 0.722451684 0.914279846 0.660406973 0.837925085 0.867032359 0.894676008 1.011259262 1.010000417 1 17.81815892 2.054397427 1.477693685 1.015273028 0.806123139 0.555189164 0.075027809 0.277160737 1.136848165 0.0458684 0.022940969 113.3437108 -2.054397427 -0.209149888 QEAKPQQAAGMLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 QEAKPQQAAGMLSPK 15 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 QEAKPQQAAGMLS(1)PK;QEAKPQQAAGMLS(1)PK;QEAKPQQAAGMLS(1)PK;QEAKPQQAAGMLS(1)PK;QEAKPQQAAGMLS(1)PK 188.32 1.84E-07 2769910000 3119430 2498070 2752350 2589820 2727250 2441890 3369300 3967660 4019530 4164520 TRUE FALSE 2997519.227 2426827.489 3249760.871 2723480.921 2814974.473 2491266.689 3410534.501 3885726.434 3563249.806 3882453.351 0.772068318 0.625075763 0.83703797 0.701484519 0.72505043 0.641673309 0.878448288 1.000843045 0.917783031 1 21.88853716 2.054437066 4.708608196 0.966555424 0.718724439 0.785608112 0.060816167 0.083949892 3.926257776 0.02296496 0.016175974 113.3540563 -2.054437066 -0.247830985 TDCSSGDASRPSSDNADS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 TDCSSGDASRPSSDNADSPK 20 1 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 TDCSSGDASRPSSDNADS(1)PK;TDCSSGDASRPSSDNADS(1)PK 161.58 1.35E-11 1178240000 782550 699880 563540 627850 562080 588070 730970 830940 922350 717560 TRUE FALSE 751967.0808 679920.1077 665384.2139 660253.4137 580159.8137 599961.1783 739915.8295 813780.7986 817648.6948 668959.0221 1.124085416 1.016385287 0.994656163 0.986986335 0.867257626 0.896857892 1.106070484 1.216488263 1.222270226 1 19.35155831 2.054512101 5.953904147 1.16843397 0.978996382 0.431313175 0.086989346 0.160726433 12.16405601 0.034141553 0.024786818 113.3736428 -2.054512101 -0.189437588 SEDRRS(ph)S(ph)EEREAGEI ddPTM_BT-474_Pertuzumab_2h_R1 2 SEDRRSSEEREAGEI 15 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 2 S(0.001)EDRRS(0.999)S(1)EEREAGEI;S(0.008)EDRRS(0.995)S(0.998)EEREAGEI 98.21 0.0054975 14095200000 2914900 2957200 2091840 2438700 2632750 2847000 2471470 2516260 2732900 2467200 TRUE FALSE 2800982.485 2872863.551 2469882.021 2564561.599 2717434.795 2904568.291 2501716.589 2464298.352 2422672.649 2300094.346 1.217768519 1.249019874 1.0738177 1.114981046 1.181444926 1.262803978 1.087658249 1.071390117 1.053292728 1 21.13326161 2.054712306 8.406303466 1.056893005 1.178158944 0.563314766 0.056665854 0.233286692 32.42441862 0.022741679 0.016752849 113.4259189 -2.054712306 0.121265939 KGPPTQELDRDS(ph)EEEEEEDDEDGEDEEEVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGPPTQELDRDSEEEEEEDDEDGEDEEEVPK 31 2 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 1 KGPPTQELDRDS(1)EEEEEEDDEDGEDEEEVPK 326.73 7.62E-106 275940000 272270 204330 202350 168300 219940 214840 252970 301810 329370 283720 TRUE FALSE 261629.3874 198502.7085 238919.1463 176985.9832 227014.5698 219184.212 256065.9225 295577.518 291981.2984 264503.3917 0.989134339 0.750473206 0.903274414 0.669125572 0.858267141 0.828663143 0.968100715 1.117481013 1.103884894 1 18.0129267 2.054906575 2.868673624 1.083369339 0.825284857 0.615814642 0.085527714 0.155760389 2.520039864 0.038083563 0.023408833 113.476668 -2.054906575 -0.258084482 VCTIS(ph)PAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VCTISPAPR 9 0 O43439-2;O43439-5;O43439;O43439-4 O43439-2 CBFA2T2 Protein CBFA2T2 1 VCT(0.012)IS(0.988)PAPR 80.916 0.023873 217080000 642690 523260 470630 512690 535130 442550 594560 681660 609040 568830 TRUE FALSE 617572.9643 508337.1371 555683.3101 539149.9923 552342.9424 451498.6642 601836.4031 667583.4828 539904.3325 530302.6374 1.164567024 0.958579312 1.047860732 1.016683596 1.041561749 0.851398112 1.134892344 1.258872643 1.018106067 1 19.0164564 2.055043419 24.99967659 1.140039984 1.012205118 0.118117318 0.101342114 114.1264304 51833.42243 0.036748578 0.02714062 113.5124295 -2.055043419 -0.127834866 S(ph)ASPST(ph)QQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASPSTQQEK 10 0 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 2 S(0.999)AS(0.231)PS(0.321)T(0.45)QQEK 102.9 0.015307 117030000 294150 255470 226220 239970 252910 244980 279470 303860 335360 314710 TRUE FALSE 282654.2928 248184.2457 267102.9862 252354.8805 261045.0798 249933.6634 282890.2375 297585.1848 297291.3387 293394.4114 0.963393582 0.845906521 0.9103888 0.860121634 0.889741146 0.851869203 0.964197771 1.014283753 1.013282214 1 18.16248187 2.055266968 4.20488848 1.006984159 0.885292533 0.749387035 0.032160768 0.094675909 3.475658119 0.012275829 0.008450365 113.570874 -2.055266968 -0.121691626 TPLS(ph)PSPMK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPLSPSPMK 9 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 TPLS(0.925)PS(0.075)PMK 106.4 0.003086 435460000 459310 518000 444710 542990 586800 491320 435740 433120 426100 408950 TRUE FALSE 441359.6574 503227.1472 525078.9895 571013.779 605674.9549 501254.827 441072.7165 424175.9206 377730.9144 381251.4522 1.157660265 1.31993503 1.37725112 1.497735354 1.588649568 1.314761751 1.156907636 1.112588341 0.990765837 1 18.54038331 2.055481479 1.826031498 1.033989638 1.392842148 0.670774401 0.109933498 0.23290164 1.468686716 0.070456481 0.037400095 113.6269838 -2.055481479 0.35885251 GEEKPAGHRT(ph)SPVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GEEKPAGHRTSPVAK 15 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GEEKPAGHRT(0.884)S(0.116)PVAK;GEEKPAGHRT(0.611)S(0.389)PVAK 145.52 0.00019282 2640030000 2310100 2222300 1869140 1891600 1969400 2223710 2167740 2553090 2748860 2367070 TRUE FALSE 2219818.738 2158922.18 2206935.177 1989225.703 2032747.54 2268674.94 2194269.451 2500367.799 2436820.937 2206746.241 1.005923879 0.978328246 1.000085618 0.901429293 0.921151468 1.028063353 0.994346069 1.133056331 1.104259698 1 21.07348931 2.055606721 2.185553704 1.089898664 0.965705022 0.468477942 0.049116648 0.238328579 2.172076202 0.026134784 0.014700707 113.6597564 -2.055606721 -0.124193642 ENTLFDIHRS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENTLFDIHRSPAR 13 1 Q9ULI0-2;Q9ULI0;C9JG15 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 ENTLFDIHRS(1)PAR 104.09 0.00094413 293560000 264140 329650 186540 252240 258710 258610 223520 202920 211990 228540 TRUE FALSE 253817.1168 320248.7048 220251.9276 265258.1366 267031.6421 263839.2714 226255.5046 198729.6311 187925.7839 213060.7822 1.191289707 1.503086121 1.033751614 1.244988091 1.253312033 1.238328653 1.061929381 0.932736795 0.882028978 1 17.70090554 2.055636612 2.350217638 0.930864732 1.249440083 0.611490894 0.110474692 0.193612031 2.05257948 0.055461381 0.031953024 113.6675795 -2.055636612 0.31857535 TYLGEEGKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TYLGEEGKR 9 1 Q9BV86;S4R338;Q9BV86-2 Q9BV86 NTMT1 "N-terminal Xaa-Pro-Lys N-methyltransferase 1;N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processed" 0 ; 99.815 0.0081482 1309660000 534190 492090 439990 466370 482410 440360 530450 556270 631660 594500 FALSE TRUE 513313.2642 478056.075 519505.9805 490439.4116 497927.1558 449264.3809 536941.8058 544782.8301 559956.6049 554233.9855 0.926167066 0.862552798 0.937340535 0.884895954 0.898406032 0.810604172 0.968799857 0.982947355 1.010325277 1 19.08013565 2.056015567 9.977745208 0.99089186 0.888311428 0.702215912 0.033432222 0.221283644 37.88822269 0.012224653 0.009021781 113.7668063 -2.056015567 -0.102580432 KLEEEGEQFVK ddPTM_BT-474_Pertuzumab_2h_R1 5 KLEEEGEQFVK 11 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ;;;; 195.77 1.01E-07 7815620000 7112110 6748170 5753010 6391590 6917770 6558700 7522960 9019730 8674920 8526360 FALSE TRUE 6834160.878 6555718.799 6792706.882 6721460.726 7140286.355 6691321.408 7615028.235 8833469.424 7690179.45 7948862.043 0.859765944 0.824736769 0.854550858 0.845587795 0.898277806 0.841796143 0.958002315 1.111287298 0.967456651 1 22.92231691 2.056032274 4.126194908 1.03849905 0.855121948 0.798173581 0.039074583 0.079914524 2.811853097 0.015501924 0.010630512 113.7711829 -2.056032274 -0.183377103 QEEEDRDS(ph)PGPQVPDPK ddPTM_BT-474_Pertuzumab_2h_R1 3 QEEEDRDSPGPQVPDPK 17 1 M0R353;Q6NSJ2-2;Q6NSJ2 M0R353 PHLDB3 Pleckstrin homology-like domain family B member 3 1 QEEEDRDS(1)PGPQVPDPK;QEEEDRDS(1)PGPQVPDPK;QEEEDRDS(1)PGPQVPDPK 132.48 2.27E-05 957170000 681550 647880 558260 584020 627400 614390 699910 803400 843670 777800 TRUE FALSE 654914.2725 629403.0967 659150.0004 614161.3422 647580.8908 626813.3868 708475.7079 786809.5092 747900.1186 725118.9132 0.903181893 0.867999835 0.909023318 0.846980172 0.893068542 0.864428407 0.977047619 1.085076523 1.031417199 1 19.46785808 2.056146481 3.813005801 1.045861549 0.88087454 0.877741787 0.02671938 0.06220523 1.852144397 0.010579091 0.007108059 113.8011056 -2.056146481 -0.164987009 LHDFLAHSSEESEETS(ph)SPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHDFLAHSSEESEETSSPPR 20 0 P46100;P46100-4;A0A096LNL9;P46100-6;A0A096LNW1;A0A087WWG0 P46100 ATRX Transcriptional regulator ATRX 1 LHDFLAHSSEES(0.001)EET(0.115)S(0.52)S(0.365)PPR 88.264 0.0014465 211800000 75156 82021 63337 103640 82998 84675 65688 39546 74141 59065 TRUE FALSE 72218.82043 79681.84139 74783.40482 108988.8728 85667.70605 86387.18652 66491.90939 38729.36128 65724.8245 55064.47494 1.311531991 1.4470644 1.3581062 1.979295597 1.555770869 1.568837015 1.207528256 0.703345693 1.193597589 1 15.74883424 2.056264798 3.968623027 0.934750992 1.543476959 0.613523125 0.204262101 0.136521701 4.422591695 0.086776594 0.058939833 113.8321132 -2.056264798 0.608725966 TSS(ph)PRSPPSSSEIFTPAHEENVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSPRSPPSSSEIFTPAHEENVR 23 1 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 T(0.081)S(0.081)S(0.464)PRS(0.373)PPS(0.001)SSEIFTPAHEENVR 167.22 6.68E-12 272300000 99228 127680 62138 68237 87080 104120 67514 55729 69553 48600 TRUE FALSE 95350.06006 124038.6914 73367.71885 71758.71975 89881.00728 106225.3777 68340.25653 54578.17668 61657.63503 45308.27871 2.104473239 2.737660643 1.619300511 1.583788257 1.983765657 2.344502611 1.508339281 1.204596119 1.360846997 1 15.46748706 2.056266059 4.833470473 1.24071207 2.045728571 0.600163019 0.323874755 0.153073218 7.469294368 0.136341148 0.096606596 113.8324437 -2.056266059 0.805016501 ATLPSPDKLPGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATLPSPDKLPGFK 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 160.48 3.99E-05 824490000 1256700 1170400 965360 1068500 1123500 1205500 1233100 1423300 1583100 1456700 FALSE TRUE 1207586.775 1137021.338 1139822.026 1123645.413 1159638.398 1229876.036 1248191.047 1393908.358 1403393.125 1358036.412 0.889215314 0.837253941 0.839316249 0.827404482 0.853908178 0.905628174 0.919114566 1.026414569 1.033398746 1 20.37309073 2.056332905 1.442233836 1.028245671 0.847886126 0.913574684 0.022305858 0.103551211 0.404374302 0.014638053 0.007294138 113.8499659 -2.056332905 -0.180359544 DYGHSSSRDDYPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYGHSSSRDDYPSR 14 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 186.05 6.65E-07 464280000 214080 318610 158746 220804 207122 248923 177022 147696 150386 183186 FALSE TRUE 205713.5169 309523.5548 187434.9335 232199.7209 213784.2672 253956.3936 179188.4482 144646.026 133314.8117 170778.6491 1.204562269 1.812425362 1.097531422 1.359653108 1.251820813 1.487050021 1.049243856 0.846979566 0.780629268 1 17.38176809 2.05658031 3.89919699 0.873073487 1.370100602 0.588153511 0.187998269 0.146490184 4.568573492 0.075561582 0.051100425 113.9148414 -2.05658031 0.497027115 GVIVDKDFSHPQMPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GVIVDKDFSHPQMPK 15 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 125.61 5.37E-05 8284130000 13830640 13385190 11124340 11456480 13091300 13391050 14031210 14626940 17497910 16063400 FALSE TRUE 13290123.3 13003457.49 13134755.7 12047750.31 13512393.55 13661826.21 14202928.15 14324888.58 15511620.61 14975411.61 0.887462972 0.868320539 0.877088125 0.804502114 0.902305319 0.912283853 0.948416545 0.956560591 1.035805961 1 23.83609232 2.0566285 0.950754347 1.01207738 0.862496727 0.81558622 0.027575294 0.23062366 0.385703321 0.022219925 0.011038981 113.9274822 -2.0566285 -0.149580652 DRPVGGS(ph)PGGPR ddPTM_BT-474_Pertuzumab_2h_R1 8 DRPVGGSPGGPR 12 1 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR 154.46 4.33E-05 3594705000 1642023 1900211 1529198 1790839 1615291 1694031 1593928 1694222 1596043 1720822 TRUE FALSE 1577850.926 1846018.843 1805558.095 1883264.415 1667248.302 1728285.467 1613434.968 1659235.724 1414866.89 1604269.193 0.983532522 1.150691449 1.125470777 1.173907985 1.039257195 1.077303906 1.005713364 1.03426266 0.881938577 1 20.61348481 2.056676502 1.040146974 0.958083998 1.106161515 0.457796186 0.061316922 0.458244217 0.917787827 0.045991958 0.022457104 113.9400752 -2.056676502 0.148077517 RSYS(ph)PDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 RSYSPDGK 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RSYS(1)PDGK;RS(0.001)YS(0.999)PDGK;RS(0.099)Y(0.001)S(0.901)PDGK 109.39 0.002222 2641190000 1460690 1282790 1040390 1128820 1189960 1170130 1306070 1448620 1459980 1414890 TRUE FALSE 1403604.62 1246206.085 1228411.616 1187078.535 1228236.144 1193790.83 1322054.075 1418705.491 1294249.191 1319058.24 1.064096017 0.944769569 0.931279286 0.89994399 0.931146258 0.905032692 1.002271193 1.075544239 0.981191847 1 20.33107683 2.056683999 6.477857216 1.030175645 0.942948683 0.319285609 0.048608211 0.198344334 17.14679719 0.018669164 0.013642054 113.9420422 -2.056683999 -0.087226962 QVDEGVWPPPNNLLSQS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 QVDEGVWPPPNNLLSQSPK 19 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 QVDEGVWPPPNNLLS(0.102)QS(0.898)PK;QVDEGVWPPPNNLLS(0.134)QS(0.866)PK;QVDEGVWPPPNNLLS(0.003)QS(0.997)PK;QVDEGVWPPPNNLLS(0.042)QS(0.958)PK 153.87 2.67E-08 479081000 1570290 1413010 1339770 1364720 1487700 1425430 1577360 1833590 1774840 1677900 TRUE FALSE 1508921.331 1372712.338 1581896.242 1435153.363 1535553.222 1454253.171 1596664.204 1795725.726 1573367.604 1564254.338 0.964626591 0.877550603 1.011278155 0.91746804 0.981651886 0.929678209 1.020719051 1.147975544 1.005825949 1 20.57704367 2.056792686 4.995605422 1.071691432 0.947862756 0.444916627 0.05203248 0.140521737 7.304900186 0.019356749 0.013792137 113.970561 -2.056792686 -0.123828676 NNDALHMSLESLICESR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNDALHMSLESLICESR 17 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 175.39 1.15E-13 0 62286 91134 74202 102500 75429 86136 79782 75735 86317 92707 FALSE TRUE 59851.79426 88534.94755 87611.95201 107790.0373 77855.24229 87877.72894 80758.39598 74171.04578 76518.65603 86427.87232 0.6925057 1.02437958 1.013700207 1.247167544 0.900811743 1.016775336 0.934402223 0.858184331 0.885346983 1 16.39920902 2.057112951 5.002976061 0.897977888 0.993719107 0.044209272 0.133296093 0.491625012 25.57051574 0.052333276 0.037304565 114.0546382 -2.057112951 0.095741219 HAPTYTIPLS(ph)PVLS(ph)PTLPAEAPTAQVPPSLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 HAPT(0.007)Y(0.004)T(0.032)IPLS(0.957)PVLS(0.943)PT(0.057)LPAEAPTAQVPPSLPR;HAPTYT(0.003)IPLS(0.997)PVLS(0.971)PT(0.029)LPAEAPTAQVPPSLPR;HAPT(0.122)Y(0.11)T(0.128)IPLS(0.656)PVLS(0.492)PT(0.488)LPAEAPT(0.003)AQVPPSLPR;HAPTYTIPLS(1)PVLS(0.989)PT(0.011)LPAEAPTAQVPPSLPR 193.4 1.26E-20 1198448000 354201 425997 327132.8 422153 431265 416448 327135.4 243033.5 344567 313986.9 TRUE FALSE 340358.4333 413847.9827 386252.974 443940.3669 445137.0304 424868.8639 331138.9809 238014.7733 305453.1987 292720.2876 1.162742891 1.413800137 1.319529224 1.51660266 1.520690739 1.451450008 1.131247115 0.813113349 1.04349856 1 18.15916321 2.057209944 3.967377064 0.937380635 1.404235022 0.762241806 0.112541097 0.098102161 3.168040658 0.047761489 0.032467535 114.0801133 -2.057209944 0.466854387 YPIEHGIITNWDDMEK ddPTM_BT-474_Pertuzumab_2h_R1 32 YPIEHGIITNWDDMEK 16 0 P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P68133 ACTA1;ACTC1;ACTG2;ACTA2 "Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle" 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 229.56 7.15E-15 3.69052E+11 108822378 103679639 89677836 95808878 98809525 104477179 107713107 121239363 133475463 121096769 FALSE TRUE 104569479.2 100722797.2 105884615.8 100753585.7 101987823.1 106589779.1 109031332.2 118735727.8 118323888 112894777 0.926256129 0.892182968 0.937905355 0.892455686 0.903388322 0.944151554 0.965778357 1.051738007 1.048090011 1 26.7504035 2.05734896 1.973034605 1.038697312 0.911615744 0.862243382 0.020965721 0.10216252 0.754875645 0.011157512 0.006080374 114.1166358 -2.05734896 -0.127081567 S(ph)SPVRPSSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPVRPSSEK 10 1 B3KV94;A0A3B3ISE6;A0A3B3ITA8;A0A3B3ITJ7;A0A3B3ITE7;A0A3B3IT25;A0A3B3IS40;Q9UGL1;Q9UGL1-2 B3KV94 KDM5B Lysine-specific demethylase 5B 1 S(0.764)S(0.236)PVRPSSEK 112.5 0.0042425 82613000 148270 135380 141070 155390 145590 142360 168690 197230 201800 188180 TRUE FALSE 142475.4445 131519.095 166564.4871 163409.6965 150273.0346 145238.6167 170754.4787 193157.1316 178892.51 175434.401 0.812129455 0.749676769 0.949440282 0.931457545 0.856576782 0.827879914 0.973323805 1.10102198 1.019711693 1 17.42057215 2.057478857 4.244070346 1.049262344 0.858341047 0.671804094 0.058999378 0.126283436 4.68772018 0.025678716 0.017750346 114.150773 -2.057478857 -0.190921297 QCHQDGHQDHDTHHHHWR ddPTM_BT-474_Pertuzumab_2h_R1 2 QCHQDGHQDHDTHHHHWR 18 0 D6RJB4;H0YA20;P52824 D6RJB4 DGKQ Diacylglycerol kinase;Diacylglycerol kinase theta 0 ; 77.468 0.03881 43191000 34085.5 40737.1 28761.8 31475 31741.7 30006.8 25872.6 6454.7 31232.5 18409.2 FALSE TRUE 32753.40098 39575.31779 33959.69706 33099.42852 32762.70061 30613.55806 26189.23662 6321.408189 27687.11754 17162.32849 1.908447388 2.305941051 1.978734825 1.928609428 1.908989251 1.783764836 1.525972227 0.368330451 1.613249482 1 14.06695768 2.057536001 3.335155134 0.925173317 1.981527101 0.655455353 0.313166239 0.128561265 2.873479283 0.134046796 0.08670747 114.165794 -2.057536001 1.056353784 QLDDKDEEINQQSQLVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLDDKDEEINQQSQLVEK 18 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 273.46 4.75E-39 2041130000 1350580 1180150 1041210 952210 1177330 1166760 1338670 1528620 1711590 1554500 FALSE TRUE 1297797.84 1146493.277 1229379.809 1001353.672 1215199.889 1190352.687 1355053.044 1497053.463 1517297.479 1449212.33 0.895519458 0.791114769 0.848308963 0.690964085 0.838524392 0.821379077 0.935027267 1.033011817 1.046980796 1 20.46683756 2.057590378 2.180083512 1.031553727 0.807536687 0.781785378 0.050688611 0.134214151 1.217871673 0.026496844 0.014920969 114.1800891 -2.057590378 -0.22401704 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_BT-474_Pertuzumab_2h_R1 4 NKDSGSDTASAIIPSTTPSVDSDDESVVK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPSTT(0.001)PS(0.031)VDS(0.934)DDES(0.035)VVK;NKDSGSDTASAIIPSTTPS(0.056)VDS(0.944)DDESVVK;NKDSGSDTASAIIPSTTPS(0.002)VDS(0.994)DDES(0.004)VVK;NKDSGSDTASAIIPSTTPS(0.035)VDS(0.964)DDES(0.001)VVK 175.39 3.44E-13 2454780000 1861760 1955890 1390157 1436382 1377281 1734630 1890480 2449210 2563410 1951150 TRUE FALSE 1789000.361 1900109.932 1641389.294 1510513.847 1421582.494 1769705.407 1913616.26 2398632.958 2272422.443 1818996.873 0.983509311 1.044592193 0.902359602 0.83041036 0.781520032 0.972901842 1.052017345 1.318656999 1.24927232 1 20.79471163 2.057755707 2.986556511 1.219756245 0.912812157 0.563824666 0.105168721 0.170394131 3.006811025 0.049998274 0.031232601 114.2235641 -2.057755707 -0.306944088 LKS(ph)PSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKSPSQK 7 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LKS(0.956)PS(0.044)QK;LKS(0.97)PS(0.03)QK 123.11 0.0025892 2369800000 3560400 3275800 2937000 3022100 3253900 3400500 3771200 3981000 4270900 4526500 TRUE FALSE 3421255.632 3182377.391 3467781.233 3178070.943 3358564.649 3469260.44 3817353.074 3898790.959 3786085.337 4219916.123 0.810740198 0.754132854 0.821765441 0.753112349 0.795884219 0.822115971 0.904604016 0.923902477 0.897194453 1 22.00878289 2.057869811 0.896468424 0.96349302 0.779391333 0.843851995 0.030033233 0.205337042 0.30589209 0.023482294 0.011886656 114.2535785 -2.057869811 -0.184101687 EVIEIEDAS(ph)PTKCPITTK ddPTM_BT-474_Pertuzumab_2h_R1 6 EVIEIEDASPTKCPITTK 18 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 EVIEIEDAS(0.984)PT(0.015)KCPITTK;EVIEIEDAS(0.992)PT(0.008)KCPITTK;EVIEIEDAS(0.907)PT(0.093)KCPITTK;EVIEIEDAS(0.997)PT(0.003)KCPITTK;EVIEIEDAS(0.986)PT(0.014)KCPITTK;EVIEIEDAS(0.944)PT(0.056)KCPITTK 213.16 6.84E-17 9289350000 4529040 3862520 3637578 3505750 3904680 3881820 4550300 5096850 5562580 5441180 TRUE FALSE 4352040.11 3752364.711 4294969.262 3686682.178 4030277.578 3960313.06 4605987.933 4991598.266 4931139.239 5072644.032 0.857943132 0.739725612 0.846692422 0.72677723 0.794512202 0.780719687 0.908005353 0.984022974 0.972104332 1 22.27430649 2.057896097 2.627843588 0.982464292 0.787591173 0.83385626 0.039268506 0.098598779 1.324113053 0.017748591 0.010633822 114.2604938 -2.057896097 -0.194873119 ALKDEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 ALKDEEK 7 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;; 101.64 0.0081244 15771920000 20075600 16894660 14579510 13273750 15646110 15969330 18726510 21208130 23970120 21004740 FALSE TRUE 19291023.36 16412840.84 17214351.78 13958809.83 16149381.34 16292240.79 18955690.63 20770174.7 21249132.47 19582070.25 0.985137072 0.83815657 0.879087428 0.712836265 0.824702451 0.831997873 0.968012595 1.060673077 1.085132072 1 24.22302996 2.058182616 2.875909072 1.052217626 0.83903947 0.660617977 0.065935505 0.156830715 2.55285646 0.031622057 0.019521299 114.3359005 -2.058182616 -0.213178155 S(ph)PPKADEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPKADEK 8 1 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)PPKADEK 61.435 0.052072 319130000 910950 713420 671400 617470 643130 637560 818800 907440 1031500 907860 TRUE FALSE 875349.0669 693073.9601 792736.9152 649337.7007 663816.8605 650451.9 828820.7193 888701.0469 914408.4444 846369.8336 1.034239445 0.818878382 0.936631817 0.767203266 0.784310634 0.768519711 0.97926543 1.050015031 1.080388747 1 19.69092868 2.058215325 5.182660924 1.041658327 0.847554459 0.546520163 0.079894985 0.145707144 8.058180515 0.031517013 0.022591881 114.344512 -2.058215325 -0.194103868 GAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTKVDAAEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTKVDAAEGR 40 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.084)S(0.464)S(0.452)PESQHGGTQSPGGGQPLLQPTKVDAAEGR;GAAAADLLS(0.08)S(0.451)S(0.451)PES(0.014)QHGGT(0.004)QSPGGGQPLLQPTKVDAAEGR 280.7 1.30E-77 1302510000 451650 632510 373430 379750 368330 632300 373990 373920 432710 411210 TRUE FALSE 433999.0187 614471.4341 440917.1079 399348.943 380177.669 645085.5392 378567.0015 366198.4213 383590.5749 383358.3804 1.132097382 1.602864227 1.150143392 1.041711786 0.991703034 1.682721892 0.987501567 0.955237814 1.000605685 1 18.54833419 2.058335257 24.99999976 0.978062014 1.260849136 0.297958809 0.211129099 97.89866286 41954.50833 0.079506529 0.058719456 114.376093 -2.058335257 0.282787122 HRGS(ph)EEDPLLS(ph)PVETWK ddPTM_BT-474_Pertuzumab_2h_R1 2 HRGSEEDPLLSPVETWK 17 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 HRGS(1)EEDPLLS(1)PVETWK;HRGS(1)EEDPLLS(1)PVETWK 127.96 2.19E-05 82889000 202008 236693 216651 283609 345390 289959 167052 63742 145554 126215 TRUE FALSE 194113.304 229942.7474 255804.6551 298246.0945 356499.783 295822.1696 169096.4323 62425.70542 129031.3201 117666.3456 1.649692637 1.954192987 2.17398317 2.534676274 3.029751465 2.51407629 1.437084082 0.530531522 1.096586449 1 16.84434222 2.058397035 3.994140789 0.848653573 2.325439901 0.751551039 0.373854582 0.112015156 3.656716311 0.172622639 0.117683131 114.392364 -2.058397035 1.476786328 SKIETEIK ddPTM_BT-474_Pertuzumab_2h_R1 6 SKIETEIK 8 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;;; 123.75 0.0012169 4196490000 6869130 6387920 5448330 5678860 6345600 6723540 7147730 8085140 9315800 8668860 FALSE TRUE 6600676.805 6205742.776 6432964.428 5971946.645 6549711.987 6859494.585 7235206.058 7918179.034 8258309.439 8081710.391 0.816742556 0.767874927 0.795990467 0.738945886 0.810436364 0.848767681 0.895256785 0.979765254 1.021851692 1 22.94622922 2.05848382 1.172900513 1.01627953 0.780772706 0.947103519 0.022120313 0.09403321 0.240621968 0.015935097 0.007745971 114.4152253 -2.05848382 -0.235506824 LLGS(ph)SEDLSSDSESHLPEEPAPLSPQQAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLGSSEDLSSDSESHLPEEPAPLSPQQAFR 30 0 C9JIE2;Q86TI0-2;Q86TI0;H0Y8P0;H0YA01;H7C380;H7C0Z7 C9JIE2 TBC1D1 TBC1 domain family member 1 1 LLGS(0.882)S(0.113)EDLS(0.002)S(0.002)DSESHLPEEPAPLSPQQAFR 150.04 1.61E-08 24425000 9205.2 13634 9299.7 8978.9 8904.2 10510 11296 13910 11865 13979 TRUE FALSE 8845.450607 13245.17167 10980.36266 9442.302105 9190.61168 10722.5194 11434.24383 13622.75364 10518.13494 13032.18988 0.678738623 1.016342748 0.842556989 0.724536873 0.705223893 0.822771883 0.877384686 1.045315773 0.807088835 1 13.66979191 2.058493282 3.824373707 0.957260815 0.803276384 0.294184393 0.105501506 0.282726194 8.430523683 0.044799986 0.030196615 114.417718 -2.058493282 -0.153984431 VESGDPSLHPPPSPGTPSATPAS(ph)PPASATPSQR ddPTM_BT-474_Pertuzumab_2h_R1 3 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPSPGTPS(0.029)AT(0.357)PAS(0.613)PPASATPSQR;VESGDPSLHPPPSPGTPS(0.001)AT(0.059)PAS(0.929)PPAS(0.008)AT(0.002)PS(0.001)QR;VESGDPSLHPPPSPGTPS(0.001)AT(0.216)PAS(0.782)PPAS(0.001)ATPSQR 193.4 1.13E-20 865080000 332063 467789 405042 520163 480896 502285 384436 351445 355908 409336 TRUE FALSE 319085.6108 454448.1157 478242.0995 547008.6748 496364.4566 512441.5468 389140.8428 344187.5379 315506.8159 381611.3081 0.836153447 1.190866481 1.253217841 1.433418411 1.300706887 1.342836378 1.0197309 0.901932229 0.826775332 1 18.5417444 2.058550062 4.483304628 0.910636032 1.23785795 0.471403474 0.152675906 0.1816791 7.508293512 0.0642399 0.044971995 114.4326781 -2.058550062 0.327221918 SSEAVIWEVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSEAVIWEVLR 11 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 ; 111.06 0.0039813 44549000 65244 73585 59829 63923 64853 60252 68268 65101 63033 68843 FALSE TRUE 62694.19235 71486.42785 70641.43119 67222.07369 66939.05564 61470.33672 69103.48421 63756.6416 55877.7581 64180.20229 0.976846288 1.113839242 1.10067324 1.04739579 1.042986049 0.957777235 1.07671029 0.993400446 0.870638547 1 15.96984072 2.05858021 0.790141295 0.951309935 1.063186614 0.316031039 0.057844577 0.765926986 0.896680876 0.048952426 0.026241958 114.4406222 -2.05858021 0.111876679 VDDLLESYMGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDDLLESYMGIR 12 0 O14908;O14908-2;K7EM11;A0A2R8Y651;Q8TF64 O14908 GIPC1;GIPC3 PDZ domain-containing protein GIPC1;PDZ domain-containing protein GIPC3 0 121.83 0.00047378 0 166810 184010 181960 186050 191290 175050 206580 230670 277980 179020 FALSE TRUE 160290.8808 178762.215 214844.2197 195652.0628 197443.0166 178589.6309 209108.1878 225906.5839 246424.8758 166894.8159 0.960430555 1.071107056 1.287303134 1.17230761 1.183038643 1.070072967 1.252933991 1.353586585 1.476528042 1 17.34857962 2.058601947 5.321483842 1.31341721 1.13456269 0.197242361 0.138640852 0.262718219 15.24897022 0.052425447 0.037710891 114.4463502 -2.058601947 -0.17885452 DKFSFDLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKFSFDLGK 9 1 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 141.88 9.64E-05 19265000000 16934000 15541500 15653100 16072000 17820700 16760400 22102000 24386000 27958000 27519000 FALSE TRUE 16272200.56 15098271.64 18481963.37 16901477.85 18393919 17099306.77 22372490.89 23882420.58 24784325.05 25655113.62 0.634267336 0.588509249 0.720400761 0.658795673 0.716968916 0.666506765 0.872048014 0.930902936 0.966057895 1 24.61274308 2.058625634 1.386163599 0.983730309 0.65546572 0.921535909 0.040307051 0.106655677 0.384264294 0.027015707 0.013381591 114.4525924 -2.058625634 -0.328264589 KRPES(ph)PPSILTPPVVPTADK ddPTM_BT-474_Pertuzumab_2h_R1 4 KRPESPPSILTPPVVPTADK 20 2 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 1 KRPES(0.955)PPS(0.045)ILTPPVVPTADK;KRPES(0.462)PPS(0.462)ILT(0.077)PPVVPTADK;KRPES(0.466)PPS(0.466)ILT(0.068)PPVVPTADK;KRPES(0.487)PPS(0.487)ILT(0.026)PPVVPTADK 159.66 1.98E-11 2952368000 1849310 1627600 1621279 1547970 1794730 1528450 1985540 2268270 2415340 2213160 TRUE FALSE 1777036.921 1581182.442 1914280.18 1627860.917 1852459.12 1559356.306 2009839.632 2221429.432 2141160.729 2063260.702 0.861275998 0.766351261 0.927793651 0.788974905 0.897830855 0.755772794 0.974108425 1.076659595 1.037755785 1 20.97649469 2.058647337 5.356959134 1.042170897 0.835846662 0.749825411 0.054377851 0.084030999 4.938759381 0.019347908 0.013928548 114.4583121 -2.058647337 -0.206324235 SS(ph)LPNGEGLQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSLPNGEGLQLK 12 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 S(0.037)S(0.963)LPNGEGLQLK;S(0.053)S(0.947)LPNGEGLQLK 224.5 5.51E-06 0 1752560 1592550 1747120 1904130 1848310 1738200 2154100 2529800 2543700 2695000 TRUE FALSE 1684068.018 1547132.033 2062863.448 2002402.377 1907762.57 1773347.595 2180462.52 2477558.746 2254949.84 2512465.25 0.670285099 0.61578246 0.821051534 0.796987094 0.759318988 0.70581975 0.867857783 0.986106672 0.897504887 1 21.26067221 2.058742278 3.5159969 0.95550709 0.732011775 0.746785628 0.061429979 0.127218648 3.178133284 0.028488451 0.018750476 114.4833366 -2.058742278 -0.223495315 KDSENT(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDSENTPVK 9 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 KDS(0.001)ENT(0.999)PVK;KDS(0.016)ENT(0.984)PVK 82.774 0.010255 491370000 751730 576410 633450 567380 558230 563040 710340 786660 810540 893160 TRUE FALSE 722351.5605 559971.3512 747928.506 596662.5498 576185.9749 574425.0546 719033.3534 770415.1961 718530.8973 832665.4777 0.867517124 0.672504585 0.898234076 0.716569338 0.691977739 0.68986294 0.863532082 0.925239747 0.862928651 1 19.66737749 2.05875654 5.195251789 0.915371893 0.75445194 0.506932931 0.077354273 0.163451355 9.041134737 0.029278066 0.020999899 114.4870962 -2.05875654 -0.160919953 RLHPPS(ph)PVPQGVCPAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLHPPSPVPQGVCPAHR 17 1 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 RLHPPS(1)PVPQGVCPAHR 74.12 0.011673 164470000 116500 149900 100250 130090 134150 141830 113160 94119 138360 121840 TRUE FALSE 111947.0512 145624.9988 118367.405 136803.9605 138465.0566 144697.8998 114544.8859 92175.40976 122653.9529 113587.6683 0.98555638 1.282049372 1.042079716 1.204390957 1.219014869 1.273887403 1.008427127 0.811491345 1.079817508 1 16.79344669 2.058850393 6.491276548 0.934717385 1.170217177 0.427584739 0.108603778 0.156306109 13.15492754 0.039403538 0.028813217 114.5118401 -2.058850393 0.235499792 DGTAPPPQSPGSPGTGQDEEWS(ph)DEESPRK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGTAPPPQSPGSPGTGQDEEWSDEESPRK 29 1 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 DGTAPPPQSPGSPGTGQDEEWS(0.999)DEES(0.001)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.997)DEES(0.003)PRK 248.98 3.02E-46 2468000000 481330 526450 400430 396520 445420 463110 498380 584270 612270 523220 TRUE FALSE 462519.0915 511436.1614 472796.6085 416984.4447 459747.3388 472474.4015 504479.3235 572204.6203 542767.6764 487781.8434 0.948208913 1.048493642 0.969278818 0.854858479 0.942526552 0.968618262 1.034231451 1.173074866 1.112726281 1 18.89587653 2.05899764 3.436573928 1.113181747 0.955099063 0.517247222 0.060129727 0.171484519 4.080878324 0.02696651 0.017631781 114.5506717 -2.05899764 -0.158082684 LLHEDLDES(ph)DDDMDEK ddPTM_BT-474_Pertuzumab_2h_R1 6 LLHEDLDESDDDMDEK 16 0 O43150;O43150-2 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK 374.5 1.13E-104 4804090000 4212470 3807080 3645080 3624310 3796060 3935660 4273000 4882310 5358760 4645540 TRUE FALSE 4047842.015 3698505.806 4303827.04 3811361.073 3918163.717 4015241.742 4325294.252 4781488.592 4750456.031 4330893.438 0.934643642 0.853982177 0.993750389 0.880040372 0.904701022 0.927116263 0.998707152 1.104042078 1.096876683 1 22.04623324 2.05920155 2.797021983 1.076191417 0.913502066 0.708604367 0.043606316 0.128341476 1.969155686 0.019588123 0.011995755 114.6044682 -2.05920155 -0.162689351 ST(ph)PDSTYSESFK ddPTM_BT-474_Pertuzumab_2h_R1 5 STPDSTYSESFK 12 0 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 S(0.165)T(0.835)PDSTYSESFK;S(0.229)T(0.593)PDS(0.137)T(0.041)YSESFK;S(0.226)T(0.774)PDSTYSESFK;S(0.113)T(0.887)PDSTYSESFK;S(0.234)T(0.766)PDSTYSESFK 373.15 1.38E-85 4507160000 4209580 3929110 3661580 3661420 3790260 4179820 4635740 5030690 5874760 5545010 TRUE FALSE 4045064.96 3817055.63 4323308.957 3850386.325 3912177.155 4264338.824 4692473.573 4926804.493 5207881.874 5169441.534 0.782495543 0.738388394 0.836320312 0.744836033 0.756789129 0.824912865 0.907733174 0.953063201 1.007436072 1 22.301577 2.059222063 1.33255091 0.999079413 0.770463287 0.923276396 0.027497384 0.107863779 0.358531691 0.018737208 0.009223263 114.6098813 -2.059222063 -0.228616126 LVGLNLS(ph)PPMSPVQLPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVGLNLSPPMSPVQLPLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 LVGLNLS(0.815)PPMS(0.185)PVQLPLR;LVGLNLS(0.515)PPMS(0.485)PVQLPLR;LVGLNLS(0.996)PPMS(0.004)PVQLPLR;LVGLNLS(0.977)PPMS(0.023)PVQLPLR 169.67 1.85E-11 1176414000 722820 746140 576810 715010 662320 591300 684240 676520 637970 651950 TRUE FALSE 694571.3953 724860.8177 681052.3981 751911.7518 683624.1243 603256.4911 692613.9338 662549.6256 565550.3202 607792.8458 1.142776523 1.192611632 1.120533752 1.237118464 1.124765007 0.992536347 1.139555917 1.090091188 0.930498482 1 19.21322017 2.059260169 0.558977069 0.983184191 1.176395162 0.533279235 0.061900642 0.708546789 0.45815699 0.059600338 0.04240924 114.6199381 -2.059260169 0.193210971 LLSSSLTADCSLRS(ph)PSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLSSSLTADCSLRSPSGR 18 1 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLSSSLTADCSLRS(1)PSGR;LLSSSLTADCS(0.005)LRS(0.993)PS(0.002)GR 240.31 3.63E-24 519680000 187389 221190 173503 192399 214700 214527 148049 123207 126164 126470 TRUE FALSE 180065.6307 214881.8778 204858.8517 202328.7354 221606.0205 218864.8829 149860.8679 120662.7324 111842.3916 117904.0743 1.527221446 1.822514439 1.737504433 1.716045325 1.879545061 1.856296182 1.271040623 1.023397479 0.948588014 1 16.84725405 2.059279624 3.108418265 1.008113107 1.762625739 0.925481574 0.09871652 0.063256127 1.215842009 0.046088566 0.029211448 114.6250726 -2.059279624 0.754512632 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHT(ph)PTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPT(0.003)DALDQFET(0.019)VDS(0.015)T(0.015)PLS(0.11)VHT(0.742)PT(0.095)LR;GIEHQDSQHSFLAFLNTPTDALDQFETVDS(0.065)T(0.043)PLS(0.192)VHT(0.571)PT(0.128)LR 214.42 5.77E-44 258101000 61516 98008 70685 92118 62931 81291 58498 18509.8 66914 70779 TRUE FALSE 59111.88671 95212.9078 83459.35188 96872.22102 64955.23277 82934.75972 59213.91602 18127.56616 59318.20325 65985.07529 0.895837225 1.442946111 1.264821651 1.468092907 0.984392796 1.256871487 0.897383473 0.274722217 0.89896394 1 16.00985213 2.059341995 4.467592639 0.63018671 1.228411068 0.437307478 0.248170913 0.148729803 6.079740822 0.095917209 0.067142667 114.6415355 -2.059341995 0.598224358 SLLENDQLLSHGGQDLSADAFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLENDQLLSHGGQDLSADAFHR 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 301.12 3.68E-62 294050000 86477 99903 80289 90926 91844 90929 80495 54849 86540 107920 FALSE TRUE 83097.38323 97053.86426 94799.00832 95618.70176 94798.24567 92767.64668 81480.12189 53716.34898 76716.34201 100610.4823 0.825931666 0.964649628 0.942237888 0.950385085 0.942230308 0.92204753 0.809857184 0.5339041 0.762508441 1 16.6184211 2.059458593 4.555265006 0.704300727 0.927564745 0.238795984 0.115524053 0.181651153 7.715151764 0.043942165 0.030879903 114.6723185 -2.059458593 0.223264019 LLVDVDESTLSPEEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLVDVDESTLSPEEQK 16 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 204.85 5.61E-11 52525000 91010 92045 97187 90436 98919 101170 110280 130750 136430 139100 FALSE TRUE 87453.22858 89419.96672 114750.8528 95103.4128 102100.8195 103215.7267 111629.6396 128049.9668 120943.0384 129678.6331 0.674384257 0.689550503 0.884886354 0.733377662 0.787337258 0.795934721 0.860817522 0.987440751 0.932636591 1 16.98458126 2.059604481 1.323226752 0.985020007 0.753266641 0.740042053 0.056827828 0.227827264 0.746518913 0.040000591 0.019675304 114.7108456 -2.059604481 -0.231753365 IGEVSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 IGEVSSPK 8 0 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 IGEVS(0.075)S(0.925)PK;IGEVS(0.002)S(0.998)PK;IGEVS(0.004)S(0.996)PK 118.04 0.0020592 1435960000 5118220 3888530 3700570 3588260 4161360 3422770 4662920 5567700 4627530 4617210 TRUE FALSE 4918194.304 3777632.932 4369345.318 3773450.529 4295213.924 3491980.755 4719986.21 5452725.049 4102232.195 4304482.254 1.142575114 0.877604485 1.015068726 0.876632846 0.997846819 0.81124292 1.096528207 1.266755147 0.95301408 1 22.03740829 2.059689794 12.52488359 1.122571771 0.951493731 0.183114461 0.117473119 0.965464986 200.610744 0.041894279 0.030938487 114.7333816 -2.059689794 -0.17107804 ILEEFRK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILEEFRK 7 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 101.28 0.014707 964290000 764870 855740 632700 693220 815100 812550 823050 921900 976450 1012590 FALSE TRUE 734978.0348 831335.1331 747042.9643 728997.1673 841318.4318 828980.3177 833122.7321 902862.4428 865607.4896 944006.3774 0.778573167 0.880645675 0.791353726 0.772237545 0.891221131 0.878151184 0.882539305 0.956415618 0.916950892 1 19.84843708 2.059835798 0.549123049 0.99117356 0.8043284 0.726502161 0.037431568 0.440333645 0.276881086 0.035266059 0.025579244 114.7719599 -2.059835798 -0.18684516 LVGATATSS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 5 LVGATATSSPPPK 13 0 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 LVGATAT(0.01)S(0.003)S(0.987)PPPK;LVGATATS(0.012)S(0.988)PPPK;LVGATAT(0.005)S(0.077)S(0.918)PPPK;LVGATAT(0.017)S(0.056)S(0.928)PPPK;LVGAT(0.007)AT(0.072)S(0.178)S(0.744)PPPK 244.37 5.14E-17 3771370000 4984370 4646210 4215800 3885940 4580930 4299510 4648780 5298770 4553430 4723410 TRUE FALSE 4789575.31 4513704.64 4977688.84 4086493.829 4728279.774 4386449.038 4705673.16 5189348.548 4036543.716 4403489.234 1.087677307 1.025029108 1.130396505 0.928012676 1.073757542 0.996130297 1.068623746 1.178462867 0.916669373 1 22.07021571 2.059969047 24.99943818 1.069542064 1.039373296 0 0.081454023 321.4634657 134007.1155 0.02977586 0.021990922 114.8071794 -2.059969047 -0.030168769 EVQDKDYPLT(ph)PPPS(ph)PTVDEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVQDKDYPLTPPPSPTVDEPK 21 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 2 EVQDKDYPLT(1)PPPS(0.989)PT(0.011)VDEPK;EVQDKDYPLT(1)PPPS(0.978)PT(0.022)VDEPK 144.49 2.91E-07 430020000 856730 710570 598440 550900 684200 737410 761910 949660 1017460 859040 TRUE FALSE 823248.0444 690305.2393 706591.4202 579332.015 706207.9144 752320.9354 771234.4825 930049.1891 901962.2063 800856.4556 1.027959553 0.861958762 0.882294717 0.723390579 0.881815848 0.939395481 0.963012132 1.161318214 1.126247032 1 19.61118415 2.06031236 2.166533273 1.110229143 0.872663002 0.560957494 0.081814646 0.210698892 1.889506312 0.043966538 0.024773547 114.8979712 -2.06031236 -0.237566141 ARPFPDGLAEDIDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARPFPDGLAEDIDK 14 1 P13639;M0R0I6 P13639 EEF2 Elongation factor 2 0 ; 131.24 5.24E-05 559880000 457770 412050 452550 503320 462500 412100 574230 674030 688870 707680 FALSE TRUE 439879.8423 400298.7374 534335.8519 529296.4055 477376.7325 420432.9444 581257.5985 660111.045 610672.3656 659748.2033 0.666738977 0.606744718 0.809908764 0.802270325 0.723574131 0.637262735 0.881029453 1.00054997 0.925614291 1 19.33155599 2.060338629 4.633290111 0.968762568 0.713556503 0.783914047 0.064043251 0.098733315 4.316168964 0.027374399 0.01931034 114.9049212 -2.060338629 -0.255206066 SQLEEKENK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQLEEKENK 9 1 P04080;A0A1W2PS52 P04080 CSTB Cystatin-B 0 112.13 0.0018361 172690000 184080 172660 115650 145320 175620 243540 248770 400220 401940 444660 FALSE TRUE 176885.9501 167735.9059 136550.5276 152819.9826 181268.9768 248464.5457 251814.5217 391955.3171 356313.4563 414542.7821 0.426701315 0.404628697 0.329400326 0.368647071 0.437274473 0.599370092 0.607451227 0.945512343 0.859533615 1 18.66116147 2.060536237 1.013194212 0.98129417 0.377517439 0.94312243 0.056847606 0.107336318 0.203966128 0.043238466 0.021252875 114.9572159 -2.060536237 -0.603776731 down YCDPDSYHRR ddPTM_BT-474_Pertuzumab_2h_R1 2 YCDPDSYHRR 10 1 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 90.108 0.0071768 1411940000 627240 794300 448170 549560 577540 670900 538210 500660 579330 586570 FALSE TRUE 602726.7673 771647.3417 529164.2885 577922.8575 596117.0986 684466.0577 544796.775 490321.196 513566.8871 546841.0914 1.102197287 1.411099776 0.967674699 1.056838754 1.090110286 1.251672686 0.99626159 0.896642926 0.939151968 1 19.06076213 2.060767368 6.568188696 0.936683335 1.14334807 0.39707862 0.114891894 0.201870034 16.89326968 0.044124508 0.032299227 115.0184123 -2.060767368 0.206664735 FRPDMEEEEAK ddPTM_BT-474_Pertuzumab_2h_R1 7 FRPDMEEEEAK 11 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ;;;;;; 234.92 1.50E-15 7974370000 4952170 4288690 4107000 4088040 4574440 4282610 5019730 5709920 6062590 5601920 FALSE TRUE 4758633.721 4166380.76 4849226.26 4299024.234 4721581.017 4369207.308 5081162.957 5592008.157 5374390.2 5222496.969 0.911179796 0.797775621 0.92852639 0.823174099 0.90408497 0.836612704 0.972937464 1.070753739 1.029084408 1 22.31630832 2.060821501 4.060613286 1.038052266 0.866684131 0.764904211 0.041976762 0.087660505 2.9396113 0.015708194 0.01077721 115.0327495 -2.060821501 -0.171368135 LKEDLLSHTTAELNYGLAHFVNEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKEDLLSHTTAELNYGLAHFVNEIR 25 1 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 ; 242.05 7.87E-39 207920000 99608 129866 93680 102747 110170 112704 92348 54759 116999 115299 FALSE TRUE 95715.20924 126162.3488 110610.0599 108049.785 113713.7181 114982.9521 93478.18245 53628.20751 103717.764 107489.696 0.890459391 1.173715747 1.029029423 1.005210629 1.05790343 1.069711389 0.869647844 0.498914868 0.964908897 1 16.71383884 2.061110643 5.146893548 0.746716568 1.040517264 0.279598457 0.147295321 0.169909159 9.052862089 0.055193323 0.0395905 115.109361 -2.061110643 0.293800696 (ac)MDKNELVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 MDKNELVQK 9 1 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 76.899 0.0091152 889830000 954730 970310 710060 751050 862440 868420 904470 975880 1093630 996530 FALSE TRUE 917418.0961 942637.7088 838383.6372 789811.7805 890181.1658 885980.0474 915539.1744 955727.737 969485.7073 929034.1355 0.98749665 1.014642706 0.902425008 0.850142907 0.95817918 0.953657152 0.985474203 1.028732638 1.043541534 1 19.82537208 2.061457813 1.989674427 1.027717828 0.940415385 0.406869205 0.043276904 0.353570074 2.661768294 0.026515676 0.014545864 115.2014149 -2.061457813 -0.087302443 AQEEAERLEADR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQEEAERLEADR 12 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 167.98 4.35E-05 659330000 2097500 2363870 1476350 1909060 1999290 2239350 1798980 1824700 1842740 1926840 FALSE TRUE 2015527.381 2296454.742 1743159.286 2007586.815 2063598.979 2284631.191 1820996.455 1787019.307 1633559.881 1796333.411 1.122022988 1.278412308 0.970398522 1.117602558 1.148783943 1.271830262 1.013729659 0.994814936 0.90938568 1 20.77662372 2.061601956 8.950165949 0.976601471 1.147356202 0.504674858 0.084212812 0.262045396 35.23242467 0.03187323 0.023509539 115.2396568 -2.061601956 0.17075473 TKGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKGSPR 6 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.016)KGS(0.984)PR 63.48 0.067914 23390000 151000 137430 121700 100090 137900 138750 159080 194670 244330 152210 TRUE FALSE 145098.7531 133510.631 143693.8972 105255.6569 142335.6787 141555.6201 161026.8686 190649.9965 216594.6827 141900.6811 1.022537397 0.940873785 1.012637121 0.741755826 1.003065508 0.997568292 1.134785734 1.343545323 1.526382263 1 17.11452199 2.061774739 2.20550649 1.324675113 0.942188484 0.527040403 0.142914062 0.213479668 1.98773815 0.07197461 0.04085309 115.2855138 -2.061774739 -0.382486629 TELDAHFENLLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TELDAHFENLLAR 13 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39;F8WFB9 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 113.76 0.00079672 890660000 666460 756910 650220 795040 772540 769960 728010 732040 820030 796960 FALSE TRUE 640414.0064 735323.6679 767729.2181 836072.1097 797389.4507 785529.1187 736919.6042 716923.1182 726943.6322 742981.1893 0.861951844 0.989693519 1.033309092 1.125293778 1.073229662 1.057266496 0.991841536 0.964927684 0.978414585 1 19.50296616 2.061778105 6.872465998 0.977471805 1.029132771 0.079133236 0.064942555 0.501429269 44.72632201 0.026526502 0.019459015 115.2864072 -2.061778105 0.051660967 SDDNSYDEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SDDNSYDEK 9 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;; 151.83 0.00019061 288800000 665690 665280 562000 588150 610070 602420 673040 731440 777720 759750 FALSE TRUE 639674.0988 646306.8658 663565.9016 618504.492 629693.4556 614601.3452 681276.8648 716335.5084 689436.4861 708291.4558 0.90312271 0.91248717 0.936854308 0.873234439 0.889031557 0.867723788 0.961859499 1.011356981 0.973379645 1 19.43398361 2.0619642 4.958400083 0.994260571 0.898458076 0.827167009 0.02044561 0.079874374 3.93947071 0.008402085 0.005999008 115.335818 -2.0619642 -0.095802495 MSQPGS(ph)PSPK ddPTM_BT-474_Pertuzumab_2h_R1 18 MSQPGSPSPK 10 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 MS(0.001)QPGS(0.942)PS(0.057)PK;MSQPGS(0.932)PS(0.067)PK;MSQPGS(0.998)PS(0.002)PK;MSQPGS(0.999)PS(0.001)PK;MSQPGS(1)PSPK;MS(0.007)QPGS(0.99)PS(0.003)PK;MS(0.001)QPGS(0.966)PS(0.033)PK;MSQPGS(0.999)PS(0.001)PK;MS(0.002)QPGS(0.602)PS(0.396)PK;MSQPGS(0.995)PS(0.005)PK;MSQPGS(0.961)PS(0.039)PK;MSQPGS(0.961)PS(0.039)PK;MSQPGS(0.994)PS(0.006)PK;MSQPGS(0.987)PS(0.013)PK;MSQPGS(0.989)PS(0.011)PK;MSQPGS(0.975)PS(0.025)PK;MSQPGS(0.991)PS(0.009)PK;MSQPGS(0.996)PS(0.004)PK 225.92 3.43E-09 51929390000 20719200 18765080 15862490 16657780 17619740 16737060 19762780 21921370 22878820 21412490 TRUE FALSE 19909470.76 18229918.29 18729194.8 17517490.02 18186494.94 17075494.82 20004642.81 21468686.05 20281712.27 19962202.98 0.997358397 0.913221768 0.93823286 0.877532908 0.911046489 0.855391303 1.00212601 1.075466774 1.016005713 1 24.25076761 2.061978638 6.362803572 1.038958639 0.914871268 0.643062791 0.039640271 0.112055294 8.725000374 0.014895344 0.010888846 115.3396525 -2.061978638 -0.12408737 YSPPAIS(ph)PLVSEK ddPTM_BT-474_Pertuzumab_2h_R1 3 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK 247.17 3.15E-17 505460000 784760 773360 723820 770670 818200 832990 701260 667190 725450 716490 TRUE FALSE 754090.7116 751304.53 854630.3753 810444.3711 844518.1461 849833.6285 709842.2297 653412.2933 643099.9573 667961.4941 1.128943387 1.124772216 1.279460542 1.213310016 1.264321602 1.272279369 1.062699326 0.978218504 0.962779985 1 19.34940541 2.06208894 4.089693797 0.985358577 1.214537917 0.808798074 0.05173903 0.096742553 3.27841154 0.023195739 0.015959757 115.3689499 -2.06208894 0.22917934 AESGDSLGS(ph)EDRDLLYSIDAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AESGDS(0.161)LGS(0.839)EDRDLLYSIDAYR 144.18 6.18E-08 125320000 44036 52067 48613 49795 44969 50579 43988 45719 41775 51295 TRUE FALSE 42315.02444 50582.10014 57398.45049 52364.92592 46415.46872 51601.74203 44526.3383 44774.88667 37032.87714 47820.74396 0.884867548 1.057743898 1.200283512 1.09502533 0.970613689 1.079066065 0.931109276 0.936306777 0.77441031 1 15.54534895 2.062121368 1.906649244 0.891119368 1.056061926 0.32923797 0.094111526 0.385000618 2.656855635 0.053928569 0.02919912 115.3775648 -2.062121368 0.164942558 ALSSGGSITS(ph)PPLS(ph)PALPK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALSSGGSITSPPLSPALPK 19 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9JW88;C9JRZ2;C9J0V6;C9JXQ0;C9JPV7;F8WCD5;C9JHT0;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 2 ALSSGGSIT(0.002)S(0.998)PPLS(1)PALPK;ALSSGGSIT(0.001)S(0.999)PPLS(1)PALPK;ALS(0.005)S(0.006)GGS(0.005)IT(0.38)S(0.606)PPLS(1)PALPK 287.08 4.08E-40 1057600000 788550 871900 867460 896420 995980 1033780 796170 775030 804260 817860 TRUE FALSE 757732.5942 847034.2657 1024229.319 942684.3436 1028016.601 1054683.74 805913.7666 759025.3597 712963.7765 762465.6137 0.993792481 1.110914709 1.343312144 1.236363092 1.348279296 1.38325417 1.056983754 0.995487988 0.93507663 1 19.54031275 2.062380214 6.58377776 0.988225204 1.239998144 0.534052798 0.111070463 0.172164354 14.14992196 0.045587535 0.033385436 115.446352 -2.062380214 0.25177294 TDLKGDDLEEGVTSEEFDKFLEER ddPTM_BT-474_Pertuzumab_2h_R1 3 TDLKGDDLEEGVTSEEFDKFLEER 24 2 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 ;; 181.37 1.87E-17 438240000 385710 305645 237862 220062 274766 287078 313037 345940 403970 330620 FALSE TRUE 370636.0268 296928.3039 280848.9546 231419.4262 283604.0979 292882.9139 316868.0404 338796.2181 358113.0192 308226.8129 1.202478212 0.963343523 0.91117626 0.750808874 0.920114948 0.950218805 1.028035288 1.09917828 1.161849016 1 18.23363284 2.062594058 2.507872565 1.096178826 0.937076736 0.237236078 0.109775868 0.393677979 4.798166975 0.056990955 0.033784936 115.5032112 -2.062594058 -0.15910209 TEVLS(ph)PNSK ddPTM_BT-474_Pertuzumab_2h_R1 4 TEVLSPNSK 9 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 TEVLS(0.992)PNS(0.008)K;TEVLS(0.997)PNS(0.003)K;TEVLS(0.995)PNS(0.005)K;TEVLS(0.991)PNS(0.009)K 165.07 6.48E-05 2311100000 4736020 4404860 3920150 4328480 4325860 4124630 4792370 5337300 5381530 5354090 TRUE FALSE 4550931.102 4279237.706 4628608.308 4551873.372 4465005.216 4208032.845 4851020.458 5227082.89 4770641.276 4991452.715 0.911744809 0.857313081 0.927306853 0.911933585 0.894530204 0.843047723 0.971865454 1.047206733 0.955762089 1 22.25102833 2.062711972 6.101434159 1.007130141 0.892650921 0.720935571 0.031598941 0.094643693 6.781355901 0.011767612 0.008582724 115.5345752 -2.062711972 -0.11447922 VADNS(ph)FDAK ddPTM_BT-474_Pertuzumab_2h_R1 3 VADNSFDAK 9 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 VADNS(1)FDAK;VADNS(1)FDAK;VADNS(1)FDAK 211.02 6.12E-06 1111480000 2236910 1874960 2172470 1803280 1913710 1975130 2281280 2669560 2382290 2895200 TRUE FALSE 2149489.084 1821487.977 2565083.655 1896347.497 1975266.22 2015068.482 2309198.987 2614432.653 2111862.427 2699105.525 0.796370895 0.674848745 0.950345821 0.702583682 0.731822525 0.746568989 0.855542314 0.968629284 0.782430478 1 21.36404995 2.062841486 4.440012552 0.913646529 0.767333304 0.375345104 0.087557299 0.215361611 8.554164123 0.03371395 0.02363371 115.5690348 -2.062841486 -0.146313224 MFPMDSKPSLLNPTGSILVSS(ph)PLKPNPLDLPQLQHR ddPTM_BT-474_Pertuzumab_2h_R1 3 MFPMDSKPSLLNPTGSILVSSPLKPNPLDLPQLQHR 36 2 O75376;O75376-2;A0A088AWL3;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 MFPMDSKPSLLNPTGSILVS(0.227)S(0.773)PLKPNPLDLPQLQHR;MFPMDSKPSLLNPTGSILVS(0.276)S(0.724)PLKPNPLDLPQLQHR;MFPMDSKPSLLNPTGSILVS(0.216)S(0.784)PLKPNPLDLPQLQHR 191.43 8.17E-24 1738490000 959050 869530 683410 672199 700304 819400 810760 945520 898700 958150 TRUE FALSE 921569.2657 844731.8558 806917.3894 706891.2709 722829.9142 835968.8294 820682.3234 925994.6816 796683.3437 893253.6471 1.031699416 0.945679717 0.903346314 0.79136679 0.809210146 0.935869484 0.918756197 1.036653681 0.891889271 1 19.76871037 2.063238176 2.9679396 0.979407913 0.895013146 0.15645438 0.072824526 0.446968712 7.78593913 0.035857072 0.022484416 115.6746453 -2.063238176 -0.084394767 RFS(ph)DQAAGPAIPTSNSYSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFSDQAAGPAIPTSNSYSK 19 1 Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7 Q7KZI7-12 MARK2 Serine/threonine-protein kinase MARK2 1 RFS(1)DQAAGPAIPTSNSYSK 149.16 5.41E-08 514470000 443860 499280 484630 547410 600890 620300 497840 519070 584030 496820 TRUE FALSE 426513.4605 485041.0232 572213.4215 575661.8957 620218.1726 632842.891 503932.7148 508351.0231 517733.3629 463169.9389 0.920857389 1.047220431 1.23542867 1.242874046 1.339072596 1.366329802 1.08800825 1.097547532 1.117804329 1 18.8211821 2.063287478 24.99997985 1.085153915 1.198928637 0.165735757 0.126387014 130.1311024 51403.54513 0.052114411 0.03848904 115.6877775 -2.063287478 0.113774722 ELEDLEAMIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEDLEAMIK 10 0 O75400-3;H0YG38 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 139.96 9.34E-05 39363000 152202 144448 118066 129698 137307 139688 147927 164495 176958 166881 FALSE TRUE 146253.7776 140328.4845 139403.1526 136391.7293 141723.6044 142512.5871 149737.3749 161098.1208 156870.4697 155578.0012 0.94006721 0.901981536 0.896033832 0.876677475 0.91094887 0.91602017 0.962458533 1.035481363 1.008307527 1 17.24727855 2.06335377 2.520184424 1.017521885 0.903972425 0.883065094 0.017591375 0.08558328 1.054253391 0.008848848 0.005258335 115.7054377 -2.06335377 -0.11354946 DGLNDDDFEPYLS(ph)PQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGLNDDDFEPYLSPQAR 17 0 Q9Y5A9;S4R3J8 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 1 DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR 261.66 2.79E-27 1083918000 895187 947709 1014387 1063761 1196850 1098063 961151 919273 990588 1045041 TRUE FALSE 860202.1024 920681.2672 1197709.296 1118661.833 1235347.767 1120266.586 972913.8535 900289.6913 878140.6031 974259.4422 0.882929192 0.945006255 1.229353542 1.148217594 1.267986446 1.149864746 0.99861886 0.924075921 0.90134164 1 19.89394648 2.063455897 4.226119596 0.938482768 1.111304329 0.299781408 0.112597716 0.275476847 9.915191638 0.050198521 0.034842088 115.7326498 -2.063455897 0.172821561 ILSDDVPIRDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILSDDVPIRDYR 12 1 P54725-2;P54725;A0A494C0B4;K7ENJ0;K7ELW1;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 75.566 0.030521 290810000 493680 578650 367160 441750 503880 544750 433860 424780 479840 451340 FALSE TRUE 474386.4398 562147.4686 433513.9794 464548.7704 520087.7578 555765.2182 439169.7085 416008.1446 425370.5749 420770.3398 1.127423668 1.335995947 1.030286449 1.104043528 1.236037117 1.320827933 1.043727818 0.988682198 1.010932888 1 18.68267349 2.06363275 8.682735843 1.002951131 1.189411299 0.50892823 0.088131069 0.239892039 29.88223924 0.033918232 0.025012968 115.779788 -2.06363275 0.186460168 WHQPPPS(ph)PLPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 WHQPPPSPLPLR 12 0 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 WHQPPPS(1)PLPLR;WHQPPPS(1)PLPLR;WHQPPPS(1)PLPLR 128.06 0.00011516 953010000 804590 823810 654850 811390 749600 793290 608250 319950 661050 690280 TRUE FALSE 773145.7333 800315.7454 773195.9621 853265.9351 773711.5648 809330.8673 615693.9454 313342.9207 586010.3753 643526.7208 1.201419783 1.243640271 1.201497835 1.325921531 1.20229905 1.257649203 0.95674962 0.486915167 0.910623221 1 19.29564053 2.06368726 4.227189652 0.7366584 1.237400112 0.686253651 0.1331754 0.097887646 3.522025805 0.051670032 0.035872141 115.794321 -2.06368726 0.500741712 ETVVEVPQVTWEDIGGLEDVKR ddPTM_BT-474_Pertuzumab_2h_R1 8 ETVVEVPQVTWEDIGGLEDVKR 22 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;; 283.75 1.22E-45 9447350000 7274092 7002719 5671766 6010779 6355866 6867921 7132791 7816836 8705268 8353375 FALSE TRUE 6989812.443 6803008.31 6696780.284 6320996.025 6560308.202 7006795.068 7220084.23 7655415.605 7717082.472 7787593.471 0.897557438 0.873570036 0.859929362 0.81167514 0.842405067 0.899738166 0.927126494 0.983027123 0.990945727 1 22.89274614 2.063758287 1.483150028 0.995681089 0.856383409 0.875299472 0.021936713 0.142886655 0.591545704 0.015686995 0.007916937 115.8132601 -2.063758287 -0.139297681 AEGS(ph)PSEGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEGSPSEGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(0.564)PS(0.436)EGKK 82.069 0.011711 266670000 405840 322850 318520 336770 344160 364480 400560 488220 507790 459340 TRUE FALSE 389979.3241 313642.6341 376083.6494 354150.7401 355230.219 371850.0353 405462.1731 478138.0864 450147.808 428228.4927 0.910680468 0.732418883 0.878231262 0.82701349 0.829534291 0.868344918 0.946836047 1.116548979 1.051186027 1 18.70802126 2.063850907 2.61213609 1.065987248 0.83459228 0.774104426 0.051918125 0.111236518 1.47830571 0.023645493 0.014226465 115.8379617 -2.063850907 -0.231394968 APAPPPKPET(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 1 APAPPPKPETPEK 13 1 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 APAPPPKPET(1)PEK 85.493 0.014971 253630000 256430 167860 225840 201380 214930 160880 271560 322680 298280 328730 TRUE FALSE 246408.4321 163072.7972 266654.3118 211773.2459 221843.4186 164133.1038 274883.4325 316016.5452 264420.5049 306464.8243 0.804034958 0.532109346 0.870097612 0.691019749 0.723878896 0.535569145 0.896949375 1.03116743 0.862808662 1 18.22536197 2.063985408 7.279322395 0.967230782 0.69544474 0.588194918 0.105601218 0.142654022 13.54213516 0.037622117 0.027658783 115.8738424 -2.063985408 -0.271786042 AS(ph)PSVTCK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPSVTCK 8 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 AS(0.965)PS(0.035)VTCK;AS(0.667)PS(0.33)VT(0.003)CK 157.34 0.00039692 940570000 1248240 1157310 925010 1021710 1033480 1228900 1129700 1318180 1437900 1385330 TRUE FALSE 1199457.401 1124304.652 1092179.884 1074440.576 1066722.823 1253749.2 1143525.607 1290959.122 1274675.62 1291500.365 0.928731755 0.87054149 0.845667499 0.831932073 0.825956269 0.970769528 0.885424145 0.999580919 0.986972714 1 20.30061662 2.064100765 1.127129127 1.000887087 0.862419689 0.629351025 0.040995623 0.313116209 0.739127325 0.030537057 0.014906685 115.9046248 -2.064100765 -0.138467398 EAEALLQSMGLTPESPIVPPPMS(ph)PSSK ddPTM_BT-474_Pertuzumab_2h_R1 8 EAEALLQSMGLTPESPIVPPPMSPSSK 27 0 Q13409-2;Q13409-3;Q13409-6;E7EQL5;E7EV09;E7EQU2;E7ETL8;E9PGG1 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 1 EAEALLQSMGLTPESPIVPPPMS(0.677)PS(0.141)S(0.182)K;EAEALLQSMGLTPES(0.001)PIVPPPMS(0.812)PS(0.156)S(0.031)K;EAEALLQSMGLTPESPIVPPPMS(0.672)PS(0.145)S(0.183)K;EAEALLQSMGLTPESPIVPPPMS(0.788)PS(0.179)S(0.033)K;EAEALLQSMGLTPESPIVPPPMS(0.86)PS(0.122)S(0.018)K;EAEALLQSMGLTPES(0.004)PIVPPPMS(0.663)PS(0.166)S(0.166)K;EAEALLQSMGLTPESPIVPPPMS(0.806)PS(0.161)S(0.033)K;EAEALLQSMGLTPESPIVPPPMS(0.918)PS(0.065)S(0.018)K 152.23 4.74E-08 2854035000 2382417 2519935 2258608 2462718 2577141 2690869 2246826 2251536 2384990 2146820 TRUE FALSE 2289309.51 2448068.921 2666788.708 2589819.171 2660037.081 2745280.215 2274323.329 2205040.995 2114255.934 2001413.969 1.143846073 1.223169698 1.332452331 1.293994751 1.329078902 1.371670358 1.136358277 1.101741583 1.056381122 1 20.93258817 2.064373289 4.817590354 1.075578593 1.284295462 0.716304286 0.065346542 0.121172485 5.571720336 0.027495212 0.01957413 115.9773787 -2.064373289 0.208716869 EDLRLPEGDLGK ddPTM_BT-474_Pertuzumab_2h_R1 9 EDLRLPEGDLGK 12 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;;;;;;; 181.67 1.63E-05 83296020000 61329300 57548020 50955940 51887730 53731690 57640440 59939950 67683540 72664490 67880870 FALSE TRUE 58932483.15 55906806.82 60164811.87 54565661.96 55460018.61 58805969.19 60673513.04 66285851.25 64415921.73 63283238.21 0.931249487 0.883437833 0.950722712 0.862245098 0.876377698 0.929250317 0.958761194 1.047447209 1.017898634 1 25.91532009 2.064801362 2.345401515 1.025652929 0.901716246 0.777058371 0.027868141 0.126283633 1.338396396 0.013982501 0.00812461 116.091751 -2.064801362 -0.123936683 MNILGSQS(ph)PLHPSTLSTVIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 MNILGSQSPLHPSTLSTVIHR 21 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 MNILGSQS(1)PLHPSTLSTVIHR;MNILGS(0.036)QS(0.964)PLHPSTLSTVIHR 203.78 9.45E-22 2422400000 898710 1311990 1159430 1393330 1114570 1408460 1034110 776280 1245860 1380550 TRUE FALSE 863587.4196 1274573.33 1368964.792 1465239.928 1150421.156 1436940.026 1046765.748 760249.5467 1104435.196 1287044.119 0.670985094 0.990310519 1.063650245 1.138453536 0.893847491 1.116465244 0.813309919 0.590694239 0.858117589 1 20.29563008 2.064867976 7.605934805 0.753816838 0.985853979 0.171113638 0.158800486 0.274188336 27.52353554 0.058844942 0.043311174 116.1095591 -2.064867976 0.232037141 PYECRECGMAFIRSS(ph)QLTEHQR ddPTM_BT-474_Pertuzumab_2h_R1 1 PYECRECGMAFIRSSQLTEHQR 22 2 Q8N9K5-2;Q8N9K5 Q8N9K5-2 ZNF565 Zinc finger protein 565 1 PYECRECGMAFIRS(0.171)S(0.79)QLT(0.039)EHQR 47.745 0.079958 173430000 64315 114620 65180 118080 96840 115830 69316 57773 47671 82354 TRUE FALSE 61801.4987 111351.1498 76959.47592 124174.123 99954.94655 118172.162 70164.30994 56579.96736 42259.58793 76776.09023 0.804957618 1.45033629 1.002388578 1.617354082 1.301902015 1.539179211 0.9138823 0.736947755 0.550426413 1 16.22836947 2.064932328 5.58118093 0.753959935 1.29517591 0.485071359 0.248413756 0.153713962 9.184283548 0.09130254 0.066184174 116.1267651 -2.064932328 0.541215975 QEQLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 QEQLSPK 7 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 QEQLS(1)PK;QEQLS(1)PK;QEQLS(1)PK;QEQLS(1)PK 132.39 0.0035386 3648150000 6306100 5385600 4644100 4509740 5113700 5252600 5659700 6311200 6824800 6283500 TRUE FALSE 6059650.64 5232007.961 5483392.177 4742488.222 5278186.805 5358811.171 5728965.102 6180871.515 6050077.316 5857912.948 1.034438493 0.893152221 0.936065835 0.809586667 0.901035377 0.914798704 0.977987408 1.055132019 1.032804238 1 22.48195532 2.06530002 2.960835794 1.033616287 0.908988072 0.481466391 0.05330551 0.208508861 3.614272095 0.024649241 0.015478014 116.2251244 -2.06530002 -0.124628215 KAGNFYVPAEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAGNFYVPAEPK 12 1 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 ; 123.95 0.00053185 1631730000 3628600 3413400 2940700 2754200 3124500 3340200 3442900 4011800 4103100 3986700 FALSE TRUE 3486790.3 3316053.174 3472149.906 2896344.592 3225002.38 3407741.133 3485035.24 3928954.928 3637333.29 3716677.258 0.938147183 0.892209074 0.934208075 0.77928332 0.867711172 0.916878409 0.937674971 1.057114905 0.978651908 1 21.82558198 2.065311665 2.499483352 1.016313841 0.882853844 0.583281158 0.046444443 0.19472478 2.359265344 0.023584107 0.014004285 116.2282409 -2.065311665 -0.133459996 VSGEEELHTGPPAPQGPLSVPQGLPTQSLAS(ph)PPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSGEEELHTGPPAPQGPLSVPQGLPTQSLASPPAR 35 0 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 VSGEEELHTGPPAPQGPLSVPQGLPTQS(0.007)LAS(0.993)PPAR;VSGEEELHTGPPAPQGPLSVPQGLPT(0.022)QS(0.098)LAS(0.88)PPAR 167.77 5.89E-15 427060000 69650 83570 82179 92725 98182 103856 72216 70039 63435 73270 TRUE FALSE 66928.001 81186.66542 97030.57336 97510.54836 101340.1132 105956.0395 73099.80101 68592.67017 56234.12474 68307.35764 0.979806617 1.188549349 1.420499588 1.427526283 1.483590007 1.551165835 1.070159988 1.004176893 0.823251355 1 16.05975336 2.065316714 6.00320442 0.964934079 1.348323583 0.566428983 0.159889082 0.160238679 10.82910476 0.066582082 0.048544828 116.2295921 -2.065316714 0.383389504 ASLQVLGTVGEPINPEAWLWYHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASLQVLGTVGEPINPEAWLWYHR 23 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 246.73 1.29E-37 3554900000 1559230 1602470 1417690 1501540 1649930 1658300 1427560 1240610 1637810 1622040 FALSE TRUE 1498293.568 1556769.125 1673898.119 1579034.659 1703001.497 1691831.962 1445030.906 1214990.97 1451892.675 1512177.786 0.990818396 1.029488159 1.106945317 1.04421231 1.12619132 1.11880493 0.955595909 0.803470982 0.960133582 1 20.52819634 2.065340873 5.433857833 0.894552284 1.06977379 0.535346728 0.062745229 0.125827607 7.143506282 0.024198929 0.017499673 116.2360581 -2.065340873 0.175221506 RPST(ph)SQTVSTPAPVPVIESTEAIEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSTSQTVSTPAPVPVIESTEAIEAK 26 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 RPS(0.253)T(0.345)S(0.345)QT(0.049)VS(0.007)T(0.001)PAPVPVIESTEAIEAK 166.19 6.92E-12 175700000 41773 36828 34286 31399 41179 34064 29131 34911 31137 30185 TRUE FALSE 40140.46498 35777.7015 40482.24289 33019.50615 42503.55993 34752.79742 29487.51389 34190.07565 27602.4583 28140.54306 1.426428228 1.271393428 1.438573619 1.173378427 1.510402974 1.234972521 1.047865843 1.214975687 0.980878664 1 14.78036255 2.065397421 0.893591174 1.016905616 1.361501458 0.611680552 0.110425929 0.404837499 0.599704058 0.086292317 0.043949124 116.2511937 -2.065397421 0.344595843 KSNFSNSADDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSNFSNSADDIK 12 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 92.063 0.0057726 0 205640 204480 128010 180780 183810 187620 196430 217120 244240 227020 FALSE TRUE 197603.3615 198648.4306 151144.2546 190110.0775 189722.4156 191413.8049 198833.9691 212636.3961 216514.8991 211643.7332 0.933660347 0.938598217 0.71414472 0.89825517 0.896423498 0.90441518 0.939474872 1.004690254 1.023015876 1 17.69127825 2.065408141 1.271331199 1.017969896 0.870259767 0.491369791 0.059012169 0.387729824 1.171521713 0.042567014 0.020927882 116.2540632 -2.065408141 -0.147710129 EGEEPTVYS(ph)DEEEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGEEPTVYSDEEEPK 15 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 EGEEPTVYS(1)DEEEPK;EGEEPTVYS(1)DEEEPK 293.52 5.83E-44 740900000 606810 581150 602900 728850 606610 535720 893850 1217320 1168620 867870 TRUE FALSE 583095.1943 564576.171 711857.4414 766466.0358 626122.1616 546552.6255 904789.2037 1192181.917 1035963.157 809088.3919 0.720681696 0.697792944 0.879826541 0.94732052 0.773861259 0.675516583 1.11828227 1.473487852 1.280407885 1 19.6259378 2.065566659 4.790231125 1.303251972 0.792374755 0.714405166 0.135309307 0.095744707 4.324548374 0.053000343 0.037724367 116.296504 -2.065566659 -0.510877217 HS(ph)S(ph)ISPVRLPLNSSLGAELSR ddPTM_BT-474_Pertuzumab_2h_R1 6 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.664)S(0.702)IS(0.621)PVRLPLNS(0.009)S(0.003)LGAELSR;HS(0.666)S(0.666)IS(0.666)PVRLPLNS(0.001)S(0.001)LGAELSR;HS(0.761)S(0.807)IS(0.43)PVRLPLNS(0.001)S(0.001)LGAELSR;HS(0.666)S(0.666)IS(0.666)PVRLPLNS(0.001)SLGAELSR;HS(0.68)S(0.713)IS(0.602)PVRLPLNS(0.004)S(0.001)LGAELSR;HS(0.689)S(0.731)IS(0.58)PVRLPLNSSLGAELSR 133.29 1.35E-05 251630000 103984.6 118606.7 101632.5 117323.8 109289.9 115345.5 97269.2 66250.2 123324.3 109004.6 TRUE FALSE 99920.76687 115224.153 119999.7536 123378.8954 112805.3089 117677.865 98459.60957 64882.11022 109325.0425 101621.6214 0.983262868 1.133854701 1.180848642 1.214100835 1.110052245 1.158000271 0.968884458 0.638467576 1.075804942 1 16.63284786 2.065621079 4.884357975 0.850595394 1.133475084 0.393389018 0.123092172 0.154182718 7.213511015 0.047416322 0.03385014 116.3110775 -2.065621079 0.282879689 EKDLDLEPLS(ph)DLEEGLEETR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKDLDLEPLSDLEEGLEETR 20 1 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 EKDLDLEPLS(1)DLEEGLEETR;EKDLDLEPLS(1)DLEEGLEETR 165.48 1.01E-11 91785000 152955 148029 127850 132457 147617 140092 155482 178901 172332 168056 TRUE FALSE 146977.3495 143807.3579 150955.339 139293.1216 152365.2349 142924.7562 157384.8352 175206.6318 152769.5938 156673.4174 0.938112871 0.917879754 0.9635032 0.889066722 0.972502147 0.912246369 1.004540769 1.118292016 0.975083051 1 17.25740089 2.065622154 5.077322472 1.048327594 0.933544953 0.528188018 0.042213686 0.124337974 6.239556035 0.015598862 0.0111952 116.3113654 -2.065622154 -0.114782641 GGGFGGNDNFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGGFGGNDNFGR 12 0 F8W6I7;P09651-2;P09651;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ; 187.97 2.28E-05 275110000 318630 389070 341090 351330 375910 439210 333170 351270 363670 359140 FALSE TRUE 306177.5873 377974.1045 402732.5505 369462.1834 388001.4865 448091.1271 337247.4341 344016.1517 322387.7062 334815.1279 0.914467603 1.128903903 1.202850519 1.103481153 1.158852914 1.338324018 1.007264625 1.027480908 0.962882735 1 18.35300519 2.065833486 25 1.004214325 1.145013566 0.328272459 0.099150831 67.90230485 25784.83654 0.037460862 0.027666678 116.3679775 -2.065833486 0.140799241 NMQNVEHVPLSLDR ddPTM_BT-474_Pertuzumab_2h_R1 9 NMQNVEHVPLSLDR 14 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;;;;;; 134.81 2.78E-05 7123780000 15226570 19059650 15487290 20242380 17800630 18225020 16777460 16638610 16701780 19215280 FALSE TRUE 14631498.81 18516087.44 18286187.82 21287091.66 18373203.43 18593542.39 16982787.57 16295016.89 14805863.95 17913811.97 0.816771932 1.033620732 1.02078708 1.188306079 1.02564454 1.037944488 0.948027567 0.909634248 0.826505491 1 24.09456903 2.065957695 2.867383512 0.904229557 1.029280091 0.216945805 0.092785613 0.372321969 6.031321384 0.043764596 0.027213681 116.4012638 -2.065957695 0.125050534 GYAFIEFASFEDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GYAFIEFASFEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 210.91 2.03E-07 243170000 359590 355660 302067 318325 349432 368600 397000 473030 488040 514980 FALSE TRUE 345536.8253 345516.925 356657.2263 334753.7914 360671.7976 376053.3445 401858.6048 463261.7652 432639.7452 480099.9459 0.719718526 0.719677076 0.742881205 0.697258548 0.751243154 0.783281372 0.837031139 0.96492776 0.901145166 1 18.87297525 2.065970661 1.180805595 0.970160894 0.721297052 0.93285427 0.026779288 0.102815036 0.267014518 0.018408179 0.009003092 116.404739 -2.065970661 -0.248863842 IDNSQVESGSLEDDWDFLPPKK ddPTM_BT-474_Pertuzumab_2h_R1 3 IDNSQVESGSLEDDWDFLPPKK 22 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;; 226.16 8.81E-26 843436000 1068110 1100210 909454 969765 978640 1092820 1126570 1231230 1418810 1306430 FALSE TRUE 1026367.08 1068833.088 1073812.568 1019814.688 1010118.844 1114917.569 1140357.301 1205804.67 1257752.637 1217944.332 0.842704427 0.87757138 0.88165981 0.837324548 0.829363722 0.9154093 0.936296734 0.990032663 1.032684831 1 20.21601676 2.066011725 1.363366299 1.014990548 0.856365309 0.909626932 0.020883904 0.122080976 0.425701931 0.01479289 0.0073514 116.4157459 -2.066011725 -0.158625239 YDS(ph)DGDKSDDLVVDVSNEDPATPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDSDGDKSDDLVVDVSNEDPATPR 24 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 YDS(0.858)DGDKS(0.142)DDLVVDVSNEDPATPR;YDS(1)DGDKSDDLVVDVSNEDPATPR 227.48 2.65E-33 362970000 262020 211875 209831 233150 255930 248320 293150 318940 394090 354350 TRUE FALSE 251779.9687 205832.5324 247752.1294 245182.8994 264162.2209 253341.2005 296737.6574 312353.7775 349354.5554 330349.5589 0.762162267 0.623074943 0.749969609 0.742192302 0.799644539 0.766888266 0.89825353 0.945525033 1.057529959 1 18.33363389 2.066525926 0.883617441 1.036141758 0.71354618 0.875548426 0.045302567 0.180337938 0.261386938 0.03572087 0.018280256 116.5536628 -2.066525926 -0.322595579 QNGSNDSDRYS(ph)DNEEDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QNGSNDSDRYSDNEEDSK 18 1 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 QNGSNDSDRYS(0.999)DNEEDSK 124 1.99E-05 77707000 99978 105140 98692 149350 104450 98205 133110 168290 143900 111790 TRUE FALSE 96070.74923 102141.5101 116527.8398 157057.9714 107809.7291 100190.7724 134739.04 164814.7527 127565.0753 104218.3637 0.9218217 0.980072096 1.118112352 1.507008609 1.034460005 0.961354303 1.292853152 1.581436772 1.224017253 1 16.66924998 2.066620524 7.565173165 1.358724384 1.10145266 0.120115495 0.20793748 0.335790599 32.55513812 0.080276402 0.059087818 116.5790533 -2.066620524 -0.257271724 ANSWQLVET(ph)PEKR ddPTM_BT-474_Pertuzumab_2h_R1 7 ANSWQLVETPEKR 13 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR 202.96 5.25E-08 7961050000 2826072 2856029 2658770 3003925 2932255 2994736 3388000 4106980 4131709 4055490 TRUE FALSE 2715625.982 2774577.849 3139268.883 3158957.929 3026573.645 3055291.614 3429463.357 4022169.428 3662694.716 3780808.05 0.718266028 0.733858427 0.830316917 0.835524546 0.800509734 0.808105456 0.907071534 1.06383857 0.968759764 1 21.85026318 2.066639545 2.760556697 1.015497985 0.788492914 0.851110203 0.04199845 0.100655143 1.504982072 0.021253638 0.01306122 116.5841592 -2.066639545 -0.227005071 AGGGGGLGAGS(ph)PALSGGQGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGGGGGLGAGSPALSGGQGR 20 0 A0A3B3ITT1;Q6IQ22 A0A3B3ITT1 RAB12 Ras-related protein Rab-12 1 AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(0.999)PALS(0.001)GGQGR 318.99 1.44E-66 4735780000 1968300 2773550 2047280 2625930 1964860 2255110 2481730 2750900 2861580 2542800 TRUE FALSE 1891376.66 2694451.07 2417269.037 2761454.562 2028061.506 2300709.869 2512102.154 2694092.954 2536745.435 2370573.891 0.797856024 1.136623954 1.019697824 1.164888626 0.855514993 0.970528646 1.05970211 1.136472887 1.070097602 1 21.17680493 2.066733214 5.931434627 1.087421338 1.001015008 0.092311672 0.109245668 0.436146583 28.43074369 0.040823148 0.029751318 116.609307 -2.066733214 -0.08640633 ATLPDADKER ddPTM_BT-474_Pertuzumab_2h_R1 4 ATLPDADKER 10 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8 P12814-3 ACTN1 Alpha-actinin-1 0 ;;; 125.97 0.00036021 2994370000 2658700 2542450 2642670 3383140 2568830 2075620 3434610 3570290 4057140 4382610 FALSE TRUE 2554795.065 2469941.815 3120259.255 3557744.261 2651458.75 2117590.459 3476643.785 3496562.264 3596590.476 4085771.921 0.625290671 0.604522686 0.763689045 0.870764284 0.648949281 0.51828406 0.850914797 0.85578988 0.880271965 1 21.96217724 2.06674867 10.34953681 0.885370384 0.681038865 0.565463453 0.096619338 0.368367643 54.82980473 0.038659371 0.02854209 116.613457 -2.06674867 -0.204331519 RPSQGPPARS(ph)PSQDFSFIEDTEILDSAMYR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(0.126)QGPPARS(0.838)PS(0.035)QDFSFIEDTEILDSAMYR 141.69 2.67E-08 47864000 27135 33187 12064 13003 27692 32672 13475 9668.5 12812 10808 TRUE FALSE 26074.5342 32240.53925 14244.23316 13674.08639 28582.73833 33332.65023 13639.91108 9468.842096 11357.63547 10075.96453 2.587795353 3.199747195 1.413684329 1.357099496 2.836724785 3.30813493 1.35370773 0.939745477 1.127200819 1 13.29863033 2.066866532 8.011104307 1.04774552 2.403778617 0.539118199 0.614010157 0.213704126 22.5018602 0.250751915 0.184761314 116.6451086 -2.066866532 1.356033097 TFLEGDWTS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 7 TFLEGDWTSPSK 12 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TFLEGDWT(0.005)S(0.995)PS(0.001)K;TFLEGDWTS(1)PSK;TFLEGDWT(0.014)S(0.985)PS(0.001)K;TFLEGDWTS(0.938)PS(0.062)K;TFLEGDWTS(0.639)PS(0.361)K;TFLEGDWTS(1)PSK;TFLEGDWTS(0.998)PS(0.002)K 297.77 2.52E-36 2942380000 5963070 5424890 4436510 4594760 5033520 4758870 5569490 6233020 6090360 6152190 TRUE FALSE 5730026.632 5270177.449 5238286.047 4831896.114 5195427.742 4855097.612 5637651.085 6104305.959 5399007.866 5735496.691 0.99904628 0.91887028 0.913309924 0.842454695 0.905837458 0.846499941 0.982940343 1.064302934 0.941332226 1 22.451487 2.066887736 6.890805426 1.012620455 0.903046076 0.457508014 0.049378595 0.16947457 14.13223545 0.018780475 0.013789035 116.650804 -2.066887736 -0.109574379 KPSGS(ph)PDLWK ddPTM_BT-474_Pertuzumab_2h_R1 4 KPSGSPDLWK 10 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.283)GS(0.717)PDLWK;KPS(0.045)GS(0.955)PDLWK;KPS(0.076)GS(0.924)PDLWK;KPS(0.067)GS(0.933)PDLWK 116.58 0.00065661 5924180000 7139850 6116240 5721430 6333420 6348440 6031910 7662420 9143570 9258030 8783620 TRUE FALSE 6860816.768 5941810.824 6755419.674 6660288.565 6552643.338 6153879.353 7756194.988 8954752.084 8207097.247 8188697.594 0.837839802 0.725611217 0.824968757 0.813351389 0.800205804 0.751508928 0.94718298 1.093550224 1.002246957 1 22.96520258 2.066917523 4.168543557 1.038720365 0.792730323 0.880787362 0.040179502 0.060890961 2.108883526 0.015657939 0.01086454 116.6588049 -2.066917523 -0.245990042 EREVEER ddPTM_BT-474_Pertuzumab_2h_R1 4 EREVEER 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 211.35 9.73E-05 1684980000 1642950 1838680 1518610 1805870 1719040 1816540 1651270 1644560 1739300 1867090 FALSE TRUE 1578741.698 1786242.647 1793056.608 1899071.167 1774334.483 1853271.683 1671478.736 1610599.261 1541861.956 1740630.331 0.906994248 1.026204482 1.030119133 1.091024977 1.019363188 1.064712966 0.960272096 0.925296562 0.885806669 1 20.73117841 2.066941408 5.338862439 0.931818241 1.026208107 0.368740579 0.051782532 0.192939239 10.47340827 0.019914792 0.014384677 116.665221 -2.066941408 0.094389866 EIRPALELLEPIEQK ddPTM_BT-474_Pertuzumab_2h_R1 6 EIRPALELLEPIEQK 15 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;; 196.22 8.25E-09 2002540000 2354950 2140960 2290640 2565120 2392420 1882530 2877340 3149400 3447710 3378690 FALSE TRUE 2262915.95 2079901.917 2704609.603 2697506.151 2469374.362 1920596.046 2912553.748 3084363.789 3056340.415 3149848.317 0.71842061 0.660318119 0.85864757 0.856392397 0.78396612 0.609742392 0.924664763 0.97921026 0.970313522 1 21.58685093 2.067018806 7.975021882 0.97376519 0.755748805 0.686989389 0.073549872 0.154834113 16.15680999 0.029390165 0.02165423 116.6860143 -2.067018806 -0.218016385 TEGAQVDEPVVIT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 TEGAQVDEPVVITPR 15 0 A0A0J9YWL0;A0A494C1M5 A0A0J9YWL0 1 TEGAQVDEPVVIT(1)PR;TEGAQVDEPVVIT(1)PR;TEGAQVDEPVVIT(1)PR 174 1.05E-05 579890000 372843 386484 373050 448168 435132 454096 358838 343154 344229 389101 TRUE FALSE 358271.8834 375461.8547 440468.4335 471298.0042 449128.416 463278.1322 363229.5668 336067.75 305153.567 362746.8427 0.987663685 1.035052027 1.21425849 1.299247709 1.23813184 1.277138979 1.001330746 0.926452585 0.841230112 1 18.46860353 2.067041259 5.014952282 0.924995622 1.178556334 0.575251998 0.099619472 0.156305323 7.594949091 0.043130454 0.030926175 116.6920473 -2.067041259 0.253560712 AHS(ph)SPASLQLGAVS(ph)PGTLTPTGVVSGPAATPTAQHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 2 AHS(0.778)S(0.222)PASLQLGAVS(0.998)PGT(0.002)LTPTGVVSGPAATPTAQHLR 190.51 7.65E-24 773900000 85664 97827 65253 112900 71279 84603 70600 39991 70320 73010 TRUE FALSE 82316.15617 95037.06974 77045.66865 118726.7825 73571.75377 86313.73063 71464.02392 39165.17187 62337.56841 68064.96767 1.209376262 1.396269961 1.131943073 1.744315565 1.080904851 1.268108009 1.04993841 0.575408661 0.915853934 1 16.05462483 2.067082649 3.272485316 0.786130486 1.312561573 0.525429862 0.201114936 0.165936196 3.546319391 0.085082484 0.055260866 116.7031688 -2.067082649 0.526431087 GSEEDS(ph)PKK ddPTM_BT-474_Pertuzumab_2h_R1 5 GSEEDSPKK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(1)PKK;GSEEDS(1)PKK;GSEEDS(1)PKK;GSEEDS(1)PKK;GSEEDS(1)PKK 120.57 0.00039383 2611378000 8009245 5361243 5865281 5525068 5835067 5006661 7372403 8247968 8532088 9187232 TRUE FALSE 7696234.851 5208345.599 6925267.749 5810217.422 6022757.229 5107899.116 7462628.673 8077644.578 7563561.14 8564972.594 0.898570867 0.608098338 0.808556907 0.678369645 0.703184647 0.596370748 0.87129627 0.94310221 0.8830806 1 23.0300172 2.067082697 6.493294025 0.928987197 0.713045071 0.583499985 0.087708999 0.137385435 10.37511287 0.031092884 0.022776705 116.7031817 -2.067082697 -0.215942126 SFFDNISCDDNRER ddPTM_BT-474_Pertuzumab_2h_R1 2 SFFDNISCDDNRER 14 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ; 104.55 0.00095879 394400000 241880 286300 148265 208625 202014 258230 185254 181747 190188 188740 FALSE TRUE 232427.0622 278135.0043 175059.7836 219392.1613 208511.9638 263451.5875 187521.1939 177993.8609 168598.6556 175956.4717 1.320935001 1.580703464 0.994903921 1.246854743 1.185020146 1.497254321 1.065724904 1.011578939 0.958183885 1 17.42485905 2.067295621 8.291227201 1.002905613 1.294543987 0.480523572 0.151611409 0.23931232 26.31804875 0.057455594 0.042356113 116.7604127 -2.067295621 0.291638374 GEWIKPGAIVIDCGINYVPDDK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEWIKPGAIVIDCGINYVPDDK 22 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 123.19 7.55E-06 0 125460 86941 106990 98830 105270 105190 118910 133390 142140 138650 FALSE TRUE 120556.8845 84461.5278 126325.473 103930.6281 108656.1052 107317.0139 120365.2561 130635.4499 126004.8631 129259.112 0.9326761 0.653428037 0.977304199 0.804048756 0.840606929 0.830247185 0.931193587 1.010647898 0.974823834 1 16.97990646 2.067398781 3.025565022 0.994033938 0.835528086 0.432904347 0.080423204 0.22582453 4.097095882 0.034102316 0.021611872 116.7881506 -2.067398781 -0.158505852 PFPTPS(ph)PASLDVYVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 PFPTPSPASLDVYVAR 16 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 PFPT(0.025)PS(0.926)PAS(0.049)LDVYVAR 88.561 0.0063861 20539000 30186 29221 35574 30622 30086 33871 51534 83683 52008 83275 TRUE FALSE 29006.29775 28387.64569 42003.01314 32202.40509 31053.74351 34555.89483 52164.68851 81954.91681 46104.26988 77634.71008 0.373625376 0.36565662 0.541033941 0.414793912 0.39999819 0.445108828 0.671924819 1.055647876 0.593861558 1 16.2444142 2.067671734 3.481249927 0.886747056 0.424664392 0.739407039 0.122818066 0.1096372 2.659129301 0.050205433 0.033246019 116.8615746 -2.067671734 -0.462082664 WGQPPSPTPVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_BT-474_Pertuzumab_2h_R1 2 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.402)PT(0.116)PVPRPPDADPNT(0.405)PS(0.077)PKPLEGRPER;WGQPPS(0.199)PT(0.285)PVPRPPDADPNT(0.3)PS(0.216)PKPLEGRPER 146.03 4.65E-10 7957200000 3016470 2907430 2242120 2519880 2598240 2672660 2820140 3097360 3280340 3045260 TRUE FALSE 2898583.018 2824512.943 2647320.96 2649931.309 2681814.749 2726703.016 2854653.717 3033398.434 2907969.556 2839001.828 1.020986668 0.994896486 0.932483006 0.933402467 0.944632977 0.960444262 1.005513166 1.068473575 1.024292949 1 21.43695235 2.067791735 3.945560223 1.038451253 0.962314217 0.491317095 0.030326522 0.170622976 5.304491794 0.013353674 0.009152421 116.8938695 -2.067791735 -0.076137036 AAQQQQPSAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAQQQQPSASPR 12 0 Q86U86-8;Q86U86 Q86U86-8 PBRM1 Protein polybromo-1 1 AAQQQQPSAS(1)PR;AAQQQQPSAS(1)PR 293.96 8.03E-22 676430000 505120 533870 462200 511980 492190 521700 477510 469240 495980 531810 TRUE FALSE 485379.352 518644.5503 545729.8216 538403.3492 508021.7383 532249.1314 483353.9102 459550.03 439678.4297 495790.035 0.979001831 1.046097166 1.100727693 1.085950324 1.024671136 1.073537372 0.97491655 0.926904531 0.886823854 1 18.91936975 2.068012833 3.549379006 0.932765742 1.05391409 0.613187913 0.041219323 0.146608294 3.696693817 0.017695849 0.01178873 116.9533948 -2.068012833 0.121148348 KEASEVCPPPGYGLDGLQYS(ph)PVQGGDPSENKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEASEVCPPPGYGLDGLQYSPVQGGDPSENKK 32 2 E9PHH8;Q9Y6X2 E9PHH8 PIAS3 E3 SUMO-protein ligase PIAS3 1 KEASEVCPPPGYGLDGLQYS(1)PVQGGDPSENKK 140.97 3.35E-10 231860000 206980 179230 154120 134390 148130 161670 196230 230850 244290 226010 TRUE FALSE 198890.9928 174118.5359 181972.9124 141325.884 152894.736 164939.0782 198631.5214 226082.8668 216559.2233 210702.1414 0.943943861 0.826372882 0.863650038 0.670737768 0.725643959 0.782806843 0.9427124 1.07299748 1.027797923 1 17.68484545 2.068098498 3.463850523 1.037150586 0.796793912 0.681283527 0.07172205 0.140131732 3.362988919 0.033317595 0.022039416 116.9764663 -2.068098498 -0.240356675 HSVVAGGGGGEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSVVAGGGGGEGR 13 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 0 ; 129.54 0.00015253 369280000 111469 109563 98842 136236 116297 118776 105393 95752 119139 101381 FALSE TRUE 107112.6682 106438.3705 116704.9481 143267.1563 120037.7986 121177.7321 106682.8311 93774.68774 105614.8402 94514.37457 1.133295001 1.126160661 1.234785171 1.515823989 1.270048066 1.282109019 1.128747151 0.992173817 1.11744738 1 16.52824614 2.06823164 3.629397192 1.039052605 1.264921469 0.479690239 0.105425154 0.215495724 5.680557569 0.04880173 0.032725641 117.0123335 -2.06823164 0.225868864 TQS(ph)PGGCSAEAVLAR ddPTM_BT-474_Pertuzumab_2h_R1 5 TQSPGGCSAEAVLAR 15 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7 Q96MH2 HEXIM2 Protein HEXIM2 1 TQS(1)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR;T(0.022)QS(0.978)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR;T(0.011)QS(0.989)PGGCSAEAVLAR 284.05 6.35E-34 2707502000 1041606 1044932 872404 1079404 997544 992673 1151585 1186962 1245335 1342251 TRUE FALSE 1000898.886 1015131.562 1030066.809 1135112.17 1029630.909 1012745.528 1165678.442 1162450.82 1103969.792 1251339.144 0.799862204 0.81123616 0.823171571 0.907117926 0.822823224 0.809329376 0.931544775 0.928965441 0.882230686 1 20.25504142 2.068247757 0.114174551 1.117528175 0.656654929 0.684914141 0.036437513 6.021826887 0.509404044 0.820709388 1.063480063 117.016676 -2.068247757 -0.460873246 SIRPDNMSEYSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIRPDNMSEYSK 12 1 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ; 109.6 0.0016585 953870000 352720 341490 283710 315790 300300 308800 346250 379180 391170 388840 FALSE TRUE 338935.3124 331751.0396 334982.7081 332087.9597 309959.4222 315044.1476 350487.5111 371349.8005 346766.0215 362503.5205 0.934984885 0.915166394 0.924081255 0.91609582 0.855052171 0.869078864 0.96685271 1.024403294 0.956586631 1 18.46763548 2.068279001 5.524346202 0.996309764 0.90282164 0.697222563 0.027672051 0.111339354 6.33566264 0.011343178 0.008224522 117.0250946 -2.068279001 -0.093488124 RSECNMCNTPK ddPTM_BT-474_Pertuzumab_2h_R1 5 RSECNMCNTPK 11 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 ;;;; 140.16 6.21E-05 882624000 720513 681565 536353 611504 624429 625673 659814 703166 752631 690797 FALSE TRUE 692354.5554 662127.4335 633283.9182 643063.7947 644514.3259 638324.5367 667889.0011 688645.3764 667195.4842 644008.7039 1.075070183 1.028134293 0.983346831 0.99853277 1.000785117 0.991173773 1.037080706 1.069310666 1.036003831 1 19.29672066 2.068430241 7.696001428 1.04536965 1.01111175 0.096425883 0.029213424 0.361919357 35.06077985 0.011287658 0.008312344 117.065855 -2.068430241 -0.0342579 GNRPVILTYHDIGMNHK ddPTM_BT-474_Pertuzumab_2h_R1 4 GNRPVILTYHDIGMNHK 17 1 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1 Q92597 NDRG1 Protein NDRG1 0 ;;; 283.49 2.66E-36 9375540000 3478200 3497560 2612520 2946280 2933440 2873560 2295820 745481 2580030 1633880 FALSE TRUE 3342268.099 3397813.013 3084660.479 3098337.864 3027796.762 2931665.352 2323916.932 730086.5568 2287155.811 1523215.852 2.1942183 2.230683858 2.025097411 2.034076693 1.987766052 1.924655227 1.525664881 0.479306039 1.501530993 1 20.53868897 2.068501657 3.183510531 0.942706089 2.070259446 0.785347456 0.25058768 0.099245393 2.002155324 0.108033798 0.069665805 117.0851071 -2.068501657 1.127553357 DLGEELEALKTELEDTLDSTAAQQELR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLGEELEALKTELEDTLDSTAAQQELR 27 1 P35579 P35579 MYH9 Myosin-9 0 232.06 1.69E-35 673840000 1000600 856540 741960 693500 814960 885690 902990 1070700 1181000 1015200 FALSE TRUE 961495.4458 832112.3178 876048.6768 729291.6181 841173.9285 903599.2586 914041.0617 1048589.671 1046937.831 946439.5998 1.015907878 0.87920277 0.925625552 0.770563297 0.888777191 0.954735261 0.965767981 1.107930893 1.106185573 1 19.85215091 2.068598206 1.951247019 1.081266449 0.893890233 0.557136588 0.065436534 0.229495021 1.664232258 0.036589655 0.020081862 117.1111394 -2.068598206 -0.187376216 LWSLGQDDMAIPSKPPAAS(ph)PEKPSALLGNSLALPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LWSLGQDDMAIPSKPPAASPEKPSALLGNSLALPR 35 2 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 LWSLGQDDMAIPS(0.017)KPPAAS(0.983)PEKPSALLGNSLALPR;LWSLGQDDMAIPSKPPAAS(0.981)PEKPS(0.018)ALLGNSLALPR 207.02 4.70E-28 1517640000 1101400 1092700 988630 877620 1031410 1083440 1100820 1197110 1361270 1245400 TRUE FALSE 1058356.07 1061537.266 1167297.433 922914.0734 1064586.239 1105347.899 1114292.164 1172389.26 1206744.337 1161047.949 0.911552423 0.914292357 1.005382624 0.794897467 0.91691841 0.952026056 0.95972967 1.009768168 1.039357882 1 20.14699612 2.068780274 1.472343227 1.020795573 0.910096022 0.468301508 0.048983069 0.366990947 1.49830934 0.031850981 0.016118242 117.1602459 -2.068780274 -0.110699551 S(ph)GGGDLTLGLEPS(ph)EEEAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGGDLTLGLEPSEEEAPR 19 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 2 S(1)GGGDLTLGLEPS(1)EEEAPR;S(1)GGGDLTLGLEPS(1)EEEAPR 291.49 2.18E-49 223902000 243910 422710 185590 496020 202140 174462 467380 754280 399450 265103 TRUE FALSE 234377.7275 410654.7247 219130.2414 521619.6516 208642.0167 177989.7412 473099.9362 738703.8544 354106.1106 247147.3377 0.948331994 1.661578589 0.886638082 2.110561483 0.844200948 0.720176648 1.914242495 2.988920946 1.432773316 1 17.91501184 2.068815251 7.77622295 2.132682687 1.231678335 0.139590212 0.638375038 0.288706111 28.24425508 0.233909032 0.172289497 117.1696819 -2.068815251 -0.901004353 KGKPSSDTVPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGKPSSDTVPKPK 13 3 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 63.185 0.031091 454270000 293410 271690 192610 230330 256630 271620 232740 215520 276940 274370 FALSE TRUE 281943.2128 263941.6672 227418.9116 242217.3589 264884.737 277112.3425 235588.3417 211069.4367 245502.9322 255786.6755 1.102259186 1.031882004 0.889096006 0.946950651 1.035568942 1.083372861 0.921034457 0.825177607 0.959795626 1 17.96458159 2.06886162 9.114998446 0.899999092 1.00756315 0.232470389 0.072784625 0.379727145 46.4739273 0.028557082 0.021072064 117.1821925 -2.06886162 0.107564057 KEEENADS(ph)DDEGELQDLLSQDWR ddPTM_BT-474_Pertuzumab_2h_R1 6 KEEENADSDDEGELQDLLSQDWR 23 1 Q96NB3;J3QQQ3 Q96NB3 ZNF830 Zinc finger protein 830 1 KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR 294.6 7.74E-62 4584520000 1180809 1044457 905257 935728 1094634 1075390 1118472 1312121 1346315 1298641 TRUE FALSE 1134661.679 1014670.109 1068857.077 984021.0342 1129843.897 1097135.123 1132160.195 1285025.243 1193486.965 1210682.888 0.937207992 0.838097341 0.882854699 0.812781814 0.9332286 0.906211803 0.935141816 1.061405307 0.985796509 1 20.2073896 2.068946392 2.157545732 1.021328798 0.878637698 0.661832401 0.041258916 0.171340481 1.528811496 0.021334508 0.012106612 117.2050682 -2.068946392 -0.142691099 DYEMNANHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYEMNANHK 9 0 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 0 109.88 0.0023779 182690000 194750 195870 161960 182210 174150 171710 203530 224690 233270 232290 FALSE TRUE 187138.9547 190283.9794 191229.7748 191613.8799 179751.6929 175182.0938 206020.861 220050.073 206790.1675 216556.7914 0.864156481 0.878679344 0.883046768 0.884820461 0.830044127 0.808942969 0.951347957 1.016131018 0.954900404 1 17.72438589 2.069331616 5.582426207 0.990321977 0.860691558 0.838284176 0.026693082 0.077141685 4.425502143 0.010865557 0.007888088 117.3090765 -2.069331616 -0.129630419 DSLS(ph)PVLHPSDLILTR ddPTM_BT-474_Pertuzumab_2h_R1 5 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 DS(0.188)LS(0.812)PVLHPSDLILTR;DSLS(1)PVLHPSDLILTR;DS(0.001)LS(0.999)PVLHPSDLILTR;DS(0.002)LS(0.998)PVLHPSDLILTR;DS(0.044)LS(0.956)PVLHPSDLILTR 247.36 1.78E-20 1725692000 1284640 1911630 1639637 2214100 1896890 2097770 1572644 1431613 1521267 1802842 TRUE FALSE 1234434.849 1857112.184 1935955.879 2328369.966 1957905.19 2140188.347 1591890.488 1402049.691 1348579.148 1680733.906 0.734461799 1.104941227 1.151851505 1.385329325 1.164910866 1.273365367 0.947140105 0.834188973 0.802375167 1 20.6806599 2.069373761 5.821464854 0.867303543 1.147030591 0.343112022 0.163798986 0.213697891 13.1377383 0.064610535 0.047058927 117.320461 -2.069373761 0.279727048 IEVLPVDTGAGGYSGNSGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 IEVLPVDTGAGGYSGNSGSPK 21 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 IEVLPVDTGAGGYS(0.001)GNS(0.24)GS(0.759)PK;IEVLPVDTGAGGYSGNS(0.001)GS(0.999)PK;IEVLPVDTGAGGYSGNS(0.203)GS(0.797)PK 342.11 9.75E-81 434700000 547265 562699 398824 529404 424862 483599 565488 708290 639820 554155 TRUE FALSE 525877.2788 546651.3755 470900.3686 556726.6039 438528.0721 493377.7031 572408.6113 693663.564 567190.3159 516621.5883 1.017915803 1.05812724 0.911499595 1.077629384 0.84883807 0.95500791 1.107984305 1.342691788 1.097883497 1 18.97874841 2.069385653 4.893600678 1.194224065 0.978808804 0.333075898 0.104479077 0.171016613 7.837811032 0.039779755 0.028461884 117.3236735 -2.069385653 -0.215415261 FLVYVANFDEKDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLVYVANFDEKDPR 14 1 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 105.65 0.00090059 6950100000 7268700 7467400 6442200 7074500 7135900 6375000 7900200 8519600 8750700 8794400 FALSE TRUE 6984631.168 7254437.063 7606448.846 7439615.793 7365432.704 6503906.868 7996885.011 8343667.283 7757357.222 8198747.455 0.851914418 0.884822603 0.927757427 0.907408825 0.898360725 0.793280547 0.975378868 1.01767585 0.946163699 1 22.96697209 2.069398524 10.9702623 0.991563172 0.882275427 0.654394853 0.038239021 0.297602322 45.54537488 0.014443516 0.010665318 117.3271506 -2.069398524 -0.109287745 SWSHYTVPAGMTVIQWVSDFSER ddPTM_BT-474_Pertuzumab_2h_R1 2 SWSHYTVPAGMTVIQWVSDFSER 23 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 278.36 7.82E-52 600870000 192409 261300 219410 226029 261620 264630 213521 208570 226860 219150 FALSE TRUE 184889.4436 253847.9798 259062.2677 237694.3838 270035.2449 269980.9999 216134.1339 204262.9566 201107.8039 204306.7753 0.904959923 1.242484394 1.268006249 1.163418998 1.321714586 1.321449078 1.057890193 0.999785525 0.984342314 1 17.64037752 2.069505866 6.294552455 1.002750258 1.211485436 0.423307221 0.111869128 0.193970861 13.52713934 0.042810723 0.03132821 117.3561534 -2.069505866 0.208735178 EKVAS(ph)DTEEADR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKVASDTEEADR 12 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 EKVAS(0.997)DT(0.003)EEADR;EKVAS(0.955)DT(0.045)EEADR;EKVAS(0.986)DT(0.014)EEADR 183.6 9.32E-06 1757230000 2256080 2038350 1821080 1913590 1951840 2091790 2215210 2556390 2775960 2436360 TRUE FALSE 2167909.899 1980218.254 2150189.666 2012350.609 2014622.706 2134087.427 2242320.403 2503599.653 2460844.659 2271343.167 0.954461629 0.87182698 0.946659975 0.885973832 0.886974164 0.939570672 0.987222202 1.102255128 1.083431467 1 21.11511426 2.069656533 2.501603166 1.070992961 0.909550049 0.769527938 0.036144658 0.115082114 1.399297335 0.016816559 0.010032993 117.3968742 -2.069656533 -0.161442912 IAPSGDQWEEEALDEFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IAPSGDQWEEEALDEFDR 18 0 Q5SZR4;F6TB26;Q9Y2W6-3;Q9Y2W6 Q5SZR4 TDRKH Tudor and KH domain-containing protein 0 72.321 0.051314 8458200 1921.8 4918.6 2522 5760.6 3446.9 3361.8 3513 2421.1 3494.7 2667 FALSE TRUE 1846.693931 4778.326344 2977.781502 6057.905256 3557.772669 3429.777899 3555.993145 2371.103439 3097.996307 2486.361714 0.742729395 1.92181464 1.197646137 2.436453723 1.430915159 1.379436419 1.430199445 0.953643802 1.245995821 1 11.27982048 2.069738387 1.63459383 1.060830864 1.580495012 0.175673842 0.425650811 0.594137063 3.002490085 0.250075654 0.130128579 117.4190027 -2.069738387 0.519664148 KDYEEIGPSICR ddPTM_BT-474_Pertuzumab_2h_R1 6 KDYEEIGPSICR 12 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;;;; 194.85 1.60E-06 6055390000 3408890 3712440 2825980 3247580 3283400 3195090 3510490 3676460 4095020 3872340 FALSE TRUE 3275666.81 3606564.846 3336697.45 3415187.993 3389013.543 3259696.909 3553452.427 3600539.816 3630170.497 3610062.963 0.907371102 0.99903101 0.924276802 0.946018955 0.938768542 0.902947384 0.984318685 0.997362055 1.005569857 1 21.78359257 2.069809915 7.198314971 0.998292588 0.939319266 0.587457225 0.024984643 0.159057812 13.65094322 0.009127444 0.006712496 117.438343 -2.069809915 -0.058973322 SGSS(ph)QELDVKPSAS(ph)PQER ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.282)GS(0.33)S(0.388)QELDVKPS(0.342)AS(0.658)PQER 104.33 0.00029018 654870000 440990 392540 402310 419280 412340 400360 518930 590550 659340 616900 TRUE FALSE 423755.6233 381345.1435 475016.3663 440919.091 425603.2906 408455.5535 525280.8206 578354.9361 584494.4874 575116.8135 0.736816614 0.663074239 0.825947625 0.76666006 0.740029296 0.710213202 0.913346312 1.005630374 1.016305685 1 19.13349549 2.070302466 3.236692985 1.002415316 0.741846986 0.9015439 0.040160166 0.07371898 1.538045262 0.018604841 0.012081937 117.5716101 -2.070302466 -0.26056833 ALIQTCLNSPDS(ph)PPRSDPTTDQR ddPTM_BT-474_Pertuzumab_2h_R1 5 ALIQTCLNSPDSPPRSDPTTDQR 23 1 P11831 P11831 SRF Serum response factor 1 ALIQTCLNSPDS(0.998)PPRS(0.002)DPTTDQR;ALIQTCLNSPDS(0.995)PPRS(0.005)DPTTDQR;ALIQTCLNSPDS(1)PPRSDPTTDQR;ALIQTCLNSPDS(1)PPRSDPTTDQR;ALIQTCLNS(0.003)PDS(0.996)PPRSDPTTDQR 277.45 5.14E-52 6061850000 1079440 1250960 902230 1037770 1168680 1243950 1006540 1036780 1073610 1061310 TRUE FALSE 1037254.291 1215283.846 1065283.031 1091329.434 1206271.654 1269103.521 1018858.338 1015370.131 951738.2937 989426.5284 1.048338873 1.228270933 1.07666714 1.102991887 1.219162433 1.282665751 1.029746331 1.026220848 0.961909011 1 19.91623306 2.070469432 10.4766446 1.006193588 1.159125621 0.547282294 0.069479788 0.339661157 48.39888638 0.026488089 0.019557522 117.6168196 -2.070469432 0.152932032 LVVEEYYEVLDHCSSILNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVVEEYYEVLDHCSSILNK 19 0 O00170;E9PMH2;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 ; 200.67 6.36E-16 1067440000 611130 627280 745390 541310 581600 611000 673540 591480 603130 651380 FALSE TRUE 587246.364 609390.5886 880098.5541 569247.074 600307.6922 623354.8386 681782.984 579265.7313 534665.2109 607261.4524 0.96704041 1.003506128 1.449290994 0.93740031 0.988548985 1.026501577 1.122717375 0.953898406 0.880453071 1 19.21195827 2.070547054 0.765547162 0.941949233 1.091823391 0.10735975 0.142768074 1.491145311 1.647276781 0.124503109 0.068472322 117.6378434 -2.070547054 0.149874159 TVSASS(ph)TGDLPK ddPTM_BT-474_Pertuzumab_2h_R1 5 TVSASSTGDLPK 12 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 TVSAS(0.002)S(0.994)T(0.004)GDLPK;TVSASS(0.998)T(0.002)GDLPK;TVSAS(0.001)S(0.996)T(0.003)GDLPK;TVSAS(0.002)S(0.767)T(0.23)GDLPK;TVSAS(0.011)S(0.986)T(0.003)GDLPK 277.82 6.87E-28 2283230000 4723670 4165670 3590620 3825690 3959630 4215790 4403960 5143550 5218440 4884300 TRUE FALSE 4539063.754 4046869.17 4239524.907 4023134.319 4086995.095 4301036.162 4457856.98 5037333.895 4626064.569 4553482.011 0.996833576 0.888741662 0.931051204 0.8835292 0.897553803 0.944559823 0.978999581 1.106259755 1.015940012 1 22.11853875 2.070630205 3.041686955 1.05124159 0.918816566 0.614279413 0.040986201 0.141584832 2.597161665 0.01784747 0.011367949 117.6603687 -2.070630205 -0.132425024 RHVFGESDELIGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RHVFGESDELIGQK 14 1 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 61.212 0.056338 245870000 198610 205960 168580 175300 173820 178880 143960 57431 165700 149460 FALSE TRUE 190848.1016 200086.2225 199046.156 184347.254 179411.0782 182497.0762 145721.8255 56245.02978 146890.4307 139336.9411 1.369687752 1.435988338 1.42852394 1.323032159 1.287605977 1.309753715 1.045823343 0.403662011 1.054210244 1 17.08821827 2.070745307 3.779000129 0.746335503 1.35977497 0.65388252 0.174430708 0.114366271 3.250786422 0.070998131 0.048248324 117.6915566 -2.070745307 0.613439467 IS(ph)PVPYEDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISPVPYEDLK 10 0 Q9Y2I9;F8VZ81;Q9Y2I9-2;Q9Y2I9-3 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 IS(1)PVPYEDLK;IS(1)PVPYEDLK 169.89 4.71E-06 366370000 596580 495930 564780 581150 612240 536130 739350 901320 869050 937910 TRUE FALSE 573264.994 481786.562 666848.3095 611143.2211 631933.2556 546970.9159 748398.3865 882707.427 770399.0874 874384.5203 0.655621161 0.551000791 0.762648805 0.698941034 0.722717799 0.625549633 0.855914497 1.009518589 0.881075853 1 19.73790833 2.070767981 3.988319799 0.959458307 0.672608548 0.818516797 0.06302041 0.088359835 2.783464005 0.026046217 0.017942808 117.6977013 -2.070767981 -0.286849759 EEAS(ph)SPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEASSPLK 8 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 EEAS(0.632)S(0.368)PLK;EEAS(0.899)S(0.101)PLK 142.83 0.00097391 184590000 1377650 1177800 1175460 1250050 1202110 1183920 1454750 1635870 1700900 1780130 TRUE FALSE 1323809.915 1144210.297 1387891.77 1314565.23 1240776.96 1207859.674 1472553.666 1602088.713 1507820.963 1659560.21 0.797687187 0.689465975 0.836300944 0.792116624 0.747654079 0.727819133 0.887315602 0.965369442 0.908566591 1 20.66236954 2.070796241 4.045267618 0.949332921 0.765788998 0.800674191 0.043721043 0.092913041 3.00552688 0.017593662 0.012160955 117.7053603 -2.070796241 -0.183543923 S(ph)GDLGDMEPLK ddPTM_BT-474_Pertuzumab_2h_R1 12 SGDLGDMEPLK 11 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK 229.95 2.26E-12 10159270000 7917460 7410850 8123650 9592690 7585240 7200070 10377720 12588610 12099290 11968880 TRUE FALSE 7608036.91 7199499.814 9591774.265 10087769.88 7829226.133 7345660.349 10504725.64 12328650.8 10725829.32 11158217.1 0.681832666 0.64521955 0.859615311 0.904066464 0.701655656 0.658318465 0.941434062 1.10489433 0.961249385 1 23.41160319 2.070849104 5.195357795 1.031699943 0.74938805 0.692292815 0.085938101 0.117235381 5.89125784 0.035865518 0.02586999 117.7196884 -2.070849104 -0.282311893 DTEEQNPETVNWEDRPST(ph)PTILGYEVMEER ddPTM_BT-474_Pertuzumab_2h_R1 1 DTEEQNPETVNWEDRPSTPTILGYEVMEER 30 1 A0A0C4DGW2;P57768-2;P57768;E5RGS8;E5RH07;E5RGQ6 A0A0C4DGW2 SNX16 Sorting nexin-16 1 DTEEQNPETVNWEDRPS(0.035)T(0.841)PT(0.124)ILGYEVMEER 161.29 6.74E-12 88271000 62971 72195 56694 71149 56657 58031 70223 77885 75524 68173 TRUE FALSE 60510.0237 70136.06929 66939.86695 74821.00842 58479.42386 59204.42658 71082.41008 76276.64753 66950.83214 63555.58199 0.952080397 1.103539093 1.053249217 1.177253139 0.920130412 0.931537793 1.118429064 1.200156542 1.053421746 1 15.95573122 2.07094056 24.99962591 1.11990064 1.029895773 0.096227826 0.089831783 78.40563612 27628.76666 0.034435754 0.025432489 117.7444811 -2.07094056 -0.090004867 VNKDDIQK ddPTM_BT-474_Pertuzumab_2h_R1 3 VNKDDIQK 8 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ;; 110.14 0.0031775 4900100000 8753800 8829000 7150400 7796500 8825200 9251100 10402800 12208200 14190100 13103400 FALSE TRUE 8411691.818 8577205.564 8442636.34 8198878.299 9109070.573 9438163.58 10530112.58 11956096.4 12579299.34 12215895.05 0.688585796 0.702134844 0.691118932 0.671164763 0.745673611 0.772613349 0.862000904 0.978732738 1.029748478 1 23.54225624 2.071283393 1.162298618 1.025763142 0.692188723 0.982750744 0.017655328 0.054501946 0.137139798 0.012954403 0.006359546 117.8374655 -2.071283393 -0.333574419 EETPGQRPAVTETHQLAELNEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EETPGQRPAVTETHQLAELNEK 22 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1;I3L1C0 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 296.04 9.20E-56 4404430000 2554260 2605770 2156320 2381510 2415030 2578270 2561080 2698710 3139940 2867560 FALSE TRUE 2454436.695 2531455.991 2546014.991 2504420.017 2492711.633 2630404.386 2592423.263 2642980.695 2783507.175 2673337.607 0.918116997 0.946927161 0.952373162 0.93681397 0.932434282 0.983940217 0.969732837 0.988644565 1.041210496 1 21.35021061 2.071433582 0.911898713 1.016587918 0.937702623 0.76505749 0.017117504 0.277345522 0.427744922 0.013679173 0.006947909 117.8782234 -2.071433582 -0.078885296 EDKPAETK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDKPAETK 8 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 87.913 0.013668 538240000 917380 695860 706890 706070 761320 695270 920080 1051200 1099820 1127030 FALSE TRUE 881527.7754 676014.7541 834640.7477 742510.3573 785808.5492 709328.8358 931340.2143 1029492.353 974973.0444 1050695.254 0.838994725 0.643397552 0.794369961 0.706684792 0.747893879 0.675104254 0.886403751 0.979820122 0.92793133 1 20.00291286 2.071440499 4.318661316 0.960677799 0.732903388 0.788077898 0.05547964 0.085356374 3.10614068 0.020392175 0.014302799 117.880101 -2.071440499 -0.227774411 LPVGSQCSVDLES(ph)ASGEKDLAPPSEPSESFQEHTVDGENQIVFTHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPVGSQCSVDLESASGEKDLAPPSEPSESFQEHTVDGENQIVFTHR 46 1 F5H7V9;E9PC84;J3QSU6;P24821-6;P24821-5;P24821-2;P24821-3;P24821-4;P24821 F5H7V9 TNC Tenascin 1 LPVGS(0.001)QCS(0.001)VDLES(0.499)AS(0.499)GEKDLAPPSEPSESFQEHTVDGENQIVFTHR 67.716 0.00046412 129690000 51485 59222 38790 46748 50462 50724 43467 30176 59135 44235 TRUE FALSE 49472.90928 57533.04654 45800.21588 49160.66988 52085.15606 51749.67403 43998.96215 29552.85505 52422.24271 41238.92405 1.199665375 1.395115122 1.11060647 1.192093902 1.263009578 1.254874496 1.066927985 0.716625269 1.27118357 1 15.33171907 2.071592418 4.849153076 0.947951265 1.234773906 0.355148813 0.143975316 0.178321755 7.938614507 0.054939759 0.039300966 117.9213434 -2.071592418 0.286822641 MADKDGDLIATK ddPTM_BT-474_Pertuzumab_2h_R1 1 MADKDGDLIATK 12 1 O43852;O43852-3;O43852-15;O43852-6;O43852-10;O43852-2;O43852-4;O43852-8 O43852;O43852-2 CALU Calumenin 0 115.91 0.00081961 903110000 2004000 2085200 1706200 1667900 1783000 1669300 2103800 2209500 2592300 2439700 FALSE TRUE 1925681.464 2025732.138 2014548.294 1753980.519 1840351.814 1703054.39 2129546.934 2163873.053 2298032.972 2274456.946 0.846655492 0.89064431 0.885727161 0.771164529 0.809138998 0.748774072 0.936288083 0.95138009 1.010365563 1 21.11709069 2.071597742 6.197910498 0.972840383 0.828049037 0.730473021 0.044886139 0.122446829 8.139063661 0.018775572 0.013734214 117.9227889 -2.071597742 -0.144791346 PLSEEQLDGILS(ph)PELDK ddPTM_BT-474_Pertuzumab_2h_R1 2 PLSEEQLDGILSPELDK 17 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 PLSEEQLDGILS(1)PELDK;PLSEEQLDGILS(1)PELDK 147.06 4.34E-07 29666000 119019 88373 103058 107951 120696 94128 134027 156724 163980 148729 TRUE FALSE 114367.6059 85852.68857 121682.8731 113522.364 124578.2965 96031.33265 135667.2625 153487.5946 145365.6779 138655.4524 0.824833095 0.61918004 0.877591693 0.818737108 0.898473838 0.69258966 0.978448811 1.106971216 1.048394963 1 17.08114482 2.071670976 5.337393443 1.059198478 0.792138551 0.689000624 0.081548695 0.107568476 5.617474462 0.031110002 0.022509793 117.9426757 -2.071670976 -0.267059926 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPRR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.724)S(0.276)PEQLAAGAEEGGGPRR 223.72 1.66E-36 86037000 116140 134420 85457 66359 116440 164450 83897 88866 96259 81483 TRUE FALSE 111601.1204 130586.4732 100900.9809 69783.79594 120185.3983 167775.2917 84923.75658 87030.88605 85332.08187 75964.08383 1.469130078 1.719055462 1.328272202 0.918641974 1.582134507 2.208613376 1.11794617 1.145684666 1.123321411 1 16.21302985 2.07218822 25 1.11224281 1.523009346 0.33256051 0.305271707 57.46654932 19900.28147 0.121602556 0.089809432 118.0832289 -2.07218822 0.410766536 GFGFVTFSSMAEVDAAMAARPHSIDGR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;; 239.96 2.29E-45 2364138000 367169 519884 312791 316611 391891 476755 303219 273042 310625 300605 FALSE TRUE 352819.6296 505057.4173 369319.2917 332951.3317 404496.5299 486395.3128 306929.8848 267403.5873 275364.1522 280244.7556 1.258969606 1.802201138 1.317845506 1.188073372 1.443368776 1.735608974 1.095220798 0.954178738 0.982584497 1 18.09632785 2.072215067 7.169507982 0.98616457 1.453288651 0.600259283 0.181533938 0.152423432 12.59086142 0.069359839 0.051014688 118.0905287 -2.072215067 0.467124081 VWDEDDDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 VWDEDDDIK 9 0 O14795;O14795-2;A0A1B0GUS7;B1AM27;I6L9J0;F8W8M9;A0A1B0GVW8;F8VZH8;F8W0P6;F8W059;A0A3B3ISZ1;Q9UPW8;Q8NB66 O14795 UNC13B;UNC13A;UNC13C Protein unc-13 homolog B;Protein unc-13 homolog A;Protein unc-13 homolog C 0 ; 137.14 0.00040287 121598000 282270 273210 277310 269150 305390 296130 331880 410930 390470 400090 FALSE TRUE 271238.5763 265418.3183 327426.0857 283040.8638 315213.1467 302117.9515 335941.6467 402444.1519 346145.4826 372991.5479 0.727197648 0.711593385 0.877837816 0.758839886 0.84509461 0.809986052 0.900668255 1.078963194 0.928025004 1 18.50878341 2.072836852 2.939618345 1.00917205 0.788889354 0.727861683 0.058700217 0.129623215 2.214503329 0.026890364 0.016978318 118.2597216 -2.072836852 -0.220282696 VMTIPYQPMPASS(ph)PVICAGGQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VMTIPYQPMPASSPVICAGGQDR 23 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 VMTIPYQPMPAS(0.458)S(0.542)PVICAGGQDR;VMTIPYQPMPAS(0.358)S(0.642)PVICAGGQDR;VMTIPYQPMPAS(0.013)S(0.987)PVICAGGQDR;VMTIPYQPMPAS(0.06)S(0.94)PVICAGGQDR 257.04 8.67E-44 1939540000 1529960 1722140 1443790 1633920 1640230 1769970 1535320 1570630 1668530 1742760 TRUE FALSE 1470167.472 1673026.253 1704714.97 1718246.807 1692989.488 1805760.006 1554109.705 1538195.942 1479125.469 1624721.313 0.90487363 1.029731216 1.04923531 1.057564022 1.042018391 1.111427536 0.95653925 0.946744484 0.910387189 1 20.63176084 2.072900034 13.02030151 0.947754789 1.034677944 0.350226466 0.052612446 0.874680096 154.0217536 0.019716488 0.014561307 118.2769274 -2.072900034 0.086923155 AS(ph)PIKMDLAPSK ddPTM_BT-474_Pertuzumab_2h_R1 7 ASPIKMDLAPSK 12 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK 161.91 3.88E-05 6565560000 14169820 12201830 14344870 12224750 12492510 12528250 16955580 19259690 21160060 21358170 TRUE FALSE 13616047.77 11853845.76 16937307.11 12855670.81 12894342.93 12781579.8 17163087.46 18861970.67 18758058.7 19911562.12 0.683826195 0.595324751 0.850626737 0.645638486 0.64758068 0.641917481 0.861965895 0.947287338 0.942068663 1 24.24710307 2.073011867 3.294409353 0.950875876 0.678782121 0.79463969 0.066035076 0.110161846 2.379968871 0.02911448 0.019061765 118.3073883 -2.073011867 -0.272093756 LKFS(ph)DEEDGRDS(ph)DEEGAEGHR ddPTM_BT-474_Pertuzumab_2h_R1 6 LKFSDEEDGRDSDEEGAEGHR 21 2 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 2 LKFS(1)DEEDGRDS(1)DEEGAEGHR;LKFS(1)DEEDGRDS(1)DEEGAEGHR;LKFS(1)DEEDGRDS(1)DEEGAEGHR;LKFS(1)DEEDGRDS(1)DEEGAEGHR;LKFS(1)DEEDGRDS(1)DEEGAEGHR;LKFS(1)DEEDGRDS(1)DEEGAEGHR 168.26 5.92E-12 6692520000 2219670 2088400 1922820 1834830 2026820 1977010 2282980 2526480 2761890 2536430 TRUE FALSE 2132922.842 2028840.877 2270316.347 1929525.796 2092014.506 2016986.497 2310919.792 2474307.305 2448371.826 2364635.337 0.902009206 0.857993131 0.96011267 0.815992964 0.884709145 0.852979935 0.977283793 1.046380077 1.03541201 1 21.17318628 2.073042069 3.954163728 1.02897597 0.879381496 0.770802382 0.036941042 0.095576245 2.946378815 0.014620631 0.010069301 118.315616 -2.073042069 -0.149594475 KLNELESDLTFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLNELESDLTFK 12 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 106.32 0.0031016 876590000 1122060 988840 800570 852170 1017380 1000070 1032970 1173530 1335570 1172350 FALSE TRUE 1078208.655 960639.2514 945250.8076 896150.5958 1050104.952 1020292.101 1045611.796 1149296.195 1183961.693 1092945.69 0.986516223 0.878945093 0.864865305 0.819940646 0.9608025 0.933524977 0.956691449 1.051558376 1.083275869 1 20.05979028 2.073201515 1.37934672 1.054320578 0.894699682 0.60892801 0.049011662 0.272546396 0.97456326 0.033252302 0.016662277 118.3590622 -2.073201515 -0.159620896 IREESNTK ddPTM_BT-474_Pertuzumab_2h_R1 2 IREESNTK 8 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 ; 161.27 0.00031786 730060000 601100 585920 464150 500280 582650 537420 599650 666800 706300 643890 FALSE TRUE 577608.3474 569210.1353 548032.23 526099.5108 601391.4664 548287.0006 606988.6961 653030.347 626123.7851 600278.7568 0.962233531 0.94824301 0.912962892 0.876425335 1.001853655 0.913387313 1.011178039 1.087878489 1.043055044 1 19.19527309 2.07345253 4.465128421 1.05287016 0.936048447 0.634004767 0.037422221 0.119109809 4.560496659 0.014669998 0.010367554 118.4274915 -2.07345253 -0.116821713 RKLEGDSTDLSDQIAELQAQIAELK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKLEGDSTDLSDQIAELQAQIAELK 25 2 P35579 P35579 MYH9 Myosin-9 0 137.52 1.06E-05 215000000 528330 437360 357480 429020 444620 473200 543320 596040 701220 658710 FALSE TRUE 507682.2795 424886.921 422084.5881 451161.7736 458921.6061 482768.4282 549969.3127 583731.5657 621620.4454 614094.985 0.826716212 0.691891208 0.687327854 0.734677509 0.747313717 0.786146183 0.895576948 0.950555826 1.012254554 1 19.2281023 2.073786851 1.229274526 1.005411692 0.727920844 0.901186984 0.036944893 0.128005194 0.361443411 0.025924015 0.012790462 118.5186924 -2.073786851 -0.277490847 EES(ph)EES(ph)DEDMGFGLFD ddPTM_BT-474_Pertuzumab_2h_R1 14 EESEESDEDMGFGLFD 16 0 F8VWS0;P05388;P05388-2;Q8NHW5;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 2 EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD 202.4 6.80E-11 668555300 889642 880562 803613 885326 865457 899676 994452 1115902 1202450 1178582 TRUE FALSE 854873.8071 855449.2339 948843.7454 931017.781 893295.2104 917868.0651 1006622.401 1092858.234 1065952.917 1098755.591 0.778038186 0.778561894 0.863562154 0.847338378 0.813006293 0.835370552 0.916147694 0.994632694 0.970145613 1 20.06743908 2.07378944 2.112277969 0.989011333 0.817943083 0.896199822 0.026069816 0.102003339 0.872749502 0.015099758 0.008548908 118.5193988 -2.07378944 -0.171068249 TKEDLDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKEDLDSR 8 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 0 ; 109.66 0.0032602 716270000 2103030 2121480 1858840 1975520 2020120 2020620 2312900 2519700 2670100 2840900 FALSE TRUE 2020841.263 2060977.468 2194773.738 2077476.824 2085098.994 2061478.321 2341205.962 2467667.314 2367001.442 2648483.313 0.763018311 0.778172722 0.828690793 0.784402459 0.787280397 0.778361831 0.88397988 0.931728474 0.893719598 1 21.33673499 2.073894665 2.744055906 0.933091594 0.787533562 0.848206262 0.029746798 0.100918335 1.492948966 0.013576297 0.008389546 118.5481184 -2.073894665 -0.145558032 FHDTSS(ph)PLMVTPPSAEAHWAVR ddPTM_BT-474_Pertuzumab_2h_R1 7 FHDTSSPLMVTPPSAEAHWAVR 22 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 FHDTS(0.003)S(0.997)PLMVTPPSAEAHWAVR;FHDT(0.004)S(0.117)S(0.879)PLMVTPPSAEAHWAVR;FHDT(0.021)S(0.121)S(0.858)PLMVTPPSAEAHWAVR;FHDTS(0.024)S(0.976)PLMVTPPSAEAHWAVR;FHDT(0.012)S(0.056)S(0.932)PLMVTPPSAEAHWAVR;FHDTS(0.021)S(0.978)PLMVTPPSAEAHWAVR;FHDTS(0.043)S(0.957)PLMVTPPSAEAHWAVR 211.71 3.37E-23 7133053000 364316 448673 322681 409977 354623 384084 307882 117124.5 407825 397358.6 TRUE FALSE 350078.1279 435877.2853 380996.6347 431135.9621 366029.7709 391850.4416 311649.952 114705.8381 361530.4157 370445.1481 0.945020146 1.176631109 1.028483263 1.16383212 0.988080888 1.057782626 0.841285015 0.309643246 0.975935081 1 18.49890041 2.073895438 4.592634761 0.660924815 1.062811911 0.289133692 0.196173489 0.175729105 7.047421833 0.074856443 0.05317118 118.5483294 -2.073895438 0.401887096 FLPS(ph)PVVIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLPSPVVIKK 10 1 Q13618;Q13618-2;Q13618-3;A0A087WTG3;H7C399 Q13618 CUL3 Cullin-3 1 FLPS(1)PVVIKK 62.14 0.042739 0 160140 158560 113540 108010 155970 160330 126390 143540 164710 149310 TRUE FALSE 153881.5518 154038.024 134059.2037 113584.409 160986.9167 163571.9825 127936.7986 140575.8488 146012.8113 139197.1007 1.105493943 1.106618049 0.963089051 0.815996946 1.156539295 1.175110556 0.91910534 1.009905006 1.048964458 1 17.08676964 2.073937678 0.006287196 2.77E-08 2.045268451 0.015992465 0.105389368 22143.90152 97.78618909 15781.71969 16019.67134 118.5598599 -2.073937678 2.045268423 RPLLAFACDDKDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPLLAFACDDKDGK 14 2 Q96J01;D6REC9 Q96J01 THOC3 THO complex subunit 3 0 ; 137.46 1.19E-05 1230810000 1789690 1523990 1424820 1490190 1595350 1509900 1795570 2032170 2171440 1975100 FALSE TRUE 1719746.936 1480527.297 1682316.669 1567098.884 1646665.882 1540431.213 1817544.723 1990204.979 1924947.235 1841324.718 0.933972655 0.804055517 0.913644754 0.851071443 0.894283266 0.83658857 0.987085388 1.080854974 1.045414324 1 20.81231264 2.074020716 4.269346523 1.048041589 0.871557726 0.789778364 0.040074046 0.080204725 2.833199932 0.014754388 0.010342526 118.5825311 -2.074020716 -0.176483863 AAMYDIISS(ph)PSKDSTK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAMYDIISSPSKDSTK 16 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AAMYDIIS(0.022)S(0.962)PS(0.016)KDSTK;AAMYDIIS(0.205)S(0.795)PS(0.001)KDSTK;AAMYDIIS(0.084)S(0.909)PS(0.007)KDSTK;AAMYDIIS(0.004)S(0.994)PS(0.003)KDSTK 195.78 2.88E-11 2770910000 3681660 3053710 2646280 2365710 2815950 2759290 3154140 3422050 3625050 3517800 TRUE FALSE 3537776.657 2966621.181 3124521.662 2487804.577 2906527.589 2815084.734 3192741.309 3351383.472 3213549.521 3279536.273 1.078742957 0.904585568 0.952732765 0.758584254 0.88626176 0.858378899 0.973534379 1.021907731 0.979879243 1 21.6450604 2.074143142 5.789464456 1.001851459 0.901235799 0.244535676 0.075837573 0.274715047 15.99878181 0.029621877 0.021592055 118.6159639 -2.074143142 -0.10061566 SSS(ph)PAPPSQQSLYK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPAPPSQQSLYK 14 0 I3L3F1;A0A494BZY0;A0A494C199;A0A494C0J4;A0A494C1N2;Q9BXL6-3;Q9BXL6-2;Q9BXL6 I3L3F1 CARD14 Caspase recruitment domain-containing protein 14 1 S(0.013)S(0.013)S(0.974)PAPPSQQSLYK;S(0.001)S(0.001)S(0.998)PAPPSQQSLYK 173.44 2.83E-06 483840000 753430 793650 623730 700250 705930 686360 785380 882370 869660 842510 TRUE FALSE 723985.1226 771015.8791 736451.8858 736389.9864 728636.8796 700238.6695 794991.7154 864148.7512 770939.8427 785446.0473 0.921750291 0.981628059 0.937622499 0.937543691 0.927672731 0.891517211 1.012153181 1.100201286 0.981531253 1 19.58315265 2.074207697 6.174337231 1.042684197 0.935823735 0.58961731 0.036391745 0.121193547 7.790862105 0.013668454 0.010001084 118.6335966 -2.074207697 -0.106860462 HS(ph)STGDSADAGPPAAGSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSSTGDSADAGPPAAGSAR 19 0 F5H1N7;Q6ZU35 F5H1N7 KIAA1211 Uncharacterized protein KIAA1211 1 HS(0.312)S(0.246)T(0.312)GDS(0.13)ADAGPPAAGSAR;HS(0.391)S(0.298)T(0.298)GDS(0.013)ADAGPPAAGSAR 153.65 2.81E-08 721220000 206990 218190 184130 238730 220730 234350 169104 113672 180703 183746 TRUE FALSE 198900.602 211967.4348 217406.3869 251050.8839 227829.9809 239088.7176 171173.5453 111324.6335 160190.353 171300.7198 1.161119476 1.237399558 1.269150458 1.465556504 1.330000138 1.39572512 0.999257596 0.649878375 0.935141155 1 17.38617169 2.074240515 4.53987026 0.822171241 1.310784624 0.752924123 0.117154326 0.091026167 3.573815827 0.047007511 0.033332127 118.6425616 -2.074240515 0.488613383 NEDLTELLNGMDEELDSPEELGK ddPTM_BT-474_Pertuzumab_2h_R1 4 NEDLTELLNGMDEELDSPEELGK 23 0 Q12955;H0Y9E9;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 0 ;;; 254.68 1.58E-43 103889000 258173 249623 221372 214722 247011 235507 274124 308265 343004 295538 FALSE TRUE 248083.3137 242503.9964 261378.8448 225803.8282 254956.3331 240269.1129 277478.8115 301899.22 304067.6239 275520.948 0.900415433 0.880165367 0.948671405 0.819552305 0.925360975 0.872053884 1.007106042 1.095739624 1.10360982 1 18.07180249 2.074307602 3.522731489 1.073531285 0.891489939 0.78672143 0.041655173 0.09290278 2.291997047 0.016720952 0.011181154 118.6608902 -2.074307602 -0.182041346 ITVQAS(ph)PGLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 ITVQASPGLDR 11 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 ITVQAS(1)PGLDR;ITVQAS(1)PGLDR;ITVQAS(1)PGLDR 133.47 0.00016894 1981600000 1458610 1634190 1492630 1824550 1550980 1650770 1527380 1602520 1557160 1741290 TRUE FALSE 1401605.909 1587584.501 1762381.444 1918715.244 1600868.68 1684149.7 1546072.533 1569427.402 1380397.725 1623350.877 0.863402933 0.977967563 1.085644188 1.181947336 0.986150747 1.037452669 0.952395785 0.966782612 0.850338485 1 20.63054343 2.074354708 1.943259705 0.93259895 1.029691802 0.167619569 0.084601745 0.60198361 4.337752181 0.049501804 0.027281941 118.6737614 -2.074354708 0.097092852 RSS(ph)SSGDQSSDSLNS(ph)PTLLAL ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 2 RS(0.363)S(0.442)S(0.146)S(0.049)GDQS(0.001)S(0.001)DS(0.117)LNS(0.874)PT(0.007)LLAL 91.166 0.0013737 70645000 141860 177490 125410 199550 181860 190710 113010 91341 89460 86201 TRUE FALSE 136315.9544 172428.159 148074.3767 209848.7994 187709.6921 194566.2869 114393.0502 89454.77643 79304.87585 80362.52949 1.696262614 2.145628816 1.84257984 2.611276683 2.335786258 2.421107052 1.423462538 1.113140378 0.98683897 1 16.29423535 2.0745242 3.789581703 1.082395788 2.184482503 0.805963333 0.255330435 0.100760711 2.859903126 0.112048301 0.076446324 118.7200854 -2.0745242 1.102086715 S(ph)HTSEGAHLDITPNSGAAGNSAGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHTSEGAHLDITPNSGAAGNSAGPK 25 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.355)HT(0.355)S(0.29)EGAHLDITPNSGAAGNSAGPK;S(0.477)HT(0.477)S(0.045)EGAHLDITPNSGAAGNSAGPK 220.38 2.07E-33 4640510000 1592860 2030400 1329580 1621860 1562920 1616660 1010490 46318 1177780 580990 TRUE FALSE 1530609.27 1972494.98 1569864.682 1705564.389 1613192.741 1649349.973 1022856.679 45361.51711 1044083.352 541639.0298 2.825884373 3.641715001 2.898359601 3.148894919 2.978353945 3.045109163 1.888447144 0.083748612 1.927636848 1 19.04697218 2.07470949 3.567593792 0.909688224 3.103500681 0.799054896 0.471458069 0.08718912 2.203904538 0.189723385 0.127369354 118.7707475 -2.07470949 2.193812458 SNS(ph)SEALLVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSSEALLVDR 11 0 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 S(0.024)NS(0.847)S(0.129)EALLVDR;S(0.003)NS(0.947)S(0.05)EALLVDR 150.76 3.54E-05 606100000 348190 399540 329310 368250 360530 352340 377950 397580 439620 379480 TRUE FALSE 334582.3499 388145.5104 388823.6425 387255.4266 372126.7749 359464.5562 382575.4652 389369.8341 389716.1806 353777.4816 0.945742359 1.097145891 1.099062724 1.094629949 1.051866764 1.016075287 1.081401404 1.100606608 1.101585604 1 18.4324827 2.074738942 24.99999999 1.081690773 1.056406226 0.011905295 0.051245518 130.1590238 43533.70356 0.018963667 0.014005596 118.7788023 -2.074738942 -0.025284548 S(ph)PVGKSPPS(ph)TGSTYGSSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(1)PVGKS(0.362)PPS(0.535)T(0.094)GS(0.006)T(0.002)YGSSQK 92.412 0.0010929 1142400000 169580 137350 176550 167670 165510 145940 221280 253920 277340 286560 TRUE FALSE 162952.6261 133432.9125 208456.5123 176323.4688 170833.7795 148891.0068 223988.0908 248676.4633 245857.5259 267151.036 0.609964418 0.499466199 0.780294606 0.660014168 0.639465158 0.557328952 0.838432425 0.930845963 0.920294114 1 18.02729609 2.074754732 3.942798481 0.932703239 0.628603876 0.808631702 0.072193577 0.098421573 3.006099932 0.030525881 0.021036952 118.7831211 -2.074754732 -0.304099363 LKEELEK ddPTM_BT-474_Pertuzumab_2h_R1 3 LKEELEK 7 1 A0A0B4J1R9;Q8N0S2-3;Q8N0S2-2;Q8N0S2 A0A0B4J1R9 SYCE1 Synaptonemal complex central element protein 1 0 ;; 77.677 0.034107 417480000 800670 726450 624340 697230 736610 728910 790070 743380 941370 842320 FALSE TRUE 769378.9312 705732.3573 737172.1264 733214.1239 760303.7296 743649.0596 799739.113 728028.9432 834509.6241 785268.9161 0.979764913 0.89871424 0.938751186 0.933710871 0.968208106 0.946999231 1.018427059 0.927107808 1.062705536 1 19.58282727 2.074814562 0.62948189 1.010833868 0.934052421 0.349905028 0.037486855 0.873140521 0.683734751 0.032141419 0.020541243 118.7994862 -2.074814562 -0.076781447 GTHDLWDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTHDLWDSR 9 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ; 152.38 8.06E-05 672330000 388350 471600 398200 410670 403620 409040 361730 323690 378910 317850 FALSE TRUE 373172.8527 458150.4297 470163.5979 431864.7279 416602.8039 417311.0691 366156.9599 317005.6884 335897.7253 296321.7364 1.25935025 1.54612495 1.586665911 1.457418322 1.405913751 1.408303941 1.235673644 1.069802345 1.133557495 1 18.17680493 2.075059214 1.365879382 1.049264737 1.470245392 0.7937214 0.086878904 0.182243142 0.638907526 0.058372542 0.029243533 118.8664284 -2.075059214 0.420980655 EAVTEILGIEPDREK ddPTM_BT-474_Pertuzumab_2h_R1 6 EAVTEILGIEPDREK 15 1 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;;;;; 260.12 6.27E-25 3686830000 3291150 3229300 2704880 2648650 2991990 2748230 3328840 3526000 3972920 3845940 FALSE TRUE 3162528.219 3137203.526 3193711.986 2785347.144 3088230.076 2803801.094 3369579.34 3453186.868 3521930.777 3585451.058 0.882044732 0.87498155 0.890742039 0.776847069 0.861322613 0.781993966 0.939792312 0.963110864 0.98228388 1 21.77372319 2.075221966 6.030132283 0.971523145 0.84604012 0.733644004 0.037833562 0.110397329 6.77637544 0.014694425 0.010740277 118.910982 -2.075221966 -0.125483025 GRASPGGVSTS(ph)SSDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRASPGGVSTSSSDGK 16 1 P54259 P54259 ATN1 Atrophin-1 1 GRAS(0.036)PGGVS(0.099)T(0.039)S(0.275)S(0.275)S(0.275)DGK 193.67 8.86E-10 91761000 92184 89549 77613 88472 83086 91014 91945 104560 108770 104080 TRUE FALSE 88581.34737 86995.1502 91639.39559 93038.05052 85758.53665 92854.36544 93070.25041 102400.7995 96422.8856 97030.5689 0.912922065 0.896574669 0.944438404 0.958852984 0.883830092 0.95695992 0.959184837 1.05534576 0.993737197 1 16.56615171 2.075290691 2.421779569 1.020677244 0.923270217 0.673405469 0.027983947 0.156994524 1.78738601 0.013679249 0.008119535 118.9298006 -2.075290691 -0.097407027 LFEDDDS(ph)NEKLFDEEEDSSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFEDDDSNEKLFDEEEDSSEK 21 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEDDDS(1)NEKLFDEEEDSSEK;LFEDDDS(1)NEKLFDEEEDSSEK 177.6 3.88E-17 99831000 168047 122194 131418 126014 161047 135222 199044 248370 277120 222670 TRUE FALSE 161479.5375 118709.1468 155168.156 132517.5976 166227.223 137956.2815 201479.96 243241.0727 245662.4994 207588.3626 0.777883382 0.571848755 0.747480032 0.63836718 0.800754055 0.664566548 0.970574446 1.171747152 1.183411711 1 17.66336604 2.075436439 3.212590286 1.130015401 0.697449049 0.850587767 0.07981163 0.079557716 1.631701148 0.033134653 0.021577774 118.9697198 -2.075436439 -0.432566352 AKPVNSKPDSAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AKPVNSKPDSAYR 13 2 O95573;C9JC11;F5H062 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 79.466 0.011492 323470000 120600 156280 102390 175690 107510 119650 161910 188750 193730 177460 FALSE TRUE 115886.8187 151823.0474 120894.1507 184757.382 110968.1568 122069.405 163891.503 184852.2465 171738.5826 165440.4761 0.700474402 0.91768986 0.730741071 1.116760458 0.670743698 0.73784486 0.990637278 1.117333864 1.038068716 1 17.33595272 2.076165577 5.343525782 1.062561918 0.821743139 0.437766272 0.125263162 0.181790114 9.194397137 0.047025011 0.034078282 119.1696263 -2.076165577 -0.240818779 DALRDEYDDLSDLNAVQMESVR ddPTM_BT-474_Pertuzumab_2h_R1 4 DALRDEYDDLSDLNAVQMESVR 22 1 U3KQM0;O15173;O15173-2 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 0 ;;; 232.81 5.36E-28 584635000 178297 274111 167796 359946 182161 208910 278463 365358 295191 203571 FALSE TRUE 171328.9561 266293.6227 198120.4698 378522.8562 188020.374 213134.3033 281870.9135 357813.2296 261682.1552 189782.9548 0.902762612 1.403148259 1.043931843 1.994503966 0.990712649 1.123042391 1.485227763 1.885381276 1.37884962 1 17.5339909 2.076380115 7.095323756 1.560260664 1.265420465 0.024872775 0.357710485 0.454631568 35.09110044 0.131234425 0.096532401 119.2285095 -2.076380115 -0.294840199 FTLDCTHPVEDGIMDAANFEQFLQER ddPTM_BT-474_Pertuzumab_2h_R1 14 FTLDCTHPVEDGIMDAANFEQFLQER 26 0 P35268 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;;;; 346.34 8.34E-110 6760936000 2010453 2058977 1835426 1917077.9 2120360 2198006 1909597.2 1966557 2090388 2072568 FALSE TRUE 1931882.274 2000256.992 2167128.307 2016018.52 2188563.305 2242451.187 1932967.422 1925946.911 1853095.918 1932191.123 0.999840156 1.035227296 1.121591069 1.04338463 1.132684691 1.16057421 1.000401771 0.996768326 0.959064502 1 20.88180638 2.076622624 10.85081286 0.988329457 1.082375655 0.490267615 0.046694491 0.401346591 54.43443904 0.018416025 0.013599 119.2951051 -2.076622624 0.094046197 MGQAPSQSLLPPAQDQPRS(ph)PVPSAFSDQSR ddPTM_BT-474_Pertuzumab_2h_R1 14 MGQAPSQSLLPPAQDQPRSPVPSAFSDQSR 30 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.98)PVPS(0.019)AFS(0.001)DQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.946)PVPS(0.054)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.94)PVPS(0.058)AFS(0.002)DQSR;MGQAPSQSLLPPAQDQPRS(0.975)PVPS(0.025)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.997)PVPS(0.003)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.995)PVPS(0.005)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.994)PVPS(0.002)AFS(0.004)DQSR;MGQAPSQSLLPPAQDQPRS(0.998)PVPS(0.001)AFS(0.001)DQSR;MGQAPSQSLLPPAQDQPRS(0.978)PVPS(0.022)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.937)PVPS(0.056)AFS(0.005)DQS(0.002)R;MGQAPSQSLLPPAQDQPRS(0.998)PVPS(0.002)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.834)PVPS(0.161)AFS(0.005)DQSR 295.53 3.28E-81 28066400000 7254092 7737561 4963783 6121514 6639529 7511629 5605349 5423965 6129331 5142211 TRUE FALSE 6970594.065 7516893.336 5860849.007 6437446.071 6853095.48 7663519.285 5673948.938 5311958.227 5433555.041 4793924.469 1.454047537 1.568004124 1.222557645 1.342834271 1.429537642 1.59858991 1.183570783 1.108060476 1.13342525 1 22.19277575 2.076708399 6.356311993 1.105218163 1.427061519 0.70547159 0.105416604 0.124188517 8.128212238 0.041590291 0.030483828 119.3186688 -2.076708399 0.321843356 EAGVEMGDEDDLSTPNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAGVEMGDEDDLSTPNEK 18 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 333.32 1.30E-74 1051020000 1680640 1690680 1471900 1592340 1522890 1705960 1749910 1889450 2127450 2010700 FALSE TRUE 1614958.731 1642463.462 1737905.072 1674520.858 1571875.14 1740455.68 1771325.922 1850432.197 1885950.795 1874513.498 0.861534864 0.876207861 0.927123264 0.893309576 0.838550985 0.928483941 0.944952343 0.987153306 1.006101475 1 20.83808478 2.076851926 1.483745685 1.001354338 0.8829538 0.82449096 0.0234562 0.169124157 0.702611135 0.015669778 0.008000898 119.358108 -2.076851926 -0.118400537 FLGDIEVWDQAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLGDIEVWDQAEK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 244.01 1.20E-16 134054000 226510 211747 210510 274220 185389 185094 288540 336620 334810 360760 FALSE TRUE 217657.7388 205708.1829 248553.8398 288372.5271 191352.2056 188836.7275 292071.2388 329668.6794 296803.7724 336325.4039 0.647164134 0.611634389 0.739027849 0.857421187 0.568949605 0.561470306 0.868418607 0.980207488 0.882489901 1 18.35949823 2.076940032 5.480864135 0.945821444 0.670586081 0.704932169 0.086243419 0.119458231 6.246459261 0.035252846 0.025609356 119.3823249 -2.076940032 -0.275235364 WGQPPSPTPVPRPPDADPNT(ph)PS(ph)PKPLEGRPER ddPTM_BT-474_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 WGQPPS(0.308)PT(0.353)PVPRPPDADPNT(0.384)PS(0.955)PKPLEGRPER 58.257 0.068245 1760700000 75768 60591 43777 51039 59479 59643 64862 79321 80419 67607 TRUE FALSE 72806.90279 58863.004 51688.47771 53673.12891 61392.19605 60849.02232 65655.80056 77682.99363 71290.17226 63027.91767 1.155153232 0.933919542 0.820088615 0.851577061 0.974047665 0.965429679 1.041693951 1.232517216 1.131088808 1 15.94370338 2.076962157 3.211311775 1.145850669 0.939268526 0.359601188 0.100136351 0.227049388 4.650620242 0.045104988 0.029413439 119.3884068 -2.076962157 -0.206582143 STT(ph)PPPAEPVSLPQEPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.025)T(0.025)T(0.951)PPPAEPVSLPQEPPK;S(0.009)T(0.009)T(0.983)PPPAEPVSLPQEPPK;S(0.197)T(0.197)T(0.605)PPPAEPVSLPQEPPK;S(0.033)T(0.033)T(0.935)PPPAEPVSLPQEPPK 260.07 1.12E-29 5855590000 1301570 1167080 1063290 1136290 1212250 1231630 1340430 1527480 1639550 1605160 TRUE FALSE 1250703.205 1133796.021 1255450.156 1194934.063 1251243.122 1256534.402 1356834.583 1495937.004 1453435.158 1496441.083 0.83578513 0.75766165 0.83895729 0.79851728 0.836145931 0.83968184 0.906707653 0.999663148 0.971261197 1 20.51310405 2.077030112 1.624174781 0.995823231 0.810311244 0.911952606 0.024203074 0.093626227 0.467870624 0.013981245 0.00731052 119.4070892 -2.077030112 -0.185511987 EAGS(ph)PAQEFK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAGSPAQEFK 10 0 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EAGS(1)PAQEFK;EAGS(1)PAQEFK;EAGS(1)PAQEFK;EAGS(1)PAQEFK 166.62 5.76E-06 4445950000 3094330 2778490 2586870 2633120 2722310 2780610 3239600 3587850 3914960 3863470 TRUE FALSE 2973400.163 2699250.186 3054374.954 2769015.639 2809875.573 2836835.839 3279247.194 3513759.644 3470550.154 3601793.736 0.82553316 0.749418313 0.848014955 0.768787955 0.780132284 0.787617517 0.910448358 0.975558264 0.963561605 1 21.78028413 2.077201646 2.679558073 0.975381927 0.791122216 0.900779365 0.028123281 0.075338893 1.061324929 0.012723837 0.007827548 119.4542611 -2.077201646 -0.184259711 EKPDQDAEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EKPDQDAEGK 10 1 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 0 ;;; 129.84 0.00026678 2615310000 4886100 4940800 4432240 4803600 4083530 3807600 6200900 8154100 7258100 5782300 FALSE TRUE 4695145.81 4799893.222 5233244.363 5051514.372 4214880.451 3884592.281 6276788.469 7985714.986 6434190.916 5390659.671 0.870977969 0.890409248 0.970798507 0.937086494 0.781885837 0.720615383 1.164382256 1.481398469 1.193581363 1 22.3620304 2.077274314 5.709892316 1.289166404 0.869844294 0.614029244 0.132567706 0.112457222 6.239839574 0.050359778 0.036699612 119.4742502 -2.077274314 -0.41932211 AEQPS(ph)PPNS(ph)DSGQDAHPDPDANPDAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEQPSPPNSDSGQDAHPDPDANPDAAR 27 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 2 AEQPS(1)PPNS(0.997)DS(0.003)GQDAHPDPDANPDAAR;AEQPS(1)PPNS(0.999)DS(0.001)GQDAHPDPDANPDAAR 164.11 5.70E-12 1386930000 531170 631780 478960 563760 566170 626880 511970 507460 560090 542400 TRUE FALSE 510411.2892 613762.253 565518.7264 592855.7212 584381.3722 639555.9431 518235.642 496980.7737 496510.9313 505662.7649 1.009390694 1.213777829 1.118371305 1.172433017 1.155674123 1.264787498 1.024864155 0.982830472 0.98190131 1 18.94781602 2.077526875 7.609813496 0.990637784 1.157187639 0.612754628 0.062147553 0.144876912 12.18448901 0.022238943 0.016382753 119.54375 -2.077526875 0.166549854 AKT(ph)QTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 AKT(0.5)QT(0.5)PPVS(1)PAPQPT(0.048)EERLPS(0.507)S(0.445)PVYEDAASFK 168.19 2.60E-13 1648900000 343090 371330 250720 255950 347970 403950 223200 204270 219650 153070 TRUE FALSE 329681.6635 360740.032 296030.6812 269159.6102 359162.7711 412118.1458 225931.5884 200051.7531 194716.2528 142702.4326 2.310273606 2.527917888 2.074461352 1.88615993 2.516865092 2.887954595 1.583235719 1.401880469 1.364491476 1 17.1226504 2.077608146 6.413272867 1.34620091 2.344332282 0.771382004 0.277339214 0.107814607 7.083720967 0.111442335 0.081721837 119.5661227 -2.077608146 0.998131373 LFEDDDS(ph)NEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFEDDDSNEK 10 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEDDDS(1)NEK;LFEDDDS(1)NEK 182.37 1.87E-06 774760000 1137040 847750 1259650 1269710 1094750 1064570 1593870 1852370 2055100 2056430 TRUE FALSE 1092603.22 823573 1487296.776 1335239.885 1129963.628 1086096.335 1613376.258 1814117.912 1821813.664 1917146.164 0.569911278 0.429582791 0.775786846 0.696472658 0.589398789 0.56651723 0.841550993 0.946259574 0.950273744 1 20.8705289 2.077656484 3.191227752 0.95217922 0.607599983 0.781544878 0.086914112 0.123891928 2.505159959 0.040962113 0.026678063 119.5794313 -2.077656484 -0.344579238 S(ph)PILEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPILEEK 7 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 S(1)PILEEK;S(1)PILEEK 113.62 0.0063863 1506810000 2007020 1859880 1503900 1646370 1751660 1722360 1904180 2053280 2265900 2083200 TRUE FALSE 1928583.44 1806838.043 1775688.184 1731339.353 1808003.735 1757187.299 1927483.924 2010879.05 2008684.531 1942103.008 0.993038696 0.930351292 0.914312051 0.891476583 0.930951513 0.904785839 0.99247255 1.035413179 1.034283209 1 20.88918829 2.077734562 4.190158742 1.024751589 0.925761556 0.726277252 0.026898088 0.108563098 3.667597262 0.011100188 0.007770397 119.6009315 -2.077734562 -0.098990033 HRS(ph)NS(ph)FSDER ddPTM_BT-474_Pertuzumab_2h_R1 5 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 HRS(1)NS(0.985)FS(0.015)DER;HRS(1)NS(0.993)FS(0.007)DER;HRS(0.999)NS(0.974)FS(0.026)DER;HRS(1)NS(0.844)FS(0.156)DER;HRS(1)NS(0.974)FS(0.026)DER 134.4 9.77E-05 2360305000 2957134 3288510 2906695 3943530 3139450 3283110 2187799 831961 2072115 1608007 TRUE FALSE 2841565.934 3194724.915 3431999.446 4147056.056 3240433.26 3349496.734 2214573.939 814780.7146 1836897.192 1499095.254 1.8955206 2.131102014 2.289380503 2.766372614 2.161592636 2.2343455 1.477273664 0.543514972 1.225337208 1 20.51566063 2.077939051 3.224770347 0.887702038 2.266201013 0.839543148 0.261357488 0.088514724 1.827785919 0.117386066 0.07672054 119.6572592 -2.077939051 1.378498975 ARPDAEKK ddPTM_BT-474_Pertuzumab_2h_R1 5 ARPDAEKK 8 2 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;; 100.02 0.003601 1474150000 3317290 3105940 2259140 2195730 2553780 2480240 3017270 3194350 3692500 3486150 FALSE TRUE 3187646.639 3017361.632 2667416.852 2309051.888 2635924.653 2530392.152 3054196.253 3128385.556 3273342.88 3250029.955 0.98080531 0.928410407 0.820736082 0.710470956 0.811046264 0.778575025 0.939744032 0.962571299 1.007173142 1 21.63202158 2.077947279 4.962319916 0.978211758 0.834883763 0.481936383 0.071548062 0.203136827 9.050652681 0.031048772 0.022338636 119.6595263 -2.077947279 -0.143327995 MESMNRPYTSLVPPLS(ph)PQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 MESMNRPYTSLVPPLSPQPK 20 1 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 MESMNRPYTSLVPPLS(0.999)PQPK;MESMNRPYTSLVPPLS(1)PQPK 116.65 5.56E-05 2027110000 1545950 1516400 1384070 1625480 1635010 1916390 1453970 1546360 1572730 1567910 TRUE FALSE 1485532.565 1473153.757 1634202.237 1709371.218 1687601.582 1955140.719 1471764.12 1514427.126 1394200.284 1461714.059 1.016294915 1.007826221 1.11800405 1.169429279 1.154536054 1.337567157 1.006875531 1.036062502 0.953811914 1 20.47922969 2.078037166 25 1.00578787 1.13355089 0.361107276 0.087635206 41.4794486 13286.23386 0.035356079 0.026112202 119.6842951 -2.078037166 0.12776302 AAEEQGDDQDS(ph)EK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAEEQGDDQDSEK 13 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 AAEEQGDDQDS(1)EK;AAEEQGDDQDS(1)EK 245.19 4.56E-17 507400000 744210 646480 727930 785940 711660 615710 879750 987520 1073520 930580 TRUE FALSE 715125.4504 628043.0234 859483.1437 826502.4576 734551.1902 628160.0781 890516.6437 967127.3669 951658.5102 867550.9877 0.824303655 0.723926354 0.990700438 0.952684591 0.846695123 0.724061279 1.026471823 1.114778705 1.096948218 1 19.72658902 2.078192394 6.736181103 1.080280756 0.850595327 0.613710405 0.084171913 0.144316072 10.11935238 0.033504765 0.024613655 119.727081 -2.078192394 -0.229685429 VEKPDTK ddPTM_BT-474_Pertuzumab_2h_R1 6 VEKPDTK 7 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 83.005 0.020932 8313170000 7760620 7461640 6130520 6376290 6913380 7417140 8196560 9191350 10440730 9754630 FALSE TRUE 7457326.391 7248841.333 7238441.337 6705371.091 7135755.146 7567119.653 8296871.953 9001545.411 9255542.102 9093940.222 0.820032484 0.797106772 0.795963154 0.737344971 0.784671438 0.832105717 0.912351715 0.989839958 1.017770282 1 23.11647409 2.078251153 1.59471726 1.009571776 0.785186571 0.955326917 0.020544465 0.076522931 0.368489786 0.01373626 0.007153905 119.7432807 -2.078251153 -0.224385205 SPVGKS(ph)PPSTGSTYGSSQK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 SPVGKS(0.952)PPS(0.048)TGSTYGSSQK;SPVGKS(0.997)PPS(0.002)TGSTYGSSQK;SPVGKS(0.979)PPS(0.021)TGSTYGSSQK 217.7 2.14E-19 1374390000 1225920 1033110 876590 924060 1031260 990820 1163850 1344170 1404070 1251070 TRUE FALSE 1178009.691 1003646.714 1035009.313 971750.8473 1064431.414 1010855.059 1178093.544 1316412.42 1244685.86 1166333.915 1.010010664 0.860514045 0.887403941 0.83316693 0.912630081 0.866694389 1.010082558 1.128675419 1.067177971 1 20.15354945 2.078259318 4.137471239 1.078003201 0.89160026 0.67761155 0.053473904 0.108493068 3.58028853 0.020810444 0.014534637 119.7455319 -2.078259318 -0.186402941 SHT(ph)SEGAHLDITPNSGAAGNSAGPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SHTSEGAHLDITPNSGAAGNSAGPK 25 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 SHT(0.999)S(0.001)EGAHLDITPNSGAAGNSAGPK;S(0.103)HT(0.878)S(0.019)EGAHLDITPNSGAAGNSAGPK;S(0.028)HT(0.944)S(0.028)EGAHLDITPNSGAAGNSAGPK 374.07 2.39E-119 14804700000 4492900 6084200 3895400 4871300 4675200 4539900 3130130 144743 3771720 1710550 TRUE FALSE 4317312.501 5910684.573 4599385.433 5122708.377 4825582.054 4631699.889 3168437.467 141754.0065 3343570.158 1594692.925 2.707300217 3.706471936 2.884182504 3.212347843 3.026025875 2.904446252 1.986863689 0.088891099 2.096685892 1 20.60484721 2.078417419 3.337342716 0.967423194 3.102280128 0.747447307 0.524456118 0.103765043 2.294069124 0.215044659 0.142083802 119.7891323 -2.078417419 2.134856934 TNKLPGS(ph)PGLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TNKLPGSPGLSK 12 1 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 TNKLPGS(1)PGLSK 116.06 0.00053437 990480000 2039900 2765300 1699800 2064900 1676800 1893700 2599600 3374900 3182500 2356600 TRUE FALSE 1960178.453 2686436.352 2006991.672 2171469.736 1730735.795 1931991.911 2631414.682 3305207.136 2821235.942 2196985.383 0.892212788 1.222782988 0.913520721 0.988386065 0.787777565 0.879383143 1.197738821 1.504428369 1.284139605 1 21.06709384 2.078428247 4.937397077 1.32651056 0.954724175 0.446510282 0.159180662 0.155189587 6.841676078 0.061449825 0.044192517 119.792119 -2.078428247 -0.371786384 LRAELDEVNK ddPTM_BT-474_Pertuzumab_2h_R1 3 LRAELDEVNK 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ;; 180.66 1.80E-06 1293480000 1421840 1665130 1241260 1436310 1289160 1283340 1557170 1703950 1671750 1627300 FALSE TRUE 1366272.921 1617642.123 1465583.294 1510438.131 1330627.002 1309290.014 1576227.112 1668762.837 1481979.949 1517081.522 0.900592949 1.066285562 0.96605441 0.99562094 0.877096572 0.863032075 1.038986429 1.09998231 0.976862435 1 20.53286718 2.078760491 14.91541237 1.044912834 0.950514348 0.27900834 0.063949372 1.603542035 300.9479345 0.024970877 0.018442256 119.8837975 -2.078760491 -0.094398486 S(ph)GDETPGS(ph)EVPGDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 2 S(1)GDET(0.19)PGS(0.81)EVPGDK 163.64 2.83E-07 0 215800 192510 207280 226970 196580 210760 255040 287750 325740 292950 TRUE FALSE 207366.2974 187019.8033 244740.1069 238683.9489 202903.1742 215021.7116 258161.2558 281807.8619 288763.3608 273108.2356 0.759282476 0.684782731 0.896128622 0.873953685 0.742940519 0.787313173 0.945270857 1.031854134 1.057322055 1 18.05911329 2.078801096 2.837757712 1.029721241 0.791487366 0.773705095 0.058932428 0.132660449 2.107618613 0.029369259 0.018443417 119.8950065 -2.078801096 -0.238233875 DTLSNPQS(ph)PQPSPYNS(ph)PKPQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DTLSNPQSPQPSPYNSPKPQHK 22 1 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 2 DTLSNPQS(1)PQPS(0.093)PY(0.003)NS(0.904)PKPQHK;DTLSNPQS(1)PQPS(0.153)PYNS(0.847)PKPQHK 190.93 2.13E-17 1196640000 652770 735790 699130 745070 745770 891840 1275580 1126180 1707780 1552440 TRUE FALSE 627259.0267 714805.9896 825478.3431 783523.152 769758.3693 909873.6158 1291190.93 1102923.989 1513919.974 1447291.856 0.433401891 0.493892083 0.570360663 0.541371907 0.53186119 0.628673209 0.892142745 0.762060523 1.046036408 1 20.46492445 2.078827073 0.739676264 1.016551074 0.486438834 0.886319396 0.070594927 0.207173944 0.214991823 0.059575433 0.033648742 119.9021782 -2.078827073 -0.530112239 down LGDSHDLQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGDSHDLQR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 125.57 0.00049789 1918590000 4019750 4437720 3865880 4112360 3991160 3858940 4359800 4516700 4851800 4895300 FALSE TRUE 3862653.726 4311160.571 4564530.512 4324599.392 4119539.286 3936970.411 4413156.537 4423428.567 4301044.004 4563736.971 0.846379568 0.944655794 1.00017388 0.947600491 0.902667992 0.862663742 0.967005015 0.969255808 0.942439065 1 22.12178421 2.078877957 25 0.967406358 0.922382718 0.255875769 0.043132509 54.76508389 17354.30597 0.017081381 0.012615436 119.9162274 -2.078877957 -0.045023639 NQTYSFS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 NQTYSFSPSK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 NQTYS(0.004)FS(0.996)PSK;NQTYS(0.001)FS(0.994)PS(0.006)K;NQTYS(0.001)FS(0.968)PS(0.031)K;NQTYSFS(1)PSK 208.35 1.21E-07 1329030000 2296090 1924840 1795940 1608080 1647000 901180 2051810 2037980 2377650 2422630 TRUE FALSE 2206356.264 1869945.448 2120506.308 1691073.202 1699977.251 919402.477 2076920.665 1995895.001 2107749.14 2258543.112 0.976893579 0.827943216 0.938882369 0.74874515 0.752687536 0.407077674 0.919584246 0.883709056 0.933233963 1 21.10696102 2.078893733 22.85874222 0.920221822 0.772985116 0.21737036 0.146587355 28.16350165 8156.741727 0.057725425 0.042633041 119.9205834 -2.078893733 -0.147236706 T(ph)PVS(ph)PVKFSPGDFWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 2 T(1)PVS(1)PVKFSPGDFWGR;T(1)PVS(1)PVKFSPGDFWGR 187.86 2.91E-09 575580000 784240 819150 715870 788530 901380 977020 670380 683680 648100 615680 TRUE FALSE 753591.0338 795788.644 845243.6334 829226.1278 930373.7063 996776.0138 678584.311 669561.7691 574530.4051 573979.4452 1.312923381 1.386441014 1.472602618 1.444696556 1.62091816 1.736605765 1.182244968 1.166525691 1.000959895 1 19.13063955 2.078903172 7.067595446 1.098745257 1.492571925 0.734967794 0.121018812 0.128825372 9.597418941 0.049738365 0.036589597 119.9231899 -2.078903172 0.393826668 KREEILEEIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KREEILEEIAK 11 2 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6 B7Z8Z7 RBM47 RNA-binding protein 47 0 ; 107.18 0.0012556 261770000 724140 695440 549290 589340 674400 665160 734200 837030 925490 818250 FALSE TRUE 695839.8082 675606.7321 648558.9219 619755.908 696092.6885 678609.9909 743185.3592 819745.038 820432.2552 762829.1987 0.912182975 0.885659245 0.850202015 0.812443872 0.912514479 0.889596245 0.974248705 1.074611511 1.075512391 1 19.54100054 2.079031428 2.264226326 1.057714286 0.872239786 0.838357182 0.034256025 0.110333737 1.093036225 0.017958017 0.010460298 119.9586107 -2.079031428 -0.185474499 KAQPAQPADEPAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAQPAQPADEPAEK 14 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 122.33 0.00017538 57518000 68041 52530 48183 53286 48147 46584 63765 69992 78477 71042 FALSE TRUE 65381.8825 51031.89583 56890.73993 56036.09685 49695.69198 47525.9604 64545.37514 68546.64074 69568.61996 66230.26206 0.987190454 0.77052233 0.858984068 0.84607995 0.750347204 0.717586779 0.974560165 1.034974626 1.050405325 1 16.01520295 2.079039863 6.117475358 1.025826014 0.819509123 0.64924381 0.070329705 0.123659513 7.479568989 0.02679946 0.019615144 119.9609408 -2.079039863 -0.206316892 GAFCEVRPDDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAFCEVRPDDKR 12 2 O60502;O60502-2;O60502-4 O60502 MGEA5 Protein O-GlcNAcase 0 ; 95.401 0.0034128 1768010000 1102310 1135360 950320 1037750 1104340 1108850 1142550 1284640 1395670 1232910 FALSE TRUE 1059230.507 1102980.644 1122063.964 1091308.402 1139862.099 1131271.707 1156532.869 1258111.735 1237239.393 1149403.908 0.921547682 0.95961101 0.976213806 0.94945597 0.991698472 0.984224692 1.006202312 1.094577569 1.076418294 1 20.13245443 2.079165076 2.302338114 1.065973548 0.962850747 0.657700762 0.02976762 0.163107021 1.673220813 0.014820389 0.008682444 119.9955321 -2.079165076 -0.103122801 TDWDAGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDWDAGFK 8 0 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 98.299 0.017729 79139000 159930 171930 118630 140470 147810 147630 160460 177470 193490 167300 FALSE TRUE 153679.7588 167026.7247 140069.0799 147719.6735 152564.4429 150615.1797 162423.7575 173805.1825 171525.8264 155968.622 0.985324848 1.070899535 0.898059354 0.947111487 0.978173949 0.965676159 1.041387398 1.114359929 1.099745732 1 17.25089629 2.079170316 3.908201142 1.083172182 0.974283663 0.443420955 0.049380556 0.185215805 5.514872752 0.020428795 0.014096205 119.9969799 -2.079170316 -0.10888852 SFQSLACS(ph)PGLPAADR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFQSLACSPGLPAADR 16 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR 217.67 1.47E-14 276600000 379510 427480 311090 382450 382690 354510 277520 301780 263570 254850 TRUE FALSE 364678.3296 415288.6889 367310.8832 402188.2903 394999.5714 361678.4351 280916.3728 295548.1375 233650.6386 237588.7825 1.534913921 1.74793054 1.545994214 1.692791579 1.6625346 1.522287506 1.182363788 1.243948197 0.983424538 1 17.8581072 2.079187737 1.154947951 1.027353416 1.651729596 0.89655563 0.087141526 0.138312019 0.343930644 0.061144307 0.030201782 120.0017936 -2.079187737 0.62437618 ITPFNLQEEMEEGHFDADGNYFLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITPFNLQEEMEEGHFDADGNYFLNR 25 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 0 ; 246.31 6.76E-39 349660000 46451.5 53628 44040.2 61921.1 50481.8 57143 47083.3 41930.7 54667 54298 FALSE TRUE 44636.12403 52098.58195 51999.24381 65116.85539 52105.59294 58298.47061 47659.51951 41064.81639 48461.43134 50620.3481 0.881782242 1.029202364 1.027239949 1.286377076 1.029340866 1.151680555 0.941509122 0.811231411 0.957350812 1 15.62742981 2.079638598 6.345837563 0.895711858 1.071555818 0.279192477 0.107721383 0.226715106 14.37456237 0.041348259 0.030315868 120.1264375 -2.079638598 0.17584396 HHNHGS(ph)PHLK ddPTM_BT-474_Pertuzumab_2h_R1 3 HHNHGSPHLK 10 0 Q9UK58 Q9UK58 CCNL1 Cyclin-L1 1 HHNHGS(1)PHLK;HHNHGS(1)PHLK;HHNHGS(1)PHLK 135.02 0.00025926 284844000 727210 742360 579940 558720 470180 600190 360620 27308.55 398550 88178 TRUE FALSE 698789.8292 721188.6196 684748.0587 587555.6062 485303.7667 612326.253 365033.3754 26744.6189 353308.2749 82205.62552 8.500511064 8.772983784 8.329698295 7.147389275 5.903534748 7.448714722 4.440491428 0.325338062 4.297860063 1 16.3269495 2.079798713 2.977580249 1.846928455 7.689750976 0.818537298 1.233558792 0.104063537 1.826463119 0.571820642 0.365118991 120.1707339 -2.079798713 5.84282252 YS(ph)GAYGASVSDEELK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSGAYGASVSDEELK 15 0 C9JRZ6;Q9NX63;A0A286YEX5;F8WAR4 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 1 YS(1)GAYGASVSDEELK;YS(1)GAYGASVSDEELK 205.66 4.50E-09 155473000 386860 373650 278710 322090 284290 332940 380620 458300 489800 369010 TRUE FALSE 371741.0835 362993.8678 329079.0969 338713.1035 293434.446 339672.2749 385278.1414 448835.9448 434199.9574 344016.624 1.080590464 1.055163741 0.956579054 0.984583534 0.85296589 0.987371688 1.119940475 1.304692604 1.262148184 1 18.39211876 2.079849223 3.709823911 1.221320487 0.982213499 0.47554505 0.095224714 0.165799814 4.484240684 0.03957171 0.026967936 120.1847108 -2.079849223 -0.239106988 T(ph)PPKSPSSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPKSPSSAK 10 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 T(0.998)PPKS(0.002)PSSAK 80.469 0.038664 361010000 710510 615220 630230 626590 577000 618940 774350 825520 989440 899910 TRUE FALSE 682742.4837 597674.528 744126.5804 658928.385 595559.729 631455.3909 783826.7269 808472.7235 877122.9193 838958.2941 0.813797883 0.712400762 0.886964925 0.785412564 0.709880018 0.752666009 0.934285688 0.963662591 1.045490491 1 19.67823957 2.079924192 2.888300225 0.994983139 0.776000844 0.795549138 0.052446183 0.121727933 2.006454841 0.024867044 0.015724379 120.2054592 -2.079924192 -0.218982295 APKPPTDGST(ph)SPTSTPSEDQEALGK ddPTM_BT-474_Pertuzumab_2h_R1 1 APKPPTDGSTSPTSTPSEDQEALGK 25 1 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;S4R3G4;F6SRV7;Q8NHM5-5;F8WBN2 Q8NHM5-4;F8WBN2 KDM2B Lysine-specific demethylase 2B 1 APKPPTDGS(0.082)T(0.458)S(0.458)PT(0.001)STPSEDQEALGK 173.68 6.73E-12 608940000 471360 402880 339760 369780 446530 373670 460700 539720 515360 459830 TRUE FALSE 452938.7301 391390.2569 401162.1899 388864.3901 460893.043 381225.8634 466338.1844 528574.5934 456858.4934 428685.3045 1.056576293 0.913001339 0.935796459 0.907109215 1.075131427 0.889290721 1.087833381 1.233013093 1.065719978 1 18.70955944 2.079943973 6.254330115 1.133896671 0.962620687 0.375328162 0.08101819 0.164681772 10.19685887 0.029392692 0.021537914 120.2109345 -2.079943973 -0.171275985 SPS(ph)IDSIQKDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSIDSIQKDPR 12 1 A0A0D9SF60;Q99569-2;Q99569;B4DRK2;E9PHB5;E7EPC8;Q9UQB3-2;Q9UQB3 A0A0D9SF60;E7EPC8 PKP4;CTNND2 Plakophilin-4;Catenin delta-2 1 S(0.405)PS(0.594)IDS(0.001)IQKDPR 52.5 0.089756 185710000 516720 628910 384170 601150 455180 524640 581260 723730 641990 570040 TRUE FALSE 496526.0111 610974.1026 453598.0648 632175.4235 469821.2781 535248.5803 588373.6338 708784.7226 569113.9866 531430.6831 0.934319427 1.149677883 0.853541354 1.189572683 0.884068785 1.007184187 1.107150288 1.333729393 1.07090916 1 19.019522 2.080095021 4.622827481 1.182634719 1.00705472 0.154263322 0.129200459 0.258488541 10.19053892 0.047752187 0.034060159 120.2527512 -2.080095021 -0.17558 LKQFEER ddPTM_BT-474_Pertuzumab_2h_R1 2 LKQFEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 81.548 0.024536 334810000 720690 809700 619200 698580 706160 623070 819530 936080 840800 924560 FALSE TRUE 692524.638 786608.1488 731103.214 734633.7975 728874.2777 635668.9023 829559.6533 916749.6209 745355.9089 861938.7277 0.803449962 0.912603325 0.848207872 0.852303968 0.845621915 0.737487343 0.962434598 1.063590243 0.864743496 1 19.71722579 2.080141298 8.243248739 0.990553239 0.8392819 0.543464076 0.062113562 0.178728374 16.22667723 0.022838496 0.016843527 120.2655655 -2.080141298 -0.151271339 HRPSAGGPDS(ph)AGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 HRPSAGGPDS(1)AGR 110.37 0.00064448 92723000 38547 35443 32551 44266 38125 39642 33819 28442 37428 37725 TRUE FALSE 37040.54062 34432.20034 38433.68979 46550.57356 39351.32525 40443.5884 34232.88704 27854.66276 33179.33035 35169.85215 1.053190115 0.979026019 1.092802143 1.323593098 1.118893679 1.149950481 0.973358856 0.792003977 0.943402611 1 15.10205165 2.080141516 4.405570672 0.887002184 1.12038178 0.489787685 0.096422367 0.168025336 6.128035476 0.040863084 0.028919983 120.265626 -2.080141516 0.233379596 FQGAGSNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FQGAGSNKK 9 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 68.893 0.091046 1425800000 947740 868670 857510 817990 838360 1003900 967650 1069800 1164600 1185500 FALSE TRUE 910701.273 843896.3821 1012481.132 860206.5619 865326.6108 1024199.546 979492.3902 1047708.256 1032399.49 1105205.029 0.824011155 0.763565456 0.916102538 0.778323062 0.78295573 0.92670547 0.886254011 0.947976374 0.934124858 1 20.0758826 2.080335793 0.77460454 0.981832721 0.811297094 0.633184059 0.047597526 0.415243197 0.46901133 0.039685666 0.021806904 120.3194376 -2.080335793 -0.170535627 EDVSTLIGDDLASCKDETDES(ph)SKEETEPQVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDVSTLIGDDLASCKDETDESSKEETEPQVLK 32 2 Q9BV44;H7C0R6;H7C3J3 Q9BV44 THUMPD3 THUMP domain-containing protein 3 1 EDVSTLIGDDLAS(0.001)CKDET(0.019)DES(0.724)S(0.234)KEET(0.022)EPQVLK 63.761 0.0044286 51182000 37724 27863 27428 25059 30097 32252 34821 47337 40772 41575 TRUE FALSE 36249.70437 27068.37452 32384.84973 26352.29799 31065.09734 32904.15754 35247.14981 46359.47441 36143.73349 38759.08822 0.935256892 0.698374904 0.835542094 0.679899843 0.801491954 0.848940443 0.909390583 1.196093008 0.9325228 1 15.24224701 2.080356006 2.978349206 1.062964444 0.789565921 0.564890492 0.093978472 0.15748129 2.765540164 0.04047892 0.025863198 120.3250376 -2.080356006 -0.273398524 TSSVSNPQDSVGS(ph)PCSR ddPTM_BT-474_Pertuzumab_2h_R1 5 TSSVSNPQDSVGSPCSR 17 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(0.993)PCS(0.007)R;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR 465.3 2.95E-206 3928870000 1397167 1552453 1337230 1691570 1683930 1720850 1311917 1289167 1260019 1276936 TRUE FALSE 1342564.169 1508178.56 1578897.208 1778872.13 1738095.138 1755646.766 1327972.633 1262545.251 1116986.926 1190447.987 1.12778062 1.266900004 1.326305075 1.49428799 1.460034505 1.474778222 1.115523439 1.060563136 0.938291246 1 20.18307316 2.080448764 4.512131698 1.0231257 1.362817644 0.698816113 0.10746536 0.133056635 5.038892401 0.047315776 0.033627159 120.3507397 -2.080448764 0.339691944 SLLS(ph)PLHR ddPTM_BT-474_Pertuzumab_2h_R1 5 SLLSPLHR 8 0 Q9BY84 Q9BY84 DUSP16 Dual specificity protein phosphatase 16 1 SLLS(1)PLHR;S(0.001)LLS(0.999)PLHR;SLLS(1)PLHR;SLLS(1)PLHR;SLLS(1)PLHR 123.11 0.00087703 1450670000 860633 1069084 873583 1078082 1019025 1001022 812912 710275 772675 782212 TRUE FALSE 826998.5109 1038594.771 1031458.881 1133721.941 1051802.865 1021263.351 822860.6602 695607.573 684964.1733 729232.0845 1.134067642 1.424230767 1.414445281 1.554679183 1.442343099 1.400464094 1.128393385 0.953890521 0.939295168 1 19.47601851 2.08088159 2.637801207 0.963654023 1.409384082 0.790003538 0.100778274 0.122004628 1.665087048 0.049526316 0.030423406 120.4707433 -2.08088159 0.445730059 KILIEDWK ddPTM_BT-474_Pertuzumab_2h_R1 1 KILIEDWK 8 1 K7ELL7;P14314-2;P14314;K7EPW7 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 114.5 0.0079026 0 2369500 2562700 1915500 2070800 2244600 2314700 2526600 2800700 3064600 2946900 FALSE TRUE 2276897.32 2489614.305 2261673.46 2177674.236 2316799.597 2361504.82 2557521.287 2742864.566 2716719.456 2747303.838 0.828775212 0.906202754 0.82323383 0.792658681 0.843299371 0.859571769 0.930920436 0.998384135 0.988867492 1 21.38958504 2.081507358 1.99838069 0.9973402 0.839308175 0.870640925 0.026874023 0.116339884 0.890366659 0.015613149 0.008744097 120.6444529 -2.081507358 -0.158032025 FSGKDPNSK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSGKDPNSK 9 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 66.92 0.056877 1039620000 2794400 2672100 1971900 2184100 2501100 2537900 2596500 2947100 3262000 2911500 FALSE TRUE 2685191.759 2595894.324 2328266.195 2296821.663 2581550.153 2589218.077 2628276.744 2886241.355 2891711.435 2714301.512 0.989275417 0.956376553 0.85777729 0.84619253 0.951091889 0.953916897 0.968306849 1.063345889 1.06536117 1 21.37214956 2.08168243 1.681216949 1.049851037 0.916754147 0.567551252 0.045356769 0.269801606 1.448533139 0.029117945 0.015443546 120.6930967 -2.08168243 -0.13309689 FHEVFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FHEVFK 6 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 74.743 0.079523 342200000 1028200 1073600 959790 845570 894180 939370 843580 439770 1173700 1005300 FALSE TRUE 988016.8073 1042981.979 1133245.403 889209.969 922942.1118 958364.705 853903.9844 430688.5958 1040466.497 937210.1356 1.054210544 1.112858194 1.209168958 0.948783987 0.984776068 1.022571853 0.911112622 0.459543254 1.110174183 1 19.83801303 2.081843614 4.438571923 0.772635748 1.055362327 0.162957344 0.176325562 0.23609778 8.662909078 0.069527274 0.049313983 120.7378988 -2.081843614 0.282726579 EYSSELNAPSQESDSHPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EYSSELNAPSQESDSHPR 18 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 ; 232.15 4.02E-20 1895040000 519640 568260 487840 651090 574030 565620 523180 505490 529070 565970 FALSE TRUE 499331.8943 552053.7812 576003.5399 684692.8329 592494.1963 577057.2239 529582.8333 495051.4549 469012.1916 527636.3478 0.946356134 1.046277012 1.091667665 1.297660474 1.122921495 1.093664654 1.003689066 0.938243654 0.888892878 1 19.00918443 2.081950402 2.416023528 0.936926012 1.1085725 0.410809178 0.085351756 0.299192389 3.398695642 0.045715706 0.027297086 120.7675907 -2.081950402 0.171646488 WNIKPESK ddPTM_BT-474_Pertuzumab_2h_R1 2 WNIKPESK 8 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EPX3;B9ZVU2;F8WAN0;E5RJ35 E5RIA4 DNPEP Aspartyl aminopeptidase 0 ; 94.692 0.0092837 718470000 1340730 1231560 1188110 1381270 1294500 1158940 1524550 1678700 1801950 1764330 FALSE TRUE 1288332.789 1196437.115 1402827.906 1452557.51 1336138.768 1182374.561 1543207.899 1644034.258 1597400.19 1644830.358 0.783261802 0.727392408 0.852870875 0.883104755 0.812326184 0.718842861 0.938217058 0.999515999 0.971164098 1 20.64950737 2.082025555 5.790736439 0.985214943 0.800921639 0.778572473 0.047767089 0.100494846 5.478092585 0.019598898 0.014309132 120.7884909 -2.082025555 -0.184293304 SPMFPALGEASS(ph)DDDLFQSAKPKPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPMFPALGEASSDDDLFQSAKPKPAK 26 2 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;Q5SRD0 Q641Q2;A0A0A0MR88 FAM21A;FAM21C;FAM21D WASH complex subunit FAM21A;WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 1 SPMFPALGEAS(0.318)S(0.682)DDDLFQSAKPKPAK 314.47 3.84E-82 667600000 516520 430040 388200 323050 445180 443590 539500 560990 697780 635170 TRUE FALSE 496333.8274 417775.6803 458356.3755 339722.6492 459499.619 452559.6937 546102.5624 549405.3605 618570.9397 592149.3701 0.838190248 0.705524149 0.774055329 0.573711071 0.775985996 0.764266107 0.922237851 0.927815494 1.044619771 1 19.17560162 2.082111865 1.358251228 1.005386569 0.72336503 0.745327115 0.068562255 0.211528741 0.734061823 0.04512939 0.02272377 120.8124983 -2.082111865 -0.28202154 SLPESTSAPASGPSDGS(ph)PQPCTHPPGPVKEPQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPESTSAPASGPSDGSPQPCTHPPGPVKEPQEK 34 1 O00221;Q7LC14;H3BNC2 O00221 NFKBIE NF-kappa-B inhibitor epsilon 1 SLPESTSAPASGPS(0.002)DGS(0.998)PQPCTHPPGPVKEPQEK;SLPESTSAPASGPS(0.006)DGS(0.987)PQPCT(0.007)HPPGPVKEPQEK 316.01 9.84E-105 625210000 242800 221827 244340 221567 247202 269650 308660 337060 413660 381300 TRUE FALSE 233311.1076 215500.7112 288497.6733 233002.0994 255153.4768 275102.5078 312437.4734 330099.5932 366703.051 355474.2114 0.656337647 0.606234445 0.811585381 0.655468363 0.717783368 0.773902857 0.878931476 0.928617556 1.031588338 1 18.43938537 2.082181765 0.945134438 1.02045885 0.678451824 0.868898299 0.051548833 0.185227667 0.306989732 0.040328973 0.020425552 120.8319447 -2.082181765 -0.342007026 GPSSVEDIK ddPTM_BT-474_Pertuzumab_2h_R1 3 GPSSVEDIK 9 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;; 130.31 0.00084861 1984970000 1680400 1654370 1264470 1494440 1585080 1494810 1719090 1955170 2019820 1803770 FALSE TRUE 1614728.11 1607188.987 1492987.857 1571568.227 1636065.538 1525036.082 1740128.738 1914795.056 1790538.501 1681599.051 0.960233719 0.955750413 0.887838189 0.934567742 0.972922491 0.906896374 1.03480597 1.138675153 1.064783249 1 20.68140233 2.082254804 4.724386094 1.084201308 0.937171805 0.691927901 0.040171287 0.098602824 3.983692048 0.015266479 0.010933546 120.8522678 -2.082254804 -0.147029503 S(ph)SPRPTAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPRPTAEK 9 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.5)S(0.5)PRPTAEK;S(0.5)S(0.5)PRPTAEK;S(0.605)S(0.395)PRPTAEK;S(0.5)S(0.5)PRPTAEK 75.695 0.02273 2953330000 2971690 2812200 2475120 2478070 2550180 2288500 2991050 3018280 3446530 3433150 TRUE FALSE 2855553.069 2731998.809 2922429.243 2605963.49 2632208.856 2334775.038 3027655.365 2955951.463 3055294.363 3200619.693 0.892187559 0.853584328 0.913082316 0.814205916 0.822406005 0.729475933 0.945959113 0.923555982 0.954594628 1 21.60991983 2.082278456 24.99999783 0.946861471 0.839729761 0.572992881 0.049858303 22.29535965 6772.205736 0.019288364 0.014245399 120.8588496 -2.082278456 -0.10713171 S(ph)FEEKVENLK ddPTM_BT-474_Pertuzumab_2h_R1 7 SFEEKVENLK 10 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK 164.64 1.60E-05 4024068000 3161950 2569392 1409080 1780513 3329940 2253183 3356510 4518900 4577390 3147430 TRUE FALSE 3038377.498 2496115.456 1663732.101 1872405.489 3437050.544 2298743.904 3397587.973 4425583.136 4057783.877 2934251.763 1.035486299 0.850682102 0.567003869 0.638120257 1.171355024 0.783417406 1.157906086 1.508249289 1.382902425 1 21.48456123 2.082465477 3.936348837 1.351084472 0.835391533 0.505724604 0.204637396 0.162799265 4.877144526 0.084931187 0.058842331 120.9109065 -2.082465477 -0.515692939 SEDGVEGDLGETQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDGVEGDLGETQSR 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 136.7 4.95E-05 147640000 83360 89999 84337 103170 82806 89519 112970 130780 136160 143170 FALSE TRUE 80102.19904 87432.31664 99578.57197 108494.6161 85469.53019 91329.13551 114352.5607 128079.3473 120703.6876 133472.9684 0.600137991 0.655056359 0.746057971 0.812858344 0.640350861 0.684251925 0.856746966 0.959590162 0.904330585 1 17.02618806 2.082553111 3.062972166 0.945852357 0.693546904 0.802851449 0.059655206 0.118768624 2.208353167 0.028340198 0.01830966 120.9353068 -2.082553111 -0.252305454 AIGS(ph)SPLGSGEGLLGLS(ph)PGPNGHSHLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIGSSPLGSGEGLLGLSPGPNGHSHLLK 28 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 2 AIGS(0.499)S(0.499)PLGS(0.001)GEGLLGLS(0.871)PGPNGHS(0.129)HLLK 76.972 0.0037016 51018000 22767 23694 22089 20341 24151 26287 19648 15202 25587 23911 TRUE FALSE 21877.24047 23018.27032 26080.97367 21390.80145 24927.83885 26818.54115 19888.4581 14888.07339 22682.47103 22291.48667 0.981416843 1.032603642 1.169997051 0.959595103 1.118267221 1.203084458 0.892199717 0.667881582 1.017539627 1 14.44420522 2.082652808 7.144507313 0.839122219 1.075321312 0.338862615 0.11761091 0.190428833 13.80960947 0.043700823 0.03216383 120.9630721 -2.082652808 0.236199093 AAS(ph)PPASASDLIEQQQK ddPTM_BT-474_Pertuzumab_2h_R1 7 AASPPASASDLIEQQQK 17 0 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(0.999)PPAS(0.001)ASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK 436.54 2.62E-161 6497326000 1128666 1119801 957159 1054946 1109527 1128798 1199073 1323836 1411850 1432810 TRUE FALSE 1084556.485 1087865.372 1130138.923 1109391.889 1145215.944 1151623.069 1213747.614 1296498.324 1251582.707 1335764.502 0.811936897 0.814414045 0.846061503 0.830529549 0.857348688 0.862145286 0.908653892 0.970603966 0.936978565 1 20.34923425 2.082667712 0.731811834 0.992699978 0.819803957 0.936921176 0.015863026 0.147305662 0.149950958 0.013696176 0.00780897 120.9672234 -2.082667712 -0.17289602 SIS(ph)REPS(ph)PALGPNLDGSGLLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SISREPSPALGPNLDGSGLLPR 22 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 2 S(0.459)IS(0.541)REPS(1)PALGPNLDGSGLLPR;S(0.131)IS(0.869)REPS(1)PALGPNLDGSGLLPR 165.98 6.95E-12 569620000 493930 434520 364530 482410 407040 388860 486180 590740 449790 466540 TRUE FALSE 474626.6695 422127.915 430408.6799 507307.2379 420132.8113 396723.0156 492130.0163 578541.0126 398731.7249 434940.8302 1.091244226 0.970541015 0.989579846 1.16638219 0.965953946 0.912131003 1.131487278 1.330160271 0.916749353 1 18.73045962 2.082826804 10.67708893 1.146886374 1.017413484 0.02633662 0.123481479 0.665633243 81.16175716 0.046182577 0.034102751 121.0115444 -2.082826804 -0.12947289 DLGEELEALK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGEELEALK 10 0 P35579;P35749;P35749-2;P35749-4;P35749-3 P35579;P35749 MYH9;MYH11 Myosin-9;Myosin-11 0 ; 178.22 5.21E-06 132527000 139001 142198 152942 161713 155876 148710 200391 224240 250990 251170 FALSE TRUE 133568.6872 138142.6523 180582.0216 170059.0273 160889.8931 151717.0181 202843.445 219609.3656 222498.6674 234158.0322 0.570421121 0.589954788 0.771197212 0.726257501 0.687099612 0.647925748 0.866267294 0.937868172 0.950207283 1 17.837123 2.082848439 2.705720803 0.953449073 0.669302403 0.842039012 0.058753922 0.116111839 1.672108563 0.030204583 0.018749395 121.0175731 -2.082848439 -0.28414667 KKLEEER ddPTM_BT-474_Pertuzumab_2h_R1 4 KKLEEER 7 2 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5;B1AK53;A0A0J9YY76;H0Y7L4;A0A2R8YG57;A0A0J9YWQ8;A0A0A0MSQ4;B1AK53-2 Q15637-6;Q15637-5;B1AK53 SF1;ESPN Splicing factor 1;Espin 0 ;;; 122.52 0.0024372 2195540000 3769060 3760240 2978730 2918270 3345010 2926840 3756820 3829940 4506540 4128960 FALSE TRUE 3621760.968 3653001.637 3517052.772 3068882.264 3452605.285 2986022.71 3802797.087 3750850.401 3994976.472 3849301.862 0.94088775 0.949003681 0.913685884 0.797256847 0.89694324 0.775730981 0.987918647 0.974423554 1.037844424 1 21.87616538 2.082884717 13.39227891 0.996229528 0.880799141 0.541182286 0.054630529 0.676382562 107.0164236 0.021328931 0.015752377 121.0276825 -2.082884717 -0.115430387 ESSPTS(ph)PVAETEGTIMEESSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESSPTSPVAETEGTIMEESSR 21 0 Q8IWV8;Q8IWV8-4 Q8IWV8 UBR2 E3 ubiquitin-protein ligase UBR2 1 ESSPT(0.002)S(0.998)PVAETEGTIMEESSR;ESSPT(0.001)S(0.999)PVAETEGTIMEESSR 363.27 1.12E-96 159831000 295459 336710 311589 369440 380410 372090 307290 285998 305770 364350 TRUE FALSE 283912.1356 327107.3605 367900.0636 388506.8427 392646.2331 379613.9147 311050.7069 280092.0414 271060.2715 339672.25 0.83584142 0.963008784 1.08310309 1.143769745 1.15595617 1.117588837 0.915737765 0.824595007 0.798005346 1 18.37378383 2.082922018 5.058218976 0.858042229 1.055849491 0.385703849 0.10221323 0.202483011 9.03350262 0.042483307 0.030684678 121.0380777 -2.082922018 0.197807262 VTSSMSS(ph)PSMQPK ddPTM_BT-474_Pertuzumab_2h_R1 5 VTSSMSSPSMQPK 13 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 VTSSMS(0.003)S(0.92)PS(0.078)MQPK;VTSSMS(0.008)S(0.923)PS(0.069)MQPK;VTSSMS(0.002)S(0.993)PS(0.005)MQPK;VTSSMS(0.013)S(0.987)PSMQPK;VTSSMSS(0.996)PS(0.004)MQPK 355.89 3.82E-76 5456670000 7449060 7633190 6440650 6988380 6964090 7681190 7556510 8670270 9316950 8761750 TRUE FALSE 7157942.5 7415498.895 7604618.726 7349051.129 7188096.279 7836508.925 7648988.83 8491225.895 8259328.896 8168308.868 0.876306542 0.907837719 0.930990594 0.899702894 0.879998099 0.959379604 0.936422576 1.039532911 1.011143069 1 22.96160599 2.082977943 1.575382665 1.020729697 0.903204458 0.794794285 0.024471173 0.157450035 0.740384719 0.014708206 0.007667561 121.0536652 -2.082977943 -0.117525239 GDKEEVAYEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GDKEEVAYEER 11 1 Q9NRV9;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 126.1 0.00028689 3257500000 6509300 6711500 5210100 6450300 5819000 6116400 6711500 7498100 7564900 7459900 FALSE TRUE 6254909.36 6520094.591 6151680.968 6783200.756 6006173.42 6240077.799 6793637.345 7343261.615 6706164.267 6954634.328 0.899387238 0.93751796 0.88454413 0.975349736 0.863621743 0.897254622 0.976850403 1.055880334 0.964272735 1 22.72954323 2.08303069 4.491547382 1.013804684 0.911034725 0.609030216 0.035546095 0.126332434 4.703599051 0.0135367 0.009625703 121.0683685 -2.08303069 -0.102769959 S(ph)NSLPHSAVSNAGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSLPHSAVSNAGSK 15 0 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.66)NS(0.34)LPHSAVSNAGSK;S(0.675)NS(0.325)LPHSAVSNAGSK 239.1 5.54E-18 1664460000 1564400 1586810 1228010 1534160 1516800 1532870 1624650 1966990 1835380 1610870 TRUE FALSE 1503261.518 1541555.732 1449938.724 1613338.181 1565589.25 1563865.682 1644532.953 1926370.969 1627035.357 1501764.34 1.000996946 1.026496429 0.965490181 1.074295173 1.04249995 1.041352255 1.095067254 1.282738521 1.083415895 1 20.51822701 2.083056218 4.18840998 1.160849064 1.026068032 0.21517573 0.073785412 0.208226915 6.924120295 0.028816833 0.020237927 121.0754851 -2.083056218 -0.134781032 ITVGNDHFCVST(ph)PERR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITVGNDHFCVSTPERR 16 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.008)T(0.992)PERR;ITVGNDHFCVS(0.041)T(0.959)PERR 198.6 3.07E-11 644440000 400450 376700 322820 371360 352660 420080 329740 332340 351180 361900 TRUE FALSE 384799.9713 365956.8848 381160.7551 390525.9341 364003.6292 428574.3054 333775.4568 325477.0629 311315.5187 337388.1907 1.140525904 1.084676035 1.129739468 1.157497343 1.078886693 1.270270618 0.989292056 0.964696074 0.922722037 1 18.36404995 2.083069237 9.105650168 0.96314638 1.137844023 0.728703745 0.052254573 0.144942383 14.43785853 0.018677637 0.013785563 121.0791148 -2.083069237 0.174697643 S(ph)LDLPSIGGSSVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDLPSIGGSSVGK 14 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(1)LDLPSIGGSSVGK;S(1)LDLPSIGGSSVGK 324.7 1.20E-56 522640000 669830 615680 809950 816910 749290 658440 983750 1119860 1166060 1315660 TRUE FALSE 643652.3031 598121.4092 956325.9822 859070.823 773391.5933 671754.1079 995789.4268 1096734.5 1033693.757 1226549.176 0.524766814 0.487645682 0.779688251 0.700396559 0.630542671 0.547678088 0.811862619 0.894162681 0.842765849 1 20.22617365 2.083237366 4.324543884 0.89127298 0.619227354 0.703707533 0.088769414 0.133417112 4.672655622 0.037534919 0.02652213 121.1259973 -2.083237366 -0.272045627 IQFKPDDGTTPER ddPTM_BT-474_Pertuzumab_2h_R1 7 IQFKPDDGTTPER 13 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;;;;;; 132.86 0.00010392 8585780000 5860390 5887560 4886280 5087580 5291240 5715950 5500490 6046440 6565550 6087520 FALSE TRUE 5631359.48 5719652.553 5769339.491 5350150.613 5461437.54 5831530.425 5567806.642 5921578.901 5820256.289 5675206.848 0.992273873 1.007831557 1.016586645 0.942723456 0.962332772 1.027545001 0.981075543 1.043411995 1.025558441 1 22.43624155 2.08339305 1.713208247 1.02471522 0.987812091 0.201848107 0.026427266 0.537461979 3.000432996 0.016152119 0.008628765 121.1694259 -2.08339305 -0.036903129 VPLS(ph)PLSLLAGPADARR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPLSPLSLLAGPADARR 17 1 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 VPLS(1)PLSLLAGPADARR 133.24 1.28E-05 71892000 70023 76857 69793 62047 67033 82431 48365 39623 39917 43458 TRUE FALSE 67286.42375 74665.11361 82406.14764 65249.25311 69189.17732 84097.8113 48956.90534 38804.7712 35385.78951 40514.55095 1.660796483 1.842920922 2.033988918 1.610514039 1.70776118 2.075743389 1.208378328 0.957798378 0.873409397 1 15.30615253 2.083594935 4.655456635 0.969068724 1.81569487 0.88536086 0.1451184 0.065462758 2.571147031 0.058125658 0.041566904 121.2257654 -2.083594935 0.846626146 EVDRNEGLK ddPTM_BT-474_Pertuzumab_2h_R1 4 EVDRNEGLK 9 1 H0Y6T8;Q9NP72;Q9NP72-2;Q5W0J0;A0A087X163;Q9NP72-3 H0Y6T8 RAB18 Ras-related protein Rab-18 0 ;;; 142.43 9.52E-05 1663880000 1071220 1336450 870120 1353220 977350 1047670 1331850 1671180 1447560 1259150 FALSE TRUE 1029355.538 1298335.755 1027370.04 1423059.846 1008787.35 1068854.605 1348149.579 1636669.549 1283239.057 1173866.649 0.876893077 1.106033429 0.87520166 1.212284076 0.859371336 0.910541761 1.148469104 1.394255089 1.093172771 1 20.1628371 2.083620914 5.672527365 1.22163292 0.981897327 0.256833983 0.143813276 0.207583252 10.86211857 0.052685583 0.038427446 121.2330173 -2.083620914 -0.239735593 RLS(ph)AQGQAISVVGSLSSMSPLEEEAPQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSAQGQAISVVGSLSSMSPLEEEAPQAK 29 1 Q92797;A0A087WUE9;M0R3C7;Q92797-2 Q92797 SYMPK Symplekin 1 RLS(0.901)AQGQAIS(0.041)VVGS(0.055)LS(0.004)SMSPLEEEAPQAK 119.11 4.70E-05 67854000 35371 38384 25073 38276 50671 43636 31980 30138 34046 32526 TRUE FALSE 33988.66222 37289.3259 29604.24885 40251.42895 52300.87873 44518.34982 32371.38081 29515.63977 30181.24081 30322.98505 1.120887741 1.229737964 0.976297314 1.327423038 1.72479321 1.468138765 1.067552576 0.973375138 0.995325518 1 14.88812416 2.083670437 6.336065265 0.994747207 1.308291675 0.383138661 0.187540098 0.248348845 15.13338062 0.080437622 0.058999544 121.2468422 -2.083670437 0.313544468 QLNHNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLNHNPR 7 0 Q8IX18-4;Q8IX18-3;Q8IX18-2;Q8IX18;F5H625 Q8IX18-4 DHX40 Probable ATP-dependent RNA helicase DHX40 0 ; 97.068 0.012269 43345000 28262 36696 28295 32667 31763 27002 32657 27037 28210 30926 FALSE TRUE 27157.48979 35649.46601 33408.53592 34352.94778 32784.68574 27547.99894 33056.66613 26478.6765 25007.71907 28831.35447 0.941942905 1.236482526 1.158757073 1.19151349 1.137119166 0.955487505 1.146552659 0.918398632 0.867379265 1 14.81535099 2.083697312 1.07383251 0.921838397 1.138695903 0.382995191 0.098432656 0.485337205 1.04063967 0.071797491 0.035657259 121.2543457 -2.083697312 0.216857506 EVWEETDGLDPNDFDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVWEETDGLDPNDFDPK 17 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 225.13 5.81E-15 160872000 270630 269660 245787 278940 268939 218196 344910 381030 431370 414050 FALSE TRUE 260053.4804 261969.5608 290206.1784 293336.1268 277589.6672 222608.0726 349131.1118 373161.5973 382402.6861 386006.0247 0.673703165 0.678667026 0.751817743 0.759926291 0.719132991 0.57669585 0.904470628 0.966724801 0.990665071 1 18.55826384 2.083713737 5.745102953 0.971234106 0.700179786 0.880593838 0.049598581 0.069648865 3.707154163 0.019954208 0.014565937 121.2589315 -2.083713737 -0.27105432 FSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSGFSAKPNNSGEAPSSPTPK 21 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 FSGFSAKPNNSGEAPS(0.147)S(0.852)PT(0.001)PK;FSGFSAKPNNSGEAPS(0.049)S(0.951)PTPK 181.03 3.13E-17 3715700000 4182000 3523000 3150100 3115500 3356300 3167900 3996900 4427400 4714400 4505300 TRUE FALSE 4018562.817 3422527.489 3719393.144 3276291.328 3464258.438 3231957.108 4045815.258 4335972.643 4179241.076 4200152.018 0.956766041 0.814858004 0.885537744 0.78004113 0.824793584 0.769485746 0.963254482 1.032337074 0.995021385 1 22.00201011 2.083719559 5.49291607 1.009325427 0.836884294 0.703901932 0.051119681 0.105163275 5.256451145 0.019243002 0.014004301 121.260557 -2.083719559 -0.172441133 AS(ph)PNLKQEEGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPNLKQEEGEK 12 1 Q05GC8;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 AS(1)PNLKQEEGEK 90.259 0.0054269 401690000 289260 234410 181020 188390 185100 208480 237120 264720 285440 251240 TRUE FALSE 277955.3994 227724.8563 213734.3408 198112.8305 191053.9096 212695.6084 240021.9455 259253.4395 253038.0479 234223.291 1.186711186 0.972255386 0.912523856 0.845828908 0.815691338 0.908089061 1.024756951 1.106864473 1.080328292 1 17.83752502 2.083743862 4.379596421 1.072690636 0.930916417 0.243164309 0.097573654 0.281230553 10.0355455 0.041322791 0.029271491 121.267343 -2.083743862 -0.14177422 TLPQQES(ph)LEIELAEEKPVKR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLPQQESLEIELAEEKPVKR 20 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TLPQQES(1)LEIELAEEKPVKR;TLPQQES(1)LEIELAEEKPVKR;TLPQQES(1)LEIELAEEKPVKR;TLPQQES(1)LEIELAEEKPVKR 229.76 1.12E-25 2362740000 1427347 1274018 737358 1072783 1486201 1152479 1480458 1982420 1646175 1523475 TRUE FALSE 1371564.701 1237684.254 870614.993 1128149.459 1534006.005 1175782.915 1498576.288 1941482.334 1459308.115 1420288.681 0.965694312 0.87143147 0.612984532 0.79430997 1.080066345 0.827847839 1.055120911 1.366963181 1.02747289 1 20.43775276 2.083762397 4.425642455 1.181035252 0.856394411 0.407025127 0.147811048 0.178602672 6.479710233 0.060223031 0.042735696 121.2725186 -2.083762397 -0.324640841 KGAEKEEL ddPTM_BT-474_Pertuzumab_2h_R1 2 KGAEKEEL 8 2 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ; 91.087 0.050599 8162000000 6541300 6595300 5192200 5491200 6047000 6071000 6787100 7162500 8603100 7305300 FALSE TRUE 6285658.764 6407208.501 6130546.04 5774601.49 6241507.247 6193759.78 6870162.56 7014591.872 7626512.155 6810505.524 0.922935712 0.9407831 0.900160204 0.847896161 0.916452857 0.909442002 1.008759561 1.029966402 1.119815868 1 22.69933046 2.08380313 1.9885567 1.055891067 0.903197354 0.76902787 0.036206446 0.153319184 1.162514054 0.019827616 0.011111034 121.2838933 -2.08380313 -0.152693713 YDEMVESMK ddPTM_BT-474_Pertuzumab_2h_R1 4 YDEMVESMK 9 0 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 137.13 0.00040317 1653640000 1876730 1792550 1846400 2140610 1960840 1794470 2359220 2623600 2878850 2789760 FALSE TRUE 1803385.317 1741428.229 2180085.553 2251087.139 2023912.199 1830755.413 2388092.84 2569421.743 2552055.017 2600807.07 0.693394499 0.669572245 0.838234246 0.865534074 0.778186211 0.703918193 0.918212222 0.987932466 0.981255029 1 21.31052795 2.08382064 4.486790861 0.981260173 0.764056085 0.765956002 0.058646527 0.11420545 4.232988957 0.025834302 0.018374224 121.2887835 -2.08382064 -0.217204089 DVIEEYFK ddPTM_BT-474_Pertuzumab_2h_R1 4 DVIEEYFK 8 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;; 139.19 0.0015663 2970110000 3618260 3532350 2940540 3111820 3407720 3286410 3684080 3963260 4283220 4298590 FALSE TRUE 3476854.399 3431610.837 3471960.99 3272421.403 3517332.409 3352863.462 3729166.873 3881417.296 3797006.822 4007442.671 0.867599286 0.856309402 0.866378206 0.816585956 0.877699994 0.836659121 0.930560255 0.96855217 0.947488744 1 21.93425045 2.083832963 3.494659656 0.965868249 0.853634735 0.871108627 0.020730216 0.075830587 1.825948061 0.008331342 0.005605782 121.2922252 -2.083832963 -0.112233514 LAAEIDDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAAEIDDRK 9 1 Q96P16;A0A0C4DGQ6;Q96P16-3;K7EP82 Q96P16 RPRD1A Regulation of nuclear pre-mRNA domain-containing protein 1A 0 103.55 0.0054593 215750000 236280 223070 170330 157940 206050 205880 204880 223440 247530 228370 FALSE TRUE 227045.9164 216708.262 201112.42 166091.3023 212677.7854 210043.0347 207387.3827 218825.8859 219431.4321 212902.2965 1.066432444 1.017876583 0.944623066 0.780129219 0.998945474 0.986570075 0.974096504 1.027823041 1.030667286 1 17.69983199 2.083924696 1.563145889 1.02174099 0.957065793 0.097951574 0.070897347 0.925944064 4.286227361 0.047460557 0.024711206 121.3178474 -2.083924696 -0.064675197 EKVLATVTKPVGGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKVLATVTKPVGGDK 15 2 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ; 180.1 3.62E-07 2132450000 2931800 2636300 2192050 1952540 2333850 2698100 2682000 3156500 3486400 3228000 FALSE TRUE 2817222.015 2561115.305 2588202.197 2053310.823 2408920.405 2752657.431 2714823.118 3091317.172 3090638.488 3009364.685 0.93615175 0.851048501 0.860049369 0.682307078 0.800474737 0.914697193 0.902125001 1.027232488 1.027006964 1 21.52102752 2.083956261 1.575771655 1.023007155 0.825547595 0.609226028 0.064096519 0.268649228 1.264223736 0.042144239 0.021991321 121.3266653 -2.083956261 -0.197459561 SLSSS(ph)LDDTEVKK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSSSLDDTEVKK 13 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 SLSS(0.008)S(0.992)LDDTEVKK;SLS(0.002)S(0.033)S(0.964)LDDTEVKK;SLSS(0.01)S(0.99)LDDTEVKK 312.42 7.63E-51 3336910000 1766260 2507630 1336760 2483980 1671380 1732380 2665270 3898900 3121610 1770280 TRUE FALSE 1697232.606 2436114.848 1578342.268 2612178.505 1725141.456 1767409.911 2697888.372 3818386.353 2767257.92 1650377.359 1.028390627 1.476095655 0.956352352 1.582776504 1.045301213 1.070912601 1.63471 2.313644411 1.676742537 1 20.6543645 2.083958193 5.299967428 1.84765235 1.209858521 0.235717871 0.363623889 0.195944079 9.296621839 0.132650584 0.096267043 121.3272051 -2.083958193 -0.637793829 EVAATEEDVTRLPS(ph)PT(ph)SPFSSLSQDQAATSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 EVAATEEDVT(0.001)RLPS(0.971)PT(0.924)S(0.103)PFS(0.001)SLSQDQAATSK;EVAATEEDVTRLPS(0.998)PT(0.87)S(0.131)PFS(0.001)SLSQDQAATSK 184.03 5.85E-18 337130000 267004 287618 274274 330730 346550 319178 280773 278972 288473 298890 TRUE FALSE 256569.1885 279415.4162 323841.413 347799.0149 357697.0955 325631.9978 284209.184 273211.1307 255726.7544 278645.9141 0.9207714 1.002761577 1.162196884 1.248175542 1.283697616 1.168622906 1.019965374 0.980495736 0.917748086 1 18.08807347 2.084436636 3.834897804 0.970340999 1.138543731 0.350921376 0.102233441 0.282984534 8.069234085 0.047740886 0.032921436 121.4609396 -2.084436636 0.168202732 AS(ph)PVAALK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPVAALK 8 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 AS(1)PVAALK;AS(1)PVAALK;AS(1)PVAALK;AS(1)PVAALK 135.55 0.00086962 2348760000 1635950 1658410 1535340 1642360 1563050 1554390 1860660 2048290 2219460 2130060 TRUE FALSE 1572015.265 1611113.771 1812810.091 1727122.396 1613326.923 1585820.831 1883431.314 2005992.096 1967516.206 1985789.139 0.791632523 0.811321675 0.912891533 0.869741083 0.81243617 0.798584704 0.948454837 1.010173767 0.99079815 1 20.92128101 2.084459887 4.380230726 0.997102549 0.836589979 0.83012349 0.034749051 0.091049966 3.242361089 0.015135224 0.010725458 121.4674423 -2.084459887 -0.16051257 VVAGQIFLDSEESELESSIQEEEDSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVAGQIFLDSEESELESSIQEEEDSLK 27 0 G3V3B3;Q9UBV2-2;Q9UBV2 G3V3B3 SEL1L Protein sel-1 homolog 1 0 ; 156.43 2.03E-08 25118000 14316.3 20013.7 15902.4 23018 15449.2 15149.8 26735 37097 34287 23745 FALSE TRUE 13756.80317 19442.92887 18776.31743 24205.96174 15946.13755 15456.13934 27062.19093 36330.93399 30394.8835 22136.73 0.621446942 0.878310793 0.848197427 1.093475041 0.720347474 0.698212398 1.222501739 1.641205995 1.373052095 1 14.4341545 2.084480943 4.845672445 1.414911381 0.826005175 0.611519697 0.192921353 0.118486067 4.923612687 0.073533995 0.052881898 121.4733317 -2.084480943 -0.588906206 GSDS(ph)DSEGDNPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSDSDSEGDNPEK 13 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 GSDS(0.971)DS(0.029)EGDNPEK;GSDS(1)DSEGDNPEK 327.79 2.55E-62 654100000 1439350 1366140 1228810 1322940 1379340 1358220 1534900 1729060 1800550 1786210 TRUE FALSE 1383098.611 1327179.025 1450883.302 1391217.092 1423707.724 1385684.139 1553684.565 1693354.307 1596159.113 1665228.406 0.830575917 0.796995187 0.871281859 0.835451213 0.85496243 0.832128574 0.933015891 1.016890116 0.958522631 1 20.66728864 2.084491069 3.246625991 0.991527746 0.837061455 0.904860766 0.022821218 0.066091249 1.380067997 0.009792892 0.006453649 121.4761639 -2.084491069 -0.154466291 FNLTYVSHDGDDK ddPTM_BT-474_Pertuzumab_2h_R1 4 FNLTYVSHDGDDK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 209.41 3.81E-08 3220890000 4518360 3822990 4281950 5032700 3740790 3663380 5618100 6280000 6991800 6990100 FALSE TRUE 4341777.496 3713962.068 5055793.616 5292438.25 3861115.908 3737456.054 5686855.988 6150315.805 6198120.176 6516654.301 0.666258681 0.569918534 0.77582658 0.812140403 0.592499729 0.573523756 0.872664979 0.943784267 0.95111999 1 22.63570003 2.084504027 4.942343224 0.947682746 0.669860829 0.758374381 0.077538859 0.111131875 4.753591788 0.032610922 0.023506707 121.4797885 -2.084504027 -0.277821918 KGSLESPATDVFGSTEEGEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGSLESPATDVFGSTEEGEKR 21 2 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 205.13 2.77E-22 284330000 229160 237740 173330 161460 199990 231080 215090 257950 303100 248190 FALSE TRUE 220204.1739 230959.888 204654.5867 169792.9699 206422.86 235752.5959 217722.3358 252623.2424 268693.3587 231379.8702 0.95169979 0.99818488 0.884496073 0.733827752 0.892138369 1.018898471 0.940973541 1.091811669 1.161265059 1 17.81990383 2.084560611 1.410057786 1.092915511 0.895592089 0.472482425 0.081450607 0.37788543 1.416673385 0.057103957 0.029024165 121.4956171 -2.084560611 -0.197323422 KVENEDMNK ddPTM_BT-474_Pertuzumab_2h_R1 4 KVENEDMNK 9 1 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 ;;; 176.48 8.52E-05 783880000 1152710 1065440 1062790 1091890 1206310 1051770 1383290 1533340 1691100 1685330 FALSE TRUE 1107660.819 1035054.694 1254859.795 1148242.574 1245112.057 1073037.51 1400219.117 1501675.993 1499133.418 1571181.098 0.70498609 0.658774915 0.79867292 0.730814911 0.792468837 0.682949605 0.891188876 0.955762512 0.954144255 1 20.58341805 2.084668593 3.855041892 0.957997299 0.731424032 0.864645031 0.043682396 0.079868486 2.297613471 0.018171162 0.012548234 121.5258291 -2.084668593 -0.226573267 SKLDAEVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKLDAEVSK 9 1 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 96.015 0.0056427 0 250200 282080 245880 241060 184080 138060 270080 278770 293250 312550 FALSE TRUE 240421.9074 274035.3546 290315.9856 253501.1355 190001.1004 140851.6678 273385.3198 273013.3021 259961.4894 291380.7101 0.825112641 0.940471847 0.996345933 0.869999718 0.65207165 0.483393934 0.938240969 0.936964228 0.89217124 1 18.15254585 2.08479776 19.78638412 0.937071591 0.799282779 0.212630018 0.138522651 9.407045214 2189.139792 0.058577963 0.043262742 121.5619784 -2.08479776 -0.137788813 SSGRNS(ph)PSAASTSSNDSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.001)S(0.003)GRNS(0.709)PS(0.288)AASTSSNDSK;S(0.001)S(0.004)GRNS(0.854)PS(0.141)AASTSSNDSK;SSGRNS(0.996)PS(0.004)AASTSSNDSK;S(0.027)S(0.027)GRNS(0.751)PS(0.196)AASTSSNDSK 195.8 1.23E-15 2389260000 1125390 991010 795820 869680 902450 976710 1019100 1089590 1271880 1117410 TRUE FALSE 1081408.515 962747.3651 939642.3769 914564.289 931478.1238 996459.7454 1031572.051 1067089.586 1127501.515 1041726.825 1.038092222 0.924184097 0.902004589 0.877931015 0.894167359 0.956546113 0.990251979 1.024346844 1.082338946 1 19.99054558 2.084844228 1.794805408 1.039821004 0.923650164 0.520135862 0.045234713 0.28051495 1.72332348 0.026855366 0.014573544 121.5749859 -2.084844228 -0.11617084 DIVPGDIVEVAVGDKVPADLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DIVPGDIVEVAVGDKVPADLR 21 1 Q93084-4;Q93084-2;Q93084-3;Q93084-7;Q93084;Q93084-6;Q93084-5 Q93084-4 ATP2A3 Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 0 ;; 173.43 3.94E-12 425015000 365523 580955 292854 608586 389233 430674 545311 759620 557886 429658 FALSE TRUE 351237.9571 564386.7322 345779.2323 639995.1964 401753.0329 439382.5234 551984.6791 743933.5815 494557.1201 400556.881 0.876874106 1.40900521 0.863246267 1.597763581 1.002986223 1.096929161 1.378043183 1.857248288 1.234673884 1 18.6116476 2.08507878 5.452750992 1.496123147 1.157393222 0.070261707 0.299376241 0.303197108 14.86896838 0.108815348 0.079171514 121.6406633 -2.08507878 -0.338729925 ETLEDGFPVHDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETLEDGFPVHDGK 13 0 I3L1Y2;A0A087WT44;P30519-2;P30519 I3L1Y2 HMOX2 Heme oxygenase 2 0 ; 131.26 0.00013252 545770000 419590 615740 359350 648290 415660 482730 601200 781510 725270 505930 FALSE TRUE 403191.9589 598179.6981 424292.5387 681748.3246 429030.0814 492491.1313 608557.6654 765371.5454 642940.3902 471662.9105 0.854830749 1.268235608 0.899567317 1.445414319 0.909611657 1.044159124 1.290238541 1.622708779 1.363135358 1 18.84739663 2.085362196 4.772692375 1.411003843 1.082909177 0.202332831 0.223674977 0.238484894 9.652318508 0.082201261 0.059022588 121.7200707 -2.085362196 -0.328094666 GDKVDILYNNIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDKVDILYNNIK 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 166.62 4.69E-05 779970000 2058400 1876000 1706800 1459600 1641300 1554100 2013400 2151800 2348700 2383300 FALSE TRUE 1977955.452 1822498.317 2015256.728 1534930.131 1694093.905 1585524.967 2038040.591 2107364.578 2082085.423 2221876.968 0.890218262 0.82025168 0.907006444 0.690825889 0.762460716 0.713597103 0.917260776 0.948461417 0.93708403 1 21.0833475 2.085476361 6.554881358 0.950484412 0.797308813 0.569299676 0.065922418 0.167690059 10.52633327 0.026143613 0.019202107 121.7520719 -2.085476361 -0.153175599 QGS(ph)FSEDVISHK ddPTM_BT-474_Pertuzumab_2h_R1 2 QGSFSEDVISHK 12 0 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5;E9PNZ4 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 QGS(0.998)FS(0.002)EDVISHK;QGS(0.984)FS(0.016)EDVISHK 216.71 2.47E-11 1299240000 1114230 1014400 794450 923460 917850 929970 998660 1092710 1102250 1030560 TRUE FALSE 1070684.66 985470.3052 938024.7874 971119.8813 947373.4788 948774.6306 1010881.9 1070145.157 977127.201 960759.2533 1.114415142 1.025720337 0.97633698 1.010783792 0.986067504 0.987525884 1.05216983 1.113853604 1.017036472 1 19.87381544 2.085697483 7.297177272 1.062827977 1.013892655 0.03987947 0.046677037 0.380459861 27.4771261 0.017812339 0.013117432 121.8140783 -2.085697483 -0.048935322 KCLELFTELAEDKENYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KCLELFTELAEDKENYK 17 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 179.46 5.14E-10 15687300000 926080 707920 750660 790000 781540 778690 1003480 1197280 1244010 1188310 FALSE TRUE 889887.7698 687730.8147 886320.9603 830771.9947 806678.9439 794435.6453 1015760.888 1172555.75 1102795.2 1107824.705 0.803274891 0.620793896 0.80005524 0.749912861 0.72816479 0.717113133 0.916896765 1.058430764 0.995460017 1 20.07929819 2.085768135 3.410904788 1.019508905 0.734160846 0.864083594 0.050831175 0.074793563 1.717507014 0.020726227 0.013874049 121.8338969 -2.085768135 -0.285348059 DVEFEVVGDAPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVEFEVVGDAPEK 13 0 Q9UBT2;Q9UBT2-2;U3KQ93 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 227.36 2.15E-11 214980000 256310 207020 234690 249380 244070 220490 287470 312030 353050 341200 FALSE TRUE 246293.1218 201115.9923 277103.7037 262250.5317 251920.7332 224948.4589 290988.1439 305586.4715 312973.2441 318090.2201 0.774286999 0.632260848 0.87114814 0.8244533 0.79197887 0.707184455 0.914797518 0.960691188 0.983913444 1 18.27907649 2.085821686 4.60575781 0.96893751 0.769700867 0.716021725 0.061856166 0.12169138 4.661487209 0.025314776 0.01809262 121.8489205 -2.085821686 -0.199236643 TEDGDWEWS(ph)DDEMDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TEDGDWEWSDDEMDEK 16 0 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 TEDGDWEWS(1)DDEMDEK 281.92 1.90E-28 0 76605 67106 69882 75558 74668 61305 93324 109750 112600 99811 TRUE FALSE 73611.19191 65192.20258 82511.23192 79457.55743 77069.76403 62544.6291 94466.12703 107483.6241 99818.12006 93050.71207 0.79108682 0.70060939 0.886734019 0.853916705 0.8282555 0.672156373 1.015211221 1.155108024 1.07272817 1 16.50572957 2.085958141 5.77578876 1.091346417 0.79495525 0.780918768 0.07084729 0.087127545 4.596808766 0.027198473 0.019867864 121.8872112 -2.085958141 -0.296391167 AEEGKS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEEGKSPFR 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 AEEGKS(1)PFR;AEEGKS(1)PFR;AEEGKS(1)PFR;AEEGKS(1)PFR 118.61 0.00058258 3004450000 3225560 2887290 2651150 2741750 2870610 2850410 3353550 3823020 4023100 3826960 TRUE FALSE 3099501.549 2804947.316 3130271.78 2883252.046 2962945.778 2908047.243 3394591.748 3744073.301 3566414.554 3567756.59 0.868753647 0.786193577 0.877378179 0.808141467 0.830478678 0.815091268 0.951463942 1.04941949 0.999623843 1 21.76658576 2.086041851 3.598740695 1.018695641 0.830028838 0.894903249 0.028960236 0.060771705 1.542427475 0.011293217 0.007673592 121.9107073 -2.086041851 -0.188666803 GGLLTSEEDSGFSTS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 GGLLTSEEDSGFSTSPK 17 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 GGLLTSEEDSGFST(0.043)S(0.957)PK;GGLLTSEEDSGFST(0.027)S(0.973)PK;GGLLTSEEDSGFSTS(1)PK;GGLLTSEEDSGFST(0.001)S(0.999)PK;GGLLTSEEDSGFSTS(1)PK 377.75 3.84E-105 1127580000 2247030 1897410 1665760 1994940 1910830 1711930 2244330 2664660 2406670 2179680 TRUE FALSE 2159213.583 1843297.725 1966799.887 2097899.092 1972293.582 1746546.398 2271796.782 2609633.84 2133474.911 2032048.332 1.062579836 0.907113131 0.967890308 1.032406099 0.970593834 0.859500421 1.117983636 1.284238076 1.049913468 1 20.95450329 2.08616097 7.316483981 1.15719919 0.96777183 0.357461015 0.090003285 0.182290495 13.14742701 0.032973946 0.024284466 121.9441497 -2.08616097 -0.18942736 RPHS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 7 RPHSPEK 7 1 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK 119.22 0.0029584 7303310000 6528550 5797970 4632370 5296290 5768230 5507870 6007100 6384020 7046410 6655830 TRUE FALSE 6273407.048 5632617.572 5469542.306 5569632.162 5953770.357 5619242.905 6080616.687 6252187.756 6246531.078 6205024.706 1.011020479 0.907751031 0.881469868 0.89760032 0.959507921 0.905595573 0.979950439 1.007600784 1.006689155 1 22.56500552 2.086163122 4.234555717 1.003366895 0.924462804 0.511078254 0.034690696 0.173842979 5.836481983 0.014075343 0.009923511 121.9447541 -2.086163122 -0.078904092 TSS(ph)DPVLLK ddPTM_BT-474_Pertuzumab_2h_R1 6 TSSDPVLLK 9 0 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 TS(0.002)S(0.998)DPVLLK;TS(0.002)S(0.998)DPVLLK;TSS(1)DPVLLK;TS(0.001)S(0.999)DPVLLK;TSS(1)DPVLLK;T(0.001)S(0.003)S(0.996)DPVLLK 200.71 2.38E-05 3300140000 7407360 6926420 5774570 6267070 6808600 6929710 7411860 8596270 9046520 8499300 TRUE FALSE 7117872.182 6728885.283 6818163.254 6590514.234 7027604.802 7069833.484 7502568.56 8418754.02 8019596.976 7923634.841 0.898308961 0.849216984 0.860484284 0.831753907 0.886916793 0.892246251 0.946859454 1.06248637 1.012110873 1 22.91773096 2.086711583 2.261652584 1.030646 0.864663934 0.88796731 0.024691765 0.085662109 0.849350202 0.012413239 0.00728347 122.0988526 -2.086711583 -0.165982065 SKEEVNDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKEEVNDKR 9 2 R4GMX3;P35226;Q5T8Z2 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 0 ; 113.47 0.0010095 646810000 1355760 1238590 1013210 973060 1092250 1184540 1263530 1424260 1544540 1454550 FALSE TRUE 1302775.4 1203266.626 1196319.586 1023279.743 1127383.213 1208492.21 1278993.458 1394848.533 1369210.294 1356032.033 0.960726125 0.887343807 0.882220742 0.754613253 0.83138391 0.891197391 0.943188234 1.028625062 1.009718252 1 20.37095983 2.086746498 2.246143581 1.014926102 0.860409629 0.636447644 0.049339796 0.203115899 1.985254912 0.02735284 0.016012575 122.1086691 -2.086746498 -0.154516473 AVDIPHMDIEALK ddPTM_BT-474_Pertuzumab_2h_R1 6 AVDIPHMDIEALK 13 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 214.81 3.02E-11 4052059000 5680520 5571200 4507660 5102560 5585740 5056760 5733300 6151310 6474840 6334360 FALSE TRUE 5458518.998 5412314.831 5322294.434 5365903.733 5765410.4 5159011.152 5803465.84 6024283.299 5739843.308 5905328.155 0.924337963 0.916513814 0.901269886 0.908654624 0.976306523 0.873619724 0.982750778 1.020143697 0.971977028 1 22.4935858 2.086912454 6.848160183 1.00004775 0.9186104 0.671535025 0.026454245 0.117550606 7.7162835 0.0095323 0.007010751 122.1553392 -2.086912454 -0.08143735 DTSEDIEELVEPVAAHGPK ddPTM_BT-474_Pertuzumab_2h_R1 4 DTSEDIEELVEPVAAHGPK 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 267.55 1.16E-31 1780040000 1439440 1329340 1202980 1287490 1378850 1430980 1486830 1535150 1796090 1748930 FALSE TRUE 1383185.093 1291428.525 1420385.246 1353937.513 1423201.962 1459915.396 1505026.27 1503448.616 1592205.393 1630473.413 0.848333424 0.792057395 0.871148977 0.830395333 0.872876522 0.895393561 0.923060909 0.922093304 0.976529504 1 20.63685949 2.0870253 0.462309555 1.003617638 0.816643573 0.885088603 0.020666437 0.286275973 0.138043174 0.019522836 0.01747594 122.1870838 -2.0870253 -0.186974065 RAT(ph)SLPSIPNPFPELCS(ph)PPSQSPILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.523)S(0.475)LPS(0.002)IPNPFPELCS(0.966)PPS(0.029)QS(0.005)PILGGPSSAR 107.71 4.08E-06 231720000 39351 47099 24357 31832 38368 44213 27465 25960 26267 25797 TRUE FALSE 37813.11942 45755.78263 28758.85172 33474.85333 39602.14156 45107.01715 27801.12489 25423.91693 23285.28028 24049.74621 1.572287669 1.902547421 1.195806869 1.391900482 1.646676069 1.875571441 1.155984127 1.057138678 0.968213139 1 14.55373405 2.08707244 6.404365134 1.036973206 1.584773289 0.658539078 0.1963511 0.139189001 8.355930194 0.078215179 0.057411636 122.2003472 -2.08707244 0.547800084 HRGS(ph)EEDPLLSPVETWK ddPTM_BT-474_Pertuzumab_2h_R1 2 HRGSEEDPLLSPVETWK 17 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 HRGS(1)EEDPLLSPVETWK;HRGS(1)EEDPLLSPVETWK 127.28 2.47E-05 431710000 531930 551100 467220 541690 542310 511370 403700 231907 396940 367660 TRUE FALSE 511141.5875 535383.1676 551657.0473 569646.6858 559753.8937 521710.2518 408640.6014 227118.0394 351881.0353 342758.0607 1.491260589 1.561985636 1.60946484 1.661949786 1.633087468 1.52209477 1.192212958 0.662619105 1.026616368 1 18.38683107 2.087125873 3.030861795 0.866528994 1.590233101 0.893845678 0.106168384 0.068095158 1.239194674 0.046334503 0.029969184 122.2153829 -2.087125873 0.723704107 TAFDDAIAELDTLNEDSYK ddPTM_BT-474_Pertuzumab_2h_R1 6 TAFDDAIAELDTLNEDSYK 19 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;; 497.85 1.04E-266 1401655000 1374596 1192474 1262339 1370701 1395518 1335368 1705788 1927581 2147347 2073045 FALSE TRUE 1320875.269 1158465.809 1490471.738 1441443.043 1440406.104 1362370.056 1726663.944 1887775.779 1903589.171 1932635.816 0.683457927 0.599422716 0.771211899 0.745843077 0.745306535 0.704928494 0.893424374 0.976788158 0.984970451 1 20.88213837 2.087182969 2.28206936 0.986451046 0.706599363 0.887242704 0.045386976 0.101554277 1.02618316 0.024860014 0.014637901 122.2314515 -2.087182969 -0.279851683 EVPTQFLDRDEEEEDADFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVPTQFLDRDEEEEDADFLK 20 1 A0A3B3ISR7;E9PIF2;Q13206 A0A3B3ISR7 DDX10 Probable ATP-dependent RNA helicase DDX10 0 148.75 9.75E-08 69440000 86694 76989 84355 73189 73031 74168 87782 93591 100080 100540 FALSE TRUE 83305.90263 74793.3491 99599.82497 76966.29306 75380.10844 75667.72778 88856.30237 91658.31314 88719.33797 93730.33625 0.888782714 0.797963094 1.062621014 0.821146025 0.804223173 0.807291756 0.947999398 0.977893784 0.946538138 1 16.51622844 2.087188082 6.728358158 0.970052756 0.865332041 0.327574124 0.07389681 0.27069539 17.31956769 0.028478214 0.020935724 122.2328905 -2.087188082 -0.104720715 HHHHDS(ph)DSNS(ph)PCCK ddPTM_BT-474_Pertuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 HHHHDS(0.996)DS(0.007)NS(0.997)PCCK 136.35 1.31E-05 161030000 116970 122850 85432 94970 88736 93162 66836 523.87 88440 35652 TRUE FALSE 112398.6831 119346.4383 100871.4628 99871.41308 91590.27403 95045.79947 67653.95896 513.0519014 78400.66197 33237.25828 3.381707424 3.590742572 3.034891204 3.00480299 2.755650699 2.859616117 2.03548555 0.015436048 2.358818567 1 15.02051376 2.087191832 3.284334472 1.012534207 3.110911626 0.697540293 0.583811415 0.123111005 2.626799378 0.248100088 0.164473254 122.2339459 -2.087191832 2.098377419 RLEELEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEELEAK 8 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 115.82 0.0038312 345220000 451760 399340 328940 382280 404630 409700 434610 478520 523850 512200 FALSE TRUE 434104.7198 387951.2142 388386.7752 402009.5166 417645.2914 417984.4147 439928.8872 468638.3948 464384.7442 477508.2378 0.909104148 0.81244926 0.813361413 0.841890223 0.874634736 0.875344929 0.921301147 0.981424733 0.972516718 1 18.8651661 2.087313585 1.10115369 0.995510316 0.841838796 0.831041798 0.026709804 0.18637841 0.420863557 0.019755483 0.009825181 122.2682186 -2.087313585 -0.15367152 AGMSSNQSISS(ph)PVLDAVPRT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 8 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.008)S(0.009)NQS(0.035)IS(0.204)S(0.744)PVLDAVPRT(0.834)PS(0.166)R;AGMSSNQSIS(0.024)S(0.975)PVLDAVPRT(0.952)PS(0.048)R;AGMSSNQSIS(0.016)S(0.984)PVLDAVPRT(0.948)PS(0.052)R;AGMSSNQSIS(0.064)S(0.936)PVLDAVPRT(0.877)PS(0.123)R;AGMSSNQS(0.001)IS(0.054)S(0.945)PVLDAVPRT(0.864)PS(0.136)R;AGMSSNQSIS(0.007)S(0.993)PVLDAVPRT(0.891)PS(0.109)R;AGMSSNQSIS(0.048)S(0.952)PVLDAVPRT(0.962)PS(0.038)R;AGMSSNQSIS(0.01)S(0.99)PVLDAVPRT(0.983)PS(0.017)R 192.89 1.78E-17 4028090000 1519036 1729372 898402 1040039 1344958 1616760 1042878 1094753 1043822 942100 TRUE FALSE 1459670.394 1680052.004 1060763.226 1093715.537 1388219.796 1649451.995 1055641.053 1072145.968 925331.7026 878290.7279 1.661944442 1.912865468 1.207758653 1.245277336 1.580592566 1.878025058 1.201926674 1.22071876 1.053559685 1 19.74433905 2.087608387 8.705340423 1.139677079 1.563567161 0.510039587 0.221894313 0.2638532 23.43879962 0.089483425 0.066032998 122.3512434 -2.087608387 0.423890082 HWDQDDDFEFTGSHLTVR ddPTM_BT-474_Pertuzumab_2h_R1 4 HWDQDDDFEFTGSHLTVR 18 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ;;; 366.98 9.68E-108 1397450000 926750 918500 830230 732210 723630 787790 642761 286957 716220 605143 FALSE TRUE 890531.5854 892305.2793 980271.0294 769999.4458 746906.2161 803719.6536 650627.3014 281031.2377 634917.7082 564156.1256 1.578519748 1.581663725 1.737588205 1.364869423 1.323935312 1.42464048 1.153275258 0.498144441 1.125429078 1 19.10573495 2.087697535 3.251421276 0.818478854 1.50480947 0.683377004 0.190751242 0.128447827 2.687011822 0.084409062 0.055816163 122.3763612 -2.087697535 0.686330617 DALDGPAAEAEPEHSFDGLRR ddPTM_BT-474_Pertuzumab_2h_R1 2 DALDGPAAEAEPEHSFDGLRR 21 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 254.72 1.39E-36 827400000 389040 396520 300670 306920 336730 392370 306290 304320 339300 301340 FALSE TRUE 373835.8867 385211.6378 355007.7574 322760.178 347561.2263 400303.9902 310038.4686 298035.6857 300784.0865 280929.9734 1.33070844 1.371201631 1.263687719 1.148899044 1.237181003 1.424924459 1.103614772 1.060889595 1.070672819 1 18.09985103 2.087713347 7.025484217 1.058388169 1.288239569 0.718069258 0.073264261 0.130590933 8.796192356 0.029449832 0.021673447 122.3808167 -2.087713347 0.2298514 SESVVSGLDS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SESVVSGLDSPAK 13 0 O14578-4;H7BYJ3;O14578;O14578-2 O14578-4 CIT Citron Rho-interacting kinase 1 SESVVSGLDS(1)PAK;SESVVSGLDS(1)PAK;SESVVSGLDS(1)PAK;SESVVSGLDS(1)PAK 306.15 1.54E-41 2377990000 3559130 3113480 2834710 2852270 3061480 2908190 3364730 3734820 3565810 3729300 TRUE FALSE 3420035.265 3024686.599 3347005.155 2999475.997 3159955.285 2966995.594 3405908.572 3657694.662 3161034.198 3476711.189 0.983698409 0.869985004 0.962692894 0.862733725 0.908892086 0.853391447 0.979635174 1.052055941 0.909202412 1 21.7292918 2.087771396 7.242077582 0.9984827 0.906108759 0.355214544 0.051044886 0.205320818 14.37629394 0.018246655 0.013436689 122.3971757 -2.087771396 -0.092373941 EFNKYDTDGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 EFNKYDTDGSK 11 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 118.87 0.00060464 8893300000 6246900 6354700 5055200 5256500 6011700 6056300 6682000 7801000 8306300 7772700 FALSE TRUE 6002764.242 6173470.178 5968787.092 5527788.595 6205071.79 6178762.535 6763776.315 7639906.624 7363403.647 7246248.106 0.828396179 0.851954016 0.823707249 0.762848375 0.856315116 0.852684375 0.93341771 1.05432584 1.016167752 1 22.78880277 2.087905949 2.173121512 1.029138462 0.824688597 0.906561262 0.028115889 0.084700282 0.773165584 0.01495803 0.008669403 122.4351025 -2.087905949 -0.204449865 DLAEDAPWK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLAEDAPWK 9 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 Q60FE5;O75369-8;Q14315-2 FLNA;FLNB;FLNC Filamin-A;Filamin-B;Filamin-C 0 ;;; 130.75 0.00082007 1302220000 2318050 2335210 2323860 2495230 2286070 2103730 2846290 3029060 3433250 3491940 FALSE TRUE 2227458.043 2268612.097 2743833.196 2624009.119 2359603.518 2146268.862 2881123.748 2966508.852 3043521.853 3255427.794 0.684228981 0.696870655 0.842848734 0.80604126 0.724821335 0.659289346 0.885021549 0.911250085 0.934906884 1 21.63441571 2.088311925 5.573002876 0.929370458 0.741931958 0.745509978 0.056863629 0.118475989 5.866658452 0.023409105 0.01706908 122.5496075 -2.088311925 -0.1874385 RGS(ph)PTTGFIEQK ddPTM_BT-474_Pertuzumab_2h_R1 8 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.956)PT(0.044)T(0.001)GFIEQK;RGS(0.985)PT(0.014)TGFIEQK;RGS(0.55)PT(0.446)T(0.004)GFIEQK;RGS(0.988)PT(0.012)TGFIEQK;RGS(0.999)PT(0.001)TGFIEQK;RGS(0.992)PT(0.008)TGFIEQK;RGS(0.707)PT(0.258)T(0.035)GFIEQK;RGS(0.924)PT(0.07)T(0.007)GFIEQK 235.11 5.16E-16 9612790000 8087810 7411390 6680030 6731620 7148090 7652830 8542290 9870140 10467970 10478070 TRUE FALSE 7771729.444 7200024.414 7887260.017 7079039.715 7378014.807 7807575.466 8646833.1 9666318.16 9279689.931 9768380.986 0.795600566 0.737074488 0.807427559 0.72468915 0.755295562 0.799270163 0.885185899 0.989551715 0.949972154 1 23.21968804 2.08846525 1.963396378 0.980949912 0.76304095 0.927232235 0.02665849 0.075408842 0.557919832 0.013832107 0.007753708 122.5928807 -2.08846525 -0.217908962 S(ph)PSSKPSLAVAVDSAPEVAVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSSKPSLAVAVDSAPEVAVK 21 1 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 1 S(0.586)PS(0.064)S(0.345)KPS(0.005)LAVAVDSAPEVAVK;S(0.7)PS(0.089)S(0.089)KPS(0.121)LAVAVDSAPEVAVK;S(0.894)PS(0.098)S(0.009)KPSLAVAVDSAPEVAVK;S(0.555)PS(0.434)S(0.011)KPS(0.001)LAVAVDSAPEVAVK 245.69 1.86E-30 2909400000 4236590 4014710 4164740 4345570 4358420 4117270 5181800 5878700 5927200 6611100 TRUE FALSE 4071019.379 3900214.402 4917401.162 4569845.388 4498612.538 4200524.02 5245216.418 5757302.791 5254369.105 6163324.308 0.660523311 0.632810186 0.797848842 0.741457882 0.729900345 0.681535452 0.851036901 0.934122967 0.852521925 1 22.55527728 2.088481813 3.723788042 0.916970109 0.710752374 0.770855951 0.054943088 0.113449546 3.053779614 0.023207361 0.015937231 122.5975561 -2.088481813 -0.206217735 AAIDWFDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAIDWFDGK 9 0 Q92804-2;Q92804;A0A075B7D9;P35637-2;P35637;H3BPE7 Q92804-2;P35637-2 TAF15;FUS TATA-binding protein-associated factor 2N;RNA-binding protein FUS 0 ;;; 128.38 0.00097451 2884300000 4392162 4446130 3720183 4478590 4430145 4115379 4760302 5241552 5361615 5202630 FALSE TRUE 4220511.453 4319330.726 4392502.823 4709730.567 4572644.637 4198594.783 4818560 5133312.12 4752986.943 4850251.236 0.870163472 0.890537524 0.905623773 0.971028167 0.942764491 0.865644805 0.993466063 1.058360046 0.979946545 1 22.20962805 2.088518076 5.969583237 1.020837943 0.911620252 0.660454914 0.035188225 0.122119198 6.612168435 0.013930316 0.010197269 122.6077933 -2.088518076 -0.109217691 AQKPWAK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQKPWAK 7 1 F6U236;Q9BY11;Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 F6U236;Q9UNF0-2 PACSIN1;PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 1;Protein kinase C and casein kinase substrate in neurons protein 2 0 69.998 0.053096 474820000 380210 357020 294520 321430 315290 318380 359600 382720 414870 390130 FALSE TRUE 365350.9729 346838.1392 347746.3156 338019.0408 325431.5892 324817.8617 364000.8924 374816.6983 367775.6969 363706.1476 1.004522402 0.953621877 0.956118883 0.92937401 0.89476516 0.893077733 1.000810393 1.030548152 1.011189113 1 18.47241379 2.088662185 6.927374381 1.016891812 0.93783962 0.569589013 0.030789258 0.161717242 10.60316614 0.012641956 0.009301362 122.6484843 -2.088662185 -0.079052191 MKEGENNKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 MKEGENNKPR 10 2 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 ;;; 143.96 1.86E-05 1559130000 1080840 1054730 759220 957740 890490 995210 1034030 1112810 1246890 1181390 FALSE TRUE 1038599.578 1024650.133 896427.9428 1007169.076 919133.4196 1015333.828 1046684.768 1089830.085 1105348.275 1101373.403 0.943004048 0.930338548 0.813918277 0.914466496 0.83453388 0.921879741 0.950345056 0.98951916 1.003609014 1 20.07087224 2.088733166 1.785853621 0.998586136 0.886988101 0.613491676 0.037989596 0.240536943 1.464465841 0.022039884 0.011985561 122.6685316 -2.088733166 -0.111598036 KTS(ph)PQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSPQVK 7 1 E9PSC8;E9PKA8;Q6ZUT1-3;Q6ZUT1;Q6ZUT1-2 E9PSC8 C11orf57 Uncharacterized protein C11orf57 1 KT(0.067)S(0.933)PQVK 85.958 0.012513 665740000 279520 246830 236940 214320 228880 245720 266210 304730 295190 311040 TRUE FALSE 268596.0494 239790.6501 279760.3287 225381.0809 236242.1331 250688.6268 269467.9576 298437.219 261681.2687 289972.9838 0.926279565 0.826941348 0.964780667 0.777248549 0.814703942 0.864524079 0.929286426 1.029189737 0.902433273 1 18.14555897 2.088844906 3.656615246 0.980461758 0.8594532 0.437681732 0.058689683 0.201148433 5.2396955 0.024023638 0.016427469 122.7000969 -2.088844906 -0.121008558 DSKPS(ph)STPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.119)KPS(0.294)S(0.294)T(0.294)PR;DS(0.039)KPS(0.32)S(0.32)T(0.32)PR 64.439 0.042095 302668000 618860 502950 499690 485040 458650 516090 553670 654870 552990 619970 TRUE FALSE 594674.267 488606.3584 589995.0985 510072.9725 473402.8938 526525.6934 560445.9791 641346.7057 490216.8935 577978.8797 1.028885809 0.845370611 1.020790066 0.882511438 0.819066077 0.910977394 0.969665153 1.109636923 0.848157105 1 19.14065725 2.088877977 4.916976628 1.007445942 0.913808237 0.099474642 0.086830425 0.335624566 13.9680738 0.033002159 0.023808756 122.7094408 -2.088877977 -0.093637705 QGQSQAASSSSVTS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 4 QGQSQAASSSSVTSPIK 17 0 O60583-2;O60583 O60583-2 CCNT2 Cyclin-T2 1 QGQSQAASSSSVT(0.006)S(0.993)PIK;QGQSQAASSSSVT(0.038)S(0.962)PIK;QGQSQAASSSSVT(0.005)S(0.995)PIK;QGQSQAASSSSVT(0.005)S(0.995)PIK 319.35 1.96E-58 2161030000 2980530 2749470 2239700 2496320 2613840 2477980 2876650 3199370 3201200 3085930 TRUE FALSE 2864047.592 2671057.808 2644463.612 2625155.374 2697916.537 2528086.453 2911855.303 3133301.891 2837813.197 2876917.212 0.995526594 0.928444446 0.919200455 0.912489022 0.937780387 0.878748419 1.012144281 1.089117851 0.986407667 1 21.45609228 2.089016019 6.262246697 1.038799412 0.928328536 0.588811477 0.037721484 0.122617649 7.039279977 0.013974837 0.010251371 122.7484508 -2.089016019 -0.110470875 ALPAAHIPAPPHEGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 ALPAAHIPAPPHEGSPR 17 0 P17029;E9PC66 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR 188.19 7.10E-10 1680420000 806070 805491 728540 915039 656216 753910 655047 510400 522269 602266 TRUE FALSE 774567.8932 782519.1853 860203.3843 962264.2724 677323.7836 769154.5767 663063.6611 499860.0616 462983.2127 561473.9874 1.379525874 1.393687335 1.532044945 1.713818083 1.206331547 1.369884614 1.180933892 0.890263971 0.824585329 1 19.09885966 2.089177679 1.368149045 0.87142225 1.466057943 0.775956643 0.127538972 0.192688037 0.679636887 0.086593963 0.043928428 122.7941506 -2.089177679 0.594635693 ETPPNGNLS(ph)PAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ETPPNGNLSPAPR 13 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR 253.15 9.38E-24 2372880000 531832 664529 593449 621357 675610 654866 551233 547260 534711 587181 TRUE FALSE 511047.4175 645577.2836 700698.4355 653425.3092 697341.6092 668107.8392 557979.1543 535958.8898 474012.849 547410.7079 0.933572197 1.179328929 1.280023254 1.19366556 1.273891064 1.220487341 1.019306247 0.979080025 0.865918116 1 19.06226413 2.089228158 3.303104892 0.953288925 1.1895519 0.545769241 0.096628114 0.188874342 4.071362395 0.042860493 0.028513237 122.8084241 -2.089228158 0.236262975 T(ph)SDANETEDHLESLICK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSDANETEDHLESLICK 17 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 T(0.499)S(0.499)DANET(0.002)EDHLESLICK 96.708 0.0082958 92385000 106170 137000 125890 178750 199640 177060 110360 97974 87006 106970 TRUE FALSE 102020.759 133092.8941 148641.1234 187975.3089 206061.6019 180640.2745 111710.6187 95950.80266 77129.44364 99724.82662 1.023022676 1.334601409 1.490512728 1.884939942 2.066301932 1.8113872 1.120188648 0.962155623 0.77342269 1 16.60566509 2.08934813 4.582800478 0.935843563 1.61681131 0.557242866 0.282076886 0.177579312 6.668153275 0.125665972 0.089882045 122.8423539 -2.08934813 0.680967747 ES(ph)PGSSEFFQEAVSHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESPGSSEFFQEAVSHGK 17 0 Q8N108-17;Q8N108;Q8N108-13;Q8N108-12 Q8N108-17 MIER1 Mesoderm induction early response protein 1 1 ES(0.846)PGS(0.068)S(0.085)EFFQEAVSHGK;ES(0.983)PGS(0.008)S(0.008)EFFQEAVSHGK 113.36 0.00026796 204185000 241900 244666 231636 276073 234479 252658 288233 329892 345168 334585 TRUE FALSE 232446.2806 237688.3652 273497.7779 290321.1606 242021.23 257766.9179 291760.4817 323079.6149 305985.9757 311923.2599 0.745203422 0.762009109 0.876811104 0.930745468 0.775899912 0.826379277 0.935359812 1.035766345 0.980965561 1 18.25083161 2.089487343 3.123668517 1.006751 0.822032915 0.71693397 0.053159539 0.145195549 2.806084213 0.025377876 0.016606627 122.8817373 -2.089487343 -0.184718085 LGHDPYRLT(ph)PDPYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGHDPYRLTPDPYR 14 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-6 P18583-7 SON Protein SON 1 LGHDPYRLT(1)PDPYR;LGHDPYRLT(1)PDPYR 118.24 0.0003767 204188000 130999 121842 84274 129310 113161 125377 108614 102706 128047 125052 TRUE FALSE 125879.4143 118367.1855 99504.18647 135983.7046 116800.9263 127912.2088 109943.2506 100585.0852 113511.6414 116582.1167 1.079748917 1.015311686 0.853511579 1.166419932 1.001876872 1.097185508 0.943054165 0.862783145 0.973662553 1 16.83098697 2.089852641 7.660424643 0.92353083 1.0306203 0.206639688 0.083535916 0.312902248 23.05655935 0.030900848 0.022776772 122.9851403 -2.089852641 0.107089469 ENQHPNLLGGAGEPPKPDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENQHPNLLGGAGEPPKPDK 19 1 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 0 ; 113.99 9.99E-05 253080000 790600 656390 603080 585580 696770 654520 768380 865560 928050 859620 FALSE TRUE 759702.4779 637670.3999 712069.9714 615801.854 719182.2398 667754.8428 777783.6643 847685.8835 822701.6547 801397.1717 0.947972497 0.795698341 0.888535668 0.768410316 0.897410504 0.833238332 0.970534576 1.057760014 1.026584175 1 19.61215789 2.089904552 3.649565834 1.031470773 0.851972752 0.712289894 0.050178122 0.109488631 2.839063486 0.019371489 0.013250545 122.9998415 -2.089904552 -0.179498022 EAAENSLVAYK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAAENSLVAYK 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;; 163.34 5.60E-05 522250000 466980 453450 375450 423310 395620 394010 466470 495820 518430 546570 FALSE TRUE 448729.9053 440518.05 443302.1668 445157.0798 408345.4766 401977.1522 472178.7994 485581.1437 459579.9998 509550.3271 0.880639029 0.864523142 0.869987013 0.873627307 0.801383995 0.788886064 0.926657828 0.952960126 0.901932499 1 18.95886512 2.090218128 7.241559 0.944760999 0.847767679 0.644403324 0.036212347 0.152055605 10.39962897 0.01419227 0.010452168 123.088684 -2.090218128 -0.09699332 GYLVTQDELDQTLEEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 GYLVTQDELDQTLEEFK 17 0 P19388;A0A087WVZ9;A0A0A0MQR7 P19388 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" 0 ; 242.79 4.67E-20 27512000 98226 87650 83589 87687 94767 102896 99223 108096 125012 125835 FALSE TRUE 94387.21933 85150.30782 98695.39173 92212.53658 97815.26662 104976.6276 100437.3208 105863.7798 110821.1619 117312.0834 0.804582244 0.725844307 0.841306274 0.786044659 0.833803849 0.894849231 0.856154949 0.902411557 0.944669625 1 16.8399921 2.090277662 0.318198247 1.013586649 0.741511329 0.835168717 0.030748592 0.57203404 0.163345751 0.042146141 0.05581236 123.1055584 -2.090277662 -0.27207532 QGS(ph)PSQSLVACECEASK ddPTM_BT-474_Pertuzumab_2h_R1 1 QGSPSQSLVACECEASK 17 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 QGS(0.999)PS(0.001)QSLVACECEASK 251.13 1.12E-21 150020000 175000 172550 140850 142300 155100 183590 172150 196390 212210 216700 TRUE FALSE 168160.8065 167629.0429 166304.7282 149644.1201 160088.9324 187302.3156 174256.8232 192334.4779 188120.8105 202022.716 0.832385634 0.829753437 0.823198161 0.740729177 0.792430354 0.927134925 0.862560541 0.952043818 0.931186424 1 17.624158 2.090307761 0.914217755 0.974284554 0.804098542 0.7304616 0.039756555 0.311721435 0.484149419 0.033029332 0.01698158 123.1140904 -2.090307761 -0.170186012 IADREDEYKK ddPTM_BT-474_Pertuzumab_2h_R1 4 IADREDEYKK 10 2 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 171.62 2.23E-06 4419360000 3944490 3477640 2684540 2657500 3180510 3412230 3699690 4059160 4926780 4142420 FALSE TRUE 3790334.97 3378461.112 3169696.095 2794653.893 3282813.993 3481227.629 3744967.913 3975336.928 4367512.589 3861850.204 0.981481614 0.874829663 0.820771373 0.723656731 0.850062488 0.901440358 0.969734121 1.02938662 1.130937856 1 21.88086077 2.090390775 1.600994405 1.062702204 0.844471325 0.639945503 0.066847702 0.248381193 1.209426355 0.043110119 0.02272723 123.1376256 -2.090390775 -0.218230879 DSPSVWAAVPGK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSPSVWAAVPGK 12 0 P07737;CON__P02584;I3L3D5 P07737 PFN1 Profilin-1 0 ;;; 177.06 5.53E-05 1247517000 2142350 2106650 1918230 2115590 2017450 1967310 2307840 2455930 2719030 2619360 FALSE TRUE 2058624.594 2046570.405 2264896.832 2224775.853 2082343.111 2007090.356 2336084.036 2405214.187 2410377.114 2441948.414 0.843025422 0.838089123 0.927495773 0.911065869 0.85273837 0.821921685 0.956647578 0.984957001 0.987071266 1 21.21960129 2.09045726 5.494958468 0.984777023 0.86905892 0.775053399 0.031022129 0.106918684 5.132427829 0.013021166 0.009489346 123.1564778 -2.09045726 -0.115718103 IDSRPPS(ph)PEPPKQEYWGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 IDSRPPSPEPPKQEYWGSK 19 2 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 IDS(0.289)RPPS(0.711)PEPPKQEYWGSK;IDSRPPS(1)PEPPKQEYWGSK;IDS(0.004)RPPS(0.996)PEPPKQEYWGSK;IDS(0.232)RPPS(0.762)PEPPKQEYWGS(0.006)K 158.29 1.86E-11 5161680000 2123930 1832170 1650560 1672320 1841130 1732820 2077840 2354560 2438850 2188260 TRUE FALSE 2040924.467 1779918.305 1948852.909 1758628.636 1900351.619 1767858.808 2103269.227 2305937.513 2162001.972 2040047.201 1.000430023 0.872488786 0.95529795 0.862052915 0.931523358 0.866577404 1.030990472 1.130335373 1.059780367 1 20.9601711 2.090765975 5.117111775 1.078565722 0.913614282 0.649050383 0.050566501 0.104607738 4.561175711 0.018141888 0.01314758 123.2440539 -2.090765975 -0.16495144 QEPVKPEEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEPVKPEEGR 10 1 P61586 P61586 RHOA Transforming protein RhoA 0 ; 126.76 0.00034101 1103470000 826400 971410 807890 1197510 862190 1025240 1152420 1605510 1381280 1137670 FALSE TRUE 794103.3744 943706.3379 953893.6944 1259313.635 889923.1244 1045971.055 1166523.661 1572355.657 1224482.885 1060614.598 0.748720012 0.8897731 0.899378244 1.187343298 0.839063621 0.986193343 1.099856313 1.48249483 1.154503142 1 20.01646908 2.091015026 3.552076574 1.27050534 0.929904103 0.3877535 0.15746607 0.19575375 4.829417594 0.065200157 0.044326295 123.3147498 -2.091015026 -0.340601237 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK 30 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;;; 326.55 1.13E-105 24564060000 7335430 7501190 6273762 5963558 6703500 6275854 5658808 2770875 7042517 5386174 FALSE TRUE 7048753.286 7287263.406 7407570.352 6271337.943 6919124.165 6402756.068 5728062.185 2713655.463 6243079.995 5021363.637 1.403752804 1.451251877 1.475210896 1.248931246 1.377937283 1.275103046 1.140738373 0.540422017 1.243303701 1 22.25964778 2.091467673 3.370725058 0.870676385 1.376819638 0.546781879 0.177868446 0.151905431 3.400021214 0.074130191 0.049700418 123.4433425 -2.091467673 0.506143253 LIVAYVDDLDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 LIVAYVDDLDRR 12 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 ;;; 202.16 2.24E-07 1094490000 775745 836759 666035 881735 770793 714810 768788 727718 728051 772380 FALSE TRUE 745428.0278 812895.4526 786402.3404 927241.449 795586.2569 729263.948 778196.6575 712690.369 645405.7027 720066.0146 1.035221789 1.128917955 1.092125339 1.287717279 1.104879609 1.012773736 1.080729602 0.989756987 0.896314629 1 19.45776965 2.091473737 1.132693891 0.954307386 1.1315916 0.482027459 0.071309166 0.432817106 1.036142384 0.053555893 0.026708628 123.4450663 -2.091473737 0.177284214 VVEAVNS(ph)DS(ph)DSEFGIPK ddPTM_BT-474_Pertuzumab_2h_R1 6 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 VVEAVNS(1)DS(1)DSEFGIPK;VVEAVNS(1)DS(0.999)DS(0.001)EFGIPK;VVEAVNS(1)DS(0.997)DS(0.003)EFGIPK;VVEAVNS(1)DS(0.993)DS(0.007)EFGIPK;VVEAVNS(1)DS(0.998)DS(0.002)EFGIPK;VVEAVNS(0.997)DS(0.992)DS(0.01)EFGIPK 208.4 7.61E-12 120837000 710079 700259 535070 658981 667039 641924 703923 807349 750448 716570 TRUE FALSE 682328.3276 680288.2989 631769.0516 692991.0884 688494.9152 654904.1431 712537.8202 790676.961 665260.2892 668036.0756 1.021394431 1.018340661 0.94571098 1.037355786 1.030625351 0.98034248 1.066615781 1.183584225 0.995844855 1 19.34956649 2.091630066 5.974329468 1.090883546 1.006523315 0.124248157 0.056761443 0.241791531 12.83448785 0.021236514 0.015552083 123.4895096 -2.091630066 -0.084360231 GPAAEEALNVFYYCTYEGAVDLDHVTDER ddPTM_BT-474_Pertuzumab_2h_R1 1 GPAAEEALNVFYYCTYEGAVDLDHVTDER 29 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7;H7C408 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 210.45 9.29E-26 31560000 15016 21445 15670 22120 22331 23607 17825 19029 19267 19137 FALSE TRUE 14429.15812 20833.4096 18501.91758 23261.61585 23049.2969 24084.34971 18043.14768 18636.0445 17079.89093 17840.83394 0.808771505 1.167737431 1.037054525 1.303841285 1.291940554 1.349956498 1.011339926 1.044572499 0.957348238 1 14.12289543 2.091859092 24.99999998 1.0110938 1.16832635 0.211161851 0.147403997 29.08242973 7902.499813 0.057282001 0.04230555 123.5546491 -2.091859092 0.15723255 HPDASVNFSEFSK ddPTM_BT-474_Pertuzumab_2h_R1 5 HPDASVNFSEFSK 13 0 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;;;; 201.48 1.01E-07 10230100000 8773700 8658940 8150150 8453880 9093400 8575820 8227120 7022350 9420640 9213730 FALSE TRUE 8430814.104 8411995.509 9623063.404 8890185.76 9385897.469 8749228.956 8327805.956 6877336.018 8351248.442 8589675.86 0.9815055 0.979314662 1.120305767 1.03498501 1.092695187 1.018574984 0.969513412 0.800651402 0.972242559 1 23.03417226 2.09192948 3.702283411 0.898946831 1.04133353 0.360010274 0.065361621 0.191105589 5.071736177 0.026880191 0.01847999 123.5746759 -2.09192948 0.142386699 KLEDNPK ddPTM_BT-474_Pertuzumab_2h_R1 6 KLEDNPK 7 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;;;; 119.27 0.0077261 25429100000 17095930 15235170 13183380 13067110 14204080 15227370 16991850 19079160 21146210 19906390 FALSE TRUE 16427802.16 14800677.87 15565910.03 13741505.11 14660967.13 15535277.85 17199801.34 18685168.68 18745780.89 18558112.47 0.885208675 0.797531424 0.838765799 0.740458122 0.79000314 0.83711519 0.926807689 1.006846397 1.010112473 1 24.14554665 2.092264213 2.079948855 1.007431421 0.807361721 0.860265549 0.03495505 0.110865696 0.925583173 0.01889984 0.010840168 123.6699578 -2.092264213 -0.2000697 YNLDAS(ph)EEEDSNK ddPTM_BT-474_Pertuzumab_2h_R1 6 YNLDASEEEDSNK 13 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNK;YNLDAS(1)EEEDSNK;Y(0.001)NLDAS(0.999)EEEDSNK;YNLDAS(1)EEEDSNK;YNLDAS(1)EEEDSNK;YNLDAS(1)EEEDSNK 338.92 9.17E-63 4742410000 4143410 3469130 4191130 4437000 4193550 3736700 5205820 5967490 6354540 5966250 TRUE FALSE 3981480.956 3370193.809 4948560.422 4665994.102 4328439.344 3812258.634 5269530.382 5844259.246 5633199.26 5562150.573 0.715816824 0.605915601 0.889684728 0.838883098 0.778195284 0.685392922 0.947390818 1.050719352 1.0127736 1 22.40721137 2.092312433 4.75167956 1.020897556 0.757736957 0.731512235 0.075131005 0.114346559 4.476820529 0.0313527 0.022555394 123.6836899 -2.092312433 -0.263160598 AAQGQAGS(ph)PDK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAQGQAGSPDK 11 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 AAQGQAGS(1)PDK 116.63 0.00082196 0 89195 84906 87381 92908 79094 73975 110320 127420 114450 144160 TRUE FALSE 85709.16079 82484.56401 103172.6905 97702.99301 81638.13034 75470.82518 111670.1292 124788.7325 101458.1158 134395.9148 0.637736355 0.61374309 0.767677281 0.72697889 0.607445029 0.561555947 0.830904193 0.928515816 0.754919641 1 17.03612976 2.092400856 5.879997923 0.884873843 0.658043729 0.66370086 0.079573883 0.129217631 6.690498141 0.030579272 0.022379305 123.7088745 -2.092400856 -0.226830114 KLEDGPK ddPTM_BT-474_Pertuzumab_2h_R1 10 KLEDGPK 7 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;;;;; 95.815 0.021148 1.11282E+11 79592380 66885430 61570720 57448280 66779730 66284000 78842700 88459500 96539500 92003500 FALSE TRUE 76481821.8 64977923.02 72697918.74 60413192.62 68927760.66 67624307.89 79807600.55 86632780.41 85580740.69 85772021 0.8916873 0.757565489 0.84757148 0.704346148 0.80361591 0.788419197 0.930461934 1.010035434 0.997769899 1 26.35400378 2.09243902 2.939636284 1.000664438 0.794248806 0.793396775 0.047348202 0.106525055 1.822932996 0.020438612 0.013160079 123.7197461 -2.09243902 -0.206415632 LHVGEESK ddPTM_BT-474_Pertuzumab_2h_R1 4 LHVGEESK 8 0 P78356;P78356-2 P78356 PIP4K2B Phosphatidylinositol 5-phosphate 4-kinase type-2 beta 0 ;;; 136.75 0.00077748 1148680000 2114780 2153890 2168050 2315680 2278320 2062970 2626750 2977850 2924520 3062950 FALSE TRUE 2032132.06 2092463.166 2559864.863 2435192.522 2351604.232 2104684.667 2658896.952 2916356.357 2592540.75 2855493.668 0.711657001 0.732785083 0.896470159 0.852809638 0.82353684 0.737065079 0.931151409 1.021314244 0.907913325 1 21.44530875 2.092519656 5.4010123 0.978209617 0.79917158 0.666471058 0.060287212 0.12954378 6.015366 0.024368869 0.017744681 123.7427194 -2.092519656 -0.179038037 AAQGQAGS(ph)PDKSK ddPTM_BT-474_Pertuzumab_2h_R1 6 AAQGQAGSPDKSK 13 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 AAQGQAGS(0.996)PDKS(0.004)K;AAQGQAGS(0.998)PDKS(0.002)K;AAQGQAGS(0.989)PDKS(0.011)K;AAQGQAGS(0.844)PDKS(0.156)K;AAQGQAGS(1)PDKSK;AAQGQAGS(0.999)PDKS(0.001)K 264.92 7.38E-24 2625887000 2560260 1994610 1804840 1620210 1812110 1750180 2392130 2758380 2792550 2777140 TRUE FALSE 2460202.209 1937725.676 2131014.736 1703829.232 1870398.164 1785569.839 2421405.603 2701418.489 2475551.431 2589041.834 0.950236561 0.748433513 0.823090113 0.658092585 0.722428714 0.689664344 0.935251633 1.043404727 0.956165095 1 21.30398685 2.092625231 5.023396894 1.001303964 0.761122556 0.656476296 0.078256033 0.121533447 5.12801733 0.030590808 0.022141641 123.7728043 -2.092625231 -0.240181408 LTFLEEDDKDLYILWK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTFLEEDDKDLYILWK 16 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 221.13 9.90E-15 780760000 1408090 1298960 1277320 1247790 1474540 1360680 1726940 1941790 2101600 2153500 FALSE TRUE 1353060.286 1261914.933 1508160.138 1312188.591 1521969.918 1388193.882 1748074.808 1901691.358 1863035.179 2007641.527 0.67395512 0.628555903 0.751209874 0.653597056 0.758088482 0.691455055 0.870710625 0.94722655 0.927972028 1 20.93707026 2.092781462 1.85221842 0.96091155 0.688264607 0.892857907 0.042012655 0.100387748 0.659672024 0.022635478 0.012501276 123.8173379 -2.092781462 -0.272646943 SVDVILDDDLVDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVDVILDDDLVDK 13 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ;;; 320.96 1.14E-50 630079000 1147580 1034250 967510 953070 1068520 1097410 1141480 1283990 1402330 1345280 FALSE TRUE 1102731.305 1004754.203 1142360.579 1002258.057 1102889.916 1119600.382 1155449.774 1257475.158 1243143.377 1254162.987 0.879256776 0.801135269 0.910854961 0.799144981 0.879383244 0.892707243 0.921291559 1.002640941 0.991213574 1 20.25829342 2.092845099 1.29718833 1.005312006 0.85021277 0.780862701 0.032994433 0.181683402 0.574791113 0.020834006 0.010508985 123.8354822 -2.092845099 -0.155099236 DKS(ph)FDDEESVDGNRPSSAASAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKSFDDEESVDGNRPSSAASAFK 23 2 E7ERI8;E7EW49;O75122-3 E7ERI8 CLASP2 CLIP-associating protein 2 1 DKS(1)FDDEESVDGNRPSSAASAFK 164.41 7.47E-12 438070000 368060 251700 198170 227470 392810 279230 407690 528760 552710 460350 TRUE FALSE 353675.8083 244521.7624 233983.7273 239209.754 405445.0904 284876.2219 412679.4322 517840.9212 489968.6779 429170.0845 0.824092408 0.569754909 0.54520046 0.557377512 0.944718901 0.663783969 0.961575485 1.206610013 1.141665497 1 18.71118999 2.093277771 2.890948012 1.1350657 0.675529829 0.702831338 0.127594562 0.140408735 2.323019933 0.05968402 0.038256421 123.9589164 -2.093277771 -0.45953587 RDVQEIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDVQEIFR 8 1 O00148;O00148-2;O00148-3;K7EQN7;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 125.97 0.001987 161090000 127100 191200 163000 185100 143100 136230 142680 84378 76798 120660 FALSE TRUE 122132.7915 185747.1632 192457.7259 194653.0332 147702.9415 138984.6639 144426.1605 82635.56481 68080.213 112487.5907 1.085744576 1.651268038 1.710924064 1.730440059 1.313059872 1.235555523 1.283929717 0.734619386 0.605224208 1 16.77940633 2.093501915 1.26329538 0.737530475 1.531235995 0.652065501 0.218982741 0.264203956 0.791664498 0.153368406 0.077134184 124.0229095 -2.093501915 0.793705521 NSENVDELQLPEGFRPDFRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSENVDELQLPEGFRPDFRPK 21 2 Q8IWV8;Q8IWV8-4 Q8IWV8 UBR2 E3 ubiquitin-protein ligase UBR2 0 ; 162.65 1.03E-11 454130000 193035 185563 159688 153393 161464 202655 184155 204135 245668 218737 FALSE TRUE 185490.9788 180270.9249 188547.1738 161309.6311 166657.6362 206752.8229 186408.744 199919.5409 217780.7986 203921.7482 0.909618422 0.884020104 0.924605519 0.791036918 0.817262689 1.013883143 0.914118997 0.980373809 1.067962591 1 17.63765612 2.09381832 1.087240819 1.022089204 0.871829666 0.534972155 0.056372953 0.422750908 0.931056329 0.043429001 0.021720786 124.1132992 -2.09381832 -0.150259537 TEVNYTQLVDLHAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TEVNYTQLVDLHAR 14 0 A0A087X2I2;A0A087WT12;P36969-2;P36969;K7ERP4;K7EKX7;K7ENB4;K7EJ20;A0A087X247;R4GNE4 A0A087X2I2 GPX4 "Glutathione peroxidase;Phospholipid hydroperoxide glutathione peroxidase, mitochondrial" 0 ;; 151.72 6.86E-06 599720000 664770 638090 514410 587800 582980 611520 569970 521940 643770 677250 FALSE TRUE 638790.0535 619892.298 607375.33 618136.4284 601732.0811 623885.3534 576945.4634 511161.7566 570691.9285 631379.2543 1.011737477 0.981806567 0.961981766 0.979025561 0.953043796 0.988130904 0.913785905 0.809595426 0.903881343 1 19.26814733 2.093835717 4.735409425 0.878502553 0.977004556 0.318185376 0.047378951 0.172791942 6.698653978 0.017698999 0.012734056 124.1182709 -2.093835717 0.098502003 YKDDPVDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 YKDDPVDLR 9 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 94.801 0.0077301 6985740000 12178600 11542900 9554000 10907700 10952100 11354600 11817700 13237000 13755900 13011600 FALSE TRUE 11702646.85 11213707.79 11280620.33 11470647.7 11304384.24 11584197.79 11962328.55 12963651.32 12194387.9 12130312.74 0.964744034 0.924436825 0.929952967 0.945618464 0.931912019 0.954979318 0.986151701 1.068698854 1.005282235 1 23.53211341 2.093991771 3.013380945 1.031653514 0.939697176 0.751687703 0.021206844 0.105282 1.893879442 0.009048197 0.005880392 124.1628781 -2.093991771 -0.091956338 ESESVDK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESESVDK 7 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4;D6RBQ9 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 100.39 0.022866 576520000 1634800 1659600 1581100 1851100 1388900 1549100 1994400 2326500 2362800 2226200 FALSE TRUE 1570910.209 1612269.833 1866839.941 1946635.493 1433575.23 1580423.863 2018808.064 2278456.962 2094584.85 2075417.491 0.75691287 0.776841209 0.899500919 0.937948871 0.690740651 0.761496841 0.972723836 1.097830664 1.009235423 1 20.98497015 2.094158486 4.578920831 1.044277141 0.808694077 0.689678594 0.071659579 0.123532624 4.56446681 0.030096789 0.021564567 124.2105503 -2.094158486 -0.235583064 VQEKPDS(ph)PGGSTQIQR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQEKPDSPGGSTQIQR 16 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 VQEKPDS(0.996)PGGS(0.003)T(0.001)QIQR;VQEKPDS(0.986)PGGS(0.005)T(0.009)QIQR;VQEKPDS(0.835)PGGS(0.11)T(0.055)QIQR;VQEKPDS(1)PGGSTQIQR 210.39 2.58E-11 3423010000 3027960 2856040 2494770 2573050 2683970 2952060 3099780 3368970 3884740 3599640 TRUE FALSE 2909623.976 2774588.536 2945630.435 2705845.419 2770302.333 3011752.676 3137716.035 3299399.592 3443760.601 3355833.177 0.867034749 0.826795728 0.877764263 0.806311064 0.825518489 0.897467936 0.93500358 0.983183436 1.026201369 1 21.67823957 2.094337419 1.365745524 1.010281136 0.840192249 0.907919486 0.022532502 0.117223187 0.412392383 0.015018725 0.007650737 124.2617367 -2.094337419 -0.170088887 ELS(ph)PAGSISK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELSPAGSISK 10 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK 168.58 5.13E-06 4819740000 8095200 7484200 6660550 7104330 6991660 7130100 8052800 8772800 9410500 8936400 TRUE FALSE 7778830.634 7270757.944 7864259.548 7470985.323 7216553.094 7274275.507 8151352.575 8591638.614 8342259.492 8331129.668 0.933706585 0.872721736 0.943960767 0.896755377 0.866215433 0.873143955 0.978421043 1.031269342 1.001335932 1 22.9900807 2.094371708 4.516019824 1.01240282 0.897547309 0.808843382 0.025318239 0.085122689 3.082026369 0.010084812 0.007212736 124.271548 -2.094371708 -0.114855511 KISELDAFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KISELDAFLK 10 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 91.914 0.013982 0 422940 414050 378050 358350 429920 390250 455250 496760 533850 519070 FALSE TRUE 406411.0372 402241.6994 446372.0447 376844.4864 443748.7672 398141.1224 460821.4857 486501.7324 473249.5861 483912.9266 0.839843317 0.831227432 0.922422238 0.77874441 0.917001268 0.822753641 0.952281827 1.005349735 0.97796434 1 18.88438795 2.094434513 4.364689543 0.991838514 0.854140715 0.720129696 0.0408052 0.106118171 3.655804071 0.014974704 0.010656235 124.2895207 -2.094434513 -0.137697799 GGIHTADTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGIHTADTK 9 0 O00442;O00442-2 O00442 RTCA RNA 3-terminal phosphate cyclase 0 86.136 0.014343 151010000 143250 158110 130290 146300 154400 137250 161200 171610 187390 167580 FALSE TRUE 137651.6316 153600.8576 153836.3013 153850.5605 159366.4162 140025.289 163172.8138 168066.1935 166118.2728 156229.6573 0.881085154 0.983173491 0.984680527 0.984771798 1.020077871 0.896278539 1.044441988 1.075763696 1.06329538 1 17.25330882 2.094444134 8.982111246 1.056076154 0.964775322 0.47825603 0.044133562 0.224724705 19.21723654 0.016055424 0.011850771 124.2922741 -2.094444134 -0.091300832 QDEDKDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDEDKDKR 8 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 ; 109.42 0.0020371 112569000 493950 397740 344800 315630 399040 367830 418980 471140 427250 460980 FALSE TRUE 474645.8879 386396.8446 407113.03 331919.7021 411875.484 375267.7746 424107.6026 461410.7944 378750.3712 429757.414 1.104450726 0.899104546 0.947308916 0.772342003 0.958390642 0.873208378 0.986853487 1.073654065 0.881312012 1 18.713163 2.094566763 7.4036048 1.002249776 0.920317351 0.084853615 0.089662447 0.426087554 28.82134571 0.033124088 0.024407496 124.3273746 -2.094566763 -0.081932425 AGLESGAEPGDGDS(ph)DTTK ddPTM_BT-474_Pertuzumab_2h_R1 6 AGLESGAEPGDGDSDTTK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK 472.81 7.77E-215 6488760000 7447070 6354450 6006050 5668000 5915200 6531060 7265360 8346530 8913210 8382770 TRUE FALSE 7156030.271 6173227.308 7091476.839 5960526.159 6105467.78 6663122.508 7354275.649 8174171.239 7901419.768 7814997.521 0.915679148 0.789920571 0.907418949 0.762703525 0.781250124 0.852607117 0.941046447 1.045959543 1.011058512 1 22.89781398 2.09459628 2.634881372 1.021665537 0.828822402 0.746911066 0.048497863 0.129280407 1.768216163 0.022501364 0.014010456 124.335825 -2.09459628 -0.192843135 DVDFELIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVDFELIK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 107.9 0.0091081 315050000 678360 634520 639710 609810 627260 566460 745350 776720 872500 906710 FALSE TRUE 651848.9412 616424.1109 755319.8273 641282.3672 647436.3876 577914.2093 754471.8163 760680.4606 773457.4578 845297.7241 0.771147162 0.729239052 0.893554786 0.758646745 0.765927045 0.683681256 0.892551577 0.899896497 0.915011878 1 19.68910004 2.094678247 6.915302103 0.919565687 0.770905758 0.661957835 0.056122968 0.144557828 8.996673295 0.021239717 0.015631514 124.3592938 -2.094678247 -0.14865993 DS(ph)SKGEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSKGEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 45 2 Q12906-7;Q12906-4;Q12906-6 Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 DS(0.268)S(0.268)KGEDS(0.231)AEET(0.231)EAKPAVVAPAPVVEAVS(0.001)TPSAAFPSDATAENVK 71.581 0.00044742 327040000 216920 145870 142130 113550 149510 140750 188740 210780 261460 184820 TRUE FALSE 208442.5266 141709.9304 167816.0527 119410.3291 154319.1249 143596.0614 191049.8566 206427.3193 231780.1569 172301.9768 1.20975122 0.822450984 0.973964755 0.693029362 0.895631773 0.833397644 1.108808269 1.198055433 1.345197317 1 17.39457973 2.094919647 4.120010554 1.193558577 0.894550941 0.427690378 0.147210776 0.188626101 5.947976635 0.057064037 0.040218477 124.4284374 -2.094919647 -0.299007636 HS(ph)SNPPLESHVGWVMDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.576)S(0.424)NPPLESHVGWVMDSR;HS(0.58)S(0.42)NPPLESHVGWVMDSR 198.6 2.87E-15 537220000 214841 236850 177754 172080 191429 207880 157272 90605 185392 197014 TRUE FALSE 206444.7762 230095.2699 209878.1019 180961.0694 197586.4876 212083.476 159196.7418 88733.97509 164347.0774 183670.0663 1.12399794 1.252764125 1.142690838 0.985250744 1.075768587 1.154698097 0.866753876 0.483116149 0.894795111 1 17.486757 2.094924959 4.503553024 0.721918765 1.11966044 0.515934009 0.143510951 0.136697512 4.922607974 0.05602785 0.040064747 124.4299592 -2.094924959 0.397741675 RHS(ph)DENDGGQPHKR ddPTM_BT-474_Pertuzumab_2h_R1 6 RHSDENDGGQPHKR 14 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR 129.77 3.13E-05 8503036000 706379.4 771234.5 542826.6 772842.7 856056 674012.6 555383.3 199209 639972.7 526072.1 TRUE FALSE 678773.3121 749239.6472 640927.4417 812729.2044 883591.8187 687641.5966 562180.247 195095.2645 567325.6821 490440.7681 1.384006706 1.52768631 1.30683965 1.657140387 1.801627997 1.402088981 1.146275521 0.397795773 1.156766972 1 18.90371938 2.094963781 3.358426983 0.782353081 1.526311954 0.62312674 0.229029679 0.135652142 3.010810702 0.096979294 0.065145799 124.4410828 -2.094963781 0.743958873 ERDQRPS(ph)SPIR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERDQRPSSPIR 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.957)S(0.043)PIR;ERDQRPS(0.558)S(0.442)PIR;ERDQRPS(0.5)S(0.5)PIR;ERDQRPS(0.5)S(0.5)PIR 154.72 2.51E-05 2993070000 2124489 2268311 1884731 2290230 2035629 2073828 2090964 2087116 2140445 2207502 TRUE FALSE 2041461.621 2203620.991 2225343.817 2408429.045 2101106.855 2115762.223 2116553.843 2044016.325 1897470.657 2057985.923 0.991970644 1.070765823 1.081321204 1.170284509 1.020952977 1.028074196 1.028458853 0.993212005 0.92200371 1 20.97280168 2.095083809 1.132875552 0.965668354 1.072857478 0.423681942 0.047664621 0.477858387 1.144997034 0.035698972 0.017854552 124.4754798 -2.095083809 0.107189123 KQEFLEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQEFLEQK 8 1 Q9BY43;Q9BY43-2;H0YI89;E9PQI5;E9PQ80;E9PSI1 Q9BY43 CHMP4A Charged multivesicular body protein 4a 0 107.24 0.0064785 388920000 691370 634480 576800 532350 611540 547910 697670 730870 826940 812870 FALSE TRUE 664350.4961 616385.2516 681040.5908 559824.6473 631210.7395 558989.1156 706208.2942 715777.2791 733069.238 757813.5909 0.876667434 0.813373182 0.898691445 0.738736615 0.832936684 0.73763406 0.931902387 0.944529483 0.967347705 1 19.53148349 2.095429792 6.771079895 0.958012959 0.817452282 0.669866958 0.050019789 0.131216472 7.918231091 0.018410543 0.0135435 124.5746833 -2.095429792 -0.140560677 YQPLASTAS(ph)DNDFVTPEPR ddPTM_BT-474_Pertuzumab_2h_R1 4 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 YQPLAST(0.03)AS(0.969)DNDFVTPEPR;YQPLASTAS(1)DNDFVTPEPR;YQPLAS(0.016)T(0.063)AS(0.921)DNDFVTPEPR;YQPLAST(0.001)AS(0.999)DNDFVTPEPR 348.63 1.15E-90 764120000 282255 307811 292272 341361 351732 397808 290456 318055 300616 311038 TRUE FALSE 271224.1626 299032.5317 345092.052 358978.6821 363045.7792 405851.9503 294010.6874 311487.0531 266491.332 289971.1192 0.935348883 1.031249362 1.190091113 1.237980814 1.252006683 1.399628871 1.013930933 1.074200265 0.919027152 1 18.14554969 2.095592499 24.80840608 1.015185636 1.177661007 0.317915997 0.123168621 19.60074396 5071.408064 0.050081889 0.036987925 124.6213636 -2.095592499 0.162475371 SS(ph)PVRPSSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPVRPSSEK 10 1 B3KV94;A0A3B3ISE6;A0A3B3ITA8;A0A3B3ITJ7;A0A3B3ITE7;A0A3B3IT25;A0A3B3IS40;Q9UGL1;Q9UGL1-2 B3KV94 KDM5B Lysine-specific demethylase 5B 1 S(0.173)S(0.826)PVRPS(0.001)S(0.001)EK;S(0.125)S(0.875)PVRPSSEK 147.33 1.64E-05 1112640000 1617520 1408830 1481330 1707090 1515410 1469730 1820700 2017310 2165370 2047500 TRUE FALSE 1554305.53 1368651.548 1749039.283 1795193.119 1564154.539 1499448.948 1842982.271 1975651.844 1919566.276 1908821.001 0.814275162 0.717014087 0.91629298 0.940472217 0.819434896 0.785536699 0.96550817 1.035011582 1.005629273 1 20.86425039 2.09564101 4.859945776 1.013678938 0.835615186 0.66257039 0.059807537 0.135951086 5.427666102 0.025214177 0.018204284 124.6352846 -2.09564101 -0.178063752 DAALAVAEAMADKAELEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAALAVAEAMADKAELEK 18 1 P46060;H0Y4Q3 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ; 187.31 3.97E-14 254560000 414480 355750 335020 320840 387250 422200 403770 463140 577230 496660 FALSE TRUE 398281.6634 345604.3583 395565.5665 337398.5908 399706.2479 430737.1733 408711.458 453575.9972 511705.2703 463020.7758 0.860180977 0.746412205 0.85431494 0.728689961 0.863257696 0.930276125 0.882706521 0.979601825 1.105145378 1 18.8207174 2.095896154 0.877845164 1.046790936 0.799476936 0.728310512 0.056465213 0.296474086 0.425482383 0.044457206 0.023260358 124.7085283 -2.095896154 -0.247314001 S(ph)SPGGQDEGGFMAQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPGGQDEGGFMAQGK 16 0 F5GZ78;A0A1B0GTU4;P49023;A0A1B0GV30 F5GZ78 PXN Paxillin 1 S(0.5)S(0.5)PGGQDEGGFMAQGK;S(0.691)S(0.309)PGGQDEGGFMAQGK 402.24 1.03E-139 1069960000 1700970 1731760 1512400 1441830 1572230 1784890 1751730 1881810 2200570 2041510 TRUE FALSE 1634494.212 1682371.9 1785724.323 1516243.019 1622802.206 1820981.699 1773168.196 1842949.966 1950770.519 1903236.709 0.858797124 0.883953053 0.938256558 0.796665497 0.852653902 0.956781513 0.931659308 0.968324096 1.024975249 1 20.86002357 2.095933261 1.073149981 1.005689319 0.869391335 0.6696418 0.039132646 0.329545665 0.706947847 0.030484738 0.015283572 124.7191841 -2.095933261 -0.136297984 KTGS(ph)PEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTGSPEIK 8 1 Q9BZ95-3;Q9BZ95-4;Q9BZ95-2;Q9BZ95-5;Q9BZ95;E9PKA2 Q9BZ95-3 WHSC1L1 Histone-lysine N-methyltransferase NSD3 1 KT(0.414)GS(0.586)PEIK 56.956 0.070027 246390000 629360 464650 471900 429240 523190 581730 580200 661890 809380 703670 TRUE FALSE 604763.9154 451398.6369 557182.8274 451393.1278 540018.8815 593492.9792 587300.6612 648221.7402 717502.5756 656009.8041 0.921882435 0.688097394 0.849351372 0.688088997 0.823187212 0.904701386 0.895262018 0.988128129 1.09373758 1 19.32335785 2.09595871 1.07295455 1.043455553 0.78473502 0.650507312 0.072866552 0.292936167 0.628181425 0.051432473 0.025786578 124.7264925 -2.09595871 -0.258720533 EVYELLDS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EVYELLDSPGK 11 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 EVYELLDS(1)PGK;EVYELLDS(1)PGK;EVYELLDS(1)PGK;EVYELLDS(1)PGK 269.14 1.51E-21 2277450000 5503100 4563300 5586600 4937800 4946200 5079300 6023000 6741600 6894600 7340200 TRUE FALSE 5288032.768 4433159.152 6596222.893 5192640.45 5105299.015 5182006.926 6096711.276 6602383.604 6111953.913 6843041.716 0.772760563 0.647834594 0.963931416 0.758820517 0.746056977 0.757266599 0.890935863 0.964831705 0.893163328 1 22.70620631 2.095971809 3.750999239 0.945300044 0.775393992 0.525098648 0.077253297 0.188149825 5.085312301 0.031591501 0.021848338 124.7302545 -2.095971809 -0.169906052 SREQMSSQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SREQMSSQPK 10 1 Q6FI81-3;Q6FI81;Q6FI81-2;H3BTZ8 Q6FI81-3 CIAPIN1 Anamorsin 0 ; 126.71 0.003409 67068000 158080 182748 142533 146409 158213 142548 198972 224910 234620 241610 FALSE TRUE 151902.0588 177536.206 168291.8837 153965.186 163302.0648 145430.4182 201407.0789 220265.5299 207986.9212 225245.5395 0.674384315 0.788189663 0.747148574 0.683543774 0.724995777 0.645652822 0.89416678 0.977890752 0.923378646 1 17.78113901 2.096216193 4.842728805 0.958372668 0.715908282 0.886469774 0.04223293 0.064983868 2.577318454 0.016395901 0.011835117 124.8004621 -2.096216193 -0.242464386 ADFTVVAGDEGSSTTGGS(ph)SEENKGPSGSAVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ADFTVVAGDEGSSTTGGSSEENKGPSGSAVSR 32 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 ADFTVVAGDEGSSTTGGS(0.585)S(0.411)EENKGPS(0.003)GSAVSR;ADFTVVAGDEGS(0.007)S(0.007)T(0.007)T(0.204)GGS(0.751)S(0.025)EENKGPSGSAVSR;ADFTVVAGDEGS(0.001)S(0.002)T(0.002)T(0.016)GGS(0.49)S(0.49)EENKGPSGSAVSR 171.93 1.35E-14 245680000 150750 135202 131475 139291 136400 142383 155964 180179 177624 179348 TRUE FALSE 144858.5233 131346.1713 155235.4571 146479.8252 140787.4299 145262.0818 157872.7341 176458.2407 157460.8682 167200.6002 0.866375618 0.785560406 0.928438396 0.876072365 0.84202706 0.868789237 0.944211527 1.055368464 0.941748223 1 17.3512205 2.096313057 3.397540157 1.00459409 0.860305754 0.686968835 0.042092606 0.126919503 2.876720115 0.017635816 0.011898174 124.8283003 -2.096313057 -0.144288336 ESEKS(ph)LENETLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESEKSLENETLNK 13 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ES(0.024)EKS(0.976)LENETLNK 86.8 0.0052448 215530000 314160 295300 299920 304540 298190 306120 376780 431230 489600 413140 TRUE FALSE 301882.2799 286878.3331 354122.2157 320257.3459 307781.5522 312309.9561 381391.1463 422324.9498 434022.6606 385157.6598 0.783788852 0.744833514 0.919421454 0.831496759 0.799105365 0.810862638 0.990220853 1.096498899 1.126870126 1 18.55508959 2.096606162 3.046797751 1.080510658 0.815557202 0.840203182 0.051803048 0.094561434 1.738839493 0.023444328 0.015326185 124.9125751 -2.096606162 -0.264953456 SFS(ph)PTMK ddPTM_BT-474_Pertuzumab_2h_R1 6 SFSPTMK 7 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 SFS(0.996)PT(0.004)MK;SFS(0.864)PT(0.136)MK;SFS(0.998)PT(0.002)MK;SFS(0.972)PT(0.028)MK;S(0.004)FS(0.962)PT(0.035)MK;S(0.015)FS(0.984)PT(0.001)MK 181.41 0.00070524 4116290000 4542030 4228900 3997730 3922980 4320010 4564920 4976700 5673660 6364340 5968230 TRUE FALSE 4364522.446 4108295.913 4720208.74 4125445.468 4458967.045 4657225.81 5037606.343 5556496.938 5641886.805 5563996.466 0.784422217 0.738371409 0.848348623 0.741453646 0.801396455 0.837028894 0.90539352 0.998652133 1.013998991 1 22.40769007 2.096904416 1.392787899 1.014601835 0.78024538 0.915657954 0.029442646 0.103609321 0.379683551 0.018394289 0.009427497 124.9983892 -2.096904416 -0.234356455 LKPEYDIMCK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKPEYDIMCK 10 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 130.56 0.00024927 2240600000 5454600 5333800 4250000 4486200 4712800 4198300 5534800 5683400 6624200 6285100 FALSE TRUE 5241428.202 5181685.246 5018069.541 4717733.32 4864391.492 4283192.502 5602536.538 5566035.804 5872248.587 5859404.579 0.894532564 0.884336484 0.856412878 0.805155755 0.83018529 0.730994497 0.956161409 0.949931982 1.002192033 1 22.48232264 2.096929604 9.098570544 0.972121992 0.835605821 0.708615 0.045126266 0.168956302 14.30447484 0.017872713 0.013193148 125.005639 -2.096929604 -0.136516172 LDSEDKDK ddPTM_BT-474_Pertuzumab_2h_R1 6 LDSEDKDK 8 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 107.15 0.0037006 31660600000 43188400 31368000 31435400 27223200 34171700 31169600 42217800 48101300 52822400 49085100 FALSE TRUE 41500549.58 30473415.35 37116476.06 28628192.61 35270863.76 31799870.67 42734474.07 47107991.35 46826222.6 45760522.46 0.90690725 0.665932418 0.811102541 0.625608955 0.770770565 0.69491931 0.933872075 1.029446099 1.023288636 1 25.44760019 2.097052344 3.962460485 1.013754444 0.741144302 0.73557679 0.074682486 0.103643291 3.06272855 0.028280401 0.019805555 125.0409729 -2.097052344 -0.272610142 SPLEHSS(ph)PEKEAPSPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLEHSSPEKEAPSPEK 17 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 S(0.003)PLEHS(0.167)S(0.831)PEKEAPSPEK 106.39 0.00045626 158190000 178870 146500 113350 113760 145690 154500 150210 169150 212010 167560 TRUE FALSE 171879.5626 142321.9634 133834.8665 119631.1672 150376.2512 157624.0959 152048.3149 165656.9934 187943.5136 156211.012 1.100303753 0.911087904 0.856756926 0.765830563 0.962648211 1.009045994 0.97335209 1.06046937 1.203138699 1 17.25313663 2.097106162 1.246659995 1.097615136 0.91091028 0.351715196 0.094568817 0.499815137 1.458310105 0.067765818 0.034133751 125.0564689 -2.097106162 -0.186704856 T(ph)PSSEEISPTKFPGLYR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSSEEISPTKFPGLYR 17 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.804)PS(0.18)S(0.016)EEISPTKFPGLYR 235.35 2.36E-19 149120000 209790 216120 139730 177410 185250 198010 212500 234740 250960 261360 TRUE FALSE 201591.1749 209956.4692 164982.3193 186566.1514 191208.7345 202013.8979 215100.6386 229892.537 222472.0729 243657.8544 0.827353484 0.861685619 0.677106509 0.765689051 0.784742749 0.829088389 0.882797885 0.943505546 0.913051104 1 17.8944972 2.09722403 1.271204634 0.959383274 0.77939111 0.703840438 0.048252861 0.262966875 0.798676754 0.034642083 0.017491168 125.0904139 -2.09722403 -0.179992164 APKPPTDGSTS(ph)PTSTPSEDQEALGK ddPTM_BT-474_Pertuzumab_2h_R1 2 APKPPTDGSTSPTSTPSEDQEALGK 25 1 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;S4R3G4;F6SRV7;Q8NHM5-5;F8WBN2 Q8NHM5-4;F8WBN2 KDM2B Lysine-specific demethylase 2B 1 APKPPTDGS(0.011)T(0.097)S(0.889)PT(0.003)STPSEDQEALGK;APKPPTDGS(0.011)T(0.098)S(0.887)PT(0.003)STPSEDQEALGK 207.9 1.84E-25 1424520000 856170 761410 642120 616270 758490 697290 838190 960590 1014240 852250 TRUE FALSE 822709.9299 739695.3323 758165.3679 648075.7686 782887.5197 711389.6816 848448.02 940753.4808 899107.7272 794526.3484 1.03547218 0.930989053 0.954235652 0.815675616 0.985351236 0.895363235 1.067866436 1.184043151 1.131627326 1 19.59973554 2.09740309 4.643184773 1.125867647 0.934067116 0.55566491 0.069611843 0.13245685 4.945806811 0.0262578 0.018869468 125.1419995 -2.09740309 -0.191800531 SS(ph)PVESLKK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPVESLKK 9 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.028)S(0.972)PVESLKK;S(0.193)S(0.807)PVESLKK;S(0.393)S(0.607)PVESLKK 167.11 3.69E-05 8936900000 10534700 9893500 8582100 7894400 8558000 8474000 10761200 11899800 13135400 11908500 TRUE FALSE 10122992.28 9611347.067 10133076.38 8301830.93 8833275.842 8645350.086 10892898.78 11654064.97 11644324.46 11101926.69 0.911823016 0.865736852 0.912731336 0.7477829 0.795652511 0.7787252 0.981171925 1.049733555 1.048856184 1 23.40430674 2.097762031 4.853890989 1.033321618 0.835062132 0.754255699 0.052124056 0.106167476 4.203412369 0.021879481 0.015804137 125.2454713 -2.097762031 -0.198259486 LQPTWNDLGDKYNSMEDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQPTWNDLGDKYNSMEDAK 19 1 Q8NBS9 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 218.69 3.01E-19 1050580000 867120 840490 699490 706490 719950 850820 845030 1033090 1098080 942450 FALSE TRUE 833231.9917 816520.0481 825903.4031 742952.0336 743107.8456 868024.1633 855371.7299 1011756.33 973430.5619 878617.0221 0.948344923 0.929324185 0.940003872 0.845592579 0.845769917 0.987943713 0.973543317 1.151532812 1.10791225 1 19.74487492 2.097817149 2.09404928 1.098469604 0.906558518 0.650433186 0.055163911 0.178404878 1.513845571 0.029122007 0.016833232 125.2613677 -2.097817149 -0.191911087 LAGLEQAILS(ph)PGQNSGNYFAPIPLEDHAENKVDILEMLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAGLEQAILSPGQNSGNYFAPIPLEDHAENKVDILEMLQK 40 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 LAGLEQAILS(1)PGQNSGNYFAPIPLEDHAENKVDILEMLQK 307.24 1.13E-94 661690000 576810 528650 526960 539830 575070 594760 464250 407200 522350 448690 TRUE FALSE 554267.6275 513573.4196 622193.3942 567690.691 593567.6488 606786.4547 469931.6304 398791.1777 463055.0179 418299.8266 1.325048667 1.227763883 1.487434023 1.357138241 1.419000466 1.450601736 1.123432525 0.953362044 1.106993091 1 18.67417787 2.097960388 4.543066942 1.01974767 1.375994819 0.822872372 0.07639657 0.083159418 3.008813686 0.030496724 0.021859016 125.3026882 -2.097960388 0.356247149 GTQEVAPPT(ph)PLTPTSHTANTSPRPVSGMER ddPTM_BT-474_Pertuzumab_2h_R1 1 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPT(0.496)PLT(0.496)PT(0.004)S(0.004)HTANTSPRPVSGMER 72.113 0.0082543 811160000 44452 40415 52469 48805 66917 73491 40131 44995 31999 53686 TRUE FALSE 42714.7667 39262.40377 61951.31547 51323.8319 69069.44608 74977.03837 40622.13518 44065.83753 28366.60767 50049.7994 0.853445313 0.784466756 1.237793482 1.025455297 1.380014444 1.498048729 0.811634326 0.880439843 0.56676766 1 15.61107667 2.098338362 24.99955557 0.812949246 1.128135351 0.315729321 0.227280431 17.04439063 4313.500209 0.09070127 0.066987323 125.4117886 -2.098338362 0.315186105 DGKS(ph)PTVPCLQEEAGEPLGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGKSPTVPCLQEEAGEPLGGK 21 1 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 DGKS(0.785)PT(0.215)VPCLQEEAGEPLGGK 109.26 0.00023325 0 83341 81554 86297 73394 87029 102280 73580 75928 81444 84219 TRUE FALSE 80083.94158 79228.15977 101892.7876 77181.87314 89828.36682 104348.1717 74480.49405 74360.06027 72198.81856 78514.77212 1.019985659 1.009086031 1.297753083 0.98302359 1.14409511 1.329025976 0.948617592 0.947083692 0.919557131 1 16.26067649 2.098395548 24.3246334 0.949026722 1.127526283 0.384291968 0.10945305 11.17457575 2748.181126 0.040792476 0.030127241 125.4283034 -2.098395548 0.178499561 YS(ph)PRHS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 9 YSPRHSR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 Y(0.015)S(0.985)PRHS(1)R;Y(0.055)S(0.945)PRHS(1)R;Y(0.035)S(0.965)PRHS(1)R;Y(0.149)S(0.851)PRHS(1)R;Y(0.02)S(0.98)PRHS(1)R;Y(0.219)S(0.781)PRHS(1)R;Y(0.175)S(0.827)PRHS(0.998)R;Y(0.225)S(0.775)PRHS(1)R;Y(0.033)S(0.967)PRHS(1)R 96.015 0.0074213 30619393000 7609510 8164860 6024869 6829267 7047692 7715875 6557579 6432605 7498774 6661955 TRUE FALSE 7312121.936 7932006.187 7113696.851 7181726.288 7274387.414 7871895.279 6637832.613 6299769.459 6647544.613 6210734.854 1.177336033 1.277144553 1.145387304 1.156340829 1.17126034 1.267466003 1.068767669 1.014335599 1.070331413 1 22.56633255 2.098676215 5.891223639 1.032681082 1.196576244 0.761627447 0.04442023 0.099251807 4.97954575 0.016879565 0.012363364 125.509389 -2.098676215 0.163895162 SDES(ph)PKPGK ddPTM_BT-474_Pertuzumab_2h_R1 6 SDESPKPGK 9 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK 131.43 0.00020183 7492830000 19290000 13274800 13188600 10398190 11420600 11808000 15550600 17201200 17440800 17635500 TRUE FALSE 18536125.47 12896215.7 15572073.4 10934841.83 11787953.97 12046765.85 15740912.89 16845989.21 15460993.5 16441031.88 1.127430785 0.784392111 0.947146962 0.665094619 0.716983828 0.732725655 0.95741636 1.024630895 0.940390702 1 23.97079751 2.098861613 6.572579404 0.990955994 0.820231403 0.25932651 0.125707858 0.279761582 15.94237102 0.04819834 0.03543724 125.5629796 -2.098861613 -0.170724591 LKAEAELLQQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKAEAELLQQQK 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 144.27 0.000305 445060000 1238530 1183050 966850 954760 1071050 1088520 1225740 1316490 1479250 1396600 FALSE TRUE 1190126.878 1149310.572 1141581.302 1004035.278 1105501.296 1110530.62 1240740.973 1289304.021 1311331.742 1302007.038 0.914071002 0.882722242 0.876785815 0.771144279 0.849074747 0.852937494 0.952944905 0.990243512 1.007161792 1 20.31230582 2.098947673 2.679979564 0.996487971 0.854596412 0.77363397 0.034941651 0.138173677 1.96000127 0.017723326 0.01114597 125.5878638 -2.098947673 -0.141891559 GLESTTLADKDGEIYCK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLESTTLADKDGEIYCK 17 1 P21291;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 248.75 5.93E-21 1361720000 1905410 1739420 1465730 1538680 1753670 1777640 1899220 2150450 2363900 2250440 FALSE TRUE 1830944.471 1689813.445 1730620.016 1618091.459 1810078.388 1813585.099 1922463.222 2106042.456 2095559.982 2098015.694 0.872702943 0.80543413 0.824884209 0.771248501 0.862757315 0.864428757 0.916324519 1.003825883 0.998829507 1 21.00059404 2.099483518 1.367069588 1.009236758 0.821778997 0.888474259 0.026870391 0.124297724 0.438609347 0.017510794 0.008962193 125.7429133 -2.099483518 -0.187457761 RLS(ph)LGQGDSTEAATEER ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSLGQGDSTEAATEER 17 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(0.995)LGQGDS(0.001)T(0.004)EAATEER;RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER 197.15 9.41E-12 7613300000 1112490 1234890 1213310 1352700 1228340 1338470 1175780 1203270 1182130 1367100 TRUE FALSE 1069012.661 1199672.146 1432582.107 1422513.009 1267850.672 1365534.78 1190169.547 1178422.054 1047939.558 1274505.099 0.838766876 0.941284697 1.12403011 1.116129712 0.994778814 1.071423552 0.933828784 0.924611486 0.822232535 1 20.28150571 2.099680084 6.092354762 0.91256123 1.019547216 0.213872869 0.088521938 0.319973565 16.61976738 0.035285558 0.025882848 125.7998386 -2.099680084 0.106985986 CTLAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 CTLAEK 6 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 122.79 0.04436 1444850000 2137700 2182400 1792360 1957580 2005960 1816170 2287200 2451500 2596900 2545400 FALSE TRUE 2054156.321 2120160.089 2116279.323 2058610.938 2070483.525 1852894.202 2315191.438 2400875.668 2302110.799 2372997.791 0.865637688 0.893452197 0.891816811 0.867514899 0.872518101 0.780824242 0.975639947 1.011747958 0.970127662 1 21.17827933 2.099740836 7.81889658 0.994812752 0.865696459 0.802006461 0.031071019 0.099912721 6.917716128 0.011784698 0.008690547 125.8174375 -2.099740836 -0.129116292 QLNNHFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLNNHFGR 8 0 E7EMW7;O95071-2;O95071;E5RFK7 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 0 ; 86.794 0.015781 134945000 324250 296700 254640 252160 262730 282110 302690 334540 349990 340540 FALSE TRUE 311577.9515 288238.4065 300659.1124 265174.0078 271180.9491 287814.4575 306394.4108 327631.6321 310260.6025 317474.9225 0.981425396 0.907909211 0.947032635 0.835259698 0.854180692 0.906573833 0.965097994 1.031992163 0.977275937 1 18.27628311 2.099799098 3.390519721 1.00545921 0.901713031 0.538601558 0.040939649 0.183909408 4.146781764 0.018323204 0.012390033 125.8343176 -2.099799098 -0.103746179 KEEGEAFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEEGEAFAR 9 1 P61019;P61019-2;H7C125 P61019 RAB2A Ras-related protein Rab-2A 0 124.67 0.00083888 1774000000 895690 1116500 849110 1212000 964760 1037000 1183100 1364000 1446600 1285500 FALSE TRUE 860685.4446 1084658.513 1002563.065 1274551.465 995792.3816 1057968.851 1197579.132 1335832.923 1282388.033 1198431.94 0.718176323 0.905064758 0.836562371 1.063515935 0.830912752 0.882794271 0.999288397 1.114650635 1.070054953 1 20.19271655 2.099805543 3.365273555 1.071856204 0.879017879 0.506821697 0.08486749 0.192885384 4.289707231 0.035650727 0.024058106 125.8361849 -2.099805543 -0.192838325 VIET(ph)PENDFK ddPTM_BT-474_Pertuzumab_2h_R1 3 VIETPENDFK 10 0 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 VIET(1)PENDFK;VIET(1)PENDFK;VIET(1)PENDFK 191.31 9.00E-06 637630000 1892440 1678280 1609520 1595430 1684730 1752180 1889500 2115100 2170160 2272730 TRUE FALSE 1818481.353 1630417.098 1900396.068 1677770.333 1738920.87 1787610.28 1912624.266 2071422.446 1923812.535 2118795.973 0.858261662 0.769501697 0.896922635 0.791850822 0.820711807 0.84369156 0.902693931 0.977641298 0.907974415 1 21.01481324 2.100197205 2.382432726 0.958927077 0.826501812 0.698099512 0.039126934 0.154641362 1.718623109 0.017958817 0.010871015 125.9497196 -2.100197205 -0.132425265 IGS(ph)DPLAYEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGSDPLAYEPK 11 0 P19634 P19634 SLC9A1 Sodium/hydrogen exchanger 1 1 IGS(1)DPLAYEPK;IGS(1)DPLAYEPK 177.64 8.28E-06 416900000 655850 933790 584280 1136000 786330 592680 1058150 1452780 1009730 565490 TRUE FALSE 630218.6569 907159.2235 689872.3932 1194629.096 811623.0186 604664.3957 1071099.956 1422779.585 895109.6835 527188.8586 1.195432427 1.720748094 1.308586822 2.266036311 1.539529915 1.146959739 2.031719637 2.698804351 1.697891882 1 19.00796036 2.100203665 9.988411292 2.08166315 1.562634056 0.019542689 0.508988429 0.525086782 47.98421405 0.186233785 0.137513007 125.9515929 -2.100203665 -0.519029094 STGS(ph)PTQETQAPFIAK ddPTM_BT-474_Pertuzumab_2h_R1 5 STGSPTQETQAPFIAK 16 0 O15231-3;H0Y704;O15231-2 O15231-3 ZNF185 Zinc finger protein 185 1 S(0.001)TGS(0.999)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;S(0.003)T(0.002)GS(0.995)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK 394.12 1.32E-121 3854510000 2622790 2588250 2324110 2549840 2432090 2659590 2766080 3240820 3156230 3309610 TRUE FALSE 2520288.467 2514435.644 2744128.377 2681437.548 2510320.384 2713368.732 2799932.114 3173895.934 2797948.002 3085447.167 0.816830861 0.814933949 0.889377853 0.869059622 0.813600184 0.879408587 0.907463963 1.028666434 0.906820908 1 21.55704816 2.100346276 2.552595583 0.980161645 0.845248603 0.700212318 0.038414708 0.149067514 1.912686805 0.017942119 0.011118044 125.992959 -2.100346276 -0.134913042 GFFDPNTEENLTYLQLMER ddPTM_BT-474_Pertuzumab_2h_R1 2 GFFDPNTEENLTYLQLMER 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 208.47 6.26E-16 81252000 19450.4 21685 20393.9 25451.3 28867 27939 20458.8 19073.7 20880 28244 FALSE TRUE 18690.25686 21066.56503 24079.53139 26764.84464 29795.53327 28503.94572 20709.18091 18679.82143 18509.78994 26331.00872 0.70981925 0.800066767 0.914493313 1.016476236 1.131575838 1.08252388 0.786494021 0.709422933 0.702965471 1 14.68447517 2.100594806 9.057506803 0.765963141 0.946507361 0.183997458 0.140746585 0.400461639 32.59913064 0.056912277 0.042011424 126.0650805 -2.100594806 0.18054422 DIAWTEDSKR ddPTM_BT-474_Pertuzumab_2h_R1 6 DIAWTEDSKR 10 1 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;;;;; 175.15 4.63E-06 8234630000 4244360 4010560 3807310 4334060 4118070 3661510 4755060 5066010 5330010 5609510 FALSE TRUE 4078485.719 3896182.756 4495375.61 4557741.356 4250531.461 3735548.241 4813253.847 4961395.123 4724969.61 5229572.891 0.779888875 0.745028865 0.859606645 0.871532236 0.812787497 0.7143123 0.920391387 0.948718992 0.903509657 1 22.31826169 2.100714588 7.456295444 0.942383057 0.802001447 0.676433987 0.049602028 0.146316009 9.529121514 0.019435281 0.014324863 126.0998552 -2.100714588 -0.14038161 DAELQDQEFGKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DAELQDQEFGKR 12 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;;; 117.03 0.0012471 3389510000 3243940 3185870 2603740 2864050 2989970 2937440 3386960 3848560 4048340 3524560 FALSE TRUE 3117163.238 3095012.107 3074293.738 3011863.964 3086145.1 2996837.049 3428410.63 3769085.891 3588789.415 3285838.412 0.948666017 0.941924623 0.935619271 0.916619622 0.939226071 0.912046386 1.043389905 1.147069764 1.092198996 1 21.6478301 2.100736887 4.285876459 1.096071394 0.93286375 0.776235871 0.036343435 0.082496548 2.732346267 0.01367897 0.009733426 126.1063302 -2.100736887 -0.163207644 TPVLLHDHDER ddPTM_BT-474_Pertuzumab_2h_R1 2 TPVLLHDHDER 11 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 109.16 0.001137 848900000 601380 706170 634000 801430 736410 841490 611780 537650 773700 728620 FALSE TRUE 577877.4047 686030.723 748577.9033 842791.8983 760097.2964 858505.5044 619267.1466 526547.3396 685872.8196 679269.9184 0.850733102 1.009953046 1.102033055 1.240731962 1.118991546 1.263865043 0.91166579 0.77516658 1.009720585 1 19.37362544 2.100795128 9.280904349 0.888474123 1.101163733 0.300779852 0.125421415 0.302407585 25.26831925 0.049082087 0.036234673 126.1232425 -2.100795128 0.21268961 GS(ph)PLAEGPQAFFPER ddPTM_BT-474_Pertuzumab_2h_R1 6 GSPLAEGPQAFFPER 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER 253.1 1.22E-24 2164850000 250999 308899 316087 381821 383695 379967 273338 272883 256674 262782 TRUE FALSE 241189.6816 300089.503 373210.9522 401526.8276 396036.8981 387650.1931 276683.1922 267247.8707 227537.4436 244983.5411 0.984513819 1.224937405 1.523412351 1.638995117 1.616585736 1.582351987 1.129395024 1.09088092 0.928786655 1 17.9023253 2.1010219 5.069209028 1.038011602 1.44066424 0.502654291 0.192196683 0.196984894 8.16594377 0.082558931 0.059925911 126.1891167 -2.1010219 0.402652638 TTPES(ph)PPYSSGSYDSIK ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPESPPYSSGSYDSIK 17 0 A0A087WTU5;A0A087X0N3;Q96MY1-2;Q96MY1 A0A087WTU5 NOL4L Nucleolar protein 4-like 1 TTPES(0.998)PPYS(0.001)S(0.001)GSYDSIK;TTPES(0.915)PPYS(0.077)S(0.008)GSYDSIK 227.63 1.78E-15 398230000 456280 433390 371480 397000 423110 433750 448740 501840 552900 486120 TRUE FALSE 438448.0732 421030.1415 438614.6995 417489.2176 436719.7174 442520.7222 454231.8144 491476.8286 490137.1099 453194.6594 0.967460812 0.929027147 0.967828483 0.921213895 0.963647096 0.976447346 1.002288542 1.084471801 1.081515635 1 18.78977133 2.101030787 2.089462212 1.063309727 0.949976931 0.729447073 0.027461733 0.142189793 1.202601892 0.013672161 0.007922141 126.1916987 -2.101030787 -0.113332796 WFQLTPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 WFQLTPPR 8 0 O15296-4;O15296;I3L1D5;O15296-3;O15296-2 O15296-4 ALOX15B Arachidonate 15-lipoxygenase B 0 86.953 0.039114 0 123840 143510 109040 144730 141870 123960 122190 114290 121870 120840 FALSE TRUE 119000.1959 139417.2353 128745.9536 152199.5326 146433.3774 126466.5561 123685.3978 111929.8716 108035.8285 112655.3992 1.056320396 1.237554847 1.142829856 1.351018538 1.299834526 1.122596494 1.097909188 0.993559762 0.958993793 1 16.78155693 2.101217571 1.712917843 0.981006898 1.218823979 0.612776419 0.078845414 0.247128005 1.386509031 0.047354111 0.025722877 126.2459838 -2.101217571 0.237817081 DSES(ph)PSQKK ddPTM_BT-474_Pertuzumab_2h_R1 3 DSESPSQKK 9 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DSES(1)PSQKK;DS(0.001)ES(0.997)PS(0.002)QKK;DSES(0.995)PS(0.005)QKK 193.73 2.04E-05 790900000 3443360 2654530 2247040 1864120 2374550 2419310 2755400 2917730 3193550 3257870 TRUE FALSE 3308789.684 2578825.403 2653130.113 1960327.457 2450929.557 2468230.106 2789121.409 2857477.856 2831031.592 3037211.563 1.089416926 0.849076645 0.873541424 0.645436584 0.806967018 0.812663212 0.918316473 0.94082279 0.932115374 1 21.53431598 2.10136257 4.21270616 0.946758675 0.836841114 0.189469356 0.103262587 0.383721707 12.38070458 0.042677533 0.030292629 126.2881408 -2.10136257 -0.109917561 EGAGS(ph)PAAPGTLPLEK ddPTM_BT-474_Pertuzumab_2h_R1 8 EGAGSPAAPGTLPLEK 16 0 O60248-2;O60248 O60248-2 SOX15 Protein SOX-15 1 EGAGS(1)PAAPGTLPLEK;EGAGS(1)PAAPGTLPLEK;EGAGS(1)PAAPGTLPLEK;EGAGS(1)PAAPGTLPLEK;EGAGS(1)PAAPGTLPLEK;EGAGS(1)PAAPGTLPLEK;EGAGS(1)PAAPGTLPLEK;EGAGS(1)PAAPGTLPLEK 279.91 2.04E-35 8988590000 9603710 8821000 7836040 8430170 8379800 9113100 9883670 11219090 11864650 11881330 TRUE FALSE 9228386.396 8569433.717 9252186.74 8865252.084 8649343.877 9297373.126 10004629.31 10987411.87 10517824.67 11076596.94 0.833142747 0.773652212 0.835291452 0.800358823 0.780866536 0.839370899 0.903222295 0.991948333 0.949553796 1 23.40101137 2.101405497 2.018594731 0.980478655 0.804570453 0.918213793 0.023017142 0.078222694 0.615941854 0.011571374 0.006629816 126.3006242 -2.101405497 -0.175908201 GDDDEES(ph)DEEAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDDDEESDEEAVK 13 0 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 GDDDEES(1)DEEAVK;GDDDEES(1)DEEAVK 271.73 4.48E-32 512520000 716980 585730 727570 640480 728150 639910 827240 938620 949360 962160 TRUE FALSE 688959.6289 569025.5539 859058.0837 673535.2496 751571.606 652849.4186 837364.0106 919237.169 841592.6328 896992.0462 0.768077746 0.634370791 0.957709812 0.750882076 0.8378799 0.727820744 0.933524454 1.024799688 0.938238679 1 19.77473567 2.101431403 4.888502679 0.987945237 0.782884336 0.590650438 0.080164092 0.142399681 5.632072178 0.030287862 0.021914848 126.3081583 -2.101431403 -0.205060901 NFLNAIATDIIHLHSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFLNAIATDIIHLHSQR 17 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ; 118.47 9.67E-05 165113000 79472 81429 67681 79886 73561 68654 65390 22780.5 85423 75503 FALSE TRUE 76366.14638 79106.72465 79912.46226 84008.92603 75927.15637 70042.23092 66190.26238 22310.07471 75726.13916 70389.11456 1.08491415 1.123848839 1.135295745 1.19349315 1.078677532 0.995071914 0.94034799 0.316953479 1.075821732 1 16.10306472 2.101550795 3.514593348 0.705687793 1.109071123 0.271905284 0.201934626 0.211202756 5.077622203 0.082494293 0.056384874 126.3428867 -2.101550795 0.40338333 DADDAVYELDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 DADDAVYELDGK 12 0 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 257.88 7.52E-21 3459580000 4354040 3698260 3476910 3609630 3942350 3655260 4546800 5149600 5533700 4939700 FALSE TRUE 4183879.303 3592789.246 4105264.98 3795923.437 4069159.268 3729171.862 4602445.099 5043258.96 4905537.575 4605129.719 0.908525831 0.780171128 0.891454797 0.824281544 0.883614473 0.809786497 0.999417037 1.095139392 1.06523331 1 22.13481036 2.101687117 4.350508153 1.060701053 0.84917753 0.824979555 0.043330107 0.072954095 2.464848816 0.015714549 0.011211802 126.3825509 -2.101687117 -0.211523523 VTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_BT-474_Pertuzumab_2h_R1 3 VTFFEPGSGDENGTSNKEDEFR 22 1 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 VTFFEPGS(1)GDENGTSNKEDEFR;VTFFEPGS(1)GDENGTSNKEDEFR;VTFFEPGS(1)GDENGTSNKEDEFR 216.82 7.95E-26 1000260000 672406 660098 516622 603509 622101 621805 709894 813562 843963 801892 TRUE FALSE 646127.6301 641272.6513 609987.0876 634656.1718 642111.4436 634378.3231 718581.8951 796761.6604 748159.8584 747579.1406 0.864293284 0.857799016 0.81594985 0.848948476 0.858921028 0.848576811 0.961211805 1.065789048 1.000776798 1 19.51186679 2.101696759 3.293790021 1.02748635 0.847859028 0.929274976 0.021760531 0.05364461 1.145785778 0.009173316 0.006163504 126.3853569 -2.101696759 -0.179627323 S(ph)TSYQELSEELVQVVENSELADEQDKETVR ddPTM_BT-474_Pertuzumab_2h_R1 1 STSYQELSEELVQVVENSELADEQDKETVR 30 1 Q9H813 Q9H813 TMEM206 Transmembrane protein 206 1 S(0.256)T(0.256)S(0.256)Y(0.218)QELS(0.014)EELVQVVENSELADEQDKETVR 112.11 0.00011493 3687900 5397 8364.5 3287.1 6285.1 4359.6 5423 7850.1 10778 9796.1 7854.2 TRUE FALSE 5186.079273 8125.95265 3881.152091 6609.474764 4499.830493 5532.656776 7946.171872 10555.43053 8684.087797 7322.228038 0.708265196 1.109765034 0.530050699 0.902658963 0.614543889 0.755597442 1.085212292 1.441559929 1.185989804 1 12.83806699 2.101862274 3.997073632 1.259712103 0.774233664 0.550047321 0.181015014 0.143477196 4.272407064 0.069629306 0.048978679 126.433533 -2.101862274 -0.485478439 GINLPTPPGLS(ph)PGDLDVFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GINLPTPPGLSPGDLDVFVR 20 0 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GINLPT(0.035)PPGLS(0.965)PGDLDVFVR;GINLPT(0.009)PPGLS(0.991)PGDLDVFVR 106.86 0.00024665 34128000 92905 104898 98102 113787 126490 114548 91953 88960 91283 90693 TRUE FALSE 89274.16989 101906.4117 115831.2137 119659.5607 130558.6657 116864.239 93078.34832 87122.94491 80920.93653 84550.28233 1.055870748 1.20527583 1.369968384 1.415247323 1.544154107 1.382186266 1.100863838 1.030427605 0.957074705 1 16.36752195 2.101956581 3.730416003 1.011016355 1.338462281 0.601388314 0.123861589 0.177204491 4.719882184 0.057032259 0.039550721 126.4609911 -2.101956581 0.327445926 AGEPNS(ph)PDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_BT-474_Pertuzumab_2h_R1 6 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 2 AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR 281.92 6.77E-72 12083640000 882380 958090 732725 854290 872080 885580 854440 846720 962030 987770 TRUE FALSE 847895.6141 930766.2113 865144.7069 898380.0093 900131.2452 903487.0344 864896.8923 829234.9361 852824.3876 920867.4581 0.920757495 1.010749379 0.939488847 0.975580146 0.97748187 0.981126031 0.939219738 0.900493256 0.926109811 1 19.812634 2.102129035 5.641139564 0.92851313 0.968870442 0.086475766 0.033340587 0.282018522 13.2525175 0.011838399 0.008656374 126.5112173 -2.102129035 0.040357312 YMEENDQLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 YMEENDQLKK 10 1 P51572;P51572-2;C9JSP1;C9JQ75;C9J0M4;A0A2R8Y5M6;C9JMD7 P51572 BCAP31 B-cell receptor-associated protein 31 0 ; 155.97 1.89E-05 819000000 746660 1143190 684240 1085960 760440 871860 1218610 1607340 1539600 1185800 FALSE TRUE 717479.7017 1110587.341 807897.3888 1142006.526 784900.2432 889489.6066 1233523.714 1574147.867 1364831.063 1105484.71 0.649018205 1.004615741 0.730808289 1.033036925 0.710005517 0.804615024 1.115821596 1.423943591 1.234599674 1 20.07624764 2.102267197 4.075195025 1.267654527 0.831330725 0.590322053 0.151276702 0.129851451 3.98160136 0.056874874 0.040158492 126.5514707 -2.102267197 -0.436323803 QIEYEYK ddPTM_BT-474_Pertuzumab_2h_R1 3 QIEYEYK 7 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;; 123.92 0.0097643 732420000 912770 902580 714670 1013870 783280 772800 1017850 1096130 1214510 1127190 FALSE TRUE 877097.9393 876839.3021 843826.7667 1066195.952 808474.9126 788426.5455 1030306.753 1073494.532 1076643.916 1050844.417 0.834660131 0.834414008 0.802998763 1.014608761 0.769357385 0.750279045 0.980456037 1.021554204 1.024551207 1 20.00311766 2.102349689 6.435845428 1.013576123 0.83863337 0.613078636 0.067355422 0.147081598 8.032912748 0.026113211 0.019192592 126.5755108 -2.102349689 -0.174942752 REEQLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 REEQLFK 7 1 C9JYI4;P52294;C9J352;C9JWD9;F2Z3G4;C9J4U1;O15131;Q5TD90 C9JYI4;O15131 KPNA1;KPNA5 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed;Importin subunit alpha-6" 0 ; 93.429 0.023958 409290000 240842 258467 216618 208598 209158 205849 251986 267585 270607 290188 FALSE TRUE 231429.6284 251095.7742 255765.6912 219363.7678 215885.757 210011.4078 255069.88 262059.2762 239888.8278 270533.3083 0.855457059 0.92815105 0.945412943 0.810856782 0.798000654 0.776286695 0.942840945 0.968676567 0.886725666 1 18.04544671 2.102478413 10.59026952 0.950160867 0.855724263 0.416075474 0.056389394 0.392367943 37.49691123 0.02315491 0.017099037 126.6130333 -2.102478413 -0.094436604 VPDEEENEES(ph)DNEKETEK ddPTM_BT-474_Pertuzumab_2h_R1 5 VPDEEENEESDNEKETEK 18 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK 267.18 1.86E-31 6684370000 4741339 3313087 3463619 3596205 3914298 3403261 4947259 5759633 6060471 5632243 TRUE FALSE 4556042.23 3218601.003 4089572.001 3781805.571 4040204.95 3472077.269 5007805.036 5640694.566 5372511.74 5250766.165 0.86769094 0.612977402 0.778852433 0.720238809 0.769450557 0.661251551 0.953728442 1.074261239 1.02318625 1 22.32409652 2.1026112 4.645444921 1.034996974 0.733128002 0.807367712 0.067125116 0.077716003 2.868349267 0.024151606 0.017386347 126.6517514 -2.1026112 -0.301868973 QAAPPIELDAVWEDIR ddPTM_BT-474_Pertuzumab_2h_R1 4 QAAPPIELDAVWEDIR 16 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 179.56 6.07E-09 170869000 86760 92309 85668 89685 98722 93085 87402 88465 91008 97630 FALSE TRUE 83369.32328 89676.4377 101150.1133 94313.6536 101897.4828 94967.24248 88471.65182 86638.16684 80677.15338 91017.43314 0.915970934 0.985266609 1.111326806 1.036215265 1.119538085 1.043396185 0.972029739 0.951885412 0.886392316 1 16.47385528 2.102636703 3.235992392 0.943870382 1.040405439 0.313888865 0.060365766 0.297290972 6.140904029 0.02717908 0.018185283 126.659189 -2.102636703 0.096535056 SEEEQSSSS(ph)VKKDETNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEEEQSSSSVKKDETNVK 18 2 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SEEEQSSS(0.046)S(0.954)VKKDETNVK 206.85 4.21E-16 524060000 416050 286250 363030 266480 289690 318470 440290 532280 578090 491690 TRUE FALSE 399790.306 278086.4303 428637.5966 280233.0647 299008.1419 324909.6816 445678.4007 521288.232 512467.6468 458387.3983 0.872166878 0.606662468 0.935098997 0.611345481 0.652304455 0.708810239 0.972274548 1.137221996 1.117979352 1 18.80620786 2.103068041 3.485702896 1.093297181 0.725259505 0.703491532 0.105219595 0.119606214 2.831731877 0.042493083 0.029016381 126.7850484 -2.103068041 -0.368037677 LGASNS(ph)PGQPNSVK ddPTM_BT-474_Pertuzumab_2h_R1 8 LGASNSPGQPNSVK 14 0 P49756 P49756 RBM25 RNA-binding protein 25 1 LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK 324.59 1.27E-56 29081080000 27818010 26289470 22738840 24591570 24030200 24702800 27876630 29461320 33289160 31492250 TRUE FALSE 26730851.41 25539720.06 26848254.21 25860743.87 24803153.21 25202307.54 28217792.54 28852933.45 29510314.12 29359251.86 0.910474543 0.86990364 0.914473378 0.880837972 0.844815574 0.858411095 0.961120967 0.982754383 1.005145303 1 24.80731187 2.103087038 4.025242554 0.989786232 0.879544149 0.863852007 0.021135702 0.083187485 2.500684452 0.009175038 0.006466597 126.7905944 -2.103087038 -0.110242083 LRQENMELAER ddPTM_BT-474_Pertuzumab_2h_R1 1 LRQENMELAER 11 1 P40222 P40222 TXLNA Alpha-taxilin 0 105.4 0.0022529 322480000 343700 512790 338870 352580 398030 500000 346560 359990 387160 395680 FALSE TRUE 330267.824 498165.7313 400111.3471 370776.6961 410832.9964 510110.3426 350801.3049 352556.0807 343211.2199 368880.2412 0.895325331 1.35048093 1.084664621 1.005141113 1.113730015 1.38286166 0.950989687 0.95574672 0.930413673 1 18.49279299 2.103107305 20.62459984 0.955266024 1.141037816 0.291208568 0.137026403 4.051479291 796.2902505 0.049687121 0.03669641 126.7965114 -2.103107305 0.185771792 ETEGSLS(ph)DSDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETEGSLSDSDFK 12 0 P78411-3;P78411-2;P78411 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 ETEGS(0.007)LS(0.948)DS(0.045)DFK;ETEGS(0.022)LS(0.916)DS(0.061)DFK 193.51 2.85E-06 374140000 874320 774370 754560 734240 814280 810940 948060 1104190 1163610 1082030 TRUE FALSE 840150.6078 752285.7258 890925.7771 772134.2144 840472.0557 827337.7624 959662.6419 1081388.091 1031521.871 1008743.144 0.832868716 0.745765391 0.883203799 0.765441846 0.833187378 0.820166925 0.951344896 1.072015306 1.022581295 1 19.94412744 2.103225165 2.878297206 1.036979177 0.810690968 0.862465005 0.039637114 0.080325365 1.319375197 0.016690964 0.010786761 126.8309265 -2.103225165 -0.226288208 S(ph)PGNLTEREELAGSLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPGNLTEREELAGSLAR 17 1 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTEREELAGSLAR;S(0.999)PGNLT(0.001)EREELAGSLAR;S(1)PGNLTEREELAGSLAR;S(1)PGNLTEREELAGSLAR 178.73 5.79E-10 2232030000 108248 120177 84338 96113 88915 102936 80645 92626 66711 85550 TRUE FALSE 104017.5485 116749.6696 99579.75269 101073.4034 91775.03173 105017.4364 81631.95763 90713.24073 59138.24696 79755.6223 1.304203334 1.463842501 1.248560914 1.267288757 1.150702973 1.31674023 1.023526057 1.137389918 0.741493142 1 16.2832986 2.10340511 0.71231954 0.904500057 1.336022803 0.647387875 0.115254239 0.421813608 0.409291143 0.095506131 0.056188137 126.8834884 -2.10340511 0.431522746 KYDDVTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYDDVTEK 8 1 P51572;P51572-2;C9JSP1;C9JQ75;C9J0M4;A0A2R8Y5M6;C9JMD7;C9JM14 P51572 BCAP31 B-cell receptor-associated protein 31 0 ; 94.692 0.016397 205830000 691190 1002490 762350 1327640 760510 735730 1331910 1724860 1591630 1226700 FALSE TRUE 664177.5306 973899.9667 900123.6034 1396159.66 784972.4948 750606.9647 1348210.313 1689241.038 1410954.835 1143614.516 0.580770462 0.851598115 0.787086549 1.220830655 0.686396057 0.656346132 1.178902763 1.477107027 1.23376786 1 20.12516941 2.103410964 5.51777376 1.298561691 0.815098331 0.519247092 0.197565933 0.150198052 6.847725535 0.0755596 0.055193174 126.8851987 -2.103410964 -0.48346336 GFEDEVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFEDEVKK 8 1 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4;C9J188;C9JWF5 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ; 135.79 0.0013127 1694790000 2563400 2258700 2196700 2164900 2524400 2461100 2983000 3086400 3964000 3353400 FALSE TRUE 2463219.494 2194284.087 2593692.555 2276630.748 2605599.619 2510865.128 3019506.846 3022664.761 3514023.338 3126271.231 0.787909721 0.701885385 0.829644123 0.728225602 0.833452834 0.803150124 0.965849289 0.966859411 1.12403022 1 21.57601152 2.103628209 1.17733092 1.052349213 0.765260141 0.833468448 0.051999185 0.168704385 0.438084049 0.034223944 0.017253222 126.9486856 -2.103628209 -0.287089071 YS(ph)DDGNRETDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSDDGNRETDEK 12 1 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 YS(1)DDGNRETDEK 155.22 4.37E-05 375690000 630910 596760 639290 625000 610230 703530 895830 951790 1218200 1071000 TRUE FALSE 606253.3397 579740.9891 754823.9239 657256.3249 629858.6021 717755.8586 906793.4355 932135.2039 1079915.043 998460.2161 0.607188278 0.580635042 0.755987982 0.658269918 0.630829944 0.718862752 0.908191855 0.933572704 1.081580443 1 19.92934542 2.103695698 1.35725523 1.024755935 0.644340029 0.902005111 0.05329052 0.126738379 0.441023198 0.036060564 0.018499512 126.9684151 -2.103695698 -0.380415906 RRS(ph)SS(ph)PFLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSSSPFLSK 10 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RRS(0.995)S(0.237)S(0.75)PFLS(0.017)K 128.74 0.0015817 1483800000 2143600 2025000 1725900 1810100 1959700 2141000 2025800 2281300 2522600 2426100 TRUE FALSE 2059825.742 1967248.983 2037808.522 1903519.478 2022735.53 2184292.487 2050592.346 2234190.358 2236245.024 2261778.086 0.910710805 0.86977984 0.900976331 0.841603113 0.894312109 0.96574129 0.906628444 0.987802637 0.988711066 1 21.10902596 2.103710758 0.852813397 1.000793785 0.880242708 0.726762138 0.027325169 0.307394258 0.417402703 0.022014291 0.011710464 126.9728179 -2.103710758 -0.120551076 EKS(ph)QDGGELTSPALGLASHQVPPSPLVSANGPGEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKSQDGGELTSPALGLASHQVPPSPLVSANGPGEEK 36 1 Q9NSC5-2;Q9NSC5;M0R1B8;M0R2U7 Q9NSC5-2 HOMER3 Homer protein homolog 3 1 EKS(0.998)QDGGELT(0.001)SPALGLASHQVPPSPLVSANGPGEEK;EKS(1)QDGGELTSPALGLASHQVPPSPLVSANGPGEEK;EKS(0.978)QDGGELT(0.011)S(0.011)PALGLASHQVPPSPLVSANGPGEEK 238.14 7.36E-50 505670000 411842 282900 187376 242539 407016 291637 421292 539100 554050 450670 TRUE FALSE 395746.7593 274831.969 221239.0114 255056.4669 420108.0393 297534.1 426447.8975 527967.3966 491156.5668 420145.7195 0.941927386 0.654134878 0.526576854 0.60706668 0.999910316 0.708168824 1.014999982 1.256629241 1.169014806 1 18.68053026 2.103718277 3.3625889 1.166455292 0.730393807 0.606678052 0.147820047 0.155958959 3.45942784 0.065012661 0.044001529 126.9750162 -2.103718277 -0.436061485 ETERAS(ph)PIKMDLAPSK ddPTM_BT-474_Pertuzumab_2h_R1 8 ETERASPIKMDLAPSK 16 2 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.016)ERAS(0.984)PIKMDLAPSK;ET(0.049)ERAS(0.951)PIKMDLAPSK;ET(0.248)ERAS(0.752)PIKMDLAPSK;ET(0.011)ERAS(0.989)PIKMDLAPSK;ET(0.001)ERAS(0.999)PIKMDLAPSK;ET(0.048)ERAS(0.952)PIKMDLAPSK;ET(0.016)ERAS(0.984)PIKMDLAPSK;ET(0.068)ERAS(0.932)PIKMDLAPSK 159.26 7.24E-09 8854500000 8715610 7820950 6258560 5413580 6722490 7965920 7655800 9298790 10183890 9134500 TRUE FALSE 8374994.326 7597904.164 7389621.013 5692975.513 6938724.996 8126996.36 7749493.971 9106766.737 9027857.502 8515812.179 0.983463955 0.892211336 0.867752935 0.66851821 0.814804842 0.954341898 0.910012317 1.069394973 1.060128771 1 23.0217127 2.104000036 1.618255341 1.048545311 0.84524581 0.491570407 0.081745352 0.326906244 1.633180056 0.052608769 0.028172155 127.057421 -2.104000036 -0.203299501 IVPEGEWGQFMDALR ddPTM_BT-474_Pertuzumab_2h_R1 2 IVPEGEWGQFMDALR 15 0 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 100.93 0.0045748 158212000 66353 55915 51569 60570 64491 55010 71009 77597 81722 84934 FALSE TRUE 63759.8514 54320.35895 60888.66545 63696.02496 66565.41158 56122.33989 71878.02938 75994.59483 72445.26117 79181.34453 0.805238302 0.68602471 0.768977413 0.804432222 0.840670387 0.708782356 0.907764699 0.959753781 0.914928404 1 16.27287294 2.104113688 5.276205013 0.949072955 0.770587954 0.773319329 0.047274306 0.097842897 4.221985619 0.01817002 0.013236931 127.0906754 -2.104113688 -0.178485001 GKLS(ph)AEENPDDSEVPSSSGINSTK ddPTM_BT-474_Pertuzumab_2h_R1 6 GKLSAEENPDDSEVPSSSGINSTK 24 1 A0A494C1S7;Q9Y5Q9;Q9Y5Q9-2 A0A494C1S7 GTF3C3 General transcription factor 3C polypeptide 3 1 GKLS(1)AEENPDDSEVPSSSGINSTK;GKLS(1)AEENPDDSEVPSSSGINSTK;GKLS(1)AEENPDDSEVPSSSGINSTK;GKLS(1)AEENPDDSEVPSSSGINSTK;GKLS(1)AEENPDDSEVPSSSGINSTK;GKLS(1)AEENPDDSEVPSSSGINSTK 208.62 3.75E-25 8773760000 6515540 5786610 4917880 5092020 6122800 6173150 6335710 7562330 8661100 7338600 TRUE FALSE 6260905.493 5621581.548 5806650.314 5354819.762 6319745.423 6297975.323 6413248.314 7406165.243 7677928.238 6841550.085 0.915129673 0.821682437 0.848733144 0.782691012 0.923730053 0.920548011 0.937396969 1.082527373 1.122249803 1 22.7058918 2.104200983 1.317203727 1.081288191 0.850982022 0.754057612 0.050881824 0.198054312 0.648043551 0.033731822 0.017222421 127.1162237 -2.104200983 -0.230306169 AQPAAGQQGPEVEPPPPTPGGPQGEAGVAPT(ph)GHVTSIEPAPQGHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQPAAGQQGPEVEPPPPTPGGPQGEAGVAPTGHVTSIEPAPQGHPR 46 0 A0A494C1T9 A0A494C1T9 1 AQPAAGQQGPEVEPPPPT(0.004)PGGPQGEAGVAPT(0.332)GHVT(0.332)S(0.332)IEPAPQGHPR 111.08 2.17E-07 257940000 75794 76877 65101 89633 72353 89521 65564 56595 79866 80741 TRUE FALSE 72831.88669 74684.54323 76866.19886 94258.96987 74680.29995 91331.17596 66366.39184 55426.29347 70799.94651 75272.34015 0.96757835 0.992191064 1.02117456 1.252239132 0.992134691 1.213343119 0.881683653 0.736343435 0.940583837 1 16.1998322 2.104415712 7.85228846 0.849822998 1.071100226 0.380871298 0.110664785 0.203283929 13.70914393 0.041079963 0.030298045 127.1790895 -2.104415712 0.221277229 YMLTHQELAS(ph)DGEIETK ddPTM_BT-474_Pertuzumab_2h_R1 4 YMLTHQELASDGEIETK 17 0 Q02241;H7BYN4;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK 298.23 2.02E-46 2984310000 2967230 2814640 2831340 2866450 2660460 3168830 3038450 3278830 3925610 3384180 TRUE FALSE 2851267.371 2734369.223 3343026.121 3014387.828 2746036.112 3232905.914 3075635.46 3211121.015 3479991.21 3154966.474 0.903739356 0.866687252 1.059607494 0.955442111 0.870385196 1.02470373 0.974855196 1.017798776 1.103020028 1 21.58919324 2.104455908 1.169860924 1.045861447 0.938011014 0.344628807 0.060873865 0.581282993 1.490045056 0.044158802 0.022270107 127.1908613 -2.104455908 -0.107850434 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_BT-474_Pertuzumab_2h_R1 21 MESEGGADDSAEEGDLLDDDDNEDRGDDQLELIKDDEK 38 2 P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 MES(0.02)EGGADDS(0.98)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.051)EGGADDS(0.949)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.001)EGGADDS(0.999)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.006)EGGADDS(0.994)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.092)EGGADDS(0.908)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.032)EGGADDS(0.968)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.027)EGGADDS(0.973)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.001)EGGADDS(0.999)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK 306.92 9.21E-94 91325494000 4806948 4196848 5895136 5318199 4274770 5291111 7577024 8564183 10172310 9648018 TRUE FALSE 4619087.158 4077158.004 6960518.212 5592671.888 4412271.859 5398100.89 7669753.886 8387329.628 9017592.015 8994549.147 0.513542934 0.453292093 0.773859601 0.621784572 0.49054953 0.60015247 0.852711321 0.932490277 1.00256187 1 23.10061954 2.10451303 2.245404506 0.972469551 0.572821312 0.826970224 0.084652772 0.132141287 1.300148671 0.045514574 0.027119471 127.2075914 -2.10451303 -0.39964824 QEES(ph)ESPVERPLKENPPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 QEESESPVERPLKENPPNK 19 2 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 QEES(0.559)ES(0.441)PVERPLKENPPNK 108.59 0.00014188 531560000 246800 246660 217560 205390 197910 234470 274120 318270 342090 324240 TRUE FALSE 237154.7831 239625.4983 256877.9316 215990.2025 204275.9549 239211.144 277474.7626 311697.6133 303257.3774 302278.936 0.7845561 0.792729727 0.849804273 0.714539377 0.675786271 0.791358959 0.917942766 1.031158894 1.003236882 1 18.20552092 2.104563553 2.688277667 1.011407562 0.764440487 0.86047215 0.044628268 0.103269759 1.476698356 0.022994097 0.014556066 127.2223908 -2.104563553 -0.246967076 AAVGQES(ph)PGGLEAGNAK ddPTM_BT-474_Pertuzumab_2h_R1 6 AAVGQESPGGLEAGNAK 17 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK 351.16 1.16E-87 7619720000 5369860 5118400 4512850 4786230 4867380 5031870 5450920 6062290 6212090 6315880 TRUE FALSE 5159999.935 4972428.243 5328422.383 5033247.904 5023943.698 5133617.859 5517629.99 5937101.593 5506919.586 5888099.822 0.876343827 0.844487762 0.904947699 0.854817013 0.853236842 0.871863252 0.937081598 1.008322171 0.935262606 1 22.4893707 2.104734311 3.200134485 0.98098569 0.866572846 0.823576692 0.023868522 0.090897172 1.837971326 0.009807995 0.006553407 127.2724227 -2.104734311 -0.114412844 S(ph)SPQLDPLRK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.697)S(0.303)PQLDPLRK;S(0.5)S(0.5)PQLDPLRK;S(0.508)S(0.492)PQLDPLRK;S(0.591)S(0.409)PQLDPLRK 166.62 3.36E-06 43279860000 5701171 5397222 5525672 5572485 5237922 4815360 6326895 6784832 7040662 6958401 TRUE FALSE 5478362.934 5243298.513 6524283.848 5860081.619 5406404.518 4912729.878 6404325.434 6644722.848 6241435.567 6487102.302 0.844500777 0.808265119 1.005731611 0.903343488 0.833408241 0.757307292 0.987239777 1.024297527 0.962129974 1 22.62914276 2.104798239 9.53788025 1.000023763 0.864127834 0.523201934 0.062835643 0.247165799 20.61153092 0.024971652 0.018437131 127.2911583 -2.104798239 -0.135895929 TTS(ph)PSSDTDLLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTSPSSDTDLLDR 13 0 K7ENU0;K7ERZ4;K7EJ43;Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3 K7ENU0;Q96QT6 PHF12 PHD finger protein 12 1 TT(0.003)S(0.997)PS(0.001)SDTDLLDR;TT(0.002)S(0.993)PS(0.005)SDTDLLDR 282.54 1.68E-32 616720000 589510 576120 485730 547000 574830 558870 549120 558300 614000 585740 TRUE FALSE 566471.2975 559689.6217 573512.216 575230.7356 593319.929 570170.7343 555840.2948 546770.9099 544301.2941 546067.3081 1.037365338 1.024946217 1.050259203 1.053406287 1.086532594 1.044140028 1.017897037 1.001288489 0.996765941 1 19.05871926 2.104815783 2.647334257 1.000370526 1.050541173 0.707259736 0.014711725 0.170867058 2.367583354 0.007697511 0.004849502 127.2963008 -2.104815783 0.050170647 EFS(ph)GGSYSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFSGGSYSAK 10 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 EFS(1)GGSYSAK;EFS(0.987)GGS(0.013)YSAK 92.19 0.010108 159972000 357190 350360 243910 297970 343890 324260 367650 428910 431970 429950 TRUE FALSE 343230.6199 340368.0758 287989.9627 313348.2674 354951.5342 330816.7594 372149.4107 420052.8586 382934.5766 400829.1035 0.856301643 0.849160086 0.718485659 0.781750289 0.885543318 0.825331186 0.928449076 1.047959978 0.955356218 1 18.61262774 2.104882583 2.768879018 1.005290122 0.815659188 0.746416039 0.047951716 0.134207623 2.038778521 0.023114519 0.01477804 127.3158821 -2.104882583 -0.189630934 DIEIIHEELQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DIEIIHEELQLK 12 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 210.15 4.69E-08 518360000 421340 377510 525720 650020 469350 454260 726070 726860 938010 1035670 FALSE TRUE 404873.567 366743.7844 620729.2986 683567.6101 484447.069 463445.4484 734955.8619 711850.087 831531.0373 965523.1484 0.419330772 0.379839453 0.642894269 0.707976408 0.50174568 0.479994135 0.761199628 0.737268794 0.861223305 1 19.88095132 2.104886385 0.166454587 1.184424481 0.190249594 0.73574524 0.098556611 2.781188272 0.348175112 0.718319519 1.044568867 127.3169965 -2.104886385 -0.994174886 down VTQGAAS(ph)PGHGIQEK ddPTM_BT-474_Pertuzumab_2h_R1 3 VTQGAASPGHGIQEK 15 0 Q9HB58;Q9HB58-6;G5E9C0;Q9HB58-2;Q9HB58-5;Q9HB58-3;Q9HB58-7;Q9HB58-4 Q9HB58 SP110 Sp110 nuclear body protein 1 VT(0.214)QGAAS(0.786)PGHGIQEK;VT(0.057)QGAAS(0.943)PGHGIQEK;VT(0.124)QGAAS(0.876)PGHGIQEK 161.58 1.06E-06 3143630000 3302370 3206580 2839290 3275550 3076920 3093230 3397940 3674230 3787120 3755700 TRUE FALSE 3173309.729 3115131.478 3352412.863 3444601.528 3175891.926 3155777.23 3439525.006 3598355.867 3357222.015 3501323.094 0.90631731 0.889701234 0.957470297 0.983799962 0.907054802 0.901309918 0.982350076 1.027713173 0.958843821 1 21.73946877 2.104923232 5.602597867 1.000054637 0.926389377 0.538090906 0.030847113 0.163386392 7.546872773 0.012502363 0.00914185 127.3277989 -2.104923232 -0.07366526 AKEEELR ddPTM_BT-474_Pertuzumab_2h_R1 5 AKEEELR 7 1 O75525-2;O75525;H0YAQ1;H0YAQ3;E5RJZ9;E5RG12;Q9H6N6;Q5STV6;A0A0A0MRT5;Q9UBC1-2;Q9UBC1-3;Q9UBC1;Q07666-2;Q07666;Q5VWX1 O75525-2;Q07666-2 KHDRBS3;MYH16;NFKBIL1;KHDRBS1;KHDRBS2 "KH domain-containing, RNA-binding, signal transduction-associated protein 3;Putative uncharacterized protein MYH16;NF-kappa-B inhibitor-like protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 2" 0 ;;;; 120.07 0.0042307 6023000000 11563690 11287470 9321460 10556590 11001150 10858380 11571380 12518900 13402900 12774400 FALSE TRUE 11111768.21 10965562.41 11006055.18 11101416.88 11355011.98 11077943.88 11712994.01 12260380.34 11881458.98 11909178.51 0.933042376 0.920765643 0.924165774 0.932173186 0.953467275 0.930202186 0.983526614 1.029490013 0.997672423 1 23.50557056 2.105053269 3.414235717 1.011600278 0.932151616 0.900004193 0.011685046 0.066146299 1.507937481 0.005039777 0.00342833 127.3659294 -2.105053269 -0.079448662 KVMDDLDR ddPTM_BT-474_Pertuzumab_2h_R1 6 KVMDDLDR 8 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;;; 137.95 0.0011642 5858200000 8292310 8751750 7224670 8272300 7883270 7755690 8756640 9132870 9862980 10010090 FALSE TRUE 7968237.358 8502158.659 8530328.581 8699234.394 8136842.539 7912515.366 8863806.38 8944273.043 8743375.859 9332097.688 0.853852759 0.911066187 0.914084793 0.93218424 0.871919992 0.847881755 0.949819288 0.958441858 0.936914309 1 23.15376998 2.105092181 7.844364472 0.958884144 0.892022272 0.60031407 0.029073073 0.18340783 12.30714971 0.011212048 0.008269335 127.3773416 -2.105092181 -0.066861871 MAADDVEEYMIERPEPEFQDLNEK ddPTM_BT-474_Pertuzumab_2h_R1 4 MAADDVEEYMIERPEPEFQDLNEK 24 1 C9J363;Q9BUL8;C9J6F3;C9J5C3;H7C5M9;C9JSA3;C9JND6 C9J363 PDCD10 Programmed cell death protein 10 0 ;;; 219.04 1.02E-32 770860000 456650 435551 371385 396813 383101 396400 464204 506830 536563 533467 FALSE TRUE 438803.6131 423129.5119 438502.5309 417292.5665 395423.7916 404415.4796 469885.0674 496363.7834 475654.6177 497334.8049 0.882310284 0.850794088 0.881704893 0.839057638 0.7950857 0.813165448 0.944806321 0.99804755 0.956407259 1 18.92385787 2.105230085 4.606936603 0.981734834 0.843659848 0.845437322 0.02779497 0.083378301 3.028614751 0.011815682 0.008504671 127.417795 -2.105230085 -0.138074986 IAS(ph)DEEIQGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 IASDEEIQGTK 11 0 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;A0A3B3ISX8 Q8WX93-8 PALLD Palladin 1 IAS(1)DEEIQGTK;IAS(1)DEEIQGTK 230.06 2.18E-12 1473100000 1718790 1570020 1720480 1761360 2108580 2191050 1193230 992080 1167490 994510 TRUE FALSE 1651617.787 1525244.567 2031409.008 1852264.001 2176404.391 2235354.532 1207833.106 971593.2013 1034961.43 927150.9519 1.78139038 1.645087635 2.191022944 1.997801973 2.347411051 2.410993083 1.302736198 1.047934211 1.116281472 1 19.82244472 2.105451747 5.458072878 1.087680028 2.056470073 0.815535346 0.22214731 0.093242717 4.172210784 0.093905179 0.068570919 127.482845 -2.105451747 0.968790046 KDS(ph)DDEKSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KDSDDEKSDR 10 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 KDS(1)DDEKSDR;KDS(1)DDEKSDR;KDS(0.989)DDEKS(0.011)DR;KDS(0.936)DDEKS(0.064)DR 141.46 1.96E-05 2479979000 3422690 2316200 2070123 1782217 2188613 2148408 2808860 3060170 3392460 3354490 TRUE FALSE 3288927.491 2250144.244 2444240.276 1874197.433 2259011.725 2191850.282 2843235.669 2996976.42 3007362.163 3127287.404 1.051686994 0.719519492 0.781584792 0.599304506 0.72235501 0.700879068 0.909169929 0.958330985 0.961651992 1 21.57648038 2.105553092 4.543908935 0.961178719 0.752651765 0.434708374 0.109743691 0.202475962 7.217357165 0.043227723 0.031066626 127.5125974 -2.105553092 -0.208526954 NTDVAQS(ph)PEAPKQEAPAK ddPTM_BT-474_Pertuzumab_2h_R1 4 NTDVAQSPEAPKQEAPAK 18 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 NTDVAQS(1)PEAPKQEAPAK;NTDVAQS(1)PEAPKQEAPAK;NTDVAQS(1)PEAPKQEAPAK;NTDVAQS(1)PEAPKQEAPAK 267.25 1.82E-31 5390110000 6116000 5330800 4758350 4112960 5158900 5634030 5790840 7129800 8117900 6086500 TRUE FALSE 5876979.958 5178770.803 5618289.694 4325230.358 5324840.704 5747953.947 5861710.032 6982567.138 7196390.025 5674255.934 1.035726979 0.912678396 0.990136814 0.762255071 0.938420961 1.012988137 1.033035891 1.23056965 1.268252632 1 22.43599979 2.105930204 1.951975414 1.186811817 0.926896334 0.513557602 0.096719405 0.237212877 1.745363538 0.051268984 0.029175873 127.6233688 -2.105930204 -0.259915482 EGPDLDRPGS(ph)DRQER ddPTM_BT-474_Pertuzumab_2h_R1 4 EGPDLDRPGSDRQER 15 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 EGPDLDRPGS(1)DRQER;EGPDLDRPGS(1)DRQER;EGPDLDRPGS(1)DRQER;EGPDLDRPGS(1)DRQER 185.09 2.28E-07 1712840000 1218500 1274720 833242 953413 1105607 1254150 922596 948498 982349 938590 TRUE FALSE 1170879.673 1238366.234 983827.3648 1002618.759 1141169.853 1279509.772 933887.0058 928911.1848 870836.8599 875018.4633 1.338119962 1.415245833 1.124350406 1.145825833 1.304166599 1.462266027 1.067276915 1.061590382 0.995221125 1 19.73895393 2.105961103 8.099340358 1.035501699 1.288731966 0.632302905 0.099945799 0.179161753 12.39053959 0.040445713 0.029838806 127.6324492 -2.105961103 0.253230267 GPYVLGPADREDEEEDEEEEEQTDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPYVLGPADREDEEEDEEEEEQTDPK 26 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ; 167.1 9.85E-12 863200000 340910 290150 277200 319320 324220 291620 376520 418130 450520 434080 FALSE TRUE 327586.8603 281875.2061 327296.2063 335800.1435 334648.8307 297516.7562 381127.9644 409495.4694 399378.8583 404679.375 0.809497297 0.69653959 0.808779064 0.829793076 0.826948077 0.735191301 0.941802296 1.011901013 0.986901935 1 18.6264198 2.106129205 4.617711214 0.995720686 0.786007558 0.86015486 0.040053916 0.07513907 2.733653319 0.016169459 0.011644806 127.6818613 -2.106129205 -0.209713128 IEEDFPHIR ddPTM_BT-474_Pertuzumab_2h_R1 4 IEEDFPHIR 9 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 ;;; 207.68 1.13E-05 1042910000 1323790 1409410 1083040 1353920 1346010 1328210 1244720 1254810 1334130 1345710 FALSE TRUE 1272054.823 1369215.007 1278769.42 1423795.973 1389305.634 1355067.316 1259953.256 1228897.735 1182685.156 1254563.863 1.013941865 1.091387252 1.019294001 1.134893181 1.107401285 1.080110273 1.00429583 0.979541792 0.942706219 1 20.25875448 2.106534839 3.039033804 0.974229166 1.077319236 0.60954154 0.036878318 0.171024162 3.130485688 0.016387199 0.010802397 127.8011728 -2.106534839 0.103090071 TSKEPPS(ph)SPLQPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSKEPPSSPLQPQK 14 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 T(0.001)S(0.001)KEPPS(0.604)S(0.394)PLQPQK;TSKEPPS(0.591)S(0.409)PLQPQK 114.34 0.00029277 1214040000 1484630 1409780 1155820 1155360 1432810 1474180 1186080 1228760 1280080 1141550 TRUE FALSE 1426609.018 1369574.455 1364702.385 1214988.268 1478897.635 1503988.93 1200595.602 1203385.677 1134770.685 1064231.802 1.340505909 1.286913671 1.282335656 1.141657547 1.389638641 1.413215549 1.128133551 1.130755231 1.066281503 1 20.02138099 2.106607467 6.523620865 1.092346846 1.302432914 0.680256021 0.076603131 0.14321209 7.799985059 0.030355892 0.022324219 127.822547 -2.106607467 0.210086068 ENIAEWK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENIAEWK 7 0 P11908;P11908-2;H7C540;D3YTJ7 P11908 PRPS2 Ribose-phosphate pyrophosphokinase 2 0 ; 101.64 0.020724 786700000 1271800 1188350 1034560 1054470 1214880 1114080 1300550 1443830 1479120 1433990 FALSE TRUE 1222096.65 1154459.422 1221528.006 1108891.323 1253957.719 1136607.461 1316466.52 1414014.406 1311216.499 1336864.58 0.914151417 0.86355749 0.91372606 0.82947169 0.937984099 0.850203886 0.984741865 1.057709529 0.98081475 1 20.3504219 2.106790079 5.027963091 1.019666269 0.885477899 0.735369128 0.035696478 0.090970517 3.680778604 0.012648706 0.009186273 127.876305 -2.106790079 -0.134188369 FNADEFEDMVAEK ddPTM_BT-474_Pertuzumab_2h_R1 9 FNADEFEDMVAEK 13 0 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;;;;; 249.2 3.79E-17 2086350000 2051623 2054561 2015931 2140018 2154121 2080381 2452381 2691412 2886291 2888519 FALSE TRUE 1971443.305 1995966.932 2380254.576 2250464.585 2223410.258 2122447.729 2482393.972 2635833.402 2558651.346 2692877.035 0.732095554 0.741202404 0.883907637 0.835710118 0.825663493 0.788171053 0.921837106 0.978816844 0.950155285 1 21.36071692 2.106793637 3.514533037 0.970385805 0.804633278 0.772656238 0.043520204 0.122512153 2.938892853 0.019600983 0.013448863 127.8773526 -2.106793637 -0.165752527 VPS(ph)SDEEVVEEPQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VPS(0.982)S(0.018)DEEVVEEPQSR 205.33 4.67E-09 275590000 65916 63839 61030 68057 65180 65613 72543 79086 87082 78778 TRUE FALSE 63339.92985 62018.37422 72059.47861 71569.42993 67276.57389 66939.73981 73430.80293 77452.84646 77196.81644 73442.29589 0.86244485 0.844450374 0.981171377 0.97449881 0.916046715 0.911460338 0.99984351 1.054608186 1.051122048 1 16.16432354 2.106872117 3.460927929 1.039206696 0.917349081 0.631888943 0.04214628 0.165130873 3.85517864 0.019345145 0.013223593 127.9004632 -2.106872117 -0.121857615 NKETLEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NKETLEGR 8 1 A0A494C0P0;A0A494C0K7;Q6P2C8-4;Q6P2C8-2;Q6P2C8 A0A494C0P0 MED27 Mediator of RNA polymerase II transcription subunit 27 0 81.525 0.020643 80862000 223070 257850 183510 197300 238390 243540 243100 280290 308640 302380 FALSE TRUE 214352.1778 250496.3705 216674.3392 207482.6766 246058.0309 248464.5457 246075.1305 274501.9136 273604.4811 281899.5333 0.760385004 0.888601579 0.768622554 0.736016389 0.872857177 0.881393959 0.872917836 0.973757957 0.970574438 1 18.10482156 2.106877795 0.841753491 0.999384064 0.797048293 0.742621446 0.044936145 0.313723162 0.415538072 0.037363852 0.020028043 127.9021354 -2.106877795 -0.202335771 WGQPPS(ph)PTPVPRPPDADPNTPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPK 24 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 WGQPPS(0.924)PT(0.076)PVPRPPDADPNT(0.29)PS(0.71)PK 124.99 5.81E-05 319250000 328540 278620 272900 312950 301160 311770 355860 425700 434590 400200 TRUE FALSE 315700.2936 270674.0304 322219.1006 329101.387 310847.0849 318074.203 360215.1211 416909.1462 385257.1651 373094.0975 0.846168019 0.725484622 0.863640306 0.882086823 0.833160018 0.852530783 0.965480621 1.117436992 1.032600536 1 18.50918001 2.107140988 2.90032676 1.060803869 0.830650394 0.803057475 0.048504477 0.104835154 1.749735179 0.022147476 0.014400654 127.9796707 -2.107140988 -0.230153475 KYGGSVGSQPPPVAPEPGPVPS(ph)SPSQEPPTKR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 32 2 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 KYGGSVGSQPPPVAPEPGPVPS(0.509)S(0.404)PS(0.071)QEPPT(0.016)KR;KYGGSVGSQPPPVAPEPGPVPS(0.451)S(0.451)PS(0.095)QEPPT(0.003)KR 141.25 3.30E-10 665680000 628090 636820 538330 580990 676680 704510 534170 551330 556840 534670 TRUE FALSE 603543.5484 618658.5171 635618.2061 610974.9635 698446.0267 718755.6749 540707.3322 539944.8428 493629.8577 498456.3247 1.210825339 1.241148896 1.275173319 1.225734198 1.401218105 1.441963196 1.08476371 1.083234009 0.990317172 1 18.92710757 2.107280663 7.041294771 1.046290301 1.296409816 0.748349232 0.074038742 0.124398901 7.343560752 0.030435483 0.022418074 128.0208373 -2.107280663 0.250119515 AVPAPSPGPT(ph)HNSPELGRPPAAGVLAPDMSDKDK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVPAPSPGPTHNSPELGRPPAAGVLAPDMSDKDK 34 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 AVPAPS(0.143)PGPT(0.767)HNS(0.09)PELGRPPAAGVLAPDMSDKDK 156.29 1.48E-09 420120000 344380 250490 267550 232550 243120 301470 339040 385250 460460 401160 TRUE FALSE 330921.2489 243346.2705 315902.2366 244551.9334 250940.1756 307565.93 343189.2729 377294.4529 408190.5112 373989.0759 0.884842019 0.650677483 0.844683059 0.653901274 0.670982635 0.822392818 0.91764518 1.008838165 1.091450359 1 18.5126366 2.107385646 1.746179465 1.039678339 0.737747611 0.734908887 0.076823238 0.174331221 1.01954181 0.042478078 0.023348326 128.0517877 -2.107385646 -0.301930729 EATNTTSEPSAPSQDLLDLS(ph)PSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EATNTTSEPSAPSQDLLDLSPSPR 24 0 J3KQU4;I3L4I4;O75674;O75674-2;O75674-3;I3NI44 J3KQU4 TOM1L1 TOM1-like protein 1 1 EATNTTSEPSAPSQDLLDLS(0.984)PS(0.016)PR;EATNTTSEPSAPSQDLLDLS(0.939)PS(0.061)PR 171.19 4.51E-12 328520000 247870 292470 249790 330970 343470 307860 249500 253280 237379 249420 TRUE FALSE 238182.9664 284129.042 294932.6095 348051.4014 354518.0245 314085.1401 252553.4556 248049.6795 210432.7311 232526.5612 1.024325845 1.221920801 1.26838245 1.496824275 1.52463453 1.350749516 1.086127341 1.066758473 0.904983628 1 17.827036 2.107479807 3.175895119 1.008765531 1.326283076 0.535317454 0.137975884 0.222550438 4.434971302 0.066402839 0.044376444 128.079554 -2.107479807 0.317517545 YLMAS(ph)DPNLQVLGAAYIQHK ddPTM_BT-474_Pertuzumab_2h_R1 4 YLMASDPNLQVLGAAYIQHK 20 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK 285.87 2.45E-45 5755470000 5356790 5528290 4309640 4925530 5065620 5154240 5264490 5791990 5798160 5806480 TRUE FALSE 5147440.725 5370628.582 5088487.815 5179737.194 5228560.268 5258462.264 5328918.403 5672383.382 5139977.185 5413201.938 0.950904988 0.992135273 0.940014408 0.956871229 0.965890489 0.971414391 0.984430004 1.047879508 0.949526222 1 22.36805078 2.107947922 3.746213236 1.006682589 0.962949416 0.266997354 0.025952553 0.24020918 6.417867328 0.010299321 0.007176174 128.2176821 -2.107947922 -0.043733174 KWQDEDGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KWQDEDGKK 9 2 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 129.16 0.00022339 4859900000 9182900 7804200 6783300 6337700 7833000 8610100 9850200 12649000 13632600 12106100 FALSE TRUE 8824022.116 7581631.857 8009193.204 6664789.457 8084955.559 8784202.121 9970749.694 12387793.73 12085084.4 11286143.06 0.781845673 0.671764642 0.709648385 0.590528529 0.716361251 0.778317453 0.883450585 1.097610907 1.070789581 1 23.42804921 2.107963684 1.823510268 1.068587001 0.690602824 0.894375203 0.054005267 0.097620646 0.624407715 0.030112933 0.016790742 128.2223358 -2.107963684 -0.377984178 GGPPFAFVEFEDPRDAEDAVYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GGPPFAFVEFEDPRDAEDAVYGR 23 1 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 162.49 1.51E-11 4569530000 876785 1047972 611407 719036 832198 934255 675381 683923 692236 642305 FALSE TRUE 842519.2729 1018084.865 721901.8456 756145.5341 858966.4045 953146.2762 683646.5147 669799.751 613656.2714 598801.1102 1.407010205 1.700205372 1.205578669 1.262765752 1.434476974 1.591757697 1.14169213 1.118567985 1.024808172 1 19.19171737 2.108213609 6.13934299 1.077931802 1.426830106 0.626783931 0.137632514 0.152871431 7.749989389 0.054649349 0.040124978 128.2961455 -2.108213609 0.348898304 AELGEYIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AELGEYIR 8 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 101.41 0.012593 327080000 330410 368870 376690 321290 372840 364360 348510 338130 369790 415190 FALSE TRUE 317497.2119 358350.1888 444766.2624 337871.8154 384832.7372 371727.6088 352775.1696 331147.4973 327812.9895 387068.8115 0.820260384 0.925804865 1.149062516 0.872898579 0.994223057 0.960365697 0.911401692 0.855526169 0.846911401 1 18.56223054 2.10826438 3.948626371 0.884491102 0.959481294 0.059295257 0.089902444 0.482327662 14.00988742 0.035912565 0.025290408 128.3111448 -2.10826438 0.074990193 ETVSEAPPLLFS(ph)DEEEKEAQLGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETVSEAPPLLFSDEEEKEAQLGVK 24 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 ETVSEAPPLLFS(1)DEEEKEAQLGVK;ETVSEAPPLLFS(1)DEEEKEAQLGVK 246.37 4.32E-38 333220000 611700 479400 510920 460880 517580 542550 671310 789070 875770 788370 TRUE FALSE 587794.0877 465727.9814 603254.6094 484666.072 534228.4308 553520.7327 679525.6926 772775.4288 776356.2611 734972.9977 0.799749228 0.633666792 0.820784724 0.659433848 0.726868106 0.7531171 0.924558718 1.051433769 1.056305828 1 19.48733172 2.108339475 2.345316461 1.040385611 0.724086657 0.865125085 0.054681251 0.090636368 0.978011955 0.024917188 0.015126233 128.3333334 -2.108339475 -0.316298954 MVIQGPS(ph)SPQGEAMVTDVLEDQK ddPTM_BT-474_Pertuzumab_2h_R1 3 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.911)S(0.089)PQGEAMVTDVLEDQK;MVIQGPS(0.746)S(0.254)PQGEAMVTDVLEDQK;MVIQGPS(0.665)S(0.335)PQGEAMVTDVLEDQK 322.29 6.19E-74 645224000 579342 496152 547958 573508 580463 567130 664230 759931 799542 761108 TRUE FALSE 556700.6741 482002.2307 646986.1999 603106.8166 599134.1196 578597.7572 672359.0454 744238.1593 708781.3441 709557.4772 0.784574459 0.67929977 0.911816478 0.849975986 0.844377149 0.815434656 0.947575168 1.048876494 0.998906173 1 19.43656003 2.108390461 3.056690234 1.018925286 0.814450667 0.721452187 0.057260424 0.139744744 2.587382525 0.026569851 0.017574238 128.3484007 -2.108390461 -0.20447462 MANSS(ph)PVLSK ddPTM_BT-474_Pertuzumab_2h_R1 13 MANSSPVLSK 10 0 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 MANS(0.001)S(0.999)PVLSK;MANS(0.019)S(0.981)PVLSK;MANS(0.037)S(0.963)PVLSK;MANS(0.082)S(0.918)PVLSK;MANS(0.081)S(0.919)PVLSK;MANS(0.003)S(0.997)PVLSK;MANS(0.002)S(0.998)PVLSK;MANS(0.023)S(0.977)PVLSK;MANS(0.021)S(0.979)PVLSK;MANS(0.026)S(0.974)PVLSK;MANS(0.023)S(0.977)PVLSK;MANS(0.007)S(0.993)PVLSK;MANSS(1)PVLSK 267.91 6.57E-18 18002020000 18519130 18154990 15549840 17191710 16749060 16794810 18897180 20478830 20512940 21985250 TRUE FALSE 17795381.93 17637227.46 18360041.99 18078976.21 17287808.73 17134412.57 19128449.34 20055935 18184397.05 20496169.44 0.868229646 0.860513352 0.895779187 0.882066099 0.84346535 0.835981212 0.933269478 0.978521136 0.88720954 1 24.28885097 2.108715986 5.549587058 0.953485554 0.865730708 0.644305026 0.03134157 0.12875284 5.825450257 0.011717482 0.008567814 128.4446399 -2.108715986 -0.087754846 NLETFCEETRR ddPTM_BT-474_Pertuzumab_2h_R1 4 NLETFCEETRR 11 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;;; 217.09 1.86E-11 2008610000 1028210 1226290 965660 1202800 1149640 1188400 1042450 1027200 1138390 1121950 FALSE TRUE 988026.4165 1191317.41 1140176.243 1264876.652 1186619.215 1212430.262 1055207.815 1005987.961 1009164.74 1045959.327 0.944612654 1.138971066 1.090077036 1.209298124 1.134479309 1.159156222 1.00884211 0.961784971 0.964822162 1 19.99639532 2.108747824 5.017718519 0.974555293 1.117918752 0.486199251 0.065316076 0.16960759 6.820950049 0.0251625 0.018279002 128.4540566 -2.108747824 0.143363459 EQS(ph)AEEDAEAEVDNSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQSAEEDAEAEVDNSK 16 0 Q8NEZ4;Q8NEZ4-3;H0YMU7;C9J4Z5 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 EQS(1)AEEDAEAEVDNSK;EQS(1)AEEDAEAEVDNSK 265.96 4.02E-27 210448000 284990 249680 250500 290870 278120 264290 357020 430740 409750 441390 TRUE FALSE 273852.2757 242559.3709 295770.9223 305881.8356 287065.9824 269634.1249 361389.3176 421845.0685 363236.8978 411494.2622 0.665506912 0.58945991 0.718772896 0.743344109 0.697618433 0.655256099 0.87823659 1.025154194 0.882726519 1 18.65051279 2.108839113 3.843378982 0.96865554 0.679941424 0.867113007 0.05222472 0.076494091 2.128950508 0.021778855 0.015262716 128.4810605 -2.108839113 -0.288714117 HAQDSDPRS(ph)PTLGIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HAQDSDPRSPTLGIAR 16 1 Q99618;F5GX58;F8WDL1;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 1 HAQDS(0.003)DPRS(0.912)PT(0.085)LGIAR 74.618 0.019246 453140000 292910 351020 261810 222780 255250 282440 198920 133570 180000 207380 TRUE FALSE 281462.7534 341009.2533 309124.8909 234277.7025 263460.3481 288151.1303 201354.4425 130811.7328 159567.1546 193333.9679 1.455837049 1.763835176 1.598916602 1.211777243 1.362721466 1.490431989 1.041485077 0.67661019 0.825344643 1 17.56073561 2.108928067 3.287106297 0.805703339 1.483754271 0.784552773 0.154968283 0.111025859 2.359866318 0.071323232 0.048179806 128.5073792 -2.108928067 0.678050932 IEASKNELHNLLDKPQLQGIPVLVLGNKR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEASKNELHNLLDKPQLQGIPVLVLGNKR 29 3 Q96BM9 Q96BM9 ARL8A ADP-ribosylation factor-like protein 8A 0 128.49 1.04E-05 60411000 76067 91105 62237 69300 66672 79433 82664 103520 108800 77120 FALSE TRUE 73094.21754 88506.7746 73484.61035 72876.5813 68816.56543 81039.18968 83675.66676 101382.2758 96449.48013 71896.59371 1.016657588 1.23102876 1.022087509 1.013630515 0.957160303 1.127163131 1.163833534 1.410112365 1.341502777 1 16.1336358 2.10895908 2.908985005 1.293517318 1.057989015 0.300382749 0.12387506 0.249169257 4.184922681 0.053852403 0.035107821 128.5165564 -2.10895908 -0.235528303 S(ph)PGAPGPLTLK ddPTM_BT-474_Pertuzumab_2h_R1 5 SPGAPGPLTLK 11 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 1 S(1)PGAPGPLTLK;S(1)PGAPGPLTLK;S(1)PGAPGPLTLK;S(1)PGAPGPLTLK;S(1)PGAPGPLTLK 118.87 0.00069544 10005250000 12679170 14348260 13214450 14711050 17180800 16321800 12784270 13073410 13141340 12863620 TRUE FALSE 12183654.02 13939061.67 15602595.07 15470289.05 17733436.04 16651837.98 12940727.72 12803439.51 11649590.18 11992355.56 1.0159517 1.162328919 1.301045069 1.29001254 1.47872834 1.388537714 1.079081391 1.067633415 0.97141801 1 23.51561173 2.109256047 5.976835473 1.033437264 1.278569854 0.503022796 0.119057435 0.198245185 9.731713897 0.050013648 0.036690491 128.6044648 -2.109256047 0.24513259 SKDEYEKS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 6 SKDEYEKSR 9 2 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R 127.79 0.00034295 9914990000 5879890 4723400 4403930 4417200 4958030 4859390 6045450 7077730 7654650 6577380 TRUE FALSE 5650097.398 4588693.257 5199818.116 4645172.221 5117509.538 4957650.195 6119436.025 6931572.402 6785726.223 6131888.194 0.92142864 0.748332832 0.847996237 0.757543529 0.834573198 0.808503032 0.997969277 1.130414023 1.10662915 1 22.54789996 2.109290302 3.343059924 1.089448087 0.814822988 0.81851016 0.055894902 0.08433687 1.848959647 0.022035961 0.014956961 128.6146089 -2.109290302 -0.274625098 VEEPSQCLASGTAISELIIEDNNAS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 4 VEEPSQCLASGTAISELIIEDNNASPQK 28 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 VEEPSQCLASGTAISELIIEDNNAS(1)PQK;VEEPSQCLASGTAISELIIEDNNAS(1)PQK;VEEPSQCLASGTAISELIIEDNNAS(1)PQK;VEEPSQCLASGTAISELIIEDNNAS(1)PQK 324.57 8.85E-84 456325000 379599 330632 289071 334955 337984 294863 385692 409767 437870 441930 TRUE FALSE 364763.8514 321202.6991 341312.56 352242.0677 348855.5623 300825.3319 390412.2141 401305.1683 388164.8333 411997.6875 0.885354123 0.779622578 0.828433194 0.854961274 0.846741554 0.730162671 0.94760778 0.974047138 0.942152942 1 18.65227671 2.109338928 7.677858986 0.966999405 0.822315294 0.740786538 0.042173205 0.113171989 7.272431746 0.015228679 0.011230302 128.6290103 -2.109338928 -0.14468411 KAEPSEVDMNS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 KAEPSEVDMNSPK 13 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK 197.51 8.16E-08 3284200000 4927300 3664890 3701550 2904070 3543890 3453880 4211530 4552800 4684000 4889200 TRUE FALSE 4734735.669 3560370.926 4370502.426 3053949.401 3657882.44 3523719.82 4263071.964 4458783.089 4152291.957 4558050.129 1.038763404 0.781117106 0.958853523 0.670012245 0.802510358 0.773076144 0.935284133 0.9782216 0.910979879 1 22.11998536 2.109379854 6.227131329 0.959562968 0.831508126 0.261079279 0.098220537 0.277678427 14.25183843 0.036303693 0.026669087 128.6411324 -2.109379854 -0.128054842 SGDLGDMEPLKGT(ph)TPLMQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGDLGDMEPLKGTTPLMQK 19 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-27;O60716-29;O60716-32;O60716-31 O60716-13 CTNND1 Catenin delta-1 1 SGDLGDMEPLKGT(0.5)T(0.5)PLMQK 132.48 2.19E-05 90891000 168990 154350 143260 127420 94759 128090 153820 164560 171470 178020 TRUE FALSE 162385.684 149948.0891 169150.2688 133996.1615 97807.00929 130680.0676 155702.4952 161161.7785 152005.4445 165962.5468 0.978447771 0.903505592 1.019207478 0.807387956 0.589331817 0.787406979 0.938178512 0.971073182 0.915902096 1 17.34049818 2.109423063 6.611619906 0.957879656 0.844627452 0.185940528 0.112004915 0.417786049 22.87457457 0.047484895 0.034937049 128.6539316 -2.109423063 -0.113252204 SAQGSSSPVPSMVQKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAQGSSSPVPSMVQKSPR 18 1 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SAQGS(0.002)S(0.001)S(0.001)PVPS(0.048)MVQKS(0.947)PR 55.827 0.067371 0 58235 65334 39015 49446 51605 63236 42045 40192 43605 47222 TRUE FALSE 55959.11182 63470.73829 46065.87838 51997.91399 53264.92169 64514.67525 42559.55929 39362.02115 38655.14321 44023.61188 1.271115872 1.441743091 1.046390253 1.181136935 1.20991712 1.465456206 0.966743924 0.89411158 0.878054788 1 15.42598989 2.109448693 7.343020879 0.9170729 1.259637743 0.659351579 0.11789085 0.13774256 8.436980244 0.045136267 0.033268737 128.6615244 -2.109448693 0.342564843 RPS(ph)VSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSVSK 6 1 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5;A0FGR8-4 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 RPS(0.958)VS(0.042)K;RPS(0.984)VS(0.016)K 105.1 0.020375 4421900000 2851200 4283500 2113200 4658200 2954800 3076900 4120000 5511700 4275500 2946700 TRUE FALSE 2739771.952 4161338.774 2495102.248 4898610.26 3049843.825 3139117.026 4170421.792 5397881.469 3790163.164 2747117.384 0.997326131 1.514801951 0.90826197 1.783181996 1.110197854 1.1426949 1.518108333 1.964925671 1.379687372 1 21.38948713 2.109503546 6.09220386 1.599623308 1.25986146 0.044307703 0.333144022 0.344679581 17.26791759 0.120110513 0.088174492 128.6777761 -2.109503546 -0.339761848 LEPNS(ph)PMHGGTLLEDVVGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEPNSPMHGGTLLEDVVGGR 20 0 Q5VY60;Q7Z4H7-3;Q7Z4H7 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 LEPNS(1)PMHGGTLLEDVVGGR;LEPNS(1)PMHGGTLLEDVVGGR;LEPNS(1)PMHGGTLLEDVVGGR 229.69 1.41E-25 239911000 101554 115898 103080 131128 124046 122326 100904 96549 97271 112880 TRUE FALSE 97585.15741 112592.7025 121708.849 137895.5318 128036.0522 124799.5155 102138.8933 94555.22941 86229.20387 105234.5371 0.927311129 1.069921583 1.156548529 1.310363837 1.216673307 1.185917846 0.970583386 0.898518985 0.81940023 1 16.68324874 2.109548765 3.903137635 0.902218915 1.152280124 0.535149862 0.102376551 0.181199408 5.164973643 0.044832942 0.031525596 128.6911746 -2.109548765 0.25006121 ELNSNHDGADET(ph)SEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELNSNHDGADETSEK 15 0 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.858)S(0.142)EK 145.19 1.51E-05 368840000 133650 130950 157600 189380 146620 128790 208190 250440 217500 254010 TRUE FALSE 128426.8102 127215.4342 186081.8258 199153.9245 151336.1655 131394.222 210737.8915 245268.3265 192810.3118 236805.6765 0.542329948 0.537214463 0.785799684 0.841001481 0.639073217 0.554860948 0.889919087 1.035736686 0.814213218 1 17.85334414 2.109571659 5.643527078 0.955745363 0.660182496 0.624409136 0.10863848 0.144568975 6.654021068 0.04425266 0.032387695 128.6979588 -2.109571659 -0.295562866 LQEVPHEGPMCDLLWSDPDDR ddPTM_BT-474_Pertuzumab_2h_R1 11 LQEVPHEGPMCDLLWSDPDDR 21 0 P67775;P62714;H0YC23;E5RHC1 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform;Serine/threonine-protein phosphatase 0 ;;;;;;;;;; 225.26 2.87E-25 10113814000 3588384 3342534 3122449 3392225 3397776 3283508 3276156 3226323 3273156 3630689 FALSE TRUE 3448145.986 3247208.203 3686744.993 3567298.139 3507068.551 3349902.781 3316250.577 3159698.303 2901601.053 3384779.2 1.018721099 0.959355991 1.089212848 1.05392344 1.036129196 0.989696102 0.979753887 0.933502044 0.857249729 1 21.69063029 2.109578795 1.601770466 0.922926984 1.030524364 0.475394155 0.045122122 0.32097233 1.572562812 0.02716913 0.014582374 128.7000735 -2.109578795 0.10759738 DVNSSS(ph)PVMLAFK ddPTM_BT-474_Pertuzumab_2h_R1 4 DVNSSSPVMLAFK 13 0 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1;Q9NRI2 C4P0D6 DISC1;TSNAX;TRAX Translin-associated protein X 1 DVNSS(0.008)S(0.992)PVMLAFK;DVNS(0.001)S(0.025)S(0.974)PVMLAFK;DVNSSS(1)PVMLAFK;DVNSS(0.005)S(0.995)PVMLAFK 313.32 1.22E-50 428620000 1357320 1351030 1112290 1284070 1195530 1105410 1450990 1509370 1637350 1726050 TRUE FALSE 1304274.434 1312499.947 1313305.546 1350341.007 1233985.308 1127762.148 1468747.65 1478200.982 1451484.892 1609143.096 0.810539744 0.81565148 0.816152118 0.839167759 0.766858654 0.700846401 0.912751422 0.918626184 0.902023503 1 20.6178612 2.109670016 8.475181365 0.927248868 0.794949846 0.720169921 0.043294097 0.146900398 10.47282645 0.016678144 0.012308477 128.7271092 -2.109670016 -0.132299022 SLLS(ph)SPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLSSPTK 8 0 Q92667-2;Q92667;I3NI36 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 SLLS(0.493)S(0.493)PT(0.015)K 73.841 0.044604 508230000 905010 1154200 993890 1129100 820490 721480 1231600 1355400 1267600 1261900 TRUE FALSE 869641.2087 1121283.346 1173508.032 1187372.986 846881.806 736068.8199 1246672.689 1327410.516 1123707.362 1176430.389 0.739220286 0.953123412 0.997515912 1.009301526 0.719874133 0.625679876 1.059707995 1.128337493 0.955183896 1 20.16598453 2.109770539 20.05278105 1.055913157 0.854100892 0.361609906 0.125057837 2.761650891 489.8259937 0.050693306 0.037439528 128.756908 -2.109770539 -0.201812265 ETEEILADVLK ddPTM_BT-474_Pertuzumab_2h_R1 5 ETEEILADVLK 11 0 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ;;;; 183.64 1.22E-05 164078000 375482 326910 402638 433816 387357 344281 492267 531978 579438 615915 FALSE TRUE 360807.7483 317586.8469 475403.6432 456205.2957 399816.6897 351242.5977 498291.5108 520992.4684 513662.6274 574198.5284 0.628367595 0.553095891 0.827942984 0.79450795 0.696303926 0.611709331 0.867803532 0.907338564 0.894573222 1 19.13119011 2.109854676 5.370032703 0.91508536 0.691824357 0.661872999 0.081766971 0.145089372 6.308284786 0.033597378 0.024525619 128.7818548 -2.109854676 -0.223261003 EHNFQPGDNVEVCEGELINLQGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHNFQPGDNVEVCEGELINLQGK 23 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 168.78 9.26E-12 159970000 78387 83944 62256 66621 70851 75619 65436 48179 85973 85064 FALSE TRUE 75323.54938 81549.99931 73507.04408 70059.31779 73129.98676 77148.06799 66236.82534 47184.08681 76213.70547 79302.53951 0.949825186 1.028340326 0.92691917 0.88344356 0.922164501 0.972832251 0.835242172 0.594988346 0.961049998 1 16.27507945 2.110053327 5.368811081 0.78577728 0.945253394 0.076014171 0.112157417 0.256806112 11.15870121 0.042473178 0.031005318 128.8407744 -2.110053327 0.159476114 SLST(ph)EVEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSTEVEPK 9 0 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 SLS(0.299)T(0.701)EVEPK;SLS(0.322)T(0.678)EVEPK 209.97 8.43E-05 409420000 912300 914730 577540 826840 987990 891820 1154140 1625990 1483290 1150260 TRUE FALSE 876646.3074 888642.796 681914.3253 869513.3115 1019769.596 909853.2114 1168264.711 1592412.738 1314913.138 1072351.866 0.817498748 0.82868583 0.635905384 0.810847017 0.95096547 0.848465173 1.08944158 1.484972227 1.226195598 1 20.03234694 2.11010956 3.26462783 1.291247015 0.811240047 0.664137147 0.134834452 0.12617807 2.64782529 0.057240848 0.038632167 128.8574581 -2.11010956 -0.480006967 RS(ph)STAKPEVEHPEPDHSKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSTAKPEVEHPEPDHSKR 19 3 Q9NZI5-3;Q9NZI5;B7Z1S6;F8WFB0 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RS(0.439)S(0.439)T(0.121)AKPEVEHPEPDHSKR;RS(0.442)S(0.442)T(0.115)AKPEVEHPEPDHSKR 139.79 7.39E-08 344140000 396200 357270 315210 272370 361130 345730 266460 132934 363940 304520 TRUE FALSE 380716.066 347081.0094 372175.4588 286427.0483 372746.0744 352720.8975 269721.0172 130188.8664 322627.057 283894.5892 1.341047278 1.222570005 1.310963551 1.008920421 1.312973507 1.24243614 0.950074526 0.458581711 1.136432568 1 18.11499583 2.110342666 4.356497931 0.783476086 1.234136889 0.442034383 0.188493038 0.15854091 5.30586456 0.072394128 0.051834937 128.9266405 -2.110342666 0.450660803 QMMS(ph)PVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QMMSPVSK 8 0 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 QMMS(1)PVSK 98.182 0.0080808 304350000 300400 359240 287150 330850 391590 336100 278880 262100 278630 261980 TRUE FALSE 288660.0359 348994.8269 339044.3926 347925.2081 404185.848 342896.1723 282293.0169 256687.5434 247001.0905 244235.8613 1.181890466 1.428925405 1.388184319 1.424545955 1.654899677 1.403955056 1.155821325 1.050982203 1.011321962 1 17.89791552 2.110391082 2.806965889 1.034125296 1.426619137 0.734937366 0.107721965 0.143651223 2.246620155 0.051219006 0.033064611 128.9410141 -2.110391082 0.392493841 MAGNEALSPTS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 1 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALS(0.006)PT(0.042)S(0.951)PFR 114.54 0.00049474 67385000 153690 202020 181110 176630 195380 219660 153430 150250 171560 153250 TRUE FALSE 147683.6249 196258.5874 213840.6058 185745.8955 201664.5751 224101.6757 155307.7222 147147.285 152085.228 142870.241 1.033690598 1.373684163 1.496747008 1.300102066 1.411522608 1.568567913 1.087054387 1.029936563 1.064498996 1 17.12434592 2.1105024 7.41011632 1.040954787 1.369164767 0.579864544 0.133333634 0.161172567 9.932720456 0.050333374 0.037104516 128.9740686 -2.1105024 0.32820998 KQQEYEEQFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQQEYEEQFK 10 1 H3BQQ6;H3BTI2;H3BTP8;H3BSY6;H3BP64;H3BUL4;H3BMX9;Q9GZU8;Q6P4H7;H3BSF0 H3BQQ6 FAM192A;NIP30 Protein FAM192A 0 ; 107.97 0.0035497 368900000 245944 223390 207329 193236 251822 221434 254278 275844 301158 285274 FALSE TRUE 236332.2366 217019.1359 244797.9623 203208.9331 259922.0833 225911.5472 257389.9302 270147.725 266971.8064 265952.1379 0.888626948 0.81600824 0.920458712 0.764080841 0.977326542 0.849444374 0.967805457 1.015775722 1.00383403 1 18.02080711 2.110537741 3.693763842 1.00569831 0.869163072 0.57604044 0.054187785 0.156610398 4.08347101 0.020860381 0.014514348 128.9845644 -2.110537741 -0.136535237 LSASTASELS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSASTASELSPK 12 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 LSASTASELS(1)PK;LSASTASELS(1)PK;LSASTAS(0.009)ELS(0.991)PK 209.21 6.06E-08 1172500000 1937710 1566430 1572670 1429750 1654920 1499510 1896730 2158600 1939270 2249360 TRUE FALSE 1861982.151 1521756.95 1856886.453 1503539.569 1708152.005 1529831.12 1919942.749 2114024.156 1719132.2 2097008.844 0.887922889 0.725679796 0.885492905 0.716992479 0.814565952 0.729530123 0.915562543 1.008114087 0.819802074 1 20.99990152 2.110605677 6.038414565 0.947739835 0.792447367 0.470282448 0.074337892 0.163785076 8.105694732 0.026117075 0.019168759 129.0047426 -2.110605677 -0.155292468 RGGADVNIR ddPTM_BT-474_Pertuzumab_2h_R1 3 RGGADVNIR 9 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 137.46 0.00026308 1643330000 836960 940630 595360 740990 812300 863730 690210 677720 734360 747440 FALSE TRUE 804250.6779 913804.1534 702954.7957 779232.5827 838428.3672 881195.2124 698656.9964 663724.8452 650998.5315 696815.223 1.154180694 1.311400961 1.008810905 1.118277209 1.203229119 1.264603848 1.00264313 0.952511976 0.934248435 1 19.41041662 2.110676965 6.004005125 0.96215444 1.173222346 0.622637542 0.078303119 0.140795259 6.923579711 0.030543433 0.022413213 129.0259201 -2.110676965 0.211067906 RT(ph)PTMPQEEAAEK ddPTM_BT-474_Pertuzumab_2h_R1 3 RTPTMPQEEAAEK 13 1 Q9NYV4-2 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 RT(0.982)PT(0.018)MPQEEAAEK;RT(0.999)PT(0.001)MPQEEAAEK;RT(0.999)PT(0.001)MPQEEAAEK 225.94 2.24E-11 2925050000 1975050 1700330 1457800 1561440 1605080 1634890 1800620 1925100 2082660 2013800 TRUE FALSE 1897862.862 1651838.253 1721256.889 1642026.106 1656708.856 1667948.596 1822656.526 1885346.012 1846245.168 1877403.532 1.010897673 0.879852533 0.916828406 0.874626087 0.882446862 0.888433716 0.970838978 1.004230566 0.983403481 1 20.84030735 2.110847291 4.448207522 0.994456508 0.905312276 0.53268727 0.037425878 0.159025705 5.472418943 0.014416634 0.010352119 129.0765329 -2.110847291 -0.089144232 SIQEIQELDKDDESLRK ddPTM_BT-474_Pertuzumab_2h_R1 5 SIQEIQELDKDDESLRK 17 2 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;; 286.68 9.82E-37 14661520000 4040730 3293130 3049427 2806850 3340210 3393690 3813410 4301940 4819500 4140290 FALSE TRUE 3882813.804 3199213.157 3600526.293 2951711.865 3447650.888 3462312.737 3860079.652 4213103.436 4272410.565 3859864.471 1.005945632 0.8288408 0.932811585 0.764719043 0.893205167 0.897003707 1.000055749 1.091515899 1.106880979 1 21.88011876 2.110903734 2.517094448 1.074342552 0.878940284 0.612056874 0.064748976 0.170660644 2.135107628 0.029454763 0.018359387 129.0933093 -2.110903734 -0.195402268 KKDS(ph)VESHPTWVDDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 KKDSVESHPTWVDDTR 16 2 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 KKDS(0.993)VES(0.007)HPTWVDDTR 74.325 0.017009 399790000 376950 382330 376230 428110 574230 447270 392310 394230 406610 402010 TRUE FALSE 362218.3773 371426.3227 444223.1302 450204.8084 592700.6295 456314.1058 397111.2071 386089.0127 360453.3374 374781.5046 0.966478796 0.991047632 1.185285626 1.201246067 1.581456454 1.217547025 1.059580588 1.030170934 0.961769279 1 18.51569023 2.110974214 3.938920296 1.009610405 1.199026603 0.238499854 0.157237936 0.377532453 10.9056906 0.070857504 0.049947975 129.1142611 -2.110974214 0.189416198 GLPWSCS(ph)VEDVQNFLSDCTIHDGAAGVHFIYTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR 33 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 1 GLPWS(0.009)CS(0.991)VEDVQNFLSDCTIHDGAAGVHFIYTR;GLPWS(0.015)CS(0.985)VEDVQNFLSDCTIHDGAAGVHFIYTR 259.91 3.22E-59 276760000 85156 82144 50510 75505 74195 63668 62347 41118 61097 48527 TRUE FALSE 81828.00938 79801.33355 59638.28059 79401.8221 76581.54956 64955.41058 63110.02124 40268.89893 54161.5247 45240.22307 1.808744604 1.763946509 1.318257881 1.755115619 1.692775684 1.43578891 1.394998012 0.89011274 1.197198445 1 15.46531842 2.111054582 1.756110701 1.018177726 1.651888992 0.743907527 0.157922925 0.175439196 1.039316098 0.089663473 0.049545464 129.1381563 -2.111054582 0.633711266 TGQIWPNDGEGAFHGDADGSFGT(ph)PPGYGCAADR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 33 0 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 TGQIWPNDGEGAFHGDADGS(0.076)FGT(0.924)PPGYGCAADR 155.99 2.08E-10 228610000 75448 85868 73564 90100 82896 90588 102310 136900 116800 129600 TRUE FALSE 72499.40875 83419.12871 86858.65122 94750.0718 85562.42512 92419.75143 103562.1004 134072.9672 103541.3537 120822.0766 0.600051007 0.690429523 0.718897189 0.784211582 0.708168801 0.764924375 0.85714551 1.10967276 0.856973797 1 16.88252456 2.111138576 2.722902072 0.999109323 0.710194157 0.740367939 0.073851073 0.128452661 1.88912258 0.03343599 0.021391371 129.1631346 -2.111138576 -0.288915166 AEEFKK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEEFKK 6 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 97.071 0.066524 9673500000 8577520 8051520 6921640 6338920 7244430 8143210 8594800 9941500 10904400 10232800 FALSE TRUE 8242301.035 7821898.533 8172534.319 6666072.421 7477453.67 8307871.286 8699985.733 9736204.551 9666578.227 9539723.342 0.863997911 0.819929284 0.856684626 0.698769994 0.783822906 0.870871302 0.911974637 1.020596112 1.013297543 1 23.185516 2.111140297 1.74959406 1.015144862 0.804534495 0.794933416 0.045144626 0.16071596 0.944847493 0.027269687 0.015052068 129.1636463 -2.111140297 -0.210610367 VKAS(ph)PITNDGEDEFVPSDGLDKDEYTFS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKASPITNDGEDEFVPSDGLDKDEYTFSPGK 31 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 VKAS(1)PITNDGEDEFVPSDGLDKDEYT(0.314)FS(0.686)PGK 262.71 5.68E-59 182230000 176640 140790 109430 110660 124870 118670 150540 168640 179810 142480 TRUE FALSE 169736.7135 136774.807 129206.4353 116371.1759 128886.557 121069.5887 152382.3536 165157.5251 159398.7226 132829.7027 1.277852092 1.029700468 0.972722461 0.876093024 0.970314277 0.911464727 1.147200893 1.243377962 1.200023183 1 17.01921827 2.111668158 6.564395154 1.179575752 0.998827406 0.240932764 0.118270718 0.249999252 13.50500047 0.045430018 0.033423437 129.320733 -2.111668158 -0.180748347 TDGSIS(ph)GDRQPVTVADYISR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 T(0.001)DGS(0.49)IS(0.509)GDRQPVTVADYISR 141.23 5.09E-07 492730000 425770 435580 397930 440650 427070 480510 484080 585900 604890 623500 TRUE FALSE 409130.4377 423157.6849 469844.8029 463391.9993 440807.0944 490226.2414 490004.3158 573800.9603 536225.4231 581269.7896 0.703856359 0.727988436 0.808307625 0.797206405 0.758351977 0.843371271 0.842989477 0.987150839 0.922506954 1 19.1488484 2.111843018 0.709301434 1.000816862 0.743700393 0.857765347 0.036692845 0.242167687 0.233269349 0.032505628 0.0192822 129.3728119 -2.111843018 -0.257116469 LEKPETQSS(ph)PITVQSSK ddPTM_BT-474_Pertuzumab_2h_R1 3 LEKPETQSSPITVQSSK 17 1 Q96CB8;A0A087WXN4;E9PGI3 Q96CB8 INTS12 Integrator complex subunit 12 1 LEKPETQS(0.007)S(0.976)PIT(0.016)VQSSK;LEKPET(0.001)QS(0.242)S(0.756)PITVQSSK;LEKPETQS(0.215)S(0.784)PITVQSSK 228.23 9.06E-16 1449410000 2415230 2232300 1932070 1899350 2140290 2342360 2451660 2627730 2983330 2942650 TRUE FALSE 2320840.141 2168636.99 2281238.028 1997375.681 2209134.372 2389724.124 2481664.148 2573466.457 2644674.886 2743341.694 0.845990183 0.790509252 0.831554462 0.728081261 0.805271314 0.871099699 0.904613579 0.938077259 0.96403408 1 21.3875029 2.11201118 1.083887478 0.978988067 0.796625384 0.840219703 0.032037211 0.196049686 0.430292831 0.024229941 0.012294469 129.422916 -2.11201118 -0.182362683 TALPTSGSSAGELELLAGEVPARS(ph)PGAFDMSGVR ddPTM_BT-474_Pertuzumab_2h_R1 5 TALPTSGSSAGELELLAGEVPARSPGAFDMSGVR 34 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;T(0.002)ALPT(0.116)S(0.107)GS(0.103)S(0.103)AGELELLAGEVPARS(0.566)PGAFDMS(0.002)GVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR 273.56 6.09E-74 918491000 277819 332413 156445 166556 257607 304795 140171 126789 127311 95278 TRUE FALSE 266961.5263 322932.9067 184718.0916 175151.9751 265893.1631 310958.1637 141886.4546 124170.7628 112859.189 88824.7362 3.005486284 3.635619091 2.0795794 1.971882863 2.993458517 3.500805936 1.597375469 1.397929993 1.270582879 1 16.43867388 2.112093709 6.081861531 1.324250415 2.825408308 0.69194667 0.508320196 0.135587685 6.742721403 0.208612521 0.153166051 129.4475124 -2.112093709 1.501157893 RGNGLIK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGNGLIK 7 1 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 112.59 0.010133 1562220000 1578050 1497190 1278770 1368370 1356210 1391950 1485520 1562160 1689460 1590590 FALSE TRUE 1516378.061 1454491.607 1509872.185 1438991.74 1399833.726 1420096.183 1503700.238 1529900.85 1497679.584 1482857.923 1.022605091 0.98087051 1.018217701 0.970417811 0.944010687 0.95767515 1.014055504 1.031724501 1.009995335 1 20.49994894 2.112135803 7.911457486 1.018746438 0.981650878 0.288842906 0.023941035 0.284619779 18.70042564 0.009615489 0.007093142 129.4600597 -2.112135803 -0.03709556 ARENIQK ddPTM_BT-474_Pertuzumab_2h_R1 7 ARENIQK 7 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72 P29692 EEF1D Elongation factor 1-delta 0 ;;;;;; 130.27 0.0032645 3188930000 2684120 2746140 2171990 2311760 2387230 2052620 2870680 3004940 3124000 3402040 FALSE TRUE 2579221.623 2667822.776 2564516.909 2431070.211 2464017.421 2094125.383 2905812.241 2942886.939 2769376.617 3171616.801 0.813219813 0.841155456 0.808583467 0.766508177 0.77689632 0.660270617 0.916192725 0.927882252 0.873175037 1 21.59678704 2.112327291 10.78630355 0.924729429 0.781561704 0.658096212 0.053461465 0.226583786 20.59109392 0.020351108 0.015029079 129.5171536 -2.112327291 -0.143167724 VDIDTPDIDIHGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 252.17 1.60E-26 2760120000 3218460 3337020 3027120 3563140 3003780 3283780 3686400 3998740 4357740 4233980 FALSE TRUE 3092679.025 3241851.457 3574187.922 3747034.082 3100399.312 3350180.281 3731515.266 3916164.622 3863067.624 3947208.763 0.783510377 0.821302255 0.905497565 0.94928703 0.785466262 0.848746667 0.945355437 0.992135166 0.978683383 1 21.91240139 2.112592125 3.356266149 0.986240112 0.851713278 0.647533065 0.047752178 0.169164347 3.734101594 0.021634845 0.014737359 129.5961575 -2.112592125 -0.134526833 NFDFEGS(ph)LSPVIAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 NFDFEGSLSPVIAPK 15 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 NFDFEGS(0.609)LS(0.391)PVIAPK 112.3 0.0008126 165950000 472200 486710 384250 410330 424350 489410 397210 390310 472070 421390 TRUE FALSE 453745.902 472829.5073 453692.5226 431507.1805 437999.6031 499306.2055 402071.1748 382249.9621 418482.5927 392848.88 1.155013862 1.203591334 1.154877984 1.098405016 1.114931531 1.270987983 1.023475426 0.973020369 1.065250823 1 18.58361492 2.112714141 8.51398052 1.007018082 1.161857819 0.688871662 0.049597536 0.140731805 9.968763985 0.018650891 0.013765096 129.6325731 -2.112714141 0.154839737 IQVTPPGFQLVFLPFADDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQVTPPGFQLVFLPFADDKR 20 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 163.78 3.06E-11 2633300000 1497470 1448310 1367860 1531330 1344650 1389760 1680530 1825610 1947900 1971860 FALSE TRUE 1438947.217 1407005.617 1615062.73 1610362.125 1387901.888 1417861.899 1701096.829 1787910.516 1726782.558 1838304.166 0.782757959 0.76538238 0.878561209 0.876004175 0.754990341 0.771287976 0.925362005 0.972586881 0.939334518 1 20.80994406 2.11273574 4.69758618 0.96339774 0.80771374 0.759919151 0.042945091 0.112888085 4.163705953 0.018016092 0.013023022 129.6390203 -2.11273574 -0.155684001 KEFSPFGTITSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEFSPFGTITSAK 13 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YAP2;H0YB86 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ; 206.06 1.04E-07 1946010000 3350500 3261500 2816000 3157100 3110200 3526600 3523800 3833100 4206500 4257100 FALSE TRUE 3219558.756 3168485.213 3324913.842 3320038.309 3210242.408 3597910.268 3566925.318 3753945.146 3728995.755 3968762.825 0.811224782 0.798355899 0.837770859 0.836542383 0.808877363 0.906557138 0.898749932 0.945872886 0.939586445 1 21.92025792 2.112832336 0.562525626 0.994749682 0.802916094 0.916316304 0.019067482 0.207936979 0.135019272 0.01724925 0.012576421 129.6678579 -2.112832336 -0.191833588 NMADRYER ddPTM_BT-474_Pertuzumab_2h_R1 1 NMADRYER 8 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 86.882 0.014336 81040000 132720 155890 99852 101050 119310 129510 102420 84243 116750 118960 FALSE TRUE 127533.1557 151444.1698 117897.4776 106265.2026 123147.7145 132128.7809 103673.4466 82503.35261 103497.0295 110902.7332 1.149955028 1.365558498 1.063070983 0.958183802 1.110411898 1.191393369 0.934814171 0.743925332 0.933223433 1 16.7589354 2.112924329 4.874042822 0.858562067 1.136186203 0.497173916 0.115357783 0.164727549 6.359781879 0.047096027 0.034161131 129.695327 -2.112924329 0.277624135 EAARSPDKPGGSPSAS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(0.148)PDKPGGS(0.042)PS(0.042)AS(0.769)R 61.276 0.056167 380300000 225850 201440 156140 147110 167770 165110 191340 198810 218100 204730 TRUE FALSE 217023.5323 195695.1284 184357.9713 154702.3647 173166.4744 168448.6373 193681.6762 194704.504 193342.2023 190863.4547 1.137061742 1.025314818 0.96591551 0.810539477 0.907279367 0.882560978 1.014765642 1.020124593 1.012987021 1 17.54218137 2.112964704 23.47559746 1.014400528 0.949677141 0.102715651 0.081854486 11.97366126 2426.692058 0.03357488 0.024796695 129.7073851 -2.112964704 -0.064723387 MANS(ph)SPVLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 MANSSPVLSK 10 0 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 MANS(0.499)S(0.499)PVLS(0.001)K 117.27 0.0038314 463050000 711090 727140 628930 679470 642070 676250 748870 808600 827490 891590 TRUE FALSE 683299.8166 706402.6791 742591.6415 714537.5281 662722.7647 689924.2383 758034.8951 791902.1274 733556.8043 831201.8152 0.822062469 0.849856998 0.893395115 0.85964385 0.797306686 0.83003216 0.911974542 0.952719439 0.882525508 1 19.66483928 2.112969885 4.292370103 0.938257359 0.843664842 0.633762005 0.035757131 0.149400623 4.888391943 0.014258648 0.010198907 129.7089326 -2.112969885 -0.094592517 KLEMDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEMDLK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 112.84 0.010043 1033700000 2631400 2596900 2277900 2216500 2378400 1949700 3002500 3152100 3675300 3313300 FALSE TRUE 2528561.979 2522838.955 2689567.202 2330893.831 2454903.396 1989124.27 3039245.493 3087008.033 3258095.352 3088887.24 0.818599639 0.81674686 0.87072366 0.754606319 0.794753322 0.643961438 0.983928922 0.999391624 1.054779634 1 21.55865578 2.11303115 7.809587727 1.011273238 0.788298583 0.790061893 0.057259926 0.107227782 6.933421211 0.021984704 0.016216118 129.7272315 -2.11303115 -0.222974655 T(ph)PPAPSPFDLPELK ddPTM_BT-474_Pertuzumab_2h_R1 4 TPPAPSPFDLPELK 14 0 O95239 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(1)PPAPSPFDLPELK;T(1)PPAPSPFDLPELK;T(1)PPAPSPFDLPELK;T(1)PPAPSPFDLPELK 133.48 0.00049574 339999000 315905 273081 300113 261307 296811 309994 330096 363488 411883 380740 TRUE FALSE 303559.0833 265292.9973 354350.0951 274793.0856 306358.1954 316262.2911 334135.8136 355981.8458 365127.7686 354952.1407 0.855211305 0.747404979 0.998303868 0.774169399 0.86309719 0.890999813 0.941354553 1.002900969 1.028667605 1 18.43726499 2.113150234 1.413239413 1.017759004 0.845857424 0.566285909 0.062492195 0.296617651 1.124041835 0.038489427 0.020076208 129.7628076 -2.113150234 -0.17190158 KDPDMVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDPDMVK 7 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 81.594 0.042935 568470000 1107000 1068400 986500 1054300 1084100 1026600 1332500 1417500 1661400 1597100 FALSE TRUE 1063737.216 1037930.278 1164782.495 1108712.549 1118971.061 1047358.555 1348807.534 1388228.13 1472804.837 1488926.994 0.714432084 0.69709951 0.782296579 0.744638625 0.751528493 0.703431773 0.905892323 0.932368165 0.989171963 1 20.50584159 2.113419313 3.396918067 0.959273314 0.734005905 0.926967019 0.031120136 0.064132998 1.446568886 0.013771947 0.00941579 129.8432308 -2.113419313 -0.22526741 SIQEIQELDKDDESLR ddPTM_BT-474_Pertuzumab_2h_R1 8 SIQEIQELDKDDESLR 16 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;;;; 293.2 1.25E-45 34821450000 18440630 16156390 14808470 15282650 16563570 17068020 18855360 21457030 22944920 22322400 FALSE TRUE 17719949.79 15695625.58 17484689.94 16071389.4 17096352.27 17413147.06 19086117.54 21013934.83 20340308.87 20810483.97 0.85149148 0.75421723 0.840186608 0.772273697 0.821525934 0.836748779 0.917139533 1.009776364 0.977406816 1 24.31080718 2.113499326 1.90883768 0.998716997 0.805133531 0.893800085 0.028630721 0.08983003 0.632814271 0.014312142 0.008144482 129.867155 -2.113499326 -0.193583466 SHPSDGYNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHPSDGYNR 9 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8VWU8;F8VPY7;F8VRK2 F8W0Q9 PPHLN1 Periphilin-1 0 75.378 0.028261 0 23665 38386 28728 36314 30911 31408 28466 26563 26940 30200 FALSE TRUE 22740.14564 37291.26886 33919.78865 38188.16989 31905.28039 32043.09128 28814.37542 26014.46477 23881.88414 28154.5271 0.807690556 1.32452123 1.204772097 1.3563776 1.133220255 1.138115059 1.023436669 0.923988695 0.848243128 1 14.7810793 2.11379606 1.805420593 0.912709068 1.185324939 0.354746523 0.143604348 0.354250434 2.224111245 0.078332364 0.043783301 129.9559176 -2.11379606 0.272615871 AALEAIDELDLFGAHGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AALEAIDELDLFGAHGGR 18 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 0 150.39 5.53E-08 14222000 19106 19738 17960 21186 20306 21656 18677 17221 21429 24588 FALSE TRUE 18359.3164 19175.09157 21205.77152 22279.412 20959.16093 22093.89916 18905.57471 16865.38033 18996.46976 22922.63286 0.800925291 0.836513488 0.925101913 0.971939486 0.914343525 0.963846487 0.824755814 0.735752321 0.82872111 1 14.48448514 2.113817396 8.313228082 0.814335242 0.903756045 0.043409609 0.080491634 0.388594423 26.7690335 0.030405624 0.022437827 129.9623023 -2.113817396 0.089420803 EDS(ph)PGPEVQPMDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDSPGPEVQPMDK 13 0 O75382;O75382-3;O75382-2;E9PMK8;E9PMW5 O75382 TRIM3 Tripartite motif-containing protein 3 1 EDS(1)PGPEVQPMDK 108.58 0.0012641 59026000 50615 43389 38620 37523 41526 36158 49465 49657 62190 55781 TRUE FALSE 48636.90984 42151.5882 45599.4931 39459.56653 42861.7215 36889.13953 50070.36747 48631.5656 55130.45192 52002.90319 0.935272973 0.810562211 0.876864373 0.758795454 0.824217859 0.709366925 0.962837926 0.935170204 1.06014181 1 15.66630455 2.113938822 8.107623207 0.980637787 0.819098633 0.626989032 0.064353373 0.16574025 11.12017234 0.023927871 0.017654768 129.998644 -2.113938822 -0.161539154 S(ph)PGGTPLTNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGGTPLTNK 10 0 Q96HE9;J3QQS2;J3QRE1 Q96HE9 PRR11 Proline-rich protein 11 1 S(1)PGGTPLTNK 110.11 0.0020237 245020000 210370 226890 281510 310880 217940 236330 326060 397350 345540 375820 TRUE FALSE 202148.5078 220419.3193 332385.1192 326924.5541 224950.238 241108.7545 330050.4198 389144.5836 306315.7478 350365.3767 0.576964852 0.629112732 0.948681409 0.933096064 0.642044714 0.688163759 0.942017796 1.110682189 0.874275166 1 18.41850069 2.114049811 5.002894231 1.011363396 0.746566562 0.47144211 0.127286456 0.192868207 7.676787051 0.052702306 0.038317225 130.0318709 -2.114049811 -0.264796834 DRDNQDREENDKDPER ddPTM_BT-474_Pertuzumab_2h_R1 2 DRDNQDREENDKDPER 16 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 142.35 6.64E-07 973420000 622980 498530 546200 526570 550800 555590 687440 778950 852290 802180 FALSE TRUE 598633.2529 484312.4125 644910.4902 553746.3408 568516.9822 566824.4105 695853.0964 762864.4103 755541.6123 747847.6341 0.80047489 0.647608404 0.86235546 0.740453423 0.760204293 0.757941036 0.930474424 1.020079994 1.010288163 1 19.51238484 2.114097768 2.953131063 1.008567861 0.758487454 0.833746871 0.050863636 0.093527073 1.619947389 0.02148297 0.01413657 130.0462304 -2.114097768 -0.250080407 QAS(ph)ESSSRPH ddPTM_BT-474_Pertuzumab_2h_R1 6 QASESSSRPH 10 1 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 1 QAS(0.939)ES(0.02)S(0.031)S(0.01)RPH;QAS(0.868)ES(0.078)S(0.037)S(0.018)RPH;QAS(0.998)ES(0.001)SSRPH;QAS(0.998)ES(0.002)SSRPH;QAS(0.997)ES(0.003)SSRPH;QAS(0.889)ES(0.046)S(0.046)S(0.018)RPH 92.039 0.025621 475779800 429954.6 430325.8 344601.5 390705.5 385749.7 441798.8 349865.9 339929.5 380802.3 390779.6 TRUE FALSE 413151.4989 418053.3295 406878.6567 410869.8577 398157.6894 450732.2744 354147.6635 332909.837 337575.2194 364311.7496 1.134060319 1.147515363 1.116841982 1.127797438 1.092903783 1.23721586 0.972100581 0.913804832 0.926610848 1 18.474814 2.114491005 6.567488343 0.938892301 1.138337492 0.833722721 0.041480053 0.074236621 3.991825323 0.014872089 0.010943171 130.1640356 -2.114491005 0.199445192 EQEEELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQEEELRR 8 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 168.83 0.00048835 468870000 466600 515830 394840 523120 458120 484960 468170 476040 513850 524620 FALSE TRUE 448364.7561 501119.0335 466196.3712 550118.2859 472855.8459 494766.2235 473899.6045 466209.6076 455519.9022 489087.0201 0.916738203 1.024600966 0.953197186 1.124786108 0.96681332 1.011611846 0.968947416 0.953224249 0.931367801 1 18.89973165 2.114678781 4.290174824 0.957294921 1.002810679 0.094904868 0.053974394 0.447557679 14.61950674 0.020535249 0.014696981 130.2203267 -2.114678781 0.045515759 INPPSSGGTSSS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 6 INPPSSGGTSSSPIK 15 0 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 INPPSSGGTSS(0.008)S(0.992)PIK;INPPSSGGTS(0.001)S(0.053)S(0.946)PIK;INPPS(0.001)S(0.001)GGT(0.002)S(0.003)S(0.038)S(0.955)PIK;INPPSSGGTSS(0.029)S(0.971)PIK;INPPSSGGTSS(0.027)S(0.973)PIK;INPPSSGGT(0.002)S(0.006)S(0.157)S(0.835)PIK 289.5 7.48E-44 6794382000 2079700 1911850 1624180 1665770 1747590 1795110 1894340 2023820 2065230 2134170 TRUE FALSE 1998423.025 1857325.91 1917705.456 1751740.589 1803802.819 1831408.354 1917523.5 1982027.41 1830793.749 1989620.765 1.004424089 0.933507502 0.963854765 0.880439439 0.90660635 0.920481122 0.963763313 0.996183516 0.920172216 1 20.92406204 2.114832629 5.552117746 0.973582362 0.932520844 0.177146603 0.037091768 0.338250702 15.16688508 0.014365183 0.010511869 130.2664653 -2.114832629 -0.041061518 IFYDMK ddPTM_BT-474_Pertuzumab_2h_R1 2 IFYDMK 6 0 P60981;F6RFD5 P60981 DSTN Destrin 0 ; 149.94 0.024602 5593100000 6479200 6369000 5285800 6012300 5981000 5428100 6628900 7195000 6890100 7126500 FALSE TRUE 6225985.701 6187362.356 6241061.642 6322595.524 6173384.297 5537859.901 6710026.461 7046420.736 6107964.734 6643815.807 0.93710992 0.931296492 0.939379089 0.951651236 0.929192572 0.833536037 1.009965757 1.060598448 0.919345887 1 22.66358065 2.114933598 24.97243744 1.009031021 0.923390953 0.403865419 0.044941986 6.234881959 1325.302091 0.0168564 0.012449277 130.2967545 -2.114933598 -0.085640068 KNS(ph)WEPKPITVPQFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KNSWEPKPITVPQFK 15 2 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 KNS(1)WEPKPITVPQFK;KNS(1)WEPKPITVPQFK 140.16 2.60E-06 1485100000 1221740 1037170 889070 824650 1115960 1047330 1179940 1389030 1457100 1327920 TRUE FALSE 1173993.05 1007590.927 1049744.726 867210.2853 1151855.867 1068507.73 1194380.459 1360346.045 1291696.117 1237978.796 0.948314345 0.813899988 0.84795049 0.700504959 0.93043263 0.863106649 0.964782646 1.098844382 1.043391148 1 20.23955517 2.115006854 2.34090825 1.057479489 0.841884385 0.63155154 0.067695387 0.1760032 1.896696486 0.032830682 0.020051082 130.3187345 -2.115006854 -0.215595105 GAGQQQS(ph)QEMMEVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GAGQQQSQEMMEVDR 15 0 Q15435;B5MBZ8;Q15435-3;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 1 GAGQQQS(1)QEMMEVDR 172.95 2.65E-11 0 35541 45158 35362 37731 34598 41578 33474 31271 35977 39437 TRUE FALSE 34152.01843 43870.13805 41752.70002 39678.30143 35710.87609 42418.73565 33883.66483 30625.24292 31893.04179 36765.89686 0.92890481 1.193229101 1.135636652 1.079214838 0.971304365 1.153752234 0.921605828 0.832979623 0.867462635 1 15.16608056 2.11516993 5.765524731 0.880831481 1.079691822 0.487923614 0.085401409 0.153496781 7.172887294 0.031485338 0.023078562 130.3676778 -2.11516993 0.198860341 CVFELPAENDKPHDVEINK ddPTM_BT-474_Pertuzumab_2h_R1 3 CVFELPAENDKPHDVEINK 19 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ;; 292.31 8.50E-50 2539340000 3014903 3663390 2210285 3340870 2660050 3105310 3568210 4558580 4341314 3372632 FALSE TRUE 2897077.258 3558913.704 2609732.667 3513292.701 2745612.924 3168101.496 3611878.821 4464443.73 3848506.235 3144200.631 0.921403434 1.131897777 0.830014676 1.117388206 0.873230829 1.007601571 1.148743113 1.419897855 1.224001483 1 21.58426185 2.11519483 3.692522566 1.265560849 0.981240088 0.378149026 0.133253197 0.184333681 4.797338025 0.051005035 0.035588502 130.3751528 -2.11519483 -0.284320762 LGAGGGS(ph)PEKSPSAQELK ddPTM_BT-474_Pertuzumab_2h_R1 5 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(0.993)PEKS(0.007)PSAQELK;LGAGGGS(0.994)PEKS(0.006)PSAQELK;LGAGGGS(0.972)PEKS(0.028)PSAQELK;LGAGGGS(1)PEKSPSAQELK;LGAGGGS(1)PEKSPSAQELK 285.4 7.35E-40 27158400000 8802480 6734490 6466380 5774100 6596540 6882550 8367160 9364430 10495000 9509900 TRUE FALSE 8458469.35 6542428.939 7634998.71 6072101.993 6808723.7 7021719.877 8469559.807 9171051.248 9303651.599 8865786.002 0.954057469 0.73794122 0.861175615 0.684891559 0.767977447 0.792001958 0.955308396 1.034431831 1.049388243 1 23.07981711 2.115539909 3.017216422 1.027476796 0.791857184 0.695878305 0.069067212 0.135312682 2.444942611 0.029425116 0.019511886 130.4787864 -2.115539909 -0.235619612 TS(ph)PINEDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPINEDIR 9 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 T(0.373)S(0.627)PINEDIR 159.94 6.89E-05 395650000 346040 326950 309610 343720 343890 318950 381500 407880 444530 430520 TRUE FALSE 332516.3742 317625.7061 365563.4142 361459.4304 354951.5342 325399.3875 386168.9111 399457.1355 394068.818 401360.4969 0.828473098 0.791372615 0.910810648 0.900585467 0.884370876 0.810740942 0.962149773 0.995257726 0.981832594 1 18.6145391 2.115587384 5.554068829 0.988580582 0.85789381 0.757842585 0.036311009 0.110393101 4.948663925 0.014917266 0.010917012 130.4930505 -2.115587384 -0.130686771 SASS(ph)DTSEELNSQDSPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASSDTSEELNSQDSPPK 18 0 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 SAS(0.12)S(0.76)DT(0.12)SEELNSQDSPPK 557.89 0 1391900000 593900 524910 428130 593590 615030 490270 671670 748070 747370 787270 TRUE FALSE 570689.7314 509940.0807 505502.6147 624225.251 634812.9985 500183.5953 679890.0984 732622.0931 662531.6908 733947.5017 0.77756206 0.694790948 0.688744922 0.850503952 0.864929708 0.681497783 0.926347044 0.998194137 0.902696295 1 19.48531735 2.11561728 5.918911008 0.965410433 0.762954711 0.693969946 0.064444185 0.122734429 5.899139813 0.025548249 0.01874591 130.5020337 -2.11561728 -0.202455722 QYAENYTRPSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QYAENYTRPSSR 12 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 0 67.456 0.050446 93563000 43469 43776 35481 38900 39768 43996 37962 38779 40523 43881 FALSE TRUE 41770.18342 42527.55134 41893.20597 40907.63366 41047.17384 44885.62926 38426.59031 37978.2001 35922.99893 40908.90078 1.021053673 1.039567197 1.024060905 0.999969026 1.003380024 1.09720937 0.939321018 0.928360317 0.878121833 1 15.32012715 2.115632431 8.427098875 0.929183697 1.028182019 0.602490699 0.037428525 0.157055907 10.93318627 0.013443969 0.009921918 130.5065866 -2.115632431 0.098998323 KKNDIYGED ddPTM_BT-474_Pertuzumab_2h_R1 7 KKNDIYGED 9 2 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;;; 153.05 0.00031395 8669540000 7077440 6643300 5697020 5760510 6221050 6582420 6989590 7670030 8428330 8040430 FALSE TRUE 6800845.82 6453839.588 6726598.244 6057810.611 6421155.723 6715521.042 7075130.693 7511641.2 7471581.313 7495844.514 0.907282136 0.860988989 0.897376971 0.808155852 0.856628724 0.895899192 0.943873726 1.002107392 0.996763113 1 22.8376596 2.11594258 1.870541194 1.001085298 0.864864977 0.842131759 0.025369919 0.127953859 0.865083453 0.014249961 0.008074211 130.5998205 -2.11594258 -0.13622032 ENSSPSVT(ph)SANLDHTKPCWYWDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSSPSVTSANLDHTKPCWYWDKK 24 2 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 1 ENS(0.001)S(0.039)PS(0.368)VT(0.582)S(0.01)ANLDHTKPCWYWDKK 213.77 2.14E-24 1707400000 1821200 1679800 1465400 1364900 1610500 1759000 1667000 1903100 2181000 1910100 TRUE FALSE 1750025.491 1631893.749 1730230.378 1435342.653 1662303.195 1794568.185 1687401.245 1863800.32 1933422.023 1780727.226 0.982758878 0.916419834 0.97164257 0.806042965 0.933496816 1.007772644 0.947591085 1.046651218 1.085748561 1 20.76403511 2.115947577 1.276463227 1.048318917 0.921962411 0.444870465 0.054421972 0.404906558 1.244718186 0.037168126 0.019080868 130.6013232 -2.115947577 -0.126356506 EQDRVHS(ph)PCPTSGSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQDRVHSPCPTSGSEK 16 1 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 EQDRVHS(0.995)PCPT(0.002)S(0.002)GS(0.001)EK;EQDRVHS(0.998)PCPT(0.002)SGSEK 78.088 0.013354 665820000 417920 403290 330130 341870 389170 409790 362610 369900 417450 404250 TRUE FALSE 401587.2244 391788.5641 389791.8347 359513.9517 401688.0065 418076.2346 367047.7296 362261.4357 370062.8261 376869.7874 1.065586146 1.039586024 1.03428783 0.953947394 1.065853565 1.109338685 0.973937795 0.961237668 0.981938161 1 18.52370662 2.11595585 24.24724119 0.974371575 1.04095369 0.412357011 0.037955929 5.888818676 1207.258429 0.014923869 0.011021998 130.6038112 -2.11595585 0.066582115 FIGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 FIGSPR 6 0 P23443-5;P23443;P23443-3;P23443-2;P23443-4;K7ERJ3 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 FIGS(1)PR;FIGS(1)PR;FIGS(1)PR;FIGS(1)PR 102 0.037671 7961900000 3844740 4365130 4142250 4732130 4387020 4291980 4051710 4234460 4152270 4403120 TRUE FALSE 3694483.31 4240640.766 4890846.719 4976355.796 4528132.482 4378766.776 4101296.039 4147016.921 3680921.717 4104892.761 0.900019446 1.033069806 1.191467598 1.212298612 1.103106158 1.066718921 0.999123796 1.010261939 0.896715683 1 21.9689131 2.116059208 1.665867703 0.965477337 1.096840868 0.28120535 0.085473044 0.521000012 2.772606505 0.054244723 0.029631597 130.6348972 -2.116059208 0.131363531 RTPDS(ph)TFSETFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RT(0.433)PDS(0.566)T(0.001)FSETFK 184.48 8.74E-06 2415500000 1166500 1152200 994640 958990 1058600 1073900 1176800 1274100 1400500 1279300 TRUE FALSE 1120911.89 1119340.384 1174393.574 1008483.589 1092650.83 1095614.994 1191202.03 1247789.39 1241521.111 1192651.872 0.939848347 0.93853069 0.984691008 0.845580855 0.916152363 0.918637718 0.998784355 1.046231025 1.040975276 1 20.18574156 2.116076102 3.540888154 1.032311261 0.92322857 0.664642376 0.034363784 0.139533958 3.383996743 0.014647769 0.010133372 130.639979 -2.116076102 -0.109082691 ANVNEILDFFHGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 ANVNEILDFFHGYR 14 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 0 ; 228.25 1.73E-12 340140000 337610 361750 288110 349470 354260 346930 320450 321560 352570 332540 FALSE TRUE 324415.828 351433.2442 340177.886 367506.1886 365655.0946 353945.1623 324371.763 314919.6736 312547.7317 310016.7696 1.046446063 1.133594304 1.097288661 1.185439707 1.179468759 1.141696827 1.046303925 1.015814964 1.008163952 1 18.24198673 2.116117386 3.449119527 1.013195049 1.134145344 0.68999335 0.03761344 0.143903046 3.33430317 0.016635176 0.011438367 130.6523983 -2.116117386 0.120950295 DSES(ph)PSQK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSESPSQK 8 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DSES(0.999)PS(0.001)QK;DSES(0.969)PS(0.031)QK;DSES(1)PSQK;DSES(1)PSQK 192.12 0.00012884 362410000 655283 590488 541577 483892 623721 615523 703750 953780 754980 787330 TRUE FALSE 629673.8159 573647.8604 639452.0112 508865.7241 643783.5524 627969.2968 712362.703 934084.1097 669277.8355 734003.4378 0.857862216 0.781532934 0.871183946 0.693274306 0.8770852 0.855539994 0.970516848 1.272588195 0.911818394 1 19.48542729 2.116224006 3.450531994 1.097208227 0.818342545 0.522334935 0.101334484 0.153456459 3.558206665 0.040902916 0.02812979 130.6844775 -2.116224006 -0.278865682 KAAS(ph)LTEDRDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KAASLTEDRDR 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 KAAS(0.987)LT(0.013)EDRDR;KAAS(0.819)LT(0.181)EDRDR;KAAS(0.853)LT(0.147)EDRDR;KAAS(0.782)LT(0.218)EDRDR 145.43 2.85E-05 11424200000 6629280 5866650 3912080 4859050 5770180 5276870 6163700 7283600 6932820 6434060 TRUE FALSE 6370200.409 5699338.886 4619079.88 5109826.153 5955783.08 5383571.927 6239133.204 7133191.115 6145835.338 5998275.385 1.062005326 0.950162925 0.770067992 0.851882554 0.992915913 0.897519967 1.040154512 1.189207006 1.024600397 1 22.51611633 2.116247266 4.421468852 1.097136163 0.915664855 0.376753163 0.088193515 0.194946987 6.630600491 0.035850059 0.025770696 130.6914771 -2.116247266 -0.181471309 AFEEAEK ddPTM_BT-474_Pertuzumab_2h_R1 6 AFEEAEK 7 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 157.52 0.0034214 2148420000 2918510 2808650 2289570 2574720 2619520 2858710 2972720 3392100 3593960 3611210 FALSE TRUE 2804451.403 2728550.052 2703346.23 2707601.608 2703779.24 2916515.075 3009101.037 3322051.95 3185988.728 3366619.53 0.83301703 0.810471759 0.80298537 0.804249362 0.803113989 0.866303735 0.893804901 0.986761919 0.946346535 1 21.68286926 2.116279137 1.414529081 0.982281955 0.809543242 0.938972237 0.018307541 0.086282094 0.327817671 0.011235352 0.005878132 130.7010682 -2.116279137 -0.172738713 KGYNVNDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGYNVNDEK 9 1 P80723;P80723-2;U3KQP0 P80723 BASP1 Brain acid soluble protein 1 0 109.59 0.0038875 120080000 149840 181060 120280 165600 123770 159240 197360 288960 224880 185720 FALSE TRUE 143984.0871 175896.3461 142017.2716 174146.6358 127751.1745 162459.9419 199775.3507 282992.875 199352.5652 173141.019 0.831600091 1.015913774 0.820240475 1.00580808 0.737844649 0.938309956 1.153830282 1.63446465 1.151388425 1 17.40158803 2.11628824 3.771473724 1.344181608 0.891628544 0.464676906 0.175329757 0.154088292 4.149587038 0.068191922 0.047815001 130.7038078 -2.11628824 -0.452553064 GGGPQAQSHGEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 GGGPQAQSHGEAR 13 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 0 ;; 146.67 4.24E-05 462382000 196154 232663 190561 223674 227628 219879 200543 200080 201500 228227 FALSE TRUE 188488.0848 226027.679 224999.6117 235217.8419 234949.8613 224325.104 202997.3052 195948.2781 178626.5648 212768.982 0.885881405 1.06231499 1.057483142 1.105508142 1.104248651 1.054313001 0.954073772 0.920943815 0.83953292 1 17.69892832 2.1163117 3.170117965 0.915118033 1.052162925 0.413958962 0.068147206 0.230079607 4.570789566 0.029470421 0.019831466 130.7108684 -2.1163117 0.137044892 ISMPDLDLHLKS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISMPDLDLHLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ISMPDLDLHLKS(1)PK;ISMPDLDLHLKS(1)PK;ISMPDLDLHLKS(1)PK 235.73 1.83E-17 14773460000 20693730 20615650 20400610 19015460 22478350 21625600 16870230 16617260 17738180 14280210 TRUE FALSE 19884996.15 20027711.85 24087454.04 19996850.17 23201386.54 22062884.45 17076692.92 16274107.77 15724616.17 13312998.66 1.493652682 1.504372708 1.809318446 1.502054547 1.742761878 1.657243797 1.282708228 1.2224224 1.181147582 1 23.66633223 2.116565838 3.201783329 1.171880434 1.623173659 0.788216259 0.114478994 0.115601538 2.33987513 0.048882168 0.032990317 130.7873793 -2.116565838 0.451293225 LIPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 LIPSPK 6 0 Q96HE9 Q96HE9 PRR11 Proline-rich protein 11 1 LIPS(1)PK;LIPS(1)PK;LIPS(1)PK 73.665 0.086396 602690000 1632290 1740900 1505360 1565760 1391740 1519280 1819010 2224540 1824550 1885730 TRUE FALSE 1568498.302 1691251.237 1777412.039 1646569.061 1436506.581 1550000.883 1841271.589 2178602.472 1617434.733 1758007.827 0.892202115 0.962027137 1.011037614 0.936610768 0.817121835 0.881680308 1.047362566 1.239245035 0.920038414 1 20.74551006 2.116606353 5.385940299 1.09425584 0.920139991 0.313027515 0.091531551 0.198983477 8.612072317 0.035834447 0.026187918 130.799581 -2.116606353 -0.174115849 ELISNSSDALDK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELISNSSDALDK 12 0 P07900;P07900-2;G3V2J8;Q14568 P07900 HSP90AA1;HSP90AA2P Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 ;; 254.19 9.76E-21 1705982000 2204840 2279220 2046740 2139320 2023910 2250730 2397280 2703080 2837490 2732800 FALSE TRUE 2118672.415 2214218.877 2416631.447 2249730.562 2089010.903 2296241.303 2426618.63 2647260.453 2515390.031 2547705.022 0.831600361 0.869103314 0.948552296 0.883042009 0.819957917 0.901297946 0.952472366 1.039076514 0.987316039 1 21.28076682 2.116634414 2.651086474 1.011250874 0.874940363 0.745579546 0.035309626 0.140372337 1.958008985 0.017065642 0.01088201 130.8080328 -2.116634414 -0.136310511 EVDKT(ph)PPPQPPLISSMDSISQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVDKTPPPQPPLISSMDSISQK 22 1 Q92625;A0A3B3ISP1;A0A3B3ITU5 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 EVDKT(1)PPPQPPLISSMDSISQK 131.09 2.04E-05 77498000 62141 50241 61071 53912 60275 69353 73135 82442 101660 92940 TRUE FALSE 59712.46102 48808.17587 72107.88822 56694.40478 62213.80012 70755.36518 74030.04801 80739.54389 90119.98299 86645.09102 0.689161501 0.563311496 0.832221276 0.654329104 0.718030293 0.816611355 0.854405566 0.931842104 1.040104892 1 16.40283039 2.116675034 0.804096742 1.027880126 0.673323484 0.804451945 0.064772873 0.257559766 0.312881719 0.052029262 0.02867985 130.8202679 -2.116675034 -0.354556642 ERESLQQMAEVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERESLQQMAEVTR 13 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 127.03 0.00016573 295100000 82067 98008 60905 66407 77676 83541 65952 52421 83914 78290 FALSE TRUE 78859.73091 95212.9078 71911.88832 69834.27323 80174.51908 85230.25626 66759.1403 51338.48803 74388.43452 72987.34857 1.080457538 1.30451249 0.985265114 0.9567997 1.098471456 1.167740135 0.91466729 0.703388862 1.019196285 1 16.15535879 2.116857472 5.676064876 0.859428081 1.095781967 0.343383408 0.12273947 0.195609546 8.974320214 0.04772551 0.034966027 130.8752343 -2.116857472 0.236353886 KTSTS(ph)PPPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.024)S(0.036)T(0.338)S(0.602)PPPEK 73.386 0.027651 1065900000 1393700 1270900 1393800 1435600 1330800 1314300 1812000 1930300 2343000 2167000 TRUE FALSE 1339232.663 1234655.176 1645690.665 1509691.488 1373606.391 1340876.046 1834175.798 1890438.63 2077032.463 2020227.16 0.662911919 0.611146707 0.814606742 0.747287987 0.679926702 0.663725384 0.907905722 0.935755477 1.028118275 1 20.94608609 2.116883553 3.497542728 0.971233339 0.699323198 0.844839223 0.057392051 0.098555517 2.339809567 0.025696737 0.017736726 130.8830941 -2.116883553 -0.27191014 VDGETAS(ph)DSESR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDGETASDSESR 12 0 O95674 O95674 CDS2 Phosphatidate cytidylyltransferase 2 1 VDGET(0.025)AS(0.975)DSESR;VDGET(0.005)AS(0.995)DSESR 289.83 4.53E-36 501620000 312340 497880 342740 806880 378650 384100 644160 875020 650220 482200 TRUE FALSE 300133.4075 483680.9499 404680.7422 848523.1735 390829.6211 391866.7652 652043.4228 856950.5312 576409.7515 449540.1645 0.667645366 1.075946018 0.900210424 1.887535843 0.86939867 0.871705792 1.450467554 1.906282461 1.282220805 1 18.77809049 2.116953234 6.448380159 1.540076365 1.07195137 0.150138911 0.378530892 0.302801764 15.93111609 0.143084025 0.105254094 130.9040956 -2.116953234 -0.468124996 S(ph)SPSPQKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPSPQKR 8 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 S(0.649)S(0.351)PSPQKR;S(0.5)S(0.5)PSPQKR 112.11 0.0019016 285885000 205717 213860 158577 191829 179722 173300 211924 218712 240646 247847 TRUE FALSE 197677.3522 207760.9222 187235.3914 201729.3177 185502.9213 176804.2447 214517.5893 214195.5208 213328.875 231060.1019 0.855523522 0.899163986 0.810331987 0.873059935 0.802834067 0.765187253 0.928406019 0.927012145 0.923261408 1 17.81790864 2.116986562 8.491898047 0.938350261 0.836649235 0.635358741 0.040869173 0.17907821 12.54344982 0.015636882 0.011540934 130.9141416 -2.116986562 -0.101701026 HVGDLGNVTADKDGVADVS(ph)IEDSVISLSGDHCIIGR ddPTM_BT-474_Pertuzumab_2h_R1 3 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 1 HVGDLGNVTADKDGVADVS(0.999)IEDS(0.001)VISLSGDHCIIGR;HVGDLGNVTADKDGVADVS(1)IEDSVISLSGDHCIIGR;HVGDLGNVTADKDGVADVS(1)IEDSVISLSGDHCIIGR 317.03 5.56E-110 759158000 355705 393056 311241 277123 297588 366024 257308 154997 378390 307504 TRUE FALSE 341803.6553 381846.4277 367489.1722 291425.3512 307160.1883 373425.2561 260457.0123 151796.2578 335436.7535 286676.4802 1.192297516 1.331976824 1.281895089 1.016565262 1.07145235 1.30260165 0.908539871 0.529503703 1.170088154 1 18.12906402 2.117029392 5.647960047 0.817758455 1.193806364 0.368323356 0.180796737 0.178876836 8.161217715 0.069457777 0.050878344 130.9270528 -2.117029392 0.376047909 AKTQT(ph)PPVSPAPQPTEER ddPTM_BT-474_Pertuzumab_2h_R1 3 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.039)QT(0.961)PPVSPAPQPTEER;AKT(0.198)QT(0.802)PPVSPAPQPTEER;AKT(0.184)QT(0.816)PPVSPAPQPTEER 114.57 0.00034639 18942900000 20000800 18679200 15996400 17648500 15972400 17766300 19770500 21412200 22670300 23294000 TRUE FALSE 19219146.62 18146487.5 18887305.32 18559341.2 16486166.75 18125546.76 20012457.29 20970030.59 20096862.59 21716276.63 0.885011135 0.835616888 0.86973037 0.854628144 0.759161758 0.8346526 0.921541829 0.965636557 0.925428559 1 24.37227343 2.117489563 3.559980894 0.957047608 0.837869462 0.714495553 0.035708525 0.132816233 3.250525454 0.015243925 0.010568503 131.0658544 -2.117489563 -0.119178145 LQALVNSLCAGQS(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 2 LQALVNSLCAGQSP 14 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 1 LQALVNSLCAGQS(1)P;LQALVNSLCAGQS(1)P 259.48 2.12E-24 767660000 1063540 1190030 1030190 1321630 1306980 1241770 992080 989500 941180 1007700 TRUE FALSE 1021975.681 1156091.51 1216368.249 1389839.483 1349020.199 1266879.44 1004221.372 969066.4792 834341.1921 939447.5814 1.087847477 1.230607787 1.294769685 1.479422067 1.435971762 1.348536592 1.068948807 1.031527994 0.888118942 1 19.84145314 2.117625472 3.301213278 0.987790415 1.322035654 0.67707441 0.107722434 0.160758447 3.443402604 0.050727527 0.034541933 131.1068769 -2.117625472 0.334245239 EDLSPAFDHS(ph)PNK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDLSPAFDHSPNK 13 0 K7EIY0;K7ENP9;K7EIE9;D3DUJ3;K7EQG9;P17706-3;P17706-2;P17706-4;P17706 K7EIY0 PTPN2 Protein-tyrosine-phosphatase;Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 2 1 EDLSPAFDHS(1)PNK;EDLSPAFDHS(1)PNK;EDLSPAFDHS(1)PNK;EDLSPAFDHS(1)PNK 186.85 4.80E-06 3375300000 4314110 3727070 3433070 3500560 3648490 3330450 4243060 4438040 4711720 5062300 TRUE FALSE 4145509.812 3620777.613 4053502.117 3681224.321 3765846.994 3397793.981 4294987.838 4346392.923 4176865.299 4719425.912 0.878392815 0.767207216 0.858897288 0.780015279 0.797945993 0.719959174 0.910065741 0.920957973 0.885036735 1 22.17017994 2.117658509 8.00130621 0.923684259 0.800692368 0.615262503 0.049851672 0.16010856 10.5406012 0.017780498 0.013118465 131.1168505 -2.117658509 -0.122991891 NTDVAQS(ph)PEAPKQEAPAKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NTDVAQSPEAPKQEAPAKK 19 2 Q9P2E9;A0A087WVV2;Q9P2E9-3;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 NTDVAQS(1)PEAPKQEAPAKK;NTDVAQS(1)PEAPKQEAPAKK 188.49 8.39E-15 925630000 695860 587500 517640 453190 582200 642200 647380 783910 944750 701710 TRUE FALSE 668665.0219 570745.0752 611189.0628 476579.1902 600926.9917 655185.724 655302.8301 767721.9846 837505.9407 654182.5567 1.022138263 0.872455356 0.934279058 0.728511003 0.918592197 1.001533467 1.001712478 1.173559241 1.280232761 1 19.31933377 2.11780484 1.582079976 1.168045783 0.891596838 0.544946607 0.097666992 0.268387526 1.284782259 0.057884962 0.031199022 131.1610366 -2.11780484 -0.276448945 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHS(ph)LDQPPAT(ph)SPRPLIEVGELLDLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HTPSPGLPAEGAPEAPRPS(0.386)S(0.386)PPPEVLEPHS(0.408)LDQPPAT(0.408)S(0.408)PRPLIEVGELLDLT(0.003)R 70.922 1.90E-05 86983000 7170.4 8170.4 5860.5 7055.1 7634.5 7389.8 4904.3 2275.2 6303 4224.4 TRUE FALSE 6890.172841 7937.388192 6919.622716 7419.214556 7880.070626 7539.226819 4964.32029 2228.216325 5587.509864 3938.277625 1.749539646 2.015446585 1.757017502 1.883872917 2.000892617 1.914346203 1.260530811 0.565784472 1.418769928 1 11.9433491 2.117852593 3.944714323 0.939391506 1.892028504 0.787473653 0.21219251 0.086672262 2.503304088 0.081580826 0.057723625 131.175459 -2.117852593 0.952636997 SKS(ph)DLSER ddPTM_BT-474_Pertuzumab_2h_R1 3 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.299)KS(0.701)DLSER;S(0.301)KS(0.696)DLS(0.003)ER;S(0.495)KS(0.505)DLSER 121.04 0.00087828 4844930000 4158300 3650900 2950040 3429800 3600500 3446900 3947900 4470700 4457100 4020700 TRUE FALSE 3995789.039 3546779.907 3483177.851 3606812.389 3716313.352 3516598.68 3996215.581 4378378.483 3951148.694 3748374.408 1.066005848 0.946218152 0.929250249 0.962233757 0.991446677 0.938166335 1.066119642 1.168073945 1.054096593 1 21.83783363 2.117897163 5.284816587 1.098220896 0.969897827 0.426481624 0.054424094 0.152912747 6.473624426 0.020282468 0.0148097 131.1889219 -2.117897163 -0.128323069 SIYYITGESK ddPTM_BT-474_Pertuzumab_2h_R1 3 SIYYITGESK 10 0 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 ;; 233.46 1.07E-11 2819200000 2211420 2306570 1991060 2119890 2193130 2159380 2498810 2755840 2896680 2870670 FALSE TRUE 2124995.262 2240788.882 2350888.833 2229297.777 2263674.018 2203044.143 2529391.184 2698930.941 2567861.03 2676236.964 0.794023582 0.83729091 0.878430746 0.832997155 0.845842147 0.823187249 0.945129754 1.008479809 0.959504358 1 21.35177443 2.118055246 3.882868565 0.987814511 0.837674157 0.901689389 0.023407455 0.063935054 1.8022223 0.009447591 0.006667063 131.2366832 -2.118055246 -0.150140354 S(ph)AEDLTDGSYDDVLNAEQLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEDLTDGSYDDVLNAEQLQK 21 0 Q8N2F6-6;Q8N2F6-4;Q8N2F6-5;Q8N2F6-2 Q8N2F6-6 1 S(0.999)AEDLTDGSYDDVLNAEQLQK 224.99 1.91E-25 48427000 34462 59269 31224 71626 27158 39729 62557 79843 72059 59907 TRUE FALSE 33115.18694 57578.70615 36866.87137 75322.62644 28031.56173 40532.3476 63322.59128 78194.21415 63879.16442 55849.44553 0.592936718 1.030962897 0.660111681 1.348672771 0.501912982 0.725743062 1.133808772 1.400089355 1.143774371 1 15.76925534 2.118085483 5.209747421 1.234620383 0.825028852 0.331873317 0.245811342 0.214683135 8.940156099 0.09084379 0.066277741 131.2458207 -2.118085483 -0.409591531 RPQS(ph)PSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPQSPSPR 8 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 RPQS(0.986)PS(0.014)PR 107.06 0.0030466 0 41199 49777 28071 56948 52556 49267 40714 42110 40301 42556 TRUE FALSE 39588.89753 48357.4087 33144.05414 59887.0931 54246.51147 50263.2125 41212.27011 41240.41378 35726.19944 39673.64422 0.997863905 1.21887993 0.835417436 1.509493123 1.367318595 1.266916954 1.038782066 1.039491446 0.900502088 1 15.2758933 2.118195573 4.95465558 0.997091134 1.204926592 0.244358248 0.177240953 0.332458367 13.05102458 0.07113516 0.051723987 131.2790947 -2.118195573 0.207835458 TLS(ph)MDK ddPTM_BT-474_Pertuzumab_2h_R1 5 TLSMDK 6 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 T(0.002)LS(0.998)MDK;TLS(1)MDK;TLS(1)MDK;T(0.001)LS(0.999)MDK;TLS(1)MDK 147.19 0.011459 1222895000 2436780 1934420 1541637 2052160 2673190 1834610 2922140 3797640 3099620 2993790 TRUE FALSE 2341547.944 1879252.236 1820245.099 2158072.224 2759175.584 1871707.071 2957902.023 3719217.407 2747764.132 2791017.937 0.8389584 0.673321447 0.652179649 0.773220478 0.988591133 0.670618073 1.059793269 1.332566645 0.984502499 1 21.41235997 2.118244676 5.225284508 1.154595698 0.768261568 0.594207484 0.130981473 0.126276755 5.276480973 0.050403785 0.036781068 131.2939383 -2.118244676 -0.386334129 AGFNYES(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 5 AGFNYESPSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29;E7EVN4;F8W8T0 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.776)PS(0.224)K;AGFNYES(0.98)PS(0.02)K;AGFNYES(0.991)PS(0.009)K;AGFNYES(0.997)PS(0.003)K;AGFNYES(0.983)PS(0.017)K 211.52 6.01E-08 2814260000 2597780 2215480 2220930 2244360 2224940 2114600 2798620 3068980 3103070 3484170 TRUE FALSE 2496255.886 2152296.68 2622301.455 2360191.689 2296507.216 2157358.661 2832870.349 3005604.491 2750822.503 3248184.063 0.768508138 0.662615369 0.807313072 0.726618826 0.707012648 0.664173772 0.872139723 0.925318403 0.846880118 1 21.63120196 2.118265397 5.332230811 0.911544402 0.723768426 0.74843072 0.053896579 0.101735677 4.35066286 0.019747394 0.014426971 131.3002028 -2.118265397 -0.187775976 ATVT(ph)PS(ph)PVKGK ddPTM_BT-474_Pertuzumab_2h_R1 6 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 ATVT(1)PS(1)PVKGK;ATVT(1)PS(1)PVKGK;ATVT(1)PS(1)PVKGK;AT(0.034)VT(0.966)PS(1)PVKGK;ATVT(1)PS(1)PVKGK;AT(0.001)VT(0.999)PS(1)PVKGK 174.39 6.13E-05 10611650000 24173000 19409950 20224990 17708350 19308680 19335420 23138620 25770600 25492430 26682500 TRUE FALSE 23228292.44 18856397.23 23880095.6 18622280.07 19929761.23 19726395.44 23421797.35 25238428.1 22598636.22 24875270.51 0.933790546 0.758037876 0.959993403 0.748626233 0.801187719 0.793012298 0.941569554 1.014599142 0.908478009 1 24.56820888 2.118318175 5.103455446 0.976282539 0.830018763 0.472708727 0.069638933 0.168514809 6.851042413 0.025434186 0.018532776 131.3161601 -2.118318175 -0.146263776 TLTDEELADWK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLTDEELADWK 11 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 102.52 0.0066466 55587000 89819 89342 81061 89188 92922 79707 99855 106810 112550 104340 FALSE TRUE 86308.77418 86794.05363 95710.52589 93791.00337 95910.92052 81318.73015 101077.0554 104604.3362 99773.79585 97272.95886 0.887284351 0.892273193 0.983937643 0.964204281 0.98599777 0.835984955 1.039107441 1.07536912 1.025709478 1 16.56975118 2.118416593 10.4392451 1.045804692 0.930762155 0.556017202 0.047677497 0.235766277 20.40662953 0.018047526 0.013327597 131.345922 -2.118416593 -0.115042538 SMQHS(ph)PNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SMQHSPNLR 9 0 O76041-2;O76041 O76041-2 NEBL Nebulette 1 S(0.001)MQHS(0.999)PNLR;SMQHS(1)PNLR;S(0.001)MQHS(0.999)PNLR;SMQHS(1)PNLR 133.05 0.00018542 2882770000 1923984 2219810 2044951 2313880 2246150 2278640 1923524 1906237 1996667 1978353 TRUE FALSE 1848792.578 2156503.192 2414519.135 2433299.624 2318399.455 2324715.662 1947064.662 1866872.54 1770013.733 1844357.389 1.002404734 1.169243664 1.309138429 1.319321103 1.25702289 1.260447501 1.055687294 1.012207586 0.959691296 1 20.81468681 2.118510392 3.898377033 1.000022059 1.227577722 0.600304002 0.085758661 0.166435024 4.720324045 0.037304154 0.026349904 131.3742931 -2.118510392 0.227555663 KDSGS(ph)SSVFAES(ph)PGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 KDS(0.493)GS(0.505)S(0.001)S(0.001)VFAES(1)PGGK;KDS(0.422)GS(0.457)S(0.092)S(0.03)VFAES(1)PGGK;KDS(0.243)GS(0.349)S(0.249)S(0.159)VFAES(1)PGGK 194.1 1.79E-10 1752160000 1430820 1440390 1533780 1461220 1810580 1677580 1364300 1359330 1403530 1434700 TRUE FALSE 1374901.973 1399311.487 1810968.165 1536633.739 1868818.95 1711501.817 1380996.712 1331259.36 1244207.158 1337526.491 1.027943732 1.046193475 1.353968072 1.148862284 1.397220139 1.279602182 1.032500456 0.995314388 0.930229918 1 20.35113604 2.118641703 5.075078425 0.983989074 1.21341094 0.477646333 0.113223934 0.195525236 7.896841053 0.046267448 0.033702462 131.4140206 -2.118641703 0.229421867 VSEEIEDIIK ddPTM_BT-474_Pertuzumab_2h_R1 5 VSEEIEDIIK 10 0 O75223;M0QZK8;O75223-3 O75223 GGCT Gamma-glutamylcyclotransferase 0 ;;;; 199.46 6.47E-07 746811000 1126783 1023723 1014129 1120919 1076698 1035550 1296302 1437842 1524429 1495945 FALSE TRUE 1082747.075 994527.4224 1197404.669 1178769.764 1111330.969 1056489.531 1312166.532 1408150.06 1351382.211 1394623.313 0.776372419 0.713115444 0.858586443 0.84522448 0.7968682 0.757544723 0.940875231 1.009699212 0.968994422 1 20.41144407 2.1187654 4.453766138 0.98989699 0.793789019 0.841996836 0.040390269 0.085141367 2.922149583 0.016927274 0.012188436 131.4514557 -2.1187654 -0.196107971 EQSELDQDLDDVEEVEEEETGEETK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQSELDQDLDDVEEVEEEETGEETK 25 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VUX1;F8W020;F8VXI6;F8VVB5 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 316.82 1.07E-74 315860000 253058 214938 233259 276910 252990 244420 326570 376620 388940 406180 FALSE TRUE 243168.2136 208808.1787 275414.0901 291201.3583 261127.6531 249362.3399 330566.6613 368842.6654 344789.1618 378669.0668 0.642165508 0.551426554 0.727321332 0.769012797 0.689593305 0.658523132 0.872969805 0.974050161 0.910528987 1 18.53057805 2.11890698 3.428954474 0.953410665 0.674350584 0.838924209 0.057994288 0.099253503 2.276107933 0.026395716 0.018160478 131.4943158 -2.11890698 -0.279060081 QTPSLPEPKPVYAQVGQPDVDLPVS(ph)PSDGVLPNSTHEDGILRPSMK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTPSLPEPKPVYAQVGQPDVDLPVSPSDGVLPNSTHEDGILRPSMK 46 2 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 QTPSLPEPKPVYAQVGQPDVDLPVS(0.832)PS(0.165)DGVLPNS(0.002)T(0.002)HEDGILRPSMK 106.02 8.45E-08 277170000 174400 212440 161360 189780 203040 220190 155570 158070 160020 151700 TRUE FALSE 167584.2552 206381.4192 190521.3414 199574.5685 209570.966 224642.3927 157473.9122 154805.7993 141855.2005 141425.2239 1.184967226 1.459297101 1.347152482 1.411166715 1.481849986 1.588418151 1.11347826 1.094612368 1.00304031 1 17.10967993 2.118909011 6.505071934 1.058448373 1.413664345 0.753047887 0.101188182 0.108106535 5.736463159 0.038643221 0.028434638 131.494931 -2.118909011 0.355215972 MVIQGPSS(ph)PQGEAMVTDVLEDQK ddPTM_BT-474_Pertuzumab_2h_R1 6 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.057)S(0.943)PQGEAMVTDVLEDQK;MVIQGPS(0.215)S(0.785)PQGEAMVTDVLEDQK;MVIQGPS(0.007)S(0.993)PQGEAMVTDVLEDQK;MVIQGPS(0.173)S(0.827)PQGEAMVTDVLEDQK;MVIQGPS(0.031)S(0.969)PQGEAMVTDVLEDQK;MVIQGPS(0.249)S(0.751)PQGEAMVTDVLEDQK 297.14 3.42E-61 732468000 947264 873037 898410 910188 990563 948891 1113591 1243275 1323890 1329700 TRUE FALSE 910243.8756 848138.8396 1060772.672 957162.9118 1022425.359 968078.2262 1127219.46 1217600.937 1173607.557 1239638.235 0.734281866 0.684182543 0.855711483 0.77213084 0.824777205 0.780936082 0.90931324 0.982222799 0.946733914 1 20.24148773 2.119088224 2.116185789 0.976657936 0.773256328 0.802736801 0.045562537 0.14153345 1.237951589 0.024231329 0.014356695 131.5492039 -2.119088224 -0.203401608 S(ph)IDQDYER ddPTM_BT-474_Pertuzumab_2h_R1 4 SIDQDYER 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER 174.77 0.00028324 2981470000 1403150 1477260 1313473 1530487 1381940 1293290 1636940 1796390 1743870 1830560 TRUE FALSE 1348313.347 1435129.991 1550846.789 1609475.617 1426391.355 1319441.21 1656973.361 1759293.919 1545913.188 1706574.541 0.79007 0.840941873 0.908748345 0.943103028 0.835821302 0.773151819 0.97093524 1.030891928 0.905857407 1 20.702672 2.119317919 7.774320471 0.986762554 0.854963859 0.558944442 0.055530543 0.180581495 11.53562403 0.021938802 0.016183307 131.6187975 -2.119317919 -0.131798696 SAHATAPVNIAGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAHATAPVNIAGSR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 161.04 4.66E-06 477340000 56706 73871 54765 77044 59759 68201 55212 51125 51917 65653 FALSE TRUE 54489.86683 71764.27141 64662.25374 81020.25007 61681.20251 69580.07095 55887.70097 50069.25088 46023.59981 61206.26383 0.890266182 1.172498808 1.056464644 1.323724812 1.007759642 1.136812911 0.913104272 0.818041288 0.751942643 1 15.90139169 2.119422521 3.855953945 0.841718514 1.105779395 0.460216067 0.120780503 0.179720379 5.010899561 0.046601674 0.032868998 131.6505025 -2.119422521 0.264060881 DAFELFDTDKDEAIDYHELK ddPTM_BT-474_Pertuzumab_2h_R1 1 DAFELFDTDKDEAIDYHELK 20 1 H0YBL5;E5RH67;E5RFM2;E5RK82;E5RJF8;O15182 H0YBL5 CETN3 Centrin-3 0 108.92 0.00012322 18007000 28648 21779 19241 14399 21126 22578 25765 28160 34563 29240 FALSE TRUE 27528.40449 21157.88424 22718.27671 15142.13412 21805.53698 23034.54263 26080.31978 27578.48616 30639.55314 27259.54876 1.009862809 0.776164141 0.833406192 0.555479999 0.799922888 0.845008215 0.956740701 1.011700025 1.123993409 1 14.73447406 2.119430629 1.706703653 1.052328594 0.784444337 0.517211261 0.10734469 0.296535595 1.660654002 0.063257999 0.034923602 131.6529604 -2.119430629 -0.267884257 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(ph)SADLSCDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSSADLSCDSR 41 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(0.474)S(0.361)ADLS(0.163)CDS(0.002)R 167.34 5.51E-20 185170000 38090 42922 37940 38471 31513 43288 24829 7905.3 34362 34905 TRUE FALSE 36601.40069 41697.90659 44796.60197 40456.49292 32526.64426 44163.31302 25132.86473 7742.052792 30461.36982 32540.85326 1.124783066 1.281401758 1.376626532 1.243252369 0.999563349 1.357165181 0.772348055 0.237917941 0.936096223 1 14.98996446 2.119614311 5.125192612 0.609714585 1.227745364 0.517597563 0.224973529 0.132656768 5.419326773 0.084593986 0.06167079 131.7086537 -2.119614311 0.618030779 FYVEDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYVEDLK 7 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 121.52 0.010306 58710000 125070 106030 89518 99229 111320 104720 117870 129270 131160 136960 FALSE TRUE 120182.1261 103006.1282 105695.8939 104350.2206 114900.7089 106837.5101 119312.5283 126600.5293 116271.2667 127683.5772 0.94124968 0.806729655 0.827795526 0.817256399 0.899886355 0.836736505 0.934439111 0.99151772 0.910620373 1 16.96221345 2.12014611 4.225488573 0.965787334 0.851909853 0.579415296 0.043996327 0.147038341 4.695828362 0.016790751 0.012017655 131.8700316 -2.12014611 -0.113877482 VKFEER ddPTM_BT-474_Pertuzumab_2h_R1 2 VKFEER 6 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 94.262 0.040751 4299800000 9568200 9700100 7724800 7533000 9029800 7961600 9595300 10216600 10862700 9983300 FALSE TRUE 9194264.166 9423462.645 9120843.197 7921779.033 9320251.718 8122589.007 9712730.152 10005623.64 9629611.836 9307122.199 0.987874014 1.012500152 0.979985328 0.851152361 1.001410696 0.872728308 1.043580383 1.075050206 1.034649769 1 23.14990372 2.12018868 10.78901528 1.048465506 0.952859776 0.391069699 0.052811153 0.326832432 29.27311763 0.019694401 0.014544276 131.8829582 -2.12018868 -0.095605729 LITSEEERS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 3 LITSEEERSPAK 12 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LITSEEERS(1)PAK;LITSEEERS(1)PAK;LITSEEERS(1)PAK 161.08 4.02E-05 1389430000 2650830 2477270 2217440 2467940 2363570 2101470 2838470 3034510 3017270 3343110 TRUE FALSE 2547232.633 2406620.685 2618180.735 2595310.679 2439596.376 2143963.163 2873208.045 2971846.308 2674762.159 3116678.182 0.817290873 0.772174907 0.840054886 0.832716927 0.782755303 0.687900078 0.921881528 0.953530052 0.858209287 1 21.57157776 2.120195846 9.08575373 0.933366768 0.792243178 0.655054774 0.051424305 0.169794538 12.74356548 0.019181438 0.01416116 131.8851344 -2.120195846 -0.14112359 VKPTLIAVRPPVPLPAPSHPASTNEPIVLED ddPTM_BT-474_Pertuzumab_2h_R1 1 VKPTLIAVRPPVPLPAPSHPASTNEPIVLED 31 2 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 0 47.757 0.05218 189110000 488160 435610 406380 484250 505480 506260 442560 453860 493320 486070 FALSE TRUE 469082.1675 423186.8293 479821.9059 509242.2005 521739.2233 516496.9241 447976.1817 444487.6324 437320.3818 453148.046 1.03516317 0.933882057 1.058863456 1.1237877 1.151365934 1.139797311 0.988586811 0.980888335 0.965071759 1 18.78962294 2.120386249 9.039413485 0.981151865 1.072480393 0.359464302 0.058988089 0.34694102 25.90541459 0.025506447 0.01883047 131.9429679 -2.120386249 0.091328528 DVDFEGTDEPIFGK ddPTM_BT-474_Pertuzumab_2h_R1 4 DVDFEGTDEPIFGK 14 0 P42285;H0Y8U3 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ;;; 276.95 9.40E-33 294600000 484374 456405 390652 422536 454024 470730 479272 507664 582852 552150 FALSE TRUE 465444.1286 443388.7763 461251.5064 444343.1336 468628.0943 480248.4831 485137.4741 497180.561 516689.0845 514752.3887 0.90420975 0.861363222 0.89606482 0.863217235 0.910395181 0.932969897 0.94246765 0.965863533 1.003762383 1 18.97351909 2.120459893 0.759358604 1.003819608 0.878706886 0.89749158 0.015396324 0.182206007 0.198874127 0.012477507 0.007116212 131.9653435 -2.120459893 -0.125112722 LTGRDPNDVRPIQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTGRDPNDVRPIQAR 15 2 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 0 68.168 0.030053 143490000 345540 357690 281070 294630 306480 300400 266060 180440 315130 219440 FALSE TRUE 332035.9148 347489.0314 331865.6014 309835.8896 316338.2075 306474.2938 269316.1219 176713.8509 279357.7635 204577.1333 1.623035328 1.6985722 1.622202814 1.514518678 1.546302866 1.498086755 1.316452711 0.863800602 1.36553758 1 17.64228537 2.120491681 2.648156272 1.063863152 1.593419647 0.755472918 0.129690829 0.124085683 1.729052314 0.058457046 0.037401973 131.9750033 -2.120491681 0.529556496 S(ph)SSSPELQTLQDILGDPGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSSPELQTLQDILGDPGDK 20 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 1 S(0.294)S(0.294)S(0.23)S(0.18)PELQT(0.002)LQDILGDPGDK;S(0.227)S(0.227)S(0.227)S(0.227)PELQT(0.092)LQDILGDPGDK 177.6 4.18E-17 71155000 211216 189834 194723 212182 217611 199542 269200 312940 325640 311350 TRUE FALSE 202961.4452 184420.1202 229913.7777 223132.7384 224610.6554 203576.876 272494.5501 306477.6796 288674.7124 290261.9872 0.69923536 0.635357464 0.792090552 0.768728763 0.773820429 0.70135562 0.938788275 1.055865712 0.994531579 1 18.14699612 2.120676206 3.911374345 1.018259183 0.730868575 0.893021844 0.046063688 0.069776776 1.988975361 0.019751102 0.013974659 132.0310892 -2.120676206 -0.287390608 LDLRDDKDTIEK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDLRDDKDTIEK 12 2 P63000;P63000-2;B1AH77;B1AH80;P15153;B1AH78 P63000 RAC1;RAC2 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 2 0 ;;; 128.96 0.00013649 1618810000 5407770 7723410 3668720 5351310 4164030 4632420 7120310 9399340 8521700 5377920 FALSE TRUE 5196428.37 7503145.909 4331739.314 5627491.75 4297969.807 4726090.706 7207450.484 9205240.344 7554352.342 5013668.688 1.036452285 1.496538039 0.863985952 1.122429921 0.857250463 0.942641208 1.437560184 1.836028848 1.506751405 1 22.25743523 2.120699887 5.276804027 1.56200646 1.06054638 0.322734052 0.261720864 0.189678163 8.015238216 0.098239919 0.071755765 132.0382888 -2.120699887 -0.50146008 AKEAQDDLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKEAQDDLVK 10 1 P15311;E7EQR4 P15311 EZR Ezrin 0 71.548 0.046197 212330000 582210 557390 510010 502270 513500 537860 570770 612410 680180 586210 FALSE TRUE 559456.5895 541493.7829 602180.1521 528192.2149 530017.1938 548735.8977 577755.254 599763.5195 602968.8179 546505.4746 1.023698052 0.990829567 1.101873961 0.966490254 0.969829615 1.004081246 1.057181091 1.097451988 1.103317068 1 19.05987642 2.120979544 4.203327441 1.077608861 1.009140103 0.260944843 0.04434487 0.255146587 8.088262877 0.017493362 0.012515739 132.1233401 -2.120979544 -0.068468758 VDINT(ph)PDVDVHGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDINT(1)PDVDVHGPDWHLK;VDINT(1)PDVDVHGPDWHLK 229.99 2.94E-19 3316800000 1829610 2459090 2228330 1702580 1977420 2396090 1671760 609650 3230700 2409500 TRUE FALSE 1758106.818 2388959.161 2631038.8 1790450.358 2041025.51 2444540.581 1692219.499 597060.5145 2863964.48 2246302.419 0.782667019 1.063507363 1.171275416 0.797065588 0.90861564 1.088250879 0.753335564 0.265797031 1.274968346 1 21.09912074 2.121205453 6.836790146 0.703378112 0.970692208 0 0.271786216 0.385607754 21.57180194 0.101863275 0.075030114 132.1920852 -2.121205453 0.267314096 DVDLEFLAK ddPTM_BT-474_Pertuzumab_2h_R1 6 DVDLEFLAK 9 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 214.64 1.56E-06 3137610000 5026390 4835120 4293290 4375980 4629980 4761510 5227430 5671250 6095140 6127300 FALSE TRUE 4829953.122 4697227.112 5069183.007 4601824.852 4778907.512 4857790.995 5291404.852 5554136.706 5403245.26 5712292.513 0.845536728 0.822301572 0.887416566 0.805600351 0.836600629 0.850410056 0.926318959 0.972313076 0.945897859 1 22.44563843 2.121449379 2.334187667 0.969604493 0.838913104 0.870941076 0.023121209 0.096503211 1.036342995 0.010861648 0.006670067 132.266353 -2.121449379 -0.13069139 DPWDAVLLEER ddPTM_BT-474_Pertuzumab_2h_R1 2 DPWDAVLLEER 11 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 0 ; 129.88 0.00054867 21968000 33794 40795 33448 32061 41757 34723 41215 46108 43242 45690 FALSE TRUE 32473.29312 39631.56654 39492.79765 33715.67205 43100.15183 35425.12285 41719.4015 45155.85369 38333.34945 42595.3756 0.762366634 0.930419464 0.927161625 0.791533625 1.011850494 0.831665934 0.979434995 1.060111645 0.899941576 1 15.37840919 2.121631637 6.466212936 0.999561644 0.883306408 0.31541087 0.077490789 0.237646323 12.54204013 0.027832863 0.02048027 132.3218721 -2.121631637 -0.116255236 ESEITDEDIDGILER ddPTM_BT-474_Pertuzumab_2h_R1 2 ESEITDEDIDGILER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 267.02 5.18E-25 2122500000 1933820 1976120 1657690 2101820 1916770 2103120 1872160 2018030 2039840 2002060 FALSE TRUE 1858244.176 1919762.992 1957271.458 2210295.182 1978424.648 2145646.527 1895072.054 1976356.975 1808285.915 1866458.693 0.995598876 1.028559057 1.048655117 1.184218644 1.059988445 1.149581577 1.015330294 1.05888064 0.968832539 1 20.83187215 2.121652969 19.22054682 1.020254172 1.07861254 0.248927888 0.056038861 3.100021745 501.2131732 0.021743422 0.016058602 132.328372 -2.121652969 0.058358368 DSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSGSDTASAIIPSTTPSVDSDDESVVKDK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTTPSVDS(0.99)DDES(0.01)VVKDK;DSGSDTASAIIPSTTPS(0.012)VDS(0.984)DDES(0.004)VVKDK 323.86 4.86E-93 1504920000 897590 934840 738850 836310 804020 855760 1183650 1404490 1608260 1284710 TRUE FALSE 862511.1905 908179.2785 872376.6306 879472.0593 829882.0335 873064.0535 1198135.863 1375486.791 1425697.067 1197695.447 0.72014233 0.758272297 0.728379349 0.734303584 0.692899046 0.728953304 1.000367719 1.148444535 1.190366942 1 20.19182967 2.121776035 3.095067706 1.122407383 0.725390205 0.930613563 0.048480231 0.055444792 1.053366952 0.020384777 0.013689343 132.3658749 -2.121776035 -0.397017178 YVHPLTEEAIEEMER ddPTM_BT-474_Pertuzumab_2h_R1 2 YVHPLTEEAIEEMER 15 0 P22830;P22830-2;K7ELX4;A0A499FJN5 P22830 FECH "Ferrochelatase, mitochondrial" 0 ; 119.05 0.0002428 622940000 1489220 1332170 1123280 1312330 1244030 1294010 1607910 1819930 1987200 1819050 FALSE TRUE 1431019.636 1294177.816 1326281.683 1380059.509 1284045.355 1320175.769 1627588.084 1782347.81 1761621.387 1695844.123 0.843839134 0.763146682 0.782077589 0.813789127 0.757171804 0.778477073 0.959750994 1.05100922 1.038787329 1 20.69357214 2.121812777 3.456084616 1.030792617 0.787208797 0.942632103 0.027259838 0.048200993 1.121005993 0.011197327 0.007733856 132.377074 -2.121812777 -0.243583821 EDKEEEKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDKEEEKEK 9 2 P07900;P07900-2;Q14568 P07900 HSP90AA1;HSP90AA2P Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 53.237 0.080378 120530000 129420 108540 112030 117420 114290 132410 136420 169580 185460 158130 FALSE TRUE 124362.1233 105444.5455 132276.3131 123480.0603 117966.2416 135087.4209 138089.5488 166078.1137 164407.3583 147419.7143 0.843592215 0.715267602 0.89727696 0.83760887 0.80020669 0.916345698 0.936710191 1.126566515 1.115233191 1 17.16956994 2.122130851 1.694781602 1.093153984 0.820563657 0.775701998 0.059318298 0.15390002 0.850196496 0.033290454 0.018386845 132.4740614 -2.122130851 -0.272590326 TDLADKR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDLADKR 7 1 P20340-2;P20340;P20340-4;J3KR73;Q9NRW1-2;Q9NRW1;C9JU14;Q53S08;Q9H0N0 P20340-2 RAB6A;RAB6B;RAB6C Ras-related protein Rab-6A;Ras-related protein Rab-6B;Ras-related protein Rab-6C 0 ;;; 114.6 0.009409 6336200000 6953200 8237600 5825300 7734600 6508200 6861100 8861400 10319200 11081200 9005100 FALSE TRUE 6681461.257 8002671.713 6878061.293 8133783.633 6717542.164 6999836.143 8969848.464 10106104.91 9823308.632 8395176.556 0.795869058 0.953246386 0.819287271 0.968863916 0.800166872 0.833792607 1.068452629 1.203798973 1.170113406 1 23.00112924 2.122142645 4.275225026 1.144815538 0.866436374 0.724309989 0.075226409 0.100279384 3.255869565 0.028044783 0.02011829 132.4776589 -2.122142645 -0.278379165 SLGYHGSSYS(ph)PEGVEPVS(ph)PVSSPSLTHDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 SLGYHGS(0.001)S(0.007)YS(0.991)PEGVEPVS(0.969)PVS(0.024)S(0.006)PS(0.001)LTHDK 193.76 5.92E-19 519070000 86480 136040 98615 172160 123880 133010 115860 121090 94188 156010 TRUE FALSE 83100.26599 132160.2724 116436.9242 181045.1982 127864.7127 135699.5533 117277.9293 118589.4492 83496.17311 145443.3037 0.571358487 0.908672101 0.800565727 1.244781943 0.879137846 0.933006538 0.806348084 0.81536548 0.574080559 1 17.15009735 2.122144415 4.497158578 0.783616178 0.901929285 0.052151622 0.181812297 0.587369826 20.42180828 0.07050506 0.050874003 132.478199 -2.122144415 0.118313107 SVEEGKIDGIIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEEGKIDGIIDK 13 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 194.48 8.99E-07 343550000 464780 462390 293890 376410 449100 576170 509200 593920 753120 733180 FALSE TRUE 446615.8838 449203.0899 347002.4605 395836.5652 463545.7094 587820.5522 515431.7419 581655.3445 667628.9749 683521.0656 0.65340471 0.657189826 0.507669007 0.579113922 0.67817326 0.859988933 0.754083185 0.850969156 0.97674967 1 19.38262628 2.122750244 0.634453455 0.99620114 0.586654209 0.830728955 0.064689948 0.319247906 0.252985277 0.062439951 0.040769517 132.6631312 -2.122750244 -0.409546931 HEPLVLFCESCDTLTCR ddPTM_BT-474_Pertuzumab_2h_R1 6 HEPLVLFCESCDTLTCR 17 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;; 379.35 2.44E-105 5091200000 2046960 2077990 1845100 2071800 1895210 1954290 1734920 1247413 1953380 2006970 FALSE TRUE 1966962.54 2018727.76 2178550.614 2178725.846 1956171.151 1993807.083 1756152.47 1221653.486 1731640.492 1871036.134 1.051269136 1.078935742 1.16435518 1.164448835 1.045501535 1.065616557 0.938598907 0.652928858 0.925498156 1 20.83540599 2.12297261 3.419774408 0.816324742 1.099859593 0.549963071 0.094470722 0.144148141 3.291239422 0.038848981 0.026788756 132.7310746 -2.12297261 0.283534851 PANKQEDEVMR ddPTM_BT-474_Pertuzumab_2h_R1 3 PANKQEDEVMR 11 1 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ;; 165.58 1.95E-05 1135410000 1566280 1304350 1043840 1031570 1270120 1258840 1371150 1502310 1723830 1424830 FALSE TRUE 1505068.046 1267151.215 1232485.108 1084809.451 1310974.563 1284294.607 1387930.544 1471286.774 1528148.045 1328324.995 1.133057084 0.953946677 0.927849068 0.816674726 0.986938112 0.9668527 1.044872715 1.107625603 1.15043235 1 20.34117674 2.122993482 2.486437296 1.09648446 0.954490965 0.317349709 0.080681476 0.313984313 3.846554274 0.038973209 0.024485211 132.7374537 -2.122993482 -0.141993495 DDEYDYLFK ddPTM_BT-474_Pertuzumab_2h_R1 4 DDEYDYLFK 9 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907;B4DQU5 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;; 161.37 0.00015025 593543000 653734 714303 683170 910926 722111 673499 1074177 1350212 1316735 1066595 FALSE TRUE 628185.3525 693931.7778 806634.016 957939 745338.3561 687117.6112 1087323.099 1322329.65 1167264.763 994353.5706 0.631752498 0.697872264 0.811214481 0.96337865 0.749570754 0.691019403 1.093497456 1.329838489 1.173893067 1 19.92339941 2.123378804 4.685672137 1.20570942 0.767026942 0.737097378 0.114217581 0.101797203 3.73331395 0.045599606 0.033044925 132.8552755 -2.123378804 -0.438682479 HGGS(ph)PQPLATT(ph)PLSQEPVNPPSEAS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 HGGS(1)PQPLAT(0.227)T(0.773)PLSQEPVNPPS(0.004)EAS(0.944)PT(0.052)R 207.17 6.69E-25 913390000 162730 135450 157370 182390 183140 214660 136560 105680 202900 189520 TRUE FALSE 156370.3317 131587.0986 185810.2597 191803.1698 189030.8644 219000.5723 138231.2621 103497.6711 179867.6426 176683.6416 0.885030047 0.744761074 1.051655139 1.085574013 1.069883226 1.239506783 0.782365933 0.58577959 1.018020916 1 17.43080895 2.12362959 23.0598516 0.78668093 1.008497548 0.152042764 0.170042334 6.157968531 1209.531187 0.06686374 0.04938217 132.9320156 -2.12362959 0.221816618 MITNSLNHDS(ph)PPSTPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 MITNSLNHDSPPSTPPR 17 0 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;Q8N9M1-3 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 1 MITNSLNHDS(0.993)PPS(0.007)T(0.001)PPR;MITNSLNHDS(0.998)PPS(0.001)TPPR;MITNSLNHDS(1)PPSTPPR;MITNSLNHDS(1)PPSTPPR 181.23 5.25E-10 1351070000 617145 711310 607868 829130 759648 794190 641470 676970 660412 664130 TRUE FALSE 593026.2911 691024.1352 717723.2696 871921.4987 784082.7678 810249.0659 649320.5017 662990.3329 585444.7984 619147.8836 0.957810415 1.116088989 1.159211375 1.408260485 1.266390128 1.308651919 1.04873249 1.070810949 0.945565371 1 19.23992451 2.123636991 6.987106958 1.025030635 1.208709347 0.379517797 0.116738456 0.265675501 15.24592908 0.047742629 0.035180487 132.9342812 -2.123636991 0.183678712 KVSGDSSHTET(ph)TAEEVPEDPLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVSGDSSHTETTAEEVPEDPLLK 23 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;H7C2V9;H7C231 H7BYY2 BCOR BCL-6 corepressor 1 KVS(0.065)GDS(0.065)S(0.065)HT(0.065)ET(0.37)T(0.37)AEEVPEDPLLK 117.73 0.00026774 320930000 852290 781710 624290 649600 744670 729310 803940 848230 955240 896040 TRUE FALSE 818981.5645 759416.3962 737113.0903 683125.9338 768622.9868 744057.1479 813778.8582 830713.7541 846805.1599 835350.4127 0.980404812 0.909099205 0.882399864 0.817771708 0.920120437 0.890712612 0.97417664 0.994449445 1.013712506 1 19.67202198 2.123734306 2.902797183 1.000472994 0.896219996 0.603461707 0.038203533 0.187137662 3.139963712 0.017743406 0.011717587 132.9640717 -2.123734306 -0.104252998 SAS(ph)SDTSEELNSQDSPPK ddPTM_BT-474_Pertuzumab_2h_R1 5 SASSDTSEELNSQDSPPK 18 0 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 S(0.002)AS(0.499)S(0.499)DT(0.001)SEELNSQDSPPK;SAS(0.999)S(0.001)DTSEELNSQDSPPK;S(0.002)AS(0.952)S(0.046)DTSEELNSQDSPPK;S(0.145)AS(0.813)S(0.043)DTSEELNSQDSPPK;S(0.106)AS(0.861)S(0.024)DT(0.01)SEELNSQDSPPK 521.21 2.19E-295 5561010000 2169640 1978240 1766710 2121040 2148160 1951200 2557160 2907190 2952550 3029940 TRUE FALSE 2084848.07 1921822.532 2085993.797 2230507.129 2217257.517 1990654.601 2588455.289 2847155.511 2617388.902 2824719.465 0.738072611 0.680358724 0.738478218 0.78963846 0.784947866 0.704726478 0.916358357 1.007942752 0.926601361 1 21.42967616 2.123801438 4.33990511 0.975439064 0.741210366 0.897384647 0.037344707 0.064922408 2.152907606 0.015317368 0.011014742 132.9846266 -2.123801438 -0.234228698 GEAGVPAEFSIWTR ddPTM_BT-474_Pertuzumab_2h_R1 3 GEAGVPAEFSIWTR 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;; 194.39 3.46E-07 229189000 285075 319769 253419 334040 319063 315302 285966 289411 291473 328869 FALSE TRUE 273933.9538 310649.5012 299217.4506 351279.8444 329325.9512 321677.6225 289465.7375 283434.5617 258386.207 306594.4097 0.893473414 1.013226241 0.975939029 1.145747715 1.074142061 1.049195981 0.94413247 0.924460958 0.842762291 1 18.22597187 2.123822894 4.288814326 0.918389117 1.030064071 0.312897867 0.070792448 0.256781311 8.377368249 0.02881449 0.020691278 132.9911966 -2.123822894 0.111674955 SEGGFIWACK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEGGFIWACK 10 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 207.95 5.58E-06 460410000 597000 622030 527260 600260 542440 523030 650770 705010 690170 717510 FALSE TRUE 573668.58 604290.3134 622547.6108 631239.4905 559888.0752 533606.025 658734.3179 690451.2971 611824.795 668912.4086 0.857613901 0.903392291 0.930686294 0.943680342 0.837012542 0.797721821 0.98478412 1.032199864 0.91465607 1 19.35145778 2.123837577 9.932911273 0.991430813 0.883030881 0.518168023 0.049031979 0.251716166 20.84757386 0.019442869 0.014357255 132.9956931 -2.123837577 -0.108399932 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPAT(ph)SPRPLIEVGELLDLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HTPSPGLPAEGAPEAPRPS(0.354)S(0.354)PPPEVLEPHS(0.354)LDQPPAT(0.466)S(0.466)PRPLIEVGELLDLT(0.005)R 47.382 0.0030744 691500000 19323 22467 14309 19574 19214 18126 13992 9293.8 14936 10752 TRUE FALSE 18567.8358 21826.26316 16894.9546 20584.21649 19832.03576 18492.52014 14163.23828 9101.879782 13240.5279 10023.75746 1.852382788 2.177453239 1.685491161 2.053542951 1.978503154 1.844869073 1.412966977 0.908030728 1.320914632 1 13.29113579 2.124131732 2.660657029 1.073428651 1.949735906 0.860117792 0.15688716 0.086758404 1.222027015 0.067573632 0.043452973 133.0858038 -2.124131732 0.876307255 NRPPLPAGTNSK ddPTM_BT-474_Pertuzumab_2h_R1 1 NRPPLPAGTNSK 12 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 61.042 0.079949 395020000 242420 271630 193870 301120 237110 268400 280460 330000 352720 301190 FALSE TRUE 232945.9584 263883.3784 228906.6216 316660.8393 244736.8585 273827.2319 283892.3534 323185.3847 312680.7043 280790.133 0.829608775 0.939788644 0.815223167 1.127749169 0.871600636 0.975202472 1.011048181 1.150985546 1.113574401 1 18.09913271 2.124215339 2.345245815 1.102021552 0.925283886 0.394923604 0.089812546 0.277801389 3.015961637 0.042262566 0.026066765 133.111427 -2.124215339 -0.176737666 NWDDMK ddPTM_BT-474_Pertuzumab_2h_R1 4 NWDDMK 6 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 120.65 0.046517 3155010000 5129880 5145050 4457870 4715410 5084490 5137990 5397240 6076180 6550830 6118310 FALSE TRUE 4929398.618 4998318.212 5263506.274 4958772.875 5248037.238 5241883.678 5463293.038 5950704.76 5807207.242 5703911.414 0.86421374 0.876296606 0.922788924 0.869363585 0.920076919 0.918998087 0.957815198 1.043267388 1.018109648 1 22.44352015 2.12481403 1.71012498 1.026088931 0.89074033 0.869149365 0.02188404 0.115929171 0.653022198 0.012462361 0.006920189 133.2950524 -2.12481403 -0.135348601 GLFIIDDK ddPTM_BT-474_Pertuzumab_2h_R1 4 GLFIIDDK 8 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;; 178.6 0.00057867 4493920000 4901550 4410400 3828960 4275250 4331760 4209410 4910700 5461720 5623350 5170100 FALSE TRUE 4709992.007 4284619.71 4520938.247 4495896.165 4471094.994 4294527.154 4970798.616 5348933.573 4985010.883 4819924.522 0.977192067 0.888939171 0.937968681 0.932773147 0.927627595 0.89099469 1.031302169 1.109754634 1.034250819 1 22.20057912 2.124888014 5.234247427 1.062355748 0.9255218 0.723632681 0.035380589 0.090994702 3.818599758 0.012847287 0.009385564 133.3177619 -2.124888014 -0.136833948 AFESDVFHNR ddPTM_BT-474_Pertuzumab_2h_R1 3 AFESDVFHNR 10 0 O14545;F8VNX8 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 0 ;; 139.43 4.11E-05 2041140000 2019630 2342550 1716190 2221420 2149320 2258510 1877360 1853400 1949670 2122610 FALSE TRUE 1940700.627 2275742.768 2026343.709 2336067.752 2218454.83 2304178.62 1900335.693 1815126.642 1728351.635 1978843.734 0.980724548 1.150036624 1.024003904 1.180521591 1.121086416 1.164406557 0.960326306 0.917266286 0.873414917 1 20.91622626 2.124959141 5.474740172 0.925551912 1.105833971 0.61110386 0.064915421 0.127561822 5.635859206 0.023737755 0.017380152 133.3395979 -2.124959141 0.180282059 QLYQTLTDYDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLYQTLTDYDIR 12 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YF43;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YDY7 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 98.156 0.010509 69767000 63333 75234 66274 59013 88060 79249 63421 61310 71574 71189 FALSE TRUE 60857.87634 73088.39998 78251.18606 62058.668 90892.52987 80851.46908 64197.16517 60043.92707 63449.21958 66367.30562 0.916985793 1.101271165 1.179062271 0.935078913 1.369537742 1.218242451 0.967301061 0.904721482 0.956031272 1 16.01818508 2.12496562 6.940509832 0.941657796 1.124391065 0.287929837 0.12505899 0.267938322 15.30343563 0.048024233 0.035386235 133.3415871 -2.12496562 0.182733269 VSPS(ph)PSQESLSSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPSPSQESLSSSK 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VS(0.036)PS(0.964)PSQESLSSSK;VS(0.136)PS(0.801)PS(0.063)QESLSSSK 309.91 1.13E-55 1381950000 728320 616820 749980 796160 706820 696960 915030 976520 1104010 1138500 TRUE FALSE 699856.4492 599228.8975 885518.0692 837249.913 729555.5072 711053.0087 926228.4109 956354.5207 978687.4132 1061388.381 0.659378284 0.56457081 0.834301642 0.788825211 0.687359613 0.669927259 0.872657387 0.901041068 0.922082275 1 20.01752123 2.12518579 3.998054089 0.921448005 0.704031552 0.690896196 0.073654092 0.146437795 4.318673799 0.031477621 0.022399161 133.4092032 -2.12518579 -0.217416453 RVHNNS(ph)PDTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVHNNSPDTSR 11 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RVHNNS(1)PDTSR 110.98 0.0010541 139670000 15373 17984 12185 13615 14410 14608 12618 11178 13625 12193 TRUE FALSE 14772.20616 17471.11393 14387.10055 14317.67178 14873.51074 14903.38377 12772.42286 10947.17039 12078.34712 11367.15725 1.299551492 1.53698181 1.265672695 1.259564856 1.308463533 1.311091546 1.12362507 0.963052604 1.062565324 1 13.47258388 2.125388092 2.612973327 1.006606194 1.336355486 0.784961234 0.07684299 0.126205572 1.713867792 0.036790272 0.023548987 133.4713619 -2.125388092 0.329749291 KKEPPRAS(ph)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR ddPTM_BT-474_Pertuzumab_2h_R1 7 KKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR 47 3 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 KKEPPRAS(0.999)PPGGLAEPPGS(0.001)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(1)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.981)PPGGLAEPPGS(0.017)AGPQAGPT(0.003)VVPGSATPMETGIAETPEGR;KKEPPRAS(0.945)PPGGLAEPPGS(0.054)AGPQAGPT(0.001)VVPGSATPMETGIAETPEGR;KKEPPRAS(0.998)PPGGLAEPPGS(0.002)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.999)PPGGLAEPPGS(0.001)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.87)PPGGLAEPPGS(0.126)AGPQAGPT(0.003)VVPGSATPMETGIAETPEGR 237.1 8.28E-61 12302350000 1801550 1763200 1425274 1572508 1662036 1758390 1709735 1983672 2169440 1847655 TRUE FALSE 1731143.434 1712915.262 1682852.717 1653665.326 1715496.897 1793945.851 1730659.248 1942708.48 1923174.266 1722511.681 1.005011143 0.994428822 0.976976084 0.960031415 0.995927584 1.041470935 1.004730051 1.12783472 1.11649418 1 20.71608234 2.125400535 1.701124812 1.090617998 0.987864248 0.462978744 0.039386108 0.270620558 1.508127153 0.022046503 0.012228998 133.4751861 -2.125400535 -0.102753749 SGFEPASLKEEVGEEAIVELVENGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGFEPASLKEEVGEEAIVELVENGK 25 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 166.06 1.32E-11 42116000 70647 61001 55649 53063 66022 63513 72687 78822 87751 86309 FALSE TRUE 67886.03714 59261.31121 65706.01221 55801.58779 68145.65759 64797.27638 73576.56525 77194.29816 77789.87436 80463.21455 0.843690344 0.73650191 0.816596908 0.693504331 0.846916917 0.805303103 0.914412451 0.959373778 0.966775623 1 16.29604176 2.125838856 1.257671387 0.986282823 0.777159963 0.788269107 0.044157737 0.185418717 0.553912275 0.027873644 0.01440402 133.6099667 -2.125838856 -0.20912286 MSGGS(ph)TMSSGGGNTNNSNSK ddPTM_BT-474_Pertuzumab_2h_R1 2 MSGGSTMSSGGGNTNNSNSK 20 0 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 MS(0.004)GGS(0.994)T(0.002)MSSGGGNTNNSNSK;MS(0.175)GGS(0.819)T(0.005)MSSGGGNTNNSNSK 472.97 7.48E-224 407840000 410360 416040 377170 391430 416300 414920 457530 502860 547390 516270 TRUE FALSE 394322.6775 404174.9465 445333.0091 411631.7492 429690.6676 423309.9667 463129.389 492475.7653 485252.582 481302.5731 0.819282297 0.839752308 0.925266213 0.85524527 0.892766197 0.879509046 0.962241664 1.023214487 1.008206914 1 18.87658461 2.126015411 2.321098101 1.012896099 0.86807744 0.846779188 0.02762342 0.111779968 1.188511248 0.013883104 0.008548186 133.6642946 -2.126015411 -0.144818659 TFVLTPELS(ph)PGKLQVLPFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFVLTPELSPGKLQVLPFEK 20 1 Q96DY7 Q96DY7 MTBP Mdm2-binding protein 1 TFVLTPELS(1)PGKLQVLPFEK 171.72 4.49E-12 82504000 221260 203190 173270 152830 175830 188460 198150 217550 225400 220090 TRUE FALSE 212612.9146 197395.2201 204583.7434 160717.5746 181485.7316 192270.7903 200575.019 213057.5165 199813.537 205183.1083 1.036210614 0.962044204 0.997078878 0.783288527 0.884506201 0.937069294 0.977541576 1.038377468 0.973830344 1 17.64655244 2.126019659 3.437800204 1.008220999 0.928232759 0.191267738 0.06539001 0.38323269 8.836333267 0.029140041 0.020160973 133.6656022 -2.126019659 -0.07998824 DKDDELSFMEGAIIYVIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDDELSFMEGAIIYVIK 18 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 ; 142.3 1.04E-07 282650000 838280 659710 652970 575710 659740 675660 774140 839440 956230 832920 FALSE TRUE 805519.0908 640895.7167 770976.2042 605422.4621 680961.1363 689322.3081 783614.1569 822105.2707 847682.7792 776505.5865 1.037364193 0.825358797 0.992879147 0.779675604 0.876955875 0.887723566 1.009154564 1.058724219 1.091663465 1 19.56663678 2.126210966 3.427258713 1.052984633 0.893869442 0.473907765 0.0728093 0.190608869 4.37142478 0.028804647 0.019917701 133.7244949 -2.126210966 -0.159115191 VPFS(ph)PGPAPPPHMGELDQER ddPTM_BT-474_Pertuzumab_2h_R1 2 VPFSPGPAPPPHMGELDQER 20 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 VPFS(1)PGPAPPPHMGELDQER;VPFS(1)PGPAPPPHMGELDQER 120.85 2.15E-05 395510000 86618 108584 104014 124201 135623 115035 83209 71698 74044 78667 TRUE FALSE 83232.8728 105487.2906 122811.6436 130611.0285 139985.437 117361.0865 84227.33663 70217.41124 65638.83554 73338.81402 1.134908901 1.438355556 1.674579078 1.780926379 1.908749669 1.600258855 1.148468758 0.957438598 0.89500814 1 16.16228932 2.126719915 3.18696217 0.961909815 1.612278144 0.689545161 0.19652419 0.153278274 3.080634959 0.092814535 0.063075923 133.8812982 -2.126719915 0.650368329 RS(ph)PVPAQIAITVPK ddPTM_BT-474_Pertuzumab_2h_R1 6 RSPVPAQIAITVPK 14 1 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 RS(1)PVPAQIAITVPK;RS(1)PVPAQIAITVPK;RS(0.999)PVPAQIAIT(0.001)VPK;RS(1)PVPAQIAITVPK;RS(1)PVPAQIAITVPK;RS(1)PVPAQIAITVPK 132.74 2.98E-05 2793090000 3708600 3781830 3214160 3454870 3590420 3725670 3923030 4422670 4542900 4643210 TRUE FALSE 3563663.812 3673975.911 3795030.211 3633176.255 3705909.12 3801005.6 3971041.215 4331340.319 4027209.037 4328721.251 0.823260174 0.848743936 0.876709308 0.839318599 0.856120989 0.878089713 0.917370508 1.000605044 0.930346124 1 22.04550947 2.126836556 1.969211042 0.977348698 0.850586043 0.853238285 0.0231142 0.112932421 0.85287341 0.011779651 0.006863202 133.9172603 -2.126836556 -0.126762654 LVLAES(ph)PQPK ddPTM_BT-474_Pertuzumab_2h_R1 3 LVLAESPQPK 10 0 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312 E7EUR8 FAM193A Protein FAM193A 1 LVLAES(1)PQPK;LVLAES(1)PQPK;LVLAES(1)PQPK 146.36 3.02E-05 1237110000 2122320 1967170 1614160 1494800 1771230 1798570 2014310 2263190 2294390 2255490 TRUE FALSE 2039377.388 1911068.238 1905874.619 1571946.807 1828203.222 1834938.318 2038961.728 2216454.336 2033940.466 2102723.653 0.969874184 0.908853731 0.906383783 0.747576509 0.869445311 0.872648346 0.969676507 1.054087318 0.967288527 1 21.00382783 2.127255424 3.791489573 1.012981702 0.875086192 0.521954874 0.056159552 0.178278593 4.846197848 0.023971376 0.016927393 134.0464832 -2.127255424 -0.13789551 GYWASLDASTQTTHELTIPNNLIGCIIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GYWASLDASTQTTHELTIPNNLIGCIIGR 29 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ; 296.97 7.46E-81 843420000 500020 606720 488190 561680 573950 597980 514550 507750 594780 566380 FALSE TRUE 480478.6656 589416.9396 576416.7927 590668.3721 592411.623 610071.5653 520847.2168 497264.7851 527263.0679 528018.5781 0.909965455 1.116280684 1.09166006 1.118650738 1.121952233 1.155397917 0.986418354 0.941756229 0.99856916 1 19.01022917 2.127391104 7.279536992 0.971524189 1.090235451 0.380061688 0.064587351 0.212247324 12.82673541 0.024112129 0.017778497 134.0883678 -2.127391104 0.118711262 TDNSSLS(ph)SPLNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TDNSSLSSPLNPK 13 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 TDNSS(0.001)LS(0.499)S(0.499)PLNPK;TDNSS(0.003)LS(0.498)S(0.498)PLNPK 212.35 1.54E-08 472580000 746060 638730 594840 626870 566660 606290 734970 848280 750960 850300 TRUE FALSE 716903.1504 620514.0458 702340.8201 659222.8358 584887.1335 618549.5992 743964.7827 830762.7216 665714.1691 792708.4236 0.904371808 0.782777156 0.886001459 0.831608213 0.737833882 0.780299011 0.93851 1.048005416 0.839797016 1 19.59643078 2.127396977 5.378520386 0.973516147 0.818924253 0.492053688 0.067606621 0.160586468 6.974861852 0.025623445 0.018751548 134.0901809 -2.127396977 -0.154591894 SIYGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIYGEK 6 0 P62937;F8WE65;C9J5S7;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37;P62937-2 P62937;P62937-2 PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D" 0 ; 127.66 0.039465 4127950000 1563580 1509370 1497200 1858810 1569300 1437630 1971820 2145710 2241720 2281420 FALSE TRUE 1502473.565 1466324.245 1767777.345 1954743.407 1619777.96 1466699.864 1995951.723 2101400.339 1987249.344 2126897.391 0.706415632 0.689419363 0.831153093 0.919058632 0.761568455 0.689595967 0.938433481 0.988012091 0.934341897 1 21.020319 2.127665086 6.24572855 0.970025972 0.772870682 0.675046186 0.067780858 0.140078291 7.188959233 0.028044144 0.020626888 134.1729862 -2.127665086 -0.19715529 ETKPEPMEEDLPENK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETKPEPMEEDLPENK 15 1 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 148.36 3.23E-06 403110000 417880 357650 297620 302170 372270 409480 392810 485610 541340 507140 FALSE TRUE 401548.7876 347450.1722 351406.5545 317765.0299 384244.4026 417759.9662 397617.3263 475581.9838 479889.3527 472790.9561 0.849315712 0.734891748 0.743259891 0.672104713 0.812715213 0.883603971 0.84100028 1.005903302 1.015013816 1 18.85084291 2.127695974 1.028677453 1.021258288 0.751963096 0.793259854 0.052356586 0.226079582 0.447195706 0.039960733 0.020611062 134.1825295 -2.127695974 -0.269295192 (ac)AVADLALIPDVDIDSDGVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVADLALIPDVDIDSDGVFK 20 0 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ; 51.211 0.00068056 652130000 153618 151053 118553 163286 147599 135365 172219 192105 187724 190929 FALSE TRUE 147614.4387 146745.1163 139978.1643 171713.21 152346.6559 138102.173 174326.6676 188137.9646 166414.3585 177997.2088 0.829307604 0.824423694 0.786406513 0.964696083 0.855893511 0.775867071 0.979378659 1.056971432 0.934926787 1 17.44149509 2.127741022 6.265008507 1.006768693 0.843191339 0.643516985 0.055788505 0.129070219 6.647367705 0.021423509 0.015758497 134.1964483 -2.127741022 -0.163577354 QGPPCS(ph)DS(ph)EEEVER ddPTM_BT-474_Pertuzumab_2h_R1 1 QGPPCSDSEEEVER 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 QGPPCS(1)DS(1)EEEVER 85.29 0.011396 219780000 323560 355980 289470 366230 347410 400170 306990 322670 346240 345090 TRUE FALSE 310914.9175 345827.7989 341783.6682 385131.1742 358584.7582 408261.7116 310747.0355 316006.7517 306936.2868 321716.7469 0.96642441 1.07494497 1.0623745 1.197112609 1.114597737 1.269009821 0.965902579 0.982251483 0.954057536 1 18.29543151 2.12776433 20.77133118 0.974619803 1.114110043 0.442072168 0.076231094 2.724351031 497.6544127 0.029249955 0.021602539 134.2036508 -2.12776433 0.13949024 GQS(ph)PLAPLLETLEDPSASHGGQTDAYLTLTSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GQSPLAPLLETLEDPSASHGGQTDAYLTLTSR 32 0 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 GQS(0.986)PLAPLLET(0.014)LEDPSASHGGQTDAYLTLTSR;GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR;GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR;GQS(0.998)PLAPLLET(0.002)LEDPSASHGGQTDAYLTLTSR 226.85 2.05E-36 438213000 66060.6 73637.9 60768.8 78740.2 73927.1 73358.5 65220.8 66285.4 73147.8 62240.1 TRUE FALSE 63478.87872 71537.81919 71751.07395 82803.99116 76305.03231 74841.85913 66018.99166 64916.58333 64844.3684 58024.52259 1.094000879 1.232889406 1.236564658 1.427051658 1.315047999 1.289831537 1.137777421 1.118778413 1.117533855 1 15.82437513 2.128435222 3.57150705 1.098303951 1.272863482 0.501576345 0.084627355 0.219853977 5.418105894 0.036822909 0.025727184 134.4111269 -2.128435222 0.174559532 RGDDSFGDK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGDDSFGDK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 161.67 0.0001032 3802440000 1725090 1563470 1733380 1658280 1589160 1441920 1999380 2090180 2273650 2383500 FALSE TRUE 1657671.576 1518881.366 2046640.325 1743864.03 1640276.775 1471076.61 2023849.011 2047017.053 2015554.784 2222063.422 0.746005519 0.683545461 0.921053965 0.784794895 0.738177299 0.662031784 0.91079714 0.921223504 0.907064472 1 21.08346856 2.128468742 7.568966003 0.929254782 0.760930834 0.613436222 0.069542913 0.171561899 10.84612769 0.026976174 0.019898066 134.4215013 -2.128468742 -0.168323948 EELQANGSAPAADKEEPAAAGS(ph)GAASPSAAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EELQANGSAPAADKEEPAAAGSGAASPSAAEK 32 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 EELQANGSAPAADKEEPAAAGS(0.637)GAAS(0.363)PSAAEK 385.7 2.59E-166 477960000 675870 642690 819740 760560 769950 745680 977280 1158100 1182700 1110300 TRUE FALSE 649456.2532 624361.1105 967885.253 799812.5927 794716.141 760758.1605 989240.245 1134184.83 1048444.854 1035098.392 0.627434318 0.603190108 0.935065942 0.772692334 0.767768694 0.73496217 0.955696823 1.095726589 1.012893907 1 19.98133648 2.128494016 3.607012342 1.043405384 0.744792413 0.705604201 0.088199929 0.132746706 3.326625727 0.038134021 0.026697255 134.4293244 -2.128494016 -0.298612971 RQPS(ph)EPKR ddPTM_BT-474_Pertuzumab_2h_R1 3 RQPSEPKR 8 2 Q9UL26 Q9UL26 RAB22A Ras-related protein Rab-22A 1 RQPS(1)EPKR;RQPS(1)EPKR;RQPS(1)EPKR 80.24 0.020446 296384000 255279 286718 147708 283675 275087 224494 336275 448190 351750 306228 TRUE FALSE 245302.4145 278541.0834 174402.1213 298315.5007 283935.4232 229033.4225 340390.434 438934.7199 311820.8147 285486.9048 0.859242264 0.975670263 0.610893594 1.044935847 0.994565489 0.80225544 1.192315403 1.537495109 1.092242094 1 18.12306505 2.128534593 5.202346169 1.290959052 0.88685968 0.422552747 0.177587945 0.159769054 6.686874918 0.066580839 0.048652067 134.4418849 -2.128534593 -0.404099371 KSPLS(ph)SILFSALDSDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPLSSILFSALDSDTR 17 1 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A0G2JQF5;A0A3B3IT55;A0A0G2JQF4;A0A1W2PPV8;A0A1W2PRR3;I3L233 A0A1W2PRB5 KANSL1 KAT8 regulatory NSL complex subunit 1 1 KS(0.415)PLS(0.552)S(0.029)ILFS(0.004)ALDSDTR 131.25 2.92E-05 133150000 86197 80780 68310 75439 80001 78970 84142 94193 91736 92016 TRUE FALSE 82828.32594 78476.23349 80655.13655 79332.41583 82574.30482 80566.82751 85171.75497 92247.88163 81322.51387 85783.67436 0.965548825 0.914815483 0.940215456 0.924796197 0.962587642 0.939186018 0.992866715 1.075354749 0.947995227 1 16.38841549 2.128601972 4.236889753 1.019937602 0.940173415 0.457292378 0.032840548 0.157248971 5.055541006 0.01255764 0.009019885 134.4627448 -2.128601972 -0.079764186 RKPDTIEVQQMK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKPDTIEVQQMK 12 2 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 171.05 2.22E-05 1899930000 1746800 1761790 1529810 1861990 1322620 1358270 2014780 2124170 2278000 2333030 FALSE TRUE 1678533.125 1711545.474 1806280.697 1958087.527 1365163.273 1385735.15 2039437.48 2080305.147 2019410.99 2175011.8 0.771735181 0.78691319 0.830469378 0.900265243 0.62765787 0.637116153 0.937667318 0.956456948 0.928459786 1 21.0525918 2.128635939 8.430877734 0.954106491 0.764219065 0.603035615 0.078168047 0.195980093 13.90969068 0.031901359 0.023546888 134.4732617 -2.128635939 -0.189887427 SLGDDISSETSGDFRK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLGDDISSETSGDFRK 16 1 P12429;D6RA82;D6RFG5 P12429 ANXA3 Annexin A3;Annexin 0 ;; 232.28 8.99E-16 1826520000 779610 986060 734600 812380 913400 922420 793160 807280 895350 831190 FALSE TRUE 749141.9793 957938.5343 867358.5611 854307.0292 942780.3405 941071.9644 802866.9293 790609.3859 793713.6216 774892.761 0.966768587 1.236220781 1.119327222 1.102484205 1.216659115 1.214454453 1.036100697 1.020282323 1.024288342 1 19.56363714 2.128701945 7.078168367 1.020101193 1.147136707 0.40462982 0.072859751 0.214854222 12.6534803 0.026490963 0.019527008 134.4937011 -2.128701945 0.127035514 EYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYVSNDAAQSDDEEKLQSQPTDTDGGR 27 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 EYVSNDAAQS(1)DDEEKLQSQPTDTDGGR 227.58 7.18E-35 812360000 389680 293100 301120 301570 326020 309680 379670 414610 416050 474970 TRUE FALSE 374450.8748 284741.075 355539.0824 317134.0638 336506.7294 315941.9418 384316.515 406048.1586 368821.7482 442799.8588 0.845643618 0.643046896 0.802934046 0.716201818 0.759952206 0.713509581 0.867923752 0.917001554 0.832931043 1 18.75629524 2.129139635 4.608533458 0.903961597 0.744117511 0.598392798 0.063763325 0.138944795 5.009839845 0.022600462 0.016378712 134.6293147 -2.129139635 -0.159844086 TLVS(ph)PNKAETK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLVSPNKAETK 11 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 TLVS(1)PNKAETK;TLVS(1)PNKAETK 196.18 3.72E-08 2569500000 1346060 1140770 1099060 997530 1152520 1009570 1470680 1802770 1481920 1585980 TRUE FALSE 1293454.487 1108236.357 1297684.59 1049012.643 1189591.852 1029984.197 1488678.622 1765542.17 1313698.654 1478560.162 0.874806802 0.749537547 0.877667763 0.709482556 0.804561007 0.696612978 1.006843455 1.19409559 0.888498614 1 20.49576152 2.129160985 5.821671371 1.06069649 0.78615828 0.610671742 0.091420081 0.118186408 5.632806623 0.033346045 0.024482584 134.6359332 -2.129160985 -0.27453821 S(ph)PLAEHRPDAYQDVSIHGTLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLAEHRPDAYQDVSIHGTLPR 22 1 O75815 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 S(1)PLAEHRPDAYQDVSIHGTLPR 218.98 6.86E-26 93172000 21846 28149 28534 31872 26255 29482 26193 22986 30492 34811 TRUE FALSE 20992.23417 27346.21808 33690.72854 33516.91774 27099.51592 30078.14624 26513.55777 22511.33107 27030.67599 32453.21996 0.646845958 0.842634972 1.038132074 1.03277634 0.835033194 0.926815468 0.816977724 0.693654777 0.832911989 1 14.98607401 2.129592953 5.966095474 0.795734132 0.895850618 0 0.127323921 0.484385401 23.74888339 0.049674684 0.036498947 134.7699145 -2.129592953 0.100116486 EVPWSPSAEKAS(ph)PQENGPAVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVPWSPSAEKASPQENGPAVHK 22 1 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EVPWSPSAEKAS(0.999)PQENGPAVHK;EVPWSPS(0.011)AEKAS(0.989)PQENGPAVHK 181.37 3.01E-17 456660000 225074 193957 171983 174889 195349 193454 234862 250370 282330 280840 TRUE FALSE 216277.8592 188425.5363 203064.1538 183915.0422 201632.578 197365.7724 237736.3114 245199.772 250281.082 261818.4567 0.826060401 0.719680112 0.77559144 0.702452549 0.770123621 0.753826812 0.908019681 0.936525924 0.955933685 1 17.99820728 2.129628135 2.396425646 0.957261727 0.752732873 0.875510673 0.035767307 0.092145754 1.048390584 0.016257774 0.01015544 134.7808326 -2.129628135 -0.204528853 VASEAPLEHKPQVEASSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 0 103.2 0.00022674 232860000 174410 205760 178110 181000 189790 210010 203410 253420 261640 247940 FALSE TRUE 167593.8644 199891.9263 210298.439 190341.4317 195894.7677 214256.5461 205899.3924 248186.7884 231939.7241 231146.803 0.725053785 0.864783435 0.909804662 0.823465561 0.847490708 0.926928443 0.890773265 1.073719322 1.003430379 1 17.81844988 2.129712761 1.363935515 1.032980511 0.839868898 0.669677617 0.055071488 0.247946937 0.87650557 0.035397101 0.018602246 134.8070983 -2.129712761 -0.193111613 SREDMIDIK ddPTM_BT-474_Pertuzumab_2h_R1 6 SREDMIDIK 9 1 P20340-2;P20340;P20340-4;P20340-3;F5H3K7 P20340-2 RAB6A Ras-related protein Rab-6A 0 ;;;;; 157.78 6.18E-05 5165300000 6038190 7358260 5362470 6878800 5712580 5837560 7802220 8877060 9389370 7903730 FALSE TRUE 5802210.859 7148409.629 6331587.617 7233815.692 5896330.324 5955599.463 7897705.902 8693745.609 8323528.081 7368403.327 0.787444797 0.970143641 0.859288958 0.981734491 0.800218183 0.808261871 1.071834094 1.179868314 1.129624386 1 22.8129206 2.129853704 5.329522716 1.123218946 0.874809206 0.681611983 0.075757067 0.110031461 4.748219346 0.028207475 0.020640745 134.8508549 -2.129853704 -0.24840974 GHYEVT(ph)GSDDETGKLQGSGVSLASK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHY(0.288)EVT(0.334)GS(0.334)DDET(0.043)GKLQGSGVSLASK;GHYEVT(0.5)GS(0.5)DDETGKLQGSGVSLASK;GHYEVT(0.498)GS(0.498)DDET(0.004)GKLQGSGVSLASK;GHY(0.226)EVT(0.258)GS(0.258)DDET(0.258)GKLQGSGVSLASK 290.54 1.17E-62 10913071000 3779048 3277664 3519267 3405547 3015174 3547343 3927095 4138026 4819209 4469809 TRUE FALSE 3631358.626 3184188.232 4155276.833 3581307.689 3112159.81 3619072.706 3975155.963 4052574.317 4272152.598 4167064.855 0.871442791 0.764132151 0.997171145 0.859431714 0.746846982 0.868494452 0.953946267 0.972524897 1.025218648 1 21.99060012 2.130002969 2.511452002 0.993755125 0.848314387 0.526566453 0.064660272 0.245746842 3.081131164 0.031193717 0.019798925 134.8972106 -2.130002969 -0.145440738 THTGEKPYPCDVCGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 THTGEKPYPCDVCGQR 16 1 Q9Y2D9;D6RF85;D6RDG5;Q9UFB7-2;Q9UFB7 Q9Y2D9 ZNF652;ZBTB47 Zinc finger protein 652;Zinc finger and BTB domain-containing protein 47 0 139.08 1.86E-06 96461000 256380 246940 194100 206010 195570 200930 173730 91681 166320 171760 FALSE TRUE 246360.3862 239897.513 229178.1877 216642.2008 201860.6867 204992.9423 175856.1597 89787.75531 147440.0509 160126.5422 1.538535603 1.498174567 1.431231728 1.352943727 1.260632272 1.280193399 1.098232418 0.560729996 0.92077209 1 17.28885294 2.13003888 2.355038699 0.783602505 1.405543183 0.775260896 0.136340893 0.126326453 1.3864401 0.067463218 0.041911476 134.9083655 -2.13003888 0.621940679 ALEVIKPAHILQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALEVIKPAHILQEK 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 136.81 1.50E-05 837250000 973420 1083300 894490 1006000 1040500 1066400 1171400 1233800 1394600 1421200 FALSE TRUE 935377.6702 1052405.345 1056144.241 1057919.781 1073968.627 1087963.339 1185735.944 1208321.599 1236290.855 1324940.858 0.705976923 0.794303639 0.797125573 0.798465663 0.810578541 0.821141058 0.894934998 0.911981536 0.93309135 1 20.33749653 2.130206939 0.364450805 1.012247181 0.728700805 0.929550035 0.021700458 0.324892063 0.109756274 0.026749194 0.032178184 134.960581 -2.130206939 -0.283546376 TPS(ph)PEPVDKDFYSEFGNK ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSPEPVDKDFYSEFGNK 18 1 Q9Y2I1;Q9Y2I1-2 Q9Y2I1 NISCH Nischarin 1 T(0.294)PS(0.706)PEPVDKDFYSEFGNK;T(0.243)PS(0.757)PEPVDKDFYSEFGNK;T(0.036)PS(0.964)PEPVDKDFYSEFGNK 189.82 1.86E-14 903420000 1311060 1216700 1118910 1067110 1272160 1224530 1469460 1730400 1767490 1634270 TRUE FALSE 1259822.326 1182000.907 1321121.927 1122183.675 1313080.182 1249290.836 1487443.691 1694666.635 1566851.945 1523579.437 0.826883256 0.775805238 0.867117194 0.736544251 0.861839002 0.819970922 0.976282335 1.112292929 1.028401872 1 20.53903329 2.130354805 3.197338274 1.057666247 0.812375085 0.847761216 0.045132984 0.078934902 1.597591404 0.018012558 0.012286558 135.0065394 -2.130354805 -0.245291162 S(ph)SPKEELHPAAPSQLAPSFSSSSSSSSGPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPKEELHPAAPSQLAPSFSSSSSSSSGPR 30 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 S(0.5)S(0.5)PKEELHPAAPSQLAPSFSSSSSSSSGPR;S(0.5)S(0.5)PKEELHPAAPSQLAPSFSSSSSSSSGPR;S(0.5)S(0.5)PKEELHPAAPS(0.001)QLAPSFSSSSSSSSGPR 177.73 5.10E-18 1681320000 760623 724148 609420 583809 611412 711845 762600 859413 960971 875834 TRUE FALSE 730897.0122 703496.0081 719555.7505 613939.4525 631078.6223 726238.9936 771932.9269 841665.8212 851885.6008 816512.9831 0.895144385 0.86158582 0.881254512 0.751904091 0.77289478 0.889439615 0.945401902 1.030805191 1.043321562 1 19.6391163 2.130407604 2.043319437 1.026875806 0.833176319 0.780283401 0.044282313 0.156596491 1.278862344 0.025136268 0.014882842 135.0229535 -2.130407604 -0.193699486 EVDEDFDGKLSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVDEDFDGKLSFR 13 1 Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2;C9JTV4 Q9BUP0 EFHD1;PP1187 EF-hand domain-containing protein D1 0 ;;; 163.27 3.56E-05 2075330000 2768890 2972810 2029160 2426960 2579910 2711880 2767700 3259460 3447150 2950660 FALSE TRUE 2660678.718 2888028.369 2395874.35 2552215.696 2662895.148 2766716.072 2801571.941 3192151.012 3055843.984 2750809.17 0.967234931 1.049883213 0.870970759 0.927805434 0.968040669 1.005782626 1.018453759 1.160440734 1.110889122 1 21.39142463 2.130469255 2.208998688 1.105163953 0.959077261 0.472599864 0.058199187 0.235832154 2.26576308 0.029106651 0.017700513 135.0421224 -2.130469255 -0.146086692 SSS(ph)LESQGK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSLESQGK 9 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SS(0.002)S(0.998)LESQGK;S(0.004)S(0.057)S(0.939)LESQGK;S(0.001)S(0.008)S(0.992)LESQGK;SS(0.003)S(0.997)LESQGK 140.09 0.00011532 1655750000 4256670 4199780 3639510 3828980 3908830 4190760 4420100 4953090 5298500 5066450 TRUE FALSE 4090314.63 4080006.386 4297250.417 4026594.117 4034561.067 4275500.039 4474194.506 4850806.961 4697036.493 4723294.829 0.865987574 0.863805148 0.909799319 0.852496883 0.854183618 0.905194402 0.947261322 1.026996437 0.994440674 1 22.17136216 2.130469306 2.071271399 1.009436366 0.871050326 0.9118645 0.018629805 0.083302074 0.699842364 0.009584937 0.00570185 135.0421384 -2.130469306 -0.13838604 AAPEAS(ph)S(ph)PPASPLQHLLPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.752)S(0.771)PPAS(0.478)PLQHLLPGK 62.203 0.023378 39921000 61665 62335 49464 76362 79208 77695 53777 57365 52171 52677 TRUE FALSE 59255.06363 60557.26683 58403.24512 80303.05197 81755.79725 79266.04613 54435.13901 56180.3927 46248.7668 49109.13987 1.2065995 1.233116015 1.189254083 1.635195652 1.664777625 1.614079301 1.108452299 1.143990566 0.941754772 1 15.58370393 2.130791956 7.052051813 1.065422808 1.424402506 0.526824668 0.174291113 0.21456654 12.68169169 0.074828481 0.055158762 135.1425024 -2.130791956 0.358979698 SYNPFDDDGEDEGARPAPWR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYNPFDDDGEDEGARPAPWR 20 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ; 146.89 1.17E-07 653540000 318453 288737 255391 261134 297359 258205 324276 362094 301934 402622 FALSE TRUE 306007.5047 280502.5035 301545.8348 274611.157 306923.8223 263426.082 328244.5867 354616.6324 267659.7181 375352.0533 0.815254644 0.747305099 0.803368017 0.731609577 0.817695866 0.701810686 0.874497911 0.944757406 0.713089793 1 18.51788485 2.131101476 7.807822433 0.886950122 0.77069769 0.346558716 0.076465057 0.252986913 16.72252071 0.026825531 0.019792592 135.2388521 -2.131101476 -0.116252432 LYSILGTTLKDEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYSILGTTLKDEGK 14 1 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 244.36 1.26E-17 3193000000 2677100 2791700 2088000 2113500 2471200 2702400 2907000 3375100 3739400 3536000 FALSE TRUE 2572475.972 2712083.449 2465348.047 2222577.988 2550688.392 2757044.38 2942576.736 3305403.006 3314918.989 3296503.57 0.780364989 0.822715156 0.74786755 0.674222837 0.773755689 0.836354131 0.892635689 1.002699659 1.005586349 1 21.65250521 2.131155484 1.479499941 1.009850697 0.758388424 0.892709191 0.036567652 0.131461812 0.549950256 0.025083854 0.013445716 135.2556714 -2.131155484 -0.251462273 AEPSEVDMNS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 AEPSEVDMNSPK 12 0 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 AEPSEVDMNS(1)PK;AEPSEVDMNS(1)PK;AEPSEVDMNS(1)PK 211.45 3.34E-08 718370000 941620 782460 724580 693346 707940 719719 860430 920290 935180 1004920 TRUE FALSE 904820.4494 760145.0069 855527.7242 729129.6702 730711.533 734272.2113 870960.1997 901285.6899 829022.287 936855.8733 0.965805387 0.811378814 0.91319033 0.778273042 0.779961522 0.78376219 0.929662955 0.962032385 0.884898425 1 19.83746759 2.131319405 6.759535861 0.944752573 0.835686202 0.403355842 0.062943356 0.219799853 12.42971749 0.023729111 0.017482099 135.3067321 -2.131319405 -0.109066371 DLVMGS(ph)SPQLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLVMGSSPQLKR 12 1 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.645)S(0.355)PQLKR;DLVMGS(0.629)S(0.371)PQLKR 81.311 0.011019 1350870000 312940 314860 220642 244180 273530 282350 300480 314130 350180 347310 TRUE FALSE 300709.9588 305880.5011 260516.9176 256782.1591 282328.3409 288059.3105 304157.3641 307643.1057 310429.0345 323786.3843 0.928729475 0.944698467 0.804595036 0.793060399 0.871958657 0.889658504 0.939376635 0.950142194 0.958746413 1 18.30468279 2.13132621 1.524238996 0.969678995 0.865300736 0.499376123 0.045368734 0.38501766 1.713007379 0.03077159 0.016625679 135.3088521 -2.13132621 -0.104378259 GESDPAYQQYQDAANNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GESDPAYQQYQDAANNLR 18 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 248.68 2.75E-22 0 31215 33664 31745 36930 36093 32806 32369 26021 36112 36549 FALSE TRUE 29995.08329 32703.93568 37482.02766 38835.96173 37253.96412 33469.3598 32765.1415 25483.65726 32012.71715 34073.50368 0.880305224 0.959805484 1.100034444 1.13977013 1.093341163 0.982269394 0.961601772 0.747902461 0.939519383 1 15.05636268 2.131369594 2.995956086 0.866816992 1.036570289 0.249705342 0.09464048 0.277948452 4.971428731 0.043102162 0.028918793 135.3223696 -2.131369594 0.169753296 SKEYFSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKEYFSK 7 1 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 104.2 0.0074828 20772430000 12536670 11965030 10038860 10180040 10659290 10634520 12040080 12753540 13839560 12882390 FALSE TRUE 12046723.08 11623799.06 11853105.32 10705433.08 11002155.74 10849557.28 12187430.1 12490174.94 12268551.17 12009854.25 1.003069881 0.967855131 0.986948307 0.891387427 0.916094027 0.903387922 1.014785846 1.039993882 1.021540388 1 23.51771531 2.131619617 6.979914879 1.02535562 0.944188805 0.523245976 0.034638588 0.178558628 10.4707244 0.014144975 0.010425759 135.400297 -2.131619617 -0.081166815 LATELPDAELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LATELPDAELRR 12 1 Q93034 Q93034 CUL5 Cullin-5 0 ; 126.34 0.00046365 377140000 429170 436610 377540 374680 405240 411690 356930 335310 390640 360540 FALSE TRUE 412397.5619 424158.3103 445769.8763 394017.2797 418274.9126 420014.6539 361298.2161 328385.7313 346296.1849 336120.3047 1.226934393 1.261924092 1.326221208 1.172250751 1.244420247 1.249596195 1.07490744 0.976988676 1.030274518 1 18.35861817 2.131778598 3.271153665 1.003483065 1.248839801 0.897860172 0.037926985 0.070331763 1.48547131 0.016144355 0.011086708 135.4498718 -2.131778598 0.245356736 EVMSLHEASR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVMSLHEASR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 92.538 0.0083415 0 81697 88467 81317 115090 101950 86535 80896 77258 71865 82613 FALSE TRUE 78504.19092 85944.00778 96012.79079 121029.8087 105229.3143 88284.79699 81886.02945 75662.5953 63707.18648 77017.54793 1.019302653 1.115901637 1.246635259 1.57145757 1.366303098 1.14629457 1.063212627 0.982407222 0.827177548 1 16.23289957 2.131899421 1.802214521 0.932988198 1.268085207 0.489346787 0.14500251 0.333478609 2.098872838 0.089623199 0.050954561 135.4875598 -2.131899421 0.335097009 EKEPS(ph)RER ddPTM_BT-474_Pertuzumab_2h_R1 4 EKEPSRER 8 2 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 EKEPS(1)RER;EKEPS(1)RER;EKEPS(1)RER;EKEPS(1)RER 81.625 0.017623 3415814000 2412286 2101687 1673071 1841872 1968452 1876372 2250938 2399245 2657038 2419497 TRUE FALSE 2318011.196 2041748.945 1975432.147 1936931.235 2031769.046 1914313.527 2278485.653 2349699.752 2355422.185 2255622.313 1.027659277 0.905182101 0.875781435 0.858712571 0.900757647 0.848685312 1.010136156 1.041707975 1.044244939 1 21.10509409 2.132269247 6.098201346 1.031170119 0.899883159 0.609686706 0.047564463 0.136747045 6.923390793 0.018317416 0.01346934 135.6029842 -2.132269247 -0.13128696 FYEAFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 FYEAFSK 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 139.31 0.0062827 8235400000 9672500 10647800 8282500 9253200 9294700 9418300 10312600 10869900 11648100 12018900 FALSE TRUE 9294488.006 10344135.17 9779331.993 9730758.761 9593672.467 9608744.479 10438808.68 10645432.77 10325856.52 11204849.2 0.829505854 0.923183792 0.872776761 0.868441742 0.856207192 0.857552325 0.931633126 0.950073721 0.921552476 1 23.4176199 2.132271858 4.383967945 0.949257744 0.870227336 0.669406058 0.028705009 0.135605177 4.588240354 0.010802461 0.007798841 135.6037993 -2.132271858 -0.079030408 S(ph)GGGDLTLGLEPSEEEAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGGDLTLGLEPSEEEAPR 19 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 S(1)GGGDLTLGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR 274.17 2.23E-39 3205890000 129080 183579 109756 200363 125078 127174 218992 310318 224744 159881 TRUE FALSE 124035.4109 178343.5067 129591.3507 210703.7584 129101.2475 129745.5454 221672.0896 303909.8249 199232.0033 149052.1175 0.832161347 1.196517766 0.869436496 1.413624724 0.866148362 0.870470998 1.487211946 2.038950067 1.33666 1 17.18545735 2.132333973 5.602125507 1.617147748 1.023935281 0.311936934 0.305282179 0.183498442 8.437771473 0.112238139 0.082324761 135.6231954 -2.132333973 -0.593212467 SYESSEDCSEAAGS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYESSEDCSEAAGSPAR 17 0 Q6P6C2-3;Q6P6C2;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 SYESSEDCSEAAGS(1)PAR;SYESSEDCSEAAGS(1)PAR 294.22 4.66E-46 392910000 182554 206555 153613 229820 217960 191889 182442 173285 179152 200943 TRUE FALSE 175419.5879 200664.2536 181374.2862 241681.0377 224970.8813 195769.1271 184674.7798 169706.6042 158815.416 187332.9516 0.936405402 1.071163679 0.968192113 1.29011493 1.200914625 1.045033057 0.985810442 0.905908986 0.847770852 1 17.51524516 2.132545808 2.385118798 0.911435754 1.096640701 0.357296344 0.102225097 0.325166938 3.667414494 0.051798554 0.032398362 135.6893643 -2.132545808 0.185204947 AKDRES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 AKDRESPR 8 2 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-2;O94875-8;H7BZK1;H7C1R7 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 AKDRES(1)PR 58.676 0.081463 25804000 66393 57362 39873 55227 49586 54308 55423 59052 61921 63265 TRUE FALSE 63798.28816 55726.09192 47078.93807 58077.27209 51180.97872 55406.14497 56101.28325 57832.55556 54891.98767 58980.0052 1.081693498 0.944830231 0.798218615 0.984694252 0.867768298 0.939405563 0.951191562 0.980545108 0.930688078 1 15.84793833 2.132831744 3.123993285 0.967711187 0.929115109 0.039301662 0.070848734 0.851841885 16.51680669 0.030357772 0.020624777 135.7787305 -2.132831744 -0.038596078 HTTDLDASK ddPTM_BT-474_Pertuzumab_2h_R1 2 HTTDLDASK 9 0 P12532;P12532-2;F8WCN3;C9JSQ1;P17540;C9J8F6;C9J6W7;C9JT96;D6RHV3;D6R998 P12532 CKMT1A;CKMT1B;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ; 138.08 0.00014665 1252420000 1456190 1866570 1520860 1999340 1638600 1560050 1649320 1301930 1541310 1656270 FALSE TRUE 1399280.485 1813337.251 1795713.233 2102526.177 1691307.057 1591595.28 1669504.872 1275044.691 1366346.95 1544089.358 0.906217298 1.174373259 1.1629594 1.361660947 1.095342733 1.030766304 1.081222964 0.825758357 0.884888523 1 20.55832481 2.13295089 1.605698551 0.891347569 1.149226411 0.392377578 0.118070059 0.353858009 1.754079086 0.070882715 0.038920445 135.8159859 -2.13295089 0.257878842 LEDFRDYRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEDFRDYRR 9 2 O43707;O43707-2;K7EJH8;F6THM6;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0;Q08043;A0A087WSZ2 O43707;P12814-3 ACTN4;ACTN2;ACTN1;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 48.64 0.097323 431900000 1279300 1555700 1028600 1203600 1182600 1430400 1163700 1238900 1376400 1223300 FALSE TRUE 1229303.542 1511332.959 1214490.901 1265717.94 1220639.403 1459323.668 1177941.709 1213316.282 1220156.842 1140444.801 1.077915862 1.325213599 1.064927386 1.109845859 1.070318705 1.279609207 1.032879195 1.06389742 1.069895571 1 20.12116519 2.133409403 20.49384183 1.048280709 1.152817659 0.299796332 0.084302654 4.143133963 792.1200628 0.030616668 0.022611927 135.9594511 -2.133409403 0.10453695 NNEYGDTVYTIEVPFHGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NNEYGDTVYTIEVPFHGK 18 0 J3QLM1;Q14849-2;Q14849-3;Q14849 J3QLM1 STARD3 StAR-related lipid transfer protein 3 0 130.11 1.98E-05 218460000 39515 58854 34407 64750 29991 42646 59787 71353 66086 66389 FALSE TRUE 37970.71011 57175.54154 40625.11028 68091.75526 30955.68775 43508.33134 60518.69119 69879.53562 58584.19434 61892.4139 0.613495382 0.923789168 0.656382709 1.100163186 0.500153182 0.70296711 0.977804667 1.129048476 0.946548868 1 15.91747497 2.133641418 5.050899898 1.041989444 0.758421951 0.386361268 0.162671319 0.206502572 8.419954893 0.060284179 0.044018222 136.0321049 -2.133641418 -0.283567494 EKYDYVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKYDYVGR 8 1 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 0 ; 105.4 0.0040091 859120000 568420 1084170 509700 1188740 838510 809180 1150290 1583800 1251360 922030 FALSE TRUE 546205.518 1053250.533 601814.1282 1250091.014 865481.4357 825542.174 1164367.593 1551093.977 1109310.859 859580.0868 0.635432959 1.225308205 0.700125721 1.454304297 1.006865386 0.960401697 1.354577207 1.804478722 1.290526474 1 19.71327254 2.133762369 4.847134155 1.481840704 1.016005424 0.241779752 0.293208217 0.225873774 8.749109744 0.107861052 0.078560612 136.069995 -2.133762369 -0.465835281 TAS(ph)PWK ddPTM_BT-474_Pertuzumab_2h_R1 8 TASPWK 6 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A1B0GTD1 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK 117.72 0.023578 11816620000 10329350 8872280 9101160 7751120 7983250 8267200 10202640 10995700 11287220 12006350 TRUE FALSE 9925667.582 8619251.261 10745942.07 8151156.232 8240038.486 8434368.448 10327502.96 10768634.95 10005942.11 11193149.22 0.886762732 0.770047025 0.960046351 0.728227246 0.736168019 0.753529528 0.92266285 0.962073742 0.893934487 1 23.41611266 2.133808237 5.974758299 0.946088982 0.804826413 0.476591333 0.071594489 0.190186443 9.457852335 0.027512527 0.020222856 136.0843669 -2.133808237 -0.141262569 YLLGDAPVS(ph)PSSQK ddPTM_BT-474_Pertuzumab_2h_R1 6 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.98)PS(0.018)S(0.002)QK;YLLGDAPVS(0.999)PS(0.001)SQK;YLLGDAPVS(0.991)PS(0.008)SQK;YLLGDAPVS(0.628)PS(0.372)SQK;YLLGDAPVS(0.98)PS(0.02)SQK;YLLGDAPVS(0.498)PS(0.498)S(0.003)QK 336.95 1.22E-68 25098976000 11249644 10932551 9327422 10526011 10174589 10388374 11460958 12843676 12284882 12538076 TRUE FALSE 10809995.48 10620765.35 11013094.64 11069259.69 10501863.9 10598434.04 11601220.63 12578449.6 10890353.7 11688860.94 0.92481171 0.908622782 0.942187155 0.946992161 0.89845058 0.906712304 0.992502237 1.076105675 0.931686479 1 23.47863101 2.134057906 5.053285451 1.016182131 0.922003308 0.521626987 0.036213055 0.141931153 5.795781051 0.01376216 0.010049873 136.1626222 -2.134057906 -0.094178823 RKQDAPSQSENK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKQDAPSQSENK 12 2 C9J470;E9PHA2;Q15003;Q15003-2 C9J470 NCAPH Condensin complex subunit 2 0 ; 168.94 2.54E-05 133794000 234317 209346 180757 169194 183743 188256 220940 233696 264219 244240 FALSE TRUE 225159.6326 203375.6571 213423.8108 177926.1226 189653.2605 192062.6653 223643.9298 228870.0959 234225.9668 227697.4073 0.988854618 0.893183895 0.937313312 0.781414794 0.832917962 0.843499571 0.982197964 1.005150207 1.028672086 1 17.79675834 2.134407901 5.099508655 1.007349018 0.876449719 0.561633372 0.054138503 0.164266577 6.789036744 0.022154384 0.016187388 136.2723989 -2.134407901 -0.130899299 VRVDLPDKYPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 VRVDLPDKYPFK 12 2 C9JZY6;P62256-2;P62256;H7C4M9;C9JZG9;C9J8Q9 C9JZY6 UBE2H Ubiquitin-conjugating enzyme E2 H 0 157.52 4.17E-05 522220000 1223300 1215800 1048800 1058600 1170100 1208000 1291400 1452100 1584300 1470900 FALSE TRUE 1175492.084 1181126.574 1238341.49 1113234.473 1207737.329 1232426.588 1307204.54 1422113.628 1404456.906 1371274.633 0.857225865 0.861334809 0.903058702 0.811824595 0.880740663 0.898745268 0.953276979 1.037074262 1.024198124 1 20.38708611 2.134443526 1.80906215 1.02542961 0.862894149 0.891383298 0.024074364 0.099948481 0.634581293 0.013021958 0.007431179 136.2835776 -2.134443526 -0.162535461 GQAGASRPHAPGTPAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQAGASRPHAPGTPAGR 17 1 Q8TDD1-2 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ; 92.439 0.0019879 56894000 97542 99796 76641 92341 90019 83800 92082 91327 87955 93999 FALSE TRUE 93729.9508 96949.91579 90491.73357 97106.73008 92914.54289 85494.49342 93208.92706 89441.06554 77970.71714 87632.364 1.069581448 1.106325464 1.03262915 1.108114921 1.060276576 0.975604098 1.063635885 1.020639652 0.88974796 1 16.41917616 2.13445319 0.717115992 0.964026844 1.08017937 0.474312464 0.045334513 0.637320723 0.626903158 0.038761231 0.023144759 136.2866102 -2.13445319 0.116152526 RSCFES(ph)SPDPELK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSCFESSPDPELK 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.025)CFES(0.589)S(0.386)PDPELK 98.507 0.0020137 216090000 416950 371010 334430 350500 385130 406410 417040 483700 530710 502110 TRUE FALSE 400655.133 360429.1581 394868.9404 368589.347 397518.0562 414627.8887 422143.8603 473711.426 470466.0257 468101.6425 0.85591482 0.769980546 0.843553845 0.787413061 0.84921312 0.885764652 0.901820934 1.011984114 1.005051004 1 18.8364623 2.134630634 1.139875596 1.016466895 0.814435994 0.887362722 0.028134539 0.135277751 0.330527528 0.018783239 0.009702856 136.3423055 -2.134630634 -0.202030901 ISDSEGFK ddPTM_BT-474_Pertuzumab_2h_R1 4 ISDSEGFK 8 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 121.85 0.0032934 767450000 1240930 1218550 1062440 1008770 1171780 1113220 1237890 1289750 1421700 1391540 FALSE TRUE 1192433.084 1183798.147 1254446.542 1060832.741 1209471.368 1135730.071 1253039.668 1263116.212 1260314.576 1297289.756 0.919172512 0.912516376 0.96697483 0.817729991 0.932306265 0.875463685 0.965890359 0.97365774 0.971498133 1 20.30706932 2.134839427 6.233786702 0.976418058 0.904789344 0.484557374 0.037351253 0.187862872 9.842811136 0.013662534 0.010053251 136.40787 -2.134839427 -0.071628714 KVSHVADTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVSHVADTK 9 1 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 ; 135.86 0.00013568 1320210000 4126200 4333000 3570700 3477500 3973000 3960500 4275600 4734300 4979700 4516700 FALSE TRUE 3964943.542 4209427.082 4216004.92 3656974.192 4100795.153 4040584.024 4327926.072 4636535.051 4414425.333 4210779.886 0.941617384 0.999678729 1.001240871 0.868479068 0.973880199 0.959580917 1.027820544 1.101110762 1.048362881 1 22.00565603 2.134868906 3.687279359 1.061787874 0.957704253 0.502007117 0.042192854 0.170987766 4.458382439 0.01718883 0.012129341 136.4171293 -2.134868906 -0.104083621 HLGVCISVANNR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLGVCISVANNR 12 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 120.96 0.00038476 356290000 448100 466580 411550 428300 448760 433980 411900 356650 465220 442080 FALSE TRUE 430587.7566 453273.5952 485926.2399 450404.6143 463194.773 442755.3729 416940.9554 349285.0529 412410.176 412137.5278 1.044767165 1.099811506 1.179039051 1.092850284 1.123883999 1.07429036 1.011654914 0.847496356 1.000661546 1 18.65276631 2.134878881 2.999347077 0.932168485 1.108205344 0.628801471 0.052549131 0.139516197 2.503510964 0.022403873 0.015081387 136.4202624 -2.134878881 0.176036859 (ac)S(ph)DNDDIEVESDADKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDNDDIEVESDADKR 15 1 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130 Q6V3B1 MAX Protein max 1 S(1)DNDDIEVESDADKR 143.17 4.71E-56 1467900000 794160 799730 693760 797390 820110 796860 980370 1021600 1177600 1131800 TRUE FALSE 763123.3492 776922.4834 819137.8646 838543.3935 846489.583 812973.0552 992368.0613 1000503.603 1043923.785 1055142.178 0.723242199 0.736320185 0.776329372 0.79472076 0.802251678 0.770486738 0.940506485 0.94821686 0.989367885 1 20.00900598 2.134957341 1.30462272 0.992784288 0.759728495 0.920929358 0.028923885 0.116588676 0.376399819 0.019717697 0.010326872 136.4449106 -2.134957341 -0.233055792 EELVAAVEDVRK ddPTM_BT-474_Pertuzumab_2h_R1 2 EELVAAVEDVRK 12 1 P35221-2;P35221;G3XAM7;P26232;P26232-5;P26232-2;P26232-3;E5RIB1;E5RJL0;E5RHV7;E5RG03;E5RIE0;E5RGY6;C9IZ88 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 0 ; 202.44 2.19E-07 623890000 387820 428970 446680 510780 373050 425850 536630 636650 560400 630830 FALSE TRUE 372663.5656 416736.1956 527405.0123 537141.417 385049.492 434460.9788 543197.4385 623502.955 496785.7414 588103.3222 0.633670227 0.708610511 0.896789718 0.91334532 0.654731027 0.738749404 0.923642867 1.06019288 0.844725276 1 19.16571011 2.135065435 4.655106067 0.978337822 0.764445795 0.494174292 0.099074513 0.185543145 6.836098781 0.040448311 0.029383664 136.4788752 -2.135065435 -0.213892027 KLQELSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLQELSSK 8 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 155.42 0.00065622 4830200000 6328300 6422300 5687400 5420900 5650000 4757900 7063100 7092100 8003700 8523300 FALSE TRUE 6080983.04 6239142.292 6715239.696 5700673.299 5831737.381 4854107.998 7149540.331 6945645.657 7095153.53 7946009.299 0.765287682 0.785191919 0.845108462 0.717425954 0.733920281 0.610886272 0.899764909 0.874104899 0.892920366 1 22.92179905 2.135075372 12.7579486 0.90294963 0.747982204 0.633435572 0.064340953 0.387461058 45.29978364 0.024748918 0.018278367 136.4819982 -2.135075372 -0.154967425 GLPS(ph)PYNMS(ph)SAPGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 GLPS(0.993)PY(0.007)NMS(0.729)S(0.271)APGSR;GLPS(0.907)PY(0.094)NMS(0.553)S(0.445)APGS(0.001)R 156.67 3.05E-06 213431000 424490 419530 345630 391520 377260 364620 292200 368830 347040 297770 TRUE FALSE 407900.4615 407565.4152 408093.0295 411726.3941 389394.9105 371992.8662 295776.031 361213.5316 307645.4741 277601.7727 1.469372683 1.468165751 1.470066367 1.483154773 1.402710461 1.340023382 1.065468812 1.301193174 1.108225899 1 18.08265725 2.135310851 0.514386113 1.023798241 1.512810355 0.824865495 0.07394334 0.369724167 0.207742746 0.071759204 0.058430477 136.5560201 -2.135310851 0.489012113 GIDIHGVPYVINVTLPDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GIDIHGVPYVINVTLPDEK 19 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 101.62 0.00025957 1009220000 1172420 1162140 900740 1118630 1093530 1156720 1167310 1271520 1407500 1360090 FALSE TRUE 1126600.53 1128996.905 1063523.755 1176362.628 1128704.386 1180109.671 1181595.889 1245262.668 1247726.501 1267969.893 0.888507319 0.89039725 0.838761047 0.927752808 0.89016655 0.930707959 0.931880083 0.982091668 0.984034801 1 20.27408906 2.135472664 0.716085437 1.00275771 0.878004773 0.824004366 0.020387126 0.257070695 0.252225976 0.016770839 0.010030559 136.6069088 -2.135472664 -0.124752937 KTPSKPPAQLS(ph)PSVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTPSKPPAQLSPSVPK 16 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 KTPSKPPAQLS(0.86)PS(0.14)VPK;KTPSKPPAQLS(0.989)PS(0.011)VPK 184.7 1.40E-09 5166540000 4183100 3614190 3341180 3145840 3501070 3694750 3962600 4508300 4556200 4573200 TRUE FALSE 4019619.827 3511116.84 3945005.55 3308197.179 3613685.096 3769460.376 4011095.484 4415202.03 4038999.277 4263453.091 0.942808503 0.823538283 0.925307601 0.77594314 0.847595838 0.884133189 0.940809104 1.035592966 0.947353985 1 22.02359095 2.135723651 2.722035968 0.997154237 0.860550328 0.580302326 0.049118891 0.175270083 2.595299606 0.021268022 0.013926948 136.6858794 -2.135723651 -0.136603909 NQGGYGGSSSSSSYGS(ph)GR ddPTM_BT-474_Pertuzumab_2h_R1 1 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-2;P09651;P09651-3;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 NQGGYGGSSSSSSYGS(1)GR 188.86 1.09E-18 0 90206 92105 84418 70915 76053 88283 75781 79034 75138 73136 TRUE FALSE 86680.64979 89478.25558 99674.21047 74574.93165 78499.31381 90068.14275 76708.43055 77401.92028 66608.64924 68182.43358 1.271304722 1.312335904 1.461875226 1.093755792 1.151312878 1.320987504 1.125046827 1.135217918 0.976918038 1 16.05711247 2.135796142 0.421048948 0.972882307 1.340749049 0.554428701 0.097161613 0.876836726 0.363832478 0.106109106 0.109133067 136.7086964 -2.135796142 0.367866742 SRPFTVAASFQSTSVKS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRPFTVAASFQSTSVKSPK 19 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SRPFTVAASFQSTSVKS(1)PK;SRPFTVAASFQSTS(0.005)VKS(0.995)PK 165.34 1.74E-11 1450370000 1060150 859730 710820 699590 1047920 949630 762860 767500 869830 740230 TRUE FALSE 1018718.166 835211.3422 839280.9861 735695.9237 1081627.298 968832.1692 772196.1089 751650.8568 771090.545 690093.5628 1.476202969 1.210287108 1.216184343 1.066081418 1.567363263 1.403914225 1.118973065 1.089201374 1.117371016 1 19.39643245 2.135807436 6.27502289 1.085585505 1.312221892 0.426000554 0.137576237 0.236668343 12.54472413 0.054368551 0.040013762 136.7122515 -2.135807436 0.226636387 DKDAYS(ph)SFGSRDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKDAYSSFGSRDSR 14 2 O15523-2;O15523;O15523-3;C9J8G5;C9J081 O15523-2 DDX3Y ATP-dependent RNA helicase DDX3Y 1 DKDAY(0.009)S(0.495)S(0.495)FGSRDSR 65.943 0.044698 2403100000 241110 410340 328980 502480 412850 377980 209910 203340 132510 141860 TRUE FALSE 231687.1546 398637.505 388434.0041 528413.053 426129.6952 385623.0146 212478.9414 199140.9579 117468.0203 132251.6958 1.751865284 3.014233598 2.937081462 3.995510603 3.222111387 2.915826615 1.606625458 1.505772434 0.888215607 1 17.0129267 2.135901576 2.191996672 1.177226654 3.057055316 0.714359628 0.537459043 0.177267094 1.679362576 0.280069326 0.170793761 136.7418893 -2.135901576 1.879828662 AQGEPVAGHES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQGEPVAGHESPK 13 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 1 AQGEPVAGHES(1)PK;AQGEPVAGHES(1)PK 224.07 3.67E-08 646500000 964700 801890 951220 1012500 951280 871020 1206250 1316230 1451200 1395320 TRUE FALSE 926998.4575 779020.8823 1123126.614 1064755.246 981878.7851 888632.6212 1221012.448 1289049.391 1286465.86 1300813.734 0.712629667 0.598871969 0.863403103 0.818530139 0.754818895 0.683135947 0.938652796 0.990956166 0.988970078 1 20.31098296 2.135907667 5.07589459 0.985438364 0.742684583 0.752068142 0.068144921 0.111936198 4.616614515 0.027992944 0.020453876 136.7438071 -2.135907667 -0.24275378 NRPLLDFVSMEELNDMDDYDS(ph)EDDNDWRPTVVK ddPTM_BT-474_Pertuzumab_2h_R1 3 NRPLLDFVSMEELNDMDDYDSEDDNDWRPTVVK 33 2 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK 228.14 1.62E-36 728530000 92511.5 86200 69551.7 101695.6 79127.6 79022.2 108417.5 120456.8 126804.8 123543.6 TRUE FALSE 88896.0483 83741.6604 82121.23936 106944.1221 81672.81112 80620.08303 109744.3458 117969.325 112410.4507 115175.8819 0.771828675 0.727076355 0.713007254 0.928528788 0.709113833 0.699973655 0.952841376 1.024253715 0.975989494 1 16.81347912 2.136109827 5.25275034 0.998853675 0.760767053 0.763132778 0.06304937 0.100093659 4.308730324 0.024598287 0.018004448 136.807475 -2.136109827 -0.238086622 KDS(ph)AQDDQAK ddPTM_BT-474_Pertuzumab_2h_R1 3 KDSAQDDQAK 10 1 Q13045-3;Q13045;Q13045-2;J3KS54 Q13045-3 FLII Protein flightless-1 homolog 1 KDS(1)AQDDQAK;KDS(1)AQDDQAK;KDS(1)AQDDQAK 178.23 1.37E-06 759290000 852270 672550 605270 536020 635680 647090 748010 802010 825260 930930 TRUE FALSE 818962.3462 653369.5325 714655.7532 563684.0564 656127.2245 660174.6032 757164.3701 785448.2132 731579.9446 867877.2819 0.943638419 0.752836312 0.823452541 0.649497421 0.756013826 0.760677364 0.872432527 0.905022207 0.842953214 1 19.72713153 2.136282472 4.061955342 0.901962702 0.774502045 0.380184973 0.078041954 0.242013941 7.365476533 0.030548866 0.021894255 136.8618707 -2.136282472 -0.127460657 WS(ph)PPQNYK ddPTM_BT-474_Pertuzumab_2h_R1 4 WSPPQNYK 8 0 H3BRF9;Q96K21-2;Q96K21;H3BRM1;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK 154.84 0.000439 6880200000 2937660 2809670 2465740 2608810 2696650 2592930 2980660 3244250 3283030 3179130 TRUE FALSE 2822852.999 2729540.963 2911354.068 2743450.997 2783390.196 2645360.821 3017138.209 3177255.104 2910354.198 2963804.693 0.952442314 0.920958445 0.982302941 0.925651749 0.9391274 0.892555716 1.017994949 1.072019054 0.981965581 1 21.49901895 2.136461613 6.945279494 1.0303901 0.936882007 0.619797943 0.031145795 0.125766137 7.508019733 0.011483057 0.008464756 136.9183362 -2.136461613 -0.093508094 KS(ph)PLSSILFSALDSDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPLSSILFSALDSDTR 17 1 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A0G2JQF5;A0A3B3IT55;A0A0G2JQF4;A0A1W2PPV8;A0A1W2PRR3;I3L233 A0A1W2PRB5 KANSL1 KAT8 regulatory NSL complex subunit 1 1 KS(0.997)PLS(0.003)SILFSALDSDTR;KS(1)PLSSILFSALDSDTR 162.11 1.77E-09 793650000 323390 323900 300500 293940 338200 306800 349400 372420 392850 385250 TRUE FALSE 310751.5613 314662.6891 354807.0346 309110.2786 349078.5101 313003.7062 353676.0617 364729.3969 348255.315 359156.6744 0.865225634 0.876115388 0.987889297 0.86065581 0.971939365 0.871496282 0.984740329 1.015516132 0.969647343 1 18.4542538 2.136816122 6.503068097 0.997341833 0.909120499 0.499874232 0.042523887 0.172920381 9.59356247 0.015299575 0.011268 137.0301466 -2.136816122 -0.088221333 SAS(ph)QSSLDKLDQELK ddPTM_BT-474_Pertuzumab_2h_R1 4 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 SAS(0.997)QS(0.002)S(0.001)LDKLDQELK;SAS(0.999)QS(0.001)SLDKLDQELK;SAS(0.962)QS(0.037)S(0.001)LDKLDQELK;S(0.001)AS(0.954)QS(0.044)S(0.001)LDKLDQELK 237.16 6.02E-18 2922430000 1728410 1505280 1529360 1563870 1647250 1627990 2127120 2415760 2644570 2518010 TRUE FALSE 1660861.826 1462350.888 1805749.372 1644581.518 1700235.292 1660909.073 2153152.331 2365873.712 2344369.501 2347462.94 0.707513545 0.62294951 0.769234454 0.700578267 0.724286319 0.707533672 0.917225271 1.007842838 0.99868222 1 21.16267095 2.136932052 2.89056047 0.999115921 0.70276857 0.940014111 0.034550297 0.057004203 0.952125217 0.015239882 0.010170924 137.06673 -2.136932052 -0.29634735 GCTALHYAVLADDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 GCTALHYAVLADDYR 15 0 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2R8Y602;A0A2U3TZY2;A0A2R8YDH5;F5H7A5;F5H392;A0A2R8Y6R5 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 ; 134.9 3.23E-05 318020000 710370 755230 661520 777850 632710 670880 691400 641140 680530 654780 FALSE TRUE 682607.955 733691.5798 781071.3794 817994.9317 653061.6918 684445.6533 699861.56 627900.2349 603279.0874 610431.1674 1.118239028 1.201923524 1.279540464 1.340028123 1.069836743 1.12124952 1.146503648 1.028617588 0.98828356 1 19.2194691 2.137020828 0.821577642 0.988536106 1.222736694 0.587552963 0.071229347 0.45753126 0.580356457 0.061590398 0.034063539 137.0947513 -2.137020828 0.234200588 DIFQEIYDK ddPTM_BT-474_Pertuzumab_2h_R1 4 DIFQEIYDK 9 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;; 155.42 0.00017066 293390000 435479 413510 396080 464061 429830 388755 525279 563852 597425 621112 FALSE TRUE 418459.9992 401717.0997 467660.4668 488011.2438 443655.8723 396615.8925 531707.5215 552208.2592 529607.8186 579043.531 0.722674509 0.693759758 0.807643021 0.842788526 0.766187426 0.684950045 0.91825138 0.953655865 0.914625223 1 19.14331228 2.137034393 6.15331695 0.94677065 0.757878443 0.786205759 0.049583217 0.104006341 5.419244835 0.020008287 0.014720895 137.0990334 -2.137034393 -0.188892207 QPPPASS(ph)PTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPPPASSPTKR 11 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 QPPPAS(0.28)S(0.711)PT(0.009)KR 60.196 0.058298 170970000 84259 84023 81175 84020 72821 78375 93370 101460 102300 108030 TRUE FALSE 80966.06513 81626.74631 95845.12823 88356.28227 75163.3536 79959.7962 94512.68999 99364.81554 90687.33288 100713.0319 0.803928386 0.810488422 0.951665603 0.877307342 0.746312093 0.793936939 0.938435555 0.986613288 0.900452813 1 16.61989085 2.137190943 5.756592699 0.960866385 0.833782124 0.540672171 0.056959106 0.177429087 8.556426874 0.023212989 0.017050379 137.1484623 -2.137190943 -0.127084261 NLLHVTDTGVGMTR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLLHVTDTGVGMTR 14 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ; 162.29 4.46E-06 1929010000 1286400 1468410 1137810 1235350 1303510 1337630 1260720 1272010 1473510 1326540 FALSE TRUE 1236126.066 1426532.385 1343437.577 1299106.562 1345438.583 1364677.795 1276149.068 1245742.549 1306243.322 1236692.264 0.999542167 1.153506354 1.086315178 1.050468738 1.087933209 1.103490201 1.031905111 1.007318138 1.056239584 1 20.23805512 2.13726697 5.935527248 1.021610962 1.08267829 0.332427402 0.039165842 0.225836143 11.29412399 0.014141884 0.010396226 137.1724735 -2.13726697 0.061067328 EKEELEQR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKEELEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 107.15 0.0037006 2865750000 4479000 4342100 3728040 3937600 4282600 4606900 4620800 5116300 5748400 5568500 FALSE TRUE 4303955.728 4218267.559 4401779.758 4140820.008 4420353.718 4700054.674 4677350.733 5010646.617 5095865.731 5191340.535 0.82906442 0.812558439 0.847908113 0.797639835 0.851485987 0.905364355 0.900990929 0.965193206 0.981608834 1 22.3076757 2.137294843 0.798639758 1.000087788 0.818770996 0.93854068 0.017174298 0.136433009 0.163958153 0.013956274 0.007826853 137.1812774 -2.137294843 -0.181316792 MEVDRS(ph)PGLPMSDLK ddPTM_BT-474_Pertuzumab_2h_R1 5 MEVDRSPGLPMSDLK 15 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK 161.8 9.88E-07 1290170000 1868540 1898400 1443300 1667810 1776500 1758790 1283980 1276310 1249960 1113160 TRUE FALSE 1795515.391 1844259.491 1704136.416 1753885.874 1833642.736 1794353.939 1299693.731 1249953.752 1108069.781 1037764.682 1.730175851 1.777146133 1.642122194 1.690061249 1.766915726 1.729056664 1.252397344 1.204467424 1.067746668 1 19.98504791 2.137332861 2.654369158 1.120646783 1.7269816 0.951667726 0.065709909 0.058437432 0.822688882 0.031238447 0.020327174 137.1932869 -2.137332861 0.606334818 GEEDWLYER ddPTM_BT-474_Pertuzumab_2h_R1 4 GEEDWLYER 9 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ;;; 201.07 5.13E-05 1203421000 783320 881341 691967 910642 866905 851854 991186 1327220 941992 995317 FALSE TRUE 752706.9884 856206.0176 817020.8296 957640.3428 894789.7866 869079.0715 1003316.431 1299812.443 835061.0173 927903.2931 0.811191203 0.922731953 0.880502134 1.032047574 0.964313623 0.936605224 1.081272626 1.400805938 0.899944017 1 19.82361493 2.137361132 4.352367774 1.165303203 0.929114211 0.235016262 0.135209942 0.220549657 7.43828896 0.05242111 0.037882137 137.202218 -2.137361132 -0.236188991 DLLVGPGVELLLT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLLVGPGVELLLTPR 15 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR 192.24 1.59E-06 74862000 82590 97813 88083 130048 126957 112274 70815 67009 55704 61153 TRUE FALSE 79362.29149 95023.46901 104001.5575 136759.7929 131040.6872 114544.2572 71681.65515 65625.24073 49380.71545 57011.05284 1.392050971 1.666755204 1.824234992 2.398829456 2.298513721 2.009158777 1.257329089 1.151096804 0.866160385 1 15.79895402 2.137648202 3.570354917 1.055577582 1.954357274 0.696417911 0.281328036 0.151435335 3.745772486 0.130195289 0.09148078 137.2929389 -2.137648202 0.898779692 YS(ph)T(ph)MERMEEALQVAINNNRGFVS(ph)PMLTQS ddPTM_BT-474_Pertuzumab_2h_R1 1 YSTMERMEEALQVAINNNRGFVSPMLTQS 29 2 Q8IVU3-2;Q8IVU3 Q8IVU3-2 HERC6 Probable E3 ubiquitin-protein ligase HERC6 3 Y(0.18)S(0.902)T(0.916)MERMEEALQVAINNNRGFVS(0.403)PMLT(0.315)QS(0.283) 41.834 0.096894 236980000 78515 80751 81200 119180 94638 91518 69951 27856 94725 92463 TRUE FALSE 75446.547 78448.06054 95874.64628 125330.8941 97682.11722 93368.55666 70807.08126 27280.76387 83972.21512 86200.39865 0.875245917 0.910066099 1.112229732 1.453947964 1.133197975 1.083156901 0.821424058 0.316480716 0.974151123 1 16.39540692 2.137711833 4.107089645 0.663275923 1.105697294 0.275044485 0.234182869 0.217563371 6.743768573 0.095572423 0.068633149 137.313056 -2.137711833 0.442421371 KPADLQNLAPGTHPPFITFNSEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPADLQNLAPGTHPPFITFNSEVK 24 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 ; 197.12 1.23E-24 1316560000 685780 681400 635570 631880 616260 744240 669070 766900 887940 755210 FALSE TRUE 658978.9594 661967.1392 750431.6372 664491.4025 636082.5626 759289.0427 677258.2788 751063.247 787144.7737 704058.954 0.935971279 0.940215497 1.065864773 0.943800798 0.903450711 1.078445261 0.961934047 1.066761871 1.118009748 1 19.42533671 2.137784848 1.247688929 1.06359157 0.966834959 0.289127813 0.059890523 0.583537563 1.71896782 0.040231028 0.020985893 137.3361436 -2.137784848 -0.09675661 LLDPEDVDVPQPDEK ddPTM_BT-474_Pertuzumab_2h_R1 6 LLDPEDVDVPQPDEK 15 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 328.26 2.00E-68 1583542000 1789360 1651290 1459940 1559810 1604580 1699610 1769460 1954710 2154860 1984410 FALSE TRUE 1719429.833 1604196.826 1723783.634 1640311.981 1656192.773 1733977.279 1791115.181 1914344.555 1910249.327 1850004.143 0.92941945 0.867131477 0.931772851 0.886653139 0.895237332 0.937282916 0.9681682 1.034778523 1.032564891 1 20.81909707 2.137898453 1.788997494 1.02645672 0.901508962 0.857389924 0.021229157 0.110365253 0.685480991 0.010999199 0.00627529 137.3720735 -2.137898453 -0.124947758 KQQTLEAEEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KQQTLEAEEAK 11 1 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 ;;; 145.83 5.78E-05 1121350000 1736170 1582090 1425770 1336520 1539830 1621580 1822790 1989390 2272630 2119210 FALSE TRUE 1668318.557 1536970.342 1683438.355 1405497.957 1589360.03 1654369.459 1845097.849 1948308.401 2014650.57 1975674.019 0.844430073 0.777947337 0.852083056 0.711401751 0.804464712 0.837369648 0.933908039 0.986148718 1.01972823 1 20.9139135 2.138030827 1.692269157 1.005653133 0.794867111 0.859650238 0.036782664 0.124698696 0.690186477 0.020656643 0.011579764 137.4139511 -2.138030827 -0.210786022 DYFEQYGK ddPTM_BT-474_Pertuzumab_2h_R1 9 DYFEQYGK 8 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;;;;;;; 174.16 0.00063642 36562642000 10484455 10227410 8709581 9064060 9639860 9681860 10307020 11367850 11373090 10959240 FALSE TRUE 10074710.91 9935734.28 10283596.03 9531857.223 9949934.852 9877633.843 10433160.39 11133099.92 10082064.5 10216960.91 0.986077073 0.972474532 1.00652201 0.932944474 0.973864433 0.966787866 1.021160841 1.089668446 0.986796816 1 23.28446279 2.138059351 4.763930585 1.039816895 0.972896298 0.363258625 0.03144949 0.174311674 6.662151485 0.011935534 0.008691713 137.4229766 -2.138059351 -0.066920597 RQS(ph)PLPPQKK ddPTM_BT-474_Pertuzumab_2h_R1 4 RQSPLPPQKK 10 2 Q01105;B2REB7 Q01105 SET Protein SET 1 RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK 100.22 0.0021707 4916770000 4776310 4483060 3798550 3911940 4370110 4787280 4792010 5476690 6538580 5501030 TRUE FALSE 4589646.525 4355207.518 4485032.483 4113835.692 4510678.557 4884082.082 4850656.052 5363594.438 5796347.81 5128440.338 0.894940025 0.849226515 0.874541223 0.802161168 0.879541978 0.952352325 0.945834548 1.045852946 1.130235984 1 22.29008871 2.13807728 1.224566539 1.069171512 0.856973082 0.799505863 0.042082097 0.189416072 0.536857362 0.028425418 0.014799101 137.4286499 -2.13807728 -0.212198431 EFNEDGALAVLQQFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFNEDGALAVLQQFK 15 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 233.59 2.89E-17 268640000 490040 510050 433930 460090 492330 456010 523370 561470 554350 594600 FALSE TRUE 470888.695 495503.8734 512350.8037 483835.3 508166.2416 465230.8346 529775.1586 549875.4483 491422.512 554327.2124 0.849477862 0.893883364 0.924275035 0.87283339 0.916726133 0.839271146 0.955708374 0.991969068 0.886520634 1 19.08037831 2.138184398 8.274606675 0.962215498 0.886330761 0.490295242 0.03772465 0.207253167 15.2913668 0.013515416 0.009976276 137.4625506 -2.138184398 -0.075884736 KGTENGVNGTLTSNVADS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 KGTENGVNGTLTSNVADSPR 20 1 G3XAN4;Q15629-2;Q15629 G3XAN4 TRAM1 Translocating chain-associated membrane protein 1 1 KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR 262.19 1.24E-36 9531640000 3428650 5951030 2582906 6290340 3526690 3529310 6149810 8553540 5865980 4392170 TRUE FALSE 3294654.567 5781312.451 3049694.571 6614985.201 3640129.187 3600675.066 6225073.214 8376906.41 5200098.543 4094684.414 0.804617459 1.411906723 0.744793557 1.615505502 0.888988947 0.879353499 1.520281561 2.045800253 1.269963205 1 21.96532083 2.138239386 6.421983511 1.608472191 1.078424393 0.183190277 0.36602352 0.248058033 13.66269755 0.13238873 0.097490958 137.4799564 -2.138239386 -0.530047798 ISNYGWDQSDKFVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISNYGWDQSDKFVK 14 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 234.21 3.03E-17 5427100000 3306300 3149800 2393000 2604300 2856000 3128000 3056700 3620900 3962100 3425600 FALSE TRUE 3177086.141 3059970.788 2825468.332 2738708.235 2947865.834 3191250.303 3094108.809 3546127.15 3512339.018 3193581.061 0.994834977 0.958162868 0.884733557 0.857566532 0.923059655 0.999270174 0.968852442 1.11039209 1.099812077 1 21.60674364 2.138430721 1.629868976 1.078032993 0.923078 0.578978164 0.050367877 0.253879413 1.300100057 0.030591178 0.016959984 137.5405386 -2.138430721 -0.154954994 MDPSAKPSAS(ph)QSPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MDPSAKPSASQSPEK 15 1 P35716 P35716 SOX11 Transcription factor SOX-11 1 MDPS(0.001)AKPS(0.059)AS(0.545)QS(0.395)PEK 69.522 0.050801 0 154260 133370 110310 96781 126350 116780 146140 159650 164920 170070 TRUE FALSE 148231.3487 129566.4182 130245.4708 101775.879 130414.1625 119141.3716 147928.505 156353.1717 146198.973 158551.0074 0.934912689 0.81719076 0.821473625 0.641912534 0.822537583 0.751438755 0.933002618 0.98613799 0.922094255 1 17.27458752 2.138490625 5.248469737 0.96550669 0.794472315 0.556667457 0.071179164 0.157031237 6.801995815 0.027735308 0.020307524 137.5595117 -2.138490625 -0.171034375 TRS(ph)PEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TRSPEKK 7 2 Q5TCQ9;Q5TCQ9-1 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 T(0.013)RS(0.987)PEKK 82.749 0.018621 199390000 274110 198490 192070 155950 188180 196290 229650 251610 249190 281360 TRUE FALSE 263397.4782 192829.2595 226781.3216 163998.5982 194232.9806 200259.1183 232460.5254 246414.1656 220902.9959 262303.2366 1.004171666 0.735138697 0.864576909 0.625225218 0.740490217 0.763464153 0.886228201 0.9394248 0.842166489 1 18.00087608 2.13859563 4.425431752 0.91859446 0.780290389 0.288190005 0.099135118 0.272332309 9.423199812 0.038038428 0.027543321 137.592775 -2.13859563 -0.138304071 SDTALEEAVAEVLDHRPIEPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDTALEEAVAEVLDHRPIEPK 21 1 A0A3B3ITN0;Q86TP1 A0A3B3ITN0 PRUNE Protein prune homolog 0 ;;; 238.56 4.08E-30 171493000 264409 264951 219095 240712 266293 264732 292701 301199 360838 336175 FALSE TRUE 254075.604 257394.8569 258690.3402 253135.1752 274858.5562 270085.0624 296283.1624 294979.1354 319877.183 313405.5678 0.810692694 0.821283612 0.825417181 0.807692017 0.877005977 0.861774934 0.94536662 0.941205791 1.020649331 1 18.25767128 2.138683771 0.772504708 1.010896529 0.813916293 0.930521091 0.020033956 0.143430193 0.161902023 0.015580128 0.008903167 137.6207028 -2.138683771 -0.196980236 WFSNPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 6 WFSNPSR 7 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R 112.8 0.0065797 2045880000 1294070 1315390 1234100 1325560 1184770 1265500 1143090 1321990 1161700 1251020 TRUE FALSE 1243496.314 1277876.365 1457129.322 1393972.31 1222879.203 1291089.277 1157079.477 1294690.445 1029828.686 1166287.301 1.06620068 1.095678881 1.24937425 1.19522206 1.048523123 1.107007918 0.992105012 1.110095637 0.882997427 1 20.15349179 2.13876114 0.819240855 0.977749628 1.146418533 0.437682588 0.074113921 0.642266849 0.810414363 0.062123052 0.034444526 137.6452219 -2.13876114 0.168668905 EKEPIAASTNR ddPTM_BT-474_Pertuzumab_2h_R1 5 EKEPIAASTNR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;; 162.32 2.30E-05 1553320000 1681260 1682870 1388900 1498260 1509780 1563780 1678730 1783810 1950080 1842430 FALSE TRUE 1615554.5 1634876.195 1639905.126 1575585.378 1558343.445 1595400.703 1699274.8 1746973.7 1728715.094 1717640.575 0.940566102 0.951815076 0.95474289 0.91729632 0.90725817 0.928832683 0.989307556 1.017077569 1.006447518 1 20.71199675 2.138960945 3.966994395 1.008356843 0.933232332 0.85544763 0.014177633 0.087602837 2.578332315 0.006476591 0.00463272 137.7085626 -2.138960945 -0.075124511 DLLDTVLPHLYNETK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLLDTVLPHLYNETK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 197.2 8.54E-09 1597950000 1337881 1363936 1071905 1133982 1273204 1315353 1410219 1382141 1754303 1545542 FALSE TRUE 1285595.131 1325037.881 1265622.078 1192506.947 1314157.763 1341950.339 1427477.682 1353599.305 1555161.878 1440861.064 0.892240872 0.919615301 0.878378984 0.827634931 0.912064179 0.931353045 0.990711539 0.939437771 1.07932813 1 20.4584998 2.139071496 0.979972604 1.018130933 0.882171529 0.68057307 0.0381123 0.342066175 0.614476092 0.029642141 0.015530458 137.7436211 -2.139071496 -0.135959404 WDDSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 WDDSQK 6 0 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 109.11 0.069422 365630000 1068250 1054430 928760 969510 1070680 1076890 1083600 1166080 1333610 1277040 FALSE TRUE 1026501.609 1024358.689 1096607.592 1019546.527 1105119.395 1098665.454 1096861.421 1142000.041 1182224.184 1190544.943 0.862211557 0.860411608 0.921097182 0.856369626 0.928246683 0.922825686 0.921310386 0.959224637 0.993010966 1 20.18319065 2.139890023 0.443269447 1.008221809 0.86199327 0.817200499 0.021044064 0.417456951 0.186703283 0.021042862 0.020425183 138.0034751 -2.139890023 -0.14622854 VLKQDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLKQDGK 7 1 P52788;P52788-2 P52788 SMS Spermine synthase 0 ; 68.224 0.057485 2195800000 2818600 2669900 1973910 2087010 2529750 2696700 2567300 2863000 3302000 3074900 FALSE TRUE 2708445.996 2593757.066 2330639.446 2194720.836 2611121.706 2751229.122 2598719.385 2803878.05 2927170.803 2866634.284 0.944817416 0.904809197 0.813022944 0.76560894 0.910866698 0.95974193 0.906540259 0.978108043 1.021117629 1 21.45092643 2.139898095 0.969831919 1.006144822 0.86233778 0.523181101 0.052575131 0.484306941 0.852064124 0.04413106 0.023180312 138.0060402 -2.139898095 -0.143807042 SS(ph)PELTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.227)S(0.773)PELTR;S(0.315)S(0.685)PELTR;S(0.418)S(0.582)PELTR;S(0.418)S(0.582)PELTR 194.29 0.00050786 2951750000 1790320 1765680 1669350 1912290 1614400 1782910 2031920 2169010 2419920 2340590 TRUE FALSE 1720352.315 1715324.535 1971038.679 2010983.516 1666328.642 1818961.662 2056787.245 2124219.186 2145220.827 2182059.755 0.788407518 0.786103374 0.903292715 0.921598738 0.763649409 0.833598465 0.94258979 0.973492674 0.983117361 1 21.05725918 2.140056471 3.38614178 0.978414662 0.834276077 0.688103615 0.047369292 0.156238631 3.525447158 0.021206047 0.014765277 138.0563768 -2.140056471 -0.144138585 LPPGEYVVVPSTFEPNKEGDFVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPPGEYVVVPSTFEPNKEGDFVLR 24 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 154.79 4.97E-08 477540000 378260 374070 331920 383480 390720 390670 426590 501690 511120 464950 FALSE TRUE 363477.181 363401.8899 391905.3275 403271.4488 403287.8636 398569.6151 431810.736 491329.9262 453099.8004 433458.5224 0.838551239 0.83837754 0.904135707 0.930357642 0.930395512 0.91951039 0.996198514 1.133510822 1.045312935 1 18.72553442 2.140084155 2.614529719 1.073638875 0.891953035 0.743154343 0.044166241 0.133736263 1.827293765 0.021304091 0.013833021 138.0651774 -2.140084155 -0.181685841 HSS(ph)NPPLESHVGWVMDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.126)S(0.874)NPPLESHVGWVMDSR;HS(0.056)S(0.944)NPPLESHVGWVMDSR 266.74 2.26E-31 1793210000 462330 458400 382670 430150 433510 382100 379860 188221 400950 430420 TRUE FALSE 444261.6325 445326.8808 451826.9814 452350.093 447454.2429 389826.3238 384508.8403 184334.1706 355435.8369 401267.27 1.107146447 1.109801158 1.126000088 1.127303737 1.115102766 0.971487966 0.958236241 0.45938003 0.885783276 1 18.61420396 2.140173279 2.63939255 0.723700527 1.105493827 0.467320854 0.14129443 0.185032817 2.577515627 0.06209101 0.040440256 138.0935133 -2.140173279 0.3817933 DSGSSSVFAES(ph)PGGK ddPTM_BT-474_Pertuzumab_2h_R1 5 DSGSSSVFAESPGGK 15 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 DSGSSSVFAES(1)PGGK;DSGSSSVFAES(1)PGGK;DSGSSSVFAES(1)PGGK;DSGSSSVFAES(1)PGGK;DSGSSSVFAES(1)PGGK 366.42 2.05E-97 5072770000 4630570 4373730 3873440 3958790 3952040 4225990 4922990 5426950 5631180 5971980 TRUE FALSE 4449602.205 4248995.503 4573456.772 4163103.626 4079160.956 4311442.413 4983239.024 5314881.586 4991952.054 5567492.475 0.799211175 0.763179388 0.821457199 0.747751999 0.732674714 0.774395732 0.895059858 0.954627529 0.896624841 1 22.40859627 2.140400544 3.275095935 0.942262055 0.771027819 0.855928802 0.033349282 0.086629543 1.839831059 0.013834632 0.009564294 138.1657961 -2.140400544 -0.171234235 RGATVEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGATVEAK 8 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 0 ; 81.263 0.037379 79759000 201937 207883 164606 173276 203814 199358 218075 251012 284390 225378 FALSE TRUE 194045.0788 201954.3804 194353.9658 182218.7951 210369.8624 203389.1554 220743.8671 245828.5145 252107.2395 210112.9473 0.923527471 0.961170565 0.924997571 0.867242107 1.001222748 0.967999155 1.050596215 1.169982705 1.199865323 1 17.68080554 2.140415963 2.043728358 1.140747608 0.935009955 0.661231934 0.058952126 0.173039243 1.419036883 0.02932515 0.017538503 138.1707017 -2.140415963 -0.205737653 ATEDGTPYDPYK ddPTM_BT-474_Pertuzumab_2h_R1 3 ATEDGTPYDPYK 12 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;; 172.27 8.42E-05 227839000 500590 495230 411520 436330 497160 500590 508430 550430 625630 598680 FALSE TRUE 481026.3894 481106.5253 485890.8182 458849.0436 513151.6029 510712.2728 514652.3184 539063.4281 554611.1053 558130.8704 0.861852327 0.861995906 0.870567897 0.822117299 0.919410895 0.91504036 0.922099718 0.965836969 0.993693656 1 19.09024392 2.140593931 0.689712391 1.003751241 0.854348545 0.874516345 0.020125274 0.230302918 0.211262677 0.017476357 0.010774872 138.2273339 -2.140593931 -0.149402696 HEQQQLLGVEEVTDPDVVLHNLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEQQQLLGVEEVTDPDVVLHNLLR 24 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 0 86.551 0.0068055 71129000 16528 15090 15552 18530 16170 17462 13710 8261.6 19478 18864 FALSE TRUE 15882.06749 14659.64797 18362.59235 19486.33552 16690.12274 17815.0936 13877.78708 8090.995073 17266.9391 17586.32448 0.903091917 0.833582253 1.044140427 1.108039121 0.949039849 1.013008354 0.789123793 0.460073114 0.981838992 1 14.10216637 2.140697475 5.249538185 0.72453759 0.976180082 0.139680373 0.162121947 0.239227848 10.44333123 0.062204594 0.045562436 138.2602936 -2.140697475 0.251642493 NRNEQESAVHPR ddPTM_BT-474_Pertuzumab_2h_R1 3 NRNEQESAVHPR 12 1 Q9UJU6-2;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;; 172.09 2.20E-05 445297000 430456 503405 305698 392664 390313 433905 364390 368510 396650 392309 FALSE TRUE 413633.3036 489048.3823 360944.4288 412929.4361 402867.7721 442678.8564 368849.5138 360900.1397 351623.9549 365737.562 1.130956584 1.337156566 0.986894611 1.129032068 1.101521457 1.210372962 1.008508702 0.986773515 0.961410562 1 18.48044928 2.140711905 6.272708501 0.985740509 1.147056889 0.471015164 0.08332352 0.191714125 10.40805981 0.031356721 0.023085377 138.2648875 -2.140711905 0.161316379 SSEELDMDKVTAAMVLTSLST(ph)SPLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSEELDMDKVTAAMVLTSLSTSPLVR 26 1 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 SSEELDMDKVTAAMVLTSLS(0.02)T(0.62)S(0.36)PLVR 138.7 8.66E-06 194430000 211170 206030 178370 193520 218520 220960 219760 271760 303240 263220 TRUE FALSE 202917.2429 200154.2261 210605.4268 203507.5904 225548.8943 225427.9626 222449.4886 266148.061 268817.4665 245391.8749 0.826911009 0.815651399 0.858241239 0.829316743 0.919137581 0.91864477 0.906507148 1.084583836 1.095461969 1 17.90472796 2.14085171 1.068835106 1.073256945 0.840300793 0.807954887 0.04288264 0.204640023 0.438659335 0.031726477 0.016484647 138.3094042 -2.14085171 -0.232956152 SKVDDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKVDDLR 7 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 125.96 0.0036465 2961110000 10172600 10071100 7980000 8643200 9382600 8675500 10545700 11660200 11591200 11217200 FALSE TRUE 9775043.546 9783882.089 9422163.514 9089276.588 9684399.85 8850924.554 10674761.43 11419412.8 10275415.57 10457449.05 0.934744554 0.935589745 0.901000183 0.869167666 0.926076694 0.846375106 1.02078063 1.091988375 0.982592936 1 23.31802763 2.141054165 6.627871271 1.039825719 0.903497114 0.703248989 0.038292243 0.105247983 6.114296424 0.014284249 0.010525686 138.3738948 -2.141054165 -0.136328605 LDKAS(ph)PDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDKASPDSR 9 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 LDKAS(1)PDSR;LDKAS(0.994)PDS(0.006)R;LDKAS(0.933)PDS(0.067)R 100.38 0.0048873 1205660000 1883800 1711850 1797940 1870980 1779740 1822580 2187940 2375620 2523490 2665510 TRUE FALSE 1810179.013 1663029.714 2122867.753 1967541.502 1836986.953 1859433.816 2214716.664 2326562.617 2237033.995 2484972.634 0.728450281 0.669234619 0.854282146 0.791775924 0.739238303 0.748271346 0.891243885 0.936252812 0.900224801 1 21.24479853 2.141116284 3.556802063 0.934111525 0.75620776 0.751006335 0.050353649 0.125398046 3.088388219 0.021296982 0.014985569 138.3936883 -2.141116284 -0.177903765 TDSLFVLPSRDDAT(ph)PVRDEPMDAESITFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDSLFVLPSRDDATPVRDEPMDAESITFK 29 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 TDSLFVLPSRDDAT(1)PVRDEPMDAESITFK 195.91 2.17E-23 192240000 115730 106240 98432 113520 107250 113960 125410 145010 153310 135980 TRUE FALSE 111207.1437 103210.1392 116220.852 119378.7808 110699.7937 116264.3493 126944.8051 142015.4928 135906.8915 126769.9535 0.877235817 0.81415301 0.916785475 0.941696179 0.873233685 0.917128595 1.001379283 1.120261457 1.07207495 1 16.95185332 2.141221225 2.661205382 1.075676523 0.886775896 0.778208748 0.04233567 0.117726681 1.668206714 0.019577265 0.012796255 138.4271332 -2.141221225 -0.188900627 KNREELDK ddPTM_BT-474_Pertuzumab_2h_R1 5 KNREELDK 8 2 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;; 170.5 0.00016583 13538740000 11711090 10729150 9362160 9039400 9711090 10804730 11468020 12646500 14266300 12978340 FALSE TRUE 11253407.66 10423165.15 11054110.57 9505924.517 10023456.03 11023209.04 11608369.06 12385345.36 12646849.43 12099305.47 0.930087077 0.861468055 0.913615298 0.785658693 0.828432347 0.911061306 0.959424414 1.023641017 1.045254165 1 23.5284209 2.14139565 1.93311565 1.025211554 0.863037491 0.748933373 0.04012314 0.167742357 1.225461752 0.022085779 0.012973763 138.4827407 -2.14139565 -0.162174063 NPRPGEENGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NPRPGEENGK 10 1 B1ANH0;B1ANG9;Q16774;Q16774-2;B1ANH2;Q16774-3;B1ANH6 B1ANH0 GUK1 Guanylate kinase 0 ; 115.57 0.00162 162350000 190249 176985 177054 224850 204661 180015 243700 281550 271410 252180 FALSE TRUE 182813.8587 171937.5611 209051.5963 236454.5354 211244.1069 183655.0266 246682.4735 275735.8941 240600.6746 235099.624 0.777601664 0.731339158 0.889204299 1.005763138 0.898530178 0.781179585 1.049267835 1.172847023 1.023398807 1 17.84291271 2.141547045 5.839495996 1.090175921 0.853944054 0.597989837 0.085059035 0.143391183 7.17072912 0.034847066 0.02561741 138.5310242 -2.141547045 -0.236231867 EFTGS(ph)PPSSATKK ddPTM_BT-474_Pertuzumab_2h_R1 4 EFTGSPPSSATKK 13 1 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFT(0.015)GS(0.985)PPSSATKK;EFT(0.001)GS(0.986)PPS(0.004)S(0.006)AT(0.003)KK;EFT(0.035)GS(0.949)PPS(0.011)S(0.005)ATKK;EFTGS(0.976)PPS(0.023)S(0.001)ATKK 140.81 2.42E-05 3553900000 4355550 4379630 3270580 3448830 3946970 4207580 4121170 4531380 5151970 4744450 TRUE FALSE 4185330.291 4254727.241 3861646.56 3626824.53 4073927.875 4292660.15 4171606.111 4437805.419 4567139.964 4423104.176 0.946242757 0.961932406 0.873062539 0.819972668 0.921056279 0.970508489 0.943139918 1.003323739 1.032564412 1 22.07662779 2.141712558 1.199976973 1.015154802 0.903345579 0.549284729 0.040487211 0.395202771 1.074952869 0.03094257 0.01612819 138.5838296 -2.141712558 -0.111809223 GSQNSSEHRPPASSTSEDVKAS(ph)PSSANK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSQNSSEHRPPASSTSEDVKASPSSANK 28 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 GSQNSSEHRPPAS(0.001)S(0.001)T(0.001)S(0.001)EDVKAS(0.946)PS(0.041)S(0.009)ANK;GSQNSSEHRPPAS(0.002)S(0.002)T(0.002)S(0.002)EDVKAS(0.949)PS(0.035)S(0.007)ANK;GSQNSSEHRPPASSTSEDVKAS(0.966)PS(0.028)S(0.006)ANK 115.3 0.00017283 239935000 142917 143341 110479 109268 95491 135193 159838 173882 203597 201591 TRUE FALSE 137331.6456 139253.055 130445.0129 114907.3346 98562.55474 137926.6951 161794.1453 170291.2759 180485.5221 187937.062 0.730732109 0.740955794 0.694088816 0.611413913 0.52444448 0.733898325 0.860895363 0.906108003 0.960350876 1 17.51989008 2.141771461 2.041211428 0.945984194 0.661903005 0.812213611 0.062860733 0.155443355 1.272105163 0.036333578 0.021750315 138.6026266 -2.141771461 -0.284081188 GFGSEEGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFGSEEGSR 9 0 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;; 205.7 3.38E-05 1795600000 1982870 2008910 1761570 1799870 2019410 1904730 1796390 1796140 1903100 1920950 FALSE TRUE 1905377.248 1951617.854 2079924.885 1892761.506 2084366.157 1943244.946 1818374.758 1759049.081 1687068.066 1790842.345 1.063955883 1.089776472 1.161422662 1.056911297 1.163902653 1.08510107 1.015374001 0.982246754 0.942052811 1 20.77220691 2.141803217 2.361603437 0.97432742 1.108023802 0.734458297 0.035708492 0.145324172 1.611121516 0.016578537 0.010430179 138.6127618 -2.141803217 0.133696382 RLS(ph)EVIYEPFQLLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSEVIYEPFQLLSK 15 1 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 RLS(0.999)EVIY(0.001)EPFQLLSK;RLS(1)EVIYEPFQLLSK 94.01 0.0049108 123111000 165969 227820 213400 197849 177022 225810 221880 279480 271650 251510 TRUE FALSE 159482.748 221322.7967 251966.1271 208060.0106 182716.0734 230376.0329 224595.4338 273708.6403 240813.4308 234475.0037 0.680169508 0.94390785 1.074596964 0.887344098 0.779256085 0.982518517 0.957865147 1.167325455 1.027032422 1 17.83907461 2.141874032 2.320391096 1.078147438 0.892015248 0.329848264 0.109290027 0.339486878 3.628714271 0.053676688 0.033572989 138.6353656 -2.141874032 -0.186132189 IEGDMIVCAAYAHELPK ddPTM_BT-474_Pertuzumab_2h_R1 7 IEGDMIVCAAYAHELPK 17 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;; 221.49 3.67E-15 3050430000 3143838 3102533 2694044 2665628 2992973 3213300 3288250 3557190 4031830 3890730 FALSE TRUE 3020973.335 3014051.797 3180917.679 2803201.381 3089244.695 3278275.128 3328492.587 3483732.783 3574153.561 3627207.392 0.832864794 0.830956566 0.87696052 0.772826331 0.851686811 0.903801402 0.917646064 0.960444884 0.985373367 1 21.79042781 2.142220789 0.973891689 0.993843514 0.829379196 0.862193253 0.026018883 0.192901679 0.342378432 0.020131634 0.010584804 138.7461014 -2.142220789 -0.164464317 T(ph)HAVSVSETDDYAEIIDEEDTYTMPSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;Q05397-2;Q05397-4;Q05397-3;H0YB99;H0YB33 E7ESA6 PTK2 Focal adhesion kinase 1 1 T(0.378)HAVS(0.378)VS(0.103)ET(0.115)DDY(0.026)AEIIDEEDTYTMPSTR 66.772 0.05082 49302000 19452 17333 11827 12747 17880 14209 14189 10276 16357 13610 TRUE FALSE 18691.79433 16838.67981 13964.40199 13404.8742 18455.12644 14496.31572 14362.64923 10063.79701 14500.22193 12688.18258 1.473165619 1.327115188 1.100583311 1.056484971 1.454512995 1.14250529 1.131970567 0.793163004 1.142813153 1 13.63119782 2.142275347 2.632233637 0.959343953 1.260033139 0.398760505 0.152831877 0.267544322 3.708944121 0.070574311 0.046017887 138.7635326 -2.142275347 0.300689186 (ac)AS(ph)PSLERPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPSLERPEK 10 1 Q13601-2;Q13601 Q13601-2 KRR1 KRR1 small subunit processome component homolog 1 AS(0.99)PS(0.01)LERPEK;AS(0.981)PS(0.019)LERPEK 55.064 0.0051787 482280000 176545 165205 176546 126974 162107 180204 154340 159970 166897 189182 TRUE FALSE 169645.4262 160493.5152 208451.7894 133527.1434 167321.3189 183847.8483 156228.8591 156666.5636 147951.5522 176368.5346 0.961880341 0.909989503 1.18191031 0.757091641 0.948702779 1.042407302 0.885809135 0.888290896 0.838877255 1 17.42823367 2.142306985 24.50987122 0.893037663 0.963852633 0.075229287 0.106796136 32.12174986 8153.277895 0.038852149 0.02869422 138.7736417 -2.142306985 0.07081497 EDLYEAADKWVAAVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDLYEAADKWVAAVGK 16 1 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 176.83 2.78E-09 601720000 1194290 1191980 1091660 1235280 918230 1126290 1253210 1383310 1433590 1309120 FALSE TRUE 1147615.826 1157985.897 1288947.246 1299032.949 947765.7019 1149064.355 1268547.159 1354744.165 1270854.873 1220452.136 0.940320224 0.948817133 1.056122733 1.06438664 0.776569333 0.941507103 1.039407545 1.110034654 1.041298413 1 20.21898429 2.14241079 4.965023916 1.065019977 0.956077186 0.246413215 0.078379189 0.284044719 11.60464744 0.031862238 0.02328359 138.8068153 -2.14241079 -0.108942791 DKGQKS(ph)PAEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKGQKSPAEQK 11 2 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 DKGQKS(1)PAEQK;DKGQKS(1)PAEQK 135.47 6.23E-05 313380000 808700 599330 383800 343700 527910 535260 541600 610640 643890 560070 TRUE FALSE 777095.1099 582237.6952 453161.1976 361438.3982 544890.7046 546083.3239 548228.2628 598030.0706 570798.3066 522135.96 1.488300308 1.115107443 0.867898847 0.692230426 1.043580114 1.04586423 1.049972239 1.145353158 1.093198612 1 18.994066 2.142704355 2.689130223 1.095092566 1.020210187 0 0.192861722 1.413626208 20.47017374 0.093370691 0.061311924 138.9006745 -2.142704355 -0.074882379 IKEEPVS(ph)EEGEEDEEQEAEEEPMDTSPSGLHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKEEPVSEEGEEDEEQEAEEEPMDTSPSGLHSK 33 1 A0A0C4DH01;Q9NVU0-3;Q9NVU0-2;Q9NVU0-5;Q9NVU0-4;Q9NVU0 A0A0C4DH01 POLR3E DNA-directed RNA polymerase III subunit RPC5 1 IKEEPVS(1)EEGEEDEEQEAEEEPMDTSPSGLHSK 153.24 7.98E-11 280510000 72231 64614 66765 63035 66019 67741 73635 81051 84057 80542 TRUE FALSE 69408.13266 62771.27198 78830.92068 66288.2439 68142.56109 69110.76943 74536.16716 79377.26853 74515.20176 75086.8186 0.924371733 0.835982575 1.04986364 0.882821315 0.907516957 0.920411475 0.99266647 1.057139855 0.992387254 1 16.19627205 2.142933859 3.818567471 1.02324229 0.919693835 0.412274175 0.053124894 0.205912517 5.726112584 0.020759577 0.014797708 138.9740966 -2.142933859 -0.103548455 EEAS(ph)DDDMEGDEAVVR ddPTM_BT-474_Pertuzumab_2h_R1 9 EEASDDDMEGDEAVVR 16 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 1 EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR 495.2 9.66E-258 15205840000 3655456 3861578 4167311 7671080 3867299 3648871 7457130 8004680 8936870 9997990 TRUE FALSE 3512596.738 3751449.576 4920436.799 8066985.358 3991694.185 3722653.672 7548392.588 7839380.561 7922393.984 9320817.232 0.376855017 0.402480757 0.527897573 0.865480479 0.428255815 0.399391339 0.809842356 0.841061504 0.849967743 1 23.15202502 2.143007345 5.720202859 0.865321619 0.510922535 0.634611441 0.139649276 0.154283794 7.575488061 0.056409318 0.041452896 138.9976139 -2.143007345 -0.354399085 AYEKPPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYEKPPEK 8 1 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 87.913 0.013668 616420000 2257000 2141750 2002880 2167930 2473600 2432200 2581200 3193500 3543300 3360800 FALSE TRUE 2168793.945 2080669.387 2364844.97 2279817.127 2553165.59 2481380.75 2612789.498 3127553.109 3141079.439 3133170.023 0.692204358 0.664078033 0.754777096 0.727639136 0.814882554 0.791971305 0.833912453 0.998207275 1.002524413 1 21.57919163 2.143133834 0.747999754 1.032547892 0.701874618 0.91252394 0.036375683 0.179371119 0.190747309 0.031949224 0.018663136 139.038103 -2.143133834 -0.330673274 EKEEEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEEEEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 98.044 0.0071153 547230000 1558540 1367480 1177520 1187940 1293790 1352300 1471250 1552950 1753370 1670020 FALSE TRUE 1497630.534 1328480.809 1390324.058 1249249.726 1335405.93 1379644.433 1489255.598 1520881.04 1554334.788 1556908.058 0.961926124 0.853281478 0.893003316 0.802391457 0.857729474 0.886143806 0.956546914 0.976859894 0.998347192 1 20.57025232 2.143194792 2.110627469 0.989746967 0.869179865 0.664272072 0.037942812 0.193085924 1.695150436 0.019297822 0.011701935 139.0576201 -2.143194792 -0.120567102 EEFWEMFDGSLYHK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEFWEMFDGSLYHK 14 0 A0A0A0MTI1;Q15392-2;Q15392 A0A0A0MTI1 DHCR24 Delta(24)-sterol reductase 0 ; 222.94 3.71E-12 1024530000 599370 866360 582260 1088310 563900 605220 987190 1109400 1170650 950880 FALSE TRUE 575945.9578 841652.2611 687487.3343 1144477.81 582038.3556 617457.9631 999271.5265 1086490.502 1037762.72 886476.0506 0.649702784 0.949435984 0.775528379 1.291041996 0.656575387 0.696530902 1.127240297 1.225628714 1.170660752 1 19.75772213 2.143265906 7.324516053 1.16090628 0.851847749 0.373346454 0.184917912 0.237296986 15.79037202 0.069211264 0.051057715 139.080392 -2.143265906 -0.309058531 S(ph)PSLDNPTPFPNLGPSENPLKR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSLDNPTPFPNLGPSENPLKR 22 1 M0R0R8;M0R0X9;M0QXC8;M0QX56;M0R3C2;M0QYT9;M0R205;M0QZB8;M0QZB7;Q14653-3;Q14653-2;Q14653;Q14653-4 M0R0R8 IRF3 Interferon regulatory factor 3 1 S(0.986)PS(0.014)LDNPTPFPNLGPSENPLKR;S(0.82)PS(0.176)LDNPT(0.004)PFPNLGPSENPLKR;S(0.975)PS(0.025)LDNPTPFPNLGPSENPLKR 154.14 1.76E-08 1866770000 863040 807710 718286 1015130 952140 870860 1229700 1427030 1452720 1535020 TRUE FALSE 829311.4427 784674.9016 848096.2584 1067520.981 982766.4478 888469.3859 1244749.436 1397561.332 1287813.316 1431051.728 0.579511856 0.548320432 0.592638436 0.745969527 0.686744182 0.620850643 0.869814425 0.976597354 0.899906894 1 20.44864439 2.143394324 3.416141116 0.951264653 0.630150998 0.872298159 0.05826438 0.087794933 2.016519455 0.026586059 0.018587711 139.1215232 -2.143394324 -0.321113655 CACASHVAK ddPTM_BT-474_Pertuzumab_2h_R1 4 CACASHVAK 9 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RFI1;D6RCR4 Q16643 DBN1 Drebrin 0 ;;; 93.551 0.0093226 507256000 594687 554541 497997 545862 494851 414651 643561 616423 730387 740875 FALSE TRUE 571445.9746 538726.0336 587996.1358 574034.0032 510768.3318 423035.5273 651437.092 603693.6496 647476.5298 690694.8763 0.827349375 0.779976878 0.851310985 0.831096368 0.739499234 0.61247816 0.9431619 0.874038118 0.93742773 1 19.397689 2.14359008 20.97235164 0.922911537 0.77832577 0.569866114 0.069633548 4.260795049 935.3115215 0.027182521 0.02007564 139.1842456 -2.14359008 -0.144585767 GGS(ph)REYDTGGGSSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSREYDTGGGSSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 GGS(0.675)REYDT(0.009)GGGS(0.119)S(0.039)S(0.119)S(0.039)R 68.173 0.046764 0 135150 172560 78959 104490 128640 151350 89683 89165 103210 80039 TRUE FALSE 129868.1886 167638.7578 93228.64773 109882.7414 132777.8224 154410.4007 90780.56738 87323.71159 91494.03349 74617.88724 1.740443121 2.246629648 1.249414198 1.472605906 1.779436906 2.069348335 1.216605974 1.170278533 1.22616757 1 16.18723389 2.14362573 7.768984385 1.163244485 1.745617209 0.554371728 0.266365387 0.198102611 14.20030167 0.104099959 0.076825244 139.1956715 -2.14362573 0.582372725 GEAAAERPGEAAVAS(ph)SPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.815)S(0.169)PS(0.016)K;GEAAAERPGEAAVAS(0.674)S(0.32)PS(0.006)K 252.75 1.94E-30 6607500000 2737690 2668450 3131940 3070500 2936200 2730640 3658600 4356800 3767400 3888400 TRUE FALSE 2630698.048 2592348.419 3697951.228 3228968.873 3030645.54 2785855.412 3703375.041 4266830.557 3339740.546 3625035.205 0.725702759 0.715123653 1.02011457 0.890741383 0.83603203 0.768504374 1.02161078 1.177045275 0.92129879 1 21.78956358 2.143878689 5.807194993 1.06285415 0.833696807 0.477324102 0.102719747 0.171750763 8.63237243 0.040548085 0.029811784 139.2767709 -2.143878689 -0.229157343 NTVDLVTTCHIHS(ph)SSDDEIDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 NTVDLVTTCHIHSSSDDEIDFK 22 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;E9PQP7;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 NTVDLVTTCHIHS(0.76)S(0.12)S(0.12)DDEIDFK;NT(0.038)VDLVT(0.032)T(0.032)CHIHS(0.299)S(0.299)S(0.299)DDEIDFK 73.805 0.023042 349373800 218864.2 254224 165133.2 210664.2 193276.2 193441 123456.1 18696.1 153134 89151.9 TRUE FALSE 210310.7451 246973.7804 194976.4426 221536.6046 199493.1045 197352.5096 124966.9927 18310.019 135750.8703 83113.5624 2.530402247 2.971522015 2.345904049 2.665468766 2.400247309 2.374492247 1.503569202 0.220301218 1.633317913 1 16.34279629 2.143896557 3.072259947 0.860998939 2.573140836 0.798853103 0.365013605 0.096060218 1.811229517 0.150406622 0.102660482 139.2825011 -2.143896557 1.712141897 KPPAPPS(ph)PVQSQSPSTNWS(ph)PAVPVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(0.985)PVQS(0.013)QS(0.024)PS(0.282)T(0.213)NWS(0.484)PAVPVKK;KPPAPPS(1)PVQSQSPST(0.001)NWS(0.999)PAVPVKK 191.46 3.07E-18 3742800000 1060050 903420 770530 754390 856040 906720 936660 1040960 1123720 1045710 TRUE FALSE 1018622.074 877655.3461 909781.9113 793324.1583 883575.304 925054.4996 948123.1253 1019463.812 996160.0166 974883.1303 1.044865833 0.900267241 0.933221515 0.813763346 0.906339721 0.948887586 0.972550551 1.045729258 1.021825064 1 19.89486975 2.143935852 2.107583375 1.026024986 0.915101767 0.393764109 0.05438532 0.303848738 2.660277587 0.027916384 0.016932293 139.295104 -2.143935852 -0.110923219 S(ph)TEEVKPIDENLGQTGK ddPTM_BT-474_Pertuzumab_2h_R1 1 STEEVKPIDENLGQTGK 17 1 B7Z2R7;Q5T8D3-4;Q5T8D3-2;Q5T8D3-3;Q5T8D3;X6RDD7;Q5T8E0 B7Z2R7 ACBD5 Acyl-CoA-binding domain-containing protein 5 1 S(0.804)T(0.196)EEVKPIDENLGQTGK 113.71 0.00024158 141460000 111410 131400 96691 145740 103440 122610 161780 194910 202510 178510 TRUE FALSE 107055.974 127652.6007 114165.2146 153261.6589 106767.2415 125089.2582 163759.912 190885.0404 179521.9138 166419.3587 0.643290389 0.767053795 0.686009221 0.920936483 0.64155542 0.751650885 0.984019608 1.147012234 1.078732157 1 17.34446374 2.144008689 3.39967157 1.087155246 0.736822437 0.786244533 0.081953091 0.09912907 2.257959507 0.032697679 0.022847576 139.3184675 -2.144008689 -0.350332808 RGS(ph)MEQAPAVALPPTHK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGSMEQAPAVALPPTHK 17 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 RGS(1)MEQAPAVALPPTHK;RGS(1)MEQAPAVALPPTHK 112.85 0.00027 941470000 508210 422580 282300 419270 420910 238884 566430 614050 648030 562790 TRUE FALSE 488348.5913 410528.4321 333317.8897 440908.5749 434448.9524 243714.3982 573362.1398 601369.6529 574468.3512 524671.732 0.930769778 0.782448162 0.635288447 0.840351305 0.828039564 0.464508345 1.09280166 1.146182682 1.094910048 1 19.00105554 2.144239738 11.61515613 1.102016123 0.751470978 0.635428297 0.124561524 0.274781263 32.02601574 0.045685853 0.033741184 139.3926061 -2.144239738 -0.350545146 SEEIS(ph)ESESEETNAPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEISESESEETNAPK 16 0 P54259 P54259 ATN1 Atrophin-1 1 SEEIS(0.5)ES(0.5)ESEETNAPK;SEEIS(0.862)ES(0.138)ESEETNAPK 326.78 2.05E-71 191010000 199787 175411 155380 169028 184094 185294 214374 252603 262438 241168 TRUE FALSE 191979.1032 170408.45 183460.6224 177751.5553 190015.5507 189040.7716 216997.5731 247386.6598 232647.1385 224833.4765 0.853872413 0.757931838 0.815984458 0.790592033 0.84513905 0.840803489 0.965147968 1.10031061 1.034753107 1 17.77849734 2.144411971 2.528592472 1.054726314 0.810808912 0.897428986 0.035138821 0.074215002 0.948332528 0.015695383 0.010125025 139.4478975 -2.144411971 -0.243917403 LESPSFTGTGDTEIAHATEDLENNGSKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LESPSFTGTGDTEIAHATEDLENNGSKK 28 1 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 113.5 0.00030505 262120000 58132 78613 63776 69077 58009 78559 82719 85876 106250 97965 FALSE TRUE 55860.13717 76371.03421 75301.74189 72642.07225 59874.91217 80147.51681 83731.33987 84102.63059 94188.94544 91329.74329 0.611631383 0.836212076 0.824504035 0.79538242 0.655590501 0.877562051 0.916802532 0.920867918 1.031306364 1 16.47879716 2.144583359 1.213447025 0.994705412 0.756673386 0.667209388 0.073868482 0.304809801 0.848911919 0.050969851 0.026661084 139.5029397 -2.144583359 -0.238032026 S(ph)VSGS(ph)PEPAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(0.725)VS(0.275)GS(1)PEPAAK 148.68 5.08E-05 237210000 591350 524340 466510 462270 483850 512790 576970 645100 673100 634730 TRUE FALSE 568239.3882 509386.3366 550818.7345 486127.8101 499413.4747 523158.9651 584031.1315 631778.4596 596692.5099 591739.1717 0.960286923 0.860829164 0.930847172 0.821523795 0.843975688 0.884103994 0.986973923 1.067663744 1.008370813 1 19.17460188 2.144600122 3.588003464 1.031827384 0.87950951 0.713281565 0.041406976 0.115196539 2.88809124 0.016778826 0.011850487 139.5083243 -2.144600122 -0.152317874 ASNEDGDIKR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASNEDGDIKR 10 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;; 92.866 0.012195 823170000 1278160 1376760 1017110 1174180 1216230 1293100 1246070 1396640 1549660 1383950 FALSE TRUE 1228208.094 1337496.153 1200924.402 1234779.571 1255351.143 1319247.368 1261319.777 1367798.896 1373749.094 1290213.834 0.951941501 1.036646886 0.930794858 0.957034825 0.972979137 1.022502885 0.977605219 1.060133491 1.064745283 1 20.29917876 2.144625198 1.348633228 1.044687005 0.972332826 0.387949129 0.034783978 0.417969238 1.448380276 0.022099089 0.011745335 139.5163795 -2.144625198 -0.072354179 LGVTNTIISHYDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGVTNTIISHYDGR 14 0 P46087-2;P46087;P46087-4;P46087-3 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 0 ; 115.1 0.00043906 1060890000 867740 969200 765120 746780 881440 708040 714060 706600 594540 650970 FALSE TRUE 833827.7615 941559.3649 903394.204 785321.4053 909792.3181 722357.0539 722798.8799 692008.4631 527050.3117 606879.2221 1.373959976 1.551477346 1.488589774 1.294032448 1.499132422 1.190281406 1.191009436 1.140273778 0.868459971 1 19.2110499 2.144682029 0.762969137 0.948316053 1.468134 0.809120285 0.093029419 0.265753236 0.293259732 0.07541986 0.043579993 139.5346378 -2.144682029 0.519817947 KGAANASGSS(ph)PDAPAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KGAANASGSSPDAPAK 16 1 O75962-5;O75962;E7EPJ7;O75962-4 O75962-5 TRIO Triple functional domain protein 1 KGAANAS(0.005)GS(0.283)S(0.712)PDAPAK;KGAANAS(0.001)GS(0.063)S(0.936)PDAPAK;KGAANAS(0.001)GS(0.122)S(0.877)PDAPAK;KGAANAS(0.007)GS(0.166)S(0.827)PDAPAK 134.29 1.78E-05 856790000 1420820 1339880 1244710 1252200 1304010 1452630 1535260 1691180 1909930 1825670 TRUE FALSE 1365292.784 1301667.934 1469656.785 1316826.192 1345954.666 1482003.174 1554048.971 1656256.542 1693122.753 1702015.745 0.802162252 0.764780196 0.863480135 0.773686258 0.790800361 0.870734115 0.913063804 0.973114701 0.994775024 1 20.69881295 2.145067421 1.248116033 0.997841445 0.797610562 0.908066743 0.026433483 0.124118534 0.366439645 0.017649417 0.009265903 139.6585152 -2.145067421 -0.200230884 TAAPS(ph)PSLLYK ddPTM_BT-474_Pertuzumab_2h_R1 4 TAAPSPSLLYK 11 0 Q9BTC0;Q9BTC0-1;Q9BTC0-2;Q9BTC0-3 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 TAAPS(0.991)PS(0.009)LLYK;TAAPS(1)PSLLYK;T(0.001)AAPS(0.98)PS(0.019)LLYK;TAAPS(0.998)PS(0.002)LLYK 212.9 4.57E-09 764550000 1815810 1693190 1576730 1605420 1541040 1691330 1811570 2000190 1965580 2157430 TRUE FALSE 1744846.138 1644901.879 1861680.185 1688275.919 1590608.951 1725529.851 1833740.536 1958885.378 1742455.599 2011305.344 0.867519267 0.817828026 0.925607934 0.839393145 0.790834149 0.857915411 0.911716632 0.97393734 0.866330716 1 20.93970069 2.145146674 3.449571579 0.94360456 0.848222229 0.482968657 0.045672047 0.204731945 4.790676556 0.018458138 0.012945438 139.6840035 -2.145146674 -0.095382331 KKEEGVIDSSDKEIVAEAER ddPTM_BT-474_Pertuzumab_2h_R1 1 KKEEGVIDSSDKEIVAEAER 20 3 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 136.64 2.20E-06 499420000 465310 361300 351890 332790 360040 387980 463650 480680 605340 506650 FALSE TRUE 447125.1708 350996.0777 415484.3508 349965.3318 371621.0136 395825.2214 469324.2874 470753.79 536624.341 472334.1442 0.946628941 0.743109686 0.879640729 0.740927447 0.786775672 0.838019496 0.993627696 0.996654161 1.136111686 1 18.8494483 2.145206045 2.082817607 1.045477816 0.812210625 0.696936171 0.06801612 0.171049182 1.461807859 0.032926582 0.019915719 139.7031005 -2.145206045 -0.233267192 SESPKEPEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 SESPKEPEQLRK 12 2 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ; 142.91 3.47E-05 6668700000 11164800 10496600 7492900 6897400 8902500 10159300 9065800 10803700 12137000 10355500 FALSE TRUE 10728467.27 10197247.25 8847033.709 7253375.641 9188856.998 10364728.01 9176749.972 10580599.82 10759258.64 9654112.761 1.111284645 1.056259389 0.916400495 0.751324935 0.951807507 1.073607515 0.950553427 1.095968121 1.114474101 1 23.20271225 2.14546713 1.447095794 1.071790454 0.957297556 0.139978288 0.100238014 0.793245332 3.181351345 0.067904772 0.036684797 139.7871111 -2.14546713 -0.114492898 DLQEQDADAGS(ph)ER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLQEQDADAGSER 13 0 Q6P158-2;Q6P158;A0A087WW12;A0A087WZ11;Q6P158-3 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 1 DLQEQDADAGS(1)ER;DLQEQDADAGS(1)ER 207.21 5.85E-08 1771140000 2279900 2669700 2289900 2615200 2241900 2661500 2323900 2415000 2551300 2587000 TRUE FALSE 2190798.987 2593562.77 2703735.869 2750170.785 2314012.75 2715317.354 2352340.583 2365129.406 2261687.12 2411780.186 0.908374238 1.075372783 1.121054018 1.140307397 0.959462543 1.125856067 0.975354469 0.980657118 0.937766689 1 21.20166699 2.145507972 10.95716354 0.972594061 1.058491075 0.242249746 0.070572595 0.567513848 62.74624704 0.02617738 0.019332972 139.8002577 -2.145507972 0.085897014 RPDPDS(ph)DEDEDYERER ddPTM_BT-474_Pertuzumab_2h_R1 3 RPDPDSDEDEDYERER 16 2 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 1 RPDPDS(1)DEDEDYERER;RPDPDS(1)DEDEDYERER;RPDPDS(1)DEDEDYERER 209.75 9.02E-12 2309380000 720805 856044 461277 546150 652742 754113 503305 512122 545743 485267 TRUE FALSE 692635.1437 831630.4633 544640.015 574336.867 673738.0392 769361.6815 509464.5971 501546.5017 483792.5426 452399.4339 1.531025664 1.838265924 1.203891902 1.269534893 1.489254824 1.700624766 1.126138892 1.108636449 1.069392458 1 18.7872376 2.145562772 7.323106181 1.084111423 1.494746682 0.591499988 0.174833951 0.180488922 12.23971301 0.069835455 0.051522314 139.8178991 -2.145562772 0.410635259 EDSGLFS(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EDSGLFSPIR 10 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 EDS(0.001)GLFS(0.999)PIR;EDSGLFS(1)PIR;EDSGLFS(1)PIR;EDSGLFS(1)PIR 155.61 1.30E-05 985670000 1156700 1313510 1102310 1352870 1290270 1047810 1257710 1009140 1089500 1242340 TRUE FALSE 1111494.885 1276049.981 1301521.938 1422691.783 1331772.706 1068997.436 1273102.231 988300.9064 965824.5276 1158195.205 0.959678369 1.101757264 1.123750066 1.228369602 1.149868952 0.922985548 1.099212141 0.853311171 0.833904788 1 20.143447 2.145809445 1.352007883 0.890448904 1.110754233 0.420426974 0.096099464 0.389828749 1.358244446 0.062773636 0.03341564 139.897336 -2.145809445 0.220305329 QGRPVVICDKEDTETIK ddPTM_BT-474_Pertuzumab_2h_R1 1 QGRPVVICDKEDTETIK 17 2 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 139.88 3.84E-07 340170000 386460 322650 272890 293630 345050 335140 398460 457900 496290 451050 FALSE TRUE 371356.7159 313448.3379 322207.2934 308784.2795 356148.8466 341916.7604 403336.4727 448444.205 439953.2398 420499.9817 0.883131349 0.745418196 0.766248056 0.734326499 0.846965189 0.813119561 0.959183092 1.066454755 1.046262209 1 18.68174621 2.14581827 2.281820644 1.044797888 0.788814591 0.854784921 0.045177672 0.100323557 1.037107129 0.021672408 0.013531747 139.9001791 -2.14581827 -0.255983297 GADS(ph)GEEKEEGINR ddPTM_BT-474_Pertuzumab_2h_R1 7 GADSGEEKEEGINR 14 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINR;GADS(1)GEEKEEGINR;GADS(1)GEEKEEGINR;GADS(1)GEEKEEGINR;GADS(1)GEEKEEGINR;GADS(1)GEEKEEGINR;GADS(1)GEEKEEGINR 248.18 3.95E-18 19541140000 11339560 9489890 10286330 10821300 11029130 9886210 13311460 14518120 15812560 14865690 TRUE FALSE 10896397.46 9219247.629 12145298.65 11379788.59 11383891.98 10086115.94 13474369.63 14218315.75 14017584.48 13858823.58 0.786242598 0.665225845 0.876358558 0.821122264 0.821418349 0.727775766 0.972259265 1.025939588 1.011455583 1 23.72430146 2.145929518 5.414078613 1.010806473 0.785759091 0.79782177 0.054263996 0.090978563 4.223698263 0.021209111 0.015566053 139.9360201 -2.145929518 -0.225047381 KVDT(ph)TPNQGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVDTTPNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KVDT(0.5)T(0.5)PNQGK 137.62 5.05E-05 1116600000 1059200 985060 975780 1001100 885270 1038600 1292800 1577900 1615300 1381800 TRUE FALSE 1017805.293 956967.0533 1152125.152 1052766.891 913745.5135 1059601.204 1308621.673 1545315.814 1431937.916 1288209.455 0.790093015 0.742866037 0.894361664 0.8172327 0.709314397 0.82253798 1.015845418 1.199584281 1.111572276 1 20.29693576 2.146044018 3.234976206 1.122966169 0.792915492 0.824868677 0.065219364 0.088709294 1.846378501 0.02715222 0.018796816 139.9729185 -2.146044018 -0.330050677 RAPFDLFENKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RAPFDLFENKK 11 2 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ; 136.27 5.77E-05 13220700000 7369000 6941600 5527700 5856500 5734900 5885300 7408400 7828300 9248400 7758000 FALSE TRUE 7081011.333 6743632.365 6526678.353 6158754.667 5919368.267 6004304.798 7499066.215 7666642.869 8198560.404 7232543.75 0.979048531 0.932401185 0.902404269 0.85153369 0.818435183 0.830178842 1.036850446 1.060020255 1.133565269 1 22.78607171 2.146150746 5.718091684 1.065109083 0.8842835 0.709328498 0.054028972 0.118769229 5.925895273 0.022185178 0.016309021 140.0073211 -2.146150746 -0.180825583 DLEWVIFDEVHYINDVER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEWVIFDEVHYINDVER 18 0 Q15477 Q15477 SKIV2L Helicase SKI2W 0 ; 162.15 3.63E-11 74198000 90031 99588 89768 92499 95812 97834 91694 83914 107286 119242 FALSE TRUE 86512.48899 96747.84775 105991.0745 97272.88448 98893.87999 99812.27051 92816.1786 82181.14658 95107.34306 111165.6331 0.778230525 0.870303573 0.953451813 0.875026586 0.889608391 0.897869852 0.834935906 0.739267562 0.855546273 1 16.76235132 2.146356643 6.310131602 0.824352407 0.880859239 0 0.074441561 0.480641291 27.22637862 0.027514974 0.020267751 140.0737137 -2.146356643 0.056506832 QSDS(ph)KGKDQER ddPTM_BT-474_Pertuzumab_2h_R1 2 QSDSKGKDQER 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 QS(0.009)DS(0.991)KGKDQER;QS(0.036)DS(0.964)KGKDQER 89.624 0.0095247 206440000 487080 318490 270660 276200 330300 311280 373940 406220 450590 359900 TRUE FALSE 468044.3751 309406.977 319574.2828 290454.7151 340924.3995 317574.2949 378516.3896 397831.415 399440.9122 335523.6524 1.394966858 0.922161448 0.952464247 0.865675826 1.016096472 0.946503451 1.128136234 1.185703041 1.190500012 1 18.35605495 2.14655937 6.485313564 1.148129025 1.002556483 0.110379945 0.145022634 0.366993351 21.5519412 0.053629735 0.039520327 140.1391149 -2.14655937 -0.145572542 FVIKPIDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FVIKPIDKK 9 2 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 84.17 0.0088154 1454300000 2715200 2669100 2150500 2237400 2380700 2744800 2772500 3320700 3588700 3301900 FALSE TRUE 2609086.982 2592979.881 2539143.188 2352872.482 2457277.378 2800301.737 2806430.684 3252126.385 3181325.821 3078259.372 0.847585166 0.842352631 0.824863301 0.764351602 0.798268463 0.909702984 0.911694027 1.056482249 1.033482055 1 21.55368337 2.146584834 1.579262113 1.035875954 0.816868206 0.873366216 0.034315394 0.124968938 0.600890865 0.020995327 0.011623149 140.147332 -2.146584834 -0.219007748 RGEGDAPFSEPGT(ph)T(ph)STQRPSSPETATK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGEGDAPFS(0.075)EPGT(0.529)T(0.243)S(0.39)T(0.378)QRPS(0.311)S(0.074)PETATK 105.49 0.0032869 597280000 587700 523770 483630 545200 535490 535210 612570 680200 728960 629660 TRUE FALSE 564732.0343 508832.5924 571032.6993 573337.8373 552714.5222 546032.3129 620066.8149 666153.6323 646211.5168 587012.5674 0.962044197 0.866817204 0.972777639 0.976704536 0.941571872 0.930188455 1.056309267 1.134820052 1.10084784 1 19.16303186 2.146737339 4.27008213 1.093779105 0.941175368 0.680976472 0.043725932 0.109507971 3.654499686 0.016758142 0.012128492 140.1965542 -2.146737339 -0.152603737 VQGLLENGDSVTS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VQGLLENGDSVTSPEK 16 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 VQGLLENGDSVT(0.001)S(0.999)PEK;VQGLLENGDSVT(0.009)S(0.991)PEK 265.37 4.57E-27 368970000 776100 634980 662960 690540 705630 678970 862380 996600 966760 964400 TRUE FALSE 745769.154 616870.9921 782771.6195 726178.8522 728327.2298 692699.2386 872934.0644 976019.8617 857017.4578 899080.329 0.829480003 0.686113323 0.870635909 0.807690735 0.810080263 0.770453113 0.970918878 1.085575816 0.95321567 1 19.77809049 2.146811139 4.523101829 1.023323165 0.795382123 0.776366531 0.054457977 0.088468668 3.217386169 0.020486322 0.014899478 140.2203798 -2.146811139 -0.227941042 SRDDALEAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRDDALEAIK 10 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;A0A087WW94;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 0 ; 127.87 0.00031437 663010000 611540 633560 534640 591530 596600 542690 662940 716910 696220 724750 FALSE TRUE 587640.3407 615491.4891 631261.341 622058.9342 615790.1808 553663.5636 671053.258 702105.558 617188.0244 675662.037 0.86972526 0.910945792 0.934285644 0.920665807 0.911387864 0.819438615 0.993178869 1.039137201 0.913456714 1 19.36594227 2.146947177 12.00864129 0.995360792 0.898958598 0.527111417 0.042241614 0.388625258 48.6553209 0.015831678 0.011692553 140.2643093 -2.146947177 -0.096402194 ETHPDSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETHPDSLR 8 0 P56597 P56597 NME5 Nucleoside diphosphate kinase homolog 5 0 83.206 0.018325 295370000 202870 201840 168850 202180 197430 190320 195530 184440 211830 215940 FALSE TRUE 194941.6161 196083.7208 199364.951 212614.534 203780.5153 194168.4008 197922.9546 180631.2495 187783.9465 201314.1915 0.968345126 0.974018371 0.990317422 1.056132866 1.012251117 0.964504288 0.983154507 0.897260388 0.932790406 1 17.61908935 2.146954246 2.18058822 0.934573598 0.999008559 0.267063881 0.035084102 0.331579557 3.120063108 0.017814689 0.010965023 140.2665923 -2.146954246 0.064434961 AS(ph)PPRSPAEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPPRSPAEPK 11 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 AS(0.998)PPRS(0.002)PAEPK;AS(0.998)PPRS(0.002)PAEPK 80.507 0.014667 545170000 952300 917750 592320 706820 777730 847980 1003240 1159920 1274430 1196450 TRUE FALSE 915083.0632 891576.6686 699365.4001 743299.0649 802746.3918 865126.7366 1015517.951 1135967.247 1129762.049 1115413.376 0.820398144 0.799323989 0.627001088 0.666388875 0.719685104 0.775610868 0.910440894 1.018427133 1.012863996 1 20.08914705 2.147014246 2.014736396 1.013472804 0.722009983 0.848929686 0.053321316 0.12761497 1.018272816 0.030408533 0.018217539 140.285972 -2.147014246 -0.291462821 RADLNQGIGEPQS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 RADLNQGIGEPQSPSR 16 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(0.985)PS(0.015)R;RADLNQGIGEPQS(0.999)PS(0.001)R;RADLNQGIGEPQS(0.5)PS(0.5)R;RADLNQGIGEPQS(0.985)PS(0.015)R 260.12 9.51E-27 2964690000 2285770 2383290 2245790 2206480 2336320 2344040 2536240 2836430 2847320 2714200 TRUE FALSE 2196439.581 2315320.903 2651654.21 2320356.697 2411469.855 2391438.095 2567279.264 2777856.729 2524104.171 2530364.816 0.86803277 0.91501466 1.04793356 0.917004806 0.953012719 0.945096169 1.014588587 1.097808787 0.997525793 1 21.27091397 2.147059368 4.004501305 1.045390278 0.943911254 0.406416164 0.050450077 0.201579237 6.088265311 0.020175165 0.014502771 140.3005483 -2.147059368 -0.101479024 GDFYTAHGEDALLAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDFYTAHGEDALLAAR 16 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 ;;; 240.2 7.46E-20 2060750000 1378280 1637850 1344180 1718010 1619920 1573400 1491370 1536730 1572380 1656130 FALSE TRUE 1324415.294 1591140.122 1587103.227 1806676.702 1672026.198 1605215.226 1509621.832 1504995.988 1393890.014 1543958.84 0.857804793 1.03055864 1.027944001 1.170158592 1.082947391 1.039674883 0.977760412 0.97476432 0.902802574 1 20.55820286 2.147317714 2.984331686 0.959245259 1.043164225 0.171579423 0.075881798 0.450748152 8.044650477 0.034255496 0.023271214 140.3840329 -2.147317714 0.083918966 YSGGNYR ddPTM_BT-474_Pertuzumab_2h_R1 3 YSGGNYR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ;; 111.73 0.015154 1038870000 982920 1132510 906020 1147920 1090430 812790 1253060 1069990 1071480 1253380 FALSE TRUE 944506.3997 1100211.924 1069757.968 1207164.289 1125504.671 829225.1707 1268395.323 1047894.333 949850.0824 1168487.456 0.808315395 0.941569306 0.915506592 1.033099913 0.963215022 0.709656887 1.085501874 0.896795534 0.812888557 1 20.15621082 2.14736987 21.26251785 0.940708348 0.906762376 0.049509338 0.105703626 32.98341282 7663.991252 0.039595092 0.029242953 140.400893 -2.14736987 -0.033945972 STDSEVSQS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 4 STDSEVSQSPAK 12 0 O75175;H7C3F5;A0A2H2FJL5;B7Z6J7;A0A0G2JNJ7;H7C148 O75175 CNOT3 CCR4-NOT transcription complex subunit 3 1 STDSEVSQS(1)PAK;STDSEVSQS(1)PAK;STDSEVSQS(1)PAK;STDSEVSQS(1)PAK 305.78 4.94E-37 3231540000 3960430 3436500 3216350 3034240 3175860 3164730 4000850 4282390 4497000 4789210 TRUE FALSE 3805652.017 3338494.385 3797615.992 3190837.49 3278014.421 3228723.009 4049813.599 4193957.15 3986519.413 4464832.541 0.852361647 0.747731153 0.850561798 0.71466006 0.734185301 0.723145377 0.907047143 0.939331344 0.892870981 1 22.09017464 2.147883656 5.641896708 0.933359152 0.769157297 0.709894801 0.051648556 0.114202075 5.65394962 0.019410604 0.01426762 140.5670905 -2.147883656 -0.164201855 AGKEPAKPS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGKEPAKPSPSR 12 2 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.935)PS(0.065)R;AGKEPAKPS(0.891)PS(0.109)R;AGKEPAKPS(0.883)PS(0.117)R;AGKEPAKPS(0.621)PS(0.379)R 121.31 0.00019749 2996060000 2187720 1990570 1586260 1601950 1775190 1937920 2117650 2322740 2649210 2399410 TRUE FALSE 2102221.484 1933800.893 1872932.468 1684626.831 1832290.599 1977106.07 2143566.434 2274774.607 2348482.787 2236895.824 0.939794094 0.864501991 0.837290878 0.753109203 0.819122008 0.883861488 0.958277275 1.016933638 1.049884739 1 21.09306664 2.14798662 1.944529171 1.024520015 0.839247972 0.756563756 0.044999593 0.171120321 1.268547159 0.025675679 0.015212138 140.6004207 -2.14798662 -0.185272042 EELQANGSAPAADKEEPAAAGSGAAS(ph)PSAAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EELQANGSAPAADKEEPAAAGSGAASPSAAEK 32 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 EELQANGSAPAADKEEPAAAGS(0.36)GAAS(0.636)PS(0.004)AAEK 342.95 5.26E-118 640720000 281720 291150 305560 323050 287870 308740 401150 504430 457920 430750 TRUE FALSE 270710.0709 282846.6871 360781.4891 339722.6492 297129.6 314982.9343 406059.3937 494013.3442 405938.8414 401574.9188 0.674120963 0.704343508 0.898416391 0.845975765 0.739910752 0.784369042 1.011167219 1.230189738 1.01086702 1 18.61530964 2.148055025 3.822716267 1.108737892 0.777633524 0.729871443 0.086014059 0.109595295 3.071898197 0.035324462 0.025250897 140.622568 -2.148055025 -0.331104368 NAVEEYVYEMR ddPTM_BT-474_Pertuzumab_2h_R1 5 NAVEEYVYEMR 11 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;;; 190.53 5.19E-06 1602330000 942777 1125200 827545 991760 1021110 1028920 1095330 1266170 1222320 1295130 FALSE TRUE 905932.2325 1093110.398 977100.7901 1042944.852 1053954.93 1049725.467 1108734.976 1240023.147 1083567.358 1207409.692 0.750310552 0.90533512 0.809253725 0.863787047 0.872905806 0.869402883 0.918275697 1.027011093 0.89743139 1 20.20348386 2.148168619 2.43352023 0.977698026 0.845660951 0.578358114 0.050037003 0.195281414 2.308860536 0.022087697 0.01412353 140.6593541 -2.148168619 -0.132037075 DWVLNEFR ddPTM_BT-474_Pertuzumab_2h_R1 8 DWVLNEFR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 200.16 0.00028405 2247464000 3733312 5226303 4319950 4896583 4225106 2990351 4771649 3092566 2630278 3635193 FALSE TRUE 3587410.04 5077253.956 5100661.062 5149296.235 4361010.372 3050817.946 4830045.868 3028703.431 2331699.868 3388978.14 1.058552133 1.498166629 1.505073462 1.519424447 1.286821629 0.900217653 1.425221901 0.89369223 0.688024464 1 21.6924189 2.148176163 0.877433516 0.848290092 1.398171782 0.465654199 0.212243261 0.518214283 0.747999952 0.170107034 0.09233803 140.6617976 -2.148176163 0.549881689 GS(ph)IDEVDKR ddPTM_BT-474_Pertuzumab_2h_R1 5 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 1 GS(1)IDEVDKR;GS(1)IDEVDKR;GS(1)IDEVDKR;GS(1)IDEVDKR;GS(1)IDEVDKR 99.283 0.0033334 7003430000 6065440 5015460 5871870 5392590 5623210 4987380 6736540 7299730 7462770 7419960 TRUE FALSE 5828395.899 4872423.991 6933047.528 5670902.216 5804085.657 5088228.241 6818983.792 7148988.025 6615627.636 6917399.5 0.842570376 0.704372213 1.002262126 0.819802617 0.839056015 0.735569522 0.98577273 1.033479131 0.956374955 1 22.72179835 2.148547107 7.708321894 1.002032281 0.827355302 0.544870061 0.076000051 0.178158909 13.24809194 0.028090422 0.020732579 140.7819923 -2.148547107 -0.17467698 NGS(ph)PNKQPSSEPEWTPEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGSPNKQPSSEPEWTPEPR 19 1 Q5JSZ5;A0A494C0D3 Q5JSZ5 PRRC2B Protein PRRC2B 1 NGS(0.888)PNKQPS(0.101)S(0.012)EPEWTPEPR;NGS(1)PNKQPSSEPEWTPEPR 161.51 1.78E-11 873120000 550110 455400 418330 416520 470550 468480 541740 582750 640680 631940 TRUE FALSE 528611.093 442412.4379 493931.5367 438016.6471 485685.6681 477952.9866 548369.9762 570716.0089 567952.6923 589138.1409 0.897261705 0.750948559 0.838396808 0.743487167 0.824400314 0.8112749 0.93080033 0.968730369 0.96403993 1 19.16824643 2.148549434 2.578183597 0.973035951 0.804997191 0.768178635 0.042126041 0.122591305 1.632415933 0.017910442 0.011671914 140.7827468 -2.148549434 -0.168038761 DSPFYQHYDLDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSPFYQHYDLDLK 13 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 160.31 4.41E-05 261680000 517280 540550 407710 432640 448200 463420 501040 521920 577310 553130 FALSE TRUE 497064.1257 525134.0433 481392.2665 454968.6022 462616.76 472790.6699 507171.8774 511142.1696 511776.1891 515666.0124 0.963926483 1.018360781 0.933534991 0.882293173 0.897124784 0.916854434 0.983527836 0.991227184 0.9924567 1 18.97607743 2.148866139 5.964841673 0.991862097 0.934997257 0.382384191 0.035246139 0.263798645 14.13657435 0.015422322 0.011351776 140.8854486 -2.148866139 -0.05686484 AVSGGS(ph)PERR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVSGGSPERR 10 1 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 AVS(0.001)GGS(0.999)PERR 73.082 0.02821 175730000 49724 49893 45966 52153 51714 47144 40331 25669 34175 56512 TRUE FALSE 47780.73111 48470.10049 54273.07871 54844.62258 53377.42778 48097.28398 40824.58284 25138.92618 30295.59727 52684.3919 0.906923842 0.92000873 1.030154791 1.041003238 1.013154482 0.912932317 0.774889514 0.477160792 0.575039327 1 15.685088 2.148958749 2.965309232 0.626664603 0.980437029 0.466006827 0.13634387 0.176683323 3.116092812 0.056459823 0.038343573 140.9154946 -2.148958749 0.353772426 ELPDLEDLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELPDLEDLMK 10 0 Q9HC38-2;F6TLX2;Q9HC38 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 136.33 0.00028073 12980000 57315 51143 51365 52206 51694 42414 62339 61823 70864 70348 FALSE TRUE 55075.06643 49684.45171 60647.79811 54900.35792 53356.78446 43271.64014 63101.92333 60546.33345 62819.81581 65583.2673 0.839773142 0.757578171 0.924744994 0.837109223 0.813573136 0.659796956 0.962164984 0.923197882 0.957863467 1 16.00104016 2.149813154 25 0.951342788 0.810458732 0.569259568 0.065921017 16.82283043 4734.93921 0.024876997 0.018372883 141.1929959 -2.149813154 -0.140884057 LEQEHTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEQEHTNR 8 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 123.6 0.0013408 463660000 366520 364180 323010 392540 362870 381290 341380 343630 364890 394170 FALSE TRUE 352195.9932 353793.943 381385.0923 412799.0364 374542.0431 388999.945 345557.9106 336533.9204 323469.2169 367472.5148 0.958428125 0.962776612 1.037860185 1.123346699 1.01923825 1.058582423 0.940363964 0.915807052 0.880254179 1 18.48727682 2.149814707 5.798612526 0.924361192 1.028179505 0.428568658 0.052087754 0.194206122 10.08724562 0.020832655 0.01532689 141.193501 -2.149814707 0.103818312 LDTDDLDEIEK ddPTM_BT-474_Pertuzumab_2h_R1 5 LDTDDLDEIEK 11 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ;;;; 256.9 3.83E-20 2246360000 3124940 2896260 2575460 2492230 2779810 2914010 3117340 3397330 3755330 3561170 FALSE TRUE 3002813.89 2813661.501 3040902.913 2620854.289 2869225.113 2972933.279 3155490.939 3327173.948 3329040.682 3319968.784 0.904470519 0.847496372 0.915943224 0.789421365 0.864232558 0.895470251 0.950458015 1.002170251 1.002732525 1 21.66273825 2.149898323 1.835200169 1.003095759 0.862583478 0.780370716 0.032171463 0.153188476 1.007336164 0.017159312 0.009989596 141.2206882 -2.149898323 -0.140512282 TQLAS(ph)WSDPTEETGPVAGILDTETLEK ddPTM_BT-474_Pertuzumab_2h_R1 4 TQLASWSDPTEETGPVAGILDTETLEK 27 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 T(0.002)QLAS(0.489)WS(0.489)DPT(0.019)EETGPVAGILDTETLEK;T(0.033)QLAS(0.934)WS(0.033)DPTEETGPVAGILDTETLEK;T(0.012)QLAS(0.986)WS(0.001)DPTEETGPVAGILDTETLEK;T(0.007)QLAS(0.985)WS(0.007)DPTEETGPVAGILDTETLEK 310.68 3.44E-82 320502000 366170 380268 346338 383430 452437 416310 291886 277406 282448 290242 TRUE FALSE 351859.6716 369423.129 408928.9808 403218.8683 466990.047 424728.0734 295458.1882 271677.4692 250385.6872 270583.6508 1.300372992 1.365282521 1.511284882 1.490181935 1.725862023 1.569673822 1.091929196 1.004042441 0.925354087 1 18.04571515 2.15003422 4.601035327 0.994125869 1.498886875 0.826592207 0.110204425 0.092957648 3.499921506 0.047882873 0.0349013 141.2648848 -2.15003422 0.504761007 AERPDVDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AERPDVDEK 9 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 115.57 0.001326 1544300000 1137300 1068800 976230 974440 1181800 1195700 1218900 1332200 1653500 1498200 FALSE TRUE 1092853.059 1038318.87 1152656.477 1024730.965 1219813.67 1219877.873 1233817.263 1304689.604 1465801.612 1396725.58 0.782439353 0.743395042 0.825256224 0.733666642 0.873338105 0.873384071 0.88336412 0.9341059 1.049455694 1 20.41361717 2.150231824 0.643864551 1.024103432 0.765732284 0.840429292 0.039484111 0.273109442 0.222015059 0.033898235 0.02222514 141.3291751 -2.150231824 -0.258371148 SPLAPSEGAGS(ph)DVFDGDLGMGAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPLAPSEGAGSDVFDGDLGMGAAK 24 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 SPLAPS(0.002)EGAGS(0.998)DVFDGDLGMGAAK;SPLAPS(0.001)EGAGS(0.999)DVFDGDLGMGAAK;SPLAPSEGAGS(1)DVFDGDLGMGAAK;SPLAPS(0.013)EGAGS(0.987)DVFDGDLGMGAAK 223.09 5.11E-33 482289000 859917 1579100 676717 1534650 652152 760459 1686960 2430740 1622870 992010 TRUE FALSE 826310.493 1534065.614 799014.8154 1613853.47 673129.0613 775836.002 1707605.521 2380544.37 1438648.601 924820.2791 0.893482238 1.6587716 0.863967663 1.745045504 0.727848509 0.838904617 1.846418769 2.574061602 1.555598027 1 19.81881351 2.150356399 6.688518805 1.960761152 1.146112204 0.22988249 0.500264328 0.226261277 14.24959691 0.182739228 0.134746939 141.3697202 -2.150356399 -0.814648948 DLLSDLQDIS(ph)DSERK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLLSDLQDISDSERK 15 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;Q9UQ88-9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 DLLSDLQDIS(0.994)DS(0.006)ERK 80.238 0.01076 26457000 43221 36456 35388 34753 39750 41390 46271 53661 55180 58889 TRUE FALSE 41531.87554 35416.31057 41783.3988 36546.60649 41028.59485 42226.93416 46837.27834 52552.8816 48916.19773 54900.39558 0.756495014 0.645101191 0.761076462 0.665689311 0.747327855 0.769155372 0.853131892 0.957240491 0.890999003 1 15.74452892 2.150402455 1.240677813 0.960070084 0.706496304 0.856612479 0.042299026 0.146736755 0.428375194 0.026296752 0.01386016 141.3847131 -2.150402455 -0.25357378 EIEIDIEPTDKVER ddPTM_BT-474_Pertuzumab_2h_R1 4 EIEIDIEPTDKVER 14 1 Q15843;F8VSA6;E9PS38;S4R3E9;E9PL57 Q15843 NEDD8;NEDD8-MDP1 NEDD8 0 ;;; 204.28 1.26E-08 31204900000 27815900 26737500 22443800 23762300 25631100 26773300 27362800 29649000 33082900 31242900 FALSE TRUE 26728823.88 25974972.68 26499893.92 24988675.15 26455547.61 27314674.47 27697674.13 29036737.79 29327467.89 29126790.55 0.917671442 0.89178973 0.909811669 0.857927519 0.908289142 0.937785247 0.950934641 0.99690825 1.006889785 1 24.79584341 2.150430002 1.233005121 1.005785052 0.894837356 0.883937141 0.016290239 0.142455302 0.410575897 0.011143076 0.005868832 141.3936814 -2.150430002 -0.110947695 SCS(ph)PLAFSAFGDLTIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.23)CS(0.77)PLAFSAFGDLTIK 134.14 3.14E-05 107860000 172870 174850 155240 157810 169250 187750 144410 146760 161490 150580 TRUE FALSE 166114.0493 169863.4492 183295.3213 165954.593 174694.08 191546.4336 146177.3328 143729.3547 143158.3322 140381.0825 1.183307938 1.210016665 1.305698161 1.182172057 1.244427503 1.364474687 1.041289397 1.023851307 1.019783647 1 17.09898901 2.150557262 7.812998606 1.021795445 1.24573167 0.818037385 0.052509681 0.099129443 7.657196567 0.019738501 0.014570094 141.4351196 -2.150557262 0.223936225 DKNSVNFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKNSVNFK 8 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 132.01 0.00089427 4001900000 6669600 6705200 5231400 5481100 6318500 6513200 7106000 7736100 8867900 8263500 FALSE TRUE 6408944.658 6513974.261 6176830.352 5763980.228 6521740.291 6644901.367 7192965.354 7576346.832 7861253.169 7703805.785 0.831919293 0.845552762 0.801789469 0.748199058 0.846560839 0.862547882 0.933689861 0.983455067 1.020437611 1 22.8771399 2.150578512 1.317221159 1.009557374 0.810331118 0.907823862 0.026392346 0.128996146 0.426291936 0.018568722 0.009878647 141.4420402 -2.150578512 -0.199226255 EVDGEGKPYYEVR ddPTM_BT-474_Pertuzumab_2h_R1 6 EVDGEGKPYYEVR 13 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;E9PQ14 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;;;;; 152 3.73E-05 5570160000 5324400 5332500 4643870 4962780 5304030 5180190 5772800 6374620 6508730 6461880 FALSE TRUE 5116316.562 5180422.321 5483120.611 5218909.671 5474638.942 5284936.991 5843449.253 6242981.869 5769886.257 6024211.112 0.849292375 0.859933728 0.910180687 0.866322507 0.908772757 0.877282833 0.969994103 1.036315254 0.957782878 1 22.5223409 2.150888977 3.835530937 1.002357879 0.879630509 0.824086968 0.025602999 0.084023428 2.377615752 0.010046729 0.00719564 141.5431891 -2.150888977 -0.12272737 DSYVGDEAQSK ddPTM_BT-474_Pertuzumab_2h_R1 11 DSYVGDEAQSK 11 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 C9JTX5;P60709;P63261;P68133 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle" 0 ;;;;;;;;;; 372.48 1.46E-85 38804069000 11056290 9984050 9353480 9940040 9614010 9405070 11369730 12366480 12743740 11985800 FALSE TRUE 10624197.96 9699314.669 11043861.9 10453046.66 9923253.363 9595246.959 11508876.16 12111107.87 11297124.06 11173991.09 0.950797068 0.868025989 0.988354279 0.935480132 0.888067055 0.858712602 1.02997005 1.083865896 1.011019605 1 23.41364124 2.150957749 7.130422134 1.044351675 0.916039934 0.640215923 0.042330353 0.130786542 9.006505141 0.016049735 0.011841511 141.5656051 -2.150957749 -0.128311741 SGSS(ph)PEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSSPEVK 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGS(0.002)S(0.998)PEVK;S(0.001)GS(0.107)S(0.892)PEVK;SGS(0.025)S(0.975)PEVK;SGS(0.065)S(0.935)PEVK 144.28 0.00061673 2752660000 10751300 8970550 7556130 7853060 8413360 8776110 9386700 10308100 10141200 10930300 TRUE FALSE 10331127.31 8714718.697 8921690.776 8258357.368 8683983.365 8953568.957 9501577.242 10095234.13 8990013.491 10189981.05 1.013851475 0.85522423 0.875535562 0.810438933 0.852208 0.878663946 0.932443073 0.990701954 0.882240453 1 23.28064803 2.151107917 3.77734243 0.957542076 0.874762909 0.267592767 0.057464884 0.28416222 7.837238445 0.022814322 0.016307123 141.6145631 -2.151107917 -0.082779168 ITKPGSIDSNNQLFAPGGRLS(ph)WGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITKPGSIDSNNQLFAPGGRLSWGK 24 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 ITKPGSIDSNNQLFAPGGRLS(1)WGK;ITKPGSIDSNNQLFAPGGRLS(1)WGK 211.87 1.34E-25 3926400000 1423380 1381960 1020550 833810 945050 1083870 1230700 1293960 1429600 1377380 TRUE FALSE 1367752.736 1342547.854 1204986.087 876843.034 975448.3915 1105786.594 1245761.675 1267239.274 1267317.801 1284088.826 1.065154301 1.045525689 0.938397767 0.68285232 0.759642458 0.861144939 0.970152259 0.986878204 0.986939358 1 20.29231357 2.151167221 5.522683134 0.986694759 0.885839402 0.151164533 0.108823929 0.454743829 22.29612024 0.047626455 0.035004559 141.6339024 -2.151167221 -0.100855357 GVGSGPHPPDTQQPS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 3 GVGSGPHPPDTQQPSPSK 18 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 GVGSGPHPPDTQQPS(0.996)PS(0.004)K;GVGSGPHPPDTQQPS(1)PSK;GVGSGPHPPDT(0.001)QQPS(0.998)PS(0.001)K 195.39 1.55E-15 1471604000 1275625 1258267 1138664 1210154 1248320 1284614 1470968 1472668 1597710 1682900 TRUE FALSE 1225772.165 1222382.457 1344445.914 1272610.193 1288473.346 1310589.775 1488970.146 1442256.891 1416344.659 1568915.684 0.781286195 0.779125653 0.856926811 0.811139952 0.821250855 0.835347488 0.949044083 0.919269854 0.90275384 1 20.58133639 2.151292428 0.380007017 1.000349718 0.769552817 0.818130042 0.030094133 0.529920445 0.188444549 0.036403702 0.042460758 141.6747411 -2.151292428 -0.230796901 KPPAPPS(ph)PVQSQSPSTNWS(ph)PAVPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(1)PVQSQSPST(0.001)NWS(0.998)PAVPVK 100.88 0.020401 440330000 472070 448810 407760 450040 465860 485510 475190 554500 606610 594220 TRUE FALSE 453620.9825 436010.3782 481451.3026 473266.6183 480844.81 495327.3448 481005.5174 543049.3812 537750.1759 553972.9501 0.818850419 0.787060773 0.869088107 0.854313587 0.867993302 0.894136338 0.868283401 0.980281404 0.970715584 1 19.07945601 2.151582529 0.482422214 1.012016939 0.80901655 0.854829376 0.025586588 0.340310864 0.172617049 0.025708977 0.022752014 141.7694091 -2.151582529 -0.203000389 EQDVVTGVS(ph)PLLFR ddPTM_BT-474_Pertuzumab_2h_R1 5 EQDVVTGVSPLLFR 14 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 EQDVVT(0.125)GVS(0.875)PLLFR;EQDVVTGVS(1)PLLFR;EQDVVTGVS(1)PLLFR;EQDVVTGVS(1)PLLFR;EQDVVTGVS(1)PLLFR 267.46 5.59E-25 352034800 552693 619049 470029 518226 512820 544931 587360 644024 653331 665123 TRUE FALSE 531093.1465 601394.3286 554973.696 544971.706 529315.321 555949.8782 594548.2874 630724.6793 579167.6039 620073.6268 0.856500137 0.969875677 0.895012579 0.878882253 0.853633017 0.89658688 0.958834986 1.017177077 0.934030378 1 19.24208 2.151644299 3.793659967 0.986007534 0.892834401 0.58215713 0.035972789 0.160427979 4.460561739 0.014515568 0.010384712 141.7895746 -2.151644299 -0.093173134 IEEVPELPLVVEDKVEGYK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEEVPELPLVVEDKVEGYK 19 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 182.95 2.57E-14 184340000 91055 77762 81074 67612 74449 82816 103580 122110 126200 121830 FALSE TRUE 87496.46993 75544.3039 95725.87528 71101.46342 76843.7197 84490.59626 104847.643 119588.3858 111874.3051 113578.3456 0.770362251 0.665129462 0.842818011 0.626012494 0.676570162 0.74389705 0.923130571 1.052915371 0.984996783 1 16.79332828 2.152040565 2.910056165 1.014856266 0.714504115 0.840114972 0.058594578 0.092077858 1.566745152 0.024811722 0.016809764 141.9190075 -2.152040565 -0.300352151 VFNDMK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFNDMK 6 0 P23528;E9PP50;E9PK25;E9PS23;Q9Y281;G3V2U0;F8WDN3 P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ; 108.24 0.07115 3924040000 5217300 5232500 4600800 4844900 5112600 4957000 5621900 6208600 6267800 6013000 FALSE TRUE 5013402.148 5083274.223 5432266.904 5094945.87 5277051.422 5057233.936 5690702.494 6080390.24 5556305.621 5605734.154 0.894334624 0.906799017 0.969055391 0.908881108 0.941366693 0.902153723 1.015157397 1.084673314 0.991182505 1 22.4184719 2.152656303 5.192321203 1.037855844 0.922578076 0.708203124 0.031806799 0.09941566 4.508440254 0.011904831 0.008735385 142.1203614 -2.152656303 -0.115277768 KDDDS(ph)DDESQSSHTGK ddPTM_BT-474_Pertuzumab_2h_R1 9 KDDDSDDESQSSHTGK 16 1 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.998)DDES(0.002)QSSHTGK;KDDDS(0.981)DDES(0.019)QSSHTGK;KDDDS(0.966)DDES(0.033)QSSHTGK;KDDDS(0.943)DDES(0.057)QSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(0.999)DDES(0.001)QSSHTGK;KDDDS(0.665)DDES(0.335)QSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK 337.22 5.18E-72 11096839000 6063495 5550658 4578219 4965544 4488934 5045837 6356439 6662904 8223082 7034084 TRUE FALSE 5826526.912 5392358.669 5405605.015 5221816.321 4633324.639 5147867.281 6434231.002 6525312.704 7289632.205 6557659.225 0.88850712 0.822299312 0.824319293 0.796292723 0.706551603 0.78501598 0.981178006 0.995067368 1.111621076 1 22.6447495 2.152744932 3.8875867 1.025266481 0.800456025 0.80847243 0.052317915 0.101662481 2.951289973 0.022355138 0.016054874 142.1493676 -2.152744932 -0.224810456 SGS(ph)TESLNPRPQTTISPADLHGMWYPTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSTESLNPRPQTTISPADLHGMWYPTVR 29 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.126)GS(0.757)T(0.108)ES(0.001)LNPRPQT(0.004)T(0.004)ISPADLHGMWYPTVR 189.91 2.47E-18 249650000 288560 317420 221320 247260 274960 285960 251350 242370 312320 263030 TRUE FALSE 277282.7562 308367.4924 261317.4472 260021.1182 283804.3381 291742.3071 254426.0965 237364.9748 276866.743 245214.7438 1.130775221 1.257540585 1.065667762 1.060381257 1.157370612 1.189742112 1.037564432 0.967988185 1.129078695 1 17.9036862 2.153114364 6.881533882 1.022945371 1.141860156 0.397667117 0.065867579 0.218682073 14.66637211 0.025407225 0.018742871 142.2703383 -2.153114364 0.118914785 IGKPAPDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGKPAPDFK 9 1 P32119;A6NIW5;P32119-2 P32119 PRDX2 Peroxiredoxin-2 0 ; 99.568 0.004787 22852000000 28854000 26578000 24956000 21851000 25054000 25663000 28626000 31227000 32740000 31941000 FALSE TRUE 27726353.78 25820021.46 29466104.34 22978732.73 25859884.66 26181923.44 28976333.55 30582151.54 29023492.46 29777607.62 0.931114216 0.867095228 0.989539009 0.77167827 0.868433925 0.879248722 0.973091389 1.02701842 0.974675092 1 24.82772451 2.153283945 3.961684009 1.00274826 0.882361097 0.508367543 0.052968143 0.17596644 5.27777042 0.020836382 0.015002828 142.3259022 -2.153283945 -0.120387162 FTDKDQQPS(ph)GSEGEDDDAEAALKK ddPTM_BT-474_Pertuzumab_2h_R1 2 FTDKDQQPSGSEGEDDDAEAALKK 24 2 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 1 FTDKDQQPS(1)GSEGEDDDAEAALKK;FTDKDQQPS(0.974)GS(0.025)EGEDDDAEAALKK 212.66 8.82E-26 824056000 966421 775987 736939 659083 807469 823761 1053656 1199990 1404770 1132850 TRUE FALSE 928652.1989 753856.6105 870120.2704 693098.3526 833441.9737 840418.0118 1066550.957 1175209.787 1245306.399 1056121.06 0.879304687 0.713797536 0.823883078 0.656267902 0.789153824 0.795759164 1.009875664 1.112760489 1.179132247 1 20.01034379 2.153462711 2.522622235 1.106807215 0.76592302 0.819340049 0.069653045 0.103373213 1.318556305 0.03037811 0.019753186 142.3844987 -2.153462711 -0.340884196 STAYEDYYYHPPPR ddPTM_BT-474_Pertuzumab_2h_R1 5 STAYEDYYYHPPPR 14 0 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;; 180.54 1.74E-06 7979030000 2058370 2127660 1905570 2106840 2142780 2077640 1911090 1930960 2046420 1996700 FALSE TRUE 1977926.625 2066981.22 2249948.888 2215574.265 2211704.465 2119651.304 1934478.491 1891085.001 1814118.981 1861461.731 1.062566365 1.110407582 1.208700051 1.190233583 1.188154679 1.138702596 1.039225496 1.015913983 0.974566896 1 20.82800453 2.153527974 2.418709119 1.000061671 1.156405532 0.748264135 0.040983424 0.158509004 1.85400974 0.021130036 0.013554893 142.405897 -2.153527974 0.156343861 LDKENALDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LDKENALDR 9 1 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;D6RGJ6;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKP3;A0A087WTJ7;H0YLS7 J3KN67;P09493-3 TPM3;TPM1 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain 0 ;;;;; 152.7 7.28E-05 8762880000 12536490 13302740 10888680 11866750 11938180 11286780 13340500 14146370 14685560 14395680 FALSE TRUE 12046550.11 12923358.88 12856506.69 12479194.39 12322182.4 11515006.42 13503765.03 13854242.52 13018516.8 13420647.77 0.897613164 0.962945984 0.957964691 0.929850377 0.918151092 0.858006754 1.006193237 1.032308034 0.970036396 1 23.67795097 2.153558911 12.04287057 1.007988857 0.924676471 0.61236918 0.031490838 0.379255861 51.84705647 0.012217754 0.009023563 142.4160416 -2.153558911 -0.083312385 VKYEETVFYGLQYILNK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKYEETVFYGLQYILNK 17 1 P43490;A0A0C4DFS8;C9JG65 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 145.55 4.29E-07 383700000 867830 860100 680210 696610 786150 743960 836880 844990 1036820 866120 FALSE TRUE 833914.2442 835570.7901 803139.0782 732562.1256 811437.2287 759003.3809 847121.9878 827540.6612 919124.5403 807456.9209 1.032766235 1.034817795 0.994652541 0.907246079 1.004929437 0.939992415 1.049123446 1.024872832 1.138295451 1 19.62302577 2.153565257 9.903784333 1.051973819 0.985712051 0.310057273 0.049207402 0.449711164 48.69800697 0.018628736 0.013757897 142.4181229 -2.153565257 -0.066261767 EKYEITEQR ddPTM_BT-474_Pertuzumab_2h_R1 6 EKYEITEQR 9 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 149.23 8.04E-05 22126300000 22214200 23056100 20132200 22514700 22800500 22844700 25469600 27649700 29913600 29123100 FALSE TRUE 21346044.5 22398562.6 23770536.38 23676686.37 23533898.79 23306635.49 25781304.58 27078724.03 26517933.54 27150566.5 0.786209912 0.824975884 0.875507934 0.872051284 0.866792182 0.858421701 0.949567833 0.997353924 0.976699088 1 24.69447896 2.153583452 2.330584986 0.991259436 0.847088492 0.872787183 0.02537145 0.108133841 1.171252026 0.013166219 0.008343359 142.4240896 -2.153583452 -0.144170945 QLPALDGSLMGPES(ph)PPAQEEEAPVSPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLPALDGSLMGPESPPAQEEEAPVSPHK 28 0 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 1 QLPALDGS(0.001)LMGPES(0.999)PPAQEEEAPVSPHK 105.05 0.0032411 168120000 65796 60875 60532 70410 62960 70567 70734 86611 89548 94822 TRUE FALSE 63224.61958 59138.9046 71471.47893 74043.86854 64985.16558 71993.91309 71599.66385 84822.45258 79382.88646 88399.62148 0.715213691 0.668994998 0.808504355 0.837603909 0.735129455 0.814414269 0.809954417 0.959534115 0.898000298 1 16.43175257 2.153592689 0.342569202 1.019828018 0.682820377 0.763020088 0.048507329 0.720779378 0.220872071 0.066302424 0.086050103 142.4271189 -2.153592689 -0.337007641 KSDGIYIINLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSDGIYIINLK 11 1 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 147.24 0.0028097 0 3881100 3699000 3512700 3500100 3716300 3513400 4151600 4485500 4587600 4575100 FALSE TRUE 3729422.321 3593508.142 4147523.03 3680740.58 3835838.165 3584443.355 4202408.523 4392872.858 4066834.881 4265224.402 0.874378924 0.842513266 0.972404413 0.862965282 0.899328571 0.840387988 0.98527255 1.029927723 0.953486733 1 22.02419022 2.153632678 6.67844157 0.999682589 0.88442965 0.653659022 0.039191227 0.125974529 8.153099046 0.014411534 0.010629044 142.4402339 -2.153632678 -0.115252939 KAGEIWK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAGEIWK 7 1 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 75.043 0.071417 815710000 2375400 1919600 1726400 1466200 2139100 1992600 2191800 2294100 2838700 2408000 FALSE TRUE 2282566.742 1864854.887 2038398.884 1541870.758 2207906.094 2032891.737 2218623.904 2246726.033 2516462.677 2244904.015 1.016776988 0.830705845 0.908011599 0.686831485 0.983519152 0.905558422 0.988293437 1.000811624 1.120966714 1 21.09822233 2.154182176 1.226366443 1.050723847 0.871071988 0.386372433 0.088709964 0.462832826 1.320177528 0.058396021 0.03083799 142.6205726 -2.154182176 -0.179651859 EFESVLVDAFSHVAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EFESVLVDAFSHVAR 15 0 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;; 171.21 1.10E-06 383681000 545098 602306 532133 554372 593966 575517 527978 522365 568953 571521 FALSE TRUE 523794.9675 585128.8226 628301.2703 582983.2054 613071.4558 587154.3481 534439.5527 511577.9802 504367.8407 532811.3736 0.983077677 1.098191314 1.179218953 1.094164341 1.150635077 1.101992895 1.003055826 0.960148386 0.94661613 1 19.02326535 2.154738982 3.346692486 0.967449967 1.107316483 0.605385862 0.049349681 0.159004311 3.54460873 0.020775891 0.014578876 142.8035428 -2.154738982 0.139866516 APELPNTSSS(ph)PSLK ddPTM_BT-474_Pertuzumab_2h_R1 4 APELPNTSSSPSLK 14 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 APELPNTSS(0.048)S(0.952)PSLK;APELPNTS(0.001)S(0.049)S(0.95)PSLK;APELPNTS(0.001)S(0.038)S(0.961)PSLK;APELPNTS(0.001)S(0.49)S(0.509)PSLK 268.12 4.29E-25 1614060000 2632680 2500740 2168750 2263780 2221030 2514710 2743170 2995150 3234170 3304790 TRUE FALSE 2529791.955 2429421.344 2560691.369 2380613.957 2292471.447 2565559.159 2776741.735 2933299.106 2867040.58 3080953.63 0.821106793 0.788529019 0.831135965 0.77268737 0.74407853 0.832715927 0.901260476 0.952075058 0.930569208 1 21.55494554 2.154977314 2.027264397 0.956046398 0.792028019 0.874124684 0.028372726 0.110410045 0.895001889 0.014757177 0.008930533 142.8819319 -2.154977314 -0.164018379 FMSVQRPGPYDRPGTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FMSVQRPGPYDRPGTAR 17 2 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 187.56 2.59E-10 6588000000 1474720 1518450 1245110 1371690 1337620 1467660 1289290 1346910 1332950 1420400 FALSE TRUE 1417086.312 1475145.293 1470129.074 1442483.085 1380645.762 1497337.091 1305068.717 1319095.838 1181639.104 1324195.043 1.070149235 1.11399397 1.110205843 1.089328263 1.042630215 1.130752678 0.985556262 0.996149204 0.89234521 1 20.3366842 2.155161409 5.999821937 0.969766593 1.091968279 0.741672483 0.036004477 0.106472147 6.020637533 0.013412069 0.009880498 142.9425119 -2.155161409 0.122201686 FFTVEPQHIPCVLMAFLDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FFTVEPQHIPCVLMAFLDHR 20 0 O43592 O43592 XPOT Exportin-T 0 ; 150.58 4.96E-08 193684000 102359 100769 88913 88321 108029 91226 87793 63251 102498 92575 FALSE TRUE 98358.69712 97895.16678 104981.557 92879.25739 111503.8509 93070.65222 88867.437 61944.84475 90862.85675 86304.81279 1.139666421 1.13429557 1.216404434 1.076177033 1.291977206 1.078394694 1.029692715 0.717744964 1.052813323 1 16.39715339 2.155449075 2.908708952 0.891022741 1.164479905 0.499382535 0.102671727 0.172870176 2.942615888 0.042338111 0.028764138 143.0372248 -2.155449075 0.273457165 S(ph)PTKTDPK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPTKTDPK 8 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.997)PT(0.003)KTDPK;S(0.988)PT(0.012)KTDPK;S(0.876)PT(0.122)KT(0.002)DPK;S(0.993)PT(0.007)KTDPK;S(0.852)PT(0.121)KT(0.027)DPK;S(0.843)PT(0.154)KT(0.003)DPK 103.34 0.0029016 10306880000 24202180 17037280 17705400 16856900 18735790 17107340 23928660 26623390 25944890 28480270 TRUE FALSE 23256332.05 16551393.46 20905159.63 17726886.63 19338443.7 17453262.14 24221506.1 26073607.69 22999734.86 26551275.95 0.875902616 0.623374692 0.787350472 0.66764726 0.728343291 0.657341748 0.91225394 0.982009593 0.866238402 1 24.66227786 2.155462425 5.855062805 0.946365919 0.71974214 0.669352438 0.074802898 0.110811322 6.067336012 0.026010677 0.019154648 143.0416216 -2.155462425 -0.226623779 VLGS(ph)EGEEEDEALS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 5 VLGSEGEEEDEALSPAK 17 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 2 VLGS(1)EGEEEDEALS(1)PAK;VLGS(1)EGEEEDEALS(1)PAK;VLGS(1)EGEEEDEALS(1)PAK;VLGS(1)EGEEEDEALS(1)PAK;VLGS(1)EGEEEDEALS(1)PAK 358.05 7.43E-88 2499040000 5342940 4509960 3835620 3993950 4248020 3993470 4923720 5292360 5318840 5417490 TRUE FALSE 5134131.998 4381340.357 4528801.857 4200078.238 4384661.421 4074220.7 4983977.958 5183070.917 4715067.582 5050558.577 1.016547362 0.867496197 0.896693264 0.831606678 0.868153761 0.806687149 0.986817177 1.026237165 0.933573487 1 22.26801152 2.155571347 9.183367319 0.993397801 0.878520131 0.455221304 0.056300081 0.256577424 25.93399116 0.020939214 0.015463766 143.0775012 -2.155571347 -0.11487767 SGSPS(ph)DNSGAEEMEVSLAKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.019)GS(0.205)PS(0.751)DNS(0.025)GAEEMEVSLAKPK;S(0.001)GS(0.17)PS(0.827)DNS(0.002)GAEEMEVSLAKPK 217.5 3.50E-25 1748680000 469910 414010 355200 365020 370110 387470 462150 505400 535730 515200 TRUE FALSE 451545.3977 402202.8402 419392.5414 383858.7259 382014.9243 395304.9089 467805.9299 494963.3134 474916.1764 480305.0451 0.940122121 0.837390413 0.873179546 0.79919778 0.795358966 0.82302885 0.973976715 1.030518664 0.98878032 1 18.87359144 2.155643253 4.608399884 1.007664463 0.841358546 0.77858937 0.040284413 0.094874966 3.651378957 0.016147747 0.011791867 143.1011924 -2.155643253 -0.166305916 AMKDEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 AMKDEEK 7 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 101.72 0.0080722 3640880000 6413820 5024440 4477890 4088320 4422130 4661180 5418560 5681310 6170730 6226170 FALSE TRUE 6163160.824 4881147.891 5287144.333 4299318.685 4564371.828 4755432.253 5484873.958 5563988.963 5470254.6 5804465.96 1.061796359 0.840929712 0.910875241 0.740691515 0.786355172 0.819271279 0.944940326 0.958570349 0.942421687 1 22.46873191 2.15586294 6.147084799 0.959319252 0.852839325 0.266915161 0.082054249 0.29119235 17.13675417 0.031789585 0.023429296 143.1735983 -2.15586294 -0.106479928 LIQESDQHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LIQESDQHLK 10 0 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 77.64 0.032393 440300000 554840 598310 513920 606960 553030 569460 648530 715020 758980 677740 FALSE TRUE 533156.2394 581246.7846 606796.7761 638285.2783 570818.7122 580974.8714 656466.9041 700254.5871 672823.7723 631836.0661 0.843820522 0.9199329 0.960370591 1.010207097 0.903428504 0.919502546 1.038982957 1.108285241 1.064870792 1 19.26919077 2.155940238 4.475242533 1.070269815 0.930184746 0.63051737 0.047248171 0.132538066 4.87702393 0.018880457 0.013762856 143.1990833 -2.155940238 -0.140085069 TPTGNAPSS(ph)ESDIDISSPNVSHDESIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPTGNAPSSESDIDISSPNVSHDESIAK 28 0 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 1 TPTGNAPS(0.022)S(0.569)ES(0.409)DIDISSPNVSHDESIAK 156.43 7.84E-09 167800000 62901 58644 54131 52042 46964 50287 66144 70202 75186 76815 TRUE FALSE 60442.75938 56971.53054 63913.67584 54727.89386 48474.63971 51303.83759 66953.49006 68752.30417 66651.20049 71612.25163 0.844028194 0.795555638 0.892496387 0.764225291 0.676904281 0.716411458 0.934944629 0.960063433 0.93072343 1 16.12791881 2.156080183 6.686404221 0.95548512 0.782011477 0.679388797 0.058923737 0.142539346 9.458730272 0.024545846 0.01810722 143.2452345 -2.156080183 -0.173473643 GLQPST(ph)PPPKPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLQPSTPPPKPPR 13 1 A0A1B0GTL5 A0A1B0GTL5 1 GLQPS(0.205)T(0.795)PPPKPPR 72.175 0.065094 532410000 963910 1113400 791950 935950 845210 927120 990830 1102100 1061900 1013800 TRUE FALSE 926239.3315 1081646.922 935072.9818 984254.4917 872396.9473 945867.0016 1002956.074 1079341.25 941357.5638 945134.423 0.980008038 1.144437125 0.989354487 1.04139101 0.923040073 1.000775105 1.06117823 1.141997608 0.996003892 1 19.85016001 2.156112974 6.237980997 1.071122632 1.015348966 0.031700663 0.06615313 0.442973557 26.67265499 0.025226227 0.018596077 143.2560506 -2.156112974 -0.055773666 SSSASS(ph)PEMK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSSAS(0.021)S(0.979)PEMK;SSSAS(0.025)S(0.975)PEMK;SSSAS(0.105)S(0.895)PEMK 240.8 2.86E-12 1108740000 2666560 2382810 2044090 1987510 2063210 2214420 2641190 2913010 3179100 2830480 TRUE FALSE 2562347.887 2314854.592 2413502.534 2090085.629 2129575.023 2259197.09 2673513.673 2852855.326 2818221.896 2638769.068 0.971039079 0.877247888 0.914631963 0.792068413 0.807033495 0.856155666 1.013166974 1.081131108 1.068006265 1 21.33143367 2.156154598 4.150133053 1.055919456 0.865421948 0.72460062 0.051780469 0.112990262 3.68294017 0.02146432 0.015552052 143.2697813 -2.156154598 -0.190497508 STKPGAAPTEHK ddPTM_BT-474_Pertuzumab_2h_R1 4 STKPGAAPTEHK 12 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;;; 146.5 3.89E-05 1544230000 1867340 1822490 1419590 1441620 1649490 1772600 1797890 1833640 2262010 1989180 FALSE TRUE 1794362.288 1770514.37 1676141.492 1516022.181 1702547.344 1808443.187 1819893.116 1795774.693 2005236.108 1854451.067 0.967597539 0.954737713 0.903847786 0.817504548 0.918086961 0.975190567 0.981364862 0.968359169 1.081309798 1 20.82256077 2.156681329 1.182690351 1.020563749 0.911324899 0.489998671 0.046430819 0.459486539 1.216597424 0.034704003 0.018301734 143.4436505 -2.156681329 -0.10923885 DVPPDILLDS(ph)PERK ddPTM_BT-474_Pertuzumab_2h_R1 7 DVPPDILLDSPERK 14 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK 254.59 1.80E-24 1782970000 1375003.4 1281231.4 1152500.9 1167351.8 1276371.7 1302891.3 1357278.4 1493010 1582229.8 1563939.7 TRUE FALSE 1321266.747 1244691.935 1360783.45 1227598.966 1317427.355 1329236.655 1373889.179 1462178.822 1402621.706 1458012.671 0.906210744 0.853690753 0.933313871 0.841967282 0.903577439 0.911677025 0.942302633 1.002857417 0.962009271 1 20.47557183 2.156713251 1.661402691 0.9898779 0.886040829 0.726975225 0.026841387 0.177380443 0.950433621 0.014247222 0.008086838 143.4541944 -2.156713251 -0.103837071 TSTS(ph)PPPEK ddPTM_BT-474_Pertuzumab_2h_R1 9 TSTSPPPEK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TST(0.003)S(0.997)PPPEK;TST(0.001)S(0.999)PPPEK;TST(0.002)S(0.998)PPPEK;TST(0.002)S(0.998)PPPEK;TSTS(1)PPPEK;T(0.003)S(0.003)T(0.023)S(0.972)PPPEK;TS(0.002)T(0.115)S(0.883)PPPEK;TST(0.023)S(0.977)PPPEK;TS(0.003)T(0.21)S(0.787)PPPEK 182.28 4.88E-05 26386011000 10256070 9689600 10462310 11745560 10021820 10281020 12966790 13696610 15563040 15282070 TRUE FALSE 9855251.446 9413262.095 12353082.15 12351749.76 10344180.94 10488909.27 13125481.45 13413770.22 13796388.94 14247001.79 0.691742136 0.660718812 0.867065389 0.866971868 0.726060198 0.736218709 0.921280256 0.941515304 0.968371391 1 23.76415501 2.156813395 4.573530064 0.955808298 0.762122472 0.696919245 0.0647393 0.138946886 5.3074914 0.027514188 0.020090715 143.4872774 -2.156813395 -0.193685825 KQVAPEKPVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQVAPEKPVKK 11 3 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ; 92.925 0.0042196 4577900000 2420280 2164190 1722760 1743300 2017960 2045960 2208060 2413250 2786910 2134760 FALSE TRUE 2325692.782 2102469.42 2034101.055 1833271.922 2082869.516 2087330.713 2235082.899 2363415.544 2470551.66 1990170.804 1.168589539 1.056426622 1.022073608 0.921163107 1.04657827 1.048819885 1.123060842 1.187544074 1.241376698 1 20.92446082 2.156969054 3.040190396 1.16255697 1.036796161 0.23663302 0.080511971 0.299782104 5.570158334 0.034182561 0.023518134 143.538715 -2.156969054 -0.125760809 KET(ph)SFGSSENITMTSLSK ddPTM_BT-474_Pertuzumab_2h_R1 3 KETSFGSSENITMTSLSK 18 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 KET(0.442)S(0.442)FGS(0.106)S(0.01)ENITMTSLSK;KET(0.637)S(0.332)FGS(0.028)S(0.003)ENITMTSLSK;KET(0.425)S(0.425)FGS(0.118)S(0.031)ENITMTSLSK 263.32 4.02E-31 1456330000 1814500 1789260 1413740 1500740 1647390 1768390 1851350 2042160 2283280 2168870 TRUE FALSE 1743587.334 1738232.057 1669234.266 1578193.371 1700379.795 1804148.057 1874007.375 1999988.682 2024091.627 2021970.503 0.862320855 0.859672312 0.825548278 0.78052245 0.84095183 0.892272194 0.926822311 0.989128516 1.001049038 1 20.94733052 2.157108577 1.364568567 1.001626181 0.831639923 0.908769856 0.022448438 0.12901167 0.45941857 0.015986736 0.008614799 143.5848363 -2.157108577 -0.169986258 REPLQMEDSNMEQGVEGVEPGMPES(ph)PGHLTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 REPLQMEDSNMEQGVEGVEPGMPESPGHLTGR 32 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 REPLQMEDSNMEQGVEGVEPGMPES(1)PGHLTGR 120.71 8.48E-08 86318000 22520 28439 25734 35716 24396 28063 23650 20130 25264 27527 TRUE FALSE 21639.8935 27627.94756 30384.70625 37559.30704 25180.7195 28630.45309 23939.43577 19714.30847 22396.13664 25662.57177 0.843247267 1.076585301 1.184008622 1.463583127 0.981223539 1.115650191 0.932854119 0.768212502 0.872715986 1 14.64737814 2.157375694 3.328491306 0.85299761 1.124819853 0.308080392 0.158198337 0.267225147 5.908105774 0.067693637 0.047538688 143.6731766 -2.157375694 0.271822243 EEQRS(ph)PFNDRFPLK ddPTM_BT-474_Pertuzumab_2h_R1 6 EEQRSPFNDRFPLK 14 2 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 EEQRS(1)PFNDRFPLK;EEQRS(1)PFNDRFPLK;EEQRS(1)PFNDRFPLK;EEQRS(1)PFNDRFPLK;EEQRS(1)PFNDRFPLK;EEQRS(1)PFNDRFPLK 212.55 1.19E-09 3641410000 3211250 3055040 2645870 2904580 3115930 3203500 3357980 3611450 3951320 3997710 TRUE FALSE 3085750.8 2967913.25 3124037.566 3054485.722 3216156.718 3268276.965 3399075.964 3536872.295 3502782.719 3726941.541 0.827957929 0.796340167 0.838230901 0.819568992 0.862947992 0.876932715 0.912028248 0.949001281 0.939854484 1 21.82956076 2.157396163 0.546918744 0.995197088 0.80611742 0.954348164 0.013363989 0.146731743 0.090693016 0.011579772 0.008933175 143.6799482 -2.157396163 -0.189079668 IKEWVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKEWVDK 7 1 J3KQ32;Q9NTK5;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 124.23 0.0038 6400700000 7579600 6945200 6603000 6636600 6873800 7633800 7868500 8932400 9945200 9137000 FALSE TRUE 7283380.852 6747129.696 7796308.983 6979115.721 7094902.02 7788160.666 7964797.057 8747942.819 8816262.59 8518142.852 0.855043286 0.792089287 0.915259244 0.81932363 0.832916534 0.91430266 0.935039151 1.026977708 1.034998208 1 23.02210749 2.157728132 1.447625176 1.026600343 0.842904985 0.836476255 0.033615048 0.146738768 0.590792474 0.020023074 0.010943222 143.7898172 -2.157728132 -0.183695358 T(ph)RTSQEELLAEVVQGQSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TRTSQEELLAEVVQGQSR 18 1 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;A0A087WTC9;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 T(0.443)RT(0.279)S(0.279)QEELLAEVVQGQSR;T(0.442)RT(0.279)S(0.279)QEELLAEVVQGQSR;T(0.486)RT(0.257)S(0.257)QEELLAEVVQGQSR 224.83 7.09E-19 235293000 179475 211243 148102 233849 255103 192159 138100 132002 117024 104442 TRUE FALSE 172460.9186 205218.5565 174867.3259 245917.9749 263308.6197 196044.5866 139790.1091 129276.1126 103739.9261 97368.05031 1.771226989 2.107658065 1.795941537 2.525653683 2.704260985 2.013438556 1.435687668 1.327705671 1.065441136 1 16.57116083 2.1582733 2.429940225 1.183045021 2.190063901 0.737975776 0.281036224 0.166616336 1.970726705 0.142842738 0.092197189 143.9704293 -2.1582733 1.00701888 DAPTS(ph)PASVASSSSTPSSK ddPTM_BT-474_Pertuzumab_2h_R1 6 DAPTSPASVASSSSTPSSK 19 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 DAPTS(0.997)PAS(0.003)VASSSSTPSSK;DAPTS(0.987)PAS(0.013)VASSSSTPSSK;DAPT(0.043)S(0.956)PAS(0.001)VASSSSTPSSK;DAPT(0.027)S(0.97)PAS(0.003)VASSSSTPSSK;DAPT(0.002)S(0.998)PASVASSSSTPSSK;DAPT(0.001)S(0.998)PAS(0.001)VASSSSTPSSK 436.99 5.22E-170 13682230000 2744870 2790090 2360620 2550530 2582170 2715190 2816510 2982250 3294880 3175020 TRUE FALSE 2637597.446 2710519.365 2787236.546 2682163.159 2665227.843 2770093.002 2850979.292 2920665.495 2920859.036 2959973.067 0.891088326 0.915724334 0.941642536 0.906144447 0.900423005 0.935850746 0.963177444 0.986720294 0.98678568 1 21.49715262 2.158439428 1.642539012 0.991561799 0.912512799 0.879421238 0.013060758 0.128633392 0.673418862 0.00783319 0.004438051 144.025512 -2.158439428 -0.079049 HLEFSHDQYR ddPTM_BT-474_Pertuzumab_2h_R1 6 HLEFSHDQYR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 221.5 3.09E-09 8120410000 630556 712983 684020 644802 636569 654135 559036 431327.6 604424 630032 FALSE TRUE 605913.1744 692649.4229 807637.6299 678080.3085 657044.82 667362.0579 565877.6498 422420.5343 535812.3215 587359.3715 1.031588502 1.179260018 1.375031487 1.154455588 1.118641928 1.136207389 0.963426613 0.719185825 0.912239333 1 19.16388395 2.158583368 3.017502077 0.844603727 1.177213527 0.609292797 0.105216841 0.151982932 2.784919442 0.045700751 0.031426118 144.073255 -2.158583368 0.3326098 VYSGHQGR ddPTM_BT-474_Pertuzumab_2h_R1 6 VYSGHQGR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;;; 192.58 0.00017515 971142000 833369 922834 792062 875087 819047 800887 836852 785917 774377 877907 FALSE TRUE 800800.0181 896515.6779 935205.2227 920250.3449 845392.3906 817081.4839 847093.6451 769687.5393 686472.9694 818445.5769 0.978440156 1.095388262 1.142660244 1.124387951 1.032924381 0.998333312 1.035003022 0.940426048 0.838752128 1 19.64252696 2.158608992 1.103374983 0.918917319 1.083489315 0.509203831 0.060174975 0.397015744 0.911406239 0.043812616 0.023079616 144.0817558 -2.158608992 0.164571996 KLEELEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEELEQK 8 1 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 83.499 0.035644 0 138740 127930 103530 97396 130410 129810 151890 178100 197700 179860 FALSE TRUE 133317.8874 124281.5617 122240.174 102422.6192 134604.7561 132434.8471 153748.8753 174422.1728 175257.9248 167677.922 0.795083132 0.741192163 0.729017706 0.610829488 0.802757778 0.789816844 0.916929751 1.04022146 1.04520573 1 17.35533322 2.158718948 1.604820042 1.038952599 0.728010219 0.869856326 0.050212722 0.125068481 0.623936468 0.029761878 0.016748849 144.1182395 -2.158718948 -0.31094238 LDPFQEVVLESSSVDELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDPFQEVVLESSSVDELR 18 0 Q96K76-2;Q96K76-4;Q96K76;Q96K76-3 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 0 96.247 0.0037878 11793000 6332.1 6719.5 7805.9 5462.9 6199.9 6116.1 8275.9 10270 8028.1 8142.7 FALSE TRUE 6084.634531 6527.866439 9216.599771 5744.840924 6399.325414 6239.771732 8377.18294 10057.92091 7116.783745 7591.187676 0.801539205 0.859926894 1.214118286 0.756777618 0.842993967 0.821975691 1.103540486 1.324946944 0.937505967 1 12.8901099 2.158752485 6.108487818 1.14422606 0.889765298 0.285614202 0.153362843 0.22362914 13.37144105 0.058576201 0.043183503 144.1293688 -2.158752485 -0.254460762 QYDIDDAIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 QYDIDDAIAK 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 125.74 0.00093304 341120000 1001220 1040410 947180 1055070 952040 927210 1180410 1250860 1312870 1363610 FALSE TRUE 962091.2155 1010738.525 1118356.496 1109522.289 982663.2312 945958.8215 1194856.211 1225029.304 1163838.502 1271251.48 0.756806368 0.795073627 0.879728766 0.872779546 0.772988859 0.744116201 0.939905463 0.963640415 0.915506113 1 20.27781802 2.158797506 7.381301158 0.954022609 0.8086101 0.720362051 0.046118504 0.137371165 10.78291108 0.018553805 0.013697442 144.1443109 -2.158797506 -0.145412509 S(ph)LEGLNQELEEVFVK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLEGLNQELEEVFVK 15 0 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK 314.29 3.06E-56 851119300 160864 143879 137999 153463 155859 146812 183140 199647 213626 205816 TRUE FALSE 154577.257 139775.7118 162938.4891 161383.2438 160872.3463 149780.6392 185381.3221 195524.2197 189376.0721 191875.899 0.805610594 0.728469352 0.849186844 0.841081369 0.838418723 0.780612052 0.966152201 1.01901396 0.986971647 1 17.54981398 2.158975706 4.830373065 1.000923223 0.808539092 0.876938054 0.034215743 0.069558752 2.92181348 0.013847475 0.010147514 144.2034683 -2.158975706 -0.192384131 KEESEES(ph)DDDMGFGLFD ddPTM_BT-474_Pertuzumab_2h_R1 18 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.003)EES(0.997)DDDMGFGLFD;KEES(0.03)EES(0.97)DDDMGFGLFD;KEES(0.077)EES(0.923)DDDMGFGLFD;KEES(0.295)EES(0.705)DDDMGFGLFD;KEES(0.002)EES(0.998)DDDMGFGLFD;KEES(0.052)EES(0.948)DDDMGFGLFD;KEES(0.002)EES(0.998)DDDMGFGLFD;KEES(0.083)EES(0.917)DDDMGFGLFD;KEES(0.003)EES(0.997)DDDMGFGLFD;KEES(0.047)EES(0.953)DDDMGFGLFD;KEES(0.006)EES(0.994)DDDMGFGLFD;KEES(0.375)EES(0.625)DDDMGFGLFD;KEES(0.297)EES(0.703)DDDMGFGLFD;KEES(0.034)EES(0.966)DDDMGFGLFD;KEES(0.007)EES(0.993)DDDMGFGLFD;KEES(0.006)EES(0.994)DDDMGFGLFD;KEES(0.002)EES(0.998)DDDMGFGLFD;KEES(0.013)EES(0.987)DDDMGFGLFD 239.93 2.82E-20 11469605000 11270593 10084962 9780876 9269391 10453329 11706077 11874339 14015268 15737003 14514280 TRUE FALSE 10830125.77 9797348.758 11548497.87 9747785.38 10789569.82 11942781.9 12019660.71 13725847.82 13950604.39 13531214.89 0.800380886 0.724055367 0.853470879 0.720392475 0.797383673 0.882609728 0.888291318 1.014383995 1.030994224 1 23.68978804 2.159129646 1.169165709 1.026603705 0.774557194 0.856261752 0.041222343 0.157064077 0.406305091 0.027211508 0.014368728 144.2545919 -2.159129646 -0.252046511 LALS(ph)PEDKPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LALSPEDKPIR 11 1 H9KVB4;O15417;O15417-2;O15417-3 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 LALS(1)PEDKPIR;LALS(1)PEDKPIR 134.21 8.82E-05 399650000 367780 356680 351010 339850 362580 391590 408790 498950 502140 475940 TRUE FALSE 353406.751 346507.8356 414445.3152 357389.6992 374242.715 399508.2181 413792.8943 488646.5081 445139.1723 443704.1599 0.796491859 0.780943401 0.934057763 0.805468444 0.843450995 0.900393222 0.932587367 1.101288995 1.003234165 1 18.75923855 2.159172079 1.922063729 1.043627945 0.835693318 0.743787145 0.050480679 0.157434765 1.143621313 0.026258037 0.015669885 144.2686869 -2.159172079 -0.207934627 AQHTLPQDPAIVQSSLGSASASPFQPHVPYS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQHTLPQDPAIVQSSLGSASASPFQPHVPYSPFR 34 0 Q9BX40;Q9BX40-2;Q5TBQ1;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 1 AQHTLPQDPAIVQSSLGSAS(0.004)AS(0.145)PFQPHVPY(0.004)S(0.847)PFR 150.46 2.25E-10 63471000 49989 60582 62294 62981 67310 67773 49685 46398 50094 61299 TRUE FALSE 48035.37461 58854.26068 73551.91152 66231.45696 69475.08728 69143.41649 50293.05989 45439.86509 44407.53913 57147.16413 0.840555701 1.029871938 1.287061443 1.158963143 1.215722396 1.209918594 0.880062216 0.795137708 0.777073365 1 15.80239429 2.159410952 5.886764976 0.83677437 1.132208766 0.492216849 0.128831374 0.165648968 9.431901143 0.050820602 0.037450405 144.3480601 -2.159410952 0.295434395 SSSPAPEFLASS(ph)PPDNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPAPEFLASSPPDNK 17 0 C9JME2;Q9Y4F1;Q9Y4F1-2;M0QXT1 C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 SSSPAPEFLAS(0.153)S(0.847)PPDNK;SSSPAPEFLAS(0.036)S(0.964)PPDNK 165.9 2.53E-09 77781000 115247 194334 122033 227120 118631 121769 211890 271820 205688 157738 TRUE FALSE 110743.0198 188791.7846 144087.0777 238841.6904 122446.8739 124231.2526 214483.1732 266206.822 182339.1606 147054.2648 0.75307588 1.283823933 0.979822503 1.624173844 0.832664554 0.844798706 1.458530792 1.810262507 1.23994473 1 17.1659891 2.159581962 8.753465437 1.486786433 1.07652903 0.171282074 0.311934033 0.371111208 37.16525898 0.115146436 0.085039786 144.4049105 -2.159581962 -0.410257403 RKT(ph)SDANETEDHLESLICK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKTSDANETEDHLESLICK 19 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RKT(0.5)S(0.5)DANET(0.001)EDHLESLICK;RKT(0.5)S(0.5)DANETEDHLESLICK 173.47 3.03E-10 458320000 549710 586550 328480 398190 564300 542530 296900 270650 293550 245142 TRUE FALSE 528226.7255 569822.1683 387843.643 418740.6336 582451.222 553500.3283 300533.551 265060.9829 260227.4347 228538.314 2.31132678 2.493333211 1.697061802 1.832255723 2.548593327 2.421914814 1.315024802 1.159809829 1.138659991 1 17.80207652 2.159750478 5.378350895 1.150148594 2.20273359 0.798314762 0.262737719 0.098775201 4.921144595 0.108777236 0.080022011 144.4609537 -2.159750478 1.052584997 up LEGDLTGPSVGVEVPDVELECPDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEGDLTGPSVGVEVPDVELECPDAK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 146.06 2.67E-07 138415000 122228 123979 107621 106945 100926 123900 120329 144951 140573 137831 FALSE TRUE 117451.1946 120443.2403 127070.5087 112464.4443 104172.3764 126405.3429 121801.6223 141957.7112 124615.7424 128495.5836 0.914048494 0.937333696 0.988909542 0.875239764 0.810707835 0.983732976 0.947905125 1.10476724 0.969805645 1 16.97135925 2.159961705 2.340912503 1.032465007 0.912098912 0.386162495 0.058546536 0.278781157 3.054086591 0.028265782 0.018051313 144.531232 -2.159961705 -0.120366095 DTLSNPQS(ph)PQPSPYNSPKPQHK ddPTM_BT-474_Pertuzumab_2h_R1 3 DTLSNPQSPQPSPYNSPKPQHK 22 1 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 DT(0.002)LS(0.059)NPQS(0.939)PQPSPYNSPKPQHK;DTLSNPQS(1)PQPSPYNSPKPQHK;DT(0.002)LS(0.009)NPQS(0.989)PQPSPYNSPKPQHK 218.93 6.88E-26 1929420000 1203110 1286890 1116070 1330700 1129930 1246060 1539900 1627690 1924780 1782950 TRUE FALSE 1156091.131 1250189.157 1317768.676 1399377.586 1166275.225 1271256.187 1558745.757 1594077.633 1706287.044 1662189.208 0.695523184 0.752134084 0.792791019 0.841888264 0.7016501 0.764808351 0.937766741 0.959022971 1.026529973 1 20.66465318 2.160211607 3.081903958 0.984532998 0.75909846 0.868339281 0.04281315 0.093544417 1.787751284 0.019173764 0.013269693 144.6144222 -2.160211607 -0.225434538 KGISLNPEQWSQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGISLNPEQWSQLK 14 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 128.96 0.00011333 419030000 468950 483360 364100 401890 442440 427720 516940 594960 572920 555950 FALSE TRUE 450622.9155 469575.0461 429900.9694 422631.5911 456671.4844 436368.7915 523266.4664 582673.8681 507884.5235 518295.0113 0.869433249 0.905999548 0.829452262 0.815426701 0.881103376 0.841931298 1.009591941 1.124212766 0.979913973 1 18.98341398 2.160285544 4.582882747 1.052162063 0.857226349 0.781757985 0.044044593 0.08475229 3.29187278 0.016931855 0.012379836 144.6390444 -2.160285544 -0.194935714 KPLAAPGDGEGLGQTAQPS(ph)PPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KPLAAPGDGEGLGQTAQPSPPAR 23 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 KPLAAPGDGEGLGQT(0.025)AQPS(0.975)PPAR;KPLAAPGDGEGLGQTAQPS(1)PPAR;KPLAAPGDGEGLGQTAQPS(1)PPAR;KPLAAPGDGEGLGQTAQPS(1)PPAR 204.34 1.07E-24 3981140000 2342460 2551780 2253680 2642690 2662350 2725900 2343570 2423840 2498900 2679990 TRUE FALSE 2250914.073 2479005.733 2660970.109 2779079.548 2747986.906 2781019.566 2372251.311 2373786.857 2215235.348 2498471.89 0.900916309 0.992208775 1.065039042 1.112311713 1.099867049 1.113088195 0.949480889 0.950095483 0.88663609 1 21.25261456 2.16032569 8.872466464 0.942874831 1.050808351 0.361996183 0.065328706 0.330866706 34.07716556 0.026362386 0.019470135 144.6524155 -2.16032569 0.10793352 DYEIESQNPLAS(ph)PTNTLLGSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYEIESQNPLASPTNTLLGSAK 22 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 DYEIESQNPLAS(0.945)PT(0.02)NT(0.035)LLGSAK;DYEIESQNPLAS(0.987)PT(0.013)NTLLGSAK 349.1 3.63E-96 1188400000 1145920 1099870 940840 993650 1146910 1174260 970570 1022330 1065890 1003870 TRUE FALSE 1101136.18 1068502.784 1110870.717 1044932.396 1183801.402 1198004.342 982448.126 1001218.528 944894.6358 935876.9907 1.176582169 1.141712848 1.186983683 1.116527499 1.264911322 1.280087398 1.049762026 1.06981851 1.009635502 1 19.83595939 2.160391392 9.053913971 1.041158133 1.191274387 0.713962789 0.050145035 0.187038023 19.80261968 0.020023914 0.014788997 144.6743006 -2.160391392 0.150116254 DFLSCRPTEIPENDILLCESR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFLSCRPTEIPENDILLCESR 21 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9 Q86U86-8 PBRM1 Protein polybromo-1 0 ; 200.17 6.95E-22 1113820000 199124 228600 171684 218259 207526 199891 189279 190794 189268 206273 FALSE TRUE 191342.0139 222080.5518 202711.1179 229523.3731 214201.2623 203932.933 191595.453 186854.0372 167783.0901 192301.946 0.995008204 1.154853378 1.054129311 1.193557205 1.113879847 1.06048294 0.996326127 0.971670028 0.87249814 1 17.55301384 2.160491591 1.693406332 0.942771113 1.107004559 0.576519214 0.058600633 0.248338478 1.386123223 0.031641135 0.018134201 144.7076833 -2.160491591 0.164233446 ISELDSMMSESDNSKS(ph)PCNNGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISELDSMMSESDNSKSPCNNGFK 23 1 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 ISELDSMMSESDNS(0.159)KS(0.841)PCNNGFK 156.69 4.24E-14 0 52088 50553 43784 43995 48488 56328 50252 61348 68859 62382 TRUE FALSE 50052.34337 49111.27794 51696.74277 46265.58722 50047.66056 57466.99075 50866.99901 60081.14236 61042.415 58156.81158 0.860644558 0.844463041 0.888919825 0.795531701 0.860564037 0.988138607 0.874652472 1.033088657 1.049617635 1 15.82766056 2.160590659 0.981728688 1.033992114 0.848479491 0.698990324 0.046523866 0.295136117 0.534053188 0.034667451 0.018462336 144.7406966 -2.160590659 -0.185512622 RGSDPAS(ph)GEVEASQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGSDPASGEVEASQLR 16 1 Q8WWA1-3;Q8WWA1-2;Q8WWA1 Q8WWA1-3 TMEM40 Transmembrane protein 40 1 RGS(0.057)DPAS(0.934)GEVEAS(0.008)QLR;RGS(0.334)DPAS(0.653)GEVEAS(0.014)QLR 171.52 5.19E-09 388040000 254643 353800 230442 383370 253748 287770 364080 445360 409030 304710 TRUE FALSE 244691.27 343709.9704 272087.9956 403155.7716 261910.0349 293588.9066 368535.7199 436163.1604 362598.6292 284071.7203 0.861371451 1.209940821 0.95781444 1.419204176 0.921985598 1.033502759 1.297333362 1.535398032 1.276433391 1 18.11589569 2.161091392 5.499522367 1.349224051 1.078519761 0.183089951 0.196065664 0.251229484 13.07434265 0.071238409 0.052448379 144.9076761 -2.161091392 -0.270704289 LEEALSEAAPDPSLPPLAQS(ph)PPKHER ddPTM_BT-474_Pertuzumab_2h_R1 3 LEEALSEAAPDPSLPPLAQSPPKHER 26 1 A0A1B0GW72;Q96PX9 A0A1B0GW72 PLEKHG4B Pleckstrin homology domain-containing family G member 4B 1 LEEALSEAAPDPS(0.002)LPPLAQS(0.998)PPKHER;LEEALSEAAPDPS(0.001)LPPLAQS(0.999)PPKHER;LEEALSEAAPDPS(0.072)LPPLAQS(0.928)PPKHER 107.01 0.0017459 881320000 429655 379811 355363 391462 392474 400780 483949 447643 579770 517981 TRUE FALSE 412863.6076 368979.1622 419584.9991 411665.4007 405098.2826 408884.0462 489871.7126 438399.0156 513956.9402 482897.6855 0.854971187 0.764093872 0.86889006 0.852489902 0.838890504 0.846730184 1.014442039 0.907850729 1.0643185 1 18.88135802 2.16109542 0.985918817 1.01096455 0.826108326 0.699931132 0.04912944 0.302870917 0.552839809 0.035522278 0.018912231 144.9090202 -2.16109542 -0.184856224 HDDSSDNFCEADDIQSPEAEYVDLLLNPER ddPTM_BT-474_Pertuzumab_2h_R1 3 HDDSSDNFCEADDIQSPEAEYVDLLLNPER 30 0 Q96HE7;G3V3E6;G3V5B3 Q96HE7 ERO1L ERO1-like protein alpha 0 ;; 295.78 5.30E-81 354964000 110231 130699 82164 107541 95010 105075 73947 35707.5 104536 81735 FALSE TRUE 105923.0507 126971.5925 97012.86253 113091.2039 98066.08294 107199.6885 74851.98551 34970.12765 92669.51153 76199.01565 1.390084239 1.66631539 1.273151125 1.484155706 1.286973094 1.406838233 0.982322211 0.458931488 1.216151032 1 16.21748474 2.161261358 4.029000952 0.808697676 1.421839197 0.575630207 0.208473088 0.132059983 4.14340797 0.080133995 0.058030137 144.9643987 -2.161261358 0.613141521 HS(ph)SLGDHK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSSLGDHK 8 0 O43295-2;O43295 O43295-2 SRGAP3 SLIT-ROBO Rho GTPase-activating protein 3 1 HS(0.5)S(0.5)LGDHK 51.436 0.096137 171460000 87423 81897 68043 102320 83709 92272 66200 57715 83640 64135 TRUE FALSE 84006.41251 79561.37775 80339.88371 107600.7475 86401.57601 94137.80306 67010.1754 56523.16508 74145.53785 59791.07932 1.404999098 1.330656323 1.343676759 1.79961206 1.445057975 1.574445622 1.120738681 0.945344451 1.240076926 1 15.86764263 2.161650152 5.598237773 1.052277224 1.481993783 0.654077217 0.144925025 0.125717765 6.75308243 0.056575388 0.041672426 145.0942333 -2.161650152 0.429716559 QYPWGVAEVENGEHCDFTILR ddPTM_BT-474_Pertuzumab_2h_R1 4 QYPWGVAEVENGEHCDFTILR 21 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;; 314.08 1.25E-66 1891820000 1166070 1225340 930243 1117470 1051380 1110520 1001261 939460 1149890 1075260 FALSE TRUE 1120498.695 1190394.503 1098358.603 1175142.761 1085198.593 1132975.475 1013514.732 920059.8227 1019359.308 1002431.682 1.117780608 1.187506863 1.095694223 1.172292118 1.082566135 1.130227122 1.011056164 0.917827957 1.016886563 1 19.93507249 2.161687407 3.680613301 0.967994517 1.132505777 0.773093968 0.038478162 0.093118441 2.489777023 0.01473076 0.010553515 145.1066803 -2.161687407 0.16451126 EDRYEEEIK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDRYEEEIK 9 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ; 134.84 0.00021659 628200000 736420 626490 588210 563420 665380 663710 739000 800560 939540 803520 FALSE TRUE 707639.8922 608623.1186 694512.6317 592498.1737 686782.552 677130.6709 748044.1031 784028.1562 832887.3581 749096.8747 0.944657382 0.812475848 0.927133266 0.790950001 0.916814067 0.903929377 0.998594612 1.046631194 1.111855337 1 19.51479278 2.161695396 1.672873771 1.061383379 0.87211274 0.697133118 0.051672966 0.184951489 1.006817378 0.027049902 0.015461807 145.1093498 -2.161695396 -0.18927064 QDGPMPKPHSVSLNDTETR ddPTM_BT-474_Pertuzumab_2h_R1 6 QDGPMPKPHSVSLNDTETR 19 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ;;;;; 283.73 4.56E-40 2916550000 1127572 1636537 817610 1514083 1038947 1193221 1384233 1692843 1523232 1010449 FALSE TRUE 1083505.24 1589864.567 965370.3146 1592225.005 1072365.674 1217348.746 1401173.658 1657885.2 1350321.089 942010.3892 1.150205191 1.687735704 1.024797949 1.690241449 1.13837988 1.292288026 1.487429092 1.759943648 1.433446069 1 19.84538345 2.161703818 6.488973456 1.515685345 1.34084425 0 0.27471763 0.548952089 36.92812514 0.096958548 0.071548577 145.1121639 -2.161703818 -0.174841095 TSPTTPEASATNS(ph)PCTSKPATPAPSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPTTPEASATNSPCTSKPATPAPSEK 27 1 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 TSPTTPEASATNS(0.955)PCT(0.043)S(0.002)KPATPAPSEK;TSPTTPEASAT(0.001)NS(0.999)PCTSKPATPAPSEK 218.98 1.88E-34 1054070000 730610 673600 649300 639800 655020 652460 809710 875930 950930 902470 TRUE FALSE 702056.9535 654389.5875 766642.9536 672820.1547 676089.3132 665653.1882 819619.4732 857841.7394 842984.413 841344.9031 0.834446077 0.777789923 0.911211265 0.799696001 0.803581635 0.791177537 0.974177736 1.019607697 1.001948678 1 19.68233782 2.161942618 5.038768242 1.005780817 0.820352186 0.862136824 0.035227292 0.069415931 3.166435499 0.013435603 0.009870438 145.1919767 -2.161942618 -0.185428632 FTDKDQQPSGS(ph)EGEDDDAEAALKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTDKDQQPSGSEGEDDDAEAALKK 24 2 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 1 FTDKDQQPS(0.169)GS(0.831)EGEDDDAEAALKK 123.31 5.94E-05 511950000 402960 283010 244420 248690 295670 330240 405240 461520 535400 495160 TRUE FALSE 387211.8777 274938.8319 288592.1311 261524.9207 305180.4941 336917.6791 410199.4483 451989.4507 474623.6366 461622.3722 0.838806568 0.59559252 0.625169291 0.566534329 0.661104211 0.729855612 0.888603918 0.979132464 1.028164286 1 18.81635362 2.162469907 1.637172927 1.009037902 0.646023043 0.832280731 0.068993428 0.14104579 0.734277175 0.039316618 0.022341 145.3683654 -2.162469907 -0.363014859 KSEEEIDFLR ddPTM_BT-474_Pertuzumab_2h_R1 6 KSEEEIDFLR 10 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ;;;;; 158.3 1.29E-05 2823620000 7065850 7332700 6100990 6465470 7078050 7234970 7728290 7995080 9105140 8872920 FALSE TRUE 6789708.77 7123578.575 7203574.609 6799153.682 7305721.906 7381266.05 7822871.125 7829978.804 8071562.679 8271949.225 0.820811224 0.861172909 0.870843668 0.821953024 0.883192305 0.892324874 0.945710728 0.946569979 0.975775172 1 22.9797959 2.162767379 0.705388357 0.995389615 0.840949616 0.911572625 0.017599442 0.187134565 0.179004755 0.014854339 0.009138638 145.4679702 -2.162767379 -0.154439999 NSS(ph)EASSGDFLDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSEASSGDFLDLK 14 0 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 NS(0.212)S(0.788)EASSGDFLDLK 286.73 8.07E-34 388770000 373650 291360 410540 409920 408400 394370 528540 628490 630350 595070 TRUE FALSE 359047.3449 283050.6981 484733.7104 431076.0203 421536.5569 402344.4316 535008.4306 615511.4619 558795.3106 554765.3789 0.647205753 0.510216947 0.873763448 0.777042037 0.759846546 0.725251515 0.96438684 1.109498691 1.007264209 1 19.08151823 2.162918944 3.430910854 1.049113536 0.716032002 0.724579312 0.092734128 0.128737177 3.027131886 0.040294526 0.028568647 145.5187463 -2.162918944 -0.333081535 ERECNPPNSQPASYQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERECNPPNSQPASYQR 16 1 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 117.18 0.00033779 61673000 36223 40286 23901 32325 35355 37705 28487 28858 31834 30222 FALSE TRUE 34807.36511 39137.08272 28220.44237 33993.29712 36492.22568 38467.42093 28835.63243 28262.07222 28220.33778 28175.03702 1.235397316 1.389069434 1.001611545 1.20650408 1.29519708 1.365301522 1.023446124 1.003089089 1.001607833 1 14.78212989 2.162954957 8.271287278 1.005837262 1.243930389 0.586585507 0.099436495 0.198653568 19.28912005 0.038547985 0.028470994 145.5308134 -2.162954957 0.238093126 KVEEDLKADEPSS(ph)EESDLEIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEEDLKADEPSSEESDLEIDK 22 2 P50502;Q3KNR6;F6VDH7 P50502 ST13 Hsc70-interacting protein 1 KVEEDLKADEPS(0.189)S(0.811)EESDLEIDK 128.06 8.99E-06 109630000 118120 74174 95075 108160 96475 105640 156850 198010 188490 191270 TRUE FALSE 113503.7398 72058.63014 112257.1674 113742.1506 99578.20599 107776.1132 158769.5772 193921.0243 167093.4054 178315.1125 0.636534605 0.404108374 0.629543766 0.637871625 0.558439521 0.604413791 0.890387668 1.087518728 0.93706811 1 17.44406945 2.163006329 3.110557555 1.014263837 0.570586107 0.882289477 0.072562332 0.074563072 1.453078303 0.030132372 0.020944868 145.548029 -2.163006329 -0.443677729 RT(ph)SMGGTQQQFVEGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSMGGTQQQFVEGVR 16 1 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0 A0A2R8Y804 CTNNB1 Catenin beta-1 1 RT(0.885)S(0.115)MGGTQQQFVEGVR 205.84 1.26E-11 752330000 101540 182540 75901 185950 88356 106290 148120 188310 142530 96990 TRUE FALSE 97571.70454 177334.1379 89617.99911 195546.9018 91198.05098 108439.2566 149932.7369 184421.3327 126350.5919 90420.78091 1.079084958 1.96120998 0.991121711 2.162632304 1.008596144 1.199273613 1.658166799 2.039590134 1.397362317 1 16.46436676 2.163199346 22.43422639 1.658107901 1.424059819 0 0.448355279 50.65297572 15074.12983 0.159722375 0.117962891 145.6127305 -2.163199346 -0.234048083 GRYPDHS(ph)VDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 GRYPDHSVDRR 11 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 GRYPDHS(1)VDRR;GRYPDHS(1)VDRR;GRYPDHS(1)VDRR;GRYPDHS(1)VDRR 153.09 1.70E-05 1107440000 159975 127815 87251 336418 158467 166196 320319 424401 352906 360406 TRUE FALSE 153723.0001 124169.8413 103019.1966 353780.5733 163564.235 169556.597 324239.1597 415636.971 312845.5904 335995.3806 0.457515219 0.36955818 0.306608967 1.052932849 0.486805011 0.504639667 0.965010766 1.237031802 0.931100868 1 18.35808187 2.163311929 4.378715868 1.085252186 0.533289665 0.595483708 0.203453864 0.145869007 5.311810897 0.081711611 0.059642919 145.6504828 -2.163311929 -0.551962521 TEIIPDRDGSDPYQEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 TEIIPDRDGSDPYQEPK 17 1 Q99447-3;Q99447;Q99447-4;I3L1L9;Q99447-2;I3L3V9 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 ;; 124.26 4.64E-05 1550160000 1663770 1534690 1195530 1262070 1497520 1596870 1635650 1848640 2181750 1920450 FALSE TRUE 1598748.029 1490922.144 1411588.865 1327205.584 1545689.091 1629159.806 1655667.574 1810464.938 1934086.887 1790376.211 0.892967645 0.832742378 0.788431424 0.741299832 0.863332009 0.909953894 0.924759592 1.011220394 1.080268423 1 20.77183134 2.163375639 1.167649078 1.040704963 0.816237749 0.799943153 0.044487191 0.211616443 0.546435433 0.032571859 0.017260875 145.6718512 -2.163375639 -0.224467214 SALS(ph)PSKSPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SALSPSKSPAK 11 1 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 1 SALS(0.996)PS(0.004)KSPAK 136.14 6.39E-05 421300000 389860 338580 235940 235060 265380 290060 335040 359670 404230 367880 TRUE FALSE 374623.8402 328924.0299 278579.6065 247191.4748 273916.1887 295925.2119 339140.3197 352242.6888 358343.5051 342963.1599 1.092315105 0.959065195 0.812272684 0.720752266 0.798675254 0.862848395 0.988853496 1.027056926 1.044845473 1 18.38769409 2.163692253 3.868677237 1.022835642 0.864453723 0.347601083 0.094733182 0.2695515 7.912114443 0.041725896 0.030121024 145.7780891 -2.163692253 -0.158381919 WLDGASFDNER ddPTM_BT-474_Pertuzumab_2h_R1 1 WLDGASFDNER 11 0 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 0 75.387 0.088931 77822000 145890 177630 144660 158420 160090 153830 137990 94985 183090 147760 FALSE TRUE 140188.4575 172564.1663 170803.2799 166596.0752 165239.4402 156940.548 139678.7629 93023.52656 162306.3908 137752.0836 1.017686657 1.252715471 1.239932461 1.209390601 1.199542221 1.13929709 1.013986571 0.675296693 1.178249988 1 17.07171462 2.1639399 3.528749864 0.901989199 1.187682403 0.356946789 0.133330207 0.19477362 4.832796682 0.052764658 0.037613624 145.8612397 -2.1639399 0.285693205 VLESLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VLESLDR 7 0 A0A5F9ZHY7;Q8WY22 REV__Q96PE2 BRI3BP BRI3-binding protein 0 ;; 155.51 0.0037367 219900000 251356 398052 224944 477667 272003 273303 381529 466573 337958 283670 FALSE TRUE 241532.7296 386699.9467 265596.3847 502319.4511 280752.2235 278829.3739 386198.266 456938.1045 299594.4247 264456.7782 0.913316464 1.462242523 1.004309235 1.899438746 1.061618558 1.054347617 1.4603455 1.727836615 1.132867256 1 18.01267243 2.164252977 25 1.429494995 1.255139935 0 0.328322117 125.6953098 42284.73338 0.119815377 0.088489542 145.9664268 -2.164252977 -0.17435506 LICCDILDVLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LICCDILDVLDK 12 0 P62258;P62258-2;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 213.34 2.26E-08 774370000 792610 798260 637850 785560 733310 702130 866290 906830 1013440 948700 FALSE TRUE 761633.9249 775494.4064 753123.6839 826102.8457 756897.5821 716327.5497 876891.9162 888103.6436 898398.5399 884443.704 0.861144606 0.876816018 0.851522466 0.934036663 0.85578944 0.809918762 0.991461539 1.004138126 1.015778094 1 19.75441079 2.164498788 7.462081673 1.004075741 0.867702936 0.842835275 0.029190286 0.089535327 7.661867458 0.011209113 0.008278595 146.0490673 -2.164498788 -0.136372805 RVPLS(ph)PLSLLAGPADAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVPLSPLSLLAGPADAR 17 1 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 RVPLS(0.999)PLS(0.001)LLAGPADAR;RVPLS(1)PLSLLAGPADAR 144.18 3.19E-07 492990000 384830 464050 313670 352990 399300 407320 235160 221590 196616 200917 TRUE FALSE 369790.4181 450815.7484 370357.1466 371207.8562 412143.8471 415556.2895 238037.9584 217014.0891 174296.976 187308.7126 1.974229671 2.40680608 1.977255309 1.981797061 2.200345309 2.218563588 1.27083228 1.158590468 0.930533201 1 17.51505848 2.164510475 4.244668141 1.085304229 2.130938938 0.926624864 0.143547278 0.054505006 1.888750918 0.057359605 0.041794853 146.0529978 -2.164510475 1.04563471 AETPTESVS(ph)EPEVATK ddPTM_BT-474_Pertuzumab_2h_R1 1 AETPTESVSEPEVATK 16 0 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 AETPT(0.002)ES(0.011)VS(0.987)EPEVATK 315.66 8.55E-58 1528400000 381970 324880 299910 305240 365710 317180 388500 414210 432810 443970 TRUE FALSE 367042.1901 315614.7405 354110.4085 320993.473 377473.3943 323593.5969 393254.5792 405656.4188 383679.2233 413899.5165 0.886790575 0.762539525 0.855546804 0.775534786 0.911992837 0.781816803 0.950120895 0.980084302 0.926986401 1 18.65892104 2.164647134 6.709284427 0.965662074 0.828737516 0.652362096 0.048427032 0.122624062 8.961082486 0.016717961 0.012343386 146.0989634 -2.164647134 -0.136924557 EESREPAPAS(ph)PAPAGVEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EESREPAPASPAPAGVEIR 19 1 Q14195-2 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 1 EESREPAPAS(1)PAPAGVEIR 138.23 1.40E-06 470480000 159200 191190 157160 196960 183450 181860 133830 128260 129930 127550 TRUE FALSE 152978.288 185737.4484 185562.308 207125.1292 189350.8359 185537.3338 135467.8516 125611.3862 115180.8911 118910.9249 1.286494812 1.56198809 1.560515219 1.741851133 1.592375436 1.560305195 1.139238062 1.056348576 0.968631698 1 16.85952174 2.164652693 3.258188401 1.027674175 1.565742586 0.844239866 0.107960745 0.094081922 2.00792136 0.046762371 0.032871439 146.1008333 -2.164652693 0.538068411 NLLEDDS(ph)DEEEDFFLR ddPTM_BT-474_Pertuzumab_2h_R1 5 NLLEDDSDEEEDFFLR 16 0 O75379 O75379 VAMP4 Vesicle-associated membrane protein 4 1 NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR 271.68 3.89E-35 733082000 606542 851439 571828 899441 624105 711231 853146 983259 996273 809684 TRUE FALSE 582837.6681 827156.7934 675170.0398 945861.2578 644179.9041 725612.5781 863587.056 962954.358 883180.2658 754843.3815 0.772130593 1.095799226 0.8944505 1.253056304 0.853395446 0.961275671 1.144061241 1.275700869 1.170017897 1 19.52581781 2.164939282 4.990894704 1.185390465 0.981272527 0.258330425 0.140804022 0.240401581 10.98715414 0.051304858 0.037711816 146.1972764 -2.164939282 -0.204117938 SLSFPILNPALSQPSQPS(ph)SPLPGSHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSFPILNPALSQPSQPSSPLPGSHGR 27 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 SLSFPILNPALSQPSQPS(0.483)S(0.483)PLPGS(0.033)HGR 209.65 1.04E-25 469750000 146880 182420 212700 204890 204000 215710 158860 151490 171510 182370 TRUE FALSE 141139.7672 177217.5602 251139.6215 215464.3975 210561.8453 220071.804 160804.1762 148361.6786 152040.9038 170017.9175 0.83014643 1.042346377 1.477136206 1.267304062 1.238468559 1.294403597 0.945807234 0.872623784 0.894264005 1 17.37532727 2.164973904 6.483556599 0.910025436 1.203000299 0.384630901 0.16252522 0.219115518 15.24565633 0.065075428 0.04804055 146.2089318 -2.164973904 0.292974863 RS(ph)PLGQK ddPTM_BT-474_Pertuzumab_2h_R1 6 RSPLGQK 7 1 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK 96.331 0.0078463 7771400000 8526570 8337600 7104560 7468010 7699970 7779090 8522160 9062900 9604200 9379200 TRUE FALSE 8193342.218 8099819.811 8388512.032 7853434.891 7947646.528 7936388.53 8626456.743 8875747.948 8513971.48 8743938.43 0.937031097 0.926335412 0.959351681 0.898157616 0.908932124 0.907644604 0.986564214 1.015074388 0.973699843 1 23.05985181 2.165060129 5.62188621 0.998249013 0.923035479 0.774031032 0.018775762 0.093323364 5.185794083 0.007378901 0.005439423 146.2379629 -2.165060129 -0.075213533 RKS(ph)VEEESK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKSVEEESK 9 2 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 RKS(1)VEEESK 97.463 0.0052561 53107000 68999 76782 58309 69698 57051 71270 77107 96471 91476 73852 TRUE FALSE 66302.4428 74592.25254 68846.73338 73295.12213 58886.09723 72711.12823 78050.65853 94478.84014 81092.02798 68849.93826 0.962999307 1.083403332 0.999953451 1.064563368 0.855281772 1.056081241 1.133634401 1.372242917 1.177808289 1 16.07116774 2.16518433 3.296711944 1.228695387 1.000941341 0.3551036 0.106167836 0.199943915 4.366539434 0.042218956 0.029758669 146.2797908 -2.16518433 -0.227754046 (ac)SSILPFT(ph)PPVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSILPFTPPVVK 12 0 Q15796-2;Q15796;B7Z5N5;K7EJX0;K7ESI8;K7EL92;K7ERC7 Q15796-2 SMAD2 Mothers against decapentaplegic homolog 2;Mothers against decapentaplegic homolog 1 S(0.005)S(0.005)ILPFT(0.989)PPVVK;SS(0.001)ILPFT(0.999)PPVVK 60.518 0.001395 354170000 140585 150632 131927 140587 149197 151264 162195 193817 176794 191042 TRUE FALSE 135090.7828 146336.1228 155769.1436 147842.7119 153996.057 154322.6617 164179.9909 189814.6112 156725.0863 178102.5552 0.75849997 0.82163966 0.874603643 0.83009877 0.864648218 0.86648202 0.921828386 1.06576018 0.879971015 1 17.44234869 2.165362649 2.638532415 0.989976797 0.835125637 0.612168992 0.052498607 0.172304944 2.418848296 0.023131452 0.015423119 146.3398646 -2.165362649 -0.15485116 RNS(ph)LQHHQDDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSLQHHQDDTK 12 1 Q6ZU80;H0YJH2 Q6ZU80 CEP128 Centrosomal protein of 128 kDa 1 RNS(1)LQHHQDDTK 112.82 0.00057976 177610000 205650 198310 166950 110810 172670 161810 121610 28693 185690 161380 TRUE FALSE 197612.9706 192654.393 197121.5788 116528.9174 178224.0874 165081.9091 123098.2996 28100.47952 164611.2497 150449.5889 1.313482956 1.280524556 1.310216799 0.774537958 1.184609999 1.097257296 0.818202964 0.186776712 1.094128943 1 17.19892064 2.165366144 3.878308125 0.636318994 1.158784998 0.287135251 0.276241247 0.214297217 6.339323447 0.109539363 0.079168806 146.3410423 -2.165366144 0.522466004 YGVYEDENYEVGS(ph)DDEEIPFK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGVYEDENYEVGSDDEEIPFK 21 0 O15541 O15541 RNF113A RING finger protein 113A 1 YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK 134.32 5.44E-06 348340000 528300 514490 407470 467570 515050 500010 534320 586330 655910 599900 TRUE FALSE 507653.4519 499817.2489 481108.8931 491701.3437 531617.051 510120.5448 540859.168 574222.0806 581453.8466 559268.2387 0.907710141 0.893698613 0.860247123 0.879186962 0.950558273 0.912121429 0.967083647 1.026738228 1.039668993 1 19.09318088 2.165412916 1.192981002 1.030916463 0.89051442 0.843998237 0.023628303 0.171478107 0.46307185 0.016638455 0.008848087 146.3568035 -2.165412916 -0.140402043 NEGVNWLR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEGVNWLR 8 0 F8VUA2;F8VVT7;Q9HD42 F8VUA2 CHMP1A Charged multivesicular body protein 1a 0 121.53 0.0033248 191950000 232530 238260 224940 193620 208080 214820 178200 140280 189410 187980 FALSE TRUE 223442.4705 231465.0581 265591.6618 203612.7514 214773.0822 219163.8076 180380.8649 137383.169 167908.9709 175247.9472 1.275007634 1.320786131 1.515519389 1.161855272 1.225538362 1.250592724 1.02928946 0.783935967 0.958122327 1 17.41903802 2.165457268 2.700188159 0.890466163 1.300610066 0.74682172 0.100911648 0.128702337 1.893711991 0.046057043 0.030920928 146.3717508 -2.165457268 0.410143903 DYTGCSTSESLS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYTGCSTSESLSPVK 15 0 O95297-4;O95297-2;O95297 O95297-4 MPZL1 Myelin protein zero-like protein 1 1 DYTGCSTSESLS(1)PVK 261.64 6.14E-25 116590000 84994 127250 88690 148920 93729 93624 153200 192300 151100 143560 TRUE FALSE 81672.34051 123620.9546 104718.2559 156605.779 96743.87841 95517.14143 155074.9074 188328.9378 133947.7615 133836.5533 0.610239419 0.923671086 0.782433896 1.170127108 0.72285094 0.713685006 1.158688741 1.407156215 1.000830925 1 17.03011267 2.165523119 6.778900968 1.204012384 0.83541743 0.415353909 0.180574116 0.184624689 13.84850188 0.067396252 0.049767989 146.3939465 -2.165523119 -0.368594954 QS(ph)PGPALAR ddPTM_BT-474_Pertuzumab_2h_R1 3 QSPGPALAR 9 0 P85037 P85037 FOXK1 Forkhead box protein K1 1 QS(1)PGPALAR;QS(1)PGPALAR;QS(1)PGPALAR 80.014 0.02655 1251800000 1523960 1539230 1291550 1441380 1379350 1613140 1348950 1370710 1524340 1558840 TRUE FALSE 1464401.958 1495332.667 1524961.815 1515769.795 1423718.045 1645758.796 1365458.854 1342404.359 1351303.314 1453258.378 1.007667996 1.028951692 1.049339772 1.043014661 0.979673035 1.132461247 0.939584367 0.923720365 0.929843814 1 20.4708598 2.165663546 24.99858282 0.939894624 1.03746851 0.533019474 0.041799059 29.22176969 10020.20854 0.014657059 0.010824958 146.4412901 -2.165663546 0.097573886 MQQQLDEYQELLDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 MQQQLDEYQELLDIK 15 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 173.68 2.22E-06 100269000 103087 91632 74247 81078 90942 87604 94801 99265 123711 84089 FALSE TRUE 99058.24607 89018.74508 87665.08452 85262.4453 93867.23202 89375.4129 95961.203 97215.14306 109667.8459 78393.57713 1.263601556 1.135536205 1.118268712 1.087620293 1.197384218 1.140085912 1.224095219 1.240090663 1.398939172 1 16.25844784 2.16598266 4.959972852 1.237669256 1.153003423 0.058343636 0.101354803 0.414382452 18.85817917 0.036686303 0.026969541 146.5489328 -2.16598266 -0.084665833 AKPEGALQNNDGLYDPDCDESGLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKPEGALQNNDGLYDPDCDESGLFK 25 1 P16422;B5MCA4;C9JKY3 P16422 EPCAM Epithelial cell adhesion molecule 0 ; 222.72 9.18E-34 628320000 400160 673670 319580 720520 365280 460550 768870 1034820 861780 591560 FALSE TRUE 384521.3048 654457.5912 377335.215 757706.1235 377029.5629 469862.6365 778279.6611 1013450.605 763954.3473 551493.1143 0.697236819 1.186701292 0.684206575 1.37391765 0.683652349 0.85198278 1.411222807 1.837648702 1.3852473 1 19.07298335 2.166080878 5.202374925 1.526883714 0.925795866 0.391381759 0.290187838 0.165843489 8.179424075 0.104857347 0.077194519 146.5820792 -2.166080878 -0.601087847 VPGGS(ph)PLGVSLVYSDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VPGGSPLGVSLVYSDKK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 VPGGS(1)PLGVSLVYSDKK 118.46 0.00010259 356640000 659870 570000 476090 488440 571050 550470 620350 705260 713210 598980 TRUE FALSE 634081.5509 553744.1581 562130.0536 513648.4469 589418.3419 561600.8806 627942.0289 690696.1345 632249.3908 558410.5511 1.135511408 0.991643437 1.006660874 0.919840153 1.055528662 1.005713233 1.124516769 1.23689664 1.132230381 1 19.09096668 2.166088976 4.683076285 1.156078232 1.01432927 0.280062341 0.075937018 0.193814664 8.005984313 0.028411744 0.020839875 146.5848125 -2.166088976 -0.141748963 LGAGGGSPEKS(ph)PSAQELK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(0.293)PEKS(0.707)PSAQELK 244.52 9.89E-24 114140000 109220 90175 71096 70504 89434 87239 106580 117760 129830 121060 TRUE FALSE 104951.5617 87603.29729 83944.62872 74142.71989 92310.72583 89003.03235 107884.3579 115328.2148 115092.2427 112860.4984 0.929922897 0.77620867 0.743791051 0.656941277 0.817918822 0.788611017 0.955908927 1.021865192 1.019774362 1 16.7841811 2.166191064 2.766058584 1.01415326 0.775925857 0.730358051 0.064190471 0.139436581 2.154790713 0.029171718 0.019732656 146.6192739 -2.166191064 -0.238227403 RCDDLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RCDDLTR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 117.39 0.0084057 462110000 414990 529480 342110 400000 432300 376380 368660 362240 348240 349520 FALSE TRUE 398771.732 514379.7488 403936.8872 420644.0479 446205.3221 383990.6615 373171.7714 354759.6174 308709.2551 325846.6991 1.223801662 1.578594321 1.239653151 1.290926221 1.369371927 1.178439624 1.145237231 1.088731659 0.947406422 1 18.31383385 2.166347268 0.790980097 0.972069573 1.365640587 0.683888858 0.097656084 0.349367829 0.413656609 0.076507401 0.043983721 146.6720183 -2.166347268 0.393571014 S(ph)PENSPPVKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPENSPPVKPK 11 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.99)PENS(0.01)PPVKPK;S(0.924)PENS(0.076)PPVKPK 135.02 7.79E-05 983090000 1388830 1213200 1246690 1280840 1248270 1248870 1562200 1670190 1852220 1777710 TRUE FALSE 1334552.988 1178600.724 1471994.615 1346944.306 1288421.738 1274123.007 1581318.671 1635699.993 1641963.751 1657304.118 0.805255338 0.71115537 0.888186181 0.81273213 0.777420224 0.768792519 0.954151174 0.986964296 0.990743782 1 20.66040693 2.166383855 4.897125574 0.985700329 0.79453448 0.829823905 0.042086919 0.082192155 3.669262347 0.016401642 0.012053726 146.6843752 -2.166383855 -0.191165849 APS(ph)PTSSAGEEGTKKPEPLSPASYHQPEGVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPTSSAGEEGTKKPEPLSPASYHQPEGVAR 32 2 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 APS(0.607)PT(0.159)S(0.18)S(0.054)AGEEGTKKPEPLSPASYHQPEGVAR 92.819 5.16E-05 683680000 102870 113960 87500 95896 101000 109930 126910 141800 153430 156850 TRUE FALSE 98849.72667 110709.9724 103313.1964 100845.2041 104248.7567 112152.8599 128463.1625 138871.7804 136013.2696 146226.4098 0.676004607 0.757113387 0.706528982 0.689651098 0.712927007 0.766980876 0.878522305 0.949703823 0.930155297 1 17.15784437 2.166403394 1.571140922 0.962900863 0.708124655 0.95287363 0.024928099 0.07367199 0.352453267 0.014217052 0.008010446 146.6909747 -2.166403394 -0.254776208 MSQPGSPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 MSQPGSPSPK 10 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 MS(0.001)QPGS(0.129)PS(0.87)PK 102.4 0.003862 0 421300 382950 323150 358640 379380 384360 414850 444950 495570 462320 TRUE FALSE 404835.1302 372028.6409 381550.3934 377149.4534 391583.1022 392132.0225 419927.0584 435761.627 439314.9712 431006.6546 0.939278143 0.863162174 0.885254066 0.875043226 0.908531453 0.909805031 0.974293677 1.011032248 1.019276539 1 18.71735062 2.166880582 1.808158896 1.01318988 0.890503618 0.874204678 0.019782221 0.106441884 0.682468024 0.010266964 0.006048852 146.8522422 -2.166880582 -0.122686262 LSIGDLDFSDLGEDEDQDMLNVESVEAGK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSIGDLDFSDLGEDEDQDMLNVESVEAGK 29 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 0 ;; 287.57 4.07E-72 115338000 108588 114533 107106 112980 119665 122302 133805 149019 172022 166088 FALSE TRUE 104344.2609 111266.631 126462.4368 118810.9113 123514.1334 124775.0302 135442.5456 145941.7056 152494.7837 154838.7118 0.673890009 0.718596982 0.816736559 0.767320458 0.797695434 0.805838726 0.874733095 0.942540169 0.984862131 1 17.24040668 2.16704094 0.540913354 1.020508012 0.717052308 0.906184225 0.032034515 0.255302534 0.1548736 0.031939535 0.025081257 146.9064757 -2.16704094 -0.303455704 AGCECLNESDEHGFDNCLR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGCECLNESDEHGFDNCLR 19 0 O43396;K7ER96;K7EML9 O43396 TXNL1 Thioredoxin-like protein 1 0 ;;; 271.73 2.47E-39 4674860000 1710150 1888130 1473290 1942080 1811630 1863050 1686520 1719310 1873600 1869000 FALSE TRUE 1643315.447 1834282.381 1739546.276 2042310.982 1869902.724 1900722.147 1707160.136 1683805.648 1660916.783 1742410.965 0.943127356 1.052726606 0.998355905 1.172117843 1.073169741 1.090857545 0.979768935 0.966365388 0.953229069 1 20.73265351 2.167408136 7.107376799 0.970855777 1.058413783 0.321655548 0.056884314 0.260542772 21.51869388 0.021880446 0.016162851 147.0307376 -2.167408136 0.087558006 S(ph)S(ph)QDVS(ph)LDS(ph)NSNSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSQDVSLDSNSNSK 14 0 Q96Q89-3;Q96Q89;Q96Q89-2;Q96Q89-4 Q96Q89-3 KIF20B Kinesin-like protein KIF20B 4 S(0.999)S(0.999)QDVS(0.999)LDS(0.999)NS(0.002)NSK 56.793 0.055065 255040000 63285 87388 95136 140310 147740 126800 222100 361540 164410 317460 TRUE FALSE 60811.75223 84895.7798 112329.1915 147551.4159 152492.1913 129363.9829 224818.1262 354074.0727 145746.8661 295958.1514 0.205474159 0.286850622 0.379544172 0.498554999 0.515249168 0.43710228 0.759628093 1.196365334 0.492457685 1 18.17503367 2.167616803 3.444917033 0.930142274 0.3886146 0.615455406 0.185391815 0.148066797 3.525009409 0.075382223 0.053654056 147.1013991 -2.167616803 -0.541527674 KVGDDIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVGDDIAK 8 1 P30050 P30050 RPL12 60S ribosomal protein L12 0 ; 79.16 0.046108 2355700000 4281100 4118800 3432100 3626400 3970100 4353500 4645100 5185800 6086800 5446900 FALSE TRUE 4113789.879 4001335.857 4052356.817 3813558.939 4097801.872 4441530.753 4701948.123 5078711.418 5395851.982 5077976.611 0.810123834 0.787978394 0.798025892 0.750999705 0.806975334 0.874665461 0.925949149 1.000144705 1.062598825 1 22.27582232 2.167673616 1.239601802 1.032062865 0.786334347 0.94990199 0.023080174 0.090704594 0.265307418 0.015618346 0.008358121 147.1206437 -2.167673616 -0.245728517 EGEIIHLISK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGEIIHLISK 10 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ;; 127.42 0.00035647 688030000 1797840 1781450 1537770 1678790 1714210 1787570 1833500 1996740 2109050 2121800 FALSE TRUE 1727578.425 1730644.79 1815679.247 1765432.553 1769349.121 1823715.89 1855938.921 1955506.621 1869639.486 1978088.596 0.873357457 0.874907622 0.917895816 0.892494177 0.894474153 0.921958649 0.938248633 0.988583942 0.945174796 1 20.91567561 2.167935919 0.79805496 0.989286825 0.885184087 0.828776327 0.017297288 0.244299296 0.294264564 0.014228105 0.008151845 147.2095275 -2.167935919 -0.104102738 DRTEEEEISLIHFFGEEYLEYK ddPTM_BT-474_Pertuzumab_2h_R1 1 DRTEEEEISLIHFFGEEYLEYK 22 1 O60725 O60725 ICMT Protein-S-isoprenylcysteine O-methyltransferase 0 117.74 7.28E-05 17225000 9654.5 14982 8373.4 16979 11441 12213 16382 20733 19541 12433 FALSE TRUE 9277.191466 14554.72803 9886.659645 17855.28822 11809.01016 12459.95523 16582.48782 20304.8563 17322.7876 11590.90184 0.800385647 1.255702812 0.852967248 1.540457203 1.0188172 1.074977202 1.430646903 1.751792621 1.494515944 1 13.5007052 2.168025561 4.870034801 1.518544893 1.104265871 0.24197469 0.265105257 0.222992892 9.952738603 0.096495955 0.070941105 147.2399161 -2.168025561 -0.414279022 ESQNTAEIISPPS(ph)PDRPPHSQTSGSCYYHVISK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESQNTAEIISPPSPDRPPHSQTSGSCYYHVISK 33 1 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 ESQNTAEIIS(0.002)PPS(0.998)PDRPPHSQTSGSCYYHVISK;ES(0.001)QNTAEIIS(0.047)PPS(0.699)PDRPPHS(0.042)QT(0.042)S(0.042)GS(0.042)CY(0.04)Y(0.04)HVIS(0.004)K 154.54 5.82E-11 400530000 154776 177125 102173 145426 171611 122891 120526 97989 105114 104215 TRUE FALSE 148727.1828 172073.5684 120637.9339 152931.4533 177131.0237 125375.9402 122001.0332 95965.49291 93181.89939 97156.42522 1.530801308 1.771098185 1.241687656 1.574074519 1.823152954 1.290454439 1.255717601 0.987742115 0.959091477 1 16.56802179 2.168273693 1.651244671 0.979675799 1.574183385 0.723048067 0.159133604 0.198164212 1.05200221 0.090371302 0.051780793 147.3240649 -2.168273693 0.594507586 AGTEKLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGTEKLR 7 1 A0A0G2JR78;Q9NY99-2;Q9NY99 A0A0G2JR78 SNTG2 Gamma-2-syntrophin 0 125.86 0.0036557 905770000 728310 804020 597760 713930 710740 713310 799230 847760 913080 910530 FALSE TRUE 699846.84 781090.1368 705788.5291 750776.0129 733601.5976 727733.6169 809011.2158 830253.4597 809430.9863 848858.9921 0.824455942 0.920164767 0.831455561 0.884453154 0.8642208 0.857308014 0.953057249 0.978081716 0.953551761 1 19.6951654 2.168302356 4.420167557 0.972499425 0.865588344 0.788342196 0.027407699 0.089323579 3.368129191 0.009745022 0.007132356 147.3337885 -2.168302356 -0.106911081 ASS(ph)LEDLVLK ddPTM_BT-474_Pertuzumab_2h_R1 8 ASSLEDLVLK 10 0 Q15477 Q15477 SKIV2L Helicase SKI2W 1 ASS(1)LEDLVLK;ASS(1)LEDLVLK;AS(0.004)S(0.996)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK 301.58 1.58E-32 8728633000 8218940 8383330 6992700 7419560 7483160 8203820 8549370 9403030 10181410 9821630 TRUE FALSE 7897734.738 8144245.637 8256436.442 7802484.381 7723862.637 8369706.861 8653999.747 9208854.145 9025659.021 9156402.252 0.862536892 0.889459136 0.901711853 0.852134295 0.843547763 0.914082478 0.945131014 1.005728439 0.985721113 1 23.12634941 2.168482965 1.900805053 0.997326295 0.872299072 0.898728157 0.018489033 0.102642984 0.730806447 0.010208038 0.006125634 147.3950724 -2.168482965 -0.125027223 EEIVDKYDLFVGSQATDFGEALVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEIVDKYDLFVGSQATDFGEALVR 24 1 O43852;O43852-3;O43852-15;O43852-6;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4;O43852-8 O43852;O43852-2 CALU Calumenin 0 ; 243.76 9.76E-38 2954700000 2783010 2875870 2458300 2969360 2726190 2869680 3231080 3515920 3759680 3754530 FALSE TRUE 2674246.892 2793853.003 2902569.495 3122609.025 2813880.377 2927706.896 3270622.924 3443315.023 3332896.888 3500232.339 0.764019823 0.798190729 0.829250522 0.892114786 0.803912456 0.83643216 0.934401664 0.983738989 0.952193045 1 21.73901926 2.168614485 2.726491937 0.975283893 0.820498074 0.836380347 0.032330541 0.111131422 1.669432553 0.015025909 0.01014479 147.4397159 -2.168614485 -0.15478582 TSPADGKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPADGKPR 9 1 Q12955;A0A087WY90;H0Y951;A0A087WX55;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 0 ; 93.551 0.0085023 158102000 341370 339840 248050 299650 289520 308560 339700 373880 393080 367280 FALSE TRUE 328028.883 330148.0959 292878.1528 315114.9724 298832.6737 314799.2946 343857.3502 366159.2473 348459.2063 342403.7985 0.958017652 0.964206873 0.855358948 0.92030221 0.872749295 0.919380264 1.004245139 1.069378462 1.01768499 1 18.38533918 2.16868318 3.700140473 1.03659101 0.912208685 0.69151704 0.035400255 0.12107233 3.303654458 0.014504614 0.010442752 147.4630389 -2.16868318 -0.124382325 RT(ph)PDSTFSETFK ddPTM_BT-474_Pertuzumab_2h_R1 5 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RT(0.955)PDS(0.045)TFSETFK;RT(0.982)PDS(0.018)TFSETFK;RT(0.992)PDS(0.008)TFSETFK;RT(0.96)PDS(0.039)T(0.001)FSETFK;RT(0.991)PDS(0.009)TFSETFK 214.63 2.54E-11 4120510000 3103260 2950780 2506870 2635650 2753960 2927980 3091730 3441520 3611850 3535830 TRUE FALSE 2981981.168 2866626.644 2959917.174 2771676.212 2842543.624 2987185.762 3129567.517 3370451.409 3201847.93 3296345.085 0.904632583 0.869637908 0.897939111 0.840833147 0.862331932 0.906211481 0.949405307 1.022481361 0.971332748 1 21.65243585 2.168842091 2.227402649 0.999411236 0.874946561 0.863178686 0.021371699 0.09880496 0.979188175 0.01017561 0.006447518 147.5170067 -2.168842091 -0.124464676 NNTAAET(ph)EDDES(ph)DGEDRGGGTSGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 2 NNT(0.216)AAET(0.784)EDDES(1)DGEDRGGGTSGVR 63.008 0.050864 0 64963 80717 60593 61105 75829 72323 53134 44950 66014 51473 TRUE FALSE 62424.17414 78415.03019 71543.50298 64258.63637 78268.10865 73785.42061 53784.26979 44021.76679 58520.36747 47986.68786 1.300864405 1.634099657 1.490903127 1.33909297 1.631037943 1.537622701 1.120816464 0.917374563 1.219512537 1 15.55034662 2.168926603 4.831584656 1.03425984 1.495474746 0.739315957 0.123699023 0.095288901 4.21599516 0.045876793 0.033728397 147.5457157 -2.168926603 0.461214906 GAGDGS(ph)DEEVDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GAGDGSDEEVDGK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 1 GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK 220.85 2.11E-11 2900500000 1763640 1632530 1760370 2055580 1702930 1797850 2285170 2488700 2717800 2643500 TRUE FALSE 1694714.999 1585971.843 2078508.018 2161668.73 1757706.29 1834203.759 2313136.594 2437307.475 2409286.738 2464453.39 0.687663644 0.643538989 0.843395142 0.877139222 0.713223588 0.744263927 0.93860026 0.988985016 0.977615055 1 21.23283627 2.169070722 4.143238502 0.982135803 0.754214967 0.74337164 0.065045877 0.122861103 4.134505292 0.028023112 0.02042349 147.5946861 -2.169070722 -0.227920835 AKEPAGENGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AKEPAGENGGR 11 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ;;; 165.58 1.95E-05 616720000 466688 759430 436565 877130 489160 588710 794190 1004550 852740 670760 FALSE TRUE 448449.317 737771.8 515462.0068 922398.7844 504894.2756 600614.1196 803909.5348 983805.6915 755940.5302 625328.8277 0.717141602 1.179814151 0.824305524 1.475061989 0.807406045 0.960477261 1.285578881 1.573261375 1.208868833 1 19.2542555 2.169218688 5.494264249 1.347495266 1.008377086 0.2039467 0.245136687 0.24807923 13.7354104 0.089041534 0.065679353 147.6449809 -2.169218688 -0.339118181 TAPAAPAEDAVAAAAAAPSEPSEPS(ph)RPSPQPKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPSEPS(0.107)EPS(0.513)RPS(0.38)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.024)EPS(0.564)RPS(0.412)PQPKPR 163.43 1.52E-14 1258630000 576830 576950 414510 455980 459240 501000 565720 636630 629380 622940 TRUE FALSE 554286.8459 560495.9509 489421.1777 479513.1824 474011.8717 511130.5633 572643.4506 623483.368 557935.421 580747.7189 0.954436544 0.965128114 0.842743177 0.825682421 0.816209614 0.880124961 0.986045114 1.073587287 0.960719092 1 19.14755206 2.169289758 4.117517638 1.021417887 0.876966325 0.566986649 0.05320047 0.158820968 5.287625643 0.022913978 0.016693084 147.6691442 -2.169289758 -0.144451562 GPHVDVSGPDIDIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 GPHVDVSGPDIDIEGPEGK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 274.23 2.12E-39 2805710000 2607460 2612910 2564930 2927980 2429820 2734970 2997660 3287650 3480540 3325110 FALSE TRUE 2505557.581 2538392.365 3028469.908 3079093.399 2507977.367 2790272.967 3034346.26 3219758.879 3085443.691 3099897.338 0.808271148 0.818863365 0.97695813 0.99328883 0.80905175 0.900117863 0.978853791 1.038666294 0.995337379 1 21.56378901 2.169538402 3.42191037 1.014134076 0.886308158 0.479907363 0.061290323 0.223923347 5.273264779 0.026839618 0.01910666 147.7537124 -2.169538402 -0.127825917 DSFIENSSSNCTSGSSKPNS(ph)PSIS(ph)PSILSNTEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSFIENSSSNCTSGSSKPNSPSISPSILSNTEHK 34 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 2 DSFIENSSSNCTSGSSKPNS(1)PS(0.003)IS(0.982)PS(0.015)ILSNTEHK 194.79 4.88E-21 312060000 214020 260770 225160 239010 247390 309700 350380 315550 469690 433520 TRUE FALSE 205655.8618 253333.0949 265851.4207 251345.3347 255347.524 315962.3462 354668.0553 309033.7822 416372.7603 404157.3043 0.508851033 0.626818054 0.657791948 0.62189977 0.631802324 0.781780616 0.877549537 0.76463738 1.030224509 1 18.6245574 2.16954104 0.482629924 1.018775091 0.555778068 0.846500417 0.06446444 0.371605298 0.188020151 0.063716296 0.056978485 147.7546102 -2.16954104 -0.462997023 EIQMDS(ph)PMLLADLPDLQDP ddPTM_BT-474_Pertuzumab_2h_R1 2 EIQMDSPMLLADLPDLQDP 19 0 Q13164-2;Q13164 Q13164-2 MAPK7 Mitogen-activated protein kinase 7 1 EIQMDS(1)PMLLADLPDLQDP;EIQMDS(1)PMLLADLPDLQDP 74.769 0.0161 26614000 73741 83770 69919 87965 80870 84685 66765 59915 75759 79543 TRUE FALSE 70859.1202 81380.96162 82554.91864 92504.88419 83471.25699 86397.38872 67582.09004 58677.73431 67159.15593 74155.48176 0.955547972 1.097436895 1.113267916 1.24744499 1.125624903 1.165084316 0.911356631 0.791279794 0.905653289 1 16.17826572 2.169744322 5.501636064 0.871218639 1.122445308 0.604533443 0.084161329 0.122047439 6.802707741 0.032477214 0.023959869 147.8237864 -2.169744322 0.251226669 HSPIAPSS(ph)PSPQVLAQK ddPTM_BT-474_Pertuzumab_2h_R1 3 HSPIAPSSPSPQVLAQK 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 HSPIAPS(0.019)S(0.975)PS(0.006)PQVLAQK;HSPIAPS(0.005)S(0.973)PS(0.022)PQVLAQK;HSPIAPS(0.002)S(0.967)PS(0.031)PQVLAQK 206.64 4.38E-12 1009440000 1838280 1796140 1322130 1744390 1577790 1394700 1546540 1142880 1266920 1390090 TRUE FALSE 1766437.985 1744915.846 1561068.302 1834418.177 1628541.048 1422901.79 1565467.019 1119279.129 1123104.553 1295937.966 1.363057516 1.346450132 1.204585669 1.415513879 1.256650465 1.097970603 1.207979903 0.863682644 0.866634501 1 20.30556523 2.169790814 1.117016387 0.89229599 1.322546435 0.779770629 0.088815255 0.213042169 0.502703049 0.061510341 0.032712694 147.8396121 -2.169790814 0.430250445 S(ph)ESPMQEIVTDDGENLRPIVIDGSNVAMSHGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SESPMQEIVTDDGENLRPIVIDGSNVAMSHGNK 33 1 E9PP00;Q9C0D7;Q9C0D7-2 E9PP00 ZC3H12C Probable ribonuclease ZC3H12C 1 S(0.515)ES(0.483)PMQEIVT(0.002)DDGENLRPIVIDGSNVAMSHGNK 78.499 0.0010279 40018000 22754 20165 19438 19895 20827 17207 25749 30187 23648 27695 TRUE FALSE 21864.74852 19589.91394 22950.879 20921.78333 21496.91937 17554.93733 26064.12396 29563.6279 20963.57818 25819.19298 0.846840896 0.758734557 0.888907682 0.810319027 0.83259455 0.679918127 1.009486392 1.14502525 0.811937778 1 14.65615629 2.170007967 9.975145314 1.019688596 0.806577628 0.486710752 0.093145975 0.289341357 39.9909134 0.03419325 0.02525906 147.9135522 -2.170007967 -0.213110967 KIPDPDS(ph)DDVSEVDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KIPDPDSDDVSEVDAR 16 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0;A0A2R8Y583 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KIPDPDS(1)DDVSEVDAR;KIPDPDS(1)DDVSEVDAR;KIPDPDS(1)DDVSEVDAR;KIPDPDS(1)DDVSEVDAR 169.85 3.36E-09 3364990000 1624240 1581340 1400760 1584260 1669480 1549960 1808330 1975450 2027560 1958540 TRUE FALSE 1560762.905 1536241.731 1653908.492 1666023.848 1723180.34 1581301.253 1830460.883 1934656.267 1797399.889 1825886.341 0.854797404 0.841367667 0.905811306 0.912446635 0.943750058 0.866045831 1.002505382 1.059571028 0.984398562 1 20.80016553 2.170040984 5.522656879 1.02297843 0.889888842 0.763941051 0.03369237 0.096132235 5.407055525 0.013556945 0.010002908 147.9247978 -2.170040984 -0.133089588 RDENWDKEIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDENWDKEIEK 11 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 136.24 5.81E-05 877520000 577179 563610 385169 377951 476905 477042 515388 546797 580850 593630 FALSE TRUE 554622.2066 547536.3946 454777.6063 397457.0964 492245.0824 486688.1161 521695.4725 535505.4509 514914.3431 553422.9113 1.00216705 0.989363439 0.821754208 0.718179693 0.889455554 0.87941447 0.942670536 0.967624289 0.930417467 1 19.07802285 2.170054365 3.373057241 0.961296271 0.877574312 0.19414317 0.076945386 0.447115868 10.2466342 0.034927041 0.024810485 147.9293554 -2.170054365 -0.083721958 EANNFLWPFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EANNFLWPFK 10 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 140.45 9.14E-05 705720000 1167950 1222360 1129350 1196430 1195570 999750 1376860 1421330 1414580 1588960 FALSE TRUE 1122305.223 1187499.49 1333448.667 1258177.896 1234026.595 1019965.63 1393710.425 1391979.039 1254002.809 1481338.324 0.757629236 0.801639619 0.900164835 0.849352154 0.83304845 0.688543335 0.940845452 0.939676653 0.846533698 1 20.49846975 2.17014225 24.9999606 0.928627997 0.812512188 0.487788624 0.063297291 48.70139072 17794.53694 0.023925396 0.01767008 147.959294 -2.17014225 -0.116115809 AKNS(ph)PPQAPSTR ddPTM_BT-474_Pertuzumab_2h_R1 5 AKNSPPQAPSTR 12 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR 124.5 0.00019497 2665600000 918680 955190 801270 886970 854100 976090 1004550 1101540 1215380 1189270 TRUE FALSE 882776.9699 927948.9164 946077.3132 932746.628 881572.9022 995827.2086 1016843.983 1078792.814 1077415.158 1108719.684 0.79621295 0.836955391 0.85330614 0.841282645 0.795126952 0.898177622 0.917133518 0.973007722 0.971765157 1 20.08046323 2.17020287 1.277507857 0.986292031 0.826836204 0.904842691 0.021982092 0.128037501 0.398866317 0.014448936 0.007784188 147.9799478 -2.17020287 -0.159455827 EILSPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 EILSPLR 7 0 A0A140T9S5;Q9Y334-2;Q9Y334 A0A140T9S5 VWA7 von Willebrand factor A domain-containing protein 7 0 ;; 99.919 0.046579 794480000 1081730 1186920 932800 990940 1055220 999970 840590 897640 810920 864840 FALSE TRUE 1039454.796 1153070.204 1101377.71 1042082.532 1089162.11 1020190.079 850877.3919 879103.4203 718867.7613 806263.6165 1.289224485 1.430140441 1.366026803 1.292483638 1.350875926 1.265330666 1.055333981 1.090342417 0.891603871 1 19.62089209 2.170211174 1.155073077 0.968138923 1.35926424 0.885717678 0.057770935 0.145186737 0.367127411 0.038647225 0.020587793 147.9827772 -2.170211174 0.391125317 KIS(ph)LEDIQAFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KISLEDIQAFEK 12 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 1 KIS(1)LEDIQAFEK;KIS(1)LEDIQAFEK 183.77 9.29E-06 347142000 1042630 793760 508508 727345 977430 820290 1080340 1351820 1220300 1186220 TRUE FALSE 1001882.867 771122.742 600406.7073 764883.3626 1008869.924 836876.8258 1093561.524 1323904.445 1081776.66 1105876.263 0.905962901 0.697295681 0.542923949 0.691653658 0.912281019 0.756754489 0.988864271 1.197154229 0.978207686 1 20.07675854 2.170303709 3.279975012 1.083983432 0.740560524 0.604888155 0.114911861 0.156725918 3.402669188 0.049748122 0.035161951 148.0143115 -2.170303709 -0.343422908 SPSVPKS(ph)PTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSVPKSPTPK 11 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 SPSVPKS(0.903)PT(0.097)PK;SPSVPKS(0.5)PT(0.5)PK 122.97 0.00023 2491000000 2004640 1809690 1760840 1690070 2158680 2087370 2157800 2631500 2967200 2756800 TRUE FALSE 1926296.453 1758079.413 2079062.958 1777294.715 2228115.903 2129578.052 2184207.802 2577158.605 2630375.896 2570079.48 0.749508514 0.684056437 0.808948896 0.691532977 0.866944357 0.828603966 0.849860021 1.002754438 1.023460915 1 21.29338155 2.170740987 0.780540012 1.033874195 0.733911518 0.826878367 0.04942364 0.238052721 0.274990742 0.039338309 0.022843097 148.1634177 -2.170740987 -0.299962676 AKS(ph)LDGVTNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AKSLDGVTNDR 11 1 Q9UBM7;E9PRL8;E9PQ71;E9PIP9;E9PJ54;E9PM00 Q9UBM7 DHCR7 7-dehydrocholesterol reductase 1 AKS(1)LDGVTNDR;AKS(0.998)LDGVT(0.002)NDR 103.16 0.0016787 741770000 795580 1002280 420800 1032110 870540 767740 1230130 1614710 1429940 922230 TRUE FALSE 764487.854 973695.9557 496847.9206 1085377.321 898541.7097 783264.2288 1245184.699 1581365.674 1267619.206 859766.5407 0.889180746 1.132512036 0.577887016 1.262409351 1.045099649 0.911019668 1.448282342 1.839296599 1.474376061 1 19.71358544 2.170899606 5.138220921 1.555046949 0.975947154 0.416975153 0.260907485 0.155924483 7.7833073 0.095438783 0.070341919 148.2175419 -2.170899606 -0.579099794 VVPQQITHTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 VVPQQITHTSPR 12 0 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 VVPQQITHT(0.475)S(0.525)PR 138.33 4.92E-05 184960000 189570 225630 172230 220900 221200 218910 183620 181600 200710 204050 TRUE FALSE 182161.3948 219195.2533 203355.7922 232300.6755 228315.0989 223336.5102 185867.1965 177849.8965 177926.2422 190229.5118 0.957587459 1.152267339 1.069002335 1.221160026 1.200208615 1.174037131 0.977068147 0.934922741 0.935324076 1 17.53738155 2.171192741 5.878940179 0.952124415 1.134628601 0.560232062 0.072443683 0.144965637 9.178687625 0.027916306 0.020618086 148.3176177 -2.171192741 0.182504186 YDEIVK ddPTM_BT-474_Pertuzumab_2h_R1 5 YDEIVK 6 0 A0A2U3TZH3;Q05639;A0A2R8Y488 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;;; 115.3 0.057112 1929420000 2816180 2734710 2464950 2788650 2810730 2877650 3192170 3581930 3827220 3733380 FALSE TRUE 2706120.572 2656718.748 2910421.298 2932572.561 2901139.683 2935838.055 3231236.731 3507961.894 3392770.031 3480514.847 0.777505826 0.763312 0.836204247 0.842568611 0.833537511 0.843506833 0.928378953 1.007885916 0.974789702 1 21.7308693 2.171228259 1.480930608 1.001397614 0.807930519 0.914066639 0.025047144 0.116370678 0.492936852 0.016717199 0.00930847 148.3297482 -2.171228259 -0.193467095 RPQLDLDILSSLIDLCDSPVS(ph)PAEASR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPQLDLDILSSLIDLCDSPVSPAEASR 27 1 Q9BQ89 Q9BQ89 FAM110A Protein FAM110A 1 RPQLDLDILSSLIDLCDS(0.001)PVS(0.999)PAEASR 144.86 1.02E-07 161770000 55616 62577 54705 68294 80219 84386 52614 64252 57824 57637 TRUE FALSE 53442.46523 60792.36523 64591.41041 71818.66152 82799.31699 86092.34274 53257.90587 62925.17375 51260.06194 53733.19465 0.994589389 1.131374481 1.202076497 1.336579036 1.540934194 1.60221895 0.991154652 1.17106705 0.953973838 1 15.71352599 2.1713861 24.99999789 1.055129958 1.301572651 0.358949253 0.176867459 74.36900853 27676.34731 0.073519187 0.054297529 148.383667 -2.1713861 0.246442694 S(ph)ESETSTMAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SESETSTMAAK 11 0 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.999)ES(0.001)ETSTMAAK;S(0.981)ES(0.019)ETSTMAAK;S(1)ESETSTMAAK 265.82 5.78E-21 1157530000 906700 739320 638020 778140 793080 792990 847190 972370 975150 885090 TRUE FALSE 871265.1616 718235.3175 753324.4067 818299.8987 818590.1385 809024.8011 857558.1646 952290.2197 864455.0602 825142.0659 1.055897157 0.870438373 0.91296328 0.991707892 0.992059637 0.980467285 1.039285476 1.154092439 1.04764391 1 19.65428301 2.171515557 3.055561975 1.086538224 0.960914643 0.359273635 0.059556502 0.220358722 4.165125492 0.024993499 0.01741952 148.4279049 -2.171515557 -0.125623581 S(ph)LENFFLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLENFFLR 8 0 Q6ZMT1;J3QKZ0 Q6ZMT1 STAC2 SH3 and cysteine-rich domain-containing protein 2 1 S(1)LENFFLR;S(1)LENFFLR;S(1)LENFFLR 115 0.0026719 98646000 50917.7 40494.7 38897.5 53542.4 55451.5 40554.6 68493 83268 67541 72460 TRUE FALSE 48927.77999 39339.8308 45927.14352 56305.72968 57235.14786 41374.6418 69331.23782 81548.4867 59874.02883 67552.21966 0.724295667 0.582361779 0.679876157 0.833514131 0.847272645 0.612483824 1.026335451 1.207191816 0.886336957 1 16.04371555 2.171551293 6.723704991 1.06737556 0.717768343 0.664621998 0.109046759 0.120837159 9.637127368 0.042342334 0.031292193 148.4401187 -2.171551293 -0.349607217 IGIARPEEEFHVPLDSYR ddPTM_BT-474_Pertuzumab_2h_R1 1 IGIARPEEEFHVPLDSYR 18 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 59.003 0.047621 96831000 49459 57731 46238 54957 54830 54400 50571 51487 54239 57445 FALSE TRUE 47526.0876 56084.5684 54594.23516 57793.33736 56593.65675 55500.00527 51189.90303 50423.77546 48082.01611 53554.19898 0.887439052 1.047248759 1.019420255 1.079156041 1.056754798 1.036333403 0.955852277 0.941546628 0.897819723 1 15.70871208 2.171979456 4.955851442 0.942348349 1.026460558 0.29807497 0.053827544 0.230575113 10.86763328 0.020414173 0.015037398 148.5865352 -2.171979456 0.084112209 REEAEESGPQLAPLGAPAPEPKPEPEPPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 REEAEESGPQLAPLGAPAPEPKPEPEPPAR 30 2 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ;; 197.83 1.49E-25 2703120000 2342307 2108451 1992834 2205293 2198069 2272401 2431269 2766019 2845760 2667457 FALSE TRUE 2250767.053 2048320.042 2352983.434 2319108.436 2268771.886 2318350.505 2461023.597 2708899.741 2522721.255 2486787.761 0.905090128 0.823681085 0.94619391 0.932571919 0.912330325 0.932267136 0.989639581 1.089316822 1.014449763 1 21.24585195 2.172192701 2.545469216 1.044060879 0.905011793 0.693774646 0.038119515 0.148172124 1.937019481 0.017621263 0.011696501 148.6595112 -2.172192701 -0.139049086 DKEADEEGGENGPADQGFQPQEEEEREDS(ph)DTEEQVPEALER ddPTM_BT-474_Pertuzumab_2h_R1 1 DKEADEEGGENGPADQGFQPQEEEEREDSDTEEQVPEALER 41 2 Q9NU22 Q9NU22 MDN1 Midasin 1 DKEADEEGGENGPADQGFQPQEEEEREDS(0.945)DT(0.055)EEQVPEALER 95.51 7.10E-05 182500000 31043 22475 19803 21018 28258 24864 27049 32027 31987 34009 TRUE FALSE 29829.80524 21834.03501 23381.84262 22102.7415 29166.94423 25366.76712 27380.03375 31365.63126 28355.96986 31705.54014 0.940838892 0.688650466 0.737468673 0.697125531 0.919932104 0.800073647 0.863572538 0.989279196 0.894353786 1 14.95244733 2.172382029 0.882166248 0.977519535 0.769595631 0.43483389 0.082918686 0.517204666 0.757323427 0.063937777 0.035262478 148.7243328 -2.172382029 -0.207923904 RNSTIPTK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSTIPTK 8 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ; 104.42 0.0073486 1587940000 1565030 1626370 1292230 1535660 1525530 1784730 1732750 1903940 2146270 2182890 FALSE TRUE 1503866.897 1579987.52 1525764.707 1614915.597 1574600.058 1820818.463 1753955.913 1864622.974 1902634.427 2035040.916 0.738986074 0.776391034 0.749746452 0.793554362 0.773743685 0.894733098 0.861877468 0.916258223 0.934936695 1 20.95662637 2.172588052 0.467972473 0.998920751 0.734510513 0.930143491 0.022533124 0.225448045 0.108680562 0.021410891 0.019887161 148.794902 -2.172588052 -0.264410239 AEDMYSAQSHQAAT(ph)PPKDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 AEDMYSAQSHQAATPPKDGK 20 1 A8MXZ4;J9JIE0;A0A0C4DFY5;Q9NQ84;Q9NQ84-2 A8MXZ4 GPRC5C G-protein coupled receptor family C group 5 member C 1 AEDMYSAQSHQAAT(0.999)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK 193.88 8.40E-18 2308730000 1053022 1316774 939553 1259270 931819 1048063 1537544 1682040 1988520 1578930 TRUE FALSE 1011868.736 1279220.895 1109351.127 1324261.076 961791.8044 1069255.552 1556360.923 1647305.286 1762791.546 1471987.665 0.687416587 0.869043216 0.753641592 0.899641422 0.653396647 0.726402522 1.05731927 1.119102643 1.19755864 1 20.48933415 2.173325937 5.113252198 1.110055851 0.770170946 0.787219322 0.083755782 0.086938839 4.376120872 0.031316732 0.023097961 149.0479258 -2.173325937 -0.339884905 PSPAQQTDRS(ph)SPVRPSSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 PSPAQQTDRSSPVRPSSEK 19 2 B3KV94;A0A3B3ISE6;A0A3B3ITA8;A0A3B3ITJ7;A0A3B3ITE7;A0A3B3IT25;A0A3B3IS40;Q9UGL1;Q9UGL1-2 B3KV94 KDM5B Lysine-specific demethylase 5B 1 PSPAQQTDRS(0.5)S(0.5)PVRPSSEK;PSPAQQT(0.002)DRS(0.825)S(0.173)PVRPSSEK 226.81 7.39E-20 833240000 699620 535000 530290 532970 634970 571070 699920 762140 857930 693950 TRUE FALSE 672278.0769 519742.3238 626125.1992 560476.6456 655394.3867 582617.4267 708485.8303 746401.5427 760541.3831 646948.1484 1.03915295 0.803375549 0.967813573 0.866339361 1.01305551 0.900562786 1.09511996 1.153726994 1.175583213 1 19.30329056 2.173537779 5.173687783 1.125505828 0.928209942 0.542461992 0.077902704 0.131293649 6.762365277 0.02750372 0.020292236 149.120647 -2.173537779 -0.197295886 VDKETNTETPAPS(ph)PTVVRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDKETNTETPAPSPTVVRPK 20 2 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 VDKETNTETPAPS(0.998)PT(0.002)VVRPK 173.47 2.52E-12 251920000 214410 246090 232470 218280 245110 240590 284810 315180 333290 327360 TRUE FALSE 206030.6202 239071.7541 274482.5003 229545.457 252994.1858 245454.8946 288295.59 308671.4229 295456.3165 305187.6156 0.675094957 0.783359946 0.89938938 0.752145386 0.828979201 0.80427541 0.944650357 1.011415297 0.968113715 1 18.21933689 2.173609555 2.945941084 0.992993042 0.792859199 0.751196062 0.054239237 0.130572171 2.296898647 0.023304899 0.016130235 149.1452942 -2.173609555 -0.200133842 AVLFCLSEDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVLFCLSEDKK 11 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 174.4 1.77E-05 23812000000 4622400 3593600 3051400 2685600 3309000 3229900 4261000 4841600 4935600 4194200 FALSE TRUE 4441751.498 3491114.047 3602855.858 2824204.138 3415436.99 3295210.791 4313147.393 4741619.268 4375331.38 3910123.098 1.135962062 0.892839933 0.921417502 0.722280109 0.873485797 0.842738376 1.103072022 1.212652172 1.118975354 1 21.8987826 2.174710593 5.837187418 1.138433693 0.88998516 0.466770777 0.108529183 0.157006755 10.17483368 0.041477503 0.030659503 149.5238921 -2.174710593 -0.248448533 VSQGVEDGPDTKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSQGVEDGPDTKR 13 1 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 128.76 0.00025899 2194700000 1488800 1438390 1084650 1233480 1369140 1379480 1418390 1569760 1718070 1604920 FALSE TRUE 1430616.05 1397368.526 1280670.383 1297140.051 1413179.632 1407374.031 1435748.681 1537343.907 1523041.896 1496217.339 0.956155241 0.933934188 0.855938739 0.866946276 0.944501574 0.940621388 0.959585646 1.027487028 1.017928249 1 20.51288832 2.175254064 1.358447424 1.019638904 0.9065368 0.675259937 0.030882526 0.258794834 0.917003141 0.021106209 0.011555698 149.7111217 -2.175254064 -0.113102104 KIIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 37 1 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 KIIPTLEEGLQLPS(0.997)PT(0.003)ATSQLPLESDAVECLNYQHYK 203.11 1.20E-30 1570100000 1154300 1230800 825800 852980 1041000 984290 688290 615660 699140 547480 TRUE FALSE 1109188.68 1195698.789 975040.4298 897002.4 1074484.71 1004193.018 696713.4989 602946.4059 619776.5582 510398.692 2.173180883 2.342676045 1.910350566 1.757454347 2.105187038 1.967467852 1.365037783 1.181324356 1.214298877 1 18.96126511 2.175342945 2.548579773 1.158489674 2.053741882 0.881499865 0.154995169 0.099601044 1.306603616 0.076157873 0.050719884 149.7417639 -2.175342945 0.895252207 LLCEQNEEEVSPQLFTFHEAVSQMVEMEEQVVEDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLCEQNEEEVSPQLFTFHEAVSQMVEMEEQVVEDHR 36 0 O00139-1;O00139-5;O00139;O00139-4;O00139-2 O00139-1 KIF2A Kinesin-like protein KIF2A 0 ; 276.85 1.96E-76 158781000 18631.6 18179.1 15799.5 23748.3 22575.4 19739.2 17204.8 14021.2 17437.1 24167.8 FALSE TRUE 17903.45647 17660.64987 18654.82111 24973.95261 23301.55824 20138.34015 17415.35749 13731.65732 15457.71351 22530.89338 0.794618135 0.783841527 0.82796633 1.108431529 1.034204807 0.893810104 0.772954592 0.60945907 0.686067492 1 14.4596169 2.175432366 3.9298351 0.716108742 0.913824858 0.175678761 0.135801513 0.287224152 8.90166104 0.055913577 0.040695887 149.7725989 -2.175432366 0.197716116 EGASGRPGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGASGRPGSPK 11 1 E7EMV7;A0A0A0MRZ4;Q15025-7;Q15025-8;Q15025-5;Q15025-6;Q15025-4;Q15025-3;Q15025-2;Q15025;E7EW15 E7EMV7 TNIP1 TNFAIP3-interacting protein 1 1 EGAS(0.001)GRPGS(0.999)PK;EGAS(0.158)GRPGS(0.842)PK;EGASGRPGS(1)PK;EGASGRPGS(1)PK 92.151 0.0064881 1202190000 1403100 1185110 972340 1050130 1140020 1150910 1403570 1538070 1695220 1524860 TRUE FALSE 1348265.301 1151311.823 1148063.468 1104327.335 1176689.779 1174182.189 1420747.31 1506308.317 1502785.733 1421579.874 0.948427398 0.80988191 0.807596878 0.776831014 0.827733848 0.825969902 0.999414339 1.059601606 1.057123669 1 20.43906373 2.175525865 3.858180549 1.042147358 0.82681958 0.819549169 0.04528693 0.085210409 2.549369867 0.017945488 0.013037597 149.8048468 -2.175525865 -0.215327778 AKT(ph)QTPPVS(ph)PAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 AKT(0.5)QT(0.5)PPVS(1)PAPQPTEERLPS(0.462)S(0.538)PVYEDAASFK 172.69 1.23E-13 1612700000 546220 558660 326520 331170 485820 613120 274830 305760 280280 249490 TRUE FALSE 524873.1185 542727.5638 385529.4274 348261.7234 501446.8415 625517.7065 278193.4518 299445.9492 248463.7894 232591.8201 2.256627591 2.333390588 1.657536483 1.497308561 2.155909186 2.689336651 1.196058622 1.287431127 1.068239585 1 17.82744083 2.175837865 12.85287346 1.17583504 2.064191588 0.676865535 0.324156839 0.643187711 130.506273 0.130945819 0.096719622 149.9125065 -2.175837865 0.888356548 VS(ph)PAHS(ph)PPENGLDK ddPTM_BT-474_Pertuzumab_2h_R1 6 VSPAHSPPENGLDK 14 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 2 VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK 231.21 9.11E-13 9094120000 4141840 3635990 3579010 3911220 3919890 3530290 4692970 4938040 5628390 5020470 TRUE FALSE 3979972.314 3532295.125 4225816.722 4113078.533 4045976.822 3601674.883 4750403.971 4836067.748 4989478.763 4680429.095 0.850343469 0.75469472 0.90286951 0.878782361 0.864445703 0.769518095 1.014950526 1.033253074 1.0660302 1 22.15820937 2.176014193 7.521432589 1.032362621 0.839393445 0.809357868 0.04559428 0.09824791 10.0226173 0.01733125 0.012815157 149.9733849 -2.176014193 -0.192969176 GATRPNGPNTGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GATRPNGPNTGNK 13 1 P20339-2;P20339;F8WCY6;F8WD79 P20339-2 RAB5A Ras-related protein Rab-5A 0 82.515 0.01107 40414000 29083 34916 26833 38447 29270 33292 38505 40864 47559 43236 FALSE TRUE 27946.40421 33920.22987 31682.32 40431.25428 30211.49613 33965.18705 38976.23571 40020.14412 42160.3017 40307.58721 0.69332863 0.841534615 0.786013805 1.003068084 0.749523805 0.842649967 0.966970201 0.99286876 1.045964411 1 15.29876381 2.176058637 2.804943067 1.008122788 0.821893813 0.58358286 0.076212786 0.199990398 3.190226525 0.03268554 0.022387699 149.9887333 -2.176058637 -0.186228975 S(ph)GSPRPTEPTDFLMLFEGSPSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.548)GS(0.451)PRPT(0.001)EPTDFLMLFEGSPSGK;S(0.5)GS(0.5)PRPTEPTDFLMLFEGSPSGK;S(0.497)GS(0.497)PRPT(0.002)EPT(0.003)DFLMLFEGSPSGK 182.64 2.35E-17 311385000 200489 194130 154471 165666 189559 217652 211930 239883 285909 267323 TRUE FALSE 192653.6682 188593.6025 182387.3459 174216.0421 195656.3374 222053.0726 214523.6627 234929.3322 253453.8089 249216.9751 0.773035898 0.756744609 0.731841584 0.699053674 0.785084312 0.891003 0.860790733 0.942669865 1.017000583 1 17.92704281 2.176146236 0.836404658 1.007775363 0.737226774 0.906867911 0.032892753 0.182398462 0.240769582 0.02838266 0.016009556 150.0189897 -2.176146236 -0.270548589 NDKSEEEQSSS(ph)SVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVK 14 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKSEEEQS(0.001)S(0.008)S(0.974)S(0.017)VK 160.47 2.88E-06 459790000 391340 267470 315440 270540 218540 289240 428980 495820 548670 438450 TRUE FALSE 376046.0002 259842.0175 372447.0249 284502.6018 225569.5376 295088.631 434229.9856 485581.1437 486387.2818 408753.391 0.919982582 0.635693852 0.911177823 0.696025056 0.551847502 0.721923383 1.062327543 1.187956246 1.189928433 1 18.64087117 2.176420192 4.321576904 1.140760468 0.731060433 0.708047357 0.116730574 0.108039271 4.031736113 0.045085611 0.033078338 150.1136526 -2.176420192 -0.409700035 GGSFWSSIPAS(ph)PASRPGSFTFPGDSDSLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGSFWSSIPASPASRPGSFTFPGDSDSLQR 30 1 O75962-5;O75962;E7EPJ7;O75962-4 O75962-5 TRIO Triple functional domain protein 1 GGSFWSS(0.002)IPAS(0.997)PASRPGSFTFPGDSDSLQR;GGSFWSSIPAS(0.998)PAS(0.002)RPGSFTFPGDSDSLQR 256.2 2.35E-58 995510000 357320 436870 359010 437200 430140 435630 317870 345830 279050 315710 TRUE FALSE 343355.5394 424410.8953 423891.0931 459763.9444 443975.8437 444438.7371 321760.1881 338688.4896 247373.4139 294326.6805 1.16657973 1.441972215 1.440206142 1.562087214 1.508445796 1.510018515 1.093207682 1.15072303 0.840472272 1 18.1670588 2.176711561 5.240705715 1.041194032 1.447327015 0.728590121 0.124584682 0.11275934 6.094635659 0.048940977 0.036157784 150.2143978 -2.176711561 0.406132984 IQQFDDGGS(ph)DEEDIWEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IQQFDDGGSDEEDIWEEK 18 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK 237.01 4.99E-24 255450000 782660 690350 617440 645530 705310 741160 760190 861250 944990 881330 TRUE FALSE 752072.7819 670661.8939 729025.1429 678845.8807 727996.9367 756146.763 769493.4326 843464.8865 837718.6969 821636.7341 0.915334905 0.816251107 0.887284018 0.826211697 0.886032606 0.920293278 0.936537281 1.026566671 1.019573082 1 19.64814116 2.176752159 1.296909598 1.021612281 0.86114376 0.818350987 0.030026783 0.160056318 0.515231032 0.018215811 0.009897472 150.2284406 -2.176752159 -0.160468522 TIEAAEALLHMES(ph)PTCLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TIEAAEALLHMESPTCLR 18 0 Q15723-2;Q15723-3;Q15723-1;Q15723;Q15723-4;D6RHI1 Q15723-2 ELF2 ETS-related transcription factor Elf-2 1 TIEAAEALLHMES(0.963)PT(0.037)CLR 74.698 0.060684 53385000 23475 36965 28786 42137 36858 30556 29955 26036 24963 33483 TRUE FALSE 22557.57105 35910.79439 33988.27054 44311.69562 38043.57104 31173.86326 30321.59825 25498.3475 22129.30489 31215.16659 0.722647787 1.150427767 1.088838352 1.419556596 1.21875278 0.998676819 0.971373905 0.816857646 0.708927977 1 14.92995954 2.176850692 1.954768171 0.829411395 1.131742898 0.302098919 0.177115269 0.386148014 2.92282337 0.093050096 0.056846179 150.2625283 -2.176850692 0.302331502 KSQS(ph)PS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSQSPSPK 8 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 KS(0.34)QS(0.859)PS(0.801)PK 76.143 0.024439 14359000 103150 79515 71146 59469 72140 81315 92715 111780 114210 93128 TRUE FALSE 99118.78396 77247.31005 84003.66483 62538.20222 74460.44862 82959.24501 93849.6739 109471.7039 101245.3596 86820.35761 1.141653717 0.889737294 0.967557231 0.720317261 0.857638124 0.955527566 1.080963918 1.260899021 1.166147692 1 16.40574574 2.177623365 3.01651914 1.170893579 0.907124154 0.425848716 0.116357045 0.207939109 3.842681334 0.049200805 0.03435925 150.5301053 -2.177623365 -0.263769426 TVSPQSNSS(ph)RPTCAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSPQSNSSRPTCAR 15 1 Q9H7N4;M0R3G4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 TVS(0.06)PQS(0.203)NS(0.239)S(0.469)RPT(0.029)CAR 121.13 0.00030767 57438000 38788 43039 34636 36895 40690 45059 35459 38521 37258 40277 TRUE FALSE 37272.12208 41811.56986 40895.49567 38799.15537 41998.8308 45970.12385 35892.95785 37725.52789 33028.62804 37549.00291 0.992626147 1.11352011 1.089123345 1.033293892 1.118507218 1.224270161 0.95589643 1.004701189 0.879613984 1 15.19648698 2.178538027 24.99999807 0.965023457 1.094022127 0.509491979 0.064894643 63.09836982 26280.47191 0.024208605 0.017879246 150.8474687 -2.178538027 0.12899867 RRT(ph)PS(ph)PPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RRTPSPPPR 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRT(1)PS(1)PPPR;RRT(1)PS(1)PPPR 72.496 0.051413 9698890000 315620 335070 286610 337210 287930 351540 295050 308900 345250 323810 TRUE FALSE 303285.2215 325514.1317 338406.8026 354613.4485 297191.5299 358648.3797 298660.9102 302521.1071 306058.6674 301878.0603 1.004661356 1.078296751 1.121004959 1.174691027 0.984475419 1.188057123 0.989342882 1.002130154 1.013848662 1 18.20360638 2.178573282 24.99999886 1.001139812 1.091456975 0.349645157 0.060487469 81.07735831 33788.55366 0.021751404 0.016064483 150.8597147 -2.178573282 0.090317163 DFTVSALHGDMDQK ddPTM_BT-474_Pertuzumab_2h_R1 7 DFTVSALHGDMDQK 14 0 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;;;;; 263.83 1.21E-24 5522110000 6533560 6709160 5763940 5981780 6344500 6863450 6429030 7065930 8165820 7411170 FALSE TRUE 6278221.252 6517821.326 6805612.176 6290500.383 6548576.604 7002233.662 6507710.392 6920016.076 7238870.348 6909204.855 0.908674932 0.943353318 0.98500657 0.910452145 0.947804667 1.013464474 0.941889918 1.001564756 1.047713955 1 22.72008826 2.178705909 0.728075734 1.020125983 0.937489733 0.494328751 0.031280337 0.611410061 0.620645887 0.026475476 0.01611018 150.905792 -2.178705909 -0.08263625 SINKLDS(ph)PDPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SINKLDSPDPFK 12 1 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 S(0.003)INKLDS(0.997)PDPFK 82.259 0.0093465 486130000 949100 742550 728240 637850 845300 817710 899490 1022900 1107700 1030900 TRUE FALSE 912008.1227 721373.201 859849.1676 670769.5149 872489.8422 834244.6565 910498.2277 1001776.758 981958.5399 961076.2248 0.94894463 0.750588957 0.894673227 0.697935812 0.907825852 0.868031728 0.947373584 1.042348912 1.021728053 1 19.87429133 2.17872455 1.59250318 1.02879545 0.829924526 0.566577743 0.070093119 0.250791279 1.238375892 0.037655803 0.021558944 150.9122694 -2.17872455 -0.198870924 FSDSTSKT(ph)PPQEELPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSDSTSKTPPQEELPTR 17 1 F6Q6H0;I6L8A6;Q99708-3;Q99708;Q99708-2 F6Q6H0 RBBP8 DNA endonuclease RBBP8 1 FSDS(0.237)T(0.19)S(0.19)KT(0.383)PPQEELPTR;FSDST(0.002)S(0.002)KT(0.995)PPQEELPTR 198.48 2.29E-11 1264710000 1585120 1551570 1157030 1293640 1379110 1418650 1460790 1578710 1599050 1665230 TRUE FALSE 1523171.758 1507320.743 1366131.059 1360404.915 1423470.326 1447336.075 1478667.585 1546109.087 1417532.548 1552442.489 0.981145369 0.970934997 0.879988192 0.876299718 0.916923065 0.932296098 0.952478173 0.995920363 0.913098268 1 20.56610839 2.178752859 3.118362021 0.970044696 0.922878602 0.206909553 0.038274267 0.396673466 7.839024178 0.016959693 0.011941699 150.9221066 -2.178752859 -0.047166093 LLQNGNS(ph)PAEVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLQNGNSPAEVAK 13 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 LLQNGNS(1)PAEVAK 155.88 1.20E-06 0 227370 233470 191970 207230 211190 225320 234130 267330 254470 277950 TRUE FALSE 218484.129 226811.6642 226663.2493 217925.1651 217983.1181 229876.1248 236995.353 261809.5421 225583.6324 259124.1989 0.843163741 0.875300976 0.87472822 0.841006614 0.841230264 0.887127199 0.914601392 1.010363151 0.870561813 1 17.98328423 2.178884555 2.568928966 0.961346636 0.857753065 0.588139536 0.037784021 0.182268198 2.433005957 0.016131666 0.01080486 150.9678796 -2.178884555 -0.103593571 GSPS(ph)PEKPDVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPSPEKPDVEK 12 1 Q7Z3Z5;Q93074-3;Q93074;Q93074-2 Q7Z3Z5 TNRC11;MED12 Mediator of RNA polymerase II transcription subunit 12 1 GS(0.445)PS(0.555)PEKPDVEK 63.062 0.04442 341630000 331410 292620 290490 297110 339950 348630 391920 414980 520320 476130 TRUE FALSE 318458.1308 284274.7641 342988.0049 312443.8827 350884.8005 355679.5375 396716.4342 406410.518 461255.455 443881.291 0.717439859 0.640429705 0.772702098 0.703890633 0.79049243 0.801294275 0.893744436 0.915583797 1.039141465 1 18.75981438 2.179014452 0.691642023 1.024484501 0.694234785 0.904804068 0.038306298 0.185335516 0.171292136 0.030887149 0.019482036 151.0130407 -2.179014452 -0.330249716 VADNS(ph)FDAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VADNSFDAKR 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 VADNS(1)FDAKR;VADNS(1)FDAKR 153.7 9.67E-06 1432780000 907520 863290 866190 715310 828330 873440 901650 1022660 931710 1087510 TRUE FALSE 872053.1151 838669.8144 1022729.801 752227.2348 854973.9867 891101.5552 912684.6624 1001541.714 825946.1868 1013851.979 0.860138495 0.827211301 1.008756527 0.741949762 0.843292714 0.878926681 0.900214904 0.987857926 0.814661513 1 19.95141561 2.179220863 2.982748958 0.934431364 0.8579461 0.157659942 0.077050651 0.463565989 8.381465674 0.031670277 0.02208799 151.0848309 -2.179220863 -0.076485264 KTS(ph)DANETEDHLESLICK ddPTM_BT-474_Pertuzumab_2h_R1 3 KTSDANETEDHLESLICK 18 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 KT(0.168)S(0.831)DANET(0.001)EDHLESLICK;KT(0.086)S(0.914)DANETEDHLESLICK;KT(0.212)S(0.788)DANETEDHLESLICK 303.65 5.37E-50 2538990000 2165000 2201610 1955200 2215890 3077170 2386480 1565840 1483380 1522180 1291080 TRUE FALSE 2080389.406 2138822.238 2308548.133 2330252.348 3176149.968 2434736.261 1585003.218 1452747.685 1349388.508 1203634.002 1.728423594 1.776970604 1.91798182 1.936014059 2.638800469 2.022821105 1.316848158 1.206967968 1.121095371 1 20.19896534 2.179352535 4.168100706 1.163446586 2.017541766 0.748653084 0.240403558 0.119513332 4.199276679 0.102825216 0.075377744 151.1306448 -2.179352535 0.85409518 IVLDSDAAEYGGHQR ddPTM_BT-474_Pertuzumab_2h_R1 3 IVLDSDAAEYGGHQR 15 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ;; 194.59 1.37E-11 683920000 665850 744590 566082 692310 631630 675790 555453 552298 611660 542247 FALSE TRUE 639827.8459 723355.0222 668385.6098 728040.2021 651946.9526 689454.9368 562250.8 540892.8533 542226.9211 505520.1277 1.265682237 1.430912406 1.32217408 1.440180444 1.289655776 1.363852593 1.112222381 1.069972932 1.072611932 1 18.94740901 2.179823281 3.776886626 1.062258485 1.356985218 0.865675246 0.055882458 0.072249827 2.091437695 0.020674455 0.015024678 151.2945489 -2.179823281 0.294726733 CLELFSELAEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 CLELFSELAEDK 12 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 172.8 8.09E-05 37164000 51751 56457 58588 60653 55898 58663 72907 81963 81811 85885 FALSE TRUE 49728.51371 54846.90164 69176.15488 63783.3086 57696.00994 59849.20605 73799.25767 80270.43541 72524.15826 80067.93245 0.621079029 0.685004595 0.863968292 0.796614907 0.720588233 0.747480349 0.921708047 1.002529139 0.905782828 1 16.28893693 2.180219638 3.872107124 0.96796732 0.742990255 0.731440293 0.065225873 0.123935805 3.772284258 0.027329991 0.01991899 151.4326903 -2.180219638 -0.224977066 LDS(ph)PPPSPITEASEAAEAAEAGNLAVSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 LDS(0.466)PPPS(0.466)PIT(0.067)EAS(0.001)EAAEAAEAGNLAVSSR;LDS(0.965)PPPS(0.015)PIT(0.018)EAS(0.002)EAAEAAEAGNLAVSSR 163.94 3.45E-12 149718000 56807 49440 43370 45993 49995 59708 80134 91544 106829 103257 TRUE FALSE 54586.91964 48030.01961 51207.92376 48366.70424 51603.13458 60915.33667 81114.70386 89653.58441 94702.21978 96263.31142 0.567058403 0.498944187 0.531956807 0.502441725 0.536062326 0.632799098 0.842633633 0.931337008 0.983783109 1 16.55469843 2.18028637 1.465823126 0.983245706 0.519503975 0.988477373 0.021497589 0.037178808 0.154528923 0.012699767 0.007113956 151.4559608 -2.18028637 -0.463741731 EKDDLS(ph)PQPLMTDFER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDDLSPQPLMTDFER 16 1 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 EKDDLS(1)PQPLMTDFER 111.45 0.00049412 406060000 149000 147100 124840 128020 138760 110510 163320 169380 181900 162400 TRUE FALSE 143176.9153 142904.852 147401.3651 134627.1275 143223.3414 112744.5879 165318.759 165882.2438 161251.4746 151400.5033 0.945683218 0.943886241 0.9735857 0.889211889 0.945989863 0.744677761 1.091930049 1.095651865 1.065065644 1 17.20801048 2.180471635 24.99997325 1.074503223 0.912806713 0.578377398 0.06485137 53.50249212 23025.58594 0.023787345 0.017568126 151.5205838 -2.180471635 -0.16169651 SRWS(ph)GSHQFEQLSGSILWMAPEVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRWSGSHQFEQLSGSILWMAPEVIR 25 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.064)RWS(0.917)GS(0.018)HQFEQLSGSILWMAPEVIR 183.8 1.21E-17 219630000 160980 151290 99958 82002 168480 116920 106220 83451 112370 98683 TRUE FALSE 154688.7236 146975.3573 118022.6342 86234.13305 173899.3122 119284.2025 107519.9521 81727.70769 99614.22869 91999.11251 1.68141539 1.597573643 1.282867094 0.937336575 1.89022815 1.296579926 1.168706406 0.888353218 1.0827738 1 16.48933232 2.180479569 2.678696441 0.988149491 1.451663831 0.425439759 0.243867012 0.273778627 3.982964642 0.109625871 0.074435504 151.5233521 -2.180479569 0.46351434 SKPAGS(ph)DGER ddPTM_BT-474_Pertuzumab_2h_R1 1 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 SKPAGS(1)DGER 80.706 0.014053 779410000 1327200 1230700 1029700 1237900 1181500 1152000 1275100 1433200 1284700 1281600 TRUE FALSE 1275331.557 1195601.641 1215789.696 1301788.167 1219504.021 1175294.229 1290705.055 1403603.919 1138866.242 1194796.09 1.067405197 1.000674216 1.017570869 1.089548399 1.020679621 0.983677666 1.080272245 1.174764406 0.953188792 1 20.18833299 2.180491054 24.99544431 1.078694731 1.030324466 0 0.062745255 176.4556754 75951.88974 0.023482487 0.017342973 151.5273591 -2.180491054 -0.048370265 WGTDEEKFITIFGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 WGTDEEKFITIFGTR 15 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 190.82 1.83E-07 2422000000 2650600 2881300 1861750 2521200 3014700 2783200 2709000 3331900 3900600 3544500 FALSE TRUE 2547011.622 2799128.145 2198209.639 2651319.434 3111670.563 2839478.211 2742153.552 3263095.101 3457820.241 3304427.858 0.77078748 0.847084054 0.665231542 0.802353554 0.941666968 0.859294962 0.82984216 0.987491705 1.046420255 1 21.65596907 2.180807802 0.612598174 1.03305895 0.768611485 0.645790628 0.066624 0.513082999 0.382916734 0.062163913 0.043438376 151.637914 -2.180807802 -0.264447465 ISGWTQALPDMVVSHLFGK ddPTM_BT-474_Pertuzumab_2h_R1 4 ISGWTQALPDMVVSHLFGK 19 0 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ;;; 188.38 1.63E-14 2071340000 1909950 1922590 1511030 1583250 1548560 1478590 1272290 1451060 1388580 917620 FALSE TRUE 1835307.042 1867759.616 1784106.734 1664961.722 1598370.839 1508488.103 1287860.666 1421095.104 1230954.22 855468.7801 2.145381673 2.183317099 2.085531086 1.946256557 1.868415161 1.763346761 1.505444378 1.661188739 1.438923604 1 19.70635568 2.180936803 0.185559738 0.731346135 2.658369726 0.964193624 0.066509418 0.711869359 0.095276579 0.319000022 0.501016341 151.6829627 -2.180936803 1.92702359 up ITRPGNTDDPSGGNK ddPTM_BT-474_Pertuzumab_2h_R1 3 ITRPGNTDDPSGGNK 15 1 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;B7WPG3;Q8WVV9-5;Q8WVV9-3;Q8WVV9-2;H7BXH8;C9JJZ7 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 0 ;; 121.92 0.0001022 603220000 1274270 1167520 1046770 1102420 1106820 1181660 1229510 1319100 1454170 1341940 FALSE TRUE 1224470.12 1134223.473 1235944.624 1159316.028 1142421.87 1205553.975 1244557.111 1291860.124 1289098.718 1251049.209 0.978754562 0.906617793 0.987926467 0.926675002 0.913171011 0.963634337 0.994810678 1.032621351 1.030414079 1 20.25470711 2.181003457 2.439908279 1.023260509 0.942208599 0.640653071 0.025804029 0.165428447 1.987492807 0.011281516 0.007452422 151.7062442 -2.181003457 -0.08105191 MLWGSDPYPHAEPQQATT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 MLWGSDPYPHAEPQQATTPK 20 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 MLWGSDPYPHAEPQQAT(0.209)T(0.791)PK;MLWGSDPYPHAEPQQAT(0.207)T(0.793)PK;MLWGSDPYPHAEPQQAT(0.017)T(0.983)PK;MLWGSDPYPHAEPQQAT(0.031)T(0.969)PK 185.34 1.35E-16 1986630000 996580 954420 883280 861140 1001790 1054060 841780 808470 970550 1044140 TRUE FALSE 957632.5518 927200.8761 1042908.344 905583.5386 1034013.485 1075373.815 852081.9554 791774.812 860377.2329 973419.4678 0.983782001 0.952519347 1.071386364 0.930311719 1.062248619 1.104738349 0.875349203 0.813395292 0.883870994 1 19.8927021 2.181144392 11.97226169 0.870495365 1.015040913 0.433581087 0.067636795 0.603278024 124.1336053 0.024967084 0.018444324 151.7554834 -2.181144392 0.144545549 VSTTTDSPVS(ph)PAQAASPFIPLDELSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSTTTDSPVSPAQAASPFIPLDELSSK 27 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 VS(0.051)T(0.051)T(0.051)T(0.044)DS(0.323)PVS(0.479)PAQAASPFIPLDELSSK 109.02 0.0010263 34860000 26643 25530 21181 20887 22350 24030 26150 30307 27493 29434 TRUE FALSE 25601.7621 24801.9094 25008.87787 21964.98057 23068.90805 24515.90306 26470.03152 29681.14986 24372.1099 27440.40896 0.932994918 0.903846201 0.911388671 0.800461123 0.840691116 0.893423385 0.964636918 1.081658437 0.888183188 1 14.74401436 2.181158832 3.697501461 1.003627782 0.876546131 0.440867713 0.056601413 0.187816025 5.224406873 0.022989644 0.016680018 151.7605292 -2.181158832 -0.127081651 SGS(ph)PRPTEPTDFLMLFEGS(ph)PSGK ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 2 S(0.426)GS(0.562)PRPT(0.01)EPT(0.001)DFLMLFEGS(0.857)PS(0.143)GK;S(0.426)GS(0.574)PRPTEPTDFLMLFEGS(0.994)PS(0.006)GK;S(0.098)GS(0.902)PRPTEPTDFLMLFEGS(0.929)PS(0.071)GK;S(0.104)GS(0.896)PRPTEPTDFLMLFEGS(0.978)PS(0.022)GK 216.19 1.47E-32 125763000 202803 182640 164339 149016 168532 167879 202463 217415 220810 236783 TRUE FALSE 194877.2345 177431.286 194038.713 156706.7336 173952.9848 171273.6284 204940.8028 212925.3043 195744.5745 220745.4765 0.88281417 0.803782206 0.87901558 0.709897825 0.788025139 0.775887375 0.928403182 0.964573805 0.88674331 1 17.75202435 2.181304205 6.186559782 0.945568988 0.804576348 0.616129408 0.053556956 0.13386691 10.42706031 0.02010328 0.014889947 151.811337 -2.181304205 -0.14099264 LEAVSHTSDMHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEAVSHTSDMHR 12 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6;Q5T0S3;Q5T0R8 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ; 205.02 6.16E-08 1167500000 572670 1238000 883690 1345720 907300 659320 1007450 82525 626580 856690 FALSE TRUE 550289.4233 1202693.452 1043392.441 1415172.77 936484.1285 672651.9021 1019779.474 80820.82991 555453.2652 798665.6232 0.689011029 1.505878577 1.306419621 1.771921477 1.172560958 0.842219676 1.276854099 0.101194827 0.695476616 1 19.60723209 2.181421176 1.591811314 0.551446681 1.307871482 0.310587348 0.376965436 0.37278019 1.840488939 0.212543257 0.121992975 151.8522306 -2.181421176 0.756424801 S(ph)KSDLSER ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.715)KS(0.284)DLS(0.001)ER 96.113 0.024126 791320000 1325900 1185600 979560 1018000 1071600 1149800 1299900 1575800 1421500 1292000 TRUE FALSE 1274082.362 1151787.849 1156588.282 1070539.102 1106068.987 1173049.744 1315808.565 1543259.179 1260137.279 1204491.689 1.057775968 0.956243915 0.960229359 0.888789115 0.91828694 0.973896088 1.092418135 1.281253489 1.046198401 1 20.19999301 2.181666393 3.875685881 1.149665621 0.952810889 0.40342509 0.082204842 0.166291625 5.08702286 0.032106638 0.023423297 151.9379955 -2.181666393 -0.196854732 INVYYNEATGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 INVYYNEATGGK 12 0 P68371 P68371 TUBB4B Tubulin beta-4B chain 0 190.53 1.52E-05 131250000 212370 217820 184140 195470 203000 231270 208970 257450 257750 264960 FALSE TRUE 204070.3456 211607.9869 217418.1942 205558.2301 209529.6794 235946.4379 211527.4374 252133.5675 228491.3006 247014.0232 0.826148827 0.856663861 0.880185632 0.832172309 0.848250138 0.955194506 0.856337768 1.020725723 0.925013477 1 17.91423342 2.181682407 0.843478206 0.989330131 0.846320544 0.608964404 0.042021147 0.385415034 0.517604764 0.031816773 0.017957206 151.9435983 -2.181682407 -0.143009588 EQSSDLTPSGDVS(ph)PVKPLSR ddPTM_BT-474_Pertuzumab_2h_R1 5 EQSSDLTPSGDVSPVKPLSR 20 1 Q8WYQ5-3;Q8WYQ5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 1 EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR 253.7 2.51E-36 8291670000 3419250 3236080 2753300 2979970 3019670 3151030 3436750 3864640 3776260 3733080 TRUE FALSE 3285621.93 3143790.167 3250882.557 3133766.609 3116800.428 3214745.986 3478809.975 3784833.833 3347594.796 3480235.167 0.944080435 0.903326935 0.934098531 0.900446797 0.895571787 0.923715161 0.99959049 1.087522438 0.961887527 1 21.73075336 2.181869218 3.889709682 1.029625556 0.91465447 0.662595104 0.033030607 0.112221523 3.459487483 0.012672628 0.009249712 152.0089707 -2.181869218 -0.114971087 TPASTPVSGT(ph)PQAS(ph)PMIER ddPTM_BT-474_Pertuzumab_2h_R1 2 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 2 TPASTPVS(0.001)GT(0.999)PQAS(1)PMIER;TPASTPVSGT(1)PQAS(1)PMIER 305.44 1.12E-49 1547040000 1374730 1383730 1160700 1244860 1261970 1247500 1027480 1290800 1184320 1119820 TRUE FALSE 1321004.032 1344267.375 1370464.31 1309107.374 1302562.411 1272725.305 1040054.608 1264144.529 1049880.959 1043973.594 1.265361537 1.287644997 1.312738481 1.253965983 1.247696703 1.219116376 0.996246087 1.210897034 1.005658538 1 19.99365379 2.181918225 0.575740152 1.011111076 1.304302538 0.716740929 0.064218679 0.451018263 0.302974081 0.057436769 0.04264889 152.0261246 -2.181918225 0.293191461 RGS(ph)PVPPVPER ddPTM_BT-474_Pertuzumab_2h_R1 6 RGSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER 95.755 0.004607 17676770000 2620890 2711360 2374930 2554580 2567000 2781060 2942520 3441320 3372890 3587080 TRUE FALSE 2518462.721 2634034.667 2804132.681 2686422.18 2649569.886 2837294.939 2978531.44 3370255.539 2990013.668 3344123.877 0.753100906 0.787660614 0.838525361 0.803326156 0.792306142 0.848441937 0.890676168 1.007814203 0.894109721 1 21.67319686 2.182110326 1.892351746 0.967984044 0.798085718 0.806729693 0.036406062 0.137588795 0.974860657 0.018423384 0.01119055 152.0933852 -2.182110326 -0.169898326 EKVESELR ddPTM_BT-474_Pertuzumab_2h_R1 9 EKVESELR 8 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;;;;; 138.66 0.00063462 53749230000 46004650 47290530 41980880 43948170 47277340 44257810 54286260 58132770 62555250 60034260 FALSE TRUE 44206737.42 45941850.39 49567758.88 46216340.32 48798058.58 45152733.24 54950631.49 56932307.98 55454240.27 55968086.1 0.789856157 0.820857985 0.885643272 0.825762386 0.871890786 0.806758572 0.981820808 1.017228066 0.99081895 1 25.73810108 2.18216672 5.93572955 1.002373095 0.836705905 0.893476802 0.027746611 0.058197497 4.224646096 0.010400819 0.007706022 152.1131359 -2.18216672 -0.16566719 KDS(ph)GSSSVFAES(ph)PGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 KDS(0.979)GS(0.02)S(0.001)SVFAES(1)PGGK;KDS(0.79)GS(0.209)S(0.001)SVFAES(1)PGGK 225.88 4.32E-15 1207090000 1025960 963850 1037620 1042740 1194930 1101820 881720 868510 952920 906350 TRUE FALSE 985864.3489 936361.9417 1225141.016 1096555.936 1233366.009 1124099.555 892510.7531 850574.965 844748.5166 844962.1072 1.166755693 1.108170335 1.449936045 1.297757529 1.459670201 1.33035499 1.05627311 1.006642733 0.999747219 1 19.68852712 2.182299323 4.925054774 1.010922362 1.307277797 0.654384044 0.102261674 0.133089869 6.630453102 0.042049058 0.031101215 152.1595879 -2.182299323 0.296355435 QGRPS(ph)PTSPVKPSSPASKPDGPAELPLTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGRPSPTSPVKPSSPASKPDGPAELPLTDR 30 3 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 QGRPS(0.344)PT(0.344)S(0.29)PVKPS(0.016)S(0.004)PAS(0.001)KPDGPAELPLTDR 75.515 0.0031084 333600000 89203 86613 77528 74686 88442 90066 103960 121100 132110 116630 TRUE FALSE 85716.84814 84142.88204 91539.0342 78540.55341 91286.81725 91887.19623 105232.2936 118599.2427 117113.4267 108730.5462 0.788341925 0.773866084 0.841888847 0.722341202 0.839569196 0.84509091 0.967826404 1.09076287 1.07709775 1 16.73039778 2.182371433 1.909534193 1.066784168 0.791477093 0.897911629 0.039399306 0.089745338 0.648044541 0.019513766 0.011892383 152.1848545 -2.182371433 -0.275307075 SQDVAVS(ph)PQQQQCSK ddPTM_BT-474_Pertuzumab_2h_R1 7 SQDVAVSPQQQQCSK 15 0 Q96F86;H3BPW9;H3BQ37;H3BTD6 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK 411.96 3.70E-133 10645212000 5636325 5315731 4378957 4807041 4698608 5279232 5314606 5702819 6287384 6059500 TRUE FALSE 5416051.188 5164131.557 5170331.939 5055132.962 4849742.993 5385981.688 5379647.738 5585053.795 5573666.527 5649084.668 0.958748453 0.914153683 0.915251274 0.894858771 0.858500674 0.953425556 0.952304321 0.988665266 0.986649494 1 22.42958569 2.182556925 1.799210034 0.989470736 0.909177052 0.652654759 0.02551129 0.2260939 1.441887702 0.014122977 0.008437924 152.2498682 -2.182556925 -0.080293684 QKS(ph)PEIHR ddPTM_BT-474_Pertuzumab_2h_R1 23 QKSPEIHR 8 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR 139.76 0.00039996 1.25038E+11 44542988.1 40589210 36212712 37748482.1 40328998.5 39138914.1 43069702 44040878.6 50852663.1 47215143.3 TRUE FALSE 42802198.88 39431645.47 42757154.61 39696685.78 41626217.36 39930329.76 43596801.9 43131419.07 45080081.98 44017219.59 0.972396696 0.895823176 0.971373363 0.901844463 0.945680299 0.907152477 0.99044879 0.979876046 1.024146514 1 25.39156468 2.182734565 8.350283778 0.995177202 0.931746523 0.588777772 0.027059579 0.185797005 24.97570956 0.009297446 0.006878041 152.3121556 -2.182734565 -0.063430679 RDS(ph)LGAYASQDANEQGQDLGK ddPTM_BT-474_Pertuzumab_2h_R1 4 RDSLGAYASQDANEQGQDLGK 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGAYASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK;RDS(0.999)LGAY(0.001)ASQDANEQGQDLGK 396.99 8.28E-132 4097030000 1760500 1537410 1575980 1731940 1759780 1717650 2025420 2283230 2313880 2511610 TRUE FALSE 1691697.714 1493564.572 1860794.643 1821325.631 1816384.922 1752382.06 2050207.696 2236080.503 2051218.043 2341496.418 0.722485715 0.637867545 0.794703178 0.777846858 0.775736793 0.748402623 0.875597195 0.954979254 0.876028692 1 21.1589994 2.182761616 0.473713368 1.00197597 0.689819356 0.78962729 0.047864184 0.437770769 0.214651109 0.049508169 0.04561608 152.321643 -2.182761616 -0.312156614 EKEQFR ddPTM_BT-474_Pertuzumab_2h_R1 10 EKEQFR 6 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;; 143.37 0.010404 1.135E+11 46809820 48431690 42652430 46436400 46602870 44140710 49781100 52785830 55081000 51556230 FALSE TRUE 44980440.48 47050465.62 50360672.9 48832988.17 48101893.64 45033265.4 50390335.99 51695784.16 48828435.8 48064280.62 0.935839253 0.978907101 1.047777523 1.015993323 1.000782557 0.9369383 1.048394678 1.075555142 1.015898608 1 25.51846181 2.182762644 24.99895309 1.045188076 0.990553203 0.272925221 0.037232451 105.5104197 47270.51861 0.014459818 0.01067929 152.3220036 -2.182762644 -0.054634874 GSGTAEVELKK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSGTAEVELKK 11 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 174.24 1.80E-05 5704070000 5218350 4548580 3731420 3944420 4273210 4458670 4903440 5498390 5821360 5086290 FALSE TRUE 5014411.113 4418858.952 4405770.599 4147991.989 4410661.68 4548827.362 4963449.766 5384846.325 5160543.618 4741791.048 1.057493057 0.931896599 0.929136386 0.874773255 0.93016787 0.959305738 1.046745779 1.135614427 1.088311055 1 22.17700066 2.182780438 3.207052721 1.090009537 0.939895926 0.545589635 0.053648341 0.161040237 3.375114785 0.022095009 0.015695127 152.3282447 -2.182780438 -0.150113611 TKTEMYQNMDDEMK ddPTM_BT-474_Pertuzumab_2h_R1 4 TKTEMYQNMDDEMK 14 1 Q5TEZ5 Q5TEZ5 C6orf163 Uncharacterized protein C6orf163 0 ;;; 77.078 0.026943 2285030000 947220 911600 777360 886810 858680 904010 978650 1034910 1134380 1120380 FALSE TRUE 910201.5952 885602.0605 917846.2443 932578.3704 886300.222 922289.7016 990627.0114 1013538.747 1005609.938 1044495.665 0.871426877 0.847875286 0.878745863 0.892850398 0.848543706 0.883000028 0.948426159 0.970361851 0.962770811 1 19.99437507 2.182818807 2.4978112 0.973468668 0.868029219 0.911974987 0.015452812 0.078141512 0.985789175 0.006969705 0.004645754 152.3417032 -2.182818807 -0.105439448 LRLEQER ddPTM_BT-474_Pertuzumab_2h_R1 2 LRLEQER 7 1 Q99583 Q99583 MNT Max-binding protein MNT 0 ; 122.52 0.0039519 457770000 325290 377290 296590 385640 358110 325540 325780 317860 307300 353100 FALSE TRUE 312577.3072 366530.0586 350190.4106 405542.9266 369628.9334 332122.6418 329766.9931 311296.0799 272416.5923 329184.2225 0.949551302 1.113449654 1.063812864 1.231963438 1.122863455 1.008926368 1.001770348 0.945659174 0.827550574 1 18.32853566 2.183174827 1.562482806 0.919343503 1.09986621 0.465704061 0.078083517 0.338580796 1.608846964 0.045787616 0.026181135 152.466639 -2.183174827 0.180522707 MDVNVGDIDIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 MDVNVGDIDIEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 220.97 2.56E-14 816775000 1044212 1054244 885272 986873 934843 1025878 1080607 1238872 1225367 1139764 FALSE TRUE 1003403.041 1024177.993 1045260.343 1037805.634 964913.0741 1046621.956 1093831.792 1213288.86 1086268.475 1062566.769 0.94431999 0.963871658 0.983712623 0.976696866 0.908096415 0.98499406 1.029424055 1.141847172 1.022306086 1 20.01912207 2.18366864 3.241656701 1.072769456 0.958477725 0.514095188 0.041338675 0.158467427 3.395834075 0.016611862 0.011832306 152.6400994 -2.18366864 -0.114291731 EGLSGDALSSPSAPEPVVGT(ph)PDDKLDADYIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGLSGDALSSPSAPEPVVGTPDDKLDADYIKR 32 2 K7EJ08;Q92503-3;Q92503;Q92503-2 K7EJ08 SEC14L1 SEC14-like protein 1 1 EGLSGDALS(0.001)S(0.05)PS(0.327)APEPVVGT(0.622)PDDKLDADYIKR 157.42 1.10E-09 456230000 220780 199760 161900 152330 181220 203960 224040 250250 276520 274510 TRUE FALSE 212151.6735 194063.0404 191158.9314 160191.7696 187049.1059 208084.2109 226781.8685 245082.25 245130.6089 255917.1932 0.828985622 0.758304036 0.746956189 0.625951573 0.730896989 0.813091955 0.886153313 0.957662309 0.957851271 1 17.96531755 2.18390728 1.590454178 0.97202214 0.734245544 0.818032639 0.048350887 0.16677665 0.822525906 0.029841167 0.01716534 152.7239963 -2.18390728 -0.237776595 RPS(ph)QGPPARSPSQDFSFIEDTEILDSAMYR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(0.613)QGPPARS(0.386)PS(0.002)QDFSFIEDTEILDSAMYR 287.3 1.62E-72 47274000 26058 30055 11629 13593 25456 34197 10670 12532 12177 9973.6 TRUE FALSE 25039.62455 29197.86083 13730.61899 14294.53636 26274.81536 34888.48677 10800.58265 12273.20982 10794.71801 9298.079188 2.692988954 3.140203502 1.476715643 1.537364446 2.825832608 3.752225171 1.161592887 1.319972606 1.160962151 1 13.182717 2.184134162 24.99982156 1.200589252 2.511643146 0.533867414 0.64370873 83.40825092 38311.44132 0.259934478 0.191974463 152.8038027 -2.184134162 1.311053894 KDESPATWR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDESPATWR 9 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ; 104.22 0.0052837 950600000 544600 610100 476620 498410 554710 546770 637780 694760 730900 720720 FALSE TRUE 523316.4299 592700.5454 562755.8364 524132.9998 572552.7509 557826.064 645585.3424 680412.9632 647931.2962 671904.9924 0.778854802 0.882119573 0.837552694 0.780070108 0.852133497 0.830215686 0.960828316 1.012662461 0.964319812 1 19.35789772 2.184405669 3.782905404 0.992398339 0.82787778 0.861523264 0.03112188 0.074879877 2.193691522 0.01197403 0.008728787 152.8993607 -2.184405669 -0.16452056 AAPPPPPPPPPLESS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAPPPPPPPPPLESSPR 17 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 AAPPPPPPPPPLES(0.186)S(0.814)PR;AAPPPPPPPPPLES(0.209)S(0.791)PR 141.99 6.33E-07 1328420000 371300 357040 347220 318710 365440 359360 331690 323020 386440 360760 TRUE FALSE 356789.1855 346857.5688 409970.3779 335158.6613 377194.7095 366626.5054 335749.3214 316349.5241 342572.9513 336325.4039 1.060845186 1.031315401 1.218969406 0.996530912 1.121517153 1.090094596 0.998287128 0.940605498 1.018575901 1 18.35949823 2.184583714 4.638342975 0.977863932 1.087798359 0.396061596 0.058504038 0.186663062 8.3283868 0.021558355 0.015936321 152.9620565 -2.184583714 0.109934427 IAQLEEQLDNETK ddPTM_BT-474_Pertuzumab_2h_R1 4 IAQLEEQLDNETK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 339.5 1.84E-62 586168000 690680 660545 565767 607056 650031 669570 715682 806800 868770 791910 FALSE TRUE 663687.462 641706.9033 668013.6823 638386.2329 670939.8375 683109.1642 724440.7304 790139.2981 770150.8718 738273.2303 0.898972677 0.869199745 0.904832594 0.864701857 0.908796107 0.925279607 0.981263712 1.070253215 1.04317865 1 19.49379532 2.184627958 1.928715663 1.045117746 0.888384366 0.896278085 0.02214148 0.088143787 0.650368122 0.010923589 0.006695028 152.9776405 -2.184627958 -0.156733381 SLS(ph)SPGGPSKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSPGGPSKPK 12 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 S(0.005)LS(0.498)S(0.498)PGGPSKPK 124.62 0.00019365 692680000 804910 744110 704740 714440 740640 715630 872620 920360 985570 1004300 TRUE FALSE 773453.2273 722888.7114 832102.1949 751312.334 764463.3582 730100.5289 883299.3846 901354.2444 873692.2254 936277.8665 0.826093679 0.772087793 0.888734237 0.802445899 0.816491968 0.779790439 0.943415856 0.962699511 0.933154843 1 19.83657723 2.184661479 6.845788598 0.958099628 0.815393678 0.81748136 0.033704409 0.083718131 8.296832238 0.012184091 0.009029198 152.9894486 -2.184661479 -0.142705949 KITSLSS(ph)SLDTSLDFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KITSLSSSLDTSLDFSK 17 1 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 KIT(0.071)S(0.071)LS(0.071)S(0.373)S(0.373)LDT(0.019)S(0.022)LDFSK 53.779 0.055495 0 110570 121210 91832 95701 99045 110910 107220 116570 136180 110360 TRUE FALSE 106248.8022 117753.2095 108428.0852 100640.1401 102230.8724 113152.6762 108532.1904 114162.7888 120721.4173 102885.2189 1.03269258 1.144510463 1.053874272 0.978178801 0.993640034 1.099795261 1.05488613 1.10961312 1.173360164 1 16.65067621 2.184680938 1.868188744 1.101145834 1.046209277 0.094093945 0.059728928 0.744346521 5.138441362 0.032075289 0.019448409 152.9963033 -2.184680938 -0.054936557 EVLDEDTDEEKETLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLDEDTDEEKETLK 15 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 144.73 3.82E-06 463620000 204290 151220 144700 130660 141580 185240 183310 225500 246430 224130 FALSE TRUE 196306.1209 146907.3537 170850.5088 137403.3783 146134.0493 188985.6797 185553.4026 220843.3462 218456.2995 208949.4755 0.939490853 0.703075963 0.817664215 0.657591401 0.699375047 0.904456349 0.88803 1.056922233 1.045498195 1 17.67279461 2.184903422 1.615350565 1.037259337 0.761154449 0.65572802 0.081682075 0.218194307 1.111873432 0.045501402 0.026322696 153.0747017 -2.184903422 -0.276104888 RHDS(ph)LHDPAAPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RHDSLHDPAAPSR 13 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 RHDS(1)LHDPAAPSR;RHDS(1)LHDPAAPSR 122.49 0.00011025 1430680000 892970 912240 739740 761660 647340 692670 569550 101195 651630 582070 TRUE FALSE 858071.7452 886223.8084 873427.4734 800969.3639 668162.279 706676.262 576520.3233 99105.28789 577659.6943 542645.8804 1.581273858 1.633153112 1.609571739 1.476044309 1.231304435 1.302278866 1.062424583 0.182633447 1.064524241 1 19.04965151 2.18520677 2.400098755 0.655898034 1.4983992 0.608175081 0.25798681 0.170272433 1.979853906 0.119884999 0.079101088 153.1816596 -2.18520677 0.842501166 ASAPERT(ph)PS(ph)PAPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASAPERTPSPAPK 13 1 Q96P11-2;Q63ZY6;Q63ZY6-6;Q3KNT7-3 Q96P11-2 NSUN5;NSUN5P2 Probable 28S rRNA (cytosine-C(5))-methyltransferase;Putative methyltransferase NSUN5C 2 AS(0.003)APERT(0.998)PS(1)PAPK;AS(0.003)APERT(0.997)PS(1)PAPK 134.14 0.0024836 466820000 2309600 2187500 1960190 2072480 2093090 2143710 2419800 2627700 2761900 2613800 TRUE FALSE 2219338.279 2125114.642 2314439.937 2179440.941 2160416.141 2187057.285 2449414.236 2573437.077 2448380.691 2436764.998 0.910772389 0.872104878 0.949800223 0.894399313 0.886591913 0.89752491 1.005190996 1.056087509 1.00476685 1 21.21653569 2.185448769 4.599332771 1.02703335 0.90135618 0.845239382 0.024000512 0.06847017 3.014953282 0.009022971 0.006671012 153.2670397 -2.185448769 -0.12567717 TFIIGELHPDDRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFIIGELHPDDRPK 14 1 P00167-2;P00167;J3KNC7 P00167-2 CYB5A Cytochrome b5 0 166.6 2.27E-06 155180000 73904 98447 67080 102860 74670 77220 92951 103200 106010 80425 FALSE TRUE 71015.74997 95639.38795 79202.84819 108168.6169 77071.82836 78781.44131 94088.56214 101068.8839 93976.18923 74977.74311 0.947157743 1.275570376 1.056351457 1.442676352 1.027929425 1.050731031 1.25488656 1.347985145 1.25338781 1 16.19417478 2.185979751 21.9058981 1.254728772 1.145626259 0.03153157 0.157774192 71.32549392 29713.20703 0.056748741 0.041911904 153.4545432 -2.185979751 -0.109102513 SAS(ph)PPQKR ddPTM_BT-474_Pertuzumab_2h_R1 3 SASPPQKR 8 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 S(0.04)AS(0.96)PPQKR;S(0.021)AS(0.979)PPQKR;S(0.161)AS(0.839)PPQKR 79.148 0.017632 1103860000 409240 576850 456143 534440 421511 400437 423990 297089 325540 321793 TRUE FALSE 393246.4484 560398.8028 538578.1869 562022.5124 435069.2841 408534.1105 429178.9164 290954.0083 288586.064 299997.6735 1.31083166 1.868010496 1.795274546 1.873422903 1.450242194 1.361790929 1.430607483 0.969854216 0.961961007 1 18.19459179 2.186151977 0.962217562 0.937007864 1.713314787 0.725289326 0.177673546 0.278159671 0.485600775 0.134102874 0.073119192 153.5154102 -2.186151977 0.776306922 LLEEHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEEHAK 7 0 P51572;P51572-2;A0A2R8Y5M6 P51572 BCAP31 B-cell receptor-associated protein 31 0 ; 117.17 0.0052914 1397950000 2137100 3225900 1974100 3354200 2081300 2276200 3279100 3899700 3580000 2708700 FALSE TRUE 2053579.769 3133900.49 2330863.784 3527310.664 2148246.905 2322226.324 3319230.607 3819169.832 3173613.409 2525237.336 0.81322248 1.241032059 0.92302761 1.396823425 0.850710891 0.919607155 1.314423226 1.51240035 1.256758469 1 21.26798756 2.186325475 8.987068748 1.335925969 1.03854802 0.228062476 0.208223938 0.371297081 59.41526702 0.075010672 0.055494878 153.5767509 -2.186325475 -0.29737795 (ac)MELDLSPPHLSSSPEDLCPAPGT(ph)PPGT(ph)PRPPDTPLPEEVKR ddPTM_BT-474_Pertuzumab_2h_R1 2 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 MELDLS(0.017)PPHLS(0.047)S(0.048)S(0.049)PEDLCPAPGT(0.861)PPGT(0.961)PRPPDT(0.017)PLPEEVKR;MELDLS(0.001)PPHLS(0.003)S(0.004)S(0.004)PEDLCPAPGT(0.99)PPGT(0.988)PRPPDT(0.01)PLPEEVKR 52.963 3.02E-06 531150000 35886 59497 42523 73801 48134 50932 32321 29151 22749 33361 TRUE FALSE 34483.53545 57800.20381 50207.85202 77609.87845 49682.27382 51961.87994 32716.55407 28549.02166 20166.62889 31101.42976 1.10874438 1.858442016 1.614326171 2.495379764 1.597427328 1.67072319 1.05193087 0.917932773 0.648414849 1 14.92469328 2.186435155 2.174582411 0.844611729 1.77572932 0.59793698 0.331387009 0.209879179 1.989778742 0.159063329 0.10173252 153.615541 -2.186435155 0.931117591 PGMYPDPHS(ph)PFAVS(ph)PIPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 PGMYPDPHSPFAVSPIPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 2 PGMY(0.001)PDPHS(0.999)PFAVS(1)PIPGR 83.245 0.0017892 61129000 127760 118300 102230 110620 124970 107330 91854 92649 96583 80382 TRUE FALSE 122766.998 114926.1998 120705.2351 116329.1115 128989.7735 109500.2861 92978.13673 90735.76577 85619.30275 74937.65554 1.638255121 1.533624171 1.610742079 1.552345221 1.72129449 1.461218467 1.240739866 1.210816713 1.142540451 1 16.19340322 2.186436243 1.590144576 1.122489963 1.607210281 0.909424529 0.069638663 0.108648938 0.536011468 0.03957118 0.022817604 153.6159259 -2.186436243 0.484720318 EELAQFHR ddPTM_BT-474_Pertuzumab_2h_R1 3 EELAQFHR 8 0 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ;; 197.3 0.00014515 1890700000 874700 1457470 919710 1852710 1033920 955500 1533170 1778870 1512560 1161810 FALSE TRUE 840515.757 1415904.383 1085922.056 1948328.585 1067176.976 974820.8647 1551933.393 1742135.713 1340860.53 1083119.574 0.776013819 1.307246602 1.002587417 1.798812091 0.985280851 0.900012232 1.432836624 1.608442646 1.237961682 1 20.04676109 2.186719745 24.99989022 1.398232513 1.154716231 0.059990962 0.30461913 215.4491748 103897.2548 0.112831641 0.083331777 153.7162374 -2.186719745 -0.243516282 EVS(ph)PAPAVAGQSK ddPTM_BT-474_Pertuzumab_2h_R1 5 EVSPAPAVAGQSK 13 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 EVS(1)PAPAVAGQSK;EVS(1)PAPAVAGQSK;EVS(1)PAPAVAGQSK;EVS(1)PAPAVAGQSK;EVS(1)PAPAVAGQSK 257.15 7.19E-24 6653700000 7772410 7987300 7154520 7452020 7420810 8198090 8809120 10156570 10301490 10426490 TRUE FALSE 7468655.624 7759510.024 8447500.915 7836619.645 7659507.093 8363860.997 8916928.646 9946833.28 9132108.043 9720294.545 0.768356925 0.79827931 0.869058121 0.806212158 0.787991255 0.860453452 0.917351692 1.023305748 0.939488819 1 23.2125686 2.186747928 2.109810741 0.989032608 0.809875807 0.853272388 0.032803534 0.110721532 0.985782961 0.016020073 0.010145047 153.7262128 -2.186747928 -0.179156801 LAS(ph)PELER ddPTM_BT-474_Pertuzumab_2h_R1 2 LASPELER 8 0 P05412;P17535 P05412;P17535 JUN;JUND Transcription factor AP-1;Transcription factor jun-D 1 LAS(1)PELER;LAS(1)PELER 130.98 0.0010747 2068800000 1907020 2024920 1529820 1848680 1741660 1819710 1359730 1292890 1403040 1340930 TRUE FALSE 1832491.55 1967171.264 1806292.505 1944090.596 1797682.076 1856505.783 1376370.782 1266191.37 1243772.781 1250107.617 1.465867039 1.573601535 1.444909607 1.55513859 1.438021856 1.485076771 1.101001837 1.012865895 0.994932568 1 20.25362087 2.186788001 3.345303925 1.012310741 1.499621809 0.967223949 0.042317668 0.03665732 0.839258083 0.016558831 0.011888281 153.7403981 -2.186788001 0.487311067 KNELEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNELEQK 7 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 101.72 0.014192 426060000 658840 623190 523300 481120 580000 486080 657410 658750 737000 670580 FALSE TRUE 633091.8044 605417.2314 617871.9507 505950.6609 598656.2267 495908.8706 665455.5802 645146.5823 653338.8498 625161.0193 1.012685988 0.968418076 0.988340494 0.809312553 0.957603255 0.793249827 1.064454692 1.031968665 1.045072917 1 19.2538683 2.186821965 24.99998339 1.038331461 0.923294696 0.394625985 0.068975603 104.5183628 50502.24694 0.025757825 0.019023437 153.7524219 -2.186821965 -0.115036765 AMSTTSIS(ph)SPQPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMSTTS(0.001)IS(0.499)S(0.499)PQPGK 113.25 0.0021355 322430000 391720 421810 417430 382430 378430 443780 454740 503110 547600 538220 TRUE FALSE 376411.1493 409780.3918 492868.8867 402167.2581 390602.5446 452753.5357 460305.2441 492720.6027 485438.7437 501765.88 0.750172868 0.816676478 0.982268636 0.801503797 0.77845577 0.902320293 0.917370556 0.981973112 0.967460649 1 18.93665485 2.187041447 1.687998454 0.98138919 0.833635388 0.555896407 0.060041735 0.306589839 1.713657113 0.034574899 0.020321915 153.8301443 -2.187041447 -0.147753802 AGS(ph)PLCNSNLQDSEEDIEPSYSLFR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGSPLCNSNLQDSEEDIEPSYSLFR 25 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR 213.35 2.59E-26 455468000 271879 272206 204734 254652 241530 282012 257672 303356 321516 314852 TRUE FALSE 261253.6681 264442.9514 241733.9881 267794.6202 249299.0318 287714.4759 260825.467 297091.5926 285018.8516 293526.7936 0.890050496 0.900915886 0.823549991 0.912334499 0.849322914 0.98019834 0.888591681 1.012144714 0.971014769 1 18.16313268 2.187248561 0.916800614 0.999009279 0.87434986 0.582489743 0.039643404 0.376982371 0.59737424 0.02842738 0.015678022 153.903523 -2.187248561 -0.124659419 RS(ph)PVSTRPLPSASQK ddPTM_BT-474_Pertuzumab_2h_R1 4 RSPVSTRPLPSASQK 15 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 RS(1)PVSTRPLPSASQK;RS(1)PVSTRPLPSASQK;RS(1)PVSTRPLPSASQK;RS(1)PVSTRPLPSASQK 214.26 1.30E-12 4496170000 2772270 2576910 2103840 2253810 2408290 2392080 2505840 2719780 2692640 2579870 TRUE FALSE 2663926.623 2503419.05 2484050.688 2370129.404 2485754.835 2440449.497 2536507.22 2663615.593 2386982.796 2405133.107 1.107600497 1.040865074 1.032812147 0.985446251 1.033520693 1.014683757 1.054622387 1.107471177 0.992453511 1 21.19768531 2.187263162 24.12062332 1.054259394 1.033519501 0 0.042194726 260.1226701 122309.7308 0.01601033 0.01182445 153.9086974 -2.187263162 -0.020739893 IYVDDGLISLQVK ddPTM_BT-474_Pertuzumab_2h_R1 2 IYVDDGLISLQVK 13 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 220.25 4.91E-11 544570000 1266600 1310760 1173990 1359490 1280400 1192580 1470650 1567180 1666510 1534500 FALSE TRUE 1217099.872 1273378.408 1386156.108 1429653.442 1321585.229 1216694.785 1488648.255 1534817.185 1477334.771 1430566.948 0.850781484 0.890121507 0.968955777 0.999361438 0.923819211 0.850498319 1.040600202 1.072873372 1.03269181 1 20.44815558 2.187655453 11.71835997 1.045907856 0.919696818 0.61506358 0.047158395 0.507548226 115.3277484 0.018930385 0.013989131 154.0477832 -2.187655453 -0.126211038 ADEICIAGSPLT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADEICIAGSPLTPR 14 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 ADEICIAGSPLT(1)PR 147.12 9.97E-06 0 78181 81255 64886 71653 74628 76607 61646 64805 59184 66163 TRUE FALSE 75125.60009 78937.68696 76612.34358 75351.01992 77028.4774 78156.04603 62400.44219 63466.7541 52465.68044 61681.72108 1.21795564 1.279758178 1.24205911 1.221610205 1.248805579 1.267086013 1.011652092 1.028939417 0.850587168 1 15.9125554 2.188040281 4.716422702 0.97706393 1.247078659 0.88763352 0.047730003 0.064097744 3.020746799 0.018362627 0.013606602 154.1843451 -2.188040281 0.270014728 LSGAEPDDEEYQEFEEMLEHAESAQDFASR ddPTM_BT-474_Pertuzumab_2h_R1 8 LSGAEPDDEEYQEFEEMLEHAESAQDFASR 30 0 Q96GC9;K7EPE7;Q96GC9-2 Q96GC9 VMP1 Vacuole membrane protein 1 0 ;;;;;;; 364.82 1.57E-136 1456988000 291972.3 490869 260287.9 605839 315647.8 322719.2 472221 520354 451305 357344.1 FALSE TRUE 280561.6997 476869.8967 307327.7136 637106.4234 325800.8982 329244.8033 478000.1819 509608.5081 400074.7484 333140.8658 0.842171371 1.431436205 0.922515804 1.912423508 0.977967375 0.98830506 1.434829019 1.529708782 1.200917658 1 18.34577281 2.188833478 24.99990322 1.359860923 1.203125059 0.007565981 0.324088693 378.044579 190056.1263 0.117601898 0.0868549 154.4662053 -2.188833478 -0.156735864 LQQQQRPEDAEDGAEGGGKR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQQQQRPEDAEDGAEGGGKR 20 2 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;; 200.39 7.67E-22 1141250000 493046 471550 405947 480850 467355 520441 526219 593194 648808 650175 FALSE TRUE 473777.2172 458101.8557 479310.6531 505666.7261 482387.898 530964.6736 532659.0255 580944.3366 575158.0359 606138.0681 0.781632506 0.755771465 0.790761509 0.834243471 0.795838314 0.87597975 0.878775074 0.958435655 0.948889479 1 19.20928693 2.18890759 0.587861979 1.001661141 0.767756698 0.941171107 0.019454692 0.164997823 0.114779542 0.017042721 0.012450146 154.4925674 -2.18890759 -0.233904443 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 98.636 4.34E-05 105710000 167630 192450 138160 175680 168830 188140 158700 167880 178690 183620 FALSE TRUE 161078.8343 186961.5144 163128.5854 184746.8659 174260.5703 191944.3197 160642.2181 164413.2193 158405.8603 171183.2538 0.940973084 1.092171753 0.9529471 1.079234456 1.017976738 1.121279771 0.938422506 0.960451537 0.925358391 1 17.38518205 2.189363685 24.99982174 0.953073966 1.034367627 0.314578957 0.056363036 123.0754464 62540.92363 0.01947197 0.014381022 154.6549001 -2.189363685 0.081293661 MVSQSQPGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 3 MVSQSQPGSR 10 0 E3W994;J3KR49;O75122;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 MVSQSQPGS(1)R;MVSQSQPGS(1)R;MVSQSQPGS(1)R 148.13 2.69E-05 968020000 442280 621300 499440 546650 596870 625820 504120 501250 588550 588270 TRUE FALSE 424995.2086 603581.1323 589699.918 574862.672 616068.8656 638474.5092 510289.5714 490899.0123 521740.2714 548425.9489 0.77493636 1.100569974 1.075258965 1.048204727 1.12334011 1.164194565 0.93046212 0.895105371 0.95134133 1 19.06493731 2.189428095 24.19819347 0.930979612 1.054858541 0.191995498 0.10198831 114.5785619 56429.89541 0.037837661 0.027945042 154.6778386 -2.189428095 0.123878929 YKDLVPDNSK ddPTM_BT-474_Pertuzumab_2h_R1 2 YKDLVPDNSK 10 1 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ; 77.593 0.029671 1299770000 3338400 3194400 2738800 2891200 3152000 2860370 3330400 3384300 3835800 3650400 FALSE TRUE 3207931.637 3103298.84 3233762.084 3040415.178 3253386.943 2918208.641 3371158.431 3314413.022 3400376.065 3403155.157 0.942634552 0.911888732 0.950224699 0.893410685 0.955991365 0.857500909 0.990597923 0.973923571 0.999183378 1 21.6984415 2.189528866 24.99983453 0.987230336 0.920293926 0.61236607 0.028106831 74.51976756 37994.92151 0.009648406 0.007125835 154.7137332 -2.189528866 -0.06693641 VQEQVHTLLSQDQAQAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQEQVHTLLSQDQAQAAR 18 0 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 252.12 1.79E-30 293840000 148370 238950 138800 250410 168380 160440 222500 249110 204740 177920 FALSE TRUE 142571.5364 232135.38 163884.2476 263333.6901 173796.0956 163684.2067 225223.0216 243965.7914 181498.7735 165869.3199 0.859541333 1.399507637 0.988032312 1.587597334 1.047789282 0.986826297 1.357834117 1.470831324 1.094227514 1 17.33968754 2.189638429 24.99847453 1.29461958 1.165035021 0 0.237844953 344.0926881 175823.7681 0.085917325 0.063454258 154.752769 -2.189638429 -0.129584559 YDEIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 YDEIRR 6 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 89.427 0.080459 693190000 1436300 1414600 1266300 1283200 1378800 1366100 1463500 1584400 1629200 1529100 FALSE TRUE 1380167.808 1374256.993 1495148.579 1349426.106 1423150.354 1393723.478 1481410.751 1551681.586 1444260.046 1425532.695 0.968176888 0.964030497 1.048834996 0.946611825 0.998328807 0.977686084 1.039198018 1.088492457 1.01313709 1 20.4430697 2.18967217 5.790278638 1.048176165 0.98492306 0.326079046 0.034228183 0.179386046 13.48903919 0.012550935 0.009327778 154.7647927 -2.18967217 -0.063253105 AEDGENYDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEDGENYDIK 10 0 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 156.48 2.53E-05 241830000 313560 273330 255330 274120 299800 294740 322110 350270 386590 376590 FALSE TRUE 301305.7285 265534.896 301473.8108 288267.3661 309443.3393 300699.8447 326052.0785 343036.8021 342705.9239 351083.2239 0.858217391 0.756330346 0.858696145 0.821079865 0.881395972 0.856491636 0.9287031 0.977081156 0.976138706 1 18.42145353 2.189725724 0.799647263 1.003675634 0.817473146 0.833360698 0.0301044 0.221786079 0.268984048 0.023002231 0.013369915 154.7838782 -2.189725724 -0.186202488 SSSAS(ph)SPEMK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSSAS(0.655)S(0.345)PEMK 224.03 4.36E-09 254290000 830360 730880 603600 639970 632270 691700 825550 919770 971250 855690 TRUE FALSE 797908.6132 710036.018 712683.947 672998.9284 652607.5388 705686.6479 835653.3278 900776.4281 860997.7718 797733.3541 1.000219696 0.890066855 0.893386171 0.843638949 0.818077288 0.884614695 1.047534647 1.12916982 1.079305218 1 19.60554707 2.189896259 4.372929818 1.084193861 0.882706186 0.716541477 0.053877366 0.102116799 4.119133543 0.021254962 0.015721041 154.8446694 -2.189896259 -0.201487675 KQEELVQQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQEELVQQVR 10 1 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 134.13 0.0067735 0 351280 353810 303160 290090 286470 272890 362750 380410 350160 382570 FALSE TRUE 337551.5892 343719.6852 357947.7558 305061.5797 295684.5677 278408.0228 367189.443 372554.4006 310411.3048 356658.1931 0.94642881 0.963722948 1.003615682 0.855333161 0.829041848 0.780601787 1.02952757 1.044569865 0.870332746 1 18.44418259 2.190004845 24.99998604 0.99710572 0.899451261 0.24559067 0.075895293 166.548753 85750.08652 0.030912195 0.022830212 154.8833898 -2.190004845 -0.09765446 DLQSSPPS(ph)LPLGFLGEGDAVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLQSSPPSLPLGFLGEGDAVTK 22 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLQS(0.246)S(0.304)PPS(0.449)LPLGFLGEGDAVTK 135.3 4.02E-06 150280000 71471 63275 51385 55776 68521 73341 68514 81176 96964 88128 TRUE FALSE 68677.8343 61470.45895 60671.41255 58654.60604 70725.04019 74824.00527 69352.49483 79499.68723 85957.05323 82159.01206 0.835913585 0.748188877 0.738463268 0.713915669 0.860831191 0.910721823 0.844125228 0.967631977 1.046227931 1 16.32613121 2.19012501 0.760547082 1.023478158 0.758348715 0.786820624 0.050037631 0.303014576 0.334117537 0.043280486 0.025841807 154.9262504 -2.19012501 -0.265129443 EKPSYDTETDPSEGLMNVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKPSYDTETDPSEGLMNVLK 20 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 192.64 9.35E-18 365160000 354770 330620 299210 292710 311130 373270 368760 450600 460910 472360 FALSE TRUE 340905.1962 321191.0413 353283.9029 307816.7982 321137.779 380817.7751 373272.9952 441294.9525 408589.4291 440366.6365 0.774139474 0.72937188 0.802249475 0.699001179 0.72925093 0.864774358 0.847641407 1.002108053 0.927839203 1 18.74834564 2.190258676 1.351162715 0.979850296 0.74691723 0.841431288 0.041832274 0.151961235 0.534395288 0.025281666 0.014021898 154.9739406 -2.190258676 -0.232933067 KPSS(ph)ETDIENWASK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSSETDIENWASK 14 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 KPS(0.147)S(0.844)ET(0.009)DIENWASK 221.85 2.52E-12 562970000 627270 519380 443950 492630 505520 563210 599210 658350 731210 706780 TRUE FALSE 602755.5949 504567.7909 524181.6406 518054.6933 521780.5099 574598.4921 606543.3112 644754.8424 648206.1063 658909.1611 0.914777985 0.765762294 0.795529447 0.786230825 0.791885347 0.87204508 0.92052645 0.978518558 0.983756403 1 19.32972006 2.190537705 1.505209306 0.989470423 0.805796084 0.797295015 0.038866074 0.164366363 0.723950883 0.022285249 0.01269836 155.0735416 -2.190537705 -0.183674339 NVMEEGKDFQPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 NVMEEGKDFQPSR 13 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;;; 232.78 1.63E-13 3802910000 4010470 3981610 3118820 3110540 3614250 3829130 3766730 4158530 4706430 4198110 FALSE TRUE 3853736.399 3868058.381 3682460.152 3271075.342 3730505.634 3906557.632 3812828.368 4072654.902 4172175.797 3913768.27 0.984661363 0.988320747 0.940898872 0.835786668 0.953174888 0.998157623 0.974209024 1.040596842 1.06602525 1 21.90012691 2.190722356 1.432010589 1.037762665 0.93990699 0.433068219 0.044506517 0.409461335 1.625465921 0.02914065 0.016389576 155.1394889 -2.190722356 -0.097855675 SGFEPASLKEEVGEEAIVELVENGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGFEPASLKEEVGEEAIVELVENGKK 26 2 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 256.88 6.77E-53 851280000 1075470 897250 704880 606320 814980 898260 924170 1015580 1209180 1034030 FALSE TRUE 1033439.443 871661.3085 832267.496 637612.2479 841194.5718 916423.4326 935480.2689 994607.9181 1071918.956 963994.2271 1.072039038 0.904218391 0.863353195 0.661427455 0.872613703 0.950652407 0.970421028 1.031757131 1.111955783 1 19.87866498 2.191136882 1.610679825 1.050470236 0.867403278 0.3656108 0.097292677 0.426161974 2.162386557 0.058667677 0.034118744 155.2876373 -2.191136882 -0.183066958 LLQIIER ddPTM_BT-474_Pertuzumab_2h_R1 1 LLQIIER 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 86.833 0.046031 131730000 212020 269680 195910 222880 232410 248450 199420 199740 238960 200040 FALSE TRUE 203734.024 261988.9904 231315.295 234382.8635 239885.6787 253473.8292 201860.5616 195615.2992 211834.2626 186491.1126 1.092459695 1.40483365 1.240355595 1.256804468 1.286311585 1.359173773 1.082413841 1.048925584 1.135894679 1 17.50874735 2.191538528 9.48825308 1.068432457 1.277569084 0.597731175 0.082953264 0.232986419 44.64899464 0.028927213 0.021410878 155.4313173 -2.191538528 0.209136627 HQGTFTDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HQGTFTDEK 9 0 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 0 ; 151.15 8.35E-05 443670000 793650 719920 595220 640030 734000 718500 658740 566980 873080 825100 FALSE TRUE 762633.2806 699388.5865 702789.4946 673062.025 757609.7766 733028.5623 666801.8572 555271.6649 773971.6186 769215.2421 0.991443277 0.909223515 0.913644785 0.874998295 0.98491259 0.952956367 0.866859912 0.721867735 1.006183414 1 19.55302782 2.191595459 7.563206129 0.858326792 0.934704927 0 0.084462601 0.436533796 58.76063601 0.031520445 0.023386047 155.4516939 -2.191595459 0.076378135 EDMAALEK ddPTM_BT-474_Pertuzumab_2h_R1 8 EDMAALEK 8 0 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;;;;;; 140.5 0.0015088 7455940000 11646220 11616350 10400400 10630030 11093770 10932390 12757570 13178730 14861420 14613070 FALSE TRUE 11191072.85 11285063.07 12279983.64 11178647.12 11450611.19 11153450.42 12913700.96 12906584.62 13174413.91 13623313.75 0.82146481 0.828364029 0.90139476 0.820552718 0.840515854 0.818703189 0.94791188 0.947389516 0.967049144 1 23.69957433 2.191721142 6.39952536 0.960376328 0.840189977 0.847154294 0.026417741 0.07585107 7.304916331 0.009940692 0.007389855 155.4966874 -2.191721142 -0.120186352 HEDGTQS(ph)DSEDPLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEDGTQSDSEDPLAK 15 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 HEDGT(0.077)QS(0.922)DS(0.001)EDPLAK 104.84 0.0013899 0 209630 189310 154780 156580 178470 162920 160470 96520 211660 174260 TRUE FALSE 201437.4278 183911.0642 182752.1891 164661.1126 184210.6496 166214.354 162433.8799 94526.82827 187633.2442 162457.215 1.239941408 1.132058457 1.12492504 1.013566018 1.133902546 1.023126945 0.999856361 0.581856757 1.154970213 1 17.30970029 2.191808379 2.889822495 0.855722282 1.11518367 0.231497036 0.149746397 0.273660944 4.664674186 0.062443931 0.043680786 155.5279255 -2.191808379 0.259461388 DNSTMGYMMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DNSTMGYMMAK 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 123.67 0.00084938 160140000 227370 298190 212270 258650 265860 236440 217910 200090 218470 216660 FALSE TRUE 218484.129 289685.9132 250631.9109 271998.9575 274411.6283 241220.9788 220576.8478 195958.0716 193670.2015 201985.4252 1.081682645 1.434192159 1.240841564 1.346626655 1.358571432 1.194249429 1.092043386 0.970159463 0.958832556 1 17.62389167 2.191809221 1.883560428 0.973978821 1.29961255 0.707690955 0.088742301 0.168685499 1.18720948 0.042992457 0.026327933 155.5282271 -2.191809221 0.325633729 SVS(ph)GS(ph)PEPAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(0.175)VS(0.825)GS(1)PEPAAK 129.37 0.0014813 0 1039700 914150 770360 846750 875540 922460 1021700 1088700 1225000 1147400 TRUE FALSE 999067.3746 888079.337 909581.1886 890450.869 903702.5392 941112.7732 1034203.87 1066217.965 1085943.136 1069685.576 0.933982281 0.830224654 0.850325749 0.83244169 0.844830069 0.879803182 0.96682978 0.996758289 1.015198447 1 20.02875536 2.191836412 2.259481071 1.003021097 0.85457216 0.849082513 0.027836476 0.105800649 1.087800949 0.012869382 0.008380809 155.5379649 -2.191836412 -0.148448937 RYDEIVK ddPTM_BT-474_Pertuzumab_2h_R1 4 RYDEIVK 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 152.63 0.0028873 2114100000 1819750 1983750 1724940 1825930 1950320 1973440 2162080 2450000 2624110 2394950 FALSE TRUE 1748632.158 1927175.392 2036675.029 1920166.466 2013053.814 2013344.309 2188540.182 2399406.644 2326232.034 2232737.903 0.783178427 0.863144478 0.912187242 0.860005316 0.901607757 0.901737865 0.980204698 1.074647696 1.041874208 1 21.09038248 2.19193751 1.907820155 1.047589204 0.86654255 0.814511976 0.036966673 0.135334147 0.978324057 0.019237066 0.011833252 155.5741761 -2.19193751 -0.181046655 EGTINVHDVETQFNQYK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGTINVHDVETQFNQYK 17 0 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;P15941-13 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 0 83.758 0.0054511 265520000 186900 131770 110040 105670 144050 128480 153000 158190 181430 168520 FALSE TRUE 179595.7414 128012.0486 129926.6758 111123.6414 148683.4991 131077.9536 154872.4598 154923.3212 160834.827 157105.9903 1.143150182 0.814813289 0.827000139 0.707316387 0.946389751 0.834328172 0.985783289 0.986107028 1.023734529 1 17.26137866 2.192155257 7.685168561 0.996761457 0.868898428 0.229523559 0.106845354 0.334903729 46.91638109 0.039699547 0.029454189 155.6521977 -2.192155257 -0.127863029 RLTVSSLQESGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLTVSSLQESGLK 13 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 79.639 0.03201 429560000 604700 541360 535600 565740 513750 588990 630140 691990 727670 743070 FALSE TRUE 581067.6555 525920.9428 632394.8344 594937.9092 530275.2353 600899.7813 637851.8418 677700.1647 645067.9522 692741.207 0.838794704 0.75918819 0.912887566 0.858816977 0.765473787 0.867423181 0.920764977 0.978287646 0.931181725 1 19.40195697 2.192207263 2.41215592 0.965417406 0.829097426 0.662288432 0.044762905 0.180022264 2.119141365 0.020455686 0.013608756 155.670838 -2.192207263 -0.13631998 AAEEQGDDQDSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAEEQGDDQDSEK 13 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 259.75 1.28E-23 627090000 720570 634560 574650 593660 607460 633280 712910 766810 824840 775280 FALSE TRUE 692409.3278 616462.9701 678502.038 624298.8637 626999.5026 646085.3555 721634.8058 750975.1055 731207.6212 722769.5951 0.957994543 0.852917685 0.938752879 0.863759168 0.867495682 0.893902234 0.998429943 1.039024207 1.011674573 1 19.46317629 2.192543875 4.277693022 1.020357704 0.892539743 0.759249898 0.032176028 0.089724316 3.48394257 0.011761365 0.008703563 155.7915415 -2.192543875 -0.127817961 DLAEDAPWKK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLAEDAPWKK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 Q60FE5;O75369-8;Q14315-2 FLNA;FLNB;FLNC Filamin-A;Filamin-B;Filamin-C 0 ;;; 136.48 0.0001871 6393280000 8330600 8080700 6429440 6616590 7799350 8609750 8917100 10015200 11522200 10973100 FALSE TRUE 8005030.942 7850246.348 7591382.83 6958073.003 8050223.176 8783845.044 9026230.137 9808382.62 10214248.16 10229882.16 0.782514482 0.767383849 0.742079206 0.680171374 0.786932151 0.85864577 0.8823396 0.958797224 0.998471732 1 23.28628619 2.19269592 1.040130019 0.999013024 0.743653333 0.919707233 0.030143568 0.144635284 0.296167889 0.023778325 0.012911839 155.8460932 -2.19269592 -0.255359692 QAGEVTFADAHRPK ddPTM_BT-474_Pertuzumab_2h_R1 5 QAGEVTFADAHRPK 14 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;;; 180.74 1.03E-06 7940080000 9094070 9325090 7258490 8320570 8787160 9240590 9422190 10223460 11006750 11144260 FALSE TRUE 8738663.69 9059147.563 8570260.607 8749995.615 9069806.982 9427441.061 9537501.58 10012341.98 9757309.884 10389449.34 0.841109418 0.871956469 0.82490037 0.842200133 0.872982454 0.907405267 0.917998757 0.963702853 0.939155634 1 23.30861586 2.192746513 0.707539917 0.985352099 0.840570337 0.904963557 0.016857219 0.194128318 0.187226363 0.014379377 0.009005225 155.8642497 -2.192746513 -0.144781762 LNDS(ph)PTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNDSPTLK 8 0 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 LNDS(0.998)PT(0.002)LK;LNDS(0.893)PT(0.107)LK 139.98 0.00068903 2205800000 1663180 1427270 1282370 1254690 1303010 1399770 1567440 1644830 1866720 1722980 TRUE FALSE 1598181.087 1386565.657 1514122.785 1319444.701 1344922.5 1428074.308 1586622.8 1610863.686 1654817.772 1606281.03 0.994957331 0.863214862 0.942626326 0.821428303 0.837289662 0.889056324 0.987761649 1.00285296 1.030216843 1 20.61529289 2.192991525 4.047342216 1.007585024 0.886253572 0.578621337 0.047703487 0.154144012 5.30821042 0.018730891 0.013815416 155.9522069 -2.192991525 -0.121331453 KLAEEEDLFDSAHPEEGDLDLASESTAHAQSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLAEEEDLFDSAHPEEGDLDLASESTAHAQSSK 33 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 217.58 2.40E-36 316040000 181460 187720 160090 142550 191740 190290 164210 138690 245120 204150 FALSE TRUE 174368.3426 182366.4094 189021.8242 149907.0226 197907.4912 194137.7942 166219.6511 135826.003 217295.0052 190322.7387 0.916171887 0.958195593 0.993164692 0.787646414 1.039852057 1.02004519 0.873356764 0.713661457 1.141718571 1 17.53808841 2.192991979 24.98228802 0.886217236 0.95109508 0 0.12270112 412.8817088 226353.3895 0.046013849 0.0339836 155.95237 -2.192991979 0.064877844 YMAENPTAGVVQEEEEDNLEYDS(ph)DGNPIAPTKK ddPTM_BT-474_Pertuzumab_2h_R1 2 YMAENPTAGVVQEEEEDNLEYDSDGNPIAPTKK 33 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3;J3KRE3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 1 YMAENPTAGVVQEEEEDNLEYDS(1)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEY(0.018)DS(0.982)DGNPIAPTKK 270.12 1.68E-61 458600000 179233 186770 137429 146327 151710 171305 167020 193248 194675 185102 TRUE FALSE 172228.3762 181443.5025 162265.4774 153878.954 156589.8899 174768.9045 169064.0407 189257.3613 172576.3101 172564.8767 0.998050006 1.051450944 0.940315785 0.891716536 0.907426198 1.012772169 0.979712929 1.096731646 1.000066256 1 17.39677933 2.193026502 2.262131714 1.039690548 0.960466413 0.219222641 0.052243792 0.408100377 4.207560114 0.026481923 0.017272266 155.9647675 -2.193026502 -0.079224135 (ac)SQAEFEKAAEEVRHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQAEFEKAAEEVRHLK 16 2 P07108;P07108-6 P07108 DBI Acyl-CoA-binding protein 0 ; 94.461 5.76E-11 165061000 377000 373360 284280 254100 363750 361100 394750 556610 477730 295190 FALSE TRUE 362266.4232 362712.1384 335655.7198 267214.1315 375450.3491 368401.6894 399581.0686 545115.809 423500.0932 275196.5184 1.316391738 1.318011363 1.219694645 0.970993867 1.364299052 1.338685866 1.451984462 1.980823784 1.538900622 1 18.07010269 2.193247185 2.988866918 1.631299823 1.240443264 0.118731266 0.253575043 0.298156342 5.447311766 0.103572939 0.07310677 156.0440398 -2.193247185 -0.390856559 GNFGGSFAGSFGGAGGHAPGVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNFGGSFAGSFGGAGGHAPGVAR 23 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 266.46 3.91E-44 2740700000 845890 923000 763480 928660 950420 888190 822430 792200 894970 953180 FALSE TRUE 812831.6836 896676.9437 901457.8195 976588.2539 980991.1224 906149.8103 832495.1444 775840.7932 793376.7576 888620.2696 0.914712067 1.009066498 1.014446609 1.098993898 1.103948622 1.019726695 0.936840147 0.873084736 0.892818659 1 19.76120752 2.193286824 3.783836041 0.90768111 1.033100558 0.410127966 0.058634657 0.197990589 5.901786782 0.024160521 0.017717359 156.0582827 -2.193286824 0.125419448 SRGSPS(ph)SYNSSSSSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 S(0.001)RGS(0.441)PS(0.449)S(0.048)YNS(0.048)S(0.009)S(0.003)SSPR;SRGS(0.092)PS(0.408)S(0.052)YNS(0.408)S(0.021)S(0.012)S(0.003)S(0.005)PR 136.34 4.73E-05 207035000 164137 172185 133250 160149 144165 157983 182674 193686 205281 221363 TRUE FALSE 157722.3446 167274.4524 157331.2391 168414.3091 148802.1982 161177.5245 184909.6191 189686.3164 181978.3615 206369.8868 0.764270151 0.810556496 0.762374984 0.816079863 0.721046081 0.781012807 0.896010663 0.919156953 0.881806761 1 17.65487294 2.193544845 3.884009841 0.92082777 0.775363033 0.792487653 0.037385181 0.097094499 3.062442221 0.013897086 0.010218787 156.151027 -2.193544845 -0.145464737 DSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSGSDTASAIIPSTTPSVDSDDESVVK 27 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTTPS(0.085)VDS(0.903)DDES(0.011)VVK;DSGSDTASAIIPSTTPS(0.017)VDS(0.937)DDES(0.045)VVK 185.71 7.58E-18 377010000 677500 785630 644360 932150 682950 726100 1070880 1174840 1272890 1195190 TRUE FALSE 651022.551 763224.6016 760810.1857 980258.3732 704917.707 740782.2395 1083985.75 1150579.143 1128396.864 1114238.717 0.58427565 0.684974046 0.682807171 0.879756159 0.632645138 0.664832615 0.972848756 1.032614579 1.012706565 1 20.08762692 2.193588808 5.453831991 1.013120958 0.693701482 0.820262708 0.072593674 0.079319116 5.423182167 0.028259472 0.02104672 156.1668348 -2.193588808 -0.319419476 MNLSEEVDLEDYVARPDK ddPTM_BT-474_Pertuzumab_2h_R1 5 MNLSEEVDLEDYVARPDK 18 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;;; 324.29 4.75E-62 2652960000 1465316 1433475 1273532 1612824 1379807 1286695 1805054 1836804 2109850 2153864 FALSE TRUE 1408049.831 1392593.697 1503687.562 1696062.04 1424189.745 1312712.854 1827144.791 1798873.356 1870348.673 2007980.873 0.701226715 0.693529363 0.748855521 0.844660456 0.709264597 0.653747689 0.909941332 0.895861798 0.931457415 1 20.9373141 2.193626638 9.874978592 0.922267072 0.729607916 0.783215452 0.053715686 0.206654641 43.65774566 0.021077326 0.015601569 156.1804384 -2.193626638 -0.192659156 LDDFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDDFFK 6 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 101.52 0.084748 390820000 873590 846060 645740 734860 746900 761070 826310 871000 913140 925840 FALSE TRUE 839449.137 821931.1972 762439.5824 772786.2127 770924.7168 776459.3569 836422.629 853013.5456 809484.1754 863132.0321 0.972561677 0.952265895 0.883340618 0.895327927 0.893171251 0.899583526 0.969055252 0.988277012 0.937845133 1 19.71922174 2.193643562 7.520814105 0.974683002 0.91424487 0.469459636 0.030045375 0.206413901 28.61091089 0.012001818 0.008911681 156.1865248 -2.193643562 -0.060438132 TLEEDEEELFK ddPTM_BT-474_Pertuzumab_2h_R1 4 TLEEDEEELFK 11 0 P43487;F6WQW2;P43487-2;C9JJ34;C9JDM3 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;; 273.9 9.73E-27 1505270000 2120910 1829730 1545810 1545930 1810990 1994620 1991000 2188200 2521380 2382540 FALSE TRUE 2038022.492 1777547.892 1825172.253 1625715.633 1869242.138 2034952.583 2015366.454 2143012.905 2235163.513 2221168.444 0.917545222 0.800276043 0.821717173 0.731919111 0.841558029 0.916163107 0.907345168 0.964813322 1.006300769 1 21.08288737 2.193765816 1.09000614 0.996732009 0.816070484 0.708050189 0.046168541 0.282228639 0.636350738 0.033514287 0.018188052 156.2304975 -2.193765816 -0.180661526 IPS(ph)PNILK ddPTM_BT-474_Pertuzumab_2h_R1 5 IPSPNILK 8 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK 120.63 0.0015397 5313950000 7661520 7392740 6171190 6921440 7227500 7261410 7864930 8566160 8924490 8766320 TRUE FALSE 7362099.328 7181906.293 7286461.31 7278656.348 7459979.101 7408240.685 7961183.366 8389265.803 7911419.31 8172569.338 0.900830452 0.878781935 0.891575343 0.890620324 0.912807074 0.906476333 0.974134698 1.026515096 0.968045541 1 22.96235828 2.193819883 2.964589502 1.001485894 0.894685045 0.901184865 0.015626943 0.06865845 1.233943241 0.00649767 0.004580134 156.2499484 -2.193819883 -0.106800849 MLISAVS(ph)PEIR ddPTM_BT-474_Pertuzumab_2h_R1 6 MLISAVSPEIR 11 0 A0AVK6;E9PMT9 A0AVK6 E2F8 Transcription factor E2F8 1 MLISAVS(1)PEIR;MLIS(0.375)AVS(0.625)PEIR;MLIS(0.012)AVS(0.988)PEIR;MLISAVS(1)PEIR;MLISAVS(1)PEIR;MLISAVS(1)PEIR 225.63 5.59E-12 618332000 864323 884452 654528 826033 786073 709114 718176 716847 633361 720362 TRUE FALSE 830544.3016 859228.2949 772815.7695 868664.6621 811357.7519 723452.7709 726965.2527 702043.8589 561464.5145 671571.2401 1.23671809 1.279429856 1.150757691 1.293481034 1.208148449 1.07725395 1.082484194 1.04537511 0.836046098 1 19.35718092 2.19425333 0.899515234 0.939649493 1.243571558 0.780027547 0.063217 0.265890483 0.406171303 0.048259869 0.026897772 156.4059716 -2.19425333 0.303922065 LEADYDKK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEADYDKK 8 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ;;; 113.62 0.0070485 717710000 2233740 1896580 1647270 1511060 1543170 1114270 2362180 2230760 2813110 2941670 FALSE TRUE 2146442.971 1842491.395 1944968.332 1589045.988 1592807.465 1136801.303 2391089.065 2184694.026 2493777.546 2742428.071 0.78267977 0.671846753 0.709213982 0.579430325 0.580801911 0.414523653 0.871887613 0.796627649 0.90933198 1 21.38702235 2.194531686 24.98885781 0.868647226 0.625308251 0.62019024 0.103244222 101.3774221 57536.68377 0.040027441 0.029562381 156.5062501 -2.194531686 -0.243338976 IGALHSIVFAGFSSESLCER ddPTM_BT-474_Pertuzumab_2h_R1 2 IGALHSIVFAGFSSESLCER 20 0 Q9NR19;Q9NR19-2;C9J7L5 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 218.37 9.94E-25 833590000 475760 494640 451250 563520 563680 536960 466030 467270 526750 505090 FALSE TRUE 457166.7732 480533.3515 532800.913 592603.3347 581811.2791 547817.6991 471733.4145 457620.7112 466955.5483 470879.8044 0.970877852 1.020501085 1.13150088 1.258502338 1.23558342 1.163391791 1.001812798 0.971841873 0.991666119 1 18.84499932 2.194614192 6.807519417 0.98646336 1.13574913 0.407310358 0.081780653 0.219926511 25.36907622 0.03507808 0.026092578 156.5359857 -2.194614192 0.149285769 TSDIFGSPVT(ph)ATSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSDIFGSPVTATSR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 1 TSDIFGS(0.36)PVT(0.64)ATSR 206.67 1.18E-07 3160500000 1244100 1294200 1220100 1177800 1125800 1337900 1285100 1500900 1473000 1525900 TRUE FALSE 1195479.197 1257290.683 1440599.211 1238586.399 1162012.379 1364953.255 1300827.438 1469905.891 1305791.215 1422549.434 0.840377964 0.883829168 1.01268833 0.870680744 0.816852021 0.959512002 0.914433908 1.03328985 0.917923261 1 20.44004736 2.194646443 2.025588088 0.983105487 0.89317981 0.294287459 0.059340022 0.417084062 3.419368621 0.029842636 0.018786113 156.5476107 -2.194646443 -0.089925677 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSR 44 2 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 2 VGDPPQPLPEEPMEVQGAERAS(1)PEPQRENAS(0.995)PAPGT(0.002)T(0.002)AEEAMS(0.001)R;VGDPPQPLPEEPMEVQGAERAS(0.998)PEPQRENAS(0.91)PAPGT(0.034)T(0.033)AEEAMS(0.025)R 70.686 0.00072677 213768000 29782 31130 18987.9 22497 31610 32096 22578 23261 27002 25010 TRUE FALSE 28618.08651 30242.20288 22419.43591 23658.07287 32626.76436 32745.00311 22854.31632 22780.65222 23936.84616 23316.05042 1.227398551 1.297055133 0.961545181 1.01466897 1.399326377 1.404397508 0.980196727 0.977037354 1.026625253 1 14.50903581 2.194737774 24.96633627 0.991733176 1.208444287 0.390012567 0.135346871 157.983068 90003.64706 0.055654758 0.041103994 156.5805355 -2.194737774 0.216711111 GIMVLAGDTLPIEVYCHLPVMCEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIMVLAGDTLPIEVYCHLPVMCEDR 25 0 D6RC52;D6RCB9;Q9NX24;H0YC83 D6RC52 NHP2 H/ACA ribonucleoprotein complex subunit 2 0 ; 305.18 1.18E-63 556390000 211887 220633 178235 227990 205150 237933 192031 211480 203977 221874 FALSE TRUE 203606.2218 214340.7629 210446.0293 239756.5912 211748.8361 242744.1683 194381.1328 207112.8641 180822.3861 206846.2764 0.98433593 1.036232156 1.017403035 1.159105184 1.023701465 1.17354865 0.939737163 1.001288821 0.874187292 1 17.65819946 2.19474465 24.99999932 0.958480617 1.064519416 0.410888347 0.065545861 140.1285562 79952.06195 0.023828406 0.017598541 156.5830148 -2.19474465 0.106038799 EHTTSSSVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHTTSSSVSK 10 0 Q9P013 Q9P013 CWC15 Spliceosome-associated protein CWC15 homolog 0 ; 119.34 0.00070596 300920000 200345 241220 182553 209844 203197 190201 193404 136636 192971 211310 FALSE TRUE 192515.2959 234340.6418 215544.388 220674.074 209733.016 194046.9945 195770.936 133814.4189 171065.7411 196997.7855 0.97724599 1.189559777 1.094146249 1.120185557 1.064646567 0.985021197 0.993772268 0.679268645 0.868363777 1 17.58781989 2.194868807 1.966562565 0.821079318 1.091871379 0.499859406 0.096013635 0.21861251 1.685134177 0.04674967 0.029140826 156.6277854 -2.194868807 0.270792061 SPYLYPLYGLGELPQGFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPYLYPLYGLGELPQGFAR 19 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 182.33 6.86E-14 211510000 124730 128458 107168 120857 124045 116414 129632 136112 141625 131249 FALSE TRUE 119855.4137 124794.5036 126535.6415 127094.4443 128035.0201 118767.9708 131218.4752 133301.2396 125548.3237 122359.3883 0.979535901 1.019901336 1.03413104 1.038697937 1.046384931 0.970648615 1.072402183 1.08942388 1.026062041 1 16.90076527 2.194941132 24.9999989 1.058816102 1.018500462 0.143937325 0.033005136 190.5152945 109190.5212 0.012247923 0.009045719 156.6538712 -2.194941132 -0.04031564 AS(ph)PS(ph)PPPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPSPPPKR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 AS(1)PS(1)PPPKR 51.927 0.068689 0 66473 69253 53628 57184 59466 71041 67356 86870 87547 79226 TRUE FALSE 63875.16167 67277.97225 63319.77255 60135.27309 61378.7779 72477.49769 68180.32288 85076.10414 77609.03159 73859.95245 0.864814552 0.91088567 0.857295062 0.814179689 0.83101567 0.981282756 0.923102718 1.151857012 1.050759295 1 16.17250471 2.19501775 1.66417459 1.076166256 0.860266626 0.692025313 0.056531282 0.189099908 1.028425716 0.030900924 0.018224631 156.6815107 -2.19501775 -0.21589963 KIEFPLPDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KIEFPLPDEK 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 128.85 0.00051112 1393440000 2892200 2511800 2189900 2296200 2553200 2504300 2957600 3249300 3394400 3177300 FALSE TRUE 2779169.627 2440165.923 2585663.644 2414707.157 2635325.997 2554938.662 2993795.994 3182200.82 3009081.942 2962098.641 0.938243443 0.823796308 0.872916117 0.815201467 0.889682052 0.86254341 1.010700978 1.074306161 1.015861491 1 21.49818825 2.195039555 4.396820809 1.038934506 0.863328209 0.813282285 0.037062825 0.073848922 3.0795753 0.013483456 0.01000783 156.6893773 -2.195039555 -0.175606297 AEGTTYRDELLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEGTTYRDELLTK 13 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 132.93 0.00010313 660420000 369010 334950 301960 322930 334460 365100 411490 429250 515120 472870 FALSE TRUE 354588.6812 325397.554 356530.8891 339596.456 345218.2096 372482.5721 416525.9377 420385.8375 456645.7372 440842.0937 0.804343973 0.738127231 0.80874965 0.770335821 0.783088127 0.844934224 0.944841574 0.953597316 1.035848762 1 18.74990246 2.195227793 1.22470184 1.007419708 0.775095364 0.938580864 0.024849364 0.098057954 0.281423136 0.015684609 0.008590991 156.7573067 -2.195227793 -0.232324344 VVPSFLPVDQGGS(ph)LVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVPSFLPVDQGGSLVGR 17 0 Q14126 Q14126 DSG2 Desmoglein-2 1 VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR 223.5 3.17E-15 189255000 115019 235870 95252 245687 113955 132465 194714 236756 175905 126102 TRUE FALSE 110523.9303 229143.2185 112466.1553 258366.9355 117620.4661 135143.5331 197096.9682 231866.9059 155937.0019 117560.9992 0.940141127 1.949143169 0.956662124 2.197726603 1.000505838 1.149560942 1.676550637 1.972311459 1.326434812 1 16.84305 2.196314843 24.99807906 1.621067669 1.39478372 0 0.465323092 481.3900584 284849.9386 0.165577073 0.122287695 157.1501657 -2.196314843 -0.22628395 AGQAVDDFIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGQAVDDFIEK 11 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 175.91 2.16E-05 442790000 484270 454940 385850 431350 482210 472440 486860 577110 606860 587980 FALSE TRUE 465344.193 441965.5566 455581.6782 453612.0252 497720.7226 481993.0605 492818.3383 565192.4768 537971.797 548155.5909 0.848927204 0.806277568 0.831117452 0.827524215 0.907991692 0.879299725 0.899048275 1.031080383 0.981421709 1 19.06422593 2.196476579 0.902176669 1.01672803 0.829237821 0.842148492 0.029646167 0.208150046 0.319970741 0.023328738 0.013013721 157.2087008 -2.196476579 -0.187490208 AHHGEAGHHLPEPS(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHHGEAGHHLPEPSSR 16 0 O76061 O76061 STC2 Stanniocalcin-2 1 AHHGEAGHHLPEPS(0.5)S(0.5)R 93.5 0.0073724 164570000 112540 117160 89382 130820 79419 92100 82778 28522 73616 46513 TRUE FALSE 108141.8124 113818.7115 105535.3157 137571.6359 81973.58426 93962.3251 83791.06193 27933.01073 65259.4203 43362.63308 2.493894044 2.62481089 2.433784763 3.172584922 1.890419895 2.166896206 1.932333347 0.644172384 1.504969041 1 15.40416474 2.197104885 1.228448936 0.984519593 2.594562142 0.745120643 0.368349516 0.214710766 0.620395206 0.238062362 0.130670921 157.4363037 -2.197104885 1.610042549 DIKPIIKDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIKPIIKDEK 10 2 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 84.289 0.0084493 528460000 382740 345320 250370 225600 362890 401830 447600 500880 577700 612390 FALSE TRUE 367782.0977 335471.8117 295617.4285 237243.243 374562.6864 409955.2779 453077.8627 490536.653 512121.9179 570912.2798 0.644200713 0.587606579 0.517798336 0.41555113 0.656077474 0.71807052 0.793603288 0.859215453 0.897023827 1 19.12290957 2.197153458 0.914486268 0.94927167 0.543172742 0.853489809 0.065658121 0.222060233 0.350744671 0.054300556 0.030197189 157.453913 -2.197153458 -0.406098928 ELSNSPLRENS(ph)FGSPLEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELSNS(0.11)PLRENS(0.89)FGSPLEFR 188.96 3.96E-14 1256600000 307050 349070 246260 282050 320700 349730 268390 295620 305600 292540 TRUE FALSE 295050.1465 339114.8654 290764.66 296606.6343 331015.6068 356801.7802 271674.6371 289515.3437 270909.5692 272726.0052 1.081855565 1.243426952 1.066142042 1.087562714 1.213729532 1.308279274 0.996144966 1.061561194 0.993339704 1 18.05709275 2.197198207 24.99999993 1.021793641 1.164266166 0.505921373 0.074350583 135.7682992 82059.3941 0.028516442 0.021060977 157.4701376 -2.197198207 0.142472526 LKVSELKEELKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKVSELKEELKK 12 3 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 79.614 0.0098831 669160000 3328300 2508900 2234500 1462600 2258700 2535800 2534600 3021000 3194100 2628000 FALSE TRUE 3198226.356 2437348.628 2638323.856 1538084.961 2331353.137 2587075.613 2565619.193 2958615.294 2831519.159 2450003.219 1.305396798 0.994834868 1.076865465 0.627788955 0.951571459 1.055947842 1.047190131 1.207596493 1.155720587 1 21.22435221 2.197346035 2.266627399 1.138729315 0.980484285 0.08464086 0.164299816 0.613766753 6.361716498 0.079395868 0.052036274 157.5237473 -2.197346035 -0.15824503 DVTGS(ph)PPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVTGSPPAK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 DVT(0.053)GS(0.947)PPAK;DVT(0.311)GS(0.689)PPAK 100.55 0.0045066 984290000 3374510 3206140 2681360 2893640 3129190 3102620 3370840 3692850 3674860 3706420 TRUE FALSE 3242630.418 3114704.026 3165941.399 3042981.107 3229843.238 3165357.102 3412093.348 3616591.357 3257705.299 3455380.872 0.938429232 0.901406861 0.916235146 0.880649983 0.934728575 0.916066049 0.987472431 1.04665491 0.942791958 1 21.72041331 2.197565836 4.230174819 1.004978131 0.912940432 0.652848171 0.028257593 0.112605096 4.338820335 0.010608882 0.007871827 157.6034919 -2.197565836 -0.092037699 QHTGERPFTCAECGK ddPTM_BT-474_Pertuzumab_2h_R1 2 QHTGERPFTCAECGK 15 1 Q9BWE0;Q9BWE0-4 Q9BWE0 REPIN1 Replication initiator 1 0 ; 118.52 0.00017097 130564000 258730 242630 196502 215970 227230 209630 207470 139224 235950 237700 FALSE TRUE 248618.5456 235710.43 232014.2826 227116.2376 234539.0593 213868.8622 210009.0799 136348.9757 209165.9452 221600.3673 1.121922985 1.063673463 1.046994125 1.02489107 1.058387503 0.965110595 0.947692833 0.615292192 0.94388808 1 17.75760075 2.197749134 2.531360122 0.809260782 1.054220489 0.38643206 0.103845772 0.218337918 2.842697267 0.045046075 0.030568978 157.6700242 -2.197749134 0.244959707 SENSEDGAAWMQEPGRYS(ph)PPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SENSEDGAAWMQEPGRYSPPPR 22 1 P35548 P35548 MSX2 Homeobox protein MSX-2 1 SENSEDGAAWMQEPGRYS(1)PPPR;SENSEDGAAWMQEPGRYS(1)PPPR;SENSEDGAAWMQEPGRYS(1)PPPR 175.39 9.31E-13 1141990000 879790 820310 689460 892910 802020 904030 766120 759500 883120 980440 TRUE FALSE 845406.8341 796915.562 814060.759 938993.1921 827817.7017 922310.106 775496.0057 743816.0596 782871.9199 914033.9255 0.924918442 0.871866503 0.890624228 1.027306718 0.905675029 1.009054566 0.848432409 0.813772923 0.856502038 1 19.80188819 2.198139506 24.99992634 0.858197811 0.935627772 0.128379517 0.065634508 217.1103025 134278.6336 0.024022335 0.017741863 157.811812 -2.198139506 0.077429961 GHFFVEDQIYCEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHFFVEDQIYCEK 13 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 0 ;;; 192.14 2.97E-06 1523010000 2152980 2097890 1739590 2007030 2060820 2037280 1958990 1917430 2312450 2181000 FALSE TRUE 2068839.161 2038060.231 2053972.61 2110613.059 2127108.147 2078475.197 1982964.706 1877834.4 2049950.371 2033278.927 1.017489108 1.002351524 1.010177493 1.038034197 1.046146753 1.022228269 0.975254639 0.923549826 1.00819929 1 20.95537671 2.198160644 4.884135531 0.964532202 1.02316592 0.42176658 0.02501385 0.152280656 8.275945393 0.009742648 0.007269853 157.8194932 -2.198160644 0.058633718 YEPSDKDRQS(ph)PPPAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 YEPSDKDRQSPPPAKR 16 3 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 YEPSDKDRQS(1)PPPAKR 121.26 0.00055103 1330200000 144060 132400 158270 140800 153900 140990 190650 197970 233270 212100 TRUE FALSE 138429.9759 128624.0816 186872.9097 148066.7049 158850.3333 143840.9144 192983.2317 193881.8503 206790.1675 197734.2781 0.700080822 0.65048955 0.945070888 0.748816575 0.803352534 0.727445518 0.975972571 0.980517148 1.045798278 1 17.59320346 2.198207496 6.794132362 0.997828386 0.766980492 0.708361839 0.074808403 0.112977594 13.81900178 0.028488725 0.021230939 157.8365198 -2.198207496 -0.230847894 S(ph)LHS(ph)AHS(ph)LASR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 3 S(1)LHS(1)AHS(0.995)LAS(0.005)R 45.342 0.074965 0 179320 214810 161150 212860 197650 203430 168070 156220 199600 195620 TRUE FALSE 172311.9762 208683.8291 190273.3898 223845.7301 204007.5918 207543.494 170126.8909 152994.0024 176942.2448 182370.4832 0.944845751 1.144285114 1.043334351 1.227423025 1.118643698 1.138032265 0.932864178 0.838918666 0.970235105 1 17.47651272 2.198296078 6.651179486 0.912030326 1.108350506 0.502614132 0.080123638 0.134921993 15.73894516 0.029322485 0.021860549 157.8687166 -2.198296078 0.196320181 SQDATFS(ph)PGSEQAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQDATFSPGSEQAEK 15 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SQDATFS(1)PGSEQAEK;SQDATFS(1)PGSEQAEK 370.38 1.55E-97 825050000 819410 783440 702800 753050 714900 796840 897930 1024520 1024050 1005550 TRUE FALSE 787386.5513 761097.0583 829811.5937 791915.0007 737895.4078 812952.6508 908919.1359 1003363.304 907804.1372 937443.2028 0.839929874 0.811886049 0.885185994 0.844760513 0.787136123 0.867202032 0.969572485 1.070319035 0.968383081 1 19.83837176 2.198308813 3.114309038 1.020492186 0.835582069 0.849390752 0.034006782 0.0829793 1.653445777 0.013807447 0.009870927 157.8733458 -2.198308813 -0.184910117 GIDLLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 GIDLLKK 7 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 117.02 0.023313 0 1649680 1744500 1314990 1186200 1468810 1403090 1572370 1593480 1863700 1644500 FALSE TRUE 1585208.682 1694748.568 1552637.945 1247419.924 1516055.608 1431461.441 1591613.134 1560574.081 1652140.589 1533116.55 1.033977933 1.105427091 1.012733144 0.813649767 0.988871725 0.933693815 1.038155341 1.017909617 1.077635349 1 20.54803595 2.198554169 24.93513648 1.033210969 0.981170053 0.109320769 0.072757231 392.4740962 244618.0928 0.029550116 0.021824467 157.9625619 -2.198554169 -0.052040916 SFPIKPVPS(ph)PSWSGSCR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.947)PS(0.05)WS(0.002)GS(0.001)CR 97.69 0.0012188 670760000 1366400 1308200 1154400 1360000 1297700 1238300 1041900 1110400 1060800 1028200 TRUE FALSE 1312999.577 1270891.417 1363025.759 1430189.763 1339441.699 1263339.274 1054651.084 1087469.852 940382.4312 958559.0982 1.369763826 1.325835224 1.421952764 1.492020435 1.397349106 1.317956584 1.100246282 1.134483887 0.98103751 1 19.87050786 2.198706675 1.475340407 1.033624083 1.406977465 0.902082529 0.054649763 0.127604871 0.540172357 0.034806186 0.019881803 158.0180416 -2.198706675 0.373353382 RTLS(ph)MDK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTLSMDK 7 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 RT(0.01)LS(0.99)MDK;RT(0.001)LS(0.999)MDK 105.13 0.0048971 459300000 563270 555530 378390 467740 616400 335350 692370 780020 656720 639070 TRUE FALSE 541256.7857 539686.8283 446773.4902 491880.1175 636227.0658 342131.0068 700843.4312 763912.3144 582171.8988 595785.2197 0.908476357 0.90584125 0.749890188 0.825599732 1.067879908 0.574252256 1.176335713 1.282194135 0.977150623 1 19.18443281 2.198762081 24.99996128 1.150049995 0.847501146 0.443457672 0.145231975 123.5777079 77626.2128 0.052370498 0.038678715 158.0382023 -2.198762081 -0.302548849 KYELGRPAANTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYELGRPAANTK 12 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 131.06 0.00011554 5013400000 5928500 5749600 4316700 4398800 4742700 4932300 5620200 5732500 6621000 6427400 FALSE TRUE 5696807.666 5585627.037 5096823.714 4625822.595 4895253.253 5032034.485 5688981.689 5614121.872 5869411.837 5992066.473 0.950725045 0.932170406 0.850595323 0.771991201 0.816955766 0.839782821 0.949418988 0.936925833 0.979530495 1 22.5146222 2.198771532 6.852003174 0.958905241 0.857202888 0.504536881 0.051248617 0.195207051 24.59102592 0.021637907 0.016128398 158.0416415 -2.198771532 -0.101702352 S(ph)DSNFQVPNGGIPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDSNFQVPNGGIPR 14 0 D6RIF6;H0Y9L2;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 S(1)DSNFQVPNGGIPR;S(0.997)DS(0.003)NFQVPNGGIPR;S(0.999)DS(0.001)NFQVPNGGIPR;S(0.979)DS(0.021)NFQVPNGGIPR 239.51 2.42E-17 680090000 395610 395822 449872 400067 412454 407173 519524 578480 528106 619764 TRUE FALSE 380149.1238 384533.5441 531173.8777 420714.5058 425720.9575 415406.317 525882.0901 566534.1858 468157.6209 577786.8323 0.657940096 0.665528397 0.919324997 0.728148311 0.736813187 0.718961205 0.910166277 0.980524571 0.810260108 1 19.1401778 2.198813784 6.250900316 0.930961446 0.742199005 0.556280267 0.08196986 0.144340298 14.63207263 0.030971523 0.023117279 158.0570182 -2.198813784 -0.188762441 QEKPAEKPAETPVATS(ph)PTATDSTSGDSSR ddPTM_BT-474_Pertuzumab_2h_R1 7 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.174)S(0.825)PT(0.001)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.165)S(0.806)PT(0.027)AT(0.001)DSTSGDSSR;QEKPAEKPAET(0.012)PVAT(0.092)S(0.789)PT(0.094)AT(0.01)DS(0.002)T(0.001)SGDSSR;QEKPAEKPAET(0.001)PVAT(0.055)S(0.881)PT(0.058)AT(0.003)DS(0.001)TSGDSSR;QEKPAEKPAET(0.001)PVAT(0.118)S(0.863)PT(0.015)AT(0.003)DSTSGDSSR;QEKPAEKPAETPVAT(0.069)S(0.926)PT(0.005)AT(0.001)DSTSGDSSR;QEKPAEKPAETPVAT(0.057)S(0.943)PTATDSTSGDSSR 196.09 3.56E-25 1.4044E+11 8258170 8209060 7511310 7427810 8541510 8015490 6891270 7007390 7642200 6544090 TRUE FALSE 7935431.587 7974945.646 8868770.805 7811160.164 8816255.426 8177568.7 6975607.424 6862684.948 6774689.495 6100852.955 1.300708548 1.307185357 1.453693585 1.280339031 1.44508571 1.340397607 1.143382323 1.12487303 1.110449562 1 22.54057953 2.198869697 3.417740307 1.100273932 1.35992971 0.805809461 0.06285975 0.100948083 2.442634413 0.024436339 0.017762014 158.0773681 -2.198869697 0.259655778 LKDEEIR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKDEEIR 7 1 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 ;; 95.099 0.012508 1603070000 2946190 2942350 2580440 2582580 2887170 3158290 3027130 3268190 3720400 3624790 FALSE TRUE 2831049.638 2858437.059 3046782.91 2715867.263 2980038.445 3222152.788 3064176.922 3200700.734 3298075.789 3379279.745 0.837767173 0.845871687 0.901607188 0.803682284 0.881856097 0.953502826 0.906754443 0.947154712 0.97597004 1 21.68828435 2.198953729 0.526996247 0.998767181 0.838859498 0.755139375 0.030108307 0.450393105 0.261168893 0.028756286 0.023697624 158.1079578 -2.198953729 -0.159907683 S(ph)RSESETSTMAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.581)RS(0.411)ES(0.008)ETSTMAAK 163.45 2.35E-05 2300600000 1034800 890700 682610 784060 916400 843300 932200 1081300 971800 849100 TRUE FALSE 994358.872 865298.1081 805972.8116 824525.4306 945876.8383 860352.1038 943608.5425 1058970.777 861485.3381 791589.7007 1.256154383 1.093114409 1.018169907 1.041607072 1.194907965 1.086866217 1.192042471 1.337777356 1.088297811 1 19.59439332 2.199287417 8.509217296 1.199930117 1.110034982 0 0.106766153 0.55174579 107.6016639 0.039858406 0.029609019 158.2294857 -2.199287417 -0.089895135 SLGVLPFTLNSGS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGVLPFTLNSGSPEK 16 0 P42695 P42695 NCAPD3 Condensin-2 complex subunit D3 1 SLGVLPFTLNS(0.012)GS(0.988)PEK;SLGVLPFTLNS(0.017)GS(0.983)PEK 324.39 1.63E-58 958050000 1489220 1390560 919800 1076600 1205020 1206240 1303020 1400290 1422350 1433420 TRUE FALSE 1431019.636 1350902.59 1086028.321 1132163.455 1243780.563 1230630.999 1318966.749 1371373.522 1260890.791 1336333.187 1.07085542 1.010902523 0.812692771 0.847216447 0.930741356 0.920901323 0.98700441 1.026221257 0.94354522 1 20.34984833 2.199379817 5.747144853 0.99574219 0.926361181 0.127535934 0.071393051 0.367570075 30.40483908 0.029198528 0.021820202 158.2631541 -2.199379817 -0.06938101 LKDLSR ddPTM_BT-474_Pertuzumab_2h_R1 5 LKDLSR 6 1 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 120.49 0.018344 11023360000 11361180 12863850 11354450 11379490 10744040 8319840 14771580 12887430 14062440 14998290 FALSE TRUE 10917172.53 12496985.59 13406451.69 11966786.84 11089631.8 8488072.865 14952359.01 12621300.07 12466130.77 13982442.46 0.780777218 0.893762705 0.958806141 0.855843811 0.793111206 0.607052229 1.069366748 0.90265346 0.891556021 1 23.73711306 2.199382583 24.99997735 0.955860246 0.825889175 0.358343356 0.097963493 215.6048381 137578.826 0.038460677 0.028405549 158.264162 -2.199382583 -0.129971071 VTLDWAKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTLDWAKPK 9 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 85.377 0.013549 2315200000 4082800 3853700 3814200 3782100 3713300 3001400 4813500 4822200 5334000 5784400 FALSE TRUE 3923239.662 3743796.249 4503510.786 3977294.634 3832741.667 3062090.364 4872409.053 4722619.885 4728506.682 5392617.436 0.727520487 0.694244732 0.835125213 0.737544371 0.710738656 0.567830075 0.903533231 0.875756521 0.876848161 1 22.36255426 2.199730189 24.99855351 0.900683947 0.718030154 0.666751147 0.069586231 106.2940723 68430.22066 0.026371789 0.019477198 158.3908863 -2.199730189 -0.182653793 IS(ph)PDLNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISPDLNIK 8 0 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 IS(1)PDLNIK;IS(1)PDLNIK 128.01 0.001208 376670000 926180 823080 890950 813780 888060 936400 1022040 1149580 1187410 1230360 TRUE FALSE 889983.8617 799606.5643 1051964.484 855779.2833 916625.2564 955334.6496 1034548.031 1125840.771 1052620.195 1147026.621 0.775905149 0.697112473 0.91712299 0.746084936 0.799131633 0.83287923 0.901938989 0.981529766 0.917694651 1 20.12946744 2.199742981 1.670468991 0.967421809 0.786263552 0.669826576 0.055605786 0.21816683 1.197525069 0.029861645 0.01771609 158.3955519 -2.199742981 -0.181158257 KIGEEEIQKPEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KIGEEEIQKPEEK 13 2 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 171.76 1.38E-05 358240000 570320 488810 443460 344500 470490 426090 506680 514140 631920 485350 FALSE TRUE 548031.2639 474869.6174 523603.0867 362279.6863 485623.7381 434705.8317 512880.9014 503522.8293 560187.0908 452476.8122 1.211180881 1.049489398 1.157193192 0.80065912 1.073256629 0.960725102 1.133496541 1.112814659 1.238045963 1 18.78748434 2.199759504 24.65552434 1.128704165 1.038095931 0.096834525 0.116904651 302.411916 192160.5762 0.042938275 0.031712647 158.4015782 -2.199759504 -0.090608234 KVTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVTFFEPGSGDENGTSNKEDEFR 23 2 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 KVTFFEPGS(1)GDENGTSNKEDEFR 155.45 1.49E-08 231810000 268050 248840 175870 169500 219760 217100 230680 255180 271110 214630 TRUE FALSE 257574.3097 241743.3268 207653.6212 178247.9153 226828.78 221489.9107 233503.1308 249910.4438 240334.7294 200092.9189 1.287273488 1.208155332 1.037785956 0.890825704 1.133617227 1.106935278 1.166973485 1.248971953 1.201115615 1 17.61031059 2.19986519 4.350250677 1.184357541 1.102466998 0.005676011 0.115662235 0.552318863 22.89747812 0.046974619 0.034962544 158.44013 -2.19986519 -0.081890543 LREDGIQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LREDGIQK 8 1 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 ;;; 146.79 0.00049955 2302780000 2090510 2143050 2050980 2057580 1989280 1757850 2430850 2349470 2495430 2555480 FALSE TRUE 2008810.558 2081932.312 2421637.71 2163771.95 2053266.998 1793394.931 2460599.469 2300952.623 2212159.248 2382395.063 0.843189523 0.873882063 1.016471931 0.908233896 0.861849921 0.752769748 1.03282596 0.965814889 0.928544255 1 21.18398124 2.200408726 24.99994347 0.979464657 0.883164545 0.378135491 0.066022004 204.2203843 133819.1376 0.026143662 0.019308763 158.6385478 -2.200408726 -0.096300112 KAEGAPNQGR ddPTM_BT-474_Pertuzumab_2h_R1 6 KAEGAPNQGR 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;;; 177.44 3.73E-06 838295000 704993 843166 577697 811832 675898 674549 791865 869281 803852 675309 FALSE TRUE 677441.0941 819119.7312 682099.6987 853730.7468 697638.873 688188.8429 801556.0807 851330.0436 712602.091 629569.7199 1.076038241 1.301078666 1.083437905 1.356054333 1.108120119 1.09310982 1.273180802 1.352241089 1.131887491 1 19.26400663 2.200447778 24.9926348 1.234937197 1.177372797 0 0.126196839 593.8664298 389426.7614 0.045447612 0.033565866 158.6528136 -2.200447778 -0.0575644 FGDEDLTWQDEHSAPFSWETK ddPTM_BT-474_Pertuzumab_2h_R1 1 FGDEDLTWQDEHSAPFSWETK 21 0 Q9H425;Q9H425-3;E5RI90 Q9H425 C1orf198 Uncharacterized protein C1orf198 0 139.11 5.26E-07 92895000 62804 69271 53108 67583 56139 62859 76960 83502 84452 92810 FALSE TRUE 60349.55025 67295.4589 62705.79698 71070.96673 57944.76192 64130.05205 77901.8595 81777.65452 74865.36301 86523.89603 0.697489977 0.777767322 0.7247223 0.821402757 0.669696634 0.74118313 0.900350806 0.94514531 0.865256495 1 16.40081101 2.200513728 4.554503953 0.928210768 0.739782396 0.778481343 0.049568172 0.089808893 4.167604085 0.017968161 0.013405005 158.6769075 -2.200513728 -0.188428372 KDVHMPK ddPTM_BT-474_Pertuzumab_2h_R1 3 KDVHMPK 7 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ;; 84.476 0.013968 2111340000 6821950 6208900 5600680 5599700 6047540 5168710 7030920 6875300 7691790 7407030 FALSE TRUE 6555340.652 6031828.251 6612847.462 5888701.188 6242064.616 5273224.858 7116966.502 6733322.652 6818650.246 6905345.261 0.94931396 0.873501327 0.957641829 0.852774331 0.90394678 0.76364391 1.030646004 0.975088486 0.987445231 1 22.71928212 2.200911952 24.99997575 0.995184574 0.885923868 0.53501075 0.052380075 132.7641912 88159.12463 0.018974253 0.014013728 158.8224723 -2.200911952 -0.109260706 GFGFVYFQNHDAADK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVYFQNHDAADK 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 167.32 1.32E-06 5864300000 1014340 931440 862250 889410 964130 864440 1026450 1045020 1158150 1027630 FALSE TRUE 974698.4714 904876.2432 1018077.756 935312.5567 995142.1171 881919.5691 1039012.002 1023439.972 1026681.667 958027.7048 1.017401132 0.944519912 1.062680913 0.976289675 1.038740437 0.920557479 1.084532313 1.068278054 1.071661772 1 19.86970785 2.200931922 24.99998876 1.063312724 0.995581648 0.315383551 0.044723988 174.8076487 116138.8365 0.01547211 0.011427168 158.8297755 -2.200931922 -0.067731076 ISMPDLDLHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISMPDLDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 148.28 3.49E-05 1411370000 2053900 2079000 1709870 2034100 1620760 1878160 2148530 2200700 2518000 2452600 FALSE TRUE 1973631.317 2019708.956 2018881.545 2139080.145 1672893.217 1916137.682 2174824.353 2155254.776 2232167.196 2286483.217 0.863173323 0.883325511 0.88296364 0.935532843 0.731644652 0.838028317 0.951165675 0.942606864 0.976244732 1 21.1246989 2.201041029 7.196460335 0.960768996 0.856257651 0.535679072 0.050816729 0.179351706 26.36177257 0.019918828 0.014854241 158.869683 -2.201041029 -0.104511345 QLIDKETNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLIDKETNDR 10 1 P15924 P15924 DSP Desmoplakin 0 ; 103.91 0.0025097 648530000 853150 853000 636630 711820 796770 872760 701310 797030 828730 799530 FALSE TRUE 819807.9548 828673.2752 751683.2028 748557.1155 822398.8307 890407.8052 709892.8416 780571.052 734656.0447 745377.121 1.099856612 1.11175035 1.008460257 1.004266289 1.103332538 1.194573566 0.952394193 1.047216275 0.985616575 1 19.50761101 2.201098284 24.9999964 1.003565677 1.081569832 0.387073592 0.055379088 216.0408432 144170.7649 0.021924158 0.016192403 158.8906287 -2.201098284 0.078004154 TT(ph)PDQELVPASEPVWERPWSVEEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPDQELVPASEPVWERPWSVEEIR 25 1 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 T(0.188)T(0.812)PDQELVPASEPVWERPWSVEEIR 132.78 0.00010851 185860000 9887.6 7880.1 7629.5 9124.5 7353.3 6140.2 10731 10909 11550 12717 TRUE FALSE 9501.181661 7655.367263 9008.320367 9595.416538 7589.825573 6264.359051 10862.32919 10683.72534 10238.89242 11855.66626 0.801404278 0.645713796 0.759832486 0.809352788 0.640185495 0.528385239 0.91621415 0.901149299 0.863628597 1 13.53328912 2.201108338 24.99550795 0.910997158 0.700441198 0.622128262 0.08491243 118.2387025 78911.38927 0.032431933 0.023953139 158.8943071 -2.201108338 -0.21055596 EWAMNVGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EWAMNVGDK 9 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 134.68 0.00056348 154990000 286970 280190 240290 260570 280100 277760 318250 348770 349840 375910 FALSE TRUE 275754.8951 272199.2555 283715.7482 274018.0489 289109.6709 283376.4975 322144.8387 341567.7776 310127.6298 350449.2809 0.786861067 0.776715121 0.809577202 0.781905011 0.824968652 0.808609157 0.919233841 0.974656808 0.884942977 1 18.41884614 2.201179909 3.190250466 0.950468949 0.796255154 0.852882041 0.030095704 0.083507774 1.751903193 0.011680401 0.008407891 158.9204949 -2.201179909 -0.154213795 EELEEVIKDI ddPTM_BT-474_Pertuzumab_2h_R1 4 EELEEVIKDI 10 1 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 166.33 4.55E-05 1254020000 2350550 2272620 1847970 1912910 2143250 2207250 2381320 2673540 2791950 2665010 FALSE TRUE 2258687.907 2207807.103 2181939.287 2011635.514 2212189.583 2251882.107 2410463.306 2618330.465 2475019.541 2484506.499 0.909109277 0.888630037 0.878218386 0.809672068 0.890393961 0.906369981 0.970198028 1.053863399 0.996181552 1 21.24452789 2.201261189 2.245025854 1.022141077 0.873774754 0.823768155 0.028985155 0.116486796 1.184924194 0.014060704 0.009221712 158.9502405 -2.201261189 -0.148366323 KVMDS(ph)DEDDDY ddPTM_BT-474_Pertuzumab_2h_R1 6 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(0.985)DEDDDY(0.015);KVMDS(1)DEDDDY;KVMDS(0.994)DEDDDY(0.006) 136.3 0.00010815 10387640000 10032480 9212830 8132480 8180130 8554620 9284150 9655120 10478760 11603350 10581340 TRUE FALSE 9640399.59 8950089.109 9602200.042 8602307.49 8829787.121 9471881.874 9773282.247 10262369.94 10286186.35 9864656.417 0.977266636 0.907288478 0.973394271 0.872033158 0.895093225 0.960183657 0.990737217 1.040317018 1.042731335 1 23.23383737 2.201464935 2.180814162 1.030206168 0.924379084 0.648175991 0.03286411 0.181908724 1.742423694 0.015542985 0.010098912 159.024828 -2.201464935 -0.105827084 LMGEDEKPAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMGEDEKPAAK 11 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 106.01 0.002179 408090000 219530 233100 183610 197950 263220 274510 283220 334820 410470 390180 FALSE TRUE 210950.5249 226452.2162 216792.4114 208166.2232 271686.7104 280060.7803 286686.1311 327905.85 363875.1664 363752.7611 0.579928313 0.622544323 0.59598836 0.572273933 0.746899376 0.7699207 0.788134584 0.901452539 1.000336507 1 18.47259867 2.201699758 0.635033505 1.018180828 0.578799881 0.944375255 0.037279221 0.164672854 0.130901278 0.033987779 0.023307228 159.1108362 -2.201699758 -0.439380947 GDDDEES(ph)DEEAVKK ddPTM_BT-474_Pertuzumab_2h_R1 4 GDDDEESDEEAVKK 14 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK 256.96 1.53E-24 6031400000 3946920 3174430 3805940 3224400 3847470 3305580 4761240 5463540 5299320 4493300 TRUE FALSE 3792670.003 3083898.364 4493758.021 3390811.67 3971227.367 3372421.092 4819509.479 5350715.99 4697763.41 4188964.789 0.905395532 0.736195819 1.072760992 0.80946292 0.948021186 0.805072676 1.150525183 1.27733611 1.121461661 1 21.99816233 2.201772088 8.868542788 1.173399823 0.88175096 0.567185438 0.108530567 0.177247646 39.2854943 0.038396694 0.02853573 159.1373376 -2.201772088 -0.291648863 ADLDVSGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADLDVSGPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 125.82 0.0011421 509560000 1174420 1030900 915300 953450 962590 941860 1089500 1058510 1273190 1141450 FALSE TRUE 1128522.368 1001499.741 1080715.071 1002657.669 993552.5816 960905.0545 1102833.627 1036651.399 1128662.809 1064138.575 1.060503204 0.941136582 1.015577385 0.942224718 0.93366842 0.902988649 1.036362794 0.974169552 1.06063518 1 20.0212546 2.201798126 24.99999804 1.01193627 0.964586385 0.221107466 0.047050311 289.3144172 196744.0658 0.017404141 0.012854152 159.146879 -2.201798126 -0.047349885 S(ph)PQQTVPYVVPLSPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 S(1)PQQTVPYVVPLSPK;S(1)PQQTVPYVVPLSPK;S(1)PQQTVPYVVPLSPK 241.68 7.17E-18 375020000 460900 439150 395720 431130 390120 519700 561190 627550 752660 681830 TRUE FALSE 442887.5184 426625.872 467235.4067 453380.671 402668.5641 530208.6901 568058.0111 614590.8732 667221.1922 635649.0468 0.696748498 0.671165754 0.735052478 0.713256274 0.633476234 0.834121742 0.89366611 0.966871383 1.049669146 1 19.27787092 2.202000657 1.340812024 1.013714208 0.690946383 0.931337217 0.037342237 0.102634998 0.356200976 0.023458558 0.013134435 159.2211137 -2.202000657 -0.322767825 SKRPPKS(ph)PEEEGQMS(ph)S ddPTM_BT-474_Pertuzumab_2h_R1 1 SKRPPKSPEEEGQMSS 16 3 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 2 S(0.003)KRPPKS(0.997)PEEEGQMS(0.535)S(0.465) 98.121 0.0040788 339590000 449970 338100 239620 213430 284970 281320 348920 394510 406640 297440 TRUE FALSE 432384.6749 328457.719 282924.6643 224445.1479 294136.3189 287008.4831 353190.1873 386363.2306 360479.932 277294.1239 1.559299811 1.184510203 1.0203053 0.809411843 1.060737656 1.035032691 1.273702387 1.393333639 1.29999124 1 18.08105752 2.202029966 9.867257462 1.287559009 1.094710801 0.069491188 0.202428694 0.746369208 193.6720684 0.078616255 0.0583328 159.2318591 -2.202029966 -0.192848208 RPGS(ph)VSSTDQER ddPTM_BT-474_Pertuzumab_2h_R1 3 RPGSVSSTDQER 12 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RPGS(0.862)VS(0.021)S(0.039)T(0.078)DQER;RPGS(0.926)VS(0.035)S(0.035)T(0.005)DQER;RPGS(0.993)VS(0.005)S(0.001)T(0.001)DQER 136.33 0.00011847 615460000 423601 444098 361112 424379 462765 443329 360704 370829 388067 374926 TRUE FALSE 407046.2046 431432.7599 426372.9713 446281.251 477650.2565 452293.4161 365118.4035 363171.2516 344015.2611 349531.9281 1.16454656 1.234315738 1.21983984 1.276796811 1.366542562 1.293997429 1.044592422 1.039021681 0.984216987 1 18.41506472 2.202083996 6.568908732 1.021260379 1.26214026 0.840483399 0.051733377 0.077980711 9.417230299 0.021425508 0.01601446 159.2516702 -2.202083996 0.24087988 S(ph)SVKTPESIVPIAPELQPSTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSVKTPESIVPIAPELQPSTSR 22 1 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.362)S(0.362)VKT(0.275)PES(0.001)IVPIAPELQPSTSR;S(0.357)S(0.357)VKT(0.281)PES(0.004)IVPIAPELQPSTSR;S(0.363)S(0.363)VKT(0.272)PES(0.001)IVPIAPELQPSTSR 101.93 0.0003829 768710000 579410 502090 499360 478510 503080 587320 533810 630570 696310 631550 TRUE FALSE 556766.0166 487770.8848 589605.4602 503205.9584 519262.0251 599196.0128 540342.9265 617548.5091 617267.808 588774.556 0.945635322 0.828451026 1.001411243 0.854666618 0.881936931 1.01770025 0.91774164 1.048870918 1.048394163 1 19.1673558 2.20213742 1.149797268 1.03410942 0.903388431 0.432340247 0.05764487 0.428489656 1.08059958 0.037515999 0.020546329 159.2712614 -2.20213742 -0.130720989 MLAES(ph)DES(ph)GDEESVSQTDKTELQNTLR ddPTM_BT-474_Pertuzumab_2h_R1 8 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 2 MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(0.997)GDEES(0.003)VSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR 190.77 3.22E-18 6782210000 3335980 3369710 2843630 3075640 3265400 3408600 3482250 3900680 4130160 4126970 TRUE FALSE 3205606.213 3273609.17 3357537.197 3234374.149 3370434.557 3477524.227 3524866.817 3820129.595 3661321.552 3847446.646 0.833177561 0.850852389 0.872666344 0.840654711 0.87601853 0.903852489 0.916157426 0.992899953 0.951623736 1 21.87546989 2.202178564 0.915709324 0.991835065 0.848367134 0.908453366 0.017421245 0.149789578 0.237448217 0.012928594 0.007215482 159.2863512 -2.202178564 -0.143467931 IDEDGKK ddPTM_BT-474_Pertuzumab_2h_R1 5 IDEDGKK 7 1 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;;;; 100.45 0.015688 2706430000 5801150 5028820 4526630 4340130 5334940 5753270 6929340 7927310 8634770 8820630 FALSE TRUE 5574434.644 4885402.977 5344692.735 4564124.629 5506543.19 5869605.061 7014143.336 7763608.278 7654587.11 8223200.873 0.677891095 0.59409992 0.649952837 0.555030176 0.669635009 0.713785927 0.852969962 0.944110256 0.930852502 1 22.97126864 2.202311491 1.339845386 0.968410368 0.619336496 0.944831557 0.035466532 0.085498417 0.296303832 0.021126098 0.011830175 159.3351122 -2.202311491 -0.349073872 EEVGEEAIVELVENGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEVGEEAIVELVENGKK 17 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 184.22 1.04E-09 438430000 428260 403930 410560 485490 511860 531230 651750 774960 888980 889340 FALSE TRUE 411523.1257 392410.3119 484757.3249 510546.1971 528324.4418 541971.8346 659726.3115 758956.8052 788066.7173 829104.2097 0.496346685 0.473294319 0.58467599 0.615780491 0.637223205 0.653683612 0.79570976 0.915393742 0.950503819 1 19.66119392 2.202361968 0.62426836 1.023243932 0.503527046 0.965667888 0.033462669 0.13595326 0.104886909 0.032725627 0.022792455 159.3536326 -2.202361968 -0.519716886 NVRS(ph)DIS(ph)DQEEDEESEGCPVSINLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 NVRSDISDQEEDEESEGCPVSINLSK 26 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;H0YBA1 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 2 NVRS(1)DIS(1)DQEEDEESEGCPVSINLSK;NVRS(1)DIS(1)DQEEDEESEGCPVSINLSK 115.92 0.00062381 335860000 301490 301980 237570 263350 292750 304290 310110 336800 376200 367930 TRUE FALSE 289707.4375 293367.8261 280504.1837 276941.5251 302166.5696 310442.9523 313905.2189 329844.9623 333495.3532 343009.7734 0.844604032 0.855275414 0.817773152 0.807386689 0.880926997 0.905055705 0.915149489 0.96161972 0.972261956 1 18.38789016 2.202630857 0.788931133 0.992932841 0.830544817 0.919811486 0.017883964 0.176892456 0.209467229 0.015807082 0.009335377 159.4523253 -2.202630857 -0.162388025 LKEGHETPMDIDS(ph)DDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEGHETPMDIDSDDSK 17 1 Q8TDB6 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 1 LKEGHETPMDIDS(1)DDSK 189.47 2.13E-10 184250000 186490 164080 151230 137960 159750 154140 209110 219310 249280 238220 TRUE FALSE 179201.7646 159400.5991 178560.6251 145080.1321 164888.5038 157256.8164 211669.1507 214781.1719 220982.7795 222085.1472 0.806905671 0.717745428 0.804018762 0.653263552 0.742456242 0.708092452 0.953099086 0.967111824 0.995036283 1 17.76075338 2.202713662 6.380439532 0.976244764 0.736929338 0.879185365 0.043612138 0.057149218 6.475916776 0.015815537 0.011832028 159.4827304 -2.202713662 -0.239315426 SPSSQETHDS(ph)PFCLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSSQETHDSPFCLR 15 0 Q8TB45;Q8TB45-2 Q8TB45 DEPTOR DEP domain-containing mTOR-interacting protein 1 SPSSQETHDS(1)PFCLR;SPSSQETHDS(1)PFCLR;SPSSQETHDS(1)PFCLR 190.31 1.43E-07 1620120000 891360 959300 829860 911380 763130 916000 728330 650960 886110 874210 TRUE FALSE 856524.6657 931941.7033 979834.1621 958416.431 787676.7695 934522.1476 737243.5204 637517.4485 785522.5077 814998.978 1.050951828 1.143488186 1.202252013 1.175972556 0.966475776 1.14665438 0.904594411 0.782230979 0.963832506 1 19.63643872 2.202764896 6.65807053 0.881152805 1.115786241 0.570852504 0.083944595 0.119145657 15.05888329 0.031843441 0.023807103 159.5015457 -2.202764896 0.234633436 VDKWWGNR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDKWWGNR 8 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 107.15 0.0037006 2275000000 2382300 2304280 2352200 2660500 2403800 1994890 2962800 3063900 3071700 3305500 FALSE TRUE 2289197.082 2238564.191 2777294.864 2797808.724 2481120.41 2035228.043 2999059.633 3000629.394 2723013.494 3081615.541 0.742856158 0.726425526 0.901246384 0.907903237 0.80513626 0.660441906 0.973210186 0.973719581 0.883631802 1 21.55525545 2.202838456 24.99879656 0.958042208 0.798760824 0.535410337 0.075973095 153.7400757 107588.2822 0.030236368 0.022331815 159.5285641 -2.202838456 -0.159281384 SRS(ph)PLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPLLK 7 1 A0A0U1RQD2;Q6ZUS6-6;Q6ZUS6;Q6ZUS6-5;Q6ZUS6-4 A0A0U1RQD2 CCDC149 Coiled-coil domain-containing protein 149 1 S(0.255)RS(0.745)PLLK;S(0.044)RS(0.956)PLLK 85.355 0.01264 808520000 746660 766830 661970 668870 704720 735160 866520 948250 962800 1029750 TRUE FALSE 717479.7017 744960.7592 781602.7044 703390.4609 727387.9588 750025.4389 877124.731 928668.3061 853506.9804 960004.1153 0.747371485 0.775997464 0.814165994 0.732695256 0.757692542 0.78127315 0.913667678 0.967358672 0.88906596 1 19.87268106 2.202937062 3.504217124 0.947147818 0.766838818 0.875062842 0.032528945 0.073818225 1.89127065 0.012527663 0.009166345 159.564789 -2.202937062 -0.180309 RNS(ph)FSENEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RNSFSENEK 9 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 RNS(0.958)FS(0.042)ENEK;RNS(0.5)FS(0.5)ENEK;RNS(0.753)FS(0.247)ENEK;RNS(0.997)FS(0.003)ENEK;RNS(0.913)FS(0.087)ENEK;RNS(1)FSENEK 229.37 7.90E-08 6157600000 3813920 3607760 2933550 2968730 3208130 3479460 3580830 3839640 4302440 3973600 TRUE FALSE 3664867.79 3504870.217 3463707.741 3121946.511 3311322.415 3549817.065 3624653.269 3760350.092 3814045.049 3704464.533 0.989311075 0.946120603 0.935009017 0.842752437 0.893873429 0.958253759 0.978455384 1.015086002 1.029580663 1 21.82083359 2.202955024 1.98167887 1.014819083 0.92013253 0.548045388 0.036577154 0.26842579 2.107447592 0.02001337 0.012609369 159.5713886 -2.202955024 -0.094686553 RGSDELTVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSDELTVPR 10 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 110.84 0.002939 256860000 62068 66596 53174 61504 70795 57727 61179 47032 69097 68411 FALSE TRUE 59642.31394 64696.74728 62783.72465 64678.22881 73072.18547 58894.27949 61927.7269 46060.77276 61253.39824 63777.46204 0.935162862 1.014413952 0.984418675 1.014123591 1.145736803 0.923434041 0.970997041 0.722210814 0.960423891 1 15.96075907 2.203172546 2.579430295 0.865263234 1.014204689 0.180762056 0.090828205 0.310147073 4.20286196 0.039005629 0.026746639 159.6513318 -2.203172546 0.148941455 SLLSS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLLSSPTK 8 0 Q92667-2;Q92667;I3NI36 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 SLLS(0.039)S(0.961)PTK;SLLS(0.001)S(0.999)PT(0.001)K 190.57 0.00019482 713870000 1760720 2096400 1867510 2312700 1467280 1332150 2547700 2626000 2433800 2564500 TRUE FALSE 1691909.116 2036612.725 2205010.6 2432058.724 1514476.394 1359086.986 2578879.515 2571772.182 2157525.227 2390804.131 0.707673663 0.851852604 0.922288267 1.01725553 0.633459 0.568464379 1.078666162 1.075693382 0.902426593 1 21.18906451 2.203254115 24.99993483 1.028494787 0.796719542 0.417542234 0.132505509 189.9696748 134513.2159 0.053678919 0.039646032 159.6813202 -2.203254115 -0.231775245 PTRPDK ddPTM_BT-474_Pertuzumab_2h_R1 2 PTRPDK 6 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 103.91 0.031268 765620000 735770 591320 722300 689050 747090 737930 911390 923810 1122540 1074290 FALSE TRUE 707015.295 574456.1326 852835.6775 724611.9531 771120.8283 752851.4502 922543.8634 904733.0007 995113.9653 1001527.381 0.70593706 0.573580057 0.851535059 0.723506882 0.769944829 0.751703313 0.921136936 0.903353236 0.993596365 1 19.93377043 2.203390383 0.569281458 1.018911162 0.679905855 0.739463433 0.06673097 0.410822742 0.270635252 0.059596353 0.045373614 159.7314313 -2.203390383 -0.339005307 VDTFPQPLAAPQCHTLLAPEMEDNEMS(ph)CSP ddPTM_BT-474_Pertuzumab_2h_R1 1 VDTFPQPLAAPQCHTLLAPEMEDNEMSCSP 30 0 B7Z4K4;Q9UET6-2;Q9UET6 B7Z4K4 FTSJ1 Putative tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase 1 VDTFPQPLAAPQCHTLLAPEMEDNEMS(0.5)CS(0.5)P 63.491 0.00072425 0 34098 36768 22426 29127 27916 35380 25183 25457 31610 25805 TRUE FALSE 32765.41246 35719.41264 26478.87706 30630.24796 28813.94349 36095.40784 25491.19709 24931.30405 28021.76532 24057.20437 1.361979221 1.484769888 1.100663097 1.273225579 1.19772618 1.500399103 1.059607621 1.036334217 1.164797243 1 14.55418138 2.203753017 24.74303012 1.064489452 1.309667003 0.521205772 0.119312535 135.7971855 96530.77288 0.044690581 0.033007704 159.8648619 -2.203753017 0.245177551 ASS(ph)PPDRIDIFGR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.147)S(0.853)PPDRIDIFGR;AS(0.085)S(0.915)PPDRIDIFGR;AS(0.189)S(0.811)PPDRIDIFGR;AS(0.115)S(0.885)PPDRIDIFGR 201.16 6.30E-08 13130120000 3913790 4422220 2649200 3179620 3445140 4159700 2959750 3280730 3458290 2929820 TRUE FALSE 3760834.76 4296102.615 3127969.371 3343720.569 3555956.057 4243811.984 2995972.306 3212981.779 3065719.418 2731380.682 1.376898791 1.572868493 1.14519715 1.224186944 1.301889583 1.553724097 1.096871017 1.176321485 1.122406495 1 21.38119897 2.203796739 24.98867173 1.119716659 1.35311089 0.492237621 0.130247265 179.2326667 128833.4633 0.050449806 0.037261326 159.8809569 -2.203796739 0.233394232 ADTSQEICS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADTSQEICSPR 11 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;H7C3P6 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 ADTSQEICS(1)PR 95.854 0.0078127 387400000 206550 257470 184050 232650 250160 255450 209130 217580 244080 240020 TRUE FALSE 198477.7976 250127.2077 217311.9292 244657.0944 258206.6236 260615.374 211689.3955 213086.897 216373.0617 223763.2316 0.886999156 1.117820859 0.971169068 1.09337487 1.153927845 1.164692573 0.946041912 0.952287359 0.966973261 1 17.77161347 2.203803902 24.97722609 0.960688979 1.068193058 0.264810818 0.079921548 231.2873371 166208.7701 0.030122123 0.022247644 159.8835941 -2.203803902 0.107504079 EEMHLEDSANFIK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEMHLEDSANFIK 13 0 P16615-5;P16615-2;P16615-3;P16615;H7C5W9;P16615-4 P16615-5 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 0 ; 220.9 2.00E-11 356870000 298930 471400 259070 601370 327010 377820 502820 587890 572170 423170 FALSE TRUE 287247.4851 457956.1335 305889.712 632406.7778 337528.5736 385459.7793 508973.6616 575749.8661 507219.6603 394508.319 0.728115153 1.160827571 0.775369485 1.603025202 0.855567696 0.977063754 1.290146841 1.459411217 1.285700798 1 18.5896962 2.203851879 7.911912823 1.315395246 1.031605718 0.161715206 0.256242152 0.336594905 64.37279216 0.091868486 0.068503071 159.9012575 -2.203851879 -0.283789528 VVTATLWGEDADKFDGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVTATLWGEDADKFDGSR 18 1 P27694;I3L4R8 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 ; 250.1 7.25E-25 500800000 495320 482140 403860 452540 461340 466330 528900 587980 601400 534860 FALSE TRUE 475962.3468 468389.8393 476846.4858 475895.6436 476179.4201 475759.5121 535372.8364 575838.0075 533131.5933 498633.4558 0.954533518 0.939346997 0.956306642 0.954399746 0.954968854 0.954126737 1.073680136 1.154832274 1.069185365 1 18.92762016 2.203883898 4.630951927 1.09661277 0.951501808 0.713321304 0.037111516 0.087052623 4.277330572 0.013569883 0.010154013 159.9130468 -2.203883898 -0.145110962 CSATPSAQVKPIVSAS(ph)PPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 CSATPSAQVKPIVSASPPSR 20 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 CSATPSAQVKPIVS(0.005)AS(0.994)PPS(0.001)R;CSATPSAQVKPIVS(0.026)AS(0.862)PPS(0.113)R;CSATPSAQVKPIVS(0.045)AS(0.955)PPSR;CSATPSAQVKPIVSAS(0.999)PPSR 282.1 5.05E-45 2265690000 1947270 1863350 1604220 1818130 1783670 2025200 2036500 2193660 2341350 2432530 TRUE FALSE 1871168.536 1810209.082 1894138.24 1911963.907 1841043.365 2066150.932 2061423.296 2148360.154 2075569.764 2267772.576 0.825112957 0.798232195 0.835241708 0.843102138 0.811828922 0.911092652 0.909007948 0.94734374 0.915245993 1 21.11284454 2.204025631 0.515140693 0.988769681 0.803150681 0.867737131 0.022913216 0.293971737 0.164195055 0.021297245 0.01805761 159.9652434 -2.204025631 -0.185619 KQAEILQESR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQAEILQESR 10 1 E5RJD8;O75347;E5RIW3;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 133.05 0.0003326 1841850000 3032600 3515100 2571900 3348800 2655100 2490600 3610400 3675800 3555300 3027300 FALSE TRUE 2914082.639 3414852.79 3036699.542 3521631.969 2740503.703 2540961.638 3654585.155 3599893.445 3151717.249 2822258.275 1.032535777 1.209971752 1.075982155 1.247806411 0.971032215 0.900329237 1.294915206 1.275536501 1.116735941 1 21.42841859 2.204053488 24.99998938 1.206990057 1.082625249 0.103619576 0.124563314 318.3436383 230634.3087 0.047199779 0.034860841 159.9755045 -2.204053488 -0.124364808 SGGGPGPSGSET(ph)PPPPRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGGPGPSGSETPPPPRR 18 1 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 SGGGPGPSGS(0.005)ET(0.995)PPPPRR;SGGGPGPSGS(0.002)ET(0.998)PPPPRR 99.059 0.0006484 850680000 271740 337250 224220 293110 279790 330240 247920 278110 316680 269630 TRUE FALSE 261120.1004 327631.9602 264741.5417 308237.4422 288789.6994 336917.6791 250954.1191 272366.9313 280731.814 251367.7199 1.038797267 1.303397112 1.053204213 1.226241151 1.148873449 1.340337889 0.998354599 1.083539809 1.116817283 1 17.93943987 2.204105367 24.99998453 1.057440134 1.184739798 0.325168619 0.0953401 218.9710708 158879.4251 0.033142627 0.024478712 159.9946156 -2.204105367 0.127299665 NIDEHANEDVER ddPTM_BT-474_Pertuzumab_2h_R1 2 NIDEHANEDVER 12 0 P61026 P61026 RAB10 Ras-related protein Rab-10 0 ; 181.71 1.78E-05 1522750000 1759910 2564600 1587320 2781400 1730530 1633760 2585600 2568000 2478300 2051500 FALSE TRUE 1691130.772 2491460.119 1874184.034 2924948.387 1786194.069 1666795.747 2617243.346 2514969.903 2196973.774 1912550.078 0.884228231 1.302690135 0.979939849 1.529344733 0.933933229 0.871504368 1.368457421 1.31498251 1.148714379 1 20.86706609 2.204207086 24.99998795 1.247724725 1.102309839 0.059215304 0.21376103 455.0066881 331118.0425 0.078447607 0.057940137 160.0320933 -2.204207086 -0.145414886 AEEYEFLTPVEEAPK ddPTM_BT-474_Pertuzumab_2h_R1 3 AEEYEFLTPVEEAPK 15 0 P52565;J3KTF8;J3QQX2;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;; 270.67 5.19E-33 419027000 740380 737340 582949 658660 683490 738900 812830 944560 997540 914010 FALSE TRUE 711445.1311 716311.7851 688300.8519 692653.5215 705475.0766 753841.0643 822777.6567 925054.5059 884303.4412 852103.2886 0.834928278 0.84063962 0.807766924 0.812875071 0.827922021 0.884682731 0.965584416 1.085613116 1.037789025 1 19.70066879 2.204621686 2.02215024 1.04945912 0.824993304 0.939294741 0.024149236 0.066192534 0.542317069 0.011747121 0.007464619 160.1849413 -2.204621686 -0.224465816 NELESYAYSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NELESYAYSLK 11 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 197.3 1.34E-07 858730000 535870 557680 417020 495900 469760 449170 553390 540760 637750 590340 FALSE TRUE 514927.608 541775.5124 492384.7906 521493.4584 484870.257 458252.5252 560162.5524 529593.117 565355.2937 550355.746 0.935626841 0.984409659 0.894666394 0.947557034 0.881012437 0.832647844 1.017819032 0.962274167 1.027254277 1 19.07000494 2.204678538 24.99982611 0.995474132 0.915245634 0.522024471 0.041584753 172.8170103 127511.7122 0.016240161 0.011994782 160.2059119 -2.204678538 -0.080228498 PAS(ph)PEPELLPEADSK ddPTM_BT-474_Pertuzumab_2h_R1 4 PASPEPELLPEADSK 15 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 PAS(1)PEPELLPEADSK;PAS(1)PEPELLPEADSK;PAS(1)PEPELLPEADSK;PAS(1)PEPELLPEADSK 263.53 4.80E-25 946950000 644619 594134 698012 675212 741284 777885 979147 916666 1312389 1212665 TRUE FALSE 619426.5768 577189.88 824158.2956 710059.7722 765128.0731 793614.3677 991130.0939 897736.5268 1163412.103 1130530.119 0.547908071 0.51054799 0.729001626 0.628076829 0.676786987 0.701984276 0.876694992 0.794084573 1.029085455 1 20.108568 2.204781216 0.453024486 1.030137765 0.539716087 0.834684123 0.067978563 0.398394324 0.181429687 0.067270178 0.066227219 160.2437929 -2.204781216 -0.490421678 LLQDFFNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLQDFFNGK 9 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652;P17066 P11142;P54652;P17066 HSPA8;HSPA2;HSPA6 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6 0 ; 222.18 9.13E-07 2859700000 2080470 2192350 1928220 2101510 1909560 1549840 2577900 2340000 2577700 2729600 FALSE TRUE 1999162.932 2129826.325 2276692.247 2209969.183 1970982.732 1581178.827 2609449.111 2291678.182 2285090.303 2544721.761 0.785611599 0.836958428 0.894672369 0.868452189 0.774537618 0.621356272 1.025435925 0.900561396 0.897972556 1 21.27907649 2.205288583 24.99999299 0.945430758 0.805426295 0.491933175 0.078615679 191.5182726 143902.2299 0.030860274 0.022793206 160.4311081 -2.205288583 -0.140004464 MES(ph)HS(ph)EDEDLAGAVGGLGWNSR ddPTM_BT-474_Pertuzumab_2h_R1 2 MESHSEDEDLAGAVGGLGWNSR 22 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7;K7EIM4 Q96MH2 HEXIM2 Protein HEXIM2 2 MES(1)HS(1)EDEDLAGAVGGLGWNSR;MES(1)HS(1)EDEDLAGAVGGLGWNSR 146.15 4.63E-08 72310000 61549 76833 60005 69084 62140 71631 63622 63465 79448 68261 TRUE FALSE 59143.59703 74641.79807 70849.2383 72649.43352 64138.78953 73079.4279 64400.62507 62154.42557 70429.39611 63637.62167 0.929381009 1.172919354 1.113323164 1.141611387 1.007875339 1.148368308 1.011989816 0.976693094 1.106725774 1 15.9575923 2.205610767 24.83053816 1.016710908 1.089825694 0.136173896 0.074852984 297.9293184 224513.4186 0.02671667 0.019732976 160.5501689 -2.205610767 0.073114786 DFSMADK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFSMADK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 139.68 0.0062246 596240000 799940 786990 712100 695270 750740 730070 799370 837090 893640 859280 FALSE TRUE 768677.4604 764545.8157 840792.3106 731152.968 774888.2339 744832.5156 809152.9292 819803.799 792197.7336 801080.2002 0.959551191 0.954393599 1.049573202 0.912708825 0.96730419 0.929785202 1.010077304 1.023372939 0.988911888 1 19.61158716 2.205726684 24.6372909 1.009325582 0.96381493 0.271132941 0.034561588 210.8592549 158219.0731 0.01279216 0.009448313 160.5930271 -2.205726684 -0.045510652 EKS(ph)PVREPVDNLSPEER ddPTM_BT-474_Pertuzumab_2h_R1 6 EKSPVREPVDNLSPEER 17 2 Q86U06-3;Q86U06-5;Q86U06-2;Q86U06 Q86U06-3 RBM23 Probable RNA-binding protein 23 1 EKS(0.999)PVREPVDNLS(0.001)PEER;EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER 223.7 1.54E-15 11777590000 4634990 4457740 3660000 3953640 4036940 4403900 4526450 5175460 5245860 5055730 TRUE FALSE 4453849.467 4330609.62 4321443.416 4157687.834 4166791.841 4492949.875 4581846.049 5068584.942 4650371.965 4713300.904 0.944953347 0.9188061 0.916861347 0.882118057 0.884049613 0.953249107 0.972109811 1.075379028 0.986648648 1 22.16830636 2.20586949 2.316801923 1.027385208 0.910158546 0.711938152 0.029882842 0.143289573 1.557489055 0.013743365 0.009146123 160.6458425 -2.20586949 -0.117226662 KEANQAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEANQAPK 8 1 Q96AG4 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 93.111 0.01812 75436000 129140 200930 100590 180350 103900 60029 228090 251900 186760 148400 FALSE TRUE 124093.066 195199.6731 118768.8506 189657.8851 107242.0379 61242.82751 230881.4336 246698.177 165559.7878 138348.7358 0.896958438 1.410924877 0.858474419 1.370868219 0.775157339 0.442669947 1.668836598 1.783161772 1.1966845 1 17.07794994 2.205876139 24.99992152 1.517026734 0.985480531 0.277630234 0.340026996 212.5730666 162593.1 0.127962669 0.094513241 160.6483018 -2.205876139 -0.531546203 RDETALQEEEELQLALALSQSEAEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDETALQEEEELQLALALSQSEAEEK 26 1 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 94.192 0.013408 46630000 17100 17976 18802 18135 18297 22054 21451 27456 29092 27562 FALSE TRUE 16431.71309 17463.34208 22199.93965 19070.94952 18885.53962 22499.94699 21713.52375 26889.02401 25789.59812 25695.20119 0.639485676 0.679634378 0.863972206 0.742198879 0.734983139 0.875647823 0.845041983 1.046460925 1.003673718 1 14.64921133 2.206187181 1.011194029 1.033236098 0.727506203 0.778602101 0.063705242 0.246914849 0.478605979 0.047710622 0.026259133 160.7633993 -2.206187181 -0.305729894 RDYLLLVMEGTDDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDYLLLVMEGTDDGR 15 1 Q9HDC9;H0Y512;Q9HDC9-2 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 182.15 8.95E-07 82154000 34663 52066 29900 58393 32023 27806 56075 54633 54561 43365 FALSE TRUE 33308.33164 50581.12866 35303.59512 61406.66973 33053.04888 28368.25637 56761.26262 53504.80946 48367.46402 40427.84992 0.823895698 1.251145652 0.873249386 1.518919998 0.817581171 0.701700843 1.404013885 1.323464136 1.196389719 1 15.30306186 2.206212845 24.99960177 1.27016214 1.019107413 0.167744656 0.245679495 322.097214 248927.2802 0.090729153 0.067012774 160.7728999 -2.206212845 -0.251054726 EGPVQFEEDPFGLDKFLEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGPVQFEEDPFGLDKFLEEAK 21 1 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 70.942 0.0091979 0 33291 25024 23359 20661 23003 27047 26695 29910 34034 28156 FALSE TRUE 31989.95091 24310.34002 27580.49092 21727.31669 23742.91239 27593.90887 27021.7014 29292.34805 30170.603 26248.96904 1.218712661 0.926144565 1.050726635 0.827739811 0.904527425 1.051237815 1.029438579 1.115942801 1.149401447 1 14.67997314 2.206241578 2.092551202 1.095213393 0.979564213 0.12771291 0.105006086 0.547987234 4.82340717 0.050490231 0.032508762 160.783537 -2.206241578 -0.11564918 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLR 32 2 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 2 KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR 201.57 1.37E-26 8434000000 194603 153392 151543 145173 186602 173026 245159 256635 310983 277210 TRUE FALSE 186997.6996 149017.4103 178930.1912 152665.3959 192604.2228 176524.7043 248159.3292 251335.3976 275681.5136 258434.3198 0.723579205 0.57661618 0.692362343 0.590731897 0.745273395 0.683054419 0.960241385 0.972531039 1.066737242 1 17.97943815 2.206262545 1.959699392 1.017204409 0.655366373 0.891573666 0.056495672 0.092798012 0.712487393 0.026314651 0.016571601 160.7912996 -2.206262545 -0.361838036 GVEITGFPEAQALGLEVFHAGTALK ddPTM_BT-474_Pertuzumab_2h_R1 1 GVEITGFPEAQALGLEVFHAGTALK 25 0 P22102;P22102-2 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 122.39 0.00017293 67568000 66366 67765 68878 72789 64125 68150 78368 82329 89818 86578 FALSE TRUE 63772.34335 65832.40855 81325.78678 76545.64901 66187.63886 69528.03969 79327.09103 80628.87738 79622.23719 80713.99494 0.790102675 0.815625699 1.007579749 0.94835659 0.820026798 0.861412445 0.982817058 0.998945442 0.986473749 1 16.30053122 2.206278284 7.286159166 0.992988101 0.878207799 0.473231245 0.061006398 0.196188819 33.18181057 0.024757684 0.018525015 160.7971268 -2.206278284 -0.114780302 FDGGEEVLISGEFNDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FDGGEEVLISGEFNDLR 17 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 134.08 4.23E-05 15097000 10947 9254.4 7877.6 16178 8059.2 6656.3 14164 14527 9728 9588.9 FALSE TRUE 10519.17914 8990.473573 9301.257556 17012.94852 8318.431487 6790.894947 14337.34327 14227.01237 8623.718223 8939.435262 1.176716295 1.005709344 1.040474849 1.903134596 0.930532102 0.759655923 1.603830986 1.591488943 0.964682664 1 13.12596798 2.206397883 24.99999063 1.375760139 1.151295507 0.021090916 0.347884918 532.587498 413975.6133 0.13349129 0.098597574 160.841414 -2.206397883 -0.224464632 AGGKPSQS(ph)PSQEAAGEAVLGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGGKPSQSPSQEAAGEAVLGAK 22 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 AGGKPS(0.416)QS(0.566)PS(0.018)QEAAGEAVLGAK 215.53 1.79E-32 0 136070 123400 102220 121770 135780 141700 146380 167370 196170 186350 TRUE FALSE 130752.234 119880.7528 120693.4279 128054.5643 140147.487 144565.2711 148171.4422 163913.751 173901.604 173728.3485 0.75262463 0.690047156 0.694725005 0.737096538 0.806704768 0.832134032 0.85289156 0.943506068 1.000997278 1 17.40647366 2.206707098 0.67278034 1.014593067 0.704280612 0.949246978 0.025145964 0.148150392 0.130554951 0.022576923 0.014812389 160.9559729 -2.206707098 -0.310312455 VDQICHK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDQICHK 7 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054;M0R286;M0QYP2 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 101.99 0.0087016 605520000 1224070 1203580 1036970 1122370 1165140 1018050 1322740 1288670 1499050 1405150 FALSE TRUE 1176231.991 1169255.077 1224373.546 1180295.65 1202617.786 1038635.669 1338928.088 1262058.514 1328884.129 1309977.939 0.897902137 0.892576159 0.934652035 0.901004219 0.918044305 0.792865008 1.022099722 0.96341967 1.014432449 1 20.32111109 2.206829273 24.99998214 0.994246794 0.893518464 0.664616553 0.038298101 125.8645893 99163.46096 0.014007933 0.010346451 161.0012595 -2.206829273 -0.100728329 KEEEEEEEENR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEEEEEEEENR 11 1 G3V583;Q8N128;Q8N128-2 G3V583 FAM177A1 Protein FAM177A1 0 117.92 0.0012675 76592000 160810 158840 142080 164790 155470 159170 188920 194860 229010 211410 FALSE TRUE 154525.3674 154310.0387 167757.0166 173294.8316 160470.8337 162388.5265 191232.0595 190836.0729 203013.7449 197091.0124 0.784030512 0.782937978 0.851165228 0.879262984 0.814196608 0.823926594 0.970272856 0.9682637 1.030050749 1 17.58850246 2.206857638 4.392358359 0.989610465 0.823504067 0.879862637 0.030750345 0.074202949 3.230115964 0.012926356 0.009674711 161.0117751 -2.206857638 -0.166106397 VNNGNTAPEDS(ph)SPAKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNNGNTAPEDSSPAKK 16 1 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 VNNGNTAPEDS(0.609)S(0.391)PAKK;VNNGNTAPEDS(0.6)S(0.4)PAKK 111.66 0.00048974 387181000 281038 234935 180027 178651 184230 187219 238019 243285 287925 239522 TRUE FALSE 270054.7243 228234.8838 212561.8836 187871.1995 190155.9253 191004.6965 240931.9477 238261.0797 255240.9611 223298.9616 1.209386386 1.022104546 0.951916131 0.841343812 0.851575502 0.855376555 1.078965822 1.067004871 1.143045894 1 17.76861702 2.207088178 24.24878945 1.076717656 0.94827495 0.222490055 0.106509554 219.5662598 169168.97 0.042927414 0.031707556 161.0972689 -2.207088178 -0.128442706 RGHTAS(ph)ESDEQQWPEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGHTASESDEQQWPEEK 17 1 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 RGHT(0.035)AS(0.93)ES(0.035)DEQQWPEEK;RGHT(0.134)AS(0.611)ES(0.255)DEQQWPEEK 210.64 7.12E-12 1312410000 1013780 918870 733860 741250 868170 810730 718260 558010 831410 821080 TRUE FALSE 974160.3568 892664.7273 866484.8266 779506.0013 896095.4765 827123.5161 727050.2807 546486.8985 737031.8224 765467.5203 1.272634476 1.166169307 1.131968116 1.018339748 1.170651207 1.080546848 0.949812058 0.713925652 0.962851856 1 19.54598164 2.207185206 3.004321681 0.855790295 1.141682904 0.594581547 0.09427854 0.154320951 2.865243642 0.039057776 0.02791664 161.1332646 -2.207185206 0.285892608 GS(ph)PRPQAPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSPRPQAPK 9 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GS(1)PRPQAPK;GS(1)PRPQAPK;GS(1)PRPQAPK;GS(1)PRPQAPK 106.67 0.007625 4147280000 3258030 3045650 2719640 2996470 2816600 2995070 3293150 3402300 3765140 3786530 TRUE FALSE 3130702.586 2958791.044 3211139.446 3151118.176 2907198.497 3055632.367 3333452.555 3332041.316 3337737.092 3530064.95 0.886868267 0.83816901 0.909654494 0.892651614 0.823553826 0.865602308 0.944303462 0.943903685 0.94551719 1 21.7512633 2.207666573 5.371181978 0.953384817 0.868624177 0.70527689 0.028146244 0.108078885 8.104362604 0.01061016 0.007980568 161.3119619 -2.207666573 -0.084760639 EANANGSS(ph)PEPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EANANGSSPEPVK 13 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 EANANGS(0.013)S(0.987)PEPVK 297.96 9.47E-41 357460000 650150 596580 603940 654070 636440 709920 766190 889540 963040 934360 TRUE FALSE 624741.4192 579566.1225 713085.3926 687826.6311 656911.6706 724275.0688 775566.8624 871170.6881 853719.7366 871074.965 0.71720741 0.665345861 0.818626894 0.789629663 0.754139078 0.831472718 0.890356047 1.000109891 0.980076079 1 19.73243736 2.207827545 0.993385072 1.012588958 0.738438951 0.881308487 0.039158726 0.178123523 0.333110592 0.030580814 0.016886873 161.3717636 -2.207827545 -0.274150006 SDPDHLAELVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDPDHLAELVK 11 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 145.28 3.63E-05 333170000 850290 925060 785400 881160 856940 867140 972070 1009200 1122500 1088400 FALSE TRUE 817059.7268 898678.1945 927339.2511 926636.7732 884504.2534 884674.1649 983966.4834 988359.6673 995078.5059 1014681.699 0.805237473 0.885674981 0.913921334 0.91322902 0.871706127 0.87187358 0.969729211 0.974058829 0.980680451 1 19.9525958 2.207918361 6.212609952 0.978907044 0.880338876 0.75232614 0.029247525 0.09596315 10.95354042 0.011338704 0.008521287 161.4055118 -2.207918361 -0.098568168 PVT(ph)PTSMCQGSSSGATIK ddPTM_BT-474_Pertuzumab_2h_R1 2 PVTPTSMCQGSSSGATIK 18 0 H7C5W6;F5H619;Q86XA9-2;Q86XA9 H7C5W6 HEATR5A HEAT repeat-containing protein 5A 1 PVT(0.988)PT(0.011)S(0.002)MCQGSSSGATIK;PVT(0.97)PT(0.03)SMCQGSSSGATIK 206.21 7.28E-18 217370000 57751 49019 51395 46479 65556 55479 68978 71619 90629 81622 TRUE FALSE 55494.02707 47621.02611 60683.21978 48877.78676 67664.66828 56600.82339 69822.1734 70140.04262 80341.17587 76093.66924 0.729285729 0.625821131 0.797480531 0.642337099 0.889228617 0.743830912 0.917581897 0.921759239 1.055819448 1 16.21548881 2.208159356 0.683027161 1.032345168 0.693895687 0.737826857 0.071495676 0.334399958 0.302887264 0.056205748 0.036487925 161.4951021 -2.208159356 -0.338449481 GGYVLHIGTIYGDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGYVLHIGTIYGDLK 15 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 212.95 6.17E-10 2004100000 2997100 2937400 2617800 2506000 2717800 2252000 3306000 2924800 3496200 3447000 FALSE TRUE 2879970.019 2853628.228 3090894.693 2635334.96 2805220.505 2297536.983 3346459.817 2864401.858 3099326.033 3213531.62 0.896200928 0.888003781 0.961837336 0.820074383 0.872940066 0.714957018 1.041365144 0.891356363 0.964461035 1 21.61572824 2.208254515 24.99993307 0.960044294 0.863858668 0.390289292 0.069532184 253.7795544 209344.9135 0.025998457 0.019203452 161.5304915 -2.208254515 -0.096185625 IIWELIK ddPTM_BT-474_Pertuzumab_2h_R1 2 IIWELIK 7 0 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 123.96 0.009755 344020000 818660 845020 742430 757910 808200 663280 958940 946410 967570 1053120 FALSE TRUE 786665.8621 820920.857 876603.6163 797025.8259 834196.487 676691.976 970675.7946 926866.3028 857735.51 981791.2444 0.801255732 0.836146036 0.892861513 0.811807836 0.849667882 0.689242219 0.988678398 0.944056395 0.87364347 1 19.90505678 2.208426267 24.99999952 0.948115391 0.81970111 0.573411082 0.058174676 157.4929851 130658.1155 0.021468802 0.015857732 161.5943853 -2.208426267 -0.128414281 IKNENTEGS(ph)PQEDGVELEGLK ddPTM_BT-474_Pertuzumab_2h_R1 5 IKNENTEGSPQEDGVELEGLK 21 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 IKNENTEGS(1)PQEDGVELEGLK;IKNENT(0.021)EGS(0.979)PQEDGVELEGLK;IKNENT(0.001)EGS(0.999)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENT(0.04)EGS(0.96)PQEDGVELEGLK 298.4 3.41E-55 7333800000 3090315 2606055 2221338 2179812 2593821 2919140 2934461 3411199 4050600 3363256 TRUE FALSE 2969542.073 2531732.863 2622783.19 2292312.359 2677253.608 2978167.011 2970373.812 3340756.549 3590792.87 3135459.675 0.947083484 0.807451897 0.836490806 0.731092916 0.853863192 0.949834257 0.947348752 1.065475845 1.145220555 1 21.58024553 2.208459944 1.327031888 1.078404253 0.828596746 0.708773847 0.063774336 0.227872013 0.77519039 0.040040866 0.02250798 161.6069166 -2.208459944 -0.249807508 WYPEVR ddPTM_BT-474_Pertuzumab_2h_R1 4 WYPEVR 6 0 P63000;J3KSC4;J3QLK0;P60763;P63000-2 P63000 RAC1;RAC3 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 3 0 ;;; 109.88 0.067884 1348640000 1063740 1812440 1087230 2153170 1140810 832980 2103260 1957230 1638850 1515190 FALSE TRUE 1022167.865 1760750.986 1283716.646 2264295.362 1177505.19 849823.4263 2129000.325 1916812.517 1452814.619 1412564.832 0.723625452 1.246492158 0.908784232 1.60296739 0.833593732 0.60161729 1.50718769 1.356973127 1.028494117 1 20.42988565 2.208525557 24.99930966 1.273142023 1.015593775 0.117796351 0.299289345 411.8756056 342817.1587 0.11227074 0.082928258 161.6313337 -2.208525557 -0.257548248 SPAS(ph)PLNNQGIPTPAQLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPASPLNNQGIPTPAQLTK 19 0 A0A2U3U043;J3QLL6;J3KSG1;J3QRK1;Q719H9 A0A2U3U043 KCTD1 BTB/POZ domain-containing protein KCTD1 1 S(0.02)PAS(0.98)PLNNQGIPTPAQLTK;SPAS(1)PLNNQGIPTPAQLTK 246.67 1.17E-24 187916000 308380 320575 288138 313620 304289 312117 330500 350800 382420 338130 TRUE FALSE 296328.1687 311432.5149 340210.9462 329805.9658 314076.732 318428.2196 334544.7579 343555.8574 339009.2848 315228.1539 0.940043473 0.987959073 1.079253049 1.046245272 0.996347338 1.010151586 1.061278169 1.089864129 1.075441012 1 18.26603687 2.208545814 5.97074141 1.067284223 1.013102821 0.219062385 0.041056497 0.245653916 25.22044104 0.01596141 0.012008096 161.6388731 -2.208545814 -0.054181402 VSNLQVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 VSNLQVSPK 9 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK 190.68 3.86E-05 1476030000 2508900 2535840 2244360 2326910 2633940 2499960 1764770 1772190 1942630 1519240 TRUE FALSE 2410849.414 2463520.326 2649965.778 2447002.104 2718663.072 2550510.904 1786367.783 1735593.657 1722110.787 1416340.522 1.70216793 1.739355959 1.870994819 1.727693352 1.919498193 1.800775213 1.26125586 1.225407048 1.215887536 1 20.43373673 2.208572139 4.750640587 1.190621681 1.799463472 0.922497522 0.087849044 0.049096272 2.637909119 0.032714789 0.024586663 161.6486712 -2.208572139 0.608841791 YHGHS(ph)MSDPGVSYR ddPTM_BT-474_Pertuzumab_2h_R1 2 YHGHSMSDPGVSYR 14 0 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3;P29803 P08559-3 PDHA1;PDHA2 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial;Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial" 1 YHGHS(0.99)MS(0.01)DPGVSYR;YHGHS(0.997)MS(0.003)DPGVSYR 173.03 1.78E-06 4314800000 1420910 1751650 996170 2323650 967430 1053890 1329240 157198 946190 484100 TRUE FALSE 1365379.266 1701694.657 1176200.079 2443573.855 998548.2645 1075200.378 1345507.637 153951.8064 838782.478 451311.4758 3.025359069 3.770554812 2.606182519 5.41438449 2.212547914 2.382390955 2.981328215 0.341120965 1.858544537 1 18.78376394 2.208572936 1.088911392 0.997660163 3.532881708 0.510498419 0.938944245 0.385490489 0.870089853 0.638166746 0.350778819 161.6489678 -2.208572936 2.535221546 YPSSISSS(ph)PQKDLTQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSS(0.008)IS(0.041)S(0.303)S(0.647)PQKDLTQAK;YPSSIS(0.001)S(0.003)S(0.996)PQKDLTQAK 267.93 4.43E-28 3373600000 4109500 3726700 3491700 3352600 3723300 3877100 4783000 5008600 5671000 5753800 TRUE FALSE 3948896.197 3620418.165 4122727.862 3525628.088 3843063.326 3955497.618 4841535.785 4905170.66 5027251.855 5364090.001 0.736172621 0.674936133 0.768579174 0.657264902 0.716442738 0.737403291 0.902582877 0.914446003 0.937204979 1 22.35490201 2.208617783 2.275894686 0.941423543 0.707995815 0.904810301 0.035743929 0.082895676 0.869049369 0.015732348 0.01043789 161.6656612 -2.208617783 -0.233427728 FVPAENDSILMNPAQDGEVQLS(ph)QNDDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVPAENDSILMNPAQDGEVQLSQNDDK 27 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 FVPAENDSILMNPAQDGEVQLS(1)QNDDK;FVPAENDSILMNPAQDGEVQLS(1)QNDDK 145.86 2.94E-09 112790000 45572 65552 73963 101973 87228 78808 60287 63157 53583 68826 TRUE FALSE 43790.99586 63682.52114 87329.7594 107235.8388 90033.76784 80401.55176 61024.81034 61852.78588 47500.48248 64164.35372 0.682481679 0.99249065 1.361032323 1.671268119 1.403174233 1.253056364 0.951070288 0.963974268 0.740293944 1 15.96948442 2.208835736 4.834873821 0.912837456 1.251973769 0.266255035 0.253489871 0.283267257 15.98081934 0.106146476 0.079824309 161.7468143 -2.208835736 0.339136314 RGAEDDRGPWR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGAEDDRGPWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 116.03 0.00058734 249510000 90220 134570 74214 77153 91955 113040 76054 85110 84283 82949 FALSE TRUE 86694.10266 130732.1954 87626.12068 81134.87558 94912.81609 115325.7462 76984.7716 83352.44876 74715.54718 77330.79035 1.121081296 1.690558118 1.133133649 1.049192375 1.227361258 1.491330242 0.995525473 1.077868833 0.966181088 1 16.23875534 2.208902072 24.99568369 1.022225611 1.283555339 0.359616836 0.17982605 248.7102895 209607.0768 0.068314152 0.050460539 161.7715223 -2.208902072 0.261329728 KYEEVAR ddPTM_BT-474_Pertuzumab_2h_R1 7 KYEEVAR 7 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;;;; 150.05 0.0031664 54038300000 45054500 44728700 37504200 41391500 41119400 40246700 45241700 45979000 50729300 49108300 FALSE TRUE 43293720.33 43453081.27 44282043.22 43527720.28 42442042.84 41060515.85 45795381.46 45029517.58 44970722.54 45782151.1 0.945646268 0.949127121 0.967233783 0.950757429 0.92704344 0.896867335 1.000288985 0.983560547 0.982276312 1 25.44828191 2.208903053 24.99998334 0.989815979 0.941099424 0.660995261 0.018234116 144.2013323 121554.3635 0.007368188 0.005442535 161.7718876 -2.208903053 -0.048716555 TAVAPSAVNLADPRT(ph)PTAPAVNLAGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAVAPSAVNLADPRTPTAPAVNLAGAR 27 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 TAVAPS(0.005)AVNLADPRT(0.981)PT(0.014)APAVNLAGAR;TAVAPS(0.013)AVNLADPRT(0.943)PT(0.043)APAVNLAGAR 107.04 0.0029892 685210000 552440 566590 417153 415560 485900 599120 380790 417520 454640 433480 TRUE FALSE 530850.034 550431.4079 492541.8266 437007.1014 501529.4148 611234.6169 385450.2219 408898.0661 403031.1732 404120.0135 1.313595012 1.362049365 1.218800876 1.081379508 1.241040775 1.512507662 0.953801369 1.011823351 0.997305651 1 18.62442428 2.208936708 24.99993983 0.992517698 1.276881459 0.660139396 0.104379508 138.1517868 116587.0135 0.041166302 0.030407576 161.7844243 -2.208936708 0.284363761 DDGSTLMEIDGDKGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDGSTLMEIDGDKGK 15 1 O96019-2;O96019;H7C5S0;C9JQT2 O96019-2 ACTL6A Actin-like protein 6A 0 ; 163.8 1.38E-06 1509440000 629960 519510 513190 414920 524360 509040 626220 647570 760900 678210 FALSE TRUE 605340.4667 504694.0835 605934.8488 436334.0709 541226.5156 519333.1376 633883.8677 634197.4532 674525.822 632274.2326 0.957401766 0.79822023 0.958341836 0.690102567 0.85599964 0.821373244 1.002545786 1.003041751 1.066824785 1 19.2701909 2.209088482 7.084914091 1.017092531 0.84298274 0.558499445 0.074534478 0.131717888 22.0884663 0.026580434 0.019947923 161.8409734 -2.209088482 -0.17410979 YQYAIDEYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 YQYAIDEYYR 10 0 G3V583;Q8N128;Q8N128-2 G3V583 FAM177A1 Protein FAM177A1 0 147.2 0.012522 0 85800 98773 70869 84147 82940 65552 104120 96504 94372 95171 FALSE TRUE 82446.84114 95956.09075 83676.60477 88489.83675 85607.84042 66877.50635 105394.2517 94511.15868 83659.2862 88724.9834 0.929240423 1.081500239 0.943100822 0.997349713 0.964867359 0.753761836 1.187875699 1.065214724 0.942905628 1 16.43705278 2.209126621 24.99999029 1.060354342 0.954375984 0.211649148 0.096355946 327.0825529 277808.1356 0.036147027 0.026700312 161.8551865 -2.209126621 -0.105978358 GTPLT(ph)PPACACSSLQVEVER ddPTM_BT-474_Pertuzumab_2h_R1 2 GTPLTPPACACSSLQVEVER 20 0 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 GT(0.002)PLT(0.998)PPACACSSLQVEVER;GTPLT(1)PPACACSSLQVEVER 109.28 0.002232 304540000 49753 66156 61038 68489 68401 60459 53144 45318 53814 60361 TRUE FALSE 47808.59776 64269.29565 72068.92438 72023.7255 70601.18029 61681.5224 53794.39217 44382.16746 47705.26033 56272.69571 0.849587836 1.142104441 1.280708583 1.279905371 1.254625878 1.096118137 0.95595904 0.788698087 0.847751467 1 15.78014746 2.209157604 2.717989728 0.858578564 1.17292572 0.490179406 0.12757844 0.211461657 3.195218013 0.056854184 0.039754959 161.8667341 -2.209157604 0.314347156 GGSPLAAPQGGS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGSPLAAPQGGSPTK 15 0 E7EPC8;Q9UQB3-2;Q9UQB3 E7EPC8 CTNND2 Catenin delta-2 1 GGSPLAAPQGGS(0.999)PT(0.001)K;GGSPLAAPQGGS(0.997)PT(0.003)K 229.02 5.44E-13 339470000 677510 721770 534320 733490 625340 667060 776220 953330 767210 699140 TRUE FALSE 651032.1602 701185.8263 630883.5099 771345.5068 645454.629 680548.4102 785719.6126 933643.4024 680119.5372 651786.6251 0.998842466 1.075790449 0.967929512 1.183432549 0.99028517 1.044127609 1.20548594 1.432437191 1.043469613 1 19.31404022 2.209176969 5.594870366 1.232614724 1.045000929 0.127685713 0.126993613 0.209876348 17.94762192 0.046547825 0.035055611 161.8739518 -2.209176969 -0.187613795 EVQQGEEFERR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVQQGEEFERR 11 1 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ;;; 227.48 6.36E-12 2240340000 1028610 1239560 816643 1037620 1106596 1140110 986290 1054470 1129530 1062140 FALSE TRUE 988410.784 1204208.962 964228.5562 1091171.693 1142190.665 1163163.805 998360.5121 1032694.826 1001310.49 990200.3117 0.998192762 1.216126624 0.973771211 1.101970661 1.153494552 1.174675257 1.008240959 1.042915069 1.011220132 1 19.91736088 2.209389701 24.98972031 1.021323999 1.104548041 0.269389748 0.070269618 293.3088668 251265.985 0.025432543 0.018785911 161.9532626 -2.209389701 0.083224042 YLNDEELITQQLNDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YLNDEELITQQLNDLEK 17 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 192.65 4.06E-10 32025000 77934 76436 62202 76156 69621 76960 90305 103630 98483 108150 FALSE TRUE 74888.25312 74256.12012 73443.28508 80086.42029 71860.42269 78516.18393 91410.1796 101490.0043 87303.62271 100824.9042 0.74275551 0.736485898 0.72842405 0.794311891 0.712724929 0.778737997 0.906623025 1.006596586 0.865893436 1 16.62149251 2.209411226 3.077996321 0.958261168 0.744687316 0.849569569 0.04095475 0.08303247 1.622704012 0.015823282 0.011386595 161.9612894 -2.209411226 -0.213573852 SDLEDKR ddPTM_BT-474_Pertuzumab_2h_R1 3 SDLEDKR 7 1 P11233;H7C3P7 P11233 RALA Ras-related protein Ral-A 0 ;; 113.7 0.0097355 1506050000 496590 741800 384110 803090 438800 396910 795010 884840 845950 666130 FALSE TRUE 477182.7138 720644.5903 453527.2215 844537.5711 452914.4005 404935.7921 804739.5702 866567.7448 749921.3025 621012.4218 0.768394797 1.160435065 0.730302979 1.35993668 0.729316169 0.652057476 1.295851004 1.39541129 1.207578587 1 19.2442626 2.209591215 24.98802515 1.273784282 0.917332713 0.320302306 0.226385081 223.359107 192660.6691 0.082635492 0.061040337 162.0284266 -2.209591215 -0.356451569 VLTEIIASR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLTEIIASR 9 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 135.71 0.00049586 102970000 238610 246650 193660 255170 235390 218410 221120 171800 238010 249620 FALSE TRUE 229284.8574 239615.7835 228658.6699 268339.3543 242961.5331 222826.3998 223826.1327 168252.27 210992.1026 232713.0151 0.985268733 1.02966215 0.982577918 1.153091305 1.044039299 0.957515848 0.961811838 0.723003266 0.906662236 1 17.82819237 2.209741217 2.283661512 0.849016715 1.037122937 0.371585832 0.082727585 0.246620829 2.604482134 0.037727185 0.025085173 162.0843997 -2.209741217 0.188106222 ANNHQQQQGLQDSSSK ddPTM_BT-474_Pertuzumab_2h_R1 5 ANNHQQQQGLQDSSSK 16 0 Q8WVV4-1;Q8WVV4 Q8WVV4-1 POF1B Protein POF1B 0 ;;;; 203.53 1.29E-12 573560000 428786 476301 358401 441933 417939 442757 451946 496534 523542 486909 FALSE TRUE 412028.5691 462717.3618 423172.0333 464741.2151 431382.3875 451709.8499 457477.0503 486280.3994 464111.707 453930.2197 0.907691427 1.019357914 0.932240276 1.023816426 0.950327537 0.995108566 1.007813603 1.071266856 1.022429631 1 18.79211101 2.2097577 2.467432734 1.038619593 0.971371998 0.338225007 0.037894679 0.278719875 3.452861795 0.015569724 0.010603271 162.0905517 -2.2097577 -0.067247595 CDLEDER ddPTM_BT-474_Pertuzumab_2h_R1 2 CDLEDER 7 0 F5H823;B7ZB78;F5GZG1;P61224-2;P61224-4;P61224-3;P62834;P61224;A6NIZ1;F5H004;A0A075B6Q0;F5GX62;E7ESV4;F5H7Y6;O95716 F5H823;O95716 RAP1B;RAP1A;RAB3D Ras-related protein Rap-1b;Ras-related protein Rap-1A;Ras-related protein Rap-1b-like protein;Ras-related protein Rab-3D 0 ; 114.78 0.013557 940080000 1858160 2706400 1688110 2870300 1947840 1613190 2925300 2928900 2824800 2411400 FALSE TRUE 1785541.053 2629216.122 1993189.029 3018436.527 2010494.043 1645809.807 2961100.696 2868417.191 2504140.547 2248073.73 0.794253778 1.169541767 0.886620844 1.342676838 0.894318552 0.732097789 1.317172412 1.275944447 1.11390499 1 21.10025792 2.20985997 24.99999783 1.212108058 0.98871278 0.214112763 0.187279425 301.3344191 262478.7576 0.069014885 0.050979727 162.1287259 -2.20985997 -0.223395278 LDQLIYIPLPDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDQLIYIPLPDEK 13 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 160.38 9.62E-05 640350000 1825800 1677600 1530490 1433230 1612210 1732480 1787890 2015110 2115800 2058830 FALSE TRUE 1754445.717 1629756.491 1807083.589 1507199.172 1664068.199 1767511.933 1809770.733 1973497.274 1875623.254 1919383.61 0.91406726 0.849104099 0.941491622 0.785251663 0.866980519 0.920874766 0.942891626 1.028193251 0.977200828 1 20.87221165 2.20992282 1.861593591 1.003316304 0.870673047 0.643848387 0.041486652 0.203353649 1.404008161 0.020824432 0.012935462 162.1521906 -2.20992282 -0.132643257 DDDKHVMR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDDKHVMR 8 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ; 116.52 0.0013551 262450000 461470 442110 395060 438140 459930 445190 455710 483450 559050 549000 FALSE TRUE 443435.2422 429501.4557 466456.1301 460752.4579 474724.0661 454192.0468 461287.1153 473466.5886 495588.9877 511815.741 0.866396257 0.839172033 0.911375115 0.90023112 0.927529242 0.887413204 0.901275749 0.925072347 0.968295713 1 18.96526499 2.21009709 0.018710328 1.833883031 2.12E-08 0.768577365 0.021277345 211.4632536 2.427344374 115.3356108 122.0109706 162.2172708 -2.21009709 -1.833883009 ICVNGDDAHPLWK ddPTM_BT-474_Pertuzumab_2h_R1 2 ICVNGDDAHPLWK 13 0 A0A087X2I2;A0A087WT12;P36969-2;P36969;K7ERP4;K7EKX7;K7ENB4;K7EJ20;A0A0A0MTT1 A0A087X2I2 GPX4 "Glutathione peroxidase;Phospholipid hydroperoxide glutathione peroxidase, mitochondrial" 0 ; 117.7 0.00048545 702350000 1370830 1416180 1170050 1206940 1335180 1424580 1224110 1291490 1419030 1478050 FALSE TRUE 1317256.448 1375791.933 1381504.063 1269230.318 1378127.277 1453385.984 1239091.024 1264820.28 1257947.663 1377940.357 0.955960424 0.998440844 1.002586255 0.921106862 1.000135652 1.054752462 0.899234149 0.917906406 0.912918805 1 20.39408201 2.210131996 24.99995698 0.923897219 0.987328107 0.300536204 0.041221233 234.5047099 206220.6252 0.015149651 0.011190888 162.2303092 -2.210131996 0.063430888 GKQS(ph)PPGPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKQSPPGPGK 10 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 GKQS(1)PPGPGK;GKQS(1)PPGPGK 110.08 0.0050874 266832000 545132 528640 502543 467150 554640 546887 637208 672761 750760 742228 TRUE FALSE 523827.6388 513563.7048 593363.6991 491259.6675 572480.4993 557945.4298 645006.3421 658868.2502 665536.8722 691956.2365 0.757024232 0.74219102 0.857516224 0.709957714 0.827336281 0.806330517 0.932149041 0.952181967 0.961819313 1 19.40032127 2.210147881 1.318732841 0.979119632 0.772617133 0.827738157 0.040311295 0.165256263 0.555097696 0.023934278 0.013458393 162.236243 -2.210147881 -0.206502499 KFQEQECPPS(ph)PEPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 KFQEQECPPSPEPTR 15 1 P62070-2;P62070-3;P62070;P62070-4 P62070-2 RRAS2 Ras-related protein R-Ras2 1 KFQEQECPPS(1)PEPTR 111.18 0.00052853 412790000 103160 223450 102020 249400 106220 125110 203330 251070 179660 138870 TRUE FALSE 99128.39315 217077.4248 120457.2834 262271.5639 109636.6628 127639.8099 205818.4134 245885.3168 159265.75 129464.2112 0.765681822 1.676736936 0.930429207 2.025822901 0.846849193 0.985908065 1.589770728 1.899253195 1.230191329 1 16.98219381 2.210194652 24.57903016 1.550047655 1.235187301 0.029916873 0.432979605 403.7817099 349872.8231 0.156066331 0.115286287 162.253716 -2.210194652 -0.314860354 KLAPEYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLAPEYEK 8 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 110.14 0.0055864 194552000 487620 491150 412440 422240 430680 407520 506730 491240 571170 552280 FALSE TRUE 468563.2713 477142.8829 486977.0827 444031.857 444533.2133 415760.3336 512931.5133 481095.7223 506333.1761 514873.5837 0.910054985 0.926718515 0.945818737 0.862409475 0.863383221 0.807499835 0.996228064 0.934395816 0.983412613 1 18.97385873 2.21039346 24.99998753 0.969729522 0.888453772 0.555951647 0.040169788 196.4174581 174330.6974 0.016177275 0.011950063 162.3280081 -2.21039346 -0.08127575 VSLEDLYNGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSLEDLYNGK 10 0 O60884;A0A087WT48 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 114.5 0.0054043 0 128510 145720 134140 125810 130280 129600 157120 168680 167920 180840 FALSE TRUE 123487.6871 141564.2083 158382.0819 132303.0692 134470.5745 132220.6008 159042.8816 165196.6991 148858.4256 168591.5457 0.732466664 0.839687469 0.939442611 0.784755064 0.797611612 0.784265903 0.943362141 0.979863482 0.882953086 1 17.36317267 2.210468946 10.54493309 0.952986929 0.818018051 0.580761257 0.057553178 0.347725772 127.0948084 0.021901726 0.016306038 162.3562253 -2.210468946 -0.134968879 QKAEADKNDK ddPTM_BT-474_Pertuzumab_2h_R1 10 QKAEADKNDK 10 2 P08238;Q58FF7;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha 0 ;;;;;;;;; 176.78 1.35E-06 25661646000 24968718.7 20644285.6 16561650.6 16074132.2 19732695.7 20269287.9 25395717.5 27524240.6 29654914.4 30213949.2 FALSE TRUE 23992913.57 20055530.79 19554709.28 16903720.09 20367415.78 20679146.79 25706517.89 26955855.41 26288612.84 28167531.51 0.851793263 0.712008817 0.694228718 0.600113648 0.723081317 0.73414835 0.912629418 0.956983235 0.933294876 1 24.7475298 2.210494453 2.950601901 0.956024917 0.7088823 0.787205968 0.05934742 0.117760472 2.108416235 0.025565004 0.018251377 162.3657611 -2.210494453 -0.247142617 SS(ph)PPSAGNSPSSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPPSAGNSPSSLK 14 0 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 1 S(0.007)S(0.993)PPSAGNSPSSLK;S(0.046)S(0.954)PPSAGNSPSSLK 305.8 2.18E-44 519620000 740170 660930 575900 664290 642800 629880 708950 777330 772870 687560 TRUE FALSE 711243.3381 642080.9235 679977.9408 698574.0865 663476.2458 642616.6052 717626.3422 761277.8639 685137.0377 640990.9488 1.109599659 1.001700453 1.060822999 1.089834557 1.035078962 1.002536161 1.119557684 1.187657744 1.068871626 1 19.28994446 2.210505392 24.63101066 1.118370374 1.0493707 0.068190804 0.055973217 248.4613304 218134.0115 0.020422661 0.01508649 162.3698508 -2.210505392 -0.068999673 ELLAKPIGPDDAIDALSSDFTCGS(ph)PTAAGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLAKPIGPDDAIDALSSDFTCGSPTAAGKK 31 2 P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0 P20810-5 CAST Calpastatin 1 ELLAKPIGPDDAIDALSS(0.001)DFT(0.159)CGS(0.74)PT(0.099)AAGKK 133.13 1.53E-06 203420000 123920 119640 79818 76691 106130 126600 78368 96488 103570 114880 TRUE FALSE 119077.0694 116227.9843 94242.88814 80649.0317 109543.7678 129159.9387 79327.09103 94495.48908 91813.1678 107099.0753 1.111840313 1.085237982 0.879959868 0.753032008 1.022826458 1.205985564 0.740688851 0.882318441 0.857273208 1 16.7085865 2.210549693 24.99992442 0.858355952 0.996259489 0.207079891 0.131581262 373.9296631 333732.3319 0.05208866 0.038477992 162.3864148 -2.210549693 0.137903537 VRALEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VRALEVK 7 1 Q8TBH0-2 Q8TBH0-2 0 89.142 0.030866 0 414040 377190 351240 327350 349520 251550 487110 434410 491720 509670 FALSE TRUE 397858.8591 366432.9105 414716.8813 344244.5727 360762.6282 256636.5134 493071.3979 425439.2817 435902.0071 475149.5969 0.837333887 0.771194826 0.872813287 0.724497242 0.759261148 0.540117291 1.037718228 0.895379654 0.917399509 1 18.85802228 2.210634225 24.99999659 0.950628605 0.756518882 0.56485614 0.090726153 174.3459351 156075.2347 0.034132801 0.025213974 162.418025 -2.210634225 -0.194109723 DQDELNPYAAWR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDELNPYAAWR 12 0 O43615;M0QXM9 O43615 TIMM44 Mitochondrial import inner membrane translocase subunit TIM44 0 121.02 0.00047214 0 56667 72808 51927 83595 55039 58352 73566 79914 75639 66970 FALSE TRUE 54452.39099 70731.58713 61311.36401 87909.34797 56809.37942 59531.91742 74466.32271 78263.74797 67052.77782 62434.06225 0.872158386 1.132900609 0.982017857 1.40803505 0.909910029 0.953516643 1.192719487 1.25354246 1.073977496 1 15.93004572 2.210672444 24.99071066 1.163638192 1.054930814 0.049745337 0.156379298 526.2431035 471565.6709 0.057924557 0.042789468 162.4323188 -2.210672444 -0.108707378 IHTGERPYACPDCDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IHTGERPYACPDCDR 15 1 Q9BWE0;Q9BWE0-4 Q9BWE0 REPIN1 Replication initiator 1 0 97.836 0.0018989 262850000 218130 209240 186960 190570 201910 169430 172430 113020 138150 171390 FALSE TRUE 209605.2384 203272.6801 220747.8309 200405.3405 208404.6185 172855.9907 174540.2499 110686.0975 122467.7912 159781.6026 1.311823358 1.27219077 1.381559749 1.254245403 1.304309226 1.081826617 1.092367626 0.692733679 0.766469914 1 17.28574178 2.210704704 1.522524182 0.794867571 1.304357672 0.808944498 0.09816194 0.14553954 0.66004137 0.054298878 0.031660404 162.4443848 -2.210704704 0.509490101 DIAAHIK ddPTM_BT-474_Pertuzumab_2h_R1 6 DIAAHIK 7 0 P63167;F8VXL2;F8VRV5 P63167 DYNLL1 "Dynein light chain 1, cytoplasmic" 0 ;;;;; 104.45 0.0081492 6148250000 8466800 8797700 7318800 8460100 8038600 7597400 9181600 9169600 10009900 9684000 FALSE TRUE 8135908.095 8546798.21 8641469.966 8896726.775 8297168.869 7751024.633 9293967.167 8980244.556 8873618.117 9028094.054 0.90117671 0.946689097 0.957175447 0.985449057 0.919038816 0.858544958 1.029449528 0.994699934 0.982889419 1 23.10599002 2.210730115 24.99999996 1.001613667 0.932389699 0.531253342 0.033786837 191.0246523 171595.3242 0.013313253 0.009834545 162.4538899 -2.210730115 -0.069223967 KSGTS(ph)CPSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSGTSCPSSK 10 1 K7EQL6;Q8NFA0;P35125-2;P35125 K7EQL6 USP32;USP6 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 32;Ubiquitin carboxyl-terminal hydrolase 6 1 KS(0.005)GT(0.2)S(0.795)CPSSK 94.551 0.0049163 101700000 187660 170880 128580 137180 145470 157960 183750 197260 201660 227310 TRUE FALSE 180326.0397 166006.6697 151817.2662 144259.8762 150149.1747 161154.0594 185998.7875 193186.5121 178768.4022 211914.0912 0.850939353 0.783367773 0.716409491 0.680746973 0.708537945 0.760468822 0.877708445 0.911626551 0.843589028 1 17.69312 2.210906693 3.420569007 0.905976477 0.743285131 0.656312484 0.056422534 0.154135309 3.773406817 0.023321089 0.017109065 162.5199549 -2.210906693 -0.162691346 DVKPDEDLASK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVKPDEDLASK 11 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 ; 90.731 0.010277 888180000 3040860 2939800 2581830 2445960 2710140 2656880 2941220 2985500 3397500 3248490 FALSE TRUE 2922019.829 2855959.782 3048424.113 2572196.289 2797314.114 2710603.934 2977215.53 2923848.382 3011830.043 3028466.879 0.964851176 0.943038143 1.00658988 0.849339415 0.923673339 0.895041631 0.983076801 0.965454964 0.994506516 1 21.5301562 2.210909383 24.90557229 0.981020798 0.930465523 0.314728324 0.039757253 287.8191074 259237.985 0.015229358 0.011250342 162.5209617 -2.210909383 -0.050555274 KAEGSPSEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAEGSPSEGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 78.692 0.046885 43729000 84927 85826 72225 85098 69370 72756 90430 99433 97592 85617 FALSE TRUE 81607.95895 83378.32651 85277.66414 89489.91798 71601.34905 74227.17617 91536.70939 97379.6738 86513.7653 79818.08433 1.022424425 1.044604455 1.068400286 1.121173462 0.897056722 0.929954368 1.146816666 1.220020182 1.083886766 1 16.28442803 2.210929041 24.9387562 1.14111649 1.017367091 0.234205832 0.081062058 247.7671436 223619.6667 0.03160664 0.023348229 162.5283182 -2.210929041 -0.123749399 TYEDLKR ddPTM_BT-474_Pertuzumab_2h_R1 3 TYEDLKR 7 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 91.9 0.025758 1833130000 3970800 4083700 3210570 3780400 3703300 3631870 4017000 4267600 4135400 4486300 FALSE TRUE 3815616.746 3967236.874 3790791.418 3975506.897 3822420.008 3705308.9 4066161.248 4179472.569 3665966.729 4182438.905 0.912294676 0.948546282 0.906359066 0.950523603 0.913921302 0.885920628 0.9721986 0.999290764 0.876514113 1 21.99591304 2.210931189 24.97817831 0.966309785 0.921456668 0.237772189 0.036784406 294.6899327 266410.4467 0.013392732 0.00989347 162.5291218 -2.210931189 -0.044853117 SVGRPS(ph)PLASGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVGRPSPLASGR 12 1 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 SVGRPS(1)PLASGR 84.508 0.0073868 416710000 217250 175480 138660 144670 174810 151370 190420 209220 202190 152620 TRUE FALSE 208759.6298 170475.4822 163718.9465 152136.436 180432.9224 154430.8051 192750.4169 204899.5339 179238.2388 142282.9115 1.467215055 1.198144461 1.150657832 1.069253043 1.268127849 1.085378444 1.35469829 1.440085333 1.259731313 1 17.11840288 2.210973767 24.94584529 1.317221976 1.20011416 0 0.151374491 459.9434798 415908.4641 0.055253967 0.040816615 162.545057 -2.210973767 -0.117107815 ERQELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERQELEK 7 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 0 113.71 0.0055352 869170000 340680 319850 346100 319070 312510 360860 358870 388970 455560 388020 FALSE TRUE 327365.849 310728.1912 408647.969 335537.2409 322562.168 368156.8364 363261.9584 380937.6336 403846.7387 361739.0598 0.904977884 0.85898435 1.129676096 0.927567073 0.891698475 1.017741453 1.004209937 1.053072991 1.116403462 1 18.46458986 2.210992155 1.64309845 1.059639081 0.948987717 0.28720556 0.074797887 0.506729238 2.695442571 0.04190669 0.025011852 162.5519391 -2.210992155 -0.110651364 DLPS(ph)PDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPSPDSR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 DLPS(0.999)PDS(0.001)R 99.973 0.0082191 0 118170 159870 114890 141680 144860 149850 128280 142230 131040 142110 TRUE FALSE 113551.7858 155310.6641 135653.1787 148992.1218 149519.5535 152880.0697 129849.929 139292.9008 116164.8886 132484.7631 0.857093171 1.172290764 1.023915321 1.124598167 1.128579241 1.153944545 0.980112173 1.051388081 0.87681697 1 17.01546692 2.211013547 24.83697375 0.988819792 1.083211246 0.207414818 0.093816384 330.825663 298276.6554 0.033594942 0.024816983 162.5599464 -2.211013547 0.094391454 KGVSASAVPFTPS(ph)SPLLSCSQEGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGVSASAVPFTPSSPLLSCSQEGSR 25 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 KGVSASAVPFT(0.001)PS(0.626)S(0.372)PLLSCSQEGSR 95.302 5.07E-06 0 302330 342250 267350 319330 333310 363100 275790 310410 302050 339270 TRUE FALSE 290514.6094 332489.3651 315666.0922 335810.6596 344031.2189 370442.1308 279165.2005 303999.925 267762.5503 316290.9407 0.918504364 1.051213684 0.99802445 1.061714442 1.087704941 1.171206896 0.882621551 0.961140159 0.846570407 1 18.27089271 2.211061334 24.99997118 0.922511222 1.048352981 0.425223143 0.071468144 211.9426121 192678.6792 0.026662034 0.019695771 162.5778342 -2.211061334 0.125841759 S(ph)RSPLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPLLK 7 1 A0A0U1RQD2;Q6ZUS6-6;Q6ZUS6;Q6ZUS6-5;Q6ZUS6-4 A0A0U1RQD2 CCDC149 Coiled-coil domain-containing protein 149 1 S(0.617)RS(0.383)PLLK;S(0.607)RS(0.393)PLLK 74.165 0.028416 747320000 665040 772720 575230 649110 736440 698150 816110 910700 890820 897020 TRUE FALSE 639049.5016 750682.7822 679186.8569 682610.6449 760128.2614 712267.0713 826097.7983 891893.7268 789697.8482 836264.0364 0.764171929 0.8976624 0.812167961 0.816262108 0.908957253 0.851725102 0.987843268 1.066521682 0.944316405 1 19.673599 2.211306345 3.982749909 1.014790465 0.843565661 0.72009417 0.048128727 0.10575565 3.662547398 0.018083056 0.013497679 162.66958 -2.211306345 -0.171224804 KMEEEQR ddPTM_BT-474_Pertuzumab_2h_R1 6 KMEEEQR 7 1 Q9BQ61;K7EN60;K7ELS0;K7ERU7 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 ;;;;; 121.09 0.00717 1910193000 3646180 3562720 2991400 3277300 3370780 3294810 3588380 3801050 3945200 3866120 FALSE TRUE 3503683.255 3461114.714 3532012.523 3446441.846 3479204.2 3361433.316 3632295.668 3722556.989 3497357.436 3604264.249 0.97209389 0.960283285 0.979953821 0.956212311 0.965302198 0.932626768 1.007777293 1.032820219 0.970338797 1 21.78127336 2.211431928 24.41296782 1.008482056 0.961871299 0.538479344 0.018581538 114.5848725 103113.3968 0.006878698 0.00508167 162.7166251 -2.211431928 -0.046610757 EQPGSYSDAPEYLWSGT(ph)L ddPTM_BT-474_Pertuzumab_2h_R1 1 EQPGSYSDAPEYLWSGTL 18 0 Q96A59-2 Q96A59-2 1 EQPGSYSDAPEYLWS(0.083)GT(0.917)L 173.03 1.04E-10 22136000 14722 40890 16331 52219 18557 18822 41082 49445 30996 21778 TRUE FALSE 14146.64796 39723.85724 19282.37498 54914.02885 19153.90276 19202.59374 41584.77381 48423.94347 27477.46403 20302.95666 0.696777725 1.956555289 0.949732362 2.704730634 0.943404602 0.945802823 2.048212706 2.385068553 1.35337254 1 14.30940222 2.211535268 24.98320194 1.88191 1.415701178 0.024051797 0.668573827 523.2245162 483684.2768 0.243206169 0.179665025 162.755348 -2.211535268 -0.466208821 EAVELPLTHFELYK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAVELPLTHFELYK 14 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 212.11 2.90E-09 1097120000 1884190 1872370 1609840 1745660 1925960 1928070 1956670 2074330 2361390 2394660 FALSE TRUE 1810553.772 1818971.841 1900773.899 1835753.722 1987910.253 1967056.896 1980616.313 2031494.361 2093334.907 2232467.545 0.81101012 0.814780866 0.851422858 0.822298056 0.890454267 0.881113323 0.887187058 0.909977108 0.937677643 1 21.09020777 2.211735166 0.167814493 1.054661036 0.725136668 0.938690904 0.013994342 1.127337109 0.130129533 0.085069879 0.13305673 162.8302787 -2.211735166 -0.329524368 SLEQYDQVLDGAHGAS(ph)LTDLANLSEGVSLAER ddPTM_BT-474_Pertuzumab_2h_R1 6 SLEQYDQVLDGAHGASLTDLANLSEGVSLAER 32 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2;M0R3I1 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 SLEQYDQVLDGAHGAS(0.993)LT(0.007)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(1)LTDLANLSEGVSLAER;SLEQYDQVLDGAHGAS(1)LTDLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.999)LT(0.001)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.999)LT(0.001)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.99)LT(0.01)DLANLSEGVSLAER 373.02 2.42E-148 2751696000 605349 574156 484461 579935 544320 581097 512129 483619 615470 609168 TRUE FALSE 581691.2918 557781.633 572013.8795 609865.5148 561828.5471 592847.1795 518396.5879 473632.0986 545604.4259 567908.5088 1.024269372 0.982168121 1.00722893 1.073879869 0.989294118 1.043913184 0.912817082 0.833993665 0.960725922 1 19.115299 2.211788089 10.06494941 0.904427675 1.018850244 0.446295457 0.048346435 0.272418816 98.34719672 0.017685015 0.01319364 162.8501221 -2.211788089 0.114422569 LKEDQIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEDQIK 7 1 Q2TB90;Q2TB90-3;Q2TB90-2 Q2TB90 HKDC1 Putative hexokinase HKDC1 0 82.543 0.022074 320210000 213060 246940 205520 237360 354880 243730 445250 415570 534100 562840 FALSE TRUE 204733.3796 239897.513 242662.0358 249610.178 366295.0375 248658.3876 450699.1027 406988.3343 473471.2071 524718.3455 0.390177667 0.457192921 0.462461505 0.475703166 0.698079342 0.473889258 0.858935287 0.77563199 0.902334007 1 19.00118371 2.211837916 0.477840366 1.011268144 0.388548984 0.847735677 0.082699391 0.335573629 0.16596814 0.075671809 0.070278598 162.8688075 -2.211837916 -0.62271916 down IIHGQDFDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 IIHGQDFDQR 10 0 Q14344 Q14344 GNA13 Guanine nucleotide-binding protein subunit alpha-13 0 132.25 0.0041653 0 150950 275990 135600 300580 143880 135850 271220 253230 225350 176860 FALSE TRUE 145050.7071 268119.0354 160105.9364 316092.9698 148508.0309 138596.9801 274539.2715 248000.712 199769.2127 164881.1147 0.879729055 1.62613551 0.971038659 1.917096269 0.90069764 0.840587355 1.665074087 1.504118361 1.211595477 1 17.33106664 2.211853963 24.99806822 1.409656631 1.219127743 0.026154912 0.368164909 715.7863729 669988.8691 0.134241127 0.09917135 162.8748253 -2.211853963 -0.190528888 RWS(ph)APAAAGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RWSAPAAAGQR 11 1 C9JI98 C9JI98 TMEM238 Transmembrane protein 238 1 RWS(1)APAAAGQR 79.652 0.016269 96483000 56280 67482 53750 62608 53283 47605 73185 76752 71454 63639 TRUE FALSE 54080.51538 65557.47943 63463.82066 65839.20638 54996.89609 48567.60572 74080.65992 75167.04438 63342.84148 59328.67385 0.911540944 1.104988114 1.069698959 1.109736694 0.926986776 0.818619439 1.248648505 1.266959794 1.067659824 1 15.85644191 2.211964497 24.9999674 1.181537745 1.001641849 0.283497216 0.114852306 251.1080054 236036.336 0.044275988 0.032709069 162.9162846 -2.211964497 -0.179895896 TDENIDTPGT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDENIDTPGTPK 12 0 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 TDENIDTPGT(1)PK 176.29 0.00037668 0 351920 280900 283410 268540 311580 318770 283570 297020 317690 302470 TRUE FALSE 338166.5773 272889.007 334628.4914 282399.3816 321602.2537 325215.7478 287040.4145 290886.4332 281627.1631 281983.4375 1.199242694 0.967748352 1.186695553 1.001475066 1.140500508 1.15331507 1.017933596 1.031572761 0.998736541 1 18.1052509 2.212183407 23.71298478 1.016616124 1.101970492 0.305416342 0.070496222 164.6960534 148059.0686 0.024465141 0.01807591 162.9984246 -2.212183407 0.085354368 SRS(ph)GEGEVSGLMR ddPTM_BT-474_Pertuzumab_2h_R1 6 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.005)RS(0.995)GEGEVSGLMR;S(0.08)RS(0.92)GEGEVSGLMR;S(0.002)RS(0.998)GEGEVSGLMR;S(0.002)RS(0.998)GEGEVSGLMR;S(0.433)RS(0.559)GEGEVS(0.008)GLMR;S(0.064)RS(0.88)GEGEVS(0.055)GLMR 246.47 2.11E-17 17039700000 3712150 4057660 2909680 3530840 4010470 3302070 3067630 2940070 3030000 2986080 TRUE FALSE 3567075.074 3941939.51 3435523.901 3713067.076 4139470.41 3368840.118 3105172.574 2879356.527 2686047.103 2783830.142 1.281355145 1.416012942 1.234099685 1.333798 1.486969463 1.210145715 1.115431767 1.034314732 0.964874639 1 21.40863976 2.212224042 1.876802854 1.005625351 1.346496064 0.824416817 0.07062725 0.137150141 0.96377598 0.036116879 0.022548451 163.0136764 -2.212224042 0.340870714 MELLAHLLGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MELLAHLLGEK 11 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 124.42 0.00034944 419080000 1204460 1370290 1036280 1261840 1146830 952440 1474800 1318610 1392460 1370360 FALSE TRUE 1157388.372 1331210.671 1223558.848 1326963.714 1183718.828 971698.9894 1492849.044 1291380.243 1234393.778 1277544.297 0.905947743 1.042007447 0.957742797 1.038683134 0.926557953 0.760599059 1.168530162 1.010830111 0.966223858 1 20.28494188 2.212254581 24.99998945 1.039149345 0.948163657 0.220927128 0.088833529 378.941598 360125.436 0.033679376 0.024881524 163.0251399 -2.212254581 -0.090985688 SKS(ph)PVGNPQLIQFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSPVGNPQLIQFSR 15 1 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 S(0.087)KS(0.913)PVGNPQLIQFSR;S(0.012)KS(0.988)PVGNPQLIQFSR 138.28 7.01E-06 1977290000 337160 331640 224140 292980 324640 331680 277700 297230 346890 301550 TRUE FALSE 323983.4144 322181.9519 264647.084 308100.7329 335082.3404 338386.7969 281098.5757 291092.0966 307512.5015 281125.7499 1.152450156 1.146042125 0.941383292 1.095953441 1.191930446 1.203684817 0.999903338 1.035451561 1.093861027 1 18.10085608 2.212371078 24.99975178 1.034016305 1.116801974 0.267032407 0.072408118 363.1242091 346625.316 0.029246849 0.021607384 163.0688763 -2.212371078 0.082785668 EYENELAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EYENELAK 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 116.52 0.0097481 0 173470 160630 138790 161070 147030 159340 146290 151390 164670 154710 FALSE TRUE 166690.6006 156048.9897 163872.4404 169382.842 151759.3535 162561.964 148080.3408 148263.7436 145977.352 144231.3539 1.155716813 1.081935276 1.136177647 1.174382944 1.052193919 1.127091715 1.026686201 1.027957789 1.012105537 1 17.1380253 2.212425962 1.034513705 1.003455827 1.12845279 0.689910683 0.034031531 0.294310152 0.59843816 0.023444328 0.012947637 163.0894852 -2.212425962 0.124996964 KEDEVEEWQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEDEVEEWQHR 11 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 226.73 2.93E-12 1758930000 1703910 1603630 1631740 1851430 1540370 1539400 1928670 1995410 2103110 2267200 FALSE TRUE 1637319.313 1557896.043 1926631.716 1946982.524 1589917.4 1570527.723 1952273.64 1954204.086 1864373.77 2113640.525 0.774644172 0.737067644 0.911522888 0.921151209 0.752217504 0.743043911 0.923654528 0.924567855 0.882067574 1 21.0112986 2.21244722 23.61434644 0.926008508 0.810950082 0.4592109 0.066715697 128.1201427 115857.5377 0.026664485 0.019701679 163.0974684 -2.21244722 -0.115058426 SPS(ph)LDNPTPFPNLGPSENPLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSLDNPTPFPNLGPSENPLKR 22 1 M0R0R8;M0R0X9;M0QXC8;M0QX56;M0R3C2;M0QYT9;M0R205;M0QZB8;M0QZB7;Q14653-3;Q14653-2;Q14653;Q14653-4 M0R0R8 IRF3 Interferon regulatory factor 3 1 S(0.027)PS(0.973)LDNPTPFPNLGPSENPLKR 193.14 5.03E-18 808790000 213600 181960 160090 216150 225050 224360 317960 363440 405590 396590 TRUE FALSE 205252.2759 176770.679 189021.8242 227305.5274 232288.9376 228896.7129 321851.2896 355934.837 359549.1236 369728.6061 0.555143077 0.478109284 0.511244792 0.61479021 0.628268773 0.619093868 0.870506865 0.962692178 0.97246769 1 18.49610714 2.212586559 1.147011039 1.007872035 0.534870873 0.954775629 0.041597231 0.094619693 0.237965914 0.029808353 0.016474965 163.149805 -2.212586559 -0.473001162 AHSQYYAAQQAGTRPHAGDRDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHSQYYAAQQAGTRPHAGDRDPR 23 2 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3;D6RCL7;D6RJA4;D6RF61 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 0 52.483 0.038001 70940000 16088 17316 14854 16017 14913 19713 11911 11345 14109 16051 FALSE TRUE 15459.26317 16822.16463 17538.44823 16843.63929 15392.69019 20111.61037 12056.77038 11110.72179 12507.40547 14963.85147 1.033107232 1.124186822 1.172054418 1.125621924 1.028658311 1.344012964 0.805726414 0.742504148 0.835841327 1 13.86919393 2.212648563 24.99501173 0.815095453 1.133338472 0.652098709 0.103444489 119.2024859 114983.0933 0.03681094 0.027195476 163.1730994 -2.212648563 0.318243019 KPMVLGHEASGTVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPMVLGHEASGTVEK 15 1 Q00796;A0A6I8PIS1;H0YKB3;Q00796-2 Q00796 SORD Sorbitol dehydrogenase 0 ; 208.92 1.72E-09 1448430000 1879220 1895350 1579690 1841270 1823470 2061530 2136600 2100220 2563600 2544600 FALSE TRUE 1805778.005 1841296.474 1865175.123 1936298.165 1882123.569 2103215.549 2162748.35 2056849.723 2272590.875 2372251.976 0.761208347 0.776180816 0.786246631 0.816227865 0.793391085 0.886590282 0.911685762 0.867045215 0.957988822 1 21.17782583 2.212666398 0.326396501 1.010853689 0.730251925 0.906761389 0.023852309 0.466679062 0.12976158 0.033204762 0.046801745 163.1798004 -2.212666398 -0.280601764 S(ph)PPLMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPLMAK 7 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(1)PPLMAK 62.714 0.087894 343980000 631910 594830 646830 668900 572570 581470 713600 749140 776320 790310 TRUE FALSE 607214.2586 577866.0308 763726.5697 703422.0092 590987.234 593227.7218 722333.2503 733669.9972 688195.4082 736781.5998 0.824144168 0.784311159 1.036571176 0.954722552 0.802119969 0.805160881 0.980389915 0.995776764 0.934056182 1 19.49087751 2.212808409 24.61666733 0.979307619 0.872673397 0.338976705 0.074860884 247.3936059 236482.9094 0.030273189 0.022366373 163.2331679 -2.212808409 -0.106634222 GRDILK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRDILK 6 1 H0Y8U1;Q8IWV2-3;Q8IWV2-4;Q8IWV2 H0Y8U1 CNTN4 Contactin-4 0 83.801 0.051597 196110000 202660 227510 188200 207360 221450 225910 230340 265370 292660 282600 FALSE TRUE 194739.8231 221021.6376 222211.9265 218061.8745 228573.1404 230478.055 233158.9698 259890.0168 259438.4637 263459.2503 0.739164873 0.838921531 0.843439455 0.827687296 0.867584418 0.874814814 0.884990637 0.986452427 0.984738488 1 18.00722031 2.213099326 0.560982143 1.016981057 0.797073685 0.860672859 0.029456077 0.29457784 0.189274009 0.027296029 0.021229008 163.3425481 -2.213099326 -0.219907372 RDYYDR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDYYDR 6 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;; 130 0.025576 1675960000 1764680 1933630 1584150 1724560 1714990 2125700 1430040 1636960 1847710 1815210 FALSE TRUE 1695714.355 1878484.766 1870441.144 1813564.748 1770154.211 2168683.11 1447541.257 1603156.204 1637965.707 1692264.21 1.002038774 1.110042247 1.105289076 1.071679433 1.046027092 1.281527493 0.855387267 0.947343916 0.967913697 1 20.6905234 2.213237741 24.99998498 0.936284872 1.099220588 0.513121733 0.076255474 175.8155238 173572.6017 0.027443751 0.020276198 163.3946157 -2.213237741 0.162935716 FDKEEEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 FDKEEEIR 8 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ;;; 135.79 0.00074663 1774850000 2514324 2502209 2473775 2548556 2709786 2823520 3180680 3283908 3942580 4006760 FALSE TRUE 2416061.438 2430848.449 2920841.171 2680087.281 2796948.728 2880613.509 3219606.113 3216094.152 3495034.847 3735378.576 0.646804973 0.650763611 0.781939799 0.717487458 0.748772493 0.771170432 0.861922305 0.860982116 0.935657464 1 21.83282304 2.213253018 0.329004209 1.022975178 0.62024218 0.914476127 0.032331502 0.429798326 0.120852185 0.04413774 0.061811934 163.4003632 -2.213253018 -0.402732998 VRDVFEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VRDVFEAK 8 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 132.01 0.00089427 897840000 587310 550820 482066 515019 539134 415974 670830 607870 655700 703840 FALSE TRUE 564357.2759 535111.1529 569186.0497 541599.1923 556475.7347 424385.2793 679039.8182 595317.2721 581267.6849 656168.2899 0.860080081 0.815509011 0.867439129 0.825396778 0.848068618 0.646762859 1.034856193 0.907263093 0.885851532 1 19.32370635 2.213354369 24.99999994 0.947821266 0.815735454 0.504266247 0.070790755 205.4544543 203772.0476 0.025933089 0.019160396 163.4385005 -2.213354369 -0.132085812 GQDMETEAHQNK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQDMETEAHQNK 12 0 Q15363;F5GX39 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 ; 115.34 0.00096004 678050000 440490 571210 532150 643260 482860 444050 679340 641100 802630 701140 FALSE TRUE 423275.1638 554919.6501 628321.3426 676458.7257 498391.6304 453028.9952 687653.9661 627861.061 711518.8073 653651.1633 0.64755513 0.848953817 0.961248718 1.03489256 0.762473408 0.693074564 1.0520198 0.960544548 1.088529857 1 19.31816139 2.213398352 24.99991612 1.016475343 0.838734639 0.428026251 0.112707286 265.1402745 263427.8707 0.04498067 0.033233314 163.4550535 -2.213398352 -0.177740704 GVDLHEQSQQNK ddPTM_BT-474_Pertuzumab_2h_R1 4 GVDLHEQSQQNK 12 0 P61020;P61020-2 P61020 RAB5B Ras-related protein Rab-5B 0 ;;; 194.39 1.58E-06 1121730000 1150600 1484320 1066100 1713070 1258950 1118250 1681180 1766780 1812450 1709470 FALSE TRUE 1105633.28 1441988.647 1258767.985 1801481.748 1299445.27 1140861.781 1701754.784 1730295.376 1606708.274 1593686.074 0.693758512 0.904813483 0.789846887 1.130386829 0.815370913 0.715863557 1.067810538 1.085719078 1.00817112 1 20.60393604 2.213400526 24.9996795 1.05237905 0.854115381 0.407965166 0.116362929 231.4422218 229965.1579 0.043843974 0.032393559 163.4558718 -2.213400526 -0.198263669 APANKDPSESWTLPVAAGPGQDTDKTPGHAPAQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 APANKDPSESWTLPVAAGPGQDTDKTPGHAPAQDK 35 2 O75363;G3XAF7;O75363-2 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 175.75 6.11E-16 313500000 334250 298600 277510 248920 304950 255730 347490 386360 367740 310580 FALSE TRUE 321187.1405 290084.2204 327662.2302 261766.791 314758.9937 260901.0358 351742.6866 378381.531 325995.6969 289544.14 1.109285584 1.001865278 1.131648633 0.904065235 1.087084663 0.901075172 1.214815422 1.306818128 1.125892919 1 18.14342377 2.213437688 24.93290718 1.201216704 1.024078967 0.268126458 0.105036304 214.3622338 212739.4197 0.03733269 0.027583119 163.4698589 -2.213437688 -0.177137737 KGSPT(ph)PGFSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.44)PT(0.56)PGFSTR 90.966 0.0065005 5263700000 891810 789540 568030 601700 815370 749900 828100 910650 992760 963880 TRUE FALSE 856957.0793 767023.0922 670685.6568 632753.8091 841597.1166 765063.4918 838234.5355 891844.7593 880066.0468 898595.5491 0.953662724 0.853579893 0.746370998 0.704158628 0.936569425 0.851399156 0.932827384 0.992487399 0.979379486 1 19.77731239 2.213504524 1.246366405 0.997254646 0.823576039 0.484030999 0.070517607 0.404293412 1.208365077 0.048226733 0.026930357 163.4950183 -2.213504524 -0.173678607 IAILHENFTTVKPEDAYEDFIVKPPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 IAILHENFTTVKPEDAYEDFIVKPPVR 27 2 O43237;O43237-2;J3KRI4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ; 170.97 2.96E-12 534570000 240860 212100 221740 187234 223077 224420 259680 281410 308580 275380 FALSE TRUE 231446.9249 206051.1157 261813.3506 196897.1692 230252.4743 228957.9262 262858.0415 275598.7852 273551.2921 256728.2673 0.901524898 0.802603928 1.019807259 0.766947759 0.896872311 0.891829827 1.023876507 1.073503857 1.065528525 1 17.96988263 2.213735636 3.411736568 1.053856689 0.87637328 0.594835829 0.065190247 0.148580387 3.623942044 0.024478769 0.017990868 163.5820459 -2.213735636 -0.177483409 QAPAS(ph)PQEAALDLDVVLIPPPEAFR ddPTM_BT-474_Pertuzumab_2h_R1 3 QAPASPQEAALDLDVVLIPPPEAFR 25 0 Q9BW04 Q9BW04 SARG Specifically androgen-regulated gene protein 1 QAPAS(1)PQEAALDLDVVLIPPPEAFR;QAPAS(1)PQEAALDLDVVLIPPPEAFR;QAPAS(1)PQEAALDLDVVLIPPPEAFR 88.222 0.0098722 51086000 49564 47963 44196 51547 47844 55038 42727 44561 51660 50607 TRUE FALSE 47626.98408 46595.1422 52183.20033 54207.34685 49382.94571 56150.90607 43249.90581 43640.79978 45795.77338 47179.34281 1.009488078 0.987617449 1.106060348 1.148963585 1.046706943 1.190158716 0.916712765 0.924998043 0.970674254 1 15.5258677 2.213766941 24.99999855 0.943428998 1.079833382 0.513061459 0.060978848 181.8216653 183333.5992 0.02354421 0.017396332 163.5938378 -2.213766941 0.136404384 LVS(ph)PGSANETSSILVESVTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVSPGSANETSSILVESVTR 20 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 LVS(0.999)PGS(0.001)ANETSSILVESVTR;LVS(0.997)PGS(0.003)ANETSSILVESVTR;LVS(0.885)PGS(0.115)ANETSSILVESVTR;LVS(0.995)PGS(0.005)ANETSSILVESVTR 240.21 1.13E-29 762599000 180446 194546 157994 176225 164767 181235 151160 148859 169828 171947 TRUE FALSE 173393.9708 188997.7386 186547.0304 185319.9934 170066.8802 184899.6959 153009.9413 145785.0096 150549.8374 160300.8765 1.081678245 1.179018747 1.16373057 1.156075983 1.060922959 1.153454054 0.954517184 0.909446116 0.939170394 1 17.29042279 2.213769937 7.189127941 0.939093303 1.133940182 0.825466974 0.04079492 0.06389109 12.37881105 0.015074971 0.011362522 163.5949663 -2.213769937 0.194846879 AAPGAEFAPNKR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAPGAEFAPNKR 12 1 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 161.99 0.00010244 4858620000 4445460 4695700 3744560 4040900 4097700 3997800 4579700 4768900 4723400 4847500 FALSE TRUE 4271726.508 4561783.234 4421285.289 4249451.333 4229506.242 4078638.255 4635747.739 4670420.548 4187219.434 4519174.507 0.945244868 1.009428431 0.978339137 0.940315831 0.935902394 0.902518424 1.025795249 1.033467626 0.926545197 1 22.10762784 2.213984735 24.99999263 1.003856494 0.954510563 0.239447958 0.037776463 318.9402682 324442.132 0.014858338 0.010978758 163.675899 -2.213984735 -0.049345931 PGPGVWDPNWDR ddPTM_BT-474_Pertuzumab_2h_R1 1 PGPGVWDPNWDR 12 0 Q96HS1;Q96HS1-2 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 76.465 0.072221 330470000 727340 704440 687020 940730 609150 672130 849430 919830 891290 809740 FALSE TRUE 698914.7487 684350.0609 811179.7967 989281.188 628743.863 685720.9291 859825.5784 900835.1891 790114.4958 754895.5886 0.925842937 0.906549291 1.074558931 1.310487441 0.832888511 0.908365262 1.138999342 1.19332422 1.046654011 1 19.52591759 2.214019298 24.97283956 1.120695976 1.000025493 0.109046474 0.133483597 455.8142153 463825.8691 0.052667846 0.03891549 163.6889256 -2.214019298 -0.120670483 IYASS(ph)SPPDTGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 IYASSSPPDTGQR 13 0 A0A494C0H7;A0A494C094;F8WDA1;A0A494C188;A0A494C155;A0A494C1K7;Q9UGJ0-3;Q9UGJ0;E9PGP6 A0A494C0H7 PRKAG2 5-AMP-activated protein kinase subunit gamma-2 1 IYAS(0.021)S(0.722)S(0.257)PPDTGQR 140.82 4.15E-05 330240000 215200 232370 174370 216500 224220 231940 195300 204260 219360 205670 TRUE FALSE 206789.7461 225743.0351 205882.5378 227673.5909 231432.2399 236629.9857 197690.1398 200041.9596 194459.1724 191739.7877 1.078491577 1.177340592 1.073760122 1.187409216 1.20701208 1.234120412 1.031033476 1.043299161 1.014182684 1 17.54879021 2.214198726 23.89689009 1.027807747 1.159996521 0.653170211 0.049036889 92.39321824 90628.63416 0.018973985 0.014021397 163.7565674 -2.214198726 0.132188775 FVNLFPEVKPTIQDVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVNLFPEVKPTIQDVLR 17 1 O94973-3;O94973;O94973-2;A0A0G2JQM1;A0A0G2JS82 O94973-3 AP2A2 AP-2 complex subunit alpha-2 0 122.22 5.26E-05 92107000 116610 128380 114520 117030 105060 105750 134330 131850 150600 143400 FALSE TRUE 112052.7523 124718.7281 135216.3115 123069.9323 108439.3503 107888.3375 135973.9707 129127.2514 133504.5194 133687.3903 0.838169943 0.932913178 1.01143654 0.92057996 0.811141201 0.807019549 1.017103935 0.965889536 0.998632101 1 17.02850387 2.214218906 24.99750374 0.990582348 0.892720512 0.444700262 0.059099362 266.8453693 274032.6712 0.024621922 0.018193002 163.7641766 -2.214218906 -0.097861836 S(ph)EDRRSS(ph)EEREAGEI ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDRRSSEEREAGEI 15 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 2 S(1)EDRRS(0.343)S(0.657)EEREAGEI 157.82 2.16E-06 449550000 472520 553930 368270 428320 456300 513350 395100 424410 419480 418200 TRUE FALSE 454053.396 538132.4588 434824.5811 450425.6465 470977.3039 523730.2887 399935.352 415645.7852 371862.389 389874.9415 1.164612925 1.380269418 1.115292456 1.15530802 1.20802148 1.343328932 1.025804199 1.066100282 0.953799153 1 18.57265191 2.214260728 24.62338914 1.022518676 1.225426845 0.628657304 0.081279924 134.1795124 135964.7903 0.030389478 0.022455637 163.7799477 -2.214260728 0.202908169 AKLDNNK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKLDNNK 7 1 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 106.04 0.0071055 1981120000 3990400 3355200 2820900 2724100 3082100 2274420 4135600 3624800 3778300 4249200 FALSE TRUE 3834450.756 3259512.981 3330699.381 2864691.127 3181238.546 2320410.331 4186212.71 3549946.613 3349403.224 3961397.899 0.967953953 0.82281888 0.8407889 0.723151574 0.803059583 0.58575543 1.056751383 0.896134825 0.845510426 1 21.91757819 2.214278149 24.99691533 0.940278691 0.791836378 0.354701893 0.104761148 280.3938243 288641.8592 0.039236348 0.028991819 163.7865177 -2.214278149 -0.148442313 GTVMYVGLTDFKPGYWIGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTVMYVGLTDFKPGYWIGVR 20 1 K7EP07;Q99426-2;Q99426 K7EP07 TBCB Tubulin-folding cofactor B 0 73.057 0.01405 192050000 38068 54510 38699 49533 43518 55570 35570 30783 58150 49807 FALSE TRUE 36580.26047 52955.42817 45692.77015 52089.40407 44917.79599 56693.66347 36005.3163 30147.32029 51549.05578 46433.52753 0.787798438 1.140456713 0.984046929 1.121805877 0.967356959 1.220963956 0.775416347 0.649257592 1.110168848 1 15.50287927 2.214353226 24.98850823 0.829669981 1.040043389 0.144492429 0.16270549 296.5122293 306078.0257 0.058912713 0.043530429 163.8148338 -2.214353226 0.210373408 LADVAAPPGGPPPPHS(ph)PY(ph)SGPPS(ph)RGSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LADVAAPPGGPPPPHSPYSGPPSRGSPVR 29 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 3 LADVAAPPGGPPPPHS(0.983)PY(0.776)S(0.369)GPPS(0.51)RGS(0.362)PVR 44.674 0.07703 118120000 34808 52836 39648 51101 51583 51965 38654 42324 36311 41611 TRUE FALSE 33447.66488 51329.16901 46813.27556 53738.32873 53242.21404 53015.7679 39127.05921 41449.99461 32189.12751 38792.64991 0.862216553 1.323167382 1.206756323 1.385270892 1.372482008 1.366644662 1.00862043 1.068501242 0.829773877 1 15.24349571 2.214424165 16.57608181 0.992576503 1.265329307 0.431871192 0.15426931 5.257437448 3608.892703 0.057649085 0.042711558 163.8415941 -2.214424165 0.272752804 S(ph)FNGTDNHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFNGTDNHIR 10 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 S(0.985)FNGT(0.015)DNHIR 54.772 0.086916 288680000 711720 731300 650750 670630 654310 647280 778020 794870 906050 874840 TRUE FALSE 683905.1956 710444.04 768355.0009 705241.2947 675356.4754 660368.4451 787541.6415 778455.6567 803199.0025 815586.3076 0.838544234 0.871083825 0.942089137 0.864704677 0.828062547 0.809685546 0.965614104 0.954473671 0.984811779 1 19.63747803 2.214445592 21.20771522 0.970264053 0.862202365 0.72676376 0.035095743 25.49271973 22418.34933 0.014304341 0.010576621 163.849678 -2.214445592 -0.108061688 KIHLFDIDVPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KIHLFDIDVPGK 12 1 Q9NQR4;H7C579 Q9NQR4 NIT2 Omega-amidase NIT2 0 ; 92.925 0.0048433 463150000 1372620 1376050 1170560 1213020 1288670 1245540 1366970 1324450 1612610 1420470 FALSE TRUE 1318976.493 1336806.401 1382106.231 1275624.108 1330121.241 1270725.672 1383699.388 1297099.645 1429553.273 1324260.302 0.996009992 1.009474043 1.043681691 0.963272935 1.004425821 0.959573938 1.044884745 0.979489941 1.079510782 1 20.3367553 2.214485707 24.9994596 1.020201667 0.997734955 0.152007778 0.033366044 579.9588558 602226.008 0.012110005 0.008948925 163.864813 -2.214485707 -0.022466713 MKEEEQAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 MKEEEQAGK 9 1 Q9H446-2;Q9H446 Q9H446-2 RWDD1 RWD domain-containing protein 1 0 108.7 0.0023433 395040000 555570 450050 364030 410540 424290 394290 492780 491310 537300 473900 FALSE TRUE 533857.7102 437215.0146 429818.3188 431728.0186 437937.6732 402262.8139 498810.789 481164.2768 476307.9565 441802.3309 1.208363272 0.989616813 0.97287472 0.977197241 0.991252519 0.910504055 1.129036119 1.08909402 1.078101955 1 18.7530415 2.214544957 24.99990786 1.083996372 1.003652993 0.137648511 0.078565739 386.5039143 402341.5227 0.029080349 0.021487971 163.8871703 -2.214544957 -0.08034338 DGLAFNALIHR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGLAFNALIHR 11 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;; 218.18 1.08E-11 3774760000 2923720 3398770 3064810 4313870 3097080 2033040 4895010 4006410 4285400 4915070 FALSE TRUE 2809457.79 3301840.407 3618689.343 4536509.348 3196700.391 2074149.462 4954916.597 3923676.233 3798939.358 4582167.931 0.613128509 0.720584766 0.789733025 0.990035594 0.697639292 0.452656798 1.081347666 0.856292544 0.829070304 1 22.1275989 2.214545202 24.99900456 0.927252534 0.726787366 0.379076866 0.143502141 298.0922021 310299.1092 0.056030524 0.041402384 163.887263 -2.214545202 -0.200465168 RTAFYNEDDS(ph)EEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 RTAFYNEDDSEEEQR 15 1 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 RTAFYNEDDS(1)EEEQR;RTAFYNEDDS(1)EEEQR 191.07 1.17E-07 705480000 188194 258530 166854 254500 185315 235260 193684 216137 202014 228885 TRUE FALSE 180839.1704 251156.9775 197008.2294 267634.7755 191275.8253 240017.1184 196054.3627 211673.6954 179082.2176 213382.4151 0.847488629 1.177027533 0.92326366 1.254249444 0.896399196 1.124821454 0.918793438 0.991992219 0.839254807 1 17.70308176 2.214569526 24.98814108 0.942107019 1.041849554 0.128577897 0.126581192 459.1629255 478242.4795 0.043107355 0.03185352 163.8964422 -2.214569526 0.099742536 QSVENDIHGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 QSVENDIHGLR 11 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 234.24 1.71E-15 1746070000 1469782 1507815 1332548 2180849 1910133 1578570 1505545 1223840 1678833 1630900 FALSE TRUE 1412341.295 1464813.593 1573369.066 2293402.878 1971574.163 1610489.767 1523970.31 1198567.276 1488258.916 1520437.69 0.928904422 0.963415733 1.034813249 1.508383338 1.29671487 1.059227732 1.002323423 0.788304107 0.978835848 1 20.53605526 2.214617246 2.806241079 0.901017937 1.149827046 0.241224745 0.167874258 0.365962729 5.913138808 0.078478246 0.055576212 163.9144519 -2.214617246 0.24880911 S(ph)PGPPPPVGVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPGPPPPVGVK 11 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 S(1)PGPPPPVGVK;S(1)PGPPPPVGVK;S(1)PGPPPPVGVK 119.45 0.00061338 1736490000 1060717 1051412 965216 1014787 1068347 967811 1013656 991942 1050954 1052692 TRUE FALSE 1019263.007 1021426.759 1139652.002 1067160.279 1102711.352 987380.8015 1026061.425 971458.0511 931654.1079 981392.2332 1.038588826 1.040793604 1.161260466 1.087394257 1.123619399 1.006102115 1.045516146 0.98987746 0.949318811 1 19.90447033 2.214664903 1.285632094 0.978769776 1.089586264 0.549973594 0.0409595 0.34726653 1.107456702 0.026700891 0.015004749 163.9324401 -2.214664903 0.110816488 QTSDGNWLMVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 QTSDGNWLMVHR 12 0 O75131;A0A087WYQ3 O75131 CPNE3 Copine-3 0 ; 114.79 0.0010201 441640000 587310 625370 453000 671090 537200 511900 683710 690260 796370 772120 FALSE TRUE 564357.2759 607535.0599 534867.1769 705725.0353 554479.5259 522250.9687 692077.4475 676005.8898 705969.4163 719823.6247 0.784021608 0.844005447 0.743053102 0.980413828 0.77029915 0.725526297 0.9614542 0.939127123 0.980753329 1 19.45728393 2.214692149 24.58241826 0.962325034 0.812715005 0.575220202 0.068174019 149.778998 154257.9732 0.025340994 0.018726234 163.9427247 -2.214692149 -0.149610029 RTVQSLEIDLDSMR ddPTM_BT-474_Pertuzumab_2h_R1 4 RTVQSLEIDLDSMR 14 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 195.6 4.17E-08 1190360000 666871 793470 552989 645420 704980 760260 581614 594183 648542 650575 FALSE TRUE 640808.9441 770841.0125 652926.4135 678730.2035 727656.3219 775632.9781 588731.9661 581912.9134 574922.2311 606510.9758 1.056549625 1.27094322 1.076528603 1.119073241 1.199741391 1.278844092 0.970686417 0.959443335 0.947917274 1 19.21017423 2.214741777 24.24525427 0.965577854 1.166878469 0.657840908 0.069733172 96.47099315 98197.1294 0.025574471 0.018899834 163.9614599 -2.214741777 0.201300615 SKPAVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKPAVSR 7 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 0 68.735 0.056221 119900000 203960 245210 175760 220230 203820 192290 242040 245550 283500 250440 FALSE TRUE 195989.0177 238216.8509 207523.7418 231596.0967 210376.0554 196178.2355 245002.1579 240479.3067 251318.2685 233477.4757 0.83943437 1.020299068 0.888838382 0.991941925 0.901055036 0.840244803 1.049361002 1.029989321 1.076413336 1 17.83292385 2.214862444 24.99971183 1.040496117 0.920344321 0.534591264 0.057064172 182.2144795 192220.7564 0.020426095 0.015094034 164.0070226 -2.214862444 -0.120151796 EKT(ph)PPRPQGQRPEPENR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKTPPRPQGQRPEPENR 17 3 A9X3U0;Q96GF1 A9X3U0 RNF185 E3 ubiquitin-protein ligase RNF185 1 EKT(1)PPRPQGQRPEPENR;EKT(1)PPRPQGQRPEPENR 81.884 0.0085884 278090000 88942 104455 73383 113241 82811 106818 122136 153496 161144 118193 TRUE FALSE 85466.04831 101476.0457 86644.9405 119085.3816 85474.69102 108977.9331 123630.7369 150326.254 142851.6087 110187.6828 0.775640672 0.920938194 0.786339619 1.080750393 0.775719108 0.989021008 1.122001423 1.364274573 1.296438994 1 16.74960344 2.214869795 2.519092088 1.256835058 0.879197647 0.599107843 0.125583549 0.16526529 2.138839382 0.052008693 0.035801462 164.0097984 -2.214869795 -0.377637411 IQHEELNNR ddPTM_BT-474_Pertuzumab_2h_R1 4 IQHEELNNR 9 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;;; 119.16 0.00087304 974070000 888200 892310 709750 876190 776850 697670 700690 825920 640690 687030 FALSE TRUE 853488.162 866862.1925 838017.6133 921410.2709 801838.0858 711777.3654 709265.2538 808864.4634 567961.5572 640496.8462 1.332540772 1.353421485 1.308386791 1.438586742 1.251900131 1.111289415 1.107367285 1.26287033 0.886751528 1 19.28883194 2.214926315 0.540845432 0.988007751 1.376181007 0.674352476 0.09389244 0.574994142 0.347551242 0.090922438 0.07358095 164.0311445 -2.214926315 0.388173257 TPIS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 8 TPISPLK 7 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK;T(0.001)PIS(0.999)PLK 112.11 0.0067433 36889420000 41994300 37422900 33922600 36724700 37783900 35433200 41377000 44511100 40352700 45090100 TRUE FALSE 40353116.33 36355635.53 40053168.42 38620066.17 38999253.46 36149683.58 41883384.1 43591930.23 35772030.67 42036107.36 0.959963204 0.864866845 0.952827722 0.918735549 0.927756063 0.859967439 0.996366855 1.037011583 0.850983426 1 25.32512574 2.214956131 24.9692027 0.981699877 0.914388013 0.197858786 0.054646556 312.6178427 330689.9568 0.019865167 0.014679329 164.0424062 -2.214956131 -0.067311864 TDVAVQIISNIYHNFPEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDVAVQIISNIYHNFPEQR 19 0 O60306 O60306 AQR Intron-binding protein aquarius 0 245.03 1.49E-24 127170000 180910 174340 180610 151400 203690 199180 165460 184480 189350 193040 FALSE TRUE 173839.8372 169367.9939 213250.2446 159213.7721 210241.8738 203207.5561 167484.949 180670.4235 167855.7818 179965.2289 0.965963471 0.941115097 1.184952482 0.884691855 1.168236082 1.129148988 0.930651716 1.003918505 0.932712296 1 17.45735866 2.215102471 24.95689131 0.969783556 1.045514569 0.142550518 0.094643344 486.2908031 517356.6686 0.034904165 0.025793324 164.0976911 -2.215102471 0.075731013 ARPFPDGLAEDIDKGEVSAR ddPTM_BT-474_Pertuzumab_2h_R1 8 ARPFPDGLAEDIDKGEVSAR 20 2 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 261.69 1.21E-36 18844450000 8146150 7884350 7080250 7348570 7902190 8570000 8804650 9524160 10536510 10557240 FALSE TRUE 7827789.452 7659496.058 8359808.674 7727830.578 8156371.118 8743291.272 8912403.94 9327482.768 9340449.557 9842188.731 0.795330151 0.778230967 0.849385122 0.785173988 0.828715171 0.888348264 0.905530689 0.947704116 0.949021586 1 23.23054775 2.215293136 0.650608181 0.992320601 0.79087832 0.922932552 0.020405417 0.180798676 0.150138491 0.017391123 0.011788794 164.1697497 -2.215293136 -0.201442281 DGFDMFAQTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGFDMFAQTR 10 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6;B7Z2U2 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 110.47 0.0060431 0 40872 46530 37633 39369 41625 33944 51155 51184 51220 48865 FALSE TRUE 39274.67705 45203.00996 44434.12024 41400.83881 42963.90593 34630.37094 51781.05019 50127.03251 45405.72033 45555.33003 0.862131325 0.992266107 0.975387956 0.9088034 0.943114799 0.760182638 1.136662827 1.100354942 0.996715869 1 15.47533224 2.215357599 24.99976002 1.072887129 0.915692243 0.502545525 0.072948686 186.9813216 201459.1154 0.027255079 0.020141575 164.1941196 -2.215357599 -0.157194886 SCLLHQFTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCLLHQFTEK 10 0 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 131.12 0.00025866 1443200000 1683600 2310300 1526900 2189700 1636700 1464900 2478700 2517600 2705600 2476700 FALSE TRUE 1617803.051 2244412.506 1802844.796 2302710.679 1689345.942 1494521.282 2509035.072 2465610.68 2398471.631 2308950.903 0.700665852 0.972048606 0.7808069 0.997297377 0.731650872 0.647272872 1.086655879 1.067848899 1.03877117 1 21.13880607 2.21543318 24.99819846 1.056627104 0.816865031 0.557299062 0.105837785 177.6949633 192067.3662 0.039474191 0.029172019 164.2226968 -2.21543318 -0.239762074 ILPKPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILPKPTR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 79.116 0.030549 3324300000 2635300 2657900 2437800 2821900 2646500 2469500 3023700 3320200 3058300 3249200 FALSE TRUE 2532309.563 2582099.294 2878364.689 2967538.597 2731627.076 2519434.982 3060704.945 3251636.71 2711134.605 3029128.79 0.8359861 0.852423081 0.95022856 0.979667358 0.901786377 0.831735841 1.010424171 1.073456078 0.89502124 1 21.53047149 2.215609469 24.69923294 1.008968413 0.897253976 0.397660888 0.060745517 201.3901457 216727.5024 0.023843061 0.017621618 164.2893718 -2.215609469 -0.111714437 KVEEVVYDLSIR ddPTM_BT-474_Pertuzumab_2h_R1 5 KVEEVVYDLSIR 12 1 E9PGT1;Q15631 E9PGT1 TSN Translin 0 ;;;; 176.91 3.84E-05 1642181000 2165290 2312890 2006790 2118060 2208300 1960970 2456720 2354100 2547140 2540310 FALSE TRUE 2080668.073 2246928.642 2369461.594 2227373.33 2279331.975 2000622.157 2486786.074 2305487.012 2257999.346 2368252.541 0.878566807 0.948770709 1.000510525 0.940513434 0.96245309 0.844767238 1.050051053 0.973497113 0.953445339 1 21.1753915 2.215712114 24.99967406 0.992124873 0.935408712 0.311296214 0.046777894 335.3936051 366968.556 0.01750605 0.012937476 164.3282058 -2.215712114 -0.056716161 LAWVGDVFTATPAEPRPLTS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAWVGDVFTATPAEPRPLTSPLR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 LAWVGDVFTATPAEPRPLT(0.065)S(0.935)PLR 211.44 2.93E-25 2073500000 315060 369210 221950 247860 294100 347790 211110 233610 222620 190870 TRUE FALSE 302747.1069 358680.4923 262061.3023 260652.0843 303559.9936 354822.5521 213693.6273 228785.8719 197349.1109 177942.2049 1.701378867 2.015713431 1.472732691 1.464813165 1.705947129 1.99403257 1.200915924 1.285731353 1.109062974 1 17.44104921 2.21612365 24.31379335 1.185850768 1.71468447 0.699429827 0.184532793 108.5182331 117594.6181 0.072015412 0.053231325 164.4839967 -2.21612365 0.528833702 LS(ph)PDFAEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSPDFAEELR 10 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LS(1)PDFAEELR;LS(1)PDFAEELR 182.41 1.87E-06 111441000 138463 167402 126437 235080 145117 122687 225800 269020 201920 180538 TRUE FALSE 133051.7129 162627.8589 149286.9785 247212.507 149784.8201 125167.8152 228563.4079 263464.643 178998.8881 168310.0005 0.790515789 0.966240024 0.886976282 1.468792741 0.889934167 0.743674261 1.357990656 1.565353468 1.063507145 1 17.36076137 2.216177305 24.95515957 1.325209647 0.975015574 0.230978202 0.24071455 279.0761018 311140.0393 0.091444965 0.067587051 164.5043193 -2.216177305 -0.350194073 DIWPTRDEIQAVER ddPTM_BT-474_Pertuzumab_2h_R1 3 DIWPTRDEIQAVER 14 1 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ;; 255.72 2.48E-24 631370000 253937 288898 224627 255155 280317 288420 239097 262744 267938 258762 FALSE TRUE 244012.8613 280658.9119 265222.0957 268323.5801 289333.6509 294252.05 242023.1406 257318.2446 237522.8015 241235.8193 1.011511732 1.163421389 1.099430825 1.112287474 1.19938097 1.219769315 1.0032637 1.066666822 0.984608348 1 17.88008461 2.216370395 24.99813221 1.023708214 1.135996642 0.50722676 0.057911613 213.9612814 241034.0672 0.021973632 0.01624093 164.5774751 -2.216370395 0.112288429 SEDLDNSIDKTEAGIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDLDNSIDKTEAGIK 16 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 133.71 2.94E-05 210500000 145640 135020 115330 110370 152870 121890 150100 158470 165240 158190 FALSE TRUE 139948.2278 131169.3618 136172.6965 116066.2089 157787.2024 124354.6993 151936.9687 155197.5391 146482.6479 147475.6504 0.9489582 0.889430638 0.923357152 0.787019475 1.06992037 0.843221908 1.03025122 1.052360432 0.993266668 1 17.17011725 2.216378854 24.97143063 1.026690179 0.911611406 0.360643197 0.070560528 233.7387457 263132.9705 0.024931894 0.018428027 164.5806806 -2.216378854 -0.115078773 QPEKEEEEEAGES(ph)VEDIFSEVVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPEKEEEEEAGESVEDIFSEVVGR 24 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 QPEKEEEEEAGES(1)VEDIFSEVVGR 82.157 0.0090857 38285000 35339 35872 30185 29459 31898 30301 36523 40271 37412 33475 TRUE FALSE 33957.91281 34848.96568 35640.10096 30979.38252 32924.02814 30913.70698 36969.9794 39439.38978 33165.1466 31207.70843 1.088125803 1.116678136 1.142028773 0.992683669 1.054996659 0.990579204 1.184642553 1.263770772 1.062722906 1 14.9296148 2.216433718 24.98506374 1.16322552 1.066439253 0.064633812 0.082063998 347.6263564 392527.1704 0.03099791 0.022911593 164.6014732 -2.216433718 -0.096786267 VTS(ph)GGVSESPSGFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTSGGVSESPSGFSK 15 0 E7EPP6;O14757-2;O14757-3;O14757 E7EPP6 CHEK1 Serine/threonine-protein kinase Chk1 1 VT(0.014)S(0.986)GGVSESPSGFSK 163.23 1.63E-06 228500000 274220 277040 222680 306270 367550 323730 259140 278220 278320 294390 TRUE FALSE 263503.1792 269139.0905 262923.2295 322076.6314 379372.5796 330276.0424 262311.4328 272474.6598 246726.2804 274450.7031 0.960111147 0.980646387 0.957998018 1.173531814 1.382297714 1.203407529 0.95576885 0.992800006 0.89898214 1 18.06618751 2.21649058 24.81838457 0.964466881 1.112202353 0.251636173 0.124771059 365.8302088 411383.7084 0.053646474 0.039652885 164.6230258 -2.21649058 0.147735472 LLDEVFFSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDEVFFSEK 10 0 P25789;H0YN18;H0YMZ1;H0YL69;H0YLC2;H0YMI6;H0YMA1;H0YKT8;H0YLS6 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type;Proteasome subunit beta type 0 ; 167.12 1.24E-05 197517000 450690 449530 402435 417450 449910 406990 491530 503570 542500 548070 FALSE TRUE 433076.5365 436709.8445 475163.9566 438994.6445 464381.7637 415219.6167 497545.4912 493171.1035 480917.6743 510948.7307 0.847592939 0.854703845 0.929964061 0.859175526 0.908861762 0.812644384 0.973767936 0.965206632 0.941224912 1 18.96281901 2.216573367 24.99974118 0.967178544 0.872342396 0.687819403 0.033336091 138.3494127 157303.7607 0.011978825 0.008854236 164.6544098 -2.216573367 -0.094836148 EEVLKDFEDLAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEVLKDFEDLAGK 13 1 Q9BV44;C9J9V2 Q9BV44 THUMPD3 THUMP domain-containing protein 3 0 ; 125.28 0.00018424 70152000 120626 106434 109038 99322 106657 106806 140190 146253 162041 162367 FALSE TRUE 115911.8026 103398.6065 128743.5921 104448.0203 110087.7193 108965.6905 141905.6872 143232.8244 143646.785 151369.7385 0.76575281 0.683086379 0.850523978 0.690019164 0.727276934 0.71986443 0.937477257 0.946244777 0.948979542 1 17.20771729 2.216866933 7.385176331 0.953198813 0.738992804 0.841299087 0.046532042 0.062167346 14.04285571 0.016532309 0.012498603 164.7657476 -2.216866933 -0.214206009 KDSGSSSVFAES(ph)PGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 KDSGSSSVFAES(1)PGGK 187.57 8.07E-10 530500000 482200 465110 441490 437550 405160 444210 581410 629930 651330 642970 TRUE FALSE 463355.0909 451845.5182 521277.0639 460132.0079 418192.3394 453192.2306 588525.4695 616921.7254 577393.749 599421.0692 0.773004345 0.753803197 0.869634203 0.767627352 0.697660394 0.756049885 0.981823129 1.029195931 0.963252342 1 19.19321027 2.217148064 6.717166943 1.000348883 0.769860428 0.869287136 0.042526074 0.056711043 9.558771995 0.016822012 0.012746407 164.8724394 -2.217148064 -0.230488455 VSSDNVADLHEK ddPTM_BT-474_Pertuzumab_2h_R1 5 VSSDNVADLHEK 12 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;; 214.42 4.39E-11 6620420000 8743590 8216190 7096900 7767290 8080270 7486500 8936610 8999680 9981450 10003430 FALSE TRUE 8401880.836 7981872.306 8379467.7 8168160.768 8340179.223 7637882.159 9045978.906 8813833.463 8848397.642 9325888.776 0.90092012 0.855883283 0.898516796 0.875858694 0.894303956 0.818997775 0.969985717 0.945093135 0.948799396 1 23.15280979 2.217186537 24.99861292 0.959954351 0.87536384 0.737594706 0.026747638 122.9171276 143760.0379 0.009423521 0.006966231 164.8870458 -2.217186537 -0.08459051 LT(ph)PPPADLPLALPAHGLWSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTPPPADLPLALPAHGLWSR 20 0 Q15742 Q15742 NAB2 NGFI-A-binding protein 2 1 LT(1)PPPADLPLALPAHGLWSR;LT(1)PPPADLPLALPAHGLWSR 155.05 1.27E-07 567410000 442230 395780 356400 369340 405810 377110 422130 434320 470410 382770 TRUE FALSE 424947.1627 384492.7419 420809.4081 388401.6817 418863.2472 384735.4226 427296.1532 425351.1402 417011.0289 356844.647 1.190846399 1.07747936 1.179251004 1.088433538 1.173797199 1.078159434 1.197429069 1.191978481 1.168606654 1 18.44493661 2.217191961 24.99756204 1.160907353 1.131039141 0 0.065923751 837.3660964 979564.1226 0.022616356 0.016717091 164.8891052 -2.217191961 -0.029868211 ASVLDTSMSAGSGS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASVLDTSMSAGSGSPSK 17 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 ASVLDTSMSAGS(0.029)GS(0.955)PS(0.017)K;ASVLDTSMSAGS(0.004)GS(0.994)PS(0.002)K;ASVLDTSMSAGS(0.001)GS(0.999)PSK;ASVLDTSMSAGSGS(1)PSK 329.9 5.94E-72 634420000 918250 817310 704600 723910 744200 737400 883370 974650 908530 962040 TRUE FALSE 882363.7748 794001.119 831936.8937 761271.0819 768137.8689 752310.7332 894180.9463 954523.1369 805397.4833 896880.1739 0.983814561 0.885292308 0.927589792 0.848799097 0.856455401 0.838808522 0.996990426 1.064270529 0.897998982 1 19.77455572 2.217530601 21.65320758 1.002639745 0.888200772 0.431808233 0.055216604 43.40042396 44685.01971 0.020829237 0.01541292 165.0177269 -2.217530601 -0.114438974 LENTS(ph)PMVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LENTSPMVK 9 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 LENT(0.284)S(0.716)PMVK 65.172 0.070608 80206000 232780 208580 206320 197660 198220 221690 227880 254850 254150 265880 TRUE FALSE 223682.7002 202631.5026 243606.6136 207861.2563 204595.9263 226172.7237 230668.8636 249587.2584 225299.9575 247871.7108 0.902413186 0.817485392 0.982793126 0.838584022 0.825410555 0.9124588 0.930597779 1.006921111 0.90893776 1 17.9192341 2.217535948 2.493560443 0.971309587 0.874747749 0.400266704 0.05138735 0.27523114 3.490091833 0.022049932 0.015170976 165.0197589 -2.217535948 -0.096561838 LPGS(ph)PGLSK ddPTM_BT-474_Pertuzumab_2h_R1 4 LPGSPGLSK 9 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 LPGS(1)PGLSK;LPGS(0.999)PGLS(0.001)K;LPGS(1)PGLSK;LPGS(1)PGLSK 180.19 5.13E-05 1471890000 2276490 3237590 2529500 4394670 2842080 2878380 4646100 5497800 5029600 4272000 TRUE FALSE 2187522.254 3145257.103 2986636.918 4621479.445 2933498.084 2936582.816 4702960.362 5384268.509 4458660.894 3982653.635 0.54926249 0.789739051 0.749911288 1.160402051 0.736568719 0.73734326 1.180861002 1.351929895 1.119520125 1 21.92529859 2.217557457 9.764609489 1.209610844 0.800267711 0.543671165 0.166277975 0.213513025 92.9594039 0.062545965 0.046984288 165.0279317 -2.217557457 -0.409343133 FLVHNVK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLVHNVK 7 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 89.673 0.0177 5248500000 7853100 8007200 7233100 7418300 7495100 7357100 8370000 8593900 9380000 9487500 FALSE TRUE 7546192.17 7778842.496 8540282.069 7801159.352 7736186.698 7505865.603 8472434.564 8416432.962 8315221.724 8844903.174 0.853168432 0.879471753 0.965559702 0.881994884 0.874649111 0.848609132 0.957888899 0.951557388 0.9401145 1 23.07641492 2.217608939 24.91721933 0.95760863 0.886910663 0.567370769 0.033407837 195.327463 232295.7538 0.012941411 0.009567713 165.0474956 -2.217608939 -0.070697967 EKPTTALLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKPTTALLDK 10 1 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EKY0;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 119.69 0.00060106 2444460000 4876890 4879860 4257940 4595240 4641600 4491310 5858030 6091570 6751940 6790360 FALSE TRUE 4686295.747 4740691.171 5027444.475 4832400.887 4790901.279 4582127.365 5929722.323 5965776.951 5985488.078 6330442.869 0.740279289 0.748871962 0.794169473 0.763359055 0.756803494 0.72382414 0.936699445 0.94239488 0.945508585 1 22.593875 2.217694273 10.37999422 0.950049946 0.756593352 0.945536436 0.023682328 0.078601423 37.60697839 0.008730813 0.006548801 165.0799289 -2.217694273 -0.193456595 LTTLPSDFCGLTHLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTTLPSDFCGLTHLVK 16 0 Q96AG4 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 160.48 8.77E-09 245720000 212320 345370 212020 306750 202730 229980 308080 360950 317830 220880 FALSE TRUE 204022.2997 335520.3858 250336.7304 322581.4043 209250.9946 234630.3532 311850.3752 353496.2564 281751.2709 205919.6009 0.990786204 1.629375661 1.215701319 1.566540547 1.016178128 1.139427001 1.514427834 1.716671239 1.368258629 1 17.65172164 2.217754249 24.73544337 1.489069029 1.277355543 0.019176159 0.262094802 439.8498919 522907.3752 0.094936476 0.070194115 165.1027279 -2.217754249 -0.211713486 TRKEPKGEAS(ph)S(ph)S(ph)NPAT(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TRKEPKGEASSSNPATPIK 19 3 Q08378 Q08378 GOLGA3 Golgin subfamily A member 3 4 T(0.113)RKEPKGEAS(0.971)S(0.971)S(0.971)NPAT(0.975)PIK 40.962 0.086388 439200000 189580 162520 144940 110760 157040 176810 184130 198520 229200 228600 TRUE FALSE 182171.004 157885.0887 171133.8822 116476.3369 162091.3342 180385.2193 186383.438 194420.4926 203182.1769 213116.7184 0.854794525 0.740838588 0.80300543 0.546537774 0.760575404 0.846415151 0.874560379 0.912272365 0.953384504 1 17.70128425 2.217765235 1.280663732 0.955467028 0.735806877 0.590016252 0.077791965 0.336782443 1.066160305 0.051181912 0.02882581 165.1069045 -2.217765235 -0.219660151 VSELKEELK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSELKEELK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 121.9 0.00054807 3735200000 9326600 9026100 6955600 5953200 9096100 6040900 11326800 12010800 12532400 12322000 FALSE TRUE 8962106.161 8768684.465 8212631.646 6260445.365 9388684.317 6163051.137 11465420.77 11762772.78 11109774.49 11487419.96 0.780167016 0.76332932 0.714923949 0.544982719 0.817301391 0.536504381 0.998084931 1.023969944 0.967125301 1 23.45355147 2.217839876 24.96611315 1.001893585 0.696007462 0.743585933 0.087549492 112.6016358 135671.1838 0.031525411 0.023308439 165.1352833 -2.217839876 -0.305886122 GWEFHSVELNR ddPTM_BT-474_Pertuzumab_2h_R1 2 GWEFHSVELNR 11 0 Q6UXG2-2;Q6UXG2-4;Q6UXG2;Q6UXG2-3;E9PB18 Q6UXG2-2 KIAA1324 UPF0577 protein KIAA1324 0 ; 155 3.17E-05 493760000 459590 794990 503780 953900 552660 459550 884840 817960 688210 674960 FALSE TRUE 441628.7147 772317.6636 594824.2525 1003130.893 570436.8108 468842.4159 895668.9366 801068.8402 610087.286 629244.358 0.701839769 1.227373204 0.945299302 1.594183373 0.906542591 0.745087993 1.423404001 1.273064796 0.969555433 1 19.26326085 2.217893097 24.999965 1.20660245 1.047016956 0.053299 0.268812886 700.0699457 846817.5149 0.100435382 0.074255135 165.1555212 -2.217893097 -0.159585495 ASGTNDKPGGPHYILR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASGTNDKPGGPHYILR 16 1 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 62.646 0.045166 103830000 98051 106770 82546 112230 85253 84858 119550 123710 142460 117120 FALSE TRUE 94219.05852 103725.0241 97463.89843 118022.2037 87995.24017 86573.8869 121013.0887 121155.3453 126288.538 109187.3581 0.862911789 0.949972835 0.892629881 1.080914547 0.805910517 0.792892954 1.108306775 1.109609642 1.156622344 1 16.7364463 2.217943423 24.99733809 1.103699653 0.903869341 0.564166311 0.084140762 176.8051083 214366.191 0.031843744 0.023544265 165.1746606 -2.217943423 -0.199830312 RGSSGSVDET(ph)LFALPAASEPVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.149)S(0.149)GS(0.149)VDET(0.553)LFALPAASEPVIR 127.05 2.80E-05 78890000 52934 62511 71618 80494 53342 65622 85117 92181 98639 89750 TRUE FALSE 50865.28076 60728.24748 84560.96573 84648.30499 55057.79387 66948.9218 86158.68731 90277.43014 87441.91425 83671.15256 0.607918969 0.725796713 1.010634647 1.011678487 0.658026 0.800143416 1.029729897 1.07895526 1.045066449 1 16.35244269 2.217963489 6.5330505 1.049562061 0.811017378 0.460528244 0.124795736 0.161662685 25.19047437 0.049932405 0.037889204 165.1822922 -2.217963489 -0.238544682 T(ph)PSS(ph)EEISPTKFPGLYR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSSEEISPTKFPGLYR 17 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 2 T(1)PS(0.014)S(0.959)EEIS(0.028)PTKFPGLYR 113.53 0.00093414 122380000 183930 173790 179750 156020 175770 178640 186610 201160 206700 202360 TRUE FALSE 176741.8123 168833.6794 212234.8235 164072.2109 181423.8017 182252.2232 188893.789 197005.9757 183236.2826 188653.977 0.936857071 0.894938353 1.124995226 0.86969919 0.961674938 0.966066161 1.001271174 1.044271522 0.971282374 1 17.52538299 2.21823809 3.798087495 1.012784858 0.959169514 0.09944191 0.065604581 0.477132968 14.90328814 0.024937482 0.018635292 165.2867689 -2.21823809 -0.053615345 VLPFFERPDFQLFTGNK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLPFFERPDFQLFTGNK 17 1 Q96HE7 Q96HE7 ERO1L ERO1-like protein alpha 0 ; 164.62 2.34E-09 432450000 311930 341820 285480 268650 300190 327810 280520 278340 350390 325040 FALSE TRUE 299739.4307 332071.6283 337072.5865 282515.0587 309845.884 334438.5428 283953.0877 272592.1817 310615.1962 303024.7513 0.989158244 1.09585645 1.112359915 0.932316774 1.02251015 1.103667411 0.937062357 0.899570681 1.025048927 1 18.20907611 2.218353725 24.99443598 0.95017881 1.042302285 0.262106258 0.061380413 282.4201938 349330.7777 0.023410739 0.017311963 165.3307839 -2.218353725 0.092123475 GMKDDKEEEEDGTGSPQLNNR ddPTM_BT-474_Pertuzumab_2h_R1 3 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 196.43 5.43E-22 859630000 577270 496930 451700 442180 513350 519130 563310 608520 666230 643400 FALSE TRUE 554709.6502 482758.0429 533332.238 465000.9628 529862.369 529627.1643 570203.9563 595953.8493 590602.3635 599821.9449 0.924790523 0.80483558 0.889150926 0.775231661 0.883366095 0.88297397 0.950622032 0.99355126 0.98462947 1 19.19417478 2.218380994 1.611080064 0.994998355 0.849428923 0.704576939 0.039794303 0.191550285 0.979752646 0.020644147 0.012336609 165.3411652 -2.218380994 -0.145569432 FKDIFQEIYDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKDIFQEIYDK 11 1 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 179.93 6.28E-06 5729600000 7164400 6576700 6059900 5962200 6667100 5368200 8354700 8314200 9449600 9188000 FALSE TRUE 6884407.327 6389138.955 7155058.732 6269909.857 6881553.326 5476748.682 8456947.318 8142508.865 8376921.024 8565688.576 0.803719078 0.745899048 0.835316235 0.731979665 0.803385888 0.639382185 0.987305018 0.950595949 0.977962361 1 23.0301378 2.218390515 24.99754136 0.972695258 0.763437596 0.812312163 0.051523882 96.92050839 120116.3823 0.018201956 0.013459672 165.3447902 -2.218390515 -0.209257662 ESWEMNSEEKLEQSTIVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESWEMNSEEKLEQSTIVK 18 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 251.75 1.66E-30 1389580000 581450 506640 507350 458990 594660 592720 639920 728830 814330 794560 FALSE TRUE 558726.2912 492191.1233 599039.4309 482678.5289 613787.779 604705.2045 647751.5324 713779.4058 721890.6723 740743.7435 0.754277435 0.664455323 0.808699954 0.651613373 0.828610143 0.816348717 0.874461024 0.963598292 0.974548457 1 19.49861501 2.218870368 0.827279321 1.003603369 0.719356208 0.82799472 0.048203615 0.220682981 0.287160468 0.035411338 0.020705776 165.5275808 -2.218870368 -0.284247162 NPPS(ph)PRPSQLPVLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 NPPSPRPSQLPVLDR 15 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR;NPPS(0.999)PRPS(0.001)QLPVLDR 100.67 0.0012516 2670280000 1433170 1602670 1232610 1457260 1452890 1454270 1344510 1388300 1421740 1527540 TRUE FALSE 1377160.132 1556963.421 1455370.046 1532469.363 1499623.526 1483676.336 1360964.516 1359631.12 1260350.036 1424078.355 0.967053622 1.093313029 1.021973293 1.076113093 1.053048465 1.041850212 0.955680922 0.9547446 0.885028574 1 20.4415971 2.218875135 4.172456204 0.944649945 1.046351047 0.554862453 0.040925695 0.140437283 5.536745713 0.014637825 0.011030182 165.5293979 -2.218875135 0.101701102 EQPGSYSDAPEYLWS(ph)GTL ddPTM_BT-474_Pertuzumab_2h_R1 1 EQPGSYSDAPEYLWSGTL 18 0 Q96A59-2 Q96A59-2 1 EQPGSYSDAPEYLWS(0.5)GT(0.5)L 147.92 7.67E-08 26198000 36869 94418 31851 115010 39784 44397 95142 125970 69465 46377 TRUE FALSE 35428.11872 91725.29108 37607.18422 120945.6799 41063.68849 45294.73776 96306.37626 123368.6755 61579.62442 43235.84448 0.819415444 2.121510339 0.869814957 2.797347463 0.949760297 1.047620055 2.227466062 2.853388825 1.424272503 1 15.39994025 2.218913425 24.97491894 2.125899297 1.479765349 0.03495277 0.756511897 467.569654 594356.747 0.273297091 0.202122993 165.5439926 -2.218913425 -0.646133948 CDMDDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 CDMDDKR 7 1 P61026 P61026 RAB10 Ras-related protein Rab-10 0 ; 75.38 0.069955 783580000 552700 758610 483460 811300 515840 543690 769900 835630 801930 665030 FALSE TRUE 531099.873 736975.1856 570831.9765 853171.2902 532432.4621 554683.7843 779322.2665 818373.9485 710898.2684 619986.9258 0.856630763 1.188694721 0.920716152 1.376111745 0.858780145 0.894670131 1.256997905 1.319985817 1.14663429 1 19.24187827 2.218969763 24.98800669 1.221379877 1.028686969 0.161521242 0.173200498 363.7574595 463967.3445 0.062974921 0.046575242 165.5654688 -2.218969763 -0.192692908 TAEALDKDGWLHTGDIGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TAEALDKDGWLHTGDIGK 18 1 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ; 227.04 1.92E-19 3074900000 5532500 5081900 4607300 4851400 5128000 5667900 6124300 6363000 8011700 6924500 FALSE TRUE 5316283.783 4936969.188 5439941.599 5101781.335 5292946.777 5782508.821 6199251.015 6231601.826 7102245.404 6455497.447 0.823528137 0.764769753 0.842683564 0.790300264 0.819913077 0.895749533 0.960305703 0.965317062 1.100185611 1 22.62209684 2.218983719 1.03911629 1.036424771 0.800261809 0.877317312 0.035672484 0.162952351 0.334826729 0.024511597 0.013609263 165.5707894 -2.218983719 -0.236162962 ALGS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 6 ALGSPTK 7 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 1 ALGS(0.998)PT(0.002)K;ALGS(0.988)PT(0.012)K;ALGS(0.966)PT(0.034)K;ALGS(0.991)PT(0.009)K;ALGS(0.903)PT(0.097)K;ALGS(1)PTK 120.31 0.0048113 9127110000 18179600 16482100 14573140 14506330 15620170 17211930 17164800 18429000 20521400 19901700 TRUE FALSE 17469121.13 16012046.65 17206830.58 15255003.43 16122606.95 17559967.02 17374867.96 18048434.71 18191896.7 18553740.13 0.94154176 0.863009104 0.927404957 0.822206376 0.868968027 0.946438125 0.93646175 0.972765307 0.980497548 1 24.1452067 2.219054768 1.344117325 0.983397294 0.883890872 0.603081216 0.034158911 0.300217791 1.051571168 0.02098506 0.011948398 165.5978784 -2.219054768 -0.099506422 GDAVANHVPAGWPDQSLAES(ph)DSEDPSGKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDAVANHVPAGWPDQSLAESDSEDPSGKPR 30 1 Q9NYQ6;A0A6I8PL36;A0A6I8PRU0 Q9NYQ6 CELSR1 Cadherin EGF LAG seven-pass G-type receptor 1 1 GDAVANHVPAGWPDQS(0.428)LAES(0.554)DS(0.018)EDPSGKPR;GDAVANHVPAGWPDQS(0.193)LAES(0.765)DS(0.04)EDPS(0.003)GKPR;GDAVANHVPAGWPDQS(0.041)LAES(0.859)DS(0.094)EDPS(0.006)GKPR 121.15 1.12E-05 500840000 207920 331369 189243 356003 212034 229525 332416 405152 346836 248196 TRUE FALSE 199794.2565 321918.6806 223443.4198 374376.3575 218854.2662 234166.1528 336484.2064 396785.4696 307464.6313 231385.4638 0.863469352 1.391265792 0.965676132 1.617976995 0.945842762 1.012017561 1.454214975 1.714824531 1.328798388 1 17.81993871 2.219066899 22.95791124 1.464834928 1.150432229 0.123349172 0.274095233 135.7435654 159863.5561 0.098258815 0.072717634 165.6025039 -2.219066899 -0.314402699 VASEAPLEHKPQVEAS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.667)S(0.333)PR 276.66 1.07E-39 1864050000 635970 714910 622990 663110 762640 760750 600480 623540 677020 663740 TRUE FALSE 611115.5893 694521.4668 735578.1513 697333.1866 787171.0082 776132.8862 607828.8539 610663.6811 600167.5279 618784.2986 0.987606813 1.122396719 1.188747279 1.126940661 1.272125052 1.254286652 0.982295212 0.986876497 0.969913958 1 19.23907706 2.219091451 24.98484573 0.983971047 1.162114503 0.568500206 0.074189459 184.0584377 236201.2688 0.029457712 0.021786962 165.6118661 -2.219091451 0.178143456 SLANGT(ph)PPMGAASK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLANGTPPMGAASK 14 0 A0A1B0GV68 A0A1B0GV68 1 SLANGT(1)PPMGAASK;SLANGT(1)PPMGAASK 189.56 2.10E-07 338400000 945940 1556780 887460 1809590 740270 939840 1665150 2014910 1570380 1366840 TRUE FALSE 908971.619 1512382.159 1047843.763 1902983.157 764081.4568 958844.2087 1685528.604 1973301.404 1392117.046 1274262.709 0.713331413 1.186868412 0.822313763 1.493399393 0.599626318 0.752469802 1.32274812 1.548582871 1.092488257 1 20.28123131 2.219093386 24.73441969 1.316020838 0.945737979 0.210825611 0.280790945 276.6135501 351453.5278 0.103464277 0.0765288 165.612604 -2.219093386 -0.370282859 YESHPVCADLQAK ddPTM_BT-474_Pertuzumab_2h_R1 3 YESHPVCADLQAK 13 0 C9JRZ6;Q9NX63 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 0 ;; 155.66 4.25E-05 436080000 1047060 1142870 862930 1244710 778040 910060 1181250 1193540 1212570 1176400 FALSE TRUE 1006139.738 1110276.467 1018880.647 1308949.632 803066.3632 928462.0367 1195706.491 1168892.982 1074924.137 1096721.38 0.917406878 1.012359645 0.929024149 1.193511548 0.732242826 0.846579682 1.090255476 1.065806688 0.980125086 1 20.06476563 2.219136139 24.99913084 1.044157584 0.943659622 0.140213445 0.114374144 486.9080656 626642.5769 0.043723198 0.032339836 165.6289084 -2.219136139 -0.100497962 LYQVEYAMEAIGHAGTCLGILANDGVLLAAER ddPTM_BT-474_Pertuzumab_2h_R1 2 LYQVEYAMEAIGHAGTCLGILANDGVLLAAER 32 0 P25789;H0YMZ1;H0YL69;H0YLC2;H0YMI6;H0YMA1;H0YLS6 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type 0 ; 207.7 3.71E-27 791330000 75441 67610 64378 74468 74971 72939 78164 80660 105353 93166 FALSE TRUE 72492.68232 65681.829 76012.53668 78311.3024 77382.5103 74413.87655 79120.59441 78994.34281 93393.76912 86855.78384 0.834632757 0.7562171 0.87515803 0.901624497 0.890930999 0.856752116 0.910942149 0.909488572 1.075274035 1 16.4063343 2.219184714 0.381219931 1.028441737 0.797665953 0.644483571 0.049326076 0.866657047 0.301962272 0.057757929 0.070098057 165.6474346 -2.219184714 -0.230775784 RPRPPNAPS(ph)QDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPRPPNAPSQDGK 13 2 P16989;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 1 RPRPPNAPS(1)QDGK;RPRPPNAPS(1)QDGK 111.7 0.0007553 155538000 118867 100944 62898 87676 101434 82640 111654 115165 130569 111708 TRUE FALSE 114221.5462 98065.17595 74265.06776 92200.96887 104696.7167 84311.03742 113020.4551 112786.8025 115747.3545 104141.9177 1.09678743 0.941649416 0.71311408 0.885339649 1.005327337 0.809578307 1.085254215 1.083010617 1.111438671 1 16.66819135 2.219210434 24.98451204 1.077804658 0.904582691 0.378876718 0.100890968 248.1336758 320382.4938 0.038567744 0.028527182 165.6572449 -2.219210434 -0.173221967 VSELHLEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSELHLEVK 9 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 125.97 0.00048667 344440000 897520 978930 850150 874870 872660 845670 1011100 1034680 1115270 1069900 FALSE TRUE 862443.9261 951011.8749 1003791.016 920022.1455 900729.9014 862770.0268 1023474.144 1013313.496 988669.2252 997434.72 0.864662026 0.953457761 1.006372644 0.92238833 0.903046468 0.864988966 1.026106394 1.015919615 0.991211961 1 19.9278629 2.219212967 24.99987062 1.010897607 0.924091529 0.543688388 0.039832342 205.4166504 265425.432 0.015896015 0.011756972 165.6582111 -2.219212967 -0.086806078 KS(ph)QENLGNPSK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSQENLGNPSK 11 1 C9J1M4;C9J8V3;C9JJN3;C9JR71;C9JTF7;C9JP72;C9J3Y6;C9IYB9;C9K0C5;B4DGG1;Q9H0X4-2;Q9H0X4 C9J1M4 ITFG3 Protein ITFG3 1 KS(1)QENLGNPSK;KS(1)QENLGNPSK;KS(1)QENLGNPSK 131.48 0.00012397 604050000 659960 1131010 582220 1431070 630390 556000 1449290 1793930 1413830 790840 TRUE FALSE 634168.0336 1098754.702 687440.1054 1504927.694 650667.0669 567242.7009 1467026.845 1756884.719 1253337.946 737275.7024 0.860150459 1.49029013 0.932405752 2.04120072 0.882528835 0.769376638 1.989794103 2.382941297 1.699958295 1 19.49184469 2.219302251 24.98684779 1.940738262 1.194285593 0.238978602 0.490282071 267.0028359 346421.7871 0.178912031 0.13233606 165.6922712 -2.219302251 -0.746452668 TVFDEAIR ddPTM_BT-474_Pertuzumab_2h_R1 3 TVFDEAIR 8 0 P63000;J3KSC4;J3QLK0;P60763;P63000-2;B1AH77;B1AH80;P15153 P63000 RAC1;RAC3;RAC2 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 3;Ras-related C3 botulinum toxin substrate 2 0 ;; 116.73 0.0096687 125680000 543960 739730 468680 702180 499900 434780 779140 700420 744600 629320 FALSE TRUE 522701.4418 718633.6247 553380.9017 738419.5939 515979.7375 443571.5495 788675.3484 685956.0822 660076.1296 586695.5959 0.890924434 1.224883278 0.94321639 1.258607699 0.879467549 0.756050587 1.344266693 1.169185668 1.125074288 1 19.16225264 2.21930351 24.99999515 1.179334009 1.007528283 0.192357609 0.164337436 397.86752 516517.2629 0.060966822 0.045096585 165.6927517 -2.21930351 -0.171805726 S(ph)RSHSDNDRPNCSWNTQYSSAYYTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.478)RS(0.478)HS(0.044)DNDRPNCSWNTQYSSAYYTSR;S(0.49)RS(0.49)HS(0.02)DNDRPNCSWNTQYSSAYYTSR;S(0.482)RS(0.482)HS(0.036)DNDRPNCSWNTQYSSAYYTSR 341.23 8.29E-96 2892240000 416159 494320 302694 421369 360613 432915 357627 353935 395996 450946 TRUE FALSE 399895.0462 480222.4776 357397.5392 443115.9046 372212.4446 441668.8379 362003.7462 346626.1186 351044.1942 420403.0258 0.951218287 1.142290726 0.850130749 1.05402644 0.885370518 1.050584346 0.861087395 0.824509096 0.835018239 1 18.68141353 2.219365255 24.57541708 0.860975684 0.987849156 0.242042628 0.091819806 231.5818405 296487.0771 0.031924427 0.02361668 165.7163101 -2.219365255 0.126873472 KLEEFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEEFQK 7 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 69.598 0.095091 249480000 421230 430280 352020 328460 391200 353440 440690 454490 458900 476000 FALSE TRUE 404767.8659 418008.8357 415637.8446 345411.86 403783.3033 360586.799 446083.296 445104.6227 406807.5959 443760.096 0.912132185 0.941970311 0.936627354 0.778375215 0.909913503 0.812571482 1.005235261 1.00302985 0.916728655 1 18.75942042 2.219403666 24.95856387 0.98465528 0.88371165 0.444895723 0.054273163 225.274475 293496.1166 0.020672765 0.015291504 165.7309676 -2.219403666 -0.10094363 DWDHYK ddPTM_BT-474_Pertuzumab_2h_R1 1 DWDHYK 6 0 O14646;O14646-2 O14646 CHD1 Chromodomain-helicase-DNA-binding protein 1 0 76.592 0.07465 56813000 161230 171600 153840 158840 143950 138990 189360 176160 209680 209530 FALSE TRUE 154928.9534 166706.136 181642.3102 167037.7514 148580.2825 141800.473 191677.4443 172522.2344 185878.0055 195338.3465 0.793131283 0.85342248 0.929885573 0.855120126 0.760630389 0.725922358 0.981258661 0.883196963 0.951569463 1 17.57561566 2.219445562 24.99999198 0.939049795 0.825154302 0.536546317 0.06039396 241.0516041 315262.0415 0.02445798 0.018091658 165.7469562 -2.219445562 -0.113895493 DRS(ph)SPPPGYIPDELHQVAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRSSPPPGYIPDELHQVAR 19 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 DRS(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.637)S(0.363)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR 241.29 1.41E-24 3194290000 1240980 1384040 1081420 1255720 1305910 1338200 1192660 1256090 1327410 1323340 TRUE FALSE 1192481.13 1344568.534 1276856.65 1320527.86 1347915.781 1365259.321 1207256.13 1230151.303 1176727.982 1233709.003 0.966582173 1.089858736 1.034973926 1.070372232 1.092571893 1.106629941 0.978558255 0.997116256 0.95381324 1 20.23457071 2.219456744 24.91632322 0.983609469 1.062306522 0.491705529 0.038703202 194.366803 253502.3063 0.014189389 0.010496553 165.7512239 -2.219456744 0.078697053 KVEEDLKADEPS(ph)SEESDLEIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEEDLKADEPSSEESDLEIDK 22 2 P50502;Q3KNR6;F6VDH7 P50502 ST13 Hsc70-interacting protein 1 KVEEDLKADEPS(0.572)S(0.419)EES(0.009)DLEIDK 69.765 0.0095091 175560000 95113 80536 95884 97647 88951 88895 154330 175220 182890 146390 TRUE FALSE 91395.87881 78239.19213 113212.3717 102686.5734 91812.1897 90692.51781 156218.7367 171601.6458 162129.0939 136474.8749 0.669690145 0.573286418 0.829547357 0.752421084 0.672740603 0.664536369 1.144670305 1.257386357 1.187977597 1 17.05827585 2.219471099 7.135354471 1.179699354 0.695718725 0.863270085 0.088126337 0.051517296 11.11108226 0.032681049 0.024809123 165.7567028 -2.219471099 -0.483980629 LALSPEDKPIRLS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LALSPEDKPIRLSPSK 16 2 H9KVB4;O15417;O15417-2;O15417-3 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 LALS(0.001)PEDKPIRLS(0.99)PS(0.009)K 70.094 0.023159 202420000 316810 251360 252750 241830 292790 224350 330280 311930 321500 329330 TRUE FALSE 304428.7149 244191.4589 298427.5474 254310.8753 302207.8563 228886.5107 334322.0654 305488.5365 285004.6678 307024.1858 0.991546364 0.79534926 0.972000126 0.828308932 0.984312866 0.745499936 1.08891117 0.994998279 0.928280836 1 18.22799278 2.219596447 24.99999406 1.004894404 0.887773747 0.31104552 0.085178194 280.5960378 369900.4612 0.029231685 0.021624029 165.804551 -2.219596447 -0.117120657 MLDAEDIVNTARPDEK ddPTM_BT-474_Pertuzumab_2h_R1 8 MLDAEDIVNTARPDEK 16 1 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;;;;;; 294.93 1.10E-45 6471660000 3436880 3422813 3167709 4107280 3296729 2648828 4892580 4777140 5210860 5308720 FALSE TRUE 3302562.93 3325197.725 3740184.482 4319257.213 3402771.282 2702389.117 4952456.858 4678490.39 4619345.019 4949155.666 0.667298253 0.671871719 0.75572173 0.872726078 0.687545818 0.546030333 1.000667021 0.945310818 0.933360219 1 22.23875099 2.219736359 24.99996955 0.964401847 0.70870213 0.734087768 0.079376125 138.6976531 184199.3468 0.031587779 0.02336804 165.8579751 -2.219736359 -0.255699718 QNEHCLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QNEHCLK 7 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2;Q9ULV0-3 Q9ULV0 MYO5B Unconventional myosin-Vb 0 87.616 0.019211 85730000 141220 155960 122190 132440 147700 143960 157730 157460 185760 174110 FALSE TRUE 135700.9663 151512.1735 144272.4511 139275.2443 152450.9046 146870.9698 159660.3469 154208.396 164673.3036 162317.3746 0.836022432 0.933431642 0.888829378 0.858042736 0.939214948 0.904838254 0.983630664 0.950042448 1.014514336 1 17.30845791 2.219774117 0.712052626 1.004479626 0.880969613 0.692182242 0.031261026 0.395220757 0.386815318 0.024932443 0.015836803 165.8723957 -2.219774117 -0.123510013 IKDLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKDLHK 6 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 72.234 0.051754 2983900000 11683500 10896200 10380900 10708400 10904800 9557400 13300000 12997000 14644400 14477300 FALSE TRUE 11226895.9 10585451.04 12256959.55 11261061.81 11255562.8 9750657.176 13462769.38 12728607.41 12982029.11 13496739.58 0.831822815 0.784296903 0.908142258 0.834354234 0.833946801 0.722445382 0.997483081 0.943087576 0.961864088 1 23.6861076 2.219799784 24.99999999 0.968840375 0.822989322 0.729423232 0.046570063 134.1026395 178699.1764 0.017407982 0.012878417 165.8821991 -2.219799784 -0.145851052 HPDSSVNFAEFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HPDSSVNFAEFSK 13 0 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 73.91 0.035545 1354200000 482310 499660 590870 379460 526990 501870 469170 468070 539510 486430 FALSE TRUE 463460.792 485410.186 697653.3528 399043.9761 543941.112 512018.1553 474911.8428 458404.1909 478267.0866 453483.6628 1.022001077 1.070402808 1.538431062 0.879952265 1.199472344 1.129077401 1.047252375 1.010850508 1.054651194 1 18.79069105 2.21980607 3.403997644 1.02429089 1.147227933 0.108048755 0.158287374 0.542421498 13.21001818 0.061726417 0.045566176 165.8845999 -2.21980607 0.122937044 GFSQYGVSGS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 5 GFSQYGVSGSPTK 13 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 1 GFSQYGVS(0.001)GS(0.985)PT(0.014)K;GFSQYGVSGS(1)PTK;GFSQYGVSGS(1)PTK;GFSQYGVSGS(1)PTK;GFSQYGVS(0.083)GS(0.905)PT(0.012)K 303.77 3.85E-41 4003740000 4644820 4295690 4067810 4484450 4648960 4991440 5227690 5806970 6620330 6568830 TRUE FALSE 4463295.299 4173181.127 4802953.755 4715893.002 4798498.02 5092370.337 5291668.034 5687054.04 5868817.893 6123917.293 0.728830108 0.681456154 0.784294354 0.77007784 0.783566758 0.831554394 0.864098547 0.928662777 0.958343755 1 22.54602337 2.219982812 0.501882325 1.009595906 0.70625767 0.951785276 0.021549206 0.179732911 0.096065857 0.020663271 0.018226583 165.9521227 -2.219982812 -0.303338236 TEIIILATR ddPTM_BT-474_Pertuzumab_2h_R1 1 TEIIILATR 9 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82 P23396 RPS3 40S ribosomal protein S3 0 90.37 0.021758 0 155460 141920 119780 122340 141460 126960 150250 150860 149820 166780 FALSE TRUE 149384.4513 137872.5806 141426.9105 128653.9821 146010.1894 129527.2182 152088.8044 147744.6883 132813.0617 155483.842 0.960771546 0.886732529 0.909592332 0.827442777 0.939069857 0.833059027 0.978164692 0.95022535 0.854192049 1 17.24640514 2.220146644 24.99998917 0.943742273 0.892401875 0.196696519 0.052280345 408.1153654 554079.9142 0.018649211 0.013798018 166.0147379 -2.220146644 -0.051340398 KFLDAGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFLDAGHK 8 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 107.15 0.0026341 4027800000 15444000 16257600 12639800 15514400 14863600 13922000 16772900 16264100 18428700 18075400 FALSE TRUE 14840431.41 15793949.17 14924093.03 16315100.04 15341701.19 14203512.38 16978171.77 15928240.65 16336751.24 16851137.06 0.88067834 0.937263112 0.885643086 0.968189861 0.910425281 0.842881541 1.007538643 0.945232396 0.969474711 1 24.00634261 2.22048565 24.99998408 0.973827678 0.908034755 0.520860177 0.035540716 223.783709 309519.5795 0.013070283 0.009672134 166.1443781 -2.22048565 -0.065792923 SNDS(ph)GEEAEKEFIFV ddPTM_BT-474_Pertuzumab_2h_R1 4 SNDSGEEAEKEFIFV 15 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SNDS(1)GEEAEKEFIFV;S(0.025)NDS(0.975)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV 175.39 2.26E-06 1148740000 2597460 2536290 2088190 2306660 2412570 2520820 2913430 3367730 3279230 3159740 TRUE FALSE 2495948.392 2463957.492 2465572.385 2425706.999 2490172.505 2571792.708 2949085.428 3298185.199 2906985.558 2945727.995 0.847311223 0.836451124 0.836999339 0.823466051 0.845350456 0.873058447 1.001139763 1.119650288 0.986847924 1 21.49019279 2.220630408 3.103032558 1.05139246 0.838809521 0.869787402 0.034887336 0.073168278 1.459934205 0.013858099 0.01007866 166.199766 -2.220630408 -0.212582939 AFLS(ph)PPTLLEGPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AFLSPPTLLEGPLR 14 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 AFLS(0.997)PPT(0.003)LLEGPLR;AFLS(0.957)PPT(0.043)LLEGPLR;AFLS(0.991)PPT(0.009)LLEGPLR 150.26 7.62E-06 538937500 727994 975335 605477 1028559 777235 750096 1003691 1175564 1058814 814892 TRUE FALSE 699543.1896 947519.4008 714900.1627 1081643.053 802235.4696 765263.4551 1015974.471 1151288.193 938621.8736 759698.639 0.920816695 1.247230615 0.941031254 1.423779111 1.055991716 1.007325031 1.337338806 1.515453804 1.235518698 1 19.53506771 2.220683502 24.2995176 1.337302845 1.111661652 0.132561676 0.187400392 241.2240374 327881.5659 0.067184661 0.049735034 166.2200856 -2.220683502 -0.225641193 NGVAAEVS(ph)PAKEENPRR ddPTM_BT-474_Pertuzumab_2h_R1 3 NGVAAEVSPAKEENPRR 17 2 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 NGVAAEVS(1)PAKEENPRR;NGVAAEVS(1)PAKEENPRR;NGVAAEVS(1)PAKEENPRR 208.46 2.69E-12 2935990000 1593930 1359030 1004410 1015920 1151210 1272750 1310340 1475960 1534190 1389420 TRUE FALSE 1531637.453 1320271.795 1185929.23 1068351.753 1188239.715 1298485.877 1326376.333 1445480.91 1360035.183 1295313.346 1.182445513 1.019268271 0.915553934 0.824782479 0.917337661 1.002449238 1.02398106 1.115931458 1.049966163 1 20.30486971 2.220730472 2.715467028 1.067248647 0.963955856 0.122284175 0.091109024 0.476311432 7.200904066 0.041824728 0.029534185 166.2380637 -2.220730472 -0.103292791 RPS(ph)LPV ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSLPV 6 1 Q15053 Q15053 KIAA0040 Uncharacterized protein KIAA0040 1 RPS(1)LPV;RPS(1)LPV 71.342 0.073307 327000000 146223 304300 118362 402740 143457 164829 312499 371800 234663 172804 TRUE FALSE 140508.4435 295621.6619 139752.6463 423525.4597 148071.4247 168161.9553 316323.4562 364122.2001 208025.04 161099.8312 0.872182438 1.83502155 0.867490955 2.628962778 0.919128367 1.043836943 1.963524443 2.260227074 1.291280311 1 17.29759546 2.220765655 24.97016693 1.79838753 1.397748675 0.012827205 0.612696224 614.0743566 861673.1645 0.221957653 0.164271683 166.2515315 -2.220765655 -0.400638855 QVTEEVRK ddPTM_BT-474_Pertuzumab_2h_R1 2 QVTEEVRK 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 80.455 0.0412 296560000 379810 419640 285390 377010 382270 355300 400670 413510 452610 399400 FALSE TRUE 364966.6053 407672.2781 336966.3215 396467.5313 394566.0617 362484.4094 405573.5193 404970.874 401231.6103 372348.2823 0.980175343 1.094868158 0.904976168 1.064776045 1.059669349 0.973509015 1.089231611 1.087613112 1.07757073 1 18.50629318 2.220781438 24.99531548 1.073349648 1.016282354 0.152105223 0.056378913 394.6525605 554828.9562 0.020011126 0.014810274 166.2575737 -2.220781438 -0.057067293 VVSSIEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 VVSSIEQK 8 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 159.46 0.00083534 1124110000 1128760 1157170 1012960 1120800 1056930 1029390 1234080 1236250 1329570 1322880 FALSE TRUE 1084646.811 1124168.645 1196024.405 1178644.622 1090927.113 1050204.971 1249183.04 1210721.005 1178642.788 1233280.159 0.879481279 0.91152739 0.969791329 0.955699006 0.884573635 0.851554258 1.012894784 0.981708006 0.955697518 1 20.23406914 2.220782918 24.99986466 0.986544172 0.912703263 0.540391902 0.035487427 218.9330053 307872.2264 0.014383516 0.010645282 166.2581402 -2.220782918 -0.07384091 SS(ph)GSETEQVVDFSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 S(0.007)S(0.708)GS(0.285)ETEQVVDFSDR;S(0.455)S(0.481)GS(0.064)ETEQVVDFSDR;S(0.078)S(0.915)GS(0.007)ETEQVVDFSDR 379.11 4.40E-98 1448130000 927810 982290 817430 869330 883890 969120 834210 905560 906280 954250 TRUE FALSE 891550.1595 954276.051 965157.7846 914196.2255 912321.1246 988716.2704 844419.3115 886859.8695 803402.8938 889617.7975 1.002172126 1.072680935 1.084912855 1.027628076 1.025520316 1.111394436 0.949193366 0.996899873 0.903087704 1 19.76282613 2.22089898 24.99999101 0.965313491 1.053803115 0.571467771 0.038890268 178.0016369 251959.2622 0.013990762 0.010354746 166.3025775 -2.22089898 0.088489624 LAEEENK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAEEENK 7 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 127.12 0.0090405 409540000 481530 455480 383890 434500 474520 492420 490450 550530 630030 599780 FALSE TRUE 462711.2752 442490.1564 453267.4626 456924.5971 489783.3667 502377.0698 496452.2738 539161.3631 558511.6357 559156.3664 0.827516779 0.791353158 0.810627384 0.817167835 0.875932738 0.898455423 0.887859468 0.964240766 0.998846958 1 19.09289226 2.221063402 0.618917865 1.010461044 0.800430871 0.937441172 0.018531472 0.17474349 0.132900974 0.016807885 0.011942927 166.3655509 -2.221063402 -0.210030173 KQYQDS(ph)PNQK ddPTM_BT-474_Pertuzumab_2h_R1 4 KQYQDSPNQK 10 1 H0Y9T5;Q8IU60 H0Y9T5 DCP2 m7GpppN-mRNA hydrolase 1 KQYQDS(1)PNQK;KQYQDS(1)PNQK;KQYQDS(1)PNQK;KQYQDS(1)PNQK 210.73 4.40E-08 1272860000 3052680 2757220 2495860 2157450 2300100 2374000 2987150 3173390 3273740 3347180 TRUE FALSE 2933377.891 2678586.785 2946917.422 2268796.253 2374084.805 2422003.907 3023707.635 3107858.388 2902118.76 3120472.517 0.940042854 0.858391404 0.94438179 0.727068173 0.760809394 0.776165755 0.968990311 0.995957622 0.930025419 1 21.57333307 2.22122151 23.55655484 0.975665091 0.832328605 0.495672909 0.068788137 109.8663987 149260.3198 0.027611174 0.020452204 166.4261282 -2.22122151 -0.143336486 REQEVNILK ddPTM_BT-474_Pertuzumab_2h_R1 1 REQEVNILK 9 1 P35579 P35579 MYH9 Myosin-9 0 100.88 0.006994 404000000 196490 178880 153860 127760 177700 178340 152720 166100 153740 179090 FALSE TRUE 188810.9536 173778.5175 181665.9246 134353.7089 183415.8819 181946.157 154589.033 162669.977 136288.0797 166960.0748 1.130874874 1.040838762 1.088080038 0.804705611 1.09856133 1.089758478 0.925904191 0.974304648 0.816291439 1 17.34914363 2.221247883 24.89117197 0.932015285 1.035938318 0.248530768 0.095855211 368.9036594 530383.2301 0.035894733 0.026574244 166.4362349 -2.221247883 0.103923033 SFS(ph)ADNFIGIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFSADNFIGIQR 12 0 Q8N7R7-3;Q8N7R7;Q8N7R7-2 Q8N7R7-3 CCNYL1 Cyclin-Y-like protein 1 1 SFS(1)ADNFIGIQR;SFS(1)ADNFIGIQR 247.93 1.14E-16 157498000 123417 216092 121487 241910 151438 138517 233590 275260 219711 159665 TRUE FALSE 118593.7272 209929.2677 143442.4034 254395.0041 156309.1408 141317.9086 236448.7443 269575.7848 194770.3284 148850.7473 0.796729135 1.410333986 0.963665994 1.70906098 1.050106523 0.949393343 1.588495513 1.811047574 1.308494125 1 17.18350694 2.221308138 24.96135781 1.531855693 1.171410773 0.122832347 0.317430301 351.8856109 509114.5095 0.1148961 0.085058608 166.4593284 -2.221308138 -0.36044492 DRVTDALNATR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRVTDALNATR 11 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 132.06 0.00017365 1474470000 1448410 1686990 1327060 1737080 1401700 1470420 1672290 1791920 1747080 1626480 FALSE TRUE 1391804.536 1638878.697 1566889.262 1826730.907 1446786.953 1500152.9 1692755.985 1754916.226 1548758.803 1516317.061 0.917884901 1.080828502 1.033351997 1.204715659 0.954145403 0.989339854 1.116360179 1.157354402 1.021395091 1 20.53214002 2.221360376 24.97632181 1.095492512 1.036992741 0.032331933 0.085005043 603.5277506 876371.9208 0.031800268 0.023544665 166.4793516 -2.221360376 -0.058499771 LLLPGELAK ddPTM_BT-474_Pertuzumab_2h_R1 3 LLLPGELAK 9 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;A0A2R8Y619;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 0 ;; 128.69 0.00095471 3231527000 5164559 5421349 3791549 5335571 4465580 4525500 5447618 5734350 5650206 5673067 FALSE TRUE 4962722.325 5266737.435 4476766.247 5610940.459 4609219.436 4617008.711 5514287.579 5615933.669 5008818.302 5288825.119 0.938341165 0.995823707 0.846457606 1.060904895 0.871501578 0.872974358 1.042629971 1.061849001 0.947056896 1 22.33451584 2.22139301 24.99762489 1.023610383 0.933304435 0.264136484 0.065923764 298.714937 434954.0059 0.024067461 0.017817732 166.4918617 -2.22139301 -0.090305949 MKQEPVKPEEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 MKQEPVKPEEGR 12 2 P61586 P61586 RHOA Transforming protein RhoA 0 101.53 0.0014723 469860000 260170 290100 192820 234650 198670 192270 303990 312090 327180 274250 FALSE TRUE 250002.2688 281826.632 227666.8633 246760.3146 205060.401 196157.8311 307710.3206 305645.2324 290039.8981 255674.8032 0.977813479 1.102285515 0.890454829 0.965133488 0.802036018 0.767216122 1.203522274 1.195445263 1.134409392 1 17.96395046 2.221421479 24.99995639 1.156464703 0.921578539 0.509488903 0.102714605 194.4392963 283616.5466 0.040626382 0.030078004 166.5027761 -2.221421479 -0.234886164 ETFS(ph)SAEGTVDKDTTIMELR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETFSSAEGTVDKDTTIMELR 20 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 ETFS(0.801)S(0.199)AEGTVDKDTTIMELR;ETFS(0.891)S(0.109)AEGTVDKDTTIMELR 204.53 5.78E-22 381940000 433670 390030 404550 308460 483770 514910 294000 378550 436220 362430 TRUE FALSE 416721.697 378906.7263 477661.1842 324379.6576 499330.9014 525321.833 297598.0599 370732.8102 386702.1344 337882.2933 1.233333931 1.121416345 1.41369108 0.960037457 1.477825004 1.554748039 0.880774358 1.097224737 1.144487717 1 18.36616122 2.221445522 24.99993835 1.039350725 1.284369414 0.352867393 0.17398325 301.8006765 440836.1269 0.065834428 0.048740933 166.5119944 -2.221445522 0.245018689 LQRPPS(ph)VDSIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQRPPSVDSIIR 12 1 Q1MSJ5-1;Q1MSJ5;Q1MSJ5-2 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 LQRPPS(1)VDSIIR 178.03 1.36E-05 253100000 101420 110800 90729 121680 113220 118390 96261 103430 95973 116820 TRUE FALSE 97456.39427 107640.0925 107125.7486 127959.9194 116861.8241 120783.9269 97439.07091 101294.1344 85078.54739 108907.6773 0.894853298 0.988360923 0.983638171 1.174939384 1.073035685 1.109048782 0.894694234 0.93009177 0.781198805 1 16.73274613 2.221487299 24.81719642 0.89932358 1.0405274 0.367499992 0.087209259 245.9434033 357492.4645 0.03368018 0.024936517 166.5280124 -2.221487299 0.141203821 GWEVVESDLYAMNFNPIISR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWEVVESDLYAMNFNPIISR 20 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 184.31 9.43E-17 43020000 95795 93793 77837 81482 83503 87838 104640 115910 117120 107230 FALSE TRUE 92051.22549 91118.11547 91903.87737 85687.29578 86188.94983 89614.14454 105920.6156 113516.418 103825.0286 99967.21659 0.920814129 0.911479969 0.919340165 0.857153962 0.862172148 0.896435327 1.059553514 1.135536448 1.038590772 1 16.60916743 2.221503314 5.294228448 1.078325923 0.892631388 0.806902909 0.038866755 0.066419068 5.270632958 0.014689063 0.011196332 166.5341535 -2.221503314 -0.185694535 NAGSS(ph)SDGTEDSDFSTDLEHTDSSESDGTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NAGSSSDGTEDSDFSTDLEHTDSSESDGTSR 31 0 O95251-4;O95251;O95251-2;O95251-3;O95251-5 O95251-4 KAT7 Histone acetyltransferase KAT7 1 NAGS(0.138)S(0.806)S(0.056)DGT(0.001)EDSDFSTDLEHTDSSESDGTSR;NAGS(0.12)S(0.683)S(0.196)DGT(0.001)EDSDFSTDLEHTDSSESDGTSR 214.53 6.00E-35 570750000 115224 120853 98592 115060 106257 124141 96262 101788 113668 106492 TRUE FALSE 110720.9187 117406.3908 116409.7676 120998.2604 109674.8529 126651.2161 97440.08315 99686.04223 100764.8852 99279.20199 1.115247871 1.182587978 1.172549388 1.218767455 1.104711266 1.275707435 0.981475286 1.00409794 1.014964697 1 16.5992039 2.221504841 24.99971867 1.00018539 1.176696833 0.782464818 0.046007295 101.2364603 148387.7243 0.015910587 0.011780048 166.5347392 -2.221504841 0.176511443 ELS(ph)PEGPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSPEGPGK 9 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 ELS(1)PEGPGK 120.06 0.0016925 0 178030 175550 173780 253880 171550 185840 280920 348080 269400 255990 TRUE FALSE 171072.3908 170543.4859 205185.9117 266982.7772 177068.0615 189597.8121 284357.983 340892.0264 238818.8414 238651.5693 0.716829105 0.714612883 0.859771894 1.118713688 0.74195222 0.794454496 1.191519435 1.428408903 1.000700905 1 17.8645463 2.221584123 8.746701909 1.21708099 0.830534513 0.488547901 0.160821444 0.143694442 60.49880792 0.061072816 0.046287736 166.5651435 -2.221584123 -0.386546477 RLS(ph)DCESTDVKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSDCESTDVKR 12 2 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 RLS(0.88)DCES(0.086)T(0.034)DVKR;RLS(0.999)DCES(0.001)TDVKR 136.63 5.56E-05 912680000 680480 760160 572010 652570 831550 767290 615520 646930 683010 657330 TRUE FALSE 653886.0893 738480.9811 675384.9313 686249.2159 858297.5609 782805.1295 623052.9179 633570.6694 605477.5682 612808.4536 1.067031771 1.205076361 1.102114253 1.119842933 1.400596803 1.277405892 1.016717237 1.033880433 0.988037232 1 19.22507667 2.22171011 24.84891992 1.014925945 1.197447009 0.504470325 0.090082523 207.5992718 306138.1369 0.036250318 0.02684301 166.6134701 -2.22171011 0.182521064 LSS(ph)TSS(ph)EETQLFHIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.1)S(0.715)T(0.2)S(0.246)S(0.739)EETQLFHIPR;LS(0.193)S(0.794)T(0.142)S(0.341)S(0.529)EETQLFHIPR 127.59 3.46E-05 51906000 50570 95824 49606 121857 56964 64865 95365 113937 83200 63400 TRUE FALSE 48593.66849 93091.19334 58570.90768 128146.0544 58796.29879 66176.61474 96532.1054 111584.1611 73755.4848 59105.86153 0.822146353 1.574990888 0.990949225 2.168076923 0.994762571 1.11962863 1.633206976 1.887869633 1.247853984 1 15.85101359 2.221747227 24.92112058 1.560219269 1.30638376 0.002225309 0.4248217 654.9969339 970842.4347 0.153927759 0.113985623 166.6277104 -2.221747227 -0.253835509 ISKPGAVST(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISKPGAVSTPVK 12 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ISKPGAVS(0.193)T(0.807)PVK 92.773 0.012201 1026900000 799210 668190 820840 721920 656510 767820 966100 1034200 1048800 1219000 TRUE FALSE 767975.9896 649133.8754 969184.0475 759178.3777 677627.2404 783345.8465 977923.4208 1012843.409 929744.6209 1136436.044 0.675775811 0.571201414 0.852827621 0.668034406 0.596273978 0.689300423 0.860517779 0.89124541 0.818123136 1 20.11608506 2.221804165 4.219776186 0.887232864 0.673432524 0.632127944 0.081344666 0.139721353 5.702131853 0.030824731 0.023302701 166.6495576 -2.221804165 -0.21380034 SLETEHK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLETEHK 7 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;;; 105.39 0.0079373 1862650000 1644580 2475450 1521970 2635360 1798740 1925640 2318880 2568250 2578380 1984250 FALSE TRUE 1580307.995 2404852.59 1797023.835 2771371.245 1856598.106 1964577.76 2347259.147 2515214.74 2285693.112 1849854.98 0.854287505 1.300022226 0.971440386 1.49815595 1.003645218 1.062017175 1.268888195 1.359682119 1.235606648 1 20.81898074 2.221845978 24.61993039 1.259012931 1.129180417 0.04195004 0.190765632 488.3524301 719316.2375 0.067588562 0.050062422 166.6656031 -2.221845978 -0.129832514 TVS(ph)SDGCSTPSREEGGCSLASTPATTLHLLQLSGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQR 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.139)VS(0.43)S(0.396)DGCS(0.012)T(0.013)PS(0.004)REEGGCS(0.004)LAS(0.001)T(0.001)PATTLHLLQLSGQR 64.665 0.0039475 876330000 15751 18536 10695 11689 11949 13434 16859 18298 17813 19391 TRUE FALSE 15135.43351 18007.37143 12627.82441 12292.27069 12333.35044 13705.64468 17065.32549 17920.13991 15790.94292 18077.6303 0.837246545 0.996113491 0.698533171 0.679971351 0.682243758 0.758154938 0.94400235 0.991288106 0.873507349 1 14.14191795 2.221892585 8.365849839 0.955895555 0.773279796 0.46379906 0.093097874 0.172240269 65.41417488 0.037838649 0.028724872 166.6834901 -2.221892585 -0.182615759 EESEKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESEKPR 7 1 P83916;J3KS05;K7ELA4 P83916 CBX1 Chromobox protein homolog 1 0 ; 124.34 0.00379 1198520000 1776340 1809730 1306570 2086800 1456410 1482550 2018960 1987030 1999390 2220500 FALSE TRUE 1706918.669 1758118.272 1542696.263 2194499.998 1503256.75 1512528.177 2043668.636 1945997.136 1772427.629 2070103.557 0.82455714 0.849290011 0.745226613 1.060091893 0.726174662 0.730653388 0.987230146 0.940048206 0.856202398 1 20.98127151 2.221993296 24.99443936 0.942441279 0.826761996 0.279092336 0.096809022 347.8417658 524771.3221 0.03600136 0.026663128 166.7221477 -2.221993296 -0.115679283 VTRS(ph)PPTQVAISSDSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTRSPPTQVAISSDSAR 17 1 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 VT(0.126)RS(0.765)PPT(0.109)QVAISSDSAR;VT(0.126)RS(0.874)PPT(0.001)QVAISSDSAR 125.73 2.78E-05 316860000 150805 161584 122654 121781 148658 154294 124686 131038 152597 125169 TRUE FALSE 144911.3739 156975.7825 144820.3062 128066.132 153439.7196 157413.9304 126211.9446 128332.0195 135274.8283 116691.1921 1.241836434 1.345223917 1.241056018 1.097478993 1.314921176 1.34897868 1.081589298 1.099757549 1.159254832 1 16.83233614 2.221998223 24.99792498 1.093713767 1.262143897 0.569122435 0.076459851 195.6523545 295299.8378 0.029453774 0.021812402 166.724039 -2.221998223 0.16843013 LKEVFSMAGVVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEVFSMAGVVVR 13 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 130.98 0.00012381 248060000 160590 161420 118920 140650 146500 137020 158150 153660 178400 154340 FALSE TRUE 154313.9653 156816.4596 140411.4894 147908.9634 151212.3055 139790.6383 160085.487 150486.8673 158148.7799 143886.4143 1.072470712 1.089862864 0.975849527 1.02795642 1.050914405 0.971534658 1.112582364 1.045872663 1.099122392 1 17.13457085 2.22199896 24.99969993 1.067407479 1.032288569 0.112623966 0.044972914 521.664216 787443.8046 0.016376629 0.012131029 166.724322 -2.22199896 -0.03511891 GAGTNEDALIEILTTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAGTNEDALIEILTTR 16 0 P12429;D6RA82;D6RFG5;D6RCA8 P12429 ANXA3 Annexin A3;Annexin 0 ; 191.06 1.76E-09 63142000 103775 107889 79406 91104 108024 102514 93731 95453 105517 108271 FALSE TRUE 99719.35827 104812.1114 93756.43058 95805.88836 111498.6901 104586.9033 94878.10802 93481.86219 93539.15252 100937.7087 0.98792968 1.038384095 0.928854357 0.949158541 1.104628701 1.036152937 0.939966928 0.926134181 0.926701762 1 16.62310572 2.222015558 24.14849948 0.94026621 1.007106842 0.24580949 0.050133424 221.2725323 322957.2325 0.019717175 0.014606137 166.7306942 -2.222015558 0.066840632 VPTANVSVVDLTCR ddPTM_BT-474_Pertuzumab_2h_R1 4 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 227.06 5.05E-12 2006610000 371701 426210 301023 367247 362033 415844 311895 346671 378106 360208 FALSE TRUE 357174.514 414054.9081 355424.5523 386200.6617 373678.1202 424252.6506 315712.0643 339512.1227 335184.992 335810.7913 1.063618333 1.233000603 1.058407179 1.150054351 1.112763883 1.263368127 0.940148657 1.011022074 0.998136453 1 18.35728907 2.222048995 24.99990451 0.988967915 1.145357447 0.604155667 0.063252992 158.2746055 239638.8584 0.022116577 0.016380463 166.7435315 -2.222048995 0.156389532 TTQLIEMLHADMNVPFPEGFVIANDVDNKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTQLIEMLHADMNVPFPEGFVIANDVDNKR 30 1 Q08J23;Q08J23-2 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 208.82 5.62E-26 409720000 269600 275370 232400 241870 237920 270990 292130 315020 343930 343360 FALSE TRUE 259063.7339 267516.7172 274399.8497 254352.9397 245572.9129 276469.6035 295705.1743 308514.7269 304888.5083 320103.9214 0.809311341 0.835718338 0.857221144 0.794594888 0.767166212 0.863687025 0.923778669 0.963795525 0.952467271 1 18.28818082 2.222073938 2.142464532 0.966410759 0.815407315 0.878326459 0.026162216 0.109248649 1.013937428 0.013099823 0.008634314 166.7531084 -2.222073938 -0.151003444 EQTLSPTIT(ph)SGLHNIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQT(0.002)LS(0.037)PT(0.309)IT(0.583)S(0.069)GLHNIAR 209.24 1.64E-11 5689500000 499050 626870 466870 613900 569140 604980 508000 550970 543720 548200 TRUE FALSE 479546.5743 608992.2814 551243.7945 645583.4526 587446.905 617213.1101 514217.056 539592.277 481999.1851 511069.9257 0.938318907 1.191602657 1.078607382 1.263199848 1.149445263 1.207688183 1.006157925 1.055809097 0.94311788 1 18.96316117 2.222123057 24.99179443 1.011275408 1.144065537 0.37496943 0.085981407 261.8612448 398133.4187 0.031148709 0.023069774 166.7719694 -2.222123057 0.132790128 RWQS(ph)PVTK ddPTM_BT-474_Pertuzumab_2h_R1 6 RWQSPVTK 8 1 A9Z1X7 A9Z1X7 SRRM1 1 RWQS(0.999)PVT(0.001)K;RWQS(0.997)PVT(0.003)K;RWQS(0.996)PVT(0.004)K;RWQS(0.999)PVT(0.001)K;RWQS(0.957)PVT(0.043)K;RWQS(1)PVTK 94.767 0.0062022 4590280000 5837670 5552220 4672250 4955330 5378030 5036600 5833590 5982070 6329280 6301580 TRUE FALSE 5609527.403 5393876.122 5516629.509 5211075.175 5551019.219 5138443.503 5904983.219 5858538.164 5610806.669 5874768.374 0.954850821 0.918142772 0.93903779 0.887026491 0.944891588 0.874663166 1.005143155 0.997237302 0.955068577 1 22.48610054 2.222129098 24.99719307 0.990572296 0.920224383 0.625680626 0.026362472 147.9906548 225136.0505 0.0093287 0.00690968 166.7742893 -2.222129098 -0.070347913 KFVEEQHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFVEEQHTK 9 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 108.67 0.001671 1086450000 1594590 1762660 1423460 1457730 1539450 1435220 1801890 1773590 1965970 1974780 FALSE TRUE 1532271.66 1712390.663 1680710.887 1532963.62 1588967.807 1464241.132 1823942.069 1736964.747 1742801.328 1841026.392 0.832292066 0.930128254 0.912920583 0.832667922 0.863088011 0.795339566 0.990720218 0.943476288 0.946646575 1 20.81207888 2.222182356 24.99988757 0.964041449 0.865368808 0.635321302 0.040321179 176.3188519 269132.5379 0.015528167 0.011502265 166.7947422 -2.222182356 -0.098672641 RIFQEPTEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RIFQEPTEPK 10 1 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 0 86.313 0.021876 423960000 557410 513550 449260 433710 491950 450180 562750 570170 615620 583820 FALSE TRUE 535625.801 498904.0568 530451.2757 456093.8251 507774.0185 459282.948 569637.1028 558395.7903 545737.3985 544277.3514 0.984104519 0.916635711 0.974597371 0.837980533 0.932932479 0.843839904 1.046593435 1.025939788 1.002682542 1 19.05398248 2.222203278 24.99997391 1.022413841 0.915109886 0.549691572 0.04597407 174.4090012 266558.8327 0.016742214 0.012401257 166.8027775 -2.222203278 -0.107303956 KT(ph)SPASLDFPESQK ddPTM_BT-474_Pertuzumab_2h_R1 4 KTSPASLDFPESQK 14 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KT(0.5)S(0.5)PASLDFPESQK;KT(0.5)S(0.5)PASLDFPESQK;KT(0.553)S(0.447)PASLDFPESQK;KT(0.5)S(0.5)PASLDFPESQK 133.16 2.71E-05 8270000000 4698160 4272980 4033650 3825710 4378810 4313680 5014700 5329600 5705030 5508410 TRUE FALSE 4514550.713 4151118.794 4762620.283 4023155.352 4519658.4 4400905.565 5076071.399 5219541.898 5057418.912 5135320.484 0.879117618 0.808346588 0.927424159 0.783428291 0.880112237 0.85698752 0.988462437 1.01640042 0.984830241 1 22.29202288 2.222213289 4.941003563 1.002072106 0.854133111 0.770878574 0.037820289 0.077930101 4.987980816 0.013132946 0.010003323 166.8066224 -2.222213289 -0.147938994 QFYINVER ddPTM_BT-474_Pertuzumab_2h_R1 1 QFYINVER 8 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;Q14240;Q14240-2;E7EQG2;J3KTN0 P60842;Q14240;J3KTN0 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 108.74 0.0087288 615150000 668900 660740 566400 673640 595570 655540 589100 656720 575910 729720 FALSE TRUE 642758.6485 641896.3421 668761.0795 708406.6411 614727.0499 668795.4679 596309.582 643158.5025 510535.1112 680295.4144 0.944822844 0.943555297 0.983045109 1.041322088 0.903617806 0.983095658 0.876545056 0.94541061 0.750460903 1 19.37580184 2.222220865 1.567787642 0.888296998 0.969514142 0.189993202 0.069035406 0.619070744 2.993988206 0.03687385 0.021936257 166.8095326 -2.222220865 0.081217143 DGTGWASK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGTGWASK 8 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-3;P48634;P48634-2;P48634-3;P48634-4 E7EPN9;P48634 PRRC2C;PRRC2A Protein PRRC2C;Protein PRRC2A 0 87.308 0.035865 97732000 94369 99819 86388 97373 84885 89135 103610 107460 111530 114940 FALSE TRUE 90680.95515 96972.25985 102000.2333 102398.4322 87615.40312 90937.37077 104878.0102 105240.9134 98869.58197 107155.0114 0.846259582 0.904971765 0.951894195 0.955610296 0.817651008 0.848652523 0.978750399 0.982137112 0.922678097 1 16.7093398 2.222305758 24.95778203 0.971101083 0.891147516 0.44611576 0.045408647 251.0161192 385408.6774 0.01825448 0.013521652 166.8421425 -2.222305758 -0.079953567 SVTDSIRDEYAFLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVTDSIRDEYAFLQK 15 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;F8VZ52;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 203.27 5.01E-09 71906000 68299 70456 54699 70921 67434 58762 80323 78325 92197 79010 FALSE TRUE 65629.79957 68446.66386 64584.32607 74581.24131 69603.07585 59950.2079 81306.0169 76707.56138 81731.18308 73658.58233 0.891000037 0.929242211 0.876806531 1.012526157 0.944941834 0.813893046 1.103822723 1.041393399 1.109594843 1 16.16856601 2.22237765 24.99528655 1.065702007 0.916761178 0.639689599 0.055901875 153.3482607 236851.4526 0.020434435 0.015137917 166.8697633 -2.22237765 -0.148940829 TLS(ph)QELVNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLSQELVNLR 10 0 Q9ULD2;Q9ULD2-2;Q9ULD2-4;Q9ULD2-7;Q9ULD2-3;Q9ULD2-6;A0A0U1RQI2 Q9ULD2 MTUS1 Microtubule-associated tumor suppressor 1 1 T(0.004)LS(0.996)QELVNLR;T(0.017)LS(0.983)QELVNLR 86.288 0.014329 26788000 24504.8 40035 21214.2 49440 27782 27687 44048 52868 41352 35839 TRUE FALSE 23547.12532 38893.241 25048.07785 51991.60432 28675.63326 28246.85011 44587.0726 51776.25732 36657.89432 33411.59261 0.704759142 1.164064265 0.749682248 1.556094764 0.858254008 0.845420643 1.334479117 1.549649486 1.097160939 1 15.02806113 2.222403472 24.78531152 1.320373837 0.998314575 0.16453284 0.271073384 308.7628545 473643.6902 0.098429199 0.072924348 166.8796851 -2.222403472 -0.322059262 DALSDLALHFLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DALSDLALHFLNK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 253.54 8.74E-24 5986000000 6072700 5548300 5086800 5058000 5352700 4826100 6414600 6053000 6865600 7117900 FALSE TRUE 5835372.17 5390067.916 6006097.915 5319043.986 5524874.457 4923687.049 6493103.794 5928003.435 6086245.871 6635798.293 0.879377569 0.812271211 0.905105558 0.801568063 0.832586256 0.741988655 0.978496257 0.893336894 0.917183676 1 22.6618386 2.222576408 24.9999998 0.934974348 0.830464667 0.567991044 0.050134785 194.8381508 304733.4079 0.018233105 0.013508741 166.9461498 -2.222576408 -0.104509681 EIYDDSFIRPVTFWIVGDFDSPSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIYDDSFIRPVTFWIVGDFDSPSGR 25 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 232.69 1.81E-35 263160000 200227 265970 176876 227462 236880 244330 198155 211336 238110 207968 FALSE TRUE 192401.9075 258384.796 208841.4278 239201.3411 244499.4603 249270.52 200580.0802 206971.8377 211080.751 193882.1421 0.992365286 1.332690021 1.077156594 1.233746123 1.261072617 1.285680658 1.034546441 1.067513673 1.088706514 1 17.5648204 2.222605217 24.99961821 1.054168337 1.202399969 0.364546861 0.096346739 255.269753 399965.2779 0.03397941 0.025174554 166.9572247 -2.222605217 0.148231632 GRLGS(ph)VDSFER ddPTM_BT-474_Pertuzumab_2h_R1 2 GRLGSVDSFER 11 1 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 GRLGS(1)VDSFER;GRLGS(1)VDSFER 192.68 7.78E-07 1120970000 660520 784830 534400 632030 609100 736360 514730 579750 555830 559480 TRUE FALSE 634706.1482 762447.4168 630977.9677 664649.144 628692.2547 751249.7037 521029.4197 567777.9599 492734.5086 521585.9213 1.216877454 1.461786804 1.209729676 1.274285054 1.205347439 1.440318216 0.998933059 1.088560747 0.944685216 1 18.9925454 2.222755111 24.99990533 1.02267173 1.298917405 0.714743028 0.090591714 130.616188 206597.0557 0.032380755 0.023993936 167.0148588 -2.222755111 0.276245675 KGS(ph)VSHDTVQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGSVSHDTVQPR 12 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;F2Z3L2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 KGS(0.983)VS(0.017)HDTVQPR;KGS(0.5)VS(0.5)HDTVQPR 185.14 8.22E-06 278200000 208370 221410 186386 220060 240760 235010 193345 201100 221210 210720 TRUE FALSE 200226.67 215095.6036 220070.0963 231417.323 248504.2641 239762.0632 195711.2139 196947.2147 196099.1682 196447.7467 1.019236277 1.094925278 1.120247496 1.178009556 1.264989129 1.220487724 0.996250745 1.002542498 0.998225592 1 17.58378609 2.222836042 24.98304813 0.999681237 1.15235717 0.575192841 0.063291855 192.7500919 306237.4768 0.026634485 0.01973808 167.0459851 -2.222836042 0.152675933 EPSAT(ph)PPISNLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 EPSATPPISNLTK 13 0 J3KP58;P30622-2;P30622-1;P30622;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 EPSAT(1)PPISNLTK;EPS(0.005)AT(0.995)PPIS(0.001)NLTK 113.65 0.0089969 286560000 776370 756760 761320 789470 762950 864370 954280 993450 1026050 1226350 TRUE FALSE 746028.6021 735177.9457 898907.4595 830214.6413 787490.9796 881848.1536 965958.7641 972934.9103 909577.1056 1143288.222 0.652528897 0.643038152 0.786247459 0.726163906 0.688794798 0.771326194 0.844895229 0.850997055 0.795579879 1 20.12475772 2.222950921 0.054188069 1.584185418 1.19E-13 0.827749716 0.042339143 20.73384044 0.689063016 9.063566138 10.69025436 167.0901777 -2.222950921 -1.584185418 GQECVEECR ddPTM_BT-474_Pertuzumab_2h_R1 3 GQECVEECR 9 0 P04626-5;P04626-4;P04626;B4DTR1;J3QLU9;P04626-6;F5H1T4 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ;; 125.71 0.0011489 261580000 401040 654030 345690 724460 399660 421430 628600 683280 527450 425420 FALSE TRUE 385366.9134 635377.7048 408163.8728 761849.4674 412515.4269 429951.6033 636292.9948 669170.0292 467576.0873 396605.9245 0.971662019 1.602037856 1.029142148 1.920923063 1.040114132 1.084077612 1.604345663 1.687241637 1.178943779 1 18.5973467 2.222966841 24.89963627 1.45941922 1.297094835 0 0.336736079 795.5533372 1270305.369 0.121455247 0.090020783 167.0963028 -2.222966841 -0.162324385 LWDWDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LWDWDKK 7 1 P35606;P35606-2;D6RBT6 P35606 COPB2 Coatomer subunit beta 0 ; 119.29 0.0077202 1704520000 2553800 2661800 2350840 1955060 2811700 2121650 3234100 3175200 3696500 3748700 FALSE TRUE 2453994.673 2585888.07 2775689.082 2055960.881 2902140.884 2164551.217 3273679.883 3109631.01 3276888.817 3494797.21 0.702185141 0.73992507 0.794234662 0.588291897 0.830417535 0.619363896 0.936729569 0.889788684 0.937647772 1 21.73677731 2.222976581 24.99998365 0.927523972 0.717096539 0.703388622 0.072485671 132.7221227 212912.1249 0.025095911 0.018598777 167.1000506 -2.222976581 -0.210427433 YESLTDPSKLDSGK ddPTM_BT-474_Pertuzumab_2h_R1 6 YESLTDPSKLDSGK 14 1 P08238;Q58FF7;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ;;;;; 182.1 1.42E-06 26411290000 28661700 26175400 20663900 18801290 23216400 26327600 25628900 30120200 33971400 28125100 FALSE TRUE 27541569.08 25428903.22 24398326.4 19771626.83 23963176.59 26859962.11 25942554.14 29498207.34 30115109.09 26220161.93 1.050396605 0.969822509 0.930517762 0.754061965 0.913921762 1.024401077 0.989412431 1.12502003 1.148547792 1 24.64417326 2.222989122 1.662402217 1.097666177 0.921451486 0.405972724 0.082181659 0.35953688 1.966127438 0.04716609 0.028597558 167.1048757 -2.222989122 -0.176214691 VSS(ph)PPNAMMSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSSPPNAMMSSR 12 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 VS(0.007)S(0.993)PPNAMMSSR;VS(0.019)S(0.981)PPNAMMSSR 162.1 6.67E-05 810820000 1095480 1154890 1031670 1056810 999870 1023610 1175290 1176750 1292670 1201200 TRUE FALSE 1052667.43 1121953.668 1218115.718 1111352.091 1032031.727 1044308.096 1189673.551 1152449.701 1145931.521 1119841.654 0.940014534 1.001885993 1.087757107 0.992418961 0.921587193 0.932549787 1.062358724 1.029118445 1.023297818 1 20.09486332 2.223064223 24.9949849 1.032021451 0.983285897 0.208661535 0.046505018 433.0927764 698554.6341 0.019079878 0.014139263 167.1337752 -2.223064223 -0.048735554 SKS(ph)LENFFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKSLENFFLR 10 1 Q6ZMT1;J3QKZ0 Q6ZMT1 STAC2 SH3 and cysteine-rich domain-containing protein 2 1 S(0.001)KS(0.999)LENFFLR;S(0.487)KS(0.513)LENFFLR;S(0.041)KS(0.959)LENFFLR;S(0.066)KS(0.934)LENFFLR 194.55 2.73E-07 1098130000 1739530 1407140 933230 1294810 1591700 1164830 1763460 1809273 1970770 1627660 TRUE FALSE 1671547.244 1367009.745 1101885.421 1361635.299 1642898.476 1188383.661 1785041.751 1771910.88 1747056.452 1517417.138 1.101573985 0.900879337 0.726158544 0.897337499 1.08269403 0.783162145 1.176368518 1.167715083 1.151335653 1 20.53318631 2.223132836 24.99691238 1.142409325 0.912840268 0.426131252 0.117760082 212.7034902 344631.2981 0.043984345 0.032601746 167.1601821 -2.223132836 -0.229569057 VVLIGGKPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVLIGGKPDR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 137.46 8.26E-05 22763000000 15181300 14426800 12787600 14323000 13790800 14288500 14577900 15510500 15892600 15707000 FALSE TRUE 14587998.01 14015361.79 15098603.78 15062211.75 14234393.61 14577423.26 14756308.7 15190202.75 14088538.68 14643150.9 0.996233537 0.957127457 1.031103475 1.028618215 0.972085428 0.995511373 1.007727695 1.037358889 0.962124803 1 23.80372269 2.223188294 10.65051208 1.008500809 0.996861523 0 0.027262136 1.409973494 934.9769671 0.010327934 0.007807094 167.1815295 -2.223188294 -0.011639285 DITDPLSLNTCTDEGHVVLAS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 7 DITDPLSLNTCTDEGHVVLASPLK 24 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK 278.03 2.67E-52 15907779000 4266790 3696021 2937814 3085570 3458685 3219219 3891184 3831946 4090609 4304229 TRUE FALSE 4100039.13 3590614.1 3468742.341 3244816.637 3569936.744 3284313.814 3938805.474 3752814.976 3626260.216 4012699.736 1.021765744 0.894812554 0.864441042 0.808636791 0.889659576 0.818479834 0.981584901 0.935234436 0.903695879 1 21.93614177 2.223275289 24.99918408 0.949316012 0.879588016 0.257583764 0.059527386 359.0888042 587286.7538 0.022567723 0.016729923 167.2150215 -2.223275289 -0.069727996 VEPAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEPAHK 6 0 Q93084-4;Q93084-2;Q93084-3;Q93084-7;Q93084;Q93084-6;Q93084-5 Q93084-4 ATP2A3 Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 0 74.597 0.079907 72670000 145390 229250 111690 242830 138560 154250 216480 257840 195010 173190 FALSE TRUE 139707.9981 222712.0145 131874.8675 255362.4854 143016.9082 157369.0407 219129.347 252515.5139 172873.2823 161459.687 0.865280991 1.379366073 0.816766525 1.581586649 0.885774715 0.974664596 1.357176835 1.563953941 1.070690062 1 17.30081447 2.223362896 24.83940688 1.325995475 1.09880966 0.050212149 0.271240826 437.41028 714905.6789 0.096724302 0.071711398 167.2487559 -2.223362896 -0.227185815 KFHTVSGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFHTVSGSK 9 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 125.48 0.00032484 7036100000 16050200 15583000 12310100 13055400 13961300 13657000 15283600 15089100 16745600 17240500 FALSE TRUE 15422940.44 15138588.1 14534808.91 13729190.76 14410377.89 13933153.9 15470645.27 14777504.81 14844709.69 16072785.58 0.959568605 0.941877064 0.904311753 0.854188634 0.896570033 0.866878602 0.962536655 0.919411557 0.923592841 1 23.93811665 2.223402813 24.99977677 0.942601453 0.903051428 0.281221439 0.036100379 397.4142183 655451.4195 0.014148061 0.010488632 167.264129 -2.223402813 -0.039550025 AGTQIENIDEDFRDGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGTQIENIDEDFRDGLK 17 1 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ; 277.98 7.51E-36 3247900000 1585450 1600610 1415450 1529380 1343490 1273640 1934360 1992240 1929000 2062870 FALSE TRUE 1523488.861 1554962.17 1671253.302 1608311.485 1386704.576 1299393.873 1958033.276 1951099.548 1710028.007 1923149.977 0.792184114 0.808549613 0.869018704 0.836290203 0.721058988 0.675659147 1.018138626 1.014533224 0.889180785 1 20.87503985 2.223472527 24.99925098 0.986497211 0.788327259 0.709520216 0.061558556 138.6952599 229800.8051 0.024851854 0.018425243 167.2909805 -2.223472527 -0.198169952 KFLDGIYVSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFLDGIYVSEK 11 1 A0A2R8Y5Y7;P32969;D6RAN4;H0Y9R4;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 178.15 1.23E-05 4061100000 10023500 10142600 8869700 8495700 9448500 8905100 10817400 11276700 11835500 11859400 FALSE TRUE 9631770.538 9853342.979 10472652.1 8934164.095 9752419.583 9085167.223 10949786.58 11043832.2 10491983.66 11056152.27 0.871168405 0.891209051 0.947223938 0.80807173 0.882080795 0.821729567 0.990379501 0.998885682 0.948972427 1 23.39834606 2.22347417 24.99575492 0.986222667 0.872410728 0.683432313 0.038090114 138.3282259 229185.5819 0.014228561 0.010549434 167.2916135 -2.22347417 -0.113811939 DFQQALYELSYHVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFQQALYELSYHVIK 15 0 Q8NI27;F2Z2V2 Q8NI27 THOC2 THO complex subunit 2 0 125.45 9.04E-05 131460000 200970 211190 182740 172980 187860 177450 225050 233720 239410 242970 FALSE TRUE 193115.8702 205167.068 215765.183 181907.5185 193902.6875 181038.1606 227804.2292 228893.6003 212233.1805 226513.4255 0.852558164 0.905761182 0.952549204 0.803076101 0.856031765 0.799238103 1.005698575 1.010507875 0.936956298 1 17.78923704 2.223522755 24.99876582 0.992043409 0.864775536 0.643062317 0.046192041 156.5569852 260256.8034 0.018023153 0.013363045 167.3103296 -2.223522755 -0.127267873 DDETMYVESK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDETMYVESK 10 0 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ; 185.81 3.28E-06 494840000 416160 384740 357730 368270 399500 396770 452690 478170 545080 478350 FALSE TRUE 399896.0071 373767.5919 422379.7687 387276.4588 412350.2803 404792.9612 458230.1556 468295.6224 483204.8036 445950.9284 0.896726482 0.838136145 0.94714405 0.868428417 0.924653934 0.907707408 1.027534929 1.050105724 1.083538059 1 18.76652544 2.223546045 3.149435722 1.048973507 0.894456981 0.815432318 0.033448269 0.093681784 1.930583863 0.012955848 0.009470579 167.3193024 -2.223546045 -0.154516526 FDSSLDRK ddPTM_BT-474_Pertuzumab_2h_R1 6 FDSSLDRK 8 1 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;;;; 162.59 0.00054654 12140880000 8288350 8170570 7243370 7274850 7572490 7307660 9068760 9536240 10390970 9876810 FALSE TRUE 7964432.119 7937553.343 8552408.087 7650305.88 7816066.018 7455425.892 9179746.198 9339313.312 9211430.648 9207844.861 0.864961589 0.862042472 0.92881757 0.830846522 0.848848578 0.809681962 0.9969484 1.014277874 1.000389427 1 23.1344321 2.223563907 24.2749944 1.004929804 0.859370522 0.857090284 0.029069887 60.74406809 98324.78125 0.011277497 0.00836547 167.326184 -2.223563907 -0.145559282 EQFWEQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQFWEQAK 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 113.62 0.0065447 392610000 278810 262510 246350 209970 227400 172660 329910 265210 295140 322110 FALSE TRUE 267913.797 255023.4718 290870.925 220806.5769 234714.5275 176151.3035 333947.5373 259733.3208 261636.9445 300293.2028 0.89217403 0.849248233 0.968623073 0.73530328 0.78161785 0.586597705 1.112071583 0.864932401 0.871271618 1 18.19601229 2.223568372 24.99974283 0.947370881 0.807976531 0.313220451 0.114920904 348.3780427 580920.825 0.043909131 0.032557071 167.3279043 -2.223568372 -0.139394349 TAESQT(ph)PTPSATSFFSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 TAESQTPTPSATSFFSGK 18 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAES(0.002)QT(0.964)PT(0.03)PS(0.003)AT(0.001)SFFSGK;TAESQT(0.992)PT(0.003)PS(0.005)ATSFFSGK;TAESQT(0.99)PT(0.006)PS(0.004)ATSFFSGK 417.28 7.33E-147 1032330000 1060840 1146930 939900 1302590 1609190 1194720 829960 848050 811880 730730 TRUE FALSE 1019381.2 1114220.679 1109760.838 1369816.826 1660951.058 1218878.057 840117.2987 830537.4711 719718.7861 681237.0062 1.496367917 1.635584487 1.629037806 2.010778647 2.438139799 1.789212926 1.233223226 1.219160826 1.056488094 1 19.37779728 2.223596805 4.270113416 1.143996381 1.855313465 0.657481627 0.250404545 0.144037737 6.084453104 0.106480733 0.080683659 167.3388595 -2.223596805 0.711317084 TDEFQLHTNVNDGTEFGGSIYQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TDEFQLHTNVNDGTEFGGSIYQK 23 0 P21796 P21796 VDAC1 Voltage-dependent anion-selective channel protein 1 0 ; 299.4 8.02E-62 215380000 105896 158342 120918 231781 93019 103784 207870 199531 205880 173120 FALSE TRUE 101757.4672 153826.2412 142770.5724 243743.2452 96011.04061 105882.5836 210413.9752 195410.6151 182509.3655 161394.4282 0.630489345 0.953107508 0.884606575 1.510233333 0.594884481 0.656048569 1.303725151 1.21076432 1.130828168 1 17.30023125 2.223619616 24.98804453 1.186766171 0.89231548 0.231803608 0.255085078 363.6164058 608125.5713 0.09746093 0.072268529 167.3476492 -2.223619616 -0.294450691 RPMS(ph)SPEMK ddPTM_BT-474_Pertuzumab_2h_R1 5 RPMSSPEMK 9 1 P51610-2;P51610;A6NEM2;P51610-4;H7C1C4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 RPMS(0.5)S(0.5)PEMK;RPMS(0.5)S(0.5)PEMK;RPMS(0.5)S(0.5)PEMK;RPMS(0.5)S(0.5)PEMK;RPMS(0.5)S(0.5)PEMK 87.719 0.0065673 2278950000 2831140 2625540 2239320 2679280 2794460 2663240 3067200 3409980 3204380 3280790 TRUE FALSE 2720495.919 2550662.17 2644014.937 2817557.962 2884346.344 2717092.538 3104737.311 3339562.721 2840632.216 3058579.171 0.889463953 0.833936945 0.864458557 0.92119831 0.943034717 0.88835122 1.015091367 1.091867346 0.928742418 1 21.54443019 2.223700344 6.111768582 1.025491343 0.889884283 0.598462936 0.046956713 0.10193623 13.52053415 0.018150783 0.013882253 167.3787593 -2.223700344 -0.135607059 KMEESK ddPTM_BT-474_Pertuzumab_2h_R1 1 KMEESK 6 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 86.953 0.084967 513130000 564730 510370 421210 478490 480540 454330 571910 617380 547360 645520 FALSE TRUE 542659.7273 495814.7473 497332.0168 503184.9262 495997.0055 463516.8639 578909.2057 604630.8873 485225.9875 601798.3554 0.90173016 0.823888505 0.826409731 0.836135429 0.824191361 0.770219559 0.961965417 1.004706779 0.806293309 1 19.19892064 2.223769422 24.99908054 0.950831905 0.829924966 0.462859772 0.059309644 197.4396354 333697.0321 0.021635111 0.016043837 167.4053843 -2.223769422 -0.120906939 QSLS(ph)SIDKNPSER ddPTM_BT-474_Pertuzumab_2h_R1 2 QSLSSIDKNPSER 13 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 QS(0.001)LS(0.646)S(0.353)IDKNPSER;QSLS(0.5)S(0.5)IDKNPSER 157.11 2.88E-05 857760000 434950 434160 330560 400910 437050 495110 489880 521760 685630 612220 TRUE FALSE 417951.6731 421778.1819 390299.5453 421601.0131 451108.1102 505121.4634 495875.298 510985.4737 607800.1568 570753.7941 0.732280149 0.738984456 0.683831714 0.738674044 0.790372512 0.885007631 0.868807712 0.895281782 1.064907782 1 19.12250902 2.223791387 0.637103094 1.021073303 0.707983185 0.883780967 0.040483715 0.251371185 0.201218204 0.036885383 0.025594886 167.4138514 -2.223791387 -0.313090118 LPS(ph)GSGAAS(ph)PTGSAVDIR ddPTM_BT-474_Pertuzumab_2h_R1 3 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPS(1)GSGAAS(1)PTGSAVDIR;LPS(0.989)GS(0.011)GAAS(0.973)PT(0.025)GS(0.002)AVDIR;LPS(0.998)GS(0.002)GAAS(0.999)PT(0.001)GSAVDIR 379.78 4.40E-108 1146960000 870610 1061650 922540 1414300 1358760 1195320 778620 852690 723380 759760 TRUE FALSE 836585.5987 1031372.781 1089263.5 1487292.192 1402465.749 1219490.189 788148.9845 835081.6535 641264.9351 708300.7785 1.181116306 1.456122615 1.537854444 2.099803131 1.980042649 1.721712338 1.11273206 1.178992991 0.905356812 1 19.4340026 2.223801268 8.046143121 1.076650315 1.682317883 0.58598323 0.251910116 0.128332653 46.51295132 0.103281111 0.078722225 167.4176603 -2.223801268 0.605667568 EQPLDEELKDAFQNAYLELGGLGER ddPTM_BT-474_Pertuzumab_2h_R1 2 EQPLDEELKDAFQNAYLELGGLGER 25 1 P05023-4;P05023;P05023-3;P05023-2 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ; 197.54 7.36E-25 224710000 95405 171855 67433 195210 81876 80296 195982 238330 164036 89352 FALSE TRUE 91676.46712 166953.8637 79619.64314 205284.8115 84509.6159 81919.64014 198380.4863 233408.4022 145415.321 83300.10945 1.100556383 2.00424543 0.955816789 2.464400261 1.014519866 0.983427761 2.381515314 2.802017953 1.745679831 1 16.34603077 2.223853363 24.99985615 2.213103128 1.454903683 0.11397757 0.646299075 339.1438014 576483.6598 0.23328168 0.173019005 167.4377436 -2.223853363 -0.758199445 IFAPNHVVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IFAPNHVVAK 10 0 Q02543;M0R3D6;M0R1A7;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 127.4 0.00035716 3570200000 7527100 7906900 7243800 7583200 7252700 6734900 8964300 8679600 9266700 9552700 FALSE TRUE 7232932.61 7681402.954 8552915.797 7974569.861 7485989.682 6871084.292 9074007.785 8500363.227 8214783.065 8905687.12 0.812170079 0.862527826 0.960388085 0.895446893 0.8405853 0.771538928 1.018900357 0.954487072 0.922419905 1 23.0862955 2.223860514 24.99999798 0.970220703 0.863041779 0.539131141 0.05270737 215.067412 365756.0808 0.020909472 0.015508354 167.4405008 -2.223860514 -0.107178924 FIDFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 FIDFFK 6 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 132.72 0.034376 496610000 910410 875920 879060 941830 893310 792810 1109850 1097500 1113060 1178860 FALSE TRUE 874830.1707 850939.6192 1037925.697 990437.9592 922044.1274 808841.1614 1123432.676 1074836.241 986710.0951 1099014.762 0.796013121 0.774274967 0.9444147 0.901205328 0.838973378 0.735969333 1.022218004 0.977999822 0.897813323 1 20.06777933 2.22392309 24.99999271 0.97501444 0.837791845 0.546594821 0.063529681 200.6195366 342643.6359 0.02501496 0.018554466 167.4646285 -2.22392309 -0.137222595 ANSALT(ph)PPKPESGLTLQESNTPGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ANSALTPPKPESGLTLQESNTPGLR 25 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 ANS(0.001)ALT(0.999)PPKPESGLTLQESNTPGLR;ANSALT(0.992)PPKPES(0.007)GLTLQESNTPGLR;ANSALT(1)PPKPESGLTLQESNTPGLR;ANS(0.001)ALT(0.999)PPKPESGLTLQESNTPGLR 147.42 3.82E-07 4304830000 1823530 1636030 1435600 1557320 1531880 1554820 1749620 1810900 2047890 1835650 TRUE FALSE 1752264.432 1589372.026 1695044.855 1637693.472 1581154.311 1586259.526 1771032.373 1773504.282 1815422.113 1711319.79 1.023925768 0.928740517 0.990489834 0.956976879 0.923938542 0.926921745 1.034892708 1.036337155 1.060831601 1 20.70667795 2.224036444 24.93172832 1.036033862 0.956960258 0.562814332 0.032113043 156.7982032 269152.9252 0.011707368 0.008684944 167.5083434 -2.224036444 -0.079073604 SGPS(ph)PLSSPNGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGPSPLSSPNGK 12 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 SGPS(1)PLSSPNGK;SGPS(1)PLSSPNGK;SGPS(1)PLSSPNGK 218.6 3.56E-11 411850000 814510 749360 527950 685610 725540 666200 797930 875930 818250 887500 TRUE FALSE 782678.0487 727988.9865 623362.3092 720994.4143 748877.653 679671.0204 807695.306 857841.7394 725365.6904 827388.8345 0.945961579 0.879863199 0.753409139 0.871409408 0.905109692 0.821465062 0.976197977 1.036806038 0.876692626 1 19.65820596 2.224037945 23.56759562 0.982086106 0.860974815 0.432848655 0.061012557 105.2585667 170812.8158 0.022974071 0.017057771 167.5089225 -2.224037945 -0.12111129 QQVAFYGQTLGQAQAHS(ph)QEQ ddPTM_BT-474_Pertuzumab_2h_R1 1 QQVAFYGQTLGQAQAHSQEQ 20 0 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 1 QQVAFYGQTLGQAQAHS(1)QEQ 242.71 8.83E-30 73366000 69106 77289 61006 72438 64751 76597 59608 58303 71998 79929 TRUE FALSE 66405.26112 75084.79339 72031.14127 76176.53386 66833.77472 78145.84382 60337.50053 57099.02268 63825.08888 74515.33764 0.891162319 1.007642128 0.966661946 1.022293346 0.896912996 1.048721596 0.809732633 0.766272079 0.856536264 1 16.18524979 2.224083624 24.97629995 0.82986921 0.972440612 0.33373757 0.07482842 199.8082828 344715.2118 0.026234281 0.0194612 167.5265419 -2.224083624 0.142571402 AKEFTNVYIK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKEFTNVYIK 10 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YBN4;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ; 172.17 3.46E-06 1565370000 4063400 4664000 3745900 3539500 3614800 3148200 5167400 4568200 5325700 5694600 FALSE TRUE 3904597.836 4530987.287 4422867.457 3722174.019 3731073.325 3211858.761 5230640.187 4473865.074 4721148.863 5308899.67 0.735481565 0.853470129 0.833104359 0.701119677 0.702795976 0.604995189 0.985258813 0.842710421 0.889289525 1 22.33998145 2.224138504 24.99999622 0.910798693 0.744699563 0.582433464 0.078424338 205.1696822 355648.8642 0.031070541 0.023050517 167.5477129 -2.224138504 -0.166099131 YLSVPPS(ph)PNISTSES(ph)RSPPEGDTTLFLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 YLS(0.001)VPPS(0.854)PNIS(0.13)T(0.127)S(0.124)ES(0.416)RS(0.328)PPEGDT(0.007)T(0.007)LFLS(0.006)R 59.694 0.020889 105000000 54563 53913 32989 45006 44067 54430 31890 38253 36640 32316 TRUE FALSE 52430.61764 52375.45403 38950.84614 47328.76505 45484.45508 55530.61189 32280.27936 37463.06218 32480.78081 30127.20854 1.740307854 1.738476831 1.292879362 1.570964167 1.509746747 1.843204684 1.071465991 1.243495963 1.078121153 1 14.87877938 2.224141065 24.99994787 1.13026575 1.599945735 0.728738925 0.154045388 136.3546364 236403.7675 0.058354442 0.043290735 167.5487011 -2.224141065 0.469679985 SLVQDSLSTNSSDLVAPS(ph)PDAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLVQDSLSTNSSDLVAPSPDAFR 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SLVQDSLSTNSSDLVAPS(1)PDAFR;SLVQDSLSTNSSDLVAPS(1)PDAFR 151.94 4.34E-08 159266000 161230 185725 158342 208391 242380 221650 137273 143009 134261 151051 TRUE FALSE 154928.9534 180428.3048 186957.9217 219146.0845 250176.3728 226131.9149 138952.988 140055.8142 119020.2541 140820.1812 1.100189987 1.281267381 1.327635855 1.556212203 1.77656619 1.605820365 0.986740585 0.994572035 0.845193161 1 17.10349458 2.224294661 23.84364591 0.961379473 1.449307123 0.634342903 0.180189729 97.98127256 163760.7722 0.075901376 0.056357568 167.6079679 -2.224294661 0.487927649 KT(ph)SDANETEDHLESLICK ddPTM_BT-474_Pertuzumab_2h_R1 4 KTSDANETEDHLESLICK 18 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK 257.2 9.82E-31 3691030000 1447660 1414850 1258730 1581600 2009080 1518170 979093 984033 956086 847097 TRUE FALSE 1391083.847 1374499.863 1486210.511 1663226.566 2073703.883 1548868.438 991075.433 963712.3747 847555.1255 789722.3657 1.761484678 1.740484913 1.88194051 2.106090239 2.625864447 1.961282224 1.254966905 1.220317945 1.073231761 1 19.59098602 2.224428694 4.372435537 1.151620166 2.032338384 0.763577478 0.239486377 0.109396057 4.93479522 0.10158423 0.077141361 167.6597037 -2.224428694 0.880718218 GGHGAASPSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGHGAASPSEK 11 0 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 ; 113.93 0.00085759 118010000 99661 153167 77485 165147 102168 99226 145152 134056 144113 109584 FALSE TRUE 95766.13794 148798.8271 91488.26314 173670.2565 105454.3265 101232.4177 146928.4136 131287.6968 127753.8964 102161.7781 0.937396938 1.456501932 0.895523403 1.699953346 1.03222877 0.990903052 1.438193582 1.285096043 1.250505804 1 16.64049601 2.224620389 24.99992443 1.275230126 1.187351306 0.011093933 0.254659766 1114.725092 1999096.815 0.090028975 0.066810892 167.7337237 -2.224620389 -0.08787882 LREEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LREEGK 6 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 122.79 0.01739 873860000 1113440 1111510 877440 1008190 1020100 1034920 1137530 1204080 1285510 1217380 FALSE TRUE 1069925.534 1079810.823 1036012.927 1060222.807 1052912.443 1055846.791 1151451.432 1179215.327 1139584.294 1134925.768 0.942727325 0.951437401 0.912846422 0.934178108 0.927736837 0.930322336 1.014561009 1.03902419 1.004104696 1 20.11416651 2.224621691 6.782962407 1.020264506 0.932785228 0.890930997 0.013865372 0.042225527 8.384561622 0.005133236 0.003928594 167.7342269 -2.224621691 -0.087479278 LEEEPSASS(ph)PQYACDFNLFLEDSADNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEEEPSASSPQYACDFNLFLEDSADNR 27 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 LEEEPSAS(0.019)S(0.977)PQY(0.003)ACDFNLFLEDSADNR;LEEEPS(0.135)AS(0.161)S(0.656)PQY(0.048)ACDFNLFLEDSADNR 223.12 1.40E-34 84104000 42307 49387 49251 59364 58827 59723 39515 38115 44480 46988 TRUE FALSE 40653.59567 47978.53111 58151.75128 62427.78315 60719.22388 60930.63998 39998.59639 37327.91193 39430.81688 43805.46091 0.928048577 1.095263698 1.327500044 1.425114172 1.386110832 1.390937082 0.91309612 0.85212919 0.900134733 1 15.41882311 2.224625438 24.37350873 0.898782026 1.267859613 0.565126033 0.146733295 132.0798497 231013.9379 0.060469942 0.044901501 167.7356741 -2.224625438 0.369077587 IEDGNNFGVAVQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEDGNNFGVAVQEK 14 0 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 211.25 1.98E-07 0 66815 76797 73036 72731 66021 68425 83208 85549 92559 94317 FALSE TRUE 64203.79593 74606.82475 86235.22988 76484.65563 68144.62542 69808.60038 84226.32439 83782.38325 82052.09036 87928.82558 0.730179159 0.848491087 0.980739016 0.869847347 0.774997562 0.793921674 0.957892066 0.952843197 0.933164862 1 16.42404858 2.224661936 24.86383436 0.956625358 0.839481937 0.483719275 0.06448684 224.8994222 402327.5511 0.025875062 0.01920789 167.7497711 -2.224661936 -0.117143421 SLGSASPGPGQPPLSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLGSASPGPGQPPLSSPTR 19 0 Q9C0B5;Q9C0B5-2 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5 1 SLGSASPGPGQPPLS(0.168)S(0.829)PT(0.003)R;SLGSASPGPGQPPLS(0.027)S(0.973)PTR;SLGSASPGPGQPPLS(0.007)S(0.993)PTR;SLGSASPGPGQPPLS(0.012)S(0.984)PT(0.005)R 393.74 3.87E-127 669920000 466872 833920 428293 1017890 504337 532420 845210 934120 686570 560820 TRUE FALSE 448626.1261 810137.4181 505695.0724 1070423.425 520559.4576 543185.8972 855553.9328 914830.0956 608633.4519 522835.1619 0.858064183 1.549508291 0.96721703 2.047343987 0.995647377 1.038923808 1.636374129 1.749748606 1.164101989 1 18.99599664 2.224711257 24.99668043 1.488802297 1.269537721 0.00331037 0.38813679 696.743059 1257541.814 0.14065892 0.104416904 167.7688226 -2.224711257 -0.219264576 SLS(ph)TSGESLYHVLGLDK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.015)LS(0.911)T(0.067)S(0.005)GES(0.002)LYHVLGLDK;S(0.001)LS(0.954)T(0.032)S(0.01)GES(0.002)LYHVLGLDK;S(0.038)LS(0.954)T(0.008)SGESLYHVLGLDK 286.16 1.37E-36 6327630000 3804970 6960900 4122790 8559500 4270110 3972450 8245700 8181000 7417700 6577800 TRUE FALSE 3656267.566 6762381.947 4867869.864 9001256.821 4407461.966 4052775.661 8346613.343 8012059.491 6575673.794 6132279.747 0.596233002 1.102751705 0.793810795 1.467848368 0.718731393 0.660892169 1.361094681 1.306538485 1.072304928 1 22.54799208 2.224748089 24.9966802 1.226193415 0.913815629 0.23145126 0.256794904 329.2506202 595844.5611 0.094933058 0.070472393 167.7830517 -2.224748089 -0.312377786 AVCMLSNTT(ph)AIAEAWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVCMLSNTTAIAEAWAR 17 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 1 AVCMLS(0.247)NT(0.301)T(0.452)AIAEAWAR 113.69 0.0044728 12556000 10813 12375 7426.5 11377 9348 12893 7974.9 10945 10524 12798 TRUE FALSE 10390.41601 12022.07712 8768.633752 11964.16833 9648.68691 13153.70529 8072.499212 10718.98193 9329.35964 11931.18006 0.870862392 1.007618446 0.734934324 1.002764879 0.808695105 1.102464737 0.676588499 0.898400818 0.781931007 1 13.54244912 2.224749568 24.99996791 0.832504188 0.915274244 0.091476792 0.125036393 559.2058539 1012235.845 0.042674546 0.031682748 167.7836231 -2.224749568 0.082770056 EANQQQQFNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EANQQQQFNR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 140.83 8.98E-05 94344000 40507 33362 29126 29992 34912 34903 32144 31153 38130 41711 FALSE TRUE 38923.94166 32410.54842 34389.7161 31539.89071 36034.97619 35608.76257 32537.38789 30509.67966 33801.64225 38885.87682 1.000978886 0.833478658 0.884375483 0.811088583 0.926685448 0.915724821 0.836740497 0.784595389 0.869252413 1 15.24695865 2.224770597 24.97729407 0.846544537 0.88966472 0 0.071970558 644.3674316 1167108.777 0.025901339 0.019229459 167.7917475 -2.224770597 0.043120183 AHS(ph)SPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 AHS(0.459)S(0.459)PAS(0.081)LQLGAVSPGTLTPTGVVSGPAATPTAQHLR;AHS(0.333)S(0.333)PAS(0.333)LQLGAVS(0.001)PGTLTPTGVVSGPAATPTAQHLR;AHS(0.5)S(0.5)PAS(0.001)LQLGAVSPGTLTPTGVVSGPAATPTAQHLR 209.93 6.29E-31 5025810000 468403 549832 296386 552587 457412 497295 405560 435251 403288 457874 TRUE FALSE 450097.2929 534151.3297 349949.5433 581106.0813 472125.0724 507350.6456 410523.3646 426262.9147 357508.437 426861.7861 1.054433326 1.251344925 0.819819329 1.36134482 1.106037335 1.188559534 0.961724328 0.998597037 0.837527388 1 18.70340949 2.224786172 24.09867368 0.955064249 1.131052906 0.289782657 0.138545238 196.0592256 343006.2385 0.048953769 0.036363588 167.797765 -2.224786172 0.175988657 YAEEDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 YAEEDRR 7 1 P38646;H0Y8S0 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 104.45 0.013067 1593994000 2307719 2011273 1466112 2313984 1529687 1708147 2276949 2222964 2728128 1951648 FALSE TRUE 2217530.79 1953913.463 1731071.052 2433408.992 1578890.772 1742686.903 2304814.983 2177059.017 2418442.347 1819461.143 1.218784363 1.07389678 0.951419633 1.337433889 0.86777933 0.957803858 1.266756914 1.196540539 1.329208022 1 20.79507981 2.224804381 24.99617102 1.214446169 1.065994679 0.150701432 0.149473381 396.1823959 719890.1922 0.054228254 0.040263746 167.8048006 -2.224804381 -0.14845149 VPS(ph)GIFDVNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPSGIFDVNSR 11 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 VPS(1)GIFDVNSR 136.01 0.0012623 0 31872 40418 33413 32897 34133 32050 25514 31602 26271 25910 TRUE FALSE 30626.407 39265.31821 39451.47237 34594.81811 35230.91894 32698.07296 25826.24796 30949.40766 23288.82622 24155.09262 1.267906834 1.625550306 1.633256928 1.432195631 1.458529656 1.353672017 1.06918439 1.281278782 0.964137318 1 14.56003976 2.224815436 0.814000882 1.023967885 1.524433033 0.699605977 0.124892585 0.352870024 0.445415217 0.098544441 0.058281282 167.809072 -2.224815436 0.500465148 DWPAQYCEALADEENR ddPTM_BT-474_Pertuzumab_2h_R1 1 DWPAQYCEALADEENR 16 0 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 0 165.86 1.60E-08 45769000 18761 18828 10060 22263 12715 19635 12426 16201 13357 16339 FALSE TRUE 18027.79938 18291.04387 11878.06578 23411.9961 13123.98952 20032.03315 12578.07311 15866.44369 11840.76936 15232.34498 1.183520949 1.20080289 0.77979233 1.536992245 0.861586942 1.315098442 0.825747652 1.041628437 0.777343828 1 13.89485044 2.224980052 24.99853108 0.925078912 1.136934378 0.225084929 0.212672126 374.1777595 688766.1938 0.073388924 0.054490997 167.8726911 -2.224980052 0.211855466 EPNEDCKPR ddPTM_BT-474_Pertuzumab_2h_R1 5 EPNEDCKPR 9 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ;;;; 117.7 0.0010118 2069913000 1459380 1649160 1168950 1605830 1315590 1536510 1612810 1824350 1871320 1746610 FALSE TRUE 1402345.816 1602127.571 1380205.268 1688707.079 1357907.147 1567579.285 1632548.051 1786676.535 1658895.599 1628310.549 0.861227496 0.983920157 0.847630244 1.03709153 0.833936222 0.962702898 1.002602392 1.097257852 1.018783303 1 20.63494444 2.224998239 2.813459552 1.048504174 0.919095663 0.42187068 0.063753239 0.221554455 3.606195746 0.024608034 0.017591376 167.8797213 -2.224998239 -0.129408511 RKPS(ph)VPDSASPADDSFVDPGER ddPTM_BT-474_Pertuzumab_2h_R1 4 RKPSVPDSASPADDSFVDPGER 22 2 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 1 RKPS(0.998)VPDS(0.002)ASPADDSFVDPGER;RKPS(0.998)VPDS(0.002)ASPADDSFVDPGER;RKPS(0.988)VPDS(0.012)ASPADDSFVDPGER;RKPS(0.885)VPDS(0.103)AS(0.012)PADDSFVDPGER 216.81 6.85E-26 3071860000 1357170 1567560 1310840 1468200 1751290 1689810 1147050 1189490 1247380 1196170 TRUE FALSE 1304130.296 1522854.724 1547737.947 1543973.978 1807621.833 1723979.116 1161087.941 1164926.616 1105782.652 1115152.34 1.169463802 1.36560241 1.387916154 1.384540858 1.620964031 1.545958389 1.04119222 1.044634507 0.99159784 1 20.08880938 2.225016139 24.70812261 1.026032403 1.417380001 0.74543413 0.112475801 109.0503543 198930.4616 0.045444404 0.033754088 167.8866406 -2.225016139 0.391347598 FGLGT(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FGLGTPEK 8 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 FGLGT(1)PEK 123.11 0.01522 257990000 729740 692180 700160 659610 623130 614030 878290 979620 851570 968060 TRUE FALSE 701220.954 672439.7041 826694.487 693652.5511 643173.5424 626446.1073 889038.7757 959390.5047 754903.3437 902492.4339 0.77698264 0.745091791 0.916012651 0.768596528 0.712663639 0.69412893 0.985092775 1.063045482 0.836465011 1 19.78355531 2.225137763 24.96752571 0.985997926 0.771945149 0.620049806 0.077185563 147.0164453 273459.8748 0.029685085 0.022047509 167.9336637 -2.225137763 -0.214052778 LTGGAAGHQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTGGAAGHQDR 11 0 O95274 O95274 LYPD3 Ly6/PLAUR domain-containing protein 3 0 73.848 0.042438 113910000 102340 198550 111880 194190 110150 113960 187080 199030 149250 112330 FALSE TRUE 98340.43966 192887.5484 132099.2048 204212.1692 113693.0748 116264.3493 189369.541 194919.9609 132307.7657 104721.789 0.939063786 1.841904633 1.261429985 1.950044695 1.085667804 1.11022119 1.808310789 1.861312366 1.263421556 1 16.67620212 2.225156511 24.99629892 1.596897785 1.395638282 0 0.386347127 749.8034013 1398241.705 0.140384148 0.104270093 167.9409135 -2.225156511 -0.201259503 ALERPYTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ALERPYTSK 9 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;; 108.7 0.0023433 1550100000 1707060 2113010 1481680 1779680 2092440 1579180 2410000 2462710 2437530 2591840 FALSE TRUE 1640346.208 2052749.024 1749452.536 1871529.498 2159745.233 1611112.102 2439494.301 2411854.178 2160831.813 2416292.368 0.678869093 0.849544968 0.724023532 0.774545963 0.89382612 0.666770347 1.009602287 0.998163223 0.894275809 1 21.2043636 2.225193926 24.9995628 0.979023844 0.772940026 0.67183165 0.072057023 133.035306 248812.666 0.025460423 0.018910844 167.9553823 -2.225193926 -0.206083818 DDDVPLMWR ddPTM_BT-474_Pertuzumab_2h_R1 4 DDDVPLMWR 9 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 210.26 1.65E-05 1691110000 1258760 1201730 1036400 1164810 1203480 1139590 1306660 1387050 1380490 1451660 FALSE TRUE 1209566.268 1167457.837 1223700.535 1224925.984 1242191.027 1162633.291 1322651.296 1358406.933 1223782.563 1353337.775 0.893765245 0.862650743 0.90420925 0.905114751 0.917872131 0.859085819 0.977325336 1.003745671 0.904269862 1 20.36809053 2.225211127 24.98802334 0.975289274 0.891724578 0.624398112 0.030662504 143.6173966 268826.1709 0.011208902 0.008326342 167.9620348 -2.225211127 -0.083564696 LKELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKELEK 6 1 Q3V6T2;A0A2U3TZV9;A0A2R8Y4X4;A0A2R8YG73;A0A2R8Y7B1;A0A2R8Y4W8;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;H7C2C6;A0A2R8Y820;A0A2R8Y885;A0A2R8YCU9;A0A2R8YGU1;A0A2R8YDS8;A0A2R8Y7D4;E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1;Q9P219 Q3V6T2;E7EX90;Q9P219 CCDC88A;DCTN1;DKFZp686E0752;CCDC88C Girdin;Dynactin subunit 1;Protein Daple 0 91.9 0.043199 1389600000 1398500 1225600 1078800 971910 1226500 1077600 1371800 1487400 1376100 1231000 FALSE TRUE 1343845.074 1190647.088 1273763.158 1022070.392 1265951.486 1099389.81 1388588.499 1456684.67 1219890.897 1147623.274 1.170981022 1.037489493 1.109914017 0.890597477 1.103107192 0.957970996 1.209968925 1.26930562 1.062971556 1 20.1302177 2.225214294 24.9997209 1.171784787 1.043240391 0.118437753 0.103571031 313.846704 587879.4659 0.037520409 0.027868483 167.9632597 -2.225214294 -0.128544395 LKEEYQSLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKEEYQSLIR 10 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ; 140.63 3.55E-05 2680300000 3188000 3433100 2883800 2726600 3167400 2817100 3737500 3648300 4166000 4284300 FALSE TRUE 3063409.435 3335191.349 3404966.81 2867320.153 3269282.298 2874063.692 3783240.643 3572961.33 3693093.145 3994120.545 0.766979715 0.835025211 0.852494754 0.717885232 0.818523693 0.719573598 0.947202419 0.894555207 0.92463237 1 21.92944644 2.225236426 24.99996323 0.929225693 0.788880703 0.708229974 0.048921961 136.4947439 256101.1959 0.017842057 0.013252819 167.9718194 -2.225236426 -0.14034499 RTPS(ph)EADR ddPTM_BT-474_Pertuzumab_2h_R1 2 RTPSEADR 8 1 P49757-3;P49757;G3V3Z8;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;P49757-9 P49757-3 NUMB Protein numb homolog 1 RT(0.007)PS(0.993)EADR;RT(0.003)PS(0.997)EADR 81.92 0.013239 94891000 79702 99683 67073 82805 90360 96538 61822 70501 64577 59914 TRUE FALSE 76587.15772 96840.13844 79194.58313 87078.57597 93266.51146 98490.0645 62578.59613 69045.12971 57246.48969 55855.97141 1.371154342 1.733747279 1.417835571 1.558984183 1.66976796 1.763286216 1.120356419 1.236127991 1.024894711 1 15.7694239 2.225237677 24.99996853 1.128188101 1.587484612 0.766775954 0.132013463 113.0523808 212136.8995 0.048322366 0.035893878 167.972303 -2.225237677 0.459296511 KKVEAQLQELQVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKVEAQLQELQVK 13 2 P35579 P35579 MYH9 Myosin-9 0 ; 104.98 0.00083765 4163200000 2463950 2382030 2119390 2081870 2190390 2499210 2508180 2879540 3098890 2890210 FALSE TRUE 2367656.11 2314096.837 2502410.919 2189315.56 2260845.884 2549745.739 2538875.857 2820076.493 2747116.999 2694453.502 0.878714778 0.858837176 0.928726703 0.812526755 0.839074002 0.946294206 0.942260037 1.046622809 1.019545149 1 21.36156126 2.225297265 1.663208362 1.024204668 0.865762618 0.780165803 0.035281382 0.162488346 0.890008121 0.019142867 0.011635404 167.9953514 -2.225297265 -0.15844205 ALLSLRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALLSLRSPK 9 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 ALLSLRS(1)PK;ALLS(0.004)LRS(0.996)PK 91.549 0.0064665 1658230000 1647200 1620510 1337980 1337410 1538840 1237700 1972820 1931680 1999980 2050330 TRUE FALSE 1582825.603 1574294.641 1579782.749 1406433.89 1588338.186 1262727.142 1996963.961 1891790.133 1772950.655 1911459.323 0.828071821 0.823608759 0.826479921 0.735790646 0.830955787 0.660608953 1.044732649 0.989709857 0.927537737 1 20.86624307 2.225305897 24.99673683 0.991613007 0.787881026 0.760346519 0.05670101 108.6403137 204880.5686 0.020664343 0.01535028 167.9986906 -2.225305897 -0.203731981 TPQEAIMDGTEIAVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPQEAIMDGTEIAVSPR 17 0 Q06587 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR 262.92 2.38E-27 618320000 300431 322831 279617 370161 313515 326721 298063 305857 337093 322239 TRUE FALSE 288689.8244 313624.176 330150.0119 389265.0536 323599.4947 333327.5225 301710.7842 299540.9461 298827.6158 300413.4655 0.960974981 1.043975094 1.098985398 1.295764332 1.077180393 1.109562522 1.004318444 0.997095605 0.99472111 1 18.19658996 2.225311304 8.080720665 0.998550489 1.103481526 0.27341369 0.078498352 0.213559574 82.8145333 0.030867369 0.02358702 168.0007823 -2.225311304 0.104931037 SLSTSGES(ph)LYHVLGLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 SLS(0.222)T(0.058)S(0.058)GES(0.662)LYHVLGLDK 246.38 1.25E-20 1089100000 875170 1539100 772420 1968000 948420 897680 1723400 1593700 1686300 1291700 TRUE FALSE 840967.3888 1495206.375 912013.4764 2069568.716 978926.7906 915831.7046 1744491.485 1560789.538 1494878.294 1204212.008 0.698354927 1.241647122 0.757352916 1.718608269 0.812918974 0.760523644 1.448658104 1.296108598 1.241374677 1 20.19965798 2.225312467 24.99846263 1.280216004 1.022670182 0.130812017 0.304832081 459.390723 866836.8963 0.110437415 0.082037638 168.001232 -2.225312467 -0.257545823 LKTDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPAS(ph)PVVHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKTDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR 47 2 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 1 LKTDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKT(0.284)PAS(0.716)PVVHIR 123.47 1.09E-10 123170000 98913 99666 62438 61044 91365 93457 63894 58015 98269 78809 TRUE FALSE 95047.37061 96823.62326 73721.93553 64194.48816 94303.8382 95346.76457 64675.95388 56816.96998 87113.9151 73471.19623 1.293668478 1.317844655 1.003412756 0.873736804 1.283548425 1.297743462 0.880289926 0.773323056 1.185687992 1 16.16489114 2.2253506 24.99658709 0.920811056 1.16765484 0.276585608 0.167922451 289.3436255 547505.4348 0.066722404 0.049571812 168.015984 -2.2253506 0.246843784 VDKLDASESLR ddPTM_BT-474_Pertuzumab_2h_R1 6 VDKLDASESLR 11 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 178.15 6.99E-06 23054730000 16633710 16976300 14519430 15548640 15288310 14865300 19051400 20237800 20712100 21404800 FALSE TRUE 15983646.22 16492152.55 17143413.98 16351107.17 15780072.38 15165886.55 19284556.73 19819882.36 18360949.24 19955033.83 0.800983168 0.826465777 0.859102226 0.819397617 0.79078154 0.760003049 0.966400603 0.993227199 0.920116167 1 24.25024939 2.225451354 24.97291692 0.971821503 0.812088518 0.864057989 0.031170007 80.10238544 152592.6264 0.012114885 0.00900142 168.0549674 -2.225451354 -0.159732985 YRPETK ddPTM_BT-474_Pertuzumab_2h_R1 5 YRPETK 6 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;; 148.54 0.0098063 6705970000 5123000 4970290 4381820 4071160 5078610 4659660 5134100 5465450 5578100 5516610 FALSE TRUE 4922787.496 4828542.196 5173712.347 4281273.055 5241968.103 4753881.518 5196932.652 5352586.548 4944897.473 5142965.091 0.957188589 0.938863498 1.005978508 0.832452288 1.019250182 0.924346449 1.010493472 1.040758872 0.96148766 1 22.29416893 2.225583919 24.65272123 1.010383164 0.946853776 0.225429968 0.050914816 254.7681291 483996.6603 0.017957178 0.013348368 168.1062729 -2.225583919 -0.063529388 LLESLQENHFQEDEQFLGAVMPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLESLQENHFQEDEQFLGAVMPR 23 0 P49903;P49903-2;P49903-4;Q5T5U6 P49903 SEPHS1 "Selenide, water dikinase 1" 0 100.79 0.0016957 58639000 24458 25750 17557 28225 23338 28160 19482 22304 27383 25742 FALSE TRUE 23502.15432 25015.63521 20729.94045 29681.69563 24088.68797 28729.41449 19720.42654 21843.41461 24274.59664 23998.47141 0.979318804 1.042384525 0.863802536 1.236816092 1.003759262 1.197135184 0.821736777 0.910200247 1.011505951 1 14.5506549 2.225659538 24.99995424 0.922621315 1.050746005 0.210371903 0.110724538 334.1306316 647480.4138 0.040248209 0.029916101 168.1355458 -2.225659538 0.12812469 AILELHYSQELSLLYLLQDDVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AILELHYSQELSLLYLLQDDVDR 23 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 204.82 1.66E-24 42943000 22139.7 30477 25143.5 25246.6 33161 26011.2 24394.6 22572.6 23506.4 29151.7 FALSE TRUE 21274.45605 29607.8258 29687.48976 26549.58005 34227.65368 26537.16429 24693.14841 22106.46792 20838.05202 27177.22939 0.782804448 1.089435033 1.092366309 0.976905323 1.259423953 0.976448478 0.908596975 0.813418749 0.766746739 1 14.73011077 2.225694848 2.959661358 0.845534225 1.046929007 0.278611928 0.125554208 0.286154783 5.175119909 0.050333518 0.03641044 168.1492166 -2.225694848 0.201394782 SGPFGQIFRPDNFVFGQSGAGNNWAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGPFGQIFRPDNFVFGQSGAGNNWAK 26 1 Q5JP53;P07437;Q5ST81;P68371;M0QY85;M0QZL7;Q13885;Q9BVA1;P04350;M0R278;M0R1I1 Q5JP53;P68371;Q13885;Q9BVA1;P04350 TUBB;TUBB4B;TUBB4A;TUBB2A;TUBB2B Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain 0 ; 297.48 1.72E-70 30099000000 4650740 4917050 4310330 4271470 4383990 4355380 5010040 4986750 5575150 5554360 FALSE TRUE 4468983.939 4776820.548 5089302.514 4491921.079 4525005.02 4443448.768 5071354.368 4883771.87 4942282.345 5178158.25 0.863045068 0.922494122 0.982840282 0.867474662 0.873863795 0.858113745 0.979374156 0.943148439 0.954447915 1 22.30400763 2.225716811 24.99893726 0.962747845 0.897734901 0.479894621 0.037725148 243.0871931 473137.085 0.014878153 0.011059303 168.1577205 -2.225716811 -0.065012944 RKS(ph)EDGTPAEDGTPAATGGSQPPSMGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RKSEDGTPAEDGTPAATGGSQPPSMGR 27 2 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 RKS(0.775)EDGT(0.182)PAEDGT(0.044)PAATGGSQPPSMGR 91.398 0.0033112 169560000 76160 54199 56153 52988 70115 65679 57799 59362 68771 71739 TRUE FALSE 73183.583 52653.29759 66301.09622 55722.71703 72370.31265 67007.07438 58506.36145 58136.15396 60964.40439 66880.05363 1.094251261 0.787279536 0.991343347 0.833173929 1.082091128 1.001899232 0.874795373 0.869259978 0.911548378 1 16.02928838 2.225732142 24.98007723 0.898382772 0.957454697 0.050310704 0.096788686 619.6143766 1206527.374 0.03472151 0.025807257 168.1636566 -2.225732142 0.059071925 TEAPGT(ph)PEGPEPERPSPGDGNPR ddPTM_BT-474_Pertuzumab_2h_R1 3 TEAPGTPEGPEPERPSPGDGNPR 23 1 A0A0G2JNW7;Q9Y666;Q9Y666-2 A0A0G2JNW7 SLC12A7 Solute carrier family 12 member 7 1 TEAPGT(1)PEGPEPERPSPGDGNPR;TEAPGT(1)PEGPEPERPSPGDGNPR;T(0.001)EAPGT(0.999)PEGPEPERPSPGDGNPR 160.52 3.05E-11 1078360000 198576 378547 224000 538826 262829 255172 469593 537487 421747 320714 TRUE FALSE 190815.4304 367751.2102 264481.7829 566634.8744 271283.1335 260331.7527 475340.0196 526387.7056 373872.0487 298991.7551 0.638196295 1.229971074 0.88457885 1.895152173 0.907326469 0.870698767 1.589809791 1.760542545 1.25044267 1 18.18974618 2.225950386 24.99689751 1.499903369 1.099763599 0.134446069 0.372370621 362.2977513 718167.5384 0.137438186 0.102189737 168.2481841 -2.225950386 -0.400139771 HSDELTSLLGYFPNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSDELTSLLGYFPNKK 16 1 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;A0A494C0Y7;H7C0P8 Q92878-2 RAD50 DNA repair protein RAD50 0 128.96 3.76E-05 289600000 373520 401720 322030 338280 391960 386430 335890 289690 450810 427270 FALSE TRUE 358922.4255 390263.3389 380227.9845 355738.6713 404567.7494 394243.8794 340000.7223 283707.8003 399635.9387 398330.6223 0.901066615 0.979747268 0.954553738 0.893073872 1.015658166 0.989740324 0.853564108 0.712242003 1.003276967 1 18.60360687 2.225955883 24.25589313 0.851045395 0.956570585 0.035555202 0.087681229 227.4246445 437639.8187 0.032496385 0.024173981 168.2503138 -2.225955883 0.10552519 LEDQLSEGRNS(ph)PEKAENKR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEDQLSEGRNSPEKAENKR 19 3 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 LEDQLSEGRNS(1)PEKAENKR;LEDQLSEGRNS(1)PEKAENKR;LEDQLSEGRNS(1)PEKAENKR 193.54 3.61E-15 937890000 921930 743290 700690 583730 740220 787960 862560 955270 1066560 945640 TRUE FALSE 885899.9564 722092.097 827320.2698 613856.3753 764029.8486 803893.0911 873116.2673 935543.3407 945488.5802 881590.9605 1.00488775 0.819078381 0.938440055 0.696305206 0.866648914 0.911866304 0.990387046 1.061198881 1.072479894 1 19.74974991 2.225973963 2.083615877 1.049537825 0.858669927 0.51622921 0.077020419 0.240676596 2.110274465 0.036135505 0.023690071 168.2573182 -2.225973963 -0.190867898 TGHSLLHTLYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGHSLLHTLYGR 12 0 P31040;D6RFM5;P31040-2;A0A494C1T6 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 ; 164.04 3.38E-05 295370000 111347 149131 120251 155465 104601 84211 153569 64360 107707 91521 FALSE TRUE 106995.4361 144877.9299 141983.0307 163488.5673 107965.5862 85913.80412 155448.4234 63030.94351 95480.5529 85322.20115 1.25401636 1.698009755 1.664080729 1.916131617 1.265386789 1.006933752 1.821898888 0.738740242 1.119058716 1 16.38063356 2.225973982 0.79834452 0.954465079 1.612514403 0.346660537 0.307413873 0.67913556 0.825816064 0.246285723 0.147089706 168.2573258 -2.225973982 0.658049324 SVS(ph)PTFLNPSDENLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVSPTFLNPSDENLK 15 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 S(0.024)VS(0.976)PTFLNPSDENLK;S(0.066)VS(0.869)PT(0.065)FLNPSDENLK;SVS(1)PTFLNPSDENLK;SVS(1)PTFLNPSDENLK 358.12 1.08E-82 3787700000 3494850 3196140 2548060 2917720 2997160 3127960 3405470 3729890 3745500 3903840 TRUE FALSE 3358267.398 3104989.217 3008551.123 3068303.879 3093566.373 3191209.494 3447147.161 3652866.468 3320326.542 3639429.44 0.922745572 0.853152745 0.82665461 0.843072775 0.850014109 0.876843348 0.947166917 1.00369207 0.912320625 1 21.79528086 2.226002179 3.059243118 0.973231119 0.856660458 0.706834095 0.033098586 0.129519767 2.511024338 0.013347963 0.009723089 168.2682503 -2.226002179 -0.116570661 LLKPGEEPSEYT(ph)DEEDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLKPGEEPSEYTDEEDTK 18 1 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPS(0.072)EY(0.031)T(0.897)DEEDTK 76.417 0.024683 208830000 80228 101460 75109 121860 71453 75291 129510 146720 136700 104310 TRUE FALSE 77092.60106 98566.46014 88682.86709 128149.2092 73751.35064 76813.43561 131094.9821 143690.1807 121182.3891 97244.99079 0.792766809 1.013589074 0.911953062 1.317797536 0.758407709 0.789896065 1.34808982 1.477610102 1.246155592 1 16.56933632 2.22602085 24.99013549 1.327402734 0.943408101 0.415074468 0.190617439 193.2582788 385136.1349 0.070798289 0.052643143 168.2754845 -2.22602085 -0.383994633 DEPSVAAMVYPFTGDHK ddPTM_BT-474_Pertuzumab_2h_R1 4 DEPSVAAMVYPFTGDHK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 245.96 1.28E-20 1300350000 1744700 1553210 1392350 1471380 1599980 1772550 1849030 1870030 2229830 2181090 FALSE TRUE 1676515.195 1508913.972 1643978.618 1547318.098 1651444.81 1808392.175 1871658.982 1831413.227 1976709.047 2033362.832 0.824503708 0.742078073 0.808502345 0.760965074 0.81217419 0.889360299 0.92047467 0.900681963 0.972137887 1 20.95543624 2.226075475 0.656602001 0.987550233 0.771618992 0.869418865 0.029834998 0.248321256 0.209796608 0.025727884 0.017435424 168.2966514 -2.226075475 -0.21593124 TQAPPT(ph)PDKVQMTWTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQAPPTPDKVQMTWTR 16 1 A0A0G2JNW7;Q9Y666;A0A0G2JQE3;H0YB78;A0A0U1RR18 A0A0G2JNW7 SLC12A7 Solute carrier family 12 member 7 1 TQAPPT(0.994)PDKVQMT(0.002)WT(0.004)R;TQAPPT(0.998)PDKVQMT(0.002)WTR 124.4 0.00013368 355510000 297510 560600 249878 602320 290010 306420 609160 734990 541830 361610 TRUE FALSE 285882.9803 544612.2369 295036.5131 633405.8074 299338.435 312616.0223 616615.0823 719812.1997 480323.7299 337117.8326 0.848020937 1.61549519 0.875173262 1.8788855 0.887934147 0.927319744 1.829078805 2.135194671 1.424794785 1 18.36289342 2.226166853 24.83531285 1.744266615 1.19799883 0.156525495 0.430119903 273.7009692 548453.146 0.154300514 0.114773088 168.3320657 -2.226166853 -0.546267785 TLLADKGEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLLADKGEIR 10 1 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8;E7ESY4;Q13330-3;Q13330;Q13330-2 Q9BTC8;E7ESY4 MTA3;MTA1 Metastasis-associated protein MTA3;Metastasis-associated protein MTA1 0 71.555 0.045563 0 390890 391250 321760 324090 382740 328370 446370 433060 513610 495660 FALSE TRUE 375613.5866 380091.9331 379909.1895 340816.3237 395051.1797 335009.8664 451832.8096 424117.1597 455307.146 462088.5067 0.812860699 0.822552233 0.82215676 0.737556375 0.854925353 0.724990692 0.977805773 0.917826679 0.985324542 1 18.81780968 2.226291316 24.99996517 0.959024365 0.798287138 0.800477982 0.042497227 97.40189129 198465.0215 0.014953826 0.011124036 168.3803142 -2.226291316 -0.160737227 AVIFCLSADKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVIFCLSADKK 11 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 168.22 2.94E-05 4577000000 2948700 3480600 2372100 2593880 3061400 2416100 4063600 4109300 4444800 4420300 FALSE TRUE 2833461.544 3381336.696 2800791.237 2727750.458 3159872.711 2464955.197 4113331.552 4024441.519 3940244.938 4120909.144 0.687581659 0.820531727 0.679653722 0.661929289 0.766790191 0.598158103 0.998161185 0.976590694 0.956159139 1 21.97453123 2.226310589 24.99981768 0.980949389 0.70785632 0.851646214 0.057281033 79.39073989 162019.2606 0.020739997 0.015428566 168.387787 -2.226310589 -0.273093069 S(ph)LTNSHLEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLTNSHLEK 9 0 F8VX12;F8VX04;Q9H2H9 F8VX12 SLC38A1 Sodium-coupled neutral amino acid transporter 1 1 S(0.992)LT(0.008)NSHLEK;S(0.995)LT(0.005)NSHLEK;S(0.995)LT(0.005)NSHLEK;S(0.961)LT(0.019)NS(0.019)HLEK 153.75 4.98E-05 1480380000 1214117 2238403 1059883 2615630 1084483 1233549 2660549 3279020 2441581 1664257 TRUE FALSE 1166667.965 2174565.938 1251427.435 2750622.978 1119366.381 1258492.206 2693109.595 3211307.091 2164422.961 1551535.391 0.751944153 1.401557419 0.806573567 1.772839339 0.721457201 0.811126973 1.73577065 2.069760774 1.395020038 1 20.56526517 2.226318249 24.9991351 1.688853143 1.068132887 0.242165157 0.408724417 248.6473831 507738.8914 0.147702232 0.109877865 168.3907567 -2.226318249 -0.620720256 ILMVGLDAAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILMVGLDAAGK 11 0 P61204;F5H423;P61204-2;F5H0C7;F5H1V1;F5H6T5;F8WDB3;P84077;P84085;C9J1Z8;P18085;C9JPM4 P61204;P84077;P84085;P18085 ARF3;ARF4;ARF1;ARF5 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 ; 195.7 1.47E-07 286340000 544790 556860 475270 537720 540780 502910 617540 645890 656990 646740 FALSE TRUE 523499.0045 540978.898 561161.8613 565471.7936 558174.6798 513079.1848 625097.6392 632552.1458 582411.2495 602935.7237 0.868250103 0.897241409 0.930715894 0.937864139 0.9257615 0.850968295 1.03675668 1.049120364 0.965959101 1 19.20164469 2.226321238 24.99943987 1.021192003 0.90563577 0.726090644 0.033243726 115.1495182 235196.1055 0.012736175 0.009475523 168.391916 -2.226321238 -0.115556234 REDLVEEIK ddPTM_BT-474_Pertuzumab_2h_R1 2 REDLVEEIK 9 1 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 201.84 3.34E-05 511600000 856510 827290 746070 773800 810760 833500 914150 961380 1039140 1061940 FALSE TRUE 823036.6423 803696.4992 880901.4452 813735.9107 836838.8317 850353.9411 925337.6412 941527.167 921181.1836 990013.8579 0.831338507 0.811803282 0.889786984 0.82194396 0.845279917 0.858931352 0.934671403 0.95102423 0.930473019 1 19.91708919 2.226408336 2.206949428 0.955730065 0.839909693 0.825810114 0.025231866 0.122194851 1.207067351 0.01129684 0.00754968 168.4256904 -2.226408336 -0.115820372 KTPSKPPAQLSPS(ph)VPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTPSKPPAQLSPSVPK 16 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 KTPSKPPAQLS(0.201)PS(0.799)VPK 98.312 0.0014488 4558800000 2550700 2297400 1981900 1920200 2250800 2326300 2517400 2874100 2974200 2749700 TRUE FALSE 2451015.824 2231880.401 2340073.417 2019301.752 2323199.026 2373339.38 2548208.694 2814748.831 2636581.285 2563460.37 0.956135641 0.870651416 0.912857263 0.787724974 0.906274602 0.925834239 0.994050356 1.098027051 1.028524301 1 21.28966116 2.226527696 2.251725377 1.052506034 0.883544743 0.68115518 0.046911719 0.157332782 1.620039632 0.021330874 0.014348615 168.471986 -2.226527696 -0.168961292 EES(ph)EESEAEPVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EES(0.985)EES(0.015)EAEPVQR;EES(0.986)EES(0.014)EAEPVQR 392.71 3.14E-108 552810000 631720 474480 266840 493000 290330 282100 600560 475620 553470 597860 TRUE FALSE 607031.684 460948.295 315063.9238 518443.7891 299668.7281 287804.2553 607909.8329 465798.2808 490642.4059 557366.4097 1.089107046 0.827011257 0.565272536 0.930166907 0.537651216 0.51636455 1.090682579 0.835712868 0.880287002 1 19.08826653 2.226546684 24.99947254 0.932476432 0.738946447 0.236041496 0.181337789 368.9832185 767802.0642 0.068914582 0.051284806 168.4793523 -2.226546684 -0.193529985 GTEDELDKYSEALK ddPTM_BT-474_Pertuzumab_2h_R1 3 GTEDELDKYSEALK 14 1 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;D6RGJ6;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;H0YKP3;A0A087WTJ7 J3KN67;P09493-3 TPM3;TPM1 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain 0 ;; 138.19 1.54E-05 1300050000 1013170 957890 943670 1051280 1034830 905760 1359460 1411300 1541920 1619200 FALSE TRUE 973574.1963 930571.9151 1114212.161 1105536.687 1068116.247 924075.0878 1376097.478 1382156.162 1366887.706 1509530.142 0.644951809 0.616464613 0.738118524 0.732371389 0.707581927 0.612160739 0.911606493 0.915620115 0.905505407 1 20.52566813 2.226687486 24.88380304 0.924503635 0.679521983 0.873648358 0.047988262 73.59501592 154239.8915 0.018458862 0.013741665 168.5339836 -2.226687486 -0.244981652 REERPENK ddPTM_BT-474_Pertuzumab_2h_R1 5 REERPENK 8 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;;;; 120.33 0.00085606 620236000 277979 275026 241676 256182 266773 252895 298253 307954 313729 328912 FALSE TRUE 267115.2734 267182.5278 285352.2293 269403.5837 275353.9958 258008.7102 301903.1094 301594.6423 278115.7992 306634.4973 0.871119446 0.871338777 0.930594019 0.87858211 0.897987664 0.841421016 0.984569943 0.983563966 0.906994489 1 18.22616049 2.226792804 24.99975632 0.969755737 0.884165074 0.648727853 0.031310484 137.571701 292257.8115 0.01144395 0.008519367 168.5748584 -2.226792804 -0.085590662 QLQGPEKEPPKPEQVESR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLQGPEKEPPKPEQVESR 18 2 O60664-4;O60664;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ; 181.34 4.16E-14 3104400000 1303280 1224680 1159810 1116780 1284890 1309290 1324460 1516040 1648540 1531770 FALSE TRUE 1252346.377 1189753.325 1369413.467 1174417.15 1326219.654 1335764.741 1340669.138 1484733.244 1461404.65 1428021.854 0.87697984 0.833147842 0.95895834 0.822408387 0.928711035 0.935395167 0.938829566 1.039713251 1.023376951 1 20.44558663 2.226931413 1.101696502 1.027878412 0.877917041 0.676152824 0.04025588 0.271982056 0.631334555 0.026558565 0.014838089 168.6286695 -2.226931413 -0.149961371 DGISCEASNPHGNKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGISCEASNPHGNKR 15 1 P50895;A0A087WXM8 P50895 BCAM Basal cell adhesion molecule 0 ;;; 212.11 6.76E-10 956890000 897422 1568680 705011 1676940 860521 893036 1668410 1986890 1477500 898192 FALSE TRUE 862349.7561 1523942.782 832422.1706 1763487.074 888200.4395 911093.7998 1688828.501 1945860.027 1309780.394 837356.6558 1.029847616 1.81994467 0.994107069 2.106016668 1.060719388 1.088059423 2.016856842 2.323812695 1.56418461 1 19.67548272 2.227005335 24.99670514 1.895180262 1.376221454 0.088350447 0.478277504 336.3646752 727628.3605 0.170965716 0.127336371 168.6573745 -2.227005335 -0.518958808 ESYSVYVYK ddPTM_BT-474_Pertuzumab_2h_R1 8 ESYSVYVYK 9 0 P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880 P58876;Q99880 HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L 0 ;;;;;;; 190.52 8.60E-05 15875300000 8448700 8893710 6457800 8582100 7736700 7792070 8624890 8805540 9206930 9103740 FALSE TRUE 8118515.463 8640070.099 7624868.113 9025023.209 7985557.982 7949630.994 8730443.984 8623702.522 8161797.905 8487135.581 0.956567193 1.018019568 0.898403005 1.063376816 0.940901427 0.936668316 1.028667906 1.016091052 0.961666964 1 23.01684629 2.227037325 24.99987273 1.005274233 0.971023169 0.10586157 0.045718464 488.5458453 1059897.127 0.016312814 0.012150893 168.6697981 -2.227037325 -0.034251064 LLIVQDAS(ph)ER ddPTM_BT-474_Pertuzumab_2h_R1 4 LLIVQDASER 10 0 O95772-2;C9JPX5;C9JKL2;O95772 O95772-2 STARD3NL MLN64 N-terminal domain homolog 1 LLIVQDAS(1)ER;LLIVQDAS(1)ER;LLIVQDAS(1)ER;LLIVQDAS(1)ER 149.69 2.40E-05 213279000 281315 483036 301903 562630 281055 295475 557940 553810 522910 493900 TRUE FALSE 270320.8988 469260.2862 356463.5879 591667.4017 290095.3893 301449.7069 564768.2366 542373.63 463551.449 460447.7131 0.587082726 1.01913914 0.774167354 1.284982822 0.63002895 0.654688249 1.226563235 1.177926645 1.006740691 1 18.81267781 2.227129329 24.98920906 1.127985013 0.843572078 0.300282441 0.205144137 269.7198634 589613.175 0.075916646 0.05655327 168.705534 -2.227129329 -0.284412936 PSMS(ph)PTPLDR ddPTM_BT-474_Pertuzumab_2h_R1 9 PSMSPTPLDR 10 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 PS(0.001)MS(0.998)PT(0.002)PLDR;PSMS(1)PTPLDR;PS(0.001)MS(0.994)PT(0.005)PLDR;PSMS(0.929)PT(0.071)PLDR;PSMS(0.925)PT(0.075)PLDR;PSMS(0.666)PT(0.334)PLDR;PSMS(0.993)PT(0.007)PLDR;PSMS(0.973)PT(0.027)PLDR;PSMS(0.877)PT(0.123)PLDR 235.47 4.27E-12 9155180000 3966800 3297960 3447760 3739000 3748010 3495710 4330090 4490530 5012550 4765930 TRUE FALSE 3811773.07 3203905.41 4070846.927 3931970.238 3868568.146 3566395.651 4383082.937 4397798.986 4443546.338 4443129.316 0.857902798 0.721092091 0.916211669 0.884955165 0.870685472 0.802676537 0.986485566 0.989797657 1.000093858 1 22.0831447 2.227178891 24.76391264 0.992633498 0.843341621 0.690835783 0.049755207 115.1971673 250639.5101 0.018993517 0.014153949 168.7247881 -2.227178891 -0.149291877 YSPTSPTYS(ph)PTSPK ddPTM_BT-474_Pertuzumab_2h_R1 4 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYS(0.996)PT(0.002)S(0.002)PK;YSPTSPTYS(0.999)PTSPK;YSPTSPT(0.041)YS(0.957)PT(0.001)S(0.001)PK;YSPTSPTYS(1)PTSPK 317.91 5.84E-56 2362820000 1191490 1145460 1017460 1057140 1003580 1059230 1192900 1230020 1294390 1347870 TRUE FALSE 1144925.254 1112792.602 1201337.655 1111699.122 1035861.062 1080648.356 1207499.067 1204619.657 1147456.274 1256577.564 0.911145707 0.885574145 0.956039396 0.88470394 0.824351072 0.859993356 0.960942724 0.958651253 0.913159924 1 20.2610683 2.227205239 24.98166955 0.95538296 0.887095064 0.46757453 0.037183541 216.1379164 475496.9531 0.014713101 0.010963762 168.7350246 -2.227205239 -0.068287897 LTHDVELNLDYER ddPTM_BT-474_Pertuzumab_2h_R1 4 LTHDVELNLDYER 13 0 P02786;G3V0E5;H7C3V5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ;;; 260.19 5.27E-24 2235890000 1346970 1874190 1368950 2312360 1408900 1267640 2205810 1938360 1924130 1838210 FALSE TRUE 1294328.923 1820739.936 1616349.717 2431701.177 1454218.548 1293272.549 2232805.363 1898332.189 1705710.829 1713706.399 0.75528044 1.062457336 0.943189404 1.418971871 0.848580917 0.754664014 1.302910092 1.107734784 0.995334341 1 20.70868853 2.227216946 24.99875903 1.117052025 0.982846856 0.099497488 0.195740476 558.3864001 1230543.162 0.073968103 0.05511363 168.7395733 -2.227216946 -0.134205169 TVQYQNELHK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVQYQNELHK 10 0 Q9UL26 Q9UL26 RAB22A Ras-related protein Rab-22A 0 ; 152.67 1.76E-05 544020000 703190 865060 579640 837680 657090 610260 961210 971330 977920 827930 FALSE TRUE 675708.5574 840389.3358 684393.842 880912.7652 678225.8966 622599.8753 972973.5755 951271.6961 866910.6214 771853.5637 0.875436209 1.08879375 0.886688712 1.141295197 0.878697629 0.806629527 1.260567576 1.232451 1.123154264 1 19.55796764 2.227235954 24.99643666 1.182852144 0.955822643 0.421283729 0.11705909 189.8972806 419148.9223 0.042612958 0.031751817 168.7469584 -2.227235954 -0.227029501 KFQEQECPPS(ph)PEPTRK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFQEQECPPSPEPTRK 16 2 P62070-2;P62070-3;P62070;P62070-4 P62070-2 RRAS2 Ras-related protein R-Ras2 1 KFQEQECPPS(1)PEPTRK;KFQEQECPPS(1)PEPTRK 160.77 4.52E-09 571400000 242860 403520 180414 401570 203559 228550 390640 419750 368480 248350 TRUE FALSE 233368.7627 392012.0047 213018.8231 422295.0758 210106.6601 233171.4376 395420.7692 411082.0158 326651.6952 231529.0333 1.007945999 1.693144048 0.920052315 1.823940047 0.907474355 1.007093729 1.707866886 1.775509576 1.410845502 1 17.82083359 2.227296401 24.99701426 1.56966952 1.246525538 0.077169363 0.357754275 397.7000235 882550.8498 0.127286762 0.094857589 168.7704472 -2.227296401 -0.323143981 IEDYFPEFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEDYFPEFAR 10 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;P63092-2;A0A590UJB0;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 111.61 0.004027 41078000 89082 90688 74600 105440 80442 83620 103650 112590 105930 105510 FALSE TRUE 85600.57695 88101.66703 88081.87947 110881.771 83029.48999 85310.85369 104918.4997 110264.9772 93905.27049 98363.71372 0.870245477 0.895672435 0.895471268 1.127262959 0.844106905 0.867300049 1.066638252 1.120992417 0.954673903 1 16.58583858 2.227355403 24.97857742 1.054479596 0.921031402 0.308148504 0.085271628 243.1160745 541948.4842 0.032491468 0.024216943 168.7933774 -2.227355403 -0.133448194 VWDVIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VWDVIGR 7 0 J3KNF4;O14618;E9PP76 J3KNF4 CCS Copper chaperone for superoxide dismutase;Superoxide dismutase [Cu-Zn] 0 ; 121.29 0.010358 350320000 545860 553450 447400 509960 504830 490550 470290 524480 491430 505900 FALSE TRUE 524527.1877 537666.1479 528255.1324 536279.0967 521068.3154 500469.2571 476045.5497 513649.3047 435644.9266 471634.9424 1.112146579 1.140004905 1.12005088 1.137063963 1.104812788 1.061136935 1.00935174 1.089082378 0.923690947 1 18.84731108 2.227368691 0.70511501 0.986170865 1.133687511 0.6924562 0.037332715 0.417363266 0.401535411 0.03116908 0.02003731 168.7985418 -2.227368691 0.147516646 DVLSVAFSSDNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVLSVAFSSDNR 12 0 P63244;J3KPE3;D6RHH4;H0YAF8;D6R9L0;H0Y8W2;D6R9Z1;D6RFX4;E9PD14;D6RFZ9;D6RAU2;H0YAM7 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 277.7 1.54E-27 1132420000 590490 615300 477310 612630 564290 466920 713370 622450 682510 696060 FALSE TRUE 567412.998 597752.2464 563570.5347 644247.9077 582440.9003 476361.4423 722100.4355 609596.19 605034.3261 648915.2362 0.874402335 0.921156128 0.868480971 0.992807491 0.897560834 0.734088854 1.11278083 0.93940804 0.932378055 1 19.30767051 2.227421562 24.99999993 0.989900752 0.888431585 0.351191549 0.075845268 279.0996837 626394.3965 0.028171763 0.020997808 168.8190926 -2.227421562 -0.101469166 S(ph)SPELTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.75)S(0.25)PELTR;S(0.94)S(0.06)PELTR;S(0.772)S(0.228)PELTR 191.78 3.34E-05 0 1883310 1868700 1822440 1787230 1740150 1785490 2126520 2200210 2423550 2441970 TRUE FALSE 1809708.163 1815406.506 2151795.448 1879469.154 1796123.505 1821593.831 2152544.988 2154774.895 2148438.764 2276573.197 0.794926412 0.797429447 0.945190539 0.825569394 0.78895926 0.800147271 0.94551978 0.946499281 0.943716094 1 21.11843242 2.227537348 22.95622915 0.953301098 0.827900716 0.675965632 0.04521538 52.13695754 108574.3868 0.017628245 0.013168361 168.8641072 -2.227537348 -0.125400382 RPS(ph)LDSMENQVSVDAFK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSLDSMENQVSVDAFK 17 1 P07949-2;P07949 P07949-2 RET Proto-oncogene tyrosine-protein kinase receptor Ret;Soluble RET kinase fragment;Extracellular cell-membrane anchored RET cadherin 120 kDa fragment 1 RPS(1)LDSMENQVSVDAFK;RPS(1)LDSMENQVSVDAFK 213.37 4.48E-13 753470000 630550 918960 573890 1072310 720480 825690 1277820 1481460 1407750 1309190 TRUE FALSE 605907.4089 892752.1606 677604.6891 1127652.048 743654.8935 842386.0175 1293458.343 1450867.333 1247948.122 1220517.395 0.496434882 0.731453861 0.555178232 0.923913131 0.609294793 0.690187638 1.059762318 1.188731385 1.022474671 1 20.21906143 2.227638106 5.097920285 1.098333325 0.672569653 0.732798731 0.117983149 0.084974365 6.121595461 0.042335571 0.032460922 168.9032888 -2.227638106 -0.425763672 SASYKPVFVTEITDDLHFYVQDVETGTQLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASYKPVFVTEITDDLHFYVQDVETGTQLEK 31 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 363.23 5.12E-122 721810000 447950 407580 380500 391170 455420 455680 490190 467430 585430 582480 FALSE TRUE 430443.6188 395956.2175 449264.8142 411358.3306 470068.9979 464894.1618 496189.0919 457777.4072 518974.4407 543028.1108 0.792672811 0.729163389 0.827332518 0.75752677 0.865643948 0.856114357 0.913744762 0.843008673 0.955704558 1 19.05066736 2.22763961 0.240515502 1.027555221 0.701489705 0.775898174 0.038123198 1.217113827 0.219227282 0.086683566 0.143497836 168.9038736 -2.22763961 -0.326065516 VILKPDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VILKPDK 7 1 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 72.547 0.062018 0 1386500 1429500 1093400 1108700 1242200 1127100 1450400 1417200 1464800 1427300 FALSE TRUE 1332314.047 1388732.06 1291001.703 1165920.14 1282156.491 1149890.734 1468150.429 1387934.325 1298522.045 1330627.7 1.001267332 1.04366688 0.970220072 0.876218149 0.963572674 0.86417165 1.103351771 1.043067362 0.975871797 1 20.34367554 2.2276456 24.99933583 1.037586914 0.955046721 0.291879588 0.058601738 277.0297726 634493.6569 0.022965511 0.017124077 168.9062033 -2.2276456 -0.082540193 QLQPSRPGPGECTLDHGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLQPSRPGPGECTLDHGSK 19 1 Q96HA7-2;Q96HA7 Q96HA7-2 TONSL Tonsoku-like protein 0 66.874 0.015959 50013000 32183 42617 31587 39730 35810 41466 28884 31119 33590 36230 FALSE TRUE 30925.25278 41401.60489 37295.47355 41780.47006 36961.86117 42304.47093 29237.49103 30476.38178 29777.00402 33776.10983 0.915595459 1.225765936 1.104196834 1.236982893 1.094319664 1.252496843 0.865626361 0.902305858 0.881599574 1 15.04371555 2.227780175 24.999791 0.902655182 1.14315174 0.563128164 0.097242138 138.6483611 321522.5052 0.033636048 0.025088125 168.9585503 -2.227780175 0.240496558 DYDDMSPR ddPTM_BT-474_Pertuzumab_2h_R1 13 DYDDMSPR 8 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;;; 209.37 0.00011101 21981210000 19246660 19517040 16067200 17689100 18455480 18672820 18201770 19012610 20507240 20195830 FALSE TRUE 18494479.25 18960433.13 18970900.45 18602036.57 19049117.28 19050397.21 18424528.71 18619992.96 18179344.09 18827948.45 0.982288607 1.007036597 1.007592543 0.988001248 1.011746836 1.011814817 0.978573356 0.988954958 0.965550981 1 24.16637247 2.227827587 24.99938138 0.98292228 1.001809963 0.347612542 0.012165837 227.2227956 529244.1934 0.004351055 0.003247824 168.9769966 -2.227827587 0.018887683 GKEHDDIFDK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKEHDDIFDK 10 1 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 122.51 0.00029238 416650000 768580 821290 843680 986870 647780 741050 1012400 954840 1130600 1089400 FALSE TRUE 738543.0439 797867.6133 996151.7436 1037802.479 668616.432 756034.5387 1024790.054 935122.2203 1002259.028 1015613.968 0.727188742 0.785601261 0.980836987 1.021847387 0.658337177 0.744411324 1.009035014 0.920745726 0.986850378 1 19.95392071 2.227834168 24.99936124 0.968305384 0.827331425 0.34583323 0.106711998 302.7551295 705604.5497 0.043103889 0.032155456 168.9795574 -2.227834168 -0.140973959 EQLEEEEEAKHNLEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EQLEEEEEAKHNLEK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 341.5 1.12E-69 9221370000 4299120 3730700 3034490 2944130 3636730 3782700 3878680 4085020 4990250 4236180 FALSE TRUE 4131105.637 3624304.089 3582889.845 3096076.902 3753708.723 3859188.786 3926148.446 4000662.909 4423777.741 3949259.755 1.046045561 0.917717323 0.907230739 0.783963855 0.95048413 0.977192949 0.994147939 1.013015896 1.120153653 1 21.91315083 2.227924355 1.344267394 1.047313525 0.913964134 0.389782088 0.066910804 0.455069893 1.597704153 0.042432724 0.024367721 169.0146519 -2.227924355 -0.133349391 RKTS(ph)DANETEDHLESLICK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKTSDANETEDHLESLICK 19 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RKT(0.384)S(0.6)DANET(0.016)EDHLESLICK 161.66 1.52E-11 419350000 238550 226780 137510 153130 229560 228800 121570 127580 167410 133720 TRUE FALSE 229227.2023 220312.4564 162361.1159 161033.0577 236944.0059 233426.4928 123057.81 124945.4284 148406.3186 124663.0253 1.838774582 1.767263837 1.302399934 1.291746749 1.900675885 1.872459715 0.987123566 1.002265332 1.190459788 1 16.9276741 2.228144931 24.99978737 1.03848351 1.644638571 0.674466251 0.209850162 137.4599453 329929.757 0.085484268 0.063814185 169.1005154 -2.228144931 0.606155061 WDYLTQVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 WDYLTQVEK 9 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;; 163.94 0.00014572 1123120000 1131922 1086585 960920 1091893 1142077 1052601 1265209 1316429 1478448 1351785 FALSE TRUE 1087685.237 1055596.66 1134579.62 1148245.729 1178812.944 1073885.313 1280693.006 1289244.281 1310620.781 1260227.398 0.863086486 0.837623957 0.900297535 0.911141696 0.935397013 0.852136142 1.016239615 1.023025117 1.039987532 1 20.26525265 2.228254313 24.79450041 1.021674291 0.885614033 0.84635298 0.028484087 72.68314483 174856.8606 0.011290212 0.00843135 169.1431106 -2.228254313 -0.136060258 IEYDTFGELK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEYDTFGELK 10 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 140.75 0.0108 0 49521 56259 43099 58468 50374 44870 72166 81363 67616 70443 FALSE TRUE 47585.66457 54654.5484 50887.94803 61485.54049 51994.32546 45777.30214 73049.1891 79682.82562 59940.51515 65671.83287 0.724597784 0.832237293 0.774882409 0.93625437 0.79172947 0.697061436 1.112336688 1.213348587 0.912727916 1 16.0029871 2.228305005 24.99954997 1.093198601 0.800245082 0.641758737 0.096262754 118.9650463 289992.5421 0.035997587 0.026882186 169.1628545 -2.228305005 -0.292953518 RSNVSSPATPTASSSSS(ph)TTPTRK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSNVSSPATPTASSSSSTTPTRK 23 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RSNVSSPATPTAS(0.013)S(0.017)S(0.017)S(0.087)S(0.287)T(0.287)T(0.287)PT(0.004)RK 111.3 0.0005076 128310000 40953 38087 23570 34275 37129 31887 39382 40192 37474 42127 TRUE FALSE 39352.51148 37000.79605 27829.62331 36043.93686 38323.288 32531.77699 39863.9687 39362.02115 33220.10862 39273.70077 1.002006705 0.942126546 0.708607103 0.91776268 0.975800275 0.8283349 1.015029598 1.002248843 0.845861428 1 15.26127593 2.228308577 24.99951668 0.971611173 0.894009597 0.127616617 0.089085667 421.8672741 1028712.877 0.033823611 0.025260069 169.164246 -2.228308577 -0.077601576 TSVPS(ph)PEQPQPYR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSVPSPEQPQPYR 13 0 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 TSVPS(1)PEQPQPYR;TSVPS(1)PEQPQPYR;TSVPS(1)PEQPQPYR;TSVPS(1)PEQPQPYR 254.47 8.66E-24 1382250000 828840 922250 674180 849780 749020 773710 966030 1009110 1069250 1118460 TRUE FALSE 796448.0165 895948.333 796019.3231 893637.2476 773112.9085 789354.9463 977852.5641 988271.5259 947873.2227 1042705.708 0.763828193 0.859253312 0.763417057 0.857036881 0.741448812 0.757025631 0.937803022 0.947795258 0.909051533 1 19.9919006 2.22833741 24.61659789 0.944452853 0.793053898 0.763850494 0.043085872 81.72331537 196780.9219 0.015441547 0.011536239 169.1754772 -2.22833741 -0.151398954 LQLATLEAGPGAAGAGS(ph)E ddPTM_BT-474_Pertuzumab_2h_R1 2 LQLATLEAGPGAAGAGSE 18 0 C9JI98 C9JI98 TMEM238 Transmembrane protein 238 1 LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E 189.81 3.24E-14 67932000 89663 146623 81909 167992 106436 102071 165035 190587 151248 127850 TRUE FALSE 86158.87083 142441.4556 96711.77836 176662.0873 109859.6106 104134.9456 167054.7477 186651.3118 134078.9611 119190.6056 0.72286629 1.19507284 0.811404371 1.482181304 0.921713671 0.873684172 1.401576465 1.565990129 1.124912156 1 16.862911 2.228389871 24.98254481 1.349514333 1.019597275 0.194702995 0.250842545 262.0610944 643699.6076 0.090450043 0.067564291 169.1959142 -2.228389871 -0.329917058 LKVPEWVDTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKVPEWVDTVK 11 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 162.93 2.24E-05 6121900000 4099900 3694500 3296400 3373300 3689100 3562800 4051900 4340700 4498500 4232700 FALSE TRUE 3939671.375 3589136.477 3892132.808 3547396.417 3807763.252 3634842.257 4101488.364 4251063.028 3987849.139 3946015.459 0.998392281 0.90955966 0.986345048 0.898981885 0.964964099 0.921142427 1.039399974 1.077305214 1.010601499 1 21.91196518 2.228456781 24.84386446 1.042491682 0.945363951 0.567573059 0.035971676 113.7128907 279601.1411 0.012435351 0.009290467 169.2219835 -2.228456781 -0.097127731 EESGKPGAHVTVK ddPTM_BT-474_Pertuzumab_2h_R1 11 EESGKPGAHVTVK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;; 162.97 2.38E-05 92128620000 66285920 66819150 57605480 61989140 61137240 66730500 70429080 75035950 82264130 81060630 FALSE TRUE 63695392.96 64913533.26 68016071.66 65188406.94 63103774.85 68079836.43 71291012.15 73486431.41 72925850.84 75570321.33 0.84286254 0.858981835 0.90003682 0.862619158 0.83503383 0.9008806 0.943373151 0.972424493 0.965006494 1 26.17131642 2.228461698 1.886668692 0.97621715 0.862054992 0.886380339 0.018845672 0.111761297 0.797439246 0.009774879 0.006213982 169.2238993 -2.228461698 -0.114162158 DFSASYFSGEQEVT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFSASYFSGEQEVTPSR 17 0 P49454 P49454 CENPF Centromere protein F 1 DFSASYFSGEQEVT(0.974)PS(0.026)R 120.24 0.00090418 69352000 36633 40378 32100 33850 34239 38534 30246 32778 31479 37047 TRUE FALSE 35201.34186 39226.45897 37901.18406 35597.00256 35340.32853 39313.18388 30616.1596 32101.12285 27905.63589 34537.77369 1.019212824 1.135755284 1.097383531 1.030668707 1.023237017 1.1382663 0.886454346 0.929449684 0.807974369 1 15.07588747 2.228465936 24.99995141 0.902749002 1.073664343 0.657158181 0.059469538 119.0859881 294919.948 0.021198581 0.01583374 169.2255505 -2.228465936 0.170915341 EKIETELR ddPTM_BT-474_Pertuzumab_2h_R1 9 EKIETELR 8 1 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;;;; 134.68 0.00079016 1.03226E+11 47683873 48151598 40861793 45160875 46633367 47023761 51163233 55882737 56729076 54929280 FALSE TRUE 45820334.53 46778361.57 48246427.96 47491633.17 48133371.6 47974613.67 51789383.95 54728738.95 50289429.12 51208870.94 0.89477338 0.913481604 0.942149809 0.927410277 0.939942059 0.936841855 1.011336181 1.068735513 0.982045263 1 25.60989041 2.2284929 3.783216137 1.028067908 0.925533447 0.755822463 0.024832691 0.097216113 3.033527009 0.009677531 0.007288654 169.2360578 -2.2284929 -0.102534461 EDCCPGKPLNVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDCCPGKPLNVFR 13 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 95.346 0.0043213 958900000 442660 483380 379290 413440 427090 441120 420760 410690 522970 460970 FALSE TRUE 425360.3578 469594.4757 447836.1403 434777.6879 440827.7377 450039.7486 425909.3867 402209.108 463604.6381 429748.0913 0.989789987 1.092720329 1.042089888 1.011703593 1.025781723 1.047217562 0.991067547 0.935918311 1.078782309 1 18.71313171 2.228635174 23.77756957 0.989473833 1.036372944 0.108855416 0.041441016 169.208536 405353.8181 0.015206574 0.011379154 169.2915081 -2.228635174 0.046899111 AEMDQILHGLDK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEMDQILHGLDK 12 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 ;;; 161.76 6.45E-05 363760000 1097570 1164930 937480 1001630 1097970 1039730 1153500 1158740 1317100 1228490 FALSE TRUE 1054675.751 1131707.337 1106903.49 1053324.244 1133287.202 1060754.053 1167616.878 1134811.614 1167588.33 1145283.278 0.920886362 0.988146216 0.966488825 0.919706298 0.989525669 0.926193609 1.019500503 0.990856704 1.019475576 1 20.12727305 2.228667993 24.99997385 1.00545646 0.954395815 0.540102002 0.025055436 163.8685997 414114.4413 0.008755902 0.006544613 169.3043018 -2.228667993 -0.051060645 IVYLCITDDDFER ddPTM_BT-474_Pertuzumab_2h_R1 2 IVYLCITDDDFER 13 0 P51809;P51809-2 P51809 VAMP7 Vesicle-associated membrane protein 7 0 ; 162.36 9.44E-05 32881000 20161.2 25582 17887.5 23390 19781.7 20830.1 24049 25566 24897.1 25586 FALSE TRUE 19373.27801 24852.42641 21120.16916 24597.1607 20417.99635 21251.29889 24343.31886 25038.05317 22070.88559 23853.03743 0.812193335 1.041897766 0.885428919 1.031196164 0.85599146 0.890926321 1.020554255 1.049679867 0.925286167 1 14.54188537 2.228669193 24.98299533 1.008645563 0.925791645 0.211162499 0.073526389 295.533008 746428.9184 0.026043549 0.01946189 169.3047694 -2.228669193 -0.082853918 DKAVESLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DKAVESLR 8 1 P30153;C9J9C1;P30154-4;P30154;P30154-2;P30154-3;E9PNM7 P30153 PPP2R1A;PPP2R1B Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform;Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform 0 ;;;;; 140.16 0.0005964 7091590000 5002120 5160490 4224660 4731410 4573750 4542150 5391310 5513790 5821790 5741450 FALSE TRUE 4806631.62 5013317.878 4988150.039 4975598.637 4720868.823 4633995.385 5457290.465 5399928.31 5160924.806 5352576.478 0.898003352 0.936617702 0.931915697 0.92957077 0.881980639 0.86575043 1.019563286 1.008846549 0.964194501 1 22.35180207 2.228772931 24.99876735 1.000693659 0.909618206 0.760990726 0.024905002 103.3135867 263871.6469 0.009988721 0.00746715 169.3452154 -2.228772931 -0.091075452 EKDIQR ddPTM_BT-474_Pertuzumab_2h_R1 5 EKDIQR 6 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;;; 124.89 0.016563 4123800000 4919460 5899890 3961520 4998640 5293540 4617290 6114070 6084030 6435550 6774330 FALSE TRUE 4727202.064 5731630.914 4677454.788 5256620.409 5463811.522 4710654.767 6188895.818 5958392.654 5705013.344 6315498.595 0.748508133 0.907550026 0.740631118 0.832336565 0.865143336 0.745888024 0.979953637 0.943455622 0.903335383 1 22.59046521 2.228805149 24.99999955 0.952060722 0.8120833 0.631274861 0.056029377 131.453605 336869.0184 0.019507609 0.014584762 169.3577788 -2.228805149 -0.139977422 EDLAYMNHIMVS(ph)VSPPEEHAMPIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDLAYMNHIMVSVSPPEEHAMPIGR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 EDLAYMNHIMVS(0.583)VS(0.417)PPEEHAMPIGR 121.83 0.00020348 71530000 68374 70292 62241 71496 78873 72104 65097 66393 73042 72367 TRUE FALSE 65701.86849 68287.34098 73489.33324 75185.91713 81410.02168 73561.99228 65893.67656 65021.96135 64750.57838 67465.51863 0.973858496 1.012181369 1.089287309 1.114434731 1.206690815 1.090364289 0.976701549 0.963780649 0.959758106 1 16.04186271 2.228806762 8.596852485 0.971123332 1.085651271 0.437743437 0.058697889 0.143434756 79.82316415 0.024027464 0.018463272 169.3584078 -2.228806762 0.114527939 DYDHLFK ddPTM_BT-474_Pertuzumab_2h_R1 3 DYDHLFK 7 0 F5H157;Q15286-2;Q15286;F5H7F8 F5H157 RAB35 Ras-related protein Rab-35 0 ;; 105.39 0.0079373 1139680000 2771820 3981200 2844460 3974200 2844070 2932100 3918800 3834300 4159500 2987760 FALSE TRUE 2663494.21 3867660.074 3358517.197 4179308.938 2935552.094 2991389.071 3966759.447 3755120.365 3687330.998 2785396.354 0.956235261 1.38854927 1.20575917 1.500435991 1.053908213 1.073954544 1.424127464 1.348145789 1.323808367 1 21.4094512 2.228835543 24.99887419 1.312190888 1.212962717 0.020362356 0.183159694 626.3317631 1610010.093 0.066120151 0.049437353 169.3696315 -2.228835543 -0.099228172 AFHPDLEFVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AFHPDLEFVGK 11 0 O95864-3;O95864;O95864-4;O95864-2 O95864-3 FADS2 Fatty acid desaturase 2 0 103.35 0.0027462 792260000 532270 888020 521850 1153000 616890 619370 1078900 1155500 1078500 872730 FALSE TRUE 511468.2999 862694.5391 616159.9035 1212506.468 636732.8271 631894.0858 1092103.901 1131638.521 956073.2014 813619.2198 0.628633503 1.060317306 0.757307458 1.490262814 0.782593149 0.776645967 1.342278887 1.390869947 1.175086795 1 19.63399423 2.228839623 24.99921866 1.276644426 0.935352782 0.267791998 0.245365663 246.2333363 633226.9537 0.089392215 0.066839244 169.371223 -2.228839623 -0.341291644 SNS(ph)LPHSAVSNAGSK ddPTM_BT-474_Pertuzumab_2h_R1 3 SNSLPHSAVSNAGSK 15 0 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.178)NS(0.822)LPHSAVSNAGSK;S(0.196)NS(0.804)LPHSAVSNAGSK;S(0.029)NS(0.966)LPHS(0.006)AVSNAGSK 221.25 1.01E-12 1666360000 1467170 1386300 1164960 1406940 1438500 1347700 1563730 1747770 1666500 1540650 TRUE FALSE 1409831.374 1346764.081 1375494.186 1479552.342 1484770.659 1374951.417 1582867.396 1711677.939 1477325.907 1436300.403 0.981571384 0.937661842 0.957664694 1.030113435 1.0337466 0.9572868 1.102044803 1.191726978 1.028563317 1 20.45392609 2.228880679 23.84438229 1.106953295 0.984241858 0.378354564 0.057410227 93.97000213 231471.3486 0.021655076 0.016212799 169.3872349 -2.228880679 -0.122711437 DSEEAEIIRK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSEEAEIIRK 10 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 86.014 0.022202 376690000 457860 450760 398230 412310 416550 423650 461360 485060 505390 489270 FALSE TRUE 439966.325 437904.7661 470199.0196 433589.3685 429948.7091 432216.4933 467006.2617 475043.3415 448020.246 456131.3071 0.964560683 0.960041022 1.030841366 0.950580155 0.942598551 0.94757033 1.023841719 1.041461821 0.982217706 1 18.79908967 2.228897575 24.99850152 1.018438522 0.966938064 0.390967387 0.027537522 193.6622875 501005.0825 0.010706649 0.008003975 169.3938252 -2.228897575 -0.051500458 SVTLLEVCGS(ph)WPEGFGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVTLLEVCGSWPEGFGLR 18 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;K7EIE2;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 SVTLLEVCGS(1)WPEGFGLR;SVTLLEVCGS(1)WPEGFGLR 360.07 6.71E-91 405980000 291690 318740 239710 281620 312660 314030 261380 283770 314700 304070 TRUE FALSE 280290.4323 309649.8473 283030.9293 296154.4419 322716.9929 320379.9018 264578.8466 277910.0503 278976.5753 283475.0681 0.988765729 1.092335384 0.998433235 1.044728356 1.138431662 1.130187229 0.933340799 0.980368581 0.984130905 1 18.11286233 2.228960427 24.99997916 0.972222335 1.066026068 0.457678789 0.048512388 187.3477686 487870.9503 0.018789217 0.014052811 169.418342 -2.228960427 0.093803733 GETSCHQCDPDKYSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GETSCHQCDPDKYSEK 16 1 Q6UXG2-2;Q6UXG2-4;Q6UXG2 Q6UXG2-2 KIAA1324 UPF0577 protein KIAA1324 0 170.91 3.07E-09 308620000 162080 264390 171230 340430 149570 170200 317240 300480 307500 285270 FALSE TRUE 155745.7344 256849.8561 202175.07 357999.6331 154381.0549 173641.5606 321122.478 294274.983 272593.8891 265948.4088 0.585623863 0.965788279 0.760204097 1.346124366 0.580492493 0.652914456 1.20746155 1.106511539 1.024987855 1 18.02078688 2.228961815 24.99913284 1.099063751 0.83300235 0.267214963 0.216961165 282.3764917 735416.1378 0.080544876 0.060243644 169.4188833 -2.228961815 -0.266061402 QALDS(ph)EEEEEDVAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 QALDSEEEEEDVAAK 15 0 Q8NC44;H7C3D5 Q8NC44 FAM134A Protein FAM134A 1 QALDS(1)EEEEEDVAAK;QALDS(1)EEEEEDVAAK 250.26 9.71E-19 1294680000 1107910 1131910 993140 1171430 992440 1072620 1201340 1230440 1388480 1339410 TRUE FALSE 1064611.652 1099629.035 1172622.49 1231887.643 1024362.734 1094309.111 1216042.358 1205030.984 1230865.571 1248690.568 0.852582441 0.880625724 0.939081723 0.986543564 0.820349541 0.876365322 0.973854043 0.965035706 0.985725049 1 20.25198458 2.228987604 24.62464416 0.976668651 0.895147523 0.495771859 0.043615648 163.3062089 420068.4636 0.017196488 0.012869289 169.4289439 -2.228987604 -0.081521128 VEPSSQSPGRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 VEPSSQSPGRSPR 13 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 VEPSSQSPGRS(1)PR;VEPSSQSPGRS(1)PR;VEPSSQS(0.001)PGRS(0.999)PR;VEPSSQSPGRS(1)PR 149.22 2.64E-05 3359150000 2905160 3351240 2665380 2980060 2922780 3201260 2732030 3039460 3067160 3089500 TRUE FALSE 2791623.135 3255665.916 3147073.457 3133861.254 3016793.873 3265991.671 2765465.4 2976694.089 2718988.855 2880245.413 0.969230998 1.130343234 1.092640732 1.088053552 1.04740862 1.13392826 0.960149225 1.03348627 0.94401291 1 21.45776031 2.228995882 24.99878069 0.991195388 1.079239199 0.458272743 0.049021329 181.4956393 474360.8623 0.017169757 0.012843981 169.4321736 -2.228995882 0.088043811 GDAVANHVPAGWPDQS(ph)LAESDSEDPSGKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDAVANHVPAGWPDQSLAESDSEDPSGKPR 30 1 Q9NYQ6;A0A6I8PL36;A0A6I8PRU0 Q9NYQ6 CELSR1 Cadherin EGF LAG seven-pass G-type receptor 1 1 GDAVANHVPAGWPDQS(0.492)LAES(0.492)DS(0.014)EDPS(0.001)GKPR 103.17 0.00022372 247880000 104550 160740 87205 177080 98635 119520 165040 207550 166340 118040 TRUE FALSE 100464.0704 156155.8526 102964.8834 186219.12 101807.6844 121936.7763 167059.8089 203264.02 147457.7806 110045.0457 0.912935878 1.419017564 0.935661235 1.692208122 0.925145551 1.10806239 1.518103863 1.847098329 1.339976549 1 16.74773467 2.229020576 23.17218648 1.535167009 1.179596583 0.1084122 0.307028211 116.2051066 282250.045 0.108690169 0.081471092 169.4418078 -2.229020576 -0.355570427 KLS(ph)GDQPAAR ddPTM_BT-474_Pertuzumab_2h_R1 9 KLSGDQPAAR 10 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR 209.25 6.06E-08 24800730000 17153360 16528760 14256500 15694990 15838920 15967650 16646780 18039890 17807020 17192050 TRUE FALSE 16482987.73 16057375.95 16832966.68 16505010.31 16348393.25 16290526.82 16850508.27 17667359.97 15785641.74 16027617.14 1.028411621 1.001856721 1.050247616 1.029785661 1.020013961 1.016403541 1.051342076 1.102307337 0.984902597 1 23.93405662 2.22902725 24.81343853 1.049792536 1.024639151 0 0.032794779 407.8675897 1061588.43 0.012140058 0.009086944 169.4444114 -2.22902725 -0.025153385 MREDYDS(ph)VEQDGDEPGPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 MREDYDS(1)VEQDGDEPGPQR;MREDYDS(1)VEQDGDEPGPQR 256.12 3.61E-31 962440000 644650 686960 513510 640870 677200 673030 572470 625270 632770 617330 TRUE FALSE 619456.3653 667368.5734 606312.68 673945.3775 698982.753 686639.1277 579476.0591 612357.956 560940.6024 575517.6892 1.076346352 1.159596978 1.053508331 1.17102461 1.214528704 1.193080839 1.006877929 1.064012397 0.974671349 1 19.13450075 2.229118492 24.99980163 1.021439616 1.145587095 0.620792922 0.050789911 147.3311685 390083.92 0.019793833 0.014810598 169.4800142 -2.229118492 0.124147479 ANGQENGHVK ddPTM_BT-474_Pertuzumab_2h_R1 6 ANGQENGHVK 10 0 P49006;P29966 P49006;P29966 MARCKSL1;MARCKS MARCKS-related protein;Myristoylated alanine-rich C-kinase substrate 0 ;;;;; 178.46 2.21E-06 2850270000 2065410 2233630 1863580 2130150 1833470 1846230 2371020 2445370 2296250 2120410 FALSE TRUE 1984691.494 2169929.059 2200370.361 2240087.297 1892445.228 1883562.036 2400037.252 2394872.255 2035589.327 1976792.742 1.003995741 1.097701855 1.113101194 1.133192797 0.957331129 0.952837389 1.214106669 1.211493853 1.029743424 1 20.91473019 2.229124173 24.99871237 1.142987109 1.048900326 0.099512511 0.087326191 333.6141083 883793.3016 0.033726461 0.025230594 169.4822314 -2.229124173 -0.094086783 TFPLAHS(ph)PQAECEDQLDAQER ddPTM_BT-474_Pertuzumab_2h_R1 1 TFPLAHSPQAECEDQLDAQER 21 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A0G2JQF5;A0A3B3IT55;A0A0G2JQF4;Q7Z3B3-4;Q7Z3B3-2 A0A1W2PRB5;Q7Z3B3-4 KANSL1 KAT8 regulatory NSL complex subunit 1 1 T(0.009)FPLAHS(0.991)PQAECEDQLDAQER 70.094 0.0053657 0 133440 91087 77452 93677 109490 106000 86740 86041 107750 98401 TRUE FALSE 128225.0173 88489.28794 91449.29931 98511.6812 113011.8453 108143.3926 87801.55007 84264.22328 95518.67172 91736.21262 1.397757915 0.964605856 0.996872409 1.073858168 1.231921856 1.178851726 0.957108949 0.918549184 1.041231908 1 16.48520373 2.229130354 24.9629726 0.966114071 1.127221004 0.299347643 0.119262202 253.3133078 670543.6733 0.044888524 0.033598407 169.4846433 -2.229130354 0.161106933 TTWGDGGENS(ph)PCNVVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TTWGDGGENSPCNVVSK 17 0 H3BV99;H3BP15;H3BQY9;H3BM38;O00161 H3BV99;H3BM38 SNAP23 Synaptosomal-associated protein;Synaptosomal-associated protein 23 1 TTWGDGGENS(1)PCNVVSK;TTWGDGGENS(1)PCNVVSK 303.76 1.37E-46 717210000 470080 815920 411430 909220 440230 472620 912890 1047220 763060 552300 TRUE FALSE 451708.7539 792650.7605 485784.5532 956144.9532 454390.3978 482176.7002 924062.2209 1025594.541 676440.6278 514892.2291 0.877287961 1.539449842 0.943468411 1.856980741 0.882496127 0.936461405 1.794671135 1.991862536 1.313751868 1 18.97391097 2.229150213 24.99838203 1.655560647 1.196855834 0.126371628 0.395617963 287.0472955 762524.5485 0.142641161 0.106746001 169.4923936 -2.229150213 -0.458704813 ERPS(ph)SWSSLDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPSSWSSLDQK 12 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 ERPS(0.868)S(0.132)WSSLDQK;ERPS(0.498)S(0.498)WS(0.003)S(0.001)LDQK 106.6 0.0011532 564930000 497210 457680 371920 364500 468160 403800 310460 265100 365280 273630 TRUE FALSE 477778.4835 444627.4145 439134.2173 383311.8887 483218.7916 411965.1127 314259.5023 259625.5924 323814.9458 255096.7964 1.872930159 1.742975297 1.721441522 1.502613495 1.894256605 1.614936442 1.231922575 1.017753245 1.269380684 1 17.96068526 2.229173654 3.032878469 1.101873838 1.733919907 0.856274126 0.121178413 0.086362358 1.644950885 0.048030735 0.03501726 169.5015421 -2.229173654 0.632046069 QFLEVELDQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QFLEVELDQAR 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 107.85 0.004984 79668000 38351 47945 44780 48578 44643 47504 43504 45645 44941 54171 FALSE TRUE 36852.20052 46577.65554 52872.74213 51085.1164 46078.98264 48464.56343 44036.41497 44702.4148 39839.48609 50501.94992 0.729718369 0.922294201 1.046944568 1.011547405 0.912419871 0.959657271 0.871974548 0.885162155 0.788870255 1 15.62405147 2.229179522 24.66665524 0.877636665 0.93822505 0.044437267 0.092190636 447.3374002 1176218.66 0.034720492 0.025994623 169.5038326 -2.229179522 0.060588385 ASTAPGAEAS(ph)PSPCITER ddPTM_BT-474_Pertuzumab_2h_R1 1 ASTAPGAEASPSPCITER 18 0 Q66PJ3 Q66PJ3 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 ASTAPGAEAS(1)PSPCITER 367.76 1.46E-77 0 126410 129850 131750 124680 129060 128500 147240 169340 145030 150340 TRUE FALSE 121469.7574 126146.8051 155560.1558 131114.7497 133211.3321 131098.358 149041.9672 165843.0698 128566.8024 140157.3379 0.866667128 0.900037109 1.109896621 0.935482592 0.950441369 0.93536564 1.063390397 1.183263555 0.917303399 1 17.09668775 2.229196274 20.6636981 1.070123665 0.954069499 0.177199995 0.087559451 31.34439486 69160.99642 0.032864774 0.024724059 169.5103708 -2.229196274 -0.116054167 AY(ph)DHLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AYDHLFK 7 0 P51153 P51153 RAB13 Ras-related protein Rab-13 1 AY(1)DHLFK 81.297 0.049937 0 75077 95864 71843 108420 80329 75405 128790 139330 137350 129610 TRUE FALSE 72142.90784 93130.05258 84826.62824 114015.5692 82912.85524 76929.74076 130366.1705 136452.7868 121758.6038 120831.3993 0.597054311 0.770743806 0.702024712 0.943592228 0.686186337 0.636670114 1.078909715 1.129282518 1.00767354 1 16.88263588 2.229253004 24.99874423 1.07216141 0.732334618 0.74546005 0.094488212 95.64185519 256876.6225 0.035414137 0.02650972 169.5325145 -2.229253004 -0.339826792 FKFPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 FKFPGR 6 1 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 79.033 0.062213 3239000000 3906600 3960000 3497800 3469900 3418500 3475500 4264000 4433000 4548200 4431000 FALSE TRUE 3753925.753 3847064.677 4129930.268 3648981.955 3528459.157 3545776.991 4316184.108 4341457.001 4031907.404 4130884.423 0.908746256 0.931293225 0.999769019 0.883341576 0.854165548 0.85835783 1.044857146 1.05097518 0.976039751 1 21.97801927 2.229264375 24.99930828 1.026105932 0.90798135 0.609716733 0.043695541 138.5442763 372568.2546 0.017829011 0.013346885 169.5369534 -2.229264375 -0.118124582 KPGDLSDELR ddPTM_BT-474_Pertuzumab_2h_R1 5 KPGDLSDELR 10 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;;; 138.45 0.00010327 4608640000 9241930 9406700 7449900 9380010 8775310 9017850 9795710 10560010 10601340 10714280 FALSE TRUE 8880745.158 9138430.126 8796262.652 9864113.44 9057575.816 9200197.106 9915592.829 10341942.1 9397920.328 9988592.272 0.889088764 0.91488669 0.880630865 0.9875379 0.906792025 0.921070443 0.992691719 1.035375338 0.940865346 1 23.25184994 2.229320578 5.279115431 1.000164382 0.917365558 0.530552124 0.034576378 0.127742946 10.39625232 0.012719081 0.009780459 169.5588949 -2.229320578 -0.082798825 DSSSLSSCTSGILEERS(ph)PAFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DSSSLSSCTSGILEERSPAFR 21 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DSSSLSSCTSGILEERS(1)PAFR;DSSSLSSCTSGILEERS(1)PAFR;DSSSLSSCTSGILEERS(1)PAFR;DSSSLSSCTSGILEERS(1)PAFR 266.19 3.42E-37 660000000 207450 218077 169411 196216 171834 219093 152864 189326 154214 194929 TRUE FALSE 199342.6247 211857.6575 200027.3362 206342.7313 177361.1967 223523.2106 154734.7954 185416.3519 136708.2732 181726.2852 1.096938863 1.165806351 1.100706681 1.135458919 0.975979873 1.229999338 0.851471735 1.02030563 0.752275727 1 17.47140758 2.229397309 24.9998948 0.91776136 1.113301 0.55592188 0.092308246 149.2565567 407207.6018 0.032111719 0.024046674 169.5888554 -2.229397309 0.19553964 AS(ph)PVPAPSSGLHAAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPVPAPSSGLHAAVR 16 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 AS(0.996)PVPAPS(0.001)S(0.003)GLHAAVR;AS(0.999)PVPAPS(0.001)SGLHAAVR 166.3 7.05E-09 628870000 164527 189077 157188 209679 157503 170013 203131 227053 195214 198247 TRUE FALSE 158097.1029 183684.7091 185595.3682 220500.5583 162569.227 173450.7793 205616.9779 222364.2762 173054.1251 184819.5541 0.855413291 0.993859713 1.004197684 1.193058599 0.879610536 0.938487165 1.112528265 1.203142586 0.936340995 1 17.49575788 2.229461631 24.98746084 1.094296885 0.984754885 0.100148177 0.109452451 340.9162953 936210.0724 0.041424487 0.031029657 169.6139745 -2.229461631 -0.109542001 EFPGFLENQKDPLAVDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFPGFLENQKDPLAVDK 17 1 P60903 P60903 S100A10 Protein S100-A10 0 167.28 2.04E-09 535760000 299830 336180 222560 349170 215650 231650 391760 394730 383210 329370 FALSE TRUE 288112.3121 326592.4756 262781.5428 367190.7055 222586.5781 236334.1217 396554.4761 386578.6876 339709.6073 307061.4765 0.938288695 1.063606152 0.855794565 1.195821468 0.724892554 0.769663861 1.291449779 1.25896186 1.106324412 1 18.228168 2.229574344 24.99879253 1.197381278 0.931105294 0.37485093 0.148940722 187.3883642 521289.0891 0.055530018 0.041604707 169.6580003 -2.229574344 -0.266275983 ENVEYIEREES(ph)DGEYDEFGR ddPTM_BT-474_Pertuzumab_2h_R1 8 ENVEYIEREESDGEYDEFGR 20 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(0.999)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR 280.08 6.53E-45 19490980000 4000635 4467649 2856668 3624983 4010776 4020666 3271724 3559525 3724296 3203173 TRUE FALSE 3844285.761 4340236.025 3372931.454 3812068.807 4139786.253 4101966.621 3311764.337 3486019.565 3301529.532 2986219.24 1.287342105 1.453421761 1.129498936 1.276553562 1.386296826 1.373632105 1.109015806 1.167368932 1.10558846 1 21.50988866 2.229651784 24.9682541 1.115632079 1.316636681 0.592374237 0.089715487 147.2396623 412656.6299 0.033615534 0.025191468 169.688255 -2.229651784 0.201004602 RSAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_BT-474_Pertuzumab_2h_R1 4 RSASPDDDLGSSNWEAADLGNEER 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.387)AS(0.613)PDDDLGSSNWEAADLGNEER;RS(0.058)AS(0.942)PDDDLGSSNWEAADLGNEER;RS(0.007)AS(0.993)PDDDLGSSNWEAADLGNEER;RS(0.006)AS(0.994)PDDDLGSSNWEAADLGNEER 355.96 2.40E-102 5447900000 993090 1010860 777630 887680 932920 983960 815518 856560 988730 902680 TRUE FALSE 954278.9449 982031.2625 918165.0393 933493.2712 962928.2191 1003856.345 825498.5532 838871.7367 876493.5155 841540.6796 1.133966507 1.166944494 1.091052473 1.10926696 1.144244411 1.192879168 0.980937194 0.996828504 1.041534339 1 19.68267349 2.229773107 24.99999389 1.002888546 1.137571383 0.829557895 0.029941363 76.24655515 216915.7338 0.011558861 0.008667927 169.7356652 -2.229773107 0.134682836 VCDGAIR ddPTM_BT-474_Pertuzumab_2h_R1 3 VCDGAIR 7 0 P42345 P42345 MTOR Serine/threonine-protein kinase mTOR 0 ;; 91.26 0.038468 48872000 11850.7 11962.4 11203.6 11497.3 12426.9 11399.9 10565.9 9508 11507.5 11903.4 FALSE TRUE 11387.56154 11621.24406 13228.33974 12090.67703 12826.62252 11630.41379 10695.20864 9311.656477 10201.21684 11097.17212 1.026167876 1.047225721 1.19204601 1.089527756 1.155846047 1.048052032 0.963777847 0.839101744 0.91926274 1 13.43790446 2.230027891 2.743964 0.902168686 1.102824352 0.649900468 0.059237559 0.146234669 2.262178727 0.024912178 0.01777827 169.8352721 -2.230027891 0.200655666 ALQAPHSPSKT(ph)DGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALQAPHSPSKTDGK 14 1 F2Z2Z8;Q5T173;Q96AQ6-3;Q96AQ6-2;Q96AQ6 F2Z2Z8 PBXIP1 Pre-B-cell leukemia transcription factor-interacting protein 1 1 ALQAPHS(0.219)PS(0.219)KT(0.562)DGK 103.13 0.0016617 723590000 751640 926000 586280 892860 784930 727590 916630 988110 922610 700490 TRUE FALSE 722265.0778 899591.3866 692233.8377 938940.6116 810177.9863 742302.3683 927847.9921 967705.1832 817879.1807 653045.1884 1.105995558 1.377533137 1.060009093 1.437788117 1.240615505 1.136678413 1.420802126 1.481834949 1.252408249 1 19.3168233 2.230032274 24.99553825 1.348580299 1.235991147 0 0.164996733 450.0145791 1318927.347 0.058194723 0.043652251 169.8369861 -2.230032274 -0.112589152 QVVSVVQDEEVGLPFEASPES(ph)PPPASPDGVTEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEAS(0.044)PES(0.955)PPPAS(0.001)PDGVTEIR;QVVSVVQDEEVGLPFEAS(0.002)PES(0.998)PPPASPDGVTEIR;QVVSVVQDEEVGLPFEAS(0.015)PES(0.949)PPPAS(0.036)PDGVTEIR;QVVSVVQDEEVGLPFEAS(0.015)PES(0.975)PPPAS(0.009)PDGVTEIR 251.1 1.30E-48 1469985000 454345 486209 366365 476231 454213 465375 419867 436820 455819 481789 TRUE FALSE 436588.6951 472342.7954 432575.3052 500809.339 468823.1737 474785.2014 425005.4579 427799.5144 404076.3381 449157.0019 0.97201801 1.051620688 0.963082627 1.114998401 1.043784627 1.057058444 0.946229172 0.952449839 0.899632726 1 18.7768603 2.230040233 24.97323982 0.946369576 1.035507943 0.440981007 0.046352159 161.1941245 472455.9829 0.016657892 0.012497378 169.8400983 -2.230040233 0.089138367 IKLPSVTSFILDTEAVAWDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKLPSVTSFILDTEAVAWDR 20 1 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ; 206.86 6.60E-22 197680000 372650 385180 294310 305410 335790 359490 299060 314500 341620 344440 FALSE TRUE 358086.426 374195.0435 347498.3639 321172.2467 346590.9903 366759.1341 302719.9857 308005.4651 302840.7298 321110.772 1.115149217 1.165314515 1.082175978 1.000191444 1.079350245 1.142157679 0.942727595 0.959187582 0.943103615 1 18.29271154 2.230061825 24.99990075 0.957456339 1.094547702 0.697739806 0.04384303 111.5646093 328173.9327 0.01758608 0.01319514 169.8485426 -2.230061825 0.137091364 ERPSQPEGLRK ddPTM_BT-474_Pertuzumab_2h_R1 3 ERPSQPEGLRK 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;; 147.39 1.99E-05 2011810000 1699330 1703580 1260050 1543020 1500050 1503700 1741230 1814300 1886870 1970760 FALSE TRUE 1632918.305 1654995.566 1487769.065 1622655.447 1548300.471 1534105.844 1762539.694 1776834.071 1672680.428 1837278.67 0.888770077 0.900786361 0.809767777 0.883184175 0.842714007 0.83498811 0.959320827 0.967101017 0.910411934 1 20.80913903 2.230134616 24.99208034 0.957708189 0.859867447 0.690161571 0.032546814 104.4695146 309861.1415 0.0118612 0.008903738 169.8770129 -2.230134616 -0.097840742 DQSCKPCAEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQSCKPCAEGR 11 1 Q6UXG2-2;Q6UXG2-4;Q6UXG2;Q6UXG2-3;E9PB18;E9PS21;E9PLY8;E9PLQ2 Q6UXG2-2 KIAA1324 UPF0577 protein KIAA1324 0 74.987 0.035861 162670000 75106 108030 70797 125770 76150 74828 125330 125930 111720 108020 FALSE TRUE 72170.77449 104949.0902 83591.59277 132261.0048 78599.43391 76341.07343 126863.826 123329.5015 99038.01397 100703.7092 0.716664511 1.042157146 0.830074616 1.313367758 0.780501876 0.758076083 1.259773121 1.224676851 0.983459445 1 16.6197573 2.230147596 24.99985663 1.149664776 0.922210329 0.231544434 0.182462417 254.949016 757591.7968 0.067170148 0.050416745 169.8820901 -2.230147596 -0.227454447 GILTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GILTLK 6 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38;P0CG39 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ; 159.65 0.021057 2896000000 5828200 6224400 5479300 5920600 5819100 5831200 6498600 7008100 6790700 7047200 FALSE TRUE 5600427.501 6046886.206 6469531.396 6226162.876 6006276.636 5949110.859 6578131.811 6863380.286 6019848.205 6569886.867 0.852438956 0.920394267 0.984724932 0.947681901 0.9142131 0.905511918 1.00125496 1.044672523 0.916278823 1 22.6474371 2.230169996 24.92909184 0.999923427 0.924632246 0.373359118 0.043413221 183.2125294 544331.7566 0.016549731 0.01242392 169.8908526 -2.230169996 -0.075291182 LQELNAHIVVSDPEDITDCPRT(ph)PDTPNNDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQELNAHIVVSDPEDITDCPRTPDTPNNDPR 31 1 Q16513-3;Q16513-2;Q16513;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 LQELNAHIVVSDPEDIT(0.155)DCPRT(0.814)PDT(0.031)PNNDPR 75.717 0.0044943 175800000 41221 46857 37957 45774 37773 47675 28268 32992 29757 29528 TRUE FALSE 39610.03775 45520.68424 44816.67425 48136.40163 38988.00285 48639.02116 28613.95224 32310.70367 26379.11011 27528.04226 1.438897738 1.65361139 1.628037106 1.748631493 1.416301329 1.766889948 1.03944741 1.173737797 0.958263209 1 14.74861439 2.230173169 24.9999315 1.069172263 1.609258567 0.843795631 0.119059182 66.84608399 199242.2676 0.041819505 0.031390604 169.8920937 -2.230173169 0.540086303 SRDSFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDSFLK 7 1 P46778;M0R181 P46778 RPL21 60S ribosomal protein L21 0 81.296 0.025158 213070000 256300 357340 222880 278600 297220 270650 371850 400210 387030 450040 FALSE TRUE 246283.5126 347149.0131 263159.3739 292978.5794 306780.3512 276122.7284 376400.8115 391945.5236 343095.977 419558.3899 0.587006525 0.827415257 0.62722944 0.698302278 0.731198228 0.658127057 0.897135704 0.93418588 0.817755014 1 18.67851208 2.230268789 23.91588053 0.909375996 0.694180976 0.690947544 0.073334756 58.42751387 168518.5012 0.025089051 0.018861249 169.9295036 -2.230268789 -0.21519502 AS(ph)PSKPASAPASR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPSKPASAPASR 13 1 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 AS(0.964)PS(0.036)KPASAPASR 152.88 0.00011953 32203000 69725 63021 58691 62116 62312 62781 70583 76347 77880 73410 TRUE FALSE 67000.06991 61223.70278 69297.76927 65321.8142 64316.32207 64050.47483 71446.81587 74770.40777 69039.3889 68437.87531 0.978991087 0.894588011 1.012564592 0.954468763 0.939776721 0.935892217 1.043966014 1.092529647 1.008789191 1 16.06250735 2.230309565 23.91441837 1.049225886 0.952283738 0.533841182 0.037505919 69.83426637 202401.27 0.013540557 0.010180793 169.9454591 -2.230309565 -0.096942148 AWKPSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AWKPSSK 7 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 72.547 0.046793 1618170000 2049200 1955710 1797380 1830960 1840660 1758480 2392100 2357600 2605200 2775300 FALSE TRUE 1969114.998 1899935.066 2122206.549 1925456.065 1899866.501 1794037.67 2421375.235 2308914.736 2309468.618 2587326.459 0.761061671 0.734323672 0.820231456 0.744187522 0.734297171 0.693394397 0.93585996 0.892394049 0.892608124 1 21.30303067 2.230341837 24.9999882 0.918678713 0.749796702 0.822789157 0.041302804 76.7184639 233361.2449 0.015203254 0.011416936 169.9580883 -2.230341837 -0.168882011 NS(ph)PGSQVASNPR ddPTM_BT-474_Pertuzumab_2h_R1 4 NSPGSQVASNPR 12 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 NS(0.74)PGS(0.26)QVASNPR;NS(1)PGSQVASNPR;NS(0.999)PGS(0.001)QVASNPR;NS(1)PGSQVASNPR 285.04 2.44E-28 3968740000 1347800 1338020 1196310 1232790 1107440 1203700 1413890 1445080 1553610 1494740 TRUE FALSE 1295126.486 1299860.98 1412509.829 1296414.44 1143061.813 1228039.639 1431193.609 1415238.593 1377250.706 1393499.928 0.929405492 0.932803047 1.013641838 0.93032975 0.820281214 0.881262793 1.027049646 1.015600047 0.988339273 1 20.4102815 2.23034541 24.98599581 1.010392288 0.919101283 0.473765285 0.046318464 178.1878215 541941.4459 0.019291086 0.01448884 169.9594866 -2.23034541 -0.091291006 SDYLNTFEFMDK ddPTM_BT-474_Pertuzumab_2h_R1 5 SDYLNTFEFMDK 12 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;; 226.04 3.78E-11 842610000 577459 562164 473841 522862 553461 508661 645043 655818 683970 721234 FALSE TRUE 554891.2639 546131.6331 559474.6092 549846.9705 571263.5757 518946.4739 652937.2292 642275.1291 606328.593 672384.1788 0.825259251 0.812231534 0.832075809 0.817757151 0.84960889 0.771800542 0.971077622 0.955220467 0.901759161 1 19.35892625 2.230347528 24.99999975 0.954125863 0.819903312 0.843629603 0.029277808 64.87834553 197483.053 0.010247591 0.007697238 169.9603151 -2.230347528 -0.13422255 TQEQCVHNETK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQEQCVHNETK 11 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ; 104.17 0.0026353 324240000 375470 395300 347710 423910 292640 372760 408510 415920 506600 415400 FALSE TRUE 360796.2173 384026.431 410548.9318 445788.0459 302053.0314 380297.4626 413509.4676 407331.1067 449092.8918 387264.588 0.931653005 0.991638386 1.060125156 1.151120086 0.779965534 0.982009392 1.067769893 1.051816043 1.159653905 1 18.56296006 2.230391768 9.023606422 1.071626783 0.985071554 0.165549495 0.095637114 0.27729713 200.1779272 0.035822691 0.027600274 169.9776294 -2.230391768 -0.086555229 DKQVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKQVYR 6 1 P63092-4;P63092;P63092-3;Q5JWD1;A2A2R6;P63092-2 P63092-4;P63092-2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short 0 ; 100.74 0.034032 277490000 400460 498720 311030 462570 329160 349740 497580 499700 483980 439010 FALSE TRUE 384809.5805 484496.9939 367240.0398 486443.2931 339747.7303 356811.9824 503669.5329 489381.0204 429040.6194 409275.4617 0.94022148 1.183791943 0.897293081 1.188547418 0.830119961 0.871813768 1.230637016 1.195725291 1.048293044 1 18.64271265 2.230447397 24.99997443 1.144899831 0.992505239 0.19082015 0.129622718 263.0218803 810465.452 0.047443748 0.035646998 169.9994034 -2.230447397 -0.152394592 T(ph)SPYILR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.753)S(0.247)PYILR;T(0.517)S(0.483)PYILR;T(0.793)S(0.207)PYILR 158.56 0.015829 806120000 1127660 1064970 1090830 1057020 1021560 1055800 1227510 1388530 1128330 1341420 TRUE FALSE 1083589.801 1034598.098 1287967.246 1111572.929 1054419.405 1077148.999 1242532.635 1359856.37 1000246.709 1250564.429 0.866480587 0.827304915 1.029908749 0.888856986 0.843154804 0.861330272 0.993577465 1.087394091 0.799836207 1 20.25414796 2.230477378 24.88270538 0.989835543 0.888197017 0.174516929 0.085292125 249.6158864 768387.7417 0.031840235 0.023926089 170.0111392 -2.230477378 -0.101638526 RQS(ph)PS(ph)PSTRPIR ddPTM_BT-474_Pertuzumab_2h_R1 4 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(0.995)PS(0.906)PS(0.085)T(0.015)RPIR;RQS(0.987)PS(0.691)PS(0.311)T(0.01)RPIR;RQS(1)PS(0.995)PS(0.005)TRPIR;RQS(1)PS(0.577)PS(0.235)T(0.189)RPIR 97.417 0.0027007 3401630000 326347 349987 277112 314889.5 332213 337235 290083.3 306138 320573 326150 TRUE FALSE 313592.9984 340005.7134 327192.3027 331140.9848 342898.9329 344054.1228 293633.4262 299816.1433 284182.897 304059.57 1.031353818 1.118220727 1.076079607 1.089066149 1.127736032 1.131535254 0.965710194 0.986044094 0.934629017 1 18.21399447 2.23054253 24.99992613 0.971936774 1.09695806 0.790057665 0.031327758 76.47948443 238456.8091 0.011402498 0.0085678 170.0366459 -2.23054253 0.125021285 S(ph)PSGVLSEPSQESK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSGVLSEPSQESK 14 0 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 S(0.999)PS(0.001)GVLSEPSQESK;S(0.994)PS(0.006)GVLSEPSQESK 142.54 9.83E-06 467420000 795380 891640 870330 1025860 933020 969900 831440 877010 936060 960810 TRUE FALSE 764295.6703 866211.3002 1027617.991 1078804.758 963031.4356 989512.0425 841615.4114 858899.437 829802.3931 895733.4829 0.853262365 0.967041332 1.147236328 1.204381413 1.07513167 1.104694713 0.939582395 0.958878342 0.9263943 1 19.77271001 2.230551101 24.86696793 0.952967989 1.065865193 0.224942959 0.092466216 259.1918667 804701.0235 0.03733101 0.02806086 170.0400019 -2.230551101 0.112897203 VLQGMVDDGSDDRPAGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLQGMVDDGSDDRPAGTR 18 1 Q53GG5-2;A0A087WYF8;Q53GG5;A0A2U3TZH4 Q53GG5-2 PDLIM3 PDZ and LIM domain protein 3 0 ; 220.34 6.23E-19 896790000 226610 233490 199396 238207 247180 242900 207166 196821 262180 254240 FALSE TRUE 217753.8307 226831.0938 235431.2927 250500.8918 255130.7692 247811.6044 209701.3595 192756.5776 232418.4255 237020.0983 0.918714625 0.957012065 0.993296747 1.056876162 1.076409853 1.04552992 0.884740834 0.813249927 0.980585306 1 17.85464987 2.230594193 24.99757652 0.893658792 1.010323317 0.263445426 0.066864075 187.5927792 588636.2303 0.026197914 0.019690674 170.0568744 -2.230594193 0.116664526 YGGSVGSQPPPVAPEPGPVPSS(ph)PSQEPPTKR ddPTM_BT-474_Pertuzumab_2h_R1 4 YGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 31 1 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 YGGSVGSQPPPVAPEPGPVPS(0.099)S(0.802)PS(0.099)QEPPT(0.001)KR;YGGSVGSQPPPVAPEPGPVPS(0.1)S(0.835)PS(0.061)QEPPT(0.004)KR;YGGSVGSQPPPVAPEPGPVPS(0.284)S(0.565)PS(0.131)QEPPT(0.02)KR;YGGSVGSQPPPVAPEPGPVPS(0.098)S(0.799)PS(0.098)QEPPT(0.004)KR 280.02 4.57E-72 6369000000 2579790 2593550 2265714 2681470 2937150 2762490 2234640 2320970 2428490 2411170 TRUE FALSE 2478968.955 2519584.493 2675178.92 2819860.988 3031626.097 2818349.441 2261988.193 2273041.158 2152817.996 2247859.308 1.102813217 1.120881758 1.190100693 1.254465072 1.348672529 1.253792633 1.006285484 1.011202592 0.95771919 1 21.10012031 2.230610526 24.64237991 0.996912141 1.214831719 0.717674184 0.066952361 91.23531215 282793.3416 0.028457507 0.021400589 170.0632703 -2.230610526 0.217919578 STS(ph)PTFNK ddPTM_BT-474_Pertuzumab_2h_R1 4 STSPTFNK 8 0 Q9BX63 Q9BX63 BRIP1 Fanconi anemia group J protein 1 S(0.002)T(0.033)S(0.964)PT(0.001)FNK;STS(0.933)PT(0.066)FNK;STS(1)PTFNK;S(0.019)T(0.114)S(0.867)PT(0.001)FNK 191.48 0.0001898 2938264000 5311870 5433770 4102240 5061850 5016270 4630010 5683940 5767530 5432130 5888470 TRUE FALSE 5104276.248 5278804.2 4843606.022 5323092.685 5177622.88 4723631.974 5753501.758 5648428.49 4815497.376 5489638.682 0.929801858 0.961594106 0.882317818 0.969661756 0.94316278 0.860463183 1.048065654 1.028925366 0.877197509 1 22.38827977 2.230617601 24.99888451 0.997065119 0.927170042 0.255558927 0.052638189 230.7256931 726151.8214 0.019393562 0.014580996 170.0660408 -2.230617601 -0.069895077 TAESQTPT(ph)PSATSFFSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TAESQTPTPSATSFFSGK 18 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAES(0.001)QT(0.321)PT(0.584)PS(0.089)AT(0.002)S(0.003)FFSGK 90.731 0.029639 114090000 181950 203270 179400 253440 306950 246360 164510 182390 165400 149290 TRUE FALSE 174839.1928 197472.9386 211821.5707 266520.0688 316823.3255 251341.568 166523.3226 178623.5828 146624.4854 139178.4553 1.256223116 1.418847035 1.521942245 1.914952053 2.276381964 1.80589422 1.196473421 1.283414034 1.053499876 1 17.08657638 2.230628248 23.81223129 1.171923548 1.714311154 0.501760327 0.274833052 98.16837046 294687.9254 0.115199844 0.086721401 170.07021 -2.230628248 0.542387606 LTFEVELVDID ddPTM_BT-474_Pertuzumab_2h_R1 4 LTFEVELVDID 11 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;; 114.89 0.0027828 234679000 375419 391682 313412 386190 397334 390829 356713 380267 408752 392816 FALSE TRUE 360747.2104 380511.6129 370052.5202 406121.3122 410114.609 398731.8302 361078.5604 372414.3536 362352.1866 366210.2224 0.985082306 1.039052406 1.010492055 1.108984095 1.119888479 1.088805844 0.985987114 1.016941447 0.98946497 1 18.48231254 2.230762642 24.99967682 1.000894834 1.060696937 0.354726363 0.039928898 224.2921694 719056.8437 0.016315478 0.012265843 170.1228469 -2.230762642 0.059802103 RVVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.035)S(0.294)T(0.316)T(0.34)PGGT(0.074)LFS(0.313)T(0.291)T(0.271)PGGT(0.067)R;RVVLGDGVQLPPGDY(0.006)S(0.115)T(0.416)T(0.458)PGGT(0.25)LFS(0.387)T(0.112)T(0.25)PGGT(0.005)R 72.766 0.0024602 436570000 176109 198406 141363 161330 169264 177038 150609 157299 169871 159671 TRUE FALSE 169226.4656 192747.6551 166910.4387 169656.2606 174708.5303 180617.8297 152452.198 154050.7207 150587.9562 148856.3409 1.136844185 1.294856866 1.121285379 1.139731499 1.173672073 1.213370076 1.024156559 1.034895253 1.011632795 1 17.18356115 2.230763783 24.98225504 1.022240689 1.180401186 0.74113006 0.046956614 89.14347457 285626.8866 0.017276736 0.012993524 170.1232939 -2.230763783 0.158160497 EAEPHYMVLEYVDLGDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAEPHYMVLEYVDLGDLK 18 0 C9JQR6;H0Y8F1;Q13308-3;Q13308-4;Q13308-2;Q13308;Q13308-6 C9JQR6 PTK7 Inactive tyrosine-protein kinase 7 0 94.01 0.0020431 21170000 13894 24893 10868 22065 14804 16192 23148 27048 22170 21605 FALSE TRUE 13351.00712 24183.07601 12832.08936 23203.77729 15280.1841 16519.41333 23431.29215 26489.44935 19653.35454 20141.67411 0.662854887 1.200648759 0.637091499 1.152028236 0.758635257 0.820160889 1.163323963 1.315156288 0.975755761 1 14.29789598 2.230811472 24.67086231 1.159447277 0.883757375 0.25363628 0.196254373 171.315642 545410.2304 0.067817317 0.05103787 170.1419757 -2.230811472 -0.275689902 FKNEEEVFAWNNEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKNEEEVFAWNNEVK 15 1 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GTY9;P49419-4 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ; 199.68 6.66E-09 976330000 1848700 1720530 1415090 1592390 1626990 1786940 1896890 2090630 2318260 2184470 FALSE TRUE 1776450.76 1671462.169 1670828.242 1674573.439 1679323.611 1823073.151 1920104.707 2047457.76 2055100.844 2036513.901 0.872299845 0.820746752 0.820435471 0.822274495 0.824606996 0.89519308 0.942838989 1.00537382 1.009126843 1 20.95767023 2.230825977 1.526149999 1.007823237 0.82939727 0.953691568 0.016663045 0.073181788 0.335266225 0.009460178 0.005631135 170.1476585 -2.230825977 -0.178425967 LSLDELHR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSLDELHR 8 0 P05023-4;P05023;P05023-3;P05023-2;Q5TC02;Q5TC01 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ;;; 209.84 4.39E-05 1024640000 887650 2120530 776610 3012090 958440 946870 2506020 2490140 1737500 1131060 FALSE TRUE 852959.6567 2060054.561 916960.7026 3167544.326 989269.093 966016.3602 2536689.422 2438717.739 1540266.284 1054452.299 0.808912511 1.953672597 0.86960852 3.003971189 0.938182879 0.916130925 2.405693862 2.312781471 1.460726375 1 20.0080624 2.230841358 24.98749739 1.965885986 1.465312308 0.037600368 0.739800432 432.8601023 1401170.345 0.266797861 0.200730899 170.1536845 -2.230841358 -0.500573678 ELAAEDEQVFLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELAAEDEQVFLMK 13 0 O43237;O43237-2;J3KRI4;J3KSD2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 76.332 0.030887 0 35125 34180 29845 34999 31746 30954 38157 39313 34716 40821 FALSE TRUE 33752.27617 33205.21987 35238.6554 36805.30258 32767.13892 31579.91109 38623.97678 38501.17281 30775.18522 38056.15731 0.886907101 0.872532127 0.925964624 0.967131344 0.861020692 0.829823958 1.014920568 1.011693653 0.808678211 1 15.21584227 2.230874952 24.99997944 0.967326542 0.893490377 0.203106997 0.065221429 271.3367361 882598.7031 0.024611585 0.018517948 170.1668468 -2.230874952 -0.073836165 KLFYSTFATDDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLFYSTFATDDRK 13 2 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 85.554 0.0051924 368800000 134530 168970 109660 166530 115640 105430 184400 176870 139740 135900 FALSE TRUE 129272.4189 164151.141 129478.0014 175124.6333 119359.6656 107561.8668 186656.7424 173217.5727 123877.301 126695.372 1.020340498 1.295636443 1.02196315 1.382249648 0.94209965 0.848980236 1.473271987 1.367197318 0.977757112 1 16.9510043 2.23090666 24.9998879 1.257807669 1.098898075 0.049008069 0.205283534 391.2264182 1277840.921 0.076372407 0.057462656 170.1792713 -2.23090666 -0.158909593 T(ph)WSRDEVMGDNLLLSSVFQFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TWSRDEVMGDNLLLSSVFQFSK 22 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4;E7EWM2;E7EMW0;Q96L14;E5RG47 Q5SW79 CEP170;CEP170P1 Centrosomal protein of 170 kDa;Cep170-like protein 1 T(0.578)WS(0.422)RDEVMGDNLLLSSVFQFSK 288.32 1.62E-46 216780000 283090 269790 218380 245720 304760 288430 236870 249600 311090 287460 TRUE FALSE 272026.5298 262095.8534 257846.1238 258401.6386 314562.8822 294262.2522 239768.8859 244445.6728 275776.3674 267990.0782 1.015061944 0.97800581 0.962148023 0.964220916 1.173785553 1.09803413 0.894693145 0.912144489 1.029054394 1 18.03182006 2.231146744 24.99929663 0.94538457 1.029633157 0.190830464 0.071293299 272.214999 917890.7104 0.028820977 0.021712827 170.2733748 -2.231146744 0.084248587 AELLQSDENGIPSS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AELLQSDENGIPSSPQK 17 0 Q14542-3;Q14542 Q14542-3 SLC29A2 Equilibrative nucleoside transporter 2 1 AELLQSDENGIPS(0.033)S(0.967)PQK 151.04 1.23E-08 0 55302 84149 56113 98523 61404 64701 99508 117390 97523 71695 TRUE FALSE 53140.7367 81749.15291 66253.86733 103607.7838 63379.11543 66009.29855 100725.8087 114965.8555 86452.59789 66839.03379 0.795055429 1.223075025 0.991245139 1.55010894 0.948235063 0.987586068 1.506990795 1.720040655 1.293444758 1 16.02840326 2.231187678 24.98790762 1.472501907 1.099935501 0.207093175 0.260000937 198.3367488 672184.7967 0.093874546 0.070717801 170.2894246 -2.231187678 -0.372566405 SKEQAELEAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKEQAELEAAR 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 166.45 1.86E-05 4117620000 5348920 5459450 4549190 4946810 4958040 5017130 5460900 5607900 6149600 5846800 FALSE TRUE 5139878.293 5303751.831 5371329.829 5202115.457 5117519.859 5118579.806 5527732.128 5492094.905 5451523.189 5450791.028 0.942960071 0.973024246 0.985422079 0.954378077 0.938858201 0.939052659 1.014115584 1.007577593 1.000134322 1 22.37803418 2.231230204 24.99994798 1.006534599 0.956944026 0.742609317 0.014356645 94.00198842 320585.5652 0.005882623 0.004432793 170.3061002 -2.231230204 -0.049590573 RPPT(ph)PCS(ph)DPER ddPTM_BT-474_Pertuzumab_2h_R1 2 RPPTPCSDPER 11 1 Q9BW71;Q9BW71-2;Q9BW71-3 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 RPPT(1)PCS(1)DPER;RPPT(1)PCS(1)DPER 87.66 0.011736 428070000 444320 485720 366930 445150 427360 474680 367440 392700 447990 446600 TRUE FALSE 426955.4832 471867.7412 433242.4133 468124.2448 441106.4225 484278.3548 371936.8406 384590.6078 397136.0533 416351.3842 1.025469109 1.133340152 1.040569168 1.124348958 1.059457082 1.16314818 0.893324376 0.923716414 0.953848284 1 18.66744209 2.231336612 24.99956413 0.933472873 1.090759699 0.699935617 0.047425071 80.20148898 277544.8306 0.016160305 0.012180842 170.3478327 -2.231336612 0.157286826 GYVVWQEVFDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GYVVWQEVFDNK 12 0 H3BS10;H3BP20;P06865 H3BS10 HEXA Beta-hexosaminidase;Beta-hexosaminidase subunit alpha 0 171.62 8.83E-05 51659000 105430 106150 95744 99284 108220 93234 125040 131080 125410 99146 FALSE TRUE 101309.679 103122.7059 113047.0706 104408.0591 111700.9946 95119.25536 126570.2769 128373.1522 111173.9826 92430.75311 1.096060301 1.115675275 1.223046084 1.129581396 1.208483008 1.029086664 1.369352436 1.388857581 1.202781313 1 16.49608532 2.231383507 24.99978408 1.288556717 1.14011745 0.116779865 0.11564557 215.131577 749353.8654 0.041094817 0.030978103 170.3662275 -2.231383507 -0.148439267 S(ph)QTNDNYEGDLTSGVYLLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SQTNDNYEGDLTSGVYLLSR 20 0 A0A1B0GV68 A0A1B0GV68 1 S(0.846)QT(0.153)NDNY(0.001)EGDLTSGVYLLSR;S(0.499)QT(0.499)NDNY(0.002)EGDLTSGVYLLSR;S(0.781)QT(0.219)NDNYEGDLTSGVYLLSR 187.52 3.03E-17 157613000 51740 70995 46203 95860 49097 54604 82786 92005 66904 65481 TRUE FALSE 49717.9436 68970.29211 54552.90988 100807.3461 50676.24959 55708.13029 83799.15983 90105.0646 59309.3384 61045.91355 0.814435246 1.12981014 0.893637374 1.651336514 0.830133364 0.91256117 1.372723496 1.476021233 0.971552967 1 15.8976071 2.231594549 24.97064655 1.27409342 1.054575398 0.058919384 0.270749974 339.8405418 1218185.63 0.099469713 0.075062249 170.4490359 -2.231594549 -0.219518022 EGIPALDNFLDKL ddPTM_BT-474_Pertuzumab_2h_R1 2 EGIPALDNFLDKL 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 133.32 0.0022256 294940000 409470 418660 365150 379300 386320 387260 468600 479990 548380 533000 FALSE TRUE 393467.4597 406720.2267 431140.7277 398875.7185 398746.3336 395090.6625 474334.867 470078.0388 486130.2014 496899.4353 0.791845254 0.818516178 0.867661939 0.802729265 0.802468881 0.795111917 0.954589266 0.946022485 0.978327136 1 18.92259438 2.231610275 23.87810849 0.962797754 0.814835292 0.90733815 0.024485097 27.47358415 94384.91124 0.009346972 0.00706258 170.4552081 -2.231610275 -0.147962461 KETESEAEDNLDDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 244.86 7.07E-20 250580000 389130 302070 244370 332350 291250 277670 476520 496670 553170 516540 FALSE TRUE 373922.3694 293455.2594 288533.095 349502.6233 300618.3208 283284.6776 482351.7943 486413.5909 490376.4607 481554.2857 0.776490586 0.609391855 0.599170444 0.725780319 0.624266733 0.588271533 1.001656114 1.010090877 1.018320209 1 18.87733892 2.231690677 24.99926756 1.008304151 0.651305618 0.90742387 0.055329638 42.36881211 154175.975 0.020100535 0.015172031 170.4867678 -2.231690677 -0.356998534 S(ph)VVGTPAYLAPEVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVVGTPAYLAPEVLR 15 0 F8WBA3;Q15139;H0Y5M6;O94806 F8WBA3;O94806 PRKD1;PRKD3 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1;Serine/threonine-protein kinase D3 1 S(1)VVGTPAYLAPEVLR 63.894 0.064104 0 30561 29209 34330 30724 30745 29903 36412 38967 36203 34475 TRUE FALSE 29366.64233 28375.98792 40534.19467 32309.66932 31733.94085 30507.65915 36857.62095 38162.31783 32093.38722 32139.97754 0.91371073 0.882887609 1.26117682 1.005279773 0.987366615 0.949212211 1.146784278 1.187378485 0.998550393 1 14.9720813 2.231716527 24.96463507 1.10999842 1.006164184 0.098140408 0.111460786 301.3600498 1099236.597 0.042375606 0.032003132 170.4969156 -2.231716527 -0.103834236 TESDDLHTFLLEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TESDDLHTFLLEIK 14 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 148.68 7.69E-06 91673000 60997 58330 49112 56224 59289 62331 63416 63711 77109 74701 FALSE TRUE 58613.1698 56666.48551 57987.63089 59125.72738 61196.08453 63591.37553 64192.10398 62395.34559 68355.90959 69641.43473 0.841642192 0.813689232 0.832659912 0.849002144 0.878730956 0.913125581 0.921751601 0.895951467 0.9815408 1 16.0876583 2.231922713 0.329416556 1.008131927 0.796702986 0.892889945 0.019427307 0.509923979 0.142338177 0.027184474 0.038509266 170.5778802 -2.231922713 -0.211428941 EVFDNDGKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVFDNDGKPR 10 1 Q08209-3;Q08209-2;Q08209;Q08209-4 Q08209-3 PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 0 ; 129.84 0.00026678 1374290000 1458780 1543100 1243610 1482970 1441530 1400520 1723440 1733510 2009180 1942570 FALSE TRUE 1401769.265 1499092.299 1468357.991 1559506.259 1487898.122 1428839.474 1744531.974 1697712.413 1781106.31 1810998.004 0.774031369 0.82777137 0.810800447 0.861130855 0.82159015 0.788979044 0.963298673 0.937445767 0.983494353 1 20.78835353 2.231936697 24.99775256 0.962712902 0.817009203 0.89075048 0.026862308 49.78215721 187869.2092 0.009909698 0.007487888 170.5833728 -2.231936697 -0.145703699 KFQILNDEIITILDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFQILNDEIITILDK 15 1 Q7L576;Q7L576-2;Q7L576-3 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 163.7 2.44E-06 126250000 378690 403010 323660 316210 378530 403660 393360 432290 512530 456390 FALSE TRUE 363890.3761 391516.5494 382152.5618 332529.636 390705.7612 411822.2818 398174.0573 423363.0604 454349.7431 425478.2988 0.855250144 0.920179832 0.898171688 0.781543117 0.918274239 0.967904316 0.935826947 0.995028563 1.067856444 1 18.69872602 2.23197899 0.988291613 1.026455892 0.871591911 0.667469486 0.044036736 0.347365722 0.646083687 0.033307633 0.018777316 170.5999856 -2.23197899 -0.154863981 KKWPER ddPTM_BT-474_Pertuzumab_2h_R1 1 KKWPER 6 2 A0A494C039;Q9Y4L1;A0A087X054 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 66.993 0.056214 738190000 1461200 1342700 1192600 1132800 1302000 1309700 1602200 1626700 1858200 1901800 FALSE TRUE 1404094.689 1304407.511 1408129.349 1191263.944 1343880.012 1336183.031 1621808.203 1593108.077 1647264.926 1772989.392 0.791936317 0.735710838 0.794211943 0.671895697 0.757974085 0.75363284 0.914730912 0.89854349 0.929088992 1 20.75775247 2.231982942 5.109490347 0.925322265 0.74806156 0.832299881 0.040531272 0.070021359 5.139409828 0.014587253 0.01124048 170.6015381 -2.231982942 -0.177260705 GES(ph)IEPLDPSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GESIEPLDPSEK 12 0 F8VYK4;P21860-5;P21860-4;P21860;B4DGQ7 F8VYK4 ERBB3 Receptor tyrosine-protein kinase erbB-3 1 GES(1)IEPLDPSEK 147.26 6.86E-05 329340000 752580 1167600 600210 1279200 811540 761580 1405500 1750400 1090300 765440 TRUE FALSE 723168.3416 1134301.191 708681.2986 1345219.665 837643.9211 776979.6694 1422700.929 1714253.628 966533.7149 713596.067 1.013414136 1.589556394 0.993112674 1.885127634 1.173834834 1.088822802 1.993706237 2.40227449 1.354454935 1 19.44474814 2.231991592 24.9988732 1.875274809 1.312419852 0.105194831 0.446595589 207.1612917 788359.2088 0.160258361 0.121121377 170.6049361 -2.231991592 -0.562854957 MYFPDVEFDIKS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 MYFPDVEFDIKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 MYFPDVEFDIKS(1)PK;MYFPDVEFDIKS(1)PK;MYFPDVEFDIKS(1)PK 217.91 3.38E-12 3345300000 4175030 3937750 4227000 3656720 4462950 4439790 2876390 3046050 3149130 2796920 TRUE FALSE 4011865.212 3825449.225 4990912.929 3845443.757 4606504.84 4529565.596 2911592.121 2983148.003 2791653.965 2607482.117 1.538597402 1.467104683 1.914073694 1.474772821 1.76664868 1.737141577 1.116629756 1.144072277 1.070632065 1 21.31422593 2.23200232 24.87307448 1.100892554 1.650800761 0.809909093 0.134430276 60.50202167 229458.413 0.048698464 0.03681636 170.6091502 -2.23200232 0.549908208 DSGS(ph)DQDLDGAGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSGSDQDLDGAGVR 14 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 DS(0.003)GS(0.997)DQDLDGAGVR 180.3 1.85E-06 88640000 122220 127350 106390 129390 124060 113330 146580 141960 157530 152810 TRUE FALSE 117443.5073 123718.1027 125617.0396 136067.8334 128050.5026 115621.6102 148373.8899 139028.4764 139647.8548 142460.0426 0.824396126 0.868440725 0.881770336 0.95512981 0.898852059 0.811607298 1.041512323 0.975912079 0.980259814 1 17.1201978 2.232033422 24.99999952 0.996684934 0.87839918 0.696788883 0.040639562 95.60329985 366169.7037 0.015616286 0.011804006 170.6213687 -2.232033422 -0.118285754 ISEDKNPDYR ddPTM_BT-474_Pertuzumab_2h_R1 3 ISEDKNPDYR 10 1 P14923 P14923 JUP Junction plakoglobin 0 ;; 113.63 0.0013341 2647720000 8230000 9697200 7870000 10496100 6573900 8015300 10478500 10953800 10404000 10196600 FALSE TRUE 7908362.501 9420645.351 9292284.067 11037804.98 6785355.464 8177374.858 10606739.02 10727600.2 9222981.537 9505975.2 0.831935949 0.991023557 0.977520336 1.161143885 0.713798987 0.86023524 1.115797043 1.128511276 0.970229918 1 23.18040321 2.232046899 24.99977723 1.073056541 0.92956639 0.217918738 0.118916512 229.0729854 879178.5023 0.045354225 0.034290081 170.6266637 -2.232046899 -0.143490152 DEVLYVFPSDFCR ddPTM_BT-474_Pertuzumab_2h_R1 4 DEVLYVFPSDFCR 13 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PRF6;Q14108-2 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ;;; 313.5 2.67E-50 476772000 527542 921367 552991 1152420 554930 605663 1101230 1106320 1054160 875921 FALSE TRUE 506925.0754 895090.5153 652928.7749 1211896.534 572779.8274 617909.9208 1114707.182 1083474.105 934496.1762 816594.0905 0.62077975 1.096126614 0.79957568 1.484086829 0.701425389 0.756691639 1.365068882 1.326820899 1.144382732 1 19.6392596 2.232127464 24.99962624 1.250600318 0.929876005 0.248330674 0.249496614 201.8911104 784553.8516 0.090392217 0.068360301 170.6583193 -2.232127464 -0.320724313 KEVTEEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEVTEEEK 8 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 85.807 0.026425 525140000 472700 512600 432970 512610 630560 588250 728550 889110 1020600 971770 FALSE TRUE 454226.3614 497981.1499 511217.3104 539065.8635 650842.5351 600144.818 737466.2128 870749.5678 904745.7667 905951.1523 0.501380632 0.549677705 0.564287941 0.595027516 0.718407977 0.662447215 0.814024256 0.961144059 0.998669481 1 19.78907374 2.232239746 0.72116256 1.037845995 0.535451395 0.953763428 0.03966686 0.132695998 0.133189088 0.034261225 0.021768724 170.7024469 -2.232239746 -0.5023946 IRDT(ph)SQEPCGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IRDTSQEPCGR 11 1 Q12955;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IRDT(0.813)S(0.187)QEPCGR 88.282 0.083403 166110000 272300 231570 176260 219230 217610 230120 196170 204910 212450 225310 TRUE FALSE 261658.215 224965.8503 208114.1029 230544.4866 224609.6233 234773.1841 198570.7871 200678.5369 188333.5667 210049.553 1.245697557 1.07101323 0.990785745 1.097571898 1.069317311 1.117703802 0.945352105 0.955386641 0.896614937 1 17.68037019 2.232382303 24.83894135 0.946657371 1.091134405 0.564467305 0.064043294 105.1940043 422911.5122 0.023661949 0.017918334 170.7584888 -2.232382303 0.144477034 KVVEAVNS(ph)DSDSEFGIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVVEAVNSDSDSEFGIPK 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KVVEAVNS(0.991)DS(0.009)DSEFGIPK 162.71 2.14E-11 132770000 323530 291300 193540 318150 259490 267610 324020 360900 335750 314560 TRUE FALSE 310886.0899 282992.4092 228516.9833 334569.7596 267836.7315 273021.2576 327985.4537 353447.2889 297637.0676 293254.571 1.060123594 0.965005961 0.779244404 1.140885063 0.913325001 0.931004269 1.118432536 1.205257561 1.014944342 1 18.16179407 2.232488327 24.97982931 1.113447425 0.962146601 0.221044626 0.104589125 170.4293621 701095.142 0.037884203 0.028698501 170.8001813 -2.232488327 -0.151300824 NSATCHS(ph)EDS(ph)DLEID ddPTM_BT-474_Pertuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 2 NSATCHS(1)EDS(1)DLEID;NSATCHS(1)EDS(1)DLEID 231.41 2.90E-13 834770000 656840 674650 511630 603880 594620 633460 561090 583980 681010 587770 TRUE FALSE 631169.9666 655409.6426 604092.9221 635046.3192 613746.4923 646268.9952 567956.7873 571920.6089 603704.5998 547959.8144 1.151854479 1.196090708 1.102440191 1.158928634 1.120057486 1.179409472 1.036493503 1.043727284 1.101731521 1 19.06371057 2.232500426 24.99999902 1.048101545 1.150175454 0.699342443 0.034017415 80.54646069 332273.6408 0.011992519 0.00908558 170.8049395 -2.232500426 0.102073908 NSSS(ph)PVSLDAALPESSNVYR ddPTM_BT-474_Pertuzumab_2h_R1 3 NSSSPVSLDAALPESSNVYR 20 0 Q70EL1-7;Q70EL1;H7C296;H7C1E9;Q70EL1-6;R4GN32 Q70EL1-7 USP54 Inactive ubiquitin carboxyl-terminal hydrolase 54 1 NSS(0.001)S(0.999)PVSLDAALPESSNVYR;NS(0.007)S(0.199)S(0.795)PVSLDAALPESSNVYR;NSS(0.001)S(0.999)PVSLDAALPESSNVYR 258.81 3.01E-36 494557000 215064 209235 197972 231509 184972 204224 249880 253199 283792 286867 TRUE FALSE 206659.0611 203267.8227 233749.9443 243457.2072 190921.7924 208353.5492 252938.1062 247970.3522 251577.1219 267437.2426 0.772738528 0.760058026 0.874036623 0.910333972 0.713893811 0.779074549 0.945784902 0.927209501 0.940695916 1 18.02884086 2.232511084 24.99059382 0.945141973 0.804033131 0.637738324 0.055868337 105.7203069 436725.7839 0.021858909 0.016559703 170.8091312 -2.232511084 -0.141108842 TLAEEQHK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLAEEQHK 8 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 71.379 0.048894 127230000 197670 191310 133420 155970 147770 147660 202700 205130 194660 202450 FALSE TRUE 189944.8379 185854.0261 157531.9619 164019.6304 152523.1563 150645.7864 205180.7032 200893.9938 172563.0129 188737.8812 1.006394883 0.984720317 0.834660011 0.869033971 0.808121588 0.798174619 1.087119883 1.064407381 0.914299831 1 17.52602449 2.232532694 24.99992025 1.028718552 0.881811455 0.412514315 0.07715177 142.5314032 591122.3086 0.030737934 0.023291642 170.8176309 -2.232532694 -0.146907097 GGDEYDNHCGK ddPTM_BT-474_Pertuzumab_2h_R1 4 GGDEYDNHCGK 11 0 P20645;F5GX30;F5H4U1;H0YGE9 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;;; 152.64 3.29E-05 2144020000 2678160 3458620 2433320 3610130 2792860 2591740 3936700 3641990 4084910 3754040 FALSE TRUE 2573494.546 3359983.544 2873075.053 3796449.242 2882694.878 2644146.759 3984878.512 3566781.634 3621208.142 3499775.527 0.735331317 0.960056872 0.820931237 1.084769355 0.823679935 0.755518958 1.138609743 1.01914583 1.034697258 1 21.73883096 2.232647448 24.999764 1.049609133 0.874104563 0.443263572 0.100990441 139.8151016 591106.1235 0.03655848 0.027716292 170.8627721 -2.232647448 -0.17550457 KQEELNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQEELNR 7 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 0 110.03 0.011057 173180000 153880 199880 137430 202440 169040 172080 207270 221570 234980 215820 FALSE TRUE 147866.1995 194179.6181 162266.6581 212887.9527 174477.3251 175559.5755 209806.6323 216994.5021 208306.0555 201202.3192 0.734912997 0.965096321 0.806485029 1.05807902 0.867173529 0.872552445 1.042764483 1.07848907 1.035306434 1 17.61828741 2.232724883 23.91213068 1.049091848 0.891351442 0.451161616 0.083279015 71.16730015 291605.8164 0.029130689 0.022116775 170.8932396 -2.232724883 -0.157740407 EFSGPST(ph)PTGTLEFEGGEVSLEGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFSGPSTPTGTLEFEGGEVSLEGGK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 EFS(0.002)GPS(0.053)T(0.435)PT(0.435)GT(0.075)LEFEGGEVSLEGGK 259.93 1.87E-44 335450000 271880 275680 272250 328380 281070 306730 274150 301620 313790 316530 TRUE FALSE 261254.629 267817.8763 321451.6312 345327.7312 290110.8718 312932.2908 277505.1297 295391.4416 278169.8747 295091.1412 0.885335385 0.907576809 1.089329994 1.170240929 0.983122945 1.060459794 0.940404814 1.001017653 0.942657491 1 18.17080109 2.232740616 24.89258598 0.973213323 1.019930374 0.068401753 0.080403232 431.8640191 1847093.679 0.03212381 0.024355021 170.8994308 -2.232740616 0.046717052 ESEQES(ph)EEEILAQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESEQESEEEILAQK 14 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 ESEQES(1)EEEILAQK;ESEQES(1)EEEILAQK 288.22 2.82E-34 308630000 392867 337036 388244 431240 401458 405896 514810 561690 610170 642860 TRUE FALSE 377513.3233 327424.0633 458408.3272 453496.3481 414371.2612 414103.4952 521110.3988 550090.9052 540906.0596 599318.5196 0.629904318 0.546327291 0.764882633 0.756686692 0.691404066 0.690957282 0.869504916 0.917860682 0.902535199 1 19.19296343 2.232836399 0.440152009 1.016586014 0.603195657 0.799404415 0.060757139 0.490878513 0.212380967 0.067207715 0.069681145 170.9371264 -2.232836399 -0.413390357 EVSMDDHK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSMDDHK 8 0 P05023-4;P05023;P05023-3;P05023-2;Q5TC02;Q5TC01 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ; 143.61 0.00059868 438850000 267309 584400 232626 664320 236140 256923 636050 631190 482260 283152 FALSE TRUE 256862.2688 567733.4842 274666.6929 698605.6348 243735.6576 262118.1591 643834.1702 618155.7059 427515.8666 263973.8628 0.973059476 2.150718553 1.040507155 2.64649548 0.923332541 0.992970123 2.439007269 2.341730728 1.619538624 1 18.01003556 2.232853869 24.99991753 2.0196185 1.497377446 0.05491075 0.655305352 291.4033349 1276556.221 0.233333498 0.177055102 170.9440026 -2.232853869 -0.522241054 LSS(ph)TS(ph)SEETQLFHIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.416)S(0.476)T(0.229)S(0.465)S(0.406)EET(0.007)QLFHIPR 55.453 0.071174 27514000 26342 41903 20658 48770 22934 28084 42136 48385 33575 29420 TRUE FALSE 25312.52552 40707.96747 24391.36013 51287.02554 23671.69294 28651.87772 42651.67297 47385.83284 29763.70676 27427.3572 0.922893348 1.484210352 0.889307707 1.869922252 0.863068679 1.044645954 1.555077752 1.727684972 1.085183182 1 14.743328 2.232873722 24.99933574 1.442899216 1.196756992 0.016520285 0.354626633 334.2277889 1469234.912 0.12609063 0.095700145 170.9518174 -2.232873722 -0.246142224 DLAGCIHGLSNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLAGCIHGLSNVK 13 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 132.97 0.00011268 1288900000 1185300 1955600 1367200 2497200 1151000 951450 2443300 1917200 1715100 1354500 FALSE TRUE 1138977.166 1899828.203 1614283.453 2626080.791 1188022.96 970688.9709 2473201.836 1877609.15 1520409.038 1262758.509 0.901975443 1.504506356 1.278378599 2.079638168 0.940815645 0.768705152 1.958570716 1.48691071 1.204037849 1 20.26814733 2.233013367 24.99888513 1.474651221 1.282972605 0.023984818 0.417532005 517.5374884 2332276.165 0.155454624 0.118064281 171.0067947 -2.233013367 -0.191678616 ADIDLTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADIDLTKR 8 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 69.598 0.08579 106270000 151340 162050 126820 116190 142680 139940 158930 163650 179600 183060 FALSE TRUE 145425.4655 157428.4927 149739.1951 122186.5798 147269.4318 142769.6827 160875.0329 160270.5703 159212.5609 170661.1831 0.852129716 0.922462213 0.877406287 0.715959995 0.862934553 0.836567988 0.942657433 0.939115547 0.932916074 1 17.38077543 2.233057869 19.67255559 0.947370789 0.844597428 0.510715784 0.05216659 8.744930003 31258.52614 0.020048415 0.015324377 171.0243186 -2.233057869 -0.102773361 SQSSDTEQQSPT(ph)SGGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSSDTEQQS(0.223)PT(0.712)S(0.065)GGGK 287 1.68E-35 412910000 549720 508260 549630 554000 527450 628220 637110 650270 836210 809930 TRUE FALSE 528236.3347 493764.9224 648960.3675 582592.0064 544415.9083 640923.0388 644907.1428 636841.6973 741286.9465 755072.7197 0.699583392 0.65393029 0.859467374 0.771570726 0.721011227 0.848822931 0.854099381 0.843417701 0.981742456 1 19.52625607 2.23308498 0.257249667 1.040030154 0.637463518 0.732456233 0.055893843 1.305429964 0.256610356 0.115823024 0.189833915 171.0349954 -2.23308498 -0.402566636 KPENSECDATAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPENSECDATAK 12 1 Q99523;Q99523-2 Q99523 SORT1 Sortilin 0 118.52 0.00098852 41635000 75346 82319 50361 78071 63833 64819 95647 100140 103860 98363 FALSE TRUE 72401.39502 79971.34272 59462.35297 82100.25367 65886.24642 66129.68459 96817.5566 98072.07401 92070.24822 91700.7864 0.789539522 0.872090043 0.648438855 0.895305884 0.718491618 0.721146319 1.055798542 1.069479095 1.004028993 1 16.48464649 2.233161227 24.99997467 1.042108403 0.775880134 0.759957129 0.070989939 59.03514908 273338.6781 0.025129541 0.019097795 171.0650258 -2.233161227 -0.266228269 QAQQDRDEMADEVANGNLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAQQDRDEMADEVANGNLSK 20 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 ; 203.64 1.49E-22 171100000 171072 176996 160267 168575 164168 168201 191267 202962 208510 206580 FALSE TRUE 164386.3171 171948.2474 189230.812 177275.176 169448.6128 171602.1395 193607.7828 198770.7638 184840.8189 192588.1526 0.853564017 0.892828791 0.982567253 0.920488481 0.87984962 0.89103165 1.005294356 1.03210276 0.959772532 1 17.55515943 2.233187196 24.99701658 1.005315238 0.906214705 0.632193878 0.035679597 87.34334378 406314.5593 0.013903232 0.010568182 171.0752548 -2.233187196 -0.099100533 FSEGVLQS(ph)PSQDQEK ddPTM_BT-474_Pertuzumab_2h_R1 5 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 FSEGVLQS(0.5)PS(0.5)QDQEK;FSEGVLQS(0.981)PS(0.019)QDQEK;FSEGVLQS(0.826)PS(0.174)QDQEK;FSEGVLQS(0.936)PS(0.064)QDQEK;FSEGVLQS(0.68)PS(0.32)QDQEK 427.94 2.55E-153 2274070000 3377000 3147740 3047200 2911110 2882400 3115220 3583910 3835420 3843960 3980940 TRUE FALSE 3245023.107 3057969.537 3597896.825 3061352.736 2975115.014 3178211.883 3627770.963 3756217.237 3407609.776 3711307.388 0.87436118 0.823960189 0.969441884 0.824871781 0.801635301 0.856359108 0.977491375 1.012100816 0.918169642 1 21.82349607 2.233240565 8.132365013 0.981832873 0.857703396 0.58916135 0.048411746 0.085356376 43.89043092 0.017873732 0.013872654 171.0962791 -2.233240565 -0.124129477 KVVDNTTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVVDNTTAK 9 1 Q9H0U4;E9PLD0;Q92928 Q9H0U4 RAB1B;RAB1C Ras-related protein Rab-1B;Putative Ras-related protein Rab-1C 0 83.081 0.026667 620820000 678530 763870 532080 732870 577330 626490 801530 810600 915370 800860 FALSE TRUE 652012.2974 742085.1755 628238.6921 770693.5085 595900.3438 639158.057 811339.3639 793860.8267 811461.0351 746617.0389 0.873288799 0.993930137 0.841447033 1.032247415 0.798133866 0.856072154 1.086687447 1.063277136 1.08685041 1 19.51000891 2.233247722 24.9999894 1.065141565 0.90232348 0.560663238 0.069280621 93.02924546 437747.3746 0.02461606 0.018711959 171.0990989 -2.233247722 -0.162818084 TDEERPPVEHS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TDEERPPVEHSPEK 14 1 Q15170-2 Q15170-2 TCEAL1 Transcription elongation factor A protein-like 1 1 TDEERPPVEHS(1)PEK;TDEERPPVEHS(1)PEK 136.66 1.56E-05 1126620000 536930 429140 411050 467520 476090 453020 596170 606010 701500 691330 TRUE FALSE 515946.182 416901.3474 485335.8788 491648.7632 491403.8672 462180.3748 603466.1068 593495.6817 621868.6609 644505.6033 0.800530173 0.646854496 0.753035934 0.762830859 0.762450884 0.717108389 0.936324066 0.920854184 0.964877043 1 19.29783338 2.233282477 24.7340622 0.945461728 0.73880019 0.859225279 0.042561753 39.40812608 184669.4707 0.015190021 0.011555024 171.1127916 -2.233282477 -0.206661538 RDS(ph)DSFLNIFPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSDSFLNIFPEK 13 1 A0A0A6YYJ5;O94854-2;O94854 A0A0A6YYJ5 MACF1;KIAA0754 Uncharacterized protein KIAA0754 1 RDS(0.98)DS(0.02)FLNIFPEK;RDS(0.963)DS(0.037)FLNIFPEK 141.6 2.45E-05 68106000 180656 233215 172441 234497 194840 198159 270720 315380 277510 243420 TRUE FALSE 173595.7638 226563.9365 203604.9246 246599.4183 201107.2055 202165.9107 274033.1523 308867.2928 246008.2282 226932.9466 0.76496501 0.998373925 0.897203018 1.086662038 0.886196599 0.890861877 1.207551202 1.361050907 1.084056907 1 17.79190655 2.233283548 24.9273947 1.211741491 0.929146489 0.476188795 0.120141009 90.31710372 426627.891 0.043143715 0.032815921 171.1132139 -2.233283548 -0.282595001 TNIIPVLEDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TNIIPVLEDAR 11 0 A6NHQ2 A6NHQ2 FBLL1 rRNA/tRNA 2-O-methyltransferase fibrillarin-like protein 1 0 ; 113.77 0.0031348 234570000 233790 242682 198009 253090 259570 245060 222823 233070 245750 243120 FALSE TRUE 224653.2283 235760.947 233793.631 266152.0052 267919.3048 250015.2811 225549.9745 228257.0231 217853.4903 226653.2659 0.991175783 1.040183322 1.031503473 1.174269447 1.182066818 1.103073808 0.99513225 1.007075818 0.961175165 1 17.79012742 2.233358814 24.66401161 0.993243214 1.090674596 0.403274563 0.057196073 123.9055897 587482.9217 0.023637176 0.017986321 171.1428714 -2.233358814 0.097431382 EAQTSFLHLGYLPNQLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAQTSFLHLGYLPNQLFR 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 167.14 3.03E-11 1474690000 1299070 1467170 1250000 1434410 1445790 1353460 1307640 1274280 1364400 1491070 FALSE TRUE 1248300.908 1425327.748 1475902.806 1508440.072 1492295.148 1380827.889 1323643.289 1247965.673 1209519.032 1390078.501 0.898007492 1.025357739 1.061740618 1.085147401 1.073533004 0.993345259 0.952207583 0.897766329 0.870108437 1 20.40673493 2.233500478 2.460427656 0.913952243 1.033160087 0.388838449 0.058044765 0.266446729 3.296486608 0.026021774 0.018095832 171.1987061 -2.233500478 0.119207845 SGEDGEKDTK ddPTM_BT-474_Pertuzumab_2h_R1 6 SGEDGEKDTK 10 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 112.94 0.0014177 2772480000 3272770 2556190 2414180 2281610 2715830 2565970 3424370 3582880 3700730 4108410 FALSE TRUE 3144866.53 2483289.964 2850476.029 2399364.166 2803187.138 2617855.671 3466278.464 3508892.276 3280638.645 3830143.731 0.821083163 0.648354249 0.744221687 0.626442331 0.731875181 0.68348758 0.904999579 0.916125483 0.856531471 1 21.8689671 2.233545965 24.74125008 0.912555992 0.705331173 0.743807151 0.060346986 51.0140439 251689.5683 0.020475319 0.015596447 171.216638 -2.233545965 -0.207224819 GPALTPIRDEEWGGHS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPALTPIRDEEWGGHSPR 18 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR;GPALT(0.001)PIRDEEWGGHS(0.999)PR 191.99 1.19E-14 1071200000 447501 1064143 475998 1408138 532666 592973 1180025 1185140 945859 731508 TRUE FALSE 430012.1662 1033794.684 562021.4271 1480812.171 549799.6856 604963.3203 1194466.499 1160666.445 838489.0517 681962.3116 0.630551218 1.515911753 0.824123881 2.171398838 0.806202449 0.887092014 1.751513945 1.70195101 1.229524033 1 19.37933249 2.233606716 24.99997716 1.512828635 1.17379443 0.063949338 0.46722122 285.6940017 1441745.28 0.166627108 0.126938686 171.2405902 -2.233606716 -0.339034205 RAEILAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RAEILAK 7 1 P30038-2;P30038;P30038-3;Q5TF55 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 86.833 0.031726 781170000 924900 1106400 889870 1450100 862960 796570 1473000 1366300 1237300 1077800 FALSE TRUE 888753.8855 1074846.555 1050689.304 1524939.835 890717.8921 812677.1912 1491027.015 1338085.428 1096846.891 1004799.646 0.884508558 1.069712315 1.045670456 1.517655625 0.886463183 0.80879526 1.483904797 1.331693769 1.091607561 1 19.93847643 2.233617791 24.99995778 1.270914602 1.052632633 0.138640364 0.22057337 219.9331896 1112372.207 0.082857506 0.063117131 171.2449569 -2.233617791 -0.218281969 RGSQNSSEHRPPASSTSEDVKAS(ph)PSSANK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGSQNSSEHRPPASSTSEDVKASPSSANK 29 3 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGSQNSSEHRPPAS(0.009)S(0.009)T(0.009)S(0.009)EDVKAS(0.835)PS(0.088)S(0.042)ANK;RGSQNSSEHRPPASSTSEDVKAS(0.956)PS(0.038)S(0.006)ANK 211.62 4.56E-26 254011000 117893 111501 79185 75985 75985 95015 120082 127465 137190 141782 TRUE FALSE 113285.6112 108321.1007 93495.49096 79906.59496 78429.12653 96936.2684 121551.5994 124832.8032 121616.7663 132178.9789 0.857062236 0.819503234 0.707340091 0.604533305 0.593355519 0.733371291 0.919598566 0.944422512 0.920091586 1 17.01213323 2.233629294 4.351358427 0.944386306 0.710484456 0.666600606 0.078783635 0.136814182 6.157138309 0.033624818 0.025742606 171.2494927 -2.233629294 -0.23390185 ESYTEEIVS(ph)EAESHVSGISR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR 348.63 3.14E-95 551330000 431652 728550 566280 550493 594817 690350 355685 450278 453751 502582 TRUE FALSE 414782.5626 707772.4673 668619.3928 578904.0097 613949.829 704309.35 360037.9794 440979.6019 402243.0888 468541.6735 0.885262904 1.510585947 1.427022249 1.235544334 1.31034199 1.503194678 0.768422533 0.94117477 0.858500132 1 18.83781785 2.233706685 24.99999127 0.888674284 1.322697773 0.578103419 0.175608458 81.32373177 418849.8108 0.061751059 0.047061285 171.280012 -2.233706685 0.434023489 S(ph)RS(ph)PATAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(1)PATAK;S(0.992)RS(0.995)PAT(0.013)AK;S(0.999)RS(0.806)PAT(0.195)AK 117.86 0.023887 2287340000 3226830 2633270 2219850 2454900 2548930 2466610 3030890 2931050 3335770 3334020 TRUE FALSE 3100721.916 2558171.718 2621026.275 2581597.683 2630918.648 2516486.544 3067982.938 2870522.793 2957107.374 3108203.856 0.997592841 0.82303859 0.843260737 0.830575407 0.846443403 0.809627251 0.987059756 0.923531057 0.951387847 1 21.5676497 2.233783865 24.99999605 0.956306686 0.854315127 0.489785483 0.053108172 105.092469 550014.1024 0.018978866 0.014471004 171.3104535 -2.233783865 -0.101991559 RPWRPEEAVEDPDEEDEDNT(ph)SEAENGFSLEEVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.564)S(0.436)EAENGFSLEEVLR 118.05 0.00013437 105650000 17647 25528 17509 23962 17268 24095 22170 27567 25050 28821 TRUE FALSE 16957.33573 24799.96643 20673.26579 25198.68169 17823.4409 24582.21741 22441.32309 26997.73182 22206.42902 26868.928 0.631113222 0.922997986 0.769411634 0.937837255 0.663347674 0.914893866 0.83521468 1.004793783 0.82647246 1 14.71365114 2.233815167 1.826646122 0.937569224 0.802198544 0.249052249 0.10744445 0.494876864 3.304972545 0.050750302 0.032086549 171.3228013 -2.233815167 -0.135370681 PAAAEEEEQQGADGAAAEDGADEAEAEIIQLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 PAAAEEEEQQGADGAAAEDGADEAEAEIIQLLK 33 0 Q6DKK2;K7EJA1;K7EKS0;K7ELX2 Q6DKK2 TTC19 "Tetratricopeptide repeat protein 19, mitochondrial" 0 ; 109.62 7.97E-06 19166300 21285 21970.4 24234 21038.6 17703.4 20963.6 27569 28436 35089 25247 FALSE TRUE 20453.15867 21343.8257 28613.62288 22124.40467 18272.84594 21387.49836 27906.39767 27848.78666 31105.84383 23536.9982 0.868979064 0.906820212 1.215687006 0.939984125 0.77634564 0.908675702 1.185639623 1.183191944 1.321572256 1 14.52264272 2.23382259 24.91173505 1.187286567 0.940377819 0.449765237 0.127694626 105.0783217 552477.1915 0.048493964 0.036984698 171.3257296 -2.23382259 -0.246908748 DCKEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 DCKEPK 6 1 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ; 68.422 0.087718 1062040000 1285550 947160 1004740 902270 1019240 990060 1277920 1306090 1317370 1542070 FALSE TRUE 1235309.285 920147.9242 1186318.868 948836.2628 1052024.78 1010079.692 1293559.567 1279118.785 1167827.68 1437624.225 0.859271333 0.640047592 0.825193988 0.660002973 0.731780087 0.702603416 0.899789767 0.889744874 0.812331665 1 20.45525519 2.233839636 24.99668769 0.891418315 0.73244194 0.527265963 0.075816295 89.6885084 474877.8019 0.025560925 0.019492688 171.3324543 -2.233839636 -0.158976375 KKELEEIVQPIISK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKELEEIVQPIISK 14 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 124.62 5.40E-05 1277100000 2485300 2568000 2007700 2023900 2042500 2434800 2557500 2832000 3234300 2742200 FALSE TRUE 2388171.728 2494763.154 2370536.051 2128353.722 2108198.867 2484033.324 2588799.45 2773518.21 2867155.823 2556468.352 0.934168313 0.975863109 0.92726986 0.832536699 0.824652833 0.971665979 1.012646782 1.084902228 1.12152995 1 21.28572074 2.233849536 2.25348631 1.073206771 0.901738446 0.65996319 0.052813929 0.190328266 1.96583396 0.02608266 0.017672027 171.3363599 -2.233849536 -0.171468325 ETAENYLGHTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETAENYLGHTAK 12 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 119.69 0.00049041 403780000 198940 290140 222820 447730 183000 132750 428800 294850 268220 296240 FALSE TRUE 191165.2049 281865.4913 263088.5306 470837.399 188886.3612 135434.296 434047.7827 288761.2445 237772.7901 276175.4009 0.692187661 1.020603176 0.952613918 1.704849155 0.683936225 0.490392321 1.571638101 1.045571921 0.860948474 1 18.0752253 2.233944061 24.9985768 1.131015853 0.954352295 0.065789591 0.348755254 408.4840471 2211908.384 0.131752402 0.100561067 171.3736556 -2.233944061 -0.176663558 NS(ph)WDSPAFSNDVIR ddPTM_BT-474_Pertuzumab_2h_R1 4 NSWDSPAFSNDVIR 14 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 NS(0.999)WDS(0.001)PAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(0.997)WDS(0.003)PAFSNDVIR;NS(0.994)WDS(0.006)PAFSNDVIR 212.92 1.85E-09 1078150000 859410 874680 705340 788670 825460 802810 865990 887180 962600 900730 TRUE FALSE 825823.3071 849734.9828 832810.6282 829373.3532 852011.6706 819043.3682 876588.2447 868859.423 853329.6835 839722.7548 0.983447575 1.011923254 0.991768561 0.987675216 1.014634492 0.975373555 1.043901978 1.034697962 1.016204073 1 19.67955356 2.233973746 24.99976699 1.028079137 0.995475885 0.447233833 0.015762537 91.0337165 496154.8768 0.005478598 0.004179781 171.38537 -2.233973746 -0.032603252 CNAEEHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 CNAEEHVR 8 0 P11279-2;P11279 P11279-2 LAMP1 Lysosome-associated membrane glycoprotein 1 0 ; 146.23 0.00055664 903200000 676080 937000 606580 1016450 599270 647920 1052260 957280 1102730 939520 FALSE TRUE 649658.0462 910277.6774 716202.4993 1068909.106 618546.0638 661021.3863 1065137.873 937511.8335 977552.7134 875885.4736 0.741715745 1.03926564 0.817689665 1.220375424 0.706195139 0.75468929 1.2160698 1.070358925 1.116073668 1 19.74038272 2.23404314 24.99897239 1.106531379 0.891969027 0.329465507 0.15354003 138.5740837 766837.3399 0.055256593 0.042191215 171.412757 -2.23404314 -0.214562352 NRS(ph)AEEGELAESK ddPTM_BT-474_Pertuzumab_2h_R1 3 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(1)AEEGELAESK;NRS(1)AEEGELAESK;NRS(1)AEEGELAESK 176.09 1.04E-05 1716090000 1657270 1662880 1275810 1423700 1948770 1713850 1257900 1451240 1472630 1200560 TRUE FALSE 1592502.056 1615456.291 1506377.247 1497177.328 2011453.957 1748505.221 1273294.556 1421271.387 1305463.216 1119245.002 1.422835977 1.443344655 1.345886955 1.3376672 1.797152503 1.562218476 1.137637027 1.269848321 1.166378419 1 20.09409445 2.234063086 24.98043547 1.176073568 1.484153129 0.589978549 0.138358461 93.00102148 516545.512 0.054059229 0.04128225 171.4206295 -2.234063086 0.308079561 GVQVPAS(ph)PDTVPQPSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVQVPASPDTVPQPSLR 17 0 Q92613;F2Z2B6;F2Z3N8 Q92613 JADE3 Protein Jade-3 1 GVQVPAS(0.96)PDT(0.04)VPQPSLR;GVQVPAS(0.995)PDT(0.005)VPQPSLR 210.91 3.09E-12 234790000 258370 270560 231730 263920 262280 270030 237120 260120 252380 267550 TRUE FALSE 248272.6148 262843.8937 273608.7658 277540.9428 270716.4744 275490.1916 240021.9455 254748.4311 223730.8805 249428.6002 0.995365466 1.053784103 1.096942234 1.112706974 1.085346565 1.104485177 0.962287185 1.021328071 0.896973644 1 17.92826737 2.234071701 24.99865894 0.976873591 1.077030522 0.580789708 0.043370016 86.32288369 480723.9408 0.016192341 0.012366216 171.4240302 -2.234071701 0.100156932 LLEQWEKDDDIEEGDLPEHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEQWEKDDDIEEGDLPEHK 20 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 ; 223.89 3.70E-25 751930000 698112 605923 581976 583180 620679 599233 749272 728511 894091 824251 FALSE TRUE 670829.0112 588642.6693 687152.0092 613277.9897 640643.7037 611349.9018 758441.8149 713466.9933 792597.538 768423.7456 0.872993599 0.766039145 0.894235782 0.798098696 0.833711487 0.79558955 0.987009862 0.928481189 1.031458935 1 19.55154258 2.23414023 24.99853979 0.975397016 0.826094989 0.768857212 0.042785451 52.13295174 294823.0458 0.014746197 0.011266264 171.4510821 -2.23414023 -0.149302027 LWKEEEDGQWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LWKEEEDGQWK 11 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 99.531 0.0042917 327090000 344590 316500 265050 285550 313250 289350 405110 417340 463400 408810 FALSE TRUE 331123.0418 307473.7299 312950.431 300287.2697 323325.9707 295200.8552 410067.8574 408721.7832 410796.7747 381120.9346 0.868813575 0.806761587 0.821131569 0.787905472 0.848355316 0.774559539 1.075952067 1.072420185 1.077864629 1 18.53988933 2.234141385 24.99999992 1.064124128 0.817578859 0.925757673 0.033079373 24.04397932 136017.3597 0.011259543 0.008601558 171.451538 -2.234141385 -0.246545269 MLSFQGLAELAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLSFQGLAELAHR 13 0 O15294;C9JZL3 O15294 OGT UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit 0 164.2 3.74E-05 120750000 111550 117330 107630 131490 99137 90748 147910 128270 127590 137400 FALSE TRUE 107190.5027 113983.8633 127081.1352 138276.2147 102325.8316 92582.98674 149720.1668 125621.1797 113106.5181 128093.7756 0.836812735 0.88984701 0.992094539 1.079492067 0.798835315 0.722775063 1.168832491 0.980696986 0.882997769 1 16.96684085 2.23414733 24.99830715 1.009552839 0.896356333 0.213675183 0.113244564 204.2014901 1156650.773 0.04402583 0.033629017 171.453885 -2.23414733 -0.113196506 GWGS(ph)PGRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GWGSPGRPK 9 1 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2;S4R3B3;H7C453;S4R3U7 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 GWGS(1)PGRPK;GWGS(1)PGRPK 62.338 0.05043 1103630000 1169690 1300030 1047500 1065250 1041070 1093510 1374670 1399380 1492920 1544020 TRUE FALSE 1123977.222 1262954.417 1236806.552 1120227.68 1074556.962 1115621.521 1391493.623 1370482.314 1323449.98 1439442.15 0.780842232 0.877391576 0.859226299 0.778237375 0.746509307 0.775037414 0.966689507 0.952092666 0.919418665 1 20.45707838 2.234149317 24.99825797 0.955584236 0.805140775 0.77354312 0.041496668 58.31335235 330450.032 0.0167113 0.012769094 171.4546692 -2.234149317 -0.150443462 ALS(ph)PAELR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALSPAELR 8 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 ALS(1)PAELR 80.231 0.024335 0 316540 350010 291910 358300 295910 308690 389360 414760 392390 373100 TRUE FALSE 304169.2668 340028.0575 344664.6305 376791.9059 305428.2139 314931.9233 394125.1042 406195.0611 347847.5322 347829.6047 0.874477798 0.977570779 0.990900791 1.083265774 0.878097234 0.905420123 1.133098215 1.16779899 1.000051541 1 18.4080212 2.234152621 24.99988999 1.099206644 0.957228727 0.367835364 0.076651061 106.8494267 605988.2925 0.028871034 0.022059177 171.4559739 -2.234152621 -0.141977917 MEEFKDQLPADECNK ddPTM_BT-474_Pertuzumab_2h_R1 3 MEEFKDQLPADECNK 15 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;; 256.18 8.70E-25 1077200000 1441270 1702290 1117860 2088030 1179800 1261740 2224220 2206170 2281030 1779700 FALSE TRUE 1384943.575 1653742.356 1319882.169 2195793.479 1217749.338 1287253.247 2251440.67 2160611.819 2022097.037 1659159.334 0.834726085 0.996735107 0.795512608 1.323437378 0.733955633 0.775846672 1.356976768 1.302232868 1.21874795 1 20.66202101 2.234228962 24.9999922 1.254853118 0.919558229 0.407807208 0.180468206 100.1581527 578052.0063 0.064837917 0.04956117 171.4861152 -2.234228962 -0.335294888 EPEDEEEEEEEEEEDEDEDLEELEVLER ddPTM_BT-474_Pertuzumab_2h_R1 2 EPEDEEEEEEEEEEDEDEDLEELEVLER 28 0 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2;F8W914 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4;Reticulon 0 ; 161.68 9.03E-12 186110000 141325 163917 148579 209224 136101 153257 217769 222547 238457 231103 FALSE TRUE 135801.8628 159242.2477 175430.5304 220022.0757 140478.8123 156355.9615 220434.1222 217951.3267 211388.3611 215450.188 0.630316752 0.739113988 0.814250997 1.021220161 0.652024552 0.725717452 1.023132652 1.011608895 0.981147258 1 17.71699483 2.234239519 24.98187024 1.006303969 0.771570055 0.573877555 0.101257244 85.06917308 491810.2943 0.039026581 0.029832496 171.4902837 -2.234239519 -0.234733914 DLKDEIVR ddPTM_BT-474_Pertuzumab_2h_R1 5 DLKDEIVR 8 1 P15924;P15924-3 P15924 DSP Desmoplakin 0 ;;;; 119.68 0.0015025 5374810000 4535110 4549565 3752385 3891997 4268351 4458562 4479730 5092500 5470640 4815280 FALSE TRUE 4357872.887 4419815.861 4430524.441 4092863.432 4405646.386 4548717.178 4534554.276 4987338.095 4849635.882 4489136.797 0.970759655 0.98455807 0.986943513 0.911726155 0.981401678 1.013272124 1.010117197 1.110979309 1.080304767 1 22.09800663 2.234250707 1.766241345 1.072496306 0.967453002 0.555465236 0.035403055 0.230935038 1.437745855 0.01821854 0.011395292 171.4947017 -2.234250707 -0.105043304 EGLPLMVFANWR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGLPLMVFANWR 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 142.83 0.00014352 208712000 334510 399160 302070 303130 330670 332450 395000 400530 471310 424600 FALSE TRUE 321436.9794 387776.3476 356660.7685 318774.5756 341306.3009 339172.3668 399834.1282 392258.9155 417808.8647 395841.4638 0.812034637 0.979625388 0.901019224 0.805308703 0.862229787 0.856838906 1.010086524 0.990949538 1.055495452 1 18.59456321 2.234357765 24.99791812 1.010858004 0.872697859 0.68230121 0.048296327 66.38117174 394820.2425 0.018172055 0.013900712 171.536982 -2.234357765 -0.138160145 EAGSQKDENLALYVENQFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAGSQKDENLALYVENQFR 19 1 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 269.9 1.57E-32 634620000 592920 856270 500880 816910 611540 622490 884880 929570 901300 775220 FALSE TRUE 569748.0309 831850.018 591400.158 859070.823 631210.7395 635077.1743 895709.4261 910374.0547 798988.2026 722713.6589 0.788345459 1.151009128 0.818304941 1.188673844 0.873389802 0.878739687 1.239369721 1.259660785 1.105539092 1 19.46306464 2.23440793 24.99996535 1.184467566 0.960307553 0.314128048 0.141911341 108.8593018 655346.026 0.04898213 0.037470009 171.5567972 -2.23440793 -0.224160012 S(ph)CSVTDAVAEQGHLPPPSVAYVHTTPGLPSGWEER ddPTM_BT-474_Pertuzumab_2h_R1 2 SCSVTDAVAEQGHLPPPSVAYVHTTPGLPSGWEER 35 0 Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.542)CS(0.458)VT(0.001)DAVAEQGHLPPPSVAYVHTTPGLPSGWEER;S(0.487)CS(0.487)VT(0.026)DAVAEQGHLPPPSVAYVHTTPGLPSGWEER 199.25 3.14E-27 344180000 132252 153647 116644 151480 129606 154314 111793 132489 131054 148549 TRUE FALSE 127083.4456 149265.138 137724.1655 159297.901 133774.8947 157434.3348 113161.1562 129753.0559 116177.2993 138487.6439 0.917651872 1.077822785 0.994487029 1.150267969 0.965969894 1.136811418 0.817120957 0.936928755 0.838900107 1 17.07939774 2.234458679 24.99999999 0.89498085 1.041708208 0.41826758 0.082149941 92.81910096 565695.6089 0.02754589 0.021085212 171.5768457 -2.234458679 0.146727358 KVDQYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVDQYK 6 1 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 105.12 0.053316 2336400000 4402100 4465500 3808700 4167400 3823000 4054500 4528400 4491300 5150700 4744900 FALSE TRUE 4230061.065 4338148.312 4497016.814 4382480.013 3945970.267 4136484.768 4583819.914 4398553.085 4566014.129 4423523.697 0.95626504 0.980699689 1.016614157 0.990721496 0.892042303 0.935110797 1.036237224 0.994355041 1.032211975 1 22.07676462 2.234555544 24.9995581 1.013744209 0.963383549 0.381094527 0.033514396 128.6539012 803044.8729 0.013518002 0.010351483 171.6151182 -2.234555544 -0.05036066 AS(ph)LSDLTDLEDIEGLTVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASLSDLTDLEDIEGLTVR 18 0 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 AS(0.999)LS(0.001)DLTDLEDIEGLTVR;AS(1)LSDLTDLEDIEGLTVR;AS(1)LSDLTDLEDIEGLTVR;AS(1)LSDLTDLEDIEGLTVR 413.74 1.58E-147 293890000 143001 178427 152386 241228 168301 171309 256343 287212 268686 238056 TRUE FALSE 137412.3628 173338.4367 179925.54 253677.806 173714.5545 174772.9854 259480.2023 281280.9718 238185.8917 221932.2551 0.61916355 0.781042109 0.810722803 1.143041627 0.782736851 0.787506013 1.169186526 1.267418167 1.073236928 1 17.75975983 2.234590328 24.99262632 1.163047462 0.831371905 0.530224295 0.139642698 76.24598965 479955.7278 0.052949176 0.040560749 171.6288641 -2.234590328 -0.331675557 GQAALDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQAALDR 7 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 85.212 0.048802 156430000 135970 151130 138730 156570 130030 111330 183310 158350 148860 156040 FALSE TRUE 130656.1421 146819.9204 163801.597 164650.5965 134212.533 113581.1689 185553.4026 155080.0172 131962.0369 145471.2718 0.898157694 1.009270893 1.126006496 1.131842696 0.922605071 0.780780751 1.275532965 1.066052529 0.907134689 1 17.15037475 2.234694576 24.99933274 1.074932665 0.990714379 0.082888912 0.130358631 279.7202627 1808756.475 0.050064214 0.038381516 171.6700667 -2.234694576 -0.084218287 SMDAMSS(ph)PTKTETVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SMDAMSSPTKTETVK 15 1 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 SMDAMS(0.016)S(0.982)PT(0.003)KTETVK 221.79 9.01E-13 890710000 993080 866660 901030 813100 971780 1196700 1189800 1264500 1737000 1493900 TRUE FALSE 954269.3357 841943.7053 1063866.164 855064.1884 1003038.186 1220898.094 1204361.128 1238387.633 1539823.042 1392716.822 0.685185474 0.604533306 0.763878304 0.613954089 0.720202535 0.876630536 0.864756646 0.889188393 1.105625363 1 20.40947052 2.234703104 0.740274849 1.032787515 0.653738152 0.825090161 0.065270238 0.269776088 0.284475066 0.053491557 0.033491273 171.6734376 -2.234703104 -0.379049362 AET(ph)PTESVSEPEVATK ddPTM_BT-474_Pertuzumab_2h_R1 2 AETPTESVSEPEVATK 16 0 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 AET(0.8)PT(0.2)ESVSEPEVATK;AET(0.976)PT(0.024)ESVSEPEVATK 172.43 5.11E-08 463740000 426110 387100 350510 368350 379440 378210 430270 450820 463060 462460 TRUE FALSE 409457.1501 376060.287 413854.9541 387360.5876 391645.0322 385857.6653 435535.773 441510.4095 410495.3701 431137.1723 0.949714329 0.872252061 0.959914804 0.898462514 0.908400058 0.894976565 1.010202323 1.024060178 0.952122425 1 18.71778743 2.234717695 24.99999328 1.001743328 0.91319047 0.649163446 0.029664104 54.76610349 356274.4241 0.010346157 0.007932908 171.6792056 -2.234717695 -0.088552857 TGST(ph)SSKEDDYESDAATIVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSTSSKEDDYESDAATIVQK 21 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.007)GS(0.288)T(0.577)S(0.123)S(0.006)KEDDYESDAATIVQK 293.77 1.36E-54 561520000 607020 455230 482490 370830 577310 477300 354720 366150 390390 274220 TRUE FALSE 583296.9873 442247.2861 569686.6759 389968.5807 595879.7004 486951.333 359061.1695 358588.8745 346074.5638 255646.8352 2.281651509 1.729914966 2.228412785 1.525419161 2.330870633 1.904781386 1.404520299 1.402672849 1.353721292 1 17.96379264 2.234725604 3.610487484 1.319870118 1.999642952 0.652583797 0.255011451 0.143423688 4.013812285 0.092255127 0.069458248 171.6823319 -2.234725604 0.679772835 NKTEDLEATSEHFK ddPTM_BT-474_Pertuzumab_2h_R1 2 NKTEDLEATSEHFK 14 1 C9JXZ5;Q9BV40 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ; 162.29 2.68E-06 1302340000 1913220 2606700 1667070 2316900 1714180 2000440 2886400 2983200 3549100 2915600 FALSE TRUE 1838449.247 2532359.468 1968346.633 2436475.487 1769318.156 2040890.267 2921724.627 2921595.878 3146221.047 2718123.815 0.676366999 0.931657143 0.724156354 0.896381347 0.650933613 0.750845218 1.074904907 1.07485754 1.157497326 1 21.37417974 2.234750571 24.87955179 1.081884043 0.777006823 0.735625383 0.089547687 44.54990401 290906.113 0.031210821 0.023932997 171.6922022 -2.234750571 -0.30487722 LQHSSALTASVEEGGVPGEDPS(ph)S(ph)RPATPELAEPESAPTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQHSSALTASVEEGGVPGEDPSSRPATPELAEPESAPTLR 40 1 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 2 LQHSSALTASVEEGGVPGEDPS(0.679)S(0.68)RPAT(0.64)PELAEPES(0.001)APTLR 78.746 0.0017642 114350000 17057 25327 20094 28700 18362 25919 13851 18297 13065 22977 TRUE FALSE 16390.39358 24604.69876 23725.43279 30181.21044 18952.63041 26443.09994 14020.51268 17919.16056 11581.91597 21420.74732 0.765164414 1.148638672 1.107591273 1.408970938 0.88477914 1.234462063 0.654529577 0.836532932 0.54068683 1 14.38672119 2.234756362 24.99996881 0.75098891 1.099945441 0.40158178 0.199311737 91.67178424 602420.4257 0.069364057 0.053192877 171.6944914 -2.234756362 0.348956531 KTFPTVNPSTGEVICQVAEGDKEDVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTFPTVNPSTGEVICQVAEGDKEDVDK 27 2 P05091;F8VP50 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ; 270.88 5.35E-61 847370000 222743 248990 181085 270828 184609 186688 329243 342546 313839 252700 FALSE TRUE 214037.9573 241889.049 213811.0877 284805.4655 190547.1161 190462.9593 333272.3743 335472.3054 278213.3124 235584.4039 0.908540437 1.026761725 0.907577429 1.208931749 0.80882738 0.808470154 1.414662298 1.424000485 1.180949621 1 17.84588451 2.234783855 24.9999998 1.309012138 0.952701125 0.463666803 0.159028496 74.29320337 491771.9916 0.05768727 0.044239964 171.705361 -2.234783855 -0.356311013 QASESSS(ph)RPH ddPTM_BT-474_Pertuzumab_2h_R1 1 QASESSSRPH 10 1 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 1 QAS(0.384)ES(0.057)S(0.03)S(0.528)RPH 121.58 0.0013453 60868000 132220 131200 109420 125190 109120 127450 101950 106180 117250 119090 TRUE FALSE 127052.6962 127458.3045 129194.628 131651.0709 112629.9439 130027.1263 103197.6946 103987.3459 103940.2716 111023.9282 1.144372193 1.148025534 1.163664717 1.185790064 1.014465491 1.171163085 0.929508587 0.936621029 0.936197027 1 16.76051112 2.234795703 24.99959436 0.943806167 1.136108602 0.785561709 0.047890983 41.19381908 273529.3422 0.017347654 0.01330636 171.7100454 -2.234795703 0.192302435 SNELWTEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNELWTEIK 9 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 143.89 0.00023465 77671000 248480 239540 219370 221390 221160 224560 268000 274860 298580 272060 FALSE TRUE 238769.1269 232708.5537 259015.0389 232815.9644 228273.8123 229100.7571 271279.8642 269184.0449 264686.4501 253633.1339 0.941395642 0.917500605 1.02121925 0.917924093 0.900015738 0.903276136 1.069575808 1.061312617 1.043579938 1 17.9523837 2.234797107 24.99993486 1.050819625 0.934575181 0.683012839 0.03659707 54.16908973 359825.2324 0.013818249 0.010593683 171.7106006 -2.234797107 -0.116244443 RSDS(ph)MTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.082)DS(0.459)MT(0.459)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.148)DS(0.636)MT(0.216)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 236.7 3.39E-50 1040160000 149760 138557 101977 91590 131234 129239 84195 99340 87476 79817 TRUE FALSE 143907.2136 134605.49 120406.5124 96316.97088 135455.2608 131852.3011 85225.4036 97288.59429 77546.09121 74410.9235 1.933952797 1.808947984 1.618129526 1.294392898 1.820367957 1.771948189 1.145334577 1.307450435 1.042133165 1 16.1832268 2.234842108 24.99941586 1.166146181 1.694775317 0.716075529 0.179313966 59.28334678 398554.6158 0.069356494 0.053204016 171.7283939 -2.234842108 0.528629136 ASAS(ph)PDRIPSLPQETVDQEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASASPDRIPSLPQETVDQEPK 21 1 A0A494C1R1;A0A2R8Y5U1;Q76L82;Q8IXJ9 A0A494C1R1 ASXH1;ASXL1 Putative Polycomb group protein ASXL1 1 AS(0.025)AS(0.975)PDRIPSLPQETVDQEPK;AS(0.007)AS(0.993)PDRIPSLPQETVDQEPK 188.29 7.26E-24 241290000 210663 198026 194146 173598 201288 196790 221891 242817 240989 223459 TRUE FALSE 202430.0571 192378.4924 229232.501 182557.4136 207762.6113 200769.2286 224606.5684 237802.7441 213632.939 208323.9229 0.971708166 0.923458476 1.100365708 0.876315168 0.997305583 0.963735829 1.078160229 1.141504734 1.025484429 1 17.668469 2.234869954 24.58770432 1.08059218 0.972550526 0.295305071 0.064766839 76.60457829 510341.792 0.022710496 0.017431481 171.7394048 -2.234869954 -0.108041655 YSEDPTVPLPSETDGY(ph)VAPLTCSPQPEYVNQPDVRPQPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPR 42 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 2 YSEDPTVPLPS(0.052)ET(0.041)DGY(0.907)VAPLTCSPQPEYVNQPDVRPQPPS(1)PR 145.51 4.01E-13 168480000 20308 38821 12723 58200 19322 23081 51145 60688 37368 26060 TRUE FALSE 19514.34091 37713.86309 15022.32912 61203.70897 19943.50968 23547.71363 51770.92781 59434.77159 33126.1413 24294.93299 0.803226785 1.552334518 0.618331778 2.519196452 0.820891734 0.969243819 2.130935197 2.446385492 1.363500007 1 14.56836783 2.234879489 24.99971423 1.92884958 1.243655884 0.109241208 0.636583865 147.75938 1003467.385 0.22603541 0.173446097 171.7431756 -2.234879489 -0.685193696 KPIDSLRDS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 8 KPIDSLRDSR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 KPIDSLRDS(1)R;KPIDS(0.001)LRDS(0.999)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R 145.71 2.36E-05 23946510000 12570840 13398930 12539640 14466060 12770880 12784760 16167780 16830610 16673780 17086370 TRUE FALSE 12079557.68 13016805.64 14805831.89 15212655.09 13181666.95 13043276.61 16365646.13 16483052.02 14781042.4 15929094.94 0.758332957 0.817171703 0.929483561 0.955023192 0.8275214 0.818833503 1.0274059 1.034776432 0.927927321 1 23.92516096 2.234899637 24.99820978 1.005069519 0.856740849 0.587529374 0.059874491 71.13913865 485751.2656 0.02361112 0.018121138 171.7511434 -2.234899637 -0.14832867 RS(ph)SDPALIGLSTSVSDSNFSSEEPSR ddPTM_BT-474_Pertuzumab_2h_R1 5 RSSDPALIGLSTSVSDSNFSSEEPSR 26 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.644)S(0.356)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR 303 5.34E-71 6986550000 647138 675269 602341 739161 707471 743417 595508 682489 709584 714734 TRUE FALSE 621847.1315 656010.9893 711197.4177 777309.1878 730227.4472 758449.4011 602796.005 668395.3637 629034.9991 666324.4296 0.933249786 0.984521894 1.067344054 1.166562643 1.095903759 1.138258433 0.904658419 1.003107997 0.944037126 1 19.34586526 2.234911993 24.999056 0.965393565 1.066902456 0.34215597 0.068760134 119.7459128 820445.8934 0.027293731 0.020938172 171.7560299 -2.234911993 0.10150889 DFNHINVELSLLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFNHINVELSLLGK 14 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 198.59 2.18E-08 4533900000 5793200 5141200 4764700 5319600 5414300 4999700 6304100 6174200 6789500 6589000 FALSE TRUE 5566795.339 4994578.01 5625787.28 5594145.194 5588455.877 5100797.36 6381251.462 6046700.612 6018784.424 6142721.161 0.906242558 0.813088838 0.91584611 0.910694959 0.90976877 0.830380743 1.038831374 0.984368402 0.979823805 1 22.55044647 2.234930656 24.99999863 0.999243395 0.88215748 0.727131585 0.035929491 49.31123099 339607.6403 0.013062842 0.010025247 171.7634108 -2.234930656 -0.117085914 RPS(ph)TSQTVSTPAPVPVIESTEAIEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSTSQTVSTPAPVPVIESTEAIEAK 26 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 RPS(0.669)T(0.098)S(0.098)QT(0.131)VS(0.004)T(0.001)PAPVPVIESTEAIEAK 163.51 9.07E-12 150060000 80787 69200 58877 62091 71374 75318 53796 64878 59962 66436 TRUE FALSE 77629.75473 67226.48375 69517.38361 65295.52395 73669.80953 76840.98156 54454.37154 63538.24663 53155.36514 61936.23054 1.253381971 1.085414517 1.122402558 1.054237938 1.189446127 1.240646725 0.879200608 1.025865573 0.85822732 1 15.91849596 2.234930741 24.99999998 0.949581757 1.149458669 0.665705527 0.075016941 60.0142697 413330.1592 0.027092819 0.020797957 171.7634447 -2.234930741 0.199876911 WLNDAENLSSDSSLSSPSALNS(ph)PGIEGLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 WLNDAENLSSDSSLSSPSALNSPGIEGLSR 30 0 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 WLNDAENLSSDSSLSSPS(0.001)ALNS(0.995)PGIEGLS(0.004)R 124.82 9.55E-06 23997000 14099 15920 12277 15645 14144 14690 16038 19808 13535 15230 TRUE FALSE 13547.99549 15465.97719 14495.727 16452.44032 14598.95461 14987.04186 16234.27784 19398.95788 11998.56354 14198.45853 0.95418777 1.089271568 1.020936672 1.158748345 1.028207011 1.055540066 1.143383122 1.366272108 0.845060998 1 13.79344669 2.23493449 8.436344182 1.146680351 1.055284433 0 0.135907754 0.300629835 193.681865 0.048987631 0.038159902 171.7649273 -2.23493449 -0.091395918 AAVPSGASTGIYEALELRDNDKTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAVPSGASTGIYEALELRDNDKTR 24 2 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 125.73 5.44E-05 189580000 116940 91769 75085 60770 114250 71157 60878 27885 72597 39067 FALSE TRUE 112369.8555 89151.83797 88654.52976 63906.34698 117924.955 72595.84329 61623.04317 27309.16501 64356.09291 36420.95729 3.085307578 2.447816988 2.434162536 1.754658629 3.237832385 1.99324369 1.691966597 0.749820077 1.767007177 1 15.15248122 2.234937751 2.411544122 1.165355378 2.52890383 0.633688109 0.463664455 0.178246481 2.116803437 0.197810484 0.136943561 171.766217 -2.234937751 1.363548452 IMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDR 33 2 P62136;P62136-2;P62136-3;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 ; 270.95 1.02E-73 1763665000 888708 921876 719401 697068 817405 801830 913324 971009 948175 1011452 FALSE TRUE 853976.3088 895584.9991 849412.7637 733043.763 843697.5742 818043.552 924501.5323 950957.3248 840542.1491 942945.4551 0.905647622 0.949773918 0.900807951 0.777397843 0.894746954 0.867540691 0.980440096 1.008496642 0.891400605 1 19.84681479 2.234998031 24.99784784 0.975176708 0.88229416 0.416176534 0.05058675 90.41117414 634385.9316 0.01932242 0.014838094 171.7900598 -2.234998031 -0.092882548 SKIEDYFPEFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKIEDYFPEFAR 12 1 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;P63092-2;A0A590UJB0;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 73.834 0.034776 245600000 391500 508010 317330 524110 342720 388600 541990 566830 555390 500250 FALSE TRUE 376199.7472 493522.0522 374678.59 551159.3799 353743.9001 396457.7583 548623.0357 555124.7624 492344.4556 466367.6219 0.806659231 1.058225376 0.803397518 1.181813132 0.758508703 0.85009709 1.176374624 1.190315829 1.055700337 1 18.83110811 2.235050395 24.99997778 1.130796398 0.917183988 0.339916879 0.131578852 92.61217914 659579.3169 0.046131947 0.035436402 171.8107744 -2.235050395 -0.21361241 VKS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKSPSK 6 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A3B3ISF7;A0A3B3ISJ7;A0A3B3IRN6;A0A3B3ITZ5;N0DVX5;Q9HCK1 Q5T4S7-3;A0A3B3ITZ5 UBR4;ZDBF2 E3 ubiquitin-protein ligase UBR4;DBF4-type zinc finger-containing protein 2 1 VKS(0.882)PS(0.118)K;VKS(0.858)PS(0.142)K 60.973 0.07641 636010000 961170 822790 727930 650090 770120 734000 964180 914800 999260 1160920 TRUE FALSE 923606.4138 799324.8348 859483.1437 683641.2228 794891.6092 748841.9829 975979.9233 895909.0603 885828.194 1082289.854 0.853381754 0.738549688 0.794133975 0.63166186 0.734453535 0.691905204 0.901773143 0.827790316 0.818475929 1 20.0456555 2.235107585 24.99987419 0.868891478 0.73777532 0.488319053 0.072400702 83.45127611 604176.7011 0.025930846 0.019927281 171.8334007 -2.235107585 -0.131116158 RAPQASGPST(ph)PGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 RAPQASGPSTPGYR 14 1 Q2QGD7-2;Q2QGD7 Q2QGD7-2 ZXDC Zinc finger protein ZXDC 1 RAPQASGPS(0.206)T(0.794)PGYR 78.441 0.012816 219450000 35859 48977 28409 37027 44697 42090 28260 35059 25476 31721 TRUE FALSE 34457.59064 47580.22391 33543.13825 38937.96791 46134.7196 42941.08864 28605.85433 34335.0194 22584.07128 29572.50842 1.165189985 1.608934327 1.134267604 1.316694795 1.560054323 1.452061084 0.967312408 1.161045215 0.763684668 1 14.851969 2.235188514 24.99963214 1.004456808 1.378707171 0.571707793 0.16862644 66.72405657 494662.3688 0.060427163 0.046453245 171.8654242 -2.235188514 0.374250363 EGPSCPS(ph)PGPFCR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGPSCPSPGPFCR 13 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 EGPSCPS(1)PGPFCR;EGPSCPS(1)PGPFCR 255.63 8.03E-24 523320000 617300 709150 504570 637810 588430 647030 549310 586700 617750 683810 TRUE FALSE 593175.2335 688925.7363 595757.0231 670727.4505 607357.3853 660113.3899 556032.6201 574584.44 547625.6098 637494.9396 0.930478341 1.0806764 0.934528239 1.052129843 0.95272503 1.035480204 0.872214955 0.90131608 0.859027383 1 19.28205436 2.235207804 24.99957216 0.89907663 0.99900517 0.355015468 0.058595177 79.42297846 592192.699 0.019266474 0.014813034 171.8730578 -2.235207804 0.09992854 S(ph)PLSPTETFSWPDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 S(1)PLSPTETFSWPDVR;S(1)PLSPTETFSWPDVR;S(1)PLSPTETFSWPDVR;S(1)PLSPTETFSWPDVR 280.97 1.03E-33 428384000 107237 106126 76227 98257 82614 92806 121956 121109 142899 148319 TRUE FALSE 103046.0595 103099.3904 90002.91456 103328.0555 85271.35434 94682.60091 123448.534 118608.0568 126677.7046 138273.222 0.745235108 0.7456208 0.650906323 0.747274519 0.616687404 0.684750088 0.892786992 0.857780379 0.916140542 1 17.07716227 2.235214874 24.07573703 0.899354942 0.696905061 0.800865623 0.05303524 24.34150817 175155.9379 0.019147202 0.014733257 171.8758559 -2.235214874 -0.202449881 LPASPETHLDMLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPASPETHLDMLR 13 0 P04626-5;P04626-4;P04626;J3QLU9;P04626-6;F5H1T4;J3QL83;J3KRI9;J3QLV2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ; 233.7 1.21E-16 708280000 185259 410280 204329 575430 244097 200367 535230 481140 378950 297330 FALSE TRUE 178018.8735 398579.2161 241255.7956 605128.0113 251948.6017 204418.558 541780.3048 471204.2909 335933.1847 277191.5743 0.642223249 1.437919667 0.870357608 2.18306784 0.908933117 0.737463101 1.954533814 1.69992285 1.211917013 1 18.08052388 2.235243849 24.99985805 1.559013841 1.170007842 0.089151006 0.482797462 182.4982047 1375544.98 0.174036747 0.133850524 171.8873233 -2.235243849 -0.389005998 RHS(ph)YAGEQPETVPYLLLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 RHSYAGEQPETVPYLLLNR 19 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 RHS(1)YAGEQPETVPYLLLNR;RHS(1)YAGEQPETVPYLLLNR 149.99 4.91E-08 1071780000 278600 273120 187692 239880 224520 246200 200299 204733 215479 240406 TRUE FALSE 267712.004 265330.885 221612.1196 252260.2355 231741.8897 251178.3327 202750.3191 200505.192 191018.7273 224123.0875 1.194486507 1.18386235 0.988796478 1.125543282 1.03399383 1.120716011 0.904638256 0.894620872 0.852293842 1 17.77393175 2.235276176 24.98309712 0.903109261 1.103381435 0.665811643 0.067496457 49.26378932 374718.9231 0.024668929 0.018977199 171.9001183 -2.235276176 0.200272174 SANAEDAQEFSDVER ddPTM_BT-474_Pertuzumab_2h_R1 3 SANAEDAQEFSDVER 15 0 Q9HCY8 Q9HCY8 S100A14 Protein S100-A14 0 ;; 281.6 2.10E-33 440330000 289197 574450 261111 726030 303046 339536 635340 686190 496600 327882 FALSE TRUE 277894.8615 558067.2484 308299.5661 763500.4953 312793.7498 346401.6506 643115.481 672019.9367 440228.0499 305674.2601 0.90912091 1.825692645 1.008588574 2.497758546 1.0232911 1.13323788 2.103924226 2.198483891 1.44018685 1 18.22163555 2.235308668 24.99998023 1.841139736 1.434018182 0.029303079 0.553683644 192.1585094 1477233.11 0.195546532 0.150428174 171.9129797 -2.235308668 -0.407121554 RFEELK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFEELK 6 1 P53990-2;P53990;P53990-4;P53990-5;J3KR23;P53990-6 P53990-2 IST1 IST1 homolog 0 107.43 0.050146 98678000 228960 181220 161860 172660 207950 165590 241920 222500 254500 224330 FALSE TRUE 220011.9901 176051.783 191111.7026 181571.0033 214638.9006 168938.3433 244880.6893 217905.2972 225610.227 209135.9293 1.052004746 0.841805536 0.913815733 0.868196124 1.026312893 0.807792061 1.170916399 1.041931427 1.078773158 1 17.67408141 2.235348243 25 1.076082114 0.91726871 0.464360729 0.081301854 68.30214694 531547.0075 0.027462555 0.021132882 171.9286462 -2.235348243 -0.158813405 KPS(ph)ASERLPDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPSASERLPDEK 12 2 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 KPS(0.999)AS(0.001)ERLPDEK;KPS(0.998)AS(0.002)ERLPDEK 99.044 0.0020964 261270000 280910 268040 275420 264330 342420 309200 218136 241270 249370 249620 TRUE FALSE 269931.7266 260395.7616 325194.5207 277972.103 353434.2503 315452.2358 220805.6136 236287.6902 221062.563 232713.0151 1.159933949 1.118956589 1.397405816 1.194484558 1.518755838 1.355541871 0.94883225 1.015360873 0.949936397 1 17.82819237 2.235427197 24.99997469 0.98251473 1.293856317 0.64802072 0.112733219 53.71735636 428576.7911 0.0432534 0.033297455 171.9599052 -2.235427197 0.311341588 NSTGGTSVGWDS(ph)PPASPLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSTGGTSVGWDSPPASPLQR 20 0 Q13424-2;Q13424 Q13424-2 SNTA1 Alpha-1-syntrophin 1 NSTGGTSVGWDS(1)PPASPLQR;NSTGGTSVGWDS(1)PPASPLQR 198.45 1.63E-21 388620000 285850 293210 227402 280220 250459 261880 314480 340330 322350 316450 TRUE FALSE 274678.666 284847.9379 268498.5999 294682.1878 258515.2412 267175.393 318328.7003 333302.0666 285758.1794 295016.5596 0.931061857 0.965532031 0.910113657 0.9988666 0.876273662 0.905628462 1.07901977 1.129774095 0.968617422 1 18.17043641 2.235441139 24.99951946 1.064012804 0.932418847 0.513388772 0.052563145 56.23978419 450699.1135 0.01917973 0.014771523 171.9654256 -2.235441139 -0.131593957 GQRDSS(ph)YYWEIEASEVMLSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQRDSSYYWEIEASEVMLSTR 21 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 GQRDS(0.276)S(0.401)Y(0.134)Y(0.19)WEIEASEVMLSTR 104.96 0.00024343 21071000 9194.7 10218 8607.3 10770 11551 11631 7665.7 9782.8 9713.5 9045.4 TRUE FALSE 8835.360959 9926.592644 10162.83058 11325.84099 11922.54841 11866.18679 7759.51513 9580.781761 8610.864202 8432.747001 1.047744105 1.177148163 1.205162514 1.343078476 1.413839216 1.407155555 0.920164583 1.136140069 1.021122085 1 13.04178696 2.235530586 24.99999338 1.03805091 1.269164202 0.521488118 0.11501264 74.18391164 612062.2478 0.045795161 0.035284747 172.0008471 -2.235530586 0.231113292 KTNHS(ph)SPEAQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTNHSSPEAQSK 12 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 KT(0.179)NHS(0.615)S(0.206)PEAQSK 92.265 0.0047973 35676000 43576 42316 31243 37017 34236 39107 45267 48090 55536 46999 TRUE FALSE 41873.00174 41109.18911 36889.3051 38927.45181 35337.23203 39897.77033 45820.99109 47096.92469 49231.78611 43815.71587 0.955661705 0.938229316 0.841919489 0.888435828 0.806496741 0.910581273 1.045766118 1.074886574 1.123610219 1 15.41916081 2.235555634 3.729822815 1.071219168 0.884189259 0.748192645 0.048771891 0.107242358 3.241606185 0.019284142 0.014584852 172.0107675 -2.235555634 -0.187029908 ALQLILDVLNPETSEDENDRVVVTDDSDERR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALQLILDVLNPETSEDENDRVVVTDDSDERR 31 2 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 ;; 119.85 8.92E-06 155936000 86515.5 109858.1 70805.1 74131.2 99295.2 95447.4 70826.1 79953.2 83843.8 82817.9 FALSE TRUE 83134.37861 106725.0546 83601.15662 77957.12012 102489.1203 97377.41182 71692.891 78302.13848 74326.20333 77208.56987 1.076750661 1.382295446 1.082796337 1.009695171 1.327431922 1.261225431 0.928561313 1.014163824 0.96266779 1 16.23647337 2.235584497 24.99999769 0.979704909 1.191945633 0.47244751 0.110586279 70.80949235 594803.7805 0.04083875 0.031469529 172.0221999 -2.235584497 0.212240724 LASS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 LASSPK 6 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 LAS(0.012)S(0.988)PK;LAS(0.044)S(0.956)PK 103.83 0.036029 851490000 3644980 4037670 2871620 4225740 3236010 3371190 4459730 4831500 4003830 4259380 TRUE FALSE 3502530.152 3922519.605 3390585.613 4443830.948 3340099.201 3439357.772 4514309.51 4731727.837 3549332.004 3970888.399 0.882052025 0.987819151 0.853860716 1.119102453 0.841146581 0.866143146 1.136851268 1.191604337 0.893838267 1 21.92103038 2.235591324 24.9999943 1.086737016 0.929650048 0.239117321 0.108348194 91.76480507 772600.9051 0.039168116 0.030188746 172.0249038 -2.235591324 -0.157086968 KDS(ph)PEPQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSPEPQVK 9 1 Q96JQ2 Q96JQ2 CLMN Calmin 1 KDS(1)PEPQVK 61.375 0.044859 0 151410 150590 122670 156400 125220 137380 198910 209870 222660 204260 TRUE FALSE 145492.7298 146295.3206 144839.1978 164471.8227 129247.815 140157.9177 201344.3201 205536.1112 197384.5703 190425.2883 0.764041011 0.768255739 0.760609051 0.863707884 0.678732411 0.736025761 1.05734024 1.079353026 1.036545997 1 17.53886555 2.235808945 24.99950566 1.053340802 0.762973649 0.896800516 0.046716964 20.24078864 183888.6257 0.017203058 0.013278987 172.1111258 -2.235808945 -0.290367154 NALVSHLDGTTPVCEDIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NALVSHLDGTTPVCEDIGR 19 0 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 ; 247.31 9.74E-25 287230000 134709 203416 119655 278535 120539 143852 205846 202513 185880 113009 FALSE TRUE 129444.4234 197614.7748 141279.3202 292910.2247 124416.2464 146760.786 208365.2049 198331.0358 164779.6817 105354.7998 1.22865236 1.875707374 1.340986082 2.780226676 1.180926229 1.393014711 1.977747624 1.882505934 1.564045321 1 16.68489652 2.235839787 24.58233946 1.712002342 1.66256309 0 0.501941608 994.0663305 8981111.816 0.178330015 0.137767071 172.1233487 -2.235839787 -0.049439253 TVS(ph)SPIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.069)VS(0.465)S(0.465)PIPY(0.007)T(0.046)PS(0.944)PS(0.059)S(0.225)S(0.197)RPIS(0.521)PGLS(0.001)YASHTVGFTPPTSLTR 156.56 6.57E-13 232640000 116670 115390 93316 119610 107850 124300 93612 101800 133680 122590 TRUE FALSE 112110.4074 112099.1902 110180.277 125783.0864 111319.0932 126813.4312 94757.65166 99697.79443 118505.2068 114286.8701 0.980956144 0.980857994 0.964067674 1.100590876 0.974032215 1.109606301 0.829121067 0.872346879 1.036910073 1 16.80230014 2.235874241 24.9999992 0.915040143 1.015903739 0.220083349 0.07356434 88.40854495 822734.8221 0.026609651 0.020541204 172.1370046 -2.235874241 0.100863596 SSS(ph)PVTELASRS(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.191)S(0.271)S(0.538)PVTELAS(0.08)RS(0.92)PIR 193.15 5.96E-08 917440000 834830 879080 653700 766890 851330 850130 652400 760060 735220 679490 TRUE FALSE 802203.9206 854009.4991 771838.1315 806469.2848 878713.8026 867320.2111 660384.2664 744364.4954 651760.9079 633467.5371 1.266369425 1.348150377 1.2184336 1.273102784 1.387148908 1.369162838 1.042491095 1.175063364 1.02887815 1 19.27291116 2.236022712 24.99997437 1.085585817 1.30972453 0.772932407 0.065546145 34.55961475 340428.0987 0.024454131 0.018901467 172.1958626 -2.236022712 0.224138713 KNY(ph)MSNPSY(ph)NY(ph)EIVNRAS(ph)LACGPMVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNYMSNPSYNYEIVNRASLACGPMVK 26 2 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 4 KNY(0.576)MS(0.459)NPS(0.49)Y(0.845)NY(0.845)EIVNRAS(0.786)LACGPMVK 42.121 0.055776 35874000 7520.3 5555.7 6653.7 6633.6 6687.8 7223.6 4933.5 4377.9 7186 7726 TRUE FALSE 7226.398362 5397.256876 7856.171601 6975.960891 6902.919161 7369.666141 4993.877649 4287.494835 6370.275406 7202.711138 1.003288654 0.74933685 1.090724236 0.968518764 0.958377898 1.023179467 0.693333045 0.59526125 0.884427445 1 12.81432433 2.236093525 24.99490506 0.739563182 0.961237979 0.249734385 0.133831346 66.34079893 672107.04 0.047766324 0.036939906 172.2239418 -2.236093525 0.221674796 EKKEEWDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKKEEWDR 8 2 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ;;; 98.943 0.0040296 7476240000 8858300 8258500 5863670 5838630 7554950 7686600 7871950 8776300 10024200 8389560 FALSE TRUE 8512107.843 8022975.666 6923365.606 6139962.394 7797961.828 7842028.319 7968289.279 8595066.338 8886294.841 7821327.629 1.088320071 1.025781817 0.885190588 0.785028155 0.997012553 1.002646698 1.01878986 1.098926774 1.136161949 1 22.89898209 2.236110778 1.654694196 1.085757093 0.948805468 0.276395303 0.083524726 0.480442915 2.610627923 0.048552264 0.029785223 172.2307839 -2.236110778 -0.136951625 KLADMYGGGEDD ddPTM_BT-474_Pertuzumab_2h_R1 3 KLADMYGGGEDD 12 1 A0A087WXI5;P12830-2;P12830;P22223 A0A087WXI5 CDH1;CDH3 Cadherin-1;E-Cad/CTF1;E-Cad/CTF2;E-Cad/CTF3;Cadherin-3 0 ;; 114.83 0.0082476 643380000 953400 1660590 877530 1880260 989620 1119050 1932980 2203600 1698880 1257400 FALSE TRUE 916140.074 1613231.599 1036119.192 1977300.444 1021452.026 1141677.958 1956636.387 2158094.89 1506030.265 1172235.178 0.781532658 1.37620132 0.88388338 1.686777944 0.871371245 0.973932517 1.669150034 1.841008469 1.284750955 1 20.16083061 2.236123302 24.99779833 1.558701792 1.115424127 0.181832869 0.334397834 80.57148131 826347.7444 0.117284094 0.090712982 172.2357504 -2.236123302 -0.443277666 LDQEVAEVDKNIELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDQEVAEVDKNIELLK 16 1 F5H442;Q99816;Q99816-2 F5H442 TSG101 Tumor susceptibility gene 101 protein 0 237.59 8.35E-20 70985000 113630 91014 80687 78285 93245 98828 101550 117110 123950 117060 FALSE TRUE 109189.214 88418.36983 95268.93577 82325.29823 96244.31011 100826.3699 102792.7993 114691.6376 109879.7156 109131.4219 1.000529564 0.810200841 0.872974383 0.754368419 0.881911996 0.923898618 0.941917529 1.050949722 1.006856813 1 16.73570703 2.236148597 1.613865636 1.022946294 0.856554798 0.534628935 0.061409237 0.269956233 1.392129965 0.032931267 0.020044008 172.2457827 -2.236148597 -0.166391496 FIIGSVS(ph)EDNSEDEISNLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 FIIGSVSEDNSEDEISNLVK 20 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087X2F8;A0A087X126;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 FIIGS(0.254)VS(0.643)EDNS(0.103)EDEISNLVK 89.982 0.0012892 30085000 30842 31622 29287 34249 40195 38759 24644 30810 33671 31072 TRUE FALSE 29636.66054 30720.17152 34579.81239 36016.59499 41487.90868 39542.73354 24945.60064 30173.76273 29848.80924 28967.46576 1.023101599 1.060506009 1.193746552 1.243346425 1.43222431 1.365073972 0.861159235 1.041643165 1.030425288 1 14.82214585 2.236168741 24.99995493 0.988169335 1.221991811 0.467662173 0.123481046 64.60977943 675290.4991 0.050459568 0.039039483 172.2537722 -2.236168741 0.233822476 LMDLLGEGLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 LMDLLGEGLKR 11 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 100.04 0.0069399 1416180000 1247720 1284230 1085200 1112500 1152330 1155550 1384490 1391620 1545020 1497120 FALSE TRUE 1198957.723 1247605.018 1281319.78 1169916.258 1189395.741 1178916.013 1401433.803 1362882.561 1369635.807 1395718.729 0.859025317 0.893879972 0.918035815 0.838217783 0.852174379 0.844665897 1.004094717 0.976473649 0.981312193 1 20.4125768 2.23617936 24.99999483 0.98777667 0.869104787 0.867271479 0.02352191 23.22160283 243790.9032 0.009243635 0.007151442 172.257984 -2.23617936 -0.118671883 LLNSTNREDEDT(ph)PPNSPNVDLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLNSTNREDEDTPPNSPNVDLGK 23 1 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 LLNSTNREDEDT(0.999)PPNSPNVDLGK;LLNSTNREDEDT(1)PPNSPNVDLGK 184.3 5.47E-17 701020000 929260 959980 738150 816660 834820 862530 921020 1023730 978920 900620 TRUE FALSE 892943.4918 932602.3103 871550.1251 858807.9205 861672.7435 879970.9476 932291.7183 1002589.618 867797.1056 839620.2052 1.063508818 1.110743053 1.038029004 1.022852851 1.026264897 1.048058327 1.110373134 1.194098965 1.033559102 1 19.67937736 2.236242301 23.80880675 1.111037705 1.051193659 0 0.055260743 53.88288779 553348.5539 0.020306746 0.015720654 172.2829504 -2.236242301 -0.059844046 PLSGQAPGS(ph)PPSTRPPPWLSELPENTSLQEHGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 PLSGQAPGSPPSTRPPPWLSELPENTSLQEHGVK 34 1 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 PLS(0.002)GQAPGS(0.635)PPS(0.163)T(0.163)RPPPWLS(0.037)ELPENTSLQEHGVK 77.077 0.0014422 48007000 34059 32268 33151 31163 31781 32475 38805 43696 37928 39062 TRUE FALSE 32727.93663 31347.74823 39142.12314 32771.32616 32803.26473 33131.66675 39279.9072 42793.66233 33622.57245 36416.29595 0.898716791 0.860816495 1.074851852 0.899908278 0.900785318 0.909803314 1.078635434 1.175123972 0.9232837 1 15.15229657 2.236289089 24.99588962 1.072018379 0.925954904 0.320903197 0.081676952 58.28674848 641374.863 0.029907285 0.02316329 172.3015123 -2.236289089 -0.146063475 SANPTRPS(ph)SPVTSHISK ddPTM_BT-474_Pertuzumab_2h_R1 1 SANPTRPSSPVTSHISK 17 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 SANPT(0.005)RPS(0.497)S(0.497)PVTSHISK 205.43 4.78E-12 1074000000 165290 220320 177940 222520 189900 206340 183010 192080 194300 239500 TRUE FALSE 158830.2841 214036.6893 210097.7163 234004.2839 196008.306 210512.3362 185249.7311 188113.4809 172243.8786 223278.4517 0.711355184 0.958608803 0.940967275 1.048037919 0.877864857 0.942824239 0.829680293 0.842506205 0.771430818 1 17.7684845 2.236308289 24.9940858 0.846568393 0.921111534 0.054396436 0.096818735 128.8338924 1429641.319 0.034127334 0.026430272 172.3091296 -2.236308289 0.07454314 GAPPSTFKGT(ph)PTAENPEYLGLDVPV ddPTM_BT-474_Pertuzumab_2h_R1 2 GAPPSTFKGTPTAENPEYLGLDVPV 25 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GAPPS(0.191)T(0.191)FKGT(0.597)PT(0.022)AENPEYLGLDVPV;GAPPS(0.012)T(0.064)FKGT(0.915)PT(0.009)AENPEYLGLDVPV 138.4 1.59E-05 761240000 960360 1816930 881710 1686320 983190 1285950 1912680 2497500 1779310 1225880 TRUE FALSE 922828.0695 1765112.935 1041054.611 1773351.177 1014815.199 1311952.79 1936087.95 2445925.752 1577330.188 1142850.056 0.807479568 1.544483396 0.910928433 1.551691903 0.887968806 1.14796581 1.694087462 2.140198305 1.380172474 1 20.1242047 2.236336841 12.65629766 1.703006161 1.156623327 0.189847846 0.367516941 0.170732028 839.43882 0.12658044 0.098784935 172.3204584 -2.236336841 -0.546382834 IYQGEDLPHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IYQGEDLPHPK 11 0 Q6DD88;F5H6I7 Q6DD88 ATL3 Atlastin-3 0 ; 88.803 0.012707 1043260000 978940 1387480 819010 1498880 1077710 1140760 1496890 1690230 1599890 1266970 FALSE TRUE 940681.9425 1347910.429 967023.3258 1576237.376 1112375.521 1163826.949 1515209.388 1655326.16 1418277.194 1181156.993 0.796407207 1.141178045 0.818708547 1.33448592 0.941767713 0.985327908 1.282817946 1.401444659 1.200752485 1 20.1717693 2.236338987 24.9483521 1.271433321 1.013171177 0.253014801 0.174931234 63.55566358 713700.0632 0.060363996 0.046746486 172.32131 -2.236338987 -0.258262144 ANESS(ph)PKPVGPPPER ddPTM_BT-474_Pertuzumab_2h_R1 1 ANESSPKPVGPPPER 15 1 Q9BQI0-3;Q9BQI0;Q9BQI0-2;A6PVM9 Q9BQI0-3 AIF1L Allograft inflammatory factor 1-like 1 ANES(0.33)S(0.67)PKPVGPPPER 112.74 0.00044798 619040000 248290 220660 218540 229270 194690 221110 278550 299010 298400 292910 TRUE FALSE 238586.5523 214366.9928 258035.0394 241102.6522 200952.3807 225580.9957 281958.9782 292835.339 264526.883 273070.9448 0.873716361 0.785023075 0.944937733 0.88293045 0.735898068 0.826089337 1.032548441 1.072378239 0.968711201 1 18.05891629 2.236373982 24.99805125 1.02986671 0.84066246 0.684005236 0.0587219 32.11179797 367100.756 0.02214804 0.017161556 172.3351959 -2.236373982 -0.18920425 GEYWECK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEYWECK 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;;; 117.17 0.01231 2261440000 1595180 1631190 1288840 1566320 1567430 1482650 1738440 1701310 1929350 1846870 FALSE TRUE 1532838.602 1584670.058 1521762.058 1647157.963 1617847.809 1512630.199 1759715.549 1666177.354 1710338.276 1721779.85 0.890263992 0.920367408 0.883830798 0.95666003 0.939636859 0.878527065 1.022032839 0.967706385 0.993354799 1 20.71546926 2.236378539 24.99998288 0.991397463 0.91401607 0.712398274 0.026129853 33.56116666 384501.4924 0.009448422 0.007317844 172.3370041 -2.236378539 -0.077381394 QKPELLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKPELLNK 8 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 93.111 0.010987 0 512230 471530 420300 445790 450320 457480 548460 565330 619670 591670 FALSE TRUE 492211.4853 458082.4261 496257.5595 468797.2753 464804.9518 466730.559 555172.2175 553655.7379 549327.6595 551595.6639 0.892341107 0.830467779 0.899676325 0.849892967 0.842655195 0.846146171 1.006484013 1.003734754 0.995888285 1 19.07325159 2.236380434 24.99998943 1.002207171 0.859374122 0.920203612 0.020387471 13.64502481 156463.1032 0.007129732 0.00552393 172.3377561 -2.236380434 -0.142833048 LSFDKDAMVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSFDKDAMVAR 11 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 162.49 2.29E-05 6551200000 10045000 10165400 7841000 8946100 8989000 8652900 10681600 10660500 10736200 10932100 FALSE TRUE 9652430.295 9875492.745 9258043.122 9407809.293 9278139.349 8827867.567 10812324.62 10440356.95 9517471.586 10191659.13 0.947091163 0.968977928 0.90839411 0.923089084 0.91036594 0.86618552 1.060899357 1.024402094 0.933849088 1 23.2808856 2.236398176 24.9999831 1.010636177 0.921960833 0.528772325 0.038727368 44.93913231 519530.3707 0.01459709 0.011314559 172.3447966 -2.236398176 -0.088675345 EKPVCGTTYK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKPVCGTTYK 10 1 Q14444-2;Q14444;G3V153 Q14444-2 CAPRIN1 Caprin-1 0 ; 114.72 0.001202 737760000 421160 426580 350980 389210 385680 385770 480860 481110 519080 547990 FALSE TRUE 404700.6016 414414.3561 414409.8935 409297.1747 398085.7475 393570.5337 486744.9085 471174.9104 460156.2146 510874.1492 0.792172793 0.81118678 0.811178045 0.80117026 0.779224684 0.770386473 0.952768719 0.922291549 0.900723232 1 18.96260841 2.23643104 24.99997171 0.936390286 0.795396214 0.88130264 0.026859855 18.18366786 213460.9664 0.009569036 0.007417056 172.3578387 -2.23643104 -0.140994072 GLIDVKPLGVIWGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLIDVKPLGVIWGK 14 1 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 59.898 0.088679 66542000 60390 62638 52582 60031 50112 60164 44894 49132 46896 55210 FALSE TRUE 58029.89204 60851.62557 62084.73708 63129.2071 51723.89799 61380.5573 45443.4262 48117.40703 41572.56268 51470.57752 1.127438137 1.1822604 1.206218 1.226510565 1.004921656 1.19253679 0.882901036 0.934852674 0.807695672 1 15.65146035 2.236470034 24.99998842 0.903923558 1.156343981 0.739158641 0.072832473 27.09360111 323988.0825 0.025996283 0.020154156 172.3733151 -2.236470034 0.252420423 LILPHVDIQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LILPHVDIQLK 11 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 145.99 0.0017821 0 322820 484330 281800 604260 295140 261330 576690 471120 432970 368290 FALSE TRUE 310203.8375 470517.3826 332727.5286 635445.931 304633.4461 266614.2717 583747.7047 461391.2074 383821.0608 343345.3903 0.903474595 1.370390854 0.969075275 1.850748398 0.887250724 0.776519153 1.700176328 1.343810695 1.117886163 1 18.38930107 2.236481746 24.99998867 1.335373783 1.152265598 0.044280068 0.336936136 173.4524896 2085848.926 0.12144824 0.094155857 172.3779638 -2.236481746 -0.183108184 IKEDRPITIKDDK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKEDRPITIKDDK 13 3 E9PM90;Q9UK41;Q9UK41-2;E9PQR7 E9PM90 VPS28 Vacuolar protein sorting-associated protein 28 homolog 0 92.265 0.0026951 256720000 363020 334790 321290 268960 340270 325430 389810 408850 440950 404900 FALSE TRUE 348832.7771 325242.117 379354.2501 282841.0578 351215.0936 332010.4176 394580.6114 400407.1046 390895.2046 377475.7624 0.92411967 0.861623843 1.004976446 0.749295944 0.930430848 0.879554267 1.045313768 1.060749178 1.035550474 1 18.52602449 2.236571272 24.96674943 1.042812176 0.890742268 0.559050207 0.062395842 34.74689586 436071.6789 0.021486081 0.016662667 172.4135017 -2.236571272 -0.152069908 VFDPQNDKPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFDPQNDKPSK 11 1 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ; 94.688 0.0075857 1157990000 2825900 2681800 2407400 2380100 2704100 2723400 2969600 3306600 3480400 3211700 FALSE TRUE 2715460.704 2605317.69 2842470.732 2502937.246 2791079.832 2778469.014 3005942.853 3238317.554 3085319.583 2994168.698 0.906916402 0.870130561 0.949335531 0.835937283 0.932171869 0.927960076 1.003932362 1.08154145 1.030442802 1 21.51372408 2.236585249 2.25834952 1.046957039 0.89779061 0.758780346 0.035103833 0.127715502 1.325681435 0.015210709 0.010339542 172.4190505 -2.236585249 -0.149166429 CEYSAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 CEYSAHK 7 0 Q9GZN8-2;Q9GZN8 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 81.784 0.026263 67431000 218510 240660 202100 241980 202810 227960 194360 185170 209750 274760 FALSE TRUE 209970.3876 233796.6124 238623.9657 254468.6168 209333.5678 232569.5074 196738.6358 181346.1748 185940.0593 256150.2605 0.81971569 0.912732285 0.931578072 0.993434933 0.817229572 0.907941717 0.76805948 0.70796795 0.725902285 1 17.96663083 2.23660205 24.67912039 0.768552742 0.90013054 0.181672297 0.090725549 50.25005634 633163.9277 0.031527127 0.024468828 172.4257207 -2.23660205 0.131577799 GLQSLPTHDPSPLQR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLQSLPTHDPSPLQR 15 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ;;; 162.29 1.60E-06 1760750000 801770 1654040 832240 2173490 966970 1074750 1853330 2028240 1454020 1081360 FALSE TRUE 770435.942 1606868.399 982644.2811 2285664.079 998073.4682 1096482.181 1876011.607 1986356.135 1288965.745 1008118.524 0.76423151 1.593928055 0.974730905 2.267257297 0.990035838 1.087652052 1.860903815 1.970359722 1.278585518 1 19.94323384 2.236603849 24.99998783 1.656135583 1.3117936 0.031922895 0.476805918 120.8196143 1543577.161 0.168523926 0.130796552 172.4264351 -2.236603849 -0.344341983 LLDIDETEYHADGGK ddPTM_BT-474_Pertuzumab_2h_R1 6 LLDIDETEYHADGGK 15 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ;;;;; 222.16 1.44E-12 3975090000 1477435 2972220 1518340 4472930 1782270 1844210 4537490 4812070 3737310 2725550 FALSE TRUE 1419695.207 2887455.196 1792737.813 4703778.453 1839598.333 1881501.19 4593021.16 4712699.073 3313066.237 2540946.071 0.558727012 1.136370122 0.705539497 1.85119177 0.723981652 0.740472697 1.807602772 1.854702517 1.303871135 1 21.27693433 2.236605817 24.99804896 1.602791959 0.98026959 0.272340053 0.414409513 58.59082916 749244.3344 0.148059318 0.114896591 172.4272163 -2.236605817 -0.622522368 TEYLSNADER ddPTM_BT-474_Pertuzumab_2h_R1 2 TEYLSNADER 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 142.83 8.16E-05 805680000 368900 429820 363620 380460 349000 361390 450830 438430 481710 469310 FALSE TRUE 354482.9802 417561.9544 429334.2227 400095.5862 360225.902 368697.5534 456347.3924 429376.2673 427028.3003 437523.2157 0.810203819 0.954376681 0.981283295 0.914455672 0.823329801 0.842692548 1.043024407 0.981379392 0.976012895 1 18.73900005 2.236613765 24.99991491 0.998300771 0.893294131 0.508825968 0.053913546 49.4260579 634676.1692 0.02110341 0.01637547 172.4303721 -2.236613765 -0.10500664 SHVCEHCNAAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHVCEHCNAAFR 12 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 0 ; 107.09 0.0010706 118834000 113421 142337 102801 130777 115480 89588 113780 55146 93441 79214 FALSE TRUE 108988.3819 138277.6881 121379.4275 137526.4166 119194.5191 91399.53074 115172.4737 54007.21583 82833.96942 73848.76522 1.47583215 1.872444146 1.643621625 1.862271038 1.61403537 1.237658212 1.559572097 0.731321853 1.121670338 1 16.17228618 2.23661523 1.132775249 0.934854482 1.718543807 0.687008054 0.200378086 0.251724586 0.620204907 0.129357832 0.072996146 172.4309536 -2.23661523 0.783689324 SLGTIQQCCDAIDHLCR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGTIQQCCDAIDHLCR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 243.01 1.96E-20 1065270000 657230 723370 594430 795930 714820 729570 622710 672470 704270 677690 FALSE TRUE 631544.725 702740.1959 701856.724 837008.0427 737812.8345 744322.4053 630330.9113 658583.2595 624324.2221 631789.4527 0.999612644 1.112301247 1.110902882 1.324821171 1.167814422 1.178117808 0.997691412 1.042409392 0.98818399 1 19.26908433 2.236617151 24.99662586 1.013551664 1.154388655 0.446999669 0.077019502 51.71370834 665119.1122 0.029657773 0.023018332 172.4317162 -2.236617151 0.140836991 QS(ph)SSSRDDNMFQIGK ddPTM_BT-474_Pertuzumab_2h_R1 2 QSSSSRDDNMFQIGK 15 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 QS(0.866)S(0.126)S(0.008)S(0.001)RDDNMFQIGK;QS(0.492)S(0.492)S(0.013)S(0.003)RDDNMFQIGK 132.14 2.98E-05 1216400000 216415 233378 163050 160767 206950 205562 150383 174569 163553 153549 TRUE FALSE 207957.2625 226722.2879 192516.762 169064.2041 213606.7347 209718.6045 152223.4321 170964.0891 144987.1491 143148.9895 1.452733011 1.583820387 1.344869864 1.181036658 1.492198691 1.465037268 1.063391594 1.194308739 1.012840885 1 17.12715796 2.236712492 24.9998236 1.094935047 1.416409712 0.702948435 0.111622148 31.1600124 421495.8075 0.042998479 0.033389175 172.4695746 -2.236712492 0.321474665 KLDNTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDNTK 6 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 97.033 0.066594 4263800000 4280500 3734900 3030000 3262600 3067700 3427500 3837400 4135400 3799400 4246000 FALSE TRUE 4113213.328 3628384.309 3577588.402 3430983.177 3166375.357 3496806.398 3884363.249 4050002.545 3368108.04 3958414.638 1.039106234 0.916625629 0.903793243 0.866756894 0.799909976 0.883385577 0.981292665 1.023137522 0.850872975 1 21.91649131 2.236758272 24.99145862 0.972457126 0.896173559 0.151515704 0.070277689 78.54586154 1089093.887 0.026477568 0.020573097 172.4877557 -2.236758272 -0.076283567 S(ph)GGGDLTLGLEPSEEEAPRS(ph)PLAPSEGAGSDVFDGDLGMGAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAK 43 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 2 S(0.832)GGGDLT(0.161)LGLEPS(0.015)EEEAPRS(0.988)PLAPS(0.003)EGAGS(0.001)DVFDGDLGMGAAK;S(0.942)GGGDLT(0.058)LGLEPSEEEAPRS(0.995)PLAPS(0.004)EGAGSDVFDGDLGMGAAK;S(0.942)GGGDLT(0.058)LGLEPS(0.002)EEEAPRS(0.985)PLAPS(0.011)EGAGS(0.002)DVFDGDLGMGAAK 176.71 2.95E-22 240541000 201740 357960 198790.2 494917 243524 255226 480415 576178 363507 248421 TRUE FALSE 193855.7778 347751.3313 234716.0112 520459.7257 251357.1706 260386.8446 486294.4625 564279.723 322243.2093 231595.2244 0.837045661 1.501547936 1.013475178 2.247281769 1.085329679 1.124318713 2.09976032 2.436491186 1.391406969 1 17.82124598 2.236815462 24.99935858 1.923148864 1.330665047 0.096478872 0.524031549 69.45830709 994965.3461 0.186684681 0.145072342 172.5104715 -2.236815462 -0.592483817 IEDVGS(ph)DEEDDSGKDKKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEDVGSDEEDDSGKDKKK 18 3 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGKDKKK 133.98 8.22E-06 411930000 1130500 868690 235680 154070 363300 585290 348180 437320 608460 304520 TRUE FALSE 1086318.81 843915.8117 278272.6187 162021.5712 374985.8744 597124.9648 352441.131 428289.1892 539390.1717 283894.5892 3.826486491 2.972637887 0.980196979 0.570710318 1.320863055 2.103333377 1.241450681 1.508620472 1.899966369 1 18.11499583 2.236854455 24.99808526 1.453027818 1.871231467 0.074356623 0.912745135 188.7782416 2765840.948 0.366120493 0.284613297 172.525961 -2.236854455 0.41820365 AHSLGGLDPAFT(ph)STEDLNCKENLEQDLGDDNSNDLLLSCPHFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHSLGGLDPAFTSTEDLNCKENLEQDLGDDNSNDLLLSCPHFR 43 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AHSLGGLDPAFT(0.333)S(0.333)T(0.333)EDLNCKENLEQDLGDDNSNDLLLSCPHFR 76.728 0.00055085 422510000 78274 90268 54926 71445 64863 72597 54420 43790 76544 72723 TRUE FALSE 75214.96554 87693.64502 64852.35002 75132.28501 66949.3773 74064.96108 55086.00824 42885.7212 67855.04602 67797.40644 1.109407712 1.293466072 0.956560928 1.108188188 0.987491717 1.092445345 0.812509079 0.632556958 1.000850174 1 16.04894246 2.23685654 10.51460699 0.808822322 1.090454321 0.397952736 0.132259225 0.080217075 191.3397083 0.04789478 0.037475 172.5267892 -2.23685654 0.281631999 DFLLKPELLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFLLKPELLR 10 1 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0G2JJL7;F6QYI9;K7EIL8;K7ENP6;K7EN69;K7EL56;F6SXL5;Q13838-2;Q13838;Q5STU3;F6WLT2;F6S4E6;A0A0A0MT12;F6TRA5;F6R6M7;F6U6E2;F6S2B7;A0A0G2JHN7 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ; 125.97 0.00036021 22383400000 14385100 17002300 14682900 14840300 15223900 14023600 20198200 18932200 20460900 22166100 FALSE TRUE 13822914.39 16517411.05 17336426.65 15606209.66 15713590.57 14307166.8 20445391.61 18541243.45 18138264.41 20664770.3 0.668912075 0.799302911 0.838936334 0.755208475 0.760404802 0.692345794 0.989383928 0.897239272 0.877738496 1 24.30066999 2.236920418 25 0.930776811 0.7590538 0.721016713 0.057234457 25.24142691 384720.574 0.020853377 0.016217966 172.5521672 -2.236920418 -0.171723011 SVYATMGDHENRS(ph)PVKEPVEQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVYATMGDHENRSPVKEPVEQPR 23 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 SVYATMGDHENRS(1)PVKEPVEQPR;SVYATMGDHENRS(1)PVKEPVEQPR;SVYATMGDHENRS(1)PVKEPVEQPR;SVYATMGDHENRS(1)PVKEPVEQPR 280.92 2.82E-52 3206380000 1817960 1761580 1427460 1573740 1598390 1613100 1831060 1847910 2009380 2017800 TRUE FALSE 1746912.113 1711341.463 1685433.776 1654960.91 1649803.666 1645717.987 1853469.06 1809750.013 1781283.606 1881132.609 0.928649105 0.909739938 0.895967551 0.879768339 0.877026775 0.874854851 0.985294206 0.962053395 0.946920806 1 20.84317012 2.236943363 24.99999992 0.970041852 0.8936601 0.787977419 0.020099579 20.48066991 316587.7604 0.007656989 0.005956881 172.5612838 -2.236943363 -0.076381752 SQGS(ph)SQFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQGSSQFR 8 0 Q15172 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 1 S(0.083)QGS(0.66)S(0.257)QFR 76.682 0.036893 250810000 251840 236910 197300 244860 216220 229250 275110 272940 324110 312070 TRUE FALSE 241997.8144 230153.5588 232956.4989 257497.2539 223174.9127 233885.5921 278476.8785 267303.6936 287318.3916 290933.2209 0.831798492 0.79108724 0.800721548 0.885073396 0.767100134 0.80391504 0.957184874 0.918780237 0.987575055 1 18.15032852 2.236969029 24.99567791 0.95472599 0.812866802 0.81234246 0.03577111 18.28366569 287135.0974 0.012878999 0.010017816 172.571482 -2.236969029 -0.141859189 GGLNTPLHESDFSGVT(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGLNTPLHESDFSGVTPQR 19 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 1 GGLNTPLHESDFS(0.056)GVT(0.944)PQR 153.59 1.63E-07 218310000 110490 175340 147340 154650 147060 160020 112450 128100 120510 137140 TRUE FALSE 106171.9286 170339.4749 173967.6156 162631.505 151790.3185 163255.714 113826.1967 125454.6902 106830.21 127851.3856 0.830432366 1.332324042 1.360701839 1.272035529 1.187240308 1.276917831 0.890300845 0.981254052 0.835581167 1 16.96410827 2.237013282 24.99999064 0.929978088 1.224148083 0.47675534 0.144851125 34.41524092 556024.2934 0.051593884 0.040146997 172.5890674 -2.237013282 0.294169995 IETSIGQSTVIIDLTEDS(ph)NEQPDSLVDHNK ddPTM_BT-474_Pertuzumab_2h_R1 1 IETSIGQSTVIIDLTEDSNEQPDSLVDHNK 30 0 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 IETSIGQSTVIIDLT(0.002)EDS(0.794)NEQPDS(0.204)LVDHNK 69.523 0.0042524 84737000 8544.3 8495 5751.6 5716 7898.1 6816.1 9013.9 9006.3 8976 9807.7 TRUE FALSE 8210.37931 8252.730917 6791.042064 6011.003445 8152.149559 6953.926212 9124.214805 8820.316758 7957.08211 9143.415743 0.897955375 0.902587299 0.742724848 0.657413336 0.891586885 0.760539213 0.997900026 0.964663207 0.870252686 1 13.1585175 2.237110393 25 0.957789711 0.806942414 0.454262789 0.080207629 37.01951702 638151.1094 0.030382974 0.023659106 172.6276636 -2.237110393 -0.150847297 GFKDQIYDIFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFKDQIYDIFQK 12 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 157.52 6.57E-05 7425100000 8465000 8497200 6624400 6692300 6941300 6878900 8948900 8093800 9844000 9737200 FALSE TRUE 8134178.441 8254868.176 7821576.439 7037690.405 7164573.218 7017996.071 9058419.315 7926660.202 8726550.389 9077690.771 0.896062517 0.909357719 0.861626226 0.775273204 0.789250636 0.773103672 0.997877053 0.873202272 0.961318314 1 23.11389391 2.237117014 24.99997862 0.941366935 0.834069533 0.534718779 0.055793482 37.48907147 649207.3058 0.021944657 0.017090065 172.6302955 -2.237117014 -0.107297402 ENPEDVLSPTS(ph)VATYLSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENPEDVLSPTSVATYLSSK 19 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 ENPEDVLS(0.357)PT(0.258)S(0.358)VAT(0.02)Y(0.005)LS(0.001)S(0.001)K 66.893 0.027833 28341000 41120 48417 43275 51682 56950 50957 37156 39194 38540 48072 TRUE FALSE 39512.98494 47036.19457 51095.75515 54349.31421 58781.84847 51987.38545 37610.72624 38384.6302 34165.10077 44816.04062 0.881670589 1.04953927 1.140122029 1.212720121 1.311625205 1.160017367 0.839224655 0.856493114 0.762340901 1 15.45172758 2.237180234 24.99636195 0.852501465 1.135504128 0.538702979 0.11811078 28.23516645 511274.3962 0.045608752 0.035539985 172.6554272 -2.237180234 0.283002663 EEDIGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEDIGK 6 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3;C9JAX4;A0A0C4DG51;Q9NP80-3;Q9NP80-2;Q9NP80 P22314 UBA1;PNPLA8 Ubiquitin-like modifier-activating enzyme 1;Calcium-independent phospholipase A2-gamma 0 ; 117.7 0.05234 1110870000 1470620 1401540 1167300 1201240 1374860 1389830 1479200 1612720 1746380 1690130 FALSE TRUE 1413146.545 1361569.451 1378257.076 1263236.14 1419083.621 1417933.315 1497302.892 1579416.768 1548138.264 1575655.99 0.896862357 0.86412863 0.874719536 0.801720774 0.90063036 0.899900311 0.950272713 1.002386802 0.982535702 1 20.58752116 2.237261844 1.468258712 0.99802111 0.862993283 0.83057543 0.025513022 0.153301226 0.648722056 0.014783852 0.008759516 172.6878743 -2.237261844 -0.135027827 GPSQEEEDNHS(ph)DEEDRAS(ph)EPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSQEEEDNHSDEEDRASEPK 21 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 GPS(0.022)QEEEDNHS(0.978)DEEDRAS(1)EPK;GPSQEEEDNHS(1)DEEDRAS(1)EPK 250.38 8.44E-31 1125840000 1145170 1028380 863640 931250 951630 962780 1126100 1079940 1374770 1177970 TRUE FALSE 1100415.49 999051.6093 1019718.96 979311.9241 982240.0432 982248.0713 1139881.549 1057638.862 1218711.873 1098185.043 1.002031031 0.909729755 0.928549306 0.891754928 0.894421254 0.894428564 1.037968561 0.963078917 1.109750931 1 20.06668974 2.237283198 24.9999985 1.018505496 0.917599984 0.56395408 0.046012687 26.47423909 518101.6835 0.016397869 0.012782783 172.6963656 -2.237283198 -0.100905512 YRPENT(ph)PEPVSTSVSHYGAEPTTVSPCPSSSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 YRPENTPEPVSTSVSHYGAEPTTVSPCPSSSAK 33 1 J3QRU1;P07947 J3QRU1 YES1 Non-specific protein-tyrosine kinase;Tyrosine-protein kinase Yes 1 Y(0.005)RPENT(0.995)PEPVSTSVSHYGAEPTTVSPCPSSSAK 162.88 6.90E-14 127310000 31719 62983 27929 76158 38616 47343 64409 70662 73628 51747 TRUE FALSE 30479.38641 61186.78651 32976.39158 80088.52351 39858.11871 48300.3079 65197.25661 69202.80501 65270.05811 48242.1296 0.631800185 1.268326813 0.68356003 1.660136569 0.826209768 1.001205965 1.351458925 1.434489016 1.352968011 1 15.55800597 2.237284783 24.95953801 1.334192893 1.029634123 0.156936501 0.299521474 53.32228292 1043124.896 0.10198433 0.079503693 172.6969957 -2.237284783 -0.304558769 EEIQETQTPTHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEIQETQTPTHSR 13 0 Q9BYG3;H7BZL0 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 ; 176.83 1.60E-05 543260000 527510 520650 463630 425270 515340 510950 439770 492430 466420 491440 FALSE TRUE 506894.326 505801.5718 547418.2544 447218.2357 531916.3791 521281.7591 445152.0368 482261.1484 413473.957 458154.3311 1.106383355 1.103998233 1.194833743 0.976130106 1.160998255 1.137786383 0.971620274 1.052617242 0.90247746 1 18.80547413 2.237352527 24.99974631 0.992678428 1.112561395 0.502583933 0.063798198 28.71693935 594233.5641 0.022418503 0.017491987 172.7239364 -2.237352527 0.119882968 LKS(ph)VEDEMDSPGEEPFYTGQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKSVEDEMDSPGEEPFYTGQGR 22 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2;A0A590UK73;B1AKN7 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 LKS(1)VEDEMDSPGEEPFYTGQGR 91.655 0.0013278 208570000 63689 76739 56886 70147 93654 75109 55544 61899 57576 59018 TRUE FALSE 61199.96347 74550.47886 67166.56562 73767.29508 96666.46596 76627.75544 56223.76409 60620.76402 51040.21386 55020.65829 1.112308819 1.354954324 1.220751763 1.340719965 1.756912203 1.392708808 1.021866438 1.101781874 0.927655456 1 15.74768578 2.237393209 24.97548637 1.029949888 1.373109386 0.532511281 0.16027587 26.46660773 566204.865 0.061832357 0.048248759 172.7401167 -2.237393209 0.343159498 KAPSDLYQIILK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAPSDLYQIILK 12 1 P07384;E9PL37 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 146.5 0.00010389 1393500000 3565900 3625200 2940400 3225300 3215100 3232800 3815100 3778400 4132200 4194200 FALSE TRUE 3426540.686 3521812.845 3471795.689 3391758.12 3318516.611 3298169.431 3861790.335 3700374.72 3663129.98 3910123.098 0.876325527 0.900691041 0.887899332 0.86743001 0.848698757 0.843495038 0.987639069 0.946357602 0.936832393 1 21.8987826 2.237444318 24.99987497 0.962300059 0.871742645 0.805030136 0.023310348 13.92335587 311806.2092 0.008880916 0.00693118 172.7604465 -2.237444318 -0.090557414 RS(ph)SVSTIQVEWPEPDLAPAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSVSTIQVEWPEPDLAPAIK 21 1 Q96B33 Q96B33 CLDN23 Claudin-23 1 RS(0.497)S(0.497)VS(0.005)T(0.001)IQVEWPEPDLAPAIK;RS(0.499)S(0.499)VS(0.001)T(0.002)IQVEWPEPDLAPAIK 160.52 1.29E-11 146250000 149304 223440 141269 221240 154257 178225 249820 279910 260400 232100 TRUE FALSE 143469.0346 217067.71 166799.4508 232658.2229 159218.8165 181828.8316 252877.3719 274129.7607 230840.4837 216379.6603 0.663043072 1.003179826 0.770864741 1.075231483 0.735830791 0.840323122 1.16867441 1.266892463 1.066830789 1 17.72320537 2.237512173 24.99604065 1.161340145 0.856842064 0.505839133 0.132337898 19.88158236 473980.028 0.045342487 0.035406658 172.787441 -2.237512173 -0.304498081 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR ddPTM_BT-474_Pertuzumab_2h_R1 5 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR 32 1 P31942;P31942-3;P31942-4;P31942-5 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;; 325.44 5.38E-105 3928100000 974312 1086294 880776 1028052 991997 1099363 870147 1009564 1131107 991719 FALSE TRUE 936234.8099 1055313.959 1039951.816 1081109.887 1023905.484 1121592.873 880796.1193 988716.1506 1002708.475 924548.9888 1.012639483 1.141436497 1.124820673 1.169337591 1.107464825 1.213124331 0.952676527 1.069403745 1.084537961 1 19.81839024 2.237573323 24.99999985 1.033550177 1.129524075 0.415840229 0.058684064 27.00220911 683718.1725 0.020618316 0.016120303 172.8117718 -2.237573323 0.095973898 VTFFEPGSGDENGTSNKEDEFR ddPTM_BT-474_Pertuzumab_2h_R1 3 VTFFEPGSGDENGTSNKEDEFR 22 1 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ;; 270.58 2.42E-45 1410250000 1022960 939310 826595 938680 900120 1036330 1109150 1253490 1347490 1318120 FALSE TRUE 982981.5923 912521.7985 975979.104 987125.3873 929073.1773 1057285.303 1122724.109 1227604.993 1194528.584 1228842.558 0.799924763 0.742586422 0.794226321 0.803296875 0.756055502 0.860391183 0.913643576 0.998992902 0.972076184 1 20.22886866 2.237579362 1.560407218 0.992694225 0.778111041 0.943715946 0.022497937 0.076539316 0.36794753 0.011924824 0.007193668 172.8141747 -2.237579362 -0.214583183 SYMNPGDQS(ph)PADSNK ddPTM_BT-474_Pertuzumab_2h_R1 8 SYMNPGDQSPADSNK 15 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 1 SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(0.999)PADS(0.001)NK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK 460.58 1.42E-198 6916770000 7846300 7208620 5950460 6901950 6502890 6840560 7597640 7974130 8128130 8106370 TRUE FALSE 7539657.921 7003037.216 7025840.489 7258160.467 6712061.363 6978880.81 7690622.191 7809461.429 7205458.758 7557318.339 0.997663137 0.926656375 0.929673751 0.960414811 0.888153848 0.923459949 1.017639041 1.033364095 0.953441212 1 22.84944296 2.237579851 24.99935868 1.007540209 0.935589287 0.468669218 0.032762663 20.63837767 526042.1487 0.011883531 0.009285027 172.8143695 -2.237579851 -0.071950923 DLELPLS(ph)PSLLGGPGPER ddPTM_BT-474_Pertuzumab_2h_R1 4 DLELPLSPSLLGGPGPER 18 0 P19419 P19419 ELK1 ETS domain-containing protein Elk-1 1 DLELPLS(0.995)PS(0.005)LLGGPGPER;DLELPLS(0.832)PS(0.168)LLGGPGPER;DLELPLS(0.768)PS(0.232)LLGGPGPER;DLELPLS(1)PSLLGGPGPER 306.07 3.76E-50 355610000 492909 597172 534945 642727 665904 617672 366751 421807 357938 402263 TRUE FALSE 473645.5713 580141.2393 631621.4613 675898.2175 687323.4069 630161.751 371239.4084 413096.538 317306.3788 375017.3687 1.262996359 1.546971654 1.684245888 1.80231177 1.83277753 1.680353508 0.989925906 1.101539749 0.846111155 1 18.51659789 2.237693227 24.98291935 1.004395807 1.649785371 0.799639357 0.159301134 10.56000189 304138.6181 0.062000549 0.048481399 172.8594897 -2.237693227 0.645389563 EVSSSFDHVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSSSFDHVIK 11 0 E9PIE4;Q9Y6C9 E9PIE4 MTCH2 Mitochondrial carrier homolog 2 0 80.758 0.017196 0 123580 215970 135460 281680 117010 130790 267910 237090 214710 215050 FALSE TRUE 118750.357 209810.7471 159940.6353 296217.5386 120773.7329 133434.6634 271188.7627 232194.0086 190337.0209 200484.472 0.59231698 1.046518691 0.797770689 1.477508635 0.602409412 0.665561089 1.352667167 1.158164552 0.949385352 1 17.61313097 2.23770707 24.9999992 1.13945684 0.885021103 0.173137893 0.264542547 41.02386016 1201511.61 0.095618111 0.074786378 172.8649998 -2.23770707 -0.254435737 LQDISELLATGAGLS(ph)ESEAEPDGDHNITELPQAVAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQDISELLATGAGLSESEAEPDGDHNITELPQAVAGR 37 0 A8MV53;A0A0A6YYI3;A0A0B4J1V8;Q9NQ55-2;Q9NQ55;Q9NQ55-3;C9J3W3 A8MV53 PPAN;PPAN-P2RY11 Suppressor of SWI4 1 homolog 1 LQDISELLATGAGLS(0.995)ES(0.005)EAEPDGDHNITELPQAVAGR 298.65 4.71E-92 44700000 32496 32206 28570 29192 30812 25542 38876 37602 31209 31964 TRUE FALSE 31226.02039 31287.51641 33733.23454 30698.60262 31803.09596 26058.47674 39351.77612 36825.50556 27666.28516 29799.04981 1.047886446 1.049950136 1.132023831 1.030187298 1.067252015 0.874473411 1.320571507 1.235794624 0.928428434 1 14.86297871 2.237786995 24.99999969 1.157439679 1.040215142 0.080685669 0.121189646 37.05546166 1197408.595 0.043925584 0.034382238 172.8968159 -2.237786995 -0.117224538 RYDSNSGGER ddPTM_BT-474_Pertuzumab_2h_R1 2 RYDSNSGGER 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 174.42 4.99E-06 144341000 97526 98280 69560 82282 96543 92778 73991 78392 90315 85593 FALSE TRUE 93714.5761 95477.15063 82131.03935 86528.58388 99648.39327 94654.03473 74896.52399 76773.17781 80062.81983 79795.70987 1.17443126 1.196519848 1.029266354 1.084376391 1.248793869 1.186204558 0.938603392 0.962121622 1.003347423 1 16.28402356 2.237883364 24.99999626 0.970487343 1.150806069 0.678056544 0.059770181 11.21328949 413898.9866 0.023353049 0.018282407 172.9351854 -2.237883364 0.180318727 QQVSWEQEFLVGSS(ph)PGGSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 QQVSWEQEFLVGSSPGGSGR 20 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 QQVSWEQEFLVGS(0.001)S(0.999)PGGSGR;QQVSWEQEFLVGS(0.182)S(0.817)PGGS(0.001)GR;QQVSWEQEFLVGSS(1)PGGSGR 297.3 1.20E-54 607920000 534740 582370 502790 558560 558370 593260 503744 540250 633240 630310 TRUE FALSE 513841.7696 565761.3778 593655.3375 587387.3485 576330.4781 605256.1237 509908.9698 529093.6487 561357.25 587618.5423 0.874447848 0.962803821 1.010273323 0.999606558 0.98079015 1.030015359 0.867755071 0.900403256 0.955308945 1 19.1645204 2.237971141 24.99999999 0.918234828 0.978512952 0.141155159 0.051101747 23.27250874 986934.736 0.018547825 0.014536179 172.9701415 -2.237971141 0.060278124 S(ph)SPLLNYNTGVYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPLLNYNTGVYR 13 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 S(0.559)S(0.441)PLLNYNTGVYR 61.423 0.085809 0 49367 54526 48084 58923 46634 50520 64968 71616 63739 59402 TRUE FALSE 47437.68306 52970.97187 56773.84842 61964.02309 48134.02496 51541.54901 65763.09782 70137.10457 56503.61594 55378.64963 0.856605991 0.956523357 1.025193803 1.118915385 0.869180186 0.930711553 1.18751718 1.266500809 1.02031408 1 15.75704225 2.237974953 24.99978906 1.155929079 0.965509241 0.342475069 0.10269166 14.93780071 637590.7505 0.037993278 0.029767162 172.9716599 -2.237974953 -0.190419837 MEDTLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEDTLKR 7 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 113.89 0.0096659 907600000 1351910 1271460 1116980 1223940 1255750 1252600 1420920 1480920 1561280 1553950 FALSE TRUE 1299075.863 1235199.206 1318843.133 1287107.69 1296142.339 1277928.43 1438309.644 1450338.484 1384050.04 1448699.582 0.896718601 0.85262619 0.910363438 0.88845728 0.894693665 0.882121073 0.992828093 1.001131292 0.955374086 1 20.46632702 2.238061635 25 0.989088779 0.887321869 0.878058128 0.018222034 4.024740259 201632.1284 0.006398087 0.005015763 173.0061871 -2.238061635 -0.101766909 VDAVHLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDAVHLLK 8 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 96.253 0.0090721 789930000 1975670 1872560 1560240 1686140 1734820 1780650 1903370 1953350 2130820 2151590 FALSE TRUE 1898458.632 1819156.422 1842210.075 1773161.887 1790622.061 1816655.963 1926664.011 1913012.64 1888938.247 2005860.893 0.946455778 0.906920529 0.918413676 0.883990457 0.892695035 0.905673953 0.960517261 0.953711519 0.941709494 1 20.93579013 2.238067063 25 0.95945374 0.907475813 0.618840066 0.02098958 9.127757437 462308.0702 0.007498079 0.005876787 173.0083497 -2.238067063 -0.051977928 DIFQEIFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DIFQEIFDK 9 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 163.64 0.00014625 200710000 264810 326290 234266 420180 237900 249160 419170 431310 354120 283140 FALSE TRUE 254460.9324 316984.5287 276603.0774 441865.5402 245552.2696 254198.1859 424299.9278 422403.2978 313921.7822 263962.6756 0.964003459 1.200868751 1.04788708 1.673969773 0.930253753 0.963008067 1.607423954 1.600238734 1.189265799 1 18.00997442 2.238201855 24.99999982 1.428221007 1.14513419 0.111893778 0.265811799 15.51761249 1081207.688 0.095531561 0.074968361 173.0620544 -2.238201855 -0.283086817 SRS(ph)WEDS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSWEDSPER 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 S(0.065)RS(0.935)WEDS(1)PER;S(0.014)RS(0.986)WEDS(1)PER 130.61 0.003252 3055400000 2073210 1967010 1746660 2013420 1957990 1962330 2305500 2426600 2442500 2539400 TRUE FALSE 1992186.661 1910912.801 2062320.316 2117332.847 2020970.527 2002009.657 2333715.399 2376489.862 2165237.64 2367404.176 0.841506778 0.807176409 0.871131485 0.894368975 0.853665186 0.845656047 0.98576974 1.003837826 0.914604131 1 21.1748746 2.238213705 24.99999684 0.979651056 0.85303893 0.792883121 0.030974825 4.067283487 293071.2871 0.011575914 0.009086116 173.0667767 -2.238213705 -0.126612126 LKGDDLQAIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKGDDLQAIKK 11 2 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;P07910-2;G3V4C1;B2R5W2;G3V2D6 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 121.04 0.0016682 749410000 899580 773440 805790 686590 640680 864380 962780 1029500 1192100 1169800 FALSE TRUE 864423.4191 751382.2485 951414.1777 722024.9922 661288.0541 881858.3558 974562.7896 1008240.465 1056777.806 1090568.404 0.792635671 0.688982228 0.872402111 0.662063003 0.606370083 0.808622689 0.893628301 0.924509147 0.969015609 1 20.05664883 2.238287875 2.288736091 0.950110677 0.726479177 0.685137093 0.07148307 0.185672597 1.981629789 0.033240689 0.022725374 173.0963359 -2.238287875 -0.2236315 SEEQLKEEGIEYK ddPTM_BT-474_Pertuzumab_2h_R1 4 SEEQLKEEGIEYK 13 1 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ;;; 200.55 9.94E-08 3225210000 3017570 3461500 2392460 3902790 2367960 2783530 4295200 4622260 4284610 3133580 FALSE TRUE 2899640.028 3362781.409 2824830.742 4104213.46 2444127.584 2839814.884 4347765.942 4526808.716 3798239.035 2921339.835 0.992571968 1.151109285 0.966964099 1.404907916 0.836646101 0.972093301 1.488278046 1.549565943 1.300170213 1 21.47819876 2.238307492 24.9999998 1.402292633 1.060568412 0.298687964 0.199868225 6.643102885 656003.1307 0.069993053 0.054972917 173.1041549 -2.238307492 -0.341724221 KVDTT(ph)PNQGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KVDTTPNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KVDT(0.123)T(0.877)PNQGK;KVDT(0.273)T(0.727)PNQGK;KVDT(0.237)T(0.763)PNQGK 125.61 0.00023702 1387590000 2869280 2840280 2784880 2789890 2595140 3092900 3736900 4420100 4421200 3931700 TRUE FALSE 2757145.365 2759277.995 3288169.765 2933876.557 2678615.035 3155440.557 3782633.3 4328823.39 3919323.911 3665402.457 0.752208086 0.752789913 0.897082873 0.800424126 0.730783336 0.860871513 1.031983075 1.180995386 1.069275191 1 21.80554018 2.238335357 2.971071258 1.104055915 0.792156839 0.829522843 0.06096937 0.091720961 1.674652277 0.024871609 0.018192179 173.1152619 -2.238335357 -0.311899076 EYQLNDSASYYLNDLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYQLNDSASYYLNDLDR 17 0 P08754 P08754 GNAI3 Guanine nucleotide-binding protein G(k) subunit alpha 0 257.81 8.94E-27 113640000 32471 56111 32682 71210 35680 36596 64473 66870 44582 41559 FALSE TRUE 31201.99742 54510.76922 38588.36441 74885.15663 36827.6796 37335.99619 65262.03986 65489.11113 39521.23826 38744.17191 0.805333961 1.406941135 0.995978556 1.93281087 0.950534694 0.963654515 1.684435017 1.690295802 1.020056342 1 15.24169169 2.238436941 24.99999999 1.446594142 1.202364861 0.020481628 0.373279063 8.656098902 1749137.913 0.132909737 0.104459332 173.1557592 -2.238436941 -0.24422928 SEVLSESSELLQQELEELRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEVLSESSELLQQELEELRK 20 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 195.78 2.91E-21 54034000 44894 49797 37412 44339 47920 44009 55141 55566 57785 61012 FALSE TRUE 43139.49285 48376.83832 44173.18063 46627.3411 49461.39032 44898.89213 55815.83205 54418.54268 51225.48905 56879.6029 0.758435197 0.850512941 0.776608457 0.819755039 0.869580444 0.789367187 0.98129785 0.956732113 0.900595054 1 15.79562377 2.238459437 25 0.957025319 0.814056112 0.777947819 0.038949378 1.224962874 302523.4752 0.013493461 0.010609116 173.1647288 -2.238459437 -0.142969207 YALYDATYETK ddPTM_BT-474_Pertuzumab_2h_R1 5 YALYDATYETK 11 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ;;;; 273.9 9.73E-27 6065730000 2588940 2468470 2106740 2313830 2496490 2423240 2719040 2861940 2963170 2980030 FALSE TRUE 2487761.363 2398071.652 2487474.782 2433247.044 2576791.868 2472239.573 2752316.425 2802839.939 2626803.364 2778189.914 0.895461232 0.863177726 0.895358078 0.875838988 0.927507459 0.889874217 0.990686926 1.008872693 0.945508927 1 21.40571379 2.238564361 25 0.989480788 0.891069779 0.818559389 0.021905322 0.040632131 255786.3203 0.007861543 0.00618739 173.2065697 -2.238564361 -0.098411009 RAS(ph)PSKPASAPASR ddPTM_BT-474_Pertuzumab_2h_R1 8 RASPSKPASAPASR 14 2 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 RAS(0.998)PS(0.002)KPASAPASR;RAS(0.992)PS(0.008)KPASAPASR;RAS(1)PSKPASAPASR;RAS(0.997)PS(0.003)KPASAPASR;RAS(0.925)PS(0.075)KPASAPASR;RAS(0.402)PS(0.195)KPAS(0.402)APASR;RAS(0.949)PS(0.051)KPASAPASR;RAS(0.903)PS(0.095)KPAS(0.002)APASR 124.84 7.46E-05 8157680000 2317290 2294960 2140690 2286700 2040730 2165350 2544710 2592300 2582770 2724270 TRUE FALSE 2226727.745 2229509.988 2527560.302 2404716.861 2106371.934 2209134.861 2575852.922 2538768.099 2289584.777 2539752.766 0.876749806 0.877845284 0.99519935 0.946831082 0.829361016 0.869822799 1.014214043 0.999612298 0.901499078 1 21.27625663 2.238593551 25 0.982293862 0.901666578 0.364017797 0.051360271 1.035459884 786223.192 0.019759161 0.015552685 173.2182117 -2.238593551 -0.080627284 QIESTETSCHGCR ddPTM_BT-474_Pertuzumab_2h_R1 1 QIESTETSCHGCR 13 0 Q9Y508;A0A096LNV3;A0A096LP02;Q9Y508-2 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 215.09 2.97E-11 517520000 83951 139580 98741 137060 114250 127590 95822 108070 114640 130250 FALSE TRUE 80670.10211 135599.3151 116585.6952 144133.683 117924.955 130169.9572 96994.6983 105838.3167 101626.5478 121428.0515 0.664344862 1.116705023 0.960121601 1.186988355 0.971150847 1.071992473 0.798783289 0.871613399 0.836928095 1 16.88974222 2.238635148 25 0.864314248 1.006767061 0.143003511 0.138933779 3.186176391 1069111.486 0.047414066 0.037322939 173.2348037 -2.238635148 0.142452813 ELVSEFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELVSEFSR 8 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ; 169.37 0.00070118 467340000 245010 525210 268830 704480 304930 278130 695210 670890 469810 378330 FALSE TRUE 235434.7383 510231.525 317413.5611 740838.2972 314738.3504 283753.9792 703718.1879 657035.8871 416479.1384 352705.3721 0.667511064 1.446622494 0.899939684 2.100445175 0.892354853 0.804507109 1.995201218 1.862846271 1.180813141 1 18.42810402 2.238687701 25 1.626521255 1.171522907 0.108079552 0.475600348 6.042610869 1188968.106 0.168711721 0.132859237 173.2557675 -2.238687701 -0.454998348 KNANKPLLDEIVPVYR ddPTM_BT-474_Pertuzumab_2h_R1 1 KNANKPLLDEIVPVYR 16 2 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 55.589 0.075155 191620000 256470 275970 219080 207480 262120 240280 268440 264020 312960 271110 FALSE TRUE 246446.8689 268099.6058 258672.6294 218188.0677 270551.3279 245138.6262 271725.249 258567.8947 277434.0928 252747.4782 0.975071524 1.060740972 1.023442969 0.863265063 1.070441255 0.969895439 1.075085896 1.023028584 1.09767304 1 17.94733717 2.238878379 25 1.048748355 0.995748269 0.170675075 0.059449972 16.0913423 1266129.318 0.020872748 0.016463916 173.3318528 -2.238878379 -0.053000086 GGS(ph)TVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGSTVPK 7 0 Q92504;A2AAT0 Q92504 SLC39A7 Zinc transporter SLC39A7 1 GGS(0.99)T(0.01)VPK;GGS(0.912)T(0.088)VPK 72.485 0.053998 863600000 2016770 1909890 1878020 1626890 1710670 1836120 2213760 2314220 2324320 2452140 TRUE FALSE 1937952.399 1855421.807 2217419.99 1710853.988 1765695.254 1873247.604 2240852.657 2266430.548 2060472.938 2286054.374 0.847728042 0.81162628 0.969976924 0.748387268 0.772376753 0.819423906 0.980227191 0.991415854 0.901322804 1 21.12442829 2.238887327 24.99997389 0.97053936 0.827769294 0.562857066 0.060423499 6.53240659 499912.9203 0.022236875 0.017536965 173.3354241 -2.238887327 -0.142770066 AGVNFSEFTGVWK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGVNFSEFTGVWK 13 0 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 220.25 4.91E-11 462600000 408350 397490 310290 373670 382810 368470 417510 437820 441830 415640 FALSE TRUE 392391.2305 386153.9744 366366.3054 392955.1535 395123.4313 375920.7159 422619.6123 428778.864 391675.3107 387488.3326 1.012653021 0.996556391 0.945489901 1.01410835 1.019704074 0.970147187 1.090664097 1.106559419 1.01080543 1 18.56379335 2.238892085 24.99999204 1.066844106 0.993265247 0.345702597 0.037537002 7.788392189 587486.4854 0.013524644 0.010660878 173.3373229 -2.238892085 -0.073578859 EGSGSSGTGEQKEDQKEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGSGSSGTGEQKEDQKEEK 19 2 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;; 171.79 5.40E-12 1319210000 2088360 2172050 1822880 2530740 1579080 1792330 3611760 3752970 3728330 2456450 FALSE TRUE 2006744.582 2110105.261 2152314.966 2661351.795 1629872.542 1828572.141 3655961.799 3675469.858 3305105.609 2290072.454 0.876279953 0.921414193 0.939845795 1.162125587 0.711712217 0.798477855 1.596439359 1.604957892 1.443231896 1 21.12696181 2.238904424 24.99999943 1.481750184 0.907484718 0.61391458 0.194722179 5.251979285 381934.9983 0.068341602 0.05389988 173.3422478 -2.238904424 -0.574265466 EDPQARPLEGSSSEDSPPEGQAPPSHS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDPQARPLEGSSSEDSPPEGQAPPSHSPR 29 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 EDPQARPLEGSSSEDSPPEGQAPPS(0.255)HS(0.745)PR 152.77 1.55E-08 909670000 98157 110600 58307 74502 98759 90161 62816 72896 69604 63263 TRUE FALSE 94320.91592 107445.7963 68844.37193 78347.05715 101935.6729 91984.11719 63584.761 71390.67213 61702.84572 58978.14066 1.59925211 1.82179016 1.167286238 1.328408395 1.728363624 1.559630673 1.078107249 1.210459864 1.046198558 1 15.84789272 2.238924074 24.99887677 1.112107112 1.530001946 0.59431779 0.181687936 7.689646084 528950.4484 0.068855733 0.054322748 173.3500912 -2.238924074 0.417894835 LKEDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEDFR 6 1 Q96HE7;G3V2H0 Q96HE7 ERO1L ERO1-like protein alpha 0 70.268 0.083281 136360000 717640 850690 649500 721300 692760 765700 604030 635990 781710 674550 FALSE TRUE 689593.8354 826429.1541 766879.098 758526.3794 715043.2545 781182.9786 611422.2998 622856.5842 692973.558 628862.1277 1.096573963 1.314165884 1.219470953 1.20618868 1.137042959 1.242216607 0.972267645 0.990450143 1.101948309 1 19.26238423 2.238972696 24.99999997 1.01116123 1.205629358 0.674329583 0.063416432 6.056169646 367443.6557 0.022227589 0.01754274 173.3694998 -2.238972696 0.194468128 GDAEKPEEELEEDDDEELDETLSER ddPTM_BT-474_Pertuzumab_2h_R1 1 GDAEKPEEELEEDDDEELDETLSER 25 1 Q9NS69 Q9NS69 TOMM22 Mitochondrial import receptor subunit TOM22 homolog 0 220.5 1.12E-33 380530000 106390 150260 101500 219170 88787 134900 222400 259000 217520 185130 FALSE TRUE 102232.1612 145974.7319 119843.3079 230481.39 91642.91449 137627.7704 225121.7977 253651.5595 192828.0415 172590.9802 0.592337798 0.845784245 0.694377584 1.335419671 0.53098322 0.79742157 1.304365949 1.469668688 1.117254455 1 17.39699754 2.239083059 24.99894243 1.285730206 0.808887998 0.424941713 0.236679661 11.72761938 561206.3084 0.08342983 0.065882478 173.4135618 -2.239083059 -0.476842208 IGELVGVLVNHFK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGELVGVLVNHFK 13 0 J3QRN6;O94832;K7EIG7 J3QRN6 MYO1D Unconventional myosin-Id 0 ; 196.38 1.42E-07 145064000 280410 292820 230915 292880 245663 261340 323380 335510 328820 326180 FALSE TRUE 269451.2672 284469.0603 272646.4772 307995.5719 253564.9735 266624.4739 327337.6212 328581.6013 291493.7321 304087.5381 0.886097697 0.935484111 0.896605231 1.012851674 0.833855195 0.876801712 1.07645852 1.080549382 0.958584932 1 18.21412717 2.239113053 24.99999087 1.041884382 0.909267405 0.536384113 0.054989706 10.6224925 480738.9533 0.01992302 0.015727475 173.4255391 -2.239113053 -0.132616977 TQS(ph)ASPPPKER ddPTM_BT-474_Pertuzumab_2h_R1 1 TQSASPPPKER 11 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 T(0.002)QS(0.499)AS(0.499)PPPKER 50.806 0.093677 732470000 1217000 1037700 837880 857490 946970 1047500 1109300 1288500 1366400 1123200 TRUE FALSE 1169438.295 1008105.812 989303.5545 901745.1617 977430.1501 1068681.168 1122875.945 1261892.025 1211292 1047124.664 1.116809044 0.962737148 0.944781065 0.861163138 0.933442009 1.020586378 1.072342181 1.205101998 1.156779171 1 19.99800178 2.239121342 2.429557461 1.141342266 0.958891513 0.421569876 0.078523522 0.234881224 2.834077919 0.034871777 0.024286016 173.4288491 -2.239121342 -0.182450754 AKPPVKPKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AKPPVKPKPR 10 3 Q9C0C2;E9PKK0;E9PKE7 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 82.749 0.0074818 1422260000 953670 948910 774310 852220 917570 972450 983310 1142370 1289660 1071610 FALSE TRUE 916399.5221 921848.0159 914245.0414 896203.1763 947084.4724 992113.6053 995344.0419 1118779.66 1143263.203 999028.9002 0.917290302 0.922744092 0.915133728 0.897074325 0.94800508 0.993077983 0.99631156 1.119867163 1.144374505 1 19.93016689 2.239277883 1.379713505 1.098195466 0.917185543 0.750729279 0.040698125 0.186834058 0.694478097 0.023695047 0.013841537 173.4913728 -2.239277883 -0.181009922 KYEAAYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYEAAYGK 8 1 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 ; 79.148 0.043585 554310000 1062680 1453520 983010 1735370 834580 822270 1803180 1538430 1374520 1050460 FALSE TRUE 1021149.291 1412067.033 1160661.774 1824932.654 861425.0236 838896.8628 1825247.856 1506660.883 1218490.252 979311.4085 1.042721735 1.441897869 1.18518151 1.863485545 0.879623188 0.856619105 1.863807406 1.538490076 1.244231652 1 19.90140817 2.239298506 24.9999732 1.479836804 1.235398918 0.058873419 0.344014332 48.12793736 1630673.104 0.123982952 0.098058691 173.4996113 -2.239298506 -0.244437885 EEDFKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEDFKR 6 1 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 86.512 0.085772 586750000 542420 1035700 617410 1281300 692680 858070 1186100 1404400 1179800 930070 FALSE TRUE 521221.6267 1006162.85 728989.7212 1347428.047 714960.6813 875420.7633 1200615.847 1375398.649 1045874.05 867075.5305 0.601125979 1.160409693 0.840745351 1.553991549 0.82456563 1.009624574 1.384672735 1.586250103 1.206208702 1 19.72579815 2.239315902 24.85395395 1.370668347 1.015959081 0.195501385 0.275847146 24.24409963 797831.5127 0.095581039 0.075598996 173.506561 -2.239315902 -0.354709267 FKDIFQEIFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKDIFQEIFDK 11 1 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 180.09 6.22E-06 3326700000 2971400 3850500 2611270 4602000 2172990 2167490 5055100 4541400 3570500 2873900 FALSE TRUE 2855274.403 3740687.51 3083184.576 4839509.772 2242886.197 2211318.133 5116965.826 4447618.503 3165191.809 2679248.193 1.065699852 1.396170582 1.150764824 1.806293939 0.837132671 0.825350238 1.909851368 1.660024821 1.181373124 1 21.3533968 2.23941904 24.9999961 1.525623916 1.201572699 0.090718848 0.354886297 43.57932551 1269217.382 0.128277114 0.101552604 173.5477708 -2.23941904 -0.324051217 NSDLLTS(ph)PDVGLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSDLLTSPDVGLLK 14 0 P05412 P05412 JUN Transcription factor AP-1 1 NSDLLT(0.067)S(0.933)PDVGLLK 220.59 4.81E-12 112360000 547610 539250 406880 427110 482100 498830 336430 339530 491490 361570 TRUE FALSE 526208.7958 523871.118 480412.267 449153.1983 497607.1843 508916.6844 340547.331 332518.5868 435698.1157 337080.5418 1.56107734 1.554142269 1.425215067 1.33248035 1.476226369 1.509777698 1.01028475 0.986466276 1.292563829 1 18.36273382 2.239491368 24.99999955 1.059946572 1.471128278 0.790953314 0.101687415 10.97311207 294748.5789 0.037720057 0.0298763 173.5766762 -2.239491368 0.411181706 KLLEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLLEDR 6 1 P35579;Q9Y6N9-5;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 P35579;Q7Z406 MYH9;MYH14 Myosin-9;Myosin-14 0 ; 94.662 0.070915 2104300000 5507700 5895400 4763000 5443700 5235200 5225800 6090800 6160900 6259100 6373700 FALSE TRUE 5292452.995 5727268.964 5623780.052 5724650.009 5403594.962 5331469.256 6165341.032 6033675.262 5548593.208 5942003.622 0.890684916 0.963861574 0.946445073 0.963420821 0.909389375 0.897251095 1.037586212 1.015427732 0.933791623 1 22.50251805 2.23951826 24.99997799 1.001269938 0.931648882 0.485050545 0.034200939 22.19951748 579555.2754 0.012526753 0.009922668 173.5874247 -2.23951826 -0.069621056 KPRPS(ph)EGDEDCLPASK ddPTM_BT-474_Pertuzumab_2h_R1 4 KPRPSEGDEDCLPASK 16 2 P78346;P78346-2;Q5VU10 P78346 RPP30 Ribonuclease P protein subunit p30 1 KPRPS(1)EGDEDCLPASK;KPRPS(1)EGDEDCLPASK;KPRPS(1)EGDEDCLPASK;KPRPS(1)EGDEDCLPASK 149.32 6.67E-07 1939520000 1218180 1203290 1002590 1142870 1271520 1221250 959070 1024090 1166840 1123670 TRUE FALSE 1170572.179 1168973.347 1183780.315 1201853.658 1312419.596 1245944.512 970807.3856 1002942.184 1034385.215 1047562.83 1.117424316 1.115898077 1.130032759 1.147285512 1.252831389 1.189374495 0.926729507 0.957405279 0.987420692 1 19.99860534 2.239521581 24.99998927 0.962253152 1.159299441 0.832030025 0.041993453 10.44135372 271647.6979 0.016706499 0.013235907 173.588752 -2.239521581 0.197046288 AKEELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKEELEK 7 1 C9J406;B9A067;Q16891-2;Q16891-4;Q16891;H7C463;Q16891-3 C9J406 IMMT MICOS complex subunit MIC60 0 104.17 0.0074896 290930000 229040 355930 226870 538170 193620 234490 551950 540490 467940 325170 FALSE TRUE 220088.8636 345779.2249 267870.4557 565945.0182 199847.9631 239231.5485 558704.9292 529328.6926 414821.413 303145.9463 0.726016186 1.14063615 0.883635289 1.866906106 0.659246695 0.789162947 1.843022927 1.746118327 1.368388455 1 18.209653 2.239536157 24.9999999 1.582814036 1.033965193 0.253835047 0.387681714 31.39476325 804575.0368 0.137749469 0.109133549 173.5945783 -2.239536157 -0.548848842 (ac)GTRDDEYDYLFK ddPTM_BT-474_Pertuzumab_2h_R1 4 GTRDDEYDYLFK 12 1 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907;B4DQU5 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;; 94.692 8.94E-11 2772430000 1799410 2556580 1609300 2634580 2013570 2142740 2875500 3083980 3173230 2613630 FALSE TRUE 1729087.068 2483668.842 1900136.309 2770550.99 2078338.308 2186067.671 2910691.229 3020294.735 2813018.234 2436606.512 0.709629175 1.019314702 0.779828954 1.137053101 0.852964275 0.897177144 1.194567615 1.239549644 1.154481948 1 21.21644186 2.239578399 24.99903726 1.175854 0.908048296 0.473733194 0.126322974 20.73214324 509245.6764 0.042567783 0.033738433 173.611464 -2.239578399 -0.267805704 HKEQCNPETRPVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HKEQCNPETRPVEK 14 2 Q15649-2;Q15649 Q15649-2 ZNHIT3 Zinc finger HIT domain-containing protein 3 0 56.527 0.074498 77309000 93308 84607 63142 80305 79403 79431 69901 60036 97272 78615 FALSE TRUE 89661.4202 82194.0912 74553.16399 84449.55067 81957.06961 81037.14924 70756.46935 58796.23562 86230.09036 73290.33603 1.223373027 1.121486074 1.017230484 1.152260383 1.118252065 1.105700337 0.965427001 0.802237223 1.176554714 1 16.16133536 2.239717752 5.103842493 0.9500593 1.120296437 0.290928543 0.09898604 0.182830519 13.45524584 0.036507777 0.028383243 173.66718 -2.239717752 0.170237136 KVEGAQNQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVEGAQNQGK 10 1 Q9P2E9 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 143 5.57E-05 217940000 329130 370440 258850 323910 294120 310290 387210 411070 417060 351300 FALSE TRUE 316267.2357 359875.4139 305629.9531 340627.0339 303580.6369 316564.2764 391948.7918 402581.2608 369717.0973 327506.1381 0.965683384 1.098835631 0.93320374 1.040063053 0.926946404 0.966590361 1.196767774 1.22923272 1.128886009 1 18.32116242 2.23972408 24.99886865 1.166866102 0.990591648 0.472852534 0.07534936 21.97764121 472237.6116 0.026003313 0.020629628 173.6697104 -2.23972408 -0.176274454 LEYCEALAMLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEYCEALAMLR 11 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 91.867 0.024245 65095000 198420 202550 176590 202990 241410 221140 183050 213430 207210 218980 FALSE TRUE 190665.527 196773.4723 208503.7412 213466.3382 249175.1719 225611.6023 185290.2207 209022.5959 183688.3895 204148.2896 0.933956035 0.963875195 1.021334745 1.04564353 1.220559685 1.105135893 0.907625634 1.023876303 0.899779224 1 17.63925795 2.239806615 24.99985742 0.964810507 1.051042197 0.227441278 0.081306523 59.22691555 1188359.562 0.031979986 0.025376739 173.7027184 -2.239806615 0.08623169 WDFDTQEEYSEYMNNK ddPTM_BT-474_Pertuzumab_2h_R1 1 WDFDTQEEYSEYMNNK 16 0 Q13123 Q13123 IK Protein Red 0 257.95 2.53E-26 153600000 114580 121900 110710 113200 116880 112250 133860 127650 152120 136620 FALSE TRUE 110102.0869 118423.5314 130717.7597 119042.2656 120639.5513 114519.7719 135498.2187 125013.9829 134851.9753 127366.6057 0.864450193 0.929784779 1.026311088 0.934642679 0.947183531 0.899134991 1.063844153 0.981528731 1.058770269 1 16.95862754 2.239979598 24.99972946 1.021298097 0.938292903 0.501767486 0.044886079 35.4840562 625175.0989 0.016199292 0.012873603 173.7719192 -2.239979598 -0.083005195 EILTLLQGVHQGAGFQDIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EILTLLQGVHQGAGFQDIPK 20 0 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 186.06 3.42E-17 121520000 238580 227750 214900 201770 217840 220680 280880 278830 314660 310930 FALSE TRUE 229256.0298 221254.793 253737.2104 212183.3739 224847.0214 225142.3008 284317.4935 273072.0631 278941.116 289870.4342 0.790891387 0.763288583 0.875346984 0.731993846 0.775681115 0.776699774 0.98084337 0.942048691 0.96229585 1 18.14504867 2.239993537 24.99999986 0.964364816 0.785818873 0.857841503 0.036980267 13.35350234 232982.2893 0.012999172 0.010332576 173.7774968 -2.239993537 -0.178545943 REEEMR ddPTM_BT-474_Pertuzumab_2h_R1 2 REEEMR 6 1 Q15233;Q15233-2;H7C367;P49755 Q15233;P49755 NONO;TMED10 Non-POU domain-containing octamer-binding protein;Transmembrane emp24 domain-containing protein 10 0 ; 130.77 0.025046 104087000 122825 168367 160558 139578 141940 126808 147682 101428 117855 139783 FALSE TRUE 118024.8632 163565.338 189574.4022 146781.6373 146505.629 129372.1446 149489.3765 99333.47636 104476.5945 130315.3729 0.905686417 1.255149982 1.454735523 1.126357037 1.124239034 0.992761957 1.147135393 0.762254477 0.80172118 1 16.99164776 2.240013594 1.12633866 0.843864567 1.197817909 0.389355976 0.155744632 0.462915803 1.128026033 0.107040258 0.060566775 173.7855226 -2.240013594 0.353953342 ALTLDQWLEQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALTLDQWLEQHK 12 0 I3L1Y8;Q9HBL8;I3L3Z0 I3L1Y8 NMRAL1 NmrA-like family domain-containing protein 1 0 ; 113.69 0.0011381 1133920000 1126720 1004800 959960 1063040 1040130 1043910 1235180 1281880 1268440 1399640 FALSE TRUE 1082686.537 976144.0878 1133446.126 1117903.622 1073586.726 1065018.575 1250296.502 1255408.73 1124452.009 1304841.136 0.829745865 0.748094201 0.868646837 0.856735422 0.822771981 0.816205549 0.958198257 0.96211615 0.861753954 1 20.31544274 2.240164791 24.99996657 0.945042483 0.823765807 0.648028161 0.043981016 26.49596234 412929.2294 0.015658628 0.012465014 173.8460352 -2.240164791 -0.121276677 DEIT(ph)KET(ph)TEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DEITKETTEK 10 1 A0A0A0MTH5;Q9NR20-2 A0A0A0MTH5 DYRK4 Dual specificity tyrosine-phosphorylation-regulated kinase 4 2 DEIT(0.998)KET(0.998)T(0.005)EK;DEIT(0.996)KET(0.996)T(0.008)EK 67.726 0.069179 350523000 437146 403100 321316 366870 388786 342118 478156 479076 443114 396224 TRUE FALSE 420061.851 391603.9827 379384.9488 385804.2047 401291.6548 349035.8604 484007.8162 469182.9132 392813.5564 369387.3956 1.137185123 1.06014441 1.027065226 1.044443339 1.086370731 0.94490463 1.310298678 1.270164924 1.06341895 1 18.49477511 2.240238502 24.99996082 1.197300656 1.05083474 0.202473621 0.097756114 49.95042115 744260.5566 0.03430944 0.027311304 173.875544 -2.240238502 -0.146465916 VDIVAINDPFIDLNYMVYMFQYDSTHGK ddPTM_BT-474_Pertuzumab_2h_R1 8 VDIVAINDPFIDLNYMVYMFQYDSTHGK 28 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;; 290.1 2.94E-71 11788610000 5320346 5993860 4173296 4819706 5122849 5236612 4587551 4754093 5786852 4947536 FALSE TRUE 5112420.996 5822920.981 4927503.422 5068451.604 5287630.091 5342499.883 4643694.821 4655919.318 5129952.821 4612434.98 1.10839958 1.262439689 1.068308484 1.098866786 1.146385827 1.158281885 1.006777297 1.009427632 1.112200572 1 22.13709714 2.240265664 24.99999446 1.029441007 1.141093079 0.469269479 0.056416396 39.38684934 577514.6812 0.02014901 0.016042309 173.8864191 -2.240265664 0.111652071 EKEEDKDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEEDKDKK 9 3 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 73.067 0.019701 115630000 133320 105010 84254 70162 113080 88968 129780 121700 124030 126540 FALSE TRUE 128109.707 102015.2176 99480.57202 73783.06923 116717.3209 90766.99392 131368.2865 119186.8525 109950.6344 117969.3331 1.085957712 0.864760484 0.843274853 0.625442793 0.989386969 0.769411775 1.11357997 1.010320643 0.932027261 1 16.84805234 2.240281847 24.99802835 1.017883936 0.857162235 0.268315153 0.121811982 59.15453801 859137.9933 0.043297438 0.034480815 173.8928987 -2.240281847 -0.160721701 ELIDWLIEHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELIDWLIEHK 10 0 Q8TB45 Q8TB45 DEPTOR DEP domain-containing mTOR-interacting protein 0 ; 132.78 0.0002146 206339000 487710 431060 381770 391480 399240 444030 328020 341350 464370 398870 FALSE TRUE 468649.754 418766.5909 450764.3314 411684.3297 412081.9172 453008.5908 332034.4069 334301.0032 411656.6644 371854.1796 1.260305194 1.126158085 1.212207247 1.107112283 1.108181486 1.218242568 0.892915624 0.899011014 1.107037885 1 18.50437746 2.240429573 24.99999976 0.95649134 1.165921815 0.62950899 0.073528813 29.73111814 397703.2525 0.02615959 0.020855049 173.9520588 -2.240429573 0.209430476 YYAGWADK ddPTM_BT-474_Pertuzumab_2h_R1 2 YYAGWADK 8 0 P05091;P05091-2;F8VP50;H0YKL3;H0YMG7;O94788-4;O94788-2;O94788-3;O94788 P05091 ALDH2;ALDH1A2 "Aldehyde dehydrogenase, mitochondrial;Retinal dehydrogenase 2" 0 ; 129.4 0.0025415 992460000 658140 949820 758210 1375750 699390 604470 1463800 1311130 1012860 897350 FALSE TRUE 632419.1612 922732.0636 895235.4133 1446752.622 721886.5145 616692.7976 1481714.422 1284054.707 897884.3791 836571.6852 0.755965295 1.102992224 1.07012397 1.729382727 0.862910528 0.737166711 1.771174483 1.534900989 1.073290424 1 19.67412964 2.240521736 24.99980976 1.418638346 1.070047033 0.146536572 0.334737753 87.58882577 1116575.038 0.122050884 0.097360045 173.9889776 -2.240521736 -0.348591313 LSSSSS(ph)NDSGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSSSSNDSGNK 12 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LSSS(0.013)S(0.032)S(0.953)NDS(0.002)GNK 263.9 1.75E-21 214240000 434560 407250 349960 512110 460710 421040 626730 651550 622890 602840 TRUE FALSE 417576.9148 395635.6287 413205.5568 538540.0585 475529.1556 429553.7173 634400.1092 638095.2648 552182.1386 562009.1098 0.743007377 0.703966576 0.735229286 0.958240799 0.846123572 0.764318068 1.128807519 1.135382423 0.982514569 1 19.10023399 2.240528512 24.999999 1.081640979 0.795282578 0.722830158 0.081474452 27.42046003 348352.9768 0.031367039 0.025018219 173.9916923 -2.240528512 -0.286358401 GAPGSPT(ph)QERPAGGLGEAPNGAPSVCAEEGSLGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAPGSPTQERPAGGLGEAPNGAPSVCAEEGSLGPR 35 1 A0A0J9YWL0;A0A494C1M5 A0A0J9YWL0 1 GAPGS(0.37)PT(0.63)QERPAGGLGEAPNGAPSVCAEEGSLGPR;GAPGS(0.294)PT(0.706)QERPAGGLGEAPNGAPSVCAEEGSLGPR 240.93 3.26E-47 3634990000 93961 113766 114802 130945 117366 121240 92306 99290 102395 123931 TRUE FALSE 90288.90024 110521.5051 135549.2752 137703.0871 121141.184 123691.5559 93435.66844 97239.6268 90771.54887 115537.043 0.781471448 0.956589352 1.173210528 1.191852272 1.048505145 1.070579207 0.808707459 0.841631604 0.785648884 1 16.81799595 2.240593197 24.99999436 0.84402831 1.047126434 0.339371368 0.120479414 57.58110443 708237.5051 0.045241058 0.036109432 174.0176089 -2.240593197 0.203098124 SEEET(ph)SPLVTHQNPAGPVASAPELESK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEEETSPLVTHQNPAGPVASAPELESK 27 0 P43007;P43007-2 P43007 SLC1A4 Neutral amino acid transporter A 1 S(0.001)EEET(0.548)S(0.451)PLVTHQNPAGPVASAPELESK 155.55 1.16E-07 260460000 93525 231730 108000 281740 114910 139790 299130 322330 244060 167750 TRUE FALSE 89869.9396 225121.2873 127518.0024 296280.6352 118606.1845 142616.6496 302790.8424 315673.7729 216355.332 156388.1431 0.574659548 1.439503551 0.815394313 1.894521089 0.758409059 0.911940297 1.936149611 2.018527534 1.383450994 1 17.25477161 2.240615277 24.99936831 1.716341315 1.0950505 0.220702211 0.449139827 64.98007156 790634.1331 0.154550311 0.12336641 174.0264563 -2.240615277 -0.621290815 LEGELQAPDLELSLPAIHVEGLDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEGELQAPDLELSLPAIHVEGLDIK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 180.37 2.58E-17 446490000 303103 300523 241246 257691 245911 275350 282672 309630 319380 279320 FALSE TRUE 291257.3997 291952.3783 284844.5187 270990.4634 253820.9506 280917.7657 286131.4245 303236.0323 283125.3214 260401.4076 1.118493953 1.121162827 1.093867047 1.040664357 0.974729565 1.078787431 1.098809055 1.164494597 1.087264942 1 17.99037772 2.240678116 4.599538191 1.108570954 1.068447872 0 0.0556398 0.5015207 26.53164562 0.02186973 0.016920127 174.0516384 -2.240678116 -0.040123081 LLDIDETEYHADGGKVPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDIDETEYHADGGKVPIK 19 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 229.6 4.60E-20 137600000 257360 491040 214050 482920 252970 314230 556630 618800 528560 328370 FALSE TRUE 247302.0867 477036.02 252733.5965 507843.5591 261107.0098 320583.9459 563442.2044 606021.5638 468560.0847 306129.2074 0.807835648 1.558283262 0.825578189 1.658919001 0.852930735 1.04721777 1.840537233 1.979626736 1.530595818 1 18.22378117 2.240773636 24.99992577 1.708686812 1.143091094 0.248524836 0.370108769 61.79763612 698121.7835 0.124374859 0.099392486 174.0899239 -2.240773636 -0.565595718 KLSVPTS(ph)DEEDEVPAPKPR ddPTM_BT-474_Pertuzumab_2h_R1 6 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KLSVPT(0.206)S(0.794)DEEDEVPAPKPR;KLSVPT(0.052)S(0.948)DEEDEVPAPKPR;KLSVPT(0.022)S(0.978)DEEDEVPAPKPR;KLSVPT(0.011)S(0.988)DEEDEVPAPKPR;KLSVPT(0.081)S(0.919)DEEDEVPAPKPR;KLSVPT(0.02)S(0.98)DEEDEVPAPKPR 205.9 2.03E-16 13959370000 3273480 2993950 2665990 2586410 2673600 2811380 3364360 3530330 3527040 3374090 TRUE FALSE 3145548.783 2908565.477 3147793.698 2719894.93 2759598.772 2868228.03 3405534.044 3457427.452 3126665.206 3145559.879 0.999996472 0.924657482 1.00071015 0.864677525 0.877299711 0.911833867 1.082647978 1.09914533 0.993993224 1 21.58488539 2.240864561 24.99988598 1.05832479 0.927494102 0.528183742 0.052090449 42.85471616 465018.4858 0.019175565 0.015329782 174.1263759 -2.240864561 -0.130830688 MDRT(ph)PPPPTLS(ph)PAAITVGR ddPTM_BT-474_Pertuzumab_2h_R1 8 MDRTPPPPTLSPAAITVGR 19 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C4H9 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 2 MDRT(1)PPPPT(0.02)LS(0.98)PAAITVGR;MDRT(1)PPPPT(0.018)LS(0.982)PAAITVGR;MDRT(1)PPPPT(0.024)LS(0.976)PAAITVGR;MDRT(1)PPPPT(0.022)LS(0.978)PAAITVGR;MDRT(1)PPPPT(0.004)LS(0.996)PAAITVGR;MDRT(1)PPPPT(0.004)LS(0.996)PAAITVGR;MDRT(1)PPPPTLS(1)PAAITVGR;MDRT(1)PPPPT(0.013)LS(0.987)PAAITVGR 167.28 4.19E-11 6260140000 3300596 3582523 2924847 3474319 3497860 3439565 3056616 3368540 3270500 3333684 TRUE FALSE 3171605.059 3480352.952 3453431.916 3653629.02 3610371.844 3509115.361 3094023.781 3298978.472 2899246.551 3107890.613 1.020500865 1.119844095 1.111181938 1.175597688 1.161679188 1.129098735 0.995538185 1.061484744 0.932866343 1 21.5675043 2.240902383 24.99981555 1.008653472 1.123727759 0.597095868 0.048754128 45.96948659 490757.3489 0.017797572 0.014241893 174.1415409 -2.240902383 0.115074287 CRS(ph)PGMLEPLGSSR ddPTM_BT-474_Pertuzumab_2h_R1 7 CRSPGMLEPLGSSR 14 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(0.985)PGMLEPLGS(0.011)S(0.003)R 172.63 1.71E-06 7967450000 1522298 1725381 1403248 1396716 1565586 1600400 1287041 1444034 1525881 1433736 TRUE FALSE 1462804.911 1676174.823 1656846.129 1468800.68 1615944.496 1632761.185 1302792.193 1414214.193 1352669.386 1336627.784 1.0943996 1.254032606 1.239571816 1.098885343 1.2089712 1.22155263 0.974685854 1.058046384 1.012001548 1 20.35016634 2.240941184 24.99999999 1.019047149 1.188804582 0.714930379 0.054046491 33.77921622 354742.8248 0.018964495 0.015174835 174.1570997 -2.240941184 0.169757433 NTVAAIEEALDVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NTVAAIEEALDVDR 14 0 O43150;O43150-2 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 0 126.63 0.00073806 0 13384 14612 11184 14337 12664 13427 16941 18830 16894 16235 FALSE TRUE 12860.93848 14195.28007 13205.19759 15076.93429 13071.34906 13698.50314 17148.32903 18441.15392 14976.26395 15135.38899 0.849726326 0.937886702 0.872471636 0.996137879 0.863628221 0.905064492 1.132995593 1.218412948 0.989486557 1 13.88563813 2.240990444 24.99378687 1.116801126 0.906584985 0.572812709 0.07462069 38.16721471 392601.6274 0.026125487 0.02090963 174.1768547 -2.240990444 -0.210216142 KPDQPYEWLSYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPDQPYEWLSYK 12 1 E7EPM6;P33121-2;P33121;P33121-3;D6RER0 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ; 173.68 5.20E-05 2611500000 3490300 3563500 3050600 3383600 3403700 3321400 4180100 3898100 4854400 4565200 FALSE TRUE 3353895.217 3461872.469 3601911.28 3558228.001 3513183.102 3388560.984 4231257.314 3817602.873 4303348.863 4255994.938 0.788040227 0.813410852 0.846314747 0.836050807 0.825466936 0.796185389 0.994187582 0.896994223 1.011126406 1 22.021065 2.241040187 24.99999999 0.960464579 0.819893181 0.832028952 0.034502666 27.29602872 275212.7258 0.012221317 0.009781421 174.1968057 -2.241040187 -0.140571399 LPQTS(ph)DDEKKDF ddPTM_BT-474_Pertuzumab_2h_R1 1 LPQTSDDEKKDF 12 2 Q9GZT3-2;Q9GZT3 Q9GZT3-2 SLIRP "SRA stem-loop-interacting RNA-binding protein, mitochondrial" 1 LPQT(0.099)S(0.901)DDEKKDF 143.02 4.87E-05 733860000 725880 779140 600910 868840 496840 628500 1124500 1181600 1091200 753230 TRUE FALSE 697511.8071 756919.6901 709507.8042 913680.9365 512821.3098 641208.7006 1138261.967 1157199.547 967331.5507 702213.0612 0.993305089 1.077906026 1.010388219 1.30114489 0.730293038 0.913125568 1.620963822 1.647932246 1.377547078 1 19.42154931 2.241045478 24.99980004 1.49068874 1.009009997 0.441101154 0.217368074 49.72342698 500265.4365 0.076113439 0.060919851 174.1989279 -2.241045478 -0.481678743 KQESTVMVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQESTVMVLR 10 1 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5 A0A0J9YVP6 PUF60 Poly(U)-binding-splicing factor PUF60 0 ; 109.72 0.0031765 1261820000 1386500 1243710 1058940 1115090 1265040 1144310 1357660 1278060 1406440 1474870 FALSE TRUE 1332314.047 1208240.609 1250314.014 1172639.929 1305731.16 1167448.732 1374275.449 1251667.614 1246786.827 1374975.741 0.968972766 0.878735946 0.909335326 0.852844085 0.949639416 0.849068603 0.999490688 0.91031978 0.906770054 1 20.39097473 2.241059129 24.99997293 0.944663305 0.900742881 0.228827343 0.046100355 111.7895432 1118569.273 0.015478841 0.012388275 174.2044037 -2.241059129 -0.043920424 NGAPIIMSFPHFYQADER ddPTM_BT-474_Pertuzumab_2h_R1 2 NGAPIIMSFPHFYQADER 18 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PRF6;Q14108-2 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ; 191.95 1.99E-14 925340000 584020 1002750 621900 1167120 586250 694060 1163290 1137140 1119700 802690 FALSE TRUE 561195.8527 974152.5518 734291.1641 1227355.203 605107.2637 708094.3687 1177526.691 1113657.662 992596.3502 748323.0913 0.749937907 1.301780692 0.981248838 1.640140759 0.808617655 0.946241506 1.573553863 1.488204326 1.326427531 1 19.51330177 2.241118706 24.99980834 1.40513178 1.091622273 0.175749461 0.279426225 99.59433757 973330.7159 0.096551249 0.077326424 174.2283026 -2.241118706 -0.313509506 S(ph)SPATSLFVELDEEEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPATSLFVELDEEEVK 17 0 A0A087WTL4;A0A087WX97;Q9BXK5-4;Q9BXK5 A0A087WTL4 BCL2L13 Bcl-2-like protein 13 1 S(0.5)S(0.5)PATSLFVELDEEEVK;S(0.5)S(0.5)PATSLFVELDEEEVK;S(0.499)S(0.499)PAT(0.002)SLFVELDEEEVK;S(0.5)S(0.5)PATSLFVELDEEEVK 357.92 5.44E-88 147946000 134986 183581 156511 268104 126135 177291 306349 329014 312265 265121 TRUE FALSE 129710.5979 178345.4496 184796.0193 281940.8796 130192.2468 180875.9455 310098.1907 322219.7459 276817.9863 247164.1185 0.524795422 0.721566911 0.747665237 1.140703114 0.526744123 0.731805031 1.25462463 1.303667166 1.119976427 1 17.91510979 2.241253105 24.99145623 1.208663251 0.741659896 0.589121942 0.177633144 46.17210208 428570.0229 0.063713134 0.051069005 174.2822288 -2.241253105 -0.467003355 DYFLEFEGDPHCLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYFLEFEGDPHCLR 14 0 Q14344;Q14344-2 Q14344 GNA13 Guanine nucleotide-binding protein subunit alpha-13 0 118.24 0.00025691 67775000 42523 76458 40241 83223 44561 47851 73947 69653 62188 54316 FALSE TRUE 40861.15415 74277.4927 47513.44386 87518.149 45994.34503 48818.58001 74851.98551 68214.64121 55128.67895 50637.12894 0.806940579 1.466858297 0.938312358 1.728339478 0.908312655 0.96408665 1.478203584 1.347126953 1.088700724 1 15.62790799 2.241293074 24.9998902 1.274929468 1.158198801 0.010552001 0.291373708 295.0321019 2699343.419 0.099788233 0.080003067 174.2982691 -2.241293074 -0.116730667 ADEWLMK ddPTM_BT-474_Pertuzumab_2h_R1 3 ADEWLMK 7 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;; 137.77 0.0066323 571420000 1228010 1188780 992700 1066930 1143820 1117490 1300220 1310740 1387930 1432510 FALSE TRUE 1180018.012 1154877.158 1172102.972 1121994.385 1180612.009 1140086.413 1316132.481 1283672.761 1230378.005 1335484.822 0.883587737 0.864762474 0.877661021 0.840140125 0.884032518 0.853687286 0.985509127 0.961203557 0.921296884 1 20.34893215 2.241334487 24.99999999 0.964270875 0.867191338 0.821788984 0.022728664 27.87593941 251239.2025 0.007734481 0.006201755 174.3148904 -2.241334487 -0.097079537 NLVS(ph)PAMR ddPTM_BT-474_Pertuzumab_2h_R1 3 NLVSPAMR 8 0 Q14686 Q14686 NCOA6 Nuclear receptor coactivator 6 1 NLVS(1)PAMR;NLVS(1)PAMR;NLVS(1)PAMR 104.3 0.004833 418260000 672140 799720 731270 936600 1017390 833910 556098 587629 558740 563947 TRUE FALSE 645872.0257 776912.7686 863426.756 984938.0382 1050115.273 850772.2316 562903.6937 575494.2558 495314.1776 525750.3674 1.228476604 1.47772178 1.642275136 1.873394864 1.997364792 1.618205682 1.070667238 1.094615033 0.942109047 1 19.00401843 2.241402507 5.252728312 1.037542087 1.66250121 0.695891885 0.198356953 0.108436393 8.793858231 0.081184321 0.063330878 174.3421939 -2.241402507 0.624959123 EKQDETQTK ddPTM_BT-474_Pertuzumab_2h_R1 6 EKQDETQTK 9 1 P35221-2;P35221;P35221-3;E5RGY7 P35221-2 CTNNA1 Catenin alpha-1 0 ;;;;; 129.88 0.00034377 1009194000 1893610 1896210 1458706 1701353 1320436 1598369 1989180 2084020 1885980 2020700 FALSE TRUE 1819605.628 1842131.947 1722326.623 1789160.032 1362909.023 1630689.116 2013524.18 2040984.259 1671891.457 1883836.189 0.965904381 0.977862066 0.9142656 0.949742893 0.723475338 0.865621505 1.068842499 1.08341918 0.887493014 1 20.84524209 2.241445392 24.99690579 1.025873811 0.897998231 0.286356286 0.083913411 90.24927691 782027.1915 0.031829431 0.025544058 174.3594107 -2.241445392 -0.12787558 VFWDPSVNLFGHVGSTTASR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFWDPSVNLFGHVGSTTASR 20 0 R4GMQ1;O60341;O60341-2;R4GMP9 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ; 202.39 1.16E-21 382640000 83147 98249 91747 91634 97576 99093 82461 90651 96319 103551 FALSE TRUE 79897.52332 95447.03472 108327.7238 96363.24172 100714.6207 101096.7284 83470.18238 88779.02517 85385.27092 96537.39854 0.827632861 0.98870527 1.122132204 0.998195965 1.043270506 1.047228638 0.864640892 0.919633495 0.884478681 1 16.55880033 2.241529066 24.99979113 0.909833097 1.010627288 0.229842346 0.077376983 102.7782856 865589.5438 0.027712039 0.022252347 174.393007 -2.241529066 0.100794191 AEVEVADELLENLAK ddPTM_BT-474_Pertuzumab_2h_R1 3 AEVEVADELLENLAK 15 0 Q7L5D6;Q7L5D6-2;C9JPA8;C9JHN8 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 ;; 283.42 1.58E-33 75808600 120214 122866 116948 114846.7 135287 130808 145984 159729 177158 182862.2 FALSE TRUE 115515.904 119361.982 138083.1051 120773.952 139638.6292 133453.0274 147770.5959 156430.5403 157047.7665 170476.7803 0.677604913 0.700165628 0.809981892 0.708448105 0.819106443 0.782822312 0.866807759 0.91760614 0.921226728 1 17.37921573 2.241610909 0.391102007 1.011875699 0.676408838 0.878272871 0.035396366 0.392026298 0.140883184 0.038518835 0.046089193 174.4258746 -2.241610909 -0.335466861 LTSVSS(ph)SVDFDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTSVSSSVDFDQR 13 0 E9PNG1;H3BLW6;Q5T3F8-2;Q5T3F8-3;Q5T3F8 E9PNG1 TMEM63B CSC1-like protein 2 1 LTS(0.001)VS(0.202)S(0.63)S(0.167)VDFDQR 170.42 2.81E-05 51845000 116070 149640 129330 190320 113450 142530 173210 189600 169430 170230 TRUE FALSE 111533.8561 145372.4137 152702.8079 200142.438 117099.2223 145412.0543 175329.7958 185684.6937 150197.0167 158700.1705 0.70279607 0.916019266 0.962209476 1.261135621 0.737864502 0.916269049 1.104786436 1.170034621 0.946420009 1 17.27594415 2.241652223 24.96938377 1.08151451 0.925732293 0.156927766 0.152406457 135.4760193 1094182.849 0.055257589 0.044414569 174.4424684 -2.241652223 -0.155782217 DGQS(ph)SPQPSPR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.619)S(0.38)PQPS(0.001)PR;DGQS(0.821)S(0.179)PQPSPR;DGQS(0.801)S(0.188)PQPS(0.011)PR 115.33 0.0011938 106553000 242291 255822 207857 269403 231123 244569 287233 297679 303601 312973 TRUE FALSE 232821.9999 248526.207 245421.3837 283306.9211 238557.2812 249514.3527 290748.2434 291531.8246 269137.4873 291775.0599 0.797950311 0.851773305 0.841132151 0.970977167 0.817606828 0.855159974 0.996480794 0.99916636 0.922414299 1 18.15449705 2.241671859 24.99951135 0.9821672 0.858422197 0.617447617 0.047673297 53.82019872 432460.2628 0.017053575 0.013704633 174.4503557 -2.241671859 -0.123745003 HLLGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLLGLK 6 0 P43155-2;P43155;P43155-3;H0Y4Z7 P43155-2 CRAT Carnitine O-acetyltransferase 0 ; 112.58 0.026876 799680000 1236740 1563350 1165570 1775370 1177920 953080 1972100 1397930 1659840 1628540 FALSE TRUE 1188406.834 1518764.789 1376214.427 1866997.058 1215808.867 972351.9306 1996235.15 1369062.257 1471421.922 1518237.535 0.782754217 1.00034728 0.906455278 1.229713411 0.800802798 0.640447827 1.314837174 0.901744441 0.9691645 1 20.53396609 2.241898633 24.99952996 1.033501249 0.909949204 0.146900684 0.176897463 214.4462795 1606071.766 0.063498981 0.051124739 174.5414713 -2.241898633 -0.123552045 DCDLPAADSCAIMEGEDVEDDLIFTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DCDLPAADSCAIMEGEDVEDDLIFTSK 27 0 Q6UXG2-2;Q6UXG2-4;Q6UXG2;Q6UXG2-3;H0YDD2 Q6UXG2-2 KIAA1324 UPF0577 protein KIAA1324 0 95.123 0.0049855 19159000 11150 14995 7906.4 16789 10826 12472 18532 18582 19508 19766 FALSE TRUE 10714.24567 14567.35728 9335.262357 17655.4823 11174.22812 12724.19239 18758.80016 18198.27521 17293.53362 18427.23121 0.581435461 0.790534243 0.506601467 0.958119106 0.606397564 0.690510269 1.017993422 0.987575127 0.938477052 1 14.16955169 2.241933802 24.99574843 0.986433691 0.693747542 0.605312654 0.117481644 56.07013304 415490.1704 0.039043561 0.031432908 174.5556063 -2.241933802 -0.29268615 VFIGEFAYTYAAMYDKGPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VFIGEFAYTYAAMYDKGPFR 20 1 P15559-2;P15559;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 73.918 0.013085 137860000 160670 175250 120480 137830 154990 151430 140510 139890 172860 159140 FALSE TRUE 154390.8388 170252.0416 142253.4161 144943.4228 159975.3941 154492.0184 142229.6034 137001.2226 153237.6575 148361.3061 1.040640871 1.147550167 0.958830977 0.976962435 1.07828246 1.041322852 0.958670473 0.923429607 1.032868081 1 17.17875535 2.241998495 24.67686738 0.966629546 1.040563435 0.216953348 0.055700506 100.9673498 724742.7843 0.020462258 0.016467936 174.5816105 -2.241998495 0.073933889 DKTLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKTLKR 6 2 Q8IWF6 Q8IWF6 DENND6A Protein DENND6A 0 ; 77.748 0.040271 623890000 1008110 973450 843230 907050 902660 902490 1084310 1048740 1158870 1177050 FALSE TRUE 968711.9467 945688.1591 995620.4186 953862.9592 931694.8787 920738.9661 1097580.11 1027083.153 1027319.936 1097327.355 0.882792124 0.861810429 0.907313951 0.869260166 0.849058282 0.839074103 1.000230337 0.935986101 0.936201883 1 20.06556254 2.242027608 24.99999998 0.961238244 0.868880451 0.765186511 0.026999066 45.46525134 327846.048 0.009691955 0.007807753 174.5933139 -2.242027608 -0.092357793 KSSS(ph)LESLQTAVAEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSSLESLQTAVAEVR 16 1 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 R4GN62 PARD3B Partitioning defective 3 homolog B 1 KS(0.143)S(0.143)S(0.714)LESLQTAVAEVR 86.625 0.0041318 268740000 67161 74415 55194 54942 65660 63904 51236 50610 65753 54578 TRUE FALSE 64536.27387 72292.75706 65168.78358 57777.5632 67772.01353 65196.18266 51863.04149 49564.88581 58288.9951 50881.38345 1.268367122 1.42080958 1.280798185 1.135534439 1.331960905 1.281336675 1.019293069 0.974126143 1.145585893 1 15.63485028 2.24224208 11.64954279 1.025805477 1.287571078 0.713205993 0.078113761 0.083955701 229.7780759 0.028762486 0.022897729 174.6795563 -2.24224208 0.261765601 SINNAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SINNAEK 7 0 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ; 114.89 0.013499 161708000 211760 205020 183323 193513 193505 181960 241670 223110 234870 256390 FALSE TRUE 203484.1851 199173.0303 216453.5441 203500.2291 199729.2641 185639.3559 244627.6298 218502.7005 208208.5423 239024.4769 0.851311078 0.833274621 0.905570621 0.851378201 0.83560172 0.776654166 1.023441753 0.91414362 0.871076238 1 17.86679884 2.242312905 24.99999993 0.944504623 0.844872569 0.541810057 0.049261141 81.74523828 544638.8927 0.017526604 0.014143858 174.7080453 -2.242312905 -0.099632053 QQGNEPSQILSLTGDRVPLHCVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQGNEPSQILSLTGDRVPLHCVDR 24 1 Q8NFH3 Q8NFH3 NUP43 Nucleoporin Nup43 0 116.94 0.00047817 87252000 52057 59009 42165 50314 58415 57241 40403 49981 48978 50476 FALSE TRUE 50022.55489 57326.1211 49785.15346 52910.71157 60293.97153 58398.45224 40897.464 48948.87488 43418.22277 47057.21556 1.063015614 1.218221699 1.057970661 1.124391041 1.281290676 1.241009515 0.869100807 1.040199134 0.922668761 1 15.52212834 2.242387037 24.9998109 0.966496735 1.165435081 0.615623391 0.079752648 68.20464 445616.1945 0.028657159 0.023130514 174.7378698 -2.242387037 0.198938346 EGPLGWSSDGSLGSVLLDSPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGPLGWSSDGSLGSVLLDSPSSPR 24 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 EGPLGWSSDGSLGSVLLDS(0.001)PS(0.154)S(0.845)PR 209.01 3.71E-25 40989000 48970 54078 45970 57437 57896 57702 45939 55841 53424 52582 TRUE FALSE 47056.19826 52535.74839 54277.8016 60401.33045 59758.27742 58868.77397 46501.21522 54687.86384 47359.53149 49020.5743 0.959927519 1.071708138 1.107245322 1.232162848 1.219044825 1.200899312 0.948606088 1.115610427 0.966115395 1 15.58109977 2.242422427 24.99997594 1.025308919 1.136505679 0.323648078 0.086328684 140.735662 911078.1866 0.032871369 0.026535814 174.7521095 -2.242422427 0.11119676 MS(ph)PSKSPFLPSMK ddPTM_BT-474_Pertuzumab_2h_R1 1 MSPSKSPFLPSMK 13 1 A0A3F2YNW7;Q8NFD5;Q8NFD5-2;Q8NFD5-3;A0A1B0GV63;A0A1B0GWJ2;A0A1B0GTJ8;A0A1B0GVK1;H0Y7H8;Q8NFD5-4 A0A3F2YNW7 ARID1B AT-rich interactive domain-containing protein 1B 1 MS(0.984)PS(0.016)KSPFLPSMK 139.88 2.37E-05 695950000 710710 630680 457900 438980 504820 542610 628080 648220 671510 665650 TRUE FALSE 682934.6675 612693.6239 540652.7159 461635.8104 521057.9938 553581.946 635766.6309 634834.0305 595283 620564.9326 1.100504768 0.987315898 0.871226664 0.743896063 0.839651044 0.892061277 1.024496547 1.022993723 0.959259811 1 19.24322265 2.242607561 24.91195998 1.006427351 0.897548024 0.212873613 0.089331209 153.5606917 945286.1978 0.035043799 0.028317481 174.8266198 -2.242607561 -0.108879327 LQLWDTAGQER ddPTM_BT-474_Pertuzumab_2h_R1 9 LQLWDTAGQER 11 0 P20340-2;P20340;P20340-4;J3KR73;Q9NRW1-2;Q9NRW1;C9JU14;C9JB90;Q14964 P20340-2;Q14964 RAB6A;RAB6B;RAB39A Ras-related protein Rab-6A;Ras-related protein Rab-6B;Ras-related protein Rab-39A 0 ;;;;;;;; 211.86 1.84E-08 6374400000 4035671 5735559 4018703 6149458 4456059 4435067 6156196 5919030 5629139 5601973 FALSE TRUE 3877952.516 5571986.473 4744972.028 6466832.264 4599392.185 4524747.093 6231537.368 5796799.962 4990142.74 5222546.379 0.742540561 1.066909907 0.908555269 1.238252721 0.880680008 0.866387154 1.193199048 1.109956627 0.955499938 1 22.31632197 2.242634977 24.9999862 1.081961275 0.963835229 0.132259276 0.137925787 204.4572472 1254542.537 0.048177354 0.0389492 174.8376566 -2.242634977 -0.118126046 (ac)SDQEAKPS(ph)TEDLGDKKEGEYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDQEAKPSTEDLGDKKEGEYIK 22 3 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.053)DQEAKPS(0.818)T(0.129)EDLGDKKEGEYIK 100.29 5.09E-08 510330000 1966500 1459600 535410 253030 694830 980550 481080 690560 779070 367010 TRUE FALSE 1889647.006 1417973.637 632170.4971 266088.9086 717179.838 1000377.393 486967.6009 676299.6947 690633.2397 342152.0858 5.522827667 4.144278804 1.847630114 0.777691909 2.096084951 2.923779905 1.423248962 1.9766055 2.018497821 1 18.38427822 2.242676617 24.98568123 1.707728167 2.763753086 0.196883276 1.245958859 231.8674908 1407531.864 0.487565446 0.394225446 174.8544209 -2.242676617 1.056024919 TGMGSGS(ph)AGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGMGSGSAGK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 TGMGS(0.002)GS(0.998)AGK;TGMGS(0.002)GS(0.998)AGK 137.6 9.12E-05 379750000 599500 563420 437690 493390 502400 524090 544780 615730 552100 543750 TRUE FALSE 576070.8772 547351.8132 516790.3194 518853.917 518560.1523 534687.4589 551447.1806 603014.9603 489427.9226 506921.3282 1.13641081 1.079756922 1.019468487 1.023539331 1.022959823 1.054774043 1.087835824 1.189563206 0.965490887 1 18.95140234 2.242679497 7.133960943 1.089126705 1.052488204 0 0.066261957 0.428083721 120.1293617 0.024362234 0.01924618 174.8555805 -2.242679497 -0.0366385 AYDPDYER ddPTM_BT-474_Pertuzumab_2h_R1 1 AYDPDYER 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 77.046 0.079626 250410000 444710 484210 406510 512790 436450 452040 527650 544250 541070 530310 FALSE TRUE 427330.2415 470400.8049 479975.3998 539255.1534 450488.8106 461180.5585 534107.5385 533011.0473 479650.002 494391.6313 0.864355734 0.951474044 0.970840462 1.090744906 0.911198293 0.932824363 1.080332887 1.078115028 0.970182284 1 18.9152948 2.242711898 24.99915441 1.04438176 0.95857141 0.263384551 0.062737694 136.1199402 819722.7375 0.022977334 0.018582915 174.8686261 -2.242711898 -0.08581035 GGS(ph)PLAAPQGGSPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSPLAAPQGGSPTK 15 0 E7EPC8;Q9UQB3-2;Q9UQB3 E7EPC8 CTNND2 Catenin delta-2 1 GGS(1)PLAAPQGGSPTK 195.38 1.32E-08 185590000 272570 339930 210430 316110 229150 280460 358270 399090 354870 341330 TRUE FALSE 261917.6631 330235.5292 248459.382 332424.475 236520.8179 286131.0934 362654.6154 390848.652 314586.6453 318211.4151 0.823093235 1.037786558 0.780799714 1.044665462 0.743282003 0.899185509 1.139665638 1.228267226 0.988608926 1 18.27962606 2.242738776 23.53964841 1.122151916 0.890589526 0.41946298 0.113186273 40.5136393 228255.0632 0.038188505 0.030850384 174.8794488 -2.242738776 -0.231562391 AENYDIPSADR ddPTM_BT-474_Pertuzumab_2h_R1 3 AENYDIPSADR 11 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 169.52 3.91E-05 4653800000 2744580 2656390 2218100 2477800 2575490 2561480 2724830 2933910 2957620 2687040 FALSE TRUE 2637318.779 2580632.358 2618960.011 2605679.555 2658332.975 2613274.881 2758177.285 2873323.733 2621883.377 2505044.387 1.052803213 1.030174304 1.045474493 1.040173008 1.061191965 1.04320502 1.101049266 1.147015098 1.046641485 1 21.25640474 2.242956358 24.81962901 1.093012855 1.045276347 0.027710159 0.037882619 134.201794 757745.3656 0.013108527 0.010607005 174.9670855 -2.242956358 -0.047736508 CPQDQS(ph)PDRVGTEMEQVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 CPQDQSPDRVGTEMEQVSK 19 1 Q9H116 Q9H116 GZF1 GDNF-inducible zinc finger protein 1 1 CPQDQS(1)PDRVGTEMEQVSK;CPQDQS(1)PDRVGTEMEQVSK 196.02 5.18E-16 571550000 948180 807050 714730 740270 769260 795020 838690 884810 901730 873020 TRUE FALSE 911124.0773 784033.7242 843897.6101 778475.4234 794003.9465 811095.8491 848954.1391 866538.3643 799369.3908 813889.5778 1.119468909 0.963317071 1.036869906 0.956487765 0.975567163 0.996567435 1.043082701 1.064687874 0.982159512 1 19.63447355 2.243151529 24.96219345 1.032360808 1.003503483 0 0.048931239 315.9954139 1718172.479 0.016778978 0.013610532 175.0457332 -2.243151529 -0.028857325 SGGGDLT(ph)LGLEPSEEEAPRS(ph)PLAPSEGAGSDVFDGDLGMGAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAK 43 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 2 S(0.474)GGGDLT(0.531)LGLEPS(0.139)EEEAPRS(0.799)PLAPS(0.054)EGAGS(0.003)DVFDGDLGMGAAK;S(0.443)GGGDLT(0.556)LGLEPS(0.032)EEEAPRS(0.968)PLAPS(0.001)EGAGSDVFDGDLGMGAAK 118.8 9.04E-06 161801000 56806 82872 51394.2 112491 66628 67196 122924 143444 90855 61913 TRUE FALSE 54585.95872 80508.5717 60682.2752 118296.674 68771.15013 68554.74916 124428.3807 140481.8313 80541.5213 57719.57736 0.945709605 1.394822613 1.051329167 2.049506933 1.191470092 1.187720914 2.155739636 2.433867982 1.395393469 1 15.81677312 2.243218292 24.99638124 1.936967381 1.324945721 0.125256294 0.474466681 152.1217897 816396.7382 0.165190322 0.133966928 175.0726445 -2.243218292 -0.61202166 AST(ph)PYIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASTPYIEK 8 0 Q969Z0;Q969Z0-2;C9J7P5;C9IZN7;C9J5A2;C9J347;C9J618 Q969Z0 TBRG4 Protein TBRG4 1 AS(0.015)T(0.985)PYIEK 109.15 0.041074 186080000 539940 659120 466890 716880 449460 582550 752500 829020 774390 670250 TRUE FALSE 518838.5479 640322.5429 551267.4089 753878.2627 463917.2891 594329.5601 761709.3201 811900.4473 686484.4937 624853.3705 0.830336479 1.024756484 0.882234833 1.206488271 0.742441845 0.951150443 1.219020903 1.299345551 1.098632937 1 19.25315816 2.243276526 24.25714523 1.193490916 0.944006604 0.353123204 0.138248677 74.09502778 381123.4538 0.047094532 0.03817503 175.0961213 -2.243276526 -0.249484311 RDSFDDRGPS(ph)LNPVLDYDHGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(0.499)FDDRGPS(0.501)LNPVLDYDHGSR 117.83 6.18E-05 245780000 72968 67835 53090 63465 66002 57644 56936 52766 58356 54261 TRUE FALSE 70116.32989 65900.41222 62684.54398 66740.43626 68125.01427 58809.60118 57632.7998 51676.36366 51731.67153 50585.85414 1.386085717 1.302743886 1.239171406 1.319349794 1.346720648 1.162570093 1.139306646 1.021557598 1.022650945 1 15.62644638 2.243337966 1.254129629 1.007529289 1.316644479 0.903788873 0.04281269 0.131935296 0.402196486 0.027663395 0.015902807 175.1208941 -2.243337966 0.30911519 SLQLPAS(ph)PAPDPSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLQLPASPAPDPSPR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 SLQLPAS(1)PAPDPSPR 118.32 0.00031554 260400000 79986 92447 100060 101730 80101 92485 109130 124620 99444 98312 TRUE FALSE 76860.05869 89810.50208 118143.0678 106980.2975 82677.52141 94355.11007 110465.5656 122046.5535 88155.53402 91653.24067 0.838596193 0.979894452 1.289022264 1.167228749 0.902068719 1.029479257 1.205255425 1.331611982 0.961837611 1 16.48389827 2.243379249 24.8780574 1.173412342 1.043503763 0.037925862 0.155787628 243.338681 1256336.441 0.057596352 0.046739889 175.1375416 -2.243379249 -0.12990858 TGQVYYNT(ph)DDEREGGSVLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGQVYYNTDDEREGGSVLVK 20 1 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 T(0.005)GQVY(0.005)Y(0.019)NT(0.97)DDEREGGSVLVK 71.882 0.027237 287850000 195970 179860 131600 174390 163190 169430 126060 145470 132910 148270 TRUE FALSE 188311.2757 174730.5689 155383.0474 183390.2888 168439.1546 172855.9907 127602.76 142465.9937 117822.614 138227.5408 1.362328192 1.26407927 1.124110626 1.326727566 1.218564358 1.250517731 0.923135572 1.030662868 0.852381611 1 17.07668557 2.243450475 24.99857407 0.961197489 1.253293907 0.803446071 0.07410814 51.5085314 263329.734 0.025547431 0.020746766 175.1662672 -2.243450475 0.292096418 QVDGDNSHVEMK ddPTM_BT-474_Pertuzumab_2h_R1 2 QVDGDNSHVEMK 12 0 P02786;F8WBE5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 162.93 6.14E-05 853550000 1563670 2178150 1304730 2391900 1618110 1749180 2628900 2565600 2732900 2361300 FALSE TRUE 1502560.048 2116031.295 1540523.735 2515346.246 1670157.978 1784549.618 2661073.265 2512619.463 2422672.649 2201367.048 0.682557708 0.961235109 0.699803214 1.14262919 0.758691277 0.810655188 1.208827609 1.141390513 1.100530987 1 21.06996828 2.243450493 24.99971133 1.129295542 0.851321513 0.487207943 0.135140938 95.61267835 488825.8777 0.045167116 0.036672118 175.1662743 -2.243450493 -0.27797403 RKS(ph)VEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 RKSVEDR 7 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 RKS(1)VEDR;RKS(1)VEDR;RKS(1)VEDR 104.22 0.0064579 356947000 737443 704500 669499 725302 690688 718494 664941 703092 761239 729252 TRUE FALSE 708622.9123 684408.3498 790492.3622 762734.9231 712904.6068 733022.441 673078.7469 688572.9045 674826.3401 679859.1125 1.042308471 1.006691441 1.162729671 1.121901449 1.048606386 1.078197567 0.990026808 1.012817056 0.99259733 1 19.37487628 2.243535928 24.9476204 1.000955683 1.078237916 0.465711366 0.040821713 115.7658176 580485.0722 0.015408783 0.012518946 175.2007365 -2.243535928 0.077282233 YNHSHDQLVLTGSSDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YNHSHDQLVLTGSSDSR 17 0 A8MUM1;Q53HC9;C9JVR6 A8MUM1 TSSC1 Protein TSSC1 0 53.773 0.076585 148360000 165590 215750 149320 243560 171100 188840 275550 251780 313700 291430 FALSE TRUE 159118.5597 209597.0212 176305.4456 256130.1608 176603.5869 192658.4742 278922.2633 246580.655 278090.0911 271691.1865 0.58565963 0.771453148 0.648918531 0.94272532 0.650015884 0.709108296 1.026615058 0.907576938 1.023552124 1 18.05160824 2.243569526 24.99811731 0.975391601 0.724397938 0.659581783 0.095257899 77.79050994 388232.9988 0.032517986 0.026422742 175.2142912 -2.243569526 -0.250993663 TNLVWDEVSGQWR ddPTM_BT-474_Pertuzumab_2h_R1 3 TNLVWDEVSGQWR 13 0 Q15050 Q15050 RRS1 Ribosome biogenesis regulatory protein homolog 0 ;; 152.31 9.63E-05 162599000 242368 249527 202835 218857 225880 231198 243553 254464 271517 256380 FALSE TRUE 232895.9906 242410.7343 239491.7965 230152.236 233145.6353 235872.982 246533.6745 249209.2295 240695.5285 239015.1542 0.974398428 1.014206547 1.001994193 0.962919011 0.975442901 0.986853669 1.031456249 1.04265033 1.007030409 1 17.86674257 2.243623017 24.95105079 1.026126067 0.986454853 0.458011211 0.017835417 97.13440259 478748.5854 0.006572176 0.005334916 175.2358733 -2.243623017 -0.039671214 VSSSS(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.003)S(0.082)S(0.417)S(0.498)ELDLPSGDHCEAGLLQLDVPLLR 258.02 8.46E-54 93551000 34728 42044 36600 38634 41644 40534 37661 40705 43635 41729 TRUE FALSE 33370.79137 40844.94629 43214.43416 40627.90537 42983.51708 41353.62525 38121.90658 39864.42753 38681.73773 38902.65766 0.857802355 1.049926888 1.110835011 1.044347811 1.104899245 1.063002575 0.979930649 1.024722472 0.994321212 1 15.2475811 2.243646014 24.97434181 1.003478179 1.045565937 0.067944845 0.066679796 339.7693571 1668604.827 0.023861518 0.019383008 175.2451525 -2.243646014 0.042087758 LALLIHNDS(ph)LTSLIYGEQSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LALLIHNDSLTSLIYGEQSEK 21 0 G3V4J5;Q9P1W3 G3V4J5 TMEM63C Calcium permeable stress-gated cation channel 1 1 LALLIHNDS(0.451)LT(0.451)S(0.098)LIYGEQSEK;LALLIHNDS(0.852)LT(0.148)SLIYGEQSEK 241.45 3.40E-30 675150000 432870 584470 392790 649730 476020 517300 718160 759580 739890 641930 TRUE FALSE 415952.9618 567801.4879 463775.8906 683262.6432 491331.6156 527760.1604 726949.0569 743894.4076 655900.7891 598451.5093 0.695048731 0.948784453 0.774959848 1.141717637 0.82100489 0.881876229 1.214716724 1.243032052 1.095996549 1 19.19087483 2.243674957 24.99780135 1.169726764 0.885301879 0.493044894 0.128038137 93.69779309 457976.436 0.043567705 0.03541803 175.256832 -2.243674957 -0.284424885 TDVKDDLSDPPVASSCISEKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDVKDDLSDPPVASSCISEKSPR 23 2 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 TDVKDDLSDPPVAS(0.031)S(0.113)CIS(0.061)EKS(0.795)PR;TDVKDDLSDPPVAS(0.001)S(0.001)CIS(0.012)EKS(0.986)PR 133.4 1.21E-05 545430000 1612620 1441130 1336380 1320110 1636220 1458900 1163000 1266500 1228560 1105310 TRUE FALSE 1549597.028 1400030.383 1577893.594 1388241.035 1688850.502 1488399.958 1177233.142 1240346.332 1089099.019 1030446.369 1.50381143 1.358663998 1.531271923 1.347222987 1.638950413 1.444422536 1.142449697 1.203698096 1.056919653 1 19.97483799 2.243744559 4.915563005 1.124641851 1.472646148 0.789586023 0.093384775 0.084562686 5.48201456 0.033443007 0.026065585 175.2849218 -2.243744559 0.348004297 QIFLGGVDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QIFLGGVDKR 10 1 P05141 P05141 SLC25A5 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed" 0 ; 154.05 2.43E-05 1779380000 878290 1527770 678350 1444050 680420 705250 1629580 1420090 1162630 883100 FALSE TRUE 843965.4558 1484199.495 800942.9348 1518577.594 702306.3272 719510.6382 1649523.288 1390764.645 1030653.117 823286.8504 1.025117133 1.802773231 0.972860109 1.844530364 0.853051797 0.873948901 2.003582696 1.6892832 1.251876082 1 19.65103566 2.243761221 24.99998414 1.575658928 1.254093714 0.066891027 0.414581753 276.0429762 1326979.228 0.142941635 0.116254086 175.2916469 -2.243761221 -0.321565214 TLLISSLS(ph)PALPAEHLEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 TLLISSLSPALPAEHLEDR 19 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TLLIS(0.003)S(0.004)LS(0.993)PALPAEHLEDR;TLLIS(0.024)S(0.003)LS(0.974)PALPAEHLEDR;T(0.004)LLIS(0.038)S(0.038)LS(0.921)PALPAEHLEDR 219.78 1.97E-19 188238000 120147 127821 124544 139974 129574 135460 119265 123327 147458 148222 TRUE FALSE 115451.5224 124175.6702 147051.8713 147198.0749 133741.8654 138199.094 120724.6007 120780.2544 130719.186 138182.7919 0.835498551 0.898633386 1.064183675 1.06524172 0.967861942 1.000117975 0.873658717 0.874061471 0.945987443 1 17.07621844 2.243819514 24.98353301 0.907364708 0.976842387 0.075786302 0.073809412 248.2886503 1179553.281 0.027774066 0.022596288 175.3151766 -2.243819514 0.069477679 QSKPVTTPEEIAQVATISANGDKEIGNIISDAMK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSKPVTTPEEIAQVATISANGDKEIGNIISDAMK 34 2 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 171.95 5.90E-15 126490000 65400 73739 51743 69051 47112 52457 93433 90923 89935 53998 FALSE TRUE 62844.0957 71636.03592 61094.11112 72614.73039 48627.40027 53517.71648 94576.461 89045.40828 79725.95584 50340.66736 1.248376293 1.423025154 1.213613452 1.442466582 0.96596654 1.063110985 1.878728788 1.768856333 1.583728624 1 15.61943672 2.243844762 24.9997252 1.646817611 1.232488574 0.256865767 0.25918261 135.1506011 639411.0256 0.088958866 0.072379948 175.325369 -2.243844762 -0.414329037 EKLQSFDS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 6 EKLQSFDSPER 11 1 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 EKLQSFDS(1)PER;EKLQSFDS(1)PER;EKLQS(0.001)FDS(0.999)PER;EKLQSFDS(1)PER;EKLQSFDS(1)PER;EKLQSFDS(1)PER 179.97 4.16E-06 4068460000 4330040 4247370 3459120 3814990 3910970 4131400 4227930 4516910 4824180 4851340 TRUE FALSE 4160817.25 4126239.166 4084259.932 4011882.091 4036769.902 4214939.739 4279672.672 4423634.23 4276559.311 4522754.421 0.919974171 0.912328812 0.903047027 0.887043982 0.892546782 0.931940881 0.946253604 0.97808411 0.945565227 1 22.10877023 2.243895855 1.730662314 0.972193205 0.902853431 0.792433973 0.015835646 0.159499257 0.953870127 0.008216771 0.005154972 175.3459967 -2.243895855 -0.069339774 TQADLDSLVR ddPTM_BT-474_Pertuzumab_2h_R1 3 TQADLDSLVR 10 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;; 180.15 4.72E-06 805730000 869760 967600 805070 966760 885960 823620 1105870 1054900 1022650 1058700 FALSE TRUE 835768.8176 940004.9954 950564.0577 1016654.599 914457.708 840274.1607 1119403.968 1033115.946 906563.0593 986993.306 0.846782661 0.952392473 0.963090683 1.030052173 0.926508521 0.851347376 1.134155582 1.046730449 0.918509836 1 19.91268077 2.24405173 24.99999233 1.034435106 0.935571172 0.303373082 0.070530811 168.1558023 765583.841 0.025555917 0.02081144 175.4089425 -2.24405173 -0.098863934 ESDDPMAYIHFTAEGEVTFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESDDPMAYIHFTAEGEVTFK 20 0 P14625 P14625 HSP90B1 Endoplasmin 0 111.65 0.00016508 59309000 42597 44271 36333 40967 41893 43614 35874 36835 47464 47095 FALSE TRUE 40932.26215 43008.43443 42899.18132 43081.31178 43240.52639 44495.90496 36313.03674 36074.34438 42076.08571 43905.2137 0.93228705 0.979574652 0.977086266 0.981234531 0.984860857 1.013453784 0.827078009 0.821641471 0.958339162 1 15.42210465 2.244051966 24.99943363 0.877772756 0.978556718 0.276428331 0.055281046 123.8248688 563716.3493 0.019232152 0.015663167 175.4090378 -2.244051966 0.100783962 TDFEEFFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDFEEFFLR 9 0 B1AKV2;B1AKV6;B1AKV3;Q9NVA1-5;Q9NVA1-2;Q9NVA1 B1AKV2 UQCC1 Ubiquinol-cytochrome-c reductase complex assembly factor 1 0 ;;; 255.13 1.40E-14 122786000 135828 197396 143901 278404 131592 129579 252764 219403 181957 162565 FALSE TRUE 130519.6916 191766.4594 169907.1118 292772.4638 135824.7762 132199.1762 255857.4014 214872.2514 161302.0042 151554.3278 0.861207288 1.265331464 1.121097063 1.931798769 0.896211795 0.872289021 1.688222337 1.417790271 1.064318034 1 17.20947552 2.244080729 24.99736848 1.349969892 1.184465775 0.02168843 0.343102414 483.7367787 2190567.452 0.122545801 0.099795636 175.4206553 -2.244080729 -0.165504117 RIS(ph)IVENCFGAAGQPLTIPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RISIVENCFGAAGQPLTIPGR 21 1 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 1 RIS(1)IVENCFGAAGQPLTIPGR;RIS(1)IVENCFGAAGQPLTIPGR 168.75 1.10E-11 302160000 158909 175092 118372 143091 147624 160561 123927 149882 143580 158483 TRUE FALSE 152698.6606 170098.5476 139764.4536 150475.9437 152372.46 163807.6534 125443.6557 146786.8843 127281.4003 147748.8052 1.03350183 1.151268515 0.945959958 1.018457939 1.031294025 1.108690207 0.8490333 0.993489484 0.861471605 1 17.17278694 2.24411562 24.99999889 0.930015965 1.046113536 0.435520986 0.068066779 131.1304158 590147.4179 0.023157744 0.018864671 175.434749 -2.24411562 0.11609757 ETSFGSS(ph)ENITMTSLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETSFGSSENITMTSLSK 17 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;A0A087WZS7;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 ETSFGS(0.02)S(0.98)ENITMTSLSK 410.69 1.88E-140 2170600000 435870 442820 355940 390470 408080 408300 502130 508660 536860 514890 TRUE FALSE 418835.7185 430191.2072 420266.2758 410622.2035 421206.2638 416556.1057 508275.2171 498155.9932 475917.9035 480016.0417 0.872545253 0.89620173 0.875525481 0.855434335 0.877483724 0.867796218 1.058871315 1.037790303 0.991462497 1 18.87272309 2.244142753 24.99998481 1.027734562 0.874527503 0.928203672 0.020121606 30.96434972 138676.4606 0.007196136 0.005863209 175.4457099 -2.244142753 -0.153207059 ETGANLAICQWGFDDEANHLLLQNNLPAVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ETGANLAICQWGFDDEANHLLLQNNLPAVR 30 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 253.67 4.57E-58 1412872000 386980 473468 352994 396297 407757 431070 375370 410515 470963 438780 FALSE TRUE 371856.3938 459965.1562 416787.8681 416749.9357 420872.8742 439786.5307 379963.8903 402037.7218 417501.2547 409061.0398 0.909048669 1.124441371 1.018889182 1.018796451 1.028875481 1.07511224 0.928868441 0.982830636 1.020633143 1 18.64195661 2.244203338 24.9997243 0.979893392 1.032567842 0.140403276 0.055294064 232.2909892 1029155.622 0.018343846 0.014949535 175.4701866 -2.244203338 0.052674451 KYQEDS(ph)DPERSDYEEQQLQK ddPTM_BT-474_Pertuzumab_2h_R1 3 KYQEDSDPERSDYEEQQLQK 20 2 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 KYQEDS(0.987)DPERS(0.013)DYEEQQLQK;KYQEDS(1)DPERSDYEEQQLQK;KYQEDS(1)DPERSDYEEQQLQK 197.44 8.63E-22 1695720000 1230610 1054720 1064110 1123760 1067730 1113760 1479360 1420110 1668180 1521010 TRUE FALSE 1182516.401 1024640.418 1256418.348 1181757.388 1102074.505 1136280.99 1497464.85 1390784.232 1478815.2 1417990.638 0.833938088 0.72260027 0.886055461 0.833402814 0.777208591 0.8013318 1.056047064 0.98081341 1.042894897 1 20.43541658 2.244206301 24.99995402 1.01566595 0.808312618 0.845218466 0.044187238 49.11247393 217478.2683 0.015288576 0.012463236 175.4713837 -2.244206301 -0.207353333 KLDDFVETGDIR ddPTM_BT-474_Pertuzumab_2h_R1 6 KLDDFVETGDIR 12 1 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PRF6;Q14108-2 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ;;;;; 128.9 0.00039085 5295510000 6400810 10922010 6096480 12385100 6505940 7771190 14038320 14268010 12725180 9605680 FALSE TRUE 6150659.269 10610524.97 7198249.551 13024296.5 6715209.469 7928328.786 14210125.16 13973370.61 11280670.91 8955078.738 0.68683475 1.184861159 0.803817561 1.454403348 0.749877211 0.885344397 1.586823028 1.560385008 1.259695335 1 23.09427469 2.244295491 24.9998059 1.422506026 0.976744263 0.331398857 0.263870081 134.7650844 587477.6226 0.089087281 0.072648937 175.5074235 -2.244295491 -0.445761763 KLLLDPSS(ph)PPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLLLDPSSPPTK 12 1 F5GX19;F5H3Y3;Q6IAA8;H0YFI1;F5H479 F5GX19 LAMTOR1 Ragulator complex protein LAMTOR1 1 KLLLDPS(0.091)S(0.909)PPTK 96.993 0.003168 340380000 499670 757610 561110 864240 480860 671290 1015100 1085800 994290 1002500 TRUE FALSE 480142.344 736003.7046 662515.0588 908843.53 496327.2986 684863.9437 1027523.097 1063377.851 881422.3676 934599.7821 0.513741126 0.787506822 0.708875683 0.97244141 0.53105865 0.732788469 1.099425783 1.137789534 0.943101405 1 19.83398918 2.244340979 21.52687026 1.066795623 0.715414131 0.611454081 0.1311986 15.47805717 57643.09845 0.045413086 0.036892353 175.5258074 -2.244340979 -0.351381492 RGPCIIYNEDNGIIK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGPCIIYNEDNGIIK 15 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 211.75 1.96E-09 3318000000 1587830 1667280 1377240 1406440 1485500 1576570 1648490 1736800 1935910 1837790 FALSE TRUE 1525775.848 1619730.807 1626137.905 1479026.537 1533282.457 1608449.326 1668664.714 1700934.473 1716153.613 1713314.846 0.89054026 0.945378376 0.949117967 0.863254375 0.894921596 0.938793783 0.97393933 0.992774023 1.001656885 1 20.70835886 2.24434232 2.108776052 0.996234065 0.910661503 0.731979411 0.024042187 0.181181828 1.635075233 0.012102198 0.008109457 175.5263494 -2.24434232 -0.085572562 KDDSHS(ph)AEDSEDEKEDHKNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDS(0.02)HS(0.955)AEDS(0.025)EDEKEDHKNVR 133.62 6.85E-06 23720000 40386 30331 22485 16705 27275 26002 34643 31033 44667 30308 TRUE FALSE 38807.67047 29465.98958 26548.53968 17567.14705 28152.32515 26527.77826 35066.9714 30392.15771 39596.58942 28255.21216 1.373469441 1.042851471 0.939597959 0.621731203 0.996358653 0.938863177 1.241079741 1.075630136 1.401390624 1 14.7862294 2.244364457 24.91528959 1.175994059 0.96996157 0.186343008 0.196994523 225.1836543 966692.7744 0.071162767 0.05804583 175.5352963 -2.244364457 -0.206032488 LYSLLGIDLTAPSNNSSPRDS(ph)PCKENK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPRDSPCKENK 27 2 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 LYSLLGIDLTAPS(0.004)NNS(0.016)S(0.016)PRDS(0.964)PCKENK 170.29 2.88E-12 182770000 272720 246290 191820 196350 231220 225920 246130 246620 292970 240460 TRUE FALSE 262061.8009 239266.0503 226486.141 206483.647 238657.4013 230488.2572 249142.2126 241527.2108 259713.2738 224173.43 1.169013655 1.067325643 1.010316615 0.921088851 1.064610562 1.028169383 1.111381543 1.0774123 1.158537271 1 17.77425577 2.244397806 24.87611223 1.092229634 1.038405259 0.083470172 0.068357812 293.8493929 1252291.365 0.024543267 0.02001956 175.548776 -2.244397806 -0.053824375 MDKEETK ddPTM_BT-474_Pertuzumab_2h_R1 2 MDKEETK 7 1 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 95.502 0.012238 1955810000 1090310 1131920 950040 1162390 1175580 1156610 1749590 1701610 1840000 1986980 FALSE TRUE 1047699.48 1099638.75 1121733.362 1222381.087 1213393.598 1179997.447 1771002.006 1666471.159 1631130.914 1852400.075 0.565590282 0.593629187 0.605556746 0.659890433 0.655038625 0.63701004 0.956058051 0.8996281 0.880550015 1 20.82096429 2.24446834 23.48803921 0.923986307 0.621102657 0.93577675 0.040341035 15.68138036 62346.61535 0.014658406 0.0119425 175.5772894 -2.24446834 -0.30288365 EAIDSYIK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAIDSYIK 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 111.04 0.0077015 731770000 754630 768240 659110 593590 690140 691520 756600 743610 849720 834670 FALSE TRUE 725138.2253 746330.5474 778225.8388 624225.251 712338.9799 705503.0082 765859.4971 728254.1936 753263.3479 778137.0575 0.931890106 0.959124797 1.000114095 0.80220476 0.915441532 0.906656484 0.984221854 0.935894502 0.968034282 1 19.56966476 2.244540473 24.96069291 0.964021365 0.919235475 0.206834208 0.049670123 276.1614307 1152737.775 0.018140693 0.014804991 175.606454 -2.244540473 -0.04478589 QFGFIVLTTSAGIMDHEEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QFGFIVLTTSAGIMDHEEAR 20 0 P62244 P62244 RPS15A 40S ribosomal protein S15a 0 ; 191.8 1.33E-17 730870000 866310 940710 781680 820400 866590 866290 796860 793660 901460 959940 FALSE TRUE 832453.6474 913881.8719 922946.9644 862740.9423 894464.6544 883806.9773 806612.211 777270.6437 799130.04 894922.4088 0.93019645 1.021185594 1.031315067 0.964039937 0.999488498 0.987579447 0.901320833 0.868534117 0.892960141 1 19.77140308 2.244572289 6.641112399 0.90045992 0.991953385 0.397711178 0.042476429 0.111216085 22.31857987 0.014713477 0.011637238 175.619319 -2.244572289 0.091493465 CRSPGMLEPLGSS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 CRSPGMLEPLGSSR 14 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 CRS(0.008)PGMLEPLGS(0.144)S(0.848)R;CRSPGMLEPLGS(0.126)S(0.874)R 162.86 1.15E-05 2275200000 1712920 1767450 1258350 1536700 1655470 1626430 1344530 1557600 1528780 1427300 TRUE FALSE 1645977.193 1717044.057 1485761.837 1616009.271 1708719.696 1659317.529 1360984.76 1525435.016 1355239.304 1330627.7 1.236993032 1.290401558 1.116587185 1.214471389 1.284145593 1.247018628 1.02281409 1.146402571 1.018496236 1 20.34367554 2.244575082 24.98818722 1.067182291 1.230657195 0.695346591 0.059279327 90.27136221 375049.6917 0.021178362 0.017294206 175.6204485 -2.244575082 0.163474904 AEEPPS(ph)PPVPK ddPTM_BT-474_Pertuzumab_2h_R1 5 AEEPPSPPVPK 11 0 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 AEEPPS(1)PPVPK;AEEPPS(1)PPVPK;AEEPPS(1)PPVPK;AEEPPS(1)PPVPK;AEEPPS(1)PPVPK 199.51 5.25E-08 3167840000 2259610 2256190 1867150 2055070 2203010 2245500 2395880 2700640 2823650 2663350 TRUE FALSE 2171301.943 2191845.67 2204585.54 2161132.409 2273871.817 2290905.549 2425201.496 2644870.84 2503121.09 2482958.932 0.874481617 0.882755507 0.887886429 0.870385886 0.915791151 0.922651405 0.976738465 1.065209257 1.008120214 1 21.24362897 2.24459236 1.789730327 1.031915812 0.884902487 0.895532308 0.020767489 0.096397576 0.618500379 0.01061325 0.006737395 175.6274355 -2.24459236 -0.147013324 DGPGFYTTR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGPGFYTTR 9 0 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 ; 126.24 0.0011143 228180000 124877 149235 104782 174663 113344 124320 171677 182545 140623 143914 FALSE TRUE 119996.6688 144978.9639 123718.4383 183677.3784 116989.8127 126833.8356 173778.0345 178775.382 124660.0666 134166.5766 0.894385709 1.080589276 0.922125625 1.369024857 0.871974345 0.945345993 1.295240878 1.332488214 0.929143977 1 17.03366579 2.244638363 24.99971358 1.189247158 1.022456888 0.079870932 0.177135342 262.0048217 1077711.28 0.061902476 0.050551777 175.6460401 -2.244638363 -0.16679027 WYMQFDDDEKQK ddPTM_BT-474_Pertuzumab_2h_R1 1 WYMQFDDDEKQK 12 1 M0R0N4;M0QYZ2;P53680;X6R390;P53680-2 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 108.17 0.00063975 0 237010 193350 159800 146060 164220 172870 205770 198510 217650 221930 FALSE TRUE 227747.3872 187835.8473 188679.4147 153598.1741 169502.2854 176365.5498 208288.2748 194410.6991 192943.2845 206898.4834 1.100768761 0.907864786 0.91194199 0.742384244 0.819253397 0.852425532 1.006717262 0.939642939 0.932550501 1 17.65856354 2.244731721 24.99783597 0.963514151 0.881152749 0.160959302 0.088618567 285.9611885 1158370.488 0.032935234 0.026905295 175.6838018 -2.244731721 -0.082361401 EAAEMGK ddPTM_BT-474_Pertuzumab_2h_R1 6 EAAEMGK 7 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;; 113.7 0.014125 9023270000 10782240 10207040 8608140 10247990 9875470 10117590 11217500 11836400 12091900 12374700 FALSE TRUE 10360858.14 9915945.213 10163822.39 10776889.99 10193123.46 10322174.6 11354783.12 11591974.2 10719278.21 11536550.55 0.89808978 0.859524272 0.881010519 0.934151846 0.883550366 0.894736651 0.984244214 1.004804179 0.929157998 1 23.45970858 2.244830002 7.935533219 0.982899858 0.891299726 0.732435085 0.025939649 0.062659198 28.22680177 0.009367689 0.007451987 175.7235635 -2.244830002 -0.091600132 LDVTILS(ph)PSRK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDVTILSPSRK 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 LDVTILS(0.96)PS(0.039)RK 84.297 0.0058375 0 197810 197240 200000 153300 196980 196560 171920 186880 198280 204710 TRUE FALSE 190079.3665 191614.9083 236144.449 161211.8314 203316.0406 200534.5779 174024.0084 183020.8627 175772.0857 190844.8094 0.995989187 1.00403521 1.23736375 0.844727357 1.0653475 1.050773026 0.911861365 0.959003618 0.921021045 1 17.54204042 2.244970325 24.97850629 0.944935555 1.033917367 0.168201085 0.092564878 257.7824804 1004575.133 0.031521471 0.025782182 175.7803501 -2.244970325 0.088981812 DLPHYF ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPHYF 6 0 A0A087X2I2;A0A087WT12;P36969-2;P36969 A0A087X2I2 GPX4 "Glutathione peroxidase;Phospholipid hydroperoxide glutathione peroxidase, mitochondrial" 0 104.64 0.078306 184220000 264030 266160 208180 240050 254590 239980 226400 226040 238980 249920 FALSE TRUE 253711.4157 258569.3774 245802.7569 252439.0093 262779.1186 244832.56 229170.7509 221372.195 211851.9923 232992.6958 1.088924332 1.109774607 1.054980527 1.083463189 1.127842732 1.050816461 0.983596289 0.950125043 0.909264522 1 17.8299252 2.24499909 2.367982812 0.949935508 1.091473926 0.840127064 0.027408723 0.104225962 1.19414703 0.011877059 0.008254327 175.7919929 -2.24499909 0.141538417 LFQEDDEIPLYLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFQEDDEIPLYLK 13 0 D6RIE3;D6RGV5;H0UI06;P14406 D6RIE3 COX7A2 "Cytochrome c oxidase subunit 7A2, mitochondrial" 0 110.86 0.0023857 22140000 30645 52862 27743 82860 29270 34238 75522 70967 56489 42021 FALSE TRUE 29447.35952 51354.42752 32756.77724 87136.41453 30211.49613 34930.31582 76446.26083 69501.50665 50076.60554 39174.88024 0.751689842 1.310901966 0.836167897 2.224293067 0.771195622 0.891650864 1.951410198 1.774134502 1.278283564 1 15.25764124 2.245102472 24.9999025 1.601609016 1.159102584 0.110998632 0.476292691 278.7331991 1065190.223 0.16484002 0.13488691 175.8338444 -2.245102472 -0.442506432 TQPSMVSNPGSCSDPQPS(ph)PEMKPHSYLDAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQPSMVSNPGSCSDPQPSPEMKPHSYLDAIR 31 1 C9J494;Q9H000-2;Q9H000 C9J494 MKRN2 Probable E3 ubiquitin-protein ligase makorin-2 1 TQPSMVSNPGSCSDPQPS(0.959)PEMKPHS(0.039)Y(0.001)LDAIR 116.84 2.66E-05 99583000 48274 45247 45743 53285 52025 48812 39403 39575 41885 45195 TRUE FALSE 46387.39871 43956.59986 54009.77765 56035.04524 53698.43137 49799.01208 39885.2257 38757.76242 37130.3904 42133.90239 1.100951872 1.04325964 1.281860321 1.329927732 1.274470873 1.181922615 0.94663023 0.919871178 0.881247363 1 15.36269392 2.245113614 4.499586206 0.926522473 1.209934401 0.704449636 0.084216669 0.116149017 5.741914123 0.035141399 0.027264822 175.8383557 -2.245113614 0.283411928 ACALSIEESCRPGDK ddPTM_BT-474_Pertuzumab_2h_R1 1 ACALSIEESCRPGDK 15 1 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3;H0Y8X1 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 97.836 0.0028822 215040000 62553 83077 66336 114720 60351 69152 106020 105490 96474 69916 FALSE TRUE 60108.3596 80707.7253 78324.39084 120640.7129 62292.24472 70550.30082 107317.5045 103311.5946 85522.67597 65180.52705 0.92218278 1.23821836 1.20165323 1.850870473 0.955687957 1.082383098 1.646465737 1.585007046 1.312089359 1 15.9921534 2.245146697 24.9998982 1.458316925 1.227246274 0.057440289 0.293319445 336.2758035 1276461.825 0.103374372 0.084609682 175.8517509 -2.245146697 -0.231070652 KGEDFVK ddPTM_BT-474_Pertuzumab_2h_R1 5 KGEDFVK 7 1 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;;;; 96.027 0.020898 7989080000 10559800 13617600 10093700 16912900 9482300 10358600 17350500 16645400 14745200 11926100 FALSE TRUE 10147111.34 13229239.38 11917856.12 17785776.8 9787306.791 10568057.99 17562840.61 16301666.67 13071386.71 11118334.62 0.912646694 1.189857998 1.071910185 1.599679934 0.880285323 0.950507279 1.579628713 1.466196802 1.175660488 1 23.40643737 2.245363944 24.99852489 1.365697459 1.116199824 0.124950222 0.243187018 263.5274061 968321.2357 0.08527035 0.069851229 175.9397391 -2.245363944 -0.249497635 KESYSVYVYK ddPTM_BT-474_Pertuzumab_2h_R1 4 KESYSVYVYK 10 1 P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880 P58876;Q99880 HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L 0 ;;; 161.99 1.11E-05 86332910000 63577550 64191610 47092120 60550160 51638040 54405880 69445030 66497440 70342660 69520800 FALSE TRUE 61092869.06 62360928.13 55602713.64 63675161.01 53299024.45 55506004.17 70294919.05 65124244.63 62357656.14 64812094.29 0.942615259 0.96218042 0.857906449 0.982458007 0.822362323 0.856414297 1.084595704 1.004816236 0.962129936 1 25.94975972 2.245467381 24.99998314 1.014926008 0.904396248 0.486234348 0.054820424 137.3640813 497209.2473 0.019492426 0.015972013 175.9816484 -2.245467381 -0.11052976 DGQSS(ph)PQPSPR ddPTM_BT-474_Pertuzumab_2h_R1 5 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.035)S(0.965)PQPSPR;DGQS(0.02)S(0.978)PQPS(0.001)PR;DGQS(0.246)S(0.753)PQPS(0.001)PR;DGQS(0.358)S(0.641)PQPSPR;DGQS(0.022)S(0.977)PQPSPR 193.62 9.17E-07 403447000 566390 620717 471439 597274 560774 565438 669696 690482 679758 695776 TRUE FALSE 544254.8526 603014.7589 556638.5144 628099.3827 578811.805 576871.5438 677891.94 676223.3054 602594.7216 648650.4718 0.839057206 0.92964514 0.858148631 0.96831716 0.892332358 0.88934113 1.04508047 1.042507999 0.928997585 1 19.30708176 2.245566855 24.99791117 1.012754889 0.899043993 0.577201569 0.04500379 107.011502 381812.5117 0.015429288 0.012652248 176.0219608 -2.245566855 -0.113710895 RKQEEEER ddPTM_BT-474_Pertuzumab_2h_R1 6 RKQEEEER 8 2 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;;;; 169.77 0.00016821 1059890000 856571.8 906360.2 748010.8 729750.2 830249.1 820733.9 910486.1 914943.3 995648.7 996018.8 FALSE TRUE 823096.0271 880511.6945 883192.991 767412.6953 856954.8163 837329.7018 921628.9012 896049.4011 882626.8337 928557.5595 0.886424346 0.948257526 0.95114512 0.826456785 0.922888202 0.901753147 0.992538257 0.964990691 0.950535403 1 19.82463182 2.245583803 24.98181925 0.973781352 0.907251037 0.489817451 0.035357212 147.8102767 525769.6201 0.012553828 0.010290135 176.0288301 -2.245583803 -0.066530315 EVGKDVSDEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVGKDVSDEK 10 1 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ;; 125.28 0.0003768 2475090000 2512370 3001160 2087320 3445200 2060750 2342180 4124300 4122800 3820100 2462740 FALSE TRUE 2414183.803 2915569.855 2464545.156 3623007.185 2127035.895 2389540.484 4174774.417 4037662.739 3386458.263 2295936.426 1.051502897 1.26988266 1.073437891 1.578008495 0.926435014 1.040769447 1.818331888 1.758612605 1.474979109 1 21.13065126 2.245642089 24.99934534 1.604390602 1.166721488 0.271306305 0.269623597 166.1007306 586377.6277 0.091444885 0.074997167 176.0524566 -2.245642089 -0.437669114 S(ph)CSPLAFSAFGDLTIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.5)CS(0.5)PLAFSAFGDLTIK 129.93 5.53E-05 138290000 90986 79094 62162 64925 85675 77180 60842 63819 82108 68293 TRUE FALSE 87430.16653 76838.31656 73396.05619 68275.78703 88430.81418 78740.63248 61586.6026 62501.11535 72787.44406 63667.45428 1.373231701 1.206869623 1.152803375 1.072381294 1.388948485 1.236748561 0.96731687 0.981680767 1.143244141 1 15.95826846 2.245653324 24.99738302 1.015327543 1.232452392 0.533543393 0.098480575 130.2554949 459070.5128 0.035528476 0.029137163 176.0570107 -2.245653324 0.217124849 SSYPDHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSYPDHK 7 0 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 0 ; 69.998 0.058219 145659000 105074 109530 94473 112040 114749 108944 100922 110461 108573 110558 FALSE TRUE 100967.5919 106406.3116 111546.3726 117822.3978 118440.0058 111146.9223 102157.1136 108179.9417 96248.24822 103069.8082 0.979603957 1.032371298 1.082241003 1.143132018 1.149124151 1.078365472 0.991144889 1.049579345 0.933816119 1 16.65326227 2.245937819 23.38985942 1.003081557 1.081881041 0.366750939 0.053206531 94.74506302 300395.5546 0.020317894 0.016651491 176.172379 -2.245937819 0.078799483 DDRNEEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DDRNEEKR 8 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 140.75 0.00036249 845015000 380518 341728 285264 316004 268116 316120 384039 404277 372370 386148 FALSE TRUE 365646.9359 331982.252 336817.5505 332313.0043 276740.1946 322512.163 388738.9842 395928.5387 330100.1187 359993.852 1.015703279 0.922188671 0.935620285 0.923107443 0.768735891 0.895882419 1.079848953 1.099820279 0.916960434 1 18.45761274 2.245938698 24.97593768 1.041383158 0.906062085 0.354081944 0.073821207 161.834006 547833.6581 0.027024867 0.022191517 176.1727357 -2.245938698 -0.135321073 EKDIQEESTFSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDIQEESTFSSR 13 1 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 115.56 0.00059716 492130000 250750 354030 228090 496360 248880 268240 469340 432850 421490 316490 FALSE TRUE 240950.4128 343933.411 269310.9368 521977.1991 256885.4512 273663.9966 475083.9233 423911.4962 373644.2222 295053.8504 0.816631989 1.165663185 0.912751813 1.769091298 0.87063921 0.927505254 1.610160053 1.436725858 1.266359418 1 18.17061876 2.246073787 24.99994839 1.381187913 1.095681549 0.138130017 0.293707363 295.3619179 982812.717 0.101508657 0.083384955 176.2275434 -2.246073787 -0.285506363 (ac)VNPTVFFDIAVDGEPLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VNPTVFFDIAVDGEPLGR 18 0 P62937;F8WE65;C9J5S7;E5RIZ5 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 113.24 4.10E-13 689990000 5114.1 5346.4 2103.2 3642.2 6730.5 6386.8 0 2401.6 4897.6 2497.7 FALSE TRUE 4914.235318 5193.925907 2483.295025 3830.174378 6946.992645 6515.945472 0 2352.006121 4341.64498 2328.528554 2.110446663 2.230561398 1.066465352 1.644890449 2.983426006 2.798310315 0 1.010082576 1.864544445 1 11.18520286 2.246132133 24.99999775 0.939220496 2.110347383 0.43244562 0.65600533 175.2002224 578485.3277 0.246046526 0.202161599 176.2512205 -2.246132133 1.171126887 S(ph)NSPPALGPEACPVSLPSPPEASTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSPPALGPEACPVSLPSPPEASTLK 26 0 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(0.5)NS(0.5)PPALGPEACPVSLPSPPEASTLK 130.15 4.76E-05 83929000 137260 134690 112770 127190 126330 129480 158130 159160 163350 171700 TRUE FALSE 131895.7275 130848.7731 133150.0476 133754.2911 130393.5192 132098.1743 160065.2422 155873.2904 144807.1928 160070.6061 0.823984682 0.817444104 0.831820725 0.835595581 0.814600022 0.825249417 0.999966491 0.973778348 0.904645746 1 17.28834888 2.24617478 24.99996332 0.969257208 0.824797432 0.88705999 0.025314259 50.77369255 166707.9423 0.008754127 0.007194304 176.2685289 -2.24617478 -0.144459776 ALS(ph)HDSIFIPESGQDATRPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALSHDSIFIPESGQDATRPVR 21 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 ALS(1)HDSIFIPESGQDATRPVR;ALS(1)HDSIFIPESGQDATRPVR;ALS(1)HDSIFIPESGQDATRPVR;ALS(0.963)HDS(0.037)IFIPESGQDATRPVR 172.34 3.46E-12 1400030000 587510 804730 567710 751900 696080 717640 582090 675880 673170 678520 TRUE FALSE 564549.4597 781779.8883 670307.8256 790705.6491 718470.0454 732151.1725 589213.7915 661922.8418 596754.5638 632563.236 0.892479087 1.235892072 1.059669275 1.250002536 1.135807465 1.157435543 0.93147018 1.046413709 0.943391158 1 19.27085018 2.246225201 24.99211717 0.988971032 1.130692253 0.32875472 0.098304774 190.3727145 620754.0863 0.032275663 0.026530194 176.2889948 -2.246225201 0.141721221 SPGSGSQSSGWHEVEPGMPS(ph)PTTLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGSGSQSSGWHEVEPGMPSPTTLKK 26 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.001)PGS(0.001)GS(0.001)QS(0.005)S(0.004)GWHEVEPGMPS(0.883)PT(0.077)T(0.027)LKK 94.631 0.0038128 639690000 143580 185940 130510 148840 153670 160090 161430 174550 184780 183740 TRUE FALSE 137968.7349 180637.1733 154096.0602 156521.6502 158612.9351 163327.1295 163405.6286 170945.4815 163804.5491 171295.1261 0.805444603 1.054537729 0.899593956 0.913754254 0.92596292 0.95348381 0.953942078 0.997958817 0.956270927 1 17.38612458 2.246343506 1.492860347 0.984436415 0.925930422 0.182690277 0.057867267 0.740919179 3.253402092 0.030945083 0.018588414 176.3370236 -2.246343506 -0.058505994 GKDSLYAQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKDSLYAQGR 10 1 Q969Q0 Q969Q0 RPL36AL 60S ribosomal protein L36a-like 0 ; 117.45 0.00087232 331860000 260810 338840 226790 242760 297180 234637 367620 313730 352090 323630 FALSE TRUE 250617.2569 329176.615 267775.9979 255288.8727 306739.0646 239381.5209 372119.0435 307251.3659 312122.2193 301710.2518 0.830655423 1.091035565 0.887527011 0.846139205 1.016667689 0.79341527 1.233365593 1.01836568 1.034509823 1 18.20280419 2.246393543 24.99999917 1.072951456 0.91989502 0.370038317 0.102281256 190.1719602 606964.2263 0.034075713 0.0280209 176.3573411 -2.246393543 -0.153056436 DRT(ph)PPHLLYSDRDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRTPPHLLYSDRDR 14 2 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 DRT(1)PPHLLYSDRDR;DRT(1)PPHLLYSDRDR;DRT(1)PPHLLYSDRDR;DRT(1)PPHLLYSDRDR 153.04 0.00030974 3926070000 1298837 1192571 987369 1094137 1162351 1233056 994806 1187182 1212344 1173104 TRUE FALSE 1248077.014 1158560.043 1165808.542 1150605.542 1199739.076 1257989.237 1006980.733 1162666.277 1074723.792 1093648.621 1.141204762 1.059353087 1.065980901 1.052079726 1.097005978 1.150268206 0.920753443 1.063107706 0.982695695 1 20.06071786 2.246517522 24.99999931 1.001272604 1.089640795 0.554427025 0.044643483 150.4621283 472740.9333 0.015390767 0.012660547 176.4076935 -2.246517522 0.088368191 TPSNELYKPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPSNELYKPLR 11 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 140.24 3.53E-05 1892210000 1497450 1490490 1233450 1409450 1427180 1378380 1590140 1577400 1595780 1724990 FALSE TRUE 1438927.998 1447982.685 1456361.853 1482191.883 1473086.541 1406251.788 1609600.609 1544826.139 1414633.744 1608154.891 0.894769532 0.900400013 0.905610437 0.921672341 0.91601036 0.874450462 1.000898992 0.960620241 0.87966262 1 20.61697494 2.246653397 24.9999997 0.958967549 0.903746938 0.420314152 0.033405364 182.7278917 564478.4869 0.011551091 0.009506249 176.4628938 -2.246653397 -0.055220612 QDAAGKDS(ph)PNR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDAAGKDSPNR 11 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 QDAAGKDS(1)PNR;QDAAGKDS(1)PNR 103.88 0.0016203 298890000 584890 538750 487360 519860 519920 576320 644780 679030 742000 779690 TRUE FALSE 562031.8522 523385.3775 575436.7933 546690.0369 536643.699 587973.5853 652671.0105 665007.7932 657771.2707 726880.9018 0.773210372 0.720042824 0.791652101 0.752104004 0.738282843 0.808899482 0.897906396 0.914878616 0.904923034 1 19.47135947 2.246693292 1.621269964 0.936050334 0.753336361 0.886115783 0.029811954 0.115920189 0.605093239 0.015451572 0.009518925 176.4791048 -2.246693292 -0.182713973 LKDSEAELQR ddPTM_BT-474_Pertuzumab_2h_R1 6 LKDSEAELQR 10 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;;;; 158.47 7.28E-06 8720080000 9041550 9030680 7757150 7871190 8348330 8527110 9498650 9954570 10083210 9699740 FALSE TRUE 8688196.23 8773133.848 9159039.562 8277423.059 8616861.616 8699534.007 9614897.32 9749004.651 8938606.273 9042767.97 0.960789468 0.970182347 1.012857965 0.915363867 0.952900887 0.962043263 1.063269272 1.078099613 0.988481215 1 23.10833302 2.246735852 24.98363619 1.044030999 0.962441734 0.495448436 0.033863323 128.9657219 394121.2981 0.01203543 0.009909243 176.4964004 -2.246735852 -0.081589265 GEFSAS(ph)PMLK ddPTM_BT-474_Pertuzumab_2h_R1 14 GEFSASPMLK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFS(0.003)AS(0.997)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFS(0.028)AS(0.972)PMLK;GEFS(0.002)AS(0.998)PMLK;GEFSAS(1)PMLK;GEFS(0.005)AS(0.995)PMLK;GEFS(0.001)AS(0.999)PMLK;GEFS(0.101)AS(0.899)PMLK 237.76 3.66E-12 52084200000 35489650 34045210 29483200 31597990 32430810 33783930 36855860 39828920 41190930 40635120 TRUE FALSE 34102675.24 33074273.94 34811470.09 33228766.05 33473976.46 34467064.21 37306913.04 39006438.88 36515108.31 37882867.13 0.90021368 0.87306681 0.918923849 0.877144962 0.88361782 0.909832513 0.984796449 1.0296591 0.963895055 1 25.17504219 2.246777949 3.358694746 1.002633585 0.89095221 0.869437005 0.019261939 0.071592532 1.699420555 0.007275293 0.005474683 176.5135092 -2.246777949 -0.111681375 KSSS(ph)LVDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSSLVDIR 9 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 KS(0.167)S(0.167)S(0.667)LVDIR 58.274 0.049072 0 95495 103730 101830 111240 93449 105720 135960 135120 150710 139610 TRUE FALSE 91762.94982 100771.722 120232.9462 116981.1097 96454.87195 107857.7308 137623.9192 132329.7248 133602.0326 130154.0903 0.705033162 0.774249366 0.923773858 0.898789346 0.741082141 0.828692595 1.057392194 1.016715836 1.026491233 1 16.98986113 2.246813563 22.03933694 1.0265917 0.816034174 0.731264611 0.063288885 23.01423278 61459.18012 0.023624864 0.019388664 176.5279848 -2.246813563 -0.210557526 ESQSVEEALKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESQSVEEALKK 11 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 122.45 0.00062628 1240040000 438320 391910 328160 336690 374670 406380 451020 510750 524020 535090 FALSE TRUE 421189.9698 380733.1105 387465.8119 354066.6112 386721.6008 414597.282 456539.7177 500202.834 464535.4465 498847.8777 0.844325472 0.763224878 0.77672138 0.709768703 0.77522952 0.831109644 0.915188253 1.002716171 0.931216644 1 18.92824041 2.24715745 1.985398234 0.978139931 0.770357568 0.862349418 0.036155587 0.109492523 0.872563029 0.017458347 0.011501596 176.6678201 -2.24715745 -0.207782364 S(ph)GSLDDSFSDFQELPASSK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGSLDDSFSDFQELPASSK 19 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.5)GS(0.5)LDDSFSDFQELPASSK;S(0.488)GS(0.488)LDDS(0.018)FS(0.007)DFQELPASSK;S(0.5)GS(0.5)LDDSFSDFQELPASSK 335.46 2.06E-75 190634000 237461 227136 210387 202914 218321 230370 279186 295427 323265 313237 TRUE FALSE 228180.7616 220658.3037 248408.6109 213386.4159 225343.4932 235028.2392 282602.7618 289326.3292 286569.3124 292021.179 0.78138429 0.755624316 0.850652723 0.730722397 0.771668322 0.804832855 0.967747486 0.990771732 0.981330578 1 18.15571348 2.247160761 3.660149969 0.988121921 0.77875807 0.92308513 0.028772372 0.054885263 1.58388023 0.010882451 0.008289268 176.6691668 -2.247160761 -0.20936385 ADGYEPPVQES(ph)V ddPTM_BT-474_Pertuzumab_2h_R1 2 ADGYEPPVQESV 12 0 P61247;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 1 ADGYEPPVQES(1)V;ADGYEPPVQES(1)V 97.716 0.0049981 143826000 180361 198737 157548 162224 182436 178754 162566 177553 175411 188059 TRUE FALSE 173312.2927 193069.2153 186020.4282 170596.4001 188304.2196 182368.5284 164555.5313 173886.4685 155499.0787 175321.5964 0.988539326 1.101228937 1.061024038 0.973048407 1.074050336 1.040194318 0.938592476 0.991814312 0.886936246 1 17.4196442 2.247236898 24.57094054 0.957204365 1.041982192 0.455425298 0.045635146 134.3099519 380361.4056 0.015390155 0.012684234 176.7001416 -2.247236898 0.084777827 EKDVER ddPTM_BT-474_Pertuzumab_2h_R1 4 EKDVER 6 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 81.297 0.056772 3540370000 3830760 3524760 2865000 3136960 3250140 3198120 3819820 3825690 3627810 4057550 FALSE TRUE 3681049.664 3424237.296 3382769.232 3298858.882 3354683.705 3262788.178 3866568.1 3746688.165 3215996.218 3782728.524 0.973120233 0.905229459 0.894266985 0.872084491 0.886842311 0.86254886 1.022163783 0.990472391 0.850178964 1 21.85099581 2.247239 24.99959931 0.969693452 0.897304559 0.288204328 0.051147463 227.9512209 656653.6648 0.018043287 0.014878638 176.7009969 -2.247239 -0.072388894 QYADKLEFMHILTR ddPTM_BT-474_Pertuzumab_2h_R1 2 QYADKLEFMHILTR 14 1 P42574 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 ; 213.94 2.01E-10 1460550000 3560100 3511300 2989300 2863700 3357800 3286300 2995800 2975200 3588600 3773400 FALSE TRUE 3420967.356 3411161.162 3529533.007 3011495.9 3465806.686 3352751.238 3032463.497 2913761.08 3181237.173 3517824.257 0.972466816 0.969679243 1.003328407 0.856067751 0.985213141 0.953075251 0.862028139 0.828285004 0.904319528 1 21.74625198 2.247287967 23.91964153 0.877544614 0.956080952 0.164441965 0.056502726 131.7295661 361040.6177 0.019226265 0.015836502 176.7209213 -2.247287967 0.078536338 TYEDMTLEELEDHEDEFNEEDER ddPTM_BT-474_Pertuzumab_2h_R1 2 TYEDMTLEELEDHEDEFNEEDER 23 0 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 ; 258.91 1.16E-43 105230000 56798 48094 43901.4 54711 49883 51781.1 41095.1 44061 51165 52688 FALSE TRUE 54578.27137 46722.40621 51835.35956 57534.64127 51487.532 52828.14932 41598.03413 43151.12495 45356.9637 49119.39483 1.111134849 0.95120077 1.055293123 1.171322274 1.048211856 1.07550489 0.846875949 0.878494637 0.923402331 1 15.58400517 2.247323817 24.99911263 0.897570949 1.066546903 0.586244027 0.063958296 122.3602866 349061.9067 0.022502485 0.018559659 176.7355098 -2.247323817 0.168975954 TLTDEVNSPDSDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 ; 161.04 7.47E-06 2603000000 608080 747620 603010 664830 642730 615240 627340 546110 637420 640040 FALSE TRUE 584315.5613 726298.6096 711987.3209 699141.956 663403.9942 627680.5743 635017.5746 534832.6377 565062.7539 596689.5207 0.979262315 1.217213617 1.193229135 1.171701415 1.111807684 1.051938324 1.064234501 0.896333217 0.946996276 1 19.18662091 2.247323882 1.38012512 0.940176041 1.145715547 0.553964505 0.069173702 0.283612863 1.05685582 0.040671488 0.023948237 176.7355362 -2.247323882 0.205539506 AEGS(ph)PNQGKK ddPTM_BT-474_Pertuzumab_2h_R1 3 AEGSPNQGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGKK;AEGS(1)PNQGKK;AEGS(1)PNQGKK 90.689 0.0065294 719706000 1064896 980860 730474 875582 930151 930149 1187422 1242154 1218986 1101979 TRUE FALSE 1023278.687 952886.8332 862486.9011 920770.892 960070.1517 948957.2501 1201954.026 1216503.086 1080611.82 1027340.981 0.996045817 0.927527326 0.839533239 0.896266098 0.934519473 0.923702323 1.169966007 1.184127869 1.051853124 1 19.97048367 2.247325334 24.95547213 1.125938835 0.91593764 0.658721851 0.063131183 95.33726014 271450.5987 0.022276565 0.018372121 176.7361272 -2.247325334 -0.210001195 TSLDWWITDK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSLDWWITDK 10 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PRF6 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 131.52 0.00057706 160180000 257340 362540 270820 437630 248420 323020 460930 453890 503490 385880 FALSE TRUE 247282.8683 352200.7142 319763.1984 460216.1367 256410.6549 329551.6857 466570.9992 444517.0129 446335.926 359744.0039 0.687385657 0.979031507 0.888863177 1.27928786 0.712758662 0.916072769 1.296952817 1.23564815 1.240704282 1 18.45661112 2.247426406 24.91272332 1.218393753 0.920460861 0.398183979 0.168917769 171.0759862 480721.0341 0.057470297 0.047414447 176.7772633 -2.247426406 -0.297932891 IESDVQEPT(ph)EPEDDLDIMLGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IESDVQEPT(1)EPEDDLDIMLGNK 180.37 1.97E-16 38918000 143070 140500 138500 111350 154640 172050 98333 153620 151490 141130 TRUE FALSE 137478.6662 136493.0776 163530.0309 117096.7868 159614.136 175528.9689 99536.42867 150447.6933 134293.4903 131571.1394 1.044899868 1.03740895 1.24290199 0.889988392 1.213139422 1.33409933 0.75652175 1.143470323 1.020691095 1 17.00548354 2.247536793 24.99996396 0.999927564 1.121397783 0.1886812 0.14668343 387.4225493 1079029.091 0.05062902 0.04178452 176.8222014 -2.247536793 0.121470219 YKPS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 YKPSPER 7 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 YKPS(1)PER 68.893 0.037073 185880000 325300 329100 275390 302610 266770 293000 367300 356140 380700 368130 TRUE FALSE 312586.9164 319714.3902 325159.099 318227.7384 275350.8993 298924.6608 371795.1273 348785.5845 337484.532 343196.2272 0.910811051 0.931578977 0.947443687 0.927247193 0.802313305 0.871002176 1.083331044 1.016286185 0.983357349 1 18.38867417 2.247566312 24.99956629 1.023664626 0.89908055 0.638957826 0.045030697 128.5963807 356980.2301 0.017130532 0.014139157 176.8342204 -2.247566312 -0.124584076 SGMS(ph)PPPCK ddPTM_BT-474_Pertuzumab_2h_R1 5 SGMSPPPCK 9 0 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 1 SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK 129.88 0.0003954 5694340000 3450960 3254100 2998540 3187200 3149850 3365050 3869880 4037130 4559950 4360310 TRUE FALSE 3316092.668 3161296.254 3540442.88 3351691.774 3251167.786 3433093.617 3917240.749 3953761.855 4042323.593 4064982.32 0.815770502 0.777690038 0.870961446 0.824528008 0.799798752 0.844553148 0.963655052 0.972639373 0.994425873 1 21.95481765 2.247592156 3.11217734 0.983305707 0.818617881 0.921268964 0.023155762 0.065432437 1.317187378 0.009493726 0.007058232 176.8447435 -2.247592156 -0.164687827 SRSS(ph)KEENR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSSKEENR 9 2 Q14696 Q14696 MESDC2 LDLR chaperone MESD 1 S(0.003)RS(0.013)S(0.984)KEENR;S(0.01)RS(0.01)S(0.98)KEENR 89.403 0.0095532 514790000 447430 390590 291900 335800 374720 354500 419560 400300 434000 463880 TRUE FALSE 429943.9409 379450.7556 344652.8233 353130.6782 386773.2091 361668.2329 424694.7008 392033.6651 384734.1395 432460.9944 0.994179698 0.877421919 0.796957015 0.81656076 0.894353974 0.836302551 0.982041632 0.906517975 0.889638937 1 18.72221049 2.247744404 24.99987192 0.935136531 0.865119155 0.274014162 0.05898599 283.6300489 772090.9312 0.02102125 0.017358183 176.9067498 -2.247744404 -0.070017376 AYVFER ddPTM_BT-474_Pertuzumab_2h_R1 3 AYVFER 6 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PSE4;A0A1W2PS70;A0A1W2PNX7 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ;; 121.68 0.045473 1727430000 684100 1411510 791930 1771310 848020 881250 1659850 1427730 1386850 1131990 FALSE TRUE 657364.6157 1371255.117 935049.3674 1862727.521 875297.3335 899069.4788 1680163.741 1398246.877 1229420.602 1055319.309 0.622905892 1.299374611 0.886034548 1.765084279 0.829414686 0.851940708 1.5920904 1.324951476 1.164974991 1 20.00924815 2.247837452 24.99307789 1.311033918 1.070189699 0.095816406 0.327451888 439.3297599 1183615.756 0.111615169 0.092198013 176.9446565 -2.247837452 -0.24084422 LQELESCSGLGS(ph)TSDDTDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQELESCSGLGSTSDDTDVR 20 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7;B4DGD8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 LQELESCS(0.014)GLGS(0.935)T(0.042)S(0.009)DDTDVR 127.01 2.34E-05 77049000 46766 60692 56032 66611 65953 61163 57531 65595 55523 64417 TRUE FALSE 44938.33302 58961.12358 66158.22883 70048.80169 68074.43814 62399.75777 58235.08159 64240.44033 49220.26181 60053.97921 0.748299007 0.981802111 1.101646047 1.166430645 1.133554163 1.039061168 0.969712288 1.069711636 0.81960034 1 15.87397222 2.247856371 20.88355693 0.981157724 1.040718843 0.048737722 0.123103975 96.75584344 217368.596 0.045440433 0.037360071 176.9523648 -2.247856371 0.059561119 WGLLSMPVDEEVESLHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 WGLLSMPVDEEVESLHLR 18 0 O75165;A0A3B3IRM0 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 112.3 0.00027985 26154000 7167.4 8930 5944.5 10330 9832.9 8954.6 5512.1 6163.5 8296.2 8549.2 FALSE TRUE 6887.290084 8675.325143 7018.803385 10863.13254 10149.18416 9135.668147 5579.558729 6036.221571 7354.450157 7970.155069 0.864135017 1.088476331 0.880635737 1.362976309 1.273398581 1.14623468 0.700056483 0.75735309 0.922748691 1 12.96039208 2.247902556 24.99980365 0.813134692 1.111502626 0.365570772 0.163862234 191.0318578 511217.1915 0.059697319 0.049319914 176.9711838 -2.247902556 0.298367934 VEYLDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEYLDDR 7 0 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1;A0A087WT22;J3KP33;A0A087WXZ1;E7ESS1;P04637-5;P04637-9;P04637-8;P04637-6;P04637-2;P04637-3;E7EQX7;E9PFT5 P04637-7 TP53 Cellular tumor antigen p53 0 121.52 0.010307 373210000 319200 353560 313110 334700 316250 352020 300810 316110 364970 433860 FALSE TRUE 306725.3111 343476.815 369695.9421 351973.9071 326422.4685 359138.0856 304491.4028 309582.218 323540.1357 404474.2758 0.758330825 0.849193226 0.914015957 0.87020097 0.807028995 0.887913292 0.752807832 0.765394085 0.799902874 1 18.62568843 2.248024327 24.99861995 0.803157388 0.850022217 0 0.076754994 525.6537588 1388528.517 0.025645515 0.021199618 177.0208112 -2.248024327 0.046864829 GSCDS(ph)PSLLSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSCDSPSLLSEK 12 0 P16471-2;P16471 P16471-2 PRLR Prolactin receptor 1 GSCDS(0.986)PS(0.014)LLSEK 158.11 7.80E-05 78669000 156000 215840 148370 244260 170530 211680 276560 311870 331190 305300 TRUE FALSE 149903.3475 209684.4545 175183.7595 256866.2879 176015.2523 215960.3146 279944.624 305429.7755 293594.6997 284621.7591 0.526675641 0.736712665 0.615496721 0.902482961 0.618418117 0.75876249 0.983567191 1.07310761 1.031525842 1 18.11868643 2.248059229 3.080414409 1.040988659 0.69110964 0.751062378 0.093838348 0.118087042 2.326018515 0.036244717 0.026905731 177.0350381 -2.248059229 -0.349879019 VYENYPTYDLTER ddPTM_BT-474_Pertuzumab_2h_R1 3 VYENYPTYDLTER 13 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 ;; 261.22 1.10E-23 577790000 283816 291168 249673 293619 266043 245636 258564 267708 227298 266814 FALSE TRUE 272724.1569 282864.1737 294794.465 308772.7118 274600.5147 250602.9282 261728.3836 262179.7362 201496.084 248742.4501 1.096411798 1.137176922 1.185139348 1.24133501 1.103955174 1.007479536 1.052206342 1.05402088 0.810059095 1 17.92429321 2.248080969 0.887487981 0.945494645 1.162571441 0.589362974 0.071905337 0.450663536 0.677248169 0.057015887 0.033274774 177.0439005 -2.248080969 0.217076796 SSDKPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSDKPIR 7 1 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 87.323 0.017717 195610000 428370 431310 340280 407340 414530 410460 472130 496120 484070 476460 FALSE TRUE 411628.8268 419009.4611 401776.1655 428362.8662 427863.7339 418759.7824 477908.0682 485874.9486 429120.403 444188.9398 0.926697605 0.943313585 0.904516366 0.964370852 0.963247158 0.942751485 1.075911679 1.093847471 0.96607629 1 18.76081395 2.248184713 24.77869317 1.048577202 0.941369937 0.578448668 0.038143838 110.0812409 283420.7047 0.013525096 0.011179372 177.0861978 -2.248184713 -0.107207265 GMGGAFVLVLYDELKK ddPTM_BT-474_Pertuzumab_2h_R1 3 GMGGAFVLVLYDELKK 16 1 P12236 P12236 SLC25A6 "ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed" 0 ;; 191.09 1.21E-09 446913000 503835 785530 442718 1050150 496972 602130 1056540 1059150 960150 590494 FALSE TRUE 484144.5712 763127.4535 522726.9908 1104348.367 512957.5557 614305.4812 1069470.253 1037278.182 851157.7973 550499.3154 0.879464438 1.386245963 0.949550665 2.006084906 0.931804166 1.115905986 1.94272767 1.884249723 1.54615596 1 19.07038124 2.248253684 24.99821359 1.700099172 1.230947875 0.164171303 0.392048368 273.9174637 706427.3976 0.13179614 0.108975835 177.1143233 -2.248253684 -0.469151297 DLAGEEAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLAGEEAFR 9 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;H7BZT5;H7C1R1;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 ; 137.14 0.00040287 271590000 400120 410520 330380 377290 364060 355270 425180 405630 406860 462310 FALSE TRUE 384482.868 398812.3715 390087.0153 396761.9821 375770.3205 362453.8028 430383.48 397253.5988 360674.9585 430997.3319 0.892077142 0.925324456 0.905079884 0.920567142 0.871862289 0.840965305 0.998575741 0.921707791 0.836838031 1 18.71731941 2.248269447 24.99999001 0.93392301 0.895021035 0.178984822 0.048228578 424.5988099 1093330.736 0.016861022 0.013936271 177.120752 -2.248269447 -0.038901976 SDRPELTGAK ddPTM_BT-474_Pertuzumab_2h_R1 6 SDRPELTGAK 10 1 H0YL12;P13804-2;P13804;H0YK49;H0YNX6;H0YKF0;H0YLU7 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 ;;;;; 151.98 1.72E-05 2164560000 1191899 1556730 1022362 1885180 1053901 1085307 1870940 1725170 1469920 1233540 FALSE TRUE 1145318.269 1512333.585 1207125.556 1982474.366 1087800.683 1107252.651 1893837.123 1689544.637 1303060.844 1149991.237 0.995936519 1.315082703 1.049682395 1.723903889 0.945920845 0.962835729 1.646827439 1.469180444 1.13310502 1 20.13319144 2.248329877 24.99994768 1.374550284 1.182485332 0.043948864 0.273685143 483.4667316 1237211.199 0.09457295 0.078210209 177.1453991 -2.248329877 -0.192064952 TGS(ph)TSSKEDDYESDAATIVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGSTSSKEDDYESDAATIVQK 21 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.005)GS(0.953)T(0.02)S(0.02)S(0.001)KEDDYESDAATIVQK;T(0.127)GS(0.836)T(0.033)S(0.002)S(0.002)KEDDYESDAATIVQK 276.46 5.03E-45 293660000 360500 292390 299640 236670 347970 290220 228720 218240 265690 200273 TRUE FALSE 346411.2614 284051.3235 353791.6135 248884.5671 359162.7711 296088.4472 231519.1438 213733.2677 235529.9851 186708.3313 1.855360492 1.521363945 1.894889269 1.333012648 1.923656907 1.585834146 1.240004354 1.144744138 1.261486209 1 17.51042678 2.248437783 3.330128445 1.160093822 1.691117312 0.680150835 0.178159022 0.134032556 3.121325181 0.064466635 0.048510074 177.1894186 -2.248437783 0.53102349 YDERPGPS(ph)PLPHR ddPTM_BT-474_Pertuzumab_2h_R1 6 YDERPGPSPLPHR 13 1 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR 144.97 2.44E-05 17209640000 4666820 4796470 4040120 4326120 4362160 4513640 4250590 4494990 4757770 4971210 TRUE FALSE 4484435.515 4659679.372 4770259.556 4549391.572 4502472.838 4604908.893 4302609.992 4402166.886 4217687.896 4634505.519 0.967618983 1.005431831 1.029292022 0.98163473 0.971510945 0.993613855 0.928385989 0.949867654 0.910062115 1 22.14398399 2.248501822 24.77389336 0.943129244 0.992508038 0.390512117 0.027000684 163.5233512 407506.9489 0.009146972 0.007565377 177.215548 -2.248501822 0.049378795 YSASKPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSASKPLK 8 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 66.299 0.056584 294920000 675300 855940 564980 732710 832370 866020 1066600 1144700 1297600 1362000 FALSE TRUE 648908.5294 831529.4293 667084.4539 770525.2509 859143.937 883531.5178 1079653.37 1121061.545 1150301.888 1269750.527 0.511051987 0.654876223 0.52536655 0.606831999 0.676624202 0.695830794 0.85028779 0.882899059 0.905927474 1 20.27611364 2.248556008 0.683427341 0.984441271 0.556208427 0.932302479 0.041656971 0.158947016 0.14474605 0.033507498 0.022357296 177.23766 -2.248556008 -0.428232845 EKQS(ph)SEEEEKETR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQSSEEEEKETR 13 2 Q92504;A2AAT0 Q92504 SLC39A7 Zinc transporter SLC39A7 1 EKQS(0.5)S(0.5)EEEEKETR 82.259 0.0066969 372380000 250290 326610 193320 292380 239050 261040 308770 332950 327750 243230 TRUE FALSE 240508.3901 317295.4026 228257.2244 307469.7668 246739.2603 266318.4077 312548.8196 326074.4661 290545.194 226755.8155 1.06064927 1.399282316 1.006621259 1.355950965 1.088127596 1.174472227 1.378349742 1.437998252 1.281313088 1 17.79078003 2.248603813 24.86980789 1.326939554 1.186604207 0.036790261 0.159988107 346.2965106 857528.805 0.051952329 0.042985667 177.2571706 -2.248603813 -0.140335347 DIEEIIDELK ddPTM_BT-474_Pertuzumab_2h_R1 4 DIEEIIDELK 10 0 E7EPT4;P19404 E7EPT4 NDUFV2 "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial" 0 ;;; 205.14 4.05E-07 72160200 180701.7 218381 161813.3 270044 145263 170878 289903 279858 244353.1 191407 FALSE TRUE 173639.6778 212152.9877 191056.5628 283981.0032 149935.5163 174333.2702 293450.9196 274078.8345 216615.1605 178442.8334 0.973082945 1.188912906 1.070687789 1.591439666 0.840243979 0.976969862 1.644509415 1.53594756 1.213919082 1 17.44510244 2.248740874 24.99968334 1.417518006 1.118877086 0.160195788 0.251176697 292.0608351 717214.6465 0.087004785 0.072017285 177.3131209 -2.248740874 -0.29864092 LLALSNES(ph)DSEENVCEVELDTDLFPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLALSNESDSEENVCEVELDTDLFPRPR 28 1 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 LLALS(0.096)NES(0.545)DS(0.359)EENVCEVELDT(0.001)DLFPRPR 46.106 0.0721 32545000 12224 14305 13327 10580 14119 12326 10239 10325 10707 9810.3 TRUE FALSE 11746.27257 13897.03541 15735.48536 11126.03507 14573.15046 12575.24017 10364.30794 10111.78514 9491.586247 9145.839643 1.2843296 1.519492572 1.720507463 1.216513246 1.593418541 1.374968363 1.133226511 1.105615836 1.037803703 1 13.15889991 2.248899713 2.494498013 1.065706788 1.472835031 0.658830347 0.136766025 0.173684038 2.214531374 0.057678992 0.040822568 177.3779832 -2.248899713 0.407128243 IRDTS(ph)QEPCGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IRDTSQEPCGR 11 1 Q12955;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IRDT(0.011)S(0.989)QEPCGR 139.64 2.36E-05 448960000 207110 202630 201870 196800 213430 218180 177980 199400 226200 221830 TRUE FALSE 199015.9122 196851.1908 238352.3996 206956.8716 220295.1698 222591.7491 180158.1725 195282.3203 200522.7243 206805.2565 0.962334882 0.951867443 1.15254517 1.00073313 1.065230031 1.076335064 0.871148904 0.944281222 0.969621023 1 17.65791333 2.248958958 24.99997028 0.939387918 1.036250589 0.322788922 0.062517946 229.3811418 551483.9306 0.021948907 0.01817917 177.4021822 -2.248958958 0.09686267 MTEEEVEMLVAGHEDS(ph)NGCINYEELVR ddPTM_BT-474_Pertuzumab_2h_R1 4 MTEEEVEMLVAGHEDSNGCINYEELVR 27 0 P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 P60660-2 MYL6 Myosin light polypeptide 6 1 MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR 274.76 4.82E-61 266803000 220073 225176 165279 188662 200060 207549 143776 161366 203404 196597 TRUE FALSE 211472.3039 218754.201 195148.5919 198398.8684 206495.1116 211745.783 145535.5737 158033.7357 180314.4307 183281.3101 1.153812703 1.193543416 1.064749002 1.082482815 1.126656676 1.155304831 0.794055726 0.862246869 0.983812428 1 17.48370015 2.248966989 24.99989384 0.890927862 1.127140043 0.728340172 0.06521685 99.10950645 238097.0369 0.02310599 0.019137002 177.4054628 -2.248966989 0.236212182 EFDEDSEDRLVNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFDEDSEDRLVNEK 14 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 182.02 1.43E-06 541060000 531540 506760 397930 432270 475800 486110 574340 630010 640600 607130 FALSE TRUE 510766.8292 492307.701 469844.8029 454579.5065 491104.5391 495939.4773 581368.9447 617000.0733 567881.7736 566008.5443 0.90240127 0.869788462 0.830101962 0.80313188 0.867662766 0.876204931 1.027138107 1.090089681 1.003309542 1 19.11046431 2.24910858 3.955752705 1.045681175 0.853100882 0.856789874 0.034370605 0.071349977 2.483535117 0.013535536 0.010418403 177.463311 -2.24910858 -0.192580293 SGGGDLTLGLEPS(ph)EEEAPR ddPTM_BT-474_Pertuzumab_2h_R1 5 SGGGDLTLGLEPSEEEAPR 19 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 SGGGDLTLGLEPS(1)EEEAPR;SGGGDLTLGLEPS(1)EEEAPR;SGGGDLTLGLEPS(1)EEEAPR;SGGGDLTLGLEPS(1)EEEAPR;SGGGDLTLGLEPS(1)EEEAPR 326.85 3.88E-75 1177489000 436995 955585 481126 1303410 524349 697085 1588860 1486550 1365860 1018850 TRUE FALSE 419916.7523 928332.6514 568076.1708 1370679.146 541215.1618 711180.5363 1608304.944 1455852.223 1210813.299 949842.382 0.442090983 0.977354421 0.598074145 1.443059577 0.569794707 0.748735316 1.693233503 1.532730325 1.274751813 1 19.85732861 2.249174428 24.99966464 1.441470683 0.814800378 0.448064117 0.310775337 170.4498024 401475.6171 0.104343688 0.086454842 177.4902203 -2.249174428 -0.626670306 LPQT(ph)SDDEKKDF ddPTM_BT-474_Pertuzumab_2h_R1 1 LPQTSDDEKKDF 12 2 Q9GZT3-2;Q9GZT3 Q9GZT3-2 SLIRP "SRA stem-loop-interacting RNA-binding protein, mitochondrial" 1 LPQT(0.5)S(0.5)DDEKKDF 94.487 0.010583 563060000 357540 392640 252800 462190 254450 333140 535840 543090 518370 344370 TRUE FALSE 343566.9415 381442.2916 298486.5835 486043.6813 262634.6153 339876.3191 542397.7702 531875.0017 459526.8108 321045.5132 1.070150267 1.188125284 0.929732923 1.513940116 0.818060383 1.05865463 1.689473137 1.656696574 1.431344753 1 18.29241831 2.249220761 24.99880717 1.522787245 1.099356733 0.300976323 0.248506151 200.07372 469187.1684 0.082665008 0.068500436 177.5091567 -2.249220761 -0.423430512 EKEELDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKEELDR 7 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 123.92 0.0038278 13943940000 14743570 14672220 11938590 13144930 13429510 13953770 14900600 15756920 16823530 16433100 FALSE TRUE 14167374.98 14253782.65 14096158.79 13823341.41 13861482.39 14235924.79 15082958 15431534.1 14913793.4 15320071.5 0.924759064 0.930399225 0.920110509 0.90230267 0.904792278 0.929233574 0.98452269 1.007275592 0.973480666 1 23.86891969 2.249234993 3.553735988 0.994838732 0.916686352 0.91055602 0.011244018 0.062654582 1.687190508 0.004566163 0.003470545 177.5149738 -2.249234993 -0.07815238 RQPEAVHLLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQPEAVHLLDK 11 1 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 94.725 0.0053812 313680000 308510 342450 292730 285050 316500 314910 374560 355660 412520 418540 FALSE TRUE 296453.0881 332683.6613 345632.8227 299761.4647 326680.5099 321277.696 379143.9773 348315.4967 365692.459 390191.913 0.759762256 0.85261547 0.885802117 0.768241101 0.837230345 0.82338379 0.971685893 0.892677385 0.937211784 1 18.57382435 2.2492728 24.99488588 0.937304398 0.823863354 0.672640585 0.043759795 135.1628685 315377.3252 0.014942667 0.01238431 177.5304278 -2.2492728 -0.113441044 AAPPPPPPPPPLES(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAPPPPPPPPPLESSPR 17 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 AAPPPPPPPPPLES(0.564)S(0.436)PR 109.87 0.00061446 561000000 170710 125500 159960 127920 135190 161000 104080 125410 149450 173060 TRUE FALSE 164038.4645 121920.8629 188868.3303 134521.9665 139538.5091 164255.5303 105353.7622 122820.2397 132485.0625 161338.4921 1.016734831 0.755683664 1.170634037 0.833787181 0.864880459 1.018080238 0.652998307 0.761258136 0.821162147 1 17.29973115 2.249312532 24.99940484 0.781135718 0.93656302 0.17982695 0.135129012 295.0652804 686059.7626 0.044516268 0.036895905 177.5466703 -2.249312532 0.155427302 EVKPEETTCSEHCLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVKPEETTCSEHCLQK 16 1 Q9Y5J7 Q9Y5J7 TIMM9 Mitochondrial import inner membrane translocase subunit Tim9 0 139.67 1.07E-06 505180000 395800 406190 340780 362960 294310 366000 389290 393530 449870 415370 FALSE TRUE 380331.6984 394605.8589 402366.5266 381692.4091 303776.7484 373400.7708 394054.2475 385403.468 398802.6436 387236.6199 0.982168728 1.019030326 1.039071477 0.985682628 0.784473195 0.964270298 1.017605844 0.995266068 1.029868104 1 18.56285587 2.249327789 19.85593093 1.008941981 0.961470189 0.115884033 0.065165584 44.88651356 82775.4591 0.025055585 0.02065239 177.5529078 -2.249327789 -0.047471792 VPGPAEGPAEPAAEAS(ph)DEAERR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPGPAEGPAEPAAEASDEAERR 22 1 Q24JP5-4;Q24JP5;Q24JP5-2;H0YFQ2 Q24JP5-4 TMEM132A Transmembrane protein 132A 1 VPGPAEGPAEPAAEAS(1)DEAERR;VPGPAEGPAEPAAEAS(1)DEAERR 193.42 4.42E-18 1022830000 95137 137726 87643 151865 105202 98075 157031 156741 118044 99054 TRUE FALSE 91418.94086 133798.1893 103482.0397 159702.7708 108585.9179 100058.1437 158952.7924 153504.2436 104644.14 92344.98435 0.989971913 1.448895035 1.12060271 1.729414672 1.175872395 1.083525482 1.721293186 1.662291078 1.133187046 1 16.49474598 2.249381913 24.99990055 1.469049198 1.278165114 0.000604688 0.286842236 531.3793065 1227619.073 0.098091604 0.081311328 177.5750368 -2.249381913 -0.190884084 GGNFPSFPHDEVTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGNFPSFPHDEVTDR 15 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 81.656 0.013353 121320000 623990 552040 469100 538310 544350 574470 586850 673130 716140 582740 FALSE TRUE 599603.7809 536296.3597 553876.8051 566092.2436 561859.5121 586086.177 594032.0458 659229.6303 634846.7895 543270.5007 1.103692875 0.987162673 1.019523063 1.042008066 1.034216861 1.078810972 1.093436962 1.213446394 1.16856481 1 19.05131119 2.249424877 2.231286755 1.14953743 1.035347706 0.261590786 0.059696187 0.28663831 2.90880315 0.02585686 0.017724106 177.5926048 -2.249424877 -0.114189724 AGKEPAKPSPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 AGKEPAKPSPSR 12 2 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.397)PS(0.603)R 102.28 0.0012374 271280000 268460 250350 216460 232550 226990 259240 275800 305830 335790 302850 TRUE FALSE 257968.2864 243210.2631 255579.1371 244551.9334 234291.3395 264482.0104 279175.3229 299514.5036 297672.5269 282337.6997 0.913687002 0.861416181 0.905224975 0.866168186 0.829826621 0.936757686 0.988799311 1.060837798 1.054313778 1 18.10706226 2.24943437 2.208128797 1.042147622 0.876130388 0.861703588 0.028637033 0.097457437 0.968003819 0.012745598 0.008708634 177.5964869 -2.24943437 -0.166017234 YEDKDGKQPVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 YEDKDGKQPVGR 12 2 A0A499FJT0;Q8NHP1;O43488;H3BLU7 A0A499FJT0;O43488 AKR7L;AKR7A2 Aflatoxin B1 aldehyde reductase member 4;Aflatoxin B1 aldehyde reductase member 2 0 50.145 0.092748 133240000 126990 134870 112050 107780 143930 134030 107830 127640 138940 119990 FALSE TRUE 122027.0904 131023.6397 132299.9275 113342.5387 148559.6392 136740.1784 109149.6558 125004.1894 123168.1137 111862.9704 1.090862239 1.17128697 1.182696356 1.013226614 1.32805019 1.222390018 0.9757443 1.117476042 1.101062427 1 16.77137302 2.249500541 24.99854354 1.061743601 1.169127146 0.310488865 0.086355595 293.9048936 671594.9994 0.030305648 0.025124831 177.6235482 -2.249500541 0.107383546 LKGEIDASVPELEGDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKGEIDASVPELEGDLR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 179.78 8.18E-10 1477150000 660000 674000 572270 718490 585880 653880 680030 728330 727580 701930 FALSE TRUE 634206.4703 654778.1799 675691.9191 755571.355 604725.3623 667101.9016 688352.4106 713289.731 644988.1687 654387.6559 0.969160198 1.000596778 1.032556029 1.154623484 0.924108755 1.019429226 1.05190311 1.090010981 0.985636209 1 19.31978601 2.249530192 22.33886424 1.045259271 1.018786728 0 0.061684183 234.4811544 477505.3283 0.021850135 0.018071476 177.6356758 -2.249530192 -0.026472543 YGGEGAESMMGFFHELLK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGGEGAESMMGFFHELLK 18 0 Q96HY7 Q96HY7 DHTKD1 "Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial" 0 ; 193.32 1.30E-14 204994000 190929 233810 167425 302760 163831 181666 287300 267460 244150 207980 FALSE TRUE 183467.2836 227141.9677 197682.4218 318385.4799 169100.7729 185339.411 290816.0633 261936.8575 216435.1156 193893.3294 0.94622793 1.171479021 1.01954215 1.642065155 0.87213301 0.95588338 1.499876578 1.350932796 1.116258699 1 17.56490364 2.249597097 24.99864419 1.287748213 1.114873278 0.062854249 0.237500309 497.324152 1126485.122 0.082512859 0.068425492 177.6630431 -2.249597097 -0.172874935 SSGS(ph)ETEQVVDFSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 SS(0.01)GS(0.99)ETEQVVDFSDR;SS(0.003)GS(0.997)ETEQVVDFSDR;SS(0.02)GS(0.98)ETEQVVDFSDR 469.53 6.02E-199 3305210000 1709560 1652060 1378940 1585060 1582820 1585030 1375510 1404090 1509550 1621100 TRUE FALSE 1642748.505 1604944.866 1628145.132 1666865.137 1633732.843 1617080.393 1392343.903 1375095.051 1338192.213 1511301.453 1.086976064 1.061962101 1.077313285 1.10293359 1.081010568 1.069991952 0.921288006 0.909874763 0.885456842 1 20.52736003 2.249691007 5.693407859 0.919589904 1.080957459 0.862764454 0.029404591 0.049632584 5.232927762 0.010046915 0.007951826 177.7014647 -2.249691007 0.161367555 IQQALT(ph)SPLPMTPILEGSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 IQQALTSPLPMTPILEGSHR 20 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 IQQALT(0.5)S(0.5)PLPMTPILEGSHR 85.376 0.0097735 38943000 23556 25948 25481 27657 30637 28358 14814 22581 18648 20659 TRUE FALSE 22635.40548 25207.98845 30085.98352 29084.38108 31622.46693 28931.41819 14995.29816 22114.69446 16531.15722 19259.74753 1.175270104 1.308843141 1.562117233 1.510112271 1.641894157 1.502170168 0.778582281 1.148233871 0.858326787 1 14.23330117 2.249759339 24.99977069 0.972521758 1.460190442 0.721318943 0.15297987 119.9675863 267812.7716 0.05567481 0.046181951 177.7294263 -2.249759339 0.487668683 QEAGDS(ph)PPPAPGTPK ddPTM_BT-474_Pertuzumab_2h_R1 4 QEAGDSPPPAPGTPK 15 0 J3KR72;P49848-4;P49848-2;P49848;P49848-3 J3KR72 TAF6 Transcription initiation factor TFIID subunit 6 1 QEAGDS(1)PPPAPGTPK;QEAGDS(1)PPPAPGTPK;QEAGDS(1)PPPAPGTPK;QEAGDS(1)PPPAPGTPK 265.08 3.70E-25 1262160000 2563220 2504030 2140000 2326600 2506910 2589480 2659910 3031930 3336390 3010480 TRUE FALSE 2463046.529 2432617.516 2526745.604 2446676.105 2587547.037 2641841.06 2692462.774 2969319.586 2957656.994 2806577.508 0.8775979 0.866755865 0.900294254 0.871765023 0.921958161 0.941303439 0.959340252 1.057985955 1.053830506 1 21.42038047 2.249839655 1.185901172 1.045222713 0.881887268 0.883995177 0.023203538 0.138430245 0.376179022 0.014993576 0.008601216 177.7622977 -2.249839655 -0.163335445 QEAEQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEAEQLR 7 0 P62879;C9JZN1;C9JIS1;C9JXA5;Q9HAV0;C9JD14;Q9BRK4 P62879;Q9BRK4 GNB2;GNB4;LZTS2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2;Guanine nucleotide-binding protein subunit beta-4;Leucine zipper putative tumor suppressor 2 0 87.435 0.045003 116650000 166300 194580 161340 221850 170530 187000 161400 177180 185040 190440 FALSE TRUE 159800.8121 189030.7689 190497.727 233299.7051 176015.2523 190781.2681 163375.2615 173521.1711 164035.035 177541.3292 0.900076691 1.06471417 1.072976799 1.31405857 0.991404385 1.074573842 0.920209746 0.977356494 0.923925915 1 17.43779538 2.24986318 24.13757447 0.95485519 1.077116735 0.237145245 0.099854865 200.675216 428558.25 0.03540554 0.029354011 177.7719268 -2.24986318 0.122261545 EGSGSSGTGEQKEDQKEEKQ ddPTM_BT-474_Pertuzumab_2h_R1 4 EGSGSSGTGEQKEDQKEEKQ 20 3 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 136.04 7.46E-06 1741500000 879084 1007310 520067 694808 527197 678347 1044335 1073111 1010303 599643 FALSE TRUE 844728.4254 978582.5051 614054.6757 730667.1241 544154.7703 692063.6411 1057115.884 1050950.883 895617.639 559028.6455 1.511064652 1.750505118 1.098431504 1.307029845 0.973393358 1.237975275 1.890986969 1.87995891 1.602096147 1 19.09256269 2.250006172 24.99957143 1.697465499 1.307479912 0.13057015 0.310511236 296.1489787 646852.9959 0.108957394 0.090427796 177.8304682 -2.250006172 -0.389985587 LS(ph)PHKVQGR ddPTM_BT-474_Pertuzumab_2h_R1 7 LSPHKVQGR 9 1 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR 109.24 0.0014989 43325480000 8127990 7430180 6471040 6739830 6967270 7019900 7935120 7608540 8666870 8616760 TRUE FALSE 7810339.165 7218278.541 7640500.876 7087673.434 7191378.567 7161847.188 8032232.372 7451420.99 7683043.252 8033139.17 0.972264889 0.898562615 0.951122682 0.882304325 0.89521399 0.891537796 0.999887118 0.927585198 0.956418542 1 22.93753244 2.250132626 24.99996744 0.962184228 0.913646478 0.394831717 0.033107206 248.011683 535799.5807 0.011306243 0.009383051 177.882255 -2.250132626 -0.048537751 RVEISAPSNFEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVEISAPSNFEHR 13 1 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 113.25 0.00054301 503450000 452850 509450 384320 458880 424690 440590 458330 450450 471070 479720 FALSE TRUE 435152.1213 494920.9848 453775.1732 482562.8518 438350.5395 449499.0317 463939.1796 441148.0501 417596.1085 447228.1371 0.972998086 1.106640982 1.014639142 1.079008255 0.980149734 1.00507771 1.037365812 0.986404954 0.933742924 1 18.77065143 2.250135056 0.757389069 0.972706354 1.041827636 0.231033336 0.042602377 0.909654679 1.004062674 0.033276246 0.020790929 177.8832501 -2.250135056 0.069121281 DGDILGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGDILGK 7 0 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ; 94.662 0.032653 275540000 941190 1193190 814680 1284960 773900 986150 1283080 1350560 1251150 974750 FALSE TRUE 904407.2543 1159161.389 961910.7985 1351276.94 798793.1963 1006090.629 1298782.717 1322670.464 1109124.697 908729.3143 0.995243842 1.275584898 1.05852291 1.486996093 0.879022151 1.107140061 1.429229471 1.455516448 1.220522635 1 19.79349109 2.25016524 24.85556142 1.333515114 1.141257063 0.084364963 0.195887879 340.5316312 729372.9744 0.065848426 0.054653889 177.8956139 -2.25016524 -0.192258051 SRDPQLCR ddPTM_BT-474_Pertuzumab_2h_R1 6 SRDPQLCR 8 1 Q8TAT6;Q8TAT6-2;I3L4S2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;;;; 160.63 0.00032124 1576277000 607814 736992 635844 739112 657017 549022 683112 370761 625203 601881 FALSE TRUE 584059.9569 715973.7098 750755.1551 777257.6589 678150.5485 560123.601 691472.129 363104.6558 554232.5765 561115.0638 1.040891601 1.275983762 1.337970059 1.385201911 1.208576622 0.998233049 1.232317886 0.64711265 0.987734268 1 19.09793712 2.250206294 1.399201039 0.866722369 1.259682971 0.445411817 0.15594413 0.333227596 1.278768697 0.091587933 0.054267546 177.9124312 -2.250206294 0.392960602 DDTIYEDEDVKEAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDTIYEDEDVKEAIR 15 1 B7Z2R2;P14927;P14927-2;E5RHG9 B7Z2R2 UQCRB Cytochrome b-c1 complex subunit 7 0 ; 195.15 2.03E-08 603730000 230187 360371 182646 436843 174873 246934 440804 427189 386898 245687 FALSE TRUE 221191.0376 350093.5719 215654.1951 459388.5196 180497.9489 251927.1747 446198.6912 418367.3979 342978.961 229046.4007 0.965704054 1.528483185 0.9415306 2.005657012 0.788040975 1.099895803 1.948071177 1.826561765 1.497421309 1 17.80528037 2.250403534 24.98150688 1.668328799 1.238711189 0.130703384 0.404544543 334.2558783 705080.4013 0.134711808 0.111873232 177.9932506 -2.250403534 -0.42961761 TTTS(ph)PFFSEDTFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTTSPFFSEDTFR 13 0 A0A494C0H4;H0Y9M2;Q17R98-2;Q17R98;H0Y9K9;G5E9Z1;A0A590UJE4;Q17R98-3;A0A5F9ZGT0;A0A5F9ZHK5 A0A494C0H4 ZNF827 Zinc finger protein 827 1 TTT(0.009)S(0.991)PFFSEDTFR;T(0.001)T(0.001)T(0.095)S(0.903)PFFSEDTFR 237.65 9.91E-17 230990000 572970 598490 509320 564730 549970 586760 609110 684830 653640 687660 TRUE FALSE 550577.6989 581421.6512 601365.4538 593875.783 567660.2845 598624.6892 616564.4704 670688.0212 579441.5275 641084.1757 0.858822788 0.90693496 0.938044451 0.926361632 0.885469188 0.933769249 0.961752752 1.046177782 0.903846249 1 19.29015427 2.250424734 2.863075263 0.990780797 0.90716279 0.441792748 0.039100523 0.221624247 3.747362359 0.015800223 0.011580121 178.0019394 -2.250424734 -0.083618006 ENPETEEDVGPVVQHIYELR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENPETEEDVGPVVQHIYELR 20 0 P06756-3;P06756-2;P06756 P06756-3 ITGAV Integrin alpha-V;Integrin alpha-V heavy chain;Integrin alpha-V light chain 0 ; 131.18 1.48E-05 71644000 45599 73516 42962 79711 52554 57884 78972 81276 73200 63660 FALSE TRUE 43816.94067 71419.39566 50726.18908 83824.89426 54244.44714 59054.45414 79938.48296 79597.6222 64890.64288 59348.2515 0.738302133 1.20339511 0.854720869 1.412423991 0.914002448 0.995049604 1.346939142 1.341195742 1.09338761 1 15.85691791 2.250425397 24.80385577 1.240787607 1.03355565 0.136779984 0.202082731 316.6394637 661948.5854 0.067014911 0.055646595 178.002211 -2.250425397 -0.207231956 TLHEWCDGCEAVLLGIEQQVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLHEWCDGCEAVLLGIEQQVLR 22 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2;J3QT95;J3KQ41;Q9H9Q2-3 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 ; 146.1 8.79E-08 31622000 25924 32715 22985 28872 27867 30193 24683 27497 32381 32506 FALSE TRUE 24910.86142 31782.00023 27138.9008 30362.08738 28763.36736 30803.52315 24985.07794 26929.17734 28705.24463 30304.33967 0.822022908 1.048760692 0.895545031 1.001905592 0.949150111 1.016472343 0.824471947 0.888624456 0.947232144 1 14.88723679 2.250442783 24.99955553 0.901055895 0.958951415 0.054194654 0.073503142 441.3481312 928576.8107 0.023771728 0.019744907 178.0093372 -2.250442783 0.057895519 LSVPTS(ph)DEEDEVPAPKPR ddPTM_BT-474_Pertuzumab_2h_R1 6 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 LSVPT(0.044)S(0.956)DEEDEVPAPKPR;LSVPT(0.173)S(0.827)DEEDEVPAPKPR;LSVPT(0.159)S(0.841)DEEDEVPAPKPR;LSVPT(0.006)S(0.994)DEEDEVPAPKPR;LSVPT(0.034)S(0.966)DEEDEVPAPKPR;LSVPTS(1)DEEDEVPAPKPR 283.05 5.27E-39 13998870000 7909070 7398270 6335850 7396390 7156320 7564690 8589500 9499130 9398640 9387870 TRUE FALSE 7599974.8 7187278.583 7480879.035 7778118.574 7386509.532 7717653.215 8694620.87 9302969.646 8331745.79 8752021.203 0.86836796 0.821213571 0.854760159 0.888722547 0.843977564 0.881813816 0.993441477 1.062950995 0.951979617 1 23.0611848 2.250526509 3.595235036 1.015764333 0.856043711 0.841552019 0.030325611 0.077368708 2.138558815 0.011579199 0.008823315 178.0436583 -2.250526509 -0.159720622 IEVPLYSLLEQTHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEVPLYSLLEQTHLK 15 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 306.69 4.09E-45 1066000000 1277250 1152000 1118970 987380 1165560 1110700 1334660 1324040 1378690 1258690 FALSE TRUE 1227333.658 1119146.088 1321192.77 1038338.8 1203051.296 1133159.115 1350993.968 1296698.111 1222186.891 1173437.805 1.045929876 0.95373277 1.125916316 0.884869054 1.025236524 0.965674627 1.151312803 1.105042044 1.041543817 1 20.16230995 2.250533105 24.99999783 1.087996973 0.999719641 0.201982824 0.07026907 283.0483761 591038.8265 0.023133235 0.019218518 178.0463624 -2.250533105 -0.088277332 LHLIYLINDVLHHCQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHLIYLINDVLHHCQR 16 0 Q8IWX8 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 173.06 1.51E-09 274830000 56120 67961 62793 64351 60147 51585 55005 18071 58780 53402 FALSE TRUE 53926.76836 66022.81882 74141.09192 67672.16282 62081.68288 52628.08404 55678.16764 17697.82753 52107.54083 49785.03497 1.083192336 1.326157928 1.489224462 1.359287241 1.246994863 1.057106499 1.118371568 0.355484887 1.046650682 1 15.60342452 2.250538842 1.88375947 0.745388918 1.308826911 0.450700156 0.217398844 0.251451671 1.797666441 0.10708353 0.069560114 178.0487145 -2.250538842 0.563437993 LPGEYFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPGEYFR 7 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 100.07 0.023419 159850000 47922 49075 41243 53624 44369 44256 55385 47747 64307 52820 FALSE TRUE 46049.15526 47675.42905 48696.52755 56391.54107 45796.16918 45150.88664 56062.8182 46761.00776 57007.13896 49242.45435 0.935151504 0.968177352 0.988913493 1.145181364 0.930013944 0.916909753 1.138505766 0.949607577 1.157682729 1 15.58761505 2.2506798 24.99982209 1.048618594 0.985696764 0.178461134 0.082632518 494.8861318 1020865.592 0.028649949 0.023801478 178.1065126 -2.2506798 -0.06292183 DLTQNTVVSINFKDPQFAEDYIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLTQNTVVSINFKDPQFAEDYIFK 24 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 128.75 6.87E-05 200490000 107710 94602 73570 60518 97679 97061 74791 94283 105800 95242 FALSE TRUE 103500.5741 91904.04359 86865.73556 63641.34123 100820.9337 99023.63992 75706.31463 92336.0231 93790.02755 88791.17451 1.165662857 1.035058316 0.978314974 0.716753006 1.135483727 1.11524192 0.852633328 1.039923434 1.056298985 1 16.43812867 2.250842548 0.003278955 6.34E-05 2.004555816 0.002952729 0.128875087 228060.9391 433.9835032 131934.7255 133349.3488 178.173269 -2.250842548 2.004492449 TQSEESRPQSLQQPATSTTETPAS(ph)PAHTTPQTQSTSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQSEESRPQSLQQPATSTTETPASPAHTTPQTQSTSGR 38 1 B8ZZU6;E9PBF9;P15336-5;P15336;P15336-4;F5H629;P15336-2 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 TQSEESRPQSLQQPATSTTET(0.003)PAS(0.997)PAHTTPQTQSTSGR 198.44 1.53E-30 895930000 125000 151750 113350 140170 114610 136630 102540 122460 120640 143680 TRUE FALSE 120114.8618 147422.2386 133834.8665 147404.1905 118296.5347 139392.7522 103794.9152 119931.1582 106945.453 133948.4256 0.8967247 1.100589558 0.999152217 1.100454819 0.88314987 1.040644946 0.774887161 0.89535325 0.798407689 1 17.0313181 2.25098194 24.99995033 0.859412207 1.006613415 0.361844992 0.088370285 212.3448273 427378.5027 0.028555504 0.023734232 178.2304648 -2.25098194 0.147201207 IKDHIQNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKDHIQNGK 9 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 111.61 0.0012602 2697500000 4458300 3922500 3761600 3539300 3909000 3948000 4384300 4273000 4941000 4752300 FALSE TRUE 4284064.707 3810634.141 4441404.796 3721963.697 4034736.535 4027831.265 4437956.375 4184761.057 4380118.394 4430422.488 0.966965277 0.860106265 1.00247884 0.840092273 0.910688889 0.909130286 1.001700489 0.94455124 0.988645757 1 22.07901285 2.251058294 24.93034011 0.976208628 0.912806886 0.341477758 0.046292228 252.8172933 504318.8049 0.015074159 0.0125286 178.2618028 -2.251058294 -0.063401742 ELELS(ph)DLDDFDPLEAEPPACELKPPFHSLDGGLER ddPTM_BT-474_Pertuzumab_2h_R1 3 ELELSDLDDFDPLEAEPPACELKPPFHSLDGGLER 35 1 P78413-2;P78413 P78413-2 IRX4 Iroquois-class homeodomain protein IRX-4 1 ELELS(1)DLDDFDPLEAEPPACELKPPFHSLDGGLER;ELELS(1)DLDDFDPLEAEPPACELKPPFHSLDGGLER;ELELS(1)DLDDFDPLEAEPPACELKPPFHSLDGGLER 176.01 4.51E-16 161099000 103149.9 97498 75989.5 99763.2 92873 95306 105424.3 109096 111775 110429 TRUE FALSE 99118.68787 94717.4525 89722.49303 104911.9907 95860.34439 97233.15262 106714.5141 106843.1295 99086.7706 102949.5455 0.96278898 0.920037598 0.871519079 1.019062204 0.931139074 0.944473841 1.036571008 1.037820313 0.962478952 1 16.65157793 2.251109169 23.4722685 1.0159605 0.940400882 0.403804564 0.039960262 97.40921389 182205.1958 0.013993478 0.011619241 178.2826861 -2.251109169 -0.075559618 KCEPIVMTVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KCEPIVMTVPR 11 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 166.04 3.35E-05 2129600000 2423500 2453300 2016210 2420000 2348200 2282000 2790100 2787500 2697900 2762500 FALSE TRUE 2328786.941 2383334.286 2380583.997 2544896.49 2423731.986 2328143.604 2824246.078 2729937.151 2391645.703 2575393.414 0.904245125 0.925425324 0.924357414 0.988158343 0.941111355 0.903995324 1.096627048 1.060007817 0.928652566 1 21.2963614 2.251230796 24.99996928 1.032442533 0.93367868 0.467041635 0.046508182 185.2888536 365599.3797 0.016558411 0.013768235 178.3326224 -2.251230796 -0.098763854 KESEDQKR ddPTM_BT-474_Pertuzumab_2h_R1 3 KESEDQKR 8 2 C9JRZ6;Q9NX63;A0A286YEX5;F8WAR4 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 0 ;; 105.78 0.0024304 113145000 350532 394151 263027 404330 247085 307840 440510 420698 372418 419071 FALSE TRUE 336832.8219 382910.1994 310561.8299 425197.5198 255032.7134 314064.7357 445901.0932 412010.4393 330142.6699 390686.9479 0.862155298 0.980094681 0.794912222 1.088333056 0.652780224 0.803878239 1.141325799 1.054579482 0.845031224 1 18.57565353 2.251307446 24.98938152 1.023565813 0.866480967 0.236307129 0.128106832 311.7820298 611229.1887 0.044474036 0.036981623 178.3640995 -2.251307446 -0.157084846 KMEIYRPHK ddPTM_BT-474_Pertuzumab_2h_R1 2 KMEIYRPHK 9 2 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ; 145.89 5.77E-05 1885600000 2240120 2052920 1997110 1861210 1969280 1892690 2314390 2153040 2357860 2291610 FALSE TRUE 2152573.634 1994372.732 2358032.202 1957267.271 2032623.68 1930961.489 2342714.197 2108578.972 2090205.618 2136397.214 1.007571822 0.9335215 1.103742407 0.91615326 0.951425918 0.903840108 1.096572389 0.9869789 0.978378742 1 21.02674848 2.251327174 24.99949257 1.014394562 0.970618575 0.120126557 0.061046749 532.0141699 1041788.984 0.021030378 0.01748951 178.3722023 -2.251327174 -0.043775987 SAS(ph)VSSISLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASVSSISLTK 11 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 S(0.005)AS(0.994)VS(0.001)SISLTK 94.122 0.0035045 0 161260 164120 117430 157520 144830 154300 79635 135190 97349 87926 TRUE FALSE 154957.7809 159439.4583 138652.2132 165649.6261 149488.5885 157420.0517 80609.59695 132398.2793 86298.34964 81970.6937 1.890404655 1.945078797 1.691485175 2.020839627 1.82368334 1.920443083 0.983395325 1.615190421 1.052795161 1 16.32282059 2.25151078 24.99787394 1.248844037 1.879858797 0.766272047 0.192239264 113.184421 218481.199 0.06427176 0.053455703 178.4476283 -2.25151078 0.63101476 YDERPGPSPLPHR ddPTM_BT-474_Pertuzumab_2h_R1 3 YDERPGPSPLPHR 13 1 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 77.078 0.016179 2040000000 1498950 1937590 1577330 2005060 1772210 1652410 1785220 1526410 1831630 1926270 FALSE TRUE 1440369.377 1882331.83 1862388.619 2108541.387 1829214.744 1685822.862 1807068.056 1494889.1 1623711.041 1795802.017 0.802075821 1.048184495 1.037079033 1.17415025 1.018606019 0.938757639 1.006273542 0.832435361 0.904170407 1 20.77619687 2.25156416 1.742125425 0.903043733 1.023623628 0.123268298 0.09772045 0.572920394 3.480128635 0.051177205 0.032426947 178.4695627 -2.25156416 0.120579895 LFECDRDQMYYNLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFECDRDQMYYNLLK 15 1 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 234.21 1.09E-17 735430000 322460 510890 345360 647560 373850 323310 721350 593990 550260 406190 FALSE TRUE 309857.9067 496319.9174 407774.2345 680980.6492 385875.2248 329847.5497 730178.0971 581723.8989 487796.7917 378678.3895 0.818261394 1.310663431 1.07683524 1.798308718 1.019005139 0.87104931 1.928227534 1.536195133 1.288155874 1 18.53061357 2.25167157 24.99968622 1.50445277 1.176690183 0.135042301 0.338072734 395.8890008 754871.9126 0.116248391 0.096710141 178.5137077 -2.25167157 -0.327762587 S(ph)PPGAGGS(ph)PPGAAVAPSALQLSPAAAAAAAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPGAGGSPPGAAVAPSALQLSPAAAAAAAHR 32 0 P78415 P78415 IRX3 Iroquois-class homeodomain protein IRX-3 2 S(0.999)PPGAGGS(0.998)PPGAAVAPS(0.002)ALQLSPAAAAAAAHR 46.714 0.049542 68045000 13376 12426 11151 12961 11551 11596 17136 18523 11768 13650 TRUE FALSE 12853.25113 12071.62265 13166.23375 13629.91876 11922.54841 11830.47907 17345.71549 18140.49358 10432.14598 12725.47334 1.010041103 0.948618752 1.034636072 1.071073617 0.93690412 0.929669078 1.363070357 1.425526037 0.819784514 1 13.6354317 2.251802666 24.96619269 1.219320945 0.990184562 0.138075345 0.16972256 287.2710802 541612.3614 0.05971978 0.049690333 178.5676017 -2.251802666 -0.229136383 NADSGVHLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 NADSGVHLNR 10 0 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;G3V3Y4;A0A3B3IT62;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 ;;; 134.57 0.0001851 754810000 1705510 1911260 1533000 1840660 1678070 1774100 1670540 1793590 1868940 1935110 FALSE TRUE 1638856.784 1856752.736 1810047.201 1935656.683 1732046.646 1809973.518 1690984.568 1756551.74 1656785.766 1804043.276 0.908435405 1.029217403 1.003328038 1.072954684 0.960091517 1.003287195 0.937330379 0.973674946 0.918373627 1 20.78280252 2.251863977 24.86528574 0.956499244 0.999887934 0.149371375 0.044919937 365.3548509 682883.493 0.01506465 0.012534155 178.5928128 -2.251863977 0.04338869 IALLPLLQAETDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 IALLPLLQAETDRR 14 1 U3KQP3;B4DEZ3;K7EJE1;E7ENQ6;Q9P0J0;Q9P0J0-2 U3KQP3 NDUFA13 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 0 ; 170 5.20E-06 230946000 82924 171170 93052 244770 87432 100944 213800 195212 143811 98135 FALSE TRUE 79683.2384 166288.3992 109868.5663 257402.609 90244.32968 102985.1568 216416.5484 191180.804 127486.1782 91488.22904 0.87096711 1.817593377 1.200903848 2.81350521 0.986403722 1.12566565 2.365512489 2.089676519 1.393470827 1 16.48129852 2.25193206 24.99952872 1.853780658 1.511978439 0.012531452 0.630780895 708.8788314 1325333.026 0.215798844 0.179581564 178.6208124 -2.25193206 -0.34180222 NS(ph)PVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPVTK 6 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(0.998)PVT(0.002)K 108.57 0.031783 1529500000 4755000 4173100 4201400 3666900 3839200 4325600 5032900 5563000 5390900 5567400 TRUE FALSE 4569169.343 4054087.274 4960686.44 3856149.148 3962691.355 4413066.596 5094494.136 5448122.106 4778947.632 5190315.039 0.880326013 0.781086937 0.955758254 0.742950884 0.763478002 0.850250238 0.981538519 1.049670794 0.920743268 1 22.30739068 2.252118332 4.148882347 1.000222427 0.823689853 0.594682768 0.064406269 0.13476894 5.284310306 0.024018583 0.018623615 178.6974405 -2.252118332 -0.176532574 TVKEEAEKPER ddPTM_BT-474_Pertuzumab_2h_R1 6 TVKEEAEKPER 11 2 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 122.46 0.00021954 20768900000 16014790 16666010 11774570 11617660 13493040 15220060 16063830 17743990 20097480 17804050 FALSE TRUE 15388914.3 16190711.71 13902496.72 12217248.82 13927055.89 15527820.04 16260423.96 17377570.41 17816098.33 16598165.84 0.927145472 0.975451859 0.83759235 0.736060174 0.839071981 0.935514213 0.979651855 1.046957271 1.073377535 1 23.98452049 2.252138035 1.964895573 1.041625312 0.862474033 0.606927981 0.062023298 0.246867116 1.927336008 0.033749946 0.02226772 178.7055479 -2.252138035 -0.179151279 DLSLDDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSLDDFK 8 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ; 164.53 0.00076665 151607000 534580 687050 532630 817310 489790 542170 850230 801730 738960 588140 FALSE TRUE 513688.0226 667456.0067 628888.0893 859491.467 505544.5402 553133.0489 860635.3691 785173.9953 655076.3588 548304.7539 0.936865892 1.217308444 1.14696815 1.567543343 0.922013783 1.00880586 1.569629595 1.432002896 1.194730401 1 19.06461846 2.252159088 24.99796866 1.353850819 1.147834122 0.095579671 0.223385912 424.6971338 780716.8999 0.077569737 0.064568812 178.7142111 -2.252159088 -0.206016697 IQEIIEQLDVTTSEYEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQEIIEQLDVTTSEYEK 17 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 146.47 1.01E-06 12790000 26702 31679 27550 52565 21504 27807 52775 47957 41102 36828 FALSE TRUE 25658.45632 30775.54594 32528.89785 55277.88595 22195.69569 28369.27659 53420.87624 46966.67119 36436.27327 34333.60676 0.747327728 0.896367986 0.947436081 1.610022691 0.646471425 0.826283029 1.55593546 1.367950403 1.061242226 1 15.0673338 2.252168695 24.99844963 1.29665919 0.96009204 0.20359165 0.28353076 336.8496461 618802.358 0.100441908 0.083609571 178.7181643 -2.252168695 -0.336567151 RSS(ph)PESDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSPESDR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.161)S(0.839)PESDR 119.53 0.001027 99362000 27083 28820 23279 31713 29969 29561 21987 27054 27690 26306 TRUE FALSE 26024.56642 27998.08182 27486.03314 33349.71173 30932.9801 30158.74367 22256.08348 26495.32545 24546.74729 24524.27119 1.061175935 1.141647864 1.120768602 1.359865558 1.261321075 1.229750864 0.907512534 1.080371573 1.000916484 1 14.58192264 2.252222494 24.99978054 1.008649064 1.200326973 0.557178092 0.086418604 189.1686398 346158.0577 0.032039891 0.026673477 178.7403047 -2.252222494 0.191677909 KEGGLGPLNIPLLADVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEGGLGPLNIPLLADVTR 18 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ; 180.86 1.23E-13 5041400000 1325030 1374640 1010390 1180750 1243630 1204930 1376120 1390490 1399940 1390490 FALSE TRUE 1273246.363 1335436.613 1192989.949 1241688.649 1283632.488 1229294.51 1392961.368 1361775.896 1241024.68 1296310.874 0.982207577 1.030182374 0.920296183 0.957863329 0.990219641 0.948302244 1.074558114 1.05050102 0.95735113 1 20.30598031 2.252234227 24.99981225 1.02934018 0.972080707 0.257486965 0.039739509 276.556155 505634.539 0.014037199 0.011684247 178.7451336 -2.252234227 -0.057259473 FEVNISELPDEIDISSYIEQTR ddPTM_BT-474_Pertuzumab_2h_R1 1 FEVNISELPDEIDISSYIEQTR 22 0 Q13838-2;Q13838;A0A0G2JJZ9 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 71.174 0.016677 8279000 6417.2 9851.5 8737.3 7516.4 8283.3 8200.3 9208.2 8660.6 11001 9058.2 FALSE TRUE 6166.408729 9570.544866 10316.32447 7904.322305 8549.739867 8366.115684 9320.892706 8481.755584 9752.2126 8444.680046 0.73021224 1.133322377 1.221635919 0.936012053 1.012440948 0.990696585 1.103759131 1.004390402 1.154835061 1 13.04382705 2.25243134 24.85518196 1.060843538 1.017107809 0.047006711 0.12747845 1069.06109 1915667.938 0.044092414 0.036702942 178.8262789 -2.25243134 -0.043735728 VGNPWDPNVLYGPLHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGNPWDPNVLYGPLHTK 17 0 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ; 225.11 2.50E-15 983730000 1873030 1982660 1575390 1892930 1626740 1642150 2122070 1912910 2140630 2019340 FALSE TRUE 1799829.917 1926116.478 1860098.017 1990624.344 1679065.569 1675355.398 2148040.527 1873407.74 1897634.657 1882568.303 0.956050261 1.023132321 0.988064026 1.057398205 0.89190154 0.889930737 1.141015985 0.995134008 1.008003085 1 20.84427078 2.252486446 24.99999252 1.03505734 0.971814908 0.224339457 0.061922361 397.8491343 714227.3089 0.022142757 0.018439035 178.8489711 -2.252486446 -0.063242431 RPGRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 9 RPGRSPK 7 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 RPGRS(1)PK;RPGRS(1)PK;RPGRS(1)PK;RPGRS(1)PK;RPGRS(1)PK;RPGRS(1)PK;RPGRS(1)PK;RPGRS(1)PK;RPGRS(1)PK 102.07 0.006839 11408270000 9164549 7684218 6086257 6788617 7603064 7478690 8400985 8290602 9372598 8781105 TRUE FALSE 8806388.293 7465071.626 7186179.028 7138978.337 7847623.458 7629914.236 8503798.767 8119398.172 8308659.968 8186352.937 1.07574012 0.911892229 0.877824238 0.87205846 0.958622664 0.932028498 1.038777443 0.991821173 1.014940356 1 22.96478944 2.252563975 24.42200129 1.00968275 0.932040713 0.300140895 0.054393305 213.7032097 372699.9947 0.019237018 0.016015573 178.8809014 -2.252563975 -0.077642037 KVVEAVNS(ph)DS(ph)DSEFGIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVVEAVNSDSDSEFGIPK 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KVVEAVNS(1)DS(0.967)DS(0.033)EFGIPK;KVVEAVNS(1)DS(0.5)DS(0.5)EFGIPK 127.16 9.11E-05 1131920000 852810 782040 644020 710930 730440 754770 804450 891490 868440 771350 TRUE FALSE 819481.2424 759736.9849 760408.7401 747621.1825 753935.266 770031.9665 814295.0997 873080.42 769858.332 719105.7775 1.139583728 1.056502407 1.057436561 1.039653979 1.048434444 1.070818773 1.132371795 1.214119602 1.070577314 1 19.45584448 2.252700239 6.314611046 1.132530897 1.06515969 0 0.058886119 0.233467062 35.33163532 0.020817564 0.016633293 178.9370359 -2.252700239 -0.067371208 MASNIFGT(ph)PEENQASWAK ddPTM_BT-474_Pertuzumab_2h_R1 5 MASNIFGTPEENQASWAK 18 0 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 MASNIFGT(1)PEENQASWAK;MASNIFGT(0.996)PEENQAS(0.004)WAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK 253.21 1.88E-29 696328000 1053945 1025947 1068540 993246 966029 1079002 1239526 1298530 1371370 1494440 TRUE FALSE 1012755.664 996687.9961 1261648.948 1044507.545 997102.2001 1100820.16 1254695.69 1271714.902 1215697.827 1393220.248 0.72691713 0.715384375 0.905563173 0.749707411 0.715681675 0.790126444 0.900572391 0.912788128 0.872581222 1 20.40999191 2.252713322 3.685479373 0.916257653 0.765958582 0.620436174 0.059449792 0.161933128 4.735728411 0.023053409 0.017652585 178.9424265 -2.252713322 -0.150299071 GLSLVDKENT(ph)PPALSGTR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLSLVDKENTPPALSGTR 18 1 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 GLSLVDKENT(1)PPALSGTR;GLSLVDKENT(1)PPALSGTR;GLSLVDKENT(1)PPALSGTR;GLSLVDKENT(1)PPALSGTR 132.26 2.45E-05 3206580000 1386910 1282830 1282060 1278370 1293830 1325210 1754160 1848380 1385960 1776180 TRUE FALSE 1332708.024 1246244.944 1513756.761 1344346.829 1335447.217 1352006.654 1775627.935 1810210.307 1228631.631 1655877.747 0.804834793 0.752618934 0.914171813 0.811863576 0.806489018 0.816489416 1.072318254 1.093202871 0.74198209 1 20.65916473 2.252969081 24.98878204 0.999405417 0.818388412 0.383946317 0.097083954 213.2563778 369852.7104 0.033850721 0.028202367 179.0478379 -2.252969081 -0.181017005 IYQNIQDGSLDLNAAESGVQHKPSAPQGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 IYQNIQDGSLDLNAAESGVQHKPSAPQGGR 30 1 P61106 P61106 RAB14 Ras-related protein Rab-14 0 ;; 301.15 1.75E-81 2874970000 749230 1065470 734300 1033690 793990 904650 1143440 1150810 1183590 1044870 FALSE TRUE 719949.2633 1035083.839 867004.3444 1087038.865 819529.4094 922942.6428 1157433.761 1127045.371 1049233.825 974100.0242 0.739091721 1.06260529 0.890056794 1.115941729 0.841319566 0.947482414 1.188208328 1.157011953 1.077131505 1 19.8937104 2.253009159 23.85149286 1.125263505 0.940882457 0.364327099 0.11031724 129.7478666 214185.7953 0.036085398 0.030045607 179.0643619 -2.253009159 -0.184381048 VEEVGPYTYR ddPTM_BT-474_Pertuzumab_2h_R1 3 VEEVGPYTYR 10 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;Q14108-2;A0A1W2PSE4;A0A1W2PS70;A0A1W2PNX7;D6RDG0 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ;; 204.36 4.38E-07 898500000 214799 352347 231791 398287 221283 287499 422832 439400 357409 330459 FALSE TRUE 206404.4176 342298.4085 273680.7899 418842.6398 228400.7687 293312.4268 428006.7445 430326.2364 316837.4287 308076.7176 0.669977333 1.111081718 0.888352719 1.359540062 0.741376273 0.952075928 1.38928624 1.396815182 1.028436784 1 18.23293013 2.253043099 24.99678274 1.259306829 0.966707342 0.222575224 0.218330502 288.8959283 498634.0502 0.073758705 0.061454431 179.078356 -2.253043099 -0.292599487 LPSGS(ph)GAASPTGSAVDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LPS(0.428)GS(0.571)GAAS(0.001)PTGSAVDIR 74.78 0.018861 770530000 288200 324390 253590 339230 336300 316760 283910 318330 336330 299930 TRUE FALSE 276936.8254 315138.7148 299419.3541 356737.701 347117.3949 323165.1042 287384.5755 311756.3743 298151.2284 279615.474 0.990420242 1.127043187 1.070825408 1.275815304 1.241409819 1.155748284 1.027784949 1.114946787 1.06629016 1 18.09308468 2.253260003 24.42024266 1.06630894 1.149949134 0.226611056 0.08045018 309.6995243 514505.6382 0.029633975 0.024688101 179.1678174 -2.253260003 0.083640194 EISEVFPDQFIHLGGDEVEFK ddPTM_BT-474_Pertuzumab_2h_R1 4 EISEVFPDQFIHLGGDEVEFK 21 0 P07686;Q5URX0;H0Y9B6 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ;;; 286.05 1.97E-45 481338000 664258 629949 564297 611690 592462 626937 667654 695269 757902 731031 FALSE TRUE 638298.063 611983.4713 666278.0206 643259.3942 611519.0783 639614.0957 675824.9494 680911.4522 671868.1423 681517.6192 0.936583362 0.897971606 0.977638731 0.94386319 0.897290196 0.938514394 0.991647069 0.999110563 0.985841192 1 19.37839143 2.253270164 4.796791324 0.995069502 0.93095585 0.663423951 0.021754528 0.115435105 6.789193844 0.008163612 0.006415906 179.1720095 -2.253270164 -0.064113652 DLFDLNS(ph)SEEDDTEGFSER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLFDLNSSEEDDTEGFSER 19 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 DLFDLNS(0.5)S(0.5)EEDDTEGFSER;DLFDLNS(0.5)S(0.5)EEDDTEGFSER 250.94 1.56E-25 125035000 104866 106352 89462 102222 93632 100873 111677 117300 112095 116364 TRUE FALSE 100767.7208 103318.9451 105629.7735 107497.6897 96643.75831 102912.7212 113043.7365 114877.714 99370.44554 108482.5626 0.928884038 0.952401405 0.973702786 0.990921371 0.890869057 0.948656804 1.042045226 1.058950962 0.916003855 1 16.72710364 2.253454878 24.43617879 1.015671434 0.948372751 0.275388073 0.043477245 201.4763149 330550.2572 0.015389168 0.012823556 179.2482307 -2.253454878 -0.067298683 RDS(ph)PLQGSGQQNSQAGQR ddPTM_BT-474_Pertuzumab_2h_R1 3 RDSPLQGSGQQNSQAGQR 18 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 RDS(1)PLQGSGQQNSQAGQR;RDS(1)PLQGSGQQNSQAGQR;RDS(1)PLQGSGQQNSQAGQR 357.44 6.63E-91 1037929000 283109 344405 281585 366382 294378 330038 418737 449047 431773 469561 TRUE FALSE 272044.7873 334582.9066 332473.6733 385291.0189 303846.9357 336711.5945 423861.6287 439774.0225 382759.9392 437757.2152 0.621451293 0.764311575 0.759493303 0.880147729 0.694099206 0.769174288 0.968257321 1.004607137 0.874365803 1 18.73977143 2.253573769 5.91885868 0.967771983 0.751902344 0.694274012 0.069458562 0.091260151 10.78026595 0.024968732 0.019903235 179.297308 -2.253573769 -0.215869639 DDIVDR ddPTM_BT-474_Pertuzumab_2h_R1 3 DDIVDR 6 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;; 115.78 0.056159 3062150000 1718270 1711640 1445630 1592310 1583540 1616980 1753530 1788210 1874990 1836500 FALSE TRUE 1651118.109 1662825.703 1706887.499 1674489.31 1634476.002 1649676.443 1774990.225 1751282.839 1662148.996 1712112.219 0.964374934 0.971213034 0.996948377 0.978025442 0.954654715 0.963532895 1.0367254 1.022878535 0.970817787 1 20.70734583 2.253584062 24.9996916 1.011916017 0.972140439 0.455405604 0.019125406 200.6054241 333816.0672 0.006926843 0.005773712 179.3015576 -2.253584062 -0.039775579 SIKDTICNQDER ddPTM_BT-474_Pertuzumab_2h_R1 3 SIKDTICNQDER 12 1 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0;H0YHL7 Q9ULV4 CORO1C Coronin-1C;Coronin 0 ;; 131.69 0.00017713 1394320000 1226040 1351290 1023920 1117980 1160400 1152950 1331500 1305180 1392560 1350040 FALSE TRUE 1178125.001 1312752.532 1208965.121 1175679.082 1197725.32 1176263.439 1347795.295 1278227.577 1234482.427 1258600.588 0.936059471 1.043025519 0.960562971 0.934116107 0.951632576 0.934580398 1.070868159 1.015594295 0.980837319 1 20.26338909 2.253620928 24.99999969 1.019737095 0.96223947 0.364228526 0.036629698 262.3350473 435473.5068 0.013051432 0.010878749 179.3167784 -2.253620928 -0.057497625 SSLDVLPSQVYSLVGSS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSLDVLPSQVYSLVGSSPLR 20 0 Q5SQL3;J3KP92;Q86Z02;H3BLW0;Q86Z02-4;Q86Z02-3;Q86Z02-2 Q5SQL3 HIPK1 Homeodomain-interacting protein kinase 1 1 SSLDVLPSQVYSLVGS(0.114)S(0.886)PLR;SSLDVLPSQVYSLVGS(0.429)S(0.571)PLR 222.13 7.73E-25 174045000 262590 288000 249840 254470 266670 274100 213820 250390 273180 258730 TRUE FALSE 252327.6925 279786.522 294991.6457 267603.2272 275247.6827 279642.4898 216436.7931 245219.359 242169.7517 241205.9866 1.046108747 1.159948498 1.222986418 1.10943858 1.141131224 1.159351365 0.897311033 1.016638776 1.00399561 1 17.87990619 2.254232134 24.99550192 0.981720621 1.143199996 0.698043857 0.051626223 127.8740171 203954.0926 0.017751977 0.014804888 179.5693184 -2.254232134 0.161479375 IIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_BT-474_Pertuzumab_2h_R1 1 IIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 36 0 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IIPTLEEGLQLPS(0.955)PT(0.042)AT(0.003)S(0.001)QLPLESDAVECLNYQHYK 159.41 3.28E-17 388540000 299870 343600 288030 340670 363190 329150 251780 261160 315490 269970 TRUE FALSE 288150.7489 333800.8644 340083.4282 358252.0195 374872.3362 335805.6385 254861.359 255766.9547 279676.8978 251684.6914 1.144887864 1.326266061 1.351228103 1.423416011 1.489452275 1.334231481 1.012621616 1.016219752 1.111219345 1 17.94125794 2.254365067 7.793736809 1.033044903 1.355105001 0.751487335 0.087195571 0.077462411 24.65733217 0.03270954 0.026457952 179.6242912 -2.254365067 0.322060099 RDFNHINVELSLLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDFNHINVELSLLGK 15 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 68.972 0.033134 213360000 803130 772810 681810 695570 735790 735640 816250 792170 891620 888540 FALSE TRUE 771742.7917 750770.2155 805028.2338 731468.4511 759457.3536 750515.1448 826239.5117 775811.4127 790407.0356 828358.3944 0.931653252 0.906335012 0.971835668 0.883033788 0.916822186 0.906027089 0.99744207 0.936564919 0.954184856 1 19.65989557 2.254582263 24.99753575 0.964622069 0.919324889 0.45295285 0.027934102 242.3790921 378167.9348 0.009397847 0.007840191 179.714146 -2.254582263 -0.04529718 (ac)SDAAVDT(ph)SSEITTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 S(0.013)DAAVDT(0.411)S(0.411)S(0.142)EIT(0.011)T(0.011)K 66.289 2.34E-43 1954400000 1443100 1418800 1090800 1327800 1308200 1329500 1434900 1496600 1514500 1472000 TRUE FALSE 1386702.057 1378337.213 1287931.825 1396327.917 1350279.441 1356383.401 1452460.735 1465694.687 1342580.309 1372300.129 1.010494736 1.004399245 0.938520516 1.017509135 0.983953446 0.988401424 1.05841332 1.068056948 0.978343061 1 20.38816461 2.254905199 24.69659816 1.036699213 0.989737162 0.202244475 0.032066494 240.2101125 362955.5947 0.01111547 0.009273502 179.8478287 -2.254905199 -0.046962051 HGT(ph)PQKYDPTFK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGTPQKYDPTFK 12 1 K7EMR2;K7ER17;K7EPV6;Q8IWA5;Q8IWA5-2 K7EMR2 SLC44A2 Choline transporter-like protein 2 1 HGT(1)PQKYDPTFK;HGT(1)PQKYDPTFK 150.76 9.84E-05 320210000 548410 768030 417840 901300 488160 501890 1153700 742260 1286470 728630 TRUE FALSE 526977.5309 746126.5364 493352.9828 947816.201 503862.1097 512038.5597 1167819.326 726932.0716 1140435.319 679279.2411 0.775789247 1.098409154 0.726288915 1.395326316 0.741759911 0.753796861 1.719203613 1.070152049 1.678890285 1 19.37364524 2.255450886 24.99981649 1.352837242 0.928904335 0.372705425 0.286601596 258.2362184 382222.767 0.09314827 0.07774347 180.0739478 -2.255450886 -0.423932907 ILKS(ph)PEIQR ddPTM_BT-474_Pertuzumab_2h_R1 4 ILKSPEIQR 9 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 1 ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR 168.82 3.57E-05 2285640000 3295180 3149390 2938410 2919750 3158830 3578320 3710490 4159230 4602510 4519150 TRUE FALSE 3166400.723 3059572.481 3469446.052 3070438.647 3260436.636 3650676.082 3755900.087 4073340.447 4080052.36 4213063.945 0.751567212 0.726210786 0.823497126 0.728789947 0.773887289 0.866513333 0.891488982 0.966835657 0.968428776 1 22.00643838 2.255546032 1.009370742 0.990624922 0.753458823 0.919383539 0.028160599 0.134091765 0.261693774 0.019709437 0.011313624 180.1134029 -2.255546032 -0.237166099 SEALS(ph)SVLDQEEAMEIK ddPTM_BT-474_Pertuzumab_2h_R1 5 SEALSSVLDQEEAMEIK 17 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEALS(0.983)S(0.017)VLDQEEAMEIK;SEALS(0.977)S(0.023)VLDQEEAMEIK;S(0.003)EALS(0.537)S(0.461)VLDQEEAMEIK;SEALS(0.91)S(0.09)VLDQEEAMEIK;SEALS(0.999)S(0.001)VLDQEEAMEIK 377.31 4.18E-105 137631000 202497 186554 181146 192271 206883 224646 244081 270079 315232 302229 TRUE FALSE 194583.1934 181233.6626 213883.1118 202194.1294 213537.5796 229188.496 247068.1363 264501.7743 279448.1849 281758.7606 0.690602106 0.643222813 0.75910013 0.717614348 0.757873789 0.813421011 0.876878276 0.938752618 0.991799454 1 18.10410094 2.255683843 0.676037703 1.014141006 0.681658294 0.956886054 0.025031428 0.129567055 0.115760964 0.020999031 0.014196641 180.170566 -2.255683843 -0.332482712 LGPGRPLPTFPTSECT(ph)SDVEPDTR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPTFPT(0.018)S(0.059)ECT(0.461)S(0.461)DVEPDTR;LGPGRPLPTFPT(0.003)S(0.016)ECT(0.552)S(0.43)DVEPDTR;LGPGRPLPTFPTS(0.001)ECT(0.499)S(0.499)DVEPDTR 175.46 2.62E-12 990820000 586270 620980 479150 515540 552150 587300 493280 587360 574250 604840 TRUE FALSE 563357.9202 603270.2584 565743.0636 542147.0812 569910.4062 599175.6084 499316.9082 575230.8107 509063.5475 563873.6481 0.999085384 1.069867798 1.003315309 0.961469086 1.01070587 1.062606154 0.885512047 1.020141325 0.902797194 1 19.1050124 2.256013961 24.99997861 0.958461466 1.016659391 0.312283738 0.047392581 320.7933193 459499.7612 0.015911664 0.013284032 180.3075702 -2.256013961 0.058197925 APAPS(ph)PAKEER ddPTM_BT-474_Pertuzumab_2h_R1 1 APAPSPAKEER 11 1 O75781-2;O75781 O75781-2 PALM Paralemmin-1 1 APAPS(1)PAKEER 59.709 0.059512 218490000 255380 325850 198410 314450 203170 248770 334970 357760 282490 234660 TRUE FALSE 245399.4673 316557.077 234267.1006 330678.8022 209705.1476 253800.2998 339069.4631 350372.131 250422.9195 218766.2692 1.121742708 1.447010447 1.070855674 1.511562104 0.95858081 1.160143658 1.549916559 1.601582055 1.144705353 1 17.73903079 2.25615198 24.97788191 1.404823277 1.218077041 0.007427614 0.230543353 484.7042948 688227.6363 0.077710056 0.064884655 180.3648814 -2.25615198 -0.186746236 GAGFGPQHNR ddPTM_BT-474_Pertuzumab_2h_R1 3 GAGFGPQHNR 10 0 Q56VL3 Q56VL3 OCIAD2 OCIA domain-containing protein 2 0 ;; 135.79 0.00013482 280118000 166743 350812 201779 584360 179936 176624 530460 420659 296211 209755 FALSE TRUE 160226.4992 340807.1852 238244.9538 614518.8896 185723.8049 180195.4583 536951.9282 411972.2446 262586.3691 195548.107 0.819371262 1.742830398 1.218344465 3.142545837 0.949760178 0.921489147 2.745881494 2.106756496 1.342822353 1 17.57716404 2.256608088 24.99918243 1.944730066 1.519841398 0.027125908 0.766183817 735.2230962 1018421.796 0.265211565 0.22147562 180.5544048 -2.256608088 -0.424888668 TVWSSGDDKEQLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVWSSGDDKEQLVK 14 1 K7EM91;O43291-2;O43291;K7ES27 K7EM91 SPINT2 Kunitz-type protease inhibitor 2 0 166.86 3.41E-06 620880000 360650 439280 305150 465480 442450 511460 724240 894910 918610 899500 FALSE TRUE 346555.3993 426752.1645 360297.393 489503.4786 456681.8061 521802.0716 733103.4658 876429.7958 814333.2439 838576.0638 0.413266505 0.508900961 0.429653801 0.583731756 0.544591988 0.622247753 0.874224173 1.045140487 0.971090494 1 19.67758213 2.256622082 1.61683186 1.020879209 0.490551334 0.955572582 0.049364324 0.069731697 0.362744416 0.026804059 0.016664635 180.5602227 -2.256622082 -0.530327875 down LTTTGQVTS(ph)PVKGASFVTSTNPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTTTGQVTSPVKGASFVTSTNPR 23 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.11)S(0.89)PVKGASFVTSTNPR 202.69 1.23E-24 3604800000 908800 813920 569940 648430 665170 884390 763220 761960 817790 812650 TRUE FALSE 873283.0913 790707.7985 672940.8362 681895.55 686565.7971 902272.9717 772560.5147 746225.2597 724957.9077 757608.4917 1.152683874 1.043689197 0.888243524 0.900063235 0.906227695 1.190948863 1.019735818 0.984974783 0.956903091 1 19.53109298 2.256688896 0.003468249 4.12E-05 1.999506026 0.010968085 0.097052445 152338.0946 307.7633769 88205.30945 89207.79609 180.5880032 -2.256688896 1.999464871 KTSFDQDSDVDIFPSDFPTEPPSLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 89.829 0.017439 61170000 68260 69777 36831 65981 58585 54340 70977 66983 67888 61370 FALSE TRUE 65592.32373 67787.02828 43487.181 69386.28732 60469.43973 55438.79203 71845.63776 65599.77764 60181.63885 57213.35524 1.146451269 1.184811273 0.760087934 1.212763821 1.056911266 0.96898341 1.255749422 1.146581552 1.051880957 1 15.80406433 2.256702486 24.99961597 1.132640393 1.054754634 0.035498569 0.135626517 697.5228778 961189.5434 0.046174108 0.038563995 180.5936541 -2.256702486 -0.077885758 SAKPGDDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SAKPGDDVR 9 1 P55809;E9PDW2 P55809 OXCT1 "Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial" 0 ;;; 99.653 0.0047346 943090000 2172840 3077230 1937600 4169820 2100410 2436950 4118760 3958170 3273150 2513060 FALSE TRUE 2087923.011 2989470.413 2287767.422 4385024.91 2167971.595 2486226.799 4169166.617 3876432.406 2901595.734 2342848.208 0.89119005 1.275998335 0.976489819 1.871664112 0.925357259 1.061198412 1.779529123 1.654581118 1.238490707 1 21.15983205 2.256792818 24.95801501 1.503144403 1.18432742 0.097702649 0.333872033 411.5139666 563319.1873 0.113539508 0.094822164 180.6312211 -2.256792818 -0.318816983 FDQLLAEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FDQLLAEEK 9 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;A0A0C4DFM8;A1L2Z2 P35579;P35580;P35749;Q7Z406 MYH9;MYH10;MYH11;MYH14 Myosin-9;Myosin-10;Myosin-11;Myosin-14 0 80.706 0.05433 36399000 32344 41328 32802 34008 37501 35449 40655 40474 42412 39762 FALSE TRUE 31079.96072 40149.3659 38730.05108 35763.15696 38707.25372 36165.80307 41152.54805 39638.19776 37597.56757 37068.88432 0.838437986 1.083101546 1.044812969 0.96477565 1.044197969 0.975637755 1.110164193 1.069311863 1.014262184 1 15.17792107 2.257110208 24.97029819 1.057826913 0.999535443 0.129631163 0.068463688 453.2573573 610145.7339 0.022793172 0.019038121 180.763278 -2.257110208 -0.05829147 KEAEQEAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEAEQEAAR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 110.84 0.0041007 0 107710 134509 96219 121021 99645 111330 156996 141669 144756 161352 FALSE TRUE 103500.5741 130672.935 113607.9137 127266.9083 102850.1719 113581.1689 158917.364 138743.4856 128323.9057 150423.4853 0.688061268 0.868700354 0.755253832 0.846057436 0.683737461 0.755076035 1.05646644 0.922352552 0.853084247 1 17.1986703 2.257201883 24.99998688 0.952130311 0.770200331 0.619907259 0.073488608 161.0133194 215936.0847 0.024888971 0.020789671 180.801439 -2.257201883 -0.18192998 LLDVDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDVDNR 7 0 P00403 P00403 MT-CO2 Cytochrome c oxidase subunit 2 0 78.178 0.083843 257220000 281550 646680 327320 1079700 331530 314630 969130 801020 496000 323530 FALSE TRUE 270546.7147 628237.3196 386474.0052 1135423.446 342193.9635 320992.0342 980990.5028 784478.6571 439696.1594 301617.0249 0.896987545 2.082897408 1.281340154 3.764454101 1.134531327 1.064237121 3.252437435 2.600909737 1.457796222 1 18.20235834 2.257337596 24.99978736 2.290138107 1.769844229 0.013581856 0.967385177 753.1159868 1002701.19 0.333019795 0.278175019 180.8579469 -2.257337596 -0.520293879 TST(ph)SPPPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSTSPPPEK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TS(0.001)T(0.5)S(0.5)PPPEK 112.13 0.022498 7887000000 1357100 1254300 1266600 1410300 1235000 1398600 1666800 1731700 1979800 1909000 TRUE FALSE 1304063.032 1218528.592 1495502.795 1483085.752 1274724.897 1426880.65 1687198.797 1695939.79 1755061.404 1779701.73 0.732742465 0.684681355 0.840310919 0.833333882 0.716257604 0.801752691 0.948023351 0.952934844 0.9861548 1 20.76320404 2.257666429 3.224945452 0.970296725 0.764600308 0.823309473 0.046600948 0.107141441 2.322007379 0.019595696 0.014773803 180.9949379 -2.257666429 -0.205696417 HEHQVMLMR ddPTM_BT-474_Pertuzumab_2h_R1 3 HEHQVMLMR 9 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;; 72.643 0.02559 43623000 153808 158639 128327 142450 144071 119081 150092 110589 120544 140095 FALSE TRUE 147797.0133 154114.771 151518.5435 149801.8616 148705.1746 121488.8994 151928.8708 108305.2985 106860.3505 130606.2409 1.131622902 1.179995458 1.160117178 1.146973227 1.138576331 0.930192146 1.16325889 0.829250561 0.818187169 1 16.99486431 2.257809132 0.980781533 0.879179086 1.159058477 0.570830204 0.089125168 0.366225509 0.674422545 0.062635089 0.036124419 181.0544202 -2.257809132 0.279879391 SLSEEIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSEEIKR 8 1 P15924 P15924 DSP Desmoplakin 0 ; 149.57 0.00080661 1065100000 1433640 1431400 1072120 1229550 1315560 1296490 1406890 1416300 1541540 1447610 FALSE TRUE 1377611.764 1390577.873 1265875.933 1293007.223 1357876.182 1322705.916 1424107.941 1387052.91 1366550.842 1349562.085 1.020784282 1.030391924 0.937990143 0.958093916 1.006160589 0.980100086 1.05523707 1.027779993 1.012588348 1 20.36405992 2.257982952 24.97461032 1.027420345 0.987872693 0.255214623 0.028994359 311.3255581 400322.8991 0.010606985 0.008862558 181.1268992 -2.257982952 -0.039547653 MCTLIDKFDEHDGPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MCTLIDKFDEHDGPVR 16 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 232.78 5.89E-17 381360000 595170 600940 493410 530500 597400 619380 624010 675640 783240 735980 FALSE TRUE 571910.0984 583801.7796 582580.1628 557879.1686 616615.9135 631904.288 631646.821 661687.7979 694329.8788 686131.4191 0.833528509 0.850860001 0.849079559 0.813079176 0.898684853 0.920966845 0.9205916 0.964374724 1.011948818 1 19.38812541 2.258069107 0.702598734 1.008007564 0.833930259 0.914059214 0.019473405 0.193330189 0.185515834 0.016871702 0.011111866 181.1628344 -2.258069107 -0.174077306 TVLEGSTAST(ph)SPADHSALPNQSLTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVLEGSTASTSPADHSALPNQSLTVR 26 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 TVLEGS(0.014)T(0.086)AS(0.073)T(0.449)S(0.378)PADHSALPNQSLTVR;TVLEGS(0.001)T(0.016)AS(0.068)T(0.523)S(0.392)PADHSALPNQSLTVR 236.08 2.29E-44 421300000 138034 155509 125780 149325 134004 152301 127830 151553 147000 166403 TRUE FALSE 132639.4787 151074.0356 148511.244 157031.6811 138314.3604 155380.6306 129394.4218 148423.3776 130313.1763 155132.3766 0.855008359 0.973839497 0.957319466 1.012243122 0.891589257 1.001600272 0.834090372 0.95675307 0.840012763 1 17.24314029 2.258083763 24.99815077 0.907249689 0.950445034 0.089638782 0.063662308 553.7786858 709077.1759 0.020448224 0.017084464 181.1689484 -2.258083763 0.043195346 GGVTGS(ph)PEASISGSK ddPTM_BT-474_Pertuzumab_2h_R1 8 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(0.802)PEAS(0.198)ISGSK;GGVTGS(1)PEASISGSK;GGVTGS(0.99)PEAS(0.01)ISGSK 380.74 2.34E-98 30897060000 13344698 13221060 12696150 14389090 11819004 13832300 15566030 16493660 17330640 18052850 TRUE FALSE 12823172.45 12844008.31 14990626.73 15131712.66 12199173 14111998.58 15756531.73 16153060.16 15363338.4 16830114.39 0.761918318 0.763156329 0.890702605 0.89908555 0.724841954 0.838496891 0.936210614 0.959771264 0.912848127 1 24.00454165 2.258112931 3.901585717 0.951681023 0.812351897 0.609327946 0.055059027 0.160361749 5.345364416 0.021703376 0.016803144 181.1811162 -2.258112931 -0.139329125 GNVAGDSK ddPTM_BT-474_Pertuzumab_2h_R1 3 GNVAGDSK 8 0 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;; 97.431 0.019163 247760000 878130 822630 772150 852390 815100 815300 1069370 999910 924080 1192110 FALSE TRUE 843811.7088 799169.3978 911694.6814 896381.9501 841318.4318 831785.9246 1082457.27 979261.5091 819182.3125 1111367.328 0.759255457 0.71908664 0.820336048 0.806557767 0.757012025 0.748434747 0.973986946 0.881132173 0.737094111 1 20.0839043 2.258363633 24.99492207 0.890461703 0.769774547 0.445930353 0.070563052 234.2115528 295615.8062 0.024173391 0.020199389 181.2857357 -2.258363633 -0.120687156 LITSEEERS(ph)PAKR ddPTM_BT-474_Pertuzumab_2h_R1 6 LITSEEERSPAKR 13 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LITSEEERS(1)PAKR;LITSEEERS(1)PAKR;LITSEEERS(1)PAKR;LITSEEERS(1)PAKR;LITSEEERS(1)PAKR;LITSEEERS(1)PAKR 261.59 2.37E-24 4244580000 2534120 2371630 1975136 1953217 2096540 2242200 2426060 2640360 2530200 2736910 TRUE FALSE 2435083.789 2303993.434 2332087.012 2054022.763 2163977.113 2287538.82 2455750.848 2585835.643 2242982.303 2551536.648 0.954359715 0.902982693 0.913993148 0.805014016 0.8481074 0.89653379 0.962459563 1.013442486 0.879071169 1 21.28293493 2.258450155 4.350996461 0.970900096 0.882340483 0.361651974 0.049894795 0.209988081 9.231985692 0.019175074 0.015017584 181.3218557 -2.258450155 -0.088559612 VVLDDKDYFLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVLDDKDYFLFR 12 1 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ; 99.669 0.0033437 10142800000 2563620 3082800 2273780 3592500 2132490 2455100 3691400 3387500 3191000 2834300 FALSE TRUE 2463430.896 2994881.562 2684702.626 3777909.356 2201083.478 2504743.804 3736576.457 3317546.941 2828771.058 2642330.336 0.932294824 1.133424357 1.016035955 1.429764214 0.833008442 0.947929852 1.414121621 1.255538301 1.070559203 1 21.33337941 2.258873831 24.99995103 1.219040418 1.058618479 0.105579927 0.182669693 458.4651617 564242.3404 0.063102606 0.052736828 181.4988304 -2.258873831 -0.16042194 GDLGIEIPAEK ddPTM_BT-474_Pertuzumab_2h_R1 7 GDLGIEIPAEK 11 0 P14618;P14618-3;B4DNK4;P30613;P30613-2;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM;PKLR Pyruvate kinase PKM;Pyruvate kinase;Pyruvate kinase PKLR 0 ;;;;;; 218.49 2.46E-11 4665441000 6098930 5867360 5076680 5733940 5717090 5903080 6162650 6792800 6943720 6465800 FALSE TRUE 5860577.073 5700028.638 5994149.006 6029869.331 5900985.392 6022444.322 6238070.354 6652526.306 6155498.016 6027865.607 0.972247468 0.945613092 0.994406544 1.00033241 0.978951054 0.999100629 1.034872169 1.103628836 1.021173732 1 22.52321582 2.25887456 2.942519058 1.056067421 0.979515479 0.471483347 0.029399112 0.182121011 3.256549887 0.011952785 0.008869728 181.499135 -2.25887456 -0.076551942 MGPGAASGGERPNLK ddPTM_BT-474_Pertuzumab_2h_R1 3 MGPGAASGGERPNLK 15 1 Q9H0U4;E9PLD0 Q9H0U4 RAB1B Ras-related protein Rab-1B 0 ;; 236.05 9.76E-18 3520460000 2054240 2520470 1783390 2472590 2145440 2301110 2755670 2968010 3040580 2898030 FALSE TRUE 1973958.03 2448588.663 2105688.244 2600200.666 2214450.026 2347640.021 2789394.714 2906719.556 2695426.106 2701743.847 0.730623679 0.906299339 0.779381157 0.962415689 0.819637298 0.868935086 1.032442331 1.075867929 0.997661606 1 21.36545947 2.259043562 4.773712533 1.038823813 0.84693498 0.662802818 0.063505499 0.104939741 5.963013699 0.02192116 0.01731833 181.5697779 -2.259043562 -0.191888834 S(ph)SPGPDTLVVLEFNPASK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPGPDTLVVLEFNPASK 18 0 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 S(0.5)S(0.5)PGPDTLVVLEFNPASK;S(0.5)S(0.5)PGPDTLVVLEFNPASK 203.99 1.18E-15 117057000 167641 167534 165109 164036 167488 172648 196704 207969 217271 210684 TRUE FALSE 161089.4044 162756.0944 194947.8691 172501.9176 172875.4036 176139.0609 199111.3224 203674.3675 192607.307 196414.185 0.820151581 0.82863717 0.992534572 0.878255904 0.880157427 0.896773626 1.013731887 1.036963636 0.98061811 1 17.5835396 2.259044685 5.20235182 1.014494992 0.884027621 0.642329478 0.045685508 0.115380092 8.494575581 0.017263742 0.013730828 181.5702471 -2.259044685 -0.130467371 REAILAK ddPTM_BT-474_Pertuzumab_2h_R1 1 REAILAK 7 1 Q2M1P5 Q2M1P5 KIF7 Kinesin-like protein KIF7 0 84.568 0.034394 675190000 701560 861230 664250 1229300 643920 689350 1250200 1082400 976780 830680 FALSE TRUE 674142.2596 836668.5636 784294.7512 1292744.32 664632.2716 703289.1293 1265500.322 1060048.062 865900.0294 774417.3037 0.870515491 1.080384645 1.012754683 1.669312287 0.858235306 0.908152654 1.63413229 1.36883313 1.118131045 1 19.56275166 2.259152094 24.99916156 1.328745826 1.082670601 0.120196005 0.268734084 443.8251398 538826.2519 0.093808951 0.07840342 181.6151584 -2.259152094 -0.246075225 SSS(ph)PVGLAK ddPTM_BT-474_Pertuzumab_2h_R1 7 SSSPVGLAK 9 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.018)S(0.256)S(0.726)PVGLAK;S(0.002)S(0.029)S(0.969)PVGLAK;S(0.002)S(0.187)S(0.811)PVGLAK;SS(0.002)S(0.998)PVGLAK;SS(0.014)S(0.986)PVGLAK;SS(0.018)S(0.982)PVGLAK;SS(0.012)S(0.988)PVGLAK 197.21 2.98E-05 16828660000 39482190 38087100 30196320 33764660 35855040 38528560 37964070 42862190 46384430 43983410 TRUE FALSE 37939182.36 37000893.2 35653466.74 35507258.15 37008349.92 39307633.88 38428685.64 41977070.8 41119063.97 41004374.46 0.925247193 0.902364533 0.869503979 0.865938296 0.902546385 0.958620498 0.937185023 1.02372177 1.002797006 1 25.28927449 2.259222207 1.222629005 1.010981946 0.890000683 0.815137666 0.022906837 0.188110599 0.545803758 0.015185416 0.008825659 181.6444811 -2.259222207 -0.120981264 VCGS(ph)SQAAGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VCGSSQAAGSR 11 0 H9KV82;Q8N7U6-2;Q8N7U6 H9KV82 EFHB EF-hand domain-containing family member B 1 VCGS(0.5)S(0.5)QAAGSR;VCGS(0.5)S(0.5)QAAGSR 68.171 0.037338 1448990000 200993 221152 165801 226773 188932 188529 233818 223729 216048 231132 TRUE FALSE 193137.9714 214844.9615 195764.9289 238476.7817 195009.1694 192341.1856 236679.5346 219108.918 191523.1368 215477.2238 0.896326619 0.997065758 0.908517965 1.106737768 0.90501059 0.892628846 1.098396993 1.016854191 0.888832395 1 17.71717586 2.25934273 24.99970072 1.007398995 0.956190699 0.087254659 0.077028532 605.4421809 728310.6548 0.026606437 0.022237639 181.694897 -2.25934273 -0.051208296 EHAPLAS(ph)PVENK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHAPLASPVENK 12 0 Q9ULJ3 Q9ULJ3 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 EHAPLAS(1)PVENK 106.36 0.0012437 286070000 585340 546000 498720 559210 598000 476800 536100 416690 538170 522110 TRUE FALSE 562464.2657 530428.6146 588849.798 588070.8951 617235.2131 486441.2227 542660.9522 408085.2059 477079.1978 486747.0247 1.155557686 1.089741874 1.209765583 1.208165362 1.268082149 0.999371744 1.114872664 0.83839281 0.980137882 1 18.89281263 2.259369269 1.667348359 0.935576346 1.178613156 0.598106244 0.079306473 0.232085627 1.288413944 0.041138095 0.025900011 181.7060004 -2.259369269 0.243036809 AKEDFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKEDFLK 7 1 P22694-2;P22694-4;A0A0A0MS54;P22694-9;P22694-6;P22694-7;P22694-5;P22694;P22694-3;P22694-10;P22694-8;B1APG3;B1APF9;B1APF8;B1APG2;B1APG1;B1APF7;B1APG0;K7ENJ5;P17612-2;P17612;Q15136 P22694-2;P17612-2 PRKACB;PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit beta;cAMP-dependent protein kinase catalytic subunit alpha 0 80.239 0.027773 929270000 1795200 1925500 1321200 1786400 2066800 1876600 2386900 2845200 2923200 2751100 FALSE TRUE 1725041.599 1870586.625 1559970.23 1878596.318 2133280.499 1914546.138 2416111.596 2786445.626 2591370.591 2564765.547 0.672592316 0.729340203 0.608231124 0.732463176 0.831764331 0.746479982 0.942039946 1.086432883 1.010373285 1 21.29039552 2.259485841 1.351669449 1.053107928 0.698769402 0.85834739 0.058303204 0.147020763 0.525962692 0.035888215 0.021279255 181.7547799 -2.259485841 -0.354338525 MGS(ph)VER ddPTM_BT-474_Pertuzumab_2h_R1 1 MGSVER 6 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 MGS(1)VER 77.674 0.075312 174820000 162120 150680 81753 88863 135050 117230 149040 140850 147770 139460 TRUE FALSE 155784.1712 146382.7539 96527.58569 93449.23008 139394.0059 119600.4709 150863.9961 137941.3983 130995.7691 130014.25 1.198208436 1.125897769 0.742438507 0.718761444 1.072144061 0.919902787 1.160365084 1.06097138 1.00754932 1 16.98831023 2.259688162 24.96201473 1.065662068 0.954150024 0.085285741 0.148682921 567.3428796 670308.8258 0.05551958 0.046409518 181.8394722 -2.259688162 -0.111512044 KKQPAS(ph)PDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 KKQPASPDGR 10 2 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 KKQPAS(1)PDGR;KKQPAS(1)PDGR;KKQPAS(1)PDGR;KKQPAS(1)PDGR 96.591 0.0052259 451124000 1304877 1155967 1213558 1210184 1273223 1325260 1474198 1611087 1748937 1700215 TRUE FALSE 1253880.964 1122999.953 1432874.926 1272641.741 1314177.374 1352057.665 1492239.676 1577817.49 1550405.004 1585057.924 0.791063182 0.708491429 0.903988999 0.802899202 0.82910369 0.853002054 0.941441731 0.99543207 0.978137758 1 20.59610413 2.259695021 1.231633692 1.000736756 0.800358062 0.774146375 0.044655847 0.213423388 0.628849035 0.028600271 0.016649051 181.842344 -2.259695021 -0.200378693 FLTPIYHPNIDSAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLTPIYHPNIDSAGR 15 0 Q9NPD8 Q9NPD8 UBE2T Ubiquitin-conjugating enzyme E2 T 0 ; 136.17 2.45E-05 710270000 605250 659660 530840 669730 657710 619140 582180 569560 606920 723060 FALSE TRUE 581596.1609 640847.1427 626774.5965 704294.8456 678865.8395 631659.435 589304.893 557798.387 538024.986 674086.5022 0.862791584 0.950689771 0.929813302 1.044813749 1.007090095 0.937059907 0.874227404 0.827487845 0.79815422 1 19.36257421 2.259754056 3.426767693 0.855310932 0.962334837 0.243627482 0.067120067 0.265420374 6.55380194 0.025893062 0.019738968 181.8670639 -2.259754056 0.107023905 RIEYIEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RIEYIEAR 8 1 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 78.098 0.050517 186590000 370790 483560 358690 567430 354870 367460 531680 471260 475230 421000 FALSE TRUE 356299.1169 469769.3423 423513.262 596715.1303 366284.7158 374890.293 538186.8589 461528.3163 421283.8827 392485.295 0.907802461 1.196909408 1.079055107 1.520350285 0.933244431 0.95517029 1.371228084 1.175912377 1.073374947 1 18.58227908 2.259865595 24.99977498 1.177638901 1.1139617 0.011776114 0.18802445 1188.248517 1394315.151 0.065369281 0.054644975 181.9137785 -2.259865595 -0.063677202 NNGAGYFLEHLAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 NNGAGYFLEHLAFK 14 0 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 83.729 0.0084145 448690000 276130 431470 271230 578670 242740 306450 558800 463970 496040 339750 FALSE TRUE 265338.5343 419164.8981 320247.2945 608535.228 250547.9526 312646.629 565638.7616 454388.8574 439731.6188 316738.4299 0.837721316 1.32337872 1.011078115 1.921254798 0.791024798 0.987081451 1.785822964 1.434587074 1.388311544 1 18.27293239 2.260026652 24.99984253 1.450396255 1.166425224 0.107233265 0.349162352 480.5974519 559713.4196 0.118045875 0.09867939 181.9812536 -2.260026652 -0.283971031 WVTYFNKPDIDAWELR ddPTM_BT-474_Pertuzumab_2h_R1 2 WVTYFNKPDIDAWELR 16 1 H3BRI0;H3BNX8;P20674 H3BRI0 COX5A "Cytochrome c oxidase subunit 5A, mitochondrial" 0 ; 162.41 7.38E-09 682500000 340990 553140 288000 852730 283460 362580 712610 597900 543460 401070 FALSE TRUE 327663.7338 537364.9888 340048.0065 896739.4975 292577.7483 369911.616 721331.1343 585553.1561 481768.6992 373905.1717 0.876328435 1.43716918 0.909449861 2.398307286 0.782491847 0.989319336 1.92918202 1.566047224 1.288478298 1 18.5123129 2.260281277 24.99880985 1.516488402 1.259391758 0.034460187 0.488858307 743.8449982 856106.0947 0.166090157 0.138849801 182.0879794 -2.260281277 -0.257096643 NSFNNPAYYVLEGVPHQLLPPEPPS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSFNNPAYYVLEGVPHQLLPPEPPSPAR 28 0 O15357;A0A0A0MTP6;O15357-2 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 1 NSFNNPAYYVLEGVPHQLLPPEPPS(1)PAR;NSFNNPAYYVLEGVPHQLLPPEPPS(1)PAR 131.95 1.30E-05 485250000 198858 202759 170222 194276 189351 194982 154913 194772 170856 193194 TRUE FALSE 191086.4095 196976.5118 200984.902 204302.6076 195441.6469 198924.6696 156808.8716 190749.8901 151461.1432 180108.7983 1.060949889 1.093652913 1.115908295 1.134328859 1.085131036 1.104469474 0.870634156 1.059081466 0.8409425 1 17.45850913 2.26128467 24.86517101 0.956785372 1.100561076 0.613879209 0.060348605 147.1188439 160980.2683 0.019733805 0.016499756 182.5091617 -2.26128467 0.143775704 ATETDKEPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATETDKEPQR 10 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 0 ;;; 113.47 0.001353 1290830000 1833170 1794190 1567420 1639600 1636090 1787710 1949900 2028870 2270030 2248540 FALSE TRUE 1761527.69 1743021.458 1850687.661 1724219.952 1688716.321 1823858.721 1973763.459 1986973.125 2012345.711 2096244.383 0.840325538 0.831497259 0.882858733 0.822528121 0.80559134 0.870060159 0.941571257 0.947872844 0.959976674 1 20.99937549 2.26132667 2.521636538 0.961211927 0.837641747 0.874690659 0.022672281 0.098514858 1.285333456 0.009895268 0.007100067 182.5268128 -2.26132667 -0.12357018 EKPYDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKPYDSK 7 1 P16422;B5MCA4 P16422 EPCAM Epithelial cell adhesion molecule 0 87.181 0.017812 345070000 577040 1091400 504190 1255400 662720 949080 1628300 1964000 1769600 1264100 FALSE TRUE 554488.6388 1060274.341 595308.3486 1320191.344 684036.9907 968271.0479 1648227.622 1923442.714 1568722.427 1178481.381 0.470511158 0.899695454 0.505148709 1.120247944 0.58043937 0.821626089 1.398603023 1.632136701 1.331138915 1 20.16849753 2.261497627 4.768873391 1.423805357 0.734538865 0.609309288 0.235534338 0.108765836 6.100926119 0.081178563 0.064273735 182.5986773 -2.261497627 -0.689266492 ANHLVPEVPTVPAHPLTYEEEEVAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ANHLVPEVPTVPAHPLTYEEEEVAGR 26 0 O15156;O15156-2 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 0 ; 95.255 0.0044812 334580000 115308 112688 97930 124983 113993 107851 96007 87673 103385 105764 FALSE TRUE 110801.6359 109474.2486 115628.1294 131433.3876 117659.6884 110031.8211 97181.96238 85862.52191 91649.16823 98600.51008 1.123743029 1.110280753 1.172693015 1.332988922 1.193296954 1.115935618 0.985613181 0.870812147 0.92949994 1 16.58930749 2.261572096 2.481812588 0.920005448 1.187951561 0.759290022 0.06418538 0.137418457 1.735834253 0.029780784 0.021283322 182.6299902 -2.261572096 0.267946113 QFTPCQLLADHANSPNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 QFTPCQLLADHANSPNKK 18 1 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 143.46 6.84E-08 392520000 124780 179540 119910 217590 117810 139040 221290 209010 178490 146610 FALSE TRUE 119903.4596 174419.695 141580.4044 228819.846 121599.4656 141851.4841 223998.2132 204693.8705 158228.5635 136679.9741 0.877256968 1.276117413 1.035853316 1.674128543 0.88966556 1.037836632 1.638851739 1.497614203 1.157657254 1 17.06044235 2.261592657 24.99903525 1.388988123 1.147651828 0.086259903 0.271471389 433.8061306 470852.8684 0.092284396 0.077163334 182.6386369 -2.261592657 -0.241336296 LKS(ph)EDGVEGDLGETQSR ddPTM_BT-474_Pertuzumab_2h_R1 7 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(0.991)EDGVEGDLGET(0.009)QSR;LKS(0.823)EDGVEGDLGET(0.088)QS(0.088)R;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR 258.31 2.23E-27 19085330000 5891920 5783360 4948610 5475870 6135600 5424740 3385470 4084550 3206900 2601400 TRUE FALSE 5661657.253 5618424.235 5842933.908 5758480.307 6332957.146 5534431.96 3426902.395 4000202.615 2842866.156 2425204.861 2.334506806 2.316680263 2.409253751 2.374430466 2.61130812 2.282047199 1.413036255 1.649428747 1.172216913 1 21.20967519 2.261766674 4.264829255 1.384680562 2.406530758 0.896459022 0.179350747 0.064320101 2.661787829 0.066742934 0.05231754 182.7118327 -2.261766674 1.021850197 up QPLTS(ph)PSALVDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPLTSPSALVDSK 13 0 Q14865;Q14865-2 Q14865 ARID5B AT-rich interactive domain-containing protein 5B 1 QPLT(0.044)S(0.95)PS(0.005)ALVDSK 123.76 0.00023044 67528000 150000 153210 127600 152060 186370 168830 125540 167810 156690 153710 TRUE FALSE 144137.8342 148840.6008 150660.1584 159907.8348 192364.7603 172243.8583 127076.3961 164344.6649 138903.2081 143299.0848 1.005853138 1.03867098 1.051368602 1.115902694 1.342400481 1.201988544 0.8867914 1.146864721 0.969323763 1 17.12866987 2.262104916 24.99965802 1.02282108 1.128040708 0.232813443 0.108459589 434.4477061 461301.0241 0.040658527 0.033999027 182.8541899 -2.262104916 0.105219628 KMESDFEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KMESDFEQK 9 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 124.1 0.00086432 283910000 570340 535000 489310 466600 474490 551760 609760 636350 756370 683490 FALSE TRUE 548050.4823 519742.3238 577739.2016 490681.2819 489752.4018 562916.9652 617222.4253 623209.1501 670510.0486 637196.6135 0.860096351 0.815670254 0.906689065 0.770062602 0.768604841 0.883427428 0.968653022 0.978048434 1.052281249 1 19.28137907 2.262350185 2.295357834 1.00356892 0.825041037 0.795989856 0.042169292 0.137862912 1.48527264 0.019450935 0.013609263 182.9574866 -2.262350185 -0.178527883 ISMPDFDLHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISMPDFDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 172.17 1.37E-05 4010700000 6456700 6786300 6165000 6990900 5888800 6397000 7272000 6932300 7893300 7496800 FALSE TRUE 6204365.026 6592761.368 7279152.64 7351701.187 6078218.6 6526351.723 7360996.911 6789145.582 6997285.675 6989035.059 0.887728417 0.943300658 1.041510391 1.05189073 0.869679226 0.933798682 1.053220774 0.97139956 1.001180509 1 22.73666185 2.262452609 24.99978339 1.002322323 0.958641155 0.16014832 0.057368712 544.225863 569458.1555 0.021247795 0.017768686 183.0006401 -2.262452609 -0.043681168 LEDTYFDRDVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEDTYFDRDVEK 12 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;;; 218.5 3.12E-11 9379990000 9217550 8029530 7679430 7888970 9147410 8828030 10718940 10483110 12909730 12039130 FALSE TRUE 8857317.955 7800535.666 9067273.829 8296120.687 9441644.75 9006538.815 10850121.59 10266630.12 11444271.57 11223709 0.789161404 0.69500516 0.807867865 0.739160351 0.841223231 0.802456551 0.966714443 0.91472704 1.019651487 1 23.42004617 2.262490584 0.79449147 1.006384132 0.749921028 0.830259358 0.043725767 0.227968681 0.276431014 0.031808361 0.019570966 183.0166426 -2.262490584 -0.256463104 RAPS(ph)TSPSFEGTQETYTVAHEENVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RAPSTSPSFEGTQETYTVAHEENVR 25 1 Q9BUT9 Q9BUT9 FAM195A Protein FAM195A 1 RAPS(0.333)T(0.333)S(0.333)PS(0.002)FEGTQETYTVAHEENVR;RAPS(0.327)T(0.327)S(0.327)PS(0.019)FEGTQETYTVAHEENVR 266.24 9.34E-46 462410000 25538 28058 21860.5 25072.8 37526 28278 18093.5 23600 28189 24856 TRUE FALSE 24539.94673 27257.81331 25811.17863 26366.81021 38733.05787 28849.80053 18314.93367 23112.65175 24989.1029 23172.48098 1.059012488 1.176301033 1.113872039 1.137850118 1.671511044 1.245002663 0.79037431 0.997418091 1.078395659 1 14.5001249 2.263376798 24.77210636 0.96337835 1.241372052 0.36711003 0.171800551 226.0572042 225654.8994 0.06307271 0.052748063 183.3904845 -2.263376798 0.277993702 ELQAQIAELQEDFESEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELQAQIAELQEDFESEK 17 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 286.74 3.96E-36 71924000 219338 205807 189034 179818 208426 211345 225734 242275 272270 248704 FALSE TRUE 210766.0285 199937.5859 223196.6488 189098.4285 215130.2116 215618.5407 228496.6002 237271.9366 241363.051 231859.0566 0.909026508 0.862323814 0.962639339 0.815574907 0.927849077 0.929955223 0.985497843 1.023345562 1.040990396 1 17.82288855 2.263445077 1.546170756 1.025658304 0.892028491 0.694878908 0.037351521 0.203280328 0.964460061 0.019385742 0.011969615 183.419319 -2.263445077 -0.133629814 S(ph)PPDGQSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPDGQSFR 9 0 P78314;P78314-3;P78314-4;H0YAD9 P78314 SH3BP2 SH3 domain-binding protein 2 1 S(1)PPDGQSFR 82.954 0.017825 363610000 148080 118100 104650 138040 124260 128310 111210 127880 124020 141100 TRUE FALSE 142292.8699 114731.9036 123562.5829 145164.2609 128256.9358 130904.5161 112571.0212 125239.2333 109941.7695 131543.1713 1.081719929 0.872199617 0.939331032 1.103548436 0.975017817 0.9951449 0.855772444 0.952077041 0.835784697 1 17.00517683 2.26351959 24.91973998 0.909927237 0.990499217 0.228443304 0.075030095 334.785011 334257.631 0.02538824 0.021232676 183.4507915 -2.26351959 0.080571979 RIENAK ddPTM_BT-474_Pertuzumab_2h_R1 4 RIENAK 6 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 105.2 0.053201 3027370000 2915580 2888940 2364010 2621840 2586340 2604330 3000160 2878990 2920830 3367520 FALSE TRUE 2801635.91 2806550.26 2791239.194 2757153.477 2669531.975 2656991.337 3036876.856 2819537.85 2589269.624 3139434.871 0.892401348 0.893966709 0.889089696 0.878232418 0.850322458 0.846327905 0.967332332 0.898103629 0.824756598 1 21.58207345 2.263539258 24.99985227 0.914250278 0.875574233 0.198448779 0.045546385 442.7791123 443153.8664 0.015550073 0.013005281 183.4590999 -2.263539258 -0.038676046 ASLRDEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASLRDEK 7 1 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753;Q8N9L9 Q86TX2;Q8N9L9 ACOT1;ACOT2;ACOT4 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial;Acyl-coenzyme A thioesterase 4" 0 ;; 127.56 0.0035044 814170000 870700 927890 721510 991510 796300 856260 1151520 1071180 1100740 1030860 FALSE TRUE 836672.0814 901427.4857 851902.9069 1042681.95 821913.7127 873574.1639 1165612.646 1049059.759 975788.6099 961038.934 0.870591244 0.93797187 0.886439536 1.08495287 0.855234563 0.908989358 1.212867247 1.091589239 1.015347636 1 19.87423535 2.263652395 24.99957466 1.092487107 0.927142546 0.47249746 0.08023281 181.5069504 180839.3459 0.027327757 0.022855549 183.5068984 -2.263652395 -0.165344561 SEFYANEACKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEFYANEACKR 11 1 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753;P49753-2 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ; 96.745 0.010877 589150000 222546 284880 178912 219740 212507 223950 265460 256740 274170 260340 FALSE TRUE 213848.6563 276755.5013 211245.3783 231080.8077 219342.4806 228478.4224 268708.7789 251438.2293 243047.371 242706.9399 0.881098235 1.140286724 0.870372221 0.952098065 0.903733864 0.941375729 1.107132655 1.035974618 1.001402643 1 17.88885584 2.263866168 24.98483898 1.041216634 0.951517489 0.24332469 0.075643965 309.0354397 305117.8104 0.025495466 0.021323639 183.5972485 -2.263866168 -0.089699145 ASPVPSDPEKPGT(ph)PGEGMLSSDLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPVPSDPEKPGTPGEGMLSSDLDR 25 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ASPVPSDPEKPGT(0.998)PGEGMLS(0.001)S(0.001)DLDR;ASPVPS(0.001)DPEKPGT(0.989)PGEGMLS(0.005)S(0.006)DLDR 114.61 0.0028384 455280000 705480 654700 529180 584770 660670 654790 714540 801470 828240 804820 TRUE FALSE 677909.0617 636028.597 624814.5975 614950.0498 681921.0506 668030.3024 723284.7543 784919.3644 734221.6675 750308.8245 0.903506715 0.84768908 0.832743235 0.819595918 0.908853832 0.890340458 0.963982737 1.046128392 0.978559286 1 19.517125 2.263960197 1.705771031 1.015128982 0.856371542 0.817295863 0.030782791 0.140252504 0.817418404 0.016288286 0.010378824 183.6370034 -2.263960197 -0.15875744 TCPSLS(ph)PTSPLNNK ddPTM_BT-474_Pertuzumab_2h_R1 1 TCPSLSPTSPLNNK 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 TCPS(0.001)LS(0.984)PT(0.012)S(0.003)PLNNK 116.96 0.00095543 0 104240 108220 83999 92419 96455 103920 82405 88257 128700 105090 TRUE FALSE 100166.1856 105133.6716 99179.48785 97188.75567 99557.56267 106021.3336 83413.49704 86434.46211 114090.5156 97972.1607 1.02239437 1.073097407 1.012323166 0.9920038 1.016182168 1.082157756 0.851399994 0.882234928 1.164519745 1 16.58008424 2.2639668 24.99997754 0.951839252 1.031276465 0.081563807 0.083085194 401.8649982 395438.511 0.029228958 0.024446069 183.6397952 -2.2639668 0.079437213 RVEEELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVEEELEK 8 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 137.95 0.0011642 314630000 406110 424370 367380 375050 444430 432330 346180 414890 461080 411960 FALSE TRUE 390238.7722 412267.3831 433773.7383 394406.3754 458725.4946 441072.0088 350416.6544 406322.3765 408740.1314 384057.5823 1.016094435 1.073452009 1.129449745 1.026945942 1.194418534 1.148452808 0.912406552 1.057972542 1.064267835 1 18.55096311 2.264223934 24.99999542 1.014648118 1.099577565 0.321548702 0.063411629 285.5489733 278167.3609 0.022266844 0.01862331 183.7485559 -2.264223934 0.084929447 VNLDALTQHLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNLDALTQHLDK 12 0 Q8NFV4;Q8NFV4-4;Q8NFV4-6 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 ; 159.52 6.66E-05 1594680000 2582100 3346200 2263000 4608700 2378600 2375400 4536000 3706400 3510700 2736300 FALSE TRUE 2481188.677 3250769.652 2671974.44 4846555.559 2455109.829 2423432.216 4591512.925 3629861.545 3112180.054 2550967.964 0.972645957 1.274327902 1.047435514 1.899888838 0.962422839 0.950004959 1.799910069 1.422934979 1.219999662 1 21.28261335 2.264464509 24.99680867 1.413274038 1.204738936 0.055036274 0.323732257 577.2242069 557009.5754 0.111309536 0.093098231 183.8503704 -2.264464509 -0.208535102 DFYLATS(ph)PPDSFLDDHHLTR ddPTM_BT-474_Pertuzumab_2h_R1 3 DFYLATSPPDSFLDDHHLTR 20 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 DFYLAT(0.081)S(0.917)PPDS(0.001)FLDDHHLTR;DFYLAT(0.007)S(0.993)PPDSFLDDHHLTR;DFYLAT(0.218)S(0.775)PPDS(0.006)FLDDHHLT(0.001)R 100.08 0.00094569 382030000 527110 509280 501177 395625 440893 410850 374883 141222 391232 415129 TRUE FALSE 506509.9584 494755.833 591750.8325 416043.2537 455074.7238 419157.6685 379470.9303 138305.7163 346820.9835 387011.9431 1.308770873 1.278399393 1.529024732 1.075013991 1.175867391 1.083061327 0.98051478 0.357368083 0.896150596 1 18.56201856 2.264833413 1.89989938 0.684877384 1.276046343 0.544971466 0.199365805 0.219597003 1.602673469 0.097495244 0.064421561 184.0066051 -2.264833413 0.59116896 DSENKGPAFVNPLIPESPEEEELFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSENKGPAFVNPLIPESPEEEELFR 25 1 H7C5Q2;Q9Y305-3;Q9Y305-2;Q9Y305;Q9Y305-4 H7C5Q2 ACOT9 "Acyl-coenzyme A thioesterase 9, mitochondrial" 0 ; 120.85 0.00017206 105289000 146001 212357 132709 250833 122507 174087 249854 245325 221999 173978 FALSE TRUE 140295.1195 206300.7863 156692.4684 263778.5212 126447.5489 177607.1584 252911.788 240258.953 196798.6042 162194.3151 0.864981731 1.271935987 0.966078671 1.626311755 0.779605308 1.095027026 1.559313518 1.481303169 1.213350814 1 17.30736373 2.264924837 24.9279688 1.374629821 1.111625038 0.118072786 0.263624172 346.5485234 327668.265 0.08771516 0.073367408 184.0453449 -2.264924837 -0.263004783 RLS(ph)LPGLLS(ph)QVSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSLPGLLSQVSPR 14 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 2 RLS(1)LPGLLS(0.733)QVS(0.267)PR 109.05 0.0026279 0 144860 160380 131650 148270 140040 143000 149340 138410 161320 154020 TRUE FALSE 139198.711 155806.1194 155442.0835 155922.2325 144544.5138 145891.558 151167.6676 135551.7851 143007.6299 143588.0882 0.969430771 1.085090841 1.082555562 1.085899495 1.006660898 1.016042207 1.052786965 0.944032244 0.995957476 1 17.13157655 2.265036808 1.101194145 0.978765153 1.054252655 0.273149611 0.040815799 0.57372046 1.341756136 0.027737469 0.016036709 184.0928019 -2.265036808 0.075487502 VS(ph)SQAEDTSSSFDNLFIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSSQAEDTSSSFDNLFIDR 19 0 H8Y6P7;P0CAP2-3;P0CAP2;Q9BZD3 H8Y6P7 GCOM1;POLR2M;GCOM2 DNA-directed RNA polymerase II subunit GRINL1A;Putative GRINL1B complex locus protein 2 1 VS(0.5)S(0.5)QAEDTSSSFDNLFIDR 77.468 0.012079 37271000 45924 48582 43640 53870 55943 49330 29553 37790 35209 37255 TRUE FALSE 44129.23931 47196.48893 51526.71877 56650.23716 57742.4574 50327.4864 29914.67845 37009.62329 31212.22193 34731.68567 1.2705758 1.35888852 1.483565159 1.631082283 1.662529655 1.449036677 0.861307992 1.065586728 0.898667062 1 15.08396481 2.265069095 9.829371107 0.9694131 1.48696629 0.818737824 0.119634136 0.147086366 52.22128391 0.045596103 0.037710487 184.1064885 -2.265069095 0.517553191 VREAAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VREAAEK 7 1 P38646;H0YBG6;A0A3B3ITN1 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 99.136 0.0098044 1171040000 1073580 1285030 947160 1243190 879130 952070 1415050 1261040 1226590 1098930 FALSE TRUE 1031623.307 1248382.203 1118332.881 1307351.185 907408.0149 971321.5077 1432367.805 1234999.083 1087352.645 1024498.492 1.006954441 1.218530053 1.091590559 1.27608893 0.885709468 0.948094619 1.398116069 1.20546696 1.061351143 1 19.96648643 2.265084991 24.99980882 1.193395248 1.079673864 0.078427215 0.146669423 484.4303655 456584.9219 0.051484638 0.043063021 184.1132272 -2.265084991 -0.113721384 ASTVS(ph)PGGYMVPK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASTVSPGGYMVPK 13 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 AST(0.003)VS(0.996)PGGY(0.001)MVPK;ASTVS(1)PGGYMVPK;ASTVS(1)PGGYMVPK;ASTVS(1)PGGYMVPK 323.68 2.58E-51 1266590000 1361710 1264940 1108630 1203230 1207080 1268280 1380530 1493380 1504930 1486840 TRUE FALSE 1308492.868 1228865.15 1308984.102 1265328.844 1245906.824 1293925.491 1397425.339 1462541.181 1334096.656 1386135.002 0.9439866 0.886540739 0.944340991 0.912846759 0.898835122 0.93347725 1.008145193 1.055121744 0.962457952 1 20.40263634 2.265101456 4.086864278 1.016747307 0.916976885 0.703643323 0.027351719 0.100434324 3.705787647 0.009908609 0.007753583 184.1202077 -2.265101456 -0.099770422 TLNDELEIIEGMK ddPTM_BT-474_Pertuzumab_2h_R1 4 TLNDELEIIEGMK 13 0 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 229.97 1.14E-11 225854000 344154 468915 317033 624733 331165 396527 643503 607085 511794 412830 FALSE TRUE 330704.0812 455542.0033 374327.9155 656975.545 341817.223 404545.0476 651378.3822 594548.4826 453697.2907 384868.6564 0.85926478 1.183629781 0.972612109 1.707012338 0.888139934 1.051124951 1.692469292 1.544808788 1.178836684 1 18.55400666 2.265115798 24.98966727 1.425471693 1.124397476 0.127892123 0.287202626 345.8632395 325472.3768 0.097788347 0.081793641 184.1262881 -2.265115798 -0.301074218 DDAMLLK ddPTM_BT-474_Pertuzumab_2h_R1 3 DDAMLLK 7 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 108.09 0.017057 302611000 547040 743050 591540 999820 533590 615500 985170 890490 809140 674670 FALSE TRUE 525661.072 721858.9415 698444.4367 1051420.83 550753.4069 627945.8317 997226.8052 872101.0703 717289.8194 628974 0.835743722 1.147676918 1.110450411 1.671644345 0.875637796 0.998365325 1.585481761 1.386545502 1.140412512 1 19.26264086 2.265141707 24.9994441 1.328316366 1.123816626 0.080191873 0.259577423 473.5738233 445393.294 0.090557306 0.075745713 184.137273 -2.265141707 -0.204499741 VNGDAS(ph)PAAAESGAK ddPTM_BT-474_Pertuzumab_2h_R1 6 VNGDASPAAAESGAK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK 284.96 5.18E-34 7247720000 5386210 5292940 5402460 5237430 5529510 5868310 6671320 7721980 7865420 6932620 TRUE FALSE 5175710.958 5141990.534 6378804.699 5507734.39 5707371.711 5986971.249 6752965.61 7562518.415 6972570.496 6463067.472 0.800813388 0.795595985 0.986962418 0.85218581 0.883074753 0.926335873 1.044854574 1.170112868 1.078833004 1 22.62378762 2.265260864 2.471516247 1.103650289 0.867735957 0.70617413 0.063784426 0.145341753 1.820891554 0.027641563 0.019795927 184.1878014 -2.265260864 -0.235914332 EGNQEVPFDVPELWYEDEKHSLNSSSASTTEPDFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGNQEVPFDVPELWYEDEKHSLNSSSASTTEPDFQK 36 1 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 243.58 4.37E-50 130392000 139022 211626 113553 215347 121365 150705 229657 211048 206046 155323 FALSE TRUE 133588.8665 205590.6337 134074.5531 226461.0845 125268.8154 153752.3584 232467.6111 206689.785 182656.5219 144802.8349 0.922556984 1.419797022 0.925911107 1.563927148 0.865099192 1.061804891 1.605407873 1.427387698 1.261415373 1 17.14373032 2.265360622 24.99830623 1.375272077 1.13872831 0.112735151 0.253392225 373.0084573 347930.7853 0.082950559 0.069383377 184.2301143 -2.265360622 -0.236543768 SQEEPKDTFEHDPSESIDEFNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQEEPKDTFEHDPSESIDEFNK 22 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 220.25 6.20E-26 1115190000 919420 741900 583090 569880 717730 759510 775940 788790 1008070 841740 FALSE TRUE 883488.0499 720741.7384 688467.3338 599291.5751 740816.4373 774867.8126 785436.1858 772501.2109 893638.1198 784728.2001 1.125852301 0.918460351 0.87733222 0.763693181 0.944042074 0.987434646 1.000902205 0.984418823 1.138786805 1 19.58183352 2.265488876 1.379411453 1.039893134 0.916297689 0.226811152 0.091995595 0.661731247 2.473400039 0.056499764 0.033865456 184.2845286 -2.265488876 -0.123595446 VGGTSDVEVNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGGTSDVEVNEK 12 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 212.72 3.94E-08 149780000 121340 162470 118580 207220 103180 139270 178720 179330 169950 133340 FALSE TRUE 116597.8987 157836.5147 140010.0438 217914.649 106498.8784 142086.1348 180907.2288 175626.7728 150657.9885 124308.763 0.937970066 1.269713501 1.12630872 1.753011161 0.856728647 1.143009804 1.455305518 1.412826968 1.211965953 1 16.92356848 2.265562378 24.9763298 1.32142984 1.193908529 0.011346854 0.254219005 713.2801895 659773.8205 0.086639712 0.072470878 184.3157203 -2.265562378 -0.127521312 DYQDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYQDNK 6 0 P47813;O14602;X6RAC9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 102.72 0.082123 376400000 816600 676580 698940 651310 722550 680790 842390 760120 802710 933810 FALSE TRUE 784686.3692 657284.6008 825254.0058 684924.1872 745791.477 694556.0402 852699.4208 744423.2564 711589.726 870562.2169 0.901355875 0.755011633 0.947955229 0.786760755 0.856677975 0.797824701 0.97948131 0.855106323 0.817391006 1 19.73158788 2.265707491 24.99984419 0.898817447 0.840143839 0.180786606 0.072675488 426.0862027 392385.6966 0.023657841 0.019789097 184.3773171 -2.265707491 -0.058673608 KEDEGQYECHVTEWVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEDEGQYECHVTEWVR 16 1 O75054;O75054-2 O75054 IGSF3 Immunoglobulin superfamily member 3 0 136.2 1.21E-05 110370000 71548 102500 65884 120250 59387 85547 120650 116730 114460 84130 FALSE TRUE 68751.82506 99576.80036 77790.70438 126456.1169 61297.23679 87276.81895 122126.5508 114319.4847 101466.9807 78431.80016 0.87658099 1.269597283 0.991826073 1.6123067 0.781535508 1.112773375 1.557105033 1.457565483 1.29369695 1 16.25915109 2.265775029 24.42003325 1.381969166 1.117687356 0.137875196 0.253929188 259.1673145 232554.9282 0.084087564 0.070333823 184.4059922 -2.265775029 -0.26428181 DKFEEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DKFEEDR 7 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;; 96.331 0.011683 5681100000 8290100 8184500 7982400 8312600 8893100 9398700 10882100 10933800 13588200 13081100 FALSE TRUE 7966113.727 7951086.073 9424997.248 8741614.282 9179154.638 9588748.154 11015278.4 10708013.21 12045724.5 12195105.45 0.65322221 0.65198994 0.77285082 0.716813341 0.752691699 0.786278413 0.903254051 0.878058272 0.987750746 1 23.5397989 2.265839077 0.497349644 1.014529578 0.657238764 0.915074403 0.035028626 0.251664818 0.131859738 0.033335679 0.03059925 184.4331898 -2.265839077 -0.357290814 AMEVDERPTEQYSDIGGLDK ddPTM_BT-474_Pertuzumab_2h_R1 8 AMEVDERPTEQYSDIGGLDK 20 1 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;;;;;; 203.64 9.50E-22 4718900000 6582980 6240320 5155170 5696080 6091110 6364000 6565860 7440430 7635890 7718040 FALSE TRUE 6325709.864 6062352.184 6086823.895 5990055.371 6287036.085 6492684.44 6646214.959 7286782.52 6769095.779 7195290.276 0.879145889 0.842544491 0.845945565 0.832496695 0.873771015 0.902351982 0.923689622 1.012715574 0.940767574 1 22.77862146 2.267279084 1.368269271 0.987292339 0.850449127 0.852524517 0.023217068 0.141706279 0.520963003 0.013351509 0.008000949 185.0457366 -2.267279084 -0.136843212 GVDDLDFFIGDEAIEKPTYATK ddPTM_BT-474_Pertuzumab_2h_R1 4 GVDDLDFFIGDEAIEKPTYATK 22 1 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 292.19 1.86E-55 2475480000 3407090 3240490 2858880 2890660 3163770 3261660 3651590 3937420 4178070 3986200 FALSE TRUE 3273937.156 3148074.398 3375543.211 3039847.309 3265535.535 3327613 3696279.251 3856110.901 3703793.009 3716211.123 0.880987933 0.847119363 0.908329236 0.817996397 0.87872713 0.895431634 0.994636507 1.03764581 0.996658394 1 21.82540104 2.267287536 2.82633243 1.016777024 0.866232022 0.8829731 0.024439394 0.07533679 1.239193766 0.009541259 0.007068088 185.0493383 -2.267287536 -0.150545001 TIVEELLADSEFRR ddPTM_BT-474_Pertuzumab_2h_R1 2 TIVEELLADSEFRR 14 1 Q5QJE6 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 ; 212.17 4.52E-09 59257000 47712 53557 34581 44308 43547 47830 40589 47282 45381 44239 FALSE TRUE 45847.36229 52029.6068 40830.55595 46594.74119 44947.7288 48797.15537 41085.74032 46305.61018 40229.53913 41242.65313 1.111649199 1.261548491 0.990007986 1.129770702 1.089836017 1.183172072 0.996195376 1.122760217 0.975435286 1 15.33184952 2.267417277 0.213304728 0.96772341 1.196686472 0.256390565 0.077657093 4.902291238 0.731475429 0.233613549 0.399156825 185.1046281 -2.267417277 0.228963063 DDFLDLAESPNAS(ph)DTECSDEIPLKVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDFLDLAESPNASDTECSDEIPLKVPR 27 1 Q6IC98;X6RIP6 Q6IC98 GRAMD4 GRAM domain-containing protein 4 1 DDFLDLAES(0.13)PNAS(0.703)DT(0.141)ECS(0.026)DEIPLKVPR 51.234 0.063072 21169000 14406 19437 11158 20602 12325 18861 15895 24710 18107 16019 TRUE FALSE 13842.99759 18882.67579 13174.49881 21665.27169 12721.44482 19242.38234 16089.52776 24199.72986 16051.56927 14934.01886 0.926943894 1.264406853 0.882180405 1.450732846 0.851843361 1.28849324 1.077374276 1.620443237 1.07483253 1 13.86631484 2.267612256 2.327270187 1.292478583 1.099773429 0.00499147 0.241765146 0.654755457 7.259710546 0.099806756 0.07044716 185.1877505 -2.267612256 -0.192705154 FEDYLREPAQGDLGCGSPPHRPPAPS(ph)SPEGPDTGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 FEDYLREPAQGDLGCGSPPHRPPAPSSPEGPDTGQK 36 2 Q8N573-2 Q8N573-2 OXR1 Oxidation resistance protein 1 1 FEDYLREPAQGDLGCGSPPHRPPAPS(0.538)S(0.462)PEGPDTGQK 147.37 1.85E-13 73830000 29451 34163 26433 27610 33572 33387 23774 30570 32100 35112 TRUE FALSE 28300.02236 33188.70469 31210.0311 29034.95541 34651.87387 34062.10802 24064.95332 29938.71882 28456.14257 32733.83297 0.864549605 1.013896073 0.953448719 0.887001392 1.05859506 1.040578048 0.735170652 0.914610851 0.869318989 1 14.99849492 2.267635925 24.99999915 0.872243573 0.97123397 0.21494217 0.083646833 287.1005585 246858.4412 0.028038175 0.023454834 185.1978435 -2.267635925 0.098990397 TNILQYASTRPPTLS(ph)PIPHIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TNILQYASTRPPTLSPIPHIPR 22 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TNILQYASTRPPT(0.005)LS(0.995)PIPHIPR;TNILQYASTRPPT(0.001)LS(0.999)PIPHIPR 297.62 7.99E-56 4352500000 2551100 2342400 2004420 2568500 2223500 2160300 2362100 2218200 2282000 2445000 TRUE FALSE 2451400.192 2275597.045 2366663.282 2701060.593 2295020.897 2203982.746 2391008.086 2172393.395 2022956.927 2279397.972 1.075459495 0.998332487 1.038284368 1.184988592 1.00685397 0.96691441 1.048964733 0.953055772 0.887496151 1 21.1202214 2.267671474 1.059492827 0.947241293 1.061905517 0.364195539 0.060312347 0.594248251 1.284268734 0.042917257 0.02485255 185.2130035 -2.267671474 0.114664225 DRYSAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRYSAGK 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 114.2 0.0054338 2811900000 3078500 2833100 2415470 2802500 2756290 2851100 3139100 3253800 3565200 3425700 FALSE TRUE 2958188.817 2752302.762 2851999.161 2947137.361 2844948.571 2908751.195 3177517.245 3186607.893 3160493.443 3193674.288 0.926265032 0.861798203 0.893015037 0.922804612 0.890807363 0.910785175 0.994940923 0.997787378 0.989610448 1 21.60678575 2.268273267 4.499849701 0.996376838 0.898244143 0.882155805 0.016986542 0.060681601 2.828118589 0.006168698 0.004886765 185.4698272 -2.268273267 -0.098132695 TTFEDLIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTFEDLIQR 9 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8;H0YAF5 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 141.52 0.0002478 457310000 541010 546450 476540 518950 547380 526160 617550 631430 575450 591540 FALSE TRUE 519866.7311 530865.781 562661.3786 545733.0717 564986.9748 536799.3157 625107.7616 618390.7498 510127.3285 551474.4689 0.942685039 0.962629842 1.020285453 0.989589006 1.024502505 0.973389243 1.133520765 1.121340669 0.92502438 1 19.07293457 2.268723803 24.99950371 1.064983596 0.988011341 0.156217636 0.060805544 275.0096315 227929.2876 0.021422256 0.017921133 185.662333 -2.268723803 -0.076972255 EVHDELEDLPSPPPPLS(ph)PPPTTSPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVHDELEDLPSPPPPLSPPPTTSPHK 26 0 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 1 EVHDELEDLPSPPPPLS(0.865)PPPT(0.041)T(0.041)S(0.052)PHK 86.304 0.021573 98851000 52267 51721 48941 54179 49570 56082 66037 70644 75028 78982 TRUE FALSE 50224.34786 50245.96772 57785.72739 56975.18468 51164.46407 57216.01646 66845.18056 69185.17671 66511.13598 73632.47879 0.68209503 0.682388649 0.784785849 0.773777898 0.694862714 0.777048626 0.907821951 0.939601353 0.903285304 1 16.16805465 2.268831958 2.67148727 0.939288186 0.727220566 0.86888971 0.03964758 0.097351315 1.428142471 0.017024046 0.012469046 185.7085753 -2.268831958 -0.212067619 LFVGNLPADITEDEFKR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFVGNLPADITEDEFKR 17 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 260.24 4.96E-27 6175260000 1712880 1567690 1239390 1264970 1409380 1458530 1538220 1633150 1649490 1712410 FALSE TRUE 1645938.756 1522981.016 1463375.343 1330255.253 1454713.988 1488022.476 1557045.196 1599424.882 1462246.81 1596426.945 1.031014141 0.953993554 0.91665663 0.833270359 0.911231166 0.932095565 0.975331318 1.001877904 0.915949718 1 20.6064151 2.269033222 4.747397904 0.976876026 0.924463221 0.146163097 0.050654501 0.353141156 18.88662145 0.019685498 0.015681943 185.7946574 -2.269033222 -0.052412804 DKAIT(ph)PPLPESTVPFSNGVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKAITPPLPESTVPFSNGVLK 21 1 Q92667-2;Q92667;I3NI36 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 DKAIT(1)PPLPESTVPFSNGVLK;DKAIT(1)PPLPESTVPFSNGVLK 117.08 0.00018534 715570000 522230 564420 423190 519650 428850 541400 639000 759870 712200 626300 TRUE FALSE 501820.6742 548323.2942 499669.8468 546469.1988 442644.3497 552347.4789 646820.2731 744178.419 631354.0418 583880.1431 0.859458367 0.939102486 0.855774687 0.935927014 0.758108243 0.945994628 1.107796319 1.274539694 1.081307609 1 19.15531272 2.269788187 3.468369078 1.15730294 0.875113481 0.657091748 0.082303574 0.118967514 2.994721785 0.030572333 0.023521404 186.1179187 -2.269788187 -0.282189459 AFVDFLSDEIKEER ddPTM_BT-474_Pertuzumab_2h_R1 6 AFVDFLSDEIKEER 14 1 Q07021 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;;;; 283.82 1.59E-33 2712762000 2393655 3195950 2300333 4181140 2125461 2801720 4499780 4149650 3619700 3052220 FALSE TRUE 2300108.316 3104804.635 2716054.344 4396929.136 2193828.383 2858372.698 4554849.654 4063958.277 3208806.831 2845490.421 0.808334584 1.091131642 0.954511856 1.545227179 0.77098428 1.004527261 1.600725703 1.428210142 1.127681474 1 21.44024589 2.269920492 24.99947404 1.345767315 1.040272833 0.190627426 0.251282136 268.6649754 214173.434 0.085630604 0.071637303 186.174627 -2.269920492 -0.305494482 AGVNSDS(ph)PNNCSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGVNSDSPNNCSGK 14 0 Q9Y4C1;F8WE62 Q9Y4C1 KDM3A Lysine-specific demethylase 3A 1 AGVNSDS(1)PNNCSGK;AGVNSDS(1)PNNCSGK 347.24 8.76E-82 356600000 576590 559190 507900 552470 559520 567790 653820 696090 690470 640410 TRUE FALSE 554056.2253 543242.4487 599688.8282 580983.0429 577517.4689 579271.1028 661821.6447 681715.4982 612090.7403 597034.4603 0.928013812 0.909901329 1.004445921 0.973114756 0.967310109 0.97024735 1.108514983 1.141836098 1.025218444 1 19.18745468 2.269954952 7.585530381 1.088268711 0.959355799 0.569308961 0.045677256 0.122951809 23.47431267 0.016283274 0.013393128 186.1893998 -2.269954952 -0.128912912 WGQPPSPT(ph)PVPRPPDADPNTPSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 WGQPPSPTPVPRPPDADPNTPSPK 24 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.425)PT(0.573)PVPRPPDADPNT(0.001)PS(0.001)PK;WGQPPS(0.171)PT(0.829)PVPRPPDADPNTPSPK 192.55 1.11E-17 3370200000 1280620 1106330 1141980 1290370 1279690 1220930 1401660 1614250 1673590 1744990 TRUE FALSE 1230571.955 1074778.552 1348361.189 1356966.15 1320852.391 1245618.041 1418813.934 1580915.173 1483611.079 1626800.273 0.756437022 0.660670255 0.82884249 0.834131991 0.811932733 0.765685906 0.872150047 0.971794264 0.911981086 1 20.63360571 2.270267245 0.39916173 1.014549304 0.711210902 0.729668015 0.050617515 0.661422574 0.243052054 0.059201001 0.070498846 186.3233334 -2.270267245 -0.303338402 GLQLT(ph)PGIGGMQQHFFDDEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GLQLTPGIGGMQQHFFDDEDR 21 0 P12270 P12270 TPR Nucleoprotein TPR 1 GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR 212.78 2.82E-22 354090000 266198 340050 342583 451220 501980 362130 168707 202998 161229 154095 TRUE FALSE 255794.6879 330352.1069 404495.3688 474507.5183 518126.6426 369452.5167 170771.6867 198806.0204 142926.9598 143658.0084 1.780580775 2.299573206 2.815682699 3.303035616 3.606667309 2.571750234 1.188737674 1.383884007 0.994911188 1 17.13227889 2.270469451 4.869715217 1.187872174 2.795138369 0.723344834 0.481152215 0.112519063 6.392000593 0.194153862 0.15519855 186.4101051 -2.270469451 1.607266195 KCSTPEEIKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KCSTPEEIKK 10 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 126.76 0.00021031 2246260000 3195900 2742000 2301150 2346450 2516450 2785000 3024300 3329000 3557200 3299000 FALSE TRUE 3071000.695 2663800.845 2717018.994 2467550.566 2597393.9 2841314.608 3061312.288 3260254.987 3153401.569 3075555.792 0.998518935 0.86612015 0.883423738 0.802310455 0.844528299 0.923837771 0.995368803 1.060053924 1.025311125 1 21.55241572 2.270485096 2.576805276 1.033642035 0.874870218 0.650293082 0.049041791 0.163224964 2.225815685 0.021103389 0.015344275 186.4168204 -2.270485096 -0.158771816 INSTATPDQDRDK ddPTM_BT-474_Pertuzumab_2h_R1 2 INSTATPDQDRDK 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 151.56 1.43E-06 787520000 663770 606820 528820 515370 546150 601210 667020 691490 783090 759250 FALSE TRUE 637829.1346 589514.0877 624389.5375 541968.3075 563717.4108 613366.8781 675183.1903 677210.4899 694196.9062 707825.3212 0.901110932 0.832852499 0.882123765 0.76568087 0.796407523 0.866551195 0.953883917 0.956748042 0.980746076 1 19.43303385 2.270725836 2.938327659 0.971045982 0.833732727 0.75174532 0.037602954 0.134535827 2.394053201 0.01573068 0.011777478 186.5201843 -2.270725836 -0.137313255 KKEPVGDDESVPENVLSFDDLTADALANLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKEPVGDDESVPENVLSFDDLTADALANLK 30 2 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 267.09 4.98E-59 610290000 664210 560030 549270 438420 532450 670420 638930 777580 877340 752900 FALSE TRUE 638251.9389 544058.4927 648535.3074 461046.9087 549576.7378 683976.3517 646749.4165 761522.7013 777748.0413 701905.4124 0.909313317 0.775116537 0.923963964 0.656850482 0.782978345 0.974456586 0.921419617 1.084936357 1.108052492 1 19.4209171 2.271085608 1.509182649 1.065346383 0.809319348 0.612621508 0.083661696 0.255326412 1.15341376 0.046152782 0.02851071 186.6747628 -2.271085608 -0.256027035 SGAGSS(ph)PETK ddPTM_BT-474_Pertuzumab_2h_R1 6 SGAGSSPETK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGAGS(0.022)S(0.978)PETK;SGAGS(0.031)S(0.969)PETK;SGAGS(0.031)S(0.969)PETK;SGAGS(0.001)S(0.999)PETK;SGAGS(0.013)S(0.987)PETK;SGAGS(0.346)S(0.654)PETK 273.23 7.14E-14 185867000 9620560 8460110 6936330 7257580 7821910 7935290 9002660 9035740 8732080 9405550 TRUE FALSE 9244577.879 8218835.946 8189879.129 7632144.574 8073508.839 8095747.001 9112837.246 8849148.811 7740850.886 8768503.721 1.05429366 0.93731339 0.934011023 0.87040444 0.920739626 0.923275767 1.03926936 1.009197132 0.882801802 1 23.06389925 2.271113073 24.94574633 0.988316674 0.935571901 0.111878573 0.057463365 350.107364 268294.5834 0.020339145 0.017015779 186.6865685 -2.271113073 -0.052744773 SSQPSPTAVPASDS(ph)PPTKQEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSQPSPTAVPASDSPPTKQEVK 22 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 SSQPSPTAVPASDS(0.999)PPT(0.001)KQEVK 211.62 1.86E-23 128310000 135910 112410 106160 100130 144510 136510 146350 162780 217990 175030 TRUE FALSE 130598.4869 109204.1769 125345.4735 105297.7213 149158.2954 139270.3257 148141.0751 159418.5361 193244.6891 163175.0622 0.800358126 0.669245505 0.768165624 0.645305232 0.914099822 0.853502514 0.907865902 0.976978553 1.184278323 1 17.31606106 2.271257498 0.802462898 1.07631446 0.723354624 0.72866303 0.080147086 0.319090176 0.395155345 0.061506358 0.037925547 186.7486616 -2.271257498 -0.352959835 SSFASSSASDASKPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSFASSSASDASKPSSPR 18 1 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 SSFASSSASDASKPS(0.5)S(0.5)PR 149.73 1.58E-07 220630000 200870 188040 169590 172550 178940 212730 210380 254930 269850 248060 TRUE FALSE 193019.7783 182677.2833 200238.6855 181455.3262 184695.7676 217031.5464 212954.6934 249665.6064 239217.7593 231258.6753 0.834648811 0.789926186 0.865864536 0.784642245 0.798654439 0.938479588 0.920850615 1.079594554 1.03441637 1 17.81914796 2.271311544 1.482248434 1.042470181 0.814821762 0.846041257 0.039850072 0.134786581 0.586380806 0.021556892 0.013250221 186.7719032 -2.271311544 -0.227648419 ERVEAVNMAEGIIHDTETK ddPTM_BT-474_Pertuzumab_2h_R1 6 ERVEAVNMAEGIIHDTETK 19 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;; 274.27 1.27E-39 884303000 816642 1181409 824952 1643400 757455 974663 1579700 1390107 1283023 1128638 FALSE TRUE 784726.7278 1147716.372 974039.1774 1728216.071 781819.228 994371.3537 1599032.841 1361400.805 1137379.608 1052194.343 0.745800178 1.090783637 0.925721739 1.642487514 0.743036905 0.945045333 1.519712448 1.293868204 1.08095963 1 20.00496977 2.271449642 24.9916322 1.262725381 1.030938867 0.11679669 0.270053522 366.7591343 278690.6984 0.092678565 0.077535567 186.8313025 -2.271449642 -0.231786514 S(ph)PSIDSIQKDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSIDSIQKDPR 12 1 A0A0D9SF60;Q99569-2;Q99569;B4DRK2;E9PHB5;E7EPC8;Q9UQB3-2;Q9UQB3 A0A0D9SF60;E7EPC8 PKP4;CTNND2 Plakophilin-4;Catenin delta-2 1 S(0.547)PS(0.453)IDSIQKDPR 61.212 0.05236 377340000 1073400 1366900 849360 1308600 957200 1198700 1291900 1579700 1349900 1242500 TRUE FALSE 1031450.341 1327917.35 1002858.246 1376137.003 987989.2073 1222938.535 1307710.659 1547078.643 1196665.011 1158344.368 0.890452243 1.146392547 0.865768655 1.188020627 0.852932197 1.055764217 1.128948087 1.335594738 1.033082254 1 20.14363279 2.271974825 3.608296558 1.174125431 0.998838236 0.141303201 0.136564906 0.30217979 8.271554986 0.049017326 0.037979621 187.0573704 -2.271974825 -0.175287195 GLPWSCSADEVQR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLPWSCSADEVQR 13 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;E7EN40;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;D6RDL0;D6RF17;D6R9D3;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ;;;; 257.88 1.51E-23 3554170000 1767380 1956120 1510290 1775350 1720150 1754600 1674450 1694240 1934380 1797370 FALSE TRUE 1698308.836 1900333.373 1783232.999 1866976.026 1775480.187 1790079.214 1694942.42 1659253.352 1714797.292 1675632.529 1.013532983 1.134099118 1.064214837 1.114191802 1.05958804 1.068300587 1.011523941 0.990225078 1.023373122 1 20.67627437 2.271998965 2.756901752 1.002046679 1.080821928 0.540894082 0.031323063 0.182276567 2.849400426 0.011946035 0.008834912 187.0677681 -2.271998965 0.078775249 DSDQVAQS(ph)DGEES(ph)PAAEEQLLGEHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDQVAQSDGEESPAAEEQLLGEHIK 26 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 2 DSDQVAQS(1)DGEES(1)PAAEEQLLGEHIK;DS(0.001)DQVAQS(0.999)DGEES(1)PAAEEQLLGEHIK 200.03 2.91E-25 385210000 327510 315230 306090 354470 362550 314630 405860 427580 494000 497850 TRUE FALSE 314710.5471 306239.949 361407.2719 372764.2392 374211.75 320992.0342 410827.0361 418750.3236 437923.191 464130.1761 0.678065257 0.659814778 0.778676523 0.803145881 0.806264641 0.691599148 0.885154763 0.902226024 0.94353527 1 18.82416997 2.272056553 0.321296741 1.028817459 0.64252578 0.786789747 0.051183921 0.803727445 0.211986235 0.074729405 0.111122264 187.0925754 -2.272056553 -0.386291679 AAEDSPYWVS(ph)PAYSK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAEDSPYWVSPAYSK 15 0 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 AAEDSPYWVS(1)PAYSK 247.5 4.75E-16 0 136750 104390 105180 106770 100090 112680 125810 142780 116710 125150 TRUE FALSE 131405.6588 101412.8994 124188.3657 112280.4125 103309.4857 114958.4668 127349.7004 139831.5431 103461.5701 116673.479 1.126268454 0.869202669 1.064409553 0.962347343 0.885458174 0.985300754 1.091505126 1.198486102 0.886761678 1 16.83211713 2.272157466 7.366763191 1.076595672 0.975138184 0.042453328 0.103587168 0.337330484 57.17398657 0.035522331 0.029226936 187.1360534 -2.272157466 -0.101457488 EREKEPS(ph)RER ddPTM_BT-474_Pertuzumab_2h_R1 2 EREKEPSRER 10 3 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 EREKEPS(1)RER;EREKEPS(1)RER 135.04 0.00085462 986630000 603580 498570 373752 375678 468222 463950 503990 488740 626590 489180 TRUE FALSE 579991.4263 484351.2718 441297.3005 395066.7866 483282.7859 473331.3869 510157.9804 478647.3482 555462.1301 456047.4029 1.271778816 1.062063436 0.967656646 0.866284479 1.059720509 1.037899534 1.118651213 1.049556132 1.217992092 1 18.79882426 2.272527891 11.92005131 1.095834408 1.034155035 0.048338012 0.10829732 2.482731457 865.2231671 0.038726449 0.032295122 187.2957362 -2.272527891 -0.061679374 KGS(ph)PTPGFSTR ddPTM_BT-474_Pertuzumab_2h_R1 7 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.747)PT(0.252)PGFS(0.001)TR;KGS(0.744)PT(0.25)PGFS(0.005)T(0.001)R;KGS(0.668)PT(0.332)PGFSTR;KGS(0.886)PT(0.114)PGFSTR;KGS(0.5)PT(0.5)PGFS(0.001)TR;KGS(0.644)PT(0.356)PGFSTR;KGS(0.682)PT(0.317)PGFS(0.001)TR 134.39 0.00015027 21992520000 4099400 3886220 3188120 3307730 3651330 3865700 4160310 4423010 4883130 4793160 TRUE FALSE 3939190.916 3775388.811 3764284.203 3478442.342 3768778.346 3943867.103 4211225.118 4331673.298 4328817.554 4468515.004 0.881543625 0.844886681 0.842401603 0.778433627 0.843407338 0.8825901 0.942421613 0.969376469 0.968737388 1 22.09136404 2.273152202 1.698514732 0.977441853 0.835109641 0.864540575 0.024990431 0.131819329 0.762893248 0.013636003 0.008757764 187.5651729 -2.273152202 -0.142332211 SPQTLAPVGEDAMKT(ph)PS(ph)PAAEDAREPEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPQTLAPVGEDAMKTPSPAAEDAREPEAK 29 2 Q92797 Q92797 SYMPK Symplekin 2 S(0.109)PQT(0.115)LAPVGEDAMKT(0.779)PS(0.997)PAAEDAREPEAK 65.58 0.018988 97630000 128300 96749 83504 83278 115170 107610 136530 154930 169280 140950 TRUE FALSE 123285.8942 93989.81325 98595.03034 87575.98756 118874.5476 109785.9479 138200.895 151730.6414 150064.0441 131403.331 0.93822503 0.71527725 0.750323676 0.666467029 0.90465399 0.835488318 1.051730531 1.154694027 1.14201096 1 17.00364232 2.273254914 1.939337654 1.120984765 0.779789581 0.723804398 0.086458513 0.158399285 1.208204358 0.040593783 0.027229453 187.6095382 -2.273254914 -0.341195184 YLLGDAPVSPS(ph)SQK ddPTM_BT-474_Pertuzumab_2h_R1 3 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.012)PS(0.988)SQK;YLLGDAPVS(0.065)PS(0.933)S(0.002)QK;YLLGDAPVS(0.008)PS(0.983)S(0.01)QK 339.48 8.44E-69 4577400000 7000200 6986300 5737500 6387800 6630300 6769900 7452200 8165200 7660100 8269300 TRUE FALSE 6726624.445 6787057.564 6774393.88 6717475.124 6843569.621 6906792.016 7543402.253 7996585.767 6790557.562 7709212.945 0.872543604 0.880382681 0.878740012 0.8713568 0.887713139 0.895914027 0.978491878 1.037276545 0.880836683 1 22.87815215 2.273349344 4.102990982 0.984672676 0.879329829 0.595850022 0.037391168 0.131926642 4.819108482 0.013645053 0.010748923 187.6503351 -2.273349344 -0.105342847 NISHDTFGTTYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NISHDTFGTTYGR 13 0 Q9H7B2 Q9H7B2 RPF2 Ribosome production factor 2 homolog 0 144.8 4.15E-05 294330000 73633 87147 57460 69695 70728 75713 55295 75028 63223 80146 FALSE TRUE 70755.34095 84661.65289 67844.30019 73291.9673 73003.03035 77243.96874 55971.71675 73478.64558 56046.19009 74717.64003 0.946969697 1.133087887 0.908009142 0.980919195 0.977052144 1.033811677 0.749109805 0.983417645 0.750106535 1 16.18916127 2.273379682 24.99985067 0.877214063 0.997209921 0.29670931 0.094803892 222.0557299 159433.7303 0.030541202 0.025551577 187.6634438 -2.273379682 0.119995858 FNGIVEDFNYGTLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FNGIVEDFNYGTLLR 15 0 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 0 ; 149.82 7.65E-06 137460000 291390 304582 277650 259730 297410 275733 335220 300980 350560 338570 FALSE TRUE 280002.1567 295895.6196 327827.5313 273134.6964 306976.4628 281308.5102 339322.5226 294764.6578 310765.8985 315638.3523 0.887098018 0.937451414 1.038617547 0.865340648 0.97255755 0.891236784 1.075035781 0.93386832 0.984563175 1 18.26791299 2.273433882 24.99998936 0.989471121 0.935948805 0.241889386 0.056393592 306.0307224 219386.6847 0.018820524 0.015745796 187.6868658 -2.273433882 -0.053522315 VQAYEEPSVASS(ph)PNGK ddPTM_BT-474_Pertuzumab_2h_R1 4 VQAYEEPSVASSPNGK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 VQAYEEPSVAS(0.001)S(0.999)PNGK;VQAYEEPSVASS(1)PNGK;VQAYEEPSVAS(0.002)S(0.998)PNGK;VQAYEEPSVASS(1)PNGK 427.02 4.02E-160 5097350000 6316940 5870240 4863540 5228590 5712610 5915670 6178650 6724730 6972520 7327190 TRUE FALSE 6070067.001 5702826.503 5742489.867 5498438.156 5896361.289 6035288.901 6254266.167 6585861.976 6181028.761 6830912.895 0.888617246 0.834855691 0.840662142 0.804934603 0.86318789 0.883525964 0.915582772 0.964126183 0.904861306 1 22.70364696 2.273735512 1.343056644 0.9562307 0.841673476 0.731334563 0.029295462 0.217058159 0.768638233 0.016968488 0.010188105 187.8172651 -2.273735512 -0.114557224 DRTQQYDDLIDEFMK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRTQQYDDLIDEFMK 15 1 A0A1W2PQ37;A0A1W2PQF8;A0A1W2PR68;A0A1W2PQT3;A0A1W2PPH1;A0A1W2PQH3;A0A1W2PQY8;P23368-2;P23368 A0A1W2PQ37 ME2 "NAD-dependent malic enzyme, mitochondrial" 0 ; 146.16 3.59E-06 112500000 164038 233070 169047 302480 141700 208461 299590 295450 258510 197369 FALSE TRUE 157627.2136 226423.0718 199597.5533 318091.029 146257.9092 212676.2242 303256.472 289348.8543 229165.0286 184001.0218 0.856664882 1.230553339 1.084763287 1.728745992 0.794875527 1.155842626 1.648123847 1.572539388 1.245455195 1 17.48935425 2.274167749 23.00468423 1.439554539 1.154239215 0.104125975 0.291628705 126.1859057 81523.87247 0.098720914 0.082590459 188.0042853 -2.274167749 -0.285315324 IFDLQDWTQEDERDKDAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IFDLQDWTQEDERDKDAAK 19 2 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 ; 211.43 7.28E-17 133774000 130666 179811 113759 199413 116698 157880 224470 242000 238940 164593 FALSE TRUE 125559.4283 174682.9663 134317.7819 209704.7288 120451.6972 161072.4418 227217.131 237002.6154 211816.5329 153444.9695 0.818270085 1.138407905 0.875348226 1.366644534 0.78498303 1.049708194 1.48077276 1.544544707 1.380407149 1 17.22736182 2.274262879 7.249431287 1.415646283 1.010627505 0.378086396 0.211039023 0.166642255 25.99392582 0.069795228 0.05746635 188.0454714 -2.274262879 -0.405018778 KS(ph)MSEDGGLQESNPCADDFVSASTADVSHTNLGTIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSMSEDGGLQESNPCADDFVSASTADVSHTNLGTIR 36 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6;A0A1W2PRP5 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 1 KS(0.789)MS(0.211)EDGGLQESNPCADDFVSASTADVSHTNLGTIR 247.08 1.93E-50 370840000 65431 79791 68370 71982 74717 67300 47613 49050 52337 37610 TRUE FALSE 62873.88418 77515.4388 80725.97988 75696.99965 77120.34016 68660.85211 48195.70214 48037.10036 46395.92317 35062.6412 1.793187336 2.2107701 2.302335966 2.158907517 2.199501735 1.958233885 1.374559944 1.370036561 1.323229557 1 15.09764706 2.274313431 2.489551553 1.27795573 2.149381067 0.873628414 0.157308447 0.09451451 1.202179159 0.066214227 0.047881822 188.0673612 -2.274313431 0.871425337 LVEKPSPLTLAPHDFANIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEKPSPLTLAPHDFANIK 19 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 180.08 2.07E-14 1416860000 2311100 2245500 1944680 2029740 1990920 2149860 2318700 2346600 2602900 2587600 FALSE TRUE 2220779.657 2181460.539 2296126.935 2134495.125 2054959.75 2193331.642 2347076.944 2298141.89 2307429.704 2412339.547 0.920591655 0.904292491 0.951825765 0.884823667 0.851853443 0.909213483 0.972946345 0.952661035 0.956511162 1 21.20200156 2.274375662 6.601918149 0.965356626 0.902456708 0.596385708 0.026776601 0.143445527 17.80925793 0.009967246 0.008168343 188.0943117 -2.274375662 -0.062899919 SRDPHYDDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRDPHYDDFR 10 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 0 ; 113.22 0.00091116 372320000 85194 149874 99389 166606 102442 110253 185906 160683 127005 153863 FALSE TRUE 81864.52429 145599.7403 117350.8032 175204.5556 105737.14 112482.3912 188181.1732 157364.8399 112587.9248 143441.722 0.570716268 1.015044565 0.818107881 1.221433717 0.737143549 0.784167881 1.311899848 1.097064632 0.784903606 1 17.13010519 2.274480422 24.9998036 1.070016245 0.874162329 0.170417213 0.20198294 298.4928847 207746.7743 0.069198632 0.057893844 188.1396889 -2.274480422 -0.195853916 TMDADHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TMDADHSK 8 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;F5H5K2 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 0 69.423 0.053956 74565000 114880 123860 87290 104870 97497 102690 127900 110840 137750 127970 FALSE TRUE 110390.3626 120327.6341 103065.2448 110282.3533 100633.0795 104766.4622 129465.2785 108551.1153 122113.1975 119302.4779 0.925298154 1.008592916 0.863898609 0.924392814 0.843512065 0.878158308 1.085185159 0.909881481 1.023559608 1 16.86426448 2.274608314 24.99999783 0.990941348 0.907816121 0.390803393 0.058547732 206.3111623 143081.2999 0.02036913 0.01704152 188.1951012 -2.274608314 -0.083125228 SATTTGS(ph)PGTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SATTTGSPGTEK 12 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 SATTT(0.001)GS(0.999)PGTEK;SATTT(0.008)GS(0.992)PGTEK 351.37 1.60E-71 687260000 1007910 928190 876010 812630 853000 939740 1021320 1051890 1241130 1102090 TRUE FALSE 968519.7629 901718.93 1034324.494 854569.9317 880437.5197 958742.1867 1033819.22 1030168.104 1100242.126 1027444.463 0.94264926 0.87763277 1.006696256 0.831743187 0.856919816 0.933132857 1.006204478 1.002650889 1.070853137 1 19.97062898 2.274655267 3.025224105 1.02076417 0.902756158 0.56706416 0.048527438 0.191451381 3.612052411 0.019406737 0.014653844 188.2154485 -2.274655267 -0.118008012 TS(ph)PINLGLNVNDLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.174)S(0.826)PINLGLNVNDLLK;T(0.157)S(0.843)PINLGLNVNDLLK 171.71 1.12E-06 1157491000 4479416 4315806 3806982 3655633 4498020 4717225 4658729 5523517 6577637 5229612 TRUE FALSE 4304355.47 4192723.438 4494988.333 3844300.657 4642702.898 4812610.522 4715743.919 5409454.444 5830971.223 4875405.721 0.882871235 0.859974262 0.921972158 0.78850887 0.95227006 0.987120005 0.967251587 1.10953934 1.195997125 1 22.21709085 2.274733582 1.121737556 1.111381612 0.871537646 0.682432453 0.063477925 0.267136393 0.650480087 0.041152277 0.024031108 188.2493918 -2.274733582 -0.239843966 FAELPEFRPEEVLPS(ph)PTLQSLATS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.99)PT(0.01)LQSLAT(0.074)S(0.926)PR 199.76 3.19E-25 652010000 322930 333680 286160 374150 352980 313770 292750 298340 297110 299350 TRUE FALSE 310309.5386 324163.7731 337875.4776 393459.9263 364333.9223 320114.6444 296332.7621 292179.1747 263383.3184 279074.7579 1.111922629 1.161566082 1.210698811 1.409872858 1.305506543 1.147056964 1.061840076 1.046956654 0.943773347 1 18.09029211 2.275290135 2.086561304 1.008073597 1.242304455 0.642410785 0.080093787 0.229937656 2.04059618 0.041170561 0.028324553 188.4907899 -2.275290135 0.234230858 NQLNPIGSLQELAIHHGWR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQLNPIGSLQELAIHHGWR 19 0 O75569;O75569-3;O75569-2 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 0 ; 195.46 5.16E-16 1124290000 964720 955640 857030 947940 1014020 840030 847070 500770 1047280 953370 FALSE TRUE 927017.6758 928386.0829 1011914.386 996863.297 1046636.874 857015.9821 857436.696 490428.9245 928397.165 888797.4007 1.043002235 1.044541852 1.138520865 1.121586648 1.177587686 0.964242224 0.964715576 0.551789333 1.04455432 1 19.76149507 2.275304905 2.481629919 0.812732491 1.10031379 0.313615762 0.137260413 0.249188542 3.14928781 0.057524343 0.041598784 188.4972005 -2.275304905 0.287581298 VINIDFRDPEESK ddPTM_BT-474_Pertuzumab_2h_R1 2 VINIDFRDPEESK 13 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 96.135 0.0039911 626960000 839070 735990 656710 702280 780700 793320 787560 884790 1002600 900960 FALSE TRUE 806278.2168 715000.2858 775392.1054 738524.755 805811.9245 809361.4739 797198.3949 866518.7773 888789.0512 839937.1767 0.959926813 0.851254481 0.923154882 0.879261897 0.959371661 0.963597631 0.949116692 1.031647129 1.058161343 1 19.6799219 2.275339116 0.918711701 1.035383583 0.902827634 0.6523206 0.035448548 0.323716143 0.524356724 0.025241769 0.014935461 188.51205 -2.275339116 -0.132555949 DSTEYFIVFEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSTEYFIVFEPR 12 0 A6NHR9;A6NHR9-2;J3KTL8;A6NHR9-3 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 0 108.9 0.0038517 54728000 73999 68240 62317 77257 75839 71488 56900 57940 73542 73797 FALSE TRUE 71107.03727 66293.86201 73579.06813 81244.24303 78278.43031 72933.53634 57596.35922 56743.51875 65193.82047 68798.66346 1.033552597 0.963592295 1.069483976 1.180898566 1.137789986 1.060101064 0.837172647 0.824776469 0.947603008 1 16.07009292 2.275385434 7.948612417 0.879280551 1.077248074 0.562069349 0.073172328 0.154179393 28.43094829 0.027541814 0.022778893 188.5321561 -2.275385434 0.197967522 NMTVEQLLTGSPTS(ph)PTVEPEKPTR ddPTM_BT-474_Pertuzumab_2h_R1 4 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 NMTVEQLLTGSPT(0.065)S(0.926)PT(0.009)VEPEKPTR;NMTVEQLLTGSPT(0.043)S(0.953)PT(0.004)VEPEKPTR;NMTVEQLLTGSPT(0.004)S(0.996)PT(0.001)VEPEKPTR;NMTVEQLLTGSPT(0.022)S(0.977)PT(0.001)VEPEKPTR 247.61 3.30E-38 1188530000 658590 643100 626150 660010 715690 640650 502441 527414 544760 512346 TRUE FALSE 632851.5747 624759.4177 739309.2336 694073.1952 738710.8188 653604.3819 508590.0233 516522.7166 482921.1286 477644.3491 1.324943079 1.308001275 1.547823679 1.45311715 1.546570833 1.368391321 1.064788109 1.081396059 1.011047508 1 18.86557727 2.275736517 3.85793735 1.045885382 1.437971279 0.859700637 0.076670659 0.082355175 2.599031757 0.030715702 0.024066464 188.6846265 -2.275736517 0.392085898 DIVPGDIVEIAVGDKVPADIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIVPGDIVEIAVGDKVPADIR 21 1 P16615-5;P16615-2;P16615-3;P16615 P16615-5 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 0 ; 173.09 4.33E-12 138132000 116537 152350 104024 161403 116013 140251 156344 168817 208201 131923 FALSE TRUE 111982.6052 148005.1272 122823.4508 169733.0282 119744.6635 143086.9713 158257.3846 165330.87 184566.8953 122987.7377 0.910518457 1.203413689 0.998664201 1.380080904 0.973630914 1.163424696 1.286773686 1.344287431 1.500693474 1 16.90815496 2.2759899 3.44189698 1.318089329 1.106964979 0.205554093 0.169686112 0.319978343 7.881314969 0.061067143 0.047140244 188.7947443 -2.2759899 -0.21112435 KQLATK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQLATK 6 1 K7EK07;Q71DI3;Q16695;P84243;P68431;Q6NXT2;K7EMV3;A0A590UJJ6;B4DEB1;K7ES00;K7EP01;Q5TEC6 K7EK07;Q5TEC6 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A;H3F3C;HIST2H3PS2 Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3C 0 ; 91.906 0.075939 1521000000 1614300 1948980 1067260 2801560 1420080 1092040 3209700 1932280 2348300 1730630 FALSE TRUE 1551211.371 1893396.999 1260137.623 2946148.847 1465758.163 1114121.797 3248981.269 1892377.743 2081730.829 1613412.889 0.961447242 1.173535313 0.781038525 1.826035275 0.908482989 0.690537311 2.013732066 1.172903574 1.290265402 1 20.62168426 2.276172782 24.99980445 1.383563625 1.077833265 0.137556566 0.38034109 337.4571786 224297.5269 0.128586723 0.107581027 188.8742627 -2.276172782 -0.30573036 QVNTISEAIVAEEDEEGRLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVNTISEAIVAEEDEEGRLDR 21 1 Q96NB3;J3QQQ3 Q96NB3 ZNF830 Zinc finger protein 830 0 ; 240.85 5.10E-30 100458000 57198 62136 51987 54878 58447 59445 51403 59302 64734 59110 FALSE TRUE 54962.63892 60363.94212 61382.20734 57710.26016 60327.00084 60647.01863 52032.08529 58077.39298 57385.66771 55106.42705 0.997390719 1.095406568 1.113884725 1.047250988 1.094736205 1.100543473 0.944210831 1.053913238 1.041360705 1 15.74993297 2.276196912 24.99999459 1.016095653 1.077223489 0.365269874 0.041583444 184.8604578 122793.3235 0.014093007 0.011790813 188.8847573 -2.276196912 0.061127835 MKETQK ddPTM_BT-474_Pertuzumab_2h_R1 4 MKETQK 6 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;; 104.45 0.030846 1608100000 1542540 1464010 1246190 1254740 1332690 1334630 1573860 1472170 1503760 1766620 FALSE TRUE 1482255.831 1422257.868 1471404.254 1319497.282 1375557.184 1361617.133 1593121.369 1441769.175 1333059.469 1646965.254 0.899992169 0.863562765 0.893403337 0.801168864 0.835207167 0.826743084 0.967307213 0.875409588 0.809403517 1 20.65137869 2.276513904 24.99993316 0.902038772 0.852435199 0.207452944 0.055493968 304.452936 200542.8415 0.019008464 0.015903304 189.0226747 -2.276513904 -0.049603572 LDNS(ph)PNMNITQPSK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDNSPNMNITQPSK 14 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 LDNS(1)PNMNITQPSK;LDNS(0.984)PNMNIT(0.016)QPSK;LDNS(1)PNMNITQPSK;LDNS(1)PNMNITQPSK 289.59 2.04E-43 1016390000 953040 893590 852533 785767 821136 952090 1014320 1107150 1200550 1191340 TRUE FALSE 915794.1432 868105.6881 1006604.678 826320.529 847548.5852 971341.9121 1026733.552 1084286.966 1064268.597 1110649.481 0.824557306 0.781619857 0.906320757 0.743997583 0.763110774 0.874571077 0.924444273 0.976263875 0.958239855 1 20.08297215 2.276616477 2.071410831 0.972497576 0.805673001 0.755358492 0.043452298 0.158812238 1.38866083 0.02019809 0.013881828 189.0673238 -2.276616477 -0.166824574 DAQMLIEDVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DAQMLIEDVKR 11 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 84.892 0.025051 114600000 86810 92791 77492 82863 87068 87867 98585 96911 117100 103740 FALSE TRUE 83417.36923 90144.69153 91496.5282 87139.56936 89868.62129 89643.73094 99791.51272 94909.75398 103807.2989 96713.5974 0.862519557 0.932078776 0.946056508 0.901006391 0.929224263 0.92689894 1.031825053 0.981348606 1.07334751 1 16.56143112 2.276620592 6.737403028 1.016367569 0.917810693 0.73589129 0.030850811 0.099546819 12.48678524 0.010546382 0.008665386 189.0691154 -2.276620592 -0.098556876 S(ph)EALSSVLDQEEAMEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEALSSVLDQEEAMEIK 17 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.971)EALS(0.014)S(0.014)VLDQEEAMEIK 62.924 0.060734 12824000 14376 11983 10507 9506.7 10453 12163 13486 14972 15032 15466 TRUE FALSE 13814.17003 11641.25657 12405.84863 9997.341926 10789.23024 12408.94419 13651.0457 14662.82297 13325.63038 14418.47404 0.958088213 0.807384785 0.860413424 0.693370318 0.748292101 0.860628119 0.946774649 1.016946934 0.924205317 1 13.81563087 2.277032603 2.97946014 0.981553734 0.808988333 0.543089709 0.068883641 0.192636881 3.521084733 0.028355584 0.021388141 189.2485685 -2.277032603 -0.172565401 LSASETSLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSASETSLHR 10 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 155.06 1.34E-05 129630000 68584 103200 80649 89498 85594 83038 83087 79411 80274 95830 FALSE TRUE 65903.66146 100256.837 95224.06833 94117.00251 88347.20874 84717.08525 84103.84356 77771.1351 71161.63206 89339.34874 0.737677881 1.122202461 1.065869291 1.053477598 0.988894703 0.948261728 0.941397545 0.87051379 0.796531798 1 16.44700812 2.277093824 1.587691243 0.879253882 1.007544267 0.135954987 0.107105626 0.609734668 3.066816579 0.055765135 0.03519516 189.2752481 -2.277093824 0.128290385 IPSTENSSQEISVEERT(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 2 IPSTENSSQEISVEERTPTK 20 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 IPSTENSSQEIS(0.001)VEERT(0.994)PT(0.004)K;IPSTENSSQEISVEERT(0.978)PT(0.022)K 107.29 0.00037014 564120000 513210 485210 382350 441290 430780 453980 489710 497420 493000 543190 TRUE FALSE 493153.1858 471372.2859 451449.1503 464065.0298 444636.4299 463159.7866 495703.2175 487148.1032 437036.7068 506399.2575 0.973842632 0.930831313 0.891488571 0.916401482 0.878035312 0.914613874 0.978878247 0.961984237 0.863027938 1 18.94991576 2.27726185 24.11904065 0.950433643 0.915108872 0.137018847 0.040829189 214.3112352 133559.9942 0.014127703 0.011819813 189.3484919 -2.27726185 -0.03532477 S(ph)NSELEDEILCLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSELEDEILCLEK 14 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5;Q86UF2;A4D2H0;A0A5F9ZHA4;G3V5K6;A0A2R8YE69;Q8IX94;P0CG41;A4FU28 Q96PC5 MIA2;CTAGE6;CTAGE15;CTAGE5;CTAGE4;CTAGE8;CTAGE9 Melanoma inhibitory activity protein 2;cTAGE family member 6;cTAGE family member 15;cTAGE family member 4;cTAGE family member 8;cTAGE family member 9 1 S(0.842)NS(0.158)ELEDEILCLEK;S(0.977)NS(0.023)ELEDEILCLEK 140.81 1.03E-05 62102000 83467 99526 79845 99326 81831 99280 111714 126738 133237 118804 TRUE FALSE 80205.01736 96687.61593 94274.76764 104452.2268 84463.16843 101287.5096 113081.1893 124120.816 118112.4943 110757.2993 0.724151075 0.872968342 0.851183338 0.943073075 0.762596858 0.914499634 1.020981823 1.120655856 1.06640822 1 16.75704225 2.277311897 2.715883058 1.074250817 0.840272293 0.728097473 0.063511821 0.130914713 1.98464283 0.025283078 0.018715411 189.3703129 -2.277311897 -0.233978524 LATQS(ph)NEITIPVTFESR ddPTM_BT-474_Pertuzumab_2h_R1 3 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.083)QS(0.917)NEITIPVTFESR;LAT(0.004)QS(0.996)NEITIPVTFESR;LAT(0.012)QS(0.988)NEITIPVTFESR 306.4 4.63E-47 395205000 261479 241131 201263 215899 197128 250111 179206 211139 215716 181789 TRUE FALSE 251260.1116 234254.18 237635.7012 227041.5733 203468.8011 255168.4158 181399.1766 206778.9059 191228.824 169476.2691 1.482568108 1.382224079 1.40217685 1.339665869 1.200573993 1.505629178 1.070351487 1.220105369 1.128351627 1 17.37072375 2.277369434 0.249449397 0.94794206 1.549673465 0.644396227 0.099007532 1.609388159 0.294361723 0.203023094 0.34638 189.3954033 -2.277369434 0.601731405 GSS(ph)PSIRPIQGS(ph)QGSSSPVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSPSIRPIQGSQGSSSPVEK 21 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 2 GS(0.455)S(0.545)PSIRPIQGS(0.492)QGS(0.2)S(0.167)S(0.141)PVEK 133.95 5.15E-06 268780000 344260 325540 324620 327170 354670 373780 366760 423820 488280 465980 TRUE FALSE 330805.9386 316255.9179 383286.0551 344055.2829 366078.2827 381338.0877 371248.5186 415067.9689 432852.5014 434418.7595 0.761490915 0.727997838 0.882296279 0.79198993 0.842685254 0.877812202 0.854586756 0.955455905 0.996394589 1 18.72872688 2.277434778 0.43420283 1.020646828 0.752957208 0.804778035 0.039368345 0.472313405 0.197948921 0.040607051 0.044026179 189.4239018 -2.277434778 -0.26768962 SGGGDLTLGLEPSEEEAPRS(ph)PLAPSEGAGSDVFDGDLGMGAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAK 43 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 SGGGDLTLGLEPS(0.007)EEEAPRS(0.993)PLAPSEGAGSDVFDGDLGMGAAK 124.4 3.83E-09 174590000 83050 151920 85815 197060 105360 123490 227310 199160 172260 121720 TRUE FALSE 79804.31418 147587.3903 101323.6794 207230.2902 108749.0001 125987.0524 230091.8878 195047.2764 152705.767 113475.796 0.703271684 1.300606786 0.892910057 1.826206976 0.958345338 1.110254846 2.027673706 1.718844752 1.345712234 1 16.79202508 2.277448207 24.99150308 1.613403438 1.152402212 0.190019431 0.37618172 209.7577204 134802.1161 0.125840588 0.105284132 189.4297591 -2.277448207 -0.461001227 RPNT(ph)SPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.5)S(0.5)PDR 67.726 0.034193 88602000 37831 41733 29256 39796 37900 37097 34820 36446 36871 39268 TRUE FALSE 36352.5227 40542.8157 34543.21 41849.87633 39119.08792 37847.12676 35246.13758 35693.37736 32685.55866 36608.34338 0.993011957 1.107474744 0.94358845 1.143178643 1.068583943 1.033838826 0.962789745 0.975006626 0.892844517 1 15.15988487 2.277617738 3.186223773 0.95595304 1.053472917 0.374948372 0.057651538 0.252245002 5.285485862 0.021521697 0.016434539 189.5037192 -2.277617738 0.097519877 ASSHSSQTQGGGS(ph)VTK ddPTM_BT-474_Pertuzumab_2h_R1 7 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ASSHSSQTQGGGS(0.986)VT(0.014)K;ASSHSSQTQGGGS(0.99)VT(0.01)K;ASSHSSQTQGGGS(0.994)VT(0.006)K;ASSHSSQTQGGGS(1)VTK;ASSHSSQT(0.004)QGGGS(0.995)VT(0.001)K;ASSHSSQTQGGGS(0.998)VT(0.002)K;ASSHSSQTQGGGS(0.996)VT(0.004)K 191.97 6.39E-10 1770831000 1457526 2252906 1504555 1839877 1447143 1693364 1294596 1531694 1095846 1416327 TRUE FALSE 1400564.273 2188655.327 1776461.557 1934833.272 1493691.669 1727604.98 1310439.653 1500063.984 971450.1562 1320397.911 1.06071379 1.657572546 1.345398643 1.465341059 1.131243587 1.308397239 0.992458139 1.136069643 0.735725305 1 20.33254133 2.278311491 0.855223404 0.91685915 1.393054859 0.499169444 0.178574231 0.47579476 0.668562881 0.128171817 0.077521843 189.8066793 -2.278311491 0.476195709 QLWGLLIEETEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLWGLLIEETEKR 13 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 212.17 2.58E-08 307150000 314690 379760 259489 310040 348190 385650 377690 412440 458400 479290 FALSE TRUE 302391.5669 368929.6166 306384.4346 326041.2016 359389.8476 393448.1072 382312.2832 403922.9699 406364.3538 446827.2614 0.676752725 0.825664968 0.685688769 0.729680639 0.804314953 0.880537383 0.855615394 0.903980139 0.909443959 1 18.76935768 2.278523992 0.43665978 0.992946633 0.701397261 0.807787537 0.043593039 0.476712455 0.201563709 0.044884973 0.04837481 189.8995747 -2.278523992 -0.291549371 ISMPDVDLHVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISMPDVDLHVK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 97.214 0.0064334 368760000 693380 742270 588430 690590 658040 703850 647750 727030 765840 722880 FALSE TRUE 666281.943 721101.1864 694772.3906 726231.4327 679206.4542 718082.3292 655677.3583 712016.5764 678905.0539 673918.6937 0.988668142 1.070012144 1.030943936 1.077624704 1.007846288 1.065532587 0.972932439 1.056531868 1.007399053 1 19.36221502 2.278534658 24.99983672 1.0170272 1.041286813 0.161029451 0.032580699 322.5566698 201725.9873 0.010514916 0.008797286 189.9042385 -2.278534658 0.024259613 EFFVDDSEEIVEVPQPDPNQPKPEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFFVDDSEEIVEVPQPDPNQPKPEGR 26 1 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 0 94.899 0.0072542 81800000 27650 27024 28004 27955 25158 31078 34916 39999 40346 41025 FALSE TRUE 26569.40743 26253.30198 33064.94575 29397.7609 25967.22992 31706.41845 35343.31245 39173.00667 35766.09122 38246.34021 0.6946915 0.686426514 0.864525745 0.768642457 0.67894679 0.829005293 0.924096587 1.024228892 0.935150684 1 15.22303408 2.278541171 2.410599584 0.986492316 0.744645133 0.795327722 0.055797549 0.128612053 1.532859218 0.0247062 0.01777991 189.9070863 -2.278541171 -0.241847183 QKVDSLLENLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QKVDSLLENLEK 12 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4;A0A0G2JNQ3;O60812;B2RXH8;A0A0G2JPF8;P0DMR1;B7ZW38 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2;HNRNPCL4;HNRNPCL3 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3 0 ; 226.59 1.36E-11 11942000000 3351800 2967800 3330800 3064100 2704280 3613100 3859900 4231000 4889600 4491500 FALSE TRUE 3220807.95 2883161.25 3932749.653 3222238.568 2791265.622 3686159.358 3907138.611 4143628.371 4334553.107 4187286.704 0.769187347 0.688551192 0.939211936 0.769529004 0.666604849 0.880321702 0.933095555 0.989573598 1.035169888 1 21.99758427 2.278776909 2.072328541 1.000621154 0.772414563 0.683564384 0.071559202 0.193713695 1.695874109 0.033663082 0.023187018 190.0101973 -2.278776909 -0.228206591 VVDVEEQQLEES(ph)GPHDLTETSYLPR ddPTM_BT-474_Pertuzumab_2h_R1 3 VVDVEEQQLEESGPHDLTETSYLPR 25 0 P38398-7;P38398;P38398-4;P38398-8;P38398-6;E7EUM2;B7ZA85;H0Y8B8;P38398-5;P38398-3;A0A2R8Y7V5;K7EPC7 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 VVDVEEQQLEES(1)GPHDLTETSYLPR;VVDVEEQQLEES(1)GPHDLTETSYLPR;VVDVEEQQLEES(1)GPHDLTETSYLPR 290.54 5.13E-63 163904000 89830 92181 69308 90557 80500 82761 76193 79637 73599 88904 TRUE FALSE 86319.34429 89552.08813 81833.49735 95230.65762 83089.35561 84434.48412 77125.47273 77992.46812 65244.35007 82882.45289 1.041467057 1.080471017 0.987344058 1.148984547 1.002496339 1.018725691 0.930540422 0.941000965 0.787191351 1 16.33877908 2.279100397 1.44417168 0.899900699 1.057672023 0.513835213 0.063950098 0.311668743 1.286133516 0.034153869 0.021003614 190.151781 -2.279100397 0.157771324 ELEDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEDFK 6 0 P00367;P00367-2;P00367-3;P49448;A6NF36 P00367 GLUD1;GLUD2;CCDC182 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial;Coiled-coil domain-containing protein 182" 0 110.36 0.066925 249840000 335720 433090 286300 591760 303960 389000 598170 564940 457890 410110 FALSE TRUE 322599.6912 420738.6972 338040.7787 622300.8045 313737.1494 396865.8465 605490.5834 553273.7916 405912.2468 382332.8844 0.84376653 1.100451241 0.884153031 1.62764133 0.820586359 1.038011279 1.58367383 1.447099672 1.061672337 1 18.54446977 2.279192794 24.99908281 1.33478063 1.062575286 0.122944401 0.268484225 244.4616097 150404.9047 0.091325521 0.076407569 190.1922401 -2.279192794 -0.272205343 GKENQLQLSCFINQEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKENQLQLSCFINQEVK 17 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 160.97 2.76E-09 615650000 281820 237770 228840 252840 238210 266760 280520 319940 326110 299330 FALSE TRUE 270806.1628 230989.0324 270196.4785 265889.1027 245872.241 272154.07 283953.0877 313333.1272 289091.36 279056.1125 0.970436234 0.827751202 0.968251425 0.952815906 0.881085309 0.975266471 1.017548353 1.12283198 1.035961396 1 18.09019572 2.279540131 2.470292892 1.06600861 0.92008308 0.564062254 0.050743709 0.17827249 2.232551185 0.020804747 0.015081479 190.3444116 -2.279540131 -0.14592553 ALALDLGS(ph)PAALR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALALDLGSPAALR 13 0 Q8TER5;Q8TER5-4;Q8TER5-3;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 ALALDLGS(1)PAALR 97.69 0.0038422 17172000 43664 41934 39312 41403 41896 42238 48306 50085 44212 47833 TRUE FALSE 41957.56261 40738.08338 46416.55289 43539.81379 43243.62289 43092.0813 48897.18328 49050.72725 39193.23911 44593.2283 0.940895383 0.913548647 1.040887925 0.976377254 0.969735194 0.966336884 1.096515887 1.099959099 0.878905623 1 15.44453703 2.279662852 24.66080849 1.037449871 0.969267782 0.100699807 0.065599839 211.5579912 126931.1401 0.023141805 0.019361619 190.398206 -2.279662852 -0.068182089 GSQSSDSSSSLSSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSQSSDSSSSLSSHR 15 0 O75376;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 0 81.656 0.013353 16096000 6649.6 7403.4 5524.4 8102.7 5740.1 6706.7 7772.8 8390.6 5389.7 8830.2 FALSE TRUE 6389.72628 7192.262281 6522.78197 8520.881318 5924.73553 6842.314069 7867.925852 8217.331178 4777.883851 8232.122689 0.776194248 0.873682591 0.792357235 1.035077056 0.719709333 0.831172509 0.955759061 0.998203196 0.580395122 1 13.00704877 2.279882235 24.98546305 0.898318723 0.84115474 0.021469757 0.135942794 569.7314245 344490.6317 0.045989249 0.038476977 190.4944094 -2.279882235 -0.057163983 NVLGHMQQGGAPSPFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NVLGHMQQGGAPSPFDR 17 0 Q01813;Q01813-2;B1APP6;H0Y757 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 124.68 0.00040737 0 141930 149600 109720 148380 107310 124190 113380 122980 110370 106710 FALSE TRUE 136383.2187 145333.5545 129548.8447 156037.9096 110761.7236 126701.2069 114767.5784 120440.42 97841.26031 99482.43665 1.370927606 1.46089661 1.302228303 1.568497062 1.113379681 1.273603775 1.153646636 1.210670185 0.983502853 1 16.60215422 2.280308597 0.477806053 0.990874919 1.446138068 0.645885619 0.107517797 0.61948344 0.303237202 0.099964231 0.09701303 190.6815163 -2.280308597 0.455263148 VNLEESSGVENS(ph)PAGARPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNLEESSGVENSPAGARPK 19 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 1 VNLEESSGVENS(1)PAGARPK;VNLEESSGVENS(1)PAGARPK 290.36 9.65E-50 1290130000 527200 468920 433600 508410 459930 513020 583110 642110 614710 688510 TRUE FALSE 506596.4411 455546.8607 511961.1654 534649.101 474724.0661 523393.6159 590246.2746 628850.2041 544930.6979 641876.6044 0.789242726 0.709710959 0.797600601 0.832946858 0.739587738 0.81541158 0.919563465 0.979705756 0.848964885 1 19.29193645 2.280443494 3.191187974 0.942801785 0.774987258 0.722121688 0.048171477 0.125082599 2.625465274 0.018345996 0.014041425 190.7407534 -2.280443494 -0.167814527 EKAEGDVAALNR ddPTM_BT-474_Pertuzumab_2h_R1 6 EKAEGDVAALNR 12 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;;; 194.98 7.63E-07 5898020000 6240430 5864680 5010760 5236700 5660920 5840190 6239920 6624400 7259180 6880060 FALSE TRUE 5996547.096 5697425.069 5916315.796 5506966.715 5843008.633 5958282.643 6316286.008 6487603.825 6435148.319 6414067.408 0.934905531 0.88827022 0.922396885 0.85857637 0.910967762 0.928939823 0.984755165 1.011464865 1.003286668 1 22.61280809 2.280773485 2.097247922 1.00635641 0.900958551 0.850962438 0.019353767 0.106750137 0.95803714 0.008584624 0.00594627 190.8857398 -2.280773485 -0.105397859 S(ph)VEEVASEIQPFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEEVASEIQPFLR 14 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(1)VEEVASEIQPFLR 78.486 0.022809 3157400 8120.4 7527.5 5103.9 6654.7 7423.3 6476.4 6216.5 5089.4 7262.9 7397.4 TRUE FALSE 7803.04579 7312.82307 6026.288266 6998.149865 7662.077186 6607.357245 6292.579387 4984.302111 6438.446041 6896.367509 1.131471863 1.060387669 0.87383514 1.014758836 1.111030869 0.958092392 0.912448384 0.722743111 0.933599613 1 12.75162094 2.280857552 2.894929494 0.849979488 1.028558054 0.309784646 0.095510384 0.258225126 4.449278916 0.038843429 0.029220476 190.9226932 -2.280857552 0.178578566 YEEIVK ddPTM_BT-474_Pertuzumab_2h_R1 7 YEEIVK 6 0 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;; 129.96 0.037149 8981260000 14783330 14012120 12720190 13997520 14237320 15624430 16093270 17130710 19433610 19309050 FALSE TRUE 14205581.12 13612508.06 15019011.29 14719933.68 14695276.33 15940366.68 16290224.25 16776954.85 17227588.07 18001230.84 0.789144989 0.756198739 0.834332464 0.817718178 0.816348418 0.885515375 0.904950578 0.931989318 0.957022784 1 24.10159222 2.280879729 0.474452517 1.002503877 0.7679375 0.944496742 0.017652947 0.206744094 0.100024529 0.017062044 0.016701003 190.9324427 -2.280879729 -0.234566376 EGNDKDFTLNDFGFMIFHSPYCK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGNDKDFTLNDFGFMIFHSPYCK 23 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ; 256.9 8.17E-44 3082000000 2160800 1896140 1641490 1863870 1973020 2321120 2360360 2202830 3040620 2775480 FALSE TRUE 2076353.547 1842063.944 1938143.758 1960064.554 2036483.98 2368054.637 2389246.792 2157340.791 2695461.565 2587494.267 0.802457255 0.711910348 0.749042725 0.757514549 0.787048693 0.915192225 0.923382448 0.833756742 1.041726584 1 21.30312424 2.281046254 0.543340524 1.000133962 0.730766066 0.750352081 0.053147886 0.465973758 0.283134788 0.050499797 0.042465642 191.0056676 -2.281046254 -0.269367897 WLSDECTNAVVNFLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 WLSDECTNAVVNFLSR 16 0 A0A0C4DGA2;O75521-2;O75521 A0A0C4DGA2 ECI2 "Enoyl-CoA delta isomerase 2, mitochondrial" 0 145.43 2.24E-05 0 64868 59616 38192 51785 56693 53190 68277 62274 65814 63871 FALSE TRUE 62332.88684 57915.81005 45094.14398 54457.63006 58516.58183 54265.53824 69112.59435 60988.02014 58343.07063 59544.96028 1.046820529 0.972639998 0.757312521 0.914563211 0.982729379 0.911337215 1.160679158 1.024234794 0.979815426 1 15.86169179 2.281284957 24.99932021 1.045365642 0.926520521 0.296363352 0.08298315 170.0142925 99479.91121 0.029753664 0.024893531 191.1106795 -2.281284957 -0.118845121 SFGTRPLSSGFS(ph)PEEAQQQDEEFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.041)S(0.041)GFS(0.918)PEEAQQQDEEFEK;SFGTRPLS(0.184)S(0.046)GFS(0.77)PEEAQQQDEEFEK 312.41 9.47E-75 3223900000 424470 386280 383770 320990 361540 423490 411850 459870 527200 460670 TRUE FALSE 407881.2431 375263.6726 453125.7759 337556.3324 373169.2624 432053.258 416890.3435 450373.5238 467354.4662 429468.4106 0.949735145 0.873786438 1.055085228 0.785986406 0.868909688 1.006018714 0.970712474 1.048676719 1.088216164 1 18.71219249 2.281973446 1.681014099 1.044081227 0.909483453 0.392385125 0.07104582 0.376348799 2.135112411 0.036529528 0.023592272 191.4138885 -2.281973446 -0.134597774 EKETLAVNYEKEEEFLTNELSR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKETLAVNYEKEEEFLTNELSR 22 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 292.19 1.14E-55 828830000 491450 476624 363391 371092 446377 510563 458964 576481 609762 580532 FALSE TRUE 472243.5907 463031.1502 429063.8373 390244.1026 460735.1216 520886.9337 464580.9387 564576.4659 540544.3741 541212.0506 0.872566659 0.85554479 0.79278323 0.721055827 0.851302407 0.962445188 0.858408342 1.043170538 0.998766331 1 19.04583444 2.282099945 1.121915 1.01385967 0.813648071 0.655175078 0.057025304 0.307750922 0.750855117 0.039447275 0.023193833 191.4696507 -2.282099945 -0.200211599 SDKNNEFIVIHNGIITNYK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDKNNEFIVIHNGIITNYK 19 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 262.25 2.03E-31 2228800000 2693900 2449000 2262100 2308400 2498500 2681600 2990500 3137700 3546600 3492000 FALSE TRUE 2588619.41 2379156.918 2670911.79 2427536.801 2578866.522 2735823.789 3027098.634 3072905.399 3144004.837 3255483.73 0.795156611 0.730815177 0.820434692 0.74567622 0.792160777 0.840373971 0.929846034 0.943916681 0.965756581 1 21.6344405 2.282557317 1.244181903 0.975495414 0.770185045 0.919833333 0.025809376 0.110445271 0.334055152 0.015044391 0.008967853 191.671401 -2.282557317 -0.205310369 SQESDGVEY(ph)IFISK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQESDGVEYIFISK 14 0 S4R337;Q5T2T1-2;Q5T2T1;U5GXS2 S4R337 MPP7 MAGUK p55 subfamily member 7 1 SQESDGVEY(0.85)IFIS(0.15)K;SQESDGVEY(1)IFISK 243.3 1.63E-16 104183000 132756 148685 115725 156270 149353 158773 211960 246980 219920 238692 TRUE FALSE 127567.7488 144444.6494 136639.0818 164335.1134 154157.0749 161983.4988 214554.0299 241879.7767 194955.6036 222525.1782 0.573273325 0.649115981 0.614038748 0.73850121 0.692762393 0.727933352 0.964178668 1.086977117 0.876105819 1 17.76360906 2.282604744 2.981716439 1.005697218 0.658732035 0.857638687 0.063555524 0.087547904 1.600151292 0.025839328 0.019573439 191.6923335 -2.282604744 -0.346965182 KPSVGS(ph)PSLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSVGSPSLTR 11 1 Q9NRJ4-2;Q9NRJ4 Q9NRJ4-2 TULP4 Tubby-related protein 4 1 KPS(0.03)VGS(0.824)PS(0.146)LTR 69.331 0.033563 132440000 217780 240570 175270 250980 199430 246420 255440 301010 289050 311560 TRUE FALSE 209268.9168 233709.1791 206945.1879 263933.1079 205844.8471 251402.7812 258566.1511 294794.0383 256238.2558 290457.7637 0.720479681 0.804623626 0.71247945 0.908679818 0.708691152 0.865539891 0.890202237 1.014929106 0.882187663 1 18.14796887 2.283198087 1.952626638 0.964859003 0.777055869 0.611739912 0.066455623 0.209295982 1.621667033 0.029399937 0.0199577 191.9544067 -2.283198087 -0.187803133 GSPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPVSPR 7 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 GS(0.001)PVS(0.999)PR 91.064 0.027152 0 380180 403310 382360 428450 383240 392600 356420 384430 359030 401210 TRUE FALSE 365322.1453 391807.9937 451460.9576 450562.3558 395567.2626 400538.641 360781.9746 376491.3862 318274.4196 374035.6893 0.976703977 1.047514996 1.206999681 1.204597231 1.057565558 1.070856746 0.964565641 1.006565408 0.850919922 1 18.51281641 2.283243312 1.528463224 0.948798554 1.109142303 0.44421879 0.076189751 0.389939908 1.81355211 0.043983437 0.027610267 191.974397 -2.283243312 0.160343749 T(ph)SPQELSEELSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPQELSEELSR 12 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;K7ERN1;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 T(0.598)S(0.402)PQELSEELSR 147.83 0.00073681 104480000 120870 119030 117300 136300 111130 135420 147900 164150 172030 171780 TRUE FALSE 116146.2668 115635.3809 138498.7193 143334.4593 114704.5974 138158.2852 149710.0444 160760.2451 152501.8756 160145.1876 0.725256054 0.722065912 0.864832228 0.895028202 0.716253789 0.862706443 0.934839483 1.003840625 0.952272609 1 17.28902092 2.283515743 2.402882685 0.982843564 0.791318098 0.699452923 0.058254411 0.173808526 2.058583377 0.026343204 0.019023483 192.0948592 -2.283515743 -0.191525466 NAEEFTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NAEEFTKK 8 1 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 70.363 0.082617 332530000 880510 996570 609210 807940 981280 1035700 1069500 1388700 1541800 1358100 FALSE TRUE 846098.6957 968148.7993 719307.7988 849637.8802 1012843.762 1056642.564 1082588.861 1360022.86 1366781.328 1266114.677 0.668263871 0.764661224 0.568122155 0.671059182 0.799962105 0.834555181 0.85504803 1.074170361 1.07950832 1 20.27197665 2.283947521 1.002495565 1.069168655 0.672197293 0.853402863 0.063674502 0.189687683 0.36738646 0.046018913 0.027094338 192.2859364 -2.283947521 -0.396971362 VSS(ph)QAEDTSSSFDNLFIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSSQAEDTSSSFDNLFIDR 19 0 H8Y6P7;P0CAP2-3;P0CAP2;Q9BZD3 H8Y6P7 GCOM1;POLR2M;GCOM2 DNA-directed RNA polymerase II subunit GRINL1A;Putative GRINL1B complex locus protein 2 1 VS(0.127)S(0.873)QAEDTSSSFDNLFIDR;VS(0.262)S(0.738)QAEDTSSSFDNLFIDR 195.77 9.09E-16 141397000 188970 209550 188791 217050 279420 211490 130590 162899 141683 155132 TRUE FALSE 181584.8435 203573.8392 222909.7333 228251.9765 288407.7981 215766.4727 132188.1995 159535.0787 125599.7398 144624.7715 1.255558378 1.407600075 1.541297048 1.578235694 1.994179802 1.491905367 0.914008009 1.103096497 0.868452469 1 17.14195515 2.283991857 6.145196072 0.990637464 1.564117954 0.69724019 0.184925 0.114175087 10.26826777 0.069861145 0.057350229 192.3055673 -2.283991857 0.57348049 LGDLYEEEMR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGDLYEEEMR 10 0 P08670;B0YJC4 P08670 VIM Vimentin 0 ; 144.5 7.47E-05 225630000 251340 296280 204867 220352 230540 231910 166215 172515 206177 163636 FALSE TRUE 241517.3549 287830.3845 241891.0241 231724.3931 237955.5285 236599.3791 168249.1889 168952.505 182772.6513 152552.788 1.583172344 1.886759254 1.585621786 1.518978422 1.559824187 1.550934481 1.102891603 1.107501916 1.198094468 1 17.21894902 2.28407636 4.042938319 1.106304805 1.626385317 0.853783769 0.10409918 0.081555287 2.800024725 0.040859916 0.03237316 192.3429889 -2.28407636 0.520080512 NLGFSPEDREENVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLGFSPEDREENVR 14 1 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 171.76 2.70E-06 1195140000 551630 626530 451220 580100 565900 557940 509010 565030 537220 562770 FALSE TRUE 530071.6897 608661.9778 532765.4913 610039.0305 584102.6874 569221.9291 515239.4166 553361.933 476237.0378 524653.0866 1.010327973 1.160122743 1.015462417 1.162747435 1.11331221 1.084949167 0.982057344 1.054719675 0.907717976 1 19.00100427 2.284084831 6.165917371 0.997210201 1.09574295 0.430078326 0.058579423 0.186558567 16.88568941 0.019588365 0.01608433 192.3467406 -2.284084831 0.098532749 VELGEKPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VELGEKPLR 9 1 Q9BSJ8-2;Q9BSJ8;F8VZB1 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ; 119.16 0.00079622 445060000 392890 524040 390780 576170 400190 497750 600980 694820 651040 531350 FALSE TRUE 377535.4244 509094.8923 461402.6389 605906.2027 413062.4748 507814.846 608334.973 680471.7242 577136.6686 495361.1912 0.762141708 1.027724621 0.931446886 1.22316042 0.833861195 1.025140554 1.228063449 1.373688 1.165082527 1 18.91812132 2.284461221 4.354314863 1.24091789 0.970065918 0.348803756 0.145804969 0.192088321 7.754677386 0.051721664 0.041316864 192.513514 -2.284461221 -0.270851972 DKPSGDTAAVFEEGGDVDDLLDMI ddPTM_BT-474_Pertuzumab_2h_R1 13 DKPSGDTAAVFEEGGDVDDLLDMI 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;;;;;;; 238.03 1.94E-37 1182623000 2601260 2496310 2192731 2372678 2453370 2666288 2628906 2992983 3251588 3061255 FALSE TRUE 2499599.883 2425117.683 2589006.269 2495132.196 2532284.874 2720202.17 2661079.338 2931176.855 2882481.362 2853913.472 0.875849919 0.84975165 0.907177563 0.874284459 0.887302611 0.953148088 0.932431682 1.027072784 1.010010076 1 21.44451016 2.284560136 1.02969417 1.017868925 0.87394403 0.869379209 0.02170226 0.16415409 0.335863817 0.014603058 0.008590042 192.5573658 -2.284560136 -0.143924895 LVYQIFDTFFAEQIEKDDREDKENAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVYQIFDTFFAEQIEKDDREDKENAFK 27 3 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 124.36 3.50E-05 89100000 101990 82864 58921 51508 52408 70519 79059 84580 95430 68449 FALSE TRUE 98004.11804 80500.79985 69569.33539 54166.33405 54093.75092 71944.9425 80026.54769 82833.39344 84597.18648 63812.88826 1.535804454 1.261513184 1.090208221 0.848830629 0.847693192 1.127435922 1.254081266 1.298066828 1.325706903 1 15.96156021 2.285026552 5.35329479 1.250737963 1.097746819 0.042639935 0.203552016 0.483676249 31.21916943 0.078673197 0.064029661 192.7642762 -2.285026552 -0.152991144 TCVQEITAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TCVQEITAHR 10 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317;Q13033-2;Q13033 F5GYK2;Q13033-2 STRN4;STRN3 Striatin-4;Striatin-3 0 127.87 0.0003447 357450000 198430 202870 153340 217900 173340 190130 222170 209150 233580 219980 FALSE TRUE 190675.1362 197084.3462 181051.949 229145.8451 178915.6385 193974.5589 224888.9829 204830.9794 207064.9776 205080.5587 0.92975725 0.961009408 0.882833313 1.117345528 0.87241638 0.945845672 1.096588503 0.998783018 1.00967629 1 17.64583121 2.28573882 24.99875579 1.025742754 0.952782971 0.226450408 0.067635308 179.6699949 95202.54753 0.022597722 0.018906556 193.08068 -2.28573882 -0.072959783 QGTTPPIWHLTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 QGTTPPIWHLTDK 13 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 153.24 4.14E-05 986460000 1645400 1778430 1452620 1612880 1640370 1664780 1812260 1852710 1977690 1908440 FALSE TRUE 1581095.949 1727710.918 1715140.747 1696120.93 1693133.991 1698442.992 1834438.98 1814450.891 1753190.922 1779179.659 0.888665707 0.971071645 0.964006495 0.953316278 0.951637448 0.954621409 1.031058876 1.019824435 0.985392854 1 20.76278077 2.285746015 8.014455245 1.012374969 0.949355385 0.615195367 0.023875367 0.156199352 23.26735644 0.00816392 0.006782517 193.0838789 -2.285746015 -0.063019584 KTQS(ph)FEIPQPDSGPR ddPTM_BT-474_Pertuzumab_2h_R1 3 KTQSFEIPQPDSGPR 15 1 A0A1B0GW72;Q96PX9 A0A1B0GW72 PLEKHG4B Pleckstrin homology domain-containing family G member 4B 1 KT(0.205)QS(0.795)FEIPQPDSGPR;KT(0.023)QS(0.977)FEIPQPDSGPR;KT(0.069)QS(0.931)FEIPQPDSGPR 125.03 5.69E-05 3087440000 1647600 1432610 1056190 1210700 1601570 1430520 1614960 1963820 2057820 1629690 TRUE FALSE 1583209.97 1391753.365 1247067.028 1273184.372 1653085.954 1459446.095 1634724.364 1923266.431 1824224.901 1519309.645 1.04205879 0.916043264 0.820811631 0.838001902 1.08805072 0.96059819 1.075965238 1.265881802 1.200693293 1 20.5349845 2.285814609 1.543451259 1.183758487 0.922194651 0.463369342 0.100678666 0.300834299 1.428733048 0.055410851 0.034977099 193.1143777 -2.285814609 -0.261563836 VEENPDADS(ph)DFDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEENPDADSDFDAK 14 0 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 VEENPDADS(1)DFDAK;VEENPDADS(1)DFDAK 230.45 9.51E-13 283310000 421250 370880 362190 378240 378540 436120 464060 513030 558250 556850 TRUE FALSE 404787.0843 360302.8655 427645.7899 397761.0117 390716.0829 444938.6452 469739.3051 502435.7512 494879.8004 519134.0535 0.779735179 0.694045908 0.823767555 0.766200963 0.752630424 0.857078518 0.90485165 0.967834315 0.953279403 1 18.9857476 2.286005181 1.241381467 0.978861456 0.758594179 0.886416916 0.033117412 0.136844006 0.412272035 0.019949371 0.011926726 193.1991367 -2.286005181 -0.220267277 KEGNASGVSLLEALDTILPPTRPTDKPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEGNASGVSLLEALDTILPPTRPTDKPLR 29 3 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 120.6 3.69E-05 76633000 126800 121060 113750 125900 128210 128740 137530 147890 174710 165490 FALSE TRUE 121844.5158 117607.4873 134307.1554 132397.7141 132333.9911 131343.211 139213.1333 144836.0198 154877.6532 154281.2149 0.789756004 0.762292982 0.870534727 0.858158358 0.857745327 0.851323417 0.90233366 0.938779358 1.003865917 1 17.23520289 2.286305678 0.389867112 1.020299488 0.774744364 0.853208707 0.029042108 0.487181904 0.171639822 0.034194787 0.042268962 193.3328609 -2.286305678 -0.245555124 LQFHNVKPECLEAYNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQFHNVKPECLEAYNK 16 1 O75323;F8WBI5 O75323 GBAS Protein NipSnap homolog 2 0 ; 226.7 3.43E-15 2470600000 1154890 1663680 991290 1943970 1014710 1225110 1994760 1848150 1489610 1134490 FALSE TRUE 1109755.622 1616233.475 1170438.154 2044298.525 1047349.069 1249882.564 2019172.47 1809985.057 1320515.718 1057649.982 1.049265486 1.528136438 1.106640358 1.93286868 0.990260565 1.181754442 1.909112187 1.711327082 1.248537551 1 20.01243083 2.286505678 24.99999715 1.559991114 1.314758407 0.025996652 0.349250857 270.0404883 140806.0107 0.11733923 0.098172811 193.4219145 -2.286505678 -0.245232707 MEDSVGCLETAEEVKR ddPTM_BT-474_Pertuzumab_2h_R1 4 MEDSVGCLETAEEVKR 16 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 322.89 4.30E-58 2249130000 1348920 1370090 1136951 1315710 1280440 1481500 1394730 1664590 1734230 1723520 FALSE TRUE 1296202.715 1331016.375 1342423.337 1383613.951 1321626.515 1511456.945 1411799.123 1630215.635 1537367.481 1606784.455 0.806706034 0.828372698 0.835471947 0.861107379 0.822528816 0.940671874 0.878648731 1.014582653 0.956797582 1 20.61574498 2.287464733 0.809028947 1.001049389 0.822724757 0.807879907 0.03211208 0.241358071 0.304666627 0.023514621 0.014632281 193.8495213 -2.287464733 -0.178324632 VPLS(ph)PLSLLAGPADAR ddPTM_BT-474_Pertuzumab_2h_R1 5 VPLSPLSLLAGPADAR 16 0 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 VPLS(0.999)PLS(0.001)LLAGPADAR;VPLS(0.928)PLS(0.072)LLAGPADAR;VPLS(1)PLSLLAGPADAR;VPLS(0.997)PLS(0.003)LLAGPADAR;VPLS(0.968)PLS(0.032)LLAGPADAR 154.46 3.71E-07 1969301000 176236 212684 227811 258988 220088 187623 155636.2 138357.3 130134.3 143503.9 TRUE FALSE 169348.5023 206618.4606 268981.5153 272354.4017 227167.3304 191416.8656 157540.9224 135500.1734 115361.9998 133784.253 1.26583285 1.544415399 2.01056185 2.035773236 1.698012473 1.430787714 1.177574481 1.012826026 0.862298792 1 17.02954879 2.287670928 1.658025811 0.959900203 1.736476761 0.713908081 0.210849817 0.216746726 1.19605624 0.120559317 0.077967122 193.9415793 -2.287670928 0.776576557 TADSVS(ph)PLEPPTK ddPTM_BT-474_Pertuzumab_2h_R1 4 TADSVSPLEPPTK 13 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 TADS(0.011)VS(0.989)PLEPPTK;TADS(0.001)VS(0.999)PLEPPTK;TADSVS(1)PLEPPTK;TADSVS(1)PLEPPTK 315.32 1.04E-50 1071780000 2338680 2428690 2526600 2854410 2966830 2472090 2129130 2167470 2211290 2071280 TRUE FALSE 2247281.8 2359426.139 2983212.824 3001726.442 3062260.781 2522077.354 2155186.93 2122710.987 1960273.63 1930990.361 1.163797524 1.221873598 1.544913369 1.554500998 1.585849854 1.306105615 1.116104448 1.099286164 1.015164897 1 20.88090953 2.287757811 2.869660897 1.061431234 1.420582789 0.618801007 0.1325631 0.197542535 3.33954011 0.059355505 0.044804662 193.9803825 -2.287757811 0.359151554 RVS(ph)S(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_BT-474_Pertuzumab_2h_R1 5 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.479)S(0.521)S(0.521)S(0.479)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.482)S(0.508)S(0.508)S(0.482)ELDLPS(0.02)GDHCEAGLLQLDVPLLR;RVS(0.826)S(0.395)S(0.372)S(0.407)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.5)S(0.5)S(0.5)S(0.5)ELDLPS(0.002)GDHCEAGLLQLDVPLLR;RVS(0.485)S(0.514)S(0.514)S(0.485)ELDLPS(0.001)GDHCEAGLLQLDVPLLR 106.21 0.00049026 105209000 100357.6 89645.6 74480 87795.3 87527.9 71281.8 71623.7 78905.1 70228.4 67605.2 TRUE FALSE 96435.51404 87088.99526 87940.1928 92326.42595 90343.31439 72723.16683 72500.25227 77275.68211 62256.36645 63026.23959 1.530085162 1.381789487 1.395294934 1.464888696 1.43342384 1.153855399 1.150318546 1.226087462 0.987784879 1 15.94366497 2.288060857 0.60027807 1.005324026 1.475196759 0.834438453 0.075331241 0.339476067 0.2455236 0.070102674 0.053613354 194.1157871 -2.288060857 0.469872733 FKGDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 FKGDSR 6 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7;K7ELW5;K7EKX4 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 86.086 0.049227 979160000 6350300 6312300 4865900 6002700 5852700 5966000 6257100 6446300 6793400 6935100 FALSE TRUE 6102123.255 6132279.384 5745276.371 6312500.066 6040957.411 6086636.608 6333676.262 6313181.652 6022241.712 6465379.5 0.943815171 0.948479418 0.888621677 0.976354144 0.934354652 0.941419851 0.979629465 0.976459565 0.931459895 1 22.62430362 2.288069398 7.404192216 0.970944725 0.93836531 0.284552097 0.025655837 0.289336316 35.83465241 0.008670753 0.007190878 194.1196046 -2.288069398 -0.032579415 DS(ph)FDDRGPSLNPVLDYDHGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSFDDRGPSLNPVLDYDHGSR 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 DS(1)FDDRGPSLNPVLDYDHGSR;DS(1)FDDRGPSLNPVLDYDHGSR 190.93 9.82E-18 150633000 139673 184368 139954 187111 184957 166167 150724 163825 147721 169602 TRUE FALSE 134214.4247 179110.0052 165246.8011 196767.8211 190906.3099 169527.0106 152568.6054 160441.9565 130952.3314 158114.7055 0.848842139 1.132785244 1.045107098 1.244462497 1.207391237 1.07217738 0.964923566 1.014718751 0.828210956 1 17.27061203 2.288151648 3.865875485 0.958528672 1.106264022 0.275937862 0.110486965 0.300851174 9.298365807 0.041825562 0.033052608 194.156372 -2.288151648 0.14773535 DALLDHDLALPLCLLMAQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DALLDHDLALPLCLLMAQQR 20 0 Q8NI27;A0A0C4DG98 Q8NI27 THOC2 THO complex subunit 2 0 140.28 2.04E-07 107890000 67323 68853 66862 80597 72072 73549 65815 70355 81342 85908 FALSE TRUE 64691.94273 66889.37985 78945.45074 84756.62083 74390.26133 75036.21117 66620.46366 68902.14466 72108.39717 80089.37464 0.807746883 0.835184195 0.985716908 1.058275473 0.928840582 0.936905944 0.831826493 0.860315678 0.90034911 1 16.28932323 2.28816298 24.99708784 0.881726568 0.930274019 0.009383435 0.078002024 315.3995952 158943.9801 0.028881953 0.024164344 194.1614381 -2.28816298 0.048547451 LVDQSGPPHEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVDQSGPPHEPK 12 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 187.97 9.80E-06 875150000 1445610 1354710 1218820 1209120 1352990 1452340 1376570 1535150 1747620 1590130 FALSE TRUE 1389113.963 1316074.997 1439087.887 1271522.828 1396510.152 1481707.31 1393416.875 1503448.616 1549237.504 1482429.079 0.93705256 0.887782772 0.970763396 0.857729281 0.942041796 0.999513117 0.939955169 1.014179118 1.045066861 1 20.49953166 2.288494743 0.934634547 1.021487337 0.914945834 0.554895566 0.036767129 0.416121763 0.69981191 0.026184021 0.015613765 194.309817 -2.288494743 -0.106541503 KGDECELLGHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGDECELLGHSK 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 166.6 3.34E-05 2468800000 3359400 4588400 3023400 5714300 2790840 3810000 5925000 5206600 4997700 4059500 FALSE TRUE 3228110.934 4457543.325 3569795.635 6009215.708 2880609.903 3887040.81 5997511.922 5099081.891 4430382.048 3784546.449 0.852971678 1.177827617 0.943255865 1.58782982 0.761150627 1.027082337 1.5847373 1.347342927 1.170650726 1 21.85168898 2.28856027 24.9992419 1.319210537 1.069109613 0.141929507 0.252053913 176.8642392 88429.18969 0.084595554 0.070777609 194.339137 -2.28856027 -0.250100924 KGVAINMVTEEDKR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGVAINMVTEEDKR 14 2 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;; 189.1 4.26E-07 19210000000 5707210 5063120 4758170 4743560 5257350 5725340 5770060 6497900 7328190 6704000 FALSE TRUE 5484165.924 4918724.775 5618077.164 4988375.7 5426457.437 5841110.298 5840675.72 6363716.094 6496324.593 6249932.109 0.877476079 0.787004513 0.898902111 0.798148782 0.868242621 0.9345878 0.934518267 1.018205635 1.039423226 1 22.57540909 2.289251342 1.111728603 1.025219223 0.838740375 0.811827476 0.035773342 0.187955129 0.450729935 0.022291771 0.013186104 194.6486259 -2.289251342 -0.186478848 S(ph)PSSDLDTDAEGDDFELLDQSELSQLDPASSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSSDLDTDAEGDDFELLDQSELSQLDPASSR 32 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 S(0.331)PS(0.331)S(0.331)DLDT(0.008)DAEGDDFELLDQSELSQLDPASSR;S(0.333)PS(0.333)S(0.333)DLDTDAEGDDFELLDQSELSQLDPASSR;S(0.353)PS(0.353)S(0.294)DLDT(0.001)DAEGDDFELLDQSELSQLDPASSR 252.67 2.87E-59 297599000 71457 95981 79611 118832 71888 93612 121352 121989 125020 123484 TRUE FALSE 68664.38144 93243.71586 93998.47864 124964.9338 74200.34281 95504.89878 122837.1421 119469.8845 110828.2537 115120.3187 0.596457534 0.809967492 0.816523788 1.085515877 0.644546016 0.829609402 1.067032679 1.037782781 0.962716704 1 16.81278297 2.289297995 6.606978629 1.023471311 0.803465147 0.428058958 0.124362224 0.197657675 19.22580544 0.043950371 0.036299974 194.6695365 -2.289297995 -0.220006164 KEGVFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEGVFAK 7 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 90.657 0.027223 2178640000 3726100 3798300 2982300 3162300 4063100 3825200 5377700 5485700 6351600 6213000 FALSE TRUE 3580479.893 3689976.203 3521267.951 3325506.682 4193793.302 3902548.165 5443513.901 5372418.378 5630592.996 5792187.976 0.618156715 0.637060851 0.607933991 0.574136526 0.724043025 0.673760621 0.9398027 0.927528319 0.97210122 1 22.46567699 2.289332171 1.455853532 0.976807992 0.618716848 0.929588497 0.043119382 0.092238654 0.387921609 0.022860165 0.014235809 194.6848562 -2.289332171 -0.358091144 AELGSWSS(ph)QEHLEWEPACQTPQPSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AELGSWSSQEHLEWEPACQTPQPSAR 26 0 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AELGS(0.001)WS(0.18)S(0.819)QEHLEWEPACQTPQPSAR 180.71 1.36E-17 285850000 101660 130560 86572 98752 103140 101930 112300 92279 122100 104130 TRUE FALSE 97687.01481 126836.5566 102217.4862 103848.6026 106457.5918 103991.0944 113674.361 90373.4064 108239.7199 97077.18235 1.006281934 1.30655375 1.05295069 1.069752954 1.096628365 1.071220774 1.170968895 0.930943855 1.114986213 1 16.56684461 2.289347146 0.414979497 1.000782718 1.142543972 0.105145844 0.092698595 2.185716891 0.84938758 0.094422071 0.108820061 194.6915693 -2.289347146 0.141761255 NNESQWKDS(ph)PLATR ddPTM_BT-474_Pertuzumab_2h_R1 2 NNESQWKDSPLATR 14 1 O95155-2;O95155;O95155-4;K7EP75;O95155-3 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 NNES(0.011)QWKDS(0.989)PLATR;NNESQWKDS(1)PLATR 116.29 0.00022402 869870000 475940 451940 409300 447870 526590 467490 418700 451400 514780 473200 TRUE FALSE 457339.7386 439051.1137 483269.6148 470984.6244 543528.2456 476942.9681 423824.1758 442078.4323 456344.3325 441149.7425 1.036699548 0.99524282 1.095477495 1.067629829 1.232072 1.081136227 0.960726336 1.002105158 1.034443157 1 18.75090892 2.289996837 9.502338485 0.998445933 1.087204033 0.33151899 0.059340801 0.443024702 77.88872801 0.022221049 0.018540881 194.9830401 -2.289996837 0.0887581 (ac)AALHTTPDS(ph)PAAQLER ddPTM_BT-474_Pertuzumab_2h_R1 5 AALHTTPDSPAAQLER 16 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 AALHTTPDS(1)PAAQLER;AALHTT(0.001)PDS(0.999)PAAQLER;AALHT(0.011)T(0.267)PDS(0.722)PAAQLER;AALHTTPDS(1)PAAQLER;AALHTTPDS(1)PAAQLER 139 6.84E-72 5634770000 67893 108483 140475 113902 115175 129305 78300.9 133721 92598 120277 TRUE FALSE 65239.6665 105389.1711 165861.9573 119780.4959 118879.7085 131919.6357 79259.16984 130959.6146 82086.66324 112130.5317 0.581818935 0.939879349 1.479186399 1.06822374 1.060190358 1.176482745 0.706847356 1.167921107 0.732063445 1 16.77481963 2.290023757 24.99999682 0.935259523 1.066582748 0.07507276 0.241908487 320.2577673 155574.624 0.0850038 0.071119192 194.9951266 -2.290023757 0.131323225 RRPES(ph)APAESSPSK ddPTM_BT-474_Pertuzumab_2h_R1 4 RRPESAPAESSPSK 14 2 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 RRPES(0.679)APAES(0.16)S(0.16)PSK;RRPES(1)APAESSPSK;RRPES(0.736)APAES(0.162)S(0.102)PSK;RRPES(0.524)APAES(0.266)S(0.193)PS(0.017)K 129.46 5.34E-05 503500000 299404 296806 242073 258134 274751 241263 211136 211924 221440 193448 TRUE FALSE 287702.9607 288341.3835 285820.976 271456.3267 283588.6154 246141.5032 213719.9455 207547.6953 196303.0596 180345.5947 1.595286878 1.598826875 1.584851443 1.505200763 1.572473206 1.364832358 1.185057755 1.150833186 1.088482699 1 17.46040466 2.290336075 0.955744018 1.042316685 1.595261747 0.973400924 0.036711146 0.080337458 0.141404803 0.026500511 0.015770832 195.1354054 -2.290336075 0.552945062 DNKPLVER ddPTM_BT-474_Pertuzumab_2h_R1 4 DNKPLVER 8 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;;; 123.86 0.0012124 2304070000 2058090 2197910 1817670 1968510 1990810 2086900 2294650 2396090 2591780 2474550 FALSE TRUE 1977657.567 2135227.759 2146163.403 2070105.037 2054846.212 2129098.548 2322732.613 2346609.904 2297572 2306946.524 0.85726199 0.925564479 0.93030479 0.89733551 0.890721215 0.922907629 1.00684285 1.017193021 0.995936393 1 21.13755313 2.290552285 3.987871074 1.008419232 0.903526461 0.864125478 0.019730254 0.07363531 2.413878496 0.007345669 0.005834622 195.2325761 -2.290552285 -0.104892771 SITS(ph)PTTLYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SITSPTTLYDR 11 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 SIT(0.126)S(0.423)PT(0.423)T(0.028)LYDR;SIT(0.008)S(0.482)PT(0.482)T(0.028)LYDR 241.39 1.06E-15 952090000 1299970 1398730 1093210 1145780 1149020 1096650 1153920 1089220 1014600 1039250 TRUE FALSE 1249165.735 1358839.59 1290777.365 1204913.843 1185979.272 1118825.014 1168042.018 1066727.226 899426.8616 968860.6718 1.28931411 1.402512899 1.332263145 1.243639956 1.224096825 1.154784219 1.205583065 1.101012 0.928334577 1 19.88592969 2.290678917 0.497747079 0.964905601 1.364630116 0.842550851 0.055159324 0.366861459 0.192001822 0.054013777 0.050350992 195.2895105 -2.290678917 0.399724515 EFKEEGEEIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFKEEGEEIPR 11 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 141.13 3.49E-05 695320000 608670 612030 471790 500530 540150 569170 605950 651050 696080 649940 FALSE TRUE 584882.5035 594575.5036 557052.9479 526362.4133 557524.4153 580679.0074 613365.7974 637605.59 617063.9166 605918.9849 0.965281693 0.981278881 0.919352194 0.868700976 0.920130297 0.958344303 1.012290112 1.052295118 1.018393435 1 19.20876538 2.290850049 2.829507357 1.029986723 0.930220512 0.654405491 0.030772395 0.166025397 2.727366954 0.01376595 0.010386241 195.366479 -2.290850049 -0.09976621 TKS(ph)WGEQCPETSGTDSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKSWGEQCPETSGTDSGR 18 1 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 T(0.137)KS(0.863)WGEQCPETSGTDSGR;T(0.463)KS(0.537)WGEQCPETSGTDSGR 166.75 1.51E-11 1099100000 412560 427290 323130 366290 395550 390990 349500 400320 415400 405070 TRUE FALSE 396436.6991 415104.1076 381526.779 385194.2708 408273.225 398896.0857 353777.2855 392053.2521 368245.5335 377634.2481 1.049790111 1.09922262 1.010307674 1.020019431 1.081133999 1.056302726 0.936825215 1.038182458 0.975138074 1 18.52663008 2.291381869 24.99996301 0.993878767 1.052773443 0.467348542 0.033861465 92.62361107 43837.69157 0.011620802 0.009722651 195.6058633 -2.291381869 0.058894676 YVELFLNSTAGASGGAYEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 YVELFLNSTAGASGGAYEHR 20 0 P31943;G8JLB6;H0YB39 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 80.752 0.0042463 0 228230 229780 174930 185950 230540 208840 221070 235820 271100 235310 FALSE TRUE 219310.5193 223226.8994 206543.7423 195546.9018 237955.5285 213062.8879 223775.5208 230950.2346 240325.8645 219372.2441 0.99971863 1.017571299 0.941521764 0.891393087 1.084711192 0.971239041 1.020072169 1.052777828 1.095516279 1 17.74302148 2.291543657 1.113694909 1.054569292 0.976416288 0.232512809 0.052038157 0.69841942 1.68184447 0.034702946 0.020573979 195.678746 -2.291543657 -0.078153004 KDSETGENIR ddPTM_BT-474_Pertuzumab_2h_R1 5 KDSETGENIR 10 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;; 153.95 2.46E-05 5146440000 3546700 5259410 3178930 6298740 3168630 4162860 5962850 5707390 4718430 4291810 FALSE TRUE 3408091.043 5109416.776 3753433.366 6623818.726 3270551.862 4247035.881 6035825.142 5589530.402 4182813.608 4001121.886 0.85178386 1.276996033 0.938095233 1.655490364 0.817408706 1.061461261 1.508533185 1.396990784 1.045410194 1 21.93197315 2.292134547 24.99996174 1.292828524 1.113258782 0.043163913 0.267288183 227.7825098 106292.1124 0.089659301 0.07501429 195.9451631 -2.292134547 -0.179569742 VIREPKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 VIREPKPR 8 2 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 146.79 0.00030808 14111740000 3192180 3191360 2702021 2793210 2635645 3016600 3130860 3308562 3616270 3377790 FALSE TRUE 3067426.076 3100345.537 3190336.301 2937367.903 2720422.915 3077597.719 3169176.401 3240239.039 3205766.19 3149009.275 0.974092424 0.984546334 1.013123818 0.932791125 0.863898032 0.977322532 1.006404277 1.028970942 1.018023737 1 21.58646658 2.292558095 3.815250194 1.017663564 0.954714733 0.355105439 0.03750297 0.263610209 7.85723845 0.01546735 0.01223712 196.1363525 -2.292558095 -0.06294883 ELS(ph)PAALEK ddPTM_BT-474_Pertuzumab_2h_R1 8 ELSPAALEK 9 0 O75683 O75683 SURF6 Surfeit locus protein 6 1 ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK 183.99 4.67E-05 6269840000 6421410 5967220 6379990 6196380 6198720 7213410 7630990 8221690 9489280 8898190 TRUE FALSE 6170454.198 5797040.728 7532996.115 6516175.914 6398107.458 7359270.092 7724380.338 8051909.228 8412096.717 8295507.666 0.743830811 0.698816873 0.908081388 0.785506587 0.771273768 0.887139207 0.931152215 0.970634897 1.014054481 1 22.98389884 2.292806212 0.933414139 1.011268241 0.773247304 0.772995094 0.051173502 0.274591127 0.461026509 0.038518311 0.023059141 196.2484393 -2.292806212 -0.238020937 HAS(ph)PILPITEFSDIPR ddPTM_BT-474_Pertuzumab_2h_R1 8 HASPILPITEFSDIPR 16 0 P42167;G5E972;H0YJH7 P42167 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR 245.66 2.50E-20 2165722200 630435 795911 530536 849913 583455 608284 640367 454669 625523 581499 TRUE FALSE 605796.9032 773212.3976 626415.6569 893777.1118 602222.36 620583.9192 648204.0029 445279.9263 554516.2514 542113.5548 1.117472341 1.426292316 1.155506354 1.648689843 1.110878624 1.144748944 1.195697833 0.821377592 1.022878411 1 19.04823555 2.293084255 1.264039959 0.940025516 1.3153288 0.420456152 0.165804109 0.390816052 1.224496614 0.097283804 0.058761437 196.3741216 -2.293084255 0.375303285 TRQELEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TRQELEK 7 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;; 117.89 0.0046782 987070000 718680 853880 639650 709480 762210 754000 839800 843620 899750 867880 FALSE TRUE 690593.1911 829528.1784 755248.9839 746096.3478 786727.1769 769246.3966 850077.7236 826198.9522 797614.1521 809097.7146 0.853534967 1.025250923 0.933445949 0.922133797 0.972351253 0.950745976 1.050649023 1.021136183 0.985806952 1 19.62595442 2.293099387 9.518262099 1.017875733 0.946490929 0.39334475 0.043272946 0.352619443 58.4920056 0.014206593 0.011858169 196.3809637 -2.293099387 -0.071384804 AQGEPVAGHES(ph)PKIPYEK ddPTM_BT-474_Pertuzumab_2h_R1 9 AQGEPVAGHESPKIPYEK 18 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 1 AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK 227.25 1.85E-19 45891020000 13072100 11496980 9323670 8873660 11145720 11359780 11411900 12489580 14635170 11798270 TRUE FALSE 12561227.88 11169097.39 11008664.57 9331630.656 11504232.21 11589482.53 11551562.25 12231665.81 12973846.86 10999162.66 1.142016739 1.015449787 1.000863876 0.848394641 1.045918908 1.053669528 1.050221967 1.11205427 1.179530411 1 23.39089036 2.293354806 1.611239026 1.104092171 1.003131028 0.167305058 0.07934725 0.594579454 3.093771573 0.042547373 0.027424929 196.4964942 -2.293354806 -0.100961143 KDPEDTGAEKSPTTSADLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 195.56 4.93E-16 579100000 443480 400844 256710 227529 301795 339459 342404 411814 396922 305941 FALSE TRUE 426148.3113 389412.3216 303103.2075 239271.799 311502.5103 346323.0936 346594.4426 403309.897 351865.0786 285219.3436 1.494107328 1.365308246 1.062702142 0.838904529 1.092150716 1.214234242 1.215185612 1.414034167 1.23366485 1 18.1217123 2.293775053 3.035148715 1.269202015 1.158068289 0 0.192054957 0.865744259 16.33225544 0.081879715 0.062722975 196.686727 -2.293775053 -0.111133726 GYAYVEFENPDEAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GYAYVEFENPDEAEK 15 0 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BV80;H3BPG5 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 0 ; 256.95 2.10E-24 431900000 877830 748230 669110 717400 817830 831910 824620 927650 1040130 981610 FALSE TRUE 843523.4331 726891.213 790033.0613 754425.1 844136.2447 848731.7902 834711.9462 908493.7033 922058.803 915124.6804 0.921757932 0.794308392 0.863306474 0.824395972 0.92242758 0.92744935 0.912129204 0.992754018 1.007577244 1 19.80360879 2.293776111 0.766172629 1.00996352 0.847066281 0.71085134 0.037070753 0.33290789 0.378631061 0.028594329 0.018349815 196.6872059 -2.293776111 -0.162897239 YSQKEDRYEEEIK ddPTM_BT-474_Pertuzumab_2h_R1 3 YSQKEDRYEEEIK 13 2 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;; 133.47 6.01E-05 2236900000 1210390 1119930 951220 947190 1188670 1194190 1218090 1429530 1608570 1400580 FALSE TRUE 1163086.621 1087990.693 1123126.614 996074.5894 1226904.65 1218337.34 1232997.35 1400009.706 1425971.877 1305717.469 0.890764387 0.833251234 0.860160517 0.762856141 0.93964022 0.933078839 0.94430639 1.072214885 1.092098338 1 20.31641133 2.294161489 1.114985093 1.062995966 0.844203118 0.750256467 0.048796545 0.229692851 0.554764966 0.031927438 0.018976404 196.8618169 -2.294161489 -0.218792848 VEEGGRHPS(ph)PCQFTIATPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEEGGRHPSPCQFTIATPK 19 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VEEGGRHPS(0.999)PCQFT(0.001)IATPK 111.11 0.00013481 555360000 346560 320920 346830 283680 341110 346250 384840 431780 407480 408040 TRUE FALSE 333016.0521 311767.6758 409509.8962 298320.7588 352082.1129 353251.4122 389549.787 422863.5921 361224.5787 380403.0874 0.875429415 0.819571886 1.076515701 0.784222759 0.925550093 0.928623936 1.024044757 1.111619769 0.94958372 1 18.53716943 2.294221721 3.188559727 1.041108518 0.898040465 0.335209142 0.082029234 0.249474386 5.187251414 0.030935304 0.023900354 196.8891216 -2.294221721 -0.143068053 SDLDYIRS(ph)PLPFQNR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDLDYIRSPLPFQNR 15 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 1 SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR 200.99 4.02E-09 1032080000 1263260 1458240 1408830 1552000 1508340 1409300 1051689 1165231 1095977 1229992 TRUE FALSE 1213890.403 1416652.423 1663436.92 1632098.906 1556857.126 1437797.012 1064559.885 1141168.573 971566.2857 1146683.546 1.058609768 1.235434508 1.450650378 1.423321117 1.357704252 1.253874285 0.928381582 0.995190501 0.847283707 1 20.12903587 2.294335238 4.454121299 0.945901746 1.314595768 0.714394656 0.109737323 0.117123802 4.759013806 0.04266397 0.034357306 196.9405913 -2.294335238 0.368694022 VHIDIGADGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VHIDIGADGR 10 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;; 167.93 5.09E-06 6151980000 2752949 3186680 2326918 2834200 2849400 2656080 2256450 1835556 2857020 2818360 FALSE TRUE 2645360.71 3095799.006 2747443.845 2980473.402 2941053.539 2709787.757 2284065.11 1797651.127 2532703.067 2627469.967 1.006809114 1.178243346 1.04566137 1.134351083 1.119348109 1.031329679 0.869302081 0.684175709 0.963932262 1 21.32524284 2.294346921 3.339795209 0.831890733 1.098436516 0.528318909 0.09346298 0.148127485 3.375387994 0.034837785 0.027109238 196.9458895 -2.294346921 0.266545783 LS(ph)ASSSISSADLFEEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSASSSISSADLFEEPR 17 0 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 LS(1)ASSSISSADLFEEPR 263.45 2.21E-27 35775000 36216 31833 22866 28801 33224 30131 20343 28485 24866 22706 TRUE FALSE 34800.63868 30925.15401 26998.39485 30287.42306 34292.68013 30740.26946 20591.96372 27896.7748 22043.31593 21168.1024 1.644013149 1.460931803 1.275428205 1.430804826 1.620016735 1.452197693 0.972782696 1.317868474 1.041345866 1 14.36960432 2.294480407 9.163771133 1.127212103 1.475160346 0.678766102 0.132580019 0.21647629 33.26929213 0.046779753 0.039033271 197.0064325 -2.294480407 0.347948243 YHTVNGHNCEVR ddPTM_BT-474_Pertuzumab_2h_R1 12 YHTVNGHNCEVR 12 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;F8VTQ5;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;;;;;;;;;;; 231.52 1.87E-12 39075851000 4644058 4597064 3666427 4220276 3838855 3190728 3646393 424322 3856917 3111311 FALSE TRUE 4462563.079 4465960.236 4329031.918 4438084.95 3962335.257 3255246.706 3691018.648 415559.6024 3419095.952 2900579.135 1.538507612 1.539678812 1.492471578 1.530068564 1.3660497 1.122274744 1.272510929 0.143267804 1.178763203 1 21.46790955 2.294871814 1.630408822 0.710444545 1.498445684 0.493992 0.286052423 0.262117456 1.398368621 0.146698132 0.095056629 197.1840642 -2.294871814 0.78800114 GVQLQTHPNVDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 GVQLQTHPNVDKK 13 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 159.08 3.00E-05 2838600000 2823550 2463120 2096050 1928180 2445370 2534140 2551380 2909380 3114740 2891350 FALSE TRUE 2713202.544 2392874.229 2474852.861 2027693.601 2524027.547 2585382.047 2582604.552 2849300.286 2761167.773 2695516.289 1.006561361 0.887723899 0.91813686 0.752246836 0.936380001 0.959141689 0.958111276 1.057051778 1.024355811 1 21.3621302 2.294872961 1.544650488 1.029411935 0.893473355 0.422078526 0.062236578 0.357246814 1.702369059 0.03402597 0.021681424 197.1845851 -2.294872961 -0.135938579 DYNKYEEGINIHLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYNKYEEGINIHLAK 15 1 Q12996;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 0 142.1 2.79E-06 610790000 1116200 1015900 821500 875120 1014300 967180 1068300 1053300 1219400 1167900 FALSE TRUE 1072577.67 986927.5267 969963.3242 920285.0481 1046925.881 986737.0423 1081374.175 1031548.987 1080978.824 1088797.093 0.985103356 0.906438429 0.890857746 0.845230993 0.961543604 0.90626348 0.99318246 0.947420776 0.992819352 1 20.05430369 2.294936305 1.387754926 0.981061563 0.909546686 0.381113066 0.039608391 0.467397962 1.78031788 0.022763405 0.014072163 197.2133476 -2.294936305 -0.071514877 YKYEVEDFTGVYEEVDEEQYSK ddPTM_BT-474_Pertuzumab_2h_R1 1 YKYEVEDFTGVYEEVDEEQYSK 22 1 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 0 209.38 5.25E-23 127540000 171990 144970 125810 127920 138830 153850 165950 181950 197340 186950 FALSE TRUE 165268.4407 140835.5975 148546.6656 134521.9665 143295.593 156960.9524 167980.9457 178192.6689 174938.7905 174287.71 0.948250687 0.808063848 0.852307174 0.771838511 0.822178414 0.900585316 0.963814062 1.022405246 1.003735665 1 17.41111131 2.295345197 2.086279322 1.009117067 0.836181539 0.74608992 0.043488506 0.149908543 1.333089945 0.019585082 0.013731192 197.3991129 -2.295345197 -0.172935528 LVPTGPTHREPS(ph)PVRYDNLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVPTGPTHREPSPVRYDNLSR 21 2 Q9C0B5;Q9C0B5-2 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5 1 LVPTGPTHREPS(1)PVRYDNLSR 150.94 3.47E-08 505140000 233790 348080 201910 293550 228160 270880 339270 357170 334180 279980 TRUE FALSE 224653.2283 338153.0992 238399.6285 308700.1507 235498.9736 276357.3792 343422.0877 349794.3147 296245.2874 261016.7052 0.860685251 1.295522825 0.91335008 1.182683501 0.902237171 1.058772767 1.315709228 1.340122328 1.134966772 1 17.99378262 2.295909594 8.137764386 1.24124078 1.04176381 0.188668525 0.154285785 0.321085328 40.47755733 0.050351032 0.041935923 197.6558143 -2.295909594 -0.19947697 LREEEVDADAADAAAAEEEDGEFLGMK ddPTM_BT-474_Pertuzumab_2h_R1 1 LREEEVDADAADAAAAEEEDGEFLGMK 27 1 D6RGY8;D6RFI3;E7EQR8;Q9GZM5 D6RGY8 YIPF3 "Protein YIPF3;Protein YIPF3, 36 kDa form III" 0 162.07 1.14E-11 111680000 66244 87161 63404 72936 77908 84103 85121 99630 106240 106630 FALSE TRUE 63655.11124 84675.25362 74862.51321 76700.2357 80413.98157 85803.62028 86162.73626 97572.60568 94180.08059 99407.85512 0.64034287 0.851796405 0.753084483 0.771571176 0.808929852 0.863147285 0.866759837 0.981538185 0.947410851 1 16.60107224 2.29609139 0.622590551 1.005683216 0.74098587 0.77815222 0.049603774 0.341205797 0.263611044 0.040860479 0.030404152 197.7385703 -2.29609139 -0.264697346 VIDIFDTDGNGEVDFK ddPTM_BT-474_Pertuzumab_2h_R1 4 VIDIFDTDGNGEVDFK 16 0 F6U1T9;D3YTA9;H7BYZ3;P63098 F6U1T9 PPP3R1 Calcineurin subunit B type 1 0 ;;; 212.18 1.20E-11 151413000 259469 271058 249821 285756 284717 290653 335394 384836 404921 413344 FALSE TRUE 249328.6646 263327.6912 294969.2119 300503.9014 293875.1809 296530.2028 339498.6521 376889.0021 358956.0656 385347.8427 0.647022344 0.68335063 0.765462212 0.779825052 0.762623138 0.769513073 0.881018691 0.978048818 0.931511808 1 18.55580179 2.2962856 0.576603431 1.013906834 0.683649438 0.896797427 0.036987355 0.264298964 0.178092056 0.036954195 0.029543687 197.827016 -2.2962856 -0.330257396 SSFVCVLLSHGEEGIIFGTNGPVDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSFVCVLLSHGEEGIIFGTNGPVDLK 26 0 P42574;A8MVM1 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 142.94 2.71E-07 133620000 48423 48449 39137 46965 45869 51734 48177 50928 61326 58378 FALSE TRUE 46530.57563 47067.28196 46209.9265 49388.86928 47344.41804 52780.09693 48766.60454 49876.319 54364.52958 54424.00606 0.854964178 0.864825752 0.849072493 0.907483165 0.869917918 0.969794411 0.896049521 0.916439686 0.998907165 1 15.73195553 2.296601167 0.260709254 1.016635477 0.819120639 0.713116642 0.029402914 1.384303756 0.265880613 0.05708687 0.097596534 197.9708131 -2.296601167 -0.197514838 SEVELAAALSDKR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEVELAAALSDKR 13 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ;;; 181.76 1.89E-05 886570000 652930 695410 561110 696520 594130 661810 678650 753010 742970 674370 FALSE TRUE 627412.7737 675577.5877 662515.0588 732467.4807 613240.731 675192.2516 686955.5217 737460.0804 658631.1604 628694.3192 0.997961576 1.074572438 1.053795205 1.165061395 0.975419552 1.073959524 1.092670159 1.173002615 1.047617483 1 19.2619992 2.297026188 4.335561965 1.101585849 1.057890624 0 0.063763172 0.535049052 20.35859634 0.022790241 0.018331092 198.1646516 -2.297026188 -0.043695225 SVESTS(ph)PEPSK ddPTM_BT-474_Pertuzumab_2h_R1 5 SVESTSPEPSK 11 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 1 SVEST(0.268)S(0.732)PEPSK;SVEST(0.292)S(0.708)PEPSK;SVEST(0.16)S(0.839)PEPSK;SVEST(0.01)S(0.99)PEPSK;SVES(0.001)T(0.048)S(0.951)PEPSK 318.18 7.27E-46 4881450000 7276650 7260420 6086750 6472380 6606780 7245480 7353500 7922820 8680670 8361580 TRUE FALSE 6992270.473 7053359.93 7186761.124 6806420.307 6819293.079 7391988.57 7443494.333 7759210.998 7695276.734 7795242.739 0.896992013 0.904828774 0.921941929 0.873150527 0.87480189 0.948269197 0.954876529 0.995377727 0.987176024 1 22.89416252 2.297701057 1.698094416 0.991892742 0.895799235 0.867775148 0.016716203 0.128538914 0.746837119 0.008846533 0.005823757 198.4728274 -2.297701057 -0.096093507 SCSPS(ph)PVSPQVQPQAADTISDSVAVPASLLGMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCSPSPVSPQVQPQAADTISDSVAVPASLLGMR 33 0 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.025)CS(0.121)PS(0.697)PVS(0.156)PQVQPQAADTISDSVAVPASLLGMR 179.54 8.70E-20 200210000 109200 103780 80738 111070 96303 99377 84907 95280 81296 110300 TRUE FALSE 104932.3433 100820.296 95329.15261 116802.336 99400.67346 101386.471 85946.11726 93312.4347 72067.6189 102829.2828 1.020451961 0.980462893 0.927062312 1.135885935 0.966657267 0.985968863 0.835813641 0.90745002 0.700847239 1 16.64989163 2.298127389 5.30127369 0.858429165 1.004242103 0.39654307 0.085737436 0.195152048 10.98048334 0.029123217 0.023835089 198.6677571 -2.298127389 0.145812939 FKDPGLVDQLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKDPGLVDQLVK 12 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 131.26 0.00018414 383110000 437370 406100 319210 381420 407470 442020 470260 574450 597280 533120 FALSE TRUE 420277.0969 394518.4256 376898.3478 401105.1319 420576.6426 450957.9473 476015.1826 562587.4068 529479.2784 497011.3075 0.845608723 0.793781589 0.758329523 0.807034218 0.846211417 0.907339411 0.957755237 1.13194086 1.065326423 1 18.92291915 2.29821087 1.458671702 1.078774575 0.80216255 0.872326313 0.04213915 0.124007033 0.524558359 0.023634104 0.014858384 198.7059491 -2.29821087 -0.276612025 MSTS(ph)QNS(ph)IPFEHHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 MSTSQNSIPFEHHGK 15 0 P48730-2 P48730-2 CSNK1D Casein kinase I isoform delta 2 MS(0.273)T(0.329)S(0.397)QNS(1)IPFEHHGK;MS(0.127)T(0.145)S(0.728)QNS(1)IPFEHHGK 68.189 0.025242 372841000 274726 284372 237452 237887 249450 241831 185058 142072 251200 237550 TRUE FALSE 263989.4042 276261.989 280364.8585 250164.3766 257473.7858 246720.9885 187322.7952 139138.1636 222684.8291 221460.5269 1.192038183 1.247454762 1.265981177 1.129611584 1.162617056 1.114063043 0.845851844 0.62827523 1.005528309 1 17.75669005 2.298432231 3.385338331 0.812226498 1.197228425 0.660139205 0.109392421 0.123867267 2.888417755 0.042192672 0.032982953 198.8072561 -2.298432231 0.385001927 SKS(ph)PRDPDANWDSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSPRDPDANWDSPSR 16 2 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.179)KS(0.82)PRDPDANWDS(0.001)PSR 107.78 0.00086733 406190000 316170 316260 220100 305500 291380 284270 261170 269560 300970 270140 TRUE FALSE 303813.7269 307240.5745 259876.9661 321266.8916 300752.5023 290018.1342 264366.2766 263993.4918 266805.1474 251843.1772 1.206360761 1.21996783 1.031899966 1.275662479 1.19420548 1.151582256 1.049725784 1.048245558 1.059409869 1 17.94216612 2.298665333 3.206041057 1.041909118 1.183443014 0.575939355 0.059672413 0.186387279 3.907016532 0.022853183 0.01772364 198.9139917 -2.298665333 0.141533897 EEGSLS(ph)DTEADAVSGQLPDPTTNPSAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 EEGS(0.243)LS(0.743)DT(0.014)EADAVSGQLPDPTTNPSAGK;EEGS(0.007)LS(0.73)DT(0.263)EADAVSGQLPDPTTNPSAGK 235.21 2.70E-45 1176840000 880200 754390 956670 1032380 954450 929620 1182720 1399140 1462970 1588540 TRUE FALSE 845800.8109 732875.5358 1129561.55 1085661.256 985150.7511 948417.5533 1197194.481 1370247.27 1296899.779 1480946.771 0.571121682 0.4948696 0.762729338 0.73308594 0.665216853 0.640412993 0.80839805 0.925250858 0.875723425 1 20.49808836 2.299007112 0.344419528 1.032318123 0.52281752 0.759677265 0.074202718 0.797175424 0.230526965 0.101994707 0.145028276 199.0705939 -2.299007112 -0.509500603 TSPVADAAGWVDVDKETLQHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPVADAAGWVDVDKETLQHR 21 1 Q9Y6N5 Q9Y6N5 SQRDL "Sulfide:quinone oxidoreductase, mitochondrial" 0 106.03 0.00022634 131440000 22066 39806 20463 50643 21740 30751 48513 41564 43923 29046 FALSE TRUE 21203.63632 38670.77185 24161.1193 53256.6913 22439.28684 31372.80629 49106.71661 40705.68888 38937.04518 27078.68855 0.783037786 1.428088801 0.892255888 1.966738205 0.828669631 1.158579236 1.813482086 1.503237086 1.437922118 1 14.72487025 2.299086512 24.99916623 1.49491728 1.194902055 0.097305103 0.373701032 141.0603029 58261.38445 0.122554971 0.102536804 199.1069925 -2.299086512 -0.300015225 DT(ph)CYSPKPSVYLSTPSSASK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTCYSPKPSVYLSTPSSASK 20 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 DT(0.524)CY(0.046)S(0.412)PKPS(0.014)VY(0.004)LSTPSSASK 64.152 0.046119 433470000 136700 124750 133640 113420 136080 128270 116370 125810 122080 130000 TRUE FALSE 131357.6129 121192.2521 157791.7208 119273.6198 140457.1368 130863.7073 117794.1709 123211.9795 108221.9902 121194.9842 1.083853542 0.999977457 1.301965769 0.984146502 1.158935229 1.079778244 0.971939323 1.016642564 0.892957666 1 16.88697047 2.29930527 4.276258395 0.97589667 1.105290531 0.350126448 0.08778654 0.244276708 8.968670694 0.030570547 0.024584736 199.2073095 -2.29930527 0.129393861 SHFVLIAGEPLREPVIQHGPFVMNTNEEISQAILDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHFVLIAGEPLREPVIQHGPFVMNTNEEISQAILDFR 37 1 O00625 O00625 PIR Pirin 0 50.627 0.037269 126460000 49397 65863 51685 61707 58241 55137 41516 35761 60571 44545 FALSE TRUE 47466.51063 63984.65173 61025.62923 64891.70566 60114.37466 56251.90792 42024.08523 35022.52285 53695.23401 41527.92747 1.143002156 1.540761979 1.469508183 1.562604002 1.447565008 1.354556111 1.011947568 0.843348681 1.292990941 1 15.34179425 2.299560792 3.853324483 1.001090747 1.443718063 0.608396885 0.150119547 0.133646569 4.004405844 0.05501163 0.043753322 199.3245497 -2.299560792 0.442627316 EREWQK ddPTM_BT-474_Pertuzumab_2h_R1 3 EREWQK 6 1 O75937;S4R3J5 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ;; 130.05 0.014528 925670000 853630 913690 675260 804000 822520 838520 867380 927270 985280 956770 FALSE TRUE 820269.1959 887632.4558 797294.5031 845494.5364 848977.1028 855475.4489 877995.2559 908121.5505 873435.145 891967.1157 0.919618203 0.995140337 0.893860871 0.947898775 0.951803141 0.959088551 0.984335903 1.018111021 0.979223482 1 19.766631 2.299580747 1.899496251 1.001678585 0.942072248 0.500039314 0.025642858 0.266628409 1.955679222 0.011690019 0.007992793 199.3337086 -2.299580747 -0.059606337 SNEEGSEEKGPEVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SNEEGSEEKGPEVR 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;;; 268.61 2.90E-25 6225510000 5407630 4983640 4241660 4595230 4821330 5145590 5717660 6045850 6920130 6179420 FALSE TRUE 5196293.841 4841511.467 5008222.317 4832390.371 4976412.458 5249637.355 5787634.433 5921001.085 6134585.854 5760882.379 0.90199617 0.840411442 0.869349865 0.838828161 0.863828166 0.911255778 1.004643742 1.027794129 1.064869138 1 22.45785837 2.299869301 2.046085721 1.033945282 0.860280766 0.92344839 0.022083019 0.073913794 0.631869496 0.009622029 0.006734958 199.4661942 -2.299869301 -0.173664516 DRPGS(ph)PESPLLDAPFSR ddPTM_BT-474_Pertuzumab_2h_R1 6 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 DRPGS(1)PESPLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(0.998)PES(0.002)PLLDAPFSR;DRPGS(0.997)PES(0.003)PLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(1)PESPLLDAPFSR 282.37 3.00E-36 12597330000 2233130 2335230 1877900 2065300 1976760 2218790 2416430 2517590 2729270 2809470 TRUE FALSE 2145856.811 2268631.527 2217278.304 2171890.381 2040344.281 2263655.454 2446002.993 2465600.887 2419454.712 2619182.094 0.81928508 0.866160292 0.846553704 0.82922466 0.779000546 0.864260434 0.933880465 0.941362913 0.923744369 1 21.32068493 2.300271559 3.22677891 0.94609151 0.83048818 0.807655633 0.028083648 0.108348591 2.297637901 0.010867279 0.00844528 199.6510317 -2.300271559 -0.11560333 EYWFVLTAESLSWYKDEEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EYWFVLTAESLSWYKDEEEK 20 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 140.16 1.88E-07 47902000 40912 44491 33213 30192 40345 38784 45090 44874 49016 46581 FALSE TRUE 39313.11381 43222.16024 39215.32792 31750.21274 41642.73357 39568.23905 45641.82491 43947.33622 43451.90917 43426.02738 0.905289205 0.995305416 0.903037424 0.731133255 0.958934908 0.911164144 1.051024643 1.012004525 1.000595997 1 15.40627236 2.300366562 6.626285236 1.017435524 0.899365423 0.425498607 0.065535614 0.210017653 17.50323936 0.024085606 0.01995873 199.6947105 -2.300366562 -0.1180701 MQMLEDEDDLAYAETEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MQMLEDEDDLAYAETEK 17 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 196.95 3.61E-11 119790000 205540 206560 195710 196960 210360 246180 230570 250120 306120 300430 FALSE TRUE 197507.2696 200669.111 231079.1505 207125.1292 217126.4204 251157.9283 233391.7846 244954.9346 271370.541 280081.6085 0.705177575 0.716466576 0.825042215 0.739517065 0.775225555 0.896731241 0.833299215 0.874584147 0.968898109 1 18.09548773 2.300849156 0.297142987 1.023875601 0.670324431 0.835820427 0.039327463 0.773299149 0.178917171 0.060871118 0.097882183 199.9167376 -2.300849156 -0.35355117 APSPT(ph)KR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPTKR 7 1 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82;H3BTV0 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 APS(0.189)PT(0.811)KR 83.998 0.012815 6558100000 2091500 1852200 1537900 1670200 1700800 1805500 1920500 2023100 2123400 2018300 TRUE FALSE 2009761.868 1799377.069 1815832.74 1756399.222 1755507.777 1842008.447 1944003.653 1981322.278 1882360.534 1881598.743 1.068113951 0.956302228 0.965047807 0.933461094 0.932987324 0.978959225 1.033165897 1.052999363 1.000404864 1 20.84352757 2.301285211 4.913328447 1.029277914 0.967013139 0.268816308 0.038643604 0.224224911 10.64906729 0.01402195 0.011426825 200.1175657 -2.301285211 -0.062264774 YPSSISS(ph)SPQKDLTQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSS(0.004)IS(0.149)S(0.829)S(0.017)PQKDLTQAK;YPSS(0.003)IS(0.128)S(0.584)S(0.285)PQKDLTQAK 269.39 1.72E-28 3435700000 2685520 2445440 2189850 2121380 2544650 2632930 3172270 3393150 3780770 3619370 TRUE FALSE 2580566.909 2375698.446 2585604.608 2230864.676 2626500.978 2686169.649 3211093.189 3323080.267 3351592.84 3374226.846 0.764787617 0.704071941 0.766280611 0.661148399 0.77840083 0.796084487 0.951653026 0.984841986 0.993292091 1 21.68612554 2.301807124 1.732104526 0.996043869 0.728280661 0.932296793 0.031848842 0.07778864 0.471327688 0.014954355 0.009948478 200.358201 -2.301807124 -0.267763208 LYDDIDFDIEEFAK ddPTM_BT-474_Pertuzumab_2h_R1 4 LYDDIDFDIEEFAK 14 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;;; 271.14 1.39E-32 953830000 1253220 1179520 1112260 1152970 1250990 1298310 1447040 1565550 1748140 1668750 FALSE TRUE 1204242.777 1145881.244 1313270.124 1212474.92 1291229.229 1324562.718 1464749.308 1533220.845 1549698.476 1555724.076 0.774072212 0.736558148 0.844153629 0.779363731 0.829986017 0.851412367 0.941522556 0.985535204 0.99612682 1 20.56915478 2.302504921 1.011413431 1.008172339 0.780202759 0.925976914 0.025661478 0.126754981 0.251034109 0.01759914 0.010528807 200.6803827 -2.302504921 -0.22796958 ALSSLHGDDQDS(ph)EDEVLTIPEVK ddPTM_BT-474_Pertuzumab_2h_R1 7 ALSSLHGDDQDSEDEVLTIPEVK 23 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 ALS(0.001)S(0.001)LHGDDQDS(0.998)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALS(0.001)S(0.006)LHGDDQDS(0.993)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALS(0.077)S(0.064)LHGDDQDS(0.859)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK 219.27 1.36E-32 4692510000 2304110 3321250 2132870 3271010 2557280 2921310 3498710 3641350 3966920 3565200 TRUE FALSE 2214062.834 3226531.202 2518327.054 3439827.218 2639537.234 2980380.89 3541528.26 3566154.85 3516611.872 3323725.828 0.66613883 0.970757327 0.757681946 1.034931097 0.79415011 0.896698778 1.065529602 1.072938935 1.058033079 1 21.66436995 2.30321573 4.3936568 1.058190007 0.856705049 0.484349328 0.099401655 0.170770668 6.504892136 0.033416202 0.026995535 201.009105 -2.30321573 -0.201484958 LKLS(ph)PSPS(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 2 LKLS(0.896)PS(0.157)PS(0.863)S(0.085)R;LKLS(0.971)PS(0.03)PS(0.978)S(0.021)R;LKLS(0.977)PS(0.039)PS(0.98)S(0.004)R 116.19 0.025522 706700000 1914870 1843900 1936720 1971370 1725520 2098870 2239490 2495970 2568640 2591820 TRUE FALSE 1840034.763 1791313.777 2286728.386 2073112.642 1781022.918 2141310.589 2266897.549 2444427.347 2277058.756 2416273.723 0.761517516 0.741353829 0.946386316 0.857979219 0.73709485 0.886203649 0.938179117 1.01165167 0.942384439 1 21.20435247 2.303540996 2.529790086 0.982570575 0.815323386 0.612104603 0.061519977 0.20003878 2.627222616 0.026605875 0.019788059 201.1597076 -2.303540996 -0.167247189 HNNCMASHLTPAVYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNNCMASHLTPAVYAR 16 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J8F6;C9J6W7;C9JT96;C9JJX8;C9J995 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 131.24 2.64E-05 122807000 73168 85864 76163 97084 66261 70762 79799 48342 70886 73101 FALSE TRUE 70308.51367 83415.24279 89927.34834 102094.5169 68392.34524 72192.85612 80775.60403 47343.72081 62839.31846 68149.80416 1.031675946 1.223998276 1.319554024 1.498089659 1.00355894 1.059325951 1.185265387 0.694700761 0.922076288 1 16.05642189 2.30363408 1.203740703 0.862486979 1.24425238 0.405697647 0.163624006 0.423927068 1.202485699 0.105128907 0.063607864 201.2028278 -2.30363408 0.381765401 EKELS(ph)PPPGLPSK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKELSPPPGLPSK 13 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78;H0YIM6 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 EKELS(1)PPPGLPSK;EKELS(1)PPPGLPSK;EKELS(1)PPPGLPSK 115.34 0.00040691 1367000000 2445000 2197150 2347640 2066860 2395930 2724410 2772190 3169320 3528300 3393600 TRUE FALSE 2349446.697 2134489.433 2771910.771 2173530.892 2472997.264 2779499.437 2806116.89 3103872.434 3127782.176 3163748.449 0.742614887 0.674671033 0.876147651 0.687011286 0.781666844 0.878546282 0.886959547 0.981074344 0.988631753 1 21.59320346 2.303724715 0.962727204 1.002615244 0.741492572 0.788880162 0.053439791 0.23790266 0.426264547 0.037003163 0.022258185 201.2448219 -2.303724715 -0.261122672 INEKPQVIADYESGR ddPTM_BT-474_Pertuzumab_2h_R1 4 INEKPQVIADYESGR 15 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;; 162.59 1.45E-06 4862290000 2633970 2740000 2172410 2240430 2500340 2549630 2715960 3028290 2939890 2788730 FALSE TRUE 2531031.54 2661857.883 2565012.812 2356058.861 2580765.707 2601185.265 2749198.731 2965754.753 2606166.012 2599846.833 0.97353102 1.023851809 0.98660151 0.906229871 0.992660673 1.000514812 1.057446422 1.140742107 1.002430597 1 21.3099952 2.304009661 3.197374371 1.071327721 0.977419869 0.319579257 0.047172963 0.228800779 4.755693107 0.018537543 0.014420656 201.3769047 -2.304009661 -0.093907852 YCHDLGER ddPTM_BT-474_Pertuzumab_2h_R1 2 YCHDLGER 8 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 ; 103.56 0.0047486 743300000 173174 184038 166993 201484 167272 165333 175793 145524 172602 179736 FALSE TRUE 166406.1686 178789.4164 197172.3498 211882.6134 172652.4558 168676.1465 177944.4073 142518.8785 153008.9446 167562.3206 0.993100167 1.067002508 1.176710546 1.264500352 1.030377564 1.006647234 1.061959554 0.850542521 0.913146488 1 17.35433824 2.304048256 1.346884942 0.915755157 1.11694559 0.434024232 0.084835623 0.385943796 1.383593575 0.05217876 0.032308895 201.3948014 -2.304048256 0.201190433 DCLADVDTKPAYQNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCLADVDTKPAYQNLR 16 1 Q8NFC6;Q96IK1-2;Q96IK1 Q8NFC6 BOD1L1;BOD1 Biorientation of chromosomes in cell division protein 1-like 1;Biorientation of chromosomes in cell division protein 1 0 ; 197.88 3.84E-11 1238850000 875650 840780 706030 722090 779450 829780 863370 948450 1013600 922720 FALSE TRUE 841428.6299 816801.7776 833625.3266 759357.1514 804521.7171 846558.7201 873936.1803 928864.1761 898540.3774 860223.3525 0.978151346 0.949522906 0.969080093 0.882744172 0.935247474 0.984115018 1.015941009 1.079794188 1.044543112 1 19.71435177 2.305263168 2.262621725 1.049144072 0.942263739 0.661794705 0.030878937 0.166367205 1.746412031 0.013658989 0.009891172 201.9589798 -2.305263168 -0.106880333 DGFYEAELCPDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGFYEAELCPDR 12 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4;E9PQS6;E9PI38;E9PMD5;E9PNV4;E9PRX2;E9PJR1 Q04206 RELA Transcription factor p65 0 ;;; 159.83 0.00016216 1070560000 990950 1057480 868610 1034340 1000190 971820 940240 949420 1020740 1026520 FALSE TRUE 952222.5784 1027321.706 1025587.149 1087722.411 1032362.02 991470.8662 951746.9384 929814.1452 904869.8745 956992.8861 0.995015315 1.073489386 1.071676879 1.13660449 1.078756211 1.036027415 0.9945183 0.971599851 0.945534588 1 19.86814867 2.305728228 2.10126193 0.970950807 1.074443246 0.62165328 0.03443078 0.205725817 1.858071454 0.016018081 0.011363578 202.1753614 -2.305728228 0.103492439 ELISNASDALDK ddPTM_BT-474_Pertuzumab_2h_R1 5 ELISNASDALDK 12 0 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ;;;; 270.67 2.49E-27 2416270000 2654760 2661197 2538031 2550949 2803266 2933770 3099132 3441690 3892584 3716210 FALSE TRUE 2551009.044 2585302.267 2996709.66 2682603.784 2893435.597 2993092.839 3137060.104 3370617.899 3450714.183 3464507.787 0.736326544 0.746224984 0.864974145 0.774310219 0.835164986 0.863930181 0.905485078 0.972899502 0.996018597 1 21.72421897 2.306021675 0.635567722 1.017242857 0.763735047 0.884873362 0.031874091 0.23947498 0.192265427 0.027869846 0.020518278 202.3120149 -2.306021675 -0.25350781 VKEEEVHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VKEEEVHR 8 1 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 ;;; 138.1 0.00043254 570360000 1082800 1390190 1086750 1360890 1155560 1444800 1344470 1644230 1818800 1599860 FALSE TRUE 1040482.979 1350543.142 1283149.9 1431125.696 1192729.637 1474014.846 1360924.026 1610276.076 1612337.449 1491500.057 0.697608407 0.905493188 0.860308314 0.959521047 0.799684607 0.988276761 0.912453217 1.079635276 1.081017356 1 20.5083326 2.306567234 0.890586751 1.064611992 0.842971258 0.55579245 0.076310043 0.429822115 0.658755092 0.054586557 0.033398747 202.566318 -2.306567234 -0.221640735 QDEFKR ddPTM_BT-474_Pertuzumab_2h_R1 6 QDEFKR 6 1 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ;;;;; 117.93 0.035752 6006050000 7390550 7367520 6324040 7044470 6764460 7393810 8070640 8301640 9439320 9100770 FALSE TRUE 7101719.135 7157405.543 7466934.706 7408035.941 6982044.999 7543317.904 8169410.907 8130208.233 8367807.966 8484366.742 0.837035851 0.843599265 0.880081559 0.873139524 0.822930598 0.889084375 0.962878097 0.95825752 0.986261936 1 23.01637555 2.306696726 2.754341801 0.974337386 0.853443105 0.908247517 0.018874652 0.079125968 1.229287423 0.007810806 0.005930873 202.6267253 -2.306696726 -0.120894281 QQHIEQLLAER ddPTM_BT-474_Pertuzumab_2h_R1 1 QQHIEQLLAER 11 0 J3KP58;P30622-2;P30622-1;P30622;F5H0N7;Q9UDT6;Q9UDT6-2 J3KP58;Q9UDT6 CLIP1;CLIP2 CAP-Gly domain-containing linker protein 1;CAP-Gly domain-containing linker protein 2 0 112.44 0.00084685 0 208030 222010 181410 208570 195510 194630 196690 197670 190380 213270 FALSE TRUE 199899.9576 215678.4922 214194.8224 219334.3227 201798.7567 198565.552 199097.1511 193588.0454 168768.8605 198825.0329 1.005406385 1.084765278 1.07730309 1.103152452 1.014956486 0.998694928 1.001368631 0.973660321 0.848831045 1 17.60113988 2.306819405 1.007509453 0.936566976 1.066681306 0.545702184 0.045929288 0.399833546 0.786403374 0.031579071 0.018969915 202.6839713 -2.306819405 0.13011433 LDINEGAARPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDINEGAARPR 11 1 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ; 150.51 3.09E-05 430120000 278530 686590 335780 917190 495090 441990 386860 260200 272030 400010 FALSE TRUE 267644.7397 667009.1254 396462.9154 964526.2858 511015.0195 450927.3406 391594.5084 254826.7791 241150.2948 372916.9664 0.717705988 1.788626385 1.063139924 2.586437123 1.370318504 1.209189662 1.050084989 0.68333383 0.646659489 1 18.50849491 2.307426115 1.798057458 0.761070058 1.547329414 0.311376352 0.468204844 0.393400159 2.578116762 0.223377044 0.151240886 202.9673188 -2.307426115 0.786259356 EGETQGVAFEHESPADFQNS(ph)QSPVQDQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGETQGVAFEHESPADFQNSQSPVQDQDK 29 0 P78332;E9PGM9;P78332-3;F8WCA5 P78332 RBM6 RNA-binding protein 6 1 EGETQGVAFEHESPADFQNS(0.649)QS(0.351)PVQDQDK 374.1 7.53E-137 201200000 49683 63653 48141 56925 53410 60424 62188 67417 78937 66998 TRUE FALSE 47741.33343 61837.67876 56841.14959 59862.90607 55127.98116 61645.81468 62949.07535 66024.81539 69976.40269 62460.16578 0.76434849 0.990033856 0.910038404 0.958417342 0.882610228 0.986962073 1.007827542 1.057070768 1.120336487 1 15.93064878 2.307508309 1.387669721 1.065669455 0.907380806 0.54620789 0.062764923 0.316523313 1.208477689 0.033884668 0.021213061 203.0057361 -2.307508309 -0.158288649 VEDVEALDRK ddPTM_BT-474_Pertuzumab_2h_R1 6 VEDVEALDRK 10 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;;;; 175.15 4.63E-06 4315640000 4867430 4778030 3850740 4197440 4607880 4832670 4723620 5584520 5800990 5399030 FALSE TRUE 4677205.454 4641765.263 4546654.377 4414070.381 4756096.645 4930389.899 4781429.075 5469197.71 5142485.935 5033348.889 0.929243245 0.922202169 0.903306025 0.876964915 0.944916943 0.979544635 0.94994986 1.086592213 1.02168279 1 22.26308717 2.307584044 1.297446924 1.040353859 0.911256143 0.69244379 0.032623016 0.22793615 0.756350918 0.0195249 0.012028035 203.0411405 -2.307584044 -0.129097717 S(ph)RSPLLVTVVESDPRPQGQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRSPLLVTVVESDPRPQGQPR 21 2 A0A2R8YH03;Q5VWN6;Q5VWN6-2 A0A2R8YH03 FAM208B Protein FAM208B 1 S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR 99.711 0.00041562 3121590000 1141240 1062330 930000 1181990 972450 1095150 1001020 1101800 1026410 1203590 TRUE FALSE 1096639.079 1032033.389 1098071.688 1242992.646 1003729.737 1117294.683 1013270.782 1079047.445 909896.2399 1122069.777 0.977335903 0.919758654 0.978612658 1.10776769 0.894534153 0.995744388 0.903037229 0.96165806 0.810908785 1 20.09773096 2.308163972 1.463922754 0.916638629 0.981732344 0.131802663 0.070028216 0.843372791 3.601140047 0.037647903 0.023932581 203.3124492 -2.308163972 0.065093714 LFTLPLLHYLEVSGCGSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFTLPLLHYLEVSGCGSLR 19 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 146.76 1.12E-07 246120000 86271 116331 90563 104158 108209 97397 88669 77735 105151 107220 FALSE TRUE 82899.43394 113013.3538 106929.7487 109533.6069 111689.6408 99366.43407 89754.15775 76129.74509 93214.69931 99957.8939 0.829343544 1.130609593 1.069747916 1.095797466 1.117366887 0.99408291 0.897919656 0.761618139 0.932539649 1 16.60903288 2.30837185 3.216449847 0.863551534 1.056556466 0.320076794 0.098573191 0.221493901 4.644723832 0.036873583 0.028789991 203.4097892 -2.30837185 0.193004931 ERELLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERELLGK 7 1 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ; 105.25 0.0072679 1149860000 558720 777990 561520 796620 574530 730890 921840 1050260 961620 849250 FALSE TRUE 536884.6047 755802.4869 662999.1549 837733.6537 593010.2792 745669.0966 933121.7537 1028571.764 852460.929 791729.5411 0.678116171 0.954622062 0.83740611 1.058105843 0.74900613 0.941823006 1.178586506 1.299145365 1.07670724 1 19.59464816 2.308595005 4.19125258 1.179841726 0.869548813 0.527856214 0.12368282 0.147125569 5.042553547 0.043383674 0.034977987 203.514335 -2.308595005 -0.310292912 LINYHQEQAVNCLLGNVFYER ddPTM_BT-474_Pertuzumab_2h_R1 1 LINYHQEQAVNCLLGNVFYER 21 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 114.88 0.00016697 168310000 83181 107550 83659 95598 105080 94530 91537 95580 94584 104240 FALSE TRUE 79930.19456 104482.7793 98778.04228 100531.8242 108459.9936 96441.46137 92657.25719 93606.2396 83847.22085 97179.73195 0.822498611 1.075149902 1.016446951 1.034493739 1.116076279 0.992403039 0.953462778 0.963228008 0.86280564 1 16.56836783 2.308698016 3.701083991 0.943578069 1.020568726 0.138394074 0.078661484 0.408444055 11.15006389 0.028586242 0.022742993 203.5626126 -2.308698016 0.076990656 LKEEIDLLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 LKEEIDLLNR 10 1 Q96IZ0;H0YHP5 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 0 ;;; 140.31 3.60E-05 1184640000 2192917 2323797 1971573 1952184 2154848 2181948 2334018 2407330 2556468 2624438 FALSE TRUE 2107215.379 2257524.585 2327880.099 2052936.45 2224160.643 2226068.484 2362582.41 2357617.794 2266268.47 2446682.477 0.861254126 0.92268801 0.951443483 0.839069421 0.909051609 0.909831376 0.965626898 0.963597776 0.926261782 1 21.22239545 2.308847294 4.109960967 0.961549564 0.89897287 0.476370084 0.033477568 0.205481113 6.793042861 0.012136045 0.009766909 203.632594 -2.308847294 -0.062576693 ATSLGRPEEEEDELAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSLGRPEEEEDELAHR 17 1 P36551;D6RER6;P36551-2 P36551 CPOX "Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial" 0 185.61 3.42E-10 704200000 441140 581260 415290 630330 445060 492070 417290 448950 417920 442780 FALSE TRUE 423899.7611 564683.0339 490342.1411 662861.4068 459375.7591 502019.9925 422396.9198 439679.0256 370479.4737 412790.1162 1.026913544 1.36796646 1.187872776 1.60580736 1.112855519 1.216162822 1.023272853 1.065139422 0.897500834 1 18.6550489 2.309143266 1.381068689 0.983390378 1.285546373 0.41528128 0.150452839 0.406677531 1.537782984 0.08292242 0.051933645 203.7714171 -2.309143266 0.302155995 SAKSEES(ph)LTSLHAVDGDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAKSEESLTSLHAVDGDSK 19 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.158)AKS(0.38)EES(0.411)LT(0.04)S(0.01)LHAVDGDSK 147.45 6.38E-08 617380000 581930 590140 444400 446590 523980 556050 632310 730630 727170 586730 TRUE FALSE 559187.5322 573309.785 524712.9656 469638.5634 540834.2926 567293.712 640048.3989 715542.2352 644624.7101 546990.2545 1.022298894 1.048117001 0.959272969 0.858586711 0.988745756 1.037118499 1.17012761 1.308144394 1.178493958 1 19.0611556 2.309419223 2.925626508 1.20572949 0.974534323 0.494400806 0.086835058 0.179316827 3.13225672 0.034523066 0.02656266 203.9009377 -2.309419223 -0.231195168 ENYTWSQDYTDLEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENYTWSQDYTDLEVR 15 0 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 0 151.72 6.88E-06 153430000 122450 129710 102130 126200 122020 121140 116630 120000 134620 129000 FALSE TRUE 117664.5186 126010.7978 120587.1629 132713.1971 125944.8841 123589.5338 118057.3528 117521.9581 119338.502 120262.7151 0.978395661 1.04779605 1.002697825 1.103527365 1.047247969 1.027662927 0.981662128 0.977210251 0.992315049 1 16.87582991 2.309741479 4.387825717 0.984678598 1.038329302 0.350320325 0.031088009 0.21862792 8.09994241 0.011294708 0.009149986 204.0522927 -2.309741479 0.053650705 KGETLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGETLR 6 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 110.61 0.045786 387110000 926420 845880 765430 788740 872050 836840 826790 852630 866290 978800 FALSE TRUE 890214.4822 821756.3306 903760.2279 829446.9659 900100.2802 853761.4782 836908.5033 835022.8925 767952.391 912505.0042 0.975572165 0.900549944 0.990416736 0.908977991 0.986405857 0.935623886 0.917154974 0.915088562 0.841587046 1 19.79947295 2.309980169 3.386020437 0.911375184 0.950058208 0.101069824 0.045315946 0.468985748 10.82780236 0.015937127 0.012546708 204.1644713 -2.309980169 0.038683024 RVTSIADR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVTSIADR 8 1 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;P11908;P11908-2 B1ALA9;P11908 PRPS1;PRPS2 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2 0 ; 85.807 0.026425 409970000 628950 855100 640570 717380 723260 439890 661590 435750 401440 482760 FALSE TRUE 604369.9387 830713.3852 756335.2484 754404.0678 746524.3147 448784.8772 669686.7363 426751.6102 355870.2142 450062.2352 1.34285859 1.845774474 1.680512581 1.676221662 1.658713521 0.997161819 1.487986958 0.948205774 0.790713342 1 18.77976499 2.310283447 0.902378131 0.899862642 1.67535422 0.665998 0.208099856 0.333326282 0.524941065 0.148921731 0.091119361 204.3070943 -2.310283447 0.775491578 SS(ph)PGGQDEGGFMAQGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPGGQDEGGFMAQGK 16 0 F5GZ78;A0A1B0GTU4;P49023;A0A1B0GV30 F5GZ78 PXN Paxillin 1 S(0.001)S(0.999)PGGQDEGGFMAQGK;S(0.115)S(0.885)PGGQDEGGFMAQGK;S(0.165)S(0.835)PGGQDEGGFMAQGK 311.9 1.15E-57 1148570000 1959000 1936570 1643360 1692680 1824640 1966770 2074000 2318340 2417430 2355370 TRUE FALSE 1882440.114 1881340.92 1940351.708 1780039.418 1883331.203 2006539.437 2099382.232 2270465.469 2143013.481 2195838.692 0.857276138 0.856775558 0.883649475 0.810642159 0.857681946 0.913791821 0.956073067 1.033985546 0.975943037 1 21.06634065 2.311469621 1.839387739 1.005969933 0.852775528 0.892685931 0.022852475 0.098698282 0.678326089 0.010954325 0.007500546 204.8658742 -2.311469621 -0.153194405 LNNLS(ph)PAPHLAS(ph)GSPPPGLPSGLPS(ph)GLQSGSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 34 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 3 LNNLS(0.995)PAPHLAS(0.502)GS(0.502)PPPGLPS(0.022)GLPS(0.433)GLQS(0.254)GS(0.214)PS(0.077)R 57.801 0.017395 137080000 41197 39985 34498 47930 36258 43456 53422 58154 53713 56770 TRUE FALSE 39586.97569 38844.66695 40732.556 50403.67304 37424.2715 44334.71009 54075.79442 56953.09958 47615.72542 52924.91733 0.747983704 0.733958009 0.769629091 0.952361866 0.707120075 0.837690682 1.021745468 1.076111262 0.899684455 1 15.69165949 2.311913276 4.33150084 1.014455983 0.787272145 0.65146247 0.07488694 0.12618905 4.535270692 0.027430797 0.022216581 205.0752623 -2.311913276 -0.227183838 VT(ph)QGAASPGHGIQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTQGAASPGHGIQEK 15 0 Q9HB58;Q9HB58-6;G5E9C0;Q9HB58-2;Q9HB58-5;Q9HB58-3;Q9HB58-7;Q9HB58-4 Q9HB58 SP110 Sp110 nuclear body protein 1 VT(0.903)QGAAS(0.097)PGHGIQEK 120.11 0.00058632 2028200000 1063500 1101800 950780 1055500 1029600 1094100 1190900 1246300 1336600 1332400 TRUE FALSE 1021937.244 1070377.743 1122607.096 1109974.481 1062718.019 1116223.452 1205474.59 1220563.469 1184874.771 1242155.361 0.822712904 0.861710037 0.903757397 0.893587482 0.855543559 0.89861823 0.970470062 0.982617398 0.953886131 1 20.2444142 2.312025744 3.131430109 0.977476684 0.870830953 0.83292525 0.02316781 0.102348081 2.035483368 0.009303157 0.007251002 205.1283773 -2.312025744 -0.106645731 EKYELAHPPEEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKYELAHPPEEWK 13 1 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E5RFW9;E5RGA6;E5RG86 E7ESA6 PTK2 Focal adhesion kinase 1 0 68.513 0.030177 54398000 203830 187420 151930 177810 166910 185570 195190 200260 237360 209690 FALSE TRUE 195864.0983 182074.9651 179387.1307 186986.7954 172278.8117 189322.3525 197578.7936 196124.561 210415.8879 195487.5095 1.001926408 0.931389251 0.917639859 0.956515308 0.881277848 0.968462655 1.010697789 1.003258784 1.076364871 1 17.57671691 2.312514665 2.982651864 1.022239111 0.936431154 0.568705348 0.034786561 0.185853001 3.366799063 0.013350741 0.010328067 205.3594369 -2.312514665 -0.085807957 LWDVDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LWDVDR 6 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ;;;;; 135.82 0.031258 2576460000 2916150 3047360 2654450 2844360 2809510 2867980 2604990 2721860 2940670 3226100 FALSE TRUE 2802183.634 2960452.276 3134168.163 2991157.76 2899880.441 2925972.521 2636870.647 2665652.64 2606857.47 3007593.373 0.931702955 0.984325974 1.042085074 0.994535294 0.964186338 0.972861739 0.87673775 0.886307525 0.866758616 1 21.5201781 2.31281977 5.484981033 0.896093661 0.985313964 0.402489517 0.043394315 0.168952613 8.96164353 0.014986882 0.012348039 205.5037588 -2.31281977 0.089220303 LSQTSNVDKEEEAVTIEMNEPVQLTFALR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSQTSNVDKEEEAVTIEMNEPVQLTFALR 29 1 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 289.88 1.13E-80 783880000 720840 752240 626130 654550 696770 785230 779710 858500 1008160 886600 FALSE TRUE 692668.7759 730786.8517 739285.6192 688331.4039 719182.2398 801107.8886 789252.3242 840771.675 893717.9034 826549.7923 0.838024257 0.884141353 0.894423574 0.832776695 0.870101531 0.969219152 0.954875715 1.017206323 1.081263236 1 19.65674221 2.313145725 1.143947879 1.036771563 0.862283418 0.843320053 0.031226357 0.182216099 0.466005122 0.020210061 0.012257869 205.6580555 -2.313145725 -0.174488146 DISDIEGEKDGIR ddPTM_BT-474_Pertuzumab_2h_R1 3 DISDIEGEKDGIR 13 1 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ;; 145.43 3.81E-05 2021950000 2657960 2476400 1993860 2347860 2338000 2452620 2627800 2921360 3067410 2330800 FALSE TRUE 2554083.985 2405775.497 2354194.855 2469033.336 2413203.893 2502213.657 2659959.802 2861032.895 2719210.476 2172932.84 1.175408617 1.107155938 1.08341814 1.13626767 1.110574542 1.151537503 1.224133463 1.316668809 1.251401068 1 21.05121215 2.313450165 3.529066943 1.23520437 1.121254824 0.096704527 0.081976637 0.288388316 7.166511285 0.02925418 0.023200528 205.8022719 -2.313450165 -0.113949545 HSGPNSADSANDGFVR ddPTM_BT-474_Pertuzumab_2h_R1 6 HSGPNSADSANDGFVR 16 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;; 289.59 1.71E-45 6837690000 1756641 1844501 1533851 2030004 1732206 1706809 1643627 1274087 1943796 2097109 FALSE TRUE 1687989.528 1791897.637 1811051.996 2134772.75 1787923.979 1741321.847 1663742.199 1247776.658 1723144.427 1955069.94 0.863390866 0.916538893 0.926336168 1.091916308 0.914506404 0.890669849 0.850988584 0.638226098 0.881372268 1 20.89878879 2.314609481 2.55182673 0.791656236 0.945629343 0.111535442 0.103531391 0.349508476 4.667817827 0.042662674 0.032072478 206.3523794 -2.314609481 0.153973108 (ac)MEDEEVAESWEEAADSGEIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 MEDEEVAESWEEAADSGEIDR 21 0 Q7Z422-5;Q7Z422 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 0 67.136 7.00E-08 0 5298.2 6456 2595.2 1766.4 6398.1 5461.9 4718.9 9971.5 5418.3 7594.9 FALSE TRUE 5091.140487 6271.881201 3064.21037 1857.564116 6603.900697 5572.34336 4776.65131 9765.58504 4803.237299 7080.490658 0.719037809 0.885797539 0.432768083 0.262349632 0.932689698 0.786999606 0.674621511 1.379224338 0.678376335 1 12.78963362 2.314813516 1.375620331 1.035258085 0.62192827 0.242274873 0.254600597 0.536730436 2.015049062 0.14908079 0.093806622 206.4493481 -2.314813516 -0.413329815 QEFAQHANAFHQWIQETR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEFAQHANAFHQWIQETR 18 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 182.34 3.98E-14 1085320000 394190 450480 355930 470840 379610 363560 395570 187064 442570 464320 FALSE TRUE 378784.619 437632.7515 420254.4686 495140.1088 391820.5004 370911.4323 400411.104 183201.063 392331.309 432871.1928 0.875051575 1.010999943 0.970853398 1.143850912 0.905166495 0.856863285 0.92501213 0.423223042 0.906346543 1 18.72357827 2.315469718 1.902897471 0.72100795 0.987531746 0.141740459 0.165014201 0.394774245 2.91142409 0.076696761 0.053285694 206.761521 -2.315469718 0.266523796 MRDAGDPS(ph)PPNK ddPTM_BT-474_Pertuzumab_2h_R1 4 MRDAGDPSPPNK 12 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 MRDAGDPS(1)PPNK;MRDAGDPS(1)PPNK;MRDAGDPS(1)PPNK;MRDAGDPS(1)PPNK 75.445 0.020464 1593790000 1635070 1564370 1286280 1311700 1417620 1575270 1569730 1751930 1911950 1756560 TRUE FALSE 1571169.657 1519755.699 1518739.409 1379396.994 1463219.035 1607123.039 1588940.825 1715752.033 1694913.452 1637586.627 0.959442164 0.928045988 0.927425386 0.842335283 0.893521607 0.981397266 0.970294212 1.047732074 1.035006896 1 20.6431398 2.315474911 1.747578963 1.027834704 0.909776949 0.672740697 0.034234066 0.211656909 1.308848451 0.017833013 0.01206099 206.7639931 -2.315474911 -0.118057755 DLS(ph)PTLIDNSAAK ddPTM_BT-474_Pertuzumab_2h_R1 5 DLSPTLIDNSAAK 13 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 DLS(0.998)PT(0.002)LIDNSAAK;DLS(1)PTLIDNSAAK;DLS(1)PTLIDNSAAK;DLS(0.998)PT(0.002)LIDNSAAK;DLS(0.662)PT(0.338)LIDNSAAK 321.81 4.32E-51 1012111000 1543660 1486130 1388240 1575700 1596350 1703990 2035290 2128600 2406440 2426850 TRUE FALSE 1483332.061 1443747.027 1639125.849 1657022.066 1647698.048 1738445.845 2060198.488 2084643.666 2133271.02 2262477.288 0.655622962 0.638126639 0.724482786 0.732392796 0.728271641 0.768381568 0.910594108 0.921398715 0.942891684 1 21.10947188 2.315568008 0.647562108 0.999362803 0.658025709 0.951120518 0.027149957 0.154447698 0.128467123 0.024512621 0.017893683 206.8083206 -2.315568008 -0.341337094 TWEQQQEVVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TWEQQQEVVSR 11 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 261.52 2.51E-20 1340080000 407862 485719 357136 456254 440669 430355 406966 425307 448362 463910 FALSE TRUE 391922.3021 471866.7697 421678.4196 479801.3236 454843.5186 439057.073 411946.5716 416524.2618 397465.8254 432488.9625 0.90620186 1.091049277 0.975003887 1.109395534 1.051688154 1.01518677 0.95250193 0.963086455 0.919019582 1 18.72230379 2.315870912 4.15439708 0.955993253 1.032041663 0.242700471 0.056885737 0.274288292 9.065442718 0.019624671 0.015859909 206.9526122 -2.315870912 0.07604841 FAELPEFRPEEVLPSPTLQSLATS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPTLQSLAT(0.197)S(0.803)PR;FAELPEFRPEEVLPSPTLQSLAT(0.231)S(0.769)PR;FAELPEFRPEEVLPSPTLQSLAT(0.076)S(0.924)PR 198.21 3.76E-25 632330000 235923 217039 164740 223874 191986 231300 263058 301294 296668 287181 TRUE FALSE 226702.8683 210849.2602 194512.1826 235428.164 198161.404 235977.0445 266277.3825 295072.1736 262991.4924 267729.9751 0.846759382 0.787544466 0.726523739 0.879349292 0.74015397 0.881399419 0.994574412 1.102126027 0.982301262 1 18.03041915 2.316078846 2.697391255 1.040742047 0.796739442 0.800623394 0.052476466 0.102852898 1.531997287 0.020247914 0.015417055 207.0517219 -2.316078846 -0.244002605 TS(ph)PGRVDLPGSSTTLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPGRVDLPGSSTTLTK 17 1 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-11;O94875-2;O94875-8;H7BZK1;H7BZX1;H7C1R7;O94875-7;O94875 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 T(0.452)S(0.548)PGRVDLPGSSTTLTK 97.69 0.0012188 449240000 111730 92726 86614 78793 87806 95289 98131 105520 114400 104090 TRUE FALSE 107363.4681 90081.54527 102267.0765 82859.51617 90630.35973 97215.80887 99331.95653 103340.9751 101413.7916 97039.89159 1.106384872 0.92829396 1.053866352 0.853870659 0.933949516 1.001812835 1.023619822 1.06493292 1.045073216 1 16.56629032 2.316171296 2.906173221 1.042733845 0.970406011 0.135679575 0.066958643 0.432859677 7.451866575 0.025918721 0.020011383 207.0958024 -2.316171296 -0.072327834 NLTANDPSQEYVAS(ph)EGEEDPEVEFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NLTANDPSQEYVASEGEEDPEVEFLK 26 0 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 NLTANDPSQEYVAS(1)EGEEDPEVEFLK;NLTANDPSQEYVAS(1)EGEEDPEVEFLK 178.59 1.56E-17 556330000 129713 118112 108322 101352 116892 119749 121540 132783 140747 132768 TRUE FALSE 124643.6726 114743.5614 127898.195 106582.7889 120651.9373 122170.4068 123027.4429 130040.9846 124769.9906 123775.5051 1.007014049 0.927029636 1.033307801 0.861097588 0.97476425 0.987032182 0.993956298 1.050619705 1.008034591 1 16.91736631 2.316570409 1.936306939 1.023552266 0.958265367 0.230015115 0.045406229 0.423791137 3.239792792 0.020244536 0.014156011 207.286209 -2.316570409 -0.065286899 YHTINGHNAEVR ddPTM_BT-474_Pertuzumab_2h_R1 21 YHTINGHNAEVR 12 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;;;;;;;;;; 281.26 2.62E-28 96418021900 10723909.5 10566150.25 8767893.03 9701629.34 8597176.1 7074224.6 9094431.54 613058.1 8420028.9 7252279.7 FALSE TRUE 10304807.26 10264813.99 10352446.34 10202331.59 8873712.077 7217270.268 9205731.914 600398.236 7464222.519 6761076.336 1.524137097 1.518221875 1.531183177 1.508980388 1.312470328 1.067473566 1.36157787 0.088802168 1.103999149 1 22.68882151 2.317324559 1.395785469 0.680349398 1.496956864 0.468642578 0.305091016 0.309005247 1.19643064 0.17000304 0.107651025 207.6464732 -2.317324559 0.816607466 VDIDVPDVNVQGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDIDVPDVNVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 283.76 1.76E-39 2088980000 2642200 2684390 2187760 2562840 2350940 2593260 2670760 2803960 3081150 2951790 FALSE TRUE 2538939.903 2607833.825 2583136.898 2695108.48 2426560.12 2645697.494 2703445.56 2746057.246 2731390.769 2751862.634 0.922625959 0.947661338 0.938686716 0.979376095 0.881788244 0.961420625 0.982405708 0.997890379 0.992560724 1 21.39197703 2.317442225 3.1917035 0.994251993 0.936521692 0.586278718 0.02327484 0.174918683 3.59696819 0.008642154 0.006777786 207.7027394 -2.317442225 -0.057730301 ALSHDS(ph)IFIPESGQDATRPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALSHDSIFIPESGQDATRPVR 21 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 ALS(0.098)HDS(0.902)IFIPESGQDATRPVR 273.45 6.24E-45 783470000 121470 198330 118530 185690 162410 158400 103840 152620 120260 131680 TRUE FALSE 116722.8181 192673.8226 139951.0077 195273.4832 167634.0651 161602.9565 105110.825 149468.3437 106608.589 122761.1963 0.950811996 1.569501018 1.140026424 1.590677584 1.365529745 1.316400959 0.856221902 1.217553658 0.868422532 1 16.90549508 2.317456191 8.173617751 1.021855563 1.340772928 0.399620798 0.199463656 0.257139058 23.48280572 0.06469843 0.053983536 207.709419 -2.317456191 0.318917364 IVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_BT-474_Pertuzumab_2h_R1 2 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR 203.06 2.46E-22 84146000 225540 235620 212840 210164 222750 223905 192750 226480 216434 226721 TRUE FALSE 216725.6475 228900.3483 251304.9226 221010.5892 229914.956 228432.5125 195108.9322 221803.1089 191865.3197 211364.9847 1.025362113 1.082962481 1.188961941 1.045634827 1.087762745 1.080749079 0.923090134 1.049384358 0.907744109 1 17.68937687 2.317566301 8.296804908 0.980576078 1.088642436 0.513462091 0.054506771 0.221870084 20.64963753 0.018559448 0.015488795 207.7620879 -2.317566301 0.108066358 EVEVIGGADKYHSVCR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVEVIGGADKYHSVCR 16 1 P04183 P04183 TK1 "Thymidine kinase, cytosolic" 0 ; 183.23 1.21E-09 1521860000 951090 1028810 603500 865380 840810 761980 818170 778090 691630 814070 FALSE TRUE 913920.3513 999469.3461 712565.8748 910042.3655 867855.4173 777387.7577 828183.0092 762022.1696 613119.0619 758932.3138 1.204218525 1.31694135 0.938905699 1.199108733 1.143521499 1.024317641 1.091247525 1.004071319 0.807870545 1 19.5336117 2.318086764 0.632206966 0.921222063 1.187446392 0.443888055 0.105108238 0.741390773 0.590310055 0.089966138 0.067115829 208.0112214 -2.318086764 0.266224329 SSGS(ph)PEPSPAIAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSGSPEPSPAIAK 13 0 K7ELE9;Q66K64 K7ELE9 DCAF15 DDB1- and CUL4-associated factor 15 1 SSGS(1)PEPSPAIAK;SSGS(1)PEPSPAIAK;SSGS(1)PEPSPAIAK 227.63 9.22E-12 2318290000 2440410 2383220 2105480 2398750 2489960 2493050 2688640 2957700 3163750 3299530 TRUE FALSE 2345036.079 2315252.899 2485987.072 2522549.775 2570051.825 2543461.179 2721544.381 2896622.461 2804614.364 3076049.894 0.76235307 0.752670788 0.808175146 0.820061397 0.835503946 0.826859533 0.884753003 0.941669531 0.911758411 1 21.55264747 2.318611101 0.336511581 1.010423564 0.728004936 0.939446945 0.018460487 0.369891445 0.102296466 0.025365555 0.037366025 208.2625115 -2.318611101 -0.282418629 TQQSPISNGS(ph)PELGIK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQQSPISNGSPELGIK 16 0 Q15723-2;Q15723-3;Q15723-1;Q15723 Q15723-2 ELF2 ETS-related transcription factor Elf-2 1 TQQSPISNGS(1)PELGIK;TQQSPIS(0.008)NGS(0.992)PELGIK 214.81 1.75E-14 589380000 510350 476850 411820 395470 490490 497720 479270 577480 585490 575680 TRUE FALSE 490404.9578 463250.7049 486245.0349 415880.2541 506267.0563 507784.2394 485135.4496 565554.8362 519027.6298 536688.6808 0.913760575 0.863164664 0.906009484 0.774900364 0.943316068 0.946143002 0.903942019 1.053785661 0.967092559 1 19.03372594 2.318745901 1.128572713 1.008179042 0.872102578 0.509356928 0.050510851 0.373104002 0.928997008 0.032037097 0.019508831 208.3271636 -2.318745901 -0.136076464 LNGDTEEGFNRLS(ph)DEFSK ddPTM_BT-474_Pertuzumab_2h_R1 3 LNGDTEEGFNRLSDEFSK 18 1 Q9BQ39;A0A087WVC1 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 1 LNGDTEEGFNRLS(1)DEFSK;LNGDTEEGFNRLS(1)DEFSK;LNGDTEEGFNRLS(1)DEFSK 253.39 1.01E-30 619670000 752029 661871 681216 628545 694001 780595 742792 838677 918409 889107 TRUE FALSE 722638.8753 642995.0871 804326.8848 660984.2828 716324.1724 796379.1657 751882.5107 821358.0269 814155.0606 828886.991 0.871818334 0.775733115 0.970369777 0.797435947 0.864200042 0.960781354 0.90709894 0.990916779 0.982226853 1 19.66081589 2.319107907 0.861358189 0.997600685 0.849444084 0.529274268 0.053280574 0.46224557 0.66476402 0.038405761 0.023968721 208.5008872 -2.319107907 -0.148156601 DHYPCVSS(ph)LEQLTELGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHYPCVSSLEQLTELGR 17 0 Q8WWK9-6;Q8WWK9-5;Q8WWK9 Q8WWK9-6 CKAP2 Cytoskeleton-associated protein 2 1 DHYPCVS(0.206)S(0.794)LEQLTELGR;DHYPCVS(0.044)S(0.956)LEQLTELGR 212.39 1.04E-12 101415000 102758 100608 70227 88897 82775 74300 71624 40258 71402 63245 TRUE FALSE 98742.10376 97738.75835 82918.58109 93484.98482 85437.53305 75802.39691 72500.55594 39426.65823 63296.7443 58961.35982 1.674691765 1.657674766 1.406320705 1.585529661 1.449042785 1.28562837 1.229628288 0.66868638 1.073529249 1 15.84748218 2.319181291 1.377372887 0.883999027 1.567863472 0.797007325 0.137271305 0.170441179 0.642112556 0.078166561 0.049418046 208.5361209 -2.319181291 0.683864445 VIAINVDDPDAANYNDINDVKR ddPTM_BT-474_Pertuzumab_2h_R1 5 VIAINVDDPDAANYNDINDVKR 22 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;; 284.88 9.55E-46 15316660000 8158610 8286840 6789900 6920660 7724150 8227390 7931970 9187880 9736000 8919420 FALSE TRUE 7839762.501 8050507.437 8016985.971 7277836.092 7972604.3 8393753.463 8029043.822 8998147.067 8630810.097 8315299.739 0.942811774 0.968156012 0.964124713 0.875234366 0.958787362 1.009434864 0.965574793 1.082119388 1.037943354 1 22.98733684 2.319492638 1.422603087 1.042434363 0.94156024 0.531845208 0.036501386 0.301689896 1.215907777 0.020582034 0.013129008 208.6856749 -2.319492638 -0.100874123 HSSIS(ph)PVRLPLNSSLGAELSR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HS(0.004)S(0.004)IS(0.992)PVRLPLNSSLGAELSR 190.37 1.10E-17 154210000 75109 120390 81728 103570 80375 82272 74989 41362 68482 81674 TRUE FALSE 72173.65724 116956.5951 96498.06763 108915.2601 82960.33487 83935.59621 75906.73781 40507.86025 60708.21046 76142.14723 0.947880509 1.536029641 1.267341034 1.43042013 1.089545513 1.102353943 0.99690829 0.532003125 0.797301004 1 16.21640763 2.319550008 1.527174727 0.733713518 1.288182906 0.527284407 0.191579127 0.25797755 1.205609752 0.098512032 0.064142062 208.7132436 -2.319550008 0.554469388 RRDS(ph)DGVDGFEAEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 RRDSDGVDGFEAEGK 15 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK 235.92 8.50E-18 14379400000 6651990 5874720 5531290 5842370 6256000 6113880 6056310 6761700 7353040 6969550 TRUE FALSE 6392022.877 5707178.738 6530917.146 6143895.416 6457229.922 6237506.843 6130428.933 6622068.532 6518353.726 6497496.171 0.983767086 0.878365849 1.00514367 0.945578921 0.993802805 0.959986228 0.943506356 1.019172364 1.003210091 1 22.63145245 2.320095989 0.482271134 1.010441467 0.944406633 0.207900891 0.035712797 1.425409699 0.705183597 0.033262607 0.032788641 208.9757962 -2.320095989 -0.066034833 VDINAPDVDVQGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDINAPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 262.21 7.95E-31 4187340000 3682630 3816980 3199740 3599710 3164550 3571080 3716300 3866170 4167900 3855410 FALSE TRUE 3538708.748 3708123.468 3778004.196 3785491.464 3266340.625 3643289.684 3761781.191 3786332.238 3694777.465 3594279.647 0.984539072 1.031673613 1.051115819 1.053198926 0.908760849 1.013635566 1.046602257 1.053432846 1.02796049 1 21.77727123 2.320210095 6.516919388 1.038535137 1.007597475 0.073562397 0.040930155 0.510994654 32.93902734 0.014990315 0.012452638 209.0307096 -2.320210095 -0.030937661 KDWDDDQND ddPTM_BT-474_Pertuzumab_2h_R1 4 KDWDDDQND 9 1 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 111.31 0.043991 14893500000 8286200 7848100 6566900 6757500 7285600 7776800 8283500 8887400 9593600 9097400 FALSE TRUE 7962366.143 7624279.872 7753684.91 7106255.385 7519947.941 7934052.224 8384875.951 8703872.084 8504574.748 8481224.995 0.938822652 0.898959747 0.914217571 0.837880777 0.88665823 0.935484229 0.988639726 1.026251761 1.002753111 1 23.01584123 2.320492022 2.364900875 1.011836269 0.893896868 0.809822046 0.025013561 0.121474922 1.39417763 0.011055434 0.008204021 209.1664484 -2.320492022 -0.117939401 QPGQVIGATTPSTGS(ph)PTNK ddPTM_BT-474_Pertuzumab_2h_R1 2 QPGQVIGATTPSTGSPTNK 19 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 QPGQVIGATT(0.004)PS(0.001)T(0.034)GS(0.96)PTNK;QPGQVIGATTPSTGS(1)PTNK 241.38 2.43E-24 500250000 338050 267910 234520 263360 281400 281170 302440 315840 317680 331810 TRUE FALSE 324838.6323 260269.4691 276902.9809 276952.0412 290451.4866 286855.45 306141.3512 309317.7936 281618.2982 309336.2132 1.050115112 0.841380537 0.895152165 0.895310763 0.938950806 0.927325796 0.989671879 0.999940455 0.910395506 1 18.23881621 2.320561807 4.995823352 0.978116866 0.918004106 0.160054351 0.055236915 0.323429379 14.12642221 0.019005334 0.015604979 209.2000611 -2.320561807 -0.06011276 FSPFLQTAEDNTQDEVAGAPADHHGPS(ph)DEEQGSPPEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSPFLQTAEDNTQDEVAGAPADHHGPSDEEQGSPPEDK 38 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 FSPFLQTAEDNTQDEVAGAPADHHGPS(0.991)DEEQGS(0.009)PPEDK;FSPFLQTAEDNTQDEVAGAPADHHGPS(1)DEEQGSPPEDK 142.77 7.19E-13 714740000 111176 95362 63814 106509 107376 77209 79494 56769 79073 78121 TRUE FALSE 106831.119 92642.36913 75346.60933 112005.9423 110829.8466 78770.21888 80466.87135 55596.70031 70096.96454 72829.79509 1.466860079 1.272039404 1.034557481 1.537913736 1.521765184 1.081565845 1.104861977 0.763378508 0.962476476 1 16.15224117 2.321865965 2.117760568 0.901768619 1.347710376 0.589842554 0.160127566 0.219894992 2.019844082 0.07324183 0.052851276 209.8292193 -2.321865965 0.445941756 DNLHQIDAVEGPAAFLDILAPPYDPDDGRDCHYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNLHQIDAVEGPAAFLDILAPPYDPDDGRDCHYYR 35 1 Q96SZ5 Q96SZ5 ADO 2-aminoethanethiol dioxygenase 0 68.326 0.0033457 45505000 27355 28113 17128 24196 22449 21023 22204 15150 22517 21001 FALSE TRUE 26285.93636 27311.24477 20223.41061 25444.75846 23171.09247 21448.09946 22475.73919 14837.14721 19960.96456 19578.58356 1.342586213 1.394955088 1.032935327 1.299622027 1.183491768 1.095487801 1.147975752 0.757825363 1.019530575 1 14.25698877 2.322236793 1.224224136 0.909532784 1.259595452 0.538108196 0.122618365 0.332055639 0.979295757 0.075218581 0.04647469 210.0084615 -2.322236793 0.350062667 EGTTPKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGTTPKPK 8 1 P61927 P61927 RPL37 60S ribosomal protein L37 0 ; 71.379 0.044591 1398970000 1273140 1209320 993010 966900 1037140 1206350 1286750 1372720 1578510 1436160 FALSE TRUE 1223384.281 1174831.378 1172468.996 1016801.825 1070500.55 1230743.224 1302497.631 1344372.852 1399324.162 1338887.604 0.913731875 0.877468261 0.875703825 0.759437776 0.799544747 0.919228186 0.972820741 1.00409687 1.045139382 1 20.35260342 2.32250525 2.254480362 1.011403686 0.844601777 0.754699065 0.043153265 0.160976252 1.678362818 0.020405286 0.014985691 210.1383173 -2.32250525 -0.16680191 SKEIEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKEIEAK 7 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 110.87 0.006116 1439520000 3091370 3230230 2305800 2703210 3049360 3551850 3475480 4247330 4686510 4403790 FALSE TRUE 2970555.843 3138107.003 2722509.352 2842722.992 3147445.434 3623670.841 3518013.964 4159621.151 4154517.032 4105517.381 0.723552129 0.764363346 0.66313429 0.692415286 0.766637951 0.882634393 0.856899055 1.013178307 1.011935073 1 21.96913261 2.323157898 1.015756287 1.017587335 0.708890997 0.911681058 0.038164579 0.145352451 0.291772766 0.027151754 0.016547933 210.4543455 -2.323157898 -0.308696338 RKADSEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 RKADSEEER 9 2 H0YGZ1;H0YGK7;J3KQH6;P78364 H0YGZ1 PHC1 Polyhomeotic-like protein 1 0 53.327 0.080048 15850000 9747.9 10764 7883.2 10027 7066.4 9747.3 10709 13901 7886.5 10430 FALSE TRUE 9366.941291 10457.02126 9307.869601 10544.49467 7293.697174 9944.397084 10840.05995 13613.93949 6991.257583 9723.56681 0.96332359 1.075430597 0.957248485 1.084426618 0.750105112 1.02271083 1.114823414 1.400097285 0.719001342 1 13.24726991 2.325808506 4.58209303 1.125531598 0.970803607 0.001307261 0.181654745 0.439080868 16.48312446 0.065031972 0.053169968 211.742729 -2.325808506 -0.154727991 YSVDIPLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSVDIPLDK 9 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 133.13 0.0006642 195241000 671500 663580 562960 591500 663140 672650 724920 799400 842670 833370 FALSE TRUE 645257.0376 644655.3481 664699.395 622027.3859 684470.5003 686251.4439 733791.7878 782892.1106 747013.6344 776925.1076 0.83052669 0.82975224 0.855551441 0.800627216 0.880999331 0.883291629 0.944482011 1.007680281 0.961500185 1 19.56741601 2.326381775 1.29773926 0.994951585 0.833039246 0.90985091 0.021146728 0.112403466 0.374544379 0.011957691 0.007505919 212.0224143 -2.326381775 -0.161912339 KRES(ph)ESESDETPPAAPQLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 KRES(0.45)ES(0.45)ES(0.095)DET(0.004)PPAAPQLIK 102.89 0.00015302 590570000 345580 304370 270850 274730 280890 341790 377660 421090 453240 442770 TRUE FALSE 332074.3515 295689.6656 319798.62 288908.8482 289925.0819 348701.228 382281.9161 412394.3443 401790.0953 412780.7935 0.804481111 0.716335814 0.774742006 0.699908651 0.702370572 0.844761271 0.926113623 0.999063791 0.973374008 1 18.65501632 2.326600205 2.039203292 0.987057555 0.738343848 0.916137188 0.03368966 0.08132225 0.69176133 0.014911903 0.010690693 212.1290783 -2.326600205 -0.248713706 SIS(ph)PEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 SISPEWK 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 S(0.008)IS(0.992)PEWK 70.256 0.060337 124250000 276460 325690 270380 280470 303930 304420 370670 356210 380510 393640 TRUE FALSE 265655.6376 316401.6401 319243.6806 294945.0903 313706.1845 310575.581 375206.3703 348854.139 337316.1 366978.4122 0.723899905 0.862180525 0.86992496 0.803712373 0.854835527 0.846304771 1.022420823 0.950612154 0.919171507 1 18.48533567 2.326675739 6.485191855 0.968505241 0.829274436 0.700853629 0.046825874 0.122227826 7.388960515 0.016085989 0.013369127 212.1659758 -2.326675739 -0.139230805 IWDLEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 IWDLEGK 7 0 P63244;J3KPE3;H0YAF8;H0Y8W2;D6RAC2;D6REE5;H0YAM7;D6RF23;H0Y9P0 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;; 129.4 0.008525 2180760000 3111140 3187520 2687660 2730810 3034550 3167970 3213530 3655560 3789210 3608650 FALSE TRUE 2989553.209 3096615.051 3173379.949 2871747.431 3132159.057 3232028.524 3252858.141 3580071.409 3359074.766 3364232.921 0.888628487 0.920452039 0.943269988 0.853611358 0.931017302 0.96070296 0.96689445 1.06415682 0.998466766 1 21.68184616 2.326849028 1.557422784 1.025371418 0.906613605 0.712392628 0.030593356 0.194332507 0.947134681 0.015903962 0.01049422 212.2506497 -2.326849028 -0.118757813 KGEIFELK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGEIFELK 8 1 P63010;P63010-2;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7ERB2;K7EN71;A0A087WXS3;K7EKZ5;K7EJX1;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 94.297 0.016771 4681700000 4633100 4635600 3669700 3807900 4463600 4544500 4832100 5432400 5737400 5395200 FALSE TRUE 4452033.33 4503397.227 4332896.422 4004426.175 4607175.748 4636392.904 4891236.685 5320219.042 5086114.405 5029778.298 0.885135103 0.895347063 0.861448789 0.796143674 0.915979885 0.921788721 0.972455722 1.057744244 1.011200515 1 22.26206338 2.326855524 1.558839254 1.029166894 0.865800846 0.809579794 0.032561433 0.157057411 0.766915445 0.017685354 0.011672982 212.2538243 -2.326855524 -0.163366047 LKDPANFQYPAESVLAYK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKDPANFQYPAESVLAYK 18 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 205.62 8.59E-16 3176200000 3610200 3679400 3005100 3274600 3380500 3625800 3678700 4094400 4183900 4231500 FALSE TRUE 3469109.393 3574467.115 3548188.418 3443602.498 3489236.853 3699116.16 3723721.031 4009849.209 3708961.212 3944896.736 0.879391686 0.906099032 0.899437591 0.872925891 0.884493838 0.937696576 0.943933715 1.016464936 0.940192218 1 21.91155611 2.327334077 1.755277464 0.985708027 0.889334999 0.776417876 0.022224072 0.153197043 0.95732801 0.010473316 0.007177332 212.4878376 -2.327334077 -0.096373028 GFTGIDSDYEKPETPER ddPTM_BT-474_Pertuzumab_2h_R1 1 GFTGIDSDYEKPETPER 17 1 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 170.11 1.72E-09 314030000 216210 217380 163660 212930 209090 215640 248750 295870 240530 212920 FALSE TRUE 207760.2742 211180.5352 193237.0026 223919.3428 215815.5697 220000.3885 251794.2769 289760.1811 213226.0428 198498.7388 1.046657906 1.063888549 0.973492345 1.12806431 1.087238998 1.108321342 1.268493082 1.459758298 1.074193439 1 17.59877032 2.328186363 3.956518263 1.263886387 1.062447145 0.150805374 0.125421445 0.247380328 7.348541359 0.045719519 0.036969042 212.9052463 -2.328186363 -0.201439243 VEPYVDFAEFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEPYVDFAEFYR 12 0 Q15750 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 0 98.044 0.010656 14623000 32622 28117 25004 30696 27986 32173 31531 35899 38352 37224 FALSE TRUE 31347.09617 27315.13069 29522.77901 32280.22424 28886.19511 32823.5601 31916.88581 35157.6731 33998.44174 34702.78532 0.903302023 0.787116378 0.850732261 0.930191163 0.832388376 0.945848 0.919721155 1.013108106 0.979703543 1 15.08276384 2.328587482 0.872553216 1.006293719 0.850813785 0.656760799 0.041291236 0.339103469 0.501460336 0.029678932 0.018602014 213.1019785 -2.328587482 -0.155479934 NGS(ph)PTPAGSLGGGAVATAGGPGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGSPTPAGSLGGGAVATAGGPGSR 24 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 NGS(0.626)PT(0.374)PAGSLGGGAVATAGGPGSR;NGS(0.999)PT(0.001)PAGSLGGGAVATAGGPGSR 288.04 3.90E-53 718750000 206355 191856 155044 169374 179319 191275 206110 232514 245612 189513 TRUE FALSE 198290.4185 186384.4547 183063.8997 178115.4124 185086.9585 195142.7116 208632.4358 227712.5046 217731.1554 176677.1157 1.122332214 1.054943952 1.03614947 1.008140821 1.047600068 1.104516059 1.180868473 1.288862475 1.232367614 1 17.43075566 2.328856679 2.767898832 1.211255031 1.051697258 0.325843621 0.076569182 0.226966241 3.549491146 0.029285433 0.022614021 213.2341104 -2.328856679 -0.159557773 KNS(ph)TGSGHSAQELPTIR ddPTM_BT-474_Pertuzumab_2h_R1 4 KNSTGSGHSAQELPTIR 17 1 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 KNS(0.976)T(0.02)GS(0.004)GHSAQELPTIR;KNS(0.992)T(0.008)GSGHSAQELPTIR;KNS(0.609)T(0.244)GS(0.147)GHSAQELPTIR;KNS(0.993)T(0.007)GSGHSAQELPTIR 256.06 2.06E-27 6144170000 1684110 1648770 1399740 1480890 1451260 1608600 1360720 1545550 1590970 1489290 TRUE FALSE 1618293.119 1601748.694 1652704.155 1557318.91 1497941.096 1641126.994 1377372.898 1513633.852 1410369.755 1388419.062 1.165565328 1.153649311 1.190349658 1.121649042 1.078882549 1.182011281 0.992044071 1.090185157 1.015809848 1 20.40501165 2.328993734 0.469554565 0.99838246 1.17972269 0.627429657 0.043934897 0.655575103 0.309649821 0.040725227 0.041657838 213.3014136 -2.328993734 0.18134023 GKFNTSDVSAIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKFNTSDVSAIEK 13 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 183.6 9.32E-06 1694030000 3330300 3512000 2590600 3176000 2737800 3160100 3468300 3587300 3798700 3489500 FALSE TRUE 3200148.194 3411841.199 3058779.048 3339913.741 2825863.823 3223999.387 3510746.093 3513221.001 3367487.501 3253153.057 0.983706619 1.048779796 0.94025058 1.026669721 0.868653818 0.991038334 1.079182575 1.079943347 1.035145732 1 21.63340727 2.329472707 5.85671011 1.058450862 0.974462811 0.323017116 0.050633024 0.216687278 11.24004746 0.017615117 0.014597883 213.5367885 -2.329472707 -0.083988052 NRDNDPNDYVEQDDILIVK ddPTM_BT-474_Pertuzumab_2h_R1 3 NRDNDPNDYVEQDDILIVK 19 1 P19387 P19387 POLR2C DNA-directed RNA polymerase II subunit RPB3 0 ;; 211.89 9.84E-17 734012000 951539 928303 693850 784028 785211 898042 859776 975525 1049946 939313 FALSE TRUE 914351.8039 901828.7073 819244.1296 824491.779 810468.0249 916201.0245 870298.1959 955380.0678 930760.5318 875692.4939 1.04414713 1.029846337 0.9355386 0.941531171 0.925516697 1.046258853 0.993839963 1.090999494 1.062885132 1 19.74006482 2.329558476 1.954177671 1.053603323 0.976237591 0.270447688 0.046686898 0.398827987 3.110006486 0.022456308 0.015942342 213.5789641 -2.329558476 -0.077365732 DYPDYYK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYPDYYK 7 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 0 103.92 0.019235 145740000 315220 318130 252400 274440 288530 298380 307820 335140 314400 358300 FALSE TRUE 302900.8539 309057.2439 298014.2946 288603.8813 297810.8295 304413.448 311587.1932 328219.2419 278710.6301 334032.0219 0.906801846 0.925232384 0.892172831 0.864000642 0.891563712 0.911330136 0.932806356 0.982598136 0.834382969 1 18.34962689 2.330076208 3.131991379 0.941339891 0.896047881 0.169188933 0.04319631 0.422276444 8.341173088 0.016151421 0.012729408 213.8337284 -2.330076208 -0.045292009 YKEEYAVLISEAQAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 YKEEYAVLISEAQAIK 16 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 161.14 7.79E-09 354370000 917890 900410 813240 783430 955390 1012320 1020330 1145410 1358940 1221810 FALSE TRUE 882017.844 874731.1884 960210.5584 823862.9162 986120.987 1032789.804 1032817.104 1121756.883 1204678.828 1139055.72 0.774341262 0.76794416 0.842988224 0.723285877 0.865735512 0.906707008 0.906730975 0.984813002 1.057611851 1 20.11940689 2.330098471 0.823588536 1.028388863 0.776230467 0.857068964 0.039311478 0.215268346 0.284018787 0.029599415 0.018929611 213.8446901 -2.330098471 -0.252158396 RPAMLDNEADGNK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPAMLDNEADGNK 13 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 134.06 0.00016033 770350000 878350 776720 664360 706570 784480 825140 820660 913410 1010920 937260 FALSE TRUE 844023.1109 754568.7061 784424.6306 743036.1624 809713.5116 841824.8961 830703.4826 894547.7643 896164.5997 873778.5454 0.965946252 0.863569734 0.897738488 0.85037126 0.926680468 0.963430495 0.95070254 1.023769431 1.025619826 1 19.73690816 2.330253918 1.166152268 1.018215705 0.893501455 0.686711064 0.032953848 0.256302279 0.684574942 0.020285794 0.012537397 213.9212453 -2.330253918 -0.12471425 SST(ph)PPGESYFGVSSLQLK ddPTM_BT-474_Pertuzumab_2h_R1 6 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.064)S(0.064)T(0.871)PPGESYFGVSSLQLK;S(0.046)S(0.046)T(0.909)PPGESYFGVSSLQLK;S(0.079)S(0.079)T(0.842)PPGESYFGVSSLQLK;S(0.086)S(0.086)T(0.828)PPGESYFGVSSLQLK;S(0.158)S(0.158)T(0.684)PPGESYFGVSSLQLK;S(0.019)S(0.019)T(0.962)PPGESYFGVSSLQLK 237.4 8.43E-23 14176780000 4366330 4037630 3822670 4049250 4185900 4681060 4548010 5148530 6054810 5358930 TRUE FALSE 4195688.996 3922480.746 4513511.504 4258232.278 4320543.275 4775714.24 4603669.907 5042211.056 5367493.353 4995964.898 0.839815548 0.785129765 0.903431388 0.852334307 0.864806572 0.95591429 0.921477633 1.009256702 1.074365706 1 22.25233191 2.330771081 0.766584463 1.039925305 0.833278262 0.803910829 0.037575084 0.271982007 0.311992147 0.029355306 0.019389704 214.1761371 -2.330771081 -0.206647043 LREEIEELKR ddPTM_BT-474_Pertuzumab_2h_R1 8 LREEIEELKR 10 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;;;;;; 215.08 4.70E-09 7229415000 3906909 3772859 3154026 3297201 3755275 3869519 4095561 4474630 4881610 4732980 FALSE TRUE 3754222.677 3665260.755 3724028.659 3467369.939 3876066.831 3947763.325 4145683.701 4382227.327 4327470.098 4412411.049 0.850832489 0.830670741 0.843989515 0.78582206 0.878446452 0.894695277 0.939550657 0.993159359 0.980749538 1 22.07313576 2.331162075 1.18660487 0.995710312 0.830141106 0.9171807 0.0204819 0.119338299 0.33049401 0.012604888 0.007816469 214.3690459 -2.331162075 -0.165569206 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDITT(ph)PPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDITTPPNK 40 3 P27816-6;P27816 P27816-6 MAP4 Microtubule-associated protein 4 1 KPCNSQPSELSSETSGIARPEEGRPVVS(0.017)GT(0.014)GNDIT(0.209)T(0.76)PPNK 90.514 0.00016003 3663200000 242040 196990 240780 239340 250190 258250 275310 338710 350780 375320 TRUE FALSE 232580.8092 191372.0381 284294.3021 251692.3661 258237.5886 263471.9919 278679.3261 331715.5201 310960.925 349899.2421 0.664707954 0.546934703 0.812503338 0.719328126 0.738034147 0.752993891 0.79645593 0.948031548 0.888715629 1 18.41658001 2.331172433 0.360893076 1.020883122 0.59854576 0.759792392 0.06259333 0.690824848 0.211965022 0.075251913 0.104271168 214.3741589 -2.331172433 -0.422337362 ILPVFDEPPNPTNVEESLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILPVFDEPPNPTNVEESLKR 20 1 Q9NYL9;H0YKU1;H0YNJ8 Q9NYL9 TMOD3 Tropomodulin-3 0 97.095 0.0015881 101710000 96267 102950 95336 101350 93656 109810 108740 126850 124020 127690 FALSE TRUE 92504.77921 100013.9668 112565.3359 106580.6856 96668.5303 112030.4334 110070.7926 124230.5032 109941.7695 119041.4426 0.777080462 0.840160911 0.945597882 0.895324211 0.812057786 0.941104468 0.924642631 1.043590371 0.923558781 1 16.86110439 2.33191368 1.900828153 0.989603997 0.861260052 0.517321729 0.054231282 0.27642413 2.036767634 0.025601254 0.018064235 214.7403618 -2.33191368 -0.128343945 KDSNELS(ph)DSAGEEDSADLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSNELSDSAGEEDSADLKR 20 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KDS(0.001)NELS(0.998)DSAGEEDSADLKR 127.38 1.13E-05 424350000 188620 164080 148300 183500 161000 188820 270830 248110 284970 315220 TRUE FALSE 181248.5219 159400.5991 175101.1089 192970.457 166178.7112 192638.0698 274144.4986 242986.4418 252621.4003 293869.8686 0.616764566 0.542418996 0.595845739 0.656652749 0.565484008 0.655521679 0.932877194 0.82685048 0.859636959 1 18.16481792 2.332040533 4.697505519 0.884854727 0.59746912 0.883700417 0.053271646 0.067303723 2.568887285 0.018509079 0.015183686 214.8030942 -2.332040533 -0.287385606 KTETQEKNPLPSK ddPTM_BT-474_Pertuzumab_2h_R1 4 KTETQEKNPLPSK 13 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;; 121.99 0.00013515 15155860000 6393080 5822500 4703060 4420310 4931780 5652150 5918510 6449510 7197930 6205390 FALSE TRUE 6143231.366 5656448.001 5553007.561 4648442.729 5090415.183 5766440.346 5990942.496 6316325.365 6380851.163 5785093.408 1.061907031 0.977762605 0.959882092 0.803520773 0.879919272 0.996775668 1.035582673 1.091827723 1.102981527 1 22.46390882 2.332231648 2.638860337 1.070773326 0.933403434 0.40581437 0.068281661 0.27152622 3.869278089 0.029625521 0.022728338 214.8976408 -2.332231648 -0.137369892 LEDDAKDNQQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LEDDAKDNQQK 11 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 178.1 7.01E-06 788670000 797549 839749 542327 554411 728440 915804 793045 975526 1277191 951503 FALSE TRUE 766379.9033 815800.1807 640337.5529 583024.2182 751870.9342 934322.1843 802750.5219 955381.0472 1132209.632 887056.8543 0.863958042 0.91967068 0.721867544 0.657256877 0.847601741 1.053283315 0.904959494 1.077023465 1.276366477 1 19.75866705 2.332282462 1.127637408 1.116052427 0.795603894 0.582449206 0.110273654 0.370196782 0.922884201 0.074369706 0.045874385 214.922786 -2.332282462 -0.320448534 LKQVEDEK ddPTM_BT-474_Pertuzumab_2h_R1 5 LKQVEDEK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;;;; 157.96 0.00033616 2863070000 4240630 3974490 3385890 3439080 4212360 4596850 5088760 6074480 6675610 5951470 FALSE TRUE 4074901.491 3861141.437 3997795.642 3616571.331 4347854.385 4689801.457 5151037.767 5949039.865 5917822.739 5548371.636 0.734431966 0.695905338 0.720534943 0.651825719 0.783627102 0.845257269 0.928387301 1.072213661 1.066587303 1 22.40363299 2.332582988 1.28556804 1.05817451 0.70390074 0.941888087 0.035957898 0.090648342 0.2965394 0.020974586 0.013220196 215.0715616 -2.332582988 -0.354273769 QQDAQEFFLHLINMVER ddPTM_BT-474_Pertuzumab_2h_R1 2 QQDAQEFFLHLINMVER 17 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 249.47 4.86E-21 1362570000 883310 914820 797470 807590 856450 849600 782240 800060 875670 982880 FALSE TRUE 848789.2686 888730.2293 941590.5686 849269.8167 883998.4921 866779.4941 791813.2871 783538.4814 776267.6127 916308.6621 0.926313702 0.969902682 1.027591037 0.926838141 0.96473877 0.94594707 0.864133801 0.855103213 0.847168258 1 19.80547413 2.332692194 4.515507198 0.876427556 0.964104017 0.307922616 0.048674284 0.200667779 7.228977027 0.016690668 0.013659416 215.1256493 -2.332692194 0.087676462 MHTTFEHDIQALGTQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MHTTFEHDIQALGTQVR 17 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 99.055 0.00096886 82900000 59163 50942 58112 47323 43600 45900 45785 18851 44990 30606 FALSE TRUE 56850.84455 49489.18404 68614.13109 49765.3457 45002.4336 46828.12945 46345.33053 18461.72026 39882.92381 28533.02836 1.992457437 1.734452558 2.404726559 1.744131225 1.577204951 1.641190303 1.624269599 0.647029822 1.397780961 1 14.80034526 2.332784564 0.914577595 0.965347816 1.979334895 0.630429848 0.281666037 0.351475781 0.571636423 0.205096394 0.127597265 215.1714092 -2.332784564 1.013987079 SYSEDDIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSEDDIHR 9 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739;Q9Y5A9;Q9Y5A9-2 A0A024R7W5;Q9Y5A9 YTHDF3;YTHDF2 YTH domain-containing family protein 3;YTH domain-containing family protein 2 0 ; 195.7 3.08E-05 3041600000 2424800 2726200 2188870 2712600 2550000 2493900 2278050 2206870 2744200 2759600 FALSE TRUE 2330036.135 2648451.445 2584447.5 2852597.611 2632023.066 2544328.367 2305929.457 2161297.363 2432689.921 2572689.834 0.905680935 1.029448405 1.004570184 1.108799659 1.023062723 0.988975948 0.896310712 0.840092472 0.945582281 1 21.2948461 2.332890694 3.858083922 0.899307657 1.018705559 0.324278287 0.060923334 0.207105618 5.868777729 0.022438675 0.018136743 215.2239976 -2.332890694 0.119397902 AGDKDDITEPAVCALR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGDKDDITEPAVCALR 16 1 P14923 P14923 JUP Junction plakoglobin 0 ;;; 144.46 1.20E-06 5627130000 1934820 2126840 1670860 2292380 1459500 2105410 2387420 2652230 2633560 2443020 FALSE TRUE 1859205.095 2066184.606 1972821.57 2410690.007 1506446.143 2147982.833 2416637.96 2597460.524 2334609.31 2277552.079 0.81631727 0.907195328 0.866202616 1.05845659 0.661432139 0.943110303 1.061068145 1.140461528 1.025051998 1 21.11905261 2.332923026 4.011767496 1.07653784 0.869914814 0.456515859 0.098497025 0.183636642 5.537470507 0.034858968 0.028274139 215.240021 -2.332923026 -0.206623026 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 6 GGPEGVAAQAVASAASAGPADAEMEEIFDDASPGK 35 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK 221.93 8.17E-37 1118396000 634662 557122 606589 644284 596326 666582 683254 807637 844741 838829 TRUE FALSE 609858.7074 541233.426 716213.1258 677535.5745 615507.3674 680060.7448 691615.8668 790959.0137 748849.5431 782014.3647 0.779856145 0.692101642 0.915856739 0.866397863 0.787079362 0.869626922 0.884403021 1.01143796 0.957590521 1 19.57683558 2.333083842 0.52026522 1.020005568 0.771156294 0.636198572 0.058209013 0.600447784 0.338036885 0.056838198 0.051894223 215.3197378 -2.333083842 -0.248849273 VNLEVIKPWITK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNLEVIKPWITK 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;M0R1E7;M0QXG5;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 ; 170.52 3.73E-05 827880000 2149860 2074660 1794180 1783800 1938440 1984880 2075370 2100300 2261540 2392680 FALSE TRUE 2065841.094 2015492.728 2118428.237 1875862.132 2000791.683 2025015.634 2100768.999 2056928.071 2004819.46 2230621.652 0.926127966 0.903556516 0.949703073 0.840959349 0.896965956 0.907825687 0.941786339 0.922132209 0.898771631 1 21.0890144 2.333964994 5.603372958 0.933074567 0.902604068 0.192285169 0.035304677 0.411815387 19.70433429 0.01215144 0.01005931 215.7570493 -2.333964994 -0.030470499 GLALEAESELERQDEALDGVAAAVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLALEAESELERQDEALDGVAAAVDR 26 1 A0A087X0B7;Q5SQN1-4;Q5SQN1 A0A087X0B7 SNAP47 Synaptosomal-associated protein 47 0 71.54 0.026718 19005000 16476 16698 12853 17122 17427 15943 14076 14825 17266 16158 FALSE TRUE 15832.0997 16221.78939 15175.82301 18005.66847 17987.55528 16265.37838 14248.2663 14518.85857 15306.03606 15063.60427 1.051016704 1.076886322 1.007449661 1.195309446 1.194106999 1.079779985 0.945873647 0.963836962 1.016093877 1 13.87877938 2.334023486 5.490229393 0.976121224 1.10588711 0.512292905 0.057217322 0.174352021 8.128007958 0.021924944 0.018135715 215.7861099 -2.334023486 0.129765886 HSS(ph)VSDSQPCEPPSVGTEYSQGAS(ph)PQPQHQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSSVSDSQPCEPPSVGTEYSQGASPQPQHQLK 32 0 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1 2 HS(0.455)S(0.503)VS(0.034)DS(0.007)QPCEPPS(0.001)VGT(0.037)EY(0.025)S(0.113)QGAS(0.825)PQPQHQLK 91.295 5.95E-05 122370000 62246 58219 43384 51111 56416 45486 45955 26241 52252 52337 TRUE FALSE 59813.3575 56558.65112 51224.45387 53748.84484 58230.67188 46405.75808 46517.41104 25699.11418 46320.57202 48792.16837 1.22588029 1.159174782 1.049849916 1.101587542 1.193443002 0.951090301 0.953378638 0.52670572 0.949344404 1 15.57436198 2.334480769 2.130448318 0.77705632 1.136370724 0.4813524 0.13597771 0.219928711 2.045599312 0.058691841 0.042905677 216.0134381 -2.334480769 0.359314404 QPLLLS(ph)EDEEDTKR ddPTM_BT-474_Pertuzumab_2h_R1 6 QPLLLSEDEEDTKR 14 1 Q99613-2;Q99613;B5ME19;H3BPE4 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR 264.92 6.16E-25 79778690000 5906240 5351910 5195920 4979050 5429490 5851780 6487350 7009510 7543090 7187080 TRUE FALSE 5675417.611 5199278.767 6134938.327 5236019.367 5604134.477 5970107.001 6566744.13 6864761.169 6686830.046 6700292.67 0.847040255 0.77597786 0.915622441 0.781461292 0.836401446 0.891021825 0.980068253 1.024546465 0.997990741 1 22.67579268 2.334675126 2.142389861 1.010538591 0.830162476 0.826758778 0.036731664 0.113878685 1.071276995 0.015278241 0.011187796 216.1101307 -2.334675126 -0.180376115 VKEFLHNQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKEFLHNQGK 10 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 151.15 1.22E-05 1059750000 1457060 1439990 1213690 1312400 1356570 1396770 1556300 1524490 1724310 1704860 FALSE TRUE 1400116.484 1398922.895 1433030.781 1380133.121 1400205.306 1425013.646 1575346.465 1493008.749 1528573.558 1589388.314 0.880915301 0.880164327 0.901624083 0.868342311 0.880971185 0.89657992 0.99116525 0.939360593 0.961737006 1 20.60004021 2.3348434 5.703906111 0.965524188 0.883294736 0.853821725 0.017840506 0.07666199 3.73493126 0.006093012 0.005047834 216.1938819 -2.3348434 -0.082229452 AEEAEAQKR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEEAEAQKR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 142.55 0.00016685 2332040000 1541120 1508090 1282880 1388410 1341880 1475000 1583320 1620300 1807150 1759120 FALSE TRUE 1480891.327 1465080.75 1514724.954 1460066.006 1385042.789 1504825.511 1602697.144 1586840.239 1602009.908 1639973.236 0.902997253 0.8933565 0.92362785 0.89029868 0.844552069 0.917591506 0.977270305 0.967601303 0.976851252 1 20.64524084 2.335049855 3.905812149 0.976967427 0.891942124 0.813394677 0.020208079 0.09931814 2.863249498 0.007683797 0.006222952 216.2966806 -2.335049855 -0.085025303 LNES(ph)DEQHQENEGTNQLVMGIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNESDEQHQENEGTNQLVMGIQK 23 0 Q15545 Q15545 TAF7 Transcription initiation factor TFIID subunit 7 1 LNES(1)DEQHQENEGTNQLVMGIQK;LNES(1)DEQHQENEGTNQLVMGIQK 303.11 2.87E-62 228570000 159902 144535 153779 161538 164498 168689 212646 206255 239820 253020 TRUE FALSE 153652.8531 140413.0033 181570.2861 169874.9955 169789.2276 172100.0072 215248.4254 201995.7622 212596.639 235882.73 0.651395094 0.595266145 0.769748112 0.720167159 0.719803555 0.729599861 0.912523038 0.856339767 0.901281069 1 17.84771027 2.335668355 0.349405366 1.013597749 0.596702738 0.839980792 0.048450636 0.577907657 0.168180267 0.060000215 0.086206274 216.6049388 -2.335668355 -0.416895012 VKDPNSGLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKDPNSGLPK 10 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 85.845 0.012734 680530000 1424590 1363170 1130290 1191810 1272960 1345220 1419590 1530940 1657330 1505630 FALSE TRUE 1368915.448 1324293.726 1334558.546 1253319.457 1313905.914 1372421.27 1436963.367 1499325.554 1469196.846 1403652.339 0.975252496 0.943462772 0.950775708 0.892898777 0.936062213 0.977750139 1.02373168 1.068160193 1.046695685 1 20.42075422 2.335763041 2.363828706 1.045759457 0.938449892 0.757112083 0.02524791 0.130865483 1.500336335 0.010745105 0.008073768 216.6521689 -2.335763041 -0.107309565 GLVVDMDGFEEERK ddPTM_BT-474_Pertuzumab_2h_R1 8 GLVVDMDGFEEERK 14 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;;;;; 255.85 4.33E-24 3234880000 4111303 3803653 3513939 3652068 3994474 4344912 4375295 4829014 5458151 5264855 FALSE TRUE 3950628.733 3695176.541 4148985.944 3840551.667 4122959.884 4432769.098 4428841.169 4729293.173 4838564.581 4908261.681 0.804893665 0.752848316 0.84530659 0.782466771 0.840004089 0.903124036 0.902323767 0.963537293 0.985800044 1 22.22678074 2.335907192 0.689440462 1.002980673 0.783884852 0.912192324 0.02437988 0.179762862 0.168553643 0.019115487 0.013514209 216.7240919 -2.335907192 -0.21909582 RIQEEMEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RIQEEMEK 8 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1 Q9UM54-1 MYO6 Unconventional myosin-VI 0 129.63 0.001736 233560000 135340 140200 105490 126490 154060 138480 175450 178630 208420 204870 FALSE TRUE 130050.7632 136201.6333 124554.3896 133018.1641 159015.4798 141280.1605 177597.2096 174941.2281 184761.0354 190993.9724 0.680915536 0.713120061 0.652137803 0.696452157 0.832568053 0.739710048 0.929857667 0.915951566 0.967365792 1 17.54316758 2.336493681 0.697696856 0.998003337 0.674268216 0.885048606 0.042304432 0.211190024 0.202542243 0.033465397 0.023477331 217.0169629 -2.336493681 -0.323735122 LEHDVNIQFPDKDDGNQPQDQITITGYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEHDVNIQFPDKDDGNQPQDQITITGYEK 29 1 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 ; 302.49 2.18E-81 1118340000 870630 809410 723650 745710 807190 867830 943920 952240 1153510 1052600 FALSE TRUE 836604.8171 786326.4193 854429.6525 784196.1825 833153.9994 885378.1172 955471.9753 932575.9112 1022568.381 981306.4644 0.852541838 0.801305655 0.87070623 0.799134838 0.849025284 0.902244252 0.973673373 0.950341147 1.042047941 1 19.90434424 2.336661192 1.181369782 1.002054305 0.828166861 0.872447565 0.028482062 0.154555506 0.42460397 0.017074725 0.010638345 217.1006839 -2.336661192 -0.173887443 KTNHSS(ph)PEAQSK ddPTM_BT-474_Pertuzumab_2h_R1 4 KTNHSSPEAQSK 12 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 KT(0.017)NHS(0.097)S(0.887)PEAQSK;KT(0.028)NHS(0.126)S(0.845)PEAQSK;KT(0.01)NHS(0.311)S(0.678)PEAQSK;KTNHS(0.158)S(0.842)PEAQSK 129.93 0.00010603 365444000 286708 286177 249916 271841 255759 300585 333349 360981 387492 372963 TRUE FALSE 275503.1344 278015.5122 295081.3806 285870.7466 263985.7205 306663.0346 337428.6248 353526.6162 343505.5327 347701.8838 0.792354448 0.799580115 0.848662013 0.822171981 0.759230055 0.881971162 0.97045383 1.016752088 0.987931181 1 18.40749136 2.336780506 2.592397304 1.001268364 0.807730228 0.933661093 0.023797924 0.063968257 0.880201025 0.009752242 0.007480893 217.1603363 -2.336780506 -0.193538136 APSPT(ph)SSAGEEGTKKPEPLSPASYHQPEGVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 APSPTSSAGEEGTKKPEPLSPASYHQPEGVAR 32 2 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 APS(0.234)PT(0.48)S(0.126)S(0.16)AGEEGTKKPEPLSPASYHQPEGVAR;APS(0.123)PT(0.721)S(0.123)S(0.033)AGEEGTKKPEPLSPASYHQPEGVAR 282.45 4.31E-72 1166380000 263280 278010 254600 256080 278270 311540 325330 354690 414180 386980 TRUE FALSE 252990.7265 270081.427 300611.8835 269296.3195 287220.8073 317839.5523 329311.4859 347365.5276 367164.0228 360769.4999 0.70125309 0.748625998 0.833251934 0.746449796 0.79613384 0.881004498 0.912803011 0.96284616 1.017724677 1 18.46071785 2.336786481 0.767413805 1.015663648 0.746747054 0.911251882 0.031748544 0.183292119 0.210966165 0.025719834 0.017061398 217.1633243 -2.336786481 -0.268916594 NFDFEGSLS(ph)PVIAPK ddPTM_BT-474_Pertuzumab_2h_R1 5 NFDFEGSLSPVIAPK 15 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 NFDFEGS(0.204)LS(0.796)PVIAPK;NFDFEGS(0.188)LS(0.812)PVIAPK;NFDFEGS(0.01)LS(0.99)PVIAPK;NFDFEGSLS(1)PVIAPK;NFDFEGS(0.103)LS(0.897)PVIAPK 284.07 6.31E-34 1779130000 1687770 1613980 1436730 1535650 1672000 1567460 1404340 1543910 1585780 1500510 TRUE FALSE 1621810.082 1567950.871 1696379.071 1614905.081 1725781.398 1599155.115 1421526.733 1512027.719 1405768.903 1398879.121 1.159363992 1.120862301 1.212670234 1.154427896 1.233688724 1.143168906 1.016189828 1.080885186 1.004925216 1 20.41583987 2.336901441 4.716326854 1.037054953 1.175091855 0.790581082 0.036663885 0.098054356 3.714106983 0.012915184 0.010609709 217.2208163 -2.336901441 0.138036902 PSTQPRPDS(ph)WGEDNWEGLETDSR ddPTM_BT-474_Pertuzumab_2h_R1 5 PSTQPRPDSWGEDNWEGLETDSR 23 1 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PPN3;H0YDH0 E9PS17 SCYL1 N-terminal kinase-like protein 1 PSTQPRPDS(1)WGEDNWEGLETDSR;PSTQPRPDS(1)WGEDNWEGLETDSR;PSTQPRPDS(1)WGEDNWEGLETDSR;PSTQPRPDS(1)WGEDNWEGLETDSR;PSTQPRPDS(1)WGEDNWEGLETDSR 250.52 1.73E-38 2657011000 761095 689902 607913 648345 711707 768040 770989 863436 1021874 867766 TRUE FALSE 731350.566 670226.6704 717776.4021 681806.1631 734599.702 783570.295 780424.594 845605.7449 905875.1476 808991.4359 0.904027575 0.828471898 0.887248456 0.84278539 0.908043855 0.968576749 0.964688326 1.045259205 1.119758637 1 19.6257649 2.337314964 1.049376415 1.061869765 0.863385978 0.80667532 0.03806069 0.202574071 0.436052231 0.024502711 0.015124716 217.4277464 -2.337314964 -0.198483787 T(ph)PIQAGGYGAFPVH ddPTM_BT-474_Pertuzumab_2h_R1 2 TPIQAGGYGAFPVH 14 0 P15056;A0A2U3TZI2 P15056 BRAF Serine/threonine-protein kinase B-raf 1 T(1)PIQAGGYGAFPVH;T(1)PIQAGGYGAFPVH 96.414 0.0099968 95184000 103172 97820 97937 115409 97504 93287 79714 79365 75043 84184 TRUE FALSE 99139.92418 95030.26938 115636.3945 121365.2723 100640.3047 95173.32706 80689.56378 77726.08502 66524.43325 78482.1427 1.263216329 1.210852126 1.473410263 1.546406203 1.282333806 1.212674932 1.028126412 0.990366501 0.847637831 1 16.26007681 2.33756985 1.585802732 0.942122085 1.368003244 0.778685612 0.09883151 0.189093721 0.958287772 0.055391731 0.037153391 217.5553913 -2.33756985 0.425881159 GREGS(ph)LTGTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GREGSLTGTK 10 1 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 GREGS(1)LTGTK 66.004 0.040739 517210000 241370 246820 185250 226020 262710 263250 268920 315610 312690 353110 TRUE FALSE 231936.9936 239780.9353 218728.7959 237684.9193 271160.3057 268573.0954 272211.1234 309092.5432 277194.7421 329193.5452 0.704561183 0.728388933 0.664438289 0.72202181 0.823710883 0.815851645 0.82690298 0.938938651 0.842041851 1 18.32857652 2.339143649 0.408211032 0.989157161 0.663123103 0.842887549 0.039806705 0.448457093 0.167396355 0.042837904 0.052005212 218.3452 -2.339143649 -0.326034058 LKDDEVAQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDDEVAQLK 10 1 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 100.56 0.0035849 117090000 155900 131420 140710 143940 172850 169960 178940 206000 255800 233860 FALSE TRUE 149807.2556 127672.0303 166139.4271 151368.7606 178409.8772 173396.7076 181129.9212 201746.028 226762.6564 218020.4539 0.687124776 0.585596571 0.762035965 0.694286971 0.818317153 0.79532312 0.830793249 0.925353674 1.040098084 1 17.73410396 2.339550093 0.504560064 1.033785951 0.639390135 0.857638065 0.051189315 0.32462947 0.173232417 0.047127438 0.04471425 218.5496387 -2.339550093 -0.394395816 S(ph)ASDSGCDPASKK ddPTM_BT-474_Pertuzumab_2h_R1 3 SASDSGCDPASKK 13 1 Q7LBC6;H0Y9V5 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 S(0.985)AS(0.013)DS(0.001)GCDPASKK;S(0.981)AS(0.017)DS(0.002)GCDPASKK;S(0.996)AS(0.003)DS(0.001)GCDPASKK 111.43 0.00060027 553650000 1357830 1246970 902740 1063780 1340070 1133390 845800 1081500 998660 863730 TRUE FALSE 1304764.502 1211407.637 1065885.199 1118681.813 1383174.569 1156307.922 856151.1534 1059166.647 885296.3035 805228.7978 1.620364927 1.504426617 1.323704769 1.389271989 1.71774106 1.435999216 1.063239611 1.315361112 1.099434479 1 19.61903924 2.339725332 5.718814833 1.162212865 1.500783876 0.667403713 0.130294656 0.143398814 6.863516881 0.046765266 0.038767943 218.637842 -2.339725332 0.338571011 LTQTSS(ph)TEQLNVLETETEVLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.04)QT(0.018)S(0.075)S(0.433)T(0.433)EQLNVLETETEVLNK 240.13 8.34E-31 115540000 70905 72018 64886 63860 67031 71325 76341 82218 84464 80887 TRUE FALSE 68133.95421 69964.11715 76612.34358 67155.82225 69187.11299 72767.24037 77275.28399 80520.16957 74876.00082 75408.45144 0.90353207 0.927802067 1.01596495 0.890560951 0.917498127 0.964974601 1.024756278 1.067787072 0.992939112 1 16.2024386 2.339775014 3.270362274 1.032119399 0.933835486 0.562185162 0.037069835 0.169821831 3.617704875 0.014251603 0.011357816 218.6628548 -2.339775014 -0.098283913 RTPS(ph)DDEEDNLFAPPK ddPTM_BT-474_Pertuzumab_2h_R1 7 RTPSDDEEDNLFAPPK 16 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 RT(0.204)PS(0.796)DDEEDNLFAPPK;RT(0.017)PS(0.983)DDEEDNLFAPPK;RT(0.018)PS(0.982)DDEEDNLFAPPK;RT(0.213)PS(0.787)DDEEDNLFAPPK;RT(0.004)PS(0.996)DDEEDNLFAPPK;RT(0.018)PS(0.982)DDEEDNLFAPPK;RT(0.063)PS(0.937)DDEEDNLFAPPK 265.08 4.88E-27 6041700000 5485120 5384120 4507790 5246080 5322210 5496140 6008540 6538150 6846110 6647340 TRUE FALSE 5270755.446 5230570.169 5322447.928 5516830.817 5493403.718 5607275.717 6082074.31 6403134.918 6068968.294 6197109.741 0.850518333 0.844033814 0.858859719 0.89022642 0.886446093 0.90482111 0.981437245 1.033245365 0.979322385 1 22.56316409 2.340952781 1.705821868 1.011001905 0.863245489 0.922386635 0.018271465 0.093349034 0.550572766 0.009637288 0.006634549 219.2566535 -2.340952781 -0.147756416 TVPS(ph)TPTLVVPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.013)VPS(0.664)T(0.318)PT(0.004)LVVPHR;T(0.012)VPS(0.744)T(0.244)PTLVVPHR 134.9 5.81E-05 900200000 645578 645788 506389 440112 625101 487047 181211 308044 178505 195547 TRUE FALSE 620348.098 627370.7585 597904.7569 462826.2331 645207.9414 496895.424 183428.7144 301682.7838 158241.8608 182302.4275 3.40285155 3.441373585 3.27974106 2.538782612 3.539217498 2.725665428 1.006178123 1.654847869 0.868018396 1 17.47597425 2.341775633 4.133004293 1.228669455 3.208718711 0.899512472 0.333415985 0.066149718 2.063827346 0.120801329 0.098518237 219.67247 -2.341775633 1.980049256 up DIEVLS(ph)EDTDYEEDEVTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIEVLSEDTDYEEDEVTKK 19 1 Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3;H7C5R6 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 1 DIEVLS(0.904)EDT(0.096)DYEEDEVTKK 78.272 0.0023392 0 35806 30457 26406 29168 31421 32982 47364 37833 57044 48434 TRUE FALSE 34406.66193 29588.39618 31178.1516 30673.36398 32431.685 33648.91864 47943.6548 37051.73533 50568.60427 45153.52204 0.761992872 0.655284346 0.69049213 0.679312767 0.718253716 0.745211384 1.06179214 0.820572431 1.119926021 1 15.4625509 2.342833426 5.676905405 0.969792525 0.700364441 0.766790762 0.078397461 0.102973238 4.833999491 0.026692776 0.022129895 220.2081689 -2.342833426 -0.269428084 TCPSLSPTS(ph)PLNNK ddPTM_BT-474_Pertuzumab_2h_R1 1 TCPSLSPTSPLNNK 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 TCPSLSPT(0.064)S(0.936)PLNNK 251.87 1.09E-12 0 476830 421090 356460 415350 416690 434410 480080 508570 526470 491000 TRUE FALSE 458194.9564 409080.9255 420880.2514 436786.2633 430093.2123 443194.0678 485955.3626 498067.8518 466707.3327 457744.1327 1.000984882 0.893689064 0.919466185 0.954214881 0.939593064 0.968213542 1.061631003 1.088092269 1.019581245 1 18.80418187 2.342846929 3.797350733 1.054430526 0.939532638 0.648865937 0.034602139 0.121310806 3.321964531 0.012519124 0.010145346 220.2150157 -2.342846929 -0.114897888 EDFLQLFNLRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDFLQLFNLRPK 12 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 ; 146.36 5.76E-05 181357000 323700 352860 312450 315290 333920 355620 383110 416020 432140 442960 FALSE TRUE 311049.4461 342796.7783 368916.6654 331562.1547 344660.8401 362810.8801 387798.6148 407429.0416 383085.2789 412957.9247 0.753223095 0.830100981 0.893351703 0.802895731 0.834614907 0.878566213 0.939075367 0.98661151 0.927661769 1 18.65563527 2.342901283 1.785180387 0.971275335 0.824958695 0.768489365 0.036663457 0.170368863 1.10399162 0.017591748 0.01230629 220.2425784 -2.342901283 -0.14631664 AHHGEAGHHLPEPSS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 AHHGEAGHHLPEPSSR 16 0 O76061 O76061 STC2 Stanniocalcin-2 1 AHHGEAGHHLPEPS(0.124)S(0.876)R 57.328 0.054044 140030000 48497 40613 31050 35565 28984 31602 22383 3907 23586 13022 TRUE FALSE 46601.68362 39454.757 36661.4257 37400.51391 29916.29668 32241.01409 22656.92985 3826.319085 20908.61616 12140.00834 3.838686294 3.249977751 3.019884721 3.080765092 2.464273157 2.655765399 1.866302659 0.315182575 1.722290098 1 13.56748179 2.343297735 1.089322017 0.870839583 3.267966253 0.809888564 0.450982197 0.203018942 0.47246296 0.29991358 0.186441759 220.4437221 -2.343297735 2.39712667 VEMAPLNEEDDEDEDSTVFDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEMAPLNEEDDEDEDSTVFDIK 22 0 Q3ZCQ3 Q3ZCQ3 FAM174B Membrane protein FAM174B 0 87.156 0.0028775 12288000 15322 22277 12743 21698 16153 20635 28040 31246 29010 24662 FALSE TRUE 14723.1993 21641.68177 15045.94357 22817.83638 16672.57591 21052.25384 28383.16191 30600.75918 25716.90642 22991.62077 0.640372397 0.941285609 0.65440987 0.992441403 0.725158791 0.915648968 1.234500264 1.330952675 1.118533864 1 14.48882055 2.343454926 3.90712395 1.21467141 0.804045789 0.634293562 0.134346634 0.123696882 3.540402519 0.046027239 0.03739731 220.5235252 -2.343454926 -0.41062562 GHTAS(ph)ESDEQQWPEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHTASESDEQQWPEEK 16 0 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GHTAS(0.99)ES(0.01)DEQQWPEEK;GHTAS(0.952)ES(0.048)DEQQWPEEK;GHT(0.03)AS(0.956)ES(0.014)DEQQWPEEK;GHT(0.021)AS(0.872)ES(0.106)DEQQWPEEK 439.02 7.28E-182 2585680000 3379000 3296920 2767570 3147290 3159160 2894160 2913930 2207320 3409800 3226360 TRUE FALSE 3246944.944 3202895.07 3267731.463 3309722.014 3260777.25 2952681.898 2949591.547 2161738.071 3022733.799 3007835.763 1.079495425 1.064850385 1.086406214 1.100366601 1.084094182 0.981663272 0.980635839 0.718702163 1.004953075 1 21.52029436 2.343521128 2.074790905 0.877965654 1.081749168 0.439704858 0.079912979 0.23266562 2.051209094 0.034775202 0.025443286 220.5571435 -2.343521128 0.203783515 EVEVEVESMDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVEVEVESMDK 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 219.72 2.25E-11 306060000 543020 530670 442010 468670 505430 554690 578770 626240 708140 663020 FALSE TRUE 521798.1781 515535.8112 521891.0395 492858.1149 521687.615 565906.2118 585853.1604 613307.9252 627754.916 618113.0648 0.844179176 0.83404775 0.84432941 0.797359161 0.844000305 0.915538344 0.947809056 0.992226115 1.015598847 1 19.23751123 2.343695005 1.323606682 1.004076617 0.828823378 0.957746338 0.015723261 0.083107458 0.289450118 0.009533901 0.006117201 220.6454646 -2.343695005 -0.175253239 GFSVVADT(ph)PELQR ddPTM_BT-474_Pertuzumab_2h_R1 13 GFSVVADTPELQR 13 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR 342.38 4.35E-62 1.43923E+11 74576385 82930235 74970556 66029555 68991831 71430576 55083300 78977719 61294436 61283649 TRUE FALSE 71661857.43 80565145.89 88519403.18 69437348.25 71211015.9 72874951.19 55757425.9 77346801.5 54336548.59 57132852.87 1.254302102 1.410136933 1.54936081 1.215366374 1.246410993 1.27553496 0.975925813 1.353806044 0.951056106 1 25.76781724 2.343822909 0.419504815 1.005537176 1.423134134 0.468398726 0.135958121 1.124243624 0.438445908 0.141461657 0.166861907 220.7104566 -2.343822909 0.417596959 YLPENDLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLPENDLKR 9 1 O00743;O00743-2 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 147.75 0.00014695 890350000 579680 541240 462440 506590 538040 559640 595660 608390 702530 667290 FALSE TRUE 557025.4647 525804.3651 546013.1949 532735.1706 555346.5452 570956.3042 602949.8653 595826.5339 622781.7396 622093.8539 0.895404224 0.845217103 0.877702282 0.856358196 0.892705404 0.917797693 0.969226527 0.957775953 1.001105759 1 19.24677273 2.344534756 0.974542604 0.993255412 0.86507071 0.910139517 0.016308393 0.142735694 0.264654972 0.010790048 0.006723246 221.0725169 -2.344534756 -0.128184702 MQNGFGSPEPSLPGTPHS(ph)PAPPSGGTWK ddPTM_BT-474_Pertuzumab_2h_R1 2 MQNGFGSPEPSLPGTPHSPAPPSGGTWK 28 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 MQNGFGSPEPSLPGTPHS(1)PAPPSGGTWK;MQNGFGSPEPSLPGT(0.011)PHS(0.989)PAPPSGGTWK 240.52 1.82E-45 469560000 513740 536610 475650 529500 530770 516600 516230 514870 564640 602140 TRUE FALSE 493662.4728 521306.4082 561610.5358 556827.5585 547842.6991 527046.006 522547.7772 504237.7546 500544.4344 561356.5215 0.879409883 0.928654764 1.000452501 0.991932109 0.975926489 0.938879279 0.930866138 0.89824868 0.891669403 1 19.0985578 2.345570839 2.839251291 0.918788501 0.958165446 0.04465726 0.042689557 0.539538272 8.845282842 0.01719423 0.013486133 221.6005524 -2.345570839 0.039376945 EISSS(ph)PTSK ddPTM_BT-474_Pertuzumab_2h_R1 6 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EIS(0.005)S(0.142)S(0.837)PT(0.008)S(0.008)K;EISS(0.009)S(0.954)PT(0.027)S(0.011)K;EISSS(1)PTSK;EISS(0.002)S(0.998)PTSK;EISS(0.034)S(0.96)PT(0.006)SK;EISS(0.001)S(0.999)PTSK 206.36 1.41E-05 10086520000 11699720 11481850 9989720 10718760 10375090 11122920 12061800 12305100 13223500 12163000 TRUE FALSE 11242482.01 11154398.88 11795084.62 11271956.49 10708814.19 11347833.06 12209415.92 12050995.38 11722423.72 11339189.18 0.991471421 0.983703394 1.040205295 0.994070768 0.944407402 1.000762302 1.076745059 1.062773995 1.03379735 1 23.43481415 2.345599337 6.629645276 1.050860117 0.991404861 0.419576313 0.028927348 0.185992792 10.30082587 0.010296741 0.008572168 221.615094 -2.345599337 -0.059455256 VLDQDTDAIAVHVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLDQDTDAIAVHVVR 15 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 144.18 4.28E-06 160540000 74306 78620 66503 73816 80949 74204 71849 72135 77377 88556 FALSE TRUE 71402.03937 76377.83458 78521.57145 77625.65261 83552.7981 75704.45572 72728.30955 70645.38704 68593.48735 82558.02324 0.864870991 0.925141271 0.951107698 0.940255708 1.012049403 0.91698484 0.880935695 0.855705893 0.830851862 1 16.33312081 2.346247499 4.17519259 0.87727621 0.940751925 0.118474262 0.053840692 0.324278739 10.22548259 0.018999211 0.015527498 221.9460902 -2.346247499 0.063475715 QSLEDFPEWER ddPTM_BT-474_Pertuzumab_2h_R1 1 QSLEDFPEWER 11 0 Q86W56-3;Q86W56-2;Q86W56;Q86W56-5;Q86W56-4 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 0 144.65 8.52E-05 34708000 35793 39498 35995 37147 33078 40837 39450 49990 42607 42517 FALSE TRUE 34394.16999 38371.55571 42500.0972 39064.16112 34141.98391 41662.75212 39932.8009 48957.68903 37770.43198 39637.28572 0.867722634 0.968067188 1.072225215 0.985540771 0.86136029 1.051100028 1.007455485 1.23514232 0.952901575 1 15.27457055 2.346452137 2.569438598 1.088018788 0.961468513 0.158986825 0.093225815 0.38093803 5.14884219 0.037675641 0.029058162 222.050695 -2.346452137 -0.126550275 ERS(ph)PALKS(ph)PLQSVVVR ddPTM_BT-474_Pertuzumab_2h_R1 6 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 ERS(1)PALKS(0.686)PLQS(0.314)VVVR;ERS(1)PALKS(0.985)PLQS(0.015)VVVR;ERS(1)PALKS(1)PLQSVVVR;ERS(1)PALKS(0.931)PLQS(0.069)VVVR;ERS(1)PALKS(1)PLQSVVVR;ERS(1)PALKS(0.996)PLQS(0.004)VVVR 157.63 2.61E-08 6413860000 6002010 5407980 5304320 4991690 5716020 5900740 5947610 6784160 6761900 7100530 TRUE FALSE 5767444.814 5253749.705 6262928.618 5249311.719 5899880.974 6020057.006 6020398.63 6644064.725 5994317.46 6619604.779 0.871267244 0.793665163 0.946118209 0.792994732 0.891273901 0.909428464 0.909480072 1.003695077 0.905540083 1 22.65831365 2.347178348 1.140022616 0.971733216 0.853091694 0.47601922 0.049463306 0.396112942 1.013200631 0.029365688 0.018398184 222.4223104 -2.347178348 -0.118641523 TTS(ph)SYQNLVWSDHSQELHS(ph)PTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSSYQNLVWSDHSQELHSPTLK 23 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 2 T(0.063)T(0.08)S(0.391)S(0.391)Y(0.002)QNLVWS(0.072)DHS(0.001)QELHS(0.997)PT(0.003)LK 162.02 8.09E-12 196790000 177500 169410 106390 116990 132810 108900 59009 19784 75055 65664 TRUE FALSE 170563.1038 164578.5927 125617.0396 123027.8679 137081.9543 111102.0326 59731.16979 19375.45349 66535.07106 61216.51879 2.786226776 2.688467033 2.052012138 2.009716827 2.239296794 1.81490282 0.975736141 0.316506947 1.086880998 1 15.90163338 2.347593202 2.143558697 0.696087368 2.343317314 0.846956552 0.302655995 0.115655399 1.089293486 0.140677482 0.104208263 222.6348779 -2.347593202 1.647229947 up RVIHFVSGETMEEYS(ph)T(ph)DEDEVDGLEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVIHFVSGETMEEYSTDEDEVDGLEKK 27 2 G3V583;Q8N128;Q8N128-2 G3V583 FAM177A1 Protein FAM177A1 2 RVIHFVSGETMEEY(0.285)S(0.873)T(0.842)DEDEVDGLEKK 94.75 0.0096809 80503000 45962 40315 25066 22763 32248 33840 36924 36801 48472 33153 TRUE FALSE 44165.75423 39165.25567 29595.98379 23937.80116 33285.28621 34524.26799 37375.88696 36041.04649 42969.66177 30907.51778 1.428964776 1.267175706 0.957565858 0.774497691 1.076931718 1.117018462 1.209281419 1.166093206 1.390265698 1 14.91567017 2.348556475 3.620961889 1.201701129 1.084998392 0.046909066 0.184911936 0.712730799 18.03345472 0.073352743 0.059337113 223.1292344 -2.348556475 -0.116702737 EYHPDKNPNAGDKFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EYHPDKNPNAGDKFK 15 2 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ; 196.64 5.30E-09 531850000 964900 1043690 792040 1204020 853100 1016370 1299470 1249630 1276250 1189250 FALSE TRUE 927190.6412 1013924.983 935179.2468 1266159.616 880540.7363 1036921.698 1315373.303 1223824.704 1131375.45 1108701.038 0.836285535 0.91451613 0.843490909 1.142020773 0.794209355 0.935258164 1.186409372 1.103836527 1.020451331 1 20.08043896 2.348991356 7.216381555 1.091185498 0.911408068 0.39942796 0.099928152 0.210301535 12.61821629 0.033903335 0.028268346 223.3527769 -2.348991356 -0.179777429 NSPTFKS(ph)FEEKVENLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPTFKSFEEKVENLK 16 2 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NSPT(0.001)FKS(0.999)FEEKVENLK;NS(0.002)PT(0.015)FKS(0.984)FEEKVENLK 105.67 0.00066027 1927910000 3329800 2578460 581560 641590 2352500 1838390 1317250 2011330 2019880 1003490 TRUE FALSE 3199667.735 2504924.845 686660.8287 674702.5368 2428170.299 1875563.505 1333370.9 1969795.333 1790591.69 935522.7285 3.420192409 2.677567064 0.73398626 0.721203789 2.595522508 2.004829437 1.425268311 2.105555827 1.91400127 1 19.83541318 2.349178183 17.96717469 1.733579608 1.963164804 0.045516892 0.830208982 9.714801403 1524.854839 0.308443215 0.258059332 223.4488803 -2.349178183 0.229585196 LVEDKPGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVEDKPGSR 9 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ;;; 146.11 8.72E-05 3105300000 2165610 2233790 1803920 2016000 2014350 2217120 2134280 2363620 2579490 2401230 FALSE TRUE 2080975.567 2170084.496 2129928.472 2120046.002 2079143.397 2261951.685 2160399.957 2314810.421 2286677.109 2238592.553 0.929591034 0.969396817 0.95145875 0.947044159 0.928772587 1.01043474 0.965070644 1.034047227 1.021479816 1 21.09416054 2.350215003 1.334344662 1.017812316 0.947517256 0.6412334 0.021750907 0.257690412 0.913711996 0.011841334 0.007662789 223.9829719 -2.350215003 -0.07029506 LINRPIIVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LINRPIIVFR 10 1 Q16658;C9JPH9;C9JFC0;A0A0A0MSB2 Q16658 FSCN1 Fascin 0 ; 128.86 0.00029046 218720000 182137 198141 178124 196506 187315 175833 186472 168808 203511 181090 FALSE TRUE 175018.8847 192490.2127 210314.9691 206647.6982 193340.1571 179388.4637 188754.1001 165322.0558 180409.2845 168824.613 1.036690572 1.140178611 1.245760114 1.224037743 1.145213092 1.06257293 1.118048469 0.979253279 1.068619565 1 17.36516572 2.350472336 1.33368577 1.020005653 1.165710295 0.461634234 0.062063466 0.388190621 1.375083758 0.036963882 0.023923462 224.1157284 -2.350472336 0.145704642 LKDSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDSEK 6 1 O00148;O00148-2;C9JGA2;Q9H6S1-3;Q9H6S1-5;C9JVK8;Q9H6S1-4;Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;H0Y6V3;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8;Q9H6S1 O00148;Q5VT25-2;Q5VT25-3;Q9H6S1 DDX39A;AZI2;CDC42BPA ATP-dependent RNA helicase DDX39A;5-azacytidine-induced protein 2;Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 0 75.109 0.071644 608030000 617430 524680 537260 511280 486140 558680 638400 632100 610790 789100 FALSE TRUE 593300.153 509716.6401 634354.8333 537667.2221 501777.1346 569976.8924 646212.9302 619046.9141 541455.6798 735653.5541 0.806493967 0.692875929 0.862301052 0.730870148 0.682083478 0.77478983 0.878420184 0.841492453 0.736019933 1 19.48866698 2.351335062 5.616526865 0.850334643 0.753658219 0.303702121 0.077688497 0.282462729 12.85731821 0.026197906 0.021730766 224.5613769 -2.351335062 -0.096676424 TLESTWEKPQELK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLESTWEKPQELK 13 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 192.18 2.68E-06 431360000 351010 356120 261030 316990 384720 357710 416130 471110 514760 494210 FALSE TRUE 337292.1411 345963.8063 308203.9276 333349.8919 397094.8682 364943.1413 421222.7234 461381.4139 456326.6028 460736.7165 0.732071331 0.750892633 0.668937197 0.723514927 0.86186938 0.792086083 0.914237369 1.001399275 0.990428126 1 18.81358305 2.351534954 0.879769721 1.017261588 0.717651974 0.89063098 0.039803231 0.178369398 0.269595892 0.029982941 0.019126856 224.6647588 -2.351534954 -0.299609615 SVS(ph)HGS(ph)NHTQKPDEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 2 S(0.455)VS(0.568)HGS(0.974)NHT(0.002)QKPDEQR 63.69 0.0883 180550000 118560 121190 121960 118240 127930 103500 122170 64759 146690 122720 TRUE FALSE 113926.5441 117733.7799 144000.885 124342.3806 132044.9846 105592.8409 123665.153 63421.70402 130038.3662 114408.0651 0.995791197 1.029068884 1.25866026 1.0868323 1.154158009 0.922949277 1.080912896 0.554346444 1.136618874 1 16.80382923 2.352515871 1.909642642 0.861168081 1.104592839 0.143422816 0.166596985 0.431242533 3.211018149 0.074916821 0.053979502 225.1727701 -2.352515871 0.243424758 NSNPDEIEIDFETLKPSTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSNPDEIEIDFETLKPSTLR 20 1 O60885;O60885-2;O60885-3 O60885 BRD4 Bromodomain-containing protein 4 0 ; 165.38 1.53E-11 113737000 141828 127879 120663 134907 141698 138614 151846 164204 186489 179543 FALSE TRUE 136285.205 124232.0161 142469.4882 141869.5664 146255.8449 141416.8701 153704.3368 160813.13 165319.5505 167382.3927 0.814214702 0.742204805 0.851161738 0.847577599 0.873782735 0.844873035 0.918282588 0.960752965 0.987675871 1 17.35278825 2.352938823 0.484941524 1.014689004 0.780725314 0.861048028 0.028943065 0.342310242 0.170374019 0.028168948 0.028214779 225.392169 -2.352938823 -0.233963691 EKPQQHNFTHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKPQQHNFTHR 11 1 F8WCR3;F8WDI9;E9PF19;Q96E41;Q9Y4P3 F8WCR3 TBL2 Transducin beta-like protein 2 0 146.5 2.31E-05 55714000 57253 98908 46647 118170 65256 57250 80498 28701 76827 61640 FALSE TRUE 55015.48946 96087.24068 55077.15056 124268.7679 67355.0185 58407.63423 81483.1586 28108.31432 68105.92105 57465.0679 0.957372739 1.672098271 0.958445758 2.16250972 1.172103697 1.016402423 1.417959842 0.489137407 1.18517081 1 15.81039761 2.353577392 1.423515277 0.890424545 1.411965699 0.170309515 0.396408863 0.598019153 2.426719188 0.206949203 0.136673459 225.7238203 -2.353577392 0.521541155 AEDGATPS(ph)PSNETPK ddPTM_BT-474_Pertuzumab_2h_R1 6 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGAT(0.002)PS(0.998)PSNETPK;AEDGATPS(0.994)PS(0.006)NETPK;AEDGATPS(0.965)PS(0.035)NETPK;AEDGATPS(0.998)PS(0.002)NETPK;AEDGAT(0.002)PS(0.997)PSNETPK;AEDGAT(0.002)PS(0.977)PS(0.022)NETPK 347.03 3.17E-82 6504060000 3474770 3458350 3356480 3450570 3527840 3956790 4320280 5092580 5109050 4713850 TRUE FALSE 3338972.147 3359721.244 3963070.6 3628654.331 3641316.178 4036799.005 4373152.879 4987416.443 4529092.063 4394576.741 0.759793797 0.76451532 0.901809397 0.825711905 0.828593148 0.918586531 0.995124932 1.134902571 1.030609392 1 22.06729279 2.354119457 1.81695309 1.069879127 0.816742283 0.814838848 0.05049761 0.136603861 0.918555587 0.02434562 0.017310298 226.0057335 -2.354119457 -0.253136844 GDFDENLNYPEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 GDFDENLNYPEQK 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;;; 299.42 1.79E-40 742790000 1041780 1080080 879290 997110 1018130 1096940 1087300 1225980 1332480 1247870 FALSE TRUE 1001066.086 1049277.176 1038197.263 1048570.967 1050879.076 1119120.878 1100606.703 1200663.085 1181222.457 1163350.653 0.860502449 0.901944029 0.89241989 0.901336982 0.903321 0.961980702 0.946066175 1.032073246 1.015362353 1 20.14985458 2.354567783 0.991829059 1.020863235 0.886734321 0.884074283 0.018995706 0.158004949 0.304331628 0.012541052 0.007876409 226.2391616 -2.354567783 -0.134128914 GFCFITYTDEEPVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFCFITYTDEEPVKK 15 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 227.42 1.18E-12 668390000 504420 458010 402050 420380 464840 506290 492940 577150 601430 595900 FALSE TRUE 484706.7087 444948.0032 474709.3786 442075.8622 479792.0008 516527.5307 498972.7472 565231.6508 533158.1878 555539.1622 0.872497821 0.80093004 0.854502096 0.795760033 0.863651086 0.929776991 0.898177448 1.017446994 0.959713057 1 19.08352909 2.354977866 1.064911613 0.994874594 0.829049719 0.796645484 0.032851911 0.202799914 0.451663907 0.020450241 0.012840605 226.452889 -2.354977866 -0.165824875 TYEDIKENLESR ddPTM_BT-474_Pertuzumab_2h_R1 2 TYEDIKENLESR 12 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ; 153.81 6.19E-05 1075920000 1882730 1793850 1383240 1601510 1759650 1808650 1681070 1964410 2111730 1982960 FALSE TRUE 1809150.83 1742691.154 1633222.238 1684164.123 1816250.74 1845222.142 1701643.438 1923844.247 1872015.263 1848652.353 0.97863226 0.942681923 0.883466399 0.911022627 0.982472847 0.99814448 0.920477793 1.040673896 1.012637806 1 20.81804251 2.354994148 0.868173328 1.015849984 0.930863345 0.391832977 0.037246632 0.607573075 0.89506866 0.028743419 0.018455789 226.4613794 -2.354994148 -0.084986639 QRSS(ph)PVTK ddPTM_BT-474_Pertuzumab_2h_R1 7 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.293)S(0.707)PVTK;QRS(0.114)S(0.886)PVTK;QRS(0.05)S(0.95)PVTK;QRS(0.148)S(0.852)PVTK;QRS(0.484)S(0.516)PVTK;QRS(0.152)S(0.848)PVTK;QRS(0.343)S(0.657)PVTK 108.2 0.002336 11676318000 5569502 5160547 4147242 4749187 4646176 4912022 5370133 5388056 5544959 5698326 TRUE FALSE 5351839.704 5013373.252 4896740.884 4994293.11 4795624.471 5011346.45 5435854.294 5276790.761 4915518.501 5312373.304 1.007429147 0.943716295 0.921761443 0.940124653 0.902727311 0.94333477 1.023244035 0.99330195 0.925296138 1 22.3409251 2.355248146 9.595296135 0.987109446 0.939978767 0.266821881 0.034081754 0.365255399 29.05893477 0.011994051 0.010025952 226.5938646 -2.355248146 -0.047130679 LTTPTYGDLNHLVS(ph)ATMSGVTTCLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTTPTYGDLNHLVSATMSGVTTCLR 25 0 Q5JP53;P07437;Q5ST81;P68371;M0R2D3;Q13885;Q9BVA1;P04350 Q5JP53;P68371;Q13885;Q9BVA1;P04350 TUBB;TUBB4B;TUBB4A;TUBB2A;TUBB2B Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain 1 LTTPTYGDLNHLVS(1)ATMSGVTTCLR 110.91 0.0017514 42639000 36874 39252 28310 31540 38373 29690 30140 27023 31657 28169 TRUE FALSE 35432.92331 38132.57139 33426.24675 33167.78318 39607.30239 30290.35214 30508.86234 26464.96561 28063.43008 26261.08854 1.349255697 1.452056008 1.272843154 1.26300108 1.508212515 1.153430944 1.161751627 1.007763466 1.068631639 1 14.6806391 2.356795504 1.905758783 1.039421727 1.361536655 0.756679212 0.0828805 0.160667383 1.191492096 0.03682121 0.026621725 227.4026407 -2.356795504 0.322114928 IDFDSVSSIMAS(ph)SQ ddPTM_BT-474_Pertuzumab_2h_R1 1 IDFDSVSSIMASSQ 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;K7EK53 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 1 IDFDSVSSIMAS(0.5)S(0.5)Q 76.759 0.027865 13620000 46997 51698 36542 55436 47273 47308 47844 45128 50505 62028 TRUE FALSE 45160.30528 50223.62366 43145.95227 58297.0586 48793.57898 48264.60017 48429.52918 44196.09103 44771.88413 57826.78831 0.780958213 0.868518296 0.74612396 1.008132395 0.8437885 0.834640857 0.837492979 0.764284034 0.774241237 1 15.81945036 2.357452188 2.648014438 0.817898606 0.852476016 0 0.089021787 1.258845934 18.03802587 0.034181047 0.026719732 227.74675 -2.357452188 0.03457741 HSS(ph)PHQS(ph)EDEEDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 2 HS(0.4)S(0.6)PHQS(1)EDEEDPR 176.44 3.25E-06 40350000 54599 64856 42513 50868 54077 46878 43372 31924 55262 40494 TRUE FALSE 52465.21072 63006.37038 50196.0448 53493.30358 55816.43582 47825.90528 43902.79951 31264.75824 48988.88944 37751.30531 1.389758852 1.668985214 1.329650575 1.416992158 1.478529957 1.266867593 1.162947854 0.82817688 1.297674055 1 15.20423891 2.358066515 2.043173782 1.02149121 1.459574818 0.63201046 0.13840758 0.187114692 1.599114328 0.059364945 0.043821799 228.0691347 -2.358066515 0.438083608 YIVNGSHEANK ddPTM_BT-474_Pertuzumab_2h_R1 4 YIVNGSHEANK 11 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;; 160.15 2.78E-05 1234640000 1749610 1702170 1585390 1766760 1819130 1687640 2011250 2087380 2328550 2415040 FALSE TRUE 1681233.307 1653625.778 1871905.24 1857942.695 1877643.969 1721765.237 2035864.279 2044274.874 2064222.766 2251467.19 0.746727874 0.734465857 0.831415731 0.8252142 0.833964615 0.764730326 0.904238928 0.907974535 0.916834487 1 21.10243402 2.358164249 0.217363597 1.041605807 0.671688682 0.813803892 0.034963107 1.531129041 0.218988428 0.107172096 0.19590086 228.1204652 -2.358164249 -0.369917124 DRVTNQPIGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRVTNQPIGGR 11 1 Q9H9Y6-4;Q9H9Y6-5;Q9H9Y6-2;Q9H9Y6;Q9H9Y6-3 Q9H9Y6-4 POLR1B DNA-directed RNA polymerase I subunit RPA2 0 116.55 0.00088864 71851000 43326 46532 39386 40803 42653 39358 46015 39841 47228 44659 FALSE TRUE 41632.77202 45204.95292 46503.92634 42908.84772 44024.97248 40153.84573 46578.14533 39018.26943 41866.87544 41634.20615 0.999965554 1.085764738 1.116964406 1.030615249 1.057423128 0.96444365 1.118747051 0.93716857 1.005588416 1 15.3454817 2.358179556 0.777840145 0.985823402 1.065344287 0.184978166 0.053093033 0.968565228 1.149838603 0.040287984 0.027018062 228.1285059 -2.358179556 0.079520885 APS(ph)PPLSQVFQTR ddPTM_BT-474_Pertuzumab_2h_R1 7 APSPPLSQVFQTR 13 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 APS(0.99)PPLS(0.01)QVFQTR;APS(0.999)PPLS(0.001)QVFQTR;APS(1)PPLSQVFQTR;APS(0.997)PPLS(0.003)QVFQTR;APS(0.999)PPLS(0.001)QVFQTR;APS(1)PPLSQVFQTR;APS(0.993)PPLS(0.007)QVFQTR 147.51 4.49E-05 3707120000 840131 871380 636387 780158 771396 771544 774157 776340 853460 836465 TRUE FALSE 807297.7517 846529.0956 751396.2873 820422.0479 796208.6529 787145.1483 783631.3649 760308.3077 756578.7988 779810.4805 1.035248656 1.085557474 0.963562694 1.052078766 1.021028407 1.009405706 1.00489976 0.974991138 0.970208554 1 19.57276402 2.358260765 1.08206007 0.978748023 1.034283763 0.343192008 0.029557744 0.551295582 1.269607224 0.018697908 0.011786484 228.1711676 -2.358260765 0.05553574 DLEALMFDR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLEALMFDR 9 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ;;;;; 180.44 0.00011317 717062000 725289 808716 617259 699816 665450 556326 622508 660200 615289 543992 FALSE TRUE 696943.904 785652.2115 728811.4322 735933.5876 686854.8036 567575.2929 630126.4391 646566.6393 545443.9722 507146.9373 1.374244529 1.549160911 1.437081403 1.451124977 1.354350688 1.119153545 1.242492841 1.274909877 1.075514673 1 18.95204428 2.358622233 0.34923296 0.998477359 1.547545763 0.772079393 0.080980608 0.773805566 0.222819277 0.104316406 0.15229007 228.361156 -2.358622233 0.549068404 QPDISCILGTGGKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPDISCILGTGGKSPR 16 1 P57740;P57740-2;G3V1T4 P57740 NUP107 Nuclear pore complex protein Nup107 1 QPDISCILGT(0.003)GGKS(0.997)PR;QPDISCILGTGGKS(1)PR 190.63 5.00E-10 2117000000 1903850 2031430 1580100 1808290 1893540 1776880 1470430 1668760 1735100 1536260 TRUE FALSE 1829445.437 1973495.605 1865659.219 1901616.064 1954447.434 1812809.731 1488425.562 1634299.523 1538138.722 1432207.742 1.277360388 1.37793949 1.302645674 1.32775156 1.364639624 1.26574496 1.03925256 1.141105075 1.073963418 1 20.44980934 2.359011695 4.312041274 1.081466045 1.329874689 0.889278971 0.044421774 0.066172473 2.174423777 0.015241605 0.01252539 228.5660354 -2.359011695 0.248408644 YGPADVEDTTGSGATDSKDDDDIDLFGS(ph)DDEEESEEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAK 38 1 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAK;YGPADVEDTTGSGATDSKDDDDIDLFGS(0.998)DDEEES(0.002)EEAK 211.91 2.20E-31 153455000 161007 138146 111643 113030 136014 142447 153295 165978 183457 170804 TRUE FALSE 154714.6684 134206.2113 131819.3736 118863.4918 140389.0138 145327.3759 155171.0701 162550.4963 162631.7305 159235.2929 0.971610411 0.842816997 0.82782762 0.746464491 0.881645088 0.912658075 0.97447662 1.020819526 1.021329678 1 17.2808006 2.359057378 1.719723512 1.015423075 0.845381935 0.650368733 0.052407713 0.222802643 1.338220207 0.02623699 0.018434257 228.5900793 -2.359057378 -0.17004114 DVVMLDNLPDLPPALVPS(ph)PPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVVMLDNLPDLPPALVPSPPKR 22 1 H3BPY8;H3BPM3;H3BRE8;Q9BWH6-2;Q9BWH6 H3BPY8 RPAP1 RNA polymerase II-associated protein 1 1 DVVMLDNLPDLPPALVPS(1)PPKR;DVVMLDNLPDLPPALVPS(1)PPKR 121.86 1.63E-05 517690000 301280 265870 244196 225456 260650 283506 296120 321710 355610 331240 TRUE FALSE 289505.6445 258287.6479 288327.6493 237091.8112 269034.044 289238.6856 299744.0051 315066.5761 315242.6436 308804.8198 0.937503646 0.836410676 0.933688955 0.767772379 0.871210638 0.936639155 0.970658442 1.020277392 1.02084755 1 18.23633574 2.359107031 1.848432558 1.012665984 0.865920416 0.654112263 0.046159481 0.201571687 1.404325421 0.020853155 0.014974822 228.6162153 -2.359107031 -0.146745569 SSS(ph)APLIHGLSDLSQVFQPYTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 S(0.116)S(0.116)S(0.768)APLIHGLSDLSQVFQPYTLR;S(0.152)S(0.152)S(0.695)APLIHGLSDLSQVFQPYTLR 270.72 8.65E-52 2271900000 595960 601710 405250 583680 548380 513830 467620 493450 492060 493440 TRUE FALSE 572669.2243 584549.8199 478487.6897 613803.7947 566019.1407 524219.9947 473342.8734 483260.0851 436203.4117 460018.8693 1.244882031 1.270708353 1.040147963 1.334301342 1.230425921 1.139561939 1.028964038 1.05052231 0.94822939 1 18.81133351 2.35924691 2.134381128 1.008509885 1.222561026 0.658416782 0.073797571 0.201788718 1.883899642 0.031644301 0.023653942 228.6898609 -2.35924691 0.214051141 VLHGEQYLELYKPLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLHGEQYLELYKPLPR 16 1 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7EPL9;E7ER27 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ; 232.93 7.33E-20 1623080000 3228500 3943000 2858900 3701900 3059200 3457000 4187700 3787900 4180800 4546900 FALSE TRUE 3102326.651 3830549.501 3375566.826 3892955.503 3157601.946 3526902.909 4238950.325 3709678.541 3706213.111 4238934.413 0.731864744 0.903658591 0.796324382 0.918380688 0.744904648 0.832025827 1.000003754 0.875144123 0.8743266 1 22.01527021 2.359454598 9.445505655 0.92387526 0.824098998 0.401561713 0.068699434 0.318298985 24.89555346 0.022558918 0.018856166 228.799251 -2.359454598 -0.099776262 ASSLSESS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSLSESSPPK 11 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 ASSLS(0.001)ES(0.081)S(0.918)PPK;ASSLS(0.001)ES(0.018)S(0.982)PPK 141.58 3.99E-05 410020000 1046200 885410 978170 904800 940890 1073330 1199630 1265320 1445370 1338130 TRUE FALSE 1005313.347 860158.9737 1154947.078 951496.8364 971154.5813 1095033.468 1214311.431 1239190.7 1281297.657 1247497.263 0.805864171 0.689507704 0.925811312 0.762724588 0.778482334 0.877784265 0.973398072 0.993341418 1.027094564 1 20.25060522 2.360074589 2.042151859 1.004539328 0.791959518 0.7550105 0.055435323 0.155116744 1.324295411 0.02384946 0.017634465 229.1261137 -2.360074589 -0.212579811 S(ph)PPPKATEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPPKATEEK 10 1 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 S(1)PPPKATEEK 62.528 0.051175 193970000 277660 234850 214060 191220 214220 245660 245470 280190 311160 234760 TRUE FALSE 266808.7402 228152.3079 252745.4037 201088.8871 221110.5808 250627.4135 248474.1353 274403.9786 275838.4213 218859.4961 1.21908688 1.042460172 1.154829506 0.918803574 1.010285525 1.145152109 1.135313476 1.253790598 1.26034477 1 17.73964546 2.360226002 2.464703949 1.193290457 1.065531127 0.132255261 0.102918269 0.421135739 5.24202434 0.041180348 0.031831248 229.2060104 -2.360226002 -0.12775933 DELKEALDDVTLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DELKEALDDVTLPR 14 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 151.72 6.26E-06 83334000 163540 127990 123780 93631 122450 133820 152210 153530 177950 160590 FALSE TRUE 157148.676 124339.8505 146149.7995 98463.30713 126388.7155 136525.9321 154072.7915 150359.5518 157749.862 149713.0963 1.049665526 0.830520867 0.976199164 0.657679987 0.844206142 0.911917097 1.029120333 1.004317963 1.053681114 1 17.1918409 2.360432632 3.551864152 1.021017111 0.864133286 0.349942309 0.096553873 0.260175925 6.374899551 0.035610148 0.028907586 229.3150889 -2.360432632 -0.156883825 ANLEAFTVDKDITLTNDKPATAIGVIGNFTDAER ddPTM_BT-474_Pertuzumab_2h_R1 2 ANLEAFTVDKDITLTNDKPATAIGVIGNFTDAER 34 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 305.79 7.22E-91 1133820000 589470 570150 460120 506040 583320 592080 657330 715100 833510 715310 FALSE TRUE 566432.8607 553889.8802 543273.9193 532156.785 602083.0176 604052.2633 665374.6012 700332.9351 738893.4392 666861.4166 0.84940116 0.830592184 0.814672893 0.798002061 0.902860778 0.905813784 0.997770428 1.050192615 1.10801648 1 19.34702745 2.360528273 1.221091406 1.063540763 0.826208548 0.894645794 0.033080454 0.128314625 0.379256147 0.019313602 0.012388338 229.3655942 -2.360528273 -0.237332214 KMPFTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KMPFTEK 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 117.04 0.0085324 3479500000 3568600 3708800 2838200 3074100 3580100 3708600 3742200 4206300 4611100 4426400 FALSE TRUE 3429135.167 3603028.655 3351125.875 3232754.669 3695257.168 3783590.433 3787998.163 4119438.435 4087667.259 4126595.985 0.830983983 0.873123676 0.812079953 0.783395002 0.895473456 0.916879299 0.917947426 0.998265507 0.990566383 1 21.97652077 2.360667192 0.984082061 1.001001417 0.828727023 0.851184579 0.028677513 0.20463928 0.388475992 0.020744588 0.013108891 229.438974 -2.360667192 -0.172274394 ASTSDYQVISDRQT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASTSDYQVISDRQTPK 16 1 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 ASTSDYQVIS(0.001)DRQT(0.999)PK 107.78 0.0017805 271290000 207670 181430 145080 157240 172330 188550 188140 231240 210370 208950 TRUE FALSE 199554.0268 176255.794 171299.1833 165355.1752 177873.151 192362.6102 190442.5136 226464.8132 186489.6795 194797.6304 1.024417116 0.904814877 0.879369954 0.848856195 0.913117632 0.987499744 0.977642866 1.162564518 0.957350863 1 17.5716166 2.360934941 1.989383433 1.055058091 0.909237189 0.356869855 0.067879832 0.29083223 2.354332126 0.030440988 0.022364942 229.5804704 -2.360934941 -0.145820902 EVDEKPASTPWGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVDEKPASTPWGSK 14 1 A0A1W2PNV4;E9PF58;Q92747;Q92747-2 A0A1W2PNV4;Q92747 ARPC1A Actin-related protein 2/3 complex subunit 1A 0 ; 171.46 2.75E-06 1096720000 1064680 1112580 956730 1005700 1166260 1149820 1227950 1365150 1463020 1502920 FALSE TRUE 1023071.129 1080850.308 1129632.393 1057604.298 1203773.812 1173070.148 1242978.019 1336959.175 1296944.103 1401125.89 0.730177878 0.771415556 0.806231904 0.754824606 0.859147505 0.837233939 0.887128008 0.954203463 0.925644236 1 20.41815516 2.361093305 0.466084771 1.001428036 0.737020127 0.909897344 0.025495951 0.272972229 0.126763933 0.024260736 0.025583158 229.6642014 -2.361093305 -0.26440791 DKNSIYSGLEAFGDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKNSIYSGLEAFGDVK 16 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 161.86 7.55E-09 1260000000 1296700 1130400 1052600 1184600 1245400 1290800 1602500 1638600 1818600 1748400 FALSE TRUE 1246023.53 1098162.099 1242828.235 1245737.348 1285459.422 1316900.86 1622111.874 1604762.337 1612160.152 1629979.311 0.764441317 0.673727631 0.762480988 0.764265742 0.788635422 0.807924893 0.995173291 0.984529268 0.989067862 1 20.63642222 2.361720636 2.147385798 0.996349732 0.746050462 0.933262487 0.030551435 0.073805203 0.697507006 0.013538597 0.010157335 229.996187 -2.361720636 -0.25029927 AIMEMPSFYSHGLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AIMEMPSFYSHGLPR 15 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 136.17 2.45E-05 412010000 290900 298110 245850 294350 286590 275020 242420 249290 284090 284310 FALSE TRUE 279531.3064 289608.1947 290280.5639 309541.4388 295808.4276 280581.0928 245386.8085 244142.0744 251841.2942 265053.4305 1.054622481 1.092640809 1.09517754 1.167845435 1.116033198 1.058583141 0.925801292 0.921105129 0.950152932 1 18.01592369 2.362069332 3.704510075 0.939581067 1.106213568 0.824960352 0.03381296 0.087427355 2.295226431 0.012891308 0.010506117 230.1809253 -2.362069332 0.1666325 VSIGNITLS(ph)PAISR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSIGNITLSPAISR 14 0 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 VSIGNITLS(1)PAISR;VSIGNITLS(1)PAISR 297.55 1.14E-43 246210000 292050 316990 328830 352120 318500 321230 310550 315930 329560 353590 TRUE FALSE 280636.3631 307949.7556 388256.8958 370292.9554 328744.8418 327725.4907 314350.6038 309405.9351 292149.7304 329641.0344 0.851339287 0.934197274 1.177817248 1.123321786 0.997281308 0.994189001 0.953614905 0.938614744 0.886266271 1 18.33053632 2.363070205 1.959521304 0.936441477 1.026604852 0.125496828 0.088764451 0.670036011 5.259624714 0.043134932 0.031619433 230.7120113 -2.363070205 0.090163375 AGKPVICATQMLESMIK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGKPVICATQMLESMIK 17 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 222.06 3.18E-15 1689410000 2217510 2083280 1850980 1960510 2049890 2136800 2284770 2419800 2670300 2370230 FALSE TRUE 2130847.258 2023866.894 2185493.261 2061692.156 2115826.574 2180007.56 2312731.699 2369830.284 2367178.739 2209692.211 0.964318581 0.915904434 0.989048724 0.933022321 0.957520945 0.98656616 1.046630697 1.07247076 1.071270798 1 21.075414 2.363235671 2.396811185 1.057518901 0.951147545 0.742940546 0.026365537 0.126351324 1.487900827 0.010177541 0.007840695 230.7999291 -2.363235671 -0.106371356 KRDS(ph)QGTYSSR ddPTM_BT-474_Pertuzumab_2h_R1 7 KRDSQGTYSSR 11 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KRDS(1)QGTYSSR;KRDS(1)QGTYSSR;KRDS(0.999)QGT(0.001)YSSR;KRDS(1)QGTYSSR;KRDS(0.985)QGT(0.003)YS(0.012)SR;KRDS(0.985)QGT(0.015)YSSR;KRDS(0.986)QGT(0.008)YS(0.005)S(0.001)R 156.24 1.63E-05 7000821000 3475222 3596482 3118404 3126299 3330258 3437391 3571145 3878904 3810078 3719884 TRUE FALSE 3339406.482 3493913.855 3681968.971 3287647.666 3437378.773 3506897.401 3614849.741 3798803.277 3377573.919 3467932.943 0.962938597 1.007491757 1.061718618 0.948013621 0.991189515 1.011235643 1.042364371 1.095408515 0.973944414 1 21.72564457 2.363630189 3.785708339 1.042416342 0.996576234 0.087222972 0.041460544 0.374936276 10.19282099 0.015314948 0.012507752 231.0096857 -2.363630189 -0.045840108 LVIGDHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVIGDHK 7 0 E9PM92;O00193;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 ; 158.12 0.0014326 705580000 971740 959260 741700 883380 894780 943200 955280 1048340 1111160 1080660 FALSE TRUE 933763.3265 931902.844 875741.689 928971.3477 923561.4113 962272.1502 966971.0024 1026691.413 985025.7752 1007465.936 0.926843572 0.924996877 0.86925191 0.922087105 0.916717259 0.955141128 0.959805159 1.019083005 0.977726135 1 19.94229963 2.363790496 1.3271925 1.000639426 0.908832284 0.787070956 0.019387122 0.183524494 0.644949892 0.010917242 0.007152932 231.094972 -2.363790496 -0.091807142 TKDQPDGSSLS(ph)PAQSPSQSQPPAASSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKDQPDGSSLSPAQSPSQSQPPAASSLR 28 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 TKDQPDGS(0.004)S(0.025)LS(0.97)PAQSPSQSQPPAASSLR 135.17 6.93E-06 242410000 29419 30934 29595 33615 30709 36914 42511 50360 48257 46429 TRUE FALSE 28269.27296 30051.79261 34943.47484 35349.87418 31696.78287 37660.42637 43031.26233 49320.0484 42779.06767 43284.32248 0.653106514 0.69428816 0.807300954 0.81669002 0.732292457 0.87007083 0.994153538 1.139443696 0.988327071 1 15.40155696 2.363852508 2.116779119 1.060395674 0.745121059 0.834903681 0.060617697 0.119513187 1.097165989 0.027467219 0.020570412 231.1279715 -2.363852508 -0.315274615 ETDPVKS(ph)PPLPEHQK ddPTM_BT-474_Pertuzumab_2h_R1 3 ETDPVKSPPLPEHQK 15 1 Q96JM3;A0A2R8Y4S6;S4R3K0;A0A2R8Y735 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 ET(0.023)DPVKS(0.977)PPLPEHQK;ETDPVKS(1)PPLPEHQK;ET(0.006)DPVKS(0.994)PPLPEHQK 152.04 1.75E-06 1569670000 959530 826770 761420 760170 869480 905390 939770 1022760 1109340 1091960 TRUE FALSE 922030.5068 803191.3291 899025.5317 799402.4648 897447.6138 923697.6061 951271.1864 1001639.649 983412.3739 1018000.577 0.9057269 0.788989071 0.883128706 0.785267202 0.881578689 0.907364522 0.934450538 0.983928371 0.966023396 1 19.95730695 2.364157047 1.192550759 0.984973335 0.840122218 0.720919967 0.036849222 0.226919034 0.639151611 0.020662158 0.013246505 231.2901017 -2.364157047 -0.144851117 DLELPDMHMR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLELPDMHMR 10 0 B3KPJ4;A0A0A0MSI2;Q8IXK0-3;Q8IXK0-2;Q8IXK0-4;Q8IXK0;Q8IXK0-5 B3KPJ4 PHC2 Polyhomeotic-like protein 2 0 143.61 3.37E-05 77242000 215200 242840 170660 206960 212570 200950 191270 189050 209830 213290 FALSE TRUE 206789.7461 235914.441 201502.0583 217641.2304 219407.5071 205013.3467 193610.8195 185146.0514 186010.9781 198843.6783 1.03996138 1.186431688 1.013369195 1.094534321 1.103417061 1.031027732 0.973683554 0.931113591 0.935463373 1 17.60127517 2.364635447 2.277468855 0.948687543 1.089216704 0.627460749 0.046154521 0.174517043 1.856006349 0.018261305 0.013928828 231.5450211 -2.364635447 0.14052916 HQAVHTADRPHCCPDCGQAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 HQAVHTADRPHCCPDCGQAFR 21 1 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 0 99.092 0.00057269 47926000 21735 20891 11012 17245 14110 13938 12599 2436.9 14673 10197 FALSE TRUE 20885.57217 20295.20913 13002.11336 18135.01652 14563.86096 14219.83591 12753.19033 2386.577163 13007.38255 9506.348107 2.197013189 2.134911209 1.367729565 1.907674357 1.532014271 1.495825289 1.341544638 0.251050891 1.368283846 1 13.21467552 2.364868314 1.354916859 0.800315044 1.859767918 0.560513069 0.357598988 0.293055682 1.075142634 0.20214617 0.133274542 231.6692078 -2.364868314 1.059452875 KEEESAGGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEEESAGGTK 10 1 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 120.87 0.00084986 1135410000 2564400 2117930 1696840 1752430 1942580 2061870 2274800 2235800 2384100 2714100 FALSE TRUE 2464180.413 2057528.71 2003496.734 1842873.122 2005064.85 2103562.424 2302639.683 2189629.949 2113466.963 2530271.59 0.973879809 0.813165163 0.791810943 0.728330164 0.792430685 0.831358354 0.910036572 0.865373487 0.835272771 1 21.27086082 2.365527849 5.0817332 0.889005999 0.812831968 0.22703861 0.070848316 0.347565534 14.13578282 0.025278789 0.020939048 232.0212966 -2.365527849 -0.076174031 LKDLFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKDLFGK 7 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;Q9H361;H0YBN4;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 103.56 0.0076133 1438380000 4290700 4583000 3756800 3842400 4099000 4495900 4890200 5169300 5752700 5412800 FALSE TRUE 4123014.7 4452297.327 4435737.33 4040706.724 4230848.058 4586810.178 4950047.73 5062552.149 5099677.613 5046186.235 0.817055596 0.882309356 0.87902767 0.800744669 0.838424874 0.908965695 0.980948285 1.003243224 1.010600358 1 22.26676202 2.366260742 2.193586914 1.003571584 0.845334689 0.905346406 0.023697365 0.0912542 0.900064721 0.010621288 0.008041532 232.4131741 -2.366260742 -0.158236896 SGYSSPGS(ph)PGTPGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 SGYSS(0.005)PGS(0.995)PGTPGSR 183.41 1.39E-11 0 126020 131020 101880 120860 108730 112730 89346 100420 103350 89568 TRUE FALSE 121094.9991 127283.4379 120291.9823 127097.5991 112227.3992 115009.4778 90439.44307 98346.29191 91618.14128 83501.47958 1.450213813 1.524325539 1.440597016 1.522099964 1.344016894 1.37733461 1.083087911 1.177779033 1.097203807 1 16.34951414 2.36768441 0.890584698 1.055533332 1.494097023 0.888184986 0.061928311 0.170366761 0.26489497 0.041942896 0.02706104 233.1763016 -2.36768441 0.438563691 TGDDKGESNDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGDDKGESNDGK 12 1 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 80.522 0.018344 386180000 493110 369030 281800 273600 339920 369010 390480 406880 424640 490380 FALSE TRUE 473838.716 358505.6257 332727.5286 287720.5288 350853.8355 376471.635 395258.811 398477.7858 376436.6474 457166.1258 1.036469435 0.784191141 0.727804423 0.629356622 0.767453702 0.823489786 0.864584642 0.871625791 0.823413254 1 18.80235898 2.367941331 2.432039856 0.880585292 0.777356675 0.165405565 0.104632018 0.56048448 6.792859166 0.043912652 0.034053716 233.3142858 -2.367941331 -0.103228617 YHDMPDVIDFLVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YHDMPDVIDFLVLR 14 0 Q8WWQ0;H7BZR9;Q9NSI6-3;Q9NSI6-2;Q9NSI6;H7C409 Q8WWQ0;Q9NSI6-3 PHIP;BRWD1 PH-interacting protein;Bromodomain and WD repeat-containing protein 1 0 125.61 9.02E-05 66089000 40986 49876 39826 51644 39238 36609 38744 20453 35742 36287 FALSE TRUE 39384.22181 48453.58531 47023.44412 54309.35303 40500.12591 37349.25906 39218.16066 20030.6384 31684.718 33829.24917 1.164206205 1.432298573 1.390023287 1.605396347 1.197192574 1.104052262 1.159297402 0.59211005 0.93660719 1 15.04598354 2.368170324 1.380218706 0.820443128 1.386589553 0.618575247 0.166629022 0.247126643 0.942538314 0.091357002 0.060724086 233.437339 -2.368170324 0.566146425 LSPFVLSAGSGS(ph)PSATSILQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSPFVLSAGSGSPSATSILQK 21 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-4 SYNRG Synergin gamma 1 LSPFVLSAGS(0.32)GS(0.516)PS(0.154)AT(0.009)SILQK;LSPFVLSAGS(0.007)GS(0.988)PS(0.004)ATSILQK 234.62 9.27E-30 503670000 1164670 1080200 936050 1061030 1068790 1214520 1132940 1284360 1414650 1375180 TRUE FALSE 1119153.409 1049393.754 1105215.057 1115789.885 1103168.601 1239078.427 1146805.259 1257837.517 1254064.863 1282037.834 0.872948816 0.818535714 0.862076788 0.87032524 0.860480535 0.966491311 0.894517485 0.981123555 0.978180854 1 20.29000741 2.368589603 0.61194585 0.999917547 0.840008818 0.796494879 0.027550331 0.319523433 0.241056891 0.022392876 0.017836474 233.6628145 -2.368589603 -0.159908729 SDEDDWSKPLPPSER ddPTM_BT-474_Pertuzumab_2h_R1 3 SDEDDWSKPLPPSER 15 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;; 128.9 6.31E-05 1059440000 508642 437877 517262 556965 525546 531226 590490 672550 750570 842990 FALSE TRUE 488763.7083 425389.1767 610742.7498 585710.0304 542450.6644 541967.7537 597716.5933 658661.6075 665368.4402 785893.5364 0.621921018 0.54128092 0.777131662 0.745279104 0.690234286 0.689619813 0.760556698 0.838105388 0.84663941 1 19.58397436 2.368753957 0.065879332 1.518026572 3.51E-11 0.79096108 0.055555084 18.29850758 0.650377785 6.415230571 8.18276375 233.7512582 -2.368753957 -1.518026572 RKEQEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKEQEEK 7 2 P21127-2;P21127;P21127-3;P21127-8;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;A0A087X1I0;A0A087WYI9;A0A590UK33;Q5QPQ9;A0A590UJH0;Q9P2H0;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A;CEP126 Cyclin-dependent kinase 11B;Centrosomal protein of 126 kDa;Cyclin-dependent kinase 11A 0 60.76 0.053751 20976000 65484 74479 48486 55809 63896 62171 72306 69907 64264 80720 FALSE TRUE 62924.81288 72354.93184 57248.49877 58689.30918 65951.27287 63428.14022 73190.90246 68463.39602 56969.02014 75252.7625 0.836179441 0.961492036 0.760749464 0.779895744 0.876396702 0.842867931 0.972600872 0.909779173 0.757035599 1 16.19945692 2.369445494 23.6701989 0.905909873 0.843224127 0.148181358 0.078376875 13.45571599 2907.859889 0.027175225 0.022736392 234.123762 -2.369445494 -0.062685746 DS(ph)SQEYTDSTGIDLHEFLVNTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSSQEYTDSTGIDLHEFLVNTLK 23 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;Q15032-2;Q15032-4;Q15032;Q15032-3;H7C2F9 A0A0U1RRA6;Q15032-2 R3HDM2;R3HDM1 R3H domain-containing protein 2;R3H domain-containing protein 1 1 DS(0.5)S(0.5)QEYTDSTGIDLHEFLVNTLK;DS(0.499)S(0.499)QEYT(0.002)DSTGIDLHEFLVNTLK 236.77 2.53E-37 404890000 222900 199048 128856 167245 265790 178417 245750 297520 314040 270840 TRUE FALSE 214188.8216 193371.3459 152143.1456 175876.5345 274339.3767 182024.714 248757.562 291376.108 278391.4958 252495.7656 0.848286786 0.765839956 0.602557216 0.696552412 1.086510802 0.720902046 0.985194985 1.153984137 1.102559067 1 17.94589967 2.3695992 0.971058627 1.11121975 0.745316727 0.509320419 0.129173258 0.426255925 0.789263736 0.090953498 0.058011183 234.2066378 -2.3695992 -0.365903023 TDGFAEAIHS(ph)PQVAGVPR ddPTM_BT-474_Pertuzumab_2h_R1 6 TDGFAEAIHSPQVAGVPR 18 0 P12270 P12270 TPR Nucleoprotein TPR 1 TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR 244.31 2.50E-24 6622490000 3136970 3713370 3298020 3475280 3425350 2933430 1551244 1800819 1783758 1887598 TRUE FALSE 3014373.744 3607468.323 3894045.578 3654639.617 3535529.494 2992745.964 1570228.588 1763631.458 1581273.27 1759749.306 1.712956348 2.049989911 2.212841093 2.076795601 2.009109753 1.700666086 0.892302433 1.002206083 0.898578715 1 20.74693849 2.369674994 3.066523947 0.944791683 2.023215852 0.940231395 0.126705786 0.056676861 1.073905218 0.050355542 0.040499726 234.247516 -2.369674994 1.078424169 RGEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFS(0.006)EPGT(0.084)T(0.017)S(0.155)T(0.099)QRPS(0.386)S(0.246)PET(0.007)AT(0.001)K;RGEGDAPFS(0.048)EPGT(0.048)T(0.06)S(0.05)T(0.145)QRPS(0.51)S(0.137)PET(0.001)ATK;RGEGDAPFSEPGTTSTQRPS(0.624)S(0.375)PETATK;RGEGDAPFSEPGTTS(0.001)T(0.003)QRPS(0.496)S(0.496)PET(0.004)ATK 226.28 7.70E-35 24325900000 6461350 5478850 5403780 5288250 6278450 6317910 6065380 6489800 7505320 7341980 TRUE FALSE 6208833.299 5322598.562 6380363.252 5561177.216 6480402.046 6445662.469 6139609.935 6355783.362 6653347.538 6844701.155 0.907100713 0.777623221 0.932160968 0.812479185 0.946776477 0.94170108 0.896987289 0.928569885 0.97204354 1 22.70655612 2.369695838 0.269862262 1.010501979 0.818799689 0.442301874 0.048587768 2.147915892 0.41387021 0.081797674 0.145523883 234.2587588 -2.369695838 -0.19170229 EVGVYEALKDDSWLK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVGVYEALKDDSWLK 15 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;; 199.68 6.66E-09 6004529000 5449700 5108160 4095854 4888790 5803150 5840060 6701220 7629470 8373810 8303060 FALSE TRUE 5236719.699 4962480.278 4836065.93 5141101.038 5989813.59 5958150.015 6783231.535 7471918.778 7423250.195 7740686.351 0.676518782 0.641090474 0.624759319 0.664166045 0.773809107 0.769718568 0.876308796 0.965278586 0.958991213 1 22.88403006 2.369959918 0.815567841 1.000777948 0.640145898 0.964933859 0.025773715 0.103968255 0.135807231 0.020092189 0.013337501 234.4012471 -2.369959918 -0.36063205 THLENNR ddPTM_BT-474_Pertuzumab_2h_R1 3 THLENNR 7 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;; 176.41 0.00075288 368370000 617750 625250 557020 606600 560970 457330 581630 148592 607000 537230 FALSE TRUE 593607.647 607418.4822 657685.9048 637906.6987 579014.1095 466577.5259 588748.1619 145523.5233 538095.9048 500842.9336 1.185217175 1.212792358 1.313158 1.273666165 1.156079223 0.931584524 1.175514562 0.290557206 1.074380547 1 18.93399871 2.370038477 1.503146315 0.746274124 1.238288765 0.330842733 0.228996703 0.357571249 1.627752791 0.117191804 0.07993044 234.4436517 -2.370038477 0.492014641 IRDIDLK ddPTM_BT-474_Pertuzumab_2h_R1 6 IRDIDLK 7 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;;;; 122.18 0.0040782 4717350000 7271430 6945280 5597530 6276410 6917530 6876070 7301590 8239280 8182130 8009130 FALSE TRUE 6987254.477 6747207.415 6609128.187 6600336.272 7140038.635 7015108.847 7390949.043 8069135.989 7253328.905 7466664.491 0.935793283 0.903644113 0.885151354 0.883973865 0.956255453 0.93952378 0.989859535 1.08068817 0.971428261 1 22.83203248 2.371030441 1.639145783 1.02787149 0.906927902 0.660246902 0.033217808 0.202400757 1.102032053 0.016637814 0.011657313 234.9797518 -2.371030441 -0.120943588 TVPST(ph)PTLVVPHR ddPTM_BT-474_Pertuzumab_2h_R1 3 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.003)VPS(0.142)T(0.855)PTLVVPHR;T(0.003)VPS(0.196)T(0.802)PTLVVPHR;T(0.007)VPS(0.229)T(0.764)PTLVVPHR 179.56 5.02E-05 2026940000 1462630 1373950 1050930 915090 1235400 978560 297801 608800 336077 340537 TRUE FALSE 1405468.803 1334766.291 1240856.429 962317.9046 1275137.763 998347.1537 301445.5777 596228.0673 297926.9479 317472.1257 4.42706206 4.204357433 3.908552369 3.031188652 4.016534555 3.144676565 0.949518252 1.878048556 0.93843498 1 18.2762704 2.371071238 3.826095624 1.318547931 3.865990678 0.895679933 0.438776257 0.073153683 2.030953997 0.16642831 0.136390767 235.0018264 -2.371071238 2.547442747 up S(ph)RSGEGEVSGLMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.5)RS(0.5)GEGEVSGLMR 66.893 0.08287 185750000 302450 325200 234980 273400 295450 262210 264740 272770 261250 289270 TRUE FALSE 290629.9196 315925.6144 277446.1131 287510.2068 304953.4176 267512.0659 267979.9673 267137.2042 231593.9952 269677.4852 1.077694415 1.171494217 1.028807106 1.066126104 1.130807851 0.991970337 0.993705378 0.9905803 0.858781352 1 18.04087555 2.372284037 1.154777699 0.945794689 1.097121233 0.58819849 0.053029127 0.341844783 0.902475272 0.032070801 0.020626491 235.6590035 -2.372284037 0.151326543 QKDYDFEER ddPTM_BT-474_Pertuzumab_2h_R1 1 QKDYDFEER 9 1 Q96NC0 Q96NC0 ZMAT2 Zinc finger matrin-type protein 2 0 64.878 0.062148 667090000 900430 866900 642290 729260 751950 795690 850040 839740 975960 928740 FALSE TRUE 865240.2001 842176.8608 758366.0907 766897.196 776137.1547 811779.397 860443.0438 822399.0755 865173.1124 865835.6126 0.999312326 0.972675238 0.875877684 0.885730715 0.896402439 0.937567577 0.993771833 0.949832813 0.999234843 1 19.72373362 2.372682589 5.196653957 0.978296842 0.922987554 0.349256103 0.038202432 0.277846869 11.76986926 0.014711747 0.012205379 235.875367 -2.372682589 -0.055309288 KEVEGDDVPESIMLEMK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEVEGDDVPESIMLEMK 17 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 197.45 2.42E-11 445550000 902530 817040 679680 690320 776430 847470 862790 965930 1081580 911720 FALSE TRUE 867258.1298 793738.8192 802513.2954 725947.4979 801404.5761 864606.424 873349.0821 945983.208 958803.5728 849968.3923 1.020341624 0.933845101 0.944168398 0.85408764 0.942863974 1.017221854 1.027507717 1.112962807 1.12804615 1 19.69704967 2.373205661 1.772864258 1.087053676 0.934809768 0.586170402 0.050912354 0.227809921 1.457592776 0.023993864 0.017249403 236.1596309 -2.373205661 -0.152243909 TNIVTASVDAINFHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNIVTASVDAINFHDK 16 0 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8;O00154-2;O00154-3 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ; 187.39 1.35E-09 1182180000 975200 1005150 800320 864600 1073570 998330 1023240 1147240 1305890 1234210 FALSE TRUE 937088.1059 976484.1061 944955.627 909222.1096 1108102.354 1018516.917 1035762.717 1123549.093 1157650.842 1150615.857 0.814423076 0.848662132 0.821260737 0.790204745 0.963051523 0.885192838 0.90018116 0.976476281 1.006114104 1 20.13397483 2.373337613 0.566262165 1.012064221 0.813247354 0.749639815 0.038600552 0.429458779 0.281224836 0.034873988 0.029983623 236.2313941 -2.373337613 -0.198816866 KKEEER ddPTM_BT-474_Pertuzumab_2h_R1 3 KKEEER 6 2 Q13442;F8WFC5;Q8NFW9-5;Q8NFW9-2;Q8NFW9 Q13442;Q8NFW9-5 PDAP1;MYRIP 28 kDa heat- and acid-stable phosphoprotein;Rab effector MyRIP 0 ;; 87.754 0.029292 394592000 499616 493979 391852 323266 429001 438004 509500 510041 518985 475753 FALSE TRUE 480090.4544 479891.2026 462668.3731 339949.797 442800.2068 446860.741 515735.4134 499508.4751 460071.9986 443529.8256 1.082431049 1.081981808 1.043150531 0.766464344 0.998354972 1.007510015 1.162797593 1.126211692 1.037296642 1 18.7586716 2.37378891 7.252825145 1.097958865 0.990738892 0.155916659 0.093884088 0.36397478 22.67861204 0.034677186 0.028932932 236.4770017 -2.37378891 -0.107219973 SSFASSSASDASKPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSFASSSASDASKPSSPR 18 1 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 SSFASSSASDASKPS(0.007)S(0.993)PR;SSFASSSASDASKPS(0.035)S(0.965)PR;SSFASSSASDASKPS(0.01)S(0.99)PR 154.07 1.74E-08 4127880000 2503750 2448570 2172230 2200290 2409920 2759940 2623870 2958890 3526340 3054610 TRUE FALSE 2405900.682 2378739.181 2564800.282 2313847.231 2487437.265 2815747.878 2655981.706 2897787.887 3126044.667 2847718.544 0.844851991 0.835314005 0.900650904 0.812526658 0.873484239 0.988773235 0.932670018 1.017582266 1.097736528 1 21.44137513 2.373853714 0.957763729 1.042549197 0.845719758 0.786492917 0.040870803 0.247174507 0.445529511 0.028161303 0.018055752 236.5122903 -2.373853714 -0.196829439 AHS(ph)SPASLQLGAVSPGTLT(ph)PTGVVSGPAATPTAQHLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 2 AHS(0.776)S(0.224)PASLQLGAVSPGT(0.007)LT(0.952)PT(0.04)GVVSGPAATPTAQHLR;AHS(0.814)S(0.185)PAS(0.001)LQLGAVSPGT(0.015)LT(0.975)PT(0.008)GVVS(0.001)GPAATPTAQHLR;AHS(0.625)S(0.304)PAS(0.07)LQLGAVS(0.001)PGT(0.303)LT(0.589)PT(0.073)GVVS(0.023)GPAAT(0.008)PT(0.002)AQHLR 187.35 5.62E-23 1209010000 172955 235496 140338 236812 154962 168317 138939 101427 138034 138997 TRUE FALSE 166195.7274 228779.8847 165700.1984 249033.8957 159946.4935 171720.4851 140639.377 99332.49701 122364.959 129582.6094 1.282546541 1.765513797 1.278722501 1.92181572 1.234320672 1.325181565 1.085326015 0.766557314 0.944300779 1 16.98351259 2.373866117 1.425123767 0.875772426 1.538086041 0.611729565 0.21044011 0.242054434 0.987229736 0.105182311 0.070930644 236.5190454 -2.373866117 0.662313614 HSFATEGAGAVENFAAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSFATEGAGAVENFAAAR 18 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ; 125.18 3.22E-05 246380000 271500 318620 299240 287840 275860 277460 283250 198105 303990 341830 FALSE TRUE 260889.4798 309533.2696 353319.3246 302695.4569 284733.2874 283070.4313 286716.4982 194014.0625 269482.3296 318677.5496 0.818662878 0.97130554 1.108704786 0.949848702 0.893483986 0.888265997 0.899707239 0.608809948 0.845626967 1 18.28173786 2.374333565 1.672342585 0.780878194 0.960992322 0.127028083 0.116565557 0.465332224 2.641008629 0.057127042 0.040401128 236.7737566 -2.374333565 0.180114128 HS(ph)PTPQQSNR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSPTPQQSNR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HS(0.99)PT(0.008)PQQS(0.002)NR;HS(0.997)PT(0.003)PQQSNR;HS(0.989)PT(0.011)PQQSNR;HS(0.891)PT(0.106)PQQS(0.003)NR 136.99 6.64E-05 643127000 394478 371727 332045 369302 349467 309832 357925 179308.8 388785 373321 TRUE FALSE 379061.3636 361125.7099 392052.9178 388361.7205 360707.9234 316097.0153 362305.3932 175606.0106 344651.7567 348035.6362 1.089145261 1.037611303 1.12647349 1.115867687 1.03641089 0.908231751 1.04100085 0.504563304 0.990277204 1 18.40887551 2.374577118 1.602500209 0.796280593 1.084193995 0.271509303 0.146223142 0.369797607 1.922224686 0.071823204 0.050157304 236.9065773 -2.374577118 0.287913403 FPEFCSSPS(ph)PPVEVK ddPTM_BT-474_Pertuzumab_2h_R1 3 FPEFCSSPSPPVEVK 15 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 FPEFCSS(0.001)PS(0.999)PPVEVK;FPEFCS(0.003)S(0.01)PS(0.986)PPVEVK;FPEFCS(0.018)S(0.091)PS(0.892)PPVEVK 180.64 1.73E-11 66113000 556300 526030 369830 442770 478050 501690 498450 552210 575210 576930 TRUE FALSE 534559.181 511028.1394 436666.5078 465621.4128 493426.9124 511834.5155 504550.1802 540806.6705 509914.5723 537854.0172 0.993874107 0.95012424 0.811868079 0.865702213 0.917399325 0.951623487 0.938080156 1.005489693 0.948053851 1 19.03685513 2.374611779 1.512062445 0.981820374 0.902601616 0.297525268 0.048521284 0.509312994 2.348155231 0.026842638 0.018424551 236.9254854 -2.374611779 -0.079218758 RRYEDDGIS(ph)DDEIEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRYEDDGISDDEIEGK 16 2 I3VM54;Q9Y2K7;Q9Y2K7-3 I3VM54 KDM2A Lysine-specific demethylase 2A 1 RRYEDDGIS(1)DDEIEGK 190.91 6.15E-10 1054200000 295280 291670 242390 252650 264340 293930 312440 356790 361350 309210 TRUE FALSE 283740.1312 283351.8572 286195.2649 265689.2968 272842.7362 299873.466 316263.7342 349422.1618 320331.0629 288266.9313 0.984296499 0.982949574 0.992813375 0.921678028 0.946493359 1.04026315 1.097121105 1.212147922 1.111230697 1 18.13704582 2.375452252 2.565688025 1.134205125 0.966580563 0.579944476 0.05409628 0.164495187 2.215146661 0.021228431 0.016718124 237.3844421 -2.375452252 -0.167624562 YEDFVVDGFNVLYNK ddPTM_BT-474_Pertuzumab_2h_R1 2 YEDFVVDGFNVLYNK 15 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;H3BNL6;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 197.56 6.02E-11 41900000 148054 165276 136492 144074 144863 153066 164671 176265 166787 167664 FALSE TRUE 142267.886 160562.4903 161159.1406 151509.6764 149522.65 156161.0994 166686.293 172625.0662 147854.039 156307.9679 0.9101768 1.027218845 1.031035991 0.969302323 0.95659007 0.99906039 1.066396647 1.1043907 0.94591492 1 17.2540318 2.376855281 5.541472266 1.045658227 0.983381576 0.143195132 0.051388236 0.305702359 14.17947929 0.018270357 0.015186512 238.1525748 -2.376855281 -0.062276651 GWQDVTATSAYKK ddPTM_BT-474_Pertuzumab_2h_R1 2 GWQDVTATSAYKK 13 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ; 191.06 6.23E-06 1465770000 1114430 1254130 844310 948280 1093250 1114310 1137820 1243360 1402450 1216670 FALSE TRUE 1070876.844 1218363.44 996895.5986 997220.8444 1128415.379 1136842.112 1151744.982 1217684.182 1243249.756 1134263.857 0.944116166 1.074144638 0.878892149 0.879178895 0.994843812 1.002273064 1.015411868 1.073545784 1.096085137 1 20.11332485 2.376915383 1.500909362 1.060935467 0.951722456 0.375845068 0.057310802 0.424860806 1.929488134 0.030773586 0.02112606 238.185535 -2.376915383 -0.109213011 FNDFDHR ddPTM_BT-474_Pertuzumab_2h_R1 4 FNDFDHR 7 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;;; 146.58 0.0022091 2416260000 3771100 3955760 3239810 3789490 3688150 3559410 3367460 3393920 3608740 3804020 FALSE TRUE 3623721.243 3842945.598 3825315.736 3985066.033 3806782.694 3631383.709 3408671.983 3323834.366 3199090.964 3546370.337 1.021811288 1.083627831 1.07865659 1.123702731 1.073430672 1.023971939 0.961172032 0.937249652 0.902074702 1 21.75791177 2.378013434 2.093887745 0.940403115 1.079538946 0.771946355 0.032293347 0.136826907 1.228273534 0.01372299 0.010375814 238.7885147 -2.378013434 0.139135832 REEAAVDAQQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 REEAAVDAQQQK 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 252.37 7.49E-21 920980000 1343640 1288970 1056370 1261870 1195980 1273280 1358400 1388570 1537930 1432630 FALSE TRUE 1291129.063 1252209.838 1247279.558 1326995.262 1234449.783 1299026.594 1375024.506 1359895.544 1363350.634 1335596.694 0.966705795 0.937565841 0.933874397 0.993559858 0.924268373 0.972618905 1.029520747 1.018193254 1.02078018 1 20.349053 2.378056442 4.452205144 1.018719369 0.951504403 0.7194052 0.019406939 0.105369885 3.698482447 0.006619061 0.005472582 238.812163 -2.378056442 -0.067214966 LENEGS(ph)DEDIETDVLYSPQMALK ddPTM_BT-474_Pertuzumab_2h_R1 9 LENEGSDEDIETDVLYSPQMALK 23 0 O60502;O60502-3 O60502 MGEA5 Protein O-GlcNAcase 1 LENEGS(0.999)DEDIET(0.001)DVLYSPQMALK;LENEGS(0.997)DEDIET(0.003)DVLYSPQMALK;LENEGS(1)DEDIETDVLYSPQMALK;LENEGS(0.997)DEDIET(0.003)DVLYSPQMALK;LENEGS(0.999)DEDIET(0.001)DVLYSPQMALK;LENEGS(0.999)DEDIET(0.001)DVLYSPQMALK;LENEGS(0.999)DEDIET(0.001)DVLYSPQMALK;LENEGS(0.994)DEDIET(0.006)DVLYSPQMALK;LENEGS(0.994)DEDIET(0.006)DVLYSPQMALK 203.94 1.17E-24 625473000 836611 865374 772491 861589 880980 912887 997083 1076458 1240838 1165161 TRUE FALSE 803915.3172 840694.3808 912097.3077 906055.7115 909317.5218 931346.2006 1009285.6 1054228.766 1099983.272 1086243.608 0.740087501 0.773946447 0.839680253 0.834118337 0.837121172 0.857400857 0.929152165 0.970527015 1.012648788 1 20.05091626 2.378189792 0.571903362 1.023748666 0.769041692 0.926339413 0.024200264 0.22161613 0.14780847 0.023239325 0.019856943 238.8855014 -2.378189792 -0.254706974 MGGEEKPIGAGEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MGGEEKPIGAGEEK 14 1 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6;D6RJ97;D6RHV7;D6RCS6 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 171.91 2.68E-06 367220000 493420 420110 337370 325180 416510 444420 439310 492810 543200 523480 FALSE TRUE 474136.6009 408128.8741 398340.2638 341962.5788 429907.4224 453406.4769 444686.4072 482633.3013 481538.2133 488024.2333 0.97154315 0.836288131 0.8162305 0.700708193 0.880914088 0.929065497 0.911197389 0.988953557 0.986709635 1 18.89659326 2.378242824 1.354476702 0.98597497 0.831615511 0.491324001 0.064832495 0.375867574 1.380719616 0.037492717 0.025053973 238.9146739 -2.378242824 -0.154359459 LCYVALDFEQEMATAASSSSLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 LCYVALDFEQEMATAASSSSLEK 23 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 0 ;; 253.95 1.66E-43 487880000 340655 334806 244300 295561 296677 316272 357991 351307 406825 372191 FALSE TRUE 327341.826 325257.6607 288450.4444 310814.9386 306219.8851 322667.2365 362372.2009 344052.3877 360643.9315 346982.1721 0.943396671 0.937390122 0.831312003 0.895766306 0.882523397 0.929924539 1.044353947 0.991556384 1.039373088 1 18.40450201 2.37865636 4.566654513 1.015786498 0.897167612 0.753975484 0.032639503 0.107182638 3.902544136 0.011955311 0.00989378 239.1422768 -2.37865636 -0.118618886 SHSDNDRPNCS(ph)WNTQYSSAYYTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.267)HS(0.267)DNDRPNCS(0.467)WNTQYSSAYYTSR;S(0.291)HS(0.291)DNDRPNCS(0.417)WNT(0.001)QYSSAYYTSR 264.84 1.72E-44 1922200000 221874 190029 167599 206129 194160 163604 181648 90902 215471 190440 TRUE FALSE 213202.9188 184609.559 197887.8675 216767.3424 200405.3327 166912.185 183871.0626 89024.84193 191011.6354 177541.3292 1.200863595 1.039811743 1.114601701 1.22094018 1.128781302 0.940131437 1.035652169 0.501431652 1.075871383 1 17.43779538 2.378705216 1.872512101 0.815354651 1.136337278 0.305944389 0.160895162 0.321273093 2.298945648 0.072092201 0.052933738 239.1691806 -2.378705216 0.320982626 SESPKEPEQLR ddPTM_BT-474_Pertuzumab_2h_R1 8 SESPKEPEQLR 11 1 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;;;;;;; 194.39 4.85E-07 29207640000 7815350 7905970 5962430 6982080 7519910 8047260 8094610 9148360 10055720 9417210 FALSE TRUE 7509917.482 7680499.476 7039973.735 7342425.986 7761794.735 8209981.111 8193674.259 8959443.169 8914236.823 8779373.979 0.855404668 0.874834526 0.801876506 0.836326827 0.884094328 0.935144252 0.933286847 1.020510482 1.015361328 1 23.06568664 2.379214461 1.057486054 1.016165251 0.841210496 0.896662561 0.023681868 0.153266958 0.338295761 0.016093588 0.010339611 239.4497901 -2.379214461 -0.174954754 QLLGHMEDLEGDAQSVLDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 QLLGHMEDLEGDAQSVLDAR 20 0 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 ;;; 264.67 1.41E-36 559341000 375233 404994 344557 408761 371102 376388 342228 352357 379098 403098 FALSE TRUE 360568.4795 393443.9677 406826.1145 429857.2042 383038.8329 383998.8232 346416.2886 345080.7048 336064.3843 375795.8134 0.959479767 1.046962083 1.082572237 1.143858417 1.019273816 1.021828369 0.921820511 0.918266496 0.894273891 1 18.51958947 2.379534257 2.454513056 0.924036032 1.05677173 0.534692691 0.051124669 0.209163089 2.580436683 0.021009571 0.016465474 239.6261757 -2.379534257 0.132735698 IFWEVFHELPLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IFWEVFHELPLEK 13 0 Q5GLZ8-6;Q5GLZ8-3;Q5GLZ8-2;Q5GLZ8 Q5GLZ8-6 HERC4 Probable E3 ubiquitin-protein ligase HERC4 0 ; 169.62 2.82E-05 124943000 255190 244810 216750 220527 259170 241310 253250 277710 291120 291270 FALSE TRUE 245216.8927 237828.2585 255921.5466 231908.4249 267506.4384 246189.4535 256349.3493 271975.1915 258073.2781 271542.0235 0.903053198 0.875843287 0.942474919 0.854042486 0.985138267 0.90663482 0.944050376 1.001595215 0.950399039 1 18.05081596 2.379641152 0.536783838 0.997375032 0.890331288 0.470943846 0.035192614 0.731716357 0.435149135 0.03033658 0.027676613 239.6851634 -2.379641152 -0.107043744 KPSKYPLCSADAAVS(ph)TTPPGS(ph)PPPPPPLPEPPVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 KPSKYPLCSADAAVS(0.817)T(0.153)T(0.029)PPGS(1)PPPPPPLPEPPVLK 169.98 3.70E-15 1773200000 1556200 1391900 1132000 1232100 1272500 1489700 1432300 1656400 1765200 1658700 TRUE FALSE 1495381.984 1352204.375 1336577.581 1295688.829 1313431.118 1519822.755 1449828.916 1622194.761 1564821.896 1546354.772 0.967036809 0.874446408 0.864340839 0.837898814 0.849372435 0.982842219 0.937578454 1.049044366 1.01194236 1 20.56043992 2.379758951 1.650335507 1.016898427 0.876616375 0.646038484 0.042833376 0.221388904 1.223069936 0.021032993 0.014895093 239.750185 -2.379758951 -0.140282052 IRDDKDWK ddPTM_BT-474_Pertuzumab_2h_R1 2 IRDDKDWK 8 2 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 0 ; 91.087 0.0071631 884340000 1601710 1536700 1235230 1430690 1626750 1590320 1708900 2012900 2126080 1924260 FALSE TRUE 1539113.402 1492874.821 1458463.539 1504528.082 1679075.891 1622477.36 1729814.029 1971332.912 1884736.312 1793928.156 0.857957102 0.832182056 0.812999971 0.838678002 0.935977221 0.904427167 0.964260482 1.098891784 1.050619728 1 20.77469068 2.379844358 1.082935707 1.062071742 0.83751945 0.833797637 0.037943237 0.18435313 0.427241985 0.025044538 0.016120427 239.7973382 -2.379844358 -0.224552292 KPGTPLPPPATSPSS(ph)PRPLS(ph)PVPHVNNVVNAPLSINIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPGTPLPPPATSPSSPRPLSPVPHVNNVVNAPLSINIPR 39 2 Q06190;Q06190-2 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 2 KPGTPLPPPAT(0.012)S(0.013)PS(0.455)S(0.523)PRPLS(0.998)PVPHVNNVVNAPLSINIPR;KPGTPLPPPAT(0.014)S(0.016)PS(0.458)S(0.513)PRPLS(0.999)PVPHVNNVVNAPLSINIPR 167.36 5.95E-18 713350000 247090 253960 222764 273776 239768 250006 229766 245749 283137 269000 TRUE FALSE 237433.4496 246717.3095 263022.4102 287905.6122 247480.3555 255061.2926 232577.945 240674.1973 250996.4748 250780.3904 0.946778372 0.983798251 1.048815698 1.148038775 0.986840937 1.017070323 0.927416792 0.959701023 1.000861648 1 17.93606502 2.379944557 7.318237413 0.966314551 1.026426019 0.167143682 0.053769504 0.376100203 24.65276708 0.019906478 0.016612933 239.8526698 -2.379944557 0.060111468 HSPESPSIAVVESELVAEYITTVSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSPESPSIAVVESELVAEYITTVSHR 26 0 Q7Z589-4;E9PMC9 Q7Z589-4 EMSY;C11orf30 Protein EMSY 0 143.67 1.49E-07 7533200 3219.9 3761.5 2770.9 4572 4112.4 3346.2 2965.4 3066.6 2709.8 3521.9 FALSE TRUE 3094.062748 3654.225703 3271.663268 4807.961468 4244.679081 3413.862457 3001.691452 3003.273638 2402.194864 3283.358576 0.942346892 1.112953586 0.996438005 1.464342489 1.29278572 1.039747069 0.914213718 0.914695599 0.731627329 1 11.6809566 2.380050672 3.167622575 0.885142323 1.166905783 0.417699732 0.150490922 0.254313269 5.129064734 0.059551804 0.048334476 239.9112823 -2.380050672 0.28176346 QS(ph)SFEIPDDVPLPAGWEMAK ddPTM_BT-474_Pertuzumab_2h_R1 7 QSSFEIPDDVPLPAGWEMAK 20 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 QS(0.5)S(0.5)FEIPDDVPLPAGWEMAK;QS(0.5)S(0.5)FEIPDDVPLPAGWEMAK;QS(0.5)S(0.5)FEIPDDVPLPAGWEMAK;QS(0.5)S(0.5)FEIPDDVPLPAGWEMAK;QS(0.5)S(0.5)FEIPDDVPLPAGWEMAK;QS(0.5)S(0.5)FEIPDDVPLPAGWEMAK;QS(0.63)S(0.37)FEIPDDVPLPAGWEMAK 206.01 5.20E-22 1276067000 2898385 2848510 2187673 2575095 2864641 2778247 2886450 3407840 3353040 3299130 TRUE FALSE 2785112.91 2767273.284 2583034.176 2707995.962 2956784.779 2834425.058 2921775.239 3337466.913 2972416.956 3075676.987 0.905528416 0.899728189 0.839826219 0.880455254 0.961344378 0.921561357 0.949961667 1.085116196 0.966426894 1 21.55247257 2.38059551 1.150311418 1.024879244 0.885373007 0.609058411 0.040824997 0.300673541 0.788769768 0.025869273 0.016766284 240.2124483 -2.38059551 -0.139506237 VDLHFIALVHVDGHLYELDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDLHFIALVHVDGHLYELDGR 21 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 57.989 0.026468 5365300 8161.5 8612.7 8519.4 6929.1 7735.8 7011.9 7426.6 3776.3 7845.8 8062.4 FALSE TRUE 7842.539557 8367.074229 10059.04509 7286.711681 7984.629032 7153.685422 7517.488952 3698.318085 6955.177676 7516.326467 1.043400602 1.113186643 1.338292733 0.969451196 1.062304713 0.951752888 1.000154661 0.492037979 0.92534268 1 12.87581202 2.380601349 1.491714137 0.764306233 1.119595575 0.337870526 0.162497497 0.358706146 1.609082165 0.08421802 0.057927479 240.2156779 -2.380601349 0.355289342 IKDCPWYDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IKDCPWYDR 9 1 O95639;C9K0K2;B7Z7B0;H7C016;O95639-3;O95639-2;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 0 79.889 0.023406 843690000 1234000 1158200 975320 1156700 1080500 1115900 995670 1087000 1191900 1225700 FALSE TRUE 1185773.916 1125169.27 1151582.02 1216397.426 1115255.264 1138464.263 1007855.307 1064553.07 1056600.509 1142682.247 1.037710981 0.984673799 1.007788493 1.064510653 0.975997716 0.996308698 0.882008371 0.931626507 0.92466695 1 20.12399285 2.380849295 6.336794797 0.927732975 1.012192521 0.523464776 0.03583657 0.151425068 8.412561298 0.012036329 0.010029245 240.3528605 -2.380849295 0.084459547 RPAS(ph)MGSEGLGGDADPMKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPASMGSEGLGGDADPMKR 19 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 RPAS(0.999)MGS(0.001)EGLGGDADPMKR;RPAS(0.995)MGS(0.005)EGLGGDADPMKR 121.94 1.78E-05 1075580000 743420 679180 744980 776660 799970 833630 919050 1033110 1174250 1228560 TRUE FALSE 714366.3245 659810.4514 879614.458 816743.5157 825701.7616 850486.5698 930297.6088 1011775.917 1040954.063 1145348.537 0.623710863 0.576078312 0.767988459 0.713096048 0.720917463 0.742556997 0.81223975 0.88337819 0.908853532 1 20.12735526 2.380939832 0.293133347 1.03290181 0.549686127 0.888416289 0.041182212 0.659151837 0.14281338 0.065995614 0.113252539 240.4029715 -2.380939832 -0.483215683 DSGPPTKK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSGPPTKK 8 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;; 83.647 0.028882 1670380000 2372940 2161540 1688500 1742020 2000420 2110170 2122780 2309750 2456730 2436550 FALSE TRUE 2280202.881 2099894.996 1993649.51 1831925.861 2064765.326 2152839.083 2148759.217 2262052.855 2177852.31 2271520.298 1.003822367 0.924444742 0.877671889 0.806475673 0.908979474 0.947752518 0.945956423 0.995832112 0.958764186 1 21.11522677 2.380945785 1.811038367 0.980558535 0.899463016 0.335754306 0.047567816 0.419529095 2.804314399 0.023552347 0.017164634 240.4062673 -2.380945785 -0.081095518 VENQENVSNLVIEDTELK ddPTM_BT-474_Pertuzumab_2h_R1 2 VENQENVSNLVIEDTELK 18 0 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ; 249.6 2.46E-24 73926000 101688 97683 91686 93133 101691 105606 116124 132943 125877 128032 FALSE TRUE 97713.92054 94897.17648 108255.6997 97939.60529 104961.9834 107741.4257 117545.1602 130197.6806 111587.9707 119360.2786 0.818646887 0.795048215 0.906965877 0.820537673 0.879371132 0.902657291 0.984792945 1.090795716 0.934883631 1 16.86496328 2.381065041 1.940494366 1.022924529 0.842140874 0.720343636 0.046539875 0.162708545 1.251915536 0.0207271 0.015404255 240.4722911 -2.381065041 -0.180783655 FEREPVIVASDRPVPGPS(ph)PGPPEPVMLPQPTSQPPVPQLPEGEASR ddPTM_BT-474_Pertuzumab_2h_R1 2 FEREPVIVASDRPVPGPSPGPPEPVMLPQPTSQPPVPQLPEGEASR 46 2 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 FEREPVIVAS(0.003)DRPVPGPS(0.997)PGPPEPVMLPQPTSQPPVPQLPEGEASR;FEREPVIVASDRPVPGPS(1)PGPPEPVMLPQPTSQPPVPQLPEGEASR 197.83 1.50E-38 470920000 53993.7 54990.9 38808.8 62273.8 47771.6 52188.6 64714 59031.1 64230 56916 TRUE FALSE 51883.56651 53422.61337 45822.41346 65487.75828 49308.2169 53243.88925 65505.98929 57812.08716 56938.87967 53061.02862 0.977809286 1.006814507 0.863579441 1.234196923 0.929273672 1.003446232 1.234540509 1.089539511 1.073082847 1 15.69536502 2.381587307 24.94215445 1.110665201 1.003561396 0.168356842 0.104130222 23.73549614 6180.425068 0.034720726 0.029049444 240.761648 -2.381587307 -0.107103805 YAQVKPDGTYVKPLSNK ddPTM_BT-474_Pertuzumab_2h_R1 1 YAQVKPDGTYVKPLSNK 17 2 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 113.29 0.00023594 1133100000 284830 327810 321990 328670 315470 387800 428510 469220 554780 471100 FALSE TRUE 273698.5287 318461.1798 380180.7556 345632.6981 325617.3791 395641.5817 433754.2336 459530.443 491803.7002 439191.9774 0.62318654 0.725107006 0.86563684 0.78697407 0.741401018 0.900839729 0.987618754 1.046308828 1.119792085 1 18.74449218 2.382208728 1.38141282 1.064820226 0.748478932 0.823388189 0.063677381 0.175943558 0.673528063 0.036065801 0.024321742 241.106394 -2.382208728 -0.316341294 TPEEIRK ddPTM_BT-474_Pertuzumab_2h_R1 5 TPEEIRK 7 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;;; 107.32 0.012033 3144220000 2903260 2831770 2289690 2514820 2485290 2727260 2810120 3038450 3208370 2912640 FALSE TRUE 2789797.389 2751010.692 2703487.917 2644610.162 2565231.61 2782407.066 2844511.089 2975704.946 2844169.288 2715364.298 1.027411825 1.013127665 0.995626229 0.973943041 0.944709928 1.024690156 1.047561497 1.095876876 1.04743562 1 21.37271434 2.382225083 3.407461539 1.059953851 0.991046833 0.404528219 0.030953431 0.200344168 4.616883445 0.011795541 0.00964152 241.1154739 -2.382225083 -0.068907018 NEDVDPMAASAEYELEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEDVDPMAASAEYELEKR 18 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 143.4 1.70E-07 74981000 62055 64897 51303 44667 49156 60444 61467 72664 68030 66628 FALSE TRUE 59629.82199 63046.2011 60574.59333 46972.26922 50737.14738 61666.21909 62219.25153 71163.46301 60307.51961 62115.22621 0.959987198 1.014987869 0.975197178 0.756211835 0.816823032 0.992771384 1.001674715 1.14566858 0.970897528 1 15.92265934 2.382970243 2.93617451 1.053261519 0.906754324 0.312752592 0.084610844 0.298584073 5.225599782 0.03526757 0.028450668 241.5295335 -2.382970243 -0.146507194 SGS(ph)IVELIAGGGSS(ph)CSPVLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.398)GS(0.602)IVELIAGGGS(0.112)S(0.533)CS(0.352)PVLS(0.003)R 124.35 3.64E-05 49712000 75871 82508 65982 71071 81779 76055 68204 77290 91646 88773 TRUE FALSE 72905.87744 80154.95262 77906.41516 74738.98283 84409.4958 77592.88421 69038.70095 75693.93449 81242.73029 82760.32564 0.880927871 0.968519058 0.94134979 0.903077438 1.019927062 0.937561369 0.834200451 0.914616199 0.981662767 1 16.3366517 2.383159985 0.004245878 1.86846283 8.65E-08 0.072573584 0.052041876 52406.58734 115.9387477 25301.38746 25713.5303 241.6350806 -2.383159985 -1.868462744 KGS(ph)ISSTQDTPVAVEEDCSLASSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGSISSTQDTPVAVEEDCSLASSK 24 1 Q9BZ71;Q9BZ71-3 Q9BZ71 PITPNM3 Membrane-associated phosphatidylinositol transfer protein 3 1 KGS(0.963)IS(0.012)S(0.012)T(0.012)QDTPVAVEEDCSLASSK 236.28 1.28E-37 401750000 242000 246410 212550 201590 257050 273870 303720 333570 407060 337930 TRUE FALSE 232542.3725 239382.6281 250962.5131 211994.0841 265318.2467 279407.839 307437.0162 326681.6629 360852.2553 315041.7001 0.738132039 0.759844262 0.796600936 0.672908012 0.842168661 0.886891605 0.975861342 1.036947372 1.145411084 1 18.26518328 2.383804698 1.170676976 1.071477567 0.74722302 0.881178501 0.049263886 0.144417913 0.393018394 0.028989515 0.018895815 241.9940557 -2.383804698 -0.324254548 ISFPGSSES(ph)PLSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISFPGSSESPLSSK 14 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 ISFPGSSES(1)PLSSK;ISFPGSS(0.004)ES(0.996)PLSSK 371.89 3.78E-97 322510000 587150 532370 504780 495960 534090 569840 639920 684600 660850 705150 TRUE FALSE 564203.5289 517187.3288 596004.9748 521556.555 551269.4899 581362.5552 647751.5324 670462.7708 585833.0785 657389.5624 0.858248383 0.786728841 0.906623726 0.793375169 0.838573536 0.884350146 0.985338937 1.019886547 0.891150563 1 19.32638902 2.384190693 3.138674157 0.981317844 0.836477959 0.677474643 0.044576885 0.135266934 2.685975463 0.016202524 0.013169651 242.2092321 -2.384190693 -0.144839885 GNSS(ph)DHEGCWNEESWTFSQSGTSGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNSSDHEGCWNEESWTFSQSGTSGSK 26 0 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 GNS(0.237)S(0.763)DHEGCWNEESWTFSQSGTSGSK 203.67 2.63E-25 333400000 221580 228790 160220 184460 192120 201350 174840 187180 183920 168060 TRUE FALSE 212920.4086 222265.1332 189175.3181 193980.0027 198299.7143 205421.435 176979.7442 183314.6676 163042.1727 156677.1465 1.358975533 1.418618721 1.207421263 1.238087411 1.265658194 1.311112945 1.129582381 1.170015358 1.040625109 1 17.25743523 2.384596731 0.240827699 0.94585167 1.460092578 0.76627831 0.061252183 1.471270307 0.238104576 0.141741336 0.263207103 242.4357883 -2.384596731 0.514240908 ELQQELQEYEVVTESEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELQQELQEYEVVTESEKR 18 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ;;; 300.24 2.58E-49 1491220000 583831 550543 542570 568975 615806 647540 701900 784510 863000 872890 FALSE TRUE 561014.2391 534842.0527 640624.4684 598339.8679 635613.9593 660633.7025 710490.0622 768309.5943 765035.858 813768.3828 0.689402846 0.657241131 0.787231947 0.735270478 0.781074778 0.811820312 0.873086344 0.944137927 0.940114994 1 19.6342587 2.384874047 0.500288475 1.008343651 0.674401491 0.933041898 0.02815635 0.222377853 0.116610589 0.026723193 0.026420285 242.5906436 -2.384874047 -0.333942159 AQTLPTSVVTITSESS(ph)PGKR ddPTM_BT-474_Pertuzumab_2h_R1 6 AQTLPTSVVTITSESSPGKR 20 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 AQTLPTSVVTITSES(0.056)S(0.944)PGKR;AQTLPTSVVTITSES(0.049)S(0.951)PGKR;AQTLPTSVVTITSES(0.15)S(0.85)PGKR;AQTLPTSVVTITSES(0.027)S(0.973)PGKR;AQTLPTSVVTITSES(0.02)S(0.979)PGKR;AQTLPTSVVTITSES(0.094)S(0.906)PGKR 306.39 9.08E-56 12626200000 3242170 3073300 2963020 2907550 3058440 3409860 3915720 4155700 4259770 4509730 TRUE FALSE 3115462.412 2985652.493 3498503.626 3057609.004 3156817.5 3478809.705 3963641.753 4069883.343 3776218.768 4204281.97 0.741021281 0.710145636 0.832128685 0.727260689 0.750857702 0.827444432 0.942763064 0.968032918 0.898183993 1 22.003428 2.384905099 2.496347959 0.954476123 0.753221319 0.859860508 0.038079655 0.097609053 1.244948776 0.014910444 0.011767911 242.6079895 -2.384905099 -0.201254803 GNILIPGINEAVAAVTEEEHK ddPTM_BT-474_Pertuzumab_2h_R1 3 GNILIPGINEAVAAVTEEEHK 21 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 184.68 3.87E-17 606902000 1872880 1674570 1535270 1689180 1774250 1875510 1937610 1926360 2314850 2255010 FALSE TRUE 1799685.779 1626812.903 1812727.441 1776358.782 1831320.363 1913434.097 1961323.051 1886579.993 2052077.933 2102276.164 0.856065349 0.773834062 0.862268941 0.844969283 0.871113127 0.910172569 0.932952142 0.897398746 0.976121961 1 21.00352077 2.385095269 0.326622542 1.006387978 0.788733511 0.805189162 0.027761376 0.716364939 0.183239027 0.035258903 0.055844523 242.7142466 -2.385095269 -0.217654467 LVGIISS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 6 LVGIISSR 8 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 LVGIIS(0.027)S(0.973)R;LVGIIS(0.016)S(0.984)R;LVGIIS(0.003)S(0.997)R;LVGIIS(0.003)S(0.997)R;LVGIIS(0.006)S(0.994)R;LVGIIS(0.003)S(0.997)R 114.86 0.0027014 473346000 1494640 1496250 1239964 1384970 1389780 1363620 1177115 1362372 1295692 1298209 TRUE FALSE 1436227.816 1453578.415 1464053.078 1456448.468 1434483.536 1391193.331 1191520.885 1334238.542 1148610.476 1210280.148 1.186690386 1.201026405 1.209681147 1.2033978 1.185249166 1.149480418 0.984500066 1.10242124 0.949045126 1 20.2069096 2.385245734 4.072929615 1.025705386 1.196384975 0.839600411 0.038695532 0.088475766 2.760810079 0.013769587 0.01137349 242.7983515 -2.385245734 0.170679589 AS(ph)DKDITVSK ddPTM_BT-474_Pertuzumab_2h_R1 6 ASDKDITVSK 10 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 AS(1)DKDITVSK;AS(1)DKDITVSK;AS(0.998)DKDIT(0.002)VSK;AS(1)DKDITVSK;AS(1)DKDITVSK;AS(1)DKDITVSK 153.24 1.01E-05 9872450000 5617740 5331080 6122380 5470280 6028490 6750930 8672290 8279420 10767580 9393600 TRUE FALSE 5398192.51 5179042.818 7228830.258 5752601.806 6222401.856 6887438.43 8778424.079 8108447.084 9545289.46 8757363.105 0.616417573 0.591392952 0.825457409 0.656887437 0.710533728 0.786474004 1.002404945 0.925900524 1.089973014 1 23.0620651 2.385896208 1.519308604 1.009486794 0.67411775 0.823632112 0.070675746 0.1630518 0.759978377 0.036181183 0.02515328 243.1622809 -2.385896208 -0.335369044 QASVADYEETVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 QASVADYEETVKK 13 1 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GTY9;P49419-4;A0A0J9YWF7;H0YHM6;F8WDY6 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 136.17 0.00012101 238920000 129730 132430 104900 109390 116330 141580 158990 171570 195720 181800 FALSE TRUE 124660.0082 128653.2261 123857.7635 115035.631 120071.8601 144442.8446 160935.7672 168027.0195 173502.6861 169486.5241 0.735515752 0.759076433 0.730782368 0.678730251 0.708444879 0.852237931 0.949549046 0.991388669 1.023696055 1 17.37081104 2.38640393 1.921672874 1.000424448 0.721689617 0.966194326 0.023762902 0.06099327 0.460037491 0.011911175 0.008871883 243.4467215 -2.38640393 -0.278734832 CENTPLIGRES(ph)PPPSYTSSMR ddPTM_BT-474_Pertuzumab_2h_R1 2 CENTPLIGRESPPPSYTSSMR 21 1 Q9C0H2-3;Q9C0H2-2;Q9C0H2 Q9C0H2-3 TTYH3 Protein tweety homolog 3 1 CENTPLIGRES(1)PPPSYTSSMR;CENTPLIGRES(1)PPPSYTSSMR 173.35 2.67E-12 720710000 400470 551940 389460 589650 396930 488280 586510 584680 607730 470000 TRUE FALSE 384819.1897 536199.2116 459844.0855 620081.9072 409697.6139 498153.3561 593687.8848 572606.1537 538743.0382 438166.4814 0.878248807 1.223733979 1.049473442 1.415174217 0.935027282 1.136904299 1.354936788 1.306823269 1.229539595 1 18.7411196 2.386699523 8.357560886 1.257935029 1.113403403 0.092312784 0.165407957 0.487037193 39.93526234 0.05460418 0.045620206 243.6124747 -2.386699523 -0.144531626 RHS(ph)VTDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHSVTDKR 8 2 Q17R89-3;Q17R89 Q17R89-3 ARHGAP44 Rho GTPase-activating protein 44 1 RHS(0.976)VT(0.024)DKR 65.5 0.033451 9614500 27428 28249 24245 25721 26122 24025 21567 16327 29253 23097 TRUE FALSE 26356.08344 27443.36618 28626.61083 27048.46389 26962.23785 24510.80196 21830.9434 15989.84174 25932.32208 21532.61962 1.224007292 1.274501973 1.329453236 1.256162249 1.252157811 1.138310266 1.013854505 0.742586923 1.20432732 1 14.39423623 2.387950151 2.319393939 0.940761798 1.270023734 0.577016801 0.109714281 0.184219297 2.029564942 0.044853077 0.034994253 244.3150108 -2.387950151 0.329261936 GPSPT(ph)PEDVSMKEENLCQAFSDALLCK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSPTPEDVSMKEENLCQAFSDALLCK 27 1 H1UBN3;O95067 H1UBN3 CCNB2V;CCNB2 G2/mitotic-specific cyclin-B2 1 GPS(0.18)PT(0.738)PEDVS(0.082)MKEENLCQAFSDALLCK;GPS(0.213)PT(0.787)PEDVSMKEENLCQAFSDALLCK 153.99 8.28E-08 267070000 192281 180687 128097 140008 161974 163036 167478 177025 185589 186062 TRUE FALSE 184766.4459 175533.9837 151246.9774 147233.8297 167184.0408 166332.6996 169527.6459 173369.3719 164521.7148 173459.855 1.065182753 1.011957399 0.871942257 0.848806369 0.963819789 0.958911787 0.977330725 0.999478363 0.948471419 1 17.40424228 2.388141624 2.393724537 0.983593257 0.946063542 0.046499173 0.059619345 0.946241423 11.1017199 0.02652968 0.020829722 244.422749 -2.388141624 -0.037529715 IVDS(ph)PEKLK ddPTM_BT-474_Pertuzumab_2h_R1 4 IVDSPEKLK 9 1 E9PQC4;Q9BZD4 E9PQC4 NUF2 Kinetochore protein Nuf2 1 IVDS(1)PEKLK;IVDS(1)PEKLK;IVDS(1)PEKLK;IVDS(1)PEKLK 152.47 4.87E-05 2765200000 7853200 6674700 6605000 6109800 7234400 8216300 8115300 9262200 11219800 9135600 TRUE FALSE 7546288.262 6484344.091 7798670.427 6425127.51 7467101.046 8382439.215 8214617.469 9070932.333 9946175.341 8516837.675 0.886043453 0.761355839 0.915676772 0.754402955 0.876745728 0.984219676 0.964514974 1.065058732 1.167824928 1 23.02188642 2.388300585 1.157189518 1.081942852 0.827822285 0.712961789 0.065069068 0.241997761 0.643623952 0.037853874 0.024741998 244.5122292 -2.388300585 -0.254120567 TADKLQEFLQTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TADKLQEFLQTLR 13 1 F8W7R3;Q9NVI1-2;Q9NVI1-1;Q9NVI1;H3BQE2;H3BT54;H3BMG4;Q9NVI1-4;H3BS60 F8W7R3 FANCI Fanconi anemia group I protein 0 ; 132.44 0.00010836 249370000 429490 457510 332610 393240 436230 413330 466880 474880 526410 512940 FALSE TRUE 412705.056 444462.2627 392720.0259 413535.1635 450261.7341 421687.8158 472593.8171 465073.5621 466654.1437 478198.1169 0.863041993 0.929452139 0.821249628 0.8647779 0.941579898 0.881826592 0.988280381 0.972554148 0.975859434 1 18.86724892 2.388530273 1.082316279 0.989987012 0.873950296 0.664820353 0.034178883 0.305090612 0.707528035 0.021329261 0.013844953 244.6415802 -2.388530273 -0.116036716 LNLGTDSDSS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 6 LNLGTDSDSSPQK 13 0 Q16512;Q16512-2;Q16512-3;K7EN76 Q16512 PKN1 Serine/threonine-protein kinase N1 1 LNLGTDSDSS(1)PQK;LNLGTDSDSS(1)PQK;LNLGTDS(0.07)DS(0.006)S(0.924)PQK;LNLGTDS(0.001)DS(0.016)S(0.983)PQK;LNLGTDSDSS(1)PQK;LNLGTDSDS(0.003)S(0.997)PQK 310.9 1.45E-50 5240930000 10246640 9479050 9232150 9551660 9946770 10738900 12321100 13125900 13679100 13930300 TRUE FALSE 9846189.981 9208716.775 10900604.87 10044622.32 10266716.89 10956047.92 12471889.31 12854845.58 12126305.92 12986788.37 0.758169741 0.709083455 0.839361092 0.773449295 0.790550873 0.84363028 0.960352086 0.989840229 0.933741705 1 23.63054136 2.388578938 2.018691966 0.97745855 0.772447719 0.881727664 0.034065917 0.103213951 0.860138654 0.015004846 0.011344806 244.668995 -2.388578938 -0.205010831 S(ph)TSTSSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 STSTSSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK 41 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.171)T(0.171)S(0.171)T(0.171)S(0.171)S(0.147)PVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK 193.7 1.27E-28 319770000 181140 178850 152860 182420 166650 194880 209550 214640 251170 236600 TRUE FALSE 174060.8485 173749.3731 180485.2024 191834.7181 172010.4486 198820.6071 212114.5356 210207.609 222658.2346 220574.8713 0.789123655 0.787711547 0.818249156 0.869703412 0.779827945 0.901374694 0.961644155 0.952998897 1.009445153 1 17.75090892 2.390017659 1.308954857 0.989362005 0.806835708 0.886100155 0.029001753 0.142022656 0.486960259 0.016498701 0.011063596 245.4808732 -2.390017659 -0.182526296 PT(ph)SPEKFSVPHVCAR ddPTM_BT-474_Pertuzumab_2h_R1 2 PTSPEKFSVPHVCAR 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 PT(0.882)S(0.118)PEKFSVPHVCAR;PT(0.5)S(0.5)PEKFSVPHVCAR 116.09 0.0007697 398960000 271500 233770 219830 255440 271050 283630 347960 341980 441160 387980 TRUE FALSE 260889.4798 227103.1085 259558.1711 268623.289 279768.5694 289365.1929 352218.4386 334917.9935 391081.3663 361701.769 0.721283395 0.627873922 0.717602714 0.742665124 0.773478576 0.800010444 0.973781355 0.925950665 1.081226026 1 18.46444113 2.391256053 0.803488515 1.032227096 0.681477006 0.899197613 0.044733415 0.174179311 0.222063323 0.032258405 0.021935808 246.1818622 -2.391256053 -0.350750091 SEISQVFEIALKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEISQVFEIALKR 13 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5;Q5JW28 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 201.76 1.59E-07 168770000 142240 152480 96464 121290 134640 140450 138400 149910 173070 158280 FALSE TRUE 136681.1035 148131.4197 113897.1906 127549.7914 138970.8179 143289.9952 140093.7806 146814.3061 153423.8192 147559.5546 0.926277556 1.003875487 0.771872692 0.86439534 0.941794777 0.971065517 0.949405011 0.994949507 1.03974168 1 17.17093781 2.3913038 1.089020617 1.009580087 0.895307429 0.402511936 0.057571824 0.560046835 1.316055602 0.038589024 0.025127705 246.2089295 -2.3913038 -0.114272658 S(ph)ASDSGCDPASK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASDSGCDPASK 12 0 Q7LBC6;H0Y9V5 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 S(0.961)AS(0.025)DS(0.014)GCDPASK;S(1)ASDSGCDPASK 279.75 5.68E-28 530480000 1438910 1299410 1178780 1348960 1619110 1260510 1027560 1240490 1072850 969630 TRUE FALSE 1382675.806 1262352.099 1391811.768 1418579.987 1671190.144 1285998.376 1040135.587 1214873.448 951064.5658 903956.0964 1.529582921 1.39647501 1.539689564 1.569301864 1.84875145 1.422633667 1.150648345 1.343951828 1.05211367 1 19.78589318 2.392149803 4.393228007 1.185876186 1.570510451 0.687222881 0.138247793 0.141774118 5.068466875 0.051006468 0.042312811 246.6890104 -2.392149803 0.384634265 MSSSEEESKIDLLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 MSSSEEESKIDLLDR 15 1 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 ; 169.92 1.07E-06 679160000 899040 903300 744840 711890 841170 871990 883100 939770 1093670 941490 FALSE TRUE 863904.5229 877538.7684 879449.1569 748630.7282 868226.997 889622.2352 893907.642 920363.4211 969521.1666 877722.0437 0.984257521 0.999791192 1.001967722 0.852924606 0.989182171 1.013558041 1.01844046 1.048581869 1.10458792 1 19.74340462 2.392357713 1.64949094 1.051766657 0.963886105 0.384493894 0.04694484 0.3946475 2.179174773 0.023309013 0.016710093 246.8071366 -2.392357713 -0.087880552 LEDDDFDLIEENLGVK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEDDDFDLIEENLGVK 16 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 191.06 2.48E-12 30333000 72349.9 63896.2 69085.5 79496 75654.7 76892 95242.5 103875.4 114214 117059 FALSE TRUE 69522.38592 62073.94294 81570.78665 83598.79809 78088.20213 78446.80892 96408.10621 101730.3367 101248.9055 109130.4897 0.637057399 0.568804769 0.747461016 0.766044378 0.715548903 0.718834939 0.883420449 0.932189867 0.927778349 1 16.7356947 2.392644339 0.452140963 1.018703308 0.605684004 0.853578289 0.050956836 0.412490476 0.180914088 0.054744671 0.061127011 246.9700783 -2.392644339 -0.413019304 TPSS(ph)PLQSCTPSLSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSSPLQSCTPSLSPR 16 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 TPS(0.003)S(0.995)PLQS(0.001)CTPSLSPR 135.57 3.11E-05 0 105340 130610 84567 117010 120970 106530 98350 96281 109700 123730 TRUE FALSE 101223.1963 126885.1307 99850.13808 123048.9001 124861.1099 108684.1096 99553.63672 94292.7637 97247.3159 115349.6569 0.877533571 1.100004405 0.865630126 1.066746997 1.082457575 0.942214416 0.863059669 0.817451618 0.843065498 1 16.81565419 2.392656497 3.873987969 0.860810461 1.001562925 0.273990223 0.087307937 0.23819185 6.943872555 0.030061882 0.024852855 246.9769918 -2.392656497 0.140752464 AHS(ph)NPMADHTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHSNPMADHTLR 12 0 Q9UBP6;F8VSD9;H0YHX0;Q9UBP6-2 Q9UBP6 METTL1 tRNA (guanine-N(7)-)-methyltransferase 1 AHS(1)NPMADHTLR 86.488 0.0041898 0 108700 117810 86689 102560 111490 86991 99264 52050 108040 120710 TRUE FALSE 104451.8838 114450.1741 102355.6307 107853.1339 115076.1771 88750.01762 100478.8225 50975.14931 95775.75214 112534.2042 0.928178989 1.017025668 0.909551291 0.958403133 1.022588447 0.788649267 0.892873622 0.452974717 0.851081259 1 16.78000404 2.393825602 2.04071097 0.717229136 0.963940009 0.184420779 0.144071454 0.345665091 2.943651426 0.060472759 0.046058358 247.6427406 -2.393825602 0.246710874 RGVMLAVDAVIAELKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGVMLAVDAVIAELKK 16 2 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 146.76 6.15E-07 429470000 431370 550140 349880 544360 376980 474370 622200 595440 619840 442500 FALSE TRUE 414511.5835 534450.5458 413111.099 572454.4848 389105.9041 483962.0864 629814.6697 583143.9559 549478.3618 412529.0809 1.004805728 1.295546352 1.001410854 1.387670619 0.943220544 1.173158715 1.52671581 1.413582661 1.331974853 1 18.6541363 2.394194035 8.73554954 1.364630215 1.135058597 0.185546526 0.179977279 0.352537031 33.42621801 0.058034744 0.048501856 247.8529176 -2.394194035 -0.229571618 DNTRPGANSPEMWSEAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DNTRPGANSPEMWSEAIK 18 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 185.09 5.00E-14 1823920000 571810 515910 446150 495360 511760 540910 591580 641990 624470 647760 FALSE TRUE 549463.033 501196.7519 526779.2296 520925.589 528221.2252 551847.5708 598819.933 628732.6822 553582.7836 603886.6382 0.909877779 0.829951716 0.872314763 0.862621486 0.874702621 0.91382643 0.99160984 1.041143556 0.916699838 1 19.20391823 2.394674298 2.676263494 0.997247617 0.867872632 0.720570575 0.034284668 0.130806242 1.914025232 0.013106594 0.010530085 248.1271559 -2.394674298 -0.129374985 GRKDDDS(ph)DDESQSSHTGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRKDDDSDDESQSSHTGKK 19 3 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.314)DDES(0.314)QS(0.314)S(0.058)HTGKK 59.356 0.05095 27963000 73123 59744 47285 48376 54401 62653 70766 75154 85582 70658 TRUE FALSE 70265.27232 58040.15962 55830.45135 50872.69116 56150.85757 63919.88659 71632.05548 73602.04364 75867.09015 65872.27072 1.066689694 0.881101547 0.847556198 0.772292963 0.852420251 0.970361062 1.087438685 1.117344868 1.1517303 1 16.00738366 2.395308763 2.756655203 1.102874204 0.876536048 0.597948593 0.078779983 0.176494712 2.737496792 0.031275579 0.025237343 248.4899127 -2.395308763 -0.226338157 HVEEFSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HVEEFSPR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;;; 175.44 0.00030783 678530000 823210 924400 714490 855200 814120 730120 853220 583265 845510 926980 FALSE TRUE 791038.0431 898037.0171 843614.2367 899336.9745 840306.9092 744883.5266 863661.9616 571220.3739 749531.2495 864194.8189 0.915346894 1.039160381 0.976185252 1.040664622 0.972358189 0.861939357 0.999383406 0.66098565 0.867317453 1 19.72099706 2.396027594 1.492149716 0.825253226 0.993768652 0.195386338 0.097784648 0.441940152 1.986385516 0.048776298 0.03407771 248.9015461 -2.396027594 0.168515426 RADLNQGIGEPQS(ph)PSRR ddPTM_BT-474_Pertuzumab_2h_R1 3 RADLNQGIGEPQSPSRR 17 2 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(0.981)PS(0.019)RR;RADLNQGIGEPQS(0.596)PS(0.404)RR;RADLNQGIGEPQS(0.941)PS(0.059)RR 154.84 9.66E-08 790760000 415248 397443 310166 302723 361654 376105 376883 429186 413861 426380 TRUE FALSE 399019.6491 386108.3148 366219.8958 318346.5703 373286.9294 383710.1008 381495.4069 420323.1591 366881.2343 397500.9028 1.003820737 0.971339466 0.921305821 0.800870056 0.939084482 0.965306237 0.959734693 1.057414351 0.922969562 1 18.60059861 2.396304431 2.096776459 0.998184269 0.923567054 0.173967171 0.058518894 0.494778367 4.449455727 0.026346358 0.020242061 249.0602564 -2.396304431 -0.074617215 KDWYDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDWYDVK 7 1 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 90.629 0.027255 3839100000 8352100 8300200 7564900 7327500 9286700 9209000 9501300 11474700 11853300 11915700 FALSE TRUE 8025690.698 8063486.423 8932045.71 7705673.153 9585415.139 9395212.29 9617579.752 11237743.44 10507763.08 11108639.03 0.722472904 0.725875276 0.804063008 0.693664916 0.862879343 0.845757277 0.865774802 1.011621983 0.94590913 1 23.40517874 2.396772372 0.735376769 1.004820337 0.730871714 0.835117198 0.043813902 0.245329766 0.263429393 0.033579071 0.023933038 249.328757 -2.396772372 -0.273948623 RCS(ph)DPSLNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RCSDPSLNEK 10 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 RCS(0.97)DPS(0.03)LNEK;RCS(1)DPSLNEK 119.96 0.00038142 1039860000 1161280 1126030 867990 943190 1023290 1073820 1130610 1196460 1301440 1205160 TRUE FALSE 1115895.894 1093916.727 1024855.101 991868.1489 1056205.052 1095533.376 1144446.743 1171752.683 1153705.987 1123533.44 0.993202209 0.973639669 0.912171427 0.882811418 0.940074425 0.975078567 1.018613868 1.042917497 1.026855051 1 20.09961163 2.397405361 2.469986627 1.028638021 0.937853435 0.61760511 0.030170671 0.194675209 2.429933754 0.013280808 0.010559368 249.6924215 -2.397405361 -0.090784586 SMSHQAAIASQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMSHQAAIASQR 12 0 Q4G0F5 Q4G0F5 VPS26B Vacuolar protein sorting-associated protein 26B 0 61.212 0.097182 0 34861 50753 45891 56319 47533 35548 44902 34516 30545 44838 FALSE TRUE 33498.59358 49305.57413 54184.52454 59225.63034 49061.94211 36266.80492 45451.52411 33803.23254 27077.65966 41801.08232 0.80138101 1.179528648 1.296246928 1.416844422 1.173700282 0.867604447 1.087328882 0.808668835 0.647774128 1 15.35125268 2.397732341 1.401778301 0.831702199 1.189508974 0.363895496 0.185578464 0.443749746 1.754027171 0.102352642 0.070392551 249.8804855 -2.397732341 0.357806775 NSRDGDPLPS(ph)SLSCK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSRDGDPLPSSLSCK 15 1 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 NS(0.003)RDGDPLPS(0.497)S(0.497)LS(0.003)CK 181.51 2.07E-11 0 890510 837330 624660 707630 831090 792050 849260 899390 1026600 890400 TRUE FALSE 855707.8847 813450.1682 737549.9575 744150.8691 857822.7646 808065.7937 859653.4979 880817.2822 910064.6719 830092.4149 1.030858576 0.979951333 0.888515476 0.896467497 1.03340634 0.973464857 1.035611798 1.061107494 1.09634139 1 19.66291244 2.398678106 1.337380584 1.059608885 0.954380174 0.391385604 0.049711491 0.422609887 1.516421122 0.028323289 0.01926077 250.4252445 -2.398678106 -0.105228712 KKEPAITSQNSPEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KKEPAITSQNSPEAR 15 2 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 0 146.78 2.15E-06 366900000 611340 566400 469730 463750 534060 570980 627840 646460 708230 731550 FALSE TRUE 587448.1569 550246.8266 554620.6601 487684.1931 551238.5249 582525.6068 635523.6937 633110.3751 627834.6995 682001.4669 0.861359081 0.806811793 0.813225025 0.715077924 0.808265893 0.854141281 0.931850919 0.928312336 0.920576758 1 19.37941532 2.398811641 2.180794311 0.941283322 0.797148778 0.750311911 0.039241759 0.161006357 1.566637292 0.01673209 0.012998594 250.5022557 -2.398811641 -0.144134544 MSS(ph)PLADAK ddPTM_BT-474_Pertuzumab_2h_R1 2 MSSPLADAK 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 MS(0.051)S(0.949)PLADAK;MS(0.001)S(0.999)PLADAK 164.39 6.53E-05 511520000 1538530 1439290 1442180 1324800 1301460 1497640 1578100 1646640 1669750 1898610 TRUE FALSE 1478402.547 1398242.858 1702814.007 1393173.087 1343322.643 1527923.307 1597413.26 1612636.309 1480206.98 1770015.454 0.835248384 0.78996082 0.962033413 0.787096567 0.75893272 0.86322597 0.902485488 0.911086005 0.836267829 1 20.75533053 2.398863764 4.179514581 0.905162369 0.828383918 0.286630727 0.063110178 0.31662047 10.6557047 0.022438494 0.018633971 250.5323222 -2.398863764 -0.07677845 MDYEDDRLR ddPTM_BT-474_Pertuzumab_2h_R1 7 MDYEDDRLR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;;; 195.58 2.83E-05 8164947000 5514453 5920790 4475065 5208988 5399837 4863040 5437311 5342431 5459713 5633585 FALSE TRUE 5298942.08 5751934.866 5283808.793 5477824.495 5573527.661 4961374.001 5503854.439 5232107.933 4839949.269 5252017.27 1.008934626 1.095185825 1.006053202 1.04299438 1.061216553 0.944660641 1.04795056 0.996209202 0.921541004 1 22.32444023 2.398989419 0.74525001 0.97420423 1.045919351 0.285899165 0.042039196 0.889384059 0.98052753 0.03212278 0.022771226 250.6048198 -2.398989419 0.071715121 KAVDDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAVDDFR 7 1 P21283;E7EV59 P21283 ATP6V1C1 V-type proton ATPase subunit C 1 0 72.547 0.082269 552770000 1811300 1870900 1511800 1794800 1728400 1822300 1976600 2057200 2006700 2201000 FALSE TRUE 1740512.394 1817543.764 1785015.89 1887429.843 1783995.556 1859148.155 2000790.222 2014718.101 1778907.829 2051924.31 0.848234209 0.885775248 0.869922873 0.919834048 0.869425615 0.90605104 0.975079935 0.981867651 0.866946125 1 20.96854608 2.399092558 4.415273292 0.95778251 0.881287906 0.48893481 0.037192794 0.179994576 6.645688866 0.012942182 0.010759628 250.6643418 -2.399092558 -0.076494604 GAADVEKVEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GAADVEKVEEK 11 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 169.23 1.56E-05 1465610000 1897330 1747420 1229920 1231120 1775630 1808470 1895860 2204530 2543950 2132340 FALSE TRUE 1823180.246 1697585.293 1452193.903 1294658.251 1832744.752 1845038.502 1919062.102 2159005.685 2255171.461 1987914.713 0.917132025 0.853952779 0.73051117 0.651264485 0.921943351 0.928127596 0.965364404 1.08606555 1.134440752 1 20.92282443 2.399326573 1.290963256 1.077954884 0.796762295 0.657202807 0.081669521 0.274755453 0.916814144 0.048749865 0.032893171 250.7994461 -2.399326573 -0.281192589 ANSWQLVET(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 4 ANSWQLVETPEK 12 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 ANSWQLVET(1)PEK;ANSWQLVET(1)PEK;ANSWQLVET(1)PEK;ANSWQLVET(1)PEK 199.84 1.87E-06 1136160000 2071660 2021470 1855560 1852170 2035380 2222920 2271830 2575030 2656250 2725910 TRUE FALSE 1990697.237 1963819.655 2190900.969 1947760.716 2100849.846 2267868.965 2299633.335 2521854.731 2354723.636 2541281.688 0.783343793 0.772767405 0.862124407 0.766448177 0.82668909 0.892411485 0.904910835 0.992355449 0.926588991 1 21.27712487 2.399443026 1.109517804 0.97669085 0.795202758 0.838482133 0.032734446 0.17930848 0.438460542 0.019666667 0.012930516 250.8667054 -2.399443026 -0.181488092 QVEDDIQQLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QVEDDIQQLLK 11 0 P35998;C9JLS9 P35998 PSMC2 26S protease regulatory subunit 7 0 161.62 6.07E-05 22376000 39454 39799 36420 40004 40704 42803 46472 54888 48282 49567 FALSE TRUE 37912.09406 38663.97149 43001.90416 42068.61123 42013.28113 43668.50599 47040.73824 53754.54362 42801.22977 46209.78294 0.820434368 0.836705326 0.930580094 0.910383225 0.909185857 0.94500565 1.017982238 1.163271935 0.926237412 1 15.49591069 2.400008569 2.10345533 1.055726075 0.882248602 0.519916913 0.064355765 0.2267004 2.051232964 0.028032009 0.021621057 251.1935994 -2.400008569 -0.173477473 DTYGVRPLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DTYGVRPLFK 10 1 P08243-2;P08243;P08243-3;F8WEJ5;C9J057;C9JT45 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ; 116.52 0.00098469 1096900000 1484810 1595750 1356240 1306750 1431660 1491520 1590730 1625270 1729360 1735290 FALSE TRUE 1426781.984 1550240.772 1601342.737 1374191.524 1477710.644 1521679.556 1610197.83 1591707.607 1533050.303 1617757.263 0.881950597 0.958265377 0.98985353 0.849442346 0.913431624 0.940610555 0.995327214 0.983897673 0.947639265 1 20.62556372 2.400482304 4.445757295 0.981020275 0.92132655 0.377193907 0.038156783 0.248558845 9.332476415 0.013987571 0.011634994 251.4677546 -2.400482304 -0.059693725 KS(ph)SPSSPAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSPSSPAVR 10 1 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 KS(0.969)S(0.027)PS(0.003)S(0.001)PAVR 101.71 0.0033316 220990000 170890 177420 137080 167640 174650 187580 209000 212760 235930 247570 TRUE FALSE 164211.4299 172360.1553 161853.4053 176291.9205 180267.7759 191372.9961 211557.8045 208366.4316 209148.2155 230801.8634 0.711482253 0.746788404 0.701265592 0.763823645 0.781049915 0.829165733 0.916620869 0.902793542 0.906180793 1 17.81629535 2.402549057 0.541222089 0.980711216 0.70099343 0.942299666 0.022997189 0.194377092 0.117388593 0.021095195 0.019401537 252.6673102 -2.402549057 -0.279717787 EMEAELEDERK ddPTM_BT-474_Pertuzumab_2h_R1 6 EMEAELEDERK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 197.3 9.23E-08 4777160000 2509060 2283558 1949587 1941159 2253770 2388644 2512801 2883740 2868820 2763860 FALSE TRUE 2411003.161 2218433.162 2301920.739 2041342.449 2326264.559 2436944.018 2543553.41 2824189.761 2543163.581 2576661.3 0.935708221 0.860971972 0.893373428 0.792243221 0.902821243 0.945775845 0.987150857 1.096065579 0.986999564 1 21.29707148 2.402670988 1.86590858 1.037372764 0.871753145 0.688112114 0.044703387 0.174959578 1.242406437 0.019953247 0.014964287 252.7382581 -2.402670988 -0.165619619 GGGT(ph)PDANSLAPPGK ddPTM_BT-474_Pertuzumab_2h_R1 6 GGGTPDANSLAPPGK 15 0 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK 235.35 1.25E-16 6295770000 6761050 6508860 5883010 6101940 6340370 7014550 6863230 7786700 8166010 7992090 TRUE FALSE 6496820.691 6323233.686 6946200.774 6416861.855 6544313.759 7156389.007 6947224.262 7625901.924 7239038.78 7450778.626 0.871965336 0.848667502 0.932278507 0.861233728 0.878339579 0.960488744 0.932415874 1.023504026 0.971581514 1 22.82895977 2.402816008 1.238377202 0.998551372 0.876522686 0.74956375 0.029031801 0.213292695 0.653734052 0.01621429 0.010880492 252.8226666 -2.402816008 -0.122028686 ERPDLEAPAPGS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 6 ERPDLEAPAPGSPFR 15 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR 218.98 1.13E-12 18454990000 2687590 3159730 2834360 2774310 2825860 2953750 2995650 3221570 3298610 3121690 TRUE FALSE 2582556.012 3069617.594 3346591.902 2917492.472 2916756.353 3013476.849 3032311.661 3155043.454 2924165.622 2910255.156 0.887398483 1.054758923 1.149930753 1.002486832 1.002233893 1.035468262 1.041940139 1.084112315 1.00477981 1 21.47271422 2.403268924 4.606882492 1.044320223 1.026909329 0 0.064579737 1.413599775 57.02364584 0.023490545 0.019564882 253.0864672 -2.403268924 -0.017410894 RQPEREEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQPEREEK 8 2 Q96AY2;Q96AY2-2;D6RIT8;F8W714 Q96AY2 EME1 Crossover junction endonuclease EME1 0 76.1 0.020628 5898600 14976 18060 13099 12602 14841 15676 17538 19052 19344 15101 FALSE TRUE 14390.72136 17544.94648 15466.28069 13252.39073 15318.37424 15992.97946 17752.63529 18658.56954 17148.15022 14078.19582 1.022199261 1.246249641 1.098598207 0.941341554 1.088092142 1.136010584 1.261002157 1.325352324 1.218064476 1 13.78117484 2.40368445 3.718497109 1.239292213 1.083728456 0.18700702 0.10795437 0.284945059 7.878875738 0.039138022 0.032462961 253.3287325 -2.40368445 -0.155563756 RPAEDMEEEQAFKR ddPTM_BT-474_Pertuzumab_2h_R1 8 RPAEDMEEEQAFKR 14 2 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 182.1 8.78E-07 9594380000 3580960 3507370 2732568 3215220 3363010 3411780 3361920 3828840 3981560 3741120 FALSE TRUE 3441012.124 3407343.242 3226403.823 3381157.89 3471184.271 3480768.529 3403064.183 3749773.116 3529590.001 3487730.61 0.986604904 0.976951383 0.925072543 0.969443534 0.995255844 0.998003836 0.975724493 1.075132668 1.012001899 1 21.73385718 2.403913997 1.16225231 1.032060944 0.965241755 0.390212378 0.028076111 0.423005405 1.138472397 0.01728768 0.011483863 253.4626648 -2.403913997 -0.066819189 KSSGEIVYCGQVFEKS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSSGEIVYCGQVFEKSPLR 19 2 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 1 KSSGEIVYCGQVFEKS(1)PLR;KSSGEIVYCGQVFEKS(1)PLR 146.25 6.12E-08 1498070000 1365300 1214750 1271430 1041830 1331640 1383080 1470630 1543840 1778300 1686320 TRUE FALSE 1311942.567 1180106.519 1501205.684 1095598.971 1374473.41 1411046.825 1488628.01 1511959.164 1576434.839 1572104.044 0.83451383 0.75065421 0.954902247 0.696899785 0.874289087 0.897553079 0.946901711 0.96174243 1.002754776 1 20.58426527 2.404333801 1.21795068 0.9885729 0.814228601 0.5767628 0.064224296 0.32834571 0.972813817 0.035472707 0.023762454 253.7077891 -2.404333801 -0.174344298 HFLQQATQVNAWDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFLQQATQVNAWDR 14 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ; 223.7 3.42E-12 1976740000 1203340 1154610 998080 1161480 1195970 1084400 1023070 943620 1171490 1311100 FALSE TRUE 1156312.142 1121681.653 1178455.258 1221424.122 1234439.461 1106327.311 1035590.637 924133.9172 1038507.366 1222298.029 0.946014896 0.917682616 0.964130867 0.999285029 1.009933283 0.905120752 0.84724888 0.756062675 0.849635148 1 20.22116467 2.404756811 3.278297755 0.833647954 0.965961068 0.340056328 0.063313835 0.209193528 4.561446328 0.023164031 0.019107487 253.9550255 -2.404756811 0.132313114 LKGTS(ph)PSSSSRPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKGTSPSSSSRPQR 14 2 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 LKGT(0.066)S(0.931)PS(0.003)SSSRPQR 80.585 0.0082882 268500000 230500 191700 159710 165960 164720 190780 221280 217590 216810 244750 TRUE FALSE 221491.8052 186232.9037 188573.1497 174525.2155 170018.3684 194637.7023 223988.0908 213096.6905 192198.6377 228172.8645 0.970719308 0.816192162 0.826448623 0.764881555 0.745129658 0.853027387 0.981659635 0.933926525 0.84233784 1 17.7997677 2.404791494 6.076263857 0.934863811 0.818888947 0.387632556 0.068206177 0.215150993 13.76440449 0.024171504 0.02017305 253.9753073 -2.404791494 -0.115974864 PAQPQEHPFASSR ddPTM_BT-474_Pertuzumab_2h_R1 5 PAQPQEHPFASSR 13 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;;; 164.22 4.11E-06 1175450000 1346910 1284690 1126740 1276070 1331110 1250500 1352480 1439200 1612380 1537680 FALSE TRUE 1294271.268 1248051.899 1330366.982 1341928.126 1373926.362 1275785.967 1369032.055 1409480.017 1429349.382 1433531.564 0.902855089 0.870613477 0.928034663 0.936099462 0.958420726 0.889960151 0.955006565 0.983222171 0.997082602 1 20.45114224 2.404909565 0.375726693 1.011856357 0.883090954 0.674156677 0.024286893 0.868071704 0.27664447 0.028913946 0.040315512 254.0443642 -2.404909565 -0.128765403 IIDDSEITKEDDALWPPPDR ddPTM_BT-474_Pertuzumab_2h_R1 8 IIDDSEITKEDDALWPPPDR 20 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;;;;;;; 193.54 6.37E-18 4459961000 2118866 1883880 1673777 1684270 1910698 1992620 1973056 2270989 2414700 2122857 FALSE TRUE 2036058.374 1830153.587 1976265.737 1771195.377 1972157.336 2032912.142 1997202.85 2224092.284 2140593.379 1979074.005 1.028793451 0.924752477 0.998581019 0.89496167 0.996505099 1.027203701 1.009160266 1.123804506 1.08161361 1 20.91639413 2.405084936 1.512083889 1.075659865 0.962959905 0.415064754 0.048141724 0.316785993 1.464201485 0.02333176 0.016512365 254.1469696 -2.405084936 -0.112699961 VLIRIMVSRSEVDMLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLIRIMVSRSEVDMLK 16 2 P07355-2;P07355;A6NMY6 P07355-2 ANXA2;ANXA2P2 Annexin A2;Putative annexin A2-like protein 0 55.426 0.036954 0 80038 63247 67519 67428 78188 82359 85305 87332 118760 99892 FALSE TRUE 76910.02647 61443.25749 79721.18525 70907.96716 80702.98803 84024.35541 86348.98811 85528.56368 105278.8627 93126.22587 0.825868607 0.659784684 0.85605515 0.761417812 0.86659786 0.90226308 0.927225251 0.91841544 1.130496396 1 16.50689989 2.405746664 0.609079199 1.040370258 0.751619637 0.691064963 0.06747155 0.443819081 0.33344624 0.055422824 0.045600858 254.5345049 -2.405746664 -0.288750621 S(ph)PGASNFSTLPK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPGASNFSTLPK 12 0 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(0.994)PGAS(0.006)NFSTLPK;S(0.92)PGAS(0.08)NFSTLPK;S(0.999)PGAS(0.001)NFSTLPK;S(1)PGASNFSTLPK 172.1 3.85E-05 5884530000 1949220 1973380 1878600 2195440 2138220 2010730 1936670 2052340 2132910 2117330 TRUE FALSE 1873042.327 1917101.135 2218104.809 2308746.922 2206997.788 2051388.338 1960371.547 2009958.462 1890790.999 1973921.353 0.948894101 0.971214548 1.123704754 1.169624574 1.118077873 1.039245224 0.99313559 1.018256608 0.957885681 1 20.91263308 2.406329644 4.192762482 0.996831602 1.070739912 0.222690175 0.064541329 0.379625935 13.15447128 0.026008827 0.021659918 254.8764116 -2.406329644 0.07390831 ACAELHQNVNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ACAELHQNVNVK 12 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 119.45 0.00051641 558680000 446070 441350 335380 392160 379500 424500 485420 475870 523520 523920 FALSE TRUE 428637.0912 428763.1301 395990.6265 412399.4246 391706.9622 433083.6808 491360.7152 466043.1182 464092.2044 488434.4317 0.877573454 0.877831501 0.810734463 0.844329142 0.801964269 0.886677213 1.005991149 0.954156972 0.950162753 1 18.89780538 2.406888716 4.791494716 0.972075882 0.84274977 0.835343442 0.028266517 0.081421999 3.579199026 0.010187355 0.008496529 255.204728 -2.406888716 -0.129326113 RGSPT(ph)TGFIEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.096)PT(0.889)T(0.015)GFIEQK 161.09 0.00012827 3316200000 1521700 1469300 1356800 1256900 1361600 1572800 1732700 1846700 2036400 1883700 TRUE FALSE 1462230.282 1427397.003 1602003.942 1321768.76 1405397.101 1604603.094 1753905.301 1808565 1805236.409 1756115.321 0.832650489 0.812815073 0.912243019 0.752666265 0.800287477 0.913723076 0.998741529 1.029866876 1.027971448 1 20.74395616 2.407104279 2.525562852 1.020418587 0.823279628 0.8472385 0.038387011 0.103492804 1.34972169 0.015377064 0.012357024 255.3314309 -2.407104279 -0.197138958 QKLDILDQER ddPTM_BT-474_Pertuzumab_2h_R1 3 QKLDILDQER 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 176.78 2.19E-06 1727910000 2770570 3035500 2470290 2698120 2728410 2873450 3018310 3183100 3302360 3291180 FALSE TRUE 2662293.061 2948930.512 2916726.354 2837370.297 2816171.786 2931553.128 3055248.981 3117367.873 2927489.937 3068265.447 0.867686681 0.961106711 0.950610827 0.924747335 0.917838379 0.955443125 0.995757712 1.016003317 0.954118862 1 21.54899187 2.407559388 3.219362525 0.995481461 0.928195093 0.565320497 0.027486247 0.179987318 3.795868634 0.010049867 0.008293141 255.5991397 -2.407559388 -0.067286369 AESGDS(ph)LGSEDRDLLYSIDAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AES(0.007)GDS(0.837)LGS(0.156)EDRDLLYSIDAYR 94.003 0.0011113 111670000 23290 28978 21627 24172 25555 23993 19430 24907 20946 22661 TRUE FALSE 22379.80105 28151.57581 25535.47999 25419.51982 26376.99978 24478.1549 19667.79015 24392.66175 18568.29789 21126.15029 1.059341184 1.332546414 1.208714302 1.203225362 1.248547389 1.158666135 0.93096896 1.154619342 0.878924823 1 14.36674228 2.407795552 5.769744084 1.018397331 1.215674541 0.552324816 0.092484046 0.158226014 9.590826779 0.030682843 0.025613455 255.7381691 -2.407795552 0.19727721 RVLVDVER ddPTM_BT-474_Pertuzumab_2h_R1 3 RVLVDVER 8 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 134.26 0.0014178 1219710000 1030410 1125920 924670 1000490 971760 974360 801860 845820 977140 1027760 FALSE TRUE 990140.438 1093809.864 1091778.438 1052125.409 1003017.543 994062.2268 811673.4025 828353.5214 866219.1637 958148.8998 1.0333889 1.141586516 1.139466359 1.09808132 1.046828466 1.03748199 0.847126582 0.864535274 0.904054854 1 19.86989035 2.407969818 3.187795976 0.888064783 1.095579479 0.745191865 0.051351786 0.111257429 2.302113262 0.019076257 0.015734819 255.8408078 -2.407969818 0.207514696 VYVGSIYYELGEDTIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYVGSIYYELGEDTIR 16 0 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5;A0A0J9YVR6;E9PQ56;A0A0J9YWM1;H0YEM1;E9PN18;E9PMU7;E9PL19 A0A0J9YVP6;E9PN18 PUF60 Poly(U)-binding-splicing factor PUF60 0 ; 113.24 0.001574 67430000 21474 18541 15174.5 16540.2 18131.8 17470.2 16014.9 15965.7 20038.4 19989.9 FALSE TRUE 20634.77234 18012.22883 17916.8697 17393.8417 18715.02581 17823.45941 16210.89514 15636.00272 17763.72484 18635.96627 1.107255296 0.966530448 0.961413508 0.933347992 1.00424231 0.956401142 0.869871457 0.839022914 0.953195803 1 14.185802 2.408170603 4.689810712 0.894709295 0.987266284 0.24233604 0.060810446 0.2405189 10.25684365 0.021445188 0.017890577 255.9591166 -2.408170603 0.092556989 AS(ph)LGSLEGEAEAEASSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 AS(0.601)LGS(0.399)LEGEAEAEASSPK 137.52 2.57E-06 123040000 82645 87250 81164 105460 81424 122380 135530 116620 184500 164630 TRUE FALSE 79415.14203 84761.71543 95832.14028 110902.8032 84043.07691 124854.6074 137188.6567 114211.7562 163556.3335 153479.4635 0.517431715 0.552267473 0.624397155 0.722590506 0.547585162 0.813493901 0.893856765 0.744150088 1.065656146 1 17.2276861 2.408382178 0.417307899 1.028317669 0.501496787 0.770655078 0.087986017 0.593468452 0.225820687 0.091075208 0.112926289 256.0838427 -2.408382178 -0.526820882 S(ph)PPYTAFLGNLPYDVTEESIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.489)PPY(0.401)T(0.11)AFLGNLPYDVTEESIK;S(0.521)PPY(0.4)T(0.079)AFLGNLPYDVTEESIK 149.53 5.15E-08 51383000 70288 68090 66845 80436 72029 68584 82737 93103 100202 107321 TRUE FALSE 67541.06725 66148.13987 78925.37846 84587.3116 74345.8782 69970.81547 83749.56016 91180.39051 88827.48904 100052.0531 0.675059283 0.661137256 0.788843167 0.845433042 0.74307199 0.699344125 0.837059886 0.91132953 0.887812757 1 16.61039125 2.40853918 0.17167579 1.089530369 0.539775115 0.734473335 0.054458397 3.389906181 0.342532303 0.3400303 0.610493592 256.1764365 -2.40853918 -0.549755254 TRPLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TRPLVK 6 1 Q9BQ61;K7EN60 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 67.035 0.091051 283960000 285590 291340 237380 298900 368010 347620 391350 505170 492110 556860 FALSE TRUE 274428.8271 283031.2685 280279.8465 314326.2648 379847.3759 354649.1146 396139.4584 494738.063 436247.7359 519143.3762 0.528618566 0.54518902 0.539889093 0.605471011 0.73168106 0.683142906 0.763063686 0.952989262 0.840322261 1 18.98577351 2.409014639 0.500014772 0.997717853 0.498199164 0.914683814 0.047390909 0.254443045 0.133133821 0.045364775 0.045658098 256.4570482 -2.409014639 -0.499518689 IDVPQDLEDDLTATPLSHATVPQS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 3 IDVPQDLEDDLTATPLSHATVPQSPAR 27 0 E7EUC4;Q9NRH2 E7EUC4 SNRK SNF-related serine/threonine-protein kinase 1 IDVPQDLEDDLTATPLSHATVPQS(1)PAR;IDVPQDLEDDLTATPLSHATVPQS(1)PAR;IDVPQDLEDDLTATPLS(0.018)HAT(0.074)VPQS(0.909)PAR 261.71 2.74E-53 363320000 187108 205990 173646 195815 177182 185314 168341 168493 173707 200062 TRUE FALSE 179795.6125 200115.3669 205027.6949 205921.0356 182881.2199 189061.176 170401.2075 165013.5607 153988.5096 186511.6225 0.963991466 1.072937783 1.099275703 1.104065435 0.980535247 1.013669676 0.913622461 0.884736074 0.825624202 1 17.50890601 2.409108642 1.510607732 0.888567027 1.057050659 0.554577003 0.058570938 0.263066551 1.213781038 0.028890683 0.020523114 256.5125641 -2.409108642 0.168483632 HQDVPSQDDSKPTQR ddPTM_BT-474_Pertuzumab_2h_R1 4 HQDVPSQDDSKPTQR 15 1 Q9NRN7 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 ;;; 157.03 1.21E-06 1311060000 2170060 2127830 1774690 1970650 2057820 2200870 2118880 1741530 2727690 2498810 FALSE TRUE 2085251.656 2067146.372 2095415.961 2072355.483 2124011.649 2245373.099 2144811.487 1705566.797 2418054.067 2329563.373 0.895125533 0.887353568 0.899488713 0.889589657 0.911763841 0.963860063 0.920692483 0.732140115 1.037985957 1 21.15162815 2.40967341 0.007570158 1.802650031 1.34E-06 0.073422825 0.074716778 14219.37968 54.7490647 6419.404166 6613.234618 256.8463567 -2.40967341 -1.802648688 LFDDEAS(ph)VDEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFDDEASVDEPR 12 0 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;Q8NI35-5;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 LFDDEAS(1)VDEPR;LFDDEAS(1)VDEPR 166.48 5.43E-05 354900000 508570 549300 434840 434980 479640 455340 386510 406890 455040 448200 TRUE FALSE 488694.5221 533634.5018 513425.261 457429.3699 495068.0562 464547.2868 391240.225 398487.5793 403385.7669 417843.0148 1.169564896 1.277117202 1.228751571 1.09473978 1.184818314 1.111774687 0.936333051 0.953677734 0.965400288 1 18.67260149 2.409844793 2.876738917 0.957427625 1.191995443 0.839379619 0.046713166 0.101780663 1.720398707 0.018888602 0.015461598 256.9477343 -2.409844793 0.234567818 EEGVIDSSDKEIVAEAER ddPTM_BT-474_Pertuzumab_2h_R1 2 EEGVIDSSDKEIVAEAER 18 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 186.56 4.32E-14 384870000 394960 383810 401900 407820 435880 433950 484920 584270 582220 620890 FALSE TRUE 379524.5265 372864.1146 474532.2702 428867.6391 449900.4761 442724.7663 490854.596 572204.6203 516128.8265 578836.5673 0.655667848 0.644161298 0.819803546 0.740913175 0.777249575 0.764852795 0.848002051 0.988542626 0.891665896 1 19.14279654 2.410923904 0.430689951 1.014908347 0.653013354 0.799183841 0.052124597 0.516606658 0.207505441 0.056425396 0.067545536 257.5869783 -2.410923904 -0.361894993 NLS(ph)STTDDEAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.314)S(0.314)T(0.186)T(0.186)DDEAPR;NLS(0.984)S(0.015)TTDDEAPR 146.96 6.84E-05 1001130000 839820 821500 721580 810880 855890 781830 662980 730470 824450 810200 TRUE FALSE 806998.9059 798071.6243 851985.5575 852729.614 883420.4791 797639.1383 671093.7476 715385.5392 730861.8924 755324.4323 1.068413613 1.056594478 1.127972989 1.128958071 1.169590763 1.056021895 0.888484099 0.947123525 0.967613202 1 19.52673693 2.411752627 5.397584555 0.945431497 1.10980256 0.78298778 0.039582445 0.088788936 4.977535151 0.014477161 0.012093522 258.078976 -2.411752627 0.164371064 NAEEES(ph)ESEAEEGD ddPTM_BT-474_Pertuzumab_2h_R1 2 NAEEESESEAEEGD 14 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 1 NAEEES(0.952)ES(0.048)EAEEGD;NAEEES(0.996)ES(0.004)EAEEGD 245.4 1.24E-17 259610000 499890 530850 454040 545820 518220 572080 671500 695440 739880 747010 TRUE FALSE 480353.7461 515710.6778 536095.1281 573989.8356 534889.0169 583647.8496 679718.0179 681078.921 655891.9242 696414.3473 0.6897528 0.740522765 0.769793342 0.824207367 0.768061455 0.838075568 0.976025294 0.977979451 0.941812768 1 19.4095864 2.411922651 2.207289996 0.976657515 0.760102509 0.896567681 0.03444983 0.097321455 0.969079388 0.015141659 0.011919752 258.1800324 -2.411922651 -0.216555005 RLSES(ph)LHVVDENKNESK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSESLHVVDENKNESK 17 2 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 RLS(0.054)ES(0.946)LHVVDENKNESK 228.6 7.19E-16 775540000 781480 720500 680850 634470 752770 695450 594250 667930 759720 685280 TRUE FALSE 750938.8976 699952.0454 803894.7404 667215.0727 776983.5307 709512.4755 601522.6093 654137.0121 673479.7706 638865.3752 1.175425883 1.095617438 1.25831634 1.044375073 1.216192896 1.11058214 0.941548302 1.023904311 1.054181048 1 19.28515243 2.412145488 6.156826047 1.007232316 1.154760801 0.582341462 0.06125502 0.138098936 9.784478708 0.019903412 0.016628678 258.3125388 -2.412145488 0.147528485 KKDELER ddPTM_BT-474_Pertuzumab_2h_R1 7 KKDELER 7 2 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;;; 120.15 0.0025989 14195490000 9647360 10097710 7572300 8514100 9590580 10058220 11113520 12229480 13097250 12364460 FALSE TRUE 9270330.505 9809733.197 8940783.055 8953513.721 9899069.716 10261604.1 11249530.58 11976936.96 11610505.09 11527004.11 0.804227223 0.851021922 0.775638056 0.776742477 0.858772116 0.890222993 0.975928392 1.039032939 1.007243944 1 23.45851427 2.412907639 1.492827715 1.022133385 0.80606943 0.929235742 0.025317166 0.094987114 0.427857497 0.013311256 0.009459867 258.7662541 -2.412907639 -0.216063955 AQIEDTLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQIEDTLRR 9 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 89.171 0.019702 314390000 327160 344520 262330 315000 313550 317300 385140 323000 380870 370160 FALSE TRUE 314374.2255 334694.6269 309738.8665 331257.1877 323635.6205 323716.0234 389853.4585 316329.9371 337635.2343 345088.7335 0.910995332 0.969879902 0.897562964 0.959918872 0.937833053 0.938066045 1.129719463 0.916662604 0.97840121 1 18.39660785 2.41301544 24.99999876 0.999915694 0.93658564 0.295284817 0.052985957 85.78572621 33453.71158 0.01790248 0.01497829 258.8304931 -2.41301544 -0.063330054 EEATYGVWAERDS(ph)DDERPSFGGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EEATYGVWAERDSDDERPSFGGK 23 2 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(0.997)DDERPS(0.003)FGGK;EEATYGVWAERDS(0.907)DDERPS(0.093)FGGK;EEATYGVWAERDS(1)DDERPSFGGK 242.75 1.23E-37 4687610000 3223810 3361580 2654130 2795020 3024670 3435470 3437580 3965550 4225400 3868030 TRUE FALSE 3097819.941 3265711.03 3133790.332 2939271.317 3121961.257 3504937.557 3479650.132 3883660.007 3745750.306 3606044.883 0.859063057 0.905621293 0.869038083 0.8150956 0.865757737 0.971961712 0.964949202 1.076986042 1.038742009 1 21.78198592 2.413022699 1.629471896 1.040256892 0.862233904 0.837540603 0.033123056 0.138739087 0.747599246 0.016349081 0.011916941 258.8348193 -2.413022699 -0.178022988 LDSPPPS(ph)PITEASEAAEAAEAGNLAVSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 LDS(0.291)PPPS(0.325)PIT(0.325)EAS(0.059)EAAEAAEAGNLAVSSR;LDS(0.082)PPPS(0.448)PIT(0.448)EAS(0.021)EAAEAAEAGNLAVSSR 97.771 0.00062367 59782000 21121.5 22857.1 16728.4 23346.4 17834.1 24150.6 31714 28782 33688 36582 TRUE FALSE 20296.04843 22205.23789 19751.594 24551.3105 18407.75002 24638.94168 32102.12542 28187.64164 29863.87947 34104.26856 0.595117541 0.651098494 0.579153134 0.719889666 0.539749152 0.722459174 0.941293474 0.826513596 0.875663978 1 15.0576647 2.413602157 4.333140238 0.889230547 0.622619015 0.827667723 0.062865361 0.083375508 3.1555564 0.020951077 0.01750435 259.1804004 -2.413602157 -0.266611532 RHPQHLHQQHHGDAAQHTR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHPQHLHQQHHGDAAQHTR 19 1 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 24.594 0.094287 4015900 3779.1 2512.7 3375.7 4055.1 2718.7 2371.4 1771.9 0 2581.5 1016.7 FALSE TRUE 3631.408594 2441.040256 3985.764082 4264.384197 2806.149455 2419.351333 1793.585042 0 2288.458943 947.8380034 3.831254477 2.575377066 4.205111071 4.499064378 2.960579175 2.552494544 1.892290703 0 2.414398805 1 9.888496697 2.415345553 1.665488034 1.02931599 3.674884545 0.674499752 0.758746627 0.206352964 1.162685183 0.362742429 0.266673475 260.2229241 -2.415345553 2.645568555 EDINAIEMEEDKR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDINAIEMEEDKR 13 1 P49756;P49756-2;P49756-3;H0YE46 P49756 RBM25 RNA-binding protein 25 0 ;; 216.54 4.38E-11 2878540000 1492930 1296980 1171750 1155870 1265400 1369950 1410730 1487970 1689700 1554970 FALSE TRUE 1434584.645 1259991.4 1383511.29 1215524.589 1306102.74 1397651.328 1427994.936 1457242.9 1497892.34 1449650.497 0.989607252 0.869169088 0.954375757 0.838494928 0.900977679 0.964129858 0.98506153 1.005237402 1.033278258 1 20.46727369 2.41586997 2.054818162 1.008996638 0.907063847 0.552768027 0.040519445 0.231355726 1.994495555 0.016545084 0.012863492 260.5373373 -2.41586997 -0.101932791 T(ph)SPTPPESATTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.636)S(0.361)PT(0.003)PPESATTVK 133.71 0.0011628 195870000 322450 315550 238130 274380 296390 314470 343150 373870 382870 386720 TRUE FALSE 309848.2975 306550.823 281165.3882 288540.7847 305923.6535 320828.7989 347349.5723 366149.4538 339408.2027 360527.1099 0.859431341 0.850285081 0.779873081 0.800330341 0.848545491 0.889888139 0.963449246 1.015594788 0.941422138 1 18.45974822 2.416345903 1.851062368 0.989489566 0.823002795 0.867281392 0.028236281 0.116600522 0.814212929 0.013232459 0.010027159 260.8230102 -2.416345903 -0.166486771 LDDPGEICTFQDIPSTHVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDDPGEICTFQDIPSTHVR 19 0 A0A0G2JN42;A0A0G2JNJ8;Q6W4X9 A0A0G2JN42 MUC6 Mucin-6 0 133.94 1.07E-05 66962000 149090 231620 180150 213850 166680 194240 152810 163770 164220 202240 FALSE TRUE 143263.398 225014.4244 212707.1124 224886.8241 172041.4136 198167.6659 154680.1345 160388.0923 145578.4341 188542.1047 0.759848301 1.193443898 1.128167699 1.192767125 0.912482726 1.051052582 0.820401017 0.850675198 0.772126917 1 17.52452721 2.417146529 1.753049302 0.844692058 1.065619319 0.261610998 0.137284863 0.409597724 2.56139969 0.060813281 0.045437888 261.3042832 -2.417146529 0.220927261 GQPVAPYNTTQFLMDDHDQEEPDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GQPVAPYNTTQFLMDDHDQEEPDLK 25 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 266.46 1.88E-45 172310000 134240 153930 122170 130030 137600 143750 159860 155360 183520 172010 FALSE TRUE 128993.7524 149540.0671 144248.8367 136740.8639 142026.029 146656.7235 161816.4145 152151.7617 162687.579 160359.6095 0.804403009 0.932529504 0.899533474 0.852713874 0.885672081 0.914549019 1.009084613 0.94881599 1.014517181 1 17.29095128 2.417431661 3.50840192 0.985238149 0.879236634 0.705935369 0.035721152 0.138724213 3.500354505 0.012650353 0.010544008 261.4758966 -2.417431661 -0.106001516 ASLPQAATFGELSGPLKPGS(ph)PYRPPVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASLPQAATFGELSGPLKPGSPYRPPVPR 28 2 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 ASLPQAATFGELSGPLKPGS(1)PYRPPVPR;ASLPQAATFGELSGPLKPGS(1)PYRPPVPR 180.07 7.95E-18 4018100000 956770 919350 821210 856340 908900 1001120 1090480 1256990 1204630 1164510 TRUE FALSE 919378.3706 893131.0381 969620.9147 900535.81 938135.5939 1021363.332 1103825.62 1231032.717 1067885.453 1085636.7 0.846856384 0.822679482 0.893135719 0.829500154 0.864134009 0.940796614 1.01675415 1.133926954 0.983648998 1 20.05010997 2.417442733 2.106292428 1.057491523 0.850030362 0.799574248 0.04273887 0.121859277 1.103940438 0.017849975 0.013974545 261.4825631 -2.417442733 -0.207461161 SSS(ph)SPELQTLQDILGDPGDKADVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSSPELQTLQDILGDPGDKADVGR 25 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 1 S(0.068)S(0.068)S(0.431)S(0.431)PELQT(0.003)LQDILGDPGDKADVGR;S(0.172)S(0.172)S(0.654)S(0.002)PELQTLQDILGDPGDKADVGR;S(0.142)S(0.142)S(0.711)S(0.004)PELQTLQDILGDPGDKADVGR 131.81 4.66E-05 861821000 161582 154701 115087 135960 140589 166013 146391 175349 187073 181900 TRUE FALSE 155267.1968 150289.0789 135885.781 142976.9119 145111.1729 169369.8966 148182.5768 171727.9819 165837.2573 169579.751 0.915599863 0.886244248 0.801309002 0.843124908 0.855710496 0.998762503 0.873822352 1.012667968 0.977930775 1 17.37160439 2.417533569 1.071354208 0.990131008 0.856666472 0.551649545 0.048213821 0.386213604 0.882587688 0.030545884 0.020384745 261.5372598 -2.417533569 -0.133464536 REPAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 REPAVK 6 1 Q9UKN8;F2Z356 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 0 91.041 0.077516 59133000 169230 146960 120660 142160 141200 157430 164960 173420 200950 179490 FALSE TRUE 162616.3045 142768.8447 142465.9461 149496.8946 145741.8262 160613.3425 166978.8298 169838.8164 178138.9985 167332.9824 0.971812623 0.853202056 0.851391901 0.89340961 0.870968916 0.959842705 0.997883546 1.014975135 1.06457792 1 17.35236231 2.41932689 1.822220512 1.025289271 0.883505951 0.747860565 0.035933018 0.16425609 1.110936307 0.015783062 0.01194233 262.6194516 -2.41932689 -0.14178332 TNHRLS(ph)LPMPASGTSLSAAIHR ddPTM_BT-474_Pertuzumab_2h_R1 4 TNHRLSLPMPASGTSLSAAIHR 22 1 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 T(0.289)NHRLS(0.711)LPMPASGTSLSAAIHR;T(0.128)NHRLS(0.872)LPMPASGTSLSAAIHR;T(0.146)NHRLS(0.854)LPMPASGTSLSAAIHR;T(0.12)NHRLS(0.88)LPMPASGTSLSAAIHR 326.68 7.38E-81 7381050000 1192840 1167510 898700 1097320 998330 850554 861140 449258 875890 819063 TRUE FALSE 1146222.494 1134213.758 1061115.081 1153952.817 1030442.191 867752.7846 871678.8889 439980.6653 776462.6392 763587.1335 1.50110242 1.48537568 1.389645052 1.511226114 1.349475582 1.136416195 1.141557853 0.576202304 1.016861868 1 19.54243327 2.419540526 1.417245783 0.833411881 1.464720468 0.765118238 0.136755214 0.174945602 0.708768592 0.070499716 0.049712878 262.7486699 -2.419540526 0.631308586 RNPPGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 RNPPGGK 7 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 ;; 110.63 0.010839 143395000 241544 245615 190222 238396 225785 237698 273170 255258 285813 292769 FALSE TRUE 232104.1934 238610.3007 224599.3469 250699.6461 233047.5796 242504.4164 276513.1362 249986.8331 253368.7065 272939.4949 0.850386983 0.87422416 0.822890608 0.918517294 0.853843375 0.888491483 1.013093163 0.915905678 0.928296239 1 18.05822164 2.419650497 8.103962573 0.954734132 0.865850676 0.636984185 0.035690765 0.17379485 21.71193666 0.011942601 0.009987383 262.8152108 -2.419650497 -0.088883455 CATITPDEKR ddPTM_BT-474_Pertuzumab_2h_R1 6 CATITPDEKR 10 1 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;;; 169.76 7.27E-06 4777480000 2375020 2127520 1807500 2040670 2080180 2396350 2417990 2823310 2956640 2726200 FALSE TRUE 2282201.593 2066845.213 2134155.458 2145989.223 2147090.879 2444805.839 2447582.085 2765007.662 2621014.622 2541552.046 0.897955876 0.813221675 0.839705589 0.844361707 0.844795165 0.961934202 0.963026545 1.087920929 1.031265375 1 21.27727834 2.419654417 1.542931134 1.044135647 0.842878894 0.851883785 0.034334508 0.124180219 0.598663942 0.016269815 0.011750453 262.8175828 -2.419654417 -0.201256753 SS(ph)TPVPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTPVPSK 8 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 S(0.004)S(0.498)T(0.498)PVPSK 91.265 0.013227 263830000 764090 681390 714720 684030 622020 744830 764850 834880 799970 922100 TRUE FALSE 734228.5181 661957.4244 843885.8029 719332.8703 642027.8382 759890.9729 774210.4631 817639.4362 709160.7593 859645.3457 0.854106315 0.770035489 0.98166739 0.836778648 0.746851991 0.883958689 0.900616128 0.951135768 0.824945732 1 19.71338206 2.419713098 4.134714672 0.917633502 0.839911196 0.221604491 0.071337371 0.350053127 12.36540491 0.02523874 0.021136516 262.8530968 -2.419713098 -0.077722306 FAEWCLEYGEHGCR ddPTM_BT-474_Pertuzumab_2h_R1 1 FAEWCLEYGEHGCR 14 0 O43813;H7C2E3 O43813 LANCL1 LanC-like protein 1 0 200.13 1.97E-08 242210000 176070 175480 124650 186440 183950 168240 150080 171160 165000 194390 FALSE TRUE 169188.9897 170475.4822 147177.0278 196062.1907 189866.9188 171641.9281 151916.7239 167625.4862 146269.8917 181223.7922 0.933591488 0.940690404 0.812128618 1.081878866 1.047693112 0.947126898 0.838282447 0.924964014 0.807123005 1 17.46741285 2.419870081 9.648640864 0.88907938 0.963852436 0.141235019 0.082656469 0.728071723 116.672804 0.029163803 0.024392324 262.9481266 -2.419870081 0.074773056 VATLNS(ph)EEESDPPTYK ddPTM_BT-474_Pertuzumab_2h_R1 6 VATLNSEEESDPPTYK 16 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62;C9JQ82;C9JHN6;C9JEJ8;C9JBS3;C9JMQ6 Q00341 HDLBP Vigilin 1 VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK 393.11 1.51E-121 5957880000 5665420 5663240 4774780 5336460 5758350 5785610 6163660 7152250 7132270 6764800 TRUE FALSE 5444009.123 5501729.94 5637688.96 5611875.34 5943572.557 5902598.998 6239092.715 7004553.538 6322644.611 6306614.071 0.863222176 0.872374602 0.893932766 0.889839663 0.942434798 0.935937879 0.989293565 1.110667858 1.002541862 1 22.58843422 2.421279809 1.291454882 1.05056422 0.883300967 0.766862994 0.035215304 0.191878577 0.642685799 0.020013636 0.013808577 263.803048 -2.421279809 -0.167263253 LAPEYEAAATR ddPTM_BT-474_Pertuzumab_2h_R1 4 LAPEYEAAATR 11 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 146.11 8.36E-05 1404670000 467120 576510 462270 591750 499880 522990 504670 513590 539950 589960 FALSE TRUE 448864.434 560068.4993 545812.4721 622290.2884 515959.0942 533565.2161 510846.3024 502984.187 478657.1397 550001.4837 0.816114951 1.018303615 0.992383636 1.131433836 0.938104913 0.970115958 0.928808953 0.914514237 0.870283361 1 19.06907598 2.422379723 1.918896653 0.919333945 0.990505581 0.077055366 0.079089234 0.702286704 5.271926439 0.034274368 0.026357908 264.4720144 -2.422379723 0.071171636 RGEGDAPFSEPGT(ph)TSTQRPSSPETATK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFS(0.026)EPGT(0.217)T(0.157)S(0.157)T(0.157)QRPS(0.217)S(0.056)PET(0.011)AT(0.001)K 90.701 0.010612 4178400000 304060 271820 249720 259400 252710 282140 301230 301130 371160 299690 TRUE FALSE 292176.999 264067.9597 294849.959 272787.6651 260838.6467 287845.0641 304916.5428 294911.5603 329027.4728 279391.7294 1.045761089 0.945153102 1.055328158 0.976362707 0.933594732 1.03025621 1.091358515 1.055548641 1.177656452 1 18.09192979 2.422465543 4.46684652 1.082008336 0.990466604 0.377086798 0.054319457 0.208089083 8.711497504 0.018299848 0.015348514 264.5242812 -2.422465543 -0.091541732 S(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.564)HS(0.436)DNDRPNCSWNTQYSSAYYTSR;S(0.884)HS(0.116)DNDRPNCSWNTQYSSAYYTSR;S(0.331)HS(0.331)DNDRPNCS(0.331)WNT(0.008)QYSSAYYTSR;S(0.864)HS(0.135)DNDRPNCSWNTQYSSAYYTSR 215.98 8.28E-33 2969390000 165586 135645.2 118370.8 162485 135803.8 118575.4 130294.9 68330.3 144284 138594.8 TRUE FALSE 159114.7161 131776.7317 139763.0367 170870.8703 140172.0526 120973.0758 131889.488 66919.25543 127905.4852 129207.6507 1.231465127 1.01988335 1.081693196 1.322451645 1.084858766 0.936268674 1.020756025 0.517920224 0.989921916 1 16.97933197 2.422944721 1.725938986 0.798964285 1.147545091 0.377435623 0.158711226 0.313687047 1.900251906 0.072952002 0.054568598 264.8163047 -2.422944721 0.348580807 CSVCSEPIMPEPGRDETVR ddPTM_BT-474_Pertuzumab_2h_R1 1 CSVCSEPIMPEPGRDETVR 19 1 Q15942;Q15942-2;H0Y2Y8 Q15942 ZYX Zyxin 0 128.79 1.89E-05 298110000 92273 93710 75616 88211 74377 98553 123630 124630 125250 123110 FALSE TRUE 88666.86915 91037.48255 89281.49327 92763.58028 76769.40375 100545.8092 125143.0209 122056.3469 111032.1451 114771.65 0.772550269 0.793205313 0.77790546 0.808244721 0.668888212 0.876050916 1.090365268 1.063471222 0.967417869 1 16.8084068 2.423074464 4.482133307 1.038806979 0.768684799 0.873424746 0.047620477 0.064634958 2.733533628 0.016805875 0.0140993 264.8954288 -2.423074464 -0.27012218 LSKEDIER ddPTM_BT-474_Pertuzumab_2h_R1 8 LSKEDIER 8 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;; 131.52 0.00091355 43905090000 30133400 30428500 23253100 24630300 25635800 28074000 28857500 30933400 32573100 30860200 FALSE TRUE 28955753.41 29560708.97 27455452.43 25901472.73 26460398.79 28641675.52 29210666.72 30294614.48 28875538.25 28770011.17 1.006456106 1.027483403 0.954308021 0.90029415 0.919721533 0.995539256 1.015316489 1.052992795 1.003667954 1 24.77806245 2.423119368 3.639704892 1.025155873 0.961130545 0.327589671 0.037401439 0.273337896 7.495260735 0.015309172 0.012815807 264.9228189 -2.423119368 -0.064025328 RDDNSAANNSANEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDDNSAANNSANEK 14 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8;H0YEI7 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 246.34 1.61E-17 527670000 229680 232210 199400 205950 218640 236150 269590 273310 297710 282040 FALSE TRUE 220703.8517 225587.5982 235436.0156 216579.1042 225672.7542 240925.1148 272889.3231 267666.053 263915.2089 262937.1796 0.839378638 0.857952453 0.895407854 0.82369144 0.858276317 0.91628394 1.037849891 1.017984803 1.003719631 1 18.00435863 2.423745416 3.197932388 1.017391588 0.85659482 0.931611352 0.020373893 0.058123718 1.221732138 0.007696742 0.006409244 265.3049883 -2.423745416 -0.160796768 YDPSLTFSENVDLTEPIISR ddPTM_BT-474_Pertuzumab_2h_R1 1 YDPSLTFSENVDLTEPIISR 20 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 67.964 0.036732 0 12542 12180 10354 13818 13022 12565 10033 14753 12742 11180 FALSE TRUE 12051.84477 11832.63833 12225.19812 14531.14864 13440.86446 12819.07291 10155.78686 14448.34539 11295.58158 10422.76864 1.15629975 1.135268251 1.172931929 1.394173577 1.289567573 1.22991053 0.974384754 1.386229119 1.083740987 1 13.34745094 2.423808608 24.99997039 1.155632908 1.233331448 0.135983719 0.12792444 276.0066015 129426.3332 0.045632719 0.038179075 265.3435946 -2.423808608 0.07769854 SLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPAPVAQRPDSPGGGLQAPGQK 23 1 Q5JVS0;Q5JVS0-2 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 1 SLPAPVAQRPDS(1)PGGGLQAPGQK 139.79 1.22E-07 288300000 152190 134540 131750 123660 127130 146440 161250 162870 173250 195410 TRUE FALSE 146242.2465 130703.0509 155560.1558 130042.1074 131219.2519 149401.1171 163223.4257 159506.6776 153583.3863 182174.7066 0.802758238 0.717459923 0.853906443 0.713831848 0.720293472 0.820098025 0.895971942 0.875569834 0.843055489 1 17.47496314 2.424160908 3.549244874 0.891283464 0.761800061 0.588543569 0.055470049 0.172082241 4.485936281 0.019258135 0.016118618 265.5589284 -2.424160908 -0.129483403 KALERPYTSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KALERPYTSK 10 2 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 113.61 0.00082422 2603800000 2377910 2602930 1805130 2018220 2377470 2289390 2566910 2642780 2879390 2673860 FALSE TRUE 2284978.648 2528696.985 2131357.146 2122380.576 2453943.482 2335683.034 2598324.612 2588205.669 2552533.719 2492757.081 0.91664714 1.014417732 0.855019995 0.851418934 0.98442945 0.936987825 1.042349707 1.038290369 1.02398013 1 21.24931087 2.424376262 1.926021695 1.031913084 0.919617579 0.488906647 0.049000319 0.284493599 2.151329928 0.021903454 0.016889762 265.6906444 -2.424376262 -0.112295504 S(ph)PDKPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPDKPGK 7 1 P55317-2;P55317;P55318;Q9Y261;Q9Y261-2 P55317-2 FOXA1;FOXA3;FOXA2 Hepatocyte nuclear factor 3-alpha;Hepatocyte nuclear factor 3-gamma;Hepatocyte nuclear factor 3-beta 1 S(1)PDKPGK 62.262 0.052395 689040000 1617100 1221700 1321400 1268400 1299100 1482300 1759600 1691400 1739300 2140900 TRUE FALSE 1553901.944 1186858.312 1560206.374 1333862.276 1340886.731 1512273.122 1781134.511 1656471.999 1541861.956 1995894.936 0.778548969 0.594649694 0.781707667 0.668302851 0.671822302 0.757691747 0.892398933 0.829939477 0.772516593 1 20.92860435 2.424408159 4.128249401 0.85692008 0.697046476 0.545718954 0.074551259 0.16738432 5.98957483 0.024861972 0.020868943 265.7101585 -2.424408159 -0.159873604 TLENPVNVYNPSHS(ph)DSLASQQSVASHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLENPVNVYNPSHSDSLASQQSVASHPR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 TLENPVNVYNPS(0.186)HS(0.739)DS(0.075)LASQQSVASHPR 213.51 3.57E-26 678780000 101680 93819 82736 97290 95871 84907 77979 71798 84122 92632 TRUE FALSE 97706.23319 91143.37398 97688.23565 102311.1486 98954.77778 86623.87771 78933.33033 70315.34621 74572.82323 86357.95213 1.131409798 1.055413795 1.131201392 1.18473338 1.145867582 1.003079341 0.914025036 0.814231284 0.863531631 1 16.39804141 2.424456326 2.380878814 0.872333567 1.128333174 0.797292233 0.054691963 0.117566825 1.360700454 0.022018865 0.017752195 265.7396303 -2.424456326 0.255999607 DVFRDPALK ddPTM_BT-474_Pertuzumab_2h_R1 7 DVFRDPALK 9 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;;; 143.96 9.18E-05 8861320000 12002152 11530203 9718874 10308651 12280460 11523010 12826960 14217940 14895400 14120840 FALSE TRUE 11533094.63 11201372.9 11475290.73 10840681.71 12675472.15 11756013.16 12983940.17 13924334.57 13204536.64 13164422.93 0.876080531 0.850882181 0.871689613 0.823483245 0.962858168 0.893013938 0.986290113 1.057724645 1.00304713 1 23.65014095 2.42454061 1.14487647 1.030902818 0.861418098 0.766622057 0.036156362 0.208067847 0.545047436 0.021257209 0.014383673 265.7912074 -2.42454061 -0.169484721 GLECSDWKPEAGLS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLECSDWKPEAGLSPPR 17 1 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 GLECSDWKPEAGLS(1)PPR 111.66 0.00030209 443430000 560080 547350 421560 495210 507630 534920 554020 600100 655330 570870 TRUE FALSE 538191.4544 531740.1139 497745.2696 520767.8474 523958.38 545736.4489 560800.2625 587707.7253 580939.6858 532204.4664 1.011249413 0.999127492 0.935251959 0.978510855 0.984505792 1.025426285 1.053730846 1.104289352 1.091572361 1 19.02162109 2.424789348 1.989167506 1.076512668 0.979399518 0.573919079 0.032272125 0.203608869 1.642965223 0.013674441 0.010631488 265.9434802 -2.424789348 -0.09711315 DVFRDPALKR ddPTM_BT-474_Pertuzumab_2h_R1 3 DVFRDPALKR 10 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;; 141.08 2.15E-05 4626230000 5337350 5018140 3953930 4151610 4934290 4872050 4967060 5242730 5899880 5587120 FALSE TRUE 5128760.461 4875027.56 4668493.106 4365875.09 5093005.919 4970566.189 5027848.366 5134465.793 5230150.357 5208699.386 0.984652805 0.935939512 0.896287683 0.838189108 0.977788415 0.954281639 0.965279044 0.985748152 1.004118297 1 22.31249175 2.424913548 1.206102114 0.994043581 0.9186987 0.394097535 0.038400404 0.510201318 1.486566741 0.023506373 0.016046963 266.0195462 -2.424913548 -0.07534488 QVICVYTDDFTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QVICVYTDDFTDR 13 0 Q9H3H3-1;Q9H3H3;Q9H3H3-3 Q9H3H3-1 C11orf68 UPF0696 protein C11orf68 0 231.17 2.41E-08 0 49797 48144 39095 47833 48728 44966 40881 45205 40892 51978 FALSE TRUE 47850.87819 46770.98026 46160.33616 50301.66686 50295.38037 45875.24333 41381.31391 44271.50095 36250.11159 48457.48376 0.987481695 0.965196222 0.952594575 1.038057756 1.037928024 0.946711215 0.853971579 0.913615349 0.748080766 1 15.56443187 2.425235062 4.418504375 0.87627623 0.9945305 0.430953569 0.063400489 0.190489943 7.899759542 0.021594691 0.018135787 266.2165566 -2.425235062 0.11825427 TGS(ph)PGPELLFHEGQQK ddPTM_BT-474_Pertuzumab_2h_R1 5 TGSPGPELLFHEGQQK 16 0 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 T(0.202)GS(0.798)PGPELLFHEGQQK;T(0.102)GS(0.898)PGPELLFHEGQQK;T(0.15)GS(0.85)PGPELLFHEGQQK;T(0.467)GS(0.533)PGPELLFHEGQQK;T(0.097)GS(0.903)PGPELLFHEGQQK 188.04 8.00E-10 1646488000 1954610 1712630 1472653 1539004 1794310 1677110 1564994 1630910 2047770 1684840 TRUE FALSE 1878221.68 1663787.469 1738794.156 1618432.181 1852025.611 1711022.313 1584146.865 1597231.139 1815315.735 1570724.286 1.195767899 1.05924858 1.10700151 1.030373182 1.179090199 1.089320595 1.008545471 1.01687556 1.155718894 1 20.58299853 2.425327224 7.888472692 1.042671996 1.108927118 0.217555048 0.061270239 0.382528157 50.72822587 0.020636187 0.017267718 266.2730566 -2.425327224 0.066255123 ELDDLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELDDLKR 7 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 114.6 0.009409 539610000 1142300 1204590 959690 1136220 1222430 1210960 1307440 1533790 1482990 1601110 FALSE TRUE 1097657.653 1170236.273 1133127.331 1194860.45 1261750.571 1235446.441 1323440.842 1502116.701 1314647.192 1492665.394 0.735367523 0.783991025 0.759130168 0.800487809 0.845300344 0.827678089 0.886629279 1.006331832 0.88073804 1 20.50945937 2.425644798 0.618592654 0.988658985 0.750404493 0.815368265 0.037921583 0.31228067 0.242224498 0.032439398 0.0267482 266.4678376 -2.425644798 -0.238254493 DVDEIEAWISEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DVDEIEAWISEK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;; 209.85 1.17E-07 640277000 662629 657417 568949 623140.6 595426 690378 710981 763309 824008 827972 FALSE TRUE 636732.7261 638668.1108 671770.7405 655300.961 614578.418 704337.9162 719682.1982 747546.4024 730470.0664 771892.719 0.824897956 0.827405279 0.870290293 0.848953417 0.796196677 0.912481617 0.932360392 0.968458937 0.946336257 1 19.55804082 2.426693063 2.31060109 0.962341657 0.836236649 0.856534683 0.024745816 0.106772718 1.163429145 0.009739202 0.0078247 267.1117935 -2.426693063 -0.126105008 EGTQASEGYFSQS(ph)QEEEFAQSEELCAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGTQASEGYFSQSQEEEFAQSEELCAK 27 0 Q16643;Q16643-3;Q16643-2 Q16643 DBN1 Drebrin 1 EGTQASEGYFS(0.001)QS(0.999)QEEEFAQSEELCAK 153.87 3.40E-08 98269000 57339 51469 44839 53931 57957 61962 55004 68964 74465 76092 TRUE FALSE 55098.12849 50001.15451 52942.40474 56714.38537 59821.23954 63214.91409 55677.15541 67539.8693 66012.04538 70938.22106 0.776705811 0.704854925 0.746317062 0.799489817 0.843286435 0.891126295 0.784868222 0.952094207 0.93055682 1 16.11427553 2.426721634 0.347512734 1.009965875 0.695495251 0.79456741 0.04169671 0.685675912 0.190286452 0.050542359 0.077671385 267.1293665 -2.426721634 -0.314470624 S(ph)PS(ph)PAPPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPAPPPR 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(1)PS(1)PAPPPR 77.662 0.046733 537440000 582490 508800 539960 662340 546120 572910 529990 568830 624990 574020 TRUE FALSE 559725.6468 494289.5222 637542.7833 696523.4468 563686.4458 584494.6327 536476.1762 557083.4617 554043.7554 535141.1141 1.04594028 0.923662019 1.191354517 1.301569676 1.05334169 1.092225242 1.002494785 1.041002919 1.035322723 1 19.02955985 2.428283436 2.579431032 1.024277247 1.108396199 0.150272551 0.093371204 0.625984082 8.507175895 0.039577345 0.032383647 268.0917416 -2.428283436 0.084118951 AEGSPS(ph)EGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEGSPSEGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(0.17)PS(0.83)EGKK 72.891 0.02856 241110000 235650 184750 178910 162780 190200 222500 234550 253360 287690 275920 TRUE FALSE 226440.5375 179481.1109 211243.0168 171181.0953 196317.9557 226999.1024 237420.4931 248128.0275 255032.6373 257231.6926 0.880297972 0.697741048 0.821216914 0.665474357 0.763195055 0.882469419 0.922983053 0.964609084 0.991451072 1 17.97270888 2.428504713 1.760670761 0.975285061 0.758646541 0.734829806 0.058200049 0.17502677 1.103782013 0.025338195 0.019156747 268.2283716 -2.428504713 -0.21663852 RTAS(ph)PPPPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTASPPPPPK 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.146)AS(0.854)PPPPPK;RT(0.412)AS(0.588)PPPPPK 69.716 0.03439 420320000 960350 983700 756440 896610 894600 921640 938460 998440 1037780 1010810 TRUE FALSE 922818.4603 955645.8391 893145.5349 942884.1496 923375.6215 940276.1923 949945.1542 977821.8651 919975.5651 942346.9384 0.979276764 1.014112531 0.94778844 1.000570078 0.979868012 0.997802565 1.008063077 1.037645293 0.97625994 1 19.84589878 2.429289375 2.961723464 1.011715034 0.984929271 0.155890371 0.021482618 0.366766182 6.600030369 0.007804845 0.00648598 268.7134316 -2.429289375 -0.026785764 KPPAPPS(ph)PVQSQSPSTNWSPAVPVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KPPAPPS(1)PVQSQSPSTNWSPAVPVKK;KPPAPPS(1)PVQSQSPSTNWSPAVPVKK 257.08 6.19E-53 5584100000 2064960 1735080 1568310 1405870 1600550 1751460 1944420 1949850 2110280 1953760 TRUE FALSE 1984259.08 1685597.217 1851738.504 1478427.119 1652033.144 1786875.721 1968216.394 1909584.916 1870729.861 1821430.095 1.089396231 0.925425149 1.016639897 0.811684798 0.90699783 0.981028987 1.080588489 1.048398685 1.027066516 1 20.7966402 2.429501688 5.585743263 1.044321374 0.944490925 0.26066114 0.070171011 0.239210814 17.14048015 0.024726329 0.020761858 268.8448294 -2.429501688 -0.09983045 GSIDEVDKR ddPTM_BT-474_Pertuzumab_2h_R1 6 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;;; 132.01 0.00050837 5315560000 3778310 3749610 3282290 3504550 3684920 3893640 4131290 4364710 4870550 4569850 FALSE TRUE 3630649.468 3642674.794 3875472.817 3685420.245 3803448.798 3972372.069 4181849.963 4274577.213 4317665.583 4260329.989 0.85219912 0.855021748 0.909664938 0.865055114 0.892759201 0.93240948 0.981578886 1.00334416 1.013458017 1 22.02253375 2.429564423 1.268272774 1.009702169 0.870115523 0.939034316 0.015140521 0.099444933 0.321312914 0.008578534 0.005944327 268.8836676 -2.429564423 -0.139586646 KEES(ph)EESDDDMGFGLFD ddPTM_BT-474_Pertuzumab_2h_R1 1 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.666)EES(0.334)DDDMGFGLFD 68.944 0.007233 0 135140 123530 108840 101780 110040 135480 132450 159360 158950 151340 TRUE FALSE 129858.5794 120007.0453 128509.8091 107032.878 113579.5365 138219.4984 134070.9627 156069.1603 140906.6624 141089.607 0.92039791 0.850573248 0.910838239 0.758616317 0.805017031 0.979657548 0.950253995 1.106170494 0.998703344 1 17.10625219 2.429873492 2.132566815 1.035109647 0.849081032 0.636375609 0.058853022 0.188444605 1.747803471 0.024671568 0.019565548 269.0750885 -2.429873492 -0.186028615 QLSQQSDGDRDLQEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLSQQSDGDRDLQEHR 16 1 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 0 70.784 0.025514 257170000 62320 79453 52680 71190 58382 61719 46821 55655 48973 51442 FALSE TRUE 59884.4655 77187.07823 62200.44786 74864.12443 60259.91005 62967.00047 47394.0094 54505.7048 43413.79035 47957.78752 1.248691164 1.609479549 1.296983265 1.561042081 1.25651981 1.312967168 0.988244284 1.136535016 0.905250067 1 15.54947748 2.430358353 1.221296983 1.000879579 1.43000146 0.680500467 0.125317794 0.249229383 0.7456074 0.065431147 0.045020703 269.3756607 -2.430358353 0.429121882 SGS(ph)PRPTEPTDFLMLFEGSPSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.135)GS(0.863)PRPT(0.001)EPT(0.001)DFLMLFEGSPSGK;S(0.165)GS(0.831)PRPT(0.002)EPT(0.002)DFLMLFEGSPSGK;S(0.122)GS(0.878)PRPTEPTDFLMLFEGSPSGK 222.95 9.32E-33 682610000 1011320 959640 884030 904150 1065930 1130270 1173600 1264650 1491210 1432920 TRUE FALSE 971796.4963 932272.0068 1043793.886 950813.2899 1100216.607 1153124.834 1187962.868 1238534.536 1321934.092 1335867.052 0.727464979 0.697877835 0.781360604 0.711757423 0.823597382 0.86320329 0.889282258 0.927139069 0.9895701 1 20.349345 2.430617451 0.582976002 1.004310588 0.705841928 0.937708699 0.026358477 0.178680884 0.124037487 0.022041729 0.019238101 269.5364169 -2.430617451 -0.298468661 QVTDAETKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 QVTDAETKPK 10 1 O43684;O43684-2 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ; 98.156 0.0050788 566170000 1210020 1217160 1057720 1075550 1340550 1552910 1521150 1845140 2130000 1966180 FALSE TRUE 1162731.081 1182447.789 1248873.533 1131059.264 1383670.008 1584310.904 1539766.289 1807037.214 1888211.33 1833008.877 0.634329214 0.645085686 0.681324323 0.61705062 0.754862688 0.864322548 0.840021185 0.985831131 1.030115758 1 20.80578234 2.430768018 0.808210929 1.023273128 0.63303353 0.943202133 0.036455033 0.134296506 0.174901408 0.027427945 0.019266971 269.62988 -2.430768018 -0.390239598 REVS(ph)PAPAVAGQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 REVSPAPAVAGQSK 14 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 REVS(1)PAPAVAGQSK;REVS(1)PAPAVAGQSK 304.36 3.83E-44 386050000 512630 528800 438260 505400 489200 545450 578020 642410 643190 625380 TRUE FALSE 492595.8529 513719.1417 517463.331 531483.7546 504935.5623 556479.3727 585093.9817 629144.009 570177.7677 583022.4556 0.844900309 0.88113097 0.887553003 0.91160083 0.866065376 0.95447331 1.003553081 1.079107679 0.977968794 1 19.15319193 2.430833532 2.300423332 1.029602412 0.880477546 0.820444035 0.030013884 0.112050256 1.209568853 0.012041623 0.009697601 269.6705566 -2.430833532 -0.149124866 AIAGDEHKR ddPTM_BT-474_Pertuzumab_2h_R1 6 AIAGDEHKR 9 1 H0YDU8;P53041;A8MU39;M0R196;A0A087WY80;E7EU14 H0YDU8 PPP5C;PPP5D1 Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5;Protein PPP5D1 0 ;;;;; 165.83 3.97E-05 1099549000 2449547 2487143 2043288 2193149 2236867 2364658 2538882 2470671 2888399 2736173 FALSE TRUE 2353815.995 2416212.117 2412555.594 2306337.683 2308817.859 2412473.005 2569953.597 2419650.78 2560520.055 2550849.566 0.922757667 0.947218585 0.945785132 0.904144922 0.905117217 0.945752755 1.007489282 0.948566632 1.003791086 1 21.28254639 2.431975542 6.27975715 0.982190559 0.926109755 0.679652972 0.020803279 0.128359194 12.33203118 0.007422722 0.006229562 270.3806088 -2.431975542 -0.056080804 SLSS(ph)PPSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSPPSSK 9 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 SLS(0.002)S(0.991)PPS(0.005)S(0.002)K 66.55 0.066518 304600000 980560 905170 727420 772570 846550 881950 962170 996790 972720 1052200 TRUE FALSE 942238.6311 879355.4379 858880.9754 812442.4303 873780.0496 899783.6333 973945.3243 976205.9382 862300.9036 980933.5568 0.96055296 0.896447503 0.875575078 0.828233905 0.890763746 0.917272762 0.992875937 0.99518049 0.879061479 1 19.90379589 2.432197053 4.008227851 0.970115772 0.887394673 0.397703394 0.044151715 0.212915796 7.323104316 0.016175435 0.013632514 270.5185511 -2.432197053 -0.082721099 NVHGINFVSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 NVHGINFVSPVR 12 0 P53634;H0YCY8 P53634 CTSC Dipeptidyl peptidase 1;Dipeptidyl peptidase 1 exclusion domain chain;Dipeptidyl peptidase 1 heavy chain;Dipeptidyl peptidase 1 light chain 0 79.089 0.015127 0 166130 173580 168260 154140 144310 116120 200060 157560 173440 214840 FALSE TRUE 159637.4559 168629.6684 198668.3249 162095.1839 148951.8622 118468.026 202508.3941 154306.3309 153751.8183 200288.6954 0.797036775 0.841933031 0.991909825 0.809307702 0.743685818 0.591486333 1.011082496 0.770419572 0.767651005 1 17.61172147 2.432591961 0.008126322 1.655766656 8.31E-06 0.03969616 0.124449467 20234.22416 81.96737723 8210.472288 8484.035189 270.7646481 -2.432591961 -1.655758348 AEGAGRPPPAT(ph)PPRPPPSTSAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEGAGRPPPATPPRPPPSTSAVR 23 2 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 AEGAGRPPPAT(1)PPRPPPSTSAVR;AEGAGRPPPAT(1)PPRPPPSTSAVR 131.13 0.0015215 1212020000 62642 60808 53116 70091 68307 61619 54032 63120 61340 62869 TRUE FALSE 60193.88139 59073.81538 62715.24276 73708.40491 70504.15669 62864.9784 54693.25978 61816.54994 54376.94036 58610.82663 1.027009596 1.007899372 1.070028293 1.257590264 1.20292036 1.072583036 0.933159672 1.054695071 0.927762727 1 15.83887956 2.432678349 7.060237603 0.990254152 1.115338242 0.39578046 0.077932758 0.248878158 31.00226695 0.029966355 0.025124547 270.8185127 -2.432678349 0.12508409 YDEELEGERPHSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDEELEGERPHSFR 14 1 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 136.17 1.72E-05 548240000 431140 465220 363450 409710 422170 408540 391500 400550 448710 433440 FALSE TRUE 414290.5721 451952.3811 429133.4999 430855.1822 435749.4815 416800.9587 396291.2941 392278.5025 397774.3219 404082.7227 1.025261781 1.118464997 1.06199418 1.066254898 1.07836702 1.031474337 0.980718234 0.970787615 0.984388343 1 18.62429114 2.433240505 2.706110524 0.979770696 1.071994432 0.762038692 0.022572582 0.115142595 1.723784519 0.008111451 0.006699121 271.1692904 -2.433240505 0.092223736 ARLEIEPEWAYGK ddPTM_BT-474_Pertuzumab_2h_R1 4 ARLEIEPEWAYGK 13 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;; 148.72 3.64E-05 3566180000 4205950 4243680 3398060 3471610 3875690 4050050 3890870 4445710 4421520 4452120 FALSE TRUE 4041576.824 4122654.401 4012165.031 3650780.208 4000355.089 4131944.786 3938487.631 4353904.535 3919607.586 4150573.947 0.973739265 0.993273329 0.966653066 0.879584427 0.96380769 0.995511666 0.948901931 1.048988547 0.944353151 1 21.98487942 2.43363308 1.745121626 0.9971809 0.955144002 0.120116463 0.039409317 0.659957197 4.087020429 0.018442242 0.013976072 271.4145212 -2.43363308 -0.042036897 RHNS(ph)WSSSSR ddPTM_BT-474_Pertuzumab_2h_R1 7 RHNSWSSSSR 10 1 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 RHNS(0.999)WS(0.001)SSSR;RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(0.99)WS(0.002)S(0.002)S(0.003)S(0.003)R;RHNS(1)WSSSSR 179.21 1.31E-06 1798244000 408497 488055 314361 375904 344629 356283 345208 231560.8 319275 336319 TRUE FALSE 392532.4856 474136.1493 371173.0256 395304.4505 355714.3048 363487.2864 349432.7588 226778.9886 283032.2405 313539.8146 1.251938246 1.51220396 1.183814649 1.260779117 1.134510797 1.159301848 1.114476512 0.723286096 0.902699521 1 18.25828913 2.43391212 0.911803189 0.849696215 1.320265479 0.659676741 0.118945717 0.320538955 0.530997615 0.083586454 0.057044651 271.5889648 -2.43391212 0.470569264 QEMQEVQSSR ddPTM_BT-474_Pertuzumab_2h_R1 11 QEMQEVQSSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;; 302.65 2.90E-32 11478548000 2999305 3204104 2524979 3036256 3010714 2912882 2881696 2992724 3089163 3234722 FALSE TRUE 2882088.845 3112726.091 2981298.873 3192957.536 3107556.35 2971782.47 2916963.058 2930923.204 2738494.167 3015631.398 0.955716553 1.032197136 0.988615146 1.058802325 1.030482821 0.985459454 0.967281034 0.971910296 0.908099766 1 21.52402867 2.434244031 2.831450931 0.960595883 1.015190002 0.341083243 0.033470676 0.289689077 4.756655455 0.012300356 0.010213651 271.7966072 -2.434244031 0.05459412 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSK 39 3 P32119 P32119 PRDX2 Peroxiredoxin-2 0 116.84 2.21E-06 4102800000 291860 306880 253590 314820 241260 287210 308950 314620 331410 297590 FALSE TRUE 280453.7885 298128.0829 299419.3541 331067.8979 249020.347 293017.583 312731.0225 308122.9871 293789.7262 277433.9642 1.01088484 1.074591151 1.079245488 1.193321441 0.897584215 1.056170551 1.127226882 1.110617396 1.058953712 1 18.08178489 2.434349511 24.86414496 1.088371816 1.053389657 0.00654432 0.075802712 490.7803627 285298.6427 0.026289597 0.021995506 271.8626284 -2.434349511 -0.03498216 KLNS(ph)GGGLSEELGSAR ddPTM_BT-474_Pertuzumab_2h_R1 3 KLNSGGGLSEELGSAR 16 1 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 KLNS(1)GGGLSEELGSAR;KLNS(1)GGGLSEELGSAR;KLNS(0.851)GGGLS(0.09)EELGS(0.059)AR 248.9 1.08E-20 1032450000 613373 555056 504137 531771 505662 531249 458082 501366 466330 514578 TRUE FALSE 589401.705 539226.3463 595245.7704 559215.765 521927.0775 541991.2188 463688.1445 491012.6169 413394.1734 479725.1737 1.228623673 1.124031791 1.240805784 1.165700271 1.087971001 1.129795242 0.966570382 1.023528978 0.86173125 1 18.87184862 2.435040659 0.912236568 0.944637676 1.192124629 0.760757578 0.055723183 0.264348578 0.438451986 0.036246552 0.024761374 272.2956223 -2.435040659 0.247486953 SQANGAGALSYVS(ph)PNTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SQANGAGALSYVSPNTSK 18 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;F5H1Z4;A0A494C002;A0A494C156;A0A494C1G3;A0A494BZU6;A0A494BZW7;A0A494C0P9;A0A494C1K5;A0A494C1N1;A0A494C0Q2 A0A494C0Q6;A0A494C0Q2 PARN Poly(A)-specific ribonuclease PARN 1 SQANGAGALSYVS(1)PNTSK;SQANGAGALSYVS(1)PNTSK;SQANGAGALSYVS(1)PNTSK;SQANGAGALSYVS(1)PNTSK 443.69 1.20E-190 1302560000 1117020 1026880 985540 1034510 1070420 1113780 1285840 1292320 1194650 1351760 TRUE FALSE 1073365.623 997594.3878 1163649.001 1087901.185 1104851.031 1136301.395 1301576.495 1265633.14 1059038.34 1260204.091 0.851739517 0.791613354 0.923381387 0.863273808 0.876723889 0.901680452 1.032829923 1.004308071 0.840370499 1 20.26522597 2.435419788 5.363641718 0.975698375 0.863320264 0.444854461 0.056674284 0.170762808 11.85568428 0.020087538 0.016920484 272.5334337 -2.435419788 -0.112378111 VDDDS(ph)LGEFPVTNSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDDDSLGEFPVTNSR 15 0 Q92785;J3KMZ8;Q92785-2 Q92785 DPF2 Zinc finger protein ubi-d4 1 VDDDS(1)LGEFPVTNSR;VDDDS(1)LGEFPVTNSR 239.19 1.92E-13 246380000 190072 216466 151453 166773 193601 174465 136594 141861 188631 232762 TRUE FALSE 182643.7761 210292.6016 178823.9262 175380.1745 199828.352 177992.8018 138265.6782 138931.5208 167218.3997 216996.8224 0.841688713 0.969104521 0.82408546 0.808215404 0.920881466 0.820255338 0.637178354 0.640246798 0.770602988 1 17.72731439 2.435822088 7.169848105 0.719300382 0.871812282 0.14954236 0.106555804 0.241241296 32.94673216 0.035518088 0.029801393 272.7860065 -2.435822088 0.1525119 EVAATEEDVTRLPS(ph)PTSPFSSLSQDQAATSK ddPTM_BT-474_Pertuzumab_2h_R1 4 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EVAATEEDVT(0.011)RLPS(0.972)PT(0.013)S(0.003)PFSSLSQDQAATSK;EVAATEEDVT(0.001)RLPS(0.941)PT(0.048)S(0.009)PFS(0.001)S(0.001)LSQDQAATSK;EVAATEEDVTRLPS(0.999)PT(0.001)SPFSSLSQDQAATSK;EVAATEEDVTRLPS(0.733)PT(0.167)S(0.1)PFSSLSQDQAATSK 405.06 8.09E-176 3478840000 853926 835696 707918 779223 783310 984670 1077220 1160590 1278220 1325020 TRUE FALSE 820553.6279 811862.7683 835854.5302 819438.7924 808505.8775 1004580.702 1090403.341 1136623.411 1133121.824 1235275.215 0.664267863 0.657232298 0.676654498 0.663365364 0.654514773 0.813244441 0.882720974 0.920137794 0.917303132 1 20.23640107 2.435911921 1.555445181 0.937272988 0.659298972 0.959748951 0.0259111 0.067356422 0.330268249 0.012095382 0.008896785 272.8424378 -2.435911921 -0.277974016 AKAEASSGDHPTDTEMKEEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKAEASSGDHPTDTEMKEEQK 21 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 217.86 3.39E-25 173910000 396850 293590 303090 267070 313860 360680 406560 441710 512640 367760 FALSE TRUE 381340.6633 285217.1007 357865.1052 280853.5147 323955.5919 367973.1967 411535.6029 432588.5341 454447.2564 342851.2876 1.112262596 0.831897417 1.043791049 0.819170074 0.944886613 1.073273486 1.200332674 1.261738106 1.325493801 1 18.38722341 2.4360096 2.433445768 1.225923184 0.942154749 0.504766252 0.113671907 0.200823872 2.425281696 0.041759004 0.034074314 272.9038106 -2.4360096 -0.283768435 LENGELEHIRPK ddPTM_BT-474_Pertuzumab_2h_R1 6 LENGELEHIRPK 12 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;;;; 235.31 2.89E-16 11050860000 7240300 7350070 6450660 6702310 7044660 7645270 7893140 7960970 8994660 9007420 FALSE TRUE 6957341.071 7140453.2 7616437.756 7048217.022 7271257.887 7799862.598 7989738.608 7796573.187 7973623.905 8397339.42 0.82851731 0.85032328 0.907006062 0.839339304 0.8659002 0.928849271 0.95146072 0.92845755 0.949541695 1 23.00150087 2.436192422 0.315900408 1.004813795 0.81602206 0.809319356 0.023503173 0.848377103 0.200622422 0.033886897 0.05721207 273.0187172 -2.436192422 -0.188791735 FLHNPDAAQGFVGCALSSTIQR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLHNPDAAQGFVGCALSSTIQR 22 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 104.41 0.00055203 403030000 127360 142330 93039 122380 135890 113590 79804 103790 111340 104000 FALSE TRUE 122382.6304 138270.8878 109853.2169 128696.0465 140261.0253 115886.8676 80780.66522 101646.7002 98701.14998 96955.98737 1.262249333 1.426120155 1.133021487 1.327365643 1.44664635 1.195252308 0.833168404 1.048379816 1.017999534 1 16.56504237 2.436388037 6.369262216 0.982893666 1.316002717 0.736838949 0.0970154 0.094663176 10.06451763 0.033056009 0.027782486 273.1417183 -2.436388037 0.333109052 VLS(ph)PLIIK ddPTM_BT-474_Pertuzumab_2h_R1 5 VLSPLIIK 8 0 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 VLS(1)PLIIK;VLS(1)PLIIK;VLS(1)PLIIK;VLS(1)PLIIK;VLS(1)PLIIK 150.61 0.00051025 2393431000 3505480 3405590 2904825 3159030 3200750 3510970 3527415 3915370 4089350 3931110 TRUE FALSE 3368481.966 3308465.908 3429791.495 3322067.917 3303705.031 3581964.219 3570584.56 3834516.241 3625144.132 3664852.418 0.919131682 0.902755563 0.93586074 0.906467038 0.901456499 0.977382937 0.974277857 1.046294858 0.989165106 1 21.80532367 2.436682675 1.878282944 1.013320309 0.913281477 0.815404217 0.020153811 0.126111727 0.905751118 0.008530441 0.006608236 273.3270882 -2.436682675 -0.100038832 AKS(ph)PAPGLASGDRPPS(ph)VSSVHSEGDCNR ddPTM_BT-474_Pertuzumab_2h_R1 1 AKSPAPGLASGDRPPSVSSVHSEGDCNR 28 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 AKS(0.999)PAPGLAS(0.005)GDRPPS(0.544)VS(0.147)S(0.158)VHS(0.147)EGDCNR 64.72 0.0080534 248890000 16239 14830 13440 16478 11843 14840 18916 16353 13273 16124 TRUE FALSE 15604.36193 14407.06292 15868.90697 17328.43155 12223.94085 15140.07497 19147.49967 16015.30484 11766.30468 15031.90712 1.038082647 0.958432141 1.055681548 1.152776652 0.8131996 1.007195883 1.273790446 1.065420689 0.782755281 1 13.87574044 2.436843241 24.99981045 1.059208125 1.002089265 0 0.138012876 642.2255325 398614.0612 0.048815292 0.040841852 273.4281605 -2.436843241 -0.057118859 TLAGHEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLAGHEGK 8 0 O43172-2;O43172 O43172-2 PRPF4 U4/U6 small nuclear ribonucleoprotein Prp4 0 102.07 0.0050364 211560000 570910 564700 471990 523520 520930 551980 580500 601160 652460 599310 FALSE TRUE 548598.206 548595.3089 557289.0924 550538.9299 537686.1865 563141.4138 587604.3326 588745.8359 578395.4761 558718.1999 0.981887123 0.981881938 0.997442168 0.985360652 0.96235667 1.007916717 1.051700719 1.053743794 1.035218606 1 19.09176129 2.437191442 4.415605444 1.041184188 0.982879173 0.697885868 0.016331033 0.099847365 4.372921904 0.005636134 0.004763928 273.6474732 -2.437191442 -0.058305015 GYEEWLLNEIR ddPTM_BT-474_Pertuzumab_2h_R1 6 GYEEWLLNEIR 11 0 O43707;O43707-2;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;;;; 242.83 2.01E-15 2710580000 1014500 1142040 1247890 1790510 1303670 886850 1566550 1557600 1562850 1956200 FALSE TRUE 974852.2184 1109470.137 1473411.482 1882918.436 1345603.73 904782.7146 1585721.908 1525435.016 1385441.82 1823704.832 0.534544956 0.608360585 0.807922125 1.032468853 0.737840744 0.49612344 0.869505788 0.836448415 0.759685337 1 20.79844082 2.437415296 0.049036811 1.55223138 7.69E-13 0.271364723 0.146668213 124.0118214 3.057697348 43.02280035 52.4204079 273.788559 -2.437415296 -1.55223138 S(ph)LSSS(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 2 S(0.984)LS(0.064)S(0.198)S(0.753)PQAQPPRPAELSDEEVAELFQR 104.31 0.0012522 89943000 35398 34758 31362 39214 44070 35198 30554 34189 33416 37385 TRUE FALSE 34014.60703 33766.73587 37029.81104 41237.83924 45487.55157 35909.72768 30927.92899 33482.9852 29622.75577 34852.88065 0.975948226 0.968836298 1.062460559 1.183197442 1.305130329 1.03032309 0.887385158 0.960694915 0.849937085 1 15.08899028 2.439638925 6.490003878 0.927129177 1.101560335 0.410685821 0.09853953 0.203870745 23.93701255 0.037710834 0.031729289 275.1939773 -2.439638925 0.174431158 GS(ph)PPGSSPLQGLENCLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPPGSSPLQGLENCLK 17 0 A0A087WVC5;A0A0C4DH65;A5PL33-3;A5PL33-2;A5PL33 A0A087WVC5 KRBA1 Protein KRBA1 1 GS(0.999)PPGS(0.001)SPLQGLENCLK 58.83 0.061568 0 36607 34741 26717 34792 32503 35834 38528 44968 35222 42527 TRUE FALSE 35176.35797 33750.22069 31545.35622 36587.61929 33548.48851 36558.58803 38999.51719 44039.39509 31223.74622 39646.60841 0.887247595 0.851276365 0.795663424 0.922843611 0.846188107 0.922111361 0.983678523 1.110798549 0.787551508 1 15.27490983 2.440165044 2.925269661 0.993787109 0.860345585 0.274241166 0.080936117 0.285355386 5.013734862 0.029949058 0.025038405 275.5275587 -2.440165044 -0.133441524 VLT(ph)PTQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLTPTQVK 8 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 VLT(0.938)PT(0.062)QVK 103.34 0.053558 205070000 619790 558520 573200 540920 641410 723850 692760 741270 934480 879030 TRUE FALSE 595567.9216 542591.5564 676789.9908 568836.946 662041.5352 738486.7429 701238.2041 725962.5155 828401.7481 819492.5151 0.726752119 0.662106787 0.825864762 0.694133181 0.807867702 0.901151297 0.855698119 0.885868391 1.010871646 1 19.64437125 2.440458053 0.434369953 1.012306521 0.681312533 0.796629711 0.050976971 0.507315065 0.205636957 0.050558833 0.061172741 275.7135135 -2.440458053 -0.330993988 QKEEEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 QKEEEAR 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;; 120.07 0.0042307 1758660000 3663570 3200800 2669820 3240290 3061850 3235620 3522400 3545960 3445420 3943850 FALSE TRUE 3520393.634 3109516.318 3152315.864 3407521.755 3160337.186 3301046.453 3565508.185 3472734.687 3054310.366 3676729.527 0.957479632 0.845728873 0.857369529 0.926780643 0.859551175 0.897821401 0.969749926 0.944517311 0.830713911 1 21.80999162 2.440532428 13.79310158 0.934302704 0.886399216 0.158598188 0.051291638 2.998190802 1127.275937 0.017144812 0.014347913 275.760735 -2.440532428 -0.047903488 MESS(ph)T(ph)GPRMPLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 MESSTGPRMPLLK 13 1 E9PNY9;Q9NQ32-2;Q9NQ32 E9PNY9 C11orf16 Uncharacterized protein C11orf16 2 MESS(1)T(1)GPRMPLLK 67.993 0.080072 249070000 71634 66027 53124 63471 69111 64928 57080 69049 65578 73328 TRUE FALSE 68834.46408 64143.97461 62724.68854 66746.74592 71334.01808 66240.88865 57778.56211 67623.11402 58133.86037 68361.42925 1.006919616 0.938306517 0.917545014 0.976380199 1.043483421 0.968980453 0.845192424 0.989199828 0.850389774 1 16.06089494 2.440611591 24.99925104 0.922757151 0.97463011 0.180274399 0.056567638 311.8277853 213516.179 0.019125292 0.016001401 275.8110052 -2.440611591 0.051872959 HGLQLGAQS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 6 HGLQLGAQSPGR 12 0 Q8N1G0;A6PVV7 Q8N1G0 ZNF687 Zinc finger protein 687 1 HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR 191.78 3.18E-06 6992730000 5047270 4992670 3976180 4704190 4478730 4006370 4308190 3287390 4320840 4296610 TRUE FALSE 4850017.108 4850283.94 4694764.176 4946973.81 4622792.418 4087381.546 4360914.918 3219504.248 3830356.358 4005596.778 1.210810118 1.210876733 1.172051117 1.235015426 1.154083318 1.020417624 1.088705419 0.803751457 0.956251108 1 21.93358577 2.440726776 1.267716813 0.911680622 1.206645185 0.7537425 0.06538643 0.195868437 0.633204189 0.035486768 0.024866973 275.8841663 -2.440726776 0.294964563 LLQTDDEEEAGLLELLK ddPTM_BT-474_Pertuzumab_2h_R1 6 LLQTDDEEEAGLLELLK 17 0 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ;;;;; 313.31 8.05E-58 1823730000 983898 977758 915597 944133 1009894 1049025 1146150 1219847 1331810 1325570 FALSE TRUE 945446.1784 949873.2992 1081065.745 992859.8173 1042378.158 1070237.004 1160176.927 1194656.733 1180628.512 1235787.963 0.765055338 0.768637766 0.874798734 0.80342247 0.843492726 0.866036113 0.938815526 0.966716596 0.955364955 1 20.2369998 2.442888214 0.568927709 1.003161575 0.778536681 0.878387912 0.02791152 0.279923092 0.185849142 0.025319751 0.022833706 277.260635 -2.442888214 -0.224624894 KEYEEDGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEYEEDGAR 9 1 P61163 P61163 ACTR1A Alpha-centractin 0 ;;; 162.38 0.00010233 2935630000 3027060 2952130 2431610 2828510 2968500 3180140 3267430 3538540 3824370 3905440 FALSE TRUE 2908759.149 2867938.143 2871056.018 2974489.74 3063984.498 3244444.61 3307417.786 3465467.912 3390243.551 3640921.07 0.7989075 0.787695775 0.788552117 0.816960786 0.841541038 0.89110545 0.908401397 0.951810777 0.931149971 1 21.79587203 2.442918154 0.57102485 0.986935311 0.776616132 0.9676122 0.012891326 0.130474828 0.087226626 0.011088532 0.00996465 277.2797501 -2.442918154 -0.210319179 QIYVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QIYVGR 6 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2;H0YAW6 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 141.59 0.027066 516460000 324050 338700 279110 325960 315600 319920 289200 330150 322130 381050 FALSE TRUE 311385.7677 329040.6076 329551.3858 342782.8347 325751.5606 326389.0016 292739.3161 323332.2871 285563.1529 355241.1441 0.876547587 0.926245772 0.927683607 0.964929993 0.91698714 0.918781529 0.824058026 0.910176911 0.803857204 1 18.43843916 2.443176186 24.99884406 0.877786673 0.924590552 0.100129555 0.053238214 331.5043959 244134.7512 0.017008308 0.014230253 277.444542 -2.443176186 0.046803879 IYNDDKNTYIR ddPTM_BT-474_Pertuzumab_2h_R1 6 IYNDDKNTYIR 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;;;; 176.78 7.55E-06 2418140000 4319310 4318560 3412990 3889220 4165890 4194500 4472620 4685970 5105510 4982580 FALSE TRUE 4150506.59 4195398.897 4029793.215 4089943.11 4299889.635 4279315.664 4527357.261 4589203.082 4525953.909 4645105.419 0.893522583 0.903187015 0.867535363 0.880484454 0.925681819 0.921252647 0.974651134 0.987965324 0.974349019 1 22.14727991 2.444020688 1.171633536 0.99081468 0.88689287 0.908648 0.013730337 0.13015485 0.358560859 0.008126943 0.005627477 277.9845684 -2.444020688 -0.103921811 KAEVEGK ddPTM_BT-474_Pertuzumab_2h_R1 5 KAEVEGK 7 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;; 109.71 0.01117 16008420000 18891400 13898900 13191730 12308120 13545900 14720100 15738300 16571500 15490700 17109300 FALSE TRUE 18153103.2 13502516.98 15575769.06 12943343.55 13981616.18 15017750.51 15930910.02 16229292.73 13732260.68 15950471.87 1.138091923 0.846527745 0.976508356 0.811470886 0.876564423 0.941523902 0.998773588 1.017480415 0.860931312 1 23.92709577 2.444302752 7.212458292 0.976206053 0.920014543 0.031743603 0.092676521 0.541378082 89.72657615 0.031153583 0.026222478 278.1651714 -2.444302752 -0.05619151 GVPAGNS(ph)DTEGGQPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVPAGNSDTEGGQPGR 16 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 GVPAGNS(0.824)DT(0.176)EGGQPGR;GVPAGNS(0.999)DT(0.001)EGGQPGR 234.04 1.20E-19 1327600000 972182 976850 844060 937500 913710 1033000 1017520 1092745 1274140 1114020 TRUE FALSE 934188.0526 948991.1944 996600.418 985884.4874 943100.312 1053887.968 1029972.714 1070179.434 1129504.969 1038566.433 0.899497637 0.913751075 0.959592363 0.949274361 0.908078946 1.01475258 0.991725403 1.030439074 1.087561597 1 19.98616207 2.444534737 1.131417198 1.041685214 0.924949795 0.715326526 0.030676039 0.261203058 0.670358962 0.018139312 0.01250257 278.3137973 -2.444534737 -0.116735419 VLNT(ph)GSDVEEAVADALK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.5)GS(0.5)DVEEAVADALK 84.874 0.019044 4415400 15731 13720 12866 12949 14236 14847 17241 16412 20393 15368 TRUE FALSE 15116.21513 13328.71903 15191.1724 13617.29944 14693.91387 15147.21651 17452.00052 16073.08646 18078.07213 14327.11167 1.055077637 0.930314451 1.060309485 0.950456711 1.025601964 1.057241464 1.218110176 1.121865093 1.261808559 1 13.80646017 2.446148317 3.905629861 1.158348653 1.002495945 0.456916068 0.07462188 0.172121062 5.765576371 0.024340729 0.020688505 279.3497694 -2.446148317 -0.155852707 QDLPSLDEKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 QDLPSLDEKPR 11 1 Q92598-2;Q92598;Q92598-4;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 216.83 1.08E-11 5091880000 3558080 3474400 3107550 3394340 3505350 3873050 4174940 4300720 4991080 4781920 FALSE TRUE 3419026.3 3375313.514 3669153.412 3569522.294 3618102.766 3951365.725 4226034.165 4211908.629 4424513.523 4458036.299 0.7669355 0.75713011 0.823042516 0.80069386 0.811591141 0.886346692 0.947958671 0.944790115 0.992480372 1 22.08797693 2.44733437 0.744972642 0.998964068 0.770462576 0.957255105 0.018203923 0.128213966 0.142867145 0.014552539 0.010754607 280.1137127 -2.44733437 -0.228501493 HSTPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSTPSPTR 8 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 HS(0.003)T(0.036)PS(0.795)PT(0.166)R 63.426 0.076977 7634500 15670 14980 13238 14591 13899 11441 15013 10024 12331 13846 TRUE FALSE 15057.59908 14552.78507 15630.40108 15344.04326 14346.07396 11672.34486 15196.73358 9817.000897 10931.23658 12908.19809 1.16651441 1.127406395 1.210889465 1.188705283 1.111392455 0.904258269 1.177293181 0.7605245 0.846844502 1 13.656 2.448040672 1.000104903 0.873611818 1.17571893 0.53235375 0.104489797 0.386050945 0.772552392 0.066621181 0.045727239 280.5696382 -2.448040672 0.302107113 S(ph)GSSPGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.42)GS(0.29)S(0.29)PGLR;S(0.491)GS(0.31)S(0.199)PGLR 105.57 0.0045765 151220000 297900 289589 259644 298628 272365 301040 354100 339060 357940 338740 TRUE FALSE 286257.7387 281330.2053 306567.4465 314040.2269 281125.8676 307127.2351 358433.5817 332058.2925 317308.1518 315796.8381 0.9064617 0.890858208 0.970774275 0.994437528 0.890211154 0.972546897 1.135013206 1.051493405 1.004785715 1 18.2686372 2.44834023 11.40734123 1.054916607 0.933847863 0.585812734 0.046360781 0.435774665 170.474039 0.016229562 0.013604111 280.7632298 -2.44834023 -0.121068744 VAPEEHPVLLTEAPLNPK ddPTM_BT-474_Pertuzumab_2h_R1 8 VAPEEHPVLLTEAPLNPK 18 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;; 319.33 1.72E-61 77251650000 19822692 19736360 16627537 17892170 18531612 19343654 20277773 20737385 22940766 22336451 FALSE TRUE 19047999.28 19173498.34 19632502.81 18815587.04 19127698.13 19734795.94 20525938.45 20309150.75 20336626.42 20823583.28 0.914732063 0.920758838 0.942801369 0.903571051 0.918559398 0.947713738 0.985706359 0.975295677 0.976615127 1 24.31171501 2.448646929 2.82157991 0.981954617 0.92060691 0.877071614 0.01130849 0.089744619 1.463249711 0.004246866 0.003559135 280.9615752 -2.448646929 -0.061347706 AS(ph)PDS(ph)SSCGERSPPPPPPPPSDEALLHCVLEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPDSSSCGERSPPPPPPPPSDEALLHCVLEGK 33 1 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 2 AS(0.999)PDS(0.393)S(0.273)S(0.169)CGERS(0.166)PPPPPPPPSDEALLHCVLEGK 138.78 6.10E-09 64761000 27678 21846 23559 23070 20910 24802 36851 29748 32288 25786 TRUE FALSE 26596.31316 21222.97347 27816.63537 24260.64546 21582.58914 25303.51343 37301.99356 29133.6934 28622.8016 24039.49125 1.106359235 0.882837879 1.157122465 1.009199621 0.89779725 1.05258107 1.551696464 1.211909732 1.190657544 1 14.55311874 2.449842998 24.99920018 1.267043325 1.007974293 0.34293865 0.148639976 202.7145304 185776.975 0.04885023 0.04087189 281.7364241 -2.449842998 -0.259069033 AVTSGLPGDTALLLPPS(ph)PRPSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVTSGLPGDTALLLPPSPRPSPR 23 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;Q6W2J9-3 H7BYY2 BCOR BCL-6 corepressor 1 AVTSGLPGDTALLLPPS(0.997)PRPS(0.003)PR 100.7 3.66E-05 0 56064 85187 60991 76763 69147 65015 56913 58459 60288 68285 TRUE FALSE 53872.9569 82757.55017 72013.43044 80724.74763 71371.17605 66329.64785 57609.51832 57251.80122 53444.35899 63659.99613 0.846260763 1.299993013 1.131219523 1.268060832 1.1211307 1.041936096 0.904956359 0.899337177 0.839528153 1 15.95809945 2.45090514 2.296959641 0.899343866 1.150439647 0.42911127 0.119856493 0.252523713 2.710006161 0.045180139 0.036934674 282.4263022 -2.45090514 0.251095781 AAPAQVRPPS(ph)PGNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAPAQVRPPSPGNIR 15 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AAPAQVRPPS(1)PGNIR 69.024 0.030819 262150000 131700 135890 148250 100340 133740 128460 123880 124560 127500 130550 TRUE FALSE 126553.0184 132014.5503 175042.0728 105518.5594 138041.8686 131057.5492 125396.0805 121987.7925 113026.7345 121707.7322 1.039810833 1.08468499 1.438216534 0.866983202 1.134207877 1.076821882 1.030304963 1.002301088 0.928673409 1 16.8930613 2.451318245 0.72484103 0.96718927 1.14012461 0.173084812 0.132455381 1.214399596 1.283920791 0.102398541 0.077068245 282.6950768 -2.451318245 0.17293534 QYDISDPQRPR ddPTM_BT-474_Pertuzumab_2h_R1 5 QYDISDPQRPR 11 1 Q13228;Q13228-4;Q13228-2;Q13228-3;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;; 112.64 0.0013664 3777810000 3464060 3863320 3079490 3231370 3387340 3202490 2609060 3029870 3115140 3190690 FALSE TRUE 3328680.705 3753141.896 3636022.346 3398141.393 3496296.867 3267246.542 2640990.457 2967302.126 2761522.367 2974581.724 1.119041604 1.261737698 1.222364246 1.142393018 1.175391094 1.098388562 0.887852714 0.997552732 0.928373339 1 21.50425539 2.451355695 3.603245014 0.956001716 1.186352166 0.833134452 0.048531534 0.086346105 2.4058129 0.017239402 0.014680933 282.7194551 -2.451355695 0.23035045 RPQT(ph)PPKIDYLLPGPGPAHS(ph)PQPSKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPQTPPKIDYLLPGPGPAHSPQPSKR 26 3 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 2 RPQT(0.999)PPKIDY(0.001)LLPGPGPAHS(0.906)PQPS(0.094)KR;RPQT(0.999)PPKIDY(0.001)LLPGPGPAHS(0.93)PQPS(0.07)KR 76.519 0.01429 1115430000 534290 451400 419860 414360 420820 493010 546920 527350 653970 606080 TRUE FALSE 513409.3561 438526.514 495738.0417 435745.1693 434356.0575 502979 553613.3706 516460.0382 579734.0673 565029.6618 0.908641423 0.776112377 0.877366403 0.771189902 0.768731426 0.890181585 0.979795236 0.914040577 1.02602413 1 19.10796708 2.4517528 3.864987078 0.966014758 0.818547905 0.681378043 0.050967423 0.132954342 4.384861648 0.017675873 0.015079202 282.978083 -2.4517528 -0.147466853 QAAAQPHTEIPEGTTAEEAGIGDTPS(ph)LEDEAAGHVTQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQAR 39 0 P10636-8;P10636-5 P10636-8 MAPT Microtubule-associated protein tau 1 QAAAQPHTEIPEGTTAEEAGIGDT(0.005)PS(0.995)LEDEAAGHVTQAR;QAAAQPHTEIPEGTTAEEAGIGDT(0.004)PS(0.995)LEDEAAGHVT(0.001)QAR 162.72 8.43E-18 230810000 35636 40692 30415 32814 31132 33207 28158 24887.8 30183 30628 TRUE FALSE 34243.30572 39531.504 35911.66708 34507.53447 32133.38905 33878.46829 28502.60603 24373.85823 26756.75238 28553.53828 1.199266633 1.38446954 1.257695867 1.208520434 1.125373281 1.186489323 0.998216254 0.853619541 0.937073091 1 14.80138191 2.452332045 1.05089045 0.903009796 1.27269249 0.793293492 0.070563408 0.210688017 0.466339516 0.045150353 0.031150486 283.3557595 -2.452332045 0.369682694 NEDEMMVAIFEYIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEDEMMVAIFEYIDR 15 0 Q9H0D6 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 105.14 0.0031141 265320000 16600 17007 13139 13872 14958 19593 20890 30744 21497 17703 FALSE TRUE 15951.25365 16521.97701 15513.50958 14587.93558 15439.13765 19989.18388 21145.65807 30109.12566 19056.75068 16503.96004 0.96651068 1.001091676 0.939987102 0.883905169 0.935480795 1.211175005 1.281247532 1.824357644 1.154677461 1 14.01052461 2.45255956 2.299738916 1.432083841 0.945122061 0.373786028 0.210252481 0.239405362 2.574777093 0.083028272 0.067973636 283.504241 -2.45255956 -0.48696178 LDS(ph)SEMDHS(ph)ENEDYTMSSPLPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 LDS(0.559)S(0.559)EMDHS(0.862)ENEDY(0.008)T(0.009)MS(0.002)S(0.001)PLPGK 49.66 0.073291 102830000 104530 80718 62116 109900 95074 79321 68421 72582 75148 74986 TRUE FALSE 100444.852 78416.00167 73341.74296 115571.9522 98132.14155 80924.92497 69258.35667 71083.15634 66617.51409 69907.13143 1.436832695 1.12171677 1.049131061 1.653221207 1.403750083 1.157606146 0.990719477 1.016822674 0.952943036 1 16.09315202 2.452686197 3.433107414 0.995152477 1.321987964 0.511886325 0.157370274 0.219443937 5.473276169 0.060557005 0.051532004 283.5869207 -2.452686197 0.326835487 RGDALIEMESEQDVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGDALIEMESEQDVQK 16 1 H0Y8R1;F5H5I6;H0YAK1;Q12849;Q12849-5;H0YAM1 H0Y8R1 GRSF1 G-rich sequence factor 1 0 114.99 0.00086697 249410000 109320 112920 98368 137850 97995 119480 175030 145240 139240 129340 FALSE TRUE 105047.6535 109699.6322 116145.2858 144964.455 101147.0982 121895.9675 177172.0695 142240.7432 123434.0589 120579.6866 0.871188643 0.909768762 0.963224313 1.202229489 0.838840281 1.010916274 1.469335959 1.17964101 1.023672083 1 16.87962736 2.452991266 24.99205538 1.198873195 0.964036605 0.297532691 0.150911343 251.1559176 260127.2094 0.051867375 0.043397146 283.7861958 -2.452991266 -0.23483659 MRPGAYSTGYGGYEEYSGLSDGYGFTTDLFGR ddPTM_BT-474_Pertuzumab_2h_R1 1 MRPGAYSTGYGGYEEYSGLSDGYGFTTDLFGR 32 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 157.65 1.34E-11 432380000 195070 188630 138080 177150 192420 167400 151920 153740 190490 175850 FALSE TRUE 187446.4487 183250.4571 163034.1276 186292.7327 198609.3641 170784.9427 153779.2424 150565.2153 168866.3738 163939.5229 1.14338779 1.117793037 0.99447726 1.136350341 1.211479456 1.041755763 0.938024216 0.91841926 1.030052856 1 17.32280418 2.453257928 5.08407103 0.960766179 1.115805941 0.590446977 0.058180065 0.128430656 9.004620726 0.021296055 0.018167539 283.9604975 -2.453257928 0.155039762 LALS(ph)PLSLGK ddPTM_BT-474_Pertuzumab_2h_R1 4 LALSPLSLGK 10 0 P49454 P49454 CENPF Centromere protein F 1 LALS(0.999)PLS(0.001)LGK;LALS(1)PLSLGK;LALS(1)PLSLGK;LALS(0.999)PLS(0.001)LGK 160.52 7.71E-06 1633844000 2352671 2229307 2218648 2371846 2226413 2429440 2740888 2797924 2487912 2931466 TRUE FALSE 2260726.016 2165729.347 2619607.047 2494257.256 2298027.596 2478564.941 2774431.807 2740145.892 2205494.66 2732915.197 0.82722143 0.792461233 0.958539456 0.91267276 0.840870437 0.906930791 1.015191328 1.002645781 0.807011744 1 21.38200926 2.453701895 7.956810192 0.963402579 0.870282191 0.267369803 0.069558518 0.258231027 69.47560114 0.024585048 0.020766913 284.2509302 -2.453701895 -0.093120388 ATSTS(ph)PNSQSSK ddPTM_BT-474_Pertuzumab_2h_R1 8 ATSTSPNSQSSK 12 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 ATST(0.027)S(0.973)PNSQSSK;ATST(0.02)S(0.979)PNS(0.001)QSSK;ATST(0.007)S(0.993)PNSQSSK;ATST(0.001)S(0.998)PNS(0.001)QSSK;ATS(0.001)T(0.028)S(0.97)PNSQSSK;ATST(0.006)S(0.993)PNS(0.001)QSSK;ATS(0.002)T(0.013)S(0.984)PNS(0.002)QSSK;ATSTS(0.973)PNS(0.026)QS(0.001)SK 315.43 2.05E-46 7321336000 10665240 9979160 8413190 9523810 9194360 9770880 10848540 10568850 10291370 11954250 TRUE FALSE 10248430.63 9694564.127 9933640.583 10015334.98 9490104.94 9968453.888 10981307.68 10350599.55 9123136.823 11144578 0.919588936 0.869890643 0.89134291 0.898673326 0.851544575 0.894466698 0.985349798 0.928756527 0.818616624 1 23.40983865 2.453813295 24.95744306 0.930784486 0.884951951 0.178230035 0.048089125 401.828362 430263.1026 0.016259743 0.013604575 284.3238526 -2.453813295 -0.045832534 TTPPPGAQCEVPASPQRPSRPGALPEQT(ph)RPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPPPGAQCEVPASPQRPSRPGALPEQTRPLR 32 3 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 TTPPPGAQCEVPAS(0.254)PQRPS(0.017)RPGALPEQT(0.729)RPLR 143.88 5.49E-10 3802100000 96505 114690 99086 91368 94406 108540 164990 123170 131000 165990 TRUE FALSE 92733.47791 111419.1535 116993.0444 96083.51343 97442.65473 110734.7532 167009.197 120626.4965 116129.4292 154747.3495 0.599257294 0.720006862 0.75602616 0.620905714 0.629688683 0.715584167 1.079237852 0.779506059 0.750445352 1 17.23955517 2.454142168 24.88093308 0.881923462 0.670993259 0.558082397 0.099822173 178.7132111 193503.0947 0.034306477 0.028704461 284.5392409 -2.454142168 -0.210930203 HGS(ph)GPPSSGGGLYR ddPTM_BT-474_Pertuzumab_2h_R1 3 HGSGPPSSGGGLYR 14 0 Q9HC52 Q9HC52 CBX8 Chromobox protein homolog 8 1 HGS(1)GPPSSGGGLYR;HGS(0.696)GPPS(0.255)S(0.049)GGGLYR;HGS(1)GPPSSGGGLYR 159.14 3.20E-06 1082130000 323198 309417 269588 256942 282999 252640 258165 186178 276923 244460 TRUE FALSE 310567.0648 300592.7301 318308.5486 270202.8074 292101.9198 257748.5539 261324.5005 182333.3592 245487.862 227902.5065 1.362718952 1.318953156 1.396687353 1.185607002 1.281696829 1.130959716 1.146650401 0.80004982 1.077161747 1 17.79805727 2.454783923 1.066170145 0.940614669 1.332161675 0.724750429 0.090853443 0.244012076 0.556348408 0.055573619 0.038468646 284.9600136 -2.454783923 0.391547006 TTPATGEQS(ph)PGAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TTPATGEQSPGAR 13 0 O00308-2;O00308;O00308-4 O00308-2 WWP2 NEDD4-like E3 ubiquitin-protein ligase WWP2 1 TTPATGEQS(1)PGAR;TTPATGEQS(1)PGAR;TTPATGEQS(1)PGAR 167.37 3.36E-05 828230000 531692 554160 431591 515425 504475 549681 622470 607768 658730 698770 TRUE FALSE 510912.8888 538355.8994 509589.0944 542026.146 520701.8965 560795.9264 630087.9741 595217.3784 583953.732 651441.6855 0.784280313 0.826406893 0.782248213 0.83204093 0.799306996 0.86085361 0.96722084 0.913692494 0.896402157 1 19.31327651 2.454836089 3.709580616 0.935399089 0.80718621 0.816749929 0.030954351 0.093361469 2.796942057 0.010533063 0.008997986 284.994244 -2.454836089 -0.128212878 ARS(ph)PSVAAMASPQLCR ddPTM_BT-474_Pertuzumab_2h_R1 12 ARSPSVAAMASPQLCR 16 1 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 ARS(0.977)PS(0.023)VAAMASPQLCR;ARS(0.989)PS(0.011)VAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(0.998)PS(0.002)VAAMASPQLCR;ARS(0.997)PS(0.003)VAAMASPQLCR;ARS(0.994)PS(0.006)VAAMASPQLCR;ARS(0.989)PS(0.011)VAAMASPQLCR;ARS(0.996)PS(0.004)VAAMASPQLCR;ARS(0.977)PS(0.023)VAAMASPQLCR;ARS(0.985)PS(0.015)VAAMASPQLCR;ARS(0.968)PS(0.032)VAAMASPQLCR 230.24 1.48E-15 13786370000 3053077 3121357 2405182 2717380 2857805 2737021 2831965 2834312 3000268 2965828 TRUE FALSE 2933759.375 3032338.954 2839851.89 2857624.307 2949728.893 2792365.44 2866623.435 2775782.467 2659690.155 2764949.828 1.061053385 1.096706683 1.027089845 1.033517599 1.066829084 1.00991541 1.036772315 1.003917843 0.961930711 1 21.39882187 2.455002602 0.537259944 0.982872562 1.069846483 0.605327418 0.023043074 0.629629733 0.375799799 0.020773553 0.020023741 285.1035351 -2.455002602 0.086973921 TIGGGDDS(ph)FNTFFSETGAGK ddPTM_BT-474_Pertuzumab_2h_R1 6 TIGGGDDSFNTFFSETGAGK 20 0 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;F8VRK0;F8W0F6;F8VXZ7;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 1 TIGGGDDS(0.998)FNT(0.002)FFSETGAGK;TIGGGDDS(0.999)FNT(0.001)FFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(0.999)FNT(0.001)FFSETGAGK;TIGGGDDS(0.989)FNT(0.011)FFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK 365.27 6.00E-112 2208275000 2449662 2164672 2308943 2333421 2494854 2678155 2421448 3285122 3343042 3217308 TRUE FALSE 2353926.501 2102937.674 2726220.362 2453849.137 2575103.245 2732309.129 2451082.405 3217283.083 2963553.887 2999396.863 0.784799947 0.701120182 0.908922856 0.818114191 0.858540354 0.910952853 0.817191761 1.072643344 0.988049939 1 21.51624099 2.455220426 0.540944721 1.035765206 0.768116407 0.605912179 0.067001319 0.590336506 0.35688502 0.060350408 0.057774171 285.2465666 -2.455220426 -0.267648799 TATYNGPPAS(ph)PSLSHEATPLSQTR ddPTM_BT-474_Pertuzumab_2h_R1 4 TATYNGPPASPSLSHEATPLSQTR 24 0 H0YIY6;P27448-6;P27448-7;A2SY06;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 TATYNGPPAS(1)PSLSHEATPLSQTR;TATYNGPPAS(1)PSLSHEATPLSQTR;TATYNGPPAS(0.995)PS(0.005)LSHEATPLSQTR;TATYNGPPAS(1)PSLSHEATPLSQTR 362.41 4.67E-103 2073360000 586560 680030 580860 699960 652550 641520 619450 683370 644580 704710 TRUE FALSE 563636.5867 660636.2102 685834.3232 736085.0195 673539.8634 654491.9739 627031.0144 669258.1707 571409.9807 656979.364 0.857921295 1.005566151 1.043920648 1.120408128 1.025207031 0.996213899 0.954415083 1.018689791 0.869753316 1 19.32548853 2.455432697 4.219231217 0.968193292 1.017899268 0.091409516 0.071025474 0.54685049 22.74562392 0.025841888 0.022120393 285.3860216 -2.455432697 0.049705976 DGHRYS(ph)RS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGHRYSRSPAR 11 2 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 2 DGHRY(0.019)S(0.99)RS(0.99)PAR 67.136 0.032608 313550000 29055 32694 25811 40286 42538 27819 22321 19056 29153 27272 TRUE FALSE 27919.49848 31761.59913 30475.62186 42365.16529 43906.2734 28381.51924 22594.17107 18662.48694 25843.67366 25424.84315 1.098118809 1.249234811 1.198655256 1.666290134 1.726904396 1.116290829 0.888665112 0.734025647 1.016473278 1 14.63395125 2.456700103 4.446537145 0.877973831 1.389504601 0.563897363 0.197374054 0.150718389 7.265433196 0.075848718 0.064987087 286.2200828 -2.456700103 0.51153077 KDIHFMPCSGLTGANLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDIHFMPCSGLTGANLK 17 1 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 177.74 6.56E-10 1530420000 2489770 2465810 1996690 1968150 1992360 2235350 2486700 2276810 2628700 2785600 FALSE TRUE 2392467.036 2395487.513 2357536.299 2069726.457 2056446.069 2280550.309 2517132.978 2229793.078 2330300.996 2596928.831 0.921267848 0.922430944 0.907817061 0.796990057 0.791876175 0.878172047 0.969272992 0.858626949 0.897329557 1 21.30837505 2.457379542 24.74248662 0.915896103 0.865921619 0.205102559 0.056385331 446.4338759 559516.3442 0.020922372 0.017507062 286.6682151 -2.457379542 -0.049974484 SPMSTNSSVHTGS(ph)DVEQDAEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPMSTNSSVHTGSDVEQDAEKK 22 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 SPMSTNSSVHT(0.003)GS(0.997)DVEQDAEKK;SPMSTNSSVHTGS(1)DVEQDAEKK 189.66 9.65E-18 458310000 286640 268170 211947 215472 252390 266100 287830 294200 355870 294660 TRUE FALSE 275437.7919 260522.0542 250250.5376 226592.5357 260508.3536 271480.7243 291352.5496 288124.6672 315473.1295 274702.4157 1.002676992 0.948379189 0.910987757 0.824865464 0.948329314 0.988272067 1.060611531 1.048861061 1.148417748 1 18.06751007 2.457941862 2.045162774 1.069231565 0.920998952 0.593276409 0.053645628 0.225138434 1.913358638 0.022831074 0.018364648 287.0396302 -2.457941862 -0.148232613 TS(ph)PYILR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.346)S(0.654)PYILR;T(0.013)S(0.987)PYILR;T(0.034)S(0.966)PYILR 185.55 0.00064179 959290000 2225740 2014900 2029250 2007160 1959480 2221660 2259110 2589540 2217190 2693550 TRUE FALSE 2138755.62 1957437.025 2395980.615 2110749.768 2022508.454 2266583.487 2286757.664 2536065.094 1965503.886 2511113.459 0.851716043 0.779509591 0.95415068 0.840563281 0.805422967 0.902620899 0.910654855 1.009936482 0.782722055 1 21.25989578 2.458291117 3.225438754 0.934654059 0.848293055 0.212178104 0.071874468 0.361452697 7.848827711 0.025475892 0.021696726 287.2705576 -2.458291117 -0.086361005 RLS(ph)MENEELLWK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSMENEELLWK 12 1 Q9ULD2;Q9ULD2-2;Q9ULD2-4;Q9ULD2-7;Q9ULD2-3;Q9ULD2-6 Q9ULD2 MTUS1 Microtubule-associated tumor suppressor 1 1 RLS(1)MENEELLWK 70.942 0.028128 73119000 115790 119930 93747 115470 106460 103480 116590 93613 124130 120230 TRUE FALSE 111264.7988 116509.7138 110689.1683 121429.4205 109884.3826 105572.4365 118016.8633 91679.85884 110039.2828 112086.715 0.99266714 1.039460509 0.987531558 1.083352479 0.98035153 0.941881797 1.05290679 0.817936888 0.981733498 1 16.77425577 2.458776838 1.282119717 0.929668732 1.021543516 0.142689498 0.063655812 0.604310305 2.00323165 0.033863827 0.024228321 287.5920242 -2.458776838 0.091874784 THYDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 THYDAK 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 71.378 0.08839 542700000 368030 351730 270900 332610 343550 293470 345180 246580 372920 377290 FALSE TRUE 353646.9807 341699.0048 319857.6561 349776.042 354600.5978 299404.1645 349404.4161 241488.0368 330587.685 351735.8122 1.005433534 0.971464926 0.909369035 0.994428289 1.008144708 0.851218881 0.993371741 0.686560846 0.939874967 1 18.42413271 2.459281653 1.808281398 0.85634584 0.972862752 0.089112487 0.091651124 0.511619045 3.398109746 0.039388911 0.030839447 287.9265101 -2.459281653 0.116516912 S(ph)RSSS(ph)PVT(ph)ELASR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSSSPVTELASR 13 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.996)RS(0.128)S(0.436)S(0.837)PVT(0.604)ELASR 115.83 0.0045564 313700000 126450 117610 91212 117100 106970 121150 119040 136730 140930 122750 TRUE FALSE 121508.1942 114255.878 107696.0374 123143.545 110410.7872 123599.736 120496.8471 133906.4777 124932.2172 114436.0332 1.061800124 0.998425713 0.941102504 1.076090648 0.964825363 1.080077075 1.052962461 1.170142603 1.091720971 1 16.80418187 2.459560297 2.28870237 1.101746998 1.008064641 0.233752253 0.056585169 0.325612862 3.464268825 0.021607852 0.017769125 288.1113033 -2.459560297 -0.093682358 KTQDQISNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTQDQISNIK 10 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 176.18 4.13E-06 4649800000 8743400 8616900 7168200 7527200 8564300 8818500 9098300 10050700 10470600 10658900 FALSE TRUE 8401698.262 8371154.449 8463653.196 7915679.694 8839778.487 8996816.112 9209647.717 9843149.533 9282021.384 9936963.209 0.845499584 0.842425827 0.85173438 0.796589413 0.88958551 0.905388892 0.926807066 0.99055912 0.934090344 1 23.24437359 2.45996925 1.122742738 0.97618571 0.836128455 0.840256045 0.025118733 0.176083311 0.446120831 0.014529224 0.010160951 288.3827307 -2.45996925 -0.140057255 EKEQEDRR ddPTM_BT-474_Pertuzumab_2h_R1 7 EKEQEDRR 8 2 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 172.23 0.00016016 3225021000 4189759 3895981 3018958 3453875 3431097 3719282 3985628 4070009 4233565 4147341 FALSE TRUE 4026018.586 3784871.436 3564550.867 3632129.903 3541461.351 3794488.43 4034405.308 3985961.892 3752988.45 3866437.9 1.041273309 0.978903977 0.921921148 0.939399519 0.915949368 0.981391278 1.043442417 1.030913206 0.970657889 1 21.88257361 2.460149225 9.018631311 1.016267009 0.956489656 0.291516952 0.0375758 0.245870456 113.0000567 0.013599684 0.011514019 288.5022635 -2.460149225 -0.059777353 SRPTSEGS(ph)DIESTEPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 1 S(0.034)RPT(0.191)S(0.191)EGS(0.583)DIESTEPQK;SRPT(0.135)S(0.267)EGS(0.597)DIESTEPQK 236.04 2.15E-20 4221800000 2440200 2184700 1891920 2002860 1963450 2209300 2356800 2538000 2477900 2339400 TRUE FALSE 2344834.286 2122394.495 2233832.03 2106227.845 2026606.152 2253973.56 2385643.223 2485589.413 2196619.18 2180950.354 1.075143357 0.973151219 1.024247079 0.965738555 0.929230759 1.033482287 1.093854896 1.139681794 1.007184403 1 21.0565255 2.460689158 5.776192662 1.078615636 0.991365741 0.232942218 0.053120586 0.178580525 20.18835485 0.018388752 0.015753266 288.8611644 -2.460689158 -0.087249895 EAPS(ph)PLMIHSPQMSQFQSLT(ph)HQSPPQQNVQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 2 EAPS(0.95)PLMIHS(0.05)PQMS(0.225)QFQS(0.167)LT(0.376)HQS(0.231)PPQQNVQPK 63.73 0.018342 207310000 29395 32118 25149 29697 30406 29352 25663 31101 32748 30838 TRUE FALSE 28246.2109 31202.02609 29693.98374 31229.66573 31384.0366 29945.51755 25977.07147 30458.75348 29030.58433 28749.31479 0.982500317 1.085313731 1.032858833 1.086275132 1.091644682 1.041608044 0.903571847 1.059460154 1.009783521 1 14.81123995 2.460723264 24.99496249 0.997753923 1.058673944 0.285349506 0.046749431 312.4283754 476221.8713 0.01580147 0.013223247 288.8838503 -2.460723264 0.060920021 WAHDKFS(ph)GEEGEIEDDESGTENREEK ddPTM_BT-474_Pertuzumab_2h_R1 2 WAHDKFSGEEGEIEDDESGTENREEK 26 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENREEK;WAHDKFS(1)GEEGEIEDDESGTENREEK 206 1.66E-25 888180000 561660 467640 361400 325450 425930 436590 495410 425000 601790 492900 TRUE FALSE 539709.7063 454303.3651 426713.0193 342246.5135 439630.4253 445418.1489 501472.9758 416223.6015 533477.3221 459515.444 1.174519188 0.988657446 0.928615186 0.744798718 0.956726115 0.96932139 1.091308208 0.905788058 1.16095624 1 18.80975382 2.460730834 24.24777627 1.021556986 0.948403428 0.090921601 0.115251454 477.2337769 706006.9883 0.041219612 0.03449687 288.8888857 -2.460730834 -0.073153558 LELMDIIAENVLSEDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LELMDIIAENVLSEDRR 17 1 A0A2R8YF87;Q96AX1;H3BMM5;F5H6Y0 A0A2R8YF87 VPS33A Vacuolar protein sorting-associated protein 33A 0 87.148 0.005251 69129000 35331 37702 36385 35553 42008 37304 32401 38210 40659 38515 FALSE TRUE 33950.22546 36626.77587 42960.57888 37387.89459 43359.22547 38058.31244 32797.53313 37420.95015 36043.56078 35906.34474 0.945521626 1.020064173 1.196462051 1.041261506 1.207564451 1.059932798 0.913418878 1.042182111 1.003821498 1 15.13195117 2.462080721 24.49870086 0.99461146 1.087895324 0.234244025 0.078817857 278.1687728 453090.1581 0.027488146 0.023006237 289.7882157 -2.462080721 0.093283865 KMEENEK ddPTM_BT-474_Pertuzumab_2h_R1 4 KMEENEK 7 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 131.06 0.0056162 831980000 1183490 1042650 926820 993980 1096230 1167910 1352900 1376830 1545990 1505190 FALSE TRUE 1137237.902 1012914.643 1094316.991 1045279.427 1131491.234 1191525.94 1369457.195 1348397.979 1370495.697 1403242.141 0.810435968 0.721838814 0.779849008 0.744903105 0.806340688 0.849123545 0.975923652 0.96091611 0.976663725 1 20.42033255 2.462567795 1.625491652 0.981005928 0.763299729 0.932684796 0.026071919 0.080064101 0.429133187 0.011199144 0.008554934 290.1134044 -2.462567795 -0.217706199 LASLSS(ph)HVTELEEDLDTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 LAS(0.319)LS(0.319)S(0.361)HVTELEEDLDTAR 75.646 0.0090836 7135700 5115 6706.3 6583.5 6269.7 6264 5532.9 5192.5 4603.4 6656.1 4335.1 TRUE FALSE 4915.100145 6515.04289 7773.284899 6593.279968 6465.487249 5644.779029 5256.047368 4508.338181 5900.527433 4041.479816 1.216163477 1.612043902 1.923375905 1.631402424 1.599782145 1.396710929 1.300525453 1.115516689 1.45999181 1 11.98066793 2.46324027 1.847037483 1.206748278 1.621598945 0.460042778 0.193586203 0.308439447 2.136783451 0.084822164 0.066989455 290.5629726 -2.46324027 0.414850667 AVQDLCGWR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVQDLCGWR 9 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 93.701 0.021452 227940000 125030 113390 100650 109810 114640 118440 138020 127320 137240 148100 FALSE TRUE 120143.6894 110156.2282 118839.6939 115477.3073 118327.4997 120834.9379 139709.13 124690.7975 121661.0906 138069.0551 0.870171012 0.797834302 0.860726496 0.836373561 0.8570168 0.875177554 1.011878657 0.903104591 0.881161173 1 17.07503048 2.463363238 23.77053647 0.939949441 0.844674752 0.588687334 0.041129632 96.08766726 166014.2495 0.013949914 0.01167806 290.6452556 -2.463363238 -0.095274689 QNPHDGVVT(ph)PAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 QNPHDGVVTPAASPSLPQPGLQMPGQWGPVQGGPQPSGQHR 41 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 QNPHDGVVT(1)PAAS(0.997)PS(0.003)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.903)PS(0.097)LPQPGLQMPGQWGPVQGGPQPSGQHR 170.53 1.28E-19 1433670000 106981 94413 72478 94720 105575 79694 59445 71847 71899 65935 TRUE FALSE 102800.0642 91720.43368 85576.38686 99608.51055 108970.9158 81305.46728 60172.50569 70363.33434 63737.32695 61469.16372 1.672384298 1.492137328 1.39218401 1.620463083 1.772773683 1.322703326 0.978905553 1.14469321 1.036899204 1 15.90757524 2.463640901 4.472764663 1.063487662 1.57501818 0.857174516 0.105446106 0.076326919 3.814793598 0.038603651 0.033267378 290.8311371 -2.463640901 0.511530518 SIDDLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIDDLEEK 8 0 H7BYY1;P09493-2;P09493-3;Q6ZN40;P09493-9;P09493-8;P09493-7 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ; 122.52 0.0032269 439270000 509430 507950 413000 442140 514600 522610 507870 589900 648120 590850 FALSE TRUE 489520.9124 493463.7633 487638.2871 464958.8984 531152.5763 533177.5323 514085.465 577718.3589 574548.1347 550831.2032 0.888694957 0.895852959 0.885277167 0.844104139 0.964274669 0.967950852 0.933290384 1.048811969 1.043056623 1 19.07125076 2.463891227 0.893462011 1.032439765 0.880837587 0.746660821 0.03328801 0.285504255 0.457523548 0.023514196 0.01656734 290.9988194 -2.463891227 -0.151602178 VKEEIIEAFVQELR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKEEIIEAFVQELR 14 1 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 197.88 2.08E-08 986970000 1534160 1434520 1368100 1463450 1537880 1629330 1564840 1808580 2109100 1925630 FALSE TRUE 1474203.331 1393608.894 1615346.103 1538978.83 1587347.307 1662276.169 1583990.98 1771232.191 1869683.81 1795205.365 0.821189241 0.77629497 0.899811317 0.857271742 0.884214886 0.925953209 0.88234528 0.986645999 1.041487423 1 20.77571746 2.464016321 0.471132367 1.027955985 0.803899898 0.778269469 0.036937963 0.488848767 0.228691359 0.035919246 0.040235768 291.0826503 -2.464016321 -0.224056086 AINCATSGVVGLVNCLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AINCATSGVVGLVNCLR 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 202.25 4.08E-17 95095000 141464 140018 116680 111485 129877 133008 157033 147918 131106 157249 FALSE TRUE 135935.4305 136024.8237 137766.6715 117238.7542 134054.6117 135697.5129 158954.8168 144863.4416 116223.3965 146598.3852 0.927264174 0.927873957 0.939755724 0.79972746 0.914434436 0.925641253 1.084287638 0.98816533 0.792801342 1 17.16150969 2.464107037 24.94720372 0.97614056 0.901729987 0.130115009 0.077052128 413.8446509 793301.4289 0.027160223 0.022735372 291.1434588 -2.464107037 -0.074410573 LREDENAEPVGTTYQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LREDENAEPVGTTYQK 16 1 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 ;;; 204.26 2.34E-11 8126440000 3249560 3237890 2801190 3224120 2925670 3300700 3527890 3559800 3977420 3834820 FALSE TRUE 3122563.603 3145548.547 3307427.345 3390517.22 3019776.833 3367442.415 3571065.373 3486288.886 3525919.956 3575084.226 0.873423787 0.879852991 0.925132706 0.948374082 0.84467292 0.941919743 0.998875872 0.975162728 0.986248081 1 21.7695458 2.464153436 5.170110101 0.985922589 0.897547527 0.728289303 0.027485941 0.099499538 7.866907717 0.009671438 0.008330799 291.1745654 -2.464153436 -0.088375061 DLPRPSEVNETILRPLNVEPPLTDLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPRPSEVNETILRPLNVEPPLTDLQK 27 2 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 104.38 0.0012324 701950000 138230 131850 102400 111270 103410 122190 149230 119390 152710 146930 FALSE TRUE 132827.8188 128089.7671 120905.9579 117012.658 106736.2766 124660.7655 151056.3214 116924.5548 135375.001 136978.3002 0.969699716 0.935109918 0.882665047 0.854242299 0.779220332 0.910076744 1.102775557 0.853599107 0.988295232 1 17.06358784 2.464214503 24.9982278 0.970765471 0.881206297 0.293022353 0.073609495 340.3141525 659127.4607 0.026268134 0.02198988 291.215511 -2.464214503 -0.089559174 SQAAPGSS(ph)PCR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQAAPGSSPCR 11 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 SQAAPGS(0.247)S(0.753)PCR;SQAAPGS(0.19)S(0.81)PCR 137.62 7.81E-05 186123000 316450 334320 277840 311450 294550 319850 358440 336920 364980 388350 TRUE FALSE 304082.7841 324785.5209 328051.8685 327523.9718 304024.4683 326317.5861 362826.6959 329962.4843 323549.0005 362046.7086 0.839899319 0.897081822 0.906103717 0.904645627 0.839738247 0.9013135 1.002154383 0.91138098 0.89366646 1 18.46581631 2.464565265 24.98195298 0.9440377 0.880564452 0.446652114 0.038650309 238.1807142 473891.6309 0.01321777 0.011065797 291.4508089 -2.464565265 -0.063473248 S(ph)PYNGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPYNGVR 7 0 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 S(1)PYNGVR;S(0.999)PY(0.001)NGVR 86.744 0.020824 674610000 227480 236960 216730 291210 268660 249530 228499 277550 243870 258020 TRUE FALSE 218589.8301 230202.1328 255897.9321 306239.383 277301.6929 254575.6676 231295.4391 271818.4955 216186.9 240544.0756 0.908730883 0.957006038 1.063829702 1.273111309 1.152810321 1.058332727 0.961551177 1.130015341 0.89874132 1 17.87594174 2.464806645 23.8307211 1.018538817 1.078577749 0.080775722 0.108429082 445.3851351 861880.5032 0.04091758 0.034263908 291.6128416 -2.464806645 0.060038932 LDDLVNWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDDLVNWAR 9 0 F5H5N1;A0A087WXF6;A0A087WTI3;F5GXJ1;O75251-2;O75251 F5H5N1 NDUFS7 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial" 0 74.269 0.096709 152240000 222670 219900 169960 230470 201800 220500 270140 248180 267540 201260 FALSE TRUE 213967.8102 213628.6673 200675.5527 242364.5843 208291.0803 224958.6611 273446.0541 243054.9963 237169.9808 187628.4809 1.14038023 1.138572706 1.069536734 1.291725985 1.110125069 1.198957962 1.457380312 1.29540566 1.264040404 1 17.51751931 2.464842833 24.99284359 1.29212637 1.152997013 0.114320508 0.119106192 317.9587725 647203.5481 0.038775676 0.032461656 291.6371418 -2.464842833 -0.139129357 AELNSDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AELNSDKK 8 1 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 85.377 0.026914 340270000 349030 373870 275420 312980 435210 481300 496340 548860 662980 672030 FALSE TRUE 335389.5217 363207.5937 325194.5207 329132.9353 449208.9249 491032.2158 502414.3574 537525.8492 587721.2898 626512.8095 0.535327477 0.579728919 0.519054863 0.525341111 0.716998788 0.783754471 0.801921924 0.857964659 0.938083437 1 19.25698448 2.464922764 0.586188959 0.981790116 0.507077631 0.944522455 0.039936637 0.194187072 0.136731452 0.037937192 0.033843827 291.6908215 -2.464922764 -0.474712485 ETAIELGYLTAEQFDEWVKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETAIELGYLTAEQFDEWVKPK 21 1 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 227.95 1.69E-25 455700000 298780 290210 270780 293250 244610 310600 351120 367720 379080 319380 FALSE TRUE 287103.3473 281933.4949 319715.9695 308384.6676 252478.1028 316880.5448 355417.1116 360126.4535 336048.4276 297748.1081 0.964249107 0.946885932 1.07378002 1.035723349 0.847958714 1.064257123 1.193683862 1.209500392 1.128633293 1 18.18373282 2.465635321 6.400335819 1.155682452 0.97863319 0.475938488 0.077436803 0.1161474 20.38077795 0.026492366 0.02276874 292.1697986 -2.465635321 -0.177049262 AALQTAPESADDS(ph)PSQLSK ddPTM_BT-474_Pertuzumab_2h_R1 4 AALQTAPESADDSPSQLSK 19 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 AALQTAPESADDS(0.999)PSQLSK;AALQTAPESADDS(0.998)PS(0.002)QLSK;AALQTAPESADDS(1)PSQLSK;AALQTAPESADDS(0.995)PS(0.005)QLSK 413.81 6.67E-148 1853150000 1320340 1322080 1246210 1285030 1339430 1453610 1573610 1738430 1762570 1724850 TRUE FALSE 1268739.653 1284375.573 1471427.869 1351350.552 1382513.982 1483002.99 1592868.31 1702530.813 1562490.443 1608024.373 0.789005238 0.798728921 0.915053213 0.840379397 0.859759345 0.922251562 0.99057473 1.058771771 0.971683308 1 20.61685784 2.466002726 1.731386334 1.019682308 0.838826258 0.808393547 0.037879199 0.149907888 0.912069856 0.017650029 0.01375169 292.4170734 -2.466002726 -0.18085605 TPLSFTNPLHSDDS(ph)DSDERNSDGAVTQNK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPLSFTNPLHSDDSDSDERNSDGAVTQNK 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TPLSFTNPLHSDDS(0.82)DS(0.179)DERNSDGAVTQNK 115.13 0.00012163 67353000 35771 43531 35093 36257 37786 40475 51330 41773 48562 47651 TRUE FALSE 34373.02977 42289.5385 41435.08574 38128.22812 39001.42101 41293.43223 51958.19189 40910.37295 43049.44535 44423.55533 0.77375684 0.951962043 0.932727816 0.858288533 0.877944611 0.929539113 1.16960904 0.920916227 0.969067987 1 15.43903724 2.466075618 24.95854504 1.010313943 0.886725063 0.424899582 0.074292769 222.2405829 502167.6292 0.025313178 0.021196863 292.4661566 -2.466075618 -0.12358888 VKPPPQIS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKPPPQISPSK 11 1 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 VKPPPQIS(0.902)PS(0.098)K 123.38 0.00022473 298960000 365630 327780 326190 268120 331000 351230 355660 391030 405870 411210 TRUE FALSE 351340.7754 318432.0353 385139.7891 281957.7053 341646.9156 358332.1112 360012.6735 382955.0939 359797.3391 383358.3804 0.91648127 0.830637992 1.004646849 0.735493783 0.891194592 0.934718346 0.939102135 0.998948017 0.93854043 1 18.54833419 2.466085078 1.997484277 0.973962169 0.873115457 0.31402702 0.066042533 0.388599981 3.147096214 0.026504089 0.021356616 292.472527 -2.466085078 -0.100846712 EEKPEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEKPEAK 7 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 73.931 0.05581 0 253220 255040 200680 271000 312670 298010 384000 444910 457970 479590 FALSE TRUE 243323.8825 247766.5089 236947.3401 284986.3425 322727.3145 304035.9664 388699.5069 435722.453 405983.1656 447106.9421 0.544218529 0.554154914 0.529956746 0.637400844 0.721812354 0.680007259 0.86936585 0.974537436 0.908022505 1 18.77026042 2.466099575 0.711809766 1.002358391 0.534396566 0.939617807 0.042488932 0.154656951 0.1583726 0.034723268 0.02675045 292.4822905 -2.466099575 -0.467961826 EKHPDGK ddPTM_BT-474_Pertuzumab_2h_R1 6 EKHPDGK 7 1 P53396;P53396-2;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 65.252 0.042713 2676560000 3968350 3379690 2914900 3252190 3152430 3462910 4140030 3463320 3834430 4494830 FALSE TRUE 3813262.495 3283304.55 3441687.272 3420035.916 3253830.774 3532932.413 4190696.926 3391801.232 3399161.582 4190391.161 0.91000156 0.783531757 0.821328401 0.816161495 0.7764981 0.843103252 1.000072968 0.809423536 0.811180019 1 21.99865349 2.466415105 24.99868229 0.889300067 0.818159335 0.233121154 0.069564265 362.3763638 846136.5885 0.023605268 0.019767795 292.694866 -2.466415105 -0.071140732 STS(ph)YGYS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 2 S(0.003)T(0.002)S(0.995)YGYS(1)R 107.12 0.0059426 460520000 1406800 1536300 1363800 1497100 1508400 1453100 1308200 1559600 1521300 1432400 TRUE FALSE 1351820.701 1492486.228 1610268.998 1574365.51 1556919.056 1482482.678 1324210.143 1527393.715 1348608.402 1335382.272 1.012309905 1.117647178 1.205848715 1.178962416 1.165897652 1.110156027 0.99163376 1.143787623 1.009904377 1 20.34882136 2.467034 24.34168217 1.055815789 1.141025485 0.339559561 0.06360485 204.7769397 494144.417 0.022539224 0.01887871 293.1122705 -2.467034 0.085209695 NPDDITNEEYGEFYK ddPTM_BT-474_Pertuzumab_2h_R1 6 NPDDITNEEYGEFYK 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 355.81 3.37E-82 16448370000 3887480 3851260 3436930 3565350 3691400 4093450 4029000 4436640 4942590 4478270 FALSE TRUE 3735552.984 3741425.836 4058059.705 3749358.141 3810137.233 4176222.364 4078308.107 4345021.834 4381527.904 4174952.784 0.894753349 0.896160036 0.972001341 0.89806001 0.912618042 1.000304094 0.976851313 1.040735562 1.04947963 1 21.99332845 2.467084753 1.368543582 1.029860264 0.913996442 0.747833576 0.028594015 0.206391679 0.781435488 0.014738922 0.010801988 293.1465266 -2.467084753 -0.115863822 DIGKPIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIGKPIEK 8 1 O60869 O60869 EDF1 Endothelial differentiation-related factor 1 0 96.89 0.0078619 793080000 954430 931000 787590 842500 995410 984630 1053200 1244600 1219900 1246400 FALSE TRUE 917129.8204 904448.7915 929925.0328 885981.526 1027428.267 1004539.893 1066089.377 1218898.575 1081422.066 1161980.218 0.789281785 0.778368493 0.800293343 0.762475567 0.884204611 0.86450688 0.917476357 1.04898393 0.930671667 1 20.14815408 2.467143001 1.014190492 1.00262284 0.78317019 0.828577152 0.038362944 0.193450668 0.399838351 0.024166463 0.016901749 293.1858467 -2.467143001 -0.21945265 LQEKEELR ddPTM_BT-474_Pertuzumab_2h_R1 6 LQEKEELR 8 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ;;;;; 134.59 0.00079343 7161760000 12370500 14071200 8107400 12012400 10525600 11711100 12404200 12576900 14439000 11876900 FALSE TRUE 11887047.18 13669903.15 9572587.528 12632361.4 10864165.48 11947906.47 12556006.31 12317182.62 12799945.25 11072466.98 1.073568086 1.234585136 0.864539722 1.140880476 0.981187435 1.079064538 1.133984534 1.112415385 1.156015662 1 23.40047336 2.467317896 20.4176213 1.110520585 1.059227035 0.034666198 0.098211757 72.41975133 150816.5178 0.032377925 0.027160453 293.3039391 -2.467317896 -0.05129355 KDETNVK ddPTM_BT-474_Pertuzumab_2h_R1 5 KDETNVK 7 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;;;; 134.48 0.0050837 9991100000 10042100 9230200 9366000 9291300 7578050 9742800 11498400 10485200 10534100 13571600 FALSE TRUE 9649643.63 8966963.733 11058644.55 9770825.106 7821804.86 9939806.091 11639120.86 10268676.96 9338313.131 12652383.44 0.762673979 0.708717355 0.874036469 0.772251738 0.618208016 0.785607402 0.91991528 0.811600202 0.738067509 1 23.59290585 2.467353481 24.43478511 0.850201894 0.748324183 0.289380111 0.087432592 235.5103736 589139.8159 0.030073579 0.025193038 293.3279728 -2.467353481 -0.10187771 KEENLADWYSQVITK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEENLADWYSQVITK 15 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 205.98 6.62E-09 1459840000 3459200 3306900 2926500 3091200 3317000 3736300 3589000 3910000 4474300 4271700 FALSE TRUE 3324010.64 3212590.45 3455383.65 3250737.202 3423694.317 3811850.546 3632923.256 3829257.134 3966396.222 3982373.954 0.83468069 0.806702356 0.867669307 0.816281253 0.85971191 0.957180463 0.912250657 0.961551371 0.995987887 1 21.92519727 2.467812884 0.673415745 0.998004582 0.818879926 0.869266362 0.025324378 0.247393059 0.227526338 0.020437583 0.016339083 293.6384235 -2.467812884 -0.179124656 DSESPS(ph)QKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSESPSQKK 9 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DSES(0.083)PS(0.917)QKK 117.09 0.0012794 54752000 212580 163710 137300 127830 144510 164740 194110 175350 197290 205640 TRUE FALSE 204272.1386 159041.1511 162113.1642 134427.3216 149158.2954 168071.1557 196485.5762 171728.9612 174894.4663 191711.8196 1.065516664 0.829584485 0.845608604 0.701194751 0.778033904 0.876686456 1.02490069 0.895766164 0.912277953 1 17.54857976 2.467831421 23.94548787 0.947017999 0.834546166 0.245404266 0.09336864 180.7375434 465862.8825 0.033090428 0.027727746 293.6509573 -2.467831421 -0.112471833 KGGDGIKPPPIIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGGDGIKPPPIIGR 14 2 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 171.08 1.73E-06 2016600000 3030200 2965200 2563600 2721800 2996200 3221100 2917600 3536400 3764200 3583600 FALSE TRUE 2911776.434 2880635.399 3026899.547 2862272.424 3092575.494 3286232.849 2953306.462 3463372.104 3336903.797 3340879.58 0.871559829 0.86223862 0.906018752 0.856742171 0.925677032 0.983643011 0.883990695 1.036664753 0.998809959 1 21.67179655 2.468061202 0.676803575 1.015041193 0.867187902 0.661125089 0.036775543 0.42419417 0.39396612 0.029030535 0.023133928 293.8063663 -2.468061202 -0.147853291 VEEEDDAEHVLALTMLCLTEGAK ddPTM_BT-474_Pertuzumab_2h_R1 3 VEEEDDAEHVLALTMLCLTEGAK 23 0 O75607 O75607 NPM3 Nucleoplasmin-3 0 ;; 196.99 3.04E-24 111167000 75344.1 67159.1 81413.6 84650.8 85314 79848 97025 104164 132377 134790 FALSE TRUE 72399.56927 65243.78822 96126.84856 89019.63793 88058.20229 81462.58127 98212.42097 102012.977 117350.1179 125660.5532 0.576151922 0.519206597 0.764972349 0.708413545 0.700762491 0.64827489 0.781569223 0.811813846 0.933865998 1 16.93917231 2.468077547 0.173828236 1.118479944 0.379330153 0.791778505 0.064376812 2.794847389 0.273918672 0.352477648 0.661412043 293.8174244 -2.468077547 -0.739149791 AKSPT(ph)PESSTIASYVTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AKSPTPESSTIASYVTLR 18 1 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 AKS(0.289)PT(0.709)PES(0.001)STIASYVTLR 168.56 3.30E-11 1548300000 298810 306090 262110 306200 291450 293260 219470 368790 277350 341220 TRUE FALSE 287132.1748 297360.6129 309479.1076 322003.0187 300824.7539 299189.9181 222155.9395 361174.3576 245866.3907 318108.8655 0.90262236 0.934776252 0.972871684 1.012241574 0.945666049 0.940526815 0.698364502 1.135379729 0.772900153 1 18.27916105 2.468167661 24.99915162 0.915403552 0.955530838 0.039367514 0.113931309 972.1680856 2714350.865 0.038541797 0.032291797 293.8783962 -2.468167661 0.040127286 GNPS(ph)PPAAGEGQRPPPPLCVPGGGGGAPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNPSPPAAGEGQRPPPPLCVPGGGGGAPAR 30 1 Q92623 Q92623 TTC9 Tetratricopeptide repeat protein 9A 1 GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR 183.93 3.32E-18 1044920000 77535 83716 55743 73389 69210 75488 81811 89055 75529 82358 TRUE FALSE 74504.84648 81328.50165 65817.0001 77176.61508 71436.2025 77014.41908 82812.22749 87215.98313 66955.26456 76779.8193 0.970370172 1.059243202 0.857217439 1.00516797 0.930403368 1.003055487 1.078567627 1.135923266 0.872042487 1 16.22843954 2.468210094 6.924374268 1.045289946 0.96601632 0.07382467 0.080461447 0.250220761 63.03747084 0.027324475 0.0235195 293.907111 -2.468210094 -0.079273626 LLPYPTLAS(ph)PASD ddPTM_BT-474_Pertuzumab_2h_R1 1 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.97)PAS(0.03)D 107.18 0.0013802 10164000 31110 24605 20967 20706 26421 22402 18747 18303 29415 22304 TRUE FALSE 29894.18681 23903.28949 24756.20331 21774.63914 27270.85546 22854.98379 18976.43139 17925.03665 26075.93252 20793.33021 1.437681531 1.149565233 1.190583858 1.047193447 1.311519376 1.099149754 0.912621076 0.862057038 1.25405273 1 14.34383322 2.468665651 5.528443349 0.980096009 1.211029258 0.358135937 0.136595233 0.173683259 17.80866782 0.046734908 0.040418938 294.2155692 -2.468665651 0.230933249 EQYPGIEIESR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQYPGIEIESR 11 0 Q9BRT3;J3KTI2 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;; 240.37 2.58E-15 6026100000 2041400 2230840 1790650 2250680 2077000 2072810 1898960 2246620 2152390 2210700 FALSE TRUE 1961619.831 2167218.627 2114260.288 2366837.865 2143808.591 2114723.638 1922200.041 2200226.512 1908059.711 2060967.32 0.951795699 1.051554096 1.02585823 1.148411157 1.040195335 1.026083052 0.93266886 1.067569821 0.925807844 1 20.9748902 2.468820952 24.84079995 0.9920094 1.047277278 0.195222473 0.05792166 323.8165896 969095.7022 0.019912891 0.01668475 294.3207976 -2.468820952 0.055267878 ASLGS(ph)LEGEAEAEASSPK ddPTM_BT-474_Pertuzumab_2h_R1 5 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;AS(0.252)LGS(0.748)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK 490.08 4.57E-240 3731470000 2006140 2144140 1965410 2424270 1936630 2580720 3426640 2777840 3743560 3608090 TRUE FALSE 1927737.831 2082991.227 2320603.307 2549386.865 1998923.463 2632903.927 3468576.245 2720476.633 3318606.763 3363710.851 0.573098556 0.619253949 0.689893814 0.757909041 0.594261383 0.782737888 1.031175508 0.80877244 0.986590974 1 21.68162226 2.469370191 4.983451172 0.929214442 0.655855827 0.785773566 0.075568294 0.089246028 6.361958177 0.026145083 0.02264888 294.6932521 -2.469370191 -0.273358615 DNTRPGANS(ph)PEMWSEAIK ddPTM_BT-474_Pertuzumab_2h_R1 4 DNTRPGANSPEMWSEAIK 18 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 1 DNTRPGANS(1)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK 307.48 3.37E-51 1504430000 1150390 1065940 930470 1012390 1123910 1099030 1212350 1274590 1345850 1381630 TRUE FALSE 1105431.487 1035540.435 1098626.627 1064639.569 1160061.586 1121253.14 1227187.102 1248269.271 1193074.75 1288050.969 0.858220298 0.803959206 0.852937231 0.826550808 0.900633293 0.870503704 0.952747314 0.96911481 0.926263617 1 20.29675825 2.469812362 0.792172168 0.977795309 0.829138295 0.810230122 0.0266928 0.246333336 0.311432655 0.018726289 0.01373185 294.9934424 -2.469812362 -0.148657014 ELNHMLSDTGNRK ddPTM_BT-474_Pertuzumab_2h_R1 9 ELNHMLSDTGNRK 13 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;; 127.71 0.00011276 5813010000 4421228 5101892 4162309 4972714 4210632 4891642 5254099 5520974 5446352 5593727 FALSE TRUE 4248441.522 4956391.035 4914530.826 5229356.365 4346070.802 4990554.353 5318400.235 5406963.958 4828104.954 5214858.888 0.814680054 0.950436271 0.942409168 1.002780033 0.83340142 0.95698742 1.019855062 1.036838019 0.925836165 1 22.31419678 2.47012389 8.404053854 1.001837824 0.915862929 0.327232121 0.058158125 0.153086579 94.51208151 0.019717598 0.016937117 295.2051231 -2.47012389 -0.085974895 KSDVEAIFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSDVEAIFSK 10 1 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;B4DSU6;G3V4M8;G3V2H6;P07910;G3V2Q1;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;P07910-4;A0A0G2JNQ3;O60812;B2RXH8;A0A0G2JPF8;P0DMR1;B7ZW38 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2;HNRNPCL4;HNRNPCL3 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3 0 ; 120.87 0.00084986 11021200000 15953700 16265300 18276900 17544400 15113400 18973600 22154900 21786500 22378900 22844400 FALSE TRUE 15330211.77 15801429.57 21579942.4 18449868.59 15599536.24 19357259.19 22426038.29 21336601.16 19838541.09 21297128.44 0.719825295 0.74195118 1.013279441 0.866307805 0.732471341 0.908914047 1.053007609 1.001853429 0.931512488 1 24.34415558 2.47095753 6.31595345 0.997880479 0.82395106 0.507228794 0.084306841 0.133707876 23.56490715 0.030425581 0.026337444 295.7723216 -2.47095753 -0.173929419 IIPGFMCQGGDFTR ddPTM_BT-474_Pertuzumab_2h_R1 4 IIPGFMCQGGDFTR 14 0 P62937;F8WE65;C9J5S7;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284 P62937 PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D" 0 ;;; 234.65 7.53E-17 7849710000 697236 792711 666336 743958 770893 722301 657369 707593 746796 907311 FALSE TRUE 669987.2463 770103.6584 786757.7378 782353.7615 795689.4735 736906.4211 665414.0785 692980.9573 662022.8489 845858.0178 0.792080033 0.910440809 0.930129787 0.924923267 0.940689166 0.87119399 0.786673489 0.819263922 0.782664271 1 19.69005599 2.471783902 21.29229279 0.829072975 0.903608322 0.089804725 0.069485031 35.67656154 142312.339 0.022724525 0.019112387 296.3356501 -2.471783902 0.074535347 TVSLTPS(ph)PTTQVETPDLVDHDNTSPLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLT(0.007)PS(0.543)PT(0.225)T(0.225)QVETPDLVDHDNTSPLFR 168.88 3.04E-12 452310000 157850 145650 120730 134530 150560 168190 234260 199350 232250 248320 TRUE FALSE 151681.0475 141496.2046 142548.5966 141473.1094 155402.8991 171590.917 237126.944 195233.3528 205885.9537 231501.0652 0.655206694 0.611211894 0.615757843 0.611112132 0.671283732 0.741210054 1.02430174 0.843336736 0.889352079 1 17.82065931 2.473156467 3.30604134 0.920661012 0.631356484 0.874369016 0.054341678 0.081769606 1.877339913 0.019396734 0.016708252 297.273685 -2.473156467 -0.289304529 KSDVETIFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSDVETIFSK 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM2 Q9UKM9 RALY RNA-binding protein Raly 0 138.42 0.00010439 448960000 680090 730050 685260 788810 591250 773090 934710 806340 957360 992430 FALSE TRUE 653511.3309 709229.6888 809101.7255 829520.5786 610268.0932 788722.4095 946149.2606 789688.7972 848684.5064 925211.8321 0.70633698 0.766559251 0.8745043 0.896573682 0.659598237 0.852477651 1.022629875 0.853522155 0.917286698 1 19.81942419 2.473621977 24.94624288 0.931284024 0.788021521 0.495259553 0.078865176 99.79531253 711425.9972 0.027535292 0.023142551 297.5924969 -2.473621977 -0.143262503 DIFDCLEGAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIFDCLEGAAR 11 0 Q9Y5U2-2;Q9Y5U2;A6NCC9;E9PME3;C9JHT9;C9JJV1;E9PL88;C9JDU0 Q9Y5U2-2 TSSC4 Protein TSSC4 0 ; 112.36 0.0035752 64776000 41123 41276 40255 39954 40747 43220 49030 47090 47492 48158 FALSE TRUE 39515.8677 40098.84889 47529.97397 42016.03073 42057.66426 44093.93801 49630.04381 46117.57504 42100.90726 44896.21577 0.880160321 0.893145407 1.058663256 0.935847933 0.936775261 0.982130393 1.105439355 1.027204058 0.937738438 1 15.45430623 2.473654689 24.98637788 1.026215325 0.946016933 0.267100861 0.058994347 136.4668769 983611.7041 0.020966817 0.017619092 297.6149127 -2.473654689 -0.080198391 TEEEFKK ddPTM_BT-474_Pertuzumab_2h_R1 6 TEEEFKK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 110.78 0.010786 15453060000 10767900 11095630 9626890 10300120 16325300 19187600 23869100 30458900 32361800 31909400 FALSE TRUE 10347078.56 10779193.5 11366683.17 10831710.43 16850418.1 19575586.42 24161217.19 29829913.07 28688224.14 29748147.92 0.347822614 0.36234839 0.382097171 0.364113775 0.566435872 0.658043871 0.812192317 1.00274858 0.964370092 1 24.82629651 2.473770583 0.938637206 1.018445843 0.348438832 0.983790052 0.033841599 0.060972154 0.108075602 0.022557585 0.015934192 297.6943438 -2.473770583 -0.670007011 down KGNSPNS(ph)EPPTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGNSPNSEPPTPK 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KGNS(0.007)PNS(0.993)EPPTPK 106.19 0.0008537 1456800000 132730 117550 108230 103160 130930 112470 92528 120610 117880 105220 TRUE FALSE 127542.7649 114197.5891 127789.5686 108484.1 135141.4824 114744.2205 93660.38534 118119.3614 104498.7566 98093.35568 1.300218185 1.16417252 1.302734193 1.105927096 1.377682325 1.169745083 0.954808658 1.204152519 1.065299029 1 16.5818678 2.473803443 24.99926032 1.08031998 1.243623213 0.480651284 0.093651533 94.63334897 713036.3734 0.030391936 0.025545198 297.7168692 -2.473803443 0.163303233 S(ph)SSPPPRK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPPPRK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.333)S(0.333)S(0.333)PPPRK;S(0.45)S(0.45)S(0.101)PPPRK 55.567 0.075408 1518670000 1175240 1135180 856470 972840 1036500 1062270 1144570 1137020 1110520 1247950 TRUE FALSE 1129310.322 1102805.778 1011253.181 1023048.389 1069839.964 1083749.827 1158577.59 1113540.14 984458.4253 1163425.235 0.970677176 0.9478957 0.86920341 0.879341756 0.919560563 0.931516521 0.995833299 0.957122217 0.846172488 1 20.14994707 2.473876891 24.97524048 0.950966 0.915377684 0.091436432 0.047958931 235.8510367 1815564.209 0.017004369 0.014295985 297.7672233 -2.473876891 -0.035588316 S(ph)PHQLLSPSSFS(ph)PSATPSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPHQLLSPSSFSPSATPSQK 20 0 A0A3B3ITS5;Q14181;E9PIQ6 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 2 S(1)PHQLLSPSSFS(1)PSATPSQK;S(1)PHQLLSPSSFS(0.999)PS(0.001)ATPSQK 233.86 8.87E-30 1374220000 1103750 1047280 944560 1033870 953500 1044700 1183550 1036280 1061860 1303420 TRUE FALSE 1060614.23 1017412.6 1115263.004 1087228.155 984170.1934 1065824.55 1198034.639 1014880.456 941322.1045 1215138.202 0.87283424 0.837281387 0.917807539 0.894736214 0.809924494 0.877122082 0.985924594 0.835197555 0.774662588 1 20.21268898 2.474134068 24.95879094 0.889459798 0.866731161 0.042192759 0.067210116 465.2386543 3887117.917 0.023309389 0.019605092 297.9436046 -2.474134068 -0.022728638 HGATHVFASK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGATHVFASK 10 0 O60264;A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 O60264 SMARCA5;SMARCA1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5;Probable global transcription activator SNF2L1 0 ; 60.102 0.057987 906250000 1126160 1148340 1001130 1076630 1026810 899840 1007860 456490 1203920 1031730 FALSE TRUE 1082148.422 1115590.468 1182056.461 1132195.003 1059838.276 918035.3813 1020194.492 447063.322 1067256.049 961850.0081 1.125069827 1.159838289 1.228940532 1.177101413 1.10187479 0.954447548 1.060658609 0.464795257 1.109586775 1 19.87545241 2.474502849 1.562749936 0.815604382 1.170975808 0.309013831 0.171355558 0.357856664 1.77141429 0.080408442 0.061473952 298.1967107 -2.474502849 0.355371426 TQSAS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 5 TQSASPPPK 9 0 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 TQSAS(1)PPPK;TQSAS(1)PPPK;TQS(0.015)AS(0.985)PPPK;TQS(0.002)AS(0.998)PPPK;TQS(0.018)AS(0.982)PPPK 114.76 0.001943 390125000 942389 917942 933009 1020330 986520 979700 1204400 1298600 1371590 1420820 TRUE FALSE 905559.396 891763.1929 1101624.481 1072989.354 1018252.312 999510.2052 1219139.807 1271783.456 1215892.853 1324586.596 0.683654356 0.673238877 0.831674188 0.810056026 0.768732158 0.754582757 0.92039268 0.960136136 0.917941384 1 20.33711073 2.474686705 0.403933207 1.017247215 0.676069095 0.778729036 0.050996371 0.641780444 0.226822155 0.059516229 0.080253718 298.3229772 -2.474686705 -0.34117812 YPESNRT(ph)PVKPS(ph)SVEEEDSFFR ddPTM_BT-474_Pertuzumab_2h_R1 1 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 2 Y(0.003)PES(0.172)NRT(0.825)PVKPS(0.777)S(0.204)VEEEDS(0.02)FFR 67.911 0.038299 162850000 64250 61328 64382 51144 67825 65255 71487 77899 79217 78060 TRUE FALSE 61739.03897 59578.98549 76017.25957 53783.54797 70006.65272 66574.50081 72361.87929 76290.35843 70224.61826 72772.92667 0.848379223 0.81869712 1.044581592 0.739059846 0.961987595 0.914825112 0.994351644 1.048334345 0.964982741 1 16.15111421 2.47484051 1.57038934 1.013177255 0.876102702 0.346120138 0.078413981 0.406723336 2.033142786 0.035282927 0.027018269 298.4286471 -2.47484051 -0.137074553 GFHLDVEDYLSGVLILASELSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFHLDVEDYLSGVLILASELSR 22 0 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;; 148.44 7.07E-08 662993000 58527.1 77387.9 52656.4 57190.8 69003.1 50880.3 48186.2 36841.9 53437.4 57671.3 FALSE TRUE 56239.79623 75180.87286 62172.58282 60142.42404 71222.64738 51909.13453 48775.91713 36081.10189 47371.41038 53765.17148 1.046026539 1.398319224 1.156372817 1.118613079 1.3246986 0.965478824 0.907202856 0.671086893 0.881079871 1 15.71438429 2.47520825 2.702884108 0.82006477 1.21103892 0.624387267 0.124832291 0.154051657 2.288412473 0.045021054 0.038251479 298.6814495 -2.47520825 0.390974149 RTS(ph)SPPRK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSSPPRK 8 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.069)S(0.547)S(0.384)PPRK 50.284 0.081681 152300000 18003 18717 20790 19698 21799 19242 15505 20408 18878 23798 TRUE FALSE 17299.42286 18183.20949 24547.21547 20714.61614 22500.18463 19631.08642 15694.75483 19986.56767 16735.04858 22186.14026 0.779740083 0.819575161 1.106421179 0.933673721 1.01415498 0.884835586 0.707412585 0.900858258 0.754301937 1 14.43737108 2.476022189 24.99914549 0.830363652 0.935967806 0.120448439 0.113037838 69.63544111 1583839.44 0.038653856 0.032583405 299.2417522 -2.476022189 0.105604154 SVLELIPELNEKEEAYNSLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVLELIPELNEKEEAYNSLMK 21 1 P42704;H7C3W8 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 128.78 1.60E-05 66415000 81059 97503 68878 135360 67820 109200 145510 131600 141560 102980 FALSE TRUE 77891.12466 94722.30991 81325.78678 142345.9458 70001.49189 111408.0988 147290.7949 128882.414 125490.7023 96005.07287 0.81132301 0.986638592 0.84709885 1.48269192 0.729143677 1.160439709 1.534198043 1.342454207 1.307125744 1 16.55082302 2.476767475 24.99999274 1.335575436 0.988835038 0.306599765 0.227124906 13.64935546 964395.1174 0.074578909 0.06295582 299.7557172 -2.476767475 -0.346740398 AGGS(ph)PASYHGS(ph)TSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGGSPASYHGSTSPR 15 0 I3L2B2;O95208-3;O95208-2;F6PQP6 I3L2B2 EPN2 Epsin-2 2 AGGS(0.982)PAS(0.019)Y(0.001)HGS(0.768)T(0.224)S(0.006)PR;AGGS(0.998)PAS(0.002)YHGS(0.76)T(0.163)S(0.077)PR 292.91 8.47E-44 509290000 745850 855500 532980 730080 642720 663390 520560 711560 560530 563260 TRUE FALSE 716701.3574 831101.9776 629301.3421 767759.5163 663393.6725 676804.2003 526930.769 696866.0373 496900.9843 525109.8985 1.364859736 1.582720074 1.198418358 1.462093018 1.263342539 1.288881056 1.003467599 1.327086081 0.94627998 1 19.00225987 2.476865744 0.374538887 0.98305445 1.495641078 0.54539721 0.133884333 1.115787252 0.344944692 0.141780199 0.208456598 299.8235515 -2.476865744 0.512586629 EKDSELNQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDSELNQK 9 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 79.974 0.023188 228070000 82864 81117 70053 74169 93147 105680 108550 130650 152990 134610 FALSE TRUE 79625.58327 78803.62258 82713.13542 77996.87098 96143.15785 107816.922 109878.4674 127952.0318 135623.2166 125492.7448 0.63450348 0.627953614 0.659106911 0.621524942 0.766125229 0.859148648 0.875576254 1.019597046 1.080725557 1 16.93724443 2.477136444 0.875692654 1.049010183 0.624067677 0.953087391 0.036500911 0.11218183 0.17329821 0.02554767 0.018301307 300.0104924 -2.477136444 -0.424942506 SQS(ph)SDTEQQSPTSGGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQS(0.5)S(0.5)DTEQQSPTSGGGK;S(0.071)QS(0.464)S(0.464)DTEQQSPTSGGGK;S(0.125)QS(0.581)S(0.294)DTEQQSPTSGGGK 417.83 4.39E-141 1799554000 1012740 916190 613565 813290 987340 892520 1015970 1188050 1193240 1102280 TRUE FALSE 973161.0012 890061.1582 724449.8442 855263.9944 1019098.688 910567.3659 1028403.745 1163516.352 1057788.398 1027621.594 0.947003262 0.866137072 0.704977249 0.832275226 0.991706182 0.88609209 1.000761127 1.132242023 1.029355946 1 19.97087768 2.477253756 1.173051229 1.069345091 0.840865475 0.537017631 0.077625231 0.344699444 0.956805288 0.046542545 0.033336435 300.0915424 -2.477253756 -0.228479616 GRKDDDSDDES(ph)QSSHTGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRKDDDSDDESQSSHTGK 18 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.016)DDES(0.984)QSSHTGK 207.07 4.09E-16 743350000 511890 499550 282930 393980 382610 440130 504470 455460 565010 488460 TRUE FALSE 491884.7729 485303.3231 334061.7447 414313.355 394916.9981 449029.7302 510643.8548 446054.5918 500872.4335 455376.1691 1.080172407 1.065719631 0.73359514 0.909826607 0.867232466 0.986063305 1.121367101 0.97952994 1.09990919 1 18.79669927 2.477286489 24.99389697 1.044959854 0.926603791 0.239314652 0.099576736 9.110942175 1378543.987 0.035636225 0.030117617 300.1141615 -2.477286489 -0.118356063 FQVWDYEEGEVEALLDR ddPTM_BT-474_Pertuzumab_2h_R1 8 FQVWDYEEGEVEALLDR 17 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ;;;;;;; 230.86 1.52E-15 1048878200 343105.7 346005.5 317655.8 362781.6 347436.3 340825.6 321475.7 344047.6 370117.2 394918 FALSE TRUE 329696.7499 336137.7619 375063.2693 381504.8019 358611.9041 347717.3271 325410.0158 336942.8968 328103.0471 368169.8521 0.895501758 0.912996434 1.01872347 1.036219559 0.974039298 0.944448127 0.883858398 0.915183291 0.891173042 1 18.49001197 2.477692111 5.194883853 0.914033557 0.970320382 0.145200681 0.049422286 0.287062381 24.01052982 0.017834415 0.01559301 300.3945931 -2.477692111 0.056286825 KLLEGEEER ddPTM_BT-474_Pertuzumab_2h_R1 8 KLLEGEEER 9 1 P20700;E9PBF6;P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8;Q03252 P20700;P02545;P02545-2;Q03252 LMNB1;LMNA;LMNB2 Lamin-B1;Prelamin-A/C;Lamin-A/C;Lamin-B2 0 ;;;;;;; 173.71 8.86E-05 18291830000 17563000 17498500 14208800 16807800 16306900 16957700 17639900 18704800 18442600 17799400 FALSE TRUE 16876618.54 16999459.91 16776646.23 17675252.57 16831426.25 17300596.31 17855782.37 18318539.34 16349073.37 16593830.78 1.017041741 1.024444574 1.011017073 1.065170111 1.014318301 1.042592066 1.076049443 1.103936733 0.985250096 1 23.98414364 2.477724953 24.23819228 1.057013558 1.027675874 0 0.035986072 32.16084793 1291391.731 0.012338733 0.010450268 300.4173102 -2.477724953 -0.029337683 EAIEGTYIDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAIEGTYIDKK 11 1 P62280;M0QZC5 P62280 RPS11 40S ribosomal protein S11 0 ; 176.42 1.39E-05 4780000000 5759000 5514100 4910900 3805700 5591100 5965000 6040000 7238100 7459800 6875500 FALSE TRUE 5533931.913 5356843.267 5798408.872 4002112.633 5770942.809 6085616.387 6113919.327 7088630.706 6612994.778 6409816.261 0.863352659 0.835724933 0.904613898 0.624372442 0.900328898 0.949421347 0.953836909 1.105902325 1.031698025 1 22.61185157 2.477747274 1.58424282 1.047246707 0.816699081 0.592239764 0.079161659 0.25448519 1.294702041 0.037142797 0.028587646 300.4327503 -2.477747274 -0.230547626 T(ph)PAPEPEPCEASELPAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPAPEPEPCEASELPAKR 18 1 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 T(1)PAPEPEPCEASELPAKR;T(1)PAPEPEPCEASELPAKR 113.99 0.00013545 1285090000 554590 547720 441320 540220 555110 562370 523930 673110 668470 656310 TRUE FALSE 532916.0097 532099.5619 521076.3411 568100.8189 572965.6173 573741.5067 530342.0121 659210.0433 592588.0881 611857.5391 0.87098054 0.869646164 0.851630172 0.928485444 0.936436312 0.9377044 0.866773682 1.077391388 0.968506638 1 19.22283626 2.477886157 0.580699114 1.020026199 0.862566151 0.521335688 0.046652642 0.644578448 0.446463141 0.041259455 0.037515144 300.5288415 -2.477886157 -0.157460048 SLGYAYVNFQQPADAER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGYAYVNFQQPADAER 17 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YBN4;E5RGH3;B1ANR1;E5RJB9;E5RHG7;E5RH24;B1ANR0;Q13310-2;Q13310;Q13310-3 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 230.26 1.96E-15 147850000 53081 61042 54111 57020 58283 55986 49995 60738 60939 58469 FALSE TRUE 51006.53584 59301.14193 63890.06139 59962.80903 60157.72563 57118.07528 50606.85377 59483.73907 54021.4602 54508.84255 0.935747916 1.087917834 1.172104532 1.100056545 1.103632417 1.047868063 0.92841549 1.091267697 0.991058655 1 15.73420267 2.47822544 24.99921237 1.01255538 1.085497862 0.222601391 0.066608807 67.62175526 1531038.139 0.023260877 0.019702502 300.7637144 -2.47822544 0.072942482 IREDLPNLESSEETEQINK ddPTM_BT-474_Pertuzumab_2h_R1 3 IREDLPNLESSEETEQINK 19 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 353.96 6.50E-91 2837170000 866206 838891 745758 788320 791356 884490 920180 1010170 988452 1047190 FALSE TRUE 832353.7119 814966.65 880533.0599 829005.2897 816810.6844 902374.9938 931441.4381 989309.6365 876247.0729 976262.8886 0.852591778 0.834781963 0.901942571 0.849161941 0.836670833 0.924315576 0.954088749 1.01336397 0.897552374 1 19.89691016 2.478724402 2.654752849 0.972331777 0.856319433 0.705365955 0.033923339 0.145238009 2.077368891 0.012480358 0.010609461 301.1094615 -2.478724402 -0.116012343 SSS(ph)PIPLTPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPIPLTPSK 11 0 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 1 S(0.001)S(0.029)S(0.971)PIPLTPSK;S(0.001)S(0.018)S(0.982)PIPLTPSK 145.28 3.81E-05 2792400000 7326000 7108600 5822400 6841300 7043600 7264300 8055700 8332700 9059800 8953000 TRUE FALSE 7039691.821 6905869.688 6874637.199 7194380.313 7270163.791 7411189.123 8154288.066 8160626.833 8031369.486 8346605.335 0.843419754 0.827386633 0.823644694 0.861952857 0.871032414 0.887928544 0.976958624 0.977718067 0.962231849 1 22.99275812 2.478852816 1.156811901 0.98685399 0.835011451 0.944017418 0.015419033 0.099746162 0.269264675 0.008911276 0.006378835 301.1985082 -2.478852816 -0.151842539 GPKPEPPGSGS(ph)PAPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.166)GS(0.834)PAPPR;GPKPEPPGS(0.189)GS(0.811)PAPPR;GPKPEPPGS(0.179)GS(0.821)PAPPR;GPKPEPPGS(0.414)GS(0.586)PAPPR 150.94 4.18E-07 5592030000 1952720 1847350 1673500 1773430 1740210 1860590 1926410 1996360 2077180 2114090 TRUE FALSE 1876405.544 1794665.387 1975938.677 1864956.935 1796185.435 1898212.405 1949985.982 1955134.468 1841387.235 1970900.801 0.952054788 0.910581286 1.002556128 0.946245967 0.911352532 0.963119201 0.989388193 0.992000443 0.934287121 1 20.91042373 2.478922874 20.77120428 0.979639431 0.945111363 0.23841596 0.028983792 11.59759264 133740.9839 0.009874077 0.008422598 301.2470996 -2.478922874 -0.034528068 KDDGDAAMGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 KDDGDAAMGSR 11 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;;; 145 5.84E-05 1120960000 1064920 1123030 952390 1016220 1129260 1127210 1239560 1315800 1431220 1403580 FALSE TRUE 1023301.749 1091002.284 1124508.059 1068667.236 1165583.673 1150002.959 1254730.106 1288628.27 1268753.906 1308514.276 0.782033309 0.833771785 0.859377753 0.816702771 0.890768786 0.878861606 0.958896765 0.984802607 0.96961411 1 20.31949823 2.479141343 0.763115815 1.000400027 0.816095748 0.902309584 0.022725548 0.18319028 0.215678143 0.016856378 0.012665899 301.398678 -2.479141343 -0.184304279 AAVGRPLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAVGRPLDK 9 1 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 69.276 0.05677 0 140220 146840 113600 131810 122820 143710 165470 149230 175060 175310 FALSE TRUE 134740.0474 142652.267 134130.047 138612.7299 126770.6168 146615.9147 167495.0714 146148.3484 155187.9227 163436.0976 0.824420366 0.872832068 0.820688018 0.848115759 0.775658614 0.89708404 1.024835234 0.894223189 0.949532723 1 17.31836714 2.479237573 24.98222292 0.954729281 0.831976144 0.725748491 0.039922605 45.62664689 538613.9533 0.01326722 0.011267671 301.4654688 -2.479237573 -0.122753138 KFYPLEIDYGQDEEAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFYPLEIDYGQDEEAVK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 196.66 2.53E-11 196852000 467690 437570 369380 379490 427890 458370 476520 514640 558380 541170 FALSE TRUE 449412.1577 425090.932 436135.1828 399075.5244 441653.4704 467638.5555 482351.7943 504012.5042 494995.0433 504516.0739 0.890778671 0.842571633 0.864462413 0.791006561 0.875400197 0.926905166 0.956068239 0.999001876 0.98112839 1 18.94454071 2.479524515 1.616304748 0.990677429 0.847245193 0.859820036 0.025327211 0.128927814 0.682806086 0.011749303 0.009105992 301.6647155 -2.479524515 -0.143432235 STS(ph)GPRPGCQPSSPCVPK ddPTM_BT-474_Pertuzumab_2h_R1 4 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 S(0.029)T(0.169)S(0.802)GPRPGCQPSSPCVPK;S(0.001)T(0.003)S(0.996)GPRPGCQPSSPCVPK;S(0.005)T(0.017)S(0.978)GPRPGCQPSSPCVPK;S(0.034)T(0.163)S(0.803)GPRPGCQPSSPCVPK 148.89 4.00E-08 1654720000 687060 610660 367081 547330 713220 614540 713760 860430 849190 876630 TRUE FALSE 660208.9356 593244.5747 433420.7024 575577.7669 736161.369 626966.4199 722495.2084 842661.8198 752793.5113 817255.0693 0.807837064 0.725898923 0.530337123 0.704281672 0.900773084 0.767161249 0.884051058 1.031087908 0.921124309 1 19.6404269 2.480146929 0.903177541 0.996436685 0.689638108 0.624329866 0.088050483 0.379686273 0.624206126 0.063186206 0.045135288 302.0973595 -2.480146929 -0.306798577 VEAPSLDVHMDSPDINIEGPDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEAPSLDVHMDSPDINIEGPDVK 23 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 249.34 5.99E-38 319430000 303310 275410 267270 267000 263780 284870 313980 287540 324990 312050 FALSE TRUE 291456.3099 267555.5765 315571.6344 280779.902 272264.7233 290630.2666 317822.5812 281602.1985 288098.4977 290914.5756 1.001862177 0.919704954 1.084757042 0.965162716 0.935892341 0.999022706 1.092494525 0.967989307 0.990319915 1 18.15023606 2.481046584 24.99871347 1.013134305 0.981333871 0.076555039 0.05125568 464.1628765 2956083.514 0.017486515 0.014960804 302.723812 -2.481046584 -0.031800435 QKADEEEMLDNLPEAGDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKADEEEMLDNLPEAGDSR 19 1 Q9NPD8 Q9NPD8 UBE2T Ubiquitin-conjugating enzyme E2 T 0 ; 122.19 3.07E-05 94016000 200276 176476 138013 164090 160472 172421 183878 175755 185724 218816 FALSE TRUE 192448.9925 171443.0773 162955.0192 172558.7046 165633.7276 175907.4708 186128.354 172125.5978 164641.3901 203995.3974 0.943398699 0.840426203 0.798817136 0.845895088 0.811948356 0.862310978 0.912414478 0.843771967 0.807083847 1 17.63817708 2.481060264 24.90108653 0.876885843 0.844042709 0.083423354 0.059457338 484.5899522 3063441.381 0.019781276 0.01689422 302.733348 -2.481060264 -0.032843134 GRDEVSK ddPTM_BT-474_Pertuzumab_2h_R1 5 GRDEVSK 7 1 Q9UKY7;H0Y8K3;D6R9V8 Q9UKY7 CDV3 Protein CDV3 homolog 0 ;;;; 113.71 0.0055352 1122210000 2187260 2093870 1701530 2096810 1973810 2158180 2354740 2400760 2390040 2667280 FALSE TRUE 2101779.461 2034154.878 2009034.321 2205026.615 2037299.391 2201819.878 2383558.013 2351183.467 2118732.679 2486622.75 0.84523455 0.818039197 0.807936918 0.886755587 0.819303769 0.885465991 0.958552323 0.945532839 0.852052318 1 21.24575622 2.481090974 3.883662197 0.936154474 0.836313504 0.598897059 0.039859807 0.152873983 5.197182736 0.013610142 0.011872682 302.7547561 -2.481090974 -0.09984097 LTWHS(ph)CPEDEAQ ddPTM_BT-474_Pertuzumab_2h_R1 1 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 1 LTWHS(1)CPEDEAQ 129.17 0.00025069 624860000 941320 951620 637750 838200 801220 760810 623560 663050 791020 678870 TRUE FALSE 904532.1737 924480.7293 753005.6117 881459.6025 826991.9689 776194.0995 631191.3138 649357.7858 701226.7258 632889.5302 1.429210203 1.460730009 1.189789964 1.392754281 1.306692447 1.226429041 0.997316725 1.026020743 1.107976499 1 19.27159418 2.481522589 2.268228745 1.030716926 1.357434076 0.799738831 0.075917905 0.132745362 1.381458907 0.030269088 0.025265962 303.0557925 -2.481522589 0.32671715 SS(ph)IDSQASLSGPLSGGAPGAGAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSIDSQASLSGPLSGGAPGAGAR 23 0 A6NKD9 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 1 S(0.232)S(0.768)IDSQASLSGPLSGGAPGAGAR;S(0.038)S(0.962)IDSQASLSGPLSGGAPGAGAR;S(0.207)S(0.793)IDSQASLSGPLSGGAPGAGAR 325.98 1.15E-74 603531000 420509 429388 399566 447824 405418 427745 385746 441076 428903 442349 TRUE FALSE 404075.0434 417142.2747 471776.4645 470936.2503 418458.6382 436394.297 390466.8749 431967.6265 380215.7295 412388.3082 0.979841172 1.011527888 1.144010281 1.141972847 1.014719937 1.058212098 0.946842738 1.047477869 0.921984746 1 18.65364391 2.48272298 2.14613224 0.988706885 1.066503397 0.271829068 0.059793406 0.469676726 4.376834393 0.025026265 0.020719402 303.894598 -2.48272298 0.077796512 DGGFCEVCKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGGFCEVCKK 10 1 P07602;C9JIZ6;P07602-2;P07602-3;Q5BJH1 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 141.88 5.89E-05 295540000 844140 956960 646430 700450 717750 1009700 995010 1142000 1276300 1271300 FALSE TRUE 811150.0756 929668.4378 763254.2808 736600.3084 740837.0806 1030116.826 1007187.23 1118417.301 1131419.775 1185193.719 0.684402948 0.784402097 0.643991163 0.621502035 0.625076786 0.869154814 0.849808107 0.943657803 0.954628561 1 20.17669145 2.483504939 2.030671282 0.939334657 0.674065245 0.828188781 0.057458973 0.138894756 1.159428434 0.024798261 0.020335092 304.4422613 -2.483504939 -0.265269412 VGIDTPDIDIHGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 205.28 2.30E-11 2390690000 3481820 3367730 2908300 3419900 2960690 3362630 3422370 3540280 4054860 3733320 FALSE TRUE 3345746.625 3271685.638 3433894.505 3596401.449 3055923.283 3430624.683 3464253.988 3467171.981 3594569.292 3480458.911 0.961294677 0.94001559 0.986621188 1.033312428 0.878023089 0.985681708 0.995344027 0.99618242 1.032786016 1 21.73084611 2.483757112 24.39952217 1.002630715 0.96107275 0.249107352 0.037713303 356.5024503 1310840.801 0.012848168 0.011127208 304.6190866 -2.483757112 -0.041557965 ALRPEAPPPPPPAFSFQEFLPSLNSS(ph)PLDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALRPEAPPPPPPAFSFQEFLPSLNSSPLDIR 31 1 Q9P107;K7EJC2;Q9P107-2 Q9P107 GMIP GEM-interacting protein 1 ALRPEAPPPPPPAFSFQEFLPS(0.001)LNS(0.035)S(0.963)PLDIR 183.48 1.62E-18 74949000 22120 26524 27691 25454 24817 28909 34845 34290 26465 36119 TRUE FALSE 21255.52595 25767.56149 32695.37968 26767.68399 25615.26134 29493.55979 35271.44353 33581.89952 23460.80415 33672.62796 0.631240483 0.765237614 0.970977962 0.794938964 0.760714649 0.875891238 1.047481164 0.997305573 0.6967322 1 15.0392887 2.48521161 7.651681274 0.947936716 0.796598281 0.264423009 0.117556887 0.189473669 79.46051166 0.040438076 0.03579931 305.6409986 -2.48521161 -0.151338435 T(ph)SSLDTLAAPYLAGHWPR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.633)S(0.184)S(0.184)LDTLAAPYLAGHWPR;T(0.333)S(0.333)S(0.333)LDT(0.001)LAAPYLAGHWPR;T(0.333)S(0.333)S(0.333)LDTLAAPYLAGHWPR 237.31 2.79E-23 343799000 145533 136961 122535 137283 139003 136119 132064 142865 156206 147400 TRUE FALSE 139845.4095 133055.0064 144679.8003 144368.1921 143474.1577 138871.4194 133680.2387 139914.7878 138474.1497 137416.4667 1.017675777 0.968261007 1.052856355 1.050588736 1.044082716 1.010587907 0.972810915 1.018180653 1.007696916 1 17.06819537 2.485242957 24.93668814 1.000707586 1.026338526 0.208789592 0.02487378 687.2725932 2110192.032 0.009007677 0.007872912 305.6630604 -2.485242957 0.02563094 AALSS(ph)SELLELGDSLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 AALS(0.02)S(0.977)S(0.003)ELLELGDSLMR;AALS(0.162)S(0.823)S(0.015)ELLELGDSLMR 126.63 4.51E-05 34867000 45628 58544 45829 57267 58157 50680 46651 56697 45698 52005 TRUE FALSE 43844.80732 56874.38244 54111.31976 60222.55673 60027.67272 51704.78432 47221.92889 55526.18714 40510.55462 48482.65503 0.904340063 1.173087208 1.116096462 1.242146427 1.238126763 1.066459423 0.973996347 1.145279422 0.83556799 1 15.56518109 2.485308214 21.95075344 1.015948912 1.142865378 0.255220989 0.113460901 120.5198153 323142.5452 0.038131584 0.033414693 305.7089929 -2.485308214 0.126916466 LRPPGAEKPSWLEEQ ddPTM_BT-474_Pertuzumab_2h_R1 1 LRPPGAEKPSWLEEQ 15 2 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 119.54 0.00081063 829840000 426040 430080 376400 387890 357570 414910 434860 443290 469970 459890 FALSE TRUE 409389.8858 417814.5395 444423.853 407909.0494 369071.5638 423299.7645 440181.9468 434135.9066 416620.9759 428741.2407 0.954864722 0.974514462 1.036578269 0.951410806 0.860825899 0.987308251 1.026684408 1.012582568 0.971730583 1 18.70974767 2.485628856 24.95556823 1.005736505 0.95726101 0.220748916 0.041956645 655.5225462 1922867.967 0.015208473 0.013332035 305.9347823 -2.485628856 -0.048475495 VRTDITYPAGFMDVISIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VRTDITYPAGFMDVISIDK 19 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 144.92 1.19E-07 156200000 361560 383450 253230 314460 293960 339940 355440 394760 359900 378230 FALSE TRUE 347429.8355 372514.3814 298994.2941 330689.3183 303415.4904 346813.8197 359789.981 386608.068 319045.6608 352612.1452 0.985303088 1.056442288 0.847940997 0.937827363 0.860479409 0.983556081 1.020356179 1.096411662 0.904806216 1 18.42772264 2.486022769 8.086267076 1.020183883 0.937493827 0.160751411 0.0706528 0.216341491 112.3649199 0.024412991 0.021650806 306.2123972 -2.486022769 -0.082690056 FDREVDIGIPDATGR ddPTM_BT-474_Pertuzumab_2h_R1 5 FDREVDIGIPDATGR 15 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;; 246.03 3.50E-18 2024936000 1498800 1631500 995585 1274889 1283283 1575900 1290479 1390761 1431860 1360016 FALSE TRUE 1440225.239 1584971.217 1175509.356 1340686.174 1324560.963 1607765.778 1306272.268 1362041.299 1269321.256 1267900.905 1.135913093 1.250074995 0.927130308 1.057406118 1.044688081 1.268053183 1.030263692 1.074249016 1.001120238 1 20.27401056 2.486064458 0.014943861 8.71E-06 2.159275378 0.125606362 0.097023797 2025.938318 14.43001039 1007.920376 1074.455994 306.2417927 -2.486064458 2.159266672 VPS(ph)VESLFR ddPTM_BT-474_Pertuzumab_2h_R1 10 VPSVESLFR 9 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR 181.87 4.93E-05 4060752000 682099 677397 583491 662896 699284 644820 622932 665488 708886 676639 TRUE FALSE 655441.817 658078.3008 688940.8034 697108.142 721777.1049 657858.7022 630555.6282 651745.4402 628416.2332 630809.6378 1.039048514 1.043228038 1.092153262 1.105100652 1.144207478 1.042879916 0.999597328 1.03318878 0.996205821 1 19.26684518 2.486271648 16.63384912 1.013262962 1.084939433 0.599100709 0.029778637 4.263077847 7751.32259 0.010853261 0.009595032 306.3879272 -2.486271648 0.071676472 QEPLGS(ph)DSEGVNCLAYDEAIMAQQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEPLGSDSEGVNCLAYDEAIMAQQDR 26 0 J3KR44;Q96FW1;F5H6Q1;F5GYJ8;F5H3F0 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 1 QEPLGS(0.809)DS(0.191)EGVNCLAYDEAIMAQQDR 239.34 3.16E-45 103940000 40169 33576 27936 36374 41633 33841 28676 36178 39843 34546 TRUE FALSE 38599.15107 32618.44535 32984.65663 38251.2665 42972.16326 34525.28821 29026.94547 35430.91166 35320.18968 32206.16865 1.198501799 1.012801172 1.024172015 1.1877 1.334283619 1.072008552 0.901285272 1.100128117 1.096690204 1 14.97504942 2.486471042 24.98439204 1.029285468 1.145167058 0.265969962 0.099691031 721.0104117 1926680.795 0.035907889 0.031631895 306.5286282 -2.486471042 0.11588159 DKTEDDADREAQLLEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKTEDDADREAQLLEMR 17 2 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 138.07 2.74E-06 308610000 449850 430480 306410 339830 417080 418290 410070 489340 491750 472090 FALSE TRUE 432269.3647 418203.1319 361785.1031 357368.667 430495.757 426748.1104 415088.5593 479234.958 435928.6016 440114.9238 0.98217384 0.950213477 0.822024166 0.811989432 0.978143966 0.969628811 0.943136751 1.088885952 0.990488116 1 18.74752077 2.486573613 1.333093119 1.026747371 0.89715768 0.381182187 0.061428445 0.433006966 1.556906447 0.034009716 0.025252934 306.6010323 -2.486573613 -0.129589691 VNFDDYTVNLGGLKDHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNFDDYTVNLGGLKDHIK 18 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 273.9 3.04E-39 1601370000 1812480 1734570 1337100 1368430 1574460 1686710 1893600 1898750 2069200 1942420 FALSE TRUE 1741646.278 1685101.762 1578743.714 1439054.836 1625103.936 1720816.432 1916774.443 1859540.149 1834313.091 1810858.163 0.96177951 0.930554251 0.871820745 0.794681144 0.89742199 0.950276762 1.05848955 1.026883379 1.012952382 1 20.78824212 2.486898882 3.177109685 1.027627074 0.887723552 0.677898071 0.043095345 0.15216377 3.178358325 0.016976081 0.014725608 306.8307502 -2.486898882 -0.139903522 YVAVMPPHIGDQPLTGAYTVTLDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YVAVMPPHIGDQPLTGAYTVTLDGR 25 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ; 268.25 1.01E-45 1789310000 900400 950260 780390 977210 979350 879250 822580 916760 893200 909330 FALSE TRUE 865211.3726 923159.5152 921423.8327 1027643.925 1010851.682 897029.0374 832646.9801 897828.5856 791807.6806 847740.2692 1.020609029 1.088965039 1.086917616 1.212215537 1.192407296 1.058141355 0.982195857 1.059084508 0.93402155 1 19.69326279 2.487215492 6.365972197 1.006055867 1.12231808 0.504116837 0.058589839 0.144248757 26.27139582 0.021075154 0.018701427 307.0545181 -2.487215492 0.116262213 YKDNPFSLGESFGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YKDNPFSLGESFGSR 15 1 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 ; 168.05 1.16E-06 1013200000 517130 455590 455030 460350 449010 498030 542040 506900 584990 572830 FALSE TRUE 496919.9879 442597.0193 537264.0431 484108.7187 463452.8144 508100.5078 548673.6477 496432.3379 518584.3877 534031.7139 0.930506513 0.828784149 1.006052691 0.906516797 0.867837625 0.951442573 1.027417723 0.929593365 0.971074141 1 19.02656589 2.487551138 24.4374768 0.975050517 0.908986352 0.340172641 0.048439309 472.3313977 1106687.856 0.015921135 0.014129744 307.2919178 -2.487551138 -0.066064164 ISMPDVDLHMK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISMPDVDLHMK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 124.42 0.00034944 686840000 2067130 2140100 1720220 2092100 1798450 2035420 2062750 2139510 2436800 2205300 FALSE TRUE 1986344.274 2079066.443 2031102.02 2200073.532 1856298.778 2076577.587 2087994.552 2095328.371 2160184.68 2055933.067 0.966152209 1.011252009 0.987922249 1.070109512 0.902898449 1.010041436 1.015594615 1.019161764 1.050707688 1 20.97136187 2.487616559 24.85611293 1.021108134 0.989861351 0.13462788 0.040474228 1016.849931 2408213.032 0.013183739 0.011678342 307.3382109 -2.487616559 -0.031246782 VEQIAAIAQELNELDYYDSHNVNTR ddPTM_BT-474_Pertuzumab_2h_R1 6 VEQIAAIAQELNELDYYDSHNVNTR 25 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 290.54 7.97E-63 3512770000 768644 795896 994235 1560727 1003729 835532 1319470 1327357 1539479 1880069 FALSE TRUE 738604.5427 773197.8253 1173915.381 1641276.308 1036014.855 852427.0295 1335618.069 1299946.614 1364723.798 1752730.252 0.42140229 0.441139088 0.669763861 0.936411239 0.591086309 0.486342396 0.762021462 0.741669525 0.778627399 1 20.74117255 2.487622613 0.087391307 1.372101827 2.96E-18 0.507091729 0.132795026 24.01862838 1.040699987 6.423570794 9.258052201 307.3424957 -2.487622613 -1.372101827 LPKPPTDPLGAVFSPPQAS(ph)PPQPSHGLQSCR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPKPPTDPLGAVFSPPQASPPQPSHGLQSCR 31 1 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 LPKPPTDPLGAVFS(0.001)PPQAS(0.966)PPQPS(0.026)HGLQS(0.008)CR;LPKPPTDPLGAVFSPPQAS(1)PPQPSHGLQSCR 176.01 5.56E-14 859960000 633700 710190 607970 666200 668870 745250 753610 804020 947520 962140 TRUE FALSE 608934.3034 689936.0765 717843.7032 700582.6618 690384.811 760319.4656 762832.9046 787416.706 839961.5019 896973.4008 0.678876657 0.769182315 0.800295419 0.781051769 0.769682591 0.847649958 0.850452091 0.877859595 0.9364397 1 19.77470568 2.48770711 0.19125364 1.060052182 0.610033683 0.911043417 0.026119128 1.433050818 0.156773366 0.106545815 0.208926213 307.402298 -2.48770711 -0.450018499 RPRPTPGDGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPRPTPGDGEK 11 2 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L410;I3L1N0;Q9BUL5-3 I3L4Q4 PHF23 PHD finger protein 23 0 ; 155.48 1.77E-05 167993000 115437 112429 91416 101918 100248 108080 111635 112919 127577 118163 FALSE TRUE 110925.5944 109222.635 107936.9047 107178.0002 103472.568 110265.4517 113001.2225 110587.1832 113094.9938 110159.7148 1.006952448 0.991493444 0.979821934 0.972932804 0.939295896 1.000959851 1.025794436 1.003880442 1.026645667 1 16.7492372 2.487713092 24.68398112 1.013644645 0.977799674 0.481226431 0.01773663 385.589354 898606.0644 0.006131563 0.005454371 307.4065324 -2.487713092 -0.035844971 YQAVTATLEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YQAVTATLEEK 11 0 P40429;M0QYS1;Q8J015;Q6NVV1 P40429 RPL13A;RPL13a;RPL13AP3 60S ribosomal protein L13a;Putative 60S ribosomal protein L13a protein RPL13AP3 0 191.53 0.0019529 0 109070 107180 95277 107680 108640 111040 126330 125560 150060 135860 FALSE TRUE 104807.4238 104123.3313 112495.6733 113237.3777 112134.5043 113285.3049 127876.0643 122967.1421 133025.8179 126658.0812 0.827483117 0.822082021 0.888183938 0.894039896 0.88533241 0.894418294 1.009616308 0.970859032 1.050275013 1 16.9505796 2.487796227 0.695389185 1.026387639 0.83934593 0.841680557 0.029642475 0.267737366 0.263269947 0.023502951 0.018716933 307.4653831 -2.487796227 -0.187041709 LKSEDGVEGDLGETQSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 183.22 6.42E-10 1730240000 912120 910970 668410 715640 623760 836190 851930 951220 997010 914130 FALSE TRUE 876473.342 884990.0275 789206.5557 752574.2662 643823.8069 853098.3347 862356.1742 931576.9746 883833.6046 852215.1609 1.028464855 1.038458441 0.926064909 0.88308012 0.755470961 1.001036327 1.011899593 1.093124151 1.03710148 1 19.70085819 2.488274164 23.7528001 1.042379542 0.924936437 0.311929459 0.077074689 352.2182492 750136.7295 0.028442809 0.025364218 307.8039322 -2.488274164 -0.117443104 TLGECGFTSQTARPQAPATVGLAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLGECGFTSQTARPQAPATVGLAFR 25 1 B8ZZU8;Q15370;Q15370-2;I3L0M9 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ; 271.55 5.63E-53 870320000 47916 57814 41127 51577 35190 57714 74533 60342 64871 68129 FALSE TRUE 46043.38975 56165.20133 48559.56377 54238.89515 36321.91831 58881.01662 75445.15715 59095.91661 57507.11604 63514.56215 0.724926508 0.88428857 0.764542211 0.853959995 0.57186757 0.927047509 1.187840309 0.930430985 0.90541624 1 15.95479978 2.488933796 24.98996317 1.006621757 0.770023009 0.55380414 0.105053772 431.8996789 913704.7524 0.03430757 0.030717648 308.2717987 -2.488933796 -0.236598749 SRDS(ph)GDENEPIQER ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDSGDENEPIQER 14 1 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;Q8WX93-7 Q8WX93-8 PALLD Palladin 1 S(0.29)RDS(0.71)GDENEPIQER 69.03 0.029154 106400000 18733 19883 14742 20349 16109 20073 28291 15908 18541 31043 TRUE FALSE 18000.89365 19315.95631 17406.20733 21399.21433 16627.16061 20478.88981 28637.23372 15579.49424 16436.30341 28940.42996 0.621998142 0.66743847 0.601449507 0.73942282 0.574530532 0.707622169 0.989523437 0.538329744 0.567935702 1 14.82079874 2.489043004 24.94844568 0.739068621 0.645249087 0.136682661 0.147382684 1542.99516 3229007.317 0.049116471 0.044013491 308.3493261 -2.489043004 -0.093819534 EKLEAYQHLFYLLQTNPTYLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKLEAYQHLFYLLQTNPTYLAK 22 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 207.77 4.62E-23 455240000 723370 706950 620650 683490 662430 707180 747470 747400 826000 713250 FALSE TRUE 695099.9007 686788.4782 732815.2613 718765.0008 683737.6626 721479.6641 756617.7615 731965.9288 732235.9429 664940.9422 1.045355845 1.032856355 1.10207571 1.080945623 1.028268255 1.085028186 1.137872123 1.100798405 1.101204478 1 19.34286669 2.489092035 24.81451618 1.097716087 1.059883973 0.070479887 0.039175832 894.3125659 1853846.142 0.012488043 0.011215364 308.3841404 -2.489092035 -0.037832114 SSSLIQLTSQNS(ph)SPNQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLIQLTSQNSSPNQQR 18 0 O95639;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 SSSLIQLT(0.034)S(0.018)QNS(0.474)S(0.474)PNQQR 71.697 0.024222 74172000 70089 94198 71575 81544 72235 86889 97991 88687 99237 105560 TRUE FALSE 67349.84439 91511.56527 84510.19468 85752.49561 74558.50438 88645.95511 99190.24317 86855.58246 87972.0318 98410.32718 0.684377812 0.929897988 0.858753315 0.871376999 0.757628864 0.90077899 1.007925144 0.882586055 0.893930894 1 16.5865221 2.489399489 24.2899905 0.935778636 0.831227045 0.395280932 0.072799207 474.4177372 938541.1263 0.023400871 0.021023975 308.6025351 -2.489399489 -0.104551591 DKQLNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKQLNEK 7 1 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 93.178 0.013795 162170000 284540 265590 179610 250960 225220 253930 265870 285210 282870 260220 FALSE TRUE 273419.8622 258015.6332 212069.5224 263912.0757 232464.4058 259064.6386 269123.7966 279320.3138 250759.7835 242595.0676 1.127062742 1.063565042 0.874170792 1.08787074 0.958240446 1.067889142 1.10935395 1.151384967 1.033655737 1 17.88819069 2.490201071 21.51031034 1.093347956 1.019223248 0.07441664 0.076791038 174.0119535 286173.1194 0.025211518 0.022736497 309.1726518 -2.490201071 -0.074124708 TLLIVSHDQGFLDDVCTDIIHLDAQR ddPTM_BT-474_Pertuzumab_2h_R1 3 TLLIVSHDQGFLDDVCTDIIHLDAQR 26 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;; 299.48 8.78E-71 867878000 330458 352374 280245 365436 329154 302613 301686 247830.6 365599 334046 FALSE TRUE 317543.336 342324.6385 330891.5055 384296.1958 339741.5373 308732.0422 305378.1235 242712.8115 324097.7342 311420.7669 1.019660118 1.099235102 1.062522287 1.234009535 1.090940533 0.991366264 0.98059653 0.779372596 1.040706879 1 18.24850563 2.490499546 2.21479707 0.915483432 1.106241511 0.40742769 0.083992742 0.2553002 2.529148866 0.033557819 0.028093386 309.385208 -2.490499546 0.190758079 LSLTSDPEEGDPLALGPES(ph)PGEPQPPQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSLTSDPEEGDPLALGPESPGEPQPPQLK 29 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 LSLTSDPEEGDPLALGPES(1)PGEPQPPQLK 112.99 0.0001729 50205000 89613 95079 77562 84046 84706 100840 112220 115090 128660 126190 TRUE FALSE 86110.82489 92367.44001 91579.17876 88383.62413 87430.64542 102879.0539 113593.3819 112713.3513 114055.0562 117643.0389 0.731967022 0.785150068 0.778449619 0.751286476 0.74318588 0.874501839 0.96557674 0.958096223 0.969501105 1 16.84405643 2.490685309 2.586581406 0.969616654 0.759990015 0.965615111 0.019136409 0.048231462 0.65203771 0.007365491 0.006294781 309.517571 -2.490685309 -0.209626639 KLPS(ph)DSGDLEALEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLPSDSGDLEALEGK 15 1 O60524-4;O60524-3;O60524;G3V5V3;O60524-5;O60524-2 O60524-4 NEMF Nuclear export mediator factor NEMF 1 KLPS(0.998)DS(0.002)GDLEALEGK 130.36 3.69E-05 142160000 159430 123970 115580 148860 188540 124420 111590 130040 120720 108670 TRUE FALSE 153199.2993 120434.497 136467.8771 156542.6824 194604.5603 126935.8576 112955.6718 127354.6286 107016.3717 101309.6841 1.512188106 1.188775763 1.347036843 1.54518972 1.920888038 1.252948904 1.114954338 1.257082476 1.056329142 1 16.62841256 2.4912346 24.78345596 1.147073974 1.48985374 0.501663299 0.1853092 590.3893006 1036742.663 0.065357445 0.059379849 309.9092935 -2.4912346 0.342779766 SLQDIIAILGMDELSEEDKLTVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLQDIIAILGMDELSEEDKLTVSR 24 1 P06576;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 132.26 5.29E-05 186096000 125588 150753 111805 161134 104790 151510 171169 180739 173230 123964 FALSE TRUE 120679.8821 146453.672 132010.6506 169450.1451 108160.6655 154573.636 173263.8174 177006.6765 153565.6566 115567.8079 1.044234414 1.26725318 1.142278746 1.466240021 0.935906525 1.337514649 1.499239456 1.531626149 1.328792676 1 16.81838006 2.491271414 24.44645156 1.405900905 1.18584658 0.125330099 0.191020903 705.1803797 1218303.618 0.059665624 0.054224833 309.9355647 -2.491271414 -0.220054324 IQNTGDY(ph)YDLYGGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 IQNTGDYYDLYGGEK 15 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1 IQNTGDY(0.793)Y(0.207)DLYGGEK;IQNTGDY(0.769)Y(0.231)DLYGGEK;IQNTGDY(0.564)Y(0.436)DLY(0.001)GGEK 291.75 6.44E-43 474286000 509793 476798 411869 439843 530655 499259 543000 591040 645360 633210 TRUE FALSE 489869.726 463200.1879 486302.8903 462543.3499 547724 509354.359 549645.3964 578834.8175 572101.4384 590322.1227 0.829834606 0.784656665 0.82379242 0.783543988 0.92783919 0.862841387 0.931094017 0.980540615 0.969134336 1 19.17114288 2.491949441 0.685990384 0.998727666 0.79754656 0.833590854 0.031820549 0.25949161 0.248700381 0.024239432 0.01954248 310.4198188 -2.491949441 -0.201181106 S(ph)PVSTRPLPSASQK ddPTM_BT-474_Pertuzumab_2h_R1 8 SPVSTRPLPSASQK 14 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(1)PVSTRPLPSASQK;S(1)PVSTRPLPSASQK;S(0.99)PVS(0.01)TRPLPSASQK;S(0.996)PVS(0.004)TRPLPSASQK;S(0.901)PVS(0.097)T(0.003)RPLPSASQK;S(0.591)PVS(0.395)T(0.014)RPLPSASQK;S(0.999)PVS(0.001)TRPLPSASQK;S(0.984)PVS(0.014)T(0.001)RPLPSASQK 219.89 1.27E-11 1.15266E+11 21754310 22049500 18563520 19364850 20537740 21318720 22406840 23654990 24198540 22689320 TRUE FALSE 20904127.51 21420669.85 21918361.01 20364272.23 21198355.06 21749799.13 22681061.61 23166506.19 21451623.19 21152552.15 0.988255572 1.01267543 1.036204088 0.962733579 1.002165361 1.028235221 1.072261231 1.095210924 1.014138769 1 24.33432841 2.492799149 3.561549836 1.058248688 1.001412801 0.278839715 0.031543868 0.234629082 6.354023797 0.011212403 0.009830081 311.0277575 -2.492799149 -0.056835887 SAS(ph)WGSTDHRK ddPTM_BT-474_Pertuzumab_2h_R1 3 SASWGSTDHRK 11 1 Q9C073;D6RJ87 Q9C073 FAM117A Protein FAM117A 1 S(0.005)AS(0.991)WGS(0.003)T(0.001)DHRK;S(0.115)AS(0.823)WGS(0.031)T(0.031)DHRK;S(0.13)AS(0.715)WGS(0.13)T(0.025)DHRK 113.76 0.00082618 1608002000 1179710 1254610 931580 1205520 1133810 1150450 1277810 1261020 1426620 1370580 TRUE FALSE 1133605.629 1218829.751 1099937.229 1267737.032 1170280.028 1173712.887 1293448.221 1234979.496 1264676.078 1277749.396 0.887189329 0.95388795 0.860839561 0.992164063 0.91589167 0.918578315 1.01228631 0.966527161 0.989768481 1 20.28517348 2.492834896 0.549731428 1.001444763 0.906519606 0.433414715 0.036930671 0.856060779 0.534703523 0.031194294 0.030254445 311.0533595 -2.492834896 -0.094925158 QESEQGPCRR ddPTM_BT-474_Pertuzumab_2h_R1 1 QESEQGPCRR 10 1 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 0 75.566 0.061911 79398000 65226 91250 40264 67704 49086 55953 48321 34648 38643 36068 FALSE TRUE 62676.89581 88647.63934 47540.60047 71198.21155 50664.89577 57084.408 48912.36685 33932.50669 34256.40864 33625.08223 1.863992343 2.636354574 1.413843396 2.117413753 1.506759014 1.697673409 1.454639323 1.009142712 1.018775461 1 15.03725018 2.493155787 0.561444831 0.895134012 2.146518197 0.638659961 0.302025365 0.510203847 0.331814129 0.250233786 0.237793239 311.2832752 -2.493155787 1.251384185 EVDRPGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 EVDRPGSK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;; 99.136 0.0064093 4670241000 2792160 2812354 2588930 2688385 2536538 2871726 2988381 3020913 3493888 3245418 FALSE TRUE 2683039.3 2732148.418 3056807.241 2827132.872 2618128.048 2929794.267 3024953.701 2958530.091 3097276.482 3025602.948 0.886778386 0.90300957 1.010313413 0.934403132 0.865324398 0.968334021 0.999785415 0.977831573 1.023689008 1 21.52879124 2.493161541 13.91594482 0.994786319 0.924041739 0.505040123 0.037421651 2.206798165 1914.430151 0.012930396 0.011742267 311.2873991 -2.493161541 -0.07074458 ELDLFLAYYVQEQDSGQSGSPS(ph)HNDPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDLFLAYYVQEQDSGQSGSPSHNDPAK 28 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 ELDLFLAYYVQEQDS(0.173)GQS(0.173)GS(0.294)PS(0.36)HNDPAK 84.516 0.002554 95534000 29737 28958 23614 30119 24383 30372 33556 30639 34832 37820 TRUE FALSE 28574.84516 28132.14619 27881.57509 31673.4452 25167.30134 30986.14265 33966.66837 30006.29394 30878.01739 35258.41771 0.810440372 0.797884534 0.790777831 0.898322933 0.713795541 0.878829643 0.963363377 0.851039153 0.875762992 1 15.10568011 2.493445166 24.81102501 0.907623077 0.805663699 0.48846594 0.057608763 609.2315889 925983.4999 0.018025291 0.016573708 311.4907585 -2.493445166 -0.101959378 SATRPS(ph)PS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 5 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.045)AT(0.017)RPS(0.938)PS(1)PER;S(0.001)AT(0.002)RPS(0.998)PS(1)PER;S(0.008)AT(0.009)RPS(0.983)PS(1)PER;S(0.028)AT(0.465)RPS(0.518)PS(0.99)PER;S(0.354)AT(0.045)RPS(0.621)PS(0.98)PER 136.33 0.0012126 8621390000 2927338 2967725 2425866 2799614 2744056 2844996 2927741 3067021 3170550 2921903 TRUE FALSE 2812934.395 2883088.389 2864273.949 2944102.414 2832321.053 2902523.768 2963571.57 3003685.945 2810642.456 2723999.907 1.032648491 1.058402528 1.051495612 1.080801217 1.039765473 1.065537396 1.087948484 1.10267476 1.031807104 1 21.37729522 2.493977279 23.34772969 1.070089877 1.054267107 0 0.030274362 1007.045272 1394891.07 0.009676313 0.008920822 311.8726418 -2.493977279 -0.01582277 DRSSS(ph)APNVHINTIEPVNIDDLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRSSSAPNVHINTIEPVNIDDLIR 24 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 DRS(0.077)S(0.13)S(0.793)APNVHINTIEPVNIDDLIR 194.06 2.01E-18 256120000 56695 86772 74044 59096 62231 77261 84584 81094 85985 95894 TRUE FALSE 54479.29672 84297.34752 87425.3979 62145.95164 64232.71663 78823.27036 85619.16429 79419.38056 76224.34328 89399.01397 0.609394828 0.94293375 0.977923514 0.69515254 0.718494688 0.881701787 0.957719336 0.88836976 0.852630694 1 16.4479713 2.494298214 22.15059558 0.91471031 0.802395173 0.25308881 0.109554785 285.7422013 368481.2271 0.036818233 0.033877304 312.1031946 -2.494298214 -0.112315136 ACLISLGYDVENDRQGEAEFNR ddPTM_BT-474_Pertuzumab_2h_R1 4 ACLISLGYDVENDRQGEAEFNR 22 1 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 311.08 3.09E-67 3117760000 949450 861070 678210 1019630 965270 871780 868120 920450 918580 953630 FALSE TRUE 912344.4443 836513.1267 800777.6337 1072253.226 996318.7862 889407.9889 878744.3122 901442.3858 814306.6494 889039.7907 1.026213285 0.940917533 0.900721927 1.20608013 1.120668385 1.000414153 0.988419553 1.013950551 0.915939487 1 19.76188847 2.494747171 23.0320067 0.985803003 1.037630291 0.101002325 0.083294583 803.7415871 1050262.348 0.029778407 0.027472793 312.4260018 -2.494747171 0.051827288 KCEEEIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KCEEEIAK 8 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 96.342 0.014445 467350000 333290 422210 267870 391200 472660 574610 626410 721950 838210 870490 FALSE TRUE 320264.6583 410168.9842 316280.0677 411389.8789 487863.5382 586229.0079 634076.193 707041.4802 743059.9149 811530.9369 0.394642575 0.505426183 0.389732607 0.506930617 0.601164436 0.722374196 0.781333359 0.871244025 0.915627342 1 19.63028657 2.494939247 0.617906753 0.985175932 0.399785599 0.972275597 0.034833012 0.116056169 0.090813635 0.02904977 0.025365784 312.5642095 -2.494939247 -0.585390333 down DTRPSSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DTRPSSEK 8 1 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RCQ8;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 131.06 0.00093131 1018680000 1819510 1702850 1423050 1585750 1520700 1689070 1841930 1710480 1762310 2095850 FALSE TRUE 1748401.538 1654286.385 1680226.791 1667590.748 1569614.697 1723224.153 1864472.09 1675157.99 1562259.957 1953896.213 0.894828255 0.846660316 0.859936561 0.853469461 0.803325523 0.881942522 0.954232921 0.85734236 0.799561382 1 20.89792241 2.494972087 24.75133007 0.89312861 0.850999734 0.156911085 0.054304032 1440.491921 1997336.27 0.017416548 0.016109815 312.5878455 -2.494972087 -0.042128875 QIAEEDFYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QIAEEDFYEK 10 0 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 158.79 1.83E-05 373540000 558340 548580 480930 487790 490810 544880 560130 584210 617560 657980 FALSE TRUE 536519.4555 532935.0355 567844.7492 512964.9004 506597.3494 555897.8469 566985.0385 572145.8593 547457.1778 613414.4285 0.874644336 0.868800946 0.925711432 0.836245247 0.825864743 0.906235362 0.924309915 0.932723185 0.892475221 1 19.22650258 2.495705811 5.024596136 0.930266616 0.867615525 0.469257038 0.035375292 0.185247987 13.1934891 0.011937809 0.010649476 313.116397 -2.495705811 -0.06265109 GWDQGLLGMCEGEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWDQGLLGMCEGEKR 15 1 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 185.02 7.06E-07 343510000 286420 334450 262930 302700 319350 291170 282300 293400 334270 319730 FALSE TRUE 275226.3897 324911.8135 310447.2998 318322.3833 329622.1828 297057.6569 285754.8718 287341.1875 296325.071 298074.4023 0.923347955 1.090035947 1.041509427 1.067929285 1.10583861 0.996588954 0.958669613 0.963991491 0.994131226 1 18.18531296 2.496043417 20.18918529 0.974684239 1.049394379 0.308207327 0.047456275 66.19748636 70630.66016 0.015009 0.013866687 313.359898 -2.496043417 0.07471014 ELAEVAEHVQYMAELIER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELAEVAEHVQYMAELIER 18 0 E2QRF9;O75496 E2QRF9 GMNN Geminin 0 ; 169.25 1.87E-11 33208000 49928 62502 36048 50175 49163 40746 42310 42841 38375 42742 FALSE TRUE 47976.75856 60719.50416 42562.67548 52764.53776 50744.37254 41569.91204 42827.80244 41956.31838 34018.83088 39847.04627 1.204022959 1.523814431 1.06815133 1.324176889 1.273478897 1.043236976 1.074804947 1.052934215 0.853735322 1 15.28218517 2.496206462 0.820000815 0.953578238 1.308922006 0.564458267 0.120072096 0.452245419 0.616274845 0.082953892 0.061577187 313.4775629 -2.496206462 0.355343768 EAHVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAHVAK 6 0 E7ETZ4;Q9Y6E2;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 88.591 0.05113 136770000 642090 645120 497040 594410 553150 612010 694520 557100 668760 815220 FALSE TRUE 616996.4129 626721.8092 586866.1846 625087.5713 570942.5721 624385.2615 703019.7435 545595.6903 592845.1685 760004.4233 0.81183266 0.82462916 0.772187854 0.82247886 0.751235854 0.821554773 0.925020595 0.717884888 0.780054892 1 19.53564829 2.497197388 24.32673863 0.82954243 0.796958982 0.080983306 0.075782998 2148.262084 2603101.485 0.024356981 0.022677985 314.1936389 -2.497197388 -0.032583448 LQQQQRPEDAEDGAEGGGK ddPTM_BT-474_Pertuzumab_2h_R1 4 LQQQQRPEDAEDGAEGGGK 19 1 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;; 267.7 9.99E-32 1736550000 1406417 1254356 1133224 1225020 1149268 1373487 1474550 1473810 1726050 1652590 FALSE TRUE 1351452.669 1218582.995 1338022.785 1288243.429 1186235.249 1401259.848 1492595.984 1443375.308 1530116.04 1540658.607 0.877191522 0.790949396 0.868474546 0.836164107 0.769953345 0.909520021 0.968803846 0.936856031 0.993157104 1 20.55511578 2.49740148 4.315100143 0.964399535 0.829141223 0.798481303 0.034485706 0.09113293 4.045272088 0.011492132 0.010204814 314.3413252 -2.49740148 -0.135258312 IVFSGNLFQHQEDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IVFSGNLFQHQEDSK 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 250.19 9.68E-19 1247640000 558350 551230 476920 537470 533090 572380 603260 630820 702550 638940 FALSE TRUE 536529.0647 535509.4601 563110.053 565208.8911 550237.324 583953.9158 610642.8763 617793.3466 622799.4693 595664.0247 0.900724305 0.899012594 0.945348434 0.948871961 0.923737713 0.980341084 1.025146477 1.037150677 1.04555495 1 19.1841393 2.497489217 1.856729441 1.03311346 0.922784676 0.869472245 0.01887526 0.116551934 0.812828831 0.008372159 0.006818074 314.4048359 -2.497489217 -0.110328784 TSDIFGS(ph)PVTATSR ddPTM_BT-474_Pertuzumab_2h_R1 6 TSDIFGSPVTATSR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 1 TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(0.719)PVT(0.281)ATSR;TSDIFGS(0.997)PVT(0.003)ATSR 378.89 1.31E-97 11803875000 6192630 6420690 6051620 5760630 5616810 6501970 6544980 7082690 7290880 7655270 TRUE FALSE 5950615.173 6237578.208 7145282.352 6057936.805 5797479.795 6633444.288 6625079.423 6936429.976 6463249.868 7136771.744 0.833796482 0.874005563 1.001192501 0.848834322 0.812339248 0.929474071 0.928301991 0.971928237 0.905626535 1 22.7668402 2.497744177 21.0832456 0.948082474 0.878817468 0.327855542 0.052727468 137.6906868 140764.6 0.017715221 0.016462097 314.5894668 -2.497744177 -0.069265006 KEEEVER ddPTM_BT-474_Pertuzumab_2h_R1 3 KEEEVER 7 1 D6RCC6;E7EUJ7;Q8TC20-2;Q8TC20-4;Q8TC20;Q8TC20-3;Q8TC20-5 D6RCC6 CAGE1 Cancer-associated gene 1 protein 0 ;; 98.392 0.018113 2824110000 2843670 2546760 2277680 2447860 2516130 2784510 2831340 3119320 3331130 3090710 FALSE TRUE 2732536.233 2474128.898 2689307.443 2574194.348 2597063.607 2840814.7 2865990.786 3054904.952 2952994.088 2881373.459 0.948345042 0.858663042 0.9333422 0.893391428 0.901328357 0.985923811 0.99466134 1.06022527 1.02485642 1 21.45832523 2.498144206 1.896628258 1.031095323 0.903944566 0.782264234 0.028275723 0.134145079 0.975755605 0.011165937 0.009139583 314.8793686 -2.498144206 -0.127150757 EAPGS(ph)PPLSPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EAPGSPPLSPR 11 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;E9PNR0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 EAPGS(0.997)PPLS(0.003)PR;EAPGS(0.989)PPLS(0.011)PR;EAPGS(0.919)PPLS(0.081)PR 156 3.28E-05 974860000 1061590 1136340 916200 1048420 1068420 1131570 1175670 1332490 1219510 1406140 TRUE FALSE 1020101.889 1103932.696 1081777.721 1102529.082 1102786.7 1154451.121 1190058.201 1304973.616 1081076.337 1310900.885 0.778168587 0.842117591 0.825217019 0.841046866 0.841243386 0.880654772 0.90781707 0.995478476 0.82468198 1 20.32212718 2.498386746 1.354116506 0.942758862 0.822178291 0.530775385 0.04794544 0.321937591 1.195391994 0.0234551 0.017689209 315.0552683 -2.498386746 -0.120580571 (ac)MEDDAPVIYGLEFQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEDDAPVIYGLEFQAR 16 0 A8MUM1;Q53HC9;F8WDS8;C9J0U9;D3YTH5;F8WDX0;F8WB12 A8MUM1 TSSC1 Protein TSSC1 0 ; 45.915 2.54E-07 6490200 5779.3 5479.6 5117.1 5847.8 7173 5476.3 5510.2 5314 5947.8 6357.4 FALSE TRUE 5553.438567 5323.327173 6041.873799 6149.605659 7403.726059 5587.034538 5577.635476 5204.264043 5272.630679 5926.807635 0.937003343 0.898177822 1.019414526 1.037591573 1.249192907 0.94267182 0.941085964 0.878088908 0.889624061 1 12.53303952 2.498418483 24.82131279 0.917244946 1.028559453 0.220873884 0.091618297 1065.417467 1241713.575 0.031956347 0.029840851 315.0782922 -2.498418483 0.111314506 HGGS(ph)PQPLATTPLSQEPVNPPS(ph)EAS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 HGGS(1)PQPLATTPLSQEPVNPPS(0.999)EAS(0.862)PT(0.139)R;HGGS(1)PQPLATTPLSQEPVNPPS(1)EAS(0.836)PT(0.165)R 239.12 1.50E-45 917890000 170032 158042 146361 180595 152799 144710 159036 108585 169555 181349 TRUE FALSE 163386.9615 153534.7969 172811.6885 189915.5296 157713.9186 147636.1353 160982.3301 106342.6818 150307.8272 169066.0707 0.966408936 0.908134886 1.022154757 1.123321367 0.932853753 0.873245204 0.952185909 0.629000729 0.889047853 1 17.36722763 2.499099276 1.667898296 0.812935329 0.996915068 0.204577967 0.108707663 0.423729126 2.387076512 0.04934253 0.039250371 315.5725915 -2.499099276 0.183979739 S(ph)PFEGAVTESQSLFSDNFR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPFEGAVTESQSLFSDNFR 19 0 O95628-3;O95628-2;O95628;O95628-8;O95628-4;O95628-7;O95628-9;O95628-10;O95628-6;O95628-5 O95628-3 CNOT4 CCR4-NOT transcription complex subunit 4 1 S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR 342.3 6.08E-76 1944727000 309656.5 321178 283112.2 315168 313643.9 301876 287144.6 311783.3 323377.4 316577 TRUE FALSE 297554.7816 312018.3179 334276.8723 331433.8582 323732.5409 307980.1396 290658.7615 305344.8659 286668.9533 295134.9578 1.008199042 1.057205558 1.132623783 1.122990854 1.096896631 1.043523078 0.984833392 1.034594032 0.971314803 1 18.17101529 2.499261318 3.727081955 1.003889945 1.086572647 0.553410546 0.03607536 0.191367198 5.743768103 0.013545958 0.011960183 315.6903579 -2.499261318 0.082682701 GYNVNDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GYNVNDEK 8 0 P80723;P80723-2;U3KQP0 P80723 BASP1 Brain acid soluble protein 1 0 109.11 0.0085645 93272000 52230 61649 36949 53121 45245 52633 53975 61871 53371 50670 FALSE TRUE 50188.79386 59890.83088 43626.50623 55862.58118 46700.34652 53697.27532 54635.5622 60593.34223 47312.54783 47238.07577 1.062464824 1.267850773 0.923545371 1.182575291 0.988616614 1.136737144 1.15660008 1.282722491 1.001576526 1 15.52766258 2.500003007 24.30942204 1.150071327 1.088724193 0 0.118785753 1719.986361 1827301.554 0.037140091 0.034757499 316.2299554 -2.500003007 -0.061347134 S(ph)LSSPTVTLSAPLEGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.543)LS(0.45)S(0.006)PTVTLSAPLEGAK 89.541 0.0042208 32720000 39472 28420 31175 35098 36347 32346 30477 35719 32913 35740 TRUE FALSE 37929.3906 27609.48943 36809.01598 36909.41199 37516.13426 33000.05828 30849.98664 34981.39017 29176.85422 33319.29797 1.138361037 0.828633588 1.104735641 1.107748789 1.125958125 0.990418775 0.925889455 1.04988377 0.875674339 1 15.02407038 2.5006092 23.21449715 0.972394062 1.053690344 0.198128951 0.09319569 600.9091682 593913.284 0.030239545 0.028308008 316.6716608 -2.5006092 0.081296282 SSSSSNASGNGGDGKEERPEGS(ph)PTLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSSSNASGNGGDGKEERPEGSPTLFK 27 2 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 SSSSSNASGNGGDGKEERPEGS(0.966)PT(0.033)LFK;SSSSSNASGNGGDGKEERPEGS(0.564)PT(0.436)LFK 87.111 0.0041281 704530000 231260 227841 209336 175567 192276 224148 226960 237370 281080 239690 TRUE FALSE 222222.1035 221343.1978 247167.6719 184628.0339 198460.7322 228680.4261 229737.6044 232468.2265 249172.9768 223455.5828 0.99447998 0.990546734 1.106115447 0.826240417 0.888143987 1.023382022 1.028113066 1.040333044 1.115089512 1 17.76962856 2.500619286 19.27767157 1.044812221 0.962550258 0.234802039 0.073332733 67.63135464 55484.58955 0.025122542 0.023437438 316.6790151 -2.500619286 -0.082261963 LDS(ph)S(ph)EMDHSENEDYTMSSPLPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 LDS(0.71)S(0.79)EMDHS(0.495)ENEDY(0.003)T(0.002)MSSPLPGK 86.48 0.0035787 102100000 78571 78063 65581 81540 93943 70200 67186 60768 75998 74515 TRUE FALSE 75500.35846 75836.71967 77432.94554 85748.28917 96964.76191 71619.4921 68008.24237 59513.11956 67371.02565 69468.03268 1.086835996 1.091677952 1.1146558 1.23435609 1.395818453 1.030970496 0.978986157 0.856697927 0.969813352 1 16.08406162 2.500743858 8.517383395 0.940699419 1.181993722 0.596171956 0.091164 0.190425758 62.41082444 0.032924806 0.030103554 316.7698639 -2.500743858 0.241294304 LSHSDEKPYQCPVCQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSHSDEKPYQCPVCQQR 17 1 I3L2Z5;A0A087WWR2;P56270-3;P56270;P56270-2 I3L2Z5 MAZ Myc-associated zinc finger protein 0 79.97 0.0074582 92766000 34196 31280 35809 37485 32755 32790 29471 28473 33986 35521 FALSE TRUE 32859.58251 30387.92503 42280.48287 39419.60534 33808.59432 33453.03627 29831.67491 27885.0226 30128.05176 33115.13103 0.992283029 0.917644716 1.276772326 1.190380473 1.02094098 1.010203953 0.900847256 0.84206288 0.909797148 1 15.01520295 2.501074682 2.026901386 0.892755977 1.090211279 0.369923457 0.101271611 0.334991043 2.778295072 0.044070145 0.036634133 317.0112554 -2.501074682 0.197455301 SQYTTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQYTTGR 7 0 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 110.22 0.037086 0 119890 102660 93080 107750 90311 111320 115940 115430 121800 138930 FALSE TRUE 115204.5663 99732.23731 109901.6266 113310.9904 93215.93533 113570.9667 117358.9084 113046.3302 107973.7746 129520.1474 0.889472168 0.77001331 0.848529196 0.874852235 0.719702203 0.876859462 0.906105427 0.872808845 0.833644625 1 16.98281701 2.501409101 24.94065187 0.890982292 0.819883185 0.287762956 0.060777877 1015.125202 1042409.06 0.018627813 0.017476404 317.2554568 -2.501409101 -0.071099107 KPIDYTVLDDVGHGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPIDYTVLDDVGHGVK 16 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7 A0A0A0MRT6 ABI1 Abl interactor 1 0 186.68 9.49E-10 533750000 826590 817330 683660 796670 738980 846450 871000 925800 1013200 962050 FALSE TRUE 794285.949 794020.5486 807212.5699 837786.2342 762749.9628 863565.7989 881659.5585 906681.9065 898185.7837 896889.4966 0.885600681 0.885304769 0.900013405 0.934101957 0.850439174 0.962845258 0.983019159 1.01091819 1.001445314 1 19.77457072 2.501765589 3.413006597 0.999583368 0.893696775 0.857509725 0.020800572 0.083949038 2.038309927 0.007261026 0.006390091 317.5159814 -2.501765589 -0.105886594 LKGIEEEEILPGFILCDPNNLCHSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKGIEEEEILPGFILCDPNNLCHSGR 26 1 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 110.68 0.0012924 138690000 264660 241400 157930 175460 216380 250630 201630 227990 246910 220680 FALSE TRUE 254316.7946 234515.5084 186471.4641 184515.5116 223340.0592 255697.9103 204097.6083 223281.9268 218881.8119 205733.147 1.236148857 1.139901429 0.906375403 0.896868173 1.08558131 1.242861999 0.992050193 1.085298748 1.063911261 1 17.65041473 2.501899935 0.007493238 4.01E-07 2.124574985 0.044188776 0.111620105 20296.9165 71.51311685 9969.790142 10300.09748 317.6142177 -2.501899935 2.124574585 (ac)SILKIHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SILKIHAR 8 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ; 71.342 0.0019183 795640000 1403570 1136020 844510 780190 1304260 654260 518450 318930 651350 373170 FALSE TRUE 1348716.933 1103621.822 997131.743 820455.6994 1346212.707 667489.5855 524794.9462 312343.984 577411.4787 347894.8635 3.876794613 3.172285474 2.866187023 2.358343814 3.869596388 1.918653178 1.508487193 0.897811428 1.659729819 1 18.40829185 2.502459651 3.32896009 1.24011633 3.155864306 0.793323276 0.474005199 0.109104638 2.501857795 0.168611195 0.148226469 318.0238205 -2.502459651 1.915747977 GS(ph)PS(ph)HSKSPAYTPQNLDSESESGSSIAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSPSHSKSPAYTPQNLDSESESGSSIAEK 29 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 GS(0.92)PS(0.536)HS(0.348)KS(0.192)PAY(0.005)TPQNLDSESESGSSIAEK;GS(0.969)PS(0.537)HS(0.344)KS(0.14)PAY(0.01)TPQNLDSESESGSSIAEK 255.87 7.95E-58 843460000 484190 466520 398780 372930 436570 461780 494230 479750 578650 571650 TRUE FALSE 465267.3195 453215.3064 470848.4168 392176.962 450612.6705 471117.508 500278.5346 469842.9948 512964.0779 532931.6363 0.873033777 0.85041922 0.883506222 0.73588606 0.845535599 0.884011149 0.938729286 0.881619635 0.962532608 1 19.02359095 2.502955853 2.538269372 0.9307701 0.835344552 0.527916138 0.047237396 0.263126591 3.41167099 0.018041761 0.015515338 318.387386 -2.502955853 -0.095425548 WHPHS(ph)PNVRPSFQDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 WHPHSPNVRPSFQDDR 16 1 Q9H329-2 Q9H329-2 EPB41L4B Band 4.1-like protein 4B 1 WHPHS(0.964)PNVRPS(0.036)FQDDR;WHPHS(0.999)PNVRPS(0.001)FQDDR 108.71 0.00062146 704600000 271360 355030 265160 291300 229600 203352 250700 75517 213480 151335 TRUE FALSE 260754.9512 344904.892 313080.3105 306334.0279 236985.2925 207463.9168 253768.1416 73957.54756 189246.6454 141084.9457 1.848212437 2.444661196 2.219090839 2.171273671 1.679734797 1.470489398 1.79869043 0.524205805 1.341366682 1 17.10620453 2.503315708 0.881526653 0.931011938 2.219185322 0.690164552 0.310254882 0.305146733 0.480784983 0.209232264 0.153507848 318.6513097 -2.503315708 1.288173383 WQHWHEECER ddPTM_BT-474_Pertuzumab_2h_R1 2 WQHWHEECER 10 0 J3QLV0;J3QLD4;J3QL54;J3KT10;Q9BW27-2;Q9BW27-3;Q9BW27 J3QLV0 NUP85 Nuclear pore complex protein Nup85 0 ; 199.68 1.59E-07 394650000 356250 398100 305195 358820 339600 191890 347460 51083 280893 234147 FALSE TRUE 342327.3561 386746.5778 360350.5255 377338.7432 350523.5424 195770.1473 351712.3194 50028.1182 249007.2042 218288.0151 1.568237065 1.771726119 1.65080307 1.728627854 1.605784643 0.896843316 1.611230553 0.22918399 1.140727786 1 17.7358734 2.50367234 1.191982269 0.794867486 1.701637686 0.508749463 0.329647065 0.33140304 0.953392282 0.175882957 0.129756084 318.913086 -2.50367234 0.9067702 EGVHGGLINKK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGVHGGLINKK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;; 179.57 4.57E-06 27400060000 29316500 28156060 23218030 23889400 26549260 28576960 30619920 32516640 34746480 32117560 FALSE TRUE 28170778.77 27353076.74 27414044.5 25122334.8 27403241.06 29154805.71 30994655.74 31845160.02 30802205.26 29942209.05 0.940838357 0.913529015 0.915565196 0.839027433 0.915204386 0.973702563 1.035149267 1.063554127 1.028721869 1 24.83567733 2.504072515 2.383201816 1.040512279 0.901813856 0.812435109 0.028714571 0.117697811 1.344900645 0.011453847 0.009784436 319.2070794 -2.504072515 -0.138698423 YFHVVIAGPQDSPFEGGTFK ddPTM_BT-474_Pertuzumab_2h_R1 2 YFHVVIAGPQDSPFEGGTFK 20 0 P61088;F8VSD4;F8VV71;F8VZ29 P61088 UBE2N Ubiquitin-conjugating enzyme E2 N 0 ; 284.5 5.46E-45 2462160000 2005380 1895400 1563860 1675350 1738760 1820510 1912670 1824000 2082590 2078510 FALSE TRUE 1927007.533 1841345.048 1846484.29 1761815.014 1794688.795 1857321.96 1936077.828 1786333.763 1846183.114 1937730.666 0.994466138 0.950258506 0.952910702 0.909215633 0.926180726 0.958503672 0.999147023 0.921868964 0.952755275 1 20.88593663 2.50442324 24.43265297 0.961450649 0.944808216 0.088989313 0.029537212 1712.485849 1532506.448 0.009911311 0.00932254 319.4649671 -2.50442324 -0.016642433 ALVSEEGEGKNPVDYIQGLLDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALVSEEGEGKNPVDYIQGLLDLK 23 1 Q13618;Q13618-2;Q13618-3 Q13618 CUL3 Cullin-3 0 147.35 1.08E-07 59725000 214710 214620 164270 164810 190450 210370 206450 242770 246010 220680 FALSE TRUE 206318.8958 208499.2477 193957.2432 173315.8639 196575.9972 214623.8255 208976.5969 237756.7147 218083.9762 205733.147 1.002847129 1.01344509 0.942761271 0.842430432 0.955490158 1.043214614 1.015765324 1.155655849 1.060033248 1 17.65041473 2.504573239 2.083218357 1.080413103 0.948714193 0.419308357 0.059087207 0.285162311 2.495370699 0.025184822 0.021095203 319.5753244 -2.504573239 -0.13169891 ICDECNYGSYQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ICDECNYGSYQGR 13 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ; 234.65 2.67E-16 534910000 194445 228810 183529 199537 219000 196054 184986 201861 207660 210870 FALSE TRUE 186845.8744 222284.5628 216696.7729 209835.1285 226044.3339 200018.3462 187249.914 197692.4998 184087.3074 196587.5871 0.950445942 1.130715149 1.102291229 1.067387477 1.149840319 1.017451555 0.952501207 1.00562046 0.936413688 1 17.5848127 2.504819314 7.717356698 0.977592619 1.08363956 0.469587072 0.053448174 0.190455007 44.91909651 0.01677259 0.015381107 319.7564499 -2.504819314 0.106046941 KYVIS(ph)DEEEEDDD ddPTM_BT-474_Pertuzumab_2h_R1 6 KYVISDEEEEDDD 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD 177.93 1.59E-05 4230690000 3858790 3764420 3183670 3321400 3532270 3766520 3784210 4141950 4365140 4118070 TRUE FALSE 3707984.221 3657062.427 3759029.989 3492817.852 3645888.672 3842681.615 3830522.294 4056417.285 3869627.607 3839149.451 0.96583482 0.952570999 0.979130934 0.909789498 0.949660522 1.000920038 0.997752847 1.0565927 1.007938778 1 21.87235529 2.505288236 2.17134943 1.024486854 0.950723735 0.635844093 0.023028538 0.183592014 1.743582022 0.009198511 0.007761704 320.1018885 -2.505288236 -0.07376312 GT(ph)PDTDLEVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTPDTDLEVQR 11 0 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 1 GT(1)PDTDLEVQR 159.44 0.00343 0 239720 213740 243070 211610 211190 238080 237400 274200 247140 245330 TRUE FALSE 230351.4774 207644.3445 286998.1561 222531.2175 217983.1181 242894.1407 240305.3722 268537.6742 219085.7033 228713.5806 1.007161345 0.907879383 1.254836531 0.972968972 0.953083405 1.062001391 1.050682568 1.17412212 0.957904217 1 17.80318251 2.505959027 24.09092547 1.070091114 1.021927928 4.85E-05 0.101639507 1614.545672 1348780.062 0.033011476 0.031062963 320.5966846 -2.505959027 -0.048163186 GFAFVTFES(ph)PADAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFAFVTFESPADAK 14 0 P38159;H3BT71;H0Y6E7;H3BR27;P38159-3;O75526;Q8N7X1;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL2;RBMXL3;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2;RNA-binding motif protein, X-linked-like-3;RNA binding motif protein, X-linked-like-1" 1 GFAFVTFES(1)PADAK;GFAFVTFES(1)PADAK 267.07 6.35E-25 145268000 336300 286490 273990 259800 308510 326180 301060 358800 413450 321900 TRUE FALSE 323157.0242 278319.5857 323506.0879 273208.3091 318433.5043 332775.5831 304744.4623 351390.6546 366516.8893 300097.4263 1.076840372 0.927430765 1.07800354 0.910398708 1.061100418 1.108891826 1.015485091 1.17092192 1.221326333 1 18.19507142 2.506529548 1.190368315 1.131526323 1.000447634 0.246302356 0.080873115 0.560040674 1.607358146 0.042888078 0.031724525 321.0181211 -2.506529548 -0.131078689 DEMEEWSASEASLFEEALEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DEMEEWSASEASLFEEALEK 20 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8 Q9BTC8 MTA3 Metastasis-associated protein MTA3 0 ; 167.82 1.32E-11 25028000 35352 27628 25009.8 27541 28905 30384 32119 33772 36797 32434 FALSE TRUE 33970.40476 26840.07649 29529.6272 28962.39431 29834.75558 30998.3853 32512.08193 33074.5964 32619.95883 30237.21629 1.123463365 0.887650379 0.976598736 0.957839307 0.986689889 1.02517325 1.075233964 1.093837345 1.07880165 1 14.88403771 2.506569916 2.496520293 1.072641822 0.978473258 0.250490292 0.059643687 0.316864721 3.969738025 0.021266351 0.0182993 321.0479613 -2.506569916 -0.094168564 SEPHSLSSEALMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEPHSLSSEALMR 13 0 Q9NR28-2;Q9NR28;H7BZK7;A0A2U3TZH2 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 178.15 1.48E-05 455230000 357850 428120 293400 393730 320010 318110 299070 297290 295770 292810 FALSE TRUE 343864.8264 415910.4368 346423.9066 414050.4525 330303.4123 324542.4022 302730.1081 291150.8576 262195.4296 272977.7179 1.259680933 1.523605809 1.269055619 1.516792124 1.210001369 1.188897045 1.10899201 1.066573711 0.960501215 1 18.05842367 2.508460414 0.949807715 1.000730685 1.397046216 0.743244335 0.092880596 0.258434577 0.472828743 0.056008386 0.040895786 322.448539 -2.508460414 0.396315531 VTIAQGGVLPNIQAVLLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTIAQGGVLPNIQAVLLPK 19 0 A0A0U1RR32;A0A0U1RRH7;P20671;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;H0YFX9 A0A0U1RR32;Q7L7L0;Q99878 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A 0 ; 205.3 9.73E-16 404810000 445960 459300 310330 378660 358340 404240 395690 467690 426570 407620 FALSE TRUE 428531.3902 446201.2137 366413.5343 398202.688 369866.3315 412414.0098 400532.5726 458032.0381 378147.5619 380011.5343 1.127679956 1.17417808 0.964216875 1.047870004 0.973302908 1.085267084 1.054001093 1.205310883 0.995094958 1 18.53568368 2.508850088 24.75508834 1.090172969 1.055328926 0 0.081351852 2398.35753 1871214.418 0.027198375 0.025620836 322.7379883 -2.508850088 -0.034844043 LREELSEAMSEVEGLEANEGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LREELSEAMSEVEGLEANEGSK 22 1 G5E9B7;A0A0D9SFG6;Q99418-2;Q99418;F8W8E2;A0A286YF81;M0QZ92 G5E9B7 CYTH2 Cytohesin-2 0 ; 185.41 3.25E-17 35176000 50530 52310 42205 51801 47171 54046 57040 61105 61372 63088 FALSE TRUE 48555.23174 50818.17002 49832.38235 54474.45582 48688.29805 55138.84715 57738.07258 59843.1604 54405.30785 58814.99357 0.825558736 0.86403427 0.847273447 0.926200149 0.827821192 0.937496441 0.981689686 1.017481373 0.925024463 1 15.84389636 2.509418335 3.354556465 0.985509361 0.861817593 0.738464775 0.034568332 0.120149151 2.78188797 0.011966842 0.010573514 323.1605473 -2.509418335 -0.123691768 VHDYDMR ddPTM_BT-474_Pertuzumab_2h_R1 4 VHDYDMR 7 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ;;; 123.69 0.0042192 1376230000 1174040 1239230 979730 1069620 1134690 947210 1065350 700254 1188340 1145190 FALSE TRUE 1128157.219 1203888.374 1156789.005 1124823.216 1171188.334 966363.2352 1078388.072 685793.5102 1053444.625 1067625.261 1.056697757 1.127631967 1.083515955 1.053574936 1.097003206 0.905152089 1.010081075 0.642354143 0.98671759 1 20.02597392 2.509887744 1.669499766 0.850778855 1.0876682 0.368631867 0.10535549 0.307765787 1.73579342 0.045874543 0.036858081 323.5100258 -2.509887744 0.236889344 AEFTS(ph)PPSLFK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEFTSPPSLFK 11 0 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 AEFT(0.014)S(0.972)PPS(0.014)LFK;AEFT(0.035)S(0.964)PPS(0.001)LFK;AEFT(0.025)S(0.95)PPS(0.025)LFK;AEFT(0.003)S(0.764)PPS(0.233)LFK 142.12 3.97E-05 589451000 1852800 1841450 1746250 1805200 1852830 1984140 2114200 2294070 2209940 2388170 TRUE FALSE 1780390.528 1788933.649 2061836.22 1898366.588 1912427.96 2024260.67 2140074.212 2246696.653 1959076.876 2226417.119 0.799666205 0.803503366 0.926078138 0.852655404 0.858971099 0.909201 0.961218899 1.009108596 0.879923559 1 21.08629248 2.510056336 2.046204368 0.96928953 0.848534427 0.58070499 0.045843826 0.234566246 1.979283084 0.018834965 0.015794245 323.6356354 -2.510056336 -0.120755103 S(ph)YDVPPPPMEPDHPFYSNISK ddPTM_BT-474_Pertuzumab_2h_R1 7 SYDVPPPPMEPDHPFYSNISK 21 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(0.999)Y(0.001)DVPPPPMEPDHPFYSNISK 239.47 4.06E-30 3742920000 4584520 4325170 3630300 3694350 3812700 4157100 4142220 4444970 5046690 4105340 TRUE FALSE 4405351.89 4201820.386 4286375.966 3885015.846 3935338.958 4241159.41 4192913.727 4353179.816 4473810.909 3827281.665 1.151039373 1.097860245 1.1199531 1.015084905 1.028233431 1.108138826 1.095533095 1.137407747 1.168926486 1 21.86788865 2.510461933 24.04357971 1.112535029 1.080289183 0.012861081 0.055317994 1175.245879 847525.2833 0.018061413 0.01701353 323.9380269 -2.510461933 -0.032245846 KAEDS(ph)DSEPEPEDNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAEDSDSEPEPEDNVR 16 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 KAEDS(0.964)DS(0.036)EPEPEDNVR 154.82 1.95E-07 788010000 531280 503590 501700 524460 600440 505010 688220 684970 788120 734470 TRUE FALSE 510516.9902 489228.1063 592368.3503 551527.4435 619753.6979 515221.6482 696642.6422 670825.1301 698655.9217 684723.6927 0.745581021 0.714489818 0.865120276 0.805474455 0.905115019 0.752451907 1.017406948 0.97970194 1.020347228 1 19.38516241 2.511422633 0.60121004 1.034695967 0.752689036 0.68522066 0.064228099 0.457050576 0.340000307 0.053565534 0.048531223 324.6554015 -2.511422633 -0.28200693 ERDEDSLHQTDLFDSHMLWFLMHHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDEDSLHQTDLFDSHMLWFLMHHLR 26 1 Q5TAQ9;V9GY98 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 0 90.468 0.0035328 34019000 70949 71989 56644 71542 67804 63474 70947 56359 81882 74830 FALSE TRUE 68176.23464 69935.9442 66880.83084 75234.29119 69984.97724 64757.48777 71815.27061 55195.16696 72587.09864 69761.69745 0.977273162 1.002497742 0.958704178 1.078446969 1.003200607 0.928267088 1.029436972 0.791195871 1.040500752 1 16.09014752 2.511738851 1.862236238 0.931682537 1.004499394 0.026424171 0.073848209 0.650582545 4.555797275 0.030625949 0.025257154 324.8918753 -2.511738851 0.072816857 NYQQNYQNSESGEKNEGSESAPEGQAQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ; 204 2.32E-25 2043300000 396270 386390 344720 340720 324330 406910 443540 426020 539350 467200 FALSE TRUE 380783.3303 375370.5355 407018.5723 358304.6 334762.369 415137.999 448968.1752 417222.5381 478125.2491 435556.1279 0.874246293 0.861818975 0.934480188 0.822637031 0.768586062 0.953121705 1.030792925 0.95790763 1.097735099 1 18.73249912 2.51188423 6.001201016 1.010206943 0.855692457 0.708067879 0.051219895 0.114386671 12.19384088 0.017381697 0.015901786 325.0006502 -2.51188423 -0.154514485 AKEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 AKEEER 6 1 A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3;H3BMZ1;H3BRL8;H3BS72;Q9P035;H3BPZ1 A0A087WY00;H3BS72 MYO5A;HACD3 Unconventional myosin-Va;Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 0 ; 67.757 0.089314 253670000 722050 699270 559670 605430 623280 683400 746800 795670 667170 730160 FALSE TRUE 693831.4877 679327.5043 660814.8188 636676.3149 643328.3672 697218.8162 755939.5618 779239.1364 591435.6586 680705.6128 1.019282748 0.997975471 0.970779154 0.935318151 0.94509044 1.02425895 1.110523474 1.144752036 0.868856738 1 19.37667148 2.51190293 6.402220075 1.057808355 0.973565063 0.084130191 0.073730763 0.309703672 39.3892174 0.024927255 0.022874689 325.0146448 -2.51190293 -0.084243292 NNTAAETEDDES(ph)DGEDRGGGTSGSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 NNTAAETEDDESDGEDRGGGTSGSLR 26 1 Q6KC79 Q6KC79 NIPBL Nipped-B-like protein 1 NNTAAETEDDES(1)DGEDRGGGTSGSLR;NNTAAETEDDES(1)DGEDRGGGTSGSLR 269.08 6.67E-54 1005290000 522410 468670 435830 459960 456980 489890 494940 541120 552590 516440 TRUE FALSE 501993.6396 455303.9905 514594.176 483698.5907 471679.1767 499795.9115 500997.2238 529945.6829 489862.2998 481461.0588 1.0426464 0.945671477 1.068817855 1.004647379 0.979682922 1.038081694 1.040576833 1.100703106 1.017449472 1 18.87705959 2.512241513 4.58320698 1.052318942 1.007802861 0.098273503 0.040069303 0.318799945 15.7760214 0.013225735 0.011930129 325.2681299 -2.512241513 -0.044516081 KPSPAQAAET(ph)PALELPLPSVPAPAPL ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSPAQAAETPALELPLPSVPAPAPL 26 1 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 1 KPS(0.436)PAQAAET(0.564)PALELPLPSVPAPAPL 83.039 0.0087241 13877000 33108 33027 32343 29350 34174 36545 34406 36378 46933 40578 TRUE FALSE 31814.10276 32085.1023 38188.09957 30864.75702 35273.23775 37283.96494 34827.07092 35626.78159 41605.3626 37829.61592 0.840984028 0.848147715 1.00947627 0.815888723 0.932423893 0.98557609 0.920629778 0.941769582 1.099809279 1 15.20722851 2.51240367 0.412396698 1.028137656 0.854739263 0.415370212 0.064027057 1.392956786 0.506271414 0.066138689 0.08945649 325.3896016 -2.51240367 -0.173398392 EIDKNDHLYILLSTLEPTDAGILGTTK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIDKNDHLYILLSTLEPTDAGILGTTK 27 1 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 ; 153.17 3.70E-08 773160000 899550 946790 819800 804800 906930 959300 993210 1085860 1180700 1054510 FALSE TRUE 864394.5915 919788.4762 967956.0964 846335.8244 936102.2271 978697.7033 1005365.201 1063436.612 1046671.886 983087.0984 0.879265523 0.935612397 0.984608686 0.860896075 0.952206807 0.99553509 1.022661372 1.081731836 1.064678692 1 19.90695971 2.512592433 1.709280589 1.055321387 0.920890281 0.694024373 0.037932714 0.193816413 1.145193063 0.016464157 0.01333397 325.5310607 -2.512592433 -0.134431106 LPPQSSGVDTSPCPNS(ph)PVFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPPQSSGVDTSPCPNSPVFR 20 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 LPPQSSGVDT(0.001)S(0.001)PCPNS(0.999)PVFR 107.78 0.00023256 122790000 19191 21302 20003 28588 24384 21440 18682 25949 19281 19406 TRUE FALSE 18440.9945 20694.48782 23617.98706 30063.43011 25168.3335 21873.53149 18910.6359 25413.14408 17092.30171 18091.61433 1.019311719 1.14387182 1.305465981 1.661732864 1.391160183 1.209042548 1.045270784 1.404691898 0.944763767 1 14.14303353 2.512781131 8.415031585 1.154558946 1.314036117 0.17377588 0.196252652 0.733189638 161.7533872 0.068675041 0.063748708 325.6725323 -2.512781131 0.159477171 SRTS(ph)VQT(ph)EDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.05)RT(0.393)S(0.557)VQT(1)EDDQLIAGQSAR 196.61 2.07E-14 190600000 303860 356320 287260 297180 278800 283710 237290 288300 248850 246900 TRUE FALSE 291984.8153 346158.1025 339174.2721 312517.4954 287767.8552 289446.8106 240194.026 282346.5043 220601.5913 230177.2431 1.268521646 1.503876308 1.473535209 1.357725426 1.250201155 1.25749534 1.043517694 1.226648215 0.95839879 1 17.81238568 2.513159686 0.655964038 1.019776391 1.438174207 0.736538411 0.091037469 0.390915656 0.344833583 0.073030347 0.061844551 325.9565304 -2.513159686 0.418397815 VHCLNTLFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHCLNTLFSR 10 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 130.98 0.00026219 653740000 504370 366940 415340 355670 446000 323930 420180 227665 473220 394250 FALSE TRUE 484658.6628 356475.2305 490401.1772 374026.1713 460345.995 330480.0865 425322.2885 222963.6382 419502.0495 367547.0963 1.318630096 0.969876334 1.334253983 1.017627877 1.252481654 0.899150313 1.157191263 0.606626036 1.141355907 1 18.4875696 2.513216934 1.605397783 0.900729662 1.168666494 0.208896141 0.186403509 0.477174343 2.489256737 0.079554412 0.063507412 325.9995003 -2.513216934 0.267936832 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(ph)PAIR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESAAPAAAPTAEAPPPSVVTRPEPQALPSPAIR 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR 286.97 1.25E-74 3937520000 961670 889700 646810 897000 937240 788370 663180 946450 868120 777120 TRUE FALSE 924086.8732 864326.6271 763702.9552 943294.2775 967387.1758 804311.3816 671296.1952 926905.4768 769574.6571 724484.9702 1.275508687 1.193022164 1.054132227 1.302020492 1.3352757 1.110183668 0.926584019 1.27939918 1.062236884 1 19.46659624 2.513258315 23.37504283 1.093951154 1.223725675 0.325072564 0.110993222 404.465058 261625.0156 0.037157632 0.035015533 326.030564 -2.513258315 0.12977452 VNPHKVS(ph)PASSVDSNIPSSQGYK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNPHKVSPASSVDSNIPSSQGYK 23 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 VNPHKVS(0.905)PAS(0.043)S(0.043)VDS(0.01)NIPSSQGYK 118.32 0.00017769 374320000 502930 449620 410850 458220 507640 545210 592130 613340 732400 700000 TRUE FALSE 483274.9396 436797.2778 485099.7343 481868.7891 523968.7016 556234.5198 599376.6641 600674.3147 649261.0225 652588.3765 0.740550946 0.669330459 0.743347188 0.738396218 0.802908419 0.852351252 0.918460527 0.920448994 0.994901297 1 19.31581377 2.514472158 0.64058135 0.999681773 0.694975353 0.956742558 0.023009945 0.1332577 0.112245503 0.017788979 0.015348314 326.9430863 -2.514472158 -0.30470642 AMSTTSISS(ph)PQPGK ddPTM_BT-474_Pertuzumab_2h_R1 8 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMSTTSIS(0.004)S(0.996)PQPGK;AMSTTS(0.003)IS(0.243)S(0.754)PQPGK;AMSTTSISS(1)PQPGK;AMSTTSIS(0.029)S(0.971)PQPGK;AMSTTS(0.001)IS(0.036)S(0.963)PQPGK;AMSTT(0.041)S(0.116)IS(0.165)S(0.678)PQPGK;AMSTTSIS(0.139)S(0.861)PQPGK;AMS(0.003)T(0.003)T(0.029)S(0.205)IS(0.09)S(0.67)PQPGK 377.55 1.78E-97 9165320000 10960650 12003690 11673220 11176290 10647770 12733060 13647180 13859320 15007370 15362950 TRUE FALSE 10532295.68 11661356.51 13782830.52 11753099.67 10990265.19 12990531.2 13814198.27 13573120.2 13303796.27 14322403.71 0.735372071 0.814203869 0.962326632 0.820609438 0.767347815 0.907007752 0.964516749 0.947684514 0.928880134 1 23.7717703 2.51486162 5.058372025 0.953776843 0.827711188 0.566362611 0.057879694 0.167932696 10.70373887 0.020292561 0.018447602 327.2364101 -2.51486162 -0.126065655 RAAPT(ph)TPPPPVK ddPTM_BT-474_Pertuzumab_2h_R1 3 RAAPTTPPPPVK 12 1 Q9NZQ3-5;Q9NZQ3-4;Q9NZQ3-3;Q9NZQ3-2;Q9NZQ3;C9JC20;C9JMQ4;C9JSC3 Q9NZQ3-5 NCKIPSD NCK-interacting protein with SH3 domain 1 RAAPT(0.5)T(0.5)PPPPVK;RAAPT(0.5)T(0.5)PPPPVK;RAAPT(0.616)T(0.384)PPPPVK 110.38 0.00087647 1772780000 1550870 1697600 1313150 1471830 1407700 1596030 1633050 1711590 1761250 1736530 TRUE FALSE 1490260.286 1649186.11 1550465.416 1547791.323 1452979.949 1628302.82 1653035.754 1676245.068 1561320.284 1618913.276 0.920531265 1.018699478 0.957719872 0.956068089 0.897503264 1.005799905 1.021077397 1.035413751 0.964424906 1 20.62659427 2.515370477 24.40517341 1.011793671 0.954367807 0.389215512 0.033997302 415.1689767 264900.8427 0.011004071 0.010372023 327.6200539 -2.515370477 -0.057425864 IYPTFLHLHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IYPTFLHLHGK 11 0 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 243.53 4.61E-16 2872200000 2972600 3154000 2676600 2662600 2663900 1892100 2838500 188374 2901200 2334790 FALSE TRUE 2856427.506 3064051.008 3160321.161 2800017.105 2749586.763 1930359.558 2873238.412 184484.0111 2571867.939 2176652.594 1.312302898 1.407689503 1.451918037 1.286386773 1.263218012 0.886847797 1.320026182 0.084755836 1.181570245 1 21.05367973 2.515406945 1.263233205 0.718396557 1.377499366 0.319547841 0.315451006 0.421897472 1.364853282 0.163923828 0.123776429 327.6475652 -2.515406945 0.659102809 AGTQIENIEEDFRDGLK ddPTM_BT-474_Pertuzumab_2h_R1 5 AGTQIENIEEDFRDGLK 17 1 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ;;;; 280.25 5.96E-36 2229632000 695144 693523 598074 597846 623235 696308 741396 774019 818812 751138 FALSE TRUE 667977.004 673744.4031 706159.2759 628700.9037 643281.9198 710387.8248 750469.426 758035.2372 725863.8945 700262.7542 0.953894806 0.962130856 1.008420442 0.897807144 0.918629351 1.014458959 1.071696904 1.082501151 1.036559335 1 19.41753683 2.516588164 4.232477349 1.057337464 0.949956288 0.648222518 0.034531552 0.127939528 5.042625587 0.012237324 0.011022658 328.5399325 -2.516588164 -0.107381176 FSPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 FSPSPR 6 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 FS(0.001)PS(0.999)PR;FS(0.001)PS(0.999)PR;FSPS(1)PR 110.12 0.030394 945900000 1132470 1239430 976740 1198480 1136710 1048460 985160 1069450 1064120 975040 TRUE FALSE 1088211.82 1204082.67 1153258.645 1260333.696 1173273.309 1069660.58 997216.6828 1047365.484 943325.5588 908999.6723 1.197153149 1.324623877 1.268711838 1.386506216 1.290730179 1.176744736 1.097048451 1.152217669 1.037762265 1 19.79392025 2.516819595 2.174346116 1.088737331 1.300275687 0.758170975 0.058713868 0.160455383 1.524544464 0.022926434 0.019515289 328.715055 -2.516819595 0.211538356 GPQPPTVS(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPQPPTVSPIR 11 0 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GPQPPTVS(1)PIR;GPQPPTVS(1)PIR;GPQPPT(0.44)VS(0.56)PIR 172.21 1.43E-05 5489100000 2139970 2160860 1794610 1693230 1965470 1552650 1600040 1625010 1348500 1511150 TRUE FALSE 2056337.607 2099234.389 2118935.948 1780617.803 2028691.128 1584045.647 1619621.768 1591452.976 1195423.933 1408798.465 1.459639301 1.490088498 1.504073153 1.263926564 1.440015147 1.124394785 1.149647596 1.12965269 0.848541479 1 20.42603381 2.516832922 0.618136679 0.949436753 1.502394688 0.831269332 0.088637814 0.304789955 0.239548439 0.07164352 0.063704763 328.725142 -2.516832922 0.552957935 QLTACPELPHNVQEILGLAPPAEPHS(ph)PSPTASPLPLS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLTACPELPHNVQEILGLAPPAEPHSPSPTASPLPLSPTR 40 0 Q9HA65-2;Q9HA65 Q9HA65-2 TBC1D17 TBC1 domain family member 17 2 QLTACPELPHNVQEILGLAPPAEPHS(0.776)PS(0.209)PT(0.019)AS(0.161)PLPLS(0.802)PT(0.034)R 155.93 2.33E-14 29345000 11592 12264 7989.3 17853 12147 11476 11512 11060 12316 11890 TRUE FALSE 11138.97182 11914.24273 9433.144231 18774.39547 12537.71929 11708.05258 11652.8873 10831.60714 10917.93931 11084.67971 1.004897942 1.0748387 0.851007379 1.693724669 1.131085391 1.056237337 1.051260623 0.977169158 0.984957581 1 13.43627946 2.516933631 2.702189525 1.001156296 1.158138475 0.106130223 0.203810524 0.674907054 9.875282284 0.07741283 0.067606883 328.8013798 -2.516933631 0.156982179 EKDQADFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKDQADFR 8 1 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;; 83.948 0.016233 5930200000 9881000 9822300 7999900 9214800 9354100 9675900 10297600 10585000 11297200 10951600 FALSE TRUE 9494839.596 9542177.621 9445659.887 9690376.932 9654983.122 9871553.327 10423625.11 10366416.05 10014789.22 10209838.38 0.929969628 0.934606139 0.925152734 0.949121482 0.945654844 0.966866758 1.020939287 1.01533596 0.98089596 1 23.28345669 2.517449833 2.453703543 1.00713564 0.936120063 0.865906316 0.012404414 0.096731934 1.167095734 0.0048372 0.004184833 329.1924251 -2.517449833 -0.071015577 (ac)MDEPS(ph)PLAQPLELNQHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 MDEPSPLAQPLELNQHSR 18 0 Q13085;A0A0C4DGT1;A0A087X2F8;A0A087X126 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR 107.65 1.63E-11 1328598000 44696 23877.2 25558.5 31064.1 37376.7 33585 42744.8 48662 38663 54551.6 TRUE FALSE 42949.23091 23196.24563 30177.4895 32667.32192 38578.9555 34264.11171 43267.92365 47657.11269 34274.13833 50856.77154 0.844513515 0.456109284 0.593381935 0.642339671 0.758580506 0.673737453 0.850779991 0.9370849 0.673934607 1 15.63415226 2.519021736 0.993669565 0.884051995 0.618165189 0.390606967 0.123497028 0.508559338 1.020216854 0.07474106 0.055054199 330.3860763 -2.519021736 -0.265886805 HDKYER ddPTM_BT-474_Pertuzumab_2h_R1 3 HDKYER 6 1 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1 C4P0D6 DISC1;TSNAX Translin-associated protein X 0 ;; 81.958 0.055182 124103000 176015 161503 128920 151219 149681 139318 156622 106987 177208 169867 FALSE TRUE 169136.1392 156897.0926 152218.7118 159023.4307 154495.6253 142135.1054 158538.7869 104777.6811 157092.0908 158361.7568 1.068036517 0.990751149 0.961208785 1.004178243 0.97558671 0.89753428 1.001117884 0.661635001 0.991982496 1 17.27286445 2.519700494 1.461573968 0.860711257 1.001580658 0.115060624 0.099475916 0.55196397 2.388603579 0.047198858 0.037038261 330.9028394 -2.519700494 0.140869401 HAELSGS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HAELSGSPLK 10 0 Q9BTC8;F6RRE2;E7EV10 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 HAELSGS(1)PLK;HAELSGS(1)PLK 164.53 3.95E-06 1061460000 2791590 2603400 2218710 2371690 2449440 2226700 2738370 1855880 2723000 2733180 TRUE FALSE 2682491.577 2529153.581 2619680.252 2494093.205 2528228.462 2271725.4 2771882.991 1817555.429 2413896.456 2548059.284 1.052758699 0.992580352 1.028108046 0.978820713 0.992217284 0.891551234 1.087840855 0.71330971 0.947347054 1 21.28096741 2.519740723 1.034833464 0.884613159 1.015561065 0.129946045 0.09263396 0.75473415 1.641591508 0.055292642 0.040788005 330.9334929 -2.519740723 0.130947907 GKGGVTGS(ph)PEASISGSK ddPTM_BT-474_Pertuzumab_2h_R1 5 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVT(0.024)GS(0.973)PEAS(0.003)ISGSK;GKGGVT(0.055)GS(0.944)PEAS(0.002)ISGSK;GKGGVTGS(0.97)PEAS(0.03)ISGSK;GKGGVTGS(1)PEASISGSK;GKGGVT(0.001)GS(0.999)PEASISGSK 276.89 2.38E-35 3004530000 2875736 2721152 2332147 2324774 2196504 2790057 2794405 3127243 3315235 3197765 TRUE FALSE 2763349.058 2643547.409 2753617.841 2444755.865 2267156.546 2846473.864 2828603.764 3062664.339 2938903.421 2981177.528 0.92693207 0.886746054 0.923667851 0.820063831 0.760490284 0.954815283 0.948820973 1.027333767 0.985819661 1 21.50745086 2.519968472 9.279364402 0.989634107 0.864881057 0.606721297 0.048888409 0.34088466 71.74207304 0.017178033 0.016072277 331.1070837 -2.519968472 -0.12475305 VGALDVPASQFLGSATS(ph)PGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGALDVPASQFLGSATSPGPR 21 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 VGALDVPASQFLGSAT(0.001)S(0.999)PGPR;VGALDVPASQFLGS(0.003)AT(0.051)S(0.947)PGPR 179.78 5.90E-17 96647000 206706 261310 267650 254900 216782 231850 192599 182726 195670 246150 TRUE FALSE 198627.701 253857.6946 316020.3088 268055.4195 223754.9899 236538.1659 194956.0842 178952.6442 173458.3619 229478.0413 0.865562996 1.106239592 1.377126574 1.168109236 0.975060571 1.030766014 0.849563135 0.779824698 0.755882179 1 17.80799658 2.520290355 1.471629397 0.816527165 1.13242228 0.42481535 0.138037128 0.354119892 1.553483606 0.067983494 0.053469374 331.3525788 -2.520290355 0.315895116 T(ph)NHRLSLPMPASGTSLSAAIHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TNHRLSLPMPASGTSLSAAIHR 22 1 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 T(0.633)NHRLS(0.367)LPMPASGTSLSAAIHR 274.63 3.03E-45 6487900000 818590 756100 573560 677010 574300 564310 500160 220570 528220 513030 TRUE FALSE 786598.5978 734536.7683 677215.0508 711950.5672 592772.8811 575720.7348 506281.1077 216015.1524 468258.6801 478282.0211 1.644633423 1.535781685 1.415932485 1.48855808 1.239379393 1.203726482 1.058540956 0.451648071 0.979043032 1 18.86750204 2.52078394 1.154127715 0.755762494 1.519164758 0.735777156 0.171313341 0.223936196 0.605366773 0.098411697 0.073481783 331.7293826 -2.52078394 0.763402264 GLMAGGRPEGQYS(ph)EDEDTDTDEYKEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 1 GLMAGGRPEGQYS(1)EDEDTDTDEYKEAK;GLMAGGRPEGQYS(1)EDEDTDTDEYKEAK 141.65 1.08E-07 338210000 247930 257120 186711 202808 225010 283230 319480 311190 417450 355880 TRUE FALSE 238240.6215 249787.1893 220453.8311 213274.9452 232247.651 288957.1047 323389.8918 304763.8178 370062.8261 331775.9306 0.718076869 0.752879176 0.664466017 0.642828263 0.700013562 0.870940529 0.974723788 0.918583265 1.115399859 1 18.3398497 2.52134813 2.032114928 0.992596783 0.691186797 0.878686432 0.053766147 0.113468705 0.942712297 0.02255847 0.019059948 332.1606107 -2.52134813 -0.301409986 SRS(ph)PITTNHRPSPDPEQRPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.459)RS(0.541)PITTNHRPSPDPEQRPLR 105.73 0.00027375 519460000 224030 261520 186950 239870 213800 215470 185240 218500 197420 204950 TRUE FALSE 215274.6599 254061.7057 220736.0237 252249.7194 220677.0712 219826.951 187507.0225 213987.8986 175009.7093 191068.5539 1.126688068 1.329688745 1.155271336 1.32020531 1.154962795 1.150513501 0.981359929 1.119953515 0.915952446 1 17.54373083 2.521400613 1.4975573 1.016695009 1.233520773 0.611491749 0.079444335 0.263471912 1.196649837 0.034829788 0.027541496 332.2007537 -2.521400613 0.216825763 ARENIPTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARENIPTDR 9 1 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 94.363 0.008001 277230000 220220 264500 193850 224990 210820 212310 211470 206000 219720 217420 FALSE TRUE 211613.5589 256956.719 228883.0072 236601.7609 217601.2168 216603.0537 214058.0331 201746.028 194778.3067 202693.9497 1.044005306 1.267707888 1.129204929 1.167285758 1.073545693 1.068621209 1.056065232 0.995323384 0.960947808 1 17.6289435 2.521482474 0.829984582 0.980124714 1.16306488 0.593653547 0.055174975 0.389535382 0.547215929 0.036679847 0.027789796 332.2633764 -2.521482474 0.182940165 HNS(ph)TTSSTSSGGYR ddPTM_BT-474_Pertuzumab_2h_R1 3 HNSTTSSTSSGGYR 14 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12 A0A0A0MRT6 ABI1 Abl interactor 1 1 HNS(0.957)T(0.039)T(0.003)S(0.001)STSSGGYR;HNS(0.945)T(0.035)T(0.019)S(0.001)S(0.001)TSSGGYR;HNS(0.615)T(0.333)T(0.035)S(0.006)S(0.011)TSSGGYR 122.63 0.00011288 322801000 374350 362886 226778 310556 347611 258549 236947 210352 288862 242630 TRUE FALSE 359719.9881 352536.8466 267761.8292 326583.8324 358792.2235 263777.0379 239846.8283 206008.1577 256071.5968 226196.454 1.590298972 1.558542764 1.183757855 1.443806154 1.586197384 1.166141349 1.060347428 0.910748838 1.132076088 1 17.78721679 2.521832069 3.35765837 1.011805804 1.458829668 0.750033593 0.122337307 0.12629571 2.884162303 0.045027652 0.040101428 332.530947 -2.521832069 0.447023863 INYTEGR ddPTM_BT-474_Pertuzumab_2h_R1 5 INYTEGR 7 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ERK8 P06744 GPI Glucose-6-phosphate isomerase 0 ;;;; 169.97 0.0023079 13138130000 12288830 12284930 9573710 11468520 10344230 9517670 9107540 10760830 9351080 8908900 FALSE TRUE 11808568.94 11934575.82 11303892.36 12060411.69 10676961.55 9710123.808 9219000.799 10538615.1 8289584.601 8305492.268 1.421778331 1.436949845 1.361014134 1.452100767 1.28553025 1.169120805 1.109988487 1.268873025 0.998084681 1 22.98563425 2.521969876 0.419862793 1.00361685 1.487779973 0.811375127 0.071542586 0.568028661 0.212924154 0.076662218 0.102280146 332.6364801 -2.521969876 0.484163122 EEHYFCK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEHYFCK 7 0 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 108.98 0.0071304 1472010000 2933100 3406900 2427000 3167100 2570400 2289300 3136200 2710800 2719900 2644500 FALSE TRUE 2818471.209 3309738.548 2865612.888 3330554.411 2653079.25 2335591.215 3174581.754 2654821.033 2411148.355 2465385.66 1.143217167 1.342483086 1.162338589 1.350926334 1.076131533 0.94735329 1.28766132 1.076838028 0.978000479 1 21.23338191 2.522053566 0.410359463 0.997567141 1.275767279 0.332192012 0.115194065 1.602909607 0.575966723 0.120794659 0.16546003 332.7005864 -2.522053566 0.278200139 KSSTGSIS(ph)NVLFSTQDPVEDAVFGEATNLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSTGSISNVLFSTQDPVEDAVFGEATNLKK 31 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 KS(0.174)S(0.174)T(0.201)GS(0.201)IS(0.25)NVLFSTQDPVEDAVFGEATNLKK 111.75 4.77E-05 276420000 204530 235890 217560 231080 210760 261640 280820 290270 343710 295560 TRUE FALSE 196536.7415 229162.6482 256877.9316 243006.0665 217539.2868 266930.5401 284256.7592 284275.8231 304693.4817 275541.4579 0.713274666 0.831681192 0.932265996 0.881921974 0.78949748 0.968749102 1.031629727 1.031698915 1.105799048 1 18.07190988 2.522740889 3.195887895 1.042183808 0.838631581 0.740066567 0.059599436 0.138608251 2.848711006 0.022013203 0.019549746 333.2275414 -2.522740889 -0.203552227 S(ph)QESGYYDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQESGYYDR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.987)QES(0.013)GYYDR 124.04 0.00056729 426820000 91793 91955 77746 95169 103830 81960 79857 81293 82940 91445 TRUE FALSE 88205.62808 89332.53343 91796.43165 100080.6835 107169.7862 83617.28736 80834.31385 79614.27114 73524.99891 85251.3487 1.034653755 1.047872377 1.076773952 1.173948389 1.257103704 0.980832428 0.948188094 0.933876969 0.862449686 1 16.37943504 2.523016232 10.23495832 0.935648511 1.115482402 0.625482217 0.067629822 0.47157254 103.8078824 0.023613012 0.022164141 333.438875 -2.523016232 0.179833891 AEKEEENRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEKEEENRR 9 2 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 84.817 0.0085689 76582000 201800 196820 156670 166420 171670 187400 187980 199510 210940 213200 FALSE TRUE 193913.4329 191206.8863 184983.7541 175008.9561 177191.9215 191189.3564 190280.5555 195390.0488 186994.9755 198759.7741 0.975617092 0.961999918 0.9306901 0.880504906 0.891487839 0.961911721 0.957339363 0.983046241 0.940808956 1 17.60066628 2.524295233 14.97232872 0.968695975 0.927372249 0.313212848 0.030190095 6.474894127 2054.200147 0.010639712 0.010023619 334.4223027 -2.524295233 -0.041323726 HESQQDYSK ddPTM_BT-474_Pertuzumab_2h_R1 4 HESQQDYSK 9 0 Q14247 Q14247 CTTN Src substrate cortactin 0 ;;; 205.53 1.48E-05 2144090000 3598730 5737820 4214830 5737710 4200580 4465260 4880790 3515930 4628490 5901560 FALSE TRUE 3458087.653 5574182.992 4976543.539 6033833.901 4335695.471 4555550.617 4940522.568 3443324.817 4103083.219 5501842.085 0.628532699 1.013148488 0.904523151 1.0966934 0.788044332 0.828004611 0.897976076 0.625849445 0.745765356 1 22.3914833 2.526374064 1.513692977 0.768910756 0.90899723 0.02522053 0.149617745 0.798082115 3.702346956 0.068134177 0.054273404 336.0269148 -2.526374064 0.140086474 WGDYDSHDIER ddPTM_BT-474_Pertuzumab_2h_R1 2 WGDYDSHDIER 11 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 174.24 1.12E-05 1852000000 2270800 2398100 1970850 2094900 2272800 1992410 2307300 2053200 2337300 2370900 FALSE TRUE 2182054.625 2329708.536 2327026.436 2203018.04 2345906.676 2032697.895 2335537.428 2010800.702 2071979.503 2210316.831 0.987213505 1.054015652 1.052802206 0.996697853 1.061344077 0.919640961 1.056652781 0.909734149 0.937412896 1 21.07582175 2.526651982 1.125300186 0.953747698 1.031911443 0.250098322 0.048459812 0.587531409 1.511549093 0.026194703 0.019605669 336.2420165 -2.526651982 0.078163745 KQS(ph)SEGIPVAQPSVMDDIEVWLR ddPTM_BT-474_Pertuzumab_2h_R1 6 KQSSEGIPVAQPSVMDDIEVWLR 23 1 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 KQS(0.943)S(0.057)EGIPVAQPSVMDDIEVWLR;KQS(0.841)S(0.159)EGIPVAQPSVMDDIEVWLR;KQS(0.5)S(0.5)EGIPVAQPSVMDDIEVWLR;KQS(0.5)S(0.5)EGIPVAQPSVMDDIEVWLR;KQS(0.789)S(0.211)EGIPVAQPSVMDDIEVWLR;KQS(0.5)S(0.5)EGIPVAQPSVMDDIEVWLR 154.02 2.72E-08 858193000 574876 537440 502571 580665 638677 531281 542654 551747 584811 584685 TRUE FALSE 552409.2104 522112.7374 593396.7593 610633.1902 659220.6257 542023.8658 549295.162 540353.2316 518425.707 545083.7642 1.01343912 0.957857804 1.088634075 1.120255693 1.209393251 0.99438637 1.007726148 0.991321458 0.95109365 1 19.05611842 2.526838978 24.99868454 0.989668652 1.076963369 0.333057692 0.063002494 497.4178872 250107.0349 0.022474996 0.021189319 336.3868251 -2.526838978 0.087294717 AAFDDAIAELDTLSEESYK ddPTM_BT-474_Pertuzumab_2h_R1 9 AAFDDAIAELDTLSEESYK 19 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;;;;; 347.73 2.70E-90 1524699000 503542.9 477363.5 511208.6 586816.1 570953.1 539035.2 685794.9 768792.3 844519.5 868153.5 FALSE TRUE 483863.8868 463749.5604 603595.3658 617101.7492 589318.325 549934.8611 694187.8631 752916.4703 748653.1869 809352.6902 0.597840586 0.572988224 0.745775449 0.762463332 0.728135376 0.679474928 0.857707488 0.93026993 0.925002407 1 19.62640899 2.527076263 0.352750985 1.031030894 0.553204863 0.838023451 0.055235066 0.675874664 0.18465058 0.072413695 0.11752128 336.570667 -2.527076263 -0.477826031 LLSPQMS(ph)GEEEDSDLAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLSPQMSGEEEDSDLAAK 18 0 P42858;A0A3B3IU44 P42858 HTT Huntingtin 1 LLSPQMS(1)GEEEDSDLAAK;LLSPQMS(1)GEEEDSDLAAK 257.71 1.30E-30 137295000 85652 83872 71907 82127 104966 93008 101221 149158 134357 108328 TRUE FALSE 82304.62515 81480.05268 84902.19446 86365.58431 108342.3267 94888.68548 102459.7729 146077.8352 119105.3566 100990.8481 0.814971126 0.806806302 0.840691965 0.855182286 1.072793513 0.939577074 1.014545128 1.446446267 1.179367823 1 16.62386503 2.52797191 1.009976453 1.239606727 0.829649262 0.533740882 0.129282862 0.361622597 0.750670628 0.082032785 0.060977604 337.2654937 -2.52797191 -0.409957465 VS(ph)PAAAQLADTLFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPAAAQLADTLFSK 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VS(1)PAAAQLADTLFSK;VS(1)PAAAQLADTLFSK 189.44 2.70E-07 1040720000 1343470 1183020 1303770 1482910 1438330 1320230 1557170 1855380 1998560 2072170 TRUE FALSE 1290965.707 1149281.428 1539390.241 1559443.163 1484595.191 1346925.955 1576227.112 1817065.755 1771691.847 1931820.08 0.668263945 0.594921566 0.796860048 0.807240373 0.768495579 0.697231574 0.815928527 0.940597819 0.917110173 1 20.8815293 2.529758816 0.26544909 1.042402656 0.573296116 0.739977415 0.061352059 1.492540419 0.254168147 0.119922271 0.240974205 338.6560325 -2.529758816 -0.46910654 VEAKPEVQSQPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 VEAKPEVQSQPPR 13 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;; 177.84 1.38E-05 4141940000 2626980 2728070 2090850 2420980 2591140 2717060 2730380 2883910 3222830 3148470 FALSE TRUE 2524314.717 2650268.115 2468713.106 2545927.068 2674486.371 2772000.815 2763795.207 2824356.251 2856987.85 2935221.323 0.860008306 0.902919345 0.841065403 0.867371414 0.911170259 0.944392436 0.941596869 0.9622294 0.973346653 1 21.48503786 2.530080895 0.725368308 0.985284052 0.862998429 0.869574588 0.018078191 0.24728472 0.266838505 0.014414195 0.011636308 338.9072779 -2.530080895 -0.122285623 KTTAS(ph)PSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTTASPSVR 9 1 Q9Y3P9;Q9Y3P9-2 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 KT(0.002)T(0.002)AS(0.987)PS(0.01)VR 101.93 0.0018958 0 49128 48488 37210 46248 44422 49746 52639 56414 55175 60061 TRUE FALSE 47208.02345 47105.16971 43934.67473 48634.86482 45850.87397 50751.8982 53283.21183 55249.03119 48911.76531 55993.01497 0.843105581 0.841268679 0.784645634 0.86858807 0.818867746 0.906396954 0.951604622 0.986712918 0.873533339 1 15.77295924 2.530207663 2.671774605 0.955642502 0.830886601 0.705206068 0.03718956 0.145908689 2.075499446 0.013147761 0.011567661 339.0062174 -2.530207663 -0.124755901 GQKPALDCSQVS(ph)PPRPAT(ph)SPENNASLSDTSPMDSS(ph)PSGIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK 41 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 3 GQKPALDCS(0.157)QVS(0.826)PPRPAT(0.235)S(0.235)PENNAS(0.21)LS(0.23)DT(0.056)S(0.061)PMDS(0.42)S(0.488)PS(0.083)GIPK 65.333 0.021819 222350000 82342 76634 65786 62586 80347 72679 86634 80357 92425 92859 TRUE FALSE 79123.98361 74448.47335 77674.9936 65816.07096 82931.43422 74148.61918 87694.25281 78697.59987 81933.30148 86569.57722 0.913992954 0.859984255 0.897255088 0.760267903 0.957974347 0.856520519 1.01299158 0.909067624 0.946444514 1 16.40157249 2.532084769 1.700095334 0.954709104 0.867188477 0.335612011 0.057795452 0.433982441 2.532735256 0.023710634 0.019511042 340.4746396 -2.532084769 -0.087520627 KGHSDENSNAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGHSDENSNAK 11 1 Q7Z333-3;Q7Z333;Q7Z333-4;X6RI79 Q7Z333-3 SETX Probable helicase senataxin 0 59.418 0.064988 10537000 31314 30606 22587 25856 29969 25582 24540 24491 30409 25914 FALSE TRUE 30090.21426 29733.14685 26668.97335 27190.43126 30932.9801 26099.28557 24840.32786 23985.25229 26957.0978 24158.8217 1.245516633 1.230736632 1.103902073 1.125486648 1.280401027 1.08032113 1.028209412 0.992815485 1.115828336 1 14.56026247 2.532173467 5.839380473 1.031583899 1.189852695 0.638917974 0.05845348 0.141920249 10.69974909 0.019792692 0.018344517 340.5441832 -2.532173467 0.158268796 S(ph)PLFIFMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPLFIFMR 8 0 C9J417;O43521-11;O43521-10;O43521-14;O43521-19;O43521-4;O43521-8;O43521-12;O43521 C9J417 BCL2L11 Bcl-2-like protein 11 1 S(1)PLFIFMR;S(1)PLFIFMR 96.034 0.0096794 177839000 104674 111658 103045 100726 99304 83947 109041 85646 86826 100251 TRUE FALSE 100583.2244 108473.6232 121667.5237 105924.4809 102498.2033 85644.46586 110375.4764 83877.38017 76969.87648 93460.91048 1.07620634 1.160630927 1.301801182 1.133355971 1.096695964 0.916366697 1.18098011 0.897459481 0.823551537 1 16.51207547 2.534192567 0.826492768 0.919496209 1.181370837 0.473880171 0.101744962 0.543919574 0.760218368 0.072841627 0.055939424 342.1311107 -2.534192567 0.261874628 S(ph)RTPS(ph)ASNDDQQE ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 S(0.918)RT(0.082)PS(0.955)AS(0.045)NDDQQE;S(0.958)RT(0.042)PS(0.923)AS(0.077)NDDQQE 127.57 0.002097 135203000 348380 327620 256040 265980 268060 271930 180595 202665 201735 199547 TRUE FALSE 334764.9244 318276.5984 302312.1236 279707.2597 276682.3933 277428.6109 182805.1756 198479.8969 178834.8885 186031.504 1.799506628 1.710874726 1.625058752 1.503547806 1.487287838 1.491299081 0.982657086 1.06691551 0.961315072 1 17.50518743 2.534288587 0.790086725 0.937518063 1.717877787 0.909250992 0.093208075 0.175708428 0.224674953 0.068563314 0.053457443 342.2067621 -2.534288587 0.780359723 EAALPPVS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 10 EAALPPVSPLK 11 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK 187.11 3.91E-06 26165517000 23306610 22251020 22101550 23923490 21976190 20685180 19839310 19631640 21157350 20589660 TRUE FALSE 22395761.91 21616442.7 26095791.73 25158184.19 22683074.11 21103448.51 20082109.41 19226239.77 18755656.33 19195103.99 1.166743453 1.126143558 1.359502493 1.310656311 1.181711447 1.099418296 1.046209983 1.001622069 0.977106263 1 24.19423504 2.534574964 1.649176844 0.99944706 1.240207169 0.738655506 0.06343338 0.206152199 1.132761001 0.030711426 0.02515484 342.43249 -2.534574964 0.240760109 DKETGGILR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKETGGILR 9 1 O95347-2;O95347 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ; 94.616 0.0078445 614180000 804620 877180 696820 709960 786060 815520 879090 842630 945200 1039870 FALSE TRUE 773174.5608 852163.6852 822750.8747 746601.1207 811344.3338 832010.3732 889848.5664 825229.396 837904.8586 969438.6787 0.797548703 0.879027941 0.848687898 0.770137542 0.836921769 0.8582393 0.917900829 0.851244554 0.864319608 1 19.88679012 2.534604472 3.145037431 0.891997035 0.827643799 0.381754317 0.047171423 0.330716108 6.496713743 0.016360703 0.01461637 342.4557576 -2.534604472 -0.064353236 QQAAYYAQTS(ph)PQGMPQHPPAPQGQ ddPTM_BT-474_Pertuzumab_2h_R1 4 QQAAYYAQTSPQGMPQHPPAPQGQ 24 0 Q96AE4 Q96AE4 FUBP1 Far upstream element-binding protein 1 1 QQAAYYAQT(0.003)S(0.997)PQGMPQHPPAPQGQ;QQAAYYAQT(0.001)S(0.999)PQGMPQHPPAPQGQ;QQAAYYAQT(0.001)S(0.999)PQGMPQHPPAPQGQ;QQAAYYAQT(0.002)S(0.998)PQGMPQHPPAPQGQ 233.87 1.56E-37 2564320000 960580 1090700 865440 954420 969900 949050 883180 1008800 965690 1000160 TRUE FALSE 923039.4716 1059594.304 1021844.26 1003677.731 1001097.714 968240.4412 893988.621 987967.9275 856068.9197 932418.2723 0.989941423 1.136393757 1.095907588 1.076424348 1.073657332 1.038418562 0.958784965 1.059575897 0.918116842 1 19.83061775 2.534609145 3.194048207 0.995320843 1.079170065 0.427943407 0.048158025 0.252618488 5.119578412 0.016385696 0.014654413 342.4594424 -2.534609145 0.083849222 RGEIIAK ddPTM_BT-474_Pertuzumab_2h_R1 5 RGEIIAK 7 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;; 132.08 0.0054568 5771940000 6438170 6358550 5154060 5962790 6076800 6267330 6416020 6890080 7305170 7080390 FALSE TRUE 6186559.199 6177210.38 6085513.293 6270530.306 6272265.791 6394059.707 6494541.172 6747797.44 6475917.727 6600828.879 0.937239749 0.935823439 0.921931685 0.949961046 0.950223965 0.968675272 0.983897824 1.022265168 0.981076445 1 22.65421577 2.535101321 1.191714169 1.004372676 0.934250471 0.85029606 0.011642603 0.158041501 0.456167491 0.006380825 0.004859689 342.8477637 -2.535101321 -0.070122205 RRDEDMLYSPELAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 0 ; 138.19 6.82E-06 283600000 254350 286910 199995 227460 220260 236950 215530 214200 222060 208970 FALSE TRUE 244409.7208 278727.6077 236138.5454 239199.2379 227344.8629 241741.2913 218167.7206 209776.6951 196852.6798 194816.2758 1.254565204 1.430720337 1.212108919 1.22781958 1.166970583 1.240868046 1.119863932 1.076792451 1.010452946 1 17.57175469 2.535188284 0.40976722 0.977496851 1.356816953 0.764824515 0.059526239 0.593290402 0.211939527 0.060464162 0.083751693 342.9164222 -2.535188284 0.379320102 TKPIVKPQTS(ph)PEYGQGINPISR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKPIVKPQTSPEYGQGINPISR 22 2 O95793-2;O95793-3;O95793;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 TKPIVKPQT(0.054)S(0.946)PEYGQGINPISR;TKPIVKPQT(0.053)S(0.947)PEYGQGINPISR 195.38 2.32E-19 3241800000 1611410 1530080 1433320 1447840 1587660 1714880 1681590 1816990 2097620 1967470 TRUE FALSE 1548434.316 1486443.617 1692352.808 1522563.196 1638728.526 1749556.049 1702169.801 1779468.522 1859506.972 1834211.504 0.844196164 0.810399244 0.922659575 0.8300914 0.893423971 0.953846404 0.928011735 0.970154487 1.013790922 1 20.80672858 2.535480163 0.558122976 1.010045313 0.832960752 0.78565756 0.031183003 0.389407132 0.251317527 0.026526395 0.026238029 343.1469654 -2.535480163 -0.177084561 VLDDVSIRS(ph)PETK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLDDVSIRSPETK 13 1 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 VLDDVSIRS(1)PETK 214.82 1.83E-11 396560000 824200 743200 658900 685220 749720 817080 809500 995140 875590 909620 TRUE FALSE 791989.3528 722004.6637 777977.8872 720584.2863 773835.4247 833601.9174 819406.9031 974590.0112 776196.694 848010.6272 0.933938004 0.851409924 0.917415257 0.849734972 0.912530338 0.98300881 0.966269616 1.149266271 0.915314819 1 19.69372282 2.537049178 1.766650273 1.03479094 0.887139519 0.43377799 0.061692409 0.276533745 1.739999154 0.02566978 0.021389719 344.3889257 -2.537049178 -0.147651421 HDDYFQER ddPTM_BT-474_Pertuzumab_2h_R1 2 HDDYFQER 8 0 Q8N684-2;Q8N684;Q8N684-3 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ; 128.86 0.0011155 1639500000 1364700 1289120 1178530 1308760 1293800 1174220 1272990 898050 1569960 1462890 FALSE TRUE 1311366.015 1252355.56 1391516.587 1376305.26 1335416.252 1197963.533 1288569.232 879504.9537 1391744.723 1363807.157 0.961547979 0.918279064 1.020317704 1.009164128 0.97918261 0.878396573 0.944832431 0.644889528 1.020484982 1 20.37920823 2.537567791 2.104903371 0.850584762 0.978820921 0.052097 0.104243705 0.483792194 4.295525596 0.041026623 0.035289121 344.800424 -2.537567791 0.128236159 IEKEQSK ddPTM_BT-474_Pertuzumab_2h_R1 4 IEKEQSK 7 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4;A0A0G2JNQ3;O60812;B2RXH8 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2 0 ;;; 132.9 0.0030316 3988500000 4937140 5230600 4264560 4510330 3950200 5653910 6463800 5991340 6570630 7776900 FALSE TRUE 4744191.111 5081428.409 5035260.857 4743108.672 4077261.77 5768235.934 6542905.918 5867616.735 5824759.629 7250163.636 0.654356419 0.700870858 0.694503064 0.65420712 0.562368241 0.795600792 0.902449413 0.80930818 0.803396988 1 22.78958213 2.537934798 5.735618994 0.857841186 0.658912512 0.737839114 0.063253901 0.118170327 8.001664208 0.020423639 0.018962267 345.0919257 -2.537934798 -0.198928674 VS(ph)PPQPPPPQPPRK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSPPQPPPPQPPRK 14 1 Q15637-5 Q15637-5 SF1 Splicing factor 1 1 VS(1)PPQPPPPQPPRK 123.36 6.33E-05 169360000 218960 206990 177090 199380 210920 231840 222500 265740 276120 264740 TRUE FALSE 210402.8011 201086.8479 209094.1023 209670.0257 217704.4334 236527.9636 225223.0216 260252.3761 244776.0152 246808.924 0.85249268 0.814747071 0.847190203 0.849523681 0.88207683 0.958344455 0.912540025 1.054469068 0.991763228 1 17.91303503 2.538086807 0.91599792 1.018860505 0.832416589 0.846990636 0.029883451 0.191040725 0.327525517 0.018990647 0.014333124 345.2127335 -2.538086807 -0.186443916 TTNHS(ph)PPTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTNHSPPTPR 10 0 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;Q9UQ26-2;D6RDY0;Q9UQ26-5;Q9UQ26-4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 T(0.012)T(0.003)NHS(0.979)PPT(0.005)PR;T(0.007)T(0.007)NHS(0.986)PPTPR 66.989 0.04143 385460000 102128 104800 100046 108331 92864 96312 89207 87738 86710 103733 TRUE FALSE 98136.72485 101811.2066 118126.5377 113921.9759 95851.0549 98259.49463 90298.74195 85926.17964 76867.04432 96707.07151 1.014783338 1.052779337 1.221488107 1.178010813 0.991148356 1.01605284 0.933734633 0.888520129 0.794844091 1 16.56133377 2.538450501 1.329603933 0.885950474 1.11254868 0.577847441 0.0774677 0.301691047 1.082303553 0.040242183 0.031444968 345.5019483 -2.538450501 0.226598206 APS(ph)PTKR ddPTM_BT-474_Pertuzumab_2h_R1 13 APSPTKR 7 1 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82;H3BTV0 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 APS(0.859)PT(0.141)KR;APS(0.916)PT(0.084)KR;APS(0.901)PT(0.099)KR;APS(0.999)PT(0.001)KR;APS(0.999)PT(0.001)KR;APS(0.856)PT(0.144)KR;APS(0.981)PT(0.019)KR;APS(0.966)PT(0.034)KR;APS(0.999)PT(0.001)KR;APS(0.996)PT(0.004)KR;APS(0.983)PT(0.017)KR;APS(0.996)PT(0.004)KR;APS(0.513)PT(0.487)KR 96.034 0.0079802 7356681000 5362394.8 5011505.7 4031693.3 4690907.3 4775214.7 5028266.5 5055627.9 5380826.3 5911560.5 5542335.6 TRUE FALSE 5152826.483 4868582.464 4760309.964 4933005.588 4928813.818 5129941.494 5117500.187 5269710.357 5240504.935 5166948.273 0.997266899 0.942254926 0.921300101 0.954723238 0.953911972 0.992837788 0.990429924 1.019888351 1.014235997 1 22.30088101 2.538726242 1.592016173 1.010973781 0.950158938 0.630895621 0.019123023 0.233282136 1.195247533 0.008685434 0.007082866 345.7213831 -2.538726242 -0.060814843 WLKEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 WLKEDK 6 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 92.925 0.042137 2894800000 3206200 3542000 3301800 4153000 4185800 4476200 5379800 5908700 7051900 7199900 FALSE TRUE 3080898.159 3440985.628 3898508.708 4367336.828 4320440.058 4566711.831 5445639.602 5786683.28 6251397.876 6712244.36 0.458996722 0.512643081 0.58080554 0.65065224 0.643665491 0.68035542 0.811299367 0.862108554 0.931342416 1 22.67836381 2.53915771 0.384219723 1.026898135 0.425883059 0.973071049 0.028129432 0.225673646 0.071537234 0.033532697 0.050089121 346.0650253 -2.53915771 -0.601015076 down T(ph)SPAPWKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPAPWKR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.62)S(0.38)PAPWKR 91.085 0.0074642 313010000 562710 552180 415290 441750 469110 521470 545520 552230 619760 587300 TRUE FALSE 540718.6711 536432.367 490342.1411 464548.7704 484199.3492 532014.4807 552196.2369 540826.2575 549407.443 547521.6479 0.987574963 0.979746407 0.895566674 0.848457357 0.884347406 0.971677527 1.008537725 0.98777146 1.003444239 1 19.06255648 2.540244384 5.070021233 0.997418635 0.917565352 0.487907955 0.03926707 0.211039613 10.86204558 0.01485417 0.013720298 346.932019 -2.540244384 -0.079853283 DSS(ph)QEYTDSTGIDLHEFLVNTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSSQEYTDSTGIDLHEFLVNTLK 23 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;Q15032-2;Q15032-4;Q15032;Q15032-3;H7C2F9 A0A0U1RRA6;Q15032-2 R3HDM2;R3HDM1 R3H domain-containing protein 2;R3H domain-containing protein 1 1 DS(0.115)S(0.885)QEYTDSTGIDLHEFLVNTLK;DS(0.135)S(0.865)QEYTDSTGIDLHEFLVNTLK 328.83 1.14E-86 362740000 368989 326596 201297 274761 445660 292262 409680 504650 520820 411050 TRUE FALSE 354568.5019 317281.8019 237675.8457 288941.4481 459995.0586 298171.7379 414693.7864 494228.8011 461698.6971 383209.2174 0.925260891 0.827959734 0.620224762 0.754004432 1.200375768 0.778091247 1.08216026 1.289710108 1.204821482 1 18.54777274 2.540797979 0.980891324 1.193911595 0.793906201 0.426496433 0.160983059 0.472054655 0.927227289 0.102951701 0.077537728 347.3745353 -2.540797979 -0.400005394 ILMEHIHK ddPTM_BT-474_Pertuzumab_2h_R1 3 ILMEHIHK 8 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;; 124.98 0.00074103 5061980000 3025480 3017470 2603320 2495160 2497730 1719940 2897700 138760 2762890 1741660 FALSE TRUE 2907240.897 2931414.71 3073797.835 2623935.507 2578071.754 1754718.365 2933162.919 135894.5575 2449258.31 1623695.817 1.790508337 1.805396479 1.893087241 1.616026524 1.587780006 1.080694023 1.806473164 0.083694591 1.508446523 1 20.63084995 2.54080683 0.97753579 0.856003648 1.815413064 0.380012485 0.417432752 0.487090235 0.950297349 0.254514929 0.191704927 347.3816153 -2.54080683 0.959409416 AYEVLKDEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYEVLKDEDLR 11 1 Q8IXB1-2;Q8IXB1;Q71S60;A0A087WXH7;E7EP04;A0A494C1G5;Q8IXB1-3 Q8IXB1-2 DNAJC10 DnaJ homolog subfamily C member 10 0 113.24 0.0012935 157740000 670510 762760 609910 705070 717790 770610 877140 848200 998340 1001300 FALSE TRUE 644305.7279 741006.8316 720134.3044 741458.7472 740878.3672 786192.2622 887874.7017 830684.3736 885012.6286 933481.0591 0.690218319 0.793810249 0.771450366 0.794294367 0.79367263 0.842215548 0.951143778 0.889878124 0.948077757 1 19.83226122 2.541582967 0.384382022 1.004683603 0.703281509 0.884540419 0.031340282 0.456821597 0.144811916 0.034013901 0.050872418 348.0029837 -2.541582967 -0.301402094 KEELQK ddPTM_BT-474_Pertuzumab_2h_R1 3 KEELQK 6 1 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ;; 91.626 0.076449 1650070000 2245200 2392290 1993420 2518250 2524250 2858150 3105450 3405820 3867760 3939250 FALSE TRUE 2157455.102 2324064.231 2353675.337 2648217.184 2605444.794 2915943.751 3143455.426 3335488.627 3428708.1 3672441.089 0.587471671 0.632839078 0.640902136 0.721105423 0.709458567 0.794006951 0.855958026 0.908248368 0.933631886 1 21.80830792 2.542601041 0.463087944 1.006842565 0.573489337 0.987286008 0.015165864 0.106200976 0.047727789 0.014348505 0.017379755 348.8197299 -2.542601041 -0.433353228 EEIDSILNKVEER ddPTM_BT-474_Pertuzumab_2h_R1 4 EEIDSILNKVEER 13 1 P52788;H7C2R7 P52788 SMS Spermine synthase 0 ;;; 212.17 1.47E-08 1101030000 999330 1004090 815410 832590 964670 1058740 1109710 1244240 1324280 1183600 FALSE TRUE 960275.0788 975454.3363 962772.7257 875560.0697 995699.4866 1080148.448 1123290.963 1218546.009 1173953.286 1103433.718 0.870260772 0.884017155 0.872524294 0.793486782 0.902364565 0.978897446 1.017995866 1.10432189 1.063909202 1 20.07356854 2.54281559 1.748275395 1.063720735 0.857974744 0.856595537 0.035567275 0.120178426 0.740329996 0.015454587 0.01291288 348.9920954 -2.54281559 -0.205745991 SSHKDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSHKDSPR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(0.017)S(0.017)HKDS(0.965)PR;S(0.008)S(0.008)HKDS(0.983)PR;SSHKDS(1)PR;S(0.028)S(0.028)HKDS(0.944)PR;SSHKDS(0.999)PR;S(0.124)S(0.124)HKDS(0.751)PR 103.22 0.0029157 1282100000 3359500 3746470 2857570 2892010 2892180 2524670 3740420 1213441 2758830 3484520 TRUE FALSE 3228207.026 3639624.344 3373996.465 3041266.983 2985209.596 2575720.557 3786196.379 1188383.019 2445659.184 3248510.357 0.993749957 1.12039795 1.038628816 0.936203567 0.918947231 0.792892826 1.165517718 0.36582399 0.752855591 1 21.63134687 2.544498003 0.920577835 0.705258268 1.039706608 0.183447748 0.197252144 0.723513715 1.25458435 0.12891524 0.097868968 350.3466772 -2.544498003 0.33444834 NCVLLSRPEISTDER ddPTM_BT-474_Pertuzumab_2h_R1 2 NCVLLSRPEISTDER 15 1 O94855;O94855-2;E9PDM8 O94855 SEC24D Protein transport protein Sec24D 0 ; 89.624 0.0057711 1095270000 857780 898430 720980 868060 802940 840610 784320 835070 910400 939690 FALSE TRUE 824257.0093 872807.6561 851277.1241 912860.6806 828767.2943 857607.7101 793918.7428 817825.5127 807055.2087 876043.9593 0.940885444 0.996305775 0.971728776 1.042026112 0.946033912 0.97895511 0.906254457 0.933543921 0.92124967 1 19.74064374 2.544802016 2.210956131 0.934522137 0.984510321 0.18763346 0.035664009 0.387381643 3.782452576 0.012966476 0.011288208 350.5920114 -2.544802016 0.049988185 QVRPVTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QVRPVTEK 8 1 P38606;P38606-2;C9JVW8 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 70.256 0.047244 125150000 279390 298420 232530 330370 337250 321350 397150 436480 470060 511660 FALSE TRUE 268471.1299 289909.3538 274553.3436 347420.4353 348097.9525 327847.9172 402010.4405 427466.5355 416700.7595 477004.8125 0.562826879 0.607770291 0.575577723 0.72833738 0.729757737 0.687305261 0.842780681 0.896147218 0.873577684 1 18.8636443 2.5448449 0.367353412 1.011401981 0.511871342 0.921306185 0.039496458 0.396688495 0.115704585 0.046178096 0.072734226 350.6266319 -2.5448449 -0.49953064 ELLTLDEKDPR ddPTM_BT-474_Pertuzumab_2h_R1 5 ELLTLDEKDPR 11 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;;; 74.944 0.035968 20390180000 25707200 24341300 22748100 20209700 25385500 25544900 25996000 30574700 29217400 28414000 FALSE TRUE 24702534.2 23647109.96 26859187.7 21252725.04 26202047.66 26061435.38 26314146.82 29943321.76 25900763.24 26489494.47 0.932540794 0.892697669 1.013956221 0.802307687 0.989148649 0.983840421 0.993380483 1.130384794 0.977774916 1 24.65891698 2.546741938 1.610252989 1.046929094 0.918821031 0.345216955 0.065336303 0.359379272 1.882244777 0.02813635 0.023171807 352.1615513 -2.546741938 -0.128108063 QTELKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QTELKR 6 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2;H0YAW6 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 132.29 0.023993 1710770000 1527110 1672180 1351220 1642490 1486320 1781930 1967330 1929850 2229920 2110410 FALSE TRUE 1467428.853 1624491.064 1595415.512 1727259.106 1534128.833 1817961.845 1991406.773 1889997.923 1976788.83 1967470.051 0.745845586 0.825675117 0.810896974 0.877908716 0.779746981 0.924009921 1.012166245 0.960623478 1.004736427 1 20.90791024 2.546929674 3.663136582 0.987795925 0.813432496 0.864689339 0.034826614 0.083358906 2.174205632 0.011742505 0.010668596 352.3138154 -2.546929674 -0.174363429 GGPASVPSS(ph)SPGTSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGPASVPSSSPGTSVK 16 0 O43237;O43237-2;J3KRI4;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 GGPASVPS(0.044)S(0.647)S(0.309)PGTSVK;GGPASVPS(0.029)S(0.63)S(0.341)PGTSVK 316.54 7.85E-58 856590000 1342750 1427300 1385200 1333700 1353110 1508300 1570780 1783030 1567520 1607020 TRUE FALSE 1290273.846 1386594.801 1635536.454 1402532.417 1396634.012 1538798.859 1590003.676 1746209.807 1389581.701 1498175.104 0.861230334 0.925522523 1.091685778 0.936160542 0.932223482 1.027115492 1.061293617 1.165557886 0.927516215 1 20.51477482 2.547486051 3.658705158 1.063639983 0.955542749 0.206051153 0.07895663 0.319557659 8.305045134 0.027880813 0.025336141 352.7654559 -2.547486051 -0.108097234 KLS(ph)DASDER ddPTM_BT-474_Pertuzumab_2h_R1 3 KLSDASDER 9 1 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 KLS(0.996)DAS(0.004)DER;KLS(0.562)DAS(0.438)DER;KLS(0.994)DAS(0.006)DER 111.31 0.0022722 1386998000 3830140 3685890 3551000 4213700 4065740 3762380 3685910 4005660 4191410 3941460 TRUE FALSE 3680453.894 3580772.026 4192744.692 4431169.562 4196518.22 3838457.901 3731019.269 3922941.721 3715618.709 3674501.404 1.001619945 0.974491947 1.141037717 1.205924036 1.142064666 1.044620067 1.015381098 1.067611981 1.011189901 1 21.80911707 2.547556909 8.851906453 1.032448345 1.095305985 0.198970771 0.065513688 0.809502488 96.48542225 0.024005649 0.022586382 352.8230169 -2.547556909 0.062857641 ELRDEEQTAESIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELRDEEQTAESIK 13 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ; 217.57 2.33E-11 1410590000 659910 638920 534780 569900 572220 644670 665570 686140 765990 737640 FALSE TRUE 634119.9876 620698.6272 631426.6421 599312.6073 590625.976 657705.6691 673715.4448 671970.9692 679038.0265 687678.9858 0.922116279 0.902599381 0.918199705 0.87150054 0.858868728 0.956413796 0.979694681 0.977157923 0.987434603 1 19.39137573 2.548248575 4.719793437 0.981950195 0.895351469 0.838770334 0.019036489 0.091307024 3.8494498 0.006819934 0.006295682 353.3853776 -2.548248575 -0.086598726 DCHYLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DCHYLK 6 0 F8WC14;Q9BSY4;Q9BSY4-2 F8WC14 CHCHD5 Coiled-coil-helix-coiled-coil-helix domain-containing protein 5 0 76.592 0.07465 211470000 190420 221340 176810 188010 142370 154150 183460 25589 183100 144770 FALSE TRUE 182978.1759 215027.5999 208763.5001 197713.2186 146949.4603 157267.0186 185705.2384 25060.57821 162315.2556 134964.599 1.355749414 1.593214825 1.546801915 1.464926508 1.088800037 1.165246441 1.375955175 0.185682604 1.202650598 1 17.04222151 2.548688089 0.991306271 0.768082311 1.500575124 0.377517597 0.303798583 0.475108761 0.954481076 0.189707666 0.144005937 353.7431912 -2.548688089 0.732492814 HYYTGTQGLIFVVDCADRDR ddPTM_BT-474_Pertuzumab_2h_R1 3 HYYTGTQGLIFVVDCADRDR 20 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ;; 215.75 7.05E-25 761120000 125380 134909 115950 92062 116780 106709 103790 74253 108277 100994 FALSE TRUE 120480.011 131061.5274 136904.7443 96813.33085 120536.3348 108866.7291 105060.2131 72719.6496 95985.84889 94153.58642 1.27961149 1.391997187 1.454057668 1.028248998 1.280209701 1.156267469 1.115838674 0.77235135 1.019460358 1 16.52272843 2.548784029 0.820107135 0.903915353 1.342250288 0.592085941 0.124985206 0.405358445 0.560023451 0.090062487 0.070318238 353.8213452 -2.548784029 0.438334934 ESYVETELIFALAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESYVETELIFALAK 14 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 227.2 4.93E-12 60876000 186738 182441 155187 159586 174950 184506 203473 204042 215227 214500 FALSE TRUE 179440.0725 177237.9613 183232.743 167822.2526 180577.4256 188236.8377 205963.1634 199828.4614 190795.3333 199971.7239 0.897327227 0.886315114 0.916293261 0.839229913 0.903014797 0.941317272 1.029961433 0.999283586 0.954111559 1 17.60943649 2.54881775 2.883488134 0.997070761 0.886862745 0.791132056 0.02588778 0.113995127 1.866386751 0.009253704 0.00828403 353.8488183 -2.54881775 -0.110208016 ADCILYYGFGDIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADCILYYGFGDIFR 14 0 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 116.03 0.00089656 180020000 201230 227900 187650 217620 224750 198490 184220 194920 205320 263230 FALSE TRUE 193365.7091 221400.5151 221562.5293 228851.3943 231979.2879 202503.6038 186474.5395 190894.8339 182012.9344 245401.1976 0.787957479 0.902198185 0.902858386 0.932560218 0.945306258 0.825194032 0.75987624 0.777888762 0.741695379 1 17.90478276 2.549117245 6.008301654 0.796702547 0.896790326 0.154118477 0.07850774 0.295472261 19.16619402 0.024399528 0.022777065 354.0929216 -2.549117245 0.100087779 ASEENLLSSSSVPSADRDSS(ph)PTTNSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.29)S(0.605)PT(0.091)T(0.014)NSK;ASEENLLSSSSVPSADRDS(0.321)S(0.671)PT(0.008)TNSK;ASEENLLSSSSVPS(0.001)ADRDS(0.22)S(0.634)PT(0.114)T(0.029)NS(0.002)K;ASEENLLSSSSVPSADRDS(0.044)S(0.955)PT(0.001)TNSK 253.48 9.13E-53 5975100000 1928210 1945350 1687470 1711360 1849530 2024760 2093910 2198940 2444460 2377480 TRUE FALSE 1852853.421 1889870.523 1992433.367 1799683.495 1909021.812 2065702.034 2119535.897 2153531.121 2166975.149 2216451.162 0.835954996 0.852656063 0.898929514 0.81196623 0.861296583 0.931986263 0.956274577 0.971612259 0.977677824 1 21.07982014 2.549740743 1.960109721 0.975572441 0.851042567 0.875484915 0.02231085 0.112999277 0.870706996 0.009046651 0.00776597 354.6016428 -2.549740743 -0.124529874 LIEDTEDWRPR ddPTM_BT-474_Pertuzumab_2h_R1 6 LIEDTEDWRPR 11 1 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;H0YBI4;Q96HC4-3;Q96HC4-2;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 ;;;;; 212.89 4.00E-09 2527400000 2278643 2553746 1978950 2192396 2106681 2284043 2141623 2228137 2243418 2412292 FALSE TRUE 2189591.112 2480915.664 2336590.287 2305545.82 2174444.308 2330227.914 2167832.823 2182125.192 1988754.594 2248905.314 0.973625301 1.103165904 1.038990069 1.025185812 0.96689011 1.036160971 0.963950242 0.970305499 0.884321177 1 21.10079149 2.551019036 0.809050936 0.946484264 1.041559145 0.349482738 0.045137995 0.643992129 0.866669637 0.030807757 0.024209674 355.6469067 -2.551019036 0.095074881 AYAGDKAEEIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYAGDKAEEIGR 12 1 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 100.19 0.0014285 0 363240 380480 277870 321970 307270 358590 384080 386820 383250 357020 FALSE TRUE 349044.1792 369629.0829 328087.2902 338586.9103 317153.6186 365840.9355 388780.4859 378832.0318 339745.0667 332838.7174 1.048688632 1.110535114 0.985724536 1.017270205 0.952874777 1.099153783 1.168074703 1.138184989 1.020749838 1 18.34446374 2.551107503 15.03295935 1.104857983 1.025529752 0.169912213 0.061538677 4.102484714 832.003588 0.020206068 0.019049337 355.7193605 -2.551107503 -0.079328232 KPRPPPALGPEETSASAGLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPRPPPALGPEETSASAGLPK 21 2 Q01105 Q01105 SET Protein SET 0 70.414 0.010162 609150000 541780 457820 420160 415190 414950 511320 530350 575850 605610 558370 FALSE TRUE 520606.6386 444763.4219 496092.2584 436618.0057 428297.2436 521659.2407 536840.5819 563958.4963 536863.6917 520551.1026 1.000106687 0.85440876 0.953013558 0.838761081 0.822776556 1.002128779 1.031292757 1.083387382 1.031337152 1 18.98968027 2.551241238 4.865830133 1.044486187 0.892200744 0.621312052 0.05332061 0.13476102 5.892564071 0.017647116 0.016335053 355.8289167 -2.551241238 -0.152285443 IHS(ph)PIPDMSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHSPIPDMSK 10 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 IHS(1)PIPDMSK;IHS(1)PIPDMSK 102.62 0.0018826 808690000 1456690 1358110 1200470 1126980 1372330 1037790 1229890 745130 1400400 1288340 TRUE FALSE 1399760.944 1319378.033 1417421.633 1185143.573 1416472.241 1058774.825 1244941.762 729742.8051 1241432.463 1201079.584 1.16541898 1.09849343 1.180122993 0.986731927 1.179332543 0.881519292 1.03651896 0.6075724 1.033597173 1 20.19590032 2.552311498 1.770448949 0.853986908 1.119846196 0.334144396 0.133952738 0.328469384 2.072164461 0.054483941 0.04600687 356.7068897 -2.552311498 0.265859287 ALPTSKPEGSLHSS(ph)PVGPSSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGSLHS(0.224)S(0.776)PVGPSSSK;ALPTSKPEGSLHS(0.007)S(0.993)PVGPSSSK 164.35 8.49E-12 1098610000 1407590 1403110 1291260 1307020 1268210 1498920 1598430 1635230 1607570 1867310 TRUE FALSE 1352579.827 1363094.677 1524619.406 1374475.459 1309003.126 1529229.189 1617992.064 1601461.929 1425085.393 1740835.43 0.776971679 0.783011796 0.875797551 0.789549336 0.751939617 0.87844558 0.929434245 0.919938727 0.818621547 1 20.73134839 2.552618204 5.180200255 0.911362474 0.799322634 0.562979997 0.050861951 0.172221081 8.334287099 0.016528869 0.015353093 356.9588911 -2.552618204 -0.112039841 NSDLLT(ph)SPDVGLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSDLLTSPDVGLLK 14 0 P05412 P05412 JUN Transcription factor AP-1 1 NSDLLT(0.74)S(0.26)PDVGLLK;NSDLLT(0.5)S(0.5)PDVGLLK 192.4 4.22E-06 125510000 844800 834770 695342 671588 696815 791890 554424 604860 750125 620003 TRUE FALSE 811784.282 810963.1769 821005.7672 706248.7372 719228.6873 807902.5584 561209.2068 592369.4296 664973.9548 578009.6446 1.404447641 1.403027068 1.420401502 1.22186324 1.244319527 1.397731969 0.970933984 1.024843504 1.150454774 1 19.14073404 2.552978643 0.757874181 1.009356855 1.400301505 0.67409548 0.097731681 0.391390765 0.463169778 0.074333405 0.060014835 357.2552693 -2.552978643 0.390944649 QAS(ph)DTGSNDAHNKK ddPTM_BT-474_Pertuzumab_2h_R1 4 QASDTGSNDAHNKK 14 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EN75;D6RGF7;D6RBR1;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 QAS(0.961)DT(0.039)GSNDAHNKK;QAS(0.998)DT(0.002)GSNDAHNKK;QAS(0.998)DT(0.002)GSNDAHNKK;QAS(0.995)DT(0.005)GSNDAHNKK 209.43 3.12E-09 1056130000 584095 476892 264335 449165 555914 445567 563388 644942 633552 598505 TRUE FALSE 561267.9216 463291.5071 312106.2146 472346.4595 573795.4787 454576.67 570282.9109 631623.7223 561633.833 557967.7233 1.005914676 0.830319547 0.559362489 0.846547999 1.028366794 0.814700656 1.022071505 1.132007634 1.006570469 1 19.08982214 2.553406396 1.081027066 1.065305684 0.808111033 0.334766137 0.127079514 0.536702037 1.280542307 0.07692166 0.058901169 357.6073166 -2.553406396 -0.25719465 AHT(ph)PTPGIYMGR ddPTM_BT-474_Pertuzumab_2h_R1 6 AHTPTPGIYMGR 12 0 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(0.973)PT(0.027)PGIYMGR;AHT(0.996)PT(0.004)PGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR 177.38 8.59E-05 42980200000 8182000 7152900 7186940 8126670 7309460 6543770 7927740 4757970 8957170 7754590 TRUE FALSE 7862238.394 6948906.295 8485779.931 8546088.413 7544575.419 6676089.513 8024762.054 4659716.257 7940389.613 7229364.712 1.087542088 0.961205662 1.173793309 1.182135465 1.043601439 0.923468351 1.110023131 0.644554043 1.098352335 1 22.78543744 2.553775292 1.558917128 0.901527396 1.095180997 0.159314673 0.137036227 0.52699724 2.588521861 0.061662585 0.050732471 357.9112027 -2.553775292 0.193653601 LSLSPALQDALHTFPQLQVEQSGEGS(ph)PEEGAVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSLSPALQDALHTFPQLQVEQSGEGSPEEGAVR 33 0 Q9ULL5;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 LSLSPALQDALHTFPQLQVEQS(0.005)GEGS(0.995)PEEGAVR;LSLSPALQDALHTFPQLQVEQS(0.001)GEGS(0.999)PEEGAVR;LSLSPALQDALHTFPQLQVEQSGEGS(1)PEEGAVR 331.57 2.52E-117 829388000 206562 212129 177303 212251 208006 196396 187229 206658 208885 213746 TRUE FALSE 198489.3287 206079.2886 209345.5962 223205.2995 214696.7019 200367.2617 189520.3645 202390.4401 185173.2505 199268.793 0.996088377 1.034177432 1.050568897 1.120121702 1.077422604 1.005512497 0.951079 1.015665509 0.929263673 1 17.60435627 2.554379042 4.629724229 0.978557798 1.05731714 0.519280417 0.037079332 0.193228757 7.580528971 0.012962301 0.011980836 358.409112 -2.554379042 0.078759341 VIISAPSADAPMFVMGVNHEK ddPTM_BT-474_Pertuzumab_2h_R1 5 VIISAPSADAPMFVMGVNHEK 21 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 343.5 5.08E-81 36876490000 17316230 17247180 15115880 15842710 16099590 16136650 15896030 15931950 18591490 16488180 FALSE TRUE 16639492.59 16755307.31 17847655.77 16660354.16 16617447.93 16462944.12 16090570.37 15602949.66 16481062 15371420.88 1.082495412 1.090029831 1.161093428 1.083852579 1.08106128 1.071009912 1.046784841 1.015062289 1.072188584 1 23.87374719 2.555950348 1.058899057 1.027719791 1.107943488 0.58629483 0.027007636 0.355792352 0.815301382 0.015800947 0.012110278 359.7082078 -2.555950348 0.080223697 LEVEANNAFDQYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEVEANNAFDQYR 13 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 88.803 0.018009 216420000 322830 352080 340210 369010 367370 330550 323610 347060 329120 350550 FALSE TRUE 310213.4467 342039.0231 401693.5149 388054.6503 379186.7897 337233.9475 327570.436 339893.0897 291759.6774 326806.9363 0.949225406 1.046608824 1.229146234 1.187412528 1.160277667 1.031905722 1.002336241 1.040042459 0.892758522 1 18.31807908 2.556514951 4.112480245 0.99506891 1.120764032 0.365502171 0.08086857 0.282055627 8.881613301 0.029412569 0.027029992 360.1761497 -2.556514951 0.125695122 TLS(ph)MDKGF ddPTM_BT-474_Pertuzumab_2h_R1 5 TLSMDKGF 8 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 TLS(1)MDKGF;TLS(1)MDKGF;TLS(1)MDKGF;TLS(1)MDKGF;T(0.003)LS(0.997)MDKGF 133.23 0.0024424 3260080000 5946130 5144750 2842650 3903290 5879850 4271800 5640990 6788650 5814340 4964620 TRUE FALSE 5713748.666 4998026.767 3356380.089 4104739.265 6068980.715 4358178.723 5710026.123 6648462.005 5154320.499 4628361.865 1.234507766 1.07986949 0.72517668 0.886866538 1.311258906 0.941624456 1.233703476 1.436461149 1.113638183 1 22.14207023 2.557209918 1.380089963 1.244889732 0.999902405 0.087993567 0.194607647 0.679714054 2.626370473 0.097788297 0.078486774 360.752972 -2.557209918 -0.244987326 IGDYVQQHGGVSLVEQLLQDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IGDYVQQHGGVSLVEQLLQDPK 22 0 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 217.11 1.29E-25 601650000 240390 250040 193710 211760 243470 252940 295660 272960 338200 334270 FALSE TRUE 230995.293 242909.104 228717.7061 222688.959 251301.4337 258054.6201 299278.3755 267323.2806 299808.9539 311629.5952 0.741249537 0.779480216 0.733940902 0.714595027 0.80641068 0.828081235 0.960365704 0.857823791 0.962068297 1 18.24947273 2.557735296 1.32959072 0.934801676 0.74377468 0.823661644 0.041345234 0.182023151 0.65353733 0.020254165 0.01613004 361.1896493 -2.557735296 -0.191026996 DVHDLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVHDLFR 7 0 Q9Y2R4;A0A087X1P7;A0A087WTD6;A0A087X069 Q9Y2R4 DDX52 Probable ATP-dependent RNA helicase DDX52 0 ; 125.25 0.0058274 104750000 96078 101207 75373 94091 107057 82180 87039 74563 89588 97681 FALSE TRUE 92323.16554 98320.67545 88994.57776 98947.04779 110500.5856 83841.73591 88104.20932 73023.24799 79418.34582 91064.97886 1.013816362 1.079676037 0.977264574 1.086554338 1.213425699 0.920680342 0.967487287 0.801880689 0.872106344 1 16.47460872 2.558390752 8.932395633 0.893687814 1.069903463 0.524093542 0.07638608 0.296805697 30.66763898 0.025359447 0.023875507 361.7351839 -2.558390752 0.176215649 S(ph)PQPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQPNK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(1)PQPNK;S(1)PQPNK 71.692 0.091849 430610000 760570 760380 649800 655860 748210 780070 912390 972000 866360 776160 TRUE FALSE 730846.0835 738694.7069 767233.3147 689709.0132 772276.8542 795843.5499 923556.1017 951927.8603 768014.4449 723589.9919 1.010027905 1.020874688 1.06031499 0.953176552 1.067285152 1.09985428 1.276352786 1.315562502 1.06139451 1 19.46481293 2.558663618 2.793464516 1.204955504 1.019409517 0.287268723 0.094685761 0.251915227 3.860392085 0.033841554 0.030398589 361.9625326 -2.558663618 -0.185545986 AS(ph)SPVEELLTMEDEGNSDMLVVTTK ddPTM_BT-474_Pertuzumab_2h_R1 5 ASSPVEELLTMEDEGNSDMLVVTTK 25 0 B8ZZD4;Q86VP1-2;Q86VP1 B8ZZD4 TAX1BP1 Tax1-binding protein 1 1 AS(0.5)S(0.5)PVEELLTMEDEGNSDMLVVTTK;AS(0.5)S(0.5)PVEELLT(0.001)MEDEGNSDMLVVTTK;AS(0.5)S(0.5)PVEELLTMEDEGNSDMLVVTTK;AS(0.5)S(0.5)PVEELLTMEDEGNSDMLVVTTK;AS(0.47)S(0.47)PVEELLT(0.06)MEDEGNSDMLVVTTK 163.72 1.14E-11 115713000 80898.9 80496.3 79142.1 95194.5 87885.1 82436.2 103031.8 105970.8 124415.8 136191.5 TRUE FALSE 77737.28155 78200.62434 93444.83798 100107.4996 90712.00406 84103.11645 104292.734 103782.4659 110292.64 126967.1284 0.612263052 0.615912365 0.73597662 0.788452104 0.714452671 0.662400714 0.821415238 0.817396339 0.868670823 1 16.95409551 2.558676211 0.062322707 1.521698844 8.81E-09 0.822786473 0.04834959 22.50685023 0.642999491 6.607722415 8.77972408 361.9730279 -2.558676211 -1.521698835 ERDSASFNPELLTHILDGS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERDSASFNPELLTHILDGSPEK 22 1 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 1 ERDSASFNPELLTHILDGS(1)PEK;ERDSASFNPELLT(0.005)HILDGS(0.995)PEK 173.98 1.90E-12 137049000 98482 107783 96236 108987 108635 131003 129562 141970 169215 175491 TRUE FALSE 94633.21456 104709.1344 113627.986 114611.8321 112129.3434 133651.9704 131147.6185 139038.2699 150006.4226 163604.8383 0.578425526 0.640012456 0.694527052 0.700540604 0.685366916 0.816919425 0.801612103 0.849842042 0.916882558 1 17.31985589 2.558678658 0.271693417 1.033774801 0.510600391 0.955709019 0.02622718 0.502657485 0.087261469 0.044629798 0.090642767 361.9750681 -2.558678658 -0.52317441 RQEEEESVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQEEEESVKK 10 2 Q9Y5A9;Q9Y5A9-2 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 0 ; 112.15 0.00093326 490450000 253880 247210 220299 222146 252250 249240 250910 282920 288130 283260 FALSE TRUE 243958.0889 240159.8128 260111.9298 233610.9817 260363.8503 254279.8036 253980.7116 277077.6031 255422.6903 264074.5479 0.923822803 0.909439455 0.98499432 0.884640279 0.985948295 0.962909169 0.961776565 1.049240093 0.967237064 1 18.01058573 2.558680309 1.009252487 1.008116263 0.929172475 0.405762288 0.03480025 0.473596971 0.987700504 0.020397628 0.015643786 361.9764436 -2.558680309 -0.078943788 TPPRDLPT(ph)IPGVTSPSSDEPPMEASQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 T(0.382)PPRDLPT(0.529)IPGVT(0.066)S(0.02)PS(0.002)S(0.001)DEPPMEASQSHLR 91.1 0.0016529 1226900000 21616 18111 14792 17517 20041 23344 29898 31676 21690 41289 TRUE FALSE 20771.22282 17594.49201 17465.24345 18421.05447 20685.63697 23816.03167 30263.90067 31021.87953 19227.84213 38492.45925 0.539617973 0.45708932 0.453731556 0.47856268 0.537394528 0.61871941 0.786229336 0.805920955 0.499522309 1 15.23228823 2.560167989 1.958512591 0.764643849 0.481607709 0.56092514 0.116391746 0.245529127 1.886103924 0.04442963 0.038442839 363.2185234 -2.560167989 -0.283036141 NLDKDMYGDDLEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 NLDKDMYGDDLEAR 14 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 122.93 9.65E-05 430500000 353180 355130 258460 240570 284420 324960 327290 368740 378870 332350 FALSE TRUE 339377.3351 345002.0401 305169.4714 252985.8465 293568.6276 331530.9138 331295.4729 361125.3901 335862.266 309839.6385 1.095332207 1.113485808 0.984927148 0.81650575 0.947485703 1.070008071 1.069248191 1.165523533 1.083987406 1 18.2411622 2.560941204 4.316274039 1.097675107 0.988603198 0.189410142 0.085774445 0.351755336 11.84719842 0.032024162 0.029558151 363.8657715 -2.560941204 -0.109071909 DHRPPCAQEAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHRPPCAQEAPR 12 1 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ; 141.58 3.56E-05 570170000 206764 230840 234510 220120 213764 192303 229140 121827 257180 239050 FALSE TRUE 198683.4343 224256.6692 276891.1736 231480.4196 220639.9132 196191.4984 231944.2839 119311.2299 227986.0046 222858.9306 0.891521079 1.006271854 1.242450428 1.038685858 0.990042951 0.880339405 1.040767284 0.535366609 1.023005917 1 17.76577125 2.562672846 1.466310938 0.825645536 1.051697532 0.117620754 0.160576842 0.56129152 2.443422415 0.075254817 0.061561055 365.3194931 -2.562672846 0.226051996 TAFPSLPDTDDHKTDNTGTLPEDVAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAFPSLPDTDDHKTDNTGTLPEDVAFR 27 1 A8MXV4 A8MXV4 NUDT19 "Nucleoside diphosphate-linked moiety X motif 19, mitochondrial" 0 ; 281.85 2.26E-61 835230000 440780 480530 363020 477620 433130 523940 508250 533410 672110 597180 FALSE TRUE 423553.8303 466825.7549 428625.7893 502270.0254 447062.0198 534534.4258 514470.1155 522394.8971 595814.8905 556732.4667 0.760785217 0.838510026 0.769895443 0.902174842 0.803010506 0.960127993 0.924088582 0.938323034 1.070199649 1 19.08662469 2.563004299 0.535269364 1.024204235 0.778556365 0.749890758 0.048493767 0.454270443 0.270604014 0.040751778 0.042955855 365.5984106 -2.563004299 -0.24564787 ELEELKEIEADLER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEELKEIEADLER 14 1 K7EJH0;K7EMX1;K7EJV2;K7ESQ2;Q8NBT2 K7EJH0 SPC24 Kinetochore protein Spc24 0 ; 147.12 7.41E-06 302960000 688810 640660 569740 565910 662380 690860 627860 785070 823610 700590 FALSE TRUE 661890.5437 622389.0041 672704.6918 595116.6829 683686.0543 704829.6625 635543.9385 768858.0302 730117.2457 653138.4153 1.013400113 0.952920529 1.02995732 0.911164723 1.046770544 1.079142868 0.973061641 1.177174719 1.117859903 1 19.31702924 2.563560205 1.146808904 1.098330397 0.980888073 0.275954944 0.063991718 0.521584713 1.400208438 0.034452658 0.026844704 366.0666842 -2.563560205 -0.117442324 NIVSLLLSMLGHDEDNTR ddPTM_BT-474_Pertuzumab_2h_R1 1 NIVSLLLSMLGHDEDNTR 18 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 67.168 0.02321 32586000 37634 33055 36713 32828 36874 42055 38609 47880 50805 44168 FALSE TRUE 36163.22167 32112.30376 43347.85578 34522.25701 38060.0857 42905.38091 39081.50849 46891.26127 45037.82939 41176.46202 0.878249852 0.779870397 1.052733859 0.838397845 0.924316559 1.041988039 0.949122547 1.138788011 1.093776084 1 15.32953226 2.564235855 1.033815364 1.081098139 0.882276095 0.464639459 0.080533595 0.428241579 0.937411649 0.046648056 0.036007123 366.636632 -2.564235855 -0.198822044 S(ph)SSEAKPTSLGLAGGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSEAKPTSLGLAGGHK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.963)S(0.022)S(0.015)EAKPTSLGLAGGHK;S(0.921)S(0.02)S(0.058)EAKPT(0.001)SLGLAGGHK 231.75 2.21E-16 268190000 802870 678260 587000 616290 664690 522990 431200 601920 465180 410290 TRUE FALSE 771492.9528 658916.6889 693083.9577 648096.8008 686070.3575 533565.2161 436477.1546 589490.1417 412374.7166 382500.6929 2.016971386 1.72265489 1.811980921 1.694367652 1.793644745 1.394939215 1.141114677 1.541147906 1.078101881 1 18.54510284 2.564771323 0.351826759 0.980398265 2.044271565 0.802144238 0.147788072 0.76138405 0.203966659 0.176909057 0.295660164 367.0889596 -2.564771323 1.0638733 up RSDS(ph)PENK ddPTM_BT-474_Pertuzumab_2h_R1 3 RSDSPENK 8 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 RS(0.003)DS(0.997)PENK;RS(0.025)DS(0.975)PENK;RS(0.003)DS(0.997)PENK 94.363 0.01103 215030000 703100 615136 554323 624383 611507 660234 704040 703480 691080 816690 TRUE FALSE 675622.0747 597592.9236 654501.4969 656607.4815 631176.678 673584.3838 712656.2521 688952.8922 612631.4956 761374.8589 0.887371138 0.784886599 0.859631086 0.862397115 0.828995955 0.884694807 0.936012325 0.904880013 0.804638462 1 19.53824741 2.566006848 4.659353854 0.905429057 0.843494739 0.271830287 0.051248548 0.314017141 11.71301189 0.016319768 0.015143682 368.1347785 -2.566006848 -0.061934318 KNNHHEENISSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KNNHHEENISSK 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 116.01 0.0005763 80090000 106676 109198 94518 124859 93938 93415 105972 27164 142894 142127 FALSE TRUE 102506.984 106083.78 111599.5051 131302.988 96959.60108 95303.9153 107268.917 26603.05391 126673.2722 132500.6117 0.773634043 0.800628605 0.842256528 0.990961372 0.731767196 0.719271512 0.809572995 0.200776838 0.956020282 1 17.01563949 2.56723176 1.790949044 0.631774691 0.841009002 0 0.221373535 0.709796279 4.572663029 0.092219408 0.079012925 369.1745549 -2.56723176 0.20923431 SHS(ph)LPSSIIF ddPTM_BT-474_Pertuzumab_2h_R1 3 SHSLPSSIIF 10 0 Q86Z20-2;Q86Z20 Q86Z20-2 CCDC125 Coiled-coil domain-containing protein 125 1 S(0.097)HS(0.901)LPS(0.002)SIIF;S(0.242)HS(0.758)LPSSIIF;S(0.429)HS(0.571)LPSSIIF 91.584 0.010542 114206000 276787 321140 247940 297007 278538 193634 290253 128404 263646 241483 TRUE FALSE 265969.858 311981.4016 292748.2734 312335.5669 287497.4277 197549.4121 293805.203 125752.4125 233718.0114 225127.1413 1.18142067 1.385800929 1.300368635 1.387374108 1.277044723 0.877501535 1.305063447 0.558583971 1.038160081 1 17.78038047 2.567509344 1.310013645 0.87666978 1.326505503 0.439902179 0.188026119 0.34811225 1.21443561 0.090452805 0.072498944 369.410592 -2.567509344 0.449835723 LYNSEESRPYTNK ddPTM_BT-474_Pertuzumab_2h_R1 4 LYNSEESRPYTNK 13 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 ;;; 121.48 0.00022454 1763200000 1038750 992950 878240 944110 999300 1090320 1020390 1152930 1227870 1244720 FALSE TRUE 998154.5016 964632.0382 1036957.504 992835.6302 1031443.392 1112367.017 1032877.838 1129121.593 1088487.345 1160414.006 0.860171022 0.831282657 0.893609952 0.855587424 0.888858103 0.95859496 0.890094253 0.973033406 0.93801638 1 20.14620818 2.568048972 0.334497447 1.001740771 0.821280228 0.749312843 0.026474902 0.836594087 0.204631027 0.030991739 0.054550196 369.8698845 -2.568048972 -0.180460543 WNQQQLDDLYLIAICHR ddPTM_BT-474_Pertuzumab_2h_R1 1 WNQQQLDDLYLIAICHR 17 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 203.99 9.19E-12 283710000 309180 342320 263800 343290 333540 307420 305260 306200 349400 365740 FALSE TRUE 297096.9038 332557.3688 311474.5282 361007.238 344268.617 313636.243 308995.8632 299876.863 309737.5768 340968.104 0.871333419 0.97533278 0.913500484 1.058771286 1.009679829 0.919840417 0.906230992 0.879486554 0.908406309 1 18.37927726 2.568893766 7.583682201 0.909995767 0.968442667 0.10910017 0.056041928 0.471218194 34.48286157 0.018297268 0.017207572 370.5900596 -2.568893766 0.0584469 NPDLHEDNVTEQTHHIIIPSYAAWFDYNSVHAIER ddPTM_BT-474_Pertuzumab_2h_R1 1 NPDLHEDNVTEQTHHIIIPSYAAWFDYNSVHAIER 35 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 88.744 0.0002075 118820000 24267 27644 26909 26997 22144 19418 20420 5629 25777 16973 FALSE TRUE 23318.61881 26855.62019 31772.05489 28390.31841 22856.28187 19810.64526 20669.90607 5512.759183 22850.90303 15823.40359 1.473679078 1.697208823 2.007915345 1.794197957 1.444460526 1.251983819 1.306286979 0.348392756 1.444120596 1 13.94977233 2.569255913 1.375116441 0.887778952 1.748892829 0.530552812 0.299740699 0.290429029 1.114505073 0.145791948 0.118290004 370.8992136 -2.569255913 0.861113877 IS(ph)ESVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ISESVLR 7 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 IS(0.998)ES(0.002)VLR 107.15 0.0079105 36040000 41069 39262 37281 48275 50333 34521 29724 38175 33546 31978 TRUE FALSE 39463.97808 38142.2862 44018.50601 50766.47854 51952.00666 35219.03827 30087.7712 37386.67291 29737.99872 29812.10158 1.323756998 1.279422925 1.476531465 1.702881577 1.74264825 1.181367177 1.009246904 1.254077067 0.997514336 1 14.86361046 2.569480033 6.692218969 1.100745384 1.500830912 0.653195939 0.152718869 0.182068302 11.19597245 0.054881543 0.05152355 371.0906681 -2.569480033 0.400085529 TALINSTGEEVAMR ddPTM_BT-474_Pertuzumab_2h_R1 2 TALINSTGEEVAMR 14 0 P02545;P02545-6;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 268.95 5.93E-25 290760000 95078 119589 93456 105760 107584 101585 96185 110424 102034 115467 FALSE TRUE 91362.24665 116178.4388 110345.5781 111218.2863 111044.5371 103639.1183 97362.1408 108143.7058 90451.52808 107646.3172 0.848726171 1.079260692 1.025075274 1.033182455 1.03156838 0.962774398 0.904463277 1.004620581 0.840265886 1 16.71593944 2.569535261 5.173544764 0.942555602 1.010209898 0.156610359 0.071519383 0.397223695 17.01991364 0.022466399 0.020952363 371.1378611 -2.569535261 0.067654297 ELLDTELDLHKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLDTELDLHKR 12 1 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 0 118.48 0.00040292 203750000 134300 137020 120820 124740 131780 146290 134350 147670 172460 161350 FALSE TRUE 129051.4075 133112.3238 142654.8616 131177.8463 136018.8234 149248.084 135994.2155 144620.5629 152883.0638 150421.6208 0.857931239 0.884928131 0.948366737 0.872067763 0.904250484 0.992198351 0.904086891 0.96143468 1.016363625 1 17.19865242 2.57093652 0.329150258 1.013104888 0.856998086 0.600267521 0.034220436 1.388503826 0.329750222 0.043599724 0.078055895 372.3372786 -2.57093652 -0.156106802 TQSAS(ph)PPPKER ddPTM_BT-474_Pertuzumab_2h_R1 1 TQSASPPPKER 11 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 TQS(0.279)AS(0.72)PPPKER 85.734 0.0090813 787760000 667670 620260 490740 531420 591990 650350 688090 743960 809720 699020 TRUE FALSE 641576.7183 602570.7921 579427.6345 558846.6499 611031.896 663500.5226 696511.0513 728596.966 717803.9802 651674.7528 0.984504487 0.924649589 0.889136232 0.857554551 0.937633219 1.018146736 1.06880165 1.118037737 1.101475816 1 19.31379258 2.571483407 2.159423761 1.086067727 0.911771955 0.745957393 0.042374477 0.14554078 1.350782262 0.016635879 0.014713911 372.806441 -2.571483407 -0.174295772 QLS(ph)PQSK ddPTM_BT-474_Pertuzumab_2h_R1 5 QLSPQSK 7 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 QLS(0.995)PQS(0.005)K;QLS(0.99)PQS(0.01)K;QLS(0.997)PQS(0.003)K;QLS(0.934)PQS(0.066)K;QLS(1)PQSK 137.46 0.0030218 16206720000 13159500 12221800 10227300 11512200 12071100 12147700 12790200 13432800 14348400 13017200 TRUE FALSE 12645212.19 11873246.23 12075600.62 12106346.02 12459377.89 12393334.82 12946730.29 13155407.99 12719629.79 12135533.45 1.041998874 0.978386841 0.995061376 0.997594879 1.026685637 1.021243513 1.066844762 1.084040355 1.04813108 1 23.53273419 2.571576149 1.858779983 1.059452071 1.002972883 0.318416682 0.026768275 0.299900993 2.076783182 0.010603386 0.009177223 372.8860608 -2.571576149 -0.056479188 ATDETDRDIIREPLTELK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATDETDRDIIREPLTELK 18 2 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 121.74 2.11E-05 81575000 121120 112430 92806 97400 104670 115410 120190 125850 135560 131940 FALSE TRUE 116386.4965 109223.6065 109578.1087 102426.8257 108036.8056 117743.6693 121660.9212 123251.1535 120171.7971 123003.5863 0.946204091 0.88797091 0.890852958 0.832714141 0.878322404 0.957237694 0.989084342 1.002012683 0.976977995 1 16.90834085 2.573792781 3.082396192 0.992371525 0.884441858 0.777742178 0.02660435 0.122560783 2.241492776 0.009863191 0.008988325 374.7941304 -2.573792781 -0.107929667 LDDIEEFENIRK ddPTM_BT-474_Pertuzumab_2h_R1 3 LDDIEEFENIRK 12 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 0 ;; 185.59 2.06E-05 591864000 619410 653310 508390 573060 622540 724150 664040 837720 831210 821720 FALSE TRUE 595202.7724 634678.2385 600267.3821 602635.6953 642564.5645 738792.8092 672166.7202 820420.7893 736854.5255 766064.1725 0.776962027 0.828492261 0.783573235 0.786664769 0.838786863 0.96440068 0.877428738 1.070955696 0.961870496 1 19.54710572 2.573895032 1.106423844 1.008038329 0.79068745 0.787908553 0.04532936 0.203513521 0.509877139 0.024543098 0.019237722 374.8823828 -2.573895032 -0.217350879 ARPPS(ph)GSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARPPSGSSK 9 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 ARPPS(0.964)GS(0.027)S(0.009)K;ARPPS(0.829)GS(0.131)S(0.04)K 70.728 0.031242 388770000 328750 333130 255840 306050 309350 323070 340060 360410 352660 376970 TRUE FALSE 315902.0865 323629.4586 302075.9791 321845.2772 319300.5237 329602.6968 344221.756 352967.4076 312627.5153 351437.4861 0.898885574 0.920873473 0.85954399 0.915796663 0.908555679 0.937870062 0.979467955 1.004353325 0.889567925 1 18.42290856 2.574113087 2.232684779 0.972752567 0.899061396 0.475522024 0.03336628 0.254928925 2.523851552 0.012444471 0.011069104 375.0706553 -2.574113087 -0.073691171 GVNTGAVGSYIYDRDPEGK ddPTM_BT-474_Pertuzumab_2h_R1 6 GVNTGAVGSYIYDRDPEGK 19 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ;;;;; 280.39 1.13E-39 17832470000 8269230 7994880 6598230 7071910 7317880 7985450 8053910 8871000 9057020 8525240 FALSE TRUE 7946059.349 7766873.85 7790676.938 7436892.123 7553266.256 8146921.27 8152476.16 8687810.75 8028905.06 7947817.901 0.999778738 0.977233493 0.980228414 0.935714962 0.950357236 1.025051325 1.025750245 1.093106417 1.010202443 1 22.92212739 2.575909618 3.590730439 1.043877942 0.968134269 0.516641375 0.029141358 0.1738199 4.149179707 0.010336751 0.009503954 376.6254105 -2.575909618 -0.075743673 IAS(ph)PVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 IASPVSR 7 0 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 1 IAS(0.992)PVS(0.008)R;IAS(1)PVSR;IAS(1)PVSR;IAS(0.999)PVS(0.001)R 122.28 0.0045694 2260210000 940340 1053570 878670 1016240 969820 936820 1054590 1013440 1002890 1159900 TRUE FALSE 903590.4732 1023523.215 1037465.215 1068688.268 1001015.141 955763.1423 1067496.388 992512.1098 889046.1317 1081338.94 0.835621876 0.946533208 0.959426482 0.988300919 0.925718204 0.883870086 0.987198693 0.917854775 0.822171568 1 20.04438737 2.577445249 0.003623846 1.857401874 4.38E-08 0.042268703 0.058249112 106215.148 169.6952313 43114.21196 43857.10121 377.9594852 -2.577445249 -1.85740183 RLNHS(ph)PPQSSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLNHSPPQSSSR 12 1 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 RLNHS(0.988)PPQS(0.009)S(0.003)SR;RLNHS(0.993)PPQS(0.005)S(0.002)S(0.001)R;RLNHS(1)PPQSSSR;RLNHS(0.901)PPQS(0.033)S(0.033)S(0.033)R 117.31 0.00045793 3732060000 421512 437646 400407 323514 385963 370383 358182 321603 342476 359700 TRUE FALSE 405038.845 425164.7646 472769.4519 340210.5963 398377.8504 377872.398 362565.5385 314961.7857 303599.5603 335337.1986 1.207855397 1.267872358 1.409833009 1.014532828 1.187991825 1.126843069 1.081196897 0.939239032 0.905356046 1 18.355253 2.578142629 0.676058166 0.930755431 1.275332531 0.626700417 0.091378521 0.467193615 0.443586395 0.072103175 0.063425017 378.5668915 -2.578142629 0.344577099 YLQAHTQSVYNYHLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLQAHTQSVYNYHLSPR 17 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 YLQAHTQSVYNYHLS(1)PR;YLQAHTQSVYNYHLS(1)PR 162.43 4.75E-09 325040000 235507 256080 196330 226424 214299 171658 136825 119558 172059 145239 TRUE FALSE 226303.1261 248776.8491 231811.1983 238109.7698 221192.122 175129.0424 138499.5053 117089.0855 152527.5837 135401.8332 1.671344625 1.837322607 1.712024076 1.758541699 1.633597691 1.2934023 1.022877623 0.864752587 1.126480935 1 17.04688775 2.578347989 1.834338817 0.969422722 1.750166192 0.955717595 0.073489645 0.061290741 0.413268686 0.029741363 0.025821877 378.7459427 -2.578347989 0.780743469 S(ph)PGPAADGPIDLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGPAADGPIDLSK 14 0 Q8IX07 Q8IX07 ZFPM1 Zinc finger protein ZFPM1 1 S(1)PGPAADGPIDLSK;S(1)PGPAADGPIDLSK 222.55 4.04E-12 487370000 705490 687430 540150 634330 686610 669400 710760 805640 786800 758060 TRUE FALSE 677918.6708 667825.1695 637767.1206 667067.8473 708695.4342 682935.7266 719458.4935 789003.2525 697485.7625 706715.921 0.959252014 0.944969753 0.902437743 0.943898146 1.002801003 0.966351127 1.018030685 1.116436221 0.986939365 1 19.43077089 2.578739198 1.260308954 1.048412389 0.938577172 0.464796095 0.040085642 0.33703323 1.090572646 0.021084081 0.016954338 379.0872673 -2.578739198 -0.109835217 AIT(ph)PPQQPYKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AITPPQQPYKK 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 AIT(1)PPQQPYKK 53.351 0.081195 442020000 600780 646220 526640 549650 562730 628310 640260 702230 691570 690020 TRUE FALSE 577300.8534 627790.4383 621815.563 578017.5024 580830.7215 641014.8587 648095.6934 687728.7051 613065.8729 643284.3308 0.897427196 0.975914395 0.966626316 0.898541243 0.902914456 0.996472054 1.007479372 1.069089782 0.953024726 1 19.29509702 2.578868531 4.43122625 1.017393652 0.931683458 0.514460359 0.036823268 0.179909654 5.922695654 0.012709499 0.011808037 379.2001769 -2.578868531 -0.085710194 GPGAPGLAHLQESQAGS(ph)DTDVEEGKAPQAVPLEK ddPTM_BT-474_Pertuzumab_2h_R1 5 GPGAPGLAHLQESQAGSDTDVEEGKAPQAVPLEK 34 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 GPGAPGLAHLQESQAGS(0.999)DT(0.001)DVEEGKAPQAVPLEK;GPGAPGLAHLQESQAGS(1)DTDVEEGKAPQAVPLEK;GPGAPGLAHLQESQAGS(0.987)DT(0.013)DVEEGKAPQAVPLEK;GPGAPGLAHLQES(0.004)QAGS(0.977)DT(0.019)DVEEGKAPQAVPLEK;GPGAPGLAHLQESQAGS(1)DTDVEEGKAPQAVPLEK 412.54 7.30E-187 25693600000 7156260 6133960 5445750 5863010 6670240 7073320 7934480 8048560 9939390 7929410 TRUE FALSE 6876585.448 5959025.467 6429918.165 6165600.649 6884794.327 7216347.377 8031584.54 7882354.423 8811112.117 7392343.998 0.930230716 0.806107707 0.869807759 0.834052183 0.931341173 0.976192041 1.086473322 1.066286204 1.191923985 1 22.81760046 2.579483225 1.433905277 1.096209062 0.856992917 0.771035683 0.054866692 0.17049149 0.710218633 0.023854061 0.019725208 379.7372709 -2.579483225 -0.239216146 ALNHEIEELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALNHEIEELEK 11 0 O95347-2;O95347;Q5T821 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 138.42 5.79E-05 168340000 377410 341570 305090 341020 345670 383270 392210 401160 462510 445040 FALSE TRUE 362660.4 331828.758 360226.5497 358620.0831 356788.7895 391019.982 397009.9833 392875.9058 410007.8038 414897.0444 0.874097333 0.799785784 0.868231178 0.864359214 0.859945363 0.942450633 0.956887952 0.946923848 0.988215774 1 18.66239385 2.580164235 0.767385216 0.987052279 0.836756251 0.859049888 0.02332582 0.226411208 0.276522755 0.016494264 0.013598909 380.3331976 -2.580164235 -0.150296028 SSGSEGSS(ph)PNWLQALK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSGSEGSSPNWLQALK 16 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SSGSEGS(0.074)S(0.926)PNWLQALK;SSGSEGS(0.107)S(0.893)PNWLQALK;SSGSEGS(0.005)S(0.995)PNWLQALK;SSGSEGS(0.021)S(0.979)PNWLQALK 347.33 4.33E-87 457904000 1021400 1047700 1035770 1039060 1039120 1135690 1225030 1283420 1176960 1294350 TRUE FALSE 981482.5588 1017820.622 1222956.68 1092686.011 1072544.239 1158654.43 1240022.284 1256916.929 1043356.435 1206682.522 0.813372649 0.84348667 1.013486694 0.905528995 0.888837138 0.960198237 1.027629274 1.041630177 0.864648668 1 20.20261472 2.580990628 3.812196395 0.99438346 0.897812674 0.292323298 0.066281262 0.3029903 7.917343289 0.02331518 0.021538178 381.0576001 -2.580990628 -0.096570786 STIGGQIMYLTGMVDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 STIGGQIMYLTGMVDKR 17 1 P15170-2;P15170-3;P15170;H3BR35;H3BSV8 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 256.84 6.63E-27 931730000 462160 443720 374920 391770 425370 439010 474590 445020 545300 512650 FALSE TRUE 444098.2763 431065.54 442676.3841 411989.2966 439052.4124 447887.083 480398.1744 435830.1815 483399.8301 477927.7589 0.929216326 0.901947066 0.926241207 0.862032575 0.91865853 0.937143898 1.005169014 0.911916442 1.011449578 1 18.86643304 2.581359906 3.016867435 0.969369916 0.905560435 0.523492643 0.032403792 0.23704207 4.153035271 0.011150487 0.010188679 381.3817486 -2.581359906 -0.063809482 TLS(ph)PEFNER ddPTM_BT-474_Pertuzumab_2h_R1 3 TLSPEFNER 9 0 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 1 T(0.005)LS(0.995)PEFNER;TLS(1)PEFNER;T(0.001)LS(0.999)PEFNER 140.78 0.00011358 823910000 584660 735000 559130 729620 587150 727790 724600 829690 789340 754960 TRUE FALSE 561810.8408 714038.5196 660177.2288 767275.7756 606036.213 742506.4124 733467.8716 812556.6116 699737.4324 703825.8868 0.798224179 1.014510169 0.937983728 1.090149979 0.861059851 1.054957521 1.042115508 1.15448526 0.9941911 1 19.42485905 2.581411278 8.728611716 1.067331444 0.952752249 0.271365739 0.085624771 0.412115744 31.49364133 0.026698807 0.025144278 381.4268643 -2.581411278 -0.114579195 EAEREEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EAEREEER 8 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 140.14 0.00059677 341520000 401080 466180 369280 427720 431170 414150 408960 451400 431910 453180 FALSE TRUE 385405.3502 452885.0028 436017.1106 449794.6805 445038.9746 422524.3968 413964.9748 442078.4323 382881.3875 422485.7149 0.912232856 1.07195341 1.032028055 1.06463879 1.053382301 1.000091558 0.979831886 1.046374863 0.906258777 1 18.68854304 2.582282903 6.437635133 0.992723464 1.031613617 0.119724109 0.052935382 0.556619516 29.28868997 0.016759782 0.015737441 382.1931534 -2.582282903 0.038890154 EIGTHKPLPGITVGDIGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIGTHKPLPGITVGDIGPK 19 1 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 78.661 0.0059006 579670000 610390 764390 531780 630750 609090 728430 787590 754150 905680 890870 FALSE TRUE 586535.284 742590.3456 627884.4754 663303.0831 628681.933 743159.3537 797228.762 738576.539 802871.0033 830530.5814 0.706217564 0.894115596 0.756004041 0.7986498 0.756964219 0.89480071 0.959902958 0.889282774 0.966696497 1 19.66367377 2.582552714 4.045211427 0.938548557 0.7884475 0.701461038 0.052688945 0.138220443 3.94679978 0.016767211 0.015536436 382.4306696 -2.582552714 -0.150101057 GGGPGKS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 3 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.767)PT(0.233)R;GGGPGKS(0.5)PT(0.5)R;GGGPGKS(0.839)PT(0.161)R 79.886 0.015541 3093538000 570110 544700 450225 472818 485150 543110 543860 590870 633180 585530 TRUE FALSE 547829.4709 529165.6893 531590.6727 497220.1936 500755.2904 554092.0563 550515.9214 578668.328 561304.0609 545871.5316 1.003586813 0.969396019 0.973838425 0.910874015 0.917350075 1.015059449 1.00850821 1.060081529 1.028271358 1 19.05820193 2.58268556 5.363122442 1.029607851 0.954584967 0.567880535 0.029279311 0.168238315 7.052738 0.010393432 0.009723506 382.5476689 -2.58268556 -0.075022884 QEPCAQHNGSEPAS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEPCAQHNGSEPASPKR 17 1 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 QEPCAQHNGSEPAS(1)PKR;QEPCAQHNGS(0.006)EPAS(0.994)PKR 201.64 5.32E-12 252706000 172117 169015 135334 155020 154257 165732 175332 181103 180356 172156 TRUE FALSE 165390.4774 164194.8577 159791.8643 163020.6008 159218.8165 169083.2146 177477.7655 177363.1598 159882.743 160495.7208 1.030497739 1.023048196 0.995614484 1.015731759 0.992043998 1.053506061 1.105809953 1.10509588 0.996180722 1 17.29217531 2.584389513 5.402382046 1.068337437 1.011696645 0.179888189 0.037148681 0.262896855 11.03764637 0.012236657 0.011452387 384.0515416 -2.584389513 -0.056640792 VIQLMPS(ph)PIMHPLILNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIQLMPSPIMHPLILNPR 18 0 P41212 P41212 ETV6 Transcription factor ETV6 1 VIQLMPS(1)PIMHPLILNPR;VIQLMPS(1)PIMHPLILNPR 214.31 6.52E-19 1000860000 677120 701200 655090 728600 693650 621890 585750 646500 573760 636210 TRUE FALSE 650657.4018 681202.4625 773479.3354 766203.1333 715961.8822 634465.0419 592918.5837 633149.5491 508629.1702 593118.93 1.097010007 1.148509056 1.304088095 1.2918204 1.207113525 1.069709648 0.999662216 1.067491724 0.857550054 1 19.17796189 2.584739649 2.515827332 0.995399776 1.217606224 0.67176045 0.075339087 0.191277315 2.381508514 0.029243392 0.026475609 384.361296 -2.584739649 0.222206449 NLDSATS(ph)PQNGDQQNGYGDLFPGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 NLDSATSPQNGDQQNGYGDLFPGHK 25 0 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 NLDS(0.006)AT(0.141)S(0.853)PQNGDQQNGYGDLFPGHK;NLDS(0.047)AT(0.157)S(0.796)PQNGDQQNGYGDLFPGHK 154.1 5.65E-08 510240000 291602 282765 257893 284399 299734 312326 322384 323997 369321 402166 TRUE FALSE 280205.8715 274700.8191 304500.0019 299076.8665 309375.2163 318641.4457 326329.4318 317306.3487 327397.2284 374926.9386 0.747361266 0.732678265 0.812158238 0.797693726 0.825161343 0.849876104 0.870381395 0.846315151 0.873229407 1 18.51624996 2.585575546 0.036753139 1.663035585 8.60E-10 0.931506113 0.018588263 37.99143879 0.617544081 12.67469053 15.0757227 385.101798 -2.585575546 -1.663035584 VKGEEIYSMDEGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKGEEIYSMDEGIR 14 1 Q96P70 Q96P70 IPO9 Importin-9 0 ; 83.966 0.0075882 602560000 421320 456580 385150 392280 448730 455930 473150 488050 564100 541580 FALSE TRUE 404854.3486 443558.7854 454755.1726 412525.6178 463163.808 465149.217 478940.5512 477971.5969 500065.7329 504898.3042 0.801853255 0.878511141 0.900686671 0.817046947 0.917340787 0.921273082 0.948588156 0.946669048 0.990428624 1 18.94563331 2.585832093 0.420130369 1.00605665 0.824709395 0.779764348 0.029287591 0.601149964 0.222547815 0.029504535 0.04123566 385.3293529 -2.585832093 -0.181347254 EIFDSRGNPTVEVDLFTSKGLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIFDSRGNPTVEVDLFTSKGLFR 23 2 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 92.792 0.002684 642870000 221470 183260 146110 118800 186500 99444 69316 62331 122540 59185 FALSE TRUE 212814.7076 178033.6042 172515.3272 124931.2822 192498.9419 101454.8258 70164.30994 61043.84307 108629.7729 55176.34723 3.856991596 3.226629039 3.126617398 2.264218066 3.488794593 1.838737628 1.271637458 1.106340781 1.968774273 1 15.75176233 2.585983272 3.654434238 1.331145729 3.138259847 0.795166733 0.449708517 0.10911743 2.649895236 0.154821052 0.143019762 385.4635101 -2.585983272 1.807114118 SSS(ph)PQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPQPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)S(0.022)S(0.977)PQPK 71.425 0.064607 0 779360 791390 688480 558390 739590 792700 842560 947540 940500 784730 TRUE FALSE 748901.7496 768820.3321 812903.6512 587208.5748 763379.584 808728.9371 852871.5013 927972.9679 833738.3829 731579.5381 1.023677824 1.050904641 1.111162367 0.802658555 1.043467654 1.105455928 1.165794636 1.268451234 1.139641474 1 19.4806552 2.586724408 2.587051412 1.175050692 1.002557396 0.290750865 0.098189182 0.29897513 3.92525572 0.035821032 0.032533766 386.1218761 -2.586724408 -0.172493296 LRDDFEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRDDFEKK 8 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 103.87 0.0026374 1269170000 1409260 1364670 942040 990740 1159330 1272720 1325600 1423710 1520520 1310530 FALSE TRUE 1354184.561 1325750.948 1112287.584 1041872.21 1196620.902 1298455.27 1341823.089 1394309.891 1347916.944 1221766.636 1.108382339 1.085109798 0.910392829 0.852758767 0.979418546 1.062768644 1.098264636 1.141224396 1.103252376 1 20.22053732 2.587621893 3.293235772 1.10081373 0.981127138 0.260576738 0.077704213 0.324643054 6.624622909 0.029475371 0.027126742 386.9206357 -2.587621893 -0.119686591 AEPYCSVLPGFTFIQHLPLSER ddPTM_BT-474_Pertuzumab_2h_R1 2 AEPYCSVLPGFTFIQHLPLSER 22 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 275.23 1.98E-45 1281000000 908430 1136970 849770 1072700 732600 1014050 885520 784560 828720 1088670 FALSE TRUE 872927.5513 1104544.729 1003342.342 1128062.176 756164.7443 1034554.786 896357.2586 768358.5618 734647.1799 1014933.411 0.86008357 1.088292805 0.988579478 1.111464223 0.745038774 1.019332672 0.88316854 0.757053175 0.723837812 1 19.95295365 2.588640171 1.014486713 0.812174777 1.000932868 0.186193972 0.123192563 0.695711027 1.474074509 0.070765674 0.055976471 387.828902 -2.588640171 0.188758091 ALEELQEALAEKEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALEELQEALAEKEELR 16 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 ;;; 219.01 1.17E-14 516150000 551253 581722 456132 521835 551174 580911 564039 635729 675130 657378 FALSE TRUE 529709.4233 565131.8581 538565.199 548766.9669 568903.0123 592657.4184 570941.878 622600.974 598492.0728 612853.2025 0.864333288 0.922132504 0.878783364 0.895429712 0.928285942 0.967046294 0.931612784 1.015905557 0.97656677 1 19.22518202 2.588916568 0.752085952 1.000629805 0.884858363 0.787731121 0.022275979 0.284114655 0.334176274 0.01571934 0.013184651 388.0758063 -2.588916568 -0.115771442 NAATEDLWESLENASGKPIAAVMNTWTK ddPTM_BT-474_Pertuzumab_2h_R1 1 NAATEDLWESLENASGKPIAAVMNTWTK 28 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 289.98 3.55E-71 84382000 43761 41390 30315 36231 32436 42385 42678 45007 45188 54819 FALSE TRUE 42050.77174 40209.59773 35793.59485 38100.88625 33479.3334 43242.05374 43200.30613 44077.58972 40058.44768 51106.0603 0.822813801 0.786787271 0.700378676 0.745525795 0.655095173 0.846123796 0.845306914 0.862472855 0.783829695 1 15.64120676 2.589054658 8.075978486 0.859091015 0.742594241 0.473175671 0.066004403 0.276623615 18.08638267 0.020704975 0.01949232 388.1992194 -2.589054658 -0.116496774 HHTAAFEER ddPTM_BT-474_Pertuzumab_2h_R1 4 HHTAAFEER 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 179.8 4.94E-05 1173930000 366806 459454 336960 369158 308992 247214 302981 40226.8 304217 203377 FALSE TRUE 352470.816 446350.8218 397856.1676 388210.2886 318931.0083 252212.8365 306688.9721 39396.10252 269683.5615 189602.0946 1.859002753 2.354144993 2.098374326 2.047499999 1.682106988 1.330221783 1.61754 0.207783055 1.42236594 1 17.53261538 2.590219438 1.052638341 0.845325873 2.134725382 0.636794489 0.355500459 0.287999161 0.656093484 0.201916535 0.160237045 389.2417695 -2.590219438 1.289399509 LHTGEKPYK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHTGEKPYK 9 1 A6NHJ4;Q05481;Q8NCK3;Q05481-2;Q8NB50;Q96N58;G3V1M0;J3KR62;Q9H963;Q9Y5A6;Q96NL3;Q8NB50-3;Q8N782;Q8NCK3-2;Q0VGE8;Q8N4W9-2;Q8N4W9;Q9P0L1 A6NHJ4;Q0VGE8;Q8N4W9-2;Q9P0L1 ZNF860;ZNF91;ZNF485;ZFP62;ZNF578;ZSCAN21;ZNF525;ZNF702P;ZNF599;ZNF816;ZNF808;ZKSCAN7 Zinc finger protein 860;Zinc finger protein 91;Zinc finger protein 485;Zinc finger protein 62 homolog;Zinc finger protein 578;Putative zinc finger protein 702;Zinc finger and SCAN domain-containing protein 21;Zinc finger protein 599;Zinc finger protein 525;Zinc finger protein 816;Zinc finger protein 808;Zinc finger protein with KRAB and SCAN domains 7 0 144.77 5.93E-05 684960000 1430200 1269900 1195900 1099500 1379300 1127200 1189100 1001800 1362000 1271100 FALSE TRUE 1374306.203 1233683.695 1412025.733 1156245.327 1423666.437 1149992.756 1203652.561 981112.4799 1207391.47 1185007.265 1.15974496 1.041076905 1.191575592 0.975728471 1.201398911 0.970452073 1.015734331 0.827937945 1.018889509 1 20.17646447 2.591379081 6.166101508 0.946542406 1.10624171 0.437049114 0.082169615 0.202593464 9.647650768 0.025570213 0.024007107 390.2825026 -2.591379081 0.159699304 DLKEER ddPTM_BT-474_Pertuzumab_2h_R1 1 DLKEER 6 1 A0A087WX19;A0A087WX45;Q6IPM2-2;Q6IPM2-3;Q6IPM2-4;Q6IPM2;Q13105-3;Q13105;Q13105-2;Q6UB98-2;Q6UB98 A0A087WX19;Q6UB98-2 IQCE;ZBTB17;ANKRD12 IQ domain-containing protein E;Zinc finger and BTB domain-containing protein 17;Ankyrin repeat domain-containing protein 12 0 67.032 0.091058 468210000 376680 374120 322290 352370 361790 458460 501200 561260 536500 539160 FALSE TRUE 361958.9292 363450.4639 380534.9723 370555.8579 373427.3039 467730.3753 507333.8355 549669.7849 475598.7692 502642.213 0.720112477 0.723079866 0.757069268 0.737215953 0.742928656 0.930543363 1.009333921 1.093560729 0.946197428 1 18.93917231 2.592914663 2.368164002 1.027966749 0.733136588 0.929448544 0.036243498 0.069175613 0.765660643 0.013678157 0.012388271 391.6649091 -2.592914663 -0.294830161 RPNTS(ph)PDR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.215)S(0.785)PDR;RPNT(0.199)S(0.801)PDR;RPNT(0.048)S(0.952)PDR 94.791 0.0061917 3947665000 542509 575407 486620 577334 608560 514476 512132 541270 596377 528432 TRUE FALSE 521307.1485 558996.9557 574563.0588 607130.2769 628134.8851 524879.0572 518399.6246 530092.5854 528678.7832 492640.83 1.058189084 1.134694734 1.166292 1.232399428 1.275036186 1.065439617 1.05228717 1.076022435 1.073152591 1 18.91017668 2.59309162 10.44451715 1.058653185 1.174025369 0.523642918 0.057122179 0.394960813 33.32631379 0.019724491 0.018588975 391.824529 -2.59309162 0.115372185 ASLGS(ph)LEGEAEAEASS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 AS(0.001)LGS(0.999)LEGEAEAEASS(1)PK;AS(0.002)LGS(0.998)LEGEAEAEAS(0.28)S(0.72)PK 295.23 3.92E-49 415654000 504910 439610 470030 477480 454900 518570 611140 487810 628110 572360 TRUE FALSE 485177.559 427072.7532 554974.8768 502122.8 469532.2716 529055.8407 618619.3141 477736.553 556809.5861 533593.5474 0.909264292 0.80037091 1.040070442 0.941021125 0.879943684 0.991495949 1.159345568 0.895319209 1.043508844 1 19.02538169 2.593650616 6.0074359 1.015765306 0.916881706 0.290042481 0.081848363 0.341742287 15.66843732 0.026963753 0.025308834 392.3291852 -2.593650616 -0.098883599 NLLDDVEEFHER ddPTM_BT-474_Pertuzumab_2h_R1 2 NLLDDVEEFHER 12 0 P29375;P29375-2;E7EV89 P29375 KDM5A Lysine-specific demethylase 5A 0 ; 154.47 6.68E-05 93779000 100251 106693 83880 105200 109678 95645 97164 103423 99186 109407 FALSE TRUE 96333.08009 103650.2201 99038.9819 110629.3846 113205.8925 97579.00743 98353.1221 101287.2789 87926.8211 101996.7664 0.944471903 1.016210844 0.971001193 1.084636195 1.109896876 0.956687264 0.964276864 0.993044019 0.862054986 1 16.63816389 2.595139316 20.55746288 0.95870817 1.025860031 0.272843855 0.057013533 7.593653313 1296.47524 0.018904573 0.017823354 393.6763417 -2.595139316 0.067151862 AKVS(ph)PVNDVDVGVYQLMQSEQLLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AKVSPVNDVDVGVYQLMQSEQLLSR 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 AKVS(1)PVNDVDVGVYQLMQSEQLLSR 145.57 1.68E-07 18773000 12031 12783 10791 7712.9 10994 11930 14092 11733 13808 15800 TRUE FALSE 11560.81522 12418.44136 12741.17374 8110.963693 11347.63199 12171.23277 14264.46211 11490.70945 12240.57373 14729.85193 0.784856173 0.84307985 0.864989941 0.550648013 0.770383304 0.826297021 0.96840499 0.780096739 0.831004533 1 13.84645531 2.595942771 4.043721612 0.871962208 0.761689604 0.268956664 0.099321995 0.388391298 10.88664249 0.034388391 0.031986932 394.4053257 -2.595942771 -0.110272604 IHGVGFK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHGVGFK 7 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ; 118.06 0.0050921 3752000000 5836700 5384500 5301700 5385600 5425400 5029900 5818800 4216400 6411100 6263000 FALSE TRUE 5608595.311 5230939.332 6259835.126 5663551.461 5599912.918 5131608.024 5890012.215 4129329.867 5683338.806 5838801.431 0.960573052 0.895892658 1.07210961 0.969985283 0.959086036 0.878880381 1.00877077 0.707222178 0.973374223 1 22.47724082 2.596152718 1.516374371 0.878392769 0.975253807 0.03289053 0.092452927 0.72052053 3.346340691 0.040956495 0.034806065 394.5960361 -2.596152718 0.096861038 TEQSLAGPKGSPS(ph)ESEKER ddPTM_BT-474_Pertuzumab_2h_R1 1 TEQSLAGPKGSPSESEKER 19 2 Q9NYD6;D6RAG4;V9GYH0 Q9NYD6 HOXC10 Homeobox protein Hox-C10 1 TEQSLAGPKGS(0.444)PS(0.556)ESEKER 117.43 5.16E-05 244740000 268130 209380 176430 152700 191690 210290 208410 229260 265370 197120 TRUE FALSE 257651.1832 203408.6874 208314.8257 160580.8653 197855.8829 214542.2079 210960.5839 224525.7009 235246.3101 183768.8868 1.402039201 1.106872284 1.133569612 0.873819655 1.076656045 1.167456644 1.147966816 1.221782995 1.28012045 1 17.487533 2.596299819 4.864710765 1.181298734 1.105469912 0.014252159 0.137356804 0.740780963 26.4394331 0.04620858 0.043204697 394.7297132 -2.596299819 -0.075828821 HSTENDS(ph)PTNVQQ ddPTM_BT-474_Pertuzumab_2h_R1 3 HSTENDSPTNVQQ 13 0 P49354;P49354-2;B3KVN2 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 HS(0.034)T(0.034)ENDS(0.926)PT(0.007)NVQQ;HSTENDS(0.999)PTNVQQ;HSTENDS(1)PTNVQQ 153.79 4.51E-05 278060000 937940 743230 777580 753830 752570 743850 750120 538789 882020 896070 TRUE FALSE 901284.2679 722033.8081 918106.0032 792735.2566 776777.0975 758891.1567 759300.1929 527662.8189 781896.7873 835378.3808 1.078893455 0.864319481 1.099030121 0.948953522 0.929850611 0.908440024 0.908929666 0.631645289 0.935979199 1 19.67207028 2.597424903 1.420682767 0.818308865 0.992384785 0.16370771 0.112102494 0.509618495 2.084674447 0.051286883 0.043044583 395.7536263 -2.597424903 0.17407592 AMGIMNS(ph)FVNDIFER ddPTM_BT-474_Pertuzumab_2h_R1 1 AMGIMNSFVNDIFER 15 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L 1 AMGIMNS(1)FVNDIFER 93.058 0.019559 10292000 45310 46369 34540 41594 44159 35709 31011 39440 34180 32095 TRUE FALSE 43539.23511 45046.60152 40782.14634 43740.67132 45579.41434 36431.06045 31390.52189 38625.55022 30300.02969 29921.17706 1.455131094 1.505509005 1.36298603 1.461863323 1.52331622 1.217567757 1.049107187 1.290910118 1.012661689 1 14.86887931 2.600109967 4.282460436 1.129469319 1.457787089 0.794265071 0.089259923 0.110457831 3.339796085 0.029412736 0.027432274 398.2079869 -2.600109967 0.32831777 KTHETLSHAGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTHETLSHAGQK 12 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6;E9PNQ9;Q16890-4;Q16890-3;Q16890-2 Q16890-5 TPD52L1 Tumor protein D53 0 137.62 3.61E-05 59944000 203900 250000 213210 258590 211930 207150 205520 158780 220120 264140 FALSE TRUE 195931.3626 242870.2448 251741.7898 271935.8609 218746.9209 211338.7149 208035.2152 155501.1375 195132.9004 246249.5625 0.795661769 0.986276858 1.022303501 1.104310026 0.888313947 0.858229809 0.844814558 0.631477822 0.792419277 1 17.90976164 2.600263716 1.817995205 0.771894622 0.977793266 0.237694381 0.114856742 0.37056687 2.449712091 0.046787545 0.041273534 398.3489864 -2.600263716 0.205898644 RLDIDEKPLVVQLNWNKDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDIDEKPLVVQLNWNKDDR 20 3 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ; 193.84 2.58E-18 557770000 346140 310264 226277 278150 301960 303016 306724 339207 378450 304990 FALSE TRUE 332612.4661 301415.5745 267170.2874 292505.3548 311672.8176 309143.1911 310477.7801 332202.2569 335489.9426 284332.7556 1.16980003 1.060080376 0.939639497 1.02874308 1.096155161 1.08725845 1.091952207 1.168357322 1.179920132 1 18.11722078 2.601636753 1.498576386 1.12865093 1.046651801 0.092733395 0.070888914 0.676441046 3.069693238 0.032370662 0.027579065 399.6103732 -2.601636753 -0.081999129 MWFS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 MWFSPR 6 0 A0A494C142;Q99728-3;Q99728-2;Q99728;A0A087X2H0 A0A494C142 BARD1 BRCA1-associated RING domain protein 1 1 MWFS(1)PR 77.674 0.075312 104340000 161030 176660 134140 144900 160870 94975 156630 132580 114520 125060 TRUE FALSE 154736.7696 171621.8298 158382.0819 152378.3064 166044.5296 96895.45957 158546.8848 129842.1767 101520.1697 116589.5748 1.32719216 1.472016945 1.358458354 1.306963394 1.424179906 0.831081679 1.359871884 1.113668841 0.870748263 1 16.83107927 2.601710201 0.530740343 0.978050751 1.437442095 0.489318043 0.158846012 0.845732986 0.496308285 0.138712973 0.152288999 399.6779609 -2.601710201 0.459391343 NIDLATPLHHTWTYQALVHDVLDFHLNR ddPTM_BT-474_Pertuzumab_2h_R1 3 NIDLATPLHHTWTYQALVHDVLDFHLNR 28 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 ;; 235.63 1.25E-45 1458290000 239503 289581 231851 252810 224522 195866 184283 71685.7 256845 218963 FALSE TRUE 230142.958 281322.4334 273751.6332 265857.5544 231743.954 199826.5447 186538.3105 70205.36524 227689.0324 204132.441 1.127419811 1.378136822 1.341049134 1.302377776 1.135262739 0.97890636 0.913810218 0.343920667 1.115398568 1 17.63914595 2.603301225 1.619005487 0.741614138 1.292905533 0.464625712 0.206489238 0.271914821 1.434009127 0.089007492 0.077121803 401.1448538 -2.603301225 0.551291394 GKPSEQLT(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 6 GKPSEQLTPTR 11 1 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 GKPS(0.003)EQLT(0.994)PT(0.003)R;GKPSEQLT(0.99)PT(0.01)R;GKPSEQLT(0.996)PT(0.004)R;GKPSEQLT(0.962)PT(0.038)R;GKPSEQLT(0.971)PT(0.029)R;GKPSEQLT(0.998)PT(0.002)R 167.37 3.12E-05 6751230000 4914010 4858900 4516540 4761420 4818750 5490200 5516500 6105410 6359020 6347990 TRUE FALSE 4721965.056 4720328.929 5332779.248 5007157.457 4973749.47 5601215.606 5584012.577 5979331.15 5637170.709 5918034.983 0.797894076 0.797617612 0.901106408 0.846084464 0.840439349 0.946465444 0.943558562 1.01035752 0.952540957 1 22.49668679 2.603428535 1.081578738 0.991812607 0.828066396 0.80973653 0.032708296 0.209881267 0.505165562 0.018691407 0.015067674 401.262463 -2.603428535 -0.163746211 ATENDIANFFSPLNPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATENDIANFFSPLNPIR 17 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 159.18 7.55E-09 64867000 56728 48408 38940 46264 55902 50126 47711 59062 63342 57550 FALSE TRUE 54511.00704 47027.45124 45977.32422 48651.69058 57700.1386 51139.58206 48294.90149 57842.34906 56151.68171 53652.08724 1.016009066 0.876526034 0.856953132 0.906799588 1.075450026 0.953170411 0.900149537 1.07810063 1.046588951 1 15.71134668 2.603483549 0.699483552 1.03385874 0.91299444 0.229448901 0.069314927 1.006382914 1.028566019 0.055326494 0.048830016 401.3132959 -2.603483549 -0.120864301 RES(ph)PSPAPKPR ddPTM_BT-474_Pertuzumab_2h_R1 10 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.933)PS(0.067)PAPKPR;RES(0.683)PS(0.317)PAPKPR;RES(0.895)PS(0.105)PAPKPR;RES(0.716)PS(0.284)PAPKPR;RES(0.871)PS(0.129)PAPKPR;RES(1)PSPAPKPR;RES(0.983)PS(0.017)PAPKPR;RES(0.999)PS(0.001)PAPKPR;RES(0.659)PS(0.341)PAPKPR;RES(0.996)PS(0.004)PAPKPR 151.22 2.00E-05 85716840000 19658520 19522160 14846060 17653140 17695320 18476030 19277910 19516510 20817490 19708670 TRUE FALSE 18890243.3 18965407.11 17529073.29 18564220.67 18264506.04 18849627.99 19513838.83 19113487.25 18454375.81 18373784.23 1.028108476 1.032199294 0.954026295 1.010364574 0.994052494 1.025897973 1.062047893 1.04025861 1.004386227 1 24.13114546 2.603626308 5.362815764 1.033545629 1.003078225 0.137614248 0.026189607 0.350337611 13.87730829 0.008724131 0.008179988 401.445236 -2.603626308 -0.030467404 S(ph)PEAQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPEAQPK 7 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 S(1)PEAQPK;S(1)PEAQPK 83.998 0.022939 3535500000 4193500 3813200 3112300 3583100 3708900 3927400 4554100 4181800 3858500 5091500 TRUE FALSE 4029613.384 3704451.27 3674761.843 3768024.22 3828200.137 4006814.719 4609834.438 4095444.369 3420499.256 4746648.17 0.848938712 0.780435191 0.774180371 0.793828421 0.806505981 0.844135604 0.97117677 0.862807653 0.720613606 1 22.17847769 2.603680161 3.847593313 0.881535165 0.797852818 0.241410825 0.072248972 0.363596062 9.449843577 0.024078309 0.022415193 401.495018 -2.603680161 -0.083682347 KPTTEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KPTTEEK 7 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 101.72 0.014192 2786400000 2945400 2321610 2192280 2107680 2286430 2557670 2734170 2650900 2844650 3033520 FALSE TRUE 2830290.512 2255399.956 2588473.763 2216457.617 2359975.097 2609387.84 2767631.59 2596157.989 2521737.258 2828056.988 1.000789773 0.797508666 0.915283452 0.783738668 0.834486401 0.922678663 0.9786336 0.918000592 0.891685446 1 21.43137976 2.603972126 5.319865203 0.940427176 0.861003154 0.260410982 0.064133186 0.309767538 12.15717929 0.020126337 0.018869147 401.7650241 -2.603972126 -0.079424023 EIEIDIEPTDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIEIDIEPTDK 11 0 Q15843;F8VSA6;E9PS38;S4R3E9;E9PL57 Q15843 NEDD8;NEDD8-MDP1 NEDD8 0 102.53 0.0066443 177780000 299900 299500 301860 343630 338190 318030 396100 492180 427560 483070 FALSE TRUE 288179.5764 290958.5532 356412.8168 361364.7855 349068.1885 324460.7845 400947.5903 482016.311 379025.1813 450351.2386 0.639899598 0.646070285 0.791410762 0.802406554 0.775102095 0.720461623 0.890299739 1.070311947 0.84162127 1 18.7806911 2.604355728 0.489966925 1.016744035 0.649882224 0.650635403 0.078448611 0.663207894 0.331474739 0.079207451 0.094652338 402.1200502 -2.604355728 -0.366861811 CS(ph)PVPGLS(ph)SSPSGSPLHGK ddPTM_BT-474_Pertuzumab_2h_R1 1 CSPVPGLSSSPSGSPLHGK 19 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 2 CS(0.999)PVPGLS(0.376)S(0.33)S(0.29)PS(0.002)GS(0.002)PLHGK 64.295 0.016586 212030000 122220 130120 102100 115790 95608 137120 128270 162610 143480 148740 TRUE FALSE 117443.5073 126409.105 120551.7412 121765.9358 98683.31815 139892.6603 129839.8066 159252.0467 127192.7519 138665.7073 0.846954229 0.911610429 0.869369533 0.878125804 0.711663468 1.00884828 0.936351237 1.148460205 0.917261768 1 17.08125152 2.606117426 9.501092451 1.018188934 0.85075853 0.51293948 0.076389612 0.278569689 20.05929034 0.024738815 0.023309688 403.7545463 -2.606117426 -0.167430405 CIIVEEGKEILVGDVGVTITDPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 CIIVEEGKEILVGDVGVTITDPFK 24 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 127.01 2.42E-07 0 17150 11715 10218 8776.7 11131 12746 12868 13716 16840 11700 FALSE TRUE 16479.75904 11380.89967 12064.6199 9229.666539 11489.03872 13003.73285 13025.48243 13432.75981 14928.3938 10907.54858 1.510858184 1.043396652 1.106079869 0.846172398 1.0533108 1.192177395 1.194171389 1.231510427 1.368629595 1 13.41303928 2.606632002 4.909117606 1.215641882 1.09352678 0.046861383 0.176173456 0.579077977 20.70424545 0.058038817 0.05435513 404.2332209 -2.606632002 -0.122115103 QQLVELVAEQADLEQTFNPSDPDCVDR ddPTM_BT-474_Pertuzumab_2h_R1 3 QQLVELVAEQADLEQTFNPSDPDCVDR 27 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7;Q9BZZ5-3 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ;; 154.49 4.49E-08 197434000 122318 126358 95472 126169 114591 112003 102157 108260 125944 127994 FALSE TRUE 117537.6773 122754.3936 112725.9142 132680.5972 118276.9236 114267.7774 103407.2279 106024.3932 111647.3651 119324.8524 0.985022608 1.028741215 0.944697705 1.111927604 0.99121785 0.957619265 0.866602605 0.888535716 0.935658942 1 16.86453503 2.608518453 2.978628552 0.909501103 1.015612577 0.384220237 0.052323609 0.22948042 3.908530493 0.017684663 0.016372108 405.9929131 -2.608518453 0.106111474 IEELEEALR ddPTM_BT-474_Pertuzumab_2h_R1 4 IEELEEALR 9 0 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;Q8IUD2-5;K7EPD6 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 0 ;;; 114.89 0.0036389 86459000 206445 200705 178630 170143 190628 174486 180549 168865 182268 193076 FALSE TRUE 198376.9012 194981.0899 210912.4146 178924.1006 196759.7227 178014.2265 182758.6127 165377.8787 161577.7008 179998.7905 1.102101301 1.083235556 1.17174351 0.99402946 1.093116916 0.98897457 1.015332448 0.918772166 0.897659925 1 17.45762769 2.609366623 0.876636009 0.932933064 1.106106217 0.626824981 0.04961406 0.351958638 0.562778082 0.031054454 0.025362904 406.7865855 -2.609366623 0.173173153 SGGGGYSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGGGYSSR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 80.165 0.057889 24757000 26357 26186 19660 25044 27042 21799.4 23040 20784.4 22134.7 27937 FALSE TRUE 25326.9393 25439.20092 23212.99933 26336.52384 27911.83049 22240.1988 23321.97041 20355.19488 19622.06165 26044.80211 0.972437387 0.976747714 0.891271865 1.011200766 1.071685259 0.853920821 0.89545585 0.781545385 0.753396458 1 14.66870785 2.61101857 7.190838139 0.840082351 0.980297982 0.4095281 0.075450524 0.240564538 13.02024515 0.024461384 0.023018497 408.336846 -2.61101857 0.14021563 SLDEMEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLDEMEK 7 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 157.21 0.0034697 814440000 1322830 1338490 1071300 1189750 1265010 1346140 1329170 1458100 1573870 1501570 FALSE TRUE 1271132.341 1300317.576 1264907.741 1251153.14 1305700.196 1373359.873 1345436.78 1427989.725 1395210.876 1399867.326 0.908037724 0.928886296 0.90359116 0.893765514 0.932731389 0.98106431 0.961117354 1.020089332 0.996673649 1 20.41685867 2.611529704 1.346779176 1.002443438 0.908713351 0.868446278 0.015572219 0.141936764 0.523446789 0.007548875 0.006351069 408.8177125 -2.611529704 -0.093730088 ALKPMHSLIPLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALKPMHSLIPLGK 13 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;H0Y9N9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 93.011 0.0034909 451940000 1157560 1179230 981130 1014190 1086000 1137010 1200860 1135820 1340570 1378170 FALSE TRUE 1112321.275 1145599.515 1158442.016 1066532.467 1120932.176 1160001.121 1215556.484 1112364.92 1188394.114 1284825.318 0.865737357 0.891638341 0.901633864 0.830099199 0.872439358 0.90284734 0.946086963 0.865771326 0.924946058 1 20.2931408 2.612861052 3.975372639 0.918304521 0.872759739 0.358735082 0.036537544 0.334408306 9.123799747 0.012133377 0.011333836 410.0728839 -2.612861052 -0.045544783 SGSS(ph)SPDSEITELKFPSINHD ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 S(0.073)GS(0.073)S(0.458)S(0.384)PDS(0.01)EIT(0.003)ELKFPSINHD;S(0.241)GS(0.241)S(0.268)S(0.231)PDS(0.015)EIT(0.004)ELKFPSINHD 120.85 1.86E-05 1213002000 141842 177007 144922 174641 137216 183557 193153 196372 178511 220020 TRUE FALSE 136298.6578 171958.9337 171112.6292 183654.2429 141629.6773 187268.6483 195516.8642 192316.8496 158247.1797 205117.8494 0.664489503 0.838342125 0.834216182 0.895359636 0.690479535 0.912980751 0.953192834 0.937591975 0.771493949 1 17.64609352 2.612921425 10.94957624 0.917067057 0.796512657 0.369448979 0.084505873 0.542281832 45.50283828 0.02667249 0.025139843 410.1298936 -2.612921425 -0.1205544 (ac)MEDMNEYSNIEEFAEGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 MEDMNEYSNIEEFAEGSK 18 0 O14979-2;O14979-3;A0A087WU03 O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;; 182.1 1.21E-107 605277000 500765 480756 420085 454755 481986 505267 521634 548231 601773 586866 FALSE TRUE 481194.5502 467045.3096 496003.7042 478224.96 497489.5174 515483.8449 528017.9129 536909.8383 533462.2519 547117.0431 0.879509341 0.85364789 0.906576957 0.874081636 0.909292671 0.942182027 0.965091327 0.981343654 0.975042285 1 19.06148997 2.613847454 0.862826113 0.990547089 0.871714206 0.926273247 0.013137661 0.136873698 0.212375055 0.008221627 0.006766167 411.0053304 -2.613847454 -0.118832883 S(ph)FDHLISDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFDHLISDTK 10 0 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 S(1)FDHLISDTK;S(1)FDHLISDTK 202.65 1.93E-07 203809000 507920 494170 297989 412120 631530 489660 556790 764850 736490 666220 TRUE FALSE 488069.9249 480076.7554 351842.241 433389.5626 651843.736 499561.2607 563604.1626 749055.5802 652886.7428 621096.326 0.785820016 0.772950564 0.566485787 0.697781559 1.049505059 0.804321713 0.907434385 1.206021593 1.051184358 1 19.24445751 2.615909692 0.880805964 1.095394841 0.70617473 0.568362726 0.120582096 0.41437917 0.66979395 0.082101198 0.067452743 412.9616215 -2.615909692 -0.389220111 QSFTMVADT(ph)PENLR ddPTM_BT-474_Pertuzumab_2h_R1 13 QSFTMVADTPENLR 14 0 Q14847;Q14847-2;C9J9W2;F6S2S5 Q14847 LASP1 LIM and SH3 domain protein 1 1 QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR 393.56 3.78E-113 23701370000 11621610 11694460 11077270 10645170 10093840 10962210 9663350 11626480 9709170 10781120 TRUE FALSE 11167424.63 11360945.45 13079179.1 11194568.5 10418517.53 11183873.4 9781612.968 11386389.13 8607025.726 10050905.14 1.111086462 1.130340531 1.301293657 1.113787101 1.036575053 1.112723008 0.973207172 1.132872012 0.856343345 1 23.26082209 2.61652389 0.670262086 0.985063722 1.1770352 0.427217691 0.085320273 0.790720955 0.74425794 0.066734715 0.061198001 413.5460621 -2.61652389 0.191971478 GLLGLEPVPSS(ph)PCR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLGLEPVPSSPCR 14 0 E7EX78;O14901-2;O14901 E7EX78 KLF11 Krueppel-like factor 11 1 GLLGLEPVPS(0.203)S(0.797)PCR;GLLGLEPVPS(0.306)S(0.694)PCR 141.54 1.01E-05 156213000 489060 513250 416730 487240 500220 458430 441000 497360 477700 522340 TRUE FALSE 469946.9945 498612.6125 492042.3811 512386.5148 516310.0306 467699.7687 446397.0899 487089.3422 423473.4987 486961.4465 0.965059961 1.02392626 1.010433957 1.052211666 1.060268804 0.960445169 0.916699039 1.00026264 0.869624283 1 18.89344803 2.616585003 6.426884962 0.949936066 1.023254243 0.42156423 0.042869664 0.238659845 11.59805953 0.0135598 0.012751096 413.6042598 -2.616585003 0.073318177 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR 34 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ; 259.9 7.19E-60 969010000 139592 188491 158511 158934 141350 113844 133237 65036 121968 117150 FALSE TRUE 134136.5903 183115.4212 187157.4638 167136.6028 145896.6511 116146.0037 134867.5943 63692.98387 108122.704 109215.3262 1.228184679 1.676645831 1.713655678 1.530340188 1.335862431 1.063458837 1.234877915 0.583187233 0.989995706 1 16.7368158 2.616596681 1.196776853 0.852702179 1.56493669 0.666660651 0.190714622 0.249815114 0.733048572 0.098290205 0.081341582 413.6153819 -2.616596681 0.71223451 SGKEELDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGKEELDR 8 1 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 66.19 0.056841 325820000 648710 655830 487270 586300 623280 669480 633660 749020 755420 761620 FALSE TRUE 623357.696 637126.3705 575330.5283 616559.0133 643328.3672 683017.3443 641414.9206 733552.4753 669667.8886 710034.799 0.877925556 0.897317105 0.810284973 0.868350416 0.906051884 0.961949112 0.903357021 1.033121864 0.943147983 1 19.43753021 2.617810397 1.038813309 0.988084948 0.860607429 0.644681099 0.037203267 0.309841462 0.69104876 0.021123808 0.017236072 414.7729225 -2.617810397 -0.127477519 KDQGELER ddPTM_BT-474_Pertuzumab_2h_R1 3 KDQGELER 8 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 125.97 0.001987 2145840000 2520820 2412830 2161080 2371170 2386870 2620080 2792240 2892680 2919610 3060840 FALSE TRUE 2422303.567 2344018.451 2551635.229 2493546.368 2463645.841 2673059.813 2826412.268 2832945.147 2588188.113 2853526.58 0.848880674 0.82144616 0.894204121 0.873847254 0.863368808 0.936756584 0.990497964 0.992787369 0.907013844 1 21.44431457 2.617873737 2.787721704 0.974642795 0.859726933 0.762422444 0.029801971 0.131777839 1.988021399 0.010693366 0.009924397 414.8334196 -2.617873737 -0.114915862 GNAMVEEGHFAAEDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNAMVEEGHFAAEDVK 16 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 178.51 2.78E-09 1029260000 1966800 1900710 1668570 1848370 1868210 2086600 2206700 2229700 2529600 2480700 FALSE TRUE 1889935.282 1846503.612 1970117.716 1943764.597 1928302.671 2128792.482 2233706.255 2183655.916 2242450.413 2312679.979 0.817205709 0.798425908 0.851876496 0.840481439 0.833795721 0.92048727 0.965851858 0.944210152 0.969632821 1 21.14113421 2.618039164 2.020136189 0.964782037 0.825529759 0.927485995 0.018779794 0.084611735 0.685707251 0.007399107 0.006711624 414.9914638 -2.618039164 -0.139252278 QEQLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 QEQLSPR 7 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 QEQLS(1)PR;QEQLS(1)PR;QEQLS(1)PR 79.974 0.032697 712480000 1654610 1673860 1411930 1696520 1543020 1484260 1387600 1528840 1504090 1440650 TRUE FALSE 1589946.012 1626123.152 1667097.159 1784077.601 1592652.64 1514272.754 1404581.864 1497268.92 1333352.009 1343073.492 1.183811624 1.210747707 1.241255351 1.328354413 1.185826873 1.127468275 1.045796728 1.114807885 0.992761764 1 20.35710682 2.618320371 1.978512533 1.053332059 1.239334884 0.775025459 0.048742585 0.168174571 1.308670851 0.019510095 0.017657466 415.2602592 -2.618320371 0.186002826 KAS(ph)ISLTDDEVDDEEETIEEEEANEGVVDHQTELSNLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KASISLTDDEVDDEEETIEEEEANEGVVDHQTELSNLAK 39 1 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80 Q96L91-4 EP400 E1A-binding protein p400 1 KAS(0.967)IS(0.026)LT(0.007)DDEVDDEEETIEEEEANEGVVDHQTELSNLAK 386.02 6.46E-180 113580000 30580 21942 27132 27746 27399 35017 42015 40477 44043 39069 TRUE FALSE 29384.89979 21316.23564 32035.35595 29177.97439 28280.31372 35725.06773 42529.19214 39641.13581 39043.42328 36422.82183 0.806771642 0.585243937 0.879540748 0.801090441 0.776444885 0.980842942 1.167652312 1.08835982 1.071949435 1 15.15255508 2.619138705 2.946653751 1.09184579 0.764787514 0.773524691 0.080193006 0.117567073 1.965696928 0.027723669 0.025795335 416.0434648 -2.619138705 -0.327058277 SES(ph)LDPDSSMDTTLILK ddPTM_BT-474_Pertuzumab_2h_R1 8 SESLDPDSSMDTTLILK 17 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.006)ES(0.994)LDPDSSMDTTLILK;S(0.008)ES(0.992)LDPDSSMDTTLILK;SES(1)LDPDSSMDTTLILK;S(0.001)ES(0.999)LDPDSSMDTTLILK;S(0.004)ES(0.994)LDPDS(0.002)SMDTTLILK;S(0.025)ES(0.975)LDPDSSMDTTLILK;S(0.093)ES(0.907)LDPDSSMDTTLILK;S(0.197)ES(0.803)LDPDSSMDTTLILK 328.73 6.40E-72 1127751000 2185100 1878569 1205311 1654012 2469790 1811511 2080935 3103280 2580760 2251685 TRUE FALSE 2099703.876 1824994.051 1423137.51 1739375.758 2549233.038 1848140.994 2106402.105 3039196.184 2287802.944 2099176.369 1.000251292 0.869385764 0.677950424 0.828599151 1.214396787 0.880412442 1.003442177 1.447804114 1.089857421 1 21.00139195 2.619500193 1.004015615 1.202949598 0.850356308 0.281253717 0.17354256 0.569617449 1.18941641 0.106383721 0.086871353 416.3899059 -2.619500193 -0.35259329 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR ddPTM_BT-474_Pertuzumab_2h_R1 6 KDSLDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR 41 1 Q96TC7;H0YLG5;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 KDS(0.999)LDLEEEAAS(0.001)GASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(0.997)LDLEEEAAS(0.002)GASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR 146.48 1.08E-13 2034959300 43956.1 46659.7 40678.5 57701.9 46935.5 43928 41522.6 45033.3 45078.6 46045.7 TRUE FALSE 42238.24702 45329.01104 48030.00984 60679.90197 48445.22298 44816.25426 42030.766 44103.34662 39961.46631 42926.98373 0.983955623 1.055956117 1.118876885 1.413560812 1.128549429 1.044011257 0.979122276 1.02740381 0.930917172 1 15.38959718 2.620412587 3.249829475 0.992544514 1.149570187 0.323772574 0.106081712 0.335633232 6.683734597 0.039398541 0.036768539 417.2656047 -2.620412587 0.157025674 TATADDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TATADDKK 8 1 P20290-2;Q96K17-3;Q96K17;E9PL10;P20290 P20290-2;Q96K17;P20290 BTF3;BTF3L4 Transcription factor BTF3;Transcription factor BTF3 homolog 4 0 71.451 0.078102 110270000 334610 316950 254250 223420 370890 403660 461810 532200 544060 546710 FALSE TRUE 321533.0713 307910.8963 300198.6308 234950.733 382820.0137 411822.2818 467461.7689 521209.884 482300.5897 509680.8447 0.630851786 0.604124914 0.588993355 0.460976188 0.751097511 0.808000312 0.917165661 1.022620115 0.946279607 1 18.95923461 2.620579718 1.411628756 0.988622042 0.577169045 0.900408647 0.058726535 0.11634493 0.470033975 0.027301094 0.023383916 417.426213 -2.620579718 -0.411452997 GHFGPINSVAFHPDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GHFGPINSVAFHPDGK 16 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 229.68 1.71E-15 3016000000 3335200 3578300 3190300 3318800 3220300 2683000 3748300 1180750 3997600 4180400 FALSE TRUE 3204856.697 3476250.388 3766858.178 3490083.666 3323883.874 2737252.098 3794172.817 1156367.1 3543809.207 3897257.784 0.822336339 0.891973428 0.966540677 0.895522919 0.852877602 0.70235336 0.973549359 0.296713013 0.909308392 1 21.89402793 2.621466781 1.469984993 0.69303228 0.898599066 0.00160664 0.195758826 0.73602845 3.215973972 0.08701261 0.075186709 418.2796932 -2.621466781 0.205566786 LIS(ph)PYKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LISPYKK 7 1 O14929;O14929-2 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 1 LIS(1)PYKK 59.757 0.062236 349000000 454200 363650 420890 437640 482210 505600 485390 572960 741440 644380 TRUE FALSE 436449.3619 353279.0581 496954.1856 460226.6528 497720.7226 515823.5784 491330.348 561128.1758 657274.8396 600735.5686 0.726524922 0.588077478 0.82724282 0.766105216 0.828518817 0.8586533 0.817881234 0.934068507 1.094116736 1 19.19637056 2.621965954 0.406647306 1.044372697 0.643870132 0.73389375 0.069552138 0.703662713 0.242551476 0.071763764 0.106918641 418.7607351 -2.621965954 -0.400502565 EQEEEEQKER ddPTM_BT-474_Pertuzumab_2h_R1 1 EQEEEEQKER 10 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 146.07 0.005564 0 301570 301230 268060 249550 270810 306420 303660 327270 372630 333910 FALSE TRUE 289784.311 292639.2153 316504.405 262429.3054 279520.8496 312616.0223 307376.2819 320511.7601 330330.6046 311293.9783 0.930902398 0.940073486 1.016737962 0.843027247 0.897932081 1.004246931 0.987414802 1.029611179 1.061153211 1 18.24791814 2.622304336 4.879080031 1.018682532 0.927247732 0.515266378 0.04411622 0.20299735 7.327433998 0.015239832 0.014301728 419.0871416 -2.622304336 -0.0914348 ASS(ph)LSESS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSLSESSPPK 11 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 2 ASS(1)LSES(0.415)S(0.584)PPK;ASS(1)LSES(0.233)S(0.767)PPK 199.8 7.17E-08 763660000 1111740 915750 739760 1022510 1411520 1234100 1612740 1897830 2078070 1908450 TRUE FALSE 1068291.972 889633.7066 873451.0879 1075281.864 1456922.823 1259054.348 1632477.195 1858639.147 1842176.206 1779188.982 0.600437605 0.500022041 0.490926538 0.604366301 0.818869068 0.707656331 0.917540077 1.044655271 1.035402211 1 20.76278833 2.622379534 0.789840054 1.05427729 0.516655829 0.896781252 0.066909951 0.184914337 0.24163266 0.048175407 0.040974253 419.1597128 -2.622379534 -0.537621461 QHMENEMAHYACDCWDAESK ddPTM_BT-474_Pertuzumab_2h_R1 4 QHMENEMAHYACDCWDAESK 20 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 160.67 1.37E-11 1299000000 794530 717320 569265 606721 614616 470768 580140 60258.5 776989 544353 FALSE TRUE 763478.8892 696862.7359 672143.8487 638033.9435 634385.6818 480287.2515 587239.9269 59014.14092 688788.4661 507483.4865 1.504440853 1.373173225 1.324464474 1.257250651 1.250061724 0.946409616 1.157160661 0.116287805 1.357262816 1 18.95300135 2.622739687 1.331923445 0.753830589 1.373411488 0.298265639 0.313252209 0.426443478 1.539727034 0.148700527 0.126184581 419.5074592 -2.622739687 0.619580899 SDWEVKEEMDFPQLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDWEVKEEMDFPQLMK 16 1 O15371-2;O15371;O15371-3;B0QYA5 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 89.506 0.0045412 0 485380 402920 328520 353110 379630 417410 475260 386680 547470 452780 FALSE TRUE 466410.813 391429.1161 387890.8719 371334.0494 391841.1437 425850.3162 481076.374 378694.9229 485323.5008 422112.8073 1.104943524 0.927309263 0.918927038 0.879703347 0.92828537 1.008854289 1.139686751 0.897141514 1.149748343 1 18.68726908 2.623223258 5.17873477 1.031685536 0.944979862 0.199238325 0.087161282 0.398277485 15.47956454 0.028324095 0.026597506 419.9748248 -2.623223258 -0.086705674 EANELQQWINEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EANELQQWINEK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 176.05 6.06E-05 119658000 239600 262540 221545 223316 242730 264070 268160 283140 305940 316150 FALSE TRUE 230236.1671 255052.6163 261583.1097 234841.3655 250537.6309 269409.6763 271441.8223 277293.0601 271210.9738 294736.8789 0.781158327 0.865356983 0.887514012 0.796783105 0.850038284 0.914068431 0.920963211 0.940815622 0.920179975 1 18.16906806 2.624653649 2.13608205 0.940691453 0.836833912 0.688156558 0.03524035 0.197142852 1.780379855 0.013062876 0.011973903 421.360333 -2.624653649 -0.10385754 FLQHGTLVGLLPVPHPILIR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLQHGTLVGLLPVPHPILIR 20 0 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 0 ; 148.26 6.51E-08 165987000 147524 161522 148627 159122 149359 141380 144472 125857 161898 160084 FALSE TRUE 141758.599 156915.5507 175487.2051 167334.3055 154163.2679 144238.8005 146240.0916 123258.009 143520.0178 149241.3681 0.949861294 1.051421283 1.175861675 1.121232723 1.03297946 0.96648002 0.979889781 0.825897072 0.961663777 1 17.18728796 2.625415246 1.80266059 0.917148709 1.079069771 0.415414418 0.07038875 0.302518485 1.962643853 0.029602985 0.026601239 422.0998968 -2.625415246 0.161921062 EEELRK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEELRK 6 1 Q16643;Q16643-3;Q16643-2;D6R9W4;H0Y7V5;Q7Z3E2;P46531;O75525-2;O75525;H0YAQ1;H0YAQ3;E5RJZ9;E5RG12;Q9H6N6;Q07666-2;Q07666;Q07666-3;Q5VWX1 Q16643;O75525-2;Q07666-2;REV__F8W7S5 DBN1;CCDC186;NOTCH1;KHDRBS3;MYH16;KHDRBS1;KHDRBS2 "Drebrin;Coiled-coil domain-containing protein 186;Neurogenic locus notch homolog protein 1;Notch 1 extracellular truncation;Notch 1 intracellular domain;KH domain-containing, RNA-binding, signal transduction-associated protein 3;Putative uncharacterized protein MYH16;KH domain-containing, RNA-binding, signal transduction-associated protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 2" 0 ; 103.71 0.05524 1299610000 1254630 1257770 1121200 1283120 1239110 1358810 1405260 1554450 1672120 1659780 FALSE TRUE 1205597.673 1221899.631 1323825.781 1349341.977 1278967.098 1386286.069 1422457.992 1522350.064 1482307.948 1547361.622 0.779131171 0.789666497 0.855537427 0.872027558 0.826546995 0.895903097 0.919279612 0.983835997 0.957958325 1 20.56137897 2.625702803 0.443542195 1.010647633 0.774437992 0.896853853 0.02365974 0.37041297 0.151410011 0.024928821 0.033793699 422.3794722 -2.625702803 -0.236209641 KQEESADAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQEESADAR 9 1 Q13045-3;Q13045;Q13045-2;J3KS54 Q13045-3 FLII Protein flightless-1 homolog 0 79.659 0.042196 212600000 902190 948020 743940 836040 829800 929730 968900 991830 1014300 1073800 FALSE TRUE 866931.4174 920983.3978 878386.5069 879188.1246 856491.2706 948529.7776 980757.688 971348.3639 899160.9163 1001070.57 0.8660043 0.919998475 0.877447139 0.878247899 0.855575318 0.947515396 0.979708842 0.97030958 0.898199331 1 19.93311225 2.626117784 5.328073889 0.961543415 0.88175536 0.655841932 0.028944935 0.142733328 5.789407774 0.009322434 0.008758716 422.7832604 -2.626117784 -0.079788055 EILDKFTEEVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EILDKFTEEVVK 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 185.87 1.14E-05 1078860000 1102130 1098220 849200 880030 933130 1078700 1081250 1182800 1326820 1050380 FALSE TRUE 1059057.541 1066899.841 1002669.33 925448.4538 963144.9739 1100512.053 1094482.661 1158374.767 1176204.956 979236.827 1.081513187 1.08952177 1.023929353 0.945071129 0.983566945 1.123846676 1.11768944 1.182936277 1.201144528 1 19.90129829 2.628048396 5.259038609 1.141519584 1.024166943 0.367374708 0.06437107 0.226363766 9.101284952 0.021787094 0.020472003 424.6668845 -2.628048396 -0.11735264 LRS(ph)PSNDSAHR ddPTM_BT-474_Pertuzumab_2h_R1 4 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 LRS(0.996)PS(0.004)NDSAHR;LRS(1)PSNDSAHR;LRS(0.996)PS(0.004)NDSAHR;LRS(1)PSNDSAHR 148.18 2.12E-05 2683900000 1682410 1844530 1613250 1438010 1521470 1409490 1378980 1069990 1351960 1400050 TRUE FALSE 1616659.557 1791925.81 1904800.162 1512225.868 1570409.464 1437990.854 1395856.37 1047894.333 1198491.169 1305223.366 1.238607581 1.37288824 1.459367194 1.158595461 1.203172962 1.101720127 1.069438692 0.802846746 0.918226872 1 20.31586529 2.628129619 0.92425033 0.888988659 1.343505317 0.773687219 0.090089979 0.245014922 0.436265035 0.05734425 0.047413013 424.7463139 -2.628129619 0.454516658 LHDFGYR ddPTM_BT-474_Pertuzumab_2h_R1 6 LHDFGYR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;;; 179.16 0.0007052 3648000000 1517530 1847670 1409310 1648110 1507870 1295472 1588750 1000265 1551380 1576420 FALSE TRUE 1458223.25 1794976.261 1664003.667 1733169.155 1556372.008 1321667.331 1608193.598 979609.1782 1375273.846 1469647.669 0.992226423 1.221365024 1.132246661 1.179309294 1.059010292 0.89930897 1.094271526 0.666560563 0.935784729 1 20.4870389 2.629017736 1.311351007 0.864503507 1.139573986 0.397047293 0.118597393 0.361590411 1.267169074 0.055616639 0.047342183 425.6157948 -2.629017736 0.27507048 SYQNSPS(ph)SDDGIRPLPEYSTEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SYQNS(0.045)PS(0.477)S(0.477)DDGIRPLPEYSTEK;SYQNS(0.013)PS(0.635)S(0.353)DDGIRPLPEYSTEK;SYQNS(0.009)PS(0.495)S(0.495)DDGIRPLPEYSTEK;SYQNS(0.012)PS(0.494)S(0.494)DDGIRPLPEYSTEK 251.51 6.35E-33 2639950000 2332890 2262110 1828290 2132520 2165460 2406440 2400760 2617240 2816400 2738540 TRUE FALSE 2241718.08 2197596.838 2158702.673 2242579.613 2235113.988 2455099.866 2430141.219 2563193.079 2496694.079 2553056.247 0.878052758 0.860771023 0.845536668 0.87839021 0.875466019 0.961631718 0.951855731 1.00397047 0.977923648 1 21.28379389 2.629628993 1.393449542 0.990724376 0.860941908 0.929698507 0.015453243 0.091679496 0.361233662 0.006735232 0.005803032 426.2152577 -2.629628993 -0.129782468 AADGGERPLAAS(ph)PPGTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AADGGERPLAASPPGTVK 18 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 AADGGERPLAAS(0.986)PPGT(0.014)VK;AADGGERPLAAS(1)PPGTVK 156.92 4.91E-09 495940000 1244350 1296290 1157540 1159160 1185490 1312050 1349540 1419780 1392070 1514930 TRUE FALSE 1195719.426 1259321.078 1366733.227 1218984.387 1223622.362 1338580.55 1366056.074 1390461.047 1234048.05 1412322.442 0.846633453 0.891666833 0.967720392 0.863106293 0.866390228 0.947786787 0.967240932 0.98452096 0.873772174 1 20.42963807 2.629800723 5.56064405 0.958395659 0.890689205 0.375148907 0.043490164 0.259275891 11.23008861 0.014285955 0.013430223 426.3838263 -2.629800723 -0.067706454 QASDTGSNDAHNKK ddPTM_BT-474_Pertuzumab_2h_R1 6 QASDTGSNDAHNKK 14 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EN75;D6RGF7;D6RBR1;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;;;;; 262.37 9.62E-25 805864000 763498 691275 566026 587844 598383 700432 695071 714501 827665 828723 FALSE TRUE 733659.6541 671560.5138 668319.4894 618182.6993 617630.5326 714595.2149 703577.4868 699746.3047 733711.9391 772592.8531 0.949607094 0.869229519 0.865034522 0.800140329 0.799425636 0.924931174 0.910670457 0.905711594 0.949674769 1 19.55934881 2.630258355 9.102427573 0.928282896 0.854757061 0.425128512 0.046669613 0.398384761 30.78974427 0.015680006 0.014773657 426.83336 -2.630258355 -0.073525835 IQFKPDDGISPER ddPTM_BT-474_Pertuzumab_2h_R1 3 IQFKPDDGISPER 13 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;; 137.46 5.52E-05 1866040000 2463100 2334680 2014400 2275220 2391650 2488270 2434030 2736960 3044820 2809640 FALSE TRUE 2366839.329 2268097.212 2378446.89 2392644.377 2468579.594 2538584.524 2463818.387 2680440.82 2699184.799 2619340.58 0.903601214 0.865903896 0.908032696 0.913452949 0.942443153 0.969169318 0.940625441 1.023326573 1.030482565 1 21.32077223 2.630267287 0.645670951 1.022369874 0.882740588 0.840873306 0.02079975 0.278691497 0.244007687 0.016553791 0.015769232 426.8421384 -2.630267287 -0.139629286 KSS(ph)TTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.004)S(0.988)T(0.004)T(0.004)LR;KS(0.002)S(0.995)T(0.002)T(0.001)LR;KS(0.029)S(0.97)T(0.001)TLR;KS(0.001)S(0.997)T(0.001)T(0.001)LR 128.27 0.0023116 3350420000 2333070 2440720 2124580 2150570 2341490 2650200 2656040 3045660 2995880 3017130 TRUE FALSE 2241891.045 2371113.055 2508538.867 2261561.175 2416806.152 2703788.86 2688545.412 2982766.057 2655800.262 2812777.098 0.797038289 0.842979366 0.891837063 0.804031424 0.8592242 0.961252444 0.955833085 1.060434565 0.944191512 1 21.4235638 2.630470133 1.929937921 1.002471116 0.836504327 0.788135808 0.037952988 0.14409646 1.067116866 0.014718141 0.013399518 427.0415502 -2.630470133 -0.16596679 ASNTST(ph)PTKGNTETSASASQTNHVK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASNTSTPTKGNTETSASASQTNHVK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ASNT(0.001)S(0.027)T(0.968)PT(0.004)KGNTETSASASQTNHVK;ASNT(0.007)S(0.029)T(0.948)PT(0.017)KGNTETSASASQTNHVK;AS(0.002)NT(0.033)S(0.194)T(0.758)PT(0.013)KGNTETSASASQTNHVK;AS(0.003)NT(0.027)S(0.146)T(0.797)PT(0.027)KGNTETSASASQTNHVK 259.27 7.90E-45 2115660000 1241660 1256700 939622 953750 992153 1170320 1175600 1192530 1261750 1362840 TRUE FALSE 1193134.554 1220860.146 1109432.597 1002973.152 1024066.502 1193984.672 1189987.344 1167903.839 1118521.43 1270533.633 0.939081441 0.960903446 0.873202069 0.789410942 0.806012903 0.939750544 0.936604363 0.91922308 0.880355624 1 20.27700314 2.630912733 19.79387226 0.929490491 0.873716495 0.229198866 0.055869281 10.88361662 1985.414846 0.019891839 0.018754157 427.4769803 -2.630912733 -0.055773996 IEFGVDEVIEPSDTLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEFGVDEVIEPSDTLPR 17 0 Q14694;Q14694-3;Q14694-2;H3BQC6 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 0 146.79 9.86E-07 29576000 26201 25461 22422 21539 18710 28708 27338 33358 26752 35956 FALSE TRUE 25177.03595 24734.87721 26474.15417 22650.63037 19311.82414 29288.49543 27672.57062 32669.14564 23715.22511 33520.66809 0.751089921 0.737899291 0.789785994 0.675721328 0.576116922 0.873744382 0.825537562 0.974597092 0.707480682 1 15.03276328 2.630982914 9.934290702 0.879373605 0.710921142 0.462211139 0.091676803 0.381360877 32.82959658 0.02915929 0.027479592 427.5460656 -2.630982914 -0.168452463 VAPLWHSS(ph)SEVISMADR ddPTM_BT-474_Pertuzumab_2h_R1 1 VAPLWHSSSEVISMADR 17 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 VAPLWHS(0.005)S(0.994)S(0.001)EVISMADR 188.04 2.79E-10 463120000 99246 101870 76105 100240 91929 82468 76943 78342 94850 78169 TRUE FALSE 95367.3566 98964.76734 89858.86645 105413.3984 94885.97977 84135.55946 77884.65145 76724.21032 84083.02564 72874.544 1.308651161 1.358015596 1.233062487 1.446505084 1.302045605 1.15452605 1.06874976 1.05282594 1.15380517 1 16.15312733 2.631274321 2.624962916 1.072216937 1.335194034 0.807615806 0.060700833 0.115388535 1.554997323 0.020843448 0.01944616 427.8330404 -2.631274321 0.262977097 SLDS(ph)DESEDEEDDYQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 S(0.001)LDS(0.999)DESEDEEDDYQQK 406.17 2.78E-140 174090000 94923 85109 89196 162480 102930 113140 231930 193230 217550 237350 TRUE FALSE 91213.30422 82681.77465 105315.7014 170865.6123 106240.8369 115427.7683 234768.4287 189239.733 192854.636 221274.0731 0.41221867 0.37366228 0.475951384 0.772189936 0.480132333 0.521650669 1.060984802 0.855227774 0.871564541 1 17.75547489 2.631657237 0.545718461 1.005701244 0.383478946 0.688308092 0.136251313 0.543085383 0.337820983 0.122974567 0.134830196 428.2104253 -2.631657237 -0.622222298 AEQAEADKK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEQAEADKK 9 1 P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKP3;A0A087WTJ7;H0YLS7;P67936-2;K7ELP0 P09493-3;P67936-2 TPM1;TPM4 Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;; 101.93 0.00588 1858450000 1873820 2033610 1328920 1567260 2014400 2343340 2410180 2871930 2784130 3171510 FALSE TRUE 1800589.043 1975613.434 1569085.406 1648146.476 2079195.005 2390723.94 2439676.504 2812623.642 2468087.234 2956700.803 0.608985881 0.668181722 0.530687922 0.557427547 0.703214544 0.808578243 0.825134725 0.95127097 0.834743655 1 21.49555683 2.632429986 1.28765696 0.917149675 0.590814231 0.860275398 0.057082727 0.152628546 0.51646793 0.027698932 0.023577412 428.9730272 -2.632429986 -0.326335444 ARNS(ph)GT(ph)QSDGEEKQPGLVMER ddPTM_BT-474_Pertuzumab_2h_R1 1 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 2 ARNS(0.716)GT(0.663)QS(0.621)DGEEKQPGLVMER 40.142 0.097941 0 136220 138690 107170 108300 113850 129200 122750 145640 140070 125590 TRUE FALSE 130896.3718 134734.697 126538.003 113889.376 117512.0886 131812.5125 124252.2512 142632.4831 124169.8408 117083.6774 1.117972844 1.150755596 1.080748451 0.97271779 1.003659017 1.12579751 1.061226073 1.218209799 1.060522214 1 16.83718044 2.632775778 22.05372676 1.113035915 1.06554096 0 0.072202035 33.88357121 7037.45652 0.024666543 0.023255835 429.3147182 -2.632775778 -0.047494955 ASQKPQPNFPSPEYMIFDHEFTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASQKPQPNFPSPEYMIFDHEFTK 23 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 250.05 2.47E-38 2042800000 1349040 1380880 1086590 1301720 1276420 1372100 1505810 1368000 1606650 1629070 FALSE TRUE 1296318.025 1341498.654 1282960.984 1368901.925 1317477.209 1399844.802 1524238.553 1339750.322 1424269.828 1518731.638 0.853553052 0.883301974 0.844758186 0.901345498 0.867485193 0.921719656 1.003625996 0.882150795 0.937802171 1 20.53443554 2.634160306 4.185734605 0.943342119 0.871138204 0.551930452 0.035790145 0.201728989 6.105931758 0.0117669 0.011059616 430.6855553 -2.634160306 -0.072203915 FITIFGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 FITIFGTR 8 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 120.62 0.0034157 375550000 699680 685730 597760 643820 660990 602850 709370 444050 831340 845260 FALSE TRUE 672335.7321 666173.6518 705788.5291 677047.6274 682251.3436 615040.04 718051.4823 434880.2123 736969.7685 788009.7873 0.853207337 0.845387535 0.895659598 0.859186825 0.865790444 0.780497971 0.911221528 0.551871588 0.935229207 1 19.58785402 2.634261767 1.839337158 0.788257393 0.865491223 0 0.118040718 0.992428967 6.690800236 0.046403227 0.042104464 430.7861851 -2.634261767 0.07723383 (ac)ASPTDGT(ph)DLEASLLSFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPTDGTDLEASLLSFEK 18 0 G3V5T8 G3V5T8 LIN52 1 AS(0.297)PT(0.297)DGT(0.404)DLEAS(0.002)LLSFEK 52.555 0.036454 97329000 23525 26319 19623 26024 23556 22140 21910 22216 24577 22364 TRUE FALSE 22605.61699 25568.40789 23169.31261 27367.10176 24313.70013 22587.68597 22178.14113 21757.23184 21787.122 20849.26636 1.084240404 1.226345688 1.111277117 1.312617014 1.16616574 1.083380373 1.063737244 1.043549037 1.044982668 1 14.347709 2.634819776 2.697790805 1.044058334 1.187302411 0.558983924 0.060088201 0.206629455 2.93615086 0.020527 0.019209589 431.340042 -2.634819776 0.143244077 REEEFDLFMR ddPTM_BT-474_Pertuzumab_2h_R1 1 REEEFDLFMR 10 1 F6VDE0;P51531-2;P51531;A0A0U1RQZ9;A0A0U1RRG6 F6VDE0 SMARCA2 Probable global transcription activator SNF2L2 0 151.1 3.27E-05 24137000 11861 11675 8756.4 11996 9557.9 10730 9411 10888 9915.6 10784 FALSE TRUE 11397.45901 11342.04043 10338.87627 12615.115 9865.338534 10946.96795 9526.174633 10663.159 8790.022658 10053.59007 1.133670552 1.128158235 1.028376549 1.254787086 0.981275192 1.088861578 0.947539592 1.060631965 0.874316796 1 13.29542315 2.63507997 1.092842399 0.976746831 1.123743165 0.40307139 0.079441343 0.517665236 1.27697064 0.040841414 0.03404719 431.5985436 -2.63507997 0.146996334 DSGRGDSVS(ph)DSGSDALR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 DSGRGDS(0.488)VS(0.511)DSGSDALR 144.94 1.30E-06 215710000 165420 189060 120360 137800 152840 141650 109170 135710 128580 108190 TRUE FALSE 158955.2035 183668.1939 142111.7294 144911.8745 157756.2374 144514.2601 110506.0551 132907.5411 113984.1375 100862.1949 1.575964152 1.820981529 1.408969233 1.43673132 1.564076982 1.432789165 1.095614221 1.317714146 1.130097729 1 16.622026 2.636238406 0.317042819 0.972831854 1.790905669 0.736906467 0.121939799 1.054504732 0.227426461 0.15897111 0.308114592 432.7513252 -2.636238406 0.818073815 DSKPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSKPIK 6 1 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6;D6RBR8 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 69.344 0.0855 335390000 200280 339910 140060 317700 412100 417630 483250 551240 627000 733850 FALSE TRUE 192452.8362 330216.0996 165371.9576 334096.5351 425355.5708 426074.7647 489164.1581 539856.7014 555825.5886 684145.6859 0.28130388 0.482669271 0.241720384 0.488341214 0.621732446 0.622783675 0.714999989 0.789096113 0.812437468 1 19.38394405 2.63625163 0.362644757 1.001952258 0.217235066 0.900148678 0.071428704 0.470320922 0.129625322 0.080144068 0.136687878 432.7645015 -2.63625163 -0.784717192 down TDGS(ph)IS(ph)GDRQPVTVADYISR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 T(0.003)DGS(0.997)IS(1)GDRQPVTVADYISR;T(0.073)DGS(0.929)IS(0.996)GDRQPVT(0.001)VADYISR;TDGS(1)IS(1)GDRQPVTVADYISR;T(0.008)DGS(0.992)IS(0.997)GDRQPVT(0.003)VADYISR 161.49 1.28E-11 1771252000 1265016 1152278 976103 1133485 1181374 1205859 1264308 1361050 1440228 1402135 TRUE FALSE 1215577.776 1119416.16 1152506.525 1191984.297 1219373.968 1230242.295 1279780.98 1332943.842 1276739.355 1307167.148 0.92993293 0.856368034 0.881682597 0.911883609 0.932837067 0.94115148 0.979049223 1.019719509 0.97672234 1 20.3180122 2.636312172 0.996523359 1.0039918 0.887573454 0.8112757 0.021318756 0.203967642 0.421037651 0.012454183 0.010349506 432.8248345 -2.636312172 -0.116418346 INDRFEFPEQLPLDEFLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 INDRFEFPEQLPLDEFLQK 19 1 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 226.44 1.37E-19 200180000 415450 471870 361450 363560 396390 424150 423740 461590 481010 446090 FALSE TRUE 399213.7547 458412.7296 426772.0554 382323.3752 409140.2443 432726.6036 428925.8569 452058.0052 426407.7614 415875.927 0.959934752 1.102282435 1.026200431 0.919320765 0.983803625 1.040518519 1.031379383 1.087002098 1.025324463 1 18.66579365 2.636927247 5.810354681 1.045986053 1.00135803 0.119740316 0.048996881 0.467988036 22.23588104 0.01683968 0.015843158 433.4382629 -2.636927247 -0.044628023 ETSFGS(ph)SENITMTSLSK ddPTM_BT-474_Pertuzumab_2h_R1 11 ETSFGSSENITMTSLSK 17 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;A0A087WZS7;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 ETSFGS(0.988)S(0.012)ENITMTSLSK;ETSFGS(0.925)S(0.075)ENITMTSLSK;ETSFGS(0.994)S(0.006)ENITMTSLSK;ETSFGS(0.868)S(0.131)ENIT(0.001)MTSLSK;ETSFGS(0.883)S(0.116)ENITMTSLSK;ETSFGS(0.5)S(0.5)ENITMTSLSK;ETS(0.005)FGS(0.888)S(0.108)ENITMTSLSK;ETSFGS(0.874)S(0.125)ENITMTSLSK;ETSFGS(0.976)S(0.024)ENITMTSLSK;ETSFGS(0.973)S(0.027)ENITMTSLSK;ETSFGS(0.987)S(0.012)ENITMTSLSK 358.05 5.32E-88 7518859000 8223720 8286490 7278510 8359550 8567700 8623410 9553320 10723690 10743210 11176410 TRUE FALSE 7902327.931 8050167.419 8593898.667 8790987.377 8843287.851 8797781.259 9670236.388 10502242.05 9523685.84 10419421.8 0.758422884 0.772611722 0.82479612 0.843711633 0.848731151 0.844363673 0.928097219 1.007948642 0.914032086 1 23.31277188 2.637674214 0.511241225 1.003412028 0.758718264 0.849690842 0.031696346 0.371996639 0.202540841 0.030744092 0.036128279 434.1843987 -2.637674214 -0.244693765 GGPASVPSSS(ph)PGTSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGPASVPSSSPGTSVK 16 0 O43237;O43237-2;J3KRI4;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 GGPASVPS(0.006)S(0.183)S(0.811)PGTSVK;GGPASVPS(0.001)S(0.018)S(0.981)PGTSVK 231.13 1.70E-15 790290000 1569780 1588360 1547670 1473660 1515850 1750720 1843070 1980130 1833170 1913720 TRUE FALSE 1508431.262 1543061.528 1827368.397 1549715.769 1564608.692 1786120.758 1865626.042 1939239.624 1625076.227 1784102.04 0.845484859 0.864895333 1.024251055 0.868625076 0.876972649 1.001131504 1.045694697 1.086955555 0.910865069 1 20.7667667 2.637956388 4.593566683 1.025915773 0.900117856 0.438861936 0.062732869 0.204766026 7.16376845 0.021179667 0.019923788 434.4665928 -2.637956388 -0.125797917 ENPVYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENPVYEK 7 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 ; 90.37 0.045436 464030000 522520 614190 451150 487560 544010 536700 589100 576080 628300 613010 FALSE TRUE 502099.3407 596673.9026 532682.8408 512723.03 561508.5757 547552.4417 596309.582 564183.7467 556978.018 571490.2867 0.878578958 1.044066569 0.932094304 0.897168407 0.982533892 0.958113295 1.043429076 0.987214936 0.974606272 1 19.12436945 2.638134894 2.282949707 0.999451487 0.947005086 0.228528456 0.046053767 0.483987628 4.973404998 0.016492416 0.015336987 434.6452058 -2.638134894 -0.0524464 AVGKEELGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVGKEELGK 9 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 77.288 0.02425 0 366130 511420 299180 406680 500330 577270 592080 610150 813540 739380 FALSE TRUE 351821.2348 496834.8023 353248.4812 427668.8035 516423.5688 588942.7949 599326.0522 597550.1893 721190.3498 689301.134 0.510402809 0.72078048 0.512473379 0.620438271 0.74919878 0.854405667 0.869469123 0.866892799 1.046263112 1 19.39477486 2.640959352 0.650552319 0.997298769 0.559349858 0.849337905 0.068814606 0.292646082 0.260713849 0.054644193 0.052314477 437.4811573 -2.640959352 -0.437948911 KTPTSSGKPSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTPTSSGKPSAK 12 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ; 95.651 0.0033338 827180000 1352370 1417280 888700 1131420 1245060 1297560 1388080 1478730 1550150 1388040 FALSE TRUE 1299517.885 1376860.562 1049307.859 1189812.722 1285108.486 1323797.552 1405067.738 1448193.709 1374183.471 1294026.814 1.004243398 1.064012389 0.810885715 0.919465276 0.99310808 1.023006276 1.085810373 1.119137326 1.061943582 1 20.30343608 2.641015929 2.073975091 1.080588771 0.950177568 0.36203234 0.067619128 0.327340404 2.787404555 0.026775457 0.024754354 437.5381529 -2.641015929 -0.130411203 ADLAEEYSKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADLAEEYSKDR 11 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 160.86 2.46E-05 1792080000 2848700 3004100 2120390 2416800 2535900 2779000 2744100 2980100 3361200 2938700 FALSE TRUE 2737369.655 2918426.009 2503591.641 2541531.338 2617469.527 2835193.284 2777683.117 2918559.894 2979650.667 2739659.231 0.999164284 1.065251465 0.913833229 0.927681556 0.95539967 1.034870779 1.013879056 1.065300334 1.08759901 1 21.38556503 2.641428012 4.500475523 1.045302783 0.971826139 0.361344569 0.045102602 0.265650957 9.143042255 0.016035275 0.015096652 437.9535107 -2.641428012 -0.073476644 DLKEEFTEALR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLKEEFTEALR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 148.96 3.15E-05 332330000 601540 558130 493370 509330 538430 596130 602640 632410 703120 694020 FALSE TRUE 578031.1518 542212.6789 582532.934 535616.5823 555749.0899 608184.157 610015.2886 619350.5125 623304.7653 647013.4072 0.893383576 0.838023869 0.900341365 0.827829186 0.858945246 0.939986947 0.942817076 0.957245253 0.9633568 1 19.30343608 2.64184771 3.226723512 0.959755064 0.861940137 0.793285607 0.024909205 0.111891554 2.230728151 0.008135124 0.007666456 438.3769488 -2.64184771 -0.097814927 KLDDTDPVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDDTDPVPR 10 1 O95721;C9JAF7 O95721 SNAP29 Synaptosomal-associated protein 29;Synaptosomal-associated protein 0 ; 91.855 0.015818 572130000 1856370 1861650 1462750 1722670 1763210 1885660 1979450 2057570 2226300 2171400 FALSE TRUE 1783821.008 1808557.565 1727101.464 1811577.205 1819925.251 1923789.337 2003675.101 2015080.46 1973579.757 2024329.144 0.88119119 0.893410822 0.853172257 0.894902497 0.899026355 0.950334259 0.989797093 0.995431235 0.974930269 1 20.94901245 2.641995808 1.66015536 0.992077929 0.879063588 0.94533119 0.012126852 0.07446021 0.411282959 0.004932132 0.004434584 438.526465 -2.641995808 -0.113014341 HHS(ph)DS(ph)DEEKSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 HHSDSDEEKSHR 12 1 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 HHS(1)DS(1)DEEKSHR;HHS(1)DS(0.988)DEEKS(0.012)HR 207.79 9.87E-08 145753000 109269 102301 77646 72960 73445 80256 64251 10162.5 90362 43421 TRUE FALSE 104998.6467 99383.47564 91678.35943 76725.47434 75807.42513 81878.83131 65037.32296 9952.640824 80104.48459 40480.05699 2.593836434 2.45512193 2.264778418 1.895389484 1.872710435 2.022695554 1.606650973 0.245865287 1.97886294 1 15.3049237 2.642009489 0.712030143 0.951644177 2.467323907 0.545887274 0.450222653 0.505854945 0.540552293 0.348162566 0.315983617 438.5402796 -2.642009489 1.51567973 NLNNSNLFS(ph)PVNR ddPTM_BT-474_Pertuzumab_2h_R1 6 NLNNSNLFSPVNR 13 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3;H0YEN4 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR 289.2 1.80E-40 5231900000 3590580 3804420 3122410 3375980 3269230 2943550 2283710 2769710 2733190 2839820 TRUE FALSE 3450256.164 3695921.667 3686698.945 3550214.732 3374387.752 3003070.598 2311658.726 2712514.521 2422929.73 2647476.462 1.303224491 1.396016818 1.392533228 1.34098066 1.274567612 1.134314371 0.873155535 1.024566057 0.915184616 1 21.33618643 2.642059822 1.957367242 0.958150102 1.360661221 0.924780762 0.052231295 0.077350755 0.588255233 0.019148355 0.017610921 438.5911077 -2.642059822 0.402511119 LKEHCK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKEHCK 6 1 Q96DG6 Q96DG6 CMBL Carboxymethylenebutenolidase homolog 0 ; 86.113 0.032414 786170000 3085600 2685700 2349000 2508000 2236400 1665300 3175700 2450800 3051400 3186800 FALSE TRUE 2965011.341 2609106.466 2773516.553 2637438.181 2308335.837 1698973.507 3214565.167 2400190.124 2705017.865 2970955.197 0.997999345 0.878204581 0.933543715 0.887740812 0.776967569 0.571861033 1.081997187 0.807884995 0.910487599 1 21.50249542 2.64371569 0.002757825 1.749060984 4.13E-07 0.001688577 0.135360362 636094.4912 729.4424542 229689.9082 232918.4648 440.2665497 -2.64371569 -1.749060571 DADKDWPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DADKDWPR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 0 76.679 0.032082 287410000 438670 462220 356690 403590 433840 437490 426100 489320 488010 486670 FALSE TRUE 421526.2914 449037.9382 421151.8175 424419.3283 447794.8576 446336.3475 431314.7393 479215.371 432613.1507 453707.4074 0.929070772 0.989708193 0.928245408 0.93544721 0.986968364 0.983753715 0.950645134 1.056221175 0.953506916 1 18.79140269 2.643928316 1.06890966 1.002820715 0.948675171 0.254073421 0.032819889 0.62210954 1.4722797 0.017909979 0.015040762 440.4821521 -2.643928316 -0.054145544 EQLELFQNIRPLFINKPLIVVANK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQLELFQNIRPLFINKPLIVVANK 24 2 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 124.86 5.79E-05 109270000 159230 153930 118770 140130 152950 172580 153230 204210 177440 203720 FALSE TRUE 153007.1156 149540.0671 140234.381 147362.1261 157869.7757 176069.6858 155105.2746 199992.9921 157297.7551 189921.8629 0.805631922 0.787376792 0.738379346 0.775909228 0.8312354 0.92706381 0.816679408 1.053027751 0.828223527 1 17.53504647 2.644251906 1.053861025 0.953389238 0.771166405 0.521200425 0.067454254 0.373889206 0.861029681 0.036100214 0.030299544 440.8104746 -2.644251906 -0.182222832 ERSPS(ph)PPT(ph)IQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSPSPPTIQSK 12 1 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 2 ERS(0.152)PS(0.876)PPT(0.964)IQS(0.009)K 117.48 0.018272 610160000 391360 395810 350980 386010 379630 421980 433940 458460 488150 457340 TRUE FALSE 376065.2185 384521.8863 414409.8935 405932.0224 391841.1437 430512.7247 439250.6875 448992.6408 432737.2585 426363.9544 0.882028639 0.901863026 0.971962778 0.95207866 0.919029715 1.009730584 1.030224725 1.053073638 1.014948037 1 18.70172595 2.644907689 3.595563013 1.030724732 0.927829788 0.761978577 0.026815175 0.121669093 2.951731656 0.009692465 0.009146624 441.4766 -2.644907689 -0.102894944 IIASILHLGSVAIQAER ddPTM_BT-474_Pertuzumab_2h_R1 2 IIASILHLGSVAIQAER 17 0 Q9ULV0 Q9ULV0 MYO5B Unconventional myosin-Vb 0 ; 128.64 3.63E-05 131063000 104321 148515 107858 134418 135080 119073 116383 131219 126424 129978 FALSE TRUE 100244.02 144279.4976 127350.3399 141355.3291 139424.9709 121480.7376 117807.33 128509.2818 112072.8775 121174.4743 0.827270104 1.190675664 1.050966721 1.166543778 1.150613375 1.002527458 0.972212429 1.060530962 0.924888498 1 16.8867263 2.644961587 9.579943383 0.999208558 1.086974454 0.148422507 0.099948614 0.793249924 76.38193586 0.03096196 0.029177809 441.5313927 -2.644961587 0.087765895 SFS(ph)FEKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFSFEKPR 8 1 P78314;P78314-3;P78314-4;H0YAD9 P78314 SH3BP2 SH3 domain-binding protein 2 1 S(0.092)FS(0.908)FEKPR 111.06 0.0020026 126820000 182130 163120 83472 144980 230750 160790 212230 280270 270820 243200 TRUE FALSE 175012.1582 158467.9773 98557.24722 152462.4352 238172.2833 164041.284 214827.3342 274482.3266 240077.649 226727.8474 0.771904114 0.698934776 0.434694054 0.672446887 1.050476534 0.723516259 0.947511903 1.210624675 1.058880291 1 17.79060207 2.645049398 0.891696893 1.106720157 0.638051283 0.567375006 0.14623885 0.410885489 0.684766114 0.097258998 0.08220938 441.6206757 -2.645049398 -0.468668874 VPMYEEQWSYYDDKQPYPSRPPFDNQHS(ph)QDLDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 VPMYEEQWSYYDDKQPYPSRPPFDNQHSQDLDSR 34 2 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 VPMYEEQWSYYDDKQPYPS(0.001)RPPFDNQHS(0.999)QDLDSR;VPMYEEQWS(0.001)Y(0.001)Y(0.001)DDKQPY(0.029)PS(0.131)RPPFDNQHS(0.795)QDLDS(0.043)R;VPMYEEQWSYYDDKQPYPS(0.022)RPPFDNQHS(0.973)QDLDS(0.005)R 120.71 5.22E-08 551980000 263720 215710 143576 167235 250541 207242 229074 266957 265735 263435 TRUE FALSE 253413.5308 209558.162 169523.377 175866.0184 258599.8788 211432.5752 231877.4761 261444.2447 235569.8769 245592.3128 1.031846347 0.853276553 0.690263368 0.716089263 1.05296406 0.860908767 0.944156083 1.064545717 0.959190759 1 17.90590588 2.645380738 1.184819511 1.005294614 0.832372723 0.242622334 0.110710626 0.629723577 1.817087549 0.059148737 0.050311324 441.9577337 -2.645380738 -0.172921891 KVPEKPETR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVPEKPETR 9 2 A0A499FI31;Q15020-4;Q15020;H0YHU8 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 132.91 0.00016407 571110000 764290 664270 601920 554250 650390 692760 733960 742320 794340 774000 FALSE TRUE 734420.7018 645325.67 710700.3336 582854.9089 671310.385 706768.0818 742942.422 726990.8326 704169.8533 721576.2906 1.01780049 0.894327708 0.984927502 0.807752301 0.930338751 0.979477972 1.029610357 1.007503769 0.975877205 1 19.46079241 2.645778455 3.58782858 1.004835629 0.921635787 0.312634672 0.053468395 0.274379028 6.641321221 0.017662215 0.016673732 442.3626537 -2.645778455 -0.083199842 LEEEDEDEEDGESGCTFLVGLIQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LEEEDEDEEDGESGCTFLVGLIQK 24 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 244.92 9.11E-38 478001000 489301 464488 374724 424405 466461 482155 501014 537853 563879 580446 FALSE TRUE 470178.576 451241.257 442444.9625 446308.5929 481465.1417 491904.5045 507145.5592 526746.1476 499869.8199 541131.8754 0.868879837 0.833884082 0.81762872 0.824768625 0.889737167 0.909028883 0.937194023 0.973415486 0.923748614 1 19.0456207 2.64661431 1.189739738 0.963592102 0.834107103 0.842892985 0.023536837 0.167859266 0.488289449 0.011808722 0.010062806 443.2148566 -2.64661431 -0.129484999 LQQQAALS(ph)PTTAPAVSSVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQQQAALSPTTAPAVSSVSK 20 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR30 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LQQQAALS(0.861)PT(0.133)T(0.006)APAVSSVSK;LQQQAALS(0.924)PT(0.047)T(0.03)APAVSSVSK 346.63 5.78E-95 918330000 772030 753260 665260 715490 722010 810650 838880 892630 858040 968390 TRUE FALSE 741858.2141 731777.7623 785487.2806 752416.5246 745234.1074 827041.8984 849146.4644 874196.8786 760638.8964 902800.0827 0.821730335 0.810564572 0.870056722 0.833425405 0.825469693 0.916085315 0.940569768 0.968317234 0.842533038 1 19.78404703 2.647029224 3.714273705 0.938004941 0.832958536 0.61746179 0.040059367 0.158378935 4.080274971 0.0130336 0.012307736 443.6384962 -2.647029224 -0.105046405 GTINFLHADCDKFR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTINFLHADCDKFR 14 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ; 118.33 0.00015105 1120620000 1127310 1419990 1018610 1309860 1087610 991110 1279290 951290 1088740 1193100 FALSE TRUE 1083253.479 1379493.276 1202695.486 1377462.032 1122593.963 1011150.923 1294946.334 931645.5291 965150.7996 1112290.274 0.973894588 1.24022776 1.081278434 1.238401579 1.009263489 0.909071082 1.16421618 0.837592084 0.86771486 1 20.08510191 2.647059195 1.013402401 0.922561713 1.135433682 0.316754351 0.114141535 0.574180245 1.226666661 0.06406073 0.05384509 443.6691124 -2.647059195 0.212871969 KVASGVLS(ph)PPPAAPPPSSSSVPEAGGPPIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVASGVLSPPPAAPPPSSSSVPEAGGPPIKK 31 2 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 KVAS(0.044)GVLS(0.956)PPPAAPPPSSSSVPEAGGPPIKK 95.002 0.00020911 1807000000 1345700 1322200 1023800 1084200 1157600 1346900 1415400 1526700 1475700 1390600 TRUE FALSE 1293108.556 1284492.151 1208823.434 1140155.692 1194835.255 1374135.241 1432722.089 1495173.111 1308184.723 1296413.423 0.997450761 0.99080442 0.932436685 0.879469212 0.921646779 1.059951414 1.105142899 1.153315049 1.009079896 1 20.30609443 2.647433687 4.519354067 1.087480093 0.94281773 0.549578984 0.053403423 0.155671138 5.526893362 0.018583349 0.017520383 444.0518531 -2.647433687 -0.144662363 APS(ph)PLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPLPK 7 0 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 APS(1)PLPK 68.735 0.076239 0 418570 408220 337520 373280 423820 415230 410780 442150 513860 475600 TRUE FALSE 402211.8216 396577.9653 398517.3721 392545.0255 437452.5552 423626.2351 415807.2485 433019.448 455528.7671 443387.1884 0.907134514 0.894428111 0.898802181 0.885332359 0.986615235 0.955431835 0.937797166 0.97661696 1.027383693 1 18.75820756 2.647716548 0.502076919 1.00813286 0.885088901 0.7108949 0.025420516 0.592289088 0.310739314 0.024003027 0.028978653 444.3411635 -2.647716548 -0.12304396 SQS(ph)MDIDGVSCEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSMDIDGVSCEK 13 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 SQS(1)MDIDGVSCEK;SQS(0.999)MDIDGVS(0.001)CEK 277 3.11E-32 849040000 2120230 1958960 1122300 1532840 2231200 1768390 2050010 2472500 2468500 2222920 TRUE FALSE 2037369.068 1903092.379 1325124.575 1611950.056 2302968.574 1804148.057 2075098.636 2421442.011 2188286.229 2072359.648 0.983115585 0.91832148 0.639427899 0.777833161 1.111278429 0.870576716 1.001321676 1.168446805 1.055939412 1 20.98284297 2.648019201 1.086338068 1.082876458 0.839342145 0.332602067 0.122411548 0.540907609 1.321359487 0.070155577 0.059240323 444.6509257 -2.648019201 -0.243534313 DLHQGIEAAS(ph)DEEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLHQGIEAASDEEDLR 16 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 DLHQGIEAAS(1)DEEDLR 204.65 1.59E-11 264880000 95098 88203 75525 95847 81680 78958 86786 60622 93748 103530 TRUE FALSE 91381.46502 85687.5368 89174.04754 100793.6752 84307.31138 80554.58486 87848.11303 59370.13452 83106.12006 96517.82089 0.946783342 0.887789799 0.923912773 1.044301189 0.873489586 0.834608408 0.910175056 0.615120959 0.861044306 1 16.55850772 2.648374105 1.711591376 0.796680757 0.942761258 0.11935443 0.102984493 0.487308903 2.854245316 0.041938648 0.038084013 445.0144412 -2.648374105 0.146080501 GPEENYSRPEAPNEFYDGDHDNDKES(ph)DVEI ddPTM_BT-474_Pertuzumab_2h_R1 3 GPEENYSRPEAPNEFYDGDHDNDKESDVEI 30 2 O15379;O15379-2 O15379 HDAC3 Histone deacetylase 3 1 GPEENYSRPEAPNEFYDGDHDNDKES(1)DVEI;GPEENYSRPEAPNEFYDGDHDNDKES(1)DVEI;GPEENYSRPEAPNEFYDGDHDNDKES(1)DVEI 139.96 2.95E-08 758360000 203254 166408 170567 197247 208295 179263 206349 221375 265836 254247 TRUE FALSE 195310.609 161662.2068 201392.2511 207426.9413 214994.9978 182887.8207 208874.3608 216803.5289 235659.4118 237026.6242 0.824002829 0.682042396 0.849660884 0.875120852 0.907049993 0.771591889 0.881227421 0.914680069 0.994231819 1 17.85468959 2.6484819 0.232835569 1.036168793 0.694834955 0.574220651 0.059588999 2.80327445 0.362446471 0.13800193 0.311395918 445.1249109 -2.6484819 -0.341333839 SWSTATS(ph)PLGGERPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SWSTATSPLGGERPFR 16 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;D6RD46;H0Y8P3;D6RJ93;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(0.022)WS(0.115)T(0.115)AT(0.115)S(0.633)PLGGERPFR;SWSTAT(0.386)S(0.614)PLGGERPFR 139.46 1.09E-06 116310000 103953 105309 102765 106204 110139 98358 96744 109424 97864 102241 TRUE FALSE 99890.40183 102305.6904 121336.9215 111685.2012 113681.721 100346.8662 97927.98201 107164.3562 86754.889 95316.126 1.047990576 1.073330345 1.272994682 1.171734583 1.192680879 1.052779528 1.027402037 1.124304571 0.910180603 1 16.5404327 2.650005703 5.726778087 1.037265922 1.155007084 0.406958134 0.076854478 0.27100762 13.90338847 0.026027705 0.024518037 446.6894578 -2.650005703 0.117741162 LEENIDNIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEENIDNIKR 10 1 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494BZX8 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 124.1 0.0007126 852950000 749670 867620 691560 769960 815820 854470 931710 958300 1068640 1005180 FALSE TRUE 720372.0676 842876.3271 816540.2757 809697.7279 842061.5912 871747.9688 943112.5457 938510.7701 947332.4673 937098.2633 0.768726286 0.899453515 0.871349684 0.864047837 0.898584091 0.930263136 1.006417985 1.00150732 1.010921164 1 19.83784081 2.650253174 0.99721494 1.014061493 0.847470979 0.825735009 0.031759914 0.205285271 0.425382446 0.017822783 0.0150288 446.9440647 -2.650253174 -0.166590514 FVSELWK ddPTM_BT-474_Pertuzumab_2h_R1 1 FVSELWK 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 121.52 0.010306 180980000 345800 404790 396980 337800 328090 158480 428440 362860 412790 460290 FALSE TRUE 332285.7537 393245.7855 468723.1168 355233.8985 338643.3128 161684.5742 433683.3769 355366.8142 365931.8098 429114.1483 0.774352827 0.916413004 1.092304038 0.827830776 0.78916837 0.376786864 1.010648049 0.828140521 0.852760999 1 18.71100194 2.650489161 0.003498039 1.683920271 2.57E-07 0.007489448 0.185221945 448548.5975 656.3552087 156586.6503 159357.4655 447.1869907 -2.650489161 -1.683920015 EDSHPFDLGLYNEAVK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDSHPFDLGLYNEAVK 16 0 P35244;B5MC59 P35244 RPA3 Replication protein A 14 kDa subunit 0 ;;; 217.37 1.43E-14 2326440000 2511760 2202590 1982180 2182660 2320450 2408230 2498970 2677290 2888060 2764490 FALSE TRUE 2413597.642 2139774.29 2340404.019 2295307.344 2395089.382 2456926.061 2529553.142 2622003.026 2560219.537 2577248.63 0.936501669 0.830255283 0.908101761 0.890603769 0.929320266 0.953313558 0.981493641 1.017365184 0.99339253 1 21.29740029 2.651513422 1.086652 1.007150082 0.884780949 0.772441644 0.026040811 0.203282826 0.497101913 0.013225965 0.011208866 448.2429026 -2.651513422 -0.122369132 S(ph)APPNLWAAQR ddPTM_BT-474_Pertuzumab_2h_R1 6 SAPPNLWAAQR 11 0 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR 170 1.70E-05 9757460000 893322 909503 775232 734943 841955 691771 679160 695072 747943 656504 TRUE FALSE 858409.9886 883564.8649 915333.6673 772873.4963 869037.2472 705759.0836 687471.7632 680718.5203 663039.6463 612038.3993 1.402542699 1.44364286 1.495549411 1.262785958 1.419906411 1.153128765 1.123249397 1.112215379 1.083330142 1 19.22326264 2.651930489 0.797272411 1.045557012 1.448733585 0.859413864 0.063276866 0.214505187 0.287587631 0.041625406 0.036377174 448.6735719 -2.651930489 0.403176574 GADNDGS(ph)GSESGYTTPK ddPTM_BT-474_Pertuzumab_2h_R1 5 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 GADNDGS(0.997)GS(0.003)ESGYTTPK;GADNDGS(0.951)GS(0.049)ESGYTTPK;GADNDGS(0.778)GS(0.222)ESGYTTPK;GADNDGS(0.9)GS(0.1)ES(0.001)GYTTPK;GADNDGS(0.96)GS(0.039)ES(0.001)GYTTPK 332.29 5.01E-72 3386518000 2417322 2562056 2315721 2645700 2562645 3065169 3373424 3345309 3937979 4211420 TRUE FALSE 2322850.384 2488988.671 2734223.298 2782244.894 2645074.804 3127148.817 3414708.972 3276227.2 3490956.133 3926176.772 0.591631635 0.633947175 0.696408607 0.708639742 0.673702423 0.796487015 0.86972879 0.834457384 0.889148996 1 21.9046937 2.652427237 0.273099591 1.025210712 0.509764381 0.940927359 0.029834144 0.637138406 0.105631481 0.051748881 0.112139037 449.1870605 -2.652427237 -0.515446331 STSGPRPGCQPSS(ph)PCVPK ddPTM_BT-474_Pertuzumab_2h_R1 4 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 STSGPRPGCQPS(0.207)S(0.793)PCVPK;STSGPRPGCQPS(0.061)S(0.939)PCVPK;STSGPRPGCQPS(0.034)S(0.966)PCVPK;STSGPRPGCQPS(0.019)S(0.981)PCVPK 203.71 6.98E-16 3531200000 2012690 2087090 1813650 1777780 1822850 2002940 1749680 1820980 1963840 2142210 TRUE FALSE 1934031.85 2027568.237 2141416.899 1869531.439 1881483.626 2043440.819 1771093.107 1783376.127 1740913.116 1997116.209 0.968412274 1.015248 1.072254529 0.9361155 0.942100223 1.023195751 0.886825263 0.892975641 0.871713478 1 20.92948685 2.652752168 0.9975075 0.904151439 1.00614276 0.276080602 0.053705295 0.585728883 1.214941285 0.031099158 0.026292804 449.5232598 -2.652752168 0.101991321 AKEEELRK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKEEELRK 8 2 O75525-2;O75525;H0YAQ1;H0YAQ3;E5RJZ9;E5RG12;Q9H6N6;Q07666-2;Q07666;Q5VWX1 O75525-2;Q07666-2 KHDRBS3;MYH16;KHDRBS1;KHDRBS2 "KH domain-containing, RNA-binding, signal transduction-associated protein 3;Putative uncharacterized protein MYH16;KH domain-containing, RNA-binding, signal transduction-associated protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 2" 0 ; 101.65 0.0029511 581370000 1573440 1478730 1129920 1214550 1330730 1492600 1470340 1650950 1736220 1632300 FALSE TRUE 1511948.225 1436558.068 1334121.679 1277233.071 1373534.139 1522781.395 1488334.461 1616857.306 1539131.584 1521742.867 0.993563537 0.944021555 0.876706379 0.839322529 0.902605932 1.000682459 0.978045958 1.06250362 1.011426843 1 20.53729317 2.653937062 3.438231447 1.018788925 0.906851669 0.569748406 0.042963199 0.187095031 4.250110574 0.015957536 0.015123195 450.7513771 -2.653937062 -0.111937257 EQQDLEFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQQDLEFAK 9 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 93.448 0.02185 150830000 136560 153790 119320 109380 142500 140550 160840 156640 154160 186820 FALSE TRUE 131223.0842 149404.0598 140883.7783 115025.1149 147083.6419 143392.0173 162808.408 153405.3293 136660.4031 174166.515 0.753434633 0.8578231 0.808902781 0.660431857 0.844500115 0.823304166 0.934785932 0.880796916 0.784653715 1 17.41010775 2.655144654 2.239307695 0.88899472 0.780356409 0.358666603 0.071794171 0.373010344 3.689417074 0.025971906 0.02439183 452.0064728 -2.655144654 -0.108638311 SS(ph)DQDSTNKEAEAAGVKPAGVRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSDQDSTNKEAEAAGVKPAGVRPR 24 3 Q92625;A0A3B3ISP1;A0A3B3ITU5 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.183)S(0.805)DQDS(0.006)T(0.006)NKEAEAAGVKPAGVRPR 86.869 0.064087 164850000 103610 94911 78006 56329 75283 99120 95253 103300 139270 103550 TRUE FALSE 99560.80665 92204.23121 92103.41943 59236.14644 77704.54607 101124.2743 96418.73471 101166.8189 123460.6535 96536.46627 1.031328476 0.955123331 0.954079044 0.613614199 0.804924285 1.047524093 0.998780445 1.047964803 1.278901727 1 16.5587864 2.655457221 5.66758118 1.07107635 0.867050093 0.384514679 0.128344187 0.266482088 14.11294553 0.044725024 0.042162329 452.3319046 -2.655457221 -0.204026257 MLAESDES(ph)GDEESVSQTDKTELQNTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 MLAES(0.033)DES(0.967)GDEESVSQTDKTELQNTLR;MLAES(0.054)DES(0.946)GDEESVSQTDKTELQNTLR;MLAES(0.001)DES(0.997)GDEES(0.002)VSQTDKTELQNTLR;MLAESDES(1)GDEESVSQTDKTELQNTLR 238.26 2.64E-45 1237210000 792260 758060 653810 807660 733180 879080 962000 918390 1110330 1056130 TRUE FALSE 761297.6033 736440.871 771968.0109 849343.4294 756763.4006 896855.5999 973773.2438 899424.9256 984289.9933 984597.3744 0.773207022 0.747961441 0.784044353 0.862630199 0.768601888 0.91088563 0.989006541 0.913495149 0.99968781 1 19.90917437 2.655512321 0.764384427 0.988901726 0.762327199 0.831504644 0.039625062 0.264728737 0.326858103 0.028233942 0.025143492 452.3892967 -2.655512321 -0.226574527 LLHYAGEVTYSVTGFLDKNNDLLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLHYAGEVTYSVTGFLDKNNDLLFR 25 1 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 116.48 0.00076162 45150000 30561 36547 21504 26435 27309 28812 22565 25823 24703 21798 FALSE TRUE 29366.64233 35504.71534 25390.25115 27799.31352 28187.41879 29394.59838 22841.15722 25289.74603 21898.819 20321.60204 1.445094844 1.747141552 1.249421729 1.367968601 1.387066764 1.446470525 1.123984082 1.244476 1.077612826 1 14.31072652 2.655527194 0.267204244 0.94728706 1.685496002 0.626280297 0.12675616 1.843082683 0.294331392 0.210305784 0.461311103 452.4047897 -2.655527194 0.738208942 GAFFMDEDEEVYKR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAFFMDEDEEVYKR 14 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 ; 192.86 5.21E-07 713470000 563390 608570 514240 518280 546230 606940 617500 670550 665280 668190 FALSE TRUE 541372.0959 591214.1795 607174.6072 545028.4929 563799.984 619212.7426 625057.1497 656702.9082 589760.2035 622932.8961 0.869069685 0.949081648 0.974703072 0.874939333 0.905073384 0.994028003 1.003410084 1.054211316 0.946747566 1 19.24871724 2.65632172 4.485508102 1.009223069 0.917664697 0.546898425 0.038354799 0.170469293 6.237339334 0.012956246 0.012245905 453.233205 -2.65632172 -0.091558373 VRVELSNGEK ddPTM_BT-474_Pertuzumab_2h_R1 8 VRVELSNGEK 10 1 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;;;;; 184.44 1.42E-06 12173990000 5876640 5842750 4986241 5543406 5923120 6323850 6554503 6996290 7669370 7550880 FALSE TRUE 5646974.412 5676120.491 5887365.667 5829501.848 6113642.534 6451722.58 6634718.968 6851814.167 6798775.27 7039452.172 0.802189471 0.806329861 0.836338613 0.828118681 0.868482715 0.916509186 0.942505014 0.9733448 0.96581028 1 22.74703173 2.657463 0.706037379 0.992025523 0.801259376 0.984298411 0.008858631 0.075373451 0.079474782 0.006458563 0.005979338 454.4258208 -2.657463 -0.190766147 AEDEVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEDEVQR 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 149.48 0.0046838 367180000 386530 411880 370910 421640 404780 391110 372410 409210 444970 436980 FALSE TRUE 371423.9803 400133.5857 437941.6878 443400.8909 417800.1163 399018.5122 376967.665 400759.6705 394458.8711 407382.9554 0.911731763 0.982205025 1.0750123 1.088412966 1.02557093 0.979467862 0.925339806 0.98374187 0.968275344 1 18.63602609 2.65800095 4.726707485 0.966696057 1.021863494 0.170921289 0.049126094 0.377579868 15.2280541 0.01745791 0.01649597 454.9890554 -2.65800095 0.055167437 GSTDDKGPVAGWINALEAYQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSTDDKGPVAGWINALEAYQK 21 1 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;A0A087WVS2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 182.15 4.17E-18 276210000 615920 678420 547630 531750 609350 684140 690290 765180 822300 727050 FALSE TRUE 591849.1655 659072.1258 646598.923 559193.6812 628950.2961 697973.7795 698737.9755 749378.7656 728955.9514 677806.2559 0.873183392 0.972360642 0.953958329 0.825005193 0.927920465 1.029754113 1.030881567 1.105594348 1.075463593 1 19.37051343 2.659352873 2.718755446 1.06358877 0.909972938 0.690307433 0.046303423 0.157571441 2.286414945 0.016721928 0.015875677 456.4076054 -2.659352873 -0.153615832 VCAKPWAPDMTLPGIS(ph)PPPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VCAKPWAPDMTLPGISPPPEK 21 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 VCAKPWAPDMTLPGIS(1)PPPEK;VCAKPWAPDMT(0.001)LPGIS(0.999)PPPEK 118.9 4.34E-05 1638660000 1112110 1081440 1006130 941500 1038400 1084490 1077530 1271330 1049250 1148870 TRUE FALSE 1068647.512 1050598.39 1187960.072 990090.9278 1071801.079 1106419.131 1090717.134 1245076.591 930143.5388 1071056.012 0.997751285 0.980899578 1.10914841 0.924406303 1.000695638 1.033017059 1.018356764 1.162475704 0.868435944 1 20.0306025 2.659517199 4.218741451 1.038545172 1.002997182 0 0.080101274 0.905845497 30.25362131 0.026418284 0.02502169 456.5803314 -2.659517199 -0.03554799 WRPGDADGTDCTSIGTIEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 WRPGDADGTDCTSIGTIEQK 20 1 Q9BTC0;Q9BTC0-1;Q9BTC0-2;Q9BTC0-3 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 ; 227.95 3.09E-25 652810000 278550 339714 235387 342151 279162 298048 249896 303867 333850 301080 FALSE TRUE 267663.958 330025.6893 277926.6671 359809.4541 288141.4993 304074.7348 252954.302 297592.0403 295952.7476 280687.5834 0.953600992 1.175775876 0.990163739 1.281885895 1.026555916 1.083320933 0.901195197 1.060225168 1.054384893 1 18.09860572 2.659565623 2.645106982 1.011507857 1.098342765 0.119775574 0.097868921 0.549147075 7.547891682 0.032569827 0.03090521 456.6312431 -2.659565623 0.086834908 ISVIVETVYTHVLHPYPTQITQSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISVIVETVYTHVLHPYPTQITQSEK 25 0 P04843 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 147.41 1.37E-07 154750000 61892 66232 38581 52335 48365 46080 41285 24229 55767 45555 FALSE TRUE 59473.19221 64343.12821 45553.44493 55036.01562 49920.70415 47011.76917 41790.25818 23728.66268 49436.56395 42469.51927 1.400373567 1.515042537 1.072615036 1.295894481 1.175447827 1.106953174 0.984005915 0.558722187 1.164048117 1 15.37414016 2.659653573 1.157198398 0.849410862 1.335107162 0.476842097 0.180161808 0.365423059 1.009174015 0.095247267 0.081934663 456.7237255 -2.659653573 0.4856963 GNIETTS(ph)EDGQVFSPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GNIET(0.001)T(0.031)S(0.968)EDGQVFSPK;GNIET(0.002)T(0.21)S(0.788)EDGQVFSPK;GNIET(0.002)T(0.148)S(0.85)EDGQVFSPK 212.37 4.91E-12 562340000 1466220 1382980 1214710 1408380 1383060 1480750 1376940 1662800 1757280 1628580 TRUE FALSE 1408918.501 1343538.764 1434235.118 1481066.661 1427547.381 1510691.78 1393791.404 1628462.599 1557800.942 1518274.826 0.927973301 0.884911441 0.944647895 0.975493129 0.940243068 0.995005485 0.918009954 1.072574326 1.026033571 1 20.53400153 2.659672131 0.581786445 1.032924465 0.911421998 0.492030976 0.038002956 0.685216608 0.487454948 0.032001764 0.033967794 456.7432426 -2.659672131 -0.121502467 YEIMDGAPVKGESIPIR ddPTM_BT-474_Pertuzumab_2h_R1 3 YEIMDGAPVKGESIPIR 17 1 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ;; 180.81 7.65E-10 202359000 527521 541490 423632 518037 479146 547494 541782 598242 614740 594310 FALSE TRUE 506904.8961 526047.2354 500191.726 544772.9517 494558.1662 558564.7038 548412.4902 585888.0936 544957.2924 554056.8543 0.914896896 0.949446309 0.902780504 0.983243773 0.892612667 1.008136077 0.989812663 1.057451215 0.983576483 1 19.0796745 2.661620088 7.399243572 1.014044793 0.931449152 0.625974536 0.030387304 0.17057359 14.4870816 0.009393244 0.008852947 458.7964918 -2.661620088 -0.08259564 DAGHPLYPFNDPY ddPTM_BT-474_Pertuzumab_2h_R1 4 DAGHPLYPFNDPY 13 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 106.38 0.0032072 1721550000 1635460 1778170 1455840 1493790 1438560 1595370 1477980 1382290 1610530 1573280 FALSE TRUE 1571544.415 1727458.333 1718942.673 1570884.681 1484832.589 1627629.474 1496067.961 1353745.228 1427709.386 1466720.344 1.071468342 1.177769395 1.171963476 1.071018539 1.012348806 1.109706756 1.020009007 0.922974331 0.973402593 1 20.48416239 2.661851227 0.753087757 0.956411569 1.14005766 0.604551249 0.049672325 0.434869078 0.522088912 0.037205774 0.033552326 459.0407359 -2.661851227 0.183646092 RATASEQPLAQEPPASGGS(ph)PATTK ddPTM_BT-474_Pertuzumab_2h_R1 2 RATASEQPLAQEPPASGGSPATTK 24 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 RATASEQPLAQEPPAS(0.05)GGS(0.949)PAT(0.001)TK;RATASEQPLAQEPPAS(0.024)GGS(0.976)PATTK 207.35 4.66E-25 597950000 264160 246630 218033 200665 227313 265950 270470 288480 284480 336760 TRUE FALSE 253836.3352 239596.3539 257436.4132 211021.3447 234624.7291 271327.6912 273780.0928 282522.7872 252187.023 313950.9452 0.808522283 0.763164939 0.819989292 0.672147506 0.747329265 0.864235943 0.872047359 0.899894686 0.803268876 1 18.26017963 2.663802515 4.45311757 0.884181687 0.760477916 0.536061697 0.058583593 0.181372214 6.814250062 0.018734405 0.01775244 461.1078492 -2.663802515 -0.123703771 EHQMAK ddPTM_BT-474_Pertuzumab_2h_R1 5 EHQMAK 6 0 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;B7Z4S1;S4R3M9;O75764 A0A1W2PRL9;S4R3M9 TCEA1;TCEA3 Transcription elongation factor A protein 1;Transcription elongation factor A protein 3 0 ;;;; 83.843 0.056526 571371000 1557321 1501441 1216318 1348477 1296704 1166755 1398708 794638 1362748 1472669 FALSE TRUE 1496459.174 1458621.373 1436133.719 1418072.06 1338413.662 1190347.586 1415825.807 778228.4476 1208054.56 1372923.817 1.089979761 1.062419746 1.046040357 1.03288474 0.974863751 0.867016488 1.031248631 0.566840227 0.879913762 1 20.38882014 2.663813156 1.091472897 0.799003776 1.064895185 0.332221712 0.12020928 0.457851004 1.131010878 0.064395269 0.055292872 461.1191478 -2.663813156 0.265891409 LLEEDVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEEDVKR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 76.064 0.058957 152620000 63056 63966 57546 63435 62482 59667 52300 62887 70490 66502 FALSE TRUE 60591.70181 62141.75231 67945.8423 66708.88795 64491.79027 60873.50762 52940.06304 61588.36147 62488.27072 61997.76031 0.977320818 1.002322536 1.095940272 1.075988675 1.040227743 0.981866237 0.853902831 0.993396554 1.007911744 1 15.91992848 2.663931205 4.461502976 0.958186607 1.04174651 0.321351214 0.051322797 0.254273148 9.592638066 0.017751225 0.016820907 461.244505 -2.663931205 0.083559903 NGHVGISFVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGHVGISFVPK 11 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 ; 102.4 0.0028735 931540000 2046990 2072370 1822930 1874880 1755190 1915210 1940630 1251260 2377130 2212990 FALSE TRUE 1966991.368 2013268.037 2152374.002 1971642.781 1811647.28 1953936.858 1964380.01 1225421.044 2107288.168 2063102.216 0.953414403 0.975845026 1.043270656 0.955668976 0.878118043 0.947086791 0.95214866 0.593970107 1.021417238 1 20.97638387 2.664171471 1.202770083 0.837480907 0.982379571 0.020000666 0.119510585 0.781848456 2.325770783 0.061134021 0.053101553 461.4997513 -2.664171471 0.144898664 IWGLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IWGLGR 6 0 P41743 P41743 PRKCI Protein kinase C iota type 0 135.03 0.059848 0 104400 108750 90119 98365 113540 110700 107460 106970 126350 128360 FALSE TRUE 100319.9326 105648.5565 106405.508 103441.6294 117192.1172 112938.4298 108775.1276 104761.0321 112007.2777 119666.0629 0.838332357 0.882861473 0.889187005 0.864419092 0.979326255 0.943779942 0.90898894 0.875444797 0.935998687 1 16.86865454 2.664640443 0.015440478 1.813703258 1.40E-06 0.504102765 0.034690789 990.9049085 6.324628334 356.4415332 385.6403842 461.9983699 -2.664640443 -1.813701854 TSLPTVGPSGLYS(ph)PSTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSLPTVGPSGLYSPSTNR 18 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 TSLPTVGPSGLYS(1)PSTNR;TSLPTVGPSGLYS(0.97)PS(0.025)T(0.005)NR 289.5 4.10E-49 472930000 328960 347170 358670 328930 330470 379980 379070 425770 395080 425190 TRUE FALSE 316103.8795 337269.0515 423489.6476 345906.1167 341099.8677 387663.4559 383709.1721 416977.7007 350232.1747 396391.5026 0.797453723 0.850848339 1.068362073 0.872637568 0.860512563 0.977981247 0.968005544 1.051934005 0.883551167 1 18.59656651 2.664769886 7.011902885 0.985301511 0.896846671 0.234831628 0.076593706 0.404382631 33.08265879 0.02552195 0.024062383 462.1360906 -2.664769886 -0.088454839 RPPS(ph)PEPSTK ddPTM_BT-474_Pertuzumab_2h_R1 9 RPPSPEPSTK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RPPS(0.826)PEPS(0.123)T(0.052)K;RPPS(1)PEPSTK;RPPS(0.958)PEPS(0.034)T(0.007)K;RPPS(0.996)PEPS(0.003)T(0.001)K;RPPS(0.998)PEPS(0.002)TK;RPPS(0.984)PEPS(0.016)TK;RPPS(0.995)PEPS(0.003)T(0.001)K;RPPS(1)PEPSTK;RPPS(0.986)PEPS(0.014)TK 97.716 0.0062166 58650200000 6500300 6818820 5504970 6529290 6315380 6868040 7104710 7464140 8157540 7853570 TRUE FALSE 6246261.09 6624353.93 6499840.536 6866267.439 6518519.933 7006916.474 7191659.566 7310002.901 7231530.258 7321640.709 0.853123137 0.90476359 0.887757375 0.937804478 0.890308633 0.957014521 0.982246992 0.998410492 0.987692588 1 22.80373555 2.664787596 0.745287087 1.005106312 0.880980155 0.849432925 0.019538032 0.237363009 0.279325349 0.013632604 0.012386053 462.1549367 -2.664787596 -0.124126157 YYTSASGDEMVSLK ddPTM_BT-474_Pertuzumab_2h_R1 3 YYTSASGDEMVSLK 14 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 218.01 1.29E-11 271285000 257826 311326 241744 245844 269252 296144 298390 320902 360933 312878 FALSE TRUE 247749.8749 302447.2873 285432.5184 258532.0383 277912.7351 302132.2346 302041.7861 314275.2616 319961.399 291686.4944 0.849370402 1.036891639 0.978559254 0.886335306 0.952778893 1.035811532 1.035501444 1.077441937 1.09693594 1 18.15405906 2.665457871 2.958554458 1.05850151 0.944219365 0.513293958 0.052828853 0.221019662 3.801924937 0.018058976 0.017224399 462.8687604 -2.665457871 -0.114282145 TIGGGDDSFNTFFSETGAGK ddPTM_BT-474_Pertuzumab_2h_R1 6 TIGGGDDSFNTFFSETGAGK 20 0 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;F8VRK0;F8W0F6;F8VXZ7;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;;;; 416.91 1.37E-151 2612600000 1902710 1861890 1660490 1882540 1866560 1954470 2068310 2242810 2422590 2339240 FALSE TRUE 1828349.99 1808790.72 1960577.48 1979698.115 1926599.598 1993990.723 2093622.596 2196495.19 2147587.74 2180801.191 0.838384534 0.829415688 0.899017062 0.907784773 0.883436604 0.914338607 0.960024511 1.007196437 0.984770069 1 21.05642682 2.665703124 0.539317615 1.014983935 0.836771853 0.88084211 0.020873731 0.318697005 0.193925903 0.020149897 0.023019567 463.1302235 -2.665703124 -0.178212082 S(ph)EEPSVSIPFLQTALLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEPSVSIPFLQTALLR 17 0 Q5SW79;H0Y2V6;H0YB66 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.98)EEPS(0.02)VSIPFLQTALLR;S(0.997)EEPS(0.003)VSIPFLQTALLR 124.68 5.19E-05 72321000 53713 51109 34468 43395 52167 53456 54398 63816 68204 60762 TRUE FALSE 51613.83658 49651.42136 40697.13434 45634.62115 53844.99893 54536.91695 55063.739 62498.1773 60461.76785 56646.53562 0.911156102 0.876512938 0.718439952 0.805603037 0.950543548 0.962758205 0.972058369 1.103300963 1.067351555 1 15.78970011 2.666657425 1.237305112 1.056635448 0.826726672 0.692115116 0.060796611 0.254381669 0.798919696 0.031699345 0.027717207 464.1490063 -2.666657425 -0.229908776 FLENHEK ddPTM_BT-474_Pertuzumab_2h_R1 5 FLENHEK 7 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;;; 119.27 0.0048185 2470420000 3201410 3161360 2674890 2895690 3140130 3091840 3214450 3326450 3659760 3597160 FALSE TRUE 3076295.358 3071201.108 3158302.126 3045136.908 3241135.133 3154359.123 3253789.401 3257757.645 3244319.388 3353521.149 0.917332923 0.915813848 0.941786852 0.908041659 0.966487161 0.940611072 0.970260588 0.971443894 0.967436686 1 21.67724527 2.667127329 0.293758595 1.002566701 0.896820277 0.77302051 0.013557644 1.040895405 0.193504588 0.01829072 0.038399743 464.6514841 -2.667127329 -0.105746424 SGVEAALSEAFHEEYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGVEAALSEAFHEEYSR 17 0 G3V1N5;B4E3L3;Q96RU2-2 G3V1N5 USP28 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 28 0 80.638 0.010994 41985000 49904 45543 40340 43526 50248 52517 61677 58810 68406 69402 FALSE TRUE 47953.69651 44244.15823 47630.33536 45772.38208 51864.27255 53578.92972 62431.82158 57595.55295 60640.83766 64701.34072 0.741154603 0.683821351 0.736156853 0.707441014 0.801595021 0.828096128 0.964923151 0.890175571 0.937242366 1 15.98150799 2.667424644 1.151882731 0.944737797 0.710874845 0.894859541 0.034940779 0.136211465 0.373167045 0.01701168 0.014741571 464.9696903 -2.667424644 -0.233862952 ALLETAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALLETASPR 9 0 H3BMP6;H3BQS6;H3BN05;H3BTS2;H3BQJ0;I3L4F8;H3BUW2;H3BTR4;Q96BT3-3;Q96BT3-2;Q96BT3 H3BMP6 CENPT Centromere protein T 1 ALLETAS(1)PR;ALLETAS(1)PR 186.02 4.42E-05 467500000 721280 802790 636970 775040 664580 615640 714400 631810 571630 748540 TRUE FALSE 693091.5802 779895.2152 752084.6483 815039.9073 685956.8193 628088.6626 723143.0409 618762.9027 506740.9589 697840.7191 0.993194523 1.117583417 1.077731104 1.167945471 0.982970469 0.900045878 1.036258019 0.886682141 0.726155618 1 19.41253826 2.668669122 1.116917962 0.886776499 1.089520795 0.452279846 0.089517828 0.439049034 1.134154859 0.047204028 0.040820139 466.3039792 -2.668669122 0.202744296 RPQYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPQYIK 6 1 G8JLG1;Q14683;Q8NDV3-2;Q8NDV3-3;Q8NDV3 G8JLG1;Q8NDV3-2 SMC1A;SMC1B Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A;Structural maintenance of chromosomes protein 1B 0 140.79 0.018816 291680000 256160 295480 225600 257120 321340 323340 390540 442890 398680 453810 FALSE TRUE 246148.984 287053.1997 266370.9384 270389.994 331676.1929 329878.1563 395319.5453 433744.1667 353423.5178 423073.0445 0.581812023 0.678495601 0.629609808 0.639109481 0.783969098 0.779719154 0.934400219 1.025222884 0.835372337 1 18.69054724 2.668806355 1.099568265 0.969837001 0.6282739 0.846595536 0.058976438 0.171904608 0.430974387 0.031031203 0.026799418 466.4513506 -2.668806355 -0.341563101 S(ph)RSPITTNHRPSPDPEQRPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.499)RS(0.499)PIT(0.001)T(0.001)NHRPSPDPEQRPLR;S(0.5)RS(0.5)PITTNHRPSPDPEQRPLR;S(0.5)RS(0.5)PITTNHRPSPDPEQRPLR 128.97 1.23E-05 4732430000 838540 838620 689730 924590 803380 755990 716730 828970 740620 725820 TRUE FALSE 805768.9297 814703.3787 814379.554 972308.2007 829221.4473 771276.6358 725501.5561 811851.4798 656547.9225 676659.5649 1.19080402 1.204007777 1.203529214 1.436923752 1.225463276 1.139829651 1.07218104 1.199793104 0.970278049 1 19.36807065 2.668999082 3.062941904 1.091751042 1.258513946 0.500111491 0.088552596 0.257552701 4.760096555 0.031157405 0.029778982 466.6583938 -2.668999082 0.166762904 S(ph)PGGGSEANGLALVSGFK ddPTM_BT-474_Pertuzumab_2h_R1 8 SPGGGSEANGLALVSGFK 18 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK 287.99 3.62E-40 4649577000 2512466 2489470 2353393 2596253 2471362 2713635 3007040 3223261 3321577 3429705 TRUE FALSE 2414276.051 2418472.753 2778703.466 2730245.928 2550855.603 2768506.559 3043841.055 3156699.534 2944525.504 3197408.025 0.755072869 0.756385401 0.869048756 0.8538935 0.797788578 0.865859639 0.951971419 0.987268284 0.92091015 1 21.60847143 2.669582511 0.478860559 1.004620096 0.756383311 0.787232983 0.038930689 0.516487356 0.245562624 0.039494036 0.051027086 467.2857222 -2.669582511 -0.248236785 (ac)ATVWDEAEQDGIGEEVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATVWDEAEQDGIGEEVLK 18 0 R4GNH3;E9PN50 R4GNH3 PSMC3 0 ; 89.629 1.03E-48 56596000 60554 59309 59522 57221 60335 66860 67295 73976 75867 73913 FALSE TRUE 58187.48273 57617.56539 70278.94946 60174.18267 62275.73007 68211.95501 68118.57634 72448.36975 67254.89622 68906.80668 0.844437372 0.836166529 1.019913022 0.873269065 0.903767466 0.989916066 0.988560922 1.051396419 0.97602689 1 16.07235888 2.670086236 2.657796304 1.011382766 0.896353211 0.520959848 0.050637013 0.231869984 3.225763923 0.018198725 0.017380175 467.8280266 -2.670086236 -0.115029555 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SAEVGPSSEPEVQT(0.013)LPY(0.006)LPHY(0.006)IPGVDPET(0.031)S(0.031)HGGHPHGNMPGLDRPLS(0.914)R 114.57 1.62E-08 672660000 149230 153520 103450 105990 92059 92794 55256 1563.4 72427 30987 TRUE FALSE 143397.9266 149141.7599 122145.7162 111460.1566 95020.16134 94670.35826 55932.23946 1531.115244 64205.3906 28888.22289 4.96388882 5.162718402 4.228218423 3.858325139 3.28923526 3.277126413 1.936160617 0.053001365 2.222545528 1 14.81819384 2.67136887 0.756581404 0.793196467 4.943230338 0.844921481 0.627130731 0.242280135 0.294219619 0.467889483 0.4252849 469.21174 -2.67136887 4.150033871 RVIISAPSADAPMFVMGVNHEK ddPTM_BT-474_Pertuzumab_2h_R1 4 RVIISAPSADAPMFVMGVNHEK 22 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 225.26 4.05E-26 9553020000 3917800 3774500 2863480 2946610 3561330 3553150 2924000 3099760 3579460 2765560 FALSE TRUE 3764688.045 3666854.956 3380974.534 3098684.895 3675883.414 3624997.127 2959784.787 3035748.873 3173134.707 2578246.158 1.460174015 1.422228418 1.311346678 1.20185766 1.425730201 1.405993418 1.147983786 1.177447259 1.230733806 1 21.29795858 2.671983535 0.041997315 2.23E-06 2.569391541 0.672531242 0.082060832 80.06637994 1.394756992 37.79600719 46.84209126 469.8762947 -2.671983535 2.569389313 AKNEQEHHAGGDSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKNEQEHHAGGDSQK 15 1 Q86SF2;E9PBY3 Q86SF2 GALNT7 N-acetylgalactosaminyltransferase 7 0 64.65 0.038386 6945200 12951 20128 12793 16951 15768 11199 15316 3220.4 20695 15618 FALSE TRUE 12444.8606 19553.96915 15104.97968 17825.84314 16275.19204 11425.45145 15503.44179 3153.897615 18345.79036 14560.17895 0.854718932 1.342975881 1.037417173 1.224287367 1.117787913 0.784705428 1.06478374 0.216611185 1.259997588 1 13.82974047 2.672191297 2.304235197 0.768350475 1.134860551 0.112094551 0.288165583 0.433637614 4.538620986 0.102316922 0.09733515 470.1011323 -2.672191297 0.366510076 KELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 34 2 Q01105-2 Q01105-2 SET Protein SET 1 KELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;KELNSNHDGADET(0.578)S(0.422)EKEQQEAIEHIDEVQNEIDR;KELNS(0.001)NHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;KELNSNHDGADET(0.765)S(0.235)EKEQQEAIEHIDEVQNEIDR 181.61 9.97E-20 2194260000 636449 526763 667223 627564 639517 602563 811276 765694 920834 918998 TRUE FALSE 611575.8694 511740.235 787805.0384 659952.6532 660087.6451 614747.2367 821204.6384 749882.1513 816304.7848 856753.4469 0.713829482 0.597301635 0.919523629 0.770294716 0.770452278 0.717531092 0.95850754 0.875260151 0.952788445 1 19.70852057 2.672210686 0.263540688 1.034896544 0.613890514 0.548142911 0.084467375 2.316325749 0.358205922 0.147151443 0.328527115 470.1221206 -2.672210686 -0.421006029 NEKDNALLSAIEESR ddPTM_BT-474_Pertuzumab_2h_R1 4 NEKDNALLSAIEESR 15 1 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ;;; 228.76 5.05E-13 3273420000 2037050 1988170 1551580 1685610 1787950 1980820 1990090 2050260 2409920 2258300 FALSE TRUE 1957439.834 1931469.338 1831985.021 1772604.534 1845461.036 2020873.538 2014445.317 2007921.415 2136355.985 2105343.33 0.929748515 0.917412999 0.870159748 0.841955091 0.876560611 0.959878377 0.956825088 0.953726353 1.01473045 1 21.00562409 2.672448078 4.491746766 0.972216971 0.885327993 0.705481076 0.029001213 0.141619759 5.682388345 0.01040164 0.009886835 470.3791658 -2.672448078 -0.086888977 GWS(ph)QEGPVK ddPTM_BT-474_Pertuzumab_2h_R1 6 GWSQEGPVK 9 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK 168.85 6.18E-05 8620070000 5179770 4774130 2515250 3910780 6064940 4092920 5396990 7431470 6039140 5395880 TRUE FALSE 4977338.862 4637976.487 2969811.626 4112615.824 6260024.303 4175681.647 5463039.978 7278007.548 5353602.145 5030412.241 0.989449497 0.921987357 0.590371422 0.817550457 1.244435645 0.830087366 1.086002442 1.446801415 1.064247201 1 22.2622452 2.673743426 1.061293683 1.20647686 0.83845324 0.261706812 0.193481132 0.572279715 1.34161118 0.11017382 0.095393002 471.7842364 -2.673743426 -0.36802362 TAGAPDPAWDWQHVGPGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAGAPDPAWDWQHVGPGYR 19 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3 H3BM67 NOL3 Nucleolar protein 3 0 ; 255.19 6.35E-31 1342380000 542000 526720 426290 453320 455350 479680 451030 437950 476270 452400 FALSE TRUE 520818.0408 511698.4613 503330.0858 476715.8995 469996.7463 489379.4583 456549.8401 428906.1795 422205.8263 421758.545 1.234872528 1.213249778 1.193408152 1.130305254 1.114373975 1.160330867 1.082491026 1.016947219 1.001060515 1 18.68605777 2.674511819 0.42973515 0.977300852 1.248171116 0.90042764 0.026275617 0.396466333 0.150821188 0.028661108 0.041818494 472.6196986 -2.674511819 0.270870264 KQEGPATQVDSAVGTLPATS(ph)PQSTSVQAK ddPTM_BT-474_Pertuzumab_2h_R1 3 KQEGPATQVDSAVGTLPATSPQSTSVQAK 29 1 Q13428-6 Q13428-6 TCOF1 Treacle protein 1 KQEGPATQVDSAVGTLPAT(0.038)S(0.96)PQS(0.002)TSVQAK;KQEGPATQVDSAVGTLPAT(0.15)S(0.766)PQS(0.061)T(0.017)S(0.005)VQAK;KQEGPATQVDSAVGTLPAT(0.035)S(0.954)PQS(0.008)T(0.002)S(0.001)VQAK 178.77 7.54E-18 1855670000 1983350 1732740 1704920 1702370 1955990 2067320 2197140 2384710 2465500 2537170 TRUE FALSE 1905838.489 1683323.952 2013036.97 1790229.52 2018906.195 2109122.627 2224029.257 2335464.905 2185626.776 2365325.216 0.805740571 0.711667022 0.851061392 0.756864007 0.853542752 0.89168399 0.940263623 0.987375812 0.92402802 1 21.17360713 2.674682864 1.072538487 0.974468416 0.774663686 0.810234984 0.039346361 0.189756705 0.453968938 0.01987095 0.017233048 472.8058743 -2.674682864 -0.19980473 S(ph)KSLTNLVAAGDDVLEDQEILMHHPPQVDELDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKSLTNLVAAGDDVLEDQEILMHHPPQVDELDR 33 1 Q7Z5Y7-2;Q7Z5Y7-3;Q7Z5Y7 Q7Z5Y7-2 KCTD20 BTB/POZ domain-containing protein KCTD20 1 S(0.333)KS(0.333)LT(0.333)NLVAAGDDVLEDQEILMHHPPQVDELDR;S(0.492)KS(0.492)LT(0.015)NLVAAGDDVLEDQEILMHHPPQVDELDR;S(0.497)KS(0.497)LT(0.007)NLVAAGDDVLEDQEILMHHPPQVDELDR 216.37 3.84E-36 107962000 41564 28109.1 23265.9 29460.6 24635.1 21737.7 21852.7 9199 22201.1 19268.8 TRUE FALSE 39939.63293 27307.45599 27470.56568 30981.0651 25427.51036 22177.25119 22120.13988 9009.037435 19680.9242 17963.70701 2.223351388 1.520145924 1.529225881 1.724647651 1.415493492 1.234558723 1.231379462 0.501513269 1.095593698 1 14.13279748 2.67552713 0.870664532 0.813852284 1.782509133 0.681366846 0.246240726 0.32762373 0.524719526 0.156862489 0.137460533 473.7259001 -2.67552713 0.968656849 LTVDDFEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTVDDFEFR 9 0 F8WDV0;Q9UI26;Q9UI26-2 F8WDV0 IPO11 Importin-11 0 88.37 0.029849 37383000 105110 87240 82325 65777 78258 80784 69672 52524 64323 65549 FALSE TRUE 101002.185 84752.00062 97202.95881 69171.75885 80775.23964 82417.50783 70524.66678 51439.36105 57021.3227 61109.30785 1.652811798 1.386891844 1.590640808 1.13193491 1.321815653 1.348689925 1.154074056 0.841759838 0.933103724 1 15.89910452 2.677215982 0.554315352 0.877277415 1.559518372 0.721686095 0.135812531 0.483171583 0.311521962 0.11989744 0.134924295 475.5716773 -2.677215982 0.682240957 SLS(ph)ESSVIMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSESSVIMDR 11 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 S(0.006)LS(0.993)ESSVIMDR 180.24 7.08E-06 492270000 204940 180420 144080 180710 180030 167850 143870 213160 161610 161510 TRUE FALSE 196930.7182 175274.5982 170118.461 190036.4648 185820.8284 171244.042 145630.7241 208758.1715 143264.7103 150570.7838 1.307894621 1.164067781 1.129823839 1.262107163 1.234109458 1.137299266 0.967191114 1.386445406 0.951477482 1 17.20008234 2.67738318 6.455620607 1.124086288 1.21380338 0.186026612 0.126441597 0.579542326 49.37193524 0.041190724 0.03893138 475.7548018 -2.67738318 0.089717091 LGGAVPFAPPEVS(ph)PEQAK ddPTM_BT-474_Pertuzumab_2h_R1 4 LGGAVPFAPPEVSPEQAK 18 0 A0A096LNZ0;A0A096LP25;Q6ZSR9 A0A096LNZ0;A0A096LP25 AAK1 Uncharacterized protein FLJ45252 1 LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK 207.39 7.84E-16 507133000 1022710 943980 1045890 986500 1059850 1256610 1302980 1385240 1571280 1625520 TRUE FALSE 982741.3625 917058.6147 1234905.589 1037413.383 1093941.038 1282019.515 1318926.259 1356634.31 1392914.882 1515422.083 0.648493495 0.605150621 0.81489217 0.684570586 0.721872177 0.845981809 0.870335911 0.895218781 0.919159683 1 20.53128825 2.677599384 0.360064685 1.009628733 0.589990643 0.840381451 0.049076974 0.632807693 0.169481588 0.05569197 0.098643923 475.9917048 -2.677599384 -0.41963809 AGGPTT(ph)PLSPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 AGGPT(0.081)T(0.919)PLSPTR 136.38 0.0012412 537080000 594150 583620 524700 653090 590740 564510 496440 617490 653510 579170 TRUE FALSE 570929.9611 566975.729 619524.9619 686796.0532 609741.6886 575924.779 502515.5812 604738.6157 579326.2845 539942.3 1.05739069 1.050067255 1.147391049 1.271980456 1.12927194 1.066641341 0.930683855 1.120006 1.072941099 1 19.04244572 2.677966482 4.507225669 1.04102675 1.135590802 0.291124434 0.073177755 0.322100382 13.46244074 0.02596661 0.024738436 476.3942182 -2.677966482 0.094564052 HILLAVANDEELNQLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HILLAVANDEELNQLLK 17 0 O75367-2;O75367-3;O75367;D6RCF2;Q9P0M6 O75367-2;Q9P0M6 H2AFY;H2AFY2 Core histone macro-H2A.1;Histone H2A;Core histone macro-H2A.2 0 ; 263.99 1.94E-27 1598300000 900010 980050 944960 1185210 710470 1007580 863440 668320 1002040 1111470 FALSE TRUE 864836.6142 952099.9336 1115735.293 1246378.83 733322.9128 1027953.958 874007.037 654518.9585 888292.6201 1036189.147 0.834631994 0.918847622 1.076767978 1.20284876 0.70771144 0.992052427 0.843482138 0.631659732 0.857268794 1 19.98285595 2.678044739 1.398368718 0.794338223 0.986444289 0.101122877 0.152769766 0.658089535 2.611713147 0.069871314 0.06299296 476.4800692 -2.678044739 0.192106067 NLEFFHEDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLEFFHEDVR 10 0 Q5T5P2;Q5T5P2-3;Q5T5P2-10;Q5T5P2-6;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 0 ; 111.63 0.0017279 296350000 297120 334610 278850 325610 310530 289540 287970 284240 326690 330000 FALSE TRUE 285508.2219 325067.2504 329244.398 342414.7711 320518.4795 295394.6972 291494.263 278370.3447 289605.5208 307648.8061 0.928032927 1.056617949 1.070195598 1.113005363 1.041832353 0.960168515 0.947490311 0.904831546 0.941351031 1 18.23092487 2.678655012 3.422599347 0.938585673 1.048999021 0.455279061 0.049256309 0.201392467 4.724529606 0.016954705 0.016275295 477.1500916 -2.678655012 0.110413348 QSSLAEPVS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 QSSLAEPVSPSK 12 0 E7EMD6;O43572 E7EMD6 AKAP10 "A-kinase anchor protein 10, mitochondrial" 1 QSSLAEPVS(0.996)PS(0.004)K;QSSLAEPVS(0.766)PS(0.234)K;QSSLAEPVS(0.998)PS(0.002)K;QSSLAEPVS(0.906)PS(0.094)K 265.43 1.33E-21 2330570000 4766920 4442850 4214620 4191820 4433800 4383920 4285390 4582240 4901080 4733430 TRUE FALSE 4580623.496 4316144.268 4976295.588 4408160.333 4576417.204 4472565.866 4337835.885 4487615.143 4344729.945 4412830.57 1.038023877 0.978089732 1.127687888 0.998941669 1.037070681 1.01353673 0.983005311 1.016947075 0.984567587 1 22.07327293 2.678776531 1.875054127 0.998627136 1.037510189 0.198124717 0.037395121 0.601464122 4.197170299 0.013964283 0.013132359 477.2836215 -2.678776531 0.038883052 IQEFKPSNK ddPTM_BT-474_Pertuzumab_2h_R1 2 IQEFKPSNK 9 1 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 125.74 0.0004497 1137320000 1855050 2100430 1574860 1825920 2275250 2476450 2551100 2937400 3295500 3132200 FALSE TRUE 1782552.595 2040527.793 1859472.235 1920155.95 2348435.483 2526525.516 2582321.125 2876741.664 2921408.656 2920053.304 0.610452074 0.698798132 0.636793935 0.65757565 0.804244046 0.86523267 0.884340406 0.985167517 1.000464153 1 21.47756327 2.679115782 0.804411308 1.005187773 0.632297459 0.955087133 0.03121181 0.120234108 0.165104241 0.02143364 0.019216757 477.6565987 -2.679115782 -0.372890314 RRGS(ph)QEK ddPTM_BT-474_Pertuzumab_2h_R1 3 RRGSQEK 7 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 RRGS(1)QEK;RRGS(1)QEK;RRGS(1)QEK 116.13 0.0043508 1505330000 1038850 1155110 905870 832240 1020200 1073750 1192430 1237610 1080560 1156670 TRUE FALSE 998250.5935 1122167.394 1069580.86 875192.0061 1053015.66 1095461.961 1207023.315 1212052.921 957899.3589 1078327.711 0.925739535 1.04065525 0.991888504 0.811619694 0.976526569 1.01588965 1.119347396 1.124011661 0.888319339 1 20.04036426 2.679201891 3.360768607 1.054916119 0.948090293 0.168367788 0.083826713 0.361772289 8.176966372 0.029221056 0.028067237 477.7513153 -2.679201891 -0.106825826 S(ph)QPWDLTPMLSSSEPWGR ddPTM_BT-474_Pertuzumab_2h_R1 8 SQPWDLTPMLSSSEPWGR 18 0 Q9H201 Q9H201 EPN3 Epsin-3 1 S(1)QPWDLTPMLSSSEPWGR;S(1)QPWDLTPMLSSSEPWGR;S(0.995)QPWDLT(0.005)PMLSSSEPWGR;S(1)QPWDLTPMLSSSEPWGR;S(0.999)QPWDLT(0.001)PMLSSSEPWGR;S(1)QPWDLTPMLSSSEPWGR;S(0.965)QPWDLT(0.033)PMLS(0.001)SSEPWGR;S(0.999)QPWDLT(0.001)PMLSSSEPWGR 241.51 5.62E-24 1007816800 1076250 1032394 791171 926937 955700 843774 728149 971196 842484 860204 TRUE FALSE 1034188.96 1002951.134 934153.1992 974776.3297 986440.9584 860835.6884 737060.3053 951140.4632 746848.7483 801941.6169 1.289606298 1.250653555 1.164864349 1.215520319 1.230065802 1.073439351 0.919094719 1.186047018 0.931300649 1 19.61313768 2.679903281 4.286872409 1.034205611 1.227461318 0.656133509 0.075466319 0.1526926 5.799195652 0.024811859 0.023695826 478.5235117 -2.679903281 0.193255707 DEESGGGSNPFQHLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DEESGGGSNPFQHLEK 16 0 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;; 179.81 2.57E-09 1483770000 650780 591950 558560 622850 640290 652870 723010 759780 843060 804050 FALSE TRUE 625346.7981 575068.1656 659504.2171 654995.3631 660885.5093 666071.4787 731858.4127 744090.2775 747359.3632 749590.9773 0.834250701 0.767175944 0.879818777 0.873803692 0.881661505 0.888579904 0.976343679 0.992661732 0.997022891 1 19.51574406 2.679926235 0.598831586 1.016183618 0.806690291 0.862122248 0.027915561 0.282819827 0.214146974 0.023229247 0.024537061 478.5488042 -2.679926235 -0.209493327 QKS(ph)EEPSVSIPFLQTALLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKSEEPSVSIPFLQTALLR 19 1 Q5SW79;H0Y2V6;H0YB66 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 QKS(1)EEPSVSIPFLQTALLR;QKS(0.908)EEPS(0.092)VSIPFLQTALLR 165.85 1.27E-11 852920000 872340 762580 472060 635440 1045430 731680 876110 1283630 1067300 973050 TRUE FALSE 838247.9884 740831.965 557371.7429 668235.1346 1079057.205 746475.0709 886832.0963 1257122.592 946144.5785 907144.4568 0.924051271 0.816663718 0.61442446 0.736635857 1.189509782 0.822884454 0.977608461 1.385801988 1.042992184 1 19.79097278 2.680452718 0.981944941 1.161382439 0.778957527 0.346738851 0.171822542 0.528858822 1.069473432 0.103491846 0.090107966 479.129287 -2.680452718 -0.382424912 (ac)ADQLTEEQIAEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADQLTEEQIAEFK 13 0 P0DP25;P0DP24;P0DP23;M0QZ52;F8WBR5;G3V479 P0DP25 CALM3;CALM2;CALM1 0 ; 162.36 2.63E-75 810870000 2174660 2012000 1666810 2188260 2129770 1940820 2199410 2514200 2522500 2472700 FALSE TRUE 2089671.883 1954619.73 1968039.645 2301196.361 2198275.986 1980064.71 2226327.037 2462280.891 2236156.375 2305221.827 0.906494923 0.847909606 0.853731134 0.998253762 0.953607137 0.85894758 0.965775619 1.068131866 0.970039564 1 21.13647415 2.680475951 0.55330466 1.024337203 0.869731226 0.409612278 0.053635 0.886715794 0.569686421 0.049705292 0.056193467 479.154919 -2.680475951 -0.154605978 KMPKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KMPKPR 6 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 77.906 0.040038 2023300000 532380 660910 400710 533210 571310 473400 492560 479070 534550 490900 FALSE TRUE 511574.001 642061.4939 473127.2107 560729.032 589686.705 482972.4724 498588.0966 469177.0371 473870.125 457650.9058 1.117825824 1.40295034 1.033816835 1.225233087 1.288507676 1.055329436 1.089450693 1.025185422 1.035440156 1 18.80388801 2.68063851 8.518349959 1.044799979 1.214741534 0.45903262 0.093635851 0.34111092 47.38712684 0.028909731 0.027277207 479.3343032 -2.68063851 0.169941555 QKS(ph)PAQSDSTTQR ddPTM_BT-474_Pertuzumab_2h_R1 6 QKSPAQSDSTTQR 13 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 QKS(1)PAQSDSTTQR;QKS(0.991)PAQS(0.009)DSTTQR;QKS(0.467)PAQS(0.021)DS(0.05)T(0.078)T(0.385)QR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR 201.9 5.94E-08 2499636000 569910 564853 450131 546418 528592 595787 635267 631187 704693 609856 TRUE FALSE 547637.2871 548743.9455 531479.6848 574618.6985 545594.6417 607834.2213 643041.5876 618152.7679 624699.205 568549.9099 0.963217613 0.965164071 0.934798644 1.010674153 0.959624885 1.069095625 1.131020472 1.087244509 1.098758779 1 19.11692748 2.681306375 4.424112586 1.089223334 0.966959555 0.698996055 0.035995395 0.106952536 4.382955113 0.011136005 0.010632316 480.0719978 -2.681306375 -0.122263779 QQDLHLES(ph)PQRQPEYSPES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 QQDLHLES(1)PQRQPEYSPES(1)PR;QQDLHLES(1)PQRQPEY(0.012)S(0.36)PES(0.628)PR;QQDLHLES(0.998)PQRQPEY(0.013)S(0.049)PES(0.94)PR;QQDLHLES(1)PQRQPEY(0.02)S(0.248)PES(0.732)PR;QQDLHLES(1)PQRQPEY(0.001)S(0.025)PES(0.974)PR;QQDLHLES(1)PQRQPEY(0.005)S(0.277)PES(0.719)PR 179.85 3.19E-17 1361620000 927348 1073482 781361 1169238 918932 1047516 1101756 953558 976666 1284508 TRUE FALSE 891106.2149 1042867.344 922570.314 1229582.513 948490.2823 1068697.491 1115239.62 933866.6941 865798.9702 1197507.129 0.744134372 0.870865249 0.770409037 1.02678513 0.792053976 0.892435181 0.931301027 0.779842284 0.723001099 1 20.19160281 2.681410675 0.011467861 1.698945634 8.78E-07 0.094868067 0.097234414 6557.074496 30.67383652 2203.350738 2338.167638 480.1873054 -2.681410675 -1.698944756 RIS(ph)GLIYEETR ddPTM_BT-474_Pertuzumab_2h_R1 3 RISGLIYEETR 11 1 P62805 P62805 HIST1H4A Histone H4 1 RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR 148.7 2.13E-05 377601000 324471 323010 272345 358443 236463 269843 239769 225199 240370 233237 TRUE FALSE 311790.3146 313798.0711 321563.7998 376942.2862 244069.0471 275299.4103 242703.3647 220548.562 213084.2053 217439.6502 1.433916557 1.443150183 1.478864593 1.733548991 1.12246799 1.266095719 1.116187248 1.014297814 0.979969408 1 17.73025552 2.681575056 1.146430005 1.009211136 1.503891871 0.740678379 0.122846239 0.239361241 0.650798528 0.062722822 0.055109835 480.3690918 -2.681575056 0.494680735 ADVGRLS(ph)PEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADVGRLSPEVK 11 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 1 ADVGRLS(1)PEVK 81.632 0.012805 630360000 112470 99907 112200 123430 120740 129950 150190 166910 176390 206840 TRUE FALSE 108074.5481 97057.75018 132477.0359 129800.2371 124623.7118 132577.678 152028.0701 163463.2502 156366.9467 192830.5426 0.560463849 0.503331832 0.687012722 0.67313111 0.646286164 0.687534642 0.788402439 0.847704145 0.810903421 1 17.55697405 2.682485413 0.197943681 1.077703927 0.352123083 0.90112868 0.043321522 1.557474085 0.155582562 0.152961733 0.347029513 481.3770848 -2.682485413 -0.725580844 ALWCSEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALWCSEDK 8 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 83.206 0.048232 0 268270 248050 230420 133940 238440 190810 184840 81451 205610 154090 FALSE TRUE 257785.7118 240975.8569 272062.0197 140852.6595 246109.6391 194668.3089 187102.1272 79769.00839 182270.0148 143653.3471 1.794498472 1.677481672 1.893878738 0.980503847 1.713218969 1.355125466 1.302455745 0.555288199 1.268818434 1 17.13223208 2.682853915 0.652875444 0.878325364 1.757156678 0.482261365 0.290667349 0.615565578 0.556998184 0.227876674 0.226687889 481.785711 -2.682853915 0.878831314 S(ph)PGLPMSDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGLPMSDLK 10 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(1)PGLPMSDLK 101.71 0.0032991 138080000 230860 232890 279340 275400 249550 213850 206150 212040 211590 212430 TRUE FALSE 221837.736 226248.2052 329822.9519 289613.427 257577.0024 218174.1935 208672.9254 207661.2999 187571.1903 198041.9269 1.120155411 1.142425792 1.665419828 1.462384413 1.300618543 1.101656588 1.053680545 1.048572407 0.947128687 1 17.59544637 2.682920315 2.554826499 1.023401366 1.358320722 0.529102615 0.147295281 0.251901178 3.244999109 0.056406753 0.054244731 481.8593777 -2.682920315 0.334919356 NNTAAETEDDES(ph)DGEDRGGGTSGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 1 NNTAAETEDDES(1)DGEDRGGGTSGVR;NNTAAETEDDES(1)DGEDRGGGTSGVR 339.99 1.64E-88 1299050000 253030 206954 158104 247670 225721 231320 268830 282300 306890 292690 TRUE FALSE 243141.3079 201051.8745 186676.9098 260452.2784 232981.521 235997.4489 272120.022 276470.4063 272053.1338 272865.8456 0.891065378 0.73681583 0.684134394 0.954506702 0.853831744 0.864884531 0.997266702 1.013210011 0.99702157 1 18.0578323 2.6830615 0.810199219 1.019246097 0.782864539 0.59294553 0.070275865 0.423043429 0.589691553 0.047881037 0.04301601 482.0160505 -2.6830615 -0.236381558 KAEAGAGSATEFQFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ; 171.71 1.71E-06 745770000 640660 690330 490440 563550 566800 622680 615190 636200 691610 686870 FALSE TRUE 615622.2989 670642.4643 579073.4178 592634.883 585031.6368 635271.0162 622718.8792 623062.2477 613101.3323 640347.6831 0.961387564 1.047309894 0.904310944 0.925489228 0.913615606 0.992072015 0.97246995 0.973006172 0.957450692 1 19.28849592 2.683435387 24.99857596 0.976456485 0.951858028 0.11894067 0.038480589 843.5018092 382516.1794 0.013144277 0.012392544 482.4312002 -2.683435387 -0.024598456 ILNHSVDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILNHSVDKK 9 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 129.38 0.00025371 804780000 999030 932290 838030 801280 932510 1022500 1116200 1091700 1221600 1209100 FALSE TRUE 959986.8031 905702.002 989480.6629 842634.1568 962505.031 1043175.651 1129860.389 1069156.013 1082929.089 1127206.58 0.85165117 0.803492472 0.877816614 0.747541907 0.853885213 0.925452059 1.002354324 0.948500508 0.960719276 1 20.10432051 2.683469352 2.759827417 0.971251473 0.821500174 0.799227563 0.036012376 0.114691324 1.729214379 0.011867039 0.011433053 482.4689311 -2.683469352 -0.149751298 S(ph)IQDLTVTGTEPGQVSSR ddPTM_BT-474_Pertuzumab_2h_R1 6 SIQDLTVTGTEPGQVSSR 18 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(0.971)IQDLT(0.029)VTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR 325.65 2.02E-62 6291420000 1510430 1578420 1450940 1545420 1493500 1479820 1321500 1512860 1676680 1592990 TRUE FALSE 1451400.726 1533405.007 1713157.134 1625179.311 1541539.784 1509742.974 1337672.912 1481618.912 1486350.316 1485095.368 0.977311462 1.032529654 1.153567084 1.094326564 1.038007267 1.016596649 0.900731994 0.997659102 1.000845028 1 20.50212415 2.683735425 2.77703145 0.973901679 1.066877774 0.371715404 0.050851214 0.287227948 4.386570857 0.018500984 0.017828586 482.764609 -2.683735425 0.092976095 GSVLPNSDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSVLPNSDKK 10 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 79.036 0.045234 545380000 664480 644240 518210 598880 647780 718160 681880 779180 840770 825060 FALSE TRUE 638511.387 625866.906 611862.0745 629788.2686 668616.432 732681.6873 690225.0514 763089.6607 745329.3144 769177.9513 0.830121802 0.813682848 0.795475317 0.818780969 0.869261048 0.952551599 0.897354182 0.992084679 0.968994643 1 19.55295788 2.684645934 0.896294638 0.98393742 0.805107235 0.888889993 0.025039479 0.173445638 0.294437527 0.015423166 0.013584791 483.7777986 -2.684645934 -0.178830185 S(ph)APTTLYLVHTDHAYQATPPVTIPGSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAPTTLYLVHTDHAYQATPPVTIPGSAK 28 0 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 S(0.195)APT(0.195)T(0.195)LY(0.11)LVHT(0.195)DHAY(0.11)QAT(0.002)PPVTIPGSAK 93.568 0.0041797 857370000 1011500 888180 591370 713880 669660 621280 574250 92272 799060 538120 TRUE FALSE 971969.4617 862849.976 698243.714 750723.4324 691200.2221 633842.7073 581277.8433 90366.55096 708354.0587 501672.6531 1.937457535 1.719946205 1.391831326 1.496440812 1.37779131 1.263458758 1.158679549 0.18013051 1.411984597 1 18.93638677 2.68493119 0.965885616 0.777964325 1.682684349 0.47617467 0.324752584 0.424868703 0.833076086 0.195418995 0.171046933 484.0956613 -2.68493119 0.904720024 AS(ph)HSSERPPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AS(0.586)HS(0.354)S(0.06)ERPPPR;AS(1)HSSERPPPR;AS(0.765)HS(0.198)S(0.037)ERPPPR;AS(0.994)HS(0.005)S(0.001)ERPPPR 159.66 1.72E-05 763561000 137437.5 151842.8 113485.6 144803.9 125041.1 115151.1 80956.9 123505.9 104698.1 94797.1 TRUE FALSE 132066.2906 147512.392 133994.9724 152277.2466 129063.1605 117479.5341 81947.67476 120955.46 92813.21062 88376.40798 1.494361375 1.669137674 1.516184867 1.723053133 1.460380247 1.329308769 0.92725736 1.368639694 1.050203473 1 16.43137367 2.685125352 2.380356707 1.137254326 1.595917743 0.741977627 0.133755879 0.153331469 1.713257879 0.045648215 0.043855975 484.3121359 -2.685125352 0.458663417 ALSYAS(ph)LDKEDLLSPINQNTLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 ALSYAS(1)LDKEDLLSPINQNTLQR;ALSYAS(1)LDKEDLLSPINQNTLQR 306.75 5.74E-63 926410000 623100 598960 505770 541750 658040 629880 672410 725400 831840 748200 TRUE FALSE 598748.5631 581878.2472 597173.8898 569709.7824 679206.4542 642616.6052 680639.1547 710420.2365 737413.0106 697523.7476 0.858391654 0.834205644 0.856134134 0.816760411 0.973739542 0.921282763 0.975793523 1.01848896 1.05718696 1 19.41188281 2.685339836 0.834181485 1.029935486 0.836260356 0.825289874 0.033844353 0.230135091 0.339823249 0.021583961 0.019286676 484.5513811 -2.685339836 -0.19367513 TQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPTEERLPS(0.5)S(0.5)PVYEDAASFK 243.58 6.00E-46 3557200000 795370 734430 543340 565890 646550 737810 722180 780380 941520 792780 TRUE FALSE 764286.0611 713484.7755 641533.6245 595095.6507 667346.8679 752729.0237 731018.2549 764264.8803 834642.5968 739084.3045 1.034098622 0.965363181 0.868011431 0.805179662 0.90293741 1.018461655 0.989086428 1.034069964 1.129292818 1 19.49537941 2.686132349 4.379964571 1.034188647 0.908946029 0.447807046 0.066077436 0.220545281 9.087046621 0.023593296 0.022591028 485.4364116 -2.686132349 -0.125242617 S(ph)YSHDVLPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SYSHDVLPK 9 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.825)YS(0.175)HDVLPK;S(0.899)YS(0.1)HDVLPK;S(0.863)YS(0.137)HDVLPK 84.882 0.0097851 1100580000 4395670 4740410 3528600 4173540 3892810 4071630 3745240 4125110 4174420 4010390 TRUE FALSE 4223882.357 4605218.148 4166296.513 4388936.9 4018025.769 4153961.148 3791075.367 4039925.037 3700557.342 3738762.713 1.129754061 1.231749245 1.114351681 1.173900896 1.074693977 1.111052363 1.01399197 1.080551334 0.98978128 1 21.83412948 2.686288784 0.527388765 1.001575373 1.18755516 0.692817008 0.040710893 0.51392422 0.298759069 0.032809492 0.038996268 485.6112996 -2.686288784 0.185979787 KRPAS(ph)PSHNGSSGGGYGASK ddPTM_BT-474_Pertuzumab_2h_R1 2 KRPASPSHNGSSGGGYGASK 20 2 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 KRPAS(0.968)PS(0.032)HNGSSGGGYGASK;KRPAS(0.907)PS(0.084)HNGS(0.006)S(0.003)GGGYGASK 238.69 6.38E-30 675954000 845480 908840 776454 807555 849910 936130 920550 958640 1116970 1080070 TRUE FALSE 812437.7069 882920.773 916776.5099 849233.0103 877248.127 955059.19 931815.9663 938843.749 990176.2483 1006915.897 0.806857563 0.876856524 0.910479726 0.843400142 0.87122284 0.948499466 0.925415885 0.932395399 0.983375326 1 19.94151176 2.688399457 0.265897977 1.015789192 0.79999907 0.765184043 0.027997303 1.528243408 0.237542502 0.049406305 0.111198622 487.9771174 -2.688399457 -0.215790122 SHTCFNR ddPTM_BT-474_Pertuzumab_2h_R1 4 SHTCFNR 7 0 O00308-2;O00308;O00308-3;A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;Q9H0M0-3;Q9H0M0;Q9H0M0-6 O00308-2;A0A590UJQ1;Q9H0M0-3 WWP2;ITCH;WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP2;E3 ubiquitin-protein ligase Itchy homolog;NEDD4-like E3 ubiquitin-protein ligase WWP1 0 ;;; 117.93 0.0051196 412322000 343925 381933 326325 364858 325412 247182 376227 141746 327325 362333 FALSE TRUE 330484.0308 371040.6448 385299.1866 383688.3651 335879.1725 252180.1894 380831.3786 138818.8956 290168.4383 337791.8632 0.978365872 1.098429788 1.140640816 1.135872136 0.994337665 0.746554956 1.127414305 0.410959856 0.859015476 1 18.36577505 2.688525905 1.34545566 0.754444496 1.095665514 0.267649507 0.185506895 0.449441014 1.657655694 0.083623186 0.075652606 488.1192156 -2.688525905 0.341221018 S(ph)SIEDAQCPGLPDLIEENHVVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSIEDAQCPGLPDLIEENHVVNK 23 0 Q15398-1;Q15398;Q15398-3 Q15398-1 DLGAP5 Disks large-associated protein 5 1 S(0.5)S(0.5)IEDAQCPGLPDLIEENHVVNK 244.85 1.15E-37 261010000 112040 95101 98667 94287 94030 113140 131920 111900 120180 120760 TRUE FALSE 107661.3529 92388.81259 116498.3217 99153.16337 97054.56035 115427.7683 133534.4764 109589.2259 106537.6702 112580.8176 0.956302816 0.820644356 1.034797261 0.880728755 0.862087897 1.025288062 1.186121039 0.973427163 0.946321696 1 16.78060151 2.688550602 9.131907296 1.03386102 0.911145878 0.33796697 0.080352153 0.521125652 91.93793249 0.02614619 0.02468541 488.1469745 -2.688550602 -0.122715142 YGS(ph)FEEAEASYPILNR ddPTM_BT-474_Pertuzumab_2h_R1 4 YGSFEEAEASYPILNR 16 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR 376.16 1.46E-104 722910000 396847 359904 187891 315880 495819 327495 424779 560894 546932 479562 TRUE FALSE 381337.7805 349639.8903 221847.0833 332182.6047 511767.4684 334117.1733 429977.5725 549311.3429 484846.5723 447080.8386 0.852950401 0.782050717 0.496212461 0.743003448 1.144686652 0.74733056 0.961744578 1.228662236 1.084471824 1 18.77017619 2.688569846 0.864193322 1.114707518 0.715054895 0.432518515 0.158498627 0.539312242 0.853733711 0.105649055 0.09400633 488.1686048 -2.688569846 -0.399652623 LGVQVVITDPEKLDQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGVQVVITDPEKLDQIR 17 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 126.63 3.92E-05 1400810000 1774260 1772080 1633060 1692760 1786820 1914940 1974470 2094240 2326000 2355500 FALSE TRUE 1704919.958 1721542.013 1928190.269 1780123.546 1844294.688 1953661.399 1998634.154 2050993.212 2061962.231 2195959.887 0.77638939 0.783958771 0.87806261 0.81063573 0.839858095 0.889661697 0.910141468 0.933984826 0.938979917 1 21.06642027 2.688639894 0.286171199 1.013814764 0.735748465 0.888581363 0.023134029 0.801312054 0.140812704 0.035506278 0.07697964 488.2473496 -2.688639894 -0.278066299 KRS(ph)PPLGGAPS(ph)PSSLSLPPSTGFPLQASGVPSPYLSSLASSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRSPPLGGAPSPSSLSLPPSTGFPLQASGVPSPYLSSLASSR 42 2 I3NI13;I3L270;Q8NBZ0 I3NI13 INO80E INO80 complex subunit E 2 KRS(0.784)PPLGGAPS(0.593)PS(0.19)S(0.19)LS(0.226)LPPS(0.009)T(0.009)GFPLQASGVPSPYLSSLASSR 124.63 4.67E-09 216190000 89087 77521 65995 76045 73873 84570 89666 90662 92392 87656 TRUE FALSE 85605.38155 75310.17698 77921.76455 79969.69156 76249.19213 86280.06334 90763.35933 88789.79802 81904.0475 81718.98104 1.047558113 0.921575086 0.953533237 0.978593841 0.93306587 1.055814234 1.110676592 1.086526005 1.002264669 1 16.31838359 2.688770157 7.799599292 1.064072065 0.964309877 0.448537043 0.045513458 0.23224836 33.10924072 0.014367752 0.013584596 488.3938167 -2.688770157 -0.099762188 GRRPS(ph)GPDGAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GRRPSGPDGAAR 12 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C528 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR 95.236 0.0048516 127876000 170899 205863 120264 120722 139669 125395 86470 75107 72507 71028 TRUE FALSE 164220.0781 199991.9888 141998.3801 126952.4769 144161.5802 127930.5728 87528.24573 73556.0142 64276.30933 66217.21029 2.480021091 3.020241836 2.144433138 1.917212705 2.177101385 1.931983728 1.321835295 1.110829252 0.970688875 1 16.01491861 2.689525013 0.533990251 0.840834376 2.750968724 0.86644627 0.23892214 0.327295764 0.195322332 0.217335641 0.256009357 489.2434425 -2.689525013 1.910134347 up NQSPTEAEKPASSSLPS(ph)SPPPQLLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQSPTEAEKPAS(0.003)S(0.017)S(0.048)LPS(0.795)S(0.138)PPPQLLTR;NQSPTEAEKPAS(0.001)S(0.002)S(0.03)LPS(0.578)S(0.39)PPPQLLTR 161.13 1.06E-11 1125720000 947800 918040 830210 872660 954890 986780 982840 1086130 1248530 1099120 TRUE FALSE 910758.9282 891858.3981 980247.4149 917698.0872 985604.9041 1006733.368 994868.2899 1063701.036 1106802.109 1024675.623 0.888826578 0.870381199 0.956641685 0.895598633 0.961870158 0.982489819 0.970910469 1.038085626 1.080148765 1 19.96673584 2.690723612 0.691820369 1.044083601 0.889333922 0.756385156 0.031144194 0.337386344 0.343993125 0.022859325 0.022128931 490.5955585 -2.690723612 -0.154749679 GEAAAERPGEAAVASS(ph)PSKANGQENGHVK ddPTM_BT-474_Pertuzumab_2h_R1 6 GEAAAERPGEAAVASSPSKANGQENGHVK 29 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.169)S(0.831)PSKANGQENGHVK;GEAAAERPGEAAVAS(0.114)S(0.542)PS(0.344)KANGQENGHVK;GEAAAERPGEAAVAS(0.368)S(0.57)PS(0.062)KANGQENGHVK;GEAAAERPGEAAVAS(0.132)S(0.847)PS(0.021)KANGQENGHVK;GEAAAERPGEAAVAS(0.368)S(0.624)PS(0.008)KANGQENGHVK;GEAAAERPGEAAVAS(0.124)S(0.872)PS(0.004)KANGQENGHVK 240.26 1.11E-45 18372730000 5508400 5388340 4741300 4183800 5026570 5509130 5649460 6392740 6046090 5362230 TRUE FALSE 5293125.638 5234669.819 5598158.38 4399726.419 5188254.189 5620528.383 5718599.781 6260727.685 5359763.21 4999041.386 1.058828129 1.047134723 1.119846376 0.880114022 1.037849817 1.124321235 1.143939276 1.252385648 1.072158199 1 22.25322004 2.690966716 3.796705667 1.148333045 1.025943069 0.188040299 0.083891162 0.284779921 8.614748267 0.028021984 0.027029659 490.8702551 -2.690966716 -0.122389976 ENTHERSPSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENTHERSPSSPK 12 1 E7EV07;A0A1B0GW00 E7EV07 ARHGEF4 1 ENTHERS(0.005)PS(0.005)S(0.989)PK 75.045 0.091731 22647000 18902 18467 16319 18191 19535 17189 16528 18858 18798 23734 TRUE FALSE 18163.28894 17940.33924 19268.20631 19129.83969 20163.36102 17536.57336 16730.27461 18468.57571 16664.12985 22126.47504 0.820884886 0.810808735 0.870821325 0.864567883 0.911277598 0.792560646 0.756120194 0.834682238 0.7531308 1 14.43348601 2.691447023 24.9976856 0.812798197 0.854515664 0.018981455 0.070239412 1093.223972 580045.408 0.021301782 0.020083565 491.4134315 -2.691447023 0.041717468 YYLHDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 YYLHDDR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 155.51 0.0016062 3733900000 3673030 4414290 3408210 4017660 3578770 3642480 3192820 3337400 3687430 4152010 FALSE TRUE 3529483.927 4288398.771 4024149.362 4225011.914 3693884.387 3716133.441 3231894.686 3268481.524 3268848.405 3870790.664 0.911825059 1.10788703 1.039619476 1.091511342 0.954297121 0.960045056 0.834944322 0.844396354 0.844491136 1 21.88419686 2.691847455 1.782000311 0.866299489 1.039779155 0.465336421 0.070055493 0.25558947 1.614781908 0.02591528 0.024475103 491.8667387 -2.691847455 0.173479667 QQLPQT(ph)PPSCLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQLPQTPPSCLK 12 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 QQLPQT(0.998)PPS(0.002)CLK 171.08 0.00044062 103600000 195920 184100 172680 175560 182240 190700 203300 213280 183120 200990 TRUE FALSE 188263.2298 178849.6483 203887.1172 184620.6726 188101.9151 194556.0847 205788.0462 208875.6935 162332.9853 187376.7683 1.004730904 0.954492117 1.088113106 0.985291156 1.003869993 1.038314869 1.098258061 1.114736343 0.866345315 1 17.51558257 2.692068343 5.942247103 1.043985524 1.007627689 0 0.071612907 0.725972279 64.92152968 0.023428109 0.022291696 492.1169716 -2.692068343 -0.036357835 KLAT(ph)PPAAQESSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLATPPAAQESSR 13 1 H0Y760;Q9Y4B4 H0Y760 RAD54L2 Helicase ARIP4 1 KLAT(0.992)PPAAQES(0.004)S(0.004)R 59.372 0.05854 513120000 388520 338780 312860 402380 406660 403990 489680 519810 590100 544200 TRUE FALSE 373336.2089 329118.3261 369400.7615 423146.88 419740.5882 412158.9546 495672.8503 509075.7418 523114.3219 507340.8493 0.735868617 0.648712452 0.728111608 0.834048511 0.827334501 0.812390635 0.977001657 1.00341958 1.031090484 1 18.9525958 2.692397671 0.644923889 1.039488581 0.686695493 0.888087334 0.042917252 0.237539512 0.20999755 0.034841824 0.035274437 492.4902886 -2.692397671 -0.352793088 GGS(ph)PYNQFDIIPGDTLGGHTGPAGDSWLPAKS(ph)PPTNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSPYNQFDIIPGDTLGGHTGPAGDSWLPAKSPPTNK 37 1 Q9UPQ9-1;Q9UPQ9;H0Y720;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 2 GGS(0.972)PY(0.028)NQFDIIPGDTLGGHTGPAGDS(0.078)WLPAKS(0.844)PPT(0.077)NK 111.04 1.82E-05 67658000 165890 166260 139150 111390 128030 160700 157240 159860 191650 181290 TRUE FALSE 159406.8354 161518.4276 164297.5004 117138.8512 132148.2012 163949.4641 159164.3502 156558.8351 169894.6955 169011.0668 0.943173949 0.95566776 0.972110901 0.693083911 0.781890818 0.970051649 0.941739219 0.92632298 1.005228229 1 17.36675819 2.692781683 24.82811704 0.958802393 0.869924623 0.264306181 0.082162761 685.5436141 371802.4601 0.02930855 0.027632463 492.9259515 -2.692781683 -0.088877771 EELGFRPEYSASQLK ddPTM_BT-474_Pertuzumab_2h_R1 3 EELGFRPEYSASQLK 15 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 168.5 1.14E-06 1402850000 775290 767030 745020 839220 992670 924730 1188060 1326120 1306410 1495630 FALSE TRUE 744990.8097 745155.0554 879661.6869 882532.2448 1024600.132 943428.6742 1202599.834 1298735.159 1158111.814 1394329.648 0.534300343 0.534418139 0.630885019 0.632943756 0.734833498 0.676618098 0.862493196 0.931440539 0.83058681 1 20.41114025 2.693526296 0.425696045 0.997018244 0.483335493 0.904035114 0.047926014 0.361640004 0.13445581 0.048476046 0.072555949 493.7718145 -2.693526296 -0.513682751 DIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_BT-474_Pertuzumab_2h_R1 9 DIDHETVVEEQIIGENSPPDYSEYMTGK 28 0 P25490;A0A494C032;H0YJV7;H0YJU4 P25490 YY1 Transcriptional repressor protein YY1 1 DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHET(0.002)VVEEQIIGENS(0.869)PPDY(0.092)S(0.017)EY(0.018)MT(0.004)GK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(0.989)PPDY(0.011)SEYMTGK;DIDHETVVEEQIIGENS(0.844)PPDY(0.138)S(0.005)EY(0.006)MT(0.007)GK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK 316.65 4.62E-83 3749154000 893659.4 835125.9 774180.2 801533.9 856794.6 818187.4 806609.9 886933.4 932542.9 883815.7 TRUE FALSE 858734.2027 811308.927 914091.7837 842901.1606 884354.1764 834731.7098 816481.4332 868617.9153 826684.5395 823954.0754 1.042211245 0.984653091 1.10939652 1.022995317 1.073305179 1.013080382 0.990930754 1.05420671 1.003313855 1 19.6522044 2.694407076 24.95067995 1.017028215 1.045262743 0.194296189 0.034110332 885.6660746 500478.8773 0.010781202 0.010164695 494.7742355 -2.694407076 0.028234528 RS(ph)SSEGLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSSEGLSK 9 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 RS(0.646)S(0.351)S(0.002)EGLSK 94.688 0.0052388 344160000 291980 288490 247530 292860 289020 291470 300560 336340 375250 342790 TRUE FALSE 280569.0988 280262.5477 292264.1773 307974.5397 298316.5908 297363.7231 304238.3432 329394.4615 332653.1932 319572.528 0.877951245 0.876991991 0.914547252 0.963707806 0.933486344 0.930504649 0.952016574 1.030734599 1.040931757 1 18.28578387 2.694464602 0.494311307 1.03238861 0.87567878 0.762712286 0.026621076 0.538307247 0.273138536 0.026735201 0.034131593 494.8397762 -2.694464602 -0.15670983 GS(ph)LDESSLGFGYPK ddPTM_BT-474_Pertuzumab_2h_R1 5 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK 241.42 2.04E-17 3566015000 1577890 1658875 1249464 1542003 1527847 1723470 1733396 1885580 1964880 1992530 TRUE FALSE 1516224.314 1611565.509 1475269.939 1621585.96 1576991.586 1758319.744 1754609.819 1846642.114 1741835.06 1857574.168 0.81623891 0.867564556 0.794191674 0.872958931 0.848952151 0.946567719 0.944570531 0.994114876 0.937693412 1 20.82498838 2.694943036 1.429351641 0.975231744 0.833056912 0.838905583 0.027510901 0.141435737 0.585354302 0.01107522 0.010174024 495.3852097 -2.694943036 -0.142174833 WCEWTVLTGIEYLQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 WCEWTVLTGIEYLQQR 16 0 O60290-2 O60290-2 0 65.092 0.033725 15863000 2870.6 1318.4 1238.6 2221.3 2398.2 1420.3 1534.8 1708.1 768.08 2514.8 FALSE TRUE 2758.413778 1280.800523 1462.442573 2335.941559 2475.340281 1449.019439 1553.583342 1672.827138 680.8907785 2344.470356 1.176561594 0.546306981 0.623783776 0.996362165 1.055820678 0.618058333 0.662658556 0.713520277 0.290424136 1 11.19504632 2.695963898 24.91509447 0.646209525 0.853497829 0.173999341 0.238787457 889.7296183 520407.6942 0.076352646 0.071986462 496.5510427 -2.695963898 0.207288304 LPS(ph)QENELLENPSVVLSTNSPAALK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSQENELLENPSVVLSTNSPAALK 25 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 LPS(1)QENELLENPSVVLSTNSPAALK 172.42 3.78E-12 33886000 23909 24281 13118 18953 26514 23556 27218 32306 30679 31973 TRUE FALSE 22974.60985 23588.52965 15488.71441 19931.1666 27366.84689 24032.31846 27551.10203 31638.86981 27196.44854 29807.44023 0.770767623 0.791363816 0.519625781 0.668664147 0.918121337 0.806252341 0.924302852 1.061442028 0.912404699 1 14.86338487 2.696965614 1.125095183 0.994216984 0.68958897 0.619315693 0.09424278 0.319191379 0.838785097 0.050913618 0.045355508 497.6976777 -2.696965614 -0.304628015 KVDSSVLGSLSSVPLTGFSFS(ph)PGNSSLFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVDSSVLGSLSSVPLTGFSFSPGNSSLFGK 30 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 1 KVDSSVLGSLSSVPLTGFS(0.001)FS(0.998)PGNSS(0.001)LFGK;KVDSSVLGSLSSVPLTGFS(0.018)FS(0.977)PGNS(0.004)S(0.001)LFGK 192.06 9.92E-19 983240000 1133280 1080180 1028730 964660 941140 1167510 1180560 1223160 1227500 1311190 TRUE FALSE 1088990.165 1049374.324 1214644.395 1014446.218 971412.6228 1191117.852 1195008.046 1197901.319 1088159.346 1222381.933 0.89087554 0.858466814 0.993670114 0.829893007 0.794688302 0.974423639 0.97760611 0.979973023 0.890195868 1 20.2212637 2.697071594 24.75977859 0.965718786 0.876933925 0.403612651 0.055171656 477.5036417 284963.6512 0.018178083 0.01713865 497.8191439 -2.697071594 -0.088784861 GIPHLVTHDAR ddPTM_BT-474_Pertuzumab_2h_R1 6 GIPHLVTHDAR 11 0 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 ;;;;; 159.83 1.80E-05 7800580000 4135660 4463080 4159270 4140060 3895310 3060140 4339410 1889074 3904920 4164750 FALSE TRUE 3974033.835 4335797.328 4910942.611 4353728.993 4020606.184 3122018.127 4392516.998 1850063.962 3461649.852 3882667.773 1.023531774 1.116705724 1.264837194 1.121324112 1.03552671 0.804090978 1.131314152 0.476492986 0.891564783 1 21.88861684 2.697189653 1.267962902 0.787021441 1.143721245 0.333526612 0.171230131 0.419915826 1.384281152 0.080331777 0.07262383 497.9544906 -2.697189653 0.356699804 MQFS(ph)FEGPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 MQFSFEGPEK 10 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK 154.23 1.56E-05 1693180000 1842040 1773640 1026720 1551800 2002400 1560510 1984030 2339670 2124360 2074420 TRUE FALSE 1770051.04 1723057.524 1212271.143 1631888.584 2066809.015 1592064.581 2008311.153 2291354.997 1883211.559 1933917.686 0.915267001 0.890967354 0.626847333 0.843825255 1.068716125 0.823232857 1.038467753 1.184825504 0.973780618 1 20.88309496 2.697803404 1.050797406 1.074421142 0.819319505 0.360773217 0.117175691 0.503963486 1.163225077 0.066312252 0.058849313 498.6587044 -2.697803404 -0.255101637 FRGTEPEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 FRGTEPEPR 9 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 91.087 0.010023 258620000 355260 370440 270690 360540 304010 372210 366340 413160 364200 359970 FALSE TRUE 341376.0464 359875.4139 319609.7045 379147.5126 313788.7577 379736.3412 370823.3785 404628.1016 322857.5429 335588.9113 1.017244715 1.072369801 0.95238458 1.129797499 0.935039112 1.131552112 1.104992942 1.205725481 0.962062607 1 18.35633552 2.697914988 24.96306659 1.104711259 1.026392071 0.078594795 0.083036295 859.3573868 527784.8889 0.025604357 0.024140359 498.7868415 -2.697914988 -0.078319188 CPT(ph)PEIQKK ddPTM_BT-474_Pertuzumab_2h_R1 2 CPTPEIQKK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 CPT(1)PEIQKK;CPT(1)PEIQKK 101.6 0.0022717 1305420000 2042690 2012300 1384310 1428490 1628240 1957010 1910150 2032900 2468400 2219300 TRUE FALSE 1962859.416 1954911.174 1634485.611 1502214.54 1680613.818 1996582.083 1933526.987 1990919.905 2188197.58 2068984.834 0.948706527 0.944864912 0.789994003 0.726063582 0.812289095 0.965005664 0.934529318 0.96226897 1.057618956 1 20.98049164 2.698016154 7.078959976 0.976357958 0.840402079 0.500145619 0.069479098 0.235785354 34.30738243 0.025076852 0.023829999 498.9030444 -2.698016154 -0.135955879 VLKGDVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLKGDVEK 8 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 70.399 0.046907 2395100000 3867400 4021800 3095200 3275700 3269000 3853300 3755400 3998900 4474900 4274200 FALSE TRUE 3716257.732 3907102.202 3654571.492 3444759.27 3374150.354 3931216.366 3801359.709 3916321.318 3966928.112 3984704.627 0.932630667 0.980524924 0.917149911 0.864495513 0.846775525 0.986576606 0.953987827 0.98283855 0.995538812 1 21.92604136 2.698131992 24.84803238 0.980272437 0.910383311 0.521851038 0.036016202 468.5422172 287972.5905 0.013008198 0.01226438 499.0361332 -2.698131992 -0.069889126 LIKDDIER ddPTM_BT-474_Pertuzumab_2h_R1 5 LIKDDIER 8 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;H3BNL6;Q6P474;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 0 ;;;; 132.01 0.00089427 4136200000 7805940 8063460 6677900 7436060 8043200 8005550 8696500 9474000 9265600 9551200 FALSE TRUE 7500875.235 7833498.016 7884745.079 7819835.948 8301916.833 8167427.706 8802930.368 9278358.589 8213807.933 8904288.717 0.842389041 0.879744387 0.88549971 0.878210062 0.932350365 0.917246505 0.988616907 1.042010079 0.922455257 1 23.08606894 2.700955893 1.071591398 0.999332577 0.869029266 0.702057411 0.032731317 0.262588841 0.629374994 0.017697609 0.01577292 502.291574 -2.700955893 -0.130303311 LEQTSVRDPS(ph)PEADAPVLGS(ph)PEKEEAASEPPAAAPDAAPPPPDRPIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEQTSVRDPSPEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK 48 3 O15234 O15234 CASC3 Protein CASC3 2 LEQT(0.028)S(0.03)VRDPS(0.942)PEADAPVLGS(0.997)PEKEEAAS(0.003)EPPAAAPDAAPPPPDRPIEK 83.156 1.35E-05 121440000 86528 78872 79178 75720 91778 90156 95754 110590 113980 105020 TRUE FALSE 83146.3901 76622.64778 93487.22591 79627.91827 94730.12272 91979.01609 96925.8661 108306.2779 101041.4682 97906.90186 0.849239313 0.782607215 0.954858382 0.8133024 0.967553062 0.939453852 0.989979912 1.106216986 1.032015786 1 16.57912294 2.701056632 0.906693605 1.057712584 0.842620151 0.668354361 0.055270557 0.306755237 0.534241047 0.032687219 0.029257794 502.4080989 -2.701056632 -0.215092433 AT(ph)TPPNQGRPDS(ph)PVYANLQELK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 2 AT(0.501)T(0.499)PPNQGRPDS(0.974)PVY(0.026)ANLQELK 75.703 0.026814 1296400000 265570 254480 210310 233030 240490 272640 297270 285440 310220 290260 TRUE FALSE 255191.2308 247222.4796 248317.6953 245056.7062 248225.5793 278152.9676 300908.0792 279545.5643 275005.1261 270600.4317 0.94305552 0.913607115 0.917654469 0.90560353 0.917314055 1.027910288 1.112001475 1.033056609 1.016277485 1 18.04580462 2.702323967 4.707542165 1.046869961 0.91781462 0.80435865 0.029124532 0.080901822 4.426168174 0.009446801 0.00911764 503.876341 -2.702323967 -0.129055341 (ac)ALNGAEVDDFSWEPPTEAETK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALNGAEVDDFSWEPPTEAETK 21 0 O60232;E9PK41 O60232 SSSCA1 Sjoegren syndrome/scleroderma autoantigen 1 0 42.958 4.28E-07 29339000 111730 111780 98063 107010 109450 126260 124250 134140 149960 141460 FALSE TRUE 107363.4681 108592.1438 115785.1655 112532.7989 112970.5586 128813.0637 125770.6087 131369.9621 132937.1695 131878.7882 0.814107178 0.823423883 0.877966556 0.853304769 0.856624179 0.976753468 0.953683381 0.996141714 1.00802541 1 17.00885301 2.702391556 1.067974264 1.001142466 0.833307641 0.910699839 0.02214451 0.137689977 0.327966179 0.011935447 0.010651377 503.9547654 -2.702391556 -0.167834825 AVVS(ph)PPKFVFGSESVK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVVSPPKFVFGSESVK 16 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 AVVS(1)PPKFVFGSESVK 108.92 0.00061348 838870000 500580 375530 398530 397740 497840 549950 438790 519730 706080 596910 TRUE FALSE 481016.7802 364820.2521 470553.2363 418267.4091 513853.4757 561070.3658 444160.0433 508997.3939 625928.7585 556480.754 0.864390685 0.655584671 0.84558762 0.751629605 0.923398468 1.008247566 0.798158858 0.914672053 1.124798574 1 19.08597227 2.702588762 0.446200586 1.02318219 0.735879539 0.462001193 0.095092665 1.16283412 0.47575526 0.092468388 0.132440815 504.183655 -2.702588762 -0.287302651 TKADVTPPPDGS(ph)TTHNLEVSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKADVTPPPDGSTTHNLEVSPK 22 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 T(0.002)KADVT(0.055)PPPDGS(0.308)T(0.308)T(0.308)HNLEVS(0.019)PK 153.84 1.87E-08 590920000 194110 166170 162550 146240 155660 179570 173160 186840 215230 191400 TRUE FALSE 186523.9666 161430.9943 191926.4009 153787.4639 160666.9453 183201.0284 175279.1839 182981.6887 190797.9927 178436.3075 1.045325187 0.904698133 1.075601729 0.86186195 0.900416219 1.026702642 0.982306719 1.02547341 1.069277858 1 17.44504967 2.703405151 24.50147876 1.019356987 0.955881733 0.194564856 0.064187066 799.9320336 557508.8791 0.020362593 0.019198916 505.1323128 -2.703405151 -0.063475254 GFGS(ph)VEELCTNSSLGMEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGSVEELCTNSSLGMEK 18 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 GFGS(1)VEELCTNSSLGMEK;GFGS(1)VEELCTNSSLGMEK 304.2 7.95E-50 191385000 240210 268730 208605 234250 244520 266250 273720 296550 288760 305370 TRUE FALSE 230822.3276 261066.0835 246304.5639 246339.6706 252385.2079 271633.7574 277069.8672 290426.1389 255981.1754 284687.0179 0.810793303 0.91702841 0.865176662 0.865299979 0.886535711 0.954148733 0.973243772 1.020159405 0.899167012 1 18.11901718 2.70431627 2.311013568 0.979334261 0.868234147 0.642795961 0.037758225 0.184184842 1.940803165 0.013040478 0.01266987 506.1931568 -2.70431627 -0.111100114 TKQEVEISR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKQEVEISR 9 1 Q14694;Q14694-3;Q14694-2;H3BQP1 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 0 64.918 0.062044 301410000 267770 365420 231170 371300 436160 452410 375630 1026500 321160 462460 FALSE TRUE 257305.2524 354998.5794 272947.5613 390462.8375 450189.4825 461558.0402 380227.0723 1005302.416 284703.2632 431137.1723 0.596806003 0.823400537 0.633087516 0.905658019 1.044190832 1.070559603 0.8819167 2.331746091 0.660354248 1 18.71778743 2.70466933 1.095455159 1.42341436 0.720281987 0.159464274 0.434569265 0.631388868 1.578664516 0.230281923 0.206322799 506.6048341 -2.70466933 -0.703132373 FDLNKPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FDLNKPVR 8 1 Q9P2R3;Q9P2R3-2;Q9P2R3-4 Q9P2R3 ANKFY1 Rabankyrin-5 0 74.376 0.034794 0 323570 355680 290490 280140 320500 387410 394790 433990 429420 453350 FALSE TRUE 310924.5267 345536.3546 342988.0049 294598.059 330809.1736 395243.6956 399621.5581 425027.9548 380674.0419 422644.2007 0.735664954 0.81755849 0.811528951 0.697035612 0.78271315 0.935168861 0.94552713 1.005640097 0.900696239 1 18.68908413 2.704685187 3.529990627 0.964587914 0.768195643 0.83381225 0.042262037 0.093136841 2.447381255 0.014204522 0.013849643 506.6233326 -2.704685187 -0.19639227 SGEKPEADRNPPVLYHNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGEKPEADRNPPVLYHNSR 19 2 Q8ND04;Q8ND04-2;J3KTD7 Q8ND04 SMG8 Protein SMG8 0 130.09 1.10E-05 386390000 163970 213520 162910 193930 163160 207450 201670 209360 195300 220280 FALSE TRUE 157561.8711 207430.6187 192351.4609 203938.7505 168408.1896 211644.7811 204138.0978 205036.6428 173130.3628 205360.2394 0.767246238 1.010081695 0.93665386 0.993078072 0.820062297 1.030602524 0.994048791 0.998424249 0.84305688 1 17.64779736 2.704965257 24.95884242 0.97697394 0.917843258 0.13397059 0.082978496 1425.119832 1058756.66 0.025871492 0.024393235 506.9501508 -2.704965257 -0.059130681 DVDKFGNEITQLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVDKFGNEITQLAR 14 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ; 169.37 3.05E-06 773540000 837090 787080 674350 800120 824550 820170 909910 974740 1031380 983760 FALSE TRUE 804375.5973 764633.249 796220.0458 841414.2891 851072.3996 836754.3993 921045.7508 954611.2784 914302.0663 917129.059 0.877058239 0.833724808 0.868165759 0.917443713 0.927974521 0.91236276 1.0042706 1.040869078 0.996917563 1 19.80676524 2.70540331 0.810638354 1.025662624 0.857140413 0.848138881 0.025534106 0.225434719 0.316159414 0.01802562 0.016580852 507.4617472 -2.70540331 -0.168522212 LQKEEEIEFLYNENTVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LQKEEEIEFLYNENTVR 17 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 221.37 3.38E-15 1534050000 1129080 1180380 930580 917420 1053720 1134460 1170200 1208010 1341910 1217450 FALSE TRUE 1084954.305 1146716.718 1098756.507 964768.1561 1087613.861 1157399.558 1184521.258 1183064.171 1189582.003 1134991.027 0.955914434 1.010331087 0.96807506 0.850022717 0.958257673 1.019743356 1.043639315 1.042355528 1.048098156 1 20.11424946 2.705774724 3.831932334 1.036755905 0.946930617 0.52238884 0.039479669 0.191156686 6.153362656 0.01395805 0.013594743 507.8959193 -2.705774724 -0.089825288 ITEAEKNER ddPTM_BT-474_Pertuzumab_2h_R1 4 ITEAEKNER 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 198.25 2.43E-05 5458470000 4807850 4772890 3401620 3672020 3879990 4399200 4218540 4731120 4933150 4533130 FALSE TRUE 4619953.907 4636771.85 4016368.403 3861533.392 4004793.402 4488154.838 4270167.754 4633420.719 4373159.493 4226097.067 1.093196354 1.097175899 0.950372966 0.913735139 0.947634032 1.062009406 1.010428224 1.096382938 1.034798639 1 22.01089447 2.705813568 24.92720078 1.048192077 0.998201491 0.091637075 0.061024919 1448.157631 1102342.204 0.021874177 0.020624366 507.9413491 -2.705813568 -0.049990586 LSSWDQAETPGHT(ph)PSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LSSWDQAETPGHT(1)PSLR;LSSWDQAET(0.001)PGHT(0.999)PSLR 193.64 4.38E-10 738850000 316520 342360 338720 347010 335890 309710 276230 335170 327270 334960 TRUE FALSE 304150.0485 332596.228 399934.2388 364919.2277 346694.2069 315972.5484 279610.5854 328248.6224 290119.6816 312272.8608 0.973988094 1.06508208 1.28072045 1.168590913 1.110228426 1.011847612 0.895404694 1.051159622 0.929058263 1 18.25244767 2.705934564 3.568061267 0.976668288 1.130000312 0.429666157 0.082518891 0.240731124 6.5031868 0.028835337 0.028133279 508.082883 -2.705934564 0.153332024 LKEAETR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEAETR 7 1 P06753-2;P06753-6;P06753-5;P06753-7;A0A494C034;A0A2R8Y6A3;A0A494C0I0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 123.72 0.0038452 1593500000 2282900 2395100 1844700 2158700 2167400 2380200 2358300 2657100 2622500 2505300 FALSE TRUE 2193681.744 2326794.093 2178078.325 2270110.766 2237116.389 2428329.275 2387161.581 2602229.956 2324804.794 2335613.8 0.939231368 0.996223816 0.932550718 0.971954681 0.957828041 1.039696407 1.022070336 1.114152501 0.995372092 1 21.15537031 2.706064654 4.28368984 1.047322168 0.960365971 0.507451119 0.035676272 0.153587853 6.62366295 0.011571907 0.011236796 508.2350991 -2.706064654 -0.086956196 DGLIPLEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLIPLEIR 9 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 78.334 0.069943 143008000 222510 236720 196451 203504 226160 184066 160243 203393 206990 206780 FALSE TRUE 213814.0632 229968.9774 231954.0657 214006.8658 233434.6418 187787.9406 162204.1018 199192.8635 183493.363 192774.6064 1.109140188 1.192942274 1.203239732 1.110140333 1.21092008 0.974132144 0.841418405 1.0332941 0.951854429 1 17.5565555 2.706198044 8.520548563 0.957884605 1.165840142 0.767873037 0.056389325 0.152225062 37.58374818 0.01777712 0.016904357 508.3912229 -2.706198044 0.207955537 MRDLS(ph)S(ph)S(ph)EKQEHVKLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 MRDLSSSEKQEHVKLQK 17 3 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 3 MRDLS(1)S(1)S(1)EKQEHVKLQK 45.33 0.076132 182760000 27057 34703 26591 26889 27870 36189 38016 37582 42723 40691 TRUE FALSE 25999.58253 33713.30442 31396.58521 28276.74451 28766.46386 36920.76638 38481.25118 36805.91857 37873.26415 37934.96233 0.685372567 0.88871327 0.827642451 0.745400622 0.758310068 0.973264875 1.014400669 0.970237383 0.99837358 1 15.21124048 2.7062295 6.965146765 0.990452926 0.787635222 0.807318103 0.051295583 0.093915496 15.83634678 0.016500185 0.015768821 508.4280469 -2.7062295 -0.202817703 FAS(ph)AENIPDLPYDYSSSLESVADETSPER ddPTM_BT-474_Pertuzumab_2h_R1 1 FASAENIPDLPYDYSSSLESVADETSPER 29 0 P50747 P50747 HLCS Biotin--protein ligase;Biotin--[methylmalonyl-CoA-carboxytransferase] ligase;Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase;Biotin--[methylcrotonoyl-CoA-carboxylase] ligase;Biotin--[acetyl-CoA-carboxylase] ligase 1 FAS(1)AENIPDLPYDYSSSLESVADETSPER 164.65 3.26E-12 43606000 72104 76240 63261 67148 72753 77231 75131 89901 85763 79595 TRUE FALSE 69286.09596 74065.70985 74693.66993 70613.51633 75093.16632 78792.66374 76050.47565 88044.51293 76027.54379 74203.95975 0.933725049 0.998136893 1.006599515 0.951613857 1.011983276 1.061839072 1.024884331 1.186520412 1.024575293 1 16.17920856 2.706277449 1.627257279 1.085248124 0.976058901 0.334704799 0.053340562 0.34897579 1.849943988 0.0215596 0.020369279 508.484184 -2.706277449 -0.109189223 FKPLSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKPLSDK 7 1 P35249;C9J8M3;C9JZI1;P35249-2 P35249 RFC4 Replication factor C subunit 4 0 64.265 0.067901 617540000 598630 765500 448740 682830 881390 826590 1099900 1111800 1310500 1254600 FALSE TRUE 575234.8778 743668.6895 529837.3002 718070.9381 909740.7098 843304.2161 1113360.905 1088840.941 1161737.534 1169624.825 0.491811447 0.635818148 0.452997653 0.61393271 0.777805576 0.721004033 0.951895755 0.930931799 0.993256564 1 20.15761441 2.706327831 0.775477301 1.001240494 0.517707403 0.893871904 0.063732323 0.187566608 0.241116047 0.042148671 0.03936661 508.5431759 -2.706327831 -0.483533091 SFGWETLDSFMQHDVQELCR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFGWETLDSFMQHDVQELCR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 269.85 1.16E-37 357620000 215060 223810 162840 214190 233740 182130 211280 198580 226000 214020 FALSE TRUE 206655.2174 217427.1579 192268.8104 225244.3716 241258.4594 185812.7934 213865.7078 194479.2536 200345.4275 199524.2348 1.035739932 1.089728063 0.963636375 1.128907332 1.209168699 0.931279319 1.071878351 0.974714945 1.004115754 1 17.60620447 2.706385252 24.99992738 0.999476125 1.081323028 0.303714068 0.067182749 928.7864275 721656.6259 0.021995974 0.020739305 508.610418 -2.706385252 0.081846903 S(ph)LSGSSPCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.998)LS(0.002)GSSPCPK 110.86 0.0025725 0 112680 143880 92629 126890 103970 135620 135080 132940 157110 134740 TRUE FALSE 108276.341 139776.6833 109369.1208 133438.8081 107314.2895 138362.3293 136733.1494 130194.7425 139275.5315 125613.9398 0.861977112 1.112748183 0.870676622 1.062292993 0.854318316 1.101488653 1.088518915 1.036467312 1.108758564 1 16.93863705 2.707386314 24.99808079 1.068313728 0.96287538 0.310776489 0.084638649 837.740315 671767.1461 0.024868969 0.023448593 509.784133 -2.707386314 -0.105438348 KDS(ph)PHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDSPHSR 7 1 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 KDS(0.86)PHS(0.14)R;KDS(0.836)PHS(0.164)R 89.9 0.010739 271290000 212093 212740 184740 180317 201454 213320 239400 214050 234990 254690 TRUE FALSE 203804.1711 206672.8635 218126.6275 189623.182 207933.9509 217633.4766 242329.8488 209629.7927 208314.9204 237439.6194 0.858341045 0.870422822 0.91866146 0.798616433 0.875734013 0.916584507 1.020595676 0.882876216 0.877338503 1 17.85720116 2.707504917 4.072253768 0.936142899 0.863500191 0.364139521 0.050062003 0.270644184 10.24469246 0.016564863 0.01612772 509.9233709 -2.707504917 -0.072642708 TMDILASLATSVDKGECLGGSTLSLLHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TMDILASLATSVDKGECLGGSTLSLLHDR 29 1 F2Z2B9;Q9BSJ2-3;Q9BSJ2;Q9BSJ2-4 F2Z2B9 TUBGCP2 Gamma-tubulin complex component 2 0 236.79 1.67E-45 57594000 61290 57158 41431 56672 44322 61786 54663 53245 70273 64415 FALSE TRUE 58894.71904 55527.9098 48918.50333 59596.84871 45747.65738 63035.35525 55331.98215 52145.47214 62295.90365 60052.11468 0.980726813 0.924662022 0.814600844 0.992418819 0.761799274 1.049677527 0.921399395 0.868336984 1.037364029 1 15.87392743 2.707710377 24.9996234 0.95462638 0.897461287 0.170038067 0.082733857 1641.734111 1330384.462 0.026233014 0.024734829 510.1646671 -2.707710377 -0.057165094 HEDGEFWMSFSDFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEDGEFWMSFSDFLR 15 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 84.753 0.0082066 52355000 46192 47523 37511 49996 54734 37566 47815 31657 50300 48310 FALSE TRUE 44386.76557 46167.69057 44290.07213 52576.29955 56494.56882 38325.61026 48400.17427 31003.27189 44590.15487 45037.92067 0.98554207 1.025084859 0.983395136 1.167378484 1.254377822 0.850963137 1.074653837 0.688381511 0.990058027 1 15.4588526 2.707723957 24.99613301 0.896950211 1.079066357 0.287761298 0.124831714 810.2586285 656793.1557 0.041300755 0.038942379 510.1806194 -2.707723957 0.182116146 (ac)MNVDHEVNLLVEEIHR ddPTM_BT-474_Pertuzumab_2h_R1 16 MNVDHEVNLLVEEIHR 16 0 Q9P1F3;Q5SZC9 Q9P1F3 ABRACL Costars family protein ABRACL 0 ;;;;;;;;;;;;;;; 134.25 2.34E-35 6929238000 106001.2 93114.24 96085.7 89617.47 112089.36 85420.66 93714.91 99583.03 109505.5 104445.9 FALSE TRUE 101858.5559 90458.71304 113450.5234 94242.63837 115694.8161 87147.92427 94861.8211 97526.60563 97074.89472 97371.68616 1.04607982 0.929004278 1.165128467 0.967864911 1.188177186 0.895002723 0.974223872 1.001591011 0.996951974 1 16.5712147 2.707913038 24.99940956 0.976034579 1.052820176 0.226856646 0.078589026 1125.71568 918251.8435 0.024086048 0.022711726 510.4027884 -2.707913038 0.076785597 TIFGSIPDIFDVHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIFGSIPDIFDVHTK 15 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 0 ; 192.65 1.25E-07 191186000 190966 198373 156164 180986 172938 193210 214355 195511 193437 205629 FALSE TRUE 183502.8376 192715.5963 184386.3086 190326.7091 178500.7078 197116.8386 216978.3406 191473.6295 171478.8427 191701.5647 0.95723182 1.005289636 0.961840395 0.992828147 0.931138502 1.02824846 1.131854823 0.99881099 0.894509354 1 17.54850259 2.708095942 24.46019308 1.019726705 0.97249686 0.103074108 0.057181426 1119.134569 898555.2845 0.019199883 0.018103688 510.6177905 -2.708095942 -0.047229846 GVAINMVTEEDKR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVAINMVTEEDKR 13 1 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;; 240.18 1.24E-16 3412680000 2196150 2089380 2002800 2313550 2320170 2440100 2615570 2850440 3305210 3348310 FALSE TRUE 2110322.03 2029792.928 2364750.512 2432952.593 2394800.375 2489440.494 2647580.128 2791577.418 2930016.417 3121525.981 0.67605461 0.650256618 0.757562335 0.77941129 0.767188993 0.797507536 0.848168538 0.894298953 0.938648736 1 21.57382004 2.70824452 0.278110772 1.02814279 0.583642001 0.949129521 0.023691756 0.57978753 0.096026437 0.03939487 0.088047408 510.7925096 -2.70824452 -0.44450079 TLTLVDTGIGMTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLTLVDTGIGMTK 13 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 115.92 0.0014566 45882000 119030 151350 93117 104470 97123 136220 125600 139570 142520 138280 FALSE TRUE 114378.176 147033.6462 109945.3133 109861.7092 100247.0495 138974.4617 127137.1304 136687.8307 126341.7271 128914.1724 0.887242836 1.140554552 0.852856681 0.852208156 0.777626289 1.07803866 0.986215309 1.060301037 0.980045287 1 16.97605135 2.70932149 24.99531973 1.024659801 0.909838006 0.28886554 0.092728009 1007.427679 861207.2035 0.031226162 0.029444451 512.0607522 -2.70932149 -0.114821795 WHHEYQTR ddPTM_BT-474_Pertuzumab_2h_R1 1 WHHEYQTR 8 0 A0A494C1L5;P50851-2;P50851;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 70.856 0.050248 23638000 62135 71814 66711 57533 66981 39830 66031 29465 53761 57819 FALSE TRUE 59706.69551 69765.93503 78767.16168 60502.28502 69135.5047 40635.38989 66839.10713 28856.53745 47658.27666 53902.86763 1.107671969 1.294289861 1.461279615 1.122431657 1.282594187 0.75386323 1.239991675 0.535343271 0.884151044 1 15.71807441 2.709354316 1.323768572 0.824141493 1.282349259 0.424527388 0.201689479 0.35892479 1.284573727 0.088452734 0.081396688 512.0994581 -2.709354316 0.458207766 KMANSS(ph)PVLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KMANSSPVLSK 11 1 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 KMANS(0.02)S(0.98)PVLSK;KMANS(0.104)S(0.896)PVLSK 130.29 0.00013913 2061500000 4512650 4343340 3180170 3182120 3475740 4095170 4058370 4271970 4550890 4263660 TRUE FALSE 4336290.649 4219472.196 3754897.461 3346349.595 3587540.334 4177977.143 4108037.546 4183752.327 4034292.046 3974878.511 1.090924072 1.061534883 0.944657164 0.841874685 0.902553455 1.051095557 1.033500152 1.052548478 1.014947258 1 21.92247934 2.710164081 24.67557566 1.03543866 0.965149959 0.168082416 0.068455602 1153.91782 1002711.722 0.024948476 0.023526132 513.055185 -2.710164081 -0.070288701 SYQNSPSS(ph)DDGIRPLPEYSTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SYQNS(0.003)PS(0.358)S(0.639)DDGIRPLPEYSTEK 248.95 1.81E-31 1400000000 1303100 1322300 1020900 1242300 1313500 1291400 1364200 1548700 1508300 1536800 TRUE FALSE 1252173.411 1284589.299 1205399.34 1306415.252 1355749.92 1317512.993 1380895.488 1516718.804 1337084.107 1432711.167 0.873988729 0.896614285 0.841341484 0.911848307 0.94628279 0.919594279 0.963833827 1.058635431 0.933254474 1 20.45031636 2.710261397 0.89179662 1.004968496 0.873511768 0.627073778 0.036237087 0.353095991 0.596710558 0.02277799 0.020636856 513.1701619 -2.710261397 -0.131456728 (ac)MEVKPPPGRPQPDS(ph)GR ddPTM_BT-474_Pertuzumab_2h_R1 4 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 MEVKPPPGRPQPDS(1)GR;MEVKPPPGRPQPDS(1)GR;MEVKPPPGRPQPDS(1)GR;MEVKPPPGRPQPDS(1)GR 83.776 4.87E-05 2601460000 862460 804150 847070 772770 759610 903860 839990 941270 965970 985350 TRUE FALSE 828754.1097 781216.4293 1000154.392 812652.7523 784043.5455 922136.6685 850270.0489 921832.4456 856317.1353 918611.3668 0.902181423 0.850431921 1.088767708 0.884653491 0.853509519 1.003837642 0.925603666 1.003506465 0.932186522 1 19.80909511 2.710409802 24.99361325 0.971809694 0.920138048 0.149508939 0.067709695 1614.421997 1433358.211 0.021891661 0.020643824 513.3455501 -2.710409802 -0.051671646 SVDLHPTEPWMLASLYNGSVCVWNHETQTLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVDLHPTEPWMLASLYNGSVCVWNHETQTLVK 32 0 P35606;D6R997 P35606 COPB2 Coatomer subunit beta 0 297.08 8.57E-90 221350000 77500 101410 99011 113980 116670 86170 102510 72860 110690 111540 FALSE TRUE 74471.21432 98517.88609 116904.4902 119862.5215 120422.7965 87912.41644 103764.548 71355.41554 98124.93525 103985.2965 0.716170621 0.947421313 1.124240582 1.152687212 1.158075234 0.845431224 0.997877119 0.686206781 0.943642405 1 16.66602002 2.710752976 24.85755896 0.868433604 1.028896347 0.138694687 0.147984759 1119.164088 1000432.192 0.050258032 0.04739423 513.7513497 -2.710752976 0.160462743 EYAEDDNIYQQK ddPTM_BT-474_Pertuzumab_2h_R1 4 EYAEDDNIYQQK 12 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;; 321.7 1.96E-46 2391870000 2005250 1965560 1718960 1927930 2033990 2096830 2197300 2369290 2596840 2543740 FALSE TRUE 1926882.613 1909504.153 2029614.31 2027430.698 2099415.136 2139229.339 2224191.215 2320363.334 2302057.61 2371450.224 0.812533442 0.805205243 0.855853642 0.85493285 0.885287456 0.902076425 0.937903394 0.978457532 0.970738322 1 21.17733816 2.711075366 0.496645367 1.004883753 0.796679072 0.973746151 0.010678335 0.150537702 0.077106694 0.009917793 0.012783918 514.132865 -2.711075366 -0.208204681 KNTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 KNTFTAWSDEESDYEIDDRDVNK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 KNTFTAWS(1)DEESDYEIDDRDVNK;KNT(0.071)FT(0.188)AWS(0.737)DEES(0.004)DYEIDDRDVNK 291.06 8.37E-62 1400490000 678558 676508 482747 553929 643510 726480 762255 802553 911579 837098 TRUE FALSE 652039.2032 657214.6542 569990.1215 582517.3421 664209.0836 741169.9234 771583.7047 785980.0001 808100.3736 780400.6069 0.835518575 0.842150363 0.730381443 0.746433738 0.851112977 0.94973007 0.988702082 1.007149396 1.035494292 1 19.57385537 2.711790144 1.986671514 1.007951941 0.78837023 0.892326534 0.034790269 0.107895443 0.841875275 0.014230881 0.013775793 514.9797402 -2.711790144 -0.219581711 AESSQTCHSEQGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 AESSQTCHSEQGDK 14 0 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ; 120.3 0.00013719 271290000 144645 140114 121397 146964 148330 150061 137673 136879 159492 170828 FALSE TRUE 138992.1135 136118.0859 143336.1384 154548.8297 153101.1692 153095.3362 139357.8834 134052.4008 141387.1368 159257.6674 0.872749901 0.854703501 0.900026609 0.970432584 0.961342532 0.961305906 0.875046619 0.841732791 0.88778857 1 17.28100331 2.712493914 0.006403705 1.811805012 5.08E-05 0.131026006 0.049218755 21611.34037 55.12156255 7663.240027 7929.075207 515.8149372 -2.712493914 -1.811754254 VLHNAQEVEKEPGQR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLHNAQEVEKEPGQR 15 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5 P49916-3 LIG3 DNA ligase 3 0 ;;; 207.72 1.95E-09 1781340000 1280770 1265880 1001640 1135720 1258100 1347840 1353460 1617970 1485340 1512890 FALSE TRUE 1230716.092 1229778.342 1182658.629 1194334.645 1298567.929 1375094.248 1370024.048 1584558.354 1316730.43 1410420.613 0.872587993 0.87192312 0.838514851 0.846793243 0.920695513 0.974953312 0.971358498 1.123465114 0.933572878 1 20.42769403 2.71262016 1.486376153 1.028782402 0.85663322 0.664102568 0.047732942 0.214484381 0.95638341 0.020351066 0.019096763 515.9649017 -2.71262016 -0.172149181 (ac)SS(ph)SPVNVKK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.095)S(0.453)S(0.453)PVNVKK;S(0.076)S(0.462)S(0.462)PVNVKK;S(0.051)S(0.474)S(0.474)PVNVKK 65.347 0.0098174 63714030000 16567630 14952470 13016090 11671450 13176120 14941870 14432250 15778220 16535890 15703860 TRUE FALSE 15920148.7 14526040.2 15368387 12273814.93 13599941.87 15244004.85 14608876.19 15452394.24 14658805.09 14640223.57 1.087425245 0.992200708 1.04973718 0.838362534 0.928943591 1.041241261 0.997858818 1.055475291 1.00126921 1 23.80343425 2.71295345 24.67373893 1.023500567 0.976128221 0.082845906 0.065046547 1575.391016 1517963.742 0.022040612 0.020788084 516.3610201 -2.71295345 -0.047372346 S(ph)PGSGSQSSGWHEVEPGMPSPTTLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGSGSQSSGWHEVEPGMPSPTTLKK 26 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.401)PGS(0.401)GS(0.096)QS(0.084)S(0.018)GWHEVEPGMPSPTTLKK 93.568 0.004101 628160000 189760 211370 165510 164750 157070 208680 200430 204030 200770 208310 TRUE FALSE 182343.9694 205341.9346 195421.3388 173252.7672 162122.2992 212899.6526 202882.9223 199816.7092 177979.4313 194200.9782 0.93894465 1.057368179 1.006284008 0.89213128 0.834817109 1.096285171 1.044705975 1.02891711 0.916470313 1 17.56719094 2.713121617 24.99986349 1.022138178 0.952467691 0.201052635 0.070195562 1400.880328 1376696.221 0.024269817 0.022888863 516.5610038 -2.713121617 -0.069670488 AYEKPPEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYEKPPEKK 9 2 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 70.808 0.028888 3691500000 3589330 4035600 2592020 3118300 4246200 5007300 5128700 5811300 7119900 5983000 FALSE TRUE 3449055.015 3920508.639 3060455.673 3279235.837 4382782.879 5108551.037 5191466.565 5691294.624 6311678.801 5577766.081 0.618357774 0.702881509 0.548688423 0.58791204 0.785759535 0.915877605 0.930742969 1.020353766 1.131578254 1 22.411256 2.713184293 1.228651902 1.038386786 0.610682863 0.908148861 0.058604981 0.13005903 0.404355963 0.029408036 0.026889236 516.6355577 -2.713184293 -0.427703922 GSQS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSQSPKR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GS(0.013)QS(0.987)PKR;GSQS(1)PKR;GS(0.074)QS(0.926)PKR;GS(0.001)QS(0.999)PKR 70.552 0.034741 456206000 715184 806528 539006 546083 648616 709499 800112 773543 723687 683393 TRUE FALSE 687233.8186 783526.6111 636416.3743 574266.4091 669479.3227 723845.5559 809904.01 757569.0667 641537.0857 637106.1834 1.078680189 1.229821075 0.998917278 0.901366874 1.050812785 1.136145865 1.271222963 1.189078189 1.006954731 1 19.28117431 2.713466328 5.802367595 1.149996391 1.050330564 0.060935702 0.108230515 0.363982252 41.76619203 0.036861554 0.035667617 516.9711737 -2.713466328 -0.099665827 NHGIHTAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 NHGIHTAHK 9 0 P24666-2;D3YTI2 P24666-2 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 128.27 0.00024408 10607000 29476 27355 26531 22763 20176 15988 17810 2125.9 20601 8219.7 FALSE TRUE 28324.04533 26574.86218 31325.74188 23937.80116 20824.97936 16311.28831 18027.96411 2081.999422 18262.46085 7662.972398 3.696221761 3.467957446 4.08793615 3.123827141 2.717611167 2.128585028 2.352607209 0.271696062 2.383208486 1 12.90368839 2.713953437 0.878420505 1.156636881 3.767764531 0.736255466 0.578965837 0.276729011 0.454548274 0.352221094 0.321139381 517.5513392 -2.713953437 2.61112765 SSSLEMTPYNTPQLS(ph)PATTPANKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLEMTPYNTPQLSPATTPANKK 24 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7;B4DGD8;B0QZ65;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 SSSLEMTPYNTPQLS(0.998)PAT(0.002)TPANKK 149.84 8.42E-08 365620000 188700 177700 127520 142120 123040 193070 174820 169390 231100 220870 TRUE FALSE 181325.3954 172632.17 150565.7007 149454.8302 126997.6933 196974.0077 176959.4995 165892.0373 204866.4969 205910.2782 0.880603907 0.838385395 0.731219937 0.725825013 0.616762283 0.956601144 0.859401002 0.805652048 0.994930893 1 17.65165632 2.714063913 24.99920132 0.897388161 0.759656638 0.457081436 0.087525421 880.4666383 898526.5424 0.029777534 0.02808544 517.6830113 -2.714063913 -0.137731524 MTPHEK ddPTM_BT-474_Pertuzumab_2h_R1 4 MTPHEK 6 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;; 124.89 0.018161 2515090000 4590480 4680520 4152060 4440910 4298000 4773880 4984490 4730300 5267740 5323180 FALSE TRUE 4411078.967 4547036.152 4902429.604 4670105.897 4436249.073 4870411.124 5045491.68 4632617.652 4669768.239 4962636.277 0.888858002 0.916254164 0.987868006 0.941053431 0.893929925 0.981416097 1.016695844 0.933499332 0.940985391 1 22.24267529 2.714141581 24.72264573 0.97092123 0.929392561 0.328078418 0.034606657 1012.80496 1025395.593 0.011830604 0.011158006 517.7756005 -2.714141581 -0.041528669 EDIEVYFTGPGWEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDIEVYFTGPGWEAR 15 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5 Q04206 RELA Transcription factor p65 0 171.32 2.54E-06 52352000 27660 37003 28408 44711 38869 31569 33059 35917 31624 36085 FALSE TRUE 26579.01662 35947.71067 33541.95753 47018.54007 40119.25668 32207.34681 33463.58593 35175.3014 28034.1761 33640.93081 0.790079703 1.068570631 0.997057951 1.397658713 1.19257273 0.957385721 0.994728301 1.04561023 0.833335328 1 15.03793 2.714433337 24.38374192 0.977738698 1.100061482 0.136377714 0.152141346 1267.397684 1280867.601 0.051544187 0.048620378 518.1235557 -2.714433337 0.122322784 RPRPPNAPSQDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPRPPNAPSQDGK 13 2 P16989;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 0 86.772 0.004878 138820000 213000 254820 234800 208990 203960 223740 210800 193330 207510 240890 FALSE TRUE 204675.7245 247552.7831 277233.5831 219775.9989 210520.5586 228264.1761 213379.8335 189337.6679 183954.3348 224574.3057 0.911394221 1.102320153 1.234484872 0.978633768 0.937420503 1.01643051 0.95015248 0.843095862 0.819124584 1 17.77683335 2.714919662 0.964561176 0.881048897 1.072775255 0.312877235 0.095770247 0.591401523 1.162704093 0.056810784 0.051347318 518.7040781 -2.714919662 0.191726357 QQSTPQAANS(ph)PPNLGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 QQSTPQAANSPPNLGAK 17 0 Q9Y4C1;F8WE62 Q9Y4C1 KDM3A Lysine-specific demethylase 3A 1 QQSTPQAANS(1)PPNLGAK;QQSTPQAANS(1)PPNLGAK 250.79 1.92E-21 576930000 902000 845860 767860 847320 885080 895780 984610 1077170 1043490 979340 TRUE FALSE 866748.8428 821736.901 906629.383 891050.2867 913549.402 913893.2853 996659.9517 1054926.063 925037.3899 913008.4295 0.949332793 0.900032108 0.993013157 0.975949682 1.000592516 1.000969165 1.091621851 1.155439566 1.013175081 1 19.80026865 2.714925758 1.304966741 1.085051278 0.950248512 0.465885232 0.049176253 0.32283321 1.124838478 0.023271683 0.02148463 518.7113586 -2.714925758 -0.134802766 EIFEQPESVVNTMR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIFEQPESVVNTMR 14 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 107.18 0.0044828 0 21189 19890 18341 20086 17473 22598 21051 25725 20466 18888 FALSE TRUE 20360.91045 19322.75667 21655.62669 21122.64087 18035.03491 23054.94704 21308.62844 25193.76976 18142.78548 17608.69894 1.156298403 1.097341532 1.229825484 1.199557159 1.024211668 1.309293045 1.210119414 1.430757028 1.030330835 1 14.1040007 2.715485655 24.98747568 1.240754029 1.147134802 0 0.130857535 1810.149665 1960177.781 0.041090676 0.038762849 519.3805177 -2.715485655 -0.093619227 KSTLT(ph)PTQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSTLTPTQR 9 1 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 KS(0.042)T(0.042)LT(0.905)PT(0.01)QR 81.017 0.019578 0 95534 102320 88397 76202 77612 104550 91599 104040 101190 120320 TRUE FALSE 91800.42566 99401.93378 104372.3043 80134.79435 80108.46047 106664.0726 92720.01596 101891.5376 89703.33542 112170.6192 0.818399919 0.886167291 0.930478097 0.714400927 0.714166161 0.95090919 0.826598057 0.908362086 0.799704379 1 16.77533532 2.715718892 24.98750174 0.887084626 0.817882391 0.20307397 0.082083182 1639.818761 1793863.616 0.027221532 0.025680549 519.659525 -2.715718892 -0.069202234 LSS(ph)ATANALYSSNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSSATANALYSSNLR 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LS(0.005)S(0.983)AT(0.012)ANALYSSNLR;LS(0.007)S(0.993)ATANALYSSNLR;LSS(1)ATANALYSSNLR;LSS(0.999)AT(0.001)ANALYSSNLR 374.55 1.02E-97 1265160000 2222520 1900900 1491870 1847440 2102380 1371040 1100890 1913610 1104530 1131600 TRUE FALSE 2135661.461 1846688.193 1761484.095 1942786.6 2170004.962 1398763.368 1114363.021 1874093.285 979148.385 1054955.724 2.02440862 1.750488813 1.669723246 1.841581173 2.056963067 1.3258977 1.056312597 1.776466293 0.928141687 1 20.00875102 2.716310886 18.01003249 1.29366806 1.849515004 0.621801093 0.250227431 17.99624282 14566.21245 0.080846957 0.076442053 520.368365 -2.716310886 0.555846944 LALVTGGEIASTFDHPELVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LALVTGGEIASTFDHPELVK 20 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 284.38 5.60E-45 763680000 407410 447250 431510 401500 382090 491290 490770 501430 539530 548100 FALSE TRUE 391487.9668 434494.8679 509493.4559 422221.4631 394380.2719 501224.2204 496776.1901 491075.2953 478284.8163 510976.6988 0.766156202 0.850322273 0.99709724 0.826302773 0.771816548 0.980914045 0.972209087 0.961052229 0.936020796 1 18.96289798 2.716464591 24.70422394 0.967307383 0.850489296 0.51743559 0.061381052 643.1916309 719112.5978 0.020742034 0.019570671 520.5525658 -2.716464591 -0.116818086 TAVEHATDEDILAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TAVEHATDEDILAK 14 0 A0A494C1L5;P50851-2;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 196.11 2.53E-08 1142490000 957620 1007830 830440 905430 981890 1039870 1046390 1048750 1286210 1203850 FALSE TRUE 920195.1517 979087.6752 980518.981 952159.3508 1013473.384 1060896.884 1059196.034 1027092.946 1140204.833 1122312.167 0.819910163 0.872384443 0.873659762 0.84839083 0.903022718 0.945277896 0.943762408 0.915157989 1.015942682 1 20.09804258 2.716485403 0.342866203 1.00889082 0.811310856 0.81788771 0.025707796 0.830034839 0.199435139 0.031456758 0.060205201 520.5775119 -2.716485403 -0.197579964 ECPPHAEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ECPPHAEQR 9 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 117.02 0.001219 140070000 101670 126140 85496 109130 115600 95409 103140 98894 98425 110660 FALSE TRUE 97696.624 122542.6107 100947.029 114762.2124 119318.379 97338.23535 104402.2582 96851.80434 87252.20663 103164.8996 0.946994805 1.187832404 0.978501694 1.112415296 1.156579218 0.943520865 1.011993988 0.938805783 0.845754776 1 16.65459267 2.716493078 24.42617519 0.949179519 1.079206646 0.39212315 0.079921861 598.9208419 662933.9064 0.024660676 0.023268049 520.5867109 -2.716493078 0.130027127 EAVFDDDMEQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAVFDDDMEQLR 12 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 0 90.827 0.0099129 0 117110 135560 96420 97691 103620 126050 138720 130080 133640 134940 FALSE TRUE 112533.2117 131693.9615 113845.2389 102732.8442 106953.0314 128598.8174 140417.6969 127393.8025 118469.7475 125800.3936 0.894537835 1.046848565 0.904967271 0.816633726 0.850180419 1.022244952 1.116194416 1.012666168 0.941727955 1 16.94077691 2.71662694 21.74956685 1.026914396 0.905997425 0.412652741 0.06873841 160.9227648 159570.831 0.024039052 0.022696885 520.7471953 -2.71662694 -0.120916971 DSSGSVS(ph)PNTLSQEEGDQICLYHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSGSVSPNTLSQEEGDQICLYHIR 25 0 H7C4T3;H7C4L8;G5E9U9;Q9H0J9 H7C4T3 PARP12 Poly [ADP-ribose] polymerase 12 1 DS(0.112)S(0.112)GS(0.112)VS(0.583)PNT(0.081)LSQEEGDQICLYHIR 95.206 0.0064976 283690000 22109 21057 21860 18488 18840 23818 27912 22403 24437 19791 TRUE FALSE 21244.95584 20456.47498 25810.58827 19442.1679 19446.00571 24299.61628 28253.59541 21940.37022 21663.01421 18450.53794 1.151454549 1.108719705 1.398907086 1.053745314 1.053953319 1.317013973 1.531315536 1.189145286 1.174112878 1 14.17137526 2.717463531 24.46965099 1.272477753 1.158983985 0.058632187 0.155594816 1444.954734 1675940.933 0.050512638 0.047673006 521.7512892 -2.717463531 -0.113493768 (ac)MFQIPEFEPSEQEDSSSAER ddPTM_BT-474_Pertuzumab_2h_R1 2 MFQIPEFEPSEQEDSSSAER 20 0 Q92934;F5GYS3;A8MXU7 Q92934 BAD Bcl2-associated agonist of cell death 0 ; 70.889 0.0012882 23363000 17464 15003.3 11101.8 11490.2 13447.7 16437.6 19131.4 15289.8 19881.6 18568.7 FALSE TRUE 16781.48757 14575.42057 13108.14222 12083.2106 13880.25748 16769.97953 19365.5358 14974.06029 17624.72412 17311.02541 0.969410371 0.841973264 0.757213505 0.698006635 0.801816019 0.968745591 1.118682189 0.865001346 1.018121324 1 14.07940356 2.717493986 5.962330893 0.987094813 0.805383173 0.516932284 0.086972714 0.15330703 20.39549134 0.029297755 0.028449668 521.787878 -2.717493986 -0.18171164 S(ph)FLEDTTPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFLEDTTPAR 10 0 Q3YEC7;Q3YEC7-2;G3V154;F2Z2T0 Q3YEC7 RABL6 Rab-like protein 6 1 S(1)FLEDTTPAR 118.77 0.00081972 156700000 52761 51528 55382 54107 58185 49854 47469 59189 54137 50393 TRUE FALSE 50699.04179 50058.47189 65390.75937 56899.46875 60056.57337 50862.08204 48049.93982 57966.72647 47991.59472 46979.83722 1.079165974 1.065530978 1.391889867 1.211146571 1.278347838 1.082636404 1.022777912 1.233863927 1.021535994 1 15.51975409 2.717775746 23.69211303 1.094514948 1.208156175 0.266806861 0.107069488 692.1265093 788934.7215 0.035924448 0.033911716 522.1265118 -2.717775746 0.113641227 DS(ph)RPLSPILHIVK ddPTM_BT-474_Pertuzumab_2h_R1 3 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.8)RPLS(0.2)PILHIVK;DS(0.639)RPLS(0.361)PILHIVK;DS(0.5)RPLS(0.5)PILHIVK 137.52 3.62E-05 708207000 1421344 1475834 1280335 1309084 1429114 1341431 1378050 1320650 1740652 1487868 TRUE FALSE 1365796.305 1433744.659 1511720.015 1376645.982 1475082.75 1368555.654 1394914.988 1293378.116 1543060.482 1387093.375 0.984646261 1.033632404 1.089847333 0.99246814 1.063434356 0.986635564 1.005638851 0.932437671 1.112441678 1 20.40363348 2.717862687 24.23391691 0.99727854 1.033779635 0.0405208 0.050794883 1262.547683 1478235.299 0.016030757 0.015133839 522.2310463 -2.717862687 0.036501095 AYGELPEHAK ddPTM_BT-474_Pertuzumab_2h_R1 4 AYGELPEHAK 10 0 P47813;O14602;X6RAC9;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;;; 133.23 0.00020274 9631400000 20968600 21381200 18671600 18491200 19255000 21139500 21060600 21248300 24499600 24012400 FALSE TRUE 20149123.93 20771429.11 22045973.47 19445533.05 19874354.56 21566955.17 21318345.92 20809515.18 21718508.12 22386018.76 0.900076255 0.927875087 0.984809926 0.86864633 0.887802104 0.963411824 0.952306265 0.92957642 0.970181806 1 24.41609464 2.718299452 24.44281018 0.955490525 0.916053356 0.341099426 0.033330769 917.5285556 1106892.508 0.011151399 0.010526793 522.7565127 -2.718299452 -0.039437169 SPS(ph)PISISSSETSSIMQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPISISSSETSSIMQK 18 0 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 S(0.082)PS(0.918)PISISSSETSSIMQK 141.86 1.69E-06 0 49909 59790 41799 50226 46672 57499 59573 59387 66116 62016 TRUE FALSE 47958.5011 58084.84774 49353.00911 52818.16988 48173.24727 58661.66918 60302.07219 58160.6377 58610.78886 57815.60108 0.829507956 1.00465699 0.853627882 0.913562583 0.833222285 1.014633906 1.043006923 1.005967881 1.013753862 1 15.81917122 2.718598639 24.10224682 1.017306567 0.893087813 0.639658606 0.048123405 319.8860062 386232.0518 0.014640839 0.013822725 523.1167659 -2.718598639 -0.124218754 GYTS(ph)DDDTWEPEIHLEDCK ddPTM_BT-474_Pertuzumab_2h_R1 2 GYTSDDDTWEPEIHLEDCK 19 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GYT(0.11)S(0.889)DDDTWEPEIHLEDCK;GYT(0.13)S(0.87)DDDTWEPEIHLEDCK 327.06 2.36E-75 670840000 1190070 1081400 797250 1217400 1068420 1002010 956060 1002940 1232100 1148360 TRUE FALSE 1143560.749 1050559.531 941330.8097 1280230.16 1102786.7 1022271.329 967760.5483 982228.9385 1092237.173 1070580.554 1.068168802 0.98129891 0.87927135 1.19582796 1.030082879 0.954875674 0.903958646 0.917473173 1.020228855 1 20.02996192 2.718751693 6.249467958 0.946282034 1.029014398 0.155559693 0.080671467 0.299029171 47.82380345 0.026493894 0.025729392 523.3011547 -2.718751693 0.082732364 ACVQGECGVCHYCR ddPTM_BT-474_Pertuzumab_2h_R1 2 ACVQGECGVCHYCR 14 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 ; 198.48 2.20E-08 609810000 273940 319050 226884 275420 290690 258260 274490 257844 299340 311420 FALSE TRUE 263234.1219 309951.0064 267886.9858 289634.4592 300040.3078 263482.1941 277849.2907 252519.4313 265360.1781 290327.246 0.906680739 1.067591866 0.922707012 0.997613773 1.033455564 0.907535196 0.957021067 0.869775175 0.914003704 1 18.14732044 2.719228513 24.79133906 0.919720827 0.987336642 0.196719389 0.054651293 953.8918022 1223261.89 0.016628714 0.015700018 523.8760124 -2.719228513 0.067615815 KVTFFEPGSGDENGTSNKEDEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVTFFEPGSGDENGTSNKEDEFR 23 2 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 73.981 0.010662 155380000 65795 66896 50345 49922 60256 67281 72716 70872 83679 71258 FALSE TRUE 63223.65866 64988.19158 59443.46142 52498.4804 62194.18896 68641.46792 73605.92016 69408.46843 74180.11073 66431.63219 0.95171015 0.978271788 0.894806577 0.790263293 0.936213471 1.033264812 1.107995058 1.044810524 1.116638389 1 16.01958274 2.719632342 3.389730208 1.069009694 0.904312709 0.653724845 0.055257289 0.153652107 3.726234833 0.019204586 0.018932521 524.3633656 -2.719632342 -0.164696986 NLFGPVDHEELTR ddPTM_BT-474_Pertuzumab_2h_R1 1 NLFGPVDHEELTR 13 0 P46527;E7ES52;H7C2T1 P46527 CDKN1B Cyclin-dependent kinase inhibitor 1B 0 159 1.20E-06 0 98824 116600 86392 103370 108860 93887 96199 99677 104310 110350 FALSE TRUE 94961.84882 113274.6822 102004.9562 108704.9381 112361.5808 95785.45947 97376.31214 97618.63512 92469.1661 102875.8962 0.923071898 1.101080878 0.991534071 1.05666091 1.092205122 0.931077765 0.946541568 0.948897057 0.898841901 1 16.65054547 2.720216449 24.91433999 0.942673875 1.035718584 0.407572117 0.05285714 717.4700814 974439.1148 0.015975502 0.015084535 525.0690849 -2.720216449 0.093044709 SHTFPELAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHTFPELAYR 10 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 77.379 0.02688 0 127120 140770 127940 117420 121210 79155 118310 29898 107860 121610 FALSE TRUE 122152.0099 136755.3774 151061.604 123480.0603 125108.8297 80755.56833 119757.9132 29280.59585 95616.18499 113373.2464 1.077432408 1.206240289 1.33242726 1.089146375 1.10351281 0.712298279 1.056315462 0.258267244 0.843375206 1 16.79072071 2.720249031 1.366059875 0.672263517 1.201704481 0.411878669 0.220678056 0.33794262 1.284138592 0.096366741 0.089975524 525.1084788 -2.720249031 0.529440964 CGQEEHDVLLSNEEDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 CGQEEHDVLLSNEEDRK 17 1 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 162.76 1.82E-09 447080000 278130 235380 232100 229440 217160 278740 256500 280020 321790 296380 FALSE TRUE 267260.3721 228667.1929 274045.633 241281.4259 224145.1486 284376.3138 259639.1237 274237.4891 285261.7483 276305.9186 0.967262567 0.827587024 0.991819627 0.873240165 0.811220946 1.029208188 0.939679921 0.992513988 1.032412732 1 18.07590694 2.720316731 24.99650908 0.992902742 0.894779872 0.455937004 0.056915473 785.9839548 1076899.342 0.017820626 0.016828852 525.1903424 -2.720316731 -0.098122871 EHPYLFSQCQAIHCR ddPTM_BT-474_Pertuzumab_2h_R1 2 EHPYLFSQCQAIHCR 15 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 210.34 1.12E-09 543350000 71477 82229 62946 75007 89115 54458 57159 58355 72183 81103 FALSE TRUE 68683.59982 79883.90943 74321.74243 78878.12026 91981.46491 55559.17807 57858.52894 57149.94886 63989.08846 75609.82157 0.908395211 1.05652821 0.982964129 1.043225848 1.216527999 0.734814299 0.765225043 0.755853508 0.846306566 1 16.20628603 2.720577861 24.98649525 0.796892745 1.039202363 0.538642277 0.101128194 561.8754603 780708.1403 0.031567781 0.029820845 525.5062203 -2.720577861 0.242309618 CQEHSKES(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 1 CQEHSKESPAR 11 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 CQEHS(0.137)KES(0.863)PAR 64.52 0.041154 573800000 297920 304990 244660 258240 255830 300910 311580 278380 314170 338450 TRUE FALSE 286276.957 296291.9838 288875.5044 271567.7973 264059.0043 306994.6064 315393.2092 272631.3557 278506.7387 315526.48 0.907299308 0.939039994 0.9155349 0.860681479 0.836883815 0.972959881 0.999577624 0.864052221 0.882673108 1 18.26740156 2.721067554 24.75929414 0.934293633 0.894087484 0.202340327 0.049715627 1645.919613 2329596.287 0.017420584 0.016461482 526.0990942 -2.721067554 -0.040206148 PSATSHSGSGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 PSATSHSGSGSK 12 0 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;;; 146.16 6.45E-05 222582000 296695 274764 241820 274295 259093 296633 313465 281382 336541 361395 FALSE TRUE 285099.8314 266927.9997 285522.2533 288451.3978 267426.9616 302631.1225 317301.2784 275571.3634 298338.2766 336917.3948 0.846200985 0.792265415 0.84745477 0.856148725 0.793746378 0.898235375 0.941777668 0.817919667 0.885493837 1 18.36203539 2.721246719 24.44118988 0.893763635 0.827962096 0.398589863 0.048357299 761.178774 1074517.607 0.015465242 0.014617406 526.3161769 -2.721246719 -0.065801539 VDIDAPDVSIEGPDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDIDAPDVSIEGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 258.78 2.36E-26 266290000 266266 298703 232816 269664 257786 294761 286398 323636 339776 313420 FALSE TRUE 255860.0303 290184.2829 274891.0302 283581.3914 266077.9208 300721.2694 289903.0244 316952.8035 301206.0529 292191.7842 0.875657853 0.993129508 0.940789731 0.970531708 0.91062766 1.029191393 0.992166926 1.084742353 1.030850521 1 18.15655609 2.72135427 22.00359266 1.033942262 0.943147814 0.576515742 0.037915826 119.2293277 152470.3319 0.011910174 0.011268247 526.4465337 -2.72135427 -0.090794449 ESKGS(ph)PVFLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESKGSPVFLPR 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ES(0.356)KGS(0.644)PVFLPR;ES(0.083)KGS(0.917)PVFLPR;ES(0.096)KGS(0.904)PVFLPR;ES(0.249)KGS(0.751)PVFLPR 111.22 0.001023 12081640000 8769200 8254200 6231200 6991700 7400500 8456800 8373700 8953100 9585600 9963100 TRUE FALSE 8426489.969 8018798.298 7357316.452 7352542.475 7638543.803 8627802.29 8476179.845 8768215.356 8497482.874 9288290.363 0.907216467 0.863323387 0.792106638 0.79159266 0.822384261 0.928890243 0.9125662 0.944007456 0.914859737 1 23.14698164 2.721562883 8.337140114 0.93511504 0.832020815 0.641930782 0.038987412 0.149016555 62.33658959 0.012973367 0.012544932 526.6994718 -2.721562883 -0.103094225 LEHAYKPVQFEGSLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEHAYKPVQFEGSLGK 16 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 0 124.29 5.01E-05 442510000 571660 550110 462430 522600 491340 579680 574300 561400 639770 686770 FALSE TRUE 549318.8952 534421.4014 546001.3877 549571.4486 507144.3973 591401.5268 581328.4552 549806.8938 567145.9917 640254.4562 0.857969655 0.834701573 0.85278811 0.858364113 0.792098192 0.923697635 0.907964716 0.85873185 0.885813423 1 19.28828586 2.722093821 24.96994249 0.902077755 0.840756593 0.468821207 0.0392296 861.4168456 1306234.762 0.012327878 0.011653114 527.3437715 -2.722093821 -0.061321162 ENLELNGSILS(ph)GGYPGSAPLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENLELNGSILSGGYPGSAPLQR 22 0 O43663-2;O43663-4;O43663;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 ENLELNGS(0.002)ILS(0.998)GGYPGSAPLQR 81.665 0.0014038 0 20200 19055 19555 18069 17841 22330 23105 22669 23952 25886 TRUE FALSE 19410.56167 18511.57006 23089.0235 19001.54326 18414.87197 22781.5279 23387.7659 22200.87723 21233.06937 24132.71816 0.804325544 0.767073561 0.956751881 0.787376835 0.763066632 0.944010026 0.969131025 0.919949302 0.879845744 1 14.5587028 2.72251096 24.56387322 0.938465461 0.819276981 0.537028982 0.058789501 549.2016742 840547.5389 0.019147512 0.018109163 527.8505276 -2.72251096 -0.11918848 GGIVDEGALLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGIVDEGALLR 11 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YFM8;A0A286YF78 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 120.12 0.0011509 145630000 171940 177670 154050 188480 184280 163460 175350 173580 175580 189530 FALSE TRUE 165220.3947 172603.0256 181890.2618 198207.4754 190207.5336 166765.2732 177495.9858 169995.5123 155648.8945 176692.9643 0.935070592 0.976852849 1.029414287 1.121762127 1.076486177 0.943813886 1.004544728 0.962095537 0.880900352 1 17.43088507 2.722771925 24.78629241 0.960339967 1.030377077 0.270645333 0.057044018 1091.609987 1713690.341 0.019964935 0.018881448 528.1678055 -2.722771925 0.07003711 SKEGLTER ddPTM_BT-474_Pertuzumab_2h_R1 5 SKEGLTER 8 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ;;;; 121.6 0.0013007 1901220000 2766790 2887800 2308620 2583030 2647500 2934900 2920200 3084270 3464590 3274480 FALSE TRUE 2658660.788 2805442.771 2725838.989 2716340.488 2732659.242 2994245.689 2955938.281 3020578.747 3071304.268 3052696.553 0.870922066 0.919004796 0.892928249 0.889816738 0.895162423 0.980852711 0.968303999 0.989478874 1.006095501 1 21.54165276 2.722784801 4.700874105 0.9874707 0.894277698 0.916809788 0.014371697 0.053125393 3.246289934 0.004638876 0.004560332 528.1834649 -2.722784801 -0.093193001 KVVVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVVVVR 6 1 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 119.7 0.033331 2958700000 2777600 2853700 2533400 2790100 2584900 3004300 2932600 3090500 3094800 3267900 FALSE TRUE 2669048.321 2772315.27 2991241.735 2934097.395 2668045.656 3065049.004 2968490.036 3026680.095 2743491.278 3046562.222 0.876085281 0.909981503 0.981841668 0.963084678 0.875756168 1.00606808 0.974373677 0.993473914 0.90052035 1 21.53875078 2.7231642 24.92273255 0.97603074 0.926397537 0.289338224 0.041558338 1134.033892 1835699.899 0.013581753 0.012846148 528.6450861 -2.7231642 -0.049633203 GQS(ph)PNKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQSPNKR 7 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 GQS(1)PNKR 58.246 0.067812 45393000 88886 86196 81855 79776 84864 89862 97982 96136 92802 92529 TRUE FALSE 85412.23685 83737.77447 96648.01935 83893.24892 87593.72763 91679.07121 99181.13303 94150.758 82267.50602 86261.92841 0.990149866 0.970738494 1.120401794 0.972540847 1.015439015 1.062798768 1.149767167 1.091452043 0.95369426 1 16.39643635 2.723255269 6.25358239 1.068331359 1.014988947 0.050412289 0.063626165 0.345149794 59.5269305 0.020604071 0.020126706 528.7559519 -2.723255269 -0.053342412 NLEELEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLEELEEK 8 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 107.57 0.0092518 195540000 265010 254350 208180 216470 289300 261440 266720 306880 318640 324250 FALSE TRUE 254653.1162 247096.187 245802.7569 227642.0426 298605.5972 266726.4959 269984.1991 300542.8208 282469.323 302288.2587 0.842418152 0.817419069 0.813140272 0.7530628 0.987817385 0.882358108 0.893134918 0.994225916 0.934436965 1 18.20556542 2.723366865 0.715349718 0.977402095 0.80573443 0.573506504 0.053349007 0.506539926 0.556395152 0.038400519 0.037784176 528.8918382 -2.723366865 -0.171667665 NLHSEISGK ddPTM_BT-474_Pertuzumab_2h_R1 4 NLHSEISGK 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 143.96 0.0001007 3069490000 5822800 5950060 5448660 5603270 5418160 5562210 5417990 5104380 6258200 6162150 FALSE TRUE 5595238.539 5780370.115 6433354.067 5892455.436 5592440.037 5674681.697 5484296.982 4998972.769 5547795.373 5744782.092 0.973968803 1.006194843 1.119860417 1.025705648 0.973481665 0.987797554 0.954657095 0.870176221 0.965710324 1 22.45382074 2.723467881 1.406459794 0.931508115 1.033541903 0.330495922 0.048533011 0.398510007 1.600280364 0.022009451 0.020692306 529.0148713 -2.723467881 0.102033788 VWEDRPSS(ph)AGSTPFPYNPLIMR ddPTM_BT-474_Pertuzumab_2h_R1 2 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.284)S(0.687)AGS(0.029)TPFPYNPLIMR;VWEDRPS(0.286)S(0.713)AGS(0.001)TPFPYNPLIMR 152.12 2.64E-08 1651450000 548030 521300 429390 490720 462560 552130 573770 527920 584590 651310 TRUE FALSE 526612.3817 506433.0344 506990.3247 516046.118 477438.6625 563294.4469 580791.9689 517018.2675 518229.794 607196.1936 0.86728538 0.834051728 0.834969537 0.849883651 0.786300487 0.927697592 0.956514509 0.851484698 0.853479978 1 19.21180322 2.723873258 24.92126637 0.907278548 0.835354291 0.443480552 0.045917801 845.2251821 1434161.847 0.01490773 0.014109671 529.5088928 -2.723873258 -0.071924258 LS(ph)PISHGNTIALFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSPISHGNTIALFFR 15 0 Q9BQ70 Q9BQ70 TCF25 Transcription factor 25 1 LS(0.996)PIS(0.004)HGNTIALFFR;LS(0.997)PIS(0.003)HGNTIALFFR 159.75 1.13E-06 374100000 120386 140442 139965 139601 129046 119471 117342 109462 131399 131144 TRUE FALSE 115681.182 136436.7317 165259.789 146805.8243 133196.8818 121886.7855 118778.0665 107201.5714 116483.1364 122261.5001 0.946178331 1.115941908 1.351691161 1.200752684 1.089442561 0.996935138 0.971508336 0.876821987 0.952737667 1 16.89961065 2.724072479 2.022395161 0.935724406 1.163302852 0.468192316 0.098206623 0.281486224 2.273983001 0.03854241 0.037677402 529.7518459 -2.724072479 0.227578446 LSYLS(ph)APGSEYSMYSTDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSYLSAPGSEYSMYSTDSR 19 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 LSYLS(0.999)APGS(0.001)EYSMYSTDSR;LSYLS(0.999)APGS(0.001)EYSMYSTDSR 203.56 5.25E-16 212300000 155703 158237 129510 152889 141428 167207 172768 184647 173723 161358 TRUE FALSE 149617.9546 153724.2357 152915.3379 160779.6196 145977.1601 170588.0401 174882.3865 180833.9749 154002.6933 150429.0789 0.994607929 1.021905052 1.016527782 1.068806781 0.970405198 1.134009736 1.162557051 1.202121134 1.023756141 1 17.19872395 2.724312713 24.52678909 1.128692821 1.01799988 0.303996131 0.06289 589.9482555 1015552.986 0.019917132 0.018862875 530.0449641 -2.724312713 -0.11069294 LGSSGLGS(ph)ASSIQAAVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGSSGLGSASSIQAAVR 17 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LGSSGLGS(0.997)AS(0.001)S(0.002)IQAAVR;LGSSGLGS(0.998)ASS(0.001)IQAAVR;LGSSGLGS(0.917)AS(0.004)S(0.078)IQAAVR 310.19 4.49E-58 1116740000 450540 492030 403520 447340 481900 421500 433960 479400 486960 471600 TRUE FALSE 432932.3987 477997.7861 476445.0403 470427.271 497400.7512 430023.0188 439270.9323 469500.2225 431682.3423 439658.1119 0.984702402 1.087203382 1.08367167 1.069984286 1.131335321 0.978085033 0.999119362 1.067875719 0.981859155 1 18.74602256 2.724463236 24.99739055 1.013843677 1.072863921 0.380142579 0.041414594 963.8952737 1709169.323 0.013501347 0.012783795 530.2287055 -2.724463236 0.059020244 DGVGMVEYLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGVGMVEYLR 10 0 Q13242;H0YIB4 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;; 201.21 5.72E-07 3065800000 1832210 1835830 1424340 1710480 1722650 1684560 1726690 1743010 1862740 1971170 FALSE TRUE 1760605.208 1783473.926 1681749.922 1798758.078 1778060.602 1718622.957 1747821.749 1707016.234 1651289.564 1837660.9 0.958068601 0.970513072 0.915157917 0.97883025 0.967567303 0.935223118 0.951112226 0.928907087 0.898582303 1 20.80943914 2.72469463 23.78339766 0.938356124 0.957495148 0.055948692 0.028570288 1017.019769 1744420.012 0.008840765 0.008380614 530.5112891 -2.72469463 0.019139024 EKEEAEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEEAEAR 8 1 Q99543;Q99543-2 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 80.688 0.022618 237350000 688020 673730 530900 549900 587670 658420 650160 672030 766580 763230 FALSE TRUE 661131.4178 654515.8801 626845.4398 578280.4049 606572.9393 671733.7035 658116.8526 658152.3457 679561.0522 711535.7523 0.929161206 0.919863658 0.880975324 0.812721501 0.852484134 0.944061773 0.924924504 0.924974386 0.955062413 1 19.44057672 2.725165721 24.11929817 0.941494004 0.877732109 0.474810789 0.0366817 521.2854078 938641.626 0.012795212 0.01212927 531.0870611 -2.725165721 -0.063761895 LQSEPESIRK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQSEPESIRK 10 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 ; 97.439 0.0097135 861550000 1396250 1443370 989260 1159830 1215870 1312240 1282820 1468920 1419410 1381240 FALSE TRUE 1341683.006 1402206.501 1168041.288 1219688.965 1254979.563 1338774.392 1298519.535 1438586.289 1258284.527 1287687.385 1.041932244 1.088933943 0.907084516 0.947193379 0.974599563 1.039673455 1.008412096 1.117185977 0.977166153 1 20.29635096 2.725229644 22.16089967 1.040716471 0.990135714 0.070336174 0.058322902 362.1225184 601975.6017 0.019891549 0.018890043 531.1652374 -2.725229644 -0.050580756 GGPNYQEGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGPNYQEGLR 10 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 80.219 0.05738 144500000 75783 90885 67269 90534 89728 72077 80845 75803 82862 88758 FALSE TRUE 72821.31658 88293.04879 79426.00469 95206.47059 92614.18261 73534.44632 81834.40529 74237.64156 73455.85315 82746.3416 0.880054818 1.067032658 0.959873309 1.150582234 1.119254106 0.888673081 0.988979134 0.897171284 0.887723272 1 16.33640791 2.725400228 24.98819546 0.928557623 1.039326646 0.290478627 0.080132565 949.9708917 1803747.631 0.025802748 0.024455227 531.3739111 -2.725400228 0.110769023 IKADPDGPEAQAEACSGER ddPTM_BT-474_Pertuzumab_2h_R1 2 IKADPDGPEAQAEACSGER 19 1 D6RC52;D6RCB9;Q9NX24;J3QSY4 D6RC52 NHP2 H/ACA ribonucleoprotein complex subunit 2 0 ; 179.87 3.18E-14 1775830000 559850 595700 465990 539310 517240 591430 572170 639230 652040 612870 FALSE TRUE 537970.4431 578711.2193 550204.7589 567143.8537 533877.4943 603389.1198 579172.3876 626029.6771 578023.1528 571359.769 0.941561643 1.012866587 0.962974274 0.99262126 0.934398121 1.056058114 1.013673729 1.09568386 1.011662326 1 19.12403993 2.725446884 24.98347953 1.04394191 0.972318209 0.486357995 0.033527083 590.1267288 1124272.01 0.010334949 0.009797513 531.4309993 -2.725446884 -0.071623701 SLSSS(ph)PVKK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 SLS(0.002)S(0.092)S(0.906)PVKK;SLSS(0.026)S(0.974)PVKK;SLS(0.001)S(0.123)S(0.875)PVKK 120.86 0.00038602 3015130000 7515100 6743100 6189100 6427000 7271400 8382900 8916600 9035900 10443700 10182400 TRUE FALSE 7221401.584 6550793.39 7307608.046 6758698.24 7505291.185 8552407.982 9025724.018 8849305.507 9258174.96 9492736.978 0.760729134 0.690084789 0.769810442 0.711986254 0.790635114 0.900942268 0.950803129 0.932218551 0.97529037 1 23.17839268 2.725807554 1.773416509 0.958504246 0.730723566 0.93764608 0.02738006 0.075985072 0.475108075 0.009958494 0.009645031 531.8725221 -2.725807554 -0.22778068 RKPS(ph)SEEGKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RKPSSEEGKR 10 3 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 RKPS(0.848)S(0.152)EEGKR;RKPS(0.982)S(0.018)EEGKR 144.27 0.00017964 740280000 294470 258290 241020 242080 266060 246990 250850 253380 304970 256190 TRUE FALSE 282961.7868 250923.8221 284577.6755 254573.7778 274618.0615 251984.307 253919.9773 248147.6145 270351.0841 238838.0231 1.184743464 1.050602491 1.19150909 1.06588463 1.149808803 1.055042676 1.063147208 1.038978682 1.131943233 1 17.86567301 2.725993301 23.96114494 1.058861266 1.124202313 0.315386537 0.051868009 550.6987537 1049973.032 0.01527986 0.014507372 532.1000517 -2.725993301 0.065341047 SRS(ph)TERPDTNLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSTERPDTNLMR 13 2 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4 A0A590UJL1 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 S(0.119)RS(0.701)T(0.18)ERPDTNLMR;S(0.109)RS(0.677)T(0.215)ERPDTNLMR 115.58 0.00051402 930060000 267280 281080 218128 272910 287110 223070 233120 265220 249400 238170 TRUE FALSE 256834.4021 273063.8736 257548.5818 286994.9178 296345.1539 227580.6282 235972.9923 259743.1143 221089.1576 222038.5338 1.156710945 1.229803985 1.159927412 1.292545546 1.334656417 1.024960057 1.062756938 1.169810978 0.995724273 1 17.76045055 2.726287969 24.97957221 1.071023307 1.233511661 0.63397808 0.069069116 574.0836117 1168480.057 0.023271584 0.022087399 532.4612034 -2.726287969 0.162488354 ETGLMYSIMVHALR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETGLMYSIMVHALR 14 0 P78527;P78527-2;H0YG84 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 200.13 1.97E-08 420310000 594220 669290 501630 573300 629210 507720 571760 496520 574410 571530 FALSE TRUE 570997.2255 650202.5045 592285.6997 602888.0817 649449.1111 517986.4463 578757.3699 486266.6885 509205.3849 532819.764 1.071651737 1.220304779 1.1116061 1.131504727 1.218890805 0.972160722 1.086216032 0.91262885 0.955680362 1 19.02328807 2.726299088 24.84633139 0.982830771 1.151405002 0.66535446 0.058655498 409.213185 829214.1478 0.01856364 0.017619429 532.4748356 -2.726299088 0.168574232 AHLS(ph)ENELEALEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHLSENELEALEK 13 0 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 1 AHLS(1)ENELEALEK;AHLS(1)ENELEALEK 218.12 1.59E-11 253450000 579240 554640 548620 569760 566210 543390 556340 499280 701600 629540 TRUE FALSE 556602.6604 538822.2102 647767.838 599165.3819 584422.6589 554377.7181 563148.6553 488969.6935 621957.3093 586900.6951 0.948376216 0.918080716 1.103709441 1.02089738 0.995777759 0.944585213 0.959529713 0.833138719 1.059731765 1 19.16275689 2.726343232 3.766833988 0.938729036 1.000784501 0.028249375 0.071107116 0.480174771 15.31498882 0.024035635 0.023791587 532.5289613 -2.726343232 0.062055465 GDVTLDPDTANPELILSEDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDVTLDPDTANPELILSEDRR 21 1 Q96F44-3;Q96F44;R4GNB9;R4GMV1 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 0 ; 167.05 2.02E-11 86948000 40527 37883 38646 42859 44759 35822 34920 43689 41871 47426 FALSE TRUE 38943.16004 36802.61393 45630.19188 45070.95813 46198.71388 36546.34538 35347.36141 42786.80688 37117.97962 44213.79478 0.880792075 0.83237854 1.032035185 1.019386785 1.044893661 0.826582418 0.799464547 0.967725279 0.839511284 1 15.43220894 2.726643109 24.749418 0.884353371 0.961792184 0.165274151 0.084466216 1289.918177 2678804.082 0.028693514 0.027252924 532.8967959 -2.726643109 0.077438813 DDREDLVYQAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DDREDLVYQAK 11 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 191.79 1.53E-06 4713750000 3332340 3611780 3397810 3753680 3890150 5138110 4585630 5433270 6536100 6511590 FALSE TRUE 3202108.469 3508775.571 4011869.851 3947407.875 4015280.208 5242006.105 4641750.312 5321071.076 5794149.33 6070554.209 0.527482065 0.577999216 0.660873738 0.650254942 0.661435525 0.863513598 0.764633698 0.876537939 0.954467933 1 22.5333968 2.726709085 0.356011233 1.02106804 0.474133517 0.920031618 0.043636748 0.448996804 0.115522811 0.049178693 0.091396759 532.9777575 -2.726709085 -0.546934523 ASESSKPWPDATYGTGSASR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASESSKPWPDATYGTGSASR 20 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 229.07 2.38E-25 1920410000 1459540 1474400 1235880 1394430 1439340 1329070 1341590 1398210 1554790 1453180 FALSE TRUE 1402499.563 1432351.556 1459231.008 1466396.699 1485637.678 1355944.706 1358008.78 1369336.475 1378296.757 1354754.824 1.035242347 1.057277324 1.077118149 1.082407439 1.096609993 1.0008783 1.002401878 1.010763313 1.017377265 1 20.36960035 2.726869039 24.86351253 1.00693185 1.070153815 0.800190456 0.015849927 322.8331601 686541.4891 0.005487145 0.005215557 533.1740936 -2.726869039 0.063221964 VSLLNERHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSLLNERHR 9 1 Q8N4B5 Q8N4B5 PRR18 Proline-rich protein 18 0 60.59 0.086394 19826000000 371310 413270 366450 317110 345550 405180 397720 407270 395120 464820 FALSE TRUE 356798.7947 401483.9442 432675.6666 333476.0851 356664.9296 413373.0172 402587.4163 398859.7322 350267.6341 433337.3274 0.823374245 0.92649287 0.998473105 0.769553103 0.823065328 0.95392894 0.929039321 0.920437052 0.808302475 1 18.72513099 2.726883076 24.80113478 0.918320829 0.873188611 0.115739235 0.073779748 1932.217211 4103693.993 0.024395511 0.023180411 533.191326 -2.726883076 -0.045132218 EVDEQMLNVQNK ddPTM_BT-474_Pertuzumab_2h_R1 11 EVDEQMLNVQNK 12 0 Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1 Q5JP53;P68371;Q13885;Q9BVA1 TUBB;TUBB4B;TUBB2A;TUBB2B Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;;;;;;;;;; 292.68 8.44E-36 7452490000 4697170 4633610 3947080 4627300 4617530 4646770 5142080 5349150 5778720 5647670 FALSE TRUE 4513599.403 4501463.98 4660405.158 4866115.508 4766057.046 4740730.873 5205010.313 5238688.183 5122743.932 5265148.28 0.857259694 0.854954835 0.885142243 0.924212434 0.905208513 0.900398359 0.988578106 0.994974482 0.972953402 1 22.32804273 2.727024127 0.551535316 1.006999339 0.852233473 0.856651274 0.02032949 0.341263051 0.218540034 0.018730713 0.022167323 533.3645257 -2.727024127 -0.154765866 GGLS(ph)PANDTGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 GGLSPANDTGAK 12 0 P30419;B7Z8J4;K7EN42 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 GGLS(1)PANDTGAK;GGLS(1)PANDTGAK;GGLS(1)PANDTGAK;GGLS(1)PANDTGAK 204.17 1.22E-07 12571300000 12901900 11780500 12102900 12023300 12523400 14795100 14549800 15453900 17509100 17885000 TRUE FALSE 12397679.48 11444531.67 14290163.26 12643823.95 12926226.53 15094267.06 14727864.8 15134771.56 15521540.37 16673633.02 0.743549979 0.686385004 0.857051564 0.758312477 0.775249552 0.905277635 0.883302684 0.907706889 0.930903322 1 23.99106515 2.727206206 0.317475358 1.008876434 0.671722928 0.795705361 0.042499629 0.926629462 0.191909154 0.054036557 0.111720425 533.5881867 -2.727206206 -0.337153506 ILGDINSDFTRVDEDEEIIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILGDINSDFTRVDEDEEIIVK 21 1 P86791;P86790 P86791 CCZ1;CCZ1B Vacuolar fusion protein CCZ1 homolog;Vacuolar fusion protein CCZ1 homolog B 0 191.79 1.20E-17 49751000 68159 68961 46506 48238 53881 64626 65898 61741 76901 71976 FALSE TRUE 65495.27093 66994.2998 54910.66872 50727.56896 55614.1313 65932.782 66704.47944 60466.02677 68171.52088 67101.00141 0.976069948 0.998409836 0.818328603 0.755988255 0.82881224 0.982590134 0.99409067 0.901119588 1.015953852 1 16.03404668 2.727220781 24.17855791 0.968066546 0.872530741 0.326516221 0.073266823 698.1341194 1488544.062 0.02645372 0.025156618 533.6060947 -2.727220781 -0.095535805 VSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFR 39 0 Q5JP53;P07437;Q5ST81;P68371;M0R2D3;Q9BVA1;P04350;M0QYM7;M0R042;K7ESM5;Q9BUF5 Q5JP53;P68371;Q9BVA1;P04350;K7ESM5 TUBB;TUBB4B;TUBB4A;TUBB2B;TUBB6 Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 42.461 0.054672 23526000 7557.2 8352.9 6834.6 10299 8872.6 7267.7 7380.3 6485.9 9417.1 9815.3 FALSE TRUE 7261.856269 8114.68347 8069.764255 10830.53262 9157.995237 7414.657873 7470.622319 6351.963898 8348.110288 9150.500988 0.793602042 0.886802098 0.881893162 1.183599962 1.000818999 0.810300757 0.816416755 0.694165697 0.912311828 1 13.15963502 2.727380573 23.64751887 0.814423564 0.955135777 0.123661626 0.122030167 546.9576722 1156896.526 0.041004794 0.039034079 533.8024626 -2.727380573 0.140712212 EYVEHTVK ddPTM_BT-474_Pertuzumab_2h_R1 3 EYVEHTVK 8 0 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ;; 72.547 0.045871 1397720000 2041510 2009600 1584700 1760870 1776490 1985880 2082770 1907950 2196950 2297160 FALSE TRUE 1961725.532 1952288.176 1871090.541 1851748.712 1833632.414 2026035.854 2108259.562 1868550.166 1947561.446 2141571.307 0.91602158 0.911614836 0.873699855 0.864668249 0.856208901 0.946051083 0.984445185 0.872513635 0.909407704 1 21.03023828 2.727391187 24.80843766 0.933066929 0.884256844 0.35408127 0.038149862 929.7659514 2065099.537 0.012920426 0.012278679 533.8155088 -2.727391187 -0.048810084 FCNTVHDIVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 FCNTVHDIVNR 11 0 G5E9W3;Q9UKF6 G5E9W3 CPSF3 Cleavage and polyadenylation specificity factor subunit 3 0 161.19 2.66E-05 135460000 111500 115090 100990 128150 122640 105610 106030 113000 127060 135040 FALSE TRUE 107142.4567 111807.7459 119241.1395 134763.8369 126584.827 107745.5066 107327.6269 110666.5105 112636.6815 125893.6205 0.851055489 0.88811288 0.947157918 1.070458029 1.005490401 0.855845643 0.852526335 0.879047803 0.894697293 1 16.94184565 2.727527694 24.89876533 0.884597791 0.955141833 0.132609125 0.068212267 1220.522606 2754434.534 0.023433647 0.022282587 533.9833237 -2.727527694 0.070544043 HS(ph)PIKEEPCGSLSETVCK ddPTM_BT-474_Pertuzumab_2h_R1 3 HSPIKEEPCGSLSETVCK 18 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 HS(0.961)PIKEEPCGS(0.035)LS(0.003)ETVCK;HS(0.911)PIKEEPCGS(0.088)LSETVCK;HS(1)PIKEEPCGSLSETVCK 187.89 2.45E-14 1649800000 2019460 1627480 1646950 1538410 1799640 1530500 1785200 1099260 2263160 2062880 TRUE FALSE 1940537.271 1581065.864 1944590.501 1617807.524 1857527.055 1561447.759 1807047.812 1076559.897 2006255.565 1923159.3 1.009036158 0.822119033 1.011143747 0.841223878 0.965872694 0.811918055 0.939624612 0.559787167 1.043208207 1 20.87504684 2.72759326 23.51867438 0.826251045 0.923481844 0 0.139700766 783.495312 1680141.576 0.043948896 0.041857683 534.0639455 -2.72759326 0.097230799 AHSLGGLDPAFTS(ph)TEDLNCK ddPTM_BT-474_Pertuzumab_2h_R1 4 AHSLGGLDPAFTSTEDLNCK 20 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AHSLGGLDPAFTS(0.977)T(0.023)EDLNCK;AHSLGGLDPAFT(0.001)S(0.979)T(0.02)EDLNCK;AHSLGGLDPAFTS(0.768)T(0.232)EDLNCK;AHSLGGLDPAFT(0.002)S(0.972)T(0.026)EDLNCK 278.52 8.15E-45 2512560000 2254750 2186420 1982180 2178920 2288340 1959470 2079020 1606160 2921260 2625750 TRUE FALSE 2166631.877 2124065.442 2340404.019 2291374.322 2361946.534 1999091.826 2104463.669 1572992.235 2589650.812 2447905.614 0.885096168 0.867707248 0.956084257 0.936055014 0.964884643 0.816653965 0.859699678 0.642586963 1.057904683 1 21.2231165 2.727687094 23.77132591 0.834808483 0.921629362 0 0.110664789 808.7230886 1767998.281 0.035461772 0.033763914 534.1793479 -2.727687094 0.086820879 DLIHGAPVGKPAANR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLIHGAPVGKPAANR 15 1 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 109.84 0.00058191 1029980000 1241140 1378260 1074960 1104790 1144280 1305860 1335560 1272350 1392400 1481720 FALSE TRUE 1192634.877 1338953.374 1269229.184 1161808.344 1181086.805 1332265.384 1351904.983 1246075.528 1234340.589 1381361.785 0.863376191 0.969299563 0.918824596 0.841060146 0.855016273 0.964457971 0.978675534 0.902063125 0.893567929 1 20.39765979 2.727743419 24.91033423 0.941081376 0.892884144 0.283595278 0.045512403 1179.612246 2716460.899 0.015544848 0.014795343 534.2486322 -2.727743419 -0.048197232 WQQHQGLLPPGMTIDLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 WQQHQGLLPPGMTIDLFR 18 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 64.2 0.037265 275790000 283240 304180 283320 265210 306480 252240 273690 255200 304690 277360 FALSE TRUE 272170.6677 295505.0842 334522.2264 278897.5199 316338.2075 257340.4656 277039.5001 249930.0308 270102.8686 258574.1602 1.052582623 1.142825269 1.2937187 1.078597798 1.223394508 0.995228856 1.071412162 0.966570019 1.044585694 1 17.98021859 2.727780046 24.94866029 1.014274076 1.160472137 0.517582597 0.068843697 548.0451367 1268296.923 0.021574853 0.02052987 534.2936915 -2.727780046 0.146198062 YGDGPRPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGDGPRPPK 9 1 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 67.563 0.055219 1134130000 2084600 2092900 1760400 1961010 1939280 2129800 2110300 2227100 2487500 2370500 FALSE TRUE 2003131.527 2033212.541 2078543.44 2062217.961 2001658.702 2172866.015 2136126.483 2181109.607 2205129.428 2209943.924 0.906417356 0.92002902 0.940541259 0.933153977 0.905750902 0.98322224 0.966597595 0.986952467 0.99782144 1 21.07557833 2.727782981 24.78898164 0.984503271 0.922855656 0.861130947 0.013173426 243.270599 559530.9679 0.004369554 0.004158536 534.2973014 -2.727782981 -0.061647615 DEWLRPEDLPIK ddPTM_BT-474_Pertuzumab_2h_R1 4 DEWLRPEDLPIK 12 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;;; 191.06 5.33E-06 2375700000 2957630 2843610 2638230 2923650 3166200 3277430 3440820 3975810 4282720 4005240 FALSE TRUE 2842042.55 2762513.027 3115016.848 3074539.927 3268043.698 3343701.88 3482929.784 3893708.134 3796563.58 3733961.527 0.761133324 0.739834357 0.834239139 0.82339893 0.875221578 0.895483752 0.932770667 1.042782071 1.016765586 1 21.83227563 2.727944729 0.630821879 1.036742084 0.752990256 0.919940203 0.028329368 0.203918715 0.17330911 0.023309589 0.024820589 534.4963324 -2.727944729 -0.283751828 LQGAEHGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQGAEHGKK 9 1 O43237;O43237-2;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 87.789 0.008584 244810000 461450 429380 306950 310830 347700 410130 401810 406400 470290 411930 FALSE TRUE 443416.0238 417134.5028 362422.6931 326871.9735 358884.0863 418423.1096 406727.471 398007.698 416904.6508 384029.6142 1.154640183 1.086203999 0.943736315 0.851163456 0.934521904 1.089559487 1.059104444 1.036398453 1.085605473 1 18.55085804 2.728047288 24.82946652 1.055092019 0.988438962 0.117668957 0.081517206 1496.312668 3533856.456 0.029105656 0.02771601 534.6225688 -2.728047288 -0.066653057 S(ph)STPPGESYFGVSSLQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.333)S(0.333)T(0.333)PPGESYFGVSSLQLK;S(0.333)S(0.333)T(0.333)PPGESYFGVSSLQLK 89.46 0.0030286 3181900000 526400 484254 480272 495354 473104 573767 569322 588219 684422 604405 TRUE FALSE 505827.706 470443.5501 567067.834 520919.2793 488321.8198 585368.9619 576289.5329 576072.0721 606729.2839 563468.111 0.897704229 0.834907142 1.006388512 0.924487596 0.866636124 1.038867951 1.022754477 1.022368544 1.076776613 1 19.10397444 2.728347007 24.8355327 1.031797553 0.908675226 0.66096159 0.045146621 404.5169751 983626.6309 0.014705774 0.014007519 534.9916542 -2.728347007 -0.123122327 TPS(ph)SEEISPTKFPGLYR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSSEEISPTKFPGLYR 17 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TPS(0.999)S(0.001)EEISPTKFPGLYR;T(0.006)PS(0.858)S(0.136)EEISPTKFPGLYR;T(0.049)PS(0.941)S(0.011)EEISPTKFPGLYR 316.66 1.56E-58 4171000000 2058330 2206790 1448510 1630680 1746380 2003540 1908610 2078720 2366980 2190620 TRUE FALSE 1977888.188 2143854.51 1710287.979 1714839.59 1802553.899 2044052.952 1931968.14 2035793.706 2098290.354 2042247.356 0.968486105 1.049752619 0.837453883 0.83968261 0.882632504 1.000884122 0.946001048 0.996839927 1.027441826 1 20.96172618 2.728429621 24.69001169 0.990255679 0.914495126 0.291571423 0.061114368 895.1274042 2181490.628 0.021668438 0.020648336 535.0934333 -2.728429621 -0.075760553 KIPSVEDSLGEGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 KIPSVEDSLGEGSR 14 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;;; 118.55 0.00038333 2206560000 902470 935540 736280 706880 761260 893260 841100 881480 1015010 894120 FALSE TRUE 867200.4747 908859.3152 869342.1745 743362.1615 785746.6193 911322.3292 851393.6334 863277.13 899790.3201 833560.456 1.040357023 1.090334011 1.042926363 0.891791539 0.942639029 1.093288822 1.021393982 1.035650292 1.079454182 1 19.66892731 2.728454109 24.70916079 1.045032135 1.002733098 0.130074017 0.057282256 1516.760657 3708283.117 0.020324532 0.019390149 535.1236049 -2.728454109 -0.042299037 LDNLHSCFCALQALIDSCAGPGSLATEPHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDNLHSCFCALQALIDSCAGPGSLATEPHVR 31 0 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 ; 208.37 2.58E-26 500330000 304810 267260 221155 253520 242410 288130 305910 248880 334500 320650 FALSE TRUE 292897.6882 259638.0065 261122.6281 266604.1976 250207.3378 293956.186 309653.8181 243740.541 296528.9623 298932.0899 0.97981347 0.868551806 0.873518223 0.891855397 0.837003943 0.9833544 1.035866769 0.815370946 0.991960958 1 18.18945825 2.728985692 24.97520273 0.948438151 0.888119662 0.228734376 0.065385993 1286.175991 3354852.015 0.021731527 0.020720846 535.7790054 -2.728985692 -0.060318489 KSPSSDSWTCADTSTER ddPTM_BT-474_Pertuzumab_2h_R1 4 KSPSSDSWTCADTSTER 17 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 ;;; 143.04 9.04E-07 1193670000 730140 789320 657470 732290 712360 797600 829370 795300 901130 901280 FALSE TRUE 701605.3216 766809.3664 776289.4543 770083.5747 735273.7063 813728.0185 839520.0782 778876.7771 798837.5002 840235.5028 0.835010327 0.912612433 0.923895089 0.916509207 0.875080503 0.968452316 0.999148543 0.926974371 0.950730477 1 19.68043422 2.72920239 24.39311812 0.964004219 0.896796633 0.595896514 0.031241315 391.4461675 1020339.908 0.010217874 0.009759338 536.0464074 -2.72920239 -0.067207586 DVYTGDALR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVYTGDALR 9 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ; 105.94 0.0070194 946200000 1108070 1175500 867810 920870 1003890 942330 945860 935140 857610 979700 FALSE TRUE 1064765.399 1141975.891 1024642.571 968396.2111 1036181.034 961384.5582 957435.7176 915829.0322 760257.7082 913344.0464 1.165787858 1.250323901 1.12185827 1.060275386 1.134491474 1.052598484 1.048274986 1.002720755 0.832389187 1 19.80079888 2.72953563 0.525210241 0.932811073 1.206780129 0.681029691 0.060617274 0.577620751 0.333279484 0.053092527 0.065866931 536.4578814 -2.72953563 0.273969056 S(ph)LSLSLADSGHLPDVHGFNSYGSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.544)LS(0.438)LS(0.018)LADSGHLPDVHGFNSYGSHR 125.85 0.00023021 127660000 113010 109350 73072 110700 72434 64567 67240 27915 69886 56039 TRUE FALSE 108593.4443 106231.4451 86277.73588 116413.2403 74763.90539 65872.58898 68062.90323 27338.54549 61952.83427 52243.42862 2.078604853 2.033393441 1.651456234 2.228284846 1.431068124 1.260877985 1.302803147 0.523291564 1.185849319 1 15.67296196 2.729595741 1.163337172 0.887355913 1.996142364 0.761326572 0.247514629 0.208326826 0.585096573 0.119797703 0.1106662 536.5321373 -2.729595741 1.108786451 KTEPATGFIDGDLIESFLDISRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTEPATGFIDGDLIESFLDISRPK 24 2 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 264 1.85E-44 848550000 572860 566210 474810 418320 498290 563390 555190 606050 618560 664960 FALSE TRUE 550471.9979 550062.2452 560618.7291 439909.5453 514317.9504 574782.1318 561984.5813 593534.8557 548343.662 619921.6669 0.887970251 0.887309276 0.904338014 0.709621181 0.829649902 0.927185099 0.90654128 0.957435249 0.884537017 1 19.2417264 2.729948718 19.85123247 0.932249893 0.842107458 0.380288991 0.058236183 44.5696792 102735.2103 0.019365651 0.018631466 536.9683868 -2.729948718 -0.090142435 LSKDPNIVIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSKDPNIVIAK 11 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 82.362 0.014515 0 2194100 2316100 1823100 2056900 2170500 2337200 2302600 2599800 2586100 2638900 FALSE TRUE 2108352.146 2250047.096 2152574.725 2163056.855 2240316.104 2384459.785 2330779.908 2546113.221 2292536.77 2460164.953 0.856996253 0.914591964 0.874971706 0.879232449 0.910636541 0.969227605 0.94740798 1.034935978 0.931863031 1 21.23032362 2.730085949 1.562498503 0.98783322 0.882024204 0.703891785 0.029437289 0.19777879 0.969897457 0.011588596 0.011107623 537.1380886 -2.730085949 -0.105809015 GRLDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_BT-474_Pertuzumab_2h_R1 5 GRLDSSEMDHSENEDYTMSSPLPGK 25 1 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GRLDS(0.12)S(0.12)EMDHS(0.735)ENEDY(0.021)T(0.004)MSSPLPGK;GRLDS(0.024)S(0.024)EMDHS(0.947)ENEDY(0.004)T(0.001)MSSPLPGK;GRLDS(0.005)S(0.005)EMDHS(0.939)ENEDY(0.023)T(0.024)MS(0.004)S(0.001)PLPGK;GRLDS(0.163)S(0.214)EMDHS(0.622)ENEDYT(0.001)MSSPLPGK;GRLDS(0.009)S(0.009)EMDHS(0.662)ENEDY(0.309)T(0.011)MSSPLPGK 136.42 1.82E-05 1736150000 1367307 1260147 1043056 1140324 1137833 1290253 1244564 1261778 1495901 1370437 TRUE FALSE 1313871.131 1224208.841 1231559.422 1199176.258 1174432.432 1316342.8 1259795.347 1235721.843 1326092.59 1277616.081 1.028377108 0.95819774 0.963951096 0.938604543 0.919237359 1.030311702 0.986051573 0.967209056 1.037942939 1 20.28502295 2.730413003 24.99724054 0.997869209 0.960325384 0.290830178 0.032482908 931.0361198 2856451.026 0.010697174 0.010261755 537.5427434 -2.730413003 -0.037543826 SSGGSGGGPLSHFYSGS(ph)PTSYFTSGLQAGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGGSGGGPLSHFYSGSPTSYFTSGLQAGLK 31 0 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 SSGGSGGGPLSHFYS(0.001)GS(0.995)PT(0.003)S(0.001)YFTSGLQAGLK;SSGGSGGGPLSHFYS(0.001)GS(0.998)PT(0.001)SYFTSGLQAGLK 327.38 9.08E-106 645660000 521260 506860 492160 507530 489670 575310 593110 591440 567160 685380 TRUE FALSE 500888.5829 492404.8491 581104.26 533723.6841 505420.6803 586943.1624 600368.6576 579226.5573 502778.3745 638958.6021 0.783913983 0.770636544 0.909455258 0.835302447 0.791006927 0.918593412 0.939604938 0.906516565 0.786871595 1 19.28536294 2.730436261 24.22280694 0.907247691 0.821463318 0.363179101 0.060930007 486.5588163 1450673.21 0.019539192 0.018727452 537.5715307 -2.730436261 -0.085784373 VRIDQYQGADAVGLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VRIDQYQGADAVGLEEK 17 1 O43396;K7ER96;K7EML9 O43396 TXNL1 Thioredoxin-like protein 1 0 ; 205.62 7.04E-12 851390000 1079250 1058610 783580 862150 886640 1052090 958100 1111930 1218150 1092070 FALSE TRUE 1037071.717 1028419.479 925190.3366 906645.6648 915159.5808 1073363.981 969825.5144 1088968.257 1079870.719 1018103.126 1.018631306 1.010132916 0.908739314 0.890524389 0.898886918 1.054278248 0.952580824 1.069605062 1.060669289 1 19.95745227 2.730480277 24.94250444 1.028571343 0.94389673 0.392222866 0.051038021 654.5485639 2020465.2 0.017677293 0.016925246 537.6260171 -2.730480277 -0.084674613 DIPVTIHNLEEYLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DIPVTIHNLEEYLR 14 0 Q14669-3;Q14669;Q14669-2;Q14669-4;H7C2Y1 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 0 ;; 181.26 1.66E-06 151366000 130745 144241 107823 124756 136653 112297 122776 124069 126823 130409 FALSE TRUE 125635.3409 140127.3879 127309.0146 131194.6721 141048.5679 114567.7223 124278.5694 121506.9318 112426.5847 121576.2823 1.033386928 1.152588196 1.047153378 1.079114032 1.160165167 0.942352572 1.022227091 0.999429572 0.924741098 1 16.89150228 2.730577539 24.99546334 0.98323142 1.094226596 0.616960259 0.045886977 407.0336957 1274441.727 0.014142366 0.013562082 537.7464344 -2.730577539 0.110995176 S(ph)SSLSDLTHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLSDLTHR 10 0 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 S(0.473)S(0.473)S(0.055)LSDLTHR 162.68 4.31E-06 302940000 312060 296600 225320 340660 320350 262300 274940 333600 275820 296610 TRUE FALSE 299864.3502 288141.2584 266040.3362 358241.5034 330654.3487 267603.8857 278304.798 326711.0434 244510.0699 276520.3405 1.084420588 1.042025545 0.962100422 1.295534002 1.19576863 0.967754796 1.006453259 1.181508177 0.884239002 1 18.07702608 2.730659122 24.63117045 1.032406452 1.113289308 0.180212929 0.109029575 1216.74488 3792924.264 0.037171011 0.035635587 537.8474595 -2.730659122 0.080882855 ENVKDYYQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENVKDYYQK 9 1 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 0 116.52 0.0011864 627040000 521730 529580 372580 382200 432980 499080 497550 529600 546760 547530 FALSE TRUE 501340.2148 514476.8969 439913.494 401925.3878 446907.1949 509171.7395 503639.1657 518663.5749 484694.097 510445.3054 0.982162456 1.007898185 0.86182298 0.787401478 0.875524155 0.997504991 0.98666627 1.016100196 0.949551484 1 18.96139686 2.730695499 23.98284661 0.992762159 0.900086133 0.345796232 0.059706802 427.7356366 1304276.995 0.021557761 0.020685103 537.8925124 -2.730695499 -0.092676025 LGEINVIGEPFLNVNCEHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGEINVIGEPFLNVNCEHIK 20 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 177.73 6.44E-17 588360000 242809 218265 190745 214657 204465 238637 235743 233635 271750 250453 FALSE TRUE 233319.7558 212040.2959 225216.8646 225735.4735 211041.8024 243462.4036 238628.0934 228810.3556 240902.0793 233489.5952 0.999272604 0.908135952 0.964569168 0.96679029 0.903859558 1.042712004 1.022007397 0.979959537 1.031746528 1 17.83299874 2.731123066 24.98743249 1.011788129 0.948187673 0.540911174 0.030666402 457.0222906 1535422.706 0.009520573 0.009148738 538.4223331 -2.731123066 -0.063600456 KMSGGSTMS(ph)SGGGNTNNSNSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.206)GGS(0.223)T(0.223)MS(0.312)S(0.037)GGGNTNNSNSK 73.322 0.0063039 182970000 72793 81689 55866 59252 64699 77981 81417 73937 97320 88938 TRUE FALSE 69948.16908 79359.3097 65962.22893 62310.00282 66780.10209 79557.82925 82413.4056 72410.17511 86272.6416 82914.15004 0.843621614 0.957126252 0.795548515 0.75150023 0.805412611 0.959520531 0.993960688 0.87331505 1.04050565 1 16.33933071 2.731174161 24.29867756 0.959785255 0.831322369 0.549250423 0.064092654 353.5965728 1163197.92 0.021819197 0.020961478 538.4856826 -2.731174161 -0.128462886 LIDWGLAEFYHPGQEYNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIDWGLAEFYHPGQEYNVR 19 0 P68400;E7EU96;A0A2R8YD58;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A2R8Y4H0;A0A2R8Y4D6 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 162.33 2.78E-11 1677480000 701990 712150 638760 661020 696940 634660 628480 649280 730040 747550 FALSE TRUE 674555.4547 691840.1793 754198.1411 695135.3214 719357.708 647493.26 636171.5262 635872.1411 647168.9198 696917.7727 0.967912545 0.992714215 1.082191 0.997442379 1.032198828 0.929081285 0.912835848 0.912406264 0.928615893 1 19.41062892 2.731335165 24.06427361 0.927727064 1.016095806 0.521921606 0.036778574 237.6184791 791382.6819 0.01157653 0.01113083 538.6853507 -2.731335165 0.088368742 HS(ph)LQEIT(ph)S(ph)VTFK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSLQEITSVTFK 12 0 H0Y5Q9;Q92835-3;Q92835-2;Q92835 H0Y5Q9 INPP5D "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1" 3 HS(1)LQEIT(0.667)S(0.667)VT(0.667)FK;HS(1)LQEIT(0.667)S(0.667)VT(0.667)FK 80.688 0.031536 90768000 9737.4 6933.2 7573.6 7338.6 8615.7 6800 6771.9 8375.8 6635.3 10299.3 TRUE FALSE 9356.851643 6735.471924 8942.317994 7717.346025 8892.831815 6937.500659 6854.776538 8202.836803 5882.088561 9601.719237 0.974497526 0.701486032 0.931324669 0.80374627 0.926170782 0.722526923 0.71391137 0.854309171 0.612607848 1 13.22907704 2.731378899 24.95575068 0.773150331 0.858235156 0.113928375 0.118704254 1212.703265 4214013.417 0.035037046 0.033675382 538.7395999 -2.731378899 0.085084825 S(ph)LGLDINMDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLGLDINMDSR 11 0 Q96H22-5;Q96H22-4;Q96H22;Q96H22-3 Q96H22-5 CENPN Centromere protein N 1 S(1)LGLDINMDSR;S(1)LGLDINMDSR;S(1)LGLDINMDSR;S(1)LGLDINMDSR 194.51 5.04E-07 208027000 211383 198905 176016 183504 194933 186980 169309 220547 204728 193922 TRUE FALSE 203121.9187 193232.4241 207826.0067 192974.6634 201203.197 190760.8637 171381.0542 215992.6274 181488.1357 180787.4902 1.123539679 1.068837362 1.149559665 1.067411596 1.112926546 1.055166281 0.947969652 1.194732153 1.00387552 1 17.46393533 2.731408916 23.28971447 1.056334199 1.102924064 0.176406902 0.064766241 524.378884 1707648.887 0.020843306 0.02006623 538.7768365 -2.731408916 0.046589865 ILNEDGSPNLDFKPEDQPHFDIKDEF ddPTM_BT-474_Pertuzumab_2h_R1 1 ILNEDGSPNLDFKPEDQPHFDIKDEF 26 2 Q9UMX5 Q9UMX5 NENF Neudesin 0 151.66 6.44E-08 59817000 13524 14589 11449 11572 11801 15958 15369 15055 20760 17627 FALSE TRUE 12995.46713 14172.936 13518.08898 12169.23231 12180.58988 16280.68169 15557.09042 14744.10899 18403.41183 16433.10759 0.79081008 0.862462314 0.822613064 0.740531408 0.741222548 0.990724463 0.946691935 0.897219769 1.119898457 1 14.00431771 2.731451703 24.94878319 0.973705074 0.794362501 0.709319994 0.063327124 341.5923473 1198818.273 0.021121352 0.020299118 538.8299194 -2.731451703 -0.179342573 GSPAS(ph)PTSPSDCPPALAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPASPTSPSDCPPALAPR 19 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 GSPAS(0.994)PT(0.006)SPSDCPPALAPR 235.02 3.95E-24 171260000 97674 94456 72597 89851 81346 81952 83813 78830 78870 98085 TRUE FALSE 93856.7921 91762.20736 85716.89281 94488.22088 83962.56797 83609.12559 84838.72857 77202.13295 69917.00825 91441.61558 1.026412225 1.003505972 0.937394777 1.033317492 0.918209586 0.914344361 0.927791225 0.844277876 0.764608191 1 16.48056327 2.731616895 1.022796221 0.863296185 0.999702312 0.392924795 0.062783897 0.479689022 1.057007868 0.03299021 0.030320766 539.0349123 -2.731616895 0.136406127 REFDRHS(ph)GSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 REFDRHSGSDR 11 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 REFDRHS(0.934)GS(0.066)DR 69.331 0.028591 104710000 104840 97872 90529 101780 88519 119260 111280 123980 114300 121800 TRUE FALSE 100742.7369 95080.78639 106889.6041 107032.878 91366.29403 121671.5189 112641.8779 121419.7697 101325.1432 113550.3775 0.887207415 0.83734452 0.941340808 0.942602573 0.804632235 1.071520162 0.99199915 1.069303091 0.892336471 1 16.79297298 2.731968678 24.99548654 1.013151837 0.886703919 0.499909387 0.060875947 423.2874882 1605028.205 0.01894512 0.018241864 539.4717135 -2.731968678 -0.126447918 RS(ph)PSLSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSPSLSSK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RS(0.998)PS(0.002)LSSK;RS(0.723)PS(0.277)LSSK 84.213 0.010787 648170000 424500 474490 423380 371970 391010 450590 342110 393440 422300 417530 TRUE FALSE 407910.0707 460958.0098 499894.184 391167.4163 403587.1918 459701.2385 346296.8445 385315.3265 374362.2744 389250.3212 1.04793766 1.184219986 1.28424861 1.004925096 1.036832007 1.180991289 0.889650761 0.989890838 0.961751999 1 18.5703387 2.732092623 0.863267523 0.960817154 1.155280293 0.366405735 0.09118163 0.613320013 0.977678065 0.057315871 0.053461834 539.6256973 -2.732092623 0.194463139 WENPGLGAESHTDSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 WENPGLGAESHTDSLR 16 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 208.13 1.56E-11 489070000 178540 187630 167380 234180 206360 171940 182160 199260 167090 207860 FALSE TRUE 171562.4594 182278.9761 197629.2893 246266.0579 212997.7568 175416.7446 184389.3286 195145.2114 148122.6437 193781.4571 0.885339919 0.940641994 1.019856556 1.270844288 1.099164802 0.905229774 0.951532367 1.007037589 0.764379864 1 17.564071 2.73209986 24.59304639 0.934968403 1.048826974 0.206046933 0.114358717 774.2436944 2947175.178 0.039352789 0.037895078 539.6346899 -2.73209986 0.11385857 YETPSDAIEVIS(ph)PASS(ph)PAPPQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YETPSDAIEVISPASSPAPPQEK 23 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 2 YETPSDAIEVIS(1)PAS(0.007)S(0.993)PAPPQEK 180.88 2.33E-17 121790000 117350 101450 96107 94386 97465 115870 105180 126920 126440 127340 TRUE FALSE 112763.8323 98556.74533 113475.6728 99257.27277 100600.0502 118212.9708 106467.2243 124299.0576 112087.0613 118715.1484 0.949868941 0.830195191 0.955865147 0.836096102 0.847407021 0.995769895 0.896829307 1.047036198 0.944168144 1 16.85714451 2.732118426 24.97279678 0.978569174 0.882247424 0.423174367 0.054178584 466.8704172 1809792.487 0.016582625 0.015978715 539.6577601 -2.732118426 -0.09632175 LGIHEDSQNRK ddPTM_BT-474_Pertuzumab_2h_R1 7 LGIHEDSQNRK 11 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;; 196.88 3.83E-08 21709290000 18903730 19844090 15979340 16856090 17074890 19502740 18684660 19110450 22527530 21416810 FALSE TRUE 18164951.33 19278155.98 18867162.2 17726034.82 17624119.34 19897098.77 18913328.46 18715812.53 19970299.24 19966230.38 0.909783719 0.965538092 0.944953646 0.887800776 0.882696383 0.996537573 0.947265863 0.937373363 1.000203787 1 24.25105864 2.732148394 24.99443589 0.967137441 0.920589464 0.455515468 0.030919607 626.2425216 2441047.665 0.010581496 0.010186661 539.6949995 -2.732148394 -0.046547977 SYQNS(ph)PS(ph)SDDGIRPLPEYSTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 SYQNS(1)PS(0.546)S(0.454)DDGIRPLPEYSTEK;SYQNS(1)PS(0.955)S(0.045)DDGIRPLPEYSTEK 251.19 2.62E-32 1088920000 1530200 1518050 1326220 1449340 1454840 1705070 1659500 1676210 1953090 2023630 TRUE FALSE 1470398.092 1474756.7 1565897.456 1524140.611 1501636.25 1739547.684 1679809.457 1641595.678 1731383.411 1886567.738 0.779403815 0.781714153 0.830024507 0.807890743 0.795962011 0.92207009 0.890405059 0.870149343 0.91774251 1 20.84733247 2.732391551 0.119254576 1.108590018 0.594662393 0.840010656 0.027755562 6.178375142 0.31413586 0.450917851 0.830294707 539.9972532 -2.732391551 -0.513927625 KDTEIFYQFTSFLSPGIIYHCDLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDTEIFYQFTSFLSPGIIYHCDLTK 25 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 213.02 3.64E-26 78415000 109070 133420 109180 97314 118330 97210 101550 92809 125970 112740 FALSE TRUE 104807.4238 129614.9922 128911.2547 102336.3872 122136.1919 99175.6528 102792.7993 90892.46172 111670.4137 105104.0194 0.997178076 1.233206808 1.226511179 0.973667685 1.16205063 0.943595244 0.978010164 0.864785783 1.062475197 1 16.68145832 2.732577196 24.85865303 0.954198819 1.122846046 0.388517901 0.092198272 420.263583 1746018.119 0.029246116 0.028238889 540.2281326 -2.732577196 0.168647227 KQELEEICHDLEAR ddPTM_BT-474_Pertuzumab_2h_R1 8 KQELEEICHDLEAR 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 287.54 3.23E-34 27632930000 11351200 11447520 8822400 10856350 10640590 11762980 12066340 12282410 13452400 12839920 FALSE TRUE 10907582.55 11121047.94 10416803.93 11416647.52 10982854.24 12000835.52 12214011.48 12028773.94 11925339.95 11970260.78 0.911223469 0.929056446 0.870223642 0.953750944 0.917511693 1.002554224 1.020363023 1.004888211 0.996247297 1 23.51295125 2.732687847 5.227569816 1.006859208 0.91617252 0.827945982 0.020159474 0.067604339 6.218206918 0.006305572 0.006258362 540.36579 -2.732687847 -0.090686688 RYPSSISSS(ph)PQKDLTQAK ddPTM_BT-474_Pertuzumab_2h_R1 4 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSISS(0.002)S(0.998)PQKDLTQAK;RYPSSISS(0.096)S(0.904)PQKDLTQAK;RYPSSISS(0.004)S(0.996)PQKDLTQAK;RYPSSISS(0.028)S(0.972)PQKDLTQAK 321.1 6.73E-62 8649840000 8120740 7262890 4979800 4832930 5758950 6857410 6314630 6936910 7822280 6930700 TRUE FALSE 7803372.503 7055759.488 5879760.635 5082358.096 5944191.857 6996071.529 6391910.331 6793660.384 6934327.568 6461277.516 1.207713565 1.092006878 0.909999705 0.786587186 0.919971607 1.082769083 0.989264169 1.051442283 1.073213084 1 22.62338801 2.732782828 24.82182511 1.039031543 0.9743017 0.059523292 0.108579227 1393.298044 5985692.836 0.038347469 0.037099774 540.4839825 -2.732782828 -0.064729843 LGSVS(ph)LDLCDGDTGEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSVSLDLCDGDTGEPR 17 0 Q8N6R0-3;Q8N6R0-4;Q8N6R0;Q8N6R0-2 Q8N6R0-3 METTL13 Methyltransferase-like protein 13 1 LGS(0.278)VS(0.722)LDLCDGDTGEPR 211.7 2.35E-12 32365000 67637 58838 44132 56427 61328 51879 52227 62499 53832 54336 TRUE FALSE 64993.67126 57159.99785 52107.63411 59339.20423 63300.67082 52928.02893 52866.16965 61208.37381 47721.21704 50655.77432 1.283045657 1.128400436 1.028661289 1.171420337 1.24962399 1.044856774 1.043635604 1.208319775 0.942068652 1 15.62843911 2.732800411 0.021066982 1.63E-06 2.241569796 0.295686728 0.091465801 797.2410817 6.609380031 330.9788916 370.9319864 540.5058651 -2.732800411 2.241568169 TLNAETPKSS(ph)PLPAK ddPTM_BT-474_Pertuzumab_2h_R1 5 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 TLNAETPKS(0.033)S(0.967)PLPAK;TLNAETPKS(0.031)S(0.969)PLPAK;TLNAETPKS(0.175)S(0.825)PLPAK;TLNAETPKS(0.14)S(0.86)PLPAK;TLNAETPKS(0.112)S(0.888)PLPAK 199.97 4.33E-09 5155320000 2874200 2499990 1772930 1565090 2140480 2483800 2383380 2613100 3264810 2541790 TRUE FALSE 2761873.086 2428692.733 2093337.89 1645864.482 2209330.483 2534024.138 2412548.517 2559138.572 2894202.456 2369632.299 1.165528123 1.024923881 0.88340199 0.694565348 0.932351607 1.069374408 1.018110919 1.07997286 1.221371964 1 21.17623178 2.732895631 6.022128735 1.07796822 0.927698123 0.234111877 0.123523889 0.24259653 39.65482674 0.042354402 0.04198792 540.6243858 -2.732895631 -0.150270097 ELMWLNEKEEEEVGFDWSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELMWLNEKEEEEVGFDWSDR 20 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 207.22 6.28E-22 124160000 130380 133250 97964 116760 113450 137060 134720 130620 159990 164300 FALSE TRUE 125284.6055 129449.8405 115668.274 122785.9976 117099.2223 139831.4471 136368.7437 127922.6514 141828.6059 153171.8147 0.817935113 0.845128334 0.755153775 0.801622661 0.764495887 0.912905859 0.890299197 0.835157902 0.925944543 1 17.22479132 2.733029019 24.98746137 0.895348117 0.797495114 0.599669227 0.046292851 368.2571455 1663496.212 0.014719182 0.014239168 540.7904562 -2.733029019 -0.097853003 HVQELRPIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 HVQELRPIAR 10 1 Q8TE77;Q8TE77-2;Q8TE77-3;E9PIT5;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;; 145.99 1.77E-05 1022270000 272730 271738 240484 326397 288480 260670 280209 243417 318700 328140 FALSE TRUE 262071.4101 263988.2983 283944.8083 343242.3883 297759.2212 265940.926 283638.2816 238390.3539 282522.5121 305914.7855 0.856681084 0.86294717 0.928182689 1.12201961 0.973340405 0.869330083 0.927180689 0.779270454 0.923533368 1 18.22277031 2.733212309 23.6082995 0.87982727 0.952370131 0.048586946 0.087048556 452.513084 1997458.621 0.029578899 0.0286803 541.0187404 -2.733212309 0.072542861 KRS(ph)PSPSPTPEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 KRS(0.477)PS(0.261)PS(0.261)PT(0.001)PEAK;KRS(0.977)PS(0.008)PS(0.015)PTPEAK 144.3 3.25E-05 410350000 457381 400603 360760 336217 383533 417023 450626 376914 508630 511848 TRUE FALSE 439506.0449 389178.1947 425957.3571 353569.1997 395869.6873 425455.4908 456140.8958 369130.5942 450892.4548 477180.0791 0.921048602 0.8155793 0.892655364 0.740955491 0.829602292 0.89160363 0.955909343 0.773566648 0.944910474 1 18.86417429 2.733291209 21.63654911 0.892541737 0.836039623 0.176064286 0.072383765 149.7992909 615080.1344 0.0229282 0.022286446 541.1170379 -2.733291209 -0.056502115 KEQTADGVAVIPVLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEQTADGVAVIPVLQR 16 1 A6NFX8;Q9UKK9;A6NCQ0;A6NJU6;H0YEY4 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 119.46 0.0019102 0 309000 287940 238190 240900 250050 305060 294750 308080 350690 281790 FALSE TRUE 296923.9384 279728.2331 281236.2315 253332.8779 258093.0853 311228.5222 298357.2387 301718.0403 310881.1414 262704.1123 1.130259956 1.064803404 1.070543697 0.964327797 0.982447831 1.184711269 1.135715905 1.148509011 1.183388942 1 18.00307926 2.733496212 24.99688362 1.140656765 1.040934608 0.307698881 0.0650784 480.4248813 2371272.43 0.02062621 0.019996515 541.3725262 -2.733496212 -0.099722157 S(ph)RTPSASNDDQQE ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 S(0.591)RT(0.395)PS(0.013)AS(0.001)NDDQQE 74.769 0.087362 11009000 24761 23730 16768 22792 21075 23558 22415 25181 25488 24323 TRUE FALSE 23793.31275 23053.24363 19798.3506 23968.29785 21752.89651 24034.3589 22689.32148 24661.00355 22594.70909 22675.58155 1.049292284 1.016655012 0.873113246 1.05700918 0.959309311 1.059922492 1.000605935 1.087557711 0.9964335 1 14.46885193 2.733542786 24.90383558 1.036297893 0.989606363 0.096902595 0.055400407 794.805645 3944657.164 0.01721422 0.016689242 541.4305857 -2.733542786 -0.04669153 HSPEDPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSPEDPEK 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 149.82 0.00049914 948870000 1081050 922520 962660 964420 1079440 880590 1080260 705030 1401060 1218540 FALSE TRUE 1038801.371 896210.6328 1136634.076 1014193.832 1114161.168 898396.1331 1093480.545 690470.8841 1242017.543 1136007.2 0.91443203 0.78891281 1.000551824 0.892770602 0.980769459 0.790836654 0.962564801 0.607805024 1.093318372 1 20.11554055 2.733810472 24.93829214 0.851496355 0.911919188 0 0.135658448 1443.71192 7579478.225 0.042098435 0.040895411 541.7644105 -2.733810472 0.060422833 EELRHT(ph)PELPLAPRPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EELRHTPELPLAPRPLK 17 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 EELRHT(1)PELPLAPRPLK 106.73 0.035197 339560000 491890 495050 314060 385510 394120 480780 481680 474360 553200 488580 TRUE FALSE 472666.395 480931.6587 370817.6282 405406.2173 406797.2277 490501.701 487574.9439 464564.3002 490403.0552 455488.0414 1.03771417 1.055860121 0.814110568 0.890047993 0.893101884 1.076870645 1.070445104 1.019926448 1.076654073 1 18.79705365 2.734130818 24.96361491 1.049287368 0.93514016 0.384968376 0.069851382 423.7442421 2387953.251 0.023948572 0.023306816 542.1641762 -2.734130818 -0.114147208 IINEVKPTEIYNLGAQSHVK ddPTM_BT-474_Pertuzumab_2h_R1 1 IINEVKPTEIYNLGAQSHVK 20 1 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 95.958 0.0006922 440310000 179640 180290 195450 165410 171320 216750 205120 220770 249950 217070 FALSE TRUE 172619.4702 175148.3057 230772.1628 173946.8299 176830.6634 221132.8335 207630.3199 216211.0224 221576.7239 202367.6556 0.852999308 0.865495552 1.140360905 0.859558458 0.873808924 1.092728148 1.026005462 1.068407013 1.094921633 1 17.6266192 2.734204804 24.96079296 1.058678474 0.924560241 0.406884343 0.083101592 394.011491 2257858.009 0.026847577 0.026128222 542.2565472 -2.734204804 -0.134118233 AEEEDDDIKQLAAWAT ddPTM_BT-474_Pertuzumab_2h_R1 2 AEEEDDDIKQLAAWAT 16 1 Q96CF2 Q96CF2 CHMP4C Charged multivesicular body protein 4c 0 ; 141.21 1.33E-05 46350000 212503 200711 160389 156606 177953 203594 191220 224463 232732 218163 FALSE TRUE 204198.1478 194986.9188 189374.8601 164688.4544 183677.0199 207710.8102 193560.2076 219827.7606 206313.2391 203386.6257 1.003990047 0.95870079 0.931107734 0.809730993 0.903092911 1.021260909 0.951686016 1.080836854 1.014389409 1 17.63386529 2.734327028 24.44172083 1.018563379 0.917744828 0.413959778 0.054676987 266.3138366 1537500.769 0.018736424 0.018248461 542.4091763 -2.734327028 -0.100818551 DIIHNPQALSPQFTGILQLLQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIIHNPQALSPQFTGILQLLQSR 23 0 Q68E01-2;Q68E01-3;Q68E01;A0A096LNW8 Q68E01-2 INTS3 Integrator complex subunit 3 0 168.56 9.51E-12 190010000 84860 77746 74402 96089 88173 75013 85079 77239 82768 90551 FALSE TRUE 81543.57738 75528.7602 87848.09646 101048.1648 91009.16462 76529.81426 86120.22225 75643.98766 73372.52363 84417.90012 0.965951265 0.89470077 1.040633519 1.19699927 1.078078992 0.906559085 1.020165417 0.896065734 0.86915836 1 16.36526132 2.734384588 24.84185314 0.935903235 1.036745834 0.248850649 0.084086193 520.0951625 3093868.436 0.029512699 0.028754568 542.4810701 -2.734384588 0.100842599 IREYPER ddPTM_BT-474_Pertuzumab_2h_R1 1 IREYPER 7 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 87.639 0.017505 184090000 100420 101710 97490 98616 105670 92702 98153 100950 111820 102820 FALSE TRUE 96495.47538 98809.33038 115108.6117 103705.5836 109068.9715 94576.49796 99354.22577 98865.34722 99126.66239 95855.90982 1.006672156 1.030811043 1.200850442 1.081890347 1.137842953 0.98665276 1.036495569 1.031395429 1.034121554 1 16.54857976 2.734387232 24.98427408 1.022179326 1.093764036 0.33138512 0.052236079 455.4128385 2726354.425 0.017152061 0.016696373 542.4843729 -2.734387232 0.071584711 DKPSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKPSLR 6 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ;; 110.63 0.026025 2973780000 4239400 4294900 3596300 3762800 3836900 4318000 4119600 4419100 4837400 4695700 FALSE TRUE 4073719.561 4172413.657 4246231.409 3956998.559 3960317.373 4405312.918 4170016.897 4327844.041 4288278.632 4377656.057 0.930570951 0.953115915 0.969978307 0.903908052 0.904666178 1.006317733 0.952568416 0.988621304 0.979583269 1 22.06172718 2.734633609 24.99980477 0.982315447 0.934095582 0.569303079 0.022934934 289.1406632 1840695.691 0.007581547 0.007395739 542.7922129 -2.734633609 -0.048219865 S(ph)STVTGGEEPTPSVAYVHTTPGLPSGWEER ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTVTGGEEPTPSVAYVHTTPGLPSGWEER 30 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-4 Q96PU5-7 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.332)S(0.332)T(0.332)VT(0.005)GGEEPTPSVAYVHTTPGLPSGWEER;S(0.314)S(0.314)T(0.314)VT(0.025)GGEEPT(0.027)PS(0.005)VAY(0.001)VHTTPGLPSGWEER 98.75 0.00037269 183520000 34742.6 44889 25942.1 33982 31979.2 39990 35243.4 47140 35879 34060 TRUE FALSE 33384.82078 43608.80967 30630.41455 35735.81509 33007.84001 40798.6252 35674.71927 46166.54253 31806.16634 31753.08586 1.051388231 1.373372335 0.96464371 1.1254281 1.039515975 1.284871189 1.123504009 1.453923021 1.001671663 1 14.95460918 2.73464947 24.91241997 1.217331842 1.11813829 0 0.162011804 884.1992503 5631975.533 0.050021862 0.048702997 542.8120369 -2.73464947 -0.099193551 SLS(ph)FEMQQDELIEKPMSPMQYAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSFEMQQDELIEKPMSPMQYAR 23 1 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 SLS(1)FEMQQDELIEKPMSPMQYAR;S(0.001)LS(0.999)FEMQQDELIEKPMSPMQYAR;S(0.012)LS(0.988)FEMQQDELIEKPMSPMQYAR 233.3 2.94E-37 676355000 379795 340321 260192 306666 371039 366172 397557 434937 481420 416829 TRUE FALSE 364952.1915 330615.3783 307214.4823 322493.069 382973.8064 373576.2487 402422.4215 425955.399 426771.2199 388596.8006 0.939153876 0.850792847 0.790573885 0.82989121 0.985530004 0.961346692 1.035578319 1.096137174 1.098236576 1 18.5679145 2.734686656 1.259674014 1.071058566 0.849712834 0.742037654 0.051692724 0.212179953 0.692419756 0.024690121 0.023122127 542.8585169 -2.734686656 -0.221345732 RIDTPSLEEPSDLEELEQFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RIDTPSLEEPSDLEELEQFAK 21 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 0 111.38 0.00040065 42117000 39104 41262 32926 37000 38971 35661 33693 37783 45209 45013 FALSE TRUE 37575.77245 40085.24816 38876.46063 38909.57443 40224.53761 36382.08985 34105.34501 37002.76785 40077.06385 41964.22942 0.895423864 0.955224216 0.926419028 0.927208124 0.958543459 0.866978623 0.812724206 0.881769268 0.955029186 1 15.35687247 2.734787357 24.97312608 0.887389629 0.933183747 0.032596362 0.050907274 608.8305323 4029500.419 0.015923002 0.015579171 542.9844063 -2.734787357 0.045794118 KLEEVER ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEEVER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 98.033 0.018536 520130000 427000 462840 376780 437100 424910 491770 476590 548400 577810 482660 FALSE TRUE 410312.3679 449640.2564 444872.5274 459658.7834 438577.616 501713.9263 482422.651 537075.3484 512219.4312 449969.0083 0.911868063 0.99926939 0.988673707 1.021534317 0.974684051 1.114996627 1.072124173 1.193582977 1.138343801 1 18.77946611 2.734857313 22.31824593 1.119404832 0.983198098 0.56157272 0.054121979 48.98065721 295183.6906 0.016966259 0.016607741 543.071877 -2.734857313 -0.136206734 SRS(ph)PHEAGFCVYLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.069)RS(0.931)PHEAGFCVYLK 195.48 1.59E-08 1058500000 531750 594170 427500 534820 539150 490840 509950 515060 590310 547740 TRUE FALSE 510968.6221 577224.8534 504758.7597 562422.1243 556492.2494 500765.1211 516190.9206 504423.831 523300.4836 510641.0819 1.000641429 1.130392508 0.988480515 1.101403988 1.08979138 0.980659682 1.010868375 0.987824617 1.024791193 1 18.96195008 2.735011782 24.98664147 0.999905316 1.064022582 0.349571716 0.041768392 324.9940841 2288206.618 0.012357606 0.012051607 543.2650691 -2.735011782 0.064117266 VGQEIEVRPGIVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGQEIEVRPGIVSK 14 1 P41091 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ; 105.14 0.00092768 649330000 764230 682670 600650 648210 645130 750210 717660 791980 802380 795410 FALSE TRUE 734363.0467 663200.92 709200.8164 681664.1958 665881.1923 765379.7602 726442.9378 775625.3362 711297.1863 741536.1722 0.990326668 0.894360848 0.956394095 0.919259534 0.897975335 1.032154315 0.97964599 1.045971006 0.959221159 1 19.50015754 2.735100785 24.99993921 1.007520774 0.930275773 0.515662689 0.034633058 215.0230929 1553701.435 0.010318447 0.010083371 543.3764157 -2.735100785 -0.077245001 KFEEMNAELEENKELAQNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KFEEMNAELEENKELAQNR 19 2 Q5VTR2 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 232.84 6.19E-22 89166000 90755 74687 76890 64864 70441 86714 77671 89503 87680 91342 FALSE TRUE 87208.19427 72556.99989 90785.73341 68211.63881 72706.79874 88467.41649 78621.56093 87654.73177 77726.93398 85155.32498 1.024107351 0.852054759 1.066119276 0.801026111 0.853813884 1.038894708 0.923272396 1.029351151 0.912766571 1 16.37780913 2.735167849 24.99450816 0.98173005 0.917253573 0.119365294 0.083310054 628.5192171 4630277.377 0.025445622 0.024897444 543.4603313 -2.735167849 -0.064476478 RGT(ph)FEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGTFEK 6 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RGT(1)FEK;RGT(1)FEK 96.331 0.024805 472260000 514590 456100 438170 419750 421410 527160 436940 594280 548520 496880 TRUE FALSE 494479.2539 443092.4746 517357.066 441413.3478 434965.0354 537819.5364 442287.4024 582007.9103 486254.3092 463225.875 1.067468983 0.956536537 1.116857011 0.952911682 0.938991233 1.161030861 0.954798569 1.256423576 1.049713186 1 18.82135632 2.73523742 24.97785465 1.102175296 1.00692231 0.133580999 0.093803264 471.553947 3544285.741 0.028933559 0.028332072 543.5473971 -2.73523742 -0.095252986 EGRPPEPTPAKR ddPTM_BT-474_Pertuzumab_2h_R1 4 EGRPPEPTPAKR 12 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 115.12 0.0005535 1289360000 1519540 1545540 1281700 1468650 1499180 1431560 1458720 1523710 1710770 1641460 FALSE TRUE 1460154.697 1501462.712 1513331.701 1544447.203 1547402.486 1460507.124 1476572.252 1492244.856 1516570.562 1530282.452 0.954173326 0.981167046 0.988923123 1.009256298 1.011187499 0.954403628 0.964901773 0.975143415 0.991039634 1 20.54536653 2.735290046 24.98486502 0.974537587 0.989637129 0.080607035 0.018969735 618.3387359 4723634.935 0.006291788 0.006170959 543.6132649 -2.735290046 0.015099542 GKDCAVIVTQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKDCAVIVTQK 11 1 G3V5Z7;P60900;G3V3I1;G3V295;P60900-2;G3V3U4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 118.37 0.00066576 925720000 1560160 1556090 1221220 1352200 1414030 1547940 1572970 1559740 1841820 1763320 FALSE TRUE 1499187.222 1511711.837 1441921.62 1421987.204 1459513.559 1579240.407 1592220.477 1527530.824 1632744.315 1643888.766 0.911976074 0.919594968 0.877140625 0.865014248 0.887842042 0.96067352 0.968569474 0.929217874 0.993220678 1 20.64868125 2.73532494 21.80633735 0.962830217 0.89146964 0.727188736 0.023669535 28.63886433 193005.4567 0.007830555 0.007686225 543.656945 -2.73532494 -0.071360577 ST(ph)PVRDR ddPTM_BT-474_Pertuzumab_2h_R1 1 STPVRDR 7 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.139)T(0.861)PVRDR 91.867 0.026011 379660000 648390 615640 483530 596220 550520 634770 641130 634540 643140 628640 TRUE FALSE 623050.202 598082.55 570914.6271 626990.9857 568227.9758 647605.4843 648976.3407 621436.5273 570133.4435 586061.6529 1.063113751 1.020511318 0.974154552 1.06983793 0.969570305 1.105012555 1.107351654 1.060360329 0.972821615 1 19.16069292 2.735431587 24.97608142 1.058253706 1.019781522 0.068385659 0.049275166 597.223348 4767062.356 0.0156015 0.015207066 543.790463 -2.735431587 -0.038472184 KADGPPGPHDGGDRPSAEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KADGPPGPHDGGDRPSAEAR 20 2 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 0 199.89 8.48E-22 192850000 266510 259450 189820 232260 222170 272710 275580 266880 301330 275770 FALSE TRUE 256094.4946 252050.74 224124.6965 244246.9664 229316.2998 278224.383 278952.6305 261368.8347 267124.2817 257091.8523 0.996120617 0.980391785 0.871768959 0.950037756 0.891962533 1.082198368 1.085031004 1.016636009 1.039022744 1 17.97192436 2.735440432 24.99603045 1.046544496 0.937391302 0.61562262 0.042069076 186.9675573 1497804.828 0.01367776 0.013398811 543.8015388 -2.735440432 -0.109153193 AKGSET(ph)PGATPGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 AKGS(0.099)ET(0.901)PGATPGSK;AKGS(0.021)ET(0.979)PGATPGSK;AKGS(0.003)ET(0.997)PGATPGSK;AKGS(0.001)ET(0.999)PGATPGSK 181.4 2.65E-06 4010980000 9720200 9384200 6618100 6470400 7589900 8823600 8112600 9451500 10074600 8505300 TRUE FALSE 9340323.838 9116571.804 7814137.889 6804338.119 7834036.026 9002019.238 8211884.426 9256323.222 8930973.644 7929228.455 1.177961247 1.149742608 0.985485276 0.858133696 0.987994743 1.135295734 1.035647349 1.167367453 1.126335771 1 22.91874906 2.735605587 24.908921 1.103657143 1.026184127 0.086560401 0.095185728 570.143832 4805896.073 0.032998073 0.032419991 544.0083761 -2.735605587 -0.077473015 VLHIDLWK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLHIDLWK 8 0 Q12996;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 0 108.46 0.0038063 173600000 637840 598500 639920 490430 653080 498450 581430 517910 641080 659660 FALSE TRUE 612912.5076 581431.366 755567.7789 515741.1511 674086.9113 508529.0005 588545.7143 507214.9775 568307.286 614980.6406 0.996637076 0.945446617 1.228604169 0.838629897 1.096110783 0.826902453 0.957015027 0.824765763 0.924105977 1 19.23018147 2.735605679 24.99894153 0.894211368 1.018275906 0.219539659 0.106641312 364.016383 3079585.69 0.031695022 0.031093065 544.0084915 -2.735605679 0.124064537 DGEEAGAYDGPR ddPTM_BT-474_Pertuzumab_2h_R1 6 DGEEAGAYDGPR 12 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 196.52 4.78E-07 7591240000 1964760 2056560 1649630 1852970 1875570 1988770 1972690 2109390 2267940 2128840 FALSE TRUE 1887975.007 1997908.922 1947754.837 1948602.004 1935899.412 2028984.292 1996832.37 2065830.359 2010492.959 1984651.771 0.951287795 1.006679838 0.981408863 0.981835722 0.975435309 1.022337683 1.006137399 1.04090319 1.013020515 1 20.92045446 2.735633652 24.94967454 1.019925581 0.981103722 0.55957201 0.016299044 172.9135464 1473922.654 0.004973576 0.004873917 544.0435328 -2.735633652 -0.03882186 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_BT-474_Pertuzumab_2h_R1 7 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 38 2 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 MDRDPLGGLADMFGQMPGS(0.182)GIGT(0.182)GPGVIQDRFS(0.589)PT(0.048)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.5)PT(0.5)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.984)PT(0.016)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.82)PT(0.18)MGR;MDRDPLGGLADMFGQMPGSGIGT(0.002)GPGVIQDRFS(0.992)PT(0.006)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.997)PT(0.003)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.97)PT(0.03)MGR 390.02 9.10E-180 10941350000 1684084 1971063 1542311 1718547 1702044 1958591 2017752 1918801 2170337 2280961 TRUE FALSE 1618268.135 1914850.213 1821040.906 1807241.417 1756791.791 1998195.052 2042445.853 1879177.089 1923969.443 2126469.48 0.761011691 0.900483281 0.856368231 0.849878841 0.826154247 0.939677278 0.960486794 0.883707529 0.904771717 1 21.02002872 2.735838553 24.98817452 0.928662723 0.843801067 0.552532677 0.044031906 210.5390953 1932707.754 0.013643483 0.01339716 544.3002739 -2.735838553 -0.084861656 QDDGSSS(ph)ASPSVQGAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QDDGSSSASPSVQGAPR 17 0 Q9NQA3 Q9NQA3 WASH6P WAS protein family homolog 6 1 QDDGS(0.005)S(0.041)S(0.606)AS(0.343)PS(0.005)VQGAPR 93.342 0.0032367 84512000 217270 166910 164270 188780 176560 218130 208950 221720 260360 230790 TRUE FALSE 208778.8482 162149.8902 193957.2432 198522.9584 182239.2127 222540.7381 211507.1926 217141.4045 230805.0243 215158.3877 0.970349566 0.753630346 0.901462616 0.922682869 0.847000271 1.034311236 0.983030199 1.009216544 1.072721481 1 17.71503956 2.735880142 24.99888874 1.016412506 0.875730711 0.603660057 0.05699114 159.6344095 1488789.81 0.017372694 0.017057221 544.3524002 -2.735880142 -0.140681795 NKDQGTYEDYVEGLR ddPTM_BT-474_Pertuzumab_2h_R1 6 NKDQGTYEDYVEGLR 15 1 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;; 281.92 7.87E-34 36955740000 14512840 13581080 10768490 12132230 12169420 13808860 12973730 14010250 16011070 14457170 FALSE TRUE 13945662.17 13193760.9 12714595.69 12758375.84 12560860.45 14088084.61 13132506.39 13720933.44 14193560.46 13477973 1.03470026 0.978912845 0.943361119 0.946609393 0.931954712 1.045267312 0.974368059 1.018026482 1.053093107 1 23.6841002 2.736079965 24.99726295 1.015493509 0.965305464 0.36624044 0.033439717 262.9035919 2649229.247 0.01092526 0.010724264 544.6029189 -2.736079965 -0.050188045 DLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.31)QS(0.31)HLRNS(0.38)PEDK 179.24 1.13E-19 1159900000 451620 411900 366260 375620 396390 463480 455300 463840 580620 523020 TRUE FALSE 433970.1911 400153.0153 432451.3294 395005.7932 409140.2443 472851.8832 460872.0976 454261.5419 514710.4518 487595.3895 0.890021113 0.820666118 0.886906108 0.810109779 0.839097853 0.969762827 0.945193715 0.931636253 1.055609759 1 18.89532496 2.736100305 24.49468813 0.969638277 0.847671381 0.727058872 0.039876263 91.89658268 914911.467 0.012460507 0.012268661 544.6284265 -2.736100305 -0.121966896 YKYPNISCELLTSDVSQMNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 YKYPNISCELLTSDVSQMNDR 21 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PNN8 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 109.64 0.00026539 419670000 302610 325290 292750 270720 325780 276590 305230 298480 356810 352210 FALSE TRUE 290783.6666 316013.0477 345656.4372 284691.8916 336259.0096 282182.8393 308965.496 292316.2837 316306.4247 328354.503 0.885578434 0.962414235 1.052692849 0.867026001 1.024073087 0.85938471 0.940950994 0.890246003 0.963307711 1 18.32489471 2.736127112 24.98561663 0.922150546 0.95874927 0.036862504 0.063196929 600.1926921 6162342.082 0.018896242 0.018582201 544.6620449 -2.736127112 0.036598724 LEHEVDLCR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEHEVDLCR 9 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;A0A087X1S3 Q7Z6Z7-2;A0A087X1S3 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 168.25 5.94E-05 1005730000 645490 729070 571880 661620 672160 596300 653560 566880 705200 733670 FALSE TRUE 620263.5372 708277.6374 675231.4374 695766.2875 693780.6368 608357.5946 661558.4628 555173.7299 625148.6524 683977.8774 0.906847367 1.035527114 0.987212393 1.017235075 1.014331983 0.889440455 0.967222018 0.811683752 0.913989579 1 19.38359014 2.736148261 24.96088148 0.901502765 0.995746467 0.286753025 0.057232127 215.0957399 2225608.106 0.017652968 0.017385763 544.6885692 -2.736148261 0.094243702 YMIVDEGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 YMIVDEGHR 9 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8YFV8;A0A2R8YCY3;A0A2R8Y4R6;F6VDE0;P51531-2;P51531;A0A0U1RQZ9 A0A2R8Y4P4;F6VDE0 SMARCA4;SMARCA2 Transcription activator BRG1;Probable global transcription activator SNF2L2 0 ; 107.15 0.0035111 377870000 567240 581860 503840 555900 618300 484130 536900 583290 613310 589740 FALSE TRUE 545071.6337 565265.9225 594895.0959 584590.0656 638188.181 493919.4403 543470.7428 571244.8577 543689.62 549796.3845 0.991406362 1.028136849 1.082028025 1.063284667 1.160771877 0.898367931 0.988494574 1.039011666 0.98889268 1 19.06853789 2.736208613 24.99963555 0.990253981 1.063907379 0.379370772 0.052122648 268.2027428 2850732.631 0.017239313 0.016971886 544.7642675 -2.736208613 0.073653398 AGFDS(ph)DYDQALADIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGFDSDYDQALADIR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 1 AGFDS(1)DYDQALADIR 119.46 0.00022113 69227000 35585 37392 33462 34268 34633 38281 35919 42646 40066 39871 TRUE FALSE 34194.29886 36325.61677 39509.32776 36036.57559 35747.0019 39055.06805 36358.58747 41765.3452 35517.87565 37170.50166 0.919931056 0.977270017 1.062921564 0.969493926 0.96170351 1.050700591 0.978157029 1.123615322 0.955539314 1 15.18187054 2.736255252 24.97736331 1.03335059 0.982424762 0.116671404 0.05447043 375.9627168 4073322.755 0.01724831 0.017003303 544.8227721 -2.736255252 -0.050925828 KKSEAPSGESR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKSEAPSGESR 11 2 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ; 114.72 0.00068587 108772000 253650 270450 183577 200419 218396 259570 245740 268760 312330 264850 FALSE TRUE 243737.0776 262737.0308 216753.4475 210762.6486 225420.9057 264818.6832 248747.4396 263210.0121 276875.6078 246911.4736 0.987143586 1.064094054 0.877858952 0.85359601 0.912962457 1.072524818 1.007435726 1.066009644 1.121355779 1 17.91363435 2.736534311 24.9605188 1.054341981 0.937917454 0.450838193 0.063082864 183.9000855 2265313.715 0.021657472 0.021384083 545.1729653 -2.736534311 -0.116424527 ILELTPEPDRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILELTPEPDRPR 12 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 0 124.21 0.00029832 67538000 43332 44652 39826 48079 46844 40727 42433 47544 43477 49202 FALSE TRUE 41638.53753 43378.56868 47023.44412 50560.36295 48350.7798 41550.52784 42952.30775 46562.19979 38541.67323 45869.50472 0.907760783 0.945695162 1.025157006 1.102265291 1.05409422 0.905842086 0.936402257 1.015101429 0.840246117 1 15.48524771 2.736558471 24.95765887 0.946396258 1.009890824 0.194870521 0.067733157 342.2100846 4265772.4 0.022816758 0.022490198 545.2032944 -2.736558471 0.063494565 STPKEDDSSASTSQSTR ddPTM_BT-474_Pertuzumab_2h_R1 3 STPKEDDSSASTSQSTR 17 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 247.91 7.68E-21 935050000 902210 882280 673180 652540 717810 869930 825030 836880 987200 874960 FALSE TRUE 866950.6358 857118.2382 794838.6008 686217.6676 740899.0105 887520.5806 835126.9639 819598.1355 875137.1947 815698.1799 1.062832623 1.050778657 0.974427332 0.841264189 0.908300434 1.088050216 1.023818594 1.004781126 1.072868882 1 19.63767591 2.736840078 24.99964327 1.034235396 0.96551555 0.226192143 0.064860244 281.57594 4091322.039 0.022858419 0.022611928 545.5569313 -2.736840078 -0.068719846 AKLEQLFQDEVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKLEQLFQDEVAK 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 162.37 3.70E-05 737610000 1170730 1158070 940980 979090 1046430 1172300 1110780 1247390 1378090 1253340 FALSE TRUE 1124976.577 1125042.977 1111036.018 1029620.952 1080089.371 1196004.709 1124374.058 1221630.961 1221655.001 1168450.165 0.962793802 0.96285063 0.95086299 0.881185165 0.924377781 1.02358213 0.962278145 1.045513961 1.045534535 1 20.15616477 2.736978683 24.9719312 1.015996026 0.935617215 0.615280714 0.031216498 100.9833908 1594082.212 0.010560632 0.010451057 545.7310742 -2.736978683 -0.080378812 YRS(ph)PYR ddPTM_BT-474_Pertuzumab_2h_R1 4 YRSPYR 6 1 Q14498-3 Q14498-3 RBM39 RNA-binding protein 39 1 Y(0.002)RS(0.996)PY(0.002)R;Y(0.003)RS(0.997)PY(0.001)R;YRS(1)PYR;YRS(0.999)PY(0.001)R 85.161 0.033326 2023710000 565830 666510 556611 646823 631090 582330 573806 635660 666854 683080 TRUE FALSE 543716.738 647501.7874 657202.9894 680205.6125 651389.583 594105.1116 580828.4095 622533.3989 591155.5296 636814.3832 0.853807251 1.016782605 1.032016561 1.068137954 1.022887674 0.932932935 0.912084313 0.977574338 0.928301158 1 19.2805134 2.737139141 24.97097085 0.948041141 1.005435181 0.144026501 0.057918341 222.0252293 3900257.984 0.018540654 0.018372632 545.9327413 -2.737139141 0.057394041 TPDVLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPDVLKK 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 86.794 0.031772 3817600000 4242000 4971000 3070800 4147700 5287800 6099500 5910800 7117300 8140200 7506300 FALSE TRUE 4076217.95 4829231.947 3625761.87 4361763.294 5457886.889 6222836.069 5983138.139 6970325.268 7216158.623 6997891.615 0.582492295 0.690098134 0.518122039 0.623296778 0.779933041 0.88924442 0.854991541 0.996060764 1.031190396 1 22.73848889 2.737152494 0.941315893 1.002730585 0.587974682 0.904577733 0.054670754 0.160726762 0.302789128 0.032830424 0.03044028 545.9495273 -2.737152494 -0.414755902 IGEHTPS(ph)ALAIMENANVLAR ddPTM_BT-474_Pertuzumab_2h_R1 3 IGEHTPSALAIMENANVLAR 20 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BR04;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 IGEHT(0.001)PS(0.999)ALAIMENANVLAR;IGEHTPS(1)ALAIMENANVLAR;IGEHT(0.008)PS(0.992)ALAIMENANVLAR 310.77 1.86E-66 157735000 156185 212666 174314 152691 185725 115907 122998 137386 126222 121645 TRUE FALSE 150081.1175 206600.9739 205816.4174 160571.4008 191699.0133 118250.719 124503.2863 134548.9311 111893.8077 113405.8758 1.323398073 1.821783681 1.814865552 1.415900187 1.690379903 1.042721271 1.097855693 1.186437035 0.986666757 1 16.79113587 2.73716127 24.9996367 1.086328784 1.625085101 0.756183367 0.155943936 61.99739497 1107587.404 0.048665441 0.048192049 545.9605593 -2.73716127 0.538756318 NPQMPQYSSPQPGSALS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 NPQMPQYSSPQPGSALSPR 19 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;A0A087WUV6 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 NPQMPQYSSPQPGS(0.009)ALS(0.991)PR;NPQMPQYSSPQPGS(0.014)ALS(0.986)PR 308.15 1.98E-61 1291320000 322170 270508 232196 275256 277962 254798 228135 299066 289574 286442 TRUE FALSE 309579.2402 262793.3767 274158.9824 289461.9951 286902.9002 259950.1901 230926.9844 292890.1826 256702.7735 267041.0282 1.159294668 0.984093637 1.026654908 1.083960757 1.074377604 0.973446634 0.86476219 1.096798438 0.961285894 1 18.02670189 2.737193189 24.89226818 0.984889934 1.059991892 0.287909965 0.06736839 181.7578597 3308623.215 0.021468971 0.021296124 546.0006874 -2.737193189 0.075101957 SAPGGGGKR ddPTM_BT-474_Pertuzumab_2h_R1 7 SAPGGGGKR 9 1 Q14847;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;; 158.87 0.0001066 4073780000 3081220 2807920 1854240 1867820 2129900 4098150 3988890 4551570 3239180 4891070 FALSE TRUE 2960802.516 2727840.871 2189342.415 1964218.414 2198410.168 4181017.401 4037707.229 4457578.489 2871481.866 4559793.472 0.649328206 0.598237812 0.480140697 0.430769162 0.482129329 0.91693131 0.885502217 0.977583418 0.629739457 1 22.12053705 2.737240017 24.97223036 0.888971182 0.523942397 0.719708936 0.110346733 61.74699737 1167610.66 0.035049764 0.034748218 546.059563 -2.737240017 -0.365028785 QPEKEEEEEAGESVEDIFSEVVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 QPEKEEEEEAGESVEDIFSEVVGR 24 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ;; 155.05 4.58E-08 165884000 133246 124695 102411 102640 116642 124512 125087 141697 137047 120810 FALSE TRUE 128038.599 121138.8207 120918.9458 107937.2627 120393.8959 127029.7179 126617.8521 138770.9074 121489.9991 112627.4311 1.136833165 1.075571195 1.073618963 0.958356784 1.068957133 1.12787548 1.124218593 1.232123525 1.078689249 1 16.78119872 2.737400153 4.302138927 1.137214101 1.05754772 0.062685293 0.069422963 0.323222447 15.25724223 0.022674015 0.022646732 546.2609467 -2.737400153 -0.079666381 GSSGGSGAKPSDAASEAARPATSTLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSSGGSGAKPSDAASEAARPATSTLNR 27 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 238.72 2.37E-45 2415950000 762241 845889 670234 799678 755283 934470 889090 987530 1030127 1046029 FALSE TRUE 732451.779 821765.0739 791360.1931 840949.4774 779577.3636 953365.6237 899970.9494 967137.1604 913191.3016 975180.5241 0.751093527 0.842679949 0.811501228 0.862352617 0.799418512 0.977629885 0.922876254 0.991751923 0.93643308 1 19.89530979 2.737496798 24.99987963 0.963875983 0.817648402 0.826796461 0.034828134 37.10065856 871860.5403 0.010363565 0.010281815 546.382521 -2.737496798 -0.146227581 HLAAVEER ddPTM_BT-474_Pertuzumab_2h_R1 2 HLAAVEER 8 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ; 111.17 0.0032855 1492610000 691750 778360 657940 721450 769030 599650 754170 519940 809930 792720 FALSE TRUE 664715.6452 756161.9349 776844.3938 758684.121 793766.5484 611775.3339 763399.7581 509203.0573 717990.1419 739028.3683 0.899445371 1.023183909 1.051169924 1.02659675 1.074067766 0.827810352 1.032977611 0.68901693 0.971532586 1 19.49527022 2.737534817 24.9985651 0.879778953 1.018018986 0.20967757 0.101898459 116.2091916 2831963.404 0.031515799 0.031274305 546.4303551 -2.737534817 0.138240033 FVKEPAFEDITLESER ddPTM_BT-474_Pertuzumab_2h_R1 4 FVKEPAFEDITLESER 16 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 200.9 3.13E-11 1996690000 854410 893600 657980 719026 739610 873890 775780 960680 934500 855750 FALSE TRUE 821018.7126 868115.4029 776891.6227 756135.018 763400.2273 891560.6545 785274.2277 940841.6223 828419.4777 797789.2903 1.02911724 1.088151237 0.97380553 0.947787877 0.956894554 1.117539011 0.984312822 1.179310921 1.038393831 1 19.60564823 2.737542131 24.99712098 1.07685646 0.999834109 0.186782556 0.064799787 135.9317114 3336203.816 0.020839535 0.020696306 546.4395571 -2.737542131 -0.077022351 SS(ph)LETLEDIEENAPLRR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.196)S(0.804)LETLEDIEENAPLRR;S(0.008)S(0.992)LETLEDIEENAPLRR;S(0.108)S(0.892)LETLEDIEENAPLRR;S(0.197)S(0.803)LETLEDIEENAPLRR;S(0.135)S(0.865)LETLEDIEENAPLRR 334.03 2.53E-72 1132442000 215686 234901 173542 200841 199759 237440 245407 249719 236867 239842 TRUE FALSE 207256.7527 228201.8535 204904.8998 211206.4281 206184.4297 242241.1995 248410.3643 244562.2154 209978.8512 223597.2877 0.926919798 1.02059312 0.916401545 0.944584034 0.922124019 1.083381654 1.110972172 1.093761995 0.93909391 1 17.77054316 2.737577449 24.99972896 1.060138471 0.94852479 0.440377183 0.054706791 75.32660082 1915368.511 0.017364135 0.017233727 546.4839971 -2.737577449 -0.111613681 LNHS(ph)PPQSSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 LNHSPPQSSSR 11 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR 134.88 8.48E-05 4183130000 1018358 1146170 931372 1144380 1070980 943477 1054550 821771 1131350 1161500 TRUE FALSE 978559.4435 1113482.354 1099691.639 1203441.589 1105429.044 962554.7514 1067455.898 804801.1417 1002923.891 1082830.57 0.90370504 1.028307091 1.015571289 1.11138494 1.020869815 0.888924618 0.985801406 0.74323829 0.926205741 1 20.04637609 2.737694789 7.191515763 0.886974536 1.022120724 0.281069444 0.081738906 0.139899119 54.51871462 0.026221495 0.026178263 546.6316693 -2.737694789 0.135146188 ENSREALAEAALES(ph)PRPALVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSREALAEAALESPRPALVR 21 2 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 ENS(0.443)REALAEAALES(0.557)PRPALVR 89.272 0.0018384 660390000 224390 164350 143660 121730 158060 183510 170930 198200 209760 206020 TRUE FALSE 215620.5907 159662.8989 169622.5577 128012.4999 163144.1434 187220.6979 173021.8925 194107.1007 185948.9242 192066.0819 1.122637525 0.831291487 0.883146863 0.666502376 0.849416731 0.974772308 0.90084564 1.010626649 0.968150765 1 17.55124324 2.737738354 24.02364785 0.968945626 0.857773645 0.173781579 0.107483203 72.41640935 2115729.329 0.034271954 0.034065123 546.6865057 -2.737738354 -0.111171981 SEHPGLSIGDTAK ddPTM_BT-474_Pertuzumab_2h_R1 6 SEHPGLSIGDTAK 13 0 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ;;;;; 210.41 3.02E-08 8565500000 10340400 10793000 10056270 10466400 10512200 9822740 10005200 10249090 10736340 10972900 FALSE TRUE 9936285.736 10485194.21 11873661.69 11006572.16 10850334.46 10021362.53 10127646.63 10037442.71 9517595.694 10229695.71 0.97131782 1.024976158 1.160705267 1.075943261 1.060670304 0.97963447 0.990024231 0.981206381 0.930388935 1 23.2862599 2.737897666 5.307492544 0.976352393 1.063864119 0.429006508 0.047416859 0.174805729 17.18177422 0.015956082 0.015942096 546.8870838 -2.737897666 0.087511726 TSNS(ph)LTEDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSNSLTEDSK 10 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0;H7C3N7 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 TSNS(0.995)LT(0.005)EDSK 120.84 0.0028454 0 178690 161870 151690 138820 158450 185180 179690 191150 217920 223110 TRUE FALSE 171706.5972 157253.6261 179103.7573 145984.5168 163546.6882 188924.4665 181889.1 187202.6857 193182.6352 207998.561 0.825518198 0.756032279 0.861081714 0.701853494 0.786287594 0.908296988 0.874472877 0.900019139 0.928769095 1 17.66621402 2.737986928 6.712836594 0.91117423 0.783717732 0.647616975 0.049872265 0.091104482 25.08284542 0.015065461 0.015050243 546.9994986 -2.737986928 -0.127456498 LNEAQPSTIATS(ph)MRDSLIDSLT ddPTM_BT-474_Pertuzumab_2h_R1 2 LNEAQPSTIATSMRDSLIDSLT 22 1 P56537;P56537-2 P56537 EIF6 Eukaryotic translation initiation factor 6 1 LNEAQPS(0.08)T(0.08)IAT(0.135)S(0.614)MRDS(0.091)LIDSLT;LNEAQPS(0.063)T(0.063)IAT(0.078)S(0.425)MRDS(0.37)LIDSLT 82.486 0.0025732 86702000 257479 258752 218070 228668 256342 223335 203358 294308 260575 235643 TRUE FALSE 247416.436 251372.6463 257480.0999 240469.5829 264587.4732 227850.9867 205846.756 288230.437 230995.6184 219682.6897 1.126244568 1.144253317 1.172054568 1.094622354 1.204407473 1.037182251 0.937018553 1.312030717 1.051496678 1 17.74506167 2.738035899 24.99998749 1.094377181 1.146426502 0.119785559 0.0965744 157.9813319 7526787.885 0.031941601 0.031813363 547.0611819 -2.738035899 0.052049321 RRTS(ph)DPSAAVNHVSSTTSLGENYEDDDLVNSDEVMK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRTSDPSAAVNHVSSTTSLGENYEDDDLVNSDEVMK 36 2 H7C3A2;Q8NHH9-2;Q8NHH9 H7C3A2 ATL2 Atlastin-2 1 RRT(0.408)S(0.427)DPS(0.125)AAVNHVS(0.008)S(0.008)T(0.008)T(0.008)S(0.008)LGENY(0.001)EDDDLVNSDEVMK 55.196 0.024136 263690000 29106 47210 31432 30990 20753 54949 46706 41951 36667 44136 TRUE FALSE 27968.50534 45863.61702 37112.4616 32589.39761 21420.53909 56060.10643 47277.602 41084.69719 32504.71588 41146.62941 0.679727738 1.114638494 0.9019563 0.792030795 0.520590372 1.362447113 1.149003033 0.998494841 0.789972747 1 15.32848663 2.738071755 24.99999948 1.062194146 0.824192049 0.29932223 0.196010865 65.57802046 3353536.377 0.063961976 0.063813245 547.106349 -2.738071755 -0.238002097 VTGQHQGYGFVEFLSEEDADYAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTGQHQGYGFVEFLSEEDADYAIK 24 0 Q5SZ64;Q15427 Q5SZ64 SF3B4 Splicing factor 3B subunit 4 0 169.08 9.66E-12 101400000 26890 33434 28412 28352 28618 32709 37116 30997 32380 32705 FALSE TRUE 25839.10907 32480.49506 33546.68042 29815.25012 29538.52396 33370.39839 37570.23671 30356.90112 28704.35815 30489.86122 0.847465618 1.065288386 1.100256908 0.977874248 0.968798242 1.094475247 1.232220653 0.995639203 0.941439449 1 14.89604196 2.738174348 24.99829401 1.06270848 1.00124832 0.082891554 0.095933639 98.43384872 6370162.698 0.03131603 0.031310574 547.235607 -2.738174348 -0.06146016 EKDRDPEAQFEMPYVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDRDPEAQFEMPYVVR 17 2 O14744-2;O14744;O14744-4;O14744-3;O14744-5;H0YJD3;H7BZ44 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 190.55 1.64E-10 946630000 472430 426900 405270 417600 418960 537740 532800 554330 552340 619620 FALSE TRUE 453966.9133 414725.23 478511.3042 439152.386 432436.2289 548613.4712 539320.5658 542882.8918 489640.6788 577652.5855 0.785882249 0.717949232 0.828372133 0.760236165 0.748609527 0.949729102 0.933641741 0.939808642 0.847638686 1 19.13984256 2.738299413 24.99999909 0.9312466 0.768316965 0.783231388 0.043639109 10.4951405 1004456.643 0.013111735 0.013085992 547.3932192 -2.738299413 -0.162929635 QNSPAGNKENIKPNET(ph)SPSFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QNSPAGNKENIKPNETSPSFSK 22 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 QNSPAGNKENIKPNET(0.927)S(0.072)PS(0.001)FSK 103.21 0.028164 517560000 120760 92046 79230 80170 86864 132360 111950 139590 166230 133780 TRUE FALSE 116040.5657 89420.9382 93548.62346 84307.58331 89658.05945 135036.4099 113320.0776 136707.4177 147360.2673 124718.9614 0.930416389 0.716979497 0.750075389 0.675980479 0.718880741 1.08272558 0.908603442 1.096123766 1.181538602 1 16.92832129 2.738552195 24.99997467 1.050566049 0.751112928 0.724068131 0.091089827 0.40600491 1202080.564 0.028885483 0.028885373 547.7119223 -2.738552195 -0.299453121 AQEALSHTEQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQEALSHTEQSK 12 0 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ; 147.18 6.54E-05 180890000 385100 377490 306650 372250 352780 432980 447660 416210 486260 493020 FALSE TRUE 370049.8662 366724.3548 362068.4764 391461.8671 364127.4891 441735.1523 453138.597 407615.1181 431061.8034 459627.3163 0.805108515 0.797873281 0.787743599 0.851694086 0.792223343 0.961072453 0.985882651 0.886838322 0.937850707 1 18.81010502 2.738662381 24.99999993 0.945047347 0.807846632 0.829669172 0.033259567 3.988625023 979979.2228 0.0107668 0.010775164 547.8509015 -2.738662381 -0.137200715 RRS(ph)PSPY(ph)YSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSPSPYYSR 10 2 P62995;P62995-3;H7BXF3;Q13595;Q13595-3 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 2 RRS(0.649)PS(0.537)PY(0.46)Y(0.31)S(0.044)R 75.96 0.061415 1457300000 804730 900490 754220 905120 832560 778100 782140 806000 891310 757790 TRUE FALSE 773280.2619 874808.9069 890524.3315 951833.3517 859340.0485 793833.7151 791712.0633 789355.8183 790132.2255 706464.2083 1.094578116 1.2382919 1.260537082 1.347319992 1.216395733 1.123671526 1.120668328 1.117333064 1.118432068 1 19.43025695 2.738851334 3.547326596 1.104193717 1.241728371 0.505077689 0.066985968 0.209238219 5.729655911 0.022303327 0.022300263 548.0893133 -2.738851334 0.137534655 VETGILRPGMVVTFAPVNITTEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VETGILRPGMVVTFAPVNITTEVK 24 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 252.21 8.61E-44 901540000 547730 493480 423660 421570 468450 570300 589760 551710 653880 687270 FALSE TRUE 526324.1061 479406.4336 500224.7863 443327.2782 483518.1197 581831.8567 596977.6593 540316.9957 579654.2837 640720.5907 0.821456519 0.748230103 0.780722195 0.691919824 0.754647387 0.908089837 0.931728538 0.84329582 0.904691206 1 19.28933583 2.739197041 24.75502909 0.903847146 0.756211117 0.729999151 0.047712878 27.67501833 1076494.456 0.014823729 0.014880324 548.5257766 -2.739197041 -0.147636029 DINLQDEDWNEFNDINK ddPTM_BT-474_Pertuzumab_2h_R1 3 DINLQDEDWNEFNDINK 17 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;; 274.09 2.59E-35 333080000 383993 352335 300835 336439 350471 381030 396199 413397 443285 398801 FALSE TRUE 368986.129 342286.7508 355202.5765 353802.6571 361744.218 388734.6877 401047.8019 404860.2075 392965.1452 371789.8531 0.992458847 0.920645757 0.955385344 0.951619992 0.972980341 1.045576377 1.078694856 1.088949051 1.056955003 1 18.50412787 2.739224288 2.663955696 1.066802946 0.952988892 0.742257539 0.028010491 0.120185073 1.699563641 0.009152697 0.009130911 548.5601909 -2.739224288 -0.113814055 LSSWDQAET(ph)PGHTPSLR ddPTM_BT-474_Pertuzumab_2h_R1 5 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR 265.41 5.54E-27 3781630000 1651176 1687340 1411112 1879285 1696018 1436131 1407693 1675060 1510973 1618845 TRUE FALSE 1586646.216 1639218.715 1666131.328 1976275.124 1750571.959 1465170.553 1424920.768 1640469.426 1339453.68 1509199.186 1.051316639 1.086151338 1.103983718 1.309485946 1.159934338 0.970826493 0.944156862 1.086980062 0.887526108 1 20.5253518 2.739553791 24.94116853 0.989008553 1.14623539 0.512133742 0.079751772 80.15777971 2012978.747 0.026406974 0.026612767 548.9765472 -2.739553791 0.157226836 HFLSDTGMACR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFLSDTGMACR 11 0 Q5TFE4;Q5TFE4-2;Q5QPD0 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 199.68 4.94E-08 255900000 264470 309080 276570 334020 302650 231180 278670 202460 284090 255340 FALSE TRUE 254134.22 300265.341 326552.3513 351258.8122 312385.0121 235854.618 282080.4468 198279.1302 251841.2942 238045.5944 1.06758632 1.261377434 1.371805902 1.475594678 1.312290668 0.99079598 1.18498495 0.832946019 1.057954023 1 17.8608784 2.739704375 24.65653663 1.003326957 1.309707958 0.560614876 0.125507554 62.95105707 1357076.22 0.041083203 0.041391078 549.1669279 -2.739704375 0.306381001 PT(ph)HSGGGGGGGGGGGGGGGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 PTHSGGGGGGGGGGGGGGGGR 21 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 PT(0.54)HS(0.46)GGGGGGGGGGGGGGGGR 74.364 0.018003 0 8531.3 7638 8265.4 8314.4 8922.6 7170.7 8193.3 7421.6 9233.5 9766.3 TRUE FALSE 8197.887364 7420.171718 9759.141643 8743.50718 9209.603532 7315.696467 8293.572056 7268.341366 8185.35179 9104.819802 0.900389853 0.814971837 1.071865436 0.960316335 1.0115086 0.803497118 0.910899088 0.798296015 0.899013047 1 13.15241475 2.73973074 24.99992457 0.866511361 0.951350542 0.13564581 0.082999603 177.190037 3785724.502 0.025806938 0.026002567 549.2002674 -2.73973074 0.084839182 GLGTDEESILTLLTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GLGTDEESILTLLTSR 16 0 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ;; 241.15 1.59E-19 127430000 140196 148042 110452 142948 137581 124011 127689 132598 136112 148009 FALSE TRUE 134716.9853 143819.9871 130413.1334 150325.5634 142006.4178 126518.5874 129251.6962 129859.805 120661.1364 137984.2186 0.976321689 1.042293014 0.945130789 1.089440263 1.029149705 0.916906213 0.936713615 0.941120704 0.874456062 1 17.07414375 2.73990646 24.99545356 0.931414552 1.017992805 0.446052089 0.045984875 104.3144445 1937380.978 0.0137423 0.013874545 549.4225241 -2.73990646 0.086578253 QGYACPYYHNS(ph)KDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGYACPYYHNSKDRR 15 2 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPYYHNS(1)KDRR 157.85 9.80E-07 125420000 172730 161290 151320 157320 161130 192630 185100 196340 234930 212110 TRUE FALSE 165979.5206 156690.1671 178666.8901 165439.3041 166312.8928 196525.1106 187365.3092 192285.5104 208261.7313 197743.6008 0.839367342 0.792390583 0.90352805 0.836635438 0.841053223 0.99383803 0.947516422 0.972398144 1.053190751 1 17.59327148 2.739968918 24.72954685 0.986283339 0.842859882 0.816729373 0.035636326 47.20006082 828829.7424 0.011256508 0.011364228 549.5015451 -2.739968918 -0.143423457 KEQSEVSVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 KEQSEVSVSPR 11 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KEQSEVS(0.132)VS(0.868)PR;KEQSEVSVS(1)PR;KEQSEVS(0.006)VS(0.994)PR;KEQSEVS(0.001)VS(0.999)PR;KEQSEVS(0.001)VS(0.999)PR 170.42 9.63E-06 8928800000 7827170 7757370 6766940 7395640 7390360 7884200 7786980 8404200 8659590 8226150 TRUE FALSE 7521275.543 7536137.403 7989876.588 7777329.867 7628077.641 8043623.926 7882279.391 8230650.333 7676589.647 7668985.533 0.980739305 0.982677222 1.041842699 1.014127597 0.994665801 1.048851102 1.027812526 1.073238474 1.000991541 1 22.87060432 2.740017905 24.98893316 1.037638661 1.004489188 0.186917755 0.026217934 168.5054362 2889481.471 0.008277415 0.008328864 549.5635311 -2.740017905 -0.033149473 RDFS(ph)PVPWSQYFESMEDVEVENETGKDTFR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDFSPVPWSQYFESMEDVEVENETGKDTFR 30 2 Q9Y570;Q9Y570-4 Q9Y570 PPME1 Protein phosphatase methylesterase 1 1 RDFS(1)PVPWSQYFESMEDVEVENETGKDTFR 192.02 8.54E-19 53199000 24016 23904 20079 22842 19524 30035 27263 27027 31075 28291 TRUE FALSE 23077.42817 23222.28132 23707.72195 24020.87836 20152.00719 30642.32828 27596.65275 26468.88301 27547.49628 26374.82537 0.874979373 0.880471472 0.898876926 0.910750233 0.764062204 1.161802129 1.046325515 1.00356619 1.044461751 1 14.68687392 2.740109183 24.99997325 1.04704836 0.870973294 0.733285894 0.055836344 75.91862857 1225634.678 0.017472706 0.017651484 549.6790471 -2.740109183 -0.176075066 DRS(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_BT-474_Pertuzumab_2h_R1 6 DRSSSAPNVHINTIEPVNIDDLIR 24 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.391)S(0.391)S(0.218)APNVHINTIEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR 268.22 6.58E-45 1504278000 457418 473918 326080 385351 403833 466430 461204 506080 478431 498142 TRUE FALSE 439541.5989 460402.3227 385009.9096 405239.0113 416822.6552 475861.5342 466848.3525 495629.2711 424121.5186 464402.3986 0.946467116 0.991386616 0.829043758 0.872603183 0.897546301 1.024675014 1.005266885 1.06724098 0.91326298 1 18.8250159 2.740185885 24.85640338 1.011518911 0.905787468 0.429626002 0.053985918 124.149593 1898716.371 0.017472575 0.017698809 549.776137 -2.740185885 -0.105731443 LREVIEIEDAS(ph)PTKCPITTK ddPTM_BT-474_Pertuzumab_2h_R1 3 LREVIEIEDASPTKCPITTK 20 2 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 LREVIEIEDAS(0.963)PT(0.037)KCPITTK;LREVIEIEDAS(0.978)PT(0.022)KCPITTK;LREVIEIEDAS(0.999)PT(0.001)KCPITTK 198.09 8.30E-22 624530000 1014170 930930 658190 672890 771690 882180 818420 906430 1028110 851090 TRUE FALSE 974535.1152 904380.7879 777139.5744 707617.9335 796512.1097 900018.284 828436.0688 887711.9037 911403.263 793444.9162 1.228232856 1.139815467 0.979449938 0.891829942 1.003865667 1.134317286 1.044100292 1.118807224 1.148666082 1 19.59777054 2.740218585 24.99470419 1.094491174 1.041148721 0.039860955 0.094238315 486.2816432 7331020.784 0.032000863 0.032259401 549.8175336 -2.740218585 -0.053342453 DILLVNDHLLNFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DILLVNDHLLNFVR 14 0 Q9NTI5-2;Q9NTI5;Q9NTI5-3 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 ; 148.85 7.65E-06 180920000 433140 446980 396180 438190 433320 396110 423440 395610 439660 470560 FALSE TRUE 416212.4099 434232.568 467778.539 460805.0384 447258.1313 404119.6156 428622.1854 387440.5153 389751.64 438688.5521 0.94876515 0.989842488 1.066311252 1.050415007 1.01953454 0.921199365 0.9770535 0.883178997 0.888447255 1 18.74283753 2.740309132 24.46630719 0.926842503 1.018398563 0.442473671 0.045024367 102.1572913 1429456.12 0.014556093 0.014730862 549.9321782 -2.740309132 0.091556061 ERPSS(ph)REDT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 ERPS(0.461)S(0.555)REDT(0.932)PS(0.052)R 61.962 0.089548 83239000 110960 119400 101900 108960 110650 129540 130010 137760 133970 143280 TRUE FALSE 106623.5605 115994.8289 120315.5968 114583.4387 114209.1577 132159.3876 131601.1013 134915.2079 118762.2872 133575.518 0.798226817 0.868383897 0.900730902 0.857817663 0.855015646 0.989398279 0.985218723 1.010029457 0.889102203 1 17.02729609 2.740322403 24.67346296 0.97911932 0.859303175 0.697897902 0.038970513 73.06161436 1023218.807 0.012097285 0.012231134 549.9489833 -2.740322403 -0.119816146 QSLSS(ph)ADNLESDAQGHQVAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSLSSADNLESDAQGHQVAAR 21 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 QS(0.005)LS(0.199)S(0.796)ADNLESDAQGHQVAAR 216.64 1.64E-32 0 46951 57658 45982 51291 54410 46277 50476 55719 42664 63213 TRUE FALSE 45116.10301 56013.65029 54291.97026 53938.13466 56160.14706 47212.75265 51093.74039 54568.38318 37820.96158 58931.52721 0.765568197 0.950486997 0.921272074 0.915267892 0.952972878 0.801145921 0.867001804 0.925962482 0.641778066 1 15.84675203 2.740429204 24.98136386 0.851281876 0.905762834 0.067022898 0.099278049 499.0814684 6672315.906 0.029646721 0.030044481 550.0842423 -2.740429204 0.054480959 AEDGSVIDYELIDQDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 AEDGSVIDYELIDQDAR 17 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28;H0YNA0 P07355-2 ANXA2 Annexin A2;Annexin 0 ;; 313.32 8.04E-58 470841000 195441 196063 111813 284329 204646 167225 142004 224641 184927 190787 FALSE TRUE 187802.9496 190471.4752 132020.0964 299003.2538 211228.6244 170606.4041 143741.8874 220002.0848 163934.8622 177864.8266 1.055874583 1.070877693 0.7422496 1.681070167 1.187579515 0.959191355 0.808152405 1.236906077 0.921682299 1 17.44042171 2.740542148 24.64264051 1.004571679 1.150397341 0.10148651 0.237980966 418.4884048 5204393.317 0.076489811 0.077567474 550.2273177 -2.740542148 0.145825662 LHVAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHVAVK 6 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6;Q96SI9;Q96SI9-2 Q12906;Q12906-7;Q96SI9 ILF3;STRBP Interleukin enhancer-binding factor 3;Spermatid perinuclear RNA-binding protein 0 ; 81.297 0.062249 2495800000 7713900 8077000 7163400 7860200 8122600 7248900 8512600 6568400 9374000 9386300 FALSE TRUE 7412432.26 7846651.868 8457985.729 8265865.864 8383870.806 7395477.725 8616779.745 6432760.245 8309902.819 8750557.541 0.84708114 0.896703077 0.966565352 0.944610195 0.958095615 0.845143603 0.984712083 0.735125758 0.949642669 1 23.06094351 2.740657571 24.98570927 0.881041937 0.924835819 0 0.078905411 576.0854256 6864206.1 0.024412808 0.024764241 550.373571 -2.740657571 0.043793881 VGLSPDSPAGDRNS(ph)VGSEGSVGSIR ddPTM_BT-474_Pertuzumab_2h_R1 3 VGLSPDSPAGDRNSVGSEGSVGSIR 25 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 VGLSPDSPAGDRNS(0.998)VGS(0.002)EGSVGSIR;VGLSPDSPAGDRNS(0.999)VGS(0.001)EGSVGSIR;VGLSPDSPAGDRNS(0.999)VGS(0.001)EGSVGSIR 210.51 1.08E-25 934800000 660470 749790 570129 642170 613720 773220 705440 753650 793560 890840 TRUE FALSE 634658.1022 728406.7233 673163.9928 675312.4707 633460.8612 788855.0382 714073.3857 738086.8641 703478.3957 830502.6133 0.764185557 0.877067346 0.81055012 0.813137081 0.762743971 0.949852566 0.859808716 0.888723109 0.847051393 1 19.66362518 2.74067598 24.99852977 0.897101566 0.810211488 0.498010923 0.05117291 183.8454247 2172622.639 0.015151835 0.015374037 550.3969007 -2.74067598 -0.086890078 IEFPLPDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEFPLPDRR 9 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 106.18 0.0047749 93743000 31433 29279 25314 28824 31661 24344 29248 28355 27787 32549 FALSE TRUE 30204.56361 28443.99159 29888.80291 30311.61009 32679.40482 24836.25236 29605.94577 27769.45934 24632.73625 30344.42724 0.995390797 0.937371181 0.984984909 0.998918512 1.07694914 0.818478206 0.975663358 0.915141984 0.811771336 1 14.88914397 2.740728675 24.99988899 0.906361927 0.99456212 0.354353337 0.063630666 236.135615 2722889.954 0.019358693 0.019637954 550.4636879 -2.740728675 0.088200193 YDHQAEEDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 YDHQAEEDLR 10 0 Q15417;Q15417-3 Q15417 CNN3 Calponin-3 0 ;; 148.28 2.54E-05 1626260000 1226506 1178540 1201242 1420902 1289860 1211191 1324307 1022681 1595780 1623271 FALSE TRUE 1178572.79 1144929.193 1418333.151 1494234.923 1331349.518 1235682.112 1340514.265 1001562.28 1414633.744 1513325.409 0.77879667 0.756565102 0.937229457 0.987385075 0.879750984 0.816534305 0.885807016 0.661828761 0.934784902 1 20.52929081 2.740751424 22.89507859 0.826674854 0.872242307 0 0.105902756 250.2143025 2614885.988 0.03432499 0.034768772 550.4925217 -2.740751424 0.045567453 TSS(ph)VSSISQVSPER ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSVSSISQVSPER 14 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 T(0.002)S(0.063)S(0.908)VS(0.027)SISQVSPER;TS(0.011)S(0.881)VS(0.107)SISQVSPER 347.65 8.54E-82 577310000 556570 632320 491050 589380 582370 551950 525140 646430 616550 596410 TRUE FALSE 534818.6291 614286.8527 579793.6583 619797.9724 601102.4599 563110.8072 531566.8204 633080.9946 546561.8288 556014.6195 0.961878717 1.104803419 1.042766931 1.114715244 1.081091106 1.012762592 0.956030295 1.138604944 0.982999025 1 19.08476329 2.740811842 24.94161033 1.030652687 1.065447325 0.093364613 0.060178502 588.6024599 6521230.326 0.018810309 0.019140764 550.5691102 -2.740811842 0.034794638 SPT(ph)FSEELPVLGDGQQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPTFSEELPVLGDGQQLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 S(0.143)PT(0.857)FSEELPVLGDGQQLR 203.99 1.25E-14 129430000 23356 20091 21469 24930 24308 18823 21774 22595 21762 20135 TRUE FALSE 22443.2217 19518.02435 25348.92588 26216.64029 25089.8889 19203.61396 22040.47673 22128.40535 19291.66899 18771.23852 1.195617523 1.039783514 1.350413072 1.396638813 1.336613398 1.023033933 1.174162094 1.178846315 1.027724888 1 14.19623622 2.740902264 24.99631412 1.106647812 1.263557464 0.401978207 0.109383275 273.8206496 2922950.205 0.037186403 0.03773778 550.6837541 -2.740902264 0.156909652 TVSPDRLELEAAQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSPDRLELEAAQK 14 1 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 ; 220.46 4.22E-12 2343800000 1249090 1283270 1259690 998770 1182450 1309860 1264180 1365330 1417910 1423160 FALSE TRUE 1200274.182 1246672.396 1487344.005 1050316.639 1220484.578 1336346.267 1279651.413 1337135.458 1256954.801 1326768.106 0.904660111 0.939630966 1.121027856 0.79163543 0.919892913 1.007219167 0.96448762 1.00781399 0.94738093 1 20.33948481 2.740909367 24.94872619 0.985942863 0.937935337 0.094708539 0.077096148 563.3975151 5984502.233 0.024197 0.024556657 550.6927597 -2.740909367 -0.048007525 SINNPDMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SINNPDMR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 84.213 0.041326 170330000 364860 500600 488380 480450 489100 399340 469840 427710 425140 467410 FALSE TRUE 350600.8678 486323.3781 576641.13 505246.0821 504832.3457 407414.9284 475590.0425 418877.639 376879.8895 435751.9044 0.804588263 1.116055657 1.323324406 1.159481065 1.158531588 0.934969932 1.091423899 0.961275521 0.864895565 1 18.73314744 2.741178049 24.71576288 0.977667744 1.126933562 0.220870499 0.131491647 311.0156911 2936846.824 0.04232436 0.043034761 551.0335591 -2.741178049 0.149265818 EWTDGLFTHVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EWTDGLFTHVLR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 145.09 6.36E-05 89607000 96878 110012 89796 98530 95278 108092 109333 101856 117373 117878 FALSE TRUE 93091.90066 106874.5655 106024.1347 103615.1451 98342.7034 110277.6943 110671.05 99752.63801 104049.3091 109894.0181 0.847106169 0.972523959 0.964785314 0.942864288 0.894886775 1.00349133 1.007070739 0.907716723 0.94681504 1 16.74575333 2.741274183 24.98011776 0.965287744 0.930370728 0.218786256 0.044017478 535.7333788 4931784.254 0.014212454 0.01446471 551.1555479 -2.741274183 -0.034917016 EDQDKVAVLSQNR ddPTM_BT-474_Pertuzumab_2h_R1 4 EDQDKVAVLSQNR 13 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ;;; 138.73 4.17E-05 3662170000 3248950 3332050 2104760 2158350 2584430 3030510 2960730 2978970 3477690 3170510 FALSE TRUE 3121977.442 3237023.196 2485136.952 2269742.702 2667560.538 3091788.989 2996964.299 2917453.228 3082917.211 2955768.534 1.056232045 1.095154495 0.840775224 0.767902722 0.902493043 1.046018642 1.013937413 0.987037109 1.043017129 1 21.49510187 2.74130263 24.94861141 1.014362766 0.927305834 0.182240578 0.09004668 472.7599295 4301491.429 0.03161372 0.032165543 551.1916503 -2.74130263 -0.087056932 AGTEDEEEEEEGRR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGTEDEEEEEEGRR 14 1 O95456;O95456-2;F8WBH7 O95456 PSMG1 Proteasome assembly chaperone 1 0 ; 286.53 1.34E-33 784710000 707610 700290 618340 643980 689240 734900 734400 807290 819200 822940 FALSE TRUE 679955.8189 680318.4149 730087.7929 677215.885 711410.0306 749760.1815 743387.8069 790619.1794 726207.8504 767201.5408 0.88628057 0.886753192 0.951624513 0.882709235 0.927279199 0.977266261 0.968960263 1.030523451 0.946567247 1 19.54924609 2.741374152 1.978750478 0.992799081 0.903425571 0.672892397 0.027446415 0.188094615 1.455255105 0.009972013 0.009852279 551.282431 -2.741374152 -0.08937351 LSKEEIER ddPTM_BT-474_Pertuzumab_2h_R1 8 LSKEEIER 8 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ;;;;;;; 134.68 0.00079016 55357350000 56746790 57093000 43722800 46800180 49300490 56857520 55074930 57790610 63574800 57581900 FALSE TRUE 54529062.71 55464763.54 51624482.57 49215542.9 50886285.03 58007218.01 55748953.47 56597213.71 56358055.23 53681826.62 1.015782549 1.033213045 0.961675223 0.916800824 0.947923874 1.080574594 1.038507014 1.054308642 1.049853531 1 25.67793043 2.741499233 24.99926151 1.047959082 0.974326424 0.483780531 0.035846453 241.081338 2050919.012 0.012123287 0.012366498 551.4412288 -2.741499233 -0.073632658 TFHVETPEER ddPTM_BT-474_Pertuzumab_2h_R1 2 TFHVETPEER 10 0 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 0 ; 131.82 0.00024004 176580000 373560 421100 366800 455800 430070 352650 423480 356320 420670 429640 FALSE TRUE 358960.8622 409090.6403 433088.9194 479323.8926 443903.5921 359780.8246 428662.6749 348961.8675 372917.3052 400540.1001 0.896192072 1.021347526 1.081262324 1.196693895 1.108262548 0.898239214 1.070211634 0.871228292 0.931036131 1 18.61158716 2.741679031 24.9667931 0.949751888 1.067254381 0.26943547 0.08729688 366.9734745 2938093.467 0.028520667 0.029095752 551.6695719 -2.741679031 0.117502493 S(ph)PVQLEEAPFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPVQLEEAPFSR 12 0 Q9BZL4-5;Q9BZL4-2;Q9BZL4-4;Q9BZL4 Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 S(1)PVQLEEAPFSR 130.24 0.00023083 136660000 49270 48848 51469 56920 52302 41905 45119 49251 38368 42804 TRUE FALSE 47344.47393 47454.90287 60770.59322 59857.64802 53984.34133 42752.34781 45671.17982 48233.94964 34012.62549 39904.84695 1.186434169 1.189201475 1.522887515 1.500009462 1.352826673 1.071357268 1.144502067 1.208724085 0.852343214 1 15.28427637 2.741711016 22.57852878 1.087185712 1.359232068 0.531959441 0.136554589 66.38261543 475755.5214 0.045351499 0.046208139 551.7102031 -2.741711016 0.272046356 FAQPGTFEFEYASR ddPTM_BT-474_Pertuzumab_2h_R1 1 FAQPGTFEFEYASR 14 0 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 195.77 2.08E-07 0 41543 35412 31618 40729 38643 34763 36098 39894 39907 37608 FALSE TRUE 39919.45363 34402.08443 37332.07594 42831.02857 39885.98719 35465.93168 36539.77812 39070.17496 35376.92466 35060.77666 1.138578703 0.981212845 1.064781773 1.221622355 1.137624177 1.011555791 1.042183933 1.114355661 1.009017142 1 15.09757033 2.741790226 24.98044178 1.048916813 1.105504251 0.227359681 0.065133676 602.6649588 4661511.602 0.021849155 0.022322146 551.8108374 -2.741790226 0.056587438 SLPTPAVLLS(ph)PTKEPPPLLAKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPTPAVLLSPTKEPPPLLAKPK 23 2 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;A0A3B3ISX8 Q8WX93-8 PALLD Palladin 1 SLPT(0.001)PAVLLS(0.922)PT(0.077)KEPPPLLAKPK;SLPTPAVLLS(0.931)PT(0.069)KEPPPLLAKPK 78.978 0.0067363 560820000 661760 578260 553540 451230 520010 654060 599750 584460 748900 763310 TRUE FALSE 635897.6876 561768.591 653576.9914 474518.0344 536736.5939 667285.5413 607089.9199 572390.6968 663888.0116 711610.3338 0.893603785 0.789432874 0.918447864 0.666822855 0.754256323 0.937711989 0.853121281 0.804359731 0.932937564 1 19.44072794 2.741921217 24.98587014 0.881942941 0.802355262 0.247401219 0.083157242 538.4635866 4003451.164 0.026226446 0.026802663 551.977299 -2.741921217 -0.079587679 ATS(ph)LPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 AT(0.181)S(0.756)LPS(0.063)IPNPFPELCSPPSQSPILGGPSSAR 100.19 0.00015287 37358000 15861 15554 12047 14978 14663 17042 16145 19437 18058 17138 TRUE FALSE 15241.13458 15110.41515 14224.16088 15751.01637 15134.64871 17386.60092 16342.58734 19035.61916 16008.13155 15977.228 0.953928591 0.945746981 0.890277142 0.985841623 0.947263738 1.088211354 1.022867505 1.191421889 1.001934225 1 13.96372951 2.741931571 23.48588924 1.079231168 0.943946651 0.494373622 0.057311559 91.82973778 639791.3882 0.01770587 0.018066102 551.9904594 -2.741931571 -0.135284517 LEDEHLVFFCQMGK ddPTM_BT-474_Pertuzumab_2h_R1 3 LEDEHLVFFCQMGK 14 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2;Q8NFU3-3 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;; 127.76 7.77E-05 3630928000 3638070 4392804 3185940 4088302 3880352 3664885 3583550 4029456 4175970 4073047 FALSE TRUE 3495890.202 4267525.531 3761710.229 4299299.756 4005167.046 3738991.486 3627406.557 3946246.325 3701931.393 3797175.899 0.920655323 1.123868276 0.990659988 1.132236133 1.054775221 0.984676924 0.95529063 1.039258236 0.974917015 1 21.8564954 2.74196086 24.28871042 0.994083885 1.050741626 0.159365546 0.060476343 350.5838464 2504303.523 0.017723578 0.018076829 552.0276866 -2.74196086 0.056657741 ERRT(ph)PS(ph)DDEEDNLFAPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERRTPSDDEEDNLFAPPK 18 2 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 2 ERRT(1)PS(1)DDEEDNLFAPPK 151.06 5.56E-08 175360000 219060 187950 158170 180560 191460 205690 207150 217750 234260 248310 TRUE FALSE 210498.893 182589.85 186754.8375 189878.7232 197618.4848 209849.1927 209685.1637 213253.3864 207667.7869 231491.7425 0.90931491 0.788753188 0.806745137 0.820239725 0.853674013 0.906508329 0.905799755 0.921213794 0.897085074 1 17.82060121 2.742113917 1.738137377 0.92489413 0.825888004 0.575471889 0.03939964 0.259228719 1.558891769 0.014578805 0.014267963 552.2222702 -2.742113917 -0.099006127 ELFDVVANPLVNDLIHGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELFDVVANPLVNDLIHGK 18 0 Q02241;H7BYN4;A0A2U3TZL8;A0A2R8Y531;H0YME6;H0YMJ4;Q02241-2 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 0 214.46 1.00E-18 50945000 121560 122790 110760 113570 117100 140510 135670 150480 155060 138270 FALSE TRUE 116809.3008 119288.1494 130776.7958 119431.3613 120866.6278 143351.2085 137330.37 147372.5354 137458.2389 128904.8497 0.906166844 0.925396908 1.014521921 0.926507897 0.937642207 1.11206994 1.065362322 1.143266027 1.066354285 1 16.97594702 2.742294565 24.98126339 1.089853684 0.94428522 0.695825073 0.044356862 164.9170433 1103346.862 0.013452005 0.013785839 552.452019 -2.742294565 -0.145568464 SRS(ph)PS(ph)PAPEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPSPAPEKK 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(0.025)RS(0.976)PS(0.999)PAPEKK 86.944 0.069319 181770000 288370 273560 251610 261620 269710 372040 379890 308560 484380 445810 TRUE FALSE 277100.1816 265758.3366 297081.524 275122.2396 278385.4671 379562.9037 384539.2075 302188.1282 429395.2131 415614.8916 0.666723419 0.639434106 0.714799999 0.661964345 0.669815911 0.913256265 0.925229618 0.727086864 1.033156467 1 18.66488782 2.742392428 24.28206057 0.888986073 0.670800641 0.700877416 0.080149027 142.7200074 904413.2892 0.025175767 0.025781366 552.5765207 -2.742392428 -0.218185433 PGHVS(ph)PLQLTNIQVPQQALPTQR ddPTM_BT-474_Pertuzumab_2h_R1 3 PGHVSPLQLTNIQVPQQALPTQR 23 0 P22670 P22670 RFX1 MHC class II regulatory factor RFX1 1 PGHVS(1)PLQLTNIQVPQQALPTQR;PGHVS(1)PLQLTNIQVPQQALPTQR;PGHVS(0.988)PLQLT(0.012)NIQVPQQALPTQR 241.22 1.77E-37 1503450000 783780 634820 649500 855850 768060 641760 733850 643480 834500 772240 TRUE FALSE 753149.0111 616715.5552 766879.098 900020.5211 792765.3474 654736.8269 742831.0758 630191.9131 739771.0585 719935.497 1.046134014 0.856626125 1.065205288 1.250140499 1.101161633 0.909438178 1.031802264 0.875344966 1.027551859 1 19.45750813 2.742454526 24.96500089 0.959359867 1.062765255 0.180458758 0.100229741 599.9407642 3846402.734 0.033616487 0.034459178 552.6555375 -2.742454526 0.103405388 YSHVQEVQER ddPTM_BT-474_Pertuzumab_2h_R1 2 YSHVQEVQER 10 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ; 191.53 7.82E-07 906320000 490000 583610 491620 531950 570160 454220 586480 430050 581120 598200 FALSE TRUE 470850.2583 566966.0142 580466.67 559404.0032 588499.7142 463404.6396 593657.5177 421169.3172 515153.6939 557683.3812 0.844296736 1.016644988 1.040853448 1.003085303 1.055257757 0.830945757 1.064506381 0.755212243 0.92373865 1 19.08908675 2.742536733 24.98231769 0.900444405 0.996722133 0.129420657 0.096092468 569.5178192 3578340.127 0.029058381 0.029809442 552.7601586 -2.742536733 0.096277729 KAPKPER ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPKPER 7 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 58.815 0.060342 149490000 317360 339540 304510 320590 313030 391180 354790 404280 438210 399060 FALSE TRUE 304957.2203 329856.6516 359541.7308 337135.6883 323098.8942 399089.9276 359132.0261 395931.4767 388466.2379 372031.3108 0.81970848 0.886636802 0.966428686 0.906202458 0.868472316 1.072732096 0.965327422 1.064242351 1.044176194 1 18.50506452 2.742728107 24.99882304 1.030446179 0.894534117 0.709713394 0.044644889 204.5352338 1226912.966 0.013976374 0.014346948 553.0037889 -2.742728107 -0.135912061 RGDYLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDYLGK 7 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 ; 92.439 0.025123 1388870000 1413210 1504050 1192900 1444300 1421060 1283050 1365160 1342840 1535730 1452430 FALSE TRUE 1357980.191 1461155.967 1408483.566 1518840.496 1466769.685 1308994.15 1381867.236 1315109.885 1361400.369 1354055.622 1.00289838 1.079095971 1.040196239 1.121697271 1.083241826 0.966721107 1.020539492 0.971237712 1.005424257 1 20.36885557 2.742984645 24.99862593 0.991703956 1.067909921 0.558973849 0.032217066 274.5968723 1551652.647 0.009834668 0.010107739 553.3305456 -2.742984645 0.076205965 S(ph)PLTQEQLIPNLAMK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLTQEQLIPNLAMK 15 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 S(0.999)PLT(0.001)QEQLIPNLAMK 179.79 6.88E-07 72326000 101950 99761 91365 98691 98617 112370 116440 112400 119380 128520 TRUE FALSE 97965.68129 96915.91396 107876.6879 103784.4543 101789.1054 114642.1984 117865.0276 110078.9007 105828.4829 119815.2259 0.817639666 0.808878114 0.900358757 0.86620422 0.849550669 0.956824957 0.983723284 0.918738832 0.88326406 1 16.87045173 2.74307571 24.08446054 0.944449191 0.850185291 0.628334858 0.038374518 168.6485073 899607.2946 0.012358413 0.012702757 553.4465829 -2.74307571 -0.0942639 GTS(ph)PRPPEGGLGYSQLGDDDLK ddPTM_BT-474_Pertuzumab_2h_R1 5 GTSPRPPEGGLGYSQLGDDDLK 22 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 GT(0.15)S(0.85)PRPPEGGLGYSQLGDDDLK;GT(0.117)S(0.883)PRPPEGGLGYSQLGDDDLK;GT(0.021)S(0.979)PRPPEGGLGYSQLGDDDLK;GT(0.004)S(0.996)PRPPEGGLGYSQLGDDDLK;GT(0.029)S(0.971)PRPPEGGLGYSQLGDDDLK 178.02 3.74E-17 2603600000 1705690 1517460 1775790 1896000 1813710 1728760 2109820 2388300 2662700 2642660 TRUE FALSE 1639029.749 1474183.527 2096714.755 1993852.787 1872049.629 1763716.712 2135640.608 2338980.77 2360441.459 2463670.284 0.665279668 0.598368839 0.851053312 0.809301797 0.759862081 0.715889915 0.866853256 0.949388717 0.958099578 1 21.23237776 2.743236398 0.294155633 1.040597828 0.585457536 0.708025861 0.068120947 1.48785424 0.266475251 0.106277786 0.235497667 553.6513938 -2.743236398 -0.455140293 TEQFYR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEQFYR 6 0 O76021;J3QSV6;I3L3U9;I3L3C4;I3L234 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 118.01 0.05172 513740000 607970 574610 470000 560040 590820 480310 498810 606120 531990 592790 FALSE TRUE 584209.8603 558222.6854 554939.4551 588943.7315 609824.2619 490022.1973 504914.586 593603.4102 471600.7255 552639.8053 1.057125916 1.010102204 1.004161209 1.065691841 1.103475095 0.886693634 0.913641365 1.074123515 0.853360038 1 19.07597995 2.743436615 24.9961818 0.957734805 1.044534667 0.388502385 0.063335304 533.7228884 2736065.225 0.020278035 0.020872924 553.906696 -2.743436615 0.086799862 NNPAIVIIGNNGQIHYDHQNDGASQALASCQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNPAIVIIGNNGQIHYDHQNDGASQALASCQR 32 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 115.27 1.19E-06 127000000 43688 45993 30922 43617 42085 29714 41838 20912 48420 34897 FALSE TRUE 41980.62466 44681.32467 36510.29326 45868.0786 43438.70225 30314.83744 42350.02596 20480.15989 42923.56459 32533.39511 1.290385603 1.373398765 1.12224049 1.409876788 1.335203476 0.931806759 1.301740129 0.629511916 1.319369357 1 14.98963377 2.743549772 24.75500669 1.004093023 1.305490646 0.315216211 0.195894273 396.9908684 1969775.591 0.058682939 0.060528392 554.0510365 -2.743549772 0.301397623 IIGEDSPS(ph)RLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IIGEDSPSRLDR 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 IIGEDS(0.051)PS(0.949)RLDR 153 0.00018488 539810000 577750 600460 459620 519700 525800 605950 631700 597000 606160 662230 TRUE FALSE 555170.8913 583335.4687 542683.5582 546521.7793 542712.8345 618202.7242 639430.9336 584671.7414 537351.258 617376.5722 0.899241915 0.944861686 0.879015471 0.885232456 0.879062891 1.001338165 1.035722705 0.947026123 0.87037844 1 19.23579121 2.743660318 24.9921848 0.971363648 0.898408491 0.405631255 0.044422374 467.7289989 2292207.93 0.014498295 0.014954479 554.192084 -2.743660318 -0.072955157 ELSVEEQIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSVEEQIKR 10 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 85.821 0.022414 867290000 971980 953910 680940 794800 801060 939340 894120 975980 954450 915960 FALSE TRUE 933993.947 926705.4208 804001.0054 835819.7232 826826.8224 958334.0984 905062.508 955825.6719 846104.8374 853921.2133 1.093770634 1.085235273 0.941540031 0.97880192 0.96827062 1.122274612 1.059889945 1.119337073 0.99084649 1 19.70374344 2.743733341 24.99535365 1.070290109 1.011579594 0.106100171 0.060418753 798.1024209 3856540.441 0.019348569 0.019873659 554.2852744 -2.743733341 -0.058710515 ERPT(ph)SPAPHRPPKR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.843)S(0.157)PAPHRPPKR;ERPT(0.5)S(0.5)PAPHRPPKR;ERPT(0.91)S(0.09)PAPHRPPKR;ERPT(0.5)S(0.5)PAPHRPPKR 152.94 3.46E-06 2190646000 272461 267641 208072 229468 243281 271671 258004 287914 324944 269067 TRUE FALSE 261812.9229 260008.1407 245675.2389 241310.871 251106.3543 277164.3738 261161.5301 281968.4753 288057.7194 250842.8524 1.043732841 1.036537969 0.979399 0.962000187 1.001050466 1.104932315 1.041136024 1.124084153 1.148359288 1 17.9364243 2.743850177 24.49259631 1.090413877 1.002561025 0.431227799 0.045098352 297.6207504 1378092.7 0.014044077 0.014488364 554.4344116 -2.743850177 -0.087852852 RGDIIGVQGNPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDIIGVQGNPGK 13 1 Q15046;Q15046-2;H3BVA8;J3KRL2;H3BPV7 Q15046 KARS Lysine--tRNA ligase 0 ; 164.53 1.48E-06 332260000 1007580 1056850 853210 936120 943120 1077680 1006200 1089450 1226830 1177440 FALSE TRUE 968202.6597 1026709.673 1007404.027 984433.2654 973456.3113 1099471.428 1018514.177 1066952.477 1087565.402 1097690.94 0.882035757 0.935335836 0.91774833 0.896821892 0.886821851 1.00162203 0.927869712 0.97199716 0.990775602 1 20.06604048 2.744060767 24.99984002 0.972143944 0.905899835 0.696749209 0.024443864 283.8960836 1290393.314 0.007486416 0.007740945 554.7033222 -2.744060767 -0.066244109 S(ph)QDDAMVDYFFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQDDAMVDYFFQR 13 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;E9PMX1;E9PM68;E9PL65 Q5T1Z4 PUM1 Pumilio homolog 1 1 S(1)QDDAMVDYFFQR;S(1)QDDAMVDYFFQR 115.38 0.00070112 61507000 78986 86449 60415 67762 73047 76211 79347 75938 87105 83980 TRUE FALSE 75899.1398 83983.55916 71333.33442 71259.20494 75396.62309 77752.03864 80318.07232 74369.85376 77217.20557 78291.9598 0.969437219 1.072697112 0.91111954 0.910172706 0.963018722 0.993103747 1.025878935 0.949904102 0.986272483 1 16.25657654 2.744068313 22.60733183 0.987725359 0.965184734 0.07215961 0.045386014 448.272813 1840017.154 0.014990339 0.015450632 554.7129605 -2.744068313 -0.022540625 VHQLYETIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHQLYETIQR 10 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 ; 160.77 7.28E-06 997320000 246759 240006 257639 242104 265194 179436 231312 168882 257738 260934 FALSE TRUE 237115.3855 233161.2639 304200.0984 254599.0165 273724.2059 183064.3189 234142.8654 165394.5277 228480.6628 243260.7078 0.974737711 0.958483045 1.25051062 1.0466097 1.125229834 0.752543724 0.962518228 0.679906464 0.939241955 1 17.89214378 2.744172099 24.9952441 0.841454144 1.073462011 0.417392974 0.118773863 399.3267188 1778723.461 0.035877829 0.03709476 554.8455393 -2.744172099 0.232007867 SRGS(ph)PSSYNSSSS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 2 S(0.365)RGS(0.635)PS(0.002)S(0.002)YNS(0.063)S(0.187)S(0.156)S(0.323)S(0.268)PR 61.985 0.045886 199000000 52233 55128 53111 56617 47349 68162 61316 63933 57202 68813 TRUE FALSE 50191.67661 53555.80342 62709.33915 59539.01015 48872.02359 69540.28234 62066.40355 62612.76121 50708.66877 64152.23422 0.782383922 0.834823667 0.977508265 0.928089425 0.761813274 1.083988472 0.967486235 0.976002815 0.790442755 1 15.96921189 2.744270632 24.99909197 0.963610956 0.86634873 0.256599094 0.090061456 756.1807245 3310645.255 0.028178859 0.029157472 554.971438 -2.744270632 -0.097262226 DRDGYSYGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRDGYSYGSR 10 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 182.71 1.59E-06 761240000 243679 284100 205014 236220 244652 218258 227744 239974 237644 250848 FALSE TRUE 234155.7553 275997.7462 242064.5903 248411.3425 252521.4538 222671.3263 230531.1992 235018.453 210667.6494 233857.8415 1.00127391 1.180194533 1.035092895 1.062232256 1.079807511 0.952165319 0.985774938 1.004962893 0.900836371 1 17.83527228 2.744346298 24.82863671 0.973460455 1.075184616 0.504546935 0.050855182 352.0744832 1510891.523 0.014982089 0.015495823 555.0681375 -2.744346298 0.101724161 SVFPEQANNNEWAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVFPEQANNNEWAR 14 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 277.15 9.25E-33 969650000 226343 251837 208955 249117 242716 216760 228991 241305 243180 251599 FALSE TRUE 217497.2653 244654.8553 246717.8167 261973.9582 250523.1806 221143.0357 231793.4604 236321.9674 215575.2259 234557.9756 0.92726442 1.043046414 1.051841516 1.116883609 1.06806507 0.942807573 0.988213936 1.007520494 0.919070116 1 17.83958503 2.744464646 24.92602908 0.976331027 1.046281924 0.317590616 0.050737057 604.8675237 2553675.59 0.016193753 0.016762311 555.2194179 -2.744464646 0.069950897 YALPLVGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 YALPLVGHR 9 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 143.85 0.00010096 2760700000 2403240 2753200 2430400 2853400 2682900 2435600 2624800 2521560 2808500 2842200 FALSE TRUE 2309318.724 2674681.432 2869627.344 3000664.316 2769197.915 2484849.501 2656923.088 2469488.905 2489690.854 2649695.262 0.871541251 1.009429827 1.083002783 1.132456384 1.045100527 0.937786898 1.002727795 0.93198978 0.939614034 1 21.33739502 2.744491787 24.42533713 0.95946787 1.036082299 0.191025758 0.066699698 551.5206065 2271234.37 0.021789218 0.022552831 555.2541164 -2.744491787 0.076614429 SFS(ph)ASQSTDR ddPTM_BT-474_Pertuzumab_2h_R1 5 SFSASQSTDR 10 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 SFS(0.989)AS(0.011)QSTDR;SFS(0.716)AS(0.284)QSTDR;SFS(0.857)AS(0.143)QSTDR;S(0.006)FS(0.99)AS(0.004)QSTDR;SFS(0.993)AS(0.007)QSTDR 205.09 1.84E-07 2381150000 1866750 1810890 1466010 1793440 1755450 1476360 1581440 1751500 1548900 1525270 TRUE FALSE 1793795.346 1759245.19 1730950.618 1885999.653 1811915.644 1506213.011 1600794.136 1715330.913 1373075.366 1421962.104 1.261493074 1.237195552 1.217297291 1.326336087 1.274236239 1.059249755 1.125764274 1.206312677 0.965620224 1 20.43945159 2.744551537 24.92039156 1.098626048 1.262805766 0.647097116 0.069423643 345.8374292 1438578.305 0.021967886 0.022748676 555.3305132 -2.744551537 0.164179717 IPNSYEVLFPES(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IPNSYEVLFPESPAR 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 IPNSYEVLFPES(1)PAR;IPNSYEVLFPES(1)PAR 103.5 0.0015395 196504000 85230 97552 73528 79033 73456 83262 79912 72635 75333 85227 TRUE FALSE 81899.11737 94769.91247 86816.14522 83111.9026 75818.77895 84945.61469 80889.98696 71135.06187 66781.51366 79454.49938 1.030767521 1.192757027 1.092652347 1.046031417 0.954241478 1.069110187 1.018066788 0.89529306 0.840500087 1 16.2778413 2.744777839 0.657912406 0.91075832 1.116454397 0.482770962 0.068402792 0.622153567 0.578582652 0.052934891 0.055782437 555.6199599 -2.744777839 0.205696077 HINWEELLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HINWEELLAR 10 0 P23443-5;P23443;P23443-3;P23443-2;P23443-4 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 0 ; 208.33 1.16E-07 875320000 675070 715610 607730 742680 693190 600930 698090 559170 697320 764330 FALSE TRUE 648687.5181 695201.5035 717560.3299 781009.8038 715487.0859 613081.2163 706633.4342 547622.9441 618163.157 712561.2483 0.910360365 0.97563754 1.007015652 1.096059891 1.004106086 0.860390904 0.991680976 0.768527541 0.867522839 1 19.4426545 2.744840393 23.679579 0.881844837 1.003236217 0.295659232 0.075861525 267.7523549 1009631.287 0.023896696 0.0247474 555.6999955 -2.744840393 0.12139138 CLVAGLLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 CLVAGLLSPR 10 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 CLVAGLLS(1)PR;CLVAGLLS(1)PR 94.465 0.0084119 296300000 228426 234164 200877 223167 257417 147915 232384 199347 177628 186073 TRUE FALSE 219498.8594 227485.872 237179.9424 234684.6756 265697.0516 150905.9426 235227.9849 195230.4148 157464.4141 173470.11 1.265341098 1.311383685 1.367266917 1.352882497 1.531658979 0.869924753 1.356014503 1.125441235 0.907732255 1 17.40432757 2.745125885 24.99975908 1.090275726 1.362062918 0.540960805 0.142364964 469.5714844 1788073.315 0.043708398 0.045390617 556.0654157 -2.745125885 0.271787192 DYAFVHFEDR ddPTM_BT-474_Pertuzumab_2h_R1 7 DYAFVHFEDR 10 0 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;;; 180.19 2.02E-06 8810958000 5071325 5246089 4477248 5154633 5213729 4381163 5032660 4860871 4794740 5242770 FALSE TRUE 4873132.012 5096475.678 5286386.309 5420664.227 5381433.328 4469753.118 5094251.199 4760492.315 4250461.216 4887672.518 0.997025065 1.042720366 1.08157539 1.109048163 1.101021664 0.914495212 1.042265246 0.973979394 0.869628888 1 22.22071619 2.745252883 24.98770965 0.966636253 1.068195327 0.502778251 0.052588645 483.555554 1805510.922 0.016643303 0.01728791 556.2280462 -2.745252883 0.101559074 EVNKFQMAYSNLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVNKFQMAYSNLLR 14 1 P37108 P37108 SRP14 Signal recognition particle 14 kDa protein 0 217.48 5.24E-12 832350000 642900 799700 535330 632990 655480 764980 832560 771790 782480 741210 FALSE TRUE 617774.7572 776893.339 632076.0394 665658.6898 676564.1095 780448.4197 842749.1183 755852.2668 693656.1508 691007.1865 0.894020741 1.124291258 0.914717027 0.963316595 0.979098514 1.129436039 1.219595302 1.093841398 1.003833483 1 19.39834119 2.745320682 24.03986592 1.105784174 0.979369838 0.314565931 0.082440101 350.1612414 1245227.61 0.025093716 0.026044762 556.3148877 -2.745320682 -0.126414336 TAPS(ph)SPLTSPSDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TAPSSPLTSPSDTR 14 0 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 T(0.002)APS(0.489)S(0.489)PLT(0.015)S(0.003)PS(0.001)DTR 68.83 0.046044 0 112740 123210 82398 108020 118060 117530 117280 139960 146100 128370 TRUE FALSE 108333.9962 119696.1714 97289.15153 113594.9251 121857.5071 119906.5371 118715.3077 137069.7771 129515.3405 119675.3856 0.905232063 1.000173685 0.812942035 0.949192055 1.018233671 1.001931488 0.99197765 1.145346442 1.082222045 1 16.86876693 2.745335079 1.009538474 1.079160455 0.913673782 0.495943216 0.061065429 0.408015154 0.878926054 0.033711739 0.031440579 556.3333292 -2.745335079 -0.165486673 NIPS(ph)PGQLDPDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 NIPSPGQLDPDTR 13 0 Q9P2D1 Q9P2D1 CHD7 Chromodomain-helicase-DNA-binding protein 7 1 NIPS(1)PGQLDPDTR;NIPS(1)PGQLDPDTR 197.73 1.38E-07 395600000 359380 310140 280270 364020 360360 270720 289320 360790 342440 310260 TRUE FALSE 345335.0323 301295.1109 330921.0236 382807.1158 371951.3067 276194.1439 292860.7847 353339.5604 303567.6468 289245.8138 1.193915403 1.041657637 1.144082326 1.323466399 1.285934969 0.954876892 1.012497919 1.221589193 1.0495144 1 18.14193655 2.745477779 24.99538862 1.071564171 1.193132026 0.356931442 0.098066458 842.9809636 3046140.976 0.033603384 0.03497291 556.5161594 -2.745477779 0.121567856 ENSENKENR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSENKENR 9 1 Q5T6F2;A0A0D9SFI5;A2A305 Q5T6F2 UBAP2 Ubiquitin-associated protein 2 0 82.417 0.016884 38094000 136410 130810 112580 109390 112780 138010 139090 125390 131930 150560 FALSE TRUE 131078.9464 127079.4269 132925.7103 115035.631 116407.6711 140800.6568 140792.225 122800.6527 116953.8595 140362.4371 0.933860576 0.905366347 0.947017686 0.819561368 0.829336349 1.003122058 1.003061987 0.874882591 0.833227621 1 17.09879738 2.745641764 24.97596327 0.935260124 0.887631804 0.153222066 0.064389369 1384.9484 4884863.509 0.021292039 0.022157972 556.726333 -2.745641764 -0.04762832 DANSSFFDNSSS(ph)PHLLDQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DANSSFFDNSSSPHLLDQLK 20 0 P49454 P49454 CENPF Centromere protein F 1 DANSSFFDNSS(0.038)S(0.962)PHLLDQLK 188.3 1.68E-17 103460000 200550 181260 198360 159670 184560 212780 222370 203440 219280 248860 TRUE FALSE 192712.2843 176090.6423 234208.0645 167910.5878 190496.54 217082.5574 225091.4306 199238.8929 194388.2537 232004.4905 0.83064032 0.758996698 1.00949798 0.723738525 0.821089883 0.935682568 0.970202905 0.858771709 0.837864186 1 17.8237932 2.745647042 24.05930467 0.91165543 0.829117963 0.231047636 0.082871736 561.6641129 1906918.831 0.025188906 0.026184318 556.7330987 -2.745647042 -0.082537467 DRDVTFSPATIENELIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRDVTFSPATIENELIK 17 1 P55145;H7C2D6 P55145 MANF Mesencephalic astrocyte-derived neurotrophic factor 0 ; 204.78 7.73E-12 424090000 302990 322970 232239 249990 270070 293000 281340 309070 316440 306640 FALSE TRUE 291148.8158 313759.2118 274209.7534 262892.0139 278757.0468 298924.6608 284783.1231 302687.5965 280519.0578 285870.9997 1.01846223 1.097555234 0.959208013 0.919617639 0.975114815 1.045662768 0.996194519 1.058825823 0.981278472 1 18.12500475 2.745679111 24.81352395 1.021513394 0.993680816 0.046316487 0.048083852 1604.4154 5592646.431 0.016032395 0.016706147 556.774211 -2.745679111 -0.027832577 YLHDESGLNRR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLHDESGLNRR 11 1 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310 Q15019-2 2-Sep Septin-2 0 ; 162.36 1.64E-05 332760000 252310 264780 197204 229260 217850 224840 209861 194153 228840 254490 FALSE TRUE 242449.4463 257228.7336 232843.1496 241092.1361 224857.3431 229386.4188 212429.3417 190143.6727 202863.0426 237253.1656 1.021901839 1.084195159 0.981412193 1.016180903 0.947752762 0.966842395 0.895369894 0.801437874 0.855048834 1 17.85606781 2.745861461 1.059968604 0.863394611 1.033828917 0.516824697 0.056003658 0.338729875 0.799978451 0.029132693 0.027200973 557.0080357 -2.745861461 0.170434306 AIIVEFAQQGLNAALFYENKDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIIVEFAQQGLNAALFYENKDPR 23 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 161.46 1.62E-11 731260000 539190 550860 452870 497670 491370 597290 560480 587360 626720 659760 FALSE TRUE 518117.8587 535150.0121 534713.683 523354.8083 507175.3623 609367.613 567339.3219 575230.8107 555577.373 615073.8675 0.842366886 0.870058119 0.869348726 0.850881229 0.824576346 0.990722652 0.922392174 0.935222322 0.903269351 1 19.23040016 2.74591958 24.99998731 0.943136865 0.853443443 0.727035902 0.030119459 319.7190358 1086154.332 0.008997747 0.009365188 557.0825823 -2.74591958 -0.089693422 QELQEEEEQTKPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QELQEEEEQTKPPR 14 1 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 0 ; 157.68 4.77E-06 894520000 354260 342520 260260 326830 307890 353630 360480 330600 395070 364730 FALSE TRUE 340415.1275 332751.665 307294.7715 343697.7355 317793.5615 360780.6409 364891.6621 323772.9945 350223.3099 340026.5122 1.001142897 0.978605059 0.90373768 1.010796873 0.934614067 1.061036795 1.073127091 0.952199263 1.029988243 1 18.37528771 2.746016858 24.98076084 1.018846832 0.965546075 0.313133676 0.042320145 797.0221239 2670276.619 0.013378093 0.013918289 557.2073779 -2.746016858 -0.053300757 MASCLEVLDLFLNQPHMVLSSFVLAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MASCLEVLDLFLNQPHMVLSSFVLAEK 27 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 158.18 1.59E-11 730260000 103930 109660 91530 92045 93342 114270 117920 100510 122430 115310 FALSE TRUE 99868.3007 106532.6042 108071.5071 96795.45348 96344.4302 116580.6177 119363.1402 98434.43338 108532.2597 107499.951 0.929007872 0.991001421 1.005316803 0.900423234 0.896227666 1.084471357 1.110355299 0.915669565 1.009602876 1 16.71397648 2.74632094 24.97559176 1.017500231 0.94792625 0.312399216 0.058550527 921.1518919 2964610.315 0.019747146 0.02057903 557.5976566 -2.74632094 -0.069573981 VCHANPSER ddPTM_BT-474_Pertuzumab_2h_R1 4 VCHANPSER 9 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;; 150.08 8.61E-05 1326260000 304057 311144 298210 311692 322055 264429 323742 274621 310849 313746 FALSE TRUE 292174.1163 302270.4778 352103.1806 327778.4615 332414.1916 269775.9356 327704.0514 268949.9804 275562.7247 292495.704 0.998900539 1.033418521 1.203789238 1.120626584 1.136475466 0.922324437 1.120372187 0.919500617 0.942108622 1 18.15805591 2.746325254 24.98311038 0.982901522 1.102081413 0.382850568 0.074683404 645.2108886 2076000.057 0.023532348 0.024554816 557.6031951 -2.746325254 0.11917989 S(ph)PAS(ph)PLNNQGIPTPAQLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPASPLNNQGIPTPAQLTK 19 0 A0A2U3U043;J3QLL6;J3KSG1;J3QRK1;Q719H9 A0A2U3U043 KCTD1 BTB/POZ domain-containing protein KCTD1 2 S(1)PAS(1)PLNNQGIPTPAQLTK 121.44 4.04E-05 0 47960 47140 38632 41381 42848 51106 47107 56533 49480 51657 TRUE FALSE 46085.67018 45795.61335 45613.66176 43516.67837 44226.24483 52139.39834 47683.50956 55365.57379 43863.23784 48158.22538 0.95696363 0.950940634 0.94716243 0.903618811 0.918352877 1.082668598 0.990142581 1.149659759 0.910815079 1 15.55549461 2.746392286 24.95783148 1.042178963 0.935157609 0.345926698 0.060893901 553.1269574 1762694.621 0.018173705 0.018960275 557.689266 -2.746392286 -0.107021354 IS(ph)EDETERNGDDGTHDK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISEDETERNGDDGTHDK 17 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 IS(0.992)EDET(0.008)ERNGDDGTHDK;IS(0.979)EDET(0.021)ERNGDDGTHDK;IS(0.983)EDET(0.017)ERNGDDGTHDK 203.71 5.71E-12 1325660000 1266690 1053250 821654 781536 951277 1100500 1019086 1060300 1413660 1156980 TRUE FALSE 1217186.354 1023212.341 970145.1554 821871.1666 981875.6886 1122752.864 1031557.879 1038404.434 1253187.243 1078616.714 1.128469769 0.948633864 0.899434565 0.761967765 0.9103101 1.040919216 0.956371124 0.962718657 1.161846675 1 20.04075086 2.74648421 24.20842973 1.011495575 0.919804682 0.175632939 0.099403757 757.0576042 2312985.962 0.03201215 0.033370464 557.8073206 -2.74648421 -0.091690893 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 35 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RLNNLSPAPHLASGSPPPGLPSGLPSGLQS(0.01)GS(0.946)PS(0.045)R;RLNNLSPAPHLASGSPPPGLPSGLPS(0.001)GLQS(0.007)GS(0.951)PS(0.041)R 177.56 2.79E-20 1795380000 339307 452006 303596 419905 326858 486949 420419 437546 452079 481732 TRUE FALSE 326046.5073 439115.2314 358462.5507 441576.3474 337371.6844 496795.4424 425564.2135 428510.5222 400760.8872 449103.8626 0.72599355 0.97775875 0.798172941 0.98323881 0.751210828 1.106192763 0.947585289 0.954145706 0.892356803 1 18.7766896 2.746489572 24.99447044 0.97264355 0.859349737 0.327148677 0.094122009 792.0426592 2496758.749 0.027005618 0.028177145 557.8142086 -2.746489572 -0.113293813 VTTVTEIGKDVIGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTTVTEIGKDVIGLR 15 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 179.14 6.23E-07 520000000 420420 474270 357560 366650 375490 482420 427040 460830 518170 497230 FALSE TRUE 403989.5216 460744.284 422179.0459 385572.8504 387567.9769 492174.8629 432266.2433 451313.6995 459349.5139 463552.1692 0.871508211 0.993942677 0.910747644 0.831778764 0.83608276 1.061746435 0.932508296 0.973598506 0.990933803 1 18.82237219 2.746834498 24.98029463 0.983839991 0.892702738 0.490996804 0.05202175 633.7198336 1913311.27 0.016845292 0.017589673 558.2574122 -2.746834498 -0.091137253 RYPSSISS(ph)SPQKDLTQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSIS(0.024)S(0.897)S(0.079)PQKDLTQAK;RYPS(0.011)S(0.009)IS(0.054)S(0.463)S(0.463)PQKDLTQAK 158.89 3.50E-11 4113470000 5322080 4791820 2923520 2959650 3735400 4467620 4112060 4548860 4963690 4329610 TRUE FALSE 5114087.23 4655161.985 3451865.097 3112397.891 3855552.533 4557958.337 4162384.62 4454924.451 4400232.721 4036361.658 1.267004214 1.153306462 0.855192222 0.771089946 0.955204925 1.129224466 1.03122192 1.10369804 1.09014828 1 21.94462402 2.747085757 23.95918821 1.076053117 0.988054552 0.059436536 0.135096363 1035.729525 2910825.281 0.045827955 0.04785534 558.5804833 -2.747085757 -0.087998566 VLSIWEER ddPTM_BT-474_Pertuzumab_2h_R1 4 VLSIWEER 8 0 Q96P16;A0A0C4DGQ6;Q96P16-3 Q96P16 RPRD1A Regulation of nuclear pre-mRNA domain-containing protein 1A 0 ;;; 186.09 0.000487 247788000 444641 515051 398240 472571 487763 418460 479850 472176 455765 523570 FALSE TRUE 427263.9381 500362.2498 470210.8268 496960.4459 503452.3399 426921.5479 485722.5478 462425.4006 404028.4679 488108.1376 0.875346886 1.025105323 0.963333308 1.018135957 1.031436072 0.874645422 0.99511258 0.9473831 0.827743766 1 18.89684128 2.747252238 24.99164919 0.933098956 0.985924843 0.148859348 0.063579722 1261.181173 3626366.998 0.018905328 0.019763168 558.7946478 -2.747252238 0.052825887 GSGDGEMGKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSGDGEMGKPR 11 1 O60547 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 ;;; 150.46 3.09E-05 1447530000 2609620 2485930 2233890 2311870 2595910 2813580 3023350 3048520 3507010 3203750 FALSE TRUE 2507633.165 2415033.71 2637603.616 2431185.888 2679409.803 2870472.515 3060350.662 2985566.997 3108908.927 2986757.159 0.83958388 0.808580538 0.883099454 0.813988469 0.897096637 0.961066589 1.024639935 0.99960152 1.04089779 1 21.51014851 2.747277971 1.731271196 1.01595874 0.836495439 0.922636235 0.023523172 0.083593875 0.498868181 0.008493683 0.008342207 558.8277591 -2.747277971 -0.179463302 NFETLR ddPTM_BT-474_Pertuzumab_2h_R1 3 NFETLR 6 0 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 ;; 140.12 0.038255 395080000 618060 673810 572630 645560 632770 605250 611830 633750 697700 701320 FALSE TRUE 593905.5319 654593.5985 676116.9791 678877.429 653123.6217 617488.5697 619317.7586 620662.841 618500.021 653818.9717 0.908363871 1.001184773 1.034104253 1.038326293 0.998936479 0.944433546 0.947231245 0.949288515 0.945980536 1 19.31853171 2.74729211 22.36278249 0.953048316 1.000909032 0.209189478 0.036670357 202.7417519 519252.9079 0.01149726 0.011995303 558.8459528 -2.74729211 0.047860715 KEDQDRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEDQDRSPR 9 2 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 KEDQDRS(1)PR;KEDQDRS(1)PR 126.65 0.00036822 336833000 524351 515693 394103 457816 485230 514576 517507 557300 571221 602812 TRUE FALSE 503858.7832 500985.9406 465326.1789 481443.9386 500837.8636 524981.0793 523840.4055 545791.5602 506378.3868 561983.0063 0.896572988 0.891461014 0.828007562 0.856687717 0.891197524 0.934158281 0.932128551 0.971188727 0.901056404 1 19.10016698 2.747386153 2.015160273 0.950344224 0.8670263 0.625008177 0.029647111 0.216680086 1.737421709 0.010755946 0.010682811 558.9669798 -2.747386153 -0.083317923 ANSFTVSSVAAPSWLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ANSFTVSSVAAPSWLHR 17 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ; 117.18 0.00023019 529750000 498010 584950 489280 575170 550700 482110 564250 479090 493820 662950 FALSE TRUE 478547.2186 568267.7987 577703.78 604854.5926 568413.7656 491858.5945 571155.4603 469196.6241 437763.6239 618047.806 0.774288354 0.919456057 0.934723454 0.97865341 0.919692231 0.795826131 0.924128287 0.759159113 0.708300587 1 19.23735891 2.747487531 24.08255327 0.824796254 0.91184853 0.111966971 0.091274479 696.416113 1878753.632 0.027636964 0.028898289 559.0974746 -2.747487531 0.087052276 GFLSSGGS(ph)PLRPANASLEEMASLEEEACSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFLSSGGSPLRPANASLEEMASLEEEACSLK 31 1 Q93075;H7C1W4;H7C1D0 Q93075 TATDN2 Putative deoxyribonuclease TATDN2 1 GFLS(0.153)S(0.153)GGS(0.647)PLRPANAS(0.046)LEEMAS(0.001)LEEEACSLK;GFLS(0.012)S(0.063)GGS(0.833)PLRPANAS(0.092)LEEMASLEEEACSLK 117.15 2.49E-05 98389000 89429 87296 74266 84731 83880 92130 88459 98122 105113 90694 TRUE FALSE 85934.01581 84806.40355 87687.51824 89103.97706 86578.07638 93992.93172 89541.5877 96095.74641 93181.01291 84551.2146 1.016354599 1.003018158 1.037093537 1.05384621 1.023972001 1.111668616 1.059021897 1.136538923 1.10206593 1 16.36753786 2.747503007 24.51526616 1.092098125 1.02760063 0.341685051 0.036818925 481.6211632 1320346.757 0.010904525 0.011411685 559.1173988 -2.747503007 -0.064497495 HNYPDLVER ddPTM_BT-474_Pertuzumab_2h_R1 1 HNYPDLVER 9 0 Q9NZT2-2;Q9NZT2;A0A087X028;Q4VXW3 Q9NZT2-2 OGFR Opioid growth factor receptor 0 116.77 0.0012606 161710000 78844 82244 76381 81737 83861 72030 85363 71240 81907 100380 FALSE TRUE 75762.68931 79898.48165 90184.74579 85955.45637 86558.46523 73486.49595 86407.69793 69768.8691 72609.26074 93581.17319 0.809593284 0.853787989 0.963706082 0.918512276 0.924955974 0.785270086 0.923344889 0.74554386 0.77589603 1 16.51393069 2.747536689 24.75509156 0.829946754 0.897092953 0.064170277 0.080552226 1153.809576 3182088.359 0.024338186 0.025470749 559.1607631 -2.747536689 0.067146199 RGT(ph)GQSDDSDIWDDTALIK ddPTM_BT-474_Pertuzumab_2h_R1 5 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 RGT(0.466)GQS(0.466)DDS(0.068)DIWDDTALIK;RGT(0.64)GQS(0.357)DDS(0.003)DIWDDTALIK;RGT(0.498)GQS(0.498)DDS(0.003)DIWDDTALIK;RGT(0.714)GQS(0.284)DDS(0.001)DIWDDTALIK;RGT(0.499)GQS(0.499)DDS(0.002)DIWDDTALIK 228.71 5.70E-20 1460980000 363946 347420 291497 303801 324859 373463 353356 389024 423591 375803 TRUE FALSE 349722.588 337511.9218 344176.9922 319480.206 335308.3848 381014.6777 357680.4764 380990.5185 375506.7255 350349.5281 0.99821053 0.963357718 0.982381778 0.911889928 0.957068179 1.087527304 1.02092467 1.087458346 1.071805998 1 18.41843543 2.747794808 24.824555 1.058510102 0.96090854 0.651962592 0.033119462 341.1180991 917038.1902 0.009895363 0.010353032 559.4931946 -2.747794808 -0.097601562 SETELKDTYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SETELKDTYAR 11 1 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 142.12 3.45E-05 1958240000 2267400 2260500 1708190 1821620 1995610 2221500 2204600 2290800 2415600 2326400 FALSE TRUE 2178787.501 2196032.753 2016897.931 1915634.027 2059800.608 2266420.252 2231580.554 2243494.179 2141391.215 2168830.856 1.004590789 1.012542194 0.929947085 0.883256535 0.949728561 1.044996315 1.0289325 1.034425609 0.987348188 1 21.04848611 2.747892659 24.55843875 1.023142812 0.953663401 0.412246101 0.037484167 532.7715654 1402055.097 0.012699015 0.01330004 559.6192678 -2.747892659 -0.06947941 KPS(ph)PAQAAETPALELPLPSVPAPAPL ddPTM_BT-474_Pertuzumab_2h_R1 5 KPSPAQAAETPALELPLPSVPAPAPL 26 1 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 1 KPS(0.945)PAQAAET(0.055)PALELPLPSVPAPAPL;KPS(0.629)PAQAAET(0.371)PALELPLPSVPAPAPL;KPS(0.5)PAQAAET(0.5)PALELPLPSVPAPAPL;KPS(0.958)PAQAAET(0.042)PALELPLPSVPAPAPL;KPS(0.87)PAQAAET(0.13)PALELPLPSVPAPAPL 158.12 1.28E-11 872281000 1024471 1028846 848169 967856 981468 1069956 1040560 1163679 1209165 1170634 TRUE FALSE 984433.5407 999504.3194 1001452.006 1017807.164 1013037.81 1091591.243 1053294.685 1139648.622 1071905.658 1091345.916 0.902036216 0.915845567 0.917630231 0.932616459 0.928246301 1.000224793 0.965133665 1.044259757 0.982186896 1 20.05767702 2.747900453 1.210139548 1.009506274 0.912437879 0.782667776 0.020683852 0.18606115 0.56364937 0.009356033 0.008836122 559.6293115 -2.747900453 -0.097068395 DKVAGHSLGYGFVNYVTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKVAGHSLGYGFVNYVTAK 19 1 Q15717;Q15717-2;M0QZR9 Q15717 ELAVL1 ELAV-like protein 1 0 ; 120.92 2.17E-05 1182280000 1651360 1654490 1241750 1264780 1389840 1607240 1533840 1538480 1847600 1685110 FALSE TRUE 1586823.026 1607305.565 1466161.848 1330055.447 1434545.466 1639739.494 1552611.593 1506709.85 1637868.194 1570975.999 1.010087377 1.023125475 0.93328087 0.846642755 0.913155559 1.043771194 0.988310193 0.959091578 1.042580024 1 20.58322971 2.747923554 24.82818675 0.998969623 0.94344029 0.254218154 0.051764562 1091.978367 2895655.278 0.017809156 0.018651256 559.6590799 -2.747923554 -0.055529333 AHFNAMFQPSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 8 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.001)S(0.996)PT(0.003)R;AHFNAMFQPS(0.159)S(0.781)PT(0.061)R;AHFNAMFQPS(0.043)S(0.934)PT(0.023)R;AHFNAMFQPS(0.235)S(0.717)PT(0.048)R;AHFNAMFQPS(0.09)S(0.881)PT(0.029)R;AHFNAMFQPSS(0.979)PT(0.021)R;AHFNAMFQPS(0.346)S(0.605)PT(0.049)R;AHFNAMFQPS(0.007)S(0.932)PT(0.06)R 288.06 3.40E-34 6491350000 2159020 2269630 2002310 2281240 2196720 1644863 2224210 1403838 2027640 2252070 TRUE FALSE 2074643.111 2204902.375 2364171.958 2398975.07 2267379.494 1678123.257 2251430.547 1374848.255 1797470.808 2099535.293 0.988143957 1.050185906 1.126045352 1.142621931 1.079943501 0.799283185 1.072347083 0.654834553 0.856127932 1 21.00163861 2.747976641 24.17227765 0.855188071 1.082204196 0.437056479 0.112626049 363.953382 934319.4628 0.034678742 0.03630624 559.7274949 -2.747976641 0.227016125 ITADLLSNGIDVYPQKEFDEDSEDRLVNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITADLLSNGIDVYPQKEFDEDSEDRLVNEK 30 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ; 331.23 1.36E-105 361060000 235500 223080 144881 136378 181910 198612 187549 219620 230990 187247 FALSE TRUE 226296.3996 216717.9768 171064.2196 143416.4849 187761.3004 202628.0707 189844.2808 215084.7703 204768.9836 174564.5939 1.296347642 1.241477278 0.979947971 0.821566858 1.075597841 1.160762708 1.087530275 1.232121391 1.17302701 1 17.41340145 2.748471299 18.93029297 1.14844015 1.071544544 0.01846556 0.135577349 86.35212212 164935.2013 0.045514649 0.047426144 560.3653835 -2.748471299 -0.076895607 KKEQSEVSVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 KKEQSEVSVSPR 12 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KKEQSEVS(0.015)VS(0.985)PR;KKEQSEVS(0.001)VS(0.999)PR;KKEQSEVS(0.001)VS(0.999)PR 157.84 3.43E-05 1030180000 3008090 2763280 2190080 2274130 2530950 2774250 2600560 2907710 3188600 2978590 TRUE FALSE 2890530.517 2684473.96 2585876.174 2391498.122 2612360.305 2830347.236 2632386.431 2847664.772 2826643.496 2776847.446 1.040939617 0.966734404 0.931227309 0.861227766 0.94076479 1.019266377 0.947976611 1.025502779 1.017932584 1 21.40501649 2.748555895 24.16731242 1.000986495 0.94343728 0.254266932 0.045823013 631.988343 1528065.945 0.014923333 0.015629294 560.4745472 -2.748555895 -0.057549215 HKPAFTEEDVLNIFPVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HKPAFTEEDVLNIFPVVK 18 1 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 70.584 0.014983 135690000 167500 178390 157630 151210 143000 200710 194960 137260 224270 230390 FALSE TRUE 160953.9148 173302.4919 186117.2475 159013.9662 147599.7249 204768.4937 197345.9788 134425.533 198811.8098 214785.4801 0.749370557 0.806863163 0.866526207 0.740338528 0.68719601 0.953362833 0.918805027 0.625859499 0.925629655 1 17.71253694 2.748632217 24.94571506 0.845212633 0.775811749 0.178422675 0.107078325 1898.265083 4701690.951 0.034921576 0.036632368 560.5730525 -2.748632217 -0.069400884 HRPSAGGPDSAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ; 120.53 0.00023973 66765000 63482 69365 60135 74156 68435 52170 67042 47162 69700 68740 FALSE TRUE 61001.05326 67386.77812 71002.7322 77983.20005 70636.27393 53224.91314 67862.48005 46188.08822 61787.94821 64084.17857 0.951889446 1.051535334 1.107960401 1.216886941 1.102242012 0.830546858 1.058958413 0.720740895 0.964168529 1 15.9676806 2.748648987 24.66458058 0.89519633 1.092662517 0.383332472 0.106976285 540.4485025 1321316.366 0.033023425 0.034652759 560.5946994 -2.748648987 0.197466187 LFDVCGS(ph)QDFESDLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFDVCGSQDFESDLDR 16 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38 Q92878-2 RAD50 DNA repair protein RAD50 1 LFDVCGS(0.996)QDFES(0.004)DLDR;LFDVCGS(1)QDFESDLDR;LFDVCGS(1)QDFESDLDR;LFDVCGS(1)QDFESDLDR 212.76 3.84E-12 320672000 162082 151820 128849 162707 142664 131959 118184 136280 138842 139309 TRUE FALSE 155747.6562 147490.2422 152134.8805 171104.3278 147252.9171 134627.3014 119630.3711 133465.7704 123081.2382 129873.4773 1.199226042 1.135645593 1.171408386 1.317469365 1.133818237 1.036603502 0.921130115 1.027659943 0.947701107 1 16.98674731 2.748715856 2.854092676 0.980888787 1.199898857 0.795934479 0.053047418 0.119179151 1.953852516 0.017972652 0.018059938 560.6810221 -2.748715856 0.21901007 TKDQILLLIDIEQSYINTNHEDFIGFANAQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKDQILLLIDIEQSYINTNHEDFIGFANAQQR 32 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 171.19 1.55E-14 370450000 200430 190870 156510 165370 175880 197770 198530 178150 243720 224140 FALSE TRUE 192596.974 185426.5745 184794.8385 173904.7655 181537.3399 201769.0449 200959.6695 174471.1402 216053.9274 208958.7982 0.921698324 0.887383427 0.884360171 0.832244285 0.86877098 0.965592484 0.961719111 0.834954746 1.03395468 1 17.67285898 2.748819055 24.01694402 0.939923811 0.87707552 0.330891894 0.053696084 620.0704762 1451700.281 0.016967755 0.01779818 560.8142693 -2.748819055 -0.062848291 QAGPASVPLRTEEEFKK ddPTM_BT-474_Pertuzumab_2h_R1 4 QAGPASVPLRTEEEFKK 17 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 182.7 4.12E-10 2632910000 2471560 2724190 1749130 1715370 2081080 2394060 2242980 2363820 2806120 2423860 FALSE TRUE 2374968.703 2646498.768 2065236.7 1803900.451 2148019.828 2442469.533 2270430.26 2315006.291 2487581.022 2259689.803 1.051015365 1.171177904 0.913946993 0.798295611 0.950581724 1.080887089 1.004753067 1.024479682 1.100850665 1 21.10769331 2.749030579 23.95416078 1.038957796 0.974359627 0.106597459 0.093975122 1115.305898 2551698.591 0.032056229 0.03363921 561.0874812 -2.749030579 -0.064598169 SRT(ph)PSASNDDQQE ddPTM_BT-474_Pertuzumab_2h_R1 3 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 S(0.152)RT(0.846)PS(0.002)ASNDDQQE;S(0.318)RT(0.68)PS(0.002)ASNDDQQE;S(0.157)RT(0.841)PS(0.001)AS(0.001)NDDQQE 107.64 0.008145 313299000 357330 377462 316140 321201 330156 388620 375816 365899 424470 419770 TRUE FALSE 343365.1486 366697.1533 373273.5305 337778.2221 340775.7676 396478.1627 380415.3486 358343.0578 376285.9451 391338.604 0.877411901 0.937032916 0.953837742 0.86313545 0.870795174 1.013133278 0.972087458 0.91568543 0.961535461 1 18.57805791 2.749074645 24.99552149 0.963037203 0.903369204 0.485438483 0.036381511 800.3097462 1902613.812 0.012016591 0.012635018 561.1444153 -2.749074645 -0.059667999 SEDTIDFLEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDTIDFLEFK 11 0 K7EIX2;Q6AI08;A0A087WXZ7 K7EIX2 HEATR6 HEAT repeat-containing protein 6 0 104.79 0.0059372 22178000 55641 55243 51890 50948 50219 64534 61933 57483 65400 71639 FALSE TRUE 53466.48821 53667.52373 61267.67729 53577.43239 51834.33974 65838.9217 62690.95458 56295.95596 57976.06618 66786.82672 0.800554403 0.803564511 0.917361706 0.802215572 0.776116224 0.985807006 0.938672455 0.84292006 0.868076371 1 16.02727595 2.749089488 24.99963126 0.912318697 0.823476614 0.454996647 0.057435174 825.2126137 1959374.686 0.018466005 0.01939513 561.1635937 -2.749089488 -0.088842082 EPFPTIYVDSQKENER ddPTM_BT-474_Pertuzumab_2h_R1 1 EPFPTIYVDSQKENER 16 1 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 170.91 4.66E-09 2033500000 1171200 1202700 771680 869520 912410 1216600 1104200 1169500 1350100 970170 FALSE TRUE 1125428.209 1168400.174 911139.7419 914396.0314 941758.4963 1241200.486 1117713.53 1145349.416 1196842.308 904459.5218 1.244310201 1.291821409 1.00738587 1.01098613 1.041238965 1.372311812 1.235780599 1.266335738 1.323267962 1 19.78669641 2.749115359 24.73043744 1.25625548 1.116523399 0.17872858 0.12646074 967.9495888 2267966.182 0.039400618 0.041394357 561.1970236 -2.749115359 -0.139732081 IRYESLTDPSKLDSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IRYESLTDPSKLDSGK 16 2 P08238;Q58FF7;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ; 203.89 1.50E-11 5749800000 9312400 8894300 5960700 5767800 7244000 8376300 7435700 8800200 9974100 8154900 FALSE TRUE 8948461.113 8640643.272 7037931.085 6065476.849 7477009.839 8545674.525 7526700.321 8618472.795 8841881.983 7602561.359 1.177032409 1.136543707 0.925731573 0.797820177 0.983485629 1.124052029 0.990021647 1.133627522 1.163013564 1 22.85805412 2.749159732 23.91302224 1.086180309 0.995663102 0.107119293 0.110988781 914.2213992 2062601.213 0.037196812 0.039053906 561.2543655 -2.749159732 -0.090517207 QPDKEFSFMDEEEEDEIRV ddPTM_BT-474_Pertuzumab_2h_R1 3 QPDKEFSFMDEEEEDEIRV 19 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 0 ;; 209.9 8.01E-16 332846000 258575 254915 208647 222293 233497 257611 247141 271868 284265 259435 FALSE TRUE 248469.6031 247645.0738 246354.1542 233765.5684 241007.6431 262820.0709 250165.5855 266253.8308 251996.4289 241863.2364 1.027314473 1.0239054 1.018568005 0.966519641 0.996462491 1.086647458 1.034326627 1.100844571 1.041896374 1 17.88383197 2.749240701 24.96400159 1.060819248 1.00596128 0.342468228 0.031001272 675.4406273 1578797.631 0.009358683 0.009838489 561.3590146 -2.749240701 -0.054857968 SVFALTNGIYPHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVFALTNGIYPHK 13 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 156.73 4.73E-05 5232700000 4539800 4730800 3561800 4262400 4126200 4762200 4801800 4573300 4810800 5269400 FALSE TRUE 4362379.597 4595882.216 4205496.492 4482382.975 4258922.97 4858494.947 4860565.865 4478859.757 4264698.153 4912498.845 0.888016412 0.935548763 0.856080912 0.912444586 0.866956534 0.989006838 0.989428399 0.911727391 0.868132144 1 22.22802564 2.749342818 24.99334324 0.946574745 0.893400883 0.327232238 0.042566349 1009.175781 2339287.322 0.013348959 0.014038411 561.4910243 -2.749342818 -0.053173862 TIGTKPVAHIDQFTADMLGSAELAEEVNLNGSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TIGTKPVAHIDQFTADMLGSAELAEEVNLNGSGK 34 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 220.62 1.83E-36 225980000 366020 373120 305660 329940 351350 413140 430750 406830 500860 478620 FALSE TRUE 351715.5337 362478.9829 360899.5614 346968.2429 362651.4918 421493.9739 436021.6474 398428.8183 444004.4726 446202.6411 0.788241712 0.812364046 0.80882435 0.777602396 0.812750662 0.944624561 0.977183027 0.892932452 0.995073609 1 18.76733953 2.749345075 4.509187597 0.952525263 0.798528024 0.878040196 0.030140729 0.069154601 3.747848623 0.00960688 0.009714346 561.4939418 -2.749345075 -0.153997239 QLPTAAPDKTEVTGDHIPTPQDLPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLPTAAPDKTEVTGDHIPTPQDLPQR 26 1 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 0 ; 162.03 9.90E-12 494470000 637120 625330 515210 549240 579210 666820 642870 668840 726550 737570 FALSE TRUE 612220.646 607496.2007 608319.9078 577586.3422 597840.8157 680303.5573 650737.6354 655028.2203 644075.0899 687613.7269 0.890355474 0.88348469 0.884682612 0.839986637 0.869442817 0.989368785 0.94637092 0.952610739 0.936681548 1 19.39123882 2.749357432 24.96642586 0.959787733 0.872889474 0.808729946 0.02215481 308.3697089 713070.1252 0.006781084 0.007128103 561.5099186 -2.749357432 -0.086898259 VLYQVEGFVDKNNDLLYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLYQVEGFVDKNNDLLYR 18 1 E9PDF6;O43795;O43795-2;A0A0U1RRI3 E9PDF6 MYO1B Unconventional myosin-Ib 0 131.71 1.49E-05 220000000 219180 229620 184680 201210 195820 246020 238930 235800 258790 214600 FALSE TRUE 210614.2033 223071.4624 218055.7842 211594.4722 202118.7281 250994.693 241854.0968 230930.6476 229413.2441 200064.9509 1.052729138 1.114995213 1.089924963 1.057628892 1.010265553 1.254566039 1.208877896 1.154278381 1.146693827 1 17.61010892 2.749524028 24.99968582 1.166236737 1.068843355 0.292930396 0.066461374 825.3184228 1881957.685 0.019633336 0.020636495 561.7253563 -2.749524028 -0.097393383 EMKPVIFLDVFLPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EMKPVIFLDVFLPR 14 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 150.57 6.54E-06 413851000 668133 711370 564235 621319 679890 548130 571907 662470 676660 707950 FALSE TRUE 642021.6237 691082.4241 666204.8158 653385.348 701759.2793 559213.5642 578906.1689 648789.763 599848.3936 659999.9159 0.97276016 1.047094715 1.009401365 0.989977926 1.063271771 0.847293387 0.877130671 0.983014918 0.908861318 1 19.33210632 2.749883081 24.98038463 0.923451897 1.016332878 0.48201029 0.048328867 645.4894089 1424122.037 0.014798942 0.015571507 562.1899545 -2.749883081 0.092880981 IAEVDCTAER ddPTM_BT-474_Pertuzumab_2h_R1 2 IAEVDCTAER 10 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 139.38 9.58E-05 715900000 430960 467700 366760 469070 468940 380300 431010 438290 443220 530560 FALSE TRUE 414117.6067 454361.6539 433041.6905 493278.7589 484023.881 387989.9266 436284.8293 429239.1583 392907.5237 494624.6986 0.837236005 0.918598799 0.875495485 0.997278867 0.978567957 0.784412763 0.882052252 0.867807773 0.794354841 1 18.91597476 2.749903611 24.99896567 0.859915592 0.922939134 0.13536283 0.069577712 1356.776981 2990216.276 0.020709246 0.021790611 562.2165309 -2.749903611 0.063023543 EWVNLYHSAAAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EWVNLYHSAAAGR 13 0 A5YKK6-3;A5YKK6-2;A5YKK6;H3BMZ2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ; 212.55 1.30E-08 699510000 669970 638670 583100 702160 647350 557420 600950 566220 676470 675300 FALSE TRUE 643786.8317 620455.7569 688479.141 738398.5617 668172.6007 568691.4143 608304.6059 554527.3591 599679.9616 629561.3295 1.022595896 0.985536639 1.093585499 1.172877887 1.061330437 0.903313764 0.966235659 0.880815471 0.952536208 1 19.2639874 2.749910881 20.56865723 0.931116427 1.069987863 0.566135289 0.055078539 49.35703834 89442.4972 0.017951482 0.018807761 562.2259423 -2.749910881 0.138871436 HPTLLQDPDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 HPTLLQDPDLR 11 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ;;; 160.52 2.74E-05 1148130000 585731 759695 624426 745027 698290 568550 721157 525083 658118 794622 FALSE TRUE 562839.985 738029.2424 737273.6685 783477.9328 720751.132 580046.4705 729982.7351 514239.8526 583411.2037 740801.5442 0.759771614 0.9962577 0.995237759 1.057608396 0.972934165 0.782998463 0.985395807 0.694166821 0.78754048 1 19.49872758 2.750149764 23.95132261 0.831323083 0.966362945 0.168923294 0.113150643 601.5777683 1243280.893 0.034353114 0.036127464 562.5352791 -2.750149764 0.135039861 ELNEYLEQFVGDQEAWHELAELYINEHDYAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELNEYLEQFVGDQEAWHELAELYINEHDYAK 31 0 Q15006 Q15006 EMC2 ER membrane protein complex subunit 2 0 ; 207.99 2.75E-26 115710000 56528 67617 46731 57059 52783 64975 71993 42886 71707 84515 FALSE TRUE 54318.82326 65688.62936 55176.33123 60003.82183 54480.81313 66288.83902 72874.07187 42000.38911 63567.12198 78790.72377 0.689406324 0.833710191 0.700289686 0.76155947 0.691462275 0.841327962 0.924906745 0.533062613 0.806784339 1 16.26573817 2.75023597 24.53527225 0.779903427 0.740269073 0.061092877 0.122738099 3151.624483 6623003.535 0.038623395 0.040620742 562.646951 -2.75023597 -0.039634354 RVEEDIQQQK ddPTM_BT-474_Pertuzumab_2h_R1 4 RVEEDIQQQK 10 1 P15924 P15924 DSP Desmoplakin 0 ;;; 205.53 2.68E-07 3474520000 4552920 4253470 3677420 4020430 4073710 4827140 4457220 4970490 5337000 4789980 FALSE TRUE 4374986.853 4132165.2 4342011.598 4227924.874 4204744.582 4924748.078 4511768.792 4867847.645 4731166.135 4465550.388 0.979719513 0.925342867 0.972335148 0.946786959 0.941596044 1.102831152 1.01034999 1.090089064 1.059481077 1 22.09040657 2.750598822 24.99835258 1.05716675 0.952322582 0.697590454 0.032648159 372.3189722 773151.4586 0.009189411 0.009679815 563.1172385 -2.750598822 -0.104844168 APS(ph)DSSLGTPSDGRPELR ddPTM_BT-474_Pertuzumab_2h_R1 4 APSDSSLGTPSDGRPELR 18 1 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3;M0R2H7;Q15642-5 Q15642 TRIP10 Cdc42-interacting protein 4 1 APS(0.951)DS(0.043)S(0.006)LGTPSDGRPELR;APS(0.905)DS(0.046)S(0.046)LGT(0.002)PSDGRPELR;APS(0.926)DS(0.032)S(0.043)LGTPSDGRPELR;APS(0.89)DS(0.054)S(0.054)LGT(0.001)PSDGRPELR 188.19 2.37E-14 3460000000 1450910 1253780 1137820 1293300 1275200 1426800 1375780 1498710 1542540 1451660 TRUE FALSE 1394206.833 1218023.422 1343449.385 1360047.368 1316217.966 1455650.874 1392617.207 1467761.115 1367437.326 1353337.775 1.030198712 0.900014353 0.992693331 1.004957811 0.97257166 1.075600563 1.029024116 1.084548988 1.010418353 1 20.36809053 2.750638275 24.68011335 1.047426928 0.977720723 0.351862954 0.039892586 596.4630751 1218842.37 0.011679554 0.012299131 563.1683963 -2.750638275 -0.069706205 IHTGDKPYECNECGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IHTGDKPYECNECGK 15 1 Q96NJ6 Q96NJ6 ZFP3 Zinc finger protein 3 homolog 0 97.417 0.0019959 53972000 91150 91737 59046 91270 58682 61561 71065 61531 55653 48781 FALSE TRUE 87587.75723 89120.75058 69716.92567 95980.45564 60569.55982 62805.8056 71934.71473 60260.36335 49335.50476 45477.01942 1.925978403 1.95968759 1.533014401 2.110526522 1.331871802 1.381044897 1.581781648 1.325072842 1.084844728 1 15.47285008 2.750872448 0.295724244 0.938918038 2.158195594 0.694295735 0.196510554 1.422181344 0.256118728 0.272068001 0.604034625 563.4721395 -2.750872448 1.219277556 YLAEVATGDDKKR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLAEVATGDDKKR 13 2 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ; 172.33 1.33E-05 2129260000 2601200 2439200 1773230 1605740 1967950 2490300 2333100 2424200 2720800 2172600 FALSE TRUE 2499542.228 2369636.404 2093692.106 1688612.434 2031250.899 2540655.572 2361653.176 2374139.423 2411946.191 2025447.867 1.234068904 1.169932064 1.033693407 0.833698295 1.002865061 1.2543673 1.165990601 1.172155286 1.190821166 1 20.94980952 2.751014837 24.80989886 1.168298735 1.047783163 0.157245754 0.115728541 1208.809402 2408053.385 0.037871353 0.039919273 563.6569123 -2.751014837 -0.120515571 YIQPWESEFIDSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIQPWESEFIDSQR 14 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 129.76 0.00015358 1263840000 634220 636710 479720 562500 597700 506640 547710 579210 625010 588070 FALSE TRUE 609433.9812 618551.6542 566416.0753 591530.6924 616925.5633 516884.6079 554413.0388 567249.1111 554061.4851 548239.4951 1.111619988 1.12825081 1.033154452 1.078964025 1.125284787 0.942808047 1.011260669 1.034673927 1.010619428 1 19.06444674 2.751219594 24.99986594 1.005647889 1.092899527 0.667219748 0.033603758 537.2117489 1060924.837 0.010770768 0.011353284 563.9227227 -2.751219594 0.087251638 KDEDLFR ddPTM_BT-474_Pertuzumab_2h_R1 5 KDEDLFR 7 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;;;; 126.41 0.0063409 24293850000 4803970 4812190 4014960 4485770 4514780 4834090 4638230 5118460 5307740 5178220 FALSE TRUE 4616225.541 4674951.053 4740552.584 4717281.127 4660001.999 4931838.612 4694994.046 5012762.012 4705227.607 4827494.547 0.956236304 0.968401105 0.981990251 0.977169644 0.965304456 1.021614538 0.972552947 1.038377561 0.974672796 1 22.2028432 2.751506825 24.86204852 1.004245936 0.970825903 0.393957308 0.019436535 691.4376976 1327843.564 0.005670119 0.005982811 564.2958094 -2.751506825 -0.033420033 APLKPYPVS(ph)PSDKVLIQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 APLKPYPVSPSDKVLIQEK 19 2 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 1 APLKPYPVS(0.5)PS(0.5)DKVLIQEK;APLKPYPVS(0.985)PS(0.015)DKVLIQEK 199.46 3.61E-16 1890230000 3092100 2580790 2187970 2021790 2443970 3181800 2752050 3045500 3890200 3278900 TRUE FALSE 2971257.314 2507188.396 2583384.85 2126134.824 2522582.515 3246138.176 2785730.411 2982609.361 3448600.805 3056817.182 0.972010145 0.820195729 0.845122458 0.695538757 0.825231724 1.061934026 0.91131731 0.975723827 1.128167175 1 21.54359884 2.751507242 23.92731746 1.002095139 0.824175164 0.553212347 0.082020457 351.5111089 649644.6558 0.025537398 0.02691318 564.2963505 -2.751507242 -0.177919974 DLSTIEPLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLSTIEPLKK 10 1 P39687;H0YN26;O95626 P39687 ANP32A;ANP32D Acidic leucine-rich nuclear phosphoprotein 32 family member A;Acidic leucine-rich nuclear phosphoprotein 32 family member D 0 84.507 0.027892 0 726860 697190 551930 465370 602480 665790 680480 548600 902170 783730 FALSE TRUE 698453.5076 677306.8238 651676.0286 489387.8015 621859.3164 679252.73 688807.9178 537271.2183 799759.4438 730647.269 0.955938025 0.926995628 0.891916053 0.669800357 0.851107426 0.929658891 0.942736594 0.73533597 1.094590342 1 19.47881557 2.751625781 22.32437096 0.908856121 0.854221346 0.083308579 0.112061752 683.4734991 1167842.388 0.035719121 0.037601908 564.4503942 -2.751625781 -0.054634775 RPAEAT(ph)SSPTSPERPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEAT(0.367)S(0.172)S(0.131)PT(0.165)S(0.165)PERPR 89.831 0.0090956 194010000 33055 37332 23315 32379 29797 41865 38414 42910 35432 38181 TRUE FALSE 31763.17406 36267.32791 27528.53914 34050.08407 30755.44757 42711.53898 38884.12202 42023.8935 31409.9079 35594.96686 0.892350151 1.018889217 0.773382912 0.95659828 0.864039225 1.199931978 1.092405063 1.180613362 0.882425541 1 15.11938564 2.751773644 24.98894424 1.092014937 0.903591647 0.396443286 0.103266021 702.0830405 1327803.551 0.03038351 0.032057798 564.6426045 -2.751773644 -0.188423291 LKDYAFVHFEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKDYAFVHFEDR 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 172.85 2.08E-05 3163500000 7766300 7476800 6699300 7062800 7323400 6232500 7123600 6851000 7043300 7143400 FALSE TRUE 7462784.41 7263568.985 7910012.535 7427311.954 7558963.812 6358525.42 7210780.748 6709524.456 6243774.112 6659571.155 1.120610357 1.090696205 1.187766051 1.11528382 1.135052639 0.954795027 1.082769533 1.007500979 0.937563991 1 22.66699785 2.751860461 24.78334374 1.005044186 1.130109636 0.70599638 0.042852563 407.9971856 760273.784 0.013041047 0.01376029 564.7554896 -2.751860461 0.125065451 TMAQHEELMK ddPTM_BT-474_Pertuzumab_2h_R1 1 TMAQHEELMK 10 0 P12270 P12270 TPR Nucleoprotein TPR 0 77.64 0.02656 0 155410 165360 139120 137060 159920 128280 147080 146370 168740 156920 FALSE TRUE 149336.4054 160644.0947 164262.0787 144133.683 165063.972 130873.9095 148880.009 143347.4084 149585.3426 146291.6686 1.020812783 1.098108294 1.1228396 0.985248746 1.12832107 0.894609452 1.017693013 0.97987404 1.022514433 1 17.15848808 2.752200598 24.9980578 0.984460964 1.070677114 0.413969921 0.052410798 785.1403066 1438929.576 0.015185751 0.016021916 565.1979758 -2.752200598 0.08621615 EVIELPVKHPELFEALGIAQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVIELPVKHPELFEALGIAQPK 22 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QSE0;J3QRR3 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 95.48 0.00096752 587590000 608010 601140 431520 480590 528950 628000 606980 569260 733030 753560 FALSE TRUE 584248.297 583996.0758 509505.2631 505393.3075 545964.1571 640698.5903 614408.4028 557504.5821 649819.5075 702520.71 0.831645656 0.831286633 0.725253015 0.71939987 0.777150267 0.911999577 0.874576926 0.793577434 0.924982706 1 19.42218123 2.752357598 23.19409056 0.878401046 0.773896968 0.490523879 0.061049099 314.6158988 528899.2517 0.019427821 0.020486211 565.4023357 -2.752357598 -0.104504078 KEVYQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEVYQR 6 1 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 0 84.244 0.089907 115520000 216180 220370 179790 197300 181160 153820 155010 146110 147850 148890 FALSE TRUE 207731.4466 214085.2634 212282.0524 207482.6766 186987.1759 156930.3458 156907.0587 143092.7774 131066.6878 138805.5477 1.496564439 1.542339387 1.529348473 1.49477222 1.347116013 1.1305769 1.130409133 1.030886588 0.944246754 1 17.0827057 2.752390684 1.05819472 0.999150106 1.541098142 0.975223527 0.036033721 0.071891526 0.169394003 0.019590035 0.018416271 565.4454114 -2.752390684 0.541948037 SLLIDFFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLIDFFR 8 0 Q9H7B2;Q5VXN0 Q9H7B2 RPF2 Ribosome production factor 2 homolog 0 91.318 0.029248 30794000 75080 80565 64868 66755 73406 53322 68380 61638 61805 66018 FALSE TRUE 72145.79059 78267.36508 76591.09058 70200.23355 75767.17066 54400.20737 69216.85489 60365.15376 54789.15551 61546.54206 1.172215175 1.271677701 1.244441816 1.140604024 1.231054875 0.883887308 1.124626219 0.980804961 0.890206885 1 15.90939018 2.752509799 24.96091792 0.987640436 1.213150254 0.731529077 0.071334734 415.0545502 742705.601 0.02152205 0.022723093 565.6005191 -2.752509799 0.225509818 MITNSLNHDS(ph)PPS(ph)TPPRRPDTSTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 MITNSLNHDSPPSTPPRRPDTSTSK 25 2 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;Q8N9M1-3 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 2 MITNSLNHDS(0.989)PPS(0.555)T(0.456)PPRRPDTSTSK 163.75 9.44E-12 457590000 621510 622840 466170 571010 562740 606240 630290 633800 587160 643700 TRUE FALSE 597220.7021 605077.213 550417.2889 600479.8945 580841.0432 618498.5882 638003.6776 620711.8085 520508.0584 600101.6257 0.995199274 1.008291241 0.917206795 1.000630341 0.967904465 1.030656412 1.063159389 1.034344488 0.867366519 1 19.19484731 2.752519878 24.2807403 1.009287819 0.977434707 0.020119074 0.054533007 1613.047672 2805729.839 0.016891983 0.017846971 565.6136452 -2.752519878 -0.031853112 NWGGPDFER ddPTM_BT-474_Pertuzumab_2h_R1 1 NWGGPDFER 9 0 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 0 84.213 0.036396 290230000 337700 305800 277800 304630 324570 271900 291810 305110 367070 332220 FALSE TRUE 324502.3107 297078.8834 328004.6396 320351.9908 335010.0888 277398.0043 295381.2581 298809.3719 325401.7525 309718.4435 1.047733248 0.95919016 1.059041354 1.034332948 1.08166012 0.895645739 0.953708971 0.964777456 1.050637311 1 18.24059777 2.75254164 24.99986413 0.968711969 1.033246549 0.311055076 0.046877064 971.9924222 1738045.067 0.01439192 0.015197401 565.6419875 -2.75254164 0.06453458 S(ph)CETLEGPQTVDTWPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCETLEGPQTVDTWPR 16 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 S(1)CETLEGPQTVDTWPR;S(0.994)CET(0.006)LEGPQTVDTWPR 266.44 3.58E-27 103810000 140513 145297 110559 141200 125897 125905 97233 151306 116131 112330 TRUE FALSE 135021.5966 141153.2718 130539.4707 148487.3489 129946.5913 128450.8854 98422.96654 148181.4782 102948.2957 104721.789 1.289336229 1.347888277 1.246535911 1.417922194 1.24087444 1.226591777 0.939851844 1.415001401 0.983064715 1 16.67620212 2.752550609 2.634982701 1.141661828 1.319787656 0.347281385 0.135599624 0.384065473 5.303075381 0.045349131 0.0456209 565.6536695 -2.752550609 0.178125828 S(ph)PPPPPPRR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPPPPPPRR 9 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 S(1)PPPPPPRR;S(1)PPPPPPRR;S(1)PPPPPPRR 63.212 0.0475 551540000 455227 551866 460824 515453 461496 632942 603022 580539 586501 597994 TRUE FALSE 437436.2256 536127.322 544105.1478 542055.5911 476340.438 645740.5209 610401.9636 568550.6668 519923.8653 557491.3337 0.784651167 0.961678307 0.975988531 0.972312139 0.854435592 1.158296967 1.094908435 1.019837677 0.932613359 1 19.08858985 2.752597795 24.99326518 1.044940348 0.919843123 0.411529381 0.077989856 863.4391182 1537356.164 0.024395378 0.025764326 565.7151314 -2.752597795 -0.125097224 MFVLDEADEMLS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 MFVLDEADEMLSR 13 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;Q14240;Q14240-2;E7EQG2;J3KTN0 P60842;Q14240;J3KTN0 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 1 MFVLDEADEMLS(1)R 109.84 0.0011594 8650800 17601 20767 16819 20378 17716 18185 16271 20494 16011 18097 TRUE FALSE 16913.13346 20174.74549 19858.56744 21429.71102 18285.85123 18552.71316 16470.12937 20070.79174 14193.4984 16871.27407 1.002481104 1.195804502 1.177063887 1.270189254 1.083845307 1.09966284 0.976223212 1.189642919 0.841281953 1 14.04228131 2.752711299 2.151142232 1.036027044 1.163288146 0.27395355 0.104865535 0.476716367 4.349586384 0.036968406 0.036969899 565.8630016 -2.752711299 0.127261102 TLLDQHGQYPIWMNQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLLDQHGQYPIWMNQR 16 0 Q9BRT6 Q9BRT6 LLPH Protein LLP homolog 0 ; 130.29 5.07E-05 625670000 662790 662840 629770 610320 655600 565200 632930 587080 706860 684810 FALSE TRUE 636887.434 643936.4522 743583.4482 641818.6883 676687.9694 576628.7312 640675.9867 574956.5928 626620.2162 638427.2087 0.997588175 1.0086294 1.1647114 1.005312242 1.059929715 0.903201999 1.003522372 0.900582846 0.981506126 1 19.28416261 2.752762216 24.61640294 0.951287817 1.049286998 0.392694242 0.055311267 607.7547899 1053452.907 0.016462529 0.017381478 565.9293472 -2.752762216 0.097999181 RRT(ph)AS(ph)PPPPPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRTASPPPPPKR 12 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRT(1)AS(1)PPPPPKR 87.99 0.019391 818390000 144130 145620 111560 136480 130910 145690 143640 140980 157930 162650 TRUE FALSE 138497.2403 141467.0602 131721.3736 143523.7492 135120.839 148635.9516 145397.9093 138068.7137 140002.4485 151633.5706 0.913367928 0.932953432 0.868682133 0.946516979 0.891101083 0.980231165 0.958876776 0.910541862 0.923294544 1 17.21022967 2.752856791 24.98984371 0.946305716 0.911445402 0.31197455 0.031526985 1208.947966 2113249.823 0.009586227 0.010130602 566.0526017 -2.752856791 -0.034860315 GQLQSHGVQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 GQLQSHGVQAR 11 0 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 0 ;; 107.85 0.0021423 503020000 344830 412650 351940 395650 382560 340050 379550 364440 400240 365810 FALSE TRUE 331353.6624 400881.626 415543.3869 416069.5439 394865.3898 346926.044 384195.0464 356914.1866 354806.4331 341033.3629 0.971616559 1.175490933 1.218483093 1.220025925 1.157849738 1.017278899 1.12656147 1.046566775 1.040386284 1 18.37955336 2.752934198 23.76622915 1.055479971 1.158022166 0.326389986 0.072421974 507.315915 838828.2852 0.022387136 0.023629331 566.1535019 -2.752934198 0.102542195 QTFLSHGDDFR ddPTM_BT-474_Pertuzumab_2h_R1 4 QTFLSHGDDFR 11 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ;;; 162.32 2.53E-05 1267340000 1797190 1883670 1622380 1848780 1799350 1745800 1819650 1715930 1935930 2211480 FALSE TRUE 1726953.828 1829949.576 1915580.156 1944195.757 1857227.727 1781101.272 1841919.421 1680495.446 1716171.342 2061694.49 0.837638087 0.88759493 0.929129008 0.94300866 0.900825867 0.86390165 0.893400759 0.81510401 0.832408172 1 20.97539913 2.753088292 7.88985954 0.866220097 0.903070891 0 0.054034147 0.448598265 181.2989401 0.016512136 0.016984504 566.354417 -2.753088292 0.036850794 GDVTAEEAAGAS(ph)PAKANGQENGHVK ddPTM_BT-474_Pertuzumab_2h_R1 4 GDVTAEEAAGASPAKANGQENGHVK 25 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GDVTAEEAAGAS(1)PAKANGQENGHVK;GDVTAEEAAGAS(1)PAKANGQENGHVK;GDVTAEEAAGAS(1)PAKANGQENGHVK;GDVTAEEAAGAS(1)PAKANGQENGHVK 263.01 2.15E-45 3739130000 1838540 1716880 1356200 1117160 1442660 1756130 1626070 1784290 1863690 1623220 TRUE FALSE 1766687.824 1667916.263 1601295.509 1174816.761 1489064.469 1791640.152 1645970.331 1747443.788 1652131.724 1513277.864 1.167457654 1.10218771 1.058163571 0.776339091 0.983999373 1.18394658 1.087685461 1.154740864 1.091757016 1 20.52924548 2.753446477 24.73511352 1.115153898 1.011174029 0.136260218 0.105671143 1281.312908 2129093.333 0.034359324 0.036307669 566.8217111 -2.753446477 -0.103979869 DTTDKGQQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTTDKGQQLR 10 1 Q13144;A0A3B3IUB1 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 ; 71.066 0.047515 400400000 510010 539160 434440 542210 493120 596930 571300 666630 653180 707430 FALSE TRUE 490078.2454 523783.6847 512952.9721 570193.5231 508981.6526 609000.3336 578291.7403 652863.8575 579033.7448 659515.136 0.7430887 0.794195093 0.777772858 0.864564726 0.771751283 0.923406152 0.876843773 0.989914896 0.877968849 1 19.33104624 2.753668856 0.410379 0.993086147 0.731677528 0.725566253 0.044953314 0.684362962 0.232767373 0.042949102 0.07019292 567.1120251 -2.753668856 -0.261408618 LLWAGDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLWAGDDR 8 0 A0A087X091 A0A087X091 WDR13 0 94.407 0.024151 52486000 88603 109290 96478 120090 105890 98327 102250 113770 103200 104180 FALSE TRUE 85140.2968 106173.1562 113913.7207 126287.8593 109296.048 100315.2393 103501.3661 111420.6097 91485.16865 97123.79581 0.876616241 1.093173463 1.172871383 1.300277221 1.125327188 1.032859543 1.065664343 1.147201969 0.941943917 1 16.56753719 2.753787835 21.80697662 1.057195053 1.126173285 0.088520471 0.110082063 433.2512386 620457.33 0.035413366 0.037366118 567.2674116 -2.753787835 0.068978232 EAGDVCYADVYR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAGDVCYADVYR 12 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 246.5 3.51E-16 8817200000 3614230 3933170 3045400 3333690 3554700 3120780 3278410 3736830 3472860 3419760 FALSE TRUE 3472981.896 3820999.843 3595771.525 3505742.14 3669040.154 3183884.31 3318532.162 3659663.155 3078635.492 3188136.609 1.089345383 1.198505682 1.127859927 1.099621055 1.150841574 0.998666212 1.04090024 1.147900358 0.965653568 1 21.60428202 2.753834833 24.54318548 1.049470131 1.134694868 0.454221403 0.054296874 714.2175063 1147630.733 0.017027084 0.01799839 567.3288028 -2.753834833 0.085224736 FIFDCVSQEYGINPER ddPTM_BT-474_Pertuzumab_2h_R1 1 FIFDCVSQEYGINPER 16 0 A6NDG6 A6NDG6 PGP Phosphoglycolate phosphatase 0 131.35 9.17E-05 0 48985 41521 42836 34378 41626 49810 48248 51426 54035 42671 FALSE TRUE 47070.61204 40336.86173 50577.41808 36152.2527 42964.93809 50817.19233 48838.47346 50364.03513 47901.17333 39780.85516 1.183247868 1.013976738 1.271400976 0.908785207 1.080040585 1.277428354 1.227687873 1.266037015 1.204126285 1 15.27978667 2.753870679 23.72371917 1.218470161 1.087028705 0.151599427 0.115830063 585.8189559 907754.5154 0.033366428 0.035250924 567.3756317 -2.753870679 -0.131441456 GTEAPAVVTEEEDDDEETAPPVIAPRPDHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 GTEAPAVVTEEEDDDEETAPPVIAPRPDHTK 31 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 ; 204.89 4.29E-26 1989340000 1578520 1714850 1393380 1563760 1542930 1821700 1701250 1770500 1993090 1974800 FALSE TRUE 1516829.693 1665944.157 1645194.762 1644465.841 1592559.745 1858536.022 1722070.406 1733938.556 1766842.779 1841045.037 0.823896028 0.904890496 0.893620052 0.893224124 0.865030302 1.009500574 0.935376578 0.941822998 0.959695577 1 20.81209349 2.754019367 24.99307992 0.960933865 0.879650978 0.697172906 0.030403292 508.1753616 821596.408 0.009128806 0.009653678 567.5699157 -2.754019367 -0.081282886 ALELDSNNEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALELDSNNEK 10 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;; 235.66 9.36E-12 814570000 1026290 999740 931810 915390 953660 1069890 1016930 1078270 1159090 1150400 FALSE TRUE 986181.4522 971228.394 1100208.795 962633.3876 984335.34 1091523.909 1029375.494 1056003.348 1027514.963 1072482.383 0.91953161 0.905589135 1.025852557 0.897575012 0.917810265 1.017754628 0.959806436 0.984634679 0.958071646 1 20.03252252 2.75411513 24.97489997 0.981227697 0.934894024 0.317472141 0.037075729 1093.415917 1755626.898 0.011207334 0.011848266 567.695079 -2.75411513 -0.046333674 DWEAIASR ddPTM_BT-474_Pertuzumab_2h_R1 3 DWEAIASR 8 0 P49750;P49750-1;F8VU51 P49750 YLPM1 YLP motif-containing protein 1 0 ;; 133.33 0.0021496 374590000 486990 497460 451430 508280 503960 458090 489320 506010 532410 536970 FALSE TRUE 467957.8924 483272.9279 533013.443 534512.3917 520170.3311 467352.8937 495308.4445 495560.7167 471973.0488 500600.5436 0.934793017 0.965386343 1.064748031 1.067742332 1.039092621 0.933584471 0.989428499 0.989932438 0.942813696 1 18.93330033 2.754245283 24.85405513 0.973680617 1.017397985 0.198341682 0.04305964 1384.129407 2193300.707 0.014290775 0.015109668 567.8652362 -2.754245283 0.043717367 KLSSERPS(ph)SDGEGVVENGITTCNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSSERPSSDGEGVVENGITTCNGK 25 2 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 KLS(0.08)S(0.08)ERPS(0.42)S(0.42)DGEGVVENGITTCNGK;KLS(0.142)S(0.142)ERPS(0.358)S(0.358)DGEGVVENGITTCNGK 205.42 2.21E-25 928780000 521310 522720 416160 423630 464410 547460 488740 569400 596520 558370 TRUE FALSE 500936.6289 507812.5374 491369.3694 445493.5951 479348.1694 558530.0163 494721.3463 557641.691 528805.5504 520551.1026 0.962319792 0.975528694 0.943940695 0.855811452 0.920847477 1.07295905 0.95037998 1.07125254 1.015857133 1 18.98968027 2.754264167 24.57884287 1.024169302 0.93059028 0.510204543 0.044256793 535.6484922 838383.8478 0.013801698 0.014592558 567.8899294 -2.754264167 -0.093579022 IWEQIQPDLHTNDECVATYK ddPTM_BT-474_Pertuzumab_2h_R1 2 IWEQIQPDLHTNDECVATYK 20 0 Q12904;Q12904-2 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 263.09 1.80E-36 520120000 317771 317763 261863 292554 293123 337525 333380 309919 385274 372940 FALSE TRUE 305352.158 308700.7104 309187.4692 307652.747 302551.5675 344349.9868 337460.0042 303519.0643 341539.3107 347680.4416 0.878255206 0.887886327 0.889286345 0.88487217 0.870200136 0.990420931 0.970603933 0.872982854 0.982336853 1 18.40740239 2.754449333 24.96594311 0.949299821 0.882974741 0.56588713 0.034473281 755.8851942 1187720.982 0.011191847 0.011835014 568.132107 -2.754449333 -0.066325079 GVVPLAGTDGETTTQGLDGLSER ddPTM_BT-474_Pertuzumab_2h_R1 4 GVVPLAGTDGETTTQGLDGLSER 23 0 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 ;;; 342.42 6.93E-87 737920000 527200 564262 430688 508943 517222 354427 460410 428935 450085 427956 FALSE TRUE 506596.4411 548169.8002 508522.9022 535209.6092 533858.9154 361593.7568 466044.6353 420077.3424 398993.2377 398970.1589 1.269760231 1.373961907 1.274588815 1.341477795 1.338092345 0.9063178 1.168119031 1.052904166 1.000057846 1 18.60592132 2.75449082 24.99044882 1.042590861 1.32131512 0.822458351 0.068086735 324.9629285 509783.7675 0.019902371 0.021050779 568.1863815 -2.75449082 0.278724258 RATS(ph)LPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 RAT(0.109)S(0.883)LPS(0.007)IPNPFPELCSPPSQSPILGGPSSAR;RAT(0.418)S(0.577)LPS(0.005)IPNPFPELCSPPSQSPILGGPSSAR 317.51 1.81E-104 3424800000 604660 718840 375740 381120 427930 662430 488550 687280 554560 510170 TRUE FALSE 581029.2187 698339.387 443644.5763 400789.6489 441694.7571 675824.7885 494529.021 673087.4278 491608.6737 475615.7315 1.22163583 1.46828488 0.932779441 0.842675341 0.928679873 1.420947088 1.039765904 1.415191684 1.033625764 1 18.85943691 2.754726254 24.95743625 1.212567767 1.079217008 0.045080647 0.215234405 2309.184798 3565049.269 0.068700562 0.072658326 568.4944823 -2.754726254 -0.133350759 GDS(ph)VSDSGSDALR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDSVSDSGSDALR 13 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 GDS(0.965)VS(0.035)DSGSDALR 169.54 2.97E-05 354860000 73990 81483 68970 83434 77539 60367 66574 74737 70701 67000 TRUE FALSE 71098.389 79159.18462 81434.41323 87740.03874 80033.11235 61587.6621 67388.75253 73193.65483 62675.31888 62462.03032 1.138265737 1.267316868 1.303742655 1.404693992 1.281308211 0.986001604 1.078875473 1.17181037 1.003414691 1 15.93069184 2.754798219 23.6645161 1.070452539 1.286763147 0.672610782 0.079742923 270.1470115 393708.72 0.025751957 0.027222832 568.588693 -2.754798219 0.216310609 TRYDSGQDLDEEGMNMGDFDPNNIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TRYDSGQDLDEEGMNMGDFDPNNIFK 26 1 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PRZ0;Q99615-2;K7ER44 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 107.23 0.002596 108220000 124520 133080 97509 102710 111140 133770 115140 139900 148140 127250 FALSE TRUE 119653.6207 129284.6887 115131.0454 108010.8754 114714.919 136474.9211 116549.1178 137011.0161 131323.7683 118631.2442 1.008618106 1.089803025 0.970495136 0.910475787 0.966987406 1.150412963 0.982448752 1.154931967 1.10699141 1 16.8561245 2.75492173 24.85442003 1.085853242 0.98943957 0.306345173 0.067073715 918.6476641 1395530.486 0.020854773 0.022067264 568.7504194 -2.75492173 -0.096413673 IIGEDS(ph)PSRLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 IIGEDSPSRLDR 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 IIGEDS(0.918)PS(0.082)RLDR;IIGEDS(0.991)PS(0.009)RLDR;IIGEDS(0.986)PS(0.014)RLDR 160.87 3.70E-05 1049380000 1215040 1268340 999640 1179500 1147230 1382030 1288810 1399880 1387320 1431990 TRUE FALSE 1167554.894 1232168.185 1180297.185 1240374.136 1184131.695 1409975.594 1304582.842 1370971.989 1229837.25 1335000.042 0.874572927 0.922972394 0.884117714 0.929119174 0.886990006 1.05616146 0.977215582 1.026945278 0.921226375 1 20.34840836 2.754987115 24.97445537 0.998768482 0.901640324 0.641834989 0.036098717 477.9488168 726661.059 0.010305736 0.010902089 568.8360537 -2.754987115 -0.097128158 LLQELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLQELR 6 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087WXM7;E9PNP6;I3L400;I3L0W2;J3KRA9;Q96Q15-2;Q96Q15;P11532-2;A0A087WTU7;A0A5H1ZRP8;A0A087WV90;P11532-3;P11532-4;A0A075B6G3;P11532-11;P11532;H0Y304 Q8N163-2;J3KRA9;P11532-2 CCAR2;SMG1;DMD Cell cycle and apoptosis regulator protein 2;Serine/threonine-protein kinase SMG1;Dystrophin 0 ; 98.133 0.093712 136795000 213677 241689 189481 208404 215354 162613 196192 180478 199550 215848 FALSE TRUE 205326.2666 234796.2664 223724.4317 219159.7554 222281.057 165901.1463 198593.0564 176751.0662 176897.9206 201228.4227 1.020364141 1.166814624 1.111793397 1.089109344 1.10462058 0.824441916 0.986903608 0.878360342 0.879090132 1 17.61847457 2.754992205 24.61424256 0.910146906 1.102545777 0.712171397 0.058685685 324.0096423 485360.429 0.016678567 0.017640893 568.8427205 -2.754992205 0.192398871 ETPDEVAQEMIESGFFHESDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETPDEVAQEMIESGFFHESDVK 22 0 Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;H0Y7R3;A6PVV2;Q9Y3S1-3 Q9Y3S1 WNK2 Serine/threonine-protein kinase WNK2 0 160.57 1.84E-11 12174000 10107 12693 10424 12993 12470 9806.8 11421 10678 13081 13761 FALSE TRUE 9712.007266 12331.00807 12307.84868 13663.57029 12871.10887 10005.10022 11560.77361 10457.49557 11596.09972 12828.95521 0.757038052 0.961185682 0.959380439 1.065057135 1.003285822 0.779884258 0.901146931 0.815147874 0.903900554 1 13.64711606 2.755001287 24.84566572 0.866101601 0.956859145 0.112478639 0.091886465 1294.154258 1955765.446 0.027883384 0.02949695 568.8546166 -2.755001287 0.090757545 FFGQHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FFGQHDR 7 0 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 0 125.81 0.011638 0 175960 193790 155590 176940 185450 156950 190120 165800 192210 190680 FALSE TRUE 169083.2887 188263.2989 183708.5741 186071.8946 191415.1677 160123.6365 192446.7454 162376.1721 170391.1266 177765.0738 0.951161469 1.059056737 1.033434579 1.046729207 1.076787265 0.900759824 1.082590305 0.913431242 0.958518583 1 17.43961237 2.75514291 24.99201527 0.970742406 1.035596013 0.237193633 0.055859157 1134.855442 1710396.24 0.016250771 0.017197346 569.0401503 -2.75514291 0.064853607 GMPTFPWDEDPEEDGS(ph)PDPEPSPEPEPKPSLEPNTSLER ddPTM_BT-474_Pertuzumab_2h_R1 2 GMPTFPWDEDPEEDGSPDPEPSPEPEPKPSLEPNTSLER 39 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 GMPTFPWDEDPEEDGS(0.975)PDPEPS(0.024)PEPEPKPSLEPNTSLER;GMPTFPWDEDPEEDGS(0.975)PDPEPS(0.025)PEPEPKPSLEPNTSLER 133.09 3.99E-09 125519000 174497 182561 154254 159120 181240 183139 190797 204589 219537 204353 TRUE FALSE 167677.4643 177354.539 182131.1292 167332.2023 187069.7492 186842.1961 193132.0308 200364.1657 194616.0801 190511.9893 0.880141271 0.930936366 0.956008752 0.878328985 0.981931635 0.980737206 1.013752633 1.051714207 1.021542428 1 17.53952227 2.75527584 1.340054469 1.029554916 0.915376352 0.740798537 0.028164534 0.202264872 0.742292614 0.012180431 0.011714906 569.2143496 -2.75527584 -0.114178563 KPEDPEECPEEVYDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPEDPEECPEEVYDPR 16 1 H3BQQ6;H3BTI2;H3BTP8;H3BSY6;H3BP64;H3BUL4;H3BMX9;Q9GZU8;Q6P4H7;H3BSF0;H3BN22 H3BQQ6 FAM192A;NIP30 Protein FAM192A 0 93.754 0.0069338 137380000 236510 229460 186360 193920 206040 232790 227970 219420 264280 252510 FALSE TRUE 227266.9277 222916.0255 220039.3976 203928.2344 212667.4637 237497.1733 230759.9651 214888.9003 234280.0424 235407.2728 0.965420163 0.946937717 0.934717925 0.866278395 0.903402266 1.008877808 0.980258436 0.912838834 0.995211573 1 17.84479937 2.755354413 24.92787182 0.969113597 0.922122413 0.367116822 0.03553233 1109.646359 1647101.59 0.011855397 0.012547702 569.3173418 -2.755354413 -0.046991184 HSDGNLCVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSDGNLCVK 9 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 86.624 0.014012 1164000000 1352900 1244600 1071600 1172600 1142400 1054200 1179500 861940 1374500 1141600 FALSE TRUE 1300027.172 1209105.227 1265261.958 1233118.027 1179146.334 1075516.646 1193935.074 844140.6378 1218472.522 1064278.415 1.221510418 1.136079816 1.188844892 1.158642334 1.107930328 1.010559484 1.121825884 0.793157717 1.144881363 1 20.02144418 2.755504746 1.148902592 0.972907798 1.181303495 0.399715617 0.091916973 0.414788031 1.140793492 0.044143065 0.04181519 569.5144473 -2.755504746 0.208395697 EKLCYVALDFEQEMATAASSSSLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKLCYVALDFEQEMATAASSSSLEK 25 1 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 0 ; 200.98 5.83E-25 2790200000 2034930 1937070 1454128 1546540 1703930 1992870 1796260 2090080 2229890 1850520 FALSE TRUE 1955402.686 1881826.66 1716921.277 1626357.115 1758738.456 2033167.197 1818243.167 2046919.118 1976762.236 1725182.632 1.133446772 1.090798519 0.995211315 0.94271591 1.019450592 1.178522876 1.053942425 1.18649416 1.145827809 1 20.71831767 2.755783972 24.36229021 1.124528382 1.031866385 0.214541612 0.071369218 794.7587418 1124177.731 0.022255435 0.023546065 569.8807296 -2.755783972 -0.092661997 IGEHTPSALAIMENANVLAR ddPTM_BT-474_Pertuzumab_2h_R1 8 IGEHTPSALAIMENANVLAR 20 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BR04;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;; 308.12 3.38E-66 26947450000 9402680 9373443 7352636 8572036 8715307 7422567 8062008 8324361 9439167 8203863 FALSE TRUE 9035212.87 9106121.583 8681420.884 9014439.805 8995642.765 7572656.39 8160673.266 8152460.036 8367672.334 7648208.052 1.181350299 1.190621584 1.135092145 1.17863423 1.176176524 0.990121652 1.067004612 1.065930736 1.094069654 1 22.86669034 2.756119949 24.99466563 1.050928541 1.171665138 0.797311608 0.032396777 371.5947324 528942.372 0.009767225 0.010337986 570.3217696 -2.756119949 0.120736597 YLAEVACGDDRK ddPTM_BT-474_Pertuzumab_2h_R1 4 YLAEVACGDDRK 12 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;; 210.79 6.33E-08 43362200000 13449900 13136900 11397310 12335700 13722100 14691700 16448200 16419600 18012800 17178300 FALSE TRUE 12924263.04 12762248.47 13457057.45 12972346.96 14163483.81 14988776.24 16649497.99 16080529.52 15968062.46 16014798.44 0.807020025 0.796903472 0.840288905 0.810022493 0.884399754 0.935932868 1.039632066 1.004104396 0.9970817 1 23.9329023 2.756293383 1.581439172 1.011849538 0.812406768 0.952107869 0.019683485 0.069799108 0.350303181 0.007646876 0.00749814 570.5495714 -2.756293383 -0.199442769 TQSLNPAPFS(ph)PLTAQQMKPEKPSTLQRPQETVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQSLNPAPFSPLTAQQMKPEKPSTLQRPQETVIR 34 3 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TQSLNPAPFS(0.989)PLT(0.01)AQQMKPEKPS(0.001)T(0.001)LQRPQET(0.001)VIR 78.542 0.0014171 281970000 151110 172350 157670 136720 153710 185580 170830 194920 177000 187970 TRUE FALSE 145204.4541 167434.7467 186164.4764 143776.1356 158654.2217 189332.5548 172920.6686 190894.8339 156907.702 175238.6245 0.828609872 0.955467137 1.062348423 0.820459165 0.905361031 1.080427077 0.986772575 1.08934223 0.895394509 1 17.41896127 2.756361317 24.26172 1.019962424 0.919722858 0.255037881 0.080912046 768.2227593 1047058.399 0.024532257 0.025967782 570.6388254 -2.756361317 -0.100239566 SSGEIVYCGQVFEKS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSGEIVYCGQVFEKSPLR 18 1 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 1 SSGEIVYCGQVFEKS(1)PLR;SSGEIVYCGQVFEKS(1)PLR;SSGEIVYCGQVFEKS(1)PLR;SSGEIVYCGQVFEKS(1)PLR;SSGEIVYCGQVFEKS(1)PLR 281 1.63E-39 6642100000 3134260 2913420 2693520 2912820 3154390 3273680 3362900 3810510 4116510 3675150 TRUE FALSE 3011769.654 2830332.114 3180298.981 3063150.989 3255853.819 3339876.053 3404056.176 3731821.637 3649221.043 3426228.817 0.879033426 0.826077961 0.928221421 0.894029895 0.950273316 0.974796556 0.993528558 1.089192181 1.065083868 1 21.70819007 2.75639854 0.83075269 1.060352256 0.865238304 0.811711446 0.033785685 0.234090478 0.348083122 0.021401972 0.020672584 570.6877364 -2.75639854 -0.195113952 AVLDLESERR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVLDLESERR 10 1 A0A0C4DGA6;Q14527-2;Q14527;H7C5K0 A0A0C4DGA6 HLTF Helicase-like transcription factor 0 110.38 0.0030361 119410000 82180 96698 77034 88888 96287 72531 86130 91152 94112 93038 FALSE TRUE 78968.31475 93940.26772 90955.75741 93475.52033 99384.1588 73997.62651 87184.0847 89269.67935 83428.80031 86736.45339 0.910439748 1.083054057 1.048645107 1.077695902 1.145817645 0.853131799 1.005160821 1.029206013 0.961865479 1 16.40435083 2.756565266 24.9077543 0.979380459 1.055908456 0.250707348 0.070941547 1239.764621 1715096.688 0.0216633 0.022934761 570.9068655 -2.756565266 0.076527996 GLLSDS(ph)MTDVPVDTGVAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 GLLSDSMTDVPVDTGVAAR 19 0 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 GLLS(0.001)DS(0.887)MT(0.112)DVPVDTGVAAR;GLLSDS(1)MTDVPVDTGVAAR;GLLSDS(0.993)MT(0.007)DVPVDTGVAAR 260.25 4.43E-31 254000000 287413 300236 211219 267457 272919 241919 230346 314611 275764 249396 TRUE FALSE 276180.5822 291673.5632 249390.9718 281260.4878 281697.6875 246810.7679 233165.0433 308114.1729 244460.4268 232504.1868 1.187852081 1.254487359 1.072630026 1.209700744 1.211581139 1.061532574 1.002842342 1.325198385 1.051423762 1 17.82689717 2.756629949 24.68434373 1.118902809 1.185865121 0.169880219 0.098374357 1794.285088 2451152.762 0.031217797 0.033049969 570.9919022 -2.756629949 0.066962311 FHKPGENYK ddPTM_BT-474_Pertuzumab_2h_R1 1 FHKPGENYK 9 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQJ6 P47897 QARS Glutamine--tRNA ligase 0 160.36 3.93E-05 658290000 786040 703320 698530 664270 756130 488410 832890 307620 875060 839920 FALSE TRUE 755320.6878 683262.0022 824769.9097 698553.0543 780451.6081 498285.9848 843083.157 301267.5395 775726.8574 783031.4703 0.964610896 0.872585622 1.053303655 0.892113639 0.996705289 0.636354992 1.076691281 0.384745123 0.990671367 1 19.57871077 2.757039985 24.81401404 0.769015994 0.953108909 0.085233202 0.196134702 1305.295653 1752742.746 0.057580216 0.06097271 571.5312547 -2.757039985 0.184092916 NS(ph)SPQRPAVSAPVGASEIAEETRPGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSPQRPAVSAPVGASEIAEETRPGQR 27 2 P0CG23 P0CG23 ZNF853 Zinc finger protein 853 1 NS(0.5)S(0.5)PQRPAVSAPVGASEIAEETRPGQR 172.74 1.79E-12 158190000 41360 32608 35496 38156 38070 33526 37022 36897 40399 39349 TRUE FALSE 39743.60547 31678.05177 41910.9168 40125.23573 39294.55612 34203.91869 37475.08631 36135.06406 35813.07489 36683.85718 1.083408576 0.86354201 1.142489368 1.093811797 1.071167515 0.932397008 1.021568864 0.985039929 0.976262521 1 15.16285772 2.75717787 24.45093173 0.985597665 1.047950054 0.182277656 0.071598038 1222.017641 1604931.33 0.02203716 0.023331573 571.7127399 -2.75717787 0.062352389 LADVAAPPGGPPPPHSPYSGPPSRGS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LADVAAPPGGPPPPHSPYSGPPSRGSPVR 29 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LADVAAPPGGPPPPHS(0.056)PY(0.007)S(0.268)GPPS(0.2)RGS(0.47)PVR;LADVAAPPGGPPPPHS(0.026)PY(0.003)S(0.112)GPPS(0.184)RGS(0.675)PVR 97.387 0.00060454 7327900000 699130 960450 622970 704750 708740 978780 906880 906400 872930 979100 TRUE FALSE 671807.2267 933058.9064 735554.5369 741122.232 731537.2658 998571.6022 917978.6687 887682.5233 773838.646 912784.6849 0.735997479 1.022211395 0.805835756 0.811935437 0.80143464 1.093983739 1.005690262 0.972499361 0.847777859 1 19.79991506 2.757327116 24.98529196 0.9833132 0.84290148 0.409376192 0.088964434 876.2663535 1166639.777 0.026937783 0.028528323 571.909243 -2.757327116 -0.14041172 RLGSLVDEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLGSLVDEFK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 125.97 0.0006333 681820000 1146750 1136320 827240 948420 1001660 1066480 1017970 1113930 1194810 1154450 FALSE TRUE 1101933.742 1103913.266 976740.6699 997368.0699 1033879.304 1088044.956 1030428.221 1090926.956 1059180.178 1076258.073 1.023856424 1.025695689 0.907533884 0.926699734 0.960623971 1.010951726 0.957417414 1.013629522 0.984132156 1 20.03759263 2.757551924 23.71944212 0.992699578 0.966286576 0.093420986 0.037466684 1110.405671 1386853.684 0.012363998 0.013090249 572.2053633 -2.757551924 -0.026413002 MEQELKEPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEQELKEPGR 10 1 C9JVE2;Q96GG9 C9JVE2 DCUN1D1 DCN1-like protein;DCN1-like protein 1 0 ; 151.13 1.86E-05 693640000 1764530 1700360 1366260 1363990 1548780 1755810 1654790 1748650 1999010 1889450 FALSE TRUE 1695570.217 1651867.398 1613173.574 1434385.687 1598597.915 1791313.681 1675041.815 1712539.766 1772090.765 1761475.869 0.962584982 0.93777464 0.915807933 0.814309019 0.907533247 1.016939098 0.95093089 0.972218693 1.006026138 1 20.74835328 2.758461077 22.2229547 0.983071519 0.904551128 0.508626391 0.039827481 180.7702181 201866.0229 0.012970303 0.013729796 573.404474 -2.758461077 -0.078520391 LFVLLPEQS(ph)PVSYSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFVLLPEQSPVSYSK 15 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 LFVLLPEQS(1)PVSYSK;LFVLLPEQS(0.995)PVS(0.004)YSK 277.94 1.41E-33 904400000 539300 513240 477850 507070 503570 583080 564680 559740 632880 614110 TRUE FALSE 518223.5598 498602.8977 564208.1247 533239.9435 519767.7864 594870.2771 571590.7228 548181.1734 561038.1156 572515.7827 0.905169037 0.870898083 0.985489207 0.931397805 0.907866302 1.039046075 0.998384219 0.957495304 0.979952226 1 19.12695594 2.758663002 24.94429581 0.989774895 0.921680351 0.558312415 0.033095424 695.9266856 863547.8177 0.010683784 0.011318852 573.6711395 -2.758663002 -0.068094544 VGDAIPAVEVFEGEPGNKVNLAELFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGDAIPAVEVFEGEPGNKVNLAELFK 26 1 P30044-2;P30044;P30044-3 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ; 291.7 2.69E-70 1173850000 1110480 1033540 720020 709050 875290 998050 911450 1057290 1161820 883720 FALSE TRUE 1067081.214 1004064.451 850143.6308 745644.1555 903444.4978 1018231.255 922604.5977 1035456.592 1029935.064 823864.8573 1.295213899 1.2187247 1.031896947 0.905056392 1.096593076 1.235920243 1.119849438 1.256828208 1.250126226 1 19.65204818 2.75876198 22.59458647 1.189445385 1.099896252 0.052252839 0.120823114 574.8473418 642945.9286 0.038881809 0.041169176 573.8018974 -2.75876198 -0.089549133 WGQPPSPT(ph)PVPRPPDADPNTPSPKPLEGRPER ddPTM_BT-474_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.373)PT(0.617)PVPRPPDADPNT(0.009)PS(0.001)PKPLEGRPER 104.35 3.12E-06 2963100000 157110 138290 119890 120410 129060 153670 142500 148110 162150 164700 TRUE FALSE 150969.9675 134346.1046 141556.7899 126624.3745 133211.3321 156777.3127 144243.9576 145051.4767 143743.4118 153544.7223 0.983231239 0.874964001 0.921925468 0.824674223 0.8675735 1.021053087 0.939426347 0.944685526 0.936166412 1 17.2282994 2.758944752 24.95724495 0.960824864 0.891037164 0.385604951 0.045994905 894.5223998 1095203.964 0.014002803 0.014836298 574.0434311 -2.758944752 -0.0697877 AHFNAMFQPS(ph)SPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.668)S(0.332)PT(0.001)R;AHFNAMFQPS(0.662)S(0.336)PT(0.001)R 136.35 9.24E-05 506790000 266770 281850 208793 278000 269450 192730 254161 211341 265450 268640 TRUE FALSE 256344.3335 273811.914 246526.5397 292347.6133 278117.104 196627.1326 257271.4983 206976.7345 235317.2289 250444.7735 1.023556331 1.093302568 0.984354899 1.167313692 1.110492745 0.785111743 1.027258404 0.826436629 0.939597283 1 17.93413298 2.758994411 24.93461276 0.907899513 1.076779558 0.489875578 0.081503309 612.5358225 747454.0245 0.023430134 0.024823576 574.1090734 -2.758994411 0.168880045 SSSAAS(ph)MAEEEASAVSTAAAQFTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSAASMAEEEASAVSTAAAQFTK 24 0 Q9HCK8-2;Q9HCK8;H0YJG4;H0YJA4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 S(0.239)S(0.239)S(0.239)AAS(0.283)MAEEEAS(0.001)AVSTAAAQFTK 127.8 5.29E-05 6334300 15660 14867 12516 13881 14543 18949 17387 20335 20872 19288 TRUE FALSE 15047.98989 14443.00772 14777.91962 14597.40007 15010.7888 19332.16176 17599.78731 19915.07514 18502.69806 17981.60658 0.836854584 0.803210083 0.821835332 0.81179621 0.834785743 1.075107593 0.97876612 1.107524795 1.028979139 1 14.1342343 2.759146689 8.87917 1.044919088 0.81991008 0.904496227 0.035118251 0.07695489 30.86756323 0.01037753 0.010805013 574.3104108 -2.759146689 -0.225009008 ETGEAGWWR ddPTM_BT-474_Pertuzumab_2h_R1 4 ETGEAGWWR 9 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ;;; 168.23 0.00013814 998680000 716228 858190 730457 822350 798360 714170 794270 812907 766629 802180 FALSE TRUE 688237.0179 833715.2615 862466.8288 864791.5821 824039.9745 728611.0067 803990.5139 796120.1864 679604.4899 747847.6341 0.920290426 1.114819682 1.153265437 1.156374029 1.101882171 0.974277344 1.075072618 1.064548646 0.908747262 1 19.51238484 2.759580855 23.64399895 1.018995454 1.098019704 0.221791788 0.076208344 676.9975369 761499.1019 0.02374569 0.025156412 574.8848381 -2.759580855 0.07902425 RYS(ph)PS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 3 RYSPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.104)S(0.9)PS(0.996)PPPK;RY(0.208)S(0.801)PS(0.992)PPPK;RY(0.014)S(0.988)PS(0.998)PPPK 90.697 0.0075221 6799690000 2017910 2032240 1602910 1867070 1878800 2062340 1929110 2143060 2311780 2165850 TRUE FALSE 1939047.846 1974282.505 1892591.494 1963429.706 1939233.308 2104041.928 1952719.025 2098805.062 2049356.426 2019155.05 0.960326373 0.977776573 0.937318555 0.972401652 0.960418224 1.042040792 0.967097116 1.039447199 1.014957433 1 20.94532027 2.759784966 24.18073055 1.013327293 0.961790042 0.576057014 0.021898109 365.5207478 416434.1888 0.006310626 0.006686343 575.1550883 -2.759784966 -0.051537251 CLHNNNFENALCR ddPTM_BT-474_Pertuzumab_2h_R1 1 CLHNNNFENALCR 13 0 F8WEL9;Q49B96 F8WEL9 COX19 Cytochrome c oxidase assembly protein COX19 0 89.629 0.0073617 121500000 59820 63143 46075 52937 51870 66145 57870 68416 70508 47122 FALSE TRUE 57482.16827 61342.22346 54401.77743 55669.08491 53538.44566 67482.49722 58578.23037 67003.18569 62504.22743 43930.38497 1.308483145 1.396350692 1.238363321 1.267211406 1.218711051 1.536123512 1.333433122 1.525212805 1.422801723 1 15.42293152 2.759821287 24.9739595 1.403660864 1.288293575 0.030780192 0.148467108 1639.146345 1925429.885 0.042244288 0.044766804 575.2031909 -2.759821287 -0.115367289 TPESQPDT(ph)PPGTPLVSQDEKR ddPTM_BT-474_Pertuzumab_2h_R1 6 TPESQPDTPPGTPLVSQDEKR 21 1 A0A0D9SFD6;M0R3C8;A0A0D9SFL2;M0QYH2;Q96T60-2;Q96T60;A0A0D9SEV0;M0R000;M0QYI1 A0A0D9SFD6 PNKP Bifunctional polynucleotide phosphatase/kinase;Polynucleotide 3-phosphatase;Polynucleotide 5-hydroxyl-kinase 1 TPESQPDT(0.996)PPGT(0.004)PLVSQDEKR;TPESQPDT(0.991)PPGT(0.009)PLVSQDEKR;TPESQPDT(0.989)PPGT(0.008)PLVS(0.003)QDEKR;TPESQPDT(0.972)PPGT(0.022)PLVS(0.006)QDEKR;TPESQPDT(1)PPGTPLVSQDEKR;TPESQPDT(0.998)PPGT(0.002)PLVSQDEKR 192.18 6.89E-18 15938900000 5686380 5352010 4245920 4572670 4903960 5344390 5024670 5501920 6035180 5677340 TRUE FALSE 5464149.983 5199375.915 5013252.194 4808666.047 5061700.327 5452457.228 5086163.415 5388303.429 5350091.668 5292808.705 1.032372468 0.98234722 0.947181822 0.908528215 0.956335399 1.03016329 0.960957348 1.018042353 1.010822791 1 22.33560208 2.759849909 24.56363332 1.002583293 0.962130698 0.245564139 0.033585438 965.9272344 1114487.003 0.010807378 0.011451738 575.2411006 -2.759849909 -0.040452595 DMKEER ddPTM_BT-474_Pertuzumab_2h_R1 1 DMKEER 6 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 67.757 0.089314 311900000 233710 259750 181240 202790 217710 242970 224100 251710 258240 269310 FALSE TRUE 224576.3548 252342.1843 213994.0997 213256.0162 224712.8399 247883.0199 226842.6028 246512.1005 228925.6778 251069.3938 0.894479217 1.005069477 0.852330491 0.849390732 0.895022832 0.987308792 0.903505598 0.981848471 0.911802408 1 17.93772664 2.760135866 24.35035852 0.9535153 0.899759379 0.253571318 0.049268209 912.7943647 1030200.318 0.015176694 0.016083871 575.619988 -2.760135866 -0.053755921 TPELRDDDFLGGAECSLGQIVSSQVLTLPLMLKPGKPAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPELRDDDFLGGAECSLGQIVSSQVLTLPLMLKPGKPAGR 40 3 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56;Q5JX54;Q5JX55;E7EV27;Q5JX57 Q99829 CPNE1 Copine-1 0 ; 164.11 6.37E-19 183354000 311950 296440 273901 276556 286930 329100 310500 312750 383420 345850 FALSE TRUE 299758.6491 287985.8214 323401.0036 290829.0883 296159.364 335754.6275 314299.9919 306291.6032 339895.769 322425.2714 0.92969961 0.893186257 1.003026227 0.902004632 0.918536449 1.041340916 0.974799495 0.949961527 1.054184641 1 18.2986053 2.760254912 24.95877359 0.994331269 0.929865365 0.461120673 0.039720391 838.9848273 965230.5789 0.012198644 0.012928277 575.7777949 -2.760254912 -0.064465905 SIEVIENR ddPTM_BT-474_Pertuzumab_2h_R1 4 SIEVIENR 8 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;; 147.06 0.0012641 2004040000 1889990 2194680 1885270 1916070 2001470 1840680 2010510 1919840 2125840 2254100 FALSE TRUE 1816127.101 2132089.875 2225980.227 2014958.602 2065849.1 1877899.811 2035115.223 1880194.633 1884523.555 2101427.799 0.864234832 1.014591068 1.059270381 0.958852169 0.983069274 0.893630422 0.968444038 0.894722452 0.896782443 1 21.00293846 2.760471352 23.41540314 0.925011683 0.981820392 0.131629937 0.056246431 592.6082926 633302.3996 0.016876544 0.017881797 576.0648172 -2.760471352 0.056808709 LQEVFGHAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQEVFGHAIK 10 0 P54136;P54136-2;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 87.363 0.012927 389240000 247260 255300 214720 206440 250350 179440 240560 174510 281020 284800 FALSE TRUE 237596.8058 248019.094 253524.6804 217094.3931 258402.7351 183068.3997 243504.0452 170906.3075 249119.7877 265510.2423 0.894868702 0.93412251 0.954858382 0.817649787 0.973230761 0.689496564 0.917117333 0.643690074 0.938268089 1 18.01840799 2.760654067 24.86154839 0.808367609 0.91282339 0.07986889 0.1104186 1257.592209 1415154.303 0.031556771 0.033444427 576.3072292 -2.760654067 0.104455781 RNNGVVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNNGVVDK 8 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 103.55 0.0076192 223067000 240290 237690 185492 210200 223830 249970 258960 256780 294390 287430 FALSE TRUE 230899.2011 230911.3139 219014.5306 221048.4472 231029.6952 255024.5647 262129.2299 251477.4033 260972.0814 267962.1101 0.861686009 0.861731212 0.817333953 0.824924267 0.862172996 0.951718751 0.978232444 0.938481202 0.973914115 1 18.03166949 2.760694406 3.296929648 0.965059958 0.841291781 0.907417786 0.019737907 0.073450742 1.66294078 0.006693181 0.006794346 576.3607609 -2.760694406 -0.123768177 VLHNDSDILFPVSGVGSYS(ph)PADAPLGSLENGTGPEDHVLPDPGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLHNDSDILFPVSGVGSYSPADAPLGSLENGTGPEDHVLPDPGLR 45 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 VLHNDSDILFPVS(0.079)GVGS(0.339)Y(0.084)S(0.454)PADAPLGS(0.022)LENGT(0.022)GPEDHVLPDPGLR 46.05 0.047671 49808000 8639.9 10758 10351 8847 7945.6 13304 10811 10385 12197 12237 TRUE FALSE 8302.243156 10451.19237 12221.65596 9303.59473 8201.17744 13573.016 10943.30825 10170.54612 10812.44769 11408.17709 0.72774494 0.916114143 1.071306648 0.815519838 0.718885881 1.189762035 0.95925126 0.891513696 0.947780492 1 13.47778066 2.760697612 24.9976694 0.979588028 0.863980857 0.268636429 0.118926575 1475.30946 1665955.584 0.038148341 0.040432366 576.3650154 -2.760697612 -0.115607171 DTSFTVCPDVPRT(ph)PVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTSFTVCPDVPRTPVGK 17 1 P30307-4;P30307-3;P30307-2;P30307;D6RJC2;A0A3B3IT42;D6RD20 P30307-4 CDC25C M-phase inducer phosphatase 3 1 DTSFTVCPDVPRT(1)PVGK 105.67 0.0012777 280320000 245980 248740 302820 190490 200660 243840 163260 191800 184070 183890 TRUE FALSE 236366.8297 241646.1787 357546.3102 200321.2117 207114.4111 248770.6119 165258.0247 187839.263 163175.1453 171434.9665 1.378755072 1.409550127 2.085609007 1.168496811 1.20812233 1.45110777 0.963969184 1.09568816 0.951819507 1 17.38730187 2.76099008 0.809434965 0.989072561 1.572520117 0.463418351 0.236412843 0.571754769 0.808916205 0.154362951 0.15088416 576.7532897 -2.76099008 0.583447556 EPS(ph)PALGPNLDGSGLLPRPIFYCSFPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EPSPALGPNLDGSGLLPRPIFYCSFPTR 28 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR 132.37 1.16E-05 128290000 12204 9826.1 7845.3 6294 10365 18422 20352 22251 22882 10140 TRUE FALSE 11727.05419 9545.869249 9263.120228 6618.834094 10698.39964 18794.50546 20601.07386 21791.50907 20284.53129 9453.208768 1.240536888 1.009802014 0.979891638 0.700167981 1.131721503 1.988161472 2.179267841 2.305197061 2.145782642 1 13.2065884 2.761005722 3.996619969 2.05800655 0.978536485 0.597080059 0.367852229 0.126560029 4.664370478 0.112091115 0.114264711 576.7740632 -2.761005722 -1.079470064 LKEEHGIELS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEEHGIELSSPR 13 1 O14647;O14647-2 O14647 CHD2 Chromodomain-helicase-DNA-binding protein 2 1 LKEEHGIELS(0.5)S(0.5)PR 64.275 0.03787 243120000 200980 228580 186570 208420 208040 179720 200310 188940 227250 221390 TRUE FALSE 193125.4794 222061.1222 220287.3492 219176.5812 214731.7955 183354.0615 202761.4537 185038.323 201453.5327 206395.0581 0.935707866 1.075903291 1.067309224 1.061927467 1.040392137 0.888364592 0.982394906 0.896524969 0.976057928 1 17.6550489 2.761082715 23.36146978 0.941385116 1.04160336 0.432655979 0.04960745 277.9583707 288316.6504 0.014414736 0.01527558 576.876324 -2.761082715 0.100218244 YIHLENLLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIHLENLLAR 10 0 Q2TAY7 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ; 188.99 1.06E-06 1352380000 918030 990830 889540 942870 983990 837740 994890 889500 1004350 1093560 FALSE TRUE 882152.3727 962572.4985 1050299.666 991531.6337 1015640.932 854679.6768 1007065.761 871131.5142 890340.3986 1019492.207 0.865286038 0.944168569 1.030218435 0.972574019 0.996222359 0.838338607 0.987811142 0.854475893 0.873317513 1 19.95941932 2.761576736 24.8063211 0.904429759 0.965131625 0.135739794 0.062916166 1244.938665 1341768.492 0.018798513 0.019928002 577.5329088 -2.761576736 0.060701866 S(ph)PTLGIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPTLGIAR 8 0 Q99618;F5GX58;F8WDL1;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 1 S(0.973)PT(0.027)LGIAR 119.75 0.0017148 107050000 24448 29267 24717 31309 28870 21349 26662 28579 20761 28435 TRUE FALSE 23492.54513 28432.33382 29183.91173 32924.86124 29798.62977 21780.69141 26988.29753 27988.83366 18404.29832 26509.07212 0.886207749 1.072551075 1.1009028 1.242022395 1.124091769 0.821631602 1.018077789 1.055820948 0.694264146 1 14.69419855 2.761802107 24.89889127 0.940891796 1.094044657 0.289350185 0.128145933 1095.072906 1173162.99 0.040054857 0.042461236 577.8326892 -2.761802107 0.153152862 SQGQLNEKPLPEGWEMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQGQLNEKPLPEGWEMR 17 1 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;A0A590UK95 A0A590UJQ1 ITCH E3 ubiquitin-protein ligase Itchy homolog 0 ; 160.45 2.82E-09 637420000 427760 467770 358650 387050 421330 489320 485610 502980 590210 552670 FALSE TRUE 411042.6663 454429.6576 423466.0331 407025.6969 434882.4621 499214.3857 491553.0404 492593.2872 523211.8352 515237.1686 0.797773708 0.881981513 0.821885646 0.789977357 0.844043265 0.968902121 0.954032571 0.956051537 1.015477662 1 18.97487715 2.761952941 4.191245521 0.973490005 0.826057494 0.872429033 0.02905316 0.075667426 3.175607077 0.009409339 0.009611031 578.03341 -2.761952941 -0.14743251 LTEEETVCLDLDKVEAYR ddPTM_BT-474_Pertuzumab_2h_R1 6 LTEEETVCLDLDKVEAYR 18 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;;; 289.95 3.48E-49 2585117000 1225829 1102531 974910 944180 1036613 1172759 1101930 1144728 1345202 1207259 FALSE TRUE 1177922.247 1071087.895 1151097.924 992909.243 1069956.599 1196472.991 1115415.749 1121088.967 1192500.309 1125490.273 1.046585898 0.951663396 1.022752441 0.882201532 0.950658237 1.063068264 0.991048769 0.996089432 1.05953853 1 20.10212216 2.762105084 24.93760206 1.017001769 0.967677881 0.221276679 0.047374534 1239.571819 1312915.637 0.014387144 0.015252817 578.2359438 -2.762105084 -0.049323888 RS(ph)SPSARPPDVPGQQPQAAK ddPTM_BT-474_Pertuzumab_2h_R1 6 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.497)S(0.497)PS(0.006)ARPPDVPGQQPQAAK;RS(0.459)S(0.459)PS(0.081)ARPPDVPGQQPQAAK;RS(0.499)S(0.499)PS(0.002)ARPPDVPGQQPQAAK;RS(0.494)S(0.494)PS(0.012)ARPPDVPGQQPQAAK;RS(0.493)S(0.493)PS(0.015)ARPPDVPGQQPQAAK;RS(0.499)S(0.499)PS(0.002)ARPPDVPGQQPQAAK 172.66 3.14E-12 20588700000 5103490 4769830 3947730 4275660 4506340 4866930 4694410 5085430 5299220 5099530 TRUE FALSE 4904039.969 4633799.119 4661172.628 4496327.325 4651290.519 4965342.659 4751861.594 4980414.093 4697674.762 4754134.291 1.031531646 0.97468831 0.980446143 0.945772048 0.978367508 1.044426252 0.999521954 1.047596426 0.98812412 1 22.18075123 2.762366927 24.15417021 1.019848902 0.979629074 0.279954514 0.026560201 561.1367191 569334.9441 0.007919606 0.008394106 578.5846756 -2.762366927 -0.040219829 FFHLAFEEEFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FFHLAFEEEFGR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 164.9 5.60E-05 1310880000 1503540 1627910 1447640 1627430 1645070 1345550 1701590 1349560 1663830 1943270 FALSE TRUE 1444779.995 1581483.601 1709260.751 1711421.857 1697985.171 1372757.943 1722414.567 1321691.114 1474958.994 1811650.592 0.797493734 0.872951775 0.943482567 0.944675461 0.93725864 0.757738799 0.950743248 0.729550787 0.814152023 1 20.7888733 2.762725342 24.91435717 0.833697007 0.902705351 0.056350269 0.086560711 1561.528755 1609967.743 0.025733832 0.027283661 579.0623674 -2.762725342 0.069008344 TLAPTWEELSKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLAPTWEELSKK 12 1 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 180.54 3.10E-05 492320000 933360 998390 576910 546000 726040 909940 827170 844800 1016700 866720 FALSE TRUE 896883.2593 969916.8947 681170.4703 574179.1254 749393.736 928339.6102 837293.1539 827354.5848 901288.4784 808016.2824 1.109981666 1.200368007 0.843015772 0.71060341 0.927448806 1.148912009 1.036233022 1.02393306 1.11543356 1 19.62402484 2.762745331 24.40383202 1.060428744 0.95156889 0.139115713 0.131851947 1327.099315 1339120.921 0.04485745 0.047552254 579.0890212 -2.762745331 -0.108859853 IKGSEADR ddPTM_BT-474_Pertuzumab_2h_R1 1 IKGSEADR 8 1 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 111.06 0.0030158 459520000 672530 731890 525100 567920 637050 680730 701100 696850 789980 798120 FALSE TRUE 646246.7841 711017.2138 619997.2508 597230.4193 657541.2918 694494.827 709680.2715 682459.804 700304.7823 744062.6215 0.868538165 0.955587868 0.833259504 0.802661499 0.883717678 0.933382227 0.953791053 0.917207483 0.94119065 1 19.50506452 2.762840613 3.83002039 0.943025545 0.866758609 0.48424932 0.041551853 0.231041475 7.568097922 0.014071305 0.014350191 579.216084 -2.762840613 -0.076266936 NTIQWLENELNR ddPTM_BT-474_Pertuzumab_2h_R1 1 NTIQWLENELNR 12 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 221.55 6.26E-11 157530000 94347 101880 91889 97509 100350 81545 79634 109000 91722 109050 FALSE TRUE 90659.81493 98974.48215 108495.3864 102541.4512 103577.8489 83193.89577 80608.58471 106749.1119 81310.10309 101663.9464 0.891759745 0.973545546 1.06719629 1.008631426 1.018825774 0.81832251 0.79289254 1.05001936 0.799792906 1 16.63344861 2.763360317 24.88281402 0.899859387 0.996069429 0.239614514 0.088205531 1162.780565 1166675.699 0.027470244 0.029124849 579.9096246 -2.763360317 0.096210041 GLFYFDNSFRPVPLEQTYVGITEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLFYFDNSFRPVPLEQTYVGITEK 24 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 220.23 9.34E-33 500540000 510750 484330 375830 379910 426010 471440 469390 483700 494880 451530 FALSE TRUE 490789.3253 470517.3826 443750.8413 399517.2006 439712.9985 480972.8398 475134.5352 473711.426 438703.2971 420947.4709 1.165915843 1.117757951 1.054171534 0.949090393 1.044579262 1.142595865 1.128726428 1.125345699 1.042180622 1 18.68328069 2.763405545 24.70690184 1.101277774 1.061975825 0.003323425 0.066190167 2004.951391 1993807.621 0.021336001 0.022618858 579.9700208 -2.763405545 -0.039301949 DLEIAKEYDLPDAKS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 DLEIAKEYDLPDAKSR 16 2 A0A087WTJ8;Q96NG3 A0A087WTJ8 TTC25 Tetratricopeptide repeat protein 25 1 DLEIAKEYDLPDAKS(1)R 79.311 0.014732 574870000 342050 279450 296260 277540 331930 300250 365990 346210 377010 359930 TRUE FALSE 328682.3078 271480.3596 349800.7723 291863.8727 342606.8299 306321.2607 370469.0951 339060.6425 334213.4054 335551.6205 0.979528298 0.809056917 1.042464858 0.869803198 1.021025705 0.912888635 1.104059919 1.010457473 0.996011895 1 18.3561752 2.763709368 1.293000303 1.024339339 0.926138046 0.204968755 0.073597015 0.601139887 2.063989934 0.030768774 0.02970847 580.3758974 -2.763709368 -0.098201293 LDELFEQER ddPTM_BT-474_Pertuzumab_2h_R1 1 LDELFEQER 9 0 Q9P0U4;Q9P0U4-2;A0A669KB29 Q9P0U4 CXXC1 CXXC-type zinc finger protein 1 0 104.17 0.0076867 34025000 34748 38879 32089 35210 37020 30427 36922 34719 34348 39627 FALSE TRUE 33390.00974 37770.20899 37888.19612 37027.19232 38210.78192 31042.25479 37373.86248 34002.04052 30448.95904 36943.02799 0.90382439 1.02239072 1.025584479 1.002278219 1.03431646 0.840273699 1.011662132 0.920391272 0.82421395 1 15.1730145 2.764088178 24.99848618 0.922671902 1.000857569 0.266349191 0.064807088 1042.624928 1021013.869 0.019109701 0.020262945 580.8823462 -2.764088178 0.078185667 FYTGNDPLDVWDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FYTGNDPLDVWDR 13 0 O60566-3;O60566;O60566-2 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 0 158.42 0.00011005 38664000 86312 80852 79661 79522 91225 69812 85778 83795 88941 96911 FALSE TRUE 82938.83162 78546.18012 94057.51475 83626.13995 94159.33497 71223.64647 86827.77682 82064.60397 78844.79055 90347.13165 0.918001824 0.869382112 1.041068079 0.925609241 1.042195068 0.788333234 0.961046303 0.908325505 0.872687258 1 16.46319118 2.764234448 24.98925376 0.90575329 0.956934891 0.120609501 0.071650178 1721.944559 1676026.714 0.020916722 0.022179631 581.07802 -2.764234448 0.051181601 SKEITVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKEITVR 7 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 105.57 0.0072026 1521850000 1862200 1861980 1522610 1555060 1678220 2017170 1909060 1965780 2020800 2057520 FALSE TRUE 1789423.165 1808878.153 1797779.497 1635316.833 1732201.47 2057958.559 1932423.647 1925185.956 1791407.256 1918162.338 0.93288411 0.943026624 0.937240536 0.8525435 0.903052592 1.072880287 1.007434881 1.003661639 0.933918481 1 20.87129339 2.765279358 24.89703617 1.004110687 0.913280697 0.568321023 0.039142261 540.4478883 503598.9402 0.012413742 0.013163085 582.477773 -2.765279358 -0.09082999 VGEAWQERPGAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGEAWQERPGAPR 13 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 ; 116.84 0.00050503 439450000 161658 176145 125343 141524 147365 169013 156722 166697 187926 171253 FALSE TRUE 155340.2266 171121.5171 147995.2683 148828.0706 152105.1291 172430.5587 158640.0107 163254.6487 166593.4283 159653.8818 0.972981207 1.071828102 0.926975697 0.932191995 0.952718013 1.080027349 0.993649568 1.022553582 1.043466194 1 17.2845881 2.765297971 24.90862733 1.025886034 0.972282268 0.296819092 0.043489385 1019.170076 949461.7641 0.01373813 0.014567653 582.5027377 -2.765297971 -0.053603767 DPQALSEHLKNPVIAQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DPQALSEHLKNPVIAQK 17 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 268.21 3.88E-28 6978700000 6466400 7634200 5179500 5098600 5781800 7466400 6437700 6923700 7968500 7384800 FALSE TRUE 6213685.939 7416480.091 6115550.867 5361739.357 5967776.848 7617375.724 6516486.498 6780723.175 7063949.287 6884620.918 0.902545836 1.077253226 0.888291591 0.778799504 0.866827225 1.106433573 0.946528004 0.98490872 1.026047675 1 22.71494579 2.765404075 24.99168699 1.004101008 0.904749801 0.325211811 0.078732582 1073.767077 999692.5781 0.025811053 0.027369889 582.645068 -2.765404075 -0.099351207 AEKDNAEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEKDNAEIR 9 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 107.55 0.0025123 4911090000 10696600 11368100 9120800 9787500 10524100 11575500 11787700 12145100 13360000 13035000 FALSE TRUE 10278565.05 11043892.92 10769131.45 10292634.05 10862617.23 11809564.54 11931961.4 11894299.44 11843428.81 12152127.84 0.845824302 0.908803221 0.886193068 0.846982042 0.893886024 0.971810427 0.981882478 0.978783271 0.974597121 1 23.53470562 2.765477321 3.451865498 0.981326785 0.875066333 0.893177407 0.018298825 0.073464484 1.847009953 0.00587204 0.005985908 582.7433431 -2.765477321 -0.106260451 S(ph)SEHLLRPSQVCPQRPLSQER ddPTM_BT-474_Pertuzumab_2h_R1 2 SSEHLLRPSQVCPQRPLSQER 21 2 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 S(0.976)S(0.024)EHLLRPSQVCPQRPLSQER;S(0.832)S(0.168)EHLLRPSQVCPQRPLSQER 183.91 2.16E-17 1420540000 125312 128560 88773 136169 121325 105043 112017 127860 121337 116965 TRUE FALSE 120414.6685 124893.5947 104816.2558 143196.6984 125227.5288 107167.0414 113387.8976 125219.6463 107563.3324 109042.8564 1.104287548 1.145362464 0.961239088 1.313214851 1.148424876 0.982797452 1.039847096 1.148352588 0.986431721 1 16.73453573 2.765534366 24.28084283 1.05016325 1.135411283 0.227724246 0.091679285 963.6546994 867446.9133 0.028392536 0.030106645 582.8198913 -2.765534366 0.085248033 GQFNFDHPDAFDNELILK ddPTM_BT-474_Pertuzumab_2h_R1 1 GQFNFDHPDAFDNELILK 18 0 A0A2R8Y653;Q9BZX2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 0 151.23 4.92E-08 85897000 105080 111700 97037 103740 99227 134700 122130 111770 136030 146030 FALSE TRUE 100973.3574 108514.4254 114573.7445 109094.0338 102418.7266 137423.7263 123624.6635 109461.9104 120588.4447 136139.258 0.741691698 0.797084007 0.84159225 0.801341475 0.752308541 1.009434959 0.908075049 0.804043683 0.885772748 1 17.05472363 2.765691844 24.99778814 0.899677863 0.791226199 0.529006912 0.061775843 758.6423819 698986.079 0.019963904 0.021169938 583.0312639 -2.765691844 -0.108451664 LLQAMEPVHVAR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLQAMEPVHVAR 12 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;; 154.28 7.14E-05 1193500000 1323400 1535180 1293170 1472220 1488470 1200670 1475580 1386630 1411830 1532200 FALSE TRUE 1271680.065 1491398.169 1526874.585 1548201.451 1536347.989 1224948.37 1493638.589 1357995.606 1251564.977 1428422.729 0.890268713 1.044087397 1.068923474 1.083853833 1.075555547 0.857553121 1.045655854 0.950695882 0.876186686 1 20.44599156 2.766186083 24.99326844 0.951972091 1.038051756 0.26091846 0.07216441 1031.634231 933336.6612 0.021905889 0.023230409 583.695148 -2.766186083 0.086079664 KFGNPGER ddPTM_BT-474_Pertuzumab_2h_R1 4 KFGNPGER 8 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 145.72 0.0009056 3228890000 3081120 3428930 2750470 2706170 3915360 3402180 4277560 4265890 4496990 4830950 FALSE TRUE 2960706.424 3331140.274 3247541.113 2845835.758 4041301.11 3470974.411 4329910.059 4177797.881 3986510.548 4503745.454 0.657387602 0.739637777 0.721075635 0.631882016 0.897320053 0.770686187 0.961402038 0.927627443 0.885154498 1 22.10269386 2.766207878 0.951264038 0.946516755 0.688762338 0.723010037 0.065460751 0.280149026 0.541034905 0.035163619 0.033623948 583.7244406 -2.766207878 -0.257754417 PTTHEKT(ph)T(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 PTTHEKTTK 9 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 2 PTTHEKT(1)T(1)K 59.245 0.072582 331210000 456860 528430 408660 478080 415720 317480 486170 16516 684320 415120 TRUE FALSE 439005.4061 513359.6938 482513.9526 502753.7661 429092.0113 323899.6631 492119.8939 16174.93883 606638.8625 387003.5526 1.134370481 1.326498659 1.246794634 1.299093413 1.108754709 0.836942351 1.271615959 0.041795324 1.567527891 1 18.56198728 2.766493598 1.556774722 0.813614987 1.260953911 0.085533381 0.377457333 0.616190635 3.002001494 0.150109834 0.148181908 584.1085961 -2.766493598 0.447338925 FAWAIDMADEDYEF ddPTM_BT-474_Pertuzumab_2h_R1 2 FAWAIDMADEDYEF 14 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 ; 109.66 0.0026813 13503800 53123 54832 33515 65052 52497 40353 43549 60499 40487 43676 FALSE TRUE 51046.89443 53268.24505 39571.90604 68409.34152 54185.61368 41168.96531 44081.96569 59249.67451 35891.0855 40717.78562 1.253675603 1.308230402 0.971858008 1.680085016 1.330760326 1.011080654 1.082621882 1.455130077 0.881459661 1 15.31337148 2.766747444 24.17885795 1.141813027 1.310777889 0.1904813 0.214843628 1064.762447 913358.1487 0.066900802 0.070943563 584.4501092 -2.766747444 0.168964863 T(ph)PPRDLPTIPGVTS(ph)PSSDEPPMEASQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.881)PPRDLPT(0.12)IPGVT(0.236)S(0.579)PS(0.137)S(0.047)DEPPMEASQSHLR 71.59 0.013353 166570000 57669 51650 42399 58515 46351 68200 56740 64830 50469 67334 TRUE FALSE 55415.23172 50176.99257 50061.44246 61534.96616 47841.92201 69579.05073 57434.40109 63491.23784 44739.9707 62773.40821 0.88278195 0.799335164 0.797494415 0.980271231 0.762136761 1.108416011 0.914947949 1.01143525 0.712721708 1 15.93786592 2.767120257 24.94664495 0.952420782 0.846842202 0.18679995 0.109500226 1179.219496 1030038.241 0.031934534 0.033865822 584.9520367 -2.767120257 -0.10557858 EDS(ph)LPEESSAPDFANLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDSLPEESSAPDFANLK 17 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 EDS(1)LPEESSAPDFANLK;EDS(1)LPEESSAPDFANLK 305.05 9.27E-47 577610000 637820 516460 304240 489460 805760 548970 678030 944490 906790 795780 TRUE FALSE 612893.2893 501731.0665 359222.9358 514721.0893 831678.0022 560070.5495 686327.934 924985.9514 803855.0008 741881.1118 0.826134106 0.676295782 0.484205528 0.693805357 1.121039462 0.754933022 0.92511849 1.246811567 1.083536146 1 19.50082848 2.767665581 0.856712272 1.114184211 0.655500572 0.509637907 0.156873504 0.469569194 0.742684534 0.101539897 0.098630409 585.6869955 -2.767665581 -0.45868364 KPELWSDNFTDFVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPELWSDNFTDFVK 14 1 F5H5B4;Q13043-2;Q13043 F5H5B4 STK4 Serine/threonine-protein kinase 4;Serine/threonine-protein kinase 4 37kDa subunit;Serine/threonine-protein kinase 4 18kDa subunit 0 ; 165.34 6.38E-06 536640000 449250 427350 331010 390030 407650 485800 539440 479770 518470 530590 FALSE TRUE 431692.8133 415162.3964 390830.8703 410159.495 420762.4325 495623.2088 546041.8281 469862.5818 459615.4592 494652.6667 0.872719066 0.839300835 0.790111722 0.829186867 0.850621983 1.001962068 1.103889385 0.949883855 0.929168061 1 18.91605633 2.767826776 5.025351571 0.999625586 0.832124561 0.746622664 0.046810168 0.101323435 7.056532731 0.015596071 0.016104038 585.9044228 -2.767826776 -0.167501024 GLGTDEDSLIEIICSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLGTDEDSLIEIICSR 16 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YMM1;H0YN52;H0YLE2 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ;;; 266.74 7.33E-27 543842000 536130 541359 207060 727497 482849 391774 322487 483696 475277 452092 FALSE TRUE 515177.4469 525919.9714 244480.348 765043.2074 498380.2766 399695.9387 326433.6924 473707.5086 421325.5475 421471.4062 1.222330719 1.247818864 0.580063901 1.815172266 1.182477077 0.948334651 0.7745097 1.123937476 0.99965393 1 18.68507523 2.768654888 7.178048223 0.972770248 1.211068855 0.148308338 0.288003018 0.453501256 86.59379166 0.088305654 0.092311543 587.0226904 -2.768654888 0.238298607 SGS(ph)MDPSGAHPSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 S(0.009)GS(0.988)MDPS(0.003)GAHPSVR 134.04 1.65E-05 0 179630 227220 152560 207220 188750 183440 167110 213560 183590 193210 TRUE FALSE 172609.861 220739.9081 180130.9857 217914.649 194821.3152 187149.2825 169155.1422 209149.9114 162749.6329 180123.7146 0.95828504 1.225490539 1.000040367 1.209805436 1.081597254 1.039004125 0.93910534 1.161145893 0.903543618 1 17.45862861 2.768811698 4.081085243 1.023806781 1.10464528 0.149503657 0.099723736 0.452899358 17.28680904 0.030106382 0.030898453 587.2346837 -2.768811698 0.080838499 NNFEGEVTKENLLDFIK ddPTM_BT-474_Pertuzumab_2h_R1 2 NNFEGEVTKENLLDFIK 17 1 P07237;H7BZ94;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 ; 198.96 1.25E-11 1920090000 2159760 1963390 1663080 1602420 1852890 2043490 1951850 2111120 2474500 2101250 FALSE TRUE 2075354.191 1907396.04 1963635.551 1685121.088 1912489.89 2084810.768 1975737.324 2067524.634 2193605.134 1958930.466 1.059432291 0.97369257 1.002401864 0.860225065 0.976292892 1.064259709 1.008579609 1.055435438 1.119797345 1 20.90163476 2.768924608 8.208712495 1.049758072 0.969445254 0.314951637 0.055221415 0.349162745 86.27014282 0.01716157 0.01800708 587.3873746 -2.768924608 -0.080312818 QQEEMMR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQEEMMR 7 0 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 78.77 0.080109 351090000 230800 270240 253290 315210 289360 214520 290530 235840 258810 341130 FALSE TRUE 221780.0808 262533.0198 299065.1374 331478.0259 298667.5272 218857.7414 294085.593 230969.8216 229430.9738 318024.9613 0.697366898 0.825510736 0.940382592 1.042301914 0.939132344 0.688177873 0.924724877 0.726263186 0.721424422 1 18.27878048 2.769226785 24.71569657 0.799139746 0.896793261 0.083402407 0.122269029 1283.879502 1034752.969 0.037786088 0.04007389 587.7962146 -2.769226785 0.097653515 GPQGPGGGGINVQEILTSIMGS(ph)PNSHPSEELLKQPDYSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPQGPGGGGINVQEILTSIMGSPNSHPSEELLKQPDYSDK 40 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 GPQGPGGGGINVQEILT(0.005)S(0.028)IMGS(0.668)PNS(0.15)HPS(0.15)EELLKQPDYSDK;GPQGPGGGGINVQEILTS(0.001)IMGS(0.814)PNS(0.174)HPS(0.011)EELLKQPDYSDK 180.11 3.68E-24 197466000 140066 132191 108306 99573 112446 145287 128174 127631 167873 132298 TRUE FALSE 134592.0659 128421.0421 127879.3035 104711.9745 116062.9277 148224.8027 129742.6318 124995.3752 148816.7608 123337.3386 1.091251582 1.041217879 1.036825546 0.848988438 0.941020205 1.201783696 1.051933123 1.013443104 1.206583201 1 16.9122501 2.76967936 24.96058279 1.085152099 0.989163492 0.246883202 0.089002893 1083.905756 869407.0855 0.028234479 0.029944873 588.4090717 -2.76967936 -0.095988607 DLDELSRYPEDK ddPTM_BT-474_Pertuzumab_2h_R1 6 DLDELSRYPEDK 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 205.96 8.72E-08 12831410000 13522900 12341450 9187480 9207630 11034030 12092900 11548510 12917960 13940150 12773940 FALSE TRUE 12994410.12 11989483.93 10847862.01 9682836.888 11388949.6 12337426.72 11689844.12 12651199.61 12357722.61 11908749.67 1.09116494 1.006779407 0.910915278 0.813085938 0.956351415 1.035996815 0.981618092 1.062344912 1.037701099 1 23.50551861 2.770491058 6.888471177 1.026763441 0.947821283 0.189393521 0.069153028 0.348174799 57.71901769 0.0231867 0.024246791 589.5098395 -2.770491058 -0.078942158 MLAES(ph)DESGDEESVSQTDKTELQNTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 MLAES(0.832)DES(0.168)GDEESVSQTDKTELQNTLR 86.304 0.0049696 312330000 33315 34741 31920 36775 36606 44070 50137 51221 51849 46953 TRUE FALSE 32013.01297 33750.22069 37688.65406 38672.96216 37783.46523 44961.12559 50750.5916 50163.26845 45963.31889 43772.83149 0.731344349 0.771031244 0.861005623 0.883492359 0.863171606 1.027146841 1.15940847 1.145990943 1.050042168 1 15.41774809 2.770515832 1.694212756 1.110302198 0.806363985 0.823441119 0.059489272 0.141801529 0.811892386 0.024016943 0.023965253 589.543468 -2.770515832 -0.303938213 KEELLK ddPTM_BT-474_Pertuzumab_2h_R1 4 KEELLK 6 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ;;; 102.71 0.056608 9048000000 6187620 6002910 5157020 4943150 6028150 6850750 6872780 7458010 8110650 8177490 FALSE TRUE 5945800.97 5831712.884 6089008.231 5198266.564 6222050.919 6989276.859 6956891.138 7303999.487 7189963.015 7623621.319 0.779918194 0.764953116 0.798702871 0.681863165 0.816154247 0.916792239 0.912544163 0.958074802 0.943116495 1 22.86204503 2.770840881 2.515593551 0.947038288 0.758826515 0.865304158 0.035751881 0.098544913 1.232931833 0.011973964 0.012174652 589.9848794 -2.770840881 -0.188211773 AKAEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AKAEKPPLSASSPQQRPPEPETGESAGTSR 30 3 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AKAEKPPLS(0.001)AS(0.146)S(0.853)PQQRPPEPETGESAGTSR;AKAEKPPLSAS(0.026)S(0.974)PQQRPPEPETGESAGTSR;AKAEKPPLSAS(0.062)S(0.938)PQQRPPEPETGESAGTSR 169.23 1.45E-12 1220020000 473931 465734 484814 419755 475920 549457 567273 551201 589830 641141 TRUE FALSE 455409.2526 452451.7223 572430.6744 441418.6059 491228.399 560567.397 574215.4567 539818.5067 522874.9712 597715.949 0.761915845 0.756967792 0.957696838 0.738508997 0.821842549 0.937849154 0.960682842 0.903135524 0.874788387 1 19.18910051 2.770895583 5.85298534 0.929477856 0.808397 0.493952254 0.0646479 0.176575967 18.75894729 0.019886797 0.020697715 590.0591954 -2.770895583 -0.121080857 GDFCIQVGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GDFCIQVGR 9 0 Q32Q12;P22392-2;J3KPD9;P22392;E7ERL0;O60361;P15531;P15531-2 Q32Q12;O60361;P15531 NME1-NME2;NME2;NME1;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase;Nucleoside diphosphate kinase A 0 ;;;;; 158.07 0.00015607 7507270000 5360510 6164230 4772630 4372770 4700460 4979990 3992270 3598490 4489920 4651830 FALSE TRUE 5151015.343 5988432.196 5635150.408 4598449.184 4851654.565 5080688.81 4041128.594 3524179.924 3980243.105 4336757.411 1.187757316 1.380854779 1.299392582 1.060342728 1.118728604 1.17154093 0.93183183 0.812630173 0.917792426 1 22.04818531 2.771005239 0.790218343 0.87678813 1.289035511 0.686655513 0.094669663 0.349213031 0.472269793 0.065627915 0.065328356 590.2082 -2.771005239 0.412247381 ISQMPVILTPLHFDRDPLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISQMPVILTPLHFDRDPLQK 20 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 198.31 8.82E-22 1328050000 980770 932700 787590 808000 860680 965590 956030 901120 1055870 1065280 FALSE TRUE 942440.4241 906100.3092 929925.0328 849700.9768 888364.5538 985114.8914 967730.1811 882511.5571 936012.0642 993127.6367 0.948962036 0.91237045 0.936360039 0.855580839 0.894511965 0.991931807 0.974426796 0.888618466 0.942489192 1 19.92161962 2.771055349 24.9305855 0.948643638 0.908203738 0.283498143 0.037742582 1071.608296 822156.6588 0.012271788 0.013014953 590.2763035 -2.771055349 -0.0404399 EELRQEWEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EELRQEWEAK 10 1 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 152.64 1.61E-05 263770000 317090 332340 261100 283460 304630 356010 337320 381710 389270 408480 FALSE TRUE 304697.7722 322861.9886 308286.5781 298089.4046 314428.7006 363208.7661 341448.2231 373827.5551 345081.7016 380813.2858 0.800123797 0.847822281 0.809547854 0.782770496 0.825676814 0.953771257 0.896628967 0.981655759 0.906170332 1 18.53872429 2.771561606 5.285891444 0.945479768 0.812197717 0.809101676 0.032672515 0.079366377 6.208559491 0.009728675 0.010095538 590.9647893 -2.771561606 -0.133282051 NPRPGEENGKDYYFVTR ddPTM_BT-474_Pertuzumab_2h_R1 4 NPRPGEENGKDYYFVTR 17 2 B1ANH0;B1ANG9;Q16774;Q16774-2;B1ANH2;Q16774-3;B1ANH6 B1ANH0 GUK1 Guanylate kinase 0 ;;; 209.23 2.51E-12 1488520000 874550 904432 713036 877530 867110 1025570 1082900 1151370 1090410 970090 FALSE TRUE 840371.6191 878638.4849 841897.4666 922819.4285 895001.3806 1046307.728 1096152.854 1127593.807 966631.2282 904384.9402 0.929218944 0.97153153 0.93090611 1.020383453 0.989624374 1.156927412 1.212042356 1.246807368 1.068827205 1 19.78657744 2.77241762 3.341698377 1.168097307 0.965044441 0.563181742 0.071995302 0.15555584 3.594863464 0.023261447 0.023807827 592.1307565 -2.77241762 -0.203052866 IKQEILPEER ddPTM_BT-474_Pertuzumab_2h_R1 6 IKQEILPEER 10 1 O75534-2;O75534;O75534-3;O75534-4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;;;; 158.4 7.30E-06 3919440000 6199710 6270430 5402890 6113520 6071970 6700390 6610080 7544670 7579440 7821890 FALSE TRUE 5957418.479 6091603.476 6379312.41 6429039.5 6267280.429 6835876.477 6690976.136 7388869.928 6719053.747 7292106.423 0.81696812 0.835369525 0.87482437 0.881643674 0.859460911 0.937435095 0.917564247 1.013269623 0.921414658 1 22.79790419 2.773212153 0.488647452 0.99737914 0.815679405 0.780001809 0.029045727 0.47378877 0.23370145 0.0259274 0.035888054 593.21504 -2.773212153 -0.181699735 DITLFHAMDTLYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DITLFHAMDTLYR 13 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8 Q9BTC8 MTA3 Metastasis-associated protein MTA3 0 ; 179.93 7.86E-07 233870000 503060 561160 439700 546610 531980 405350 508720 487540 527300 506390 FALSE TRUE 483399.859 545156.2662 519163.5711 574820.6076 549091.6198 413546.4547 514945.8675 477472.1286 467443.1146 472091.7543 1.023953193 1.154767609 1.099709043 1.217603575 1.163103602 0.875987456 1.090774967 1.011396883 0.990153101 1 18.84870776 2.773448381 24.96920593 1.00386617 1.136082868 0.507136274 0.067665954 512.3279691 366672.6251 0.020168445 0.021391045 593.5377971 -2.773448381 0.132216697 AGSS(ph)SPEPWARPSCTPQEGGCPRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGSSSPEPWARPSCTPQEGGCPRPK 25 2 Q86VE0 Q86VE0 MYPOP "Myb-related transcription factor, partner of profilin" 1 AGS(0.06)S(0.47)S(0.47)PEPWARPSCTPQEGGCPRPK 128.92 5.55E-05 133510000 128800 133110 92575 113920 112340 135120 126950 134490 126060 134290 TRUE FALSE 123766.3536 129313.8331 109305.3618 119799.4249 115953.5181 137852.219 128503.6521 131712.7345 111750.1973 125194.4187 0.988593221 1.032904138 0.873084942 0.956907074 0.9261876 1.101105148 1.026432755 1.052065546 0.892613253 1 16.93381072 2.773458951 24.99656604 1.021470223 0.955329281 0.177302702 0.062536171 977.4857425 700140.0537 0.019072449 0.020228594 593.5522436 -2.773458951 -0.066140941 HIAELIFYMEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIAELIFYMEELR 13 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 146.5 4.23E-05 65243000 51360 61580 50409 48339 53995 32211 55222 37139 47846 49664 FALSE TRUE 49352.79442 59823.79869 59519.02764 50833.78158 55731.79821 32862.32849 55897.82335 36372.06667 42414.72267 46300.21304 1.06593018 1.292084739 1.285502241 1.097916797 1.203705006 0.709766248 1.207290846 0.785570179 0.916080508 1 15.49873121 2.773500547 24.65315798 0.923943605 1.195051221 0.474142854 0.139617457 426.5733199 300983.7208 0.040261751 0.042702119 593.6090956 -2.773500547 0.271107616 LVQEQGSHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVQEQGSHSK 10 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 151.98 0.0060589 0 266000 282910 231700 255100 250210 292840 277060 269560 320230 310230 FALSE TRUE 255604.4259 274841.6838 273573.3441 268265.7416 258258.2319 298761.4254 280450.7432 263993.4918 283878.8329 289217.8458 0.883778196 0.950292964 0.945907551 0.927555977 0.892953999 1.032997893 0.969686855 0.912784241 0.981539822 1 18.14179705 2.773651979 24.99996959 0.96819546 0.92362348 0.398825893 0.034947331 855.5711296 609528.9823 0.011278007 0.011961681 593.8161152 -2.773651979 -0.04457198 T(ph)PLTQDPASITDNLLQLPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPLTQDPASITDNLLQLPAR 20 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 T(0.832)PLT(0.167)QDPASIT(0.001)DNLLQLPAR 85.457 0.029564 29545000 26689 23286 21705 28839 27486 17296 16730 28371 25482 30127 TRUE FALSE 25645.96437 22621.90608 25627.57633 30327.38425 28370.11215 17645.73697 16934.74674 27785.12894 22589.39019 28086.47146 0.91310738 0.805437811 0.912452686 1.079786199 1.010098837 0.628264643 0.602950313 0.989270901 0.804280104 1 14.77758777 2.773678566 24.99926625 0.802883248 0.942240301 0.204765286 0.137126513 1077.779388 767232.3 0.044498704 0.047196384 593.852468 -2.773678566 0.139357052 LTDISVTDPEKYPHMLSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTDISVTDPEKYPHMLSVK 19 1 Q9Y333 Q9Y333 LSM2 U6 snRNA-associated Sm-like protein LSm2 0 109.77 0.0001495 186980000 334980 301420 247970 232490 269210 328900 324280 312080 330380 284890 FALSE TRUE 321888.6113 292823.7967 292783.6951 244488.8368 277869.3841 335550.5833 328248.6356 305635.4389 292876.6475 265594.1465 1.211956722 1.102523533 1.102372544 0.920535486 1.046218028 1.263396004 1.235903125 1.150761201 1.102722523 1 18.01886383 2.773691826 24.83302376 1.166061506 1.070902795 0.118389527 0.09554073 974.2400504 688654.3651 0.029844093 0.031653594 593.8706002 -2.773691826 -0.095158711 KPPAPPSPVQSQS(ph)PSTNWSPAVPVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KPPAPPSPVQSQS(0.953)PS(0.037)T(0.009)NWSPAVPVKK 142.79 1.43E-07 362310000 193260 166930 114410 130900 146440 187420 163730 166240 210130 188590 TRUE FALSE 185707.1855 162169.3198 135086.432 137655.7647 151150.3756 191209.7608 165733.7767 162807.0859 186276.9233 175816.6313 1.056254941 0.922377585 0.768337051 0.782950758 0.859704651 1.087552181 0.942651304 0.926005035 1.059495464 1 17.42371202 2.774019499 24.68912011 0.987561212 0.869029991 0.328981102 0.087560457 691.979921 481806.7243 0.02849447 0.030221934 594.3188411 -2.774019499 -0.118531221 SYS(ph)FDEIRK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSFDEIRK 9 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 1 S(0.042)YS(0.958)FDEIRK;S(0.194)Y(0.009)S(0.797)FDEIRK 85.813 0.008919 362820000 400650 315080 252920 330320 353070 334700 393910 522350 292160 271810 TRUE FALSE 384992.1551 306094.2269 298628.2702 347367.8548 364426.8172 341467.8633 398730.7884 511563.29 258995.2216 253400.0666 1.519305659 1.207948486 1.178485366 1.370827796 1.438148072 1.347544489 1.573522824 2.018796983 1.022080322 1 17.95105738 2.774236253 1.653174825 1.531160353 1.306809405 0 0.296389876 0.948536499 5.182242532 0.117532798 0.117379605 594.6155377 -2.774236253 -0.224350947 HSGDYFTLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSGDYFTLLR 10 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 145.46 3.04E-05 66866000 47837 53252 46269 56621 55347 41753 57028 45884 54190 58567 FALSE TRUE 45967.47715 51733.3051 54630.83755 59543.2166 57127.28652 42597.27427 57725.92572 44936.47937 48038.57838 54600.20492 0.841892026 0.947492874 1.000561035 1.09053101 1.046283372 0.78016693 1.057247419 0.823009354 0.879824141 1 15.73661875 2.774556966 24.9950003 0.903563113 0.989936984 0.137621916 0.096085266 1111.908104 772080.3346 0.029271531 0.031046308 595.0548049 -2.774556966 0.086373871 VMVTDADR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMVTDADR 8 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 0 137.88 0.0016961 344650000 375590 418020 317720 375990 383450 279850 372740 340790 341230 390850 FALSE TRUE 360911.5276 406098.4789 375139.0716 395394.889 395784.0175 285508.7587 377301.7036 333752.5674 302495.001 364377.3814 0.990488285 1.114499691 1.029534463 1.085124679 1.086192606 0.783552364 1.035469606 0.915953032 0.830169534 1 18.47507388 2.774726289 24.999004 0.918806658 1.063704359 0.492033692 0.075122512 488.5178171 337680.1473 0.021653974 0.022966865 595.2868507 -2.774726289 0.144897701 KAGTQIENIEEDFRDGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAGTQIENIEEDFRDGLK 18 2 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ; 223.36 2.92E-19 535200000 771540 763610 584850 539950 642480 803700 640190 821180 865430 745130 FALSE TRUE 741387.3638 741832.5905 690545.4049 567816.8842 663145.9527 819951.3647 648024.8367 804222.346 767190.0146 694661.6814 1.067263941 1.067904867 0.994074416 0.817400613 0.954631543 1.180360723 0.932863945 1.15771802 1.104408139 1 19.40595099 2.774922114 24.79144439 1.078869131 0.976844765 0.203626308 0.093481599 849.0048329 578853.9346 0.029404321 0.031186999 595.5553279 -2.774922114 -0.102024367 KQTIDNSQGAYQEAFDISK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQTIDNSQGAYQEAFDISK 19 1 P27348 P27348 YWHAQ 14-3-3 protein theta 0 ; 150.69 1.17E-07 1289790000 815820 755300 743370 771480 801900 867920 901610 953680 1085390 1024040 FALSE TRUE 783936.8525 733759.5835 877713.4952 811296.1753 827693.8418 885469.9371 912644.1729 933986.1747 962181.0775 954680.8587 0.821150697 0.76859149 0.91937896 0.849808779 0.866984851 0.927503604 0.955967813 0.97832293 1.007856258 1 19.86465901 2.775325578 0.509928994 1.015977143 0.798121954 0.813741126 0.032928275 0.416254377 0.225347441 0.028772236 0.038281783 596.1088621 -2.775325578 -0.217855189 KTAHNSEADLEESFNEHELEPS(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTAHNSEADLEESFNEHELEPSSPK 25 1 Q8IWS0-5;Q8IWS0 Q8IWS0-5 PHF6 PHD finger protein 6 1 KTAHNSEADLEESFNEHELEPS(0.5)S(0.5)PK 151.73 6.61E-08 93172000 84938 119390 88359 95263 88792 97617 91565 79255 104880 114270 TRUE FALSE 81618.52906 115985.1141 104327.4368 100179.5348 91648.07532 99590.88262 92685.59986 77618.35655 92974.46209 106530.3911 0.766152534 1.088751415 0.979320884 0.940384559 0.860299811 0.934858885 0.870039046 0.728602944 0.872750594 1 16.70090554 2.775369872 1.230123946 0.839005597 0.954705447 0.035434597 0.100687441 0.772311922 2.41760509 0.045825323 0.044525922 596.1696626 -2.775369872 0.11569985 TSS(ph)LTQFPPSQSEER ddPTM_BT-474_Pertuzumab_2h_R1 7 TSSLTQFPPSQSEER 15 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 T(0.001)S(0.023)S(0.977)LTQFPPSQSEER;T(0.001)S(0.022)S(0.978)LTQFPPSQSEER;TS(0.002)S(0.998)LTQFPPSQSEER;TSS(1)LTQFPPSQSEER;TSS(1)LTQFPPSQSEER;T(0.001)S(0.028)S(0.971)LTQFPPSQSEER;T(0.001)S(0.025)S(0.974)LT(0.001)QFPPSQSEER 337.49 4.09E-69 1233853000 2060697 1997859 1691656 1906626 1906934 1850539 1743185 2113549 2029633 1975172 TRUE FALSE 1980162.683 1940882.017 1997375.87 2005027.196 1968272.264 1887958.166 1764518.619 2069903.475 1799237.571 1841391.841 1.075361929 1.054029878 1.084709851 1.088865038 1.06890463 1.025288656 0.958252654 1.124097234 0.977107387 1 20.81236523 2.775666967 5.564882215 1.027838416 1.074975089 0.29630033 0.042671819 0.316282626 27.3003207 0.013494489 0.014073112 596.577633 -2.775666967 0.047136672 KKQQEEEAER ddPTM_BT-474_Pertuzumab_2h_R1 4 KKQQEEEAER 10 2 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;; 160.67 4.11E-06 631848000 962130 1065660 746150 865620 894710 1031420 971910 1003540 1096340 1063440 FALSE TRUE 924528.8959 1035268.42 880995.903 910294.7519 923489.1597 1052276.019 983804.5253 982816.5483 971888.0794 991412.2616 0.932537282 1.044236046 0.888627201 0.91817984 0.93148854 1.061390967 0.992326365 0.99132983 0.980306697 1 19.91912558 2.776320845 24.99238599 1.002382014 0.944236092 0.344094063 0.042742194 710.8353246 470479.818 0.013293426 0.014099588 597.4765233 -2.776320845 -0.058145921 ASSVSTKES(ph)PARK ddPTM_BT-474_Pertuzumab_2h_R1 5 ASSVSTKESPARK 13 2 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVS(0.039)T(0.039)KES(0.922)PARK;ASSVS(0.226)T(0.226)KES(0.547)PARK;ASSVS(0.176)T(0.24)KES(0.584)PARK;ASSVS(0.014)T(0.014)KES(0.971)PARK;ASS(0.001)VS(0.009)T(0.009)KES(0.982)PARK 142.94 3.20E-05 1737520000 1130265 1061693 956039 1040681 1033689 1187043 1153741 1131007 1202982 1307451 TRUE FALSE 1086092.994 1031414.555 1128816.514 1094390.671 1066938.545 1211045.823 1167860.827 1107651.31 1066424.527 1218896.179 0.891046352 0.846187372 0.926097344 0.897853886 0.875331766 0.993559454 0.958129862 0.908733105 0.874910058 1 20.21714382 2.776460874 24.97778376 0.939723642 0.88776048 0.358451123 0.039365881 727.7551962 479618.3105 0.012304893 0.013051058 597.6691979 -2.776460874 -0.051963162 QAGPASVPLRTEEEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAGPASVPLRTEEEFK 16 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 195.89 4.32E-11 596570000 506210 582090 406970 427340 457900 629510 523790 566430 647020 578620 FALSE TRUE 486426.7536 565489.3631 480518.532 449395.0686 472628.7694 642239.1235 530200.2987 554733.0226 573573.0021 539429.552 0.901742872 1.048309943 0.890790151 0.833093157 0.876164028 1.190589431 0.982890716 1.02836973 1.063295476 1 19.04107503 2.776882085 24.9994776 1.046705451 0.912360745 0.484209283 0.073635277 524.3171648 342043.7196 0.023008643 0.024403923 598.2491429 -2.776882085 -0.134344706 IIHTDIKPENILLSVNEQYIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IIHTDIKPENILLSVNEQYIR 21 1 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 ; 170.14 5.17E-12 697820000 869060 1013400 735210 718580 799800 955230 894540 881070 1026300 971920 FALSE TRUE 835096.1744 984498.8242 868078.8017 755665.9999 825526.2934 974545.4051 905487.6481 862875.5966 909798.7266 906090.9927 0.921647143 1.086534169 0.958048153 0.833984673 0.911085421 1.075549159 0.999334124 0.952305677 1.004092011 1 19.78929641 2.777183553 24.99484683 0.99853389 0.945136988 0.18954148 0.065060028 1225.29377 792947.2547 0.021614965 0.022925739 598.6645648 -2.777183553 -0.053396902 EADKSHPEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 EADKSHPEQR 10 1 O14745 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;; 159.09 4.68E-06 4075080000 7444100 6908610 5219600 5863610 5952770 6896390 6536720 6027170 7864790 7847950 FALSE TRUE 7153176.342 6711583.207 6162897.829 6166231.615 6144246.253 7035839.731 6616718.335 5902706.833 6972012.011 7316401.356 0.977690533 0.91733393 0.842340042 0.842795702 0.83979076 0.961653057 0.904367873 0.806777341 0.952929134 1 22.80270279 2.777340065 24.97132957 0.902815536 0.881240166 0.040887307 0.063212719 2822.143846 1817264.633 0.020412158 0.021649785 598.8803515 -2.777340065 -0.021575371 EVWALVQAGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVWALVQAGIR 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 114.5 0.0029071 60225000 83533 101510 78011 72901 98959 56277 98351 70864 97857 82993 FALSE TRUE 80268.43801 98615.03419 92109.32305 76663.42935 102142.1061 57414.9595 99554.64896 69400.63364 86748.68361 77371.81019 1.037437767 1.274560256 1.190476516 0.990844458 1.320146263 0.74206561 1.286704405 0.8969757 1.121192375 1 16.23952041 2.777617461 24.99842527 1.017405657 1.160904218 0.185077332 0.160382864 939.0414088 601034.1445 0.045009837 0.047739474 599.2629961 -2.777617461 0.143498561 LTPYEVDELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTPYEVDELR 10 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 136.99 0.0002398 279260000 227340 231900 207723 243100 227280 222182 217065 240360 235070 258680 FALSE TRUE 218455.3015 225286.4391 245263.1669 255646.4201 234590.6676 226674.6723 219721.5064 235396.482 208385.8391 241159.3732 0.905854492 0.934180729 1.017016936 1.060072502 0.972761973 0.939937226 0.911104982 0.976103391 0.864100103 1 17.87962736 2.777734399 4.940497053 0.937685114 0.98274977 0.126048202 0.051916321 0.425404 25.95648467 0.016877704 0.017554233 599.4243742 -2.777734399 0.045064656 HEGALETLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 HEGALETLLR 10 0 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 177.57 2.31E-06 650840000 597819 578854 584251 648091 620779 508216 655697 491643 674500 723258 FALSE TRUE 574455.5726 562345.6507 689838.1523 681539.0542 640746.9203 518492.4757 663721.616 481490.4002 597933.5877 674271.0914 0.8519653 0.83400528 1.023087243 1.010778992 0.950280871 0.768967382 0.984354252 0.714090232 0.886785145 1 19.36296922 2.777864229 24.80145851 0.851352627 0.937679163 0.075917443 0.098773127 945.4391301 596591.6837 0.030163259 0.031992475 599.6035968 -2.777864229 0.086326536 EAAELEEASAES(ph)EDEMIHPEGVASLLPPDFQSSLERPELELSR ddPTM_BT-474_Pertuzumab_2h_R1 5 EAAELEEASAESEDEMIHPEGVASLLPPDFQSSLERPELELSR 43 1 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAAELEEAS(0.165)AES(0.835)EDEMIHPEGVASLLPPDFQSSLERPELELSR;EAAELEEAS(0.032)AES(0.968)EDEMIHPEGVASLLPPDFQSSLERPELELSR;EAAELEEAS(0.137)AES(0.863)EDEMIHPEGVASLLPPDFQSSLERPELELSR;EAAELEEAS(0.187)AES(0.813)EDEMIHPEGVASLLPPDFQSSLERPELELSR;EAAELEEAS(0.006)AES(0.994)EDEMIHPEGVASLLPPDFQSSLERPELELSR 247.32 1.94E-55 492646000 41093.7 44644.6 40240.5 49760.5 45084.9 37714.2 46928.2 42017.5 44746.9 44838 TRUE FALSE 39487.71277 43371.37972 47512.8535 52328.64537 46535.09675 38476.80696 47502.52135 41149.82394 39667.41951 41801.08232 0.944657664 1.037565951 1.136641705 1.251849054 1.113251001 0.920473941 1.136394531 0.984420059 0.948956757 1 15.35125268 2.778023196 24.68155489 1.007576516 1.104330742 0.225796699 0.090027273 762.6237741 476975.6395 0.028993879 0.030752227 599.8231128 -2.778023196 0.096754225 DFIHTASISFLTPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFIHTASISFLTPLR 15 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 184.76 4.51E-07 374950000 264431 295990 252800 257690 260913 228943 240293 216757 247308 277850 FALSE TRUE 254096.7442 287548.655 298486.5835 270989.4118 269305.5036 233572.3843 243233.7776 212280.8922 219234.6326 259030.972 0.980951205 1.110093719 1.152320053 1.046166061 1.039665263 0.901716048 0.939014264 0.819519344 0.846364552 1 17.98276508 2.778107001 1.737115339 0.878699761 1.08316692 0.626109367 0.063028415 0.206870984 1.242851657 0.023686983 0.0238176 599.9388708 -2.778107001 0.204467159 HHQEEDAGPTQPS(ph)PAKPQLK ddPTM_BT-474_Pertuzumab_2h_R1 3 HHQEEDAGPTQPSPAKPQLK 20 1 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70;H7C171;C9JKY0 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 HHQEEDAGPTQPS(1)PAKPQLK;HHQEEDAGPT(0.043)QPS(0.957)PAKPQLK;HHQEEDAGPTQPS(1)PAKPQLK 252.84 2.63E-36 661890000 549020 488380 449790 420720 350642 374220 393617 63420.6 458700 321703 TRUE FALSE 527563.6914 474451.8806 531077.0585 442433.4096 361920.7184 381786.9848 398434.2026 62110.94245 406630.299 299913.7693 1.759051252 1.581960981 1.770765843 1.475202058 1.206749257 1.272989185 1.328495866 0.207096002 1.355824042 1 18.19418823 2.779042621 0.867047941 0.813047638 1.706280424 0.480419574 0.309210783 0.455177059 0.738265054 0.191425786 0.187865846 601.2327391 -2.779042621 0.893232786 MSDDVHSLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 MSDDVHSLGK 10 0 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 0 134.68 0.00016435 213560000 433330 461970 379200 414070 398620 473080 442850 425390 491400 539650 FALSE TRUE 416394.9845 448795.0679 447729.8753 435440.2023 411441.9743 482646.0017 448269.7308 416605.5478 435618.3321 503099.0248 0.827660091 0.892061097 0.889943834 0.865515894 0.81781509 0.95934593 0.891016895 0.828078623 0.865869959 1 18.94048287 2.779151261 24.99659626 0.891092165 0.862583848 0.152042173 0.050967006 1576.639361 970925.523 0.015822539 0.016782134 601.3831572 -2.779151261 -0.028508317 RFQILGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFQILGK 7 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 84.097 0.034947 398520000 350730 426770 334740 403430 348140 299340 305610 291350 290010 318810 FALSE TRUE 337023.0838 414598.9375 395234.9643 424251.0706 359338.2393 305392.8599 309350.1466 285333.5207 257089.2806 297216.7147 1.133930453 1.394938161 1.329787137 1.42741323 1.209010871 1.027509036 1.040823518 0.960018419 0.864989309 1 18.18115573 2.779343977 2.199057278 0.968100462 1.328189048 0.789662366 0.084382084 0.134203127 1.278618908 0.029438128 0.029985499 601.6500779 -2.779343977 0.360088586 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_BT-474_Pertuzumab_2h_R1 1 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 36 3 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 196.38 3.21E-30 809330000 484960 385660 342490 323290 402170 435320 441780 474810 567820 408350 FALSE TRUE 466007.227 374661.3544 404385.5616 339975.0356 415106.1633 444122.4687 447186.6358 465005.0076 503363.4541 380692.0908 1.224105355 0.984158493 1.062237886 0.893044652 1.090398706 1.166618586 1.174667524 1.22147273 1.322232498 1 18.53826507 2.779984821 3.113855115 1.195605698 1.034760331 0.254275336 0.107648767 0.299478707 5.865519584 0.034129568 0.035047598 602.538526 -2.779984821 -0.160845367 AIIESDQEQGRK ddPTM_BT-474_Pertuzumab_2h_R1 3 AIIESDQEQGRK 12 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;; 163.51 9.59E-05 1300030000 771800 826830 648940 743640 797590 913430 903570 992880 1094170 1023380 FALSE TRUE 741637.2027 803249.618 766217.8936 782019.3495 823245.2067 931900.1804 914628.1599 972376.681 969964.4087 954065.5611 0.777344066 0.841922873 0.803108219 0.819670452 0.862881169 0.976767445 0.958663846 1.019192727 1.016664314 1 19.86372888 2.780003563 1.458765245 1.006072157 0.807632125 0.947384289 0.020797594 0.078759773 0.339438357 0.008317262 0.008251031 602.5645298 -2.780003563 -0.198440032 RKAEDS(ph)DS(ph)EPEPEDNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RKAEDSDSEPEPEDNVR 17 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 2 RKAEDS(1)DS(1)EPEPEDNVR;RKAEDS(1)DS(1)EPEPEDNVR 91.416 0.017515 756960000 1466240 1442970 978060 1156360 1318750 1328360 1159930 1303320 1307080 1176770 TRUE FALSE 1408937.72 1401817.908 1154817.199 1216039.878 1361168.791 1355220.349 1174125.57 1276405.987 1158705.758 1097066.32 1.284277618 1.277787754 1.052641192 1.108447007 1.240735192 1.235313057 1.070241196 1.163472038 1.056185699 1 20.06521931 2.780141428 0.024384245 1.06E-06 2.318460743 0.445941904 0.074027913 433.3684502 4.023881027 177.775458 203.9086882 602.7558413 -2.780141428 2.318459681 HDELTYF ddPTM_BT-474_Pertuzumab_2h_R1 2 HDELTYF 7 0 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 ; 126.68 0.0091404 232650000 619680 685140 567860 791290 648720 608790 681700 394200 886800 857140 FALSE TRUE 595462.2205 665600.478 670484.934 832128.5717 669586.668 621100.1509 690042.8485 386059.6322 786134.1818 799085.1443 0.745179941 0.832953137 0.839065697 1.041351573 0.837941579 0.777264044 0.86354108 0.48312703 0.983792763 1 19.60798971 2.780150385 3.921396192 0.767133357 0.8685085 0 0.154511286 0.62289509 20.70575732 0.050090664 0.051761565 602.7682727 -2.780150385 0.101375143 GAGAFGYFEVTHDITK ddPTM_BT-474_Pertuzumab_2h_R1 1 GAGAFGYFEVTHDITK 16 0 P04040 P04040 CAT Catalase 0 202.89 2.92E-11 488530000 241940 323240 252970 297020 298330 243200 292260 263150 331320 322870 FALSE TRUE 232484.7173 314021.5117 298687.3063 312349.2378 307926.0554 248117.6706 295836.7653 257715.8605 293709.9426 301001.7273 0.772370044 1.043254849 0.992310938 1.037699154 1.02300428 0.824306468 0.982840756 0.856193959 0.975774941 1 18.19941224 2.780589888 24.99832881 0.918449523 0.98217681 0.053302424 0.089119763 1103.652399 656432.4204 0.025932243 0.027505075 603.3785793 -2.780589888 0.063727287 DGKPEMNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGKPEMNK 8 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 70.977 0.045541 380570000 304070 402570 280910 357020 464960 521980 566460 654970 722680 696990 FALSE TRUE 292186.6082 391089.0978 331676.6858 375445.845 479915.8607 532534.7932 573392.5069 641444.6406 640644.3961 649782.2465 0.4496685 0.601877167 0.510442825 0.577802559 0.738579521 0.819558854 0.88243794 0.987168615 0.985937058 1 19.3095968 2.780605659 0.797834368 1.006528026 0.498819486 0.962243957 0.038658094 0.105336769 0.145431365 0.024375012 0.02445047 603.4004906 -2.780605659 -0.50770854 down GKEDKENR ddPTM_BT-474_Pertuzumab_2h_R1 3 GKEDKENR 8 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ;; 81.594 0.01263 208934000 434757 417643 308834 316454 379155 433031 467229 441568 440127 524952 FALSE TRUE 417766.2158 405732.2306 364647.1738 332786.2289 391350.8649 441787.1835 472947.0883 432449.4665 390165.6281 489396.5335 0.853635421 0.829045984 0.745095539 0.679993024 0.799660067 0.902718253 0.966388309 0.883638189 0.797238234 1 18.90064436 2.780650589 4.531831052 0.906503143 0.774757704 0.485025114 0.066337182 0.194926245 9.276980482 0.021746926 0.022593414 603.462919 -2.780650589 -0.13174544 TIAECLADELINAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIAECLADELINAAK 15 0 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ; 264.72 8.78E-25 66762000 148978 134599 108434 123054 126722 171134 140241 162512 163200 165504 FALSE TRUE 143155.7751 130760.3683 128030.4359 129404.8317 130798.1282 174594.4467 141957.3113 159156.0704 144674.2202 154294.2667 0.927810075 0.847473928 0.829780903 0.83868853 0.847718655 1.131567948 0.920042685 1.031509944 0.937651303 1 17.23532493 2.781284671 24.97900499 1.00117528 0.85501993 0.603678804 0.059037278 302.7887223 177027.6135 0.016841748 0.017863276 604.3446344 -2.781284671 -0.14615535 AQS(ph)YDIQAWK ddPTM_BT-474_Pertuzumab_2h_R1 3 AQSYDIQAWK 10 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 AQS(1)YDIQAWK;AQS(1)YDIQAWK;AQS(1)YDIQAWK 177.81 2.40E-06 1185370000 1249340 1259000 994560 1666860 1219750 1077070 1048510 1227520 982380 1043220 TRUE FALSE 1200514.412 1223094.553 1174299.116 1752886.844 1258984.366 1098849.093 1061341.979 1202171.283 870864.3409 972561.7802 1.234383703 1.257600882 1.207428813 1.802339841 1.294503231 1.129850171 1.091284894 1.236087319 0.89543344 1 19.89143037 2.781656502 4.144253492 1.097283388 1.374226609 0.396400584 0.177994461 0.258779632 9.789591538 0.058254636 0.060370325 604.8622793 -2.781656502 0.276943221 VVEAVNS(ph)DSDSEFGIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VVEAVNS(0.908)DS(0.092)DSEFGIPK;VVEAVNS(0.9)DS(0.1)DSEFGIPK 267.32 9.65E-28 156367000 93651 88097 58831 97007 85737 83770 95629 110673 104598 92145 TRUE FALSE 89991.01538 85584.55982 69463.07039 102013.5429 88494.80847 85463.8868 96799.33631 108387.5639 92724.47355 85903.93708 1.047577311 0.996282158 0.808613351 1.187530471 1.030160101 0.994877414 1.126832362 1.261729876 1.079397251 1 16.39043663 2.782775677 0.967930282 1.144698019 0.982727665 0.133894302 0.109125687 0.786506182 1.573649323 0.06180285 0.060105915 606.4230175 -2.782775677 -0.161970354 WRPEDAEEAEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 WRPEDAEEAEHR 12 1 F8W8D3;Q14493;E7EUV9;H0YAE8 F8W8D3 SLBP Histone RNA hairpin-binding protein 0 145.17 3.83E-05 294960000 338570 379500 249580 327360 309120 262700 275540 270300 249810 314640 FALSE TRUE 325338.3101 368677.0316 294684.6579 344255.0888 319063.1255 268011.974 278912.1409 264718.2105 221452.6161 293329.1525 1.109123683 1.25687143 1.004621107 1.173613621 1.087730704 0.913690207 0.950850396 0.902461308 0.754962861 1 18.16216094 2.782799366 2.792811904 0.898545389 1.136349726 0.647855541 0.082398207 0.167124787 2.590797389 0.026750523 0.027459407 606.4560957 -2.782799366 0.237804337 ENGLPLEYQEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ENGLPLEYQEK 11 0 O75223;M0QZK8;O75223-3 O75223 GGCT Gamma-glutamylcyclotransferase 0 ;; 242.45 2.10E-15 732910000 1302860 1296510 1199450 1405350 1344040 1320810 1457050 1669810 1776690 1883240 FALSE TRUE 1251942.791 1259534.804 1416217.297 1477880.282 1387272.267 1347517.683 1474881.814 1635327.84 1575007.6 1755686.477 0.713078791 0.717403033 0.806645899 0.841767765 0.790159453 0.767516126 0.840059904 0.931446395 0.897089327 1 20.74360381 2.783050283 0.160581258 1.080859533 0.56491388 0.825430416 0.036499678 3.87539807 0.273283583 0.250294478 0.557174736 606.8065818 -2.783050283 -0.515945653 FYEEVHDLER ddPTM_BT-474_Pertuzumab_2h_R1 7 FYEEVHDLER 10 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6;F8VRJ2;F8VVB5;Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34;E9PNW0;E9PJJ2 P55209;Q99733 NAP1L1;NAP1L4 Nucleosome assembly protein 1-like 1;Nucleosome assembly protein 1-like 4 0 ;;;;;; 270.63 1.02E-23 23163377000 14590660 16244730 14384610 15912130 15789160 14469310 16424040 14964540 16971130 18219120 FALSE TRUE 14020440.88 15781446.21 16984229.01 16733356.94 16297032.67 14761889.36 16625042.31 14655517.02 15044638.47 16985122.77 0.825454197 0.929133478 0.99994738 0.985177273 0.959488659 0.869107015 0.978800244 0.862844338 0.885753884 1 24.01776831 2.783370185 24.8819604 0.911934781 0.945103394 0.01733719 0.060454684 1308.816381 726760.5275 0.018571507 0.019697962 607.2537214 -2.783370185 0.033168614 SKS(ph)PTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSPTLR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 S(0.081)KS(0.838)PT(0.081)LR 78.149 0.021874 363590000 330740 310680 292820 381630 344830 282580 364110 297780 342770 390190 TRUE FALSE 317814.3151 301819.7106 345739.0877 401325.97 355921.7701 288293.9612 368566.0871 291630.7389 303860.1866 363762.0838 0.873687306 0.829717346 0.950453891 1.103264985 0.978446589 0.79253439 1.013206443 0.801707358 0.835326715 1 18.47263565 2.783535772 24.99980935 0.88068888 0.949452591 0.081808576 0.09614567 1087.823301 604673.2585 0.030504636 0.032354892 607.4852977 -2.783535772 0.068763712 VFCMTEEELKEHLLGDSAIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VFCMTEEELKEHLLGDSAIDR 21 1 Q86TU7 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 0 83.245 0.001936 73617000 82483 73318 63644 59063 69898 72550 73753 79609 78102 73848 FALSE TRUE 79259.47317 71227.04243 75145.88655 62111.24851 72146.33265 74017.01071 74655.61128 77965.04633 69236.18839 68846.20918 1.151253992 1.034581908 1.09150362 0.902173834 1.047934716 1.075106554 1.084382309 1.132452277 1.005664498 1 16.0710896 2.783806684 5.780483564 1.075057503 1.039202024 0 0.069258391 0.69922782 59.66065253 0.021548311 0.022614933 607.8643648 -2.783806684 -0.035855478 LKVTELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKVTELR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 97.093 0.011172 663380000 1935730 1909190 1640280 1817300 1860660 2102990 2109030 2184950 2306250 2289490 FALSE TRUE 1860079.532 1854741.77 1936715.084 1911091.071 1920509.819 2145513.899 2134840.94 2139830.019 2044454.169 2134420.803 0.871468048 0.868967248 0.907372661 0.895367525 0.899780313 1.005197239 1.000196839 1.002534278 0.957849626 1 21.0254132 2.784422635 5.100670286 0.994792961 0.88786833 0.909182993 0.016536972 0.057982774 3.614235429 0.005365474 0.005611027 608.7270971 -2.784422635 -0.106924631 TGGMAFHSYFMEAIAPPLLQELKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGGMAFHSYFMEAIAPPLLQELKK 24 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 112.58 0.0010266 335960000 276930 306950 213860 207020 233110 297300 260890 254950 349340 276640 FALSE TRUE 266107.2694 298196.0865 252509.2593 217704.327 240608.1949 303311.6097 264082.8499 249685.1934 309684.3878 257902.9264 1.031811749 1.156233823 0.979086445 0.84413283 0.932940926 1.176068895 1.023962208 0.968136333 1.200778883 1 17.97646862 2.784707697 24.99367987 1.059062773 0.989559491 0.143984404 0.100395143 1110.877815 601660.134 0.032920007 0.034916911 609.1267852 -2.784707697 -0.069503282 DLEPHSFGGLLEGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEPHSFGGLLEGIR 15 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 0 ; 196.18 9.06E-09 176457000 175138 188843 147425 169987 176104 158499 179618 166566 187350 206746 FALSE TRUE 168293.4133 183457.3825 174067.977 178760.0494 181768.5451 161703.9584 181816.2188 163126.3539 166082.8134 192742.9093 0.8731497 0.951824289 0.903109627 0.927453311 0.943062164 0.838961905 0.943309507 0.846341661 0.861680536 1 17.55631826 2.785345815 24.99628239 0.888983132 0.921010243 0.029894726 0.049427043 1005.135508 537019.3734 0.013979046 0.014827002 610.0224454 -2.785345815 0.032027111 IDRTDAISEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 IDRTDAISEEK 11 1 Q9NR31;Q9NR31-2;H0Y5E8 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ;;; 158.25 2.74E-05 1591920000 1555360 1561010 1258050 1409330 1561580 1629740 1673470 1880610 1904270 1785350 FALSE TRUE 1494574.812 1516491.523 1485407.62 1482065.69 1611809.639 1662694.459 1693950.426 1841774.746 1688105.253 1664426.654 0.897951741 0.911119465 0.892444024 0.890436167 0.968387303 0.998959284 1.017738103 1.106552062 1.014226279 1 20.66659387 2.78613676 1.409843401 1.050094897 0.897045072 0.805830285 0.029764166 0.158298424 0.639996326 0.012748627 0.012673123 611.1344412 -2.78613676 -0.153049825 VVLHDGDPNEPVSDYINANIIMPEFETK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVLHDGDPNEPVSDYINANIIMPEFETK 28 0 Q06124;Q06124-1;Q06124-3 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 52.329 0.083849 34534000 22743 24442 18671 21890 23320 22880 25302 25510 27514 27073 FALSE TRUE 21854.17842 23744.93809 22045.26503 23019.74552 24070.10898 23342.64928 25611.65344 24983.20959 24390.72607 25239.3216 0.865878203 0.940791455 0.873449191 0.912058806 0.953674959 0.924852484 1.014752055 0.989852659 0.966378037 1 14.62338551 2.786453276 1.046262832 0.993182198 0.896203756 0.688689364 0.026941644 0.280122988 0.648946905 0.013395317 0.013052452 611.5800022 -2.786453276 -0.096978442 RTES(ph)DSGLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTESDSGLKK 10 2 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7 Q12802-2 AKAP13 A-kinase anchor protein 13 1 RT(0.146)ES(0.853)DSGLKK 74.769 0.03229 201800000 140590 148360 103960 115030 167500 170420 161480 201390 212080 213660 TRUE FALSE 135095.5874 144128.9181 122747.8846 120966.7121 172887.7896 173866.0092 163456.2405 197231.2261 188005.5675 199188.6179 0.678229453 0.72358009 0.616239451 0.607297311 0.867960185 0.872871206 0.820610345 0.990173175 0.943856981 1 17.60377569 2.787355954 1.008148215 0.959242048 0.654856757 0.796910113 0.063304572 0.236440785 0.511039556 0.03517748 0.034323093 612.8524882 -2.787355954 -0.304385291 KLAAVTYNGVDNNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLAAVTYNGVDNNK 14 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 143.46 1.46E-05 310120000 159530 202350 165890 170130 178560 189170 195650 198600 204050 199040 FALSE TRUE 153295.3912 196579.1761 195870.0132 178910.4297 184303.5446 192995.147 198044.4232 194498.8406 180887.0994 185558.8435 0.826128188 1.059389962 1.055568193 0.96417086 0.993235036 1.040075177 1.067286363 1.048178771 0.974823382 1 17.50151723 2.787466212 5.75673139 1.034026698 0.987116861 0.101741945 0.065100578 0.501747916 40.33241932 0.019892532 0.020913203 613.0080988 -2.787466212 -0.046909837 ERS(ph)PS(ph)PPTIQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERSPSPPTIQSK 12 1 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 2 ERS(1)PS(1)PPTIQSK;ERS(1)PS(1)PPTIQSK 140.28 3.39E-05 1713760000 1154140 1113230 990870 1066810 1155200 1187840 1178930 1358340 1466070 1265480 TRUE FALSE 1109034.933 1081481.77 1169942.251 1121868.192 1192358.057 1211858.939 1193358.098 1330289.804 1299647.88 1179767.912 0.940045005 0.916690274 0.99167153 0.950922788 1.010671713 1.027201135 1.011519372 1.12758602 1.101613178 1 20.17007165 2.787777975 0.878959148 1.082398508 0.940178391 0.613973456 0.03929305 0.349256988 0.582379381 0.023392124 0.023125376 613.4483103 -2.787777975 -0.142220118 SGAQASST(ph)PLSPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SGAQAS(0.138)S(0.294)T(0.567)PLSPTR 153.22 7.21E-05 263010000 286940 313750 227300 227600 249200 248920 173460 231300 197760 199750 TRUE FALSE 275726.0676 304802.1572 268378.1663 239346.4633 257215.7443 253953.3329 175582.8554 226523.5742 175311.1139 186220.7546 1.48064091 1.63677866 1.441182895 1.2852835 1.381241016 1.363721963 0.942874793 1.216424961 0.941415549 1 17.50665435 2.788084254 0.504169427 0.973698871 1.593514885 0.756206402 0.112629065 0.505520417 0.266856771 0.097436851 0.132603142 613.8810877 -2.788084254 0.619816015 VKDGPGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKDGPGGK 8 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ; 92.062 0.010984 1683000000 5167900 5136200 3873400 4550700 5138700 5341800 5787400 6303700 5989000 6240000 FALSE TRUE 4965932.755 4989720.605 4573409.543 4785562.172 5303990.952 5449814.856 5858227.932 6173526.392 5309153.828 5817359.242 0.85364038 0.857729495 0.786165914 0.822634803 0.911752349 0.936819376 1.007025299 1.061224885 0.912639843 1 22.47193297 2.789276815 1.613900667 1.005546518 0.829212432 0.753176594 0.041489715 0.173970311 0.908222439 0.016721739 0.016864783 615.5691057 -2.789276815 -0.176334087 LLQIIDRDGEEEEEEEEPLDESSVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLQIIDRDGEEEEEEEEPLDESSVKK 26 2 A0A087WUB9;Q8WYA6;Q8WYA6-4;A2A2P1 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 167.72 5.69E-12 156500000 182350 145050 106370 99099 128050 161340 146760 141850 192680 132190 FALSE TRUE 175223.5604 140913.316 125593.4252 104213.5113 132168.8445 164602.4053 148556.0928 138920.7479 170807.7742 123236.6536 1.421846142 1.143436729 1.01912395 0.845637302 1.072479986 1.335661109 1.205453804 1.127268097 1.386014382 1 16.91107189 2.789985898 24.66349593 1.210530336 1.084209388 0.0952961 0.166292081 687.8310314 329881.2376 0.052094622 0.055254626 616.57498 -2.789985898 -0.126320948 LPVVIGGLLDVDCSEDVIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPVVIGGLLDVDCSEDVIK 19 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 241.51 1.07E-26 52275000 141346 144184 115811 127181 142724 144299 152264 156848 175617 166776 FALSE TRUE 135822.0421 140072.0135 136740.6239 133744.8267 147314.8471 147216.8246 154127.4524 153609.034 155681.6944 155480.113 0.873565368 0.90089987 0.879473402 0.860205361 0.947483535 0.946853085 0.991300105 0.987965799 1.001296509 1 17.24637054 2.790084858 1.309143333 0.995043344 0.879541326 0.905747473 0.016347494 0.118065494 0.415572145 0.00703895 0.006974335 616.7154925 -2.790084858 -0.115502018 LCQFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LCQFHR 6 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 88.627 0.051088 141550000 128590 154400 130860 149320 136500 114430 127750 100730 128760 147880 FALSE TRUE 123564.5606 149996.6632 154509.313 157026.4231 140890.6465 116743.853 129313.4427 98649.8903 114143.7046 137863.9559 0.896278943 1.088004926 1.120737556 1.138995484 1.021954183 0.846804752 0.937978617 0.715559696 0.827944504 1 17.07288579 2.790315017 3.382050287 0.841024881 1.068817909 0.491195776 0.094157474 0.184947168 4.285346506 0.030849855 0.031943237 617.0424137 -2.790315017 0.227793028 YGISSMIQSQEKPDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YGISSMIQSQEKPDR 15 1 P14868;H7C278 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;; 221.59 1.38E-12 2896200000 1044071 941856 892037 967603 983556 1039205 1083460 1184640 1197100 1146350 FALSE TRUE 1003267.551 914995.1891 1053247.929 1017541.107 1015192.972 1060218.437 1096719.708 1160176.77 1061210.227 1068706.693 0.938767912 0.856170542 0.985535073 0.952123827 0.949926653 0.99205745 1.02621207 1.085589505 0.992985478 1 20.02743453 2.790473466 1.041194413 1.040854338 0.921705351 0.542890009 0.038663223 0.348376723 0.800175016 0.020404627 0.019967471 617.2675777 -2.790473466 -0.119148987 VENSPQVDGS(ph)PPGLEGLLGGIGEK ddPTM_BT-474_Pertuzumab_2h_R1 6 VENSPQVDGSPPGLEGLLGGIGEK 24 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;Q8WVB6-3 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 VENS(0.056)PQVDGS(0.944)PPGLEGLLGGIGEK;VENS(0.218)PQVDGS(0.782)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK 344.1 3.83E-88 607239000 622851 593958 535141 581408 625682 700928 672879 730304 842965 809073 TRUE FALSE 598509.2943 577018.8994 631852.8828 611414.5366 645807.6298 715101.2444 681113.8945 715222.9672 747275.1472 754273.7651 0.793490801 0.764999296 0.837697017 0.810600295 0.856197921 0.948065911 0.903006211 0.948227289 0.990721382 1 19.52472872 2.790486081 0.487950992 1.000623871 0.759403941 0.908963637 0.024152279 0.300331056 0.147519503 0.021592796 0.03039991 617.2855075 -2.790486081 -0.24121993 EKAEAQQVEALPGPSLDQWHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKAEAQQVEALPGPSLDQWHR 21 1 H7BZV4;A0A0C4DG62;Q66PJ3-4;Q66PJ3-3;F5H7X4;Q66PJ3-7;F5GYV5;F8WCT1;Q66PJ3-2;Q66PJ3 H7BZV4;F5GYV5;Q66PJ3 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 0 ; 125.73 1.36E-05 583360000 822190 734280 645630 684760 729290 825280 808500 814100 942090 925640 FALSE TRUE 790057.9058 713339.0533 762309.703 720100.5457 752748.2752 841967.727 818394.6648 797288.5505 835147.8928 862945.5783 0.915536189 0.826632723 0.883380971 0.834468087 0.872300982 0.975690412 0.948373438 0.923915216 0.967787441 1 19.71891005 2.791465816 6.514650175 0.954375074 0.862905951 0.716931826 0.03009924 0.126433945 12.4346231 0.008843163 0.009337031 618.6796277 -2.791465816 -0.091469123 ASEYS(ph)PASLDAFGAFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASEYSPASLDAFGAFLK 17 0 P17029;E9PC66;B3KRF7 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 AS(0.017)EY(0.024)S(0.954)PAS(0.005)LDAFGAFLK 80.534 0.011765 12074000 18588 15743 18008 21469 19409 15666 19415 17864 19795 20195 TRUE FALSE 17861.56041 15294.02505 21262.44619 22577.01766 20033.30811 15982.77725 19652.60658 17495.10216 17547.95459 18827.17466 0.948711675 0.812337769 1.129348751 1.199171839 1.064063433 0.848920645 1.04384258 0.92924735 0.932054591 1 14.20052889 2.791471385 24.99938611 0.952837211 1.033431054 0.120637016 0.107685448 809.3773811 382414.5755 0.035664259 0.037827646 618.687562 -2.791471385 0.080593842 MMVDKDGDVTVTNDGATILSMMDVDHQIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 MMVDKDGDVTVTNDGATILSMMDVDHQIAK 30 1 P48643;B7ZAR1;E9PCA1 P48643 CCT5 T-complex protein 1 subunit epsilon 0 346.72 2.99E-120 638030000 950200 905720 731440 699410 854520 920630 924210 940840 1149300 1065700 FALSE TRUE 913065.1335 879889.7524 863627.4788 735506.6339 882006.4119 939245.7694 935520.7584 921411.3252 1018836.282 993519.1898 0.919021135 0.885629348 0.869260994 0.740304406 0.887759815 0.945372549 0.94162324 0.92742177 1.025482238 1 19.92218831 2.791914094 3.55348322 0.959493473 0.853178854 0.527661125 0.051173523 0.215825883 5.551595221 0.017168594 0.017817718 619.3185588 -2.791914094 -0.106314619 AVTGYKDPYSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVTGYKDPYSGK 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 99.531 0.0034145 572600000 1264700 1342700 1063100 1181600 1237300 1461600 1430500 1491500 1590400 1476900 FALSE TRUE 1215274.126 1304407.511 1255225.819 1242582.518 1277098.878 1491154.553 1448006.887 1460700.004 1409864.46 1376868.248 0.882636467 0.947372788 0.911652818 0.902470167 0.927538913 1.083004533 1.051666991 1.060885823 1.023964684 1 20.39295908 2.791928077 6.63270997 1.049267443 0.914653048 0.861488162 0.025943421 0.074710397 7.547720895 0.007532648 0.007956876 619.3384992 -2.791928077 -0.134614395 ECADLWPR ddPTM_BT-474_Pertuzumab_2h_R1 6 ECADLWPR 8 0 J3KTJ3;P62829 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;;;; 98.523 0.019593 213310000 3854030 3795000 3481920 3691450 3809910 3119350 3709330 3896640 3596320 3636490 FALSE TRUE 3703410.247 3686770.316 4111180.399 3881966.177 3932459.215 3182425.394 3754725.89 3816173.022 3188080.831 3390187.293 1.092391047 1.087482784 1.212670582 1.145059503 1.159953382 0.93871669 1.107527569 1.125652565 0.940384868 1 21.69293355 2.792067117 24.99985152 1.045125704 1.140993638 0.410703656 0.067414874 396.5719423 185289.4914 0.021294587 0.022586298 619.5368127 -2.792067117 0.095867934 SVS(ph)KESVASMGADS(ph)GDDFASDGSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSKESVASMGADSGDDFASDGSSSR 26 1 Q92805;Q5T165 Q92805 GOLGA1 Golgin subfamily A member 1 2 S(0.105)VS(0.602)KES(0.289)VAS(0.004)MGADS(1)GDDFASDGSSSR 120.34 0.00011645 186050000 214670 218240 160620 188770 199440 232460 220480 242020 266510 256820 TRUE FALSE 206280.4591 212016.0089 189647.607 198512.4423 205855.1687 237160.5005 223178.3002 237022.2024 236256.9021 239425.3526 0.861564813 0.885520295 0.792094926 0.829120392 0.859788516 0.990540466 0.93214147 0.989962841 0.986766437 1 17.8692164 2.793277274 4.829628106 0.976364119 0.842318992 0.847851429 0.028449972 0.081686323 4.137003654 0.00914616 0.009593056 621.2655528 -2.793277274 -0.134045126 MTGSAPPPS(ph)PTPNK ddPTM_BT-474_Pertuzumab_2h_R1 5 MTGSAPPPSPTPNK 14 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 MTGSAPPPS(1)PTPNK;MTGSAPPPS(0.997)PT(0.003)PNK;MTGSAPPPS(0.997)PT(0.003)PNK;MTGSAPPPS(0.964)PT(0.036)PNK;MTGSAPPPS(0.995)PT(0.005)PNK 190.41 6.37E-07 1585556000 2932460 2766170 2468800 2949950 2771560 2481270 2538390 2845190 2803800 2851780 TRUE FALSE 2817856.221 2687281.54 2914967.078 3102197.273 2860709.744 2531442.979 2569455.576 2786435.832 2485524.378 2658626.4 1.059891762 1.010778175 1.096418465 1.166842123 1.076010433 0.952161981 0.966459814 1.048073483 0.93489043 1 21.34224963 2.793355353 8.093007357 0.987534751 1.083805719 0.545606207 0.046150349 0.296615498 40.61910331 0.015225448 0.016125038 621.3772568 -2.793355353 0.096270968 RQS(ph)LTSPDSQSARPANR ddPTM_BT-474_Pertuzumab_2h_R1 1 RQSLTSPDSQSARPANR 17 2 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RQS(0.997)LT(0.003)SPDSQSARPANR 91.637 0.0018296 37241000 25734 26563 21625 25432 22501 34424 28321 27640 31243 33074 TRUE FALSE 24728.28683 25805.44925 25533.11855 26744.54857 23224.7651 35120.07687 28667.60087 27069.22434 27696.42562 30833.86852 0.801984571 0.836918962 0.828086769 0.867375709 0.753222551 1.13900975 0.92974389 0.877905551 0.898246861 1 14.91222829 2.793558611 24.99993605 0.951340018 0.821952627 0.509072573 0.073289265 299.6117363 136191.1289 0.02300458 0.02440003 621.66814 -2.793558611 -0.129387391 EFEFLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFEFLMR 7 0 P85037 P85037 FOXK1 Forkhead box protein K1 0 ; 117.93 0.01191 125532000 115425 122175 102980 114890 115913 95341 118527 110911 111121 118095 FALSE TRUE 110914.0634 118690.6886 121590.7768 120819.4867 119641.4469 97268.86034 119977.5689 108620.6491 98507.00994 110096.3205 1.007427523 1.078062265 1.104403637 1.097398043 1.086697961 0.883488748 1.089750942 0.986596542 0.894734806 1 16.74840673 2.794458081 24.99988335 0.981379318 1.077879632 0.427497063 0.059442403 301.9106532 135027.5095 0.017919476 0.019006466 622.9570147 -2.794458081 0.096500314 EKPEEESLAAPTWLVHLQQVER ddPTM_BT-474_Pertuzumab_2h_R1 2 EKPEEESLAAPTWLVHLQQVER 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 ; 269.25 1.89E-38 686880000 953980 928360 754520 858390 931910 958300 992880 1061170 1152800 1073210 FALSE TRUE 916697.4069 901884.0818 890878.5482 902691.6108 961885.7315 977677.4826 1005031.162 1039256.469 1021938.977 1000520.531 0.916220486 0.901414868 0.89041506 0.902221976 0.961385301 0.977168836 1.004508285 1.038715785 1.021407303 1 19.93231934 2.795822545 1.244405081 1.023087315 0.899386545 0.928892557 0.013947052 0.103485499 0.331511556 0.006516523 0.006464363 624.9172967 -2.795822545 -0.123700771 SGSKFPVFNMSYNPAENAVLLCTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSKFPVFNMSYNPAENAVLLCTR 24 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 73.676 0.024385 185780000 92636 81799 67550 91587 78163 122200 99648 99003 103080 120400 FALSE TRUE 89015.68271 79466.17261 79757.78764 96313.81605 80677.18388 124670.9677 100867.522 96958.55345 91378.79055 112245.2008 0.79304667 0.707969446 0.710567464 0.858066228 0.718758427 1.110701989 0.898635499 0.863810237 0.814099756 1 16.77629424 2.795866473 24.99975113 0.920513223 0.757879253 0.51397359 0.086626621 252.9117073 110332.4674 0.026759786 0.028384398 624.9805091 -2.795866473 -0.162633971 GRAS(ph)SHSS(ph)QTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 GRAS(0.811)S(0.405)HS(0.341)S(0.409)QT(0.033)QGGGSVTK 49.47 0.088926 400640000 192470 229370 191470 209420 201630 188720 170980 227230 173960 193310 TRUE FALSE 184948.0596 222828.5922 226072.8882 220228.1913 208115.6121 192536.0477 173072.5044 222537.6211 154212.7901 180216.9415 1.026252349 1.23644642 1.25444859 1.222017139 1.154806037 1.068357093 0.960356462 1.23483186 0.855706399 1 17.45937511 2.79596854 3.213245047 1.047727821 1.192708734 0.331535521 0.107893564 0.338854141 6.987665647 0.035024337 0.036341691 625.1274069 -2.79596854 0.144980914 GT(ph)PPPVFT(ph)PPLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTPPPVFTPPLPK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 2 GT(1)PPPVFT(1)PPLPK 91.441 0.010157 44996000 92557 86972 77356 82725 88277 91394 97610 101550 93991 109310 TRUE FALSE 88939.77011 84491.64371 91335.94997 86994.44716 91116.50988 93242.0493 98804.58038 99452.95701 83321.53572 101906.3363 0.872759961 0.829110797 0.896273512 0.853670638 0.894120161 0.914977936 0.969562678 0.975925154 0.817628606 1 16.63688423 2.796511181 2.02315236 0.943207854 0.863010689 0.334975891 0.048600341 0.363146812 2.933980267 0.017086603 0.017551034 625.9089786 -2.796511181 -0.080197165 DYQDNKADVILK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYQDNKADVILK 12 1 P47813;O14602;X6RAC9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ; 178.84 1.96E-05 1769230000 1875100 1872080 1189890 1062520 1432620 1848360 1519000 1706020 1972560 1809680 FALSE TRUE 1801819.019 1818690.111 1404929.592 1117356.785 1478701.523 1885735.106 1537589.976 1670790.091 1748643.258 1687108.762 1.067992212 1.077992215 0.832743937 0.662290903 0.876470775 1.117731796 0.911375728 0.990327434 1.036473343 1 20.68612155 2.79704454 24.99923756 1.000589812 0.895860894 0.162709047 0.120328883 566.6214562 242203.7718 0.040500851 0.042957697 626.6781312 -2.79704454 -0.104728918 LLFPEAEAEAENLPDDKPQQPTRPQEQSTGDTMGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLFPEAEAEAENLPDDKPQQPTRPQEQSTGDTMGR 35 2 A6NH27;O95229-2;O95229 A6NH27 ZWINT ZW10 interactor 0 91.407 0.00030552 129540000 35528 34766 27390 33118 35175 33377 40741 37877 44550 37161 FALSE TRUE 34139.52648 33774.50772 32339.98229 34827.22395 36306.43582 34051.90581 41239.60055 37094.82671 39492.87077 34644.05237 0.985436869 0.974900608 0.933493055 1.005287245 1.047984671 0.982907699 1.190380389 1.070741561 1.139961063 1 15.08032007 2.798167782 1.265563637 1.100728851 0.970066371 0.436838857 0.057035345 0.361752821 1.196043193 0.024123299 0.024015534 628.3010455 -2.798167782 -0.130662479 ILDEIEEHNIK ddPTM_BT-474_Pertuzumab_2h_R1 8 ILDEIEEHNIK 11 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0;C9J2Q4 Q15019-2 2-Sep Septin-2 0 ;;;;;;; 223.71 6.74E-12 5506642000 4487630 4532115 3824412 4183961 4506744 4477137 4713065 4946593 5471986 5085039 FALSE TRUE 4312248.458 4402863.518 4515568.322 4399895.729 4651707.514 4567667.778 4770744.899 4844444.126 4850829.09 4740624.779 0.909637159 0.928751741 0.952525992 0.928125708 0.981243556 0.96351599 1.006353618 1.021899929 1.02324679 1 22.17664578 2.798347971 0.766512216 1.021219518 0.92255982 0.849445079 0.01517693 0.22500737 0.288025473 0.009851992 0.010213295 628.5617809 -2.798347971 -0.098659698 TKGGQQVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKGGQQVDR 9 1 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 103.91 0.0030515 229580000 476840 463390 347920 400990 423200 466890 449850 489740 499450 500870 FALSE TRUE 458204.5656 450174.5709 410796.8834 421685.142 436812.6123 476330.8357 455355.3989 479626.6979 442754.5299 466945.6288 0.981280341 0.964083489 0.879753141 0.903071184 0.935467826 1.020099143 0.975178631 1.027157485 0.9481929 1 18.83289505 2.798552099 7.334744906 0.996753954 0.929603896 0.450959317 0.033733471 0.248659676 26.80086267 0.010687351 0.011319658 628.8572895 -2.798552099 -0.067150058 ANEQEPCGWWLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ANEQEPCGWWLAR 13 0 P51116;I3L1Z2 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 160.72 0.0001009 244440000 183160 185020 141480 158610 155240 155350 142550 157460 134000 160470 FALSE TRUE 176001.9047 179743.4108 167048.5832 166795.8811 160233.4356 158491.2834 144294.5695 154208.396 118788.8818 149601.224 1.176473695 1.201483557 1.116625779 1.114936607 1.071070352 1.059425045 0.964528001 1.030796352 0.794036831 1 17.19076245 2.799415837 0.613399728 0.927761003 1.191090127 0.700364161 0.060889975 0.453946867 0.367427121 0.045606717 0.053261721 630.1092236 -2.799415837 0.263329123 GSGS(ph)QSSVPSVDQFTGVGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSGSQSSVPSVDQFTGVGIR 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 GS(0.049)GS(0.95)QS(0.001)SVPSVDQFTGVGIR;GS(0.001)GS(0.999)QSSVPSVDQFTGVGIR 243.23 8.31E-30 142281000 197039 207960 151400 185810 172212 162161 142605 176099 150179 167858 TRUE FALSE 189338.498 202029.1844 178761.3479 195399.6764 177751.3554 165440.0065 144350.2426 172462.4941 133131.3095 156488.8281 1.209917029 1.291013466 1.14232658 1.248649368 1.135872493 1.057200111 0.922431616 1.10207544 0.850740025 1 17.25570014 2.799785046 1.810452558 0.986965538 1.223918427 0.718727095 0.070972453 0.190108901 1.237488946 0.025370897 0.025987645 630.6451294 -2.799785046 0.236952888 EAHQLFLEPEVLDPESVELK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAHQLFLEPEVLDPESVELK 20 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ;;; 246.16 5.16E-30 2036380000 4319260 4064430 3552740 3592220 3880410 4101030 4029550 4049800 4722740 4541940 FALSE TRUE 4150458.544 3948516.436 4194799.148 3777614.905 4005226.912 4183955.636 4078864.838 3966170.215 4186634.355 4234310.358 0.980197055 0.932505202 0.990668797 0.892144077 0.945898286 0.988107928 0.963289058 0.936674424 0.98874055 1 22.01369559 2.800638662 24.51807931 0.967614239 0.946642103 0.142750337 0.030209029 449.6074729 177574.0497 0.009118135 0.009671242 631.885897 -2.800638662 -0.020972136 SS(ph)FSQHAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.378)S(0.613)FS(0.009)QHAR 128.81 0.00071984 1374400000 1281500 1519000 1113100 1406800 1291600 961190 1147100 1106700 976520 1041300 TRUE FALSE 1231417.563 1475679.607 1314261.931 1479405.117 1333145.487 980625.9204 1161138.553 1083846.258 865669.5435 970771.8235 1.26849331 1.52010964 1.353831971 1.523947318 1.373284076 1.010150786 1.196098326 1.116478901 0.891733281 1 19.88877271 2.801282117 5.293878273 1.068305396 1.421424595 0.754705537 0.10358164 0.107982413 6.176904848 0.031260789 0.032977165 632.8227986 -2.801282117 0.353119199 QAYS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 QAYSPR 6 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 QAYS(1)PR;QAYS(1)PR 74.269 0.084726 3350390000 2222610 2442480 1968380 2341810 2265520 2018770 2111850 2459430 2264180 2387110 TRUE FALSE 2135747.944 2372822.862 2324110.052 2462671.095 2338392.508 2059590.913 2137695.452 2408641.911 2007159.779 2225428.913 0.959701715 1.066231704 1.044342526 1.106605149 1.05076037 0.925480432 0.96057683 1.08232705 0.901920419 1 21.08565199 2.802698992 24.80300963 0.98653313 1.050005853 0.267431471 0.057072361 300.411665 116171.6195 0.017817595 0.018898409 634.8907395 -2.802698992 0.063472722 LMEDLDR ddPTM_BT-474_Pertuzumab_2h_R1 16 LMEDLDR 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;;;;;; 235.41 1.42E-07 72558560000 23433200 25881440 20850490 25706310 24098230 22586880 24280580 25048530 24379300 24873050 FALSE TRUE 22517404.64 25143326.67 24618637.36 27033015.74 24873371.45 23043602.19 24577733 24531269.1 21611864.07 23188376.17 0.971064316 1.084307348 1.061680093 1.165800293 1.072665514 0.993756614 1.05991609 1.057912332 0.932012829 1 24.46689846 2.802782788 8.60378796 1.020338219 1.076712923 0.221422505 0.055941969 0.664895973 84.12096214 0.017359361 0.018408901 635.0132507 -2.802782788 0.056374705 QIPFHDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QIPFHDVR 8 0 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 Q06787 FMR1 Fragile X mental retardation protein 1 0 ; 118.26 0.00192 402050000 251119 294632 216840 253653 250772 220118 250007 217336 250217 256020 FALSE TRUE 241304.9919 286229.3838 256027.8116 266744.0617 258838.3091 224568.9368 253066.6605 212847.9357 221813.4152 238679.5374 1.010999914 1.199220457 1.07268438 1.117582448 1.084459573 0.94088056 1.060277991 0.891772868 0.929335701 1 17.86471536 2.803542902 4.658691302 0.960202364 1.104518354 0.543759731 0.060583857 0.156344406 6.795675532 0.018301874 0.01926293 636.1256419 -2.803542902 0.14431599 QHLVEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QHLVEVR 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 91.516 0.016347 343510000 229170 279540 223980 255320 240230 174520 232200 108240 269130 267510 FALSE TRUE 220213.783 271567.7929 264458.1684 268497.0958 247957.2161 178048.914 235041.7331 106004.8062 238579.4907 249391.3094 0.88300504 1.088922439 1.060414531 1.076609672 0.994249626 0.713933915 0.942461602 0.42505413 0.956647171 1 17.92805167 2.804531099 4.846250181 0.754868933 1.033476921 0.265338137 0.165980686 0.225125312 10.50635833 0.051047384 0.053801705 637.5747343 -2.804531099 0.278607987 IIAPPERK ddPTM_BT-474_Pertuzumab_2h_R1 6 IIAPPERK 8 1 P60709;P63267-2;Q562R1;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ;;;;; 133.86 0.0014451 40349810000 13205100 13749000 10895790 11198850 12988020 13723400 14268370 14367880 16515000 15861440 FALSE TRUE 12689030.09 13356891.98 12864901.63 11776823.99 13405791.46 14000896.55 14442990.58 14071178.26 14640286.44 14787130.54 0.858113077 0.903278154 0.870006631 0.796423888 0.906585049 0.946829847 0.976727063 0.951582744 0.990069466 1 23.81783879 2.806291137 2.678374985 0.971166956 0.860802144 0.780326912 0.029007872 0.136770184 1.930308067 0.009892558 0.010291961 640.1638372 -2.806291137 -0.110364812 KAVPMAPAPAS(ph)PGSSNDSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAVPMAPAPASPGSSNDSSAR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 KAVPMAPAPAS(0.975)PGS(0.021)S(0.004)NDSSAR 92.833 0.0011085 172390000 97362 103990 74032 72683 76967 92915 73189 66415 75092 65258 TRUE FALSE 93556.9854 101024.307 87411.22923 76434.17834 79442.71345 94793.80496 74084.70888 65043.50704 66567.87097 60838.01753 1.537804636 1.660545677 1.436786286 1.256355507 1.305807071 1.558134351 1.217737064 1.069126012 1.094182119 1 15.89268552 2.806837782 0.309497729 0.942659134 1.712122779 0.712453478 0.115557414 1.367482775 0.260224572 0.166622984 0.372765967 640.9701165 -2.806837782 0.769463645 NVHMNDNVLHSAFEVGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVHMNDNVLHSAFEVGAR 18 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 250.04 4.79E-25 545010000 221633 224173 197747 198486 188390 188077 187786 110011 236450 241341 FALSE TRUE 212971.3373 217779.8055 233484.2818 208729.8862 194449.7354 191880.0458 190084.1812 107739.2344 209609.1873 224994.7591 0.946561325 0.967932793 1.037732091 0.927709992 0.864241177 0.852820068 0.844838262 0.478852196 0.931618088 1 17.77953187 2.807047726 1.312125386 0.747523976 0.978108678 0.148750322 0.136615613 0.511757562 1.810993083 0.060464778 0.060869887 641.2800446 -2.807047726 0.230584702 YYKVDENGK ddPTM_BT-474_Pertuzumab_2h_R1 4 YYKVDENGK 9 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;; 133.81 0.00024314 3992350000 4500140 5028680 3088770 3142790 4114160 5015400 4497060 5244160 6210800 5438100 FALSE TRUE 4324269.554 4885266.97 3646979.448 3304989.769 4246495.693 5116814.824 4552096.366 5135866.263 5505776.022 5069772.643 0.852951376 0.963606716 0.719357594 0.651900983 0.837610676 1.009278953 0.897889646 1.013036802 1.086000578 1 22.27348962 2.807534928 4.600546471 0.994595809 0.79750373 0.557436398 0.087641176 0.187692015 7.752954002 0.029722218 0.031321055 641.9998518 -2.807534928 -0.197092079 TFHHVYSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TFHHVYSGK 9 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 101.65 0.0022218 1313610000 1764590 1907230 1562500 1548950 1532340 1274640 1574760 733180 1614730 1589140 FALSE TRUE 1695627.872 1852837.668 1844878.508 1628891.495 1581629.108 1300414.094 1594032.384 718039.5768 1431432.62 1481506.132 1.144529769 1.250644616 1.245272272 1.099483465 1.067581884 0.877764908 1.075953956 0.48466865 0.966200941 1 20.49863317 2.80790136 1.089708322 0.796284781 1.214296229 0.451167661 0.155619711 0.374247353 0.937680581 0.076980973 0.07676553 642.5417616 -2.80790136 0.418011449 DAFEHIVTQFSSVPVSVVSDSYDIYNACEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAFEHIVTQFSSVPVSVVSDSYDIYNACEK 30 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 332.07 2.28E-105 575440000 450370 421600 338370 390360 400120 439710 414010 433010 517780 478140 FALSE TRUE 432769.0425 409576.3808 399520.986 410506.5264 412990.2232 448601.2375 419076.7782 424068.1922 459003.7851 445755.1519 0.970867169 0.918837122 0.896279009 0.920923796 0.926495681 1.006384863 0.940150162 0.95134782 1.029721772 1 18.76589195 2.808904565 9.338207861 0.97616406 0.924135381 0.469066836 0.030439718 0.475713991 60.6516781 0.00948362 0.010060643 644.0277261 -2.808904565 -0.052028679 AVQPHISPLTINIPDTMAHLISPLPSPTGTISAANSCPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVQPHISPLTINIPDTMAHLISPLPSPTGTISAANSCPSSPR 42 0 Q01167;Q01167-2;E9PPI7;Q01167-3 Q01167 FOXK2 Forkhead box protein K2 1 AVQPHISPLTINIPDTMAHLISPLPSPTGTISAANS(0.005)CPS(0.497)S(0.497)PR 114.92 4.30E-06 82152000 22334 27620 18558 17813 23147 32024 31826 32098 27320 40649 TRUE FALSE 21461.16259 26832.30464 21911.84342 18732.33106 23891.54428 32671.54722 32215.49611 31435.16508 24218.74813 37895.80702 0.566320242 0.70805471 0.578212872 0.494311443 0.630453503 0.862141482 0.85010714 0.829515652 0.639087805 1 15.20975061 2.808965115 5.079408026 0.827207052 0.592079371 0.61354661 0.095644919 0.153262738 7.547300759 0.029105835 0.030751676 644.1175243 -2.808965115 -0.235127681 CLKDEDPYVR ddPTM_BT-474_Pertuzumab_2h_R1 4 CLKDEDPYVR 10 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;K7ERB2;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ;;; 131.37 0.00022979 6412120000 14241100 14002400 12282700 14275000 14376200 15195700 16722100 17619100 18777500 18274400 FALSE TRUE 13684542.07 13603065.26 14502457.12 15011734.46 14838623.53 15502967.47 16926750.06 17255259.43 16645956.92 17036658.61 0.803240963 0.798458522 0.851250087 0.881143116 0.870982032 0.909976998 0.993548703 1.012831203 0.977067 1 24.02213907 2.809320983 0.711889181 1.013736971 0.804410828 0.925123399 0.021160047 0.183457731 0.202849589 0.016289173 0.017622832 644.6455408 -2.809320983 -0.209326143 VS(ph)PSSTEADGELYVFNTPSGTSSVETQMR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSPSSTEADGELYVFNTPSGTSSVETQMR 29 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 VS(0.731)PS(0.179)S(0.045)T(0.045)EADGELYVFNTPSGTSSVETQMR 116.99 9.22E-05 26429000 35444 34445 25033 31968 36540 35893 36309 46566 42108 40193 TRUE FALSE 34058.80929 33462.66233 29557.01996 33617.87231 37715.34228 36618.78105 36753.3604 45604.39583 37328.07637 37470.69231 0.90894529 0.893035604 0.788803679 0.897177774 1.006529102 0.977264598 0.980856188 1.217068408 0.996193934 1 15.19347501 2.809661021 1.090089717 1.0816179 0.864066846 0.511473516 0.073904765 0.355146204 0.890572735 0.037988613 0.037952293 645.1504744 -2.809661021 -0.217551054 VHIEIGPDGR ddPTM_BT-474_Pertuzumab_2h_R1 7 VHIEIGPDGR 10 0 P52597;P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7;P55795 P52597;P31943;P55795 HNRNPF;HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;;; 176.6 2.45E-06 41794000000 15683180 16270860 13840700 17604140 15344570 13310160 16081640 10780950 16310460 16939770 FALSE TRUE 15070263.99 15806831 16342022.37 18512691.78 15838142.03 13579300.55 16278451.92 10558319.62 14458964.96 15792424.29 0.954271726 1.000912255 1.034801375 1.172251419 1.002894916 0.859861685 1.030775999 0.668568639 0.915563355 1 23.91272932 2.8101015 4.195802568 0.868421358 1.042360107 0.284382452 0.106190828 0.251589412 8.594708894 0.034262265 0.036059333 645.8051437 -2.8101015 0.17393875 LVILDEADAMTQDAQNALRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVILDEADAMTQDAQNALRR 20 1 P40937-2;P40937;E9PEP3;F5H5S0 P40937-2 RFC5 Replication factor C subunit 5 0 69.737 0.031238 11407000 5163 5858.4 3972.1 6697.7 5358.1 4796 4058.6 6115.8 6412.3 4154.7 FALSE TRUE 4961.224252 5691.324168 4689.946829 7043.3691 5530.448153 4892.978406 4108.270361 5989.506593 5684.402587 3873.298468 1.280878376 1.469374027 1.210840545 1.818442126 1.427839398 1.263258808 1.060664546 1.546358134 1.467587028 1 11.91934696 2.811111283 6.607471458 1.304153264 1.452220802 0.129442212 0.214762282 0.626458128 47.48287817 0.066489422 0.070495058 647.3084595 -2.811111283 0.148067538 LRGDVAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRGDVAIK 8 1 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 87.258 0.014092 696630000 745890 748940 648400 729240 748380 763740 818200 869410 938510 912030 FALSE TRUE 716739.7942 727580.9645 765580.3036 766876.1638 772452.3224 779183.3461 828213.3764 851456.3797 831974.2794 850257.3957 0.842968021 0.855718478 0.900410049 0.901934129 0.90849233 0.916408784 0.97407371 1.001410142 0.978496963 1 19.69754012 2.811633422 0.519793682 1.010049931 0.843668973 0.91840692 0.015555561 0.282298823 0.159329443 0.014984172 0.020261412 648.0871671 -2.811633422 -0.166380958 AGHCAVAINTR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGHCAVAINTR 11 0 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 0 ; 115.18 0.0011584 665060000 363860 379980 340720 379050 358230 313340 368910 261780 384870 406380 FALSE TRUE 349639.9489 369143.3424 402295.6833 398612.8159 369752.7933 319675.9495 373424.8309 256374.1515 341181.1711 378855.5206 0.922884662 0.974364427 1.061870981 1.052149947 0.97597309 0.843793827 0.985665539 0.676706917 0.900557475 1 18.53128825 2.811776106 3.834365247 0.854304718 1.006049252 0.261353439 0.092570837 0.259841716 7.426323871 0.029913533 0.031435124 648.3001255 -2.811776106 0.151744533 LCSS(ph)SSSDTSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.066)S(0.759)S(0.14)S(0.026)S(0.01)DTSSR 195.29 4.63E-07 267160000 207520 217550 171090 188170 191670 181330 167880 189680 198480 199470 TRUE FALSE 199409.889 211345.687 202009.7689 197881.4763 197835.2396 184996.6168 169934.5657 185763.0417 175949.3825 185959.7192 1.072328404 1.136513261 1.086309281 1.064109352 1.063860714 0.994820909 0.913824598 0.998942365 0.946169328 1 17.50463063 2.812698523 1.954041488 0.964902823 1.094003734 0.794105879 0.029473333 0.140535347 1.061176994 0.010453237 0.010841816 649.678543 -2.812698523 0.129100911 GFVQVDDGRK ddPTM_BT-474_Pertuzumab_2h_R1 4 GFVQVDDGRK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;; 136.48 0.0001871 1541060000 1675590 1594550 1379770 1619720 1630690 1804380 1742100 1916130 2090750 2179610 FALSE TRUE 1610106.09 1549074.995 1629125.132 1703313.943 1683142.625 1840865.8 1763420.341 1876561.246 1853416.825 2031983.073 0.792381645 0.762346407 0.801741488 0.838252034 0.828325121 0.90594544 0.8678322 0.923512243 0.912122177 1 20.95445695 2.813597185 0.227798939 1.021516401 0.688776903 0.917929915 0.01972262 1.029657123 0.116157178 0.042129277 0.107131619 651.0242789 -2.813597185 -0.332739498 RGQS(ph)SPPPAPPICLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGQSSPPPAPPICLR 15 1 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 RGQS(0.58)S(0.42)PPPAPPICLR 64.705 0.039031 445850000 273020 250810 228040 224010 275440 275120 297670 307380 340420 321570 TRUE FALSE 262350.0766 243657.1444 269251.9007 235571.1829 284299.7777 280683.1149 301312.9745 301032.4956 301776.9488 299789.7775 0.875113484 0.812760016 0.898135697 0.785787911 0.948330461 0.936266464 1.005080884 1.004145298 1.006628549 1 18.19359166 2.813887744 1.514623425 1.003544818 0.845149954 0.780258399 0.036544233 0.159740536 0.740150825 0.013408346 0.013728304 651.4599842 -2.813887744 -0.158394863 GAPVNISS(ph)SDLTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.067)S(0.865)S(0.067)DLTGR 309.06 1.19E-55 744480000 389900 443850 352460 379450 369770 398760 331650 417970 366550 414210 TRUE FALSE 374662.2769 431191.8326 416157.3624 399033.46 381663.9879 406823.2004 335708.8319 409338.7734 324940.7807 386155.1878 0.970237585 1.116628356 1.077694605 1.033349991 0.988369443 1.053522556 0.869362481 1.060036965 0.841477186 1 18.55882123 2.814516003 1.088130309 0.957702572 1.058560888 0.25410936 0.072477266 0.686957035 1.717786165 0.033970445 0.034109751 652.403081 -2.814516003 0.100858316 IHVFYIDYGNR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHVFYIDYGNR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 167.09 6.15E-05 1449500000 1841210 2003970 1625130 1958700 1823390 1398680 1847400 1161270 1919040 1996940 FALSE TRUE 1769253.478 1946818.738 1918827.142 2059788.742 1882040.995 1426962.268 1870009.034 1137289.369 1701198.624 1861685.475 0.950350369 1.045729133 1.030693513 1.106410706 1.01093392 0.766489446 1.00447098 0.610892325 0.913794863 1 20.82817792 2.814805435 6.027149701 0.829219614 1.036065635 0.339477547 0.114631183 0.218261317 13.64449944 0.034425539 0.036496321 652.838014 -2.814805435 0.206846021 KAAS(ph)PS(ph)PQSVR ddPTM_BT-474_Pertuzumab_2h_R1 3 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(1)PS(0.999)PQS(0.001)VR;KAAS(1)PS(0.996)PQS(0.004)VR;KAAS(1)PS(0.999)PQS(0.001)VR 124.5 0.0012174 6717400000 4444700 4474700 3836500 4282000 4372300 4840300 4847500 5077500 5888400 5299100 TRUE FALSE 4270996.21 4347085.937 4529840.892 4502994.533 4512939 4938174.182 4906825.155 4972647.851 5219973.518 4940187.237 0.864541364 0.879943559 0.916937087 0.911502807 0.913515781 0.999592514 0.993246798 1.006570725 1.056634752 1 22.23613429 2.816127738 0.838555542 1.025745604 0.878645777 0.888250693 0.02042663 0.185559943 0.284028687 0.012474339 0.0128509 654.8287485 -2.816127738 -0.147099827 MWDLSSNQAIQIAQHDAPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 MWDLSSNQAIQIAQHDAPVK 20 0 P78406;E9PQ57;E9PPG9;B0QZ36 P78406 RAE1 mRNA export factor 0 229.46 2.35E-25 389990000 252480 249400 220900 235930 242510 264190 263680 269540 290070 273750 FALSE TRUE 242612.8025 242287.3562 260821.5439 248106.3756 250310.5544 269532.1028 266906.9947 263973.9048 257142.4697 255208.6687 0.950644834 0.949369618 1.021993278 0.972170643 0.980807414 1.056124403 1.045838279 1.03434537 1.007577333 1 17.96131781 2.816229156 6.922975822 1.032492533 0.975667303 0.548129934 0.024309957 0.19569727 14.92832101 0.00758331 0.008045637 654.9816853 -2.816229156 -0.05682523 QLETVLDDLDPENALLPAGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLETVLDDLDPENALLPAGFR 21 0 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 ; 196.64 2.22E-21 30215000 55493 58250 48311 61816 55177 54305 54679 56091 61552 59036 FALSE TRUE 53324.27221 56588.76703 57041.87237 65006.33117 56951.81832 55403.08431 55348.17796 54932.70125 54564.87501 55037.43914 0.968872699 1.028186775 1.03641945 1.181129286 1.034783217 1.006643572 1.005645954 0.99809697 0.99141377 1 15.74812572 2.816774789 4.400058868 1.000383276 1.05638204 0.199986869 0.049760715 0.372881914 13.46724027 0.016404985 0.017326884 655.8050992 -2.816774789 0.055998764 S(ph)PQPPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQPPSR 7 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 S(1)PQPPSR;S(1)PQPPSR 97.965 0.012178 3815300000 1265570 1338060 1088590 1361240 1236040 1199360 1229740 1241410 1282970 1336580 TRUE FALSE 1216110.125 1299899.839 1285322.429 1431493.76 1275798.349 1223611.881 1244789.926 1215774.45 1137332.624 1246052.246 0.975970413 1.043214555 1.031515679 1.148823225 1.023872276 0.981990831 0.998986944 0.975701022 0.912748745 1 20.24893313 2.816777173 3.82480962 0.974334783 1.051591982 0.379540307 0.045810506 0.254327837 7.130001082 0.014827613 0.015615426 655.8086989 -2.816777173 0.077257199 DLSLEEIQKK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSLEEIQKK 10 1 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN2 Stathmin;Stathmin-2 0 ; 135.99 0.00020786 1443100000 2160840 2112820 1528190 1446400 1857850 2127310 1938370 2267030 2533260 2229970 FALSE TRUE 2076391.984 2052564.442 1804367.927 1521048.877 1917609.433 2170325.666 1962092.352 2220215.038 2245694.945 2078932.146 0.998778141 0.987316708 0.867930168 0.731649121 0.922401165 1.043961762 0.943798169 1.067959357 1.080215605 1 20.98741124 2.81714096 5.043226879 1.027339342 0.893090509 0.399383018 0.077153839 0.243096139 11.07859713 0.025981437 0.027506538 656.3582668 -2.81714096 -0.134248833 REELLK ddPTM_BT-474_Pertuzumab_2h_R1 2 REELLK 6 1 E7ERS3;Q86VM9;H3BRH3;Q9BSJ1 E7ERS3 ZC3H18;TRIM51 Zinc finger CCCH domain-containing protein 18;Tripartite motif-containing protein 51 0 ; 120.65 0.0503 654180000 591750 612680 484720 575470 592870 644060 611160 716440 753360 699250 FALSE TRUE 568623.7558 595206.9663 572319.6865 605170.0757 611940.202 657083.3345 618639.5589 701645.2636 667841.7311 651889.1747 0.872270591 0.913049318 0.87794016 0.928332758 0.938718153 1.007967857 0.948994987 1.076325994 1.024471271 1 19.31426719 2.817198624 0.858698093 1.034118336 0.885351044 0.761978427 0.030773416 0.261941782 0.419755697 0.017948486 0.018418222 656.4454219 -2.817198624 -0.148767292 AHGCFQDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AHGCFQDGR 9 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 0 ;;; 170.5 5.77E-05 322163000 294382 314477 251737 298386 286941 216785 296885 210436 284719 285437 FALSE TRUE 282877.226 305508.4239 297231.4758 313785.7372 296170.7179 221168.5412 300518.3674 206090.4231 252398.8928 266104.0977 1.063032206 1.148078615 1.116974441 1.179184161 1.112988189 0.831135421 1.129326343 0.77447294 0.948496828 1 18.0216312 2.817640849 7.414626061 0.926931863 1.129112227 0.501455805 0.093135098 0.214958394 17.80009723 0.027286081 0.02895495 657.1141958 -2.817640849 0.202180364 HAS(ph)TSSPADKAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HASTSSPADKAK 12 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HAS(0.505)T(0.401)S(0.052)S(0.042)PADKAK 86.467 0.0067191 61908000 57497 83320 61522 63562 63749 118740 92850 56976 132100 129890 TRUE FALSE 55249.95367 80943.79518 72640.39395 66842.44244 65799.54448 121141.0042 93986.32607 55799.42569 117104.5618 121092.4346 0.456262638 0.668446344 0.599875576 0.551995198 0.543382786 1.000401095 0.776153575 0.460800263 0.967067531 1 16.88574921 2.818140664 24.99986669 0.773869563 0.571122022 0.3916766 0.161994339 151.4083683 47563.19305 0.051835725 0.054980084 657.8708817 -2.818140664 -0.202747541 VENSWGEDHGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 VENSWGEDHGHK 12 0 Q13867;K7ESE8 Q13867 BLMH Bleomycin hydrolase 0 ; 122.42 0.00020747 710470000 1278110 1352120 1232300 1259110 1379470 403180 1591340 82445 1827670 1423600 FALSE TRUE 1228160.048 1313558.861 1455004.022 1324092.818 1423841.905 411332.5758 1610815.295 80742.48194 1620200.564 1327178.304 0.925391897 0.989738046 1.0963139 0.997675153 1.072833922 0.309930154 1.213714307 0.060837705 1.220785903 1 20.33993078 2.818348615 24.99997657 0.68823123 1.01831103 0.10114905 0.348226291 177.3126629 55555.77891 0.099752521 0.10580352 658.1859613 -2.818348615 0.3300798 RPDYAPMES(ph)SDEEDEEFQFIK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPDYAPMESSDEEDEEFQFIK 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 RPDYAPMES(0.5)S(0.5)DEEDEEFQFIK;RPDYAPMES(0.5)S(0.5)DEEDEEFQFIK 208.12 2.02E-22 173229000 134592 118656 107047 183703 135581 146990 238720 213371 223040 243490 TRUE FALSE 129331.9958 115272.0471 126392.7741 193183.9338 139942.086 149962.2385 241641.5268 208964.8143 197721.4343 226998.2054 0.569748979 0.507810389 0.556800764 0.851037274 0.616489834 0.660631824 1.064508534 0.92055712 0.87102642 1 17.79232137 2.819048429 0.58622788 0.994619525 0.517351047 0.67134492 0.11001062 0.527557799 0.388057918 0.09125616 0.112402452 659.2474043 -2.819048429 -0.477268478 SVSEINS(ph)DDELSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVSEINSDDELSGK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK 369.89 4.49E-97 1542740000 2000550 2024410 1550290 1878930 1943930 2115470 2151480 2376900 2464500 2182100 TRUE FALSE 1922366.294 1966675.809 1830461.889 1975901.802 2006458.274 2158246.253 2177810.456 2327816.184 2184740.292 2034304.423 0.94497474 0.966755903 0.899797429 0.97129111 0.98631171 1.060925901 1.070543047 1.14428114 1.073949536 1 20.95610416 2.819643977 1.623518325 1.09068557 0.941673491 0.701558398 0.038141965 0.179472729 0.94880201 0.014433199 0.014912892 660.1520517 -2.819643977 -0.149012079 DKPASSMS(ph)DDEMPVLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKPASSMSDDEMPVLVR 17 1 Q05GC8 Q05GC8 BCAR2 1 DKPASSMS(1)DDEMPVLVR 275.37 6.17E-36 162790000 144840 162030 121300 144940 148560 160160 150120 181260 180590 169100 TRUE FALSE 139179.4927 157409.063 143221.6083 152420.3708 153338.5673 163398.5449 151957.2135 177516.9177 160090.1803 157646.7064 0.882856965 0.998492558 0.908497308 0.966847797 0.972672191 1.036485625 0.963909852 1.126042667 1.015499683 1 17.2663355 2.820513301 1.005471081 1.049648053 0.934199812 0.428480596 0.048435142 0.442618065 0.95608088 0.024545987 0.024827898 661.4747965 -2.820513301 -0.11544824 GT(ph)PPPVFTPPLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GTPPPVFTPPLPK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 GT(1)PPPVFTPPLPK;GT(1)PPPVFTPPLPK 102.73 0.018627 194012000 262980 273570 211506 242040 267550 296770 335610 304390 341540 367680 TRUE FALSE 252702.4509 265768.0515 249729.8391 254531.7134 276155.9887 302770.8927 339717.2956 298104.2401 302769.8111 342776.7061 0.737221773 0.775338717 0.72854962 0.742558374 0.805643977 0.883288996 0.991074625 0.869674732 0.883285841 1 18.38690955 2.820628659 2.303339139 0.922710569 0.747446575 0.813184947 0.041200643 0.130878947 1.36508433 0.014054697 0.014714549 661.650521 -2.820628659 -0.175263994 S(ph)LESVLSLGPRPTGGGS(ph)SPPEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(0.994)LES(0.041)VLS(0.177)LGPRPT(0.019)GGGS(0.445)S(0.324)PPEIR;S(0.995)LES(0.254)VLS(0.011)LGPRPT(0.025)GGGS(0.378)S(0.337)PPEIR;S(1)LES(0.001)VLS(0.045)LGPRPT(0.306)GGGS(0.424)S(0.224)PPEIR;S(1)LESVLSLGPRPT(0.05)GGGS(0.528)S(0.422)PPEIR 138.29 2.40E-06 1833663000 1195295 1173365 933922 1134117 1118952 1176647 1172939 1346370 1254506 1305581 TRUE FALSE 1148581.55 1139901.779 1102702.48 1192648.914 1154944.107 1200439.609 1187293.778 1318566.989 1112099.738 1217152.836 0.943662551 0.936531342 0.905968789 0.979867835 0.948889961 0.986268588 0.975468112 1.083320804 0.913689477 1 20.21507891 2.821290263 1.148646279 1.008264702 0.934159151 0.239714256 0.04235396 0.544577597 1.506689054 0.019947363 0.020198309 662.6592472 -2.821290263 -0.074105551 DDNMFQIGK ddPTM_BT-474_Pertuzumab_2h_R1 8 DDNMFQIGK 9 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;;;;;;; 148.52 0.00020894 2679310000 2037162 2000916 1704127 1996556 2217828 2176855 2516095 2806635 2773277 2556987 FALSE TRUE 1957547.457 1943851.835 2012100.657 2099598.494 2289166.452 2220872.5 2546887.723 2748677.006 2458466.221 2383799.993 0.821187794 0.815442504 0.844072767 0.88077796 0.960301392 0.931652197 1.068415023 1.15306528 1.031322355 1 21.18483176 2.822592249 0.978839071 1.086758538 0.822992858 0.800201832 0.048042443 0.214426812 0.440623022 0.026967113 0.027377337 664.6488372 -2.822592249 -0.26376568 GGSISVQVNSIKFDS(ph)E ddPTM_BT-474_Pertuzumab_2h_R1 4 GGSISVQVNSIKFDSE 16 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GGSISVQVNS(0.001)IKFDS(0.999)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E 291.67 3.99E-45 3221790000 5787880 5475910 4006410 4222740 4824470 5576080 5039010 5447490 6222820 5638390 TRUE FALSE 5561683.251 5319742.408 4730457.409 4440676.117 4979653.459 5688832.158 5100678.912 5334997.428 5516431.562 5256496.823 1.058058901 1.012031889 0.899925857 0.844797641 0.947333105 1.082247807 0.970357081 1.014934015 1.049450185 1 22.32567021 2.823180778 14.193078 1.019099242 0.946819344 0.250626142 0.060746513 2.857664101 476.4135594 0.020009552 0.021224408 665.5501383 -2.823180778 -0.072279899 VIS(ph)DSESDIGGSDVEFKPDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 VISDSESDIGGSDVEFKPDTK 21 1 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1 P52701 MSH6 DNA mismatch repair protein Msh6 1 VIS(0.978)DS(0.021)ES(0.001)DIGGSDVEFKPDTK 150.59 4.23E-08 152640000 66741 60268 69540 98998 82194 106370 181100 128410 175620 190630 TRUE FALSE 64132.68793 58549.21565 82107.42491 104107.2986 84837.84466 108520.8743 183316.356 125758.2886 155684.3539 177718.4603 0.360866777 0.329449262 0.462008419 0.585799013 0.477372157 0.610633662 1.031498673 0.707626481 0.876016783 1 17.43923402 2.82355776 0.456389328 0.976216049 0.274552592 0.798858191 0.107941767 0.543552621 0.2294963 0.102188223 0.158441556 666.1281079 -2.82355776 -0.701663457 down LPLVPES(ph)PRR ddPTM_BT-474_Pertuzumab_2h_R1 6 LPLVPESPRR 10 1 C9J0I9;Q86WB0;Q86WB0-2;Q86WB0-3 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LPLVPES(1)PRR;LPLVPES(1)PRR;LPLVPES(1)PRR;LPLVPES(1)PRR;LPLVPES(1)PRR;LPLVPES(1)PRR 107.85 0.0023619 3647699000 1906732 2075013 1595214 1868900 1846576 1370928 1777348 1617347 1582167 1821797 TRUE FALSE 1832214.805 2015835.661 1883504.655 1965354.153 1905972.794 1398649.103 1799099.716 1583948.219 1402566.035 1698405.067 1.078785527 1.186899227 1.10898436 1.157176337 1.122213323 0.823507378 1.059287771 0.932609217 0.825813619 1 20.69574915 2.824068053 7.99292859 0.935992361 1.135078376 0.666220806 0.071575165 0.185061931 15.65146379 0.020969275 0.022256431 666.911264 -2.824068053 0.199086014 LNNLSPAPHLASGS(ph)PPPGLPSGLPSGLQSGS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 34 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 LNNLSPAPHLAS(0.162)GS(0.838)PPPGLPS(0.001)GLPS(0.001)GLQS(0.393)GS(0.598)PS(0.006)R 164.33 1.44E-14 736010000 256460 282820 240380 265800 274640 360040 330480 372360 338770 398690 TRUE FALSE 246437.2597 274754.2505 283822.0132 279517.9699 283474.045 367320.2555 334524.5131 364670.6359 300314.2498 371686.3712 0.66302474 0.739209914 0.763606189 0.752026417 0.762670001 0.988253226 0.900018239 0.981124583 0.807977567 1 18.50372626 2.824098416 5.295295428 0.934973444 0.736011969 0.749998994 0.057658554 0.109098281 5.102134793 0.017040815 0.018075461 666.957892 -2.824098416 -0.198961475 DVGAQILLHSHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVGAQILLHSHK 12 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 139.78 3.42E-05 2164100000 2501500 2769900 2740200 2465200 2481600 1484970 3019600 99648 3054600 2671000 FALSE TRUE 2403738.614 2690905.164 3235415.095 2592429.267 2561422.918 1514997.111 3056554.768 97590.23398 2707854.614 2490090.791 0.965321676 1.080645402 1.299316116 1.041098291 1.028646396 0.608410391 1.227487278 0.039191436 1.087452162 1 21.24776691 2.824455666 1.584728481 0.692381056 1.118809741 0.129124259 0.322862452 0.543220574 2.743544081 0.123868018 0.128286167 667.5067568 -2.824455666 0.426428686 SSS(ph)VEEKPLSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSVEEKPLSHR 12 1 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(0.003)S(0.102)S(0.896)VEEKPLSHR;S(0.018)S(0.018)S(0.964)VEEKPLSHR 143.88 3.79E-05 730500000 728490 700970 476160 619000 856650 704420 790730 966790 983450 907430 TRUE FALSE 700019.8054 680979.0219 562212.7041 650946.6642 884204.9252 718663.855 800407.1903 946825.4486 871812.879 845968.9578 0.827476941 0.804969279 0.664578409 0.769468735 1.045197837 0.849515633 0.946142507 1.119220085 1.030549491 1 19.6902452 2.826027376 0.892332456 1.049363792 0.758719113 0.603084499 0.086218914 0.387578462 0.669285741 0.052293532 0.053829767 669.9268376 -2.826027376 -0.290644679 RYIGIVK ddPTM_BT-474_Pertuzumab_2h_R1 2 RYIGIVK 7 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 132.09 0.0054554 4165300000 4913200 5835700 3966300 5092400 5796300 6975100 7071600 8292900 8305800 7806100 FALSE TRUE 4721186.712 5669271.55 4683098.64 5355219.374 5982743.254 7116141.301 7158144.356 8121648.717 7362960.405 7277385.894 0.648747611 0.779025825 0.643513853 0.735871294 0.822100592 0.977843061 0.983614784 1.116011826 1.011758963 1 22.79498888 2.826567728 1.436127155 1.049150475 0.695171274 0.907006463 0.048296691 0.103988499 0.436229401 0.019123498 0.019717838 670.7608834 -2.826567728 -0.3539792 GVTSEEFDKFLEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GVTSEEFDKFLEER 14 1 O60784;O60784-3 O60784 TOM1 Target of Myb protein 1 0 ; 177.88 1.87E-06 398480000 386260 394300 280646 323250 349540 395310 349670 425010 443590 416320 FALSE TRUE 371164.5322 383054.9501 331364.9751 339932.9712 360783.2715 403303.439 353949.3661 416233.395 393235.5229 388122.2756 0.956308245 0.986943997 0.853764383 0.87583989 0.929560848 1.039114383 0.911953238 1.072428513 1.013174321 1 18.56615171 2.82721015 5.891597823 1.008665617 0.916967226 0.414679666 0.051616226 0.23538113 12.56990494 0.016412115 0.017423888 671.7538277 -2.82721015 -0.091698391 VKTEDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKTEDEK 7 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 68.016 0.057998 162370000 225040 185720 141170 145480 180750 192850 209790 186650 232950 231500 FALSE TRUE 216245.188 180423.4474 166682.5593 152988.2402 186563.9879 196749.5591 212357.4728 182795.6123 206506.4926 215820.2988 1.001968718 0.835989239 0.772321048 0.708868633 0.864441338 0.911636024 0.983955049 0.846980628 0.956844624 1 17.71947104 2.828974989 3.727815168 0.927748831 0.82287911 0.289582257 0.080160627 0.338699853 8.799141145 0.026331433 0.027857385 674.4891825 -2.828974989 -0.104869722 VKESSIIAPAPAEDVDT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 6 VKESSIIAPAPAEDVDTPPR 20 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR 111.01 0.00028196 4080650000 4950950 4954810 3937300 4511360 4642900 5172750 5145780 5372170 5444670 5242190 TRUE FALSE 4757461.4 4813503.67 4648857.695 4744191.83 4792243.095 5277346.549 5208755.595 5261232.812 4826613.888 4887131.802 0.973466973 0.984934286 0.951244592 0.970751767 0.980583968 1.07984535 1.065810337 1.076548173 0.987616885 1 22.22055658 2.829606792 5.928784807 1.050924054 0.970762635 0.568856438 0.029916341 0.149580445 7.894992744 0.009078341 0.009640359 675.4711302 -2.829606792 -0.080161419 AKWDAWNALGSLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKWDAWNALGSLPK 14 1 A0A0C4DGA2;O75521-2;O75521;F1LLU7;F8WAW4;C9JB63;F8W6J1 A0A0C4DGA2 ECI2 "Enoyl-CoA delta isomerase 2, mitochondrial" 0 109.35 0.00070463 212920000 339810 409070 253950 332890 347780 378020 385510 429630 407770 393220 FALSE TRUE 326529.8495 397403.7241 299844.4141 350070.4928 358966.6595 385663.8234 390227.9867 420757.9904 361481.6591 366586.8592 0.890729827 1.084064293 0.817935522 0.954945558 0.979213113 1.052039411 1.064489839 1.147771612 0.986073696 1 18.48379555 2.829931953 2.228914327 1.070488375 0.939618747 0.324826678 0.075067505 0.321415387 3.141763283 0.025365534 0.026696713 675.977052 -2.829931953 -0.130869628 DIVNMLMHHDR ddPTM_BT-474_Pertuzumab_2h_R1 6 DIVNMLMHHDR 11 0 P11216;H0Y4Z6;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, muscle form" 0 ;;;;; 147.87 2.03E-05 2544344000 2063437 2191233 2083800 2349785 2147928 1479680 2552832 825389 2325473 2471974 FALSE TRUE 1982795.601 2128741.18 2460389.014 2471057.685 2217018.055 1509600.143 2584074.322 808344.4287 2061495.054 2304544.999 0.860384849 0.923714304 1.067624635 1.07225404 0.962019859 0.655053446 1.121294799 0.350760965 0.89453452 1 21.13605051 2.82997556 6.651317648 0.757277437 0.986476613 0.131363631 0.204947866 0.383912174 23.66829811 0.062315599 0.066172653 676.0449298 -2.82997556 0.229199176 LTQAEISEQPTMATVVPQVPT(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTQAEISEQPTMATVVPQVPTSPK 24 0 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 LTQAEISEQPTMATVVPQVPT(0.5)S(0.5)PK 99.366 0.017921 98636000 280460 217220 229380 242330 238570 225530 223000 264570 232750 230740 TRUE FALSE 269499.3131 211025.0983 270834.0685 254836.6803 246243.8207 230090.3711 225729.1407 259106.537 206329.1958 215111.7743 1.252833854 0.981002081 1.259038792 1.184670998 1.144724976 1.069631692 1.04935744 1.204520477 0.959172023 1 17.71472697 2.832690372 4.41562874 1.079699859 1.162389713 0.231444689 0.094063356 0.450074494 15.23007989 0.028769277 0.030529037 680.2841803 -2.832690372 0.082689854 NTKDEFEER ddPTM_BT-474_Pertuzumab_2h_R1 3 NTKDEFEER 9 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ;; 117.52 0.0010381 686830000 2443270 2702710 2076430 2434920 2473130 2730490 2767060 2802430 2973750 3072700 FALSE TRUE 2347784.307 2625631.357 2451687.091 2560586.513 2552680.472 2785702.379 2800924.108 2744558.841 2636182.367 2864583.292 0.81959017 0.916584051 0.855861688 0.893877486 0.89111756 0.97246339 0.977777157 0.958100555 0.920267312 1 21.44989386 2.834298266 3.57736292 0.963939917 0.875143344 0.692601207 0.030196771 0.141594151 3.392456239 0.009161627 0.009708786 682.8074744 -2.834298266 -0.088796573 HEGVFICR ddPTM_BT-474_Pertuzumab_2h_R1 6 HEGVFICR 8 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;;;; 131.06 0.0010211 2260090000 1374318 1353229 1336808 1636337 1396852 1219278 1419778 1042711 1525791 1709607 FALSE TRUE 1320608.133 1314636.234 1578398.943 1720788.549 1441783.013 1243932.637 1437153.668 1021178.653 1352589.602 1593813.795 0.828583701 0.824836777 0.990328323 1.079667245 0.904611955 0.780475511 0.901707384 0.640713901 0.848649702 1 20.60405166 2.83460637 5.106698617 0.804078104 0.934370438 0.116560134 0.111746626 0.351338859 14.54956568 0.035671726 0.037894829 683.2920541 -2.83460637 0.130292335 GESAEDKEHEEGRDS(ph)EEGPR ddPTM_BT-474_Pertuzumab_2h_R1 10 GESAEDKEHEEGRDSEEGPR 20 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7EPS6;A0A087WX58 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR 257.11 1.72E-36 5669567000 2138590 1877878 2003012 2138931 2120673 2113093 2460015 2396187 3050389 2879894 TRUE FALSE 2055011.538 1824322.758 2365000.825 2249321.485 2188886.373 2155821.188 2490121.399 2346704.901 2704121.629 2684836.214 0.765414116 0.679491266 0.880873408 0.837787226 0.815277432 0.8029619 0.927476092 0.874058868 1.007183088 1 21.35640265 2.835138975 0.239431404 1.036482732 0.655943669 0.679777235 0.054781675 2.356334833 0.283693055 0.110685575 0.284959376 684.130536 -2.835138975 -0.380539064 EANANGS(ph)SPEPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EANANGSSPEPVK 13 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 EANANGS(0.876)S(0.124)PEPVK 202.01 1.02E-07 475390000 617820 553580 588890 586900 644370 707830 746090 831580 870250 854690 TRUE FALSE 593674.9114 537792.4404 695315.5228 617189.9793 665096.7463 722142.8076 755220.8726 814407.5824 771462.8684 796801.085 0.74507292 0.674939393 0.872633755 0.774584763 0.834708635 0.90630249 0.94781607 1.022096478 0.968200073 1 19.60386009 2.835353084 0.662286203 1.016681905 0.725696256 0.831217862 0.045162801 0.282596807 0.270275354 0.032829007 0.037943249 684.4678975 -2.835353084 -0.29098565 HMGIGK ddPTM_BT-474_Pertuzumab_2h_R1 6 HMGIGK 6 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;;;; 74.849 0.060109 4995250000 15991130 16256870 14316840 15570940 15770930 16309250 16349780 14209210 19312750 18959070 FALSE TRUE 15366178.96 15793239.98 16904211.46 16374558.08 16278216.29 16639034.21 16549873.5 13915784.85 17120447.59 17674955.3 0.869375831 0.893537761 0.956393449 0.926427128 0.920976376 0.941390455 0.936345989 0.787316551 0.96862749 1 24.07520323 2.835859336 0.005036686 1.819802248 5.35E-07 0.086175227 0.053842577 49311.50089 90.75748227 16151.23129 16637.2549 685.2662396 -2.835859336 -1.819801713 (ac)MDPLSELQDDLTLDDTSEALNQLK ddPTM_BT-474_Pertuzumab_2h_R1 3 MDPLSELQDDLTLDDTSEALNQLK 24 0 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;; 119.01 3.52E-38 59749000 49221 52322 37727.5 45109 50988 51140 55726 57652 57110 66311 FALSE TRUE 47297.3889 50829.82779 44545.69849 47437.0809 52628.07533 52174.08584 56407.99146 56461.46605 50627.11222 61819.69691 0.765086069 0.822227062 0.720574521 0.767345737 0.851315648 0.84397188 0.912459851 0.913324861 0.81894792 1 15.91577896 2.836045371 1.361766173 0.905164433 0.768632747 0.610423742 0.049249292 0.285869405 1.086349796 0.019917881 0.020639534 685.5598437 -2.836045371 -0.136531686 TTIIWDAHTGEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTIIWDAHTGEAK 13 0 Q9BZK7;A0A0D9SF63;A0A1B0GVH3;O60907;A0A2R8YFW3;Q9BQ87;O60907-2 Q9BZK7;O60907 TBL1XR1;TBL1X;TBL1Y F-box-like/WD repeat-containing protein TBL1XR1;F-box-like/WD repeat-containing protein TBL1X;F-box-like/WD repeat-containing protein TBL1Y 0 123.02 0.00022828 476900000 364750 312820 287700 375340 325730 352900 350450 397690 439650 429910 FALSE TRUE 350495.1667 303898.6799 339693.7899 394711.3424 336207.4013 360035.8798 354738.9119 389477.5625 389742.7752 400791.8128 0.874506803 0.758245728 0.847556709 0.984828856 0.838857957 0.898311463 0.885095206 0.971770256 0.972431978 1 18.61249351 2.836267153 0.273267231 1.017606325 0.774101302 0.505184867 0.052144706 2.535878904 0.380057352 0.083795327 0.207322885 685.9100294 -2.836267153 -0.243505023 ELLFHPALFEVPSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLFHPALFEVPSLK 15 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 0 ; 133.48 4.11E-05 433060000 649800 659220 555140 626760 665080 719410 690190 767140 854510 842780 FALSE TRUE 624405.0976 640419.691 655466.147 659107.1587 686472.9022 733956.9631 698636.7517 751298.2909 757509.6072 785697.7599 0.794714112 0.815096751 0.834247188 0.838881301 0.873711161 0.934146692 0.88919275 0.956217937 0.964123415 1 19.58361492 2.836354381 0.356911116 1.005316953 0.762187404 0.941263807 0.016186261 0.392202442 0.097345331 0.017835554 0.035949814 686.0478077 -2.836354381 -0.243129549 QKEIEER ddPTM_BT-474_Pertuzumab_2h_R1 4 QKEIEER 7 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ;;; 109.71 0.0063531 1734540000 2572340 2708000 2165790 2360610 2542280 2792480 2797330 2887050 3235720 3079030 FALSE TRUE 2471810.109 2630770.491 2557196.431 2482441.365 2624054.745 2848945.859 2831564.561 2827431.409 2868414.631 2870484.556 0.861112492 0.916490035 0.890858801 0.864816137 0.914150449 0.992496494 0.986441316 0.985001436 0.999278894 1 21.45286286 2.836961713 3.417083447 0.991123035 0.886382486 0.920810109 0.015297799 0.06418232 1.414608298 0.004812073 0.005103246 687.0078712 -2.836961713 -0.104740549 VLHEAEGHIVTCETNTGEVYR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLHEAEGHIVTCETNTGEVYR 21 0 P62318;P62318-2;H3BT13 P62318 SNRPD3 Small nuclear ribonucleoprotein Sm D3 0 ;;; 278.82 3.90E-45 3088170000 1120643 1079095 969985 1006483 994404 558751 1001712 290550 1071479 1001194 FALSE TRUE 1076847.033 1048320.267 1145282.867 1058427.708 1026389.908 570049.3281 1013971.251 284550.041 949849.1959 933382.2386 1.153704225 1.123141435 1.227024491 1.133970269 1.099645853 0.610735136 1.086340846 0.30485907 1.017642244 1 19.83210849 2.837021222 5.437314017 0.748045699 1.155689882 0.372283379 0.217672255 0.206838685 9.196847167 0.065114004 0.069196902 687.1020141 -2.837021222 0.407644183 FEELFPDWIFPSESER ddPTM_BT-474_Pertuzumab_2h_R1 2 FEELFPDWIFPSESER 16 0 P45984-3;P45984-2;P45984-4;P45984 P45984-3 MAPK9 Mitogen-activated protein kinase 9 0 ; 165.7 1.61E-08 86166000 114418 111885 104009 110027 114327 129827 127861 138476 149271 126201 FALSE TRUE 109946.4181 108694.1493 122805.74 115705.5067 118004.4318 132452.1909 129425.8012 135616.4222 132326.3819 117653.2939 0.934495027 0.923851307 1.043793471 0.983444686 1.002984514 1.125783958 1.100061009 1.152678499 1.124714639 1 16.84418219 2.838065253 3.446584292 1.11386305 0.974507691 0.607599021 0.049179839 0.155722902 3.479720036 0.015575556 0.016526785 688.7557744 -2.838065253 -0.13935536 REPLPSR ddPTM_BT-474_Pertuzumab_2h_R1 6 REPLPSR 7 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39;Q8IZ40 P38159;Q96E39;Q8IZ40 RBMX;RBMXL1;RCOR2 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1;REST corepressor 2" 0 ;;;;; 122.19 0.0069993 8103670000 2819040 2839690 2751500 2984390 2916590 2511070 2918610 2909400 2954040 3028190 FALSE TRUE 2708868.8 2758704.822 3248757.257 3138414.726 3010404.766 2561845.556 2954328.822 2849319.873 2618709.764 2823087.994 0.959541044 0.977194061 1.150781436 1.111695679 1.06635173 0.90746217 1.046488394 1.00929191 0.927604725 1 21.42884267 2.838616267 24.91418562 0.986943436 1.057576285 0.244810566 0.064667867 66.18793814 16468.96392 0.02096795 0.022239869 689.6301933 -2.838616267 0.070632849 DSMTVSEVTASISSPS(ph)EEDASEMPEFLDK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSMTVSEVTASISSPSEEDASEMPEFLDK 29 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 DSMTVSEVTASISS(0.001)PS(0.808)EEDAS(0.19)EMPEFLDK;DSMTVSEVTASISS(0.004)PS(0.83)EEDAS(0.166)EMPEFLDK;DSMTVSEVTASISS(0.005)PS(0.995)EEDASEMPEFLDK;DSMTVSEVTASISS(0.001)PS(0.987)EEDAS(0.012)EMPEFLDK 210.19 6.42E-26 257729800 342684 341569 308867 325140 361590 375591 395042 405266 471532 473575 TRUE FALSE 329291.5304 331827.7866 364686.1376 341920.5144 373220.8707 383185.7074 399876.6422 396897.1155 418005.6642 441499.3434 0.74584829 0.751592933 0.826017395 0.774453053 0.845348643 0.867919088 0.905724206 0.898975551 0.946786604 1 18.75205177 2.841665671 0.275876184 1.015344028 0.677258051 0.939353308 0.019722084 0.639135877 0.097103929 0.029452955 0.072814258 694.4894789 -2.841665671 -0.338085977 DFSDITK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFSDITK 7 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 79.597 0.097098 0 137590 122890 126320 118370 130200 146500 140240 156300 155800 153200 FALSE TRUE 132212.8307 119385.2975 149148.834 124479.0899 134388.0012 149462.3304 141956.2991 153072.3504 138114.2372 142823.6275 0.925706992 0.835893189 1.044286835 0.871558103 0.940936759 1.046481825 0.993927276 1.071757895 0.967026532 1 17.12387514 2.841698914 5.028486065 1.022433342 0.920761914 0.396104565 0.056938901 0.213518579 8.359636927 0.016837181 0.017905081 694.5426408 -2.841698914 -0.101671428 S(ph)LTELVQQPCPPIEASK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLTELVQQPCPPIEASK 17 0 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1 1 S(0.891)LT(0.109)ELVQQPCPPIEASK 194.37 8.16E-11 118550000 131680 138420 159730 200800 163040 161000 232290 240520 301190 332360 TRUE FALSE 126533.8 134472.3971 188596.7642 211163.3121 168284.3297 164255.5303 235132.8345 235553.1779 267000.1739 309848.9612 0.408372517 0.433993377 0.608673218 0.681504018 0.543117295 0.530114833 0.758862749 0.760219357 0.861710728 1 18.24120561 2.842371399 0.150527651 1.186854138 0.079567269 0.838910559 0.072257072 4.296397997 0.26824421 0.570697823 1.272527942 695.618941 -2.842371399 -1.107286869 down HQEHKGEIDAHEDSFK ddPTM_BT-474_Pertuzumab_2h_R1 1 HQEHKGEIDAHEDSFK 16 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 61.097 0.029586 144690000 137780 133110 129220 118100 109920 104680 122690 7011.6 200290 125250 FALSE TRUE 132395.4053 129313.8331 152572.9285 124195.1552 113455.6766 106796.7013 124191.5169 6866.80801 177553.9189 116766.7059 1.13384551 1.107454664 1.306647535 1.063617871 0.971644063 0.914616033 1.063586713 0.058807928 1.520586861 1 16.83326945 2.842435683 1.294836308 0.770233129 1.168801694 0.048132413 0.3510327 0.760535901 2.632510617 0.152350975 0.158354971 695.7219131 -2.842435683 0.398568565 KSAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSAEPSANTTLVSETEEEGSVPAFGAAAK 29 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KSAEPSANT(0.001)T(0.001)LVS(0.973)ET(0.026)EEEGSVPAFGAAAK;KSAEPSANTT(0.001)LVS(0.983)ET(0.016)EEEGSVPAFGAAAK;KSAEPSANTTLVS(0.976)ET(0.024)EEEGSVPAFGAAAK 326.78 3.06E-105 3364770000 864360 762330 693840 650190 776370 930850 819730 991730 1083620 945060 TRUE FALSE 830579.8556 740589.0948 819232.3224 683746.3838 801342.6461 949672.4248 829762.1009 971250.4289 960612.0005 881050.2444 0.942715652 0.840575324 0.929836099 0.776058333 0.909531155 1.077886796 0.941787493 1.102378026 1.090303313 1 19.74886477 2.843568495 4.748465741 1.044456728 0.871044357 0.637592894 0.061663313 0.138304294 4.983123137 0.018553198 0.019737573 697.5390011 -2.843568495 -0.173412371 KEKEEAEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEKEEAEAR 9 2 Q99543;Q99543-2 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 ; 76.927 0.019149 80485000 192377 180850 145408 135611 172679 192686 186824 195485 241489 218518 FALSE TRUE 184858.6942 175692.3351 171686.4602 142609.9 178233.3769 196582.2429 189110.408 191448.1664 214076.1811 203717.5812 0.907426316 0.862430891 0.842767027 0.700037273 0.874904246 0.964974362 0.928296944 0.93977243 1.050847845 1 17.63621097 2.844581659 3.982893057 0.966475352 0.827581416 0.584003694 0.05918555 0.185932387 5.2074077 0.019355785 0.020597849 699.1681867 -2.844581659 -0.138893937 AQAGEGVRPSPMQLELR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQAGEGVRPSPMQLELR 17 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ; 124.84 4.46E-05 1199600000 290208 321461 243583 284361 280866 220928 256430 257986 262690 290856 FALSE TRUE 278866.3505 312293.247 287603.8666 299036.9053 289900.31 225395.3155 259568.267 252658.4989 232870.5325 271156.0641 1.028434866 1.151710356 1.060658066 1.10282212 1.06912715 0.831238336 0.957265212 0.931782587 0.858806287 1 18.04876391 2.845255191 6.585668783 0.917174164 1.088101569 0.711739121 0.053080941 0.123923488 6.641344389 0.01517749 0.016128481 700.2533433 -2.845255191 0.170927405 EALEAYRR ddPTM_BT-474_Pertuzumab_2h_R1 3 EALEAYRR 8 1 Q9NRF9 Q9NRF9 POLE3 DNA polymerase epsilon subunit 3 0 ;; 149.65 0.00080453 535700000 541536 612520 486388 520892 522836 463730 510397 474867 485403 546449 FALSE TRUE 520372.1744 595051.5293 574289.1312 547775.2985 539653.4948 473106.9383 516643.3912 465060.8305 430302.0864 509437.5225 1.021464167 1.16805595 1.127300416 1.075255109 1.05931242 0.928684907 1.014144754 0.912890806 0.844661156 1 18.9585457 2.846017499 1.291677934 0.928172514 1.112200828 0.636469777 0.05681388 0.259082496 0.892974782 0.02391018 0.024932571 701.4835628 -2.846017499 0.184028314 EPLGPALAHELR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPLGPALAHELR 12 0 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 184.31 1.45E-05 326010000 340860 376920 352750 361730 350270 278240 274080 327230 333970 370810 FALSE TRUE 327538.8144 366170.6106 416499.7719 380398.9286 361536.7527 283866.2034 277434.273 320472.5861 296059.1257 345694.7084 0.947479977 1.059231171 1.204819633 1.100389793 1.04582669 0.821147089 0.802541278 0.927039316 0.85641787 1 18.39913899 2.84632248 4.901167553 0.875116284 1.083933536 0.595854871 0.078322092 0.153256605 5.699778339 0.024752975 0.026342465 701.9763493 -2.84632248 0.208817251 VLTELLEQER ddPTM_BT-474_Pertuzumab_2h_R1 1 VLTELLEQER 10 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 114.5 0.0031355 17057000 24956 29614 21342 24104 24602 20820 24929 20629 26749 23470 FALSE TRUE 23980.69193 28769.43772 25198.97415 25348.01033 25393.34567 21240.99466 25234.08856 20203.00394 23712.56566 21880.356 1.095991854 1.31485236 1.151671123 1.158482537 1.160554503 0.970779208 1.15327596 0.923339819 1.083737653 1 14.41734859 2.846725911 5.095411486 1.024304702 1.184487493 0.481603482 0.077855711 0.185086782 7.220370914 0.022919523 0.024388684 702.6287417 -2.846725911 0.160182791 EDS(ph)FESLDSLGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDSFESLDSLGSR 13 0 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EDS(0.994)FES(0.006)LDSLGSR;EDS(0.999)FES(0.001)LDSLGSR;EDS(0.994)FES(0.006)LDSLGSR 196.74 1.46E-07 487690000 597120 507860 442631 608510 595760 559730 612590 704720 721440 767300 TRUE FALSE 573783.8902 493376.33 522624.268 639915.274 614923.1615 571048.1241 620087.0597 690167.2857 639545.1557 715330.0876 0.802124642 0.689718409 0.73060574 0.894573408 0.859635534 0.798300161 0.866854436 0.96482351 0.894055999 1 19.4482496 2.847335425 0.297960557 1.008550782 0.674500477 0.664289108 0.053386854 1.568607694 0.272808702 0.077019529 0.182543094 703.6155439 -2.847335425 -0.334050306 IDEDGENTQIEDTEPMS(ph)PVLNSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDEDGENTQIEDTEPMSPVLNSK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 IDEDGENTQIEDT(0.001)EPMS(0.999)PVLNSK;IDEDGENTQIEDTEPMS(1)PVLNSK 177.6 3.49E-17 358370000 125210.9 111740.9 97355 113221 120707 138637.1 150184 155034 143950.5 163791 TRUE FALSE 120317.5196 108554.1589 114949.2142 119064.3494 124589.6503 141440.4371 152021.9967 151832.4937 127609.8427 152697.2897 0.787947971 0.710910843 0.75279145 0.779741079 0.815925748 0.926279945 0.995577571 0.994336534 0.8357047 1 17.22031493 2.847563776 1.939037721 0.962686259 0.752146243 0.785432123 0.048207188 0.144013571 1.072917234 0.017230867 0.018296735 703.9855996 -2.847563776 -0.210540015 GKDSTEMR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKDSTEMR 8 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 0 ; 87.913 0.013668 538910000 1100980 1149820 975560 1103280 1109010 1284450 1325570 1177010 1400790 1403680 FALSE TRUE 1057952.484 1117028.259 1151865.393 1160220.413 1144682.314 1310422.459 1341792.722 1152704.332 1241778.192 1308607.503 0.808456685 0.853600684 0.880222214 0.886606878 0.874733112 1.001386937 1.025359184 0.880863306 0.948930973 1 20.31960102 2.847854735 5.626489682 0.961401973 0.861343816 0.6299178 0.042117253 0.1852231 8.116991218 0.014141592 0.015042199 704.4573997 -2.847854735 -0.100058157 LGHGLLSGEYSKPVPESGDGERVPEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGHGLLSGEYSKPVPESGDGERVPEQK 27 2 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 125.78 4.34E-05 84361000 116610 108220 100640 105910 109190 123720 119910 119520 144200 119740 FALSE TRUE 112052.7523 105133.6716 118827.8867 111376.0278 112702.1955 126221.7032 121377.4944 117051.8702 127831.0205 111629.9031 1.003787956 0.941805633 1.064480783 0.997725741 1.009605781 1.130715871 1.087320611 1.04857092 1.145132415 1 16.76836402 2.849017738 7.318122862 1.082512184 1.002438966 0.416851913 0.046684427 0.257420089 15.21087334 0.013709287 0.014562425 706.3464029 -2.849017738 -0.080073217 DFTEVLS(ph)PNMYNSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFTEVLSPNMYNSK 14 0 B7ZLP8;A2RTX5-2;A2RTX5 B7ZLP8 TARSL2 "Probable threonine--tRNA ligase 2, cytoplasmic" 1 DFTEVLS(0.986)PNMY(0.009)NS(0.005)K;DFTEVLS(1)PNMYNSK 153.24 2.97E-07 37220000 123191 121877 104362 108854 118168 123758 130097 133408 131390 133608 TRUE FALSE 118376.5595 118401.1873 123222.5349 114471.968 121968.981 126260.4716 131689.166 130653.0782 116475.158 124558.6112 0.950368332 0.950566052 0.989273514 0.919020909 0.979209546 1.013663129 1.057246583 1.048928508 0.935103217 1 16.92646524 2.849404514 3.389564217 1.020972353 0.954425857 0.360703784 0.035423654 0.241837006 5.194090785 0.011432564 0.012187954 706.9757452 -2.849404514 -0.066546496 HFEALANR ddPTM_BT-474_Pertuzumab_2h_R1 3 HFEALANR 8 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;; 126.52 0.0012156 789870000 278448 361956 271713 309516 303118 204764 327839 203109 273283 301747 FALSE TRUE 267565.9443 351633.3693 320817.5833 325490.1579 312868.0658 208904.4684 331851.1917 198914.7282 242261.0595 281309.4069 0.951144675 1.249987951 1.140443851 1.157053941 1.112184869 0.742614585 1.179666174 0.707103009 0.861190751 1 18.10179827 2.849521552 7.297183183 0.88979343 1.134339939 0.384517693 0.141304697 0.252755975 14.83671927 0.041235225 0.043802352 707.1662925 -2.849521552 0.244546509 DYALHVGDGS(ph)SDPEVLLNIENQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYALHVGDGSSDPEVLLNIENQR 23 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 DYALHVGDGS(0.5)S(0.5)DPEVLLNIENQR 140.41 1.26E-07 56001000 33384 34144 28223 28821 32336 35548 34178 38446 39459 38251 TRUE FALSE 32079.31637 33170.24655 33323.52392 30308.45526 33376.11681 36266.80492 34596.28059 37652.07666 34979.77975 35660.2257 0.899582539 0.930174891 0.934473163 0.84992326 0.935947997 1.017009966 0.970164375 1.055856376 0.98091863 1 15.12202821 2.850278368 4.028706485 1.009284148 0.906257579 0.709585011 0.030674329 0.124037135 3.498675267 0.009581755 0.010213199 708.3996996 -2.850278368 -0.103026569 DLADAPAEELQEKGS(ph)PAGPPPSQGQPAARPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLADAPAEELQEKGSPAGPPPSQGQPAARPPK 32 2 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 DLADAPAEELQEKGS(1)PAGPPPSQGQPAARPPK 127.78 5.86E-08 213510000 51534 42258 32849 32360 42661 50231 49869 48413 61243 62485 TRUE FALSE 49519.99431 41052.84321 38785.54502 34030.10348 44033.22981 51246.70524 50479.31174 47413.25463 54290.95139 58252.83529 0.85008728 0.704735538 0.665813858 0.58417935 0.755898483 0.879728943 0.866555447 0.813921836 0.931988136 1 15.83004065 2.850865536 3.822586652 0.878609599 0.696378734 0.591127254 0.077324849 0.184076197 4.795829862 0.024786338 0.026429839 709.3581067 -2.850865536 -0.182230864 VAAIEALNDGELQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VAAIEALNDGELQK 14 0 P50502;Q3KNR6;F6VDH7;Q8IZP2;H7C3I1 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 172.92 6.47E-06 29810000 64888 54647 50922 59891 63257 65989 63426 74473 83331 76293 FALSE TRUE 62352.10522 53088.52107 60124.73815 62981.98169 65291.71885 67323.34279 64202.22636 72935.10652 73871.61423 71125.60716 0.876647774 0.746405172 0.845331809 0.885503607 0.917977666 0.946541555 0.9026598 1.025440899 1.038607854 1 16.11808144 2.85114323 0.576447833 1.025569537 0.798442853 0.749381969 0.042287407 0.425250064 0.302129201 0.03388579 0.043695203 709.8118247 -2.85114323 -0.227126684 YNLEELYQAVENLCSHK ddPTM_BT-474_Pertuzumab_2h_R1 1 YNLEELYQAVENLCSHK 17 0 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 0 103.1 0.00091533 382090000 171130 198570 139710 161640 172430 192690 202890 187410 197810 225390 FALSE TRUE 164442.0504 192906.978 164958.7048 169982.2598 177976.3675 196586.3238 205373.0285 183539.918 175355.4381 210124.1345 0.782594778 0.918061975 0.785053584 0.808961142 0.847005833 0.935572319 0.977389051 0.873483279 0.834532589 1 17.68088235 2.851207852 4.663860977 0.917134043 0.827842219 0.418073964 0.056589029 0.25565077 8.794726886 0.017563114 0.018710147 709.9174513 -2.851207852 -0.089291824 FVHGPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 FVHGPSPR 8 0 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 FVHGPS(1)PR;FVHGPS(1)PR;FVHGPS(1)PR 102.52 0.0031875 873770000 848130 876370 720640 819650 751020 749360 672330 756980 782220 774630 TRUE FALSE 814984.1419 851376.7857 850875.6786 861952.2347 775177.2404 764512.5726 680558.1757 741348.0985 693425.6649 722163.6201 1.128531152 1.178925055 1.178231158 1.193569173 1.073409431 1.058641769 0.942387787 1.026565279 0.960205756 1 19.46196622 2.851274907 1.723557544 0.989154179 1.171108224 0.861195921 0.032772309 0.116458288 0.691448314 0.01152948 0.012235049 710.0270708 -2.851274907 0.181954045 GSNYWR ddPTM_BT-474_Pertuzumab_2h_R1 5 GSNYWR 6 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 123.99 0.043155 9615400000 8778690 10308940 9045550 10668080 9825210 8217780 10356010 9137080 9347910 10054290 FALSE TRUE 8435609.089 10014939.12 10680282.1 11218660.89 10141246.8 8383949.142 10482749.95 8948396.105 8286774.446 9373303.983 0.899961113 1.068453466 1.139436225 1.196873686 1.081928722 0.894449722 1.118362316 0.954668292 0.884082546 1 23.16012624 2.852303572 9.438901157 0.978908563 1.087408114 0.242443552 0.093165049 0.553486591 42.53758484 0.029191045 0.030979557 711.7108267 -2.852303572 0.108499552 ESVEDKLELR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESVEDKLELR 10 1 Q6I9Y2;A0A5S6STF9 Q6I9Y2 THOC7 THO complex subunit 7 homolog 0 97.911 0.0052312 310240000 752400 743940 596350 656870 761960 763020 780990 856650 916890 871950 FALSE TRUE 722995.3762 722723.5596 704123.7107 690771.1394 786469.1354 778448.7872 790547.9892 838959.8781 812808.4911 812892.0498 0.889411302 0.88907692 0.866195839 0.849769831 0.967495174 0.957628737 0.972512881 1.032068007 0.999897208 1 19.63270425 2.853049075 1.289765539 1.006625689 0.873666222 0.841664282 0.024030554 0.16048709 0.551935152 0.010662912 0.011191316 712.933586 -2.853049075 -0.132959467 SCGTDSQSENEAS(ph)PVKRPR ddPTM_BT-474_Pertuzumab_2h_R1 5 SCGTDSQSENEASPVKRPR 19 2 H0Y398;C9JQ48;Q9H8U3 H0Y398 ZFAND3 AN1-type zinc finger protein 3 1 SCGTDSQSENEAS(1)PVKRPR;SCGTDSQSENEAS(1)PVKRPR;SCGTDSQSENEAS(1)PVKRPR;SCGTDSQSENEAS(1)PVKRPR;SCGTDSQSENEAS(1)PVKRPR 207.24 1.71E-16 1742533000 615967 623959 458319 511280 555869 614376 588853 616606 669490 682600 TRUE FALSE 591894.3287 606164.3002 541147.4386 537667.2221 573749.0312 626799.1037 596059.5592 603872.8706 593492.3019 636366.894 0.930114898 0.952539024 0.850370193 0.84490131 0.901601005 0.984964978 0.936660227 0.948938225 0.932625986 1 19.27949926 2.853396161 6.555570981 0.954662068 0.892946476 0.444362336 0.035902515 0.262596384 13.37295619 0.011674362 0.012409828 713.5035866 -2.853396161 -0.061715591 EIVHLQAGQCGNQIGAK ddPTM_BT-474_Pertuzumab_2h_R1 6 EIVHLQAGQCGNQIGAK 17 0 P68371;M0R2D3;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;M0R2T4;P04350;M0QYM7;M0R042;M0R278 P68371;P04350 TUBB4B;TUBB4A Tubulin beta-4B chain;Tubulin beta-4A chain 0 ;;;;; 288.42 4.47E-37 25574200000 12868800 12745100 10877600 12237700 12502400 14032400 14231700 13897600 15107900 15911200 FALSE TRUE 12365873.07 12381622.23 12843424.29 12869289.16 12904551.05 14316144.74 14405871.8 13610609.7 13392914.53 14833520.25 0.833643859 0.834705587 0.865837918 0.867581595 0.869958771 0.965121192 0.971170131 0.917557631 0.902881737 1 23.82235768 2.853436949 4.215450692 0.945447438 0.852251672 0.751633423 0.027894366 0.128738599 3.853865345 0.009079721 0.009683587 713.5706005 -2.853436949 -0.093195765 S(ph)SFSQHAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.571)S(0.429)FSQHAR;S(0.972)S(0.028)FSQHAR;S(0.5)S(0.5)FS(0.001)QHAR 153.88 0.00027957 3345740000 2279520 2810010 2032710 2332120 2272590 1669070 2029070 2117260 1655240 1843510 TRUE FALSE 2190433.838 2729871.266 2400065.914 2452480.993 2345689.921 1702819.739 2053902.366 2073537.841 1467344.095 1718647.426 1.274510295 1.588383531 1.396485328 1.426983194 1.364846499 0.990790614 1.195069061 1.20649402 0.853778426 1 20.71284218 2.853684307 4.764994703 1.086719608 1.427593 0.68325327 0.121825508 0.143208627 5.033008134 0.03758541 0.04005013 713.9771404 -2.853684307 0.340873392 AQPFGFIDSDT(ph)DAEEERIPATPVVIPMKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQPFGFIDSDTDAEEERIPATPVVIPMKK 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.382)DT(0.618)DAEEERIPATPVVIPMKK 287.59 1.92E-70 377440000 221230 245070 178930 188740 220090 250660 242830 257920 306440 259360 TRUE FALSE 212584.087 238080.8435 211266.6313 198480.894 227169.3947 255728.5169 245801.8262 252593.8619 271654.2159 241793.3162 0.879197533 0.984646091 0.873748847 0.82087006 0.939518918 1.057632696 1.01657825 1.044668504 1.123497623 1 17.88341484 2.853742675 3.913677438 1.048031485 0.893875336 0.706573228 0.048636224 0.136420196 3.669840496 0.015627902 0.01667691 714.0731035 -2.853742675 -0.15415615 GNWAHSGFPEIAFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNWAHSGFPEIAFGR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 ; 185.67 4.13E-07 760460000 586670 670880 555260 652410 610380 579970 633300 576900 641370 688680 FALSE TRUE 563742.2878 651747.1593 655607.8337 686080.9583 630013.427 591697.3908 641050.5148 564986.8134 568564.3664 642035.0902 0.87805526 1.015127007 1.02114019 1.068603521 0.981275691 0.921596654 0.998466477 0.879993667 0.885565875 1 19.29229262 2.854144719 4.591012127 0.9309499 1.001579867 0.178649193 0.058724916 0.340089089 11.39178798 0.018429148 0.019645033 714.734456 -2.854144719 0.070629968 CSDVSELSSS(ph)PPGPYHQEPYVCKPEER ddPTM_BT-474_Pertuzumab_2h_R1 6 CSDVSELSSSPPGPYHQEPYVCKPEER 27 1 Q9Y478;F5H610;F5H2X8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 CSDVSELS(0.002)S(0.255)S(0.743)PPGPYHQEPYVCKPEER;CSDVSELS(0.199)S(0.168)S(0.633)PPGPYHQEPYVCKPEER;CSDVSELS(0.002)S(0.154)S(0.844)PPGPYHQEPYVCKPEER;CSDVSELS(0.033)S(0.163)S(0.804)PPGPYHQEPYVCKPEER;CSDVSELS(0.001)S(0.143)S(0.856)PPGPYHQEPYVCKPEER;CSDVSELS(0.001)S(0.171)S(0.829)PPGPYHQEPYVCKPEER 234.01 3.47E-45 12257790000 2799640 2826580 2090350 2500730 2612740 3031810 2947450 2904270 3493040 3267200 TRUE FALSE 2690226.974 2745968.706 2468122.745 2629792.975 2696781.155 3093115.275 2983521.775 2844295.81 3096524.743 3045909.634 0.883226128 0.901526649 0.810307278 0.863385094 0.885377926 1.015498044 0.979517495 0.933808337 1.016617403 1 21.53844171 2.855287446 4.995371936 0.979698813 0.864717178 0.783643247 0.03152034 0.115515021 4.285667834 0.010236597 0.010905986 716.6175604 -2.855287446 -0.114981634 DVDDGLQAAEEVGYPVMIK ddPTM_BT-474_Pertuzumab_2h_R1 3 DVDDGLQAAEEVGYPVMIK 19 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 226.19 3.63E-19 134109000 208139 204778 204262 206459 239999 255865 276363 278778 352285 338918 FALSE TRUE 200004.6978 198937.9319 241176.6872 217114.3737 247718.7858 261038.7656 279745.2131 273021.1369 312295.0837 315962.782 0.633000813 0.629624574 0.763307266 0.687151735 0.784012548 0.826169348 0.88537394 0.864092711 0.988391993 1 18.2693951 2.856618506 0.347014832 1.017965636 0.563533692 0.915946924 0.036494415 0.502808701 0.116941478 0.040526267 0.085244297 718.8172747 -2.856618506 -0.454431944 DDILNGSHPVSFDK ddPTM_BT-474_Pertuzumab_2h_R1 3 DDILNGSHPVSFDK 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;; 177.88 2.05E-06 1268050000 1866680 1759810 1650890 1650030 1856310 1936170 1869210 2066320 2305200 2160230 FALSE TRUE 1793728.082 1709621.942 1949242.547 1735188.246 1916019.897 1975320.684 1892085.951 2023649.77 2043523.36 2013915.698 0.890666915 0.848904422 0.967886863 0.861599246 0.951390318 0.980835834 0.939506034 1.004833406 1.01470154 1 20.94157186 2.85700223 0.548636193 1.012050569 0.87272013 0.629782907 0.034673294 0.595403087 0.379065646 0.027529385 0.037138696 719.4526714 -2.85700223 -0.139330439 FNEYWR ddPTM_BT-474_Pertuzumab_2h_R1 2 FNEYWR 6 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 105.2 0.077189 1695800000 1269600 1688010 1538030 1728970 1543160 1109470 1437460 1263680 1339080 1598320 FALSE TRUE 1219982.628 1639869.608 1815986.234 1818202.349 1592797.143 1131904.244 1455052.065 1237584.566 1187073.252 1490064.363 0.818744921 1.10053609 1.218730063 1.220217324 1.068945196 0.759634464 0.976502829 0.830557792 0.796659045 1 20.50694322 2.85727162 6.209911902 0.869073844 1.104474206 0.418773374 0.1248192 0.222095702 10.49682181 0.038657 0.04111439 719.8990823 -2.85727162 0.235400362 HIVLSGGSTMYPGLPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIVLSGGSTMYPGLPSR 17 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 73.464 0.026215 383520000 250870 262850 222600 233350 224720 235140 246470 206790 285870 240120 FALSE TRUE 241065.723 255353.7754 262828.7717 245393.2215 231948.3229 239894.6919 249486.3736 202519.7142 253419.2361 223856.4585 1.076876337 1.140703186 1.174095103 1.096207914 1.036147558 1.071645167 1.114492632 0.904685599 1.132061312 1 17.77221442 2.858096514 0.850793096 1.015047893 1.131779667 0.243375414 0.064835316 0.736550484 1.166752084 0.03865809 0.041641947 721.2677501 -2.858096514 0.116731775 HPLLSSGGPQS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 5 HPLLSSGGPQSPLR 14 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR 208.52 5.11E-09 5085010000 2017970 2136610 2086620 2263070 2124580 1721650 2235980 1599670 2187180 2576410 TRUE FALSE 1939105.501 2075675.975 2463718.651 2379867.314 2192919.045 1756462.943 2263344.592 1566636.255 1938900.496 2401907.456 0.80731899 0.864178164 1.025734212 0.9908239 0.912990648 0.731278359 0.942311323 0.652246718 0.807233639 1 21.19574914 2.85943558 6.909851245 0.802694694 0.928321602 0.1376322 0.10880324 0.376655335 19.83840019 0.033111362 0.035191343 723.4950758 -2.85943558 0.125626908 GEEGRPGK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEEGRPGK 8 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 85.67 0.015119 941730000 1976390 1964750 1715010 2103350 1899280 1724400 1850620 1842430 1931720 1993680 FALSE TRUE 1899150.494 1908717.254 2024950.457 2211904.146 1960372.066 1759268.549 1873268.441 1804383.177 1712439.244 1858646.278 1.021792321 1.026939486 1.08947597 1.190061913 1.054731118 0.9465322 1.007867104 0.970805041 0.921336816 1 20.8258208 2.859520865 5.071755777 0.971432458 1.083286447 0.549969257 0.04884624 0.186772233 6.99551232 0.016080388 0.01713815 723.6371673 -2.859520865 0.111853988 GKAS(ph)PFEEDQNR ddPTM_BT-474_Pertuzumab_2h_R1 6 GKASPFEEDQNR 12 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR 188.12 2.53E-05 7443560000 5268490 5499730 4310160 4822900 5052110 5631700 5271660 5644750 6321000 6250020 TRUE FALSE 5062591.586 5342883.085 5089101.791 5071810.447 5214615.706 5745576.833 5336176.152 5528183.94 5603466.58 5826700.578 0.868860776 0.916965444 0.873410556 0.870442951 0.89495172 0.986077241 0.915814376 0.948767465 0.961687752 1 22.47424774 2.859846013 5.928127694 0.9543971 0.884160803 0.701378368 0.025096118 0.140911394 6.286203135 0.007437635 0.007914575 724.1791445 -2.859846013 -0.070236297 VGNHTAEGTGTNKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VGNHTAEGTGTNKK 14 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ; 105 0.00066541 620577000 469146 434510 353620 385140 417595 468180 442650 446630 582530 510580 FALSE TRUE 450811.2557 422118.2002 417527.0002 405017.1216 431027.3224 477646.9204 448067.2831 437406.9344 516403.6366 475997.9618 0.947086525 0.886806739 0.877161319 0.850879949 0.905523462 1.003464213 0.941321852 0.918926066 1.084886235 1 18.86059587 2.860029365 5.293434665 0.975003461 0.888146852 0.49244411 0.047790836 0.225241255 8.855369248 0.015021639 0.016003176 724.4849451 -2.860029365 -0.086856609 DHGLEVLGLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHGLEVLGLVR 11 0 Q96DE0-3;Q96DE0;K7EIN2;Q9BRJ7 Q96DE0-3;K7EIN2 NUDT16;NUDT16L1 U8 snoRNA-decapping enzyme;Protein syndesmos 0 ; 206.97 2.46E-08 261060000 256210 249970 241570 239180 232590 150887 256080 83646 243970 220532 FALSE TRUE 246197.0299 242841.1003 285227.0727 251524.1085 240071.4686 153938.0385 259213.9836 81918.68087 216275.5484 205595.1712 1.197484496 1.181161498 1.387323793 1.223395019 1.16769021 0.748743454 1.260798014 0.398446522 1.05194858 1 17.64944685 2.860500013 4.152830996 0.848405372 1.247576041 0.371800292 0.21814353 0.224493944 6.526591643 0.067452033 0.072071113 725.2704992 -2.860500013 0.399170669 RT(ph)ETSLPETEVDHNMDVNTEEDDDGELALWSPEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTETSLPETEVDHNMDVNTEEDDDGELALWSPEVK 35 1 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;Q8NI35-5 A0A2R8Y549 INADL InaD-like protein 1 RT(0.2)ET(0.2)S(0.2)LPET(0.2)EVDHNMDVNT(0.2)EEDDDGELALWSPEVK 46.772 0.065243 55422000 24734 22009 16377 20987 21372 20227 22996 18757 26204 21141 TRUE FALSE 23767.36794 21381.32487 19336.6882 22070.14159 22059.44979 20636.0038 23277.43193 18369.6614 23229.43178 19709.10124 1.205908258 1.08484525 0.981104515 1.11979442 1.11925194 1.047029164 1.181049894 0.932039527 1.178614463 1 14.26657437 2.86072591 0.011612798 3.19E-07 2.164004938 0.094423276 0.083963704 4740.611296 19.776859 1777.634894 1905.991367 725.6478449 -2.86072591 2.164004618 KWQTMIEAHVDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KWQTMIEAHVDVK 13 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ; 130.88 8.89E-05 944880000 3769200 3184100 3176200 2668000 3203800 3422400 3470700 3252600 3970100 3746400 FALSE TRUE 3621895.497 3093292.586 3750209.994 2805695.8 3306853.137 3491603.273 3513175.465 3185432.673 3519430.892 3492652.991 1.037004107 0.885657004 1.073742511 0.803313644 0.946802658 0.99969945 1.005875898 0.912038122 1.007666923 1 21.73589188 2.860757184 9.460696943 0.975773132 0.944404019 0.045317449 0.074704191 1.406568795 102.7588954 0.021972613 0.023319324 725.7001025 -2.860757184 -0.031369113 MGPLGLDHMASSIER ddPTM_BT-474_Pertuzumab_2h_R1 8 MGPLGLDHMASSIER 15 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;; 238.03 9.35E-18 7130400000 4317220 5038540 4183310 4529660 4478550 3985670 4517080 4127488 4606376 4707724 FALSE TRUE 4148498.269 4894845.772 4939327.174 4763436.295 4622606.628 4066262.978 4572361.376 4042253.93 4083479.508 4388865.66 0.945232457 1.115287218 1.125422275 1.08534566 1.053257718 0.926495202 1.041809372 0.921024757 0.930417977 1 22.06541668 2.861175515 4.981710444 0.962766435 1.074591751 0.434980193 0.057388697 0.203856247 7.457836978 0.017543385 0.018704969 726.3994639 -2.861175515 0.111825316 DLLIDEWK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLLIDEWK 8 0 Q16539-2;Q16539;B4E0K5 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 ;; 143.01 0.0014152 95296000 300607 281654 255128 259683 301685 317910 306748 350634 369163 357610 FALSE TRUE 288858.9461 273621.5037 301235.3049 273085.2708 311388.972 324338.358 310502.0738 343393.2854 327257.1639 333388.7562 0.866432778 0.82072805 0.903555682 0.819119618 0.934011619 0.972853319 0.931351367 1.030008598 0.981608281 1 18.34684592 2.861431008 1.205306426 0.995797071 0.849773138 0.762464095 0.033847842 0.202799449 0.61563245 0.01450742 0.015314094 726.8269258 -2.861431008 -0.146023933 SGDAAIVDMVPGKPMCVESFSDYPPLGR ddPTM_BT-474_Pertuzumab_2h_R1 7 SGDAAIVDMVPGKPMCVESFSDYPPLGR 28 1 P68104;A0A087WVQ9;Q5VTE0 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ;;;;;; 260.46 9.61E-54 12986590000 5039436 4801405 4100528 4635313 4885152 5116120 5125252 5356673 5895372 6130980 FALSE TRUE 4842489.27 4664473.63 4841584.625 4874542.059 5042287.351 5219571.452 5187976.367 5246055.831 5226154.086 5715723.264 0.847222485 0.816077584 0.847064213 0.852830313 0.882178356 0.91319527 0.907667521 0.917828871 0.914346942 1 22.44650464 2.862190313 0.126434104 1.07149348 0.690494717 0.922559068 0.01388564 3.759537167 0.18729135 0.177002659 0.360424288 728.0987957 -2.862190313 -0.380998763 AGVVGPELHEQLLSAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGVVGPELHEQLLSAEK 17 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 233.52 4.12E-20 493950000 705280 717700 592760 708990 721840 694730 780500 816800 918400 829430 FALSE TRUE 677716.8779 697231.8987 699884.9179 745581.0589 745058.6392 708777.9166 790051.9925 799932.7946 814147.0822 773251.9673 0.876450247 0.901687843 0.905118832 0.964214888 0.963539274 0.91661961 1.021726456 1.0345047 1.052887179 1 19.56057907 2.86294358 0.587277939 1.040879318 0.883111742 0.755347935 0.0291614 0.429201825 0.317911402 0.02405646 0.03097225 729.3627516 -2.86294358 -0.157767576 IEHLYK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEHLYK 6 0 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 90.285 0.049203 573330000 1544100 1475000 1263700 1474000 1561000 1560700 1728000 1757500 1960900 1913000 FALSE TRUE 1483754.865 1432934.444 1492078.701 1550073.317 1611210.983 1592258.423 1749147.781 1721207.011 1738306.853 1783430.806 0.8319666 0.803470726 0.836633917 0.869152485 0.903433415 0.892806392 0.980776924 0.965110059 0.974698232 1 20.76622381 2.863558157 0.596829508 0.996058264 0.804524537 0.9347117 0.017137451 0.188837217 0.144922201 0.013046561 0.016614455 730.3956152 -2.863558157 -0.191533726 SPIIFIGTGEHIDDFEPFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPIIFIGTGEHIDDFEPFK 19 0 G3V4F7;P61011-2;P61011 G3V4F7 SRP54 Signal recognition particle 54 kDa protein 0 ; 260.29 4.21E-31 884960000 1257530 1176110 1043080 1126910 1167990 1357660 1254140 1323980 1476510 1447910 FALSE TRUE 1208384.337 1142568.494 1231587.759 1185069.96 1205559.459 1385112.815 1269488.54 1296639.35 1308902.775 1349841.766 0.895204436 0.846446245 0.912394171 0.877932503 0.893111689 1.026129766 0.940472115 0.960586183 0.969671266 1 20.36435887 2.864175927 6.963177502 0.972193877 0.88294019 0.753286549 0.026879571 0.127706867 6.702565898 0.007948886 0.008448726 731.4353188 -2.864175927 -0.089253688 VRPAS(ph)TGGLSLLPPPPGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VRPASTGGLSLLPPPPGGK 19 1 Q9NVZ3;Q9NVZ3-2;D6RB24;Q9NVZ3-4 Q9NVZ3 NECAP2 Adaptin ear-binding coat-associated protein 2 1 VRPAS(0.47)T(0.47)GGLS(0.06)LLPPPPGGK 51.834 0.080127 282620000 164060 157690 117740 140220 142510 124510 115400 137160 126150 119620 TRUE FALSE 157648.3538 153192.8356 139018.2371 147456.771 147093.9636 127027.6775 116812.2997 134327.5981 111829.9809 111518.0309 1.413657976 1.373704633 1.246598743 1.322268425 1.319015073 1.13907748 1.047474555 1.204537034 1.002797306 1 16.76691747 2.864712412 0.363433857 0.989701278 1.459742105 0.802036027 0.06486175 0.836075947 0.21319981 0.074008781 0.149852804 732.3394212 -2.864712412 0.470040828 S(ph)PPLATGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPLATGYR 9 0 Q86U06-3;Q86U06-5;Q86U06-2;Q86U06 Q86U06-3 RBM23 Probable RNA-binding protein 23 1 S(1)PPLATGYR 70.496 0.054805 376010000 174470 164010 140290 137210 161850 174390 178340 176960 207500 198380 TRUE FALSE 167651.5195 159332.5954 165643.5237 144291.4245 167056.0522 177916.2853 180522.5783 173305.7142 183945.4699 184943.5459 0.906501055 0.861520171 0.895643711 0.780191727 0.903281331 0.962003212 0.976095583 0.937073599 0.994603348 1 17.49672543 2.865437909 3.717574823 0.967636272 0.861609207 0.685584701 0.035974394 0.143879271 3.553024321 0.011134573 0.01193205 733.5638292 -2.865437909 -0.106027065 SVPIWER ddPTM_BT-474_Pertuzumab_2h_R1 3 SVPIWER 7 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ;; 113.14 0.014418 1509910000 2180870 2164640 2136860 1289970 1704030 1789290 1415740 862910 1501210 1408650 FALSE TRUE 2095639.189 2102906.587 2523038.136 1356545.506 1758841.673 1825470.67 1433066.25 845090.607 1330798.934 1313240.881 1.595776693 1.601310633 1.921230273 1.032975386 1.339313829 1.39005014 1.091244014 0.643515306 1.013370018 1 20.32470014 2.865512122 0.670811925 0.838905567 1.694268207 0.608978358 0.223552769 0.492584574 0.485736998 0.16723948 0.198441903 733.689192 -2.865512122 0.855362641 ALEHVPNSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEHVPNSVR 10 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 83.397 0.015631 582670000 302460 309650 276560 298540 300290 277310 298100 302830 322560 348910 FALSE TRUE 290639.5288 300819.0852 326540.544 313947.6852 309949.1006 282917.3982 301748.237 296576.4547 285944.3411 325278.0149 0.893511137 0.924806078 1.003881385 0.965167244 0.952874422 0.869771043 0.927662563 0.911762988 0.879076753 1 18.31131379 2.866541911 20.08472527 0.912909076 0.950817523 0.108152638 0.042185532 6.924415303 1068.832667 0.012614678 0.013379917 735.4309634 -2.866541911 0.037908446 EELLDGEDYNFLQGASDQES(ph)NGSANFYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 EELLDGEDYNFLQGASDQESNGSANFYIK 29 0 Q05BQ5 Q05BQ5 MBTD1 MBT domain-containing protein 1 1 EELLDGEDYNFLQGAS(0.422)DQES(0.511)NGS(0.066)ANFY(0.001)IK 90.55 0.0010209 20340000 20162 17124 14781 19952 16220 21658 20365 20460 25858 22387 TRUE FALSE 19374.04675 16635.64029 17452.2555 20981.72511 16741.73103 22095.9396 20614.23296 20037.49385 22922.70825 20870.70855 0.928288884 0.797080763 0.836208098 1.005319252 0.802163999 1.058705772 0.987711218 0.960077316 1.098319599 1 14.34919196 2.866725019 0.945522816 1.018655765 0.857900627 0.43422349 0.075026461 0.528683698 1.023940498 0.039259594 0.041989501 735.7411024 -2.866725019 -0.160755138 TMLEDLGMDDEGDDDPVPLPNVNAAILK ddPTM_BT-474_Pertuzumab_2h_R1 9 TMLEDLGMDDEGDDDPVPLPNVNAAILK 28 0 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3;E5RI56 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;;;;;;; 264.36 4.83E-54 1625655000 1230498 1239977 1092817 1226694 1204959 1351818 1343439 1471693 1593262 1602143 FALSE TRUE 1182408.778 1204614.07 1290313.341 1290003.824 1243717.601 1379152.686 1359880.408 1441302.025 1412401.577 1493628.428 0.791635159 0.806501837 0.863878404 0.863671179 0.832682063 0.923357283 0.910454289 0.964966921 0.945617766 1 20.51038986 2.866739184 0.334587525 1.007925277 0.760068247 0.898084689 0.021092237 0.6133124 0.132013127 0.025465005 0.055817307 735.7651 -2.866739184 -0.247857029 TKEEVNEWFTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKEEVNEWFTK 11 1 Q9UKD2 Q9UKD2 MRTO4 mRNA turnover protein 4 homolog 0 68.513 0.054874 0 831580 828770 665030 647980 772080 872160 819570 858420 1068900 967940 FALSE TRUE 799080.9342 805134.2911 785215.7145 681422.3255 796914.6544 889795.6728 829600.1428 840693.327 947562.9532 902380.5616 0.885525429 0.892233638 0.870160271 0.755138524 0.883124802 0.986053679 0.919346203 0.931639447 1.050070218 1 19.78337647 2.866967143 4.813014556 0.964547778 0.851379743 0.591395957 0.049813553 0.184275797 6.439453018 0.016018557 0.017100568 736.1514009 -2.866967143 -0.113168035 DLDEEIFDDDDFYHQLLR ddPTM_BT-474_Pertuzumab_2h_R1 5 DLDEEIFDDDDFYHQLLR 18 0 Q9NY61;A0A087WTH8;A0A087WWS8 Q9NY61 AATF Protein AATF 0 ;;;; 300.03 1.65E-49 531178000 504870 507450 438473 485880 517059 519387 474242 493780 560668 584824 FALSE TRUE 485139.1222 492978.0228 517714.8249 510956.325 533690.6723 529889.361 480045.9155 483583.2704 497023.3192 545213.3496 0.889815194 0.904192869 0.949563736 0.937167671 0.978865746 0.971893593 0.880473517 0.886961537 0.911612527 1 19.05646136 2.86761369 0.004052974 1.851361309 2.69E-05 0.11238546 0.038141884 70410.53128 101.814887 22967.19212 23537.63417 737.2481477 -2.86761369 -1.851334399 EEQKLEAHSDWVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEQKLEAHSDWVR 13 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 142.85 2.44E-05 286990000 207530 200190 179210 219770 211750 217090 249200 243370 308160 280390 FALSE TRUE 199419.4982 194480.7772 211597.2335 231112.356 218561.1311 221479.7085 252249.7841 238344.3245 273178.9687 261398.9356 0.762893306 0.743999882 0.809480089 0.884136561 0.836120968 0.847286191 0.964999278 0.911802965 1.045065345 1 17.99589374 2.867994248 0.379578153 1.024123286 0.71417733 0.823325599 0.039892348 0.67737309 0.189111945 0.04201724 0.081695647 737.8944578 -2.867994248 -0.309945956 HPTPGSSDPLIQPSSPAVCPEPPSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 HPTPGSSDPLIQPSSPAVCPEPPSSPK 27 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9 A0A0G2JQJ7 MAPT Microtubule-associated protein tau 1 HPTPGSSDPLIQPSSPAVCPEPPS(0.358)S(0.642)PK 190.81 3.62E-18 1388800000 684160 666860 504290 630350 557470 564550 570940 447990 665940 705830 TRUE FALSE 657422.2708 647841.8057 595426.4209 662882.439 575401.5288 575965.5878 577927.3345 438738.8499 590345.283 658023.5054 0.999086302 0.984526845 0.904871051 1.007384134 0.874439171 0.875296373 0.878277645 0.66675255 0.897149233 1 19.32777959 2.868086793 1.414937683 0.820029928 0.971896586 0.206680177 0.086307038 0.452102688 1.849966797 0.034916805 0.03728408 738.0517138 -2.868086793 0.151866658 VHMFEAHSDYIR ddPTM_BT-474_Pertuzumab_2h_R1 3 VHMFEAHSDYIR 12 0 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 ;; 213.63 3.68E-09 810010000 306861 354600 363431 280059 292651 158142 327162 36749.7 254175 268550 FALSE TRUE 294868.5329 344487.1552 429111.0662 294512.8786 302064.3852 161339.7396 331165.9064 35990.80585 225322.1196 250360.8693 1.177774041 1.37596245 1.713970188 1.176353475 1.206515962 0.64442874 1.32275426 0.143755715 0.899989364 1 17.93364957 2.869055736 1.279470337 0.699385325 1.414265104 0.397335963 0.318804737 0.380254024 1.290116417 0.134591081 0.143353337 739.7001992 -2.869055736 0.71487978 KVEGAPTQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEGAPTQGR 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 120.55 0.00087355 195400000 209290 204770 168890 180630 199010 210820 225540 240420 208840 207700 FALSE TRUE 201110.7154 198930.1601 199412.1799 189952.3359 205411.3374 215082.9248 228300.226 235455.243 185133.3587 193632.294 1.038621767 1.027360447 1.029849804 0.980995122 1.060832019 1.110780234 1.179040031 1.2159916 0.956107863 1 17.56296006 2.869204412 3.21597459 1.122222759 1.02058553 0.113410711 0.075415298 0.346527955 6.751691064 0.024421802 0.026266712 739.9534709 -2.869204412 -0.101637229 KNPEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KNPEFR 6 1 H0Y8S5;D6RBI1;D6RJ86;D6RFY6;Q96H20-2;Q96H20 H0Y8S5 SNF8 Vacuolar-sorting protein SNF8 0 86.113 0.0865 172040000 267860 305310 245810 269780 317790 328260 367830 384050 397870 400540 FALSE TRUE 257391.7351 296602.8577 290233.335 283703.3781 328012.004 334897.6421 372331.6136 376119.2333 352705.4656 373411.069 0.689298621 0.794306549 0.77724888 0.759761565 0.878420677 0.896860511 0.997109203 1.007252501 0.944550108 1 18.51040517 2.869458092 1.110846047 0.99477268 0.748037414 0.899421414 0.034330759 0.134387652 0.351119292 0.015885614 0.016893727 740.3858188 -2.869458092 -0.246735265 NFYVEHPEVAR ddPTM_BT-474_Pertuzumab_2h_R1 8 NFYVEHPEVAR 11 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 133.32 0.00016411 9597450000 5245260 5381360 4372800 4896730 4827790 4644400 4540160 4696250 5394990 5235230 FALSE TRUE 5040269.44 5227888.882 5163062.232 5149450.822 4983080.25 4738312.95 4595723.836 4599270.796 4782573.353 4880643.209 1.032705982 1.071147523 1.057865124 1.055076268 1.020988431 0.970837807 0.941622577 0.942349317 0.979906366 1 22.21863986 2.869835567 2.261431912 0.958052332 1.055788445 0.824505544 0.018927622 0.10814411 1.088684217 0.006344061 0.006845076 741.0296194 -2.869835567 0.097736113 LRETFER ddPTM_BT-474_Pertuzumab_2h_R1 1 LRETFER 7 1 Q9Y2W2;F5H5G4 Q9Y2W2 WBP11 WW domain-binding protein 11 0 130.28 0.0032638 130460000 65462 63771 51648 60582 59065 53640 57445 59113 56847 64611 FALSE TRUE 62903.67267 61952.31352 60981.9425 63708.64428 60964.87937 54724.63755 58148.02909 57892.29589 50393.96688 60234.83942 1.044307136 1.028512969 1.012403172 1.057671024 1.012119895 0.908521349 0.965355426 0.961109824 0.836624906 1 15.87831055 2.870578897 4.88052029 0.937293565 1.033649807 0.574929059 0.041832891 0.169034368 6.002025254 0.012517101 0.013366297 742.2990376 -2.870578897 0.096356241 ADAASSLTVDVT(ph)PPTAK ddPTM_BT-474_Pertuzumab_2h_R1 6 ADAASSLTVDVTPPTAK 17 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ADAASSLTVDVT(1)PPTAK;ADAASSLTVDVT(0.999)PPT(0.001)AK;ADAASSLTVDVT(0.987)PPT(0.013)AK;ADAASSLTVDVT(0.977)PPT(0.023)AK;ADAASSLTVDVT(1)PPTAK;ADAASSLTVDVT(0.991)PPT(0.009)AK 272.4 1.38E-34 2590260000 2201860 2079710 1996120 2043120 2254240 2487200 2394800 2581180 3021290 3022850 TRUE FALSE 2115808.877 2020398.707 2356863.287 2148565.668 2326749.677 2537492.888 2424108.279 2527877.731 2678325.825 2818109.677 0.750790111 0.716934023 0.836327737 0.762413786 0.825641988 0.900423752 0.860189473 0.897011834 0.950398009 1 21.42629633 2.870673711 0.252009455 1.021960167 0.652197199 0.865582535 0.031418489 1.212823338 0.155461721 0.055414311 0.144910873 742.4611103 -2.870673711 -0.369762968 STSTPTS(ph)PGPR ddPTM_BT-474_Pertuzumab_2h_R1 7 STSTPTSPGPR 11 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;H3BRB0;A0A0C4DGL7 Q8WWM7 ATXN2L Ataxin-2-like protein 1 STST(0.002)PT(0.012)S(0.986)PGPR;STST(0.009)PT(0.083)S(0.907)PGPR;ST(0.002)S(0.008)T(0.228)PT(0.094)S(0.668)PGPR;STST(0.003)PT(0.082)S(0.915)PGPR;STST(0.004)PT(0.195)S(0.802)PGPR;STST(0.001)PT(0.015)S(0.984)PGPR;STS(0.001)T(0.002)PT(0.046)S(0.951)PGPR 171.09 1.57E-05 12077760000 12762860 14529370 12299260 12769290 10899140 11359500 7996040 10270130 10585630 10502440 TRUE FALSE 12264073.32 14115006.59 14522009.88 13428314.59 11249720.74 11589196.87 8093897.929 10058048.23 9383993.661 9791100.384 1.252573545 1.441615961 1.483184658 1.371481658 1.148974098 1.183646007 0.826658661 1.027264335 0.958420739 1 23.22303958 2.871295194 1.425188788 0.963746919 1.403164107 0.801459915 0.092592442 0.162728396 0.675104772 0.036390082 0.038974676 743.5243473 -2.871295194 0.439417188 WPEVDDDSIEDLGEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 WPEVDDDSIEDLGEVK 16 0 O43583 O43583 DENR Density-regulated protein 0 182.02 5.15E-09 77036000 90273 76776 87601 76615 102490 96230 106360 121120 125100 121670 FALSE TRUE 86745.03136 74586.42365 103432.4494 80569.10933 105786.6839 98175.83653 107661.6655 118618.8297 110899.1725 113429.1825 0.764750564 0.657559386 0.911868067 0.710303182 0.932623171 0.865525382 0.949153146 1.04575231 0.977695246 1 16.79143233 2.871549813 0.653255936 1.025118054 0.727582931 0.659773944 0.071848966 0.43010885 0.401349488 0.049659461 0.060203668 743.9603893 -2.871549813 -0.297535123 EVIEIEDAS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVIEIEDASPTK 12 0 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 EVIEIEDAS(0.985)PT(0.015)K;EVIEIEDAS(0.993)PT(0.007)K;EVIEIEDAS(0.994)PT(0.006)K 289.72 4.55E-36 276370000 890030 790170 967740 1046140 986640 828270 1189950 1360670 1365050 1593160 TRUE FALSE 855246.6436 767635.1253 1142632.145 1100131.411 1018376.172 845018.1869 1204512.964 1332571.689 1210095.247 1485253.854 0.575825231 0.516837659 0.769317745 0.740702613 0.68565799 0.568938559 0.810981207 0.8972013 0.814739678 1 20.5022781 2.871615623 0.149053458 1.140646558 0.301691168 0.669452964 0.083854859 6.915431015 0.418363001 0.678644071 1.531631059 744.0731322 -2.871615623 -0.838955389 QESDKNGESAS(ph)PERDR ddPTM_BT-474_Pertuzumab_2h_R1 5 QESDKNGESASPERDR 16 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGES(0.098)AS(0.902)PERDR;QESDKNGES(0.005)AS(0.995)PERDR;QESDKNGES(0.151)AS(0.849)PERDR;QESDKNGESAS(1)PERDR;QESDKNGES(0.044)AS(0.956)PERDR 257.73 5.78E-27 1230972000 1412790 1260230 940867 977781 1134740 1324130 1183560 1282300 1521630 1256700 TRUE FALSE 1357576.605 1224289.474 1110902.596 1028244.395 1171239.943 1350904.816 1198044.761 1255820.057 1348900.942 1171582.59 1.158754506 1.044987767 0.948206815 0.877654212 0.999707535 1.153059825 1.022586689 1.07190058 1.151349426 1 20.16002723 2.871795784 12.35880044 1.078333456 0.997481263 0.169338181 0.080779445 1.087451643 102.5712567 0.025719084 0.027283127 744.3818648 -2.871795784 -0.080852193 KVDAETVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVDAETVGR 9 1 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 ; 140.07 0.00017632 997480000 1043040 1052630 863980 987110 1012190 1121420 1099360 1137440 1238150 1271240 FALSE TRUE 1002276.844 1022610.023 1020120.405 1038054.865 1044748.011 1144095.881 1112814.297 1113951.467 1097600.403 1185137.782 0.845704912 0.862861718 0.860761019 0.875893825 0.881541392 0.96536951 0.938974618 0.939934143 0.926137382 1 20.17662336 2.872398286 3.680664855 0.948260392 0.862643655 0.825121603 0.020450238 0.100112155 2.432667251 0.006230847 0.006693823 745.4152721 -2.872398286 -0.085616737 RLQQQQRPEDAEDGAEGGGK ddPTM_BT-474_Pertuzumab_2h_R1 4 RLQQQQRPEDAEDGAEGGGK 20 2 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;; 232.84 1.82E-27 964100000 701426 650790 534678 551112 628387 705573 658891 726786 808269 769694 FALSE TRUE 674013.4965 632230.1064 631306.2084 579554.9564 648599.6385 719840.1695 666954.7052 711777.6151 716517.6917 717561.9398 0.939310545 0.881080881 0.87979333 0.807672375 0.903893591 1.003174959 0.929473357 0.991938919 0.998544728 1 19.45274384 2.874367599 4.783569854 0.979789677 0.875205024 0.673089728 0.035849919 0.139566628 4.845541942 0.011206769 0.011978093 748.8030409 -2.874367599 -0.104584653 LFPADTS(ph)PSTATK ddPTM_BT-474_Pertuzumab_2h_R1 8 LFPADTSPSTATK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 LFPADT(0.119)S(0.877)PS(0.003)TATK;LFPADT(0.328)S(0.622)PS(0.038)T(0.011)AT(0.001)K;LFPADT(0.017)S(0.983)PSTATK;LFPADT(0.004)S(0.959)PS(0.035)T(0.002)ATK;LFPADT(0.099)S(0.901)PS(0.001)TATK;LFPADT(0.062)S(0.938)PSTATK;LFPADT(0.233)S(0.766)PSTATK;LFPADT(0.038)S(0.962)PSTATK 268.21 1.15E-24 3462730000 5192870 4983590 4770540 4921440 5009540 5556310 5450800 6167360 6371710 6443410 TRUE FALSE 4989926.899 4841462.893 5632682.698 5175436.108 5170676.404 5668662.395 5517508.521 6040001.861 5648420.193 6006992.102 0.830686443 0.805971243 0.937687715 0.861568655 0.860776295 0.943677351 0.918514363 1.005495223 0.940307578 1 22.51821134 2.874621987 0.396791969 1.005727543 0.807642936 0.674534568 0.036968017 0.899563911 0.275818868 0.037894325 0.070832031 749.2417807 -2.874621987 -0.198084607 GWVHDSIDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWVHDSIDYR 10 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 0 67.726 0.062111 79032000 79572 151960 101470 174430 118180 74870 112200 99587 57693 85032 FALSE TRUE 76462.23827 147626.2496 119807.8862 183432.3532 121981.367 76383.9227 113573.1372 97530.49365 51143.93251 79272.7069 0.964546832 1.862258214 1.511338402 2.31394083 1.538756172 0.963558905 1.432689025 1.230316176 0.645164452 1 16.27453662 2.874662808 5.273597685 1.116162899 1.694738449 0.381804862 0.368070533 0.252082954 9.808135359 0.111952921 0.119445114 749.3122081 -2.874662808 0.57857555 HELLQPFNVLYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HELLQPFNVLYEK 13 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 120.92 0.00025264 1763320000 1383780 1406580 1253240 1311440 1164340 1256190 1297420 920410 1498310 1404130 FALSE TRUE 1329700.348 1366465.716 1479728.346 1379123.576 1201792.054 1281591.022 1313298.214 901403.2119 1328228.13 1309027.024 1.015792893 1.043878919 1.130403207 1.05354859 0.918080399 0.97904092 1.003262874 0.688605502 1.014668227 1 20.32006345 2.874770573 1.151225882 0.885700124 1.06579309 0.224635481 0.098076339 0.535905915 1.496330311 0.046487386 0.049702242 749.4981641 -2.874770573 0.180092966 LNLSTRPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNLSTRPEK 9 1 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 87.298 0.012363 783600000 622800 665140 606670 923500 735740 686110 1036240 1106610 1180400 1236810 FALSE TRUE 598460.2875 646170.8584 716308.7643 971161.9457 759405.7453 699983.6143 1048921.815 1083758.117 1046405.941 1153039.757 0.51902832 0.560406399 0.621235096 0.842262324 0.658611935 0.607076738 0.909701343 0.939913919 0.907519393 1 20.13701083 2.874836323 0.337436428 1.03747725 0.448547721 0.742672461 0.086626261 1.12228568 0.244869208 0.11136701 0.243767767 749.6116422 -2.874836323 -0.588929529 EKEDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEDFR 6 1 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 67.035 0.091051 572070000 2029100 2060700 1594900 1777400 1969100 2032500 2085900 2174400 2316900 2402600 FALSE TRUE 1949800.529 2001930.854 1883133.908 1869131.827 2032437.89 2073598.543 2111427.868 2129497.88 2053895.225 2239869.762 0.870497277 0.893771097 0.840733662 0.83448237 0.907391101 0.925767461 0.942656535 0.950723973 0.916970826 1 21.09498342 2.875053627 2.205044238 0.946506264 0.861398693 0.715629585 0.025809403 0.172235285 1.651263839 0.008696705 0.009413743 749.9868128 -2.875053627 -0.08510757 VDKGGDPALIR ddPTM_BT-474_Pertuzumab_2h_R1 3 VDKGGDPALIR 11 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;; 79.492 0.024622 1320030000 622510 691450 514250 567340 634500 741640 749490 752340 808590 762880 FALSE TRUE 598181.621 671730.523 607186.4144 596620.4854 654909.2687 756636.4689 758662.4828 736803.9161 716802.2531 711209.4581 0.841076583 0.944490425 0.853737823 0.83888154 0.920838807 1.0638729 1.066721588 1.03598723 1.00786378 1 19.43991498 2.876281258 4.025963543 1.039264462 0.874217253 0.838312234 0.034508868 0.08798421 2.442691465 0.010831195 0.011626258 752.1098174 -2.876281258 -0.165047209 APAASEGNHTDGAEEAAGSCAQAPS(ph)HSPPNKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 APAASEGNHTDGAEEAAGSCAQAPSHSPPNKPK 33 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 APAASEGNHTDGAEEAAGS(0.002)CAQAPS(0.499)HS(0.499)PPNKPK 115.96 2.08E-06 195280000 19737 18125 14902 17163 21627 19893 19385 20907 27371 23399 TRUE FALSE 18965.65622 17608.09275 17595.12289 18048.78449 22322.6521 20295.25009 19622.23943 20475.26314 24263.95883 21814.16489 0.869419312 0.807186195 0.806591634 0.827388286 1.023309955 0.930370252 0.89951825 0.93862237 1.112302898 1 14.41297762 2.876589261 0.489669573 1.019220415 0.79898401 0.549690116 0.064235177 0.952196055 0.468261645 0.059971593 0.091153948 752.6434053 -2.876589261 -0.220236405 DVEQQFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVEQQFK 7 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 89.752 0.06592 0 161100 163930 150390 148660 161120 202350 180690 187680 210550 214650 FALSE TRUE 154804.0339 159254.8769 177568.8184 156332.3604 166302.5711 206441.6556 182901.3383 183804.3424 186649.2467 200111.5643 0.773588645 0.795830453 0.88734911 0.781226017 0.831049278 1.031632811 0.913996844 0.918509348 0.932725939 1 17.61044502 2.877530933 7.042042074 0.947359084 0.813202815 0.719673963 0.045234227 0.148795963 7.955430316 0.013814362 0.014686343 754.2771172 -2.877530933 -0.134156269 LGQDRPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGQDRPIK 8 1 Q9BZK7;A0A0D9SF63;A0A1B0GVH3 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 64.04 0.063385 277470000 729930 694860 555840 595040 602990 555530 534170 470280 645620 545600 FALSE TRUE 701403.5286 675043.2731 656292.6526 625750.0857 622385.721 566763.1972 540707.3322 460568.5537 572331.9243 508646.026 1.378961975 1.327137614 1.290273823 1.230227022 1.223612668 1.114258577 1.063032649 0.905479509 1.125206715 1 18.95630249 2.877662296 0.822757905 0.987499961 1.347792226 0.843391238 0.056602549 0.221003984 0.329076439 0.035004775 0.038876024 754.5053015 -2.877662296 0.360292264 RLDECEEAFQGTK ddPTM_BT-474_Pertuzumab_2h_R1 4 RLDECEEAFQGTK 13 1 K7ESG5;K9J957;P61289;P61289-2;B3KQ25;P61289-3;K7ENH2;K7EMD0;K7EPX6;K7EKR3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ;;; 238.06 1.47E-16 2183650000 2529570 2584230 1936090 2278060 2404500 2554700 2557730 2679730 2922000 2886680 FALSE TRUE 2430711.608 2510530.291 2285984.531 2395630.95 2481842.926 2606357.784 2589032.265 2624392.639 2590306.81 2691162.592 0.9032199 0.932879454 0.849441255 0.890184397 0.922219614 0.968487668 0.962049737 0.975189179 0.962523341 1 21.35979813 2.877832503 2.51427872 0.972370831 0.89376598 0.756453403 0.02147234 0.147166152 1.820615413 0.007243415 0.007848906 754.8010626 -2.877832503 -0.078604851 DSEHIDDETRR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSEHIDDETRR 11 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 145.55 2.35E-05 167253000 179567 196027 149169 183833 147686 185980 173232 168041 190533 186860 FALSE TRUE 172549.3231 190436.5019 176127.1565 193320.6432 152436.4543 189740.643 175352.065 164570.8946 168904.4926 174203.8058 0.990502603 1.093182213 1.011040808 1.109738345 0.875046637 1.089187703 1.006591471 0.944703211 0.969579808 1 17.41041662 2.878193756 0.723719921 0.973648302 1.046775866 0.10016506 0.065535278 1.407053705 1.625217034 0.042584558 0.049425443 755.4291791 -2.878193756 0.073127563 FWETLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 FWETLDR 7 0 A0A1B0GUB2;Q6P1J9 A0A1B0GUB2 CDC73 Parafibromin 0 ;; 149.48 0.0046838 306581000 381045 406240 343967 350474 363090 366535 322452 360563 394040 431100 FALSE TRUE 366153.3401 394654.433 406129.4884 368562.0051 374769.1196 373946.5888 326398.264 353117.248 349310.2312 401901.213 0.911053085 0.981968753 1.010520683 0.917046262 0.932490641 0.930444041 0.812135553 0.878617025 0.869144506 1 18.61648141 2.878303562 1.529134415 0.879675513 0.962874577 0.198278118 0.052617374 0.45634584 2.162441337 0.019675965 0.021242374 755.6202049 -2.878303562 0.083199064 RRESASS(ph)SSSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRESASSSSSVK 12 2 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 RRES(0.148)AS(0.134)S(0.707)S(0.009)S(0.001)SVK 161.24 5.19E-05 171630000 68597 64178 60663 62180 64397 51653 53299 71265 66732 62281 TRUE FALSE 65916.1534 62347.70628 71626.15354 65389.11725 66468.38799 52697.45905 53951.28911 69793.35285 59156.86312 58062.6524 1.135259081 1.073800519 1.233601129 1.126182056 1.144770093 0.907596482 0.929190915 1.202035215 1.018845345 1 15.82532286 2.879190099 19.64251344 1.031194753 1.143073886 0.37210242 0.083269735 5.139614213 814.5139453 0.027635075 0.029311508 757.1642473 -2.879190099 0.111879133 SLCLS(ph)PSEASQMK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLCLSPSEASQMK 13 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 SLCLS(0.831)PS(0.148)EAS(0.021)QMK 98.58 0.0014184 0 84430 90720 72001 74947 86892 97209 97684 97591 119620 109520 TRUE FALSE 81130.38226 88132.75442 85013.18235 78815.02365 89686.96009 99174.63258 98879.48601 95575.71175 106041.2391 102102.1128 0.794600425 0.863182475 0.832629022 0.771923533 0.878404546 0.971327917 0.968437217 0.936079667 1.038580262 1 16.6396532 2.879714406 3.163045825 0.974820575 0.820186569 0.842932937 0.034057119 0.102956996 1.95023045 0.010953219 0.011839327 758.0788958 -2.879714406 -0.154634006 HGFCGIPITDTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 HGFCGIPITDTGR 13 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;; 107.17 0.0013166 2286740000 2338690 2426250 2122270 2115200 2076530 2043870 2204020 1639560 2328530 2444610 FALSE TRUE 2247291.409 2357055.726 2505811.399 2224365.725 2143323.473 2085198.452 2230993.456 1605702.513 2064205.036 2279034.387 0.986071742 1.034234384 1.099505744 0.976012358 0.94045245 0.914948218 0.978920489 0.704553877 0.905736679 1 21.11999126 2.879726379 1.089257326 0.857629676 1.037447871 0.314317652 0.082024256 0.467633789 1.179486199 0.039901067 0.042906266 758.0997953 -2.879726379 0.179818195 DKAFELELSWVGELTNGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKAFELELSWVGELTNGR 18 1 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 145.88 8.01E-08 270930000 639960 636560 547070 525920 627800 668900 696940 697960 798250 726240 FALSE TRUE 614949.6557 618405.9321 645937.7185 553062.7942 647993.7572 682425.6163 705469.3602 683546.8821 707636.0065 677051.1179 0.908276553 0.91338145 0.954045716 0.81687007 0.957082471 1.007938098 1.041973555 1.0095942 1.045173677 1 19.36890524 2.881914197 3.407675786 1.02250835 0.901938225 0.726592997 0.035237595 0.126843678 2.730583642 0.01082117 0.011687189 761.9284626 -2.881914197 -0.120570125 FVDSCQLTADLDGSFPYSHGDWICFR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVDSCQLTADLDGSFPYSHGDWICFR 26 0 A0A1B0GW72;Q96PX9;Q96HN1 A0A1B0GW72 PLEKHG4B Pleckstrin homology domain-containing family G member 4B 0 82.849 0.015124 56621000 20710 23245 19641 18343 21649 22565 25591 23722 21688 26500 FALSE TRUE 19900.6303 22582.07536 23190.56561 19289.68443 22345.35975 23021.27976 25904.19031 23232.13241 19226.06916 24705.1314 0.805526187 0.914064167 0.938694283 0.780796674 0.90448253 0.931842029 1.048534812 0.9403768 0.778221692 1 14.59252311 2.881956279 3.87630741 0.945312329 0.867009597 0.182621262 0.077880763 0.427761569 11.28010434 0.024731486 0.026617004 762.002294 -2.881956279 -0.078302732 ISEGLPT(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISEGLPTPTK 10 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 ISEGLPT(0.994)PT(0.006)K;ISEGLPT(0.998)PT(0.002)K;ISEGLPT(0.997)PT(0.003)K 138.2 0.0007923 3078890000 4202270 5349200 4636600 4914200 4826820 4076060 5004800 5212300 5332700 5485000 TRUE FALSE 4038040.643 5196646.053 5474536.761 5167822.451 4982079.049 4158480.726 5066050.24 5104664.184 4727354.253 5113496.064 0.789682947 1.016260888 1.070605451 1.010624118 0.974299967 0.813236321 0.990721451 0.998272829 0.924485752 1 22.28587856 2.882173307 0.003621355 1.926046796 8.71E-05 0.016580321 0.085289572 193438.205 247.9804361 65210.3757 66668.35521 762.3831821 -2.882173307 -1.925959656 ILGSASPEEEQEKPILDRPTR ddPTM_BT-474_Pertuzumab_2h_R1 3 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 0 ;; 204.29 3.02E-22 564560000 216421 180260 167902 196358 216483 221028 211300 240008 263881 273313 FALSE TRUE 207963.0281 175119.1613 198245.6264 206492.0599 223446.3723 225497.3376 213885.9526 235051.7509 233926.3352 254801.2671 0.81617737 0.687277435 0.77804019 0.810404368 0.876943725 0.884992999 0.839422641 0.92249051 0.918073673 1 17.95901293 2.882531407 0.265113738 1.010063076 0.670850038 0.768367269 0.039892906 1.510391743 0.209511638 0.065197405 0.169086377 763.0120682 -2.882531407 -0.339213038 THFEYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 THFEYEK 7 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 ; 150.84 0.0019219 829510000 993140 990550 905280 833390 912550 725400 1053660 453250 1111880 983140 FALSE TRUE 954326.9908 962300.4838 1068884.234 876401.3578 941902.9995 740068.085 1066555.006 443890.2291 985664.0438 916551.0521 1.041215313 1.049914766 1.166202615 0.956194809 1.027660159 0.807448841 1.163661319 0.484304969 1.075405501 1 19.80585572 2.882559503 1.109852766 0.846485123 1.076078827 0.098991742 0.181294458 0.764739392 1.997247456 0.083548033 0.09007265 763.0614312 -2.882559503 0.229593704 ASHS(ph)SERPPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AS(0.07)HS(0.924)S(0.006)ERPPPR 228.02 2.17E-12 622570000 119010 125890 91984 127120 104540 78673 80778 96746 85891 83318 TRUE FALSE 114358.9576 122299.7405 108607.555 133680.6784 107902.624 80263.82196 81766.58533 94748.16129 76141.01376 77674.79765 1.472278797 1.574509933 1.398234154 1.721030276 1.38915874 1.033331588 1.052678447 1.219805705 0.980253777 1 16.24515896 2.883517866 4.020291249 1.083773166 1.536049029 0.838667983 0.100682625 0.0911476 2.538602064 0.03075087 0.033075338 764.7471477 -2.883517866 0.452275863 TQLEWTEAILEDEQTQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TQLEWTEAILEDEQTQR 17 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 270.07 1.71E-28 115732000 65661.2 78363 50903.2 66680 68870 72657.7 70965.5 85548 82147 72043.7 FALSE TRUE 63095.08771 76128.16397 60102.54058 70121.36279 71085.2661 74126.88848 71833.99702 83781.4039 72822.01695 67164.11603 0.939416633 1.133464839 0.894860889 1.04403016 1.058381622 1.103668043 1.069529404 1.247413185 1.084239937 1 16.03540303 2.883855148 1.433595213 1.131126368 1.002370508 0.209622967 0.083735499 0.49760304 2.089426454 0.032494809 0.035185425 765.3412967 -2.883855148 -0.12875586 EYWMDPEGEMKPGRK ddPTM_BT-474_Pertuzumab_2h_R1 3 EYWMDPEGEMKPGRK 15 2 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;; 139.3 2.98E-06 2812270000 6109990 6231880 4965800 5122710 7497050 7228580 7756070 9767700 9009900 8054190 FALSE TRUE 5871204.836 6054152.884 5863230.524 5387093.677 7738199.422 7374746.84 7850991.105 9565993.582 7987133.925 7508672.537 0.781923144 0.806288043 0.78086113 0.717449543 1.030568237 0.982163865 1.045589758 1.273992644 1.063721168 1 22.84012644 2.884624375 1.314134842 1.129284711 0.771481755 0.717574755 0.087101707 0.209514399 0.747968488 0.037109433 0.040128397 766.6980789 -2.884624375 -0.357802956 KIS(ph)PVKFSNTDSVLPPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KISPVKFSNTDSVLPPKR 18 3 G3V2F4;E7EPD8;Q9NUW8;G3V3Q0;G3V5F9;G3V5B8;G3V554;G3V4W8;G3V5H9;G3V2U6;Q9BRS7 G3V2F4 TDP1 Tyrosyl-DNA phosphodiesterase 1 1 KIS(1)PVKFSNTDSVLPPKR 105.46 0.0026369 737580000 693860 532430 354430 342920 473370 579620 468930 587620 675840 514280 TRUE FALSE 666743.1841 517245.6177 418483.3853 360618.1423 488596.376 591340.3135 474668.9056 575485.4417 599121.4766 479447.3575 1.390649408 1.078837144 0.872845326 0.75215378 1.019082425 1.233379023 0.990033417 1.200309967 1.249608465 1 18.87101289 2.885460807 8.124223505 1.138796406 1.000793193 0.087845796 0.173983608 0.668257868 43.21197092 0.055675935 0.059135402 768.1761288 -2.885460807 -0.138003213 TSYGWIEIVGCADR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSYGWIEIVGCADR 14 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 140.24 2.33E-05 213013000 173712 167897 142174 171210 153088 170934 167238 170820 192206 187674 FALSE TRUE 166923.143 163108.7419 167868.0044 180046.1686 158012.2146 174390.4026 169284.7087 167292.5073 170387.5807 174962.6728 0.954050029 0.932248801 0.959450389 1.029054745 0.903119574 0.996729187 0.967547569 0.956161132 0.973851039 1 17.41668764 2.887020079 0.005006888 1.927882243 1.41E-08 0.123048023 0.031758045 25441.82112 44.95076817 8520.691733 8785.997244 770.939111 -2.887020079 -1.927882229 EKHQTLEVSLSRDS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKHQTLEVSLSRDSPLK 17 2 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 EKHQTLEVS(0.127)LS(0.034)RDS(0.839)PLK 101.15 0.00060462 177780000 197010 217960 164110 163240 187280 224920 207240 201740 241910 244650 TRUE FALSE 189310.6314 211743.9942 193768.3276 171664.836 193304.0313 229468.0365 209776.2651 197573.9985 214449.391 228079.6376 0.830019871 0.928377458 0.849564344 0.752653055 0.847528667 1.006087343 0.919750081 0.866250055 0.94023909 1 17.79917813 2.88750705 10.24671477 0.930052541 0.841291625 0.461022708 0.055309898 0.485661112 41.31199195 0.017924279 0.019020183 771.8040441 -2.88750705 -0.088760916 QVVS(ph)ASYNSPIGLYSTSNIQDALHGQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QVVSASYNSPIGLYSTSNIQDALHGQLR 28 0 Q53GG5-2;Q53GG5-3 Q53GG5-2 PDLIM3 PDZ and LIM domain protein 3 1 QVVS(0.255)AS(0.255)Y(0.234)NS(0.255)PIGLYS(0.001)T(0.001)SNIQDALHGQLR 72.951 0.0065609 95224000 13788 17614 16645 15121 17286 22056 21134 22246 23059 18876 TRUE FALSE 13249.14972 17111.66597 19653.12177 15901.39662 17842.01989 22501.98743 21392.64421 21786.61233 20441.43899 17597.51171 0.752899043 0.972391225 1.116812541 0.903616198 1.013894475 1.278702797 1.215663019 1.238050736 1.161609626 1 14.10308383 2.88898912 4.832933242 1.199087292 0.952485192 0.521393202 0.109209456 0.174262231 6.280185082 0.033117918 0.035470246 774.4423958 -2.88898912 -0.2466021 RRSS(ph)PS(ph)ARPPDVPGQQPQAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 2 RRS(0.631)S(0.685)PS(0.685)ARPPDVPGQQPQAAK 127.83 2.75E-05 207020000 110020 103850 98251 115730 104830 94156 98721 107040 115540 93985 TRUE FALSE 105720.2968 100888.2997 116007.1413 121702.8392 108201.9522 96059.89883 99929.17713 104829.5866 102424.3836 87619.31224 1.2065867 1.151439073 1.323990549 1.3889956 1.234909855 1.096332491 1.140492599 1.196421016 1.168970413 1 16.41896127 2.890169818 5.571165149 1.140096886 1.268889781 0.442560901 0.077996835 0.25643104 11.05572521 0.025252707 0.026955218 776.550705 -2.890169818 0.128792895 GAPGS(ph)PTQERPAGGLGEAPNGAPSVCAEEGSLGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAPGSPTQERPAGGLGEAPNGAPSVCAEEGSLGPR 35 1 A0A0J9YWL0;A0A494C1M5 A0A0J9YWL0 1 GAPGS(0.967)PT(0.033)QERPAGGLGEAPNGAPSVCAEEGSLGPR;GAPGS(0.783)PT(0.217)QERPAGGLGEAPNGAPSVCAEEGSLGPR 412.68 3.34E-187 4197760000 109701 99417 108156 89438 96437 81708 64433 79122 92248 102799 TRUE FALSE 105413.7636 96581.7245 127702.1951 94053.9059 99538.98369 83360.19174 65221.55033 77488.10305 81776.39378 95836.33217 1.099935288 1.007777764 1.332502948 0.981401351 1.038635155 0.869818261 0.680551403 0.808546209 0.85329219 1 16.54828507 2.890615833 1.840471726 0.810323795 1.119190568 0.54792001 0.114280682 0.234433691 1.584442029 0.039838589 0.043543341 777.3486224 -2.890615833 0.308866774 VSLQVHPDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSLQVHPDR 9 0 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;; 120.65 0.00063592 6145700000 3340950 3849130 3103550 3471560 3409160 3049520 3603570 3139990 3465420 3676810 FALSE TRUE 3210381.98 3739356.581 3664430.523 3650727.628 3518818.728 3111183.384 3647671.568 3075148.109 3072040.05 3427776.384 0.936578592 1.090898636 1.069040134 1.065042529 1.026560176 0.907638958 1.064150971 0.897126231 0.896219504 1 21.70884157 2.890907268 5.708924116 0.952223373 1.04602675 0.32051456 0.061557821 0.260113899 11.58539657 0.018563775 0.019806616 777.8704392 -2.890907268 0.093803378 DHINLPGFSGQNPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DHINLPGFSGQNPLR 15 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;; 211.7 1.25E-09 2310380000 1184690 1226560 1155756 1463650 1214970 757618 1311140 534644 1452740 1308650 FALSE TRUE 1138391.005 1191579.71 1364626.819 1539189.152 1254050.613 772937.555 1327186.124 523603.4146 1287831.046 1220013.97 0.933096697 0.976693496 1.118533765 1.261616006 1.027898569 0.633548118 1.087845022 0.429178212 1.05558713 1 20.21846624 2.89117562 6.788163212 0.796684438 1.077907195 0.21421021 0.20533547 0.309639308 16.94153368 0.061392856 0.065321191 778.3512366 -2.89117562 0.281222757 SKDGVCVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKDGVCVR 8 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 111.06 0.0030151 1185930000 1031110 1332310 934930 1195560 1329660 1458980 1655000 1683310 1819030 1863930 FALSE TRUE 990813.0812 1294313.823 1103892.648 1257262.995 1372429.721 1488481.575 1675254.385 1648549.06 1612541.34 1737684.361 0.570191632 0.744849785 0.635266492 0.72352783 0.789803806 0.856589153 0.964072891 0.94870455 0.927982882 1 20.72873462 2.891523774 0.898549149 0.971373535 0.643729862 0.900394984 0.044067629 0.156898099 0.276928747 0.023102645 0.025596491 778.9754549 -2.891523774 -0.327643673 HDLDLICR ddPTM_BT-474_Pertuzumab_2h_R1 7 HDLDLICR 8 0 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;P62140;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ;;;;;; 158.07 0.00036709 11424910000 6505560 6473540 5474240 6293210 5813860 4537800 6074760 3695491 6300190 6083690 FALSE TRUE 6251315.523 6288920.977 6463556.942 6618003.322 6000868.087 4629557.425 6149104.73 3619177.819 5585018.844 5671636.258 1.102206707 1.108837149 1.139628257 1.166859619 1.058048827 0.816264869 1.084185313 0.638118817 0.984727967 1 22.43533358 2.891676519 4.173284748 0.877862819 1.127591736 0.452938144 0.115548827 0.188020363 5.589469788 0.035412654 0.038128929 779.2494767 -2.891676519 0.249728917 GGGGNFGPGPGSNFR ddPTM_BT-474_Pertuzumab_2h_R1 3 GGGGNFGPGPGSNFR 15 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;; 272.97 4.54E-33 1830690000 1270530 1140030 876370 896130 952940 876370 832960 490960 978060 608670 FALSE TRUE 1220876.283 1107517.461 1034749.554 942379.3767 983592.1805 894090.8018 843154.0136 480821.5044 867034.7292 567444.2388 2.151535252 1.951764394 1.823526407 1.66074358 1.733372397 1.575645219 1.485879944 0.847345821 1.527964635 1 19.1141191 2.892671685 0.416449313 0.985419432 2.198985292 0.75442014 0.187973361 0.698330061 0.237130259 0.191299434 0.345743904 781.0371389 -2.892671685 1.21356586 SRT(ph)SVQT(ph)EDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.086)RT(0.545)S(0.368)VQT(1)EDDQLIAGQSAR;S(0.237)RT(0.427)S(0.336)VQT(1)EDDQLIAGQSAR 238.71 2.35E-26 366200000 337740 373350 320930 344220 278640 310060 243020 300320 285340 250820 TRUE FALSE 324540.7474 362702.4235 378929.19 361985.2355 287602.7087 316329.6256 245994.1515 294118.2871 252949.3994 233831.738 1.387924283 1.551125723 1.620520778 1.548058611 1.229955827 1.352808769 1.052013527 1.257820215 1.081758198 1 17.83511123 2.892673052 1.233329704 1.13173428 1.539535324 0.732591755 0.108838971 0.233406764 0.741306621 0.046198596 0.050294489 781.0395967 -2.892673052 0.407801045 LEDQLSEGRNS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDQLSEGRNSPEK 14 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 LEDQLSEGRNS(1)PEK;LEDQLSEGRNS(1)PEK 142.26 5.72E-06 698340000 286110 234850 294480 329370 320770 278180 384660 417140 469050 496970 TRUE FALSE 274928.5049 228152.3079 347699.0867 346368.8252 331087.8584 283804.9902 389367.5841 408525.9132 415805.4104 463309.7792 0.59340104 0.492440087 0.750467834 0.74759662 0.71461444 0.612559896 0.840404415 0.881755429 0.897467373 1 18.82161761 2.89339479 0.229129204 1.059286567 0.406759404 0.745075627 0.07500669 2.351403647 0.255200979 0.17614265 0.474313592 782.3386569 -2.89339479 -0.652527163 FVSEDDRNSFTLK ddPTM_BT-474_Pertuzumab_2h_R1 5 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;;; 164.33 3.39E-05 3921600000 5017500 5252760 3935730 4404080 4937970 5482240 5442750 5616450 6292160 6302910 FALSE TRUE 4821410.553 5102956.428 4647003.961 4631375.097 5096804.29 5593094.649 5509360.003 5500468.345 5577900.376 5876008.292 0.820524804 0.868439283 0.79084367 0.788183894 0.86739229 0.95185275 0.93760249 0.936089276 0.949266934 1 22.486405 2.894810105 3.255764294 0.948594509 0.81907742 0.852496476 0.027108193 0.097223175 1.948566829 0.008754368 0.009519425 784.8923661 -2.894810105 -0.129517089 ASYDTLCVLDGDKDSVNCAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASYDTLCVLDGDKDSVNCAR 20 1 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 265.64 1.06E-36 1063420000 875580 778160 668410 718550 814540 914990 871020 951190 1110220 1025550 FALSE TRUE 841361.3656 755967.6387 789206.5557 755634.4516 840740.4188 933491.7247 881679.8033 931547.5941 984192.48 956088.585 0.880003567 0.790687861 0.825453382 0.790339372 0.879354102 0.976365307 0.922173758 0.974331886 1.029394656 1 19.86678477 2.895000316 2.832366266 0.974724536 0.819758299 0.823190927 0.034797818 0.110261252 1.715128833 0.011218311 0.012246985 785.2362053 -2.895000316 -0.154966237 RTNPPGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 RTNPPGGK 8 1 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ;; 87.806 0.024152 239934000 339818 333215 268488 304987 319697 343217 340479 367753 376203 359946 FALSE TRUE 326537.5369 323712.0345 317009.7541 320727.4156 329980.3443 350157.0829 344645.8839 360158.772 333498.0126 335566.5368 0.973093265 0.964673169 0.944700139 0.955778901 0.983352951 1.043480337 1.027056771 1.07328572 0.993835726 1 18.35623933 2.895140097 3.273508737 1.035432784 0.959327356 0.665191458 0.022505567 0.134240147 2.716789469 0.007117959 0.007739791 785.4889805 -2.895140097 -0.076105427 IKLDVPEDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKLDVPEDLR 10 1 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 Q06787 FMR1 Fragile X mental retardation protein 1 0 ; 116.01 0.001046 373280000 1374220 1372130 1125280 1215420 1299060 1479570 1338600 1513210 1624940 1525420 FALSE TRUE 1320513.963 1332998.196 1328643.128 1278147.972 1340845.445 1509487.919 1354982.187 1481961.685 1440483.624 1422101.945 0.928564909 0.937343628 0.934281211 0.898773802 0.942861691 1.06144846 0.952802429 1.042092439 1.012925711 1 20.43959346 2.896763135 6.330261527 1.013177055 0.925672896 0.699545661 0.02819312 0.126222496 6.592124625 0.008099467 0.008628997 788.4299891 -2.896763135 -0.087504159 ELCSER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELCSER 6 0 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 103.02 0.081529 278760000 304920 312460 254450 318520 294310 266600 297420 303920 286470 298140 FALSE TRUE 293003.3893 303548.9467 300434.7752 334958.8554 303776.7484 271990.8347 301059.9149 297643.9458 253951.1266 277946.7122 1.054171092 1.092112025 1.080907821 1.205118969 1.092931613 0.978571873 1.083156957 1.070866942 0.913668395 1 18.08444879 2.897293108 6.837046099 1.024889875 1.11023044 0.391350204 0.058310339 0.306435776 17.67062462 0.018286637 0.019460105 789.3927038 -2.897293108 0.085340565 RRDS(ph)EEFGVK ddPTM_BT-474_Pertuzumab_2h_R1 4 RRDSEEFGVK 10 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RRDS(1)EEFGVK;RRDS(1)EEFGVK;RRDS(1)EEFGVK;RRDS(1)EEFGVK 151.56 1.54E-05 3146780000 2140590 2188600 1962110 1934740 2247210 2626090 2440120 2705780 3120480 2912890 TRUE FALSE 2056933.376 2126183.271 2316706.924 2034592.163 2319493.551 2679191.339 2469982.918 2649904.697 2766256.193 2715597.366 0.757451529 0.782952325 0.853111346 0.749224531 0.854137502 0.986593732 0.909554174 0.975809128 1.018654764 1 21.37283816 2.897416115 3.379719018 0.971023517 0.790476167 0.852140832 0.037911326 0.094319952 2.021205446 0.012013637 0.013061955 789.6163187 -2.897416115 -0.18054735 VCTFSPQRVS(ph)PTTSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VCTFSPQRVSPTTSPR 16 1 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 VCTFSPQRVS(0.631)PT(0.288)T(0.065)S(0.015)PR 93.269 0.0027186 203720000 53699 56315 51294 50477 56255 61815 60146 70799 61728 63804 TRUE FALSE 51600.38371 54708.95134 60563.96683 53082.12402 58064.49316 63064.94165 60882.08474 69336.97591 54720.89622 59482.49825 0.867488509 0.919748715 1.01818129 0.892399035 0.97616097 1.060226848 1.023529383 1.165670205 0.919949529 1 15.86017762 2.897445469 3.42495165 1.053250181 0.930661029 0.338938451 0.069018049 0.250828158 5.499529643 0.021802877 0.023694411 789.6696897 -2.897445469 -0.122589152 SYS(ph)HDVLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SYSHDVLPK 9 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.45)Y(0.008)S(0.542)HDVLPK 78.908 0.01832 211610000 758170 830370 601020 737740 692250 673130 622500 719840 736990 713870 TRUE FALSE 728539.8782 806688.6606 709637.6836 775814.8498 714516.8499 686741.1498 630118.3412 704975.0524 653329.9849 665518.9491 1.094694417 1.212119748 1.066292229 1.165729167 1.0736236 1.031888199 0.946807513 1.059286221 0.981685023 1 19.34412022 2.897546966 2.406597789 1.005506815 1.135412587 0.643817644 0.0458346 0.180784554 2.059677943 0.014379539 0.015768076 789.8542619 -2.897546966 0.129905772 FNDS(ph)EGDDT(ph)EETEDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FNDSEGDDTEETEDYR 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 2 FNDS(1)EGDDT(1)EETEDYR;FNDS(1)EGDDT(1)EETEDYR 233.34 6.33E-19 272570000 677030 635360 566210 620350 598410 611720 573440 605200 689860 689680 TRUE FALSE 650570.9191 617240.1549 668536.7423 652366.3378 617658.4011 624089.3975 580457.9303 592702.4085 611549.9849 642967.3593 1.011825732 0.959986764 1.039767778 1.014618127 0.960637258 0.970639316 0.902779779 0.92182348 0.951136906 1 19.29438597 2.897663009 1.942217283 0.936731632 1.004832969 0.396358098 0.031827282 0.288797603 2.167680512 0.01102503 0.012110377 790.0653387 -2.897663009 0.068101337 LQIWDTAGQESFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQIWDTAGQESFR 13 0 P61019;P61019-2;E9PKL7;A0A3B3ITL1;Q8WUD1 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 81.565 0.034251 293270000 191860 178620 172510 140760 156910 170900 155760 118140 181500 162230 FALSE TRUE 184361.8991 173525.9325 203686.3945 148024.6405 161957.1527 174355.7151 157666.2375 115700.3677 160896.8809 151242.0176 1.21898598 1.147339445 1.346757982 0.978726962 1.070847607 1.1528259 1.042476423 0.765001483 1.063837176 1 17.20649947 2.898588505 0.697836887 0.925794791 1.224856164 0.390469633 0.115254318 0.688706971 0.74002154 0.082492187 0.099629608 791.7507895 -2.898588505 0.299061373 TAS(ph)ETRS(ph)EGSEYEEIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TASETRSEGSEYEEIPK 17 1 P48634 P48634 PRRC2A Protein PRRC2A 2 T(0.411)AS(0.584)ET(0.197)RS(0.8)EGS(0.008)EY(0.001)EEIPK 84.946 0.0016043 0 122220 101810 78321 87103 111880 116510 122120 129390 140570 145390 TRUE FALSE 117443.5073 98906.47848 92475.34694 91598.39627 115478.7218 118865.912 123614.5411 126718.0513 124613.0829 135542.6058 0.866469304 0.729707666 0.682260359 0.675790433 0.8519736 0.876963456 0.911997673 0.934894608 0.919364669 1 17.04838689 2.898611985 2.133958075 0.929207718 0.73524924 0.703300727 0.057662319 0.177535629 1.600588027 0.020043234 0.022021338 791.793597 -2.898611985 -0.193958478 NMFHPMDFEDDPLVLNEIR ddPTM_BT-474_Pertuzumab_2h_R1 5 NMFHPMDFEDDPLVLNEIR 19 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ;;;; 218.88 3.26E-19 757287000 518905 484541 438159 469049 451889 434966 404956 406945 504828 560176 FALSE TRUE 498625.6189 470722.3651 517344.0781 493256.6751 466424.4201 443761.3105 409911.9727 398541.4435 447522.0419 522234.7806 0.954792054 0.901361576 0.99063505 0.944511345 0.893131667 0.849735267 0.784918944 0.763146114 0.856936494 1 18.99433902 2.899213341 2.180116698 0.823098164 0.947431546 0.292001696 0.064757457 0.292655845 2.751077017 0.021364667 0.023477996 792.8907303 -2.899213341 0.124333382 GDHAGVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDHAGVLK 8 0 Q16658 Q16658 FSCN1 Fascin 0 105.14 0.0076586 0 267060 288900 269360 274960 279150 250830 282520 278200 314640 297000 FALSE TRUE 256622.9999 280660.8549 318039.3439 289150.7186 288129.1133 255901.9545 285977.5643 272455.0728 278923.3863 276883.9255 0.926825201 1.01364084 1.148637803 1.044303016 1.040613365 0.924221058 1.032842783 0.984004659 1.007365761 1 18.07892177 2.899612588 23.75709013 0.99097017 1.040502424 0.133365752 0.056532725 53.24242695 12586.35113 0.01769437 0.018767723 793.6199712 -2.899612588 0.049532254 VGYELKDEIER ddPTM_BT-474_Pertuzumab_2h_R1 4 VGYELKDEIER 11 1 Q8WWY3-4;Q8WWY3;Q8WWY3-3;Q8WWY3-2 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 ;;; 111.31 0.0015294 1479720000 2017290 1984310 1461210 1612780 1818620 2053730 1871090 2161420 2299740 2106960 FALSE TRUE 1938452.077 1927719.422 1725283.151 1696015.769 1877117.564 2095257.828 1893988.959 2116785.922 2038683.156 1964253.723 0.986864403 0.981400417 0.878340273 0.863440272 0.955639051 1.066694085 0.964228265 1.077654021 1.037891965 1 20.90554986 2.900447338 5.231944566 1.031654039 0.925794688 0.518023729 0.046881359 0.184277671 7.703623261 0.01511521 0.016181019 795.146842 -2.900447338 -0.10585935 ALHELNPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALHELNPR 8 0 Q5T6V5 Q5T6V5 C9orf64 UPF0553 protein C9orf64 0 65.246 0.064767 66111000 70463 85390 72737 72370 74506 61699 77339 63728 75407 82366 FALSE TRUE 67709.22806 82954.76081 85882.19393 76105.02437 76902.55315 62946.59605 78285.49782 62411.99453 66847.11349 76787.27746 0.881776647 1.080319078 1.118443013 0.991115024 1.001501234 0.819752935 1.01951131 0.812790824 0.870549337 1 16.22857968 2.900929803 6.003296517 0.896251359 1.025780705 0.290453698 0.085435309 0.26253679 13.20023103 0.025553081 0.027260262 796.0306743 -2.900929803 0.129529346 AGTGYAS(ph)PDRTHVLAAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGTGYASPDRTHVLAAGK 18 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 AGT(0.289)GYAS(0.711)PDRTHVLAAGK;AGT(0.003)GYAS(0.98)PDRT(0.017)HVLAAGK 223.07 3.24E-19 1243450000 1423360 1305750 1222990 1215720 1295830 1465350 1474290 1180130 1604840 1798650 TRUE FALSE 1367733.518 1268511.288 1444011.498 1278463.455 1337511.549 1494980.381 1492332.802 1155759.903 1422665.291 1676825.833 0.815668205 0.756495554 0.861157712 0.762430677 0.797644885 0.891553763 0.88997484 0.68925459 0.848427584 1 20.67730142 2.901473388 21.04712949 0.835247173 0.797759027 0.095068555 0.078795738 43.47295754 9269.415751 0.02460045 0.026092776 797.0276501 -2.901473388 -0.037488146 IQNNDNVGKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQNNDNVGKPK 11 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 60.49 0.095571 0 130740 122520 92982 101440 115850 122730 121840 132930 137160 132750 FALSE TRUE 125630.5363 119025.8496 109785.9158 106675.3306 119576.4205 125211.6847 123331.1144 130184.949 121590.1718 123758.7243 1.015124687 0.961757244 0.887096376 0.861962106 0.966205988 1.011740267 0.99654481 1.051925429 0.982477579 1 16.9171707 2.90258964 3.953910521 1.013696668 0.928939165 0.41876226 0.042281197 0.224057611 6.273875319 0.014166422 0.015336653 799.0788572 -2.90258964 -0.084757503 QSGLSSLVNGKS(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSGLSSLVNGKSPIR 15 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 QSGLSSLVNGKS(1)PIR;QSGLSSLVNGKS(1)PIR 130.47 3.61E-05 1325860000 907490 959610 730600 820600 859430 911590 938820 907150 969890 992060 TRUE FALSE 872024.2875 932242.8624 862635.6721 862951.2643 887074.3465 930022.9744 950309.56 888417.0355 859792.1533 924866.8926 0.942864638 1.007975169 0.932713322 0.933054552 0.959137313 1.005574945 1.027509545 0.960589078 0.929638806 1 19.81888622 2.90369304 8.628632193 0.983977816 0.955190425 0.178931698 0.031704296 0.674591397 55.33622213 0.010191988 0.010824016 801.1116368 -2.90369304 -0.028787391 TLPAHSDPVSAVHFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLPAHSDPVSAVHFNR 16 0 P61964 P61964 WDR5 WD repeat-containing protein 5 0 ; 201.24 1.94E-11 291190000 154954 189317 148741 202532 161231 132953 172172 109621 152781 187006 FALSE TRUE 148898.2264 183917.8645 175621.8074 212984.7008 166417.1415 135641.4008 174279.0924 107357.288 135437.9414 174339.9171 0.854068471 1.05493835 1.007352822 1.221663429 0.954555585 0.778028366 0.999651115 0.615792928 0.776861339 1 17.4115434 2.904325585 4.536273013 0.809664532 1.039703103 0.321610272 0.134815185 0.23514621 8.176310511 0.041734833 0.044941424 802.2792963 -2.904325585 0.230038571 IIEHNIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IIEHNIR 7 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 0 ; 151.29 0.0041813 115710000 221647 266310 215061 249030 232959 217225 231270 236705 231361 240180 FALSE TRUE 212984.7902 258715.0995 253927.3067 261882.4681 240452.3378 221617.4383 234100.3514 231816.959 205097.8692 223912.3947 0.951196965 1.155430006 1.134047568 1.169575577 1.073867921 0.989750651 1.045499745 1.03530204 0.915973721 1 17.77257487 2.904410928 4.442474069 1.006979167 1.110015318 0.366641744 0.065167744 0.2528019 8.521995973 0.020024683 0.021582422 802.4369676 -2.904410928 0.10303615 ACEVALEEIKAETEKQS(ph)PPHGEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ACEVALEEIKAETEKQSPPHGEAK 24 2 Q9Y6D6;E5RJN9 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 ACEVALEEIKAET(0.437)EKQS(0.563)PPHGEAK;ACEVALEEIKAET(0.069)EKQS(0.931)PPHGEAK 138.16 4.07E-06 595040000 364800 294710 236460 250980 296630 351750 349910 324070 414920 340180 TRUE FALSE 350543.2127 286305.1594 279193.582 263933.1079 306171.3733 358862.626 354192.3032 317377.8413 367820.0211 317139.3056 1.105328815 0.902774126 0.880349982 0.832230831 0.965416043 1.131561493 1.116835085 1.000752148 1.159805847 1 18.27475717 2.904517315 5.364141365 1.077119539 0.921725159 0.43981776 0.081920422 0.210008719 9.296595481 0.025293205 0.027073526 802.6335611 -2.904517315 -0.155394379 ALDKLDGTEINGR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALDKLDGTEINGR 13 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 152.88 4.14E-05 8573200000 9463500 9576700 7553600 8588700 8948900 10070200 9285100 10143000 11052400 10599800 FALSE TRUE 9093655.958 9303581.893 8918703.549 9031963.836 9236749.496 10273826.34 9398733.831 9933543.505 9797777.887 9881866.105 0.92023671 0.941480262 0.902532321 0.913993748 0.934717127 1.039664597 0.951109207 1.005229518 0.991490654 1 23.23635208 2.90484137 6.598265787 0.99440102 0.920416159 0.742974116 0.022124939 0.120725099 7.094293479 0.006386078 0.00680254 803.2326797 -2.90484137 -0.073984861 AEGYEVAHGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEGYEVAHGGR 11 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ; 150.46 3.39E-05 688690000 571740 618980 504120 609380 565740 493080 521890 554760 604740 611080 FALSE TRUE 549395.7687 601327.2964 595225.6981 640830.1748 583937.5409 503050.4154 528277.0459 543304.0121 536092.4505 569691.0073 0.964375006 1.055532365 1.044822001 1.12487325 1.025007475 0.883023269 0.92730452 0.953681917 0.941023193 1 19.11982011 2.904985665 6.290881879 0.938884208 1.050986689 0.564256172 0.045026394 0.16591044 9.159261797 0.013691877 0.014597876 803.4995996 -2.904985665 0.11210248 ISLPGQMAGT(ph)PITPLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISLPGQMAGTPITPLK 16 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ISLPGQMAGT(0.999)PIT(0.001)PLK;ISLPGQMAGT(1)PITPLK;IS(0.077)LPGQMAGT(0.923)PITPLK 307.52 2.34E-46 509720000 937934 864365 766776 804249 826497 714458 670307 904672 901032 836533 TRUE FALSE 901278.5023 839714.1565 905349.48 845756.3873 853082.0266 728904.8303 678510.4176 885990.2071 798750.6248 779873.8748 1.15567213 1.076730717 1.160892177 1.08447842 1.093871784 0.934644503 0.870025833 1.136068582 1.024204875 1 19.5728813 2.904998624 6.053825163 1.002397498 1.115925746 0.44108715 0.068285664 0.265092425 13.89760373 0.02257137 0.024084567 803.5235764 -2.904998624 0.113528248 AAVPSGASTGIYEALELR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAVPSGASTGIYEALELR 18 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798;P13929-3;P13929-2;P13929;E5RGZ4;P09104-2;F5H0C8;P09104;E5RI09;E5RG95;K7EPM1;K7EKN2;F5H1C3 P06733 ENO1;ENO3;ENO2 Alpha-enolase;Enolase;Beta-enolase;Gamma-enolase 0 ; 246.86 5.86E-24 248690000 26447.1 25413.2 23590.4 22178 22875.8 22102.6 23560.2 22854 22818.1 23483 FALSE TRUE 25413.51809 24688.44042 27853.71005 23322.60924 23611.62088 22549.52972 23848.53678 22382.05691 20227.88495 21892.47549 1.160833461 1.127713512 1.272296048 1.065325355 1.07852677 1.030012788 1.089348566 1.022363 0.923965175 1 14.41814748 2.905611845 0.593276107 0.983410589 1.190543078 0.632300095 0.055101872 0.598738957 0.454461162 0.043492578 0.058187713 804.6589476 -2.905611845 0.207132489 DLKDYFTK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLKDYFTK 8 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 97.456 0.0074955 6148900000 9087300 8536700 6166000 6156500 7697800 8829700 8045200 9199300 9964900 8773100 FALSE TRUE 8732158.269 8293241.674 7280333.362 6474237.703 7945406.728 9008242.584 8143659.564 9009331.24 8833726.328 8178890.123 1.067645871 1.013981304 0.890137079 0.791579005 0.971452924 1.10140159 0.995692501 1.101534695 1.080064189 1 22.96347365 2.905708535 5.835753634 1.059256132 0.935469645 0.340857873 0.076202982 0.265271577 13.30125583 0.024983971 0.026684302 804.8381151 -2.905708535 -0.123786487 AEPS(ph)PQSWSSLWK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEPSPQSWSSLWK 13 0 Q8WXH0;Q8WXH0-2;A0A0C4DGK3;Q8WXH0-7 Q8WXH0 SYNE2 Nesprin-2 1 AEPS(1)PQSWSSLWK 151.54 4.70E-05 19957000 63960 78196 63147 87435 70633 59717 63662 75666 65811 55897 TRUE FALSE 61460.37249 75965.92664 74559.0676 91947.53083 72904.97459 60924.51866 64441.1146 74103.47066 58340.41118 52111.0464 1.179411598 1.457770125 1.430772797 1.764453742 1.3990311 1.169128675 1.236611411 1.422029987 1.119540198 1 15.6693016 2.906298791 5.735552776 1.238158563 1.470403472 0.353576862 0.168163111 0.295163184 14.51403382 0.052459492 0.056059047 805.9327253 -2.906298791 0.232244909 FHMYEGYPLWK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHMYEGYPLWK 11 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 ; 127.76 0.00027983 908550000 2391100 2501900 2311500 2324500 2284000 1409910 2410400 1007040 2762000 2713800 FALSE TRUE 2297653.168 2430548.262 2729239.469 2444467.724 2357466.934 1438419.346 2439899.196 986244.2721 2448469.339 2529991.909 0.908166212 0.960694085 1.078754228 0.966195866 0.931808092 0.568547014 0.964390118 0.389821117 0.967777537 1 21.27070134 2.906852916 6.597384529 0.727790564 0.980261704 0.189518639 0.185161864 0.300435006 17.98358524 0.054220927 0.057765665 806.9616874 -2.906852916 0.25247114 WS(ph)PIASTLPELVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 WSPIASTLPELVQR 14 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 1 WS(0.999)PIAS(0.001)T(0.001)LPELVQR 94.717 0.0042529 37021000 78366 82996 59327 58817 73400 80555 84132 88209 83737 74772 TRUE FALSE 75303.37008 80629.03534 70048.70862 61852.55242 75760.97766 82183.87729 85161.63258 86387.45332 74231.52681 69707.62584 1.080274492 1.15667453 1.004893048 0.887314001 1.086839162 1.178979721 1.221697505 1.239282679 1.064898222 1 16.08902887 2.9070153 4.758528561 1.168038445 1.033763931 0.203451012 0.093225646 0.285471699 10.78228073 0.029816151 0.032066156 807.2634685 -2.9070153 -0.134274514 S(ph)PKPGPAPHDQELGFFLETGLQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPKPGPAPHDQELGFFLETGLQR 23 1 Q86TV6;Q86TV6-2;G3V3H1 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 S(1)PKPGPAPHDQELGFFLETGLQR;S(1)PKPGPAPHDQELGFFLETGLQR;S(1)PKPGPAPHDQELGFFLETGLQR;S(1)PKPGPAPHDQELGFFLETGLQR 199.04 1.62E-24 289684000 190005 175623 150152 163446 171423 185977 171315 199318 205395 185108 TRUE FALSE 182579.3945 170614.404 177287.8065 171881.4676 176936.9765 189737.5824 173411.6042 195202.0136 182079.4207 172570.4703 1.057999055 0.988665116 1.027335709 0.996007413 1.025302743 1.099478851 1.004874148 1.131143778 1.05510184 1 17.39682609 2.90740822 7.080933294 1.066912928 1.015477498 0.171445968 0.040868004 0.34177276 22.62705278 0.011849527 0.0126104 807.9941566 -2.90740822 -0.051435431 NLSDIGWPVFEIPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 NLSDIGWPVFEIPSPR 16 0 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4;F5H1X6 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 NLSDIGWPVFEIPS(1)PR;NLSDIGWPVFEIPS(1)PR;NLSDIGWPVFEIPS(1)PR 134.21 3.41E-05 4836700 86378.5 101069.2 101635.7 98966.5 97044.5 90589 91737.5 94608.5 101044.8 124132.8 TRUE FALSE 83002.73272 98186.80537 120003.5319 104074.1729 100166.0245 92420.77165 92860.21097 92654.80141 89574.61792 115725.1749 0.717240072 0.848448105 1.036969976 0.899321803 0.865550858 0.798622873 0.802420139 0.800645162 0.774028797 1 16.82034322 2.907457929 4.70709363 0.818770127 0.884901551 0.022406725 0.094155117 0.567366419 21.12693822 0.029162924 0.031380848 808.0866442 -2.907457929 0.066131425 GKDETDSPTVHLGLDS(ph)DS(ph)ESELVIDLGEDHSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 GKDETDSPTVHLGLDSDSESELVIDLGEDHSGR 33 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 2 GKDETDSPTVHLGLDS(0.994)DS(0.865)ES(0.14)ELVIDLGEDHSGR;GKDET(0.001)DS(0.004)PT(0.004)VHLGLDS(0.832)DS(0.859)ES(0.3)ELVIDLGEDHSGR;GKDETDSPTVHLGLDS(1)DS(0.965)ES(0.035)ELVIDLGEDHSGR 229.16 7.22E-37 192391000 161001 147238 118862 144071 142304 169606 145771 150168 181410 169646 TRUE FALSE 154708.9029 143038.9164 140343.0075 151506.5216 146881.3374 173035.5495 147554.9891 147066.9783 160817.0973 158155.7253 0.978206149 0.9044182 0.887372286 0.957957869 0.928713375 1.094083374 0.932972795 0.92988716 1.016827541 1 17.27098626 2.90756145 19.90806969 0.983414254 0.928791385 0.275614616 0.049650285 16.30204499 3506.556074 0.015733299 0.016687754 808.2792868 -2.90756145 -0.054622869 TSGAPGS(ph)PQTPPER ddPTM_BT-474_Pertuzumab_2h_R1 2 TSGAPGSPQTPPER 14 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7;K7EIM4 Q96MH2 HEXIM2 Protein HEXIM2 1 TSGAPGS(0.98)PQT(0.02)PPER;TSGAPGS(0.907)PQT(0.092)PPER 213.29 7.44E-08 0 221350 223896 180238 206055 205983 209570 203534 216957 236273 239194 TRUE FALSE 212699.3973 217510.7053 212811.016 216689.5232 212608.6303 213807.649 206024.91 212476.7621 209452.2796 222993.1773 0.953838139 0.975414171 0.954338687 0.971731628 0.9534311 0.95880803 0.923906787 0.952839745 0.939276628 1 17.76664004 2.908424359 2.449078031 0.949421194 0.963829065 0.007858692 0.019534823 0.675054879 7.971203979 0.005987881 0.006606032 809.8868709 -2.908424359 0.014407871 DQDLASCDRDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDLASCDRDR 11 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 125.03 0.00030711 108740000 159170 174560 137060 177450 159970 153810 156980 161260 178390 176220 FALSE TRUE 152949.4604 169581.7197 161829.7909 186608.2158 165115.5803 156920.1436 158901.1682 157929.9246 158139.9151 164284.4624 0.93100381 1.03224442 0.985058407 1.135884751 1.005059017 0.95517337 0.967231872 0.96131991 0.962598122 1 17.32583652 2.909847977 5.872483161 0.966963804 1.025119883 0.198057413 0.049112013 0.337912516 17.66616789 0.0149601 0.015984092 812.5460376 -2.909847977 0.058156079 SDESPKPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDESPKPGK 9 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 ; 110.14 0.0021305 387560000 605190 585370 400820 471850 562250 578950 610150 617830 686440 712490 FALSE TRUE 581538.5057 568675.8207 473257.0902 496202.235 580335.2819 590656.7657 617617.1982 605071.5946 608518.209 664232.4177 0.875504553 0.856139817 0.712487192 0.747031042 0.873693103 0.889232067 0.929820921 0.910933551 0.916122419 1 19.34132861 2.911956578 2.514594215 0.924610809 0.796908165 0.578707159 0.052251977 0.227518125 2.830084069 0.018082266 0.019978857 816.5007307 -2.911956578 -0.127702644 LIEDKPR ddPTM_BT-474_Pertuzumab_2h_R1 6 LIEDKPR 7 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;;;; 136.16 0.0027429 6130150000 7238920 7472370 6057830 6901150 7432280 8315920 8153780 8938630 9382690 9415750 FALSE TRUE 6956015.003 7259265.324 7152614.637 7257319.179 7671346.036 8484073.6 8253568.399 8754044.167 8317606.367 8778012.866 0.792436182 0.826982762 0.814833009 0.826761055 0.873927409 0.966514145 0.940254762 0.997269462 0.947550031 1 23.06546295 2.91205211 1.631263299 0.974922792 0.811862346 0.935328596 0.019358566 0.0786093 0.422434985 0.006705077 0.007440561 816.6803566 -2.91205211 -0.163060446 LLQDHPWLLSQNLVVKPDQLIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLQDHPWLLSQNLVVKPDQLIK 22 1 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ; 293.67 1.11E-55 1922960000 1646260 1457940 1359820 1501400 1611790 1793780 1876070 1914510 2118470 2074970 FALSE TRUE 1581922.339 1416360.979 1605569.723 1578887.434 1663634.689 1830051.461 1899029.906 1874974.699 1877990.167 1934430.434 0.817771635 0.732185016 0.829996104 0.816202747 0.860012674 0.946041496 0.981699767 0.969264475 0.970823315 1 20.88347742 2.912352938 1.230417815 0.982296733 0.785476033 0.917724385 0.025083984 0.109626622 0.347245745 0.010370827 0.011507911 817.2462535 -2.912352938 -0.196820699 FHS(ph)PSTTWSPNK ddPTM_BT-474_Pertuzumab_2h_R1 3 FHSPSTTWSPNK 12 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.439)PS(0.439)T(0.047)T(0.075)WSPNK;FHS(0.556)PS(0.433)T(0.011)TWSPNK;FHS(0.5)PS(0.5)T(0.001)TWSPNK 198.03 1.97E-07 820004000 1811760 1872280 1690210 1821240 1685280 1383270 1951210 810042 2145830 1898400 TRUE FALSE 1740954.416 1818884.408 1995668.546 1915234.415 1739488.562 1411240.667 1975089.492 793314.3496 1902244.374 1769819.677 0.983690281 1.027723011 1.127611231 1.08216359 0.982862031 0.797392348 1.115983463 0.448245864 1.074823836 1 20.75517094 2.913049135 3.286296091 0.838592434 1.057880861 0.134277703 0.180412842 0.372984305 7.716731249 0.057131823 0.06262556 818.5573929 -2.913049135 0.219288427 LEDNDSAAS(ph)DPDAETTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDNDSAASDPDAETTAR 18 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8;F8WF85;C9J6R3;C9J9X8;C9JCX6;C9JXA0 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 1 LEDNDS(0.019)AAS(0.981)DPDAETTAR;LEDNDS(0.36)AAS(0.64)DPDAETTAR 187.39 4.53E-14 282680000 318100 345260 258850 320990 328640 366240 369900 397270 425510 404780 TRUE FALSE 305668.3003 335413.5228 305629.9531 337556.3324 339211.0041 373645.6237 374426.9468 389066.2357 377207.8887 377363.8901 0.810009406 0.888833118 0.809907787 0.894511482 0.898896299 0.990146735 0.992217212 1.031010772 0.999586602 1 18.52559685 2.913107294 1.265561261 1.014150602 0.841636029 0.890086586 0.025713008 0.119871745 0.400037447 0.010008571 0.01111158 818.6670182 -2.913107294 -0.172514573 RPSPT(ph)SGDSRPAAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSPTSGDSRPAAGR 15 2 Q8N1G1 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 RPS(0.156)PT(0.713)S(0.104)GDS(0.027)RPAAGR 122.61 0.00017336 197140000 57873 69198 54892 61189 60143 56201 61575 59841 61650 65007 TRUE FALSE 55611.25918 67224.54079 64812.20547 64346.97162 62077.55422 57337.42273 62328.57327 58605.26244 54651.75046 60604.01799 0.917616703 1.109242308 1.069437434 1.061760817 1.024314167 0.946099362 1.028456121 0.967019422 0.901784276 1 15.88712583 2.914892362 4.770858652 0.971974165 1.046398358 0.269224616 0.05561868 0.286634717 11.31968225 0.016717825 0.01801415 822.0388864 -2.914892362 0.074424193 THLMSESEWR ddPTM_BT-474_Pertuzumab_2h_R1 6 THLMSESEWR 10 0 P61024;Q5T179;Q9BZU3 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ;;;;; 196.27 3.36E-07 1790150000 1828736 1930123 1543268 1686242 1601605 1048565 1797858 716243 1641194 1605974 FALSE TRUE 1757266.975 1875077.782 1822170.857 1773269.152 1653122.079 1069767.703 1819860.724 701452.3318 1454892.538 1497199.951 1.173702267 1.25238969 1.217052443 1.184390335 1.104142489 0.714512248 1.215509474 0.468509454 0.971742309 1 20.51383548 2.914894072 4.035767529 0.839734259 1.206256146 0.416295036 0.1852523 0.204051794 6.100568899 0.056472581 0.061349459 822.0421232 -2.914894072 0.366521887 HHYLRPSLFVYPEESLVIGSSTLFSALLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 HHYLRPSLFVYPEESLVIGSSTLFSALLIK 30 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 121.3 1.19E-05 354060000 284430 291730 181090 187430 195110 150140 191560 34401 142800 76201 FALSE TRUE 273314.1611 283410.146 213816.9913 197103.2848 201385.8903 153175.9337 193904.3686 33690.60733 126589.9427 71039.8384 3.847336471 3.989453698 3.009818099 2.774545793 2.834830356 2.156197665 2.729515902 0.474249493 1.781957075 1 16.11634068 2.916162716 0.425412273 0.819938678 4.265122368 0.782020377 0.500788192 0.620134166 0.219703528 0.490233026 0.885393605 824.4469502 -2.916162716 3.44518369 KNLQEEIDALESR ddPTM_BT-474_Pertuzumab_2h_R1 4 KNLQEEIDALESR 13 1 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 ;;; 195.54 2.39E-07 659850000 753030 826650 689682 731178 778370 881450 814627 889410 950780 963050 FALSE TRUE 723600.7551 803074.7514 814322.8793 768914.1842 803406.9779 899273.5229 824596.6489 871043.3727 842851.4404 897821.7657 0.805951451 0.89447013 0.906998371 0.856421857 0.894840166 1.001616977 0.918441366 0.970174043 0.938773677 1 19.77606955 2.916282156 5.481441901 0.960253374 0.871345303 0.653268903 0.034547112 0.146154509 7.267482436 0.010150065 0.010879727 824.6737223 -2.916282156 -0.088908071 GRAS(ph)SHS(ph)SQTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 GRAS(0.732)S(0.308)HS(0.808)S(0.15)QT(0.002)QGGGSVTK 80.844 0.0045128 214260000 213160 269300 233960 199760 221560 221010 165510 234820 207370 200360 TRUE FALSE 204829.4715 261619.8277 276241.7764 210069.6375 228686.6786 225478.9736 167535.5609 229970.8849 183830.227 186789.4387 1.096579512 1.400613597 1.47889398 1.124633378 1.224301974 1.207129135 0.896922021 1.231177129 0.9841575 1 17.51105336 2.916672349 1.129106423 1.061305932 1.314342426 0.382650172 0.136501463 0.520014805 1.406168778 0.061794278 0.068994986 825.4149858 -2.916672349 0.253036494 VQEFDSGLLHWR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQEFDSGLLHWR 12 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 0 138.02 8.19E-05 37753000 43525 49196 39679 46319 44117 40123 47516 38197 44834 56286 FALSE TRUE 41823.99488 47792.97825 46849.87795 48709.52914 45536.06337 40934.31455 48097.51502 37408.2186 39744.63228 52473.69909 0.797046818 0.910798725 0.892825907 0.928265588 0.867788324 0.780092032 0.916602333 0.712894636 0.757420059 1 15.67930687 2.916782654 6.165217819 0.814704203 0.886578728 0.049005913 0.083640444 0.460652715 27.59626003 0.024787012 0.026475111 825.6246564 -2.916782654 0.071874525 VELFFKDDANNDPQWSEEQLIAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VELFFKDDANNDPQWSEEQLIAAK 24 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 315.3 1.21E-73 352580000 456950 415780 391470 324670 408630 483250 409590 482610 569620 468180 FALSE TRUE 439091.8888 403922.3615 462217.3372 341426.2576 421773.9551 493021.6461 414602.6849 472643.9348 504959.1256 436469.7516 1.006007604 0.925430365 1.058990538 0.782244947 0.966330321 1.129566583 0.949900156 1.082879015 1.156916656 1 18.73552215 2.917234359 7.706396307 1.059831699 0.94095297 0.31440814 0.08607956 0.358558693 29.87407427 0.025627043 0.027257462 826.4838268 -2.917234359 -0.118878729 RDQDNMQAELNR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDQDNMQAELNR 12 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 182.72 2.65E-05 1618530000 460464 499669 370396 431085 494532 487108 502956 571883 539597 589695 FALSE TRUE 442468.5578 485418.9293 437334.7966 453333.3485 510439.0709 496957.6575 509111.326 560073.4162 478344.2107 549754.4324 0.804847641 0.882974108 0.79550936 0.824610629 0.928485594 0.903962985 0.926070434 1.018770169 0.870105237 1 19.06842781 2.917270521 1.185666654 0.960745958 0.82621477 0.580647512 0.046810741 0.316996026 0.938078456 0.020260942 0.022604672 826.5526466 -2.917270521 -0.134531188 KAAS(ph)PSPQS(ph)VR ddPTM_BT-474_Pertuzumab_2h_R1 4 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(0.696)PS(0.582)PQS(0.722)VR;KAAS(0.989)PS(0.012)PQS(0.999)VR;KAAS(0.956)PS(0.044)PQS(1)VR;KAAS(0.998)PS(0.003)PQS(1)VR 153.41 2.17E-05 5027170000 3443350 3436500 3119890 3328270 3520840 3769950 4000180 4056570 4738680 4275420 TRUE FALSE 3308780.075 3338494.385 3683723.525 3500042.414 3634091.016 3846180.972 4049135.399 3972800.412 4200764.913 3985841.995 0.830133277 0.837588241 0.924202096 0.878118706 0.911749894 0.964960723 1.015879557 0.996728023 1.053921585 1 21.92645309 2.918831517 0.687282504 1.029743198 0.840505027 0.871196142 0.026274048 0.245365851 0.255916991 0.018208694 0.022676632 829.5288921 -2.918831517 -0.18923817 RGFCFITYTDEEPVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGFCFITYTDEEPVKK 16 2 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 141 9.26E-07 1572900000 1729700 1679700 1253100 1440000 1623000 1888100 1798700 1876400 2115500 2125300 FALSE TRUE 1662101.412 1631796.601 1479563.045 1514318.573 1675205.269 1926278.676 1820713.029 1837651.684 1875357.309 1981351.538 0.838872547 0.823577527 0.746744339 0.764285662 0.845486143 0.972204396 0.918924781 0.927473822 0.946504077 1 20.91805344 2.918899972 3.912370408 0.943521989 0.792825475 0.837092472 0.033351901 0.09574726 2.74266516 0.010806723 0.011777679 829.6596568 -2.918899972 -0.150696513 GLPQLGTLGAGNHYAEIQVVDEIFNEYAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLPQLGTLGAGNHYAEIQVVDEIFNEYAAK 30 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 317.19 1.83E-92 206310000 236900 210880 206310 210890 232870 223460 245410 239470 298740 264960 FALSE TRUE 227641.6861 204865.9089 243594.8063 221774.0582 240360.475 227978.5143 248413.401 234524.8608 264828.2876 247014.0232 0.921573938 0.829369548 0.986157803 0.897819708 0.973064087 0.922937538 1.005665175 0.94943946 1.072118434 1 17.91423342 2.919185998 0.421811804 1.020278556 0.87465087 0.442179085 0.047722853 1.316050801 0.45701642 0.043348525 0.079163203 830.2062497 -2.919185998 -0.145627686 YPLFEGQETGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 YPLFEGQETGKK 12 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 137.84 0.00013649 2530100000 2433500 2354200 1972440 2076400 2430500 2689200 2546700 2892900 3263600 2962500 FALSE TRUE 2338396.13 2287060.521 2328903.785 2183563.253 2508679.24 2743577.467 2577867.276 2833160.604 2893129.81 2761847.236 0.846678302 0.828090885 0.843241347 0.790616955 0.908333816 0.993384946 0.933385179 1.025820895 1.047534336 1 21.39720209 2.920460814 2.557284769 0.999835551 0.828235174 0.868761184 0.031579739 0.099494581 1.281490252 0.010690452 0.011864593 832.6467933 -2.920460814 -0.171600377 NFEWVAER ddPTM_BT-474_Pertuzumab_2h_R1 6 NFEWVAER 8 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;; 129.38 0.0025427 3752790000 2969600 3569190 3034470 3368330 3167730 2783520 3264480 3080790 2902680 3298360 FALSE TRUE 2853544.749 3467400.196 3582866.23 3542169.915 3269622.912 2839804.682 3304431.683 3017170.61 2573179.935 3074959.139 0.927994363 1.127624804 1.165175233 1.151940483 1.063306133 0.923525989 1.074626209 0.981206733 0.836817603 1 21.55213581 2.920828853 5.355194879 0.973613763 1.101703674 0.354351759 0.083460798 0.256719667 12.76138943 0.025940451 0.027858426 833.3527115 -2.920828853 0.128089911 AQPGS(ph)PESSGQPK ddPTM_BT-474_Pertuzumab_2h_R1 5 AQPGSPESSGQPK 13 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 AQPGS(0.972)PES(0.023)S(0.006)GQPK;AQPGS(0.869)PES(0.128)S(0.003)GQPK;AQPGS(1)PESSGQPK;AQPGS(0.991)PES(0.008)S(0.001)GQPK;AQPGS(0.994)PES(0.006)SGQPK 164.22 3.92E-05 2024097000 2883184 2843810 2286978 2579215 2851126 2972608 2959183 3171561 3596208 3324705 TRUE FALSE 2770505.982 2762707.323 2700285.798 2712328.595 2942835.057 3032716.17 2995398.367 3106067.157 3187981.544 3099519.769 0.893850076 0.89133399 0.871194894 0.87508027 0.949448713 0.978447113 0.966407247 1.002112388 1.028540478 1 21.56361327 2.922215305 1.483488572 0.999181909 0.880740366 0.90757509 0.016842195 0.115395363 0.518526955 0.006900936 0.007720554 836.0173778 -2.922215305 -0.118441543 SNQWHGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SNQWHGR 7 0 Q9BTL3;A0A3B3IU46 Q9BTL3 FAM103A1 RNMT-activating mini protein 0 ;;; 103.91 0.0082707 574330000 888020 983770 798890 916780 884990 711400 874270 787850 935930 961560 FALSE TRUE 853315.1966 955713.8428 943267.1942 964095.1257 913456.5071 725784.9954 884969.5778 771580.6222 829687.1501 896432.6847 0.951901031 1.066130072 1.052245428 1.075479667 1.018990631 0.809636917 0.987212529 0.860723438 0.925543172 1 19.77383573 2.922270503 9.081515324 0.910250812 1.04063434 0.47966163 0.060550098 0.304518544 33.72613379 0.017126995 0.018191678 836.1236401 -2.922270503 0.130383528 KSPSGPVKS(ph)PPLSPVGTTPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPSGPVKSPPLSPVGTTPVK 21 2 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 KS(0.014)PS(0.014)GPVKS(0.972)PPLS(0.001)PVGTTPVK;KS(0.107)PS(0.107)GPVKS(0.775)PPLS(0.011)PVGTTPVK 168.55 5.56E-12 1961290000 1998710 1851900 1465040 1522260 1837960 1980930 1975700 2083680 2412470 2159230 TRUE FALSE 1920598.204 1799085.625 1729805.318 1600824.021 1897079.653 2020985.762 1999879.208 2040651.28 2138616.519 2012983.429 0.954105322 0.893740902 0.859324172 0.795249478 0.942421892 1.00397536 0.993490149 1.013744699 1.062411388 1 20.94090387 2.923023116 3.545484841 1.0132803 0.874911574 0.716357508 0.041039691 0.134935466 3.257310405 0.013485154 0.014799563 837.5738625 -2.923023116 -0.138368726 HRPS(ph)AGGPDSAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 HRPS(1)AGGPDSAGR 170.89 1.58E-05 187440000 91317 92697 76945 88689 83034 70717 86525 71725 85983 78027 TRUE FALSE 87748.23068 90053.37232 90850.67313 93266.24992 85704.86402 72146.94619 87583.91883 70243.85369 76222.57031 72742.16179 1.206291214 1.237980424 1.248941067 1.282148449 1.178200674 0.991817461 1.204032389 0.965655295 1.047845822 1 16.15050418 2.923329258 4.333456927 1.04781967 1.243061102 0.698062799 0.06311642 0.125417717 4.384059917 0.019002754 0.020633368 838.164491 -2.923329258 0.195241432 ALDYCHSMGIMHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDYCHSMGIMHR 13 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;P68400-2;A0A2R8Y4H0;A0A2R8Y4D6;A0A2R8YDY7;V9GYW6 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 159.5 2.63E-05 105320000 66136 64199 61895 69433 59746 35181 69292 15432 69524 72145 FALSE TRUE 63551.332 62368.10738 73080.80335 73016.44545 61667.78435 35892.38392 70140.01622 15113.32381 61631.92699 67258.55489 0.944881021 0.92728884 1.086565173 1.0856083 0.91687644 0.533647861 1.042841559 0.224704855 0.916343313 1 16.03743016 2.923867612 5.505943587 0.683347211 1.009928057 0.209817929 0.23229441 0.269825855 14.43343201 0.069502634 0.074616792 839.204129 -2.923867612 0.326580846 GIVEFSGKPAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GIVEFSGKPAAR 12 1 Q15233;Q15233-2;H7C367;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 144.47 5.75E-05 2746100000 4046800 5007100 3579100 4090700 4463200 4935700 4969600 5286300 5366500 5102500 FALSE TRUE 3888646.582 4864302.41 4225922.987 4301821.517 4606762.881 5035503.236 5030419.451 5177136.058 4757317.418 4756903.13 0.81747441 1.022577563 0.888376927 0.904332377 0.968437396 1.058567538 1.057498821 1.088341704 1.000087092 1 22.18159122 2.925181558 3.029609152 1.051240998 0.91547816 0.570748413 0.053707634 0.178061066 3.193627269 0.016313701 0.018052106 841.7469632 -2.925181558 -0.135762838 HGS(ph)PLPAGPCLFGPPLAGAPAGYSPGGVPSAYPELHAALDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGSPLPAGPCLFGPPLAGAPAGYSPGGVPSAYPELHAALDR 41 0 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 HGS(1)PLPAGPCLFGPPLAGAPAGYSPGGVPSAYPELHAALDR 50.85 0.050215 146800000 47120 57325 42013 42988 37516 53241 32227 36009 46918 43602 TRUE FALSE 45278.49831 55690.14713 49605.68367 45206.61583 38722.73621 54317.5695 32621.40367 35265.40157 41592.06534 40648.7977 1.113895142 1.37003184 1.220348115 1.112126764 0.952617012 1.336265094 0.802518291 0.867563214 1.023205302 1 15.31092506 2.925377202 0.773398209 0.918320343 1.250369827 0.350338729 0.144104742 0.654603528 0.868310854 0.090681473 0.108475946 842.126244 -2.925377202 0.332049484 EHIYDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHIYDLR 7 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 149.4 0.0020189 3307110000 3403150 4139680 2972450 4011550 3414660 3172960 3759640 2430210 4035580 4089380 FALSE TRUE 3270151.136 4021620.38 3509637.837 4218586.576 3524495.64 3237119.425 3805651.599 2380025.314 3577477.877 3812402.65 0.857766463 1.054878183 0.920584251 1.106542767 0.924481479 0.849102186 0.998229187 0.624284876 0.938378814 1 21.86226907 2.926385385 4.243202906 0.850337729 0.988456099 0.111313426 0.119861851 0.344546038 11.7430274 0.036811337 0.040066502 844.0834498 -2.926385385 0.138118369 IKPVTENLVLSSHTGFCQS(ph)SGDEALSK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKPVTENLVLSSHTGFCQSSGDEALSK 27 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 1 IKPVTENLVLSSHTGFCQS(0.589)S(0.411)GDEALSK 101.45 0.0016154 989970000 304480 357830 305450 361170 342230 346330 397070 369340 478920 489380 TRUE FALSE 292580.585 347625.0388 360651.6097 379810.027 353238.1388 353333.0299 401929.4614 361712.9999 424555.0094 456233.8567 0.641295206 0.761944853 0.790497251 0.832489789 0.774247973 0.774455961 0.880972456 0.792823668 0.930564453 1 18.79941399 2.926802271 0.043755002 1.59819207 7.45E-12 0.755225668 0.046815049 72.21741453 1.098435365 17.22737715 22.66706751 844.894088 -2.926802271 -1.59819207 VAWHIDPFGHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VAWHIDPFGHSR 12 0 O00754;O00754-2 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 ; 146.36 3.73E-05 777260000 291270 348570 319890 354790 311640 270220 375580 148993 358370 455150 FALSE TRUE 279886.8464 338629.1249 377701.2389 373100.7544 321664.1836 275684.0335 380176.4604 145916.2425 317689.34 424322.2851 0.659609114 0.798046996 0.890128217 0.879286258 0.758065732 0.649704348 0.895961569 0.343880695 0.748698221 1 18.69480092 2.927960803 4.247726415 0.673891637 0.813109179 0 0.174669483 0.504146981 17.33367038 0.054389776 0.059235779 847.1509512 -2.927960803 0.139217542 RPPSAFFLFCSEHRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPPSAFFLFCSEHRPK 16 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 153.95 2.41E-07 5256400000 1169660 1260420 1010540 945040 977740 1034810 907350 825810 977140 949240 FALSE TRUE 1123948.394 1224474.056 1193167.057 993813.6277 1009189.895 1055734.567 918454.4207 808756.7349 866219.1637 884947.1293 1.270074061 1.383669165 1.348291912 1.123020342 1.140395693 1.192991685 1.037863608 0.913904015 0.978837193 1 19.75523174 2.928455894 0.634313938 0.943225471 1.358827904 0.803436951 0.067221743 0.346057771 0.304513573 0.052856094 0.069487266 848.1172447 -2.928455894 0.415602433 VKVETYNDESR ddPTM_BT-474_Pertuzumab_2h_R1 6 VKVETYNDESR 11 1 P27694;I3L4R8 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 ;;;;; 177.81 7.13E-06 3854830000 5291590 4972080 4220860 4809900 4943440 5197330 5358170 5670590 5650110 5607220 FALSE TRUE 5084788.813 4830281.147 4983663.295 5058139.515 5102450.237 5302423.574 5423744.887 5553490.335 5008733.2 5227437.995 0.972711454 0.92402457 0.953366314 0.967613489 0.976090054 1.014344614 1.037553175 1.062373258 0.958162145 1 22.31767261 2.92947725 1.745923338 1.025224727 0.950196959 0.488808311 0.028401627 0.258435642 1.584739828 0.010338603 0.011618801 850.1141591 -2.92947725 -0.075027768 AKS(ph)PTPDGSER ddPTM_BT-474_Pertuzumab_2h_R1 3 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 AKS(0.846)PT(0.154)PDGSER;AKS(0.826)PT(0.174)PDGSER;AKS(0.868)PT(0.132)PDGSER 133.48 9.74E-05 1486540000 1011650 990900 915380 981130 1051790 1167850 1244890 1254170 1383780 1302240 TRUE FALSE 972113.5996 962640.5022 1080809.529 1031766.237 1085621.781 1191464.727 1260125.336 1228270.951 1226699.096 1214038.125 0.800727407 0.792924442 0.890259957 0.849863127 0.894223796 0.981406352 1.037961914 1.011723541 1.010428808 1 20.2113823 2.93026272 1.217940926 1.020888636 0.821592287 0.911504408 0.026109921 0.123716466 0.385148631 0.011721262 0.013238281 851.6530775 -2.93026272 -0.19929635 (ac)AASAAAASAAAASAASGS(ph)PGPGEGSAGGEKR ddPTM_BT-474_Pertuzumab_2h_R1 11 AASAAAASAAAASAASGSPGPGEGSAGGEKR 31 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 AASAAAASAAAASAASGS(0.999)PGPGEGS(0.001)AGGEKR;AASAAAASAAAAS(0.001)AAS(0.025)GS(0.95)PGPGEGS(0.025)AGGEKR;AASAAAASAAAASAAS(0.071)GS(0.924)PGPGEGS(0.005)AGGEKR;AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR;AASAAAASAAAAS(0.001)AAS(0.062)GS(0.923)PGPGEGS(0.014)AGGEKR;AASAAAASAAAASAASGS(0.999)PGPGEGS(0.001)AGGEKR;AASAAAASAAAAS(0.003)AAS(0.201)GS(0.793)PGPGEGS(0.003)AGGEKR;AASAAAASAAAASAASGS(0.999)PGPGEGS(0.001)AGGEKR;AASAAAASAAAAS(0.001)AAS(0.041)GS(0.91)PGPGEGS(0.048)AGGEKR;AASAAAASAAAASAAS(0.007)GS(0.929)PGPGEGS(0.063)AGGEKR;AASAAAASAAAASAAS(0.005)GS(0.989)PGPGEGS(0.006)AGGEKR 193.4 3.00E-155 18738351000 8446948 8469466 6248158 6734074 7579994 8515917 8021561 8566445 9145729 8834656 TRUE FALSE 8116831.934 8227925.122 7377339.14 7081620.366 7823811.391 8688114.676 8119731.263 8389544.917 8107544.186 8236276.88 0.985497701 0.998985979 0.895712862 0.859808439 0.949920881 1.054859471 0.985849721 1.018608898 0.984370038 1 22.9735609 2.930345126 8.181890276 1.008279946 0.93285356 0.423011939 0.041572235 0.342552403 37.22349002 0.013651469 0.014524072 851.8146904 -2.930345126 -0.075426386 ALQESATGQPEPTSS(ph)PDNKPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALQESATGQPEPTSSPDNKPFK 22 1 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 ALQESATGQPEPT(0.001)S(0.349)S(0.649)PDNKPFK 187.75 1.65E-17 919170000 319300 259190 222480 275180 331510 335830 350780 400820 455550 381020 TRUE FALSE 306821.403 251798.155 262687.085 289382.0728 342173.3202 342620.7127 355072.9506 392542.9269 403837.8738 355213.176 0.863766954 0.708864907 0.739519541 0.814671562 0.963290056 0.96454956 0.999605236 1.105091121 1.136888779 1 18.43832557 2.930540859 1.020404696 1.078744764 0.756669557 0.820107102 0.058213013 0.196486857 0.441348335 0.028794232 0.032832129 852.1986834 -2.930540859 -0.322075207 EFNAEVHR ddPTM_BT-474_Pertuzumab_2h_R1 6 EFNAEVHR 8 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 229.55 1.62E-06 18405240000 9050078 10291143 9102766 10003126 9754621 7946852 10911088 9515754 10693649 11449947 FALSE TRUE 8696390.946 9997649.678 10747838.31 10519388.53 10068387.24 8107542.792 11044621.16 9319250.355 9479750.797 10674431.89 0.814693563 0.936597824 1.006876845 0.985475259 0.943224646 0.759529207 1.034679997 0.873044154 0.888080124 1 23.34765595 2.932137291 24.99999552 0.905169335 0.943948902 0.018596909 0.084110837 638.9875069 235395.7407 0.025141313 0.026666402 855.3370622 -2.932137291 0.038779566 LTQEPESIRK ddPTM_BT-474_Pertuzumab_2h_R1 3 LTQEPESIRK 10 1 P09497-2;P09497;H0Y9Q6 P09497-2 CLTB Clathrin light chain B 0 ;; 142.89 5.60E-05 1895060000 2278430 2515300 1700240 1984860 2225100 2496890 2358910 2605540 2710240 2702690 FALSE TRUE 2189386.437 2443566.107 2007511.19 2087298.862 2296672.362 2547378.827 2387779.046 2551734.688 2402584.917 2519634.399 0.868930206 0.96980979 0.796747016 0.828413385 0.911510163 1.011011291 0.947668855 1.012740058 0.953545053 1 21.26478298 2.932408839 4.429409436 0.984272 0.868272234 0.599538865 0.046029858 0.158304631 6.027387228 0.014479017 0.015762175 855.8720397 -2.932408839 -0.115999766 DVPIDHSDLVADLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVPIDHSDLVADLLK 15 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 0 ; 183 5.24E-07 119858000 189933 181920 164536 183490 195066 217412 207877 223580 265380 266420 FALSE TRUE 182510.2084 176731.8197 194271.3153 192959.9409 201340.475 221808.2196 210421.0609 218962.9949 235255.175 248375.1361 0.734816742 0.711551979 0.782168933 0.77688912 0.810630558 0.893037134 0.847190521 0.881581781 0.947176834 1 17.92216123 2.932652089 0.23549833 1.027025497 0.615086183 0.928424245 0.023538735 1.053555565 0.116727234 0.048786646 0.134977321 856.3515524 -2.932652089 -0.411939314 SSGSPYGGGYGSGGGSGGYGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 399.2 3.33E-132 311860000 38767 34401 31717 33559.7 32015.8 32406.1 33358.9 32872.8 36185.9 33837.5 FALSE TRUE 37251.94278 33419.91716 37448.96744 35291.72014 33045.61728 33061.37355 33767.1562 32193.96519 32078.22834 31545.65599 1.180889781 1.05941424 1.187135479 1.118750555 1.047548902 1.048048377 1.070421747 1.020551457 1.016882589 1 14.94515373 2.932784573 0.546617866 1.006333999 1.154605216 0.650858592 0.037095062 0.637520099 0.402196259 0.029951728 0.043821799 856.6128266 -2.932784573 0.148271217 STFS(ph)PISDIGLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 STFSPISDIGLAK 13 0 Q8TEK3;Q8TEK3-1;H7C2S2 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 ST(0.001)FS(0.995)PIS(0.004)DIGLAK;STFS(0.937)PIS(0.063)DIGLAK 187.63 7.13E-06 53244000 158052 153704 126405 147910 155071 153628 152397 177945 173094 178082 TRUE FALSE 151875.1531 149320.5124 149249.1954 155543.6528 160058.9995 156734.4634 154262.0801 174270.3736 153445.0948 166020.3475 0.914798429 0.899410913 0.898981345 0.936895116 0.964092667 0.944067795 0.929175745 1.049692861 0.92425475 1 17.34100054 2.933085283 0.588649804 0.994328498 0.89600152 0.418580805 0.034264339 0.794408922 0.592917147 0.026763733 0.037096279 857.2061586 -2.933085283 -0.098326978 GGDVAVELPFTLMHPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGDVAVELPFTLMHPKPK 18 1 P49407-2;H0YET9 P49407-2 ARRB1 Beta-arrestin-1 0 137.14 2.88E-06 105420000 411360 341070 284770 285080 343210 415900 378170 387980 461050 434930 FALSE TRUE 395283.5964 331343.0175 336234.2737 299793.013 354249.6613 424309.783 382798.1576 379968.0774 408713.5369 405471.8037 0.974873204 0.817178937 0.82924206 0.739368336 0.873672739 1.046459406 0.944080831 0.93710111 1.007994966 1 18.62924207 2.933145771 6.778929929 0.975037615 0.833954038 0.561808703 0.061924781 0.190587014 16.22442841 0.019024561 0.020327745 857.3255582 -2.933145771 -0.141083577 FLLSLPEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLLSLPEHR 9 0 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 121.64 0.00060824 1124080000 1463340 1775640 1429690 1642680 1598380 1387880 1682980 1564730 1692630 1724930 FALSE TRUE 1406151.055 1725000.486 1688066.786 1727458.912 1649793.344 1415943.885 1703576.813 1532417.779 1500489.738 1608098.955 0.874418238 1.072695484 1.049728178 1.074224261 1.025927751 0.880507932 1.059373124 0.952937488 0.933082964 1 20.61692476 2.934214199 24.99986311 0.967777142 1.027236918 0.130753918 0.068265401 364.8143779 138635.5814 0.020148961 0.021371218 859.4373023 -2.934214199 0.059459776 YFDACADAVSKDELQR ddPTM_BT-474_Pertuzumab_2h_R1 1 YFDACADAVSKDELQR 16 1 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2R8YE59;A0A2U3TZL3;A0A2R8YEK8;A0A2R8Y5H3;A0A2R8YFI2;A0A2R8YCI0;A0A2R8YDX6 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 121.03 9.21E-05 367460000 473140 453730 374090 407660 446110 514640 462570 502050 606750 542300 FALSE TRUE 454649.1657 440790.0646 441696.3846 428699.3815 460459.5333 525046.3734 468231.07 491682.4921 537874.2837 505569.538 0.89928117 0.871868322 0.873660993 0.847953346 0.910773887 1.038524543 0.926145732 0.972531878 1.06389773 1 18.94755001 2.934732054 5.215756071 0.989766053 0.87355207 0.725672046 0.037010985 0.121433155 6.493414056 0.011440677 0.012356091 860.4627096 -2.934732054 -0.116213983 LHSYS(ph)SPSTK ddPTM_BT-474_Pertuzumab_2h_R1 5 LHSYSSPSTK 10 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LHSYS(0.789)S(0.198)PS(0.013)TK;LHSYS(0.976)S(0.023)PSTK;LHSYS(0.726)S(0.274)PSTK;LHSYS(0.702)S(0.298)PSTK;LHSYS(0.655)S(0.333)PS(0.011)TK 256.92 3.67E-17 3897790000 4260140 4194720 3478020 3790530 3578510 3840990 4110060 2565050 4741620 4826970 TRUE FALSE 4093649.019 4075090.693 4106575.582 3986159.708 3693616.024 3918657.449 4160360.144 2512080.821 4203371.176 4500035.022 0.909692702 0.905568662 0.912565249 0.885806374 0.820797173 0.870805989 0.924517281 0.558235838 0.934075214 1 22.1015048 2.936723178 1.049015788 0.801604849 0.909284796 0 0.11555551 1.149642675 2.719033463 0.056522883 0.064738807 864.4167583 -2.936723178 0.107679947 GLVEDTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLVEDTLR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 134.06 0.0020773 188950000 168140 173470 147250 195670 172590 145450 180010 175490 159510 197040 FALSE TRUE 161568.9029 168522.8054 173861.3506 205768.5521 178141.5141 148391.0987 182213.0162 171866.0702 141403.0935 183694.3053 0.879553139 0.917408981 0.946471097 1.120168379 0.969771566 0.807815454 0.991936119 0.935609136 0.769773964 1 17.48694738 2.937779168 24.99714602 0.905995872 0.971539872 0.117136213 0.089109954 528.3305798 212255.4553 0.027747862 0.029431076 866.521151 -2.937779168 0.065544 ILDSVGIEADDDR ddPTM_BT-474_Pertuzumab_2h_R1 5 ILDSVGIEADDDR 13 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;;; 353.5 1.10E-75 3293883000 1331554 1415267 1506418 2161127 1567073 1207608 1926181 1967854 1980761 2442270 FALSE TRUE 1279515.398 1374904.971 1778661.243 2272663.023 1617479.326 1232026.661 1949754.179 1927217.127 1755913.315 2276852.878 0.561966656 0.603862017 0.781192874 0.998159805 0.710401336 0.541109473 0.856337359 0.846439024 0.771201922 1 21.11860964 2.938422972 0.053838614 1.503085142 1.96E-12 0.347203159 0.126495755 121.5402477 2.271018976 26.1555846 36.72415106 867.8066467 -2.938422972 -1.503085142 WVDLTMDDIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 WVDLTMDDIRR 11 1 F5GWE5;Q00169 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ; 253.71 3.27E-20 180002000 221951 249310 197232 207998 219240 75796 225959 206726 208823 211980 FALSE TRUE 213276.9095 242199.9229 232876.2098 218732.8017 226292.0537 77328.64705 228724.3538 202457.0359 185118.2885 197622.4058 1.079214215 1.225569145 1.178389712 1.106821875 1.145072862 0.391294938 1.157380677 1.024463977 0.936727229 1 17.592387 2.938560388 24.99995576 0.918160034 1.151621379 0.288627848 0.191465664 325.0136543 132248.5642 0.058768876 0.062333894 868.0812752 -2.938560388 0.233461345 DLPEEYLSSIYEEIEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPEEYLSSIYEEIEGK 17 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 148.68 8.21E-07 17043000 33804 35838 27525 32402 36646 39383 44268 40711 48193 48013 FALSE TRUE 32482.90231 34815.93533 32499.37979 34074.2711 37824.75187 40179.35124 44809.76503 39870.30362 42722.33268 44761.03674 0.725695933 0.777817894 0.726064054 0.761248478 0.845037439 0.897641211 1.001088632 0.890736822 0.9544536 1 15.44995583 2.938801704 1.648690545 0.948032054 0.744215076 0.885435396 0.034427024 0.11594765 0.637718072 0.012300018 0.01392989 868.5637573 -2.938801704 -0.203816978 DHQYQFLEDAVR ddPTM_BT-474_Pertuzumab_2h_R1 5 DHQYQFLEDAVR 12 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;; 228.7 9.95E-12 20375700000 6659800 6624660 6390400 6231990 5744810 3844670 6063130 2166210 6028630 6068130 FALSE TRUE 6399527.653 6435731.183 7545287.434 6553623.751 5929597.031 3922411.862 6137332.399 2121477.007 5344285.196 5657130.15 1.131232177 1.137631805 1.333765926 1.158471447 1.048163446 0.69335719 1.084884427 0.375009404 0.944699 1 22.43163893 2.939501937 2.499389996 0.766883535 1.198538206 0.435189119 0.194392029 0.236189193 2.923697979 0.06302191 0.070764776 869.9653139 -2.939501937 0.431654671 LEPTAPALS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEPTAPALSPR 11 0 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 LEPTAPALS(1)PR;LEPTAPALS(1)PR;LEPTAPALS(1)PR 157.5 0.0013296 460500000 860160 988540 800510 862850 885470 753880 911850 926130 915930 977740 TRUE FALSE 826543.9962 960347.8071 945179.9642 907381.7919 913951.9467 769123.9701 923009.4931 907005.0919 811957.4663 911516.7989 0.906778676 1.053571155 1.036930932 0.995463598 1.002671534 0.843784745 1.012608319 0.99505033 0.890776196 1 19.79790972 2.93976621 24.99942193 0.95398268 1.004180556 0.143943932 0.060377881 494.3406906 205170.3681 0.01829244 0.019402094 870.4948573 -2.93976621 0.050197876 KLSCS(ph)LEDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 KLSCSLEDLR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLS(0.161)CS(0.839)LEDLR;KLS(0.219)CS(0.781)LEDLR;KLS(0.007)CS(0.993)LEDLR;KLS(0.429)CS(0.571)LEDLR;KLS(0.202)CS(0.798)LEDLR;KLS(0.247)CS(0.753)LEDLR 147.56 1.63E-05 10404550000 16747760 17739000 13142480 15775130 16760940 17501850 17457080 20471100 19375100 17258350 TRUE FALSE 16093239.02 17233101.09 15517618.49 16589286.35 17300070.86 17855749.4 17670724.97 20048364.63 17175719.88 16089426.58 1.000236953 1.071082366 0.964460629 1.031067594 1.075244712 1.109781589 1.098281836 1.246058368 1.067515973 1 23.93960957 2.939899924 1.688729231 1.132992417 1.015312475 0.245170132 0.064843376 0.379797883 2.187370117 0.023460689 0.026581277 870.7629134 -2.939899924 -0.117679943 GQNQDYR ddPTM_BT-474_Pertuzumab_2h_R1 5 GQNQDYR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;; 133.9 0.0075065 4885130000 10120790 11068270 9032290 10438520 9925950 9019370 10256220 9616920 10144710 10558540 FALSE TRUE 9725258.338 10752613.78 10664625.73 10977253.27 10245227.2 9201747.841 10381738.69 9418327.241 8993125.051 9843400.681 0.987997812 1.092367783 1.083428997 1.115189112 1.04082192 0.934813906 1.054690246 0.956816404 0.913619728 1 23.23072539 2.940180143 5.753000387 0.97575077 1.073133774 0.493598782 0.047153526 0.181384182 12.50267179 0.014275818 0.015379944 871.3249358 -2.940180143 0.097383004 CNTDQAGRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 CNTDQAGRPK 10 1 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 86.114 0.012566 182577000 262390 238640 224600 265020 254070 274680 291590 322400 327590 353850 FALSE TRUE 252135.5087 231834.2209 265190.2162 278697.714 262242.3923 280234.2178 295158.5656 315742.3273 290403.3566 329883.4243 0.764316998 0.702776204 0.803890698 0.844836974 0.794954741 0.849494692 0.89473597 0.957133048 0.880321153 1 18.33159676 2.941590253 0.300054788 1.00611035 0.669021523 0.825855125 0.035185628 1.037358693 0.17457831 0.048232649 0.122021828 874.1586369 -2.941590253 -0.337088827 VNGRPLEMIEPR ddPTM_BT-474_Pertuzumab_2h_R1 7 VNGRPLEMIEPR 12 1 P62249;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ;;;;;; 145.6 5.42E-05 4604180000 4939190 5328590 4452100 5183620 4999720 3838620 5183820 4826190 4353940 4779910 FALSE TRUE 4746160.994 5176623.83 5256693.506 5451147.249 5160540.534 3916239.526 5247261.14 4726527.49 3859698.984 4456162.438 1.065078094 1.161677543 1.179645845 1.223282886 1.158068317 0.878836798 1.177529144 1.060672172 0.866148629 1 22.08737039 2.942507555 24.80773302 1.020221853 1.163233033 0.423843639 0.091668536 274.4511677 118424.1827 0.028114923 0.029820486 876.0069574 -2.942507555 0.14301118 HLEIIYAINQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLEIIYAINQR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 172.8 1.29E-05 2394500000 2858000 3186600 2652800 3117700 2852300 2381380 3124900 2224540 3063500 3202800 FALSE TRUE 2746306.2 3095721.288 3132219.971 3278604.871 2944046.82 2429533.135 3163143.461 2178602.472 2715744.323 2985871.503 0.919767042 1.036789857 1.049013652 1.098039506 0.98599247 0.813676386 1.059370257 0.729637049 0.909531546 1 21.50972065 2.942869861 6.635007262 0.886793773 1.030084435 0.269199075 0.095066727 0.266624632 25.23170972 0.028341314 0.030390459 876.7380617 -2.942869861 0.143290663 MIPCDFLIPVQTQHPIR ddPTM_BT-474_Pertuzumab_2h_R1 4 MIPCDFLIPVQTQHPIR 17 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;;; 152.71 2.02E-07 3797490000 1750560 1845330 1581670 1720940 1631510 1134370 1518530 1515390 1571580 1411700 FALSE TRUE 1682146.18 1792702.995 1867512.953 1809757.92 1683989.001 1157307.739 1537114.224 1484096.667 1393180.827 1316084.302 1.278144704 1.362149061 1.418991892 1.3751079 1.279544934 0.879356845 1.16794511 1.127660793 1.058580233 1 20.32782047 2.943166718 7.160317757 1.070595418 1.359127151 0.773207624 0.080557433 0.12740455 13.88063951 0.024811424 0.0265425 877.3375502 -2.943166718 0.288531733 NEVTLEFHQNDDAEVSLMEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEVTLEFHQNDDAEVSLMEVR 21 0 Q08945;E9PMD4;E9PPZ7 Q08945 SSRP1 FACT complex subunit SSRP1 0 95.622 0.0011293 0 7110.3 11352 7965.7 8592.4 8782.6 8776.3 7306.8 10372 9886.4 8160.9 FALSE TRUE 6832.421615 11028.25207 9405.279186 9035.854794 9065.100305 8953.762799 7396.222804 10157.81458 8764.137319 7608.154974 0.898039227 1.44953042 1.236210253 1.187653883 1.191497851 1.176863882 0.972144078 1.335121933 1.151939905 1 12.89333092 2.943329647 2.27940512 1.150815858 1.21432807 0.024961948 0.156727302 1.347729812 13.92260372 0.05075802 0.057273912 877.6667531 -2.943329647 0.063512212 KREVS(ph)PPGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KREVSPPGAR 10 2 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 KREVS(1)PPGAR 65.563 0.035791 70320000 65471 57831 45113 61216 57325 82140 65388 60066 62989 61793 TRUE FALSE 62912.32094 56181.7165 53265.92263 64375.3651 59168.91069 83800.92708 66188.2379 58825.61611 55838.75279 57607.70507 1.092081708 0.975246565 0.924631915 1.117478383 1.027100639 1.454682615 1.148947659 1.021141461 0.969293131 1 15.81397417 2.943345356 24.99999179 1.127012552 1.023295497 0.099547543 0.136275557 665.5909793 293704.4678 0.0440306 0.04670166 877.6984988 -2.943345356 -0.103717055 QFFVAVER ddPTM_BT-474_Pertuzumab_2h_R1 1 QFFVAVER 8 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 88.177 0.034431 57379000 66029 63964 57146 61136 62128 49009 54638 63753 60544 71759 FALSE TRUE 63448.51368 62139.80935 67473.55341 64291.23629 64126.40354 49999.99556 55306.67619 62436.47827 53671.29894 66898.69901 0.94842672 0.928864242 1.008592908 0.961023715 0.9585598 0.747398624 0.826722747 0.933298841 0.80227717 1 16.02969053 2.943516268 24.99474207 0.860419025 0.962360402 0.350487039 0.067482748 310.9888654 137616.0807 0.020122812 0.02134354 878.0439776 -2.943516268 0.101941378 LTDCVVMRDPASK ddPTM_BT-474_Pertuzumab_2h_R1 8 LTDCVVMRDPASK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 172.1 2.18E-05 14747200000 8681200 8810380 6684030 7489780 7925230 9197590 8608880 9156240 9403130 8579210 FALSE TRUE 8341929.106 8559116.589 7891982.906 7876328.443 8180152.22 9383571.572 8714238.049 8967160.444 8335726.104 7998132.465 1.042984615 1.070139389 0.986728207 0.984770942 1.022757782 1.173220325 1.089534099 1.12115678 1.042209058 1 22.93123174 2.943783263 24.99002 1.095576652 1.019891556 0.285327359 0.049085427 306.795249 136379.4438 0.014612413 0.015498838 878.5839454 -2.943783263 -0.075685097 YHPDKNPEGR ddPTM_BT-474_Pertuzumab_2h_R1 4 YHPDKNPEGR 10 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ;;; 141.71 2.23E-05 470876000 456208 499268 405049 442500 441588 406241 481100 367067 521460 495683 FALSE TRUE 438378.887 485029.3655 478250.3646 465337.478 455792.0791 414455.4714 486987.8457 359486.9382 462266.0469 462109.9489 0.948646287 1.049597323 1.034927652 1.006984332 0.986328211 0.896876322 1.053835449 0.777925122 1.000337794 1 18.81787662 2.944740032 3.568050901 0.928429431 1.01389885 0.119945372 0.074709789 0.369219993 9.411625307 0.02302721 0.025548783 880.5216371 -2.944740032 0.085469419 SDLNGLPS(ph)PVEER ddPTM_BT-474_Pertuzumab_2h_R1 2 SDLNGLPSPVEER 13 0 E7EWN3;Q9C0A6 E7EWN3 SETD5 SET domain-containing protein 5 1 SDLNGLPS(1)PVEER;SDLNGLPS(1)PVEER 174.78 4.13E-06 215120000 377430 392230 289910 332890 342310 351490 336290 356090 355870 349640 TRUE FALSE 362679.6183 381043.9844 342303.186 350070.4928 353320.712 358597.3686 340405.6176 348736.6171 315473.1295 325958.5714 1.112655565 1.168995136 1.050143227 1.07397235 1.083943614 1.100131735 1.044321725 1.069880186 0.96783198 1 18.31432909 2.944761339 0.225846925 0.976770503 1.177855914 0.571117368 0.035297697 3.616355426 0.372382923 0.079306644 0.221530484 880.5648369 -2.944761339 0.201085411 EVEERPAPTPWGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 EVEERPAPTPWGSK 14 1 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ;;; 150.76 6.50E-06 3667960000 1477150 1596080 1264420 1616260 1559790 1833480 1757880 2115340 2066990 2133960 FALSE TRUE 1419421.345 1550561.361 1492928.821 1699675.372 1609962.062 1870554.222 1779393.461 2071657.49 1832353.961 1989424.988 0.713483219 0.779401772 0.750432326 0.854355094 0.809259998 0.940248681 0.894426013 1.041334809 0.921047022 1 20.92392007 2.945205157 0.627357528 1.001154974 0.724962553 0.82303153 0.043173639 0.301705232 0.25936069 0.030047825 0.040525618 881.4651716 -2.945205157 -0.276192421 LTYEIEDEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTYEIEDEKR 10 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 196.76 5.25E-07 3679720000 3174010 3195090 2592630 3178890 3283340 3584620 3678320 4080840 4357590 3900390 FALSE TRUE 3049966.18 3103969.162 3061175.914 3342952.894 3388951.613 3657103.472 3723336.38 3996569.228 3862934.652 3636213.111 0.83877542 0.853626855 0.841858225 0.919350102 0.932000273 1.005745087 1.023959891 1.099102034 1.062351005 1 21.79400532 2.946890697 0.973345447 1.064931767 0.841043322 0.905428372 0.027498847 0.138170698 0.284743338 0.013782861 0.016088128 884.8928726 -2.946890697 -0.223888445 RVS(ph)HS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK 92.856 0.03427 32540800000 5479720 5250760 4330800 4983290 4855950 4947190 5069810 4904500 5832390 5384110 TRUE FALSE 5265566.484 5101013.466 5113471.898 5240478.194 5012146.042 5047225.571 5131855.851 4803220.361 5170321.539 5019439.434 1.049034768 1.016251622 1.018733658 1.044036543 0.998546971 1.005535705 1.02239621 0.956923661 1.030059553 1 22.25909482 2.947148501 1.163148023 0.995205882 1.030626003 0.257155116 0.02154613 0.570206434 1.632782143 0.009411091 0.010828763 885.4183141 -2.947148501 0.035420121 RRS(ph)PPPGPDGHAK ddPTM_BT-474_Pertuzumab_2h_R1 7 RRSPPPGPDGHAK 13 2 P57081;P57081-2;P57081-3 P57081 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 1 RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK 144.17 2.03E-05 9933200000 867456 805321 691220 768287 784693 857766 820358 815614 956920 949425 TRUE FALSE 833554.8605 782354.0336 816138.8301 807938.3841 809933.363 875110.6162 830397.7866 798771.2859 848294.4533 885119.5991 0.941742632 0.883896407 0.92206616 0.912801372 0.91505528 0.988691943 0.938175798 0.902444468 0.958395288 1 19.75551288 2.948154169 24.96439032 0.946512242 0.913458604 0.312437969 0.029225282 513.808119 247404.4747 0.009093063 0.009644789 887.4709962 -2.948154169 -0.033053638 SKLEVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKLEVGR 7 1 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 85.676 0.01882 225640000 312670 287840 258420 283290 285030 233220 271420 299990 286340 301540 FALSE TRUE 300450.5107 279631.085 305122.2425 297910.6308 294198.2488 237935.8682 274741.7192 293795.1017 253835.8836 281116.4272 1.068776072 0.994716274 1.085394566 1.059741097 1.046535244 0.846396173 0.977323602 1.045101151 0.902956423 1 18.10080824 2.948479144 24.99994438 0.964350059 1.050767196 0.429573098 0.055125202 385.6987913 187155.9674 0.017380498 0.018435035 888.1353238 -2.948479144 0.086417137 S(ph)PLLLGAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLLLGAQR 9 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 S(1)PLLLGAQR 62.78 0.084312 90578000 38698 49491 43200 46432 45104 31971 39600 48892 37857 50454 TRUE FALSE 37185.63938 48079.56514 51007.20098 48828.36108 46554.81112 32617.47553 40084.63665 47882.36311 33559.63207 47036.70564 0.790566407 1.022171185 1.0844127 1.038090581 0.989754926 0.693447279 0.852199067 1.017978671 0.71347752 1 15.5214994 2.948959962 24.99981047 0.866887712 0.996259828 0.217086872 0.121194599 564.5452423 276518.2454 0.037407798 0.03967736 889.1191458 -2.948959962 0.129372116 RQS(ph)VS(ph)PPYKEPSAYQSSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 RQSVSPPYKEPSAYQSSTR 19 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RQS(0.723)VS(0.896)PPY(0.284)KEPS(0.07)AY(0.01)QS(0.012)S(0.002)T(0.004)R;RQS(1)VS(0.999)PPY(0.001)KEPSAYQSSTR;RQS(1)VS(0.996)PPY(0.002)KEPS(0.001)AYQSSTR;RQS(0.999)VS(0.994)PPY(0.005)KEPS(0.001)AYQSSTR 100.94 0.00029798 5147910000 858540 763270 769810 874760 864210 860980 985650 1078860 1122350 1187320 TRUE FALSE 824987.3076 741502.2869 908931.7913 919906.4684 892008.0995 878389.6055 997712.6795 1056581.164 994945.5333 1106901.759 0.74531213 0.66988988 0.821149469 0.83106424 0.805860224 0.79355697 0.901356124 0.95453924 0.898856222 1 20.07809575 2.949022314 0.289569029 1.01612924 0.641370122 0.795621004 0.042303514 1.277549261 0.200383528 0.06302639 0.164090209 889.2468059 -2.949022314 -0.374759118 LFENLR ddPTM_BT-474_Pertuzumab_2h_R1 8 LFENLR 6 0 Q92769;Q92769-3;Q13547;Q96G03 Q92769;Q13547;Q96G03 HDAC2;HDAC1;PGM2 Histone deacetylase 2;Histone deacetylase 1;Phosphoglucomutase-2 0 ;;;;;;; 151.14 0.024247 2789961000 2048021 2246061 1848333 2042492 2053761 1572112 2141257 2010820 2111014 2220034 FALSE TRUE 1967982.075 2182005.539 2182367.889 2147905.257 2119822.088 1603901.182 2167462.344 1969295.864 1871380.541 2069669.12 0.95086797 1.054277478 1.054452554 1.037801278 1.02423236 0.774955362 1.047250656 0.951502753 0.904193102 1 20.98096871 2.949713596 24.99994404 0.939126306 1.028935566 0.276294429 0.071546185 471.8225041 234566.6696 0.021126358 0.022408175 890.6633781 -2.949713596 0.08980926 LSQELEYLTEDVKR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSQELEYLTEDVKR 14 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;;; 238.17 4.11E-17 483569000 434142 424242 328135 347042 399246 436160 419766 466061 486925 435621 FALSE TRUE 417175.2507 412143.0335 387436.2938 364952.8792 412088.1102 444979.454 424903.2219 456436.6775 431651.3154 406116.0017 1.027231749 1.014840666 0.954004009 0.898641959 1.014705425 1.095695447 1.046260724 1.123907149 1.062876896 1 18.63153235 2.950081542 5.357933006 1.074744516 0.972994243 0.479260464 0.044774994 0.163937238 10.79726313 0.014094224 0.015316977 891.4182924 -2.950081542 -0.101750273 RNS(ph)SEASSGDFLDLK ddPTM_BT-474_Pertuzumab_2h_R1 20 RNSSEASSGDFLDLK 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 RNS(0.988)S(0.005)EAS(0.005)S(0.002)GDFLDLK;RNS(0.941)S(0.046)EAS(0.007)S(0.005)GDFLDLK;RNS(0.999)S(0.001)EASSGDFLDLK;RNS(0.998)S(0.002)EASSGDFLDLK;RNS(1)SEASSGDFLDLK;RNS(0.975)S(0.025)EASSGDFLDLK;RNS(0.879)S(0.112)EAS(0.008)S(0.002)GDFLDLK;RNS(0.996)S(0.004)EASSGDFLDLK;RNS(0.824)S(0.176)EASSGDFLDLK;RNS(0.888)S(0.112)EASSGDFLDLK;RNS(0.829)S(0.17)EAS(0.001)SGDFLDLK;RNS(0.418)S(0.418)EAS(0.082)S(0.082)GDFLDLK;RNS(0.998)S(0.002)EAS(0.001)SGDFLDLK;RNS(0.979)S(0.021)EASSGDFLDLK;RNS(0.994)S(0.006)EASSGDFLDLK;RNS(0.848)S(0.152)EASSGDFLDLK;RNS(0.905)S(0.095)EASSGDFLDLK;RNS(0.441)S(0.007)EAS(0.317)S(0.235)GDFLDLK;RNS(0.937)S(0.063)EASSGDFLDLK;RNS(0.988)S(0.012)EASSGDFLDLK 307.58 6.39E-46 1.61128E+11 35369118 30378535 35693146 38282680 41151182 38548164 46475348 51386137 61289981 56820937 TRUE FALSE 33986853.77 29512168.93 42143691.47 40258453.7 42474847.14 39327634.29 47044127.21 50324995.31 54332599.31 52972404.33 0.641595453 0.557123455 0.795578226 0.759989172 0.801829701 0.742417392 0.888087445 0.950022865 1.025677426 1 25.65873766 2.950246236 0.369239935 1.04338648 0.547349244 0.822108471 0.060767697 0.747952836 0.191375091 0.067465979 0.144141008 891.756402 -2.950246236 -0.496037236 SSLS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSLSPGR 7 0 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 SSLS(1)PGR;SSLS(1)PGR 120.15 0.004847 2314700000 2306400 2278900 1891450 2271300 2069300 1769130 1950810 1977970 2118800 2175900 TRUE FALSE 2216263.338 2213908.003 2233277.09 2388522.065 2135860.914 1804903.021 1974684.596 1937124.228 1878282.707 2028524.355 1.092549534 1.091388426 1.100936789 1.177467778 1.052913616 0.889761573 0.973458658 0.954942554 0.925935497 1 20.95199919 2.950269328 5.402242119 0.949839444 1.113459649 0.83271528 0.03543178 0.076188379 5.127340235 0.010538947 0.011449449 891.8038197 -2.950269328 0.163620205 DKFSFDLGKGEVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKFSFDLGKGEVIK 14 2 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 113.69 0.00029313 1083600000 2075300 2055700 1419800 1037100 1627800 2259100 1573200 1881900 2100000 1753200 FALSE TRUE 1994194.982 1997073.449 1676389.443 1090624.855 1680159.665 2304780.55 1592453.292 1843038.107 1861616.804 1634454.202 1.220098415 1.221859533 1.02565703 0.667271591 1.027963746 1.410122441 0.974302792 1.127616855 1.138983767 1 20.64037752 2.950911926 24.99982573 1.133582972 1.02171236 0.066728825 0.180225738 1089.796872 555016.6506 0.05808537 0.061609894 893.1243408 -2.950911926 -0.111870612 APRPSAPS(ph)PPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 APRPSAPSPPPR 12 1 Q8IV50 Q8IV50 LYSMD2 LysM and putative peptidoglycan-binding domain-containing protein 2 1 APRPSAPS(1)PPPR;APRPS(0.003)APS(0.997)PPPR;APRPS(0.001)APS(0.999)PPPR;APRPS(0.006)APS(0.994)PPPR 115.56 0.00056735 1391760000 207067 222843 178599 222139 213495 212882 206609 222244 203835 260341 TRUE FALSE 198974.5927 216487.7358 210875.8122 233603.6204 220362.2606 217186.6199 209137.5427 217654.5837 180696.5053 242707.8722 0.819811038 0.891968332 0.868846199 0.962488848 0.907932069 0.894847859 0.861684217 0.896775954 0.744502037 1 17.88886138 2.95109308 0.00590421 1.765231897 5.70E-07 0.075218475 0.064390245 36234.19982 72.36574722 10611.82974 11021.84386 893.4969616 -2.95109308 -1.765231327 RVPS(ph)PTPAPK ddPTM_BT-474_Pertuzumab_2h_R1 10 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RVPS(0.977)PT(0.023)PAPK;RVPS(0.914)PT(0.086)PAPK;RVPS(0.903)PT(0.097)PAPK;RVPS(0.5)PT(0.5)PAPK;RVPS(0.914)PT(0.086)PAPK;RVPS(0.958)PT(0.042)PAPK;RVPS(0.99)PT(0.01)PAPK;RVPS(0.912)PT(0.088)PAPK;RVPS(0.897)PT(0.103)PAPK;RVPS(0.975)PT(0.025)PAPK 147.58 2.82E-05 82160080000 64788200 63791240 52151400 56055650 60457760 63427570 61502020 67378580 72691180 66610170 TRUE FALSE 62256205.52 61971976.29 61576318.08 58948688.81 62402438.76 64710118.92 62254700.12 65987188.78 64439581.99 62098603.86 1.002537926 0.997960863 0.991589412 0.94927559 1.004892782 1.042054328 1.002513684 1.062619523 1.037697758 1 25.8880575 2.951899063 5.472361545 1.032511296 0.985542643 0.465606158 0.021887707 0.168988516 11.94059749 0.006746821 0.007332109 895.1566931 -2.951899063 -0.046968653 HELIEFR ddPTM_BT-474_Pertuzumab_2h_R1 8 HELIEFR 7 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;; 176.66 0.00074355 10153120000 4793880 4800160 5100230 5335870 5062460 4054000 6057400 3097639 5975050 6494390 FALSE TRUE 4606529.87 4663264.137 6021955.015 5611254.89 5225298.624 4135974.658 6131532.273 3033671.672 5296787.373 6054519.181 0.760841568 0.770212134 0.994621511 0.926787863 0.863041055 0.683121902 1.012719935 0.501059057 0.874848558 1 22.52958096 2.952021232 23.46808097 0.77665686 0.869503293 0 0.155098251 553.3038843 270639.2734 0.046797212 0.04963786 895.4085393 -2.952021232 0.092846432 IIECTHCGCR ddPTM_BT-474_Pertuzumab_2h_R1 4 IIECTHCGCR 10 0 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 ;;; 180.36 2.01E-06 1477700000 1176510 1338610 1084180 1189080 1142630 965230 1172250 1065590 1074260 1158890 FALSE TRUE 1130530.688 1300434.153 1280115.443 1250448.561 1179383.732 984747.6119 1186596.346 1043585.194 952314.5085 1080397.348 1.046402687 1.203662852 1.184856151 1.157396918 1.09162035 0.911468002 1.098296241 0.965927208 0.881448395 1 20.04313057 2.952080873 4.334027823 0.979957955 1.152681757 0.613772197 0.066474449 0.146533133 5.889714373 0.020319806 0.02238794 895.5315128 -2.952080873 0.172723802 LNLQFLTLHDYLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNLQFLTLHDYLLR 14 0 O60306;H0YH15 O60306 AQR Intron-binding protein aquarius 0 ; 176.32 2.24E-06 164677000 194103 217190 195281 200203 203433 141641 236620 180940 215062 231570 FALSE TRUE 186517.2402 210995.9539 230572.6207 210535.5008 209976.6072 144505.0781 239515.8263 177203.5258 190649.0634 215885.5576 0.863963492 0.977350945 1.068031707 0.975218088 0.972629246 0.669359635 1.109457385 0.820821586 0.883102443 1 17.71990721 2.952386005 24.99998922 0.890322629 0.977933276 0.091875128 0.116133926 854.706069 448767.6018 0.033770521 0.035819822 896.1609287 -2.952386005 0.087610647 ITADLLSNGIDVYPQKEFDEDSEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ITADLLSNGIDVYPQKEFDEDSEDR 25 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ;;; 284.33 1.51E-53 2031930000 993930 916940 832580 929420 1029520 998380 1096760 1235280 1258340 1117390 FALSE TRUE 955086.1168 890789.769 983045.7266 977387.4776 1062635.446 1018567.928 1110182.477 1209771.036 1115498.519 1041708.18 0.916846133 0.855124099 0.943686289 0.938254586 1.020089375 0.977786243 1.065732705 1.161333912 1.070835902 1 19.99051975 2.952618525 0.877667886 1.095562344 0.891853251 0.668004495 0.04851592 0.312181591 0.530153399 0.027411179 0.032758659 896.640859 -2.952618525 -0.203709093 SHEAEVLK ddPTM_BT-474_Pertuzumab_2h_R1 6 SHEAEVLK 8 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ;;;;; 134.48 0.00087486 14231480000 18412200 18027100 15099100 15425500 15120200 12165360 17377700 5919330 18668700 17286200 FALSE TRUE 17692630.87 17512984.76 17827843.25 16221611.9 15606554.96 12411351.91 17590373.49 5797093.767 16549507.44 16115390.28 1.097871697 1.086724209 1.106261961 1.006591316 0.968425505 0.770155218 1.091526373 0.359724069 1.026938048 1 23.94193579 2.952731706 1.130762388 0.772123003 1.09943008 0.192393088 0.196420092 0.57780308 1.571281407 0.087245745 0.101125385 896.8745606 -2.952731706 0.327307078 DTIPQTSEQKEYENR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTIPQTSEQKEYENR 15 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;A0A087WZS7;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 0 96.993 0.0036949 0 62900 57034 33365 46573 49145 63411 51786 55106 60120 51319 FALSE TRUE 60441.79846 55407.44616 39394.7977 48976.63811 50725.79356 64693.21387 52419.77256 53968.04184 53295.42964 47843.11842 1.26333317 1.158106913 0.823416178 1.023692429 1.06025266 1.352194757 1.095659612 1.128020991 1.113962288 1 15.54602381 2.952986286 24.99692578 1.147275098 1.054444143 0.063626743 0.132863399 1014.778541 539551.5765 0.041662872 0.044191198 897.4004557 -2.952986286 -0.092830955 SFGS(ph)PNR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFGSPNR 7 0 D6RAD4;P50613;D6REC6;D6R9G1 D6RAD4 CDK7 Cyclin-dependent kinase 7 1 S(0.036)FGS(0.964)PNR;S(0.007)FGS(0.993)PNR;S(0.004)FGS(0.996)PNR;S(0.002)FGS(0.998)PNR 98.009 0.012145 3185120000 2793710 2962150 2461880 2915230 2782940 1381900 2995450 2827100 2968960 3124790 TRUE FALSE 2684528.725 2877672.382 2906796.48 3065685.37 2872455.793 1409842.965 3032109.213 2768719.397 2631936.108 2913145.19 0.921522461 0.987823193 0.997820668 1.052362711 0.986032486 0.483959045 1.04083697 0.950422727 0.903468909 1 21.47414618 2.954412159 24.99952573 0.877168411 0.993915125 0.131802801 0.145346378 919.3622502 504160.827 0.045009035 0.047741068 900.3516371 -2.954412159 0.116746715 CPTQFPLILWHPYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 CPTQFPLILWHPYAR 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 164.09 1.50E-06 449490000 453580 504000 429990 421410 417630 372750 437740 359100 412030 417040 FALSE TRUE 435853.5921 489626.4135 507698.7581 443159.0206 431063.4482 380287.2604 443097.1931 351684.4595 365258.0818 388793.5093 1.121041328 1.259348219 1.305831363 1.139831324 1.108720794 0.978121422 1.1396723 0.90455332 0.939465482 1 18.56864461 2.954465027 1.047162046 0.971184835 1.233361691 0.657724148 0.073816 0.298069017 0.703643668 0.035327738 0.041262322 900.4612473 -2.954465027 0.262176856 GEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_BT-474_Pertuzumab_2h_R1 7 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEGDAPFSEPGTTST(0.001)QRPS(0.053)S(0.945)PETATK;GEGDAPFSEPGTTSTQRPS(0.046)S(0.927)PET(0.025)AT(0.001)K;GEGDAPFSEPGTTSTQRPS(0.009)S(0.99)PET(0.001)ATK;GEGDAPFSEPGTTS(0.001)T(0.022)QRPS(0.223)S(0.726)PET(0.025)AT(0.003)K;GEGDAPFSEPGT(0.003)T(0.003)S(0.003)T(0.003)QRPS(0.438)S(0.549)PET(0.002)ATK;GEGDAPFSEPGTTSTQRPS(0.048)S(0.952)PETATK;GEGDAPFSEPGTTS(0.001)T(0.003)QRPS(0.213)S(0.782)PETATK 286.44 1.49E-61 52402220000 13094450 13439100 12847610 13538260 13809970 14251870 15410480 17388770 18501160 17274340 TRUE FALSE 12582704.42 13055830.03 15169458.92 14236971.22 14254180.23 14540052.58 15599078.06 17029685.82 16400985.88 16104333.57 0.78132413 0.810702906 0.941948877 0.884045972 0.885114567 0.902865835 0.968626115 1.057459829 1.018420651 1 23.94094562 2.954842795 0.47572591 1.044692557 0.793308715 0.751271345 0.042186849 0.631535533 0.287723787 0.041676709 0.070143651 901.2448476 -2.954842795 -0.251383842 AGVLAHLEEER ddPTM_BT-474_Pertuzumab_2h_R1 6 AGVLAHLEEER 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;;; 195.51 6.36E-08 18024300000 4289450 4932650 3991720 4314620 4385970 3200300 4751870 4024510 4159740 4482230 FALSE TRUE 4121813.552 4791975.652 4713112.599 4537298.055 4527048.708 3265012.259 4810024.807 3941402.462 3687543.754 4178644.57 0.986399653 1.146777519 1.12790464 1.085830101 1.083377309 0.781356778 1.151096899 0.943225105 0.882473657 1 21.99460362 2.955463724 24.99632056 0.961194949 1.092789265 0.326539848 0.095888116 527.7306229 296192.6847 0.028102642 0.029808778 902.5343162 -2.955463724 0.131594316 IIPVLLEHGLER ddPTM_BT-474_Pertuzumab_2h_R1 2 IIPVLLEHGLER 12 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ; 172.92 3.45E-05 616450000 503320 560390 454420 546640 502500 431950 537450 456400 477890 567310 FALSE TRUE 483649.698 544408.2259 536543.8025 574852.1559 518663.3689 440684.325 544027.4739 446975.1805 423641.9307 528885.5884 0.914469421 1.029349708 1.014479907 1.08691212 0.980672153 0.833231865 1.028629794 0.845126414 0.801008649 1 19.01259614 2.955492187 8.561492982 0.89950192 1.015432957 0.316568718 0.07702143 0.409799689 74.77190389 0.022930008 0.024534398 902.5934698 -2.955492187 0.115931037 SVVS(ph)DLEADDVK ddPTM_BT-474_Pertuzumab_2h_R1 6 SVVSDLEADDVK 12 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 SVVS(1)DLEADDVK;SVVS(1)DLEADDVK;SVVS(1)DLEADDVK;SVVS(1)DLEADDVK;SVVS(1)DLEADDVK;SVVS(1)DLEADDVK 281.01 4.91E-28 3777552000 4812070 4359800 4054010 4406220 5021460 4866010 5248860 5839100 6009260 5874560 TRUE FALSE 4624008.984 4235462.773 4786659.788 4633625.542 5182979.821 4964404.056 5313097.119 5718520.544 5327113.998 5476670.819 0.844310191 0.773364497 0.874009037 0.846066104 0.946374174 0.906463839 0.97013264 1.044159989 0.972692019 1 22.38486774 2.955844824 0.710104015 1.015252853 0.806898561 0.80626448 0.034865715 0.278581388 0.311754656 0.022738116 0.029138398 903.326653 -2.955844824 -0.208354292 EDVLSFIQMHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDVLSFIQMHR 11 0 Q8N1G2 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 167.18 1.95E-05 148040000 200410 196350 179180 199300 194800 176370 199670 191570 217140 232490 FALSE TRUE 192577.7556 190750.2902 211561.8118 209585.8969 201065.9189 179936.3222 202113.6212 187614.0126 192491.1775 216743.2452 0.888506377 0.880074902 0.976094141 0.966977756 0.927668674 0.830181914 0.932502515 0.865604888 0.888106927 1 17.72562751 2.955847644 24.99234291 0.893490264 0.930361025 0.038180643 0.050392073 1014.478733 574242.5948 0.014980224 0.015889786 903.3325172 -2.955847644 0.036870761 VVDRDSEEAEIIRK ddPTM_BT-474_Pertuzumab_2h_R1 3 VVDRDSEEAEIIRK 14 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 221.59 2.37E-12 1981740000 2161820 2146450 1244740 1497530 1741400 2389220 1763800 1980350 2055520 1841800 FALSE TRUE 2077333.684 2085235.348 1469692.207 1574817.703 1797413.712 2437531.665 1785385.912 1939455.08 1822185.987 1717053.245 1.20982485 1.214426724 0.855938633 0.917162998 1.046801383 1.419601676 1.039796475 1.129525299 1.061228586 1 20.71150335 2.956582738 24.9991698 1.140018322 1.039148829 0.065436674 0.149142043 1203.267608 692827.4549 0.047280022 0.050150582 904.8628074 -2.956582738 -0.100869493 DYDS(ph)PERER ddPTM_BT-474_Pertuzumab_2h_R1 1 DYDSPERER 9 1 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3 P52756 RBM5 RNA-binding protein 5 1 DYDS(1)PERER 115.29 0.0024501 0 94916 95059 74587 85105 87630 97324 89028 95775 101290 97807 TRUE FALSE 91206.57778 92348.01039 88066.53008 89497.27925 90448.69853 99291.95796 90117.5513 93797.21278 89791.98384 91182.44477 1.000264667 1.012782785 0.965827691 0.98151875 0.991952988 1.08893722 0.988321288 1.028676222 0.984750783 1 16.47646847 2.956893128 24.99997298 1.020355958 0.989578889 0.177483852 0.029601726 743.5477451 431222.4785 0.008767647 0.009300102 905.5097435 -2.956893128 -0.030777069 YWDGWFR ddPTM_BT-474_Pertuzumab_2h_R1 2 YWDGWFR 7 0 Q9Y570;Q9Y570-4;Q9Y570-2;Q9Y570-3 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ; 116.11 0.012861 4544200000 2516400 2755700 2362200 2783200 2624400 2319500 2718300 2666700 2642500 2870700 FALSE TRUE 2418056.306 2677110.134 2789102.087 2926841.286 2708816.209 2366401.879 2751567.369 2611631.713 2342534.478 2676264.932 0.903519034 1.000315814 1.042162177 1.093629129 1.01216295 0.884218095 1.028137138 0.975849469 0.875299919 1 21.35178951 2.956994324 24.96554524 0.958436202 1.016696834 0.169779317 0.062412799 859.6316028 499031.1953 0.019458556 0.020640405 905.7207638 -2.956994324 0.058260632 TPQPCSRPAS(ph)PEPELLPEADSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPQPCSRPASPEPELLPEADSK 22 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 TPQPCS(0.006)RPAS(0.994)PEPELLPEADSK;TPQPCS(0.003)RPAS(0.997)PEPELLPEADSK 181.62 2.97E-17 605830000 451810 631370 226873 433730 437820 790780 492870 417810 656280 523810 TRUE FALSE 434152.7657 613363.9458 267873.9979 456114.8573 451902.8779 806770.1134 498901.8905 409182.0775 581781.8458 488331.8821 0.889052674 1.256039116 0.548549066 0.934026374 0.925401135 1.652093879 1.021645133 0.837918007 1.191365682 1 18.89750245 2.957226056 24.99882707 1.115691237 0.909187701 0.167251405 0.253816868 1026.41886 599880.549 0.080595797 0.085490743 906.2041687 -2.957226056 -0.206503536 LTHVNTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTHVNTGR 8 0 Q99470;K7ELI9 Q99470 SDF2 Stromal cell-derived factor 2 0 ;;; 110.76 0.0033646 586059000 554977 621698 516938 634373 586017 535321 635864 535385 621470 689554 FALSE TRUE 533287.8853 603967.7817 610360.1958 667113.0666 604866.769 546145.5574 643645.8938 524329.1127 550923.331 642849.8934 0.829568288 0.939516033 0.949459901 1.037743139 0.940914474 0.849569337 1.001238237 0.815632262 0.857001513 1 19.29412238 2.95725721 22.27103763 0.895087226 0.946030938 0.041895567 0.073579275 328.7818907 171310.3502 0.022392975 0.023755061 906.2691784 -2.95725721 0.050943712 KTGSPGS(ph)PGAGGVQSTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTGSPGSPGAGGVQSTAK 18 1 O43237;O43237-2;J3KRI4;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 KT(0.008)GS(0.004)PGS(0.989)PGAGGVQSTAK;KT(0.003)GS(0.004)PGS(0.992)PGAGGVQSTAK 209.64 3.06E-16 405300000 363490 369830 286870 282840 326680 385260 349130 354570 405420 357650 TRUE FALSE 349284.4089 359282.8105 338713.7904 297437.4063 337187.9589 393050.2212 353402.7574 347248.0056 359398.4213 333426.0469 1.047561857 1.077548721 1.015858819 0.892064099 1.011282598 1.178822785 1.059913467 1.041454346 1.077895457 1 18.34700729 2.957355985 24.99663961 1.072893487 1.005990814 0.206966315 0.061352878 775.4244454 454530.0479 0.019662206 0.020856595 906.4753206 -2.957355985 -0.066902672 GFAFVEYESHR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFAFVEYESHR 11 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;F8W9F8;Q5T0W7;Q8TBY0-2;Q8TBY0-3;Q8TBY0;Q9NQ94-6;Q9NQ94-3;Q9NQ94-2;Q9NQ94;Q9NQ94-4;Q9NQ94-5 B7Z8Z7 RBM47;A1CF;RBM46 RNA-binding protein 47;Probable RNA-binding protein 46;APOBEC1 complementation factor 0 ;; 152.54 3.29E-05 1267830000 1423959 1701861 1441396 1802684 1596347 977699 1767940 1318581 1377050 1541886 FALSE TRUE 1368309.108 1653325.591 1701888.321 1895720.737 1647694.951 997468.7437 1789576.579 1291351.842 1220733.057 1437452.688 0.951898535 1.150177397 1.183961278 1.318805658 1.146260301 0.693914139 1.244963813 0.898361283 0.849233556 1 20.45508304 2.957655962 24.99547349 0.950647038 1.163358468 0.320259094 0.154099222 576.1902027 340122.181 0.045997478 0.048791617 907.1016615 -2.957655962 0.21271143 DVESYIHR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVESYIHR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;;; 175.44 0.00026609 3731630000 4256500 4289220 4307700 4699480 4436170 3862120 4616930 4346460 4491880 5191210 FALSE TRUE 4090151.274 4166895.645 5086197.214 4942020.726 4578863.437 3940214.713 4673433.37 4256704.082 3981980.614 4839604.723 0.845141599 0.860999169 1.050953023 1.02116206 0.946123433 0.81416044 0.965664272 0.879556147 0.822790464 1 22.20645779 2.957855936 24.9317996 0.89270922 0.950875384 0.083036746 0.078916675 1110.505263 656957.8556 0.024802763 0.02630971 907.5194376 -2.957855936 0.058166164 LKDTQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDTQDR 7 1 A0A3B3IRY9;O15079;O15079-2 A0A3B3IRY9 SNPH Syntaphilin 0 66.073 0.062803 118250000 233310 254940 173740 209550 221840 239040 240830 221290 281120 269150 FALSE TRUE 224191.9873 247669.3608 205138.6828 220364.9006 228975.6851 243873.5526 243777.3496 216720.2842 249208.4362 250920.2308 0.893479121 0.987044209 0.81754541 0.878226917 0.912543737 0.97191666 0.971533259 0.863701916 0.993177933 1 17.93686927 2.958425841 6.797889384 0.945266562 0.895198755 0.239975841 0.053012078 0.421355876 54.63446517 0.016568132 0.017900622 908.7111161 -2.958425841 -0.050067808 LCSDHCFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LCSDHCFNR 9 0 Q9UBW7;Q9UBW7-2 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 ; 140.83 0.0015646 0 106128 142768 104725 121491 112770 89955 108380 109638 107117 109994 FALSE TRUE 101980.4004 138696.3964 123651.1371 127761.1651 116397.3495 91773.95173 109706.3869 107373.937 94957.52723 102544.0084 0.994503745 1.352554855 1.205834831 1.245915457 1.135096543 0.89497137 1.069846874 1.047101032 0.926017314 1 16.64588367 2.958772096 5.826461529 1.002289059 1.209249452 0.523308344 0.095919716 0.155011212 13.94046564 0.027912885 0.030382838 909.4359044 -2.958772096 0.206960393 FTDFDEVR ddPTM_BT-474_Pertuzumab_2h_R1 4 FTDFDEVR 8 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4 P50570-2 DNM2;DNM3 Dynamin-2;Dynamin-3 0 ;;; 214.41 2.06E-05 1354810000 2119510 2378930 2008210 2436250 2254260 1731160 2465780 2329300 2356950 2518660 FALSE TRUE 2036677.206 2311085.246 2371138.219 2561985.154 2326770.32 1766165.241 2495956.953 2281199.141 2089398.917 2348068.915 0.867383914 0.984249325 1.009824799 1.09110305 0.990929315 0.75217777 1.062982836 0.971521375 0.889837136 1 21.16304332 2.959385506 24.99987597 0.939797133 0.995862121 0.075319651 0.091328995 1425.296932 877327.9563 0.028295304 0.03001547 910.7213254 -2.959385506 0.056064988 RGPPPPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RGPPPPPR 8 1 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ;; 113.41 0.0045757 257818000 164312 183866 156683 166451 168735 138581 195319 153398 187470 175702 FALSE TRUE 157890.5054 178622.3217 184999.1035 175041.5561 174162.5145 141383.2028 197709.3723 150230.2777 166189.1915 163801.547 0.963913395 1.090480065 1.129409989 1.068619676 1.063253172 0.863137164 1.207005525 0.9171481 1.014576447 1 17.32158946 2.959745268 24.99249071 1.001768534 1.069314669 0.103544929 0.091563093 1125.294809 698648.7978 0.026641185 0.028261103 911.4760641 -2.959745268 0.067546135 YWSQFDENIR ddPTM_BT-474_Pertuzumab_2h_R1 1 YWSQFDENIR 10 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 120.45 0.0012978 173330000 207100 224740 192190 218070 210670 141920 233070 194710 216570 236110 FALSE TRUE 199006.303 218330.6352 226923.0082 229324.6188 217446.3919 144789.7196 235922.3804 190689.1705 191985.8815 220118.0594 0.90408894 0.991879702 1.030914996 1.041825552 0.98786257 0.657782101 1.071799293 0.866304069 0.872195049 1 17.74791799 2.959789208 24.99913442 0.891167278 0.99741341 0.175196015 0.105713823 833.3689173 518107.2302 0.030890002 0.032768252 911.5682868 -2.959789208 0.106246132 GYAFIEYEHER ddPTM_BT-474_Pertuzumab_2h_R1 4 GYAFIEYEHER 11 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;; 161.62 2.61E-05 3120080000 4381580 4915010 3771550 4293270 4283970 2514860 4545620 3428690 4012490 4338480 FALSE TRUE 4210343.01 4774838.727 4453152.983 4514846.179 4421767.786 2565712.192 4601250.657 3357886.353 3557008.957 4044630.885 1.040970889 1.180537573 1.101003555 1.116256664 1.093243836 0.634350146 1.137619424 0.830208355 0.879439696 1 21.94757662 2.960064676 24.9493506 0.897719801 1.112959361 0.420670669 0.123357841 456.8198694 285395.4128 0.034818297 0.03693557 912.146668 -2.960064676 0.21523956 T(ph)SPDSLRR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSPDSLRR 8 1 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 1 T(0.951)S(0.043)PDS(0.006)LRR;T(0.967)S(0.029)PDS(0.004)LRR;T(0.932)S(0.061)PDS(0.008)LRR;T(0.994)S(0.005)PDSLRR 106.2 0.0082045 1147460000 1538620 1478230 1320760 1418000 1471860 1604320 1490250 1595450 1926570 1754870 TRUE FALSE 1478489.029 1436072.328 1559450.712 1491183.15 1519203.714 1636760.45 1508488.125 1562503.4 1707873.85 1636011.092 0.903715774 0.87778887 0.953203019 0.911474963 0.928602331 1.00045804 0.922052505 0.955068953 1.043925594 1 20.6417511 2.960258128 0.305535596 1.013375579 0.868285193 0.551494324 0.032796701 2.145324626 0.370470346 0.043270147 0.109611357 912.5530646 -2.960258128 -0.145090387 AREEAER ddPTM_BT-474_Pertuzumab_2h_R1 2 AREEAER 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 96.948 0.01127 102357000 97137 102134 79273 107105 96162 80036 105696 88711 91191 109869 FALSE TRUE 93340.77865 99221.23832 93599.39452 112632.7019 99255.13806 81654.38276 106989.5393 86879.08685 80839.37998 102427.4748 0.911286536 0.968697496 0.913811404 1.099633689 0.969028459 0.797192188 1.044539461 0.848201003 0.789235312 1 16.64424322 2.960468687 24.59557893 0.894551792 0.976966189 0.155148724 0.089304258 783.3447557 487381.1184 0.02664213 0.028263407 912.9956042 -2.960468687 0.082414397 SYVAWDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYVAWDR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 123.69 0.0098156 581890000 757430 864020 679410 811880 772010 412770 765120 720670 767450 813040 FALSE TRUE 727828.7982 839378.9956 802194.5004 853781.2241 796842.4028 421116.4922 774483.7674 705787.9127 680332.2934 757972.0766 0.960231677 1.107400947 1.058343078 1.126401949 1.051282003 0.555583121 1.021784036 0.93115292 0.897569072 1 19.53178518 2.960819252 24.99999251 0.884284542 1.068785325 0.335527119 0.126260723 605.0438166 386059.1436 0.037681514 0.039973519 913.7328771 -2.960819252 0.184500783 IVNHPTMLQDPDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 IVNHPTMLQDPDVR 14 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;;; 179.39 1.87E-06 2121050000 1120290 1376170 1187920 1315680 1262980 1042820 1373600 1176270 1235700 1422570 FALSE TRUE 1076507.828 1336922.979 1402603.569 1383582.402 1303604.899 1063906.535 1390410.528 1151979.613 1095428.516 1326218.067 0.811712534 1.008071759 1.057596488 1.043254075 0.982949133 0.802210859 1.048402644 0.868620057 0.825979184 1 20.33888658 2.960889415 24.92975234 0.908247603 0.990861052 0.124350185 0.093398721 977.6003775 623139.1261 0.028071936 0.029779821 913.8805085 -2.960889415 0.08261345 MCEDLWR ddPTM_BT-474_Pertuzumab_2h_R1 2 MCEDLWR 7 0 Q14376;Q14376-2;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ; 92.677 0.036046 577550000 1076100 1268820 925840 1029820 1066860 707220 1068820 1049110 1058920 1131090 FALSE TRUE 1034044.822 1232634.496 1093159.883 1082969.134 1101176.521 721520.473 1081900.539 1027445.512 938715.841 1054480.267 0.980620363 1.168949799 1.036681214 1.027016975 1.044283668 0.684242746 1.02600359 0.97436201 0.890216603 1 20.00810067 2.960995083 24.99881679 0.921395579 1.057296238 0.323991036 0.098401244 649.9330544 416551.6245 0.029643436 0.031446467 914.1028913 -2.960995083 0.135900659 IVELFR ddPTM_BT-474_Pertuzumab_2h_R1 1 IVELFR 6 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 137.5 0.029562 80567000 131130 134740 125030 130790 131480 121560 150540 119200 144030 158250 FALSE TRUE 126005.2946 130897.3471 147625.7023 137540.0876 135709.1736 124018.0265 152382.3536 116738.4783 127680.3182 147531.5865 0.854090284 0.88724964 1.000637936 0.932275527 0.919865208 0.840620164 1.032879515 0.791277862 0.865443945 1 17.17066434 2.961039882 24.77120459 0.893933189 0.922674335 0 0.075417152 2126.148501 1351825.651 0.022833457 0.024224141 914.1971903 -2.961039882 0.028741146 ELVLDNSR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELVLDNSR 8 0 P39687;H0YN26;H7BZ09 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;; 140.14 0.0015223 1994740000 1735810 1892340 1596880 1924700 1792720 1467920 1876590 1734120 1894320 1836770 FALSE TRUE 1667972.626 1838372.316 1885471.738 2024033.998 1850384.467 1497602.348 1899556.27 1698309.816 1679284.735 1712363.932 0.97407601 1.073587385 1.101092883 1.182011581 1.080602337 0.874581811 1.10931808 0.991792565 0.980682146 1 20.70755792 2.961068174 24.99299247 0.998388312 1.089349923 0.287474482 0.070889834 707.0206263 453884.7413 0.021583516 0.022896543 914.2567471 -2.961068174 0.090961611 ASGQAFELILSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 105.66 0.0033393 207570000 204430 204280 180000 183800 192980 165920 200370 192700 206470 209110 FALSE TRUE 196440.6496 198454.1344 212530.0041 193285.94 199187.377 169275.0161 202822.188 188720.6777 183032.3912 194946.7934 1.007662892 1.017991273 1.090194921 0.991480478 1.021752517 0.868313929 1.040397661 0.968062487 0.938883825 1 17.5727209 2.96112824 24.99969559 0.965889638 1.027713064 0.301757314 0.047627011 680.1006406 437394.8328 0.014093965 0.014951807 914.3832042 -2.96112824 0.061823426 STS(ph)TPTS(ph)PGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 STSTPTSPGPR 11 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;H3BRB0;A0A0C4DGL7 Q8WWM7 ATXN2L Ataxin-2-like protein 2 S(0.001)T(0.004)S(0.994)T(0.014)PT(0.097)S(0.89)PGPR;ST(0.001)S(0.999)T(0.004)PT(0.202)S(0.794)PGPR 165.72 3.11E-05 271450000 598270 579870 489770 490950 491800 498360 398860 494010 480960 440390 TRUE FALSE 574888.947 563332.6754 578282.3339 516287.9883 507619.1936 508437.1807 403741.368 483808.5209 426363.4371 410561.993 1.400248822 1.372101375 1.408514046 1.257515301 1.236400841 1.238393201 0.983387101 1.178405525 1.038487352 1 18.64724055 2.961425842 0.531890251 1.025193482 1.442988164 0.830784962 0.062587249 0.399973766 0.236531945 0.050413629 0.077667556 915.0100027 -2.961425842 0.417794683 DLDGFRK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDGFRK 7 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0;C9JTZ5;C9JUW1;F2Z3H1 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 87.616 0.030803 474350000 1134750 1211920 811040 973930 1034810 1200890 1072720 1158630 1287280 1151200 FALSE TRUE 1090402.715 1177357.228 957612.9695 1024194.644 1068095.603 1225172.819 1085848.268 1134703.886 1141153.371 1073228.199 1.01600267 1.097024127 0.892273396 0.954312089 0.995217611 1.141577178 1.011758981 1.057281096 1.063290522 1 20.03352544 2.961447099 24.98074254 1.055967977 0.988603966 0.223353769 0.059525004 816.9678157 529362.5204 0.018397582 0.019517207 915.0547897 -2.961447099 -0.067364011 HHCAAITPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HHCAAITPGR 10 0 Q92896;Q92896-3;Q92896-2 Q92896 GLG1 Golgi apparatus protein 1 0 ; 91.584 0.01005 66610000 19872.4 22558.4 15733.5 17367.5 13199.9 13553.1 13760.5 3043 17832.2 11506 FALSE TRUE 19095.76464 21915.05652 18576.89344 18263.83876 13624.48677 13827.15297 13928.90512 2980.160987 15807.96341 10726.68837 1.780210628 2.04304029 1.731838644 1.70265399 1.270148465 1.289042106 1.298527992 0.277826752 1.473703986 1 13.38891712 2.961502485 0.888020815 0.872027402 1.918959807 0.57296659 0.308049726 0.37541001 0.65226655 0.169153531 0.203808932 915.171495 -2.961502485 1.046932405 QIANS(ph)QDGYVWQVTDMNR ddPTM_BT-474_Pertuzumab_2h_R1 4 QIANSQDGYVWQVTDMNR 18 0 P10155-3;P10155-5;P10155-4;P10155;D6RE09;P10155-2;D6RDN1 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 1 QIANS(1)QDGYVWQVTDMNR;QIANS(1)QDGYVWQVTDMNR;QIANS(1)QDGYVWQVTDMNR;QIANS(1)QDGYVWQVTDMNR 378.84 4.22E-108 517690000 529682 566037 360471 488555 437117 383754 379286 419630 353460 401855 TRUE FALSE 508981.4418 549894.179 425616.1283 513769.3821 451177.2653 391513.7688 383927.8155 410964.4939 313336.7026 374637.0029 1.358598958 1.467805301 1.136076055 1.37137917 1.204305132 1.045048315 1.024799506 1.096967173 0.836374144 1 18.51513388 2.961774774 0.620985454 0.955571777 1.403518156 0.724635683 0.097730411 0.446078451 0.375109454 0.070715558 0.097791557 915.7454604 -2.961774774 0.44794638 ARNS(ph)GTQSDGEEKQPGLVMER ddPTM_BT-474_Pertuzumab_2h_R1 2 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 ARNS(0.956)GT(0.043)QSDGEEKQPGLVMER;ARNS(0.961)GT(0.039)QSDGEEKQPGLVMER 179.79 2.93E-17 1161120000 270470 329600 214097 229655 263834 326570 271920 314760 308980 314510 TRUE FALSE 259899.7334 320200.1307 252789.0905 241507.5221 272320.4602 333173.4692 275247.8383 308260.096 273905.8857 293207.9576 0.886400681 1.092058119 0.862149488 0.82367315 0.928762174 1.136304321 0.93874614 1.05133605 0.934169345 1 18.16156473 2.962792846 24.98189527 1.014159684 0.918717909 0.23374401 0.084801104 842.3070129 565547.7441 0.025764745 0.027334619 917.8946659 -2.962792846 -0.095441775 GSCSTEVEKETQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSCSTEVEKETQEK 14 1 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 136.81 2.27E-05 584710000 126910 134430 93045 84167 109990 137460 114030 127730 152730 109980 FALSE TRUE 121950.2169 130596.188 109860.3013 88510.86896 113527.9282 140239.5354 115425.5333 125092.3309 135392.7307 102530.9566 1.189398996 1.273724466 1.071484212 0.863259954 1.107255135 1.367777498 1.125762765 1.220044511 1.320505876 1 16.64570004 2.962796472 24.84336096 1.21580302 1.094332871 0.130173747 0.135606334 1022.332355 682681.7985 0.042463391 0.045051197 917.9023296 -2.962796472 -0.121470149 DGFQHPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGFQHPAR 8 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;;; 123.98 0.0013243 1030380000 1767860 1920910 1617470 1773920 1772070 1339440 1945000 1700940 1910690 2079500 FALSE TRUE 1698770.077 1866127.528 1909782.809 1865472.224 1829070.241 1366524.395 1968803.492 1665814.995 1693796.481 1938653.613 0.876262817 0.962589457 0.985107807 0.962251437 0.943474496 0.704883217 1.015551968 0.859263864 0.873697328 1 20.88662362 2.963508335 24.99542453 0.884001738 0.950753761 0.094307315 0.084002398 1174.440711 804447.9352 0.024358056 0.025843662 919.4081192 -2.963508335 0.066752022 HPGCTT(ph)PVTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HPGCTTPVTVK 11 0 Q96Q89-3;Q96Q89;Q96Q89-2;Q96Q89-4;Q96Q89-5 Q96Q89-3 KIF20B Kinesin-like protein KIF20B 1 HPGCT(0.061)T(0.939)PVTVK 109.44 0.0070944 227380000 594010 498990 433040 480710 433230 441630 416630 382780 415500 495040 TRUE FALSE 570795.4325 484759.2938 511299.9609 505519.5007 447165.2364 450560.0612 421728.8426 374875.4592 368334.1819 461510.4999 1.236798367 1.050375439 1.107883702 1.095358612 0.968916713 0.976272612 0.913801187 0.812279373 0.798105746 1 18.81600395 2.96402564 0.847012126 0.852595671 1.145893882 0.703546206 0.069756955 0.309396025 0.491408232 0.038387777 0.046872242 920.5039151 -2.96402564 0.293298211 DSYESYGNSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DSYESYGNSR 10 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 251.75 1.13E-16 6052480000 1519210 1541240 1346020 1447760 1413460 1348550 1344330 1455680 1515890 1476490 FALSE TRUE 1459837.594 1497285.344 1589275.756 1522479.067 1458925.225 1375818.605 1360782.313 1425619.699 1343812.522 1376486.017 1.060553885 1.087759211 1.154589103 1.106062138 1.059891061 0.999515133 0.988591454 1.03569501 0.976263112 1 20.39255852 2.964032782 2.863328292 1.004061929 1.104640506 0.77187672 0.026196068 0.13302183 2.185473691 0.008790087 0.009963992 920.5190532 -2.964032782 0.100578577 WEWLVNQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 WEWLVNQHR 9 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 159.79 6.58E-05 2524900000 2238300 2377200 2169000 2238400 2262900 1649990 2567400 2060170 2510800 2720900 FALSE TRUE 2150824.761 2309404.584 2560986.549 2353924.092 2335688.234 1683353.928 2598820.609 2017626.77 2225784.51 2536611.019 0.847912725 0.910429138 1.009609487 0.927979921 0.920790857 0.663623203 1.024524686 0.795402509 0.877463865 1 21.27447087 2.96410415 24.99401444 0.859637526 0.928537861 0.052139501 0.101565835 1389.885188 967766.8936 0.029325496 0.031115103 920.6703355 -2.96410415 0.068900335 HTPYGNQTDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTPYGNQTDYR 11 0 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 0 110.31 0.0018122 93988000 103460 108010 99037 102450 98020 46695 91373 57097 109840 100770 FALSE TRUE 99416.66882 104929.6606 116935.189 107737.4568 101172.9023 47639.20489 92491.25011 55917.927 97371.42369 93944.75814 1.058246046 1.116929381 1.24472287 1.146817118 1.076940367 0.507098063 0.984528056 0.595221363 1.036475325 1 16.51952505 2.964201387 17.59043345 0.795939005 1.142848506 0.454035498 0.166434557 13.40426919 6586.215223 0.047018904 0.04996501 920.876493 -2.964201387 0.3469095 GIHNSIGDYR ddPTM_BT-474_Pertuzumab_2h_R1 3 GIHNSIGDYR 10 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 136.02 0.00012868 1337400000 925790 1632180 1234740 1525950 1188900 1014270 1257680 929910 998200 1236010 FALSE TRUE 889609.1033 1585631.824 1457884.985 1604704.462 1227142.048 1034779.234 1273071.864 910707.0335 884888.5208 1152293.942 0.772033134 1.3760654 1.265202334 1.392617286 1.064955741 0.898016727 1.104815202 0.790342638 0.767936452 1 20.13607735 2.965022209 4.271320907 0.909444331 1.220719671 0.351068678 0.184160408 0.221817115 9.106531321 0.055950585 0.06225638 922.6186075 -2.965022209 0.31127534 DIEREDIEFICK ddPTM_BT-474_Pertuzumab_2h_R1 6 DIEREDIEFICK 12 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;; 218.5 3.12E-11 5311840000 5221570 5211900 3930440 4084170 4624440 5211350 4628060 5025240 5874960 5633250 FALSE TRUE 5017505.272 5063261.715 4640757.94 4294954.503 4773189.312 5316727.068 4684699.583 4921467.038 5208059.171 5251704.96 0.955405018 0.964117702 0.883666919 0.817820981 0.908883753 1.012381143 0.892034038 0.93711796 0.991689215 1 22.32435444 2.965453051 24.58077511 0.955088907 0.90234507 0.253479948 0.050062233 856.1222987 609146.4426 0.016242026 0.017236095 923.5343444 -2.965453051 -0.052743837 MDYVEINIDHK ddPTM_BT-474_Pertuzumab_2h_R1 5 MDYVEINIDHK 11 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ;;;; 203.11 3.77E-08 2383766000 3201615 3217339 2696891 3064871 3431676 3360152 3729808 3679172 4329009 4166032 FALSE TRUE 3076492.346 3125583.642 3184279.196 3223049.36 3542058.975 3428096.576 3775454.506 3603195.812 3837598.047 3883862.942 0.792121759 0.804761571 0.819874245 0.829856616 0.911993813 0.882651274 0.972087471 0.927735058 0.988087918 1 21.88906086 2.965573629 0.458798495 0.997580848 0.7642526 0.913936068 0.021897953 0.324543706 0.135551256 0.018772623 0.032999757 923.7907929 -2.965573629 -0.233328248 ENQRS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 10 ENQRSPVR 8 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR 110.08 0.0021168 2996252000 1920560 1987616 1559543 1636877 1730989 1121320 1698366 1503262 1612675 1663247 TRUE FALSE 1845502.392 1930931.138 1841387.112 1721356.418 1786667.833 1143993.859 1719151.111 1472219.114 1429610.895 1550593.799 1.190190747 1.24528496 1.187536744 1.110127242 1.152247503 0.737777914 1.108705008 0.949455051 0.921976404 1 20.56438937 2.965844072 24.5867703 0.954023131 1.180913508 0.621491211 0.091178135 333.878027 240338.4328 0.02686659 0.028513109 924.3662317 -2.965844072 0.226890377 DLQHPNEFIR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLQHPNEFIR 10 0 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 ;;; 139.32 4.13E-05 4725190000 4641210 5242810 4364340 4700130 4712770 2879440 5266820 4453200 4739190 5250950 FALSE TRUE 4459826.382 5093290.192 5153073.322 4942704.273 4864360.527 2937664.25 5331276.919 4361239.864 4201217.02 4895298.479 0.911042789 1.040445279 1.052657635 1.009683943 0.993680068 0.600099108 1.089060645 0.890903769 0.85821468 1 22.2229654 2.966097172 24.99990965 0.888473224 1.008622411 0.17824445 0.122159469 1041.276405 767836.3937 0.036079479 0.03829053 924.905095 -2.966097172 0.120149187 FEEMFASR ddPTM_BT-474_Pertuzumab_2h_R1 5 FEEMFASR 8 0 Q9BTL3 Q9BTL3 FAM103A1 RNMT-activating mini protein 0 ;;;; 188.76 0.00045427 686580000 655613 720391 577001 676620 653444 508068 653687 658711 646318 678186 FALSE TRUE 629990.9191 699846.154 681277.916 711540.4393 674462.6197 518341.4831 661687.017 645108.3877 572950.6902 632251.8582 0.99642399 1.106910395 1.077541975 1.12540664 1.066762574 0.819833863 1.046556065 1.020334506 0.906206416 1 19.27013985 2.966449563 24.92914219 0.969302956 1.080966959 0.420193057 0.067560303 621.992414 462162.0594 0.020493456 0.021749483 925.6558764 -2.966449563 0.111664002 YSYQLLQCDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSYQLLQCDSPR 12 0 E7EWN3;Q9C0A6;Q9C0A6-2;Q9C0A6-3 E7EWN3 SETD5 SET domain-containing protein 5 1 YSYQLLQCDS(1)PR;YSYQLLQCDS(1)PR 217.79 3.76E-11 303810000 258960 287400 254080 247750 253720 244780 248360 254670 261910 260378 TRUE FALSE 248839.5569 279203.6334 299997.908 260536.4072 261881.1342 249729.6193 251399.504 249410.9755 232179.0748 242742.3661 1.025117951 1.150205619 1.235869588 1.073304225 1.078843955 1.028784646 1.035663893 1.027471963 0.956483528 1 17.8890664 2.967695296 1.37234291 1.009286732 1.135570302 0.502020642 0.053623338 0.353644303 1.378939824 0.021608857 0.025181255 928.3148455 -2.967695296 0.126283571 GGGQSVQFTDIETLKQES(ph)PNGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGGQSVQFTDIETLKQESPNGSR 23 1 Q02241;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23 1 GGGQSVQFTDIETLKQES(1)PNGSR;GGGQSVQFTDIETLKQES(1)PNGSR 247.98 5.81E-38 2530420000 732190 686080 576700 642830 686730 786070 764070 792550 766450 750140 TRUE FALSE 703575.2053 666513.6701 680922.5186 676006.5333 708819.2941 801964.874 773420.9172 776183.5655 679445.8092 699332.3496 1.006067009 0.953071412 0.973675133 0.966645592 1.013565717 1.146757868 1.105941857 1.109892265 0.971563534 1 19.41561872 2.967711903 6.448858903 1.080113688 0.974962194 0.412153733 0.050722067 0.161705805 21.92321157 0.015185908 0.016585498 928.3503454 -2.967711903 -0.105151494 APVPSTCSSTFPEELS(ph)PPSHQAK ddPTM_BT-474_Pertuzumab_2h_R1 4 APVPSTCSSTFPEELSPPSHQAK 23 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;F5H763;F5H0Z7 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(0.998)PPS(0.002)HQAK;APVPSTCSSTFPEELS(1)PPSHQAK 234.71 2.89E-37 9762200000 751945 723184 627104 628531 687324 753483 728207 756115 772391 760667 TRUE FALSE 722558.1581 702559.5004 740435.6427 660969.5602 709432.4007 768718.9425 737119.0151 740500.961 684712.4118 709146.3466 1.018912615 0.990711584 1.044122481 0.93206369 1.000403378 1.084006068 1.039445551 1.044214589 0.965544581 1 19.43572386 2.967966286 24.99733461 1.032687334 0.995295756 0.114520507 0.039178934 1147.760813 895648.1161 0.011773045 0.012497054 928.8942737 -2.967966286 -0.037391578 EQISDIDDAVRK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQISDIDDAVRK 12 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 116.98 0.0012555 190720000 162130 177390 139960 181740 187190 199590 234220 256480 219090 253140 FALSE TRUE 155793.7804 172331.0109 165253.8854 191119.6232 193211.1364 203625.8465 237086.4544 251183.5984 194219.8217 235994.6023 0.660158236 0.730232849 0.700244344 0.809847434 0.818709981 0.862841118 1.004626598 1.064361625 0.822984169 1 17.84839434 2.969135805 0.932859524 0.991359256 0.692316038 0.741684109 0.065991947 0.269870877 0.514649289 0.03509114 0.042284306 931.3990805 -2.969135805 -0.299043218 ELPPLS(ph)PSLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELPPLSPSLSR 11 0 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 ELPPLS(0.856)PS(0.144)LSR;ELPPLS(0.988)PS(0.011)LSR 150.51 3.55E-05 315030000 276830 300380 254552 268520 225706 265064 191416 250419 237163 238712 TRUE FALSE 266011.1775 291813.4565 300555.2089 282378.3494 232966.0385 270423.7757 193758.6063 245247.7601 210241.2505 222543.8236 1.195320424 1.311262886 1.350543924 1.268866261 1.046832191 1.21514842 0.870653713 1.10202007 0.944718425 1 17.76372994 2.969776547 1.200490407 1.004001333 1.295800467 0.636633309 0.09308969 0.278972995 0.848337225 0.037832244 0.044460821 932.7742476 -2.969776547 0.291799135 DSTFDLPADSIAPFHICYYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSTFDLPADSIAPFHICYYGR 21 0 Q8N1G2 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 199.15 8.17E-22 62681000 54969 60460 50776 50150 54822 59649 56762 57090 63782 68280 FALSE TRUE 52820.75071 58735.74 59952.35271 52738.24751 56585.39942 60855.14365 57456.67034 55911.07155 56541.73476 63655.33478 0.829792992 0.922715122 0.941827624 0.8284969 0.888934126 0.956010111 0.902621446 0.878340704 0.888248172 1 15.95799381 2.969858322 24.36956927 0.913519475 0.884404471 0.149425079 0.047066423 1368.832761 1106702.543 0.014339158 0.015231856 932.9498986 -2.969858322 -0.029115004 T(ph)LTPPLRR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.564)LT(0.436)PPLRR;T(0.902)LT(0.098)PPLRR 91.265 0.0073892 1162400000 446490 438020 352190 400120 410760 432760 404830 465010 462930 461150 TRUE FALSE 429040.6772 425528.0985 415838.5674 420770.2412 423972.4684 441510.7037 409784.4306 455407.381 410380.1272 429915.8998 0.997964201 0.989793815 0.967255614 0.978726866 0.986175363 1.026969935 0.953173472 1.059294111 0.954559083 1 18.71369494 2.970509722 23.77883463 1.003656533 0.982698314 0.04535435 0.03024759 881.6286579 710882.5764 0.00878832 0.009339695 934.3502836 -2.970509722 -0.02095822 ALS(ph)VGNIDDALQCYSEAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALSVGNIDDALQCYSEAIK 19 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 1 ALS(1)VGNIDDALQCYSEAIK;ALS(1)VGNIDDALQCYSEAIK 231.44 2.17E-20 84960000 72479 69309 49200 70439 71563 71165 68711 90129 83643 77909 TRUE FALSE 69646.44055 67332.37518 58091.53445 74074.36523 73864.88889 72604.00506 69551.90577 88267.80465 74148.1973 72632.15404 0.958892676 0.927032608 0.799804649 1.019856374 1.016972302 0.999612445 0.957591121 1.215271746 1.020872894 1 16.14832075 2.970736889 0.896988615 1.079464612 0.903603614 0.319186783 0.080694158 0.592678487 1.05013783 0.044753598 0.054408408 934.8391429 -2.970736889 -0.175860998 HTENVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HTENVAK 7 0 A0A2R8Y595;A0A2R8YFL0;P49711-2;P49711 A0A2R8Y595 CTCF Transcriptional repressor CTCF 0 76.774 0.039847 46246000 139220 128640 106480 120620 111240 90386 103990 97488 99513 108680 FALSE TRUE 133779.1285 124971.3132 125723.3046 126845.2127 114818.1356 92213.66685 105262.6607 95474.83873 88216.70143 101319.0068 1.320375443 1.233443922 1.24086594 1.251938966 1.133233924 0.910131966 1.03892314 0.942319134 0.870682651 1 16.62854531 2.970740196 2.70755011 0.954981962 1.259060171 0.896659114 0.04952032 0.080918654 1.188546751 0.015727553 0.017937345 934.8462633 -2.970740196 0.304078209 QPAQELS(ph)PTPGGTAHQALK ddPTM_BT-474_Pertuzumab_2h_R1 3 QPAQELSPTPGGTAHQALK 19 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 QPAQELS(0.928)PT(0.072)PGGTAHQALK;QPAQELS(0.999)PT(0.001)PGGTAHQALK;QPAQELS(0.5)PT(0.5)PGGTAHQALK 229.77 3.78E-22 1098190000 934040 828310 775630 857630 906810 1013010 1044710 1079960 1117200 1180240 TRUE FALSE 897536.6842 804687.4098 915803.5948 901892.3871 935978.3672 1033493.756 1057495.473 1057658.449 990380.1397 1100301.294 0.815719012 0.731333694 0.832320747 0.819677658 0.850656427 0.939282506 0.961096274 0.961244393 0.900099041 1 20.0694672 2.970777746 1.305647167 0.957573832 0.786669564 0.8250729 0.033587126 0.161785986 0.57496148 0.013157731 0.015409531 934.9270953 -2.970777746 -0.170904269 SESELIDELSEDFDRSECK ddPTM_BT-474_Pertuzumab_2h_R1 2 SESELIDELSEDFDRSECK 19 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 125.73 2.44E-05 163214000 89744 93860 68350 77794 85152 94525 88438 96765 105620 92257 FALSE TRUE 86236.70526 91183.2047 80702.36544 81808.95766 87890.99141 96436.36026 89520.3307 94766.76893 93630.4604 86008.35122 1.002655022 1.060166872 0.938308482 0.951174584 1.021889039 1.121244145 1.040833006 1.101832178 1.088620571 1 16.39218913 2.971053678 7.785783224 1.075973461 0.989211197 0.440542757 0.043749472 0.206662195 47.91311017 0.013115253 0.014273486 935.5212949 -2.971053678 -0.086762264 YGGGGYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGGGGYGR 8 0 Q01130;J3KP15 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ; 133.99 0.0020842 3311200000 1848790 2104910 1750060 1999230 1928450 1677980 1816330 2104390 2050430 2080850 FALSE TRUE 1776537.243 2044880.028 2066334.772 2102410.5 1990480.346 1711909.905 1838558.79 2060933.611 1817673.783 1939912.176 0.915782304 1.05410959 1.065169237 1.083765815 1.026067247 0.882467736 0.947753621 1.062385007 0.936987666 1 20.88755991 2.971846532 24.7267337 0.973745498 1.036599564 0.204206254 0.060703295 1079.527812 948132.0745 0.019398211 0.020617878 937.2307552 -2.971846532 0.062854066 AYSSFGGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 AYSSFGGGR 9 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 191.38 8.37E-05 1032960000 728060 851710 696670 717330 715510 422190 813310 447338 722060 716040 FALSE TRUE 699606.6103 827420.0647 822573.7663 754351.4873 738525.029 430726.9711 823263.5311 438100.314 640094.7759 667541.973 1.048033889 1.23950268 1.232242765 1.130043529 1.10633497 0.645243278 1.233276055 0.65628879 0.958883189 1 19.34849903 2.97208721 20.28459423 0.886163962 1.166099926 0.369671079 0.165717047 65.48572198 47589.2479 0.047241814 0.050327013 937.7502964 -2.97208721 0.279935963 S(ph)QESDGVEYIFISK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQESDGVEYIFISK 14 0 S4R337;Q5T2T1-2;Q5T2T1;U5GXS2 S4R337 MPP7 MAGUK p55 subfamily member 7 1 S(0.981)QES(0.019)DGVEYIFISK;S(0.956)QES(0.044)DGVEYIFISK 161.91 4.74E-06 115020000 185675 170155 164761 198414 183622 203502 227554 248130 255200 247806 TRUE FALSE 178418.6157 165302.346 194536.9778 208654.1703 189528.3684 207616.9499 230338.8739 243006.0288 226230.7659 231021.8789 0.772301812 0.715526801 0.842071663 0.903179263 0.820391425 0.898689556 0.997043549 1.051874524 0.979261215 1 17.81766996 2.972212544 0.600942003 1.035273226 0.742230007 0.807345397 0.045776517 0.374152776 0.292501217 0.037425724 0.05345109 938.0209634 -2.972212544 -0.293043219 RPNPDILDHER ddPTM_BT-474_Pertuzumab_2h_R1 4 RPNPDILDHER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 184.31 3.22E-06 2378730000 941070 1092050 936800 1100370 1016780 834620 1083050 951590 1047960 1124900 FALSE TRUE 904291.944 1060905.803 1106100.599 1157160.228 1049485.652 851496.5882 1096304.69 931939.334 928999.9742 1048709.521 0.862290201 1.0116298 1.054725429 1.103413485 1.000740082 0.811947037 1.045384511 0.88865345 0.885850615 1 20.00018369 2.97246606 24.61471619 0.924895209 1.016667861 0.187326038 0.082815857 905.1603476 809193.2479 0.024906621 0.026482859 938.5686855 -2.97246606 0.091772652 IMGPNYTPGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IMGPNYTPGKK 11 1 P13639 P13639 EEF2 Elongation factor 2 0 80.979 0.036764 445670000 271910 354560 225640 292030 339590 326620 394950 378790 400260 418760 FALSE TRUE 261283.4566 344448.296 266418.1673 307101.7033 350513.2208 333224.4802 399783.5162 370967.8541 354824.1628 390397.0122 0.669276271 0.882302592 0.682428807 0.786639482 0.897837867 0.853552844 1.024043483 0.950232308 0.908880324 1 18.57458249 2.972632078 1.250266179 0.963558826 0.75179908 0.651629168 0.067811252 0.269590495 0.884064177 0.026800388 0.03151161 938.9275409 -2.972632078 -0.211759746 LAVPAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 LAVPASPR 8 0 A6NHQ4 A6NHQ4 C17orf96 Uncharacterized protein C17orf96 1 LAVPAS(1)PR;LAVPAS(1)PR;LAVPAS(1)PR;LAVPAS(1)PR 114.51 0.002771 1258370000 1498630 1647290 1359360 1465780 1464730 1080380 1468820 1486720 1258810 1413680 TRUE FALSE 1440061.883 1600310.902 1605026.591 1541429.081 1511844.371 1102226.024 1486795.859 1456018.712 1115915.166 1317930.194 1.092669315 1.214260747 1.217838849 1.169583251 1.147135392 0.836331111 1.128129445 1.104776807 0.84671796 1 20.32984253 2.972709605 24.34524742 1.009273408 1.176992204 0.479391567 0.094810126 512.2110196 456934.1595 0.029344293 0.031211705 939.0951655 -2.972709605 0.167718796 NSEGWEQNGLYEFFR ddPTM_BT-474_Pertuzumab_2h_R1 4 NSEGWEQNGLYEFFR 15 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ;;; 336.93 9.72E-69 340353000 182664 186575 165823 191686 181847 163022 188839 182805 191389 211960 FALSE TRUE 175525.2889 181254.0637 195790.9048 201578.9374 187696.2739 166318.4165 191150.0682 179030.0129 169663.3231 197603.7604 0.888268971 0.917260194 0.990825804 1.02011691 0.949861852 0.841676374 0.967340236 0.906005091 0.858603717 1 17.59225088 2.972864274 24.91093108 0.911421876 0.957967535 0.107160547 0.054875923 1404.188182 1289063.649 0.016767808 0.017832284 939.4296742 -2.972864274 0.046545659 T(ph)SPPCS(ph)PANLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 T(0.5)S(0.5)PPCS(1)PANLSR;T(0.569)S(0.431)PPCS(1)PANLSR 91.62 0.0082674 621390000 551686 529010 482168 538810 516589 499272 475799 559292 540621 615998 TRUE FALSE 530125.5012 513923.1528 569306.4834 566618.0487 533205.5543 509367.6219 481621.9705 547742.4248 479251.9705 574275.9068 0.923119871 0.894906345 0.991346627 0.986665193 0.92848324 0.886973693 0.838659545 0.95379663 0.834532609 1 19.13138451 2.972875339 6.804930289 0.899814728 0.949346031 0.144623725 0.052848418 0.345119334 60.16414736 0.015603443 0.017107515 939.4536097 -2.972875339 0.049531304 VKELQAEQEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VKELQAEQEDR 11 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ;; 176.25 8.09E-06 4943240000 4114400 4472600 3611600 3957000 4273000 4676600 4632700 4976400 4872300 4895000 FALSE TRUE 3953604.699 4345045.827 4264296.46 4161221.244 4410444.926 4771164.056 4689396.368 4873635.601 4319216.93 4563457.29 0.866361718 0.952139036 0.934444258 0.911857169 0.966470079 1.045515221 1.027597295 1.067970026 0.946479096 1 22.1216958 2.972955289 3.404443372 1.026032447 0.92051497 0.623105085 0.036708505 0.14840827 3.566785666 0.011240752 0.012718032 939.6265712 -2.972955289 -0.105517477 MEWWSR ddPTM_BT-474_Pertuzumab_2h_R1 1 MEWWSR 6 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 115.78 0.056159 36622000 85190 87513 70826 82945 80806 61274 88496 78576 81945 98876 FALSE TRUE 81860.68062 85017.21492 83625.83372 87225.80139 83405.19838 62513.00226 89579.04052 76953.37814 72642.94714 92179.04045 0.888061757 0.922305271 0.907210938 0.946265018 0.904817385 0.678169375 0.971794023 0.834825116 0.788063607 1 16.49215113 2.973051036 24.99676621 0.847314855 0.917008019 0.105320363 0.085383029 1443.08458 1338547.588 0.024578466 0.026135869 939.8337483 -2.973051036 0.069693164 RVDAENR ddPTM_BT-474_Pertuzumab_2h_R1 8 RVDAENR 7 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 176.41 0.0012072 1539213000 1197573 1320747 1119171 1152050 1126810 721432 1158028 1016930 937377.1 1069173 FALSE TRUE 1150770.523 1283080.589 1321430.096 1211507.439 1163054.867 736019.8493 1172200.293 995930.0401 830969.9814 996756.9604 1.15451466 1.287255208 1.325729489 1.215449188 1.166838972 0.738414557 1.176014154 0.999170389 0.833673618 1 19.92688225 2.97326857 14.63350554 0.97044291 1.246518557 0.598418148 0.115700174 3.142360021 1719.981151 0.03471539 0.037243451 940.3046211 -2.97326857 0.276075647 FENLDMSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FENLDMSHR 9 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 ; 145.89 9.61E-05 325000000 423390 449150 390540 475910 430450 340700 456180 399060 420060 466800 FALSE TRUE 406843.4507 436340.6818 461119.2655 500471.7721 444295.8152 347589.1874 461762.8673 390819.2715 372376.5498 435183.2202 0.934878533 1.002659711 1.05959799 1.150025435 1.020939674 0.798719186 1.061076912 0.898056849 0.855677638 1 18.7312634 2.973663603 24.89765147 0.924850394 1.042169246 0.303787434 0.084039272 851.4532123 804939.4057 0.025452376 0.027079315 941.1603076 -2.973663603 0.117318852 EQLEWER ddPTM_BT-474_Pertuzumab_2h_R1 1 EQLEWER 7 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 114.99 0.01345 574170000 423930 508020 420400 491880 463640 377440 490940 486520 470970 555820 FALSE TRUE 407362.3469 493531.767 496375.6317 517265.9857 478553.4017 385072.0954 496948.2706 476473.192 417507.4601 518173.8163 0.786150002 0.952444434 0.957932678 0.998248019 0.92353837 0.743133063 0.959037788 0.919523868 0.805728593 1 18.98307659 2.973814464 24.89500796 0.884315396 0.932280593 0.043730078 0.085489647 2115.487904 2011230.039 0.025742043 0.027400935 941.4872948 -2.973814464 0.047965197 QYECSLEQALR ddPTM_BT-474_Pertuzumab_2h_R1 2 QYECSLEQALR 11 0 Q8TE77;Q8TE77-2;Q8TE77-3;E9PIT5;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 146.88 0.003718 141160000 244900 223660 229940 159808 189738 176377 148816 139747 154199 149552 FALSE TRUE 235329.0372 217281.4358 271495.273 168055.71 195841.0951 179943.4638 150637.2547 136861.1756 136694.976 139422.7098 1.687881677 1.55843647 1.947281568 1.205368266 1.40465707 1.29063238 1.080435568 0.981627568 0.980435513 1 17.08910605 2.974355446 0.687177771 0.955653425 1.739783115 0.773336921 0.150254332 0.335113785 0.350569436 0.099693293 0.132545735 942.6607962 -2.974355446 0.784129691 SICEVLDLER ddPTM_BT-474_Pertuzumab_2h_R1 3 SICEVLDLER 10 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;D6RDA2 H0Y993 DEK Protein DEK 0 ;; 154.01 3.55E-05 328121000 460830 461720 355140 392690 399630 237451 378890 372880 370480 381910 FALSE TRUE 442820.2541 448552.1977 419321.698 412956.778 412484.4619 242252.4219 383526.9692 365179.8977 328424.6636 356042.8955 1.243727258 1.259826283 1.17772803 1.159851195 1.158524625 0.680402347 1.077193153 1.025662644 0.922430043 1 18.44169154 2.974387126 24.90635901 0.956796873 1.204958074 0.613545715 0.102941225 506.5756281 492602.3191 0.031593475 0.033635965 942.7295616 -2.974387126 0.248161201 DYYSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DYYSSR 6 0 C9J384;Q9BQ75-2;Q9BQ75;H7C515;Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;Q14011-3 C9J384;Q14011 CMSS1;CIRBP Protein CMSS1;Cold-inducible RNA-binding protein 0 ;;; 133.82 0.033265 5647970000 4173780 4826570 3852030 4260950 4272800 3556030 4621100 4549590 4292480 4464590 FALSE TRUE 4010664.063 4688920.949 4548177.509 4480858.14 4410238.492 3627935.363 4677654.404 4455639.377 3805215.666 4162199.343 0.963592498 1.126548866 1.092734186 1.076560196 1.059593289 0.871639022 1.123841993 1.070501197 0.914231961 1 21.98891463 2.974843483 24.98519105 1.011694546 1.07085902 0.14365116 0.077720674 1702.552153 1690959.338 0.023995414 0.025547818 943.7207039 -2.974843483 0.059164474 DDGMQIWGAVER ddPTM_BT-474_Pertuzumab_2h_R1 4 DDGMQIWGAVER 12 0 O15296-4;O15296;I3L1D5;O15296-3 O15296-4 ALOX15B Arachidonate 15-lipoxygenase B 0 ;;; 250.37 8.46E-17 1134770000 472601 513788 392705 494757 461306 383506 435349 481195 454574 486936 FALSE TRUE 454131.2304 499135.2693 463675.5292 520291.4681 476144.3264 391260.7541 440676.9313 471258.1551 402972.6652 453955.391 1.00038735 1.09952493 1.0214121 1.146129065 1.04887911 0.861892516 0.970749417 1.03811556 0.887692212 1 18.79219101 2.974872993 24.55473211 0.961876674 1.069894099 0.456400752 0.060593808 570.702253 557704.8843 0.018349618 0.019545334 943.7848307 -2.974872993 0.108017425 NLLHADSNGYTNLPDVVQPS(ph)HSPTENSK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLLHADSNGYTNLPDVVQPSHSPTENSK 28 0 Q8N4C8;Q8N4C8-4;Q8N4C8-2;Q8N4C8-3;Q8N4C8-5 Q8N4C8 MINK1 Misshapen-like kinase 1 1 NLLHADSNGYTNLPDVVQPS(0.636)HS(0.362)PT(0.002)ENSK 307.16 2.14E-72 480570000 248180 295450 221790 264210 249360 240260 251370 225190 293890 304610 TRUE FALSE 238480.8512 287024.0553 261872.3867 277845.9098 257380.8909 245118.2218 254446.3413 220539.7478 260528.8393 283978.4934 0.839784902 1.010724622 0.922155701 0.97840476 0.906339377 0.863157695 0.896005674 0.776607218 0.917424542 1 18.11542215 2.974903084 4.513101925 0.86990066 0.942242278 0.055483204 0.067503208 0.323008546 16.0411101 0.019791213 0.022138222 943.8502252 -2.974903084 0.072341617 EGS(ph)QGELTPANSQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGSQGELTPANSQSR 15 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 EGS(1)QGELTPANSQSR 168.64 7.12E-11 0 131230 116660 124480 127500 120120 111430 123950 110450 132890 132030 TRUE FALSE 126101.3865 113332.971 146976.305 134080.2903 123983.7689 113683.1909 125466.9372 108169.1689 117804.8843 123087.4905 1.024485803 0.920751334 1.194079954 1.08930883 1.007281637 0.923596626 1.019331344 0.878799043 0.95708251 1 16.90932462 2.975065532 4.470560267 0.948578082 1.056890926 0.299444686 0.072629058 0.250513873 12.11404278 0.022854012 0.025578978 944.2033402 -2.975065532 0.108312844 FSPDDKYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSPDDKYSR 9 1 Q9NPE3 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 100.48 0.0046934 0 368080 347550 277620 304250 328970 393490 337640 365440 415240 380160 FALSE TRUE 353695.0267 337638.2143 327792.1096 319952.379 339551.6188 401446.6374 341772.1393 357893.5363 368103.696 354411.4246 0.997978626 0.952673054 0.924891487 0.902771064 0.958071877 1.132713591 0.964337252 1.009825055 1.038633832 1 18.43506558 2.975134046 24.98582611 1.024919163 0.942084372 0.439325053 0.046264581 707.5151196 710926.4593 0.014002575 0.014915622 944.3523072 -2.975134046 -0.082834791 RSTGVSFWTQDSDENEQEQQS(ph)DTEEGSNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSTGVSFWTQDSDENEQEQQSDTEEGSNKK 30 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YIS3;H0YIM2;H0YIL7 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 RSTGVSFWTQDSDENEQEQQS(0.998)DT(0.002)EEGSNKK 129.63 5.18E-06 119650000 35165 35091 31113 28071 38315 48245 42802 41353 60748 57965 TRUE FALSE 33790.71292 34090.23904 36735.8112 29519.74767 39547.43677 49220.54696 43325.82368 40499.0461 53852.14172 54038.97892 0.62530258 0.630845359 0.679802097 0.546267681 0.731831681 0.910834141 0.801751338 0.749441365 0.996542547 1 15.72171279 2.975216507 4.603485474 0.856911665 0.625702583 0.702377825 0.08189787 0.126407937 6.659707504 0.025067125 0.028022304 944.5316327 -2.975216507 -0.231209082 QQMAEEMVEAAGEDER ddPTM_BT-474_Pertuzumab_2h_R1 1 QQMAEEMVEAAGEDER 16 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 263.59 1.38E-26 101090000 60636 69421 63048 87569 70739 58680 70832 72513 73277 85770 FALSE TRUE 58266.27808 67441.18105 74442.1761 92088.44658 73014.38418 59866.5498 71698.8632 71015.58121 64958.90216 79960.7215 0.728686247 0.843428871 0.930984297 1.151671031 0.913128131 0.74869947 0.896676041 0.888130821 0.812385143 1 16.28700387 2.975251085 24.8684755 0.863242158 0.92522023 0.030812786 0.115228062 2336.974531 2348266.309 0.036747453 0.039156113 944.6068386 -2.975251085 0.061978072 FGVQSER ddPTM_BT-474_Pertuzumab_2h_R1 6 FGVQSER 7 0 Q14247 Q14247 CTTN Src substrate cortactin 0 ;;;;; 123.69 0.0098156 2094650000 1450480 1582360 1312480 1464540 1432400 1037370 1510060 1420690 1409240 1572230 FALSE TRUE 1393793.638 1537232.642 1549674.332 1540125.085 1478474.447 1058346.332 1528540.566 1391352.255 1249268.983 1465741.462 0.950913701 1.048774755 1.05726308 1.05074812 1.008687061 0.72205526 1.042844598 0.949248071 0.852311964 1 20.48319922 2.975297615 24.94927341 0.918375455 1.030535787 0.291221447 0.085912443 942.5673995 951988.7084 0.025655993 0.027336697 944.7080468 -2.975297615 0.112160332 GGHMDDGGYSMNFNMSSSR ddPTM_BT-474_Pertuzumab_2h_R1 7 GGHMDDGGYSMNFNMSSSR 19 0 P38159;P38159-2;H3BT71;H0Y6E7;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;;;;; 266.7 1.15E-31 2458780000 1115798 1257628 1126665 1256434 1108901 960257 1129096 989558 1100433 1163584 FALSE TRUE 1072191.381 1221761.681 1330278.428 1321278.709 1144569.808 979674.0545 1142914.215 969123.2815 975516.4592 1084773.419 0.988401229 1.126282834 1.22631916 1.218022756 1.05512339 0.903113993 1.053597179 0.893387747 0.899281308 1 20.0489623 2.975299226 4.759954257 0.949285743 1.145022519 0.579208182 0.076321651 0.140209035 8.164106136 0.024022709 0.02681627 944.7115527 -2.975299226 0.195736776 GVEEEEEDGEMRE ddPTM_BT-474_Pertuzumab_2h_R1 5 GVEEEEEDGEMRE 13 1 P62306 P62306 SNRPF Small nuclear ribonucleoprotein F 0 ;;;; 321.23 9.51E-50 8604220000 3257820 3437910 2993990 3460380 3256570 2480620 3473300 3241930 3276300 3511880 FALSE TRUE 3130500.793 3339864.173 3535070.594 3638970.626 3361320.532 2530779.836 3515807.284 3174983.013 2904388.159 3274017.24 0.95616503 1.020111969 1.079734875 1.111469598 1.026665496 0.77298916 1.073851183 0.969751464 0.88710228 1 21.64263049 2.975569715 24.85222968 0.947294619 1.046276677 0.261927454 0.082145304 995.8768175 1013077.809 0.025028936 0.026674489 945.3001242 -2.975569715 0.098982058 GLIHPDDSVK ddPTM_BT-474_Pertuzumab_2h_R1 4 GLIHPDDSVK 10 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;; 138.66 5.88E-05 2585990000 5166770 5761830 4631130 5264830 5118610 3343480 5514830 4845580 5381670 5790460 FALSE TRUE 4964846.916 5597508.25 5468078.21 5536548.507 5283254.739 3411087.456 5582322.139 4745517.08 4770765.383 5398266.987 0.919711257 1.036908375 1.012932155 1.02561591 0.978694598 0.631885652 1.03409523 0.879081581 0.883758694 1 22.3640649 2.975687657 24.99892274 0.882294532 1.002478433 0.216448245 0.104065149 1073.449083 1103763.962 0.030347713 0.032338155 945.5568759 -2.975687657 0.120183901 TLLEEEYFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLLEEEYFR 9 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 ; 228.39 3.84E-07 421470000 307350 329280 259750 303940 296710 237865 300260 309410 302540 337160 FALSE TRUE 295338.4222 319889.2568 306692.6031 319626.3798 306253.9466 242674.7933 303934.6717 303020.5754 268196.9276 314323.8529 0.939599141 1.017705955 0.975721697 1.016869629 0.974326141 0.772053381 0.966947525 0.96403939 0.853250318 1 18.26189223 2.97611119 24.98227702 0.913788559 0.989644569 0.250506874 0.063846856 1068.993338 1117925.991 0.019187144 0.020461734 946.4794527 -2.97611119 0.07585601 FQEHIIQAPKPVEAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 FQEHIIQAPKPVEAIK 16 1 Q9UHD1-2;Q9UHD1;E9PPQ5;E9PIZ4;E9PSD5 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 0 129.62 3.27E-05 393950000 1000500 938830 830310 746740 900640 1145600 929860 959450 1219600 1095600 FALSE TRUE 961399.3539 912055.4876 980365.4871 785279.3409 929609.9035 1168764.817 941239.9048 939637.0222 1081156.121 1021394.036 0.941261961 0.892951648 0.959830832 0.768830944 0.91013837 1.144283964 0.921524771 0.919955462 1.058510313 1 19.96210811 2.976121893 24.75531873 0.993471088 0.888773607 0.346690775 0.077334291 867.1702981 899028.4326 0.024043523 0.025643087 946.5027783 -2.976121893 -0.10469748 LVVADTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVVADTR 7 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 107.74 0.017236 919920000 1995230 2224350 1886710 2090300 2021480 1332240 2162100 2056000 1986800 2186850 FALSE TRUE 1917254.206 2160913.716 2227680.467 2198180.634 2086502.74 1359178.806 2188560.427 2013542.882 1761266.793 2038732.702 0.940414702 1.059929884 1.092679028 1.078209336 1.023431242 0.666678277 1.073490617 0.987644373 0.863902753 1 20.95924121 2.976285818 24.9993816 0.927230229 1.047996821 0.236270171 0.10810213 1170.688311 1234135.372 0.033124491 0.035316542 946.8601038 -2.976285818 0.120766591 SVDFHFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVDFHFR 7 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 0 ; 100.37 0.0098425 106340000 374998 436100 370962 413330 390610 260168 430960 358212 320745 428710 FALSE TRUE 360342.6636 423662.855 438003.0854 434662.0108 403174.3254 265428.7752 436234.2174 350814.797 284335.3723 399673.0898 0.901593509 1.060023469 1.095903368 1.08754385 1.008760248 0.664114703 1.091477581 0.87775436 0.711419857 1 18.60846091 2.976392687 24.81829861 0.876938828 1.042964002 0.292055272 0.126066971 878.9997202 924090.725 0.03736474 0.039861642 947.0931317 -2.976392687 0.166025174 IQRPPEDSIQPYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IQRPPEDSIQPYEK 14 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0;C9JTZ5;C9JUW1 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 216.54 5.55E-12 2333090000 959300 927770 771660 869120 908860 954150 946250 1042590 1041300 1002550 FALSE TRUE 921809.4954 901310.908 911116.1275 913975.3874 938094.3073 973443.5667 957830.4906 1021060.152 923095.9895 934646.3955 0.986265501 0.964333584 0.974824417 0.977883606 1.003689001 1.041509999 1.024805205 1.092456096 0.987641951 1 19.83406113 2.976448415 2.197383456 1.039865316 0.97418143 0.43168778 0.027545748 0.23913208 2.312699833 0.009106527 0.010501546 947.2146698 -2.976448415 -0.065683886 QHSLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 QHSLLK 6 0 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 ; 90.986 0.048407 900240000 1895480 1834390 1746140 1745600 1736970 1365780 1876690 1153780 2244400 2278600 FALSE TRUE 1821402.546 1782074.993 2061706.341 1835690.625 1792841.218 1393397.007 1899657.494 1129954.04 1989625.121 2124268.392 0.85742581 0.838912352 0.970548895 0.864151927 0.843980555 0.65594207 0.89426435 0.531926212 0.936616639 1 21.01853463 2.97655214 14.38172606 0.761365786 0.881925427 0.026602543 0.134051569 6.81157455 4177.404042 0.038792185 0.041860584 947.4409254 -2.97655214 0.120559641 WTKEDLELINK ddPTM_BT-474_Pertuzumab_2h_R1 2 WTKEDLELINK 11 1 F5H8H2;Q03426;F5H092;A0A1B0GWC2;A0A1B0GWF3 F5H8H2 MVK Mevalonate kinase 0 ; 137.89 6.28E-05 1358420000 1000920 1054640 879400 955570 1105550 1210320 1216740 1257670 1518420 1342280 FALSE TRUE 961802.9398 1024562.7 1038327.142 1004887.082 1141111.02 1234793.5 1231630.828 1231698.675 1346055.327 1251366.18 0.768602313 0.818755306 0.829754838 0.803031997 0.911892169 0.98675633 0.984228955 0.984283174 1.075668616 1 20.25507259 2.976585677 1.564597587 1.00812573 0.801711881 0.914923065 0.028914974 0.102915871 0.514477402 0.010712506 0.012512274 947.5140901 -2.976585677 -0.206413849 EAFVHVVTLEDMR ddPTM_BT-474_Pertuzumab_2h_R1 5 EAFVHVVTLEDMR 13 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ;;;; 143.86 4.10E-05 742804000 1008409 1113467 895884 950387 966778 686326 1007959 867347 993436 1034665 FALSE TRUE 968999.2614 1081712.011 1057790.168 999436.587 997875.2924 700203.982 1020294.704 849435.9814 880665.3101 964586.218 1.004575064 1.121425945 1.096625836 1.036129864 1.034511248 0.725911245 1.057753765 0.880622142 0.912998023 1 19.87955067 2.976848746 24.84203023 0.914023192 1.066560221 0.415065116 0.085577819 636.2387042 682704.9629 0.024449526 0.026096375 948.0882103 -2.976848746 0.152537029 EGFDKIDISAVVAYTIAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGFDKIDISAVVAYTIAVK 19 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 90.654 0.0020081 9470800 38817 33869 21480 25322 29967 37688 32435 29076 45637 35276 FALSE TRUE 37299.98873 32903.08928 25361.91382 26628.87145 30930.91577 38450.07718 32831.94923 28475.57044 40456.47909 32886.7251 1.134195899 1.000497592 0.771190009 0.809714904 0.940528912 1.169167105 0.998334408 0.86586823 1.230176582 1 15.00521773 2.976893162 24.54315401 1.028125366 0.916795402 0.159747359 0.132536628 1308.649558 1389996.228 0.042662565 0.045556248 948.1851774 -2.976893162 -0.111329964 YWLEEAECR ddPTM_BT-474_Pertuzumab_2h_R1 4 YWLEEAECR 9 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 224.28 7.35E-07 2770610000 1371710 1543650 1190310 1300180 1326330 980860 1396180 1221470 1404680 1576350 FALSE TRUE 1318102.057 1499626.613 1405425.495 1367282.446 1368992.609 1000693.661 1413266.868 1196246.218 1245226.615 1469582.41 0.896922859 1.020444041 0.956343438 0.930388412 0.931552119 0.680937424 0.961679222 0.814004175 0.847333641 1 20.48697483 2.976953541 24.98122955 0.85009411 0.953189048 0.2007191 0.085478675 1002.395551 1086548.515 0.024198746 0.025834396 948.3170116 -2.976953541 0.103094938 VHPAVVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHPAVVIR 8 0 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32 J3KTJ3 RPL23 60S ribosomal protein L23 0 ; 132.09 0.00097697 1153660000 963070 1032210 1029080 1021670 978690 606470 903960 904770 829070 1038470 FALSE TRUE 925432.1597 1002772.381 1215057.648 1074398.511 1010170.453 618733.2389 915022.9329 886086.1833 734957.4493 968133.5019 0.955893126 1.035779032 1.255051752 1.109762764 1.043420614 0.639099089 0.945141276 0.915252061 0.759148865 1 19.88484648 2.976978549 24.2652072 0.85821425 1.094592169 0.489177714 0.117222889 445.9576689 470051.4904 0.03561527 0.038038234 948.37162 -2.976978549 0.236377919 LYSESLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LYSESLAR 8 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ;;; 138.83 0.0016023 2276630000 2020350 2370920 2046770 2243970 2161080 1643630 2336730 2180200 2084840 2455500 FALSE TRUE 1941392.488 2303303.683 2416666.869 2359781.561 2230593.101 1676865.325 2365327.601 2135178.108 1848177.704 2289186.798 0.848070804 1.006166769 1.055687929 1.030838358 0.974404143 0.732515724 1.03326107 0.932723406 0.807351198 1 21.12640376 2.977261908 24.97972019 0.905308713 0.993086827 0.152045236 0.095962342 1404.986397 1543497.919 0.028942561 0.030903713 948.9905932 -2.977261908 0.087778114 LMADVVEEETRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LMADVVEEETRR 12 1 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 0 134.56 0.0002297 78306000 140140 144090 118440 125470 133750 149770 135230 149110 153960 146960 FALSE TRUE 134663.1739 139980.6943 139844.7427 131945.5217 138052.1902 152798.452 136884.9852 146030.8264 136483.1063 137006.2683 0.982897903 1.021710145 1.020717843 0.963061934 1.007634117 1.11526614 0.999114762 1.065869673 0.996181474 1 17.06388238 2.977331495 24.99368478 1.040777136 0.998642961 0.184195966 0.037548449 1098.691472 1211388.465 0.010779286 0.011511794 949.1426627 -2.977331495 -0.042134175 YVGFGNT(ph)PPPQKK ddPTM_BT-474_Pertuzumab_2h_R1 2 YVGFGNTPPPQKK 13 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 YVGFGNT(1)PPPQKK;YVGFGNT(1)PPPQKK 91.207 0.0038897 1883490000 2336480 2309250 1991790 1953280 2208890 2658400 2392260 2405160 2760800 2792640 TRUE FALSE 2245167.778 2243392.451 2351750.76 2054089.015 2279940.953 2712154.669 2421537.193 2355492.606 2447405.558 2603492.005 0.862367841 0.861685938 0.903306311 0.788974581 0.8757242 1.041737276 0.930111246 0.904743552 0.940047272 1 21.31201655 2.977433077 24.80353203 0.951220273 0.854918438 0.574735432 0.044826971 567.0048272 623201.378 0.013925556 0.014877532 949.3646938 -2.977433077 -0.096301835 LVDMMER ddPTM_BT-474_Pertuzumab_2h_R1 4 LVDMMER 7 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 117.18 0.012306 406770000 518745 573960 514128 515013 521626 355994 544204 499893 542888 596660 FALSE TRUE 498471.8719 557591.2228 607042.3663 541592.8826 538404.574 363192.4426 550864.1313 489570.0349 481261.6302 556247.6868 0.896132935 1.002415356 1.091316658 0.973654175 0.967922361 0.652932949 0.990321658 0.880129566 0.865193046 1 19.08536791 2.978427668 24.84953911 0.873619671 0.995366661 0.232773346 0.098985962 965.7342723 1112447.014 0.029256022 0.03130502 951.541355 -2.978427668 0.12174699 SVNVKPLVTHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVNVKPLVTHR 11 1 Q00796 Q00796 SORD Sorbitol dehydrogenase 0 ; 63.76 0.043619 993220000 1624710 1600190 1382590 1587830 1532380 1399170 1506330 1346380 1922620 1939690 FALSE TRUE 1561214.537 1554554.148 1632454.769 1669778.097 1581670.394 1427462.176 1524764.917 1318576.782 1704372.238 1808313.069 0.863354119 0.859670914 0.902750081 0.92338994 0.874666241 0.789388851 0.843197422 0.729175056 0.942520555 1 20.78621304 2.978656598 23.06686443 0.833231711 0.887998271 0 0.074488236 643.8291586 695818.7738 0.021878241 0.023457167 952.0430742 -2.978656598 0.05476656 EVTSLFNKDDEQHLLER ddPTM_BT-474_Pertuzumab_2h_R1 1 EVTSLFNKDDEQHLLER 17 1 Q86YL5;Q86YL5-2 Q86YL5 TDRP Testis development-related protein 0 131.67 1.57E-05 115480000 107170 111470 95432 99225 108190 145870 117890 117950 146510 128230 FALSE TRUE 102981.6779 108290.9847 112678.6853 104346.0141 111670.0296 148819.5913 119332.7731 115514.2913 129878.799 119544.8679 0.861447921 0.905860592 0.94256397 0.872860676 0.934126505 1.24488482 0.998225814 0.966283985 1.086443955 1 16.86719267 2.978760884 24.95040232 1.048978792 0.900225676 0.523896503 0.074614254 664.5562095 780680.4021 0.023326038 0.024981277 952.2717129 -2.978760884 -0.148753115 WIYEDVER ddPTM_BT-474_Pertuzumab_2h_R1 7 WIYEDVER 8 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ;;;;;; 211.87 6.42E-05 6766200000 6046160 7538680 6282120 7611670 6881550 6127160 7353340 6759730 6924210 7580240 FALSE TRUE 5809869.383 7323684.228 7417438.829 8004509.201 7102901.305 6251055.373 7443332.375 6620139.213 6138202.709 7066823.593 0.822133071 1.036347396 1.049614262 1.132688413 1.005105223 0.884563664 1.053278361 0.93679135 0.868594302 1 22.75263047 2.979141649 24.28034369 0.952062384 1.021631537 0.099958915 0.087995311 1164.400138 1355431.926 0.026862527 0.028805544 953.1069769 -2.979141649 0.069569154 KQDSGHLDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQDSGHLDLR 10 1 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 107.85 0.0014474 228740000 394540 493010 362960 449940 423110 385330 424130 434840 447040 445870 FALSE TRUE 379120.9406 478949.8375 428554.946 473161.4573 436719.7174 393121.6366 429320.6298 425860.402 396293.8933 415670.8278 0.912070117 1.152233463 1.030995965 1.138308069 1.050638362 0.945752288 1.032838008 1.024513566 0.953383944 1 18.66508198 2.97944411 24.27412511 0.99881974 1.067062413 0.187091352 0.066597917 828.9633915 978911.067 0.018978023 0.020361258 953.7709937 -2.97944411 0.068242673 KLGDVS(ph)PTQIDVSQFGSFK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLGDVSPTQIDVSQFGSFK 19 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 KLGDVS(0.975)PT(0.025)QIDVSQFGSFK 172.8 4.69E-12 308900000 323010 333450 261930 306760 337390 333280 346670 391550 418130 339620 TRUE FALSE 310386.4121 323940.3325 309266.5776 322591.9204 348242.4558 340019.1499 350912.6512 383464.3557 370665.6353 316617.2349 0.980320646 1.023129182 0.976783774 1.018870373 1.099884711 1.073912322 1.108318223 1.211129128 1.170705807 1 18.27238026 2.979565788 1.099204941 1.144272519 0.991910514 0.468342399 0.055884393 0.363216078 0.939322849 0.024994712 0.029867512 954.0382524 -2.979565788 -0.152362005 LYVELHR ddPTM_BT-474_Pertuzumab_2h_R1 4 LYVELHR 7 0 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 ;;; 129.4 0.0074279 304170000 602553 652177 560515 648232 615468 528472 652612 597242 691076 761464 FALSE TRUE 579004.5626 633577.5505 661812.5291 681687.3312 635265.0872 539158.0659 660598.8609 584908.744 612627.9497 709889.365 0.815626478 0.89250182 0.932275593 0.960272635 0.894879003 0.759495905 0.930565935 0.823943522 0.862990742 1 19.43723468 2.979611681 24.80612599 0.86205355 0.905122426 0.009137551 0.069023284 1841.050878 2239979.878 0.020036449 0.021495995 954.1390726 -2.979611681 0.043068875 SEDFSLPAYMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDFSLPAYMDR 12 0 H3BN72;H3BNV9;P13073;Q86WV2;H3BNI5 H3BN72 COX4I1 "Cytochrome c oxidase subunit 4 isoform 1, mitochondrial" 0 110.39 0.0034788 221000000 439530 451080 360300 504730 433260 337950 509190 403980 508740 390870 FALSE TRUE 422352.6817 438215.6401 425414.2248 530779.1758 447196.2014 344783.5805 515421.6195 395637.6718 450989.968 364396.0267 1.159048537 1.202580731 1.167450229 1.456599789 1.227225789 0.946178211 1.414454554 1.085735416 1.237636898 1 18.4751477 2.979826026 24.77879486 1.153071986 1.25068091 0.115253715 0.143625347 1670.798748 2052170.204 0.04216001 0.045270545 954.6101017 -2.979826026 0.097608923 QEELGDLVDKEMAATSAAIETATAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEELGDLVDKEMAATSAAIETATAR 25 1 O00291-3;O00291-4;O00291 O00291-3 HIP1 Huntingtin-interacting protein 1 0 ; 80.359 0.0056379 9185800 40922 45119 30598 36510 38735 42851 40789 40900 48145 43667 FALSE TRUE 39322.723 43832.2503 36127.73925 38394.28548 39980.94645 43717.47658 41288.18798 40055.40071 42679.78144 40709.3952 0.965937293 1.076710919 0.887454581 0.943130825 0.982106127 1.073891576 1.014217671 0.983935048 1.048401265 1 15.31307417 2.980283279 23.88370478 1.019924931 0.96931895 0.225283168 0.049376321 738.6822157 894799.0098 0.015335034 0.016492755 955.6157063 -2.980283279 -0.050605981 ILSHGGFR ddPTM_BT-474_Pertuzumab_2h_R1 3 ILSHGGFR 8 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;; 166.68 0.00031706 3193240000 2770890 3013870 2999990 3101370 2998990 2598623 3256490 3147900 3126400 3379400 FALSE TRUE 2662600.555 2927917.378 3542154.927 3261432.077 3095455.237 2651168.938 3296343.899 3082894.765 2771504.179 3150510.228 0.845133125 0.929347048 1.124311515 1.035207583 0.982525056 0.841504628 1.046288906 0.97853825 0.879700105 1 21.58715406 2.980448435 24.35850742 0.953895225 0.992086832 0.032593775 0.086186148 2231.802875 2780516.173 0.027338747 0.029402469 955.9791831 -2.980448435 0.038191607 LRIEEEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 LRIEEEIR 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 189.38 0.00017511 1791700000 1532610 1671780 1365450 1623150 1536690 1265200 1629310 1564770 1624730 1757410 FALSE TRUE 1472713.907 1624102.471 1612217.189 1706920.966 1586119.029 1290783.211 1649249.983 1532456.953 1440297.462 1638379.055 0.898884725 0.991286153 0.98403186 1.041835197 0.968102604 0.787841621 1.006635173 0.935349453 0.879099044 1 20.64383775 2.98056358 24.95981191 0.921552328 0.983335614 0.14753084 0.06624362 1352.897318 1737363.211 0.019670583 0.021158516 956.2326765 -2.98056358 0.061783287 LQAVTDDHIR ddPTM_BT-474_Pertuzumab_2h_R1 8 LQAVTDDHIR 10 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;;; 222.18 5.03E-09 30627410000 13484480 14462230 11392272 14086400 13121900 11566550 12964831 13298950 13195210 14045840 FALSE TRUE 12957491.61 14049781.36 13451108.97 14813400.79 13543977.83 11800433.57 13123498.48 13024322.04 11697345.08 13094502.75 0.989536744 1.072952645 1.027233277 1.131268677 1.034325479 0.901174622 1.002214344 0.994640445 0.893301969 1 23.64245794 2.980757918 24.21421438 0.964970829 1.058047128 0.474696088 0.04891577 446.4401879 561800.8165 0.014439639 0.015554158 956.6606671 -2.980757918 0.093076299 LKDLDLDAFAEELER ddPTM_BT-474_Pertuzumab_2h_R1 5 LKDLDLDAFAEELER 15 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;;; 205.98 3.76E-09 352553000 681901 770159 588342 665958 706661 794103 706172 810759 839756 826805 FALSE TRUE 655251.555 748194.8194 694668.487 700328.1722 729391.3928 810160.3067 714814.3442 794016.5433 744430.4194 770804.7609 0.850087582 0.970667097 0.901224956 0.908567523 0.946272558 1.051057736 0.927361091 1.030113699 0.96578337 1 19.55600596 2.980783367 6.439265376 0.994478662 0.913284002 0.493613335 0.041585094 0.138731482 23.51554511 0.011568862 0.012850289 956.7167269 -2.980783367 -0.08119466 EIYHFTLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIYHFTLEK 9 0 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 99.653 0.0051914 239380000 154430 162760 124190 167600 149780 123520 167470 126560 165970 192180 FALSE TRUE 148394.7049 158118.2442 146633.8956 176249.8561 154597.8097 126017.659 169519.548 123946.4918 147129.7814 179163.4774 0.828264259 0.882536142 0.818436311 0.983737638 0.862886856 0.703366896 0.946172459 0.691806687 0.821204095 1 17.45091705 2.980793326 24.92331986 0.810133977 0.880407502 0.022269822 0.098650734 1671.563114 2169088.058 0.028117084 0.030252482 956.7386668 -2.980793326 0.070273525 ELSDFISYLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSDFISYLQR 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 259.86 2.99E-20 8341600000 2346000 2844600 2345700 2458900 2457300 1827980 2779500 2355400 2268500 2615700 FALSE TRUE 2254315.726 2763474.793 2769620.17 2585804.124 2536341.286 1864943.008 2813516.352 2306760.167 2010989.39 2438536.309 0.924454443 1.133251444 1.135771553 1.060391889 1.040108067 0.764779676 1.15377259 0.945960968 0.824670678 1 21.21758402 2.980808296 24.8464714 0.948400039 1.070695713 0.226885354 0.111136198 1086.624582 1406796.582 0.033076495 0.035587944 956.7716454 -2.980808296 0.122295674 YYIADR ddPTM_BT-474_Pertuzumab_2h_R1 2 YYIADR 6 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 106.76 0.074087 1647410000 1620820 1694670 1438090 1741160 1614220 1477390 1593310 1637460 1742660 1870030 FALSE TRUE 1557476.562 1646339.671 1697984.853 1831021.476 1666142.852 1507263.838 1612809.404 1603645.879 1544840.543 1743371.202 0.893370592 0.944342587 0.973966331 1.050276312 0.955701717 0.864568507 0.925109582 0.919853372 0.886122554 1 20.73344835 2.980837313 24.8574418 0.914726499 0.969384646 0.169748815 0.048692266 1087.662397 1410894.925 0.014813568 0.01593862 956.8355737 -2.980837313 0.054658147 VHFALLGTWDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHFALLGTWDEK 12 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ; 194.17 1.88E-06 476870000 1004770 1001470 884870 954520 950500 677630 1175480 680490 1304890 1286320 FALSE TRUE 965502.4776 972909.0561 1044785.693 1003782.892 981073.6957 691332.1429 1189865.876 666437.6437 1156764.358 1199196.401 0.805124563 0.811300847 0.871238183 0.837046285 0.818109273 0.576496179 0.992219352 0.555736861 0.964616269 1 20.19363653 2.980881765 24.67329636 0.77697415 0.831989057 0 0.149376611 2799.26202 3612629.051 0.042216898 0.045440176 956.9335147 -2.980881765 0.055014907 (ac)ADFDDRVSDEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADFDDRVSDEEK 12 1 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ; 96.342 0.00041745 2009270000 1720790 1700670 1180700 1194100 1451970 1624240 1484650 1618740 1729420 1561200 FALSE TRUE 1653539.624 1652168.557 1394078.755 1255727.644 1498673.934 1657083.246 1502819.591 1585312.453 1533103.492 1455458.533 1.136095317 1.1351533 0.957827875 0.862771158 1.029691949 1.138530029 1.0325403 1.089218564 1.053347421 1 20.47304231 2.981165575 24.87701027 1.069049391 1.016311713 0.047581107 0.081882925 2050.68491 2708602.657 0.026911297 0.028959457 957.5590708 -2.981165575 -0.052737679 GCNPSGHTQSVT(ph)TPEPAKEGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 GCNPSGHTQSVTTPEPAKEGTK 22 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 GCNPSGHTQS(0.003)VT(0.584)T(0.414)PEPAKEGTK;GCNPSGHTQSVT(0.823)T(0.176)PEPAKEGTK 155.73 2.49E-08 438380000 651300 794460 468840 500950 615030 763100 686120 710900 619930 640690 TRUE FALSE 625846.4759 771802.7787 553569.8173 526804.0895 634812.9985 778530.4048 694516.9418 696219.6666 549558.1454 597295.4956 1.047800428 1.292162396 0.926793892 0.881982358 1.062812298 1.303425876 1.162769428 1.165620152 0.920077498 1 19.18808532 2.981169018 24.42330098 1.134006076 1.038123004 0.045439926 0.139877322 1464.722223 1899709.928 0.043822805 0.047234308 957.5666619 -2.981169018 -0.095883072 T(ph)PPASPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPASPHR 8 0 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P2-8;Q5T5P2-6;Q5T5P1;Q5T5P2-4;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 T(1)PPASPHR 128.03 0.0042341 85582000 95536 106440 103420 105980 102570 90587 104470 104080 105680 109830 TRUE FALSE 91802.3475 103404.4354 122110.2946 111449.6405 105869.2572 92418.73121 105748.5351 101930.7116 93683.64945 102391.1163 0.896585083 1.009896553 1.192586808 1.088469826 1.033969167 0.902604978 1.032790138 0.995503471 0.914958767 1 16.64373102 2.981241718 23.11725939 0.975604489 1.055471087 0.185158331 0.077768618 499.5779094 615669.864 0.024636489 0.026600994 957.7269702 -2.981241718 0.079866597 S(ph)LQQLAEER ddPTM_BT-474_Pertuzumab_2h_R1 4 SLQQLAEER 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 S(1)LQQLAEER;S(1)LQQLAEER;S(1)LQQLAEER;S(1)LQQLAEER 184.98 4.55E-05 2294850000 650357 512914 480486 538998 525903 414835 444145 633368 522121 473201 TRUE FALSE 624940.3294 498286.1949 567320.5086 566815.7514 542819.1476 423223.2479 449580.5794 620288.7295 462852.013 441150.6748 1.416614244 1.129514752 1.286001679 1.284857496 1.230462014 0.959362123 1.019108901 1.40607 1.049192576 1 18.75091197 2.981291328 23.83101372 1.126743156 1.267612567 0.297341722 0.134763126 719.1492043 916050.3997 0.043274888 0.046693511 957.8363797 -2.981291328 0.140869411 DLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_BT-474_Pertuzumab_2h_R1 3 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.201)QS(0.201)HLRNS(0.598)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.052)QS(0.281)HLRNS(0.667)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.009)QS(0.044)HLRNS(0.947)PEDKR 241.67 3.26E-47 2132770000 541958 542332 448761 410170 498495 585522 495403 552187 658199 609452 TRUE FALSE 520777.6822 526865.2224 529862.0953 431338.9229 514529.5444 597361.656 501465.8901 540784.1455 583483.0089 568173.2732 0.916582505 0.927296737 0.932571313 0.759167921 0.905585617 1.051372326 0.88259324 0.95179441 1.02694554 1 19.11597144 2.981588489 24.92069931 0.969922526 0.883217319 0.354998906 0.062948933 929.6773355 1258356.531 0.019448937 0.020977705 958.4919916 -2.981588489 -0.086705206 AAVEWFDGKDFQGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAVEWFDGKDFQGSK 15 1 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 232.26 7.72E-14 4703800000 6080600 5472100 4071400 3879500 4927400 5566200 5053400 5654900 6293100 5622800 FALSE TRUE 5842963.43 5316041.066 4807192.548 4079721.46 5085894.296 5678752.378 5115245.021 5538124.339 5578733.671 5241962.748 1.114651841 1.01413179 0.917059655 0.778281277 0.970227096 1.083325588 0.975826282 1.056498225 1.064245196 1 22.32167567 2.981869737 24.53869582 1.03491119 0.947004614 0.172768562 0.083878586 1045.698446 1415319.597 0.027106041 0.029290192 959.1129094 -2.981869737 -0.087906576 GNDVAFHFNPR ddPTM_BT-474_Pertuzumab_2h_R1 6 GNDVAFHFNPR 11 0 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;;;;; 140.39 3.86E-05 3357250000 3140090 3545310 2627100 3960210 3265940 2703670 3321000 3179000 3375000 3839360 FALSE TRUE 3017371.811 3444201.23 3101875.41 4164596.913 3370991.926 2758340.06 3361643.391 3113352.539 2991884.149 3579316.727 0.843002182 0.962251036 0.866611045 1.163517294 0.941797606 0.770633132 0.939185785 0.869817559 0.835881364 1 21.77125278 2.98205061 24.78516304 0.877115337 0.965020091 0.11907985 0.097993294 1253.425128 1730776.924 0.028964561 0.031300997 959.5124398 -2.98205061 0.087904755 SESGGLGVSMVEYVLSSS(ph)PADKLDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SESGGLGVSMVEYVLSSSPADKLDSR 26 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 1 SESGGLGVSMVEYVLSS(0.041)S(0.958)PADKLDS(0.001)R;SESGGLGVSMVEYVLS(0.001)S(0.177)S(0.822)PADKLDSR 168.17 5.81E-12 496260000 413840 384570 294570 316140 363780 436000 369230 413320 478490 477880 TRUE FALSE 397666.6753 373602.4401 347805.3517 332456.0233 375481.3141 444816.2187 373748.7472 404784.7976 424173.8212 445512.7619 0.892604453 0.83858976 0.780685496 0.746232323 0.842807089 0.998436536 0.838918162 0.908581823 0.952102515 1 18.76510723 2.982159021 22.90825538 0.923259659 0.811415671 0.52006999 0.056766841 221.2703633 284117.4656 0.017339794 0.018782512 959.7519888 -2.982159021 -0.111843988 DLCNTHLMR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLCNTHLMR 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 185.61 4.27E-05 923590000 296780 345460 286700 291970 295750 198120 304300 259850 345450 326460 FALSE TRUE 285181.5095 335607.819 338513.0676 307038.6067 305263.0673 202126.1221 308024.1144 254484.0067 306235.9642 304348.5734 0.937022659 1.102708698 1.112254491 1.008838659 1.003004758 0.664127056 1.012076748 0.836159683 1.006201412 1 18.21536508 2.982409996 24.49129757 0.891567042 1.044330053 0.267198888 0.107245778 653.8646031 910404.2725 0.030725861 0.033259884 960.3067811 -2.982409996 0.152763011 QICLVMLETLSQS(ph)PQGR ddPTM_BT-474_Pertuzumab_2h_R1 9 QICLVMLETLSQSPQGR 17 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QICLVMLETLSQS(1)PQGR;QICLVMLET(0.128)LS(0.128)QS(0.745)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLS(0.018)QS(0.982)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR 480.38 1.90E-231 6542451000 1974597 1964811 1568656 1706270 1637555 1612318 1402210 1578558 1622472 1657910 TRUE FALSE 1897427.566 1908776.514 1852147.034 1794330.799 1690228.444 1644920.175 1419370.665 1545960.226 1438295.781 1545618.279 1.227617189 1.234959847 1.198321124 1.160914583 1.093561371 1.064247361 0.918319021 1.000221236 0.930563387 1 20.55975263 2.982468697 0.990411633 0.959681083 1.231006605 0.921445098 0.031701819 0.123278307 0.263023445 0.014673454 0.017795974 960.4365892 -2.982468697 0.271325522 EHLELFWSR ddPTM_BT-474_Pertuzumab_2h_R1 6 EHLELFWSR 9 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 185.27 4.30E-05 9258960000 8072750 9358530 8333090 8399980 8014160 4919300 9977960 4048130 8636760 9842710 FALSE TRUE 7757258.005 9091633.887 9839064.732 8833503.974 8271942.735 5018771.616 10100073.26 3964534.701 7656351.213 9176054.485 0.845380552 0.990799902 1.072254393 0.962669085 0.901470534 0.546942221 1.10069892 0.432052219 0.8343838 1 23.12944253 2.982480766 19.8203139 0.746090966 0.971282176 0.162564416 0.190471656 69.32193567 78428.20118 0.054802568 0.059626073 960.4632797 -2.982480766 0.22519121 GSNMDFR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSNMDFR 7 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 95.605 0.031042 3718130000 5632700 6138500 5801800 6724900 6048700 4368500 6672900 6335900 6220100 6720800 FALSE TRUE 5412567.857 5963435.99 6850314.32 7071972.895 6243261.929 4456834.063 6754564.946 6205061.451 5514020.325 6265594.23 0.863855471 0.951775007 1.093322368 1.128699471 0.996435725 0.711318655 1.078040597 0.990338861 0.880047466 1 22.57901991 2.982731924 24.99268384 0.938994967 1.017699361 0.096850445 0.112719401 1897.845889 2746822.683 0.035526256 0.038516124 961.0188888 -2.982731924 0.078704394 EIAIVHS(ph)DAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIAIVHSDAEK 11 0 Q9H307 Q9H307 PNN Pinin 1 EIAIVHS(1)DAEK;EIAIVHS(1)DAEK 170.95 9.73E-06 492930000 377133 327428 586730 711660 496540 471700 791510 823390 1032940 1157670 TRUE FALSE 362394.2254 318090.074 692765.1627 748388.8579 512511.66 481238.0972 801196.7361 806386.7088 915684.9816 1079259.98 0.335780287 0.294729796 0.64188905 0.693427786 0.474873218 0.445896361 0.742357496 0.747166321 0.848437817 1 20.041611 2.982797616 0.165177761 1.162070373 9.70E-22 0.72872752 0.113094162 5.39810884 0.347360605 0.646783116 1.661496262 961.1642664 -2.982797616 -1.162070373 down SDTSISDFLS(ph)EEDDIVPSKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDTSISDFLSEEDDIVPSKK 20 1 Q4AC94;Q4AC94-2;Q4AC94-4;Q4AC94-1;Q4AC94-3 Q4AC94 C2CD3 C2 domain-containing protein 3 1 SDTSIS(0.001)DFLS(0.999)EEDDIVPSKK;S(0.003)DT(0.004)S(0.004)IS(0.057)DFLS(0.931)EEDDIVPSKK 121.47 1.97E-05 158038000 225660 212613 196002 186913 209203 229065 212469 229459 257820 237976 TRUE FALSE 216840.9577 206549.4854 231423.9214 196559.6023 215932.2045 233696.8512 215069.2592 224720.5915 228553.3545 221857.6736 0.977387684 0.930999961 1.043118851 0.885971619 0.973291575 1.053363841 0.96940194 1.0129043 1.030180074 1 17.75927493 2.98309018 24.79873259 1.010528481 0.959113527 0.273976763 0.041904522 893.1511917 1309833.848 0.012008302 0.013030764 961.8119751 -2.98309018 -0.051414955 HVGMAVAGLLADAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVGMAVAGLLADAR 14 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 184.31 1.31E-06 2252800000 2171700 2327100 2005160 2150400 2090900 1470710 2264300 1688660 2354500 2450900 FALSE TRUE 2086827.563 2260733.386 2367537.017 2261382.402 2158155.697 1500448.764 2292011.181 1653788.581 2087227.031 2284898.36 0.913313082 0.989424049 1.036167323 0.989708094 0.944530284 0.656680748 1.00311297 0.723790874 0.913487912 1 21.12369856 2.983091798 24.8673112 0.840328755 0.984104235 0.224139279 0.106035463 806.277502 1185814.511 0.029573104 0.032086747 961.815558 -2.983091798 0.14377548 DYALHWLVLGTHTSDEQNHLVVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYALHWLVLGTHTSDEQNHLVVAR 24 0 Q16576;E9PC52;Q16576-2;C9J7L0 Q16576 RBBP7 Histone-binding protein RBBP7 0 ; 299.85 1.36E-62 1492860000 1670740 1989640 1802670 1847130 1644900 980050 1997230 913180 1797000 1859780 FALSE TRUE 1605445.634 1932897.415 2128452.569 1942460.601 1697809.702 999867.2825 2021672.698 894322.5139 1593012.094 1733815.444 0.925961087 1.114823046 1.227611956 1.120338735 0.979233233 0.576686109 1.166025314 0.515811828 0.918789886 1 20.72551891 2.983289202 7.75135067 0.806100817 1.101180511 0.289734614 0.190790981 0.189110866 63.8462134 0.054520176 0.06053038 962.252841 -2.983289202 0.295079695 IKNGSNPETTTSGGCHS(ph)PEDTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKNGSNPETTTSGGCHSPEDTPK 23 1 Q08379 Q08379 GOLGA2 Golgin subfamily A member 2 1 IKNGSNPETTTSGGCHS(0.998)PEDT(0.002)PK;IKNGSNPETTTSGGCHS(0.993)PEDT(0.007)PK 181.31 2.59E-17 234293000 248718 225334 179227 164404 210279 264616 219151 233586 270069 255108 TRUE FALSE 238997.8256 218907.6949 211617.3058 172888.9101 217042.815 269966.7168 221833.0355 228762.3675 239411.8993 237829.3079 1.004913262 0.920440365 0.889786493 0.726945353 0.912599111 1.135128043 0.932740533 0.961876269 1.006654316 1 17.85956699 2.983325967 24.89767694 0.998036311 0.879751736 0.341797673 0.08075569 842.9502636 1258695.945 0.025284651 0.027462257 962.3343029 -2.983325967 -0.118284575 AFFESHPAPSAER ddPTM_BT-474_Pertuzumab_2h_R1 3 AFFESHPAPSAER 13 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;; 172.76 2.28E-05 1599170000 1959420 2146820 1721180 1808230 1763960 1145330 1884480 1485440 1725590 1975770 FALSE TRUE 1882843.7 2085594.796 2032235.513 1901552.967 1820699.375 1168489.357 1907542.83 1454765.145 1529708.257 1841949.338 1.022201676 1.132275873 1.103306954 1.032358995 0.988463329 0.634376491 1.03561091 0.789796502 0.83048335 1 20.81280195 2.983414209 13.42147567 0.851072977 1.070452519 0.470392674 0.10772672 1.482896904 1199.641988 0.030477587 0.033522838 962.5298544 -2.983414209 0.219379542 SEDVWLEAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEDVWLEAAR 10 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 199.89 6.29E-07 314650000 345180 398660 329300 357920 355450 298650 390750 353690 382330 387590 FALSE TRUE 331689.984 387290.6071 388811.8352 376392.2941 366883.3721 304688.9076 395532.1154 346386.1779 338929.5013 361338.1841 0.917948887 1.071823085 1.076033069 1.041662107 1.015346255 0.843223664 1.094631381 0.958620465 0.937984183 1 18.46299019 2.983541652 24.9486778 0.970022364 1.032954137 0.140450058 0.07094297 1348.453932 2044081.543 0.020877601 0.022664184 962.8123485 -2.983541652 0.062931773 ALGHQLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALGHQLGR 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 152.39 0.00045787 143700000 163990 205880 190950 177630 183170 135160 205680 171230 200340 201240 FALSE TRUE 157581.0895 200008.504 225458.9127 186797.5056 189061.8294 137893.0278 208197.1734 167694.0407 177598.2431 187609.8356 0.839940449 1.066087518 1.201743565 0.99567011 1.007739434 0.734998927 1.109734853 0.893844612 0.9466361 1 17.51737594 2.983622479 24.78905169 0.934879788 1.036347881 0.110083676 0.120440911 1303.51051 1973000.311 0.035687006 0.038836359 962.9915552 -2.983622479 0.101468093 YAVWFGGSMLASTPEFYQVCHTK ddPTM_BT-474_Pertuzumab_2h_R1 2 YAVWFGGSMLASTPEFYQVCHTK 23 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 271.91 1.26E-51 323840000 206096 183028 162523 208570 186305 165419 181696 173610 233940 205722 FALSE TRUE 198041.5405 177808.2206 191894.5214 219334.3227 192297.6695 168763.8855 183919.65 170024.8928 207384.112 191788.2657 1.032605096 0.92710688 1.000554026 1.143627437 1.002656074 0.879948963 0.958972382 0.88652396 1.081318042 1 17.54915493 2.983624771 24.86760287 0.947883172 1.024101538 0.137453572 0.073037804 1126.970662 1711431.524 0.022260922 0.024202284 962.9966371 -2.983624771 0.076218366 GDYYEAHQMYR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDYYEAHQMYR 11 0 Q7L5D6 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 ;; 180.88 6.47E-06 1259420000 1075728 1224900 1134285 1202780 1164690 1001281 1292370 1140535 1265171 1392740 FALSE TRUE 1033687.36 1189967.051 1339275.532 1264855.62 1202153.312 1021527.588 1308186.411 1116982.554 1121554.092 1298408.479 0.796118769 0.916481269 1.031474727 0.974158472 0.925866806 0.786753633 1.007530705 0.860270532 0.863791411 1 20.3083129 2.98395508 24.69365375 0.896481589 0.937667572 0.015486144 0.082513254 2109.914452 3247234.513 0.024760308 0.02696832 963.7293381 -2.98395508 0.041185983 SVGQYDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVGQYDNR 8 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 79.906 0.056261 0 121150 126050 119670 125010 119870 93097 115380 117440 123020 139890 FALSE TRUE 116415.3241 122455.1774 141297.031 131461.7811 123725.7274 94979.48513 116792.055 115014.823 109055.2853 130415.1257 0.89265201 0.938964532 1.083440516 1.008025567 0.948706883 0.728285807 0.895540715 0.881913216 0.836216541 1 16.99275168 2.984238001 24.37771903 0.862547776 0.984274105 0.323656464 0.077409271 554.761868 858003.9836 0.023056194 0.025164796 964.3573636 -2.984238001 0.121726329 TIEGQS(ph)PEPVFGDADVDVSAVQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIEGQSPEPVFGDADVDVSAVQAK 24 0 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 T(0.033)IEGQS(0.967)PEPVFGDADVDVSAVQAK;T(0.02)IEGQS(0.98)PEPVFGDADVDVSAVQAK 171.52 4.25E-12 325920000 272770 256759 228592 270520 282420 269980 314110 349580 332000 328520 TRUE FALSE 262109.8468 249436.4847 269903.6594 284481.5696 291504.2958 275439.1806 317954.1721 342361.0508 294312.7519 306269.0478 0.855815659 0.814435825 0.88126326 0.928861639 0.951791563 0.899337307 1.038153135 1.117844109 0.960961462 1 18.22444005 2.984273807 0.748131674 1.047814856 0.836007239 0.637895956 0.05151458 0.41336553 0.515222782 0.034691392 0.045060303 964.4368744 -2.984273807 -0.211807617 ALVTGYFMQVAHLER ddPTM_BT-474_Pertuzumab_2h_R1 2 ALVTGYFMQVAHLER 15 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 162.29 1.60E-06 1299880000 544000 551660 512680 511750 506170 351530 537570 432840 505930 567730 FALSE TRUE 522739.8786 535927.1969 605332.6805 538161.4788 522451.4177 358638.1775 544148.9425 423901.7027 448498.9474 529277.1414 0.987648696 1.012564411 1.143697003 1.016785795 0.987103687 0.677599974 1.028098325 0.800906878 0.847380157 1 19.01366382 2.984404308 23.54689951 0.863553705 1.040139977 0.395773846 0.099620652 300.8851966 454288.0041 0.028270895 0.030893094 964.7267215 -2.984404308 0.176586272 FLIDGFPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLIDGFPR 8 0 P30085;P30085-3;A0A494BXC7;P30085-2;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ; 136.11 0.0018725 821630000 1141100 1285390 1004180 1167740 1124740 843470 1185900 1175720 1126790 1227900 FALSE TRUE 1096504.55 1248731.936 1185657.664 1228007.201 1160918.284 860525.5413 1200413.399 1151440.971 998881.5231 1144733.239 0.957869059 1.090849722 1.035750185 1.072745299 1.014138704 0.751725827 1.048640293 1.005859646 0.872588904 1 20.12658001 2.984530364 24.90461979 0.944495909 1.042820439 0.256626316 0.083959646 995.0463383 1601931.624 0.025393868 0.027730653 965.0067787 -2.984530364 0.09832453 RQT(ph)IEER ddPTM_BT-474_Pertuzumab_2h_R1 2 RQTIEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RQT(1)IEER;RQT(1)IEER 141.91 0.0014796 219440000 212685 211970 87064 193057 163456 103891 135823 271850 73015 64380 TRUE FALSE 204373.0351 205924.8231 102798.4015 203020.6949 168713.7107 105991.7472 137485.2425 266236.2025 64726.6433 60019.48526 3.405111427 3.430966165 1.712750469 3.382579741 2.8109823 1.765955618 2.290676801 4.435829487 1.078427165 1 15.87314333 2.984569161 24.36376181 2.490759706 2.945718925 0.089122183 1.035532869 2041.671218 3223603.786 0.321813466 0.351785596 965.0929897 -2.984569161 0.454959219 QGGLGPMNIPLVSDPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QGGLGPMNIPLVSDPKR 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 169.61 5.31E-09 1145570000 1146330 1191070 798770 870610 1023970 1196760 1083140 1089970 1308640 1267970 FALSE TRUE 1101530.156 1157101.85 943125.5075 915542.2864 1056906.925 1220959.307 1096395.791 1067461.739 1160088.673 1182089.263 0.931850234 0.978861653 0.797846269 0.774511973 0.894100774 1.032882495 0.927506768 0.903029722 0.981388386 1 20.17290755 2.984651781 24.65511551 0.955511999 0.868408194 0.336272143 0.064956902 816.7167643 1311962.938 0.021277561 0.023264219 965.276607 -2.984651781 -0.087103804 GGVDHAAAFGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GGVDHAAAFGR 11 0 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ;;;;; 176.33 8.78E-06 5209890000 2527580 2809650 2588050 3032040 2743260 2442880 2933680 2755090 2948860 3042000 FALSE TRUE 2428799.379 2729521.533 3055768.206 3188523.948 2831499.449 2492276.707 2969583.253 2698196.429 2614117.775 2835962.63 0.856428556 0.962467384 1.077506513 1.124318041 0.99842622 0.878811547 1.047116496 0.951421715 0.921774408 1 21.43540709 2.984725682 24.68308306 0.961191964 1.014054972 0.069439294 0.078112888 1585.600426 2562313.144 0.02470091 0.027026913 965.4408753 -2.984725682 0.052863008 EHAMLAK ddPTM_BT-474_Pertuzumab_2h_R1 6 EHAMLAK 7 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ;;;;; 91.065 0.016678 1692379000 2844290 3165830 2870710 3151100 2993910 2788340 3418590 2405560 3331720 3947680 FALSE TRUE 2733132.002 3075543.628 3389511.156 3313728.649 3090211.834 2844722.145 3460427.727 2355884.345 2953517.113 3680300.117 0.742638349 0.835677399 0.920987704 0.900396311 0.839662999 0.772959284 0.94025694 0.640133758 0.802520724 1 21.81139199 2.985071039 22.27591137 0.804547691 0.855988974 0 0.102034432 558.677944 833624.3955 0.030600607 0.033586486 966.2089115 -2.985071039 0.051441283 YCDAVFHER ddPTM_BT-474_Pertuzumab_2h_R1 2 YCDAVFHER 9 0 A0A2R8Y595;A0A2R8YFL0;P49711-2;P49711 A0A2R8Y595 CTCF Transcriptional repressor CTCF 0 ; 110.14 0.0028306 255510000 441340 413410 390180 448040 384470 265400 390430 388310 292380 319620 FALSE TRUE 424091.9449 401619.9516 460694.2055 471163.3981 396836.8267 270766.5698 395208.1991 380291.2628 259190.2482 297971.8527 1.423261765 1.347845268 1.546099745 1.581234582 1.331792997 0.908698481 1.326327287 1.276265726 0.869848094 1 18.18481653 2.985112853 11.48719043 1.128157597 1.468954596 0.60200777 0.150940913 0.519681753 398.3924829 0.046559012 0.051591773 966.3019433 -2.985112853 0.340797 LDETDDPDDYGDRESGCSFVLALMQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDETDDPDDYGDRESGCSFVLALMQK 26 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 259.77 8.62E-53 1611460000 1872260 1911570 1527030 1568660 1758480 1929950 1839270 1974490 2130630 1948730 FALSE TRUE 1799090.009 1857053.895 1802998.29 1649618.731 1815043.106 1968974.911 1861779.536 1933716.092 1888769.815 1816740.781 0.990284375 1.0221898 0.992435634 0.908009964 0.999065538 1.083795185 1.024790964 1.064387452 1.039647392 1 20.79292116 2.98514426 24.48554803 1.045943947 0.978778771 0.446034455 0.034033 465.3709557 767036.0865 0.010327849 0.011322512 966.3718255 -2.98514426 -0.067165176 QSANDFFSYYDSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSANDFFSYYDSHR 14 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 149.3 7.52E-06 326030000 185740 218260 166480 207010 192870 175690 192400 195080 210530 224820 FALSE TRUE 178481.0755 212035.4385 196566.6393 217693.8109 199073.8387 179242.5722 194754.6488 191051.5298 186631.517 209592.7412 0.85156134 1.011654494 0.937850415 1.038651481 0.949812659 0.855194561 0.929205123 0.911536959 0.890448381 1 17.67722923 2.985165221 24.8341694 0.911840615 0.966070137 0.105950465 0.057441014 1076.519593 1802152.058 0.016154549 0.017710786 966.4184689 -2.985165221 0.054229522 GSASYS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSASYSPPR 9 0 A0A087WTY1;P0DPB5 A0A087WTY1 POLR1D 1 GSAS(0.002)YS(0.998)PPR;GSASYS(1)PPR;GSAS(0.001)YS(0.999)PPR 119.22 0.00090415 888120000 1339870 1403190 1079120 1265620 1252750 1176470 1263550 1322140 1293490 1380610 TRUE FALSE 1287506.399 1363172.395 1274140.989 1330938.8 1293045.841 1200259.029 1279013.703 1294837.347 1146658.438 1287100.055 1.000315705 1.059103672 0.989931578 1.034060091 1.004619522 0.932529701 0.993717387 1.006011415 0.890885237 1 20.29569278 2.985182482 21.18871788 0.970609228 1.021121785 0.343462213 0.036705354 112.1735489 160407.6092 0.010757448 0.011823186 966.4568793 -2.985182482 0.050512557 SKESVPEFPLS(ph)PPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKESVPEFPLSPPKK 15 2 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 SKESVPEFPLS(1)PPKK 87.49 0.0037313 663420000 619230 471870 462680 449510 519050 630810 563370 591510 679440 545540 TRUE FALSE 595029.807 458412.7296 546296.5683 472709.265 535745.7146 643565.4104 570264.6906 579295.1118 602312.8196 508590.0899 1.169959499 0.901340271 1.074139231 0.929450405 1.053393932 1.265391173 1.121265833 1.139021627 1.184279505 1 18.95614383 2.985290663 24.28682912 1.148905628 1.011436997 0.285960614 0.092606034 500.4973449 826381.4442 0.025483492 0.027961549 966.6976497 -2.985290663 -0.137468632 LHACTEEGQLENQVIAFEWDEMQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHACTEEGQLENQVIAFEWDEMQR 24 0 Q96L92-3;Q96L92;A0A2R8Y8A7;Q96L92-2;A0A5H1ZRP6 Q96L92-3 SNX27 Sorting nexin-27 0 125.62 9.75E-05 28116000 20244 23405 24084 15496 17578 22220 18902 14101 22299 18899 FALSE TRUE 19452.8421 22737.51232 28436.51455 16295.75042 18143.41233 22669.30362 19133.32833 13809.80942 19767.71101 17618.9539 1.1040861 1.290514321 1.613972924 0.924898862 1.029766718 1.286642996 1.085951439 0.783804164 1.121957133 1 14.10484065 2.98533857 0.73498392 0.965447711 1.300975565 0.217941369 0.192886016 0.97607446 1.173761957 0.128472695 0.168202999 966.8042921 -2.98533857 0.335527854 FFSGYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FFSGYGR 7 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 133.47 0.0076042 1882330000 880740 888840 794260 844850 826460 736760 808630 880800 834500 904200 FALSE TRUE 846319.7071 863491.1535 937800.4502 888452.8097 853043.8365 751657.792 818526.2558 862611.1722 739771.0585 842957.7286 1.003988312 1.024358784 1.112511836 1.053970774 1.011965141 0.891690967 0.971016966 1.023314863 0.877589745 1 19.68510076 2.985424356 7.011429398 0.960375125 1.049524728 0.460551954 0.048904604 0.154852888 39.11639877 0.015102829 0.016866581 966.9952828 -2.985424356 0.089149603 DGWENVPPFDHPLIWK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGWENVPPFDHPLIWK 16 0 Q96GA7;F8VYZ3;H0YID3 Q96GA7 SDSL Serine dehydratase-like 0 ; 135.57 2.22E-05 594150000 941600 988630 852540 887470 998150 1053630 1077960 1142360 1156150 1179170 FALSE TRUE 904801.231 960435.2404 1006612.943 933272.4331 1030256.401 1074935.12 1091152.397 1118769.867 1024908.699 1099303.766 0.823067526 0.873675931 0.915682247 0.84896683 0.937189914 0.977832656 0.992584972 1.017707664 0.932325287 1 20.06815866 2.985529135 2.403174458 0.989424238 0.86887954 0.76767192 0.030559479 0.136904715 1.58567143 0.009950928 0.011501571 967.2286127 -2.985529135 -0.120544698 YWPTADGR ddPTM_BT-474_Pertuzumab_2h_R1 8 YWPTADGR 8 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 ;;;;;;; 145.34 0.0013282 7814000000 3974380 4500950 3840380 4263210 4053460 3031560 4334580 3965090 4264950 4410760 FALSE TRUE 3819056.836 4372587.313 4534422.095 4483234.779 4183843.222 3092860.22 4387627.887 3883209.506 3780810.756 4112015.297 0.928755503 1.063368445 1.102725007 1.090276776 1.017467816 0.752151925 1.067026159 0.944356775 0.919454448 1 21.9714142 2.985554788 24.82846277 0.939000944 1.051825971 0.268940865 0.086477391 801.7153996 1377993.758 0.025513053 0.028013004 967.2857463 -2.985554788 0.112825027 GGNFGGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GGNFGGR 7 0 F8W6I7;P09651-2;P09651;P09651-3;Q32P51;H0YH80;P51991;P51991-2 F8W6I7;P51991;P51991-2 HNRNPA1;HNRNPA1L2;HNRNPA3 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoprotein A3" 0 ;;;;; 144.29 0.0054992 4204740000 2484710 2754350 2211690 2658420 2490030 2256180 2607650 2471020 2566040 2652460 FALSE TRUE 2387604.786 2675798.635 2611391.582 2795621.375 2570124.076 2301801.505 2639563.201 2419992.573 2274753.897 2472806.522 0.96554452 1.082089768 1.056043633 1.130545941 1.039355103 0.930845776 1.067436202 0.978642103 0.919907755 1 21.23771793 2.985641232 24.72381625 0.985422791 1.063169125 0.331051857 0.053604575 677.2685441 1166165.511 0.01583006 0.017392881 967.4782992 -2.985641232 0.077746334 AGLQEGDQVLAVNDVDFQDIEHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGLQEGDQVLAVNDVDFQDIEHSK 24 0 Q5EBL8;Q5EBL8-2 Q5EBL8 PDZD11 PDZ domain-containing protein 11 0 ; 241.13 1.43E-37 379320000 346111 353405 271203 302439 320721 339509 327159 337569 389345 362877 FALSE TRUE 332584.5995 343326.2354 320215.415 318047.913 331037.2822 346374.1046 331162.8697 330598.0822 345148.1879 338299.0176 0.983108381 1.014860279 0.946545507 0.940138447 0.978534566 1.023869673 0.978905798 0.977236306 1.020245907 1 18.36793946 2.985690056 24.55432619 0.995731339 0.970877291 0.244283619 0.023784725 940.4267802 1613674.984 0.007654417 0.008406623 967.5870704 -2.985690056 -0.024854048 GIFGFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GIFGFR 6 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 101.25 0.085467 726770000 420790 508450 435950 506140 456050 335650 478780 487780 404170 426550 FALSE TRUE 404345.0616 493949.5038 514735.8627 532261.9461 470719.2624 342437.073 484639.4529 477707.1725 358290.316 397659.3886 1.016812562 1.24214219 1.294413957 1.33848706 1.183724755 0.861131619 1.218730066 1.201297357 0.900998006 1 18.60117371 2.985718651 24.88462259 1.071133298 1.233395967 0.294633227 0.133636207 930.0749503 1620617.695 0.041487224 0.045593303 967.6507804 -2.985718651 0.16226267 SLS(ph)PGGAALGYR ddPTM_BT-474_Pertuzumab_2h_R1 8 SLSPGGAALGYR 12 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;S(0.001)LS(0.999)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;S(0.001)LS(0.999)PGGAALGYR;SLS(1)PGGAALGYR 249.98 5.02E-17 36042020000 8010810 8835110 7292810 8174720 7935990 6831400 8195060 8270340 7869850 8296620 TRUE FALSE 7697738.689 8583141.313 8610782.995 8596618.279 8191258.326 6969535.589 8295353.596 8099554.589 6976497.621 7734682.538 0.995223611 1.109695359 1.113269091 1.111437766 1.059029674 0.901075843 1.072487921 1.047173501 0.901975949 1 22.88291065 2.985742706 24.55939937 0.997745536 1.086394347 0.365928664 0.060626676 633.1745408 1090698.977 0.01841167 0.020231988 967.7043788 -2.985742706 0.088648811 KGYNAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGYNAR 6 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ; 101.33 0.058763 1130390000 1958040 2122100 1696210 1961420 1831460 1318960 1930310 1648520 1651350 1950340 FALSE TRUE 1881517.632 2061579.786 2002752.879 2062649.121 1890370.574 1345630.275 1953933.711 1614477.486 1463895.671 1818241.735 1.034800597 1.133831518 1.101477785 1.134419633 1.039669554 0.740072263 1.074628128 0.887933356 0.805116087 1 20.79411259 2.985858234 23.53771265 0.906738323 1.101436736 0.525101857 0.090510043 234.3871516 390118.1682 0.025865634 0.028477559 967.9618348 -2.985858234 0.194698413 ALTLDQWLEQHKGDFNLL ddPTM_BT-474_Pertuzumab_2h_R1 2 ALTLDQWLEQHKGDFNLL 18 1 I3L1Y8;Q9HBL8;I3L3Z0 I3L1Y8 NMRAL1 NmrA-like family domain-containing protein 1 0 ; 242.26 4.53E-24 503260000 683720 759930 520170 593750 649460 712870 674510 672940 823480 766300 FALSE TRUE 656999.4665 738257.5404 614176.2901 624393.5087 670350.4707 727284.7198 682764.8551 659043.5538 730002.0027 714397.8185 0.919654917 1.033398369 0.859711878 0.874013739 0.93834339 1.018038831 0.955720801 0.92251619 1.02184243 1 19.44636815 2.985900534 24.40308628 0.972530436 0.922862756 0.235020131 0.051617753 913.9427384 1581839.051 0.016210944 0.017839314 968.0561172 -2.985900534 -0.04966768 HATLQK ddPTM_BT-474_Pertuzumab_2h_R1 6 HATLQK 6 0 Q13263;Q13263-2;M0R3C0 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;; 127.66 0.016964 2695230000 7028010 8609350 7811190 7971090 7226440 6475430 7747130 5930310 6839090 8165860 FALSE TRUE 6753347.599 8363819.767 9222845.792 8382478.91 7458885.005 6606367.631 7841941.694 5807847.026 6062745.175 7612779.029 0.887106742 1.098655266 1.211495271 1.101106295 0.979784777 0.867799736 1.030102367 0.762907606 0.796390536 1 22.85999177 2.98596722 2.789464704 0.878560896 1.085749406 0.388931349 0.106864991 0.260856548 4.097898097 0.03500026 0.040237008 968.2047737 -2.98596722 0.20718851 ENWLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENWLPR 6 0 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8 A0A590UJQ1 ITCH E3 ubiquitin-protein ligase Itchy homolog 0 100.74 0.086812 126680000 105720 135470 110040 134790 121490 96415 131950 125770 129350 141450 FALSE TRUE 101588.3455 131606.5282 129926.6758 141746.5281 125397.8362 98364.57736 133564.8436 123172.8055 114666.7303 131869.4655 0.770370496 0.998006079 0.985267327 1.0749003 0.950923974 0.745923834 1.012856487 0.934050996 0.869547244 1 17.00875102 2.986068343 24.99001096 0.911919791 0.968420646 0.040801564 0.099753249 2000.591002 3588582.486 0.029782059 0.032817487 968.4302411 -2.986068343 0.056500855 IQDFNDTFYR ddPTM_BT-474_Pertuzumab_2h_R1 3 IQDFNDTFYR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;; 159.79 1.76E-05 480500000 383920 403630 357350 396600 383450 330290 410070 396170 414230 434030 FALSE TRUE 368915.982 392118.8676 421931.0942 417068.5735 395784.0175 336968.6901 415088.5593 387988.9511 367208.347 404632.7615 0.911730381 0.969073454 1.042750697 1.030733577 0.97813142 0.832776587 1.025840216 0.958866874 0.907510172 1 18.62625361 2.986121704 24.61495986 0.946090858 0.992722101 0.11024384 0.059012393 1183.093913 2098375.061 0.017948628 0.019783575 968.5492384 -2.986121704 0.046631244 AGHLILQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGHLILQDR 9 0 Q96P11-2;Q63ZY6;Q63ZY6-6;Q96P11-5;Q96P11;Q96P11-4;Q63ZY6-5;Q96P11-3;Q63ZY6-2 Q96P11-2 NSUN5;NSUN5P2 Probable 28S rRNA (cytosine-C(5))-methyltransferase;Putative methyltransferase NSUN5C 0 ; 104.17 0.0033041 361600000 216660 228780 198280 211006 198627 147986 215930 164680 206124 221967 FALSE TRUE 208192.6877 222255.4184 234113.6067 221896.0449 205016.0178 150978.3783 218572.6159 161279.3005 182725.6677 206932.9774 1.006087528 1.074045429 1.131349917 1.072308763 0.990736326 0.729600377 1.05624835 0.779379403 0.883018598 1 17.65880405 2.986159373 6.572605762 0.879676413 1.070910304 0.458174305 0.092828706 0.125351636 24.91173 0.026252411 0.029390602 968.6332506 -2.986159373 0.191233891 ELALGQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELALGQDR 8 0 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ; 135 0.0019835 783610000 689810 732980 596660 646250 642580 467780 692430 636090 651800 652270 FALSE TRUE 662851.4626 712076.1281 704489.7346 679603.0399 663249.1693 477238.8321 700904.1655 622954.5192 577810.3966 608091.1719 1.090052764 1.171002246 1.158526496 1.117600569 1.090706789 0.784814604 1.152630062 1.02444263 0.95020356 1 19.21392812 2.986208059 24.70431411 0.995092284 1.134336429 0.405697907 0.087238784 601.4895537 1077399.145 0.026022784 0.028713729 968.7418447 -2.986208059 0.139244145 IHDPQLLTER ddPTM_BT-474_Pertuzumab_2h_R1 6 IHDPQLLTER 10 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;;; 181.31 1.90E-06 5647590000 2885980 3126810 2560830 2951200 2644390 2324220 2958080 2005970 2793390 2914190 FALSE TRUE 2773192.711 3037636.44 3023628.946 3103511.786 2729449.206 2371217.321 2994281.868 1964546.019 2476296.078 2716809.316 1.020753534 1.118089673 1.112933811 1.142336994 1.004652476 0.872794902 1.102131773 0.723107804 0.911472168 1 21.37348188 2.986259418 3.688864767 0.905651492 1.100347364 0.426301905 0.095364758 0.20250477 5.979345115 0.029680283 0.033777491 968.8564122 -2.986259418 0.194695872 ASTAS(ph)PCNNNINAATAVALQEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASTASPCNNNINAATAVALQEPR 23 0 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 AS(0.141)T(0.141)AS(0.718)PCNNNINAATAVALQEPR 169.13 5.70E-12 318990000 44979 53960 52084 45492 57015 75647 59604 69087 73535 77423 TRUE FALSE 43221.17095 52421.11363 61496.7374 47839.84757 58848.93925 77176.63417 60333.45158 67660.32931 65187.61508 72179.07125 0.598804753 0.726264729 0.852002337 0.662793892 0.815318599 1.069238393 0.835885673 0.937395399 0.903137349 1 16.13929296 2.986271794 8.042634054 0.936123155 0.723183934 0.647694779 0.08286506 0.110960715 46.86488719 0.024153118 0.026958003 968.8840229 -2.986271794 -0.212939221 IHSEIVK ddPTM_BT-474_Pertuzumab_2h_R1 5 IHSEIVK 7 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;; 138.33 0.0027959 2835610000 4909080 5371930 4289790 4899740 4737300 3868680 5364260 3881490 5557660 5469060 FALSE TRUE 4717227.726 5218727.816 5065050.479 5152616.169 4889679.557 3946907.36 5429909.419 3801335.875 4926777.736 5098635.695 0.925194112 1.023553776 0.993412901 1.010587239 0.959017245 0.774110487 1.064973013 0.745559421 0.966293344 1 22.28167983 2.986509125 24.34919692 0.892364727 0.990300971 0.120653509 0.093886178 703.5451631 1269807.504 0.026253017 0.028996878 969.4136386 -2.986509125 0.097936243 SVSDQFYR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVSDQFYR 8 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54;H0YK11;H0YK29 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;; 152.63 0.0010562 1657720000 886160 947330 801010 877920 861410 690670 882710 875980 941580 976020 FALSE TRUE 851527.8875 920313.0759 945770.3254 923229.5564 889118.035 704635.8206 893512.869 857890.7069 834695.7858 909913.2961 0.935834097 1.011429419 1.039407084 1.014634648 0.977145887 0.774398862 0.981975835 0.942826872 0.917335519 1 19.79536955 2.986583776 24.89335365 0.92155935 1.002908315 0.262085975 0.061620347 785.3892961 1457266.965 0.01827143 0.020187287 969.5802851 -2.986583776 0.081348965 YSPDEMNNS(ph)PNFEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSPDEMNNSPNFEEK 15 0 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 1 YSPDEMNNS(1)PNFEEK;YSPDEMNNS(1)PNFEEK 221.47 1.61E-12 199634000 384160 339750 353620 347530 403650 451440 421020 481970 539270 533320 TRUE FALSE 369146.6025 330060.6627 417527.0002 365466.0649 416633.7688 460568.4261 426172.5687 472017.1511 478054.3304 497197.7614 0.742454273 0.663841812 0.839760419 0.73505171 0.837963887 0.926328439 0.85714901 0.94935494 0.961497351 1 18.92346028 2.986698251 0.409043276 1.002267192 0.665279461 0.806322143 0.046229407 0.620987018 0.197507641 0.043246355 0.086396015 969.8358895 -2.986698251 -0.336987731 FKRPQFS(ph)PTGDCQAEAAAAANGTGGEEDDGPAAELLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKRPQFSPTGDCQAEAAAAANGTGGEEDDGPAAELLEK 38 2 Q7Z4Q2 Q7Z4Q2 HEATR3 HEAT repeat-containing protein 3 1 FKRPQFS(0.5)PT(0.5)GDCQAEAAAAANGT(0.001)GGEEDDGPAAELLEK;FKRPQFS(0.951)PT(0.049)GDCQAEAAAAANGTGGEEDDGPAAELLEK 402.03 3.16E-199 673150000 272620 250490 195666 170554 228141 263517 225335 257928 302427 283110 TRUE FALSE 261965.709 243346.2705 231027.1988 179356.3124 235479.3625 268845.4943 228092.7171 252601.6967 268096.7548 263934.7075 0.992539827 0.921994204 0.87531951 0.679548037 0.892187938 1.018606067 0.864201299 0.957061309 1.015769231 1 18.00982155 2.986712549 24.65519588 0.958333157 0.86107842 0.250258882 0.084663569 836.8627962 1552823.311 0.026600892 0.029418463 969.8678189 -2.986712549 -0.097254738 TEYNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEYNLR 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 129.2 0.037913 305940000 815440 916150 731430 830350 807490 658220 906310 786720 812510 903690 FALSE TRUE 783571.7033 890022.299 863615.6716 873204.463 833463.6492 671529.6594 917401.6929 770473.9571 720277.2711 842482.2714 0.930075006 1.05642852 1.025084682 1.036466277 0.989295179 0.797084618 1.088927001 0.914528392 0.854946502 1 19.6842868 2.98685948 24.63132088 0.933627543 1.015714898 0.190784034 0.079519106 835.0030728 1565180.943 0.022982413 0.025450803 970.1960015 -2.98685948 0.082087355 KVPLDER ddPTM_BT-474_Pertuzumab_2h_R1 4 KVPLDER 7 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 98.299 0.018222 4324410000 13204310 14779300 11257170 12485380 12598510 8914850 13909500 13208930 12948210 13685140 FALSE TRUE 12688270.97 14357808.83 13291591.03 13129751.96 13003752.52 9095114.375 14079728.62 12936160.98 11478383.48 12758233.28 0.994516301 1.125375945 1.041804985 1.029119916 1.019243984 0.712881962 1.103579807 1.013946108 0.899684403 1 23.60492523 2.986936274 24.97951488 0.955631898 1.049249795 0.190616745 0.099280862 1161.593849 2221121.742 0.030249327 0.033495856 970.3675713 -2.986936274 0.093617898 ILCAHGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILCAHGGR 8 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 102.71 0.0049121 132150000 87937 112240 88732 104230 95492 72880 114000 79804 89543 112720 FALSE TRUE 84500.32482 109039.0251 104767.8462 109609.3228 98563.5869 74353.68353 115395.1661 78156.01951 79378.45403 105085.374 0.804111187 1.037623229 0.996978383 1.043050223 0.937938204 0.707555016 1.098108725 0.74373832 0.755371095 1 16.68120236 2.987082218 24.46678561 0.853316076 0.978804958 0.141357222 0.127562391 790.3884738 1497031.033 0.036679821 0.040667101 970.6937147 -2.987082218 0.125488882 EFLLSLDDSVDETEAVKR ddPTM_BT-474_Pertuzumab_2h_R1 4 EFLLSLDDSVDETEAVKR 18 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A286YEP7;H7C0U8 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;; 296.23 3.96E-49 928010000 837673 734659 615371 723283 795325 796073 789193 933795 926691 864700 FALSE TRUE 804935.8131 713707.2446 726582.2286 760611.7223 820907.3509 812170.1415 798851.38 914511.8069 821496.9227 806133.0988 0.998514779 0.885346658 0.901317946 0.94353119 1.018327311 1.007488891 0.990967101 1.134442697 1.019058669 1 19.62065853 2.987322134 1.197338057 1.052760126 0.922042924 0.470283811 0.04825915 0.346587829 1.050207688 0.020862415 0.024956874 971.2301015 -2.987322134 -0.130717202 LYELIITR ddPTM_BT-474_Pertuzumab_2h_R1 1 LYELIITR 8 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 124.98 0.0029812 132630000 160710 159710 140690 156890 151720 86149 189660 163190 155580 168360 FALSE TRUE 154429.2755 155155.2272 166115.8126 164987.1117 156600.2116 87890.99181 191981.1158 159820.0695 137919.2106 156956.8272 0.983896516 0.988521684 1.058353533 1.051162378 0.997727938 0.559969218 1.223146003 1.018242228 0.878707942 1 17.26000826 2.987368616 24.95843741 0.94891092 1.021348026 0.060002096 0.156065498 2276.755124 4498669.156 0.047907361 0.053214727 971.3340553 -2.987368616 0.072437106 NFQNIFPPSATLHLSNIPPSVSEEDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NFQNIFPPSATLHLSNIPPSVSEEDLK 27 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 84.524 0.0051213 520890000 327030 371280 281880 297710 273710 227650 196950 211330 247650 278100 FALSE TRUE 314249.306 360691.4579 332821.9864 313074.8488 282514.1307 232253.239 199360.333 206965.9616 219537.8102 259264.0393 1.212082119 1.39121283 1.283718279 1.207552153 1.089677271 0.895817405 0.768947107 0.798282562 0.846773084 1 17.98406259 2.987368826 1.571000302 0.827296139 1.300772971 0.876242278 0.073257313 0.108910481 0.549376688 0.025947526 0.030563048 971.334525 -2.987368826 0.473476833 QDLPALEEKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 QDLPALEEKPR 11 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 174.05 1.05E-05 4360050000 2669130 2491830 2329050 2501610 2624420 2713270 2802020 2972850 3361010 3160710 FALSE TRUE 2564817.449 2420765.448 2749961.144 2630718.392 2708836.853 2768134.178 2836311.959 2911459.609 2979482.235 2946632.296 0.870423314 0.821536318 0.933255618 0.892788148 0.919299247 0.939423009 0.962560535 0.988063428 1.011148299 1 21.49063561 2.987492188 0.454653199 1.013984662 0.836088031 0.827575702 0.023738064 0.491649657 0.20015286 0.021098405 0.038191931 971.6104743 -2.987492188 -0.177896631 SELNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SELNLR 6 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ;;; 135.5 0.031577 5254750000 2437660 2560620 1993470 2407150 2248680 1834220 2270750 2325220 2253090 1947670 FALSE TRUE 2342393.552 2487593.625 2353734.374 2531383.3 2321010.834 1871309.185 2298540.118 2277203.394 1997328.669 1815752.576 1.290040054 1.370006937 1.296285851 1.39412348 1.278263826 1.030597015 1.265888397 1.254137499 1.10000046 1 20.7921362 2.987717887 23.37155721 1.164745343 1.3368781 0.54969964 0.087043474 217.4856155 413854.406 0.025854646 0.028785899 972.1155436 -2.987717887 0.172132757 LPGIALELS(ph)ELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPGIALELSELR 12 0 P25391 P25391 LAMA1 Laminin subunit alpha-1 1 LPGIALELS(1)ELR 63.624 0.044676 762250000 410040 411730 369350 452570 407700 375400 418020 402050 435370 505520 TRUE FALSE 394015.1835 399987.8635 436099.7611 475927.1919 420814.0408 382990.8452 423135.8538 393747.527 385948.6228 471280.6801 0.83605206 0.848725357 0.92535039 1.00985933 0.89291596 0.812659762 0.897842563 0.835484126 0.818935804 1 18.84622701 2.987829653 24.56944069 0.861790829 0.908550768 0.035154877 0.066876569 1166.77239 2355482.057 0.020002489 0.022300475 972.3657495 -2.987829653 0.046759939 LIDDYGVEEEPAELPEGTSLTVDNKR ddPTM_BT-474_Pertuzumab_2h_R1 3 LIDDYGVEEEPAELPEGTSLTVDNKR 26 1 Q00577 Q00577 PURA Transcriptional activator protein Pur-alpha 0 ;; 190.24 1.20E-17 391320000 224300 216180 187975 205058 221764 242497 240555 250295 272855 263202 FALSE TRUE 215534.108 210014.7581 221946.264 215641.068 228897.2405 247400.4555 243498.984 245126.3208 241881.6443 245375.0941 0.878386247 0.855892725 0.904518304 0.878822151 0.932846267 1.008254144 0.992354114 0.998986151 0.985762818 1 17.9046293 2.987925708 2.608266607 0.996972248 0.878865233 0.94908047 0.012838081 0.055345492 0.757211619 0.004095797 0.004726132 972.580836 -2.987925708 -0.118107016 T(ph)TPVDLCLLEESVGSLEGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPVDLCLLEESVGSLEGSR 20 0 Q9UKK3 Q9UKK3 PARP4 Poly [ADP-ribose] polymerase 4 1 T(0.5)T(0.5)PVDLCLLEESVGSLEGSR 84.14 0.031658 18511000 11497 11693 8963.7 12803 11100 10635 10290 10205 14421 14430 TRUE FALSE 11047.68453 11359.52709 10583.63999 13463.76436 11457.04158 10850.04699 10415.9321 9994.263184 12783.98854 13452.64325 0.821227793 0.844408558 0.786733119 1.000826686 0.851657282 0.80653644 0.774266581 0.742921893 0.950295663 1 13.71560205 2.988081538 24.74398391 0.824947997 0.865200863 0 0.091054168 1976.535208 4103507.006 0.026968396 0.030108993 972.9298716 -2.988081538 0.040252866 DAENHEAQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DAENHEAQLK 10 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 124.67 0.00042945 1022000000 638480 533290 490910 501950 565940 623900 616130 547910 763080 742950 FALSE TRUE 613527.4957 518081.0913 579628.3572 527855.6997 584143.9741 636515.6855 623670.3832 536595.467 676458.3575 692629.3347 0.885794847 0.747991841 0.836852163 0.762104163 0.843371692 0.91898459 0.900438881 0.774722409 0.976652769 1 19.40172397 2.988196952 7.259114006 0.888266564 0.805416044 0.320017141 0.068488205 0.212356133 65.27871662 0.02021178 0.022673851 973.1884631 -2.988196952 -0.08285052 IVEDEPNKICEADR ddPTM_BT-474_Pertuzumab_2h_R1 6 IVEDEPNKICEADR 14 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ;;;;; 219.52 4.54E-12 11923490000 9147700 8614700 6712360 6888300 8007830 8734960 8152040 8854880 10568130 9056930 FALSE TRUE 8790197.771 8369017.191 7925432.768 7243805.988 8265409.124 8911586.876 8251807.104 8672023.634 9368480.188 8443496.064 1.041061393 0.991179143 0.938643508 0.857915481 0.978908388 1.055438033 0.977297442 1.027065515 1.109549897 1 23.00940905 2.988249183 24.67162471 1.02880046 0.953315326 0.31266381 0.054004169 623.2145842 1308484.836 0.016895216 0.018863799 973.3055118 -2.988249183 -0.075485134 EQPEMEDANS(ph)EK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQPEMEDANSEK 12 0 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 EQPEMEDANS(1)EK;EQPEMEDANS(1)EK 235.71 4.92E-16 237120000 263771 274650 301170 313730 351210 336770 446470 441110 548210 564930 TRUE FALSE 253462.5377 266817.2509 355598.1185 329921.6429 362506.9886 343579.7201 451934.0334 432000.9244 485979.4991 526666.7879 0.481257872 0.506614917 0.675186145 0.626433355 0.68830425 0.652366407 0.858102398 0.820254731 0.922745672 1 19.00653096 2.988314501 0.264186626 1.04511852 0.336915426 0.90747366 0.049741268 0.977096258 0.127282652 0.080540504 0.225979228 973.4519082 -2.988314501 -0.708203093 down VDDSSGSIGRR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDDSSGSIGRR 11 1 P41250 P41250 GARS Glycine--tRNA ligase 0 117.94 0.0012613 207350000 185560 205290 111400 124360 165050 329620 152070 175300 160660 135180 FALSE TRUE 178308.1101 199435.3302 131532.4581 130778.2345 170358.9831 336285.1422 153931.0781 171679.9937 142422.5503 126024.1382 1.414872679 1.582516913 1.043708451 1.037723696 1.351796454 2.668418503 1.221441228 1.362278657 1.1301212 1 16.94334056 2.988317654 24.97376948 1.520242545 1.265763095 0.039852339 0.45598977 1796.311447 3840049.271 0.140246048 0.156771561 973.458975 -2.988317654 -0.254479451 T(ph)MIISPERLDPFADGGKTPDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.5)MIIS(0.5)PERLDPFADGGKTPDPK;T(0.545)MIIS(0.455)PERLDPFADGGKTPDPK 114.91 0.00028551 264830000 630550 662610 414990 385450 531590 642820 506880 580750 718910 578630 TRUE FALSE 605907.4089 643713.0116 489987.9244 405343.1207 548689.0751 655818.2608 513083.3491 568757.3096 637302.3507 539438.8747 1.123217916 1.193301117 0.908328909 0.751416221 1.017147819 1.215741563 0.951142702 1.054349874 1.181417174 1 19.04109997 2.988364617 24.98327441 1.075171605 0.987436677 0.087715265 0.132399367 1596.082959 3427090.439 0.042489923 0.047525806 973.5642477 -2.988364617 -0.087734928 ANWEAQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ANWEAQQR 8 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 88.358 0.034132 340570000 127490 144520 127650 121020 121280 61627 139340 108420 107300 124510 FALSE TRUE 122507.5499 140398.4311 150719.1946 127265.8567 125181.0813 62873.14016 141045.2846 106181.0891 95119.75384 116076.8268 1.055400576 1.209530231 1.298443442 1.096393313 1.078433007 0.541651093 1.215102863 0.914748379 0.819455153 1 16.82472046 2.988388659 24.27561202 0.910124094 1.166381499 0.363494989 0.167815852 428.4450803 895745.7193 0.049126978 0.054946841 973.6181448 -2.988388659 0.256257405 KISELDAFLKEPALNEANLSNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KISELDAFLKEPALNEANLSNLK 23 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 264.08 3.56E-44 1070280000 1653910 1397970 1009920 998170 1302910 1502910 1301940 1471360 1888870 1589100 FALSE TRUE 1589273.369 1358101.264 1192435.01 1049685.673 1344819.283 1533299.87 1317873.531 1440975.902 1674453.396 1481468.842 1.072768677 0.916726175 0.804900499 0.708543875 0.907760761 1.034986243 0.889572223 0.972667032 1.130265686 1 20.49859685 2.988402381 24.66182637 0.989562338 0.865421825 0.259338996 0.103029878 715.9914653 1522529.166 0.032348911 0.036167399 973.6489069 -2.988402381 -0.124140513 KINS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_BT-474_Pertuzumab_2h_R1 2 KINSSPNVNTTASGVEDLNIIQVTIPDDDNER 32 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 KINS(0.492)S(0.492)PNVNT(0.013)T(0.002)ASGVEDLNIIQVTIPDDDNER;KINS(0.482)S(0.482)PNVNT(0.026)T(0.005)AS(0.005)GVEDLNIIQVTIPDDDNER 114.03 1.17E-06 370100000 337770 324915 280566 290194 311462 342441 310810 324264 360610 368054 TRUE FALSE 324569.575 315648.7423 331270.5174 305170.9471 321480.4581 349365.3916 314613.7858 317567.8351 319675.0646 343125.3748 0.945921225 0.91992247 0.965450362 0.889386124 0.936918345 1.018185822 0.916906207 0.925515448 0.93165673 1 18.38837629 2.988441055 24.76660132 0.951052233 0.929607365 0.113016589 0.035156044 1457.612314 3123146.374 0.010625381 0.011892016 973.735616 -2.988441055 -0.021444868 IFPMGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFPMGDR 7 0 P49720;A0A087WXQ8;A0A087WY10;A0A087WUL2 P49720 PSMB3 Proteasome subunit beta type-3 0 ; 110.23 0.015936 315240000 196975 228350 193481 212425 197740 124309 233291 175513 171412 226250 FALSE TRUE 189276.9992 221837.6816 228447.3207 223388.2797 204100.4867 126822.6132 236146.085 171888.5952 151954.0284 210925.886 0.897362589 1.051732842 1.083069153 1.059084231 0.96764077 0.601266234 1.119569009 0.814924135 0.720414318 1 17.68637664 2.988463336 24.7446217 0.852704598 1.02720462 0.253499459 0.140235382 661.2801445 1418362.748 0.040326864 0.045113091 973.7855724 -2.988463336 0.174500022 AWEEYYK ddPTM_BT-474_Pertuzumab_2h_R1 6 AWEEYYK 7 0 A0A087WTP3;Q92945;M0R3J3;M0R251;M0QYG1;M0R263;M0R0C6;Q96AE4;E9PEB5;Q96AE4-2 A0A087WTP3;Q96AE4 KHSRP;FUBP1 Far upstream element-binding protein 2;Far upstream element-binding protein 1 0 ;;;;; 154.68 0.0038667 10129000000 4655180 4635460 4156930 4282260 4340350 2734690 4888820 4698540 4797460 4876110 FALSE TRUE 4473250.419 4503261.219 4908179.721 4503267.952 4479961.3 2789987.305 4948650.842 4601513.507 4252872.453 4545846.727 0.98403019 0.990631997 1.079706382 0.990633478 0.985506457 0.613744253 1.08860926 1.012245635 0.935551221 1 22.11611761 2.988532791 24.88464044 0.93566151 1.011342814 0.09383086 0.119710354 1494.127753 3242369.183 0.037144698 0.041578873 973.941318 -2.988532791 0.075681305 TLYDHVDEVTCLAFHPTEQILASGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLYDHVDEVTCLAFHPTEQILASGSR 26 0 Q05048;A0A0A0MSZ9 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 ; 204.31 2.22E-25 422670000 199956 214370 194973 190152 180585 87218 240331 96001 193296 185003 FALSE TRUE 192141.4985 208256.3775 230208.9583 199965.7675 186393.6805 88981.60772 243272.2427 94018.5458 171353.8484 172472.582 1.11404083 1.20747527 1.334756838 1.159406122 1.08071485 0.515917409 1.410498062 0.545121692 0.993513557 1 17.39600751 2.988673145 20.57957559 0.873516752 1.201837623 0.269963903 0.24117935 63.20574744 114840.3721 0.067532394 0.075642109 974.2561247 -2.988673145 0.328320871 YYPTEDVPRK ddPTM_BT-474_Pertuzumab_2h_R1 4 YYPTEDVPRK 10 1 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 179.1 3.44E-06 2585080000 1827720 2054390 1418020 1595130 1776660 2109230 1858790 1932610 2139470 1980720 FALSE TRUE 1756290.682 1995800.809 1674287.758 1677454.85 1833807.882 2151880.076 1881538.428 1892700.928 1896606.335 1846564.07 0.951112778 1.080818608 0.906704395 0.908419522 0.993091933 1.165342763 1.018940235 1.024985246 1.027100205 1 20.81641189 2.98872789 24.93383746 1.047920676 0.964387516 0.301751094 0.061705678 698.8242985 1545799.208 0.018736858 0.021014177 974.3789437 -2.98872789 -0.08353316 DGKDQGVNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGKDQGVNVR 10 1 Q9H201;I6L9I8;Q9H201-2;D6RFG3;D6REL6;Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9H201;Q9Y6I3 EPN3;EPN1 Epsin-3;Epsin-1 0 81.625 0.01865 212510000 468810 473820 308540 264380 388920 452460 366310 489820 454960 470770 FALSE TRUE 450488.3869 460307.1175 364300.0414 278024.6835 401429.965 461609.0512 370793.0114 479705.0458 403314.8481 438884.3286 1.026439901 1.048811925 0.830059352 0.633480545 0.914660057 1.051778387 0.844853615 1.093010196 0.918954772 1 18.74348123 2.988876949 24.91538933 0.984601773 0.877711716 0.121228028 0.123958151 1110.45858 2487410.294 0.039351614 0.044141524 974.7134281 -2.988876949 -0.106890057 YSSSFCTHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSSSFCTHDR 10 0 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 0 ; 188.28 1.14E-06 1277750000 1061130 1218840 818130 1071160 959580 620010 1067710 843120 805270 941580 FALSE TRUE 1019659.866 1184079.877 965984.2902 1126442.696 990445.7622 632547.027 1080776.954 825709.2774 713859.1256 877805.9479 1.161600544 1.348908468 1.100453116 1.283247965 1.128319721 0.720600069 1.231225372 0.940651267 0.813231133 1 19.74354252 2.988910943 23.57950717 0.958225458 1.221472536 0.482266034 0.138693393 222.475907 473070.2747 0.039597629 0.044425814 974.7897255 -2.988910943 0.263247078 DHANEELDELKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DHANEELDELKR 12 1 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 151.74 4.49E-05 310920000 348520 367520 301240 345350 327200 247900 359550 252740 421700 387560 FALSE TRUE 334899.4531 357038.6894 355680.769 363173.5549 337724.6852 252912.7078 363950.2805 247520.8307 373830.3839 361310.216 0.926902806 0.988177676 0.984419353 1.005157172 0.934722214 0.699987702 1.007306919 0.685064578 1.034652128 1 18.46287852 2.988972956 24.31788378 0.856968286 0.976652989 0.097757532 0.115024265 580.6642164 1280540.814 0.031792668 0.035684256 974.9289269 -2.988972956 0.119684703 LIQSHPESAEDLQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LIQSHPESAEDLQEK 15 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 188 3.17E-07 500990000 170350 160660 131580 146150 160250 182590 165370 173730 211800 187130 FALSE TRUE 163692.5337 156078.1341 155359.433 153692.819 165404.5868 186282.0949 167393.8475 170142.4148 187757.3519 174455.5184 0.938305278 0.894658624 0.890538943 0.880985711 0.948118972 1.067791358 0.959521654 0.975276772 1.076247709 1 17.41249971 2.989015215 6.020793198 1.006747384 0.901181428 0.678077145 0.037126348 0.100071809 14.40573456 0.011275523 0.012699129 975.023796 -2.989015215 -0.105565956 ILPEAHQR ddPTM_BT-474_Pertuzumab_2h_R1 4 ILPEAHQR 8 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;; 163.04 0.00056435 619440000 1125910 1214230 1020250 1059640 1073090 798570 1219090 1033800 1107080 1217720 FALSE TRUE 1081908.192 1179601.349 1204631.87 1114328.147 1107606.914 814717.6325 1234009.588 1012451.669 981408.9197 1135242.74 0.953019257 1.039074119 1.061122726 0.981576986 0.975656461 0.717659408 1.087000643 0.891837167 0.864492575 1 20.11456938 2.98921107 24.82089628 0.911818962 1.010113125 0.196178357 0.092906538 758.9629126 1746068.11 0.026755141 0.030079179 975.4636041 -2.98921107 0.098294163 DIEEHLQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DIEEHLQR 8 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;;; 130.96 0.0010254 1674690000 1560350 1813370 1498370 1632680 1623880 1472250 1799150 1599410 1774980 1883150 FALSE TRUE 1499369.797 1761654.463 1769158.79 1716942.81 1676113.575 1502019.904 1821168.536 1566381.625 1573491.712 1755602.573 0.85404853 1.003447187 1.007721689 0.977979206 0.954722669 0.855558044 1.0373467 0.892218802 0.896268743 1 20.74353486 2.989325834 24.64902713 0.932051235 0.967091295 0.027507372 0.063476122 1330.130087 3071577.51 0.018271045 0.020538348 975.7214085 -2.989325834 0.03504006 GGGHVAQIYAIR ddPTM_BT-474_Pertuzumab_2h_R1 4 GGGHVAQIYAIR 12 0 P62249;M0R210;M0R3H0;M0R1M5;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ;;; 152.62 6.22E-05 2632710000 2083930 2397280 2041890 2107690 2064930 1365660 2249210 2033420 1981160 2240500 FALSE TRUE 2002487.712 2328911.922 2410904.945 2216468.133 2131350.349 1393274.581 2276736.505 1991429.166 1756267.023 2088748.939 0.958701965 1.114979344 1.154233953 1.061146264 1.020395658 0.66703784 1.090000077 0.953407625 0.84082246 1 20.99420767 2.989344477 24.80091059 0.917987839 1.076121273 0.316320878 0.113191099 580.2077873 1350448.309 0.033409082 0.037585266 975.7632933 -2.989344477 0.158133435 GQYTHK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQYTHK 6 0 F5GWE5;Q00169;I3L4H1;I3L471;I3L4U7;A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7 F5GWE5;A0A0A0MSW4 PITPNA;PITPNB Phosphatidylinositol transfer protein alpha isoform;Phosphatidylinositol transfer protein beta isoform 0 ; 72.234 0.086135 293870000 420390 396320 347220 374110 368150 230550 415000 356060 386550 446110 FALSE TRUE 403960.694 385017.3416 409970.3779 393417.8619 379991.8791 235211.879 420078.8941 348707.2366 342670.4645 415894.5723 0.97130552 0.925757072 0.985755538 0.94595575 0.913673571 0.565556501 1.010061016 0.83845104 0.82393589 1 18.66585833 2.989366167 24.90243766 0.840223137 0.953591504 0.16763365 0.115006564 838.5840471 1963812.716 0.033001849 0.037158669 975.8120274 -2.989366167 0.113368367 SNLDEEVNVIPPHT(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNLDEEVNVIPPHTPVR 17 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 SNLDEEVNVIPPHT(1)PVR;SNLDEEVNVIPPHT(1)PVR 151.3 9.39E-07 666770000 297770 307440 239960 327700 280010 207539 265480 301460 260220 317680 TRUE FALSE 286132.8192 298672.1122 283326.1099 344612.6363 289016.7759 211735.5808 268729.0237 295234.7457 230680.9165 296163.2506 0.966132086 1.008471212 0.956655187 1.163590133 0.975869813 0.714928609 0.907367889 0.996864888 0.778897841 1 18.17603311 2.9894302 24.96662397 0.886909505 1.024320764 0.332072788 0.097032911 629.992849 1488092.957 0.029069211 0.032717954 975.9559144 -2.9894302 0.13741126 LKGSGNLEAIHIIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKGSGNLEAIHIIK 14 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 92.468 0.0029723 2243050000 3183400 3207900 2588000 2627800 2979000 3423400 3115500 3173100 3563300 3453600 FALSE TRUE 3058989.209 3116413.833 3055709.17 2763421.073 3074822.24 3492623.494 3153628.421 3107574.376 3158809.123 3219684.596 0.950089711 0.967925193 0.949070966 0.858289373 0.955007284 1.084771936 0.97948365 0.965179751 0.981092722 1 21.61848794 2.989525229 24.98520454 0.997676914 0.931651159 0.404014934 0.040736007 574.187972 1369600.964 0.012786565 0.014401864 976.1694877 -2.989525229 -0.066025755 LMELYER ddPTM_BT-474_Pertuzumab_2h_R1 1 LMELYER 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 120.62 0.02811 0 176060 175370 152250 173330 166050 132830 169600 169550 190110 199390 FALSE TRUE 169179.3806 170368.6193 179764.9618 182275.5821 171391.1491 135515.9136 171675.6155 166048.7332 168529.5098 185885.1377 0.910128602 0.91652631 0.967075496 0.980581795 0.922027179 0.729030386 0.923557513 0.893286765 0.906632515 1 17.5040519 2.989555636 24.99704219 0.881356618 0.944321721 0.119093368 0.066042357 916.2679049 2192959.361 0.019329999 0.021779207 976.2378376 -2.989555636 0.062965103 T(ph)TPPPGRPPAPSSEEEDGEAVAH ddPTM_BT-474_Pertuzumab_2h_R1 5 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 T(0.842)T(0.158)PPPGRPPAPSSEEEDGEAVAH;T(0.5)T(0.5)PPPGRPPAPSSEEEDGEAVAH;T(0.717)T(0.283)PPPGRPPAPSSEEEDGEAVAH;T(0.5)T(0.5)PPPGRPPAPSSEEEDGEAVAH;T(0.5)T(0.5)PPPGRPPAPSSEEEDGEAVAH 127.53 7.41E-05 9065960000 929530 895500 767073 803740 871950 949980 875010 1022590 1072640 861830 TRUE FALSE 893202.94 869961.2168 905700.1545 845221.1177 899997.0636 969189.2465 885718.6341 1001473.159 950878.4041 803457.4865 1.111699069 1.082771934 1.127253364 1.051979889 1.120155178 1.206273216 1.102383946 1.24645445 1.183483159 1 19.61586216 2.989678592 23.15778397 1.16559625 1.093954566 0.102939188 0.065757981 283.8510709 636871.2163 0.018391526 0.020739409 976.5142658 -2.989678592 -0.071641684 GNFNYIEFTR ddPTM_BT-474_Pertuzumab_2h_R1 4 GNFNYIEFTR 10 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;; 204.52 4.31E-07 3607700000 2885260 3173350 2544680 2879000 2795960 2217700 2875480 2921790 2979490 3039460 FALSE TRUE 2772500.849 3082849.165 3004560.282 3027585.535 2885894.593 2262543.413 2910670.984 2861454.015 2641270.786 2833594.667 0.978439465 1.087964062 1.06033524 1.068461051 1.018457095 0.798471087 1.027200897 1.009831804 0.932127244 1 21.43420197 2.989758307 24.98034317 0.959260109 1.051301072 0.325015139 0.06515486 616.9250133 1504736.964 0.019644666 0.022170698 976.6935209 -2.989758307 0.092040963 GGGPGKS(ph)PTQGST ddPTM_BT-474_Pertuzumab_2h_R1 2 GGGPGKSPTQGST 13 1 Q6P582 Q6P582 MZT2A Mitotic-spindle organizing protein 2A 1 GGGPGKS(0.59)PT(0.137)QGS(0.137)T(0.137);GGGPGKS(0.715)PT(0.282)QGS(0.001)T(0.001) 107.75 0.00090688 193730000 532170 534280 446160 475210 513640 580010 552460 556230 592850 610760 TRUE FALSE 511372.2081 519042.8575 526791.0368 499735.645 530161.6971 591738.1996 559221.1707 544743.6561 525552.1534 569392.6812 0.898101126 0.911572759 0.925180555 0.877664328 0.931100301 1.039244478 0.982136211 0.956709972 0.923004757 1 19.11906442 2.989944769 24.63536281 0.976930517 0.905192133 0.596821663 0.030012497 304.4988485 746026.2844 0.009189329 0.010377371 977.1129502 -2.989944769 -0.071738384 FRAPELLFRPDLIGEESEGIHEVLVFAIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 FRAPELLFRPDLIGEESEGIHEVLVFAIQK 30 2 P61163;R4GMT0 P61163 ACTR1A Alpha-centractin 0 ; 130.12 5.66E-06 581170000 490280 527320 320430 382250 442000 608230 457110 448480 527460 460180 FALSE TRUE 471119.3156 512281.3499 378338.8289 401977.9683 456217.3314 620528.8273 462704.2489 439218.7313 467584.9521 429011.5987 1.098150532 1.194096736 0.881884849 0.936986248 1.063414912 1.446415037 1.078535523 1.023792207 1.089912146 1 18.71065713 2.990038748 24.77658348 1.130153911 1.025608597 0.103617603 0.13954169 1068.437203 2657528.877 0.044062987 0.049818022 977.3244135 -2.990038748 -0.104545314 KVNNADDFPNLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVNNADDFPNLFR 13 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 226.59 1.69E-11 1287760000 1990180 2251800 1492000 1583150 1899630 2351800 2150600 1960730 2301500 2076430 FALSE TRUE 1912401.565 2187580.869 1761637.589 1664856.561 1960733.324 2399355.007 2176919.686 1920240.24 2040243.369 1935791.547 0.987917097 1.130070473 0.910034757 0.860039173 1.012884537 1.239469721 1.124563071 0.991966435 1.053958197 1 20.88449218 2.990082706 24.99684312 1.082449362 0.973575837 0.245170483 0.091569671 755.6712391 1904698.292 0.029220549 0.033044454 977.4233414 -2.990082706 -0.108873525 KNVFIIGATNRPDIIDPAILRPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KNVFIIGATNRPDIIDPAILRPGR 24 3 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 197.86 7.97E-25 13602590000 10707650 11504300 8835880 10341620 10728520 12270750 11169490 11397690 13054540 12327040 FALSE TRUE 10289183.2 11176208.63 10432720.07 10875352.25 11073612.59 12518872.97 11306185.56 11162323.72 11572643.35 11492118.6 0.895325184 0.972510728 0.907815211 0.946331362 0.963583215 1.08934422 0.983820821 0.971302517 1.007006954 1 23.45414145 2.990212821 16.65314009 1.00556686 0.934760123 0.528953926 0.035410154 5.226508166 8894.877551 0.010755671 0.012130849 977.7162216 -2.990212821 -0.070806737 IHPTSVISGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHPTSVISGYR 11 0 P17987;E7ERF2;F5H136;F5H676 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 192.5 1.37E-06 2361600000 479250 596560 531490 652590 561470 458710 636890 543090 567390 665580 FALSE TRUE 460520.3802 579546.6929 627542.0659 686270.2481 579530.1925 467985.4305 644684.4503 531875.0017 502982.2659 620499.6738 0.742176668 0.933999996 1.01134955 1.105996147 0.933973404 0.754207376 1.038976292 0.857172089 0.810608429 1 19.24307093 2.990495454 24.73110829 0.8886234 0.960367877 0.047744605 0.115005791 1127.452611 2933676.756 0.034412971 0.039041253 978.3527136 -2.990495454 0.071744476 FMEQSRS(ph)PSVSPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 FMEQSRSPSVSPSK 14 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 FMEQSRS(0.999)PSVSPSK;FMEQS(0.011)RS(0.988)PS(0.001)VSPSK 145.43 5.20E-06 870430000 892610 969540 649650 686530 826250 1045720 888120 795280 1074700 967850 TRUE FALSE 857725.8144 941889.6685 767056.2064 721961.8956 852827.0816 1066865.175 898989.0782 778857.1901 952704.5615 902296.6574 0.950602895 1.043880259 0.850115314 0.800138058 0.945173713 1.182388482 0.996334266 0.863194143 1.055866221 1 19.78324232 2.990738945 24.99360445 1.003669913 0.910844805 0.221073759 0.094704116 876.7044376 2366046.962 0.030942897 0.035161402 978.9013891 -2.990738945 -0.092825107 SNSGRELT(ph)DEEILASVMIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.314)NS(0.314)GRELT(0.372)DEEILASVMIK 60.765 0.096979 19752000 65733 66775 44711 48209 57738 65113 62581 61613 70482 68544 TRUE FALSE 63164.08169 64870.64238 52791.27229 50697.07227 59595.19521 66429.62947 63346.885 60340.67002 62481.17884 63901.45383 0.988460792 1.015166925 0.8261357 0.793363362 0.932610944 1.039563664 0.991321499 0.944276952 0.97777398 1 15.96356113 2.990774831 24.77679925 0.983932882 0.902291086 0.272899353 0.065459238 610.7142799 1640251.896 0.021426778 0.024351911 978.9822797 -2.990774831 -0.081641796 ICDPYAWLEDPDSEQTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ICDPYAWLEDPDSEQTK 17 0 P48147 P48147 PREP Prolyl endopeptidase 0 138.94 4.63E-06 58455000 106490 98521 75819 82758 92091 100440 87991 103950 110820 109260 FALSE TRUE 102328.2531 95711.27754 89521.17988 87029.1503 95053.19065 102470.9656 89067.86018 101803.3962 98240.1782 101859.7229 1.004599759 0.93963811 0.878867303 0.854401994 0.933177393 1.006000829 0.874416871 0.999447017 0.964465398 1 16.63622417 2.990790033 24.85807179 0.964120573 0.914912896 0.172741234 0.050943148 760.1365832 2051649.013 0.015339404 0.017437112 979.016549 -2.990790033 -0.049207677 EKLQGQDSER ddPTM_BT-474_Pertuzumab_2h_R1 3 EKLQGQDSER 10 1 A0A0C4DGG1;Q9UKS6;E9PIY1;E9PJ75;E9PNM9 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ;; 126.12 0.00035664 516348000 654920 774620 563060 702790 705680 818090 800320 861650 908640 833030 FALSE TRUE 629325.0023 752528.596 664817.4672 739061.0761 728378.8381 834632.3403 810114.5556 843856.6264 805494.9965 776608.1361 0.810350772 0.968993964 0.856052668 0.951652502 0.937897511 1.074714906 1.043144564 1.086592565 1.037196186 1 19.5668273 2.990813294 1.675069714 1.057591598 0.891788819 0.694483623 0.047779193 0.183970397 1.049748019 0.015712308 0.018500741 979.0689878 -2.990813294 -0.165802779 LFYADHPFIFLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFYADHPFIFLVR 13 0 P50454;E9PKH2;H0YEP8 P50454 SERPINH1 Serpin H1 0 ; 191.26 3.72E-06 1482130000 944610 1222480 1106070 1098050 1039180 632400 1184700 842530 1110640 1268590 FALSE TRUE 907693.5969 1187616.067 1305961.453 1154720.492 1072606.168 645187.5613 1199198.713 825131.4611 984564.8034 1182667.269 0.767497013 1.004184438 1.104250948 0.976369704 0.906938237 0.545535991 1.013978102 0.6976869 0.832495182 1 20.17361281 2.990859215 24.05267337 0.799337365 0.971790659 0.169183598 0.149176232 382.963765 1007720.756 0.042022028 0.047756447 979.1725154 -2.990859215 0.172453294 HEDTNLASSTLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HEDTNLASSTLLR 13 0 P49407-2;P49407;H0YET9 P49407-2 ARRB1 Beta-arrestin-1 0 ; 119.17 0.00036996 573490000 324530 318520 343300 402400 344620 310290 387480 276710 400510 457880 FALSE TRUE 311847.0088 309436.1215 405341.9467 423167.9122 355705.0153 316564.2764 392222.0961 270995.8418 355045.7839 426867.3798 0.730547762 0.724899901 0.949573488 0.99133345 0.833291631 0.741598659 0.918838297 0.634847858 0.831747284 1 18.70342839 2.990879765 24.57137166 0.796068179 0.855510125 0 0.121187096 1283.27212 3457358.024 0.036750061 0.041817016 979.218849 -2.990879765 0.059441947 KYPNKYESIIATLCENLDSLDEPDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KYPNKYESIIATLCENLDSLDEPDAR 26 2 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01 P63010 AP2B1 AP-2 complex subunit beta 0 218.93 1.89E-34 252030000 282630 282900 258110 255230 280120 325080 306270 292950 328400 319030 FALSE TRUE 271584.5071 274831.969 304756.2186 268402.4509 289130.3142 331653.3403 310018.2239 286900.4801 291121.4088 297421.8139 0.913129079 0.924047787 1.024659942 0.90243028 0.972122086 1.115094202 1.042352004 0.964624875 0.9788166 1 18.18215094 2.990904677 24.92402693 1.018248477 0.944753828 0.365005536 0.04932401 521.8234244 1429963.937 0.015440336 0.017549679 979.2750216 -2.990904677 -0.073494648 ASHTAPQVLFSHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASHTAPQVLFSHR 13 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 177.42 8.94E-06 1661548000 1354897 1615660 1407290 1489680 1360414 831097 1629357 1049738 1243456 1497230 FALSE TRUE 1301946.127 1569582.959 1661618.608 1566562.563 1404172.952 847902.3508 1649297.558 1028060.543 1102304.088 1395821.279 0.93274558 1.124487055 1.190423612 1.122323171 1.00598334 0.607457677 1.181596515 0.736527347 0.789717212 1 20.4126828 2.990933105 23.02847395 0.858652513 1.097072326 0.326408471 0.156251187 167.5873715 425649.8259 0.044248241 0.050277867 979.3391243 -2.990933105 0.238419813 EDLRVECSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDLRVECSK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 107.83 0.0024713 288370000 852940 893680 595120 670070 760680 856040 749100 825160 902080 869340 FALSE TRUE 819606.1618 868193.1214 702671.4224 704652.393 785147.963 873349.7153 758267.7099 808120.1576 799679.6602 810458.8275 1.011286612 1.071236554 0.867004465 0.869448724 0.96876971 1.077599115 0.935602999 0.997114388 0.98669992 1 19.62837937 2.990946093 24.68440099 0.996680428 0.952086787 0.0958927 0.064929532 1001.082041 2729344.678 0.020546956 0.023359074 979.3684137 -2.990946093 -0.04459364 LQDAEIAR ddPTM_BT-474_Pertuzumab_2h_R1 6 LQDAEIAR 8 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;; 171.53 0.00067197 14196030000 11525880 12272110 9979810 12179010 11298220 10325100 11888310 11735930 11575180 11872300 FALSE TRUE 11075435.87 11922121.44 11783383.67 12807570.17 11661637.51 10533880.6 12033802.69 11493578.94 10261214.09 11068178.55 1.000655692 1.077152974 1.064618141 1.157152472 1.053618485 0.95172666 1.087243275 1.038434544 0.927091486 1 23.39991449 2.990952267 24.92886423 1.012289212 1.078204992 0.284073532 0.054599906 615.354402 1695466.691 0.016341666 0.018576514 979.3823373 -2.990952267 0.065915779 EKIYVLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKIYVLLR 8 1 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 74.92 0.036234 660540000 934440 1157380 971380 1023960 969080 626970 1126460 886690 923840 993570 FALSE TRUE 897921.0517 1124372.656 1146929.974 1076806.698 1000251.338 639647.763 1140245.954 868379.5416 818969.5563 926274.6189 0.969389675 1.21386534 1.238218074 1.162513445 1.079864781 0.690559527 1.23100205 0.937496855 0.884154159 1 19.82108046 2.991087715 24.3344071 0.959515369 1.152901379 0.305764706 0.140929016 373.815605 1020684.386 0.040654824 0.046274978 979.6878333 -2.991087715 0.19338601 AHYEAEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHYEAEIK 8 0 M0QXG8;Q92990 M0QXG8 GLMN Glomulin 0 86.011 0.020225 0 74983 80796 64207 74378 71942 56199 85964 65088 81147 83992 FALSE TRUE 72052.58146 78491.77719 75810.63318 78216.65749 74256.07977 57335.38228 87016.05315 63743.91005 71935.53276 78303.14703 0.920174785 1.002408973 0.968168408 0.998895453 0.948315395 0.732223218 1.111271468 0.814065749 0.91867997 1 16.25678267 2.991097397 24.52645152 0.905566578 0.97417071 0.067644848 0.097048831 771.7768157 2126236.807 0.026946004 0.030683655 979.709676 -2.991097397 0.068604132 EVSTYIKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSTYIKK 8 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 149.94 0.00079724 2912000000 3472600 5117700 1841270 2241650 3657700 5762500 4114800 4498800 5331000 4568700 FALSE TRUE 3336886.953 4971748.207 2174028.448 2357341.825 3775353.242 5879021.698 4165158.153 4405898.208 4725847.229 4259257.88 0.783443277 1.167280392 0.510424236 0.553463043 0.88638757 1.380292498 0.977907014 1.03442861 1.1095471 1 22.02217065 2.99155116 24.8763146 1.091306902 0.760086734 0.41550631 0.194847099 402.0532675 1183789.48 0.059423047 0.06786764 980.7338379 -2.99155116 -0.331220167 DLDVSIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDVSIKR 8 1 O43747;O43747-2 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ; 96.711 0.014026 523960000 736850 814750 617050 656480 735340 818860 771710 813360 896320 879410 FALSE TRUE 708053.0874 791514.1277 728564.6612 690361.0115 758992.8789 835417.9102 781154.4178 796563.8318 794573.5113 819846.7774 0.863640752 0.965441531 0.888659541 0.842061017 0.925774059 1.018992735 0.952805377 0.971600857 0.969173184 1 19.64499478 2.991588258 24.42306138 0.97703468 0.893834038 0.619238921 0.034223912 211.5350057 614184.2959 0.010079963 0.01151551 980.8176176 -2.991588258 -0.083200642 SLDQEIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDQEIAR 8 0 P48681 P48681 NES Nestin 0 ; 113.89 0.0064252 1150920000 1104190 1228970 977640 1241110 1096030 984510 1081740 1088290 1114570 1104400 FALSE TRUE 1061037.034 1193920.979 1154321.295 1305163.836 1131284.8 1004417.467 1094978.658 1065816.431 988048.6863 1029598.004 1.030535247 1.159599158 1.121137853 1.2676441 1.098763591 0.975543331 1.063501146 1.03517725 0.959645106 1 19.97364973 2.991635478 24.68620232 1.017955101 1.148993358 0.534985012 0.060737944 271.2610046 800575.8126 0.017778373 0.020305777 980.9242652 -2.991635478 0.131038257 VARS(ph)PDKPGK ddPTM_BT-474_Pertuzumab_2h_R1 3 VARSPDKPGK 10 2 P55317-2;P55317;P55318 P55317-2 FOXA1;FOXA3 Hepatocyte nuclear factor 3-alpha;Hepatocyte nuclear factor 3-gamma 1 VARS(1)PDKPGK;VARS(1)PDKPGK;VARS(1)PDKPGK 81.494 0.010875 644210000 1651740 1420840 1229100 1083930 1424560 1639270 1486550 1605690 2093220 1662590 TRUE FALSE 1587188.175 1380319.034 1451225.711 1139871.757 1470382.266 1672417.163 1504742.844 1572531.94 1855606.441 1549981.298 1.024004726 0.890539154 0.936285949 0.735410007 0.948645166 1.078991833 0.970813548 1.014548977 1.19717989 1 20.56381938 2.991650946 24.86145916 1.040241639 0.891849993 0.41245341 0.087832551 382.9092955 1140216.332 0.025877221 0.029560053 980.9592025 -2.991650946 -0.148391646 ILDDDTIITTLENLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILDDDTIITTLENLKR 16 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 256.26 1.98E-26 1875750000 1078150 1299130 985250 994930 1133720 1267990 1137570 1241850 1407700 1371970 FALSE TRUE 1036014.706 1262080.084 1163306.592 1046278.457 1170187.133 1293629.627 1151491.922 1216205.364 1247903.798 1279045.25 0.80999066 0.986736071 0.909511678 0.818015201 0.914891114 1.011402549 0.900274578 0.950869693 0.97565258 1 20.28663587 2.991840764 24.89320699 0.958423902 0.887619681 0.355525015 0.054263167 483.0223839 1473671.504 0.015760189 0.018024746 981.3880463 -2.991840764 -0.070804221 ISAPELLLHS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 4 ISAPELLLHSPAR 13 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 ISAPELLLHS(1)PAR;ISAPELLLHS(1)PAR;ISAPELLLHS(1)PAR;ISAPELLLHS(1)PAR 173.51 1.39E-05 1561410000 1380560 1398540 1204180 1412330 1270860 1221700 1262970 1270730 1193210 1507090 TRUE FALSE 1326606.189 1358655.009 1421802.113 1485220.521 1311738.366 1246403.611 1278426.605 1244488.981 1057761.803 1405013.452 0.944194653 0.967004983 1.01194911 1.057086335 0.933612674 0.887111514 0.909903462 0.885748802 0.752848168 1 20.42215251 2.991907716 4.58464397 0.884144995 0.994936844 0.397262028 0.062442922 0.193173906 10.54957864 0.018649444 0.021187831 981.5393516 -2.991907716 0.110791848 GRPYDYNGPR ddPTM_BT-474_Pertuzumab_2h_R1 6 GRPYDYNGPR 10 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 138.36 6.09E-05 5627700000 2203160 2478560 2160750 2332530 2296860 2082400 2444950 2402750 2531850 2614090 FALSE TRUE 2117058.071 2407873.896 2551245.591 2452912.153 2370740.588 2124507.555 2474872.029 2353132.373 2244445.002 2437035.356 0.86870224 0.988034043 1.046864414 1.0065148 0.972796961 0.87175902 1.015525697 0.965571701 0.920973509 1 21.21669575 2.992133017 24.86762587 0.955163181 0.984034798 0.031738578 0.056265445 1194.28658 3775175.227 0.016823634 0.019286695 982.0486824 -2.992133017 0.028871617 HMNLILCDCDEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 HMNLILCDCDEFR 13 0 P14678-2;P14678;P14678-3;J3QLE5;P63162;P63162-2;J3KRY3;S4R3P3 P14678-2;S4R3P3 SNRPB;SNRPN Small nuclear ribonucleoprotein-associated proteins B and B;Small nuclear ribonucleoprotein-associated protein N 0 ;;; 121.76 0.00024291 1837010000 1260710 1271700 1191300 1297550 1194210 781220 1333970 1081710 1299660 1381150 FALSE TRUE 1211440.059 1235432.361 1406594.41 1364516.711 1232622.849 797016.8037 1350295.524 1059372.31 1152128.045 1287603.48 0.940848699 0.959481999 1.092412712 1.059733631 0.957300029 0.618992427 1.048688936 0.822747318 0.894784818 1 20.29625695 2.992169505 24.99101258 0.868091736 1.01414749 0.238243818 0.11462932 486.237951 1551834.795 0.032424626 0.037194314 982.1311932 -2.992169505 0.146055754 DTVTISGPQAPVFEFVEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 DTVTISGPQAPVFEFVEQLRK 21 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 276.26 1.35E-44 4270500000 671380 677690 530730 531630 619930 737200 652290 619970 782960 706650 FALSE TRUE 645141.7274 658362.9447 626644.717 559067.488 639870.6115 752106.6891 660272.9201 607167.4028 694081.6632 658787.9661 0.979285841 0.999354843 0.951208506 0.848630389 0.971284608 1.141652137 1.00225407 0.92164313 1.053573682 1 19.32945468 2.992176169 24.98195757 1.013889736 0.944119819 0.254446595 0.06339703 640.3069323 2044548.031 0.020392426 0.023407687 982.146264 -2.992176169 -0.069769917 ELREPQFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELREPQFR 8 1 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494BZX8 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 117.89 0.0041961 172330000 936830 980400 1101920 1077900 982040 667030 915470 954720 1107600 1219560 FALSE TRUE 900217.6479 952439.9519 1301061.456 1133530.548 1013628.208 680517.8036 926673.7957 935004.6984 981869.8914 1136958.115 0.791777319 0.837708918 1.144335432 0.996985318 0.891526429 0.598542545 0.815046556 0.822373917 0.863593723 1 20.11674768 2.99239832 24.50712624 0.803362193 0.948936093 0.16573023 0.127398319 430.9088847 1389219.889 0.038276254 0.043941087 982.648781 -2.99239832 0.145573899 DLVSSLTSGLLTIGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLVSSLTSGLLTIGDR 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 210.41 2.27E-11 291350000 119409 113680 90068 85419 109417 131985 131244 119031 140774 124297 FALSE TRUE 114742.3643 110437.9577 106345.2912 89827.48483 112936.4972 134653.8271 132850.2033 116572.9683 124793.9257 115878.2535 0.990197564 0.953051624 0.917732948 0.77518846 0.974613388 1.162028449 1.146463632 1.005995213 1.076939995 1 16.82225032 2.992453964 24.9558667 1.07728037 0.908068634 0.565091398 0.070385848 264.4642862 874626.6888 0.021652598 0.024880585 982.7746911 -2.992453964 -0.169211735 (ac)AAAAAAAGDS(ph)DSWDADAFSVEDPVRK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 AAAAAAAGDS(0.976)DS(0.024)WDADAFSVEDPVRK;AAAAAAAGDS(0.901)DS(0.099)WDADAFSVEDPVRK;AAAAAAAGDS(0.5)DS(0.5)WDADAFSVEDPVRK 139.61 3.42E-70 1265957000 584519 615546 523249 531898 593812 678935 601037 673246 739038 705916 TRUE FALSE 561675.3513 597991.2308 617811.7339 559349.3195 612912.5023 692663.5309 608392.6706 659343.2348 655145.5045 658103.6806 0.853475475 0.908658086 0.938775686 0.849941029 0.931331218 1.052514294 0.924463255 1.001883524 0.995505 1 19.32795536 2.992492806 23.90918011 0.989917379 0.892578538 0.642281779 0.037707321 127.7654551 406915.4819 0.01058375 0.012142304 982.8625929 -2.992492806 -0.097338841 GSSERGS(ph)PIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSSERGSPIEK 11 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(0.045)S(0.045)ERGS(0.91)PIEK;GS(0.003)S(0.142)ERGS(0.855)PIEK 115.79 0.0028299 2872790000 4793800 4841550 3687040 3981780 4376300 4742450 4330360 4752420 5417500 4603630 TRUE FALSE 4606452.996 4703473.734 4353370.146 4187280.143 4517067.664 4838345.588 4383356.241 4654280.866 4802528.112 4291822.04 1.073309413 1.095915369 1.014340787 0.975641605 1.052482517 1.127340683 1.021327585 1.084453368 1.118995165 1 22.03315883 2.992528474 24.96085278 1.073964921 1.038500116 0.083577253 0.047192441 818.2486912 2733618.067 0.014081836 0.016166663 982.9433158 -2.992528474 -0.035464804 GSLAS(ph)LDSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GS(0.465)LAS(0.535)LDSLR 229.86 1.50E-09 2117700000 1125900 1731500 1472100 1760900 1456700 1128300 1446500 1451000 1312000 1437600 TRUE FALSE 1081898.583 1682119.315 1738141.217 1851780.26 1503556.078 1151114.999 1464202.7 1421036.343 1163067.26 1340230.072 0.807248402 1.255097428 1.29689764 1.381688338 1.121864156 0.858893576 1.092501005 1.060292836 0.867811643 1 20.35404925 2.992652963 24.85276973 0.995436913 1.204896441 0.279234731 0.157779764 424.1926811 1434921.308 0.046849456 0.053873742 983.2251131 -2.992652963 0.209459527 MSSSEEESKIDLLDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 MSSSEEESKIDLLDRK 16 2 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 52.453 0.089765 150840000 86625 88719 52579 72063 80230 90283 94684 86682 101300 93377 FALSE TRUE 83239.59923 86188.82098 62081.19491 75782.18007 82810.67081 92108.58412 95842.77112 84891.98641 89800.84868 87052.49262 0.956200067 0.990078726 0.713146666 0.870534292 0.951272828 1.05808095 1.100976758 0.97518157 1.031571251 1 16.40959799 2.992779619 3.547469108 1.031850554 0.879167846 0.474686237 0.074678199 0.216397067 5.832108297 0.024318117 0.027839703 983.5118994 -2.992779619 -0.152682708 SHIEIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SHIEIIR 7 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;;; 158.08 0.0014338 1497800000 2838830 2785030 2219610 2521010 2207410 526210 3218140 833130 2254170 2821870 FALSE TRUE 2727885.385 2705603.671 2620742.902 2651119.628 2278413.347 536850.3267 3257524.56 815925.5744 1998286.072 2630742.231 1.036926139 1.028456395 0.996199046 1.007745874 0.866072442 0.204068008 1.238253038 0.310150331 0.759590221 1 21.32703846 2.99293762 22.92162186 0.661954063 1.006653739 0.211594551 0.281221648 145.4923179 472216.157 0.077051699 0.08857824 983.8697763 -2.99293762 0.344699676 RAEDGSVIDYELIDQDAR ddPTM_BT-474_Pertuzumab_2h_R1 5 RAEDGSVIDYELIDQDAR 18 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28;H0YNA0 P07355-2 ANXA2 Annexin A2;Annexin 0 ;;;; 252.58 2.79E-30 8829060000 3131570 3433360 1298037 4616150 2890760 2439590 2170410 3286050 3151190 2604870 FALSE TRUE 3009184.782 3335443.934 1532621.161 4854390.055 2983743.921 2488920.181 2196972.127 3218191.919 2793480.122 2428439.835 1.239143231 1.373492514 0.631113499 1.998974809 1.228667014 1.024905022 0.904684603 1.325209656 1.150318852 1 21.21159831 2.992998926 24.98980225 1.106948847 1.310026164 0.098989593 0.3245341 893.8280957 3190468.508 0.094346775 0.108711262 984.0086721 -2.992998926 0.203077317 QVLGQMVIDEELLGDGHSYSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 QVLGQMVIDEELLGDGHSYSPR 22 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ;;; 240.85 1.21E-30 962600000 854390 885510 720270 888700 802590 717400 771740 759730 875860 931440 FALSE TRUE 820999.4942 860256.1218 850438.8113 934565.9135 828406.0362 731906.3195 781184.785 744041.31 776436.0447 868352.7392 0.945467731 0.990675889 0.979370218 1.076251472 0.953997148 0.84286752 0.899616883 0.856842244 0.894148207 1 19.72792168 2.993038221 24.19882967 0.888440997 0.998474421 0.462437148 0.04996306 159.9024309 555817.8615 0.013972759 0.016099049 984.0977093 -2.993038221 0.110033424 QNAQCLHGDIAQSQR ddPTM_BT-474_Pertuzumab_2h_R1 3 QNAQCLHGDIAQSQR 15 0 Q9BQ39;A0A087WVC1 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 0 ;; 165.02 1.45E-06 426500000 226972 242018 208075 206070 200899 212018 202200 200554 209239 226724 FALSE TRUE 218101.6833 235115.8836 245678.7811 216705.2974 207361.0988 216305.1492 204674.5841 196412.4898 185487.0659 211367.7815 1.031858695 1.112354408 1.162328427 1.025252268 0.981044023 1.023359131 0.96833388 0.929245169 0.877556005 1 17.68939596 2.993148138 0.929877772 0.936256679 1.102479716 0.611645428 0.048789025 0.360902168 0.685085888 0.025693138 0.031861208 984.3468107 -2.993148138 0.166223036 WAYHDFFNR ddPTM_BT-474_Pertuzumab_2h_R1 1 WAYHDFFNR 9 0 Q9ULV0 Q9ULV0 MYO5B Unconventional myosin-Vb 0 159.37 6.61E-05 276480000 138190 169190 140280 133230 136530 90646 126970 108420 121780 141550 FALSE TRUE 132789.382 164364.8669 165631.7165 140106.0163 140921.6114 92478.92423 128523.8968 106181.0891 107956.0449 131962.6924 1.006264571 1.245540416 1.255140475 1.061709288 1.067889787 0.700795979 0.973941153 0.804629605 0.818080042 1 17.00977059 2.993175254 3.006602074 0.853708989 1.157620784 0.605171309 0.10790027 0.158486962 2.927357044 0.032377265 0.037281873 984.4082715 -2.993175254 0.303911795 DSLGAYASQDANEQGQDLGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSLGAYASQDANEQGQDLGKR 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 222.06 6.53E-25 407350000 131700 136540 103760 105460 120820 132780 113260 143680 137380 118890 FALSE TRUE 126553.0184 132646.0129 122511.7401 110902.8032 124706.285 135464.9026 114646.1098 140712.9578 121785.1983 110837.4744 1.141789084 1.196761417 1.105327785 1.000589411 1.125127451 1.222194058 1.034362343 1.269543163 1.098772766 1 16.75808622 2.993183234 24.86494259 1.147366997 1.110075586 0 0.088263543 1230.186369 4487284.358 0.025603651 0.029489088 984.4263604 -2.993183234 -0.037291411 ADSPSIDYAELLQHFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADSPSIDYAELLQHFEK 17 0 Q08AM6;Q08AM6-2 Q08AM6 VAC14 Protein VAC14 homolog 0 ; 205.18 8.11E-12 247500000 415190 455710 386300 401910 423890 449950 485650 416200 477490 482380 FALSE TRUE 398963.9158 442713.597 456113.0032 422652.6233 437524.8068 459048.2973 491593.53 407605.3246 423287.337 449707.9729 0.887162203 0.984446849 1.014242643 0.939837959 0.972908717 1.020769755 1.093139458 0.906377803 0.94124935 1 18.77862894 2.993230669 24.44649184 0.989197064 0.961781569 0.081844738 0.055128055 879.6862003 3176885.055 0.017225004 0.019875149 984.5338873 -2.993230669 -0.027415495 GNYSER ddPTM_BT-474_Pertuzumab_2h_R1 3 GNYSER 6 0 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q7L7L0;P04908 A0A0U1RR32;Q7L7L0 HIST1H2AD;HIST3H2A;HIST1H2AB Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E 0 ;; 113.1 0.061479 1680380000 1816210 1942650 1413610 2008360 1713500 1378550 1873360 1752620 1588270 1773780 FALSE TRUE 1745230.505 1887247.524 1669080.773 2112011.7 1768616.284 1406425.226 1896286.74 1716427.785 1407976.248 1653640.301 1.055387018 1.141268463 1.009337261 1.277189301 1.069529016 0.850502509 1.146734716 1.037969251 0.851440454 1 20.65721402 2.993737886 24.99547475 0.994749872 1.121679383 0.294019042 0.103885639 405.8092193 1619812.696 0.030103838 0.034846201 985.6844065 -2.993737886 0.126929512 LQAFGFCEYKEPESTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQAFGFCEYKEPESTLR 17 1 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 ; 191.21 2.33E-10 952470000 695490 642670 518190 572610 629180 705150 659350 698760 741300 744930 FALSE TRUE 668309.4819 624341.6808 611838.4601 602162.4707 649418.1461 719408.6161 667419.3225 684330.3618 657150.7318 694475.2276 0.962322996 0.899012169 0.881008329 0.867075522 0.935120679 1.035902488 0.961041224 0.985392041 0.946255108 1 19.40556371 2.993742113 22.94425789 0.983091895 0.900654584 0.603077938 0.032003959 64.93468028 238084.2242 0.009319702 0.010759327 985.6940004 -2.993742113 -0.082437311 HLLPVETQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLLPVETQR 9 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 105.4 0.0031047 630310000 798180 908910 768960 872280 795960 735440 868260 611530 973450 956390 FALSE TRUE 766986.2432 882988.7767 907928.1774 917298.4753 821562.7763 750311.1007 878886.0256 598901.6918 862948.037 891612.8534 0.860223403 0.990327555 1.018298664 1.028808044 0.921434424 0.84152118 0.985726061 0.671705987 0.967850602 1 19.76605789 2.993823069 5.187783231 0.865370469 0.978853371 0.096327052 0.099748555 0.275099211 22.82621176 0.029998375 0.034077054 985.877759 -2.993823069 0.113482903 LLEASR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEASR 6 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 129.2 0.037913 926460000 822050 937660 809400 815460 787760 348470 888920 755660 822040 975910 FALSE TRUE 789923.3772 910918.8549 955676.585 857545.9883 813099.0158 355516.3022 899798.8689 740055.3569 728725.4655 909810.7464 0.868228233 1.001217955 1.050412505 0.942554253 0.893701266 0.390758522 0.988995648 0.813416812 0.800963792 1 19.79520695 2.993845673 24.84188481 0.789194994 0.96719535 0.190478121 0.161963015 406.4997283 1640843.178 0.04680192 0.054190729 985.929072 -2.993845673 0.178000356 RYS(ph)DFEWLR ddPTM_BT-474_Pertuzumab_2h_R1 3 RYSDFEWLR 9 1 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR 220.53 2.77E-07 832131000 229910 236883 221885 251002 229197 203040 229120 234870 243479 248889 TRUE FALSE 220924.863 230127.3288 261984.5553 263956.2433 236569.3297 207145.6079 231924.0391 230019.8524 215840.2847 232031.5263 0.952132956 0.991793367 1.129090341 1.137587842 1.019556839 0.892747685 0.999536756 0.99133017 0.930219648 1 17.82396131 2.993899439 24.97167516 0.966571889 1.056865121 0.330932299 0.060435413 344.3980787 1409747.794 0.018920984 0.02192228 986.0511386 -2.993899439 0.090293232 FFWHLTLPER ddPTM_BT-474_Pertuzumab_2h_R1 1 FFWHLTLPER 10 0 P55212;D6RBM3;D6RHU3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 103.7 0.0027796 305790000 231310 269720 235170 242880 234060 121000 282000 216410 258230 302630 FALSE TRUE 222270.1495 262027.8497 277670.4503 255415.0659 241588.7525 123446.7029 285451.2004 211941.0579 228916.813 282132.6005 0.787821574 0.928740065 0.984184209 0.905301498 0.856295061 0.437548524 1.011762554 0.751210805 0.811380225 1 18.10601385 2.993930554 24.83383915 0.786261052 0.905791463 0.078705207 0.155107827 554.9771044 2270767.736 0.043890813 0.050853067 986.121786 -2.993930554 0.119530411 TQDECILHFLR ddPTM_BT-474_Pertuzumab_2h_R1 6 TQDECILHFLR 11 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ;;;;; 194.39 5.32E-07 2389950000 3027260 3230450 2552133 2875700 2801767 2311175 2978560 2708530 3004580 3185810 FALSE TRUE 2908951.332 3138320.729 3013360.205 3024115.222 2891888.38 2357908.542 3015012.508 2652597.909 2663512.675 2970032.251 0.979434257 1.056662172 1.014588378 1.018209557 0.973689218 0.793899979 1.015144703 0.893120911 0.896795876 1 21.50204717 2.993950794 20.80181827 0.915999656 1.016864731 0.371884844 0.059731247 29.43702669 101232.8074 0.016520504 0.019043629 986.1677445 -2.993950794 0.100865074 GADSGEEKEEGINR ddPTM_BT-474_Pertuzumab_2h_R1 2 GADSGEEKEEGINR 14 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 0 ; 119.32 0.00017737 1856340000 958140 832310 842660 995640 993160 890990 1041870 1271890 1241120 1196790 FALSE TRUE 920694.8295 808573.3337 994947.4069 1047025.1 1025105.893 909006.4283 1054620.717 1245625.027 1100233.261 1115730.347 0.825194754 0.724703183 0.891745402 0.938421279 0.918775666 0.814718745 0.945229032 1.116421212 0.986110366 1 20.08955696 2.993955204 0.46755907 1.050539923 0.765738526 0.532558471 0.071442553 0.99218102 0.431092113 0.070606054 0.125401328 986.1777588 -2.993955204 -0.284801396 VIHLVER ddPTM_BT-474_Pertuzumab_2h_R1 5 VIHLVER 7 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ;;;; 143.23 0.0024359 607720000 655168 722692 657929 681932 645286 413268 761454 594140 623593 776467 FALSE TRUE 629563.3102 702081.5317 776831.4059 717126.5922 666042.2102 421624.5621 770772.9018 581870.8014 552805.337 723876.1985 0.869711301 0.969891721 1.073155061 0.990675745 0.920105139 0.582453965 1.06478553 0.803826404 0.763673869 1 19.46538345 2.994063976 24.58285689 0.837676144 0.979008109 0.187405423 0.130658675 338.1304561 1400311.376 0.037071536 0.042948593 986.4247855 -2.994063976 0.141331965 EQQEVADRLETK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQQEVADRLETK 12 1 O75884 O75884 RBBP9 Putative hydrolase RBBP9 0 111.83 0.0012215 169260000 136840 143670 103220 115360 131920 159170 136060 152660 151340 159920 FALSE TRUE 131492.1415 139572.6723 121874.1501 121313.7434 136163.3266 162388.5265 137725.143 149507.5177 134160.5177 149088.476 0.881973879 0.936173446 0.817461909 0.813703022 0.91330551 1.089209112 0.923781279 1.002810691 0.899871816 1 17.18580922 2.994067982 24.82451628 0.982111601 0.864286277 0.500225639 0.057110363 204.5002416 855805.7577 0.016443162 0.01905616 986.4338844 -2.994067982 -0.117825324 ENFS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 ENFSPER 7 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 ENFS(1)PER;ENFS(1)PER 115.82 0.0058681 1632250000 1360290 1518070 1251920 1421750 1371480 1170790 1421160 1443640 1601860 1484060 TRUE FALSE 1307128.363 1474776.13 1478169.793 1495126.688 1415594.9 1194464.176 1438552.581 1413828.33 1420023.568 1383543.294 0.944768673 1.065941439 1.068394317 1.080650453 1.023166319 0.863337043 1.039759715 1.021889474 1.02636728 1 20.39993636 2.99410579 24.9809665 0.992746361 1.04483858 0.140933952 0.057694029 529.2772001 2243211.875 0.01737524 0.020124633 986.5197643 -2.99410579 0.052092219 TLT(ph)PPLRR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.381)LT(0.619)PPLRR;T(0.203)LT(0.797)PPLRR;T(0.053)LT(0.947)PPLRR;T(0.006)LT(0.994)PPLRR 120.45 0.0008784 4347850000 2388050 2300600 1858180 2085820 2184370 2325900 2196210 2390420 2507170 2456210 TRUE FALSE 2294722.366 2234989.141 2193994.461 2193469.42 2254632.245 2372931.292 2223087.875 2341056.992 2222566.573 2289848.709 1.002128375 0.976042274 0.958139484 0.957910194 0.984620615 1.036283001 0.970844871 1.022363173 0.970617213 1 21.12682085 2.994112221 24.93037405 1.001670182 0.972460844 0.242079743 0.022030286 327.7461518 1387771.002 0.006174296 0.007163068 986.5343706 -2.994112221 -0.029209338 EHVYDLFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHVYDLFEK 9 0 A0A499FI31;Q15020-4;Q15020;Q15020-2;A0A494C0L2;F8W667;F8VVK9;F8VZM2 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 179.51 4.97E-05 624100000 603910 594450 499640 563230 546120 487620 592070 433930 695400 718420 FALSE TRUE 580308.5295 577496.868 589936.0624 592298.3678 563686.4458 497480.0105 599315.9298 424969.1939 616461.1074 669760.7735 0.8664415 0.862243492 0.880816085 0.884343173 0.841623559 0.742772689 0.894820888 0.634508933 0.920419845 1 19.35328636 2.994383064 15.63857481 0.804523082 0.871911857 0 0.096370185 4.653075291 12960.96599 0.027196843 0.031194284 987.1498046 -2.994383064 0.067388775 FS(ph)PPRHELS(ph)PPQKR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSPPRHELSPPQKR 14 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 FS(1)PPRHELS(1)PPQKR;FS(1)PPRHELS(1)PPQKR 81.723 0.0068162 1187940000 1047070 1054190 885370 850050 975710 1046370 1013920 976330 1235670 1129240 TRUE FALSE 1006149.347 1024125.533 1045376.054 893921.1824 1007094.598 1067528.318 1026328.656 956168.4443 1095401.922 1052755.569 0.955729304 0.97280467 0.992990286 0.849125104 0.956627187 1.014032459 0.97489739 0.908253038 1.040509264 1 20.00573908 2.994384647 24.96905479 0.975835742 0.942718469 0.144108348 0.048119956 655.8060487 2916106.608 0.014688124 0.017050119 987.153404 -2.994384647 -0.033117272 AAS(ph)PQDLAGGYTSSLACHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AASPQDLAGGYTSSLACHR 19 0 H0YJ92;P51948-2;P51948 H0YJ92 MNAT1 CDK-activating kinase assembly factor MAT1 1 AAS(1)PQDLAGGYTSSLACHR;AAS(1)PQDLAGGYTSSLACHR 148.89 5.86E-08 2141080000 411650 452910 357830 426090 394620 249577 453060 409160 405330 443220 TRUE FALSE 395562.2629 439993.4502 422497.8409 448080.556 407313.3107 254623.6179 458604.6838 400710.703 359318.6377 413200.3146 0.957313557 1.06484297 1.022501256 1.084414847 0.985752663 0.616223195 1.109884643 0.96977347 0.869599139 1 18.65648183 2.994468422 24.95978481 0.919383902 1.034045622 0.175209075 0.1221557 457.2630526 2063293.782 0.035985215 0.041810862 987.3438416 -2.994468422 0.11466172 ELFQETLESLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELFQETLESLR 11 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 138.25 0.00014313 44859000 54402 63409 54374 56406 54393 35111 58490 54548 54731 66556 FALSE TRUE 52275.9097 61600.6374 64200.59134 59317.12042 56142.60024 35820.96848 59205.81812 53421.56474 48518.16633 62048.10284 0.842506174 0.992788411 1.034690642 0.955986045 0.904823801 0.577309649 0.954192238 0.860970155 0.781944397 1 15.92109948 2.994607939 24.54974508 0.829454837 0.960387711 0.199484235 0.11487336 286.858589 1306063.215 0.033073346 0.038418809 987.6610778 -2.994607939 0.130932874 VDKGAGNNPEFEETRR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDKGAGNNPEFEETRR 16 2 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 0 125.18 4.41E-05 218370000 90036 117630 64572 82254 91515 112370 85948 104190 106150 98440 FALSE TRUE 86517.29358 114275.3076 76241.5968 86499.1388 94458.66309 114642.1984 86999.85733 102038.4401 94100.29702 91772.57112 0.942735858 1.245201112 0.830766708 0.942538034 1.029269006 1.249198938 0.947994115 1.111862061 1.02536407 1 16.48577541 2.994930571 24.96147199 1.074168587 0.995718741 0.077376757 0.12285979 585.8637455 2884770.79 0.035180556 0.040965103 988.3950706 -2.994930571 -0.078449846 DCQIAHGAAQFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCQIAHGAAQFLR 13 0 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 ; 127.71 0.00017374 472040000 679630 697530 595650 662370 652630 591860 719560 647060 708510 784210 FALSE TRUE 653069.3082 677637.1274 703297.2052 696554.9951 673622.4367 603827.8147 728366.1905 633697.9849 628082.9151 731094.7582 0.893275873 0.926880024 0.96197818 0.952756106 0.921388683 0.825922779 0.996267833 0.866779549 0.859099191 1 19.47969888 2.995012579 24.84557716 0.90264351 0.935479602 0.033242757 0.054925369 571.0303806 2844699.376 0.015405211 0.017917655 988.5817276 -2.995012579 0.032836092 KIENISHLTELQEFWMNDNLLESWSDLDELK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIENISHLTELQEFWMNDNLLESWSDLDELK 31 1 Q15435;H7C003;C9J177;Q15435-2;H7C3Q5 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 192.67 4.04E-19 127460000 107610 102170 90003 77664 99337 110830 99533 111280 129220 123550 FALSE TRUE 103404.4822 99256.21163 106268.5442 81672.24835 102532.2648 113071.0585 100751.1146 108982.0291 114551.4873 115181.8485 0.897749807 0.861734839 0.922615374 0.709072214 0.890177282 0.981674283 0.874713472 0.946173643 0.994527253 1 16.81355385 2.995089325 24.99354389 0.9470311 0.847319783 0.411322875 0.062470082 233.8064116 1189999.31 0.018115788 0.021102369 988.7564399 -2.995089325 -0.099711317 APLATGEDDDDEVPDLVENFDEASKNEAN ddPTM_BT-474_Pertuzumab_2h_R1 4 APLATGEDDDDEVPDLVENFDEASKNEAN 29 1 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 ;;; 205.26 2.03E-25 1564000000 785820 713592 550330 549170 675575 740570 688883 778310 863380 777004 FALSE TRUE 755109.2856 693241.0548 649786.873 577512.7295 697305.4834 755544.8328 697313.7562 762237.6265 765372.722 724376.827 1.042426065 0.957017162 0.897028796 0.797254561 0.962628093 1.043027337 0.962639513 1.052266718 1.056594708 1 19.46638087 2.995099464 24.97207883 1.021193325 0.918444278 0.364292515 0.062111323 236.5654607 1205495.816 0.01917585 0.022342882 988.7795227 -2.995099464 -0.102749047 VNPCIGGVILFHETLYQK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNPCIGGVILFHETLYQK 18 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 260.96 9.19E-31 7021200000 4681000 5100700 4784600 5711400 5004400 4566200 5409600 4917100 5592100 5065900 FALSE TRUE 4498061.345 4955233.03 5649283.653 6006166.038 5165371.071 4658531.693 5475804.303 4815560.167 4957308.252 4722782.081 0.952417721 1.049219072 1.196177074 1.271743209 1.093713617 0.986395648 1.159444626 1.019644795 1.049658478 1 22.17120554 2.995129563 24.99318903 1.050690936 1.12622025 0.127712006 0.090389788 475.4371801 2439780.116 0.027976538 0.032588905 988.8480534 -2.995129563 0.075529314 LVS(ph)SPELGHDEFSTQALAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVSSPELGHDEFSTQALAR 19 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 LVS(0.5)S(0.5)PELGHDEFSTQALAR 88.555 0.0016347 46902000 19018 20148 20413 24087 19292 14835 16339 18814 20331 18910 TRUE FALSE 18274.75553 19573.39877 24102.08318 25330.13296 19912.5447 15134.97386 16538.96157 18425.48433 18023.11011 17629.20886 1.036618017 1.110282312 1.367167601 1.436827549 1.12952004 0.858516907 0.938156766 1.045167964 1.022343672 1 14.10568011 2.995237783 24.70404069 0.98003738 1.24353026 0.535358768 0.116691584 151.0410429 783534.3222 0.037238588 0.043394395 989.0944906 -2.995237783 0.263492881 SSYSSPTSLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSYSSPTSLSPR 12 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR 245.55 1.87E-16 750260000 767080 852080 649490 695720 680090 590210 581420 625510 657420 574550 TRUE FALSE 737101.6655 827779.5127 766867.2908 731626.1926 701965.7125 602144.4506 588535.5919 612592.9999 582792.4377 535635.2167 1.376126219 1.54541652 1.431696921 1.365903827 1.310529425 1.124168897 1.098761944 1.143675734 1.088039807 1 19.03089129 2.99526171 1.223610868 1.08879629 1.463415557 0.902508699 0.053355619 0.124674782 0.393508337 0.021560183 0.025954059 989.1489864 -2.99526171 0.374619267 EDAFYARPLPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDAFYARPLPAR 12 1 Q96N66-3;Q96N66-2;Q96N66;M0R1Z5;A9C4B8 Q96N66-3 MBOAT7 Lysophospholipid acyltransferase 7 0 75.479 0.030736 152680000 259600 279990 179660 306800 243450 187080 237190 302650 206810 220910 FALSE TRUE 249454.545 272004.9593 212128.5585 322633.9848 251280.7903 190862.8858 240092.8022 296400.1717 183333.7958 205947.5689 1.211252681 1.320748581 1.030012443 1.566583118 1.220120207 0.92675474 1.165795758 1.43920209 0.890196455 1 17.65191757 2.995270446 24.98044671 1.137971041 1.282703404 0.168744341 0.191715413 485.464797 2564141.11 0.057609671 0.067158972 989.168883 -2.995270446 0.144732363 EHVIEALR ddPTM_BT-474_Pertuzumab_2h_R1 6 EHVIEALR 8 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;; 147.29 0.00053968 9484980000 5389750 5922310 5656590 7120140 5964100 5131930 7033230 4779490 7017210 7980180 FALSE TRUE 5179112.611 5753411.517 6678861.643 7487611.279 6155940.693 5235701.141 7119304.773 4680791.861 6220645.739 7439675.301 0.696147668 0.77334175 0.897735637 1.006443289 0.827447495 0.703753985 0.956937566 0.629166149 0.83614479 1 22.82680823 2.995356469 24.95762747 0.79587653 0.851623306 0 0.127241403 792.305283 4258448.795 0.03724914 0.043452425 989.3648314 -2.995356469 0.055746775 FRPAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 FRPAIK 6 1 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ; 64.866 0.096264 1200550000 1567570 1452450 1237750 1454910 1370040 1175960 1375320 1396080 1509190 1496250 FALSE TRUE 1506307.631 1411027.548 1461438.959 1529998.079 1414108.581 1199738.717 1392151.578 1367250.46 1337873.078 1394907.655 1.079861901 1.011556244 1.047695848 1.096845425 1.013765016 0.860084689 0.998024187 0.980172742 0.959112292 1 20.41173819 2.9955421 24.95243111 0.960674977 1.054858811 0.553600255 0.042138916 146.3206906 819017.3818 0.012189721 0.014231244 989.7878091 -2.9955421 0.094183833 YSEEGLS(ph)PSKR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSEEGLSPSKR 11 1 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 YSEEGLS(0.937)PS(0.063)KR;YS(0.001)EEGLS(0.961)PS(0.038)KR 70.552 0.031516 776040000 826010 826790 718820 800230 782410 722230 800190 814740 872810 886920 TRUE FALSE 793728.616 803210.7587 848726.7641 841529.9662 807576.9282 736833.9854 809982.9646 797915.3343 773732.2679 826848.1184 0.959944878 0.971412695 1.026460296 1.017756402 0.976693192 0.891135831 0.979603081 0.965008345 0.935761055 1 19.65726282 2.995606529 24.91887021 0.953213973 0.994940342 0.250112316 0.032365162 248.4332485 1409075.422 0.009554142 0.011150565 989.9346577 -2.995606529 0.041726369 MLLNDFLNDQNR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLLNDFLNDQNR 12 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ; 165.63 0.00012582 617660000 839470 1402110 2169660 1040000 1235440 701790 1189930 697240 562230 732310 FALSE TRUE 806662.5843 1362123.196 2561765.826 1093674.525 1275179.05 715980.6746 1204492.719 682841.7503 498408.0075 682709.9914 1.181559658 1.995171028 3.75234852 1.601960625 1.867819522 1.04873326 1.764281663 1.000192994 0.730043523 1 19.38091334 2.995738315 1.686545959 1.131466027 2.266279668 0.35288057 0.665436908 0.413806306 2.393936415 0.24217962 0.286125345 990.235096 -2.995738315 1.134813641 SLGSVQAPSYGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 266.93 4.10E-24 244840000 190870 189750 143150 173240 163560 108230 185050 157740 168080 200470 FALSE TRUE 183410.5894 184338.5158 169020.3894 182180.9372 168821.0559 110418.4848 187314.6973 154482.6139 149000.263 186891.9883 0.981372134 0.986337175 0.904374719 0.974792653 0.903308148 0.590814436 1.002261782 0.826587674 0.797253346 1 17.5118452 2.995928766 24.84381708 0.835736815 0.956840198 0.203042313 0.109914248 244.2932679 1490762.358 0.030822816 0.036048513 990.66944 -2.995928766 0.121103383 DWEMHVHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DWEMHVHFK 9 0 Q12907;D6RBV2;D6RDX1;D6RIU4;D6RBH1 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 120.12 0.00041446 213080000 384330 516760 401940 486600 365050 207150 496710 30930 546330 275890 FALSE TRUE 369309.9587 502022.5108 474579.4991 511713.4843 376792.1648 211338.7149 502788.8856 30291.28469 484312.9088 257203.7246 1.435865516 1.951847749 1.845150182 1.989525949 1.464956098 0.821678284 1.95482739 0.117771563 1.882993373 1 17.97255201 2.99616883 4.829582911 1.08820954 1.814221123 0.260210183 0.509852935 0.224010205 14.54227446 0.147769196 0.168463703 991.2172019 -2.99616883 0.726011583 WDLSAQQIEER ddPTM_BT-474_Pertuzumab_2h_R1 2 WDLSAQQIEER 11 0 P52888;K7EKB6 P52888 THOP1 Thimet oligopeptidase 0 ; 113.67 0.003165 245450000 182980 226278 171632 201177 184303 145734 217740 169583 160833 199549 FALSE TRUE 175828.9393 219824.773 202649.7203 211559.7691 190231.2734 148680.8413 220404.7673 166081.0518 142575.9121 186033.3685 0.945147318 1.181641631 1.089319201 1.137214097 1.022565333 0.799215982 1.184759321 0.892748721 0.766399669 1 17.50520189 2.99633388 21.36101627 0.938008145 1.093169369 0.277819004 0.121318965 31.01494716 180725.8246 0.034729379 0.040484545 991.5939768 -2.99633388 0.155161224 GGDLMAYDR ddPTM_BT-474_Pertuzumab_2h_R1 7 GGDLMAYDR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;; 186.76 9.61E-05 8354430000 4163630 4749360 4433420 4426010 4195280 2496410 4885320 4157830 4210520 4539280 FALSE TRUE 4000910.736 4613912.903 5234637.615 4654436.907 4330224.991 2546889.121 4945108.008 4071969.358 3732559.422 4231830.522 0.945432648 1.090287732 1.236967687 1.099863731 1.023251042 0.601841002 1.168550579 0.96222411 0.882020062 1 22.01285042 2.996370164 24.67906879 0.931369288 1.09800165 0.230221586 0.146830933 200.4536908 1362894.349 0.043125245 0.050500165 991.6768255 -2.996370164 0.166632362 HFWTAES ddPTM_BT-474_Pertuzumab_2h_R1 2 HFWTAES 7 0 Q14157-4;Q14157-1 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ; 140.01 0.0061723 223800000 660730 701130 642430 722350 661850 554220 667630 647840 736290 822450 FALSE TRUE 634907.9411 681134.4589 758531.3918 759630.5701 683139.0063 565426.7081 675800.6557 634461.8776 652709.446 766744.7289 0.82805648 0.888345799 0.989288042 0.990721607 0.89096016 0.737438011 0.881389373 0.827474717 0.85127347 1 19.54838682 2.996491811 24.98439878 0.845594786 0.928034468 0.127494277 0.075122008 227.3674356 1619272.436 0.021465385 0.025157855 991.9546358 -2.996491811 0.082439682 DVYHLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVYHLNR 7 0 I3L2Z5;A0A087WWR2;P56270-3;P56270;P56270-2;J3QSH4;Q14119;Q9HBE1-4;Q9HBE1-2;Q9HBE1-3;Q9HBE1 I3L2Z5 MAZ;VEZF1;PATZ1 "Myc-associated zinc finger protein;Vascular endothelial zinc finger 1;POZ-, AT hook-, and zinc finger-containing protein 1" 0 ; 143.02 0.00245 459260000 582340 560660 493090 564630 491670 324550 529000 484130 421950 463710 FALSE TRUE 559581.509 544670.5257 582202.3317 593770.622 507485.0121 331112.6234 535474.0602 474132.5463 374052.005 432302.5087 1.294421147 1.259929135 1.346747521 1.373507232 1.173911791 0.765928064 1.238655917 1.096761034 0.865255226 1 18.72168168 2.996527124 12.13008528 1.021970043 1.311183274 0.605463555 0.122964814 0.163639085 539.4374561 0.036675545 0.042129919 992.035296 -2.996527124 0.289213231 SKFGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKFGGR 6 1 P25391 P25391 LAMA1 Laminin subunit alpha-1 0 68.398 0.087774 548750000 834470 987530 766070 918620 843860 730490 874600 804370 876580 1028300 FALSE TRUE 801857.9898 959366.6113 904515.8901 966030.0883 871003.5233 745261.0083 885303.6164 787759.4784 777074.3133 958652.3251 0.836442962 1.000745094 0.943528604 1.007695974 0.908570814 0.777404893 0.923487685 0.821736367 0.810590339 1 19.87064816 2.996569841 24.69345031 0.856260297 0.951611159 0.204851967 0.073188207 152.1205775 1095119.74 0.019822375 0.023228099 992.1328754 -2.996569841 0.095350862 LYVYNTDTDNCR ddPTM_BT-474_Pertuzumab_2h_R1 3 LYVYNTDTDNCR 12 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ;; 256.38 8.44E-21 646090000 347805 416997 298136 385765 353629 339187 339068 368054 366005 420163 FALSE TRUE 334212.3961 405104.6538 352015.8072 405674.3779 365003.7979 346045.5935 343217.6156 360453.5563 324457.6468 391704.9858 0.853224769 1.034208572 0.89867584 1.035663044 0.931833424 0.883434233 0.87621457 0.920216922 0.828321463 1 18.57940797 2.996886174 24.90453344 0.897734663 0.960356094 0.128095837 0.065464769 203.2454969 1625590.206 0.01744213 0.020470751 992.8557917 -2.996886174 0.062621431 WRPHS(ph)PDGPR ddPTM_BT-474_Pertuzumab_2h_R1 4 WRPHSPDGPR 10 1 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9IYH5;C9JH78 Q6Y7W6 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 WRPHS(1)PDGPR;WRPHS(1)PDGPR;WRPHS(1)PDGPR;WRPHS(1)PDGPR 136.24 7.42E-05 22161300000 6248700 6628020 5383580 6363620 5963600 5558350 6319980 5804260 6153080 6702430 TRUE FALSE 6004493.896 6438995.359 6356512.663 6692047.191 6155424.61 5670743.645 6397325.806 5684400.003 5454608.154 6248468.446 0.960954504 1.030491778 1.017291312 1.070989995 0.985109337 0.907541375 1.023823015 0.909726928 0.87295122 1 22.57507119 2.997072631 24.53505181 0.942241503 1.021441582 0.36310802 0.048235764 98.63823162 826729.1335 0.013845732 0.016248069 993.2821494 -2.997072631 0.079200078 VVGAMQLYSVDRK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVGAMQLYSVDRK 13 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 182.33 1.81E-05 2486900000 912180 1168210 634920 783140 1036280 1142070 1191240 1208120 1340460 1307620 FALSE TRUE 876530.9971 1134893.795 749664.1677 823557.9493 1069612.887 1165163.438 1205818.751 1183171.9 1188296.6 1219053.733 0.719025728 0.930962897 0.614955804 0.675571492 0.877412421 0.955793339 0.989143234 0.970565832 0.974769667 1 20.21733029 2.997083504 3.346837818 0.97526088 0.741273011 0.687587484 0.076831958 0.14694141 3.455566392 0.024475972 0.028152843 993.3070178 -2.997083504 -0.23398787 GQSQLS(ph)NPTDDSWK ddPTM_BT-474_Pertuzumab_2h_R1 4 GQSQLSNPTDDSWK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GQSQLS(1)NPTDDSWK;GQSQLS(1)NPTDDSWK;GQSQLS(1)NPTDDSWK;GQSQLS(1)NPTDDSWK 331.48 2.03E-68 1476670000 2578940 2786470 2382960 2632360 2892440 3184300 3337640 3366110 4046300 3813100 TRUE FALSE 2478152.174 2707002.604 2813613.881 2768216.415 2985477.959 3248688.728 3378487.037 3296598.652 3586980.987 3554835.341 0.697121508 0.761498732 0.791489228 0.778718604 0.839835794 0.91387882 0.950391991 0.927356217 1.009042795 1 21.76135131 2.99711486 0.49832017 1.005820957 0.694407724 0.949514095 0.02301105 0.24079269 0.121676081 0.020380069 0.034364249 993.3787374 -2.99711486 -0.311413233 NLS(ph)LVR ddPTM_BT-474_Pertuzumab_2h_R1 4 NLSLVR 6 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NLS(1)LVR;NLS(1)LVR;NLS(1)LVR;NLS(1)LVR 79.474 0.070336 1311920000 740816 620476 611672 1096050 858750 876340 1172770 1487560 1353390 1384030 TRUE FALSE 711864.0917 602780.632 722214.737 1152617.272 886372.4736 894060.1952 1187122.71 1456841.366 1199758.841 1290288.415 0.551709279 0.46716736 0.559731242 0.893302039 0.686956856 0.692914998 0.920044461 1.129081955 0.929837722 1 20.29926215 2.997171526 0.517365374 1.064797624 0.458664459 0.725342259 0.109907151 0.578899533 0.319735199 0.100033316 0.163587718 993.5083608 -2.997171526 -0.606133165 TKNETDEDGWTTVR ddPTM_BT-474_Pertuzumab_2h_R1 3 TKNETDEDGWTTVR 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 135.86 2.78E-05 1939140000 835000 849250 747530 715720 902330 841130 924790 879170 1070010 1033390 FALSE TRUE 802367.2769 825030.2215 882625.2997 752658.395 931354.2639 858138.2249 936107.8567 861014.8323 948546.9506 963397.5749 0.832851668 0.856375647 0.916158939 0.781254193 0.966739266 0.890741525 0.971673462 0.893727423 0.984585155 1 19.87777177 2.997268553 0.216158659 1.01860055 0.775678431 0.500874267 0.048310046 4.5421681 0.423966933 0.113095903 0.32666419 993.7303485 -2.997268553 -0.242922119 IEPEPFENCLLRPGSPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IEPEPFENCLLRPGSPAR 18 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 0 ; 122.22 3.34E-05 1119890000 462660 611780 503420 639930 517860 268089 647270 497210 467480 585630 FALSE TRUE 444578.7357 594332.6334 594399.1925 672956.864 534517.4372 273509.9433 655191.4839 486942.4397 414413.6302 545964.7585 0.814299328 1.08859157 1.088713481 1.232601287 0.979032857 0.500966297 1.200061861 0.891893537 0.759048315 1 19.0584483 2.997513323 24.98929311 0.878286796 1.066347276 0.172333439 0.19164828 174.9704882 1758359.221 0.055211265 0.064942421 994.2905761 -2.997513323 0.18806048 LKEQSIFGDHRDEEEETHMK ddPTM_BT-474_Pertuzumab_2h_R1 5 LKEQSIFGDHRDEEEETHMK 20 2 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 ;;;; 211.33 9.07E-23 2399770000 2237600 2036000 1701990 1718960 1959360 2245030 2201820 1632480 2639290 2379950 FALSE TRUE 2150152.118 1977935.273 2009577.454 1807675.732 2022384.594 2290426.045 2228766.532 1598768.718 2339688.864 2218753.867 0.969080956 0.891462232 0.905723471 0.81472567 0.911495693 1.032302897 1.004512743 0.720570561 1.054505819 1 21.0813182 2.997519001 24.94970825 0.934383508 0.89164901 0.066071527 0.09542967 404.3198826 4066032.323 0.029738986 0.034962761 994.3035761 -2.997519001 -0.042734498 LEFHQSVFDELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEFHQSVFDELR 12 0 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 168.59 4.61E-05 52018000 72443 138450 102040 120710 97516 46704 119540 76320 76476 126930 FALSE TRUE 69611.84747 134501.5416 120480.8979 126939.8576 100652.6907 47648.38688 121002.9663 74743.96533 67794.76509 118332.918 0.588271198 1.136636735 1.018152006 1.072734955 0.850589104 0.402663837 1.022563867 0.63164136 0.572915518 1 16.85249194 2.997529966 24.68238782 0.712777799 0.970343639 0.189703094 0.22072191 119.5309442 1194465.614 0.060959492 0.071679612 994.3286806 -2.997529966 0.257565839 GHEFYNPQK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHEFYNPQK 9 0 P78406 P78406 RAE1 mRNA export factor 0 ;;; 155.84 7.23E-05 2543660000 3875900 4055400 3824110 3904480 3755770 2743990 4423880 3185080 4334980 4794340 FALSE TRUE 3724425.543 3939743.963 4515211.744 4105990.681 3876577.753 2799475.358 4478020.767 3119306.985 3842891.244 4469615.081 0.833276574 0.881450391 1.010201474 0.918645254 0.867318031 0.626334775 1.001880628 0.697891637 0.859781251 1 22.09171916 2.997570247 24.3493696 0.814943395 0.913021049 0.065295295 0.117178406 137.037894 1373340.294 0.032224327 0.037883701 994.4209091 -2.997570247 0.098077654 GDSVIVVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDSVIVVLR 9 0 P62316;P62316-2;K7EJB5 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 ; 103.74 0.0078483 294630000 276000 305260 252010 325230 281500 209180 320750 296630 289800 309290 FALSE TRUE 265213.6149 296554.2837 297553.8129 342015.1593 290554.7032 213409.7629 324675.4344 290504.4868 256903.1189 288341.5128 0.919789913 1.02848279 1.031949267 1.186146094 1.007675587 0.740128471 1.126010026 1.007501431 0.890968201 1 18.13741903 2.997616091 24.99945936 0.962469855 1.047084866 0.124008053 0.109930466 222.670934 2335139.855 0.032712099 0.038471294 994.525884 -2.997616091 0.084615012 AAQMHSGYQR ddPTM_BT-474_Pertuzumab_2h_R1 6 AAQMHSGYQR 10 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;;;; 103.18 0.0028485 1670391000 1159415 1256305 1097140 1179187 1138616.4 802573 1348676 1143140.3 1207951.1 1332543 FALSE TRUE 1114103.78 1220476.411 1295417.604 1240044.982 1175241.031 818801.5759 1365181.5 1119534.053 1070829.555 1242288.676 0.896815532 0.982441871 1.042766974 0.998193903 0.946028933 0.659107333 1.098924531 0.901186717 0.861981258 1 20.24456903 2.997624084 24.93057158 0.903504479 0.983130429 0.096186565 0.109633051 219.0553337 2298599.216 0.031566114 0.037139205 994.5441875 -2.997624084 0.079625949 MDPNTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDPNTGR 7 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 83.753 0.051295 178260000 47482 51108 40782 42988 32532 37549 38392 38738 26565 33820 FALSE TRUE 45626.35095 49650.44988 48152.21459 45206.61583 33578.42132 38308.26651 38861.85278 37938.04676 23549.45257 31529.34128 1.44710765 1.574737938 1.527219176 1.433795125 1.064989624 1.215003706 1.232561519 1.203261636 0.746905949 1 14.94440741 2.99770139 0.444897991 0.955806225 1.629760999 0.69240416 0.136775644 0.847866477 0.327213476 0.132697113 0.247435704 994.7212362 -2.99770139 0.673954774 LYHNEVEIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYHNEVEIEK 10 0 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 105.46 0.0028262 523570000 2139500 2146700 1694540 1890440 2036930 2185900 2149000 2097200 2502600 2514600 FALSE TRUE 2055885.975 2085478.218 2000781.073 1988005.835 2102449.703 2230100.396 2175300.105 2053892.087 2218515.34 2344283.902 0.876978242 0.88960139 0.853472172 0.848022645 0.896840908 0.951292799 0.927916667 0.87612771 0.946350968 1 21.16071587 2.997720389 5.831352725 0.92695015 0.867950396 0.525814538 0.031705732 0.153413457 19.98991482 0.009656296 0.011015877 994.7647544 -2.997720389 -0.058999754 AAFNSGK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAFNSGK 7 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 125.25 0.0094623 3336070000 4743380 4624880 3888070 4387280 4335050 4088870 4591110 4502710 4725920 4664610 FALSE TRUE 4558003.466 4492982.951 4590730.739 4613708.047 4474490.82 4171549.753 4647297.378 4409727.465 4189453.374 4348671.81 1.048136917 1.033185107 1.055662726 1.060946479 1.028932744 0.95926985 1.068670523 1.01404007 0.963386882 1 22.0521434 2.997894265 24.70365656 1.007120527 1.048282555 0.372059045 0.029209757 89.06101964 1044848.748 0.008572199 0.010091475 995.1631011 -2.997894265 0.041162028 HILAILQDCPSLRPPIDHLCELLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HILAILQDCPSLRPPIDHLCELLPR 25 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ; 116.24 0.00085771 392690000 116962 186565 134012 223930 162888 151197 178159 136816 212546 161611 FALSE TRUE 112390.9957 181244.3489 158230.9495 235487.0541 168127.4405 154254.3069 180339.3631 133990.7018 188418.6691 150664.943 0.74596647 1.20296298 1.050217432 1.562985054 1.115902858 1.023823484 1.196956369 0.889328991 1.250580695 1 17.20098424 2.99790326 24.99980871 1.062027581 1.163653953 0.017762379 0.209100702 295.711951 3525900.475 0.060280607 0.071011688 995.1837136 -2.99790326 0.101626373 AASSDQLRDNS(ph)PPPAFKPEPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 AASSDQLRDNSPPPAFKPEPPK 22 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK;AAS(0.002)S(0.002)DQLRDNS(0.996)PPPAFKPEPPK 148.85 3.53E-08 3341260000 2065230 2518970 1925750 1743910 2289760 3333820 2849800 1612330 3288990 2917630 TRUE FALSE 1984518.528 2447131.442 2273775.863 1833913.404 2363412.21 3401232.125 2884676.705 1579034.822 2915637.644 2720016.321 0.729598022 0.899675279 0.835941992 0.674228823 0.868896334 1.250445484 1.060536542 0.580524025 1.071919172 1 21.37518388 2.998170205 24.98021496 0.952586614 0.793567158 0.235938846 0.169316331 146.8284484 2004541.491 0.054775958 0.064554333 995.7956049 -2.998170205 -0.159019456 AGPIWDLR ddPTM_BT-474_Pertuzumab_2h_R1 6 AGPIWDLR 8 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5;O43390;O43390-3;B4DT28;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 161.6 0.00080627 3299811000 5760530 6423450 5107614 5853050 5384670 3166722 6027880 5416790 5563170 6230280 FALSE TRUE 5535402.119 6240259.495 6030673.468 6155126.612 5557872.801 3230755.289 6101650.999 5304931.394 4931662.264 5808297.586 0.953016273 1.074369796 1.038285897 1.059712682 0.956884994 0.55623102 1.05050592 0.913336707 0.849071899 1 22.46968394 2.998187666 24.95042188 0.873982676 1.031587994 0.25799509 0.126101499 95.78835578 1318753.614 0.036450507 0.04295842 995.8356409 -2.998187666 0.157605318 GDFILVGDLMR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDFILVGDLMR 11 0 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 77.677 0.074356 7809100 12599 15227 12406 13829 12736 8893 13183 13201 10494 18020 FALSE TRUE 12106.61715 14792.74087 14648.04017 14542.71635 13145.66501 9072.822553 13344.3375 12928.39474 9302.765114 16799.48935 0.720653878 0.880547055 0.871933656 0.86566419 0.782503845 0.540065377 0.794329948 0.769570698 0.553752851 1 14.03612976 2.998213831 24.25260407 0.720557385 0.838565356 0.123129097 0.128002874 84.7677516 1151018.799 0.035311577 0.041587464 995.895639 -2.998213831 0.118007971 KLPVESIQIVLEELRK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLPVESIQIVLEELRK 16 2 K7ENE3;Q9BRG1;K7EKV4 K7ENE3 VPS25 Vacuolar protein-sorting-associated protein 25 0 237.59 5.15E-20 194420000 194290 193530 146260 141090 180320 214980 192840 198550 222520 207170 FALSE TRUE 186696.932 188010.7139 172692.4355 148371.6718 186120.1566 219327.0429 195200.0336 194449.8731 197260.4625 193138.1914 0.966649479 0.973451768 0.894139239 0.768215083 0.963663143 1.135596442 1.010675477 1.006791416 1.021343635 1 17.55927395 2.998456717 24.99973186 1.032773618 0.900427243 0.499881895 0.063386316 52.42465121 849255.5843 0.019369552 0.022849168 996.4527649 -2.998456717 -0.132346375 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSS(ph)GSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPR 45 1 O14686;O14686-3;F8VWW4 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLS(0.127)S(0.589)GS(0.285)PR 215.56 4.69E-45 647840000 202200 198310 163850 151020 186750 220690 201130 184940 237170 211190 TRUE FALSE 194297.8005 192654.393 193461.3398 158814.1603 192756.9834 225152.503 203591.4891 181120.9244 210247.4559 196885.9132 0.986854759 0.978507755 0.982606306 0.806630387 0.97902882 1.143568371 1.03405818 0.919928305 1.067864392 1 17.58700037 2.998536743 24.9996148 1.023488152 0.938160686 0.27626569 0.071450124 87.73853627 1499054.584 0.02222526 0.026200208 996.6363969 -2.998536743 -0.085327466 FSAS(ph)SGGGGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSASSGGGGSR 11 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 FS(0.001)AS(0.824)S(0.175)GGGGSR 100.07 0.0045171 443580000 444330 506710 456800 485150 468070 445740 450570 485110 508310 574590 TRUE FALSE 426965.0924 492259.1269 539353.9215 510188.6496 483125.8966 454753.1682 456084.2104 475092.309 450608.7798 535672.5075 0.797063666 0.918955369 1.006872509 0.952426422 0.901905343 0.848938786 0.851423592 0.886908143 0.841201991 1 19.03099173 2.9986466 24.91246069 0.876533369 0.925382102 0.042323538 0.064707742 113.6636542 2092310.234 0.018676341 0.02202763 996.8885318 -2.9986466 0.048848733 AYVWDNNKDLAEWLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYVWDNNKDLAEWLEK 16 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 228.51 3.68E-15 1081370000 946650 935510 674730 661450 860680 1007740 927190 867850 1234880 1027070 FALSE TRUE 909653.8714 908830.1708 796668.7203 695587.5138 888364.5538 1028117.193 938537.2286 849928.5942 1094701.599 957505.6341 0.950024563 0.949164306 0.832025099 0.726457881 0.927790419 1.07374532 0.980189771 0.887648661 1.14328476 1 19.86892145 2.998776471 24.99681906 0.997277387 0.863028325 0.403829458 0.086071943 55.00861586 1123874.889 0.026402726 0.031170482 997.1866858 -2.998776471 -0.134249061 GVIDYDRDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVIDYDRDR 9 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 ; 64.654 0.062727 550010000 210690 246540 202401 237330 214900 155401 237380 222740 217370 249000 FALSE TRUE 202456.0019 239508.9206 238979.3631 249578.6297 221812.4537 158543.3147 240285.1274 218140.3412 192695.0689 232135.0082 0.87214765 1.03176562 1.029484372 1.075144295 0.955532108 0.682978909 1.035109393 0.939713242 0.830099132 1 17.82460459 2.998861647 24.99954584 0.900208016 1.007347027 0.186606605 0.102850812 72.05159107 1582404.676 0.029786979 0.035170244 997.3822787 -2.998861647 0.107139011 LPLVPES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 LPLVPESPR 9 0 C9J0I9;Q86WB0;Q86WB0-2;Q86WB0-3 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR 182.28 4.88E-05 1545490000 593426 637308 552889 659796 591369 516997 609103 640626 559364 653779 TRUE FALSE 570234.2559 619132.5998 652808.3412 693848.1506 610390.921 527451.0336 616557.3847 627396.8492 495867.3438 609497.966 0.935580244 1.015807491 1.071059097 1.138392889 1.001465066 0.865386044 1.01158235 1.0293666 0.813566856 1 19.21726188 2.998925266 24.99697076 0.955867331 1.044327733 0.246619245 0.078161709 64.26062616 1494680.987 0.023373348 0.027605626 997.5283936 -2.998925266 0.088460402 NIEDYIHR ddPTM_BT-474_Pertuzumab_2h_R1 5 NIEDYIHR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ;;;; 193.1 0.00017241 2761070000 3162400 3484800 2820159 3127760 3071140 2858110 3137387 3078600 3318860 3443190 FALSE TRUE 3038809.912 3385416.916 3329824.465 3289184.068 3169926.007 2915902.942 3175783.281 3015025.834 2942116.927 3209979.674 0.946675749 1.054653692 1.037335062 1.024674422 0.987522143 0.908386731 0.98934685 0.939266332 0.916553133 1 21.61413273 2.998930588 5.0048406 0.949223977 1.019163393 0.40298059 0.037314447 0.164032711 12.02740619 0.010733913 0.012269829 997.5406175 -2.998930588 0.069939417 AGVEHQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGVEHQLR 8 0 A3KFJ0;O14965;A3KFJ1;Q5QPD4 A3KFJ0 AURKA Aurora kinase A 0 ; 123.98 0.0013243 183580000 358320 415500 363180 403110 367470 295550 428480 357020 321398 419120 FALSE TRUE 344316.4583 403650.3468 428814.7049 423914.5554 379290.0063 301526.2235 433723.8664 349647.4122 284914.2465 390732.6291 0.881207334 1.033060248 1.09746326 1.084922333 0.970714955 0.771694507 1.110027252 0.894850817 0.72917956 1 18.57582221 2.998972972 24.88526414 0.908091691 1.029757539 0.205052967 0.113894452 59.8071508 1449216.696 0.03307216 0.039059664 997.6379751 -2.998972972 0.121665848 KEPEDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEPEDGR 7 1 Q13867;J3KSD8;K7ES02;K7EMJ3 Q13867 BLMH Bleomycin hydrolase 0 ; 96.253 0.020632 218251000 1047080 994660 847250 936790 878930 282440 955260 997480 985990 1139210 FALSE TRUE 1006158.956 966293.2707 1000366.922 985137.8442 907201.5817 288151.1303 966950.7576 976881.6894 874064.5488 1062050.292 0.947374115 0.909837583 0.941920481 0.927581162 0.854198326 0.2713159 0.910456656 0.919807373 0.822997325 1 20.01842065 2.998982783 24.98000357 0.778222494 0.925854895 0.120555762 0.186187327 87.85927009 2157676.499 0.056662917 0.06692861 997.6605123 -2.998982783 0.147632401 KSSEAS(ph)PTAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSSEASPTAQR 11 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 KS(0.001)S(0.019)EAS(0.98)PTAQR;KSS(0.001)EAS(0.893)PT(0.106)AQR 132.93 0.00018244 186683000 194894 207577 159388 173993 196871 250360 212993 201862 232810 225600 TRUE FALSE 187277.327 201657.1072 188192.9572 182972.7996 203203.5345 255422.4507 215599.672 197693.4792 206382.3848 210319.9111 0.890440311 0.958811299 0.894793823 0.86997374 0.966164038 1.214447312 1.025103477 0.939965589 0.981278395 1 17.68222591 2.998998456 24.99714559 1.02752824 0.908237504 0.422863425 0.070730465 42.57334234 1062619.67 0.022447101 0.026514402 997.696516 -2.998998456 -0.119290736 EILFYDR ddPTM_BT-474_Pertuzumab_2h_R1 5 EILFYDR 7 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;;; 150.84 0.0044711 1939130000 1249005 1418680 1236020 1317190 1266640 986283 1390060 1316520 1292010 1500240 FALSE TRUE 1200192.504 1378220.635 1459396.309 1385170.334 1307382.626 1006226.318 1407071.97 1289333.402 1145346.441 1398627.409 0.858121682 0.985409429 1.043448956 0.99037837 0.934761194 0.719438438 1.006037749 0.921856239 0.818907476 1 20.41558025 2.999111815 24.95604374 0.893330834 0.974129598 0.139200991 0.089065441 62.80463679 1764758.488 0.025825071 0.030507298 997.9569678 -2.999111815 0.080798764 GSCFHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSCFHR 6 0 P62937;F8WE65;C9J5S7;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37 P62937 PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D" 0 ; 121.68 0.045473 1236450000 748980 978830 811350 1069240 855660 725970 937940 791030 799990 957570 FALSE TRUE 719709.0336 950914.7268 957978.9934 1124423.605 883183.081 740649.6108 949418.7903 774694.9541 709178.489 892712.931 0.806204334 1.065196542 1.073109798 1.259557877 0.989324844 0.829661569 1.063520822 0.867798513 0.794408218 1 19.7678368 2.999144594 24.99989316 0.912496554 1.062462164 0.214874117 0.125660349 47.1620992 1378422.269 0.036646656 0.043300012 998.0322923 -2.999144594 0.14996561 GS(ph)FSSENYWR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSFSSENYWR 10 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 GS(0.86)FS(0.139)S(0.001)ENYWR;GS(0.666)FS(0.294)S(0.04)ENYWR;GS(0.857)FS(0.135)S(0.008)ENYWR 193.22 6.26E-07 1358260000 970710 986750 890590 1108850 925180 741310 881060 1084640 791870 867570 TRUE FALSE 932773.58 958608.8561 1051539.424 1166077.881 954939.2549 756299.7961 891842.6758 1062241.805 701980.2374 808808.7111 1.153268464 1.185210845 1.300108925 1.441722703 1.180673801 0.935078697 1.102662055 1.313341202 0.86791874 1 19.62543901 2.999243958 24.99411123 1.085505026 1.271790576 0.370282281 0.134428072 37.4557446 1238332.867 0.041395932 0.048928117 998.2606644 -2.999243958 0.18628555 VFEEDALSWEDKLNR ddPTM_BT-474_Pertuzumab_2h_R1 3 VFEEDALSWEDKLNR 15 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 300.98 2.41E-44 1045400000 552330 619030 481570 516910 578350 673630 564270 640960 721400 701370 FALSE TRUE 530744.333 601375.8705 568600.4115 543587.787 596953.153 687251.2601 571175.7051 627723.952 639509.6964 653865.5852 0.811702504 0.919723999 0.869598316 0.83134485 0.912960043 1.051058927 0.873536883 0.960019867 0.978044587 1 19.31863457 2.999285829 19.91110343 0.963117763 0.86442076 0.540267874 0.049304741 1.656512653 46216.51469 0.013928486 0.016359964 998.3569118 -2.999285829 -0.098697003 MEIATKDPLNPIKQDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEIATKDPLNPIKQDVK 17 2 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 117.65 0.00011636 1254800000 853140 805040 460030 413750 684830 814300 722490 783280 976300 769420 FALSE TRUE 819798.3456 782081.0474 543167.6543 435103.6871 706858.1789 830765.7039 731332.0487 767104.9943 865474.517 717306.4981 1.142884315 1.090302471 0.757232307 0.606579877 0.985433954 1.158173955 1.019553079 1.069424293 1.206561657 1 19.45223017 2.999304246 24.99989695 1.085381877 0.889409107 0.257961633 0.152948446 38.2158147 1373266.352 0.04812962 0.056903816 998.3992489 -2.999304246 -0.19597277 VGSLYPEMSAHER ddPTM_BT-474_Pertuzumab_2h_R1 2 VGSLYPEMSAHER 13 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 71.879 0.04107 471150000 339490 398860 368280 394860 365380 308050 382170 358910 411320 422020 FALSE TRUE 326222.3555 387484.9033 434836.3883 415238.7719 377132.7795 314278.9821 386847.1108 351498.3831 364628.678 393436.2095 0.829162003 0.984873517 1.10522717 1.055415749 0.95856144 0.798805434 0.983252434 0.893406287 0.926779664 1 18.58577022 2.999313474 24.99620163 0.913624635 1.001757085 0.141011445 0.083506555 42.61530921 1551709.037 0.024506182 0.028963709 998.4204637 -2.999313474 0.08813245 ATS(ph)PRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSPRPR 7 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 AT(0.141)S(0.859)PRPR;AT(0.116)S(0.884)PRPR 69.825 0.035543 421520000 664550 750590 621290 682500 488890 504600 403620 426890 424810 480380 TRUE FALSE 638578.6513 729183.9081 733570.9235 717723.9068 504615.5908 514803.3577 408559.6223 418074.5723 376587.3497 447843.4347 1.425897092 1.628211673 1.638007542 1.60262237 1.126767865 1.149516366 0.912282263 0.933528416 0.840890634 1 18.77263493 2.999314231 1.575599426 0.931954068 1.593828991 0.895784824 0.097510282 0.105519122 0.535984281 0.035039225 0.041660195 998.4222042 -2.999314231 0.661874923 DHDTFLAVR ddPTM_BT-474_Pertuzumab_2h_R1 3 DHDTFLAVR 9 0 Q12907;D6RBV2;D6RDX1;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ;; 156.92 6.98E-05 613260000 148591 252963 179338 246045 173652 101923 213309 58753 211990 189671 FALSE TRUE 142783.8994 245748.7429 211748.366 258743.4119 179237.6743 103983.9529 215919.5393 57539.73002 187925.7839 176824.4142 0.807489735 1.389789662 1.19750639 1.463278773 1.013647776 0.588063325 1.221095742 0.325406026 1.062781883 1 17.43195796 2.999360284 24.77554124 0.791945519 1.227401071 0.268472424 0.286227799 23.07220537 893635.2639 0.079262336 0.093677204 998.5280827 -2.999360284 0.435455552 TQFEDLVPSPT(ph)SEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQFEDLVPSPTSEK 14 0 Q9Y4J8;Q9Y4J8-2;Q9Y4J8-15;Q9Y4J8-14;Q9Y4J8-13;Q9Y4J8-6;Q9Y4J8-10;Q9Y4J8-11;M0QZ28;M0R0C4 Q9Y4J8 DTNA Dystrobrevin alpha 1 TQFEDLVPS(0.289)PT(0.696)S(0.016)EK 201.57 1.97E-07 200800000 346790 366970 286360 304870 330930 351270 322860 377110 375590 341770 TRUE FALSE 333237.0634 356504.3749 338111.622 320604.3772 341574.664 358372.9201 326811.2573 369322.5467 332954.5978 318621.6135 1.045870868 1.118895768 1.061169763 1.006222942 1.072038586 1.124760233 1.025703353 1.159125844 1.044984344 1 18.28148461 2.999388721 24.99998977 1.084844491 1.059675322 0 0.050944179 79.56114996 3253958.091 0.014392074 0.017037565 998.593469 -2.999388721 -0.025169169 (ac)TECFLPPTS(ph)SPSEHRR ddPTM_BT-474_Pertuzumab_2h_R1 1 TECFLPPTSSPSEHRR 16 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.099)S(0.471)S(0.353)PS(0.076)EHRR 64.83 0.0020411 412600000 92445 99865 68482 71961 90032 105180 98267 103610 101600 111000 TRUE FALSE 88832.1472 97016.94798 80858.22077 75674.91583 92927.96104 107306.8117 99469.62094 101470.4173 90066.79394 103481.8711 0.858431977 0.937526032 0.781375712 0.731286698 0.89801199 1.036962421 0.961227506 0.980562259 0.870363021 1 16.65901852 2.999404856 24.99999213 0.968778353 0.829628843 0.531022286 0.063226796 18.13022822 761646.9751 0.019066892 0.022544729 998.6305688 -2.999404856 -0.13914951 RTEEGPTLSYGR ddPTM_BT-474_Pertuzumab_2h_R1 6 RTEEGPTLSYGR 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 252.44 7.46E-21 8186980000 2584520 2823400 2218550 2532940 2441840 2187660 2625540 2430740 2402950 2689790 FALSE TRUE 2483514.101 2742879.396 2619491.336 2663665.337 2520384.001 2231895.984 2657672.144 2380544.37 2130177.19 2507608.127 0.99039163 1.093822981 1.044617501 1.062233492 1.005094845 0.890049749 1.059843488 0.949328702 0.849485678 1 21.25788048 2.999924906 5.979450605 0.955091729 1.049319847 0.384744289 0.058368405 0.166177323 23.96808782 0.017105939 0.019576101 999.8271042 -2.999924906 0.094228118 FAQHGTFEYEYSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FAQHGTFEYEYSQR 14 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 232.78 3.99E-14 7358600000 1301300 1454480 1142610 1589800 1350100 1276740 1386130 1465540 1376100 1434410 FALSE TRUE 1250443.757 1412999.654 1349105.044 1671849.769 1393527.193 1302556.558 1403093.874 1435276.087 1219890.897 1337256.133 0.935081714 1.056640998 1.008860615 1.250209086 1.042079493 0.974051661 1.049233456 1.073299311 0.912234288 1 20.35084439 3.000134159 24.99998749 1.014984279 1.06938544 0.093174934 0.084611805 13.23593565 2465296.314 0.02504762 0.029656339 1000.308961 -3.000134159 0.054401161 DIRPVCR ddPTM_BT-474_Pertuzumab_2h_R1 5 DIRPVCR 7 1 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;;; 108.09 0.0066864 5325400000 387833 375424 379195 433076 372868 320674 405922 359936 345203 419333 FALSE TRUE 372676.0576 364717.2751 447723.9716 455427.1043 384861.6379 327158.248 410889.7949 352503.1958 306017.0026 390931.2024 0.953303434 0.932944909 1.145275611 1.164980184 0.984474085 0.836869111 1.051053977 0.901701357 0.782789915 1 18.57655521 3.000156389 24.99999913 0.918471026 1.051074209 0.297913723 0.097435518 7.436230593 1188332.846 0.02938606 0.034800598 1000.360164 -3.000156389 0.132603183 RPS(ph)QGPPAR ddPTM_BT-474_Pertuzumab_2h_R1 7 RPSQGPPAR 9 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR 131.17 0.00020861 6269346000 1354741 1458057 1210406 1448373 1328858 1236068 1248230 1557459 1378819 1223492 TRUE FALSE 1301796.224 1416474.642 1429153.29 1523123.704 1371601.924 1261062.142 1263506.212 1525296.927 1222301.248 1140623.797 1.141302003 1.241842092 1.25295763 1.335342738 1.202501585 1.105589893 1.107732642 1.337248032 1.071607703 1 20.12139161 3.000257425 24.99906829 1.158967262 1.246686091 0.223877826 0.094439954 17.72166164 1720647.922 0.028217947 0.033430305 1000.592919 -3.000257425 0.087718829 NIILEEGKEILVGDVGQTVDDPYATFVK ddPTM_BT-474_Pertuzumab_2h_R1 2 NIILEEGKEILVGDVGQTVDDPYATFVK 28 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 357.24 3.43E-111 2837600000 1859690 1659140 1191600 1129830 1490010 1629970 1514880 1712250 1825030 1431580 FALSE TRUE 1787011.259 1611822.952 1406948.627 1188140.662 1537937.525 1662929.11 1533419.555 1676891.439 1617860.246 1334617.811 1.338968537 1.207703762 1.054195902 0.890247868 1.152343024 1.245996491 1.148957808 1.25645816 1.212227374 1 20.34799523 3.000374059 24.99999737 1.192692068 1.111114948 0.018511378 0.12633318 37.38682681 2498364.834 0.038182383 0.045245975 1000.861673 -3.000374059 -0.08157712 GQHPNPLR ddPTM_BT-474_Pertuzumab_2h_R1 5 GQHPNPLR 8 0 M0R1K3;Q15102;M0R389;M0QZT2 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;;; 103.83 0.0046967 1849130000 1890810 2014500 1803980 1857900 1753850 1057000 2076490 1645470 1830450 2081190 FALSE TRUE 1816915.055 1957048.432 2129999.315 1953786.442 1810264.178 1078373.264 2101902.706 1611490.469 1622664.99 1940229.148 0.936443542 1.008668711 1.097808121 1.006987471 0.93301566 0.555796858 1.083327043 0.830567086 0.836326468 1 20.88779562 3.000480384 19.23696091 0.855414087 1.012263924 0.222959028 0.132931901 1.30229361 51959.87346 0.03761725 0.044275195 1001.106737 -3.000480384 0.156849837 EGDLIAAQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGDLIAAQAR 10 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 156.46 2.54E-05 1064040000 1429930 1517070 1231240 1503180 1401470 1355130 1444020 1426870 1486070 1707360 FALSE TRUE 1374046.755 1473804.649 1453752.457 1580759.3 1446549.555 1382531.657 1461692.349 1397404.636 1317377.564 1591718.986 0.863247072 0.925920129 0.913322307 0.993114559 0.908797073 0.868577726 0.918310557 0.877921698 0.827644562 1 20.60215422 3.000494677 24.99998435 0.891350422 0.926747887 0.042445052 0.050898686 41.70987303 2107719.239 0.014158729 0.016781304 1001.139684 -3.000494677 0.035397465 DTNFGTNCICR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTNFGTNCICR 11 0 P41223;C9JCD9;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 87.568 0.021084 0 24780 27387 19335 24868 22490 19608 21104 23571 22783 24335 FALSE TRUE 23811.5702 26605.94957 22829.2646 26151.44046 23213.41127 20004.48719 21362.27706 23084.25061 20196.76935 22686.76877 1.049579622 1.172751829 1.00628101 1.152717724 1.023213641 0.881768902 0.941618318 1.017520425 0.890244422 1 14.46956352 3.000533415 7.669668257 0.952605639 1.093967854 0.586081506 0.059000914 0.085222335 39.4221889 0.016674266 0.019154901 1001.228989 -3.000533415 0.141362215 VVDPFSKK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVDPFSKK 8 1 P61247;E9PFI5;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 116.52 0.0036163 1397990000 3415800 3311900 2637200 2501700 3204900 3567100 3282800 3794300 3919100 3864600 FALSE TRUE 3282306.76 3217447.855 3113800.704 2630813.037 3307988.519 3639229.206 3322975.888 3715946.379 3474220.198 3602847.2 0.911031353 0.893029228 0.864261106 0.730203889 0.918159538 1.010098126 0.922319406 1.031391611 0.964298513 1 21.78070604 3.000653862 24.99997788 0.983726947 0.850076898 0.599151997 0.052451501 15.86111143 606389.0534 0.015518825 0.018394303 1001.506708 -3.000653862 -0.133650049 ALDDKNCWEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDDKNCWEK 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 125.28 0.0003768 370850000 1023200 1150200 713300 793810 985640 1079300 1030800 1097000 1304700 1187000 FALSE TRUE 983212.2128 1117397.422 842209.1773 834778.6292 1017344.006 1101124.185 1043415.239 1074346.567 1156595.926 1106603.433 0.888495538 1.009754162 0.761075876 0.754361142 0.919339282 0.99504859 0.942898972 0.970850564 1.045176521 1 20.07770687 3.000675305 24.99756909 0.980889342 0.855349405 0.452395538 0.070900078 24.76082573 916491.077 0.022016222 0.026097677 1001.556156 -3.000675305 -0.125539937 DYGVYLEDSGHTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYGVYLEDSGHTLR 14 0 Q13162;H7C3T4 Q13162 PRDX4 Peroxiredoxin-4 0 ; 175.28 2.41E-06 345600000 440670 552900 502370 572750 487570 270080 617410 442410 518730 591340 FALSE TRUE 423448.1292 537131.8333 593159.4342 602309.6961 503253.1318 275541.2026 624966.0483 433274.0789 459845.9451 551288.0151 0.768106902 0.974321623 1.075951985 1.092549955 0.912867899 0.499813519 1.133647079 0.785930525 0.834130133 1 19.07244671 3.000712871 24.9998283 0.841927111 0.986780197 0.105753383 0.172463844 50.24320541 1761855.492 0.048967247 0.058046908 1001.642795 -3.000712871 0.144853085 AALSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALSSPR 7 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 AALS(0.057)S(0.943)PR;AALS(0.372)S(0.628)PR 98.997 0.011384 411030000 670590 783080 605100 737890 658890 534780 726200 671160 594610 726540 TRUE FALSE 644382.6014 760747.3251 714455.0304 775972.5913 680083.7952 545593.618 735087.4528 657300.3115 527112.3656 677330.7987 0.951355826 1.123154781 1.054809602 1.145633113 1.004064479 0.805505403 1.08527097 0.97042732 0.778219987 1 19.36950107 3.000783384 24.97912105 0.939090783 1.07203264 0.319856033 0.096267884 33.11251129 1055760.949 0.027413316 0.032500347 1001.805436 -3.000783384 0.132941858 DNTIEHLLPLFLAQLKDECPEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNTIEHLLPLFLAQLKDECPEVR 23 1 P30153;B3KQV6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 203.4 1.15E-24 2085990000 2660800 2686000 1728620 1943900 2289100 2695700 2286300 2337700 2838500 2419300 FALSE TRUE 2556812.994 2609397.91 2041020.087 2044224.912 2362730.98 2750208.901 2314280.423 2289425.678 2516285.38 2255438.656 1.133621164 1.156935882 0.904932653 0.906353585 1.047570491 1.219367635 1.026088835 1.015068919 1.115652325 1 21.10497662 3.000937572 24.99995854 1.073613843 1.020082663 0.055524062 0.095880215 109.4556456 2918438.687 0.030075456 0.035660462 1002.161172 -3.000937572 -0.05353118 EQEAEPEEQEEDSSSDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQEAEPEEQEEDSSSDPR 18 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 174.59 1.27E-11 158870000 42035 42461 32008 42479 38262 34583 36163 45754 38202 36858 FALSE TRUE 40392.22573 41250.05385 37792.55761 44671.34628 39492.73198 35282.29195 36605.57361 44809.16391 33865.46912 34361.57483 1.175505661 1.200470411 1.099849404 1.300037804 1.149328346 1.026794963 1.06530547 1.30404861 0.985562195 1 15.06850854 3.001100594 24.99723806 1.108966833 1.192329736 0.214774329 0.09711893 78.42064562 1781042.043 0.029204204 0.034624514 1002.537425 -3.001100594 0.083362903 LLDPEDISVDHPDEK ddPTM_BT-474_Pertuzumab_2h_R1 6 LLDPEDISVDHPDEK 15 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 238.22 9.21E-18 2741300000 1919740 1917410 1704620 1763530 1971130 2244620 2019930 2305240 2362210 2380970 FALSE TRUE 1844714.438 1862727.344 2012682.753 1854545.995 2034533.187 2290007.754 2044650.508 2257635.988 2094061.824 2219704.781 0.831062966 0.839177966 0.906734432 0.835492184 0.916578278 1.031672218 0.921136236 1.017088402 0.943396546 1 21.08193638 3.001188915 4.607639782 0.981293566 0.856964015 0.737486526 0.036387538 0.094680152 5.275388542 0.010317783 0.011829125 1002.741329 -3.001188915 -0.124329552 ELLPLIYHHLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLPLIYHHLLR 12 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 ; 97.214 0.0029189 434900000 411900 457680 376270 423090 365700 271480 416120 184244 417200 450880 FALSE TRUE 395802.4926 444627.4145 444270.3591 444925.7256 377463.0726 276969.5116 421212.601 180439.297 369841.205 420341.496 0.941621268 1.057776638 1.056927197 1.058486326 0.897991457 0.658915463 1.002072375 0.429268342 0.879858897 1 18.68120236 3.001231177 3.861225986 0.74966349 1.031051576 0.296514594 0.162827827 0.22340065 7.481689238 0.048716617 0.055993829 1002.838912 -3.001231177 0.281388085 HVEAVYIDIADR ddPTM_BT-474_Pertuzumab_2h_R1 4 HVEAVYIDIADR 12 0 F5GWE5;Q00169;I3L4H1;I3L2X8;I3L4C0;I3L459;I3NI10 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ;;; 162.32 6.05E-05 1179090000 1581240 1853670 1504220 2270740 1703340 965170 2051150 1631980 1978050 1987860 FALSE TRUE 1519443.393 1800805.147 1776066.015 2387933.164 1758129.478 984686.3987 2076252.587 1598279.043 1753510.057 1853220.472 0.819893486 0.971716627 0.958367362 1.288531613 0.948688785 0.531337967 1.120348398 0.862433298 0.94619614 1 20.82160309 3.001355328 24.9999607 0.884878996 1.017676959 0.087253629 0.177781909 106.0229181 1955590.806 0.051362159 0.060944937 1003.125632 -3.001355328 0.132797963 VLDWICR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLDWICR 7 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 91.041 0.061963 0 50041 62131 51592 81108 57707 49260 53616 60627 68502 47563 FALSE TRUE 48085.3424 60359.08471 60915.82206 85293.9936 59563.19806 50256.07095 54272.16865 59375.03126 60725.94014 44341.51565 1.084431637 1.36123188 1.373787548 1.923569647 1.343282862 1.133386404 1.223958357 1.339039282 1.369505288 1 15.43637046 3.001373495 24.99997856 1.242893621 1.451933332 0.18381742 0.216437985 85.95924375 1564546.503 0.064626705 0.076692294 1003.167595 -3.001373495 0.209039711 AYIDSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 AYIDSFR 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 143.37 0.005645 303020000 744150 800830 676250 798940 734520 624880 784660 763550 788520 839500 FALSE TRUE 715067.7953 777991.1125 798463.4181 840173.3891 758146.5029 637515.5017 794262.9038 747782.4257 699010.5153 782639.9173 0.913661289 0.994060098 1.020218111 1.073512059 0.968704108 0.814570644 1.014851001 0.955461649 0.893144472 1 19.57798917 3.001449189 24.99999943 0.936414433 1.003803069 0.186033688 0.063738275 80.34197262 1385930.623 0.018579326 0.022048078 1003.342454 -3.001449189 0.067388636 VFDFAGEEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFDFAGEEVR 10 0 Q9UEE9;Q9UEE9-2 Q9UEE9 CFDP1 Craniofacial development protein 1 0 ; 146.27 6.73E-05 139301000 229180 240520 195186 231760 211480 181399 207491 226810 219130 218610 FALSE TRUE 220223.3922 233660.6051 230460.4521 243721.1614 218282.4463 185067.0121 210030.3369 222126.2942 194255.2811 203803.35 1.080568068 1.146500316 1.130798155 1.195864354 1.071044447 0.908066585 1.030553899 1.08990502 0.953150579 1 17.63681824 3.001564922 23.76604131 1.009736634 1.137837539 0.617899309 0.052216292 20.73747226 314912.5809 0.015874337 0.018826174 1003.609867 -3.001564922 0.128100904 RS(ph)FSKEVEER ddPTM_BT-474_Pertuzumab_2h_R1 2 RSFSKEVEER 10 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 RS(0.852)FS(0.148)KEVEER;RS(0.951)FS(0.049)KEVEER 126.1 0.00020433 541520000 541210 526370 360870 393570 489860 536450 495200 589060 615180 565000 TRUE FALSE 520058.9149 511358.443 426087.2365 413882.1949 505616.7918 547297.3866 501260.4057 576895.7051 545347.3454 526732.0468 0.987331069 0.970813236 0.808925979 0.785754726 0.95991272 1.039043267 0.951642128 1.09523563 1.035341117 1 19.00670971 3.001728956 24.85276211 1.026414743 0.886492592 0.479032413 0.066863461 47.80545776 687152.6348 0.020998685 0.024927327 1003.989002 -3.001728956 -0.139922151 LLHDQIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLHDQIEK 8 0 P12270 P12270 TPR Nucleoprotein TPR 0 ; 113.71 0.0027969 416010000 910400 896760 738060 746040 841690 873130 885480 901430 1010930 913310 FALSE TRUE 874820.5615 871185.2828 871443.8601 784543.2138 868763.7233 890785.2868 896316.7691 882815.1555 896173.4646 851450.7002 1.02744711 1.023177599 1.023481289 0.921419424 1.020333559 1.046197139 1.052693678 1.03683649 1.052525372 1 19.69956347 3.001759377 24.99997146 1.040121029 0.998436765 0.24895558 0.031594226 77.79666001 1105419.968 0.00931424 0.011061765 1004.059332 -3.001759377 -0.041684265 LTDIFR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTDIFR 6 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;; 137.5 0.029562 3068540000 2649650 2885090 2508950 2871920 2660020 2572230 2527690 2768970 2918740 3045580 FALSE TRUE 2546098.749 2802810.058 2962373.076 3020140.135 2745581.959 2624242.253 2558624.626 2711789.802 2587416.872 2839300.154 0.896734621 0.987148208 1.043346218 1.063691745 0.966992502 0.924256722 0.901146229 0.955090922 0.911286842 1 21.43710394 3.001796918 24.89210701 0.935301896 1.002121319 0.249035226 0.048232498 71.97217935 996974.3814 0.014324234 0.017007912 1004.146127 -3.001796918 0.066819423 FLDEDFVFDIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLDEDFVFDIYR 12 0 O75794;H7BZW7 O75794 CDC123 Cell division cycle protein 123 homolog 0 ; 152.07 0.00016167 18321500 38195 43820 35660 42491 38251 33485 41679 35683 41963 43174 FALSE TRUE 36702.29717 42570.2965 42104.55525 44683.9656 39481.37815 34162.08964 42189.08007 34946.13358 37199.53616 40249.78652 0.911863151 1.057652728 1.046081455 1.110166524 0.980909008 0.84875207 1.048181462 0.868231526 0.92421698 1 15.29669351 3.002002644 24.99607934 0.932032907 1.035756342 0.274986542 0.071168724 75.11435967 937517.2914 0.019771566 0.023481633 1004.621907 -3.002002644 0.103723435 EHALLAYTLGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHALLAYTLGVK 12 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;P68104;Q5VTE0;A0A087WV01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 186.46 1.17E-05 23015000000 13659200 13590500 11138400 13073100 12641600 11537800 14783100 9830400 16896200 16676300 FALSE TRUE 13125383.36 13202912.25 13151356.65 13747804.26 13048228.54 11771102.22 14964020 9627398.805 14978214.21 15546799.35 0.844249872 0.849236679 0.845920524 0.88428518 0.839287126 0.757139908 0.962514513 0.619252786 0.963427512 1 23.89011426 3.002036204 24.995319 0.824766747 0.855612895 0 0.108075502 387.6170153 4758065.167 0.030161908 0.035808419 1004.699542 -3.002036204 0.030846148 LDAQSLNLSQEDFDRYMSGQT(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDAQSLNLSQEDFDRYMSGQTSPR 24 1 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A0A0MSJ3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 LDAQSLNLSQEDFDRYMS(0.011)GQT(0.495)S(0.495)PR 80.93 0.026998 138240000 40760 31827 21195 29235 31641 41151 28350 35760 33435 37787 TRUE FALSE 39167.05414 30919.32512 25025.40798 30743.82185 32658.7615 41983.10141 28696.95578 35021.5435 29639.59897 35227.65283 1.111826959 0.877700404 0.710391013 0.872718429 0.92707742 1.191765503 0.814614471 0.994149218 0.841373086 1 15.10442073 3.002087564 23.95143779 0.967592196 0.881612303 0.065071119 0.131815243 106.4856367 1221692.912 0.038350719 0.045520262 1004.818364 -3.002087564 -0.085979893 FTEDSLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTEDSLLR 8 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 118.05 0.0045621 229214000 331151 357910 328256 386430 347363 327301 372180 362981 340101 409680 FALSE TRUE 318209.2528 347702.7572 387579.1612 406373.6986 358536.2464 333919.2505 376734.8502 355485.3155 301494.1603 381932.0087 0.833156807 0.910378678 1.014785753 1.063994872 0.938743646 0.874289776 0.986392451 0.930755494 0.789392231 1 18.54295631 3.002202589 24.99938621 0.918100029 0.962178194 0.049908607 0.079044643 228.6177064 2594735.026 0.023750641 0.02822062 1005.084532 -3.002202589 0.044078166 RPYDLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPYDLDR 7 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;; 88.358 0.029929 1051920000 679640 767020 692280 710400 656360 363265 756240 634180 683150 827760 FALSE TRUE 653078.9174 745145.3406 817390.3957 747063.8291 677472.4155 370610.4672 765495.0913 621083.9614 605601.676 771695.0779 0.846291412 0.96559556 1.059214214 0.96808163 0.877901693 0.480255062 0.991965756 0.804830793 0.784768095 1 19.55767138 3.002219531 20.02296328 0.802182229 0.961771997 0.191264854 0.142120445 8.864468035 79938.73071 0.040462328 0.047847212 1005.123741 -3.002219531 0.159589768 IELGDVTPHNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 IELGDVTPHNIK 12 0 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;F8WCK0;C9JZU6;C9J5J3;A0A0D9SF32 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ; 131.37 0.00019995 361470000 351120 368220 263977 269979 327340 370480 339610 341340 385250 409530 FALSE TRUE 337397.8422 357718.7261 311683.516 283912.6485 337869.1884 377971.3594 343766.2488 334291.2097 341518.0351 381792.1683 0.883721224 0.936946213 0.81636959 0.74363141 0.884955786 0.989992438 0.90040152 0.875584251 0.89451294 1 18.54242798 3.002271693 24.99989294 0.919799234 0.845244271 0.312780476 0.059479849 107.9674694 1188147.325 0.018388289 0.021848365 1005.244471 -3.002271693 -0.074554963 YVESFR ddPTM_BT-474_Pertuzumab_2h_R1 3 YVESFR 6 0 P50135;P50135-3;P50135-2 P50135 HNMT Histamine N-methyltransferase 0 ;; 132.94 0.034151 482812000 485775 523074 494226 528458 490195 375735 536153 504962 514819 596472 FALSE TRUE 466790.3759 508156.4417 583543.6322 555731.7807 505962.5674 383332.6191 542714.6008 494534.3582 456378.9054 556072.4202 0.839441697 0.913831406 1.04940222 0.999387419 0.909886103 0.689357366 0.975978274 0.889334447 0.820718469 1 19.08491326 3.002390891 24.96084234 0.870635638 0.954918477 0.122349745 0.094584929 146.8398211 1532967.28 0.027563175 0.032751875 1005.520412 -3.002390891 0.084282839 GHVDILAPTVQELAALEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GHVDILAPTVQELAALEK 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 107.57 0.0004163 486370000 552570 538860 455820 474140 521490 574470 570100 510770 632360 597050 FALSE TRUE 530974.9535 523492.2404 538196.8137 498610.4222 538264.1995 586086.177 577077.0543 500222.421 560577.1439 556611.2717 0.95394215 0.940498813 0.966916843 0.895796488 0.967037907 1.052954201 1.036768538 0.898692582 1.00712503 1 19.0863106 3.002456739 24.94153237 0.990424872 0.940107054 0.300177499 0.042091327 121.5072249 1233546.17 0.013364737 0.01588132 1005.672882 -3.002456739 -0.050317818 ESWHGKPLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESWHGKPLPK 10 1 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 106.62 0.0014376 3352700000 4790900 6159000 5163600 5513100 4921300 2487900 5331200 4895100 5182300 6340700 FALSE TRUE 4603666.331 5983351.35 6096777.384 5797631.752 5079598.084 2538207.043 5396444.82 4794014.474 4594027.03 5911238.741 0.778798917 1.012199238 1.031387438 0.980781187 0.859311949 0.429386657 0.912912683 0.810999976 0.777168244 1 22.49502906 3.002457964 21.49186901 0.773848603 0.9558241 0.204356339 0.152110912 19.18175181 167695.8387 0.04357988 0.051640334 1005.675718 -3.002457964 0.181975497 LVINGNPITIFQER ddPTM_BT-474_Pertuzumab_2h_R1 2 LVINGNPITIFQER 14 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 361.34 2.96E-82 4371300000 701930 726340 670630 822070 713250 668020 724370 760690 776560 716820 FALSE TRUE 674497.7996 705625.4944 791827.7591 864497.1312 736192.334 681527.8221 733235.0567 744981.4857 688408.1644 668269.1429 1.009320581 1.055900159 1.184893493 1.293636165 1.101640472 1.019840328 1.097215193 1.114792586 1.030136094 1 19.35006973 3.002533889 24.99972091 1.067011873 1.141707579 0.191137698 0.078171193 157.9331546 1558155.558 0.024510035 0.029136435 1005.851549 -3.002533889 0.074695706 KVFASLPQVER ddPTM_BT-474_Pertuzumab_2h_R1 2 KVFASLPQVER 11 1 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 135.58 0.00018761 2253900000 2789600 3148800 2398700 2768100 2726600 2364700 2958900 2919400 2908700 3096100 FALSE TRUE 2680579.348 3058999.307 2832198.449 2910961.973 2814303.565 2412515.854 2995111.903 2859113.37 2578516.57 2886398.389 0.928693474 1.059798023 0.981222294 1.008510115 0.975022566 0.835822201 1.037664071 0.990547036 0.893333567 1 21.46083901 3.002689466 24.82033829 0.955790461 0.997451558 0.097520665 0.060958571 197.4832358 1822476.448 0.017631571 0.020961784 1006.211939 -3.002689466 0.041661097 LTVDEAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTVDEAVR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 134.3 0.0020535 162880000 605250 640030 582120 610940 579250 375360 666200 616720 595700 683090 FALSE TRUE 581596.1609 621776.9711 687322.0332 642470.6866 597882.1023 382950.0364 674353.1549 603984.5165 528078.6334 636823.7059 0.913276556 0.976372213 1.079297185 1.008867416 0.938850261 0.601343877 1.058932242 0.948432841 0.829238341 1 19.28053452 3.003142862 23.73607414 0.89067585 0.996051763 0.148359061 0.120589582 103.9492941 785036.9953 0.035698543 0.042421158 1007.262955 -3.003142862 0.105375913 LVHLWSSDSHQPLWSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVHLWSSDSHQPLWSR 16 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ELI8 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 167.69 3.61E-09 152200000 126250 147170 112240 137160 121080 95862 144980 88262 145200 152930 FALSE TRUE 121316.0104 142972.8557 132524.2648 144238.844 124974.6482 97800.39532 146754.3086 86439.35886 128717.5047 142571.9149 0.850910998 1.002812201 0.929525741 1.011691848 0.876572699 0.685972377 1.029335327 0.60628602 0.90282511 1 17.12133029 3.003310851 23.2239431 0.814775983 0.950339122 0.106241531 0.128449002 64.07457141 449430.4716 0.035062873 0.041661523 1007.65265 -3.003310851 0.13556314 DGYSYGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGYSYGSR 8 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 122.18 0.0032608 968740000 642610 715670 645720 749830 680460 657710 710550 675810 730650 820780 FALSE TRUE 617496.0908 695259.7923 762415.968 788528.8162 702347.6139 671009.3468 719245.9234 661854.2873 647709.6751 765187.8395 0.806986283 0.908613227 0.996377528 1.030503591 0.917876079 0.87692108 0.93995995 0.86495662 0.84647147 1 19.54545442 3.003413675 24.99330021 0.897602793 0.942550761 0.030787311 0.06822737 279.1944394 2044089.573 0.020364876 0.024231255 1007.891249 -3.003413675 0.044947968 EGLQNMEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EGLQNMEAR 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 170.69 0.00013381 4464650000 2120560 2386730 2032420 2269060 2150970 1828990 2394830 2130870 2395910 2517390 FALSE TRUE 2037686.171 2318662.797 2399723.505 2386166.459 2220157.904 1865973.431 2424138.646 2086866.79 2123936.341 2346884.933 0.868251418 0.98797464 1.022514343 1.01673773 0.946002027 0.795085181 1.032917555 0.889207119 0.905002334 1 21.16231568 3.003420526 24.43868846 0.919005899 0.978728959 0.091293026 0.071853265 159.2776973 1137967.291 0.020250852 0.024086458 1007.90715 -3.003420526 0.05972306 FVSEEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FVSEEHR 7 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 ; 142.64 0.0024759 655050000 640820 785460 674130 763640 675150 519960 767790 641200 708300 761060 FALSE TRUE 615776.0459 763059.4498 795960.2869 803051.5519 696866.8129 530473.9475 777186.4437 627958.9959 627896.7534 709512.7283 0.867885834 1.075469712 1.121840744 1.1318353 0.982176619 0.747659522 1.095380552 0.885056703 0.884968977 1 19.43646904 3.003456732 24.7708584 0.921237302 1.056401098 0.235319697 0.107311411 126.4906659 906411.7748 0.030463637 0.036240853 1007.991181 -3.003456732 0.135163796 TLSDVEDQKELAS(ph)PVSPELR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLSDVEDQKELASPVSPELR 20 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 TLSDVEDQKELAS(0.998)PVS(0.002)PELR 87.808 0.0013993 196050000 158860 165580 120810 123510 149140 176480 152340 148590 186230 178540 TRUE FALSE 152651.5756 160857.8205 142643.0544 129884.3659 153937.2235 180048.5465 154204.3825 145521.5646 165089.9511 166447.3268 0.917116415 0.966418768 0.856986154 0.780333145 0.924840468 1.081714858 0.926445534 0.874279974 0.991845014 1 17.34470617 3.003835433 24.99942554 0.960238989 0.880696373 0.294879285 0.067213775 182.6235213 1190325.24 0.021320808 0.025377898 1008.870524 -3.003835433 -0.079542615 DRLPEMLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRLPEMLR 8 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 0 87.913 0.013668 87031000 50456 61617 44007 53176 49303 30839 57018 49465 55980 60868 FALSE TRUE 48484.12374 59859.74349 51960.04383 55920.41973 50888.87577 31462.58571 57715.80334 48443.53046 49625.38509 56745.35614 0.85441571 1.054883563 0.915670415 0.985462486 0.896793663 0.554452167 1.017101791 0.853700351 0.874527688 1 15.79221471 3.004152836 24.45573735 0.850524788 0.955256706 0.103717378 0.126850241 189.1510926 1113874.553 0.035770285 0.042570027 1009.608122 -3.004152836 0.104731918 VDIKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDIKDR 6 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 98.418 0.036441 1693440000 4974800 4780700 3334500 3102600 4121000 4603400 4106400 4554800 4826600 4294500 FALSE TRUE 4780379.316 4644359.117 3937118.326 3262725.558 4253555.708 4696483.902 4156655.352 4460741.788 4278704.603 4003629.69 1.194011356 1.160037135 0.983387234 0.814941893 1.062424859 1.173056518 1.038221732 1.11417442 1.068706383 1 21.93287711 3.004166657 24.99882316 1.088036375 1.029870283 0.026340075 0.105241513 410.5909101 2463391.849 0.032811146 0.039080144 1009.640252 -3.004166657 -0.058166092 YRGDYDR ddPTM_BT-474_Pertuzumab_2h_R1 6 YRGDYDR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 122.18 0.0039821 3043190000 2458423 2769975 2268674 2565868 2422735 2145099 2554761 2566148 2530969 2490408 FALSE TRUE 2362345.111 2690978.025 2678673.858 2698292.755 2500664.472 2188474.372 2586026.929 2513156.147 2243664.01 2321730.448 1.017493272 1.159039813 1.153740246 1.162190364 1.07706925 0.942604846 1.113835989 1.082449579 0.966375753 1 21.14676905 3.004195621 18.94051433 1.035617545 1.12683995 0.368129051 0.061638111 7.151074215 32270.1106 0.018170827 0.02152732 1009.707591 -3.004195621 0.091222405 EVADEVTRPRPSGEEVLQDIQVMLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVADEVTRPRPSGEEVLQDIQVMLK 25 2 P33992;B1AHA9 P33992 MCM5 DNA replication licensing factor MCM5 0 ; 172.02 3.60E-12 140966000 160235 164506 131779 139673 156329 169117 157081 170447 187914 187338 FALSE TRUE 153972.8391 159814.4499 155594.3967 146881.5403 161357.4643 172536.6616 159003.4043 166927.2099 166582.7905 174649.4304 0.881610886 0.915058524 0.890895529 0.84100784 0.923893447 0.987902802 0.910414674 0.955784451 0.953812389 1 17.41410241 3.004276348 24.78856446 0.954531119 0.884785843 0.631937112 0.028301579 76.36427017 442650.8897 0.007963067 0.009480192 1009.895294 -3.004276348 -0.069745276 YLPHSAGR ddPTM_BT-474_Pertuzumab_2h_R1 7 YLPHSAGR 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;;; 182.68 0.00022728 6363010000 4591260 5104910 4438410 4945640 4409370 3202680 5030620 4087590 4639510 5007940 FALSE TRUE 4411828.483 4959322.965 5240529.419 5200885.073 4551201.391 3267440.384 5092186.232 4003179.838 4112852.275 4668747.763 0.944970409 1.06223836 1.122470025 1.113978595 0.974822719 0.699853697 1.090696369 0.857441875 0.880932636 1 22.15460422 3.004466419 18.45237652 0.902055139 1.062781478 0.329680032 0.104194168 5.41385074 22355.93305 0.02922568 0.034617257 1010.337374 -3.004466419 0.160726339 LTGIKHELQANCYEEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTGIKHELQANCYEEVK 17 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 191.99 1.27E-10 4184200000 5231000 5014300 3591900 3267900 4464400 4836100 4467100 5010100 5644500 4915900 FALSE TRUE 5026566.737 4871297.074 4241036.231 3436556.711 4608001.48 4933889.255 4521769.706 4906639.684 5003760.024 4582941.714 1.096799185 1.062919273 0.925396066 0.749858262 1.005468053 1.076576916 0.98665224 1.070631047 1.09182275 1 22.12784251 3.004566426 24.99434911 1.045782507 0.953035023 0.163700822 0.091687113 240.6128308 1316977.549 0.028638278 0.034112719 1010.570057 -3.004566426 -0.092747484 LQELSAEER ddPTM_BT-474_Pertuzumab_2h_R1 2 LQELSAEER 9 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 169.77 0.00013543 1697300000 1328690 1369210 1135170 1397820 1284850 1213120 1395570 1316070 1397740 1399400 FALSE TRUE 1276763.326 1330161.471 1340320.471 1469961.658 1326178.367 1237650.118 1412649.403 1288892.695 1239074.415 1304617.392 0.978649629 1.019579748 1.027366705 1.126737745 1.016526666 0.948669032 1.082807429 0.98794689 0.949760767 1 20.31519534 3.004765347 24.99417287 0.998341315 1.040450763 0.150285986 0.048932954 274.1088427 1437677.211 0.0144495 0.017214183 1011.033037 -3.004765347 0.042109448 KQMVIDVLHPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQMVIDVLHPGK 12 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 141.38 3.93E-05 5620800000 11294600 11037800 9854500 9385000 10837600 11141600 11154000 11929500 12984800 12570200 FALSE TRUE 10853194.55 10723012.75 11635427.36 9869360.975 11186201.25 11366890.79 11290505.99 11683151.66 11510819.94 11718809.16 0.926134593 0.915025802 0.992884789 0.842181218 0.954551021 0.969969784 0.963451647 0.996957242 0.982251676 1 23.48232264 3.004888286 24.99995381 0.979999128 0.920832628 0.415965074 0.035364504 138.1686233 706620.049 0.009939743 0.011843339 1011.319279 -3.004888286 -0.0591665 GWDSS(ph)HEDDLPVYLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWDSSHEDDLPVYLAR 16 0 Q14195-2 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 1 GWDS(0.463)S(0.537)HEDDLPVYLAR 79.311 0.012049 15495000 19975 22428 20698 23359 20520 17345 21925 19439 22982 23718 TRUE FALSE 19194.35492 21788.3754 24438.58902 24564.56079 21180.04444 17695.72778 22193.32471 19037.57786 20373.17971 22111.55873 0.86806883 0.985383964 1.105240445 1.110937546 0.957872065 0.800293095 1.003697884 0.860978554 0.921381435 1 14.43251311 3.004963097 24.7246589 0.908760561 1.023020416 0.233825669 0.084534833 156.1411979 777837.2783 0.024606344 0.029311741 1011.493503 -3.004963097 0.114259855 GEEGRPGKK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEEGRPGKK 9 2 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 80.219 0.01391 841410000 1275820 1225450 898500 1005060 1113580 1164740 1149840 1203790 1317200 1161200 FALSE TRUE 1225959.544 1190501.366 1060878.937 1056931.267 1149399.312 1188291.841 1163912.086 1178931.316 1167676.978 1082550.89 1.132472899 1.099718616 0.979980662 0.976334025 1.061750836 1.09767758 1.075156925 1.08903085 1.078634722 1 20.04600342 3.005271099 24.99168923 1.075812064 1.042706428 0.022872872 0.051045988 409.7413711 1942668.946 0.015620238 0.018618435 1012.211108 -3.005271099 -0.033105636 EYFGGFGEVESIELPMDNK ddPTM_BT-474_Pertuzumab_2h_R1 2 EYFGGFGEVESIELPMDNK 19 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 126.88 2.45E-05 115055000 177753 175035 142303 167356 179443 169340 174814 200130 205900 194550 FALSE TRUE 170806.2162 170043.1732 168020.3176 175993.2632 185214.9471 172764.1708 176953.426 195997.2456 182527.0952 181372.9552 0.941740272 0.937533234 0.926380217 0.970339062 1.021182827 0.952535457 0.975632921 1.080631042 1.006363352 1 17.46859982 3.005365116 0.654450076 1.029951623 0.928861594 0.469942088 0.032487265 0.667989425 0.630050801 0.024259366 0.034282889 1012.430257 -3.005365116 -0.101090029 LCSDLMNCLHER ddPTM_BT-474_Pertuzumab_2h_R1 3 LCSDLMNCLHER 12 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;; 220.66 2.90E-11 1065030000 1060050 1168500 996290 1160480 1051950 938680 1164290 1008080 1119590 1216110 FALSE TRUE 1018622.074 1135175.524 1176341.765 1220372.512 1085786.927 957660.7527 1178538.929 987262.7957 992498.8369 1133741.787 0.898460378 1.001264607 1.037574675 1.076411337 0.957702133 0.844690356 1.03951265 0.870800395 0.875418767 1 20.11266067 3.00541558 24.96335089 0.921496445 1.00713037 0.214030567 0.069464619 200.3484938 923504.2784 0.019802151 0.023596818 1012.547905 -3.00541558 0.085633924 EKIDLENTLEQEQEALVNR ddPTM_BT-474_Pertuzumab_2h_R1 5 EKIDLENTLEQEQEALVNR 19 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;;; 320.08 5.98E-62 1636370000 968250 984590 800080 867060 977590 1010980 1009300 1107600 1180720 1109950 FALSE TRUE 930409.7195 956510.4572 944672.2537 911809.0705 1009035.07 1031422.708 1021652.115 1084727.673 1046689.616 1034772.098 0.899144576 0.924368235 0.912927838 0.881168977 0.97512783 0.996763162 0.987320896 1.048276886 1.011517046 1 19.98088163 3.005419707 2.640357634 1.013372718 0.906419974 0.86238979 0.019503628 0.097893936 1.379192545 0.00658387 0.007674035 1012.557529 -3.005419707 -0.106952744 SPHQNVCEQAVWALGNIIGDGPQCR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPHQNVCEQAVWALGNIIGDGPQCR 25 0 O00505 O00505 KPNA3 Importin subunit alpha-4 0 99.387 0.0069505 242260000 156740 165910 132180 140160 153980 164750 171650 165770 167280 157720 FALSE TRUE 150614.4275 161178.4092 156067.8663 147393.6744 158932.9065 168081.3579 173750.704 162346.7916 148291.0757 147037.4839 1.024326746 1.096172248 1.061415512 1.002422447 1.080900613 1.143119111 1.18167626 1.104118401 1.008525661 1 17.16582446 3.005819434 24.39798213 1.103457424 1.049620097 0.074165951 0.057079556 214.1934077 897990.5838 0.016684988 0.019886265 1013.489922 -3.005819434 -0.053837327 SDLYSSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDLYSSGR 8 0 P38159;P38159-2;H3BUY5 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ;;; 226.68 6.95E-06 4188860000 1418060 1537750 1360640 1508280 1405780 1322930 1448240 1461630 1455770 1520780 FALSE TRUE 1362640.647 1493894.876 1606537.915 1586122.512 1450998.19 1349680.551 1465963.994 1431446.83 1290517.093 1417776.216 0.961111233 1.053688769 1.133139276 1.118739681 1.023432453 0.951970089 1.033988282 1.009642293 0.910240331 1 20.4351984 3.00587013 21.94954392 0.988400673 1.070564894 0.357864546 0.05348035 40.57945171 151725.9521 0.01613073 0.019198225 1013.608235 -3.00587013 0.082164221 LLS(ph)PLSSAR ddPTM_BT-474_Pertuzumab_2h_R1 7 LLSPLSSAR 9 0 A0A087WZ13;Q8IY67-2;E9PAU2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 LLS(1)PLSSAR;LLS(0.999)PLS(0.001)SAR;LLS(0.989)PLS(0.011)SAR;LLS(0.962)PLS(0.038)SAR;LLS(0.995)PLS(0.005)SAR;LLS(0.828)PLS(0.172)SAR;LLS(0.992)PLS(0.007)SAR 211.86 4.67E-06 7300080000 4703330 5309410 4239330 5080120 4690750 4236270 5065800 5001210 4700670 5128480 TRUE FALSE 4519518.664 5157990.825 5005471.234 5342305.602 4841632.234 4321930.282 5127796.776 4897933.266 4167069.648 4781123.482 0.945283819 1.078824014 1.046923647 1.11737453 1.01265576 0.903957051 1.072508751 1.024431451 0.871567042 1 22.18891824 3.005942318 24.98455983 0.98519237 1.051312255 0.196944418 0.067287015 278.0945532 1169240.155 0.019488888 0.023234265 1013.77673 -3.005942318 0.066119885 YGYTHLSAGELLR ddPTM_BT-474_Pertuzumab_2h_R1 3 YGYTHLSAGELLR 13 0 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ;; 158.01 3.90E-05 1801910000 1503288 2422830 1717640 2251730 1826010 1323313 2156930 1759120 1583347 2241070 FALSE TRUE 1444537.843 2353733.261 2028055.757 2367942.055 1884745.27 1350071.296 2183327.155 1722793.557 1403612.086 2089280.333 0.691404509 1.126576086 0.970695854 1.133376894 0.902102624 0.646189635 1.045013979 0.824587074 0.671816062 1 20.99457465 3.005945145 24.93170114 0.837005054 0.993681986 0.145503241 0.162099582 260.8727674 1093989.233 0.044794955 0.053398033 1013.783328 -3.005945145 0.156676932 AAKPGPAEAPS(ph)PTASPSGDAS(ph)PPATAPYDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 AAKPGPAEAPS(0.979)PT(0.019)AS(0.002)PS(0.1)GDAS(0.898)PPAT(0.002)APYDPR;AAKPGPAEAPS(0.935)PT(0.118)AS(0.266)PS(0.154)GDAS(0.515)PPAT(0.012)APY(0.001)DPR;AAKPGPAEAPS(0.984)PT(0.014)AS(0.002)PS(0.002)GDAS(0.991)PPAT(0.007)APYDPR;AAKPGPAEAPS(0.939)PT(0.062)AS(0.118)PS(0.069)GDAS(0.813)PPATAPYDPR 139.2 4.79E-08 4534100000 871170 893974 717109 737027 831790 856220 840855 951740 940700 913970 TRUE FALSE 837123.7133 868478.7368 846706.5483 775065.0518 858545.2808 873533.355 851145.635 932086.2364 833915.6797 852065.9978 0.982463466 1.019262286 0.993710054 0.909630303 1.007604203 1.025194477 0.998919846 1.093913193 0.97869846 1 19.70060565 3.006733686 24.99500517 1.027806974 0.977837824 0.201951297 0.038778568 237.7888973 882646.0723 0.011568118 0.01379765 1015.625709 -3.006733686 -0.04996915 DVLDGHLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVLDGHLR 8 0 P15924 P15924 DSP Desmoplakin 0 ;;;;; 173.73 0.00027608 4395760000 4546270 4918080 4112060 4772600 4423750 4110810 4734200 4392360 5004830 4675320 FALSE TRUE 4368596.742 4777821.174 4855200.714 5018914.458 4566043.936 4193933.395 4792138.556 4301656.231 4436702.68 4358656.412 1.002280595 1.096168342 1.113921414 1.151482013 1.047580608 0.962207845 1.099453158 0.986922534 1.017906038 1 22.05545205 3.006805947 24.87764645 1.01628716 1.093794355 0.366017186 0.048046537 170.6541557 623781.9337 0.013677444 0.016312044 1015.794711 -3.006805947 0.077507195 ARS(ph)MDSSDLSDGAVTLQEYLELK ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSMDSSDLSDGAVTLQEYLELK 23 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.582)MDS(0.116)S(0.116)DLS(0.186)DGAVTLQEYLELK 106.69 0.00085931 45682000 34725 32270 21212 21790 29183 31441 29613 32154 38746 33225 TRUE FALSE 33367.90861 31349.6912 25045.48026 22914.58451 30121.6977 32076.75856 29975.41275 31490.00866 34347.71652 30974.64116 1.077265381 1.012108293 0.808580159 0.73978531 0.972463169 1.035581281 0.967740436 1.016638369 1.108897964 1 14.91879995 3.006843734 24.99110734 1.019391274 0.902884651 0.249898385 0.094423593 262.5153214 958611.6718 0.029635223 0.035344173 1015.883097 -3.006843734 -0.116506623 GLQTSQDAR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLQTSQDAR 9 0 P27797 P27797 CALR Calreticulin 0 ;;;; 199.46 5.75E-05 1696800000 2472810 2941210 2501370 2769500 2510550 1975650 2766390 2469370 2671040 2759380 FALSE TRUE 2376169.851 2857329.571 2953423.202 2912434.227 2591304.121 2015598.997 2800245.908 2418376.647 2367834.737 2572484.735 0.923686667 1.110727513 1.148081915 1.132148303 1.007315645 0.783522238 1.088537425 0.940093682 0.920446565 1 21.29473109 3.006868029 16.80213958 0.948584244 1.083890843 0.31740486 0.09120012 3.653718064 8930.839519 0.026112694 0.030962282 1015.939927 -3.006868029 0.1353066 GNYAER ddPTM_BT-474_Pertuzumab_2h_R1 4 GNYAER 6 0 Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;H0YFX9;Q8IUE6 Q99878 HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;HIST2H2AB Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A;Histone H2A type 2-B 0 ;;; 143.02 0.026643 11392000000 8005200 8686600 6005300 8491500 7033400 5422060 7730700 7321600 6586240 7278200 FALSE TRUE 7692347.934 8438866.673 7090591.297 8929747.333 7259635.699 5531697.768 7825310.619 7170406.401 5838597.647 6785241.031 1.133688236 1.243709197 1.045002125 1.31605455 1.069915669 0.815254424 1.153284103 1.056765171 0.860484929 1 22.69396863 3.0069674 24.94575584 0.99571875 1.180627774 0.434109831 0.110609543 172.7639046 618549.447 0.031379314 0.037427679 1016.172412 -3.0069674 0.184909024 KIDGQQTIIACIESHQFQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIDGQQTIIACIESHQFQAK 20 1 P47755;F8W9N7;A0A0D9SET8 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 195.56 1.19E-21 418400000 525920 574030 444920 452730 519510 560810 515600 558750 613050 618620 FALSE TRUE 505366.465 557659.2264 525326.9412 476095.4496 536220.511 572149.9624 521910.067 547211.6172 543459.1341 576720.3164 0.876276508 0.966949162 0.910886831 0.825522244 0.929775657 0.992075268 0.904962167 0.948833606 0.942327015 1 19.13751232 3.007037522 24.99920934 0.950798623 0.898252383 0.333065428 0.041173579 239.5931996 851092.1331 0.011942431 0.014245306 1016.336499 -3.007037522 -0.05254624 NLDSLEEDLDFLRDQFTTTEVNMAR ddPTM_BT-474_Pertuzumab_2h_R1 4 NLDSLEEDLDFLRDQFTTTEVNMAR 25 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;; 330.44 7.01E-88 1125908000 251084 245110 200701 206365 238782 277731 251642 266142 260749 239101 FALSE TRUE 241271.3597 238119.7028 236972.1353 217015.5224 246462.6399 283346.9111 254721.6701 260646.0747 231149.8667 222906.4763 1.08238829 1.06824937 1.063101168 0.973572083 1.10567734 1.271147056 1.142728889 1.169306873 1.036981386 1 17.76607901 3.007141661 24.98540261 1.143733877 1.048283278 0.169914216 0.075038495 232.7174098 814163.0653 0.021068372 0.025132901 1016.580233 -3.007141661 -0.0954506 GHQLLSADVDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHQLLSADVDIK 12 0 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 147.26 6.54E-05 212210000 230260 224690 201850 238850 220850 218880 234320 201940 274200 263620 FALSE TRUE 221261.1846 218282.0612 238328.7851 251177.0771 227953.8408 223305.9036 237187.6783 197769.8684 243073.9655 245764.7826 0.900296545 0.888174697 0.969743438 1.022022254 0.927528503 0.908616366 0.965100352 0.804711995 0.98905125 1 17.90691867 3.007309957 24.99359423 0.914900755 0.946761221 0 0.062629854 632.0186275 2160923.311 0.0186597 0.022257334 1016.974251 -3.007309957 0.031860466 QSRPANKQS(ph)PSPSEVSQSPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSRPANKQSPSPSEVSQSPGR 21 2 A0A5F9ZH11;P55201-3;P55201;P55201-2;P55201-4;A0A5F9ZHX4;A0A5F9ZHW9;C9JHC0 A0A5F9ZH11 BRPF1 Peregrin 1 QS(0.145)RPANKQS(0.821)PS(0.034)PSEVSQSPGR 75.896 0.0061044 81796000 36203 54472 41802 36038 46419 54490 43368 52983 54552 55296 TRUE FALSE 34788.14674 52918.51189 49356.55128 37897.9255 47912.10929 55591.82513 43898.75056 51888.88253 48359.48566 51550.75267 0.674832955 1.026532284 0.957436094 0.735157559 0.92941629 1.078390174 0.851563717 1.006559165 0.938094657 1 15.65370587 3.007655908 24.98600254 0.971268663 0.864401177 0.228622372 0.107961906 311.5728767 1016847.003 0.030277743 0.036124554 1017.784677 -3.007655908 -0.106867486 DRWQER ddPTM_BT-474_Pertuzumab_2h_R1 1 DRWQER 6 1 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 68.081 0.088537 243020000 619000 545210 480540 468830 581900 673490 575380 680740 688050 672880 FALSE TRUE 594808.7957 529661.1446 567384.2676 493026.3725 600617.342 687108.4292 582421.6726 666682.4811 609945.4485 627305.2383 0.948196762 0.84434357 0.904478766 0.785943337 0.957456283 1.095333479 0.928450198 1.062772061 0.972326407 1 19.25880808 3.007942218 23.06294845 1.013952088 0.871319242 0.570762083 0.057680752 47.04908971 136619.655 0.015362927 0.018319346 1018.455876 -3.007942218 -0.142632846 FSHEEIAMATVTALR ddPTM_BT-474_Pertuzumab_2h_R1 6 FSHEEIAMATVTALR 15 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;; 212.39 8.99E-10 9988850000 5102560 5286930 4935030 5830310 4819720 3726620 5402040 4643920 5205620 4917460 FALSE TRUE 4903146.314 5136151.933 5826899.7 6131212.998 4974750.671 3801974.81 5468151.781 4548021.429 4614699.841 4584396.054 1.06952939 1.120355194 1.271028862 1.337409099 1.085148537 0.829329483 1.192774733 0.992065558 1.006610203 1 22.12830026 3.00802954 24.88875759 1.012307195 1.20055687 0.426008117 0.106741916 178.5544359 553450.4126 0.031274862 0.037319992 1018.660674 -3.00802954 0.188249675 S(ph)PLGSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLGSVR 7 0 Q92620;H3BMS7;Q92620-2;J3KSA8 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 1 S(1)PLGSVR 102.77 0.019519 0 48077 63665 40322 57778 49118 46796 51650 49477 43622 58073 TRUE FALSE 46198.09769 61849.33653 47609.08236 60759.9295 50697.92508 47742.24718 52282.10815 48455.28266 38670.21344 54139.66398 0.853313343 1.142403406 0.879375283 1.122281245 0.936428514 0.881834937 0.965689557 0.895005235 0.714267703 1 15.72439831 3.00812696 24.95908811 0.893735148 1.004538027 0.176588902 0.109647797 299.5642123 919996.806 0.029655155 0.035388478 1018.889202 -3.00812696 0.110802879 NFYNEHEEITNLTPQQLIDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NFYNEHEEITNLTPQQLIDLR 21 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;; 243.48 4.23E-30 657670000 426618 445366 334425 405745 395216 391777 383368 413958 473854 437845 FALSE TRUE 409945.2969 432664.5977 394863.0367 426685.5481 407928.4816 399698.9994 388059.7723 405409.6226 420064.0805 408189.3682 1.00430175 1.059960478 0.967352576 1.045312743 0.999360869 0.979199927 0.950685644 0.993190059 1.029091185 1 18.63887908 3.008393608 24.60551757 0.98720324 1.018923087 0.17329836 0.029335251 248.0809434 727229.8576 0.008294855 0.009898553 1019.514971 -3.008393608 0.031719847 SGSMDPS(ph)GAHPSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 S(0.103)GS(0.103)MDPS(0.794)GAHPS(0.001)VR;S(0.001)GS(0.066)MDPS(0.928)GAHPS(0.006)VR 142.1 9.96E-06 346730000 469395 635261 452668 576399 511757 505376 479146 546971 538274 568109 TRUE FALSE 451050.5245 617143.9783 534475.1771 606147.0215 528218.1287 515595.049 485009.9321 535675.8577 477171.3921 529630.4714 0.851632504 1.16523503 1.009147332 1.144471578 0.997333343 0.973499594 0.915751563 1.011414348 0.900951546 1 19.0146266 3.008465076 24.95792395 0.963892356 1.051727921 0.166684455 0.085597906 299.2560101 882300.3215 0.022943853 0.027381432 1019.682759 -3.008465076 0.087835565 EKYDTDFYILDKYPLAVRPFYTMPDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKYDTDFYILDKYPLAVRPFYTMPDPR 27 3 P14868;P14868-2 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 38.629 0.089054 1141600000 3764600 3615800 2752900 2620900 3220000 3500900 3107700 3444600 3974700 3369300 FALSE TRUE 3617475.27 3512680.924 3250410.268 2756164.963 3323574.224 3571690.597 3145732.962 3373467.806 3523508.719 3141094.31 1.151660827 1.118298458 1.034801871 0.877453744 1.058094376 1.1370848 1.001476763 1.073978516 1.121745599 1 21.58283583 3.008668043 24.99172501 1.069259904 1.039705859 0.01345588 0.078631564 948.06133 2733427.478 0.024126159 0.028803715 1020.159418 -3.008668043 -0.029554044 GYFDEEMNR ddPTM_BT-474_Pertuzumab_2h_R1 4 GYFDEEMNR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 ;;; 237.76 6.70E-10 3580850000 4250250 4742470 4125970 4534260 4267920 3628620 4762680 4452830 4548730 4645330 FALSE TRUE 4084145.531 4607219.399 4871624.561 4768273.702 4405201.523 3701993.183 4820967.103 4360877.504 4032377.24 4330697.661 0.943068727 1.063851545 1.124905256 1.101040542 1.017203663 0.854826052 1.113207958 1.006968818 0.931114928 1 22.04616803 3.008752997 23.67812613 0.988880857 1.062849991 0.183677463 0.075414561 187.7006066 507748.5063 0.022258708 0.026558355 1020.358994 -3.008752997 0.073969135 YLSVPPS(ph)PNISTSESR ddPTM_BT-474_Pertuzumab_2h_R1 4 YLSVPPSPNISTSESR 16 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 YLSVPPS(1)PNISTSESR;YLSVPPS(0.994)PNIS(0.001)T(0.004)S(0.001)ESR;YLSVPPS(0.683)PNIS(0.048)T(0.069)S(0.1)ES(0.1)R;YLSVPPS(0.884)PNIS(0.019)T(0.033)S(0.058)ES(0.005)R 163.41 6.28E-09 417210000 754550 750910 689750 791310 711360 686910 662660 781810 727900 791780 TRUE FALSE 725061.3518 729494.782 814403.1684 832149.6039 734241.5404 700799.7908 670769.8313 765665.3503 645271.8436 738152.0354 0.9822656 0.988271721 1.103300038 1.127341745 0.994702318 0.949397627 0.908715006 1.037273236 0.874172003 1 19.49355847 3.008788508 24.61986141 0.960451451 1.051072088 0.369042793 0.059103048 193.7566288 542777.9884 0.017677983 0.02109873 1020.442429 -3.008788508 0.090620637 RLDINEGAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 RLDINEGAAR 10 1 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ;; 196.11 5.44E-07 1347290000 788490 876850 827610 967400 815060 546340 981720 848990 797160 971760 FALSE TRUE 757674.9391 851843.0965 977177.5371 1017327.63 841277.1451 557387.3691 993734.583 831458.0598 706669.7388 905941.8296 0.836339502 0.94028454 1.078631657 1.122950279 0.928621593 0.61525735 1.096907716 0.917783055 0.780038757 1 19.78905889 3.008923003 24.95152693 0.885682937 1.000319136 0.125595321 0.139524237 421.7701804 1179392.132 0.041169778 0.049141089 1020.758494 -3.008923003 0.1146362 ERECSPS(ph)SPLPPLPEDEEGSEVTNSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERECSPSSPLPPLPEDEEGSEVTNSK 26 1 Q96GY3 Q96GY3 LIN37 Protein lin-37 homolog 1 ERECS(0.019)PS(0.491)S(0.491)PLPPLPEDEEGSEVTNSK 156.07 2.14E-08 236260000 307560 286330 235400 247140 273690 292060 273370 289470 319720 314020 TRUE FALSE 295540.2152 278164.1487 277942.0164 259894.925 282493.4874 297965.6533 276715.5838 283492.3433 283426.726 292751.1457 1.0095271 0.950172708 0.949413932 0.887767405 0.964961168 1.017812083 0.945224597 0.96837313 0.96814899 1 18.15931529 3.008977061 24.99967938 0.976010974 0.946434921 0.155000169 0.032918233 392.9197033 1094209.328 0.009672316 0.011547632 1020.885561 -3.008977061 -0.029576054 KAGLAS(ph)PEEEDAVGKEPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAGLASPEEEDAVGKEPLK 19 2 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 KAGLAS(1)PEEEDAVGKEPLK 48.984 0.081077 191350000 65596 74588 64908 58419 71103 73446 81491 68568 95020 82278 TRUE FALSE 63032.4358 72460.82327 76638.31947 61434.01159 73390.09257 74931.12844 82488.31123 67152.04684 84233.72796 76705.23777 0.821748783 0.94466591 0.999127591 0.800910256 0.956780719 0.97687108 1.075393462 0.87545582 1.098148319 1 16.22703747 3.009009993 24.86001463 0.99064939 0.900052624 0.312704237 0.077492778 273.3981246 754342.3942 0.021964329 0.02621655 1020.962977 -3.009009993 -0.090596766 GWEFMWNER ddPTM_BT-474_Pertuzumab_2h_R1 4 GWEFMWNER 9 0 P12532;P12532-2;P17540 P12532 CKMT1A;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ;;; 123.86 0.0012699 1345534000 1018792 1229972 1055467 1300564 1036172 804098 1142579 1053527 991852 1041049 FALSE TRUE 978976.4823 1194894.403 1246213.366 1367686.264 1069501.413 820357.4125 1156562.224 1031771.299 879261.1191 970537.824 1.008694827 1.23116727 1.284044099 1.409204495 1.101967782 0.84526063 1.191671458 1.063092312 0.90595245 1 19.88842491 3.009148593 24.73397236 1.02051984 1.239107279 0.424635438 0.126282681 181.3147979 490194.6084 0.037113399 0.044299991 1021.288857 -3.009148593 0.21858744 RNDLDDPER ddPTM_BT-474_Pertuzumab_2h_R1 1 RNDLDDPER 9 1 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 91.855 0.016789 450640000 156320 168530 162160 198830 164650 146180 155090 169670 183950 218080 FALSE TRUE 150210.8416 163723.6894 191465.9192 209091.6401 169946.1168 149135.8598 156988.0378 166166.2552 163068.7672 203309.2474 0.738829362 0.805293864 0.941747224 1.028441366 0.835899591 0.73354194 0.772163784 0.817307906 0.802072554 1 17.63331631 3.009270552 24.99598741 0.807310761 0.884644833 0.047989012 0.09768855 455.5877674 1228380.648 0.028794288 0.03437246 1021.575694 -3.009270552 0.077334072 LAAELEDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAAELEDRR 9 1 Q9NQG5;A2A2M0;A0A087X2D2 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 167.12 9.66E-05 267640000 164460 182230 124490 161520 149780 137450 156390 155180 144290 165160 FALSE TRUE 158032.7214 177032.9788 146988.1123 169856.0666 154597.8097 140229.3332 158303.9476 151975.4788 127910.8041 153973.5661 1.026362676 1.149762153 0.954632123 1.103150826 1.004054226 0.910736412 1.028124188 0.98702318 0.830732231 1 17.23232317 3.009604826 8.474242296 0.959677598 1.057232262 0.343016748 0.069449313 0.173651391 97.74244541 0.019644681 0.022965066 1022.362299 -3.009604826 0.097554664 TPS(ph)GPPARPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSGPPARPSR 11 1 Q2M2I3 Q2M2I3 FAM83E Protein FAM83E 1 T(0.053)PS(0.944)GPPARPS(0.003)R 54.09 0.081074 285260000 170210 191260 166460 225410 174380 166660 176660 182430 174270 159040 TRUE FALSE 163558.005 185805.4521 196543.0249 237043.4371 179989.0911 170029.9794 178822.0179 178662.7567 154487.6002 148268.0791 1.103123518 1.253172316 1.325592306 1.598748959 1.213943636 1.146774008 1.206072264 1.204998121 1.041947809 1 17.17784851 3.009666506 24.99842079 1.149084866 1.327085525 0.333075779 0.130195713 272.8964619 705728.2034 0.038869117 0.046402279 1022.507508 -3.009666506 0.178000659 LKAIEPNDYTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKAIEPNDYTGK 12 1 O75223;M0QZK8;O75223-3 O75223 GGCT Gamma-glutamylcyclotransferase 0 ; 140.1 5.42E-05 1108720000 1681060 1739960 1302220 1205390 1666350 1858420 1719630 2014130 2015340 1702860 FALSE TRUE 1615362.317 1690338.044 1537560.122 1267600.322 1719949.661 1895998.526 1740675.346 1972537.512 1786567.052 1587523.775 1.017535826 1.064763924 0.968527304 0.798476434 1.083416631 1.194311893 1.096471986 1.242524706 1.125379714 1 20.59834677 3.0097641 24.90256015 1.150240671 0.966443393 0.448525111 0.087769368 166.060894 423521.527 0.025500268 0.030444252 1022.73731 -3.0097641 -0.183797278 HGYIPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGYIPGK 7 0 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0;H0YHL7 Q9ULV4 CORO1C Coronin-1C;Coronin 0 62.842 0.083023 653760000 1403500 1496800 1192100 1402400 1331100 1288900 1445400 1162400 1657700 1610200 FALSE TRUE 1348649.668 1454112.73 1407538.988 1474778.032 1373916.04 1314962.441 1463089.238 1138396.034 1469524.846 1501139.72 0.89841715 0.968672476 0.937646889 0.982438885 0.915248609 0.875976049 0.974652271 0.758354481 0.978939419 1 20.51762683 3.009991867 22.06117759 0.89564279 0.947845861 0 0.068908458 114.0801292 251869.7393 0.01955333 0.02332704 1023.273829 -3.009991867 0.052203071 DIIHFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIIHFFR 7 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ; 120.52 0.0045384 1278420000 1315930 1398550 1140390 1260070 1228460 1064680 1306160 1206120 1274630 1435280 FALSE TRUE 1264502.001 1358664.723 1346483.841 1325102.364 1267974.532 1086208.559 1322145.177 1181213.201 1129939.346 1338067.207 0.945021292 1.015393484 1.006290143 0.990310768 0.947616476 0.811774291 0.988100724 0.882775689 0.844456347 1 20.35171915 3.010283734 6.080642647 0.90154407 0.990170681 0.327920266 0.056412418 0.166010489 24.14283899 0.015862811 0.01840886 1023.961751 -3.010283734 0.088626611 AHCAICTDR ddPTM_BT-474_Pertuzumab_2h_R1 4 AHCAICTDR 9 0 P41743 P41743 PRKCI Protein kinase C iota type 0 ;;; 110.87 0.0022166 310144000 138881 153481 141821 169413 138849 108897 163635 142237 118473 158201 FALSE TRUE 133453.377 149103.8722 167451.2095 178156.4252 143315.2042 111098.972 165637.6141 139299.7562 105024.4417 147485.9054 0.904855123 1.010970315 1.13537093 1.2079556 0.971721358 0.753285351 1.123074193 0.94449538 0.712098159 1 17.17021756 3.010509963 24.89559458 0.918485777 1.068967156 0.240672251 0.131562973 317.2924168 751583.6904 0.038863849 0.046408267 1024.495282 -3.010509963 0.150481378 (ac)MDGPAEPQIPGLWDTYEDDISEISQK ddPTM_BT-474_Pertuzumab_2h_R1 4 MDGPAEPQIPGLWDTYEDDISEISQK 26 0 O00204 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ;;; 76.691 5.66E-08 124529000 211291 214005 180779 202720 222467 242364 248266 253100 282972 281190 FALSE TRUE 203033.5141 207901.7869 213449.7867 213182.4035 229622.8531 247264.7661 251304.3536 247873.3966 250850.2049 262144.7508 0.774509173 0.793080107 0.814243986 0.813224002 0.875939161 0.943237526 0.958647285 0.94555926 0.95691485 1 18.00000413 3.010795041 1.283200494 0.963054015 0.789319368 0.961503684 0.015413407 0.076056077 0.262551917 0.006144466 0.007480963 1025.167999 -3.010795041 -0.173734647 ALTQTGGPHVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALTQTGGPHVK 11 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 86.772 0.011104 0 51565 64324 35611 56209 48579 45576 41937 50124 57175 64043 FALSE TRUE 49549.78279 62489.5425 42046.69986 59109.95323 50141.58765 46497.57795 42450.23755 49088.92188 50684.7337 59705.31057 0.829905788 1.046632903 0.704237185 0.990028402 0.839817885 0.778784626 0.710996009 0.822186861 0.848915 1 15.86557164 3.010929722 24.80484465 0.811160547 0.893320581 0.04925473 0.109963398 433.5099506 983835.7197 0.029802257 0.035589639 1025.485967 -3.010929722 0.082160034 HFSGLEEAVYR ddPTM_BT-474_Pertuzumab_2h_R1 4 HFSGLEEAVYR 11 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 261.87 1.04E-20 3525870000 1385030 2667840 2045080 2907270 1989500 1802150 2321560 1532900 1683730 2550400 FALSE TRUE 1330901.496 2591755.815 2414671.449 3057314.553 2053494.074 1838590.708 2349971.946 1501245.079 1492600.029 2377659.136 0.559752858 1.090045152 1.015566702 1.285850653 0.863662096 0.773277666 0.988355273 0.631396257 0.627760307 1 21.18111047 3.011084351 24.9864883 0.788016559 1.006798179 0.147383226 0.204994768 353.6676423 797235.9296 0.058924484 0.070371724 1025.851153 -3.011084351 0.218781621 DFPAMVQELHQGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFPAMVQELHQGGR 14 0 P10253 P10253 GAA Lysosomal alpha-glucosidase;76 kDa lysosomal alpha-glucosidase;70 kDa lysosomal alpha-glucosidase 0 ; 172.3 2.88E-06 909490000 625870 712960 608300 736230 648720 633270 675360 676200 667300 704690 FALSE TRUE 601410.3085 692627.0789 718233.3416 774226.9185 669586.668 646075.1533 683625.2577 662236.2337 591550.9015 656960.7186 0.915443331 1.054289943 1.093266798 1.178498039 1.019218728 0.983430417 1.040587722 1.008030183 0.900435726 1 19.32544759 3.011088433 24.99614998 0.994052902 1.066860488 0.197233645 0.068933769 372.4227834 839528.802 0.020573894 0.02456998 1025.860795 -3.011088433 0.072807585 RHEILQWVLQTDSQQ ddPTM_BT-474_Pertuzumab_2h_R1 2 RHEILQWVLQTDSQQ 15 1 Q96AG4 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 ; 140.84 7.81E-06 1780040000 835100 1679130 720360 1686000 1056880 740120 1346080 817480 1371140 814740 FALSE TRUE 802463.3687 1631242.856 850545.0763 1773014.662 1090875.505 755085.7335 1362553.73 800598.7523 1215493.935 759556.9341 1.056488767 2.147624205 1.119791076 2.334274868 1.436199784 0.99411341 1.793879653 1.054033893 1.600267052 1 19.53479858 3.011234959 24.99362275 1.304154892 1.688276637 0.138881433 0.439244218 399.6953932 889167.4029 0.115950329 0.13847832 1026.206967 -3.011234959 0.384121745 DVPNETLQVEEDDRPELPWWK ddPTM_BT-474_Pertuzumab_2h_R1 5 DVPNETLQVEEDDRPELPWWK 21 1 O95373 O95373 IPO7 Importin-7 0 ;;;; 315.38 1.02E-66 5603883000 1502581 1487958 1421813 1312227 1559200 1699002 1689676 1657295 1939243 1956912 FALSE TRUE 1443858.473 1445522.895 1678766.237 1379951.193 1609353.084 1733356.985 1710354.76 1623071.279 1719108.265 1824368.607 0.791429138 0.792341465 0.920190268 0.75639933 0.8821425 0.950113358 0.937505038 0.889661921 0.942303139 1 20.79896582 3.011392158 6.894417349 0.931289188 0.820453883 0.613517383 0.047605245 0.106952854 25.28722347 0.013631523 0.015886801 1026.578485 -3.011392158 -0.110835305 LGIHEDSQNR ddPTM_BT-474_Pertuzumab_2h_R1 11 LGIHEDSQNR 10 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;; 245.5 1.54E-12 1.04468E+11 20678788 23952193 20027239 22875690 21457348 21005320 22647140 21736286 23177100 24613850 FALSE TRUE 19870638.1 23269099.91 23646606.59 24056307.1 22147543.09 21430061.96 22924302.47 21287424.1 20546132.77 22946732.02 0.865946318 1.014048532 1.030499967 1.048354384 0.965171994 0.933904747 0.999022539 0.927688705 0.895383829 1 24.45178537 3.011443087 24.94873461 0.949241583 0.99591391 0.095039522 0.054609158 440.629651 960673.093 0.015835568 0.018911547 1026.698876 -3.011443087 0.046672327 LAAPSVSHVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAAPSVSHVSPR 12 0 A0A0U1RRM7;Q8WXE1-3;A0A0U1RQW3;A0A0U1RQJ8;Q8WXE1-5;Q8WXE1-2;Q8WXE1 A0A0U1RRM7 ATRIP ATR-interacting protein 1 LAAPSVS(0.014)HVS(0.986)PR;LAAPSVSHVS(1)PR 171.46 2.47E-05 489200000 561180 627170 538750 635370 578350 575890 598060 560000 593800 786820 TRUE FALSE 539248.4652 609283.7257 636114.1094 668161.5218 596953.153 587534.8904 605379.2372 548435.8043 526394.3134 733527.9806 0.735143688 0.830620974 0.867198152 0.910887573 0.813811019 0.800971341 0.825298084 0.747668554 0.717619951 1 19.48449247 3.011529066 24.87929487 0.799828721 0.840879299 0 0.081900301 708.6146211 1529151.636 0.022998673 0.027467837 1026.902157 -3.011529066 0.041050578 FNENNRR ddPTM_BT-474_Pertuzumab_2h_R1 4 FNENNRR 7 1 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;;; 109.86 0.011116 718900000 367908 404784 270545 409493 352106 312668 368688 365634 411610 412089 FALSE TRUE 353529.7486 393239.9566 319438.4997 430626.9828 363431.8093 318990.3612 373200.114 358083.5301 364885.7584 384177.845 0.920224196 1.023588324 0.831486 1.120905301 0.945998875 0.830319513 0.971425393 0.932077513 0.949783448 1 18.5514148 3.011529576 24.99611565 0.93072337 0.975661845 0.04402652 0.080096552 656.6749013 1423659.793 0.022097899 0.026393454 1026.903363 -3.011529576 0.044938475 LNPNFLVDFGKEPLGPALAHELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNPNFLVDFGKEPLGPALAHELR 23 1 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 117.64 0.00021641 300820000 393170 427470 357140 316530 416780 472540 429940 423030 583380 465390 FALSE TRUE 377804.4817 415278.9741 421683.1425 332866.1512 430186.1072 482095.0826 435201.7343 414294.2827 517157.1481 433868.7208 0.870780639 0.957153522 0.971914135 0.767204768 0.991512148 1.111154272 1.003072389 0.954883961 1.191966886 1 18.72689906 3.011568833 24.9987021 1.038885881 0.899308961 0.462190043 0.080864357 224.6015164 485330.1163 0.02333023 0.027864739 1026.996192 -3.011568833 -0.13957692 VLHDSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLHDSSK 7 0 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 105.12 0.020593 0 131240 197410 163320 194400 153500 128540 171960 140390 128940 191700 FALSE TRUE 126110.9957 191780.0601 192835.557 204433.0073 158437.4669 131139.1669 174064.4979 137490.8974 114303.2718 178715.9883 0.705650328 1.073099626 1.079005627 1.143898816 0.886532137 0.73378531 0.973972724 0.76932623 0.63958056 1 17.44730918 3.011598604 22.4103841 0.817729311 1.0117189 0.240857937 0.147717852 83.64334746 161607.9255 0.042007062 0.050146163 1027.066594 -3.011598604 0.193989589 GEAAAERPGEAAVAS(ph)SPSKANGQENGHVK ddPTM_BT-474_Pertuzumab_2h_R1 3 GEAAAERPGEAAVASSPSKANGQENGHVK 29 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.496)S(0.496)PS(0.008)KANGQENGHVK;GEAAAERPGEAAVAS(0.5)S(0.5)PS(0.001)KANGQENGHVK;GEAAAERPGEAAVAS(0.5)S(0.5)PS(0.001)KANGQENGHVK 172.18 9.08E-13 3055390000 1036666 930839 813953 751623 952246 978105 1008261 1158913 1047745 955116 TRUE FALSE 996151.9466 904292.3831 961052.4134 790414.3531 982875.8574 997882.9533 1020600.4 1134981.042 928809.3801 890425.1426 1.118737442 1.01557373 1.079318594 0.887681979 1.10382761 1.120681465 1.146194498 1.274650712 1.043107765 1 19.7641348 3.011749735 24.99848849 1.144216562 1.02439606 0.16446022 0.089037992 289.306821 615518.3533 0.025768175 0.030776883 1027.424067 -3.011749735 -0.119820502 T(ph)PDDFLNSVDEMDTGDTINQSTLPSQQNR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPDDFLNSVDEMDTGDTINQSTLPSQQNR 29 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8;P46937-4;H0YCI3 P46937-6 YAP1 Transcriptional coactivator YAP1 1 T(1)PDDFLNSVDEMDTGDTINQSTLPSQQNR;T(1)PDDFLNSVDEMDTGDTINQSTLPSQQNR;T(1)PDDFLNSVDEMDTGDTINQSTLPSQQNR 196.3 1.64E-24 291059000 67359 67333.5 60915 93567 63171 54545.6 54389.7 74021.8 57197 62766.4 TRUE FALSE 64726.53581 65413.21451 71923.69555 98396.00408 65202.95259 55648.5494 55055.33742 72493.22396 50704.23635 58515.17582 1.106149557 1.11788461 1.229146021 1.681546756 1.114291321 0.951010548 0.940872802 1.238879025 0.866514295 1 15.83652321 3.01184357 24.9617484 1.028281878 1.284190587 0.36506494 0.174702345 274.6568783 578867.851 0.052871121 0.063151119 1027.646081 -3.01184357 0.255908709 LLDIACWIHHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDIACWIHHK 11 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;F8WD96;F8W787;A0A1B0GV01 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 140.07 2.24E-05 2118530000 4070000 4265800 3782200 3673900 3152400 2805200 4006600 865850 3982600 4222400 FALSE TRUE 3910939.9 4144143.561 4465727.675 3863510.419 3253799.809 2861923.066 4055633.969 847969.8949 3530511.944 3936413.087 0.993528833 1.052771513 1.13446622 0.981479924 0.826590029 0.727038297 1.03028668 0.215416898 0.896885532 1 21.90845019 3.011846293 1.220034846 0.681202501 1.066634945 0.208661071 0.221972813 0.525480364 1.651496876 0.092678011 0.113443167 1027.652523 -3.011846293 0.385432444 EIEELKELLPEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIEELKELLPEIR 13 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 153.24 4.08E-05 973829000 1984290 1962800 1393330 1427664 1756270 1940330 1705290 1947190 2100410 1857600 FALSE TRUE 1906741.753 1906822.866 1645135.725 1501345.91 1812762.02 1979564.802 1726159.849 1906979.846 1861980.262 1731783.097 1.101028042 1.10107488 0.949966383 0.866936461 1.04676043 1.143078948 0.996752914 1.101165526 1.075180988 1 20.72382682 3.012156224 24.98307095 1.069320905 1.001359729 0.115346072 0.07559626 459.2823022 943894.3353 0.023064364 0.027547821 1028.386161 -3.012156224 -0.067961176 DLSELGSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSELGSVR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 158.87 0.00015466 225050000 277810 309070 272580 305360 286780 272790 302160 297540 316720 325890 FALSE TRUE 266952.8781 300255.6262 321841.2695 321119.6662 296004.5391 278306.0007 305857.9245 291395.695 280767.2734 303817.18 0.878662879 0.988277313 1.059325445 1.056950322 0.974285059 0.91603115 1.006717015 0.959115265 0.924132313 1 18.21284393 3.012399867 24.97353625 0.96080835 1.001780378 0.080803093 0.05356491 525.6922643 1058744.482 0.01600838 0.019121436 1028.963256 -3.012399867 0.040972028 AHQSYCHSNK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHQSYCHSNK 10 0 Q96S59-2;Q96S59-3;Q96S59 Q96S59-2 RANBP9 Ran-binding protein 9 0 82.261 0.010724 21019000 10140 20492 16287 22863 13405 8261.3 19141 4604.3 14451 17696 FALSE TRUE 9743.71759 19907.58822 19230.4232 24042.96217 13836.184 8428.349146 19375.25328 4509.219596 12810.58306 16497.43416 0.590620183 1.206708148 1.165661461 1.457375852 0.838687027 0.510888485 1.174440407 0.27332854 0.776519727 1 14.00995404 3.012587436 24.47442096 0.700004423 1.120595716 0.227126836 0.307001594 220.5104751 428746.1629 0.086668419 0.103522112 1029.407755 -3.012587436 0.420591292 LAVNNIAGIEEVNMIKDDGTVIHFNNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAVNNIAGIEEVNMIKDDGTVIHFNNPK 28 1 Q96K17;E9PL10 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4;Transcription factor BTF3 0 ; 219.34 1.68E-34 1099010000 704140 584920 537117 515838 630850 734510 635710 627350 802930 759330 FALSE TRUE 676621.4303 568238.6543 634185.99 542460.461 651141.8632 749362.2955 643490.0091 614395.0033 711784.7526 707899.9028 0.95581512 0.802710457 0.895869582 0.766295431 0.919821942 1.058570982 0.90901271 0.867912258 1.005487852 1 19.43318585 3.012927842 24.86759409 0.951732207 0.852923051 0.360409883 0.069239832 266.3858789 512407.5637 0.020219636 0.024153289 1030.214935 -3.012927842 -0.098809156 EKVMYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKVMYEK 7 1 E5RJD8;O75347;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 71.223 0.050068 364004000 601480 666530 454720 525340 622850 681010 656760 709180 802460 750950 FALSE TRUE 577973.4966 647521.217 536898.0192 552452.8604 642884.5359 694780.4888 664797.6253 694535.1852 711368.105 700087.4876 0.825573242 0.924914712 0.766901321 0.789119746 0.91829171 0.992419521 0.949592211 0.992069131 1.016113154 1 19.4171757 3.013072574 3.77756728 0.985206908 0.829891443 0.770792263 0.0418472 0.11221499 3.538236615 0.013291666 0.015417563 1030.55832 -3.013072574 -0.155315465 VGIIAWHPTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGIIAWHPTAR 11 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ; 147.3 3.54E-05 3324400000 1953840 2413700 2191730 2390600 2138290 1474780 2640500 2198340 2151730 2640800 FALSE TRUE 1877481.773 2344863.639 2587824.366 2513979.152 2207070.04 1504601.062 2672815.229 2152943.511 1907474.631 2461936.264 0.762603728 0.952446931 1.051133778 1.021139007 0.896477326 0.611145416 1.085655737 0.874491977 0.774786358 1 21.23136198 3.013128693 23.97137249 0.868028746 0.955198001 0.064666762 0.137896662 391.0667766 714031.1786 0.039995845 0.047774184 1030.691496 -3.013128693 0.087169255 DFDFESANAQFNKEEIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFDFESANAQFNKEEIDR 18 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 310.3 3.55E-61 4647210000 2897660 2617210 2060830 2138290 2449880 2585050 2450630 2647770 2841850 2631210 FALSE TRUE 2784416.244 2542569.733 2433267.824 2248647.403 2528682.615 2637321.482 2480621.543 2593092.624 2519255.102 2452995.803 1.135108442 1.036516137 0.991957598 0.916694354 1.030854848 1.075143088 1.011262041 1.05711254 1.027011583 1 21.22611333 3.01339198 24.97817251 1.038863026 1.013553306 0.005545335 0.054048929 897.1193566 1673258.753 0.01629594 0.019471186 1031.316533 -3.01339198 -0.02530972 YLEPLYNDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLEPLYNDYR 10 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 ; 88.819 0.027765 276741000 227077 259000 223192 257020 236494 221528 249750 234178 278700 277168 FALSE TRUE 218202.5798 251613.5736 263527.7593 270284.833 244101.0443 226007.4479 252806.5152 229342.1425 247063.1444 258395.1645 0.844453031 0.973754962 1.019863355 1.04601351 0.944681162 0.874658194 0.978371696 0.8875636 0.956144612 1 17.97921955 3.013634965 24.98424031 0.929801001 0.977285474 0.043570899 0.060826858 516.6456263 946676.7003 0.017577367 0.020998735 1031.893708 -3.013634965 0.047484472 YLVIDEAHR ddPTM_BT-474_Pertuzumab_2h_R1 5 YLVIDEAHR 9 0 O60264;A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 O60264 SMARCA5;SMARCA1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5;Probable global transcription activator SNF2L1 0 ;;;; 169.12 5.87E-05 2154830000 1812560 1944260 1705440 1983110 1714560 1523900 1823320 1633320 1628840 1803100 FALSE TRUE 1741723.151 1888811.608 2013650.945 2085458.545 1769710.38 1554714.302 1845634.336 1599591.371 1443940.912 1680974.431 1.036138991 1.123640892 1.197906945 1.240624787 1.052788399 0.924888727 1.097955032 0.951585784 0.858990408 1 20.68086635 3.013638011 6.805564467 0.974898561 1.151223431 0.567172683 0.075137306 0.115951629 24.94870942 0.022793508 0.026628679 1031.900948 -3.013638011 0.17632487 SHPPPPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHPPPPEK 8 0 A0A0U1RRE5 A0A0U1RRE5 0 78.334 0.030893 80960000 77629 79011 62963 67430 74842 79484 78394 75930 90615 87555 FALSE TRUE 74595.17286 76757.68364 74341.8147 70910.07038 77249.3609 81091.22094 79353.40922 74362.01897 80328.76509 81624.82186 0.913878538 0.940371836 0.910774603 0.868731701 0.946395461 0.993462762 0.972172526 0.911022129 0.984121781 1 16.31672032 3.01366299 24.72074946 0.962900498 0.910471462 0.511832231 0.028611263 206.7981198 374161.2267 0.008797169 0.010509237 1031.960301 -3.01366299 -0.052429037 EIHQDWANR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIHQDWANR 9 0 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 ;;; 179.8 4.94E-05 6584970000 2154090 2407930 1869940 2403730 2162850 1986290 2374160 2283670 2218920 2527590 FALSE TRUE 2069905.781 2339258.194 2207879.755 2527786.793 2232420.035 2026454.145 2403215.68 2236511.416 1967037.504 2356394.078 0.878420889 0.992727921 0.936973902 1.072735166 0.947388238 0.859981004 1.019870022 0.949124528 0.834765934 1 21.1681494 3.013710456 24.99174491 0.935060485 0.974524914 0.059314352 0.069228741 697.8178842 1271989.244 0.019674406 0.023505282 1032.073093 -3.013710456 0.039464429 TPMYGSQT(ph)PLQDGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPMYGSQTPLQDGSR 15 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 TPMYGS(0.01)QT(0.99)PLQDGSR;TPMYGS(0.002)QT(0.998)PLQDGSR 211.9 1.28E-08 764360000 568630 663450 572070 769740 570590 478870 592000 582870 555030 639530 TRUE FALSE 546407.3109 644529.0556 675455.7746 809466.3736 588943.5455 488553.0795 599245.0731 570833.5308 492025.3213 596214.0635 0.916461628 1.081036317 1.132908155 1.357677424 0.987805524 0.819425621 1.005083761 0.957430503 0.825249439 1 19.18547088 3.014186338 24.98821542 0.926500023 1.126479901 0.401043977 0.115722671 239.6891285 422192.2333 0.034032708 0.040660148 1033.204616 -3.014186338 0.199979878 LS(ph)EGS(ph)QPAEEEEDQETPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 LS(1)EGS(1)QPAEEEEDQETPSR 195.09 2.94E-21 0 123440 124940 116500 134650 116570 105800 115110 121410 128560 133990 TRUE FALSE 118615.8283 121376.8335 137554.1415 141599.3026 120319.5799 107939.3485 116518.7506 118902.8411 113966.4078 124914.738 0.949574328 0.971677446 1.101184246 1.133567623 0.963213644 0.86410419 0.932786255 0.951871997 0.912353575 1 16.93058418 3.014395125 24.75381785 0.929476257 1.039853399 0.419135807 0.059493627 208.3471111 358270.3397 0.018162274 0.021699638 1033.701448 -3.014395125 0.110377143 KKHPDASVNFSEFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKHPDASVNFSEFSK 15 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 159.02 1.07E-06 1261200000 958080 802370 646660 582440 767170 835570 774460 789610 950600 851670 FALSE TRUE 920637.1744 779487.1932 763525.8469 612499.7982 791846.7198 852465.7979 783938.0731 773304.2776 842691.8732 793985.6323 1.159513645 0.981739671 0.961636856 0.771424284 0.997306107 1.073653934 0.987345414 0.973952482 1.061343983 1 19.59875338 3.01490203 24.99911045 1.013787386 0.958440684 0.057558322 0.091804276 712.8911762 1195912.569 0.027592709 0.032969374 1034.908681 -3.01490203 -0.055346702 AIAHYEQSADYYKGEESNSSANK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIAHYEQSADYYKGEESNSSANK 23 1 P54920;M0R0Y2;M0R2M1;M0R058;M0R027;A0A087WZQ7;Q9H115-3;Q9H115-2;Q9H115 P54920 NAPA;NAPB Alpha-soluble NSF attachment protein;Beta-soluble NSF attachment protein 0 349.37 8.41E-102 1211800000 1166100 1055400 904030 903170 1054700 1079600 1082900 1153000 1236100 1212000 FALSE TRUE 1120527.523 1025301.025 1067408.331 949782.7119 1088625.383 1101430.252 1096152.854 1129190.147 1095783.11 1129910.16 0.991696121 0.907418184 0.944684249 0.840582504 0.963461894 0.974794537 0.970123902 0.999362769 0.969796669 1 20.10777664 3.01534818 24.9970404 0.981704155 0.919330619 0.391984328 0.03632209 233.9913266 381090.8813 0.010177338 0.012160568 1035.972388 -3.01534818 -0.062373536 MFADYLAHESR ddPTM_BT-474_Pertuzumab_2h_R1 4 MFADYLAHESR 11 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;; 208.17 2.05E-08 1305560000 1226440 1900220 1610680 2075940 1598200 1214230 1992600 1527890 1527580 1995190 FALSE TRUE 1178509.369 1846027.586 1901765.705 2183079.512 1649607.554 1238782.563 2016986.035 1496338.538 1354175.523 1860054.004 0.633588792 0.992459134 1.022424995 1.173664586 0.886860032 0.665992794 1.08436961 0.804459728 0.728030218 1 20.82691308 3.015375841 24.97241684 0.851955642 0.971363818 0.067826004 0.169174101 577.4064503 937778.5535 0.048637036 0.058114862 1036.038372 -3.015375841 0.119408176 GLSFHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLSFHPK 7 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23;A0A3B3IU84 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 73.039 0.049975 245790000 708450 1038900 906530 1003900 821280 398480 1035700 824660 826520 1074400 FALSE TRUE 680762.9908 1009271.589 1070360.137 1055711.399 847697.2171 406537.5386 1048375.206 807630.4828 732696.9147 1001629.931 0.6796552 1.007629223 1.068618362 1.053993463 0.846317777 0.405875989 1.046669208 0.806316243 0.731504613 1 19.93391815 3.015381143 20.77105356 0.79045449 0.96289109 0.126654646 0.190495296 62.24357131 84050.23839 0.054702091 0.065325296 1036.05102 -3.015381143 0.1724366 RAPEEELPPLDPEEIRK ddPTM_BT-474_Pertuzumab_2h_R1 4 RAPEEELPPLDPEEIRK 17 2 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 ;;; 104.2 0.00048493 1044130000 947700 964430 795338 779200 901410 974190 902110 985150 1014040 973400 FALSE TRUE 910662.8363 936925.4007 939073.2688 819414.6054 930404.6713 993888.7893 913150.292 964806.3082 898930.4304 907470.751 1.003517563 1.03245796 1.034824834 0.902965307 1.025272352 1.095229558 1.006258649 1.063181714 0.990588875 1 19.79149162 3.015605908 24.99981272 1.037681047 0.994801101 0.130675882 0.044851694 430.6879371 689933.99 0.012835739 0.015337953 1036.587358 -3.015605908 -0.042879947 EHSPYGPS(ph)PLGWPSSETR ddPTM_BT-474_Pertuzumab_2h_R1 1 EHSPYGPSPLGWPSSETR 18 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 EHSPYGPS(1)PLGWPSSETR 157.3 3.47E-09 139510000 61183 99092 64248 106570 69567 63321 71213 56672 88744 64615 TRUE FALSE 58791.90072 96265.99318 75859.04279 112070.0905 71804.68573 64601.394 72084.526 55501.7034 78670.15317 60238.5685 0.97598436 1.598079031 1.259310184 1.860437478 1.192005181 1.072425783 1.196650714 0.921364913 1.305976472 1 15.87839987 3.015667067 24.99988506 1.092603583 1.436954108 0.301615961 0.233239989 265.3126481 423355.5133 0.063518303 0.075896919 1036.733344 -3.015667067 0.344350525 S(ph)FEVEEVETPNSTPPRR ddPTM_BT-474_Pertuzumab_2h_R1 3 SFEVEEVETPNSTPPRR 17 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR 200.99 7.28E-12 1287730000 195099 229017 143714 211351 225080 197344 219431 263036 256350 237839 TRUE FALSE 187474.3154 222485.6594 169686.3167 222258.8504 232319.9026 201334.4309 222116.4622 257604.2147 227250.2227 221729.9527 0.845507398 1.00340823 0.765283691 1.002385324 1.047760575 0.908016389 1.001743154 1.161792584 1.024896366 1 17.75844415 3.01569002 0.733153114 1.068470945 0.880706239 0.333700672 0.085920803 0.764088136 0.914831194 0.055107408 0.074947881 1036.78814 -3.01569002 -0.187764706 ENSS(ph)PSVTSANLDHTKPCWYWDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSSPSVTSANLDHTKPCWYWDKK 24 2 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 1 ENS(0.173)S(0.827)PSVTSANLDHTKPCWYWDKK 193.23 2.50E-18 2287700000 2219800 1964500 1567300 1490100 1880200 2013300 1867500 2007200 2347700 2041100 TRUE FALSE 2133047.762 1908474.383 1850545.974 1567004.24 1940678.341 2054010.305 1890355.024 1965750.619 2081198.938 1902854.479 1.120972615 1.002953407 0.972510507 0.823501879 1.019877433 1.079436356 0.993431208 1.033053573 1.093724697 1 20.8597338 3.015739536 24.9996749 1.038551637 0.973666174 0.12828762 0.073058551 483.0941373 767310.2157 0.021822936 0.026076482 1036.906355 -3.015739536 -0.064885463 HVVFGK ddPTM_BT-474_Pertuzumab_2h_R1 7 HVVFGK 6 0 C9JQD4;O43447;O43447-2;H0YEL5;P62937;P23284;P45877;P62937-2 C9JQD4;P62937;P23284;P45877;P62937-2 PPIH;PPIA;PPIB;PPIC "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase H;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase B;Peptidyl-prolyl cis-trans isomerase C" 0 ;;;;;; 118.11 0.022145 51316140000 61995540 61959700 54522800 63950560 55720700 47291940 62457340 44964710 67902150 67425440 FALSE TRUE 59572685.76 60192670.02 64376282.81 67251056.07 57513006.92 48248215.43 63221711.61 44036173.03 60194182.6 62858654.89 0.947724476 0.957587625 1.0241435 1.069877429 0.914957646 0.767566782 1.005775763 0.700558628 0.957611688 1 25.90560806 3.016089407 12.0808299 0.861855055 0.997824363 0.217301724 0.096895174 0.777111678 576.9694148 0.026900288 0.031949636 1037.742032 -3.016089407 0.135969308 KGDVVIVLTGWRPGS(ph)GFTNTMR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGDVVIVLTGWRPGSGFTNTMR 22 2 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 1 KGDVVIVLTGWRPGS(0.631)GFT(0.344)NT(0.024)MR 139.16 2.00E-07 187530000 228230 218880 200910 199480 209780 200910 186830 230490 228000 186490 TRUE FALSE 219310.5193 212637.7567 237218.9062 209775.1867 216527.7642 204972.5379 189116.4814 225730.301 202118.3959 173858.8662 1.261428445 1.223048104 1.364433758 1.206583198 1.245422618 1.178959361 1.087758626 1.298353693 1.162542931 1 17.40755712 3.016432919 1.668438744 1.169922212 1.272624138 0.311471375 0.081927788 0.548309183 3.114880189 0.028732978 0.034503895 1038.563174 -3.016432919 0.102701925 ESYCQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESYCQR 6 0 B8ZZN6;P63165;B8ZZJ0;B9A032;B8ZZ67;P63165-2 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 0 103.28 0.080999 149500000 128860 155640 135290 157740 133790 113150 157970 141060 127070 129960 FALSE TRUE 123824.0087 151201.2996 159739.9125 165880.9803 138093.4769 115437.9705 159903.2841 138147.0617 112645.5463 121157.6934 1.022006983 1.247971097 1.318446299 1.369132868 1.13978298 0.952791088 1.31979472 1.140225253 0.929743239 1 16.88652649 3.016495218 24.45032673 1.097524603 1.246750371 0.251015918 0.134337499 297.4295716 440866.256 0.039756414 0.047505248 1038.712165 -3.016495218 0.149225769 SGEGEVSGLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGEGEVSGLMR 11 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 230.41 4.24E-12 1135630000 583130 597610 494220 562170 538010 471750 566620 573810 579220 597850 FALSE TRUE 560340.6349 580566.7479 583536.5479 591183.6611 555315.5803 481289.1082 573554.4651 561960.623 513469.3739 557357.087 1.005353028 1.041642354 1.046970715 1.060691027 0.996337166 0.863520209 1.029061043 1.008259581 0.921257459 1 19.0882424 3.016500198 11.94501825 0.969526115 1.038127999 0.363569088 0.046059024 0.755774047 540.4539839 0.01377562 0.016362632 1038.724076 -3.016500198 0.068601884 EEGEHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEGEHIR 7 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 0 98.997 0.010852 56737000 158670 167210 150050 166490 158050 150500 166080 164590 179830 177460 FALSE TRUE 152469.001 162441.3345 177167.3728 175082.5689 163133.8218 153543.2131 168112.5367 161191.159 159416.4523 165440.4761 0.921594307 0.981871778 1.070882876 1.05828134 0.986057497 0.92808735 1.01615119 0.97431513 0.963587969 1 17.33595272 3.016649193 24.97951189 0.976029212 1.012186529 0.101714045 0.043973224 528.368256 792728.4461 0.013394884 0.01600614 1039.080496 -3.016649193 0.036157318 DFPQMGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFPQMGR 7 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 125.62 0.023984 227810000 614180 631910 542070 642890 584620 543560 612660 608930 627180 696610 FALSE TRUE 590177.1666 613888.5455 640034.1073 676069.6299 603424.8332 554551.1556 620157.9163 596355.3827 555985.1558 649427.9842 0.908764607 0.945275782 0.985535152 1.041023249 0.929163584 0.853907083 0.954929463 0.918277926 0.85611518 1 19.30881003 3.016749633 24.98775116 0.913042422 0.971424642 0.199267565 0.050729055 357.3281004 533072.1868 0.014526975 0.017359232 1039.320833 -3.016749633 0.058382221 GVEICIAT(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVEICIATPGR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 P17844;A0A1X7SBZ2 DDX5;DDX17 Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17 1 GVEICIAT(1)PGR 122.55 0.0043429 80452000 102160 106680 97931 120970 98845 84901 90619 104260 121670 119660 TRUE FALSE 98167.47426 103637.5909 115629.3102 127213.2762 102024.4392 86617.75639 91728.02243 102106.9946 107858.5317 111555.3216 0.879989164 0.929024177 1.036519894 1.140360445 0.914563624 0.77645562 0.822264874 0.915303664 0.966861375 1 16.76739981 3.016896374 24.99061036 0.882766594 0.998634341 0.222013628 0.087909387 332.228894 491380.2856 0.026750418 0.0319658 1039.672063 -3.016896374 0.115867747 VNLFTDFDKYMTISDEWDIPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNLFTDFDKYMTISDEWDIPEK 22 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 158.02 2.87E-13 0 60257 60677 44249 39857 52524 58030 49416 56103 67287 53323 FALSE TRUE 57902.08982 58946.55137 52245.77861 41914.02455 54213.48216 59203.40636 50020.76779 54944.45344 59648.86185 49711.38571 1.164765154 1.185775663 1.050982141 0.843147378 1.090564694 1.190942588 1.006223566 1.105268997 1.199903422 1 15.6012887 3.017418627 24.99603674 1.103051616 1.05653012 0.029394937 0.105398068 999.518608 1434317.019 0.032218131 0.038501756 1040.923053 -3.017418627 -0.046521496 MGPLINRPHLER ddPTM_BT-474_Pertuzumab_2h_R1 3 MGPLINRPHLER 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ;; 146.36 3.89E-05 2496170000 464293 496265 404233 480715 420750 302590 484684 428827 444571 437198 FALSE TRUE 446147.9163 482112.0081 477286.8952 505524.7588 434283.8059 308708.5771 490615.7078 419971.5726 394105.1639 407586.19 1.094609992 1.182846769 1.171008505 1.240289223 1.065501767 0.757406862 1.203710331 1.03038715 0.966924723 1 18.63674564 3.017475588 13.36313975 1.003992759 1.170399674 0.386918205 0.106565627 1.329103226 1012.300582 0.030931283 0.036824748 1041.059587 -3.017475588 0.166406915 QHFISFDTDR ddPTM_BT-474_Pertuzumab_2h_R1 3 QHFISFDTDR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ;; 149.96 2.24E-05 2461140000 753420 828600 592158 672090 632657 438530 644010 383236 631601 586902 FALSE TRUE 723975.5135 804969.1393 699174.1231 706776.6454 653006.987 447397.3771 651891.587 375322.0427 559904.3024 547150.6048 1.323174108 1.471202137 1.277845838 1.291740591 1.193468455 0.817685977 1.191429894 0.685957467 1.0233093 1 19.06157847 3.018018259 1.712648581 0.918561189 1.364146696 0.648115707 0.136885409 0.200908617 1.200671871 0.046145436 0.055389256 1042.361253 -3.018018259 0.445585507 IPMPPS(ph)SPQPR ddPTM_BT-474_Pertuzumab_2h_R1 4 IPMPPSSPQPR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 IPMPPS(0.581)S(0.419)PQPR;IPMPPS(0.5)S(0.5)PQPR;IPMPPS(0.5)S(0.5)PQPR;IPMPPS(0.656)S(0.344)PQPR 96.604 0.0072254 2750930000 1153720 1239500 850810 1343650 1048100 851300 1229570 1107910 1038970 1097610 TRUE FALSE 1108631.347 1204150.674 1004570.293 1412995.938 1081813.088 868513.8693 1244617.845 1085031.271 921030.4813 1023267.897 1.083422386 1.176769717 0.981727557 1.380866088 1.057213943 0.848764895 1.216316713 1.060358948 0.900087342 1 19.96475247 3.018022096 24.99958969 1.022896694 1.154058401 0.222331806 0.130915202 410.6161937 569587.6936 0.037284964 0.044557359 1042.370461 -3.018022096 0.131161707 LVGILDILDEENR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVGILDILDEENR 13 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 122.42 0.00054724 27857700 56217 53430 44562 48554 53579 62392 53904 66800 52662 47943 FALSE TRUE 54019.97749 51906.22871 52615.34468 51059.87776 55302.41719 63653.60899 54563.69328 65420.55666 46684.03054 44695.77791 1.208614773 1.161322862 1.177188252 1.142387048 1.23730741 1.424152615 1.220779587 1.46368538 1.044484126 1 15.44785094 3.018271613 9.79680139 1.28052991 1.174038211 0 0.139473328 0.617126948 308.9956007 0.038403934 0.045496764 1042.96951 -3.018271613 -0.106491698 LNSGVDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNSGVDYR 8 0 P62312 P62312 LSM6 U6 snRNA-associated Sm-like protein LSm6 0 ; 78.516 0.070776 456470000 1473420 1544660 1189440 1460140 1323000 1089810 1346770 1423630 1483960 1476880 FALSE TRUE 1415837.117 1500607.809 1404398.267 1535498 1365555.497 1111846.705 1363252.174 1394231.543 1315507.082 1376849.602 1.028316466 1.089885059 1.020008478 1.115225656 0.991797139 0.807529525 0.990124246 1.01262443 0.955447189 1 20.39293955 3.018635728 15.19830655 0.955663705 1.061083651 0.436784784 0.059045136 2.765310994 2252.657953 0.017700879 0.021112338 1043.844309 -3.018635728 0.105419946 EQEVAELKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQEVAELKK 9 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 101.93 0.0072234 0 254690 269000 210350 215500 253790 257540 256560 281060 333960 248850 FALSE TRUE 244736.4332 261328.3834 248364.9242 226621.9808 261953.3858 262747.6353 259699.858 275256.0128 296050.2609 231995.1678 1.054920391 1.126438907 1.070560764 0.976839229 1.12913294 1.1325565 1.119419255 1.186473043 1.27610529 1 17.82373523 3.018653622 24.59680239 1.152533172 1.061828074 0.236350143 0.072598616 273.1227813 360138.6517 0.020671467 0.024703476 1043.88732 -3.018653622 -0.090705099 YGRPPDSHHSR ddPTM_BT-474_Pertuzumab_2h_R1 8 YGRPPDSHHSR 11 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;;;; 156.14 1.87E-05 733378000 713549.6 1311359 1013934 1514244 872464 792476.5 1127177 382705 876175 1233824 FALSE TRUE 685663.2928 1273960.325 1197174.429 1592394.314 900527.5969 808500.9178 1140971.729 374802.008 776715.2872 1150256.002 0.596096253 1.107545037 1.040789552 1.384382531 0.782893196 0.702887806 0.991928517 0.325842254 0.675254279 1 20.13352355 3.018795398 24.83424994 0.693800851 1.043878263 0.226115912 0.252779149 280.6947837 370877.6 0.073578802 0.087930988 1044.228153 -3.018795398 0.350077412 IHLGSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHLGSSPK 8 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 IHLGS(0.001)S(0.999)PK;IHLGS(0.007)S(0.993)PK 135.87 0.00052502 1173930000 2528300 2391800 1979820 2023600 2022580 2052080 2308000 1251850 2448200 2408100 TRUE FALSE 2429491.241 2323588.206 2337617.515 2128038.239 2087638.123 2093574.464 2336245.994 1225998.86 2170290.6 2244997.242 1.082180056 1.035007154 1.041256297 0.947902384 0.929906765 0.932551018 1.040645374 0.546102613 0.966723058 1 21.09828224 3.018818623 0.772171398 0.825581603 1.062433793 0.169434627 0.131379714 0.872563686 1.159772827 0.081328688 0.109000358 1044.283997 -3.018818623 0.23685219 VDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_BT-474_Pertuzumab_2h_R1 9 VDEFPLCGHMVSDEYEQLSSEALEAAR 27 0 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;;;;;;; 311.89 4.93E-82 4679537000 1488412 1525787 1259207 1364507 1463741 1731447 1439218 1461727 1639432 1759420 FALSE TRUE 1430243.214 1482273.049 1486773.716 1434929.37 1510823.559 1766458.045 1456831.58 1431541.827 1453330.552 1640252.916 0.871965048 0.903685666 0.906429552 0.87482202 0.921091829 1.076942481 0.888174967 0.872756764 0.886040523 1 20.64548686 3.018875087 18.12855919 0.934196315 0.892295234 0.155660479 0.058280791 26.71182155 25649.74545 0.018252717 0.021796613 1044.419778 -3.018875087 -0.041901081 DRPVGGSPGGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRPVGGSPGGPR 12 1 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 0 126.5 0.0002612 71174000 45583 64205 46616 61704 53093 53182 53090 57990 53403 60114 FALSE TRUE 43801.56597 62373.93626 55040.54817 64888.55083 54800.78456 54257.37648 53739.7313 56792.48624 47340.91532 56042.42524 0.781578702 1.112977106 0.982122882 1.157846945 0.97784463 0.96814826 0.958911594 1.013383807 0.844733523 1 15.77423177 3.019296507 24.99855445 0.963667519 1.020898007 0.046733807 0.101975763 704.4353811 912587.6596 0.028028747 0.033496567 1045.433726 -3.019296507 0.057230488 DKFSPFPVQDRPESSLVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKFSPFPVQDRPESSLVFK 19 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 223.51 1.23E-19 2163600000 1451700 1423270 1270850 1126030 1458820 1601500 1413070 1604280 1839070 1594440 FALSE TRUE 1394965.959 1382679.733 1500520.865 1184144.543 1505744.27 1633883.427 1430363.573 1571151.057 1630306.484 1486447.159 0.938456474 0.930190976 1.009468017 0.796627405 1.012982037 1.099187023 0.962270044 1.05698413 1.096780652 1 20.50343675 3.019482687 24.9996772 1.04218502 0.923343534 0.475985565 0.061939161 207.2793407 265973.4966 0.017141303 0.02048546 1045.881995 -3.019482687 -0.118841486 SGGIVIS(ph)PFRLEELTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGIVISPFRLEELTNR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR 297.68 2.00E-46 1128710000 337160 372190 302610 291480 358050 457070 369280 351100 409860 364030 TRUE FALSE 323983.4144 361575.5056 357298.3585 306523.3177 369567.0034 466312.2686 373799.3591 343849.6623 363334.4111 339373.9239 0.954650289 1.065419233 1.052816181 0.903202327 1.088966999 1.374036824 1.101438068 1.013188221 1.070602028 1 18.37251619 3.020490294 24.43251999 1.116296348 1.002416744 0.218898404 0.105607561 314.2848478 374748.1078 0.032563681 0.03891654 1048.311366 -3.020490294 -0.113879605 APEYLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 APEYLHR 7 0 Q9UN86-2;Q9UN86;D6RB17;D6RAC7;D6RE13;D6RBW8;D6RGJ4;D6RBM9;D6REX8;D6RBR0;D6R9X5;D6R9A4 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 144.83 0.00987 0 207340 236710 191930 234980 211960 195460 227680 216730 233470 259310 FALSE TRUE 199236.9236 229959.2626 226616.0205 247107.346 218777.8859 199412.3351 230466.4159 212254.4498 206967.4644 241746.7027 0.824155702 0.951240534 0.937411009 1.022174628 0.904988086 0.824881303 0.953338405 0.878003494 0.856133557 1 17.88313669 3.020496502 24.99848732 0.894597772 0.938797486 0.043368223 0.064363485 580.8248166 708396.0502 0.017978463 0.021486658 1048.326351 -3.020496502 0.044199714 TIVCPMIDVIDHDDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TIVCPMIDVIDHDDFR 16 0 Q86SR1-3;Q86SR1-2;Q86SR1 Q86SR1-3 GALNT10 Polypeptide N-acetylgalactosaminyltransferase 10 0 119.54 0.00018611 24254000 16625 22961 19524 23060 18684 16724 20493 19059 17207 22383 FALSE TRUE 15975.27662 22306.17476 23052.42111 24250.12936 19284.98783 17062.17074 20743.79946 18665.42499 15253.7335 20866.97947 0.76557686 1.068969986 1.104732055 1.162129353 0.92418684 0.817663657 0.994096893 0.894495776 0.730998634 1 14.34893416 3.020541128 24.33467623 0.889049994 1.035265266 0.222394269 0.121753287 252.0402818 298584.4367 0.03511386 0.041964274 1048.434076 -3.020541128 0.146215272 VASWELR ddPTM_BT-474_Pertuzumab_2h_R1 1 VASWELR 7 0 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 105.39 0.018466 143840000 175890 177480 173370 188490 172720 155030 189680 183040 185510 192880 FALSE TRUE 169016.0243 172418.4442 204701.8156 198217.9915 178275.6957 158164.8128 192001.3606 179260.16 164451.6825 179816.0658 0.939938395 0.958860063 1.138395586 1.102337495 0.991433635 0.879592222 1.067765329 0.996908476 0.914555003 1 17.4561624 3.02057757 24.86783954 0.977070396 1.038101355 0.142276279 0.072564054 488.6270702 590497.7785 0.022232752 0.026570618 1048.522055 -3.02057757 0.06103096 SPRPAS(ph)PASNVVVLPSGSTVYVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPRPASPASNVVVLPSGSTVYVK 23 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 S(0.141)PRPAS(0.677)PAS(0.182)NVVVLPSGSTVYVK 107.76 0.00079698 732630000 815900 803890 674540 706140 808180 936270 813650 860520 1076700 850020 TRUE FALSE 784013.726 780963.8443 796444.3831 742583.97 834175.8437 955202.0209 823607.6921 842749.9613 954477.5299 792447.3883 0.989357448 0.985508762 1.005043861 0.937076683 1.052657698 1.205382256 1.039321606 1.063477492 1.204468011 1 19.59595563 3.020822089 8.536906554 1.100669293 0.982946151 0.459519397 0.062978601 0.188748876 65.31726586 0.01778624 0.021048994 1049.112567 -3.020822089 -0.117723142 LYNNHEIR ddPTM_BT-474_Pertuzumab_2h_R1 8 LYNNHEIR 8 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;;; 172.25 0.00028467 6847730000 4459082 4708400 3963519 4853155 4053588 2968277 4577303 3997601 4661636 5089474 FALSE TRUE 4284816.146 4574121.042 4679815.051 5103626.911 4183975.339 3028297.595 4633321.403 3915049.142 4132466.624 4744759.393 0.903062893 0.964036459 0.986312406 1.075634503 0.881809802 0.638240497 0.976513458 0.825131228 0.870953885 1 22.1779035 3.021375813 22.46735014 0.849008314 0.980933475 0.243803466 0.099938682 93.9602741 98755.99228 0.027954114 0.033406036 1050.451034 -3.021375813 0.131925161 HGLEAISIMDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 HGLEAISIMDSR 12 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;; 218.62 3.39E-11 1065400000 1115800 1199930 995960 1165060 1060270 1001070 1156100 853960 1258440 1390380 FALSE TRUE 1072193.302 1165709.171 1175952.127 1225188.886 1094374.547 1021312.321 1170248.698 836325.4276 1115587.167 1296208.324 0.827176683 0.899322392 0.907224637 0.945209858 0.844289091 0.787922977 0.90282455 0.645209116 0.860654222 1 20.30586617 3.021419641 7.720644547 0.809391144 0.896017684 0.031522879 0.09077688 0.322453334 85.66979585 0.02608632 0.030814329 1050.557049 -3.021419641 0.08662654 LSVACFYGGTPYGGQFER ddPTM_BT-474_Pertuzumab_2h_R1 1 LSVACFYGGTPYGGQFER 18 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 116.84 0.0003463 57770000 22151 22198 19043 15703 21241 16525 15641 16329 18284 18929 FALSE TRUE 21285.31443 21564.93477 22484.49371 16513.43371 21924.23606 16859.14682 15832.41924 15991.80044 16208.47697 17646.92197 1.206177172 1.222022447 1.274131191 0.935768501 1.242383011 0.955359062 0.897177381 0.906209053 0.918487485 1 14.10712895 3.021491591 0.866619282 0.90934039 1.227259534 0.596568596 0.09563949 0.382588219 0.636483155 0.05004926 0.065149392 1050.731111 -3.021491591 0.317919144 AFFSEVER ddPTM_BT-474_Pertuzumab_2h_R1 5 AFFSEVER 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;; 193.96 0.00039056 5214640000 4130120 4386300 3633530 4083240 3854820 3249260 4182690 3916840 3944730 4468730 FALSE TRUE 3968710.344 4261207.019 4290189.698 4293976.506 3978813.786 3314962.263 4233879.011 3835955.885 3496940.788 4166058.937 0.952629429 1.022838871 1.029795729 1.030704695 0.955054608 0.795707001 1.016279192 0.920763711 0.839388218 1 21.99025182 3.021528458 7.902586575 0.91474178 1.009481525 0.322452878 0.064608625 0.214581304 60.37315383 0.018381616 0.021727056 1050.820311 -3.021528458 0.094739745 SAEVGPS(ph)SEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 S(0.091)AEVGPS(0.453)S(0.453)EPEVQT(0.001)LPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 44.333 0.011862 150300000 26803 40919 38372 44664 35985 33585 38160 39496 34315 39341 TRUE FALSE 25755.50913 39752.03018 45306.67398 46969.11439 37142.49021 34264.11171 38627.01349 38680.3938 30419.70506 36676.39903 0.702236583 1.083858591 1.235308678 1.28063593 1.012708204 0.934227804 1.05318446 1.0546399 0.829408172 1 15.16256438 3.021645526 24.84862889 0.988884596 1.094914412 0.076139992 0.156691742 582.2269859 668379.926 0.046954321 0.056117066 1051.103607 -3.021645526 0.106029816 LPLLPPES(ph)PGPLR ddPTM_BT-474_Pertuzumab_2h_R1 6 LPLLPPESPGPLR 13 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;A0A669KAX5 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR 180.84 1.32E-05 1441710000 933788 1173543 732958 1264758 892459 732946 913532 1190377 766446 595372 TRUE FALSE 897294.5326 1140074.703 865419.8152 1330032.312 921165.7542 747766.6703 924712.0779 1165795.299 679442.2633 555046.9241 1.616610224 2.054014991 1.559183156 2.396252018 1.659617798 1.34721343 1.666007031 2.100354489 1.224116798 1 19.08225022 3.021813146 24.99206153 1.588489999 1.90920309 0.218269894 0.356599008 448.4945936 513851.8353 0.102481365 0.122480327 1051.509367 -3.021813146 0.320713092 AFHAALRNS(ph)PVNTK ddPTM_BT-474_Pertuzumab_2h_R1 2 AFHAALRNSPVNTK 14 1 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 1 AFHAALRNS(1)PVNTK;AFHAALRNS(1)PVNTK 198.85 1.30E-08 1063430000 743780 739320 637260 648360 736560 868560 727450 737650 886670 816620 TRUE FALSE 714712.2553 718235.3175 752427.0578 681821.9373 760252.1213 886122.8783 736352.7507 722417.2697 786018.9388 761309.6 0.938793173 0.943420807 0.988332549 0.895590883 0.998610974 1.163945494 0.967218528 0.948913911 1.03245636 1 19.53812374 3.021984833 21.94980026 1.016163563 0.9452728 0.300323604 0.058010514 88.85431448 88710.09276 0.018027891 0.021543786 1051.925135 -3.021984833 -0.070890763 NVPHEDICEDSDIDGDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVPHEDICEDSDIDGDYR 18 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ; 178.75 8.72E-14 867360000 278715 311541 190830 242199 262126 280271 271902 277201 281163 303861 FALSE TRUE 267822.5097 302656.1557 225317.226 254698.9194 270557.5208 285938.2716 275229.618 271476.7025 249246.555 283280.2238 0.945433134 1.068398463 0.79538636 0.899105896 0.955087924 1.009383104 0.97158077 0.958332703 0.879858649 1 18.11187036 3.022524773 22.1829101 0.96375698 0.92768432 0.05867227 0.069971302 223.0122963 219621.8308 0.020783094 0.024837089 1053.233764 -3.022524773 -0.03607266 IEIESFYEGEDFSETLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 IEIESFYEGEDFSETLTR 18 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 312.05 8.08E-61 994834000 632204 758082 582263 731649 622573 560610 647664 617177 744266 716300 FALSE TRUE 607496.7687 736462.2436 687490.8765 769409.4926 642598.626 571945.9183 655590.3058 604432.0793 659780.0439 667784.363 0.909719967 1.102844398 1.029510295 1.152182554 0.962284626 0.856482946 0.981739529 0.905130627 0.988013617 1 19.34902279 3.022641135 24.57720371 0.93741517 1.051849657 0.32325716 0.070285901 191.5976833 207979.6596 0.01908739 0.022812275 1053.515999 -3.022641135 0.114434487 LAAAEETAVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 LAAAEETAVSPR 12 0 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR 194.98 8.77E-07 10117130000 3278070 3450870 3513550 4108870 3437990 3321390 3661650 3511350 3554620 4107430 TRUE FALSE 3149959.4 3352454.566 4148526.643 4320929.273 3548576.071 3388550.781 3706462.368 3438839.395 3151114.44 3829230.108 0.822609065 0.875490496 1.083384003 1.128406795 0.926707451 0.88491699 0.967939315 0.898049816 0.822910703 1 21.86862293 3.023055352 24.98304488 0.911505352 0.983978725 0.090106192 0.093970122 551.2340706 597319.5071 0.029055741 0.034726575 1054.521289 -3.023055352 0.072473372 LKLGEIVTTIPTIGFNVETVEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKLGEIVTTIPTIGFNVETVEYK 23 1 P61204;F5H423;F5H0C7;P84077;P84085;C9J1Z8;P18085;C9JPM4 P61204;P84077;P84085;P18085 ARF3;ARF1;ARF5;ARF4 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 ; 210.74 5.55E-25 543250000 747780 662860 543270 526000 690000 825480 661530 753120 847230 660280 FALSE TRUE 718555.9309 643955.8818 641450.974 553146.923 712194.4766 842171.7712 669626.002 737567.8088 751056.0023 615558.6475 1.167323266 1.046132459 1.042063135 0.898609621 1.156988826 1.368142215 1.087834611 1.198208833 1.220120951 1 19.23153679 3.023252655 24.67660272 1.18876626 1.03788614 0.266882144 0.107380295 236.4670511 250945.7764 0.029952978 0.035798816 1055.000475 -3.023252655 -0.150880119 HYYEVSCHDQGLCR ddPTM_BT-474_Pertuzumab_2h_R1 4 HYYEVSCHDQGLCR 14 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 210.14 3.27E-09 2247940000 582290 778860 620230 828910 583260 502872 678690 320667 638060 740430 FALSE TRUE 559533.463 756647.6754 732319.3579 871690.1444 602021.0876 513040.4164 686996.0112 314045.1144 565630.1038 690280.0166 0.810589108 1.096145995 1.060901866 1.262806576 0.872140397 0.743235215 0.995242503 0.454953217 0.819421235 1 19.39682219 3.023561562 10.24153274 0.764143437 1.061669351 0.307369734 0.17686609 0.39942847 167.366669 0.051528518 0.061292867 1055.751147 -3.023561562 0.297525913 QEELGAVVDKEMAATSAAIEDAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEELGAVVDKEMAATSAAIEDAVR 24 1 O75146 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 240.46 1.39E-37 31836000 38002 40470 25826 30852 36164 40353 37618 40331 43567 37825 FALSE TRUE 36516.83983 39315.83522 30493.3327 32444.27542 37327.2479 41168.96531 38078.38034 39498.15076 38621.45681 35263.07906 1.035554489 1.114929163 0.864738234 0.920063599 1.058536262 1.167480731 1.07983708 1.120099317 1.095237791 1 15.10587083 3.02369479 9.844751759 1.101706991 0.985137788 0.326586998 0.073244714 0.375558934 148.3292108 0.02185352 0.025980523 1056.075069 -3.02369479 -0.116569203 GS(ph)LASLDSLR ddPTM_BT-474_Pertuzumab_2h_R1 5 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GS(0.994)LAS(0.006)LDSLR;GS(1)LASLDSLR;GS(0.999)LAS(0.001)LDSLR;GS(0.966)LAS(0.034)LDSLR;GS(0.745)LAS(0.255)LDSLR 208.17 1.24E-07 5435630000 2610090 3642980 2952710 3710580 2889670 2466390 2920340 3459180 2829150 2724270 TRUE FALSE 2508084.797 3539085.777 3486330.38 3902083.478 2982618.86 2516262.096 2956079.994 3387746.724 2507996.753 2539752.766 0.987531082 1.393476493 1.372704629 1.536402885 1.174373703 0.990750804 1.163924313 1.333888388 0.987496415 1 21.27625663 3.023818765 24.95073488 1.133695549 1.334206519 0.286888059 0.163320269 322.3998532 337719.3076 0.048262155 0.057681702 1056.376581 -3.023818765 0.20051097 AVPLIHQEGNR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVPLIHQEGNR 11 0 O00170;E9PMH2;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 152.64 3.29E-05 1038100000 713740 895410 570770 767220 697040 606140 826650 715880 700640 799710 FALSE TRUE 685846.2517 869873.7835 673920.8357 806816.3161 719460.9246 618396.5661 836766.79 701096.8278 621106.2845 745544.9294 0.919926117 1.16676239 0.903930547 1.082183359 0.965013504 0.8294558 1.122355953 0.940381726 0.833090348 1 19.50793577 3.024054837 24.05800086 0.950240448 1.02101862 0.097823125 0.104604835 364.9685184 365012.5047 0.029014239 0.034676564 1056.950959 -3.024054837 0.070778172 VTELEDKFDLLVDANDVILER ddPTM_BT-474_Pertuzumab_2h_R1 1 VTELEDKFDLLVDANDVILER 21 1 Q01780;Q01780-2;K7EJ37 Q01780 EXOSC10 Exosome component 10 0 128.12 1.70E-05 91582000 315430 276950 249130 217070 300220 328530 291830 329940 359690 353290 FALSE TRUE 303102.6469 269051.6572 294153.3329 228273.0087 309876.849 335173.1017 295401.5028 323126.6237 318859.4991 329361.3536 0.920273868 0.816888971 0.893102149 0.693077698 0.940841558 1.017645507 0.896891817 0.981070244 0.968114491 1 18.32931176 3.024506117 24.98854619 0.967383357 0.832121095 0.533265382 0.063088617 171.7638094 175143.903 0.017236607 0.020600867 1058.049819 -3.024506117 -0.135262262 GFGSFR ddPTM_BT-474_Pertuzumab_2h_R1 8 GFGSFR 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;; 120.76 0.046406 7919030000 3991380 4455530 3837300 4448260 4036380 3314620 4638670 4412100 4155570 4678640 FALSE TRUE 3835392.457 4328462.647 4530785.47 4677835.232 4166213.828 3381643.887 4695439.431 4320988.593 3683847.115 4361751.545 0.879323918 0.992367998 1.03875368 1.072467146 0.955169909 0.775294936 1.076503185 0.990654453 0.84457977 1 22.05647616 3.024573944 24.9775267 0.944147618 1.000468575 0.081201761 0.090893644 645.0396499 655628.679 0.027095556 0.032384167 1058.215074 -3.024573944 0.056320957 RFS(ph)NVGLVHTSER ddPTM_BT-474_Pertuzumab_2h_R1 4 RFSNVGLVHTSER 13 1 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER 152.83 6.41E-07 2457610000 942960 1519390 1060950 1487230 1057530 1002080 921070 1105260 725490 1024870 TRUE FALSE 906108.0807 1476058.485 1252687.266 1563986.119 1091546.413 1022342.744 932342.3302 1082435.995 643135.4167 955454.642 0.948352795 1.544875518 1.31109025 1.636902528 1.142436663 1.07000657 0.975810142 1.132901497 0.673119778 1 19.86582786 3.024669414 7.892463044 1.002706337 1.373152665 0.444829326 0.203536065 0.179028367 45.42889474 0.056741711 0.067219309 1058.447726 -3.024669414 0.370446327 KLPIQEFHLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPIQEFHLSR 11 1 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 189.24 1.81E-06 1783270000 1965630 2976400 2363160 3216800 2342600 2248600 2687400 2158370 2221640 2839100 FALSE TRUE 1888811.006 2891515.986 2790235.58 3382819.434 2417951.856 2294068.233 2720289.205 2113798.905 1969448.741 2646805.228 0.713619191 1.092455144 1.054189991 1.278076451 0.913535998 0.866731034 1.027763273 0.798622763 0.744085254 1 21.3358206 3.024820093 24.98024461 0.881503696 1.047080027 0.175970872 0.151019693 351.3084043 353572.661 0.043531821 0.052028643 1058.815019 -3.024820093 0.16557633 KFDPMGQQTCSAHPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KFDPMGQQTCSAHPAR 16 1 Q9NPE3 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 161.14 5.54E-09 400780000 284140 387510 265060 362570 300120 280180 308250 304730 332980 362720 FALSE TRUE 273035.4947 376458.5942 312962.2382 381282.2812 309773.6324 285845.4316 312022.4557 298437.219 295181.5064 338152.6513 0.80743266 1.113280031 0.925505795 1.127544852 0.916076308 0.845314773 0.922726628 0.882551764 0.872923827 1 18.36731514 3.025000769 24.99895281 0.896120528 1.000231094 0.169429303 0.093030218 316.4138238 316388.5583 0.02455477 0.029347579 1059.2556 -3.025000769 0.104110566 LAT(ph)QSNEITIPVTFESR ddPTM_BT-474_Pertuzumab_2h_R1 1 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.902)QS(0.098)NEITIPVTFESR 163.41 3.04E-08 102650000 68411 65033 54293 55922 53449 55189 41814 51742 51914 52908 TRUE FALSE 65737.42249 63178.32251 64104.95284 58808.14112 55168.23563 56304.95939 42325.73224 50673.50962 46020.94036 49324.49403 1.332754117 1.280871173 1.299657586 1.19227054 1.118475449 1.141521277 0.858107783 1.027349811 0.933024074 1 15.59001663 3.025046361 0.891802331 0.956522894 1.318759543 0.845817987 0.060272417 0.201153016 0.353374265 0.030204546 0.039231577 1059.366807 -3.025046361 0.362236649 IDGAVIPDHWLDPSAVWEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 IDGAVIPDHWLDPSAVWEVK 20 0 P18858;P18858-3;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ; 204.78 9.29E-22 675110000 1176210 1044320 921510 957700 1052250 1065800 1088180 1087850 1266590 1200090 FALSE TRUE 1130242.413 1014537.016 1088047.356 1007127.012 1086096.577 1087351.206 1101497.472 1065385.517 1122812.013 1118806.835 1.010221226 0.906802662 0.97250689 0.90017953 0.970763265 0.971884665 0.98452873 0.952251527 1.003579865 1 20.09352954 3.025117836 24.9996883 0.976840229 0.944961448 0.197089263 0.032278106 363.5219427 361809.6073 0.008630562 0.010315136 1059.54117 -3.025117836 -0.031878781 LGELTMQLHPVADSS(ph)PAGAQIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGELTMQLHPVADSSPAGAQIK 22 0 Q8IXM2-2 Q8IXM2-2 BAP18 Chromatin complexes subunit BAP18 1 LGELTMQLHPVADS(0.355)S(0.645)PAGAQIK;LGELTMQLHPVADS(0.321)S(0.679)PAGAQIK 195.73 1.42E-22 453420000 435610 421030 391400 425490 471710 592910 513410 541780 662770 645690 TRUE FALSE 418585.8796 409022.6366 462134.6866 447449.5899 486882.9805 604899.0464 519693.2652 530592.0537 587535.1282 601956.8412 0.695375235 0.67948831 0.767720632 0.743325035 0.808833702 1.004887735 0.863339744 0.881445342 0.976041948 1 19.19930053 3.025483584 2.959446346 0.926471085 0.720796752 0.808094008 0.051038159 0.119691827 2.146781174 0.016344411 0.019205954 1060.433853 -3.025483584 -0.205674333 YLAEFATGNDRK ddPTM_BT-474_Pertuzumab_2h_R1 4 YLAEFATGNDRK 12 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 203.51 1.99E-07 3801360000 3063390 3298460 2404330 2652310 3283790 3723970 3553400 3808920 4184670 4093210 FALSE TRUE 2943669.332 3204391.15 2838845.915 2789196.037 3389416.088 3799271.225 3596887.572 3730264.471 3709643.805 3815973.241 0.771407226 0.839731033 0.743937584 0.730926519 0.888217992 0.995623131 0.94258721 0.977539473 0.972135697 1 21.86361962 3.026180794 3.902732374 0.972097911 0.775168408 0.905961204 0.031200869 0.064022026 2.15690538 0.009750744 0.011412798 1062.137626 -3.026180794 -0.196929504 GQRPETLHER ddPTM_BT-474_Pertuzumab_2h_R1 1 GQRPETLHER 10 1 Q5BJF2;Q86XC5;J3KTD1 Q5BJF2 TMEM97 Transmembrane protein 97 0 51.286 0.094695 34069000 24676 45936 27706 50043 32009 23564 46312 31370 27623 27928 FALSE TRUE 23711.63464 44625.95026 32713.09052 52625.72523 33038.59855 24040.48022 46878.78011 30722.19854 24487.35285 26036.41168 0.910710544 1.713982357 1.256436214 2.021235717 1.268938245 0.923340763 1.800508483 1.179970532 0.940504135 1 14.66824301 3.026393102 24.99362071 1.218796647 1.497980402 0.13300569 0.357238219 467.1630107 442388.5699 0.100006896 0.119528487 1062.656988 -3.026393102 0.279183755 S(ph)LPS(ph)SPLLTHQSISVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(1)LPS(0.546)S(0.454)PLLTHQSISVR 90.464 0.0028743 100690000 31030 45093 36006 45675 33702 30875 33962 40689 25966 31402 TRUE FALSE 29817.31329 43806.99179 42513.08515 48032.29222 34786.05544 31499.31365 34377.63712 39848.75793 23018.44854 29275.11457 1.018520806 1.496390106 1.452191931 1.640720897 1.188246603 1.07597576 1.174295562 1.361181963 0.786280391 1 14.8373872 3.026465555 22.43482255 1.131091058 1.412564396 0.347568527 0.20244709 86.28804155 73144.51687 0.058383786 0.069777877 1062.834283 -3.026465555 0.281473338 ISDDKYGR ddPTM_BT-474_Pertuzumab_2h_R1 5 ISDDKYGR 8 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;; 159.58 0.00032678 5589480000 5590340 5585400 4554020 5322030 5491880 5626010 5972510 6376450 6264210 6104030 FALSE TRUE 5371863.332 5426109.861 5377032.718 5596700.606 5668531.308 5739771.777 6045603.364 6244774.079 5553123.143 5690598.611 0.943989148 0.953521805 0.944897556 0.98349945 0.996122147 1.008641124 1.06238443 1.097384389 0.975841651 1 22.44014899 3.026479634 1.226997558 1.046415927 0.94834385 0.511851891 0.033171412 0.315891857 1.004308272 0.014101668 0.017504603 1062.868739 -3.026479634 -0.098072078 AAS(ph)PSPQSVR ddPTM_BT-474_Pertuzumab_2h_R1 7 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 AAS(0.984)PS(0.016)PQSVR;AAS(0.997)PS(0.003)PQSVR;AAS(0.999)PS(0.001)PQSVR;AAS(0.993)PS(0.007)PQSVR;AAS(0.658)PS(0.342)PQSVR;AAS(0.984)PS(0.016)PQSVR;AAS(0.815)PS(0.185)PQSVR 191.23 8.54E-07 7111372000 5986490 6233290 5514790 6641530 5819160 5417500 6329590 6120030 6315730 6417340 TRUE FALSE 5752531.352 6055522.672 6511435.229 6984300.159 6006338.566 5527045.562 6407053.416 5993649.242 5598794.808 5982687.846 0.961529583 1.012174265 1.088379571 1.167418448 1.003953193 0.92383987 1.07093226 1.001832186 0.935832681 1 22.51236236 3.026577666 24.98997841 0.991804085 1.060026949 0.224918064 0.062055904 358.1739117 336774.936 0.018849469 0.022528976 1063.108685 -3.026577666 0.068222863 LNVEFALIHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNVEFALIHK 10 0 P11908;P11908-2 P11908 PRPS2 Ribose-phosphate pyrophosphokinase 2 0 ; 111.86 0.001698 1277640000 1701790 1745820 1552090 1729170 1558580 1145110 1820280 1538950 1668880 1792240 FALSE TRUE 1635282.165 1696030.923 1832587.189 1818412.671 1608713.141 1168264.909 1842557.131 1507170.145 1479435.739 1670849.988 0.978712737 1.015070733 1.096799355 1.088315937 0.962811235 0.699203948 1.102766343 0.902037978 0.885438998 1 20.67215078 3.026666671 9.931719199 0.917032835 1.043905634 0.264125536 0.099953143 0.490691465 175.0586978 0.028564051 0.034007284 1063.326582 -3.026666671 0.126872799 RTEEENGKK ddPTM_BT-474_Pertuzumab_2h_R1 4 RTEEENGKK 9 2 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;H3BNL6;Q6P474;H3BPV5;H3BM88;A0A0J9YXH6;H3BU11;H3BQ54 H3BND4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 0 ;;; 143.89 5.67E-05 821200000 922700 825670 640770 727140 826350 873850 921100 916780 870690 1010050 FALSE TRUE 886639.8639 802122.7 756571.3929 764667.7825 852930.2982 891519.8457 932372.6973 897848.1726 771852.9214 941638.4138 0.941592708 0.851837275 0.803462754 0.812060947 0.905793865 0.946775145 0.990160006 0.953495694 0.819691412 1 19.84481365 3.026886465 4.679563006 0.943228833 0.848925019 0.3512717 0.057351413 0.214043003 11.59321288 0.017415176 0.020425018 1063.864863 -3.026886465 -0.094303814 IREEYPDR ddPTM_BT-474_Pertuzumab_2h_R1 16 IREEYPDR 8 1 Q5JP53;P07437;Q5ST81;A6NNZ2;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1 Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1 TUBB;TUBB1;TUBB4B;TUBB2A;TUBB8;TUBB2B Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-1 chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain 0 ;;;;;;;;;;;;;;; 192.91 0.00015818 1.80379E+11 21602210.6 23884125.4 19942476.6 24226844.2 21568785.1 18873579.9 24110056.6 22993654.8 23133243.9 24772514.3 FALSE TRUE 20757972.33 23202973.53 23546525.74 25477194.53 22262564.66 19255216.62 24405122.68 22518827.79 20507255.03 23094649.84 0.898821695 1.004690423 1.019566259 1.103164357 0.963970652 0.833752265 1.056743568 0.975066864 0.887965619 1 24.46105534 3.026907705 24.99528222 0.954054463 1.010632496 0.115420508 0.072881301 489.5852956 454785.4095 0.021425894 0.025608411 1063.916895 -3.026907705 0.056578033 EPWLLPSQHNDIIR ddPTM_BT-474_Pertuzumab_2h_R1 3 EPWLLPSQHNDIIR 14 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 127.07 8.17E-05 865240000 854220 1275960 1053930 1335450 1042330 893490 1257920 970660 1143330 1232790 FALSE TRUE 820836.138 1239570.87 1244398.596 1404372.735 1075857.491 911556.98 1273314.801 950615.5318 1013543.972 1149292.035 0.714210238 1.078551693 1.082752301 1.221945938 0.936104539 0.793146522 1.107912317 0.827131401 0.881885492 1 20.132314 3.026960637 24.98948941 0.91445866 1.038233456 0.098933403 0.145084163 431.454255 399906.7886 0.041440302 0.049529596 1064.046573 -3.026960637 0.123774796 LWPSGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LWPSGDR 7 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;; 183.89 0.0014796 10387060000 1954010 2220290 1859560 2377840 2023130 1824310 2210710 2245080 2078540 2190680 FALSE TRUE 1877645.129 2156969.503 2195623.858 2500560.607 2088205.814 1861198.798 2237765.33 2198718.313 1842592.853 2042303.292 0.919376243 1.056145535 1.075072378 1.224382596 1.022475859 0.911323409 1.095706665 1.076587558 0.902213134 1 20.9617657 3.026966931 24.99975454 1.011315907 1.075187886 0.113244557 0.089616464 545.658156 505850.3478 0.026951006 0.032211708 1064.061992 -3.026966931 0.06387198 LS(ph)LDLSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSLDLSHR 8 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 LS(1)LDLSHR 146.11 0.00035983 102020000 63993 59532 55702 71634 79908 57295 80898 96814 95860 94362 TRUE FALSE 61492.08281 57834.20565 65768.59048 75331.03932 82478.31339 58453.54416 81888.05392 94814.75707 84978.37468 87970.77769 0.699005788 0.657425195 0.747618609 0.856318897 0.9375649 0.66446547 0.930855178 1.077798328 0.965984125 1 16.42473675 3.027470141 0.423881851 1.04622213 0.627523219 0.600035864 0.090933626 1.057337358 0.361351203 0.093801027 0.188075397 1065.295619 -3.027470141 -0.418698911 SLFS(ph)PQNTLAAPTGHPPTSGVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLFSPQNTLAAPTGHPPTSGVEK 23 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 SLFS(1)PQNTLAAPTGHPPTSGVEK;SLFS(0.975)PQNT(0.025)LAAPTGHPPTSGVEK 237.1 2.48E-37 422870000 578370 579850 493230 554970 566070 612140 598460 668970 684040 701320 TRUE FALSE 555766.661 563313.2457 582367.6328 583612.0682 584278.1556 624517.8902 605784.1325 655155.5357 606390.6469 653818.9717 0.850031408 0.861573723 0.890716939 0.892620272 0.893639036 0.955184718 0.926531898 1.002044242 0.927459546 1 19.31853171 3.027726457 0.412010169 0.994766116 0.831137763 0.790742173 0.022908377 0.646938972 0.206819088 0.021493005 0.044252832 1065.92453 -3.027726457 -0.163628354 RYDGSQQALDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RYDGSQQALDLK 12 1 Q9UBU9;Q9UBU9-2;E9PIN3;B4E227 Q9UBU9 NXF1 Nuclear RNA export factor 1 0 ; 109.22 0.0025997 153040000 543460 597980 438640 445120 545560 593100 574790 631020 515780 560260 FALSE TRUE 522220.9824 580926.1959 517912.0055 468092.6965 563108.4329 605092.8884 581824.452 617989.2165 457230.8167 522313.0912 0.999823652 1.112218334 0.991573855 0.896191775 1.078105149 1.158486928 1.113938099 1.183177728 0.87539605 1 18.99455534 3.027784785 24.98092903 1.092922045 1.004844464 0.076254546 0.09611163 398.5004136 358283.5975 0.027835546 0.033269224 1066.067701 -3.027784785 -0.088077581 EAFQLFDR ddPTM_BT-474_Pertuzumab_2h_R1 10 EAFQLFDR 8 0 P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2 P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;;;; 220.88 1.34E-05 10388243000 3583702 4000594 3288942 3722354 3537527 3070023 4034212 3797603 3657387 3903501 FALSE TRUE 3443646.964 3886500.976 3883326.982 3914465.136 3651314.769 3132100.968 4083583.893 3719181.171 3242215.761 3639113.4 0.946287347 1.067980178 1.067107989 1.075664511 1.003352841 0.860676935 1.122137027 1.022001999 0.890935622 1 21.79515558 3.02781075 16.3429509 0.989475486 1.042829379 0.116169788 0.075291115 12.11585082 7115.988658 0.022204895 0.026530077 1066.131438 -3.02781075 0.053353893 EGLMLDSHEELYK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGLMLDSHEELYK 13 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 213.06 8.96E-09 1410680000 1840110 1967940 1703320 1579550 1978600 2046190 2085120 1970840 2551160 2334110 FALSE TRUE 1768196.467 1911816.278 2011147.814 1661070.765 2042243.466 2087565.364 2110638.322 1930141.465 2261563.012 2176018.651 0.812583323 0.878584509 0.924232802 0.763353184 0.93852296 0.95935086 0.969954151 0.887005938 1.039312329 1 21.05325949 3.02787606 24.0705134 0.956859495 0.852559575 0.544428917 0.053932364 122.9784658 106188.6478 0.015271576 0.018252616 1066.291778 -3.02787606 -0.10429992 FDEFDEAIDEAIEDDIKEADGGGVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDEFDEAIDEAIEDDIKEADGGGVGR 26 1 Q96T23-2;Q96T23;Q96T23-3;H0YDG9 Q96T23-2 RSF1 Remodeling and spacing factor 1 0 ; 132.26 5.19E-05 36880000 74554 62868 40085 40905 55519 62269 49836 59557 70543 58438 FALSE TRUE 71640.34726 61075.06619 47329.25119 43016.11195 57304.81906 63528.12184 50445.90788 58327.12714 62535.25438 54479.94221 1.314985742 1.121056002 0.868746354 0.789577048 1.051851686 1.166082769 0.92595377 1.070616538 1.14785831 1 15.73343755 3.028040257 24.99949232 1.060747269 1.007145503 0.01034985 0.146585263 1069.041682 953104.8238 0.045323229 0.054170974 1066.694993 -3.028040257 -0.053601766 LQLEETDHQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LQLEETDHQK 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 174.24 3.17E-06 4064100000 3168460 3155250 2535440 2991340 3105590 3246520 3293110 3260840 3889630 3756130 FALSE TRUE 3044633.08 3065265.359 2993650.409 3145723.416 3205484.123 3312166.859 3333412.065 3193502.514 3448095.509 3501723.969 0.869466899 0.875358933 0.854907593 0.898335632 0.915401714 0.945867489 0.95193456 0.911980082 0.984685126 1 21.73963393 3.028062964 0.236152914 1.01002583 0.807686463 0.829955501 0.019167214 1.968935187 0.207665021 0.041340117 0.122499318 1066.750767 -3.028062964 -0.202339367 SDPGPPTETPSQRPS(ph)PLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDPGPPTETPSQRPSPLKR 19 2 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 SDPGPPTET(0.002)PS(0.09)QRPS(0.909)PLKR 132.83 6.72E-06 330650000 158640 146490 158370 166320 160310 162090 195180 219250 206750 223480 TRUE FALSE 152440.1734 142312.2486 186990.9819 174903.7951 165466.5167 165367.5709 197568.6712 214722.4109 183280.6068 208343.5005 0.731677125 0.683065458 0.897512912 0.839497247 0.794200521 0.793725604 0.948283343 1.030617275 0.879703981 1 17.66860457 3.028273275 0.368299991 1.016485758 0.679087682 0.595577279 0.068260705 1.370361076 0.339106647 0.079266963 0.181174234 1067.267477 -3.028273275 -0.337398075 GCCFDDTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GCCFDDTVR 9 0 P04155 P04155 TFF1 Trefoil factor 1 0 107.29 0.0065065 294710000 458000 490150 442650 394810 360350 436220 367890 303500 372030 483440 FALSE TRUE 440100.8537 476171.4019 522646.7017 415186.1914 371940.985 445040.6673 372392.3479 297232.6189 329798.7141 450696.1782 0.976491204 1.056524162 1.159643074 0.92121081 0.825258795 0.987451611 0.826260274 0.659496648 0.731753962 1 18.78179569 3.028360997 0.936895519 0.775162476 1.062109298 0.406472318 0.111897305 0.479878833 0.925067991 0.057853944 0.0746888 1067.483073 -3.028360997 0.286946821 HFGAGGNQR ddPTM_BT-474_Pertuzumab_2h_R1 6 HFGAGGNQR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;;;; 132.08 0.00031497 1194658000 300773 310160 282766 315325 289140 263420 340905 256997 338162 366785 FALSE TRUE 289018.4586 301314.5405 333868.1063 331598.961 298440.4507 268746.5329 345077.0974 251689.9221 299775.2675 341942.3253 0.845225751 0.881185271 0.976387191 0.969751144 0.872780082 0.785941116 1.009167546 0.736059574 0.876683713 1 18.38339348 3.028727934 22.01632627 0.861808856 0.919859647 0.020427815 0.086805463 141.3443966 108319.3648 0.024535948 0.029324806 1068.385375 -3.028727934 0.058050791 SALSGHLETVILGLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SALSGHLETVILGLLK 16 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YNP5;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 133.48 3.35E-05 415450000 711790 831320 343020 998990 613740 463040 509380 746360 772210 736360 FALSE TRUE 683972.4599 807611.5675 405011.3444 1050547.994 633481.5045 472402.9861 515613.9448 730947.4052 684551.9582 686485.6813 0.996339004 1.176443427 0.589977847 1.530327612 0.922789101 0.688146889 0.75109206 1.064767154 0.997183156 1 19.3888701 3.028896232 24.99988763 0.89515251 1.068674979 0.107466084 0.239352825 487.7620168 421989.3455 0.068234897 0.081555247 1068.799477 -3.028896232 0.173522469 IGITNHDEYSLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGITNHDEYSLVR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ; 154.86 4.64E-05 763160000 722358 813777 642870 714310 759432 799670 820393 831480 850273 903320 FALSE TRUE 694127.4508 790568.8767 759050.9096 751175.6247 783859.82 815839.8753 830433.2149 814309.6474 753753.5737 842137.3318 0.824244959 0.938764792 0.901338631 0.891987086 0.93079809 0.96877296 0.98610189 0.966955883 0.895048284 1 19.68369599 3.029413044 2.779034099 0.963572353 0.893176595 0.473321987 0.036765416 0.249029871 3.913447898 0.011265992 0.013296911 1070.072109 -3.029413044 -0.070395759 QNGDDPLLTYR ddPTM_BT-474_Pertuzumab_2h_R1 2 QNGDDPLLTYR 11 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 240.1 2.64E-15 1158730000 907220 1045970 845890 1029750 936700 879530 998510 1025510 993150 1050290 FALSE TRUE 871764.8394 1016139.96 998761.1397 1082895.521 966829.8062 897314.6992 1010730.064 1004332.86 880411.7756 979152.9228 0.890325524 1.037774525 1.020025694 1.105951375 0.987414513 0.916419364 1.032249448 1.025716042 0.899156562 1 19.90117467 3.030500834 24.99608556 0.981856019 1.019587323 0.068314837 0.063570345 587.2742754 481280.212 0.018587071 0.022215619 1072.755708 -3.030500834 0.037731304 LIHELAAVYTEAIADIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LIHELAAVYTEAIADIKR 18 1 Q92797;A0A087WUE9 Q92797 SYMPK Symplekin 0 180.1 5.21E-14 51822000 111170 110770 97282 99030 112850 124110 116430 125760 133180 134610 FALSE TRUE 106825.3535 107610.9481 114863.0214 104140.9502 116479.9227 126619.5892 117854.9052 123163.0121 118061.9647 125492.7448 0.851247247 0.857507326 0.915296112 0.829856342 0.928180533 1.008979359 0.939137202 0.981435319 0.940787174 1 16.93724443 3.030519033 5.609359225 0.97072728 0.867352082 0.762530015 0.029019363 0.082952615 7.312992738 0.007995265 0.00943663 1072.800663 -3.030519033 -0.103375198 FQEHCPDLER ddPTM_BT-474_Pertuzumab_2h_R1 1 FQEHCPDLER 10 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 109.24 0.0020454 438410000 349400 388520 316420 416850 342300 312200 375410 371650 346320 379080 FALSE TRUE 335745.0617 377439.79 373604.1327 438363.6785 353310.3904 318512.8979 380004.3799 363975.2976 307007.2055 353404.574 0.950030324 1.068010484 1.057157038 1.240401825 0.999733496 0.90126988 1.075267294 1.029911112 0.868713164 1 18.43096119 3.03073208 24.99901586 0.985708179 1.082006376 0.242417413 0.086207205 311.7758709 253612.1333 0.025305851 0.030245996 1073.327063 -3.03073208 0.096298197 LKPGGVGAPSSSS(ph)PSPSPSARPGPPPSEEAMDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKPGGVGAPSSSSPSPSPSARPGPPPSEEAMDFR 34 2 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPS(0.001)S(0.002)S(0.04)S(0.917)PS(0.04)PS(0.001)PSARPGPPPSEEAMDFR 114.85 5.51E-06 294510000 54352 59989 45875 48728 56328 62365 57212 61201 69157 64249 TRUE FALSE 52227.86375 58278.17246 54165.63298 51242.85792 58139.84128 63626.06303 57912.17757 59937.17796 61306.58729 59897.358 0.871956051 0.972967329 0.904307549 0.855511155 0.970657859 1.062251578 0.966856962 1.000664803 1.023527403 1 15.87020475 3.031238397 7.980072317 1.007255114 0.907054285 0.666477913 0.036416548 0.136380509 29.28845191 0.010449882 0.012426258 1074.579117 -3.031238397 -0.100200829 GAAGRPLELSDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAAGRPLELSDFR 13 1 P42167;G5E972;H0YJH7;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 ; 85.271 0.008538 590080000 1729440 3109700 1640580 2898900 1887780 1308460 2400100 2239400 1570640 1562450 FALSE TRUE 1661851.573 3021014.401 1937069.301 3048512.576 1948502.158 1334917.958 2429473.142 2193155.607 1392347.532 1456623.87 1.140892723 2.073983863 1.329834929 2.092861884 1.337683803 0.916446576 1.667879534 1.505643051 0.955873071 1 20.47419696 3.031398069 24.99894555 1.282879028 1.671693036 0.253704861 0.354529608 295.3788135 235176.8783 0.09846153 0.117683138 1074.974269 -3.031398069 0.388814008 VLNTNIDGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VLNTNIDGR 9 0 P62269;A0A0G2JQH2;Q5GGW2 P62269 RPS18 40S ribosomal protein S18 0 ;; 150.35 0.00019879 541110000 639550 692900 616270 664110 633450 543110 675440 708760 649070 718490 FALSE TRUE 614555.6789 673139.1704 727643.6979 698384.7967 653825.4945 554092.0563 683706.2368 694123.8583 575390.2947 669826.0323 0.91748551 1.004946267 1.086317436 1.042636092 0.976112398 0.827217859 1.020722104 1.036274831 0.859014531 1 19.35342692 3.031558651 11.18527508 0.957755882 1.016557396 0.138177393 0.073621538 1.39200626 485.9784816 0.022449622 0.026793224 1075.371818 -3.031558651 0.058801515 GGVTEISAADKAEEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGVTEISAADKAEEFR 16 1 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 124.46 7.51E-05 160840000 153220 136340 123470 145980 138520 168480 156730 169410 185050 185270 FALSE TRUE 147231.993 132451.7167 145783.7756 153514.0453 142975.6216 171886.781 158648.1086 165911.6243 164043.8998 172721.4979 0.852424248 0.766851367 0.844039551 0.888795241 0.827781274 0.995167267 0.918519759 0.960573098 0.949759595 1 17.39808813 3.03183898 0.830824482 0.968157858 0.808744822 0.699341507 0.040296376 0.33340085 0.51161333 0.021390586 0.028501819 1076.066174 -3.03183898 -0.159413036 ERPMYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPMYGR 7 1 P50402;Q5HY57 P50402 EMD Emerin 0 ; 96.492 0.011575 216799000 247810 324900 238058 320630 252280 243680 255800 285630 254320 249120 FALSE TRUE 238125.3112 315634.1701 281080.3762 337177.7527 260394.8153 248607.3766 258930.5569 279731.6407 225450.6598 232246.8805 1.025311129 1.359045897 1.210265454 1.451807456 1.121198333 1.070444417 1.114893584 1.204458118 0.970737085 1 17.82529969 3.031884802 24.99666856 1.09783632 1.267600544 0.352275514 0.119340499 224.1357303 175713.8123 0.033049254 0.039501139 1076.179715 -3.031884802 0.169764224 AGGPATPLS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AGGPATPLS(0.98)PT(0.02)R;AGGPATPLS(0.993)PT(0.007)R 203.8 1.27E-07 1266670000 636300 736330 651290 770560 626500 571090 655240 659780 644090 693730 TRUE FALSE 611432.6925 715330.5893 768992.5909 810328.6939 646651.9415 582637.8311 663259.0231 646155.3124 570975.6034 646743.0492 0.945402805 1.10605068 1.189023356 1.252937616 0.999859128 0.900879927 1.025537149 0.999091236 0.882847685 1 19.30283312 3.031901404 18.85374383 0.968092049 1.126759659 0.456135394 0.08377344 12.95003767 7652.337931 0.02505304 0.029941681 1076.220855 -3.031901404 0.15866761 GPS(ph)PRPPATAYDAPASAFGSSLLGSGGSAFAPPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLR 35 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 GPS(0.999)PRPPAT(0.001)AYDAPASAFGSSLLGSGGSAFAPPLR;GPS(0.992)PRPPAT(0.008)AYDAPASAFGSSLLGSGGSAFAPPLR 284.58 8.17E-75 1010990000 159571 152695 128200 177156 132551 129921 133232 140419 131639 153561 TRUE FALSE 153334.7889 148340.2881 151368.5918 186299.0424 136814.6233 132548.0916 134862.5331 137519.2986 116695.8926 143160.1767 1.071071526 1.036184025 1.05733728 1.301332862 0.95567515 0.925872646 0.942039443 0.960597435 0.815142139 1 17.1272707 3.032013794 24.99997065 0.931352692 1.109269266 0.552406708 0.080995502 149.9113819 117066.71 0.023220127 0.027753166 1076.499406 -3.032013794 0.177916574 KHGLAHDEMK ddPTM_BT-474_Pertuzumab_2h_R1 1 KHGLAHDEMK 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 93.345 0.0035991 229680000 401980 393100 328180 302190 321100 217420 325890 88462 374310 300450 FALSE TRUE 386270.1772 381889.1729 387489.4263 317786.0621 331428.4731 221816.3814 329878.3393 86635.22879 331819.898 280100.2539 1.379042581 1.363401738 1.383395484 1.134543999 1.183249456 0.791917816 1.177715246 0.309300786 1.184646902 1 18.09558377 3.032223642 1.053118986 0.799275771 1.38226053 0.396551172 0.242952852 0.428595538 1.026924861 0.10837264 0.13785172 1077.019688 -3.032223642 0.582984759 T(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TPESFLGPNAALVDLDSLVSRPGPTPPGAK 30 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.946)PES(0.054)FLGPNAALVDLDSLVSRPGPTPPGAK;T(0.992)PES(0.008)FLGPNAALVDLDSLVSRPGPTPPGAK;T(0.5)PES(0.5)FLGPNAALVDLDSLVSRPGPTPPGAK 191.97 2.68E-18 1309384000 204652 213914 162677 164063 194799 200803 195497 224604 216671 187986 TRUE FALSE 196653.9736 207813.3822 192076.3526 172530.3111 201064.8867 204863.3742 197889.5508 219965.8489 192075.4164 175253.5408 1.122111272 1.185787067 1.095991281 0.9844612 1.147280026 1.168954267 1.129161499 1.255129271 1.095985939 1 17.41908407 3.032476741 24.99996029 1.154774782 1.098660765 0.003162263 0.077155083 454.5246781 349881.5259 0.022431198 0.026810232 1077.647539 -3.032476741 -0.056114017 ASPPSFPSGS(ph)PVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPPSFPSGSPVLR 14 0 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 ASPPS(0.013)FPS(0.075)GS(0.912)PVLR 103.32 0.0011776 87114000 59902 60442 45804 49886 57256 58474 67453 60439 52629 68957 TRUE FALSE 57560.96361 58718.25334 54081.8017 52460.62244 59097.69124 59656.38434 68278.50999 59190.91353 46654.77656 64286.48097 0.895382089 0.913384159 0.841262438 0.816044395 0.919286456 0.927977134 1.062097489 0.920736563 0.725732313 1 15.97222776 3.032508419 18.01786954 0.932594177 0.868010758 0.106342079 0.083959701 22.14017328 12268.41651 0.024954806 0.029824133 1077.726147 -3.032508419 -0.064583419 AHQDALPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHQDALPR 8 0 P43155-2;P43155;P43155-3;B7ZBP5;A6PVN3 P43155-2 CRAT Carnitine O-acetyltransferase 0 ; 114.99 0.0025505 351360000 330800 434640 348150 479530 367990 249140 504280 340480 420120 449420 FALSE TRUE 317871.9703 422244.4928 411068.4496 504278.6008 379826.7325 254177.7815 510451.5295 333448.969 372429.7389 418980.3831 0.758679841 1.007790603 0.98111622 1.20358523 0.906550158 0.606657953 1.218318447 0.795858189 0.888895409 1 18.67652317 3.032955395 24.99473812 0.892975777 0.997034846 0.05118442 0.17566265 532.3881946 403781.8498 0.049572706 0.059250353 1078.835913 -3.032955395 0.104059068 LLSSS(ph)LTADCSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLSSSLTADCSLR 13 0 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLS(0.001)S(0.053)S(0.928)LT(0.018)ADCSLR;LLSS(0.008)S(0.99)LT(0.002)ADCSLR;LLSS(0.022)S(0.975)LT(0.003)ADCSLR 258.62 6.39E-24 349140000 620480 602293 482900 582229 537471 522032 487225 595504 562329 577254 TRUE FALSE 596230.9556 585116.1933 570170.7721 612277.9085 554759.2428 532587.8447 493187.8053 583206.6343 498495.7694 538156.0724 1.107914574 1.087261156 1.059489619 1.137732973 1.030851961 0.989653136 0.916440101 1.083712819 0.926303344 1 19.03766511 3.03329424 4.897770785 0.992062354 1.094412006 0.568129564 0.046808273 0.153882662 9.088097322 0.013752399 0.016215217 1079.677969 -3.03329424 0.102349652 APVPEPGLDLSLS(ph)PRPDSPQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLS(0.244)LS(0.756)PRPDSPQPR 160.88 1.09E-11 105650000 72464 66603 72931 94343 67512 69286 58441 80525 71263 65380 TRUE FALSE 69632.02677 64703.54765 86111.25404 99212.05354 69683.58479 70687.01039 59156.21844 78862.13061 63173.523 60951.75437 1.142412183 1.061553491 1.412777285 1.627714486 1.143258066 1.159720686 0.970541686 1.293845131 1.036451266 1 15.89538013 3.033440306 24.99161226 1.118753635 1.311167259 0.275148196 0.166279966 291.8294866 218096.9264 0.050998681 0.060954812 1080.041157 -3.033440306 0.192413623 S(ph)PGPGPGPGAGAEPGATGGSSHFISSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPGPGPGPGAGAEPGATGGSSHFISSR 27 0 Q9ULI0-2;Q9ULI0;C9JG15 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 S(1)PGPGPGPGAGAEPGATGGSSHFISSR;S(1)PGPGPGPGAGAEPGATGGSSHFISSR;S(1)PGPGPGPGAGAEPGATGGSSHFISSR;S(1)PGPGPGPGAGAEPGATGGSSHFISSR 220.64 1.76E-34 1760820000 249802 317424 201170 297134 236319 221452 237648 291835 212113 228471 TRUE FALSE 240039.4617 308371.3783 237525.894 312469.1213 243920.4153 225929.9112 240556.4073 285808.5053 188034.8215 212996.4557 1.126964582 1.447777041 1.115163599 1.467015591 1.145185325 1.060721459 1.129391597 1.341846297 0.882807279 1 17.7004699 3.034252999 24.98116722 1.124945401 1.290369129 0.265931164 0.154535417 279.8470559 204094.3837 0.043186452 0.051617458 1082.064126 -3.034252999 0.165423728 MFEFYER ddPTM_BT-474_Pertuzumab_2h_R1 1 MFEFYER 7 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 89.298 0.041818 97571000 82159 147580 93857 190700 109600 89286 148050 114000 92509 101560 FALSE TRUE 78948.13545 143371.1629 110819.0477 200542.0499 113125.3835 91091.42409 149861.8802 111645.8602 82007.76615 94681.25074 0.83383072 1.514250834 1.170443429 2.11807563 1.194802378 0.962085137 1.582804188 1.179176017 0.866145784 1 16.53079114 3.034593867 24.9999924 1.162482051 1.431710672 0.126534319 0.351419216 398.2108223 287773.0384 0.100176549 0.119733369 1082.913747 -3.034593867 0.26922862 VSMPDVELNLKS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSMPDVELNLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VSMPDVELNLKS(1)PK;VSMPDVELNLKS(1)PK 225.6 1.64E-12 7209300000 8214800 7673000 7906300 4834100 5702900 5218900 1603420 4184800 3501700 2696100 TRUE FALSE 7893756.534 7454173.553 9335144.285 5083588.48 5886338.958 5324429.734 1623043.134 4098382.418 3104201.696 2513490.746 3.140555241 2.965665804 3.714015777 2.022521264 2.341898003 2.118340695 0.645732687 1.630554011 1.235016163 1 21.26126095 3.035227564 0.862536839 1.162440332 3.280637767 0.783445449 0.436343844 0.266831974 0.440031779 0.230131783 0.304973117 1084.495024 -3.035227564 2.118197435 up EGDLLFTVAKDPIVNVWYSVNGER ddPTM_BT-474_Pertuzumab_2h_R1 2 EGDLLFTVAKDPIVNVWYSVNGER 24 1 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 115.55 0.00095293 662750000 241115 267638 180687 191853 236931 273510 222990 253288 264762 263336 FALSE TRUE 231691.9592 260005.2263 213341.1603 201754.5563 244552.1008 279040.5596 225719.0183 248057.5143 234707.3277 245500.0182 0.943755365 1.059084346 0.869006698 0.821810759 0.99613883 1.13662134 0.919425669 1.010417499 0.956037924 1 17.90536361 3.035243051 24.99621876 1.005272599 0.926688218 0.204755288 0.076972055 307.6466586 218197.2686 0.023068538 0.027572055 1084.533699 -3.035243051 -0.078584381 SLHDALCVIR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLHDALCVIR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 215.93 7.96E-09 1944180000 348783 507363 404134 475349 380985 237366 444997 355657 400072 482615 FALSE TRUE 335152.1748 492893.504 477170.0037 499881.8189 393239.7285 242165.7032 450443.0064 348312.5587 354657.5038 449927.0562 0.744903357 1.095496475 1.060549698 1.111028581 0.874007738 0.538233253 1.001146742 0.774153396 0.78825556 1 18.7793316 3.035474332 9.398331735 0.807812391 1.011444291 0.235797887 0.154578773 0.425554757 106.6362944 0.043068272 0.051378964 1085.111414 -3.035474332 0.2036319 KDDYEYCMSEYLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDDYEYCMSEYLR 13 1 P53611;Q5T4U8 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 0 ; 131.72 0.00020393 254790000 165641 174896 177103 191202 169042 155290 188033 169305 180332 216710 FALSE TRUE 159167.5666 169908.1373 209109.4517 201069.9581 174479.3895 158430.0702 190334.2041 165808.7926 159861.4674 202032.0387 0.787833294 0.840996005 1.035031142 0.99523798 0.863622377 0.784182901 0.942099111 0.820705437 0.791267902 1 17.62422457 3.035513856 24.97721427 0.856374115 0.919511467 0.055435284 0.090157048 434.5164282 305596.5616 0.026609123 0.031803908 1085.210173 -3.035513856 0.063137352 CAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_BT-474_Pertuzumab_2h_R1 8 CAVSDVEMQEHYDEFFEEVFTEMEEK 26 0 P0DN76;Q01081 P0DN76 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;;;;;;; 245.92 2.28E-45 433596000 373946.7 338766 309363.7 280455.6 356406 361902 371421 358954 443275 421173 FALSE TRUE 359332.4495 329104.7254 365272.6023 294929.9471 367870.1227 369219.9064 375966.5613 351541.4745 392956.2804 392646.5776 0.915154926 0.838170365 0.930283423 0.75113337 0.936898839 0.940336495 0.957519008 0.895312718 1.000788757 1 18.5828718 3.035804436 24.99849417 0.946683437 0.86004446 0.432283661 0.053737754 174.375342 121747.0075 0.014636725 0.017494189 1085.936513 -3.035804436 -0.086638977 FIIGSVSEDNS(ph)EDEISNLVK ddPTM_BT-474_Pertuzumab_2h_R1 4 FIIGSVSEDNSEDEISNLVK 20 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087X2F8;A0A087X126;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 FIIGSVS(0.004)EDNS(0.996)EDEISNLVK;FIIGSVS(0.003)EDNS(0.997)EDEISNLVK;FIIGSVSEDNS(1)EDEISNLVK;FIIGSVSEDNS(1)EDEISNLVK 233.85 1.08E-29 1276800000 976259 1059598 924390 1077434 1086261 1284725 1341996 1367810 1638423 1601405 TRUE FALSE 938105.719 1029379.302 1091447.836 1133040.498 1121201.572 1310703.02 1358419.748 1339564.246 1452436.09 1492940.413 0.628361126 0.689497915 0.731072604 0.758932164 0.751002225 0.877933914 0.90989549 0.897265714 0.972869431 1 20.50972515 3.036192075 0.383938033 1.009321474 0.585297872 0.958050271 0.024518368 0.338765756 0.091788539 0.026064278 0.05773053 1086.906222 -3.036192075 -0.424023602 LPLIFHLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPLIFHLGR 9 0 P34059 P34059 GALNS N-acetylgalactosamine-6-sulfatase 0 128.1 0.0014612 0 31823 44035 38881 48181 36343 30705 42750 34822 40178 45669 FALSE TRUE 30579.32198 42779.16491 45907.6616 50667.62718 37512.0056 31325.87614 43273.18729 34102.91353 35617.16188 42575.79795 0.718232504 1.004776586 1.078257222 1.190057019 0.881064065 0.735767212 1.016379948 0.800992939 0.836558881 1 15.37774595 3.036623384 24.99989954 0.865648822 1.008007899 0.151711954 0.135912848 278.0136875 189776.3424 0.039288071 0.046958129 1087.986193 -3.036623384 0.142359077 EFEMWAPDMYVVTYVGDKDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFEMWAPDMYVVTYVGDKDSR 21 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 182.22 4.33E-17 283110000 513510 487000 408850 427070 484320 508040 491830 490380 595740 546650 FALSE TRUE 493441.4615 473111.2368 482738.2898 449111.1339 499898.5926 518312.9169 497849.1627 480253.4816 528114.0927 509624.9086 0.968244395 0.92835187 0.947242338 0.881258208 0.980914756 1.017047849 0.976893308 0.942366579 1.036279985 1 18.95907627 3.036875429 24.82600697 0.986849117 0.932066036 0.474099019 0.031209868 155.5193963 104700.807 0.009178671 0.010970583 1088.617794 -3.036875429 -0.054783081 GHDLEFCLYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHDLEFCLYGR 11 0 Q99523;Q99523-2 Q99523 SORT1 Sortilin 0 ; 128.01 0.00027463 346120000 289440 412670 286520 395890 334870 299680 407530 324310 378020 373890 FALSE TRUE 278128.3648 400901.0556 338300.5376 416321.9303 345641.3977 305739.7349 412517.474 317612.8852 335108.7544 348566.0973 0.797921447 1.15014357 0.970549173 1.194384461 0.99160934 0.877135606 1.183469871 0.911198443 0.961392278 1 18.41107273 3.037779796 24.99990685 0.98607628 1.040355088 0.021390567 0.125166951 614.8589768 406864.8961 0.034343093 0.041047778 1090.887073 -3.037779796 0.054278808 WVGGQHPCFIIAEIGQNHQGDLDVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 WVGGQHPCFIIAEIGQNHQGDLDVAK 26 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 330.26 3.48E-95 1206070000 1152670 1240880 1105020 1223240 1136260 1109830 1232330 937910 1515360 1410540 FALSE TRUE 1107622.382 1205491.317 1304721.695 1286371.563 1172808.835 1132271.523 1247411.623 918541.8307 1343342.686 1315002.869 0.842296551 0.916721435 0.992181633 0.978227191 0.89186789 0.861041104 0.948599925 0.698509374 1.021551144 1 20.32663452 3.038143022 11.20102854 0.875556558 0.935497408 0 0.093685785 1.705914388 493.537362 0.027180853 0.032467848 1091.799828 -3.038143022 0.05994085 RFDEATQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RFDEATQLR 9 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;; 180.09 7.86E-05 1353550000 506252 959610 460660 916840 511370 458010 560270 488480 505180 635950 FALSE TRUE 486467.1121 932242.8624 543911.5093 964158.2223 527818.6805 467271.276 567126.7519 478392.7173 447834.0843 592876.5401 0.82052009 1.572406394 0.917411084 1.62623777 0.890267442 0.788142631 0.956568043 0.806901075 0.755358079 1 19.17737219 3.038626375 24.99703613 0.852571031 1.238503476 0.356113755 0.242461807 154.7517597 100146.5551 0.063128416 0.075452786 1093.015636 -3.038626375 0.385932446 TPEEVIEYSAVFWER ddPTM_BT-474_Pertuzumab_2h_R1 2 TPEEVIEYSAVFWER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 180.24 1.48E-06 48316000 9087.3 11069.5 9492.6 11014.8 9453 10056.4 8465.6 10084.9 9861.6 12513.2 FALSE TRUE 8732.158269 10753.8087 11208.12398 11583.27515 9757.06433 10259.7473 8569.204545 9876.643291 8742.152511 11665.66982 0.748534667 0.921833797 0.960778434 0.992936996 0.836391264 0.879482058 0.734566011 0.846641765 0.749391389 1 13.50998153 3.038832518 24.82175641 0.828228487 0.911512116 0.09838536 0.091205671 268.0581239 171341.028 0.025551434 0.030539753 1093.534572 -3.038832518 0.083283629 WLAIDANAR ddPTM_BT-474_Pertuzumab_2h_R1 2 WLAIDANAR 9 0 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 ; 121.05 0.0037516 172120000 644620 745770 624930 699800 655090 593060 746410 684200 665550 725080 FALSE TRUE 619427.5377 724501.3698 737868.7525 735916.7619 676161.5648 605052.0795 755544.7889 670071.0309 589999.5542 675969.6858 0.916354018 1.071795652 1.091570773 1.088683084 1.000283857 0.895087594 1.117719929 0.991273788 0.872819546 1 19.36659902 3.039158789 11.91096738 0.984048141 1.04738336 0.135992917 0.077384421 1.739102214 524.1248354 0.022628675 0.027036485 1094.356417 -3.039158789 0.063335218 GSQQYR ddPTM_BT-474_Pertuzumab_2h_R1 6 GSQQYR 6 0 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;A6NNZ2;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ;;;;; 144.9 0.026088 3043751000 3356080 3630543 3123103 3560541 3177550 2523103 3737340 3193778 3099551 3807161 FALSE TRUE 3224920.683 3527003.468 3687517.185 3744300.948 3279758.782 2574121.871 3783078.685 3127825.368 2747702.965 3549298.594 0.908607883 0.993718442 1.038942509 1.054941096 0.924058288 0.725248046 1.06586656 0.881251685 0.774153792 1 21.75910252 3.039219378 9.293874416 0.889595557 1.000253711 0.218033943 0.098284661 0.506920847 113.3255129 0.028118498 0.033565934 1094.509104 -3.039219378 0.110658154 S(ph)PGDGHNAPVEGPEGEYVELLEVTLPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGDGHNAPVEGPEGEYVELLEVTLPVR 28 0 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 S(0.994)PGDGHNAPVEGPEGEY(0.006)VELLEVTLPVR;S(1)PGDGHNAPVEGPEGEYVELLEVTLPVR 108.57 0.00048981 51156000 5932.7 6562 7667.3 8962.4 6738.7 6826 5390.4 7617.9 7978.4 8550.8 TRUE FALSE 5700.843525 6374.858185 9052.951668 9424.950538 6955.456405 6964.026397 5456.369328 7460.587703 7072.72548 7971.6467 0.715140013 0.79969151 1.135643865 1.182309113 0.872524419 0.873599478 0.684472046 0.935890411 0.887235191 1 12.96066206 3.039684456 24.99996048 0.862806844 0.968032624 0.063374057 0.149325497 401.7468272 253085.3556 0.046166449 0.0551794 1095.681822 -3.039684456 0.10522578 HELLNSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HELLNSTR 8 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 133.13 0.00093243 123000000 175450 183550 127800 153510 139820 100340 136640 100260 151280 157850 FALSE TRUE 168593.22 178315.3337 150896.3029 161432.6695 144317.4373 102368.9435 138312.2412 98189.59596 134107.3286 147158.6789 1.145655977 1.21172149 1.025398597 1.096997273 0.980692667 0.695636467 0.939885043 0.667236188 0.911311039 1 17.1670131 3.039697828 3.048694551 0.817511335 1.121143083 0.59047129 0.107221456 0.15530353 2.960291552 0.031701605 0.037536903 1095.715557 -3.039697828 0.303631748 NNS(ph)GEAGGAATQELFCSACDQLFLSPHQLQQHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNSGEAGGAATQELFCSACDQLFLSPHQLQQHLR 34 0 A0A0C4DFM2;Q6ZN55;Q6ZN55-2 A0A0C4DFM2 ZNF574 Zinc finger protein 574 1 NNS(1)GEAGGAATQELFCSACDQLFLSPHQLQQHLR 209.43 2.14E-27 229610000 27291 27042 30437 26694 23767 21095 26683 13387 28845 25177 TRUE FALSE 26224.43755 26270.78864 35937.64297 28071.68054 24531.48714 21521.55535 27009.55454 13110.55377 25570.63653 23471.73936 1.117277128 1.11925189 1.531102677 1.195977857 1.045149946 0.916913528 1.150726587 0.558567628 1.08942231 1 14.51863714 3.040172626 2.023273976 0.898857688 1.257133133 0.357284221 0.184650793 0.318459298 2.643678505 0.062870861 0.07585787 1096.914119 -3.040172626 0.358275445 KDIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_BT-474_Pertuzumab_2h_R1 5 KDIDHETVVEEQIIGENSPPDYSEYMTGK 29 1 P25490;A0A494C032;H0YJV7;H0YJU4 P25490 YY1 Transcriptional repressor protein YY1 1 KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK 386.84 4.74E-155 2918200000 1240410 1184530 1029050 1015670 1156130 1192210 1154000 1237790 1365680 1246590 TRUE FALSE 1191933.406 1150748.364 1215022.226 1068088.85 1193317.971 1216317.303 1168122.997 1212229.204 1210653.732 1162157.349 1.025621364 0.990182926 1.045488571 0.919057003 1.02681274 1.046602944 1.005133253 1.043085263 1.041729619 1 20.14837398 3.040277565 24.99999063 1.029924347 0.995161944 0.176886095 0.033731459 240.3256102 149166.9456 0.009302448 0.011118543 1097.179199 -3.040277565 -0.034762404 LGDAVEQGVINNTVLGYFIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGDAVEQGVINNTVLGYFIGR 21 0 P41250 P41250 GARS Glycine--tRNA ligase 0 133.66 2.22E-05 35752000 31418 31661 25708 26672 31085 33360 32971 33446 38300 32724 FALSE TRUE 30190.14983 30758.05928 30354.00747 28048.54512 32084.87726 34034.56206 33374.50896 32755.32841 33952.34457 30507.57433 0.989595223 1.008210582 0.994966271 0.919396108 1.05170201 1.115610231 1.093974519 1.073678558 1.112915245 1 14.89687985 3.041167108 8.188512326 1.084080465 0.981611999 0.621423226 0.037316422 0.150335934 26.4098334 0.010288283 0.012275998 1099.428796 -3.041167108 -0.102468466 AVPIGT(ph)PPKQMAVPSFTQQILCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVPIGTPPKQMAVPSFTQQILCPK 24 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 AVPIGT(1)PPKQMAVPSFTQQILCPK 171.31 1.11E-11 143750000 256810 241160 199100 170070 254860 260670 246960 267760 316810 319620 TRUE FALSE 246773.5813 234282.3529 235081.799 178847.3331 263057.8034 265940.926 249982.3704 262230.6624 280847.057 297971.8527 0.828177491 0.786256657 0.788939616 0.600215529 0.882827693 0.892503515 0.838946256 0.88005179 0.942528814 1 18.18481653 3.041229923 24.99994636 0.894798721 0.754312795 0.54302159 0.069360721 122.6812186 74387.52248 0.019797012 0.023661935 1099.587827 -3.041229923 -0.140485926 ES(ph)PSLASR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESPSLASR 8 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 ES(0.997)PS(0.003)LASR;ES(0.995)PS(0.005)LASR 182.39 0.00024 558460000 683060 685660 743930 843710 718560 709250 910730 961270 997210 1182470 TRUE FALSE 656365.26 666105.6481 878374.6996 887253.9742 741673.135 723591.5209 921875.7862 941419.4386 884010.9014 1102380.254 0.595407309 0.604243088 0.796798289 0.804852927 0.672792471 0.656390133 0.836259343 0.853987937 0.801911045 1 20.07219052 3.041588212 0.062446359 1.475530856 2.05E-19 0.681198198 0.068459868 46.40715083 0.948590859 8.808064833 13.42475611 1100.495352 -3.041588212 -1.475530856 GHLLDSFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHLLDSFAR 9 0 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 76.17 0.03619 143860000 165070 207540 196120 196600 172060 118660 213510 117220 189420 213090 FALSE TRUE 158618.8819 201621.1624 231563.2467 206746.5496 177594.4662 121059.3865 216122.9992 114799.366 167917.8357 198657.2245 0.79845514 1.01491986 1.165642212 1.040720014 0.893974365 0.609388291 1.087919152 0.577876623 0.845264179 1 17.59992173 3.042182913 5.207043096 0.797347626 1.014208081 0.19545213 0.167886939 0.252880301 16.25944838 0.047908792 0.056847297 1102.003346 -3.042182913 0.216860455 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIRPEYAWIVQPVSGAVYDRPGASPKR 27 3 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR;LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR 175.75 4.72E-12 3107600000 2007600 1980790 1568370 1604690 1837100 1911920 1788710 1909030 2281050 2046860 TRUE FALSE 1929140.772 1924299.809 1851809.347 1687508.243 1896191.99 1950580.332 1810600.768 1869607.863 2022114.767 1908224.349 1.010961197 1.008424303 0.970435865 0.8843343 0.993694474 1.022196543 0.948840617 0.979763131 1.059683977 1 20.86379937 3.042198291 24.99957932 0.99600103 0.967459794 0.117015193 0.042112535 379.5747013 224869.5613 0.01286099 0.01537182 1102.042367 -3.042198291 -0.028541235 FDRPPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 FDRPPAR 7 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;; 129.68 0.0033167 2714330000 2960810 3207260 2829030 3116670 2964650 2735040 3124440 3226520 3363580 3352330 FALSE TRUE 2845098.272 3115792.085 3340298.652 3277521.712 3060010.66 2790344.383 3162677.831 3159891.234 2981760.5 3125273.703 0.910351714 0.996966148 1.068801958 1.048715096 0.979117655 0.892832004 1.011968273 1.01107664 0.954079797 1 21.57555111 3.04233517 24.99611882 0.976373143 1.010506642 0.081855253 0.050574968 381.9164591 225493.9117 0.015567304 0.018606475 1102.389759 -3.04233517 0.034133499 TNVLGHLQQGGAPTPFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TNVLGHLQQGGAPTPFDR 18 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 203.06 1.22E-15 2587700000 1369240 1483340 1180150 1288590 1234120 1262590 1198820 1287220 1300920 1337560 FALSE TRUE 1315728.587 1441036.596 1393429.357 1355094.284 1273816.591 1288120.435 1213491.518 1260638.457 1153245.016 1246965.87 1.055144025 1.155634352 1.117455891 1.086713211 1.021532843 1.033003762 0.973155358 1.010964685 0.924840883 1 20.24999055 3.042430578 1.126721119 0.98109704 1.11678091 0.72838716 0.033895189 0.234513101 0.637004706 0.013997927 0.017839423 1102.631963 -3.042430578 0.13568387 FAELPEFRPEEVLPSPTLQSLAT(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPTLQS(0.002)LAT(0.631)S(0.367)PR 227.57 2.07E-34 491410000 182010 180330 124180 124650 178320 182820 190940 205100 226730 220790 TRUE FALSE 174896.848 175187.165 146622.0884 131083.2014 184055.8247 186516.7457 193276.7808 200864.6133 200992.5609 205835.6966 0.84969153 0.851101961 0.712325854 0.636834153 0.894188072 0.906143826 0.938985725 0.975849265 0.976470866 1 17.65113367 3.042642554 7.656708412 0.952270087 0.764617361 0.686056774 0.06287292 0.144114503 21.76361737 0.020030128 0.023895596 1103.170282 -3.042642554 -0.187652726 RRS(ph)SDEDAAGEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRSSDEDAAGEPK 13 2 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 1 RRS(0.623)S(0.377)DEDAAGEPK;RRS(0.5)S(0.5)DEDAAGEPK 122.31 0.0001863 893960000 837010 764430 609090 637290 738380 760160 720990 797750 898570 782900 TRUE FALSE 804298.7238 742629.2049 719166.1121 670180.6133 762130.6633 775530.956 729813.6913 781276.1837 796568.1007 729873.4857 1.101970053 1.017476617 0.985329823 0.918214768 1.044195574 1.062555321 0.999918076 1.07042686 1.091378323 1 19.47728689 3.042773329 24.99993141 1.047776859 1.002136907 0.125688656 0.049732255 266.8900188 155988.9439 0.014744674 0.01762325 1103.50252 -3.042773329 -0.045639952 AEVAAEFLNDRVPNCNVVPHFNK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEVAAEFLNDRVPNCNVVPHFNK 23 1 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 119.06 0.00013356 269290000 274310 237360 173470 204390 231260 255750 229740 241030 261770 254710 FALSE TRUE 263589.6619 230590.7252 204819.8878 214938.5924 238698.6879 260921.4402 232551.6268 236052.6463 232054.967 237458.2648 1.110046273 0.971078961 0.862551101 0.905163661 1.005223752 1.098809681 0.979336841 0.994080566 0.977245274 1 17.85731445 3.042815775 23.04281528 1.010332871 0.95565839 0.101158022 0.067488289 139.4476439 75046.75134 0.0205828 0.024601106 1103.610377 -3.042815775 -0.054674481 RTDALT(ph)SS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 2 RTDALT(0.671)S(0.6)S(0.729)PGR 67.648 0.051415 226180000 173900 148200 130540 165270 142110 133960 136140 179210 141170 139130 TRUE FALSE 167103.7957 143973.4811 154131.4818 173799.6045 146681.0972 136668.763 137806.122 175509.2509 125144.9734 129706.6012 1.288321444 1.109993476 1.188308694 1.339944173 1.130868405 1.053676233 1.06244494 1.353125047 0.964831183 1 16.98489238 3.042888886 24.98878801 1.123162629 1.221801243 0.230311259 0.115603204 287.5171042 167517.1474 0.034620368 0.041379243 1103.796179 -3.042888886 0.098638614 QSFTMVADTPENLR ddPTM_BT-474_Pertuzumab_2h_R1 10 QSFTMVADTPENLR 14 0 Q14847;Q14847-2;C9J9W2;F6S2S5 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;;;;; 319.7 1.02E-55 5801780000 4381736 4532374 3577872 4571099 4061208 3987630 3986341 4485475 4422462 4787856 FALSE TRUE 4210492.913 4403115.131 4224473.06 4807013.967 4191840.444 4068262.611 4035127.034 4392848.374 3920442.654 4463570.249 0.94330159 0.986455883 0.946433645 1.076943724 0.939122767 0.911436896 0.904013337 0.984155761 0.878319918 1 22.0897667 3.043104667 24.99999123 0.935037029 0.988022552 0.220950708 0.047966796 205.9597762 119451.8861 0.013354947 0.015962206 1104.34474 -3.043104667 0.052985523 LILEVHQFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LILEVHQFSR 10 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 196.44 3.33E-07 782940000 500930 600230 450640 597300 505250 458190 589230 495030 575180 588830 FALSE TRUE 481353.1018 583112.0281 532080.6724 628126.7246 521501.8251 467454.9157 596441.173 484807.4575 509887.9778 548948.0196 0.876864629 1.062235416 0.969273325 1.144237163 0.950002198 0.851546775 1.086516668 0.883157312 0.928845646 1 19.06631002 3.043495391 24.99992762 0.944470345 1.017723751 0.109256681 0.087220741 264.0493804 151766.479 0.024016448 0.028705123 1105.338739 -3.043495391 0.073253406 ICQGCPHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ICQGCPHR 8 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ;;; 104.37 0.0045942 234199000 397240 425143 366020 420964 367719 341105 397799 347618 362249 397683 FALSE TRUE 381715.4216 413018.3379 432167.9561 442690.0025 379547.0156 348002.3768 402667.3832 340439.5668 321128.0122 370747.5762 1.029583054 1.114014937 1.165666302 1.194046923 1.023734314 0.938650443 1.086095794 0.918251632 0.866163484 1 18.50007774 3.044226795 5.421971963 0.965288027 1.127211763 0.574025987 0.066560874 0.142787141 9.912498533 0.0202618 0.02408194 1107.201831 -3.044226795 0.161923736 WCDDYFFIAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 WCDDYFFIAHR 11 0 P36551 P36551 CPOX "Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial" 0 115.57 0.0011049 139230000 245590 288370 225580 250150 215230 149790 238140 158280 223190 176710 FALSE TRUE 235992.0713 280145.9699 266347.324 263060.2715 222153.0684 152818.8564 241054.4286 155011.4627 197854.4069 164741.2743 1.432501189 1.700520839 1.616761344 1.596808527 1.348496722 0.927629442 1.463230326 0.940938835 1.201000828 1 17.32984253 3.044870221 3.531338482 1.118560506 1.595799128 0.67149225 0.15775798 0.130364368 3.390066972 0.045079535 0.053399119 1108.843412 -3.044870221 0.477238622 KT(ph)SDDGGDSPEHDTDIPEVDLFQLQVNTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSDDGGDSPEHDTDIPEVDLFQLQVNTLR 30 1 Q9HAJ7 Q9HAJ7 SAP30L Histone deacetylase complex subunit SAP30L 1 KT(0.453)S(0.453)DDGGDS(0.083)PEHDT(0.011)DIPEVDLFQLQVNTLR 249.38 2.09E-46 16473000 34503 35585 28958 33505 34894 37542 37290 44282 41164 31587 TRUE FALSE 33154.58461 34570.15064 34191.35477 35234.19707 36016.3972 38301.12496 37746.36617 43367.56123 36491.23529 29447.58436 1.125884698 1.173955399 1.161092005 1.196505514 1.223067969 1.300654223 1.281815368 1.472703523 1.239192827 1 14.84586167 3.045631187 1.597469451 1.306770184 1.157424085 0.067384512 0.113405277 0.53199288 2.789134965 0.039459243 0.04862912 1110.78802 -3.045631187 -0.1493461 SEPVS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEPVSPSR 8 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SEPVS(0.739)PS(0.261)R;S(0.003)EPVS(0.982)PS(0.014)R;SEPVS(0.5)PS(0.5)R;SEPVS(0.991)PS(0.009)R 161.28 0.00036549 516660000 1060920 1096100 971220 1190890 1001800 999280 1003350 1081530 1111170 1122330 TRUE FALSE 1019458.073 1064840.301 1146741.059 1252351.976 1034023.807 1019486.126 1015629.297 1059196.028 985034.64 1046313.589 0.974333205 1.017706653 1.09598219 1.196918389 0.988254207 0.974360016 0.970673905 1.012312215 0.941433476 1 19.99688387 3.045893614 24.99972123 0.982286782 1.072105262 0.380401946 0.056346231 141.7052552 77190.48569 0.017187754 0.02054329 1111.459429 -3.045893614 0.08981848 IWDILGDRPSLVHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IWDILGDRPSLVHSR 15 1 Q13610;B4DJV5 Q13610 PWP1 Periodic tryptophan protein 1 homolog 0 ; 127.75 4.58E-05 481360000 256500 274190 243680 263700 241350 212786 258490 215732 271290 270400 FALSE TRUE 246475.6964 266370.3697 287718.3966 277309.5886 249113.2419 217088.6787 261653.4779 211277.0588 240494.2965 252085.5672 0.977746165 1.056666483 1.141352121 1.100061347 0.988209062 0.861170598 1.037955012 0.838116443 0.954018508 1 17.943554 3.046154568 4.744819576 0.92854407 1.07207768 0.452011554 0.06730812 0.163373747 8.183494173 0.019636328 0.023311904 1112.127469 -3.046154568 0.14353361 GQFSTDELVAEVEKR ddPTM_BT-474_Pertuzumab_2h_R1 7 GQFSTDELVAEVEKR 15 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;;; 335.91 7.53E-69 23478750000 7799170 8152280 6665500 7508530 8588370 9043400 9070790 9769550 10836880 10350300 FALSE TRUE 7494369.814 7919784.956 7870104.123 7896046.133 8864622.721 9226263.744 9181801.041 9567805.378 9606722.814 9649264.962 0.776677793 0.820765622 0.815616957 0.818305453 0.918683729 0.956162338 0.951554453 0.991557949 0.995591151 1 23.20198762 3.047310781 1.056348762 0.989647044 0.794636989 0.959571067 0.01667312 0.089593449 0.215994524 0.007519788 0.009723305 1115.092207 -3.047310781 -0.195010056 EHIKNPDWR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHIKNPDWR 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 153.12 4.74E-05 2346200000 4290200 4658700 3636970 3862370 3684330 3667990 4295520 2222640 4767030 4713950 FALSE TRUE 4122534.241 4525838.437 4294251.383 4061707.379 3802839.82 3742159.271 4348089.859 2176741.707 4225896.739 4394669.968 0.938075958 1.029847172 0.977149914 0.924234905 0.865330013 0.851522253 0.989400772 0.495314033 0.961595927 1 22.06732339 3.047403992 1.007631838 0.796154431 0.989712224 0.069444646 0.141068239 0.815385672 1.800939303 0.066983508 0.087280591 1115.331561 -3.047403992 0.193557793 VTYLVHNFEEGGGVAMGMYNQDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTYLVHNFEEGGGVAMGMYNQDK 23 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 315.14 2.61E-73 2294000000 2412900 2403800 2127200 2349200 2503600 2564600 2686400 2921300 3168900 2944000 FALSE TRUE 2318601.2 2335245.978 2511632.359 2470442.494 2584130.568 2616457.969 2719276.967 2860974.134 2809179.757 2744600.258 0.844786484 0.850851038 0.915117731 0.90011013 0.941532582 0.953311129 0.990773414 1.042401029 1.023529656 1 21.38816461 3.047728371 0.615076749 1.03254724 0.842326771 0.910795398 0.019506372 0.23614489 0.193933863 0.014893519 0.022897022 1116.164925 -3.047728371 -0.190220469 QHIDAVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QHIDAVAR 8 0 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3;A0A087WXU8 G3V529 DDX24 ATP-dependent RNA helicase DDX24 0 81.525 0.022635 39716000 68258 67780 52217 52384 54771 30783 56395 27506 40087 44346 FALSE TRUE 65590.4019 65846.98076 61653.77346 55087.54452 56532.75896 31405.45335 57085.17888 26937.99149 35536.49182 41342.40592 1.586516325 1.592722516 1.491296215 1.332470699 1.367427891 0.759642615 1.380789957 0.651582579 0.859565161 1 15.33533473 3.047745949 0.788765038 0.860165618 1.616824297 0.665034857 0.1934544 0.363691744 0.504230444 0.107236235 0.147961754 1116.210104 -3.047745949 0.756658678 GHEYTNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 GHEYTNIK 8 0 Q06124;Q06124-1 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 128.69 0.0011229 197850000 444460 488910 422950 515540 432220 321770 575540 407070 506190 510310 FALSE TRUE 427090.0118 474966.7655 499386.4735 542147.0812 446122.7488 328276.4099 582583.6307 398663.8622 448729.4333 475746.2492 0.897726493 0.998361556 1.049690826 1.139571951 0.937732561 0.690024168 1.224567995 0.837975839 0.94321171 1 18.85983276 3.048127312 24.99919862 0.932343954 1.023838216 0.078519197 0.137233538 289.3469288 150296.1171 0.038772688 0.046342287 1117.190702 -3.048127312 0.091494262 FPTTATKIS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 FPTTATKISPK 11 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 FPT(0.013)T(0.013)AT(0.051)KIS(0.923)PK 50.155 0.096175 787880000 551390 384130 329940 274200 432230 471910 403630 438270 555380 504840 TRUE FALSE 529841.0692 373174.9885 389567.4975 288351.4949 446133.0705 481452.3435 408569.7447 429219.5713 492335.5907 470646.7371 1.12577232 0.79289828 0.827728032 0.612670762 0.947914933 1.022959059 0.868102788 0.911978215 1.046083085 1 18.84428507 3.048958145 24.99991564 0.955018636 0.828651202 0.187946437 0.126706919 191.7929327 97935.56019 0.036587127 0.043729973 1119.330002 -3.048958145 -0.126367434 YGASLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGASLR 6 0 Q6P4E4;E9PEL3;P61513;G5E9R3;E9PPK6;G3V1E1;P17405-3;P17405-4;P17405;P17405-2;E9PQT3 Q6P4E4;P17405-2 RPL37A;SMPD1 60S ribosomal protein L37a;Sphingomyelin phosphodiesterase 0 99.228 0.090816 344290000 437410 487820 512580 561030 463980 453070 469180 525180 463170 534670 FALSE TRUE 420315.5336 473907.8512 605214.6083 589984.8255 478904.3381 462231.3858 474921.9652 514334.8495 410592.8834 498456.3247 0.843234428 0.950751004 1.214177809 1.183623913 0.960774925 0.927325751 0.952785513 1.031855398 0.823728907 1 18.92710757 3.049150672 24.99993429 0.95519968 1.05529322 0.156448117 0.111158266 224.9884447 114436.2802 0.034252693 0.040939792 1119.826324 -3.049150672 0.10009354 SAGGRPGSGPQLGTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 171.56 4.45E-09 90045000 46288 46759 41420 48976 42583 35599 42374 50677 51784 44045 FALSE TRUE 44479.01379 45425.4791 48905.51538 51503.65723 43952.72087 36318.83617 42892.58569 49630.50224 45905.69742 41061.79292 1.083221424 1.106271204 1.191022406 1.254296356 1.070404328 0.884492215 1.044586284 1.208678402 1.11796622 1 15.325509 3.050187956 24.98740761 1.065531905 1.157901982 0.242441227 0.089095767 200.1611915 99654.12026 0.029365727 0.03509875 1122.504153 -3.050187956 0.092370077 ENKPSIIFIDEIDSLCGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 ENKPSIIFIDEIDSLCGSR 19 1 O75351 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 ;;; 243.06 1.77E-24 848160000 1589020 1579950 1298460 1440540 1539750 1610330 1616910 1656480 1813540 1772510 FALSE TRUE 1526919.342 1534891.373 1533120.606 1514886.442 1589277.457 1642891.976 1636698.228 1622273.109 1607674.542 1652456.319 0.924030078 0.92885443 0.927782834 0.916748252 0.961766698 0.994212045 0.990463838 0.981734337 0.972899873 1 20.65618071 3.050538461 3.574302882 0.986237212 0.925048474 0.936670273 0.007761692 0.053785786 1.424448156 0.002393504 0.002843979 1123.410453 -3.050538461 -0.061188738 RSQS(ph)IEQESQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSQSIEQESQEK 12 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 RS(0.092)QS(0.905)IEQES(0.002)QEK;RS(0.057)QS(0.943)IEQES(0.001)QEK 73.386 0.011451 118060000 175787 207577 138304 139258 183840 208354 180744 188357 215096 195668 TRUE FALSE 168917.0497 201657.1072 163298.6094 146445.1221 189753.3806 212567.0606 182955.9991 184467.3621 190679.2038 182415.2321 0.926002987 1.105483928 0.895202706 0.802811917 1.040227718 1.165292274 1.002964484 1.011249774 1.045303079 1 17.47686668 3.050805646 24.9999906 1.045626677 0.939514255 0.305447957 0.082330503 145.5510819 71620.45554 0.024989257 0.02986787 1124.101806 -3.050805646 -0.106112422 QAPQTIHLPSGEILDVFDAAER ddPTM_BT-474_Pertuzumab_2h_R1 1 QAPQTIHLPSGEILDVFDAAER 22 0 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 60.464 0.054998 51111000 25447 22180 18981 22646 24252 25458 29689 28307 26721 27023 FALSE TRUE 24452.50311 21547.44812 22411.28893 23814.76277 25032.08761 25972.7782 30052.34286 27722.45056 23687.7441 25192.70814 0.970618283 0.855304956 0.889594275 0.945303801 0.993624324 1.030964121 1.192898465 1.10041566 0.940261919 1 14.6207186 3.051347215 1.76698845 1.074990844 0.903123339 0.464955331 0.068690169 0.273377475 1.743151009 0.024303258 0.029834405 1125.504447 -3.051347215 -0.171867506 KRNDS(ph)EEEERER ddPTM_BT-474_Pertuzumab_2h_R1 4 KRNDSEEEERER 12 3 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 KRNDS(1)EEEERER;KRNDS(1)EEEERER;KRNDS(1)EEEERER;KRNDS(1)EEEERER 183.7 8.44E-05 667193000 408266 391641 316699 362110 385854 418575 379223 434015 462953 458075 TRUE FALSE 392310.5134 380471.7821 373933.5542 380798.5405 398265.3443 427038.8733 383864.0445 425052.4386 410400.5163 427049.1722 0.918654195 0.890932021 0.875621775 0.891697175 0.932598329 0.999975883 0.898875515 0.995324347 0.961014663 1 18.70404267 3.051456715 3.731993536 0.96699584 0.892956512 0.598627069 0.029486432 0.154999941 4.49030733 0.008527416 0.010134867 1125.788258 -3.051456715 -0.074039328 IMLFTNEDNPHGNDSAK ddPTM_BT-474_Pertuzumab_2h_R1 7 IMLFTNEDNPHGNDSAK 17 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;;;; 307.92 4.88E-58 4912350000 2660570 2577530 2119880 2444640 2561220 2807620 2677910 2786670 3251970 3079460 FALSE TRUE 2556591.983 2504021.368 2502989.472 2570808.163 2643603.967 2864392 2710683.064 2729124.291 2882819.999 2870885.431 0.890523862 0.872212224 0.87185279 0.895475708 0.920832277 0.997738178 0.944197575 0.950621108 1.004157103 1 21.45306433 3.051462583 2.452736208 0.971321613 0.879502262 0.824435389 0.020926202 0.122384833 1.49292726 0.006764992 0.008132985 1125.803469 -3.051462583 -0.091819351 LAQENEVDFILLGGDLFHENKPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAQENEVDFILLGGDLFHENKPSR 24 1 F8W7U8;P49959-2;P49959;P49959-3;F5GXT0;F5H742;F5H256 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ; 144.4 1.38E-07 409550000 241430 252820 193703 217760 235620 255350 241110 247350 268720 279010 FALSE TRUE 231994.6487 245609.8211 228709.441 228998.6197 243198.9313 260513.352 244060.7763 242242.1361 238216.0322 260112.4042 0.89190152 0.944244939 0.879271566 0.880383311 0.934976292 1.00154144 0.938289649 0.931297901 0.915819578 1 17.98877567 3.051722279 6.938426331 0.951600416 0.901276953 0.436399993 0.030928567 0.229893343 24.35536161 0.009173301 0.010957559 1126.476871 -3.051722279 -0.050323463 LLS(ph)PQQPALQR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLSPQQPALQR 11 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 LLS(1)PQQPALQR;LLS(1)PQQPALQR;LLS(1)PQQPALQR;LLS(1)PQQPALQR 169.58 1.75E-05 1455240000 764750 791760 705790 756460 722840 698860 708040 781860 772220 720180 TRUE FALSE 734862.7245 769179.78 833341.9532 795500.9913 746090.8051 712991.428 716705.2053 765714.3178 684560.823 671401.5671 1.094520419 1.145632983 1.24119751 1.184836364 1.111243765 1.061944837 1.067476218 1.140471448 1.01959968 1 19.35681638 3.05300173 3.868380442 1.074025043 1.169944036 0.501141138 0.049709146 0.213784781 6.657890044 0.015497625 0.018432751 1129.800416 -3.05300173 0.095918993 FRDQDLASCDR ddPTM_BT-474_Pertuzumab_2h_R1 5 FRDQDLASCDR 11 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;; 244.64 6.26E-16 7583350000 2587640 2586990 2231350 2515890 2319040 2031530 2545200 2290890 2406830 2552550 FALSE TRUE 2486512.168 2513211.578 2634604.581 2645735.384 2393634.028 2072608.929 2576348.919 2243582.321 2133616.749 2379663.515 1.04490074 1.056120566 1.107133242 1.111810711 1.005870793 0.870967225 1.082652612 0.942814943 0.896604388 1 21.18232616 3.053076824 5.703885313 0.961961319 1.07903019 0.500816218 0.057053195 0.165221963 11.64099909 0.016524784 0.019718449 1129.995785 -3.053076824 0.117068871 RNS(ph)FTPLSSSNTIR ddPTM_BT-474_Pertuzumab_2h_R1 4 RNSFTPLSSSNTIR 14 1 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 RNS(0.997)FT(0.003)PLSSSNTIR;RNS(1)FTPLSSSNTIR;RNS(1)FTPLSSSNTIR;RNS(1)FTPLSSSNTIR 175.01 1.50E-06 9022230000 3275580 3124350 2436540 2944130 2607700 2183250 2819940 2061970 3031530 2897380 TRUE FALSE 3147566.712 3035246.597 2876876.979 3096076.902 2691579.039 2227396.811 2854451.269 2019389.599 2687403.424 2701137.872 1.165274363 1.123691844 1.065061139 1.146212096 0.996461183 0.824614261 1.05675882 0.747607007 0.99491531 1 21.36513585 3.053500254 4.06735548 0.906643882 1.119649619 0.529991767 0.087928168 0.152727643 5.277583138 0.025181561 0.029960858 1131.098052 -3.053500254 0.213005737 DNFFEVFTPVFER ddPTM_BT-474_Pertuzumab_2h_R1 2 DNFFEVFTPVFER 13 0 Q99543;Q99543-2;H7C3L7;C9IZ83 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 ; 165.58 8.16E-05 669490000 445450 463680 390300 378180 443690 496590 449370 442900 487380 518050 FALSE TRUE 428041.3215 450456.3004 460835.8922 397697.9151 457961.6918 506631.39 454869.5245 433753.9602 432054.6657 482962.0121 0.886283622 0.932695096 0.954186625 0.823455893 0.948235431 1.049008778 0.941832925 0.898111962 0.894593477 1 18.88155019 3.053558454 24.99999632 0.950296634 0.903027261 0.206821787 0.053124044 192.8173427 90001.73672 0.016390383 0.019590253 1131.249641 -3.053558454 -0.047269373 LKELLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKELLR 6 1 E5RHX8;Q9NPA8-2;Q9NPA8;J3KNT2;E5RI00;E5RHT9;E5RJ84 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 ; 110.35 0.026248 1652580000 2485200 2917500 2131550 2400420 2584810 2667690 2669300 2855600 2910400 2867100 FALSE TRUE 2388075.636 2834295.757 2516768.501 2524305.964 2667952.761 2721632.52 2701967.692 2796630.862 2580023.593 2672908.763 0.893437019 1.060378789 0.941584141 0.944404088 0.998145839 1.018228739 1.01087165 1.046287438 0.965249405 1 21.34997916 3.054099494 5.688422222 1.013619391 0.965981087 0.208549188 0.043432538 0.299747989 20.76152702 0.012163105 0.014517922 1132.659818 -3.054099494 -0.047638304 KELNS(ph)NHDGADETSEKEQQEAIEHIDEVQNEIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 34 2 Q01105-2 Q01105-2 SET Protein SET 1 KELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDR;KELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDR 72.072 0.002343 687800000 248530 191925 320260 178331 260570 264900 298060 269110 275980 270526 TRUE FALSE 238817.1728 186451.4869 378138.1061 187534.6843 268951.4707 270256.4595 301707.7474 263552.7845 244651.9074 252203.0331 0.946924269 0.739291216 1.499340042 0.743586158 1.06640855 1.071582908 1.196289132 1.045002438 0.970059338 1 17.9442261 3.054441521 24.99999095 1.069691491 0.98975348 0.029919356 0.204025994 384.1443665 176399.13 0.057145981 0.068302498 1133.552191 -3.054441521 -0.079938011 RLLDQIVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLLDQIVEK 9 1 Q96AE4;E9PEB5;Q96AE4-2;C9JSZ1 Q96AE4;C9JSZ1 FUBP1 Far upstream element-binding protein 1 0 ; 101.39 0.0064348 482540000 1046610 1569230 1217850 1240600 1076580 499810 1317510 841170 742620 1005240 FALSE TRUE 1005707.324 1524477.097 1437942.586 1304627.515 1111209.173 509916.5006 1333634.081 823799.5455 658320.8909 937154.1994 1.073150315 1.626708921 1.534371384 1.39211617 1.185727145 0.544111632 1.423067924 0.879043754 0.702468058 1 19.83792692 3.054493739 4.02355285 0.93631645 1.427852736 0.45941125 0.252215111 0.195099063 6.570635108 0.073785987 0.087830697 1133.688493 -3.054493739 0.491536286 LSEHATAPTR ddPTM_BT-474_Pertuzumab_2h_R1 5 LSEHATAPTR 10 0 P33316-2;H0YNJ9;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMM5;H0YKI0 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;;; 157.78 8.57E-06 2627320000 1208240 1779520 1446150 1771990 1424610 1331280 1646960 1515750 1305720 1730040 FALSE TRUE 1161020.645 1728769.832 1707501.474 1863442.616 1470433.874 1358199.394 1667115.989 1484449.233 1157500.14 1612862.85 0.71985082 1.071864128 1.058677416 1.155363344 0.911691825 0.842104705 1.033637788 0.920381564 0.717668052 1 20.62119233 3.054653377 24.99856132 0.907327973 1.013429193 0.110960329 0.132941054 191.5738254 87624.69842 0.038177692 0.045631065 1134.105292 -3.054653377 0.10610122 TSVPENHAQSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSVPENHAQSR 11 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 190.68 2.16E-06 1282066000 1263080 1365380 1194957 1436960 1279333 1307460 1273140 1363670 1511350 1365390 FALSE TRUE 1213717.437 1326440.699 1410912.312 1511121.678 1320483.908 1333897.737 1288721.068 1335509.738 1339787.884 1272910.919 0.953497546 1.042053045 1.108414022 1.187138593 1.037373384 1.047911301 1.012420468 1.04917769 1.052538606 1 20.27970003 3.054657827 24.99999672 1.035648176 1.078017954 0.101211829 0.056620738 217.3689471 99420.88553 0.017300663 0.020678244 1134.116913 -3.054657827 0.042369778 CNAAFGAHDFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 CNAAFGAHDFHR 12 0 H3BP71;O75150-4;O75150 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 0 53.967 0.079696 84512000 39304 39599 39054 42066 34430 30537 44240 16333 46554 37464 FALSE TRUE 37767.95623 38469.67529 46111.92655 44237.0313 35537.47222 31154.47906 44781.42235 15995.71784 41269.38509 34926.52991 1.081354384 1.101445674 1.320255023 1.266573903 1.017492213 0.892000412 1.282160652 0.45798188 1.18160565 1 15.09203569 3.05531598 4.308916728 0.919404808 1.19385014 0.190560074 0.215320738 0.297714918 11.52530541 0.064807449 0.077197449 1135.836916 -3.05531598 0.274445331 SSKPEGEAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSKPEGEAGR 10 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 0 83.081 0.014669 40748000 89265 107270 74677 110330 122740 126910 136490 154110 178760 160740 FALSE TRUE 85776.42511 104210.7646 88172.79508 116024.1445 126688.0436 129476.2072 138160.4054 150927.5746 158467.9142 149852.9366 0.572404032 0.695420236 0.58839551 0.774253392 0.845415822 0.864021821 0.921973293 1.007171284 1.057489548 1 17.19318783 3.05554753 0.602416284 1.037806654 0.573011411 0.926288875 0.044427276 0.214696995 0.168118642 0.032282424 0.050700795 1136.442665 -3.05554753 -0.464795243 HTGPGILSMANAGPNTNGSQFFICTAK ddPTM_BT-474_Pertuzumab_2h_R1 4 HTGPGILSMANAGPNTNGSQFFICTAK 27 0 P62937;F8WE65;C9J5S7;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;; 302.8 5.02E-71 8854620000 2634940 2781060 2154990 2774650 2477200 2496060 2713660 2146000 3258980 3064470 FALSE TRUE 2531963.632 2701746.892 2544444.63 2917850.019 2556881.388 2546532.043 2746870.583 2101684.35 2889034.253 2856910.717 0.886259279 0.945688248 0.890627983 1.021330489 0.894981202 0.891358637 0.961482823 0.735649293 1.011244151 1 21.44602452 3.055989434 24.99995443 0.893343117 0.936521616 0 0.081669912 273.7616845 122235.573 0.02338796 0.027953957 1137.599607 -3.055989434 0.043178499 YIELFR ddPTM_BT-474_Pertuzumab_2h_R1 12 YIELFR 6 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3;Q9H6T0-2;Q9H6T0 Q6NXG1;Q9H6T0-2 ESRP1;ESRP2 Epithelial splicing regulatory protein 1;Epithelial splicing regulatory protein 2 0 ;;;;;;;;;;; 150.82 0.024342 7749439000 4962090 5315351 4428880 4710942 4344470 4300050 3871672 4224379 4583868 4955514 FALSE TRUE 4768166.037 5163762.394 5229277.136 4954074.281 4484213.823 4386999.957 3919054.68 4137144.097 4063526.522 4619872.623 1.032099027 1.117728304 1.131909376 1.072340016 0.970635814 0.949593271 0.848303622 0.895510425 0.879575446 1 22.13942164 3.056378335 1.786858872 0.898781948 1.098717265 0.761312044 0.045911849 0.146464148 0.955059906 0.015199364 0.018710678 1138.618761 -3.056378335 0.199935317 QADFEAHNILR ddPTM_BT-474_Pertuzumab_2h_R1 5 QADFEAHNILR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;; 225.15 5.69E-12 3636890000 4258120 4873780 3697310 4394110 4079900 3544510 4445190 4093290 4565490 4749560 FALSE TRUE 4091707.963 4734784.566 4365496.163 4620890.544 4211133.689 3616182.421 4499591.565 4008762.131 4047234.715 4427868.071 0.924080821 1.069314734 0.985913784 1.043592643 0.951052204 0.816687029 1.0161982 0.905348142 0.91403688 1 22.07818081 3.056718535 7.273864233 0.925735049 1.007979136 0.245500945 0.062218063 0.27604906 29.30732081 0.016953488 0.020269736 1139.511035 -3.056718535 0.082244087 LSMPTQQASGQT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSMPTQQASGQTPPR 15 0 Q15723-2;Q15723-3;Q15723-1;Q15723;Q15723-4 Q15723-2 ELF2 ETS-related transcription factor Elf-2 1 LSMPT(0.015)QQAS(0.228)GQT(0.757)PPR 90.498 0.014509 0 58181 62886 50864 61544 54191 51780 50981 62754 55663 58705 TRUE FALSE 55907.2222 61092.55285 60056.25626 64720.29322 55934.10273 52827.02708 51604.92073 61458.10797 49344.3696 54728.85806 1.021530947 1.116276769 1.097341666 1.182562464 1.022022105 0.965249942 0.942919742 1.122956154 0.901615187 1 15.74001413 3.057241233 10.18983341 1.00036265 1.104644296 0.415362603 0.065177859 0.474247113 81.37510606 0.01906056 0.022787921 1140.883326 -3.057241233 0.104281646 EFTELLSQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EFTELLSQDR 10 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 0 ;;; 229.55 3.66E-09 619080000 506294 557849 427517 561410 466631 447620 529007 494365 478564 506383 FALSE TRUE 486507.4707 541939.6927 504778.832 590384.4374 481640.6099 456671.1831 535481.1459 484156.19 424239.421 472085.2284 1.030550082 1.147970028 1.069253604 1.250588669 1.020240798 0.96734902 1.134289136 1.025569454 0.898650065 1 18.84868782 3.057780189 24.99999849 1.016525045 1.123946583 0.35461699 0.076723936 95.7703778 41436.48093 0.021865616 0.026134407 1142.300031 -3.057780189 0.107421539 MKENQK ddPTM_BT-474_Pertuzumab_2h_R1 1 MKENQK 6 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 81.635 0.055961 385970000 714180 808800 527860 638220 825600 850310 992570 914250 930120 1117100 FALSE TRUE 686269.056 785733.8159 623256.0442 671158.6107 852156.1738 867503.8508 1004717.369 895370.418 824536.677 1041437.822 0.658963062 0.754470213 0.598457278 0.644453847 0.818249689 0.832986696 0.964740619 0.859744479 0.791729146 1 19.99014528 3.058018241 2.65658689 0.885120444 0.665388326 0.712612472 0.067469318 0.152718751 2.188856305 0.020980644 0.025228355 1142.926339 -3.058018241 -0.219732119 AVTEMNGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVTEMNGR 8 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YB86;Q4VXU2;A0A6I8PLA1;A0A6I8PS38;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YEU6 P11940-2;B1ANR0 PABPC1;PABPC3;PABPC1L;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3;Polyadenylate-binding protein 1-like;Polyadenylate-binding protein 4 0 129.47 0.0025346 244650000 159940 183410 134840 159930 167970 190730 188580 175580 190390 210560 FALSE TRUE 153689.368 178179.3264 159208.5875 168184.0065 173372.9076 194586.6913 190887.8985 171954.2116 168777.7254 196298.5837 0.782936714 0.907695425 0.811053165 0.856776464 0.883210181 0.99127914 0.972436453 0.875982946 0.859801035 1 17.58269024 3.058279084 3.562272571 0.930995073 0.842656529 0.443214382 0.052365918 0.253687207 6.597827433 0.016212243 0.019343918 1143.613002 -3.058279084 -0.088338545 HADNSSDTEMEDMIAEET(ph)LEEMDSELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.24)S(0.24)DT(0.24)EMEDMIAEET(0.281)LEEMDSELLK 64.722 0.04257 14232000 8468.4 6872.6 6489.6 5721.9 5820.8 6842.3 6229.2 3052.9 7863 5197.2 TRUE FALSE 8137.445566 6676.600177 7662.41508 6017.207945 6008.031318 6980.655994 6305.434813 2989.856548 6970.425204 4845.189015 1.679489807 1.377985494 1.581448125 1.241893335 1.239999368 1.440739664 1.301380564 0.617077381 1.438628128 1 12.24233723 3.058303857 0.46875441 0.97009896 1.636897356 0.367406609 0.229282717 1.314378791 0.567321677 0.210172101 0.397154861 1143.678236 -3.058303857 0.666798397 DIPVVHQLLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIPVVHQLLTR 11 0 P30419;P30419-2 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 ; 177.1 8.13E-06 1084060000 2141000 2327700 1970530 2190300 2047590 1705660 2209700 2121400 2200900 2414200 FALSE TRUE 2057327.353 2261316.275 2326648.605 2303341.645 2113452.592 1740149.614 2236742.97 2077592.349 1951063.059 2250684.084 0.914089795 1.004723982 1.033751748 1.023396247 0.939026764 0.773164758 0.993805833 0.923093722 0.866875575 1 21.10193214 3.058359185 6.670634281 0.909312415 0.996389327 0.252476437 0.066999378 0.277255276 24.65615177 0.019289694 0.023064821 1143.823948 -3.058359185 0.087076912 LLLERPS(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 10 LLLERPSPIR 10 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR 167.73 3.12E-06 10412716000 3640003 3628996 3337816 3498989 3236615 2076809 3529503 3314667 3382712 3744973 TRUE FALSE 3497747.659 3525500.587 3941033.601 3679572.242 3340723.661 2118803.501 3572698.114 3246217.968 2998720.715 3491322.643 1.001840281 1.009789397 1.128808192 1.053919279 0.956864777 0.606877026 1.02330792 0.92979604 0.858906787 1 21.73534226 3.058833656 5.531638951 0.884963409 1.048618627 0.327580364 0.110899749 0.238319388 14.85701398 0.032811718 0.039208723 1145.07427 -3.058833656 0.163655217 GPPDFSSDEEREPTPVLGSGAAAAGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 ;;; 287.55 1.28E-61 2293470000 696800 910520 626440 961920 752650 773380 736590 886530 788250 720150 FALSE TRUE 669568.2856 884552.8611 739651.6431 1011564.806 776859.6708 789018.2735 745604.6088 868222.8457 698771.1646 671373.5991 0.997311015 1.317527026 1.10169903 1.506709242 1.157119779 1.175229819 1.110565875 1.293203735 1.040808226 1 19.35675628 3.059636041 25 1.154522039 1.24079921 0.087506916 0.146161601 204.5228231 85735.96227 0.040431245 0.048324577 1147.191817 -3.059636041 0.086277171 CYYSNTDAVIYVVDSCDRDR ddPTM_BT-474_Pertuzumab_2h_R1 4 CYYSNTDAVIYVVDSCDRDR 20 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;;; 174.29 3.30E-12 1072770000 495835 459110 320345 370706 425376 472779 403248 473179 474505 416257 FALSE TRUE 476457.22 446016.6323 378238.4675 389838.1811 439058.6054 482338.9153 408183.0696 463407.6883 420641.1817 388063.5426 1.227781452 1.149339176 0.974681788 1.004573062 1.131409053 1.242937979 1.05184596 1.194154146 1.083949239 1 18.56593338 3.061259415 24.99987675 1.132810064 1.083070507 0.004060278 0.092582445 222.5487578 90819.5363 0.027106327 0.032398254 1151.487998 -3.061259415 -0.049739557 KEEWDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEEWDR 6 1 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 101.99 0.057602 1581440000 2239000 2414000 1945410 2194400 2436900 2616900 2540600 2816300 2998600 2946200 FALSE TRUE 2151497.405 2345155.084 2296988.862 2307653.247 2515285.102 2669815.511 2571692.623 2758142.421 2658211.499 2746651.25 0.783316559 0.853823391 0.836287047 0.840169733 0.915764279 0.972025666 0.936301113 1.004183702 0.967800881 1 21.38924231 3.061435703 1.059925659 0.985018324 0.817014876 0.898196334 0.023530762 0.141113402 0.342456819 0.010131557 0.013301848 1151.955502 -3.061435703 -0.168003447 S(ph)SPEQPRPSTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPEQPRPSTSK 12 1 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BRN3;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 1 S(0.55)S(0.45)PEQPRPSTSK 79.804 0.013353 92438000 133800 120560 100900 104300 122800 126150 123630 132290 134290 142320 TRUE FALSE 128570.9481 117121.7468 119134.8745 109682.9355 126749.9735 128700.8394 125143.0209 129558.1653 119045.9622 132680.5396 0.969026418 0.88273493 0.897907672 0.82666935 0.955301914 0.970005396 0.943190473 0.976466976 0.897237549 1 17.01759726 3.061510874 24.99922938 0.957098377 0.893226534 0.36611182 0.040578935 71.32226635 28986.00365 0.011276522 0.01347802 1152.154907 -3.061510874 -0.063871843 KLTDIINNDHENVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLTDIINNDHENVK 14 1 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 150.59 4.66E-06 752630000 1145700 1125500 786740 885040 1052600 1068400 1133300 1125800 1175700 1055900 FALSE TRUE 1100924.777 1093401.842 928921.4189 930717.0205 1086457.835 1090003.78 1147169.664 1102551.837 1042239.465 984382.9525 1.118390739 1.110748453 0.94365858 0.945482668 1.103694281 1.107296482 1.165369292 1.120043611 1.058774395 1 19.90886015 3.063029253 24.99967112 1.105680884 1.02865123 0.155383328 0.067877954 101.5678495 40284.31384 0.020620338 0.024646016 1156.190117 -3.063029253 -0.077029654 VARPLPAEEPER ddPTM_BT-474_Pertuzumab_2h_R1 3 VARPLPAEEPER 12 1 P26358;P26358-2;K7ENQ6 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;; 129.37 0.00021475 1353740000 837430 989630 794740 851730 823930 725900 859710 797860 825630 890870 FALSE TRUE 804702.3098 961406.7213 938367.1969 895687.8874 850432.4567 740578.1954 870231.3881 781383.9122 731907.9437 830530.5814 0.96890148 1.157581362 1.129840632 1.078452627 1.023962845 0.891692867 1.04780174 0.940824973 0.881253454 1 19.66367377 3.063049155 3.236947394 0.955708369 1.092570216 0.475234365 0.064613294 0.204579389 4.363701721 0.019285194 0.023104289 1156.243102 -3.063049155 0.136861847 IENHEGVR ddPTM_BT-474_Pertuzumab_2h_R1 17 IENHEGVR 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;; 166.07 0.00032063 84147524000 28579255.5 29022813.5 23737400.9 29177738.4 26111478.5 25929255.6 28211674.3 27278896.4 28146677 29575620.6 FALSE TRUE 27462346.6 28195111.28 28027277.28 30683604.98 26951377.92 26453562.91 28556937.21 26715577.66 24951584.23 27572437.47 0.996007213 1.022583198 1.016496177 1.112836143 0.977475348 0.959420542 1.035705938 0.96892332 0.904946625 1 24.71672348 3.06353102 24.99994074 0.975986092 1.035822656 0.347875747 0.041927529 75.71308485 29792.74874 0.012193029 0.014573456 1157.526706 -3.06353102 0.059836564 VLSTST(ph)DLEAAVADALKKPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLSTSTDLEAAVADALKKPVR 21 2 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.003)T(0.016)S(0.444)T(0.536)DLEAAVADALKKPVR 120.64 0.0014792 557540000 498440 555280 342610 370970 477000 545440 471260 510000 505250 487760 TRUE FALSE 478960.4137 539443.9581 404527.2483 390115.8062 492343.1382 556469.1705 477027.4208 499468.3218 447896.1382 454723.5807 1.053300145 1.186311819 0.889611328 0.857918574 1.082730606 1.223752614 1.049049227 1.09839987 0.98498551 1 18.79463029 3.064434065 24.99996768 1.084736042 0.998624711 0.108947563 0.103833623 131.2706714 50930.40176 0.031599115 0.037768163 1159.9361 -3.064434065 -0.086111331 QALTEFNTAIQEIVVTHWHR ddPTM_BT-474_Pertuzumab_2h_R1 2 QALTEFNTAIQEIVVTHWHR 20 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ; 140.35 1.18E-07 114391000 60951 55460 49294 46456 40868 38538 37507 22217 45370 38364 FALSE TRUE 58568.96754 53878.3351 58202.52234 48853.59973 42182.55634 39317.26476 37966.02189 21758.21119 40219.78781 35765.57211 1.637579496 1.50643012 1.627333743 1.365939278 1.179417911 1.099304791 1.061524244 0.608356302 1.124539199 1 15.1262839 3.064464848 0.958301993 0.880166957 1.612897657 0.789059592 0.139047546 0.226762926 0.456225724 0.068727111 0.09220524 1160.018321 -3.064464848 0.7327307 AQTAPTKTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 AQTAPTKTSPR 11 1 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 AQTAPTKT(0.205)S(0.795)PR;AQTAPTKT(0.284)S(0.716)PR;AQTAPTKT(0.132)S(0.867)PR;AQT(0.002)APT(0.053)KT(0.15)S(0.795)PR;AQTAPT(0.002)KT(0.012)S(0.986)PR;AQT(0.001)APT(0.034)KT(0.195)S(0.77)PR 206.45 6.93E-08 4834000000 5746420 6735820 5246680 5764240 6184770 6727600 6780400 5930440 7755220 7406350 TRUE FALSE 5521843.553 6543721.009 6194871.788 6061733.117 6383708.744 6863636.681 6863380.563 5807974.342 6874879.938 6904711.318 0.799721132 0.947718262 0.897194901 0.877912608 0.924543902 0.994051216 0.994014123 0.841161067 0.995679562 1 22.71914967 3.064517512 4.817702362 0.949274285 0.887154234 0.310231344 0.056532745 0.339355258 15.58213216 0.01717624 0.02054601 1160.158996 -3.064517512 -0.062120051 VTVAGLAGKDPVQCSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTVAGLAGKDPVQCSR 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ; 176.21 2.96E-09 4188100000 1527990 1682690 1148160 1308320 1738530 1990710 1879480 2053750 2257400 2124800 FALSE TRUE 1468274.462 1634701.329 1355658.053 1375842.552 1794451.396 2030963.52 1902481.638 2011339.345 2001149.416 1980885.403 0.741221304 0.825237707 0.684369752 0.694559387 0.905883497 1.025280673 0.960419838 1.015373904 1.010229775 1 20.91771399 3.064563355 3.864696094 0.998941784 0.739817012 0.908956369 0.039624507 0.064008328 1.935331874 0.012431096 0.014869195 1160.281466 -3.064563355 -0.259124772 NTLQLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 NTLQLHR 7 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 107.9 0.0073747 949040000 1446080 1862630 1577320 1658470 1382040 960800 1389760 1170790 1251280 1557350 FALSE TRUE 1389565.595 1809509.616 1862376.811 1744063.835 1426494.572 980228.0343 1406768.299 1146612.777 1109239.94 1451869.297 0.957087251 1.246330933 1.282744125 1.201254024 0.98252272 0.675148952 0.96893591 0.789749311 0.764008125 1 20.46948015 3.064788873 3.934685688 0.833292156 1.183509736 0.626833666 0.120315057 0.131614836 4.11803314 0.034822557 0.041653055 1160.884126 -3.064788873 0.350217579 GVEDIPGYYYR ddPTM_BT-474_Pertuzumab_2h_R1 3 GVEDIPGYYYR 11 0 O15296-4;O15296;I3L1D5;O15296-3;O15296-2 O15296-4 ALOX15B Arachidonate 15-lipoxygenase B 0 ;; 205.12 7.19E-08 1256490000 1234830 1379850 1133980 1287670 1148880 881090 1279350 1267490 1081750 1083880 FALSE TRUE 1186571.478 1340498.029 1338915.411 1354126.803 1185834.769 898906.2435 1295007.068 1241315.889 958954.2751 1010467.842 1.174279308 1.326611272 1.325045049 1.34009886 1.17355023 0.889594113 1.28159157 1.228456599 0.949020083 1 19.94659198 3.065717101 5.75467186 1.105686044 1.294255163 0.410710325 0.121314826 0.236485026 14.78732293 0.036860298 0.044121154 1163.367965 -3.065717101 0.188569119 RGS(ph)GDTSSLIDPDTSLSELR ddPTM_BT-474_Pertuzumab_2h_R1 3 RGSGDTSSLIDPDTSLSELR 20 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.958)GDT(0.024)S(0.009)S(0.009)LIDPDTSLSELR;RGS(0.942)GDT(0.057)S(0.001)SLIDPDTSLSELR;RGS(0.795)GDT(0.181)S(0.019)S(0.005)LIDPDTSLSELR 205.65 5.17E-22 2705740000 3394650 3341490 2710940 3297200 3345310 3404650 3356270 3786480 3980630 4019260 TRUE FALSE 3261983.325 3246193.977 3200867.163 3467368.887 3452914.934 3473494.356 3397345.036 3708287.865 3528765.571 3747031.94 0.870551246 0.866337418 0.854240693 0.925364113 0.921506672 0.926998865 0.906676295 0.989660063 0.941749531 1 21.83731684 3.065749625 0.280449238 1.005223132 0.816408209 0.777225346 0.021952006 1.468015081 0.204717267 0.032158675 0.093024427 1163.455093 -3.065749625 -0.188814923 IRPWINK ddPTM_BT-474_Pertuzumab_2h_R1 2 IRPWINK 7 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 99.139 0.0098018 355270000 493320 582840 443380 615860 605660 524880 763800 722620 819500 971380 FALSE TRUE 474040.509 566217.9739 523508.6289 647644.6084 625141.6039 535493.4332 773147.6129 707697.6445 726473.7956 905587.5674 0.523461812 0.625249279 0.578087253 0.715165084 0.690316019 0.591321538 0.853752459 0.781478976 0.802212643 1 19.78849463 3.06598258 0.086793955 1.363598625 3.11E-13 0.817206115 0.059224245 14.87578125 0.425562397 2.356170128 4.237181266 1164.079335 -3.06598258 -1.363598625 TLCTLGPNETAPFKPEGELHELSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLCTLGPNETAPFKPEGELHELSTR 25 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 48.097 0.091332 44666000 14382 18408 14551 14635 17701 19612 20494 19747 21665 15860 FALSE TRUE 13819.93554 17883.02186 17180.68939 15390.3141 18270.36874 20008.56808 20744.8117 19339.21755 19205.68003 14785.78807 0.934676966 1.209473704 1.161973193 1.040885614 1.235670946 1.353229735 1.403023741 1.307959877 1.298928399 1 13.85192352 3.066237766 4.922195147 1.303031195 1.101972856 0.324631095 0.123098145 0.208293639 9.836558188 0.034208988 0.040944111 1164.763534 -3.066237766 -0.201058339 NSPT(ph)PATS(ph)TESLSPLHNVALR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPTPATSTESLSPLHNVALR 21 0 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 2 NS(0.015)PT(0.982)PAT(0.167)S(0.655)T(0.165)ES(0.015)LSPLHNVALR;NS(0.01)PT(0.984)PAT(0.403)S(0.482)T(0.119)ES(0.002)LSPLHNVALR 93.949 0.0029198 131529000 97212 109184 85379 104859 92901 94146 74391 115762 101850 108092 TRUE FALSE 93412.84757 106070.1792 100808.8845 110270.7856 95889.24504 96049.69662 75301.41931 113371.4742 90288.41499 100770.8326 0.926982989 1.0525881 1.000377609 1.094272844 0.951557535 0.953149777 0.747254115 1.125042548 0.895977662 1 16.6207186 3.067074942 24.99963418 0.95012266 1.020091709 0.120167341 0.096331689 126.5077419 47148.95882 0.027666327 0.033067583 1167.01098 -3.067074942 0.069969049 NLSLTDFVGDESPS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 3 NLSLTDFVGDESPSPER 17 0 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3 E9PDC2 PRUNE2 Protein prune homolog 2 1 NLSLTDFVGDES(0.006)PS(0.994)PER;NLSLTDFVGDES(0.001)PS(0.999)PER;NLSLTDFVGDESPS(1)PER 354.55 8.52E-88 173745000 143494 145623 128514 150583 132403 133625 132560 142294 155654 141026 TRUE FALSE 137886.0958 141469.9746 151739.3386 158354.6067 136661.8627 136326.9891 134182.3089 139355.5792 137984.8105 131474.1834 1.048769365 1.076028548 1.154137905 1.204454004 1.039457779 1.036910711 1.020598154 1.059946337 1.049520194 1 17.00442001 3.068566446 24.99992491 1.037902393 1.120266036 0.502807049 0.042025667 47.08577301 17167.01991 0.012921842 0.015444554 1171.025753 -3.068566446 0.082363643 S(ph)GSMDPSGAHPSVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 S(0.619)GS(0.381)MDPSGAHPSVR;S(0.497)GS(0.497)MDPS(0.005)GAHPSVR;S(0.499)GS(0.499)MDPS(0.001)GAHPSVR 191.15 3.36E-07 1192400000 1045593 1273637 884782 1149888 995730 995297 892786 1073603 1109365 1117776 TRUE FALSE 1004730.07 1237314.12 1044681.789 1209233.857 1027758.56 1015422.587 903712.1821 1051432.723 983434.536 1042068.036 0.964169358 1.187364046 1.002508237 1.160417378 0.986268194 0.974430222 0.867229539 1.008986637 0.94373352 1 19.99101804 3.069130754 7.511520967 0.958275173 1.08078001 0.39092096 0.071076034 0.217847532 20.15856858 0.018962774 0.022695342 1172.548334 -3.069130754 0.122504837 DREIQLEISGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DREIQLEISGK 11 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 104.59 0.002009 0 446710 393400 335630 409700 425130 456610 477090 486780 524170 533300 FALSE TRUE 429252.0793 382180.6172 396285.807 430844.6661 438804.6925 465842.967 482928.7701 476727.8229 464668.4191 497179.116 0.863375121 0.76869805 0.79706849 0.866578366 0.882588746 0.936972113 0.971337602 0.958865342 0.934609689 1 18.92340617 3.06976023 1.222401599 0.964321705 0.805788182 0.841495851 0.028619668 0.159417754 0.504474558 0.011250846 0.014590332 1174.249083 -3.06976023 -0.158533522 VQLFEISLSHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQLFEISLSHGR 12 0 Q5T370;Q8N5I2;F2Z3I4;Q5T371 Q5T370 ARRDC1 Arrestin domain-containing protein 1 0 109.44 0.0015974 52764000 73200 88785 75669 84188 76279 68713 84902 81444 72478 89057 FALSE TRUE 70339.26307 86252.93873 89344.07155 88532.95277 78732.58331 70102.42394 85941.05607 79762.15294 64250.60129 83025.09007 0.847204899 1.038877991 1.0761093 1.066339738 0.94829868 0.844352278 1.035121504 0.960699385 0.773869697 1 16.34125976 3.070110872 8.177881929 0.929518481 1.013911632 0.156533578 0.09143783 0.493356359 51.00660537 0.026648189 0.031885598 1175.197535 -3.070110872 0.084393151 IKETVDQVEELRR ddPTM_BT-474_Pertuzumab_2h_R1 1 IKETVDQVEELRR 13 2 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 152.16 2.54E-05 275900000 239960 279490 201340 232610 259750 297410 251260 290360 343260 290080 FALSE TRUE 230582.0979 271519.2188 237726.6168 244615.03 268105.0946 303423.834 254334.995 284363.9645 304294.5639 270432.6232 0.852641575 1.00401799 0.879060425 0.904532253 0.991393314 1.121994197 0.940474533 1.051515017 1.125213964 1 18.04490967 3.071372232 4.333018801 1.043430958 0.915383165 0.518248841 0.062326659 0.179109648 6.563365542 0.017921724 0.021486917 1178.615728 -3.071372232 -0.128047792 S(ph)RAS(ph)PVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RAS(0.987)PVS(0.014)R;S(1)RAS(0.997)PVS(0.003)R;S(1)RAS(0.996)PVS(0.004)R;S(1)RAS(1)PVSR 79.283 0.016181 904130000 128140 141472 97851.3 118576 99323 119468 117900 100357 110006 113644 TRUE FALSE 123132.1471 137437.3571 115535.2066 124695.7216 102517.8145 121883.7248 119342.8955 98284.59288 97518.58006 105946.7907 1.162207429 1.297230017 1.090502184 1.176965539 0.967634922 1.150423944 1.126441818 0.927678812 0.920448647 1 16.69298036 3.072166186 0.440641783 0.947269364 1.253099256 0.506560953 0.082585811 1.160111934 0.429825505 0.077093677 0.155775835 1180.772382 -3.072166186 0.305829892 HPENYDLATLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPENYDLATLK 11 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 191.29 1.90E-06 944950000 1794070 1841170 1448500 1611800 1612580 1432570 1794740 1208780 1935200 1888440 FALSE TRUE 1723955.761 1788661.634 1710276.172 1694985.191 1664450.1 1461537.547 1816704.565 1183818.271 1715524.209 1760534.277 0.97922306 1.015976603 0.971452924 0.962767504 0.945423286 0.83016705 1.031905251 0.672419893 0.974433859 1 20.74758189 3.072526004 1.304215167 0.871365191 0.993282912 0.089702661 0.098098539 0.674128292 2.408976663 0.037372405 0.048177892 1181.751069 -3.072526004 0.121917721 RQEQTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RQEQTLR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 149.4 0.0032371 552572000 553110 581970 519405 564720 512990 413387 559330 492990 558650 622890 FALSE TRUE 531493.8497 565372.7854 613273.0376 593865.2669 529490.7892 421745.9684 566175.2479 482809.5842 495234.3941 580701.1055 0.915262335 0.97360377 1.056090701 1.022669427 0.911812952 0.726270304 0.974985655 0.831425289 0.852821511 1 19.14743625 3.073206399 5.558188063 0.867198857 0.993860603 0.317704717 0.078760041 0.213854273 11.77876023 0.022147787 0.026547603 1183.60393 -3.073206399 0.126661746 RES(ph)AASGLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RES(0.998)AAS(0.002)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(1)AASGLGGLLEEEGAGAGAAQEEVLEPGR 330.01 7.35E-106 682260000 157387 186835 151681 178399 160794 170078 146668 198130 166928 148752 TRUE FALSE 151236.142 181506.6487 179093.1308 187606.1938 165966.085 173517.0937 148462.9669 194038.5463 147979.0333 138676.8945 1.090564816 1.30884564 1.291441746 1.352829499 1.196782532 1.251232906 1.070567432 1.399213235 1.067077784 1 17.08136791 3.073696208 24.99933165 1.195804871 1.267559572 0.094584334 0.124865872 117.2502621 39770.34513 0.035047443 0.041889706 1184.939583 -3.073696208 0.0717547 IDRDS(ph)YSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDRDSYSPR 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 IDRDS(0.5)YS(0.5)PR 101.38 0.010581 841170000 930710 1003800 770620 973650 838770 833100 861560 882260 845200 934710 TRUE FALSE 894336.8242 975172.6068 909888.1763 1023900.193 865749.7988 849945.8528 872104.029 864041.0227 749256.4394 871401.2591 1.026320326 1.119085607 1.044166699 1.175004262 0.993514514 0.97537827 1.000806482 0.991553562 0.85982942 1 19.73297767 3.07403602 8.650912361 0.971563848 1.089637923 0.552598246 0.053665965 0.213058856 22.50059031 0.01489804 0.017824364 1185.867098 -3.07403602 0.118074076 GPSS(ph)PPTTTAPMR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPSSPPTTTAPMR 13 0 Q9NXL9-4;Q9NXL9 Q9NXL9-4 MCM9 DNA helicase MCM9 1 GPS(0.02)S(0.979)PPT(0.001)TTAPMR 129.37 4.01E-05 0 156360 200640 139310 173620 156220 142850 168300 163190 169000 160420 TRUE FALSE 150249.2783 194917.9436 164486.4159 182580.549 161244.9582 145738.5249 170359.7057 159820.0695 149815.8285 149554.6105 1.004644911 1.303322866 1.099841826 1.220828622 1.078167752 0.974483664 1.1391137 1.068640204 1.00174664 1 17.19031286 3.074788962 6.826198128 1.04932822 1.162864933 0.306945297 0.084176205 0.262690839 19.55524779 0.022860605 0.027381136 1187.924834 -3.074788962 0.113536713 KELSDIAHR ddPTM_BT-474_Pertuzumab_2h_R1 6 KELSDIAHR 9 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;; 162.36 4.14E-05 14211320000 11719000 12740500 10148510 11972700 10893600 10248680 11495600 11485500 11836000 10789200 FALSE TRUE 11261008.52 12377153.41 11982571.51 12590612.48 11244002.54 10455915.33 11636286.59 11248320.41 10492426.9 10058437.87 1.119558391 1.230524418 1.191295473 1.251746309 1.117867673 1.039516818 1.156868168 1.118296952 1.043146762 1 23.26190293 3.075132203 6.319678871 1.08812496 1.199479593 0.551180115 0.052892624 0.169891365 11.22003617 0.015050829 0.018034792 1188.864072 -3.075132203 0.111354633 EAVILPIKFPHLFTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAVILPIKFPHLFTGK 16 1 O75351;I3L4J1;Q9UN37 O75351;I3L4J1 VPS4B;VPS4A Vacuolar protein sorting-associated protein 4B;Vacuolar protein sorting-associated protein 4A 0 ; 210.09 6.35E-12 639040000 885660 916900 727050 810340 889790 994180 936460 947820 1074050 966180 FALSE TRUE 851047.4281 890750.9097 858444.1081 852161.7445 918410.9034 1014283.001 947920.6776 928247.1858 952128.3468 900739.768 0.944831635 0.988910384 0.953043419 0.946068748 1.019618469 1.126055534 1.052380178 1.030538696 1.057051527 1 19.78075083 3.075506046 4.842631023 1.05473436 0.960787744 0.664357737 0.03177539 0.124199349 5.394105025 0.009377534 0.011252129 1189.887895 -3.075506046 -0.093946616 GLGACTLLGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 GLGACTLLGSPR 12 0 O95644-6;O95644;K7ER53;O95644-8;O95644-11;O95644-3;O95644-10;O95644-2;O95644-5;O95644-4 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 1 GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR 177.36 2.45E-05 1639280000 1154160 1211540 1031500 1226950 1057390 1045487 1045530 1171090 1087370 1074870 TRUE FALSE 1109054.151 1176988.065 1217914.996 1290273.037 1091401.91 1066627.463 1058325.509 1146906.582 963936.3162 1002068.098 1.106765253 1.174558963 1.215401427 1.287610133 1.089149442 1.064426126 1.056141306 1.144539563 0.961946916 1 19.93454912 3.075931031 8.25958206 1.063989673 1.195711595 0.562521235 0.061855595 0.216755522 20.91829883 0.018188132 0.021765659 1191.052845 -3.075931031 0.131721921 LMEEDELPSWIIKDDAEVER ddPTM_BT-474_Pertuzumab_2h_R1 4 LMEEDELPSWIIKDDAEVER 20 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;F6VDE0;P51531-2;P51531;A0A0U1RQZ9;A0A0U1RRG6 A0A2R8Y4P4;F6VDE0 SMARCA4;SMARCA2 Transcription activator BRG1;Probable global transcription activator SNF2L2 0 ;;; 252.24 4.11E-36 1049930000 1608510 1591320 1329980 1508610 1541590 1655000 1627400 1701170 1847570 1757430 FALSE TRUE 1545647.651 1545937.112 1570336.971 1586469.543 1591176.642 1688465.234 1647316.608 1666040.245 1637841.599 1638397.701 0.943389783 0.943566456 0.958458969 0.968305523 0.971178513 1.03055884 1.005443677 1.016871694 0.999660582 1 20.64385417 3.076026701 1.849598584 1.011505493 0.950045449 0.846427346 0.011462717 0.11686954 0.81715818 0.003765451 0.004687868 1191.31525 -3.076026701 -0.061460044 QMIAVADENQNHHLEPEEVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QMIAVADENQNHHLEPEEVLK 21 0 A0A5F9UP49;Q9BRK5;Q9BRK5-2;Q9BRK5-5 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 150.83 3.91E-08 129750000 89911 93062 79809 88835 73766 64015 96380 21954 104650 101010 FALSE TRUE 86397.17872 90407.96288 94232.26164 93419.785 76138.75038 65309.42716 97559.52727 21500.64223 92770.57073 94168.50273 0.917474274 0.960065842 1.000677073 0.99204917 0.808537337 0.693537916 1.036010178 0.228320952 0.985154994 1 16.52295697 3.076647168 3.295264788 0.720414295 0.969682572 0.092183683 0.222659537 0.395005961 8.640216891 0.068132642 0.082164372 1193.018471 -3.076647168 0.249268278 AYS(ph)GSDLPSSSSGGANGTAGGGGGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AYS(0.993)GS(0.007)DLPSSSSGGANGTAGGGGGAR;AYS(0.983)GS(0.016)DLPS(0.001)SSSGGANGTAGGGGGAR;AYS(0.5)GS(0.5)DLPSSSSGGANGTAGGGGGAR;AYS(0.72)GS(0.28)DLPSSSSGGANGTAGGGGGAR 303.42 8.33E-71 3307240000 1043900 1137630 952380 1073690 1006220 971900 959060 1199680 1022000 982220 TRUE FALSE 1003103.234 1105185.906 1124496.252 1129103.27 1038585.98 991552.4839 970797.2632 1174906.189 905986.8446 915693.3645 1.095457576 1.206938861 1.228027083 1.233058263 1.134207171 1.082843365 1.060177239 1.283078194 0.989399814 1 19.80450504 3.076733495 6.333757239 1.113086363 1.194252025 0.224839631 0.085607553 0.395047786 25.74928981 0.025442282 0.030490643 1193.255638 -3.076733495 0.081165661 EQSISLMSVGFLLEKPDEAVVWR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQSISLMSVGFLLEKPDEAVVWR 23 1 H3BQR2;Q9Y5Y2;H3BRE1;H3BNF0;H3BNS4 H3BQR2 NUBP2 Cytosolic Fe-S cluster assembly factor NUBP2 0 ; 216.19 2.36E-32 468170000 143711 129442 107619 124460 135612 150201 147166 148910 161603 162151 FALSE TRUE 138094.6152 125750.4409 127068.1473 130883.3955 139974.0831 153238.1671 148967.0615 145834.9565 143258.5049 151168.3683 0.913515286 0.831856838 0.840573651 0.865812054 0.92594823 1.01369201 0.985438046 0.964718731 0.947675142 1 17.20579676 3.077124062 3.102393316 0.978960461 0.858548776 0.814811583 0.026708998 0.101880876 1.982515204 0.008245011 0.009962728 1194.329233 -3.077124062 -0.120411685 SLEPEPQQSLEDGS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLEPEPQQSLEDGSPAK 17 0 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 SLEPEPQQSLEDGS(1)PAK;SLEPEPQQSLEDGS(1)PAK 317.27 2.70E-46 317560000 356880 333080 426230 463050 439840 425790 573620 628280 724290 763960 TRUE FALSE 342932.735 323580.8845 503259.2424 486948.066 453987.8531 434399.7655 580640.1331 615305.7984 642071.6357 712216.3087 0.481500818 0.454329507 0.706610107 0.683708109 0.637429735 0.609926732 0.815258126 0.863931071 0.901512122 1 19.44195595 3.077229182 0.236371417 1.064760866 0.286251226 0.839255104 0.068136906 1.899821937 0.195337935 0.147328602 0.45233128 1194.618352 -3.077229182 -0.778509639 down KSDPVVSYR ddPTM_BT-474_Pertuzumab_2h_R1 3 KSDPVVSYR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ;; 115.23 0.0024202 1329490000 293257 351745 261520 332532 374310 388878 443890 450630 479100 503910 FALSE TRUE 281796.1922 341713.577 308782.4815 349694.0164 386350.0211 396741.3796 449322.4586 441324.333 424714.5766 469779.7269 0.599847495 0.727391067 0.657292054 0.744378687 0.822406756 0.844526396 0.956453489 0.939428221 0.904071743 1 18.84162493 3.078710756 0.666498375 0.968171037 0.627809036 0.914648295 0.037206703 0.203759542 0.199308933 0.023986673 0.036734776 1198.700693 -3.078710756 -0.340362001 HIGTSALMDLLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIGTSALMDLLLR 13 0 O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170 O75170-6 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 0 ; 214 1.42E-09 228570000 149523 155794 187109 138233 158528 108959 176938 107020 157487 169337 FALSE TRUE 143679.4759 151350.9077 220923.7585 145367.2217 163627.1971 111162.2256 179103.4202 104809.9996 139609.736 157867.6542 0.910126122 0.958720192 1.399423838 0.920817013 1.036483363 0.704148207 1.134516257 0.663910541 0.884346681 1 17.26835608 3.078711411 2.283345048 0.863422033 1.072623487 0.156930686 0.182222792 0.471517312 4.998754221 0.057059418 0.070037154 1198.702501 -3.078711411 0.209201454 SLESLHSFVAAATK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLESLHSFVAAATK 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 93.206 0.0045546 0 197010 210440 183710 180620 190850 155880 219730 152830 189460 210540 FALSE TRUE 189310.6314 204438.4572 216910.4836 189941.8198 196988.8636 159032.0004 222419.1215 149674.0071 167953.2951 196279.9383 0.964493025 1.04156573 1.105107764 0.967708781 1.003611807 0.81023054 1.133172974 0.762553771 0.855682433 1 17.5825532 3.079094906 1.923256252 0.904334367 1.03339876 0.18578157 0.104212735 0.495102183 3.738697909 0.034075142 0.042372034 1199.761457 -3.079094906 0.129064393 LAGESESNLRK ddPTM_BT-474_Pertuzumab_2h_R1 6 LAGESESNLRK 11 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 169.65 2.67E-05 6910760000 5653920 5470790 3525520 4278420 5420350 6024450 5328340 6321270 7079520 5870430 FALSE TRUE 5432958.556 5314768.426 4162659.889 4499229.769 5594700.48 6146268.507 5393549.819 6190733.565 6275882.569 5472820.547 0.992716372 0.971120536 0.760605953 0.822104385 1.02227004 1.123053178 0.985515562 1.131177884 1.146736407 1 22.38385312 3.079220942 5.099518779 1.080791227 0.88475359 0.563294359 0.07936394 0.154084049 7.107531577 0.024387899 0.029278243 1200.10969 -3.079220942 -0.196037637 NPEISHMLNNPDIMR ddPTM_BT-474_Pertuzumab_2h_R1 4 NPEISHMLNNPDIMR 15 0 Q9UMX0;Q9UMX0-2 Q9UMX0 UBQLN1 Ubiquilin-1 0 ;;; 257.35 8.75E-25 1328840000 851040 842530 709540 830410 767120 726550 822350 783900 858350 887540 FALSE TRUE 817780.4159 818501.8693 837769.6616 873267.5596 791795.1115 741241.3388 832414.1653 767712.1911 760913.7065 827426.1253 0.988342513 0.989214438 1.012500858 1.05540245 0.956937529 0.895839902 1.006028381 0.927831703 0.919615278 1 19.65827098 3.080103668 9.008714034 0.946490803 1.009698172 0.400735691 0.036080461 0.284612004 29.15353995 0.010172424 0.012169782 1202.551455 -3.080103668 0.063207369 SKPLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 94.407 0.0406 1544390000 2493700 2511600 2122500 2637200 2766200 2980500 3207000 3455700 3535500 3791500 FALSE TRUE 2396243.447 2439971.627 2506082.965 2773306.208 2855177.335 3040767.752 3246248.225 3384338.587 3134164.862 3534698.328 0.677920214 0.690291335 0.708994865 0.784594879 0.807757005 0.860262311 0.918394704 0.95746179 0.886685248 1 21.75315566 3.080180114 0.530026944 0.975365884 0.641390585 0.947449825 0.024788353 0.214559455 0.124121401 0.01985065 0.034874622 1202.763151 -3.080180114 -0.333975298 EVVESEGERK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVVESEGERK 10 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 89.171 0.018751 332720000 153640 145980 125260 126620 159490 188270 174990 168610 182410 190800 FALSE TRUE 147635.5789 141816.7933 147897.2684 133154.8734 164620.1407 192076.9484 177131.58 165128.1446 161703.5815 177876.9461 0.829987147 0.797274725 0.831458329 0.748578589 0.925472043 1.079830482 0.995809653 0.928327972 0.909075544 1 17.44052002 3.08023852 5.516895835 0.977769127 0.804805301 0.758700604 0.048110445 0.106791534 5.505880672 0.014963418 0.017956533 1202.924914 -3.08023852 -0.172963826 DGWSLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGWSLDR 7 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 ; 114.59 0.01366 560350000 473870 554490 476280 503610 473880 348460 530230 495010 484490 547470 FALSE TRUE 455350.6365 538676.4881 562354.3908 529601.3725 489122.7806 355506.0999 536719.1133 484787.8705 429492.7263 510389.3693 0.892163246 1.055422625 1.101814467 1.037641856 0.958332618 0.696538998 1.051587564 0.949839279 0.841500141 1 18.96123875 3.080610897 5.412241033 0.912137815 1.028359946 0.21203101 0.102514931 0.321083854 16.05177858 0.030216481 0.036268088 1203.95678 -3.080610897 0.116222131 VNQSALEAVTPS(ph)PSFQQR ddPTM_BT-474_Pertuzumab_2h_R1 4 VNQSALEAVTPSPSFQQR 18 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 VNQSALEAVT(0.001)PS(0.998)PS(0.001)FQQR;VNQSALEAVT(0.026)PS(0.974)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(0.999)PSFQQR 265.38 5.09E-31 2510160000 2031370 2048110 1876030 1684380 1698880 1786030 1576860 1721570 1668610 1748100 TRUE FALSE 1951981.815 1989699.908 2215070.353 1771311.054 1753526.018 1822144.75 1596158.084 1686018.978 1479196.388 1629699.63 1.197755573 1.220899773 1.359189333 1.086894187 1.075981111 1.118086251 0.979418572 1.034558115 0.907649705 1 20.63617466 3.08141719 0.835758421 0.982002915 1.259056842 0.711709387 0.067535658 0.339879535 0.52724891 0.036722681 0.051957278 1206.194072 -3.08141719 0.277053927 ATAPAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATAPASPR 8 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 ATAPAS(1)PR;ATAPAS(1)PR 107.08 0.0042717 1181680000 1642700 1821800 1391970 1504580 1337440 1325060 1197450 1305740 1350410 1225940 TRUE FALSE 1578501.468 1769844.048 1643529.943 1582231.554 1380459.972 1351853.621 1212104.751 1278776.013 1197117.118 1142905.992 1.381129751 1.548547352 1.438027235 1.384393437 1.207850849 1.182821361 1.060546327 1.118881187 1.047432708 1 20.12427531 3.081908275 1.050021232 1.064794113 1.481301507 0.914332538 0.052435616 0.125984705 0.30053758 0.022094007 0.029731536 1207.558765 -3.081908275 0.416507394 EYELLSDELNQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EYELLSDELNQK 12 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 152.54 0.00016259 52911000 122520 126400 99746 116530 127320 134130 139340 147960 151710 136240 FALSE TRUE 117731.7829 122795.1958 117772.321 122544.1273 131415.3634 136842.2005 141045.2846 144904.5743 134488.5168 127012.3435 0.926931822 0.96679734 0.927250989 0.964820615 1.034666079 1.077392927 1.110484861 1.140870016 1.058861786 1 16.95460918 3.082591467 1.857514267 1.094723914 0.941791776 0.729554921 0.037265444 0.153698991 1.084518811 0.012324177 0.015409353 1209.45988 -3.082591467 -0.152932138 MEDDKVAEAAIQIFR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEDDKVAEAAIQIFR 15 1 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 ;; 138.39 9.92E-06 231507000 300000 288753 234103 264725 293963 310099 304750 329378 348045 345081 FALSE TRUE 288275.6683 280518.0472 276410.6197 278387.489 303418.5869 316369.4142 308479.6217 322576.2292 308536.3907 321708.3565 0.896077651 0.871963819 0.859196269 0.86534118 0.943147981 0.983404403 0.958879729 1.0026977 0.95905619 1 18.29539389 3.082832183 3.101280579 0.980432505 0.871719774 0.904006885 0.016523684 0.06880759 1.334744071 0.005019737 0.00608356 1210.130432 -3.082832183 -0.108712732 EAEAAMFHR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAEAAMFHR 9 0 P14618-2;H3BTN5;H3BR70 P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 163.99 6.26E-05 2615590000 2032050 2160470 1843020 2159740 1953480 1794700 2294790 1960650 2142170 2286230 FALSE TRUE 1952635.239 2098855.511 2176094.712 2271204.44 2016315.458 1830990.064 2322874.326 1920161.892 1898999.842 2131381.606 0.916135916 0.984739432 1.020978461 1.065601971 0.946013353 0.859062525 1.089844409 0.900900096 0.890971301 1 21.02335749 3.083320959 24.99978873 0.9457087 0.998731906 0.106339531 0.069439628 58.98039146 17690.2598 0.020040509 0.023952986 1211.493139 -3.083320959 0.053023206 VVIGMDVAASEFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVIGMDVAASEFFR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 149.49 1.74E-05 252277000 229440 262600 211790 187862 174979 224550 186184 162124 188628 191666 FALSE TRUE 220473.2311 255110.9051 250065.1642 197557.5803 180607.3584 229090.5549 188462.5755 158776.0827 167215.7402 178684.2911 1.233870251 1.427718707 1.399480406 1.105623662 1.010762375 1.282096783 1.054723805 0.888584451 0.935816681 1 17.44705328 3.083460597 0.584722173 0.932546463 1.391789339 0.609051021 0.113307571 0.63802036 0.46520738 0.090218808 0.149085093 1211.882731 -3.083460597 0.459242876 RQEELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQEELQR 7 1 Q9NYJ1;Q9NYJ1-2 Q9NYJ1 COA4 "Cytochrome c oxidase assembly factor 4 homolog, mitochondrial" 0 ; 194.44 0.00077278 529220000 239000 248640 180446 248060 197676 176242 225700 191856 210909 220210 FALSE TRUE 229659.6158 241549.0306 213056.6062 260862.4063 204034.4281 179805.734 228462.1841 187894.1066 186967.4945 205294.9806 1.118681105 1.176594917 1.037807187 1.270671137 0.993859799 0.875840868 1.112848368 0.915239652 0.910726088 1 17.64733883 3.08418267 8.473311648 0.963604656 1.144234939 0.552509242 0.080914649 0.19610226 17.59016631 0.022224816 0.026597275 1213.899325 -3.08418267 0.180630283 SKDAS(ph)PINRWS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.042)KDAS(0.958)PINRWS(0.906)PT(0.094)R;S(0.263)KDAS(0.737)PINRWS(0.586)PT(0.414)R 100.45 0.0087518 2689700000 2382800 2541400 1728990 1928730 2349200 2702300 2442700 2234600 2933200 2546500 TRUE FALSE 2289677.542 2468921.76 2041456.954 2028271.986 2424764.151 2756942.357 2472594.493 2188454.729 2600235.433 2374023.287 0.964471391 1.039973691 0.859914461 0.854360611 1.021373364 1.161295415 1.041520741 0.921833725 1.095286406 1 21.17890266 3.085227706 9.632445081 1.035422734 0.93280858 0.33756888 0.075881238 0.454631124 47.40231675 0.024034055 0.028747283 1216.823828 -3.085227706 -0.102614155 NLLSSWDEVIHIADQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLLSSWDEVIHIADQLR 17 0 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2R8Y6Q1;A0A2R8YFL4;A0A2R8YER9;A0A2R8Y897;A0A2R8Y6L2;A0A2R8Y809;A0A2R8Y4V6;A0A2R8Y784;A0A2R8Y4E7 Q15813-2 TBCE Tubulin-specific chaperone E 0 ; 134.37 1.72E-05 407500000 205324 238090 220424 209090 210472 189820 175005 209570 240570 252520 FALSE TRUE 197299.7111 231299.9063 260259.5201 219881.16 217242.023 193658.2905 177146.7635 205242.3063 213261.5022 235416.5955 0.838087522 0.982513173 1.105527499 0.93400875 0.922798253 0.822619536 0.752482055 0.871825989 0.905889841 1 17.8448565 3.085948409 2.629991743 0.854786869 0.97800808 0.196916102 0.085625362 0.353557343 4.964694082 0.026961006 0.03296416 1218.844801 -3.085948409 0.123221211 IEPGVDPDDTYNETPYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEPGVDPDDTYNETPYEK 18 0 Q9H4A4;A6NKB8;C9JMZ3 Q9H4A4 RNPEP Aminopeptidase B 0 ; 286.74 1.78E-39 432860000 653880 629990 627310 700360 701880 701540 807050 883120 964560 965790 FALSE TRUE 628325.6467 612023.302 740678.8714 736505.6635 724456.6076 715725.6195 816926.9193 864883.2634 855067.1926 900376.1831 0.69784792 0.679741772 0.822632679 0.817997718 0.804615472 0.794918427 0.907317335 0.960579899 0.949677711 1 19.78016837 3.086407256 0.314834504 1.024785828 0.617064211 0.867432821 0.03758074 0.963068518 0.166575681 0.05155634 0.140847612 1220.133233 -3.086407256 -0.407721617 TKEPSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKEPSTR 7 1 Q641Q2;F8W7U3;A0A0A0MR88;A0A096LPC5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A 0 ; 92.062 0.014542 69895000 91965 88803 77974 85711 90657 96208 100122 99662 107169 106360 FALSE TRUE 88370.90613 86270.42539 92065.63632 90134.55498 93573.06474 98153.39168 101347.323 97603.94487 95003.62441 99156.14246 0.891229771 0.870046204 0.928491509 0.909016353 0.943694081 0.989887154 1.022098283 0.984345926 0.958121424 1 16.59741453 3.08643512 1.576618424 0.992971772 0.893961615 0.823354921 0.019963807 0.153163834 0.786143007 0.007386912 0.009419458 1220.211518 -3.08643512 -0.099010157 SANMDHWQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SANMDHWQQR 10 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;H7C0X7 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ; 121.61 0.00051054 581880000 450200 489340 385400 463800 407840 331150 457040 403460 447020 497680 FALSE TRUE 432605.6863 475384.5023 455050.3532 487736.7736 420958.544 337846.0799 462633.3922 395128.41 396276.1637 463971.6903 0.932396729 1.024598078 0.980771807 1.051220977 0.907293597 0.728160978 0.997115561 0.851621809 0.854095566 1 18.82367726 3.086802123 6.701575129 0.877943647 0.997169905 0.312529837 0.078095903 0.234131374 14.99061614 0.021490424 0.025761553 1221.2431 -3.086802123 0.119226257 RTDDIPVWDQEFLK ddPTM_BT-474_Pertuzumab_2h_R1 4 RTDDIPVWDQEFLK 14 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;; 226.93 3.97E-12 2909440000 3968170 4056880 3418860 3738650 4026030 3957000 4363180 4483950 4395190 4403590 FALSE TRUE 3813089.529 3941181.755 4036724.054 3931602.175 4155530.911 4037013.251 4416577.902 4391354.866 3896266.457 4105330.927 0.928814168 0.960015605 0.983288345 0.957682156 1.012227999 0.98335879 1.075815319 1.069671348 0.94907488 1 21.96906709 3.088262686 1.224698295 1.03180582 0.953943555 0.327239928 0.038223737 0.458090078 1.455762704 0.015743486 0.020795705 1225.357142 -3.088262686 -0.077862266 TLTAVHDAILEDLVFPSEIVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTAVHDAILEDLVFPSEIVGK 22 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 209.9 5.14E-23 3632200000 2208400 2040000 1900890 2174120 2271430 2325240 2497290 2628920 2983100 2878500 FALSE TRUE 2122093.286 1981821.197 2244423.108 2286326.594 2344492.609 2372257.946 2527852.582 2574631.883 2644470.994 2683536.631 0.790782306 0.738510954 0.836367606 0.851982629 0.873657763 0.884004309 0.941985495 0.959417454 0.98544248 1 21.35570415 3.088406767 0.415182582 1.008672899 0.726015483 0.93276733 0.021065853 0.357977154 0.114479447 0.01988903 0.043016236 1225.763731 -3.088406767 -0.282657416 AGEAGKLEEVMQELR ddPTM_BT-474_Pertuzumab_2h_R1 7 AGEAGKLEEVMQELR 15 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;;; 202.33 5.44E-09 2747308000 3783279 3820569 2556735 2770040 3463989 3433926 3544502 3820680 3926132 3612131 FALSE TRUE 3635424.274 3711610.113 3018793.889 2913002.096 3575411.352 3503362.336 3587880.676 3741781.623 3480453.955 3367478.15 1.079568779 1.102192783 0.896455375 0.865039643 1.061747454 1.040351913 1.065450321 1.111152458 1.033549083 1 21.68323715 3.089071997 24.8694688 1.061548942 0.984699486 0.159952794 0.072393444 34.1231976 9518.339697 0.022749651 0.027191037 1227.642733 -3.089071997 -0.076849457 NTETEESLVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NTETEESLVKR 11 1 B1ANH0;B1ANG9;Q16774;Q16774-2;B1ANH2;Q16774-3;B1ANH6;B1ANH5;B1ANH3 B1ANH0 GUK1 Guanylate kinase 0 92.295 0.016198 341790000 578480 600220 493910 554360 606180 648380 641730 711830 717810 653780 FALSE TRUE 555872.3621 583102.3133 583170.524 582970.586 625678.3302 661490.6878 649583.6837 697130.4617 636327.2181 609498.8983 0.912015368 0.956691333 0.956803245 0.956475209 1.026545465 1.085302516 1.065766789 1.14377641 1.044017011 1 19.21726409 3.08931203 1.971278235 1.082950422 0.942866772 0.700705508 0.037153183 0.15987837 1.268798823 0.012049414 0.015057498 1228.321433 -3.08931203 -0.14008365 SEEDNEIES(ph)EEEVQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEDNEIESEEEVQPK 16 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;C9J7Y7 P52701 MSH6 DNA mismatch repair protein Msh6 1 SEEDNEIES(1)EEEVQPK;SEEDNEIES(1)EEEVQPK 391.63 1.78E-121 1364150000 487260 391020 458360 562500 494920 433200 661660 595010 757230 770180 TRUE FALSE 468217.3405 379868.4924 541195.8482 591530.6924 510839.5513 441959.6008 669757.593 582722.8356 671272.425 718015.0226 0.652099644 0.529053683 0.753738893 0.823841666 0.711460812 0.615529741 0.932790501 0.811574713 0.934900251 1 19.4536545 3.089415929 0.185048247 1.078454668 0.405050675 0.615731684 0.089896526 5.347725348 0.376900063 0.33312411 0.975642993 1228.615329 -3.089415929 -0.673403993 ISES(ph)VLRDS(ph)PPPHEDYEDEVFVRDPHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISESVLRDSPPPHEDYEDEVFVRDPHPK 28 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 2 IS(0.446)ES(0.59)VLRDS(0.962)PPPHEDY(0.003)EDEVFVRDPHPK 58.49 0.086307 115140000 89989 89364 58220 81923 78160 59914 61353 75128 66600 48301 TRUE FALSE 86472.13039 86815.42622 68741.6491 86151.05585 80674.08738 61125.50213 62103.85637 73576.58055 59039.84721 45029.53025 1.920342715 1.927966509 1.526590411 1.913212405 1.791581812 1.357453693 1.37918064 1.633962871 1.311136201 1 15.45858381 3.089481432 0.070046153 2.76E-10 3.320727832 0.731157405 0.155279383 32.30621751 0.724050889 12.96311557 21.07704172 1228.800648 -3.089481432 3.320727832 HYCDSEKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HYCDSEKPR 9 1 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ; 200.6 1.37E-05 907320000 1100730 1161360 969290 1043710 969750 1024610 1040400 843280 1180850 1240300 FALSE TRUE 1057712.255 1128239.15 1144462.265 1097575.998 1000942.889 1045328.316 1053132.726 825865.9733 1046804.859 1156293.376 0.91474385 0.975737795 0.989768071 0.949219308 0.865647862 0.904033818 0.910783325 0.714235669 0.90531078 1 20.14107606 3.089651597 1.416079331 0.85313897 0.964505 0.125700105 0.072793414 0.531507212 2.221550559 0.027558813 0.035706722 1229.282211 -3.089651597 0.11136603 MVDVVEKEDVNEAIR ddPTM_BT-474_Pertuzumab_2h_R1 4 MVDVVEKEDVNEAIR 15 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ;;; 186.83 3.34E-07 1272160000 1548520 1489090 1204900 1328350 1490060 1619040 1511260 1574270 1795780 1757290 FALSE TRUE 1488002.126 1446622.611 1422652.233 1396906.303 1537989.133 1651778.098 1529755.252 1541760.774 1591930.583 1638267.183 0.908278052 0.883019953 0.868388409 0.852673066 0.938790174 1.008247077 0.933764204 0.941092387 0.971716091 1 20.64373923 3.09028488 5.343468577 0.963146563 0.878278156 0.742651088 0.025581067 0.1130995 5.241107508 0.007697834 0.009253586 1231.076043 -3.09028488 -0.084868407 STSTSS(ph)PVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 STSTSSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK 41 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.065)T(0.065)S(0.065)T(0.055)S(0.128)S(0.621)PVRPAAT(0.002)FPPATHCPLGGTLDGVYPTLMEPVLLPK 207.73 8.49E-36 360430000 218760 207450 176300 188540 221960 232740 226610 251290 271370 261560 TRUE FALSE 210210.6173 201533.7291 208161.3318 198270.572 229099.545 237446.1623 229383.321 246100.7737 240565.2153 243844.3082 0.862068993 0.826485271 0.85366492 0.813103137 0.939532059 0.973761348 0.940695818 1.009253714 0.986552514 1 17.89560077 3.092447456 3.8152938 0.979905082 0.839172397 0.906359818 0.021728905 0.064141451 1.795945843 0.006631113 0.008023867 1237.221493 -3.092447456 -0.140732686 LIMVQHWPETVCEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LIMVQHWPETVCEK 14 0 D6RHI9;O00584;H0YAE9;A0A087WZM2;A0A087WWI1;O00584-2;J3QQ64 D6RHI9 RNASET2 Ribonuclease T2 0 ; 160.27 4.78E-06 591720000 951680 1013050 855090 896700 849530 865650 858050 792470 983940 961840 FALSE TRUE 914487.2935 984158.8059 1009623.784 942978.7945 876855.904 883154.0361 868551.0726 776105.2176 872247.2562 896693.7201 1.019843535 1.097541762 1.12594051 1.051617485 0.977876709 0.984900436 0.968615095 0.865518739 0.972737108 1 19.77425577 3.092742222 1.507586497 0.939408862 1.084684518 0.608134176 0.043616523 0.235831384 1.111209131 0.016340965 0.021059129 1238.06151 -3.092742222 0.145275656 HSNASQSLCEIVR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSNASQSLCEIVR 13 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PK08 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 189.09 3.67E-07 0 187600 205120 196080 213830 168870 116350 193600 147910 185060 207520 FALSE TRUE 180268.3846 199270.1784 231516.0178 224865.7919 174301.8569 118702.6767 195969.3347 144855.6068 164052.7646 193464.4856 0.931790577 1.030009089 1.196684844 1.162310443 0.900950148 0.613563137 1.012947333 0.74874521 0.84797354 1 17.56170923 3.092778528 5.655114886 0.829425932 1.083130155 0.433653822 0.127120307 0.178054326 8.76778264 0.036154224 0.043440215 1238.165013 -3.092778528 0.253704223 THTRVS(ph)VQR ddPTM_BT-474_Pertuzumab_2h_R1 8 THTRVSVQR 9 1 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 THTRVS(1)VQR;THT(0.002)RVS(0.998)VQR;THTRVS(1)VQR;THTRVS(1)VQR;THTRVS(1)VQR;THT(0.001)RVS(0.999)VQR;THT(0.001)RVS(0.999)VQR;T(0.016)HT(0.013)RVS(0.971)VQR 124.12 0.0003261 4897499000 2204556 1994727 1288098 1415932 1511956 1444156 1213045 543355 1261874 952220 TRUE FALSE 2118399.514 1937839.339 1520885.962 1489008.42 1560589.438 1473357.824 1227890.608 532134.5294 1118631.354 887725.2913 2.386323264 2.182926811 1.713239419 1.677330177 1.757964376 1.659700178 1.383187592 0.599436036 1.260109816 1 19.75975377 3.092816953 0.444815946 0.829219007 2.440197851 0.773946918 0.238421459 0.6930377 0.26128807 0.242228036 0.495440551 1238.274566 -3.092816953 1.610978844 up LEKEISK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEKEISK 7 1 A0A087X0P0;Q02224-3;Q02224 A0A087X0P0 CENPE Kinesin-like protein;Centromere-associated protein E 0 64.091 0.068854 988400000 303670 445660 318930 592040 455970 537930 876990 799150 784250 646030 FALSE TRUE 291802.2407 432950.2131 376567.7456 622595.2554 470636.6892 548807.3132 887722.866 782647.2732 695225.2278 602273.8127 0.48450096 0.718859436 0.625243432 1.033741203 0.781433094 0.911225595 1.473952291 1.29948747 1.154334147 1 19.20006001 3.09292419 0.814454734 1.261731572 0.589405847 0.638538538 0.175633822 0.38651758 0.569932371 0.099458074 0.143836058 1238.580363 -3.09292419 -0.672325725 LVDQNIFSFYLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVDQNIFSFYLSR 13 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469;F8WD96 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 85.288 0.021761 100580000 45822 61523 45531 57210 47620 46376 52160 48651 45769 62003 FALSE TRUE 44031.22558 59768.42428 53759.46453 60162.61496 49151.74055 47313.75449 52798.34968 47646.33985 40573.495 57803.48158 0.761740026 1.033993501 0.930038521 1.040812998 0.850324915 0.818527763 0.913411238 0.824281489 0.701921301 1 15.81886877 3.093668252 12.47987499 0.843707866 0.947381953 0.158494886 0.100695383 0.874522276 111.5095432 0.027597283 0.032991106 1240.704198 -3.093668252 0.103674087 SNNVEMDWVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNNVEMDWVLK 11 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;E5RGH4;H0YAQ2;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ; 121.02 0.0020644 189180000 405100 393660 309767 358389 390900 428670 384300 432300 460980 494540 FALSE TRUE 389268.2441 382433.2022 365748.7876 376885.4992 403473.6535 437338.0011 389003.1784 423372.8539 408651.483 461044.3653 0.844318407 0.829493279 0.793304973 0.817460374 0.875129779 0.948581165 0.843743482 0.918290919 0.886360432 1 18.81454606 3.093737326 3.816415599 0.908845548 0.819868744 0.561722064 0.040275965 0.173565777 4.85357928 0.011340613 0.013728942 1240.901547 -3.093737326 -0.088976804 MGLSMER ddPTM_BT-474_Pertuzumab_2h_R1 4 MGLSMER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 117.16 0.012315 732477000 813360 923110 809827 821730 768880 426692 919720 750950 717560 868940 FALSE TRUE 781572.992 896783.8066 956180.7534 864139.5838 793611.7235 435320.0046 930975.8085 735442.6201 636105.5971 810085.9198 0.964802588 1.107023076 1.180344862 1.066725841 0.979663643 0.537375103 1.149230947 0.907857552 0.785232259 1 19.62771541 3.093818077 4.550981139 0.884707561 1.087240499 0.272680316 0.155074053 0.287588214 10.54257096 0.045406356 0.054758553 1241.132297 -3.093818077 0.202532937 DEKIEELEALLQEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEKIEELEALLQEAR 15 1 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 0 ; 162.4 1.46E-06 54432000 114780 100275 106153 92147 117205 119438 119797 125960 139193 135904 FALSE TRUE 110294.2707 97415.25518 125337.2085 96902.71771 120975.0053 121853.1182 121263.1115 123358.882 123392.3942 126699.101 0.870521336 0.768870926 0.989250969 0.764825614 0.954821339 0.961752035 0.95709528 0.9736366 0.973901103 1 16.95104676 3.095048319 8.98625582 0.969269324 0.852913627 0.505801914 0.059091262 0.226743544 19.34849781 0.015836885 0.018949131 1244.653083 -3.095048319 -0.116355696 EIENEDMR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIENEDMR 8 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 99.802 0.018836 322390000 1050940 1072420 908860 1015270 1055500 1227060 1087040 1124680 1266740 1225120 FALSE TRUE 1009868.103 1041835.632 1073111.219 1067668.206 1089451.116 1251871.994 1100343.521 1101454.965 1122944.986 1142141.531 0.884188234 0.912177347 0.939560633 0.934795012 0.953867 1.096074313 0.963403826 0.964376949 0.983192499 1 20.12331001 3.095610155 3.745824612 0.995515847 0.918727836 0.510690622 0.038127838 0.214953702 5.813658494 0.012021298 0.014570392 1246.2643 -3.095610155 -0.076788011 RS(ph)SVFAAEIMDAFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSVFAAEIMDAFDR 15 1 Q9UMX3 Q9UMX3 BOK Bcl-2-related ovarian killer protein 1 RS(0.5)S(0.5)VFAAEIMDAFDR 86.546 0.004603 17927000 8882.3 10695 6088.9 8873.9 7387.8 5281 5702.9 10845 7266 5194.8 TRUE FALSE 8535.169896 10389.98907 7189.299677 9331.883042 7625.435296 5387.785438 5772.693796 10621.04696 6441.194142 4842.951569 1.762390099 2.145383641 1.484487213 1.926899931 1.57454296 1.112500375 1.191978428 2.193093779 1.330014156 1 12.24167086 3.095662666 5.599664424 1.473218911 1.825194338 0.258247151 0.34725507 0.383335969 18.36927007 0.107849952 0.129640606 1246.414997 -3.095662666 0.351975427 AKNNTVTPGGKPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKNNTVTPGGKPNK 14 2 C9K025;P18077 C9K025 RPL35A 60S ribosomal protein L35a 0 56.482 0.069972 157770000 370220 304220 248280 258080 328280 341840 320170 363450 377570 387340 FALSE TRUE 355751.3931 295543.9435 293149.719 271399.5397 338839.4243 348752.239 324088.3362 355944.6305 334709.8365 361105.1168 0.985174058 0.818442968 0.811812698 0.751580432 0.938340136 0.965791463 0.897490291 0.985709185 0.926904164 1 18.46205934 3.096142906 9.079695766 0.952100248 0.8381216 0.440747062 0.061178949 0.258483601 22.08307631 0.017506592 0.020946081 1247.794036 -3.096142906 -0.113978649 YLDESSGGWR ddPTM_BT-474_Pertuzumab_2h_R1 4 YLDESSGGWR 10 0 K7ENE5;O00115-2;O00115 K7ENE5 DNASE2 Deoxyribonuclease-2-alpha 0 ;;; 236.82 8.68E-12 656510000 1172670 1240510 1064430 1208230 1081510 931710 1147380 1144180 1144170 1252300 FALSE TRUE 1126840.76 1205131.869 1256796.179 1270586.895 1116297.751 950549.8146 1161421.98 1120552.283 1014288.618 1167480.606 0.965190132 1.032250012 1.076502833 1.088315205 0.956159568 0.814188955 0.994810513 0.959803767 0.868784127 1 20.15496715 3.09630026 6.295722015 0.929026551 1.04180588 0.440304375 0.060435924 0.200878896 11.07074812 0.017797742 0.021359941 1248.246221 -3.09630026 0.112779329 IAGEASR ddPTM_BT-474_Pertuzumab_2h_R1 7 IAGEASR 7 0 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053 Q16778;P58876 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S 0 ;;;;;; 161.89 0.0030062 21695000000 11272870 12895890 8772080 12199310 10191590 7941500 11994040 11374450 11235570 11638080 FALSE TRUE 10832313.78 12528111.84 10357389.99 12828917.85 10519411.75 8102082.571 12140826.65 11139563.63 9960155.197 10849822.48 0.998386269 1.154683579 0.954613775 1.182408088 0.9695469 0.746747939 1.118988507 1.026704691 0.918001674 1 23.3711681 3.097260828 24.65312661 0.969598305 1.070724174 0.195047538 0.10819631 23.1535696 5847.04432 0.031438416 0.037576094 1251.010133 -3.097260828 0.101125869 NFTMDTESSVYNFEGEDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 NFTMDTESSVYNFEGEDYR 19 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 97.904 0.0024236 43152000 16229 17521 16275 17068 14632 13844 11697 16467 14850 15398 FALSE TRUE 15594.75274 17021.31823 19216.25454 17948.88153 15102.65157 14123.93517 11840.15138 16126.9507 13164.29026 14355.07974 1.086357792 1.185734844 1.338637951 1.250350527 1.052077163 0.983898064 0.824805685 1.123431634 0.917047518 1 13.80927372 3.098061116 3.752042386 0.979983988 1.221624741 0.61404 0.091510635 0.160577118 4.343191373 0.028256871 0.034278547 1253.317535 -3.098061116 0.241640753 SMGTGDTPGLEVPS(ph)SPLRK ddPTM_BT-474_Pertuzumab_2h_R1 5 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.56)S(0.44)PLRK;SMGTGDT(0.278)PGLEVPS(0.474)S(0.248)PLRK;SMGTGDTPGLEVPS(0.626)S(0.373)PLRK;SMGTGDTPGLEVPS(0.598)S(0.402)PLRK;SMGTGDT(0.001)PGLEVPS(0.609)S(0.391)PLRK 146.58 5.58E-08 1050630000 1317750 1312757 1053279 1171644 1251030 1272930 1271952 1401904 1376842 1341731 TRUE FALSE 1266250.873 1275318.456 1243629.945 1232112.687 1291270.516 1298669.517 1287518.529 1372954.192 1220548.668 1250854.364 1.012308794 1.019557905 0.994224412 0.985016899 1.032310837 1.038225995 1.029311298 1.097613145 0.975772003 1 20.2544824 3.099877249 6.48566636 1.039071322 1.003497788 0.096478859 0.031343798 0.3320778 18.57024395 0.00919491 0.011033143 1258.569633 -3.099877249 -0.035573534 QSS(ph)TPSAPELGQQPDVNISEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSSTPSAPELGQQPDVNISEWK 22 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 QS(0.255)S(0.607)T(0.136)PS(0.002)APELGQQPDVNISEWK 247.74 2.81E-31 161800000 198500 181280 155790 200050 198210 219450 229290 267380 247650 220140 TRUE FALSE 190742.4005 176110.0719 183944.7185 210374.6045 204585.6047 223887.4294 232096.1196 261858.5096 219537.8102 205229.7217 0.929409244 0.858111927 0.896286936 1.025068897 0.996861483 1.090911333 1.130908904 1.275928785 1.069717429 1 17.64688015 3.100029876 1.056079909 1.154219136 0.88909069 0.588758309 0.074632886 0.30177013 0.727623972 0.033387418 0.045812035 1259.01202 -3.100029876 -0.265128446 MLSCAGADR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLSCAGADR 9 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;A6QRI9;B8A6G2;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ; 109.48 0.0056825 305340000 434340 486820 410370 425590 419200 350250 472380 378080 450690 445810 FALSE TRUE 417365.5126 472936.3702 484532.9876 447554.7509 432683.9487 357332.295 478161.1277 370272.5159 399529.5606 415614.8916 1.004212123 1.137919694 1.165822008 1.076849651 1.041069407 0.859767785 1.150490845 0.890902909 0.961297511 1 18.66488782 3.101097922 3.304642277 0.972811855 1.105049663 0.327519703 0.082629113 0.264507028 5.730309887 0.024083014 0.029379747 1262.112075 -3.101097922 0.132237808 VVPS(ph)PLQFCAATPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVPSPLQFCAATPK 14 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 VVPS(1)PLQFCAATPK 108.41 0.0018007 0 78844 81977 64513 66426 77479 84418 82010 78061 81648 86703 TRUE FALSE 75762.68931 79639.09622 76171.93418 69854.25382 79971.1824 86124.9898 83013.66291 76449.01307 72379.66134 80830.52858 0.937302906 0.985260119 0.942365905 0.864206322 0.989368544 1.065500762 1.027008785 0.945793804 0.895449561 1 16.30261266 3.101623282 21.79533138 0.988202943 0.935533366 0.218931519 0.050630088 8.620964398 1827.912663 0.015954599 0.019069395 1263.639758 -3.101623282 -0.052669577 QKEIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKEIPR 6 1 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 105.12 0.030325 257160000 335980 419440 305350 341050 397160 452090 397490 448750 468590 487800 FALSE TRUE 322849.5302 407477.9819 360533.5375 358651.6314 409935.0121 461231.5696 402354.6015 439483.1557 415397.6277 454760.8715 0.709932517 0.896026917 0.792798062 0.788659829 0.901429823 1.014228792 0.88476082 0.966404946 0.913441885 1 18.7947486 3.101633286 4.215397242 0.949703695 0.804064494 0.646734216 0.055167635 0.138060741 4.456275436 0.015269649 0.018483711 1263.668868 -3.101633286 -0.1456392 EIESEIDSEEELINK ddPTM_BT-474_Pertuzumab_2h_R1 3 EIESEIDSEEELINK 15 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 336.79 9.88E-69 144064000 356250 330460 288317 326735 352490 405562 368315 400730 435820 425200 FALSE TRUE 342327.3561 321035.6044 340422.2955 343597.8325 363828.161 413762.7415 372822.5491 392454.7855 386347.5407 396400.8253 0.863588909 0.809876226 0.858783014 0.866793938 0.91782897 1.04379889 0.940519104 0.990045329 0.974638588 1 18.59660044 3.101719652 2.659182704 0.98533379 0.844942922 0.83878163 0.028813807 0.098016126 1.406326589 0.008536519 0.010525162 1263.920191 -3.101719652 -0.140390868 APS(ph)PRPGPGPLR ddPTM_BT-474_Pertuzumab_2h_R1 7 APSPRPGPGPLR 12 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR 91.076 0.0051484 8038300000 1557608 2144250 1388355 2158280 1374574 1428710 1394220 1450367 1255152 1441500 TRUE FALSE 1496734.957 2083098.089 1639261.632 2269669.089 1418788.421 1457599.495 1411282.881 1420416.415 1112672.407 1343865.921 1.113753191 1.550078811 1.219810404 1.68891037 1.05575147 1.084631638 1.050166434 1.056962895 0.827963854 1 20.35795778 3.101731406 9.727671669 1.020881574 1.391603184 0.568720238 0.162525563 0.213774127 18.7565723 0.043593656 0.052144427 1263.9544 -3.101731406 0.37072161 RVPPPALS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 RVPPPALSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RVPPPALS(1)R;RVPPPALS(1)R 80.17 0.015233 517070000 116972 145021 128590 131922 115539 110462 115402 108299 108457 142306 TRUE FALSE 112400.6049 140885.1431 151829.0735 138730.5102 119255.4169 112695.6173 116814.3242 106062.5878 96145.41605 132667.4879 0.847235496 1.061941741 1.144433168 1.045700891 0.898904613 0.849459194 0.880504531 0.799461794 0.724709705 1 17.01745533 3.101806704 3.290354108 0.839620419 1.036343118 0.422850914 0.095308009 0.213805905 4.594460394 0.028897742 0.035270918 1264.173563 -3.101806704 0.196722699 YGMGTS(ph)VER ddPTM_BT-474_Pertuzumab_2h_R1 1 YGMGTSVER 9 0 P08559-3;P08559;P08559-2;P08559-4 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 1 YGMGT(0.032)S(0.968)VER 66.19 0.067586 292670000 770100 996690 593710 1288800 541790 553420 651610 703440 471360 227060 TRUE FALSE 740003.6406 968265.3771 701006.604 1355315.122 559217.1674 564610.5316 659584.5981 688913.7182 417853.1889 211681.024 3.49584307 4.574171832 3.311617598 6.402629282 2.641791678 2.66727041 3.115936354 3.254489728 1.97397566 1 17.69153242 3.102341522 23.66755376 2.655682137 4.392797441 0.487719419 0.991098441 7.118274797 1631.022989 0.271316228 0.324285124 1265.731307 -3.102341522 1.737115305 EHALTSGTIK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHALTSGTIK 10 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 135.86 0.00013302 399450000 646130 589160 505110 606890 541200 510990 591200 509770 613560 701420 FALSE TRUE 620878.5253 572357.7336 596394.6131 638211.6656 558608.1895 521322.5679 598435.2824 499243.0714 543911.2411 653912.1986 0.949483014 0.875282239 0.912040813 0.975989845 0.854255649 0.79723634 0.915161521 0.763471109 0.831780233 1 19.31873741 3.102473616 8.001227732 0.842851328 0.923035103 0.172482173 0.066590722 0.330038903 23.08246975 0.018296131 0.021908817 1266.116347 -3.102473616 0.080183775 ASLENSLR ddPTM_BT-474_Pertuzumab_2h_R1 8 ASLENSLR 8 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 251.94 1.46E-12 14217500000 6640790 7504500 6093560 6634010 6214340 4647630 6916060 6114830 6472000 6950010 FALSE TRUE 6381260.585 7290479.008 7194801.843 6976392.051 6414229.89 4741608.263 7000700.811 5988556.624 5737325.693 6479279.632 0.984871922 1.125199007 1.110432371 1.076723409 0.989960343 0.731811024 1.080475178 0.924262721 0.885488205 1 22.62740199 3.10253807 4.445262858 0.927176026 1.079757187 0.37657303 0.090202687 0.220439901 7.662565157 0.025949322 0.031373639 1266.304268 -3.10253807 0.152581161 KTIQGDEEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTIQGDEEDLR 11 1 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 77.078 0.053876 307930000 764570 821240 708200 723310 845190 872820 887970 942820 997740 966150 FALSE TRUE 734689.7591 797819.0393 836187.4938 760640.1158 872376.3039 890469.0184 898837.2425 923350.4375 884480.7381 900711.7999 0.815676845 0.885765058 0.928362983 0.844487788 0.968540996 0.988628126 0.997918804 1.025134163 0.981979739 1 19.78070604 3.102659318 4.211964534 1.000526081 0.874309794 0.814038492 0.029458735 0.09304937 2.995218939 0.008913381 0.010792815 1266.657847 -3.102659318 -0.126216287 TVEQHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVEQHLR 7 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 ; 127.31 0.0038676 130222000 278480 306410 254760 283000 269240 241980 305150 266970 297950 302760 FALSE TRUE 267596.6937 297671.4868 300800.7991 297605.6639 277900.3491 246873.0014 308884.517 261456.9762 264127.9651 282253.7955 0.948071197 1.054623504 1.065710378 1.054390299 0.984576128 0.874649005 1.094350269 0.926318726 0.935781801 1 18.10663346 3.103003383 5.803291482 0.965803148 1.034406248 0.196508131 0.061441766 0.320506147 15.53628467 0.017484559 0.021018799 1267.661742 -3.103003383 0.068603101 IAWTHITIPESLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IAWTHITIPESLR 13 0 E9PP67;E9PQ25;F2Z2Y8;E7EN89;Q9H0E2-2;Q9H0E2 E9PP67 TOLLIP Toll-interacting protein 0 107.39 0.0012991 250080000 158790 185060 157250 166420 156280 111030 190270 148100 165260 179380 FALSE TRUE 152584.3112 179782.27 185668.573 175008.9561 161306.8881 113275.1027 192598.5812 145041.6832 146500.3776 167230.4328 0.91241952 1.075057135 1.11025589 1.046513802 0.964578548 0.677359382 1.151695764 0.867316318 0.876038979 1 17.35147789 3.103468486 4.979294061 0.91401511 1.043089935 0.180015847 0.121082998 0.338357504 13.62854947 0.03452303 0.041630709 1269.020057 -3.103468486 0.129074825 IKVEELENER ddPTM_BT-474_Pertuzumab_2h_R1 1 IKVEELENER 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;E9PIK8;E9PJA0;A0A3B3IS15 E9PP16 PPFIBP2 Liprin-beta-2 0 110.31 0.0027872 0 168810 178060 143760 175060 197920 163230 207380 236590 227030 197090 FALSE TRUE 162212.7186 172981.9031 169740.6299 184094.8676 204286.2765 166530.6224 209917.9785 231704.3338 201258.5062 183740.9188 0.882833936 0.94144464 0.923804186 1.001926347 1.111816997 0.906333894 1.14246723 1.261038289 1.095338521 1 17.48731342 3.103779647 0.73905028 1.146877795 0.899306816 0.40464271 0.089531748 0.632468993 0.767359764 0.056729158 0.085904405 1269.929603 -3.103779647 -0.247570979 THTYECR ddPTM_BT-474_Pertuzumab_2h_R1 1 THTYECR 7 0 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 111.65 0.0065316 34153000 34234 34377 34421 31675 26328 12207 30769 10704 26439 33059 FALSE TRUE 32896.09743 33396.60162 40641.64039 33309.75055 27174.86403 12453.8339 31145.56023 10482.95866 23437.75556 30819.88448 1.06736602 1.083605671 1.318682437 1.080787651 0.881731534 0.40408438 1.010567066 0.340136209 0.760475127 1 14.91157383 3.104017185 3.134808409 0.65982832 1.150730617 0.466419503 0.215559381 0.188240913 3.699442088 0.062046938 0.075964929 1270.624383 -3.104017185 0.490902298 YHYLGGR ddPTM_BT-474_Pertuzumab_2h_R1 6 YHYLGGR 7 0 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ;;;;; 149.11 0.0094673 551190000 2010350 2296190 1797540 1821210 1526070 1239320 1302360 792593 1716390 1772520 FALSE TRUE 1931783.299 2230704.909 2122395.464 1915202.866 1575157.427 1264379.9 1318298.671 776225.6776 1521552.603 1652465.642 1.169030841 1.349925138 1.284380994 1.158997088 0.953216447 0.765147467 0.797776751 0.469737862 0.920777149 1 20.65618884 3.104113874 1.627969877 0.727099179 1.277838151 0.686705371 0.141728002 0.182012828 0.995413268 0.04920895 0.063407366 1270.907298 -3.104113874 0.550738972 ELGGLGMLSMGHVLIPQSDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELGGLGMLSMGHVLIPQSDLR 21 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 183.45 4.31E-17 520780000 492050 625980 441830 523480 512160 476390 589170 522270 573810 542950 FALSE TRUE 472820.142 608127.6633 521678.5095 550496.8655 528634.0915 486022.9322 596380.4387 511484.942 508673.4944 506175.5129 0.934103152 1.201416599 1.03062771 1.087561234 1.044369153 0.960186575 1.17820879 1.010489305 1.004935011 1 18.94927819 3.104707353 7.347501091 1.038095862 1.070745041 0.027489165 0.081643902 0.935381921 58.68970607 0.022487939 0.026949516 1272.645227 -3.104707353 0.032649179 YAEAVTR ddPTM_BT-474_Pertuzumab_2h_R1 4 YAEAVTR 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 130.04 0.0083798 5465700000 3320760 3730140 2228640 3430440 2496000 2309080 2425580 2497860 2758540 2326000 FALSE TRUE 3190981.028 3623760.059 2631404.824 3607485.42 2576286.107 2355771.18 2455264.974 2446278.318 2445402.104 2168457.948 1.471543882 1.67112305 1.213491286 1.663617882 1.188072893 1.086380846 1.132263125 1.128118864 1.127714792 1 21.04823804 3.105568826 5.974312726 1.110814539 1.494420733 0.710640008 0.124106352 0.110817449 5.503298865 0.033675196 0.040469569 1275.172169 -3.105568826 0.383606193 HYTEAIK ddPTM_BT-474_Pertuzumab_2h_R1 5 HYTEAIK 7 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 146.21 0.0022347 2736200000 4426590 4928630 4729980 4374560 4353640 3262400 4730390 3427220 4764430 5174190 FALSE TRUE 4253593.969 4788070.298 5584792.604 4600331.566 4493678.784 3328367.963 4788281.928 3356446.709 4223591.881 4823737.503 0.88180461 0.992605899 1.15777291 0.953686133 0.931576144 0.689997738 0.992649771 0.69581869 0.875584934 1 22.20171997 3.105768851 3.024787119 0.831637582 1.009841471 0.240407215 0.117339696 0.29203479 5.367197232 0.034344505 0.042154361 1275.759617 -3.105768851 0.178203889 LPIVNEDDELVAIIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LPIVNEDDELVAIIAR 16 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;; 178.32 6.53E-09 80612000 13751.4 13088.3 13453.5 12948.1 15916 18719.9 16771.7 17710.1 20480.8 18449.5 FALSE TRUE 13213.98009 12715.0345 15884.84672 13616.35299 16427.95259 19098.4292 16976.95708 17344.38025 18155.90545 17199.89893 0.76825917 0.739250536 0.923543027 0.791653082 0.955119135 1.110380316 0.987038188 1.008400126 1.055582101 1 14.07011247 3.106897931 3.859931613 1.027754785 0.809205015 0.786311846 0.055627875 0.103854143 2.915995488 0.016676287 0.020275083 1279.080655 -3.106897931 -0.21854977 FAIGS(ph)AR ddPTM_BT-474_Pertuzumab_2h_R1 1 FAIGSAR 7 0 O96017-13;O96017-4;O96017-12;O96017;O96017-9;B7ZBF2;A0A087X102;H0Y4V6;B7ZBF7;B7ZBF6;O96017-8;O96017-7 O96017-13 CHEK2 Serine/threonine-protein kinase Chk2 1 FAIGS(1)AR 71.501 0.056795 53939000 73341 67531 60193 60078 55534 55289 49245 58361 52925 49267 TRUE FALSE 70474.75264 65605.082 71071.21409 63178.63278 57320.30154 56406.98146 49847.67504 57155.82496 46917.17588 45930.10221 1.534391374 1.428367864 1.54737766 1.375538693 1.247989854 1.228104854 1.085294233 1.244408834 1.021490779 1 15.48715237 3.107004623 0.426933835 1.023061915 1.61341912 0.869517752 0.068031947 0.550745105 0.187282344 0.065708163 0.141167218 1279.394922 -3.107004623 0.590357206 HDFSFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HDFSFDR 7 0 Q9BW19 Q9BW19 KIFC1 Kinesin-like protein KIFC1 0 132.08 0.0034032 120050000 131550 128850 102800 113420 96382 67013 119610 55948 87499 98749 FALSE TRUE 126408.8806 125175.3242 121378.2468 119273.6198 99482.21456 68368.04877 121073.823 54792.65425 77566.48035 92060.64227 1.373104482 1.359705093 1.3184597 1.295598389 1.080616125 0.742641449 1.315152925 0.595180013 0.84255854 1 16.49029689 3.107329105 2.454589931 0.883923667 1.346907237 0.57684976 0.176105918 0.198618641 2.435188124 0.054784758 0.068103583 1280.351176 -3.107329105 0.462983569 GS(ph)LAS(ph)LDSLR ddPTM_BT-474_Pertuzumab_2h_R1 6 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 2 GS(1)LAS(1)LDSLR;GS(1)LAS(1)LDSLR;GS(1)LAS(1)LDSLR;GS(1)LAS(0.999)LDS(0.001)LR;GS(1)LAS(0.999)LDS(0.001)LR;GS(1)LAS(1)LDSLR 136.01 0.00018848 2885870000 3190210 3735750 2964910 2941860 2649210 2518910 1817810 3004110 2183900 1945550 TRUE FALSE 3065533.066 3629210.068 3500735.191 3093689.747 2734424.246 2569844.086 1840056.903 2942074.079 1935992.828 1813776.166 1.690138576 2.00091397 1.930081152 1.705662367 1.507586381 1.416847423 1.014489515 1.622071198 1.067382439 1 20.790565 3.107633732 1.396606285 1.260223153 1.889767827 0.693649843 0.192442748 0.242177097 0.986956532 0.070066698 0.092444322 1281.249567 -3.107633732 0.629544674 GFFNIYHPLDPVAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFFNIYHPLDPVAYR 15 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 69.594 0.049195 255380000 179720 200220 161560 180970 164860 130260 185360 160920 173000 185980 FALSE TRUE 172696.3437 194509.9216 190757.4859 190309.8834 170162.8716 132893.9464 187628.4911 157596.9458 153361.7653 173383.4089 0.996037307 1.121848525 1.10020611 1.097624534 0.981425343 0.766474412 1.082159431 0.908950555 0.884523878 1 17.40360633 3.108748305 4.747760508 0.929348255 1.082720465 0.426599966 0.082018956 0.193863193 7.278614773 0.023265755 0.028114438 1284.541988 -3.108748305 0.15337221 LQLNGNLQLELAQVLAQERPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQLNGNLQLELAQVLAQERPK 21 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 382.44 2.51E-114 1712250000 1191200 1128880 1068750 1151590 1237560 1394490 1473870 1411160 1679960 1602590 FALSE TRUE 1144646.587 1096685.448 1261896.899 1211023.698 1277367.241 1422687.543 1491907.662 1382019.053 1489257.984 1494045.152 0.76613922 0.734037687 0.844617646 0.810567001 0.854972314 0.952238653 0.998569327 0.925018264 0.996795834 1 20.51079232 3.109143869 0.820769258 0.982942973 0.754517089 0.883663636 0.032290383 0.208002017 0.31108358 0.018029204 0.026554467 1285.712507 -3.109143869 -0.228425884 LLWHGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLWHGSR 7 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 128.57 0.0037452 1216560000 1011960 1646730 1355960 1783120 1102290 936600 1238330 1048450 1041530 1721020 FALSE TRUE 972411.4844 1599766.873 1601012.135 1875147.037 1137746.159 955538.6937 1253485.053 1026799.141 923299.8809 1604453.782 0.606070112 0.997078813 0.997854941 1.16871365 0.70911744 0.595553891 0.78125345 0.639968039 0.575460565 1 20.6136508 3.109180617 10.82892917 0.692704573 0.950109542 0.284068049 0.172883059 0.394458313 36.73107526 0.048349884 0.057815009 1285.821304 -3.109180617 0.257404969 SS(ph)IEDAQCPGLPDLIEENHVVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSIEDAQCPGLPDLIEENHVVNK 23 0 Q15398-1;Q15398;Q15398-3 Q15398-1 DLGAP5 Disks large-associated protein 5 1 S(0.178)S(0.822)IEDAQCPGLPDLIEENHVVNK 281.11 3.74E-52 297980000 107270 84209 82047 88715 99005 109730 99211 112150 113830 129560 TRUE FALSE 103077.7698 81807.44177 96874.71803 93293.59178 102189.5857 111948.8158 100425.1739 109834.0633 100908.4956 120784.7858 0.853400278 0.677299225 0.802044044 0.772395225 0.846046835 0.926845339 0.831438937 0.909336905 0.835440448 1 16.88207922 3.109264651 3.100503161 0.890690889 0.76997697 0.476204399 0.060745772 0.211634388 4.070902281 0.017048329 0.020936792 1286.070127 -3.109264651 -0.120713919 ANHPMDAEVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ANHPMDAEVTK 11 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 111.79 0.0016125 210500000 601360 599800 517360 561730 566530 561960 606520 547680 668390 666280 FALSE TRUE 577858.1864 582694.2913 610858.4606 590720.9526 584752.952 573323.2162 613942.7732 536370.2166 592517.1693 621152.2621 0.930300381 0.938086081 0.983427893 0.951008293 0.941400342 0.922999482 0.988393363 0.863508433 0.953900043 1 19.24458743 3.109806707 3.943158374 0.934668085 0.952097978 0 0.037925393 0.870606847 25.21122092 0.011232821 0.013659511 1287.676313 -3.109806707 0.017429893 FVLCPECENPETDLHVNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVLCPECENPETDLHVNPK 19 0 P55010;H0YLZ1;H0YN40 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 244.86 1.53E-24 597090000 461260 460390 367690 430980 451960 477940 470130 493380 544910 548440 FALSE TRUE 443233.4493 447260.128 434139.7622 453222.9294 466497.7039 487604.2743 475883.5916 483191.5306 483054.1012 511293.6703 0.866886244 0.874761715 0.8491006 0.8864239 0.912387012 0.953667731 0.930744148 0.945037184 0.944768397 1 18.96379264 3.109889285 1.679289812 0.950076134 0.864258638 0.825950541 0.018581546 0.14108036 0.819848871 0.006014573 0.007756039 1287.921179 -3.109889285 -0.085817496 DPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.457)T(0.457)S(0.085)EGLEDAVHS(0.001)R;DPTSLLGVLQAEADS(0.333)T(0.333)S(0.333)EGLEDAVHS(0.001)R;DPTSLLGVLQAEADS(0.976)T(0.021)S(0.003)EGLEDAVHSR 159.75 9.36E-12 186491000 39677.8 41262 36324.2 40865.6 36196 34493.7 31651.7 40796.1 42236 39580.7 TRUE FALSE 38127.14771 40085.24816 42888.79097 42974.67851 37360.27721 35191.18625 32039.06297 39953.64628 37441.54635 36899.86393 1.033259846 1.086325094 1.162302144 1.164629728 1.012477371 0.953694201 0.868270491 1.082758634 1.014679794 1 15.17132788 3.109905676 5.97332342 0.986795176 1.112854456 0.495131136 0.061288779 0.192617368 9.446599956 0.019224488 0.023110003 1287.969787 -3.109905676 0.12605928 DIDAFWLQR ddPTM_BT-474_Pertuzumab_2h_R1 5 DIDAFWLQR 9 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;; 164.53 0.00014467 1240423000 776097 857720 740125 842800 750992 624122 806500 802815 853250 937390 FALSE TRUE 745766.2712 833258.6654 873882.0515 886297.009 775148.3397 636742.1745 816370.1883 786236.5897 756392.6371 873899.7404 0.85337738 0.953494579 0.999979759 1.014186145 0.886999165 0.72862154 0.934169162 0.899687405 0.865537089 1 19.73710825 3.110134344 8.689943653 0.877621197 0.958106044 0.164578234 0.075434501 0.421792786 30.89926322 0.021962215 0.026285779 1288.648119 -3.110134344 0.080484847 ATSSSNPSS(ph)PAPDWYKDFVTDADAEVLEHSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 ATSSSNPS(0.021)S(0.979)PAPDWYKDFVTDADAEVLEHSGK 230.26 8.34E-37 78927000 111590 103010 95025 84861 112830 118870 112070 108780 143370 136020 TRUE FALSE 107228.9394 100072.2557 112198.1313 89240.68638 116459.2794 121273.6328 113441.5462 106533.655 127095.2387 126807.2442 0.845605786 0.789168286 0.884792758 0.703750696 0.918396107 0.956362025 0.894598308 0.840122783 1.00227112 1 16.95227764 3.111054865 16.86798646 0.919850592 0.810282637 0.490987841 0.063355131 1.115402993 163.571359 0.018004718 0.021520162 1291.382405 -3.111054865 -0.109567956 AEYLHGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEYLHGK 7 0 Q5JR04;Q9HCE1;Q9HCE1-2 Q5JR04 MOV10 Putative helicase MOV-10 0 69.344 0.059993 108150000 241110 268310 215760 245750 259560 278960 294290 292210 318190 289020 FALSE TRUE 231687.1546 260658.0615 254752.6316 258433.187 267908.9831 284600.7623 297891.6091 286175.7614 282070.4052 269444.418 0.859869937 0.967390839 0.945473777 0.959133572 0.994301478 1.056250356 1.105577214 1.062095714 1.046859339 1 18.03962817 3.111625874 1.460321527 1.063812503 0.92671924 0.719957417 0.035788632 0.197844484 0.878156718 0.012673605 0.016671898 1293.081428 -3.111625874 -0.137093262 AQELGHSQSALASAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQELGHSQSALASAQR 16 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 228.9 3.68E-15 469450000 281860 293290 248107 264190 259123 233653 280640 247825 266336 288430 FALSE TRUE 270844.5996 284925.6564 292945.454 277824.8776 267457.9266 238377.6237 284074.5563 242707.3271 236102.6539 268894.3792 1.007252738 1.059619235 1.08944432 1.033211919 0.99465793 0.886510252 1.056454051 0.902612126 0.878049792 1 18.03668007 3.111809693 2.955260032 0.94465525 1.052618378 0.442750558 0.05399166 0.231295183 4.065698451 0.016279294 0.02006629 1293.628852 -3.111809693 0.107963128 SRWDETPASQMGGST(ph)PVLTPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRWDETPASQMGGSTPVLTPGK 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 SRWDETPASQMGGS(0.146)T(0.854)PVLTPGK;SRWDETPASQMGGS(0.03)T(0.97)PVLTPGK 218 1.97E-25 1185480000 1113110 1133280 802960 958370 1071750 1110980 1045620 1208490 1324820 1165900 TRUE FALSE 1069608.431 1100959.964 948072.7337 1007831.591 1106223.812 1133444.777 1058416.61 1183534.259 1174431.988 1086932.555 0.984061455 1.012905501 0.872246148 0.927225508 1.017748348 1.042792188 0.973764753 1.088875528 1.080501254 1 20.05183099 3.111867336 4.70949989 1.040190418 0.948538019 0.44489458 0.046678411 0.202086204 7.480470565 0.014458643 0.017485976 1293.800563 -3.111867336 -0.091652399 GLDHDFGPSR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLDHDFGPSR 10 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ;;;; 155.15 1.32E-05 1242102000 580511 704317 572118 648172 559004 425925 672236 542745 554228 656518 FALSE TRUE 557823.9883 684230.5688 675512.4493 681624.2346 576984.8713 434537.4953 680463.0253 531537.1261 491314.361 612051.4511 0.911400483 1.11792982 1.103685725 1.113671462 0.942706484 0.7099689 1.111774221 0.868451705 0.802733757 1 19.22329341 3.113158028 5.623152995 0.899251945 1.067676928 0.310183341 0.114919813 0.24413589 11.13113967 0.032693455 0.03935954 1297.651364 -3.113158028 0.168424983 RPMSS(ph)PEMK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPMSSPEMK 9 1 P51610-2;P51610;A6NEM2;P51610-4;H7C1C4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 RPMS(0.285)S(0.715)PEMK;RPMS(0.194)S(0.806)PEMK;RPMS(0.263)S(0.737)PEMK;RPMS(0.076)S(0.924)PEMK 109.16 0.0015279 2168610000 2336330 2203110 1972300 2206700 2310360 2218580 2531830 2626280 2619450 2730820 TRUE FALSE 2245023.641 2140279.46 2328738.484 2320588.051 2384674.828 2263441.208 2562815.293 2572046.4 2322101.018 2545859.129 0.881833411 0.840690451 0.914716159 0.911514712 0.936687659 0.889067734 1.006660291 1.010286222 0.912108997 1 21.27972116 3.114183726 0.56454935 0.990992238 0.855426924 0.540036495 0.037229244 0.742120416 0.496235694 0.029172777 0.051081133 1300.719726 -3.114183726 -0.135565314 RDHRPPCAQEAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDHRPPCAQEAPR 13 2 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ; 157.33 2.68E-05 74964000 49913 51954 45940 45699 44461 31117.6 43201 35292.1 54179 56990 FALSE TRUE 47962.34478 50472.32279 54242.37993 48057.53087 45891.12844 31746.81919 43729.70676 34563.3058 48028.82706 53130.01654 0.902735363 0.949977547 1.020936628 0.904526932 0.863751443 0.597530761 0.8230697 0.650541973 0.903986676 1 15.69723954 3.114194494 3.175043824 0.763828062 0.952572228 0.24871212 0.114154429 0.255637596 5.132886255 0.032533191 0.040002525 1300.751974 -3.114194494 0.188744166 LVEEHLDSEIQKLDQMDEDELER ddPTM_BT-474_Pertuzumab_2h_R1 4 LVEEHLDSEIQKLDQMDEDELER 23 1 F8WCJ3;B8ZZX4;O14530-2;O14530;F8WBV5;G3XAJ4 F8WCJ3 TXNDC9 Thioredoxin domain-containing protein 9 0 ;;; 257.86 7.59E-44 253745000 225336 219470 184463 196621 218960 230282 225086 220089 272242 252197 FALSE TRUE 216529.62 213210.9305 217799.5675 206768.6334 226003.0473 234938.4598 227840.6698 215544.0852 241338.2295 235115.4726 0.920950109 0.906834961 0.926351486 0.879434395 0.961242766 0.999247124 0.969058596 0.916758403 1.026466812 1 17.84300996 3.114216421 6.624545003 0.971942645 0.909819223 0.567868097 0.02984255 0.18586606 10.10422983 0.008933487 0.010722695 1300.817651 -3.114216421 -0.062123422 HPELNISEEGITK ddPTM_BT-474_Pertuzumab_2h_R1 1 HPELNISEEGITK 13 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 103.21 0.0016283 217440000 210730 191410 180520 181340 204850 206110 225910 198540 253010 244730 FALSE TRUE 202494.4386 185951.1742 213143.9796 190698.9791 211439.1863 210277.6854 228674.7542 194440.0796 224289.3655 228154.2191 0.887533176 0.815024044 0.934210117 0.835833674 0.926738007 0.921647148 1.002281505 0.852230918 0.983060346 1 17.79964981 3.114435101 6.308468548 0.938024977 0.869307828 0.359082085 0.051246599 0.266104383 13.72899164 0.014338483 0.017224082 1301.472814 -3.114435101 -0.068717149 SVVLMSHLGRPDGVPMPDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVVLMSHLGRPDGVPMPDK 19 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 124.35 1.77E-05 4246600000 2500600 2449500 1940500 2346900 1962100 1634600 1763100 1916900 2596000 2090000 FALSE TRUE 2402873.787 2379642.658 2291191.516 2468023.79 2025212.728 1667652.732 1784677.345 1877315.345 2301312.963 1948442.438 1.233228008 1.221305085 1.175909265 1.266664974 1.039400851 0.855890171 0.915950767 0.96349541 1.1811039 1 20.89388988 3.114811995 4.764928426 0.971770785 1.219683066 0.66254071 0.081366941 0.126017224 4.721813482 0.024438148 0.029559875 1302.602762 -3.114811995 0.247912281 ALPLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALPLSPR 7 0 J3KTI7;J3QR52;J3QLN7;Q99741 J3KTI7 CDC6 Cell division control protein 6 homolog 1 ALPLS(1)PR;ALPLS(1)PR;ALPLS(1)PR;ALPLS(1)PR 109.11 0.0074496 748310000 988860 1192390 831270 1007840 874240 771860 975680 854870 761230 917640 TRUE FALSE 950214.258 1158384.205 981498.9805 1059854.743 902360.7236 787467.538 987620.6637 837216.6358 674818.3617 855487.4255 1.110728492 1.354063391 1.147297963 1.238889914 1.054791335 0.920489904 1.154453747 0.978642831 0.78881155 1 19.70638712 3.114913856 3.834286448 0.983587192 1.218422497 0.549505294 0.103686791 0.177451975 4.908553675 0.030493458 0.037184881 1302.908316 -3.114913856 0.234835305 ACGNFGIPCELR ddPTM_BT-474_Pertuzumab_2h_R1 4 ACGNFGIPCELR 12 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 145.46 0.00014868 826720000 750640 801310 664410 711810 696290 542141 731080 709940 756380 795900 FALSE TRUE 721304.1589 778457.4234 784483.6667 748546.5994 718686.8002 553103.4625 740027.1757 695279.4909 670518.9134 741992.9841 0.972117223 1.049143914 1.057265612 1.008832449 0.968589752 0.745429505 0.997350638 0.937043214 0.903672848 1 19.50104602 3.115819357 4.0812766 0.916550815 1.026282059 0.329691896 0.0697561 0.249237678 7.573355904 0.020478042 0.024914873 1305.627704 -3.115819357 0.109731244 ACQSIYPLHDVFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ACQSIYPLHDVFVR 14 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ; 142.1 9.49E-06 8139200000 4697900 4911400 4658800 4206800 4287000 4082800 4164600 4140100 4301000 4240700 FALSE TRUE 4514300.874 4771331.681 5500748.794 4423913.452 4424895.248 4165357.013 4215567.621 4054605.488 3812768.511 3953473.612 1.141856837 1.206870755 1.391371066 1.118994051 1.119242389 1.053594237 1.066294614 1.025580511 0.964409753 1 21.91468936 3.117527122 1.456130741 1.022436515 1.239240067 0.64998938 0.068799696 0.251342374 1.109868408 0.025371335 0.033562955 1310.7719 -3.117527122 0.216803552 ILQDSNDS(ph)PLAEREPGEVIDSLVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILQDSNDSPLAEREPGEVIDSLVGK 25 1 A0A1W2PR54;Q5JUX0 A0A1W2PR54 SPIN3 Spindlin-3 1 ILQDS(0.001)NDS(0.999)PLAEREPGEVIDSLVGK;ILQDSNDS(1)PLAEREPGEVIDSLVGK 205.58 2.52E-25 80663000 143877 139955 108033 119450 116492 125389 99647 117711 116103 101724 TRUE FALSE 138254.1278 135963.6204 127556.9663 125614.8288 120239.071 127924.4515 100866.5098 115280.2267 102923.4742 94834.14287 1.45785182 1.433699049 1.345053189 1.324573882 1.267887992 1.348928219 1.063609653 1.215598341 1.085299778 1 16.53311894 3.118604852 0.241639679 0.960075546 1.630095352 0.839518073 0.060359592 1.643010121 0.171367296 0.107421806 0.33913013 1314.028704 -3.118604852 0.670019806 HNKPEVEVR ddPTM_BT-474_Pertuzumab_2h_R1 6 HNKPEVEVR 9 1 F8WCF6;P59998;P59998-3;F8WDD7;H7C0A3;A0A0A6YYG9;P59998-2;F8WE39 F8WCF6 ARPC4-TTLL3;ARPC4 Actin-related protein 2/3 complex subunit 4 0 ;;;;; 154.24 4.58E-05 5737980000 13151160 12912010 10870300 11595090 11554140 9957080 12688360 9215480 13842630 13322140 FALSE TRUE 12637198.13 12543772.12 12834805.02 12193513.98 11925789.41 10158418.98 12843643.95 9025177.118 12271272.68 12419819.59 1.017502552 1.009980219 1.033413161 0.981778672 0.960222435 0.817920011 1.03412484 0.72667538 0.988039527 1 23.56614088 3.119164712 2.422463015 0.892256694 1.01590059 0.195166309 0.087018445 0.359364597 4.296099175 0.026237607 0.032877923 1315.723742 -3.119164712 0.123643896 VLAEDEELYGDFEDLETGDVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLAEDEELYGDFEDLETGDVHK 22 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 190.83 1.64E-17 56934000 72613 64847 55727 59200 69289 70254 71873 76789 78763 81055 FALSE TRUE 69775.20368 62997.62705 65798.10854 62255.31909 71517.74361 71674.58401 72752.60327 75203.28032 69822.15444 75565.07265 0.923379033 0.83368711 0.870747638 0.823863683 0.946439156 0.948514724 0.962780829 0.995212175 0.924000361 1 16.20543193 3.119322402 5.50558698 0.966012867 0.861777357 0.701831179 0.032055678 0.108764726 4.822256583 0.00901448 0.010864324 1316.201563 -3.119322402 -0.10423551 DHFEEAMR ddPTM_BT-474_Pertuzumab_2h_R1 10 DHFEEAMR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;;; 206.09 7.42E-05 23169530000 19486000 19662410 16390020 16035400 15843830 8130530 18705650 7437540 17055050 17312840 FALSE TRUE 18724465.58 19101657.32 19352061.21 16862988.92 16353461.18 8294934.887 18934575.34 7283952.2 15119032.22 16140225.93 1.16011174 1.183481409 1.198995683 1.044780228 1.013211417 0.513929292 1.173129511 0.451291837 0.9367299 1 23.94415744 3.119683685 2.395163682 0.783081476 1.165956744 0.353735726 0.206821506 0.272260366 3.183035506 0.061203677 0.076781449 1317.296946 -3.119683685 0.382875268 HTNYTMEHIR ddPTM_BT-474_Pertuzumab_2h_R1 5 HTNYTMEHIR 10 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0;H7C5W8;H0YJ11;H0YJW3 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;;; 172.61 2.12E-06 2475470000 709380 893621 807627 930382 654866 525393 922769 440719 623551 846885 FALSE TRUE 681656.6453 868135.804 953583.1645 978399.1265 675930.3596 536016.8064 934062.1231 431617.9986 552768.1046 789524.7246 0.863375932 1.099567597 1.207793923 1.239225443 0.856123106 0.678910729 1.183068869 0.546680788 0.700127668 1 19.59062492 3.119752589 6.246903739 0.800639508 1.108476226 0.330900538 0.190547238 0.229538852 11.67836411 0.055546751 0.066755954 1317.505961 -3.119752589 0.307836719 LKVTEGGEPYR ddPTM_BT-474_Pertuzumab_2h_R1 4 LKVTEGGEPYR 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 112.44 0.0013917 1054190000 1470470 1899460 1207400 1365860 1727520 2029810 1764280 1807190 2062580 1905590 FALSE TRUE 1413002.407 1845289.261 1425604.038 1436352.198 1783087.25 2070854.149 1785871.786 1769870.895 1828444.565 1776522.692 0.795375377 1.038708522 0.802468803 0.808518914 1.003695172 1.165678411 1.005262581 0.996255721 1.029226687 1 20.76062469 3.12020462 6.065533717 1.037384685 0.870555161 0.530780169 0.079537197 0.176705185 8.711858566 0.023295135 0.028013392 1318.877988 -3.12020462 -0.166829524 WFLTCINQPQFR ddPTM_BT-474_Pertuzumab_2h_R1 2 WFLTCINQPQFR 12 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 231.23 9.15E-12 1187570000 432330 427960 430670 465800 413800 372170 467330 402020 488030 544210 FALSE TRUE 415434.0656 415754.9998 508501.6492 489839.9938 427110.2528 379695.5324 473049.3243 393718.1465 432630.8804 507350.172 0.818831033 0.819463603 1.002269591 0.965486997 0.841845093 0.748389482 0.932392163 0.776028409 0.85272639 1 18.95262231 3.120743295 16.25585924 0.842725414 0.903037624 0.037827401 0.086051047 2.307237127 314.0027293 0.024719159 0.029545827 1320.514867 -3.120743295 0.060312209 DRDFLVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRDFLVQR 8 1 Q66K14-2;Q66K14;Q6ZT07 Q66K14-2;Q6ZT07 TBC1D9B;TBC1D9 TBC1 domain family member 9B;TBC1 domain family member 9 0 128.28 0.0010399 122440000 76981 77437 74102 78647 64016 39748 87260 45527 71985 75783 FALSE TRUE 73972.49741 75228.57258 87493.87979 82705.9811 66075.13278 40551.73179 88327.91398 44586.85154 63813.56459 70650.14991 1.047025343 1.064804147 1.238410391 1.170641268 0.935244056 0.573979416 1.250215521 0.631093516 0.903233251 1 16.108405 3.121065769 4.941815783 0.853365611 1.132018412 0.306686947 0.182934685 0.232721569 9.102661646 0.051060605 0.061751888 1321.495744 -3.121065769 0.2786528 VREEVPLELVEAHVK ddPTM_BT-474_Pertuzumab_2h_R1 3 VREEVPLELVEAHVK 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 0 ;; 186.43 2.30E-07 419583000 445620 408640 348010 363830 420110 439750 423420 437860 493900 485900 FALSE TRUE 428204.6777 396985.9873 410903.1484 382607.3099 433623.2197 448642.0463 428601.9406 428818.038 437834.5426 452989.5602 0.945285974 0.876368955 0.907091873 0.844627213 0.957247711 0.990402618 0.946162954 0.946640002 0.966544444 1 18.78911828 3.121071259 8.480932171 0.964078916 0.893256616 0.618965826 0.02858333 0.169359107 11.85363336 0.008000927 0.009578458 1321.512449 -3.121071259 -0.0708223 HAEMVHTGLK ddPTM_BT-474_Pertuzumab_2h_R1 4 HAEMVHTGLK 10 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;;; 190.86 4.95E-07 2074770000 2048750 2035770 1540320 1805370 1507590 1333860 1735240 513332 2254560 2224070 FALSE TRUE 1968682.585 1977711.833 1818690.088 1898545.362 1556083.002 1360831.563 1756476.386 502731.5148 1998631.801 2073431.758 0.949480289 0.953835025 0.877140075 0.915653652 0.750486721 0.656318472 0.847134891 0.242463497 0.963924563 1 20.98358913 3.121147473 1.792796291 0.662695155 0.933391811 0.099822187 0.204796222 0.497370037 3.286724219 0.068679283 0.088632679 1321.74438 -3.121147473 0.270696656 FMKPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FMKPGK 6 1 P61353;K7EQQ9;K7ERY7 P61353 RPL27 60S ribosomal protein L27 0 65.619 0.094454 1250600000 1232200 1311200 1042500 1312200 1444800 1143200 1506800 1625700 1717300 1546700 FALSE TRUE 1184044.262 1273805.86 1230902.94 1379922.799 1491273.304 1166316.287 1525240.669 1592128.727 1522359.304 1441940.631 0.821146333 0.883396883 0.853643287 0.956990024 1.034212693 0.808851808 1.057769395 1.10415692 1.05577114 1 20.45958034 3.122103728 0.539263508 1.069582162 0.822874615 0.492776511 0.073282459 0.89406755 0.535203213 0.060387875 0.109929859 1324.657883 -3.122103728 -0.246707548 SFPIKPVPSPS(ph)WSGSCR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.355)PS(0.624)WS(0.019)GS(0.001)CR 153.36 1.08E-07 895430000 670250 650910 510120 557790 503840 468490 459670 492840 413900 459280 TRUE FALSE 644055.889 632346.6841 602310.0316 586577.6087 520046.4712 477963.1888 465295.579 482662.6818 366915.8072 428172.5565 1.504197033 1.476850103 1.406699291 1.369956107 1.21457217 1.11628637 1.086701079 1.127262069 0.856934434 1 18.7078328 3.122753921 0.557463238 0.972154852 1.558753701 0.915360436 0.059714192 0.279820145 0.181323492 0.046631889 0.083137005 1326.642546 -3.122753921 0.586598849 TDS(ph)PDMHEDT ddPTM_BT-474_Pertuzumab_2h_R1 7 TDSPDMHEDT 10 0 Q9BW61 Q9BW61 DDA1 DET1- and DDB1-associated protein 1 1 T(0.009)DS(0.991)PDMHEDT;T(0.011)DS(0.989)PDMHEDT;T(0.002)DS(0.998)PDMHEDT;TDS(1)PDMHEDT;T(0.003)DS(0.997)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT 196.06 3.57E-07 3251580000 3527470 3236600 2730235 3071720 3243090 3275050 3486710 3207130 3982450 3814480 TRUE FALSE 3389612.573 3144295.337 3223649.198 3230251.837 3347406.935 3341273.755 3529381.4 3140901.645 3530378.972 3556121.872 0.953176717 0.884192232 0.906506952 0.908363648 0.941308272 0.93958359 0.99248044 0.883237909 0.992760962 1 21.76187334 3.123126248 2.960352326 0.950695501 0.91024988 0.258220689 0.036308524 0.412145771 7.265394274 0.010855966 0.013458193 1327.780383 -3.123126248 -0.040445621 APS(ph)PARPK ddPTM_BT-474_Pertuzumab_2h_R1 3 APSPARPK 8 1 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 APS(1)PARPK;APS(1)PARPK;APS(1)PARPK 94.66 0.0061785 1164090000 1714370 1683050 1505160 1891610 1704610 2025230 1962870 2367970 2386350 2310190 TRUE FALSE 1647370.525 1635051.062 1777175.894 1989236.219 1759440.329 2066181.538 1986892.19 2319070.592 2115461.552 2153718.774 0.764895837 0.759175748 0.82516618 0.923628583 0.816931324 0.959355308 0.92254022 1.076775028 0.982236668 1 21.03839845 3.123362224 0.532436623 1.034662441 0.73701851 0.774943666 0.048168068 0.482570108 0.280072196 0.038700781 0.071161067 1328.502036 -3.123362224 -0.297643931 FLNRS(ph)PEESFDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLNRSPEESFDIK 13 1 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 FLNRS(1)PEESFDIK 108.56 0.00073085 104240000 52596 52812 38922 47551 53760 60779 58332 62968 63117 55351 TRUE FALSE 50540.49017 51305.85347 45956.07122 50005.11281 55489.23922 62007.99302 59045.88447 61667.6888 55952.22277 51602.02747 0.97942838 0.994260419 0.890586542 0.969053257 1.075330601 1.201658076 1.144255126 1.195063292 1.084302798 1 15.65514013 3.123684113 3.253644755 1.143224133 0.954679818 0.621390414 0.060658394 0.136598591 2.864737734 0.017540272 0.021635967 1329.487055 -3.123684113 -0.188544315 VDKDAELVAQWNYCTLSQEILR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDKDAELVAQWNYCTLSQEILR 22 1 Q9BY42;A2A2L6 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ; 187.81 2.47E-17 935080000 1041890 1032750 906280 937770 1021240 1065080 1022090 1119870 1217520 1179400 FALSE TRUE 1001171.787 1003296.981 1070064.956 986168.4221 1054089.112 1086616.647 1034598.643 1096744.293 1079312.234 1099518.187 0.910555003 0.912487845 0.973212602 0.896909604 0.958682743 0.988266188 0.940956371 0.997477173 0.981622902 1 20.06844004 3.124027144 0.348151697 1.003397091 0.895054535 0.559673446 0.024230799 1.648709671 0.34728427 0.026244927 0.068303768 1330.537575 -3.124027144 -0.108342555 WLGGAVEDYFMR ddPTM_BT-474_Pertuzumab_2h_R1 1 WLGGAVEDYFMR 12 0 Q969E8 Q969E8 TSR2 Pre-rRNA-processing protein TSR2 homolog 0 134.25 0.00034628 152470000 114460 122880 98884 92243 125070 78999 115570 105100 109200 106920 FALSE TRUE 109986.7767 119375.5827 116754.5385 97003.67228 129092.9901 80596.41391 116984.3802 102929.6483 96804.0738 99678.21317 1.103418422 1.197609577 1.171314521 0.97316825 1.295097354 0.808565998 1.173620358 1.032619316 0.971165822 1 16.60499059 3.124212265 0.928057151 1.02205802 1.155024411 0.165673743 0.123493728 1.082172129 2.046824623 0.056604964 0.082208612 1331.104847 -3.124212265 0.132966391 ESSTVFELKR ddPTM_BT-474_Pertuzumab_2h_R1 3 ESSTVFELKR 10 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;; 155.26 2.09E-05 1173380000 1101560 1255950 796570 1013160 1370750 1479710 1534520 1612480 1739520 1623160 FALSE TRUE 1058509.817 1220131.536 940527.9186 1065449.309 1414841.419 1509630.75 1553299.915 1579181.725 1542056.982 1513221.927 0.699507322 0.806313677 0.621539975 0.704093226 0.934986067 0.997626801 1.026485201 1.043588978 1.019055404 1 20.52919216 3.124846881 3.093538995 1.020232843 0.706623571 0.917083366 0.044075008 0.066758539 1.27741693 0.013922125 0.017230666 1333.051357 -3.124846881 -0.313609272 GTEAPAVVT(ph)EEEDDDEETAPPVIAPRPDHTK ddPTM_BT-474_Pertuzumab_2h_R1 3 GTEAPAVVTEEEDDDEETAPPVIAPRPDHTK 31 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK;GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK;GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK 222.52 7.71E-35 2284770000 2043910 2131800 1816460 1799580 2147930 2340070 2084690 2258460 2563500 2401600 TRUE FALSE 1964031.738 2071003.151 2144734.729 1892456.539 2217020.119 2387387.819 2110203.06 2211822.012 2272502.227 2238937.493 0.877215976 0.924993734 0.957925237 0.845247599 0.990210815 1.066303917 0.942501998 0.98788913 1.014991367 1 21.09438282 3.125316159 8.544658067 0.998646805 0.907263315 0.597695382 0.039695171 0.188930183 13.42919231 0.011424823 0.013677216 1334.492567 -3.125316159 -0.091383491 DRDWSHSGNPGASR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRDWSHSGNPGASR 14 1 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 0 93.51 0.0027238 92620000 68325 74168 58599 62448 62963 65320 63735 63397 72643 67790 FALSE TRUE 65654.78346 72052.80126 69189.14283 65670.94876 64988.26208 66640.81515 64515.008 62087.8298 64396.87118 63198.52292 1.03886579 1.140102615 1.094790505 1.039121576 1.028319319 1.054467922 1.020830947 0.982425331 1.01896165 1 15.94760322 3.125539257 0.751400417 1.000529333 1.098554569 0.554955182 0.029127321 0.491534707 0.615685098 0.017319541 0.026808135 1335.178274 -3.125539257 0.098025237 KLDVEEPDSANSSFYSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDVEEPDSANSSFYSTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 198.49 2.77E-15 645120000 468550 492890 366300 419300 461590 467780 477010 520590 515220 486050 FALSE TRUE 450238.548 478833.2598 432498.5583 440940.1232 476437.4616 477238.8321 482847.7911 509839.6346 456734.3856 453129.4006 0.993620249 1.056725207 0.954470307 0.973099787 1.05143798 1.053206505 1.065584777 1.125152404 1.007955752 1 18.78956358 3.125551812 5.545941813 1.063594762 0.996321585 0.280162304 0.041259718 0.230078573 10.32055584 0.012317818 0.014851769 1335.216873 -3.125551812 -0.067273177 VLNTGS(ph)DVEEAVADALK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.287)GS(0.713)DVEEAVADALK;VLNT(0.012)GS(0.988)DVEEAVADALK;VLNT(0.021)GS(0.979)DVEEAVADALK 243.23 2.00E-20 197672000 169411 155833 149760 148711 172711 173781 171913 195608 200479 191615 TRUE FALSE 162790.2308 151388.7954 176824.9634 156385.9925 178266.4062 177294.9709 174016.9227 191568.6264 177721.4644 178636.7454 0.911291966 0.847467273 0.989857731 0.875441344 0.997926859 0.99248881 0.974138453 1.072392055 0.994876301 1 17.44666935 3.12670834 0.8216716 1.025685552 0.890845556 0.524829064 0.0440887 0.450354658 0.674124637 0.022753901 0.034260352 1338.7773 -3.12670834 -0.134839996 GNHECASINR ddPTM_BT-474_Pertuzumab_2h_R1 4 GNHECASINR 10 0 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;A0A087WYY5;P62140;E7ETD8;C9JP48;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ;;; 178.46 2.21E-06 7083170000 2990190 3140640 2571260 2864690 2500350 1945050 2976640 2108950 2574780 2794120 FALSE TRUE 2873330.069 3051072.022 3035943.879 3012536.994 2580776.029 1984380.244 3013069.011 2065399.446 2282501.769 2604871.764 1.103060085 1.17129452 1.165486886 1.156501075 0.990749742 0.761795752 1.156705314 0.792898704 0.87624343 1 21.31278092 3.126943589 4.026848892 0.912402759 1.152057719 0.520920512 0.104599922 0.166082497 4.948545658 0.029646318 0.036211979 1339.502686 -3.126943589 0.239654961 GQPIYIQFSNHK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQPIYIQFSNHK 12 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 222.25 2.52E-11 4908200000 1852290 2738900 1904330 2409800 1959680 1558170 2349800 2056040 1946470 2329900 FALSE TRUE 1779900.459 2660789.254 2248484.793 2534170.067 2022714.887 1589677.265 2378557.555 2013582.056 1725514.886 2172093.798 0.819439962 1.224988192 1.035169289 1.166694583 0.931228149 0.731864005 1.095052874 0.927023528 0.794401645 1 21.05065497 3.127640892 7.974294364 0.913719896 1.070928196 0.221366615 0.136126985 0.343353962 22.86596787 0.037860881 0.045353347 1341.655119 -3.127640892 0.1572083 IVAFENAFER ddPTM_BT-474_Pertuzumab_2h_R1 4 IVAFENAFER 10 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;; 140.17 9.25E-05 558270000 474841 542902 433124 469676 451861 382141 502782 440686 475688 472484 FALSE TRUE 456283.6888 527418.9665 511399.1416 493916.0346 466395.5194 389868.1528 508935.1965 431585.6801 421689.8925 440482.2378 1.035873072 1.197367161 1.160998328 1.121307495 1.058829345 0.885093925 1.155404583 0.979802687 0.957336883 1 18.74872432 3.12810503 3.631461535 1.003871724 1.136815925 0.412221408 0.074112458 0.226098742 5.730692609 0.021489974 0.02640103 1343.089736 -3.12810503 0.132944201 LRDDFEK ddPTM_BT-474_Pertuzumab_2h_R1 6 LRDDFEK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;;;; 144.12 0.0021665 5401300000 3357490 3250150 2896960 3280710 3465700 3287100 3663220 3936300 4213930 4096290 FALSE TRUE 3226275.579 3157458.904 3420505.115 3450027.836 3577177.388 3353567.414 3708051.582 3855014.029 3735582.333 3818844.63 0.84483028 0.826809994 0.895691091 0.903421891 0.936717184 0.878162832 0.97098781 1.009471294 0.978196993 1 21.86470479 3.128525403 0.41656082 1.01429874 0.809275472 0.806461769 0.026913508 0.697289192 0.222030081 0.027398319 0.061380779 1344.3904 -3.128525403 -0.205023268 (ac)ADKEAAFDDAVEER ddPTM_BT-474_Pertuzumab_2h_R1 4 ADKEAAFDDAVEER 14 1 Q09028-3;Q09028;E9PNS2;E9PIC4;E9PNS6 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;;; 110.74 1.88E-06 2362480000 2815050 2795630 2293970 2489480 2733290 2955260 2726530 2868520 3134940 3117250 FALSE TRUE 2705034.734 2715901.37 2708541.408 2617962.361 2821208.755 3015017.382 2759898.09 2809284.06 2779074.754 2906115.881 0.930807595 0.934546825 0.932014248 0.900845826 0.970783297 1.037473214 0.94968618 0.966679986 0.956284907 1 21.4706608 3.128789426 6.938084346 0.978835068 0.926004064 0.546907955 0.024843612 0.184677398 10.64632905 0.007431766 0.008918463 1345.207953 -3.128789426 -0.052831004 HLYTLDGGDIINALCFSPNR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLYTLDGGDIINALCFSPNR 20 0 P63244;J3KPE3;H0YAF8;D6R9L0;H0Y8W2;D6RAC2;D6R9Z1;D6REE5;H0YAM7;H0Y8R5;D6RF23 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 224.4 5.81E-25 1703800000 608550 695240 556620 568630 499710 594960 628830 432680 618050 640280 FALSE TRUE 584767.1932 675412.4359 657213.6159 597977.0624 515783.626 606990.4988 636525.8096 423745.0068 547891.5551 596913.2653 0.979651864 1.131508504 1.101020289 1.001782164 0.86408471 1.016882241 1.066362312 0.709893768 0.917874651 1 19.18716179 3.129541508 0.797377707 0.887891397 1.082293795 0.214148324 0.103962695 0.845585224 1.192817776 0.060651287 0.092505447 1347.539512 -3.129541508 0.194402398 SCATFSSSHR ddPTM_BT-474_Pertuzumab_2h_R1 4 SCATFSSSHR 10 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-5;D6RCQ9;D6RE64;D6RBT0;D6RHE8 D6REX3 SEC31A Protein transport protein Sec31A 0 ;;; 152.54 1.78E-05 457451000 392562 588080 503449 543460 414057 212422 540870 377338 407479 535983 FALSE TRUE 377220.243 571308.5342 594433.4335 571508.0357 427375.5194 216717.3184 547489.3289 369545.8384 361223.6922 499680.394 0.754923042 1.14334791 1.189627291 1.143747168 0.855297755 0.433711871 1.095679029 0.739564415 0.722909477 1 18.93064609 3.129673976 5.680911838 0.789379009 1.072060572 0.27492625 0.199289418 0.25178121 11.68487248 0.056679416 0.068319718 1347.950599 -3.129673976 0.282681562 VLITTDLLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLITTDLLAR 10 0 P60842;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 101.9 0.0070241 365110000 340980 366130 312260 344990 326570 265720 391150 325380 370780 377200 FALSE TRUE 327654.1246 355688.3309 368692.3282 362794.9752 337074.4206 271093.0405 395937.0107 318660.7893 328690.6088 351651.908 0.931756994 1.011478461 1.048458205 1.031687777 0.958545689 0.770913037 1.125934487 0.906182455 0.934704466 1 18.42378852 3.129708542 6.605808328 0.945291145 1.008950613 0.09163503 0.087042121 0.50087587 27.46362576 0.024739876 0.029715337 1348.057888 -3.129708542 0.063659468 SGTHNMYR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGTHNMYR 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;; 130.22 0.0010572 740270000 768280 1069250 957980 976690 772460 404503 1024780 662750 667140 978010 FALSE TRUE 738254.7682 1038756.037 1131108.296 1027097.088 797306.8774 412682.3278 1037321.564 649063.9809 591409.0641 911768.5116 0.809695398 1.139276059 1.240565211 1.126488878 0.874461958 0.452617438 1.137702773 0.711873653 0.648639492 1 19.79830806 3.130911092 4.878284057 0.785212482 1.093792737 0.309383806 0.202978437 0.239151326 9.284134689 0.058069046 0.070376803 1351.795797 -3.130911092 0.308580255 IIGVHQEDELLECLSPATSR ddPTM_BT-474_Pertuzumab_2h_R1 3 IIGVHQEDELLECLSPATSR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;; 243.18 7.97E-30 722840000 389765 439672 337990 417937 336079 337411 299130 339222 385548 407147 FALSE TRUE 374532.5529 427132.985 399072.3115 439506.7787 346889.2863 344233.6816 302790.8424 332216.9472 341782.2074 379570.571 0.986727058 1.125305853 1.051378431 1.157905307 0.913899319 0.906902979 0.79771949 0.875244217 0.900444432 1 18.53400862 3.131164063 5.969246182 0.882428017 1.080783862 0.661472052 0.063158123 0.111614879 5.497130361 0.01757079 0.021153606 1352.583432 -3.131164063 0.198355845 MREEFDK ddPTM_BT-474_Pertuzumab_2h_R1 5 MREEFDK 7 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;;;; 150.24 0.0017894 6331860000 5550980 6130380 5008880 5129460 5281190 4272360 5389520 5224070 5041860 5131430 FALSE TRUE 5334041.565 5955547.565 5914096.038 5394192.045 5451064.273 4358750.046 5455478.558 5116191.129 4469529.19 4783873.675 1.115004686 1.244921578 1.236256732 1.127578279 1.1394666 0.911134019 1.140389343 1.069466185 0.934290806 1 22.18974786 3.132010657 2.258292416 1.030865297 1.196424873 0.531316721 0.074095869 0.248428372 2.588423478 0.023392774 0.029710843 1355.222666 -3.132010657 0.165559576 GKPLPEYHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKPLPEYHVR 10 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 104.79 0.0015829 1495420000 3603600 3371000 2959400 3138000 3083300 2440000 3078900 2988700 3459800 3871500 FALSE TRUE 3462767.328 3274862.381 3494229.411 3299952.556 3182477.145 2489338.472 3116580.499 2926982.301 3067058.009 3609279.857 0.959406714 0.907345097 0.968123712 0.914296671 0.881748512 0.68970503 0.863490952 0.810960196 0.849770073 1 21.78327958 3.132176153 3.57267858 0.828167305 0.9382734 0.251917111 0.073575095 0.263476335 6.506785006 0.020592724 0.025362693 1355.739198 -3.132176153 0.110106095 TLS(ph)PTPSAEGYQDVR ddPTM_BT-474_Pertuzumab_2h_R1 3 TLSPTPSAEGYQDVR 15 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 TLS(1)PTPSAEGYQDVR;TLS(0.994)PT(0.006)PSAEGYQDVR;T(0.004)LS(0.918)PT(0.078)PSAEGYQDVR 260.07 7.02E-17 214828000 152102 193688 128361 161620 168978 184586 178480 196103 191216 190102 TRUE FALSE 146157.6857 188164.2079 151558.6881 169961.2276 174413.3308 188318.4554 180664.2916 192053.4045 169509.9613 177226.2222 0.8246956 1.061717648 0.855170788 0.959007225 0.984128244 1.062587991 1.019399327 1.083662463 0.956460953 1 17.43523255 3.132420126 2.456271211 1.03318838 0.927284708 0.324290713 0.067237498 0.312273939 3.839490142 0.019610055 0.024742618 1356.501025 -3.132420126 -0.105903672 LVEYDIDEVVYDEDSPYQNIK ddPTM_BT-474_Pertuzumab_2h_R1 4 LVEYDIDEVVYDEDSPYQNIK 21 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 ;;; 296.16 6.97E-55 721540000 558641 523321 464987 526509 537186 574796 584933 612812 662286 651441 FALSE TRUE 536808.6921 508396.3975 549020.4945 553682.1926 554465.0755 586418.7689 592091.585 600157.218 587106.0698 607318.3208 0.883900047 0.837116846 0.904007792 0.911683665 0.912972747 0.965587154 0.974927916 0.98820865 0.966718852 1 19.21209337 3.135232778 0.695401029 0.990861196 0.856824898 0.880925639 0.0171745 0.229161466 0.244090361 0.010467968 0.01690045 1365.314736 -3.135232778 -0.134036298 KPELWSDDFTDFVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPELWSDDFTDFVK 14 1 A0A087WZ06;Q13188;Q13188-2;E5RFQ9 A0A087WZ06 STK3 Serine/threonine-protein kinase 3;Serine/threonine-protein kinase 3 36kDa subunit;Serine/threonine-protein kinase 3 20kDa subunit 0 87.932 0.010818 125120000 138920 128070 139550 124960 147120 152600 163500 171030 190590 179890 FALSE TRUE 133490.8528 124417.569 164769.7893 131409.2006 151852.2484 155685.6766 165500.9619 167498.1707 168955.0222 167705.8901 0.795981899 0.741879542 0.98249256 0.783569382 0.905467592 0.928325633 0.986852411 0.998761407 1.00744835 1 17.35557383 3.135310478 0.498079458 1.02367887 0.766993175 0.628518301 0.059138784 0.76247385 0.375205009 0.048066876 0.093908345 1365.559028 -3.135310478 -0.256685694 DVTNFTVGGFAPMS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 12 DVTNFTVGGFAPMSPR 16 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR 255.24 1.39E-26 11809810000 4548971 4986007 3788553 4335078 3956946 2975646 4048476 4197388 4213441 4188449 TRUE FALSE 4371192.184 4843810.962 4473228.803 4558811.895 4084224.762 3035815.601 4098022.46 4110710.471 3735148.842 3904761.619 1.119451739 1.240488264 1.14558307 1.167500693 1.045960077 0.777465028 1.049493634 1.052743003 0.956562578 1 21.89680305 3.135470274 4.154121467 0.978342768 1.172096673 0.592256053 0.078017065 0.164274927 5.156922665 0.023992476 0.029334657 1366.061571 -3.135470274 0.193753905 EEIFRES(ph)PIPIEIPPAAVPSYVPESR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEIFRESPIPIEIPPAAVPSYVPESR 26 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 EEIFRES(1)PIPIEIPPAAVPSYVPESR 53.819 0.062395 22082000 11037 12513 9504.6 9107.4 12284 13698 10234 14086 13612 14778 TRUE FALSE 10605.66184 12156.14149 11222.29265 9577.434005 12679.12602 13974.98295 10359.24675 13795.11918 12066.82283 13777.0729 0.769805162 0.882345734 0.814562914 0.695171905 0.92030623 1.014365174 0.751919281 1.001309878 0.875862596 1 13.74998178 3.135566081 11.14581076 0.924746748 0.79882518 0.387192194 0.084041341 0.421703427 42.53052709 0.023390339 0.027968329 1366.362962 -3.135566081 -0.125921568 HQALQAEIAGHEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQALQAEIAGHEPR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 163.8 2.44E-06 622530000 446576 496204 465056 557055 542406 654787 565503 1012380 572364 680527 FALSE TRUE 429123.3162 482052.7478 549101.9643 585804.6753 559852.9816 668027.2418 572423.7949 991473.9992 507391.6383 634434.3001 0.67638732 0.759815079 0.865498546 0.923349628 0.882444378 1.052949441 0.902258587 1.562768594 0.799754424 1 19.27511125 3.136381951 0.742797843 1.157905571 0.722067107 0.279107361 0.196630065 0.765887395 0.935946347 0.118228675 0.186347357 1368.932237 -3.136381951 -0.435838464 GPQNATDSYVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPQNATDSYVHK 12 0 B7Z982;D6RA26;O43660-2;O43660 B7Z982 PLRG1 Pleiotropic regulator 1 0 142.83 6.17E-05 187310000 127160 126580 111470 123120 132980 148610 145150 151590 173860 149240 FALSE TRUE 122190.4466 122970.0623 131615.1086 129474.238 137257.4225 151614.996 146926.3891 148459.6135 154124.1417 139131.8419 0.878234953 0.883838384 0.945974026 0.930586674 0.986527747 1.089721763 1.056022742 1.067042681 1.107756065 1 17.08609311 3.136592118 1.477413913 1.069406564 0.898087761 0.837047399 0.032101238 0.138990504 0.631684362 0.011070249 0.014857831 1369.594862 -3.136592118 -0.171318803 FVEGLPINDFSR ddPTM_BT-474_Pertuzumab_2h_R1 5 FVEGLPINDFSR 12 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;;; 181.68 6.86E-05 288188000 557916 632834 491682 600671 535437 496055 591252 567897 595194 648113 FALSE TRUE 536112.0259 614786.1939 580539.8748 631671.7023 552659.8174 506085.572 598487.9188 556169.7285 527630.0724 604215.7292 0.887285782 1.017494521 0.960815561 1.045440679 0.914673006 0.83759086 0.990520256 0.920482042 0.873247827 1 19.20470422 3.136819729 21.43883328 0.919727418 0.979518235 0.170359206 0.059189094 6.968310821 1449.21955 0.016429518 0.019637072 1370.312846 -3.136819729 0.059790817 GPASQFYITPSTSLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPASQFYITPSTSLSPR 17 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 GPASQFYITPSTSLS(1)PR;GPASQFYITPST(0.001)S(0.044)LS(0.955)PR;GPASQFYITPST(0.001)S(0.013)LS(0.986)PR 195.48 1.77E-11 750760000 686230 703100 569540 650660 612930 584140 622760 685710 600790 669800 TRUE FALSE 659411.3729 683048.2764 672468.5473 684240.6406 632645.4501 595951.711 630381.5232 671549.8489 532590.8379 624433.8494 1.056014778 1.093868113 1.076925199 1.095777625 1.013150473 0.954387261 1.009524906 1.075453948 0.852917949 1 19.25218922 3.137127739 4.830593596 0.992574896 1.081129614 0.43143051 0.054118005 0.22959367 8.906539224 0.016001567 0.019423909 1371.285043 -3.137127739 0.088554718 MGPPVGGHR ddPTM_BT-474_Pertuzumab_2h_R1 11 MGPPVGGHR 9 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;;;;; 130.27 0.00036587 2027831000 1808706 1875081 1676894 1756901 1657661 1307202 1882078 1563973 1832326 1992156 FALSE TRUE 1738019.77 1821605.526 1979946.048 1847574.871 1710981.172 1333634.52 1905111.434 1531676.411 1624328.034 1857225.5 0.935815156 0.980820868 1.066077355 0.994803739 0.921256558 0.718078941 1.025783586 0.824712137 0.874599253 1 20.82471756 3.137912407 4.439872865 0.87961466 0.998452512 0.245924197 0.086128412 0.26399374 9.150726779 0.024178756 0.029477189 1373.764872 -3.137912407 0.118837852 WREEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 WREEQR 6 1 P09497-2;P09497;H0Y9Q6;F8VW50;Q2TAC6-3;Q2TAC6-2;Q2TAC6;A0A0C4DG89;Q7L014;D6RJA6 P09497-2;A0A0C4DG89 CLTB;KIF19;DDX46 Clathrin light chain B;Kinesin-like protein;Kinesin-like protein KIF19;Probable ATP-dependent RNA helicase DDX46 0 ;;; 139.92 0.010803 3189910000 2403110 2665470 2129020 2201280 2173050 1270140 2327150 2122340 2060720 2401480 FALSE TRUE 2309193.804 2589453.405 2513781.274 2314888.325 2242948.127 1295823.101 2355630.358 2078512.937 1826795.705 2238825.621 1.031430846 1.156612369 1.122812447 1.033974376 1.00184137 0.578795905 1.052172325 0.928394297 0.815961586 1 21.09431073 3.138004396 3.334317613 0.883811722 1.09703378 0.379323132 0.125351625 0.254280937 5.583314654 0.03729758 0.046243077 1374.055882 -3.138004396 0.213222059 HLLVPER ddPTM_BT-474_Pertuzumab_2h_R1 1 HLLVPER 7 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 77.282 0.050897 0 72639 88498 73530 74377 70548 59752 73563 54647 82654 89141 FALSE TRUE 69800.18757 85974.12369 86818.50667 78215.60588 72817.24049 60960.22638 74463.286 53518.52035 73271.46443 83103.40067 0.839919751 1.03454399 1.044704621 0.941184178 0.876224558 0.733546713 0.896031756 0.643999162 0.881690326 1 16.34261989 3.13816983 2.720214852 0.801092968 0.979261652 0.23711782 0.106019203 0.283169681 4.25055052 0.031443022 0.039508345 1374.579395 -3.13816983 0.178168684 EVSSRPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 EVS(0.002)S(0.01)RPS(0.493)T(0.493)PGLS(0.001)VVSGISATSEDIPNKIEDLR 90.724 6.90E-05 1199900000 44333 36886 39961 51726 36666 57484 58606 48492 80161 64420 TRUE FALSE 42600.41735 35834.0474 47182.84163 54395.58506 37845.39519 58646.36587 59323.23776 47490.62325 71061.45934 60056.77602 0.709335735 0.596669515 0.785637271 0.905736016 0.630160287 0.976515387 0.98778592 0.790762115 1.183237997 1 15.87403941 3.138356637 0.386327496 1.036967503 0.592537449 0.507319784 0.123814468 1.649581303 0.437765503 0.124470215 0.300276479 1375.170782 -3.138356637 -0.444430053 TGDTGMLPANYVEAI ddPTM_BT-474_Pertuzumab_2h_R1 4 TGDTGMLPANYVEAI 15 0 Q14847;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;; 123.95 0.00023173 105306000 435640 449099 364187 406247 399961 385421 395395 435968 427443 436498 FALSE TRUE 418614.7072 436291.1362 430003.6922 427213.4564 412826.1088 393214.4767 400233.9623 426965.1084 378921.4626 406933.6017 1.028705188 1.072143304 1.056692518 1.049835783 1.014480267 0.966286576 0.983536284 1.049225492 0.931162875 1 18.63443389 3.138749274 3.386926185 0.993555894 1.054167128 0.510456035 0.029843249 0.216958119 4.89901675 0.009111616 0.011289745 1376.414611 -3.138749274 0.060611233 HEVGHIDNSMK ddPTM_BT-474_Pertuzumab_2h_R1 2 HEVGHIDNSMK 11 0 Q969X5;Q969X5-2;F2Z2U2;F2Z3Q5;Q969X5-3 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ; 113.22 0.00082137 1521430000 1063550 1603490 1088680 1308750 951190 511430 1560710 56772 1677860 1187360 FALSE TRUE 1021985.29 1557760.035 1285428.694 1376294.744 981785.8902 521771.465 1579810.436 55599.63836 1487396.367 1106939.05 0.923253444 1.40726812 1.161246135 1.243333809 0.886937624 0.471364223 1.427188278 0.050228274 1.343702137 1 20.07814436 3.138952259 4.68097812 0.776886452 1.197505345 0.120383066 0.39247344 0.33303963 12.44175315 0.109558197 0.133239964 1377.058083 -3.138952259 0.420618893 S(ph)PVEMDEDFDVIFDPYAPK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPVEMDEDFDVIFDPYAPK 19 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425;A0A0J9YWY6 O95425-2 SVIL Supervillin 1 S(1)PVEMDEDFDVIFDPYAPK;S(1)PVEMDEDFDVIFDPYAPK;S(1)PVEMDEDFDVIFDPYAPK;S(1)PVEMDEDFDVIFDPYAPK 143.14 9.54E-08 73085000 218245 204577 183222 182571 186638 141570 185812 173277 192973 183398 TRUE FALSE 209715.7441 198742.6643 216334.2912 191993.5112 192641.3808 144432.6424 188086.0228 169698.7694 171067.514 170976.2901 1.226577931 1.162398974 1.265288251 1.12292477 1.126714006 0.844752464 1.100070792 0.992528083 1.000533547 1 17.38343675 3.139032298 2.371327183 0.997187001 1.205052434 0.659863822 0.06963634 0.17031512 1.954869718 0.020598878 0.026167493 1377.311896 -3.139032298 0.207865433 AHEILPNLVCCSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHEILPNLVCCSAK 14 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 136.14 2.88E-05 478990000 456590 458190 448500 474740 438020 420160 511660 331080 599060 604030 FALSE TRUE 438745.958 445122.8698 529553.9268 499241.3883 452109.3111 428655.9231 517921.8481 324243.0823 531057.2203 563118.5101 0.779136097 0.790460377 0.94039517 0.886565402 0.802867075 0.761217959 0.919738632 0.575799013 0.943064756 1 19.10307905 3.139103992 8.961205902 0.799208141 0.851382344 0 0.120412168 1.074720989 87.43231948 0.03453951 0.041340086 1377.539282 -3.139103992 0.052174203 ELGITALHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELGITALHIK 10 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 150.35 2.17E-05 1303800000 1960400 1871800 1801400 1721900 1794000 1273900 1908100 1739900 1793000 2066100 FALSE TRUE 1883785.401 1818418.097 2126953.052 1810767.465 1851705.639 1299659.131 1931451.899 1703970.457 1589466.157 1926161.207 0.977999865 0.944063296 1.104244569 0.940091338 0.961345101 0.674740581 1.002746754 0.884645818 0.825198925 1 20.87729702 3.139227297 3.153640441 0.878563374 0.99871267 0.22680765 0.097248377 0.352018459 6.990465625 0.028336368 0.03527659 1377.930448 -3.139227297 0.120149295 TGFINLDKPSNPSSHEVVAWIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGFINLDKPSNPSSHEVVAWIR 22 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 236.5 1.02E-30 1520070000 1169110 1340520 1163770 1299180 1192880 1218270 1223990 1251060 1298540 1502260 FALSE TRUE 1123419.889 1302289.682 1374089.127 1366230.835 1231250.069 1242904.254 1238969.556 1225225.174 1151135.183 1400510.592 0.802150226 0.929867785 0.981134405 0.975523386 0.879143703 0.887465087 0.884655613 0.874841776 0.821939648 1 20.41752146 3.139875839 22.10019493 0.883892555 0.927015369 0.046144152 0.061902008 13.86924241 3080.90032 0.017665667 0.021114538 1379.989683 -3.139875839 0.043122815 AFVRPSGTEDVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFVRPSGTEDVVR 13 1 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;H0Y8I3 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 186.51 7.07E-06 1240600000 1038900 1195200 967110 1115900 984090 746490 1200200 1024800 1001900 1161800 FALSE TRUE 998298.6394 1161114.066 1141888.29 1173491.733 1015744.149 761584.5393 1214888.407 1003637.522 888168.5123 1083110.251 0.921696234 1.072018352 1.054267826 1.083446243 0.937803098 0.703145906 1.121666428 0.926625448 0.820016717 1 20.04674867 3.140101203 6.74374809 0.918316871 1.036730171 0.207667122 0.110062469 0.348336951 20.5125082 0.031814975 0.038217256 1380.705972 -3.140101203 0.1184133 S(ph)SDIVSSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSDIVSSVR 9 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 S(0.97)S(0.03)DIVSSVR 73.666 0.03289 0 83464 94292 65065 99730 97727 103010 106460 137320 119950 117230 TRUE FALSE 80202.13461 91602.88448 76823.69286 104877.0773 100870.4777 105092.9328 107762.8893 134484.294 106333.7789 109289.9077 0.733847583 0.838164167 0.702934923 0.959622709 0.92296242 0.961597782 0.986027819 1.230528023 0.972951493 1 16.73780066 3.140897944 0.792940148 1.084766174 0.748981139 0.629483045 0.086209598 0.39727979 0.553632624 0.048662617 0.075448288 1383.24129 -3.140897944 -0.335785034 ASS(ph)ESQGLGAGVR ddPTM_BT-474_Pertuzumab_2h_R1 6 ASSESQGLGAGVR 13 0 Q9BV36-2;H7C2D8;Q9BV36-3 Q9BV36-2;Q9BV36-3 MLPH Melanophilin 1 AS(0.001)S(0.999)ESQGLGAGVR;ASS(1)ESQGLGAGVR;AS(0.03)S(0.97)ESQGLGAGVR;AS(0.007)S(0.993)ESQGLGAGVR;AS(0.001)S(0.999)ESQGLGAGVR;AS(0.016)S(0.983)ES(0.002)QGLGAGVR 258.42 6.50E-24 5638630000 4678180 5248950 3789350 3966870 3870550 3607630 2746920 3556040 3469090 3803190 TRUE FALSE 4495351.554 5099255.085 4474169.839 4171600.636 3995049.756 3680578.75 2780537.629 3482606.531 3075293.447 3545596.554 1.267868886 1.438193829 1.261894796 1.176558182 1.126763775 1.038070377 0.784222792 0.982234295 0.867355719 1 21.75759695 3.141241442 1.023443115 0.907961502 1.349684554 0.827323896 0.078466387 0.189166241 0.429709076 0.033630236 0.048711494 1384.335775 -3.141241442 0.441723052 HWPFMVVNDAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HWPFMVVNDAGR 12 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 169.23 4.44E-05 2602900000 1509580 1492470 1419990 1520940 1244040 650220 1604800 881770 1617700 1902150 FALSE TRUE 1450583.945 1449906.217 1676613.781 1599435.896 1284055.676 663367.8939 1624440.022 863561.1414 1434065.478 1773315.686 0.818006605 0.817624424 0.945468307 0.901946511 0.724098753 0.374083362 0.916046723 0.486975415 0.808691588 1 20.75801796 3.141737163 5.363913128 0.673857017 0.871602843 0.124842522 0.17911668 0.308850981 13.89685949 0.048867916 0.059102487 1385.916812 -3.141737163 0.197745826 YQILPLHSQIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YQILPLHSQIPR 12 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 200.44 1.60E-07 3126500000 3331800 3469500 2789400 3200800 3034300 2800100 3263100 3225800 3211800 3410300 FALSE TRUE 3201589.573 3370553.257 3293506.63 3365993.672 3131901.015 2856719.94 3303034.794 3159186.103 2847209.929 3179317.343 1.007005349 1.060149992 1.035916291 1.058715852 0.985086003 0.898532494 1.038913212 0.993668062 0.895541282 1 21.6002856 3.142517799 5.680684085 0.97065425 1.041284662 0.399246126 0.04337599 0.224261983 10.8812644 0.012687772 0.015314268 1388.410213 -3.142517799 0.070630412 HREQEELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 HREQEELRR 9 2 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 123.75 0.00030878 268790000 124920 129574 101438 109407 106072 113421 114101 86695 127518 130089 FALSE TRUE 120037.9883 125878.6764 119770.1031 115053.5084 109483.9022 115714.4503 115497.4022 84904.71795 113042.6912 121277.9562 0.989775818 1.037935338 0.987566965 0.948676182 0.902751874 0.954125993 0.952336318 0.700083681 0.932095946 1 16.88795782 3.142694492 0.82831732 0.862333607 1.016758265 0.183053236 0.079500605 0.7698309 1.168981822 0.044158679 0.067700391 1388.9752 -3.142694492 0.154424658 QVVQGLLSETYLEAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVVQGLLSETYLEAHR 16 0 P33993;P33993-3;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 228.51 4.04E-15 1147690000 764720 811670 661740 750270 697280 710440 672860 688570 796630 882960 FALSE TRUE 734833.897 788521.9663 781331.1383 788991.5246 719708.6445 724805.5836 681094.662 674350.7889 706199.9021 823156.3327 0.89270272 0.957924923 0.949189245 0.958495359 0.874328017 0.880519963 0.827418359 0.819225659 0.85791711 1 19.65080693 3.14272154 4.763725124 0.859822968 0.941440396 0.235693163 0.050842156 0.223569178 8.635389777 0.014354971 0.017457284 1389.06171 -3.14272154 0.081617429 SNTENLSQHFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SNTENLSQHFR 11 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 232.17 5.29E-13 2709650000 1654750 2214540 1756740 2100630 1749140 1553280 2008660 1819030 1837420 2163260 FALSE TRUE 1590080.541 2151383.487 2074221.996 2209043.766 1805402.677 1584688.386 2033242.582 1781466.395 1628843.785 2016740.473 0.788440834 1.066762688 1.028502191 1.095353515 0.895208234 0.785767136 1.008182564 0.883339437 0.807661574 1 20.94359401 3.142827048 12.34566497 0.892869166 1.00228498 0.181304522 0.101406968 0.800407199 98.15791125 0.028557301 0.034140079 1389.399211 -3.142827048 0.109415813 RQVEEAER ddPTM_BT-474_Pertuzumab_2h_R1 3 RQVEEAER 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 142.43 0.00099036 720450000 594728 672930 575668 563607 524378 242263 598808 455301 513753 560569 FALSE TRUE 571485.3723 653738.6953 679704.0133 592694.8248 541245.0946 247161.7238 606136.3914 445898.8752 455433.9133 522601.1623 1.093540186 1.250932341 1.30061711 1.134124582 1.03567526 0.472945224 1.159845089 0.853229781 0.871475125 1 18.99535081 3.143550696 3.442026711 0.876894631 1.210341304 0.436647992 0.1711188 0.212741131 4.953085943 0.049513674 0.061418254 1391.716243 -3.143550696 0.333446673 TPGVVASAPTKPQS(ph)PAQNATSSQDSSQDTLTEQITLENQVHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPGVVASAPTKPQSPAQNATSSQDSSQDTLTEQITLENQVHQR 43 1 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80;A0A0A0MR72 Q96L91-4 EP400 E1A-binding protein p400 1 TPGVVASAPT(0.036)KPQS(0.963)PAQNATSSQDSSQDTLTEQITLENQVHQR;TPGVVAS(0.001)APT(0.028)KPQS(0.971)PAQNATSSQDSSQDTLTEQITLENQVHQR 221.46 1.47E-44 580120000 119179 110894 81625 98986 113488 124113 107152 124073 144491 139386 TRUE FALSE 114521.3529 107731.4117 96376.45324 104094.6793 117138.4446 126622.6499 108463.3582 121510.8492 128088.9874 129945.2621 0.881304567 0.829052248 0.741669621 0.8010656 0.901444522 0.974430679 0.834684978 0.935092571 0.985714949 1 16.98754451 3.143658946 4.30848685 0.93255699 0.809277919 0.567704492 0.053934884 0.171522916 5.753560952 0.016174193 0.019782897 1392.063177 -3.143658946 -0.123279071 SVS(ph)KESVASMGADSGDDFASDGSSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVSKESVASMGADSGDDFASDGSSSR 26 1 Q92805;Q5T165 Q92805 GOLGA1 Golgin subfamily A member 1 1 S(0.12)VS(0.437)KES(0.437)VAS(0.005)MGADSGDDFASDGSSSR;S(0.009)VS(0.988)KES(0.003)VASMGADSGDDFASDGSSSR 229.8 4.49E-35 580120000 277490 256660 188035 204515 269550 291120 281780 296120 285100 299170 TRUE FALSE 266645.384 249340.3081 222017.1073 215070.0437 278220.3205 297006.6459 285228.5079 290005.0185 252736.6432 278906.9494 0.956037075 0.89399102 0.796025727 0.77111755 0.997538144 1.064895107 1.022665475 1.039791296 0.906168325 1 18.08942436 3.144429665 7.441983612 1.014470714 0.853379852 0.591206546 0.06127188 0.15740025 10.76537824 0.018526633 0.022220542 1394.53579 -3.144429665 -0.161090862 EAASQRPLSSSASNR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAASQRPLSSSASNR 15 1 A0A087X2H1;Q9ULT8;H0YJP0 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 0 ; 79.837 0.0094339 0 53200 59785 42830 53456 55818 59116 63378 61858 63255 64910 FALSE TRUE 51120.88518 58079.99034 50570.33375 56214.87057 57613.43666 60311.36602 64153.63892 60580.61068 56074.55759 60513.58788 0.844783576 0.959784279 0.835685596 0.928962776 0.95207438 0.99665824 1.060152623 1.001107566 0.926644074 1 15.8849715 3.144506056 1.937637077 1.002064564 0.888186808 0.560044235 0.04431936 0.238122685 1.836083971 0.014258443 0.018544272 1394.781108 -3.144506056 -0.113877756 SRDPFWNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDPFWNR 8 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 148.14 0.00047968 220280000 54326 58058 45928 55873 49761 39415 57259 54503 52045 64253 FALSE TRUE 52202.87986 56402.24268 54228.21126 58756.61223 51361.60776 40211.99831 57959.75277 53377.494 46137.06979 59901.08708 0.871484683 0.941589634 0.905295945 0.980893922 0.857440328 0.671306653 0.967591 0.891093912 0.77022091 1 15.87029456 3.14474103 11.63959924 0.855479267 0.924588616 0.109039928 0.090865368 1.015030068 119.0592924 0.026069254 0.031168965 1395.535954 -3.14474103 0.069109349 KPQSSSTEPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KPQSSSTEPAR 11 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ;;; 150.14 5.46E-05 693080000 748810 766360 629746 719210 784210 824880 835890 888070 905280 937330 FALSE TRUE 719545.6773 744504.1631 743555.1108 756328.5143 809434.8269 841559.6388 846119.8719 869731.0442 802516.4096 873843.8042 0.823425965 0.851987689 0.850901623 0.865519113 0.926292345 0.963054993 0.968273584 0.995293484 0.918375121 1 19.7370159 3.144758809 1.498293396 0.973262761 0.840287402 0.875709751 0.021690857 0.119575032 0.558520419 0.007413597 0.009998139 1395.593087 -3.144758809 -0.132975359 DLSYCLSGMYDHR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLSYCLSGMYDHR 13 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;; 213.18 7.96E-09 7447300000 3518240 4068020 3357530 3904620 3272150 2542280 3788850 3380490 3639460 3780890 FALSE TRUE 3380743.291 3952004.053 3964310.359 4106137.906 3377401.676 2593686.643 3835219.08 3310681.7 3226323.759 3524806.953 0.959128638 1.121197304 1.124688646 1.164925615 0.95818061 0.735837928 1.088065001 0.939251921 0.915319279 1 21.74911282 3.144899925 6.964588519 0.936113587 1.096326121 0.377927544 0.096355652 0.228424817 14.46014904 0.027828823 0.033416016 1396.046631 -3.144899925 0.160212534 LFNVDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFNVDR 6 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;; 170.4 0.013377 1781010000 2104920 2218650 1782430 2058590 1827180 1774900 1614620 1921660 2059360 2301630 FALSE TRUE 2022657.399 2155376.274 2104554.751 2164834.077 1885952.904 1810789.694 1634380.203 1881977.049 1825590.086 2145738.55 0.94263926 1.004491565 0.980806702 1.008899279 0.878929497 0.843900434 0.761686554 0.87707659 0.850798009 1 21.03304287 3.145391829 4.812889691 0.852985524 0.985222243 0.480173078 0.057933945 0.154047678 6.08402913 0.016086316 0.01956425 1397.62876 -3.145391829 0.132236719 AVYLPNCDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVYLPNCDRK 10 1 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 0 85.355 0.022923 346490000 303220 336240 254970 270870 268010 207470 265330 225990 256800 276150 FALSE TRUE 291369.8272 326650.7644 301048.7508 284849.6332 276630.7851 211665.1855 268577.1879 221323.2275 227649.1406 257446.1145 1.131770148 1.268812175 1.169366068 1.106443706 1.074519169 0.822172772 1.043236517 0.859687581 0.884259376 1 17.97391097 3.145525829 1.681976362 0.917953392 1.194337554 0.717577373 0.073019121 0.172812563 1.009995399 0.023465206 0.03110664 1398.06006 -3.145525829 0.276384162 RLEELLR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEELLR 7 1 P42285;H0YAC4 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 167.24 0.0017534 232020000 143234 146045 148169 139947 129863 89220 133304 127301 134475 156816 FALSE TRUE 137636.2569 141879.9396 174946.4343 147169.6814 134040.1613 91024.08953 134935.4142 124672.1899 119209.9618 146194.7126 0.941458514 0.970486121 1.196667315 1.006668974 0.916860527 0.622622309 0.92298423 0.852781798 0.815419105 1 17.15753161 3.145871531 3.796883338 0.836838116 1.03776354 0.382696528 0.110321763 0.220727561 6.089228313 0.032338891 0.039897161 1399.173372 -3.145871531 0.200925425 WIHALEETILR ddPTM_BT-474_Pertuzumab_2h_R1 1 WIHALEETILR 11 0 Q96SU4-7;Q96SU4-2;Q96SU4;Q96SU4-6;H0YE19 Q96SU4-7 OSBPL9 Oxysterol-binding protein-related protein 9 0 146.11 0.0017866 0 28599 30423 25331 30881 25932 24235 30628 25316 30311 27893 FALSE TRUE 27481.31946 29555.36583 29908.87519 32474.77211 26766.12633 24725.0483 31002.83463 24793.21575 26870.22235 26003.78227 1.056820088 1.136579499 1.150174035 1.248848024 1.029316661 0.950825078 1.192243279 0.953446522 1.033319772 1 14.66643386 3.14812888 12.62982083 1.027137794 1.147400309 0.379869423 0.076099787 0.627577953 84.35077539 0.02160218 0.025824573 1406.464842 -3.14812888 0.120262515 ALQLEEER ddPTM_BT-474_Pertuzumab_2h_R1 4 ALQLEEER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 193.29 0.00039875 1574870000 1649100 1738950 1433800 1742660 1499850 1121500 1729080 1740250 1576260 1800480 FALSE TRUE 1584651.349 1689356.849 1692919.555 1832598.891 1548094.037 1144177.498 1750240.998 1704313.229 1397329.573 1678531.886 0.944069852 1.006449066 1.008571579 1.091786761 0.922290515 0.681653717 1.042721329 1.01535946 0.832471271 1 20.67876851 3.148351088 13.8585793 0.921183186 1.011962986 0.174219584 0.103014888 1.640985685 245.4553164 0.031464245 0.037610729 1407.184648 -3.148351088 0.0907798 ASLGLADHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASLGLADHR 9 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 81.338 0.021251 0 133110 180710 145600 145190 126330 76831 149480 100430 115720 137280 FALSE TRUE 127907.914 175556.3277 171913.1589 152683.2733 130393.5192 78384.57546 151309.381 98356.0854 102583.9507 127981.9033 0.999421877 1.371727746 1.343261464 1.19300674 1.018843413 0.612466086 1.182271689 0.76851557 0.801550439 1 16.9655803 3.148857173 3.303735872 0.872935154 1.250119847 0.48893505 0.169402506 0.188589041 4.090764776 0.048697599 0.060719401 1408.825399 -3.148857173 0.377184693 DYHQQFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYHQQFR 7 0 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-3 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 113.14 0.0061974 132870000 391030 392790 357750 338000 345390 240670 410760 200880 420750 372450 FALSE TRUE 375748.1153 381588.0138 422403.3831 355444.2205 356499.783 245536.5123 415787.0038 196731.7578 372988.2239 347223.6298 1.082150185 1.098969025 1.216516812 1.023675205 1.026715213 0.707142289 1.197461717 0.566585166 1.07420173 1 18.40550561 3.14939827 2.245921124 0.880151114 1.123131002 0.207493861 0.174176501 0.381690507 3.938811349 0.052393817 0.06731207 1410.581781 -3.14939827 0.242979888 HLTSNSPR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLTSNSPR 8 0 P14923 P14923 JUP Junction plakoglobin 0 ;; 133.12 0.0009329 114568000 50347 81999 58579 83411 47837 27454.2 78962 39717 45038 57618 FALSE TRUE 48379.38358 79660.46881 69165.52838 87715.85171 49375.72055 28009.34273 79928.36058 38896.83007 39925.47505 53715.48154 0.900659962 1.483007627 1.287627447 1.632971523 0.919208376 0.521438921 1.487994863 0.724126992 0.743276871 1 15.71305033 3.149835691 9.615285156 0.896367715 1.334061664 0.337918348 0.292609998 0.351292026 34.92009572 0.082051097 0.098172624 1412.003234 -3.149835691 0.437693949 HIEWESVLTNTAGCLR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIEWESVLTNTAGCLR 16 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 258.36 1.05E-26 520850000 194630 265850 178610 273200 178460 192240 229960 162040 217150 239180 FALSE TRUE 187023.6444 258268.2183 210888.8002 287299.8847 184200.328 196127.2245 232774.3193 158693.8174 192500.0424 222980.1256 0.838745803 1.158256673 0.945773977 1.288455121 0.826084062 0.879572671 1.043924066 0.711694896 0.86330583 1 17.7665556 3.150554173 23.88509091 0.872654299 1.057194502 0.257014489 0.140568844 18.51143285 5018.404732 0.038844801 0.046428446 1414.341135 -3.150554173 0.184540203 SLHDAIMIVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLHDAIMIVR 10 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 215.93 7.96E-09 1612370000 159176 215365 189917 188584 157092 93959 181279 132830 178825 188544 FALSE TRUE 152955.2259 209223.0011 224239.2266 198316.8428 162145.0068 95858.91536 183497.5466 130087.0141 158525.5357 175773.7469 0.870182428 1.190297213 1.275726498 1.128250642 0.922464302 0.545353996 1.043941714 0.740082159 0.901872654 1 17.42336008 3.151038078 4.302474349 0.831001629 1.133315503 0.377618507 0.162215182 0.198255191 6.746022789 0.045962787 0.056351123 1415.91792 -3.151038078 0.302313873 SLVDTVYALKDEVQELR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLVDTVYALKDEVQELR 17 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 ; 164.02 2.41E-09 404800000 407110 427740 342510 382540 425780 454320 438380 468210 518670 444390 FALSE TRUE 391199.6911 415541.274 404409.1761 402282.9352 439475.6004 463506.6617 443745.0256 458541.2999 459792.756 414291.0695 0.944262911 1.003017696 0.976147462 0.971015223 1.060789461 1.118794721 1.071094837 1.10680952 1.109830238 1 18.6602852 3.151162687 3.988823435 1.088603308 0.975513639 0.689619869 0.034239216 0.110974983 3.345626359 0.00935154 0.011522793 1416.324236 -3.151162687 -0.11308967 SYDVPPPPMEPDHPFYSNISK ddPTM_BT-474_Pertuzumab_2h_R1 3 SYDVPPPPMEPDHPFYSNISK 21 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;; 235.5 8.37E-30 1915360000 2036380 2068440 1722570 2006890 1842860 1862710 1918460 1931400 2124540 1924080 FALSE TRUE 1956796.018 2009450.116 2033876.717 2110465.833 1902137.266 1900375.272 1941938.687 1891515.915 1883371.126 1793760.348 1.090890442 1.120244473 1.133862012 1.176559531 1.060418839 1.059436549 1.082607657 1.054497563 1.04995694 1 20.77455572 3.15216106 9.052260854 1.056096877 1.129817156 0.659178288 0.027782986 0.184392864 17.4946968 0.007922244 0.009482892 1419.583883 -3.15216106 0.073720279 VAILVDDMADTCGTICHAADK ddPTM_BT-474_Pertuzumab_2h_R1 4 VAILVDDMADTCGTICHAADK 21 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;B7ZB02;P11908;P11908-2 B1ALA9;P11908 PRPS1;PRPS2 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2 0 ;;; 328.07 5.21E-80 986870000 880308 844709 681673 787128 842863 889180 877847 891706 976713 1023380 FALSE TRUE 845904.5901 820618.7264 804866.4748 827751.7704 869974.4539 907159.8288 888590.3542 873291.9595 865840.635 954065.5611 0.886631511 0.860128234 0.843617575 0.867604706 0.911860242 0.950835944 0.931372424 0.915337473 0.907527397 1 19.86372888 3.152670514 3.265272493 0.933283997 0.861931955 0.653489518 0.025951958 0.155422096 3.305874183 0.007548269 0.009436588 1421.250118 -3.152670514 -0.071352042 ARPAEVGGMQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ARPAEVGGMQLR 12 1 P33316-2;H0YNJ9;H0YNW5;P33316;H0YKC5;H0YMM5;H0YKI0 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;; 115.75 0.00083541 3645570000 3125570 3220060 2769800 2823150 2919990 2586360 2932510 2918760 2981760 3042250 FALSE TRUE 3003419.269 3128227.042 3270364.474 2968853.11 3013914.13 2638657.971 2968398.935 2858486.586 2643283.105 2836195.698 1.058960519 1.102965865 1.153081389 1.046773011 1.06266085 0.930351165 1.046612875 1.007859432 0.931981918 1 21.43552565 3.153053898 2.045551842 0.991728133 1.101562816 0.580659516 0.042804646 0.229384869 1.969091562 0.013573412 0.017648461 1422.505317 -3.153053898 0.109834683 ATMKDDLADYGGYDGGYVQDYEDFM ddPTM_BT-474_Pertuzumab_2h_R1 2 ATMKDDLADYGGYDGGYVQDYEDFM 25 1 O75822;O75822-2;O75822-3;H0YLP3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 165.87 1.34E-11 170162000 372640 372300 294370 332080 367760 407540 367730 379380 438500 432100 FALSE TRUE 358076.8168 361682.3685 347569.2072 349218.6886 379589.3344 415780.738 372230.3897 371545.6704 388723.3183 402833.4821 0.888895369 0.897845846 0.862811118 0.866905816 0.942298372 1.032140466 0.924030415 0.922330657 0.964972714 1 18.61982407 3.153199218 5.271573239 0.959404521 0.879450339 0.623784315 0.032467585 0.156806377 7.278214376 0.010108065 0.012258183 1422.981381 -3.153199218 -0.079954182 HCGLSLSST(ph)PPGK ddPTM_BT-474_Pertuzumab_2h_R1 4 HCGLSLSSTPPGK 13 0 Q09GN1;Q71F23-3;Q71F23;D6R9S4 Q09GN1 MLF1IP;CENPU Centromere protein U 1 HCGLSLS(0.003)S(0.176)T(0.821)PPGK;HCGLSLS(0.001)S(0.022)T(0.977)PPGK;HCGLSLSS(0.028)T(0.972)PPGK;HCGLSLSS(0.262)T(0.738)PPGK 165.64 0.0001287 3324830000 3729210 4228150 2788450 3279350 3030650 1850500 3158490 2636180 3071540 2786610 TRUE FALSE 3583468.35 4107567.302 3292384.944 3448597.646 3128133.61 1887918.378 3197144.545 2581741.962 2722871.656 2597870.423 1.37938687 1.58112863 1.267339939 1.327470999 1.204114563 0.726717684 1.230678989 0.993791661 1.048116808 1 21.30889804 3.153414462 2.604925366 1.015238828 1.406145163 0.632817365 0.138570157 0.175073806 2.418916943 0.041622027 0.052921707 1423.686811 -3.153414462 0.390906334 MS(ph)DEFVDSFK ddPTM_BT-474_Pertuzumab_2h_R1 6 MSDEFVDSFK 10 0 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 MS(1)DEFVDSFK;MS(1)DEFVDSFK;MS(1)DEFVDSFK;MS(1)DEFVDSFK;MS(1)DEFVDSFK;MS(1)DEFVDSFK 217.45 7.60E-09 522588000 1123616 981825 1096573 1188061 1195354 1087755 1297510 1530520 1582790 1570460 TRUE FALSE 1079703.844 953824.3123 1294748.134 1249376.971 1233803.647 1109750.151 1313389.316 1498914.227 1403118.315 1464091.345 0.737456613 0.65147869 0.884335624 0.853346326 0.842709474 0.757978766 0.897067877 1.023784637 0.958354354 1 20.48157414 3.15414884 0.316694644 1.035513644 0.637647675 0.63840743 0.067848773 1.811534442 0.307697756 0.090552387 0.259966952 1426.096256 -3.15414884 -0.397865969 RFVEVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RFVEVGR 7 1 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;; 141.52 0.004091 1211750000 675190 696950 635300 504938 685970 452552 574350 549227 590006 617560 FALSE TRUE 648802.8283 677073.6684 750112.8422 530997.9107 708034.848 461702.9115 581379.0671 537885.2705 523030.9924 575732.1111 1.126917912 1.176022069 1.302885192 0.922300321 1.229799128 0.801940525 1.009808305 0.934263106 0.908462429 1 19.13503815 3.154318957 1.223785452 0.938550428 1.18402589 0.423840059 0.115787947 0.402922439 1.27982286 0.042193505 0.059632677 1426.65498 -3.154318957 0.245475462 HKEQVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HKEQVEK 7 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EPD6 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 0 78.77 0.02069 38746000 119200 113220 103400 93393 107440 104170 111840 87764 119940 120310 FALSE TRUE 114541.5322 109991.0765 122086.6801 98213.02392 110895.9052 106276.3888 113208.7314 85951.64273 106324.914 112161.2965 1.021221542 0.980650901 1.088492055 0.875640947 0.98871811 0.947531743 1.009338648 0.766321765 0.947964381 1 16.77521541 3.154343907 0.740785205 0.90146934 1.023191675 0.130424575 0.078244682 1.098069357 1.331461014 0.046588486 0.075236301 1426.736942 -3.154343907 0.121722335 RIEESAIDEVVVTNTIPHEVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RIEESAIDEVVVTNTIPHEVQK 22 1 O60256;O60256-2;O60256-4;I3L0S1 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 0 ; 218.44 7.66E-26 489860000 246193 256940 187167 218018 242225 274690 240604 250410 278260 275620 FALSE TRUE 236571.5054 249612.3228 220992.2404 229269.9351 250016.3871 280244.42 243548.5837 245238.946 246673.0914 256952.0119 0.920683608 0.971435565 0.860052579 0.892267523 0.973008093 1.090648864 0.947836843 0.954415356 0.959996731 1 17.97113942 3.15499108 6.164978342 0.98606034 0.911993401 0.402150496 0.045863155 0.239441176 14.03096375 0.014191402 0.017107523 1428.864612 -3.15499108 -0.074066939 DHINDIIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHINDIIK 8 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 122.13 0.0014034 1412970000 4247400 4403300 3350900 3505200 3567000 2405800 4131000 1617860 4059000 3739700 FALSE TRUE 4081406.912 4277722.195 3956482.17 3686103.792 3681735.794 2454446.924 4181556.414 1584450.626 3598239.337 3486406.788 1.170662852 1.226971623 1.134830905 1.057278745 1.056025879 0.704004746 1.199388559 0.454465219 1.032076736 1 21.73330948 3.155932083 1.108859085 0.827314212 1.195432205 0.282592149 0.195199749 0.517414561 1.365145509 0.078187463 0.113089049 1431.963945 -3.155932083 0.368117993 SGSDRLPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSDRLPSR 9 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 88.496 0.011624 67472000 115580 129320 97909 110550 105010 92916 110840 95948 121230 124910 FALSE TRUE 111063.0058 125631.9202 115603.3343 116255.4987 108387.742 94794.82518 112196.4931 93966.64027 107468.4786 116449.7344 0.953742027 1.078851067 0.992731626 0.998332021 0.930768477 0.814040716 0.963475732 0.806928764 0.922874399 1 16.82934782 3.156184151 3.19969434 0.886833511 1.012046746 0.365530103 0.063410375 0.210899055 4.327110452 0.01779415 0.022316298 1432.79531 -3.156184151 0.125213235 VAEEHAPSIVFIDEIDAIGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAEEHAPSIVFIDEIDAIGTK 21 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 190.71 1.70E-17 131915000 116029 102660 97341 104879 113426 116347 125429 130943 128714 128119 FALSE TRUE 111494.4584 99732.23731 114932.684 110291.8178 117074.4503 118699.6161 126964.0376 128238.9813 114102.9263 119441.386 0.933465879 0.834988948 0.962251761 0.923397002 0.980183287 0.993789674 1.062981952 1.073656172 0.955304775 1 16.86594329 3.156365447 1.138761866 1.03374566 0.896883328 0.553991955 0.043757615 0.312933751 0.867933471 0.017752163 0.025536229 1433.393552 -3.156365447 -0.136862332 MKEEMDR ddPTM_BT-474_Pertuzumab_2h_R1 4 MKEEMDR 7 1 F5H442;Q99816;Q99816-2 F5H442 TSG101 Tumor susceptibility gene 101 protein 0 ;;; 104.17 0.0074896 1675300000 2342230 2396710 2170420 2195830 2432290 2468370 2649570 2660030 3103470 3043860 FALSE TRUE 2250693.062 2328358.177 2562663.175 2309157.049 2510526.817 2518282.133 2681996.23 2605099.451 2751177.096 2837696.651 0.793140825 0.820509894 0.90307862 0.813743445 0.884705846 0.887438808 0.945131408 0.918033099 0.96951064 1 21.43628894 3.156990871 0.230499174 1.021302764 0.729074842 0.813646587 0.028094145 2.102562026 0.198740345 0.056452745 0.183751526 1435.45926 -3.156990871 -0.292227921 LRDFLLDIEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LRDFLLDIEDR 11 1 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 ;; 192.15 1.39E-06 178887000 311584 327553 275937 305847 278760 202513 317852 305353 289207 314886 FALSE TRUE 299406.9528 318211.5091 325804.9541 321631.8003 287726.5686 206607.9516 321741.9679 299047.3538 256377.4338 293558.4907 1.019922647 1.083979919 1.109846809 1.09563106 0.980133696 0.703805061 1.096006343 1.018697681 0.873343616 1 18.16328846 3.15774414 5.457225901 0.948712687 1.079875153 0.297740637 0.099987246 0.28444728 14.27508874 0.030295268 0.036712682 1437.951176 -3.15774414 0.131162466 IFSGSSHQDLSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 IFSGSSHQDLSQK 13 0 B1ALA9;P60891;A0A2R8Y7H4;Q15244;B1ALA7;A0A0B4J207;P21108 B1ALA9;A0A0B4J207 PRPS1;PRPS1L1 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 3 0 155.08 1.36E-06 0 291880 392470 310600 340500 319090 299310 344880 330570 343970 372510 FALSE TRUE 280473.0069 381277.1399 366732.3293 358073.2458 329353.8196 305362.2533 349100.7446 323743.614 304923.9676 347279.5659 0.80762888 1.097896845 1.056014708 1.031080665 0.948382375 0.879298074 1.005244129 0.932227651 0.878036019 1 18.405738 3.157823104 6.365297848 0.937847173 1.009221413 0.101142931 0.081644973 0.404773493 25.44903915 0.022971641 0.027673203 1438.212648 -3.157823104 0.07137424 AYYEFR ddPTM_BT-474_Pertuzumab_2h_R1 6 AYYEFR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 109.88 0.067884 4260090000 4894630 5704620 4532820 4786940 4396530 2233870 5075740 4373370 4429010 4999280 FALSE TRUE 4703342.448 5541929.823 5352001.406 5033994.547 4537948.38 2279040.382 5137858.424 4283058.381 3926247.353 4660674.313 1.009154928 1.189083264 1.14833199 1.080100048 0.973667773 0.488993701 1.102385209 0.918978262 0.84242045 1 22.15210727 3.1580475 3.972209379 0.87701681 1.117259932 0.334492377 0.155183714 0.255316515 7.741652433 0.045724993 0.056508608 1438.955951 -3.1580475 0.240243122 QVSDDLTER ddPTM_BT-474_Pertuzumab_2h_R1 2 QVSDDLTER 9 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ; 121.6 0.0014173 657780000 614210 763470 664380 916210 557400 716810 713840 705480 693750 752050 FALSE TRUE 590205.9942 741696.5831 784448.2451 963495.7079 575329.2772 731304.3893 722576.1875 690911.5915 614998.4084 701112.9836 0.841812957 1.057884536 1.118861387 1.374237434 0.820594242 1.043062112 1.030613046 0.985449717 0.877174468 1 19.41928743 3.158553498 24.68040389 0.969242179 1.097035948 0.19775344 0.136011187 50.05817195 15438.1103 0.03989613 0.047685014 1440.633461 -3.158553498 0.127793769 HLTDAYFK ddPTM_BT-474_Pertuzumab_2h_R1 6 HLTDAYFK 8 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 114.28 0.0026864 6937480000 10775870 11931480 10469710 11351010 10160120 9275850 12348210 7921680 12525380 13191090 FALSE TRUE 10354737.09 11591205.87 12361819.49 11936836.99 10486929.49 9463414.042 12499331.09 7758094.54 11103551.37 12297645.72 0.842009708 0.94255487 1.005218378 0.97066034 0.852759115 0.769530547 1.016400323 0.630860143 0.902900573 1 23.55187882 3.1589226 5.826981719 0.834619901 0.944674662 0.075077279 0.112170324 0.358273697 19.99196051 0.031996502 0.038672192 1441.858359 -3.1589226 0.110054761 RQEAIAQNR ddPTM_BT-474_Pertuzumab_2h_R1 4 RQEAIAQNR 9 1 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 210.6 1.05E-05 590401000 351076 364936 318604 320086 331441 240397 366769 320726 336818 374421 FALSE TRUE 337355.5618 354528.3826 376182.8301 336605.6768 342102.1008 245257.992 371257.6287 314102.896 298583.8327 349061.1322 0.966465558 1.01566273 1.077698991 0.964317267 0.980063574 0.702621889 1.063589138 0.899850677 0.855391234 1 18.4131202 3.159518859 3.132308151 0.907565448 1.014600016 0.198746746 0.093880438 0.384010043 7.580217658 0.0273998 0.034474301 1443.839302 -3.159518859 0.107034567 HHAISAK ddPTM_BT-474_Pertuzumab_2h_R1 5 HHAISAK 7 0 P27824;P27824-2;P27824-3;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ;;;; 111.04 0.0066693 234794000 735742 1136636 740430 870965 593204 395047 856885 233434 732807 495645 FALSE TRUE 706988.3892 1104220.254 874242.1718 915915.608 612284.9454 403035.121 867371.815 228613.5063 649621.8215 462074.5227 1.530031098 2.389701661 1.891993886 1.982181581 1.325078349 0.872229697 1.877125382 0.494754623 1.405881064 1 18.81776602 3.159686877 3.699406159 1.109642201 1.982045555 0.499156582 0.388243613 0.174431499 4.681605028 0.109946593 0.136673875 1444.397994 -3.159686877 0.872403354 RQQEQQVPILEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RQQEQQVPILEK 12 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 175.88 4.25E-05 13887030000 4530300 4772030 3982910 4584520 4605050 5121190 5437560 5340440 6105240 6054620 FALSE TRUE 4353250.867 4635936.377 4702710.436 4821127.627 4753175.615 5224743.971 5504106.486 5230158.048 5412198.75 5644535.195 0.771232833 0.821314106 0.833143966 0.854123052 0.842084503 0.925628735 0.975121298 0.926587906 0.958838693 1 22.42842335 3.15992376 0.394907951 0.995829988 0.747984053 0.906087608 0.02216747 0.545393968 0.151283234 0.023332235 0.056351368 1445.186047 -3.15992376 -0.247845935 IGEGTY(ph)GVVYK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGEGTYGVVYK 11 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2;G3V317;K7ELV5;G3V5T9;P24941;P24941-2;E7ESI2;Q00526 P06493;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 IGEGT(0.108)Y(0.892)GVVYK;IGEGT(0.114)Y(0.876)GVVY(0.01)K 126.07 0.0012537 18856000000 283798 291676 227844 261357 243760 218051 245657 271784 242225 259619 TRUE FALSE 272706.8604 283357.6861 269020.4792 274845.6661 251600.7618 222460.1406 248663.4239 266171.5654 214728.6335 242034.7739 1.126725949 1.170731302 1.111495158 1.13556272 1.039523196 0.919124707 1.02738718 1.099724478 0.887180921 1 17.88485481 3.161666176 3.962780963 1.002999731 1.137627854 0.597562567 0.057012022 0.175460936 5.337469367 0.017613428 0.021803457 1450.995869 -3.161666176 0.134628123 VEYFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEYFLK 6 0 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 116.35 0.055015 379750000 1950100 1971200 1726000 1858400 1779900 1329300 2039300 1756200 2132900 2196600 FALSE TRUE 1873887.936 1914983.306 2037926.595 1954312.247 1837152.1 1356179.357 2064257.563 1719933.856 1890782.134 2047822.325 0.91506373 0.93513157 0.995167681 0.95433682 0.897124754 0.662254406 1.008025715 0.839884318 0.923313566 1 20.96565912 3.161675763 5.314448913 0.874624682 0.95199987 0.087434373 0.092682566 0.414590272 20.51441797 0.026127599 0.03173094 1451.027899 -3.161675763 0.077375187 (ac)MEDS(ph)MDMDMSPLRPQNYLFGCELK ddPTM_BT-474_Pertuzumab_2h_R1 13 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(1)MDMDMSPLRPQNYLFGCELK;MEDS(0.936)MDMDMS(0.062)PLRPQNY(0.002)LFGCELK;MEDS(0.923)MDMDMS(0.077)PLRPQNYLFGCELK;MEDS(0.944)MDMDMS(0.056)PLRPQNYLFGCELK;MEDS(0.932)MDMDMS(0.068)PLRPQNYLFGCELK;MEDS(0.883)MDMDMS(0.113)PLRPQNY(0.003)LFGCELK;MEDS(0.574)MDMDMS(0.426)PLRPQNYLFGCELK;MEDS(0.934)MDMDMS(0.066)PLRPQNYLFGCELK;MEDS(0.82)MDMDMS(0.177)PLRPQNY(0.002)LFGCELK;MEDS(0.488)MDMDMS(0.511)PLRPQNY(0.001)LFGCELK;MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.002)LFGCELK;MEDS(0.999)MDMDMS(0.001)PLRPQNYLFGCELK;MEDS(0.994)MDMDMS(0.006)PLRPQNYLFGCELK 98.689 2.16E-25 2622851000 1460549 1500280 1152928.9 1076946 1213124.6 1083904.5 853330.5 1025888.8 974794.2 1031065.2 TRUE FALSE 1403469.13 1457493.483 1361288.799 1132527.312 1252145.854 1105821.792 863773.8139 1004703.838 864139.6491 961230.2356 1.46007593 1.516279273 1.416194319 1.178206084 1.302649259 1.150423437 0.898612821 1.045227044 0.898993412 1 19.8745225 3.161697713 0.656017526 0.940944874 1.53020259 0.867895184 0.078922186 0.275104903 0.257294305 0.051866183 0.088847968 1451.101239 -3.161697713 0.589257715 LFWEWGDGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFWEWGDGIR 10 0 Q8N1G2 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 83.005 0.037949 93772000 212180 226670 174190 202550 220250 258200 246650 228640 239880 235950 FALSE TRUE 203887.771 220205.5935 205670.0078 213003.6298 227334.5413 263420.9809 249668.5765 223918.5041 212649.8281 219968.8963 0.92689364 1.001076048 0.934995862 0.968335221 1.033484938 1.197537403 1.135017635 1.017955301 0.966726804 1 17.74694002 3.16182399 4.05762707 1.070452268 0.958646248 0.366061444 0.065202229 0.244395519 7.751140855 0.020584347 0.025438674 1451.523227 -3.16182399 -0.111806019 HAHGDQYK ddPTM_BT-474_Pertuzumab_2h_R1 2 HAHGDQYK 8 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 160.26 0.00035436 328340000 587990 815810 530610 818430 361300 117172 845620 12450.4 496340 279200 FALSE TRUE 565010.7007 792543.8976 626503.0304 860669.2704 372921.5426 119541.2981 855968.9505 12193.29489 439997.564 260289.5353 2.170700793 3.044855017 2.40694667 3.306584221 1.432718154 0.45926279 3.288526177 0.046845121 1.690415881 1 17.98975779 3.161894846 7.172083601 1.275173557 2.728245478 0.39488822 0.856642641 0.217282319 16.96879793 0.236343935 0.283935724 1451.760065 -3.161894846 1.453071921 IDPWSFVSAGPRPS(ph)PLPS(ph)PQPAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDPWSFVSAGPRPSPLPSPQPAPR 24 1 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 2 IDPWS(0.002)FVS(0.002)AGPRPS(0.997)PLPS(1)PQPAPR 84.962 0.0071831 97315000 126310 150330 127360 117840 122010 115860 99137 123720 122810 124630 TRUE FALSE 121373.6656 146042.7356 150376.7851 123921.7365 125934.5625 118202.7686 100350.2683 121165.1388 108869.1237 116188.6991 1.044625394 1.256944408 1.294246224 1.066555848 1.083879615 1.01733447 0.863683551 1.042830669 0.937002691 1 16.82611023 3.163857037 1.528594057 0.971068702 1.198001116 0.574405475 0.080927917 0.264504074 1.285052521 0.02802646 0.038293432 1458.334119 -3.163857037 0.226932414 VDSPDVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDSPDVKR 8 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4;K7EPS6 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 90.657 0.020911 112580000 60508 59556 52099 48869 61930 69828 55914 68988 65262 64241 FALSE TRUE 58143.28046 57857.52119 61514.44824 51391.13495 63922.03469 71239.97 56598.29226 67563.37369 57853.73136 59889.89985 0.970836161 0.966064751 1.027125582 0.85809352 1.06732579 1.189515597 0.94503902 1.128126343 0.966001471 1 15.8700251 3.164446904 24.99999676 1.059792161 0.961390529 0.24629508 0.07886515 50.70170372 17101.19375 0.021573858 0.0257857 1460.316202 -3.164446904 -0.098401631 GSFKDDPQLYQEIQER ddPTM_BT-474_Pertuzumab_2h_R1 2 GSFKDDPQLYQEIQER 16 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ; 151.95 5.42E-07 989450000 1190360 1341370 1028740 1228290 1276160 1503900 1379110 1431100 1515350 1495800 FALSE TRUE 1143839.415 1303115.441 1214656.202 1291682.194 1317208.845 1534309.888 1395987.961 1401547.285 1343333.821 1394488.134 0.820257547 0.934475819 0.871040902 0.926276935 0.944582326 1.10026744 1.001075539 1.005062181 0.963316782 1 20.41130423 3.165938564 2.439572891 1.012492588 0.885182284 0.644771979 0.043942829 0.177604892 2.159616172 0.013268219 0.017089986 1465.340537 -3.165938564 -0.127310304 VLLGFSSDES(ph)DVEASPR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLLGFSSDESDVEASPR 17 0 Q9Y2U8 Q9Y2U8 LEMD3 Inner nuclear membrane protein Man1 1 VLLGFSSDES(1)DVEASPR;VLLGFSSDES(1)DVEASPR;VLLGFSS(0.001)DES(0.999)DVEASPR;VLLGFSSDES(1)DVEASPR 344.29 3.39E-73 174353000 123608 151082 81433 152243 94545 87388 94811 155383 100866 75165 TRUE FALSE 118777.2627 146773.2893 96149.75457 160100.2795 97586.12579 89155.04523 95971.32538 152174.2868 89416.11454 70074.0076 1.69502597 2.094546813 1.372117249 2.284731314 1.392615167 1.272298364 1.369570953 2.171622431 1.276023987 1 16.09659179 3.16651314 24.99999998 1.509185903 1.843352589 0.240493207 0.366556449 81.91415192 28421.83549 0.108106717 0.129212283 1467.28048 -3.16651314 0.334166686 IGLEVDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 IGLEVDRR 8 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ;;; 190.26 0.00030041 949660000 878530 989280 729660 868310 818410 713430 916060 858620 886610 953740 FALSE TRUE 844196.0763 961066.703 861525.7932 913123.5832 844734.9009 727856.0434 927271.0163 840889.197 785965.7498 889142.3403 0.949449867 1.080891843 0.968940241 1.026971208 0.950055871 0.818604638 1.042882533 0.945730688 0.883959423 1 19.76205487 3.166675617 6.413383802 0.939004215 1.009041228 0.198561213 0.065408631 0.329437456 22.94767778 0.018496111 0.022303072 1467.829516 -3.166675617 0.070037013 EVYFAER ddPTM_BT-474_Pertuzumab_2h_R1 8 EVYFAER 7 0 P50238 P50238 CRIP1 Cysteine-rich protein 1 0 ;;;;;;; 176.65 0.0017308 46431770000 10170000 11778960 9938400 9885890 9649130 5339980 11080280 9849550 9342400 9824720 FALSE TRUE 9772545.156 11443035.59 11734489.96 10396101.97 9959503.03 5447958.054 11215883.78 9646153.351 8281889.919 9159282.963 1.066955262 1.249337491 1.281158144 1.135034479 1.087367108 0.594801807 1.224537317 1.05315595 0.904207235 1 23.12680323 3.167052791 3.541318913 0.978404115 1.19827633 0.302303662 0.159051864 0.308110738 7.703962358 0.047987954 0.060054551 1469.104846 -3.167052791 0.219872215 QVHQCIER ddPTM_BT-474_Pertuzumab_2h_R1 4 QVHQCIER 8 0 E7EQY1;Q96C01;C9JF51 E7EQY1 FAM136A Protein FAM136A 0 ;;; 149.72 0.00050068 1531650000 707260 781990 676560 758580 610140 499394 687268 622950 631511 689200 FALSE TRUE 679619.4973 759688.4108 798829.442 797730.4047 629765.7072 509492.0888 695678.9914 610085.8648 559824.5188 642519.8701 1.057740825 1.182357848 1.243275857 1.241565346 0.980149777 0.792959273 1.082735373 0.949520619 0.871295262 1 19.29338155 3.167086238 6.029520403 0.944125688 1.185303137 0.643307149 0.085972191 0.127452739 8.073668989 0.02510833 0.030349282 1469.217991 -3.167086238 0.241177448 QQSELQSQVR ddPTM_BT-474_Pertuzumab_2h_R1 5 QQSELQSQVR 10 0 Q14847;Q14847-2;C9J9W2 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;; 259.4 6.62E-17 3573780000 777962 832304 734167 741535 724880 394128 831337 755140 769948 873115 FALSE TRUE 747558.385 808567.5048 866847.3084 779805.7102 748196.4235 402097.5382 841511.1509 739546.0951 682546.7309 813978.1434 0.918401054 0.993352845 1.064951578 0.958017997 0.919184906 0.493990584 1.033825242 0.908557682 0.838532013 1 19.63463053 3.167261607 4.166572367 0.856066269 0.991229165 0.149974944 0.141317464 0.407297234 13.73240981 0.042052621 0.051984891 1469.811384 -3.167261607 0.135162895 ELSFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSFGR 6 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ; 141.59 0.027066 322040000 236428 274070 210616 279940 215880 227890 242190 235880 265750 291140 FALSE TRUE 227188.1324 266253.7919 248678.9963 294387.7369 222823.9763 232498.0919 245153.9937 231008.9956 235583.1741 271420.8285 0.837032786 0.980963007 0.916211912 1.08461734 0.820953858 0.856596354 0.90322469 0.851110052 0.86796277 1 18.05017191 3.167289103 24.99999979 0.874488876 0.953861755 0.180943954 0.072974425 65.50527637 22976.05555 0.019849972 0.023725264 1469.904444 -3.167289103 0.079372879 LYFLQCETCHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LYFLQCETCHSR 12 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 197.36 1.96E-07 1471190000 1272540 1387310 1209990 1235260 1127360 776890 1216280 1140980 1131230 1248530 FALSE TRUE 1222807.73 1347745.277 1428662.109 1299011.917 1163622.558 792599.2481 1231165.198 1117418.364 1002817.513 1163965.951 1.050552835 1.157890638 1.22740885 1.116022265 0.99970498 0.680947108 1.057733001 0.960009495 0.861552275 1 20.15061743 3.167517937 3.75708953 0.919589204 1.147958372 0.515212389 0.102638702 0.183006003 5.112028219 0.030465666 0.037962983 1470.679154 -3.167517937 0.228369168 HYLSEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 HYLSEELR 8 0 Q7L2J0;Q7L2J0-2 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 0 152.47 0.00045665 172870000 175050 228490 157980 204390 144890 86461 207230 112110 168210 178980 FALSE TRUE 168208.8525 221973.6889 186530.5002 214938.5924 149550.5184 88209.30066 209766.1427 109794.8893 149115.506 166857.5252 1.00809869 1.330318718 1.117902834 1.288156421 0.896276738 0.528650419 1.257157221 0.658015808 0.893669649 1 17.34825723 3.167725496 6.527047637 0.850109445 1.190871923 0.370037852 0.199751522 0.200358296 14.52625853 0.054414457 0.065586078 1471.382194 -3.167725496 0.340762478 RLS(ph)AEGGDK ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSAEGGDK 9 1 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 RLS(1)AEGGDK;RLS(1)AEGGDK;RLS(1)AEGGDK 108.68 0.0027237 1110260000 1261810 1225150 1043050 1177130 1282360 1342370 1352290 1404230 1502910 1589410 TRUE FALSE 1212497.07 1190209.922 1231552.338 1237881.82 1323608.274 1369513.641 1368839.73 1375232.16 1332305.958 1481757.845 0.818282875 0.803241856 0.831142782 0.835414386 0.89326895 0.924249293 0.923794488 0.928108573 0.899138791 1 20.49887827 3.167829057 1.347479859 0.932621921 0.812233902 0.824773998 0.02472493 0.159778527 0.609261157 0.00847917 0.011907656 1471.733098 -3.167829057 -0.120388019 ELLSPLS(ph)EPDDRYPLIVK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLS(0.015)PLS(0.985)EPDDRYPLIVK;ELLS(0.058)PLS(0.942)EPDDRYPLIVK;ELLSPLS(1)EPDDRYPLIVK;ELLS(0.004)PLS(0.996)EPDDRYPLIVK 264.72 3.32E-31 2534400000 1500450 1451430 1106540 1296370 1394220 1451370 1379970 1576350 1493950 1558110 TRUE FALSE 1441810.755 1410036.637 1306516.393 1363275.811 1439066.352 1480717.696 1396858.486 1543797.822 1324363.059 1452577.822 0.992587615 0.970713318 0.899446744 0.938521703 0.990698282 1.019372369 0.961641066 1.062798701 0.911732948 1 20.47018403 3.168419377 5.734817171 0.998594958 0.948220726 0.165471012 0.042941706 0.297177389 17.55202946 0.012336358 0.014949001 1473.734928 -3.168419377 -0.050374232 VVDLMAHMASK ddPTM_BT-474_Pertuzumab_2h_R1 5 VVDLMAHMASK 11 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 176.78 8.27E-06 30796840000 28148100 29601400 24793180 26281960 25241080 18613830 27406600 25174790 28511300 27663900 FALSE TRUE 27048041.13 28757197.05 29273859.15 27638375.11 26052982.26 18990214.4 27742010.17 24654921.79 25274816.75 25790199.41 1.048772082 1.11504361 1.135076882 1.071661939 1.010189252 0.736334531 1.075680328 0.95598027 0.980016337 1 24.62031959 3.169916558 3.767666949 0.951774676 1.098913218 0.387737702 0.083919903 0.228458063 6.441383697 0.024551887 0.030621851 1478.82423 -3.169916558 0.147138542 (ac)AENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLR 33 0 Q6PCE3 Q6PCE3 PGM2L1 "Glucose 1,6-bisphosphate synthase" 0 ; 164.55 2.01E-117 258650000 5525.2 3891.1 1240.7 3290.4 4712.8 6333 3148.2 6430 5845.2 6703.4 FALSE TRUE 5309.269076 3780.129638 1464.922089 3460.217938 4864.391492 6461.057599 3186.728613 6297.218253 5181.677401 6249.372747 0.849568315 0.604881448 0.23441106 0.553690439 0.778380757 1.033872976 0.509927755 1.007656049 0.829151598 1 12.60949568 3.170186004 4.164181024 0.860393731 0.539163896 0.35962653 0.197407836 0.236127892 8.022074717 0.058023469 0.071821267 1479.742011 -3.170186004 -0.321229835 CPS(ph)QSSSRPAAMISQPPTPPTGQPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 CPSQSSSRPAAMISQPPTPPTGQPVR 26 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.968)QS(0.013)S(0.016)S(0.004)RPAAMIS(0.001)QPPTPPTGQPVR;CPS(0.996)QS(0.003)S(0.001)S(0.001)RPAAMISQPPTPPTGQPVR 185.19 8.92E-18 1005290000 133777 126082 140576 120343 115651 122997 94399 126636 128777 103580 TRUE FALSE 128548.8469 122486.2648 165981.2103 126553.9167 119371.0194 125484.0836 95554.2832 124020.9223 114158.7748 96564.43434 1.331223528 1.268440763 1.718864833 1.310564469 1.236179969 1.299485514 0.989539097 1.284333339 1.182203113 1 16.55920431 3.170357107 1.99900933 1.166263958 1.428172677 0.41367492 0.146837291 0.337787118 2.773790368 0.046897346 0.061869382 1480.325115 -3.170357107 0.261908718 QHWTMTK ddPTM_BT-474_Pertuzumab_2h_R1 2 QHWTMTK 7 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 127.56 0.0038425 1871680000 3796600 4107100 3373400 3114200 3313000 2871400 3331500 1961740 3672900 4010100 FALSE TRUE 3648224.675 3989969.529 3983048.421 3274924.235 3419565.654 2929461.675 3372271.894 1921229.383 3255967.79 3738492.355 0.975854523 1.067267002 1.065415692 0.876001319 0.914691092 0.7835944 0.902040602 0.513904858 0.870930707 1 21.83402515 3.170497286 1.095817311 0.759927669 1.040538329 0.29907598 0.128414077 0.46970675 1.21131179 0.053394437 0.07871725 1480.803 -3.170497286 0.280610661 SS(ph)SPATEQSWMENDFDELREEGFRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.17)S(0.654)S(0.177)PATEQSWMENDFDELREEGFRR 246.9 3.13E-39 335450000 23122 28840 19731 18678 26901 29907 30827 27460 25669 22044 TRUE FALSE 22218.36668 28017.51144 23296.83061 19641.97382 27766.2951 30511.74003 31204.27005 26892.9414 22755.16273 20550.94025 1.08113626 1.363320174 1.133613856 0.955770081 1.351096094 1.484688275 1.518386491 1.308599075 1.107256528 1 14.32691678 3.170566075 24.99967155 1.333811876 1.149882902 0.145367668 0.17571283 83.94914329 30864.55337 0.051179858 0.061171651 1481.037569 -3.170566075 -0.183928975 TLTGDVKTS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTGDVKTSPPR 12 1 Q9H8T0;Q9H8T0-2;H3BSX7;H3BNB8;H3BVH0;H3BRV2;H3BM79 Q9H8T0 AKTIP AKT-interacting protein 1 TLTGDVKT(0.009)S(0.991)PPR;TLTGDVKT(0.036)S(0.964)PPR 112.72 0.00075275 1767390000 2870600 2871100 1732130 1835490 2420000 2728700 2271050 2418200 2948900 2402700 TRUE FALSE 2758413.778 2789219.039 2045164.422 1930219.859 2497841.498 2783876.184 2298843.789 2368263.325 2614153.235 2239962.989 1.23145507 1.245207645 0.913034917 0.861719532 1.115126237 1.242822403 1.026286506 1.057277882 1.167051977 1 21.09504346 3.170578 0.009519943 6.22E-07 2.177610835 0.042031209 0.127809781 17643.08648 49.82571249 5496.618702 5899.5016 1481.078236 -3.170578 2.177610212 GFEKPTENSSAVLLQWHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFEKPTENSSAVLLQWHEK 19 1 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 ; 231.76 1.58E-20 4700000000 4100600 3555200 3309900 3447500 3950000 4284000 3974600 4044900 4558100 4876000 FALSE TRUE 3940344.019 3453809.177 3908072.558 3625425.888 4077055.337 4370625.415 4023242.344 3961371.401 4040683.597 4545744.177 0.866820451 0.759789606 0.859721182 0.797542877 0.896895025 0.961476327 0.885056921 0.871446181 0.888893752 1 22.11608506 3.172012372 6.260884125 0.908860591 0.819503651 0.505572355 0.046280799 0.178472335 12.69620937 0.013016897 0.015725571 1485.977973 -3.172012372 -0.08935694 MCHNVNR ddPTM_BT-474_Pertuzumab_2h_R1 6 MCHNVNR 7 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;; 148.28 0.0020945 885737000 470309 525915 423529 454259 407471 327110 490962 319398 443906 479844 FALSE TRUE 451928.8043 510916.4191 500070.1117 477703.3614 420577.6748 333724.3883 496970.5398 312802.3197 393515.6519 447343.7385 1.010249536 1.14211148 1.117865455 1.067866431 0.940166674 0.746013322 1.110936618 0.699243764 0.879671756 1 18.7710243 3.172366097 3.347676211 0.871170305 1.09417265 0.397578561 0.114059807 0.212515655 4.798999911 0.032650417 0.041146252 1487.188769 -3.172366097 0.223002345 TALIHDGLAR ddPTM_BT-474_Pertuzumab_2h_R1 10 TALIHDGLAR 10 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;;;;;;;; 188.99 1.06E-06 13639790000 8192260 8214150 6988179 8048480 7561660 7290078 8413940 8179430 8594320 8895280 FALSE TRUE 7872097.422 7979890.484 8251098.397 8463863.017 7804887.661 7437488.372 8516912.315 8010521.912 7618728.824 8292794.763 0.949269534 0.962267934 0.994971977 1.020628541 0.941164937 0.896861503 1.027025576 0.965961674 0.918716674 1 22.98342696 3.172444163 25 0.959158933 0.981338047 0.079484057 0.039092462 171.9534128 65017.10256 0.011669584 0.013947824 1487.456121 -3.172444163 0.022179114 FWEGDFHR ddPTM_BT-474_Pertuzumab_2h_R1 3 FWEGDFHR 8 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 ;; 133.86 0.00090124 832190000 571578 653766 535226 559447 555524 479487 593745 551650 563977 618253 FALSE TRUE 549240.0998 635121.2338 631953.2442 588320.1267 573392.934 489182.5557 601011.4289 540258.2347 499956.6953 576378.1736 0.952916202 1.101917565 1.096421192 1.020718954 0.994820693 0.848718043 1.042738009 0.937332917 0.867410874 1 19.13665618 3.17277321 2.880657914 0.943082285 1.053903358 0.3490669 0.065891746 0.27540841 4.644870786 0.019471998 0.024831422 1488.583531 -3.17277321 0.110821073 WISIMTER ddPTM_BT-474_Pertuzumab_2h_R1 2 WISIMTER 8 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 155 0.00096795 1240570000 892340 1072460 489650 1025390 610390 361440 667460 785570 730110 655830 FALSE TRUE 857466.3663 1041874.491 578140.6472 1078310.501 630023.7487 368748.5644 675628.5751 769347.705 647230.9737 611410.0499 1.402440746 1.704051955 0.945585777 1.763645365 1.030443887 0.603111716 1.10503348 1.258317074 1.058587398 1 19.22178074 3.173527582 15.18294819 1.025954719 1.435462378 0.416095654 0.257237935 2.062001889 479.9429724 0.075150957 0.08982854 1491.171457 -3.173527582 0.40950766 SGLIHVGDELR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGLIHVGDELR 11 0 S4R337;Q5T2T1-2;Q5T2T1 S4R337 MPP7 MAGUK p55 subfamily member 7 0 132.76 0.0001757 271810000 178260 198050 152910 201060 159810 169040 183740 175480 173840 188030 FALSE TRUE 171293.4021 192401.8079 180544.2385 211436.7307 164950.4338 172458.1046 185988.6651 171856.2767 154106.412 175294.5606 0.977174657 1.097591433 1.029947751 1.206179644 0.94099003 0.983818916 1.061006482 0.980385678 0.879128317 1 17.4194217 3.173705397 24.99999995 0.980103618 1.075740568 0.346889501 0.069271409 70.95962759 27352.39196 0.019679883 0.023521967 1491.782119 -3.173705397 0.095636949 EGPYSISVLYGDEEVPRS(ph)PFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGPYSISVLYGDEEVPRSPFK 21 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 EGPYSISVLYGDEEVPRS(1)PFK;EGPYSISVLYGDEEVPRS(1)PFK 211.18 9.88E-23 887570000 626930 562990 594690 434630 510390 600970 442410 492610 548760 547480 TRUE FALSE 602428.8825 546934.0764 702163.7118 457061.3064 526807.1579 613122.0252 447824.3459 482437.4314 486467.0654 510398.692 1.180310397 1.07158205 1.375716127 0.895498585 1.032148331 1.201260965 0.877401045 0.945216826 0.953111897 1 18.96126511 3.175320146 0.676048476 0.946354813 1.192999812 0.297299809 0.125225644 0.997696898 0.994114109 0.079558365 0.136880793 1497.339034 -3.175320146 0.246644999 HFRPELEER ddPTM_BT-474_Pertuzumab_2h_R1 1 HFRPELEER 9 1 B4DE93;G3V0I5;P49821-2;P49821 B4DE93 NDUFV1 "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial" 0 163.66 3.78E-05 178830000 124720 173780 118290 214560 93526 82799 188910 107320 128800 102630 FALSE TRUE 119845.8045 168823.9645 139667.6343 225633.4673 96534.34873 84473.25251 191221.9371 105103.8045 114179.164 95678.77869 1.252585016 1.764487035 1.459755614 2.358239417 1.008942109 0.882883892 1.998582546 1.098506962 1.193359338 1 16.54591135 3.175372508 24.99999984 1.235174979 1.695010826 0.288083965 0.391102125 89.47308073 35398.70539 0.111263648 0.132985544 1497.519576 -3.175372508 0.459835847 NCCFEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 NCCFEHR 7 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 ; 125.81 0.0040127 172354000 210170 213762 183400 196836 177334 154639 197913 169939 181098 198061 FALSE TRUE 201956.324 207665.7171 216544.4597 206994.7295 183038.1092 157765.9065 200335.1185 166429.7003 160540.5143 184646.1521 1.093747808 1.124668534 1.172753709 1.121034623 0.991291219 0.854422932 1.084967741 0.901343995 0.869449552 1 17.49440367 3.176346432 3.784625449 0.943420669 1.132661817 0.64961545 0.064713906 0.135063796 3.885665152 0.018741698 0.02344049 1500.881593 -3.176346432 0.189241148 WTLGFCDER ddPTM_BT-474_Pertuzumab_2h_R1 2 WTLGFCDER 9 0 M0R1L2;O95336;M0R0U3;M0R261 M0R1L2 PGLS 6-phosphogluconolactonase 0 ; 145.17 0.00022753 153346000 311670 372050 275650 318810 285280 169870 340410 275990 324040 412610 FALSE TRUE 299489.5918 361439.4983 325466.0868 335263.8223 294456.2903 173304.8878 344576.0394 270290.7101 287256.3377 384663.5572 0.778575423 0.939625009 0.846105852 0.871576774 0.765490478 0.450536279 0.895785507 0.702667838 0.746772946 1 18.55323763 3.176770679 5.454059478 0.736533002 0.863847133 0.096483135 0.138399877 0.359959079 20.97263338 0.038349987 0.046709393 1502.34847 -3.176770679 0.127314131 NYHIFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 NYHIFYR 7 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 93.262 0.015064 261440000 162830 193130 163150 178180 135950 116890 147750 108340 165210 173860 FALSE TRUE 156466.4236 187622.1215 192634.8343 187375.8912 140322.9552 119253.5959 149558.2087 106102.7411 146456.0534 162084.3073 0.965339743 1.157558832 1.188485409 1.156039682 0.865740537 0.735750412 0.922718622 0.654614521 0.903579476 1 17.30638489 3.176838634 5.037019192 0.814539772 1.125150917 0.58934073 0.108761317 0.119529571 5.987360122 0.030638581 0.037506392 1502.583565 -3.176838634 0.310611145 HTTSIFDDFSHYEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HTTSIFDDFSHYEK 14 0 Q9Y5A9;Q9Y5A9-2 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 0 115.82 0.0002299 82510000 121440 158060 111300 175000 102390 95590 119410 50423 191240 206300 FALSE TRUE 116693.9905 153552.2836 131414.3859 184031.771 105683.4673 97522.89529 120871.3753 49381.74743 169531.2369 192327.1172 0.606747463 0.798391229 0.683285788 0.956868556 0.549498525 0.507067837 0.62846767 0.256759151 0.881473395 1 17.55320266 3.176936717 24.99974438 0.570975278 0.758400875 0.022708589 0.213701624 125.2737672 50820.41738 0.059508841 0.071126697 1502.922954 -3.176936717 0.187425597 YWCDAEYDAYRR ddPTM_BT-474_Pertuzumab_2h_R1 2 YWCDAEYDAYRR 12 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ; 171.92 5.96E-05 894260000 395050 453930 302520 355180 397890 321010 360970 359210 387530 356850 FALSE TRUE 379611.0092 440984.3608 357192.0935 373510.8824 410688.4932 327501.0421 365387.6588 351792.188 343539.2191 332680.2317 1.141068729 1.32555024 1.073679947 1.122732422 1.234484211 0.984431929 1.09831491 1.057448428 1.032640916 1 18.34377662 3.177021328 0.378336591 1.002946721 1.25588318 0.42154339 0.076460953 1.875228027 0.467352039 0.075725055 0.192591996 1503.215787 -3.177021328 0.252936459 DRCESCSGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DRCESCSGAK 10 1 Q8WW22-3;Q8WW22;Q8WW22-2;C9JDE6;F5H170 Q8WW22-3 DNAJA4 DnaJ homolog subfamily A member 4 0 ;;; 184.58 1.41E-06 272682000 291610 328195 227641 277660 311095 326478 331564 332604 369650 350158 FALSE TRUE 280213.5588 318835.1999 268780.7925 291990.0659 321101.6532 333079.6088 335621.7794 325735.6112 327688.8817 326441.4868 0.858388318 0.976699387 0.823365912 0.894463718 0.983642295 1.020334799 1.028122322 0.997837666 1.00382119 1 18.31646489 3.177981237 3.781090822 1.009601138 0.888996122 0.710451364 0.037023987 0.119630628 3.44587909 0.010579269 0.013243553 1506.541977 -3.177981237 -0.120605016 AHQLVHEGYK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHQLVHEGYK 10 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 179.57 1.21E-06 200722000 293388 278144 260840 228575 220394 98228 278193 43637 273141 250512 FALSE TRUE 281922.0726 270211.6055 307979.5904 240371.7831 227483.1732 100214.2375 281597.6092 42735.8807 242135.1788 233544.5991 1.207144476 1.157002159 1.31871853 1.029232892 0.97404596 0.42910107 1.205755176 0.182988092 1.036783465 1 17.83333856 3.17835191 2.113578468 0.712137224 1.211592002 0.294700688 0.289306011 0.321920949 2.951660813 0.087460538 0.115232385 1507.828369 -3.17835191 0.499454779 VHSFPTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHSFPTLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 170.66 0.00029388 6839300000 5924300 6743000 5708900 6320800 5728600 5632000 6876200 4643600 7124700 6960900 FALSE TRUE 5692771.806 6550696.242 6740625.224 6647017.245 5912865.622 5745882.899 6960352.993 4547708.037 6315933.925 6489432.043 0.877237294 1.00944061 1.038708038 1.024283358 0.911153023 0.885421538 1.07256736 0.700786757 0.973264514 1 22.62966079 3.178427718 7.649667245 0.903063585 0.99253347 0.064860012 0.100524396 0.459790509 50.13820462 0.029300021 0.03521334 1508.091589 -3.178427718 0.089469885 RSPPIPLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPPIPLAK 9 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 83.862 0.028076 0 517180 566550 429180 506650 468010 425300 486790 474310 554610 573160 FALSE TRUE 496968.0338 550392.5487 506742.3731 532798.2672 483063.9667 433899.8574 492747.4816 464515.3327 491652.9979 534339.3627 0.930060685 1.030043053 0.948353066 0.997115886 0.904039643 0.812030495 0.922162049 0.869326434 0.920113756 1 19.02739677 3.178467076 6.405742302 0.892644931 0.97812233 0.303434882 0.051496309 0.197552207 15.84730736 0.013873 0.016769358 1508.228267 -3.178467076 0.085477399 AS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASPEPQRENASPAPGTTAEEAMSR 24 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 2 AS(1)PEPQRENAS(1)PAPGTTAEEAMSR;AS(1)PEPQRENAS(1)PAPGTTAEEAMSR;AS(1)PEPQRENAS(1)PAPGTTAEEAMSR 145.61 1.19E-07 1433200000 594278 621034 483775 542420 597898 654551 614690 630187 641991 681363 TRUE FALSE 571052.9588 603322.7184 571203.904 570414.3612 617129.9322 667786.4697 622212.7601 617173.4182 569114.8731 635213.6771 0.898993487 0.949794912 0.899231116 0.89798816 0.971531241 1.051278481 0.979533002 0.9715997 0.895942411 1 19.27688245 3.178503474 6.541815125 0.980419915 0.913448367 0.422458543 0.038256384 0.210107783 17.52218088 0.011451489 0.013830635 1508.354678 -3.178503474 -0.066971548 QRIDEFEAL ddPTM_BT-474_Pertuzumab_2h_R1 2 QRIDEFEAL 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 95.741 0.063935 744260000 1595430 1756970 1329350 1459060 1315970 710010 1502670 1272450 1294320 1520660 FALSE TRUE 1533078.832 1706862.936 1569593.116 1534362.261 1358299.37 724366.8887 1521060.125 1246173.463 1147394.22 1417664.344 1.081411717 1.20399652 1.107168367 1.08231703 0.958124803 0.510957965 1.072933894 0.879032804 0.809355349 1 20.43508456 3.179033887 3.606647706 0.857984429 1.127942642 0.431980796 0.142008829 0.214564584 5.641905181 0.041473509 0.052141476 1510.197988 -3.179033887 0.269958213 LLNEVMVEHFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLNEVMVEHFFR 12 0 Q9H871 Q9H871 RMND5A Protein RMD5 homolog A 0 ; 151.78 6.93E-05 159437000 172793 191349 161304 171182 166959 146278 184275 165324 184582 195732 FALSE TRUE 166040.0585 185891.9139 190455.221 180016.7235 172329.3879 149235.8414 186530.2126 161910.0016 163629.0252 182474.8973 0.9099337 1.018725954 1.043733817 0.986528702 0.94440052 0.817843131 1.022223962 0.887300138 0.896720741 1 17.47733848 3.179181243 4.1251968 0.920175539 0.996230351 0.187148079 0.062695262 0.304865757 10.45463373 0.017754315 0.022085108 1510.710485 -3.179181243 0.076054811 VQSFLASLDGEKLELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VQSFLASLDGEKLELLK 17 1 Q8IWE2;Q8IWE2-2 Q8IWE2 FAM114A1 Protein NOXP20 0 159.88 2.88E-09 61835000 111950 113190 80816 78141 113790 109250 107460 127660 123990 111930 FALSE TRUE 107574.8702 109961.932 95421.24894 82173.86637 117450.1587 111459.1099 108775.1276 125023.7764 109915.175 104348.8814 1.030915414 1.053791191 0.914444388 0.787491589 1.125552638 1.068139 1.042417764 1.198132406 1.053343108 1 16.67105561 3.179221067 24.99999976 1.094993489 0.952007296 0.37340172 0.084189381 77.29510371 32564.23885 0.025504115 0.030483262 1510.849018 -3.179221067 -0.142986193 LTGSTSS(ph)LNK ddPTM_BT-474_Pertuzumab_2h_R1 5 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGST(0.005)S(0.048)S(0.946)LNK;LTGST(0.058)S(0.28)S(0.661)LNK;LTGS(0.008)T(0.337)S(0.129)S(0.527)LNK;LTGS(0.225)T(0.225)S(0.086)S(0.464)LNK;LTGS(0.077)T(0.319)S(0.118)S(0.485)LNK 165.63 6.08E-06 2809510000 5479120 5649820 4867700 5470160 5628940 6165710 6222290 6469790 7577300 7296750 TRUE FALSE 5264989.933 5488692.665 5747401.671 5752475.613 5809999.967 6290384.881 6298440.246 6336186.576 6717156.671 6802534.623 0.773974735 0.806859938 0.844891204 0.845637094 0.854093406 0.924711924 0.925896095 0.931444958 0.987449097 1 22.69764096 3.179447387 0.316301152 1.011273664 0.724088259 0.954048657 0.015379112 0.545512019 0.091385523 0.019268578 0.0565064 1511.636559 -3.179447387 -0.287185405 GPSQEEEDNHS(ph)DEEDRASEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GPSQEEEDNHSDEEDRASEPK 21 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPSQEEEDNHS(1)DEEDRASEPK;GPSQEEEDNHS(1)DEEDRASEPK;GPSQEEEDNHS(1)DEEDRASEPK 318.74 4.72E-67 1423080000 963420 976574 800817 835567 949875 988954 934864 906875 1180539 1091938 TRUE FALSE 925768.4813 948723.0657 945542.446 878690.713 980428.592 1008951.327 946305.1453 888147.7143 1046529.162 1017980.067 0.909417101 0.93196625 0.928841808 0.863170844 0.963111778 0.991130731 0.929591036 0.872460811 1.028044847 1 19.95727788 3.184186046 24.99999268 0.950894893 0.911498734 0.243404823 0.044493826 182.7243794 84010.89263 0.013628183 0.016288805 1528.220587 -3.184186046 -0.039396158 DVTNNVHYENYR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVTNNVHYENYR 12 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;; 252.42 4.65E-21 9595400000 6482100 6838700 6056370 5922320 5779160 3231390 6677300 5243840 5951860 6602700 FALSE TRUE 6228772.366 6643666.972 7150890.782 6227971.645 5965051.93 3296730.92 6759018.795 5135552.872 5276229.805 6155493.248 1.01190467 1.079307003 1.161708818 1.011774588 0.969061567 0.535575426 1.098046659 0.834304038 0.857157923 1 22.55344304 3.184206331 3.287571412 0.864770022 1.078763578 0.303820205 0.14144473 0.278692183 6.129009939 0.040701388 0.05168894 1528.291968 -3.184206331 0.213993557 TTESHMDWEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTESHMDWEK 10 0 E9PKP7;P17480-2;P17480;E9PMM2 E9PKP7 UBTF Nucleolar transcription factor 1 0 97.813 0.0058027 291720000 662680 669630 570860 634200 568780 384840 664670 570820 663920 744180 FALSE TRUE 636781.733 650532.808 674027.1007 666931.138 587075.3253 392621.7285 672804.4303 559032.3675 588554.585 693776.0258 0.917849146 0.937669772 0.971534149 0.961306118 0.846202958 0.56592 0.969771807 0.805782193 0.848335144 1 19.40411046 3.184215042 5.915546089 0.823646287 0.948149845 0.17953203 0.110361065 0.29353232 21.67920646 0.03115754 0.037876454 1528.322622 -3.184215042 0.124503558 AS(ph)PDSSSCGERS(ph)PPPPPPPPSDEALLHCVLEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASPDSSSCGERSPPPPPPPPSDEALLHCVLEGK 33 1 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 2 AS(1)PDS(0.073)S(0.053)S(0.043)CGERS(0.831)PPPPPPPPSDEALLHCVLEGK;AS(0.994)PDS(0.15)S(0.137)S(0.115)CGERS(0.605)PPPPPPPPSDEALLHCVLEGK;AS(0.995)PDS(0.012)S(0.011)S(0.009)CGERS(0.973)PPPPPPPPSDEALLHCVLEGK 225.77 3.64E-36 621906000 186446 183586 139728 171875 196185 198525 201625 218868 251195 217288 TRUE FALSE 179159.4842 178350.307 164979.9578 180745.4893 202495.4687 202539.3115 204092.5471 214348.2993 222680.3967 202570.8902 0.884428577 0.880434039 0.814430729 0.89225796 0.999627678 0.99984411 1.007511725 1.058139692 1.099271452 1 17.62806735 3.184244834 2.069774394 1.036877595 0.858747051 0.848954611 0.03337268 0.117333824 1.032532424 0.01123118 0.014893726 1528.427467 -3.184244834 -0.178130544 TRQS(ph)PQTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TRQSPQTLK 9 1 M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63;M0QXV1;M0QX88;M0R200;M0R073;Q8IV63-3 M0QXD7 VRK3 Inactive serine/threonine-protein kinase VRK3 1 T(0.218)RQS(0.752)PQT(0.03)LK 60.08 0.059392 214760000 132210 129810 112020 140860 143160 114770 152470 169320 161490 173670 TRUE FALSE 127043.087 126107.9459 132264.5059 148129.8015 147764.8714 117090.728 154335.9735 165823.4828 143158.3322 161907.1762 0.78466619 0.778890404 0.816915649 0.914905719 0.912651773 0.723196654 0.953237386 1.024188592 0.884200043 1 17.30480741 3.184443399 0.288902372 1.015488992 0.710420269 0.441757592 0.071168249 3.139677715 0.437302995 0.104668565 0.326201399 1529.126443 -3.184443399 -0.305068724 QDDS(ph)PPRPIIGPALPPGFIK ddPTM_BT-474_Pertuzumab_2h_R1 4 QDDSPPRPIIGPALPPGFIK 20 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 1 QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK 204.53 5.78E-22 3116740000 3204020 3044420 2659430 2873630 3179210 3292790 3250560 3496530 3661610 3385640 TRUE FALSE 3078803.356 2957596.122 3140048.16 3021938.389 3281472.177 3359372.47 3290341.326 3424325.434 3245959.384 3156327.587 0.975438471 0.937037123 0.994842288 0.957422291 1.039648796 1.064329471 1.042458755 1.084908122 1.028397495 1 21.58981552 3.184887063 5.124993178 1.051808796 0.966010514 0.682634401 0.02543603 0.097777952 5.383628523 0.007056347 0.008657909 1530.689357 -3.184887063 -0.085798282 KFESEILEAISQNSVVIIR ddPTM_BT-474_Pertuzumab_2h_R1 3 KFESEILEAISQNSVVIIR 19 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 290.57 2.52E-49 2235300000 2029507 2035699 1543448 1822132 2017548 2247345 2075133 2143192 2333742 2216636 FALSE TRUE 1950191.623 1977642.858 1822383.387 1916172.451 2082444.264 2292787.856 2100529.098 2098934.336 2068825.392 2066501.269 0.943716634 0.957000553 0.88186899 0.927254427 1.00771497 1.109502273 1.016466396 1.015694676 1.001124665 1 20.97875882 3.185092541 4.573981488 1.029859733 0.925876694 0.662582683 0.034307242 0.123528646 5.353152488 0.010366082 0.012828189 1531.413745 -3.185092541 -0.103983039 LWDCETGK ddPTM_BT-474_Pertuzumab_2h_R1 3 LWDCETGK 8 0 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;; 110.12 0.0081143 286330000 458440 463760 402280 531500 484240 504680 574270 628760 673250 723690 FALSE TRUE 440523.658 450534.0189 474980.9447 558930.7787 499816.0194 514884.9754 581298.088 615775.8863 596825.4825 674673.8317 0.652943152 0.667780485 0.704015663 0.828445913 0.740826153 0.763161325 0.861598688 0.912701601 0.884613356 1 19.36383068 3.185677014 0.225728032 1.037277802 0.500952748 0.889409498 0.036065836 1.740878729 0.156663366 0.082874544 0.275163554 1533.476108 -3.185677014 -0.536325055 PSQMEHAMETMMFTFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 PSQMEHAMETMMFTFHK 17 0 P60903 P60903 S100A10 Protein S100-A10 0 ; 223.29 1.79E-15 316550000 421090 466360 351350 533800 332240 375020 486840 298110 570040 392270 FALSE TRUE 404633.3373 453059.8694 414846.7607 561349.482 342926.8013 382603.1613 492798.0936 291953.9243 505331.449 365701.2035 1.106458861 1.238879897 1.13438719 1.534994899 0.937724016 1.046217944 1.347542991 0.79834007 1.381815111 1 18.48030585 3.185738066 24.99998697 1.072650355 1.24411126 0.147351597 0.196521264 178.0854333 84283.93425 0.054395827 0.065015511 1533.691696 -3.185738066 0.171460905 GYAFNHSADFETVR ddPTM_BT-474_Pertuzumab_2h_R1 4 GYAFNHSADFETVR 14 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 179.39 1.87E-06 4177900000 2839430 3042950 2567020 2459850 2533820 1135220 2957100 2111150 2373760 2655540 FALSE TRUE 2728461.936 2956168.045 3030937.617 2586803.153 2615322.621 1158174.926 2993289.874 2067554.015 2104300.716 2475677.91 1.102106993 1.194084268 1.224285924 1.044886793 1.056406655 0.467821327 1.20907888 0.83514661 0.849989697 1 21.2393922 3.185845889 2.765715647 0.882310595 1.161801266 0.32341129 0.180244904 0.301529614 4.705825836 0.052534483 0.067715029 1534.072515 -3.185845889 0.279490671 SLDFYTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLDFYTR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;;; 153.73 0.004017 2222850000 1330890 1247870 1165440 1171270 1070160 911980 1055130 1005880 1168940 1222830 FALSE TRUE 1278877.347 1212281.969 1376060.933 1231719.385 1104582.668 930420.8604 1068042.997 985108.2265 1036246.832 1140006.635 1.121815706 1.063399047 1.207063969 1.080449313 0.968926526 0.816153899 0.936874369 0.864124994 0.908983159 1 20.12061079 3.187543138 2.945732393 0.896669855 1.125731573 0.76254244 0.05632398 0.107592589 1.903835905 0.015872476 0.020372041 1540.079493 -3.187543138 0.229061719 QDS(ph)DEDDGPQRVEEVDQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 QDSDEDDGPQRVEEVDQGR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 QDS(1)DEDDGPQRVEEVDQGR 123.14 1.93E-05 293610000 172980 147760 105290 169070 170130 161190 179330 208180 216210 175270 TRUE FALSE 166219.7504 143546.0295 124318.2452 177795.723 175602.386 164449.3722 181524.6942 203881.0103 191666.7472 163398.8068 1.017264163 0.878501088 0.76082713 1.088109066 1.074685852 1.006429456 1.110930353 1.247750912 1.172999675 1 17.31803792 3.187903689 1.062170043 1.148514287 0.891365351 0.435677359 0.099795821 0.429355325 1.043054814 0.043714844 0.066255393 1541.358598 -3.187903689 -0.257148936 ATISDEEIER ddPTM_BT-474_Pertuzumab_2h_R1 1 ATISDEEIER 10 0 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 0 129.85 0.0080233 0 80781 97744 81036 91520 81235 91512 88832 100840 84357 106810 FALSE TRUE 77623.98921 94956.43682 95681.00784 96243.35817 83847.99755 93362.43534 89919.15259 98757.61876 74781.14701 99575.66356 0.779547797 0.953610887 0.960887474 0.966534942 0.842053114 0.937602944 0.903023383 0.991784691 0.750998229 1 16.60350557 3.188276798 0.007528289 1.820664771 2.64E-06 0.046959753 0.081784969 24457.79707 54.05507277 6351.266442 6720.883424 1542.683371 -3.188276798 -1.82066213 ELYQQLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELYQQLQR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 125.58 0.0029213 114010000 127970 141100 123050 149650 118880 113210 153520 127000 125730 138630 FALSE TRUE 122968.7909 137075.9662 145287.8722 157373.4544 122703.8832 115499.1838 155398.8237 124377.4056 111457.6575 129240.4666 0.951472818 1.060627292 1.124167036 1.217679405 0.94942309 0.893676623 1.20240067 0.962371994 0.862405254 1 16.97969834 3.188818155 24.99994594 0.987001799 1.089047059 0.206135829 0.105039277 194.220435 97612.08757 0.031396618 0.037526196 1544.607557 -3.188818155 0.10204526 RPGSVSSTDQER ddPTM_BT-474_Pertuzumab_2h_R1 1 RPGSVSSTDQER 12 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 0 85.287 0.018855 218120000 505540 529740 545930 344320 430760 378160 501340 382960 378500 390800 FALSE TRUE 485782.9379 514632.3339 644591.6951 362090.3965 444615.7866 385806.6543 507475.5489 375051.7422 335534.2668 364330.7679 1.333356885 1.412541512 1.769248584 0.993850721 1.220362994 1.058946123 1.392897865 1.029426486 0.920960557 1 18.47488931 3.189306951 0.487677472 1.00352905 1.528404424 0.402830999 0.194308529 1.386408495 0.638843365 0.166302777 0.350161015 1546.346982 -3.189306951 0.524875373 IAHFLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IAHFLDR 7 0 P60228;H0YBR5;E5RHS5;E5RIP5;E5RJ25;E5RII3 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;;; 130.77 0.0035314 1311469000 1617302 1813295 1596763 1586992 1587046 1074578 1799356 1515380 1736134 1975457 FALSE TRUE 1554096.05 1761581.602 1885333.594 1668896.847 1638094.776 1096306.703 1821377.057 1484086.873 1539055.347 1841657.538 0.843857242 0.956519638 1.023715623 0.906192825 0.889467636 0.595282609 0.98898792 0.805843021 0.835690304 1 20.81257338 3.189331925 3.646249152 0.835690025 0.942767354 0.106774681 0.113092844 0.416990422 11.37655061 0.032204673 0.040678772 1546.435906 -3.189331925 0.107077328 VKFQGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKFQGGR 7 1 Q9UK45;K7ENY5;K7EML7 Q9UK45 LSM7 U6 snRNA-associated Sm-like protein LSm7 0 ; 86.866 0.018023 792130000 682840 876550 535160 643120 817070 820000 833520 919390 915890 967150 FALSE TRUE 656153.8579 851551.6522 631875.3166 676311.5003 843351.7986 836580.9618 843720.8671 900404.2752 811922.0069 901644.0691 0.727730465 0.944443247 0.700803497 0.750087006 0.935348912 0.927839477 0.93575824 0.998624963 0.900490598 1 19.78219851 3.189358602 6.840672735 0.951856232 0.786862765 0.601607559 0.067284244 0.141144934 15.08975644 0.019145332 0.023156027 1546.530901 -3.189358602 -0.164993467 AAELIANSLATAGDGLIELR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAELIANSLATAGDGLIELR 20 0 P35232;C9JW96 P35232 PHB Prohibitin 0 120.66 7.83E-05 28524000 32838 42911 31394 40678 32671 30177 36050 39586 41866 33712 FALSE TRUE 31554.65466 41687.22029 37067.59416 42777.39645 33721.89239 30787.19962 36491.19068 38768.53527 37113.5472 31428.65621 1.004009031 1.326407977 1.179420269 1.361095306 1.072966409 0.979590072 1.161080208 1.233540976 1.180882407 1 14.93979297 3.189867993 24.99950344 1.122238323 1.222761072 0.175804038 0.116045101 222.7533756 114363.9019 0.034115922 0.040776398 1548.345917 -3.189867993 0.100522749 KADYQAVDDEIEANLEEFDISEDDIDDGFRR ddPTM_BT-474_Pertuzumab_2h_R1 2 KADYQAVDDEIEANLEEFDISEDDIDDGFRR 31 2 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 360.29 2.66E-121 386420000 73709 81309 59870 73227 76944 84584 78610 90386 88192 85058 FALSE TRUE 70828.37079 78990.14693 70689.8408 77006.25425 79418.97364 86294.34643 79572.05269 88519.49751 78180.81389 79296.9459 0.893204271 0.996131012 0.891457294 0.971112486 1.001538871 1.088243002 1.003469324 1.116303995 0.985924653 1 16.27497768 3.191761029 2.316379472 1.048587579 0.934169041 0.499208313 0.047622022 0.213798668 2.350425831 0.013895436 0.01827826 1555.109695 -3.191761029 -0.114418538 AKDQDILDLVGVLHDPETLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AKDQDILDLVGVLHDPETLLR 21 1 F5H345;A0A3B3IRR1;A0A3F2YNY7;P08397-2;P08397 F5H345 HMBS Porphobilinogen deaminase 0 ; 140.64 9.81E-08 146697000 340500 295880 245090 272710 297100 298620 285880 311890 336520 334940 FALSE TRUE 327192.8836 287441.7921 289383.215 286784.5958 306656.4913 304658.301 289378.685 305449.3625 298319.6604 312254.2155 1.047841366 0.920537747 0.926755191 0.918433064 0.982073183 0.975673941 0.926740683 0.97820733 0.955374325 1 18.25236152 3.191906541 24.99937717 0.966614146 0.949141987 0.032155781 0.039102801 448.797603 240485.0041 0.011094339 0.013260316 1555.63083 -3.191906541 -0.017472159 GDRWEDLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDRWEDLSR 9 1 Q9NR50-3;Q9NR50-2;Q9NR50;H0Y580 Q9NR50-3 EIF2B3 Translation initiation factor eIF-2B subunit gamma 0 ; 172.56 5.12E-05 285220000 501520 600140 469530 510500 494550 396700 590190 478710 520890 594370 FALSE TRUE 481920.0439 583024.5948 554384.5156 536846.9662 510457.6499 404721.5458 597412.9218 468824.4712 461760.7509 554112.7905 0.869714708 1.05217675 1.000490379 0.968840596 0.921216147 0.730395603 1.078143172 0.846081302 0.8333335 1 19.07982014 3.192464884 4.231269905 0.893636541 0.981291847 0.111951596 0.098019896 0.403017891 15.21966513 0.027633531 0.034551306 1557.632082 -3.192464884 0.087655306 NSVLSDPGLDS(ph)PRTS(ph)PVIMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(1)PRT(0.327)S(0.673)PVIMAR;NSVLSDPGLDS(1)PRT(0.108)S(0.892)PVIMAR 159.65 1.27E-11 509440000 92657 105211 70774 102562 78786 87563 71828 100366 90620 87587 TRUE FALSE 89035.862 102210.4853 83564.43616 107855.2371 81320.22324 89333.58385 72707.05255 98293.40703 80333.19751 81654.65448 1.090395429 1.251741079 1.023388522 1.320870657 0.995904321 1.094041539 0.89042141 1.203769799 0.983816514 1 16.3172475 3.192947096 24.99997998 1.042861732 1.166738272 0.291866875 0.107998668 174.1012842 95421.29729 0.029386333 0.035123523 1559.362535 -3.192947096 0.123876539 DALYDVITVGAPAAHFQGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DALYDVITVGAPAAHFQGFK 20 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 227.4 3.76E-25 149290000 231200 209200 178790 205810 223900 241090 229440 241720 268350 273180 FALSE TRUE 222164.4484 203233.8208 211101.3302 216431.8788 231101.9468 245965.005 232247.9554 236728.3975 237888.033 254677.2753 0.87233715 0.798005321 0.828897395 0.849827997 0.907430577 0.96579094 0.911930423 0.929523049 0.934076402 1 17.95831071 3.193489362 2.580532903 0.939884476 0.830526255 0.769345362 0.028534094 0.126573196 1.723324845 0.008310655 0.010826269 1561.310792 -3.193489362 -0.109358221 SSLS(ph)GDEEDELFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 S(0.003)S(0.016)LS(0.981)GDEEDELFK 103.83 0.0010126 0 170520 136220 118380 108670 158070 142710 157970 166600 171350 161500 TRUE FALSE 163855.8899 132335.139 139773.8993 114278.4717 163154.4651 145595.694 159903.2841 163159.6518 151899.0664 150561.4612 1.088299015 0.878944306 0.928351108 0.759015427 1.083640288 0.967018338 1.062046575 1.083674737 1.008884114 1 17.19999301 3.193944372 24.99999238 1.040230376 0.91222209 0.337426112 0.082493597 138.3433826 77518.00212 0.023288235 0.027834886 1562.947436 -3.193944372 -0.128008285 EWYGWHFPELGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EWYGWHFPELGK 12 0 Q9Y2X3;H7BZ72 Q9Y2X3 NOP58 Nucleolar protein 58 0 ; 98.803 0.0041537 1061340000 2752200 2506200 2416500 2501300 2414600 2243000 2453300 2562500 2699700 2777400 FALSE TRUE 2644640.981 2434725.63 2853215.305 2630392.393 2492267.802 2288354.997 2483324.219 2509583.48 2393241.374 2589284.224 1.021379174 0.940308371 1.101932062 1.015876267 0.962531567 0.88377899 0.959077492 0.969219005 0.924286856 1 21.30412191 3.194162017 4.58013734 0.946395461 1.020437715 0.361091756 0.045929154 0.220641116 10.03727134 0.013334476 0.01658425 1563.730894 -3.194162017 0.074042254 HTLADNFNPVSEER ddPTM_BT-474_Pertuzumab_2h_R1 4 HTLADNFNPVSEER 14 0 P20645;H0YGT2 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;;; 177.88 2.05E-06 1182790000 574120 853834 642463 829566 614365 606141 821909 605589 790199 810364 FALSE TRUE 551682.7557 829483.4903 758570.3556 872380.0007 634126.6082 618397.5863 831967.7682 593083.3755 700498.9223 755477.3245 0.730243963 1.09795948 1.004094142 1.154740152 0.839372126 0.818552147 1.101247835 0.785044576 0.927226933 1 19.52702893 3.194404418 24.99999805 0.902153044 1.004513464 0.08339212 0.134540232 283.1529887 160312.3179 0.037496341 0.044816947 1564.603935 -3.194404418 0.10236042 KLFAPQQILQCS(ph)PAN ddPTM_BT-474_Pertuzumab_2h_R1 2 KLFAPQQILQCSPAN 15 1 P04183;K7ERV3 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 KLFAPQQILQCS(1)PAN;KLFAPQQILQCS(1)PAN 147.12 3.99E-06 719050000 1510690 1495980 1249850 1401350 1270460 1151300 1432940 1392630 1151990 1380120 TRUE FALSE 1451650.565 1453316.115 1475725.698 1473673.841 1311325.5 1174580.075 1450476.748 1363871.704 1021220.925 1286643.243 1.128246367 1.12954086 1.146957951 1.145363215 1.01918345 0.912902688 1.127334058 1.060023212 0.793709469 1 20.29518065 3.195059885 5.279208985 0.998411988 1.137963318 0.438378788 0.083726824 0.205744937 13.18707138 0.02493367 0.030695831 1566.967125 -3.195059885 0.13955133 GCQLLVYPGAFNLTTGPAHWELLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GCQLLVYPGAFNLTTGPAHWELLQR 25 0 Q9NQR4 Q9NQR4 NIT2 Omega-amidase NIT2 0 ; 207.64 3.17E-25 897380000 668270 727220 588060 649500 600990 594450 625780 585670 691620 679360 FALSE TRUE 642153.2696 706480.3976 694335.5233 683020.7728 620321.3892 606470.1863 633438.4828 573575.7098 613110.1971 633346.3421 1.013905389 1.115472453 1.096296729 1.078431701 0.979434707 0.957564836 1.000145482 0.905627256 0.968048848 1 19.27263512 3.195481347 3.973266121 0.959667396 1.081358469 0.692382031 0.034982274 0.11085975 3.674996143 0.010213911 0.012858675 1568.488531 -3.195481347 0.121691073 SIGTANRPMGAGEALR ddPTM_BT-474_Pertuzumab_2h_R1 6 SIGTANRPMGAGEALR 16 1 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EQR9;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 158.64 8.58E-09 3577510000 1776109 1859183 1673421 1756337 1576514 864623 1919014 1724984 1747642 1916501 FALSE TRUE 1706696.697 1806160.921 1975845.4 1846981.763 1627224.005 882106.2695 1942499.467 1689362.478 1549257.007 1786694.68 0.955225711 1.010895113 1.10586628 1.033742241 0.910745424 0.493708455 1.087202805 0.945523875 0.867107863 1 20.76886169 3.195685977 5.66744862 0.880642758 1.031263625 0.179970216 0.149400528 0.335157259 25.68583748 0.044674582 0.054753257 1569.227741 -3.195685977 0.150620867 KDDRVEER ddPTM_BT-474_Pertuzumab_2h_R1 2 KDDRVEER 8 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 111.06 0.0018598 202741000 123388 133203 91900 109866 126308 132753 142097 120073 143162 155223 FALSE TRUE 118565.8605 129404.1809 108508.3743 115536.1974 130370.8115 135437.3566 143836.0256 117593.4506 126910.8499 144709.608 0.819336478 0.894233511 0.749835314 0.798400321 0.900913308 0.935925116 0.993963204 0.812616745 0.877003619 1 17.14280119 3.195886867 7.042191331 0.910391802 0.816427197 0.408605386 0.061017172 0.235872378 30.03139998 0.018422293 0.02231468 1569.953779 -3.195886867 -0.093964605 FVMQEEFSR ddPTM_BT-474_Pertuzumab_2h_R1 7 FVMQEEFSR 9 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;; 233.57 8.73E-10 7153490000 2198639 2655292 2187963 2243529 1961733 1263617 2340694 1845643 1937169 2229516 FALSE TRUE 2112713.757 2579565.672 2583376.585 2359317.801 2024833.924 1289168.202 2369340.113 1807529.827 1717269.696 2078508.895 1.016456442 1.241065495 1.24289898 1.135101132 0.974176213 0.620237038 1.139923009 0.869628141 0.826202717 1 20.98711749 3.195953657 3.789211287 0.894739372 1.174452491 0.458260912 0.137081703 0.190414059 5.696491771 0.039280398 0.049652951 1570.195241 -3.195953657 0.279713119 DTHPGS(ph)PGSPGPALRPLPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 DTHPGSPGSPGPALRPLPAR 20 1 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 DTHPGS(0.886)PGS(0.114)PGPALRPLPAR;DTHPGS(0.863)PGS(0.137)PGPALRPLPAR;DTHPGS(0.981)PGS(0.019)PGPALRPLPAR 115.54 6.53E-05 1171910000 398390 429998 428840 490350 377342 413160 453600 308622 473700 588350 TRUE FALSE 382820.4784 417734.8781 506340.9275 515657.0223 389479.5481 421514.3783 459151.2925 302248.8479 419927.5619 548500.5305 0.697940033 0.761594301 0.923136623 0.940121283 0.710080531 0.768484905 0.837102732 0.55104568 0.765591898 1 19.06513349 3.195997244 24.99865482 0.740848627 0.832365468 0.015003098 0.125579322 329.6007868 193582.6227 0.036969464 0.044187286 1570.352839 -3.195997244 0.091516842 TYLPDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TYLPDFR 7 0 Q13630;H0YCP7 Q13630 TSTA3 GDP-L-fucose synthase 0 80.462 0.069435 325220000 803950 889000 769460 758550 763630 400030 863180 762490 780670 944200 FALSE TRUE 772530.7452 863646.5904 908518.5385 797698.8564 788192.8525 408118.8807 873743.855 746744.315 692051.6144 880248.493 0.877628024 0.981139527 1.032115983 0.906220076 0.895420848 0.463640533 0.992610453 0.848333534 0.786200283 1 19.74755133 3.196017689 3.49590331 0.816253688 0.960908444 0.147124543 0.144407664 0.415134897 10.46031065 0.042357806 0.05388708 1570.426769 -3.196017689 0.144654756 AFKPEETSSNSDPPS(ph)PPVLNNSHPVPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AFKPEETSSNSDPPSPPVLNNSHPVPR 27 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 AFKPEETSSNSDPPS(1)PPVLNNSHPVPR;AFKPEETSSNSDPPS(1)PPVLNNSHPVPR;AFKPEETSSNSDPPS(1)PPVLNNSHPVPR;AFKPEETSSNSDPPS(1)PPVLNNSHPVPR 237.28 2.82E-45 2663720000 3247840 3090110 2621630 2830800 3047540 3111050 3016550 3403870 3447610 3140950 TRUE FALSE 3120910.822 3001983.088 3095416.859 2976897.927 3145566.892 3173957.563 3053467.441 3333578.895 3056251.766 2928210.659 1.065808163 1.025193689 1.057101834 1.016626969 1.074228346 1.083923915 1.042775878 1.138435476 1.04372674 1 21.48158792 3.196235811 19.80400033 1.074702567 1.041177826 0.037709574 0.03664 30.31798796 14184.9098 0.010235964 0.012235053 1571.215703 -3.196235811 -0.033524741 DLGHNDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGHNDK 7 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 0 ; 130.22 0.0035843 584560000 1397840 1197180 994820 1099260 1214730 1159390 1289070 1227370 1268910 1349630 FALSE TRUE 1343210.867 1163037.599 1174606.104 1155992.94 1253802.894 1182833.66 1304846.024 1202024.381 1124868.657 1258218.358 1.067549888 0.924352749 0.933547103 0.918753834 0.996490701 0.940086156 1.037058485 0.955338454 0.894017044 1 20.26295089 3.196656171 24.9985266 0.970590524 0.956464535 0.004573445 0.05319662 898.6978706 536123.9752 0.015199346 0.018166844 1572.737241 -3.196656171 -0.014125989 QILIACS(ph)PVSSVR ddPTM_BT-474_Pertuzumab_2h_R1 4 QILIACSPVSSVR 13 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 QILIACS(0.962)PVS(0.038)SVR;QILIACS(0.983)PVS(0.017)SVR;QILIACS(0.995)PVS(0.005)SVR;QILIACS(0.992)PVS(0.006)S(0.002)VR 149.6 4.51E-05 1358660000 2339990 2362620 1867530 2159020 1949060 1988830 1938120 2072570 1900180 2362220 TRUE FALSE 2248540.604 2295240.391 2205034.214 2270447.281 2011753.285 2029045.505 1961839.292 2029770.705 1684479.533 2202224.735 1.0210314 1.042237131 1.001275746 1.030978921 0.913509531 0.921361691 0.890844273 0.921690994 0.764899016 1 21.07053027 3.196723107 4.807648839 0.898605013 1.024074696 0.540838142 0.055028286 0.144606081 7.480983444 0.015219116 0.018886834 1572.97966 -3.196723107 0.125469683 LFQEDPEAFLLYHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFQEDPEAFLLYHR 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 0 ; 175.15 2.43E-06 75209000 83927 93400 83133 84197 83498 80981 82432 90729 90992 86249 FALSE TRUE 80647.04005 90736.32345 98156.98238 88542.41726 86183.789 82618.4913 83440.82747 88855.41444 80662.96963 80407.27841 1.00298184 1.12845908 1.220747479 1.10117416 1.071840643 1.027500158 1.037727294 1.105066807 1.003179951 1 16.29503848 3.198554062 3.162380308 1.047229534 1.123577389 0.281964926 0.056875543 0.341781583 7.007736517 0.017426206 0.022377903 1579.62523 -3.198554062 0.076347855 EFVEAVLELR ddPTM_BT-474_Pertuzumab_2h_R1 8 EFVEAVLELR 10 0 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 ;;;;;;; 189.38 2.37E-06 1018034000 800399 924953 744096 1073796 646625 771147 751592 742559 767945 905657 FALSE TRUE 769118.5222 898574.2461 878570.6995 1129214.74 667424.2804 786740.1207 760790.2077 727224.8972 680771.1031 844316.0447 0.91093676 1.064262904 1.040570892 1.337431341 0.790491054 0.931807616 0.901072783 0.861318344 0.806298906 1 19.6874236 3.199112338 24.99999869 0.87771265 1.083175476 0.443944755 0.113087535 140.6568523 89139.64248 0.031929274 0.038163334 1581.65711 -3.199112338 0.205462827 DKEPEVVFIGDSLVQLMHQCEIWR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKEPEVVFIGDSLVQLMHQCEIWR 24 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ; 254.14 5.07E-44 1880560000 873480 745470 652100 627470 826960 834420 806840 852040 979420 863090 FALSE TRUE 839343.4359 724209.9255 769948.9759 659853.8019 853559.9194 851292.5441 816714.3493 834445.0762 868240.3477 804632.1455 1.043139328 0.900050948 0.95689562 0.820068904 1.06080763 1.057989727 1.01501581 1.037051628 1.079052524 1 19.61796985 3.199354369 24.99992449 1.041949817 0.929814821 0.490912724 0.055681812 125.0421775 79732.98107 0.01536557 0.018365634 1582.538807 -3.199354369 -0.112134996 GHQFSCVCLHGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHQFSCVCLHGDR 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 180.48 7.44E-06 2233400000 105785 129061 122740 115732 92648 57023 127307 63737 112748 98240 FALSE TRUE 101650.8052 125380.3066 144921.8483 121704.9424 95628.10706 58176.04413 128865.0211 62420.80868 99949.31972 91586.1173 1.109893161 1.368988121 1.582356067 1.328857975 1.044133215 0.635205923 1.407036622 0.681553171 1.091315176 1 16.48284131 3.200368244 4.13170801 0.949589211 1.369849855 0.39116464 0.227472162 0.19569876 7.176866834 0.063796267 0.080308657 1586.237613 -3.200368244 0.420260644 LPLLPHEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPLLPHEVR 9 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ; 102.61 0.0035568 1170620000 1111310 1253940 1103770 1115790 1010290 695230 1185290 909770 1118900 1325080 FALSE TRUE 1067878.777 1218178.859 1303245.792 1173376.056 1042786.895 709288.0269 1199795.934 890982.9316 991887.1628 1235331.151 0.864447379 0.986115227 1.054976871 0.949847378 0.844135513 0.574168332 0.971234258 0.721250274 0.802932203 1 20.2364664 3.200398963 4.113585245 0.796181749 0.973860035 0.249985598 0.121116707 0.24457357 8.879178306 0.033623496 0.042341778 1586.349819 -3.200398963 0.177678286 GEDVDQLVACIESK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEDVDQLVACIESK 14 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;; 239.19 5.51E-17 201924000 350428 363194 294747 340241 374001 360199 393485 422405 427144 405025 FALSE TRUE 336732.8863 352836.0627 348014.3395 357800.8788 386031.0818 367482.4706 398300.5871 413682.1891 378656.4039 377592.296 0.89178961 0.934436604 0.921666949 0.94758522 1.022348935 0.973225552 1.054842992 1.095578998 1.00281814 1 18.5264698 3.200990196 0.940441071 1.048052517 0.90694506 0.683071135 0.033700056 0.304004055 0.585836756 0.0160507 0.025545642 1588.510889 -3.200990196 -0.141107457 LTPSGYEWGR ddPTM_BT-474_Pertuzumab_2h_R1 3 LTPSGYEWGR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;; 155.84 2.79E-05 562910000 487750 451970 403450 412860 409470 387530 434780 373200 436840 470110 FALSE TRUE 468688.1908 439080.2581 476362.3897 434167.7541 422640.9744 395366.1221 440100.9677 365493.2896 387251.7546 438269.031 1.069407505 1.00185098 1.086917752 0.990642102 0.964341408 0.902108281 1.004179937 0.833947333 0.8835937 1 18.74145721 3.201739111 1.332920669 0.91086805 1.050270552 0.506515507 0.053287664 0.319482804 1.192797445 0.019223139 0.027961429 1591.252543 -3.201739111 0.139402502 FHDFDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 FHDFDHR 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 87.754 0.035194 0 904900 976230 870420 883350 726750 518390 928010 546580 793200 920420 FALSE TRUE 869535.5076 948388.8762 1027724.256 928939.7994 750126.5738 528872.201 939367.264 535292.932 703159.2614 858079.1336 1.013351186 1.105246403 1.197703354 1.082580572 0.874192769 0.616344321 1.094732674 0.623827 0.81945736 1 19.71075118 3.202065809 4.0193276 0.809281454 1.110347419 0.44001447 0.144034633 0.174681403 6.036584173 0.040179011 0.050743348 1592.450015 -3.202065809 0.301065965 VSHVSTGGGASLELLEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSHVSTGGGASLELLEGK 18 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ; 166.92 2.45E-11 1427740000 857550 1133100 837390 1225230 748130 894360 871370 898190 1022320 919430 FALSE TRUE 824035.9979 1100785.097 988725.0006 1288464.267 772194.2809 912444.572 882034.0867 879642.0626 906270.5195 857156.1872 0.96136038 1.284229308 1.153494562 1.503184935 0.900879318 1.064502113 1.029023765 1.026233113 1.057299163 1 19.70919858 3.202170599 24.99996178 1.018519715 1.224610547 0.384260103 0.13171445 175.2313657 120383.5125 0.036278359 0.04336213 1592.834299 -3.202170599 0.206090832 NVPNWHR ddPTM_BT-474_Pertuzumab_2h_R1 5 NVPNWHR 7 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;; 135.35 0.0030858 7576430000 4611460 4731330 4229640 4453250 4005670 3757970 3702040 4039700 4957630 4977560 FALSE TRUE 4431239.045 4596397.101 4994030.036 4683082.766 4134516.013 3833958.728 3747346.673 3956278.783 4394860.626 4640425.428 0.954920861 0.990512006 1.076200903 1.009192549 0.890977795 0.826208456 0.807543776 0.85256812 0.947081403 1 22.14582564 3.202469022 4.61239167 0.868457403 1.012219499 0.469833615 0.060963941 0.148771289 7.16910682 0.01769603 0.02211626 1593.929183 -3.202469022 0.143762096 KIVSWLEYESSFSNEEAQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KIVSWLEYESSFSNEEAQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 259.18 7.49E-31 544720000 524360 483810 404930 397570 512900 563030 462540 519120 595140 497590 FALSE TRUE 503867.4315 470012.2125 478109.8586 418088.6353 529397.8943 574414.8524 468200.7029 508399.9906 527582.2022 463887.7861 1.086183872 1.013202388 1.030658433 0.901271057 1.141219731 1.238262506 1.009297328 1.095954681 1.137305655 1 18.82341634 3.203475364 24.99984484 1.107191605 1.009843152 0.272881414 0.07648815 234.9847891 167436.6905 0.022120939 0.026440607 1597.626898 -3.203475364 -0.097348453 TAPFDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAPFDSR 7 0 P14854;A0A494C160;K7EQD3 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ; 124.89 0.0095448 563070000 1226720 1339420 1291470 1615630 1069690 1046010 1435160 1319470 1278690 1329340 FALSE TRUE 1178778.426 1301221.053 1524867.358 1699012.858 1104097.55 1067161.039 1452723.917 1292222.483 1133538.472 1239302.618 0.951162702 1.049962321 1.230423737 1.370942685 0.890902298 0.861098027 1.172210804 1.042701326 0.914658337 1 20.24109708 3.203540292 24.99999945 0.994130954 1.149133747 0.282903645 0.131761457 274.6372651 196054.8816 0.04105447 0.049071425 1597.865767 -3.203540292 0.155002794 GDLSSIR ddPTM_BT-474_Pertuzumab_2h_R1 5 GDLSSIR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 178.84 0.0016513 2250410000 2685210 3086420 2888580 2999980 2678440 1719050 3481100 2743820 2980700 3439590 FALSE TRUE 2580269.025 2998398.324 3410610.662 3154809.327 2764594.455 1753810.369 3523702.743 2687159.158 2642343.432 3206623.506 0.804668531 0.935064038 1.063614315 0.983841515 0.862151247 0.546933672 1.09888259 0.838002701 0.824026715 1 21.61262354 3.203690355 10.06915973 0.854462028 0.954277833 0.073565304 0.145715824 1.021188505 285.9588799 0.042040276 0.050539127 1598.417974 -3.203690355 0.099815804 LQLS(ph)PWESSVVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQLSPWESSVVNR 13 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LQLS(0.994)PWES(0.005)S(0.001)VVNR;LQLS(0.999)PWES(0.001)SVVNR 194.01 1.44E-06 444580000 309610 319860 341160 354400 305600 298630 304130 369780 299920 359610 TRUE FALSE 297510.0989 310737.906 402815.2011 372690.6265 315429.9015 304668.5032 307852.0339 362143.9138 265874.339 335253.2944 0.887418868 0.926875026 1.20152496 1.111668797 0.940870401 0.908771094 0.918266991 1.080209859 0.793055112 1 18.35489198 3.203706861 24.96645323 0.950464343 1.036490284 0.145702244 0.106798149 387.9962082 277928.3108 0.032510262 0.038858628 1598.478728 -3.203706861 0.086025941 QLEDWLHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLEDWLHSK 9 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;H7C0P8 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 123.8 0.00054754 610460000 1167650 1204410 971340 1045430 1145880 1142130 1187890 1158500 1257450 1281290 FALSE TRUE 1122016.947 1170061.406 1146882.745 1099384.768 1182738.271 1165224.651 1202427.753 1134576.57 1114709.548 1194507.087 0.939313763 0.979534922 0.960130549 0.920366886 0.990147554 0.975485758 1.006630908 0.949828245 0.933196261 1 20.18798398 3.204104367 24.9999252 0.973903123 0.952693003 0.200831957 0.025009964 369.4023539 268020.8496 0.00743316 0.008884759 1599.942469 -3.204104367 -0.02121012 IGEYLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGEYLEK 7 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 132.69 0.0077809 166517000 349230 332830 297520 282080 358150 358550 339310 391540 428330 400430 FALSE TRUE 335581.7055 323338.0143 351288.4823 296638.1826 369670.22 365800.1267 343462.5773 383454.5622 379707.7741 373308.5194 0.898939317 0.866141536 0.941013837 0.794619376 0.990253907 0.979886897 0.920050198 1.027178707 1.017142 1 18.51000891 3.204209499 24.99879908 0.987792987 0.879235535 0.62352859 0.043307517 119.0889488 86665.87155 0.012238635 0.014628649 1600.329825 -3.204209499 -0.108557452 FLDAGHK ddPTM_BT-474_Pertuzumab_2h_R1 6 FLDAGHK 7 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 150.02 0.0019771 10157520000 17545900 18180900 16040900 18917800 16065200 15985100 19134500 17474100 20387900 19165000 FALSE TRUE 16860186.83 17662398.53 18939847.46 19894149.93 16581951.75 16308329.67 19368673.73 17113253.73 18073551.07 17866937.48 0.94365287 0.988552098 1.060050021 1.113461663 0.928080247 0.912765811 1.084051128 0.957816847 1.011564018 1 24.09078903 3.204434167 24.99999595 0.98255545 1.026125562 0.112076027 0.06073659 444.9685467 325968.8973 0.018221882 0.021780348 1601.157915 -3.204434167 0.043570112 IHAENAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHAENAIR 8 0 Q7LBR1 Q7LBR1 CHMP1B Charged multivesicular body protein 1b 0 ; 87.258 0.015452 1555730000 1574970 1853330 1490090 1447300 1420450 1112600 1474740 1042250 1480380 1626990 FALSE TRUE 1513418.431 1800474.843 1759382.41 1521995.326 1466140.064 1135097.534 1492788.309 1020727.173 1312333.469 1516792.518 0.997775512 1.187027772 1.159936108 1.003430138 0.966605549 0.748353859 0.984174362 0.672951087 0.865203021 1 20.53259232 3.205467961 1.806466713 0.831551054 1.118491548 0.514158747 0.106444754 0.233632058 1.573734029 0.033413886 0.045878605 1604.973852 -3.205467961 0.286940494 YNEQHVPGSPFTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 YNEQHVPGSPFTAR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 84.508 0.0081056 1668050000 1974520 2087100 1367050 2014290 1579630 1800580 1672970 1526680 1919980 2205610 FALSE TRUE 1897353.575 2027577.951 1614106.345 2118247.748 1630440.234 1836988.961 1693444.307 1495153.524 1702031.92 2056222.07 0.922737677 0.98606954 0.784986392 1.030164873 0.792930033 0.893380627 0.823570728 0.727136211 0.827747131 1 20.97156465 3.205477962 24.99982311 0.824585044 0.924495302 0.162856767 0.089686064 275.3321856 208061.6137 0.025119694 0.03002547 1605.010811 -3.205477962 0.099910258 NMEVMGFLHGIFER ddPTM_BT-474_Pertuzumab_2h_R1 1 NMEVMGFLHGIFER 14 0 F8WDV0;Q9UI26;Q9UI26-2 F8WDV0 IPO11 Importin-11 0 80.638 0.015737 40155000 33203 32258 28814 29311 28057 27887 26299 27030 33937 30202 FALSE TRUE 31905.39005 31338.03342 34021.33076 30823.74422 28959.47889 28450.89425 26620.85503 26471.82105 30084.61404 28156.39164 1.133149107 1.112998918 1.208298677 1.094733466 1.028522378 1.010459529 0.945464013 0.940170935 1.068482582 1 14.78117484 3.205875369 1.970932397 0.981583519 1.148649309 0.735859939 0.041632756 0.157316328 1.257822456 0.013689201 0.01854867 1606.480171 -3.205875369 0.16706579 VIPELNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VIPELNGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 114.65 0.006085 3361400000 3731700 3898200 3233700 3505800 3441000 3214500 3476600 3659700 3927000 3648000 FALSE TRUE 3585861.038 3787027.153 3818101.523 3686734.758 3551682.89 3279499.392 3519147.671 3584125.916 3481223.423 3400917.711 1.054380418 1.113530957 1.122668011 1.084041154 1.044330734 0.964298366 1.034764134 1.053870226 1.023612954 1 21.69749267 3.206307546 3.41555942 1.021831327 1.098643261 0.628607053 0.028134547 0.164270497 3.976255714 0.008784795 0.011264147 1608.079613 -3.206307546 0.076811935 ALMDSLGPEWR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALMDSLGPEWR 11 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ; 175.91 2.16E-05 101830000 95732 112399 99136 101365 96672 76634 109194 100932 105695 117464 FALSE TRUE 91990.6876 109193.4906 117052.0805 106596.4598 99781.54268 78183.59199 110530.3488 98847.71893 93696.94671 109508.0587 0.840035781 0.997127444 1.068890106 0.973412013 0.911179907 0.713952863 1.009335296 0.902652464 0.855616909 1 16.74067752 3.20648782 5.164864479 0.892986795 0.979298455 0.120056664 0.092958554 0.352052797 23.41957981 0.026909015 0.033446874 1608.747258 -3.20648782 0.086311659 GPHLVQSDGTVPFWAHAGNAIPSSDQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPHLVQSDGTVPFWAHAGNAIPSSDQIR 28 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 161 5.46E-12 593910000 111580 162670 106000 157130 100810 92997 120020 100720 113510 128300 FALSE TRUE 107219.3302 158030.8109 125156.558 165239.4981 104052.6452 94877.46306 121488.8407 98640.0968 100624.8207 119610.1267 0.896406794 1.321215981 1.046370917 1.381484182 0.869931736 0.793222661 1.015706981 0.824680146 0.841273422 1 16.86798001 3.206671172 24.97948946 0.882405674 1.164572933 0.464269385 0.142198232 150.3948186 117806.151 0.037872333 0.045269582 1609.42659 -3.206671172 0.28216726 GTTTVDGAGFGIDRPAELSKEDDEYEAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTTTVDGAGFGIDRPAELSKEDDEYEAFR 29 2 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 0 129.72 8.62E-06 110190000 130050 110100 80368 86130 116960 110730 114310 120660 143250 108570 FALSE TRUE 124967.5022 106960.0558 94892.28538 90575.17962 120722.1246 112969.0365 115708.96 118168.3288 126988.8606 101216.4572 1.234655961 1.056745699 0.937518344 0.894866133 1.19271241 1.116113324 1.143183265 1.167481377 1.25462661 1 16.62708436 3.206882324 24.99993216 1.153270145 1.026115678 0.226329678 0.103202785 270.7754709 213690.4332 0.030297735 0.036215634 1610.209274 -3.206882324 -0.127154467 TAS(ph)ET(ph)RSEGSEYEEIPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASETRSEGSEYEEIPKR 18 2 P48634 P48634 PRRC2A Protein PRRC2A 2 T(0.191)AS(0.803)ET(0.622)RS(0.375)EGS(0.008)EY(0.001)EEIPKR 49.106 0.057381 0 325130 298730 230770 237320 317150 311350 324460 343810 377730 339860 TRUE FALSE 312423.5601 290210.5129 272475.2725 249568.1136 327351.4178 317645.7103 328430.8385 336710.2034 334851.674 316840.9795 0.986057929 0.915950056 0.859974846 0.787676247 1.033172598 1.002539857 1.036579419 1.062710398 1.056844587 1 18.27339942 3.207213647 23.5463873 1.035896802 0.887493081 0.668611499 0.049812064 62.29863141 46795.49739 0.015200761 0.018170875 1611.438173 -3.207213647 -0.148403721 LQTMKEELDFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQTMKEELDFQK 12 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 220.19 2.75E-11 4314100000 5380300 5381100 3157700 3629900 5261400 5814900 5213300 5521300 6052500 5115600 FALSE TRUE 5170031.928 5227636.297 3728366.633 3817239.574 5430637.709 5932481.262 5277101.925 5407283.226 5365445.574 4769115.855 1.084065073 1.096143699 0.781773131 0.800408229 1.138709537 1.243937334 1.106515775 1.133812511 1.125039889 1 22.1852904 3.207752073 24.49929828 1.135558658 0.940363385 0.400325241 0.109884129 161.1224447 128125.8122 0.033711451 0.040297569 1613.437227 -3.207752073 -0.195195274 LKSIFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKSIFR 6 1 E9PGK7;O94759-3;O94759-2;O94759 E9PGK7 TRPM2 Transient receptor potential cation channel subfamily M member 2 0 ; 103.29 0.031752 660950000 494640 611140 491770 421460 628960 744770 631270 677000 568780 421800 FALSE TRUE 475308.9219 593710.8856 580643.7784 443211.6011 649191.0696 759829.7597 638995.6711 663019.7134 504214.4789 393231.1103 1.208726648 1.509826842 1.476596747 1.127102077 1.650914825 1.932272752 1.624987582 1.686081533 1.282234456 1 18.58501794 3.207780941 24.99964228 1.59611059 1.353798354 0.087287411 0.262805012 351.7441534 285690.142 0.073300389 0.087619822 1613.544477 -3.207780941 -0.242312236 IEYQFFEDR ddPTM_BT-474_Pertuzumab_2h_R1 7 IEYQFFEDR 9 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;;;;;; 149.27 0.00020479 1447441000 859990 1087949 787407 900726 880049 726254 1017559 939964 948588 1012724 FALSE TRUE 826380.64 1056921.76 929708.9607 947212.5768 908356.5753 740939.3535 1030012.191 920553.4149 840908.267 944131.3014 0.875281477 1.119464801 0.984724221 1.003263609 0.962108315 0.784784227 1.090962867 0.975026899 0.890668772 1 19.84862799 3.207966316 5.797108189 0.952827677 1.003901634 0.052066155 0.091765161 0.548780687 51.4184898 0.0261804 0.032323612 1614.233352 -3.207966316 0.051073956 IDMNLTDLLGELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDMNLTDLLGELQR 14 0 F5H365;Q15436;Q15436-2;A0A2R8YFH5;Q15437;Q5QPE2 F5H365;A0A2R8YFH5 SEC23A;SEC23B Protein transport protein Sec23A;Protein transport protein Sec23B 0 ; 120.14 0.00034171 132702000 303700 344900 213310 194520 344660 445260 296640 308320 237130 222610 FALSE TRUE 291831.0682 335063.7897 251859.8621 204559.2005 355746.3019 454263.4623 300270.3691 301953.0843 210211.9965 207532.4264 1.406195038 1.614512949 1.213592817 0.985673439 1.714172132 2.188879445 1.446860012 1.454968216 1.012911573 1 17.66297725 3.207999159 24.99963787 1.520452787 1.320572504 0.037709864 0.35211212 622.2892549 509038.2769 0.106427892 0.127219354 1614.355429 -3.207999159 -0.199880284 IHIVMK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHIVMK 6 0 B8ZZF8;Q9Y4Y9 B8ZZF8 LSM5 U6 snRNA-associated Sm-like protein LSm5 0 ; 85.077 0.055124 845790000 4806100 4898100 4153200 4618300 4141600 4110600 4638900 3145500 5592100 5594900 FALSE TRUE 4618272.299 4758410.984 4903775.627 4856651.016 4274818.325 4193719.148 4695672.246 3080544.326 4957308.252 5215952.44 0.885413039 0.912280363 0.940149605 0.931114897 0.819566201 0.804017904 0.900252121 0.59060054 0.950412855 1 22.31449928 3.208014978 6.841984254 0.809821791 0.918596489 0.048157931 0.106789416 0.304181894 45.70293603 0.030761594 0.037611267 1614.414235 -3.208014978 0.108774697 LGAPENSGIST(ph)LER ddPTM_BT-474_Pertuzumab_2h_R1 4 LGAPENSGISTLER 14 0 A0A1B0GV68;M0QYB0;Q9Y4F1-3;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 LGAPENS(0.001)GIS(0.05)T(0.949)LER;LGAPENSGIS(0.025)T(0.975)LER;LGAPENSGIS(0.001)T(0.999)LER;LGAPENSGIS(0.032)T(0.968)LER 260.07 2.14E-23 2088230000 2267930 4149830 1537700 3908280 1652750 1597000 2358040 3626210 2053060 1362560 TRUE FALSE 2179296.788 4031480.912 1815596.596 4109986.799 1705912.205 1629292.434 2386898.399 3551327.496 1820005.236 1270272.598 1.715613477 3.173713201 1.429296829 3.235515595 1.342949701 1.28263212 1.879044233 2.795720779 1.432767454 1 20.2767067 3.208046239 24.99976811 1.785902181 2.376104108 0.202089634 0.701976269 404.0055019 330991.8615 0.203742586 0.243544741 1614.530446 -3.208046239 0.590201927 KAQPQDSR ddPTM_BT-474_Pertuzumab_2h_R1 6 KAQPQDSR 8 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;;;; 133.57 0.0014649 927954000 2746920 2735730 2162080 2429490 2283250 1641330 2583090 2420000 2370840 2622210 FALSE TRUE 2639567.33 2657709.659 2552815.951 2554876.27 2356692.81 1674518.817 2614702.628 2370026.154 2101712.183 2444605.381 1.07975191 1.087173283 1.044265046 1.045107848 0.964038134 0.684985327 1.069580656 0.969492325 0.859734744 1 21.22117017 3.20819016 4.007428247 0.923239854 1.066359958 0.343053579 0.095933509 0.261938937 9.111394022 0.02864789 0.036334494 1615.065573 -3.20819016 0.143120104 ELYLSHNGIEVIEGLENNNK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELYLSHNGIEVIEGLENNNK 20 0 Q15435;C9JD73;H7C003;C9J177;Q15435-2 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 ;; 209.43 4.69E-22 322960000 399080 373518 315708 372780 413030 390600 439080 432750 489590 481000 FALSE TRUE 383483.5124 362865.6324 372763.4585 392019.2205 426315.4851 398498.1996 444453.5924 423813.5613 434013.7957 448421.4416 0.855185495 0.809206694 0.831279292 0.874220508 0.950702722 0.888668923 0.991151518 0.945123319 0.967870301 1 18.77449574 3.208231393 0.815843164 0.971176147 0.817898973 0.797219269 0.029184575 0.27334343 0.399417088 0.014666198 0.024598457 1615.218921 -3.208231393 -0.153277174 VYQSLCPTSWVTDWDEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 VYQSLCPTSWVTDWDEQR 18 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;; 324.48 1.11E-61 838887000 331529 395335 329693 459395 275187 352164 352858 348641 337273 334718 FALSE TRUE 318572.4802 384060.4329 389275.8591 483104.431 284038.6398 359284.9974 357176.3818 341441.4415 298987.183 312047.2517 1.020911027 1.230776527 1.247490106 1.54817717 0.910242401 1.151380105 1.144622745 1.094197881 0.958147144 1 18.25140498 3.208434328 24.99999778 1.062708246 1.258595784 0.365910188 0.139615372 244.7863083 203132.8126 0.040585697 0.048514917 1615.973849 -3.208434328 0.195887539 FVEDTKNEVHER ddPTM_BT-474_Pertuzumab_2h_R1 3 FVEDTKNEVHER 12 1 O75828 O75828 CBR3 Carbonyl reductase [NADPH] 3 0 ;; 203.39 7.54E-08 914830000 1013380 1053290 784940 868350 997470 1056700 1027800 1016980 1120180 1088100 FALSE TRUE 973775.9892 1023251.2 926796.1189 913165.6476 1029554.528 1078067.198 1040378.524 995979.0076 993021.8626 1014402.018 0.959950761 1.008723546 0.91363789 0.900200938 1.014937382 1.062761291 1.025607703 0.981838551 0.97892339 1 19.95219809 3.20875661 24.9079993 1.011271585 0.94785005 0.45368204 0.034932555 200.5774778 167627.3396 0.011130254 0.013304919 1617.173478 -3.20875661 -0.063421535 GQPSNKEDVDDLVSQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GQPSNKEDVDDLVSQLR 17 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 201.12 1.07E-11 1826370000 1926440 1816250 1570250 1708890 1919130 1987670 1859690 2163340 2208840 2076070 FALSE TRUE 1851152.595 1764452.328 1854029.105 1797086.018 1980860.559 2027862.049 1882449.443 2118666.273 1958101.743 1935455.93 0.956442648 0.911646864 0.957928867 0.928507847 1.023459397 1.047743851 0.97261292 1.094660044 1.011700506 1 20.88424203 3.208834061 6.62542131 1.031937404 0.937987491 0.622306741 0.032724652 0.103457626 14.44323278 0.009203488 0.011280475 1617.461905 -3.208834061 -0.093949913 LWGDVTEIKS(ph)PILSGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LWGDVTEIKSPILSGPK 17 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 LWGDVTEIKS(1)PILSGPK;LWGDVTEIKS(1)PILSGPK 171.06 1.07E-09 556350000 998360 965870 913030 848910 1043020 1018710 996450 1139530 1115530 1101170 TRUE FALSE 959342.9875 938324.3333 1078034.831 892722.3468 1076569.686 1039309.014 1008644.853 1115998.307 988899.7111 1026586.775 0.934497707 0.914023399 1.050115643 0.869602423 1.048688442 1.012392756 0.982522742 1.087095932 0.963288964 1 19.96942415 3.208835893 24.99983751 1.022085609 0.947775355 0.307443816 0.053327388 237.2806937 199563.1427 0.014758145 0.017641609 1617.468728 -3.208835893 -0.074310254 CSGPGLS(ph)PGMVR ddPTM_BT-474_Pertuzumab_2h_R1 7 CSGPGLSPGMVR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR 221.54 2.83E-11 9300670000 5077550 4756700 4428910 4803580 5062620 5576510 5533050 5735600 6706410 6202850 TRUE FALSE 4879113.732 4621043.573 5229312.558 5051493.339 5225463.77 5689270.853 5600765.121 5617157.856 5945126.452 5782725.445 0.843739475 0.799111702 0.904298952 0.873548881 0.903633385 0.983839006 0.968533812 0.971368589 1.028083818 1 22.46331818 3.208841863 0.582658251 1.007155561 0.809140117 0.862095043 0.026172939 0.338877007 0.239446148 0.018560503 0.035791871 1617.490964 -3.208841863 -0.198015444 THPQYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 THPQYSR 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 109.01 0.0071238 712530000 1412250 1614770 1164780 1363710 1018650 443454 1404240 863080 1191320 1330530 FALSE TRUE 1357057.709 1568718.341 1375281.656 1434091.237 1051415.802 452420.9437 1421425.509 845257.0964 1056086.348 1240412.018 1.094037859 1.264675219 1.10872971 1.156141037 0.847634324 0.364734409 1.145930133 0.681432527 0.851399642 1 20.24238798 3.209197968 5.100465723 0.790525225 1.162228183 0.417940282 0.196472749 0.165150612 10.81410205 0.054323989 0.067732436 1618.81779 -3.209197968 0.371702958 RSS(ph)TSSEPTPTVK ddPTM_BT-474_Pertuzumab_2h_R1 3 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.038)S(0.933)T(0.027)S(0.001)S(0.001)EPTPTVK;RS(0.031)S(0.936)T(0.031)S(0.001)S(0.001)EPTPTVK;RS(0.004)S(0.562)T(0.416)S(0.009)S(0.008)EPTPTVK 239.98 8.34E-17 544250000 790590 838760 695190 711070 818540 862320 744180 862550 926690 886040 TRUE FALSE 759692.8688 814839.386 820826.2974 747768.4079 844869.0825 879756.7012 753287.4974 844738.0411 821496.0362 826027.7216 0.919694157 0.986455254 0.993703088 0.905258248 1.022809599 1.065045008 0.91193973 1.022650958 0.994513882 1 19.65583067 3.20977081 24.98660386 1.001839069 0.956820674 0.244748968 0.043911747 338.568456 293841.9119 0.01256689 0.015022897 1620.954446 -3.20977081 -0.045018395 EHLLLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHLLLAR 7 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;; 118.01 0.0051023 613332000 645004 1005730 723750 1153340 508527 266961 1256310 406788 734560 639240 FALSE TRUE 619796.5306 977047.5651 854547.7247 1212864.016 524884.2328 272359.1343 1271685.098 398387.6856 651175.8283 595943.7054 1.040025299 1.639496409 1.433940349 2.03519897 0.880761434 0.457021581 2.133901384 0.668498857 1.092680101 1 19.18481653 3.209928329 24.9991884 1.046714067 1.537102032 0.211490369 0.471265254 332.0811593 289943.1024 0.133080361 0.159088044 1621.542475 -3.209928329 0.490387965 ICGDIHGQYTDLLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ICGDIHGQYTDLLR 14 0 P62140;E7ETD8;C9JP48;C9J9S3 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase 0 ;;; 137.93 1.83E-05 1626520000 1908930 2213270 1770440 1942790 1783950 1445890 2055900 1880330 1885710 2075450 FALSE TRUE 1834326.905 2150149.707 2090397.891 2043057.625 1841332.372 1475126.886 2081060.719 1841500.528 1671652.106 1934877.923 0.948032371 1.111258587 1.080377148 1.05591035 0.951652996 0.762387574 1.075551431 0.951739904 0.863957403 1 20.88381111 3.210675401 5.564598415 0.934212759 1.05603641 0.297528233 0.086308439 0.21952609 18.75353056 0.024856819 0.030846007 1624.334248 -3.210675401 0.121823651 TLNAETPKS(ph)SPLPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 TLNAET(0.004)PKS(0.596)S(0.4)PLPAK 66.827 0.034772 989530000 448970 454380 297180 286030 486470 485800 426970 505350 626680 519530 TRUE FALSE 431423.756 441421.5273 350887.0367 300792.0426 502117.7494 495623.2088 432195.3866 494914.3459 555541.9137 484341.7704 0.890742411 0.911384387 0.724461647 0.621032628 1.036701313 1.02329231 0.892335564 1.02182875 1.147003929 1 18.8856659 3.21095617 24.99876543 1.012720679 0.791336316 0.5880146 0.095511738 166.3867007 150680.4263 0.029451234 0.035208375 1625.384711 -3.21095617 -0.221384363 SELWKPEAFSQEFGDQDVDLVNCR ddPTM_BT-474_Pertuzumab_2h_R1 2 SELWKPEAFSQEFGDQDVDLVNCR 24 1 Q7LBC6;Q7LBC6-2;Q7LBC6-3 Q7LBC6 KDM3B Lysine-specific demethylase 3B 0 ; 248.74 3.55E-38 166440000 121914 126902 96670 103848 122309 131855 114892 130759 135118 124337 FALSE TRUE 117149.4661 123282.8792 114140.4194 109207.6077 126243.1801 134521.1984 116298.0827 128058.781 119779.9711 115915.5442 1.010645008 1.063557783 0.98468605 0.942130828 1.089096211 1.160510433 1.003300148 1.104759347 1.033338297 1 16.82271452 3.211371546 24.99203568 1.072744212 1.00366444 0.254719126 0.053333676 277.5457032 255117.5942 0.015231223 0.018208922 1626.940035 -3.211371546 -0.069079772 ELFDDPSY(ph)VNVQNLDK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELFDDPSYVNVQNLDK 16 0 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3;Q5T188 P29353-2 SHC1 SHC-transforming protein 1 1 ELFDDPS(0.023)Y(0.977)VNVQNLDK;ELFDDPS(0.041)Y(0.959)VNVQNLDK;ELFDDPS(0.492)Y(0.508)VNVQNLDK;ELFDDPS(0.076)Y(0.924)VNVQNLDK 278.46 2.33E-34 1308090000 2395260 2414510 2033180 2198840 2086360 1975680 1875890 2337670 2457480 2160590 TRUE FALSE 2301650.591 2345650.539 2400620.854 2312322.396 2153469.664 2015629.603 1898847.703 2289396.298 2178517.173 2014251.315 1.142682928 1.164527247 1.191817941 1.147981078 1.069116673 1.000684268 0.942706448 1.136599133 1.081551819 1 20.94181227 3.211674085 3.352217215 1.040723464 1.166546494 0.598612348 0.050070735 0.186882408 4.360500906 0.016192199 0.020858933 1628.07379 -3.211674085 0.125823031 THMQDLK ddPTM_BT-474_Pertuzumab_2h_R1 4 THMQDLK 7 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;J3QRT6;O43236-5;J3KSZ7;O43236-2;O43236-3;O43236;O43236-4;A0A5F9ZHH3 E7EPK1;A0A5F9ZHH3 SEPT7;SEPT4 Septin-7;Septin-4 0 ;;; 143.01 0.0024506 2150480000 3674670 3554680 3088890 2712780 2952210 1766740 3143840 1046770 3501950 3027560 FALSE TRUE 3531059.834 3453304.007 3647121.135 2852786.901 3047170.516 1802464.693 3182315.254 1025153.834 3104423.317 2822500.665 1.251039505 1.223490946 1.292159531 1.010730285 1.079599574 0.638605587 1.127480781 0.36320765 1.099883999 1 21.42854249 3.212379678 1.303296799 0.789491731 1.255721382 0.344625878 0.224111815 0.400496131 1.431862357 0.079362799 0.117287694 1630.721054 -3.212379678 0.466229651 QSTIVCHNR ddPTM_BT-474_Pertuzumab_2h_R1 6 QSTIVCHNR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;;; 116.3 0.0013354 2239300000 2183950 2394530 1944820 2122370 1823780 1164110 2174350 1809820 2068950 2326920 FALSE TRUE 2098598.82 2326240.349 2296292.236 2231905.77 1882443.54 1187649.102 2200960.346 1772446.585 1834091.47 2169315.636 0.967401325 1.07233835 1.058533022 1.028852479 0.867759172 0.547476394 1.014587416 0.817053339 0.845470083 1 21.04880855 3.212553303 5.05853971 0.83416323 1.037801622 0.348103488 0.122304249 0.191128619 12.48899658 0.034504586 0.043169709 1631.373123 -3.212553303 0.203638391 HPELTKPPPLMAAEPTAPLS(ph)HSASSDPADRLSPFLAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPELTKPPPLMAAEPTAPLSHSASSDPADRLSPFLAAR 38 2 Q9ULP9-2;Q9ULP9 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 1 HPELTKPPPLMAAEPT(0.051)APLS(0.206)HS(0.206)AS(0.179)S(0.179)DPADRLS(0.179)PFLAAR 51.544 0.029275 693940000 457310 486180 447110 589800 352880 405490 439100 296230 528610 570300 TRUE FALSE 439437.8196 472314.6224 527912.7229 620239.6487 364230.7057 413689.2856 444473.8371 290112.747 468604.4089 531673.073 0.826518855 0.888355357 0.992927326 1.166580894 0.685065173 0.778089594 0.835990874 0.545660034 0.881376983 1 19.02017988 3.212641178 24.99948228 0.75339879 0.964602314 0.2641702 0.141040771 250.759653 241858.799 0.040932108 0.048938249 1631.703248 -3.212641178 0.211203524 DLYCHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLYCHK 6 0 P16220-1;P16220;P16220-3;Q03060-6;G5E998;Q03060-26;Q03060-32;Q03060-21;Q03060-31;E9PAR2;Q03060-23;Q03060-9;Q03060-24;Q03060-8 P16220-1;Q03060-6 CREB1;CREM Cyclic AMP-responsive element-binding protein 1;cAMP-responsive element modulator 0 91.26 0.048095 115120000 190750 175430 172440 177310 164260 106870 194290 175480 189590 210630 FALSE TRUE 183295.2791 170426.9082 203603.7439 186460.9903 169543.5721 109030.9846 196667.7791 171856.2767 168068.538 196363.8425 0.933447201 0.867913899 1.03686983 0.949568861 0.863415433 0.555249802 1.001547824 0.875193083 0.855903693 1 17.58316978 3.213015107 6.437680507 0.849533911 0.947912712 0.110501358 0.121525394 0.365821398 50.37445237 0.035329808 0.043547268 1633.108755 -3.213015107 0.0983788 NVVGAR ddPTM_BT-474_Pertuzumab_2h_R1 5 NVVGAR 6 0 P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;A0A0J9YWZ2;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;P61981;Q04917;A2IDB2 P31946-2;P63104;P61981;Q04917 YWHAB;YWHAZ;YWHAG;YWHAH "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein zeta/delta;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein eta" 0 ;;;; 167.64 0.015345 2096830000 2080970 2177580 1730820 2133870 1826620 1871940 1743900 2150350 2100520 2075620 FALSE TRUE 1999643.392 2115477.55 2043617.676 2243999.286 1885374.891 1909791.909 1765242.37 2105944.521 1862077.776 1935036.409 1.033387994 1.093249482 1.056113294 1.159667734 0.974335616 0.986953993 0.912252794 1.088322944 0.96229599 1 20.88392928 3.213065411 24.98476044 0.993119276 1.084044205 0.467561346 0.051128509 211.1254951 206897.9682 0.014826901 0.017727945 1633.297927 -3.213065411 0.090924929 SIIDEFLHINDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIIDEFLHINDFK 13 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 0 ; 114.56 0.00073315 89951000 185051 188989 157170 162215 188479 189454 195391 184161 224742 220600 FALSE TRUE 177819.0023 183599.2188 185574.1152 170586.9356 194541.5982 193284.8897 197782.2535 180358.011 199230.2304 205658.5655 0.864632124 0.892738011 0.902340803 0.829466719 0.945944545 0.93983389 0.961701999 0.876977871 0.968742682 1 17.64989163 3.213095174 24.99976315 0.938837954 0.87590083 0.521673474 0.035073776 209.4646232 205633.635 0.010106986 0.012084546 1633.409865 -3.213095174 -0.062937124 TPSSPLQSCTPSLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPSSPLQSCTPSLSPR 16 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 TPSSPLQSCTPS(0.007)LS(0.993)PR;TPSSPLQSCTPS(0.007)LS(0.993)PR 123.02 9.46E-05 321890000 95983 103795 79637 104073 81039 66445 93658 96301 92960 99906 TRUE FALSE 92231.87825 100834.8682 94029.17742 109444.22 83645.69303 67788.56343 94804.21462 94312.3507 82407.57052 93139.27763 0.990257608 1.082624547 1.009554506 1.17505979 0.898071095 0.727819295 1.017875777 1.012594827 0.884777858 1 16.50710207 3.21314018 24.99983839 0.927706179 1.061762094 0.360169537 0.091841744 272.9729732 268455.7501 0.028030187 0.03351384 1633.579144 -3.21314018 0.134055915 DAGTIAGLNVLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DAGTIAGLNVLR 12 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 204.64 2.58E-07 1546340000 903400 965000 832300 876870 845840 628737 998360 855750 957690 1015440 FALSE TRUE 868094.1292 937479.1448 982715.1244 922125.3658 873047.2118 641450.4929 1010578.228 838078.4635 848977.0462 946663.3443 0.917004059 0.990298347 1.038083 0.974079509 0.922236207 0.677590927 1.067515959 0.885297258 0.896809886 1 19.85249194 3.213209536 4.824733465 0.901019219 0.985466137 0.113301366 0.097693739 0.383247751 21.93622398 0.027879509 0.035015842 1633.840045 -3.213209536 0.084446918 ILPPGLLAYLESSDLVPEKDADR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILPPGLLAYLESSDLVPEKDADR 23 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ; 131.65 2.73E-05 168932000 129874 115815 106794 99322 132405 150230 116137 142496 139345 136237 FALSE TRUE 124798.3805 112512.0696 126094.0514 104448.0203 136663.9271 153267.7535 117558.3193 139553.4078 123527.1398 127009.5466 0.982590552 0.885855218 0.992791918 0.822363539 1.07601303 1.206741994 0.925586481 1.098763136 0.972581535 1 16.95457742 3.214164437 24.99997492 1.053685854 0.923532161 0.343812081 0.084714615 239.4102533 245334.9405 0.023417127 0.028001342 1637.436387 -3.214164437 -0.130153693 NCPHIVVGTPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 NCPHIVVGTPGR 12 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;; 154.36 7.14E-05 2840860000 1932470 1843080 1599020 1876150 1688590 1792750 1757950 1872170 2008110 1977170 FALSE TRUE 1856946.936 1790517.163 1887998.484 1972978.326 1742905.031 1829000.633 1779464.318 1833509.035 1780157.771 1843254.515 1.007428394 0.971389002 1.024274439 1.070377591 0.945558531 0.992267003 0.965392627 0.994712895 0.965768838 1 20.81382386 3.214475654 24.99704757 0.978101735 1.015433764 0.350671934 0.027257699 285.2823078 296084.7972 0.008004115 0.009571943 1638.610202 -3.214475654 0.037332029 HYASEEIKEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HYASEEIKEK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 175.86 1.61E-06 314970000 706600 750030 550170 569010 741120 806640 760250 601650 921240 797180 FALSE TRUE 678985.2908 728639.8788 649597.9575 598376.6743 764958.7979 822950.8135 769554.1669 589225.7172 816664.6974 743186.2885 0.913613856 0.980426967 0.874071505 0.805150315 1.029296167 1.107327767 1.035479501 0.792837175 1.098869435 1 19.50336436 3.214709662 24.99984761 0.992457736 0.898163243 0.269595626 0.091580382 418.6751755 438841.5155 0.029448877 0.035215233 1639.493358 -3.214709662 -0.094294493 VLHDAQQQCR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLHDAQQQCR 10 0 A1L0T0;M0R026 A1L0T0 ILVBL Acetolactate synthase-like protein 0 ;;; 167.67 5.17E-06 1405380000 535695 868419 549771 798849 513963 326178 704300 678992 596368 560084 FALSE TRUE 514759.4472 843652.5404 649126.8493 840077.6926 530495.0867 332773.5426 712919.4341 664970.5779 528670.8048 522149.0118 0.985847786 1.615731374 1.243183142 1.608884961 1.015984086 0.637315278 1.365356283 1.273526451 1.012490291 1 18.99410206 3.21522814 24.99466845 1.081053717 1.372846986 0.272190737 0.247299465 337.5635249 361610.442 0.073058499 0.087370771 1641.451821 -3.21522814 0.291793269 DSTLIMQLLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DSTLIMQLLR 10 0 B7Z2E6;H0YB80;P63104-2;P27348;P31946-2;P31946;P63104;E7EX29;B0AZS6;P31947-2;P31947;P61981;P62258;P62258-2;K7EM20;Q04917 B7Z2E6;P27348;P31946-2;P63104;P31947-2;P61981;P62258;Q04917 YWHAZ;YWHAQ;YWHAB;SFN;YWHAG;YWHAE;YWHAH "14-3-3 protein zeta/delta;14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein sigma;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein epsilon;14-3-3 protein eta" 0 ;;;;; 229.44 3.77E-09 9330753000 2367682 2632452 2569228 2518375 2354772 1322846 3000616 2448274 2711980 3115619 FALSE TRUE 2275150.37 2557377.046 3033544.652 2648348.636 2430515.38 1349594.852 3037338.436 2397716.286 2404127.4 2904595.35 0.783293401 0.880458976 1.044394928 0.911778859 0.836782783 0.464641263 1.04570106 0.825490644 0.827697875 1 21.46990576 3.215334703 6.374564297 0.822217007 0.913399732 0.044378301 0.1564433 0.49661787 68.72838988 0.045184567 0.055862886 1641.854636 -3.215334703 0.091182725 VASPMNKS(ph)PSAMQQQDGLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VASPMNKSPSAMQQQDGLDR 20 1 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 VAS(0.019)PMNKS(0.954)PS(0.027)AMQQQDGLDR;VASPMNKS(0.5)PS(0.5)AMQQQDGLDR 128.97 1.14E-05 341990000 278610 276300 198342 224050 266190 286150 257830 267540 296270 282820 TRUE FALSE 267721.6132 268420.1945 234186.8115 235613.2474 274752.2431 291936.1491 260985.4007 262015.2055 262638.6717 263664.3495 1.015387987 1.018037497 0.888200517 0.893610561 1.042053063 1.107226478 0.989839549 0.99374529 0.996109911 1 18.00834299 3.215511225 24.99991783 1.021057821 0.953710515 0.293243117 0.051476084 331.2004143 359227.0761 0.016403348 0.019617402 1642.522114 -3.215511225 -0.067347306 (ac)VEADRPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEADRPGK 8 1 P38159;P38159-2;H3BT71;H3BR27;P38159-3;H3BNC1;O75526;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL2;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2;RNA binding motif protein, X-linked-like-1" 0 77.674 0.060538 412170000 149690 134980 123070 124390 144400 141410 166540 149830 145640 146150 FALSE TRUE 143839.9493 131130.5026 145311.4867 130809.7828 149044.7571 144269.4071 168578.1663 146735.9581 129107.5578 136251.1303 1.055697292 0.962417723 1.066497477 0.960063836 1.0938974 1.05884925 1.237260681 1.076952226 0.947570545 1 17.05590867 3.215537255 24.80418925 1.084123254 1.011638857 0.100378078 0.077455467 384.344609 414072.0051 0.022464319 0.026867472 1642.620562 -3.215537255 -0.072484398 VIPAKS(ph)PPPPTHSTQLGAPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 VIPAKSPPPPTHSTQLGAPSR 21 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 VIPAKS(0.998)PPPPT(0.002)HSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR 243.9 2.42E-30 1413890000 701130 877670 621350 765840 694130 743570 687320 746450 788470 827470 TRUE FALSE 673729.0645 852639.7109 733641.7669 805365.0942 716457.3218 758605.4949 695731.6278 731035.5466 698966.1911 771424.7199 0.873356851 1.105279218 0.951021853 1.043997001 0.92874561 0.983382403 0.901878835 0.947643403 0.906071809 1 19.55716585 3.215557253 24.97802084 0.941294323 0.998376152 0.122927639 0.062921809 390.7118789 424250.0735 0.016587465 0.019837305 1642.696203 -3.215557253 0.057081828 EIIDTNGAGDAFVGGFLSQLVSDKPLTECIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIIDTNGAGDAFVGGFLSQLVSDKPLTECIR 31 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 157.42 8.15E-10 96433000 31965 30332 23891 24563 32146 34442 34887 33061 32386 32065 FALSE TRUE 30715.77246 29466.96106 28208.63515 25830.69937 33180.00528 35138.44084 35313.95754 32378.2788 28709.67705 29893.20899 1.027516734 0.985740978 0.943646939 0.864099247 1.10995127 1.175465667 1.181337124 1.083131584 0.960408 1 14.86753016 3.215767097 24.88964314 1.099371921 0.956599965 0.40885054 0.07528117 205.7764454 224699.3355 0.022698171 0.027146838 1643.490116 -3.215767097 -0.142771956 HFAS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HFASPSK 7 0 A0A1X7SBT5;Q92664 A0A1X7SBT5 GTF3A Transcription factor IIIA 1 HFAS(0.999)PS(0.001)K 63.534 0.050792 64139000 145110 135760 128240 109030 124680 99864 123190 101410 115180 120360 TRUE FALSE 139438.9408 131888.2577 151415.8207 114657.0514 128690.4454 101883.3185 124697.6361 99315.84806 102105.2493 112207.91 1.2426837 1.175391804 1.349421985 1.021826816 1.146892812 0.907986955 1.111308785 0.885105587 0.909964808 1 16.77581486 3.215845845 0.967228309 0.950268951 1.253026014 0.621450365 0.091182206 0.341481535 0.69300546 0.038696263 0.062228756 1643.78815 -3.215845845 0.302757062 HGVIVAADSR ddPTM_BT-474_Pertuzumab_2h_R1 6 HGVIVAADSR 10 0 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;;; 111.06 0.0018039 4167900000 3574820 3712760 3275150 3254850 3003280 1875150 3596780 2384100 3392000 3850870 FALSE TRUE 3435112.082 3606875.72 3867042.46 3422833.199 3099883.229 1913066.818 3640798.47 2334867.502 3006954.38 3590047.145 0.956843168 1.004687564 1.077156456 0.953422911 0.863465883 0.532880695 1.014136674 0.650372379 0.83758075 1 21.77557136 3.216027301 3.295452574 0.785304192 1.009785439 0.289917836 0.13912367 0.251703487 5.673321084 0.038515139 0.0498102 1644.475097 -3.216027301 0.224481247 GYSFTTTAER ddPTM_BT-474_Pertuzumab_2h_R1 11 GYSFTTTAER 10 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L3I0;I3L1U9;I3L4N8 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;;;;; 223.19 1.06E-08 64999270000 5628243 6551217 5459201 5654259 5238224 3581301 6029954 5430989 5538215 6109880 FALSE TRUE 5408285.041 6364382.705 6445800.06 5946075.985 5406716.232 3653717.36 6103750.381 5318837.179 4909540.051 5696052.385 0.949479512 1.117332193 1.131625839 1.043894189 0.949204092 0.641447289 1.071575535 0.933776029 0.861919751 1 22.44153098 3.216216357 4.113166231 0.904968761 1.072045296 0.299569326 0.114232807 0.25685442 9.676411386 0.033395321 0.04251462 1645.191121 -3.216216357 0.167076535 VEILANDQGNR ddPTM_BT-474_Pertuzumab_2h_R1 6 VEILANDQGNR 11 0 P17066;P48741 P17066 HSPA6;HSPA7 Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;; 206.73 5.91E-08 13873000000 4191330 4732480 3575010 4447220 3757070 3333620 4324510 3825250 4339100 4614690 FALSE TRUE 4027528.19 4597514.304 4221093.833 4676741.557 3877919.569 3401028.08 4377434.647 3746257.251 3846543.559 4302132.936 0.936170093 1.068659284 0.981163041 1.087075092 0.90139464 0.790544628 1.017503344 0.870790677 0.894101511 1 22.03662067 3.216258314 24.72466966 0.905308172 1.019216056 0.340798811 0.071729692 207.5271992 230067.1148 0.019581759 0.023421992 1645.350068 -3.216258314 0.113907885 EMNDAAMFYTNR ddPTM_BT-474_Pertuzumab_2h_R1 3 EMNDAAMFYTNR 12 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;; 220.45 6.87E-11 1061270000 887310 924820 732094 899260 779060 687680 818860 899510 921080 1018880 FALSE TRUE 852632.9442 898445.0391 864399.6711 945670.9164 804119.1724 701585.3608 828881.4536 880934.8042 816522.8599 949870.3501 0.897630865 0.945860705 0.910018584 0.99557894 0.846556767 0.738611707 0.872625884 0.927426363 0.859615062 1 19.85737108 3.216525323 24.99385366 0.868210165 0.935939072 0.175132247 0.066353508 397.4012521 450757.1922 0.019648223 0.023502059 1646.36196 -3.216525323 0.067728907 SVIDYQTHFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVIDYQTHFR 10 0 Q9Y3B3;A0A0A6YYA0;Q86XR7-2;Q9Y3B3-2 Q9Y3B3 TMED7;TMED7-TICAM2 Transmembrane emp24 domain-containing protein 7 0 ; 188.28 1.14E-06 331510000 370850 558800 423270 510560 396120 226593 520220 434210 489000 528750 FALSE TRUE 356356.772 542863.5711 499764.3046 536910.0628 408861.5595 231174.8657 526586.608 425243.4118 433490.7701 492937.2915 0.722925163 1.101283227 1.013849658 1.089205609 0.829439295 0.468974187 1.068262874 0.862672431 0.879403481 1 18.9110446 3.21654164 24.59708429 0.843377512 0.99263743 0.113613208 0.176485222 389.6724057 435296.1425 0.050949276 0.060945936 1646.423818 -3.21654164 0.149259918 VWLYHDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VWLYHDGR 8 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 99.139 0.0070255 263510000 130710 250740 162730 276130 106570 55034 221200 189560 162010 189460 FALSE TRUE 125601.7087 243589.1407 192138.9309 290381.1024 109997.9208 56146.82519 223907.1118 185645.5198 143619.304 176627.7054 0.711109893 1.379110599 1.087818757 1.644029184 0.622767083 0.317882322 1.267678314 1.051055491 0.813118778 1 17.43035213 3.216753219 24.9797743 0.866570277 1.20951 0.225926362 0.32509459 386.887668 443168.0808 0.097213126 0.116284803 1647.226117 -3.216753219 0.342939723 FTHESQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTHESQR 7 0 A0A0A0MTI1;Q15392-2;Q15392 A0A0A0MTI1 DHCR24 Delta(24)-sterol reductase 0 ; 159.04 0.0013983 355480000 95249 251334 140403 220033 112234 41571 209130 136551 125662 164351 FALSE TRUE 91526.56378 244166.2004 165776.9453 231388.9295 115844.1085 42411.5941 211689.3955 133731.1741 111397.3766 153219.3604 0.597356389 1.593572769 1.081958213 1.510180756 0.756067042 0.276803101 1.381609967 0.872808592 0.727045044 1 17.22523908 3.216881735 24.99861834 0.844283611 1.216052638 0.193607617 0.358767548 375.2507732 432712.7486 0.101192279 0.12104775 1647.713632 -3.216881735 0.371769027 TRNS(ph)GIWESPELDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRNSGIWESPELDR 14 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 T(0.238)RNS(0.762)GIWESPELDR 152.66 4.00E-06 243400000 107970 129510 90090 121770 92767 103740 92283 105810 105230 89398 TRUE FALSE 103750.413 125816.5016 106371.267 128054.5643 95750.9348 105837.6939 93412.38696 103624.9865 93284.73156 83342.99383 1.244860645 1.509623015 1.276307247 1.536476654 1.148878033 1.269905112 1.120818711 1.243355701 1.119287024 1 16.3467733 3.216905604 24.99845513 1.171193403 1.391980941 0.5341862 0.109422095 179.5282626 207246.1746 0.028760309 0.034404024 1647.804193 -3.216905604 0.220787538 MVEDCEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 MVEDCEHR 8 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 180.87 0.00023681 118400000 93556 133870 97133 122900 95768 85129 119470 109330 109890 119890 FALSE TRUE 89899.72809 130052.1587 114687.0938 129242.8837 98848.46469 86850.36671 120932.1096 107072.2973 97415.7479 111769.7435 0.804329734 1.163572131 1.026101431 1.156331577 0.884393769 0.777047204 1.08197537 0.957972112 0.871575301 1 16.77017017 3.216990751 24.99830695 0.932446899 1.045762796 0.164405483 0.119381019 412.6667561 478257.1253 0.033885589 0.040535564 1648.127292 -3.216990751 0.113315897 IFGGLDMLAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IFGGLDMLAEK 11 0 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 140.16 0.0031983 0 131760 144450 121920 117080 144210 120890 166290 140940 135060 144390 FALSE TRUE 126610.6735 140330.4274 143953.6561 123122.5128 148848.6456 123334.4786 168325.1068 138029.5397 119728.555 134610.3367 0.940571702 1.042493696 1.069410118 0.91465868 1.105774261 0.916233342 1.25046197 1.025400747 0.889445476 1 17.03842967 3.217301969 24.98206538 1.041698851 1.000950356 0.025146466 0.103014198 995.1983748 1169502.881 0.02942438 0.035199846 1649.308774 -3.217301969 -0.040748495 DVVEQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVVEQHK 7 0 O75382;O75382-3;O75382-4;E9PMK8;Q9C040;Q9C040-2;A0A0J9YX34;C9J084 O75382 TRIM3;TRIM2 Tripartite motif-containing protein 3;Tripartite motif-containing protein 2 0 ; 86.011 0.02039 703930000 593240 625570 519810 547820 601750 600190 641330 583790 682170 681990 FALSE TRUE 570055.5249 607729.3561 613751.2301 576093.0559 621105.8352 612326.253 649178.7884 571734.5325 604732.9215 635798.2098 0.896598191 0.955852575 0.965323935 0.906094177 0.97689145 0.963082694 1.021045323 0.899238978 0.951139705 1 19.27820943 3.217539048 24.98534459 0.962588297 0.935198776 0.194859333 0.035828873 535.1266982 636027.3517 0.010633741 0.012721966 1650.209367 -3.217539048 -0.02738952 IPEQSVLLLHACAHNPTGVDPRPEQWK ddPTM_BT-474_Pertuzumab_2h_R1 1 IPEQSVLLLHACAHNPTGVDPRPEQWK 27 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 68.516 0.014677 427650000 284880 316620 268980 332570 242530 169180 455610 152120 296960 319910 FALSE TRUE 273746.5746 307590.3076 317590.6694 349733.9776 250331.1977 172600.9355 461185.8915 148978.6688 263250.3458 298242.2108 0.917866636 1.031343977 1.064874984 1.172650835 0.839355358 0.578727388 1.546346811 0.499522413 0.882672996 1 18.18612493 3.217598007 24.57232781 0.872133076 1.046887774 0.0711624 0.270194967 497.3424449 582981.9854 0.07618379 0.091145415 1650.433411 -3.217598007 0.174754698 ADFDNTVAIHPTSSEELVTLR ddPTM_BT-474_Pertuzumab_2h_R1 6 ADFDNTVAIHPTSSEELVTLR 21 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;;;;; 255.41 2.04E-36 2739910000 1712469 1972307 1466711 1718316 1404604 482743 2312839 1234712 1388804 2129211 FALSE TRUE 1645543.818 1916058.735 1731778.305 1806998.495 1449784.363 492504.3942 2341144.216 1209214.766 1231152.792 1984997.642 0.828990314 0.965270031 0.872433431 0.910327779 0.730370824 0.24811334 1.179419142 0.609176928 0.620228844 1 20.92070586 3.217704679 7.462126977 0.713271112 0.897948012 0.101846713 0.233599014 0.353850367 84.91266174 0.064980599 0.07991069 1650.838842 -3.217704679 0.1846769 KLEGETYR ddPTM_BT-474_Pertuzumab_2h_R1 3 KLEGETYR 8 1 Q709C8-3;Q709C8 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ;; 86.898 0.02944 90841000 538530 591200 474250 540360 521910 502700 572080 570760 567770 585400 FALSE TRUE 517483.6522 574339.5548 559957.5246 568248.0444 538697.7091 512864.9384 579081.2862 558973.6065 503319.1299 545750.3366 0.948205832 1.052385159 1.026032394 1.041223443 0.987077191 0.93974278 1.061073622 1.024229522 0.922251616 1 19.05788159 3.218521236 24.92551285 0.995229599 1.02013987 0.072825308 0.045126187 721.8618931 897867.002 0.013295822 0.015906819 1653.945655 -3.218521236 0.024910271 SGMNVAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SGMNVAR 7 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;; 140.98 0.0060199 1733300000 1647280 1756780 1435970 1704530 1459220 1165610 1775130 1607720 1523170 1669570 FALSE TRUE 1582902.476 1706678.354 1695481.722 1792500.998 1506157.137 1189179.433 1796854.572 1574520.02 1350266.127 1556488.537 1.016970211 1.096492723 1.089299203 1.151631352 0.967663494 0.764014257 1.154428401 1.01158472 0.867507916 1 20.56986352 3.218794542 24.59205357 0.969100638 1.089212303 0.282000866 0.09932658 285.8651323 355659.3472 0.029585556 0.035411208 1654.986828 -3.218794542 0.120111665 NEEDEGHS(ph)NSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.981)NS(0.253)S(0.766)PR 83.37 0.014962 36529000 109750 106710 95572 116120 110800 97296 112300 101680 135230 120840 TRUE FALSE 105460.8487 103666.7353 112843.9864 122112.9671 114363.9826 99263.39178 113674.361 99580.27247 119879.2573 112655.3992 0.936136656 0.92021098 1.001674018 1.083951307 1.015166459 0.881124141 1.009044944 0.883936972 1.064123497 1 16.78155693 3.218898057 0.00207138 1.945352337 7.10E-06 0.010791674 0.066966094 967032.1226 577.3139202 268946.3136 273238.97 1655.381347 -3.218898057 -1.945345233 LDLAGR ddPTM_BT-474_Pertuzumab_2h_R1 7 LDLAGR 6 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;Q9BYX7;P63261;I3L3I0;I3L1U9;I3L4N8;P68133;P68032;P63267;P62736;Q6S8J3;A5A3E0;P0CG38;P0CG39 P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;;;;;; 159.65 0.021057 39356620000 13170450 14514310 12254700 13961390 12535170 11291960 14261810 14433260 13525670 13988970 FALSE TRUE 12655734.25 14100376.09 14469396.89 14681939.01 12938375.13 11520291.17 14436350.3 14135208.14 11990292.65 13041484.6 0.970421286 1.081194091 1.109490011 1.125787398 0.992093732 0.883357342 1.106956051 1.083864956 0.919396297 1 23.63660478 3.219121176 24.9558951 1.009566308 1.075097335 0.184684205 0.073625936 479.5350985 615614.4934 0.022802239 0.027292448 1656.232019 -3.219121176 0.065531027 GLPLGSAVSSPVLFS(ph)PVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLPLGSAVSSPVLFSPVGR 19 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 1 GLPLGSAVSSPVLFS(1)PVGR 211.06 1.54E-16 107510000 118740 104540 126040 122050 111960 120240 112080 115840 135410 133200 TRUE FALSE 114099.5095 101558.6216 148818.2317 128349.0151 115561.2951 122671.3352 113451.6686 113447.8635 120038.8245 124178.2454 0.918836542 0.817845519 1.19842434 1.03358696 0.930608214 0.987864942 0.913619517 0.913588875 0.966665491 1 16.92205293 3.219143247 24.8789149 0.944513973 0.994453582 0.038420106 0.093593129 753.9851945 966057.0783 0.028346475 0.033928641 1656.316191 -3.219143247 0.049939608 TNTPVKEDWNVR ddPTM_BT-474_Pertuzumab_2h_R1 4 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 156.52 5.71E-05 4614400000 4009390 4185720 2886040 3385050 3938320 4449970 3719880 4167080 4534360 4143780 FALSE TRUE 3852698.606 4066347.364 3407611.628 3559752.836 4064999.639 4539951.442 3765405.004 4081028.342 4019638.462 3863118.09 0.997302831 1.052607575 0.882088393 0.9214714 1.052258705 1.175203899 0.974706161 1.056407867 1.04051659 1 21.88133435 3.219507705 24.29519652 1.053434698 0.963936196 0.300822656 0.064448862 216.4047868 275946.2886 0.01913662 0.022911678 1657.706747 -3.219507705 -0.089498502 LFVGGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFVGGLK 7 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 109.88 0.016119 402180000 683830 703290 590830 622160 687410 674850 731970 679310 781840 784870 FALSE TRUE 657105.1676 683232.8578 697606.1239 654269.7522 709521.1669 688495.9294 740928.0678 665282.0111 693088.8009 731710.0558 0.898040368 0.933748077 0.953391468 0.894165314 0.969675299 0.940940915 1.012597903 0.909215345 0.947217816 1 19.48091256 3.219601358 24.99670333 0.95780991 0.923226791 0.297119336 0.031906483 369.811498 487574.4582 0.009093408 0.010885109 1658.064259 -3.219601358 -0.034583119 EGKPSWGLPIDAVQWDICNLPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGKPSWGLPIDAVQWDICNLPLR 23 1 Q9BV44 Q9BV44 THUMPD3 THUMP domain-containing protein 3 0 ; 134.34 1.78E-05 206560000 337860 330930 258730 278590 327440 312610 313230 351350 348670 355180 FALSE TRUE 324656.0577 321492.2004 305488.2664 292968.0633 337972.405 318931.1884 317063.4024 344094.4997 309090.4433 331123.3422 0.980468654 0.970913733 0.92258149 0.884770193 1.020684325 0.963179419 0.957538663 1.03917319 0.933460146 1 18.33700919 3.219802374 24.9999433 0.988160338 0.940692642 0.260333634 0.037821864 331.4830993 441781.4979 0.011179295 0.013383357 1658.831884 -3.219802374 -0.047467696 S(ph)GEGEVSGLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGEGEVSGLMR 11 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(1)GEGEVSGLMR;S(1)GEGEVSGLMR 198.33 5.67E-08 3275400000 352370 277600 297540 296920 272760 248920 275180 297080 297210 286330 TRUE FALSE 338598.9908 269683.1198 351312.0967 312244.0768 281533.5731 253953.3329 278547.7352 290945.1942 263471.9668 266936.6141 1.268462148 1.010288981 1.316088083 1.169731166 1.05468324 0.951361932 1.043497671 1.089941128 0.987020712 1 18.02613768 3.219900985 4.238859154 1.026322598 1.18898019 0.512282124 0.081742623 0.179165847 7.345580249 0.023144956 0.029487028 1659.208579 -3.219900985 0.162657592 KDLEEWNQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDLEEWNQR 9 1 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 71.066 0.081187 703830000 815170 914880 756130 792820 753520 538240 887200 739790 798620 916800 FALSE TRUE 783312.2552 888788.5182 892779.511 833737.5352 777757.6551 549123.5816 898057.819 724513.078 707964.0057 854704.3194 0.916471623 1.039878351 1.044547794 0.975468962 0.909972768 0.642471986 1.050723389 0.847676865 0.828314529 1 19.70506589 3.219922834 3.883826315 0.86971403 1.003339974 0.216803669 0.10726636 0.303468186 9.971838502 0.03044429 0.039013357 1659.292055 -3.219922834 0.133625945 TAFYNEDDS(ph)EEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAFYNEDDSEEEQR 14 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR 411.9 1.04E-132 2294900000 1385640 1428110 1190290 1628880 1030690 1295300 1217500 1257630 1211310 1419800 TRUE FALSE 1331487.657 1387381.701 1405401.881 1712946.692 1063843.08 1321491.853 1232400.129 1231659.501 1073807.167 1323635.681 1.005932127 1.048159792 1.061773946 1.294122481 0.803728016 0.998380349 0.931072006 0.930512465 0.811255833 1 20.33607466 3.220385228 24.99999296 0.915732545 1.095707154 0.493463655 0.094173441 208.9473723 287403.6117 0.026678257 0.031946355 1661.059648 -3.220385228 0.179974609 CLATHGR ddPTM_BT-474_Pertuzumab_2h_R1 4 CLATHGR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 104.11 0.019134 224016000 130527 129664 114307 129503 118199 115818 133455 123989 139463 139503 FALSE TRUE 125425.8605 125966.1097 134964.8176 136186.6653 122000.9782 118159.9193 135088.2622 121428.5838 123631.7449 130054.3376 0.964411206 0.968565232 1.037757142 1.047152044 0.938076964 0.908542703 1.038706319 0.93367577 0.950616083 1 16.98875499 3.220449963 24.98851174 0.959529325 1.00428425 0.199998108 0.041878826 387.6538605 534871.5578 0.012361016 0.014801298 1661.30726 -3.220449963 0.044754925 WFNGQPIHAELSPVTDFR ddPTM_BT-474_Pertuzumab_2h_R1 4 WFNGQPIHAELSPVTDFR 18 0 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;;; 214.69 9.92E-19 3598517000 2743350 3007130 2518517 2440990 2458244 1957466 2439140 2110766 2507162 2650750 FALSE TRUE 2636136.849 2921369.597 2973669.046 2566969.786 2537315.651 1997047.304 2468990.925 2067177.944 2222559.481 2471212.341 1.066738299 1.182160492 1.20332397 1.038749177 1.026749344 0.808124527 0.999101082 0.836503569 0.899380212 1 21.23678755 3.22049798 1.882026412 0.902072807 1.14981526 0.668660953 0.071547693 0.173173459 1.264475786 0.021723596 0.0299607 1661.490948 -3.22049798 0.247742454 QVLDLEDLVFTQGSHFMANK ddPTM_BT-474_Pertuzumab_2h_R1 2 QVLDLEDLVFTQGSHFMANK 20 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 223.46 6.45E-25 284410000 211815 217275 193756 188573 229500 211713 219740 236290 235550 259800 FALSE TRUE 203537.0356 211078.5297 228772.0193 198305.2751 236882.0759 215993.9819 222429.2439 231410.5289 208811.3515 242203.5146 0.840355417 0.871492431 0.94454459 0.818754738 0.978029061 0.89178715 0.918356797 0.955438361 0.862131798 1 17.88586027 3.220589933 0.016279575 1.797440097 1.72E-08 0.32313121 0.047476893 1407.378642 6.614969164 342.3934201 387.8466194 1661.842772 -3.220589933 -1.79744008 GVQDIVVGEGTHFLIPWVQKPIIFDCR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVQDIVVGEGTHFLIPWVQKPIIFDCR 27 1 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ; 254.85 4.59E-53 5269400000 1381980 1665010 1432240 1973560 1114570 1509070 1701990 1385650 1467980 1586840 FALSE TRUE 1327970.694 1617525.545 1691077.628 2075415.668 1150421.156 1539584.429 1722819.463 1357035.843 1301341.065 1479361.913 0.897664514 1.093394071 1.14311286 1.402912735 0.777646866 1.04070844 1.164569296 0.9173116 0.879663761 1 20.49654361 3.220698067 24.99996069 0.973661048 1.131982994 0.238373147 0.148992831 392.5667845 549424.9666 0.044066861 0.052773313 1662.256604 -3.220698067 0.158321946 SDPYLEFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDPYLEFHK 9 0 O75131;A0A087WYQ3 O75131 CPNE3 Copine-3 0 ; 127.4 0.00044656 958620000 1718560 2238100 1219210 2190300 1205550 777370 1794300 1797690 1756490 1655510 FALSE TRUE 1651396.775 2174271.579 1439548.368 2303341.645 1244327.611 793088.954 1816259.18 1760567.073 1557100.619 1543380.833 1.069986577 1.40877192 0.932724016 1.492400058 0.806234977 0.513864716 1.176805582 1.140721095 1.008889436 1 20.55766266 3.220762543 24.9999449 0.957746535 1.218081813 0.27023747 0.228216807 374.2116503 525632.8015 0.069031075 0.082670128 1662.503402 -3.220762543 0.260335278 YLPDGSYEDWGVDELIITD ddPTM_BT-474_Pertuzumab_2h_R1 2 YLPDGSYEDWGVDELIITD 19 0 P61218;U3KQB0 P61218 POLR2F "DNA-directed RNA polymerases I, II, and III subunit RPABC2" 0 ; 117.98 0.00020542 82504000 63901 69422 53399 64833 57974 59364 64499 59051 66534 72034 FALSE TRUE 61403.67827 67442.15253 63049.38715 68179.0389 59838.78636 60564.38075 65288.35806 57831.57621 58981.33925 67155.07302 0.914356511 1.004274875 0.93886261 1.015247782 0.89105385 0.901858609 0.97220292 0.861164669 0.878285684 1 16.03520877 3.220916788 24.99662931 0.910307808 0.968668786 0.203311752 0.047993645 319.1391634 452134.5721 0.013219167 0.015833208 1663.093966 -3.220916788 0.058360979 GEGYAKPNEGAIVEVALEGYYK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEGYAKPNEGAIVEVALEGYYK 22 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 196.81 1.90E-22 1652104000 2435200 2310310 2300130 2367880 2621420 2790780 2815100 3104380 3518190 3588430 FALSE TRUE 2340029.692 2244422.221 2715814.657 2490086.571 2705740.355 2847211.484 2849552.036 3040273.468 3118819.821 3345382.44 0.699480473 0.670901537 0.811809922 0.744335398 0.808798517 0.851086994 0.85178663 0.908796983 0.932276018 1 21.67373972 3.221073287 0.245498408 1.026326536 0.56301907 0.91287278 0.029058026 1.174292817 0.119266003 0.049364416 0.167605074 1663.693375 -3.221073287 -0.463307465 RYEEDMYWR ddPTM_BT-474_Pertuzumab_2h_R1 2 RYEEDMYWR 9 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ; 133.81 0.0020986 271220000 173180 204985 148108 162237 148425 119688 160374 138976 129876 148187 FALSE TRUE 166411.9341 199139.0285 174874.4102 170610.071 153199.2249 122108.1734 162336.705 136106.097 115133.021 138150.1625 1.204572844 1.441467928 1.26582848 1.234961059 1.108932644 0.883880056 1.175074296 0.985204031 0.833390413 1 17.07587773 3.221172488 1.905515406 0.990102635 1.316127723 0.67555496 0.101599081 0.194369146 1.454319612 0.032284378 0.04445791 1664.073437 -3.221172488 0.326025087 AQQIHSQTSQQYPLYDLDLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQQIHSQTSQQYPLYDLDLGK 21 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 284.88 2.74E-45 529310000 712910 801430 626750 749570 678120 731190 699950 771360 846550 732540 FALSE TRUE 685048.689 778574.0011 740017.667 788255.3975 699932.3457 745975.1628 708516.1975 755431.1464 750453.193 682924.4133 1.003110558 1.14005882 1.083601131 1.154235201 1.02490456 1.092324638 1.037473817 1.106170949 1.098881777 1 19.38136638 3.22133884 24.99991705 1.067874108 1.097619827 0.095504622 0.049536158 646.0164677 937783.6765 0.013560474 0.016245985 1664.710966 -3.22133884 0.029745719 KIS(ph)PPSYAR ddPTM_BT-474_Pertuzumab_2h_R1 3 KISPPSYAR 9 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 KIS(0.997)PPS(0.003)YAR;KIS(0.963)PPS(0.037)YAR;KIS(0.823)PPS(0.177)YAR 112.02 0.0012433 3884700000 458830 471380 431250 452755 436858 430695 421993 469120 528590 493860 TRUE FALSE 440898.4163 457936.7039 509186.4681 476121.7398 450909.9343 439403.948 427157.4766 459432.5081 468586.6792 460410.4223 0.957620408 0.994627145 1.10594036 1.034124591 0.979365176 0.95437446 0.927775428 0.997875995 1.017758627 1 18.81256097 3.221430629 10.85577826 0.97598592 1.026967553 0.199291108 0.042126365 0.586804367 362.4060232 0.012889833 0.015708652 1665.062842 -3.221430629 0.050981633 FISETLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FISETLR 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 117.16 0.012315 58463000 95036 117400 103140 97164 96168 60068 116940 81377 108280 104160 FALSE TRUE 91321.88805 114051.8669 121779.6923 102178.6457 99261.33106 61282.61612 118371.1467 79696.53651 95988.50835 97105.15042 0.940443299 1.174519235 1.254101269 1.052247437 1.022204596 0.631095424 1.218999674 0.820724093 0.988500692 1 16.5672602 3.22158225 3.135353426 0.929854213 1.127255269 0.202429283 0.159021377 0.345582963 7.017452186 0.045184558 0.058852977 1665.64425 -3.22158225 0.197401056 LSNRPAFMPSEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSNRPAFMPSEGK 13 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 121.48 0.00018736 0 1951000 1790400 1734800 1801200 1596700 1376400 1784800 1579500 1749400 2094500 FALSE TRUE 1874752.763 1739339.545 2048316.95 1894160.148 1648059.306 1404231.751 1806642.916 1546882.773 1550815.446 1952637.649 0.960112985 0.890764114 1.049000029 0.970052046 0.844016967 0.7191461 0.92523204 0.792201653 0.794215684 1 20.89699282 3.221590362 6.367305969 0.831823199 0.968183414 0.34507974 0.08084274 0.155009146 23.36029488 0.022052239 0.027470433 1665.675362 -3.221590362 0.136360215 AVAAPRPDR ddPTM_BT-474_Pertuzumab_2h_R1 7 AVAAPRPDR 9 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;;;;; 108.3 0.0024015 2043450000 2504130 2689940 2345500 2607050 2357410 2012270 2734860 2598370 2555250 2722470 FALSE TRUE 2406265.831 2613225.545 2769384.025 2741600.163 2433238.234 2052959.478 2768330.035 2544712.751 2265188.732 2538074.682 0.948067387 1.029609398 1.091135751 1.080188925 0.958694498 0.808864882 1.09072048 1.002615396 0.892483089 1 21.27530309 3.221594271 24.63812468 0.964164485 1.040553537 0.192648784 0.078018061 365.5222205 530801.0674 0.023555188 0.028226521 1665.690354 -3.221594271 0.076389052 EHQTSAYSPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EHQTSAYSPPR 11 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 0 85.522 0.012371 0 103790 75112 82963 69984 106130 109610 95662 116260 113450 107790 FALSE TRUE 99733.77205 72969.8793 97956.2596 73595.88263 109543.7678 111826.3893 96832.74017 113859.1904 100571.6316 100489.2873 0.992481634 0.726145854 0.974793057 0.732375406 1.090103938 1.112819011 0.963612568 1.133048044 1.000819434 1 16.61668218 3.221623834 24.99510425 1.058730352 0.855594757 0.498186447 0.094957707 172.672089 254826.9018 0.024966286 0.029912735 1665.803743 -3.221623834 -0.203135595 EFSFEAWNAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFSFEAWNAK 10 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 150.85 4.85E-05 678770000 773230 749770 663130 692610 760380 761400 778160 816320 844700 829070 FALSE TRUE 743011.3167 728387.2937 782972.3422 728355.6851 784838.3133 776796.0297 787683.3549 799462.7067 748813.1973 772916.3504 0.961308835 0.942388259 1.013010453 0.942347364 1.015424648 1.005019533 1.019105566 1.034345704 0.968815315 1 19.55995276 3.221709732 24.99379103 1.011257938 0.966611674 0.413744453 0.024362935 217.8673206 323147.3474 0.006876486 0.008239046 1666.133253 -3.221709732 -0.044646264 EFTLEFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFTLEFSR 8 0 P16615-5;P16615-2;P16615-3;P16615;H7C5W9;P16615-4;O14983-3;O14983-2;O14983;Q93084-4;Q93084-2;Q93084-3;Q93084-7;Q93084;Q93084-6;Q93084-5 P16615-5;Q93084-4 ATP2A2;ATP2A1;ATP2A3 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2;Sarcoplasmic/endoplasmic reticulum calcium ATPase 1;Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 0 ; 193.86 0.00039181 134820000 149610 276000 144813 228480 149784 62489 235941 225146 176044 155504 FALSE TRUE 143763.0758 268128.7502 170983.9304 240271.8802 154601.9384 63752.57039 238828.5165 220496.6564 156060.2232 144971.5756 0.991663885 1.849526358 1.179430725 1.657372345 1.066429317 0.439759105 1.647416161 1.520964752 1.076488426 1 17.14541053 3.222281542 24.99196899 1.180294027 1.433067001 0.117296998 0.377070004 628.7307162 965238.3203 0.113781907 0.136372913 1668.328398 -3.222281542 0.252772973 NVMVEPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVMVEPHR 8 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R2U2;M0R1H0;M0R2B0;M0QXC9 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 104.17 0.0046324 874610000 758690 733820 721490 747880 643390 579690 617960 694230 737530 844180 FALSE TRUE 729039.556 712892.1721 851879.2925 786478.1764 664085.2237 591411.729 625522.7793 679893.9079 653808.6864 787002.9367 0.926349219 0.905831654 1.082434706 0.999333217 0.843815433 0.751473345 0.794816322 0.863902631 0.83075762 1 19.58600949 3.22233854 10.62767286 0.83437398 0.980736161 0.417179805 0.074899754 0.29868244 189.0078747 0.021378594 0.026110116 1668.547368 -3.22233854 0.146362181 DRS(ph)PAAETPPLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 DRS(1)PAAETPPLQR;DRS(1)PAAETPPLQR 124.99 0.00012439 864800000 579680 585510 449250 510870 553990 579580 564310 577630 623910 594560 TRUE FALSE 557025.4647 568811.8281 530439.4685 537236.0619 571809.5915 591299.5047 571216.1946 565701.7386 553086.3524 554289.9216 1.004935221 1.026199117 0.956971159 0.969232961 1.031607412 1.06676936 1.030536859 1.020588173 0.997828629 1 19.08028125 3.222442358 24.90478091 1.027547116 0.989656117 0.316634286 0.025116774 271.9748666 420235.1526 0.007721848 0.009256756 1668.94628 -3.222442358 -0.037890999 YGEPSEVFINR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGEPSEVFINR 11 0 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 118.41 0.0016851 177130000 127250 132070 99987 131060 127000 169780 131530 161780 154130 150610 FALSE TRUE 122276.9293 128303.4929 118056.8751 137824.0223 131085.0703 173213.0679 133139.7035 158439.1865 136633.8086 140409.0506 0.870862162 0.913783637 0.840806733 0.981589305 0.933594165 1.233631787 0.948227361 1.128411494 0.973112545 1 17.09927641 3.222462464 2.027104658 1.059357059 0.885098955 0.417912119 0.085497978 0.273501098 2.31173488 0.025057031 0.034208391 1669.023547 -3.222462464 -0.174258104 IISSDRDLLAVVFYGTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IISSDRDLLAVVFYGTEK 18 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 224.86 3.99E-19 2807200000 5511300 5704800 4538300 4965200 5485300 5469000 5783900 5451600 6564400 6064600 FALSE TRUE 5295912.303 5542104.69 5358471.764 5221454.567 5661739.656 5579586.927 5854685.098 5339022.555 5819236.832 5653839.24 0.936693117 0.980237402 0.94775807 0.923523706 1.001397354 0.986866922 1.035523801 0.944318069 1.029254032 1 22.43079943 3.222530168 24.99860638 0.995137659 0.949473738 0.470264853 0.027009122 235.9694764 367980.8643 0.007702866 0.009234183 1669.283757 -3.222530168 -0.045663921 DLDFTIDLDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLDFTIDLDFK 11 0 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 131.82 0.00045459 92205000 291890 310880 250800 225010 343990 331760 302830 316500 406900 365550 FALSE TRUE 280482.6161 302014.0068 296125.139 236622.7931 355054.7508 338468.4145 306536.1241 309964.1644 360710.4179 340790.9729 0.823034172 0.886214808 0.868934809 0.694334099 1.041854917 0.993184801 0.899484284 0.909543354 1.058450624 1 18.3785276 3.223069365 24.99982095 0.969264701 0.826621624 0.582742095 0.067846097 199.6329342 322167.4952 0.020400011 0.024464721 1671.357542 -3.223069365 -0.142643077 ERGTGDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERGTGDVK 8 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 76.679 0.032082 237010000 242820 237746 174430 231100 248120 261600 253890 291340 298660 292350 FALSE TRUE 233330.3259 230965.7169 205953.3812 243027.0987 256101.0051 266889.7312 256997.1818 285323.7272 264757.3689 272548.8741 0.856104531 0.847428622 0.755656694 0.891682637 0.939651672 0.979236227 0.942939803 1.046871788 0.971412448 1 18.05615543 3.223123467 1.789243644 0.99251847 0.822132531 0.795906475 0.036875066 0.14606583 0.965637702 0.012269865 0.017103445 1671.56576 -3.223123467 -0.170385939 DKLPNYEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKLPNYEEK 9 1 Q9BV57;Q9BV57-2 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ;;; 150.04 7.86E-05 880570000 1220200 1110840 1014080 1171540 1317610 1682130 1107890 1739160 1699990 1395640 FALSE TRUE 1172513.235 1079159.931 1197346.814 1232003.32 1359992.122 1716143.821 1121448.689 1703245.738 1507014.262 1301112.06 0.901162376 0.829413518 0.920248802 0.946884867 1.045253644 1.318982334 0.861915529 1.309069212 1.158250937 1 20.31131379 3.223171542 2.411222708 1.142215138 0.884082929 0.415305193 0.128635411 0.254392423 3.030935866 0.03778321 0.050465433 1671.750808 -3.223171542 -0.258132209 EASEVKPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EASEVKPPR 9 1 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ;;; 121.73 0.00055231 1192030000 1459300 1496220 1169290 1403110 1498110 1627800 1469230 1752670 1794770 1672050 FALSE TRUE 1402268.943 1453549.271 1380606.714 1475524.675 1546298.069 1660715.231 1487210.876 1716476.752 1591035.234 1558800.564 0.899582009 0.932479307 0.88568528 0.946576945 0.991979413 1.065380184 0.954073863 1.101152252 1.020679149 1 20.57200493 3.223717975 2.125379168 1.034059496 0.908709047 0.658318358 0.038586051 0.17325172 1.607850926 0.011697109 0.015875471 1673.855543 -3.223717975 -0.12535045 TFADCIQALLEQHQVLEVGGNTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TFADCIQALLEQHQVLEVGGNTAR 24 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 0 138.62 5.29E-06 76326000 56924 48748 44219 45440 55704 56896 58376 61564 62572 54709 FALSE TRUE 54699.34715 47357.75477 52210.35695 47785.16385 57495.76975 58046.4761 59090.42295 60292.68189 55469.08888 51003.5107 1.072462393 0.92851951 1.023662023 0.936899503 1.127290435 1.138087855 1.158555992 1.182128074 1.08755433 1 15.63830893 3.223925701 24.61203305 1.132367867 0.988343714 0.490635077 0.061072647 131.9574747 221916.8851 0.016565841 0.019884593 1674.656352 -3.223925701 -0.144024154 ARSPS(ph)VAAMASPQLCR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSPSVAAMASPQLCR 16 1 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 ARS(0.188)PS(0.81)VAAMAS(0.002)PQLCR 162.47 2.12E-08 907440000 170390 177740 142860 167430 151530 149390 165610 160040 165430 168070 TRUE FALSE 163730.9704 172671.0292 168677.9799 176071.0824 156404.1001 152410.7682 167636.7847 156735.1181 146651.0799 156686.4692 1.044959219 1.102016212 1.076531884 1.123715936 0.998197872 0.97271174 1.069886797 1.000310485 0.935952419 1 17.25752107 3.224011279 24.991528 1.000431621 1.087158415 0.597495133 0.036340167 167.215684 287227.4474 0.010556966 0.012672769 1674.986375 -3.224011279 0.086726793 AAFQSLLDAQADEAVLDHPDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAFQSLLDAQADEAVLDHPDLK 22 0 Q9UBI1;R4GN54;R4GMW6;H0Y4W0;H0Y6Z9;R4GMX3 Q9UBI1;R4GMX3 COMMD3;COMMD3-BMI1 COMM domain-containing protein 3 0 ; 268.25 6.14E-38 92650000 80794 74124 63046 70769 81298 80647 81003 89331 97168 91982 FALSE TRUE 77636.48116 72010.05609 74439.81465 74421.39657 83913.024 82277.7376 81994.33894 87486.28363 86137.896 85751.97721 0.905360829 0.839748055 0.868082779 0.867867995 0.978554976 0.95948502 0.956180156 1.020224681 1.004500407 1 16.38788232 3.224227463 5.332209471 0.987145031 0.867269305 0.854660332 0.023485304 0.064060992 5.276292763 0.007206086 0.0090903 1675.820363 -3.224227463 -0.119875727 RAAVAASSS(ph)S ddPTM_BT-474_Pertuzumab_2h_R1 2 RAAVAASSSS 10 1 P61927 P61927 RPL37 60S ribosomal protein L37 1 RAAVAAS(0.001)S(0.141)S(0.429)S(0.429);RAAVAAS(0.02)S(0.057)S(0.688)S(0.235) 63.415 0.077274 157190000 471560 493590 417080 476420 427790 441010 458830 452770 450230 523220 TRUE FALSE 453130.9139 479513.2965 492455.6339 501008.0933 441550.2539 449927.5244 464445.2988 443420.1413 399121.7779 487781.8434 0.92896224 0.983048678 1.009581723 1.027115093 0.905220766 0.922394981 0.952157824 0.909054216 0.818238283 1 18.89587653 3.224350169 24.96702556 0.91565751 0.988482402 0.327248142 0.048625307 257.4356955 452300.4521 0.013898703 0.016687525 1676.293916 -3.224350169 0.072824892 FVEWTR ddPTM_BT-474_Pertuzumab_2h_R1 2 FVEWTR 6 0 A0A2R8YD12;A0A024QZX5;A0A087X1N8;P35237 A0A2R8YD12 SERPINB6 Serpin B6 0 ; 143.97 0.026361 232590000 450290 501630 414580 450020 382570 157069 547950 388270 440260 496140 FALSE TRUE 432692.169 487324.0035 489503.8283 473245.5861 394875.7115 160245.0428 554655.976 380252.0888 390283.5305 462535.9959 0.935477828 1.053591521 1.058304289 1.023154069 0.853718878 0.346448804 1.199162835 0.822102695 0.843790611 1 18.81920612 3.224620341 6.701859876 0.835595204 1.023577695 0.1493394 0.202178022 0.280898091 53.48476605 0.05771074 0.072011878 1677.337056 -3.224620341 0.187982491 YREWHHFLVVNMK ddPTM_BT-474_Pertuzumab_2h_R1 2 YREWHHFLVVNMK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 131.26 7.96E-05 1399250000 2519810 2518310 2103540 2159120 2061650 1330760 2327580 1460790 2706750 2495740 FALSE TRUE 2421333.039 2446490.264 2483696.471 2270552.442 2127964.845 1357668.879 2356065.62 1430624.176 2399491.088 2326701.307 1.040672059 1.051484459 1.067475427 0.975867609 0.914584454 0.583516619 1.012620577 0.614872297 1.03128454 1 21.14985458 3.22463034 2.740632921 0.81735633 1.046726186 0.246500462 0.14771613 0.294556535 4.534497803 0.041578312 0.054867938 1677.375673 -3.22463034 0.229369856 AIENELLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AIENELLAR 9 0 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 0 162.49 0.00014827 114610000 105720 120960 99920 114450 92243 29181 136440 95422 104680 133770 FALSE TRUE 101588.3455 117510.3392 117977.7667 120356.7782 95210.07987 29771.05981 138109.7935 93451.50235 92797.16525 124709.6388 0.814598988 0.942271507 0.946019633 0.965096038 0.763454059 0.238723006 1.107450835 0.749352683 0.744105798 1 16.92821345 3.224675151 20.91990644 0.753751462 0.920874846 0.101733027 0.21576436 72.27152776 108883.4405 0.061861749 0.074521005 1677.548754 -3.224675151 0.167123384 ALMGS(ph)PQLVAAVVR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALMGSPQLVAAVVR 14 0 P14923;C9JTX4;C9J826;C9JK18;C9JKY1 P14923 JUP Junction plakoglobin 1 ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR 211.12 4.49E-09 1178521000 1231201 1534534 1144776 1552018 1022803 1065181 1320935 1333724 1179841 1197322 TRUE FALSE 1183084.304 1490770.593 1351662.489 1632117.835 1055702.387 1086719.69 1337100.998 1306182.133 1045910.396 1116226.314 1.059896446 1.335545107 1.210921541 1.462174663 0.945778086 0.973565733 1.197876255 1.170176797 0.937005679 1 20.09019813 3.224755489 24.99999023 1.062228639 1.268005754 0.434774314 0.126435553 246.2899785 446010.7624 0.037235812 0.044724248 1677.859104 -3.224755489 0.205777115 AVIFDR ddPTM_BT-474_Pertuzumab_2h_R1 3 AVIFDR 6 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;; 121.68 0.045473 1053780000 888940 1118230 1001200 1315650 686390 743800 1006330 968220 843970 984650 FALSE TRUE 854199.242 1086339.175 1182139.112 1383550.854 708468.3577 758840.1456 1018645.768 948225.9186 748166.0638 917958.7785 0.930542048 1.183429148 1.287791064 1.507203686 0.77178668 0.826660372 1.109685741 1.032972222 0.81503231 1 19.80806984 3.224775071 24.99969856 0.942819638 1.228437071 0.444222388 0.164413327 239.1487944 433688.8981 0.050141143 0.06022444 1677.934759 -3.224775071 0.285617433 SPDDPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPDDPSR 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 94.262 0.033338 860010000 1518330 1556120 1087280 1458670 1117130 1141820 1136940 1113550 1278110 1226750 FALSE TRUE 1458991.985 1511740.981 1283775.682 1533952.134 1153063.501 1164908.383 1150854.212 1090554.803 1133024.311 1143661.13 1.275720532 1.321843457 1.122514046 1.341264553 1.008221291 1.018578277 1.006289522 0.953564631 0.990699327 1 20.12522821 3.224843832 24.291124 0.992908233 1.259170351 0.843154018 0.056825897 57.80812142 102372.4586 0.015898347 0.019105353 1678.200447 -3.224843832 0.266262118 DANNGNLQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DANNGNLQLR 10 0 P05455 P05455 SSB Lupus La protein 0 ;; 152.11 4.33E-05 473280000 235064 270005 224136 260753 219610 228041 257177 231090 246957 254278 FALSE TRUE 225877.439 262304.7218 264642.3611 274210.4936 226673.9551 232652.1453 260324.4091 226317.9107 218923.4767 237055.5246 0.952846129 1.106511743 1.11637289 1.156735301 0.956206169 0.981424692 1.098157951 0.954704224 0.923511389 1 17.85486549 3.224870244 24.99902108 0.988974334 1.08716307 0.346472302 0.065377487 266.7013708 487003.5335 0.019280744 0.023158467 1678.302508 -3.224870244 0.098188736 YYEGYYAAGPGYGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 YYEGYYAAGPGYGGR 15 0 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 196.48 3.24E-11 0 80445 93409 71118 88314 74968 77709 86030 91217 84283 83298 FALSE TRUE 77301.12046 90745.06678 83970.60461 92871.89612 77379.4138 79280.32922 87082.86087 89333.33707 74715.54718 77656.15227 0.995428156 1.168549614 1.08131297 1.195937391 0.996436361 1.020914981 1.121390364 1.150370376 0.962133006 1 16.24481261 3.224886586 24.99637504 1.060575555 1.11239624 0.140984452 0.07455785 573.4087885 1048199.066 0.021971613 0.026391855 1678.365662 -3.224886586 0.051820685 DKQTQLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKQTQLNR 8 1 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 0 119.75 0.0014909 73744000 116630 113320 86201 94995 117190 110550 121550 125430 137570 126210 FALSE TRUE 112071.9707 110088.2246 101779.4382 99897.70333 120959.5228 112785.3967 123037.5653 122839.8267 121953.6303 117661.6843 0.95249334 0.935633594 0.865017689 0.849024931 1.028028143 0.958556708 1.045689308 1.044008739 1.036477007 1 16.84428507 3.224978334 24.99965107 1.021608762 0.900511427 0.71083369 0.036922575 129.0466597 237523.8336 0.011528956 0.013851089 1678.720268 -3.224978334 -0.121097335 LADALQELR ddPTM_BT-474_Pertuzumab_2h_R1 6 LADALQELR 9 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 223.88 7.68E-07 2951350000 2710620 2956510 2348160 2449320 2404910 1297150 2694910 2445240 2411460 2727060 FALSE TRUE 2604685.974 2872193.23 2772524.747 2575729.699 2482266.114 1323379.262 2727891.115 2394744.939 2137721.17 2542353.797 1.024517507 1.129737817 1.090534586 1.013127953 0.976365334 0.520533084 1.072978559 0.94194008 0.840843305 1 21.27773338 3.224993148 3.144114053 0.884322264 1.077693462 0.280565985 0.140685727 0.329017771 6.725228536 0.042176056 0.055035002 1678.777533 -3.224993148 0.193371197 KSPVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPVAK 6 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 83.614 0.091054 5040100000 5920400 7614100 4074100 6852600 10401500 11044000 12419700 11994300 12582000 13700000 FALSE TRUE 5689024.223 7396953.323 4810380.498 7206263.507 10736073.69 11267317.25 12571696 11746613.51 11153744.11 12772086.8 0.445426367 0.579149942 0.376632306 0.564219741 0.840588845 0.882182953 0.984310254 0.919709809 0.87329066 1 23.60649093 3.225081847 2.547290569 0.928344881 0.474198861 0.926666091 0.059504808 0.065155432 0.865988716 0.017515527 0.023284944 1679.120436 -3.225081847 -0.45414602 FGVLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 FGVLFR 6 0 Q9P1F3 Q9P1F3 ABRACL Costars family protein ABRACL 0 ; 115.97 0.05577 931640000 842020 1026690 822740 977100 775420 620780 870380 908760 895470 1045200 FALSE TRUE 809112.9275 997409.8064 971427.4198 1027528.248 800362.0885 633332.5969 881031.9708 889993.7884 793819.9997 974407.673 0.830363871 1.023606273 0.996941472 1.05451576 0.821383196 0.649966759 0.904171832 0.913369027 0.814669282 1 19.89416597 3.225359244 24.99995952 0.845469408 0.981202139 0.270178566 0.100925244 294.561299 557821.4271 0.029720192 0.035719683 1680.193282 -3.225359244 0.135732731 SPSPGGPQLS(ph)PQLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSPGGPQLSPQLPR 15 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 1 SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR 170.79 1.18E-06 1346980000 464200 568820 508510 551780 468720 478540 479730 535320 534820 535100 TRUE FALSE 446058.5508 552597.8105 600409.0687 580257.4319 483796.8045 488216.4067 485601.0792 524265.4549 474109.4757 498857.2004 0.894160795 1.107727442 1.203569014 1.163173412 0.969810206 0.97866966 0.973427023 1.050932921 0.950391165 1 18.92826737 3.225431247 24.99568394 0.992537962 1.101227751 0.289848452 0.079715809 294.3932658 560464.7626 0.023881827 0.028705349 1680.471869 -3.225431247 0.108689789 QHLLTNLVEVDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 QHLLTNLVEVDGR 13 0 Q8NFV4;Q8NFV4-4;Q8NFV4-6 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 100.11 0.0014475 0 197190 209810 155720 201520 158440 156330 180380 170420 189400 179170 FALSE TRUE 189483.5968 203826.4242 183862.068 211920.4714 163536.3665 159491.0997 182587.5444 166900.7674 167900.106 167034.6563 1.134396903 1.220264278 1.100742038 1.26872157 0.979056503 0.954838374 1.093111744 0.999198437 1.005181258 1 17.34978794 3.225434814 24.99999951 1.00848457 1.178098626 0.71893799 0.05381375 116.988801 222821.7362 0.014789213 0.01777595 1680.485673 -3.225434814 0.169614056 EGPPAPPPVKPPPS(ph)PVNIR ddPTM_BT-474_Pertuzumab_2h_R1 3 EGPPAPPPVKPPPSPVNIR 19 1 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 EGPPAPPPVKPPPS(1)PVNIR;EGPPAPPPVKPPPS(1)PVNIR;EGPPAPPPVKPPPS(1)PVNIR 185.96 1.31E-14 9217300000 10489280 11200940 9241520 10165530 8095040 7130620 7438810 9329200 9118050 9343350 TRUE FALSE 10079347.34 10881500.16 10911668.24 10690174.22 8355424.313 7274806.022 7529848.382 9136548.76 8083007.19 8710516.582 1.157146909 1.249237064 1.252700473 1.227272128 0.959234075 0.835175038 0.864454859 1.048910093 0.927959566 1 23.05432685 3.225459257 6.075351345 0.937943296 1.226833461 0.832841613 0.061984993 0.064289426 8.492975516 0.019246438 0.024153563 1680.580256 -3.225459257 0.288890165 IESLIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IESLIDR 7 0 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 96.285 0.050947 0 83977 89407 78063 91581 76160 82870 85164 83240 95535 98991 FALSE TRUE 80695.086 86857.1999 92170.7206 96307.50639 78609.75557 84545.68818 86206.26251 81521.06491 84690.26732 92286.2514 0.874399868 0.941171611 0.998748126 1.043573717 0.851803539 0.916124416 0.934118151 0.883350051 0.917691054 1 16.49382811 3.225618083 24.99998945 0.910679036 0.965257142 0.15024502 0.053767976 382.9550981 739720.524 0.015588253 0.018743233 1681.194973 -3.225618083 0.054578107 (ac)MDLFGDLPEPERS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 MDLFGDLPEPERSPR 15 1 Q9H0C8;E9PC05;F8SNU7;F8SNU6 Q9H0C8 ILKAP;ILKAP3;ILKAP2 Integrin-linked kinase-associated serine/threonine phosphatase 2C 1 MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR 114.54 2.61E-08 697300000 98251.8 107021.1 91275.1 79389.6 133031.8 145483.1 140453.7 135835.4 140241.8 119055 TRUE FALSE 94412.01103 103968.963 107770.541 83486.90677 137310.8887 148424.868 142172.6144 133030.3515 124322.1388 110991.2988 0.850625338 0.936730754 0.970981889 0.752193259 1.237132011 1.3372658 1.280934775 1.19856559 1.120107073 1 16.76008705 3.22570259 24.99651162 1.217140865 0.888521886 0.695308726 0.102447805 117.896909 229195.8567 0.029058497 0.034939934 1681.522141 -3.22570259 -0.328618978 GLLDDLRNDLDR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLLDDLRNDLDR 12 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 ;;;; 153.38 6.44E-05 352389000 475107 898628 339145 660670 447586 410588 541407 675133 539384 346340 FALSE TRUE 456539.2932 873000.0093 400436.0457 694767.2579 461983.0102 418890.3707 548032.9008 661191.2676 478155.3896 322882.0833 1.413950531 2.703773465 1.240192833 2.151767762 1.430810299 1.297347832 1.697315922 2.047779365 1.480897871 1 18.30064786 3.225748266 24.99893215 1.582964736 1.890930053 0.129074236 0.454295252 551.9035343 1076849.64 0.127549637 0.153382686 1681.699001 -3.225748266 0.307965317 S(ph)SFSHYSGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSFSHYSGLK 10 0 Q8NC51;Q8NC51-3 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.5)S(0.5)FSHYSGLK;S(0.421)S(0.421)FS(0.158)HYSGLK 186.58 8.53E-07 555990000 591160 778950 546300 729030 505360 425460 500300 681280 643950 680010 TRUE FALSE 568056.8136 756735.1087 645028.5624 766655.3257 521615.3634 434063.0927 506422.8211 667211.3299 570851.4957 633952.317 0.896056057 1.193678276 1.017471733 1.209326483 0.822799049 0.684693598 0.798834246 1.052462957 0.900464405 1 19.27401481 3.225823537 24.99974781 0.876902943 1.08291056 0.380997343 0.126468623 247.3883867 485561.6123 0.038312449 0.046072365 1681.990493 -3.225823537 0.206007617 (ac)GDS(ph)DDEYDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDSDDEYDRR 10 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A087X0F4 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 GDS(1)DDEYDRR 45.972 0.00033108 1339500000 14983 24377 13321 24542 10058 20227 10583 13170 21816 13965 TRUE FALSE 14397.4478 23681.79183 15728.40102 25808.61556 10381.5247 20636.0038 10712.51792 12898.0349 19339.53914 13019.13811 1.105867967 1.818998433 1.208098485 1.982359765 0.797404914 1.585051454 0.822828503 0.990698062 1.485470004 1 13.66834632 3.225897454 24.99898688 1.106381797 1.526648018 0.265315644 0.338389408 288.0112081 568576.4636 0.091188136 0.109674923 1682.276793 -3.225897454 0.420266221 T(ph)LDRS(ph)GDLGDMEPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLDRSGDLGDMEPLK 15 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 2 T(1)LDRS(1)GDLGDMEPLK;T(1)LDRS(1)GDLGDMEPLK 247.85 5.92E-18 316710000 408990 405080 336380 405530 338430 308520 316190 457640 379750 373310 TRUE FALSE 393006.2186 393527.515 397171.3487 426459.4519 349315.9083 314758.4858 320059.6278 448189.5741 336642.372 348025.3812 1.129245854 1.130743722 1.141213745 1.225368824 1.003708141 0.904412445 0.9196445 1.287807149 0.967292589 1 18.408833 3.22604349 24.94673847 1.034181423 1.153691 0.302111017 0.103572859 362.3699186 722205.4024 0.033590676 0.040409601 1682.842572 -3.22604349 0.119509577 STQKPLHYK ddPTM_BT-474_Pertuzumab_2h_R1 2 STQKPLHYK 9 1 Q13427;E9PG73;C9JM79;Q13427-2;C9JN15 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G;Peptidyl-prolyl cis-trans isomerase 0 ; 76.228 0.021646 875690000 1099840 1188140 1059740 1025050 1093820 909310 1137820 1036890 1115690 1285600 FALSE TRUE 1056857.037 1154255.411 1251258.592 1077952.953 1129003.714 927696.8712 1151744.982 1015477.859 989041.5486 1198525.167 0.881797951 0.96306314 1.043998596 0.899399515 0.941994165 0.774032033 0.960968541 0.847272871 0.825215503 1 20.19282877 3.226111764 2.339691457 0.877366894 0.960499221 0.140734864 0.073498729 0.458867679 5.150105405 0.021588081 0.028987823 1683.107146 -3.226111764 0.083132327 APSDTGSLS(ph)PPWDQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSDTGSLSPPWDQDR 16 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 APS(0.001)DT(0.127)GS(0.127)LS(0.746)PPWDQDR 66.965 0.041684 0 12039 11333 15229 16219 10405 11938 15970 13092 11920 14274 TRUE FALSE 11568.50257 11009.79394 17981.21907 17056.06453 10739.68627 12179.39454 16165.44564 12821.64562 10566.89157 13307.20927 0.869340997 0.827355587 1.351238919 1.281716113 0.807057743 0.91524784 1.214788564 0.963511234 0.794072699 1 13.69992043 3.226220605 24.9999044 0.965011097 1.083396432 0.107142506 0.18512371 638.7703661 1294096.86 0.057578339 0.069292049 1683.529011 -3.226220605 0.118385335 YSEQHK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSEQHK 6 0 Q5T2E6-2;Q5T2E6 Q5T2E6-2 C10orf76 UPF0668 protein C10orf76 0 74.335 0.080597 51209000 125200 151490 123130 139780 126630 126570 136680 140190 134870 172020 FALSE TRUE 120307.0456 147169.6535 145382.33 146994.0626 130703.169 129129.3321 138352.7307 137295.0275 119560.123 160368.9322 0.750189229 0.917694291 0.906549218 0.916599372 0.815015522 0.805201671 0.862715296 0.856119858 0.745531702 1 17.29103515 3.226481207 24.99690764 0.84060575 0.878381424 0.019393842 0.075707471 716.5251664 1482760.66 0.020723978 0.024940321 1684.539533 -3.226481207 0.037775674 HNIICLQNDHK ddPTM_BT-474_Pertuzumab_2h_R1 2 HNIICLQNDHK 11 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ; 127.17 0.00016894 687370000 1259310 1353630 1200160 1133340 1093940 900170 1213090 635780 1465510 1361180 FALSE TRUE 1210094.773 1315025.798 1417055.609 1191831.813 1129127.574 918372.0542 1227936.158 622650.9208 1299151.449 1268986.066 0.953591852 1.036280723 1.116683348 0.939200079 0.889787212 0.723705389 0.967651412 0.490668052 1.023771248 1 20.2752448 3.226591577 2.119339212 0.794668141 1.033807459 0.191265042 0.154869253 0.37100323 3.423781433 0.047675192 0.064856585 1684.967688 -3.226591577 0.239139318 SAMQSVVDDWIESYKHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAMQSVVDDWIESYKHDR 18 1 Q8N3U4;Q8N3U4-2;B1AMT4;B1AMT1;B1AMT2;B1AMT3;B1AMT0 Q8N3U4 STAG2 Cohesin subunit SA-2 0 ; 191.95 1.20E-14 210710000 336800 310770 294139 292580 341270 372430 340410 335130 387010 372140 FALSE TRUE 323637.4836 301907.1439 347296.4604 307680.0889 352247.2595 379960.7898 344576.0394 328209.4484 343078.2473 346934.6263 0.932848609 0.870213351 1.001042946 0.886853215 1.015313067 1.095194198 0.993201639 0.946026783 0.988884422 1 18.40430431 3.226848785 24.93138827 1.002996553 0.92458076 0.426475472 0.047429677 233.5559316 497177.9952 0.014649049 0.017648467 1685.965894 -3.226848785 -0.078415793 DRVLDDVSIRS(ph)PETK ddPTM_BT-474_Pertuzumab_2h_R1 1 DRVLDDVSIRSPETK 15 2 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 DRVLDDVS(0.001)IRS(0.997)PET(0.002)K 110.33 0.0004853 165490000 268520 240690 201760 211540 264550 266310 247700 288740 286960 281690 TRUE FALSE 258025.9415 233825.7569 238222.5201 222457.6048 273059.491 271694.9707 250731.4267 282777.4181 254385.5038 262610.8854 0.982540922 0.89038867 0.907131172 0.84709971 1.039787405 1.034591427 0.954764028 1.076792448 0.968678444 1 18.00256719 3.226904148 24.9999967 1.017389096 0.905642943 0.56508138 0.045275717 145.6981336 312482.9418 0.012636304 0.015221353 1686.18083 -3.226904148 -0.111746153 FLPEEEKLTEQER ddPTM_BT-474_Pertuzumab_2h_R1 1 FLPEEEKLTEQER 13 1 A0A1B0GUA3;Q96EK5;A0A1B0GUH6;A0A1B0GTE6;A0A0D9SFK7;A0A1B0GV79;A0A1B0GW21 A0A1B0GUA3 KIAA1279;KIF1BP KIF1-binding protein 0 143.46 3.72E-05 98789000 151510 147400 107010 117570 149740 148270 139590 145010 171800 163980 FALSE TRUE 145588.8217 143196.2963 126349.0874 123637.8018 154556.5231 151268.121 141298.3442 142015.4928 152297.9842 152873.4885 0.952348397 0.936698035 0.826494434 0.808758948 1.011009329 0.989498718 0.924282853 0.928973978 0.996235421 1 17.22197871 3.226985018 24.99998498 0.965834489 0.881149412 0.461057356 0.049152833 235.8941632 509463.2455 0.015549377 0.01873178 1686.494843 -3.226985018 -0.084685078 EVAALCR ddPTM_BT-474_Pertuzumab_2h_R1 3 EVAALCR 7 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 96.51 0.029496 408010000 703050 751900 595120 667480 655070 596920 694750 669180 760460 809250 FALSE TRUE 675574.0287 730456.5482 702671.4224 701928.7228 676140.9215 608990.1314 703252.5583 655361.1992 674135.7689 754438.7767 0.895465675 0.968211829 0.931382962 0.930398522 0.896217085 0.807209478 0.932153251 0.8686738 0.893559278 1 19.5250443 3.22699418 4.95870546 0.889250216 0.93439695 0.069082776 0.048954429 0.328718695 21.58102376 0.01321493 0.016784546 1686.530426 -3.22699418 0.045146734 HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(ph)PFLAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 HPELTKPPPLMAAEPTAPLSHSASSDPADRLSPFLAAR 38 2 Q9ULP9-2;Q9ULP9 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 1 HPELTKPPPLMAAEPTAPLSHSAS(0.029)S(0.029)DPADRLS(0.942)PFLAAR;HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR;HPELTKPPPLMAAEPTAPLSHSAS(0.001)S(0.001)DPADRLS(0.999)PFLAAR 209.93 3.24E-31 7952120000 4135090 4881330 3779210 4971280 2959805 3217150 3603030 2151453 4603180 4984750 TRUE FALSE 3973486.111 4742119.248 4462197.315 5227848.357 3055009.816 3282202.977 3647124.959 2107024.744 4080646.305 4647128.443 0.855041164 1.020440753 0.96020529 1.124963173 0.657397327 0.706286262 0.784812601 0.453403595 0.878100607 1 22.14790809 3.227366214 24.99967727 0.70259157 0.990185519 0.363850756 0.151132265 186.8673495 417317.0829 0.042467946 0.051194806 1687.975792 -3.227366214 0.287593949 VVYFGDSMHSDIFPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVYFGDSMHSDIFPAR 16 0 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 193.06 4.34E-10 1163880000 394790 501200 381780 455210 374950 374450 439430 392220 408790 451060 FALSE TRUE 379361.1703 486906.2667 450776.1387 478703.4427 387010.6073 382021.6356 444807.8758 384120.5199 362385.873 420509.3044 0.902146912 1.157896535 1.07197661 1.138389657 0.920337798 0.908473681 1.057783671 0.913464972 0.861778489 1 18.6817782 3.227404557 24.9999867 0.943833051 1.074364452 0.356159366 0.081448385 220.7171853 494611.8931 0.022769698 0.027452259 1688.124826 -3.227404557 0.130531402 ESSAMAS(ph)PLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESSAMASPLPR 11 0 Q9C0C2;E9PKK0;E9PKE7 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 ESSAMAS(1)PLPR;ESSAMAS(1)PLPR 175.54 1.02E-05 281960000 278520 329500 234152 265064 298200 327550 282610 326070 318960 288440 TRUE FALSE 267635.1305 320102.9826 276468.4751 278743.9848 307791.8738 334173.2854 286068.6657 319336.5406 282752.998 268903.7019 0.995282432 1.190400059 1.028131904 1.036594078 1.144617466 1.242724749 1.063833126 1.187549812 1.051502809 1 18.03673009 3.227456965 24.78730956 1.130819681 1.069268382 0.068754236 0.081688564 414.6002022 925534.9153 0.022367397 0.02697377 1688.328552 -3.227456965 -0.061551299 VIQHNALEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIQHNALEDR 10 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 150.94 2.07E-05 461980000 371250 480110 331730 460740 333560 378870 422210 424770 404670 428060 FALSE TRUE 356741.1396 466417.7329 391680.9903 484518.8466 344289.2603 386531.011 427377.1323 415998.3511 358733.5581 399067.1149 0.893937702 1.168770153 0.981491523 1.214128723 0.862735233 0.968586477 1.070940492 1.042427039 0.898930392 1 18.60627187 3.227752396 24.99999866 0.986905663 1.066089024 0.153589371 0.101519214 444.3250786 1027745.907 0.028255393 0.034095194 1689.477436 -3.227752396 0.079183362 GVPLYR ddPTM_BT-474_Pertuzumab_2h_R1 5 GVPLYR 6 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90;A0A2R8YEM5;P13929-3;P13929-2;P13929;E5RGZ4;E5RI09;E5RG95;K7EPM1;K7EKN2 P06733 ENO1;ENO3 Alpha-enolase;Enolase;Beta-enolase 0 ;;;; 136.94 0.030126 2038623000 2799880 2864040 2414150 2740300 2454280 2330850 2468840 2690950 2858470 2850060 FALSE TRUE 2690457.594 2782360.383 2850440.607 2881727.211 2533224.145 2377981.384 2499054.402 2635380.942 2533988.469 2657022.898 1.012583518 1.047172151 1.072794898 1.084569958 0.953406968 0.894979635 0.940546807 0.99185481 0.95369463 1 21.34137923 3.228360145 24.99725529 0.954040228 1.055094901 0.693999945 0.032039117 118.6664099 290803.1452 0.009900432 0.011956398 1691.843336 -3.228360145 0.101054673 DGLGGLPDIVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGLGGLPDIVR 11 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 144.77 0.0035543 119400000 347130 359000 294910 336300 305470 226020 359650 325520 343450 395990 FALSE TRUE 333563.7758 348761.6715 348206.7972 353656.4833 315295.72 230590.2793 364051.5043 318797.8982 304462.9959 369169.2446 0.903552451 0.944720278 0.943217243 0.95797927 0.854068221 0.62461942 0.986137143 0.863554868 0.824724704 1 18.49392284 3.228449434 22.89632731 0.8510011 0.938310371 0.132740413 0.097071462 137.276657 310856.2814 0.027744449 0.033591353 1692.191208 -3.228449434 0.087309272 VIQPMGMS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 VIQPMGMSPR 10 0 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35 Q9NPQ8-4 RIC8A Synembryn-A 1 VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR 130.44 0.00029023 782720000 876080 884870 771240 692100 701380 772050 697500 665618 739770 737040 TRUE FALSE 841841.825 859634.374 910620.2241 727819.3639 723940.5247 787661.38 706036.2136 651872.7557 655794.411 687119.6243 1.225175057 1.251069455 1.325271746 1.059232393 1.053587322 1.146323511 1.027530271 0.948703446 0.95441083 1 19.39020176 3.228484031 0.629480175 0.964405383 1.293357059 0.73913219 0.06349192 0.468325361 0.393765867 0.044930784 0.085497923 1692.326018 -3.228484031 0.328951676 DGASS(ph)SPESASR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGASSSPESASR 12 0 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;G5E9M9;Q14135-5 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 DGAS(0.004)S(0.828)S(0.167)PESASR;DGAS(0.067)S(0.466)S(0.466)PESASR;DGAS(0.003)S(0.498)S(0.498)PESASR 142.08 6.40E-05 201982600 231785 235711 199491 211146 234217 241978 234929 249019 247189 252768 TRUE FALSE 222726.5859 228988.7531 235543.4614 222043.2704 241750.8025 246870.961 237804.1314 243876.6706 219129.141 235647.7982 0.945167269 0.971741535 0.999557234 0.942267537 1.025898839 1.047626852 1.009150661 1.034920218 0.929901076 1 17.84627268 3.228573027 24.99908446 1.013233927 0.967678533 0.277663453 0.03336912 248.823674 622808.2249 0.009484213 0.011459074 1692.672843 -3.228573027 -0.045555393 EFLDFFWDIAKPEQETR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFLDFFWDIAKPEQETR 17 1 Q9BQG0;Q9BQG0-2 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 ; 168.89 1.86E-09 283150000 603930 605810 475460 495820 614120 659690 568560 595320 614010 639470 FALSE TRUE 580327.7479 588532.892 561386.1986 521409.3296 633873.7275 673029.3838 575518.2074 583026.434 544310.1589 596158.1273 0.973446006 0.987209374 0.941673313 0.87461582 1.063264423 1.128944407 0.965378447 0.977972802 0.913029839 1 19.18533552 3.228611288 24.99737498 1.007623344 0.947122579 0.208295904 0.060886271 379.1494265 952599.9261 0.019178972 0.023179379 1692.821974 -3.228611288 -0.060500765 LMLLLEVISGERLPKPER ddPTM_BT-474_Pertuzumab_2h_R1 1 LMLLLEVISGERLPKPER 18 2 O43707 O43707 ACTN4 Alpha-actinin-4 0 159.31 2.44E-11 32608000 37698 37921 24727 29965 35964 39742 30240 37263 42316 35821 FALSE TRUE 36224.72048 36839.53021 29195.71895 31511.49724 37120.81472 40545.61047 30610.08617 36493.50603 37512.46508 33394.81176 1.084740969 1.103151306 0.874259126 0.943604577 1.111574306 1.214129032 0.916612029 1.092789691 1.123302187 1 15.02733636 3.228633571 24.98417443 1.077101955 0.999619878 0.129105715 0.095322852 434.9386754 1094643.378 0.02847548 0.034417733 1692.908833 -3.228633571 -0.077482077 LLNNAFEELVAFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLNNAFEELVAFQR 14 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 208.27 1.93E-08 51809000 80472 80402 72116 67839 89153 102556 80459 92690 75836 85119 FALSE TRUE 77327.06527 78109.01368 85148.96541 71340.17892 92020.68721 104629.7526 81443.68131 90775.91911 67227.41521 79353.81431 0.974459337 0.984313285 1.07302927 0.89901386 1.159625256 1.318522033 1.026336062 1.143938951 0.847185681 1 16.27601195 3.228638368 24.99564138 1.100213515 0.989270692 0.128964484 0.121667487 376.2851667 947917.2371 0.035032937 0.042345318 1692.92753 -3.228638368 -0.110942823 LSAEKVEIATLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSAEKVEIATLTR 13 1 P25789;H0YN18;P25789-2;H0YMZ1;H0YL69 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type 0 ; 180.95 1.14E-05 1905780000 2151240 2208990 1403350 1678720 2156230 2252310 2131930 2145900 2376850 2067370 FALSE TRUE 2067167.162 2145991.768 1656966.562 1765358.94 2225587.096 2297853.251 2158021.197 2101586.415 2107039.953 1927345.188 1.07254641 1.113444432 0.859714478 0.915953692 1.154742342 1.192237522 1.119685882 1.090404785 1.093234344 1 20.87818355 3.228640886 24.99766409 1.115849685 0.989866848 0.332250113 0.081518499 234.7164069 591482.9175 0.024862312 0.030051848 1692.937346 -3.228640886 -0.125982837 TAGCCVQCSHGR ddPTM_BT-474_Pertuzumab_2h_R1 4 TAGCCVQCSHGR 12 0 O75164-2;O75164 O75164-2 KDM4A Lysine-specific demethylase 4A 0 ;;; 142.12 0.00031291 53270000 87152 93487 74627 87273 75734 71729 82294 83640 83921 79116 FALSE TRUE 83746.00349 90820.84229 88113.75897 91777.16999 78170.05289 73179.40953 83301.13859 81912.80477 74394.63991 73757.40285 1.135425059 1.231345448 1.194642918 1.244311302 1.059826538 0.992163589 1.129393598 1.110570622 1.008639635 1 16.17050024 3.228681935 24.98147671 1.062020997 1.203083039 0.678585181 0.050620707 125.4868257 317333.8242 0.014968412 0.018094967 1693.09737 -3.228681935 0.141062042 NSMDRPK ddPTM_BT-474_Pertuzumab_2h_R1 3 NSMDRPK 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;; 81.548 0.024536 250542000 439550 409900 349320 403410 370960 330110 402500 413800 434750 427940 FALSE TRUE 422371.9001 398210.0533 412449.8946 424230.0384 382892.2653 336785.0504 407425.9154 405254.8854 385399.0026 398955.2426 1.058694949 0.998132148 1.033824977 1.063352459 0.959737395 0.844167501 1.021232138 1.01579035 0.96602065 1 18.60586738 3.228768191 24.99874464 0.969833432 1.035283624 0.329236628 0.049285489 279.1454936 712619.904 0.015412259 0.01863677 1693.433672 -3.228768191 0.065450192 DWDDDQND ddPTM_BT-474_Pertuzumab_2h_R1 2 DWDDDQND 8 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 153.73 0.0010151 414840000 1176890 1233850 993340 1157800 1202580 1333390 1294070 1282870 1433890 1487820 FALSE TRUE 1130895.838 1198661.806 1172858.635 1217554.197 1241262.078 1360352.059 1309907.216 1256378.286 1271120.819 1387048.626 0.8153253 0.864181532 0.845578599 0.8778021 0.894894421 0.98075297 0.944384495 0.905792531 0.916421238 1 20.40358693 3.228827456 1.898687061 0.939861719 0.844700534 0.704985841 0.030008257 0.2025203 1.504606701 0.009775633 0.013545389 1693.664779 -3.228827456 -0.095161185 KLEAAEDIAYQLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 KLEAAEDIAYQLSR 14 1 P35232 P35232 PHB Prohibitin 0 ;;; 169.61 5.30E-06 4784240000 2872780 3339670 2875600 3888390 2246060 2916550 3295870 3097990 3005620 3077020 FALSE TRUE 2760508.582 3244425.881 3395284.887 4089070.274 2318306.56 2975524.639 3336205.843 3034015.424 2664434.618 2868610.695 0.962315516 1.131009477 1.183599048 1.425453193 0.808163535 1.037270287 1.163004046 1.057660222 0.928824055 1 21.45192076 3.228868358 24.99999953 1.018667938 1.172981474 0.280814537 0.13617215 309.6970949 798824.6311 0.040498905 0.048979327 1693.824296 -3.228868358 0.154313536 ALGNICYDSHEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALGNICYDSHEGR 13 0 P52306-4;P52306;P52306-5;D6RHH8 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ; 116.98 0.00054246 841550000 528690 565660 532320 573860 509150 530210 588740 544890 612240 558780 FALSE TRUE 508028.2103 549527.9306 628522.0654 603476.9834 525527.2721 540931.2095 595945.1762 533637.8311 542741.0819 520933.3329 0.975226921 1.054891089 1.206530713 1.158453386 1.00881867 1.038388552 1.143995092 1.024387954 1.041862841 1 18.99073923 3.228982588 24.99958164 1.049441389 1.103337729 0.133820069 0.068035527 451.0149424 1177189.573 0.020730004 0.02507168 1694.26987 -3.228982588 0.053896339 AAQEEYVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAQEEYVK 8 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 118.26 0.0044668 322180000 378660 344350 320700 336110 311798 222243 332100 362670 369430 331942 FALSE TRUE 363861.5486 334529.4752 378657.6239 353456.6774 321827.2658 226736.9057 336164.3391 355180.7378 327493.8552 309459.2727 1.175797854 1.08101293 1.223610528 1.142175105 1.039966465 0.732687387 1.0862959 1.147746308 1.058277725 1 18.23939003 3.229066001 5.157973999 1.018501481 1.156282796 0.303414779 0.107576159 0.269940642 20.27010826 0.034194899 0.043440719 1694.595313 -3.229066001 0.137781314 ENVKPSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENVKPSGR 8 1 Q8NI27;A0A0C4DG98 Q8NI27 THOC2 THO complex subunit 2 0 ; 95.608 0.0097062 187170000 420620 400800 332790 359210 412260 422040 422700 414060 459700 461310 FALSE TRUE 404181.7054 389369.5764 392932.5559 377748.8711 425520.7173 430573.938 427873.129 405509.5163 407516.7832 430065.0628 0.939815252 0.905373652 0.913658397 0.878352844 0.989433353 1.001183252 0.994903251 0.942902717 0.947570074 1 18.71419541 3.229070661 24.9999854 0.976307864 0.90933089 0.678036205 0.023586568 127.7885211 336640.7978 0.007355472 0.008900397 1694.613496 -3.229070661 -0.066976974 (ac)SQPGQKPAASPRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQPGQKPAASPRPR 14 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 0 ; 99.941 0.00081501 89851000 64722 70786 44080 59085 68541 78994 75962 68049 79390 69201 FALSE TRUE 62192.59269 68767.25259 52046.23655 62134.38393 70745.68351 80591.3128 76891.64568 66643.76437 70377.98003 64513.95463 0.964017677 1.06592834 0.806743856 0.963115411 1.096595053 1.249207451 1.191860678 1.033013164 1.090895457 1 15.97732363 3.22914852 4.864532964 1.119683834 0.946476283 0.438872535 0.08884158 0.174817981 10.86052738 0.026594931 0.033885785 1694.917329 -3.22914852 -0.173207551 TVWIAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TVWIAR 6 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;; 138.53 0.028531 2362406000 1443906 1669732 1277844 1550413 1233720 1105975 1468259 1304710 1442398 1466377 FALSE TRUE 1387476.557 1622112.878 1508778.836 1630430.001 1273403.724 1128338.572 1486227.993 1277767.283 1278663.026 1367057.98 1.014936146 1.186572115 1.103668505 1.192656072 0.931492112 0.825377262 1.087172611 0.934684045 0.93533928 1 20.382643 3.229432363 24.99242061 0.951592805 1.127409941 0.548120759 0.07653815 138.8275375 380098.2991 0.021446608 0.025979644 1696.025444 -3.229432363 0.175817136 TASPLPLRPDAPVEKS(ph)PEETATQVPSLESLTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TASPLPLRPDAPVEKSPEETATQVPSLESLTLK 33 2 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 TASPLPLRPDAPVEKS(1)PEETATQVPSLESLTLK 290.32 9.26E-90 343800000 496800 393570 331650 362770 447130 406880 447930 488510 500720 446050 TRUE FALSE 477384.5068 382345.7689 391586.5325 381492.6032 461512.3425 415107.3924 453411.9013 478422.0978 443880.3648 415838.6362 1.148004214 0.919457058 0.941679052 0.917405383 1.109835168 0.99824152 1.090355397 1.150499391 1.067434159 1 18.66566428 3.229437654 24.94888776 1.079960007 0.974340941 0.236934595 0.075289079 229.5828512 627847.429 0.021750676 0.026344571 1696.046106 -3.229437654 -0.105619065 QSIAIDDCTFHQCVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSIAIDDCTFHQCVR 15 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 230.97 2.57E-13 922690000 458740 505270 403560 467300 408260 410510 389180 451920 461590 503370 FALSE TRUE 440811.9336 490860.1943 476492.2691 491417.409 421392.0537 418810.7935 393942.9013 442587.6941 409192.2383 469276.3015 0.939344118 1.045993997 1.0153768 1.047181388 0.897961504 0.892460992 0.839468987 0.943128158 0.871964421 1 18.84007808 3.229562616 24.94735086 0.902019847 1.014647123 0.520658953 0.048914181 130.1268346 360781.9256 0.013267531 0.016078597 1696.534187 -3.229562616 0.112627275 ARFEEVLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARFEEVLSK 9 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 76.332 0.032588 851310000 704150 643720 605490 664040 576860 541990 643150 572190 680470 685760 FALSE TRUE 676631.0395 625361.7359 714915.5121 698311.184 595415.2258 552949.4091 651021.0621 560374.0765 603225.8984 639312.8644 1.05837232 0.978177932 1.118256103 1.092283955 0.931336219 0.864912064 1.018313721 0.876525576 0.943553512 1 19.2861626 3.229573286 24.99237037 0.931255426 1.059836069 0.535513372 0.055667743 137.4277813 382164.6107 0.015672271 0.018989985 1696.575872 -3.229573286 0.128580644 WYVVQTNYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 WYVVQTNYDR 10 0 A0A1B0GV06;A0A1B0GTP7;A0A1B0GUE3;A0A1B0GUG1;A0A1B0GUW4;E7EMM4;A0A1B0GW68;A0A1B0GUA4;A0A1B0GTM3;A0A1B0GTZ5;A0A1B0GUH5;Q13510-3;Q13510;Q13510-2 A0A1B0GV06 ASAH1 Acid ceramidase;Acid ceramidase subunit alpha;Acid ceramidase subunit beta 0 ; 118.18 0.0019997 507100000 298390 344260 319430 333300 282480 230810 368300 284980 286810 319480 FALSE TRUE 286728.5889 334442.0419 377158.1067 350501.6529 291566.2257 235477.1363 372807.3656 279095.0634 254252.5312 297841.335 0.96268904 1.122886593 1.266305453 1.176806614 0.978931369 0.790612681 1.251697873 0.937059537 0.853650925 1 18.18418446 3.229749067 24.06654785 0.974848381 1.141089655 0.264986172 0.13284102 164.5859783 449524.8644 0.038776315 0.047058194 1697.2627 -3.229749067 0.166241273 MEDETQKELETMR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEDETQKELETMR 13 1 A0A0A0MSW4;P48739;P48739-3 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ; 140.1 3.57E-05 446320000 349810 343750 264010 283590 340110 316000 321850 343020 363790 360660 FALSE TRUE 336139.0385 333946.5866 311722.4799 298226.1139 351049.947 322389.7365 325788.8966 335936.5171 322494.0843 336232.177 0.999722994 0.993202345 0.927104844 0.886964825 1.044070054 0.958830709 0.968940271 0.999120668 0.959141053 1 18.35909827 3.22975749 24.99994414 0.986379576 0.952949438 0.182095548 0.037829926 379.0353368 1076417.93 0.011250258 0.013643279 1697.295619 -3.22975749 -0.033430138 TSTVDLPIENQLLWQIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSTVDLPIENQLLWQIDR 18 0 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 158.93 1.03E-10 23001000 22106 20528 19962 19150 23595 22537 24715 25655 22844 25390 FALSE TRUE 21242.07308 19942.56154 23569.57745 20138.33379 24353.9546 22992.71358 25017.46956 25125.21528 20250.84489 23670.31268 0.897414131 0.84251365 0.995744237 0.850784443 1.028881829 0.971373462 1.056913354 1.061465289 0.855537701 1 14.53079114 3.229804467 24.99112698 1.006041901 0.899830517 0.337201303 0.067057643 198.2440539 565812.3071 0.019037855 0.023076736 1697.479224 -3.229804467 -0.106211384 AGSRLS(ph)AEER ddPTM_BT-474_Pertuzumab_2h_R1 2 AGSRLSAEER 10 1 Q86Y82;B1AJQ6 Q86Y82 STX12 Syntaxin-12 1 AGS(0.03)RLS(0.97)AEER;AGS(0.029)RLS(0.971)AEER 69.846 0.033766 348140000 923340 1036060 869710 951830 897310 761710 1055030 921910 1081030 1007320 TRUE FALSE 887254.852 1006512.583 1026885.944 1000954.06 926172.7911 777112.2981 1067941.773 902872.2363 958316.0064 939093.3192 0.944799451 1.071791868 1.093486582 1.065872837 0.986241487 0.827513392 1.137205165 0.96142973 1.020469411 1 19.840909 3.229953673 24.45345174 0.987976034 1.049509332 0.101469414 0.079742171 309.8625326 880358.6108 0.022675965 0.027521618 1698.062508 -3.229953673 0.061533299 EAPSPLMIHSPQMSQFQSLT(ph)HQSPPQQNVQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 EAPSPLMIHSPQMSQFQS(0.015)LT(0.626)HQS(0.358)PPQQNVQPK 124.18 9.99E-08 398220000 140430 142190 106000 144370 111230 129350 136990 123200 145940 141440 TRUE FALSE 134941.8403 138134.8804 125156.558 151820.953 114807.814 131965.5456 138666.5246 120655.8769 129373.503 131860.1428 1.023370955 1.04758631 0.949161401 1.151378648 0.870678671 1.000799353 1.051618189 0.915029169 0.981141839 1 17.00864902 3.22997858 24.99998677 0.969254628 1.036517126 0.22842477 0.065301304 295.6784005 861327.7763 0.018105774 0.021969207 1698.159896 -3.22997858 0.067262498 ALLLLCGEDD ddPTM_BT-474_Pertuzumab_2h_R1 8 ALLLLCGEDD 10 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;;;; 221.28 1.27E-08 712815000 1465517 1619905 1000626 1415574 1065517 981659 973846 1174467 1307194 1525774 FALSE TRUE 1408242.975 1573706.895 1181461.377 1488631.944 1099790.322 1001508.818 985764.2187 1150213.846 1158806.817 1422431.968 0.990024836 1.106349499 0.830592537 1.046539994 0.773176044 0.704082051 0.693013262 0.808624857 0.814665899 1 20.43992822 3.229993531 24.8320264 0.779356801 0.989818762 0.454499166 0.103003027 136.5930178 395919.6646 0.028439514 0.03450807 1698.218357 -3.229993531 0.210461962 ETPVVTIVHDCQVVDIPEELVEEHDITVDYILTPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETPVVTIVHDCQVVDIPEELVEEHDITVDYILTPTR 36 0 F5H0M7;Q2M296-4;Q2M296-2;Q2M296-3;Q2M296;H3BNE5;H3BSD1;H3BQU0 F5H0M7 MTHFSD Methenyltetrahydrofolate synthase domain-containing protein 0 247.73 2.03E-50 31651000 11117 11996 10132 12041 10164 11409 11006 11625 13128 12199 FALSE TRUE 10682.53535 11653.88583 11963.07779 12662.43745 10490.93429 11639.6978 11140.69472 11384.93969 11637.76448 11372.75086 0.939309713 1.024720049 1.051907136 1.113401463 0.922462333 1.023472503 0.979595425 1.001071757 1.023302508 1 13.47329364 3.230006074 24.99987595 0.992966321 1.033188739 0.148035677 0.047733782 376.9966061 1101737.11 0.013769782 0.016696672 1698.267404 -3.230006074 0.040222418 GGSPYNQFDIIPGDTLGGHTGPAGDSWLPAKS(ph)PPTNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSPYNQFDIIPGDTLGGHTGPAGDSWLPAKSPPTNK 37 1 Q9UPQ9-1;Q9UPQ9;H0Y720;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 GGSPYNQFDIIPGDTLGGHTGPAGDS(0.001)WLPAKS(0.999)PPTNK 201.56 1.75E-30 255350000 67342 78483 60963 65438 77083 83962 77134 78474 91337 80331 TRUE FALSE 64710.20019 76244.74168 71980.37021 68815.26302 79562.4447 85659.76917 78077.98897 76853.48448 80968.80668 74890.10982 0.864068705 1.018088261 0.961146544 0.91888319 1.062389211 1.143806163 1.042567425 1.026216742 1.081168219 1 16.19248758 3.230038711 24.99204736 1.060983766 0.947556778 0.569129695 0.050485319 139.1772261 408162.1108 0.01449793 0.017590507 1698.395034 -3.230038711 -0.113426988 RGGS(ph)DTNLNFDVPDGILDFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGGSDTNLNFDVPDGILDFHK 21 1 G3V207;Q9ULS5;F8VQF2 G3V207 TMCC3 Transmembrane and coiled-coil domains protein 3 1 RGGS(0.994)DT(0.006)NLNFDVPDGILDFHK;RGGS(1)DTNLNFDVPDGILDFHK 273.53 4.82E-45 141347000 111380 182634 102308 175001 84812 102870 112260 151426 138054 103492 TRUE FALSE 107027.1465 177425.4571 120797.3314 184032.8226 87540.055 104950.1019 113633.8715 148299.0002 122382.6887 96482.39466 1.109291979 1.838941268 1.252014234 1.90742387 0.907316359 1.087764273 1.177767943 1.537057623 1.268445804 1 16.55797809 3.230280916 24.99999578 1.2105508 1.529569276 0.28730889 0.274690368 263.3294309 795104.2742 0.07814243 0.094889755 1699.342486 -3.230280916 0.319018475 EAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK 32 0 Q3ZCM7;A0A075B736;Q5SQY0 Q3ZCM7 TUBB8 Tubulin beta-8 chain 0 ; 357.53 6.09E-132 1300610000 521350 537050 417870 481170 520350 577190 519460 519470 620630 579440 FALSE TRUE 500975.0656 521733.8598 493388.4045 506003.2414 537087.5303 588861.1773 525817.3069 508742.763 550178.6843 540194.0127 0.927398405 0.96582681 0.913354078 0.936706497 0.994249321 1.09009201 0.973386033 0.941777863 1.018483492 1 19.04311812 3.230456832 6.898589647 0.998273604 0.936198474 0.430941036 0.037599223 0.164615489 38.17671659 0.011909693 0.014980329 1700.030967 -3.230456832 -0.06207513 AGLQFPVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGLQFPVGR 9 0 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q71UI9-5;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;Q8IUE6;P16104;Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-2 A0A0U1RR32;Q7L7L0;Q99878;P16104;Q71UI9 HIST1H2AD;H2AFV;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;HIST2H2AB;H2AFX;H2AFZ Histone H2A type 1-D;Histone H2A.V;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A type 2-B;Histone H2AX;Histone H2A.Z;Histone H2A 0 ;;; 166.96 0.00014039 13826250000 3595860 3929680 2842830 3158640 2964800 1309280 3645780 3071040 2777950 3071770 FALSE TRUE 3455329.816 3817609.374 3356592.619 3321657.789 3060165.485 1335754.539 3690398.146 3007621.951 2462608.762 2863716.282 1.206589437 1.333096228 1.172110743 1.159911619 1.068599394 0.466440948 1.288674499 1.050251371 0.859934616 1 21.44945714 3.230554191 3.23149532 0.960118071 1.231669173 0.307909711 0.198097786 0.328580857 7.128208789 0.059986987 0.078380538 1700.412117 -3.230554191 0.271551103 S(ph)KEGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKEGHSLEMENENLVENGADSDEDDNSFLK 30 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 2 S(0.5)KEGHS(0.5)LEMENENLVENGADS(0.964)DEDDNS(0.036)FLK 62.052 0.028354 145340000 24478 21889 13280 18643 25126 29482 27436 28061 24633 19753 TRUE FALSE 23521.3727 21264.74715 15679.99141 19605.16746 25934.20061 30078.14624 27771.76998 27481.53054 21836.76511 18415.11172 1.277286452 1.154744401 0.85147414 1.064623868 1.408310794 1.633340416 1.508096742 1.492335804 1.185806823 1 14.16860253 3.230708948 8.605736854 1.423545667 1.074731511 0.312539801 0.197326664 0.127311158 78.38854714 0.055654026 0.069573321 1701.018152 -3.230708948 -0.348814156 DIHTLAQLISAYSLVDPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DIHTLAQLISAYSLVDPEK 19 0 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 163.45 2.57E-11 621750000 823580 781170 602400 700050 790910 820070 832220 756160 994000 931150 FALSE TRUE 791393.5831 758891.7964 711267.0803 736179.6644 816350.3384 836652.3773 842404.9573 740545.0318 881165.2872 868082.3811 0.911657235 0.874216334 0.819354356 0.848052766 0.940406528 0.963793754 0.970420522 0.853081514 1.015071042 1 19.72747244 3.230735271 22.97619529 0.944565882 0.860958049 0.476794279 0.04702381 63.77039889 187237.7664 0.013971231 0.017029818 1701.121256 -3.230735271 -0.083607832 ETHVMDYR ddPTM_BT-474_Pertuzumab_2h_R1 8 ETHVMDYR 8 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;;;; 130.96 0.00099647 13887400000 7742240 8911700 7573860 7369870 7485140 4902080 8505470 6518750 7923940 8850690 FALSE TRUE 7439664.701 8657547.041 8942624.982 7750229.874 7725906.326 5001203.416 8609562.486 6384135.534 7024447.551 8251224.883 0.901643672 1.049243859 1.083793632 0.939282347 0.936334476 0.606116484 1.043428413 0.773719736 0.851321792 1 22.97617687 3.230741312 2.791338501 0.847404515 1.011206263 0.212396242 0.122572841 0.342967683 5.481032263 0.03486141 0.046094987 1701.144918 -3.230741312 0.163801748 HS(ph)SLIDEMFK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSSLIDEMFK 10 0 A0A1B0GV68 A0A1B0GV68 1 HS(0.5)S(0.5)LIDEMFK 119.45 0.00044507 67259000 131650 160340 88819 173700 72905 90342 149730 107920 133750 117460 TRUE FALSE 126504.9725 155767.2602 104870.5691 182664.6778 75250.05554 92168.77714 151562.4405 105691.4143 118567.2607 109504.3296 1.155250874 1.422475813 0.957684226 1.668104618 0.687187948 0.841690712 1.384077151 0.965180233 1.082763222 1 16.74062839 3.230795154 24.9996911 1.009702566 1.285050487 0.28249321 0.238630986 251.1297324 808471.8834 0.066965321 0.081447968 1701.355832 -3.230795154 0.275347921 VDEEDS(ph)DEES(ph)HHDEMSEQEEELEDDPTVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDEEDSDEESHHDEMSEQEEELEDDPTVVK 30 0 A0A0D9SEI0;Q9P0P8 A0A0D9SEI0 C6orf203 Uncharacterized protein C6orf203 2 VDEEDS(0.667)DEES(0.667)HHDEMS(0.667)EQEEELEDDPTVVK 57.803 0.020788 94716000 43255 53199 35621 53965 29120 33792 46819 32558 47519 32792 TRUE FALSE 41564.54678 51681.81661 42058.50708 56750.14012 30056.67125 34475.29739 47391.98493 31885.66592 42124.84234 30570.96863 1.359608434 1.690552145 1.375766257 1.856340923 0.983176935 1.12771361 1.550228437 1.043004764 1.377936134 1 14.89987464 3.231061239 24.99999097 1.195761282 1.565222989 0.447700079 0.211882733 157.3223293 524450.6651 0.057666984 0.07020595 1702.398543 -3.231061239 0.369461707 GS(ph)PNTASAEATLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPNTASAEATLPR 14 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 1 GS(0.998)PNT(0.002)ASAEATLPR 157.37 5.58E-06 262730000 119100 102100 99798 100530 119310 120150 124240 116840 146370 134490 TRUE FALSE 114445.4403 99188.20797 117833.7186 105718.3653 123147.7145 122579.5153 125760.4863 114427.2132 129754.6912 125380.8725 0.912782293 0.791095212 0.939806178 0.843177777 0.982189006 0.977657221 1.003027685 0.912636919 1.034884258 1 16.93595775 3.231066779 24.92623091 0.977044394 0.87082041 0.576538823 0.047289292 118.4449319 393974.4661 0.01294985 0.015766252 1702.42026 -3.231066779 -0.106223984 VTGEADVEFATHEDAVAAMSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTGEADVEFATHEDAVAAMSK 21 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ; 118.52 8.05E-05 10505000 31802 32348 26260 26798 33561 32907 31222 33881 33949 38165 FALSE TRUE 30559.14268 31425.46671 31005.76615 28181.04799 34640.52004 33572.40209 31604.10418 33181.34551 30095.25185 35580.05056 0.858884184 0.883232773 0.871436821 0.792046317 0.973593896 0.94357376 0.888253493 0.932582866 0.845846236 1 15.11878094 3.231098261 24.99996985 0.925407354 0.855104989 0.41393433 0.045854651 183.3909493 614385.1621 0.012841659 0.015632195 1702.543671 -3.231098261 -0.070302365 KTRPDGNCFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTRPDGNCFYR 11 2 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 76.942 0.019108 649750000 1435400 1492000 1214400 1335400 1262000 1083400 1279700 1335900 1469300 1547600 FALSE TRUE 1379302.981 1449449.621 1433869.094 1404320.154 1302593.376 1105307.09 1295361.351 1308313.198 1302511.224 1442779.674 0.956003891 1.004622984 0.993824019 0.973343456 0.902835963 0.766095552 0.8978234 0.906800409 0.902779023 1 20.46041957 3.231266104 4.345337229 0.885839251 0.985762485 0.369406599 0.054447837 0.193870557 8.64471974 0.015659059 0.020105755 1703.201787 -3.231266104 0.099923235 RDSQDGSSYR ddPTM_BT-474_Pertuzumab_2h_R1 3 RDSQDGSSYR 10 1 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;; 187.76 6.09E-06 462350000 481208 531500 396358 443777 428817 432115 442622 473772 446203 434015 FALSE TRUE 462401.8594 516342.1404 467988.7075 466680.3842 442610.2882 440852.6614 448038.9404 463988.4426 395551.9061 404618.7775 1.142808701 1.276120064 1.156616385 1.153382913 1.093894581 1.089550673 1.10731129 1.146729881 0.97759157 1 18.62620375 3.231606619 0.187564036 0.964823071 1.321230792 0.590960609 0.051244698 6.001984239 0.398190475 0.174930469 0.567961789 1704.53773 -3.231606619 0.356407721 VHSYLER ddPTM_BT-474_Pertuzumab_2h_R1 2 VHSYLER 7 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ; 161.68 0.0013001 556450000 172306 197172 154539 157989 140372 91078 159153 108330 151436 164863 FALSE TRUE 165572.091 191548.8476 182467.635 166142.8312 144887.1929 92919.65956 161100.762 106092.9476 134245.6202 153696.6822 1.077265226 1.246278351 1.187193064 1.080978645 0.942682632 0.604565162 1.048173323 0.690274807 0.873445141 1 17.2297265 3.231622792 2.669606795 0.827033512 1.171395817 0.55154774 0.129841781 0.175506265 2.562944761 0.036614632 0.048639968 1704.601209 -3.231622792 0.344362305 APFDLFENR ddPTM_BT-474_Pertuzumab_2h_R1 3 APFDLFENR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 154.49 0.00017583 325040000 202768 216832 189352 227604 164724 93788 242925 205861 190841 257808 FALSE TRUE 194843.6024 210648.1637 223572.1185 239350.6697 170022.4971 95684.45762 245897.9888 201609.8984 169177.5298 240346.4345 0.810678148 0.876435567 0.93020776 0.99585696 0.707405947 0.398110577 1.023098135 0.838830411 0.703890324 1 17.87475588 3.231649413 24.99921058 0.774720003 0.903298476 0.11506216 0.169271076 371.9242388 1345323.581 0.05019839 0.061249964 1704.705698 -3.231649413 0.128578473 S(ph)SSSGSDDYAYTQALLLHQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSSGSDDYAYTQALLLHQR 20 0 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 S(0.362)S(0.362)S(0.271)S(0.004)GSDDYAYTQALLLHQR;S(0.384)S(0.384)S(0.231)S(0.001)GSDDYAYTQALLLHQR 273.8 1.18E-44 609450000 215850 225182 170340 198330 231846 326227 190541 260393 208757 226518 TRUE FALSE 207414.3434 218760.0298 201124.2272 208565.8351 239303.5371 332823.5335 192872.8978 255015.7936 185059.7805 211175.7341 0.982188338 1.035914618 0.952402169 0.987641104 1.133196189 1.576050084 0.913328885 1.207599891 0.876330708 1 17.68808454 3.231682616 8.554308196 1.140363118 0.990046859 0.096974446 0.184100677 0.264745607 165.4471769 0.051694255 0.064769516 1704.836035 -3.231682616 -0.150316258 EQNYCESR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQNYCESR 8 0 Q7L5D6;Q7L5D6-2;C9JPA8;C9JY46 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 143.37 0.0014016 90164000 88828 90155 78210 91462 80105 89707 91558 80436 101750 109300 FALSE TRUE 85356.50356 87583.86767 92344.28677 96182.36478 82681.65007 91520.937 92678.51419 78774.96849 90199.76657 101897.0136 0.837674241 0.859533214 0.90625116 0.943917406 0.811423683 0.898170945 0.909531211 0.773084173 0.885205202 1 16.63675224 3.231685779 24.99265441 0.864882918 0.886279459 0 0.063130753 796.6007226 2895945.93 0.01804285 0.022024085 1704.84845 -3.231685779 0.021396541 LTQYHGGS(ph)LPNVSQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTQYHGGSLPNVSQLR 16 0 Q6UUV7;Q6UUV7-3;H0YK33 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR 255.63 8.33E-27 1939040000 1918290 1922520 1460480 1791570 1623980 1573040 1660110 1911560 1878630 1827160 TRUE FALSE 1843321.106 1867691.612 1724421.224 1884033.142 1676216.792 1604847.947 1680426.923 1872085.618 1665375.798 1703404.826 1.082139183 1.09644612 1.012337877 1.106039571 0.984039006 0.942141247 0.986510604 1.099025663 0.977674698 1 20.69998991 3.231856828 24.99996256 1.006256587 1.071405162 0.403400363 0.044595107 203.4597048 758746.8968 0.014219711 0.017371786 1705.520044 -3.231856828 0.065148575 RFPQHTIMAGNVVTGEMVEELILSGADIIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFPQHTIMAGNVVTGEMVEELILSGADIIK 30 1 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YNH0;H0YLB8 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 99.976 0.00032942 83490000 68153 68900 53497 51781 77675 81164 74298 69830 67595 83284 FALSE TRUE 65489.50541 66935.03946 63165.09793 54453.42362 80173.48692 82805.19169 75207.28115 68387.9861 59921.89898 77643.1005 0.843468447 0.862086123 0.81353137 0.701329845 1.032589971 1.066484867 0.968628 0.880799268 0.771760769 1 16.24457011 3.232250113 24.99999935 0.949191523 0.809776059 0.410556298 0.086877928 174.1814349 690045.2509 0.027276435 0.033361589 1707.065215 -3.232250113 -0.139415464 CGLGQENS(ph)DNEHLVENEVSLLLEESDLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 CGLGQENSDNEHLVENEVSLLLEESDLRR 29 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 CGLGQENS(1)DNEHLVENEVSLLLEESDLRR 175.34 3.62E-13 35122000 23785 26018 17150 21193 24603 29448 19633 32281 22278 22094 TRUE FALSE 22855.4559 25275.99211 20249.3865 22286.77327 25394.37784 30043.45874 19873.27453 31614.38607 19749.09484 20597.5537 1.109619921 1.227135634 0.983096672 1.082010689 1.232883196 1.458593538 0.964836641 1.534861204 0.958807785 1 14.33018538 3.2323501 23.30854868 1.236043171 1.101130061 0.021239147 0.193702506 147.455411 553412.2233 0.052544405 0.064430553 1707.458274 -3.2323501 -0.13491311 SCLLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCLLLR 6 0 Q9H0U4;E9PLD0;Q92928;P62820;E7END7;P62820-2;P62820-3 Q9H0U4;P62820 RAB1B;RAB1C;RAB1A Ras-related protein Rab-1B;Putative Ras-related protein Rab-1C;Ras-related protein Rab-1A 0 126.04 0.041095 229130000 247650 298860 230940 290410 222240 213330 261560 300950 263320 268430 FALSE TRUE 237971.5642 290336.8054 272675.9952 305398.0949 229388.5514 217643.6788 264761.0495 294735.2773 233429.0175 250248.997 0.950939133 1.160191685 1.089618734 1.220376899 0.916641242 0.869708496 1.057990452 1.177768066 0.932787025 1 17.93300476 3.232398489 24.99990822 1.012081844 1.108084982 0.210556088 0.102826403 293.2095977 1189558.26 0.032276586 0.039496602 1707.648532 -3.232398489 0.096003138 CVEDPETGLCLLPLTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 CVEDPETGLCLLPLTDK 17 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 97.214 0.004955 22551000 47096 51431 32729 35544 53283 51346 45697 52665 56012 52956 FALSE TRUE 45255.43625 49964.23824 38643.85835 37378.4301 54996.89609 52384.2513 46256.25356 51577.44935 49653.75258 49369.24295 0.91667268 1.012051943 0.78275169 0.757119775 1.113991076 1.061070581 0.936944761 1.044728383 1.005762892 1 15.5913249 3.232629754 24.99998956 1.025718256 0.871470848 0.500841882 0.078164709 131.4272219 553996.604 0.02380285 0.029169049 1708.558109 -3.232629754 -0.154247407 HQERPPESHRVT(ph)PNLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 HQERPPESHRVTPNLNR 17 2 Q5TC79;Q5TC79-2;Q5TC79-3 Q5TC79 ZBTB37 Zinc finger and BTB domain-containing protein 37 1 HQERPPES(0.016)HRVT(0.984)PNLNR 105.96 0.00078015 137770000 99030 109280 92731 107520 93729 102860 105360 97705 113600 133370 TRUE FALSE 95159.79812 106163.4414 109489.5545 113069.1201 96743.87841 104939.8997 106649.4272 95687.35761 100704.6043 124336.7311 0.765339391 0.853838125 0.880588974 0.909378259 0.778079635 0.843997576 0.857746751 0.769582381 0.809934469 1 16.92389303 3.232705432 24.99967951 0.828754381 0.854418665 0 0.069614884 628.3435099 2682818.917 0.019180363 0.023522425 1708.855861 -3.232705432 0.025664284 HGVESTLER ddPTM_BT-474_Pertuzumab_2h_R1 4 HGVESTLER 9 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 119.21 0.0008644 1956260000 1125070 1121310 875400 1075720 885150 862770 1101810 693200 1181430 1369390 FALSE TRUE 1081101.021 1089331.337 1033604.253 1131238.038 913621.6536 880215.8005 1115294.28 678885.1778 1047319.019 1276639.996 0.846833112 0.85327997 0.809628601 0.886105748 0.715645489 0.689478478 0.873616904 0.531774956 0.820371462 1 20.28392032 3.232777765 24.90630625 0.737363768 0.846460779 0.047720623 0.119347986 239.7845069 1032733.699 0.032886804 0.040324142 1709.1405 -3.232777765 0.109097011 NSPTFKS(ph)FEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPTFKSFEEK 11 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NSPTFKS(1)FEEK 117.2 0.0010637 0 134150 116580 49290 60141 128900 92178 92918 126480 133940 87151 TRUE FALSE 128907.2697 113255.2525 58197.79945 63244.88422 133046.1856 94041.90232 94055.15828 123868.1438 118735.6927 81248.18514 1.586586451 1.393941937 0.716296608 0.778415962 1.637528092 1.157464652 1.157627806 1.524565054 1.461395015 1 16.31004797 3.233185515 24.99999571 1.341866342 1.109711545 0.098666529 0.298769343 304.1728968 1414730.598 0.090031443 0.110584139 1710.745928 -3.233185515 -0.232154797 KPGQSFQEQVEHYR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPGQSFQEQVEHYR 14 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 239.75 1.47E-17 619440000 939480 1038600 921160 997480 899960 875960 1037180 952460 1022630 1057960 FALSE TRUE 902764.0829 1008980.145 1087634.103 1048960.062 928908.0307 893672.5114 1049873.319 932791.3682 906545.3296 986303.4269 0.915300564 1.022991624 1.102737832 1.063526734 0.941807567 0.90608274 1.064452673 0.945744831 0.91913432 1 19.91167202 3.233206356 24.99978274 0.963581371 1.031385696 0.203124068 0.061029181 207.5477774 969067.9708 0.018017175 0.022134202 1710.828024 -3.233206356 0.067804325 SSVTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSVTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQR 37 1 F6WE04;Q5SRH9-5;Q5SRH9-6;Q5SRH9-4;Q5SRH9;A0A0A0MRQ0;A0A0A0MSH8;E9PAZ4;A0A0A0MSW9;Q5SRH9-3;E9PQ33;F8W961;E9PQX3;U5GXS1 F6WE04 TTC39A Tetratricopeptide repeat protein 39A 0 ; 106.21 1.24E-05 116974000 34764 29895 29992 29190 36861 42769 36588 36188 38906 36949 FALSE TRUE 33405.38445 29042.42387 35412.22157 30696.4994 38046.66754 43633.81848 37035.77489 35440.70515 34489.55399 34446.41132 0.969778365 0.843119 1.028038051 0.891137806 1.104517599 1.266715946 1.075170779 1.028864947 1.001252458 1 15.07206607 3.233210504 24.9952205 1.085509091 0.933384045 0.418588496 0.084344615 129.8453909 606625.1027 0.025308326 0.031092534 1710.844365 -3.233210504 -0.152125047 IFVGGLSPDTPEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 IFVGGLSPDTPEEK 14 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;; 160.18 5.34E-07 88184000 274229 264369 245519 252307 271920 290376 277648 313135 335338 332119 FALSE TRUE 263511.8275 256829.455 289889.7448 265328.5945 280666.5538 296247.6017 281045.9393 306668.6528 297271.8361 309624.2843 0.851069638 0.82948744 0.936262947 0.856937288 0.906474614 0.956797049 0.907699924 0.990454135 0.960105041 1 18.2401591 3.23340659 0.310104917 1.007410096 0.800192435 0.709142502 0.030433422 1.526933132 0.239647226 0.036341435 0.112819413 1711.616996 -3.23340659 -0.207217661 IINEPTAAAIAYGLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IINEPTAAAIAYGLDR 16 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;P17066 A0A0G2JIW1;P17066 HSPA1B;HSPA1A;HSPA6 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 6 0 ; 205.27 5.36E-11 183393000 73726 75845 60699 75283 55687 46201 65756 66484 65950 80971 FALSE TRUE 70844.70641 73681.97486 71668.65954 79168.36465 57478.22293 47135.21587 66560.7416 65111.08217 58463.63248 75486.76205 0.938505037 0.976091342 0.949420237 1.0487715 0.761434474 0.624416978 0.881753831 0.862549676 0.774488545 1 16.20393604 3.233433858 24.99999726 0.809879647 0.975991142 0.407938658 0.094599101 124.5316357 607263.1224 0.027371278 0.033661958 1711.724467 -3.233433858 0.166111495 HLEPALAFQLELNR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLEPALAFQLELNR 14 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4;O00763-3;O00763-2;O00763;F8W8T8;H0YGH5 Q13085 ACACA;ACACB Acetyl-CoA carboxylase 1;Biotin carboxylase;Acetyl-CoA carboxylase 2;Biotin carboxylase 0 ; 137.46 1.61E-05 302610000 356790 380350 316510 317590 339270 277860 380240 248910 353440 465170 FALSE TRUE 342846.2523 369502.7904 373710.3977 333980.858 350182.9277 283478.5196 384893.4909 243769.9215 313318.9729 433663.6216 0.790581076 0.852049312 0.86175178 0.770138055 0.80749897 0.65368296 0.887539263 0.562117525 0.722493097 1 18.7262169 3.23349732 1.700165609 0.734715 0.833491262 0.00702363 0.117219988 0.78636877 4.702678963 0.037172792 0.052746484 1711.974611 -3.23349732 0.098776262 IKDEDHS(ph)PTFENSDCTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKDEDHSPTFENSDCTLK 18 1 Q6UB98-2;Q6UB98 Q6UB98-2 ANKRD12 Ankyrin repeat domain-containing protein 12 1 IKDEDHS(0.663)PT(0.334)FENS(0.003)DCTLK 65.454 0.020195 425690000 221070 227640 178930 192350 224960 236450 201720 215010 270080 248450 TRUE FALSE 212430.34 221147.9301 211266.6313 202277.2066 232196.0427 241231.181 204188.7097 210569.9684 239421.6507 231622.2602 0.917141296 0.954778396 0.91211713 0.873306419 1.002477234 1.041485308 0.881559093 0.909109376 1.033672888 1 17.82141439 3.233648187 24.9972583 0.965523135 0.917066091 0.24824252 0.051539311 241.9075065 1230964.003 0.016150575 0.019873133 1712.569429 -3.233648187 -0.048457044 AS(ph)PRPWT(ph)PEDPWSLYGPSPGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPRPWTPEDPWSLYGPSPGGR 22 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 2 AS(1)PRPWT(0.99)PEDPWS(0.009)LY(0.002)GPSPGGR 66.479 0.050034 38800000 27069 29078 29597 29588 19937 22417 18170 20428 21720 20996 TRUE FALSE 26011.11355 28248.72391 34945.83628 31115.04023 20578.29171 22870.2871 18392.3699 20006.15466 19254.43666 19573.92222 1.328865685 1.443181576 1.785326206 1.589617036 1.051311612 1.168405946 0.939636404 1.022082056 0.983678 1 14.25664525 3.233937869 23.47253602 1.02856381 1.547820029 0.807860806 0.121614309 22.80260948 115783.3282 0.036881005 0.045553287 1713.712122 -3.233937869 0.519256219 GPRT(ph)PPITTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPRTPPITTK 10 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GPRT(1)PPITTK 79.633 0.042713 2828700000 455520 476360 388040 423110 477540 478230 474370 515610 544230 524330 TRUE FALSE 437717.7748 462774.6792 458167.4599 444946.7578 492900.5078 487900.1383 480175.482 504962.4733 482451.292 488816.6621 0.895464105 0.946724437 0.937299187 0.910252846 1.008354555 0.998125015 0.982322247 1.033030403 0.986978001 1 18.89893394 3.233976524 24.99986065 1.00366433 0.925231806 0.815389824 0.018385965 45.8923809 250279.6002 0.005229521 0.00645167 1713.864663 -3.233976524 -0.078432524 TETGQELECLQDHLDDLVVECR ddPTM_BT-474_Pertuzumab_2h_R1 5 TETGQELECLQDHLDDLVVECR 22 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ;;;; 257.96 3.67E-37 575567000 386671 542819 359920 475236 330981 282557 352791 408125 527789 426400 FALSE TRUE 371559.4698 527338.3336 424965.5504 499762.9869 341627.3045 288270.4961 357108.5618 399697.0761 467876.6054 397519.5482 0.934694838 1.326572079 1.069043151 1.257203549 0.859397496 0.725173133 0.89834214 1.005477788 1.176990182 1 18.60066628 3.23426675 24.99996861 0.935569222 1.154154011 0.313343654 0.146468626 126.6814997 737572.0779 0.042637077 0.052679401 1715.010368 -3.23426675 0.218584789 MPDMHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 MPDMHFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 65.038 0.07167 499790000 683250 739080 717880 822740 580740 495020 790930 733060 783660 805830 FALSE TRUE 656547.8346 718002.162 847616.8852 865201.71 599420.0295 505029.6436 800609.6379 717922.0548 694702.2022 751250.4163 0.873940061 0.955742781 1.128274763 1.15168217 0.797896436 0.672252065 1.065702754 0.955636149 0.924727876 1 19.51893436 3.234314134 24.99988959 0.904933761 1.029495484 0.191120801 0.125605933 200.1312798 1178213.639 0.038849893 0.048024518 1715.197494 -3.234314134 0.124561723 GS(ph)PMALLLAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPMALLLAAR 11 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 GS(1)PMALLLAAR 73.632 0.045136 11681000 7304.8 10643 10229 10335 7665.1 7575.4 8189.8 8729.7 8251.8 11714 TRUE FALSE 7019.32034 10339.47206 12077.60784 10868.39059 7911.654903 7728.579778 8290.029222 8549.428644 7315.090258 10920.60035 0.642759566 0.94678605 1.105947243 0.995219149 0.724470693 0.707706494 0.759118451 0.782871671 0.669843234 1 13.41476455 3.234315363 24.99566772 0.76070885 0.937490673 0.213052222 0.137403073 141.5638419 833515.5143 0.03903505 0.048241978 1715.202351 -3.234315363 0.176781823 SKPCGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKPCGSPR 8 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 SKPCGS(1)PR;SKPCGS(1)PR;SKPCGS(1)PR;S(0.002)KPCGS(0.998)PR 87.298 0.0093405 891645000 1444010 1481900 1195430 1404940 1261970 1175040 1495470 1357760 1406460 1573390 TRUE FALSE 1387576.493 1439637.663 1411470.793 1477449.122 1302562.411 1198800.114 1513772.009 1329721.782 1246804.557 1466822.894 0.945974118 0.981466589 0.962263951 1.007244384 0.888016145 0.817276659 1.032007351 0.906531925 0.850003475 1 20.48426326 3.234389299 24.99960346 0.914232916 0.973898405 0.179615515 0.061305577 184.7011884 1106955.535 0.01740894 0.021529542 1715.494377 -3.234389299 0.059665489 AQIHDLVLVGGSTR ddPTM_BT-474_Pertuzumab_2h_R1 6 AQIHDLVLVGGSTR 14 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;;;; 176.25 2.26E-06 12706320000 6125530 6784330 5527500 6615030 4867320 4273650 5956960 5082130 6639160 6945960 FALSE TRUE 5886137.515 6590847.551 6526442.209 6956432.491 5023881.768 4360066.131 6029863.058 4977182.24 5885510.39 6475503.942 0.908985242 1.017812298 1.007866301 1.074268899 0.775828694 0.673316883 0.931180509 0.768616973 0.908888396 1 22.62656104 3.234510818 24.99988885 0.825687466 1.00374835 0.392152157 0.095688955 91.29980707 563604.6678 0.02631349 0.032550091 1715.974453 -3.234510818 0.178060884 AYGSELYGPGRPLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYGSELYGPGRPLSPR 16 1 A7MCY6 A7MCY6 TBKBP1 TANK-binding kinase 1-binding protein 1 1 AYGSELYGPGRPLS(1)PR 91.276 0.0031286 358090000 287950 334410 305600 322330 276870 303250 283820 287960 339960 321670 TRUE FALSE 276696.5957 324872.9542 360828.718 338965.4899 285775.775 309381.9228 287293.4741 282013.5254 301369.166 299883.0044 0.922681818 1.083332331 1.203231636 1.130325777 0.952957556 1.031675414 0.958018527 0.940411831 1.004955805 1 18.19404024 3.234519187 24.99914735 0.976535909 1.093234195 0.339491106 0.070188174 110.9304124 686185.4502 0.020976125 0.025954707 1716.007523 -3.234519187 0.116698286 QDIAFAYQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDIAFAYQR 9 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8 P07355-2 ANXA2 Annexin A2;Annexin 0 ; 109.29 0.0057536 521610000 610380 692270 426820 587520 443370 360590 478960 546680 500570 516990 FALSE TRUE 586525.6748 672527.1374 503955.8686 617841.9776 457631.3987 367881.3769 484821.6558 535390.867 443747.3922 481973.8068 1.216924377 1.395360345 1.045608416 1.281899491 0.949494334 0.76328085 1.005908721 1.110829799 0.920687776 1 18.87859522 3.234561032 24.99967491 0.968173737 1.232881921 0.5818738 0.11467368 79.87593042 499270.1682 0.034703582 0.042944346 1716.172868 -3.234561032 0.264708183 LTDEGAVHVNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTDEGAVHVNDR 12 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 147.18 0.00034657 0 124570 135310 112990 118470 142740 148020 157100 138760 159770 148460 FALSE TRUE 119701.6667 131451.0913 133409.8064 124584.2509 147331.3617 151013.0658 159022.6368 135894.5575 141633.5794 138404.672 0.86486724 0.949759061 0.963911149 0.900144837 1.064497026 1.091098036 1.148968706 0.981863947 1.023329469 1 17.07853312 3.234568467 24.99995666 1.054476492 0.924979783 0.616083988 0.050932013 71.93519404 450478.3946 0.015280077 0.018915529 1716.20225 -3.234568467 -0.12949671 IPWFQYPIIYDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IPWFQYPIIYDIR 13 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5 Q99623-2 PHB2 Prohibitin-2 0 ; 105.03 0.0034544 243430000 118006 137922 121867 150242 91903 88016 128076 122194 132699 126648 FALSE TRUE 113394.1951 133988.5996 143891.0778 157996.0076 94859.14346 89795.74382 129643.4324 119670.6512 117635.5658 118070.0182 0.960397879 1.134823232 1.218692773 1.33815519 0.803414321 0.760529601 1.098021618 1.013556643 0.996320384 1 16.84928314 3.23461798 24.99998711 0.952590075 1.164980223 0.409126111 0.127986744 112.0804006 710694.2942 0.039527847 0.048929529 1716.397923 -3.23461798 0.212390148 TEAAKEESQQMVLDIEDLDNIQTPESVLLSAVSGEDTQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TEAAKEESQQMVLDIEDLDNIQTPESVLLSAVSGEDTQDR 40 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 252.18 3.88E-63 13885000 13989 15069 12656 11627 16582 18129 14348 15092 16533 14265 FALSE TRUE 13442.29441 14639.24687 14943.22073 12227.07086 17115.37509 18495.5808 14523.59512 14780.34493 14656.24315 13298.81884 1.010788595 1.100793014 1.123650221 0.919410288 1.286984603 1.390768685 1.09209662 1.111402832 1.102071043 1 13.6990105 3.234669295 24.99894279 1.17079053 1.049169266 0.218478208 0.114902486 168.6116614 1083209.782 0.034488803 0.042708593 1716.60074 -3.234669295 -0.121621265 SNAAAYLQHLCYR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNAAAYLQHLCYR 13 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 0 ; 126.63 0.00018628 1564070000 1153270 1405780 1139070 1304100 1023420 906560 1201540 1158570 1202760 1297660 FALSE TRUE 1108198.933 1365688.531 1344925.287 1371404.757 1056339.234 924891.2643 1216244.806 1134645.125 1066227.727 1209768.332 0.916042273 1.128884344 1.111721353 1.133609403 0.87317481 0.764519321 1.005353482 0.937902815 0.881348684 1 20.20629937 3.2348453 24.99591376 0.909281985 1.079384138 0.458132437 0.086276191 83.61685824 562558.1197 0.024960274 0.030942442 1717.296559 -3.2348453 0.170102153 ACPRPEGLNFQDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ACPRPEGLNFQDLK 14 1 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 ; 196.95 2.20E-08 3446100000 2608600 2512900 2079460 2300400 2529000 2473900 2615200 2659500 2855300 2791500 FALSE TRUE 2506653.028 2441234.552 2455264.679 2419123.92 2610347.582 2523923.953 2647205.6 2604580.396 2531178.314 2602429.219 0.963197389 0.938059923 0.943451089 0.929563772 1.003042681 0.969833852 1.01720561 1.000826603 0.972621386 1 21.31142749 3.234866423 24.99999114 0.994922694 0.943166249 0.720131256 0.015369867 47.75751998 323193.1437 0.004345086 0.005387129 1717.380089 -3.234866423 -0.051756445 GKDNFLFITYEELQQDLQGSVER ddPTM_BT-474_Pertuzumab_2h_R1 2 GKDNFLFITYEELQQDLQGSVER 23 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 199.94 2.30E-24 466550000 339100 307270 294850 298790 352660 379360 347060 366210 394680 367330 FALSE TRUE 325847.5971 298506.9604 348135.9539 314210.5877 364003.6292 387030.9191 351307.4241 358647.6355 349877.581 342450.4119 0.951517609 0.871679373 1.016602526 0.917536019 1.062938214 1.130180913 1.025863634 1.047298012 1.021688305 1 18.38553557 3.234874494 24.99999999 1.05232404 0.940020599 0.56477377 0.046636017 66.36237163 450082.9232 0.013141794 0.016289694 1717.412003 -3.234874494 -0.112303441 QITQEEDDS(ph)DEEVAPENFFSLPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 QIT(0.056)QEEDDS(0.944)DEEVAPENFFSLPEK;QIT(0.074)QEEDDS(0.926)DEEVAPENFFSLPEK;QIT(0.185)QEEDDS(0.815)DEEVAPENFFSLPEK 109.48 0.0013794 465257000 121260 109673 98500 104053 116110 120019 109707 121570 131734 125838 TRUE FALSE 116521.0251 106545.2334 116301.1411 109423.1878 119844.7836 122445.8664 111049.6271 119059.537 116780.1086 117314.8802 0.993233126 0.9081988 0.99135882 0.932730679 1.021565068 1.043736875 0.946594557 1.014871573 0.995441571 1 16.84002649 3.235483829 24.99988382 1.0030653 0.955437277 0.330836233 0.032951813 89.5816106 727880.6165 0.008971424 0.011156706 1719.823302 -3.235483829 -0.047628023 HQFGTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 HQFGTDK 7 0 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 ; 103.83 0.0082873 309530000 597760 602590 571540 619800 521380 514800 543600 528670 739030 726030 FALSE TRUE 574398.8783 585404.7232 674829.9918 651787.9523 538150.6612 525209.6087 550252.7394 517752.7798 655138.4127 676855.3414 0.848628715 0.864888976 0.997007707 0.962964924 0.795074853 0.775955476 0.812954712 0.764938604 0.967914963 1 19.36848801 3.235491825 24.99798186 0.829920447 0.920169119 0.089885275 0.08515635 127.4699853 1038355.154 0.024040371 0.02992435 1719.854967 -3.235491825 0.090248672 VFHGNESLWK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFHGNESLWK 10 0 Q13268;H0YJG9 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ; 130.79 0.00026734 3554400000 5851600 7368400 5626500 8004400 4469400 3908600 8859200 5723200 6943000 6685900 FALSE TRUE 5622913.003 7158260.446 6643333.711 8417508.043 4613162.31 3987634.57 8967621.54 5605013.92 6154859.747 6233058.038 0.902111447 1.14843475 1.065822534 1.350462003 0.740112202 0.639755726 1.438719403 0.899239809 0.987454266 1 22.57150872 3.235533457 24.999948 0.961899066 1.115339219 0.11739435 0.221506318 197.7628547 1633236.601 0.064150496 0.079869755 1720.019841 -3.235533457 0.153440153 ELYVAADEASIAPILAEAQAHFGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELYVAADEASIAPILAEAQAHFGR 24 0 Q8NFF5-2;Q8NFF5;Q8NFF5-3;Q5T196;Q8NFF5-4;Q8NFF5-5;Q5T191 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 0 167.73 1.14E-11 178010000 238430 212050 190580 198090 231150 206100 248690 265620 218160 207340 FALSE TRUE 229111.892 206002.5416 225022.0454 208313.4486 238585.1497 210267.4832 251733.5426 260134.8542 193395.3914 193296.6771 1.185286242 1.065732452 1.164127851 1.077687686 1.234295143 1.087796678 1.302316969 1.345780269 1.000510688 1 17.56045731 3.235600963 24.99527977 1.196264637 1.122025929 0 0.11600101 206.1408441 1740931.728 0.033358932 0.041539509 1720.287218 -3.235600963 -0.074238708 RDTFNHLTTWLEDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDTFNHLTTWLEDAR 15 1 P61019;P61019-2;E9PKL7 P61019 RAB2A Ras-related protein Rab-2A 0 ; 161.66 1.06E-06 1149470000 325950 473000 339630 418500 322080 304180 419170 392430 382420 360470 FALSE TRUE 313211.5136 459510.5031 401008.696 440098.8352 332439.9957 310330.728 424299.9278 384326.1834 339009.2848 336055.0458 0.932024433 1.367366772 1.19328277 1.309603414 0.989242685 0.923452071 1.262590558 1.143640568 1.008790938 1 18.35833804 3.235640714 24.99998583 1.075435905 1.211962975 0.199400418 0.138830044 133.357503 1141800.683 0.039665355 0.049424687 1720.444685 -3.235640714 0.13652707 NGMVLKPHFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGMVLKPHFHK 11 1 P26373;P26373-2;J3QSB4;H3BTH3 P26373 RPL13 60S ribosomal protein L13 0 ; 98.943 0.0033189 1394890000 2624800 2336790 2234140 1713330 1792540 1245150 1962180 31482.9 2633000 1816450 FALSE TRUE 2522219.914 2270147.037 2637898.796 1801755.167 1850198.677 1270327.786 1986193.746 30832.76711 2334112.878 1693420.224 1.489423522 1.340569225 1.557734317 1.063974046 1.09258095 0.750155082 1.172888878 0.018207393 1.37834239 1 20.69150859 3.23565685 1.098458541 0.742667846 1.471050827 0.309883952 0.35284112 0.497979174 1.283908483 0.141159826 0.223997876 1720.508607 -3.23565685 0.728382981 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGREETPTEGGALSLKPGLPIR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASEDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIR 41 3 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 AS(0.011)EDNRVPS(0.793)PPPT(0.188)GDDGGGGGREET(0.006)PT(0.001)EGGALSLKPGLPIR;ASEDNRVPS(0.982)PPPT(0.017)GDDGGGGGREETPTEGGALSLKPGLPIR;ASEDNRVPS(0.993)PPPT(0.007)GDDGGGGGREETPTEGGALSLKPGLPIR;ASEDNRVPS(0.997)PPPT(0.003)GDDGGGGGREETPTEGGALSLKPGLPIR;AS(0.021)EDNRVPS(0.943)PPPT(0.033)GDDGGGGGREET(0.001)PT(0.001)EGGALSLKPGLPIR 145.77 5.27E-55 21206700000 949201 1097513 817940 892459 1043300 1115212 1017144 1080538 1049557 1037633 TRUE FALSE 912105.1755 1066213.004 965759.953 938518.9159 1076858.692 1137762.351 1029592.113 1058224.513 930415.6895 967353.1927 0.94288744 1.10219619 0.998352991 0.970192607 1.113201156 1.176160227 1.064339396 1.093938099 0.961815908 1 19.88368321 3.235720128 24.99999165 1.078903587 1.010102634 0.167873991 0.067630327 124.605925 1096692.585 0.01917894 0.023901607 1720.75931 -3.235720128 -0.068800953 LAETYLHR ddPTM_BT-474_Pertuzumab_2h_R1 6 LAETYLHR 8 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ;;;;; 178.83 0.00024754 2850690000 2152800 2349570 2086950 2240180 1983610 1647540 2456370 2060110 2219620 2538430 FALSE TRUE 2068666.196 2282562.564 2464108.289 2355795.958 2047414.617 1680854.388 2486431.791 2017568.009 1967658.043 2366499.875 0.874145914 0.964531031 1.041245899 0.995476899 0.865165741 0.71027022 1.050679029 0.852553609 0.831463405 1 21.17432342 3.235798395 24.98101157 0.879457665 0.973712589 0.154535161 0.095255132 122.6640301 1109351.553 0.02691601 0.033568248 1721.069447 -3.235798395 0.094254924 AQLNIGNVLPVGTMPEGTIVCCLEEKPGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQLNIGNVLPVGTMPEGTIVCCLEEKPGDR 30 1 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 110.75 0.00019859 176400000 95740 81559 77775 75053 101650 100980 106170 88278 110470 111600 FALSE TRUE 91998.37495 79233.01717 91830.6726 78926.49432 104919.6646 103021.8848 107469.3402 86455.02845 97929.90873 104041.2326 0.884249183 0.761554003 0.8826373 0.758607836 1.008443114 0.990202463 1.03294951 0.830968899 0.941260559 1 16.66679587 3.235806904 24.99914653 0.955841939 0.821809731 0.538616794 0.065477384 63.07216842 572592.8567 0.019504153 0.024317533 1721.10317 -3.235806904 -0.134032208 SPAGPAATPAQAQAAS(ph)TPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPAGPAATPAQAQAASTPR 19 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SPAGPAATPAQAQAAS(0.5)T(0.5)PR 129.12 2.11E-05 220180000 153060 127430 116480 140810 106450 93762 117760 153760 111510 125870 TRUE FALSE 147078.246 123795.8212 137530.5271 148077.221 109874.0609 95657.93188 119201.1821 150584.8023 98851.85229 117344.7128 1.25338622 1.054975706 1.172021507 1.261899386 0.936335846 0.815187405 1.015820647 1.283268745 0.842405678 1 16.84039331 3.235884773 24.99729803 1.010279327 1.175274691 0.350457694 0.132082318 107.0480461 1000028.538 0.041942307 0.052318348 1721.41179 -3.235884773 0.164995364 LYPLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYPLRK 6 1 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 116.49 0.037725 1887780000 1540470 1511880 1283100 1350560 1509330 1481600 1516570 1468990 1675930 1687730 FALSE TRUE 1480266.729 1468762.663 1514984.712 1420262.563 1557878.97 1511558.967 1535130.237 1438654.843 1485685.452 1573418.544 0.940796545 0.933485034 0.962861864 0.902660369 0.990123687 0.960684602 0.97566553 0.914349744 0.944240462 1 20.58547106 3.235921608 24.99909354 0.957511327 0.936839886 0.199026948 0.026683014 156.2783631 1480416.375 0.00780494 0.009736969 1721.557797 -3.235921608 -0.020671441 NESSFASHK ddPTM_BT-474_Pertuzumab_2h_R1 2 NESSFASHK 9 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YC67;H0YB03;H0YB83 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ; 119.53 0.00081249 449540000 775790 818290 754750 885900 637600 710240 856190 663520 886480 857740 FALSE TRUE 745471.2691 794953.1704 891150.1143 931621.4052 658108.9831 724601.5394 866668.3093 649818.0801 785850.5068 799644.5058 0.93225335 0.994133224 1.114432861 1.165044465 0.823001944 0.90615459 1.083817 0.812633708 0.982749836 1 19.60899924 3.235938113 24.99999774 0.926751629 1.051868403 0.260538279 0.09578418 91.79647935 875085.7406 0.027762417 0.034652833 1721.623226 -3.235938113 0.125116774 DFLLQQTMLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFLLQQTMLR 10 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 123.79 0.0069899 0 129530 122100 111420 97688 106450 97028 104050 97071 102710 83470 FALSE TRUE 124467.8244 118617.8275 131556.0725 102729.6894 109874.0609 98989.97264 105323.395 95066.44993 91050.7914 77816.50255 1.599504222 1.524327407 1.690593489 1.320153001 1.411963495 1.272094856 1.35348405 1.221674668 1.170070466 1 16.24778852 3.235961172 0.207780943 0.929035144 1.919337619 0.844443304 0.077928244 2.389033654 0.183855493 0.195328559 0.662300538 1721.714639 -3.235961172 0.990302475 HVVLPVDDDSDLNVVASFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HVVLPVDDDSDLNVVASFDR 20 0 Q15291;Q15291-2 Q15291 RBBP5 Retinoblastoma-binding protein 5 0 209.85 4.29E-22 182990000 148180 169900 144120 163850 131640 138380 179030 101730 181380 182790 FALSE TRUE 142388.9618 165054.6183 170165.6899 172306.3181 135874.3202 141178.1384 181221.0227 99629.23995 160790.5028 170409.4705 0.835569534 0.968576558 0.998569442 1.011131116 0.797340193 0.828464158 1.06344455 0.584646145 0.943553796 1 17.37864599 3.236115422 24.99897401 0.842617856 0.957763284 0.067491408 0.131180396 125.2953741 1280987.586 0.037278012 0.046572528 1722.326256 -3.236115422 0.115145428 TEAACLSAPHLAS(ph)PPATPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TEAACLSAPHLASPPATPK 19 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 TEAACLSAPHLAS(0.993)PPAT(0.007)PK 102.27 0.00025483 583110000 370080 364780 308120 335110 388840 395230 387320 425890 446900 393040 TRUE FALSE 355616.8645 354376.8316 363804.1381 352405.0673 401347.3917 403221.8214 392060.138 417095.2227 396169.7856 366419.0507 0.970519583 0.96713539 0.992863601 0.961754217 1.095323485 1.100439021 1.069977495 1.138301139 1.081193199 1 18.48313499 3.236124323 24.99808529 1.091220973 0.974058372 0.698560477 0.034288389 30.61530493 314135.9094 0.00927171 0.01158892 1722.361556 -3.236124323 -0.117162601 EMEPLGWIHTQPNESPQLSPQDVTTHAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EMEPLGWIHTQPNESPQLSPQDVTTHAK 28 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 280.73 5.44E-62 192500000 434430 431530 354760 384730 428560 451690 412170 406730 520710 477760 FALSE TRUE 417451.9953 419223.1869 418873.0236 404585.9614 442345.0216 460823.4813 417214.2598 398330.8834 461601.1838 445400.8897 0.937250026 0.941226649 0.940440474 0.908363613 0.993139062 1.034626315 0.936716269 0.89431991 1.036372388 1 18.76474491 3.236206362 24.99972639 0.970955559 0.933107816 0.234879866 0.041789337 130.4067239 1384790.224 0.013237603 0.016552391 1722.686942 -3.236206362 -0.037847743 QREEHYFCK ddPTM_BT-474_Pertuzumab_2h_R1 3 QREEHYFCK 9 1 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ;; 104.05 0.0019969 594280000 1026854 1177962 818612 1010979 773502 633517 951868 840238 881074 806377 FALSE TRUE 986723.4104 1144367.677 966553.3983 1063155.747 798382.3943 646327.1478 963517.2453 822886.7917 781058.1733 751760.3675 1.312550452 1.522250609 1.285720078 1.414221597 1.062017138 0.859751559 1.281681353 1.09461316 1.038972267 1 19.51991333 3.236353236 24.99472216 1.069541461 1.386585668 0.662994076 0.114146685 35.89825945 406486.5807 0.03250989 0.040687656 1723.269638 -3.236353236 0.317044207 IRT(ph)SPTFR ddPTM_BT-474_Pertuzumab_2h_R1 2 IRTSPTFR 8 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 IRT(0.619)S(0.381)PTFR;IRT(0.649)S(0.35)PTFR 94.616 0.016543 2681400000 246750 275750 257510 299290 184614 257860 191714 254800 209656 219980 TRUE FALSE 237106.7372 267885.88 304047.7853 314736.3928 190552.277 263074.1059 194060.2533 249538.291 185856.7298 205080.5587 1.156163894 1.306247075 1.482577321 1.534696389 0.929158172 1.282784227 0.94626353 1.216781798 0.906262061 1 17.64583121 3.23645226 24.99978521 1.072176518 1.373419888 0.524038663 0.149649486 46.60399993 552607.3699 0.041863033 0.052428063 1723.662607 -3.23645226 0.301243371 ICSHSAPEQQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ICSHSAPEQQAR 12 0 O75683 O75683 SURF6 Surfeit locus protein 6 0 85.522 0.011627 69634000 71232 64513 65183 66721 59786 51959 62156 65612 68160 77776 FALSE TRUE 68448.17469 62673.1524 76963.01809 70164.47881 61709.07099 53009.64658 62916.68372 64257.08927 60422.76255 72508.16224 0.944006476 0.864359963 1.06143937 0.967676971 0.851063785 0.731085231 0.867718637 0.886204908 0.833323597 1 16.14585579 3.236472892 24.46546859 0.852561981 0.959874848 0.279308355 0.076144355 51.01951033 597888.0028 0.021562208 0.027017724 1723.744493 -3.236472892 0.107312867 QDAQSLHGDIPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 QDAQSLHGDIPQK 13 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 182.02 1.16E-05 944900000 1252600 1343940 1180650 1283000 1223660 1314530 1237330 1289840 1440730 1535100 FALSE TRUE 1203647.007 1305612.147 1394019.718 1349215.784 1263020.135 1341110.697 1252472.815 1263204.353 1277184.37 1431126.31 0.841048759 0.912296936 0.974071757 0.942764992 0.882535753 0.93710156 0.875165809 0.882664475 0.892433017 1 20.44871958 3.236491008 24.99731735 0.903009699 0.921208284 0 0.04696151 240.9170884 2909868.609 0.013263903 0.016589125 1723.816398 -3.236491008 0.018198585 LESPTTPLLDDMDGSQDS(ph)PIFMYAPEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LESPTTPLLDDMDGSQDSPIFMYAPEFK 28 0 Q9H3M7-2;Q9H3M7 Q9H3M7-2 TXNIP Thioredoxin-interacting protein 1 LESPTTPLLDDMDGS(0.029)QDS(0.97)PIFMY(0.001)APEFK;LESPTTPLLDDMDGS(0.489)QDS(0.511)PIFMYAPEFK 167.07 3.74E-12 48582000 113472 117203 105614 116719 95776 106622 107137 95375 117344 117651 TRUE FALSE 109037.3888 113860.4852 124700.7992 122742.8816 98856.72202 108777.9699 108448.1747 93405.47292 104023.6011 109682.393 0.994119346 1.038092643 1.136926318 1.119075526 0.901299829 0.991754163 0.988747343 0.851599517 0.948407472 1 16.74297243 3.236635399 24.99989477 0.938604491 1.074261468 0.538289443 0.056420169 38.93824045 505634.3089 0.017139046 0.021484769 1724.389615 -3.236635399 0.135656977 KTLDPDPAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTLDPDPAIR 10 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 91.936 0.015729 327050000 1352990 1444430 1120220 1319860 1363790 1504370 1382040 1504320 1562830 1604270 FALSE TRUE 1300113.655 1403236.271 1322668.673 1387978.133 1407657.544 1534789.392 1398953.819 1473255.266 1385424.09 1495611.364 0.869285756 0.938235898 0.884366557 0.928033957 0.941192062 1.026195327 0.935372552 0.985052201 0.926326266 1 20.51230391 3.236655914 2.46305378 0.971762878 0.902429135 0.506754764 0.032485361 0.229820827 2.856627126 0.009238266 0.012413518 1724.471076 -3.236655914 -0.069333743 VFIPGLPAPSLTMSNTMPRPS(ph)TPLDGVSTPKPLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFIPGLPAPSLTMSNTMPRPSTPLDGVSTPKPLSK 35 2 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 VFIPGLPAPS(0.033)LT(0.033)MS(0.028)NT(0.033)MPRPS(0.495)T(0.378)PLDGVSTPKPLSK 140.38 7.64E-11 297030000 123350 146870 95450 110590 159610 143910 155320 165760 197470 164090 TRUE FALSE 118529.3456 142681.4114 112699.9383 116297.5632 164744.0006 146819.9588 157220.8526 162336.9981 175054.0335 152976.0381 0.774822953 0.932704318 0.736716283 0.760233855 1.076926835 0.959757885 1.027748231 1.061192328 1.144323226 1 17.22294616 3.23672103 24.9998527 1.04382759 0.80591804 0.761549362 0.06682905 23.84788469 324093.0049 0.019284941 0.024194515 1724.729653 -3.23672103 -0.237909551 SQLLGSAHEVQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQLLGSAHEVQR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 157.5 6.20E-05 1094370000 1431650 1758420 1520960 1582380 1485740 1333810 1662880 1597830 1611280 1800300 FALSE TRUE 1375699.535 1708271.583 1795831.306 1664046.821 1533530.176 1360780.552 1683230.823 1564834.252 1428374.249 1678364.077 0.819666933 1.017819439 1.069989122 0.991469517 0.913705314 0.81077793 1.002899696 0.932356855 0.85105149 1 20.67862427 3.236783427 24.35057028 0.917199694 0.984617408 0.098634886 0.081110927 70.28717956 963068.0226 0.023129031 0.029036461 1724.97747 -3.236783427 0.067417714 HAASNPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HAASNPSK 8 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 62.546 0.078954 17425000 33088 43593 30632 37550 26814 24498 34898 24372 32759 41901 FALSE TRUE 31794.88438 42349.77032 36167.88381 39487.96 27676.49666 24993.36634 35325.09216 23868.70968 29040.33566 39063.00795 0.813938456 1.084140023 0.925885786 1.010878631 0.708509101 0.639821859 0.9043106 0.611031022 0.743422926 1 15.25351542 3.236823936 24.98906201 0.74296143 0.965325339 0.340220954 0.12727863 42.02003661 604628.764 0.033780545 0.042406895 1725.138377 -3.236823936 0.222363908 GVMGGQSAGPQHTEAETIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GVMGGQSAGPQHTEAETIQK 20 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 103.17 0.00081894 0 36142 39100 29025 33455 40135 39482 42010 40096 48705 45605 FALSE TRUE 34729.53068 37984.90628 34270.46316 35181.61656 41425.97872 40280.35309 42524.13095 39268.00359 43176.21259 42516.13273 0.816855355 0.893423363 0.806057865 0.827488633 0.974359051 0.947413382 1.000188122 0.923602432 1.015525397 1 15.37572275 3.236961035 24.99996945 0.969998505 0.837925476 0.808493375 0.033487819 17.78206713 277918.5425 0.009141978 0.011489165 1725.683057 -3.236961035 -0.132073028 TTS(ph)GDDACNLTSFRPATLTVTNFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSGDDACNLTSFRPATLTVTNFFK 25 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0U1RQT6 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 T(0.159)T(0.159)S(0.682)GDDACNLTSFRPATLTVTNFFK 61.488 0.040603 125320000 48029 59408 35396 34299 60307 50912 47968 55233 55217 52250 TRUE FALSE 46151.97358 57713.74201 41792.84458 36069.1755 62246.82942 51941.47552 48555.04673 54092.41925 48948.99765 48711.06096 0.947463937 1.184818004 0.857974426 0.740471975 1.277878745 1.066317885 0.99679715 1.110475079 1.004884654 1 15.57196179 3.237355459 24.99997053 1.077580053 0.945355569 0.226632828 0.128886469 55.34330549 1148057.368 0.037554696 0.047324428 1727.251023 -3.237355459 -0.132224484 GSYSLSHVYTPNDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSYSLSHVYTPNDVR 15 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 130.24 6.10E-05 221480000 199830 277120 202270 227990 177360 189560 196060 178060 180860 202830 FALSE TRUE 192020.4227 269216.8089 238824.6885 239756.5912 183064.9455 193393.0331 198459.4409 174382.9988 160329.531 189092.1434 1.015485991 1.423733446 1.263006935 1.267935234 0.968125603 1.022744941 1.049538269 0.922211762 0.847891023 1 17.5287299 3.237424162 24.97801464 0.969732539 1.256944694 0.612673108 0.106526942 18.60731097 408972.0017 0.029438086 0.03711634 1727.524289 -3.237424162 0.287212154 S(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_BT-474_Pertuzumab_2h_R1 10 SYEDMIGEEVPSDQYYWAPLAQHER 25 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(0.532)Y(0.468)EDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(0.958)Y(0.04)EDMIGEEVPS(0.002)DQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER 257.04 4.17E-45 6510200000 1263162 1330686 1013916 1256258 998073 996253 1031248 1298438 1191999 1069457 TRUE FALSE 1213796.233 1292736.138 1197153.176 1321093.626 1030176.924 1016397.918 1043868.722 1271624.802 1056688.271 997021.7248 1.21742205 1.296597763 1.200729278 1.32503996 1.03325424 1.019434073 1.046986937 1.275423363 1.05984478 1 19.92726542 3.237442756 24.99999047 1.09469559 1.258335304 0.554148202 0.080910898 27.8483749 622809.2795 0.025202492 0.031772595 1727.598251 -3.237442756 0.163639714 LAHYIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LAHYIDR 7 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ;;; 113.7 0.0060716 1249230000 1833130 2181910 1617870 1974380 1391060 1426260 1571720 1495390 1811340 1844780 FALSE TRUE 1761489.253 2119684.063 1910255.098 2076277.988 1435804.708 1455099.954 1590955.18 1464509.674 1605724.277 1719831.407 1.024222052 1.232495263 1.110722301 1.207256699 0.834852011 0.846071277 0.925064615 0.85154258 0.933652142 1 20.71383572 3.237698667 24.99996553 0.888003281 1.147664771 0.744435198 0.070188093 9.900102386 287146.7854 0.018410971 0.02326171 1728.616552 -3.237698667 0.259661491 S(ph)VSKESVASMGADSGDDFASDGSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSKESVASMGADSGDDFASDGSSSR 26 1 Q92805;Q5T165 Q92805 GOLGA1 Golgin subfamily A member 1 1 S(0.447)VS(0.447)KES(0.106)VASMGADSGDDFASDGSSSR 94.185 0.0050664 251130000 131920 152070 97138 127960 144400 161450 160160 153290 166120 137620 TRUE FALSE 126764.4206 147733.1125 114692.9974 134564.0309 149044.7571 164714.6296 162120.086 150124.5079 147262.754 128298.8748 0.988040002 1.151476291 0.893951701 1.04883251 1.161699643 1.28383534 1.263612687 1.170115546 1.147810176 1 16.96914899 3.237777034 3.974834667 1.192226785 1.017903004 0.378458575 0.0934939 0.198401787 6.98830379 0.026276721 0.034066261 1728.928503 -3.237777034 -0.174323781 LSLMPWFHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSLMPWFHGK 10 0 P41240;H3BUM9;K7ENL8;K7ES68;K7EQY5;P42679-3;P42679;P42679-2 P41240 CSK;MATK Tyrosine-protein kinase CSK;Non-specific protein-tyrosine kinase;Megakaryocyte-associated tyrosine-protein kinase 0 ; 104.52 0.004312 150450000 327230 370530 297360 321130 298360 240170 352320 284150 332420 381420 FALSE TRUE 314441.4898 359962.8472 351099.5667 337703.5578 307957.0204 245026.402 356631.7976 278282.2032 294685.0752 355586.0837 0.884290765 1.012308591 0.987382754 0.949709714 0.86605476 0.689077591 1.002940818 0.782601502 0.828730619 1 18.43983934 3.23780753 4.425513287 0.847128863 0.966001653 0.199028843 0.093035955 0.261840718 12.3383797 0.025443654 0.032825897 1729.04991 -3.23780753 0.11887279 QLS(ph)LEGSGLGVEDLKDNTPSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 QLSLEGSGLGVEDLKDNTPSGK 22 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 QLS(0.999)LEGS(0.001)GLGVEDLKDNTPSGK;QLS(0.998)LEGS(0.002)GLGVEDLKDNTPSGK;QLS(0.998)LEGS(0.002)GLGVEDLKDNTPSGK 250.24 9.30E-32 1294840000 781440 692030 449500 570960 849660 742710 779820 1017150 882930 870480 TRUE FALSE 750900.4609 672293.982 530734.6491 600427.314 876990.0855 757728.1051 789363.6704 996145.4971 782703.4879 811521.6143 0.925299398 0.828436323 0.6539994 0.739878401 1.080673725 0.933712783 0.972695806 1.227503346 0.964488775 1 19.63026999 3.237875948 24.99981324 1.045397209 0.780376851 0.579288476 0.100844806 12.96509911 473412.0151 0.03087536 0.039049238 1729.322325 -3.237875948 -0.265020359 VFPGSTTEDYNLIVIER ddPTM_BT-474_Pertuzumab_2h_R1 1 VFPGSTTEDYNLIVIER 17 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 132.97 5.09E-05 149460000 29659 25157 25826 24760 30405 36070 29216 28766 28051 30924 FALSE TRUE 28499.89349 24439.54699 30493.3327 26037.86657 31383.00444 36799.36011 29573.55415 28171.97205 24866.76808 28829.48994 0.988567385 0.847727346 1.057713222 0.903167785 1.088573003 1.276448532 1.025809135 0.977192871 0.862546238 1 14.81525769 3.238107562 24.99999295 1.043175171 0.949783413 0.134940172 0.110165825 26.48365238 1461431.678 0.033357151 0.04227291 1730.244835 -3.238107562 -0.093391758 QPGTCS(ph)PDLAAPLDENGAVDRGEGGSEDGSEDGLPEGIHLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPGTCSPDLAAPLDENGAVDRGEGGSEDGSEDGLPEGIHLDK 42 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 QPGT(0.194)CS(0.806)PDLAAPLDENGAVDRGEGGSEDGSEDGLPEGIHLDK 121.32 6.44E-09 73937000 71756 73184 60246 65175 72610 82203 66411 71609 84785 75786 TRUE FALSE 68951.69619 71096.86397 71133.79237 68538.68956 74945.56659 83865.20098 67223.75768 70130.24913 75160.56225 70652.94672 0.975921025 1.006283068 1.006805741 0.970075457 1.060756417 1.187002169 0.951464317 0.9926019 1.063799399 1 16.10846211 3.238159113 24.99998708 1.039208 0.992167477 0.156960481 0.05957019 25.28736614 1574551.059 0.018161795 0.023017399 1730.450232 -3.238159113 -0.047040523 IISPGSST(ph)PSSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 IISPGSSTPSSTR 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IISPGS(0.267)S(0.15)T(0.583)PSSTR 188.96 6.33E-05 369250000 429680 402380 380000 421380 351940 374830 344380 474970 394100 334860 TRUE FALSE 412887.6306 390904.5164 448674.4531 443127.4723 363260.4697 382409.3194 348594.6255 465161.7035 349363.4202 312179.6339 1.322596306 1.25217815 1.437231659 1.419463104 1.16362642 1.224965622 1.116647557 1.490045003 1.119110224 1 18.2520169 3.238220614 24.99999997 1.225828815 1.355986962 0.264925036 0.130579209 16.19935638 1191183.651 0.037980699 0.048171736 1730.695298 -3.238220614 0.130158147 VYWNDGLDQYR ddPTM_BT-474_Pertuzumab_2h_R1 3 VYWNDGLDQYR 11 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;; 219.03 2.37E-11 716075000 646233 691251 558390 640219 554991 396269 684721 657129 608722 710514 FALSE TRUE 620977.4999 671537.1983 659303.4943 673260.7793 572842.7895 404281.8307 693100.8204 643559.0565 539622.4305 662390.2539 0.937479826 1.013808996 0.995339968 1.016411059 0.864811621 0.610337831 1.046363252 0.971570842 0.814659375 1 19.33732192 3.238338984 24.9999997 0.887819929 0.992733474 0.169941306 0.114750734 11.75768838 1326330.54 0.034225395 0.043430452 1731.167076 -3.238338984 0.104913544 QAHTMDPQLR ddPTM_BT-474_Pertuzumab_2h_R1 9 QAHTMDPQLR 10 0 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;; 113.69 0.0014551 4538004000 1414035 1455456 1219051 1368664 1239205 1306629 1390928 1173760 1525233 1498561 FALSE TRUE 1358772.949 1413947.82 1439360.633 1439300.913 1279065.154 1333049.934 1407950.593 1149521.446 1352094.944 1397062.129 0.972593073 1.012086571 1.030276753 1.030234006 0.915539208 0.954180853 1.00779383 0.822813404 0.967813039 1 20.41396475 3.238559178 25 0.933060273 1.012709616 0.271237291 0.051387416 0.061713153 768381.9495 0.015004172 0.019077405 1732.045025 -3.238559178 0.079649343 KEWLTNFMEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEWLTNFMEDR 11 1 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ; 126.1 0.00050439 995650000 1834370 1921050 1482560 1707910 1526830 1189120 1851540 1646510 1630360 1852920 FALSE TRUE 1762680.792 1866263.535 1750491.571 1796055.44 1575941.874 1213164.821 1874199.7 1612508.993 1445288.368 1727420.078 1.020412356 1.080376197 1.013356041 1.039732873 0.912309573 0.702298669 1.084970427 0.933478205 0.836674522 1 20.72018753 3.238566179 24.85924101 0.912392944 1.039668849 0.299042822 0.095129245 0.187429932 805167.4255 0.027168443 0.034530593 1732.072947 -3.238566179 0.127275906 KVEEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEEELR 7 1 Q5T7U0;Q5T7U4;Q9Y5Q8-2;Q9Y5Q8;Q9Y5Q8-3;H7BY84 Q5T7U0 GTF3C5 General transcription factor 3C polypeptide 5 0 89.298 0.028822 474100000 1116200 979680 886090 969730 1105400 1147100 1079400 1188700 1245400 1273700 FALSE TRUE 1072577.67 951740.4856 1046226.174 1019777.882 1140956.195 1170295.148 1092610.02 1164152.93 1104027.413 1187431.165 0.903275661 0.801512133 0.881083641 0.858810104 0.960860915 0.985568834 0.920145986 0.980396139 0.92976119 1 20.17941245 3.238687022 9.7741401 0.961269494 0.858262565 0.693975965 0.033027043 0.049827608 80.63769689 0.008663627 0.011023046 1732.554965 -3.238687022 -0.103006929 EIFDSR ddPTM_BT-474_Pertuzumab_2h_R1 6 EIFDSR 6 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;; 148.07 0.025152 26149400000 31435100 34241200 24596200 29525200 23654700 23981500 25329600 24887500 26607200 26306300 FALSE TRUE 30206581.54 33264674.5 29041280.48 31048999.11 24415574.91 24466422.36 25639591.22 24373564.43 23586862.2 24524550.87 1.231687451 1.356382617 1.184171756 1.26603742 0.995556454 0.997629783 1.04546629 0.993843457 0.961765307 1 24.54772338 3.238696565 24.99999999 1.001510055 1.261099475 0.893016885 0.04416963 1.043392171 191837.5351 0.012186415 0.015500923 1732.593038 -3.238696565 0.259589421 IADMGHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IADMGHLK 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 73.931 0.032078 437880000 657600 746820 648030 729940 563690 441560 769490 620630 660970 846320 FALSE TRUE 631900.265 725521.4248 765143.4363 767612.2909 581821.6008 450488.6457 778907.2488 607813.7736 585939.4566 788997.9926 0.800889573 0.919547872 0.969766012 0.972895113 0.737418354 0.570962981 0.987210685 0.770361622 0.742637449 1 19.5896621 3.238736839 24.99999998 0.791066195 0.919900688 0.164560355 0.124772711 7.795079874 1105719.254 0.034903115 0.044429479 1732.753715 -3.238736839 0.128834493 KPSDEEFASR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSDEEFASR 10 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 98.105 0.0089855 330030000 338130 325460 269040 321060 241610 256410 267190 282380 284890 281320 FALSE TRUE 324915.5058 316178.1995 317661.5128 337629.9451 249381.6051 261594.7859 270459.9511 276548.7543 252550.4816 262265.9458 1.238877982 1.205563301 1.211219061 1.287357167 0.950872994 0.997440918 1.031243116 1.054459257 0.962955678 1 18.00067097 3.238778456 24.99999998 1.007789517 1.231845368 0.915050075 0.035203315 1.670105188 191646.1163 0.010528262 0.013401287 1732.919768 -3.238778456 0.22405585 ELHYLPFPS(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 4 ELHYLPFPSP 10 0 Q8N565 Q8N565 MREG Melanoregulin 1 ELHYLPFPS(1)P;ELHYLPFPS(1)P;ELHYLPFPS(1)P;ELHYLPFPS(1)P 139.15 4.80E-05 163500000 247625 444744 255706 347304 217192 132494 349392 257530 300922 284342 TRUE FALSE 237947.5412 432060.3366 301917.7623 365228.4011 224178.1779 135173.1195 353667.9638 252211.9155 266762.5961 265083.2631 0.897633213 1.629904248 1.138954451 1.37778748 0.845689672 0.509927024 1.334176891 0.951444133 1.006335115 1 18.01608606 3.238785608 24.99998937 0.946932769 1.278692655 0.271300739 0.256017557 7.85500028 872726.5527 0.070897457 0.090255051 1732.948306 -3.238785608 0.331759885 QLYLER ddPTM_BT-474_Pertuzumab_2h_R1 5 QLYLER 6 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;;; 107.43 0.072758 1473929000 1463880 1686060 1380350 1401390 1366860 1055648 1412730 1344470 1411920 1578120 FALSE TRUE 1406669.951 1637975.22 1629809.951 1473715.906 1410826.293 1076993.926 1430019.412 1316706.225 1251644.761 1471232.527 0.956116675 1.113335377 1.107785426 1.001687958 0.95894175 0.732035152 0.971987355 0.894968131 0.85074571 1 20.48859385 3.238803196 2.746482668 0.889188745 1.06139897 0.451648176 0.080087316 0.21974104 3.398346832 0.023232212 0.030912152 1733.01849 -3.238803196 0.172210225 DKEVANR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKEVANR 7 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ;; 88.948 0.016628 433152000 421719 441842 354170 415237 449576 498551 507550 470922 494799 551810 FALSE TRUE 405237.7552 429241.0988 418176.3975 436667.4313 464037.0203 508632.0428 513761.5487 461197.2961 438631.4919 514435.4172 0.787733001 0.834392587 0.812884151 0.848828476 0.902031635 0.988718945 0.998690081 0.896511556 0.852646372 1 18.97263045 3.238852328 2.443222885 0.941734262 0.815554903 0.638471111 0.045149035 0.200544759 2.452891592 0.014599685 0.019662442 1733.214556 -3.238852328 -0.126179358 QGLSMR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGLSMR 6 0 P61956;J3KRH1;A8MUA9;A8MU27;P55854 P61956;A8MUA9 SUMO2;SUMO3 Small ubiquitin-related modifier 2;Small ubiquitin-related modifier 3 0 97.068 0.09653 254950000 302840 304000 236460 275730 248570 225980 264410 269830 297390 289840 FALSE TRUE 291004.678 295330.2176 279193.582 289960.4583 256565.4798 230549.4704 267645.9287 264257.9162 263631.534 270208.8786 1.076961939 1.092970072 1.033250955 1.073097449 0.949507955 0.85322685 0.990514931 0.977976436 0.975658296 1 18.04371555 3.238954735 25 0.955663342 1.068218751 0.642051145 0.040675288 6.896092574 437417.1316 0.012112553 0.015444581 1733.623298 -3.238954735 0.112555408 S(ph)VEEELHQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEEELHQR 9 0 F5H5A3;Q8IVH8-3;Q8IVH8-2;Q8IVH8 F5H5A3 MAP4K3 Mitogen-activated protein kinase kinase kinase kinase;Mitogen-activated protein kinase kinase kinase kinase 3 1 S(1)VEEELHQR 194.48 2.09E-05 83812000 94184 92200 81590 87793 81988 80458 84954 92818 82153 94792 TRUE FALSE 90503.18515 89570.54627 96335.12796 92324.00725 84625.21848 82084.91589 85993.69246 90901.27586 72827.33585 88371.65341 1.024120084 1.013566487 1.09011345 1.044724226 0.95760592 0.928860248 0.973091361 1.028624818 0.8241029 1 16.43129606 3.238984782 23.84178335 0.958950673 1.044375213 0.401193982 0.054113042 6.866412822 385909.6802 0.015288065 0.019490003 1733.743245 -3.238984782 0.085424541 TFHIEEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TFHIEEPR 8 0 Q969N2;Q969N2-5;Q969N2-6;Q969N2-4;A0A1W2PP53;Q969N2-2;A0A1W2PNP0;A0A1W2PPR6;Q969N2-3;A0A1W2PR73 Q969N2 PIGT GPI transamidase component PIG-T 0 124.08 0.0033259 0 59124 98860 90404 91812 64624 77769 84997 42528 102500 105170 FALSE TRUE 56813.36871 96040.60959 106742.0138 96550.42832 66702.68965 79341.54246 86037.21871 41649.78194 90864.62972 98046.74222 0.579451876 0.979539018 1.088684962 0.98473877 0.680315206 0.809221609 0.877512264 0.424795164 0.926748076 1 16.58118207 3.239305215 24.9988885 0.742875217 0.926104856 0.056660179 0.195047125 37.02316612 1242971.497 0.055813768 0.071314961 1735.022914 -3.239305215 0.18322964 MKPKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 MKPKPR 6 2 E7ETZ8;Q49MG5;A0A0C4DG83;A2VCS9;Q49MG5-2;A8MSM7 E7ETZ8 MAP9 Microtubule-associated protein 9 0 59.32 0.076166 2043800000 1162200 1102300 746140 891810 1327200 1451900 1220500 1240400 1457600 1346600 FALSE TRUE 1116779.939 1070863.483 880984.0958 937836.421 1369890.593 1481258.413 1235436.844 1214785.307 1292139.359 1255393.583 0.889585509 0.853010162 0.701759279 0.747045734 1.091204075 1.179915553 0.984103202 0.967652952 1.029270323 1 20.25970831 3.23935061 24.99996176 1.037801879 0.794926511 0.719747338 0.074606348 12.56525307 397627.0421 0.023633557 0.030208094 1735.20428 -3.23935061 -0.242875367 HTLAYDK ddPTM_BT-474_Pertuzumab_2h_R1 1 HTLAYDK 7 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 80.229 0.030479 120910000 275380 302210 283450 280860 233040 159830 299150 210090 285260 307110 FALSE TRUE 264617.8452 293591.2667 334675.7203 295355.2183 240535.9432 163061.8721 302811.0872 205751.5681 252878.4807 286309.1662 0.924238119 1.025434395 1.168931211 1.031595398 0.840126589 0.569530743 1.057636719 0.718634233 0.883235714 1 18.12721433 3.239362814 5.770344216 0.824613046 1.047481096 0.307308848 0.139756081 0.169884752 19.43017575 0.038302303 0.049083975 1735.25304 -3.239362814 0.22286805 VMEHFIK ddPTM_BT-474_Pertuzumab_2h_R1 4 VMEHFIK 7 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 110.63 0.0067597 5821860000 13384890 15949520 11574090 14596210 11396130 9954720 14463370 12504740 16142430 15577410 FALSE TRUE 12861793.7 15494655.31 13665785.53 15349522.15 11762696.87 10156011.26 14640377.05 12246512.75 14310009.02 14522338.15 0.885655848 1.06695321 0.941018271 1.056959423 0.809972661 0.699337197 1.008128092 0.843287949 0.985379136 1 23.79177042 3.239495418 24.99993465 0.879912017 0.989980833 0.171582853 0.102232992 39.02673546 1043692.407 0.02810973 0.035976806 1735.78295 -3.239495418 0.110068817 S(ph)LPAGDALYLSFNPPQPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLPAGDALYLSFNPPQPSR 19 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR 287.09 2.91E-40 317828000 160573 176732 141831 165082 140900 150978 141335 177256 160680 145803 TRUE FALSE 154297.6296 171691.7764 167463.0167 173601.9018 145432.1765 154030.8786 143064.7 173595.6017 142440.28 135927.6329 1.135145417 1.263111648 1.232001272 1.277164165 1.069923556 1.133182969 1.052506374 1.277117816 1.047912606 1 17.05247925 3.239521633 24.99943246 1.120303046 1.22981289 0.36821115 0.079951321 32.37050152 842058.0015 0.022627301 0.028968934 1735.887727 -3.239521633 0.109509844 RPAETNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPAETNLR 8 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ; 158.37 0.0010415 88418000 199215 209720 191656 202340 183821 141604 251750 192260 191447 224680 FALSE TRUE 191429.4576 203738.9909 226292.5026 212782.7916 189733.7694 144467.3299 254830.9918 188289.7638 169714.7392 209462.2235 0.913909221 0.972676541 1.08034995 1.015852826 0.905813785 0.689705893 1.216596423 0.898919914 0.810240321 1 17.67633055 3.239623166 24.99883723 0.923896783 1.000099443 0.071678585 0.132305658 85.62263422 2014431.652 0.037645287 0.048223968 1736.293607 -3.239623166 0.07620266 AAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTPR 55 1 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 AAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLS(0.284)GPAEVGPGAVGERT(0.716)PR 97.541 1.01E-07 67726000 8548.9 10960 7661 9255.1 7061.4 8677.9 6763.7 7572.4 8875.1 8007.1 TRUE FALSE 8214.799537 10647.43153 9045.513118 9732.75682 7288.536344 8853.373084 6846.476184 7416.027294 7867.635855 7464.771985 1.100475614 1.426357235 1.211760136 1.303825065 0.976391022 1.186020565 0.917171509 0.993470036 1.053968677 1 12.86588248 3.239692324 24.99999998 1.019387183 1.268955139 0.578686543 0.099977413 19.84447924 438365.6314 0.026823754 0.034375644 1736.570118 -3.239692324 0.249567957 SQIDVALS(ph)QDSTYQGER ddPTM_BT-474_Pertuzumab_2h_R1 3 SQIDVALSQDSTYQGER 17 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 1 SQIDVALS(1)QDSTYQGER;SQIDVALS(1)QDSTYQGER;SQIDVALS(1)QDSTYQGER 328.19 6.61E-72 953140000 998150 1017760 777907 755640 764750 732966 547021 676730 691667 627130 TRUE FALSE 959141.1945 988734.4813 918492.0993 794638.671 789348.8783 747787.0747 553715.6066 662755.289 613151.8619 584653.9265 1.640528099 1.691144858 1.571001335 1.359160753 1.35011302 1.279025148 0.947082678 1.133585629 1.048743255 1 19.15722338 3.239711808 0.648675095 1.015221689 1.732564078 0.918123087 0.073186196 0.223682366 0.200649885 0.047454914 0.090415917 1736.648029 -3.239711808 0.717342389 TAIHEVMEQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAIHEVMEQGR 11 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 144.1 3.69E-05 557740000 498020 480140 388270 411740 420140 283010 464790 347710 455820 472690 FALSE TRUE 478556.8278 466446.8773 458439.026 432989.9507 433654.1847 288732.6561 470478.2391 340529.667 404077.2246 440674.2853 1.085964949 1.058484447 1.040312633 0.982562326 0.984069639 0.6552065 1.067632614 0.772746853 0.91695213 1 18.74935319 3.239899618 2.200119188 0.874808382 1.055133163 0.309816665 0.110206789 0.325398075 3.233091731 0.032027215 0.043732537 1737.399205 -3.239899618 0.180324781 RLTELETAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLTELETAVR 10 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18;F8VRV7 Q13561 DCTN2 Dynactin subunit 2 0 98.105 0.0089855 229720000 83074 78015 67445 73469 83593 94736 91604 84758 73896 84815 FALSE TRUE 79827.37624 75790.08858 79633.81181 77260.74389 86281.84476 96651.62683 92725.07715 83007.71768 65507.63588 79070.4045 1.009573389 0.958513986 1.007125388 0.9771133 1.091202774 1.222348961 1.172690057 1.04979503 0.828472249 1 16.27085018 3.240008661 24.96630312 1.077245407 0.987329815 0.098719187 0.100393907 77.18494396 1330753.035 0.029951127 0.038456818 1737.835487 -3.240008661 -0.089915592 GSHQISLDNPDY(ph)QQDFFPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSHQISLDNPDYQQDFFPK 19 0 P00533;E9PFD7 P00533 EGFR Epidermal growth factor receptor;Receptor protein-tyrosine kinase 1 GSHQISLDNPDY(1)QQDFFPK 132.14 8.26E-05 127490000 51592 75856 28547 63197 27144 24053 45763 49583 58010 32305 TRUE FALSE 49575.7276 73692.66115 33706.07792 66458.60474 28017.11141 24539.36814 46323.06128 48559.09372 51424.948 30116.95358 1.646106983 2.446882981 1.119172888 2.206684171 0.930277073 0.814802469 1.53810581 1.612350784 1.707508293 1 14.87828822 3.240138465 24.99996152 1.316453264 1.84447117 0.305417787 0.430121207 60.03064531 951131.8696 0.123294839 0.158470453 1738.354977 -3.240138465 0.528017906 ELPGHTGYLSCCR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELPGHTGYLSCCR 13 0 P62879;E7EP32;C9JZN1;C9JIS1;C9JXA5;P62879-2;Q9HAV0;H7C5J5 P62879 GNB2;GNB4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2;Guanine nucleotide-binding protein subunit beta-4 0 ; 164.68 3.66E-05 768220000 404670 600310 490550 504350 343780 203344 503720 384070 327960 467710 FALSE TRUE 388855.049 583189.7466 579203.2972 530379.5639 354837.9959 207455.755 509884.676 376138.8203 290731.3557 436031.5851 0.891804774 1.33749427 1.3283517 1.216378772 0.813789661 0.475781485 1.169375553 0.862641224 0.666766734 1 18.73407312 3.240162023 24.92265982 0.8341596 1.213423962 0.421546623 0.207268819 38.71234157 602470.1497 0.058517303 0.075224861 1738.449273 -3.240162023 0.379264362 TNS(ph)DSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TNSDSALHQSTMTPTQPESFSSGSQDVHQK 30 0 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 T(0.173)NS(0.789)DS(0.038)ALHQSTMTPTQPESFSSGSQDVHQK 213.1 2.91E-26 740960000 434910 614320 489530 549550 288920 356810 319880 350880 354300 428290 TRUE FALSE 417913.2364 596800.1951 577998.9605 577912.3414 298213.3742 364024.9427 323794.7871 343634.2054 314081.3493 399281.5368 1.046663063 1.494685178 1.447597515 1.447380578 0.746874941 0.911699914 0.810943551 0.860631343 0.78661626 1 18.60704684 3.24038095 25 0.846817773 1.375090189 0.777774781 0.13244463 20.01291508 274848.835 0.035696754 0.045962086 1739.325843 -3.24038095 0.528272416 SCYDLSCHAR ddPTM_BT-474_Pertuzumab_2h_R1 6 SCYDLSCHAR 10 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;;;; 180.36 2.01E-06 5053500000 3468170 4619520 3762530 4133420 3237940 3138930 4253350 3271870 3565690 4453120 FALSE TRUE 3332630.082 4487775.813 4442502.868 4346746.302 3342091.281 3202401.315 4305403.77 3204304.741 3160927.82 4151506.216 0.80275204 1.08099942 1.070094235 1.047028735 0.805031019 0.771382999 1.037070293 0.771841489 0.761393011 1 21.98520343 3.240454055 24.99962201 0.849852203 1.010979797 0.264973348 0.115207485 60.88820238 803914.7692 0.031843262 0.041008696 1739.61865 -3.240454055 0.161127594 TVIDYNGER ddPTM_BT-474_Pertuzumab_2h_R1 4 TVIDYNGER 9 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;; 205.91 3.30E-05 7856300000 3085980 3535980 3059360 3294350 2830240 2472330 3507970 3047070 3335000 3350210 FALSE TRUE 2965376.49 3435137.312 3612254.407 3464371.798 2921277.24 2522322.207 3550901.586 2984146.94 2956424.781 3123297.293 0.949437793 1.099843208 1.156551576 1.109203343 0.93531834 0.807583131 1.13690797 0.955447612 0.946571685 1 21.57463847 3.24061062 24.9999591 0.96577501 1.085821623 0.279933213 0.090128875 71.55294672 872583.7697 0.025827418 0.033298659 1740.245904 -3.24061062 0.120046613 RSDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RS(0.039)DS(0.961)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.07)DS(0.93)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.004)DS(0.996)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.039)DS(0.961)PEIPFQAAAGPSDGLDASSPGNSFVGLR 238.11 7.09E-47 1700480000 568140 637126 465907 491837 658803 744328 585998 649153 627660 523117 TRUE FALSE 545936.4607 618955.7903 550106.7589 517220.7665 679993.9968 759378.8221 593169.6188 635747.7637 556410.6682 487685.8196 1.119442967 1.269169136 1.127994165 1.060561422 1.394328007 1.557106628 1.216294579 1.303601085 1.140920334 1 18.8955925 3.240617518 24.99924709 1.294422865 1.152047608 0.130677475 0.148036746 97.46624858 1184574.791 0.041584195 0.053617407 1740.273542 -3.240617518 -0.142375257 GGEADNLDEFLKEFENPEVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGEADNLDEFLKEFENPEVPR 21 1 O60216 O60216 RAD21 Double-strand-break repair protein rad21 homolog 0 161.8 1.77E-11 30778000 44443 39666 27881 32306 41609 39305 35340 44822 42492 38903 FALSE TRUE 42706.11843 38534.76452 32919.71691 33973.31653 42947.39127 40099.77403 35772.50149 43896.41004 37668.4863 36268.06516 1.177513006 1.062498491 0.907677781 0.936728121 1.184165493 1.105649663 0.986336088 1.210332281 1.038613065 1 15.14641216 3.240879073 24.99999404 1.099376097 1.015959192 0.094660199 0.095996703 123.8106784 1335040.733 0.027626819 0.03569485 1741.321945 -3.240879073 -0.083416905 LNHVAAGLVS(ph)PSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNHVAAGLVSPSLK 14 0 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 LNHVAAGLVS(0.996)PS(0.004)LK;LNHVAAGLVS(1)PSLK 213.49 1.01E-09 3271300000 3757120 3544250 3053810 3268090 3617390 3602430 3747150 3365760 4188700 4186000 TRUE FALSE 3610287.597 3443171.46 3605701.399 3436756.517 3733746.635 3675273.603 3793008.743 3296255.88 3713216.336 3902478.491 0.92512684 0.882303764 0.923951639 0.880659951 0.956762899 0.941779336 0.971948661 0.844657027 0.951502063 1 21.89595925 3.241011722 24.99994123 0.932331583 0.903027288 0.162111609 0.04092065 160.0782978 1632693.994 0.01189864 0.015377694 1741.853885 -3.241011722 -0.029304295 RQAVDVSPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RQAVDVSPLR 10 1 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;; 197.73 4.97E-07 1504200000 910940 901230 779620 837910 729970 508908 918130 759230 777470 933190 FALSE TRUE 875339.4577 875527.8028 920514.6766 881154.6355 753450.148 519198.4684 929366.3496 743551.6352 689214.865 869984.2101 1.006155569 1.006372061 1.05808205 1.012839802 0.866050371 0.59679068 1.068256572 0.854672564 0.792215372 1 19.73062969 3.241093851 6.112108996 0.857228892 1.023399717 0.300884388 0.117815265 0.188045831 26.96121815 0.03319836 0.042602705 1742.18332 -3.241093851 0.166170825 LQAQEHGAER ddPTM_BT-474_Pertuzumab_2h_R1 1 LQAQEHGAER 10 0 Q9H5N1;B4DHR0;Q9H5N1-2 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 0 93.839 0.0085121 208190000 50173 42321 36773 40737 51803 53343 56700 50561 52777 51186 FALSE TRUE 48212.18369 41114.04652 43418.69911 42839.44145 53469.29054 54421.63201 57393.91156 49516.89768 46785.97622 47719.12663 1.010332483 0.86158422 0.909880423 0.897741524 1.120500192 1.140457419 1.202744384 1.037674014 0.980444939 1 15.54228002 3.241152513 24.99869159 1.090191912 0.915005731 0.543437496 0.071635024 49.53155302 477724.0383 0.020762843 0.026869804 1742.41866 -3.241152513 -0.175186182 DFLKGEVQFGSWFDHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFLKGEVQFGSWFDHIK 17 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 129.43 2.02E-05 226936000 332286 336243 243594 237282 309597 328156 285512 274235 355840 293154 FALSE TRUE 319299.8958 326653.6789 287616.8545 249528.1525 319555.4687 334791.5392 289006.1813 268571.9514 315446.535 273298.4185 1.168319588 1.19522711 1.052391214 0.913024502 1.169254731 1.225003573 1.057474767 0.982705838 1.154220126 1 18.06011759 3.24120679 0.014478939 4.59E-06 2.197836603 0.107605044 0.094093642 3771.284725 15.58185511 1116.207417 1248.815751 1742.636435 -3.24120679 2.197832008 LPAELQELPGLSHQYWSAPSDKEGYSGVGLLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPAELQELPGLSHQYWSAPSDKEGYSGVGLLSR 33 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 245.43 2.33E-47 746070000 491590 487430 411950 416500 527190 598190 449290 511730 525650 503700 FALSE TRUE 472378.1193 473528.9736 486398.5288 437995.6149 544147.5451 610285.8117 454788.5454 501162.5967 465980.4157 469583.9504 1.005950308 1.008401103 1.035807396 0.932731229 1.158786506 1.299630899 0.968492524 1.067248138 0.992326112 1 18.84102357 3.241223517 24.99533378 1.085451931 0.999491341 0.165776236 0.093344962 136.927205 1285249.919 0.027510218 0.035617945 1742.703556 -3.241223517 -0.08596059 TPDDFLNSVDEMDTGDTINQSTLPSQQNR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPDDFLNSVDEMDTGDTINQSTLPSQQNR 29 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8;P46937-4;H0YCI3 P46937-6 YAP1 Transcriptional coactivator YAP1 0 115.66 0.00018477 35466000 17835 17224 13656 12980 20150 17938 14512 22814 16115 18657 FALSE TRUE 17137.98848 16732.78838 16123.94298 13649.89936 20798.14305 18300.71865 14689.6022 22342.88293 14285.69276 17393.34477 0.985318736 0.962022463 0.927017959 0.784777139 1.195752934 1.052167877 0.84455304 1.284565058 0.821330972 1 14.08624777 3.24128453 24.99999764 1.051159978 0.919032124 0.137490534 0.140656159 127.8105948 1173031.076 0.038562048 0.04993641 1742.948399 -3.24128453 -0.132127854 QDGGQNESFKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDGGQNESFKR 11 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 88.101 0.021213 293870000 361720 385190 276920 333280 366850 379160 363400 380050 430930 409450 FALSE TRUE 347583.5825 374204.7583 326965.6041 350480.6207 378650.0634 386826.875 367847.3979 372201.8347 382012.633 381717.5868 0.910577858 0.980318359 0.85656416 0.918167339 0.991963893 1.013384996 0.963663742 0.975071224 1.000772944 1 18.54214613 3.241381381 24.5427162 0.987778599 0.916697529 0.583656503 0.030720786 43.84431682 381472.4011 0.008655124 0.01121413 1743.337134 -3.241381381 -0.07108107 HNAQGQGNGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNAQGQGNGLR 11 0 P35813;P35813-3;P35813-2;E9PL75;E9PJN3;E9PKB5;E9PP44 P35813 PPM1A Protein phosphatase 1A 0 ; 78.932 0.02853 148218000 29579 31401 25440 28755.3 23208.1 25757.4 26532.9 21703.1 31941 23980.7 FALSE TRUE 28423.01998 30505.47422 30037.57391 30239.36448 23954.60961 26278.23228 26857.61757 21254.9234 28315.19159 22356.46583 1.271355687 1.364503426 1.343574344 1.352600394 1.071484634 1.175419786 1.201335568 0.95072824 1.266532546 1 14.44840452 3.241414726 24.99617376 1.106852082 1.336012846 0.591995604 0.090274025 49.71626021 435408.7773 0.024914547 0.032297057 1743.470993 -3.241414726 0.229160764 ATAGDTHLGGEDFDNR ddPTM_BT-474_Pertuzumab_2h_R1 8 ATAGDTHLGGEDFDNR 16 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P17066;P48741 A0A0G2JIW1;Q53FA3;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;; 217.37 1.43E-14 82334410000 24343160 28003240 22789130 25852740 19658980 18610770 24205920 20268950 24996650 27869750 FALSE TRUE 23391802.39 27204615.01 26907632.73 27187003.01 20291328.95 18987092.52 24502159.29 19850389.1 22159135.09 25982107.01 0.90030429 1.047051919 1.035621658 1.046374068 0.780973188 0.730775703 0.943039734 0.764002284 0.852861359 1 24.63101509 3.241495755 24.9999692 0.830468076 1.012194977 0.453798091 0.086123464 59.6812924 508329.438 0.023012864 0.029853172 1743.796311 -3.241495755 0.181726901 SRFS(ph)GGFGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRFSGGFGAR 10 1 A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A2R8YFS5 1 S(0.002)RFS(0.998)GGFGAR;S(0.05)RFS(0.95)GGFGAR 112.08 0.00101 477070000 217856 207822 193480 217899 171421 203424 191375 200146 190992 209770 TRUE FALSE 209341.9467 201895.12 228446.1399 229144.7935 176934.9121 207537.3727 193717.1045 196012.9152 169311.3889 195562.0911 1.070462816 1.032383725 1.168151449 1.171723989 0.904750564 1.061235189 0.990565725 1.002305273 0.865767941 1 17.57726721 3.241546629 24.9995495 0.97848732 1.109192936 0.532326101 0.06399368 66.76275277 558947.3975 0.018240276 0.023673504 1744.000594 -3.241546629 0.130705616 RVS(ph)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK ddPTM_BT-474_Pertuzumab_2h_R1 6 RVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 33 2 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(0.984)GPDPKPGS(0.007)NCS(0.007)PAQS(0.001)VLSEVPSVPTNGMAK;RVS(0.999)GPDPKPGS(0.001)NCSPAQSVLSEVPSVPTNGMAK;RVS(0.991)GPDPKPGS(0.007)NCS(0.002)PAQSVLSEVPSVPTNGMAK;RVS(1)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK;RVS(0.998)GPDPKPGS(0.002)NCSPAQSVLSEVPSVPTNGMAK;RVS(0.997)GPDPKPGSNCS(0.001)PAQS(0.001)VLSEVPSVPTNGMAK 202.8 2.49E-27 12659420000 10327740 9916360 8897430 9179130 10691400 10716960 10110790 11322720 11705200 10644060 TRUE FALSE 9924120.503 9633555.122 10505393.52 9652865.999 11035298.59 10933664.27 10234528.87 11088901.88 10376474.77 9923128.335 1.000099985 0.970818354 1.058677583 0.972764402 1.112078592 1.101836427 1.031381287 1.117480446 1.045685838 1 23.24236358 3.241611728 24.99999024 1.075818057 1.002612635 0.377435062 0.041725157 73.22727749 599997.5306 0.011062747 0.014358143 1744.262034 -3.241611728 -0.073205422 KDS(ph)LESDSSTAIIPHELIR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDSLESDSSTAIIPHELIR 19 1 Q9UMX1-2;Q9UMX1-3;Q9UMX1 Q9UMX1-2 SUFU Suppressor of fused homolog 1 KDS(0.709)LES(0.155)DS(0.045)S(0.045)T(0.045)AIIPHELIR;KDS(0.888)LES(0.109)DS(0.002)STAIIPHELIR 121.84 2.10E-05 438750000 339380 310070 262150 291430 342550 329180 332320 369020 402320 348890 TRUE FALSE 326116.6544 301227.1072 309526.3365 306470.7372 353568.4318 335836.2451 336387.0316 361399.608 356650.3203 325259.3695 1.002635696 0.926113543 0.95162927 0.942234924 1.087035348 1.032518281 1.034211657 1.11111206 1.096510519 1 18.31123109 3.241750853 24.99905088 1.065717256 0.953255919 0.664048599 0.036298889 46.57623051 364974.0753 0.010263206 0.013334402 1744.820895 -3.241750853 -0.112461336 RT(ph)FSLTEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTFSLTEVR 9 1 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 RT(0.496)FS(0.496)LT(0.009)EVR 86.838 0.026824 93744000 112950 122940 94400 108860 92069 98084 82614 120300 91153 101320 TRUE FALSE 108535.7891 119433.8716 111460.1799 114478.2776 95030.483 100067.3257 83625.05484 117815.763 80805.69358 94457.50615 1.14904356 1.264419065 1.180003416 1.211955326 1.006065975 1.059389875 0.885319317 1.247288519 0.855471385 1 16.52737783 3.241889678 24.95117802 1.030281599 1.204334787 0.442827255 0.104082986 84.93129299 636550.666 0.028513824 0.037069956 1745.378724 -3.241889678 0.174053188 QAEMLDDLMEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QAEMLDDLMEK 11 0 F8W1A4;P54819-2;P54819;P54819-6;P54819-3;P54819-5;F8VZG5;A0A5F9ZHP2;F8VY04;A0A5K1VW67;P54819-4 F8W1A4 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 0 148.18 8.13E-05 80803000 137260 128510 123760 133000 116470 124200 115170 141290 139250 126360 FALSE TRUE 131895.7275 124845.0206 146126.185 139864.1459 120216.3633 126711.4091 116579.4849 138372.3121 123442.9238 117801.5247 1.119643637 1.059791212 1.24044392 1.187286382 1.020499214 1.075634712 0.989626282 1.174622421 1.047889016 1 16.84599869 3.24191895 24.9999909 1.064611142 1.151552186 0.350661464 0.065470406 117.6114251 875509.7282 0.019115 0.024887147 1745.496369 -3.24191895 0.086941045 EHAIEEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHAIEEWK 8 0 P45984-3;P45984-2;P45984-4;P45984;J3KNK1 P45984-3 MAPK9 Mitogen-activated protein kinase 9 0 101.64 0.0052489 154840000 345200 385260 292210 319820 371190 378080 409190 305630 422410 422850 FALSE TRUE 331709.2024 374272.762 345018.8472 336325.9485 383129.6635 385725.0366 414197.7896 299318.6337 374459.7877 394209.9929 0.841453054 0.949424847 0.875215883 0.853164442 0.971892317 0.97847605 1.050703425 0.759287281 0.949899278 1 18.58860482 3.241956159 24.99979334 0.935614747 0.884458247 0.154358751 0.076794712 245.1556153 1804949.227 0.023241949 0.030228753 1745.645924 -3.241956159 -0.0511565 GILAADESTGSIAK ddPTM_BT-474_Pertuzumab_2h_R1 4 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 240.21 5.06E-17 504160000 718630 709590 568257 656810 628313 577195 669780 720370 747370 665500 FALSE TRUE 690545.1451 689353.188 670953.6807 690708.0428 648523.2583 588866.2784 677976.968 705494.1078 662531.6908 620425.0922 1.11301937 1.111098175 1.081441884 1.113281928 1.045288571 0.949133563 1.092762005 1.13711408 1.067867337 1 19.24289751 3.242016872 24.99347569 1.059434473 1.103504585 0.222724963 0.048831719 194.056327 1403286.543 0.015570055 0.020252969 1745.889979 -3.242016872 0.044070112 SLDPADERDDVLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDPADERDDVLAK 14 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 ; 163.23 3.93E-06 790250000 1471690 1417430 1275630 1467210 1555860 1599310 1594450 1847700 1957360 1981310 FALSE TRUE 1414174.728 1377006.284 1506164.717 1542932.884 1605905.65 1631649.144 1613963.356 1809544.349 1735168.699 1847114.109 0.765613083 0.745490643 0.81541509 0.835320826 0.869413342 0.883350485 0.873775663 0.979660293 0.939394426 1 20.81684156 3.24204869 0.32155663 1.009506992 0.679923277 0.919967712 0.022721915 0.691221228 0.116616035 0.027284791 0.083257547 1746.017894 -3.24204869 -0.329583715 SKYNDDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKYNDDIR 8 1 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 ; 60.436 0.084181 1004320000 2143110 2310400 1989090 2317100 1822660 1537990 2303800 2235640 2327300 2549200 FALSE TRUE 2059354.892 2244509.654 2348562.81 2436685.809 1881287.514 1569089.212 2331994.594 2189473.253 2063114.661 2376540.413 0.866534766 0.944444135 0.988227592 1.025307962 0.791607626 0.660240913 0.981256023 0.921285933 0.868116801 1 21.1804315 3.242068452 24.9997486 0.868311897 0.95758678 0.154805122 0.098015174 182.7943502 1302732.863 0.029168936 0.037971813 1746.097345 -3.242068452 0.089274884 TEMQDNTYPEILR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEMQDNTYPEILR 13 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 176.97 3.68E-05 215970000 307700 296650 260290 289180 270770 278880 284620 294650 304520 336680 FALSE TRUE 295674.7438 288189.8325 307330.1931 304104.6145 279479.563 284519.1447 288103.2647 288565.3745 269952.1663 313876.3637 0.942010224 0.918163538 0.979144111 0.968867521 0.890412899 0.906468844 0.917887735 0.919360003 0.86005892 1 18.25983687 3.242347192 24.99967595 0.912012075 0.951561703 0.188523154 0.03646056 146.6134586 967961.0917 0.009694046 0.012639156 1747.218391 -3.242347192 0.039549627 FDWFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FDWFLK 6 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 101.52 0.084748 186520000 338970 345010 298250 305770 292560 244350 289530 309630 312880 309370 FALSE TRUE 325722.6776 335170.6526 352150.4095 321550.8263 301970.4581 249290.9244 293073.3547 303236.0323 277363.1741 288416.0943 1.129349867 1.162108007 1.220980439 1.11488517 1.046995865 0.864344707 1.016147713 1.05138388 0.961677172 1 18.13779215 3.24238347 2.874573701 0.988873853 1.168474682 0.723478885 0.051996722 0.145015378 2.460893721 0.016370431 0.021739909 1747.364345 -3.24238347 0.179600829 APEATVTLPVFIGNIAVNHAPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 APEATVTLPVFIGNIAVNHAPVSPR 25 0 Q5T370;Q8N5I2 Q5T370 ARRDC1 Arrestin domain-containing protein 1 1 APEATVTLPVFIGNIAVNHAPVS(1)PR;APEATVTLPVFIGNIAVNHAPVS(1)PR 195.92 5.70E-25 546150000 469650 457510 370700 463290 348030 348900 422150 431220 433520 476420 TRUE FALSE 451295.5588 444462.2627 437693.7362 487200.4524 359224.701 355954.9971 427316.398 422315.1563 384308.6271 444151.649 1.016084393 1.000699342 0.985460117 1.09692366 0.808788399 0.801426715 0.962095714 0.950835502 0.865264438 1 18.76069282 3.242589868 24.99999975 0.899404154 1.020261562 0.4711345 0.065696 101.5994114 630381.4381 0.019341246 0.025259935 1748.194975 -3.242589868 0.120857408 GYAVLGGER ddPTM_BT-474_Pertuzumab_2h_R1 3 GYAVLGGER 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 123.69 0.0012811 436590000 749080 954900 865200 792450 620390 535570 853160 495310 419670 643360 FALSE TRUE 719805.1254 927667.1869 1021560.886 833348.4395 640345.4078 546399.5923 863601.2273 485081.6754 372030.821 599784.6542 1.200105939 1.546667092 1.703212777 1.38941274 1.067625527 0.910992951 1.439852156 0.808759731 0.620273991 1 19.19408508 3.242658508 3.198627453 0.97469374 1.497328567 0.531316769 0.225733061 0.197716085 4.197047153 0.0688554 0.090700319 1748.471298 -3.242658508 0.522634827 DCDPTTGETDDEGYEDEYVLEDLEVTVADHIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DCDPTTGETDDEGYEDEYVLEDLEVTVADHIQK 33 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 271.13 1.04E-73 17919000 14838 16055 11371 13004 15243 15269 15007 12819 19427 17292 FALSE TRUE 14258.11456 15597.12712 13425.99265 13675.138 15733.30494 15577.74964 15190.66016 12554.28317 17221.7284 16120.79744 0.884454669 0.967515855 0.832836756 0.848291659 0.975963193 0.966313838 0.94230203 0.778763161 1.068292587 1 13.97663549 3.242835 24.99881878 0.932799054 0.885689252 0.134189612 0.077824998 324.0506094 1895204.199 0.022950218 0.030002855 1749.182001 -3.242835 -0.047109801 DFEQPLAISR ddPTM_BT-474_Pertuzumab_2h_R1 3 DFEQPLAISR 10 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 0 ;; 128.03 0.00079164 568448000 391257 443276 354944 397933 347215 308846 411386 391993 405069 389832 FALSE TRUE 375966.2439 430634.2025 419090.2765 418470.3698 358383.4858 315091.0777 416420.6649 383898.2076 359087.2653 363428.3314 1.034498996 1.184921937 1.153157969 1.15145225 0.986118733 0.866996463 1.145812335 1.056324382 0.988055235 1 18.47131137 3.242938939 24.99937313 1.016202149 1.136440973 0.392980309 0.074751642 124.9321177 713332.246 0.021926598 0.028697314 1749.600682 -3.242938939 0.120238824 QDREHLWK ddPTM_BT-474_Pertuzumab_2h_R1 1 QDREHLWK 8 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 62.262 0.048519 303860000 214360 303860 149720 240740 142870 193130 117640 206280 232330 188250 FALSE TRUE 205982.5742 295194.2103 176777.7345 253164.6203 147465.5433 197035.2209 119079.7135 202020.2459 205956.8724 175499.6598 1.173692157 1.682021553 1.007282491 1.442536245 0.840261135 1.122709988 0.678518201 1.151114744 1.173545707 1 17.42110871 3.243012642 24.99997423 0.996214699 1.328992974 0.364177084 0.214905956 119.7085665 672208.2477 0.057325154 0.075039152 1749.897626 -3.243012642 0.332778275 DKIIVNDR ddPTM_BT-474_Pertuzumab_2h_R1 5 DKIIVNDR 8 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;; 132.78 0.00086424 5220190000 6957680 7403430 5665490 6500270 6789640 6859580 6948260 7246120 7398680 7453240 FALSE TRUE 6685766.173 7192291.425 6689370.071 6835749.714 7008034.937 6998285.407 7033294.884 7096485.09 6558812.864 6948425.416 0.962198739 1.035096586 0.962717403 0.983783995 1.008578853 1.007175725 1.012214202 1.021308378 0.943927936 1 22.72825465 3.243051864 24.99056709 1.002653785 0.987800296 0.038617467 0.027364902 354.9747551 1975163.005 0.007429145 0.009759619 1750.05567 -3.243051864 -0.014853489 GLLEFEHQR ddPTM_BT-474_Pertuzumab_2h_R1 6 GLLEFEHQR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 250.08 3.15E-11 9338060000 4447690 5748270 4575310 4582430 4162380 2318350 5238790 3795400 4324410 4867660 FALSE TRUE 4273869.358 5584334.968 5402170.294 4818929.761 4296266.733 2365228.625 5302903.879 3717023.664 3833521.106 4537969.053 0.941802227 1.230580223 1.190437888 1.061913315 0.946737777 0.521208628 1.168563253 0.819094097 0.844765811 1 22.11361534 3.243150009 3.437704724 0.870068355 1.128331052 0.302621221 0.168352048 0.26685364 6.636633139 0.047832601 0.062732506 1750.451205 -3.243150009 0.258262697 ARQEFEER ddPTM_BT-474_Pertuzumab_2h_R1 2 ARQEFEER 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 148.14 0.00047968 556750000 518740 609620 441620 511410 435460 433050 491600 444030 490940 552840 FALSE TRUE 498467.0673 592234.2345 521430.5578 537803.9314 449466.9664 441806.5677 497616.3479 434860.6253 435210.5494 515395.6544 0.967154191 1.149086589 1.011709263 1.043477815 0.872081405 0.857218263 0.965503577 0.84374135 0.844420293 1 18.97532085 3.243454935 24.62842579 0.889260068 1.048220005 0.5482088 0.064484112 67.11088527 337701.6949 0.017046272 0.022365043 1751.680661 -3.243454935 0.158959936 IHEPIMLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IHEPIMLK 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 70.919 0.050085 146860000 505660 520430 446230 479520 429000 387760 553970 319850 551700 590250 FALSE TRUE 485898.2482 505587.846 526873.6873 504268.0847 442799.1746 395600.7729 560749.6506 313244.9857 489073.3289 550271.8418 0.883014923 0.918796507 0.957478917 0.916398126 0.804691683 0.718918801 1.01904115 0.569254979 0.888784946 1 19.06978498 3.243812301 6.797533053 0.803082752 0.922134619 0.070800973 0.125426287 0.250065716 55.70955695 0.034383253 0.044273517 1753.122649 -3.243812301 0.119051867 EAAGPAPS(ph)PMR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAAGPAPSPMR 11 0 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 EAAGPAPS(1)PMR;EAAGPAPS(1)PMR 163.93 2.45E-05 1388210000 665700 689040 741340 697240 643800 591190 726390 733450 627890 722890 TRUE FALSE 639683.708 669389.2538 875316.629 733224.64 664508.4117 603144.2669 735279.7781 718304.0012 556614.5595 673928.0164 0.949186994 0.993265212 1.298828076 1.087986583 0.986022833 0.894968383 1.091036075 1.065846772 0.825925835 1 19.36223498 3.243814545 12.81305583 0.990337117 1.091437595 0.167336927 0.11179265 0.685402582 1623.248276 0.032849333 0.042544685 1753.13171 -3.243814545 0.101100478 NYTEEEDRFLICMLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 NYTEEEDRFLICMLHK 16 1 O60264;A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 O60264 SMARCA5;SMARCA1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5;Probable global transcription activator SNF2L1 0 ; 189.81 5.76E-10 222488000 284330 274960 223920 269130 233980 255310 258380 255090 289770 289490 FALSE TRUE 273218.0693 267118.41 264387.3251 283019.8316 241506.1792 260472.5431 261542.1317 249822.3024 256876.5244 269882.5844 1.012359022 0.989757863 0.979638333 1.048677639 0.894856479 0.965132832 0.969095995 0.925670335 0.95180845 1 18.04197236 3.243922179 24.99994362 0.947847498 1.004335331 0.439537809 0.031046425 119.9582881 559339.19 0.008273652 0.010882615 1753.566253 -3.243922179 0.056487833 AAELEMELNEHSLVIDTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAELEMELNEHSLVIDTLK 19 0 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 ; 130 4.82E-06 15124000 94891 97407 85365 87929 102350 107480 101364 103253 102274 105242 FALSE TRUE 91182.55481 94629.04773 100792.3544 92467.02623 105642.1807 109653.3192 102604.523 101120.7895 90664.28429 98113.8656 0.929354422 0.964481902 1.027299799 0.942446062 1.076730389 1.117612873 1.045769855 1.030647288 0.924072084 1 16.58216941 3.243931586 24.99404384 1.038517425 0.970180589 0.268785406 0.053050216 184.9220074 860538.9209 0.015482416 0.020356822 1753.604236 -3.243931586 -0.068336837 AGVLAGHDNR ddPTM_BT-474_Pertuzumab_2h_R1 7 AGVLAGHDNR 10 0 P62879;E7EP32;P62879-2;Q9HAV0;P62873-2;P62873;B3KVK2 P62879;P62873-2 GNB2;GNB4;GNB1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2;Guanine nucleotide-binding protein subunit beta-4;Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 0 ;;;;;; 157.66 8.77E-06 8030660000 7076680 9890150 8381730 9392390 5082130 3144090 9011860 7113050 6909160 7904050 FALSE TRUE 6800115.522 9608092.605 9896495.062 9877132.373 5245601.327 3207665.654 9122149.838 6966163.032 6124861.122 7368701.653 0.922837678 1.30390577 1.343044613 1.34041692 0.711875928 0.435309476 1.237958906 0.945371839 0.831199499 1 22.81297901 3.24412979 24.99995497 0.870037465 1.241254701 0.392522649 0.22337249 148.99932 668851.8772 0.065521829 0.086295263 1754.404733 -3.24412979 0.371217236 LKPLEVELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKPLEVELR 9 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 101.95 0.0033407 1764290000 4220700 5545400 4063400 4692400 3798300 1697540 5123900 4825000 5020000 5111700 FALSE TRUE 4055750.378 5387250.622 4797746.77 4934575.326 3920475.769 1731865.422 5186607.821 4725362.064 4450150.646 4765480.006 0.851068596 1.130473869 1.006770937 1.035483376 0.822682241 0.363418883 1.088370492 0.991581553 0.933830514 1 22.18419011 3.244209354 24.92334779 0.867026341 1.014902533 0.10776551 0.195685182 321.8691582 1420139.783 0.057986441 0.07639016 1754.726173 -3.244209354 0.147876192 TFVDFFSQCLHEEYR ddPTM_BT-474_Pertuzumab_2h_R1 2 TFVDFFSQCLHEEYR 15 0 Q53GQ0;A0A1B0GV93 Q53GQ0 HSD17B12 Very-long-chain 3-oxoacyl-CoA reductase 0 ; 200.77 6.75E-09 372750000 367430 497110 306580 417230 303560 163665 436460 437170 428450 339880 FALSE TRUE 353070.4294 482932.9095 361985.8258 438763.2903 313324.2831 166974.4184 441801.528 428142.2867 379814.1522 316859.6249 1.114280273 1.524122582 1.142417012 1.384724515 0.988842561 0.526966534 1.394313107 1.351204928 1.198682705 1 18.27348431 3.244459154 24.98540234 1.108021728 1.297369476 0.142515963 0.250877983 354.3639765 1501027.138 0.076243578 0.100572407 1755.735756 -3.244459154 0.189347749 HPFFLDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPFFLDDR 8 0 A0A1B0GV06;A0A1B0GTP7;A0A1B0GUE3;A0A1B0GUG1;A0A1B0GUW4;E7EMM4;A0A1B0GW68;A0A1B0GUA4;A0A1B0GTM3;A0A1B0GTZ5;A0A1B0GUH5;Q13510-3;Q13510;Q13510-2 A0A1B0GV06 ASAH1 Acid ceramidase;Acid ceramidase subunit alpha;Acid ceramidase subunit beta 0 99.802 0.0065549 67829000 14498 16817 15448 15506 12152 9618.8 16752 12350 12274 18837 FALSE TRUE 13931.40213 16337.39563 18239.79724 16306.26652 12542.88012 9813.298726 16957.01599 12094.96818 10880.70698 17561.15321 0.793307932 0.930314509 1.038644616 0.928541897 0.714240117 0.558807193 0.965598089 0.688734278 0.619589548 1 14.10009997 3.244775833 24.73589203 0.744088526 0.931527623 0.242822998 0.141042719 164.875578 656181.9095 0.038234989 0.050495705 1757.016472 -3.244775833 0.187439097 GENLEHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GENLEHLR 8 0 C9JXZ5;Q9BV40;B8ZZT4 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 177.97 0.00025206 357360000 589180 933490 634990 852400 525420 344920 970400 729160 753410 756060 FALSE TRUE 566154.1942 906867.7792 749746.8183 896392.4662 542320.6115 351894.5187 982276.0455 714102.5912 667886.0554 704851.3828 0.803224918 1.286608498 1.063694896 1.271746765 0.76941129 0.499246405 1.393593131 1.013125048 0.947555856 1 19.42695957 3.244879089 24.99900439 0.954147451 1.116151999 0.10080244 0.243667716 403.2551458 1595466.065 0.070041054 0.092588229 1757.434264 -3.244879089 0.162004548 DWYPHSR ddPTM_BT-474_Pertuzumab_2h_R1 10 DWYPHSR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;; 157.58 0.0014664 83678530000 13626870 12860980 10695700 12289760 10339950 8339710 12522920 10526180 13734240 15403410 FALSE TRUE 13094316.86 12494197.44 12628650.91 12924035.99 10672543.88 8508344.65 12676179.24 10308810.7 12175186.65 14360123.32 0.911852674 0.870061988 0.879424963 0.899994777 0.74320698 0.592498021 0.882734706 0.717877589 0.847846943 1 23.7755648 3.244976956 24.98985924 0.775626669 0.88810646 0.144342827 0.102985233 228.4724033 889830.5865 0.027258939 0.036035965 1757.830339 -3.244976956 0.112479791 DCFGCLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DCFGCLR 7 0 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;;;;; 153.67 0.0040255 8281250000 4877340 5362300 3863970 4491530 4022060 3028190 4495110 4100380 4759390 4848350 FALSE TRUE 4686728.161 5209372.454 4562275.333 4723338.402 4151433.213 3089422.077 4550122.501 4015705.72 4219124 4519966.936 1.036894346 1.15252446 1.009360333 1.044994016 0.918465394 0.683505459 1.006671634 0.888436968 0.933441341 1 22.10788079 3.24511481 4.153865436 0.894339092 1.066830922 0.417456091 0.090265245 0.191663989 7.560511545 0.025767954 0.033530699 1758.388401 -3.24511481 0.17249183 AHPTLQAPS(ph)LEDVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHPTLQAPSLEDVTK 15 0 Q96PE2;H0YFZ8 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 AHPTLQAPS(1)LEDVTK;AHPTLQAPS(1)LEDVTK 208.87 1.72E-09 906470000 726320 774350 559730 711020 594920 657530 614910 732870 698330 728450 TRUE FALSE 697934.6114 752266.2962 660885.6621 747715.8274 614056.1421 670825.7071 622435.4525 717735.9784 619058.506 679111.4327 1.027717364 1.107721443 0.973162327 1.101020821 0.904205278 0.987799166 0.916543917 1.056875122 0.911571321 1 19.37328879 3.245202985 24.99980505 0.969808511 1.050696395 0.374369596 0.056278103 180.6655103 679964.667 0.01497523 0.0198212 1758.745443 -3.245202985 0.080887883 KLDVSIEMPEELDISQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 KLDVSIEMPEELDISQLR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 123.19 5.53E-05 1588840000 1795604 1744496 1391978 1591463 1844248 1783075 1793716 1928501 2100534 2039181 FALSE TRUE 1725429.811 1694744.682 1643539.389 1673598.596 1903569.912 1819129.998 1815668.033 1888676.78 1862090.186 1901065.455 0.907611995 0.891470979 0.864535929 0.880347698 1.001317397 0.956900244 0.955079179 0.9934833 0.979498198 1 20.85837677 3.245338469 24.99890751 0.978730103 0.884850459 0.870807198 0.017921017 53.83566586 198562.0117 0.005122522 0.00678352 1759.294194 -3.245338469 -0.093879643 DRLIEVER ddPTM_BT-474_Pertuzumab_2h_R1 3 DRLIEVER 8 1 Q3V6T2;A0A2U3TZV9;A0A2R8Y4X4;A0A2R8YG73;A0A2R8Y7B1;A0A2R8Y4W8;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;H7C2C6;A0A2R8Y820;A0A2R8Y885;A0A2R8YCU9;A0A2R8YGU1;A0A2R8YDS8;A0A2R8Y7D4;H0Y470 Q3V6T2 CCDC88A Girdin 0 ;; 81.548 0.02059 558040000 262956 347486 232870 266169 239622 198601 251858 225818 255792 276250 FALSE TRUE 252679.3888 337576.0395 274954.7892 279906.014 247329.6592 202616.8483 254940.3135 221154.7794 226755.5645 257539.3414 0.981129281 1.310774648 1.067622475 1.086847595 0.960356806 0.786741347 0.98990823 0.858722315 0.880469614 1 17.97443331 3.245380309 2.467849092 0.896645669 1.133463208 0.511648998 0.096288416 0.200321857 2.499294002 0.027466793 0.037099586 1759.463693 -3.245380309 0.236817539 VAELSSDDFHLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VAELSSDDFHLDR 13 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ;; 283.83 1.28E-32 1471340000 995780 1605960 1230560 1523160 919780 908550 1224200 1298190 1585360 1468340 FALSE TRUE 956863.8167 1560159.593 1452949.566 1601770.47 949365.559 926921.5035 1239182.126 1271381.923 1405396.579 1368888.024 0.6990081 1.139727696 1.061408633 1.170125271 0.693530473 0.677134643 0.905247255 0.928769849 1.026670228 1 20.38457301 3.245389327 24.99999861 0.865953975 1.029424637 0.163383897 0.160259809 276.8232096 1013446.724 0.045668588 0.060487099 1759.500225 -3.245389327 0.163470661 APHVAGGPPS(ph)PEVGSPLLCR ddPTM_BT-474_Pertuzumab_2h_R1 6 APHVAGGPPSPEVGSPLLCR 20 0 A0A087WXR4;Q8NG45;Q8NG42;P06401-5;P06401;Q8NG44 A0A087WXR4 PGR;PR Progesterone receptor 1 APHVAGGPPS(1)PEVGSPLLCR;APHVAGGPPS(1)PEVGSPLLCR;APHVAGGPPS(1)PEVGSPLLCR;APHVAGGPPS(1)PEVGSPLLCR;APHVAGGPPS(1)PEVGSPLLCR;APHVAGGPPS(1)PEVGSPLLCR 294.73 9.19E-55 15847800000 3154810 2855110 2945110 3091700 2578480 3269590 2652770 2258080 3380080 4214570 TRUE FALSE 3031516.537 2773685.058 3477356.891 3251263.008 2661419.151 3335703.35 2685235.393 2211449.859 2996387.489 3929113.42 0.77155231 0.705931533 0.885023291 0.82748006 0.677358698 0.848971 0.683420178 0.56283686 0.762611604 1 21.90577238 3.245410524 24.79260223 0.722126746 0.797208315 0 0.118926541 399.98289 1447690.027 0.033513112 0.044372824 1759.586106 -3.245410524 0.075081569 GAHVTINAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAHVTINAR 9 0 Q9UJU6-2;Q9UJU6-3;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 123.16 0.0017215 150620000 320050 355920 332550 328650 265400 239030 314890 241000 309540 329740 FALSE TRUE 307542.0922 345769.5101 392649.1825 345611.6659 273936.832 243863.3504 318743.718 236023.2658 274402.3169 307406.4161 1.000441357 1.124796009 1.27729664 1.124282539 0.891122689 0.793292975 1.036880499 0.767789003 0.892636921 1 18.22978775 3.245424428 5.744878657 0.881537058 1.143439539 0.571981211 0.098888184 0.106338159 11.80032564 0.027731992 0.035831385 1759.642439 -3.245424428 0.261902481 RS(ph)STSSEPTPTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.448)S(0.448)T(0.079)S(0.022)S(0.004)EPTPTVK;RS(0.314)S(0.314)T(0.052)S(0.124)S(0.195)EPTPTVK 144.68 2.54E-05 1016710000 1156460 1250500 1011898 1130590 1258200 1378670 1228130 1288700 1398990 1548410 TRUE FALSE 1111264.265 1214836.964 1194770.478 1188939.885 1298671.146 1406547.652 1243160.222 1262087.895 1240182.52 1443534.812 0.769821591 0.841570951 0.827670014 0.823630907 0.899646573 0.974377369 0.861191717 0.874303747 0.859128932 1 20.46117447 3.245504417 5.641725674 0.90292322 0.817738433 0.495706646 0.046877301 0.159527008 16.5411956 0.013328 0.017225533 1759.966563 -3.245504417 -0.085184788 LPESENLQEFWDNLIGGVDMVTDDDRR ddPTM_BT-474_Pertuzumab_2h_R1 3 LPESENLQEFWDNLIGGVDMVTDDDRR 27 1 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 166.59 1.39E-11 5447080000 193220 283729 171974 189014 300345 278805 270547 292349 292312 248824 FALSE TRUE 185668.7488 275637.3267 203053.5273 198769.0352 310005.8697 284442.6281 273858.0351 286311.891 259129.9672 231970.9289 0.800396626 1.18824082 0.875340407 0.856870454 1.336399657 1.226199462 1.180570499 1.234257639 1.117079491 1 17.82358449 3.245509397 24.99961996 1.198464529 0.944723283 0.484210293 0.126519391 133.7089451 481041.5249 0.033711823 0.044677645 1759.986744 -3.245509397 -0.253741246 S(ph)SSFSDTLEESSPIAAIFDTENLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.241)S(0.241)S(0.241)FS(0.241)DT(0.034)LEESSPIAAIFDTENLEK;S(0.286)S(0.286)S(0.213)FS(0.213)DT(0.003)LEESSPIAAIFDTENLEK;S(0.35)S(0.35)S(0.246)FS(0.053)DT(0.002)LEESSPIAAIFDTENLEK 298.97 2.62E-63 2240336000 933078 861663 728709 817687 930737 936756 892272 1033279 1005809 920408 TRUE FALSE 896612.2802 837089.2149 860402.9263 859887.9241 960675.0009 955697.8481 903191.8916 1011941.428 891633.779 858067.9463 1.044919909 0.9755512 1.002721206 1.002121018 1.119579172 1.113778754 1.052587846 1.179325521 1.039117919 1 19.71073237 3.246034734 24.98441154 1.097915545 1.003872292 0.348287456 0.049939103 149.4279639 499503.7228 0.013290521 0.017653836 1762.116972 -3.246034734 -0.094043253 ERPTPSLNNNCTTS(ph)EDSLVLYNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 ERPTPSLNNNCT(0.001)T(0.057)S(0.943)EDSLVLYNR 178.44 3.12E-17 283490000 73071 56596 44487 56447 74719 72177 80879 79346 79629 87000 TRUE FALSE 70215.30454 54981.93749 52526.79051 59360.23643 77122.40449 73636.46839 81868.8214 77707.47737 70589.84975 81107.41251 0.865707614 0.677890415 0.647620099 0.731871904 0.950867524 0.90788827 1.009387661 0.95808108 0.870325505 1 16.30754615 3.246555741 6.566072667 0.950766766 0.719989359 0.728937027 0.065209315 0.072151751 13.5359375 0.018367474 0.023758128 1764.232185 -3.246555741 -0.230777407 ATLLPEAGRS(ph)PEEAGFPGDPHEDKQ ddPTM_BT-474_Pertuzumab_2h_R1 2 ATLLPEAGRSPEEAGFPGDPHEDKQ 25 2 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 AT(0.027)LLPEAGRS(0.973)PEEAGFPGDPHEDKQ;AT(0.155)LLPEAGRS(0.845)PEEAGFPGDPHEDKQ 159.42 1.23E-11 1278770000 932850 908460 778280 809820 984270 973100 992750 964230 992960 955600 TRUE FALSE 896393.1907 882551.6103 918932.5087 851614.9072 1015929.938 992776.7487 1004899.571 944318.3135 880243.3436 890876.3608 1.006192588 0.990655549 1.031492752 0.955929402 1.140371418 1.114382189 1.127989938 1.059988069 0.988064542 1 19.7648657 3.246655915 24.99944769 1.079487536 0.998211373 0.345667242 0.050348637 196.5163224 606867.7955 0.014212505 0.018912162 1764.63917 -3.246655915 -0.081276162 ELWLVIHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELWLVIHGR 9 0 D6RFH4;H3BUX2;O43169;J3QR91 D6RFH4 CYB5B Cytochrome b5 type B 0 85.731 0.014617 382610000 69171 106630 87183 104710 51958 47035 90866 86572 84350 73650 FALSE TRUE 66467.72085 103589.0168 102938.9075 110114.0956 53629.27626 47986.07993 91978.04529 84784.25795 74774.94162 68661.6199 0.968047665 1.508688798 1.499220491 1.603721203 0.781066283 0.698877772 1.339584551 1.234812958 1.089035501 1 16.06721627 3.246677063 24.99997939 1.055700818 1.410495961 0.361846796 0.238797501 227.442957 700557.0336 0.071701477 0.095435519 1764.725101 -3.246677063 0.354795143 AKDEYER ddPTM_BT-474_Pertuzumab_2h_R1 2 AKDEYER 7 1 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 0 ; 73.233 0.045097 371910000 350580 354090 290940 330460 354270 365400 360540 381750 420410 403160 FALSE TRUE 336878.946 343991.6999 343519.3299 347515.0802 365665.4163 372788.6384 364952.3964 373866.7291 372686.8193 375853.6141 0.896303596 0.915227863 0.91397107 0.924602205 0.972893176 0.991845294 0.970996108 0.994713673 0.991574393 1 18.51981135 3.24669966 2.104453939 0.988792432 0.908718594 0.949525596 0.00854289 0.061901461 0.563236463 0.00263754 0.00364123 1764.816924 -3.24669966 -0.080073838 TCEEHQLCVVAVLPHILDTGAAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TCEEHQLCVVAVLPHILDTGAAGR 24 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 104.38 0.0017695 51408000 40972 48053 40390 54759 32026 50774 42140 40009 52608 59219 FALSE TRUE 39370.76894 46682.57549 47689.37147 57585.11855 33056.14538 51800.68507 42655.72193 39182.80017 46636.16039 55208.04438 0.713134642 0.845575604 0.863812004 1.043056663 0.598755956 0.938281471 0.772635988 0.709729906 0.844734874 1 15.75259088 3.246913866 24.99886605 0.793817029 0.864723077 0.033221053 0.129109087 557.2177188 1667582.796 0.034528155 0.045993696 1765.687596 -3.246913866 0.070906048 TLHPDLGTDK ddPTM_BT-474_Pertuzumab_2h_R1 8 TLHPDLGTDK 10 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;;;; 164.33 6.19E-06 7759410000 10844190 9743930 9847920 10317580 8953020 7576850 10487490 10740300 11710910 9818420 FALSE TRUE 10420387.07 9466042.657 11627658.21 10850071.54 9241002.019 7730059.098 10615839.04 10518509.05 10381536.59 9153409.668 1.138415896 1.034154812 1.270308948 1.185358455 1.009569369 0.844500506 1.15976881 1.149135615 1.134171524 1 23.12587782 3.247033657 24.99556428 1.061292281 1.156369871 0.203698485 0.102585317 380.1242978 1121363.33 0.031357288 0.041780267 1766.174692 -3.247033657 0.09507759 STMGKPQR ddPTM_BT-474_Pertuzumab_2h_R1 3 STMGKPQR 8 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;; 98.933 0.00654 3503220000 4616630 4573170 3593360 3933030 4742970 4523080 4512560 4922580 4749450 4888090 FALSE TRUE 4436206.996 4442747.669 4242760.086 4136014.15 4895531.938 4614539.777 4567786.059 4820927.003 4210312.347 4557015.31 0.973489596 0.974924894 0.931039243 0.907614714 1.074284725 1.012623277 1.002363553 1.057913278 0.92391885 1 22.11965779 3.247377471 24.99983395 1.01701195 0.947654969 0.36459475 0.041752908 195.5479054 554464.9329 0.011444261 0.015260064 1767.573456 -3.247377471 -0.069356981 SNS(ph)DNNLNASAPDWAVCSTATSHR ddPTM_BT-474_Pertuzumab_2h_R1 4 SNSDNNLNASAPDWAVCSTATSHR 24 0 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.166)NS(0.834)DNNLNASAPDWAVCSTATSHR;S(0.243)NS(0.757)DNNLNASAPDWAVCSTATSHR;S(0.321)NS(0.679)DNNLNASAPDWAVCSTATSHR;S(0.075)NS(0.925)DNNLNASAPDWAVCSTATSHR 296.34 3.63E-62 4542710000 656568 723910 542260 624160 508247 534760 468120 629320 627275 611530 TRUE FALSE 630908.5967 703264.7956 640258.4445 656372.9724 524595.2263 545573.2136 473848.9926 616324.3221 556069.3718 570110.5284 1.106642599 1.233558688 1.12304266 1.151308281 0.920164074 0.956960425 0.831152854 1.081061112 0.975371168 1 19.12088212 3.24764348 24.93700533 0.963657791 1.157161347 0.667957878 0.066575268 114.3286901 313887.5591 0.018865655 0.025186015 1768.65644 -3.24764348 0.193503557 TVSS(ph)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 T(0.004)VS(0.123)S(0.873)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR;T(0.002)VS(0.062)S(0.927)PIPY(0.001)T(0.003)PS(0.003)PS(0.001)S(0.001)S(0.001)RPISPGLSYASHTVGFTPPTSLTR 206.89 4.12E-31 2144700000 189272 211201 153507 185109 202413 225576 202415 207297 247940 228294 TRUE FALSE 181875.041 205177.7543 181249.1296 194662.4977 208923.798 230137.3013 204892.2153 203016.2445 219794.8906 212831.444 0.854549673 0.964038726 0.851608795 0.914632227 0.981639715 1.081312502 0.962697106 0.953882757 1.032718129 1 17.69935179 3.247693589 3.970665801 0.998583462 0.895866929 0.58044352 0.044434467 0.168611601 5.904546365 0.013089883 0.017096471 1768.860519 -3.247693589 -0.102716533 KQTDFEHR ddPTM_BT-474_Pertuzumab_2h_R1 3 KQTDFEHR 8 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;; 131.44 0.00065239 581427000 1085660 1153380 890030 941780 933360 731520 931120 862010 972380 843120 FALSE TRUE 1043231.207 1120486.732 1050878.22 990385.3787 963382.3721 746311.8356 942515.3251 844209.1923 861999.4989 786014.7314 1.327241291 1.425528921 1.336970132 1.260008673 1.225654347 0.949488357 1.199106438 1.074037367 1.09667092 1 19.58419683 3.247851032 1.634520566 1.080036126 1.369642439 0.763524706 0.071843134 0.169040772 0.935580828 0.022835757 0.033057324 1769.501895 -3.247851032 0.289606313 YSPTS(ph)PTYSPTTPK ddPTM_BT-474_Pertuzumab_2h_R1 3 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.133)S(0.864)PT(0.003)YSPTTPK;YSPT(0.016)S(0.983)PT(0.001)YSPTTPK;YSPT(0.015)S(0.985)PTYSPTTPK 300.33 8.32E-44 5271400000 6523100 6623900 5827700 6362000 5988200 6426700 6221500 6390200 7063500 7194000 TRUE FALSE 6268170.04 6434992.857 6880895.026 6690343.582 6180815.891 6556652.277 6297640.578 6258240.137 6261681.093 6706743.972 0.934607026 0.959480917 1.025966558 0.997554642 0.921582204 0.977620781 0.939001191 0.933126442 0.933639501 1 22.6771811 3.248067711 24.99997288 0.946993136 0.98130535 0.160061222 0.031214864 317.9488371 836077.3053 0.008773327 0.01172879 1770.384957 -3.248067711 0.034312213 GYTS(ph)DSEVYTDHGRPGK ddPTM_BT-474_Pertuzumab_2h_R1 4 GYTSDSEVYTDHGRPGK 17 1 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GYT(0.088)S(0.906)DS(0.006)EVYTDHGRPGK;GYT(0.001)S(0.993)DS(0.006)EVYTDHGRPGK;GYT(0.119)S(0.675)DS(0.206)EVYTDHGRPGK;GYT(0.119)S(0.88)DS(0.001)EVYTDHGRPGK 278.46 4.77E-36 6146820000 1695334 1663714 1387922 1521369 1704924 1641722 1724996 1695989 1936870 1913520 TRUE FALSE 1629078.473 1616266.506 1638750.38 1599887.036 1759764.429 1674918.744 1746107.017 1660966.234 1717004.638 1783915.586 0.913203789 0.906021853 0.918625518 0.896840102 0.986461715 0.938900224 0.978805853 0.931078941 0.962492088 1 20.76661592 3.248126421 24.99949098 0.960364675 0.909194362 0.649639116 0.020451682 130.7568085 341720.4578 0.00537449 0.00718638 1770.624304 -3.248126421 -0.051170313 ASSRS(ph)PVFTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 ASS(0.001)RS(0.999)PVFTPR;AS(0.081)S(0.064)RS(0.855)PVFTPR 112.68 0.00090421 1429060000 278810 350570 227190 296160 305230 346960 331690 316630 375020 347050 TRUE FALSE 267913.797 340572.0868 268248.2868 311444.8531 315048.0002 353975.7689 335749.3214 310091.4799 332449.3018 323543.9944 0.828059867 1.052629914 0.829093698 0.96260434 0.973740838 1.094057609 1.037723856 0.958421375 1.027524255 1 18.30360237 3.248391578 2.753431038 1.017152056 0.916920123 0.352236579 0.067726079 0.318510225 4.949562793 0.019575824 0.026190687 1771.705683 -3.248391578 -0.100231932 GSLAS(ph)LDSLRK ddPTM_BT-474_Pertuzumab_2h_R1 6 GSLASLDSLRK 11 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GS(0.001)LAS(0.932)LDS(0.068)LRK;GS(0.007)LAS(0.985)LDS(0.008)LRK;GSLAS(1)LDSLRK;GSLAS(1)LDSLRK;GSLAS(1)LDSLRK;GSLAS(1)LDSLRK 194.86 2.00E-07 4356580000 3465880 4254890 3415950 3832960 3261960 3753200 3292000 4021860 3919480 3344320 TRUE FALSE 3330429.578 4133544.703 4033288.152 4030779.525 3366883.906 3829092.276 3332288.481 3938807.186 3474557.062 3117806.228 1.068196461 1.325786275 1.293630155 1.292825542 1.079888762 1.228136708 1.068792682 1.263326486 1.114423671 1 21.57209984 3.248447815 24.99944379 1.1478794 1.254337986 0.242766451 0.098190132 309.7965646 783305.4939 0.026039734 0.034839134 1771.935114 -3.248447815 0.106458586 ISQMPVILTPLHFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ISQMPVILTPLHFDR 15 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 66.965 0.057007 95359000 96243 104960 102500 100370 87248 84687 103040 88816 105220 108130 FALSE TRUE 92481.71716 101966.6436 121024.0301 105550.1077 90054.41116 86399.42916 104301.0343 86981.91856 93275.86672 100806.2588 0.917420389 1.011511039 1.200560675 1.047059072 0.893341467 0.857083977 1.03466824 0.862862283 0.925298368 1 16.62122569 3.248604503 23.46586354 0.922091142 1.052980469 0.31133565 0.08320183 107.9799745 252273.6376 0.023404341 0.0312763 1772.574523 -3.248604503 0.130889328 LRPGFMEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LRPGFMEDR 9 1 Q5BKZ1 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 ;; 169.76 5.31E-05 574990000 731180 826500 639530 681300 655320 391590 741440 685520 643940 790370 FALSE TRUE 702604.6772 802929.0292 755107.2973 716461.9746 676398.9629 399508.2181 750513.9645 671363.7724 570842.6308 736837.5359 0.953540832 1.089696154 1.02479483 0.972347281 0.917975714 0.542193087 1.018560982 0.911142199 0.774719803 1 19.49098703 3.249351731 3.2376485 0.853909988 1.022844611 0.25308249 0.129256544 0.338482112 7.368541269 0.038282192 0.050591467 1775.626964 -3.249351731 0.168934622 QPS(ph)EEEIIK ddPTM_BT-474_Pertuzumab_2h_R1 9 QPSEEEIIK 9 0 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK 141.13 0.00011271 30447290000 5760530 5296600 3324934 4539180 6439940 4912600 6231450 7254260 6871190 5726810 TRUE FALSE 5535402.119 5145546.154 3925823.537 4773447.624 6647086.519 5011936.138 6307712.349 7104456.996 6091201.318 5338928.058 1.036800283 0.963778889 0.735320554 0.894083526 1.24502268 0.938753264 1.181456705 1.330689779 1.140903427 1 22.34811868 3.249385503 24.83292445 1.161279104 0.899217717 0.437467863 0.127298762 175.040867 401551.3722 0.037399928 0.05013684 1775.765046 -3.249385503 -0.262061387 GRLPLLLVANAGTAAVGHTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 GRLPLLLVANAGTAAVGHTDK 21 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;H3BNL6;Q6P474;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 0 ; 269.9 3.38E-38 1855060000 723070 794980 658450 730840 818550 870700 896020 835930 939610 944820 FALSE TRUE 694811.625 772307.9488 777446.5621 768558.74 844879.4041 888306.1506 906985.7608 818667.7534 832949.412 880826.4998 0.788817804 0.876799175 0.88263303 0.872542709 0.959189357 1.008491628 1.02969854 0.929431339 0.945645269 1 19.74849835 3.249564482 2.8567551 0.979110272 0.854452488 0.740706392 0.036150599 0.147972293 2.478263155 0.01153259 0.015389112 1776.497015 -3.249564482 -0.124657785 IASEASR ddPTM_BT-474_Pertuzumab_2h_R1 3 IASEASR 7 0 Q99880;Q96A08 Q99880 HIST1H2BL;HIST1H2BA Histone H2B type 1-L;Histone H2B type 1-A 0 ;; 96.51 0.029496 594060000 769500 782190 572350 678910 530250 349605 730370 613150 659270 705390 FALSE TRUE 739427.0893 759882.707 675786.3769 713948.6265 547305.9728 356674.2526 739308.4865 600488.2382 584432.4335 657613.307 1.124410168 1.155516014 1.027634888 1.085666331 0.832261098 0.542376878 1.124229815 0.913132736 0.888717469 1 19.32687997 3.249809416 22.87230975 0.882441259 1.097345453 0.355841515 0.141611172 91.18866233 185411.4397 0.040664499 0.054457744 1777.499207 -3.249809416 0.214904194 FKVASFR ddPTM_BT-474_Pertuzumab_2h_R1 3 FKVASFR 7 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ;; 87.181 0.029721 378070000 1813720 2336480 1467180 1777690 2573680 2075480 2488990 2455300 2835590 2793760 FALSE TRUE 1742837.817 2269845.878 1732332.063 1869436.794 2656464.755 2117447.628 2519451.004 2404597.197 2513705.711 2604536.147 0.669154782 0.871497169 0.665121145 0.717761893 1.019937757 0.812984542 0.96733194 0.923234335 0.965126061 1 21.31259503 3.249851406 24.99998979 0.938086918 0.736230184 0.666976392 0.074956156 132.1124979 292520.916 0.019650237 0.026371503 1777.671076 -3.249851406 -0.201856734 VHLVGIDIFTGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHLVGIDIFTGKK 13 1 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 165.7 2.26E-05 825840000 1560000 1837700 1393100 1635300 1291600 1251200 1951300 1177300 1760100 1569400 FALSE TRUE 1499033.475 1785290.595 1644864.159 1719698.029 1333145.487 1276500.121 1975180.593 1152988.344 1560300.827 1463103.14 1.024557623 1.2202083 1.124229806 1.17537717 0.911176697 0.87246079 1.349994091 0.788043106 1.06643256 1 20.48060004 3.249944811 24.96849207 0.992358243 1.14125408 0.172890578 0.14746708 357.8564159 784867.1376 0.03962997 0.053190725 1778.053446 -3.249944811 0.148895837 KDEEHILSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEEHILSGR 10 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-3;Q8IXQ4-2 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 0 ; 96.103 0.0045238 668210000 761650 804410 600490 700670 753170 760960 762100 771190 830120 841630 FALSE TRUE 731883.876 781469.0144 709011.9008 736831.6627 777396.3971 776347.1326 771426.8078 755264.657 735888.2577 784625.6505 0.932780971 0.995976889 0.903630796 0.939086891 0.990786366 0.989449086 0.983178166 0.962579616 0.937884528 1 19.58164497 3.250518318 24.88629447 0.97555903 0.943859588 0.283258182 0.026735997 309.6080478 644350.3545 0.007470372 0.010034976 1780.403004 -3.250518318 -0.031699443 QSDDEVYAPGLDIESSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSDDEVYAPGLDIESSLK 18 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 171.67 2.95E-11 23383000 66584 63107 51541 56827 65222 64863 59727 68758 70438 66840 FALSE TRUE 63981.82367 61307.25015 60855.60522 59759.84828 67319.92486 66174.5743 60457.95689 67338.12327 62442.17354 62312.86727 1.026783496 0.983861806 0.976613786 0.959029024 1.08035351 1.061972867 0.970232306 1.080645559 1.002075114 1 15.92724248 3.250727433 24.99983531 1.036580609 0.985667141 0.26319123 0.037307902 278.521965 572291.7454 0.010087868 0.013555048 1781.260482 -3.250727433 -0.050913468 VWFGDVEAETMYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VWFGDVEAETMYR 13 0 H0Y8R3;Q5QPV1;Q06330-3;Q06330-2;Q06330-5;Q06330-4;Q06330-6;Q06330-7;Q06330;Q9UBG7 H0Y8R3 RBPJ;RBPJL Recombining binding protein suppressor of hairless;Recombining binding protein suppressor of hairless-like protein 0 108.37 0.0028415 49756000 39910 40865 35738 35543 32691 30648 28446 35826 30170 37631 FALSE TRUE 38350.27308 39699.57021 42196.65159 37377.37849 33742.5357 31267.72356 28794.13066 35086.18058 26745.22808 35082.21885 1.093154149 1.131615146 1.202793123 1.065422305 0.961813044 0.891269839 0.820761389 1.000112927 0.76235851 1 15.09845238 3.250820013 2.318563459 0.898944262 1.141368008 0.695024445 0.072591668 0.157683133 1.737746469 0.02138063 0.029199156 1781.64024 -3.250820013 0.242423745 YSDVHNCSYNYK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSDVHNCSYNYK 12 0 H3BM82;Q6FIF0-2;Q6FIF0 H3BM82 ZFAND6 AN1-type zinc finger protein 6 0 142.83 6.17E-05 344340000 194490 212760 156650 197230 163080 153150 204070 181200 216250 231290 FALSE TRUE 186889.1158 206692.2931 184960.1397 207409.0639 168325.6163 156246.7979 206567.4697 177458.1567 191702.2066 215624.5223 0.866734051 0.958575077 0.857788055 0.961899239 0.780642269 0.724624436 0.957996185 0.822996173 0.889055681 1 17.71816173 3.25108898 24.99990813 0.852047871 0.910810867 0.070487095 0.081430702 525.9955964 1049598.961 0.021779754 0.029290952 1782.743988 -3.25108898 0.058762996 TVQS(ph)LEIDLDSMR ddPTM_BT-474_Pertuzumab_2h_R1 8 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.049)VQS(0.951)LEIDLDSMR 304.03 3.60E-41 732354000 667979 636812 529195 531852 508998 530291 456277 493083 512198 487243 TRUE FALSE 641873.6422 618650.7453 624832.3084 559300.9455 525370.3829 541013.8474 461861.0544 482900.6637 454055.4303 454241.5976 1.413066627 1.361942078 1.375550614 1.231285176 1.156588004 1.191026648 1.016774018 1.063092122 0.999590158 1 18.7931003 3.251093525 0.55431548 0.994504952 1.458197901 0.942700303 0.03663376 0.226022897 0.140161608 0.026469581 0.055273681 1782.762641 -3.251093525 0.463692949 WGDEHIPGSPYR ddPTM_BT-474_Pertuzumab_2h_R1 4 WGDEHIPGSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 110.98 0.0014316 4326400000 4745470 5319800 4055870 4629120 3782890 2643750 5136540 4125720 4858800 5523060 FALSE TRUE 4560011.786 5168084.513 4788855.931 4868029.438 3904570.092 2697208.436 5199402.513 4040522.44 4307249.394 5148978.227 0.88561489 1.003710695 0.930059464 0.945436011 0.758319402 0.523833723 1.009793067 0.784723155 0.836525074 1 22.29585474 3.251283949 24.38682939 0.806359753 0.944873873 0.170790776 0.130223566 272.7045455 522688.8266 0.035647369 0.047932513 1783.544497 -3.251283949 0.13851412 MPEMHFK ddPTM_BT-474_Pertuzumab_2h_R1 2 MPEMHFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 92.925 0.015312 1775470000 4416600 4620000 4427100 4643900 3508200 2590100 4828600 4326200 4822100 4779500 FALSE TRUE 4243994.389 4488242.123 5227175.45 4883572.236 3621044.439 2642473.597 4887693.851 4236862.458 4274715.424 4455780.208 0.95246942 1.007285349 1.173122373 1.096008332 0.812662266 0.593043973 1.096933337 0.950868818 0.959364067 1 22.08724664 3.251299219 24.87568316 0.90246515 1.061933181 0.237307302 0.13609197 338.8275054 661651.2568 0.04025235 0.054143136 1783.607207 -3.251299219 0.159468031 KVLVTVEEDDTIMEELVDNHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVLVTVEEDDTIMEELVDNHGK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 282.03 6.52E-46 113319000 175450 162176 142302 155915 171371 166298 167751 180120 196875 186063 FALSE TRUE 168593.22 157550.8993 168019.1369 163961.7918 176883.3039 169660.6595 169803.9869 176400.4591 174526.5754 173460.7873 0.971938515 0.908279628 0.968628931 0.94523837 1.01973078 0.978092295 0.978918576 1.016947183 1.006144259 1 17.40425004 3.251320178 24.99680287 0.999469881 0.94708319 0.599869503 0.020570059 151.1421636 296095.4696 0.00557582 0.007501509 1783.693288 -3.251320178 -0.052386691 VFGGTVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFGGTVHK 8 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 63.565 0.072507 291240000 637730 686300 606060 624040 598560 534180 629560 603140 738610 686420 FALSE TRUE 612806.8066 666727.396 715588.5237 656246.7792 617813.226 544981.4856 637264.7436 590684.9482 654766.0893 639928.162 0.957618125 1.041878504 1.118232586 1.025500702 0.965441533 0.851629164 0.995837942 0.923048841 1.023186864 1 19.28755043 3.251331147 4.291927971 0.950652517 1.043741319 0.287253269 0.057823462 0.223027124 9.546880794 0.016462175 0.021505178 1783.73834 -3.251331147 0.093088802 LVEGILHAPDAGWGNLVYVVNYPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEGILHAPDAGWGNLVYVVNYPK 24 0 Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;K7EJM5;A0A087WX29;A0A1W2PNU8;K7EJ99;A0A0A0MSV7 Q13148 TARDBP;TDP43 TAR DNA-binding protein 43 0 ; 274.8 5.37E-52 954910000 563100 546140 437090 476560 566190 557750 539730 553890 603680 576760 FALSE TRUE 541093.4295 530564.6219 516081.886 501155.3187 584402.0156 569028.0871 546335.3772 542451.9779 535152.7772 537695.5315 1.006319372 0.986738016 0.959803189 0.93204293 1.086864185 1.058271929 1.016068286 1.008845985 0.995271015 1 19.03642996 3.251667486 24.99810647 1.027293351 0.971517993 0.435151273 0.031437775 241.4302184 460465.6789 0.009381056 0.012624833 1785.120289 -3.251667486 -0.055775358 MGLVMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 MGLVMDR 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 107.43 0.0174 658110000 690350 719640 574110 596070 583780 327850 638580 581800 548490 657740 FALSE TRUE 663370.3588 699116.5718 677864.448 626833.2441 602557.8139 334479.3516 646395.1331 569785.6267 486227.7147 613190.6839 1.08183372 1.140129148 1.105470885 1.022248479 0.982659766 0.545473636 1.054150283 0.929214422 0.792947002 1 19.22597625 3.251842658 2.710351283 0.875212327 1.103832337 0.383275305 0.13227378 0.286361912 4.309498995 0.039769131 0.053397786 1785.840459 -3.251842658 0.22862001 S(ph)QGRLSVGS(ph)NRDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQGRLSVGSNRDR 13 2 H3BLT5;H0Y781;Q2LD37-4;Q2LD37 H3BLT5 KIAA1109 Uncharacterized protein KIAA1109 2 S(0.513)QGRLS(0.513)VGS(0.975)NRDR 54.524 0.073298 392130000 20837 10891 14301 7439.6 27443 23200 12492 20273 23233 18088 TRUE FALSE 20022.667 10580.39934 16885.50882 7823.558648 28325.72902 23669.1199 12644.88083 19854.35547 20595.68724 16862.88365 1.187380962 0.627437131 1.001341714 0.46395141 1.679767803 1.403622322 0.749864679 1.177399778 1.221362115 1 14.04156365 3.251844621 24.99993043 1.189453217 0.819222474 0.294905897 0.291252279 314.5579572 591981.2225 0.08055257 0.108442723 1785.84853 -3.251844621 -0.370230743 DMLANFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DMLANFR 7 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 146.94 0.0050827 89261000 157780 163050 141310 152340 121720 99702 166230 136430 152570 155920 FALSE TRUE 151613.7832 158399.9736 166847.8604 160202.2857 125635.2343 101718.0428 168264.3725 133612.6728 135250.8932 145359.3995 1.043027033 1.089712631 1.147829868 1.102111636 0.864307604 0.699769283 1.157574763 0.919188393 0.93045853 1 17.14926484 3.251943254 24.89245884 0.929454465 1.098970488 0.358736824 0.109422958 251.3049923 467438.5648 0.031009125 0.041747624 1786.254163 -3.251943254 0.169516023 WNTEDK ddPTM_BT-474_Pertuzumab_2h_R1 8 WNTEDK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;; 160.03 0.020789 19411640000 13571710 13111540 9549750 11990840 9217500 8918960 10774780 11326330 13532380 10283710 FALSE TRUE 13041312.57 12737611.72 11275602.26 12609688.69 9513989.259 9099307.482 10906644.98 11092437.33 11996240.95 9587185.162 1.360285876 1.328608085 1.176111869 1.315264958 0.992365235 0.949111478 1.137627447 1.157006685 1.251278738 1 23.19267587 3.251975803 24.99803632 1.091374458 1.288966642 0.546330557 0.095127758 208.5295261 388574.3225 0.028476497 0.038340739 1786.388043 -3.251975803 0.197592184 KGDVEGSQSQDEGEGSGESER ddPTM_BT-474_Pertuzumab_2h_R1 5 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;;;; 211.92 1.97E-22 964610000 367911 366481 305941 338049 364375 382010 342187 382064 407663 402297 FALSE TRUE 353532.6314 356029.3207 361231.3443 355495.7494 376095.4528 389734.5039 346374.7869 374174.2449 361386.8053 375049.0659 0.942630348 0.949287315 0.963157563 0.947864644 1.00279 1.039156045 0.92354526 0.997667449 0.963572071 1 18.51671982 3.252072262 24.86642424 0.986310683 0.951518882 0.288960513 0.028407598 308.3317005 567440.9274 0.007845186 0.010564217 1786.784851 -3.252072262 -0.034791801 S(ph)EGSEYEEIPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEGSEYEEIPKR 12 1 P48634 P48634 PRRC2A Protein PRRC2A 1 S(0.999)EGS(0.001)EYEEIPKR 128.95 0.00014877 372970000 133640 116340 137330 152350 145670 148850 194640 201780 214470 202730 TRUE FALSE 128417.2011 113022.0971 162148.5859 160212.8018 150355.6078 151859.849 197022.0625 197613.1725 190124.2647 188998.9165 0.679459985 0.598003942 0.857933944 0.847691641 0.795536877 0.803495871 1.042450751 1.045578335 1.005954257 1 17.52801844 3.252188518 0.473076415 1.058058579 0.602131289 0.74526584 0.074313011 0.720122623 0.301886422 0.068218221 0.157338538 1787.263221 -3.252188518 -0.455927291 SS(ph)TPPRQS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.261)S(0.37)T(0.37)PPRQS(0.998)PS(0.002)R 86.378 0.0082594 462270000 326340 332760 323270 294120 294120 215120 301750 282230 294550 337570 TRUE FALSE 313586.272 323270.0106 381692.0801 309299.5684 303580.6369 219469.8738 305442.9068 276401.8519 261113.9189 314706.0832 0.996441724 1.027212462 1.212852565 0.982820431 0.964648137 0.697380462 0.970565626 0.878285698 0.82970725 1 18.26364554 3.252331405 2.71560259 0.875487066 1.073482482 0.436848563 0.096247594 0.232311137 3.509653192 0.027966038 0.037553816 1787.851344 -3.252331405 0.197995417 WGQPPS(ph)PTPVPRPPDADPNTPSPKPLEGRPER ddPTM_BT-474_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.947)PT(0.053)PVPRPPDADPNTPSPKPLEGRPER 160.62 4.13E-13 1359500000 197000 185140 151850 171710 193570 185100 195440 205910 193830 212760 TRUE FALSE 189301.0222 179859.9885 179292.6729 180571.9737 199796.3548 188842.8488 197831.8532 201657.8865 171827.231 198349.5757 0.954380777 0.906782824 0.903922644 0.910372372 1.007294087 0.952070848 0.997389848 1.016679193 0.866284843 1 17.59768579 3.252437189 24.99990136 0.977682276 0.916934364 0.2785979 0.042505385 278.5270241 501788.7423 0.01152797 0.01552953 1788.286875 -3.252437189 -0.060747912 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTR ddPTM_BT-474_Pertuzumab_2h_R1 12 INHTVILDDPFDDPPDLLIPDRSPEPTR 28 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.997)PEPT(0.003)R;INHTVILDDPFDDPPDLLIPDRS(0.994)PEPT(0.006)R;INHTVILDDPFDDPPDLLIPDRS(0.969)PEPT(0.031)R;INHTVILDDPFDDPPDLLIPDRS(0.943)PEPT(0.057)R;INHTVILDDPFDDPPDLLIPDRS(1)PEPTR;INHTVILDDPFDDPPDLLIPDRS(0.744)PEPT(0.256)R;INHTVILDDPFDDPPDLLIPDRS(0.999)PEPT(0.001)R;INHTVILDDPFDDPPDLLIPDRS(0.999)PEPT(0.001)R;INHTVILDDPFDDPPDLLIPDRS(0.994)PEPT(0.006)R;INHTVILDDPFDDPPDLLIPDRS(1)PEPTR;INHTVILDDPFDDPPDLLIPDRS(0.794)PEPT(0.206)R;INHTVILDDPFDDPPDLLIPDRS(0.932)PEPT(0.068)R 321.3 2.28E-83 10704368000 788662.4 868053.6 699952.3 793582.9 714359.2 804963 768626.2 746767 851322.5 904248.4 TRUE FALSE 757840.6015 843297.5612 826449.251 834539.8086 737337.2124 821239.9034 778032.8774 731346.0005 754683.9388 843002.8504 0.898977508 1.000349596 0.980363531 0.989960838 0.874655658 0.974184017 0.922930304 0.867548669 0.895232962 1 19.68517798 3.252456358 24.9814918 0.915050267 0.970690543 0.172406169 0.046415021 330.4119875 594004.5454 0.012687881 0.01709164 1788.36581 -3.252456358 0.055640276 WTPKS(ph)PLDPDSGLLSCTLPNGFGGQSGPEGER ddPTM_BT-474_Pertuzumab_2h_R1 2 WTPKSPLDPDSGLLSCTLPNGFGGQSGPEGER 32 1 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 WT(0.003)PKS(0.994)PLDPDS(0.003)GLLSCTLPNGFGGQSGPEGER;WT(0.001)PKS(0.998)PLDPDS(0.001)GLLSCTLPNGFGGQSGPEGER 165.61 3.13E-14 1109040000 669390 643800 512300 579570 677790 703290 628580 696740 723580 655260 TRUE FALSE 643229.4988 625439.4543 604884.0061 609481.6772 699591.7309 717511.0057 636272.7501 682352.0755 641442.2319 610878.6566 1.052957886 1.023835827 0.990186839 0.997713164 1.145222089 1.174555696 1.041569784 1.117001009 1.050032155 1 19.22052631 3.25300277 24.99953568 1.096116144 1.014864543 0.317830687 0.050766567 252.4987063 437075.5403 0.013838928 0.018652119 1790.617273 -3.25300277 -0.081251601 RHDAETNITTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RHDAETNITTEK 12 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;H7C0K6 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A;Kinesin-like protein 0 ; 62.258 0.051309 301490000 122579 123315 100638 108874 125749 123022 137850 98433 152392 145929 FALSE TRUE 117788.4772 119798.1769 118825.5253 114493.0002 129793.8308 125509.5891 139537.0495 96400.32415 135093.099 136045.0988 0.865804635 0.880576941 0.873427461 0.841581219 0.954050031 0.922558697 1.025667596 0.708590938 0.993002322 1 17.05372546 3.253226161 24.90883911 0.911097562 0.86701252 0.102222655 0.084614948 781.8623587 1327952.959 0.024324816 0.032797783 1791.538565 -3.253226161 -0.044085042 KVFAENK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVFAENK 7 1 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 69.825 0.094106 1906790000 1968790 2182840 1766720 1929310 1557780 1306190 2152000 1633610 1966780 2046250 FALSE TRUE 1891847.51 2120587.54 2086005.604 2028881.92 1607887.408 1332602.057 2178336.82 1599875.383 1743519.38 1907655.665 0.991713308 1.111619659 1.093491683 1.063547242 0.842860396 0.698554818 1.14189204 0.838660463 0.913959166 1 20.86336936 3.253379544 23.55268209 0.900719323 1.070444936 0.326509949 0.111686363 133.9490162 212891.1564 0.03044148 0.041012348 1792.171406 -3.253379544 0.169725613 LGDVYVNDAFGTAHR ddPTM_BT-474_Pertuzumab_2h_R1 12 LGDVYVNDAFGTAHR 15 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;;;;;; 267.37 4.62E-25 91522917000 24141200 27204860 17169397 23526010 17806870 18895881 18468983 17849268 20435906 17036629 FALSE TRUE 23197735.21 26429004.03 20272288.97 24740190.2 18379644.15 19277968.66 18695011.94 17480674.38 18116107.63 15882722.94 1.460564117 1.664009636 1.276373645 1.557679391 1.157209895 1.21376975 1.177065923 1.100609413 1.140617241 1 23.92095493 3.254378405 0.513733633 1.049965662 1.61507112 0.707205446 0.110494392 0.625202812 0.321579663 0.081475947 0.178554606 1796.298078 -3.254378405 0.565105457 DLLDQILMLDPAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLDQILMLDPAKR 14 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ; 141 1.57E-05 271940000 252964 236160 188088 214296 252467 233535 240006 260580 278360 263790 FALSE TRUE 243077.8872 229424.948 222079.6856 225355.8422 260587.8303 238257.2377 242943.2652 255198.9319 246761.7398 245923.2683 0.988429801 0.932912732 0.903044625 0.91636649 1.05963064 0.968827551 0.987882386 1.037717714 1.003409484 1 17.90784872 3.25465705 24.9999858 1.009879493 0.932729862 0.57469998 0.031321308 171.7545736 266757.015 0.008788286 0.011861921 1797.450958 -3.25465705 -0.077149631 DAVDFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAVDFLR 7 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 121.52 0.010307 208890000 637580 642230 560850 599790 592610 571740 637850 641070 640300 639770 FALSE TRUE 612662.6687 623914.2292 662208.071 630745.2338 611671.8388 583300.9745 645656.1991 627831.6805 567615.8284 596437.8081 1.027202938 1.046067538 1.110271787 1.057520542 1.025541692 0.977974512 1.082520575 1.052635618 0.951676471 1 19.18601219 3.254749536 5.289895516 1.022774164 1.063253759 0.222571548 0.03982418 0.32027845 25.42344679 0.011801264 0.015422767 1797.833779 -3.254749536 0.040479595 MDS(ph)FDEDLARPSGLLAQER ddPTM_BT-474_Pertuzumab_2h_R1 8 MDSFDEDLARPSGLLAQER 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER 271.94 1.48E-39 2002473000 1019937 834543 533144 719590 1026535 881898 817993 1171244 885414 1008028 TRUE FALSE 980076.7344 810742.6507 629494.9805 756728.1261 1059554.431 899730.5818 828003.843 1147057.402 784905.5147 939753.3657 1.042908459 0.862718539 0.669851265 0.805241198 1.12748139 0.957411396 0.881086329 1.220594088 0.83522501 1 19.84192265 3.254930125 24.99234104 1.017996404 0.833909108 0.243863773 0.134693924 309.069252 471872.2934 0.037768524 0.050990759 1798.581513 -3.254930125 -0.184087297 VVNSCHR ddPTM_BT-474_Pertuzumab_2h_R1 6 VVNSCHR 7 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 143.11 0.002444 398408000 342498 492761 400398 399015 295835 149882.3 443438 280382 296135 426617 FALSE TRUE 329112.7995 478707.9387 472758.8254 419608.212 305350.8014 152913.0228 448864.9269 274592.0137 262518.9963 397721.8506 0.827494891 1.20362494 1.188666966 1.055029316 0.767749624 0.38447227 1.128590059 0.69041219 0.660056761 1 18.6014003 3.255036699 5.521300572 0.757979761 1.09004233 0.321839437 0.210104891 0.186858766 17.07627069 0.058061883 0.075909394 1799.022932 -3.255036699 0.332062569 IGHPAPNFK ddPTM_BT-474_Pertuzumab_2h_R1 5 IGHPAPNFK 9 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;; 130.27 0.00036587 21737220000 6222650 5930900 5231660 5635380 5391470 4754400 6040320 5473620 6521130 6430560 FALSE TRUE 5979461.958 5761756.539 6177137.34 5926222.637 5564891.529 4850537.225 6114243.243 5360587.834 5780878.661 5995012.443 0.997406096 0.961091673 1.030379403 0.988525494 0.928253541 0.809095439 1.019888332 0.894174597 0.964281345 1 22.51533132 3.255193365 6.265093452 0.928130527 0.994991764 0.193718028 0.057130326 0.230219823 32.74619442 0.015471295 0.020253819 1799.672022 -3.255193365 0.066861236 KLNEQSPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLNEQSPTR 9 1 O75396 O75396 SEC22B Vesicle-trafficking protein SEC22b 0 ; 161.67 0.0001032 472380000 325000 448600 301240 367400 272040 168882 408000 369750 374910 325510 FALSE TRUE 312298.6407 435806.3672 355680.769 386361.558 280790.4137 172296.9098 412993.226 362114.5333 332351.7886 303462.9178 1.029116318 1.436110779 1.172073253 1.27317552 0.925287398 0.567769239 1.360934737 1.193274407 1.095197367 1 18.21116071 3.255400549 24.9820677 1.046352117 1.238543735 0.173823535 0.21384371 493.4360872 732008.7298 0.063168778 0.08530726 1800.530777 -3.255400549 0.192191618 DNLEDETEDDDLFETEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNLEDETEDDDLFETEFR 18 0 Q8IZH2-2;Q8IZH2;Q8IZH2-3 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 0 350.97 5.05E-90 156110000 185780 177320 150210 165920 199760 176920 187530 210330 223550 206720 FALSE TRUE 178519.5122 172263.0072 177356.2884 174483.1511 206185.4618 180497.4436 189825.0482 205986.612 198173.5412 192718.6703 0.926321835 0.893857388 0.92028597 0.905377517 1.069877981 0.936585144 0.984985253 1.068846167 1.028304839 1 17.55613682 3.255858753 24.99987769 1.015998935 0.910833638 0.646179264 0.037441664 156.755726 226547.5252 0.010866711 0.014678552 1802.431434 -3.255858753 -0.105165297 AVEVQGPSLESGDHGK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVEVQGPSLESGDHGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 216.26 1.53E-14 1210220000 1103050 1279230 947880 1142170 983930 1161270 1080300 1046990 1273700 1203320 FALSE TRUE 1059941.587 1242747.613 1119183.001 1201117.531 1015579.002 1184751.675 1093521.035 1025369.291 1129114.916 1121818.065 0.94484268 1.107797826 0.997651078 1.070688348 0.905297422 1.056099659 0.97477574 0.914024585 1.006504487 1 20.09740729 3.256195603 24.99943967 0.971519545 1.033456326 0.172444691 0.057391475 373.756115 529835.1756 0.015194396 0.020528742 1803.829991 -3.256195603 0.061936781 HIESMIR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIESMIR 7 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 143.85 0.0023936 1351260000 11749 21102 23372 18619 16343 15009.8 18629.6 14297 20512 17496 FALSE TRUE 11289.83609 20500.19162 27595.84031 19579.92882 16868.68744 15313.30844 18857.59462 14001.76195 18183.56375 16310.98034 0.692161713 1.256833814 1.691856635 1.20041398 1.034192126 0.938834339 1.15612883 0.858425531 1.114805081 1 13.99355587 3.256428448 4.600584805 1.004108114 1.251740787 0.128816843 0.238516536 0.341276092 17.5428324 0.069766047 0.091399023 1804.797366 -3.256428448 0.247632673 VVEHPEFLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VVEHPEFLK 9 0 P06396-2;Q5T0I0 P06396-2 GSN Gelsolin 0 ;;; 152.34 8.07E-05 4155060000 7284650 7882140 6029240 6908610 4937400 2355360 7734180 5606980 8179490 8012030 FALSE TRUE 6999957.824 7657349.085 7118857.788 7265164.19 5096215.955 2402986.993 7828833.208 5491193.904 7250988.586 7469368.072 0.937155293 1.025166923 0.953073636 0.972661157 0.682282076 0.321712221 1.048125241 0.735161777 0.970763325 1 22.83255476 3.25652067 23.99941338 0.772997224 0.974458122 0.162417828 0.195979453 256.7965876 343145.1153 0.054424739 0.073515145 1805.180651 -3.25652067 0.201460899 FEELCSDLFR ddPTM_BT-474_Pertuzumab_2h_R1 8 FEELCSDLFR 10 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P17066;P48741 A0A0G2JIW1;P17066 HSPA1B;HSPA1A;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;; 276.82 1.57E-23 3359872000 2335968 2448561 2243973 2481623 1641902 1141874 2523375 2100198 2529051 2978077 FALSE TRUE 2244675.788 2378730.438 2649508.838 2609699.86 1694715.269 1164963.475 2554256.818 2056828.177 2241963.733 2776369.192 0.808493263 0.856777422 0.954307102 0.939968599 0.610407029 0.419599626 0.919998978 0.740833814 0.807516428 1 21.40476799 3.256718749 24.92368258 0.733943169 0.892123142 0.160134258 0.154704855 402.9866267 553132.0973 0.043500639 0.058784786 1806.00417 -3.256718749 0.158179973 GTCADRDNLTR ddPTM_BT-474_Pertuzumab_2h_R1 5 GTCADRDNLTR 11 1 P55212;D6RBM3;D6RHU3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 ;;;; 155.97 2.85E-05 2029206000 1957915 2117917 1527471 1824743 1986397 2183172 1960517 1991580 2091343 2104512 FALSE TRUE 1881397.517 2057516.081 1803518.988 1918918.205 2050291.264 2227317.234 1984510.394 1950453.177 1853942.51 1961971.528 0.95893212 1.048698236 0.919238104 0.978056092 1.045015809 1.135244422 1.011487866 0.994129196 0.94493854 1 20.90387267 3.256832745 23.79509695 1.024102117 0.977336388 0.143617065 0.054316143 295.2203832 384449.7456 0.015959087 0.021559451 1806.478281 -3.256832745 -0.046765729 HPSHKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HPSHKPR 7 1 A6NFR6 A6NFR6 C5orf60 Putative uncharacterized protein C5orf60 0 ; 95.62 0.012159 415600000 470870 501210 410090 460080 397780 405420 454920 437430 502350 510470 FALSE TRUE 452467.8798 486915.9815 484202.3854 483824.7839 410574.955 413617.8702 460487.447 428396.9176 445325.334 475895.4122 0.950771678 1.023157545 1.01745546 1.016662005 0.86274199 0.869136074 0.967623211 0.900191316 0.935763032 1 18.86028502 3.256943285 24.9862894 0.917155271 1.004625247 0.441965721 0.043432817 201.886813 274408.9987 0.011681818 0.015787979 1806.938142 -3.256943285 0.087469975 ALTHNGT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALTHNGTPR 9 0 Q9HB90 Q9HB90 RRAGC Ras-related GTP-binding protein C 1 ALTHNGT(1)PR;ALTHNGT(1)PR 125.97 0.0017905 1228820000 870580 986520 826750 926430 810880 970570 813000 886860 1022700 1064310 TRUE FALSE 836556.7711 958385.4155 976162.116 974243.1633 836962.6916 990195.5904 822949.7372 868546.0311 906607.3835 992223.3357 0.843113381 0.965896871 0.983812899 0.981878906 0.843522483 0.997956362 0.8293997 0.87535336 0.913713023 1 19.92030536 3.25703313 24.99814771 0.900466984 0.948129696 0.047323856 0.06501292 557.310313 754181.9908 0.017483331 0.023631156 1807.311991 -3.25703313 0.047662712 ENFQNWLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENFQNWLK 8 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 126.41 0.0028389 696510000 674350 797210 581020 708630 547260 505940 586860 695070 805410 874260 FALSE TRUE 647995.6565 774474.3514 686023.2387 745202.4792 564863.1149 516170.4534 594042.1682 680716.5616 713983.2334 815045.5915 0.79504222 0.950222122 0.84169922 0.914307723 0.693044807 0.633302552 0.728845324 0.835188324 0.876004043 1 19.63652124 3.257039015 24.96825249 0.777895276 0.878266808 0.115574702 0.103677844 430.694566 581956.5695 0.028875203 0.03902654 1807.336483 -3.257039015 0.100371532 LYPPGDVDEIPEWVHQLVIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYPPGDVDEIPEWVHQLVIQK 21 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 0 160.55 2.11E-11 116630000 60798 63207 45178 56363 62731 65836 69874 67337 62587 70808 FALSE TRUE 58421.94694 61404.39825 53342.66958 59271.90118 64748.79959 67167.24903 70729.13891 65946.46742 55482.38615 66012.11109 0.885018612 0.930198978 0.808073984 0.897894344 0.980862428 1.017498879 1.071457006 0.999005581 0.840487984 1 16.01044312 3.257517885 3.977340041 0.994232037 0.876320031 0.408748881 0.061583651 0.206283754 7.181805073 0.018285379 0.024050502 1809.330421 -3.257517885 -0.117912006 T(ph)TPDQELVPASEPVWERPWSVEEIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPDQELVPASEPVWERPWSVEEIRR 26 2 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 T(0.5)T(0.5)PDQELVPASEPVWERPWSVEEIRR;T(0.5)T(0.5)PDQELVPASEPVWERPWSVEEIRR 145.26 1.09E-05 512430000 156113 147807 101430 125032 160043 148875 129754 164475 177911 163164 TRUE FALSE 150011.9314 143591.6891 119760.6573 131484.9165 165190.9284 151885.3545 131341.9683 161078.5338 157715.2891 152112.7569 0.986189024 0.943981898 0.787315014 0.864391121 1.085976822 0.99850504 0.863451369 1.05894165 1.036831442 1 17.21478162 3.257581304 24.99916046 1.003279795 0.891209125 0.35603377 0.073462686 288.3308823 378954.9189 0.021319759 0.028822519 1809.59465 -3.257581304 -0.11207067 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_BT-474_Pertuzumab_2h_R1 3 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPS(0.001)S(0.001)DEPPMEAS(0.391)QS(0.265)HLRNS(0.342)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.385)QS(0.385)HLRNS(0.23)PEDKR;DLPTIPGVT(0.003)S(0.003)PS(0.005)S(0.018)DEPPMEAS(0.324)QS(0.324)HLRNS(0.324)PEDKR 133.46 2.10E-08 2530400000 534689 519352 448993 484247 562279 565140 518566 551597 650631 586641 TRUE FALSE 513792.7628 504540.5895 530136.0229 509239.0457 580365.2147 576567.518 524912.3658 540206.3292 576774.0965 546907.2825 0.939451309 0.922534048 0.969334364 0.931125004 1.061176607 1.054232658 0.959783098 0.987747551 1.054610379 1 19.06093675 3.257693265 24.9999246 1.014360325 0.94137159 0.584125435 0.03246571 201.274953 262996.8212 0.009699446 0.013113181 1810.061226 -3.257693265 -0.072988735 VKDLESLFHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKDLESLFHR 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 183 1.03E-06 865880000 2171540 2721700 1991010 2405000 1905060 2041850 2372600 2330200 2350200 2353100 FALSE TRUE 2086673.816 2644079.781 2350829.797 2529122.338 1966337.985 2083137.606 2401636.589 2282080.556 2083415.149 2193722.441 0.951202293 1.205293674 1.071616788 1.152890763 0.896347664 0.949590325 1.09477687 1.040277709 0.949716842 1 21.06494957 3.257843693 24.99069717 0.999298972 1.101422922 0.295501008 0.079509021 324.4579339 420491.9198 0.021929018 0.029647588 1810.688289 -3.257843693 0.10212395 ERPPNPIEFLASYLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPPNPIEFLASYLLK 16 1 Q9C005 Q9C005 DPY30 Protein dpy-30 homolog 0 ; 220.64 1.03E-14 836320000 1219620 1244180 1010970 1176180 1254660 1354250 1330980 1341790 1469910 1491670 FALSE TRUE 1171955.902 1208697.205 1193674.768 1236882.791 1295017.278 1381633.863 1347268.931 1314081.568 1303051.979 1390637.862 0.842747011 0.869167479 0.858364928 0.889435578 0.931239767 0.993525274 0.968813642 0.944948792 0.937017476 1 20.40731534 3.258094913 2.128345443 0.963879083 0.858488574 0.862678129 0.019744032 0.11209118 1.042600014 0.00630107 0.008751925 1811.735997 -3.258094913 -0.105390509 SIS(ph)VGENLGLVAEPQAHAPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SISVGENLGLVAEPQAHAPIR 21 0 O60336-4;O60336-3;O60336-6;O60336 O60336-4 MAPKBP1 Mitogen-activated protein kinase-binding protein 1 1 S(0.172)IS(0.828)VGENLGLVAEPQAHAPIR 141.23 1.02E-07 43259000 30904 33262 21857 25597 36627 26388 34829 42399 26926 31169 TRUE FALSE 29696.23751 32313.40033 25807.04611 26918.06424 37805.14072 26921.58344 35255.24772 41523.44583 23869.47336 29057.89587 1.021967924 1.112035107 0.88812508 0.926359719 1.301028157 0.926480829 1.213276002 1.428990111 0.821445347 1 14.82664262 3.258124985 24.96078268 1.154206016 0.988973109 0.087001008 0.178113443 452.0810943 576774.3701 0.05026269 0.067960711 1811.86145 -3.258124985 -0.165232907 S(ph)SPQSTDTAMDLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPQSTDTAMDLLK 14 0 Q9UGU5 Q9UGU5 HMGXB4 HMG domain-containing protein 4 1 S(0.5)S(0.5)PQSTDTAMDLLK 74.769 0.033693 70427000 67255 69719 61607 70549 77660 69226 74183 88576 99789 91492 TRUE FALSE 64626.60025 67730.68238 72740.75534 74190.04234 80158.00443 70625.79715 75090.87374 86746.87465 88461.37107 85295.16535 0.757681868 0.794074108 0.852812173 0.869803605 0.939771957 0.828016416 0.880364947 1.017019831 1.037120577 1 16.38017635 3.258484367 0.317567631 1.038998529 0.703345021 0.735439969 0.047198385 1.599120342 0.260840571 0.062388452 0.194620548 1813.3614 -3.258484367 -0.335653508 GWWYAHFDGPWIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWWYAHFDGPWIAR 14 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6 Q9UM54-1 MYO6 Unconventional myosin-VI 0 96.059 0.0035218 111020000 222820 206910 184600 177180 168290 115520 194170 117740 185310 170670 FALSE TRUE 214111.9481 201009.1294 217961.3264 186324.281 173703.2007 117855.8935 196546.3105 115308.6279 164274.3857 159110.3689 1.345681929 1.263331427 1.369875062 1.171037955 1.091715153 0.74071787 1.235282854 0.724708444 1.032455564 1 17.27966833 3.258548744 2.050688497 0.936109045 1.317090749 0.565086863 0.142623309 0.210214003 1.816842416 0.041880305 0.058531407 1813.630221 -3.258548744 0.380981704 KLDGFPLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDGFPLLR 9 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ; 137.46 0.00026308 1762030000 1164560 1158350 1026430 1108440 1002340 915360 1174050 1137400 1245340 1170770 FALSE TRUE 1119047.708 1125314.992 1211928.734 1165646.721 1034581.176 933869.2064 1188418.375 1113912.293 1103974.224 1091472.705 1.025264033 1.031006077 1.110361009 1.067957738 0.947876362 0.855604727 1.088820975 1.020559 1.011453808 1 20.05784462 3.258813626 24.9176712 0.991508102 1.060366717 0.252156949 0.059840165 378.0328201 465098.0853 0.017920025 0.024233873 1814.736717 -3.258813626 0.068858615 LKTDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKTDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR 47 2 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 11.376 0.089769 460490000 122970 97680 86465 97584 107560 105420 118340 85632 138910 128410 FALSE TRUE 118164.1964 94894.26204 102091.1489 102620.3219 111019.7651 107551.6646 119788.2803 83863.66928 123141.5192 119712.6763 0.98706503 0.79268349 0.852801491 0.857221851 0.927385207 0.898415004 1.000631545 0.700541261 1.02864227 1 16.8692164 3.2590381 24.49344068 0.900798249 0.865342887 0.028699203 0.098633709 914.7039011 1094082.829 0.027188311 0.036768088 1815.674942 -3.2590381 -0.035455362 QTWPHWK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTWPHWK 7 0 E9PDF6;O43795;O43795-2 E9PDF6 MYO1B Unconventional myosin-Ib 0 72.547 0.051308 457270000 1021100 1039000 904170 971840 882730 926950 914540 1038900 1035000 992620 FALSE TRUE 981194.2831 1009368.737 1067573.632 1021996.779 911123.8121 945693.5641 925732.4141 1017446.352 917511.1391 925388.9633 1.060304717 1.090750784 1.153648546 1.104396983 0.984584697 1.021941693 1.000371142 1.09947967 0.991487013 1 19.81970037 3.259107241 24.72958874 1.025672289 1.105121649 0.547657093 0.037666896 183.9648249 221415.4706 0.011021746 0.0149056 1815.964027 -3.259107241 0.07944936 ILLDIDNDTESTAL ddPTM_BT-474_Pertuzumab_2h_R1 1 ILLDIDNDTESTAL 14 0 Q68EM7;Q68EM7-3;Q68EM7-7;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 0 77.64 0.056079 7427000 27327 30634 19908 27390 29304 32724 33758 33858 28249 33924 FALSE TRUE 26259.03063 29760.34831 23505.81845 28803.60118 30246.58977 33385.7017 34171.1405 33158.82047 25042.29195 31626.29726 0.83029102 0.941000082 0.743236499 0.910748449 0.956374675 1.05563106 1.080466051 1.048457244 0.791818648 1 14.94883704 3.259395351 2.65854658 1.008270892 0.847021044 0.362447675 0.088238006 0.274682612 3.97421393 0.026573606 0.035911755 1817.169132 -3.259395351 -0.161249849 KGNNESYHYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGNNESYHYAR 11 1 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ; 122.51 0.00025269 138400000 280560 403060 282830 303490 272550 231415 291790 278494 268270 278540 FALSE TRUE 269595.405 391565.1234 333943.6725 319153.1553 281316.8183 236094.3699 295361.0133 272743.0016 237817.1143 259674.2377 1.038206206 1.507909013 1.286010023 1.229052054 1.08334512 0.909194427 1.137429018 1.050327533 0.91582868 1 17.98634337 3.259474173 2.668777721 1.018600546 1.295920252 0.504556907 0.122616035 0.212565669 3.099262976 0.035438239 0.047875021 1817.49897 -3.259474173 0.277319706 TVEMHNK ddPTM_BT-474_Pertuzumab_2h_R1 4 TVEMHNK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 104.11 0.0082248 1777910000 3685760 3892170 3183340 3693580 3104960 2917500 3949600 3653340 3797970 3948950 FALSE TRUE 3541716.424 3781169.122 3758640.351 3884206.106 3204833.858 2976493.849 3997936.386 3577897.252 3366840.368 3681484.099 0.962034964 1.027077402 1.020957921 1.055065295 0.870527693 0.808503791 1.085957804 0.971862748 0.914533454 1 21.81185604 3.259477373 24.99927172 0.946420597 1.017388712 0.197693783 0.073059189 452.4554372 540761.675 0.021403326 0.028950761 1817.512359 -3.259477373 0.070968115 LQAYHTQTTPLIEYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQAYHTQTTPLIEYYR 16 0 F8W1A4;P54819-2;P54819;P54819-6;P54819-5;F8VY04;A0A5K1VW67 F8W1A4 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 0 174.95 3.69E-09 940050000 312410 342620 277960 303230 194640 286370 237970 224170 291940 246490 FALSE TRUE 300200.6718 332848.8131 328193.5552 318879.7366 200900.7724 292160.5976 240882.348 219540.8112 258800.1951 229795.0127 1.306384626 1.448459691 1.428201384 1.387670397 0.874260803 1.271396599 1.048248807 0.955376744 1.126221984 1 17.80998796 3.259487179 24.383877 1.048123973 1.399200939 0.725503117 0.104456516 90.67990698 105660.3699 0.028224132 0.038171069 1817.5534 -3.259487179 0.351076966 SQESGYYDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQESGYYDR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 143.04 0.00023938 3757908000 2268588 2466043 2108863 2335981 2157201 2339692 2308124 2404751 2566734 2511348 FALSE TRUE 2179929.073 2395713.868 2489981.456 2456541.259 2226589.329 2387002.175 2336371.512 2355092.051 2275369.117 2341252.163 0.93109538 1.023261785 1.063525533 1.049242494 0.951024996 1.019540831 0.997915367 1.005911319 0.97185991 1 21.1588489 3.259729541 24.99996349 0.994088585 1.020583044 0.096234045 0.037237636 589.0362236 695632.0026 0.010457228 0.014145534 1818.567983 -3.259729541 0.026494459 RLQGQLQGGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 RLQGQLQGGSR 11 1 Q9UP83-3;Q9UP83;Q9UP83-2;U3KQU7 Q9UP83-3 COG5 Conserved oligomeric Golgi complex subunit 5 1 RLQGQLQGGS(1)R 133.16 0.00010259 148900000 39210 48650 47763 47883 29231 50473 30213 40401 39540 40518 TRUE FALSE 37677.62985 47262.54963 56394.83658 50354.24737 30171.24166 51493.59864 30582.75573 39566.70523 35051.58497 37773.67977 0.997457226 1.251203217 1.49296645 1.333051153 0.798737159 1.363213723 0.80963136 1.047467588 0.927936732 1 15.20509371 3.259762123 24.99925373 1.001694941 1.28344322 0.34661129 0.185877075 265.9316238 313564.8605 0.050150988 0.067838562 1818.704421 -3.259762123 0.281748279 LAHYNK ddPTM_BT-474_Pertuzumab_2h_R1 8 LAHYNK 6 0 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;Q99880 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;HIST1H2BL Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type 1-L 0 ;;;;;;; 118.18 0.022086 52979360000 48251300 50856600 45126000 49497600 37443700 24233500 56510200 46233300 50722300 58298800 FALSE TRUE 46365585.85 49406219.56 53281272.02 52052177.07 38648110.62 24723517.97 57201788.73 45278566.2 44964517.15 54350170.35 0.853089982 0.909035229 0.980333119 0.957718747 0.711094563 0.454893109 1.052467515 0.833089683 0.82731143 1 25.69578122 3.259848626 24.98506105 0.806949409 0.927849999 0.109865903 0.155359936 544.3465672 638878.094 0.044335591 0.059973593 1819.066708 -3.259848626 0.120900591 LLEAS(ph)LEEQGLAVDVGETGPSPPIHSKPLTPAGHTGGPEPRPPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEASLEEQGLAVDVGETGPSPPIHSKPLTPAGHTGGPEPRPPAR 45 2 Q9NW68-9;Q9NW68-8;Q9NW68;Q9NW68-7;Q9NW68-4;Q9NW68-3;Q9NW68-2 Q9NW68-9 BSDC1 BSD domain-containing protein 1 1 LLEAS(1)LEEQGLAVDVGETGPSPPIHSKPLTPAGHTGGPEPRPPAR 147.12 1.44E-14 126430000 63707 73100 57045 62873 75374 64277 77861 78802 79239 70103 TRUE FALSE 61217.26001 71015.25957 67354.30046 66117.88306 77798.47316 65576.72498 78813.88621 77174.71116 70244.12092 65354.86137 0.936690228 1.086610209 1.030593579 1.011675056 1.190400707 1.003394753 1.205937624 1.180856474 1.074810954 1 15.99600693 3.259853166 24.99596418 1.124120183 1.022422173 0.247629606 0.076400532 302.0369474 354567.9038 0.020560619 0.027813793 1819.085725 -3.259853166 -0.10169801 KLPVDSVFNKFEDEDSDDVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLPVDSVFNKFEDEDSDDVPR 21 2 P49756 P49756 RBM25 RNA-binding protein 25 0 110.67 0.00015003 557810000 487670 482630 368300 458390 483170 530520 485090 530430 604200 562030 FALSE TRUE 468611.3173 468865.8649 434860.0028 482047.5628 498711.6019 541247.4779 491026.6765 519476.4351 535613.749 523963.2075 0.894359204 0.894845016 0.829943776 0.920002695 0.951806529 1.032987565 0.937139611 0.991436856 1.022235419 1 18.99910598 3.25995604 2.409434501 0.990626848 0.875586058 0.750867296 0.030719186 0.14015559 1.666468668 0.009179281 0.012547948 1819.516673 -3.25995604 -0.115040791 KEDLELIMTEMEISR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEDLELIMTEMEISR 15 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 ;;; 188.04 5.06E-07 370645000 766424 755337 667597 724108 769771 830622 834140 827724 1011428 1034990 FALSE TRUE 736471.3028 733795.5283 788246.6285 761479.3007 794531.3833 847417.7459 844348.4548 810631.2101 896614.9337 964889.2054 0.763270331 0.760497189 0.816929679 0.78918833 0.823443126 0.87825394 0.875072962 0.8401288 0.929241335 1 19.88000377 3.260366508 0.036957512 1.637556963 1.35E-11 0.898163303 0.022851178 71.31531232 0.749393956 14.21703557 18.97480487 1821.237183 -3.260366508 -1.637556963 ELAAQLNEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELAAQLNEEAKR 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 143.94 0.00010042 1660510000 1480430 1643640 1070060 1447430 1618290 1720290 1699670 1809560 1933230 1746870 FALSE TRUE 1422573.159 1596764.996 1263443.645 1522132.036 1670343.768 1755075.442 1720471.07 1772191.954 1713777.835 1628552.939 0.873519752 0.980480866 0.775807538 0.934653089 1.025661326 1.077690139 1.056441598 1.088200396 1.052331671 1 20.63515919 3.260667794 3.038824854 1.06144692 0.883216786 0.701802413 0.051655402 0.127395561 2.419323001 0.014628137 0.01955014 1822.501077 -3.260667794 -0.178230135 VFVGGLS(ph)PDTSEEQIK ddPTM_BT-474_Pertuzumab_2h_R1 5 VFVGGLSPDTSEEQIK 16 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 1 VFVGGLS(0.997)PDT(0.003)S(0.001)EEQIK;VFVGGLS(0.994)PDT(0.005)S(0.001)EEQIK;VFVGGLS(1)PDTSEEQIK;VFVGGLS(1)PDTSEEQIK;VFVGGLS(0.934)PDT(0.056)S(0.01)EEQIK 255.21 1.40E-26 697531000 738651 647533 754246 832303 782773 742647 932031 1040706 1149779 1077948 TRUE FALSE 709783.7023 629065.9928 890555.0303 875258.2576 807951.6044 757663.8312 943437.4742 1019215.057 1019260.908 1004937.622 0.706296278 0.625975164 0.886179412 0.870957797 0.803981846 0.753941155 0.938802025 1.014207285 1.014252911 1 19.93867452 3.261275993 0.33505342 1.050214657 0.601563384 0.66217496 0.075099121 1.674161979 0.306174175 0.093828819 0.282653784 1825.055151 -3.261275993 -0.448651273 FAVLHGEAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 FAVLHGEAPR 10 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 155.06 1.34E-05 1493390000 1488010 1556240 1346980 1364220 1266050 822900 1467960 1188360 1460120 1608000 FALSE TRUE 1429856.924 1511857.559 1590409.249 1434627.558 1306773.648 839539.6018 1485925.334 1163819.951 1294373.299 1499088.728 0.953817408 1.008517729 1.060917356 0.956999763 0.87171201 0.560033296 0.991219069 0.776351612 0.863440085 1 20.51565435 3.261336881 3.51988186 0.824147728 1.006249688 0.283629825 0.118177764 0.259516909 6.754005167 0.033004209 0.043728294 1825.311043 -3.261336881 0.18210196 LGHGEEELETEKDFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGHGEEELETEKDFSR 16 1 O60306 O60306 AQR Intron-binding protein aquarius 0 171.46 2.95E-09 147570000 161150 157950 133620 142520 175470 176540 177330 145960 196850 174900 FALSE TRUE 154852.0798 153445.4206 157768.1064 149875.4743 181114.1519 180109.7598 179500.2176 142945.875 174504.4133 163053.8672 0.949698909 0.941071949 0.967582732 0.919177673 1.110762688 1.104602809 1.100864522 0.876678839 1.070225541 1 17.31498913 3.261443846 24.9968734 1.033500023 0.945803446 0.345006773 0.066217712 344.4859501 376302.1556 0.020600612 0.027874641 1825.760662 -3.261443846 -0.087696576 FTFPDPPPLS(ph)PPVLGLHGVTFGYQGQKPLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTFPDPPPLSPPVLGLHGVTFGYQGQKPLFK 31 1 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 FTFPDPPPLS(1)PPVLGLHGVTFGYQGQKPLFK 220.24 3.88E-35 645080000 1484000 1492700 1234400 1365800 1507400 1583900 1396600 1544800 1633300 1638300 TRUE FALSE 1426003.639 1450129.658 1457483.539 1436289.102 1555886.89 1615927.543 1413692.009 1512899.34 1447894.631 1527336.482 0.933653885 0.949450023 0.954264863 0.940388132 1.018692939 1.058003631 0.925593034 0.990547504 0.947986674 1 20.5425865 3.261932222 24.97186139 0.988419699 0.945498952 0.298293429 0.034260653 328.5547862 351048.7326 0.009784447 0.013240299 1827.814935 -3.261932222 -0.042920747 SSS(ph)PPILTKPTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPPILTKPTLK 13 1 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ITI3 A0A3B3IS53 KAT6A Histone acetyltransferase KAT6A 1 S(0.039)S(0.039)S(0.922)PPILTKPTLK;S(0.084)S(0.111)S(0.805)PPILT(0.001)KPTLK 88.092 0.0048855 3127800000 3399600 3513900 2815400 3378100 3390000 3752500 3645800 3830700 4218400 4038700 TRUE FALSE 3266739.874 3413687.012 3324205.408 3552444.146 3499042.429 3828378.121 3690418.391 3751594.706 3739544.917 3765155.252 0.867624216 0.906652391 0.882886677 0.943505356 0.929322218 1.01679157 0.980150391 0.99639841 0.993198067 1 21.84427792 3.263102324 1.081323143 0.997298127 0.882394781 0.86903443 0.018274797 0.156953357 0.391524093 0.006844518 0.011266302 1832.746183 -3.263102324 -0.114903347 MGANNLER ddPTM_BT-474_Pertuzumab_2h_R1 2 MGANNLER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 123.72 0.003107 703500000 263530 267220 216375 242166 231860 190300 273520 248853 264060 273570 FALSE TRUE 253230.9563 259599.1472 255478.7757 254664.2163 239317.9875 194147.9964 276867.4196 243714.0986 234085.0158 255040.8602 0.992903474 1.017872771 1.001717041 0.998523202 0.938351554 0.761242713 1.085580637 0.955588443 0.917833384 1 17.96036887 3.263183805 7.163429663 0.943351371 1.00405973 0.128803827 0.076007504 0.388368119 74.7499376 0.021627432 0.028669368 1833.090072 -3.263183805 0.060708359 APS(ph)SDEECFFDLLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 APSSDEECFFDLLTK 15 0 A0A0A0MSK4;A0A0A0MRC4;Q86YR5-4;Q86YR5 A0A0A0MSK4 GPSM1 G-protein-signaling modulator 1 1 APS(0.879)S(0.121)DEECFFDLLTK;APS(0.873)S(0.127)DEECFFDLLTK 194.77 3.96E-08 141634000 196494 183764 137308 170248 201329 194224 189586 230606 222623 235493 TRUE FALSE 188814.7972 178523.2306 162122.61 179034.5197 207804.9301 198151.3424 191906.2102 225843.9055 197351.7704 219542.8494 0.860036197 0.81315894 0.738455434 0.81548782 0.946534723 0.902563408 0.874117334 1.028700803 0.898921422 1 17.74414302 3.263247692 5.582698235 0.942968985 0.800957074 0.622081715 0.051542161 0.115829708 10.27912148 0.014963373 0.019732584 1833.359746 -3.263247692 -0.142011911 (ac)MEVKPPPGRPQPDSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 63.062 0.00035143 7348240000 2324790 2354130 2024900 2228100 2330520 2353670 2315770 2666010 2824480 2656520 FALSE TRUE 2233934.637 2286992.517 2390844.474 2343092.508 2405483.292 2401262.82 2344111.086 2610955.962 2503856.872 2476591.534 0.902019815 0.923443566 0.965376987 0.946095662 0.97128786 0.969583715 0.946506945 1.05425377 1.011009219 1 21.23992451 3.264092862 0.418846971 1.023938284 0.895546247 0.629400998 0.025542855 1.140803504 0.351824995 0.025354514 0.06465544 1836.931079 -3.264092862 -0.128392037 LLQDFFNGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLQDFFNGR 9 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 265.82 4.15E-15 4483200000 1944160 2338900 1891980 2045680 1666530 1444340 2151150 1889460 2214050 2443300 FALSE TRUE 1868180.078 2272196.862 2233902.873 2151257.79 1720135.451 1473545.544 2177476.417 1850441.991 1962720.326 2277813.115 0.820163896 0.997534366 0.980722632 0.944439988 0.755169702 0.646912398 0.955950426 0.812376564 0.861668727 1 21.11921795 3.26414476 24.44009795 0.827636958 0.94334579 0.170855595 0.102462524 264.1238453 252310.7653 0.027972645 0.037859739 1837.150603 -3.26414476 0.115708832 QLTEEDGVHSVIEENIK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLTEEDGVHSVIEENIK 17 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 138.07 4.87E-06 240680000 208190 199470 211510 208840 213760 255860 261160 250250 341490 321290 FALSE TRUE 200053.7046 193781.3109 249734.562 219618.2574 220635.7845 261033.6645 264356.1542 245082.25 302725.4868 299528.7421 0.667894851 0.646953977 0.833758257 0.733212632 0.736609726 0.87148119 0.88257358 0.818226152 1.010672581 1 18.19233492 3.264309403 0.218884052 1.044935202 0.510004474 0.757673566 0.058883183 3.038835495 0.249773469 0.13334077 0.466729634 1837.847209 -3.264309403 -0.534930727 EIGDYIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIGDYIR 7 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ;;; 138.24 0.0065249 970990000 1684080 1837550 1501700 1618280 1621870 1494210 1682810 1757180 1750370 1781440 FALSE TRUE 1618264.292 1785144.873 1773090.595 1701799.625 1674038.921 1524423.95 1703404.732 1720893.619 1551675.336 1660781.482 0.974399287 1.074882453 1.067624257 1.024698097 1.007982651 0.917895561 1.025664575 1.036195091 0.934304334 1 20.66343083 3.264764712 3.274770701 0.990783882 1.042406679 0.23683052 0.042913265 0.374513769 8.310911903 0.012953204 0.017265428 1839.774997 -3.264764712 0.051622796 DKELTGALIASLINCYIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKELTGALIASLINCYIR 18 1 O75694;O75694-2 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 116.73 0.00013865 293430000 586820 555790 485960 553050 603770 666570 620420 663750 708320 749920 FALSE TRUE 563886.4256 539939.4134 573783.7821 581592.9768 623190.8104 680048.5021 628012.8855 650043.3305 627914.4831 699127.2504 0.806557641 0.772304917 0.820714372 0.831884291 0.89138395 0.972710621 0.898281229 0.929792581 0.898140478 1 19.41519554 3.265696033 1.928697964 0.93227637 0.796966143 0.795591433 0.031661643 0.140032158 1.072062185 0.009569272 0.013586469 1843.724528 -3.265696033 -0.135310226 SKDLAEVGEGGGHSQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKDLAEVGEGGGHSQAR 17 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 153.25 1.10E-07 571170000 739900 772650 624920 705920 784620 871570 724240 837390 911880 775340 FALSE TRUE 710983.89 750614.7785 737856.9453 742352.6158 809858.0149 889193.7426 733103.4658 820097.6039 808367.2053 722825.5312 0.983617566 1.038445304 1.020795356 1.027014935 1.120405935 1.230163717 1.014219108 1.134571993 1.11834346 1 19.46328794 3.266856125 6.954392241 1.11099659 1.018676879 0.309612096 0.061857012 0.201750298 32.98288258 0.016624625 0.022103076 1848.656088 -3.266856125 -0.092319711 EKVGEQAQVVIIDMNDPSNPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKVGEQAQVVIIDMNDPSNPIR 22 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 130.65 1.21E-05 100020000 242690 232380 205720 226040 261300 270220 268930 265100 289420 305960 FALSE TRUE 233205.4065 225752.7499 242898.1802 237705.9515 269704.9518 275684.0335 272221.2458 259625.5924 256566.2549 285237.0567 0.817584535 0.791456596 0.851566003 0.833362797 0.945546679 0.966508478 0.954368443 0.910209898 0.899484302 1 18.1218019 3.266889445 5.362206655 0.941268248 0.821834707 0.801992644 0.02979347 0.083288212 6.341564641 0.008753357 0.01157506 1848.797927 -3.266889445 -0.119433541 QRLEAEAGR ddPTM_BT-474_Pertuzumab_2h_R1 3 QRLEAEAGR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 121.6 0.00055563 1281830000 701790 772640 636150 685280 610380 487180 770080 659100 676690 736300 FALSE TRUE 674363.2709 750605.0637 751116.4561 720647.3829 630013.427 497031.1134 779504.4694 645489.3547 599874.9881 686429.7452 0.9824214 1.093491459 1.094236462 1.049848711 0.917811956 0.724081549 1.135592499 0.940357494 0.873905877 1 19.38875255 3.267185091 7.536058506 0.934231704 1.061108367 0.262897611 0.10070987 0.270407318 54.085219 0.028437918 0.037900223 1850.056922 -3.267185091 0.126876663 LRNPSDRK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRNPSDRK 8 2 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ; 80.239 0.014603 779200000 360170 583650 346870 454490 318250 183146 468550 505410 476240 425410 FALSE TRUE 346094.1582 567004.8735 409557.1251 477946.2834 328486.8003 186849.3376 474284.2551 494973.1069 422179.2318 396596.6018 0.872660423 1.42967658 1.03267936 1.205119462 0.828264284 0.471131968 1.195885827 1.24805181 1.064505419 1 18.59731279 3.267220953 24.9848087 0.99130023 1.148768837 0.097597364 0.241280823 605.5255557 527866.0676 0.072671486 0.098380581 1850.209698 -3.267220953 0.157468607 AVIGIGIEEEDRK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVIGIGIEEEDRK 13 1 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ;; 217.09 4.23E-11 1782320000 618056 623833 494048 558928 631218 617334 593906 660052 679803 643978 FALSE TRUE 593901.6882 606041.8936 583333.4636 587774.3411 651521.7002 629816.9164 601174.3993 646421.6955 602634.6134 600360.7965 0.989241289 1.009462805 0.971638167 0.979035181 1.08521693 1.04906403 1.00135519 1.07672203 1.003787417 1 19.19547025 3.267477674 24.99868496 1.040515414 0.987802351 0.389710879 0.029522173 196.4470813 169826.4753 0.007885741 0.010675286 1851.303722 -3.267477674 -0.052713063 GKLPSYK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKLPSYK 7 1 Q12996;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 0 73.931 0.043371 192800000 193720 295220 167260 263210 473860 545550 482200 507330 578930 538250 FALSE TRUE 186149.2082 286800.6147 197487.6027 276794.2996 489102.1372 556581.3948 488101.3078 496853.4582 513212.2935 501793.8481 0.370967498 0.571550679 0.39356322 0.551609592 0.974707321 1.109183377 0.972712818 0.990154543 1.022755252 1 18.93673526 3.268208481 3.799678448 1.015948855 0.460221017 0.9505633 0.060675332 0.041288203 1.268999927 0.016664909 0.022107264 1854.421618 -3.268208481 -0.555727838 down LFGPYVWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFGPYVWGR 9 0 Q9H4A4;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ; 188.61 9.11E-05 691270000 584700 642040 568380 584630 531000 400960 615870 590750 600760 702420 FALSE TRUE 561849.2776 623729.6478 671098.9095 614802.8244 548080.0972 409067.6859 623407.2013 578550.8061 532564.2434 654844.4677 0.857988889 0.952485176 1.024821836 0.9388532 0.836962247 0.624679151 0.951992774 0.883493462 0.813268294 1 19.32079277 3.268849296 6.6015906 0.845058218 0.950725979 0.16428729 0.100371948 0.301125926 41.01796717 0.028485835 0.037891675 1857.159893 -3.268849296 0.10566776 NMITQYWPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NMITQYWPDR 10 0 O95373 O95373 IPO7 Importin-7 0 103.22 0.0094378 0 126070 115050 104140 112910 98397 94823 97182 120640 132020 136930 FALSE TRUE 121143.045 111768.8866 122960.4146 118737.2986 101562.0289 96740.38603 98371.34239 118148.7418 117033.6431 127655.6091 0.94898333 0.875550142 0.963219834 0.930137731 0.795593939 0.75782323 0.770599452 0.925527226 0.916792015 1 16.96189741 3.268882199 24.64468261 0.85120673 0.928031724 0.162860171 0.07396697 300.9716197 244620.4983 0.021274286 0.028801751 1857.300602 -3.268882199 0.076824994 RREEEMMIR ddPTM_BT-474_Pertuzumab_2h_R1 3 RREEEMMIR 9 2 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 163.64 3.54E-05 1487871000 590191.2 595061 518713.7 526579.3 496621 378064.5 580893 487424.4 515785.6 518650.5 FALSE TRUE 567125.8754 578090.4429 612456.8043 553756.1208 512595.2655 385709.2232 588002.1423 477358.9158 457235.781 483521.8397 1.172906431 1.195582899 1.266657996 1.145255654 1.060128465 0.797707966 1.216081869 0.987254094 0.945636254 1 18.88322153 3.268883895 3.080839207 1.002001732 1.208298188 0.492485262 0.098901007 0.215211332 4.195079634 0.028735835 0.038551462 1857.307853 -3.268883895 0.206296456 HIADLAGNSEVILPVPAFNVINGGSHAGNK ddPTM_BT-474_Pertuzumab_2h_R1 2 HIADLAGNSEVILPVPAFNVINGGSHAGNK 30 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90;A0A2R8YEM5 P06733 ENO1 Alpha-enolase;Enolase 0 ; 162.44 2.23E-12 6690100000 10802600 10495400 7963200 9435400 7354200 8196800 7935800 5991600 9546600 9363400 FALSE TRUE 10380422.45 10196081.47 9402327.38 9922362.125 7590754.522 8362544.912 8032920.694 5867871.366 8462909.991 8729208.578 1.189159631 1.168041911 1.077111092 1.136685192 0.869581068 0.957995772 0.920234707 0.672211153 0.969493387 1 23.05741943 3.269295901 1.130150888 0.852855069 1.173365601 0.573373703 0.097320612 0.312489991 0.847380105 0.038621349 0.063142821 1859.070678 -3.269295901 0.320510531 HTQFWR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTQFWR 6 0 P12236 P12236 SLC25A6 "ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed" 0 68.398 0.096242 395050000 531040 606160 541740 551770 525120 564190 538450 486950 651950 670080 FALSE TRUE 510286.3697 588872.9103 639644.4689 580246.9158 542010.9617 575598.3084 545039.7122 476894.3123 577943.3692 624694.8848 0.816856968 0.942656847 1.023931017 0.928848515 0.867641108 0.92140711 0.872489475 0.763403581 0.92516104 1 19.25279219 3.270643968 6.164621673 0.872156094 0.936509869 0.011239979 0.074469863 0.374942735 40.97763363 0.021542805 0.028652816 1864.850273 -3.270643968 0.064353775 YYTVFDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YYTVFDR 7 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;; 139.31 0.0062827 1657250000 2193440 2396930 2182110 2130600 1760930 1569250 1737320 1813540 1905620 2435150 FALSE TRUE 2107717.94 2328571.903 2576465.818 2240560.521 1817571.913 1600981.31 1758581.842 1776089.765 1689302.007 2270215.121 0.928422122 1.025705397 1.134899417 0.986937537 0.8006166 0.705211279 0.774632247 0.782344258 0.744115388 1 21.11439758 3.271686449 4.109678734 0.782212639 1.033212767 0.596418581 0.087487522 0.125580446 4.607628667 0.023850881 0.031650507 1869.332035 -3.271686449 0.251000128 SQDATFS(ph)PGSEQAEKS(ph)PGPIVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 2 SQDAT(0.024)FS(0.975)PGSEQAEKS(1)PGPIVSR 124.25 3.33E-05 472320000 940510 903160 823090 876020 997140 943020 904980 956650 1063000 1100600 TRUE FALSE 903753.8294 877402.7611 971840.6725 921231.4972 1029213.914 962088.5105 916055.416 936894.8432 942332.6965 1026055.382 0.880804141 0.855122225 0.947162005 0.897837986 1.003078325 0.937657487 0.892793345 0.913103581 0.918403347 1 19.96867717 3.271759254 0.011132002 1.827680678 1.04E-06 0.312296823 0.038153331 4073.122715 12.72028293 998.342202 1090.058367 1869.645436 -3.271759254 -1.827679635 EQEAGLLQFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQEAGLLQFLR 11 0 Q9NZL4;Q9NZL4-3;K7EN20 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ; 201.75 9.86E-08 49221000 60374 64416 58528 62674 54512 58391 65202 61214 61889 72655 FALSE TRUE 58014.51733 62578.91875 69105.31155 65908.61265 56265.42799 59571.70603 65999.96158 59949.90951 54863.62018 67734.01214 0.85650496 0.923892101 1.020245359 0.973050475 0.830682049 0.87949472 0.974399116 0.885078377 0.809986275 1 16.04759283 3.271779355 24.99949451 0.895123116 0.947515436 0.105731426 0.06619108 415.6636573 312814.11 0.018479681 0.025019998 1869.731975 -3.271779355 0.05239232 SSSGLLEWESK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSGLLEWESK 11 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 197.21 1.36E-05 174220000 711530 745960 580820 665310 762880 697320 765260 779420 820140 766590 FALSE TRUE 683722.621 724685.9512 685787.0943 699646.7288 787418.728 711420.2882 774625.4808 763324.7046 727041.1455 714668.1765 0.956699407 1.014017379 0.959588123 0.978981228 1.101796266 0.99545539 1.083895305 1.068082685 1.017312886 1 19.44691402 3.271948878 24.74544229 1.049596931 0.978675908 0.454421019 0.035738939 137.9693455 102253.9076 0.009315816 0.012612833 1870.461949 -3.271948878 -0.070921022 EKPPITVVGDVGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKPPITVVGDVGGR 14 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;I3L4G9;C9J168;B4DP31;Q14558;Q14558-2 O60256;C9J168 PRPSAP2;PRPSAP1 Phosphoribosyl pyrophosphate synthase-associated protein 2;Phosphoribosyl pyrophosphate synthase-associated protein 1 0 ;; 152.68 6.02E-06 552880000 1265870 1321170 1091460 1237430 1333320 1387030 1334530 1538190 1621320 1635240 FALSE TRUE 1216398.401 1283491.525 1288711.101 1301293.911 1376207.449 1415076.697 1350862.377 1506425.839 1437274.551 1524483.738 0.797908413 0.841918804 0.845342636 0.853596452 0.902736719 0.928233382 0.886111372 0.988154745 0.942794282 1 20.53988933 3.272035009 0.304931172 1.007025602 0.750053571 0.874461569 0.022273792 0.980789924 0.146107311 0.02747311 0.088927564 1870.832943 -3.272035009 -0.256972031 SEIDLLDIR ddPTM_BT-474_Pertuzumab_2h_R1 5 SEIDLLDIR 9 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 ;;;; 146.81 0.00021845 377253000 1068210 1183430 941966 1020263 1004285 890101 997817 1060757 1116398 1230838 FALSE TRUE 1026463.172 1149679.735 1112200.21 1072918.896 1036588.739 908099.4521 1010028.583 1038851.997 989669.1794 1147472.246 0.894542919 1.001923784 0.969261099 0.935028189 0.903367156 0.791391213 0.88022049 0.905339542 0.862477662 1 20.13002783 3.272343576 3.105916217 0.880932488 0.958354056 0.223534007 0.054330923 0.306942143 6.076529086 0.01542903 0.020729016 1872.162646 -3.272343576 0.077421568 ELDQGTPQYMENMEQVFEQCQQFEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDQGTPQYMENMEQVFEQCQQFEEK 26 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 149.99 1.44E-07 35949000 31948 28626 23713 27030 33822 28392 30389 34934 37587 31695 FALSE TRUE 30699.43684 27809.61451 27998.46659 28425.02154 34909.91535 28966.10569 30760.90967 34212.60069 33320.28134 29548.26942 1.038958878 0.941158824 0.947550132 0.961986001 1.181453805 0.980297874 1.041039299 1.157854635 1.127655934 1 14.85078602 3.272449023 24.98257881 1.086427205 0.968404918 0.397758396 0.065437948 177.4920725 130846.2886 0.018249535 0.024708578 1872.617263 -3.272449023 -0.118022287 HQYINEDEYEVNLK ddPTM_BT-474_Pertuzumab_2h_R1 3 HQYINEDEYEVNLK 14 0 Q93009;A0A669KBL1;Q93009-3 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7 0 ;; 220.21 4.73E-12 1577930000 1169870 1185590 1062780 1015480 998790 835010 850110 762390 1365280 1448330 FALSE TRUE 1124150.187 1151778.134 1254847.987 1067889.044 1030916.987 851894.4743 860513.9005 746646.3801 1210299.138 1350233.319 0.832559952 0.853021561 0.929356408 0.790892233 0.763510256 0.630923902 0.637307559 0.552975822 0.896362963 1 20.36477729 3.272627992 2.279741799 0.695448615 0.867936478 0.090051794 0.130132056 0.410056343 4.366696828 0.038950955 0.054077778 1873.389112 -3.272627992 0.172487862 SIS(ph)ESSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 S(0.33)IS(0.67)ESSR 155.95 0.0016534 785870000 920600 931930 824900 897250 848480 824880 985970 942040 941320 1016600 TRUE FALSE 884621.9342 905352.2689 973977.7798 943557.18 875772.1298 841559.6388 998036.5958 922586.5448 834465.2999 947744.7765 0.933396792 0.955270123 1.027679396 0.995581515 0.924059042 0.887960197 1.053064729 0.973454634 0.880474702 1 19.85413907 3.273886703 24.99896459 0.957192357 0.979909486 0.045937193 0.053257006 750.7035896 531240.4643 0.015360765 0.02079774 1878.826611 -3.273886703 0.02271713 FSHQGVQLIDFSPCER ddPTM_BT-474_Pertuzumab_2h_R1 3 FSHQGVQLIDFSPCER 16 0 P55884;P55884-2;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;; 197.75 4.25E-11 1498760000 1227658 1418852 1105618 1213659 1111568 1073915 1268307 1067102 1253942 1410750 FALSE TRUE 1179679.768 1378387.73 1305427.767 1276296.086 1147322.594 1095630.297 1283828.92 1045065.971 1111599.761 1315198.646 0.896959385 1.048045278 0.992570796 0.970420773 0.872356885 0.833053091 0.976148299 0.794606939 0.845195336 1 20.32684929 3.275007916 4.953566613 0.87461695 0.98487602 0.282768212 0.068462719 0.203789922 11.74755189 0.018616255 0.024748017 1883.683424 -3.275007916 0.11025907 SEAAAPHTDAGGGLS(ph)S(ph)DEEEGTSSQAEAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEAAAPHTDAGGGLSSDEEEGTSSQAEAAR 30 0 Q01831-2;Q01831 Q01831-2 XPC DNA repair protein complementing XP-C cells 2 SEAAAPHTDAGGGLS(1)S(1)DEEEGTSSQAEAAR;SEAAAPHTDAGGGLS(1)S(1)DEEEGTSSQAEAAR 174.66 2.97E-13 1154510000 569700 504250 405680 344190 435770 342340 268130 315850 241540 223780 TRUE FALSE 547435.4942 489869.2837 478995.4003 361953.6871 449786.9378 349262.3494 271411.4551 309327.5871 214121.3918 208623.1813 2.624039624 2.348105712 2.295983588 1.734963895 2.155977754 1.67413011 1.300964991 1.482709569 1.026354744 1 17.67053995 3.275694068 0.332292392 0.911305251 2.992817231 0.899845257 0.171823255 0.757921463 0.135279784 0.19255776 0.590733305 1886.661853 -3.275694068 2.08151198 up APRPTRPDK ddPTM_BT-474_Pertuzumab_2h_R1 6 APRPTRPDK 9 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;;; 119.68 0.00044312 11056770000 3474280 3653350 3069470 3637170 3908090 4404830 4365660 4496870 5259520 4845280 FALSE TRUE 3338501.297 3549160.035 3624191.509 3824884.78 4033797.264 4493898.681 4419088.253 4404008.063 4662481.339 4517104.87 0.739079874 0.78571566 0.802326183 0.846755807 0.893005007 0.994862597 0.978301009 0.974962546 1.03218355 1 22.10696698 3.275747473 0.851965186 1.003864076 0.749455708 0.963708906 0.018991014 0.110655097 0.173875958 0.009493597 0.017163033 1886.893868 -3.275747473 -0.254408369 LPS(ph)IVVEPTEGEVESGELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPSIVVEPTEGEVESGELR 19 0 B5MBX5;B5MCP4;Q53QV2 B5MBX5 LBH Protein LBH 1 LPS(1)IVVEPTEGEVESGELR;LPS(1)IVVEPTEGEVESGELR 155.79 2.34E-08 53137000 13246.5 11624.4 6845 10406.1 13747.7 11113.2 16755.6 19907.9 6933.7 7553.5 TRUE FALSE 12728.81214 11292.88349 8082.043766 10943.16007 14189.90726 11337.91652 16960.66004 19496.79491 6146.615444 7041.894717 1.80758342 1.603671163 1.147708691 1.554007907 2.015069498 1.610066179 2.408536442 2.768685942 0.872863866 1 12.78174794 3.276383746 6.277265003 1.962540809 1.502425178 0 0.576243745 0.417377207 43.97955813 0.164806673 0.220216043 1889.660332 -3.276383746 -0.460115631 HFCPNVPIILVGNKK ddPTM_BT-474_Pertuzumab_2h_R1 2 HFCPNVPIILVGNKK 15 1 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;P61586 Q5JR08;P61586 RHOC;RHOA Rho-related GTP-binding protein RhoC;Transforming protein RhoA 0 ; 160.69 1.10E-06 1280330000 2448940 2972300 2060670 2580500 2314800 2486300 2743200 2399700 3199700 2550200 FALSE TRUE 2353232.717 2887532.914 2433078.908 2713679.914 2389257.644 2536574.689 2776772.102 2350145.356 2836483.47 2377472.683 0.989804314 1.21453884 1.023388797 1.14141371 1.004956928 1.066920646 1.167951212 0.988505724 1.193066693 1 21.18099733 3.276767254 24.99996076 1.070650342 1.096097374 0.014913604 0.08555039 875.5666709 572908.46 0.021906665 0.029661285 1891.329749 -3.276767254 0.025447032 LRDPSGDFSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRDPSGDFSVR 11 1 Q96E14;A0A3B3ISX4 Q96E14 RMI2 RecQ-mediated genome instability protein 2 0 ; 166.7 1.83E-05 733080000 224270 217100 158358 235020 211770 198680 225390 257300 216410 256570 FALSE TRUE 215505.2805 210908.5206 186976.8133 247149.4104 218581.7744 202697.4457 228148.3902 251986.6651 191844.0441 239192.2854 0.900970866 0.881753022 0.781700852 1.033266646 0.913832877 0.847424679 0.953828381 1.053489935 0.802049463 1 17.86781133 3.27683434 0.510320187 0.96457126 0.858285804 0.075071321 0.085080417 2.905642097 1.459544837 0.069177098 0.156322473 1891.62193 -3.27683434 -0.106285455 LHVAILER ddPTM_BT-474_Pertuzumab_2h_R1 1 LHVAILER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 105.57 0.0043629 577450000 336260 400200 341870 326640 322980 201690 386850 240000 381380 442890 FALSE TRUE 323118.5874 388786.6878 403653.5139 343497.9295 333368.945 205768.31 391584.386 235043.9161 338087.3413 412892.6658 0.782572843 0.941616841 0.977623357 0.831930325 0.807398563 0.498357871 0.94839269 0.569261543 0.818826221 1 18.65540727 3.277095358 2.891723638 0.736713611 0.902562698 0.097580953 0.152138427 0.407949949 6.972528239 0.042221656 0.057203679 1892.759165 -3.277095358 0.165849087 IDEHHFVAVALR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDEHHFVAVALR 12 0 Q9NRN7;E9PLW6 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 75.78 0.019019 39778000 51717 49147 44902 39891 38502 23412 48818 14495 43441 49833 FALSE TRUE 49695.84246 47745.37568 53016.79024 41949.77929 39740.4518 23885.40668 49415.44929 14195.67318 38509.7598 46457.76652 1.069699346 1.027715692 1.141182502 0.902965907 0.855410296 0.514131618 1.063663903 0.305560819 0.828919741 1 15.50363218 3.277178044 1.880803779 0.693780723 1.072576879 0.293428123 0.212802862 0.346577226 2.523674616 0.065157092 0.093754507 1893.119566 -3.277178044 0.378796156 EGYAWAEDKEHCEEYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGYAWAEDKEHCEEYGR 17 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 219.01 2.68E-15 5635200000 2659800 2601900 2125020 2506000 2553500 2813500 2789300 2573700 3305700 2943300 FALSE TRUE 2555852.075 2527696.36 2509058.385 2635334.96 2635635.647 2870390.898 2823436.288 2520552.196 2930450.795 2743947.669 0.931450736 0.921189711 0.914397316 0.960417354 0.960526936 1.046080772 1.028968708 0.918586103 1.067968907 1 21.38782154 3.277192309 1.977647369 1.000613922 0.923551032 0.478162598 0.039104035 0.326643531 2.626052142 0.012831559 0.01828791 1893.181748 -3.277192309 -0.07706289 FIILFS(ph)LDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FIILFSLDLK 10 0 Q5T6F7;F1DAM0;Q13285 Q5T6F7 NR5A1 Steroidogenic factor 1 1 FIILFS(1)LDLK 59.153 0.068566 802830000 1170900 1077500 1271200 591140 918650 889710 890010 516640 835350 876760 TRUE FALSE 1125139.934 1046770.755 1500934.118 621648.8062 948199.2115 907700.5458 900902.2086 505971.2035 740524.5701 817376.2643 1.376526311 1.28064736 1.836282974 0.760541789 1.160052295 1.110505144 1.102187876 0.619018713 0.90597758 1 19.64064082 3.277398296 0.75293246 0.855694892 1.478527472 0.40140696 0.250327376 0.705932476 0.863789524 0.138706447 0.262308899 1894.079904 -3.277398296 0.622832579 AACHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AACHLK 6 0 Q15785;Q8WXU2-3;Q8WXU2-2;Q8WXU2;Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q15785;Q9H3U1;Q9H3U1-2 TOMM34;DYX1C1;UNC45A Mitochondrial import receptor subunit TOM34;Dyslexia susceptibility 1 candidate gene 1 protein;Protein unc-45 homolog A 0 72.054 0.086609 253650000 644870 669570 564350 603480 586090 447060 682350 621730 648190 717350 FALSE TRUE 619667.7675 650474.5192 666340.5989 634625.6751 604942.1171 456099.8595 690700.8034 608891.0582 574610.1886 668763.2456 0.926587655 0.972652913 0.996377423 0.948954177 0.904568427 0.682004973 1.032803175 0.910473269 0.859213171 1 19.35113604 3.27857006 4.43056624 0.894048793 0.966125222 0.107532637 0.089205643 0.453792897 19.47380254 0.025530251 0.034003854 1899.197193 -3.27857006 0.07207643 FHVEEEGK ddPTM_BT-474_Pertuzumab_2h_R1 10 FHVEEEGK 8 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;;;; 193.28 0.0001715 55013905000 48185505 44859186 33031702 40670887 31047988 30025496 35547108 19767223 45219214 31719968 FALSE TRUE 46302362.19 43579845.94 39001265.34 42769916.35 32046674.73 30632632.1 35982144.14 19359022.94 40086118.4 29571546.31 1.56577413 1.473708729 1.318878118 1.446319915 1.083699662 1.035881985 1.216782638 0.654650343 1.355563824 1 24.81770635 3.279077234 1.006402904 0.988597183 1.511044631 0.512118917 0.182620497 0.399529861 0.866848129 0.075829475 0.130230327 1901.416396 -3.279077234 0.522447448 AIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAK 39 1 Q15417;E9PDU6;Q15417-2 Q15417 CNN3 Calponin-3;Calponin 0 ; 195.55 1.05E-30 260010000 350800 329970 251460 340450 320220 384790 338760 368880 438390 388450 FALSE TRUE 337090.3482 320559.5787 296904.4157 358020.6653 330520.1671 392570.7174 342905.8462 361262.4991 388625.8051 362139.9355 0.930828984 0.88518152 0.819861017 0.988625198 0.912686326 1.084030451 0.946887688 0.997577079 1.073137114 1 18.46618776 3.279299449 1.598151642 1.009818226 0.883655627 0.501064927 0.054878946 0.306263898 1.619556655 0.017583942 0.02628147 1902.38954 -3.279299449 -0.126162599 ENGAFTVLVDNYVKEEEGTGVVHQAPYFGAEDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENGAFTVLVDNYVKEEEGTGVVHQAPYFGAEDYR 34 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 80.93 0.00079935 42984000 18870 18857 15832 17083 20751 18972 18311 20715 24404 18494 FALSE TRUE 18132.53954 18319.21682 18693.19458 17964.65568 21418.47476 19355.62684 18535.0955 20287.22801 21633.76023 17241.38491 1.051686952 1.062514231 1.084204934 1.041949691 1.242271133 1.122625992 1.07503519 1.176658843 1.254757686 1 14.07358804 3.279761445 24.99906457 1.149585328 1.061984681 0.256515202 0.070743667 198.8260984 120638.6963 0.018876988 0.025559283 1904.414349 -3.279761445 -0.087600648 ALLFIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALLFIPR 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 143.22 0.0056673 1555730000 883790 949590 885450 843050 729990 446370 873270 766070 749170 938580 FALSE TRUE 849250.5097 922508.6229 1045470.512 886559.9115 753470.7913 455395.9072 883957.3395 750250.3868 664127.3624 875009.1406 0.970561872 1.054284556 1.194810961 1.013200743 0.86110048 0.520447029 1.010226406 0.857420057 0.758994771 1 19.73893856 3.280284476 3.957737651 0.82592339 1.074381557 0.391616382 0.137799946 0.216735556 7.14140757 0.039602518 0.05286882 1906.70926 -3.280284476 0.248458167 ELQAWVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELQAWVR 7 0 O15296-4;O15296;I3L1D5;O15296-3 O15296-4 ALOX15B Arachidonate 15-lipoxygenase B 0 ; 89.142 0.042085 114049000 246217 314530 253176 227320 232631 163454 243014 199114 201076 214390 FALSE TRUE 236594.5674 305559.9124 298930.5351 239052.0124 240113.7874 166759.1519 245988.078 195002.2263 178250.6955 199869.1743 1.18374716 1.528799593 1.49563101 1.196042427 1.201354777 0.834341526 1.230745456 0.975649331 0.891836853 1 17.60869646 3.281411891 1.844631828 1.006973661 1.408878287 0.609638376 0.138923541 0.218144958 1.528491251 0.042999357 0.062315428 1911.665451 -3.281411891 0.401904626 KAEFPSSGSNSVLNTPPTTPES(ph)PSSVTVTEGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAEFPSSGSNSVLNTPPTTPESPSSVTVTEGSR 33 1 Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3;H7C5R6 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 1 KAEFPSSGSNSVLNT(0.001)PPT(0.008)T(0.034)PES(0.953)PS(0.003)S(0.002)VTVTEGSR 143.54 2.45E-10 338230000 153310 141050 110080 136130 154740 166570 170500 165630 158820 166080 TRUE FALSE 147318.4757 137027.3921 129973.9047 143155.6856 159717.3526 169938.1595 172586.63 162209.6826 140791.4194 154831.2537 0.951477639 0.88501119 0.839455224 0.924591658 1.031557575 1.097570132 1.114675661 1.047654648 0.909321704 1 17.24033719 3.281572917 3.720044629 1.046228372 0.890302663 0.550717739 0.058912759 0.159156374 4.569907122 0.017653695 0.0236236 1912.374382 -3.281572917 -0.155925708 QWSGS(ph)QDSQMGFPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QWSGSQDSQMGFPR 14 0 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 QWSGS(1)QDSQMGFPR;QWS(0.001)GS(0.999)QDSQMGFPR 278.79 3.59E-33 378740000 320400 373680 277380 302520 295900 284510 300930 299940 301130 314380 TRUE FALSE 307878.4138 363023.0123 327508.7363 318133.0935 305417.8922 290262.9871 304612.8714 293746.1342 266946.9848 293086.7626 1.050468507 1.238619612 1.117446361 1.085457053 1.042073308 0.990365394 1.03932661 1.002249749 0.910812152 1 18.16096828 3.281914753 1.262611646 0.990424524 1.149353693 0.602853641 0.052430007 0.289703662 0.96996078 0.018569115 0.029729724 1913.880213 -3.281914753 0.15892917 AHNDHPNNFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AHNDHPNNFSR 11 0 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;S4R3B3;H7C453;S4R3U7 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 0 ; 90.434 0.0066445 39049000 48915 62505 47490 54171 67212 88084 67834 52246 85077 57268 FALSE TRUE 47003.34772 60722.4186 56072.49941 56966.7718 69373.93502 89865.11883 68664.17278 51167.10184 75419.41563 53389.18735 0.880390769 1.13735424 1.050259466 1.067009532 1.299400468 1.683208217 1.286106348 0.958379484 1.412634643 1 15.70425997 3.282928984 6.166689437 1.269435963 1.039984981 0.257244236 0.199433412 0.314830035 28.8997388 0.060054359 0.080520857 1918.355025 -3.282928984 -0.229450982 SKTDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_BT-474_Pertuzumab_2h_R1 3 SKTDLLVNDNPDPAPLSPELQDFK 24 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 SKTDLLVNDNPDPAPLS(1)PELQDFK;SKTDLLVNDNPDPAPLS(1)PELQDFK;SKTDLLVNDNPDPAPLS(1)PELQDFK 241.23 8.57E-38 735970000 690208 596496 570597 586634 714978 614898 615963 753770 797420 681022 TRUE FALSE 663233.9083 579484.5181 673716.5708 616910.251 737975.9167 627331.6589 623501.3394 738204.3861 706900.2247 634895.7733 1.04463431 0.912723856 1.06114515 0.971671693 1.162357583 0.988086053 0.982053064 1.162717437 1.113411452 1 19.27616025 3.283188997 24.99996208 1.072447492 0.996028093 0.183616674 0.072514038 217.0405018 121580.4823 0.020205706 0.027358565 1919.503892 -3.283188997 -0.076419399 SSS(ph)SQTLTQFDSNIAPADPDTAIVHPVPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSSQTLTQFDSNIAPADPDTAIVHPVPIR 30 0 Q96D71;Q96D71-3;H0YE73 Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.229)S(0.229)S(0.264)S(0.264)QT(0.014)LTQFDSNIAPADPDTAIVHPVPIR 133.23 4.04E-06 132210000 5316.8 2371.8 3276.7 3442.6 4613.3 3767.1 4293.2 5034.3 2441.5 5483.1 TRUE FALSE 5109.013578 2304.158586 3868.87258 3620.272999 4761.690984 3843.273343 4345.741466 4930.339946 2164.351156 5111.724753 0.999469616 0.450759518 0.756862462 0.708229252 0.931523353 0.751854517 0.850151696 0.964515928 0.423409174 1 12.31959444 3.285607088 24.66957085 0.827397149 0.71097003 0.046134079 0.195428114 289.5630801 151834.6839 0.051105668 0.069197177 1930.22123 -3.285607088 -0.116427118 KPGGFDISLFYR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPGGFDISLFYR 12 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 164.53 9.15E-05 4086000000 2171450 2199070 1876760 1997950 1748090 890790 2377300 1909480 2223740 2319800 FALSE TRUE 2086587.333 2136354.677 2215932.28 2101064.439 1804318.902 908802.3841 2406394.109 1870048.571 1971310.358 2162677.88 0.964816514 0.987828422 1.024624287 0.971510579 0.834298496 0.420220872 1.112691877 0.864691218 0.911513627 1 21.04438737 3.286327773 5.935901865 0.849163393 0.991627991 0.124738094 0.168095915 0.406962888 32.75282109 0.047817046 0.064174547 1933.42697 -3.286327773 0.142464599 NFWSHETR ddPTM_BT-474_Pertuzumab_2h_R1 5 NFWSHETR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;; 158.57 0.00036424 3210320000 2296370 2519040 1939120 2046910 1992170 1571520 1748240 2025470 2181690 2245810 FALSE TRUE 2206625.322 2447199.446 2289562.119 2152551.27 2056249.957 1603297.211 1769635.484 1983643.337 1934033.698 2093699.288 1.053936128 1.168839985 1.093548693 1.02810909 0.982113319 0.765772439 0.845219509 0.94743469 0.92373996 1 20.99762282 3.286512408 2.107056956 0.893830276 1.1083863 0.647039919 0.066427325 0.187031459 1.703230157 0.021093549 0.029926519 1934.249122 -3.286512408 0.214556024 DAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQR 36 1 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 152.44 1.12E-13 144500000 70284 63651 48226 62430 73076 78717 72925 84844 83008 72049 FALSE TRUE 67537.22358 61835.7358 56941.51098 65652.01978 75426.55591 80308.71167 73817.47796 83091.94175 73585.27984 67169.05706 1.005481192 0.920598539 0.847734262 0.977414641 1.122936054 1.19562065 1.098980412 1.237056844 1.09552349 1 16.03550916 3.286574404 3.464794177 1.146895281 0.922812501 0.626237345 0.070609802 0.12871943 3.16298994 0.019718111 0.026534748 1934.525258 -3.286574404 -0.224082781 LFTNFHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFTNFHR 7 0 F5GWE5;Q00169;I3L4H1 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ; 185.42 0.0006137 402010000 258605 293879 285022 252183 248923 119516 294743 237829 260275 315718 FALSE TRUE 248498.4307 285497.8587 336531.8157 265198.1949 256929.8344 121932.6954 298350.153 232917.748 230729.6732 294334.1386 0.844273219 0.969978746 1.143366574 0.901010654 0.872918906 0.414266235 1.013644406 0.791337862 0.78390388 1 18.16709536 3.287581185 3.28121766 0.795076657 0.986316905 0.170120535 0.16922218 0.382048166 8.393589793 0.048538064 0.065544502 1939.015072 -3.287581185 0.191240249 HYELYR ddPTM_BT-474_Pertuzumab_2h_R1 6 HYELYR 6 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141;E7EW69;E7EX04;B5ME97;Q9P0V9;Q9P0V9-2;Q9P0V9-3;A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 D6RGI3;B1AMS2;E7EW69;A0A087X142 SEPT11;SEPT6;SEPT10;SEPT8 Septin-11;Septin-6;Septin-10;Septin-8 0 ;;;;; 154.29 0.010023 7040790000 936216 1000398 911982 804045 771226 356504 945022 531330 843586 891851 FALSE TRUE 899627.6437 971867.6285 1076797.434 845541.8588 796033.1847 363712.7551 956587.4619 520357.8498 747825.6539 831445.1374 1.082004817 1.168889666 1.295091385 1.016954482 0.957409153 0.437446488 1.150511824 0.625847487 0.899428742 1 19.66526155 3.288854448 2.58363674 0.808035237 1.175496586 0.37885601 0.193087508 0.251891239 3.43257431 0.054214705 0.074821227 1944.708213 -3.288854448 0.367461349 KPHQQATPDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPHQQATPDDR 11 1 A0A087WWW8;Q9Y6J0 A0A087WWW8 CABIN1 Calcineurin-binding protein cabin-1 0 91.961 0.0067194 16492000 25401 26527 24985 22961 20453 17103 22055 18113 21421 24408 FALSE TRUE 24408.30084 25770.47593 29500.34529 24146.01996 21110.88932 17448.83438 22324.91569 17738.96022 18989.37788 22754.82442 1.072664873 1.132528006 1.296443547 1.061138487 0.927754437 0.766819117 0.981106919 0.779569198 0.834520958 1 14.47388483 3.289109901 2.869630897 0.861402326 1.165071502 0.678640762 0.089310839 0.135398781 2.272239362 0.025454954 0.034752952 1945.85243 -3.289109901 0.303669176 TEKHESQR ddPTM_BT-474_Pertuzumab_2h_R1 3 TEKHESQR 8 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 131.44 0.00060384 140052000 262994 342872 232399 259112 226508 169461 268649 210457 197158 293597 FALSE TRUE 252715.9037 333093.6263 274398.669 272484.8014 233793.8355 172887.6175 271936.8068 206110.9894 174777.4504 273711.4137 0.923293261 1.216951905 1.002510876 0.995518593 0.854161806 0.631641974 0.993516504 0.753022998 0.638546446 1 18.06229607 3.289424297 2.56507162 0.796663292 1.059093232 0.402178226 0.134687649 0.253046795 3.399227906 0.038740565 0.053529747 1947.261588 -3.289424297 0.26242994 T(ph)NSAEVTPPVLSVMGEATPVSIEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TNSAEVTPPVLSVMGEATPVSIEPR 25 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 T(0.861)NS(0.131)AEVT(0.008)PPVLSVMGEATPVSIEPR 116.74 0.0044144 21103000 61885 52725 34352 46679 57285 47850 54600 63252 55108 46758 TRUE FALSE 59466.46578 51221.33462 40560.17056 49088.10878 59127.62405 48817.55978 55268.21113 61945.8241 48852.37087 43591.03901 1.364190144 1.175042756 0.930470378 1.1261055 1.356416947 1.119898972 1.267880105 1.42106785 1.120697556 1 15.41174397 3.289456165 24.99930249 1.246921808 1.135209692 0.01331068 0.152254017 248.8624166 122236.405 0.042607719 0.057691057 1947.404482 -3.289456165 -0.111712116 SKPNLPSESR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ; 95.018 0.0070299 196620000 321670 343025 267326 336657 366939 384220 398889 423650 445440 474870 FALSE TRUE 309098.7808 333242.2629 315637.7548 354031.9081 378741.9262 391989.1916 403770.7229 414901.4795 394875.5186 442706.6319 0.698202282 0.752738357 0.712972727 0.799698678 0.855514462 0.885437812 0.912050315 0.937192826 0.891957541 1 18.75599146 3.289688459 0.479351241 0.966781618 0.660602697 0.923062679 0.026389275 0.350439682 0.149937805 0.021928515 0.052301107 1948.446381 -3.289688459 -0.306178921 EFHGNIIK ddPTM_BT-474_Pertuzumab_2h_R1 3 EFHGNIIK 8 0 Q92804-2;Q92804;A0A075B7D9 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;; 101.25 0.0055261 1895140000 4083000 4559400 3695400 3960600 3857800 3410040 4468000 3766600 4219200 4657000 FALSE TRUE 3923431.846 4429370.376 4363240.984 4165007.041 3981889.641 3478993.345 4522680.721 3688818.394 3740254.104 4341577.242 0.903688136 1.020221484 1.004989832 0.959330402 0.917152781 0.801320154 1.041713753 0.849649376 0.861496617 1 22.04978782 3.290776389 3.654010349 0.904130932 0.980420045 0.141578246 0.071894865 0.373552743 10.18207892 0.019967731 0.026872491 1953.333458 -3.290776389 0.076289113 HITLDK ddPTM_BT-474_Pertuzumab_2h_R1 6 HITLDK 6 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 144.29 0.011291 2669550000 5383840 5715930 4741020 4973410 4833530 3881140 5422240 4279780 5975420 6166890 FALSE TRUE 5173433.581 5552917.273 5597827.777 5230088.286 4989004.882 3959619.31 5488598.995 4191401.047 5297115.373 5749201.047 0.899852612 0.965858948 0.973670555 0.909706974 0.867773599 0.688725142 0.954671606 0.729040612 0.921365478 1 22.45493005 3.291347366 3.120325661 0.83641405 0.946841358 0.124405039 0.092353092 0.354474288 7.023364274 0.025297425 0.034345839 1955.903239 -3.291347366 0.110427308 CPHSTPLWLLLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 CPHSTPLWLLLSR 13 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 85.536 0.0092405 72296000 60024 62882 60713 55561 49917 42227 55126 42104 51323 70528 FALSE TRUE 57678.19572 61088.66693 71685.18965 58428.50987 51522.62564 43080.85887 55800.64848 41234.53769 45497.0282 65751.07574 0.877220564 0.92909 1.090251206 0.888631999 0.783601258 0.655211468 0.848665179 0.627130997 0.69195869 1 16.00472688 3.291947425 3.129263625 0.738763625 0.964683569 0.372570574 0.113284364 0.216721833 4.317279829 0.03168234 0.043020057 1958.607551 -3.291947425 0.225919944 VSSS(ph)SELDLPSGDHCEAGLLQLDVPLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.045)S(0.104)S(0.716)S(0.134)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.015)S(0.118)S(0.433)S(0.433)ELDLPSGDHCEAGLLQLDVPLLR 260.68 6.63E-54 510700000 139467 148969 113052 134480 111125 122300 138509 130159 135338 145758 TRUE FALSE 134016.4755 144720.55 133483.0112 141420.5289 114699.4365 124772.9898 140204.1146 127471.1712 119974.9976 135885.6808 0.98624428 1.065016925 0.982318449 1.040731651 0.844087735 0.918220294 1.031779903 0.938076554 0.88291126 1 17.05203391 3.292232364 24.99993489 0.938922111 1.019305073 0.353589549 0.054701841 110.9402663 51674.3133 0.015198861 0.02057934 1959.89301 -3.292232364 0.080382962 HIPLAPGSDWR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIPLAPGSDWR 11 0 P26358;P26358-2;P26358-3;K7ENW7 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 107.06 0.0022486 132860000 84205 83605 64113 71629 58591 51298 68446 50547 66028 83207 FALSE TRUE 80914.17551 81220.66726 75699.64529 75325.78127 60475.63273 52335.28071 69283.66262 49503.18679 58532.77825 77571.31578 1.043094019 1.047045115 0.975871616 0.971051999 0.779613342 0.674673108 0.893160854 0.638163557 0.754567299 1 16.24323565 3.292744103 3.257863285 0.762905203 1.018816076 0.530862027 0.099954227 0.163931229 3.537264447 0.027706641 0.03753708 1962.203757 -3.292744103 0.255910873 ASYNNPHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASYNNPHR 8 0 P54725-2;P54725;A0A494C0B4;K7ELU6;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 ;;; 135.83 0.00081697 556556000 638030 722400 604970 606900 572637 428332 641430 553349 625120 683120 FALSE TRUE 613095.0822 701797.8593 714301.5365 638222.1817 591056.3892 436993.1665 649280.0122 541922.1498 554158.9983 636851.6739 0.962696821 1.101980081 1.121613659 1.002152005 0.928091129 0.686177307 1.019515279 0.85093935 0.870153948 1 19.28059787 3.293123709 3.096275716 0.880016741 1.064584242 0.401641871 0.094373234 0.224371798 4.373846925 0.026638509 0.03622289 1963.919621 -3.293123709 0.184567501 KTFEINPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTFEINPR 8 1 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 171.56 0.00046283 1830970000 2262250 2801300 2193200 2338670 2193880 2264890 2150150 2137800 2716400 2696600 FALSE TRUE 2173838.769 2721409.667 2589560.027 2459369.039 2264448.143 2310687.628 2176464.179 2093653.683 2408045.66 2513956.88 0.864708057 1.082520424 1.030073367 0.978286087 0.90075059 0.9191437 0.865752391 0.83281209 0.957870709 1 21.26152847 3.293468548 3.529081771 0.895923284 1.001930459 0.207141872 0.068019983 0.264917471 6.704806836 0.01930773 0.026057747 1965.479635 -3.293468548 0.106007175 IMADIR ddPTM_BT-474_Pertuzumab_2h_R1 1 IMADIR 6 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 97.306 0.095899 433280000 799290 903390 739760 749320 692190 366830 835870 724530 725440 830350 FALSE TRUE 768052.8631 877626.2017 873451.0879 787992.495 714454.92 374247.5539 846099.6271 709568.2023 643091.0925 774109.6549 0.992175796 1.133723364 1.128329924 1.017933945 0.922937617 0.483455479 1.092997125 0.916624922 0.83074935 1 19.56217842 3.295225806 3.393725883 0.869038005 1.085831412 0.285516502 0.153223406 0.308443967 7.205839216 0.045039992 0.060958463 1973.448538 -3.295225806 0.216793407 EILGTAQSVGCNVDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EILGTAQSVGCNVDGR 16 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 247.93 5.58E-20 378390000 48738 65485 39153 50850 61586 66665 54320 60044 63109 69902 FALSE TRUE 46833.26508 63617.43192 46228.81805 53474.37459 63566.96962 68013.01198 54984.78441 58804.07042 55945.13089 65167.47528 0.718660112 0.976214464 0.709384825 0.820568456 0.975440116 1.043664983 0.843745813 0.902353055 0.858482405 1 15.99186448 3.296793435 8.342736596 0.928835217 0.810854321 0.338736695 0.08917824 0.354731224 45.63597119 0.024432618 0.033029557 1980.584771 -3.296793435 -0.117980896 DSSTWTVDHQLLWGEALLITPVLQAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSTWTVDHQLLWGEALLITPVLQAGK 27 0 P10253 P10253 GAA Lysosomal alpha-glucosidase;76 kDa lysosomal alpha-glucosidase;70 kDa lysosomal alpha-glucosidase 0 124.45 7.93E-05 86111000 116910 118330 94201 108720 99742 107880 109960 103010 126140 132130 FALSE TRUE 112341.0279 114955.3443 111225.2162 114331.0522 102950.292 110061.4075 111305.7234 100882.8075 111821.116 123180.7174 0.912001735 0.933225156 0.902943403 0.928157058 0.835766297 0.893495425 0.903596973 0.81898214 0.90778101 1 16.91041691 3.296987275 24.99999788 0.880690689 0.918939417 0.028574504 0.04698561 156.3439005 66895.879 0.012309063 0.016666542 1981.468969 -3.296987275 0.038248728 YDWDLLAAR ddPTM_BT-474_Pertuzumab_2h_R1 6 YDWDLLAAR 9 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;;; 178.65 0.00011799 624796000 913974 1011578 899782 877937 791418 486237 963695 813906 873244 988355 FALSE TRUE 878254.8856 982728.7859 1062392.623 923247.4338 816874.6787 496069.0453 975488.9877 797098.5567 774117.0021 921412.8355 0.953161115 1.066545579 1.153003933 1.001991071 0.886545799 0.538378701 1.058688299 0.865082975 0.840141327 1 19.81348817 3.297167908 3.851014437 0.856094811 1.059768105 0.29906851 0.135695176 0.266619076 7.986535204 0.038859283 0.052383246 1982.293279 -3.297167908 0.203673294 KGFLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGFLFR 6 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 91.584 0.076526 683650000 759530 819350 632970 660100 586320 303020 609770 601630 659090 712930 FALSE TRUE 729846.7279 795982.9402 747361.7593 694167.8401 605179.5153 309147.272 617232.5477 589206.1303 584272.8663 664642.6161 1.098104019 1.197610447 1.124456574 1.044422707 0.910533722 0.465133087 0.928668329 0.886500679 0.879078248 1 19.34221927 3.29725915 2.884708634 0.827497631 1.138098106 0.498390847 0.136444581 0.214211327 3.624707501 0.041193523 0.056477776 1982.709785 -3.29725915 0.310600474 ALDVMVSTFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALDVMVSTFHK 11 0 P26447 P26447 S100A4 Protein S100-A4 0 ; 162.26 2.53E-05 1608180000 3985600 4180200 3506200 3540100 2600300 2555300 2835800 2396800 2983500 3245800 FALSE TRUE 3829838.346 4060984.789 4139848.335 3722804.985 2683941.011 2606969.917 2870505.369 2347305.242 2644825.588 3025959.075 1.265660986 1.342048814 1.368111145 1.230289271 0.886972013 0.861535088 0.948626633 0.775722733 0.874045393 1 21.52896105 3.297356748 3.57374762 0.872686487 1.323821859 0.915116518 0.061548318 0.056343231 1.454956523 0.017547258 0.023717084 1983.155406 -3.297356748 0.451135372 NQVIIPLVLS(ph)PDRDEDLMR ddPTM_BT-474_Pertuzumab_2h_R1 6 NQVIIPLVLSPDRDEDLMR 19 1 Q96G25-2;Q96G25 Q96G25-2 MED8 Mediator of RNA polymerase II transcription subunit 8 1 NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR 220.49 1.75E-19 391017000 344474 333211 295739 316796 297395 317439 290445 322128 356042 380709 TRUE FALSE 331011.5752 323708.1485 349185.616 333145.8795 306960.9803 323857.8341 293999.5528 315475.9442 315625.6048 354923.2403 0.93262863 0.912051147 0.983834182 0.938642055 0.864865823 0.912472888 0.828346863 0.888856824 0.889278494 1 18.43714752 3.297494174 8.473130636 0.887700998 0.94292702 0.173225804 0.044744193 0.370648868 48.20321552 0.011619425 0.015710684 1983.783043 -3.297494174 0.055226022 AVS(ph)EEQQPALK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVSEEQQPALK 11 0 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 AVS(1)EEQQPALK;AVS(1)EEQQPALK;AVS(1)EEQQPALK 217.2 1.21E-11 815330000 831610 629680 354843 597740 860900 623880 811930 1103560 791580 776860 TRUE FALSE 799109.7618 611722.1429 418971.0235 628589.433 888591.6303 636495.2811 821866.6422 1080771.1 701723.157 724242.5802 1.103373074 0.844637087 0.578495431 0.867926645 1.226925418 0.878842667 1.134794701 1.492277767 0.968906242 1 19.46611347 3.29779413 6.324227761 1.155109619 0.82527847 0.292277771 0.198483733 0.229991585 18.20460095 0.059074271 0.079680642 1985.153666 -3.29779413 -0.329831148 VMFENPDFQVDEESEEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMFENPDFQVDEESEEFR 18 0 Q9BSC4-2;Q9BSC4-4;Q9BSC4 Q9BSC4-2 NOL10 Nucleolar protein 10 0 206.2 2.05E-15 70659000 63915 67783 59915 60388 60266 54092 57262 67123 69741 60781 FALSE TRUE 61417.13114 65849.89521 70742.9733 63504.63192 62204.51062 55185.7773 57962.78948 65736.88659 61824.29406 56664.24873 1.083877974 1.162106561 1.248458682 1.120717795 1.097773499 0.973908214 1.022916403 1.160112206 1.091063509 1 15.79015116 3.297970651 3.079325186 1.064316006 1.166045579 0.375835456 0.062194361 0.302402078 5.818265281 0.019697675 0.026868035 1985.960703 -3.297970651 0.101729573 TVTNAVVTVPAYFNDSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVTNAVVTVPAYFNDSQR 18 0 P11142;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 278.64 8.09E-39 247520000 506400 528310 426730 468580 437130 372840 451760 472830 543840 559450 FALSE TRUE 486609.3281 513243.1161 503849.6036 492763.47 451190.6834 380379.0803 457288.774 463065.8953 482105.5632 521557.9532 0.932991866 0.984057693 0.966047206 0.944791402 0.865082549 0.729313162 0.876774616 0.887851278 0.924356651 1 18.99246804 3.29946909 4.730472643 0.868752341 0.961605359 0.242274796 0.064508019 0.255990863 11.40922618 0.018418933 0.024799501 1992.824666 -3.29946909 0.092853018 NIFDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NIFDQR 6 0 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 0 97.071 0.096521 430980000 1200100 1516700 1091500 1199400 977880 377730 1474900 977960 1224000 1441500 FALSE TRUE 1153198.765 1473445.201 1288758.33 1261301.178 1009334.398 385367.9594 1492950.267 957764.7842 1085056.651 1343865.921 0.858120403 1.096422774 0.958993237 0.93856177 0.751067783 0.28676072 1.11093692 0.712693706 0.807414367 1 20.35795778 3.30027512 4.830159593 0.760914975 0.97693252 0.155354974 0.209322534 0.345129658 15.94180147 0.058038223 0.07817156 1996.526687 -3.30027512 0.216017545 AFHPTYEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 AFHPTYEEK 9 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;; 146.79 9.40E-05 1597710000 2422070 2774980 2222240 2310650 2330440 1631360 2494310 2332300 2649890 2792320 FALSE TRUE 2327412.827 2695840.287 2623848.201 2429902.923 2405400.719 1664347.217 2524836.112 2284137.19 2349085.596 2603193.679 0.894060571 1.035589595 1.007934301 0.933431478 0.924019115 0.639348209 0.969899448 0.877436515 0.902386025 1 21.31185122 3.300470771 2.90803312 0.872594782 0.981776721 0.1536398 0.09723733 0.415761549 7.141276282 0.028192913 0.038695693 1997.426334 -3.300470771 0.109181939 DDEFSVSSVLASDVIHATR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDEFSVSSVLASDVIHATR 19 0 Q9Y5S2;H0YLY0 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 ; 204.23 4.68E-16 50817000 41846 36298 40445 34782 34494 33250 33180 34270 35875 33989 FALSE TRUE 40210.61206 35262.81658 47754.31119 36577.10319 35603.53084 33922.33778 33586.06677 33562.31252 31802.6204 31686.89476 1.268998189 1.112851759 1.507068192 1.154329052 1.123604288 1.070547873 1.059935567 1.059185912 1.003652161 1 14.95159867 3.300641347 2.51659817 1.051266821 1.281588253 0.556819307 0.096100679 0.211183284 2.728734389 0.027990938 0.039037181 1998.211009 -3.300641347 0.230321432 VQAAEHTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQAAEHTLR 9 0 Q9GZZ9-2;Q9GZZ9;E7EWE1;E7EQ61;C9JRV9;C9J5W5 Q9GZZ9-2 UBA5 Ubiquitin-like modifier-activating enzyme 5 0 ;;; 171.85 5.66E-05 1315440000 915180 1063360 910560 898810 851990 443424 1067140 818080 1016810 1112880 FALSE TRUE 879413.7538 1033034.014 1075118.447 945197.6918 879395.0321 452390.3371 1080199.979 801186.3621 901385.9916 1037503.646 0.847624735 0.995691936 1.036255102 0.911030718 0.847606691 0.436037347 1.041152947 0.772225105 0.868802722 1 19.98468498 3.301052249 3.68916062 0.809494874 0.963282007 0.118400135 0.159863172 0.418223046 11.43236304 0.044988247 0.060844071 2000.102485 -3.301052249 0.153787134 HDDYLVMLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HDDYLVMLK 9 0 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ; 75.682 0.037571 550030000 1155060 1104060 960360 991900 1001110 930470 1079600 794440 1299550 1212600 FALSE TRUE 1109918.978 1072573.29 1133918.415 1043092.078 1033311.612 949284.7409 1092812.468 778034.5364 1152030.532 1130469.522 0.981821232 0.948785676 1.00305085 0.922706944 0.91405526 0.839726081 0.966689014 0.68824017 1.019072615 1 20.10849067 3.301355068 1.821306101 0.873082982 0.974775304 0.059273356 0.091724154 0.584928381 3.99163877 0.028756163 0.042439288 2001.497574 -3.301355068 0.101692322 SDALETLGFLNHYQMK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDALETLGFLNHYQMK 16 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 295.66 1.14E-45 9773710000 2911500 2903460 2551930 2679390 2549170 2577300 2841210 2342080 3144180 2925330 FALSE TRUE 2797715.361 2820656.164 3013120.518 2817673.639 2631166.368 2629414.772 2875981.578 2293715.23 2787265.868 2727194.793 1.02585828 1.034270148 1.104842428 1.033176525 0.964788571 0.964146301 1.054556713 0.841052951 1.02202669 1 21.37898632 3.301683116 4.043062865 0.962717437 1.055049599 0.289141786 0.056550213 0.243563986 7.938654896 0.016389862 0.022116901 2003.009992 -3.301683116 0.092332162 LILDVFCGSQMHFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LILDVFCGSQMHFVR 15 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 237.48 9.72E-18 410100000 377960 435610 358250 356760 288340 107186 424440 251620 309260 477010 FALSE TRUE 363188.9053 423186.8293 422993.7442 375172.4264 297614.718 109353.3744 429634.4237 246423.9591 274154.1013 444701.6878 0.816702332 0.951619571 0.951185381 0.843649657 0.669245758 0.245902764 0.966118266 0.554133177 0.616489905 1 18.76247835 3.302266118 3.938076301 0.646220047 0.907755866 0.210467931 0.2024374 0.294035616 9.097330211 0.055379036 0.074793 2005.700665 -3.302266118 0.261535819 EEIVYLPCIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEIVYLPCIYR 11 0 Q13228;Q13228-4;Q13228-3;H0Y532;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 161.79 6.02E-05 168940000 339890 403090 334930 285090 309770 252872 256456 273890 276410 319750 FALSE TRUE 326606.723 391594.2679 395459.3015 299803.5291 319734.0334 257985.2451 259594.5852 268234.0758 245033.0956 298093.0477 1.095653607 1.313664545 1.326630408 1.005738079 1.072598089 0.86545207 0.870850854 0.899833384 0.822002048 1 18.1854032 3.302780789 1.462394296 0.887791042 1.247963581 0.721127193 0.089712726 0.190562211 0.845918442 0.029498789 0.046123401 2008.078975 -3.302780789 0.360172539 GKGPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKGPLK 6 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6;E5RGY7;Q9UI47 P35221-2;Q9UI47 CTNNA1;CTNNA2;CTNNA3 Catenin alpha-1;Catenin alpha-2;Catenin alpha-3 0 64.563 0.096993 2500300000 2099800 2134700 1555700 1899300 2172100 2009300 2275900 2176100 2502200 2257000 FALSE TRUE 2017737.495 2073820.446 1836849.596 1997323.101 2241967.569 2049929.423 2303753.145 2131162.775 2218160.746 2104131.38 0.958940831 0.985594562 0.872972864 0.949238778 1.065507406 0.974240222 1.094871341 1.012846819 1.054193083 1 21.00479336 3.30279746 7.169950662 1.034160747 0.939090366 0.540087053 0.041564301 0.163734319 15.06934362 0.011033549 0.014913056 2008.156061 -3.30279746 -0.095070381 VFSWGFGGYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFSWGFGGYGR 11 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 200.54 1.08E-07 1013220000 304360 313940 289567 272160 267049 171115 270300 301780 260124 281017 FALSE TRUE 292465.2747 304986.7386 341898.1983 286206.2102 275638.8736 174575.0625 273608.0123 295548.1375 230595.814 261983.4683 1.116350114 1.164144977 1.305037301 1.092459047 1.052123157 0.666359079 1.044371288 1.128117509 0.880192233 1 17.99911625 3.30284753 2.9424268 0.968224751 1.190819498 0.415496877 0.125315744 0.283198999 4.974315218 0.039360122 0.054038169 2008.387595 -3.30284753 0.222594748 KSDLFQDDLYPDTAGPEAALEAEEWVSGR ddPTM_BT-474_Pertuzumab_2h_R1 5 KSDLFQDDLYPDTAGPEAALEAEEWVSGR 29 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;; 224.06 2.28E-34 2784984000 545228 601771 439190 572323 596593 582328 618600 692733 668949 694331 FALSE TRUE 523919.887 584609.0803 518561.4027 601860.6586 615782.9557 594103.0711 626170.6118 678427.8215 593012.714 647303.3429 0.809388508 0.903145468 0.801110342 0.929796926 0.951305076 0.917812456 0.967352662 1.048083296 0.916127995 1 19.30408243 3.303088523 0.721173073 0.994122389 0.82663384 0.605084277 0.045577979 0.515082971 0.571593438 0.025854113 0.05143978 2009.502372 -3.303088523 -0.167488549 QLLLTADDR ddPTM_BT-474_Pertuzumab_2h_R1 4 QLLLTADDR 9 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 196.79 6.76E-05 1371130000 2179180 2077120 2047170 1762660 1625440 894980 1612900 1580560 1568260 1774720 FALSE TRUE 2094015.236 2017882.571 2417139.158 1853631.094 1677723.754 913077.1088 1632639.153 1547920.884 1390237.699 1654516.634 1.265635651 1.219620601 1.460933731 1.120346001 1.014026526 0.551869404 0.986777116 0.935572875 0.840268191 1 20.65797837 3.306063438 2.640110376 0.872428138 1.302777965 0.668364499 0.136398001 0.158894296 2.254831092 0.040296303 0.056053903 2023.314704 -3.306063438 0.430349827 VMLGETNPADSKPGTIR ddPTM_BT-474_Pertuzumab_2h_R1 4 VMLGETNPADSKPGTIR 17 1 Q32Q12;P22392-2;J3KPD9;P22392;E7ERL0;O60361;P15531;P15531-2 Q32Q12;O60361;P15531 NME1-NME2;NME2;NME1;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase;Nucleoside diphosphate kinase A 0 ;;; 228.9 1.17E-15 4001200000 1507739 1786601 1338714 1225808 1407997 1554635 1213236 1320998 1468387 1497897 FALSE TRUE 1448814.893 1735648.889 1580649.399 1289072.098 1453286.502 1586070.785 1228083.945 1293718.93 1301701.864 1396443.102 1.037503706 1.242906987 1.131911065 0.923111078 1.040705848 1.135793347 0.879437152 0.926438698 0.932155318 1 20.41332536 3.307107138 0.646316559 0.935594339 1.158827994 0.349105055 0.089156 0.949859388 0.828468181 0.058515185 0.122160499 2028.182998 -3.307107138 0.223233655 SGNFGGSR ddPTM_BT-474_Pertuzumab_2h_R1 8 SGNFGGSR 8 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 144.9 0.0013446 4284260000 2983054 3170031 2786114 2804471 2711477 2127056 2979195 2810494 3050748 3137669 FALSE TRUE 2866472.952 3079624.82 3289626.777 2949210.084 2798694.12 2170066.53 3015655.28 2752456.317 2704439.877 2925151.884 0.979939868 1.052808518 1.124600331 1.008224599 0.956768821 0.741864565 1.030939725 0.940961846 0.924546822 1 21.48008011 3.307117221 3.46981967 0.927587055 1.053441022 0.324353393 0.07871016 0.267921495 6.458415527 0.02283222 0.031055527 2028.230089 -3.307117221 0.125853967 GKLEEQRPER ddPTM_BT-474_Pertuzumab_2h_R1 13 GKLEEQRPER 10 2 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;;;;;;;; 187.42 6.93E-07 20911135000 13860390 13879377 11591689 13342992 13696970 14929148 14879885 14889064 16399609 15959379 FALSE TRUE 13318710.64 13483550.76 13686565.06 14031625.42 14137545.48 15231025.6 15061989.48 14581599.63 14537994.14 14878436.05 0.895168726 0.906247855 0.919892724 0.943084701 0.950203734 1.023698025 1.012336877 0.980049219 0.977118435 1 23.82671955 3.307156273 1.408113893 0.996530954 0.904371573 0.853780659 0.016299077 0.156909027 0.646890021 0.006079912 0.009654643 2028.412477 -3.307156273 -0.09215938 AVS(ph)LDSPVSVGSSPPVK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 AVS(0.999)LDS(0.001)PVSVGSSPPVK;AVS(1)LDSPVSVGSSPPVK;AVS(0.774)LDS(0.226)PVSVGSSPPVK 278.89 7.93E-36 329651000 627900 600870 355597 483250 819670 562720 559800 839250 699060 639580 TRUE FALSE 603360.9738 583733.7759 419861.2881 508190.5904 846035.43 574098.5839 566650.9999 821919.1942 619705.6395 596260.6769 1.011908042 0.978990899 0.704157266 0.852296001 1.418901938 0.962831537 0.950341053 1.378456145 1.039319988 1 19.18558367 3.307998653 24.99997387 1.14019163 0.880370055 0.316433638 0.170483524 56.17429236 20223.46613 0.047649927 0.06451829 2032.350706 -3.307998653 -0.259821575 FYQLER ddPTM_BT-474_Pertuzumab_2h_R1 1 FYQLER 6 0 Q9Y3P9;A0A0U1RQX4;Q5R372-4;Q5R372;Q5R372-3 Q9Y3P9;Q5R372-4 RABGAP1;RABGAP1L Rab GTPase-activating protein 1;Rab GTPase-activating protein 1-like 0 113.08 0.061517 119590000 125350 149660 131560 123090 121610 108810 118580 113010 125510 162210 FALSE TRUE 120451.1834 145391.8433 155335.8185 129442.6897 125521.6961 111010.2128 120031.2175 110676.304 111262.631 151223.3722 0.796511688 0.961437648 1.027194515 0.85597013 0.830041641 0.734081056 0.793734565 0.731873006 0.735750231 1 17.20632161 3.308433823 2.581624315 0.780013388 0.931643219 0.240579874 0.092681027 0.299012346 4.059215137 0.026383026 0.036852901 2034.388177 -3.308433823 0.151629831 MAQYLEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 MAQYLEEER 9 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 140.11 0.00025562 756160000 545570 601110 565620 546680 503080 362450 654750 514830 538610 623850 FALSE TRUE 524248.5212 583966.9313 667840.1161 574894.2203 519262.0251 369778.9873 662763.0264 504198.5806 477469.2508 581596.0838 0.901396237 1.00407645 1.148288537 0.988476773 0.892822424 0.635800339 1.139558956 0.866922241 0.820963662 1 19.14965803 3.309542292 4.659456082 0.889963226 1.023412796 0.160681644 0.13245378 0.367260798 15.10442993 0.037292642 0.050400966 2039.587265 -3.309542292 0.133449571 IFCCHGGLSPDLQSMEQIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFCCHGGLSPDLQSMEQIRR 20 1 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;F8W1A0;P62140;E7ETD8;P62136;P62136-2;P62136-3 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 202.5 7.50E-22 687300000 422920 475020 315916 333342 331647 411770 332261 294504 329200 333931 FALSE TRUE 406391.8188 461472.8947 373009.0487 350545.8206 342314.7269 420096.2715 336327.3095 288422.3895 291830.5961 311313.5559 1.305409967 1.482341151 1.198177984 1.126021703 1.099581822 1.349431348 1.080349066 0.926469098 0.937416924 1 18.24800887 3.309803755 0.378097106 0.926129564 1.474586333 0.589963022 0.111338395 1.542143164 0.364717768 0.121100677 0.348654449 2040.81555 -3.309803755 0.548456769 EKHPNSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.299)S(0.701)PR 120.6 0.00038655 178430000 512970 464070 403100 424500 389810 364520 424080 376380 418570 440280 TRUE FALSE 492922.5653 450835.178 475949.1369 446408.4959 402348.5927 371890.8442 429270.0179 368607.6215 371055.6884 410459.4434 1.200904433 1.098367172 1.159552167 1.087582471 0.980239581 0.906035542 1.045828095 0.898036645 0.904000856 1 18.64688015 3.309913593 2.407127175 0.947520657 1.147326332 0.772680382 0.049140314 0.128805475 1.52326277 0.014419679 0.02035105 2041.331762 -3.309913593 0.199805675 IS(ph)ASSATR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISASSATR 8 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;A0A1B0GV30;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 IS(0.863)AS(0.116)S(0.021)ATR;IS(0.998)AS(0.002)SATR 113.46 0.0029838 310280000 376930 401890 312710 348340 318670 328860 332050 337160 342340 374260 TRUE FALSE 362199.1589 390428.4907 369223.6532 366317.8691 328920.31 335509.7745 336113.7272 330197.5282 303478.9984 348911.0368 1.038084556 1.118991518 1.058217179 1.049889027 0.942705375 0.961591177 0.963322142 0.94636596 0.869789048 1 18.41249971 3.31003597 3.476744527 0.945828685 1.074038913 0.724552 0.036042469 0.116774682 2.817056874 0.010133709 0.013801882 2041.907058 -3.31003597 0.128210228 KLTSDLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLTSDLGR 8 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 108.43 0.010298 0 576050 640000 491080 525700 466940 251940 569040 535370 514770 483700 FALSE TRUE 553537.3291 621747.8266 579829.08 552831.44 481959.5492 257034.3994 576004.0817 524314.4224 456335.4677 450938.5682 1.227522701 1.378786093 1.285827208 1.225957323 1.068792033 0.569998704 1.277344903 1.162718072 1.011968148 1 18.78257138 3.310396721 3.499296816 1.029081953 1.297944686 0.360146531 0.174340742 0.293595326 7.16661364 0.053584357 0.072968962 2043.603893 -3.310396721 0.268862733 NFWNGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFWNGR 6 0 P47755;P52907 P47755;P52907 CAPZA2;CAPZA1 F-actin-capping protein subunit alpha-2;F-actin-capping protein subunit alpha-1 0 ; 131.65 0.035445 2102040000 879190 848010 775640 801840 723630 663010 722030 855750 871840 860130 FALSE TRUE 844830.2828 823825.5851 915815.402 843223.0585 746906.2161 676416.5165 730866.4191 838078.4635 772872.3783 801872.629 1.053571667 1.027377111 1.14209585 1.051567329 0.931452439 0.843546085 0.911449515 1.045151603 0.963834343 1 19.61301357 3.310538935 5.453601329 0.950554686 1.073233324 0.515829072 0.056846954 0.186677579 9.979803228 0.01782918 0.024099296 2044.273199 -3.310538935 0.122678638 ELAGHTGYLSCCR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELAGHTGYLSCCR 13 0 P62873-2;P62873;B3KVK2;F6X3N5;F6UT28 P62873-2 GNB1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 0 ; 175.48 1.82E-05 917890000 611510 872260 652020 654320 426750 156418 725930 468510 480980 573700 FALSE TRUE 587611.5131 847383.9988 769854.5181 688089.5336 440476.8013 159580.8791 734814.1485 458835.1048 426381.1668 534842.788 1.098662123 1.584360896 1.439403382 1.286526712 0.823563131 0.298369694 1.373888112 0.857887804 0.797208407 1 19.02875536 3.310810128 4.658836089 0.861507511 1.388081183 0.445400728 0.270523729 0.191721734 7.83591626 0.076699955 0.103703932 2045.550132 -3.310810128 0.526573673 HITIFSPEGR ddPTM_BT-474_Pertuzumab_2h_R1 5 HITIFSPEGR 10 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4;G3V4S5;G3V2S7 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;;; 211.78 5.26E-08 2149060000 1462390 1761010 1495650 1322670 1298400 575909 1626780 922590 1271480 1526780 FALSE TRUE 1405238.182 1710787.719 1765947.226 1390933.157 1340164.215 587554.2746 1646689.02 903538.1941 1127146.921 1423369.831 0.987261463 1.201927765 1.240680523 0.977211352 0.941543221 0.412791013 1.156894705 0.634788074 0.791886196 1 20.44087913 3.311262607 2.475949895 0.790883626 1.143272802 0.339443525 0.2000772 0.283281657 3.541031053 0.0567577 0.079856361 2047.682444 -3.311262607 0.352389176 DTFEHDPSESIDEFNK ddPTM_BT-474_Pertuzumab_2h_R1 4 DTFEHDPSESIDEFNK 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;; 322.99 2.61E-58 1577870000 2112570 1977290 2184290 2479660 2337120 2163260 2625020 2846880 3491810 3665400 FALSE TRUE 2030008.429 1920899.625 2579039.792 2607635.55 2412295.587 2207002.599 2657145.78 2788090.933 3095434.368 3417139.193 0.594066649 0.562136781 0.754736534 0.763104867 0.705940101 0.645862657 0.777593662 0.815913773 0.90585551 1 21.70435758 3.31131252 0.075424074 1.407311807 1.66E-11 0.789203966 0.05887219 27.53434281 0.589300114 3.90665765 7.097022512 2047.917795 -3.31131252 -1.407311807 SKDPGSAER ddPTM_BT-474_Pertuzumab_2h_R1 1 SKDPGSAER 9 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;A0A087WYS3;A0A087WV57;Q5TH12;Q5TH08;Q5TH07 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 0 60.102 0.089307 133870000 102220 108790 69407 105720 109370 126550 122040 120600 144870 129660 FALSE TRUE 98225.12939 105687.4157 81950.38885 111176.2219 112887.9854 129108.9277 123533.562 118109.5679 128424.9649 120878.0127 0.812597156 0.874331182 0.677959432 0.919738995 0.933900077 1.068092739 1.021968837 0.977097201 1.06243445 1 16.88319232 3.311331773 2.190091501 1.017136801 0.798075487 0.743071578 0.058342152 0.147473406 1.447083884 0.017193601 0.024652576 2048.008586 -3.311331773 -0.219061315 NFLIEPFVPHSQAEEFYVCIYATR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFLIEPFVPHSQAEEFYVCIYATR 24 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 206.46 8.60E-25 459740000 525540 509090 425840 457240 395510 419240 362810 390430 515890 521910 FALSE TRUE 505001.3158 494571.2517 502798.7608 480838.2112 408231.9383 427717.32 367250.1773 382367.4841 457328.33 486560.5708 1.037900204 1.016463892 1.033373419 0.988239163 0.83901566 0.879062846 0.7547882 0.785857932 0.939920654 1 18.89225989 3.311477056 3.656530562 0.843301291 1.026062666 0.533578346 0.068458506 0.154788399 4.095495736 0.019589524 0.026634893 2048.693816 -3.311477056 0.182761375 VLIAAHGNSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLIAAHGNSLR 11 0 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 ; 174.4 1.11E-05 5951300000 3117900 3390900 2696700 2671900 2314900 1245130 2611000 2242000 2410400 2339600 FALSE TRUE 2996049.021 3294194.852 3184053.678 2809797.079 2389360.861 1270307.382 2642954.199 2195701.917 2136781.497 2181136.808 1.37361811 1.510310972 1.45981383 1.288225969 1.095465838 0.5824061 1.211732427 1.00667776 0.979664132 1 21.05664883 3.311865611 2.639855241 0.972849703 1.446765939 0.672095848 0.151060949 0.162158849 2.298941752 0.045202066 0.063099127 2050.527562 -3.311865611 0.473916235 LTISPDYAYGATGHPGIIPPHATLVFDVELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTISPDYAYGATGHPGIIPPHATLVFDVELLK 32 0 P62942;Q5W0X3;Q1JUQ5;Q5VVH2 P62942 FKBP1A;FKBP12-Exip2;FKBP1C Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 148.53 2.07E-10 217030000 79141 84318 65895 119160 96301 98707 114070 98748 146430 156990 FALSE TRUE 76048.08223 81913.3332 77803.69233 125309.8619 99398.60912 100702.9232 115466.0228 96708.81929 129807.8803 146356.9275 0.519606988 0.559681968 0.531602389 0.856193581 0.679152062 0.688063933 0.788934455 0.660773774 0.886926793 1 17.15913151 3.312257617 0.086904604 1.320305716 3.69E-20 0.686853819 0.086153925 26.91472324 0.670710579 3.42313814 6.77619096 2052.379257 -3.312257617 -1.320305716 HIYLLPSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIYLLPSGR 9 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 101.11 0.0042083 719430000 561530 654220 515620 526410 454510 173678 658150 361550 575060 675780 FALSE TRUE 539584.7868 635562.2861 608804.0039 553578.0832 469129.7269 177189.8882 666204.6366 354083.8662 509781.5996 630008.8187 0.8564718 1.008814904 0.966342035 0.87868307 0.744639937 0.281249854 1.057452875 0.562030016 0.809165816 1 19.2650125 3.312498072 3.598330598 0.709841877 0.945528335 0.154698083 0.208260112 0.351992484 9.028867564 0.056996697 0.077587551 2053.515908 -3.312498072 0.235686458 KFLPLFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFLPLFDR 8 1 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 133.13 0.0014951 2367600000 3371900 5156400 3532000 3782400 1785140 817260 4001700 2687500 2418200 2625200 FALSE TRUE 3240122.42 5009344.521 4170310.969 3977610.117 1842560.649 833785.5571 4050674.002 2632002.186 2143696.074 2447392.866 1.323907766 2.0468085 1.703981011 1.625243815 0.752866724 0.340683169 1.655097577 1.075431012 0.875910077 1 21.22281428 3.312549165 6.493359095 0.98337775 1.712885459 0.509759708 0.34708261 0.183420296 12.73061291 0.100098124 0.13541075 2053.757514 -3.312549165 0.729507709 TESSPSEASQHSMQS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 3 TESSPSEASQHSMQSPQK 18 0 Q9UQR0 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 TESSPSEASQHS(0.007)MQS(0.993)PQK;TESSPSEASQHS(0.003)MQS(0.997)PQK;TESSPSEASQHS(0.026)MQS(0.974)PQK 170.56 9.95E-12 337830000 340210 361874 263602 321802 295518 306811 302591 305873 334664 362072 TRUE FALSE 326914.2171 351553.7078 311240.7452 338410.2398 305023.6049 313014.9286 306294.1992 299556.6157 296674.3457 337548.5409 0.968495423 1.041490823 0.922062185 1.002552815 0.903643677 0.927318269 0.90740786 0.88744752 0.878908689 1 18.36473546 3.313386117 1.262054993 0.907230825 0.99179485 0.30079301 0.04411315 0.44441922 1.481384231 0.014880249 0.02463228 2057.719235 -3.313386117 0.084564025 EEGGFEYKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEGGFEYKR 9 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 138.66 0.00020906 957640000 690150 762240 570320 695330 834030 875180 820660 857900 980710 895350 FALSE TRUE 663178.175 740501.6615 673389.5107 731216.0646 860857.3324 892876.7392 830703.4826 840184.0652 869383.9123 834707.147 0.794504009 0.887139477 0.806737445 0.8760151 1.031328575 1.069688624 0.99520351 1.006561485 1.04154363 1 19.6709106 3.313457356 4.177039726 1.023640265 0.836400381 0.894097818 0.03107492 0.06333394 2.120765893 0.008671198 0.011751563 2058.056797 -3.313457356 -0.187239885 S(ph)KSLDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSLDSR 7 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 S(0.496)KS(0.496)LDS(0.008)R 52.79 0.086958 305910000 301870 251610 206290 245120 272220 273450 247690 307480 274060 278200 TRUE FALSE 290072.5867 244434.3292 243571.1919 257770.6726 280976.2035 278979.3464 250721.3043 301130.4305 242949.8578 259357.2662 1.11842861 0.942461851 0.939133865 0.993882594 1.083355819 1.075656566 0.966702449 1.161064176 0.936738196 1 17.98458126 3.314398952 8.884326629 1.049901062 0.989918169 0.039307974 0.075969651 0.629029417 67.10322553 0.020357064 0.027557354 2062.523719 -3.314398952 -0.059982893 YGYTHLSTGDLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGYTHLSTGDLLR 13 0 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 133.32 0.00010855 437020000 310430 480350 380810 369360 263110 134030 425290 281140 293470 402990 FALSE TRUE 298298.0524 466650.8883 449630.8381 388422.7139 271573.1721 136740.1784 430494.8262 275334.3608 260156.5159 375695.1284 0.793989674 1.242099919 1.196797095 1.03387743 0.722855187 0.363965801 1.145862147 0.732866465 0.6924671 1 18.51920288 3.316276031 5.137963602 0.767981884 1.095730951 0.289990375 0.221959965 0.243928076 11.38118334 0.061513635 0.083261781 2071.45752 -3.316276031 0.327749067 HAFSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HAFSLK 6 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 111.69 0.027635 1155940000 3120300 3367800 2682600 2953900 2850300 2570100 3357800 2516100 3578200 3791800 FALSE TRUE 2998355.226 3271753.641 3167405.494 3106351.133 2941982.488 2622069.183 3398893.761 2464141.656 3172017.737 3534978.009 0.848196288 0.925537198 0.896018444 0.878746947 0.832249163 0.741749786 0.961503509 0.697074112 0.897323188 1 21.75326981 3.316573003 4.199358414 0.832509371 0.892368861 0 0.088634414 0.543280331 18.20062708 0.023768771 0.032246218 2072.874469 -3.316573003 0.05985949 S(ph)PACSSLTPSLCK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPACSSLTPSLCK 13 0 Q96R06;F5GZT2;J3KSV2;J3QRV8 Q96R06 SPAG5 Sperm-associated antigen 5 1 S(1)PACSSLTPSLCK 135.81 8.35E-05 308880000 181040 207910 193200 182680 167220 187550 135530 183180 180570 210020 TRUE FALSE 173964.7566 201980.6104 228115.5377 192108.1367 172598.7832 191342.3895 137188.6567 179397.269 160072.4506 195795.1583 0.888503874 1.031591445 1.165072414 0.981168985 0.88152733 0.977258024 0.700674408 0.916249771 0.817550607 1 17.57898556 3.316979476 3.559492061 0.871471905 1.034575297 0.303334216 0.100323811 0.254452352 6.364751082 0.028311245 0.038639572 2074.815462 -3.316979476 0.163103392 KPPAPPS(ph)PVQSQS(ph)PSTNWSPAVPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(1)PVQS(0.006)QS(0.825)PS(0.138)T(0.03)NWSPAVPVK 212.46 2.91E-25 3423900000 1750400 1494700 1465100 1676300 1944500 1745200 1692400 2229800 2272500 2276300 TRUE FALSE 1681992.433 1452072.619 1729876.161 1762814.044 2007046.608 1780489.14 1713112.097 2183753.851 2014535.327 2122124.173 0.792598498 0.684254313 0.815162554 0.830683739 0.945772464 0.839012703 0.807262892 1.029041504 0.949301343 1 21.01707765 3.317600719 0.318627524 1.016881334 0.65778504 0.613739062 0.063429781 1.955484588 0.312946272 0.078217637 0.255749063 2077.785538 -3.317600719 -0.359096294 EHFGTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHFGTVK 7 0 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 ; 139.31 0.0027006 1691240000 2133200 2165100 1806880 1835060 1787230 1198410 2132750 1346690 2207500 2276400 FALSE TRUE 2049832.186 2103353.468 2133423.41 1929767.667 1844717.876 1222642.671 2158851.232 1318880.381 1956913.855 2122217.4 0.965891706 0.991111216 1.005280331 0.909316673 0.869240765 0.576115657 1.017262054 0.621463372 0.9221081 1 21.01714102 3.317722146 2.552213625 0.800632277 0.984517144 0.182782148 0.137095324 0.360327857 4.77778668 0.038208898 0.053756485 2078.36656 -3.317722146 0.183884867 YHSDEYIK ddPTM_BT-474_Pertuzumab_2h_R1 4 YHSDEYIK 8 0 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19 Q92769 HDAC2 Histone deacetylase 2 0 ;;; 179.21 0.00024555 4761750000 5202510 5100620 4410100 3841630 4142840 2077650 4810210 1801430 4437190 4713910 FALSE TRUE 4999190.158 4955155.312 5207103.172 4039896.985 4276098.211 2119661.507 4869078.789 1764229.841 3933498.793 4394632.677 1.137567238 1.127547096 1.184877908 0.919279786 0.973027446 0.482329619 1.107960357 0.401451036 0.895068845 1 22.06731115 3.318483281 1.59868045 0.742347891 1.148255862 0.332505574 0.210859416 0.359747972 1.897455501 0.065329685 0.10102042 2082.012253 -3.318483281 0.405907971 GFTIPEAFR ddPTM_BT-474_Pertuzumab_2h_R1 6 GFTIPEAFR 9 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;;;;; 170.3 0.0001345 4394108000 4182269 4871925 3827202 3748865 3862190 2083787 4080322 3652317 3685110 4260582 FALSE TRUE 4018821.304 4732982.469 4518862.537 3942344.372 3986420.849 2125922.601 4130258.201 3576895.378 3266791.762 3972008.986 1.011785552 1.191584029 1.137676816 0.992531584 1.003628356 0.53522603 1.039841102 0.9005255 0.822453266 1 21.92143746 3.319082509 2.282319681 0.86989558 1.115320364 0.364356543 0.138455564 0.310088757 3.298931923 0.041309078 0.059133175 2084.88694 -3.319082509 0.245424784 ALNS(ph)ALAEEITLHYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALNSALAEEITLHYAR 16 0 A0A494C178;Q6ZSY5-2;Q6ZSY5 A0A494C178 PPP1R3F Protein phosphatase 1 regulatory subunit 3F 1 ALNS(1)ALAEEITLHYAR;ALNS(1)ALAEEITLHYAR 240.31 4.75E-20 149696000 52497 48561 40664 95111 59032 107684 78824 146872 100640 105719 TRUE FALSE 50445.3592 47176.08783 48012.88937 100019.6901 60930.81789 109861.4443 79788.67169 143839.0419 89215.76912 98558.55797 0.511831344 0.478660492 0.487150891 1.014825015 0.618219454 1.114681937 0.809555997 1.459427216 0.905205707 1 16.58869353 3.31949869 0.704257293 1.138809888 0.421663027 0.538297095 0.207486592 0.561600061 0.589311649 0.116875477 0.239951942 2086.88583 -3.31949869 -0.717146861 SQS(ph)PAASDCSSSSSSASLPSSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQSPAASDCSSSSSSASLPSSGR 23 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SQS(1)PAASDCSSSSSSASLPSSGR;S(0.003)QS(0.997)PAASDCSSSSSSASLPSSGR;S(0.012)QS(0.988)PAASDCSSSSSSASLPSSGR;S(0.001)QS(0.999)PAASDCSSSSSSASLPSSGR 414.21 1.25E-157 2766900000 580822 613810 497006 589945 554528 664640 647121 658728 766869 787954 TRUE FALSE 558122.8341 596304.7398 586826.04 620392.1321 572364.8967 678079.4762 655040.6604 645125.0366 679817.2461 734585.1737 0.759779606 0.811757113 0.79885364 0.844547582 0.779167505 0.923078086 0.891715057 0.878216795 0.925443734 1 19.48657025 3.320876568 0.124251125 1.092125037 0.574551102 0.818798672 0.030715721 8.226521618 0.305762475 0.357715398 0.91871144 2093.517365 -3.320876568 -0.517573935 RKPGQADNER ddPTM_BT-474_Pertuzumab_2h_R1 4 RKPGQADNER 10 2 Q9NU22 Q9NU22 MDN1 Midasin 0 ;;; 218.11 3.90E-09 138178000 128986 132894 108484 119374 114283 93893 125347 121967 135733 156463 FALSE TRUE 123945.0845 129103.9932 128089.472 125534.9064 117959.0165 95791.58079 126881.0341 119448.3388 120325.1589 145865.6216 0.849721018 0.885088562 0.878133384 0.860620241 0.80868278 0.656711154 0.869848787 0.818893016 0.824904165 1 17.15428038 3.321089646 5.07832531 0.815809598 0.871609624 0.037169917 0.079395535 0.505344484 22.538637 0.021551312 0.029204354 2094.54476 -3.321089646 0.055800026 LIFYDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LIFYDLR 7 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 95.62 0.031016 350000000 640850 712630 669870 583130 544750 281610 639350 486460 564240 656440 FALSE TRUE 615804.8735 692306.4901 790930.4102 613225.4092 562272.3785 287304.3471 647174.5566 476414.431 500189.8407 611978.7341 1.006252079 1.131259064 1.29241486 1.002037122 0.918777642 0.469467861 1.057511512 0.778482003 0.817332062 1 19.223122 3.321280122 2.944969753 0.820343326 1.141067585 0.412377746 0.162408527 0.231268313 4.047512539 0.046051668 0.063873449 2095.463606 -3.321280122 0.320724259 TQFEDLVPS(ph)PTSEK ddPTM_BT-474_Pertuzumab_2h_R1 6 TQFEDLVPSPTSEK 14 0 Q9Y4J8;Q9Y4J8-2;Q9Y4J8-15;Q9Y4J8-14;Q9Y4J8-13;Q9Y4J8-6;Q9Y4J8-10;Q9Y4J8-11;M0QZ28;M0R0C4 Q9Y4J8 DTNA Dystrobrevin alpha 1 TQFEDLVPS(0.948)PT(0.032)S(0.02)EK;TQFEDLVPS(0.978)PT(0.019)S(0.004)EK;TQFEDLVPS(1)PTSEK;TQFEDLVPS(0.964)PT(0.036)SEK;TQFEDLVPS(0.999)PT(0.001)SEK;TQFEDLVPS(0.998)PT(0.002)SEK 263.04 1.42E-24 2771547000 3252596 3240555 2639596 2991214 3163596 3116603 3143204 3492943 3551633 3231252 TRUE FALSE 3125480.952 3148137.544 3116629.715 3145590.913 3265355.938 3179622.848 3181671.471 3420812.506 3148466.512 3012396.424 1.037539723 1.045060842 1.034601452 1.044215459 1.08397285 1.055512755 1.056192819 1.135578465 1.045170047 1 21.52248021 3.321314579 6.254896255 1.073039767 1.03977071 0.05056926 0.032865767 0.367794009 22.1588971 0.009208574 0.012469609 2095.629866 -3.321314579 -0.033269057 LGNSCEFR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGNSCEFR 8 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;; 122.19 0.0032597 736090000 775610 823020 688750 704490 721220 528840 769340 752870 759080 774350 FALSE TRUE 745298.3037 799548.2754 813222.4462 740848.8133 744418.6963 539533.5071 778755.4131 737322.9714 672912.4207 721902.5848 1.032408416 1.10755702 1.12649887 1.026244855 1.031189958 0.747377165 1.078754155 1.021360758 0.932137431 1 19.46144464 3.321795414 2.650553346 0.968782546 1.087983065 0.283885559 0.086420776 0.37499024 5.351681759 0.026264909 0.036865935 2097.951354 -3.321795414 0.119200519 ILSQST(ph)DSLNMR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ILSQS(0.401)T(0.599)DSLNMR 271.53 1.14E-26 847750000 670360 751550 632980 653430 558410 586020 584590 663330 576480 623730 TRUE FALSE 644161.5901 730116.5298 747373.5666 687153.6006 576371.7648 597869.7259 591744.3873 649632.0037 511040.4072 581484.2115 1.107788616 1.255608519 1.285286086 1.181723574 0.991207935 1.028178778 1.017644805 1.11719629 0.878855173 1 19.14938049 3.322510832 4.894616673 1.02041901 1.221588959 0.662915866 0.07024844 0.129120056 5.411232852 0.019712643 0.02672984 2101.410183 -3.322510832 0.20116995 NFEHLNSDFDR ddPTM_BT-474_Pertuzumab_2h_R1 4 NFEHLNSDFDR 11 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 ;;; 187.51 3.56E-06 2049150000 1361640 1415200 1237830 1299870 1086920 1081420 1270210 1149530 1451330 1546970 FALSE TRUE 1308425.603 1374839.882 1461533.416 1366956.446 1121881.769 1103287.053 1285755.21 1125791.804 1286581.103 1442192.344 0.907247642 0.953298558 1.013410883 0.947832272 0.777900239 0.765006872 0.891528245 0.780611413 0.89210091 1 20.45983216 3.322601745 7.393316776 0.835427018 0.960748329 0.32734851 0.071054594 0.217358473 16.28847679 0.018699251 0.025319448 2101.850124 -3.322601745 0.125321311 LAQANGWGVMVSHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LAQANGWGVMVSHR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;; 191.19 5.17E-07 9759580000 5663740 5776050 4868030 4962080 3684280 2343110 5398470 3762810 4297900 4779600 FALSE TRUE 5442394.779 5611322.709 5747791.31 5218173.543 3802788.212 2390489.29 5464538.091 3685106.659 3810020.41 4455873.435 1.221397973 1.259309267 1.289935945 1.171077595 0.853432726 0.536480518 1.226367439 0.827022291 0.855055797 1 22.08727682 3.322694858 4.38259416 0.878947881 1.252213784 0.537244426 0.161313709 0.164643383 5.814251618 0.045361881 0.061613032 2102.300811 -3.322694858 0.373265902 LFLEFER ddPTM_BT-474_Pertuzumab_2h_R1 3 LFLEFER 7 0 O43663-2;O43663-4;O43663;O43663-3;H0YL53 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 ;; 130.77 0.0082156 75516000 159827 173834 146889 143537 148454 84360 170686 143163 147871 167203 FALSE TRUE 153580.7841 168876.4245 173435.1098 150944.9618 153229.1577 86065.817 172774.9063 140206.634 131085.304 155878.1919 0.985261519 1.083387115 1.112632292 0.968352019 0.983005742 0.552135074 1.108396911 0.899462794 0.84094704 1 17.25005958 3.323634615 2.6243643 0.889114467 1.058612987 0.217643368 0.139048346 0.411003837 5.751730069 0.040695957 0.057256438 2106.854844 -3.323634615 0.169498519 APFAAHGYGAFLTLSILDR ddPTM_BT-474_Pertuzumab_2h_R1 1 APFAAHGYGAFLTLSILDR 19 0 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 170.91 1.13E-11 444460000 278360 337240 255740 261230 256920 178710 284960 230730 257500 305150 FALSE TRUE 267481.3835 327622.2454 301957.9069 274712.1116 265184.0651 182323.6386 288447.4257 225965.3449 228269.6795 284481.9187 0.940240366 1.151645232 1.061430928 0.965657546 0.93216492 0.640897107 1.013939399 0.79430477 0.802404879 1 18.11797743 3.324288813 2.27158121 0.845809228 1.057307161 0.364294613 0.112191936 0.282168565 2.972766407 0.032253758 0.046368302 2110.030889 -3.324288813 0.211497933 NCWQNYLDFHR ddPTM_BT-474_Pertuzumab_2h_R1 5 NCWQNYLDFHR 11 0 P14854;A0A494C160 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;;; 205.12 3.09E-08 3588770000 3629660 3748010 3559820 3428240 2137599 1356357 3429730 2632368 3190640 3433800 FALSE TRUE 3487808.874 3641120.424 4203158.662 3605171.877 2206356.813 1383783.468 3471704.062 2578008.681 2828451.923 3201225.667 1.089522963 1.137414479 1.312984181 1.126184859 0.689222517 0.432266766 1.084492136 0.805319259 0.883552807 1 21.61019295 3.324375302 6.199228344 0.807825095 1.181011838 0.49386532 0.174120038 0.17667668 10.24821935 0.049641756 0.067243843 2110.451142 -3.324375302 0.373186742 TLEFVPINLHLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLEFVPINLHLQR 13 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 155.02 4.27E-05 965390000 785760 898010 783120 775100 690120 493460 829040 707280 803490 943410 FALSE TRUE 755051.6305 872399.634 924647.2044 815103.0039 712318.3366 503438.0993 839186.0395 692674.4208 712281.1837 879512.0004 0.858489287 0.991913281 1.051318463 0.926767348 0.809901782 0.572406174 0.954149618 0.787566765 0.80985954 1 19.74634374 3.325231102 4.249683996 0.80784283 0.971817314 0.243893704 0.115774248 0.267625088 8.938965477 0.032016102 0.043551557 2114.613993 -3.325231102 0.163974484 SLS(ph)NPDIASETLTLLSFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSNPDIASETLTLLSFLR 19 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.045)LS(0.955)NPDIASETLTLLSFLR 130.25 1.88E-05 857700000 297300 303730 224580 269230 309730 304540 280350 326500 325870 321950 TRUE FALSE 285681.1873 295067.9178 265166.6018 283124.9926 319692.7467 310698.0075 283781.0072 319757.6609 288878.6038 300144.0397 0.951813628 0.983087714 0.883464493 0.943297068 1.065131085 1.035163009 0.945482734 1.065347362 0.962466568 1 18.19529549 3.32528738 9.332275839 1.015284321 0.938975636 0.40026994 0.042992112 0.29377241 28.89315618 0.011646847 0.015769743 2114.888032 -3.32528738 -0.076308685 KPTSAKPSSTTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPTSAKPSSTTPR 13 2 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 ; 88.507 0.0044302 1324140000 884750 852790 798140 937340 929980 938790 1061700 1103870 1274480 1276460 FALSE TRUE 850172.9919 828469.2642 942381.6525 985716.2297 959893.6513 957772.977 1074693.402 1081074.699 1129806.373 1190004.227 0.714428548 0.696190186 0.791914542 0.828330024 0.806630455 0.804848382 0.903100491 0.908462906 0.949413748 1 20.18253527 3.326382129 0.240644268 1.029153521 0.576687143 0.917455301 0.026872878 1.394014333 0.129712331 0.051811478 0.190508723 2120.225868 -3.326382129 -0.452466378 GDVTAEEAAGAS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 8 GDVTAEEAAGASPAK 15 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVT(0.002)AEEAAGAS(0.998)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK 335.18 5.31E-69 7668630000 4864440 4707280 4978380 5231020 5146560 5315360 6214860 7007980 6856020 6906930 TRUE FALSE 4674332.307 4573032.983 5878084.009 5500993.569 5312103.776 5422840.221 6290919.316 6863262.764 6077753.352 6439117.479 0.725927477 0.710195613 0.912871062 0.85430862 0.824973887 0.842171344 0.976984709 1.065870096 0.943879867 1 22.61843154 3.326499664 0.405711093 1.03689727 0.673909883 0.686232267 0.061585575 1.143325353 0.318531177 0.064959063 0.180643127 2120.799752 -3.326499664 -0.362987387 EIEMSVDDDDINSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIEMSVDDDDINSSK 15 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 194.86 7.92E-08 105560000 160020 149680 128940 161410 156730 163000 184950 182250 188010 195150 FALSE TRUE 153766.2415 145411.273 152242.3263 169740.3894 161771.3628 166295.9717 187213.4734 178486.4738 166667.893 181932.3167 0.845183771 0.799260272 0.836807495 0.932986467 0.889184317 0.914054054 1.02902814 0.981059754 0.916098338 1 17.47304231 3.326923122 0.772286243 0.981494542 0.809392963 0.70674902 0.038277696 0.395371703 0.502724883 0.020762297 0.041635471 2122.868643 -3.326923122 -0.172101579 REDS(ph)PGPEVQPMDK ddPTM_BT-474_Pertuzumab_2h_R1 8 REDSPGPEVQPMDK 14 1 O75382;O75382-3;O75382-2;E9PMK8;E9PMW5 O75382 TRIM3 Tripartite motif-containing protein 3 1 REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK 265.43 9.65E-25 14726890000 9146080 9192930 7629090 8885260 8906580 9247620 9476350 10028090 10829220 10465320 TRUE FALSE 8788641.082 8930756.637 9007836.271 9343829.333 9193068.234 9434613.212 9592324.406 9821006.437 9599932.345 9756494.555 0.900799056 0.915365307 0.923265648 0.957703536 0.942251152 0.967008505 0.983173244 1.006612199 0.983953027 1 23.21793146 3.32711102 0.483131095 1.004845381 0.8886135 0.922948456 0.009639639 0.361120649 0.155483098 0.008364834 0.02072932 2123.787303 -3.32711102 -0.116231882 SST(ph)PPRQS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.291)S(0.332)T(0.379)PPRQS(0.997)PS(0.001)R 75.961 0.084001 390190000 331180 313630 286710 294070 271210 216760 299360 293650 354260 303140 TRUE FALSE 318237.1195 304685.5795 338524.8748 309246.9879 279933.716 221143.0357 303023.6572 287586.0249 314045.89 282608.0578 1.126072349 1.078120638 1.197859953 1.094261043 0.990536923 0.782507893 1.072239976 1.017614385 1.111241811 1 18.10844308 3.32764963 4.42081077 0.993559419 1.130445192 0.3574802 0.085281517 0.249003874 8.78851207 0.02514114 0.034191927 2126.422847 -3.32764963 0.136885774 IDYIAGLDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 IDYIAGLDSR 10 0 H3BQB1;P07741-2;P07741;H3BQF1 H3BQB1 APRT Adenine phosphoribosyltransferase 0 ;; 182.39 4.15E-06 685598000 863619 905331 772008 819239 769735 615954 903747 851358 904814 931079 FALSE TRUE 829867.8147 879511.8463 911527.0188 861520.023 794494.2253 628409.0119 914807.3261 833777.1598 802103.308 868016.19 0.956051079 1.013243597 1.050126748 0.992516076 0.915298856 0.723960013 1.053905833 0.960554848 0.924064916 1 19.72736243 3.328114992 5.346545176 0.929239599 1.008943109 0.159228456 0.082749621 0.395440827 18.30276589 0.024042134 0.032609022 2128.702605 -3.328114992 0.07970351 AT(ph)PSENLVPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATPSENLVPSSAR 13 0 Q8N684-2;Q8N684;Q8N684-3;F5H669;F5H6M0;F5H047 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 AT(0.963)PS(0.037)ENLVPSSAR;AT(0.824)PS(0.176)ENLVPSSAR;AT(0.965)PS(0.035)ENLVPSSAR;AT(0.85)PS(0.15)ENLVPSSAR 221.03 2.21E-10 3023000000 652530 534000 565815 567238 507229 444868 489362 689520 602070 628910 TRUE FALSE 627028.4062 518770.8428 668070.357 596513.2212 523544.4814 453863.5358 495350.9585 675281.171 533725.5377 586313.3655 1.069442457 0.884801325 1.139442483 1.017396594 0.892943112 0.774097202 0.844857013 1.15174105 0.910307643 1 19.16131242 3.328301446 7.81158387 0.938433371 1.026410418 0.157494185 0.110737642 0.582273675 44.15354357 0.033718519 0.045663111 2129.616711 -3.328301446 0.087977047 DLEEWNQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLEEWNQR 8 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;;; 189.53 0.00044487 6026100000 3061380 3135790 2613680 2916940 3227930 3254270 3188370 3391340 3418220 3525860 FALSE TRUE 2941737.885 3046360.339 3086030.117 3067483.623 3331759.3 3320073.569 3227390.226 3321307.644 3030197.996 3287050.362 0.894947616 0.92677629 0.938844793 0.933202502 1.013601537 1.010046456 0.981849948 1.010421891 0.921859315 1 21.64836213 3.328373797 5.870220929 0.991797693 0.923503608 0.590441128 0.027041202 0.143444428 7.514539161 0.007439089 0.010083415 2129.971522 -3.328373797 -0.068294086 STMDNPTTTQYASLMHSFILK ddPTM_BT-474_Pertuzumab_2h_R1 2 STMDNPTTTQYASLMHSFILK 21 0 Q9NP97;B1AKR6 Q9NP97 DYNLRB1 Dynein light chain roadblock-type 1 0 ; 240.13 5.96E-30 502940000 439730 514330 383130 451090 479070 541180 459470 523470 521170 531900 FALSE TRUE 422544.8655 499661.812 452370.1137 474370.809 494479.7216 552123.0304 465093.1313 512660.1616 462008.9665 495873.9392 0.852121541 1.007638782 0.912268377 0.956635894 0.997188363 1.113434256 0.937926143 1.033851794 0.931706488 1 18.91961388 3.329145543 3.500181642 1.006951368 0.932787154 0.258548707 0.05929891 0.325212153 7.806415191 0.016246646 0.022317465 2133.759868 -3.329145543 -0.074164214 S(ph)DSLLSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.998)DS(0.002)LLSFR;S(0.999)DS(0.001)LLSFR;S(0.998)DS(0.002)LLSFR;S(0.999)DS(0.001)LLSFR 175.93 0.00027613 187707000 255383 266926 211945 233174 202993 214953 195433 237271 244795 233035 TRUE FALSE 245402.35 259313.5318 250248.1762 245208.1381 209522.4542 219299.4969 197824.7675 232371.2709 217006.8979 217251.3319 1.129578115 1.193610781 1.151883277 1.128684165 0.964424256 1.009427629 0.910580229 1.069596531 0.998874879 1 17.7290055 3.329417337 4.895906345 0.99597085 1.158261165 0.788648491 0.040370482 0.093588263 3.812919981 0.011464014 0.015568552 2135.095656 -3.329417337 0.162290315 HEENLK ddPTM_BT-474_Pertuzumab_2h_R1 5 HEENLK 6 0 P42766 P42766 RPL35 60S ribosomal protein L35 0 ;;;; 129.67 0.016095 2860170000 4243540 3731370 3679280 3166320 3632680 2677000 3691240 2451140 4193390 4242710 FALSE TRUE 4077697.765 3624954.981 4344207.741 3329734.155 3749528.451 2731130.774 3736414.499 2400523.102 3717373.947 3955347.473 1.030932881 0.916469414 1.098312543 0.841831009 0.947964364 0.690490733 0.944648865 0.606905744 0.939834989 1 21.91537301 3.330293478 1.596005159 0.808335574 1.002079683 0.194104064 0.128776322 0.46296322 2.430851694 0.039879033 0.062339089 2139.407323 -3.330293478 0.193744108 LIMGIGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIMGIGHR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 105.12 0.0044497 859250000 1526460 1769240 1540860 1496950 1425740 660600 1887760 1407520 1645300 1828180 FALSE TRUE 1466804.256 1718783.007 1819327.678 1574207.769 1471600.222 673957.7846 1910862.972 1378454.22 1458532.442 1704355.74 0.86062095 1.008464939 1.067457712 0.923638024 0.863434896 0.395432578 1.121164395 0.808783159 0.855767612 1 20.70079506 3.330407507 3.709519146 0.828515049 0.982486269 0.104231486 0.181097607 0.482509877 12.79188977 0.051316649 0.070298575 2139.969124 -3.330407507 0.15397122 KLKPEYDIMCK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLKPEYDIMCK 11 2 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 108.3 0.0011705 879910000 2396030 2451830 1953700 2260890 2433600 2384970 2553200 2514420 2800460 2771250 FALSE TRUE 2302390.499 2381906.209 2306777.05 2377574.804 2511878.954 2433195.727 2584446.825 2462496.348 2482563.521 2583550.769 0.891172926 0.921950611 0.892870803 0.920274079 0.972258407 0.941802947 1.000346831 0.953144168 0.960911452 1 21.3009238 3.331813448 3.671405188 0.968891794 0.904162063 0.736296819 0.019156601 0.115942993 3.016360315 0.00515834 0.007074321 2146.908065 -3.331813448 -0.064729731 FDS(ph)NEEDSASVFSPSFGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FDSNEEDSASVFSPSFGLK 19 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 FDS(1)NEEDSASVFSPSFGLK;FDS(0.966)NEEDS(0.034)ASVFSPSFGLK 205.31 2.69E-16 200886000 415310 361970 380600 480280 435940 372870 502330 575620 588740 562000 TRUE FALSE 399079.2261 351646.97 449382.8864 505067.3084 449962.406 380409.6869 508477.6648 563733.2458 521908.7034 523935.2394 0.761695714 0.671164952 0.857706931 0.963988047 0.858813021 0.726062418 0.970497166 1.075959782 0.996132087 1 18.99902897 3.332558074 0.362682349 1.052673541 0.656025433 0.521361764 0.088357217 1.967704133 0.418043428 0.103139104 0.312652964 2150.592236 -3.332558074 -0.396648107 QGVLTHGR ddPTM_BT-474_Pertuzumab_2h_R1 5 QGVLTHGR 8 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;; 142.92 0.0006097 2356230000 3392860 3590010 3274160 3069350 3157940 2314260 3353120 3124320 3140350 3629960 FALSE TRUE 3260263.28 3487626.43 3865873.545 3227759.521 3259518.008 2361055.923 3394156.486 3059801.7 2783870.633 3384099.576 0.963406427 1.030592142 1.142364005 0.95380158 0.963186199 0.697691031 1.002971813 0.904170114 0.8226326 1 21.69034059 3.33263277 2.664794063 0.889985086 1.042822509 0.322635599 0.094241865 0.303521993 4.37166479 0.0272419 0.038461631 2150.962157 -3.33263277 0.152837423 AGVYPEKDQAENEDGAQENTFSMDPQLER ddPTM_BT-474_Pertuzumab_2h_R1 3 AGVYPEKDQAENEDGAQENTFSMDPQLER 29 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ;; 325.62 2.34E-93 1872120000 910750 891410 755600 895510 919710 961380 1028530 1063030 1094610 1012870 FALSE TRUE 875156.8831 865987.8596 892153.7282 941727.3784 949293.3074 980819.7623 1041117.458 1041078.059 970354.4618 944267.4127 0.926810426 0.917100228 0.94481046 0.997310048 1.005322533 1.038709744 1.102566332 1.102524608 1.02762676 1 19.84883596 3.333419945 1.049477693 1.070144677 0.918909917 0.73212718 0.031992517 0.245185819 0.571071683 0.013195693 0.023870921 2154.864395 -3.333419945 -0.15123476 VIAPWR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIAPWR 6 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 122.76 0.044387 228790000 303830 315630 273830 289900 255740 276480 301730 267830 313650 300040 FALSE TRUE 291955.9877 306628.5414 323317.1723 304861.7737 263966.1094 282070.615 305422.662 262299.2169 278045.7669 279718.0236 1.043751075 1.096205877 1.155868214 1.089889632 0.943686453 1.008410582 1.091894824 0.937727264 0.994021634 1 18.09361369 3.335607183 7.279265391 0.996450872 1.102040956 0.525109334 0.046779232 0.179834864 11.71489498 0.013293032 0.018009015 2165.744314 -3.335607183 0.105590084 ILSQS(ph)TDSLNMR ddPTM_BT-474_Pertuzumab_2h_R1 5 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ILSQS(0.999)T(0.001)DSLNMR;ILSQS(0.732)T(0.268)DSLNMR;ILSQS(0.732)T(0.268)DSLNMR;ILSQS(0.905)T(0.095)DSLNMR;ILS(0.001)QS(0.63)T(0.368)DS(0.001)LNMR 330.56 3.97E-58 2067510000 2448370 2624800 2226100 2335900 2068970 2115860 2101790 2573330 2213370 2247150 TRUE FALSE 2352684.994 2549943.274 2628405.789 2456456.079 2135520.299 2158644.139 2127512.335 2520189.836 1962117.517 2094948.529 1.123027588 1.217186598 1.254639793 1.172561543 1.019366476 1.030404379 1.015543965 1.202984131 0.936594618 1 20.99848337 3.335989213 5.304306376 1.053728379 1.201811358 0.527953549 0.071780169 0.185298484 8.195704648 0.02082132 0.028276228 2167.650265 -3.335989213 0.148082978 KASGPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KASGPPK 7 1 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ; 94.114 0.023151 1561110000 1101640 968350 753980 928240 1036150 1039240 1173720 1062790 926790 1121740 FALSE TRUE 1058586.691 940733.6061 890240.9582 976146.5776 1069478.706 1060254.145 1188084.336 1040843.015 821584.6846 1045763.551 1.012261988 0.89956626 0.851283216 0.933429528 1.022677359 1.013856473 1.136092701 0.995294791 0.785631402 1 19.99612526 3.336040429 5.43169046 1.002856824 0.915056346 0.115721701 0.08908432 0.385034082 17.54517614 0.02567405 0.034855915 2167.905906 -3.336040429 -0.087800478 SALSPSKS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SALSPSKSPAK 11 1 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 1 SALS(0.002)PS(0.009)KS(0.988)PAK;SALS(0.034)PS(0.111)KS(0.855)PAK 84.62 0.0095844 707100000 1122400 1052860 890230 896010 884210 638730 872930 870840 869100 918190 TRUE FALSE 1078535.367 1022833.464 1051114.364 942253.1835 912651.4177 651645.5582 883613.1785 852856.8497 770443.4116 856000.1735 1.259970968 1.194898664 1.227937092 1.100762842 1.066181347 0.761268021 1.032258177 0.996327894 0.900050532 1 19.70725156 3.336239839 1.934771858 0.950613041 1.223990506 0.719502583 0.076926827 0.178072478 1.364705809 0.023995738 0.035893759 2168.901549 -3.336239839 0.273377465 VFLLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFLLDR 6 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 116.35 0.055015 507840000 899400 1019680 824950 814790 716470 532730 689280 733710 790510 943660 FALSE TRUE 864250.4537 990599.7248 974036.8159 856841.4095 739515.9082 543502.1656 697715.6148 718558.6321 700774.6189 879745.0677 0.982387382 1.126007705 1.107180764 0.973965574 0.840602506 0.61779507 0.793088408 0.816780518 0.796565556 1 19.74672599 3.336533332 2.794969347 0.790159025 1.074236488 0.613600438 0.093899857 0.15713444 2.480902372 0.026846731 0.037770035 2170.367773 -3.336533332 0.284077463 SST(ph)PPRQSPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.012)S(0.052)T(0.936)PPRQS(0.214)PS(0.786)R 137.93 0.0017059 248620000 497700 491000 412670 439220 404770 317940 471860 427270 478160 474360 TRUE FALSE 478249.3338 476997.1607 487248.6488 461888.1968 417789.7947 324368.9646 477634.7638 418446.7252 423881.2814 442231.1747 1.08144645 1.07861496 1.101796248 1.044449653 0.944731667 0.73348281 1.080056747 0.946217158 0.958506106 1 18.7544412 3.3365561 3.828527146 0.941166984 1.084380601 0.394806411 0.081653245 0.236003403 6.552397379 0.023599127 0.032353946 2170.481557 -3.3365561 0.143213617 DYLHYHIK ddPTM_BT-474_Pertuzumab_2h_R1 4 DYLHYHIK 8 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 125.96 0.0007168 1396400000 1722050 1818760 1643490 1296760 1194580 598910 1757410 87731.7 1595300 1264420 FALSE TRUE 1654750.382 1766890.746 1940505.202 1363685.939 1233004.751 611020.3705 1778917.709 85920.00974 1414208.232 1178779.707 1.403782549 1.498915136 1.646198344 1.156862415 1.046000998 0.518349923 1.50911803 0.072888945 1.199722241 1 20.1688627 3.3365863 1.921283399 0.797149981 1.513170862 0.351936934 0.372076518 0.319223717 2.412801661 0.112218547 0.168168949 2170.632494 -3.3365863 0.716020881 AAVEWFDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAVEWFDGK 9 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 ;;; 164.57 0.00014462 629634000 720306 676203 629570 739937 754510 666771 778740 905340 890960 921480 FALSE TRUE 692155.6452 656918.3525 743347.3037 778125.2372 778779.4994 680253.5665 788270.4531 886644.4126 789821.956 859067.3388 0.805705925 0.764687846 0.865295734 0.905779096 0.906540691 0.791851274 0.917588666 1.032101178 0.919394697 1 19.7124117 3.338100235 0.288343498 1.018957123 0.71583865 0.571205744 0.053793131 2.714004731 0.350324613 0.079443218 0.27954378 2178.212444 -3.338100235 -0.303118473 ILQLCMGNHELYMR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILQLCMGNHELYMR 14 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 237.21 2.75E-17 919730000 1027070 1105330 864330 879160 819330 455540 922830 761360 872820 950650 FALSE TRUE 986930.9689 1073807.071 1020533.658 924533.553 845684.4935 464751.3309 934123.8696 745637.6499 773741.1328 886261.6287 1.113588738 1.211614083 1.151503828 1.043183551 0.954215399 0.524395185 1.054004641 0.841329045 0.873039188 1 19.75737313 3.338281875 2.46679294 0.857576179 1.159318574 0.483503508 0.134370395 0.231037134 2.859863757 0.03921192 0.056154162 2179.123653 -3.338281875 0.301742395 FLIATGERPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLIATGERPR 10 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 146.11 2.67E-05 821160000 521560 484700 425290 374850 449960 365290 399220 349230 423770 449160 FALSE TRUE 501176.8586 470876.8306 502149.3635 394196.0534 464433.372 372676.4141 404105.7738 342018.2785 375665.4062 418737.9931 1.196874577 1.124514227 1.199197044 0.941390702 1.109126422 0.889999045 0.965056385 0.816783488 0.897137141 1 18.6756883 3.338390217 0.792317986 0.889007187 1.193907581 0.643866836 0.076608628 0.396610457 0.52971192 0.037024912 0.07473665 2179.667342 -3.338390217 0.304900394 YQYVDCGR ddPTM_BT-474_Pertuzumab_2h_R1 1 YQYVDCGR 8 0 Q9NUM4 Q9NUM4 TMEM106B Transmembrane protein 106B 0 133.86 0.0037102 0 271520 339590 258030 286380 213560 243910 306450 240440 302590 291410 FALSE TRUE 260908.6982 329905.2257 304661.7608 301160.1061 220429.3514 248842.0273 310200.4268 235474.83 268241.2518 271672.5411 0.960379349 1.214348805 1.121430085 1.108540837 0.81137884 0.915963116 1.141817371 0.866759773 0.98736976 1 18.05150923 3.339048924 13.42351023 0.952991774 1.111018749 0.337634836 0.10069116 0.675586644 86.31679415 0.027255631 0.03690392 2182.975815 -3.339048924 0.158026975 MLMRRDQVLK ddPTM_BT-474_Pertuzumab_2h_R1 6 MLMRRDQVLK 10 2 F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 F8VYC4 RGPD1;RGPD2 RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 0 ;;;;; 72.79 0.027042 5224910000 15150540 14628680 16143220 7311890 11260410 11810940 10743430 5897870 10754180 10352020 FALSE TRUE 14558440.15 14211484.37 19060658.96 7689257.519 11622611.31 12049765.3 10874911.31 5776076.923 9533410.572 9650868.465 1.508510887 1.472560156 1.975020075 0.796742547 1.204307297 1.248567975 1.126832404 0.598503331 0.987829293 1 23.20222734 3.339244266 0.708677941 0.873535197 1.663736211 0.459769268 0.273696751 0.710320724 0.75048977 0.160271895 0.337351525 2183.957917 -3.339244266 0.790201014 ALPFWNEEIVPQIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALPFWNEEIVPQIK 14 0 P18669;Q8N0Y7;P15259 P18669 PGAM1;PGAM4;PGAM2 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4;Phosphoglycerate mutase 2 0 ; 186.81 2.37E-06 183418000 179597 202214 149347 165681 166873 178205 143382 179268 203119 164134 FALSE TRUE 172578.1507 196447.0547 176337.3251 174231.8163 172240.6216 181808.4272 145136.7518 175566.0532 180061.7827 153017.058 1.127836027 1.283824544 1.152403055 1.138643094 1.1256302 1.188157906 0.948500473 1.147362624 1.176743201 1 17.22333296 3.339855606 0.909037333 1.089636971 1.204289977 0.23034064 0.078449322 0.914424886 1.608013421 0.034510661 0.066393833 2187.034359 -3.339855606 0.114653006 DIVAAIQHNYK ddPTM_BT-474_Pertuzumab_2h_R1 2 DIVAAIQHNYK 11 0 Q5TFE4;Q5TFE4-2;Q5QPD0 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 170.52 1.56E-05 2857800000 4312300 4006000 3461800 3700200 3581800 2166200 4164000 3797300 4683500 4392600 FALSE TRUE 4143770.549 3891752.802 4087424.267 3891167.765 3697011.85 2210002.048 4214960.278 3718884.428 4151848.715 4095085.289 1.011888705 0.950347191 0.998129215 0.950204328 0.902792393 0.5396718 1.029272892 0.908133571 1.013861354 1 21.96546207 3.340210898 3.82659967 0.888079853 0.981386001 0.080212227 0.13133463 0.589381007 16.29829873 0.038343427 0.052640581 2188.824283 -3.340210898 0.093306148 RFSDIQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RFSDIQIR 8 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 181.53 0.00037416 730790000 460160 440830 390850 396870 389870 334910 392560 407680 414500 462150 FALSE TRUE 442176.4385 428257.96 461485.2894 417352.5083 402410.5226 341682.1097 397364.2667 399261.2655 367447.6977 430848.1689 1.026292951 0.993988117 1.071108856 0.968676528 0.933996131 0.793045287 0.922283754 0.926686695 0.8528473 1 18.71682003 3.341008736 2.721324187 0.897559587 1.026073173 0.521902647 0.053959685 0.202756467 3.039096272 0.015431795 0.021838652 2192.849043 -3.341008736 0.128513585 ILFHGEGDQEPELEPGDVIIVLDQK ddPTM_BT-474_Pertuzumab_2h_R1 4 ILFHGEGDQEPELEPGDVIIVLDQK 25 0 Q8WW22-3;Q8WW22;Q8WW22-2 Q8WW22-3 DNAJA4 DnaJ homolog subfamily A member 4 0 ;;; 240.96 1.36E-38 332532000 372347 361492 316295 347507 371216 409272 404522 403223 485737 485619 FALSE TRUE 357795.2676 351182.6021 373456.5424 365441.8779 383156.4998 417547.7603 409472.6612 394896.3041 430598.1721 452727.5926 0.790310274 0.775703995 0.824903427 0.807200365 0.84632902 0.922293598 0.904457046 0.872260296 0.951119789 1 18.78828371 3.342356225 0.179416693 1.036805285 0.641285437 0.876868919 0.024609226 3.320865738 0.195060862 0.097992565 0.334598179 2199.663381 -3.342356225 -0.395519847 LQLHESQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LQLHESQK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 144.09 0.000591 997450000 1677160 2636210 2038220 1923190 1631180 699530 2160050 1659230 1712690 2395480 FALSE TRUE 1611614.733 2561027.872 2406571.694 2022446.066 1683648.386 713674.9759 2186485.338 1624966.321 1518272.611 2233232.006 0.721651279 1.146780928 1.077618307 0.905613954 0.753906617 0.319570458 0.979067706 0.727629873 0.679854403 1 21.09070171 3.342825984 3.61970543 0.726260675 0.996987938 0.221507424 0.203045582 0.308987028 7.7901966 0.056942573 0.078512672 2202.043955 -3.342825984 0.270727264 TPPTAALSAPPPLISTLGGRPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPPTAALSAPPPLISTLGGRPVSPR 25 1 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 TPPTAALSAPPPLISTLGGRPVS(0.999)PR;TPPTAALSAPPPLIS(0.001)T(0.003)LGGRPVS(0.995)PR 129.59 6.03E-05 3693500000 757770 728070 579640 657430 580030 600750 569870 759780 590100 682460 TRUE FALSE 728155.5106 707306.1565 684393.842 691360.0411 598687.1917 612897.5766 576844.2395 744090.2775 523114.3219 636236.3763 1.144473246 1.111703422 1.075691154 1.086640228 0.940982336 0.963317408 0.906650831 1.169518602 0.822201215 1 19.27920333 3.343083069 5.772670037 0.98458186 1.105782339 0.378959679 0.084725033 0.26272286 12.55519676 0.024080651 0.032692466 2203.347864 -3.343083069 0.121200479 YFSDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFSDLR 6 0 E7ESC6;Q9UIA9 E7ESC6 XPO7 Exportin-7 0 ; 101.33 0.085259 571260000 969750 1060890 913780 871570 818970 785390 666870 810220 932180 1092010 FALSE TRUE 931851.0979 1030634.456 1078920.373 916551.8321 845312.9138 801271.1239 675031.3545 793488.6739 826362.8344 1018047.19 0.915331929 1.012364128 1.059794068 0.900303877 0.83032783 0.78706678 0.663064896 0.779422292 0.811713683 1 19.95737301 3.343184223 2.36393656 0.78433509 0.996768185 0.461347887 0.08643103 0.215206634 2.448672379 0.025086784 0.036282882 2203.861118 -3.343184223 0.212433095 HIQDLNWQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIQDLNWQR 9 0 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 ; 173.37 8.89E-05 279560000 88802 109383 91760 85827 79688 60104 97840 65620 80687 100199 FALSE TRUE 85331.51966 106263.5039 108343.0732 90256.54176 82251.23689 61319.34406 99037.39519 64264.92407 71527.75003 93412.43248 0.913492106 1.137573459 1.159835691 0.966215517 0.880517022 0.656436648 1.060216425 0.68796971 0.76571981 1 16.51132695 3.343298088 2.787651699 0.820829584 1.075543801 0.369508024 0.133266688 0.246444764 3.868661652 0.037623344 0.053156407 2204.439011 -3.343298088 0.254714217 QLS(ph)EEQPSGNGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLSEEQPSGNGVK 13 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 QLS(1)EEQPSGNGVK 128.74 5.13E-05 0 162170 142550 127980 143290 161670 154400 156080 174450 181750 170370 TRUE FALSE 155832.2171 138484.6136 151108.8329 150685.2141 166870.2624 157522.0738 157990.1537 170847.5465 161118.502 158830.6882 0.981121589 0.87190086 0.951383103 0.948715993 1.05061726 0.991760948 0.994707985 1.075658291 1.014404104 1 17.27713016 3.343459263 5.064618513 1.025046407 0.931915746 0.568649006 0.035316789 0.141167357 5.763573187 0.0099051 0.013476996 2205.257275 -3.343459263 -0.093130661 LILIESR ddPTM_BT-474_Pertuzumab_2h_R1 4 LILIESR 7 0 P62277 P62277 RPS13 40S ribosomal protein S13 0 ;;; 149.4 0.004697 688203000 883717 982493 892736 803212 837730 455449 950215 810148 814674 921428 FALSE TRUE 849180.3626 954473.2616 1054073.254 844665.8676 864676.3463 464658.4908 961844.0154 793418.1607 722195.6229 859018.8608 0.988546819 1.111120262 1.227066485 0.983291411 1.006585985 0.540917682 1.119700695 0.923632992 0.840721497 1 19.71233028 3.34372073 2.701182018 0.898325967 1.106613706 0.260861545 0.152337342 0.362194467 5.350133227 0.044465757 0.063088484 2206.585346 -3.34372073 0.208287739 SEVQQPVHPKPLS(ph)PDSR ddPTM_BT-474_Pertuzumab_2h_R1 8 SEVQQPVHPKPLSPDSR 17 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SEVQQPVHPKPLS(0.931)PDS(0.069)R;SEVQQPVHPKPLS(0.875)PDS(0.125)R;SEVQQPVHPKPLS(0.995)PDS(0.005)R;SEVQQPVHPKPLS(0.988)PDS(0.012)R;SEVQQPVHPKPLS(0.998)PDS(0.002)R;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(0.998)PDS(0.002)R;SEVQQPVHPKPLS(0.996)PDS(0.004)R 227.4 1.07E-15 29785950000 9290380 8854240 8436000 9087260 9692130 10748680 10711500 11093590 13499920 13509950 TRUE FALSE 8927301.679 8601725.744 9960572.858 9556254.578 10003886.16 10966025.67 10842590.54 10864503.49 11967465.68 12594909.05 0.708802393 0.682952589 0.79084119 0.758739467 0.794280143 0.870671287 0.860870888 0.862610714 0.950182778 1 23.58633737 3.344203277 0.206049673 1.038711496 0.534613012 0.919450714 0.027099744 1.81020344 0.129952948 0.068716923 0.250787471 2209.038459 -3.344203277 -0.504098484 FSGWYDADLSPAGHEEAK ddPTM_BT-474_Pertuzumab_2h_R1 6 FSGWYDADLSPAGHEEAK 18 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;; 328.8 7.74E-75 17478890000 7509000 7726590 7081090 7270830 6806550 6856160 7289350 7713970 8031180 7505730 FALSE TRUE 7215539.978 7506235.218 8360800.481 7646078.408 7025488.862 6994796.253 7378559.246 7554673.824 7119514.116 6997360.222 1.031180295 1.072723853 1.19485066 1.092708988 1.004019893 0.999633581 1.054477548 1.079646264 1.01745714 1 22.73837933 3.345600376 6.713483371 1.034100818 1.104272651 0.367550845 0.045384017 0.262946946 14.76299655 0.013495926 0.01829827 2216.156245 -3.345600376 0.070171832 HNESVVK ddPTM_BT-474_Pertuzumab_2h_R1 3 HNESVVK 7 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 ;; 90.308 0.017234 803880000 1199510 1267530 1121990 1096130 1144080 1010550 1268170 889475 1434840 1417980 FALSE TRUE 1152631.823 1231381.285 1324758.552 1152701.401 1180880.372 1030984.013 1283690.244 871107.0304 1271962.979 1321938.952 0.871925153 0.931496333 1.002132927 0.871977786 0.89329418 0.779902894 0.971066207 0.658961618 0.962194946 1 20.33422412 3.345973377 2.386769015 0.84696818 0.933798348 0.009247595 0.101584617 0.618221618 7.167061783 0.029582787 0.042797025 2218.060442 -3.345973377 0.086830168 TTHLIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTHLIAK 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 80.18 0.046553 0 920220 926960 793410 838670 795360 720800 905330 678720 1041400 1152500 FALSE TRUE 884256.785 900524.0084 936796.8363 881953.8592 820943.4767 735375.0699 916409.6994 664704.1948 923184.6379 1074440.148 0.82299306 0.838133245 0.871892993 0.820849687 0.76406627 0.684426276 0.852918332 0.618651672 0.859223884 1 20.03515369 3.346095225 4.072501391 0.765854457 0.843981257 0 0.100369342 0.482856885 14.63352736 0.02688771 0.036870868 2218.682844 -3.346095225 0.0781268 DILKPEIMEEIVMETR ddPTM_BT-474_Pertuzumab_2h_R1 2 DILKPEIMEEIVMETR 16 1 A3KFL2;Q13868-3;Q13868-2;Q13868 A3KFL2 EXOSC2 Exosome complex component RRP4 0 ; 175.39 3.23E-09 121377000 128498 119905 110987 126203 123866 143532 133246 149214 166800 165252 FALSE TRUE 123476.1561 116485.4268 131044.8198 132716.352 127850.2624 146434.3154 134876.7044 146132.6788 147865.5633 154059.3348 0.801484417 0.756107554 0.850612655 0.861462579 0.829876765 0.950505956 0.875485439 0.948548031 0.959796194 1 17.23312658 3.347734459 0.278144651 1.010760192 0.697198377 0.81938942 0.031682358 1.47570397 0.17674262 0.042572725 0.153407533 2227.073031 -3.347734459 -0.313561814 RPLS(ph)GPDVGTPQPAGLASGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPLSGPDVGTPQPAGLASGAK 21 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RPLS(1)GPDVGTPQPAGLASGAK;RPLS(1)GPDVGTPQPAGLASGAK 227.96 1.14E-25 500440000 519540 445650 386980 500880 497700 484280 534460 637670 536730 516630 TRUE FALSE 499235.8024 432940.4983 456915.8943 526730.4768 513708.9725 494072.4734 541000.8814 624501.8917 475802.6606 481638.1899 1.036536996 0.898891548 0.9486704 1.09362274 1.066586876 1.025816648 1.123251629 1.296620378 0.987883998 1 18.87759026 3.348277525 1.018968952 1.129027938 0.952292998 0.184702602 0.094071468 0.655884659 1.438475691 0.040175003 0.074850432 2229.859632 -3.348277525 -0.176734941 ILVATNLFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILVATNLFGR 10 0 O00148;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;H0Y400 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ; 87.258 0.030241 118848000 231560 242710 230690 221500 216242 189795 247650 215542 247260 228090 FALSE TRUE 222510.3792 235788.1484 272380.8147 232931.6415 223197.6203 193632.7849 250680.8148 211090.9824 219192.0814 212641.2611 1.046412056 1.108854167 1.280940553 1.095420711 1.049643983 0.910607772 1.178890745 0.992709417 1.03080691 1 17.69806204 3.348396377 3.81765137 1.029268707 1.14749575 0.290134823 0.083104994 0.285331841 7.823572499 0.023448394 0.032292292 2230.469953 -3.348396377 0.118227043 GIGEFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIGEFFR 7 0 H0YKX3;H0YMA4;A0A0U1RQM0;Q15004 H0YKX3 KIAA0101 PCNA-associated factor 0 ; 135.87 0.01366 217530000 285050 274910 215506 234110 238460 198798 234690 227460 196757 229459 FALSE TRUE 273909.9309 267069.836 254452.7281 246192.4452 246130.2825 202817.8318 237562.2064 222762.8715 174421.9702 213917.5375 1.280446353 1.248470972 1.189489796 1.150875463 1.150584872 0.948112222 1.110531699 1.04134927 0.815370129 1 17.70669524 3.348653437 0.468896677 0.949132154 1.330638957 0.713699972 0.072772577 0.862186627 0.34161506 0.061746854 0.15975526 2231.790564 -3.348653437 0.381506803 NILGGTVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 NILGGTVFR 9 0 O75874;C9J4N6;P48735;P48735-2 O75874;P48735 IDH1;IDH2 "Isocitrate dehydrogenase [NADP] cytoplasmic;Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 106.42 0.0068354 261020000 447740 488250 369450 420110 378040 352740 414650 461580 427750 452080 FALSE TRUE 430241.8258 474325.588 436217.8334 441791.9274 390199.9999 359872.6445 419724.6107 452048.2117 379193.6133 421460.2189 1.020836147 1.125433829 1.035015439 1.048241109 0.925828779 0.853870967 0.995881917 1.072576228 0.899713891 1 18.68503694 3.349615905 6.200987794 0.967162579 1.062680771 0.375805996 0.0621424 0.267737657 13.61781709 0.019141017 0.025976263 2236.742061 -3.349615905 0.095518192 GLS(ph)LEHQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLSLEHQK 8 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 GLS(1)LEHQK;GLS(1)LEHQK 105.98 0.0029771 267810000 714360 662970 350330 572620 941150 613750 778190 986530 887200 776740 TRUE FALSE 686442.0214 644062.7447 413642.424 602172.9868 971422.9445 626160.4455 787713.722 966157.8108 786488.7754 724130.708 0.947953199 0.889428853 0.571226188 0.831580515 1.341502209 0.864706383 1.08780599 1.334231238 1.086114381 1 19.46589061 3.349818429 7.854911063 1.134661695 0.79403655 0.466132314 0.161525103 0.200489573 13.12814903 0.045911805 0.062201923 2237.785364 -3.349818429 -0.340625144 ITHQIVDRPGQQTSVIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ITHQIVDRPGQQTSVIGR 18 1 B5MCF9;O00541-2;O00541;B3KXD6 B5MCF9 PES1 Pescadillo homolog 0 122.22 2.20E-05 315150000 140680 138760 112590 125440 118060 120750 128400 120420 135200 147910 FALSE TRUE 135182.0701 134802.7007 132937.5176 131913.9734 121857.5071 123191.6477 129971.3976 117933.2849 119852.6628 137891.924 0.980347987 0.977596779 0.964070366 0.956647566 0.883717506 0.893392769 0.942559897 0.855258825 0.869178262 1 17.07317844 3.350268242 4.546888953 0.899085793 0.97231289 0.370983227 0.039212521 0.197105689 6.947934226 0.010634033 0.014531126 2240.10431 -3.350268242 0.073227097 QS(ph)PPISTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSPPISTSK 9 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 QS(0.998)PPIS(0.002)TSK 90.697 0.0091997 0 292970 292620 319380 330810 334660 339590 405710 416410 481860 552190 TRUE FALSE 281520.4085 284274.7641 377099.0706 347883.1437 345424.6428 346456.7425 410675.2003 407810.988 427161.2729 514789.6795 0.546864904 0.552215352 0.732530363 0.67577723 0.671001492 0.673006387 0.797753367 0.792189518 0.829778238 1 18.97362361 3.35087756 0.085136176 1.348315929 1.22E-13 0.889252575 0.042883338 14.42345305 0.344378175 1.834602252 3.637623388 2243.249397 -3.35087756 -1.348315929 FIGELFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FIGELFK 7 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 Q04637-9;A0A0A0MSA7 EIF4G1;EIF4G3 Eukaryotic translation initiation factor 4 gamma 1;Eukaryotic translation initiation factor 4 gamma 3 0 91.906 0.037363 44874000 149410 197730 146230 150330 147780 140130 170010 125980 149070 180760 FALSE TRUE 143570.892 192090.934 172657.0139 158088.5493 152533.4779 142963.5246 172090.6332 123378.469 132148.1986 168516.9642 0.851966998 1.139890781 1.024567554 0.938116528 0.905152064 0.848362806 1.021206583 0.732142723 0.784183356 1 17.36253431 3.352267269 1.804785837 0.862288 1.017603115 0.205527731 0.105375931 0.451076831 3.008200102 0.033016691 0.05085352 2250.43912 -3.352267269 0.155315115 EYVTCHTCR ddPTM_BT-474_Pertuzumab_2h_R1 3 EYVTCHTCR 9 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;; 205.09 1.55E-05 989660000 937200 955290 850880 789300 723910 370070 844470 733880 729780 826060 FALSE TRUE 900573.1879 928046.0645 1004652.944 830035.8676 747195.2226 377553.069 854804.8765 718725.1215 646938.4339 770110.2204 1.169408176 1.20508213 1.304557344 1.077814377 0.970244522 0.490258484 1.109977317 0.933275656 0.840059535 1 19.55470542 3.353602206 2.865413569 0.884795391 1.220886269 0.490497686 0.154977939 0.224277596 3.708402454 0.04569114 0.064724035 2257.367177 -3.353602206 0.336090878 GS(ph)IDREDGSLQGPIGNQHIYQPVGKPDPAAPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSIDREDGSLQGPIGNQHIYQPVGKPDPAAPPK 33 2 E7ESA6;Q05397;Q05397-7;H0YBP1;E9PEI4;H0YB16;H0YBZ1;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 1 GS(0.994)IDREDGS(0.006)LQGPIGNQHIYQPVGKPDPAAPPK 130.01 3.66E-08 548440000 269770 243590 240970 333520 370470 329280 413640 474950 491440 491910 TRUE FALSE 259227.0902 236643.0517 284518.6393 350733.0072 382386.504 335938.2672 418702.2501 465142.1165 435653.7915 458592.4976 0.565266749 0.51602033 0.620417126 0.764803195 0.83382634 0.732542004 0.913015918 1.014282002 0.949980198 1 18.80685323 3.354112536 0.461366139 1.022316747 0.436120123 0.894659401 0.055774096 0.476656516 0.18095755 0.051067834 0.134276975 2260.021319 -3.354112536 -0.586196624 DKDQPPS(ph)PSPPPQSEALSSTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKDQPPSPSPPPQSEALSSTSR 22 1 H3BU99;H3BPL8;H3BR21;H3BUX9;Q7L1V2 H3BU99 MON1B Vacuolar fusion protein MON1 homolog B 1 DKDQPPS(0.997)PS(0.003)PPPQSEALSSTSR 71.927 0.0055609 0 49820 40492 31990 42020 49242 44485 50546 54036 57216 53729 TRUE FALSE 47872.97932 39337.20781 37771.30461 44188.65724 50825.91365 45384.51718 51164.59707 52920.13772 50721.07955 50089.88697 0.955741412 0.785332333 0.75407047 0.882187202 1.014694117 0.906061481 1.02145563 1.056503436 1.012601198 1 15.61223174 3.354245123 3.773874644 1.005506699 0.825559686 0.622150209 0.060814153 0.144772272 3.892761753 0.018003639 0.02486575 2260.711392 -3.354245123 -0.179947013 HMLPSGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 HMLPSGFR 8 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 91.853 0.012192 981970000 1079890 1172640 1138020 991930 872760 393670 1256080 690160 1015860 1232780 FALSE TRUE 1037686.705 1139197.455 1343685.529 1043123.626 900833.118 401630.2771 1271452.283 675907.9548 900543.8316 1149282.713 0.902899429 0.991224738 1.169151432 0.907630137 0.783822038 0.349461688 1.106300712 0.58811287 0.783570328 1 20.1323023 3.354540062 3.522397831 0.740958525 1.020120115 0.229627709 0.204593156 0.298683237 7.174576909 0.055926746 0.077645652 2262.247214 -3.354540062 0.27916159 QSSFEPEFVIS(ph)PRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSSFEPEFVISPRPK 15 1 A0A0A0MSU3;Q9H9A7 A0A0A0MSU3 RMI1 RecQ-mediated genome instability protein 1 1 QSSFEPEFVIS(1)PRPK 160.3 1.04E-06 267810000 241010 241150 197560 204280 200830 191400 186150 204690 208150 221570 TRUE FALSE 231591.0627 234272.6381 233263.4867 214822.9153 207289.8793 195270.2391 188428.1594 200463.08 184521.6846 206562.8665 1.121165031 1.134146916 1.129261472 1.039988062 1.003519572 0.945330796 0.912207322 0.970470072 0.893295527 1 17.6562214 3.354622101 1.407021622 0.941704897 1.134127183 0.880458709 0.029280313 0.118988464 0.486999154 0.009386844 0.01561864 2262.674598 -3.354622101 0.192422286 LDPHNHVLYSNR ddPTM_BT-474_Pertuzumab_2h_R1 5 LDPHNHVLYSNR 12 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 87.18 0.0061841 6307600000 9937810 11575230 9581440 7196720 6837490 2047690 9614350 198897 7481950 7079670 FALSE TRUE 9549429.398 11245115.77 11313019.35 7568143.582 7057424.076 2089095.695 9732013.291 194789.7074 6632630.403 6600157.645 1.446848683 1.703764725 1.714052899 1.146661033 1.069281138 0.31652209 1.474512249 0.029512887 1.004919997 1 22.65406905 3.354871322 1.752348815 0.710212542 1.631859884 0.460280187 0.387576641 0.275517538 1.733151573 0.117591623 0.182918093 2263.97341 -3.354871322 0.921647342 EYFADMER ddPTM_BT-474_Pertuzumab_2h_R1 2 EYFADMER 8 0 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 ; 106.91 0.0095488 748750000 1169500 1286300 960480 1006180 1008630 714050 1115270 886390 929620 1013380 FALSE TRUE 1123794.647 1249615.983 1134060.102 1058109.07 1041073.5 728488.5802 1128919.008 868085.7367 824093.4349 944742.87 1.189524349 1.322704858 1.20039022 1.119996884 1.101964919 0.771097198 1.194948429 0.918859262 0.872293892 1 19.8495622 3.355747605 1.552202153 0.964332844 1.251266083 0.548101695 0.110550958 0.283488059 1.405236406 0.035193093 0.056756147 2268.546079 -3.355747605 0.286933239 GSDSPAADVEIEYVTEEPEIYEPNFIFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSDSPAADVEIEYVTEEPEIYEPNFIFFK 29 0 Q13435;E9PPJ0;H0YCG1 Q13435 SF3B2 Splicing factor 3B subunit 2 0 120.63 2.98E-05 13021000 31723 31044 27176 30123 30219 36118 28027 38291 36848 35273 FALSE TRUE 30483.23009 30158.65552 32087.30773 31677.65164 31191.02158 36848.33071 28370.00281 37500.27747 32665.16952 32883.92829 0.926994787 0.917124476 0.975774775 0.963317137 0.94851872 1.120557446 0.862731562 1.140383142 0.993347547 1 15.00509503 3.356133182 0.723892459 1.033277872 0.918337227 0.180125653 0.074458894 1.203896487 1.323376068 0.039371393 0.08417674 2270.561044 -3.356133182 -0.114940645 HPFPGPGLAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPFPGPGLAIR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 66.056 0.072241 0 197430 206070 169820 163100 146220 82847 161960 126280 173790 169800 FALSE TRUE 189714.2173 200193.0854 200510.2516 171517.6105 150923.2991 84522.2231 163942.1149 123672.2739 154062.0878 158299.2948 1.198452701 1.264649256 1.266652842 1.083502051 0.953404747 0.533939354 1.035646528 0.781256 0.973232938 1 17.2722953 3.356181303 2.485586158 0.853438744 1.241481094 0.593409212 0.136148042 0.177967307 2.232800229 0.038771834 0.056100855 2270.812642 -3.356181303 0.38804235 LRTEQNER ddPTM_BT-474_Pertuzumab_2h_R1 1 LRTEQNER 8 1 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2;G3V4Y7;B7Z6P3;H0YJP2 Q86UP2-2 KTN1 Kinectin 0 96.331 0.0082232 117610000 79370 85934 72211 65198 70528 45829 68800 67732 59970 63490 FALSE TRUE 76268.13265 83483.24646 85261.13403 68562.87659 72796.59717 46755.69378 69641.99498 66333.31053 53162.45701 59189.76575 1.288535808 1.410433804 1.440470881 1.158356951 1.229884867 0.789928684 1.176588454 1.12068885 0.898169748 1 15.85306013 3.356907741 1.79575524 1.033656797 1.379249639 0.613049915 0.123624598 0.239135987 1.578191343 0.038763404 0.06000804 2274.614172 -3.356907741 0.345592842 SYLFNIMDTPGHVNFSDEVTAGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYLFNIMDTPGHVNFSDEVTAGLR 24 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 148.09 1.67E-07 185190000 208630 231980 168420 200740 241550 233350 223530 238750 242130 248610 FALSE TRUE 200476.5089 225364.1575 198857.2405 211100.2155 249319.6751 238068.4969 226265.627 233819.7291 214644.4175 231771.4233 0.864975095 0.972355238 0.857988607 0.910812094 1.075713613 1.027169327 0.976244715 1.008837612 0.926103894 1 17.82234317 3.357042079 9.026366482 1.002434571 0.902370929 0.540139691 0.045624929 0.208137607 15.51388451 0.012399421 0.016793201 2275.317878 -3.357042079 -0.100063642 KFGQGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFGQGSR 7 1 A0A2R8Y851;P62273;P62273-2;A0A2R8Y6P7 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ; 141.52 0.004091 6992900000 6812600 7816200 5948500 6321000 6061200 3389700 6739500 6744500 6743900 7101600 FALSE TRUE 6546356.06 7593289.629 7023526.274 6647227.568 6256164.003 3458242.056 6821980.017 6605223.718 5978360.745 6620602.307 0.988785575 1.146918253 1.06085911 1.004021577 0.944953905 0.522345535 1.030416826 0.997677162 0.902993484 1 22.65853104 3.357236739 2.954087015 0.897590987 1.069169535 0.230132276 0.138974482 0.403420137 7.066476994 0.042582196 0.060225931 2276.337952 -3.357236739 0.171578548 RQQVLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQQVLDR 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 110.12 0.011025 184750000 363590 443420 351890 329720 280260 199382 296970 257560 279770 368010 FALSE TRUE 349380.5008 430774.0958 415484.3508 346736.8887 289274.8174 203413.6406 300604.4077 252241.296 248011.6825 343084.3549 1.018351597 1.255592363 1.211026807 1.010646168 0.843159454 0.592896871 0.876182208 0.735216551 0.722888348 1 18.38820381 3.358011956 2.563544015 0.770876579 1.16790614 0.672460305 0.115741625 0.142995769 1.905862944 0.032392197 0.046703565 2280.404852 -3.358011956 0.397029561 EREDEIATMECINNGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EREDEIATMECINNGK 16 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ;;; 272.24 3.27E-35 4109520000 2018950 1852240 1665180 2061810 1961940 2083030 2237620 2345810 2513690 2499160 FALSE TRUE 1940047.202 1799415.929 1966115.068 2168220.261 2025047.582 2125150.294 2265004.663 2297368.204 2228346.449 2329889.667 0.832677714 0.772318086 0.843866169 0.930610703 0.869160291 0.912124863 0.97215104 0.986041629 0.956417156 1 21.15183021 3.358063085 0.467828308 0.998426195 0.76554938 0.818886596 0.030464956 0.611618565 0.240077196 0.026414771 0.069181338 2280.673335 -3.358063085 -0.232876814 FFLSHPAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 FFLSHPAYR 9 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4;E5RIK2 P50570-2 DNM2;DNM3 Dynamin-2;Dynamin-3 0 120.07 0.00072403 361920000 398250 436970 336000 371210 324430 236960 438070 358160 375780 415650 FALSE TRUE 382685.9497 424508.0434 396722.6743 390368.1926 334865.5856 241751.4936 443431.2317 350763.8708 333123.0298 387497.6553 0.98758262 1.095511257 1.023806645 1.007407883 0.864174482 0.623878597 1.144345587 0.905202563 0.859677537 1 18.56382806 3.359103883 5.006828465 0.900180562 1.037506161 0.206563823 0.124536963 0.343505973 13.6229899 0.035433205 0.048338781 2286.145584 -3.359103883 0.137325598 GHFDYQSLLMR ddPTM_BT-474_Pertuzumab_2h_R1 3 GHFDYQSLLMR 11 0 Q9H832-2;Q9H832 Q9H832-2 UBE2Z Ubiquitin-conjugating enzyme E2 Z 0 ;; 227.36 4.06E-12 2976730000 2899060 3513860 2819670 2749910 2524360 1391320 3314310 2273790 2834510 2993600 FALSE TRUE 2785761.53 3413648.153 3329247.092 2891833.185 2605558.332 1419453.444 3354871.517 2226835.442 2512748.308 2790840.806 0.99818002 1.223161187 1.192919025 1.03618708 0.933610519 0.508611398 1.20210064 0.797908443 0.900355299 1 21.4122684 3.359222613 3.023670835 0.877649083 1.143164362 0.298074943 0.172012963 0.292390942 5.350324118 0.048308427 0.06821741 2286.770667 -3.359222613 0.265515279 SS(ph)PSHTISRPIPMPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPSHTISRPIPMPIR 16 1 Q9Y4J8;Q9Y4J8-2;Q9Y4J8-15;Q9Y4J8-14;Q9Y4J8-13;Q9Y4J8-6;Q9Y4J8-10;Q9Y4J8-11;M0QZ28 Q9Y4J8 DTNA Dystrobrevin alpha 1 S(0.248)S(0.747)PS(0.004)HT(0.001)ISRPIPMPIR 58.304 0.067301 219510000 76309 85475 64170 66228 61941 45337 62289 59861 60007 70412 TRUE FALSE 73326.75992 83037.33669 75766.94645 69646.03502 63933.38852 46253.7452 63051.31141 58624.84943 53195.25693 65642.93252 1.117054907 1.264985178 1.154228544 1.060982993 0.973956922 0.70462643 0.960519419 0.893086996 0.810372951 1 16.00235207 3.359504804 1.962472926 0.875635467 1.187722234 0.708738123 0.084978563 0.165707915 1.302723496 0.025460193 0.038640573 2288.257021 -3.359504804 0.312086767 LWDEESAQLLPHWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LWDEESAQLLPHWK 14 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 183.89 1.36E-06 460590000 444130 429570 373260 395170 391570 343950 410050 391450 475240 496250 FALSE TRUE 426772.9086 417319.0842 440716.3851 415564.7711 404165.2047 350904.9047 415068.3146 383366.4207 421292.7476 462638.5455 0.9224759 0.90204132 0.952614929 0.898249346 0.873609016 0.758486097 0.897176248 0.82865214 0.910630452 1 18.81952595 3.35972192 3.453146717 0.862707243 0.923496925 0.079161361 0.059850772 0.401350029 9.323158233 0.016200964 0.022581536 2289.401272 -3.35972192 0.060789682 EKPEVTDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKPEVTDR 8 1 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 ;;; 96.89 0.0078619 1753610000 2528410 2541320 2028520 2373230 2589140 2634900 2630210 2696890 2824270 2931810 FALSE TRUE 2429596.942 2468844.042 2395118.688 2495712.685 2672422.039 2688179.483 2662399.297 2641198.279 2503670.71 2733235.897 0.888908617 0.903267824 0.876294172 0.913098166 0.977750234 0.983515358 0.974083247 0.9663265 0.916009742 1 21.38217855 3.360290599 4.118112775 0.968733405 0.891322527 0.74965787 0.021281081 0.108201061 3.322076356 0.005982302 0.008234036 2292.401054 -3.360290599 -0.077410878 RNSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.439)PMAQT(0.56)PPCHLPNIPGVTSPGTLIEDSK 139.04 2.66E-07 562240000 359410 317750 346090 385720 413040 344560 471610 498930 537010 522020 TRUE FALSE 345363.8599 308688.0811 408636.1617 405627.0554 426325.8067 351527.2393 477381.7043 488626.9211 476050.8761 486663.1204 0.709656938 0.6342952 0.839669465 0.833486324 0.876018315 0.722321508 0.980928458 1.004035236 0.97819386 1 18.89256393 3.360565903 0.363322283 1.035444229 0.595738111 0.686706119 0.071410194 1.368673706 0.288618116 0.077869692 0.241995676 2293.854689 -3.360565903 -0.439706118 YNADEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 YNADEAR 7 0 P47813;O14602;X6RAC9;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;; 134.81 0.0073009 397482000 795380 857770 712090 724670 730400 582120 745060 753290 794640 827540 FALSE TRUE 764295.6703 833307.2394 840780.5034 762070.3055 753893.9793 593890.8652 754178.2672 737734.2983 704435.7986 771489.9787 0.990674787 1.080127108 1.089813901 0.987790284 0.977192187 0.769797252 0.977560679 0.956246119 0.913084833 1 19.55728789 3.36079684 2.554144024 0.926107058 1.05435964 0.413323217 0.064797147 0.263558328 3.486953712 0.019229949 0.027790356 2295.074775 -3.36079684 0.128252582 LKEVDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKEVDR 6 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-5;D6RCQ9;D6RE64;D6RBT0;D6RHE8;D6REA9;U3KQC9;D6RAB3;D6REC0;U3KQR3 D6REX3 SEC31A Protein transport protein Sec31A 0 ;; 100.45 0.048328 576790000 1049650 1114450 850750 1009060 1092820 1111090 1076460 1155880 1255650 1201320 FALSE TRUE 1008628.518 1082666.977 1004499.45 1061137.708 1127971.548 1133557.001 1089634.039 1132010.674 1113113.876 1119953.526 0.900598546 0.966707057 0.896911726 0.947483697 1.007159245 1.012146464 0.972927906 1.010765757 0.993892916 1 20.09500744 3.361072938 4.240635395 0.999418204 0.925387384 0.747857494 0.020683771 0.102082687 3.268744061 0.005451875 0.007493228 2296.534309 -3.361072938 -0.07403082 DYMLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYMLFR 6 0 Q9NXG2 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 0 ; 110.54 0.066582 169982000 246870 264660 245870 214061 228559 140274 236631 226284 205718 243300 FALSE TRUE 237222.0475 257112.1559 290304.1783 225108.7139 235910.8078 143110.4364 239526.961 221611.1563 182365.7551 226821.0743 1.045855409 1.133546152 1.27988186 0.992450611 1.040074466 0.63093977 1.056017223 0.977030715 0.804007104 1 17.79119516 3.363805704 2.445165605 0.913190933 1.14785395 0.389565392 0.130282555 0.295603393 3.588854037 0.038499379 0.05613141 2311.030642 -3.363805704 0.234663017 GWVTFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWVTFDR 7 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 117.16 0.012315 73305000 169730 193420 184280 161490 163720 78351 195330 176850 150480 179830 FALSE TRUE 163096.764 187903.851 217583.4953 169824.5183 168986.2025 79935.3109 197720.507 173197.9857 133398.1413 167649.9539 0.97284109 1.120810633 1.297844051 1.012970861 1.007970468 0.476798884 1.179365114 1.033092951 0.79569447 1 17.35509256 3.364157663 3.179697647 0.922122949 1.131095915 0.201412418 0.189983565 0.422797239 8.492005599 0.056327302 0.079311889 2312.904295 -3.364157663 0.208972967 SATRPSPS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SATRPS(0.029)PS(0.971)PER;SATRPS(0.012)PS(0.988)PER 87.447 0.0083074 986830000 635740 609570 520470 490640 436630 206943 503660 382010 456690 526570 TRUE FALSE 610894.578 592185.6604 614530.5068 515961.9892 450674.6005 211127.5292 509823.9417 374121.36 404848.4658 490904.9449 1.244425391 1.206314311 1.251831975 1.051042558 0.918048606 0.430078229 1.038539023 0.762105503 0.824698284 1 18.90508417 3.364707287 2.436602322 0.805053068 1.227852762 0.579363282 0.156359666 0.191781412 2.312163539 0.044902864 0.065544406 2315.833261 -3.364707287 0.422799694 EQILEEFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQILEEFSK 9 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 131.28 0.0026523 29087000 313866 305321 248667 290809 308059 315028 309871 329651 362000 345380 FALSE TRUE 301599.7697 296613.544 293606.6585 305817.6873 317967.9975 321398.082 313663.294 322843.5917 320907.2776 321987.105 0.936682759 0.921196965 0.911858438 0.949782406 0.9875178 0.998170663 0.97414862 1.002660003 0.996646365 1 18.29664339 3.364774726 2.714618677 0.993529559 0.923269146 0.919226274 0.009438854 0.067083656 0.999429952 0.002767292 0.003973788 2316.192902 -3.364774726 -0.070260414 HGYPLIIYDVFPDACK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGYPLIIYDVFPDACK 16 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 77.746 0.023065 221710000 374230 430160 338070 359730 277020 307140 374930 297040 351230 323830 FALSE TRUE 359604.6779 417892.258 399166.7693 378295.7084 285930.5999 313350.5812 379518.5055 290906.0202 311359.8429 301896.7057 1.191151381 1.38422265 1.322196506 1.253063387 0.947114011 1.037939717 1.257113769 0.96359455 1.031345613 1 18.20369549 3.364777136 5.769081294 1.048146618 1.304269322 0.639507946 0.091468786 0.132098474 6.19020711 0.025615135 0.034838284 2316.205754 -3.364777136 0.256122704 TLTPDQWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLTPDQWAR 9 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 135 0.00054241 290940000 332680 354400 312920 323340 297250 264020 351570 328440 341860 382630 FALSE TRUE 319678.4978 344292.859 369471.6049 340027.6161 306811.3162 269358.6653 355872.6188 321657.5992 303053.486 356714.1293 0.896175597 0.965178642 1.035763864 0.953221609 0.860104187 0.755110726 0.997640939 0.901723741 0.849569616 1 18.44440884 3.365813036 6.169550999 0.891113602 0.970107191 0.171501338 0.07371719 0.348463966 17.60766609 0.020677073 0.028088961 2321.737074 -3.365813036 0.07899359 NIIHGSDSVESAEK ddPTM_BT-474_Pertuzumab_2h_R1 5 NIIHGSDSVESAEK 14 0 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 ;;;; 210.9 4.58E-09 6736310000 5763220 7966910 5250680 5912900 4961950 5928620 4590190 4874830 5691400 6875500 FALSE TRUE 5537986.991 7739701.527 6199594.677 6218065.478 5121555.628 6048500.758 4646366.118 4774163.057 5045336.132 6409816.261 0.863985295 1.207476348 0.967203181 0.970084824 0.799017541 0.943630911 0.724882887 0.744820579 0.787126483 1 22.61185157 3.366258495 1.500704887 0.80495153 1.039001745 0.322833643 0.114867203 0.36816172 1.705963628 0.036396967 0.059922004 2324.119717 -3.366258495 0.234050215 MATHTLITGLEEYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MATHTLITGLEEYVR 15 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ; 212.87 6.56E-10 630980000 346310 384890 373060 347280 321070 283420 406380 301890 355070 394180 FALSE TRUE 332775.8223 373913.314 440480.2407 365203.1624 331397.5081 289150.9466 411353.4 295655.866 314763.9422 367481.8375 0.905557196 1.017501481 1.198644928 0.993799217 0.901806496 0.786844184 1.119384302 0.80454552 0.856542855 1 18.48731342 3.366290297 4.486440462 0.904254656 1.046363271 0.212129353 0.112129675 0.29995768 10.4092594 0.031299351 0.042948563 2324.28991 -3.366290297 0.142108615 GDSFFIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDSFFIR 7 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ; 79.939 0.092244 109340000 369340 400390 345060 289030 305620 261160 277120 261720 284830 303450 FALSE TRUE 354905.7845 388971.2692 407420.0178 303946.8729 315450.5449 266440.8341 280511.4775 256315.3905 252497.2925 282897.0612 1.254540372 1.37495691 1.440170556 1.074408025 1.115071834 0.941829629 0.991567308 0.906037657 0.892541235 1 18.10991766 3.366552552 1.428189387 0.942990186 1.360415347 0.837203091 0.074781292 0.144375772 0.607315525 0.024755898 0.041462515 2325.693889 -3.366552552 0.417425161 LKPWGLFEVLVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKPWGLFEVLVEK 13 1 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 ; 120.3 0.00025579 101835000 559910 522790 541810 365510 496240 446230 466070 370320 500260 502860 FALSE TRUE 538028.0982 507880.5411 639727.1195 384374.0149 512202.0103 455253.0763 471773.9041 362672.7626 443472.5821 468800.8443 1.147668791 1.083360978 1.364603173 0.819908965 1.092579112 0.97110123 1.00634184 0.773617981 0.945972234 1 18.83861564 3.36825999 0.90451598 0.908816006 1.182433059 0.336897678 0.129659329 0.647858691 1.119520596 0.056735515 0.113561944 2334.855406 -3.36825999 0.273617053 LVGYLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVGYLDR 7 0 P07602;C9JIZ6;P07602-2;P07602-3;Q5BJH1 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 ;;; 158.38 0.0033101 1423620000 1447630 1594350 1418750 1351370 1000270 556467 1441880 1293870 1122790 1373640 FALSE TRUE 1391055.019 1548880.699 1675149.685 1421114.368 1032444.593 567719.144 1459526.159 1267151.132 995335.5863 1280602.139 1.086250738 1.209494074 1.308095335 1.109723562 0.806218076 0.443322033 1.139718664 0.989496342 0.777240296 1 20.28839089 3.369056546 4.727040919 0.868979958 1.202910789 0.434271157 0.18008959 0.216340057 8.064937706 0.053787167 0.073665458 2339.141779 -3.369056546 0.333930831 LMFEELR ddPTM_BT-474_Pertuzumab_2h_R1 6 LMFEELR 7 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;;; 134.12 0.007456 558065000 1761620 1987040 1651452 1493032 1510973 633856 1637946 1356506 1452852 1766822 FALSE TRUE 1692773.943 1930371.565 1949906.113 1570087.56 1559574.819 646673.0026 1657991.673 1328493.677 1287930.332 1647153.572 1.027696489 1.17194389 1.183803469 0.953212613 0.946830244 0.39260031 1.006579897 0.80653905 0.781912721 1 20.65154364 3.369169848 2.345556668 0.800940105 1.1274367 0.399438609 0.168002037 0.276936567 3.095646471 0.048959861 0.072151428 2339.752111 -3.369169848 0.326496594 IQEHFNK ddPTM_BT-474_Pertuzumab_2h_R1 5 IQEHFNK 7 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ;;;; 98.997 0.010852 2820930000 3321860 3412730 2809480 3120140 3354140 3362640 3525490 3565210 4030890 3915210 FALSE TRUE 3192038.039 3315402.282 3317215.533 3281170.799 3462028.959 3430634.885 3568636.001 3491587.168 3573320.266 3650029.339 0.87452394 0.908322091 0.908818868 0.898943678 0.948493461 0.939892413 0.977700635 0.956591535 0.978983984 1 21.79947663 3.370895836 0.301601589 1.002295123 0.845269332 0.895977358 0.012420802 0.983680146 0.13696914 0.015346172 0.054179327 2349.069339 -3.370895836 -0.157025792 YFSIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFSIDR 6 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 114.94 0.057818 347650000 524480 621530 505590 496130 407590 434370 343870 434550 508590 571390 FALSE TRUE 503982.7418 603804.5729 596961.3598 521735.3288 420700.5025 443153.259 348078.3839 425576.3906 450856.9954 532689.2464 0.946110223 1.133502463 1.120655924 0.979436571 0.789767215 0.831917036 0.653436101 0.798920559 0.846379007 1 19.02293463 3.371174736 3.348982326 0.797925366 1.071925228 0.58350354 0.093815535 0.145478299 3.212866647 0.026036875 0.036592864 2350.578373 -3.371174736 0.273999862 NMGGPYGGGNYGPGGSGGSGGYGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 429.86 1.63E-180 443530000 135080 118459 105856 113594 89284 95287 94190 116325 123627 120559 FALSE TRUE 129800.9243 115080.6653 124986.534 119456.6 92155.90095 97213.76843 95342.7254 113922.8481 109593.3812 112393.4315 1.154879983 1.023909171 1.112044825 1.062843249 0.819940273 0.864941724 0.848294461 1.013607704 0.975087065 1 16.7781982 3.37144428 7.256574565 0.920210049 1.089147072 0.600393529 0.067493538 0.165492641 10.16089409 0.019837483 0.026900321 2352.037706 -3.37144428 0.168937023 NADHSMNYQYR ddPTM_BT-474_Pertuzumab_2h_R1 6 NADHSMNYQYR 11 0 Q12906;K7ELV3;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 221.09 8.66E-12 3976796000 769082 845695 725500 707228 631658 547989 697312 591605 801126 776679 FALSE TRUE 739025.4252 821576.6066 856613.9887 743728.1218 651975.8532 559069.713 705845.9128 579388.15 710185.5351 724073.8395 1.020649255 1.134658597 1.183047836 1.02714403 0.900427301 0.772116989 0.974825873 0.800178267 0.980819215 1 19.4657773 3.371834688 3.326544791 0.886709046 1.114415299 0.57318916 0.080367279 0.148262218 3.236169805 0.021977128 0.030918564 2354.153018 -3.371834688 0.227706254 GTWERPGGAAPLGYDFWYQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTWERPGGAAPLGYDFWYQPR 21 1 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 167.61 1.08E-11 313060000 104210 129380 90824 75224 78842 81022 61439 56898 67916 76827 FALSE TRUE 100137.358 125690.2091 107237.9172 79106.31965 81378.02453 82660.32035 62190.90886 55723.03642 60206.46041 71623.43886 1.39810877 1.754875374 1.497246137 1.104475307 1.136192646 1.154095945 0.868303866 0.778000014 0.840597176 1 16.12814417 3.372352887 0.792858778 0.851050575 1.639588433 0.79328349 0.135345223 0.30033739 0.397284983 0.070111668 0.148298263 2356.963665 -3.372352887 0.788537857 HLLQEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLLQEAR 7 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 69.198 0.082653 0 92060 104520 106700 84635 85396 56529 83536 76833 95658 99296 FALSE TRUE 88462.19342 101539.1919 125983.0635 89003.02249 88142.83989 57672.05511 84558.33856 75246.3717 84799.30487 92570.59348 0.955618735 1.096883882 1.360940433 0.961461077 0.952168897 0.623006216 0.913447083 0.812853941 0.916050137 1 16.49826635 3.372805076 2.899541951 0.846153043 1.135275895 0.425864408 0.135646834 0.219944934 3.721473165 0.038576284 0.055171845 2359.419017 -3.372805076 0.289122851 VHSPCPT(ph)SGSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHSPCPTSGSEK 12 0 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 VHS(0.348)PCPT(0.65)S(0.002)GSEK 132.86 0.0019387 58517000 137380 116450 121890 115310 115480 103920 132550 83734 164660 143670 TRUE FALSE 132011.0377 113128.96 143918.2344 121261.1629 119194.5191 106021.3336 134172.1866 82004.86364 145968.4871 133939.1029 0.985604912 0.844629817 1.07450499 0.905345491 0.889915764 0.791563713 1.001740221 0.612254837 1.089812339 1 17.03121769 3.372897663 3.474454018 0.862434573 0.959782383 0.010986526 0.136392187 0.583960952 13.76600522 0.037787246 0.052956454 2359.922078 -3.372897663 0.09734781 AS(ph)PATPAGHPVSGLLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASPATPAGHPVSGLLLR 17 0 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 AS(0.992)PAT(0.008)PAGHPVSGLLLR;AS(0.999)PAT(0.001)PAGHPVSGLLLR;AS(0.995)PAT(0.005)PAGHPVSGLLLR 174.2 8.91E-10 961360000 509189 518992 446527 486646 513054 543413 535091 584422 623270 583753 TRUE FALSE 489289.3309 504190.8563 527224.3618 511761.8584 529556.8479 554401.1832 541639.6037 572353.4815 552519.0026 544214.8894 0.899073768 0.926455461 0.968779745 0.940367249 0.97306571 1.018717411 0.995267888 1.051704929 1.015258886 1 19.0538169 3.373132094 0.653066958 1.02858914 0.904841261 0.791236563 0.020261595 0.390113963 0.340030351 0.012523336 0.028495836 2361.196299 -3.373132094 -0.123747879 FLCSGGHNALFETFNWALSMGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLCSGGHNALFETFNWALSMGGK 23 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 88.071 0.00012128 0 16669 17602 12649 17234 22602 23558 27531 21601 22467 15387 FALSE TRUE 16017.55705 17100.00819 14934.95568 18123.44881 23329.01386 24034.3589 27867.93261 21154.9318 19916.64035 14344.82478 1.116608763 1.192068112 1.04113894 1.263413745 1.626301764 1.675472462 1.942716836 1.47474313 1.388419911 1 13.80824273 3.37369611 4.03956296 1.572136948 1.127089764 0.370658163 0.231362977 0.202432596 6.100886511 0.063939716 0.088493066 2364.264765 -3.37369611 -0.445047183 YFPEYAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YFPEYAEK 8 0 Q9NQR4;H7C579;F8WF70 Q9NQR4 NIT2 Omega-amidase NIT2 0 117.04 0.0095481 0 321580 285800 271970 207990 220090 202210 188070 175870 207240 184360 FALSE TRUE 309012.2981 277649.2638 321121.0289 218724.3888 227169.3947 206298.8247 190371.6569 172238.223 183714.984 171873.133 1.797909264 1.615431446 1.868360827 1.272592086 1.321727199 1.20029711 1.107628945 1.002124183 1.068898791 1 17.39098452 3.373944526 0.811227543 1.027880097 1.818050374 0.880429742 0.10625651 0.213179714 0.295414257 0.050461525 0.106066845 2365.617511 -3.373944526 0.790170277 ISEQFTAMFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISEQFTAMFR 10 0 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1;P04350 Q13509;Q5JP53;P68371;Q13885;Q9BVA1;P04350 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB2B;TUBB4A Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain 0 ; 171.85 9.06E-06 6898400000 664760 679730 634350 608480 610820 445500 713030 578090 688860 756110 FALSE TRUE 638780.4443 660344.7659 748991.156 639883.7257 630467.58 454508.3152 721756.2744 566152.2395 610663.5007 704897.9962 0.906202667 0.936794784 1.06255254 0.907767832 0.894409664 0.644785937 1.023915912 0.803169029 0.866314707 1 19.42705498 3.374594801 3.383855815 0.858277874 0.967273602 0.131833583 0.105702507 0.405874339 9.142504602 0.029028341 0.040821871 2369.162233 -3.374594801 0.108995729 VKLEGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKLEGSK 7 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 99.802 0.0093578 1218070000 3652200 3225400 2988100 2369800 1551730 833690 1286630 1345180 1569110 1470290 FALSE TRUE 3509467.986 3133414.75 3528116.14 2492105.662 1601642.805 850547.783 1302376.163 1317401.563 1390991.211 1370705.949 2.560336146 2.285986103 2.573940927 1.818118368 1.168480232 0.62051805 0.950149931 0.961111728 1.014799135 1 20.38648768 3.375146783 2.219738624 0.912538823 2.45817482 0.961004654 0.139045919 0.051138404 0.512166966 0.041423962 0.061938229 2372.17532 -3.375146783 1.545635997 up GWAFGSNS(ph)LPIAGSVGMGVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWAFGSNSLPIAGSVGMGVAR 21 0 M0QZ22;Q5PRF9;A0A087WZT0 M0QZ22 SAMD4B Protein Smaug homolog 2 1 GWAFGS(0.001)NS(0.999)LPIAGSVGMGVAR 169.39 1.00E-11 263810000 173470 162550 134190 141550 144330 119940 130390 156440 131300 150250 TRUE FALSE 166690.6006 157914.2332 158441.118 148855.4125 148972.5055 122365.269 131985.7518 153209.4593 116395.3745 140073.4337 1.190022949 1.127367474 1.131128965 1.062695534 1.063531475 0.87357942 0.94226113 1.093779565 0.830959672 1 17.09582383 3.375474113 1.412747229 0.966796462 1.154615988 0.583124244 0.071965686 0.327124549 1.345390796 0.024965291 0.042345738 2373.963912 -3.375474113 0.187819526 DIVENYFMR ddPTM_BT-474_Pertuzumab_2h_R1 11 DIVENYFMR 9 0 Q13263;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;;;;;;; 265.82 4.15E-15 7581060000 2786108 3049142 2565409 2617535 2538316 1844417 2903081 2753529 2755817 3002470 FALSE TRUE 2677223.819 2962183.456 3029035.474 2752626.295 2619963.239 1881712.375 2938609.774 2696667.664 2442988.207 2799110.033 0.956455369 1.058259026 1.082142337 0.983393387 0.93599866 0.672253807 1.049837177 0.963401807 0.872773195 1 21.41653677 3.375493852 3.459778396 0.915423829 1.034534986 0.220947788 0.098971068 0.368146582 8.626684403 0.029081339 0.040822152 2374.071812 -3.375493852 0.119111158 HWPFMVVNDAGRPK ddPTM_BT-474_Pertuzumab_2h_R1 4 HWPFMVVNDAGRPK 14 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 198.14 1.35E-08 18776300000 5422090 5466360 4628610 4792370 4498940 3701090 5504500 3376270 6464200 6088800 FALSE TRUE 5210188.728 5310464.765 5465102.79 5039704.79 4643652.491 3775928.576 5571865.718 3306548.845 5730411.116 5676400.153 0.917868471 0.935533899 0.962776169 0.887834658 0.818062921 0.665197744 0.981584379 0.582508061 1.009515003 1 22.43654486 3.375879505 3.275103421 0.807296779 0.93727457 0.057070304 0.134288795 0.435946654 9.266307286 0.036578121 0.051650354 2376.180924 -3.375879505 0.129977791 LRDYQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRDYQVR 7 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 147.52 0.0019572 130200000 145020 162420 133940 131750 122290 84614 133930 130330 120000 157850 FALSE TRUE 139352.4581 157787.9406 158145.9375 138549.6333 126223.5689 86324.95305 135569.0754 127638.64 106378.1031 147158.6789 0.946953718 1.072229934 1.074662661 0.941498214 0.85773785 0.586611362 0.921244173 0.867353804 0.722880253 1 17.1670131 3.376020491 2.927922282 0.81742217 1.033185806 0.415501116 0.109989702 0.240884408 4.153799704 0.031664108 0.0453138 2376.952436 -3.376020491 0.215763636 TLSNAEDYLDDEDS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 1 TLSNAEDYLDDEDSD 15 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 1 TLSNAEDYLDDEDS(1)D 444.24 4.14E-175 379020000 372000 389450 372170 444190 374980 451190 506970 495830 633500 573070 TRUE FALSE 357461.8287 378343.2673 439429.3979 467114.6991 387041.5722 460313.3709 513174.4505 485590.9372 561587.7358 534255.4585 0.669084093 0.708169213 0.822508017 0.874328361 0.724450384 0.861597881 0.960541334 0.908911513 1.051159566 1 19.02717022 3.376541692 0.309309216 1.038913866 0.585500237 0.763808999 0.059142698 1.621570482 0.237362532 0.075094856 0.262642154 2379.806748 -3.376541692 -0.45341363 LNFEAAWDEVGDEFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNFEAAWDEVGDEFEK 16 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 113.35 0.0015547 13892000 14959 15330 14906 19392 16678 17474 23149 24137 24809 26051 FALSE TRUE 14374.38574 14892.80341 17599.84578 20392.82344 17214.46302 17827.33625 23432.30439 23638.56252 21992.78633 24286.54257 0.591866286 0.613212168 0.724674817 0.839675857 0.708806656 0.734041752 0.964826686 0.973319378 0.905554435 1 14.5678695 3.376804823 0.343321004 1.025417156 0.483289435 0.795610172 0.064913014 1.232565543 0.226584877 0.078643632 0.257794361 2381.249067 -3.376804823 -0.542127721 ACS(ph)LAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ACSLAK 6 0 B7Z2E6;H0YB80;P63104-2;P31946-2;P31946;P63104;E7EX29;B0AZS6 B7Z2E6;P31946-2;P63104 YWHAZ;YWHAB "14-3-3 protein zeta/delta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 1 ACS(1)LAK 71.692 0.091849 223570000 202800 205530 164240 189460 198680 210620 198440 220390 206910 206390 TRUE FALSE 194874.3518 199668.4856 193921.8215 199238.0533 205070.7226 214878.8807 200868.5681 215838.8695 183422.4442 192411.0215 1.012802439 1.037718547 1.007851941 1.035481501 1.065795094 1.116770126 1.043955625 1.121759387 0.953284499 1 17.55383191 3.377332874 4.068100423 1.063164686 1.02129724 0.036782032 0.048255945 0.440581861 13.48429833 0.013134667 0.018191298 2384.146147 -3.377332874 -0.041867446 QPS(ph)VETLDSPTGSHVEWCK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPSVETLDSPTGSHVEWCK 19 0 F8WA39;Q13613;Q13613-2;E9PPP8;Q8NEC6 F8WA39 MTMR1 Myotubularin-related protein 1 1 QPS(1)VETLDSPTGSHVEWCK 166.05 1.33E-11 392360000 213650 224480 163470 219340 287620 275460 293230 266290 322740 333610 TRUE FALSE 205300.3218 218078.0502 193012.6654 230660.1637 296871.5585 281029.9899 296818.6365 260791.0184 286103.9082 311014.2976 0.660099305 0.70118336 0.620590972 0.741638457 0.954527045 0.903591867 0.954356886 0.83851778 0.919905967 1 18.24662138 3.377505722 4.147798828 0.915262702 0.666397592 0.88098188 0.045055192 0.070915155 2.235617074 0.012659937 0.017509721 2385.09522 -3.377505722 -0.24886511 ELWAVLNGWR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELWAVLNGWR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ; 169.12 1.10E-05 428680000 408900 428850 419080 382770 348720 230910 412940 392660 387650 413170 FALSE TRUE 392919.7359 416619.6179 494817.0784 402524.8056 359936.8955 235579.1584 417993.6832 384551.4338 343645.5972 385185.6279 1.020078911 1.08160738 1.284619785 1.045015121 0.934450482 0.611599035 1.085174661 0.998353536 0.892155813 1 18.55519435 3.377729208 4.054680201 0.923280468 1.129429646 0.336542946 0.132324492 0.266471324 8.119030184 0.03906808 0.054129538 2386.322896 -3.377729208 0.206149179 SPQNDDHSDT(ph)DSEENRDNQQFLTTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPQNDDHSDTDSEENRDNQQFLTTVK 26 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 SPQNDDHS(0.042)DT(0.479)DS(0.479)EENRDNQQFLTTVK 137.25 2.74E-05 132530000 42926 44558 35886 42265 47004 47898 51947 42856 57080 56932 TRUE FALSE 41248.40446 43287.24947 42371.39848 44446.30172 48515.92635 48866.53038 52582.74293 41971.00862 50600.5177 53075.94493 0.777158174 0.815571904 0.798316423 0.837409523 0.914085023 0.920690728 0.990707617 0.790772707 0.953360656 1 15.69577053 3.378339063 2.828038282 0.913901057 0.799555588 0.531510318 0.055618763 0.243393119 3.926779572 0.016634155 0.023947565 2389.676227 -3.378339063 -0.114345469 QGSIT(ph)SPQANEQSVT(ph)PQRR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.081)IT(0.493)S(0.426)PQANEQS(0.215)VT(0.785)PQRR 61.648 0.032775 1012700000 434490 428330 344240 416940 459860 499360 492780 514910 453910 453790 TRUE FALSE 417509.6504 416114.4478 406451.8256 438458.3234 474651.8145 509457.4013 498810.789 504276.9286 402384.0397 423054.3991 0.986893533 0.983595605 0.960755464 1.036411214 1.121964021 1.204236151 1.179070091 1.191990745 0.951140186 1 18.69048366 3.378429141 2.973551664 1.132358519 0.978954508 0.33686556 0.078639059 0.241233253 4.285938179 0.022715756 0.032488888 2390.171927 -3.378429141 -0.153404011 LEALQKQMDS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 LEALQKQMDSR 11 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 LEALQKQMDS(1)R 57.348 0.056776 121850000 197880 177850 149740 136340 166500 101770 178970 54178 197820 185590 TRUE FALSE 190146.6308 172777.8921 176801.3489 143376.5237 171855.6237 103827.8591 181160.2884 53059.20537 175364.3029 173019.824 1.098987541 0.99860171 1.021856021 0.828671076 0.99327129 0.600092271 1.047049316 0.306665468 1.013550349 1 17.40057782 3.378853338 0.917647461 0.733100608 1.065095869 0.128631402 0.22161432 0.887599284 1.573524501 0.094148901 0.190062072 2392.507666 -3.378853338 0.331995261 WDS(ph)YDNFSGHRDDGMEEVVGHTQGPLDGSLYAK ddPTM_BT-474_Pertuzumab_2h_R1 2 WDSYDNFSGHRDDGMEEVVGHTQGPLDGSLYAK 33 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;E7ERH1;E7EMG1 E9PGF5 TNS1 Tensin-1 1 WDS(0.999)YDNFS(0.001)GHRDDGMEEVVGHTQGPLDGSLYAK;WDS(0.253)Y(0.236)DNFS(0.253)GHRDDGMEEVVGHT(0.253)QGPLDGS(0.004)LYAK 207.61 1.66E-27 271870000 181896 203048 147512 134001 169758 150352 129988 110851 184412 171638 TRUE FALSE 174787.3032 197257.2698 174170.6998 140916.8077 175218.4202 153392.2205 131578.832 108561.8881 163478.3229 160012.8054 1.092333222 1.232759274 1.088479759 0.880659566 1.095027487 0.958624656 0.822301888 0.678457501 1.021657751 1 17.28782784 3.379158864 0.777124344 0.846126288 1.175372963 0.37036839 0.120147654 0.675744258 0.855501797 0.064623447 0.139018401 2394.191385 -3.379158864 0.329246675 KRPYEENR ddPTM_BT-474_Pertuzumab_2h_R1 8 KRPYEENR 8 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8;M0QZV6;M0R203 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ;;;;;;; 172.23 0.00016016 4851480000 2699264 2931582 2438161 2415120 2279089 1565643 2648534 2317975 2450665 2569826 FALSE TRUE 2593773.779 2847976.152 2878790.929 2539764.633 2352397.968 1597301.374 2680947.551 2270108.006 2172475.783 2395769.396 1.082647513 1.188752205 1.201614368 1.060103964 0.98189666 0.666717497 1.119034059 0.947548629 0.9067967 1 21.19205762 3.379448295 2.881555911 0.934460484 1.158435189 0.450858176 0.110244632 0.237513783 3.973664715 0.032105402 0.04613442 2395.7875 -3.379448295 0.223974706 NRPEDYQGGR ddPTM_BT-474_Pertuzumab_2h_R1 8 NRPEDYQGGR 10 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;;;; 243.82 1.79E-12 6985002000 1961884 2161616 1658708 1855658 1679040 1874247 1737979 1850359 2057306 1990039 FALSE TRUE 1885211.404 2099968.828 1958473.433 1951428.732 1733047.846 1912145.558 1759248.907 1812148.44 1823769.248 1855251.886 1.016148491 1.131904969 1.055637484 1.051840317 0.934130756 1.030666279 0.948253399 0.976766796 0.983030532 1 20.82318364 3.379522332 5.950931747 0.978099871 1.071048601 0.571847985 0.036183599 0.133224875 6.790085063 0.009408079 0.012802002 2396.19596 -3.379522332 0.09294873 EIPSATQS(ph)PISK ddPTM_BT-474_Pertuzumab_2h_R1 6 EIPSATQSPISK 12 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 EIPSAT(0.003)QS(0.997)PISK;EIPSAT(0.001)QS(0.997)PIS(0.002)K;EIPSAT(0.021)QS(0.979)PISK;EIPSAT(0.073)QS(0.927)PISK;EIPSAT(0.006)QS(0.994)PISK;EIPSATQS(1)PISK 190.34 7.09E-06 10275620000 9851090 9342110 8114980 8679530 8566090 8610070 9097850 9005090 9013990 9859200 TRUE FALSE 9466098.512 9075682.17 9581537.403 9127481.583 8841626.064 8784171.515 9209192.21 8819131.745 7990759.645 9191427.602 1.029883378 0.987407241 1.042442787 0.993042863 0.961942633 0.955691748 1.001932736 0.959495317 0.869370895 1 23.13185753 3.379905028 3.331738749 0.959041265 1.017000044 0.368205627 0.036485085 0.275760538 6.0571174 0.010399944 0.01468798 2398.308397 -3.379905028 0.057958779 HYPVFENPK ddPTM_BT-474_Pertuzumab_2h_R1 2 HYPVFENPK 9 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISU1;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 133.57 0.00027316 258480000 715590 698930 579140 601760 631420 531370 654040 501650 770310 767690 FALSE TRUE 687623.9517 678997.2007 683803.4809 632816.9057 651730.1977 542114.6655 662044.3372 491290.7522 682867.6382 715693.6725 0.9607797 0.948726008 0.955441563 0.884200783 0.910627302 0.757467456 0.92503869 0.686453955 0.95413396 1 19.4489827 3.379945911 1.50556713 0.838989847 0.956256419 0.099333396 0.089506706 0.573349933 2.668295603 0.028256064 0.047072729 2398.534178 -3.379945911 0.117266571 EEADEYIDIGALNGIFVLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEADEYIDIGALNGIFVLGR 20 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 234.69 3.73E-29 80728000 57091 57843 48541 55865 61390 63843 62445 68995 69954 68553 FALSE TRUE 54859.8206 56193.37427 57313.43849 58748.19934 63364.6651 65133.9492 63209.22059 67570.22914 62013.11519 63909.84425 0.858393902 0.879260072 0.896785764 0.919235527 0.991469559 1.019153621 0.989037312 1.057274195 0.970321801 1 15.96375055 3.380049829 1.459652781 1.014928129 0.871396574 0.865327351 0.022907646 0.125958041 0.55174822 0.007464983 0.01257189 2399.108164 -3.380049829 -0.143531555 HSTLDFMLGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSTLDFMLGAK 11 0 P52788;P52788-2 P52788 SMS Spermine synthase 0 79.693 0.026447 672090000 1554000 1905300 1463600 1524200 1439600 1395800 1682100 1181700 1661500 1892500 FALSE TRUE 1493267.962 1850962.709 1728105.078 1602864.145 1485906.041 1424024.032 1702686.043 1157297.482 1472893.486 1764319.289 0.846370592 1.049108696 0.979474117 0.908488704 0.842197923 0.807123768 0.965066841 0.655945604 0.834822526 1 20.75068024 3.380680251 2.545689456 0.826299028 0.96642726 0.16416373 0.10026188 0.370405996 4.863852117 0.029280399 0.042881448 2402.593242 -3.380680251 0.140128231 ANASNS(ph)PEGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 ANASNSPEGNK 11 0 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 ANASNS(1)PEGNK 130.27 0.0010821 0 118890 105120 103200 105940 116390 102200 115850 127520 105760 131140 TRUE FALSE 114243.6474 102122.0805 121850.5357 111407.5761 120133.7901 104266.554 117267.807 124886.6674 93754.56818 122257.771 0.934448963 0.835301345 0.996669043 0.911251491 0.982627027 0.852841935 0.959184893 1.021502899 0.766859787 1 16.89956664 3.380853653 0.007379691 1.849232265 5.18E-05 0.019537407 0.078650455 27273.68599 53.28550364 6469.463337 6883.269895 2403.552724 -3.380853653 -1.849180425 LGQELCGMLHRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGQELCGMLHRPR 13 1 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 85.845 0.0054668 649080000 199480 249671 196489 210326 209566 209231 231847 204922 229340 260690 FALSE TRUE 191684.1011 242550.6275 231998.9332 221180.9501 216306.8807 213461.7942 234684.4129 200690.2891 203306.2847 243033.2341 0.788715592 0.998014236 0.954597564 0.910085202 0.890030047 0.878323473 0.96564741 0.825773026 0.836536968 1 17.89079409 3.380958108 4.320874423 0.890111614 0.923598042 0 0.070459089 0.791615839 26.68507941 0.019314749 0.026665465 2404.130888 -3.380958108 0.033486427 YLELLGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLELLGYR 8 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;O94979-5;H0YAB3;H0Y8V7;H0Y9K1 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 140.98 0.0014908 386500000 409670 495980 408590 393540 355480 187029 465720 389640 343760 432410 FALSE TRUE 393659.6435 481835.136 482431.302 413850.6466 366914.337 190810.8545 471419.6207 381593.7978 304737.806 403122.4855 0.976526137 1.195257405 1.196736276 1.026612658 0.910180777 0.473332204 1.169420307 0.94659517 0.755943459 1 18.62085873 3.381073814 3.392383738 0.880069124 1.128201579 0.283907669 0.17799811 0.319103833 7.245247659 0.051979786 0.073311841 2404.771488 -3.381073814 0.248132455 FKEFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FKEFLR 6 1 P33992;B1AHB1;B1AHA9;F8WFD7 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 108.09 0.02801 393770000 681180 728040 629850 643530 591120 480070 683110 659870 680460 752290 FALSE TRUE 654558.7325 707277.012 743677.9059 676742.6604 610133.9116 489777.3443 691470.1045 646243.4539 603217.0335 701336.7282 0.93330166 1.008469945 1.060372109 0.964932583 0.869958591 0.698348346 0.985931688 0.921445331 0.86009617 1 19.41974776 3.38109803 4.611183274 0.886282206 1.003098355 0.274164776 0.082881413 0.274811858 10.16978494 0.023866309 0.032814821 2404.90558 -3.38109803 0.116816148 QLIYNYPEQLFGAAGVMAIEHADFAGVER ddPTM_BT-474_Pertuzumab_2h_R1 2 QLIYNYPEQLFGAAGVMAIEHADFAGVER 29 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 218.69 2.29E-34 215335000 135538 139444 102837 109991 106500 96562 82991 93779 107137 135220 FALSE TRUE 130241.0251 135467.1936 121421.9335 115667.6487 109925.6692 98514.5498 84006.66868 91842.43088 94975.25691 126061.429 1.033155234 1.07461255 0.96319655 0.917549877 0.872000818 0.78148051 0.666394704 0.728552989 0.753404572 1 16.9437674 3.383319638 1.131842702 0.755610414 1.049903413 0.581796295 0.086378758 0.295809242 0.789625449 0.031090147 0.057976816 2417.239255 -3.383319638 0.294292998 AKFEELNMDLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 AKFEELNMDLFR 12 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 192.86 3.23E-06 7184700000 7323400 8937800 6671100 7059300 5729000 3920000 7513600 5990800 8074700 8152600 FALSE TRUE 7037193.432 8682902.695 7876716.168 7423631.319 5913278.488 3999265.086 7605553.684 5867087.886 7158093.908 7600417.14 0.925895685 1.142424493 1.03635314 0.976739984 0.778020256 0.526190209 1.000675824 0.771942879 0.941802769 1 22.85764717 3.383331024 4.255830361 0.819393923 1.040616004 0.295179272 0.139427461 0.24068788 7.973110308 0.038622781 0.05341796 2417.302628 -3.383331024 0.221222081 RLEFLYDK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLEFLYDK 8 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 0 105.98 0.00687 412960000 380070 437930 395580 363650 311150 191240 430070 326600 313350 410540 FALSE TRUE 365216.4442 425440.6652 467070.1056 382418.0201 321158.4223 195107.0038 435333.3253 319855.5959 277779.8217 382733.7601 0.954231067 1.111583846 1.220352512 0.99917504 0.839117046 0.509772129 1.137431214 0.835713044 0.725778206 1 18.54598164 3.383358593 3.946676804 0.83917799 1.098923554 0.327776491 0.16518647 0.255541912 7.526358572 0.046740564 0.065034148 2417.456081 -3.383358593 0.259745563 SPDMLAHFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPDMLAHFR 9 0 O43747;O43747-2;H3BNR4 O43747 AP1G1 AP-1 complex subunit gamma-1 0 99.653 0.0051914 212110000 104100 131250 108290 104770 101310 49916 133800 99383 106830 134880 FALSE TRUE 100031.6569 127506.8785 127860.4119 110177.1923 104568.7282 50925.33572 135437.4844 97330.70632 94703.10627 125744.4575 0.795515436 1.014015894 1.016827417 0.876199194 0.831597116 0.404990699 1.077085123 0.774035757 0.753139408 1 16.94013529 3.383918264 3.404611835 0.794647632 0.948761349 0.103645629 0.176054406 0.487951824 11.17121018 0.049440914 0.069803126 2420.573439 -3.383918264 0.154113717 ILLWDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILLWDTR 7 0 Q9BQA1;Q9BQA1-2;H0Y711 Q9BQA1 WDR77 Methylosome protein 50 0 ; 79.146 0.077742 468270000 767900 829440 748480 736120 700650 439230 885530 717430 803830 977690 FALSE TRUE 737889.619 805785.1833 883746.9858 774111.2414 723187.0436 448111.5315 896367.381 702614.8198 712582.5883 911470.1855 0.809559798 0.884049963 0.969584085 0.849299575 0.793429182 0.491635973 0.983430281 0.770858807 0.781794731 1 19.79783594 3.384021419 4.297346218 0.789457378 0.890328659 0.066305415 0.13568292 0.510024081 17.17086601 0.037457663 0.051781212 2421.148455 -3.384021419 0.100871281 TPLGAS(ph)LDEQSSSTLK ddPTM_BT-474_Pertuzumab_2h_R1 3 TPLGASLDEQSSSTLK 16 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK 216.17 1.62E-14 472410000 317726 287057 189616 273793 419556 274322 337246 445321 416875 392964 TRUE FALSE 305308.9167 278870.4154 223883.8292 287923.4895 433051.3998 279868.9788 341373.3174 436124.9657 369553.0977 366348.1983 0.833384518 0.761216833 0.611123052 0.785928499 1.182075964 0.763942556 0.931827477 1.190465704 1.008748233 1 18.48285599 3.385298519 7.196581999 1.01607918 0.731552767 0.523425775 0.124448938 0.178434688 11.92701208 0.03612375 0.049009358 2428.278638 -3.385298519 -0.284526413 RPAEEQKR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPAEEQKR 8 2 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDQ3;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 54.982 0.071327 15026000 14045 15660 12708 13372 13968 12646 13905 14339 15930 15377 FALSE TRUE 13496.10587 15213.39213 15004.61829 14062.13052 14417.29341 12901.71078 14075.17355 14042.89464 14121.69318 14335.50209 0.941446333 1.061238876 1.046675463 0.98093045 1.005705507 0.899983182 0.981840291 0.979588615 0.985085356 1 13.80730481 3.385307258 2.380905371 0.970807934 1.019537513 0.158459975 0.040347952 0.445296755 5.119853611 0.011778757 0.017502761 2428.327499 -3.385307258 0.048729579 HTTENKPHSPKT(ph)PEPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HTTENKPHSPKTPEPR 16 2 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 HTTENKPHS(0.004)PKT(0.996)PEPR;HTTENKPHS(0.007)PKT(0.993)PEPR;HTTENKPHS(0.003)PKT(0.997)PEPR;HTTENKPHS(0.015)PKT(0.985)PEPR 153.83 4.16E-07 780040000 732470 702030 557420 507320 511360 580680 533890 201448 711690 549750 TRUE FALSE 703844.2626 682008.7918 658158.1937 533502.846 527808.3588 592421.7475 540423.9055 197288.0284 630901.9348 512514.9428 1.373314617 1.330710063 1.284173667 1.040950812 1.029839942 1.15591117 1.054454925 0.384941027 1.230992274 1 18.96723454 3.385813575 0.644185349 0.83592081 1.417528195 0.326774253 0.219031374 0.976303331 0.820855558 0.143674923 0.334471029 2431.160187 -3.385813575 0.581607385 S(ph)FDGNTLLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFDGNTLLNR 10 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(1)FDGNTLLNR 206.03 1.66E-07 1128310000 860966 750000 517946 704944 1018977 647042 876965 1136476 940976 838366 TRUE FALSE 827318.4969 728610.7343 611550.3638 741326.2443 1051753.321 660125.6326 887697.56 1113007.373 834160.3494 781582.7241 1.058516868 0.932224718 0.78245123 0.948493642 1.345671147 0.844601105 1.135769168 1.424042957 1.067270711 1 19.57603905 3.38607923 9.065230342 1.161534516 0.915353605 0.261009051 0.166547346 0.346335069 31.08679876 0.048102578 0.065159255 2432.647768 -3.38607923 -0.246180911 GISDLAQHYLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 GISDLAQHYLMR 12 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 160.15 6.88E-05 2419900000 4473700 5365900 4981600 4577800 3869950 2220730 5646400 3953600 4622400 5702000 FALSE TRUE 4298862.858 5212869.786 5881885.935 4814060.807 3994430.456 2265634.682 5715502.332 3871956.778 4097684.531 5315798.461 0.808695606 0.980637213 1.106491523 0.905613868 0.751426241 0.426207784 1.07519169 0.728386677 0.770850242 1 22.34185498 3.387987206 4.800548252 0.778941993 0.972556801 0.165098124 0.17598469 0.332515731 13.32150987 0.048561162 0.066722946 2443.358571 -3.387987206 0.193614808 VQIFEYNENTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQIFEYNENTR 11 0 K7ELV2;Q96EE3;Q96EE3-1;K7ENI5 K7ELV2 SEH1L Nucleoporin SEH1 0 ; 174.87 0.0017404 0 186558 237700 194674 203286 193449 197219 212370 221530 211490 208254 FALSE TRUE 179267.1071 230921.0287 229855.9223 213777.6148 199671.4628 201206.9033 214969.0476 216955.3281 187482.5418 194148.7711 0.923349172 1.189402474 1.183916442 1.101102076 1.028445669 1.036354246 1.107238776 1.117469489 0.965664324 1 17.56680305 3.388363545 7.088613362 1.057331531 1.113514479 0.080982584 0.08121507 0.557749329 37.602453 0.022499417 0.030534459 2445.476787 -3.388363545 0.056182948 HYGGLTGLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 HYGGLTGLNK 10 0 P18669;Q8N0Y7;P15259 P18669 PGAM1;PGAM4;PGAM2 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4;Phosphoglycerate mutase 2 0 ; 169.77 4.53E-06 7401800000 8824900 9241900 7416900 7582600 6436500 5556200 7942400 5936400 7950000 7052900 FALSE TRUE 8480013.152 8978330.061 8757298.818 7973938.895 6643535.868 5668550.171 8039601.467 5813811.265 7047549.329 6575200.801 1.289696453 1.365483783 1.33186789 1.212729335 1.010392849 0.862110579 1.222715733 0.884202847 1.071837886 1 22.64860352 3.388442212 2.864521541 1.001523525 1.329740051 0.70212969 0.095108474 0.134175513 2.221657572 0.026426643 0.038210682 2445.919797 -3.388442212 0.328216526 KLFVQDLATR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLFVQDLATR 10 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 158.3 1.29E-05 553310000 740330 863000 681950 721050 646690 428150 853990 691930 787000 894180 FALSE TRUE 711397.0851 838388.085 805193.5349 758263.4769 667491.3712 436807.4863 864441.3851 677641.4037 697663.0594 833616.3921 0.853386632 1.005724087 0.965904153 0.909607205 0.800717665 0.523990999 1.036977431 0.812893568 0.836911397 1 19.66902412 3.388456996 4.626682034 0.825317529 0.946675265 0.114470647 0.13404595 0.411811758 15.66834561 0.037347059 0.05143546 2446.00306 -3.388456996 0.121357736 GFPTWLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFPTWLK 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 97.602 0.02763 185897000 499450 517430 491270 463090 393600 281500 489810 451050 477280 515400 FALSE TRUE 479930.9418 502673.403 580053.4172 486990.1304 406260.5015 287192.1229 495804.4413 441735.6599 423101.1753 480491.4989 0.998833367 1.046165029 1.207208491 1.013524967 0.845510279 0.597704899 1.03186933 0.91934126 0.880559128 1 18.87415138 3.388570674 4.705581394 0.876762831 1.084729455 0.377313568 0.120102889 0.223597366 8.723450148 0.034914315 0.048035748 2446.643393 -3.388570674 0.207966624 DKFPGEFMK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKFPGEFMK 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 122.51 0.0005324 1556170000 1593430 1867180 1460460 1768250 1942770 1935940 2164360 2249080 2541490 2512010 FALSE TRUE 1531156.994 1813929.855 1724397.61 1859509.594 2005260.961 1975086.033 2190848.085 2202635.712 2252990.71 2341869.325 0.653818288 0.774564932 0.73633383 0.794027905 0.856265096 0.84338012 0.935512525 0.940545951 0.962048004 1 21.15922915 3.389920236 0.352425425 1.011482631 0.60381748 0.939238639 0.025955938 0.536058063 0.104032959 0.026399893 0.086072961 2454.258118 -3.389920236 -0.407665151 VAAAPDEDLDGDDEDDAEDENNIDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 VAAAPDEDLDGDDEDDAEDENNIDNR 26 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 280.8 7.82E-61 206910000 104490 101880 70753 96872 107070 108830 107490 124570 105870 123390 FALSE TRUE 100406.4153 98974.48215 83539.64099 101871.5755 110514.0038 111030.6172 108805.4948 121997.586 93852.08144 115032.6854 0.872851181 0.860403126 0.726225252 0.885588085 0.960718281 0.965209295 0.945865902 1.060547144 0.815873168 1 16.81168432 3.390037837 3.716311389 0.967240777 0.821321359 0.447356218 0.068431406 0.191329176 5.145863877 0.019154229 0.026875538 2454.922786 -3.390037837 -0.145919419 GFGFVSFER ddPTM_BT-474_Pertuzumab_2h_R1 4 GFGFVSFER 9 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;; 186.13 9.78E-05 1956772000 1669782 1929261 1682051 1644148 1511978 991754 2008117 1570975 1674857 1973272 FALSE TRUE 1604525.073 1874240.365 1986035.033 1729002.675 1560612.146 1011807.945 2032692.937 1538533.817 1484734.255 1839620.53 0.872204374 1.018819009 1.079589513 0.9398692 0.84833373 0.550009053 1.104952301 0.836332163 0.807087239 1 20.81097677 3.390466064 4.281013918 0.85237333 0.995420868 0.150423152 0.142274518 0.381615806 12.98450798 0.039802044 0.055153314 2457.344608 -3.390466064 0.143047538 EFFVTSAPWSVIDQQAIHPELNGATYR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFFVTSAPWSVIDQQAIHPELNGATYR 27 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 ; 258.31 5.93E-53 274180000 91419 92617 76029 86316 97233 102420 92406 102094 94755 94274 FALSE TRUE 87846.24441 89975.65384 89769.13156 90770.7791 100360.5877 104491.0026 93536.89227 99985.72322 83998.80965 87888.73801 0.999516507 1.023744974 1.021395159 1.032791927 1.141904981 1.188900932 1.064264824 1.137639765 0.955740309 1 16.42339069 3.390470216 7.121091741 1.095074114 1.017614898 0.163469251 0.065270266 0.320242761 22.16296559 0.017762764 0.024106951 2457.368098 -3.390470216 -0.077459216 WGTDEDKFTEILCLR ddPTM_BT-474_Pertuzumab_2h_R1 2 WGTDEDKFTEILCLR 15 1 P12429;D6RA82;D6RFJ9 P12429 ANXA3 Annexin A3;Annexin 0 ; 138.39 9.92E-06 1292170000 2034500 2056680 1674360 1839200 1577920 1759470 1574930 1825510 2116920 2167260 FALSE TRUE 1954989.491 1998025.5 1976954.098 1934121.332 1628675.23 1795047.689 1594204.464 1787812.581 1876616.116 2020469.55 0.967591663 0.988891666 0.978462703 0.957263292 0.806087491 0.888430954 0.789026721 0.884850049 0.928801979 1 20.94625918 3.390732314 7.316892655 0.871805768 0.977490262 0.377080143 0.056167909 0.199310795 14.33203899 0.014810015 0.020092944 2458.851574 -3.390732314 0.105684493 ERPGLGSNPCIPFFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPGLGSNPCIPFFYR 16 1 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 0 174.52 3.50E-09 648600000 258670 265990 226310 217990 157010 149250 186470 186100 181790 203840 FALSE TRUE 248560.8904 258404.2256 267209.2512 229240.49 162060.3692 152267.9373 188752.0756 182256.97 161153.9613 190033.7352 1.307982975 1.359780806 1.406114819 1.206314709 0.852797894 0.801267928 0.993255621 0.959076923 0.848028173 1 17.53589603 3.392434093 3.850357933 0.912107197 1.353202283 0.906581046 0.065823975 0.064335122 1.846488391 0.019801077 0.027715943 2468.505465 -3.392434093 0.441095086 WREEQMER ddPTM_BT-474_Pertuzumab_2h_R1 3 WREEQMER 8 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 ;; 186.78 0.00018757 2496320000 1375070 1595720 1287220 1325100 1267650 948480 1501030 1340980 1370810 1518990 FALSE TRUE 1321330.744 1550211.628 1519849.288 1393488.57 1308425.114 967658.9155 1519400.054 1313288.294 1215201.396 1416107.454 0.933072374 1.094699151 1.073258448 0.984027424 0.92395892 0.683323086 1.072941216 0.927393109 0.858127956 1 20.43349931 3.392753392 3.418411554 0.909646417 1.038727175 0.227416058 0.102382787 0.345218347 8.016494343 0.029334971 0.041585598 2470.321007 -3.392753392 0.129080757 NVLFSHLDDNER ddPTM_BT-474_Pertuzumab_2h_R1 4 NVLFSHLDDNER 12 0 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ;;; 204.13 1.17E-07 5432600000 4627680 5162770 4087440 4328280 3997940 4117010 3751250 4230950 4684450 5227440 FALSE TRUE 4446825.149 5015532.854 4826131.333 4551663.05 4126537.371 4200258.763 3797158.92 4143579.404 4152690.875 4873380.833 0.912472327 1.029169077 0.990304575 0.933984682 0.846750441 0.861877803 0.779163183 0.850247404 0.852117045 1 22.21649154 3.392991679 3.040514243 0.850792688 0.981412104 0.414875627 0.059001161 0.198296727 3.689798616 0.01603114 0.023056578 2471.67679 -3.392991679 0.130619416 ASQQEIQHIVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASQQEIQHIVNR 12 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4;H3BT18;H3BU44 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ; 131.26 0.00023515 0 157945 166664 121789 155648 163984 173847 167889 186236 182551 178806 FALSE TRUE 151772.3348 161910.9059 143798.9815 163681.0119 169258.6943 177362.3055 169943.6758 182390.1615 161828.5758 166695.3104 0.910477532 0.971298506 0.862645633 0.981917317 1.015377661 1.063990973 1.019486844 1.094152926 0.97080461 1 17.34685399 3.393887367 2.842348811 1.038185394 0.920183407 0.588525214 0.041200102 0.162782803 2.656634712 0.011460156 0.016644057 2476.779627 -3.393887367 -0.118001987 DRRPVHLDQAAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRRPVHLDQAAFR 13 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 156.8 2.66E-05 458910000 64246 82418 62658 65918 48756 44194 62064 61967 69895 77686 FALSE TRUE 61735.19529 80067.51934 73981.69442 69320.03588 50324.28102 45087.63296 62823.5578 60687.3598 61960.81262 72424.25802 0.852410463 1.105534548 1.021504347 0.957138365 0.69485394 0.622548773 0.867438059 0.837942444 0.85552568 1 16.14418538 3.394466147 6.627523048 0.802904702 1.001988607 0.360245489 0.111710953 0.210698125 13.76834506 0.031265842 0.042492656 2480.082611 -3.394466147 0.199083904 EGWLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGWLFK 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 104.04 0.079497 371340000 436240 436050 366920 427350 519050 475450 492700 553440 524820 542020 FALSE TRUE 419191.2585 423614.2809 433230.6061 449405.5847 535745.7146 485063.9248 498729.81 542011.2706 465244.6338 505308.5026 0.829574916 0.838328029 0.857358631 0.889368737 1.06023491 0.959936202 0.986980839 1.072634376 0.920714042 1 18.94680493 3.394575532 4.808396877 1.00524488 0.845752391 0.747629326 0.042188507 0.097786523 4.039647994 0.011831822 0.016281789 2480.707339 -3.394575532 -0.159492488 DTEQVDNWMSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTEQVDNWMSK 11 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 153.63 0.0035071 0 136090 123310 119410 93743 100920 110800 103230 90913 101320 101420 FALSE TRUE 130771.4523 119793.3195 140990.0433 98581.08746 104166.1835 113040.4519 104493.3596 89035.61478 89818.57837 94550.73306 1.383082374 1.26697399 1.49115759 1.042626369 1.101696201 1.195553416 1.105156525 0.941670275 0.949951158 1 16.52880102 3.395513227 0.492911454 0.956810938 1.451219392 0.66500846 0.101612387 0.884897993 0.390006954 0.083500336 0.221938561 2486.06928 -3.395513227 0.494408454 GIIRPGTAFELLEAQAATGYVIDPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIIRPGTAFELLEAQAATGYVIDPIK 26 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 147.11 1.79E-07 86377000 124280 127680 92126 127460 139140 145530 148130 149950 171470 164650 FALSE TRUE 119423.0002 124038.6914 108775.2175 134038.2259 143615.5645 148472.7163 149942.8593 146853.4801 152005.4445 153498.1088 0.778009587 0.808079607 0.70864207 0.873223956 0.93561781 0.967260883 0.97683848 0.956711983 0.990275682 1 17.22786136 3.395586622 2.395261193 0.971233374 0.769245882 0.910169239 0.029016296 0.075014997 0.872055246 0.008221611 0.012289784 2486.489458 -3.395586622 -0.201987492 AHSSMVGVNLPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHSSMVGVNLPQK 13 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 69.641 0.047158 737130000 1186600 1698600 1567100 1146300 1108300 786750 1196100 836340 931280 1299400 FALSE TRUE 1140226.36 1650157.591 1850309.83 1205460.68 1143949.476 802658.624 1210738.23 819069.2867 825564.9986 1211390.481 0.941254185 1.36220122 1.527426424 0.995104964 0.944327609 0.662592811 0.999461568 0.676139775 0.68150197 1 20.20823255 3.395755819 2.62751519 0.800767072 1.283308071 0.536426332 0.184173428 0.191878966 2.681378312 0.052878178 0.077807451 2487.458358 -3.395755819 0.482540999 SQASMVINSDT(ph)DDEEEVSAALTLAHLK ddPTM_BT-474_Pertuzumab_2h_R1 3 SQASMVINSDTDDEEEVSAALTLAHLK 27 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQASMVINS(0.356)DT(0.644)DDEEEVSAALTLAHLK;SQASMVINS(0.029)DT(0.971)DDEEEVSAALTLAHLK;S(0.001)QAS(0.005)MVINS(0.235)DT(0.758)DDEEEVS(0.002)AALTLAHLK 166.65 3.17E-11 189793000 207831 208610 175324 216477 209234 256484 249016 247020 265926 241485 TRUE FALSE 199708.7348 202660.6471 207008.9469 227649.4039 215964.2016 261670.2822 252063.5323 241918.9507 235739.1953 225129.0059 0.887085758 0.90019785 0.919512553 1.01119535 0.959290878 1.162312609 1.119640409 1.074579216 1.047129376 1 17.78039242 3.396326633 1.271286926 1.083430986 0.893858952 0.675120514 0.050583502 0.247196627 0.824960567 0.017717201 0.031975732 2490.729893 -3.396326633 -0.189572035 KPNIFYSGPAS(ph)PARPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPNIFYSGPASPARPR 16 2 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 KPNIFYSGPAS(1)PARPR;KPNIFYSGPAS(1)PARPR 169.43 4.43E-09 20045600000 4087500 4111400 2556500 3620700 3326700 3070900 3099100 3254100 2677100 3100800 TRUE FALSE 3927755.981 3994146.897 3018516.419 3807564.761 3433706.327 3132995.702 3137027.713 3186901.698 2373206.831 2890780.054 1.358718376 1.381684813 1.044187507 1.317140941 1.187813069 1.083789027 1.08518381 1.102436587 0.820957246 1 21.46302741 3.397515788 0.338149271 0.937242085 1.458301304 0.607748584 0.104429807 1.943559251 0.342200829 0.114675893 0.38676322 2497.559185 -3.397515788 0.521059219 ILYSQCGDVMR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILYSQCGDVMR 11 0 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;P60660-2;G8JLA2;P14649;F8W1I5 F8VPF3;P60660;P60660-2;P14649 MYL6;MYL6B Myosin light polypeptide 6;Myosin light chain 6B 0 171.5 3.36E-05 95538000 67993 78407 61344 59274 61003 28493 71010 50190 65269 73405 FALSE TRUE 65335.75839 76170.90913 72430.22539 62333.13824 62965.2169 29069.14798 71879.04162 49153.55896 57859.93675 68433.21397 0.95473754 1.113069294 1.058407478 0.910860891 0.920097322 0.424781276 1.050353147 0.718270502 0.845494949 1 16.06240908 3.398216313 2.249299982 0.800576301 1.04599686 0.248417066 0.166407838 0.368724462 3.781006407 0.047362915 0.071798393 2501.591041 -3.398216313 0.245420559 SPEDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPEDKR 6 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 92.692 0.074506 216260000 554100 559120 440280 585520 523340 594920 674880 616600 573900 726930 FALSE TRUE 532445.1594 543174.445 519848.39 615738.7574 540173.7064 606949.69 683139.3833 603866.9945 508753.278 677694.3836 0.785671495 0.801503536 0.76708381 0.908578811 0.797075672 0.895609739 1.008034595 0.89106094 0.750711958 1 19.37027529 3.398623408 1.005982861 0.906244515 0.782247147 0.291303422 0.075102173 0.746137232 1.576918388 0.030574923 0.061018208 2503.937057 -3.398623408 -0.123997367 LVAIVDPHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVAIVDPHIK 10 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 81.338 0.021311 562550000 749060 807760 613700 735820 780080 855530 784240 756980 976580 881570 FALSE TRUE 719785.9071 784723.4757 724609.2417 773795.7584 805171.9817 872829.4028 793837.7637 741348.0985 865722.7326 821860.4787 0.875800608 0.954813495 0.881669408 0.941517178 0.979694246 1.062016517 0.965903319 0.902036438 1.053369465 1 19.64853397 3.398760804 3.470370027 0.984257604 0.909168815 0.416862513 0.047118874 0.288055229 6.918881689 0.014345349 0.020365457 2504.729345 -3.398760804 -0.075088789 HFVDEK ddPTM_BT-474_Pertuzumab_2h_R1 6 HFVDEK 6 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;H0Y562 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ;;;;; 141.55 0.011639 3159520000 8708510 8669200 7480140 7697390 7729290 6989570 8781960 5674210 10950220 9947640 FALSE TRUE 8368171.801 8421962.904 8831967.693 8094653.22 7977909.632 7130903.894 8889436.253 5557035.581 9707196.933 9273877.482 0.902337972 0.908138254 0.952348973 0.872844529 0.860256095 0.768923668 0.958545794 0.599213823 1.046724733 1 23.14474124 3.399101099 2.666253811 0.835916089 0.919267674 0 0.122114464 0.725170504 10.43294499 0.03476076 0.051140918 2506.692714 -3.399101099 0.083351585 LHLGFIEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHLGFIEIR 9 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 158.76 6.66E-05 1480450000 1430120 1660940 1326360 1120310 1124810 464540 1379310 579720 1169130 1270040 FALSE TRUE 1374229.329 1613571.617 1566062.757 1178129.333 1160990.535 473933.3171 1396190.408 567748.5794 1036415.264 1184019.06 1.16064798 1.362791928 1.322666847 0.995025649 0.980550546 0.400275074 1.17919589 0.479509662 0.875336639 1 20.17526087 3.400296044 1.92489699 0.76655983 1.289757813 0.453205536 0.226014841 0.259622839 1.953564755 0.065062282 0.102411088 2513.599287 -3.400296044 0.523197983 NIYSEELR ddPTM_BT-474_Pertuzumab_2h_R1 6 NIYSEELR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 216.57 1.82E-05 10979320000 6137230 6073040 4815010 5112220 4903880 3428360 5054040 5223580 5143220 5493680 FALSE TRUE 5897380.267 5899842.845 5685189.416 5376062.287 5061617.754 3497683.788 5115892.853 5115711.248 4559383.228 5121588.16 1.15147491 1.151955733 1.110044236 1.049686566 0.988290662 0.682929529 0.99888798 0.998852521 0.890228399 1 22.28815982 3.400635062 2.188142545 0.923454788 1.139215459 0.54169727 0.089116693 0.253338565 2.458366107 0.028143848 0.042985292 2515.562211 -3.400635062 0.215760671 FVMEEGR ddPTM_BT-474_Pertuzumab_2h_R1 4 FVMEEGR 7 0 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;; 181.2 0.0015712 2057170000 2202690 2402860 2065520 1842920 1815430 592160 2242250 1648190 1741200 2268380 FALSE TRUE 2116606.44 2334332.785 2438805.411 1938033.322 1873824.955 604133.8809 2269691.326 1614154.301 1543546.276 2114740.602 1.000882301 1.103838827 1.153240926 0.91644021 0.88607792 0.285677534 1.07327174 0.763287137 0.729898633 1 21.01204928 3.400847656 2.617586117 0.771747355 1.084181667 0.301418598 0.201394064 0.324779988 4.504395016 0.057730312 0.085282852 2516.793919 -3.400847656 0.312434312 TRPDGNCFYR ddPTM_BT-474_Pertuzumab_2h_R1 8 TRPDGNCFYR 10 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;;;;;; 227.36 2.37E-09 15322710000 2030321 2217897 2039313 2030527 1844574 1527817 2229327 2099316 2156346 2514274 FALSE TRUE 1950973.811 2154644.749 2407862.223 2135322.742 1903906.398 1558710.507 2256610.171 2055964.391 1911566.642 2343979.982 0.832333819 0.919224893 1.027253748 0.910981646 0.812253693 0.664984564 0.962725871 0.877125405 0.815521744 1 21.16052882 3.400924831 6.864952561 0.850394478 0.932574778 0.103885946 0.09590213 0.446642428 32.88553577 0.027001625 0.036689508 2517.2412 -3.400924831 0.082180299 KEEDRPPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEEDRPPLR 9 2 P53618 P53618 COPB1 Coatomer subunit beta 0 ;;; 129.16 0.00022339 2777520000 2967490 2965940 2614870 2918920 3241670 3265400 3364680 3736910 3848980 3840490 FALSE TRUE 2851517.21 2881354.295 3087435.176 3069565.811 3345941.26 3331428.625 3405857.96 3659741.503 3412059.927 3580370.192 0.796430832 0.804764351 0.862322892 0.857331965 0.934523829 0.930470439 0.951258607 1.022168465 0.952990821 1 21.77167733 3.401006833 0.549585246 1.001543922 0.767685918 0.909246359 0.022190173 0.318259472 0.1830495 0.015984009 0.04056066 2517.716541 -3.401006833 -0.233858004 ASS(ph)HSSQTQGGGS(ph)VTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.448)S(0.552)HSSQTQGGGS(0.998)VT(0.002)K 98.175 0.004127 105370000 206210 256050 169780 166810 158360 143610 107050 165560 119580 133810 TRUE FALSE 198151.0852 248747.7047 200463.0227 175419.0841 163453.7932 146513.8926 108360.1099 162141.1281 106005.7797 124746.9295 1.588424549 1.994018656 1.60695757 1.406199614 1.310283098 1.174488969 0.868639496 1.299760473 0.849766645 1 16.92864478 3.402174508 1.018814099 1.047144871 1.813083742 0.780998026 0.159663099 0.242752004 0.525479007 0.061705728 0.123046438 2524.494958 -3.402174508 0.76593887 DLDAPDDVDFF ddPTM_BT-474_Pertuzumab_2h_R1 4 DLDAPDDVDFF 11 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;; 152.47 7.66E-05 460544000 1079760 1089870 888290 1006820 1115290 1072050 1088460 1171350 1154030 1167880 FALSE TRUE 1037561.785 1058787.975 1048823.763 1058782.101 1151164.316 1093727.586 1101780.899 1147161.213 1023029.352 1088778.447 0.952959519 0.972454935 0.9633032 0.972449541 1.057298956 1.004545588 1.011942238 1.053622264 0.939612053 1 20.05427898 3.403542866 10.09379018 1.016230461 0.964526524 0.341225533 0.030938669 0.378467022 49.14161847 0.008268043 0.011198076 2532.461584 -3.403542866 -0.051703937 SVS(ph)EESANSLVSVGVEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVSEESANSLVSVGVEAK 18 0 Q8NEZ4;Q8NEZ4-3;H0YMU7;C9J4Z5 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 S(0.018)VS(0.982)EESANSLVSVGVEAK;SVS(1)EESANSLVSVGVEAK;S(0.005)VS(0.995)EESANSLVSVGVEAK;S(0.129)VS(0.869)EES(0.002)ANSLVSVGVEAK 400.53 9.29E-128 589490000 813040 813170 681716 827810 955980 939040 981760 1034400 1158600 1105150 TRUE FALSE 781265.4979 789979.1878 804917.2459 870533.3733 986729.9649 958028.0322 993775.0726 1013039.279 1027080.585 1030297.206 0.758291387 0.76674884 0.781247626 0.844934227 0.957713909 0.929855993 0.964551846 0.983249564 0.996877968 1 19.97462914 3.404238489 1.187660181 0.980469535 0.752794605 0.96322781 0.018156544 0.080778667 0.235777723 0.006652085 0.012458248 2536.521154 -3.404238489 -0.22767493 KCEAEEAEPPAATQPQTSETQTSHLPESER ddPTM_BT-474_Pertuzumab_2h_R1 3 KCEAEEAEPPAATQPQTSETQTSHLPESER 30 1 S4R3H4;Q9UKV3;E7EQT4;A0A087WYN3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;; 234.34 1.38E-45 1459940000 967870 965290 785050 914560 971870 1036100 948310 1013590 1109860 1156330 FALSE TRUE 930044.5704 937760.8743 926925.9983 961760.5512 1003131.081 1057050.652 959915.7015 992659.0123 983873.3457 1078010.739 0.862741471 0.869899381 0.859848575 0.89216231 0.930539043 0.980556699 0.890450964 0.92082479 0.912674902 1 20.03994012 3.404308885 3.007515691 0.932980883 0.865319339 0.553926943 0.030344843 0.20836566 3.809289259 0.00865011 0.012544155 2536.932342 -3.404308885 -0.067661544 NEEVQFGQHLDAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEEVQFGQHLDAAR 14 0 Q9H6W3;Q9H6W3-2 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 0 141.55 1.10E-05 0 78039 79192 68429 72968 70462 74414 75477 70134 90059 80571 FALSE TRUE 74989.1496 76933.5217 80795.64249 76733.88722 72728.47422 75918.70207 76400.7101 68685.70839 79835.87988 75113.8544 0.99833979 1.024225455 1.075642345 1.021567697 0.96824314 1.010715036 1.017132068 0.9144213 1.062864907 1 16.19679141 3.405213138 6.547364463 0.98851885 1.034565836 0.140648742 0.039981376 0.320873435 23.12012154 0.011200746 0.015241512 2542.220041 -3.405213138 0.046046986 TITEYAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TITEYAR 7 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 145.88 0.0052498 751030000 856520 913570 735090 767230 757570 551980 896120 742000 786980 911390 FALSE TRUE 823046.2515 887515.8781 867937.115 806826.8322 781937.9271 563141.4138 907086.9846 726677.4407 697645.3297 849660.7435 0.968676331 1.044553235 1.021510199 0.949587042 0.920294286 0.662783844 1.067587259 0.85525599 0.821086928 1 19.69652738 3.405649685 2.619004791 0.880599726 1.013223533 0.227647937 0.102542033 0.387519844 5.380099023 0.029200048 0.043269293 2544.776731 -3.405649685 0.132623806 RGEFCIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGEFCIAK 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 81.95 0.034528 339890000 381460 378890 323270 331070 253250 157340 424770 284640 328660 366480 FALSE TRUE 366552.1215 368084.4282 381692.0801 348156.5624 261396.0162 160521.5226 429968.4623 278762.0845 291351.8947 341657.9832 1.072862744 1.077347658 1.117175945 1.019020715 0.765080956 0.469831031 1.258476264 0.815909764 0.852758926 1 18.38219331 3.407171012 5.63503706 0.859067755 1.085143067 0.243638799 0.185227628 0.292318438 16.88641633 0.052036514 0.071205205 2553.706675 -3.407171012 0.226075312 LHCESESFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHCESESFK 9 0 C9JLU1;P52434;P52434-2;P52434-4 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ; 179.51 4.97E-05 1068910000 1975200 2127320 1670570 1626710 1582560 741410 2002470 1018480 1889700 2141300 FALSE TRUE 1898007 2066650.916 1972479.161 1710664.698 1633464.48 756401.8182 2026976.827 997448.0321 1675189.178 1996267.844 0.950777726 1.035257329 0.988083421 0.85693145 0.818259175 0.378907981 1.015383198 0.499656414 0.839160528 1 20.92887387 3.407685752 2.191918493 0.715584416 0.994624643 0.220580469 0.188907442 0.369358356 3.593095294 0.052972558 0.081294193 2556.735208 -3.407685752 0.279040227 LPSGS(ph)GAAS(ph)PTGSAVDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPSGS(1)GAAS(0.999)PT(0.001)GSAVDIR 297.87 3.09E-49 859100000 659590 709970 611070 631160 498990 620230 594000 641060 567050 595850 TRUE FALSE 633812.4936 689722.3507 721503.9422 663734.2432 515040.4665 632771.4756 601269.5497 627821.887 502680.8613 555492.5488 1.140991891 1.241641049 1.298854402 1.194857149 0.927177993 1.139117846 1.082407948 1.130207576 0.90492818 1 19.08340803 3.408208723 8.659561973 1.052067218 1.231631876 0.552367792 0.082104009 0.220787155 25.16916084 0.022475644 0.030463596 2559.815842 -3.408208723 0.179564659 LTDHGLEEISSCR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTDHGLEEISSCR 13 0 O95630 O95630 STAMBP STAM-binding protein 0 124.3 0.00021337 190460000 193130 190260 206200 180830 156280 139830 159040 177170 197840 219880 FALSE TRUE 185582.2661 184833.9711 243464.9269 190162.658 161306.8881 142657.4584 160986.3791 173511.3776 175382.0326 204987.3318 0.905335293 0.901684848 1.187707186 0.927680049 0.786911497 0.695933047 0.785347942 0.846449271 0.855574982 1 17.64517523 3.408239834 5.18645068 0.814938929 0.999094646 0.351239991 0.103412146 0.200448805 10.1552282 0.028930337 0.039772618 2559.999228 -3.408239834 0.184155717 TLIEFLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLIEFLLR 8 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 135.77 0.0034853 0 151935 170847 136626 144729 135385 84346 184454 144583 143919 186945 FALSE TRUE 145997.2122 165974.6108 161317.3574 152198.481 139739.7815 86051.53391 186711.4032 141597.3105 127581.9185 174283.0486 0.837701735 0.952327906 0.925605552 0.87328333 0.801797895 0.493745861 1.071311322 0.812456011 0.732038597 1 17.41107273 3.40860471 4.227310997 0.812584401 0.908735784 0.065687865 0.147520799 0.585797368 20.68065142 0.041270506 0.057659532 2562.150933 -3.40860471 0.096151383 GLSASYLEPDRYDEEEEGEESISLAAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLSASYLEPDRYDEEEEGEESISLAAIK 28 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 0 149.66 5.77E-08 45214000 20979 20857 16536 21502 21250 24494 21840 23440 29878 26899 FALSE TRUE 20159.11749 20262.17878 19524.42304 22611.7208 21933.52555 24989.28546 22107.28445 22955.95581 26486.3747 25077.10677 0.803885299 0.807995076 0.778575584 0.901687783 0.874643385 0.996497949 0.88157237 0.915414845 1.056197389 1 14.61408329 3.408609489 0.357100793 1.006753011 0.725113605 0.695537357 0.048529219 1.542650929 0.306213153 0.052633277 0.173104494 2562.17913 -3.408609489 -0.281639406 SIQPQVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIQPQVSPR 9 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 SIQPQVS(1)PR;SIQPQVS(1)PR 136.5 0.00020034 3275400000 2184300 2259200 1855120 2015100 1883080 2011730 1950480 2074600 2146000 2375900 TRUE FALSE 2098935.141 2194769.828 2190381.451 2119099.552 1943650.978 2052408.559 1974350.558 2031758.785 1902395.077 2214978.177 0.947609851 0.990876502 0.988895274 0.956713513 0.877503444 0.926604416 0.891363436 0.917281627 0.858877571 1 21.07886105 3.40869264 5.812154694 0.908003526 0.976679351 0.383418045 0.037054199 0.174148311 10.74825769 0.009426215 0.012884924 2562.669737 -3.40869264 0.068675825 GGFCNFMHLKPISR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGFCNFMHLKPISR 14 1 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ; 174.65 1.51E-06 3377900000 4539300 4450000 3917800 3780800 3623400 2996000 4008300 3393800 4054100 4053000 FALSE TRUE 4361899.138 4323090.357 4625833.611 3975927.541 3739949.952 3056581.173 4057354.774 3323716.844 3593895.564 3778486.7 1.154403729 1.144132744 1.224255629 1.052253946 0.98980101 0.808943213 1.07380417 0.87964233 0.951146808 1 21.84937711 3.409303248 2.551981027 0.940329083 1.170352817 0.671517379 0.069915881 0.150401798 1.982308213 0.019349482 0.028868056 2566.275327 -3.409303248 0.230023733 APS(ph)PGAYK ddPTM_BT-474_Pertuzumab_2h_R1 2 APSPGAYK 8 0 P54259 P54259 ATN1 Atrophin-1 1 APS(1)PGAYK;APS(1)PGAYK 95.775 0.0098721 721020000 1205020 1157120 946620 1139850 1174920 1237480 1145360 1356910 1411760 1263800 TRUE FALSE 1157926.486 1124120.071 1117695.291 1198677.795 1212712.369 1262502.693 1159377.258 1328889.334 1251502.923 1178201.7 0.98279139 0.954098157 0.948645118 1.017379108 1.029290968 1.071550561 0.984022734 1.127896296 1.062214494 1 20.16815511 3.410043143 1.727500625 1.057098203 0.96027563 0.469057936 0.038994322 0.282918555 1.716706126 0.012279812 0.020095986 2570.651137 -3.410043143 -0.096822573 IEPEPFENCLLRPGS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 5 IEPEPFENCLLRPGSPAR 18 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 1 IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR 246.34 1.69E-24 1603909000 824248 1009911 708719 785819 641302 198777 1039353 673421 904010 1125790 TRUE FALSE 792035.4769 981109.3271 836800.2887 826375.2128 661930.0612 202796.4071 1052072.913 659514.621 801390.5747 1049539.241 0.754650657 0.934800043 0.797302527 0.787369524 0.630686339 0.193224226 1.002414081 0.62838491 0.763564185 1 20.00132468 3.410409116 4.480004894 0.678837785 0.833407503 0.0586057 0.217653687 0.516714599 20.44519824 0.060083461 0.083564636 2572.818302 -3.410409116 0.154569717 SCAHDWVYE ddPTM_BT-474_Pertuzumab_2h_R1 4 SCAHDWVYE 9 0 Q32Q12;P22392-2;P22392;O60361 Q32Q12;O60361 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 ;;; 143.61 0.00023621 8857400000 4240570 5663380 3881980 3632460 3571440 2843510 3439340 2753960 3270420 3727890 FALSE TRUE 4074843.836 5501865.947 4583540.14 3819931.696 3686318.611 2901007.72 3481431.672 2697089.764 2899175.632 3475396.69 1.172483086 1.583090058 1.318853803 1.099135447 1.060690028 0.834727077 1.001736487 0.776052349 0.834199918 1 21.72874623 3.410595045 1.350268074 0.876141889 1.395805891 0.731556379 0.120790024 0.19521227 0.730776637 0.039379013 0.070426926 2573.920005 -3.410595045 0.519664002 FESILPR ddPTM_BT-474_Pertuzumab_2h_R1 1 FESILPR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 128.86 0.0086462 205680000 243550 247910 217680 189620 207910 185350 175630 205240 192150 209880 FALSE TRUE 234031.7967 240839.8495 257019.6183 199406.3109 214597.614 189097.904 177779.4125 201001.7223 170337.9376 195664.6407 1.196086303 1.230880801 1.313572127 1.019122874 1.096762365 0.966438818 0.908592436 1.027276679 0.870560654 1 17.57802354 3.412832587 1.414445488 0.96241723 1.246885635 0.753079209 0.067986318 0.193194289 0.79155568 0.021894786 0.038533921 2587.215393 -3.412832587 0.284468405 HGVYNPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGVYNPNK 8 0 P40926;G3XAL0 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 94.662 0.0102 255090000 561900 740750 512180 521850 340400 148400 726930 331100 409840 430920 FALSE TRUE 539940.3268 719624.5353 604742.3194 548782.741 351349.2751 151400.7497 735826.3868 324262.6693 363316.6814 401733.4046 1.344026463 1.791298725 1.505332423 1.366037115 0.874583172 0.376868709 1.831628584 0.807158841 0.904372594 1 18.6158789 3.413091738 3.721099445 0.979942501 1.558252692 0.362953939 0.352575464 0.249701597 6.996571074 0.099419464 0.141105305 2588.75969 -3.413091738 0.578310191 VSPAS(ph)PAGS(ph)PSADFAVHGESLGDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSPASPAGSPSADFAVHGESLGDR 24 0 A0A0A0MRP9;Q96C92-3;Q96C92;Q96C92-2;Q96C92-4 A0A0A0MRP9;Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 2 VS(0.011)PAS(0.965)PAGS(0.892)PS(0.133)ADFAVHGESLGDR;VS(0.003)PAS(0.995)PAGS(0.957)PS(0.045)ADFAVHGESLGDR;VS(0.003)PAS(0.993)PAGS(0.963)PS(0.041)ADFAVHGESLGDR 143.06 1.55E-10 356470000 222076 238747 195385 230123 233605 263075 246236 293306 271465 269768 TRUE FALSE 213397.0244 231938.1693 230695.4158 241999.6756 241119.117 268394.5567 249249.5098 287249.1286 240649.4313 251496.3731 0.848509351 0.922232661 0.917291224 0.962239227 0.958737949 1.067190566 0.991066021 1.142160124 0.956870385 1 17.94017807 3.414130806 0.855738808 1.049147233 0.874850546 0.544583302 0.052346765 0.453558621 0.691251341 0.023470852 0.051098768 2594.960827 -3.414130806 -0.174296687 GLLEPLGLECTFIDDISAYHK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLEPLGLECTFIDDISAYHK 21 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 206.28 4.30E-22 297240000 392070 425380 328970 391330 472910 461020 465190 445640 456810 489180 FALSE TRUE 376747.4709 413248.5789 388422.1969 411526.5882 488121.5796 470342.1403 470883.1344 436437.3783 404954.8439 456047.4029 0.826114716 0.906152686 0.851714525 0.902376783 1.070330796 1.03134485 1.032531117 0.95700003 0.887966561 1 18.79882426 3.416375905 7.039027957 0.995705917 0.867547216 0.608737827 0.049799504 0.154697728 14.56738963 0.014643657 0.019917992 2608.410291 -3.416375905 -0.128158701 QHAHTVLS(ph)SPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QHAHTVLSSPPR 12 0 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 QHAHTVLS(0.5)S(0.5)PPR;QHAHTVLS(0.5)S(0.5)PPR 118.2 0.00041941 397940000 370640 359430 248680 312110 297920 316290 290500 222138 371350 288910 TRUE FALSE 356154.979 349179.4083 293622.0079 328218.0345 307502.8674 322685.6005 294055.2259 217550.7727 329195.9048 269341.8684 1.322315692 1.296417116 1.090146176 1.2185927 1.141682388 1.198052135 1.091754608 0.807712421 1.222223291 1 18.03907898 3.417977429 0.412993386 0.974895328 1.364188915 0.382407361 0.113566168 1.927328533 0.540776639 0.110837253 0.334953321 2618.04694 -3.417977429 0.389293587 EGSALSHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGSALSHVR 9 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 0 ; 200.05 2.37E-05 407780000 537800 652350 600700 541410 477390 294400 638550 497680 541360 672450 FALSE TRUE 516782.1814 633745.6167 709259.8525 569352.235 492745.6829 300352.9697 646364.7659 487402.7341 479907.0824 626904.3625 0.824339744 1.010912756 1.131368507 0.90819632 0.785998172 0.479104928 1.031042061 0.777475422 0.765518811 1 19.25788584 3.41823197 4.486843303 0.796104594 0.995526243 0.212620271 0.157203028 0.288262493 11.87962263 0.04359717 0.060841486 2619.581836 -3.41823197 0.199421649 EREVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EREVQK 6 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 69.093 0.086104 81814000 98799 95690 79096 107370 121780 132710 142830 134930 126310 155330 FALSE TRUE 94937.82585 92961.01489 93390.40668 112911.3786 125697.1643 135393.4871 144577.9963 132143.6483 111971.8183 144809.3607 0.655605586 0.641954459 0.644919681 0.779724308 0.868018225 0.934977452 0.998402282 0.912535265 0.773236052 1 17.14379534 3.421510628 1.807163259 0.923127209 0.642153212 0.804254977 0.059604279 0.146269585 0.968254709 0.018813246 0.030665358 2639.432913 -3.421510628 -0.280973997 SAST(ph)DLGTADVVLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASTDLGTADVVLGR 15 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 SAS(0.294)T(0.706)DLGTADVVLGR 326.36 2.45E-57 216190000 306870 333990 148990 311850 494280 344610 403850 549510 444790 459240 TRUE FALSE 294877.1811 324464.9322 175915.8073 327944.6159 510178.9651 351578.2503 408792.4371 538162.4265 394299.3039 428135.2658 0.688747704 0.757856122 0.410888384 0.765983655 1.191630323 0.821184982 0.954820754 1.256991585 0.920968991 1 18.70770715 3.421638662 5.890498996 1.035986548 0.62554007 0.620166348 0.144383949 0.123124127 8.982392437 0.041015866 0.056209658 2640.211159 -3.421638662 -0.410446478 CEAFGWHAIIVDGHSVEELCK ddPTM_BT-474_Pertuzumab_2h_R1 1 CEAFGWHAIIVDGHSVEELCK 21 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 218.69 3.09E-25 372720000 560550 524810 487590 361280 394260 132420 390340 216640 442740 372140 FALSE TRUE 538643.0863 509842.9326 575708.3594 379925.7041 406941.731 135097.6231 395117.0977 212166.3083 392482.0113 346934.6263 1.552578052 1.469564852 1.659414529 1.095093067 1.172963723 0.389403688 1.138880549 0.611545496 1.131285209 1 18.40430431 3.421675775 1.82794535 0.844206678 1.554166522 0.596025237 0.238735855 0.209347731 1.417420732 0.068483406 0.111264797 2640.436788 -3.421675775 0.709959844 NTADHDES(ph)PPRT(ph)PTGNAPS(ph)SESDIDISSPNVSHDESIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NTADHDESPPRTPTGNAPSSESDIDISSPNVSHDESIAK 39 1 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 3 NT(0.099)ADHDES(0.786)PPRT(0.501)PT(0.5)GNAPS(0.366)S(0.366)ES(0.366)DIDIS(0.009)S(0.006)PNVS(0.001)HDESIAK;NTADHDES(0.998)PPRT(0.994)PT(0.012)GNAPS(0.375)S(0.34)ES(0.28)DIDISSPNVSHDESIAK 120.13 4.75E-07 558990000 121649 113858 91580 89502 99269 95785 82655 75288 105860 102856 TRUE FALSE 116894.8226 110610.8813 108130.5432 94121.20895 102462.0775 97721.83833 83666.55661 73733.27649 93843.2166 95889.47151 1.21905795 1.153524778 1.127658141 0.981559367 1.068543563 1.019109156 0.87253121 0.768940274 0.978660276 1 16.5490848 3.42178277 0.662180707 0.877918731 1.22170675 0.634926468 0.07636889 0.574295128 0.505978537 0.049022944 0.118775376 2641.08738 -3.42178277 0.343788019 KIEISQHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KIEISQHAK 9 1 Q6P4E4;E9PEL3;P61513;G5E9R3;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 128.27 0.00027399 2342200000 2811200 3330000 2791200 2882900 2646400 2259100 3245100 2974000 3089700 3447000 FALSE TRUE 2701335.196 3235031.66 3295631.93 3031686.814 2731523.859 2304780.55 3284814.505 2912585.861 2738970.209 3213531.62 0.840612608 1.006690471 1.025548313 0.943412785 0.850006841 0.717211101 1.022182102 0.90635046 0.852324026 1 21.61572824 3.422197166 7.391743039 0.889446669 0.966120823 0.100503136 0.091466522 0.467520425 52.5739702 0.025623956 0.034842735 2643.608659 -3.422197166 0.076674153 LQIVEMPLAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQIVEMPLAHK 11 0 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 151.1 3.36E-05 468100000 778850 821110 748900 720010 684190 393120 842410 665630 928660 938950 FALSE TRUE 748411.6809 797692.7468 884242.8892 757169.8024 706197.5927 401069.1557 852719.6656 651884.5079 823242.4101 875354.0802 0.854981656 0.911280092 1.01015453 0.864986889 0.806756499 0.458179341 0.974142561 0.74470951 0.940467896 1 19.73950718 3.422327561 4.161414954 0.798770543 0.926159608 0.078101367 0.149302909 0.439294462 15.80225212 0.041026903 0.057811611 2644.40251 -3.422327561 0.127389064 S(ph)EGSEYEEIPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SEGSEYEEIPK 11 0 P48634 P48634 PRRC2A Protein PRRC2A 1 S(1)EGSEYEEIPK;S(1)EGSEYEEIPK;S(0.999)EGS(0.001)EYEEIPK 234.63 1.76E-15 700133000 534830 531950 603950 742320 656530 628960 874920 968040 1053050 1084100 TRUE FALSE 513928.2523 516779.3068 713097.1998 780631.2242 677647.8837 641678.0021 885627.5327 948049.6357 933512.1787 1010672.941 0.50850105 0.511321997 0.705566727 0.772387577 0.670491764 0.634901733 0.8762751 0.938038011 0.923654073 1 19.94688478 3.422409283 0.27057073 1.051119606 0.320345302 0.812512876 0.072599653 1.942355457 0.213031377 0.119517536 0.461197532 2644.90016 -3.422409283 -0.730774304 ANPQVGVAFPHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ANPQVGVAFPHIK 13 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 146.07 4.21E-05 792000000 882010 942090 767770 876990 979330 1010200 932630 957710 1101700 1107700 FALSE TRUE 847540.0741 915222.5156 906523.118 922251.559 1010831.039 1030626.936 944043.8049 937932.9538 976639.6347 1032674.492 0.820723355 0.88626428 0.877840137 0.89307092 0.978847688 0.99801723 0.914173645 0.908256145 0.945738122 1 19.97795415 3.423438352 4.424298159 0.948715202 0.866607688 0.619535139 0.033912697 0.166984423 6.859052297 0.010381458 0.01454611 2651.174735 -3.423438352 -0.082107514 EHVVAASK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHVVAASK 8 0 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;;; 117.89 0.001992 1065150000 3104860 3290760 2872120 2973680 2889950 2804540 3486320 2320260 3938480 3797730 FALSE TRUE 2983518.639 3196910.747 3391175.974 3127151.981 2982907.866 2861249.72 3528986.627 2272345.82 3491400.262 3540506.364 0.842681337 0.902952973 0.957822307 0.883249925 0.842508828 0.808147035 0.996746302 0.641813793 0.986130204 1 21.75552428 3.42356052 5.542058869 0.851974741 0.904330907 0 0.106644465 0.67816697 44.69165609 0.028974767 0.039869655 2651.920618 -3.42356052 0.052356166 MECCDVPAETLYDVLHDIEYR ddPTM_BT-474_Pertuzumab_2h_R1 27 MECCDVPAETLYDVLHDIEYR 21 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;;;;;;;;;;;;;;;;;;;;;;;;;; 242.18 4.55E-30 14047160900 1190174.8 1256889.1 1001594.3 1283915.6 1233275.3 1302162.3 1189699.7 1141375.4 1369241.6 1444473.2 FALSE TRUE 1143661.453 1221043.853 1182604.67 1350178.638 1272944.72 1328492.914 1204259.601 1117805.599 1213811.034 1346637.744 0.849271794 0.906735207 0.878190646 1.002629434 0.945276282 0.986525827 0.894271386 0.830071491 0.901364186 1 20.36093038 3.423649132 0.00523619 1.818870418 6.64E-06 0.088445196 0.055925953 66246.04062 89.88954289 15261.44455 15964.02781 2652.461761 -3.423649132 -1.81886378 CTMHCNDK ddPTM_BT-474_Pertuzumab_2h_R1 3 CTMHCNDK 8 0 E7EQY1;Q96C01;C9JF51 E7EQY1 FAM136A Protein FAM136A 0 ;; 89.698 0.013721 315556000 615082 620682 525499 552213 438918 348157 629179 534354 624796 598225 FALSE TRUE 591043.9154 602980.7571 620468.359 580712.7791 453036.1961 355196.9731 636879.0808 523319.4032 553871.7774 557706.6879 1.059775556 1.081178996 1.112535267 1.041251238 0.81231982 0.636888495 1.14196063 0.938341631 0.993123786 1 19.08914705 3.423783253 8.600916503 0.921207336 1.083008763 0.272045256 0.124307114 0.394196378 58.12920072 0.03617574 0.049077671 2653.281038 -3.423783253 0.161801427 SRS(ph)SDIVSSVR ddPTM_BT-474_Pertuzumab_2h_R1 5 SRSSDIVSSVR 11 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 S(0.013)RS(0.945)S(0.042)DIVSSVR;S(0.002)RS(0.989)S(0.009)DIVSSVR;S(0.022)RS(0.737)S(0.241)DIVSSVR;S(0.001)RS(0.942)S(0.057)DIVS(0.001)SVR;S(0.036)RS(0.946)S(0.018)DIVSSVR 193.97 4.35E-07 4440510000 1326000 1302760 769820 1222990 1682800 1284140 1586010 1707270 1657530 1651610 TRUE FALSE 1274178.454 1265606.56 908943.5986 1286108.66 1736928.79 1310106.191 1605420.065 1672014.278 1469374.143 1539744.984 0.827525641 0.821958554 0.59032087 0.835273811 1.128062639 0.850859204 1.04265322 1.085903377 0.954297081 1 20.55426 3.423963327 6.431207839 1.013126754 0.747318118 0.628420201 0.092816701 0.120399629 10.77497223 0.025578474 0.034939446 2654.381412 -3.423963327 -0.265808636 RVELSGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVELSGPK 8 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ; 101.65 0.0084132 792370000 1478360 1292450 1189550 1187250 1164270 902360 1369270 977240 1552910 1384780 FALSE TRUE 1420584.057 1255590.591 1404528.146 1248524.115 1201719.802 920606.3375 1386027.536 957059.6525 1376630.167 1290987.617 1.100385502 0.972581437 1.087948581 0.967107738 0.930853082 0.713102376 1.073617994 0.741339142 1.066338785 1 20.30004373 3.423983195 2.832775901 0.897521475 1.044972033 0.184289078 0.118256784 0.367097688 5.975040681 0.031931639 0.047303029 2654.502845 -3.423983195 0.147450558 DQS(ph)TPIIEVEGPLLSDTHVTFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQSTPIIEVEGPLLSDTHVTFK 22 0 P49116;P49116-2 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 DQS(0.5)T(0.5)PIIEVEGPLLSDTHVTFK 65.207 0.014964 214860000 59325 57486 45578 52464 43165 50646 50189 51467 56706 59130 TRUE FALSE 57006.51341 55846.55556 53814.95848 55171.67333 44553.44143 51670.09682 50803.228 50404.18846 50268.97261 55125.07243 1.034130404 1.013088112 0.976233792 1.000845367 0.808224633 0.937324788 0.921599297 0.914360494 0.911907602 1 15.75042103 3.424175373 24.99968734 0.912289246 1.005044311 0.483078066 0.045805306 75.34043758 35573.49645 0.011977444 0.016217537 2655.677738 -3.424175373 0.092755066 SLS(ph)TDTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSTDTSR 8 0 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 S(0.001)LS(0.958)T(0.041)DT(0.001)SR 128.6 0.0011816 73800000 149690 193380 124750 203470 206050 176450 200340 300570 218300 217650 TRUE FALSE 143839.9493 187864.9917 147295.1 213971.1111 212677.7854 180017.9399 202791.8208 294363.1245 193519.4992 202908.3716 0.708891152 0.925861216 0.725919285 1.054520863 1.048146923 0.887188333 0.999425599 1.450719466 0.953728511 1 17.63046886 3.424238277 0.624542765 1.154336243 0.737126908 0.32518897 0.16068817 1.086693607 0.837326045 0.107050101 0.265992777 2656.062419 -3.424238277 -0.417209335 ALEAELDAQHLS(ph)ETFDNIDNLSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLS(0.368)ET(0.368)FDNIDNLS(0.263)PK;ALEAELDAQHLS(0.441)ET(0.441)FDNIDNLS(0.118)PK 122.04 0.00020554 186396000 183784 161000 136390 155952 183719 170466 164680 163341 202466 176983 TRUE FALSE 176601.5181 156408.4376 161038.707 164000.7014 189628.4885 173912.9393 166695.4031 159967.9513 179482.9085 164995.7838 1.070339581 0.947954148 0.976017104 0.993969044 1.149292934 1.054044748 1.010300986 0.969527509 1.087802999 1 17.33206963 3.424841906 24.99995756 1.039561822 0.991737008 0.147993241 0.054996765 201.133825 96181.16864 0.016065227 0.021752423 2659.756664 -3.424841906 -0.047824813 AYPLADAHLTK ddPTM_BT-474_Pertuzumab_2h_R1 4 AYPLADAHLTK 11 0 A0A3B3IUA2;B1AHD1;P55769 A0A3B3IUA2 NHP2L1 "NHP2-like protein 1;NHP2-like protein 1, N-terminally processed" 0 ;;; 208.46 1.95E-08 1858610000 3766560 3921530 3478510 3608590 3310760 2838610 3912160 3845120 4042100 4256720 FALSE TRUE 3619358.671 3809691.804 4107154.136 3794829.762 3417253.602 2896008.639 3960038.184 3765716.928 3583257.754 3968408.563 0.912042854 0.960004935 1.034962522 0.956259846 0.861114361 0.729765747 0.997890747 0.948923698 0.902945777 1 21.92012913 3.425913274 9.730013189 0.905669786 0.972666265 0.123462227 0.077411551 0.80126165 145.8262487 0.022632624 0.030675546 2666.326162 -3.425913274 0.066996479 LREQMER ddPTM_BT-474_Pertuzumab_2h_R1 1 LREQMER 7 1 E9PF16;Q96CM8-3;Q96CM8;Q96CM8-2;Q96CM8-4 E9PF16 ACSF2 "Acyl-CoA synthetase family member 2, mitochondrial" 0 63.961 0.069571 134590000 591060 643870 480760 702170 653180 745690 759260 820590 867930 874790 FALSE TRUE 567960.7217 625507.458 567644.0264 738409.0778 674190.1279 760768.3627 768552.051 803644.5297 769406.2251 815539.6941 0.696423149 0.766985914 0.696034823 0.905423835 0.826679722 0.932840386 0.942384603 0.985414365 0.943431976 1 19.63739557 3.426100289 0.597926699 0.986738542 0.672759138 0.852708468 0.041854732 0.364703713 0.25374096 0.025965492 0.065776111 2667.474574 -3.426100289 -0.313979404 GLFIIDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLFIIDGK 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 105.95 0.0099801 1394080000 2542900 2594500 2220130 2568630 2763900 2636010 2862400 3208200 3281000 3218500 FALSE TRUE 2443520.657 2520507.4 2621356.878 2701197.302 2852803.354 2689311.928 2897430.907 3141949.549 2908554.635 3000508.128 0.814368951 0.840026853 0.873637653 0.90024662 0.950773413 0.8962855 0.965646745 1.047139156 0.969354026 1 21.51677541 3.426796145 0.455658632 1.018816863 0.782596839 0.820570155 0.029455944 0.687831064 0.245728188 0.027189057 0.078279984 2671.752011 -3.426796145 -0.236220024 VSRPENEQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSRPENEQLR 10 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 180.97 1.77E-06 3039390000 1706900 1929380 1448240 1368880 1394590 528750 1456900 1199010 1310730 1556310 FALSE TRUE 1640192.461 1874355.971 1709969.184 1439528.061 1439448.254 539441.6873 1474729.978 1174250.024 1161941.425 1450899.737 1.130465751 1.291857682 1.178557787 0.992162328 0.992107323 0.371798046 1.016424457 0.80932541 0.800841985 1 20.4685164 3.427051243 1.925824678 0.807247428 1.211378837 0.475968343 0.17550562 0.273206014 2.048993702 0.052305588 0.084096446 2673.321821 -3.427051243 0.40413141 AAAIGIDLGTTYSCVGVFQHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAAIGIDLGTTYSCVGVFQHGK 22 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 301.77 7.81E-56 914390000 1285580 1417820 1092650 1234180 964490 937770 1282620 1112260 1501550 1446440 FALSE TRUE 1235338.112 1377385.162 1290116.161 1297876.178 995513.6968 956732.3519 1298317.087 1089291.442 1331100.339 1348471.33 0.916102615 1.021441933 0.956724946 0.962479623 0.738253513 0.709494025 0.962806593 0.807797257 0.987118012 1 20.36289342 3.42713513 24.96409325 0.853763925 0.96862146 0.185710192 0.096445714 147.1485481 73488.41876 0.026246719 0.035538232 2673.838238 -3.42713513 0.114857535 SQS(ph)LPHSATVTLGGTSDPSTLSSSALSER ddPTM_BT-474_Pertuzumab_2h_R1 3 SQSLPHSATVTLGGTSDPSTLSSSALSER 29 0 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 S(0.277)QS(0.723)LPHSATVTLGGTSDPSTLSSSALSER;S(0.191)QS(0.786)LPHS(0.021)AT(0.002)VTLGGTSDPSTLSSSALSER;S(0.23)QS(0.72)LPHS(0.025)AT(0.025)VT(0.001)LGGTSDPSTLSSSALSER 269.06 3.35E-59 1433330000 293130 273340 166659 259185 326631 281859 287871 421101 267951 264213 TRUE FALSE 281674.1555 265544.6108 196777.9886 272561.5689 337137.3828 287558.3821 291394.0514 412405.1172 237534.3258 246317.6182 1.143540432 1.078057724 0.798879065 1.106545163 1.368709982 1.167429209 1.183001255 1.674281849 0.964341599 1 17.9101603 3.427867955 5.954806586 1.280145351 1.004032429 0.157580377 0.207567737 0.256283112 20.67812815 0.058533846 0.080339237 2678.353862 -3.427867955 -0.276112922 RNS(ph)TTIMSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSTTIMSR 9 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RNS(0.943)T(0.043)T(0.013)IMS(0.001)R;RNS(0.751)T(0.248)T(0.001)IMSR 149.69 5.33E-05 1251791000 295721 303921 212939 266420 239713 237782 220085 250982 243436 242524 TRUE FALSE 284163.8964 295253.4706 251421.8141 280169.9681 247423.5863 242590.115 222778.4661 245799.134 215802.1658 226097.6335 1.256819419 1.305867143 1.11200551 1.239154802 1.094321876 1.07294407 0.985319761 1.087137137 0.954464505 1 17.78658637 3.427877843 0.535052324 0.994462567 1.315735032 0.765349646 0.055353253 0.60075587 0.319902311 0.039106659 0.10401075 2678.414844 -3.427877843 0.321272465 QALQRYSEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QALQRYSEDR 10 1 B0QY60;Q9UH99-3;Q9UH99;Q9UH99-2 B0QY60 SUN2 SUN domain-containing protein 2 0 ; 59.426 0.095463 428210000 474250 503940 450720 366600 404450 338080 352660 371070 380160 382390 FALSE TRUE 455715.7857 489568.1246 532175.1302 385520.2699 417459.5016 344916.2092 356975.9586 363407.2748 337005.8306 356490.3847 1.278339628 1.373299661 1.492817627 1.081432449 1.171025978 0.967532994 1.001362095 1.01940274 0.945343395 1 18.44350364 3.428383861 1.699871119 1.000859027 1.378874216 0.79566787 0.08123461 0.14834416 0.86935121 0.024694198 0.041274481 2681.537418 -3.428383861 0.378015189 KPLPTAAAQCS(ph)FEDPDSAVDDRDSDYR ddPTM_BT-474_Pertuzumab_2h_R1 3 KPLPTAAAQCSFEDPDSAVDDRDSDYR 27 2 O14795;O14795-2;A0A1B0GUS7;A0A0U1RRL2 O14795 UNC13B Protein unc-13 homolog B 1 KPLPTAAAQCS(1)FEDPDSAVDDRDSDYR;KPLPT(0.071)AAAQCS(0.926)FEDPDS(0.004)AVDDRDSDYR;KPLPTAAAQCS(1)FEDPDSAVDDRDSDYR 181.38 8.88E-18 2493660000 1166754 1127618 528722 1056334 1611087 1243976 1422953 1586184 1455745 1474004 TRUE FALSE 1121155.964 1095459.439 624273.8268 1110851.524 1662909.077 1269130.047 1440367.524 1553428.746 1290494.931 1374168.396 0.815879602 0.79717991 0.454292086 0.808380929 1.210120303 0.923562244 1.048173956 1.13045006 0.939109744 1 20.39012738 3.428548968 6.822403017 1.047264808 0.688625811 0.641343369 0.120730781 0.1166651 12.61607985 0.032929578 0.044936673 2682.557054 -3.428548968 -0.358638997 IEHSFWR ddPTM_BT-474_Pertuzumab_2h_R1 4 IEHSFWR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 158.12 0.0014326 2531370000 1677910 1983930 1663460 1576630 1348780 772572 1916470 1369030 1567550 1922230 FALSE TRUE 1612335.422 1927350.259 1964084.225 1658000.063 1392164.734 788193.9352 1939924.333 1340759.052 1389608.296 1792035.65 0.89972285 1.075508882 1.09600734 0.925204844 0.776862187 0.439831616 1.082525525 0.748176551 0.775435631 1 20.77316791 3.428748427 3.921391297 0.792059694 1.027772394 0.259634405 0.166711422 0.275442476 8.904087597 0.046163713 0.065734134 2683.789358 -3.428748427 0.235712699 GFHQVPFAPIVFIER ddPTM_BT-474_Pertuzumab_2h_R1 2 GFHQVPFAPIVFIER 15 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8 P47897 QARS Glutamine--tRNA ligase 0 ; 104.95 0.0013531 761050000 665610 666130 544190 556550 421410 478640 560380 454160 501990 579160 FALSE TRUE 639597.2253 647132.6246 642537.2384 585273.6122 434965.0354 488318.4287 567238.0981 444781.4373 445006.1997 539932.9773 1.184586332 1.198542508 1.190031477 1.083974561 0.805590793 0.904405638 1.050571315 0.823771572 0.82418785 1 19.04242081 3.428867358 4.39145736 0.899021078 1.185813431 0.762242905 0.07357495 0.097163935 4.029097939 0.021120977 0.029708341 2684.524414 -3.428867358 0.286792353 KLEDSTR ddPTM_BT-474_Pertuzumab_2h_R1 6 KLEDSTR 7 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;;; 160.88 0.0021324 4676310000 6174590 6187840 5342720 5780740 5317150 5073580 6136720 6167370 6728200 6317530 FALSE TRUE 5933280.196 6011368.862 6308268.352 6079084.684 5488180.959 5176171.264 6211823.015 6040011.654 5964442.943 5889638.066 1.007409985 1.020668638 1.071079119 1.032166088 0.93183671 0.878860671 1.054703692 1.025531889 1.012701099 1 22.48974755 3.429912029 24.99705741 0.987485405 1.035115819 0.19102845 0.048912251 229.6961459 121622.2471 0.015133349 0.020490657 2690.98966 -3.429912029 0.047630413 AVFPSIVGRPR ddPTM_BT-474_Pertuzumab_2h_R1 5 AVFPSIVGRPR 11 1 C9JTX5;F8WCH0;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63267-2;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I" 0 ;;;; 241.4 9.18E-16 1.12457E+11 11253418.2 13181454.2 10520518.2 10556833.9 10001755.5 8222892.9 11025721.6 10818078.3 11098001.4 10357515.3 FALSE TRUE 10813622.18 12805532.03 12421809.87 11101673.36 10323471.05 8389165.428 11160657.68 10594681.2 9838202.808 9655991.563 1.119887285 1.326174733 1.286435452 1.149718627 1.069125939 0.868804138 1.155827199 1.097213179 1.018870278 1 23.20299298 3.430326568 2.946817909 1.044150536 1.250681424 0.546025593 0.085769463 0.203694687 3.598730414 0.02532494 0.037453149 2693.559468 -3.430326568 0.206530888 WTETYVR ddPTM_BT-474_Pertuzumab_2h_R1 3 WTETYVR 7 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;; 134.06 0.0074714 640150000 961590 1126320 1017020 886720 779470 393510 1061900 732350 894110 1119660 FALSE TRUE 924009.9997 1094198.456 1200818.137 932483.7255 804542.3604 401467.0418 1074895.85 717226.7166 792614.3812 1043824.431 0.885215916 1.048259098 1.150402407 0.893333877 0.770764064 0.384611655 1.029766901 0.687114322 0.759336875 1 19.99344764 3.431326319 3.678145233 0.753025036 1.030342426 0.290784267 0.177434866 0.256167744 7.243191627 0.048653225 0.069921999 2699.767215 -3.431326319 0.27731739 AHSIQIMK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 93.374 0.011114 1429650000 2195600 2376600 2179050 2018260 2032930 1229150 2590200 1764420 2388000 2537200 FALSE TRUE 2109793.525 2308821.695 2572852.808 2122422.64 2098321.04 1254004.255 2621899.642 1727984.11 2116924.251 2365353.184 0.891957082 0.976100191 1.087724584 0.897296292 0.887106862 0.530155185 1.108460107 0.730539575 0.894971738 1 21.17362419 3.431409687 3.459549907 0.840278422 0.98555339 0.112752982 0.151956234 0.428361286 10.6120142 0.041099381 0.059518588 2700.285518 -3.431409687 0.145274968 ADTQTYQPYNK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADTQTYQPYNK 11 0 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 143.5 8.64E-05 192028000 149556 146527 120435 156073 206291 202758 204296 172482 243120 217590 FALSE TRUE 143711.1862 142348.1934 142200.2836 164127.9462 212926.5374 206857.9057 206796.2356 168920.1864 215522.0368 202852.4355 0.708451865 0.70173273 0.70100358 0.809100201 1.049662218 1.019745734 1.019441719 0.832724468 1.062457231 1 17.6300711 3.43144276 3.965406248 0.980450796 0.708207519 0.824519654 0.061404769 0.097950762 3.267971509 0.01909824 0.027207218 2700.491158 -3.43144276 -0.272243277 LGYFSVDPDSHQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGYFSVDPDSHQGK 14 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RR79 P47897 QARS Glutamine--tRNA ligase 0 ; 136.3 1.76E-05 0 478180 525010 405670 479670 569230 601490 503730 505400 632970 607420 FALSE TRUE 459492.1969 510037.2288 478983.5931 504425.8262 587539.7999 613652.5399 509894.7984 494963.3134 561117.8992 566278.9024 0.811423832 0.900682026 0.845843967 0.89077277 1.037544923 1.083657783 0.900430506 0.874062783 0.990886111 1 19.11115326 3.431476909 8.343173306 0.967195949 0.859191955 0.47381142 0.06120977 0.293425833 48.2637729 0.019439201 0.026408732 2700.703511 -3.431476909 -0.108003994 QLAEDFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 QLAEDFLR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 129.72 0.0025092 700510000 1600840 1797930 1473250 1336850 1319360 686704 1491400 1237310 1268540 1460680 FALSE TRUE 1538277.403 1746654.797 1739499.047 1405844.989 1361798.413 700589.6254 1509652.199 1211759.116 1124540.657 1361746.843 1.129635373 1.282657497 1.277402666 1.032383513 1.000037871 0.514478612 1.10861443 0.88985638 0.825807428 1 20.37702709 3.432201562 2.339711218 0.879729125 1.233093232 0.501329251 0.152167557 0.236873258 2.616386044 0.044204019 0.068110415 2705.213597 -3.432201562 0.353364107 YGGPYHIGGSPFK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGGPYHIGGSPFK 13 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 164.04 3.77E-05 1291080000 3853800 4318000 3466800 3597700 3008900 2120900 3761900 3373100 4460900 4899300 FALSE TRUE 3703189.235 4194854.868 4093327.879 3783377.728 3105684.001 2163786.051 3807939.258 3303444.306 3954517.334 4567466.047 0.810775427 0.918420591 0.896192295 0.828331878 0.679957764 0.473738837 0.833709374 0.723255361 0.865801145 1 22.12296257 3.432546207 5.617416793 0.739510767 0.877160563 0.115409969 0.131779954 0.313343566 23.50452997 0.03621487 0.049981965 2707.36124 -3.432546207 0.137649796 DTLAAISEVLYVDLLEGDTECHAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTLAAISEVLYVDLLEGDTECHAR 24 0 Q4G0J3;Q4G0J3-3;H0YA82;Q4G0J3-2 Q4G0J3 LARP7 La-related protein 7 0 118.22 0.00056409 282710000 115810 115380 94362 92655 99439 98981 84055 100010 94540 110110 FALSE TRUE 111284.0172 112089.4754 111415.3125 97436.93565 102637.5457 100982.4636 85083.69023 97944.75855 83808.21554 102652.1516 1.084088501 1.091934982 1.085367532 0.949195259 0.999857715 0.983734506 0.828854426 0.954142285 0.816429215 1 16.64740434 3.432724778 0.811901408 0.903117596 1.108233054 0.588077838 0.059687894 0.470452932 0.639365707 0.027221707 0.062097373 2708.474666 -3.432724778 0.205115458 GEPNVSY(ph)ICSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GEPNVSYICSR 11 0 A0A3B3ITW1;P49841;P49841-2;P49840;A8MT37 A0A3B3ITW1;P49840 GSK3B;GSK3A Glycogen synthase kinase-3 beta;Glycogen synthase kinase-3 alpha 1 GEPNVS(0.419)Y(0.581)ICSR;GEPNVS(0.398)Y(0.602)ICSR;GEPNVS(0.376)Y(0.624)ICSR 208.15 2.12E-07 6007750000 582700 611020 544632 537122 455669 416095 568042 556669 504282 581252 TRUE FALSE 559927.4398 593594.3079 643059.1177 564842.9308 470326.0072 424508.726 574993.8679 545173.5906 447038.0215 541883.2843 1.03329897 1.095428342 1.186711486 1.042370095 0.867947067 0.78339513 1.061102796 1.006071983 0.824971049 1 19.04762262 3.432837655 5.947461584 0.933538957 1.106088692 0.470648063 0.08750737 0.177937562 15.29819855 0.025884645 0.035602202 2709.178714 -3.432837655 0.172549735 S(ph)PPPPHRPR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPPPPHRPR 9 1 O43281-3;O43281-2;O43281 O43281-3 EFS Embryonal Fyn-associated substrate 1 S(1)PPPPHRPR;S(1)PPPPHRPR;S(1)PPPPHRPR;S(1)PPPPHRPR;S(1)PPPPHRPR;S(1)PPPPHRPR 97.813 0.0038982 2318518000 55784.5 54271.5 44330.4 52564.6 62894.6 55030.6 48909.3 86654.5 45427.1 52172.5 TRUE FALSE 53604.38007 52723.72996 52341.8894 55277.46531 64917.66193 56143.35644 49507.86664 84865.05429 40270.40605 48638.8101 1.102090696 1.083984782 1.076134249 1.136488849 1.334688529 1.154291322 1.017867553 1.744801201 0.82794801 1 15.56982031 3.433439102 7.860555259 1.240064186 1.090116814 0 0.234158072 0.632202959 98.15952873 0.065189415 0.088703462 2712.93321 -3.433439102 -0.149947372 ST(ph)TPTSSPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 STTPTSSPFR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.006)T(0.496)T(0.496)PT(0.001)S(0.001)SPFR;S(0.088)T(0.446)T(0.446)PT(0.02)SSPFR 142.94 0.00038964 1027120000 1422220 1475800 1261280 1273590 1054600 777460 1298200 1346790 1413100 1448170 TRUE FALSE 1366638.07 1433711.629 1489221.353 1339320.133 1088522.167 793180.7739 1314087.76 1318978.316 1252690.812 1350084.156 1.012261394 1.061942415 1.103058166 0.992027146 0.806262456 0.58750469 0.973337665 0.976960073 0.927861279 1 20.36461791 3.433760815 5.618020923 0.878114357 1.057991865 0.341889695 0.114030464 0.2300472 17.50629228 0.034887639 0.048179276 2714.943621 -3.433760815 0.179877508 GSPDEENEEIEDLSDAAFAALHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSPDEENEEIEDLSDAAFAALHAK 24 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A0G2JQF5;A0A3B3IT55;A0A0G2JQF4;A0A1W2PPV8;A0A1W2PS83;A0A1W2PQT4;Q7Z3B3-4;Q7Z3B3-2 A0A1W2PRB5;Q7Z3B3-4 KANSL1 KAT8 regulatory NSL complex subunit 1 0 ; 196.55 1.97E-24 23253500 34048 37365 28871 33275 43952 39133 36414 41009 43241 44240 FALSE TRUE 32717.36652 36299.38678 34088.63193 34992.32674 45365.756 39924.29607 36859.64542 40162.14982 38332.46296 41243.5854 0.793271637 0.880121998 0.826519606 0.848430766 1.099946951 0.968012254 0.893706138 0.973779303 0.929416359 1 15.33188213 3.434590323 24.99970541 0.970249315 0.837900912 0.617660216 0.053994592 96.56027464 56757.89061 0.014969603 0.020268954 2720.134154 -3.434590323 -0.132348404 DAYSGGAVNLYHVR ddPTM_BT-474_Pertuzumab_2h_R1 6 DAYSGGAVNLYHVR 14 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;;; 201.48 1.78E-08 3806640000 4077290 4293280 3844310 3617460 3139150 1587833 4287030 3531510 3669050 4416220 FALSE TRUE 3917944.999 4170839.858 4539062.333 3804157.544 3240123.611 1619940.071 4339495.956 3458583.084 3252554.826 4117105.486 0.951626091 1.013051493 1.102488714 0.92398836 0.786990671 0.393465768 1.054016219 0.840052094 0.790010078 1 21.97319898 3.435245501 4.174115623 0.804296747 1.021387953 0.242331402 0.1682681 0.299289782 11.34808186 0.048044297 0.068223715 2724.240853 -3.435245501 0.217091206 SNFAEALAAHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNFAEALAAHK 11 0 P07237;H7BZ94;I3L312;I3L3U6;I3L0S0;I3NI03;I3L514;I3L3P5;I3L1Y5 P07237 P4HB Protein disulfide-isomerase 0 ; 109.84 0.0018741 4192100000 6330200 6762400 5580400 5829400 5137900 3765000 6806700 5569000 6944500 7028800 FALSE TRUE 6082808.786 6569542.973 6588902.415 6130256.033 5303165.22 3841130.88 6890002.431 5453998.204 6156189.474 6552733.115 0.928285752 1.00256532 1.005519727 0.935526585 0.809305846 0.586187597 1.051470022 0.832324178 0.939484237 1 22.64366534 3.435847471 5.675537089 0.859461405 0.979827502 0.141386081 0.120345761 0.326187036 26.07851937 0.033400608 0.046144564 2728.019501 -3.435847471 0.120366097 GRLT(ph)PSPDIIVLSDNEASS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(0.931)PS(0.069)PDIIVLSDNEAS(0.057)S(0.943)PR 172.11 1.38E-11 262110000 88021 77387 66918 76153 99507 92520 84041 84630 94732 99072 TRUE FALSE 84581.04201 75179.99853 79011.57118 80083.26546 102707.733 94390.81779 85069.5189 82882.36093 83978.42051 92361.7652 0.91575818 0.813973167 0.85545757 0.867060794 1.112015701 1.021968534 0.921046915 0.897366575 0.909233603 1 16.49500813 3.436022725 24.9995009 0.967121969 0.857671058 0.428432256 0.063805651 160.2687996 97488.17917 0.019586848 0.026520743 2729.120583 -3.436022725 -0.109450912 TTAPSHAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTAPSHAK 8 0 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 84.568 0.01736 49776000 148470 135960 131920 124320 128050 100490 135890 117350 160450 144400 FALSE TRUE 142667.6283 132082.5539 155760.8785 130736.1701 132168.8445 102521.9767 137553.0625 114926.6815 142236.3887 134619.6594 1.059783013 0.981153529 1.15704407 0.971152139 0.981794525 0.761567643 1.021790302 0.853713952 1.056579621 1 17.03852959 3.436100015 3.165420309 0.92976924 1.058404514 0.240818173 0.09107831 0.304621534 6.263126144 0.024536332 0.036062101 2729.606318 -3.436100015 0.128635274 WAEALR ddPTM_BT-474_Pertuzumab_2h_R1 1 WAEALR 6 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 97.64 0.095015 79097000 182810 212690 176820 156530 97605 61517 191120 114780 108280 127280 FALSE TRUE 175665.5831 206624.2894 208775.3073 164608.5321 100744.5535 62760.91589 193458.9837 112409.7529 95988.50835 118659.2122 1.480420945 1.741325309 1.759453003 1.387237695 0.84902429 0.528917348 1.630374752 0.947332708 0.808942741 1 16.85646458 3.436285543 4.068708832 0.985675617 1.660374272 0.579721672 0.269914762 0.15836711 5.678220015 0.07782746 0.110910364 2730.77264 -3.436285543 0.674698655 VLQGDLVMNVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLQGDLVMNVYR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 110.52 0.003445 467230000 369310 387050 363040 358590 327190 251210 413190 362910 398510 455680 FALSE TRUE 354876.9569 376011.713 428649.4038 377096.8729 337714.3635 256289.6383 418246.7428 355415.7817 353272.8155 424816.3877 0.835365507 0.885115838 1.009022759 0.887670259 0.79496548 0.603295084 0.984535331 0.836633877 0.831589425 1 18.6964799 3.437883477 8.531236786 0.833481478 0.914125577 0.071003174 0.110036781 0.625353097 123.4174241 0.030524748 0.041505129 2740.838698 -3.437883477 0.080644099 DLQSSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLQSSDR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 159.46 0.0032171 219881000 319840 306750 275780 272810 271070 311910 297460 287060 301370 336900 FALSE TRUE 307340.2992 298001.7903 325619.5807 286889.7568 279789.2127 318217.0339 301100.4045 281132.1107 267159.741 314081.4629 0.978536894 0.948804134 1.036736067 0.913424671 0.890817338 1.013167192 0.958669772 0.895092974 0.850606523 1 18.26077927 3.438164991 0.683192426 0.923076594 0.985466322 0.09549399 0.054317135 2.061642976 1.933118909 0.032092442 0.078681757 2742.615912 -3.438164991 0.062389728 DVFISAAER ddPTM_BT-474_Pertuzumab_2h_R1 6 DVFISAAER 9 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;;; 209.19 2.05E-05 2628890000 1839180 2022320 1624850 1708830 1621860 1132462 1996110 1766590 1847550 2027280 FALSE TRUE 1767302.812 1964645.414 1918496.54 1797022.921 1674028.6 1155361.158 2020538.991 1730109.299 1637823.87 1889970.52 0.935095439 1.039511142 1.015093368 0.950820609 0.885743234 0.611311735 1.069084925 0.915416024 0.866586993 1 20.8499323 3.438433876 3.679654134 0.889118637 0.999447946 0.148596328 0.113640021 0.432228236 12.37363685 0.032658966 0.047161495 2744.314474 -3.438433876 0.110329309 NDANCIHMVDNGIVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDANCIHMVDNGIVEK 16 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3;H0Y8M2 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 89.344 0.0049106 0 143960 132010 95653 120790 149930 119080 130270 167030 143110 138170 FALSE TRUE 138333.884 128245.2041 112939.6249 127023.9864 154752.6346 121487.8792 131864.2832 163580.7721 126864.7528 128811.6228 1.073923929 0.995602735 0.876781321 0.986122087 1.201387198 0.943143767 1.023698641 1.269922454 0.984885913 1 16.97490325 3.438673239 24.79233991 1.087921802 0.974785742 0.130224859 0.104545281 236.0494007 152210.4194 0.029847574 0.04041389 2745.827426 -3.438673239 -0.11313606 MPPSHQLDHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 MPPSHQLDHSK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 85.845 0.010438 111301000 124326 136031 114074 99707 103996 60071 131070 57873 117357 128280 FALSE TRUE 119467.2025 132151.5291 134689.7094 104852.8902 107341.1258 61285.67678 132674.0739 56677.90233 104035.1254 119591.4813 0.998960805 1.105024602 1.126248357 0.876758855 0.897564982 0.512458547 1.109394017 0.473929261 0.869920869 1 16.8677551 3.438914287 2.040464061 0.765248851 1.078854426 0.266224914 0.189608219 0.353277678 2.96563449 0.053986463 0.086276525 2747.351877 -3.438914287 0.313605575 LRECELSPGVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRECELSPGVNR 12 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 112.82 0.0011244 1311390000 321330 351610 276780 314380 388720 348250 378040 360270 338650 363680 FALSE TRUE 308772.0684 341582.4271 326800.3029 330605.1895 401223.5318 355291.8536 382666.5666 352830.2986 300207.8717 339047.6297 0.910704106 1.007476228 0.963877268 0.975099545 1.183383975 1.047911333 1.128651355 1.040651129 0.885444538 1 18.37112843 3.43893466 24.99959605 1.056630314 0.966051818 0.216553317 0.076733642 230.0116809 150580.9511 0.021163305 0.028655307 2747.480764 -3.43893466 -0.090578496 SPAGLQVLNDYLADK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPAGLQVLNDYLADK 15 0 P24534;C9JZW3;F2Z2G2;F8WF65 P24534 EEF1B2 Elongation factor 1-beta 0 ; 204.13 1.18E-08 213000000 199291 189027 166297 202791 187126 207160 216680 219560 252960 267810 FALSE TRUE 191502.4874 183636.135 196350.5672 213257.0678 193145.0777 211348.9171 219331.7947 215026.0093 224245.0413 249670.9902 0.767019377 0.735512504 0.786437251 0.854152369 0.773598397 0.846509709 0.878483297 0.861237459 0.898162182 1 17.92966868 3.439054802 0.039273456 1.610219646 1.26E-11 0.873859506 0.026262667 72.77987305 0.741265789 12.67382668 17.78286782 2748.240922 -3.439054802 -1.610219646 LEAHSDWVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEAHSDWVR 9 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ;; 195.79 3.07E-05 1180750000 1007310 1122330 1060160 934130 789410 362534 1188400 806010 961110 1171050 FALSE TRUE 967943.2116 1090322.247 1251754.495 982340.5612 814802.0896 369864.6859 1202943.995 789365.6118 852008.8221 1091733.74 0.886611062 0.998707109 1.146574892 0.899798664 0.746337737 0.33878653 1.10186573 0.723038579 0.780418146 1 20.05818961 3.439121647 4.574406681 0.768516244 1.012285018 0.213238107 0.19662147 0.28416046 13.64579093 0.054247431 0.076497269 2748.663955 -3.439121647 0.243768774 KNFEWVAER ddPTM_BT-474_Pertuzumab_2h_R1 2 KNFEWVAER 9 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 141.1 0.00017242 2023220000 2401800 2557850 2146110 2156280 1781880 1157220 2664100 2010960 2266890 2481700 FALSE TRUE 2307935.001 2484902.622 2533959.817 2267565.869 1839195.788 1180619.781 2696704.053 1969432.973 2009562.151 2313612.249 0.997546154 1.074035904 1.095239627 0.980097625 0.794945562 0.510292847 1.165581681 0.85123727 0.868582085 1 21.14171566 3.439392293 5.144758262 0.862404204 1.055210147 0.233801599 0.156522163 0.274985469 17.81209735 0.044202633 0.061664167 2750.377411 -3.439392293 0.192805943 RDENWDK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDENWDK 7 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 110.41 0.027676 0 235130 205540 213220 233920 244700 265230 286400 300110 306830 296540 FALSE TRUE 225940.8597 199678.2004 251753.5971 245992.6392 252570.9977 270593.1323 289905.0489 293912.6236 271999.9447 276455.0817 0.817278736 0.72228081 0.910649193 0.889810517 0.913605915 0.978796015 1.048651546 1.063147842 0.983884771 1 18.07668557 3.440136578 0.726729843 1.037447435 0.760501085 0.794267648 0.045363154 0.339557968 0.364075913 0.024469952 0.05882514 2755.094997 -3.440136578 -0.276946351 ELFDDPS(ph)YVNVQNLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELFDDPSYVNVQNLDK 16 0 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3;Q5T188 P29353-2 SHC1 SHC-transforming protein 1 1 ELFDDPS(0.616)Y(0.384)VNVQNLDK;ELFDDPS(0.83)Y(0.17)VNVQNLDK 241.39 7.00E-20 594969000 854540 863660 685200 772990 619030 706410 679030 833040 902680 730900 TRUE FALSE 821143.6321 839029.2624 809030.8822 812884.1065 638941.6621 720694.0942 687340.1723 815837.4329 800211.5507 681395.492 1.205091084 1.231339614 1.187314697 1.192969599 0.937695758 1.057673704 1.008724273 1.197303831 1.174371654 1 19.37813288 3.440146563 24.99595675 1.075916281 1.20690515 0.461222515 0.074248414 173.4824206 117278.6143 0.022283154 0.030171597 2755.158339 -3.440146563 0.130988869 TPELTWER ddPTM_BT-474_Pertuzumab_2h_R1 2 TPELTWER 8 0 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 ; 153.71 0.0010159 580850000 305270 350110 288880 285440 286550 197757 340230 264140 326020 359750 FALSE TRUE 293339.7109 340125.2056 341087.0421 300171.5926 295767.141 201755.782 344393.8365 258685.4167 289011.5764 335383.8121 0.874638848 1.014137216 1.017005084 0.895009186 0.881876615 0.601566846 1.026864816 0.771311576 0.861733828 1 18.35545353 3.440296048 2.986361446 0.841060577 0.972095879 0.142753026 0.117328697 0.404493164 7.361332778 0.032041724 0.047614858 2756.106832 -3.440296048 0.131035302 YGADALR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGADALR 7 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 107.22 0.017509 268080000 332390 388540 343100 309040 298120 180140 378180 289650 299260 365010 FALSE TRUE 319399.8313 377459.2196 405105.8022 324989.5914 307709.3005 183782.5542 382808.28 283668.6263 265289.2594 340287.5476 0.938617453 1.109236063 1.19048083 0.955044032 0.904262594 0.540080163 1.124955299 0.833614478 0.779603195 1 18.37639483 3.440480114 3.361064255 0.857922901 1.082439779 0.281081589 0.153470097 0.294250584 6.902427173 0.042806246 0.062605109 2757.275194 -3.440480114 0.224516877 AAGQPYEQHAK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAGQPYEQHAK 11 0 O14976-2;O14976;A0A087X1U9;H0Y8H5 O14976-2 GAK Cyclin-G-associated kinase 0 ;; 151.79 3.33E-05 590900000 364266 399960 305069 368183 402584 392325 426738 416607 436230 449525 FALSE TRUE 350030.082 388553.5324 360201.7545 387184.9688 415533.48 400258.0803 431960.5473 408003.9199 386710.9992 419078.2714 0.835237964 0.927162201 0.859509498 0.923896549 0.991541457 0.955091465 1.030739546 0.973574503 0.922765568 1 18.6768602 3.441060391 3.502723571 0.979715316 0.87978089 0.65280616 0.034348738 0.141724136 3.644315672 0.009407638 0.013692784 2760.961758 -3.441060391 -0.099934426 VNMEDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VNMEDLR 7 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141;A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 D6RGI3;B1AMS2;A0A087X142 SEPT11;SEPT6;SEPT8 Septin-11;Septin-6;Septin-8 0 125.58 0.0093872 187620000 723550 793010 692110 576590 588520 211470 661570 541160 553670 650960 FALSE TRUE 695272.8661 770394.1312 817189.6729 606347.879 607450.2803 215746.0683 669666.4916 529984.8569 490819.7028 606869.8994 1.145670376 1.26945517 1.346564846 0.999139815 1.000956351 0.355506293 1.103476202 0.873308855 0.808772528 1 19.21102774 3.441206044 2.444321965 0.843574464 1.252452312 0.452466943 0.194607969 0.25558126 3.079247942 0.056365359 0.08665323 2761.887879 -3.441206044 0.408877848 MMNGGHYTYSENR ddPTM_BT-474_Pertuzumab_2h_R1 6 MMNGGHYTYSENR 13 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;; 198.14 1.28E-07 3321460000 2271030 2724350 2784500 2231430 1847480 877134 2731810 1928440 2036870 2741540 FALSE TRUE 2182275.637 2646654.205 3287721.091 2346594.37 1906905.872 894870.2505 2765242.708 1888617.04 1805653.057 2555853.054 0.853834548 1.03552675 1.28634981 0.918125698 0.746093704 0.350125861 1.081925545 0.738938038 0.706477649 1 21.28537346 3.441670331 4.77115565 0.761237953 1.063815758 0.280365954 0.206863832 0.235392553 12.76244578 0.057342373 0.080675064 2764.842085 -3.441670331 0.302577805 EGSEEDLDALEHMFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGSEEDLDALEHMFR 15 0 P31944 P31944 CASP14 "Caspase-14;Caspase-14 subunit p17, mature form;Caspase-14 subunit p10, mature form;Caspase-14 subunit p20, intermediate form;Caspase-14 subunit p8, intermediate form" 0 ; 155.98 2.21E-06 41597000 43851 39621 33766 26439.8 28288 26261.2 19108.3 18382 25118.7 15641 FALSE TRUE 42137.25444 38491.04787 39868.26732 27804.36125 29197.90921 26792.21946 19342.15309 18002.40528 22267.33048 14581.62114 2.889751012 2.63969606 2.734145054 1.906808645 2.00237744 1.837396487 1.326474807 1.234595598 1.527081953 1 13.8318635 3.44172538 0.44562155 1.076078545 3.270229225 0.922192771 0.175461513 0.433765951 0.145619988 0.152366137 0.451862647 2765.192564 -3.44172538 2.194150681 HHGT(ph)PTSTKK ddPTM_BT-474_Pertuzumab_2h_R1 3 HHGTPTSTKK 10 1 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 HHGT(1)PTSTKK;HHGT(0.999)PT(0.001)STKK;HHGT(0.999)PT(0.001)STKK 148.18 1.95E-05 239673000 444930 438650 289456 256962 229535 294552 206958 7403.71 263217 128100 TRUE FALSE 427541.6437 426140.1315 341767.1381 270223.8396 236918.2017 300508.0433 209490.8139 7250.820801 233337.7097 119423.6729 3.580040986 3.568305355 2.861803944 2.262732614 1.983846217 2.516318883 1.754181636 0.060715105 1.953864791 1 16.86572932 3.442368924 0.449824803 0.810262432 4.20461768 0.714504072 0.550642185 0.925455436 0.31798661 0.508807831 1.502199037 2769.293102 -3.442368924 3.394355248 YIQEAEMLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YIQEAEMLR 9 0 Q05048;A0A0A0MSZ9 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 85.377 0.034562 60702000 58453 56678 47422 47851 43577 23236 58672 43553 48988 56898 FALSE TRUE 56168.59214 55061.59893 55992.2103 50320.59584 44978.69378 23705.84784 59390.04549 42653.61533 43427.08761 53044.24778 1.058900719 1.038031478 1.055575536 0.948653208 0.84794668 0.446907041 1.119632156 0.804113869 0.818695512 1 15.69490869 3.443486178 2.989268419 0.830115063 1.047479568 0.2564293 0.16155325 0.348941408 6.366530804 0.045824763 0.068236721 2776.426479 -3.443486178 0.217364505 SAS(ph)TDLGTADVVLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SASTDLGTADVVLGR 15 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 SAS(0.858)T(0.142)DLGTADVVLGR;S(0.001)AS(0.973)T(0.026)DLGTADVVLGR 388.7 2.07E-114 290413000 348276 367929 180910 344288 556250 359183 425062 590800 477000 478976 TRUE FALSE 334664.9889 357436.0252 213604.4613 362056.7449 574142.2864 366445.9264 430264.0359 578599.7735 422852.9597 446534.5289 0.749471692 0.80046671 0.478360457 0.810814666 1.28577355 0.820644099 0.963562744 1.295755952 0.946965872 1 18.76841221 3.443592141 8.856138561 1.064686118 0.681160087 0.540152568 0.15816093 0.198432559 48.30189374 0.044153185 0.060085707 2777.103978 -3.443592141 -0.383526032 RDPHLACVAYER ddPTM_BT-474_Pertuzumab_2h_R1 3 RDPHLACVAYER 12 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;; 96.591 0.003504 4765740000 844640 960430 650650 781390 721510 627270 797180 696710 714850 806080 FALSE TRUE 811630.535 933039.4768 768236.9286 821717.6315 744718.0244 639953.8292 806936.1273 682322.695 633703.2249 751483.4836 1.080037756 1.241596784 1.02229383 1.093460667 0.990997195 0.851587351 1.073790901 0.907967653 0.843269664 1 19.51938187 3.443744423 1.177594731 0.935496502 1.147935104 0.502356099 0.081505275 0.381842922 1.086751064 0.028403718 0.055896892 2778.077921 -3.443744423 0.212438602 S(ph)VENLPECGITHEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVENLPECGITHEQR 15 0 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR 225.82 6.11E-13 5767820000 2845660 2891420 2204750 2591660 2839750 2691190 2731330 2895860 2922980 3165620 TRUE FALSE 2734448.461 2808959.533 2603197.369 2725415.883 2931093.138 2745607.706 2764756.834 2836059.479 2591175.565 2951209.738 0.926551721 0.951799358 0.882078063 0.923491085 0.993183609 0.930332965 0.936821534 0.960982015 0.878004546 1 21.49287502 3.443796853 24.9978319 0.948027879 0.919887908 0.135253551 0.035696277 382.2477375 286736.9815 0.009465038 0.012815805 2778.413324 -3.443796853 -0.028139971 S(ph)EEENVVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEENVVLK 9 0 Q9H1A4 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 S(1)EEENVVLK;S(1)EEENVVLK 68.227 0.05991 0 443660 400730 408130 192609 325940 406440 319010 163155 310520 308430 TRUE FALSE 426321.2767 389301.5728 481888.1698 202549.5736 336424.1561 414658.4953 322914.1398 159785.7922 275271.0714 287539.7614 1.482651563 1.353905181 1.675900987 0.704422834 1.170009165 1.442090977 1.123024302 0.555699815 0.957332197 1 18.13340194 3.443959811 0.449620885 0.829017431 1.616205387 0.3361456 0.273462958 1.971183732 0.676065755 0.25077769 0.741937504 2779.456051 -3.443959811 0.787187955 TLS(ph)INEEEPEGGFSK ddPTM_BT-474_Pertuzumab_2h_R1 3 TLSINEEEPEGGFSK 15 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.004)LS(0.996)INEEEPEGGFSK;TLS(1)INEEEPEGGFSK;TLS(1)INEEEPEGGFSK 291.7 6.57E-44 1183910000 684140 701840 458690 682540 990920 793880 768960 1041380 898880 819320 TRUE FALSE 657403.0524 681824.2104 541585.4865 717765.9712 1022793.842 809932.7975 778370.7625 1019875.139 796842.9108 763826.7266 0.860670398 0.892642515 0.709042336 0.939697377 1.339039086 1.06036195 1.019041015 1.335217928 1.043224704 1 19.54288588 3.444399859 8.385017129 1.150362707 0.82721354 0.573581312 0.121898592 0.15388116 34.98396698 0.03303147 0.045022821 2782.273755 -3.444399859 -0.323149167 (ac)SQPGQKPAAS(ph)PRPR ddPTM_BT-474_Pertuzumab_2h_R1 7 SQPGQKPAASPRPR 14 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 1 SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR 123.4 7.93E-12 32871430000 9607350 9424090 7731830 8178690 7225450 8311610 7151510 7745520 8618260 8663880 TRUE FALSE 9231884.141 9155324.18 9129143.675 8600793.171 7457863.161 8479676.449 7239032.319 7585572.305 7639951.255 8077067.691 1.142974715 1.133496032 1.130254694 1.064841041 0.923337955 1.049845906 0.896245097 0.93914928 0.945881791 1 22.9454002 3.444944208 2.870029439 0.954400719 1.134916502 0.792593157 0.040755117 0.109005798 1.825723181 0.01160688 0.017405536 2785.763268 -3.444944208 0.180515783 FTGS(ph)FDDDPDPHRDPYGEEVDRR ddPTM_BT-474_Pertuzumab_2h_R1 5 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.191)GS(0.809)FDDDPDPHRDPYGEEVDRR;FT(0.143)GS(0.857)FDDDPDPHRDPYGEEVDRR;FT(0.028)GS(0.972)FDDDPDPHRDPYGEEVDRR;FT(0.179)GS(0.821)FDDDPDPHRDPYGEEVDRR;FT(0.495)GS(0.505)FDDDPDPHRDPYGEEVDRR 242.83 1.21E-37 22224600000 2210900 1855010 1163910 1705450 2531590 1943890 2055650 2392730 1901370 1937970 TRUE FALSE 2124495.584 1802106.931 1374254.428 1793468.479 2613020.891 1983196.788 2080807.66 2343319.289 1685534.449 1806709.566 1.175892143 0.997452477 0.760639371 0.992671159 1.446287185 1.097684335 1.15171121 1.2970094 0.932930495 1 20.78493318 3.4454101 24.99771501 1.17848344 0.962725961 0.198319094 0.165121115 245.2697652 193344.0493 0.044628681 0.060427981 2788.753315 -3.4454101 -0.215757479 DLMVGDEASELR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLMVGDEASELR 12 0 P61160 P61160 ACTR2 Actin-related protein 2 0 ;;; 215.89 9.39E-11 2144340000 2177980 2288430 1816010 2099870 2215540 2239170 2287590 2342420 2337510 2515970 FALSE TRUE 2092862.134 2223166.217 2144203.404 2208244.542 2286804.856 2284447.552 2315586.211 2294048.208 2072165.664 2345561.111 0.892265021 0.947818501 0.914153715 0.941456836 0.974950022 0.973945015 0.987220584 0.978038132 0.883441346 1 21.16150166 3.445606013 3.634579759 0.96775109 0.921416583 0.309755493 0.032165267 0.282574847 7.942687 0.008889811 0.01292292 2790.011628 -3.445606013 -0.046334506 ADADPSPT(ph)SPPTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADADPSPTSPPTAR 14 0 Q9NWZ5;Q9NWZ5-3;Q9NWZ5-2 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 ADADPS(0.138)PT(0.59)S(0.271)PPTAR 85.909 0.084391 294630000 209540 255060 211830 221810 205250 216510 231100 237230 215610 252900 TRUE FALSE 201350.9451 247785.9385 250112.3931 233257.6407 211852.0527 220887.9805 233928.2709 232331.1176 191134.8567 235770.8577 0.854011166 1.050960839 1.060828278 0.989340425 0.89855063 0.936875671 0.992184841 0.985410665 0.810680584 1 17.84702588 3.445743078 20.29864438 0.943652951 0.999877491 0.095087189 0.073917071 56.40233808 36485.28585 0.020266325 0.027442215 2790.892303 -3.445743078 0.05622454 MGLS(ph)MER ddPTM_BT-474_Pertuzumab_2h_R1 4 MGLSMER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 MGLS(1)MER;MGLS(1)MER;MGLS(1)MER;MGLS(1)MER 115.13 0.0060302 4341800000 2799400 2416860 1081350 2028770 3343470 1801280 2332910 3219350 2447090 2263950 TRUE FALSE 2689996.353 2347933.519 1276774 2133475.063 3451015.749 1837703.116 2361460.85 3152869.297 2169306.602 2110610.65 1.274510935 1.112442752 0.604931089 1.010833079 1.635079283 0.870697358 1.118851954 1.493818529 1.027809938 1 21.00922903 3.446016439 24.99950801 1.223675231 0.97532112 0.100218857 0.266779212 358.7617788 288342.3788 0.073993191 0.100188108 2792.649549 -3.446016439 -0.248354111 AMTGVEQWPYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AMTGVEQWPYR 11 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 164.97 5.15E-05 303550000 108060 120640 103700 104740 92815 79754 109040 105790 123250 126880 FALSE TRUE 103836.8957 117199.4653 122440.8968 110145.644 95800.47877 81366.68052 110374.4641 103605.3995 109259.1767 118286.3046 0.877843771 0.990811791 1.035123189 0.931178333 0.809903387 0.687879132 0.933112794 0.875886688 0.923684082 1 16.85192352 3.446413749 7.605278625 0.862641986 0.972407484 0.200371761 0.086185087 0.275487211 54.44483646 0.024272354 0.033219026 2795.205543 -3.446413749 0.109765498 RAS(ph)GQAFELILSPR ddPTM_BT-474_Pertuzumab_2h_R1 8 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR 197.88 1.40E-08 6250837000 1664726 1874394 1522466 1498851 1462092 1371568 1684862 1579147 1552376 1496504 TRUE FALSE 1599666.667 1820938.118 1797609.473 1576206.88 1509121.517 1399302.045 1705481.845 1546537.063 1376156.785 1395144.451 1.146595728 1.305196832 1.288475521 1.129780417 1.08169553 1.002980045 1.222441048 1.108513933 0.986390179 1 20.41198307 3.448030773 0.296599169 1.006024281 1.334500608 0.451199585 0.081490533 3.733390269 0.484958818 0.112150092 0.425502861 2805.632432 -3.448030773 0.328476328 EIEVGGGRK ddPTM_BT-474_Pertuzumab_2h_R1 4 EIEVGGGRK 9 1 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;;; 131.62 0.00052611 5814100000 4847720 4787740 3342340 3444840 3910570 4783710 4135040 4330440 4586110 4152300 FALSE TRUE 4658265.743 4651198.343 3946375.188 3622628.605 4036357.036 4880439.894 4185645.856 4241014.901 4065514.019 3871061.023 1.203356319 1.201530618 1.019455691 0.935823172 1.042700441 1.260749925 1.08126579 1.095569116 1.05023248 1 21.88429762 3.44842175 0.012013274 1.14E-05 2.208076302 0.127414251 0.091146947 7230.373183 22.24437613 1937.873247 2151.576771 2808.159362 -3.44842175 2.208064904 LSIVPVRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSIVPVRR 8 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 112.41 0.0048844 638910000 710770 788740 677910 569630 554020 357430 650850 468910 510090 565110 FALSE TRUE 682992.3226 766245.9075 800423.417 599028.6726 571840.5564 364657.4795 658815.297 459226.8446 452186.7217 526834.5964 1.296407501 1.454433541 1.519306861 1.137033666 1.085427116 0.692166919 1.250516389 0.871671769 0.858308708 1 19.00699056 3.448580551 2.328837342 0.950767812 1.425071171 0.660108452 0.148454053 0.170112916 1.856757891 0.042221183 0.065895246 2809.186358 -3.448580551 0.474303359 FVFDRPLPVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 FVFDRPLPVSR 11 1 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ; 219.92 8.69E-12 4999400000 2384360 2623900 2222850 2167040 2018750 1773310 2238080 2127900 2245450 2389900 FALSE TRUE 2291176.575 2549068.941 2624568.442 2278881.194 2083684.927 1809167.543 2265470.293 2083958.121 1990555.93 2228029.944 1.028341913 1.14409097 1.177977185 1.022823414 0.935214059 0.812003244 1.016804239 0.935336676 0.89341525 1 21.08733719 3.449492736 3.475875552 0.930275753 1.118843048 0.628589542 0.063629969 0.144179907 3.670477642 0.017934853 0.026288244 2815.092928 -3.449492736 0.188567295 S(ph)LDGVTNDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDGVTNDR 9 0 Q9UBM7;E9PRL8;E9PQ71;E9PIP9;E9PJ54;E9PM00 Q9UBM7 DHCR7 7-dehydrocholesterol reductase 1 S(1)LDGVTNDR 89.356 0.010616 0 46348 52699 29275 73668 53048 44584 68414 85826 74038 52722 TRUE FALSE 44536.66892 51196.07612 34565.64372 77470.01431 54754.3371 45485.51903 69251.271 84053.66311 65633.51663 49151.09198 0.906117588 1.041606077 0.703252813 1.576160594 1.11400042 0.92542235 1.408946744 1.710107746 1.335341983 1 15.58493585 3.449787277 0.671433539 1.403077656 0.862831126 0.202780331 0.27329725 1.265527693 1.135678124 0.166100784 0.416642545 2817.002786 -3.449787277 -0.54024653 SQDLHCGACR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQDLHCGACR 10 0 Q9Y2B0;F8VXJ7;F8W031;F8W1U5;F8VP03;Q9Y2B0-2 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ; 74.962 0.040422 910500000 1677670 2024290 1705020 1449980 1147120 545530 1599980 1084360 1341050 1740370 FALSE TRUE 1612104.802 1966559.231 2013155.042 1524813.642 1184018.157 556560.9904 1619561.034 1061967.587 1188819.626 1622493.19 0.993597269 1.212060084 1.240778732 0.939796636 0.729752312 0.343028244 0.998192809 0.654528225 0.732711628 1 20.62978099 3.451158276 3.302856022 0.721601901 1.152193315 0.490953915 0.184474469 0.184620697 4.191361392 0.050799223 0.075028695 2825.909675 -3.451158276 0.430591414 RPES(ph)PSEISPIK ddPTM_BT-474_Pertuzumab_2h_R1 5 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 RPES(0.984)PS(0.016)EISPIK;RPES(0.996)PS(0.004)EISPIK;RPES(0.996)PS(0.004)EISPIK;RPES(0.935)PS(0.033)EIS(0.032)PIK;RPES(0.968)PS(0.032)EISPIK 216.71 2.35E-11 9806400000 4885930 4899220 4066590 4873950 4921200 5336960 5049560 5645040 6444400 5389770 TRUE FALSE 4694982.454 4759499.042 4801513.274 5125495.144 5079494.867 5444876.988 5111358.026 5528467.951 5712858.729 5024716.077 0.934377661 0.947217508 0.955579022 1.020056669 1.010901868 1.083618836 1.017243153 1.100254794 1.136951549 1 22.26061065 3.45119983 0.803506417 1.078109647 0.926079839 0.644221947 0.038392986 0.428034378 0.565137067 0.017879875 0.042038425 2826.180075 -3.45119983 -0.152029808 GQETSTNPIASIFAWTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQETSTNPIASIFAWTR 17 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 193.77 2.60E-10 199206000 142835 160861 105789 134776 154847 156440 135039 157725 154100 163977 FALSE TRUE 137252.8503 156273.4018 124907.4256 141731.8055 159827.7944 159603.324 136691.6477 154467.9236 136607.214 152870.6917 0.897836261 1.022258747 0.817078958 0.92713524 1.045509722 1.044041354 0.894165167 1.010448255 0.893612847 1 17.22195232 3.451364531 24.94286259 0.981141137 0.914832887 0.183966766 0.067768258 366.8680483 355274.6051 0.018376144 0.024882157 2827.25207 -3.451364531 -0.066308249 VGRPSNIGQAQPIIDQLAEEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 VGRPSNIGQAQPIIDQLAEEAR 22 1 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5;A0A0J9YVR6;E9PQ56;A0A0J9YWM1;H0YEM1;E9PN18;E9PMU7 A0A0J9YVP6;E9PN18 PUF60 Poly(U)-binding-splicing factor PUF60 0 ;; 156.24 1.21E-08 460070000 399320 414710 345000 369990 369640 355470 366281 408920 415930 429160 FALSE TRUE 383714.1329 402882.8768 407349.1745 389085.2282 381529.8063 362657.847 370763.6564 400475.6591 368715.3701 400092.6109 0.959063283 1.00697405 1.01813721 0.972487913 0.95360373 0.906434753 0.926694586 1.000957399 0.921575055 1 18.60997446 3.451556678 3.911685029 0.951476648 0.996131023 0.265203976 0.032167434 0.292417352 9.886770945 0.009287851 0.013447888 2828.503224 -3.451556678 0.044654375 NMAPGAVCS(ph)PGESK ddPTM_BT-474_Pertuzumab_2h_R1 3 NMAPGAVCSPGESK 14 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NMAPGAVCS(1)PGESK;NMAPGAVCS(0.999)PGES(0.001)K;NMAPGAVCS(1)PGESK 218.66 5.56E-12 1138707000 976990 905650 794190 801020 868680 869810 729850 903430 949690 962220 TRUE FALSE 938808.1507 879821.7487 937717.7997 842360.7382 896621.8811 887398.1542 738782.1226 884773.8548 841885.1726 897047.9823 1.046552881 0.980796753 1.045337393 0.939036434 0.999524996 0.989242684 0.823570352 0.986317201 0.938506289 1 19.77482563 3.452138355 0.962472134 0.941755728 1.024955094 0.23861232 0.053230068 0.833936363 1.589840667 0.021321605 0.046512656 2832.294147 -3.452138355 0.083199366 IESGAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 IESGAFR 7 0 O94933 O94933 SLITRK3 SLIT and NTRK-like protein 3 0 ; 87.284 0.045261 837150000 872970 999740 828390 828300 710970 448630 1000710 801990 925510 1041110 FALSE TRUE 838853.3673 971228.394 978098.5004 871048.6623 733838.9957 457701.606 1012956.988 785428.6262 820449.9849 970594.6924 0.864267417 1.0006529 1.007731145 0.897438106 0.756071511 0.471568214 1.043645712 0.80922411 0.845306482 1 19.88850945 3.452494963 5.594378095 0.811304974 0.960949916 0.144335783 0.149128791 0.308340187 28.75287401 0.041616266 0.058254289 2834.620758 -3.452494963 0.149644943 DKPASSMS(ph)DDEMPVLEIPR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKPASSMSDDEMPVLEIPR 19 1 Q96PN7 Q96PN7 TRERF1 Transcriptional-regulating factor 1 1 DKPAS(0.1)S(0.073)MS(0.827)DDEMPVLEIPR;DKPAS(0.017)S(0.064)MS(0.919)DDEMPVLEIPR;DKPAS(0.138)S(0.138)MS(0.725)DDEMPVLEIPR 145.52 7.54E-08 284870000 595942 563358 477813 559899 611145 606974 633218 647631 725176 616087 TRUE FALSE 572651.9278 547291.5814 564164.438 588795.4545 630803.034 619247.4302 640967.5113 634257.1935 642857.0607 574358.8787 0.997028076 0.952873894 0.982250748 1.025135114 1.098273322 1.078154187 1.115970406 1.104287262 1.119260247 1 19.13159294 3.452613221 2.333465917 1.094419106 0.974093383 0.67084778 0.033987756 0.147985832 1.620599402 0.009313076 0.014571777 2835.392725 -3.452613221 -0.120325723 LPLFPEPLHVFAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPLFPEPLHVFAPR 14 0 P26358;P26358-2;P26358-3;K7ENW7 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 150.69 7.14E-06 463740000 280820 292620 260790 249590 228730 182407 275170 236550 247050 317170 FALSE TRUE 269845.2439 284274.7641 307920.5542 262471.3698 236087.3082 186095.3945 278537.6128 231665.1598 219005.9197 295687.7934 0.912601906 0.961401757 1.04137053 0.887663866 0.798434408 0.629364481 0.941999024 0.783478943 0.740666083 1 18.17371516 3.452642984 4.061601986 0.804715742 0.970994237 0.32257378 0.100525223 0.223725941 8.335386559 0.027136711 0.039163232 2835.58705 -3.452642984 0.166278494 DENQSINHQMAQEDAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DENQSINHQMAQEDAQR 17 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ; 164.82 2.55E-09 650150000 151159 156417 58323 370683 156964 157282 246266 195732 327090 335123 FALSE TRUE 145251.5392 151956.1403 68863.26349 389813.9941 162012.8896 160462.3498 249279.877 191690.0658 289960.1145 312424.8207 0.464916772 0.486376658 0.220415469 1.247704946 0.518566 0.513603079 0.797887557 0.613555816 0.928095642 1 18.25314955 3.452705856 0.119861615 1.198494322 4.93E-12 0.270521752 0.249486743 34.85305193 1.159557702 3.213698284 8.58742276 2835.997578 -3.452705856 -1.198494322 LLEEQLQHEISNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEEQLQHEISNK 13 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 0 ; 216.34 2.76E-11 438330000 763910 815330 594250 719570 835920 714470 750980 951290 866230 715920 FALSE TRUE 734055.5527 792077.5867 701644.194 756707.0939 862808.126 728917.0729 760170.7179 931645.5291 767899.2019 667430.1007 1.099823864 1.186757364 1.051262437 1.133762312 1.292731816 1.092124961 1.138951805 1.395869812 1.150531271 1 19.34825723 3.452746308 24.27243497 1.205306301 1.115442725 0.03927242 0.107596665 335.3901405 333977.9698 0.030130434 0.040798854 2836.261752 -3.452746308 -0.089863575 GSFSQADVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSFSQADVHR 10 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3 Q04206 RELA Transcription factor p65 0 ; 167.12 5.34E-06 656030000 541630 660580 538900 496460 414650 224320 601770 443740 460250 531710 FALSE TRUE 520462.5008 641740.9052 636291.2178 522082.3601 427987.5938 228855.9041 609134.6413 434576.6139 408004.3495 495696.8081 1.049961372 1.29462384 1.283629847 1.053229215 0.863405991 0.461685249 1.228845196 0.876698431 0.823092549 1 18.91909844 3.452962896 3.576852338 0.87671069 1.215104822 0.389488112 0.188088411 0.235476633 6.423792222 0.053459278 0.078290604 2837.676583 -3.452962896 0.338394132 SLDFLIELLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDFLIELLHK 11 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 156.71 3.09E-05 384750000 937630 881670 946930 1046890 1041990 1038680 1179680 1119140 1330950 1514970 FALSE TRUE 900986.383 856525.6348 1118061.315 1100920.118 1075506.555 1059682.821 1194117.277 1096029.368 1179866.136 1412359.733 0.637929815 0.606450053 0.791626446 0.77948988 0.76149619 0.750292434 0.845476722 0.776027058 0.835386417 1 20.42967616 3.45298991 0.056188341 1.465162318 1.71E-13 0.796650087 0.046735114 53.05003154 0.774808156 7.733542186 12.56454298 2837.853097 -3.45298991 -1.465162318 IAAASSDLYLRPGSEQPGRPGS(ph)HGYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 IAAASSDLYLRPGSEQPGRPGSHGYVR 27 2 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 IAAASSDLYLRPGSEQPGRPGS(1)HGYVR;IAAASSDLYLRPGSEQPGRPGS(1)HGYVR 72.687 0.0098811 589520000 249890 238930 214310 226470 192645 245400 200511 222030 266260 287640 TRUE FALSE 240124.0225 232115.9503 253040.5843 238158.1438 198841.6014 250362.1561 202964.9136 217445.0029 236035.2811 268157.8866 0.895457619 0.865594345 0.943625368 0.888126569 0.741509429 0.933637117 0.756885864 0.810884236 0.880210103 1 18.03272316 3.453195482 24.99908934 0.837299693 0.900948254 0.053278056 0.07552146 429.0010496 448244.7816 0.019504457 0.026410272 2839.196705 -3.453195482 0.063648561 DVGAYSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVGAYSK 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 95.531 0.051697 0 161440 157620 124020 145020 157150 149620 162930 156180 164740 177780 FALSE TRUE 155130.7463 153124.8319 146433.1728 152504.4996 162204.8725 152645.4189 164923.9861 152954.8284 146039.4058 165738.8023 0.935995339 0.923892473 0.883517745 0.920149642 0.978677716 0.920999892 0.995083733 0.922866742 0.881141916 1 17.33855188 3.453621196 24.49062502 0.946497083 0.913148035 0.169904022 0.03640606 330.6375428 344573.3958 0.009869461 0.013364195 2841.981171 -3.453621196 -0.033349048 QREESYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 QREESYSR 8 1 P23246;P23246-2;H0Y9K7;H0Y9U2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 207.68 5.60E-05 2556990000 1063140 1190590 896050 972820 982454 880607 1069730 930226 1024940 1119990 FALSE TRUE 1021591.313 1156635.539 1057986.168 1023027.357 1014055.525 898413.4769 1082821.676 911016.508 908593.1081 1044132.08 0.978411959 1.107748303 1.01326852 0.979787305 0.971194684 0.86044045 1.037054312 0.872510792 0.870189822 1 19.99387279 3.454028085 1.532588125 0.925485382 1.043895244 0.341396414 0.061736954 0.395224664 1.880865972 0.019132684 0.033985981 2844.645063 -3.454028085 0.118409862 YEQGTGCWQGPNR ddPTM_BT-474_Pertuzumab_2h_R1 6 YEQGTGCWQGPNR 13 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 277.1 6.85E-32 4329970000 643371 789392 637163 624953 542402 345009 743601 595509 644965 791983 FALSE TRUE 618227.35 766879.3131 752312.5277 657206.8992 559848.8529 351985.3184 752701.4115 583211.531 571751.2771 738341.286 0.83731922 1.038651539 1.018922471 0.890112624 0.75825213 0.476724416 1.01944917 0.789894243 0.774372621 1 19.49392831 3.454733247 4.448028784 0.79343884 0.970978546 0.192254161 0.148528958 0.29829281 14.25096902 0.041174716 0.058966566 2849.267651 -3.454733247 0.177539706 RIS(ph)QVSSGETEYNPTEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(0.998)QVS(0.002)SGETEYNPTEAR;RIS(0.992)QVS(0.006)S(0.002)GET(0.001)EYNPTEAR 208.34 3.94E-16 599110000 193234 182545 131881 169813 223378 178630 199473 214715 199244 216103 TRUE FALSE 185682.2016 177338.9953 155714.8304 178577.0693 230563.1562 182242.021 201914.2102 210281.0602 176626.6564 201466.1513 0.921654583 0.880242136 0.77290815 0.886387456 1.144426271 0.904578857 1.002223991 1.043753796 0.876706361 1 17.62017794 3.454817371 24.98843638 0.998465905 0.855329322 0.411048822 0.076697458 203.1209859 227568.4819 0.020400112 0.027623775 2849.819614 -3.454817371 -0.143136583 S(ph)ASFAGFSS(ph)AQSRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASFAGFSSAQSRR 14 1 A0A499FJE4;Q96MK2;Q96MK2-2 A0A499FJE4 FAM65C Protein FAM65C 2 S(0.499)AS(0.499)FAGFS(0.001)S(0.5)AQS(0.5)RR 53.756 0.097635 804840000 19985 25352 23418 20551 0 22928 17210 15711 0 19390 TRUE FALSE 19203.96411 24628.98578 27650.15353 21611.63957 0 23391.61987 17420.62113 15386.56236 0 18076.69803 1.062360176 1.362471495 1.529602004 1.195552392 0 1.294020613 0.963705932 0.851182132 0 1 14.14184355 3.455244648 24.9985301 0.724575453 1.329244202 0.348009362 0.404454283 262.0593451 299455.9329 0.109999105 0.148950363 2852.624766 -3.455244648 0.60466875 ELHINLIPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELHINLIPNK 10 0 P07900;P07900-2;G3V2J8;Q14568 P07900 HSP90AA1;HSP90AA2P Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 ; 121.9 0.00050283 3940300000 12577200 12823900 13062600 11822900 10602500 5053900 14403600 11756700 13701200 15898400 FALSE TRUE 12085669.12 12458174.93 15423302.4 12433081.29 10943539.04 5156093.321 14579875.57 11513920.04 12145897.22 14821587.21 0.815409912 0.840542565 1.040597217 0.838849518 0.738351358 0.347877272 0.983691919 0.776834483 0.819473451 1 23.82119661 3.455514019 6.749799516 0.763661967 0.900649737 0.083835532 0.176514839 0.370174013 65.92699358 0.049084475 0.068030055 2854.394652 -3.455514019 0.13698777 LLQAFLER ddPTM_BT-474_Pertuzumab_2h_R1 2 LLQAFLER 8 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 121.09 0.0033688 338640000 755770 939960 791840 633840 566470 284180 721150 464590 535690 701190 FALSE TRUE 726233.6729 913153.2611 934943.1024 666552.5584 584691.022 289926.3143 729975.6494 454996.0541 474880.717 653697.7767 1.110962434 1.39690434 1.430237543 1.019664717 0.894436302 0.443517363 1.116686756 0.696034269 0.726453009 1 19.31826426 3.455831522 2.717223549 0.793578924 1.318489167 0.58053345 0.189297696 0.175827568 2.625741601 0.052539841 0.080078166 2856.482202 -3.455831522 0.524910243 SLS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSPFR 6 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(0.004)LS(0.996)PFR 86.833 0.055729 90319000 120740 114460 99995 91996 88578 65261 95443 79529 88580 108200 TRUE FALSE 116021.3473 111195.7129 118066.3209 96743.92458 91427.19181 66580.62213 96611.05998 77886.69836 78524.76976 100871.5176 1.15018937 1.102349955 1.170462422 0.959080689 0.90637272 0.660053737 0.957763522 0.772137668 0.778463253 1 16.62215934 3.45653454 2.13123881 0.826067403 1.139068155 0.660928295 0.094141457 0.169646914 1.548219058 0.026334161 0.042194396 2861.109896 -3.45653454 0.313000752 SPQYCQVIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQYCQVIHR 10 0 Q13228;Q13228-4;A6PVX1;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 154.24 1.48E-05 384840000 322030 392720 315190 253991 274811 150260 259470 231880 246439 262183 FALSE TRUE 309444.7116 381520.0101 372151.8444 267099.5059 283650.5454 153298.3602 262645.4715 227091.597 218464.2779 244425.1119 1.26601031 1.560887125 1.522559779 1.092766221 1.160480375 0.627179257 1.07454373 0.929084558 0.893788188 1 17.89903299 3.456927901 1.919241113 0.926285013 1.460915096 0.691358528 0.149749225 0.175017794 1.296969812 0.043673971 0.072011142 2863.702516 -3.456927901 0.534630083 HIDFSLR ddPTM_BT-474_Pertuzumab_2h_R1 7 HIDFSLR 7 0 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;; 183.9 0.00063596 5449780000 1323087 1441193 1442552 1111073 1122111 541953 1389791 880117 1135510 1404232 FALSE TRUE 1271379.297 1400091.587 1703253.236 1168415.611 1158204.719 552911.661 1406799.678 861942.2764 1006611.665 1309122.116 0.971169368 1.069488911 1.301065206 0.892518426 0.884718626 0.422353006 1.074613026 0.658412432 0.768921137 1 20.32016825 3.457081821 3.205410326 0.778306037 1.109834623 0.348407953 0.187393269 0.244279137 5.196124064 0.050709966 0.075510119 2864.717629 -3.457081821 0.331528585 NREPVQLETLSIR ddPTM_BT-474_Pertuzumab_2h_R1 5 NREPVQLETLSIR 13 1 P62314;J3QLI9 P62314 SNRPD1 Small nuclear ribonucleoprotein Sm D1 0 ;;;; 290.34 1.47E-40 9223670000 4294461 4207244 3841988 3581920 3746559 2502792 3926219 3690750 4199886 4169935 FALSE TRUE 4126628.716 4087257.52 4536320.696 3766783.32 3867070.473 2553400.169 3974269.243 3614534.723 3723132.549 3887501.588 1.061511776 1.051384142 1.166898738 0.968947082 0.99474441 0.656822926 1.022319645 0.929783472 0.957718592 1 21.89041183 3.457168855 2.757181952 0.917755883 1.088055844 0.342557056 0.101484139 0.296198062 4.559055903 0.028938507 0.044042782 2865.291786 -3.457168855 0.170299961 SPALLLSQLLPYMENRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPALLLSQLLPYMENRR 17 1 Q13268;C9JZP6;Q13268-2;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ; 131.45 4.32E-05 192519000 119140 206777 98073 134355 88809 124157 138363 112911 99308 92736 FALSE TRUE 114483.8771 200879.9224 115796.9727 141289.0777 91665.62214 126667.5396 140056.3278 110579.3484 88034.97217 86454.90812 1.324203328 2.323522479 1.339391542 1.634251666 1.060270887 1.465128382 1.61999279 1.279040725 1.018276164 1 16.39966025 3.457817786 0.190542262 0.884810009 2.18591419 0.308115731 0.31180409 10.51999724 0.634522957 0.928610288 3.546039011 2869.576364 -3.457817786 1.301104182 NLVYDQS(ph)PNR ddPTM_BT-474_Pertuzumab_2h_R1 1 NLVYDQSPNR 10 0 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 NLVYDQS(1)PNR 128.57 0.0034236 0 205450 207740 201150 198730 173250 149860 220270 229870 199190 220660 TRUE FALSE 197420.7869 201815.4586 237502.2796 208986.4791 178822.7436 152890.2719 222965.7302 225123.1042 176578.7863 205714.5017 0.959683373 0.981046338 1.154523758 1.015905429 0.869276313 0.743215819 1.08386005 1.094347274 0.858368199 1 17.65028397 3.458277776 24.7873834 0.955719102 1.036436348 0.120361947 0.11072921 565.0619971 743300.2273 0.034052351 0.046114551 2872.617329 -3.458277776 0.080717247 ASSHSSQTQGGGS(ph)VTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ASSHSSQTQGGGS(0.92)VT(0.08)KK 148.44 1.70E-07 244030000 206730 234710 181540 176250 147810 167190 136600 166600 145190 165980 TRUE FALSE 198650.763 228016.3006 214348.3163 185346.2836 152564.4429 170570.6964 138271.7517 163159.6518 128708.6399 154738.0268 1.28378762 1.47356345 1.385233616 1.197806948 0.985953137 1.10231919 0.893586112 1.054425051 0.831784162 1 17.23946826 3.458703086 2.140755903 0.980973357 1.394519029 0.824754943 0.083676616 0.114999508 1.058449904 0.023624553 0.037873976 2875.431894 -3.458703086 0.413545671 SLHDALCVLAQTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLHDALCVLAQTVK 14 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 172.1 2.91E-06 233970000 806320 945540 795610 782810 693890 419690 965420 729530 856530 1121930 FALSE TRUE 774808.123 918574.125 939394.4252 823210.9179 716209.602 428176.4194 977235.0987 714464.9506 759300.3053 1045940.682 0.740776352 0.878227744 0.898133557 0.787053159 0.684751645 0.409369696 0.934312161 0.683083623 0.725949682 1 19.9963696 3.45883912 5.550234498 0.720247817 0.843346591 0.068927236 0.154332375 0.367677475 35.55643446 0.041460987 0.058444072 2876.332708 -3.45883912 0.123098774 STPALFS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 STPALFSPK 9 0 C9J3S1;C9K0Q9;K7EKK7;K7EMX4;Q9BZR8-2;Q9BZR8-3;Q9BZR8 C9J3S1 BCL2L14 Apoptosis facilitator Bcl-2-like protein 14 1 STPALFS(1)PK 63.32 0.0806 42885000 203820 202860 168610 164120 170520 105790 198530 159890 157890 174780 TRUE FALSE 195854.4891 197074.6314 199081.5777 172590.2529 176004.9307 107929.1463 200959.6695 156588.2156 139966.9891 162941.9949 1.201989022 1.209477222 1.221794159 1.059212838 1.080169239 0.662377715 1.233320297 0.961005882 0.858998868 1 17.31399895 3.458975203 1.98708503 0.965305825 1.212436707 0.394823811 0.136921796 0.345443482 2.741391794 0.040623386 0.06642876 2877.234126 -3.458975203 0.247130881 FLIWDTAGQER ddPTM_BT-474_Pertuzumab_2h_R1 1 FLIWDTAGQER 11 0 Q9UL26;J3QR51;Q13636 Q9UL26 RAB22A;RAB31 Ras-related protein Rab-22A;Ras-related protein Rab-31 0 93.096 0.022113 138630000 467350 527370 414000 448600 364930 461910 468710 392730 514550 499880 FALSE TRUE 449085.4453 512329.9239 488819.0094 471752.2998 376668.3049 471250.1367 474446.2132 384619.9883 456140.4412 466022.6824 0.963655767 1.099366926 1.048916776 1.012294718 0.808261742 1.011217167 1.018075367 0.825324609 0.978794506 1 18.83004065 3.459284694 24.99741667 0.931134083 1.041366435 0.25768806 0.075325552 276.8801719 388038.4508 0.020617707 0.027922129 2879.285257 -3.459284694 0.110232351 KTTPS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTTPSPGR 8 1 Q14686 Q14686 NCOA6 Nuclear receptor coactivator 6 1 KT(0.03)T(0.016)PS(0.954)PGR 57.019 0.06978 66157000 138340 129560 110620 117030 106650 93171 122150 123610 136260 125520 TRUE FALSE 132933.5199 125865.0757 130611.4947 123069.9323 110080.4941 95054.98146 123644.9082 121057.4103 120792.336 117018.4186 1.136005096 1.075600552 1.116161851 1.051714198 0.940710834 0.812307862 1.056627749 1.034515863 1.032250628 1 16.8363761 3.460189419 4.565242264 0.982648702 1.103704502 0.438690915 0.066174094 0.212263981 11.12447135 0.020390262 0.029276028 2885.289657 -3.460189419 0.1210558 T(ph)PDSTFSETFK ddPTM_BT-474_Pertuzumab_2h_R1 5 TPDSTFSETFK 11 0 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 T(0.953)PDS(0.046)T(0.001)FSETFK;T(0.973)PDS(0.027)TFSETFK;T(0.928)PDS(0.072)TFSETFK;T(0.999)PDS(0.001)TFSETFK;T(0.983)PDS(0.017)TFSETFK 212.93 4.77E-08 4372410000 4382540 4431330 3948610 4253970 4480100 4532560 4962860 5211270 5362730 5520330 TRUE FALSE 4211265.492 4304952.807 4662211.663 4473517.901 4624206.485 4624211.469 5023596.965 5103655.453 4753975.373 5146433.132 0.818288198 0.836492518 0.905911248 0.869246289 0.898526487 0.898527456 0.976131786 0.991687898 0.923741794 1 22.29514145 3.460328765 0.343839285 1.001742792 0.775239783 0.787372939 0.027301742 1.259980401 0.22418437 0.031358863 0.110822757 2886.215571 -3.460328765 -0.226503009 KEQQLQER ddPTM_BT-474_Pertuzumab_2h_R1 2 KEQQLQER 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 163.64 0.00053673 166769000 259040 277260 224860 233930 220190 191040 252840 233970 246200 268630 FALSE TRUE 248916.4304 269352.8163 265497.204 246003.1553 227272.6113 194902.9597 255934.3316 229138.4377 218252.4082 250435.4508 0.993934483 1.07553789 1.060142257 0.982301645 0.907509742 0.778256269 1.021957278 0.91496007 0.871491666 1 17.93407927 3.460778175 3.322463239 0.913197245 1.045216147 0.43152098 0.065777485 0.219831738 5.072858072 0.018540891 0.027557588 2889.203785 -3.460778175 0.132018902 S(ph)QS(ph)SSQGDNPLAPGYLPPHYK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSSSQGDNPLAPGYLPPHYK 21 0 A0A494C1T9;Q6ZRV2 A0A494C1T9 FAM83H Protein FAM83H 2 S(0.497)QS(0.582)S(0.482)S(0.44)QGDNPLAPGYLPPHYK 94.019 0.00036061 0 62359 63003 49168 87831 63321 84624 93206 95616 101200 98735 TRUE FALSE 59921.94134 61206.21613 58053.75134 92363.96844 65357.77747 86335.15526 94346.68291 93641.49619 89712.20027 92047.59051 0.650988701 0.664940992 0.630692786 1.003437113 0.710043328 0.937940415 1.024977214 1.017316104 0.974628448 1 16.49009234 3.460825596 0.614469766 1.02274572 0.586585889 0.696759571 0.090171639 0.578608016 0.422145264 0.056300443 0.148116031 2889.519277 -3.460825596 -0.436159831 KYHNVGLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYHNVGLSK 9 1 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 125.48 0.00032484 5397800000 9709100 10016700 8383500 8540200 8313700 6982000 8852700 8623300 9814600 9643800 FALSE TRUE 9329657.638 9731033.523 9898584.94 8980960.745 8581117.711 7123180.824 8961041.991 8445225.842 8700487.754 8990616.836 1.037710516 1.082354381 1.100990635 0.998925981 0.954452611 0.792290557 0.996710476 0.939337756 0.967729791 1 23.09998867 3.461254378 2.963673669 0.935956726 1.073764046 0.518995683 0.056632295 0.197568088 3.541498374 0.016251564 0.024533659 2892.373526 -3.461254378 0.13780732 VTFQT(ph)PLRDPQTHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTFQTPLRDPQTHR 14 1 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91;C9JWI7;Q8IX09 Q9Y6A5 TACC3;ERIC-1s Transforming acidic coiled-coil-containing protein 3 1 VT(0.001)FQT(0.999)PLRDPQTHR 86.367 0.010801 221780000 219490 231450 171060 180720 156920 140320 158430 180500 137480 141810 TRUE FALSE 210912.0881 224849.2726 201974.3472 190046.9809 161967.4743 143157.3665 160368.9137 176772.6119 121873.8468 132205.0824 1.595340242 1.700761185 1.527735118 1.437516451 1.225122903 1.08284314 1.213031382 1.337109049 0.921854475 1 17.01241811 3.462053124 1.504879969 1.152103326 1.642332632 0.785265273 0.114743988 0.193461996 0.886961908 0.038183664 0.068855304 2897.69802 -3.462053124 0.490229306 ATGPEAAGGGGAGGGGGGYRPIIQS(ph)PGYK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATGPEAAGGGGAGGGGGGYRPIIQSPGYK 29 1 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 ATGPEAAGGGGAGGGGGGYRPIIQS(0.999)PGY(0.001)K;ATGPEAAGGGGAGGGGGGYRPIIQS(1)PGYK 221.5 1.11E-34 1276230000 501040 401780 368360 427240 470760 440260 473800 536450 481750 468850 TRUE FALSE 481458.8029 390321.6278 434930.8461 449289.9076 485902.4229 449162.3588 479598.5061 525372.12 427063.7597 437094.3719 1.101498518 0.892991658 0.995050209 1.027901379 1.11166479 1.027609568 1.097242465 1.201964962 0.97705161 1 18.73758528 3.462141178 3.228416516 1.087469318 0.987378508 0.124189406 0.077065699 0.348046509 7.527387082 0.021859022 0.032639531 2898.285596 -3.462141178 -0.10009081 ASS(ph)FSGISILTR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASSFSGISILTR 12 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 ASS(0.911)FS(0.087)GIS(0.002)ILTR;AS(0.004)S(0.996)FS(0.001)GISILTR;AS(0.156)S(0.844)FSGISILTR 231.66 3.06E-12 375269000 456840 457700 245728 398790 610300 366670 412990 626720 483640 413820 TRUE FALSE 438986.1877 444646.8441 290136.5158 419371.5997 629930.8538 374084.3186 418044.2952 613778.013 428739.2148 385791.6028 1.137884248 1.152557082 0.752055031 1.087041804 1.632826762 0.969653865 1.083601333 1.59095742 1.111323346 1 18.55746222 3.462200718 24.99726361 1.269058598 1.009928493 0.138981791 0.236742681 369.9216379 619749.9182 0.06548762 0.08870197 2898.682965 -3.462200718 -0.259130105 GGGAPWPGGAQTYS(ph)PSSTCR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGGAPWPGGAQTYSPSSTCR 20 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 GGGAPWPGGAQTYS(0.999)PS(0.001)STCR 208.13 6.27E-22 205290000 64434 77237 65412 67444 57092 71202 67200 72580 70950 81957 TRUE FALSE 61915.84804 75034.27638 77233.40348 70924.79292 58928.41603 72641.75322 68022.4137 71081.19764 62896.05345 76405.97939 0.810353437 0.982047177 1.010829311 0.928262336 0.771253984 0.95073388 0.890276052 0.930309358 0.823182347 1 16.22139792 3.46288481 24.98393049 0.892029367 0.944235757 0.052094013 0.077257877 570.1865276 1000633.314 0.020637117 0.027953808 2903.252506 -3.46288481 0.05220639 RLEEEADR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEEEADR 8 1 A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 A0A669KAX4 CUL4B Cullin-4B 0 ; 117.01 0.0034643 149260000 143989 165552 124311 151403 157539 178708 173326 161246 159395 193565 FALSE TRUE 138361.7507 160830.6191 146776.763 159216.927 162606.385 182321.5982 175447.2154 157916.2138 141301.1478 180454.6701 0.76673965 0.891252185 0.813371928 0.882309817 0.901092695 1.01034569 0.9722509 0.875101839 0.78302849 1 17.46127695 3.462993696 2.466601275 0.922236733 0.830162797 0.299403843 0.068133251 0.416726645 5.096051512 0.020619249 0.032140346 2903.980501 -3.462993696 -0.092073936 ASS(ph)FSGISVLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASSFSGISVLTR 12 0 Q15032-2;Q15032-4;Q15032;Q15032-3;H7C1X4;H7BZ47;H7C207 Q15032-2 R3HDM1 R3H domain-containing protein 1 1 AS(0.002)S(0.96)FS(0.037)GIS(0.001)VLTR;AS(0.006)S(0.844)FS(0.149)GIS(0.001)VLTR;ASS(1)FSGISVLTR;ASS(0.999)FS(0.001)GISVLTR 185.57 1.35E-05 779050000 835980 887020 467625 829910 1186210 826760 959350 1281730 1090550 1122790 TRUE FALSE 803308.9774 861723.0581 552135.2398 872741.7546 1224365.522 843477.6537 971090.8123 1255261.828 966755.336 1046742.433 0.7674371 0.823242692 0.527479562 0.833769347 1.169691304 0.805812038 0.927726613 1.199207931 0.923584738 1 19.99747506 3.463231413 11.79829748 1.011600969 0.711567765 0.521713571 0.129203675 0.395209606 331.4457769 0.036207511 0.049488556 2905.570472 -3.463231413 -0.300033204 LYQTDPSGTYHAWK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYQTDPSGTYHAWK 14 0 O14818;H0Y586;O14818-2;Q8TAA3-2;Q8TAA3-5;Q8TAA3;A0A087WYS6 O14818 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 ; 223.7 3.42E-12 5139000000 9068200 10105900 9003100 8856800 8122000 5770200 10331500 9055900 10179900 10956700 FALSE TRUE 8713804.719 9817689.627 10630160.44 9313900.509 8383251.506 5886877.397 10457939.99 8868892.5 9024320.43 10214592.95 0.853074103 0.961143501 1.040683706 0.911822973 0.820713223 0.576320312 1.023823469 0.868257066 0.883473328 1 23.28412838 3.463352272 8.443515423 0.855402311 0.956530305 0.098338006 0.121295458 0.34861007 159.9533316 0.033899446 0.046865481 2906.379167 -3.463352272 0.101127995 HYLDFINHYANLFHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HYLDFINHYANLFHEK 16 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 223.76 2.93E-15 556190000 715870 818070 729850 534770 542510 257870 759510 126978 679530 703260 FALSE TRUE 687893.009 794739.4446 861750.1304 562369.5438 559960.3268 263084.3081 768805.1106 124355.8599 602392.6032 655627.5738 1.049213054 1.212181239 1.314389701 0.857757615 0.854082942 0.401270963 1.172624736 0.189674542 0.918803033 1 19.32251701 3.463544907 2.315470642 0.687635791 1.192239352 0.307046319 0.280225766 0.301540819 3.244683472 0.078879602 0.124621383 2907.668601 -3.463544907 0.504603561 GRAS(ph)SHSSQTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 4 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 GRAS(0.717)S(0.088)HS(0.194)S(0.001)QTQGGGSVTK;GRAS(0.764)S(0.089)HS(0.142)S(0.005)QTQGGGSVTK;GRAS(0.942)S(0.049)HS(0.008)SQTQGGGSVTK;GRAS(0.44)S(0.1)HS(0.388)S(0.069)QT(0.003)QGGGSVTK 258.83 6.83E-31 688381000 424739 585700 427449 335185 291847 281976 189594 301016 209006 286817 TRUE FALSE 408139.7303 568996.4095 504698.5429 352483.938 301234.5238 287677.7479 191914.3081 294799.9144 185280.5151 267390.6291 1.526380082 2.127959425 1.887495252 1.318235943 1.126570983 1.075870717 0.717730119 1.102506529 0.692920749 1 18.02858938 3.46373151 1.756267925 0.933965747 1.88924525 0.811215774 0.193392909 0.136288853 0.846478631 0.057498946 0.098057787 2908.918205 -3.46373151 0.955279503 SPSDLHIS(ph)PLAK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPSDLHISPLAK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 SPSDLHIS(1)PLAK;SPSDLHIS(1)PLAK;SPSDLHIS(1)PLAK;SPSDLHIS(1)PLAK;SPSDLHIS(1)PLAK;SPSDLHIS(1)PLAK 162.37 4.05E-05 3360710000 6829330 6670680 5570030 6024850 5668430 5883880 6307350 6092750 6373470 7500940 TRUE FALSE 6562432.233 6480438.738 6576658.326 6335793.231 5850760.199 6002856.085 6384541.236 5966932.583 5649980.405 6992894.653 0.938442885 0.926717627 0.940477249 0.906032987 0.836672149 0.85842221 0.913004064 0.853285067 0.807960178 1 22.73745834 3.463757492 6.303178271 0.871171027 0.932805761 0.205409436 0.049142071 0.203146733 32.75836413 0.012716071 0.017865712 2909.092241 -3.463757492 0.061634734 GPNGYGFHLHGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GPNGYGFHLHGEK 13 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;; 131.35 7.60E-05 1367010000 1936340 1829880 1566180 1352920 1308020 758271 1842920 319970 1824340 1644680 FALSE TRUE 1860665.692 1777693.614 1849223.565 1422744.363 1350093.651 773603.7592 1865474.206 313362.5077 1617248.571 1533284.359 1.213516385 1.159402432 1.20605389 0.927906396 0.880523983 0.504540306 1.216652473 0.204373381 1.054761018 1 20.54819385 3.464244969 1.720945203 0.736838566 1.200565283 0.261708697 0.274605941 0.40603519 2.422602793 0.082134511 0.141111844 2912.359403 -3.464244969 0.463726717 VEKFDLVPVPTNLYGDFFTGDAYVILK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEKFDLVPVPTNLYGDFFTGDAYVILK 27 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396;Q5T0I0;A0A0U1RQL8 P06396-2 GSN Gelsolin 0 159.7 1.33E-11 114120000 187410 198850 149620 162320 104040 62532 167320 185580 197020 198020 FALSE TRUE 180085.81 193178.9927 176659.6623 170697.3547 107386.5411 63796.43988 169367.7122 181747.7081 174655.1156 184607.929 0.975504199 1.04642847 0.95694515 0.924648012 0.581700589 0.345578005 0.917445492 0.984506511 0.94608675 1 17.49410499 3.464476834 24.91374209 0.792304696 0.9887213 0.180700609 0.191786698 413.8904015 815500.0432 0.059891394 0.081143842 2913.914698 -3.464476834 0.196416603 DLEWVER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEWVER 7 0 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 ; 86.833 0.046031 629410000 782720 846210 630770 813270 961180 951070 904500 994720 971390 1001240 FALSE TRUE 752130.4371 822076.9193 744764.1704 855242.9622 992097.2276 970301.287 915569.5416 974178.6844 861121.8796 933425.123 0.805774795 0.880710085 0.797883142 0.916241636 1.062856788 1.03950629 0.980870901 1.043660236 0.922539857 1 19.83217477 3.464561722 4.501193991 1.011716767 0.835333226 0.784239583 0.042409387 0.081917712 4.166491924 0.011342228 0.016377311 2914.484314 -3.464561722 -0.176383541 QSS(ph)FEPEFVISPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSSFEPEFVISPR 13 0 A0A0A0MSU3;Q9H9A7 A0A0A0MSU3 RMI1 RecQ-mediated genome instability protein 1 1 QS(0.049)S(0.951)FEPEFVISPR;QS(0.001)S(0.999)FEPEFVISPR 195.5 1.57E-07 96983000 144772 141488 100952 150013 209315 147160 182883 220490 179046 211436 TRUE FALSE 139114.1502 137452.9008 119196.2721 157755.1889 216047.8071 150135.676 185121.1769 215936.8044 158721.4487 197115.2514 0.705750312 0.697322504 0.604703447 0.800319548 1.096048152 0.761664432 0.939151971 1.095485017 0.805221552 1 17.58867988 3.464631616 6.554008257 0.9547857 0.67618283 0.595899054 0.104030453 0.098239965 18.66103031 0.028605403 0.040137216 2914.953401 -3.464631616 -0.27860287 AIS(ph)SDMFFGR ddPTM_BT-474_Pertuzumab_2h_R1 11 AISSDMFFGR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 AIS(0.943)S(0.057)DMFFGR;AIS(0.76)S(0.24)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.9)S(0.1)DMFFGR;AIS(0.775)S(0.225)DMFFGR;AIS(0.941)S(0.059)DMFFGR;AIS(0.953)S(0.047)DMFFGR;AIS(0.91)S(0.09)DMFFGR;AIS(0.812)S(0.188)DMFFGR 243.91 2.03E-12 4352753000 1370395 1466801 664910 1292599 2087265 1316333 1594086 2034449 1743803 1693708 TRUE FALSE 1316838.448 1424969.272 785074.0278 1359310.189 2154403.774 1342950.155 1613594.901 1992436.917 1545853.794 1578991.649 0.833974296 0.90245523 0.497199607 0.860872311 1.36441746 0.850511246 1.021914779 1.261841327 0.979013281 1 20.59057211 3.464846517 24.90405236 1.091515505 0.746784527 0.453861253 0.167801541 177.5131516 360152.7917 0.045616689 0.061806865 2916.396153 -3.464846517 -0.344730978 LADAMAES(ph)PSRDVVGSGTDTALDVAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LADAMAESPSRDVVGSGTDTALDVAVK 27 1 Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 LADAMAES(0.807)PS(0.193)RDVVGSGTDTALDVAVK 136.12 1.05E-05 111930000 64502 67402 53102 64168 71922 65455 73078 76369 77544 78932 TRUE FALSE 61981.19053 65479.76095 62698.71265 67479.71817 74235.43645 66778.54495 73972.35042 74791.95346 68741.53021 73585.86533 0.842297502 0.889841557 0.852048316 0.917020108 1.00882739 0.907491468 1.005252165 1.016390215 0.934167586 1 16.16714105 3.465042938 3.743427288 0.980423857 0.865398564 0.697688707 0.034676466 0.123820635 3.806090016 0.00979583 0.01440974 2917.715469 -3.465042938 -0.115025293 ELQELVQYPVEHPDK ddPTM_BT-474_Pertuzumab_2h_R1 9 ELQELVQYPVEHPDK 15 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;; 235.16 1.13E-17 90369600000 19772289 18145921 17647219 19874908 19303649 19972471 21980619 22924585 25633755 24693520 FALSE TRUE 18999566.09 17628417.1 20836464.03 20900654.38 19924568.4 20376328.05 22249624.39 22451184.31 22723918.6 23021005.9 0.825314331 0.765753555 0.905106585 0.907894923 0.865495126 0.885118927 0.966492276 0.975247755 0.987094947 1 24.45644754 3.465797481 0.326012375 1.016663281 0.73740708 0.771483163 0.034495384 1.460667574 0.230118843 0.041495104 0.152046904 2922.789113 -3.465797481 -0.279256201 RNS(ph)PSGTTTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSPSGTTTK 10 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 RNS(0.505)PS(0.263)GT(0.223)T(0.006)T(0.002)K 87.719 0.013436 44568000 138000 129610 120200 125500 122210 132420 126630 126920 136340 163010 TRUE FALSE 132606.8074 125913.6497 141922.8138 131977.07 126140.9956 135097.6231 128179.7358 124299.0576 120863.2548 151969.1875 0.872590093 0.828547232 0.933892035 0.868446244 0.830043233 0.888980361 0.843458716 0.817922762 0.795314213 1 17.21341931 3.465974994 23.41128542 0.851025936 0.877997797 0 0.058249232 358.3133126 752584.8441 0.015296205 0.020737758 2923.984015 -3.465974994 0.026971861 LGGKS(ph)PPPPPPPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGGKSPPPPPPPPR 14 1 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P2-8;Q5T5P2-6;Q5T5P2-4 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 LGGKS(1)PPPPPPPPR 93.152 0.0028313 347360000 363560 367990 310630 354900 435550 436220 371690 382590 417970 389370 TRUE FALSE 349351.6733 357495.2855 366767.7509 373216.4315 449559.8613 445040.6673 376238.8534 374689.3828 370523.7979 362997.6231 0.962407606 0.984841946 1.010386095 1.028151172 1.238465028 1.226015376 1.036477457 1.032208915 1.0207334 1 18.46960058 3.466643726 24.9956782 1.095398775 0.991357151 0.276268419 0.078046011 305.647083 729163.2307 0.024092561 0.032653743 2928.489867 -3.466643726 -0.104041624 KLEAAEER ddPTM_BT-474_Pertuzumab_2h_R1 6 KLEAAEER 8 1 P16949;P16949-2;A2A2D0;E5RIR6;E7EVN3;Q9H169-3;Q9H169;Q9H169-4;Q9H169-2;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN4;STMN2 Stathmin;Stathmin-4;Stathmin-2 0 ;;;;; 144.77 0.0009301 37362200000 45385600 45167200 39929000 41664700 40704100 33848300 46407300 44758400 48940700 47749500 FALSE TRUE 43611880.58 43879075.68 47145058.52 43815020.16 42013384.34 34532735.82 46975246.42 43834123.4 43385156.91 44515383.83 0.979703573 0.985705882 1.059073391 0.984266929 0.943794723 0.775748356 1.055258708 0.984696067 0.974610419 1 25.40780066 3.466645408 8.241025631 0.956197473 1.008530339 0.101872164 0.070360585 0.352326001 173.3343587 0.020242604 0.028143 2928.501213 -3.466645408 0.052332866 LLASTLVHSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLASTLVHSVK 11 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 68.069 0.061288 0 126610 148290 108940 120420 119530 103100 127020 125990 126560 131120 FALSE TRUE 121661.9412 144060.9144 128627.8814 126634.8906 123374.791 105184.7526 128574.5088 123388.2625 112193.4394 122239.1256 0.995278235 1.178517219 1.05226441 1.035960377 1.009290523 0.860483516 1.051827785 1.009400729 0.917819387 1 16.8993466 3.466791487 2.0204186 0.977097802 1.086528547 0.332383405 0.065246701 0.369818085 3.029023299 0.019379336 0.031741367 2929.486404 -3.466791487 0.109430745 MGLAMGGGGGAS(ph)FDR ddPTM_BT-474_Pertuzumab_2h_R1 8 MGLAMGGGGGASFDR 15 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR 180.27 6.67E-07 2624160000 2436230 2324730 1309070 2240090 3463820 2239020 2801180 3357390 2954520 2806960 TRUE FALSE 2341019.438 2258430.977 1545648.069 2355701.313 3575236.916 2284294.518 2835461.679 3288058.723 2619135.276 2616842.099 0.894597133 0.863036779 0.59065393 0.900207664 1.366240981 0.872920273 1.083543283 1.256498711 1.000876315 1 21.31939544 3.466941401 24.97228331 1.110257098 0.783230139 0.476183533 0.149644526 159.9724269 392428.2728 0.040457752 0.054838281 2930.497806 -3.466941401 -0.327026959 DKNNMQHR ddPTM_BT-474_Pertuzumab_2h_R1 13 DKNNMQHR 8 1 P31942;P31942-3;P31942-2;P31942-4 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;;;;;;;;;; 164.96 0.00019653 4815985000 4177627 4119579 3328675.4 3464479 3063107 2202620.3 3752721 3237599.2 3711651 4054834 FALSE TRUE 4014360.718 4002092.64 3930241.091 3643281.176 3161634.618 2247158.792 3798647.922 3170741.645 3290319.939 3780196.482 1.061944991 1.058699636 1.039692278 0.963780902 0.836367801 0.594455553 1.00488108 0.838776942 0.870409767 1 21.85002979 3.467031255 2.941550602 0.847620326 1.052646054 0.405446421 0.106505102 0.250048789 4.407934539 0.030391595 0.046118529 2931.104182 -3.467031255 0.205025728 VPLAPITDPQQLQLS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VPLAPITDPQQLQLSPLK 18 0 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 VPLAPITDPQQLQLS(1)PLK;VPLAPITDPQQLQLS(1)PLK;VPLAPITDPQQLQLS(1)PLK;VPLAPITDPQQLQLS(1)PLK 240.42 6.23E-24 14921036000 4392560 4065670 3390500 3439970 2568050 2551270 3348640 3745440 2797310 3039610 TRUE FALSE 4220893.899 3949721.072 4003238.771 3617507.264 2650653.66 2602858.427 3389621.658 3668095.355 2479771.096 2833734.507 1.489516357 1.39382185 1.412707775 1.276586517 0.935392378 0.918525861 1.196167689 1.294438609 0.875089423 1 21.43427317 3.467069553 4.169585532 1.073262973 1.420769417 0.663835145 0.125954288 0.153600876 6.291192093 0.039530822 0.057627293 2931.362674 -3.467069553 0.347506444 ERT(ph)PCAETPAEPVDWAFAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERTPCAETPAEPVDWAFAQR 20 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 ERT(1)PCAETPAEPVDWAFAQR;ERT(1)PCAETPAEPVDWAFAQR 165.47 2.69E-11 121598000 69459 67253 49653 61450 66339 71101 57694 72253 69092 72774 TRUE FALSE 66744.46549 65335.01029 58626.40163 64621.44186 68472.85418 72538.71094 58400.07643 70760.9503 61248.96582 67844.95216 0.983779388 0.963004737 0.864123266 0.952487102 1.009254956 1.069183611 0.860787348 1.042980326 0.902778525 1 16.04995386 3.467371747 22.72903255 0.98268802 0.934361454 0.087310708 0.064469706 151.9001465 354120.6598 0.017218996 0.023356545 2933.403102 -3.467371747 -0.048326566 GS(ph)PHYFSPFRPY ddPTM_BT-474_Pertuzumab_2h_R1 19 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GS(0.999)PHYFS(0.001)PFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(0.998)PHY(0.002)FSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY 196.11 5.54E-07 38117966800 9955371.7 11285167.9 9240540.3 8214428.2 6700999.5 4575369.6 8694502.1 6701856.3 7266700.9 8380653.8 TRUE FALSE 9566304.768 10963325.96 10910511.49 8638375.824 6916543.235 4667886.708 8800908.018 6563460.625 6441815.478 7813024.653 1.224404785 1.403211489 1.396451691 1.105637856 0.885258084 0.597449377 1.126440579 0.840066545 0.824497012 1 22.89744974 3.468131418 2.948192888 0.873509641 1.345152763 0.702503832 0.134995897 0.136368015 2.415211491 0.038158795 0.057931648 2938.538723 -3.468131418 0.471643122 KRRT(ph)ES(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 KRRTESR 7 3 Q6IQ21 Q6IQ21 ZNF770 Zinc finger protein 770 2 KRRT(1)ES(1)R 63.076 0.06502 1215500000 2180600 2048100 1896600 2431800 2344100 2198800 2460100 3092400 2845200 3066300 TRUE FALSE 2095379.741 1989690.193 2239357.81 2557305.489 2419500.105 2243261.243 2490207.44 3028540.859 2522224.824 2858616.77 0.733004775 0.696032506 0.783371116 0.894595427 0.846388411 0.784736613 0.871123218 1.059442767 0.882323525 1 21.44688579 3.468334488 0.316250621 1.018337131 0.612006767 0.641794448 0.064374911 2.097935774 0.308998906 0.083130893 0.310486543 2939.913061 -3.468334488 -0.406330364 IDIIPNPQER ddPTM_BT-474_Pertuzumab_2h_R1 7 IDIIPNPQER 10 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;;;; 132.91 0.00049099 7052450000 1470900 1632270 1330870 1590080 1465730 1496820 1542810 1577250 1622900 1785190 FALSE TRUE 1413415.602 1585719.258 1571387.814 1672144.219 1512876.537 1527086.726 1561691.37 1544679.236 1438675.196 1664277.491 0.84926679 0.952797395 0.944186184 1.004726813 0.90902902 0.917567373 0.938359966 0.928138033 0.864444303 1 20.66646457 3.468476014 0.004041326 1.855166539 1.66E-07 0.079806197 0.045684619 104488.5989 107.1480776 24156.78603 25030.77185 2940.871265 -3.468476014 -1.855166374 FTDYQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTDYQLR 7 0 Q15911;Q15911-2;E7EVZ1;Q86UP3;Q86UP3-4;Q86UP3-2;Q86UP3-5 Q15911;E7EVZ1 ZFHX3;ZFHX4 Zinc finger homeobox protein 3;Zinc finger homeobox protein 4 0 ; 92.191 0.036877 607730000 1080690 1162770 1260800 1067220 870250 676580 1252160 1022960 986120 1260720 FALSE TRUE 1038455.44 1129608.938 1488654.606 1122299.352 898242.3816 690260.9112 1267484.309 1001835.519 874179.7918 1175330.311 0.883543486 0.961099129 1.266584033 0.954879953 0.764246759 0.587290998 1.078406892 0.852386354 0.743773715 1 20.16463483 3.468498895 13.93742524 0.838873604 1.043017005 0.251226262 0.156061542 1.295768683 2088.307291 0.043720048 0.059844879 2941.026213 -3.468498895 0.204143401 HDVGAYMLMYK ddPTM_BT-474_Pertuzumab_2h_R1 1 HDVGAYMLMYK 11 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 94.297 0.0086092 261180000 934680 961780 780970 724720 685290 404670 798300 448240 913210 920480 FALSE TRUE 898151.6723 934350.9761 922108.6516 762122.8861 707332.9752 412852.7047 808069.8342 438983.6874 809546.2293 858135.0697 1.046632056 1.088815746 1.074549548 0.888115301 0.824267648 0.481104571 0.941658094 0.511555468 0.943378563 1 19.71084522 3.469161813 2.129442016 0.737236254 1.074567217 0.356662172 0.166222814 0.278987768 2.535835445 0.046406031 0.075096901 2945.518896 -3.469161813 0.337330963 AYHLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYHLQK 6 0 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ; 118.18 0.022086 1129300000 3051110 3210800 3090820 2832930 2488030 1608570 3245380 2788500 3230890 3581010 FALSE TRUE 2931869.248 3119231.128 3649399.929 2979137.857 2568059.745 1641096.388 3285097.931 2730916.501 2864132.912 3338465.003 0.878208771 0.934330935 1.093137093 0.892367556 0.769233687 0.49157214 0.984014488 0.818015614 0.857919106 1 21.67075349 3.469237478 7.269858823 0.809468261 0.969818028 0.18218329 0.140264839 0.209885413 66.67233135 0.038893347 0.054623843 2946.03212 -3.469237478 0.160349767 LES(ph)VEEYNELMVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LESVEEYNELMVR 13 0 O15018 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 LES(1)VEEYNELMVR;LES(1)VEEYNELMVR 235.71 1.13E-16 68575000 51159 48292 32922 45105 57368 45904 44416 62372 50958 47049 TRUE FALSE 49159.64972 46914.75944 38871.73775 47432.87446 59213.29382 46832.21033 44959.57629 61083.9964 45173.46147 43862.32932 1.120771525 1.069591154 0.886221465 1.081403455 1.349980604 1.067709149 1.025015702 1.392630016 1.029891986 1 15.42069481 3.469823435 24.9763522 1.171411428 1.022247355 0.111405577 0.138878222 279.4413168 956366.8411 0.038142854 0.051751222 2950.009639 -3.469823435 -0.149164072 DVFQHSQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVFQHSQSR 9 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 109.66 0.0024125 168580000 151100 165400 114310 138360 119430 124080 133380 113040 129760 148180 FALSE TRUE 145194.845 160682.9539 134968.3598 145500.7762 123271.5744 126588.9826 135012.3443 110705.6845 115030.1888 138143.6366 1.051042585 1.163158564 0.977014672 1.053257173 0.892343487 0.916357682 0.977333069 0.801380992 0.832685396 1 17.07580958 3.469986064 0.897072336 0.879772452 1.107892298 0.523882495 0.071669392 0.457133668 0.751590676 0.030144136 0.069512234 2951.114529 -3.469986064 0.228119846 KQAVGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQAVGSPR 8 1 A0A0D9SFM0;Q149N8-4;Q149N8;K4DI94;Q149N8-2 A0A0D9SFM0 SHPRH E3 ubiquitin-protein ligase SHPRH 1 KQAVGS(1)PR 51.092 0.092752 121890000 228470 243350 197150 215240 206810 201860 240660 221050 239280 253760 TRUE FALSE 219541.1398 236409.8963 232779.3906 226348.5622 213462.2315 205941.7475 243605.2691 216485.2403 212117.9375 236572.6092 0.928007433 0.999312207 0.983965943 0.956782626 0.902311693 0.870522366 1.029727279 0.915090048 0.896629319 1 17.85192352 3.470425848 24.05816204 0.933532279 0.972826467 0.09553977 0.048117234 220.0804585 790795.2074 0.013130114 0.017824137 2954.104459 -3.470425848 0.039294187 HQTLEVSLSRDS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HQTLEVSLSRDSPLK 15 1 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 HQTLEVSLSRDS(1)PLK 155.53 1.38E-06 237320000 290340 285300 250890 255200 252070 258830 278460 207110 321130 319270 TRUE FALSE 278993.1918 277163.5233 296231.404 268370.9026 260178.0605 264063.7199 281867.8768 202833.1061 284676.6687 297645.5585 0.93733363 0.931186491 0.995248864 0.901645917 0.874120419 0.887175072 0.946991711 0.681458535 0.956428411 1 18.18323584 3.470866148 3.64019915 0.866273034 0.95252639 0.058624709 0.083566896 0.414817337 11.9131881 0.024086449 0.035706998 2957.100928 -3.470866148 0.086253356 IADNHTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IADNHTPK 8 0 B8ZZN6;P63165;B8ZZ67;P63165-2 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 0 77.732 0.032452 461940000 729950 765830 557350 681380 723570 762210 716580 679220 883700 834880 FALSE TRUE 701422.747 743989.2782 658075.5432 716546.1035 746844.2862 777622.4084 725349.7204 665193.8696 783386.0808 778332.834 0.90118612 0.955875489 0.845493746 0.920616569 0.959543596 0.999087247 0.931927434 0.854639353 1.006492398 1 19.57002769 3.470935345 19.39210583 0.944533769 0.902471031 0.191474305 0.049453792 21.838884 68456.63721 0.014534728 0.019804691 2957.572131 -3.470935345 -0.042062738 FT(ph)GSFDDDPDPHRDPYGEEVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FTGSFDDDPDPHRDPYGEEVDR 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.71)GS(0.29)FDDDPDPHRDPYGEEVDR 200.99 2.32E-22 195420000 36415 39268 28094 42466 69585 34801 54264 75200 46380 56920 TRUE FALSE 34991.86154 38148.11509 33171.21075 44657.67535 71823.26472 35504.70006 54928.09906 73647.09372 41115.13684 53064.7577 0.659418097 0.718897376 0.625108117 0.841569382 1.35350217 0.669082487 1.03511448 1.387872044 0.774810602 1 15.69546641 3.471123538 24.65590684 1.06448551 0.682987097 0.382424014 0.209423171 126.6397525 520597.9743 0.058597346 0.079570797 2958.854013 -3.471123538 -0.381498413 AEVMLGHGLFSLLAER ddPTM_BT-474_Pertuzumab_2h_R1 1 AEVMLGHGLFSLLAER 16 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 170.78 5.15E-09 54668000 85479 107760 92251 85787 71278 45031 106120 84612 86804 105350 FALSE TRUE 82138.38618 104686.7903 108922.8078 90214.47735 73570.7216 45941.55767 107418.7283 82864.73263 76950.37383 98214.55066 0.836315858 1.06589899 1.109029233 0.918544928 0.74908169 0.467767325 1.09371501 0.843711365 0.783492602 1 16.58364916 3.471993024 6.977245801 0.820352031 1.010962606 0.190581029 0.16776759 0.213954492 59.01942331 0.046832124 0.066213837 2964.783769 -3.471993024 0.190610576 LMDLLADSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LMDLLADSR 9 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 120.12 0.0016674 28334000 130430 143320 115360 108290 115350 49111 128200 107650 110810 138330 FALSE TRUE 125332.6514 139232.6539 136208.1182 113878.8599 119060.3375 50104.05807 129768.9499 105426.9899 98231.31335 128960.7859 0.971866374 1.079651097 1.056197954 0.883050294 0.923229001 0.388521656 1.006266743 0.817511999 0.761714599 1 16.97657292 3.472315121 2.225546686 0.800293467 1.039453534 0.259278484 0.165603279 0.397262655 3.941345978 0.047983191 0.0769971 2966.983433 -3.472315121 0.239160066 LRPLYDIPYMFEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRPLYDIPYMFEAR 14 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 179.17 1.73E-06 1131060000 958140 1046880 925040 797010 726480 520560 811190 749450 745070 855030 FALSE TRUE 920694.8295 1017024.007 1092215.305 838143.7816 749847.889 531086.0799 821117.5859 733973.5956 660492.7772 797118.0565 1.155029449 1.275876263 1.370205199 1.051467565 0.940698662 0.666257746 1.030107873 0.920784054 0.828600948 1 19.60443388 3.472670293 3.088618603 0.894791066 1.266426874 0.704168083 0.106803345 0.134316862 2.630339866 0.030360022 0.04594617 2969.410862 -3.472670293 0.371635808 TS(ph)PPLLDR ddPTM_BT-474_Pertuzumab_2h_R1 5 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.01)S(0.99)PPLLDR;T(0.108)S(0.892)PPLLDR;T(0.168)S(0.832)PPLLDR;T(0.141)S(0.859)PPLLDR;T(0.025)S(0.975)PPLLDR 182.16 0.0002413 53656940000 8872990 8605050 7579900 8021330 7644850 7645420 7987600 8857280 9283890 9239950 TRUE FALSE 8526223.741 8359642.399 8949756.544 8435311.803 7890753.543 7800015.631 8085354.638 8674374.073 8230021.728 8614119.956 0.989796263 0.97045809 1.038963538 0.979242435 0.9160255 0.905491875 0.938616444 1.006994808 0.955410625 1 23.03827198 3.472677767 24.99640088 0.953907882 0.998859814 0.27381455 0.03384537 179.3274203 1008784.263 0.010215392 0.013886453 2969.461964 -3.472677767 0.044951931 TFDHYCEYR ddPTM_BT-474_Pertuzumab_2h_R1 4 TFDHYCEYR 9 0 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 202.44 1.98E-05 2984240000 3343950 3730120 3146810 2963920 2787580 1533540 3714500 2721610 3283520 3344450 FALSE TRUE 3213264.737 3623740.63 3715508.567 3116888.266 2877245.042 1564549.23 3759959.162 2665407.802 2910788.575 3117927.423 1.030577144 1.162227383 1.191659735 0.999666716 0.922806933 0.50179142 1.205916191 0.854865249 0.933565212 1 21.57215592 3.472777604 3.337735055 0.896836446 1.130121357 0.263873587 0.167724965 0.314251663 7.331931501 0.046690825 0.069988494 2970.144674 -3.472777604 0.233284912 SLYQSAGVAPES(ph)FEYIEAHGTGTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLYQSAGVAPESFEYIEAHGTGTK 24 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 SLYQSAGVAPES(1)FEYIEAHGTGTK 201.8 8.89E-25 168970000 147310 135660 90889 140180 158700 158980 140800 182200 193690 175170 TRUE FALSE 141552.9623 131791.1096 107314.6641 147414.7066 163804.7296 162194.6845 142523.1525 178437.5063 171703.1232 163305.5799 0.866798075 0.807021473 0.657140217 0.902692405 1.003056538 0.993197444 0.872739025 1.092660192 1.051422268 1 17.31721456 3.473040755 4.356133011 1.001607804 0.778446135 0.664155055 0.071622896 0.12124391 5.663300211 0.020626697 0.030127876 2971.944909 -3.473040755 -0.223161669 GS(ph)PTGGAQLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSPTGGAQLLK 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 GS(0.968)PT(0.032)GGAQLLK;GS(0.986)PT(0.014)GGAQLLK 121.66 0.00042701 736540000 714810 731830 623170 635240 643600 590350 653920 698160 649610 718530 TRUE FALSE 686874.4349 710958.9249 735790.6813 668024.8125 664301.9785 602287.2815 661922.8686 683742.752 575868.9962 669863.3231 1.0253949 1.061349234 1.098419119 0.997255394 0.991697792 0.899119657 0.988146157 1.020719792 0.859681335 1 19.35350724 3.473093734 2.876395624 0.964045873 1.061287191 0.459816131 0.048901047 0.247745865 4.158476497 0.014060701 0.021499848 2972.307478 -3.473093734 0.097241318 QMQVLHPAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 QMQVLHPAAR 10 0 P50991 P50991 CCT4 T-complex protein 1 subunit delta 0 ;; 101.38 0.0033706 332586000 567789 661022 526428 496507 455157 340400 516717 435977 506329 581690 FALSE TRUE 545599.1782 642170.2998 621565.2499 522131.7858 469797.5383 347283.1212 523040.7372 426973.9226 448852.6546 542291.6182 1.006099228 1.184178915 1.146182661 0.962824739 0.866319011 0.640399205 0.964500869 0.787351138 0.827696095 1 19.04870935 3.473235326 2.704105526 0.83223939 1.118276918 0.571855475 0.101854124 0.17377429 2.561462128 0.028010816 0.043255578 2973.276689 -3.473235326 0.286037528 CYEMASHLR ddPTM_BT-474_Pertuzumab_2h_R1 14 CYEMASHLR 9 0 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;;;; 255.84 5.75E-15 47210280000 27346060 28445000 23485590 23366570 21361610 12569670 27159920 22629270 25468430 27960980 FALSE TRUE 26277345.74 27633776.45 27729958.55 24572521.48 22048725.59 12823837.34 27492311.23 22161967.67 22577360.6 26067157.92 1.00806332 1.060099323 1.063789103 0.942662087 0.845843097 0.491953798 1.05467237 0.850187341 0.86612283 1 24.63572996 3.473982072 3.225349364 0.843005316 1.043875237 0.274837347 0.139817575 0.318205203 6.862703614 0.039853804 0.060039639 2978.393476 -3.473982072 0.200869921 S(ph)IEEGDGAFGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIEEGDGAFGR 11 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(1)IEEGDGAFGR 158.42 3.13E-05 310450000 52224 68068 28670 59741 99582 62798 68194 82855 73634 86668 TRUE FALSE 50183.02834 66126.76729 33851.30676 62824.24017 102785.1455 64067.81859 69028.57857 81144.0153 65275.37702 80797.89916 0.621093232 0.818421865 0.41896271 0.777547941 1.27212646 0.792939164 0.854336304 1.004283727 0.807884582 1 16.30203016 3.47398775 24.99892186 0.951230764 0.632530467 0.484448497 0.156031281 77.38683319 617383.2601 0.041388174 0.056328863 2978.432418 -3.47398775 -0.318700298 VWEDRPS(ph)SAGSTPFPYNPLIMR ddPTM_BT-474_Pertuzumab_2h_R1 1 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.571)S(0.427)AGS(0.002)TPFPYNPLIMR 94.08 0.0011043 69960000 26923 27873 18666 24689 31762 23514 29187 25493 26043 30534 TRUE FALSE 25870.8194 27078.08933 22039.36142 25963.20225 32783.65358 23989.46919 29544.19924 24966.56064 23086.70782 28465.90498 0.908835304 0.951246389 0.77423716 0.91208069 1.15168141 0.842743949 1.037880203 0.877068924 0.811030172 1 14.79694735 3.474748644 24.99604488 0.950717175 0.878376714 0.099737963 0.102024662 181.3818444 1910883.674 0.027978869 0.038121833 2983.655272 -3.474748644 -0.072340461 TS(ph)VQT(ph)EDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSVQTEDDQLIAGQSAR 17 0 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 T(0.412)S(0.588)VQT(1)EDDQLIAGQSAR;T(0.037)S(0.963)VQT(1)EDDQLIAGQSAR 235.98 1.89E-19 386560000 348090 379110 320590 293790 250920 255000 214840 344140 255710 231260 TRUE FALSE 334486.258 368298.154 378527.7445 308952.5371 258991.0697 260156.2747 217469.2762 337033.3887 226682.8728 215596.5542 1.551445287 1.70827477 1.755722608 1.433012407 1.20127648 1.206681042 1.008686233 1.563259626 1.051421595 1 17.71797459 3.475325484 3.184896454 1.215211125 1.673245356 0.653106722 0.162015089 0.164646246 3.450268943 0.046638379 0.07044041 2987.620865 -3.475325484 0.458034231 RISQVS(ph)SGETEYNPTEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(0.103)QVS(0.794)S(0.101)GET(0.001)EYNPTEAR 148.06 7.63E-08 228590000 75282 82233 53815 80271 115560 73075 86973 119040 96595 93319 TRUE FALSE 72339.89621 79887.79535 63540.56761 84413.79593 119277.0923 74552.62657 88037.40159 116581.7824 85629.94056 86998.42101 0.831508151 0.918267187 0.730364607 0.970291127 1.371025945 0.856942295 1.011942522 1.340044808 0.984270054 1 16.4087016 3.475531257 24.99889653 1.114956763 0.838278537 0.368298503 0.15550015 51.12644942 803829.9234 0.042943337 0.058569979 2989.036764 -3.475531257 -0.276678226 SES(ph)FSSEDLIPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SESFSSEDLIPSR 13 0 Q9P219;Q9P219-2;A0A0A0MR69;Q9P219-3 Q9P219 CCDC88C Protein Daple 1 S(0.024)ES(0.975)FSSEDLIPSR;S(0.033)ES(0.965)FS(0.003)SEDLIPSR 145.71 4.40E-05 239218000 279570 245140 176873 242750 311040 255770 261310 295350 279980 258840 TRUE FALSE 268644.0953 238148.8472 208837.8856 255278.3566 321044.8841 260941.8446 264507.9899 289250.9193 248197.8442 241308.5362 1.113280531 0.98690602 0.865439279 1.057891944 1.330433183 1.081361848 1.096140211 1.198676697 1.02854979 1 17.88051943 3.475698747 24.99965294 1.138169759 0.983926212 0.244173177 0.10368603 53.30286802 936746.4336 0.027767358 0.037880812 2990.189738 -3.475698747 -0.154243547 LGSSLDWDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LGSSLDWDR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;; 137.14 0.00040287 1147659000 1350650 1496750 1269170 1193990 1139220 669825 1439540 1140160 1224350 1470550 FALSE TRUE 1297865.105 1454064.155 1498537.252 1255611.967 1175864.046 683369.3204 1457157.521 1116615.298 1085366.921 1370948.339 0.946691475 1.060626513 1.093066171 0.915871103 0.857701208 0.498464677 1.062882882 0.814483862 0.791690606 1 20.38674278 3.476023392 3.28647702 0.828487832 1.035012554 0.26737268 0.144227191 0.308297753 6.936670303 0.040103455 0.060371517 2992.425811 -3.476023392 0.206524722 FDLSHGS(ph)PQMVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FDLSHGSPQMVR 12 0 A8MY87;A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5 A8MY87 KSR1 Kinase suppressor of Ras 1 1 FDLSHGS(1)PQMVR 142.45 3.95E-05 124540000 89039 119900 93153 96424 86390 100030 107890 93808 103020 105780 TRUE FALSE 85559.25744 116480.5694 109987.8193 101400.4542 89168.81281 102052.6751 109210.3901 91870.83202 91325.6015 98615.42638 0.867605207 1.18115972 1.115320628 1.0282413 0.904207547 1.034855082 1.107437184 0.931607106 0.92607825 1 16.58952572 3.476208224 24.99413422 0.986251372 1.068081534 0.102562195 0.092619815 60.23708458 1648939.176 0.025347144 0.034610045 2993.699631 -3.476208224 0.081830161 SWHDVQVSSAYVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SWHDVQVSSAYVK 13 0 O43399;O43399-7;O43399-5;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 123.02 0.00022828 520470000 751770 728100 611050 643720 567600 476370 715390 610270 808490 866260 FALSE TRUE 722389.9973 707335.3009 721480.3277 676942.4663 585857.3695 486002.5278 724145.1568 597667.7112 716713.6047 807587.4386 0.894503756 0.875862188 0.893377352 0.838228078 0.725441409 0.601795551 0.896677093 0.740065636 0.887474929 1 19.62325895 3.476356398 6.677795387 0.788004548 0.883687604 0.084822428 0.103835084 0.258685054 60.21118308 0.027481519 0.03923645 2994.721208 -3.476356398 0.095683056 TYS(ph)FEQPWPNAR ddPTM_BT-474_Pertuzumab_2h_R1 5 TYSFEQPWPNAR 12 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 T(0.022)YS(0.978)FEQPWPNAR;TYS(1)FEQPWPNAR;T(0.006)YS(0.994)FEQPWPNAR;T(0.312)YS(0.688)FEQPWPNAR;T(0.006)YS(0.994)FEQPWPNAR 237.65 4.32E-16 2601910000 1651240 1716560 1330170 1426710 1471080 1385070 1267850 1631010 1547000 1381070 TRUE FALSE 1586707.715 1667605.389 1570561.308 1500342.674 1518398.624 1413077.064 1283366.328 1597329.074 1371391.046 1287528.899 1.232366681 1.295198415 1.219826064 1.165288543 1.179312267 1.09751095 0.996767008 1.240616094 1.065134186 1 20.29617338 3.476988319 1.077916027 1.10098399 1.267575913 0.516484587 0.068828696 0.488438275 1.157938113 0.026285652 0.056157421 2999.081854 -3.476988319 0.166591923 TS(ph)PDTLR ddPTM_BT-474_Pertuzumab_2h_R1 7 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.004)S(0.996)PDTLR;T(0.237)S(0.754)PDT(0.009)LR;T(0.229)S(0.771)PDTLR;T(0.086)S(0.914)PDTLR;T(0.224)S(0.776)PDTLR;T(0.188)S(0.812)PDTLR;T(0.086)S(0.914)PDTLR 196.95 0.00045454 16584460000 15064760 14500510 13294590 13884420 13994950 14035990 13120540 15391120 16905350 15685240 TRUE FALSE 14476012.52 14086969.65 15697218.15 14600996.58 14445110.28 14319807.33 13281113.09 15073287.99 14986325.54 14622864.72 0.989957358 0.963352251 1.07347079 0.998504524 0.987844075 0.979275101 0.908242902 1.03080267 1.024855651 1 23.80172264 3.477200328 23.97790739 0.987418987 1.009639047 0.048490299 0.040474206 5.45315054 1653698.845 0.011586862 0.015878394 3000.546271 -3.477200328 0.02222006 SMSSLQDDRDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SMSSLQDDRDR 11 1 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 ; 123.2 0.00034184 1036900000 353790 421730 309210 408140 401600 537380 409640 495460 430520 484090 FALSE TRUE 339963.4957 409702.6733 365091.1253 429204.1543 414517.8287 548246.1918 414653.2969 485228.5779 381649.1745 451302.1531 0.753294646 0.90782344 0.808972709 0.951035025 0.918492912 1.214809608 0.918793084 1.075174524 0.845662206 1 18.78373414 3.477559956 1.825204713 1.011921083 0.828201765 0.365664264 0.100865223 0.354737242 2.371211306 0.029264716 0.049865563 3003.03197 -3.477559956 -0.183719318 YGPQYGHPPPPPPPPEYGPHADSPVLMVYGLDQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 YGPQYGHPPPPPPPPEYGPHADSPVLMVYGLDQSK 35 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 105.05 1.27E-05 742830000 605440 592730 441770 545230 586160 606980 576850 554470 672590 653870 FALSE TRUE 581778.7355 575825.9207 521607.6661 573369.3856 605014.3687 619253.5515 583909.6629 543020.0007 596240.4029 609582.8025 0.954388367 0.944622976 0.85567976 0.940593113 0.992505639 1.015864537 0.957884081 0.890805972 0.978112244 1 19.21746268 3.477754844 24.99631385 0.96326341 0.917080763 0.252940291 0.04048652 39.71378391 1566840.108 0.012455444 0.017064054 3004.379871 -3.477754844 -0.046182647 SIQFVDWCPTGFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIQFVDWCPTGFK 13 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ; 246.26 8.42E-17 1666730000 1627690 1602110 1367690 1452280 1373530 1327420 1547350 1546160 1669330 1669950 FALSE TRUE 1564078.075 1556419.391 1614862.007 1527232.345 1417710.84 1354261.342 1566286.932 1514231.256 1479834.657 1556842.799 1.004647403 0.999728034 1.037267223 0.980980447 0.910631979 0.869876742 1.006066209 0.972629514 0.950535698 1 20.57019185 3.477842612 24.93981169 0.951307609 1.011908645 0.342975971 0.038670811 30.5973284 1057881.752 0.011366653 0.015574833 3004.987101 -3.477842612 0.060601036 RGS(ph)LEMSSDGEPLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSLEMSSDGEPLSR 15 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 RGS(0.701)LEMS(0.137)S(0.137)DGEPLS(0.024)R 92.586 0.0019811 0 105090 115890 86176 103870 114100 101470 117180 116950 122480 115990 TRUE FALSE 100982.9666 112584.9307 101749.9202 109230.7431 117770.1301 103521.7929 118614.0839 114534.9416 108576.5839 108133.894 0.933869695 1.041162271 0.940962324 1.010143435 1.089113929 0.957348238 1.09691864 1.059195571 1.004093905 1 16.72245927 3.477970618 24.99685143 1.040415975 0.978354237 0.244549721 0.048053706 39.80855399 1171592.243 0.01255448 0.017202787 3005.872933 -3.477970618 -0.062061738 LSPPYSSPQEFAQDVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSPPYSSPQEFAQDVGR 17 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 184.51 1.47E-09 165805000 26907 33173 22693.7 29484 34062 30082 33765 36736 33531 33915 FALSE TRUE 25855.44469 32226.93852 26794.95641 31005.67277 35157.63516 30690.27865 34178.22617 35977.38876 29724.70145 31617.90684 0.817746881 1.019262239 0.847461426 0.980636477 1.111953278 0.970661303 1.080976876 1.137880156 0.940122368 1 14.94845424 3.477974422 6.574730211 1.052582379 0.90791336 0.414282092 0.076113021 0.127627708 27.75569732 0.020115435 0.028823222 3005.899262 -3.477974422 -0.14466902 GAPVNIS(ph)SSDLTGR ddPTM_BT-474_Pertuzumab_2h_R1 5 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.914)S(0.082)S(0.004)DLTGR;GAPVNIS(0.953)S(0.045)S(0.002)DLTGR;GAPVNIS(0.48)S(0.48)S(0.041)DLTGR;GAPVNIS(0.473)S(0.473)S(0.053)DLTGR;GAPVNIS(0.976)S(0.023)SDLTGR 226.74 2.40E-12 7510990000 2508160 2698650 2316630 2362500 2343810 2484980 2133680 2689630 2502960 2464510 TRUE FALSE 2410138.334 2621687.144 2735296.574 2484428.908 2419200.777 2535227.998 2159792.614 2634088.201 2218834.474 2297586.543 1.048986965 1.141061325 1.190508616 1.081321144 1.052931297 1.103430905 0.940026665 1.146458752 0.965724003 1 21.13168777 3.478086997 4.815392196 1.046687897 1.129812974 0.270729571 0.066135197 0.256650418 16.45924562 0.017516934 0.02553552 3006.678532 -3.478086997 0.083125077 ERPSS(ph)REDTPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 ERPS(0.165)S(0.835)REDTPSR;ERPS(0.385)S(0.615)REDTPSR;ERPS(0.108)S(0.892)REDTPSR;ERPS(0.257)S(0.742)REDTPSR 125.75 0.00023596 1588600000 871901 954529 641954 844610 919685 1012321 907007 957450 911349 942999 TRUE FALSE 837826.145 927306.7675 757969.368 888200.4233 949267.5033 1032790.824 918107.223 937678.3229 807896.4822 879128.8378 0.953018612 1.054801899 0.862182351 1.010318835 1.07978201 1.174788927 1.044337512 1.066599436 0.918973929 1 19.74571508 3.478455686 19.8026477 1.056306028 0.961442625 0.223413042 0.074504036 4.800247074 71235.02406 0.020472254 0.028300045 3009.232103 -3.478455686 -0.094863403 LHFFMPGFAPLT(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHFFMPGFAPLTSR 14 0 Q5JP53;P07437;Q5ST81;A6NNZ2;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 1 LHFFMPGFAPLT(0.827)S(0.173)R 100.58 0.006361 121970000 105370 130000 80851 87837 69956 66312 75061 50494 77903 76129 TRUE FALSE 101252.0239 126292.5273 95462.57422 92370.2781 72206.19827 67652.87407 75979.61897 49451.28125 69059.77804 70972.71502 1.426633092 1.779451825 1.345060199 1.301489989 1.017379682 0.953223701 1.070546885 0.696764683 0.973046868 1 16.11497688 3.47868774 1.108242412 0.896318531 1.609860524 0.791801969 0.133434584 0.203389691 0.509181456 0.047662349 0.100674383 3010.840439 -3.47868774 0.713541993 LFVWEILHSTIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFVWEILHSTIR 12 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 119.76 0.00048234 41874000 36821 42711 49266 38445 34974 21878 47042 34431 36924 45484 FALSE TRUE 35381.99461 41492.9241 58169.46212 40429.15106 36098.97047 22320.38815 47617.71407 33719.98782 32732.54232 42403.32817 0.834415508 0.978529891 1.371813596 0.953442874 0.851323989 0.526382931 1.122971147 0.795220311 0.77193333 1 15.37188988 3.478730658 11.44477926 0.841895222 1.071481356 0.206169791 0.19124627 0.154710908 690.9023178 0.052076861 0.073333901 3011.137991 -3.478730658 0.229586134 NMCNELLPIMKPHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NMCNELLPIMKPHGR 15 1 O75828 O75828 CBR3 Carbonyl reductase [NADPH] 3 0 53.777 0.091412 257280000 288170 242130 246300 239900 214650 219330 212900 277080 280860 280960 FALSE TRUE 276907.9978 235224.6895 290811.8889 252281.2677 221554.4122 223765.0029 215505.5339 271358.2012 248977.9503 261930.3289 1.057181881 0.898042966 1.110264283 0.963161726 0.845852457 0.85429207 0.822758994 1.035993817 0.95055029 1 17.99882359 3.47892097 24.95586352 0.917323835 1.0139947 0.248499653 0.08038865 102.0762351 1415458.63 0.022945144 0.031534089 3012.457787 -3.47892097 0.096670865 AIQLEYSEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AIQLEYSEAR 10 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 127.76 0.00080827 363760000 84935 89291 67971 83078 111640 81836 89975 77891 109640 96695 FALSE TRUE 81615.6463 86744.50811 80254.87171 87365.66554 115231.002 83490.77999 91076.14096 76282.52363 97194.12685 90145.76152 0.905374195 0.962269403 0.890278925 0.969159992 1.278274209 0.926175325 1.010320834 0.846213092 1.078188538 1 16.45997204 3.478946702 24.99766527 1.00925579 0.924622969 0.153895598 0.106612384 163.8889789 2244306.849 0.031084731 0.042725801 3012.636284 -3.478946702 -0.084632821 NCHTASTTTSST(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 1 NCHTASTTTSSTPPK 15 0 H0Y4A4;A0A2R8Y6E3;P81274 H0Y4A4 GPSM2 G-protein-signaling modulator 2 1 NCHT(0.038)AS(0.029)T(0.022)T(0.013)T(0.009)S(0.037)S(0.181)T(0.671)PPK 78.794 0.080416 71808000 92138 88811 98386 85671 70679 93312 94556 56987 112330 113370 TRUE FALSE 88537.1451 86278.19724 116166.5388 90092.49058 72952.45422 95198.83257 95713.20461 55810.19854 99578.76933 105691.3489 0.837695289 0.816322226 1.099111138 0.85241121 0.690240544 0.900724927 0.905591665 0.528048881 0.942165753 1 16.68949777 3.478966864 24.99999815 0.792591731 0.918935879 0.038287247 0.148291522 147.3909212 1996520.72 0.041286663 0.056745886 3012.776146 -3.478966864 0.126344148 SRDEGYQYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDEGYQYHR 10 1 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 0 85.355 0.0085899 18893000 29727 32728 28026 28819 27101 26315 31211 29740 33801 34416 FALSE TRUE 28565.23598 31794.62948 33090.92164 30306.35204 27972.72828 26847.10733 31592.96955 29125.85861 29964.05219 32084.97367 0.890299499 0.990950774 1.031352619 0.944565277 0.871832671 0.836750175 0.984665591 0.907772558 0.933896736 1 14.96961018 3.478968177 24.97507263 0.916847126 0.975389781 0.126008846 0.055626382 116.6535272 1577468.144 0.015223569 0.020936333 3012.785257 -3.478968177 0.058542655 APVPEPGLDLSLS(ph)PRPDS(ph)PQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 2 APVPEPGLDLS(0.163)LS(0.837)PRPDS(1)PQPR;APVPEPGLDLS(0.008)LS(0.992)PRPDS(1)PQPR 73.109 0.0082796 97531000 94555 112313 100117 98020 86831 107532 89381 103390 111432 123806 TRUE FALSE 90859.68606 109109.9432 118210.369 103078.8239 89623.99797 109706.3707 90474.87141 101254.9604 98782.70652 115420.5093 0.787205728 0.945325435 1.024171264 0.89307199 0.776499761 0.950492866 0.783871705 0.877270088 0.855850551 1 16.81654008 3.479803281 24.98170839 0.863375098 0.927723 0.043054305 0.083505024 229.3402498 2136202.55 0.021865476 0.030134461 3018.584105 -3.479803281 0.064347902 KGGHERPPS(ph)PGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGGHERPPSPGLR 13 2 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 KGGHERPPS(1)PGLR;KGGHERPPS(1)PGLR;KGGHERPPS(1)PGLR;KGGHERPPS(1)PGLR 130.4 7.44E-05 1428320000 333645 358692 323428 327590 305039 360687 331597 337634 382959 367322 TRUE FALSE 320605.7845 348462.4554 381878.6342 344496.9592 314850.8565 367980.3383 335655.1833 330661.7399 339487.0998 342442.9538 0.93623122 1.017578115 1.115159854 1.005998095 0.919425712 1.074574128 0.980178391 0.965596565 0.991368332 1 18.38550415 3.479906094 24.99885752 0.986570265 1.028803636 0.072790671 0.05393539 249.7772914 2242201.767 0.014908459 0.020582173 3019.298796 -3.479906094 0.042233372 INPICNDHYR ddPTM_BT-474_Pertuzumab_2h_R1 3 INPICNDHYR 10 0 Q96KB5;Q96KB5-2;E5RFX4 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 0 ;; 103.08 0.0028615 904344000 1137680 1236520 1071560 943510 888540 412406 1124280 800320 1021100 1221360 FALSE TRUE 1093218.208 1201255.66 1265214.729 992204.6642 917120.6961 420745.1319 1138039.275 783793.1123 905189.0088 1138636.199 0.960111938 1.054995143 1.111166788 0.871397436 0.805455418 0.369516736 0.999475755 0.688361316 0.79497649 1 20.11887544 3.479908648 3.032366904 0.75375077 1.041863583 0.321316987 0.17028286 0.269937409 5.067954268 0.046631896 0.071116873 3019.316551 -3.479908648 0.288112812 VYCGPSPSCLVQSSSLSNAHIDYTTKPAIIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VYCGPSPSCLVQSSSLSNAHIDYTTKPAIIFR 32 1 P51610-2;P51610;A6NEM2;P51610-4;H7C1C4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 0 204.89 3.20E-27 206330000 149080 187410 151810 153890 145410 155720 147990 162760 156870 184630 FALSE TRUE 143253.7888 182065.2503 179245.444 161832.2813 150087.2447 158868.7651 149801.1459 159398.9491 139062.7753 172124.8456 0.832266767 1.057751132 1.0413688 0.940202913 0.871967345 0.922985665 0.870305186 0.926065894 0.807918083 1 17.39309584 3.480243828 7.379445818 0.897909053 0.986253059 0.182072477 0.072967291 0.178226081 67.04621755 0.018865631 0.027029974 3021.647703 -3.480243828 0.088344006 LSSERPSS(ph)DGEGVVENGITTCNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSERPSSDGEGVVENGITTCNGK 24 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 LSSERPS(0.108)S(0.892)DGEGVVENGITTCNGK;LSSERPS(0.114)S(0.886)DGEGVVENGITTCNGK 214.47 9.02E-33 1810610000 607100 566240 506170 662810 637250 628280 713260 805380 791920 767190 TRUE FALSE 583373.8608 550091.3896 597646.1787 697017.7035 657747.725 640984.2521 721989.0892 788748.6216 702024.5616 715227.538 0.81564793 0.769113828 0.835602863 0.974539802 0.919634228 0.89619627 1.009453707 1.102793978 0.981540173 1 19.44804276 3.480745031 0.563106509 1.042113106 0.749151624 0.712841168 0.05218373 0.671167742 0.3946329 0.039524065 0.110413403 3025.136887 -3.480745031 -0.292961482 YRPYDGAASAYAQNYR ddPTM_BT-474_Pertuzumab_2h_R1 2 YRPYDGAASAYAQNYR 16 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ; 257.16 1.06E-26 595160000 229370 279880 225570 219670 194842 137573 255030 233050 220160 228320 FALSE TRUE 220405.9668 271898.0964 266335.5168 231007.195 201109.2699 140354.8203 258151.1334 228237.4361 195168.3598 212855.683 1.035471375 1.277382368 1.251249264 1.085276145 0.94481513 0.659389584 1.212798877 1.072263765 0.916904623 1 17.69951608 3.480751339 4.273661355 0.981832602 1.195127126 0.319418314 0.143913782 0.264902398 11.70374083 0.042152947 0.062149293 3025.180828 -3.480751339 0.213294524 FQDRSNPGTFMR ddPTM_BT-474_Pertuzumab_2h_R1 1 FQDRSNPGTFMR 12 1 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 0 65.395 0.05551 401330000 266500 296990 399460 313140 300560 290000 362610 329690 290130 348380 FALSE TRUE 256084.8854 288520.136 471651.3079 329301.1929 310227.7854 295863.9987 367047.7296 322881.7863 257195.6587 324783.9123 0.788477741 0.888344912 1.45220034 1.013908573 0.955182118 0.910956447 1.130129036 0.994143411 0.791897779 1 18.30912065 3.480871363 24.97483936 0.97531355 1.061793539 0.033830968 0.178975892 576.9306908 3842224.833 0.050845586 0.07040993 3026.016995 -3.480871363 0.086479989 S(ph)QEADVQDWEFR ddPTM_BT-474_Pertuzumab_2h_R1 6 SQEADVQDWEFR 12 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR 286.93 1.28E-28 4624540000 2504200 2525390 1574150 2656240 3465000 2649460 3201240 3875240 3390220 3379510 TRUE FALSE 2406333.095 2453368.35 1858633.922 2793328.865 3576454.872 2703033.896 3240417.733 3795214.94 3005376.439 3150612.778 0.763766691 0.778695614 0.589927755 0.886598596 1.135161673 0.857939102 1.028503965 1.204595807 0.953902193 1 21.58720102 3.481519162 5.330298732 1.04209126 0.718787287 0.667952425 0.100619131 0.100185129 9.165007817 0.028792278 0.041906534 3030.534009 -3.481519162 -0.323303974 S(ph)VASDVPEELDFLVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVASDVPEELDFLVPK 16 0 Q14966;Q14966-5;A0A096LNS4;A0A096LPK8 Q14966 ZNF638 Zinc finger protein 638 1 S(0.5)VAS(0.5)DVPEELDFLVPK 59.607 0.072557 0 6088.7 9111.8 4146.6 7038.9 7813.1 8516.3 6507.8 9612.6 8146.2 7610.5 TRUE FALSE 5850.746873 8851.940385 4895.982861 7402.178473 8064.415457 8688.505421 6587.444403 9414.096451 7221.477528 7095.034056 0.824625622 1.247624792 0.690057697 1.043290055 1.136628153 1.224589671 0.928458461 1.32685712 1.017821404 1 12.79259389 3.481609841 22.74688573 1.125725214 0.938991449 0.184703752 0.169414706 88.79674908 449998.8667 0.043784878 0.060994553 3031.166835 -3.481609841 -0.186733765 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR 36 1 Q96EK6;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 254.47 3.64E-62 781480000 10663 19332 0 11667 13666 15971 13950 12838 14898 17690 FALSE TRUE 10246.27817 18780.67029 0 12269.13527 14105.5793 16293.94456 14120.72427 12572.89081 13206.8415 16491.84054 0.621293793 1.138785585 0 0.743951849 0.855306554 0.98800037 0.856224885 0.762370384 0.800810647 1 14.0094648 3.48177164 24.62655719 0.856902578 0.596914676 0.192667314 0.26462704 289.9895043 1535669.909 0.071476486 0.099386623 3032.296325 -3.48177164 -0.259987902 KNIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 KNIIEATHMYDNAAEACSTTEEVFNSPR 28 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 KNIIEATHMYDNAAEACSTTEEVFNS(1)PR;KNIIEATHMYDNAAEACSTTEEVFNS(1)PR;KNIIEATHMYDNAAEACSTTEEVFNS(1)PR 246.81 5.75E-46 1656810000 708326 852307 555103 707608 740352 816152 745560 700951 843817 875967 TRUE FALSE 680643.8368 828000.0389 655422.4603 744127.7337 764166.0945 832655.1526 754684.3863 686476.1169 748030.4317 816636.9749 0.833471736 1.013914462 0.802587295 0.911209946 0.935747606 1.019614808 0.924136929 0.840613563 0.915988934 1 19.63933536 3.481909244 24.15389938 0.927609059 0.889802693 0.10184236 0.069043809 437.9725135 2209433.678 0.019464379 0.027105473 3033.257246 -3.481909244 -0.037806365 YADLSHNR ddPTM_BT-474_Pertuzumab_2h_R1 6 YADLSHNR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;;;; 157.91 0.00036932 2367510000 2592830 2950440 2551820 2465190 2255770 1390920 3028090 2506290 2710750 3119160 FALSE TRUE 2491499.337 2866296.34 3012990.639 2592418.751 2328328.891 1419045.355 3065148.671 2454534.236 2403037.024 2907896.515 0.856804678 0.985694066 1.036140944 0.891509976 0.800691799 0.487997199 1.054077632 0.844092705 0.826383268 1 21.4715445 3.481948428 5.863468236 0.829101911 0.962975831 0.125006665 0.1464201 0.313354713 41.45730546 0.040474642 0.058682602 3033.530932 -3.481948428 0.13387392 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHT(ph)LRR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHTLRR 39 1 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 NNSQIASGQNQPQAAAGS(0.024)HQLS(0.304)MGQPHNAAGPS(0.304)PHT(0.367)LRR 84.408 0.00024583 293960000 46611 66112 36920 37741 33348 48276 34879 20636 42943 36731 TRUE FALSE 44789.39059 64226.55049 43592.26528 39688.81753 34420.66871 49252.1738 35305.85964 20209.85939 38068.29067 34243.17665 1.307980011 1.875601412 1.273020483 1.159028496 1.005183282 1.438306215 1.031033423 0.590186465 1.111704415 1 15.06352892 3.482032878 0.582620397 0.882523188 1.659424697 0.416252588 0.243263419 1.052018636 0.670484837 0.169469169 0.468245774 3034.120874 -3.482032878 0.776901508 NDQWAWETLR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDQWAWETLR 10 0 Q13464;A0A0U1RQV4 Q13464 ROCK1 Rho-associated protein kinase 1 0 ; 133.81 0.00043588 139875000 190662 219870 181629 167769 178756 120721 196459 175491 162874 185231 FALSE TRUE 183210.7183 213599.5229 214453.4006 176427.5782 184505.8491 123162.0613 198863.324 171867.0495 144385.2263 172685.1394 1.06095243 1.236930541 1.24187525 1.021672037 1.068452385 0.713217488 1.15159489 0.995262535 0.836118423 1 17.39778441 3.483048891 2.410925311 0.963241297 1.183786661 0.385262512 0.122719188 0.304464905 3.53997958 0.035326349 0.056130833 3041.227373 -3.483048891 0.220545365 YGQNCHK ddPTM_BT-474_Pertuzumab_2h_R1 4 YGQNCHK 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;; 94.401 0.014227 1423030000 868230 866730 738637 797220 799921 784349 886180 824570 904920 908520 FALSE TRUE 834298.6117 842011.709 872125.1368 838364.6197 825651.1854 800209.0742 897025.3359 807542.3413 802197.2753 846985.1312 0.985021556 0.994128088 1.029681756 0.989822122 0.974811901 0.944773461 1.059080382 0.953431544 0.947120848 1 19.69197712 3.483137004 22.82325012 0.979969213 1.003343844 0.089886022 0.032897923 213.4343456 809756.2049 0.008978393 0.012604152 3041.844464 -3.483137004 0.023374631 SVISHSVTSDMQTIEQES(ph)PIMAKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVISHSVTSDMQTIEQESPIMAKPR 25 1 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 SVISHSVTSDMQTIEQES(1)PIMAKPR 309.37 1.15E-74 593680000 132510 144570 110090 113150 118790 125270 115780 134920 108270 126640 TRUE FALSE 127331.3627 140447.0051 129985.7119 118989.6851 122610.9882 127803.0452 117196.9503 132133.8549 95979.6435 118062.56 1.078507553 1.189598169 1.100990119 1.007852829 1.038525577 1.082502745 0.992668211 1.119185073 0.812955805 1 16.849192 3.483278165 0.331725182 0.969137525 1.182093934 0.310379778 0.079666283 4.059720309 0.659558772 0.088701906 0.326901084 3042.833334 -3.483278165 0.212956409 GGKNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGKNIR 6 1 Q9NYT6 Q9NYT6 ZNF226 Zinc finger protein 226 0 71.995 0.079129 368400000 926460 887840 765770 773710 715430 705160 786380 787090 667640 963390 FALSE TRUE 890252.9189 862519.6725 904161.6735 813641.2658 738442.4557 719418.8183 796003.9537 770836.3164 591852.3062 898138.7372 0.991219822 0.960341244 1.00670602 0.905919355 0.822191968 0.801010789 0.88628173 0.858259737 0.658976483 1 19.77657879 3.48337086 3.333715577 0.834718636 0.98271439 0.406854418 0.080062859 0.230067245 5.336306163 0.021536752 0.032548792 3043.482859 -3.48337086 0.147995755 RGNDPLTSS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.003)S(0.025)S(0.973)PGR;RGNDPLT(0.054)S(0.166)S(0.779)PGR 171.36 4.10E-05 5552400000 1290940 1379920 1073960 1266920 1313560 1454720 1347790 1344790 1418710 1531250 TRUE FALSE 1240488.638 1340566.033 1268048.462 1332305.893 1355811.85 1484135.435 1364284.657 1317019.617 1257663.989 1427537.074 0.868971224 0.93907616 0.888277079 0.933289872 0.949755965 1.03964756 0.955691227 0.922581725 0.881002681 1 20.44509678 3.483913279 3.254812184 0.95546841 0.902946845 0.27341268 0.042937846 0.390736638 8.576039281 0.012793724 0.019395914 3047.28644 -3.483913279 -0.052521565 DIYQDLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 DIYQDLNR 8 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 ;;; 140.5 0.0015088 603890000 789900 965570 774100 722620 735730 440760 824710 734860 741320 858760 FALSE TRUE 759029.8347 938032.889 913997.0898 759914.5048 759395.4236 449672.4692 834803.0477 719684.8842 657168.4615 800595.4203 0.94808166 1.171669067 1.141646663 0.949186675 0.948538306 0.561672547 1.042727733 0.898937049 0.820849639 1 19.61071384 3.484028774 2.704170497 0.872415568 1.093928532 0.320924035 0.134659712 0.308035421 4.528330706 0.038268753 0.059551381 3048.096931 -3.484028774 0.221512964 SGGMERPFVLAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SGGMERPFVLAR 12 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 138.89 6.05E-05 2972160000 2111200 2421050 1962730 2008410 2002400 1661350 2150760 2110030 2376520 2213150 FALSE TRUE 2028691.97 2352004.024 2317438.972 2112064.281 2066809.015 1694943.635 2177081.644 2066457.143 2106747.413 2063251.379 0.983250025 1.139950298 1.123197588 1.023658243 1.001724286 0.82149158 1.055170333 1.001553744 1.021081306 1 20.97648817 3.484162792 3.419619083 0.982978516 1.087366001 0.282958375 0.06984605 0.297027841 7.308771878 0.019903476 0.030015974 3049.037682 -3.484162792 0.104387485 RVNTTQK ddPTM_BT-474_Pertuzumab_2h_R1 6 RVNTTQK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 ;;;;; 113.94 0.0096466 1869006000 1715910 1817100 1526080 1576570 1475990 1037113 1950900 1668290 1660320 1995990 FALSE TRUE 1648850.34 1765278.087 1801876.603 1657936.967 1523466.559 1058084.135 1974775.698 1633839.229 1471847.434 1860799.819 0.886097646 0.948666304 0.968334468 0.890980829 0.818715986 0.568617927 1.061251015 0.878030625 0.790975697 1 20.82749143 3.484224644 6.059738632 0.850524555 0.935207613 0.079038962 0.12459342 0.416182764 62.54726582 0.034591978 0.050276595 3049.471955 -3.484224644 0.084683057 FEPYANPTKR ddPTM_BT-474_Pertuzumab_2h_R1 2 FEPYANPTKR 10 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 145.91 4.74E-05 2587300000 3307400 2702800 2736800 2461000 2012880 1924700 2395400 2462000 2453700 2447000 FALSE TRUE 3178143.151 2625718.79 3231400.64 2588012.505 2077626.113 1963618.753 2424715.622 2411158.84 2175166.263 2281262.51 1.393151002 1.150993706 1.416496622 1.134465014 0.91073522 0.860759664 1.062883211 1.056940544 0.953492311 1 21.12140104 3.48422751 4.829122713 0.98462197 1.301740099 0.753952286 0.088356117 0.095825264 6.178666483 0.024750522 0.036342745 3049.492083 -3.48422751 0.317118129 VHATSTYR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHATSTYR 8 0 Q9H074;Q9H074-3;Q9H074-2;D6REB4 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ; 91.853 0.012192 195769000 140051 200304 174605 126930 96541 50307 154389 64710 113347 161495 FALSE TRUE 134577.6521 194591.526 206160.0076 133480.8725 99646.32894 51324.24201 156278.4588 63373.71589 100480.3237 150556.7998 0.893866317 1.292479159 1.369317147 0.886581494 0.661852066 0.340896207 1.038003325 0.420928952 0.667391469 1 17.19994834 3.484849561 3.682752444 0.654511499 1.193753958 0.466974569 0.23523175 0.173816311 5.120355503 0.062955134 0.094307319 3053.863078 -3.484849561 0.539242459 TQS(ph)FEIPQPDSGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQSFEIPQPDSGPR 14 0 A0A1B0GW72;Q96PX9 A0A1B0GW72 PLEKHG4B Pleckstrin homology domain-containing family G member 4B 1 TQS(1)FEIPQPDSGPR;TQS(1)FEIPQPDSGPR 314.72 8.03E-56 441120000 365360 346140 218160 339150 426570 316100 363630 447150 382320 377250 TRUE FALSE 351081.3273 336268.4261 257586.3649 356653.5721 440291.0115 322491.7586 368080.2127 437916.1962 338920.6364 351698.5215 0.998245104 0.956126926 0.732406733 1.014088915 1.251898955 0.916955116 1.046578789 1.245146537 0.963668073 1 18.42397974 3.484884289 24.95262167 1.089100834 0.896913225 0.287711548 0.12116307 395.4720916 1271161.3 0.033018835 0.046747137 3054.107283 -3.484884289 -0.192187609 S(ph)FEVEEVETPNSTPPR ddPTM_BT-474_Pertuzumab_2h_R1 7 SFEVEEVETPNSTPPR 16 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR 355.38 2.22E-87 5129934000 1294550 1319857 819972 1421357 1976385 1432957 1759365 2024273 1901845 1743236 TRUE FALSE 1243957.555 1282215.971 968159.1806 1494713.405 2039957.218 1461932.372 1780896.635 1982471.055 1685955.529 1625165.073 0.765434586 0.788975835 0.595729749 0.919730205 1.255230778 0.89955931 1.095825073 1.21985827 1.037405711 1 20.63215483 3.485061284 6.16436624 1.096318145 0.727646528 0.702500544 0.107126376 0.079541098 12.77859394 0.029026508 0.042223371 3055.352226 -3.485061284 -0.368671618 SLS(ph)YEEPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSYEEPR 8 0 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 S(0.004)LS(0.996)YEEPR;S(0.007)LS(0.993)YEEPR;S(0.082)LS(0.918)YEEPR 121.5 0.0015005 1071640000 2372000 2456850 1870330 2404960 2892110 2446650 2603350 3128810 2845790 2661350 TRUE FALSE 2279299.618 2386783.044 2208340.236 2529080.274 2985137.345 2496122.939 2635210.576 3064198.98 2522747.85 2481094.394 0.91866703 0.961988004 0.890066997 1.01934061 1.203153476 1.006057224 1.062116211 1.235019106 1.01678834 1 21.24254519 3.48514455 6.475644697 1.103511413 0.931055858 0.465847533 0.077136559 0.119067232 23.55061194 0.021082683 0.030626108 3055.938082 -3.48514455 -0.172455555 LGPLFSLLNENHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGPLFSLLNENHR 13 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 208.08 4.87E-08 719630000 761760 827180 696500 657350 615970 331370 794760 636590 693930 774260 FALSE TRUE 731989.577 803589.6363 822373.0436 691275.9123 635783.2345 338070.5284 804486.5106 623444.194 615157.9756 721818.6806 1.014090653 1.113284621 1.139306956 0.95768637 0.880807399 0.468359351 1.114527141 0.863713022 0.852233382 1 19.46127695 3.485444053 3.258499685 0.857480649 1.089842081 0.290566025 0.157369311 0.307248181 6.756257152 0.044495926 0.067526315 3058.046278 -3.485444053 0.232361432 FLTWILNR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLTWILNR 8 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 216.16 1.87E-05 569040000 318800 343430 320300 284650 236300 151457 349980 270800 298390 341320 FALSE TRUE 306340.9435 333635.7127 378185.335 299340.8206 243900.8041 154519.5643 354263.1599 265207.8854 264518.0182 318202.0924 0.962724479 1.048502573 1.188506751 0.940725494 0.766496544 0.485601974 1.113327563 0.83345739 0.831289374 1 18.2795838 3.485768351 6.52945643 0.834317972 1.06549601 0.288909513 0.160480759 0.186690101 38.05900109 0.044302742 0.064416838 3060.330641 -3.485768351 0.231178038 QNS(ph)SSSDSGGSIVR ddPTM_BT-474_Pertuzumab_2h_R1 3 QNSSSSDSGGSIVR 14 0 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 QNS(0.88)S(0.106)S(0.013)S(0.001)DSGGSIVR;QNS(0.435)S(0.435)S(0.029)S(0.047)DS(0.047)GGS(0.006)IVR;QNS(0.386)S(0.386)S(0.208)S(0.019)DSGGSIVR 171.15 3.21E-06 375180000 393966 405962 279777 398914 484260 394552 432140 529450 433309 416453 TRUE FALSE 378569.3732 394384.3612 330338.9275 419501.9993 499836.6627 402530.1118 437428.6586 518516.6725 384121.5789 388246.2674 0.975075371 1.015809795 0.850848946 1.080504913 1.287421682 1.036790681 1.126678336 1.335535499 0.989376103 1 18.56661253 3.485958432 24.11376663 1.156707525 0.956030465 0.31861198 0.114849431 262.8732263 717294.7798 0.030839345 0.044017094 3061.670376 -3.485958432 -0.20067706 ARPATDS(ph)FDDYPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ARPAT(0.016)DS(0.984)FDDYPPR;ARPAT(0.006)DS(0.994)FDDYPPR;ARPAT(0.01)DS(0.99)FDDYPPR 119.4 0.00011474 1079780000 568460 532190 296251 504720 681050 488484 559430 620610 510540 552490 TRUE FALSE 546243.9547 517012.4623 349790.1458 530768.6597 702956.5918 498361.4812 566276.4717 607794.1866 452585.6396 515069.3602 1.060525042 1.003772506 0.679112704 1.030479972 1.364780447 0.967561885 1.099417895 1.180023961 0.878688725 1 18.9744072 3.486043366 24.99911907 1.10139282 0.911966318 0.183898174 0.154294203 601.3044605 1684811.587 0.041177993 0.058764208 3062.269195 -3.486043366 -0.189426501 SGMNS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGMNSPLR 8 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 S(0.01)GMNS(0.99)PLR 81.525 0.023744 209430000 342570 362690 265900 276050 258930 134570 314030 252540 235280 262340 TRUE FALSE 329181.9857 352346.4363 313954.0449 290296.9736 267258.7186 137291.0976 317873.1931 247324.9607 208572.0008 244571.4781 1.345954108 1.440668548 1.283690344 1.186961684 1.092763231 0.561353673 1.299714895 1.011258396 0.852805905 1 17.89989664 3.486334531 1.831699062 0.974279779 1.377434199 0.502888592 0.176455043 0.300123908 2.017012389 0.054232169 0.092998171 3064.322934 -3.486334531 0.40315442 SCAADS(ph)DPEPER ddPTM_BT-474_Pertuzumab_2h_R1 2 SCAADSDPEPER 12 0 Q13207 Q13207 TBX2 T-box transcription factor TBX2 1 S(0.001)CAADS(0.999)DPEPER;SCAADS(1)DPEPER 91.202 0.0088432 127974000 329590 375160 274780 330910 347130 365250 328280 390570 359270 385370 TRUE FALSE 316709.2584 364460.8041 324438.8584 347988.3048 358295.7517 372635.6053 332297.5888 382504.593 318487.1758 359268.5466 0.881539064 1.014452302 0.90305389 0.9686022 0.99729229 1.037206315 0.924928141 1.064675983 0.886487778 1 18.45470311 3.486888862 6.813431852 0.99113183 0.940179177 0.131647521 0.057721275 0.276165394 66.74059006 0.014612827 0.021271098 3068.236712 -3.486888862 -0.050952653 HAEQQALR ddPTM_BT-474_Pertuzumab_2h_R1 2 HAEQQALR 8 0 K7EQA8;Q86X55-2;Q86X55-1;Q86X55;K7EK20;K7EPK1 K7EQA8 CARM1 Histone-arginine methyltransferase CARM1 0 ; 141.2 0.0006374 144141000 157166 176283 148485 114955 101001 34969 132706 69411 112989 130034 FALSE TRUE 151023.779 171255.5814 175319.5425 120887.8413 104249.7889 35676.09714 134330.0957 67977.63859 100162.9624 121226.6814 1.24579653 1.412688853 1.446212505 0.997204905 0.859957459 0.294292451 1.108090185 0.560748161 0.82624519 1 16.88734774 3.486974635 2.527678713 0.739622994 1.37251183 0.590790659 0.219379345 0.175987857 2.250157856 0.060073648 0.094822249 3068.842745 -3.486974635 0.632888837 IYHPNINSNGSICLDILR ddPTM_BT-474_Pertuzumab_2h_R1 2 IYHPNINSNGSICLDILR 18 0 P61077-3;P61077-2;P61077;A0A087WY85;H9KV45;D6RAH7;P62837-2;D6RA11;P51668;Q9Y2X8;C9J9H9;A0A087WW00;D6RFM0;D6RAW0;A0A0A0MQU3;P62837 P61077-3;A0A0A0MQU3 UBE2D3;UBE2D2;UBE2D1;UBE2D4 Ubiquitin-conjugating enzyme E2 D3;Ubiquitin-conjugating enzyme E2 D2;Ubiquitin-conjugating enzyme E2 D1;Ubiquitin-conjugating enzyme E2 D4 0 ; 262.59 7.59E-31 1327080000 1035510 1177280 853600 911760 871690 547480 1074080 802510 953540 989410 FALSE TRUE 995041.1244 1143705.127 1007864.508 958816.0429 899728.7005 558550.4207 1087224.912 785937.8881 845298.1368 922396.3794 1.078756537 1.239928032 1.092658786 1.039483745 0.97542523 0.605542729 1.178695989 0.852060899 0.91641528 1 19.81502732 3.487243636 2.043197109 0.912756833 1.151477681 0.331853811 0.139408048 0.353214282 2.946759258 0.040289099 0.066865957 3070.744169 -3.487243636 0.238720848 ELDQDMVT(ph)EDEDDPGSHKR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELDQDMVTEDEDDPGSHKR 19 1 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 ELDQDMVT(1)EDEDDPGSHKR;ELDQDMVT(1)EDEDDPGSHKR;ELDQDMVT(1)EDEDDPGSHKR;ELDQDMVT(1)EDEDDPGSHKR 193.54 3.86E-15 2806020000 2734740 2572600 2230950 2046290 2336950 2054200 1859580 2267430 2350280 2265280 TRUE FALSE 2627863.337 2499231.967 2634132.292 2151899.272 2412120.119 2095737.331 1882338.096 2220606.778 2083486.068 2111850.568 1.244341516 1.183432202 1.247309981 1.018963796 1.142183143 0.992370087 0.891321633 1.051498061 0.986568889 1 21.01007632 3.487274482 0.988946971 0.986940107 1.240133602 0.712291745 0.061704009 0.314262987 0.625407647 0.024094137 0.054384212 3070.962279 -3.487274482 0.253193495 YIEVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 YIEVFK 6 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 118.03 0.051687 1612730000 2916500 3027900 2481600 2601300 2558800 2576700 2257800 2752600 3037100 3200500 FALSE TRUE 2802519.956 2941547.257 2930080.323 2735553.405 2641106.126 2628802.639 2285431.632 2695757.848 2692341.141 2983727.284 0.939268133 0.98586331 0.982020153 0.916824208 0.885170082 0.881046553 0.765965323 0.903486677 0.902341563 1 21.50868425 3.487847628 2.621091054 0.877097001 0.970670597 0.275989215 0.05505385 0.301128193 4.145992702 0.015503479 0.024322408 3075.017756 -3.487847628 0.093573596 SADTLWGIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SADTLWGIQK 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 133.13 0.00047738 897180000 1219380 1200210 1002770 992800 838060 709610 1042640 983210 1010440 944780 FALSE TRUE 1171725.282 1165981.186 1183992.845 1044038.527 865016.961 723958.8004 1055400.14 962906.3699 895739.0873 880789.2091 1.330312939 1.323791407 1.344240862 1.185344366 0.98209305 0.821943313 1.198243722 1.093231343 1.016973276 1 19.74843727 3.488374209 3.370372042 1.032194259 1.32940095 0.71122619 0.089775806 0.146180113 3.468495031 0.027570417 0.041776905 3078.748469 -3.488374209 0.297206691 GWGAEYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GWGAEYR 7 0 Q15796-2;Q15796;B7Z5N5;P84022-3;P84022-2;P84022;H3BQ00;P84022-4 Q15796-2 SMAD2;SMAD3 Mothers against decapentaplegic homolog 2;Mothers against decapentaplegic homolog;Mothers against decapentaplegic homolog 3 0 102.98 0.019726 239740000 492620 486400 448590 447250 448870 328470 523930 501600 482130 520130 FALSE TRUE 473367.8658 472528.3482 529660.1918 470332.6261 463308.3112 335111.8885 530342.0121 491241.7847 427400.6237 484901.1318 0.976215221 0.974483905 1.092305538 0.969955719 0.955469643 0.691093228 1.09371164 1.013076177 0.881418078 1 18.8873311 3.489205352 21.11368607 0.945586706 1.013813267 0.093474553 0.10371128 207.2101187 362040.7994 0.029163766 0.04260546 3084.646154 -3.489205352 0.068226562 AS(ph)SHSSQTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 6 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.42)S(0.308)HS(0.076)S(0.196)QTQGGGSVTK;AS(0.228)S(0.228)HS(0.228)S(0.228)QT(0.086)QGGGSVTK;AS(0.246)S(0.246)HS(0.246)S(0.246)QT(0.016)QGGGSVTK;AS(0.388)S(0.388)HS(0.112)S(0.112)QTQGGGSVTK;AS(0.531)S(0.462)HS(0.001)S(0.006)QTQGGGSVTK;AS(0.445)S(0.445)HS(0.11)SQTQGGGSVTK 215.08 1.06E-14 14286410000 12218490 17832690 10939760 8322280 8637220 7080616 4134587 6420839 5984096 7056008 TRUE FALSE 11740977.9 17324119.14 12916817.99 8751793.868 8915044.025 7223790.907 4185187.313 6288246.431 5304806.509 6578098.293 1.784858994 2.633606001 1.963609756 1.330444374 1.355261601 1.098157945 0.636230583 0.95593683 0.806434667 1 22.64923914 3.489381806 1.133229895 0.875358912 2.266819351 0.814863184 0.249388883 0.191326321 0.499153798 0.087977616 0.186234005 3085.8997 -3.489381806 1.391460438 LWEAGWK ddPTM_BT-474_Pertuzumab_2h_R1 2 LWEAGWK 7 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 135.87 0.0070624 853170000 1182700 1259460 1194610 1117170 1065250 797460 1275530 1125480 1356870 1528510 FALSE TRUE 1136478.776 1223541.434 1410502.601 1174827.278 1099514.734 813585.1876 1291140.318 1102238.445 1202843.806 1424982.656 0.797538673 0.858636018 0.989838434 0.824450229 0.771598678 0.570943923 0.906074409 0.773510077 0.84411119 1 20.44251293 3.489945467 22.97053831 0.794108079 0.884247011 0.062032566 0.112909367 451.3911684 808522.974 0.0297267 0.043676579 3089.907416 -3.489945467 0.090138932 FLTTYDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLTTYDR 7 0 P78356;P78356-2 P78356 PIP4K2B Phosphatidylinositol 5-phosphate 4-kinase type-2 beta 0 98.457 0.026169 62854000 112690 125550 134980 107290 98011 57576 130950 107940 123700 133430 FALSE TRUE 108285.9502 121969.4369 159373.8886 112827.2498 101163.6128 58740.22617 132552.6053 105711.0013 109658.0946 124392.6673 0.87051715 0.980519508 1.281216105 0.907024926 0.813260259 0.472216148 1.065598224 0.849816984 0.8815479 1 16.92454192 3.490399628 24.1696475 0.840114957 1.04712658 0.202428242 0.174560235 611.9201861 1113831.639 0.047442447 0.06995364 3093.140358 -3.490399628 0.207011623 LLLPHWAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLLPHWAK 8 0 P04062-4;P04062-5;P04062-2;P04062;A0A0G2JNZ5;A0A0G2JNZ0;A0A0G2JLB3;P04062-3 P04062-4 GBA Glucosylceramidase 0 ; 108.24 0.0038491 502350000 540890 632930 566490 488230 387290 227450 573420 451640 502150 623720 FALSE TRUE 519751.4208 614879.4561 668867.3445 513427.6088 399747.5346 232049.1948 580437.6855 442313.4762 445148.0372 581474.8888 0.893850157 1.057447996 1.150294462 0.882974688 0.687471707 0.399070019 0.998216254 0.760675112 0.76554989 1 19.14935736 3.490531672 5.312361609 0.757193928 1.035129828 0.330752593 0.16857927 0.193870331 17.06108814 0.046332256 0.068300429 3094.080949 -3.490531672 0.2779359 FATHAAALSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FATHAAALSVR 11 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 73.848 0.042438 404930000 414080 452650 462460 393570 384180 308850 449460 388170 396440 399170 FALSE TRUE 397897.2958 439740.8652 546036.8094 413882.1949 396537.4986 315095.1586 454960.6259 380154.1539 351437.7932 372133.8604 1.069231635 1.181673887 1.467312888 1.112186337 1.065577581 0.846725311 1.222572505 1.021552173 0.944385423 1 18.50546214 3.490625614 14.79481229 1.029769678 1.242987494 0.37446588 0.128248571 3.292951777 3605.295115 0.034666052 0.050906244 3094.750304 -3.490625614 0.213217816 NTSLPPLWS(ph)PEAER ddPTM_BT-474_Pertuzumab_2h_R1 6 NTSLPPLWSPEAER 14 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER 311.7 1.01E-55 1283350000 1720780 1695490 1486699 1366980 1288046 1287651 1083194 1338509 1408469 1659199 TRUE FALSE 1653530.015 1647136.285 1755378.581 1437530.002 1329477.169 1313688.185 1096450.452 1310868.321 1248585.504 1546819.974 1.068986723 1.064853256 1.134830562 0.929345383 0.859490562 0.849283179 0.708841669 0.847460172 0.8071951 1 20.56087387 3.490636713 2.53626011 0.828089981 1.087545079 0.698174448 0.070903236 0.139691342 1.796731293 0.019554412 0.030926809 3094.829391 -3.490636713 0.259455098 KAPPPPIS(ph)PTQLSDVSSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 KAPPPPISPTQLSDVSSPR 19 1 Q9P0K7-3;Q9P0K7;Q9P0K7-2 Q9P0K7-3 RAI14 Ankycorbin 1 KAPPPPIS(0.991)PT(0.009)QLSDVSSPR;KAPPPPIS(0.951)PT(0.049)QLSDVSSPR;KAPPPPIS(0.996)PT(0.004)QLSDVSSPR;KAPPPPIS(0.999)PT(0.001)QLSDVSSPR 224.99 1.13E-19 1444260000 701103 808350 674392 923698 846882 1041650 1264948 1076300 1150598 1258803 TRUE FALSE 673703.1196 785296.6495 796269.6362 971370.1645 874122.7286 1062712.877 1280428.812 1054074.029 1019986.939 1173543.152 0.574076137 0.669167255 0.67851756 0.827724284 0.744857765 0.905559267 1.091079446 0.898197929 0.869151626 1 20.16243946 3.491306267 0.718415398 0.964452347 0.57659631 0.774963129 0.071997673 0.423234249 0.43232981 0.039921608 0.103758034 3099.604391 -3.491306267 -0.387856037 SIS(ph)ADDDLQESSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SISADDDLQESSR 13 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50;A2ABK4 P18615 NELFE Negative elongation factor E 1 SIS(1)ADDDLQESSR;SIS(1)ADDDLQESSR 322.19 3.97E-51 1427860000 1219540 1227670 727640 1207690 1561690 1130780 1176190 1736680 1205090 1201790 TRUE FALSE 1171879.029 1192658.054 859140.7343 1270019.026 1611923.177 1153645.146 1190584.565 1700816.951 1068293.235 1120391.693 1.045954764 1.064500979 0.766821764 1.133549127 1.438713967 1.029680204 1.062650297 1.51805566 0.953499782 1 20.09557176 3.491335109 24.59284816 1.20828573 0.966392002 0.174368699 0.191375783 745.4296234 1289742.21 0.051076427 0.075781411 3099.810244 -3.491335109 -0.241893729 SGSYSGRS(ph)PSPYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 SGSYSGRS(0.99)PS(0.01)PYGR 86.517 0.0044258 368410000 188580 235090 171200 233400 320940 329540 313280 191700 318960 302770 TRUE FALSE 181210.0851 228385.4634 202139.6483 245445.802 331263.3266 336203.5246 317114.0144 187741.328 282752.998 282263.1182 0.64198995 0.809122583 0.716139075 0.869563844 1.17359763 1.191099732 1.123469536 0.665128796 1.001735543 1 18.10668111 3.491673027 5.485018149 1.002320303 0.738420908 0.466610512 0.144400866 0.199630467 19.58627397 0.046071953 0.067959256 3102.223095 -3.491673027 -0.263899396 TLS(ph)DESLCSGR ddPTM_BT-474_Pertuzumab_2h_R1 6 TLSDESLCSGR 11 0 O60292;M0R2Q7 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 TLS(1)DESLCSGR;T(0.002)LS(0.997)DESLCSGR;TLS(1)DESLCSGR;TLS(1)DESLCSGR;TLS(1)DESLCSGR;TLS(1)DESLCSGR 324.13 2.04E-46 7290070000 2414980 2688920 2088940 2505500 2540400 2612830 2780030 3007900 2883200 2892470 TRUE FALSE 2320599.912 2612234.634 2466457.926 2634809.155 2622114.273 2665663.213 2814052.839 2945785.814 2555911.223 2696560.431 0.860577751 0.968728386 0.914668145 0.977099985 0.972392179 0.988541989 1.043571213 1.092423437 0.947841255 1 21.36268893 3.492095925 0.705050654 1.034020595 0.893229623 0.491155403 0.043269469 0.711291348 0.697039133 0.024000424 0.062875564 3105.245386 -3.492095925 -0.140790973 NYLPAINGIVFLVDCADHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NYLPAINGIVFLVDCADHSR 20 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ; 181.4 5.11E-17 970150000 766760 779690 616420 634980 573770 563230 465310 627730 713150 752500 FALSE TRUE 736794.1715 757454.0046 727820.8062 667751.3939 592225.8331 574618.8965 471004.603 614767.1561 632196.2018 701532.5047 1.050263768 1.079713341 1.037472678 0.951846692 0.844188728 0.819090908 0.671393841 0.876320273 0.901164518 1 19.42015043 3.492263014 2.041236711 0.832540667 1.063099226 0.570715225 0.078511732 0.213006329 1.771952828 0.023402566 0.039007134 3106.440314 -3.492263014 0.230558559 FNFESFPES(ph)PGEK ddPTM_BT-474_Pertuzumab_2h_R1 3 FNFESFPESPGEK 13 0 H0YBR0;Q96Q05-3;Q96Q05;Q96Q05-2 H0YBR0 TRAPPC9 Trafficking protein particle complex subunit 9 1 FNFESFPES(1)PGEK;FNFESFPES(1)PGEK;FNFESFPES(1)PGEK 238.12 4.63E-09 126910000 208730 191208 216462 250594 229489 224591 280651 320164 336778 360431 TRUE FALSE 200572.6008 185754.9351 255581.4986 263527.1864 236870.7221 229132.3839 284085.6909 313552.5015 298548.3733 336018.6873 0.596909066 0.552811323 0.760616919 0.784263484 0.704933181 0.681903693 0.845446106 0.93314007 0.88848741 1 18.35818194 3.492308452 0.219610983 1.053583543 0.371948565 0.79067866 0.062802911 3.219026692 0.237092628 0.149810124 0.617914874 3106.765345 -3.492308452 -0.681634978 KGNCSQHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGNCSQHDR 9 1 Q9BRX2 Q9BRX2 PELO Protein pelota homolog 0 62.303 0.054208 7194700 17367 19580 18793 15203 14560 9836.1 19255 12809 12224 18730 FALSE TRUE 16688.27844 19021.59757 22189.31315 15987.62865 15028.33562 10034.99268 19490.64845 12544.48967 10836.38277 17461.40042 0.955723942 1.089351204 1.270763663 0.915598307 0.860660386 0.574695754 1.116213361 0.718412577 0.620590703 1 14.09188165 3.492461473 4.024007263 0.808247776 1.105006354 0.369996279 0.168438979 0.218147584 8.032277819 0.045675283 0.068395751 3107.86019 -3.492461473 0.296758578 KLCLNICVGESGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLCLNICVGESGDR 14 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 189.1 1.21E-06 2166510000 1201950 1264550 959410 1154880 1206350 1315970 1137520 1307650 1251690 1294820 FALSE TRUE 1154976.465 1228486.272 1132796.729 1214483.495 1245153.343 1342579.815 1151441.31 1280646.571 1109603.399 1207120.688 0.956802809 1.017699625 0.938428726 1.006099479 1.03150692 1.112216722 0.953874224 1.060910134 0.919214963 1 20.20313849 3.493574529 22.29797274 1.019419955 0.97508509 0.102281394 0.053560356 358.0947969 485298.0439 0.01369262 0.02054661 3115.835556 -3.493574529 -0.044334865 FQWDLNAWTK ddPTM_BT-474_Pertuzumab_2h_R1 2 FQWDLNAWTK 10 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 155.11 3.09E-05 648870000 1402530 1411500 1229320 1175150 1075360 693880 1380910 1143470 1274770 1368050 FALSE TRUE 1347717.577 1371245.402 1451485.47 1235799.632 1109949.931 707910.729 1397809.99 1119856.945 1130063.454 1275390.755 1.056709539 1.075157082 1.138071187 0.968957653 0.870282246 0.555053991 1.095985669 0.878050073 0.886052725 1 20.2825079 3.493903161 3.666960441 0.876202735 1.087121479 0.337679966 0.130755325 0.26211019 7.577392993 0.036743857 0.055475077 3118.194214 -3.493903161 0.210918745 KIVDQIRPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIVDQIRPDR 10 2 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 P17844;A0A1X7SBZ2 DDX5;DDX17 Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17 0 ; 169.65 2.57E-06 9342300000 6159100 6101000 4950100 5749300 6121800 6421600 6225500 6158200 6398100 6457200 FALSE TRUE 5918395.563 5927005.454 5844693.184 6046022.062 6318713.257 6551449.152 6301689.531 6031031.018 5671814.511 6019848.093 0.983146995 0.984577246 0.970903766 1.004347945 1.049646629 1.088308052 1.046818696 1.001857676 0.942185654 1 22.52129565 3.494021058 5.802746805 1.025220516 0.980933207 0.205657709 0.036392404 0.274670331 32.52071 0.010845177 0.016032576 3119.040815 -3.494021058 -0.044287309 SVAVS(ph)DEEEVEEEAER ddPTM_BT-474_Pertuzumab_2h_R1 4 SVAVSDEEEVEEEAER 16 0 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 SVAVS(1)DEEEVEEEAER;SVAVS(1)DEEEVEEEAER;SVAVS(1)DEEEVEEEAER;SVAVS(1)DEEEVEEEAER 374.06 1.94E-104 2468352900 723583.8 689769.3 582978.4 681836.8 684131 758467.4 761470.7 743246.8 722436.5 821901 TRUE FALSE 695305.3451 670097.7549 688335.5652 717026.479 706136.6949 773804.1305 770789.8062 727898.4938 640428.5372 766232.9132 0.90743341 0.874535332 0.898337246 0.935781362 0.921569255 1.009881091 1.005947138 0.949970278 0.835814445 1 19.54742347 3.494257536 1.705498009 0.958693407 0.890092107 0.242304972 0.048353142 0.526882609 3.071244602 0.015460234 0.027375325 3120.73963 -3.494257536 -0.0686013 KPVWVDEEDEDEEMVDMMNNR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPVWVDEEDEDEEMVDMMNNR 21 1 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 ; 152.32 8.60E-08 178052000 121784 127225 112732 116237 114935 120862 114520 126686 130132 144059 FALSE TRUE 117024.5466 123596.6676 133105.1801 122236.0055 118631.9887 123305.9124 115921.53 124069.8898 115359.9609 134301.7556 0.871355301 0.920290781 0.991090396 0.910159401 0.883324184 0.918125842 0.863142328 0.923814356 0.85896093 1 17.03511864 3.494320722 24.76787027 0.902415068 0.930812498 0.026507203 0.046154023 1791.48939 2579808.297 0.011641672 0.017564738 3121.193699 -3.494320722 0.02839743 SPQQLLLQGSS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQQLLLQGSSR 12 0 O14795;O14795-2;A0A1B0GUS7;A0A0U1RRL2;B1AM27 O14795 UNC13B Protein unc-13 homolog B 1 SPQQLLLQGS(0.223)S(0.777)R;SPQQLLLQGS(0.233)S(0.767)R 85.28 0.0087141 91486000 228030 259520 142732 287180 422490 294980 385510 406600 369030 397050 TRUE FALSE 219118.3355 252118.7437 168526.8475 302001.3942 436079.7745 300944.6977 390227.9867 398203.5679 327139.2615 370157.4498 0.591959815 0.681112169 0.455284224 0.815872798 1.17809266 0.813018076 1.054221621 1.075768077 0.883784081 1 18.49777954 3.494338987 5.673186573 1.004866021 0.591482782 0.756999789 0.10768045 0.077059701 8.383133186 0.028002184 0.041432637 3121.32497 -3.494338987 -0.413383238 LYYLNGIECAASAMEMSAIAAHNAALLAYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LYYLNGIECAASAMEMSAIAAHNAALLAYHR 31 0 Q9UHG3;Q9UHG3-2 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 246.31 1.87E-46 114120000 22065 31867 25397 21334 15672 22733 18892 15268 19732 17652 FALSE TRUE 21202.67541 30958.18436 29986.80285 22435.0503 16176.10411 23192.67684 19123.20595 14952.71046 17492.10608 16456.41432 1.288414049 1.881222954 1.822195423 1.363301255 0.982966508 1.409339628 1.162051804 0.908625061 1.062935445 1 14.0063624 3.494353474 4.031866068 1.092858261 1.680891708 0.638457756 0.194290395 0.13288104 4.903252362 0.055065792 0.082588524 3121.429096 -3.494353474 0.588033447 EILDAFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EILDAFDK 8 0 P07602;C9JIZ6;P07602-2;P07602-3;A0A0J9YXB8 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 ; 135.83 0.0019006 160436000 453140 445230 530490 430830 393830 391750 417280 491950 463200 536070 FALSE TRUE 435430.7878 432532.4763 626361.3437 453065.1879 406497.8996 399671.4534 422386.7975 481791.0606 410619.4779 499761.5014 0.871277172 0.865477783 1.253320518 0.906562804 0.813383781 0.799724373 0.845176742 0.964041966 0.821630871 1 18.93088024 3.494383865 24.96295746 0.872058907 0.999632284 0.181771793 0.116447707 1193.003069 1725163.833 0.031461771 0.047541618 3121.647533 -3.494383865 0.127573377 S(ph)SPLSFPSVPQEETLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPLSFPSVPQEETLR 16 0 Q9ULD5 Q9ULD5 ZNF777 Zinc finger protein 777 1 S(0.5)S(0.5)PLSFPSVPQEETLR;S(0.5)S(0.5)PLSFPSVPQEETLR 187.16 1.45E-09 278954000 375705 342362 329684 310405 276172 309797 290220 315055 320087 391536 TRUE FALSE 361022.0332 332598.171 389265.2326 326425.0392 285055.3232 316061.3076 293771.7992 308549.0042 283752.0657 365016.918 0.989055618 0.911185632 1.06643066 0.894273726 0.780937291 0.865881257 0.804816941 0.845300557 0.777366888 1 18.47760381 3.494401229 10.36933509 0.836826355 0.981062822 0.459451105 0.06889114 0.343645025 200.6830504 0.016845846 0.024956225 3121.772343 -3.494401229 0.144236467 GGPGGGFRPFVPHIPFDFYLCEMAFPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGPGGGFRPFVPHIPFDFYLCEMAFPR 27 1 Q12905;A0A0A0MRL0 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 154.24 2.89E-08 179740000 161380 184510 148350 132660 102590 90461 132550 100330 134400 133530 FALSE TRUE 155073.0912 179247.9555 175160.145 139506.5985 105889.9005 92290.1834 134172.1866 98258.15044 119143.4755 124485.8942 1.245708136 1.439905755 1.407068216 1.120661899 0.850617664 0.741370611 1.077810361 0.789311521 0.957084144 1 16.92562275 3.494436964 3.130483978 0.890996089 1.36935076 0.795388614 0.104725395 0.09885107 1.977505749 0.028645226 0.043967476 3122.029222 -3.494436964 0.478354671 SIPLDEGEDEAQRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIPLDEGEDEAQRR 14 1 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 182.33 2.46E-06 1396810000 442250 451920 342540 418680 439250 499960 440360 412290 500470 503960 FALSE TRUE 424966.3811 439031.6841 404444.5978 440288.125 453378.8752 510069.5337 445749.2574 403776.0674 443658.7437 469826.3403 0.904517999 0.934455237 0.860838491 0.937129503 0.964992458 1.085655465 0.948753229 0.85941556 0.944303683 1 18.84176807 3.494485175 13.70902645 0.957035806 0.902651627 0.214468811 0.05565605 4.594623749 3622.707872 0.017086799 0.025447763 3122.375816 -3.494485175 -0.054384178 LTDIHGNVLQYHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTDIHGNVLQYHK 13 0 O95861-3;O95861-4;O95861;A6NF51;O95861-2 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 132.79 6.63E-05 387320000 726550 753630 595050 556040 514620 236220 630030 415980 601460 664660 FALSE TRUE 698155.6228 732137.2103 702588.7718 584737.291 531173.2197 240996.5302 637740.4956 407389.8676 533184.7823 619641.9862 1.126708064 1.181548744 1.133862436 0.943669577 0.857225997 0.388928665 1.02920801 0.657460076 0.860472328 1 19.24107538 3.494766333 2.187313781 0.769518477 1.155107642 0.451368651 0.17118971 0.251450523 2.398878619 0.048032811 0.078742172 3124.397868 -3.494766333 0.385589164 DFCHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFCHSK 6 0 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;H0YC07 Q8N573-2 OXR1 Oxidation resistance protein 1 0 73.039 0.084013 109130000 392850 349940 338090 334220 335560 324300 377410 289080 439670 406930 FALSE TRUE 377496.9877 339960.0538 399190.3838 351469.1343 346353.5921 330857.5682 382028.8565 283110.397 389760.5048 379368.2686 0.995067376 0.896121479 1.052250324 0.926458967 0.912974597 0.872127681 1.007013206 0.746267994 1.02739353 1 18.53323949 3.494909464 23.43466169 0.907711734 0.975429032 0.046908564 0.085227053 713.1580475 939530.5202 0.022014929 0.033286803 3125.427749 -3.494909464 0.067717298 GLFDEEMNEILTDPSDDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLFDEEMNEILTDPSDDTK 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 99.021 0.00086298 30875000 45388 45424 43297 47586 50250 51849 51730 64522 65133 59466 FALSE TRUE 43614.18678 44128.55199 51121.73104 50041.91916 51866.33689 52897.4223 52363.08721 63189.59815 57739.3749 55438.31485 0.786715594 0.795993747 0.922137175 0.902659457 0.935568425 0.954167212 0.94452884 1.139818162 1.041506674 1 15.75859578 3.494996563 0.476151774 1.06822697 0.741710472 0.737075524 0.051267375 0.829091022 0.320750824 0.044562802 0.1360717 3126.054628 -3.494996563 -0.326516498 IEYEPFR ddPTM_BT-474_Pertuzumab_2h_R1 3 IEYEPFR 7 0 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;; 128.48 0.0087314 319337000 730340 773220 695580 618810 569580 316959 775430 604920 583970 700860 FALSE TRUE 701797.5054 751168.5227 821286.7791 650746.8583 587901.058 323368.1281 784919.9443 592428.1906 517680.1738 653390.1279 1.074086484 1.149647799 1.256962332 0.995954531 0.899770341 0.494908194 1.201303648 0.906699023 0.792298738 1 19.31758513 3.49499719 3.827104158 0.885989865 1.158274425 0.344583441 0.171019557 0.258700267 8.31635336 0.048005973 0.072300809 3126.059139 -3.49499719 0.272284561 GNHETDNMNQIYGFEGEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNHETDNMNQIYGFEGEVK 19 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 139.44 1.85E-07 188260000 247600 256300 222070 227270 221010 216800 237060 220610 278940 281840 FALSE TRUE 237923.5183 248990.5749 262202.9889 238999.4319 228118.9874 221183.8445 239961.2112 216054.3264 247275.9006 262750.7258 0.905510413 0.947630398 0.997915375 0.909605221 0.868195461 0.841801079 0.913265646 0.822278705 0.941104539 1 18.00333522 3.495408613 10.70875494 0.883533515 0.950716657 0.13517076 0.052699865 0.718755307 413.3410819 0.01342028 0.019948692 3129.021971 -3.495408613 0.067183142 LMQLVDHR ddPTM_BT-474_Pertuzumab_2h_R1 5 LMQLVDHR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;; 175.51 0.00026568 2727010000 3208607 3439472 2883396 2508388 2481626 1068410 2905909 2346062 2471242 2863760 FALSE TRUE 3083211.091 3341381.626 3404489.798 2637846.205 2561449.754 1090013.982 2941472.384 2297615 2190716.968 2669794.984 1.154849383 1.251549893 1.275187727 0.988033246 0.959418146 0.408276287 1.101759648 0.860596043 0.820556253 1 21.34829753 3.495885003 2.476178488 0.847779945 1.229436341 0.471852209 0.17406359 0.24600752 3.009651153 0.049869675 0.07954674 3132.456168 -3.495885003 0.381656397 STSFMSVS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 3 STSFMSVSPSK 11 0 Q8TB45;Q8TB45-2 Q8TB45 DEPTOR DEP domain-containing mTOR-interacting protein 1 STSFMSVS(0.809)PS(0.191)K;STSFMSVS(0.999)PS(0.001)K;STSFMSVS(1)PSK 248.36 3.35E-16 761280000 1719780 1406140 1398430 1321530 1258600 1282600 1155610 1296050 1651620 1418540 TRUE FALSE 1652569.096 1366038.264 1651157.409 1389734.322 1299084.012 1308535.051 1169752.701 1269286.115 1464135.022 1322461.022 1.249616487 1.032951626 1.248549017 1.050869779 0.982323101 0.989469654 0.884527167 0.959790945 1.107129055 1 20.33479377 3.496073109 4.110053713 0.977965572 1.162881086 0.546769542 0.076488393 0.156265959 6.054646947 0.020565331 0.030855871 3133.813223 -3.496073109 0.184915514 YPFILPHQQVDK ddPTM_BT-474_Pertuzumab_2h_R1 1 YPFILPHQQVDK 12 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 140.14 5.94E-05 436580000 799120 678230 717700 650820 663280 524430 643210 717550 816800 712940 FALSE TRUE 767889.5069 658887.5445 847404.3552 684408.8982 684615.0036 535034.3339 651081.7964 702732.3417 724080.2883 664651.9388 1.155325761 0.991327199 1.274959578 1.029725272 1.030035367 0.804984237 0.979583085 1.057293751 1.089412738 1 19.34223951 3.496106008 23.76633227 0.99422003 1.130070827 0.320405519 0.095530557 513.7623489 643158.4823 0.026132927 0.03971226 3134.050631 -3.496106008 0.135850797 GLHVVEVTYDDVPIPNS(ph)PFK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLHVVEVTYDDVPIPNSPFK 20 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 GLHVVEVTYDDVPIPNS(1)PFK;GLHVVEVTYDDVPIPNS(1)PFK 133.95 6.34E-06 131696000 289160 241490 261230 201219 211032 258230 225085 210390 239170 237949 TRUE FALSE 277859.3075 234602.9416 308440.072 211603.9367 217820.0359 263451.5875 227839.6576 206045.373 212020.4243 221832.5023 1.252563554 1.057567936 1.390418757 0.953890591 0.98191218 1.187614911 1.027079689 0.92883311 0.955768078 1 17.75911124 3.496139893 0.51707786 0.962157788 1.258572095 0.353200635 0.11677209 1.647516921 0.781440687 0.08826201 0.260316407 3134.295169 -3.496139893 0.296414306 KTGQPMINLYTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTGQPMINLYTDR 13 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ; 196.18 2.31E-07 2594500000 2145020 2274700 1793200 1857470 1738400 1432660 2007820 1796960 1886160 2106240 FALSE TRUE 2061190.247 2209827.783 2117271.13 1953334.249 1794317.215 1461629.367 2032392.302 1759852.148 1672051.024 1963582.489 1.049709018 1.125406137 1.078269511 0.994780846 0.913797727 0.744368711 1.035042996 0.896245591 0.851530829 1 20.90505678 3.496484541 2.519501046 0.902907928 1.08924722 0.524380001 0.076019128 0.217030781 2.749718049 0.02168386 0.034483815 3136.783474 -3.496484541 0.186339292 VGEFCHNR ddPTM_BT-474_Pertuzumab_2h_R1 6 VGEFCHNR 8 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 204.03 9.08E-05 14483300000 12033400 13014000 10637190 11049090 10649760 8763480 12252200 11579670 12529000 12625600 FALSE TRUE 11563121.42 12642853.46 12559566.86 11619334.86 10992319.2 8940683.57 12402146.09 11340545.77 11106760.45 11770456.87 0.982385098 1.07411748 1.067041577 0.987160906 0.933890615 0.759586792 1.053667349 0.963475411 0.943613368 1 23.48866698 3.497076931 3.870838519 0.942015188 1.043621022 0.262448382 0.074126824 0.304344485 10.04124956 0.021173028 0.031918613 3141.065053 -3.497076931 0.101605834 QVQPEGPYR ddPTM_BT-474_Pertuzumab_2h_R1 4 QVQPEGPYR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 186.91 9.57E-05 2172550000 1774040 1885020 1790860 1601010 1471870 805460 2041680 1529830 1775060 2074390 FALSE TRUE 1704708.555 1831261.075 2114508.239 1683638.318 1519214.035 821746.9531 2066666.691 1498238.476 1573562.63 1933889.718 0.881492124 0.946931492 1.093396495 0.870596861 0.785574287 0.424919242 1.068657986 0.774727981 0.813677541 1 20.8830741 3.497228592 6.809633515 0.800582251 0.973493252 0.158485688 0.16655112 0.29339543 58.83339355 0.044535156 0.066110788 3142.162141 -3.497228592 0.172911001 AES(ph)GDSLGSEDRDLLYSIDAYR ddPTM_BT-474_Pertuzumab_2h_R1 2 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AES(0.999)GDSLGS(0.001)EDRDLLYSIDAYR;AES(0.995)GDS(0.002)LGS(0.003)EDRDLLYSIDAYR 153.82 1.88E-08 384300000 80384 77626 50937 77586 85270 77232 88744 94653 74707 97361 TRUE FALSE 77242.50441 75412.18248 60142.44899 81590.22276 88012.78699 78793.68396 89830.07562 92698.38247 66226.57456 90766.65275 0.851000914 0.830835777 0.662605122 0.898900866 0.969659939 0.868090665 0.989681484 1.021282373 0.729635527 1 16.46987473 3.497600088 22.64388308 0.937892924 0.785472186 0.342284624 0.091757273 240.205842 265599.2663 0.024101355 0.036754111 3144.8511 -3.497600088 -0.152420738 TPSS(ph)PHKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSSPHKK 8 1 E7EWN3;Q9C0A6;Q9C0A6-2;Q9C0A6-3;H0Y3R4 E7EWN3 SETD5 SET domain-containing protein 5 1 T(0.011)PS(0.011)S(0.977)PHKK 62.823 0.036303 56389000 66090 69511 59977 60841 59497 61075 62257 64784 68528 72448 TRUE FALSE 63507.12973 67528.61434 70816.17808 63981.0113 61410.77504 62309.97835 63018.91979 63446.18776 60748.98873 67541.03243 0.940274785 0.99981614 1.048491199 0.947290987 0.909236546 0.922549983 0.933046439 0.939372489 0.899438261 1 16.04347661 3.497669534 23.16179169 0.930750393 0.996778753 0.386910099 0.035016801 268.1992591 302309.9641 0.008919365 0.013612434 3145.354022 -3.497669534 0.06602836 RNS(ph)LIELPDDYSCLLNQASHFR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSLIELPDDYSCLLNQASHFR 22 1 Q8IWV7 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 RNS(1)LIELPDDYSCLLNQASHFR;RNS(1)LIELPDDYSCLLNQASHFR 194.73 1.21E-18 68713000 27573 32712 23551 29575 32598 37961 31330 28904 34416 40404 TRUE FALSE 26495.41668 31779.08579 27807.18959 31101.36929 33646.54427 38728.59743 31713.42591 28307.1223 30509.23996 37667.40109 0.703404427 0.843676093 0.738229577 0.825683971 0.89325367 1.028172805 0.841932944 0.751501868 0.809964029 1 15.20102888 3.497805887 4.728111927 0.869823938 0.77070236 0.293065856 0.084786245 0.329591682 19.08609784 0.025340207 0.03783857 3146.341708 -3.497805887 -0.099121577 VFDMLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 VFDMLNR 7 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;; 113.1 0.014436 1679099000 2544840 2615900 2427130 2299630 2304760 1581622 2774080 2338400 2689140 2987510 FALSE TRUE 2445384.839 2541297.093 2865766.382 2418314.18 2378894.699 1613603.48 2808030.021 2290111.223 2383880.101 2785163.287 0.87800412 0.912440971 1.028940169 0.868284524 0.854131142 0.579356869 1.008210195 0.822253845 0.855921128 1 21.40933048 3.49781437 21.47653095 0.842889182 0.938985184 0.097048245 0.116060907 262.4243232 272356.5998 0.03020105 0.046018753 3146.403162 -3.49781437 0.096096002 HQGVMVGMGQK ddPTM_BT-474_Pertuzumab_2h_R1 31 HQGVMVGMGQK 11 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;Q562R1;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 C9JTX5;P60709;P63261;P68133 ACTB;ACTBL2;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle" 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 160.77 2.06E-05 84691030000 111910121 113892949 96595116 97465778 92792772 74670697 111419772 89354560 118744445 117769092 FALSE TRUE 107536549.7 110644833.6 114052002.2 102495998.5 95777535.78 76180589.65 112783360.5 87509357.11 105265073.4 109792486.5 0.979452722 1.007763255 1.038796058 0.93354292 0.872350548 0.693859772 1.027241154 0.797043221 0.958763908 1 26.71020409 3.498201148 3.674657736 0.876867179 1.007712807 0.231514476 0.092890199 0.283853318 8.204633906 0.024616714 0.037288471 3149.206564 -3.498201148 0.130845628 SLLSNVS(ph)IEDEEEELVAIVR ddPTM_BT-474_Pertuzumab_2h_R1 7 SLLSNVSIEDEEEELVAIVR 20 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLS(0.001)NVS(0.999)IEDEEEELVAIVR 298.1 1.11E-54 279510500 60075 60440.7 43531.7 64429.6 87017.2 66204.4 70403.2 86508.3 79319.8 73944.3 TRUE FALSE 57727.20258 58716.99041 51398.84655 67754.81938 89816.18727 67543.09833 71264.81542 84721.87337 70315.74884 68935.9867 0.837403007 0.851761079 0.745602537 0.982865737 1.302892605 0.979794467 1.033782482 1.22899341 1.020015121 1 16.07296969 3.4984213 6.8657261 1.107821324 0.822226202 0.610789475 0.10050419 0.108759819 21.847425 0.026613845 0.039591144 3150.803363 -3.4984213 -0.285595122 RDPVALEDVYPIHMILENK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDPVALEDVYPIHMILENK 19 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 0 73.783 0.010872 102040000 141040 137680 130900 83200 122630 126080 117850 97651 117170 110490 FALSE TRUE 135528.0009 133753.5012 154556.5419 87493.96197 126574.5053 128629.424 119292.2836 95634.47273 103869.3528 103006.4139 1.315723903 1.298496823 1.500455516 0.849403049 1.228802174 1.248751598 1.158105394 0.928432212 1.008377526 1 16.65237465 3.498541625 0.354458017 0.95824284 1.465821902 0.374121425 0.152224496 2.910002242 0.546111264 0.163696798 0.588973379 3151.676441 -3.498541625 0.507579062 QLLHSCTVIATNILLVDEIMR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLLHSCTVIATNILLVDEIMR 21 0 P40227;P40227-2;Q92526-3;Q92526;Q92526-2 P40227 CCT6A;CCT6B T-complex protein 1 subunit zeta;T-complex protein 1 subunit zeta-2 0 ; 232.82 2.57E-27 442250000 266310 288010 222421 213296 212917 225313 191682 183170 247440 248154 FALSE TRUE 255902.3108 279796.2368 262617.4224 224304.2321 219765.6687 229868.9832 194027.8617 179387.4755 219351.6486 231346.3085 1.106143912 1.209425984 1.135170144 0.969560455 0.949942405 0.993614226 0.838690113 0.775406691 0.948152793 1 17.81969455 3.498730295 1.075083407 0.876908563 1.177911808 0.661064868 0.072591967 0.29857118 0.699710105 0.028471443 0.062602714 3153.045912 -3.498730295 0.301003245 RDDGLSAAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDDGLSAAAR 10 1 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 0 ;;; 210.98 1.08E-07 1839720000 716230 783690 700700 658190 636980 434097 757300 701670 703400 765050 FALSE TRUE 688238.9398 761339.9285 827332.077 692159.2648 657469.0402 442874.7388 766568.0639 687180.2693 623552.9809 713232.4821 0.96495737 1.067449882 1.159975321 0.970453929 0.921815897 0.620940226 1.07478008 0.963473042 0.874263296 1 19.44401288 3.499195666 4.991328753 0.911407326 1.065686217 0.251805815 0.119290276 0.272577779 18.58087011 0.033559839 0.050110548 3156.426394 -3.499195666 0.154278892 IAVMELFRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IAVMELFRPK 10 1 Q16531;F5GY55;Q16531-2;F5H2L3;F5GWI0;F5GZY8;F5GYG8;F5H198 Q16531 DDB1 DNA damage-binding protein 1 0 ; 105.17 0.0023579 469680000 1157770 1234860 1046350 1068730 1086560 951910 1259850 1023680 1193500 1286580 FALSE TRUE 1112523.068 1199643.002 1235448.721 1123887.283 1121510.189 971158.2724 1275268.421 1002540.65 1058018.884 1199438.791 0.927536342 1.000170256 1.030022316 0.937010952 0.935029114 0.809677226 1.063220926 0.835841444 0.882094936 1 20.19392811 3.49924333 3.858706594 0.913183795 0.987566432 0.128640117 0.073406591 0.386162717 12.5922198 0.019580256 0.029577921 3156.772828 -3.49924333 0.074382637 DLPLLLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLPLLLFR 8 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ; 160.03 0.0008276 722350000 461780 492230 473520 397000 359180 149441 503010 385140 404300 496810 FALSE TRUE 443733.1271 478192.0823 559095.5974 417489.2176 370733.3509 152462.7994 509165.9868 377186.7244 358405.559 463160.6162 0.958054531 1.032454111 1.207131129 0.901391878 0.800442304 0.32917911 1.099329194 0.814375643 0.773825637 1 18.82115306 3.499322545 4.808487994 0.796715727 1.063530974 0.263291045 0.196341931 0.259475361 15.72205002 0.054018749 0.080753395 3157.348675 -3.499322545 0.266815247 CSS(ph)PTVGPPPLPQK ddPTM_BT-474_Pertuzumab_2h_R1 5 CSSPTVGPPPLPQK 14 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 CS(0.035)S(0.929)PT(0.035)VGPPPLPQK;CS(0.001)S(0.999)PTVGPPPLPQK;CS(0.001)S(0.998)PTVGPPPLPQK;CSS(1)PTVGPPPLPQK;CS(0.002)S(0.986)PT(0.012)VGPPPLPQK 271.04 6.31E-33 1784587000 2535980 2626080 2037380 2658470 2996660 2948740 3104430 3386260 3244040 2714280 TRUE FALSE 2436871.098 2551186.77 2405579.887 2795673.955 3093050.29 3008365.543 3142422.943 3316332.548 2875790.179 2530439.398 0.963022904 1.008199118 0.950656984 1.104817589 1.222337232 1.188870813 1.241848726 1.310575764 1.136478582 1 21.27095649 3.500047991 2.936082085 1.210343717 0.977520608 0.563980766 0.07994124 0.163010194 2.830795186 0.022113736 0.034365757 3162.627121 -3.500047991 -0.232823108 VFQSWWDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFQSWWDR 8 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 0 ; 109.11 0.0085645 1464210000 625870 672660 588360 543350 545520 474640 476250 578950 580920 690900 FALSE TRUE 601410.3085 653476.3954 694689.74 571392.3586 563067.1462 484237.546 482078.49 566994.4802 514976.397 644104.7276 0.933715097 1.014549913 1.078535384 0.887110953 0.874185706 0.751799397 0.748447371 0.880283059 0.799522772 1 19.29693576 3.500391762 3.170246399 0.829623978 1.008954663 0.478452437 0.076524219 0.192522556 3.944509052 0.020988778 0.032305555 3165.131526 -3.500391762 0.179330685 LHFFMPGFAPLTS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 LHFFMPGFAPLTSR 14 0 Q5JP53;P07437;Q5ST81;A6NNZ2;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 1 LHFFMPGFAPLT(0.164)S(0.836)R 145.62 5.49E-06 170910000 123490 135870 89588 96526 73432 67621 78176 57007 76934 84742 TRUE FALSE 118663.8743 131995.1206 105778.5445 101507.7184 75794.00697 68988.34295 79132.74127 55829.78553 68200.77485 79002.34886 1.502029699 1.670774636 1.338929108 1.284869626 0.959389285 0.8732442 1.001650488 0.706685134 0.86327528 1 16.26960793 3.50059617 1.143707857 0.851847619 1.59501616 0.881836548 0.101754316 0.144291718 0.38221939 0.03534896 0.075511162 3166.621603 -3.50059617 0.743168541 GFAFVYFER ddPTM_BT-474_Pertuzumab_2h_R1 2 GFAFVYFER 9 0 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ; 121.62 0.0014163 148210000 276550 367200 269550 249020 219820 103783 303180 212720 218760 290820 FALSE TRUE 265742.1203 356727.8155 318263.6811 261871.952 226890.7099 105881.5634 306890.4075 208327.2577 193927.2819 271122.5024 0.980155162 1.315744036 1.173874091 0.965880551 0.836856801 0.390530341 1.131925255 0.768387927 0.715275494 1 18.04858533 3.50062452 2.704438114 0.79807858 1.171601677 0.388363832 0.196241161 0.264857647 3.873394939 0.055070301 0.08671179 3166.828316 -3.50062452 0.373523097 S(ph)ISESSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 S(0.997)IS(0.003)ESSR;S(0.998)IS(0.002)ESSR;S(0.998)IS(0.002)ESSR 165.26 0.0012242 2346920000 2458390 2359700 2080480 2521480 2359940 2550500 2826900 2913120 2902270 2715720 TRUE FALSE 2362313.401 2292403.666 2456469.016 2651613.885 2435849.613 2602072.857 2861496.448 2852963.054 2572816.477 2531781.865 0.93306356 0.905450702 0.970253026 1.0473311 0.9621088 1.027763447 1.130230249 1.12685974 1.016207799 1 21.27172168 3.500820215 0.76235424 1.080106081 0.90867309 0.490126173 0.05081602 0.623626789 0.720945974 0.026818075 0.069120254 3168.255625 -3.500820215 -0.17143299 HCFTSNEAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HCFTSNEAAR 10 0 Q9BV44;H7C0R6;H7C3J3 Q9BV44 THUMPD3 THUMP domain-containing protein 3 0 ; 193.83 5.30E-07 410050000 134413 159499 131458 115658 96611 53129 138342 95523 119963 136989 FALSE TRUE 129159.9914 154950.2447 155215.3849 121627.1232 99718.58055 54203.30478 140035.0708 93550.41667 106345.3032 127710.613 1.011348926 1.21329184 1.215367942 0.952365041 0.780816709 0.424422869 1.096503004 0.732518735 0.832705291 1 16.9625189 3.501166208 3.511302024 0.797190354 1.150799535 0.423652485 0.174378162 0.209680293 5.413751778 0.047729662 0.072743185 3170.780712 -3.501166208 0.353609182 LEEALENLCER ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEALENLCER 11 0 A0A0J9YYJ0;Q8N129 A0A0J9YYJ0 CNPY4 Protein canopy homolog 4 0 91.855 0.024266 16239000 26605 29994 20761 26697 27368 29981 29244 30309 27841 31466 FALSE TRUE 25565.24719 29138.60049 24512.97453 28074.83537 28248.31657 30587.23636 29601.89682 29683.10856 24680.6064 29334.77979 0.871499543 0.993312399 0.83562838 0.957049467 0.962963308 1.042695278 1.009105813 1.011874259 0.841342821 1 14.84032454 3.501709241 10.66947588 0.983777116 0.907256127 0.228995022 0.063008852 0.949786719 406.543402 0.016479692 0.024873855 3174.74787 -3.501709241 -0.076520989 LYTLVLTDPDAPSRK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYTLVLTDPDAPSRK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 107.35 0.0018674 826020000 773050 740540 657660 680560 684060 663590 699600 739590 773690 816830 FALSE TRUE 742838.3513 719420.5243 776513.7916 715683.7832 706063.4111 677008.2445 708161.9141 724317.208 685863.9548 761505.3765 0.97548668 0.944734662 1.019708876 0.939827617 0.927194256 0.889039349 0.929949986 0.95116493 0.900668565 1 19.5384947 3.501762861 23.67090241 0.930122902 0.977005167 0.29062733 0.032797709 457.1381741 439128.238 0.00830923 0.012791524 3175.139864 -3.501762861 0.046882265 AWSS(ph)QDEVSTNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 AWSSQDEVSTNVR 13 0 A1L390-3;A1L390;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 AWS(0.001)S(0.999)QDEVSTNVR 213.73 3.74E-09 338500000 148200 149270 75800 140290 191720 132380 128040 166150 160840 147400 TRUE FALSE 142408.1802 145012.9658 89498.74616 147530.3837 197886.8479 135056.8143 129606.9918 162718.9444 142582.1175 137416.4667 1.036325439 1.05528085 0.651295644 1.073600473 1.440051929 0.98282846 0.943169293 1.184129881 1.037591207 1 17.06819537 3.502573231 24.95363282 1.109786335 0.917406881 0.195141568 0.167246252 1133.131594 1110942.501 0.044741875 0.068994124 3181.070036 -3.502573231 -0.192379454 LLMHGK ddPTM_BT-474_Pertuzumab_2h_R1 3 LLMHGK 6 0 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;F8VXH9;H3BSP4;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;Q15365 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15365 PCBP2;PCBP3;PCBP1 Poly(rC)-binding protein 3;Poly(rC)-binding protein 2;Poly(rC)-binding protein 1 0 ;; 86.627 0.053362 9447000000 26843000 28453000 23811900 23037200 21867400 13615000 25393000 23691100 25931000 27443200 FALSE TRUE 25793945.88 27641548.3 28115240.02 24226152.65 22570784.78 13890304.63 25703767.13 23201870.51 22987421.59 25584447.62 1.008188501 1.080404342 1.098919173 0.946909349 0.882207234 0.542919856 1.004663752 0.906874006 0.898492003 1 24.60876375 3.503701373 3.240522821 0.865763087 1.063153587 0.323971394 0.122282175 0.291290379 6.247715267 0.035309556 0.054342597 3189.34406 -3.503701373 0.197390501 SPQQLLLQGS(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQQLLLQGSSR 12 0 O14795;O14795-2;A0A1B0GUS7;A0A0U1RRL2;B1AM27 O14795 UNC13B Protein unc-13 homolog B 1 SPQQLLLQGS(0.546)S(0.454)R;SPQQLLLQGS(0.607)S(0.393)R 99.451 0.0039744 799590000 407640 475000 275170 513200 724520 540610 665630 656750 693810 697040 TRUE FALSE 391708.9781 461453.4651 324899.3401 539686.3135 747824.8438 551541.5046 673776.1791 643187.883 615051.5975 649828.8599 0.602787907 0.710115376 0.499976779 0.830505302 1.150802757 0.848748861 1.036851732 0.989780422 0.946482429 1 19.30970029 3.504517643 5.499972293 0.991525846 0.619545028 0.807091112 0.085503109 0.071177848 6.352754666 0.021524876 0.032299384 3195.344168 -3.504517643 -0.371980818 VTYS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTYSPR 6 0 Q96K76-2;Q96K76-4;Q96K76;Q96K76-3 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 VT(0.001)YS(0.999)PR;VT(0.008)YS(0.992)PR 87.696 0.054699 829160000 950720 1089720 915890 847080 866260 494980 1018170 862960 875630 1044760 TRUE FALSE 913564.8113 1058642.253 1081411.697 890797.9003 894124.0396 504988.8347 1030630.669 845139.5744 776232.1533 973997.4746 0.937953984 1.086904515 1.110281828 0.914579271 0.917994207 0.518470374 1.058145114 0.867702018 0.796954996 1 19.89355851 3.504701917 3.071376887 0.853482347 1.048145746 0.250728122 0.141969033 0.341641091 6.513951054 0.039624471 0.061411613 3196.700264 -3.504701917 0.194663399 ALEFAPACHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEFAPACHR 10 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ER44;K7EPP7;A0A6I8PUC2 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ; 111.61 0.0019261 217050000 349070 405720 371100 325630 305760 222270 400640 341530 356180 395440 FALSE TRUE 335427.9585 394149.2628 438166.0251 342435.8033 315595.0481 226764.4517 405543.1522 334477.2862 315747.9396 368656.4966 0.909865855 1.06915046 1.188548226 0.928875 0.85606805 0.615110418 1.10005698 0.907287107 0.856482776 1 18.49191766 3.504887254 18.10306364 0.8884736 1.05744055 0.243337129 0.131706192 33.41200996 21782.4376 0.035472698 0.054552295 3198.064758 -3.504887254 0.16896695 KGDVVIVLTGWRPGSGFTNTMR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGDVVIVLTGWRPGSGFTNTMR 22 2 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 161.16 9.94E-12 10774200000 3695720 3981140 3363710 3469530 3388360 3531450 3676060 3661340 4059650 4004550 FALSE TRUE 3551287.177 3867601.785 3971607.222 3648592.859 3497349.677 3602858.339 3721048.722 3585732.05 3598815.551 3733318.262 0.951241477 1.035968946 1.063827658 0.977305604 0.936793874 0.965055237 0.996713503 0.960467819 0.963972343 1 21.83202707 3.505182517 24.16374472 0.968516785 1.019184723 0.308182305 0.031274586 512.3860762 441217.396 0.008212653 0.012687398 3200.239764 -3.505182517 0.050667938 TGNAWHSK ddPTM_BT-474_Pertuzumab_2h_R1 4 TGNAWHSK 8 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 89.886 0.013588 4299240000 6890530 7020510 5746410 5923290 5788780 4540470 6546620 5753850 6989600 6723120 FALSE TRUE 6621240.47 6820291.929 6784914.115 6228991.707 5974981.366 4632281.414 6626739.494 5635030.987 6196169.911 6267757.094 1.056397108 1.088155113 1.082510699 0.99381511 0.953288597 0.739065242 1.057274459 0.899050634 0.988578501 1 22.57951784 3.505557582 2.650088295 0.931478525 1.076998388 0.368627628 0.079322222 0.277368082 3.884052613 0.022168134 0.035151015 3203.004747 -3.505557582 0.145519863 HFVLDECDK ddPTM_BT-474_Pertuzumab_2h_R1 5 HFVLDECDK 9 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0D9SEM9 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;;; 185.81 4.24E-05 5086280000 6119510 5268310 5003360 4915630 4815580 4134520 5910830 3360160 7016520 6840500 FALSE TRUE 5880352.784 5118062.957 5907578.451 5169326.253 4970477.504 4218122.827 5983168.506 3290771.522 6220034.065 6377186.842 0.922091971 0.8025581 0.926361199 0.810596644 0.77941538 0.66143943 0.938214397 0.516022441 0.975357037 1 22.60448872 3.505565874 4.309661746 0.772374306 0.875710524 0.006283851 0.14448718 0.508746914 21.85580895 0.037884542 0.057203868 3203.065903 -3.505565874 0.103336218 SCS(ph)VTDAVAEQGHLPPPSAPAGR ddPTM_BT-474_Pertuzumab_2h_R1 3 SCSVTDAVAEQGHLPPPSAPAGR 23 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-4 Q96PU5-7 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.147)CS(0.852)VT(0.001)DAVAEQGHLPPPSAPAGR;S(0.05)CS(0.949)VT(0.001)DAVAEQGHLPPPSAPAGR;S(0.176)CS(0.822)VT(0.002)DAVAEQGHLPPPSAPAGR 282.1 3.27E-52 3503910000 1620240 1845250 1268500 1477850 1279960 1450730 1077050 1566940 1397660 1313400 TRUE FALSE 1556919.23 1792625.277 1497746.168 1554122.016 1321131.076 1480064.755 1090231.26 1534582.141 1239003.496 1224442.248 1.271533412 1.464034159 1.223206868 1.269248932 1.078965609 1.208766487 0.890390104 1.253290748 1.011892148 1 20.2236933 3.505875856 1.151087986 1.081203705 1.363193967 0.51171825 0.112276631 0.406782178 1.089826524 0.037824141 0.081055337 3205.352938 -3.505875856 0.281990262 LDFNLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDFNLIR 7 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 115.69 0.013082 261590000 354890 397140 343000 326340 318840 226731 395570 304670 366750 411040 FALSE TRUE 341020.5064 385813.956 404987.73 343182.4465 329095.7782 231315.6562 400411.104 298378.458 325118.0775 383199.8947 0.889928497 1.006821665 1.056857623 0.895570305 0.858809678 0.603642275 1.044914442 0.778649635 0.848429454 1 18.54773764 3.506145526 4.300882305 0.843416976 0.986853784 0.184145708 0.119153108 0.305330609 13.0176296 0.031487882 0.047573964 3207.343881 -3.506145526 0.143436808 VQDT(ph)SNTGLGEDIIHQLSK ddPTM_BT-474_Pertuzumab_2h_R1 3 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.614)S(0.362)NT(0.024)GLGEDIIHQLSK;VQDT(0.594)S(0.387)NT(0.019)GLGEDIIHQLSK;VQDT(0.639)S(0.359)NT(0.003)GLGEDIIHQLSK 192.12 3.00E-14 193773000 207064 184044 184335 200783 211291 240548 234425 246441 260973 266980 TRUE FALSE 198971.71 178795.2453 217648.435 211145.4347 218087.3669 245412.0454 237293.9633 241351.9072 231348.4391 248897.2068 0.79941319 0.718349746 0.874451095 0.848323842 0.876214602 0.985997587 0.953381383 0.969685077 0.929493915 1 17.92519051 3.507199616 0.786734167 0.971254276 0.751262371 0.799039418 0.038242466 0.315769143 0.389227147 0.017681107 0.045430102 3215.137982 -3.507199616 -0.219991906 S(ph)MGYDDLDYGMMSDYGTAR ddPTM_BT-474_Pertuzumab_2h_R1 10 SMGYDDLDYGMMSDYGTAR 19 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(0.998)MGY(0.002)DDLDYGMMSDYGTAR;S(0.994)MGY(0.006)DDLDYGMMSDYGTAR;S(0.976)MGY(0.024)DDLDYGMMSDYGTAR 408.44 1.24E-147 4725671000 1973656 2078765 1452880 1403274 1228751 765865 1033254 1188661 963873 1129015 TRUE FALSE 1896523.342 2019480.658 1715447.735 1475697.139 1268274.892 781351.315 1045899.272 1164114.735 854458.1779 1052545.808 1.801843992 1.918662961 1.629808148 1.402026522 1.20495933 0.742344237 0.993685275 1.105999117 0.811801416 1 20.00545159 3.50732957 1.330767309 0.955456858 1.862819161 0.911596598 0.115861001 0.121957912 0.435074737 0.040147751 0.080151394 3216.100195 -3.50732957 0.907362304 GSLS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSLSPAR 7 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 GS(0.016)LS(0.984)PAR 82.563 0.025333 279030000 303480 327550 280400 234570 215000 103800 290730 194650 203900 269840 TRUE FALSE 291619.6661 318208.5947 331074.5175 246676.1858 221915.6703 105898.9071 294288.0407 190630.4095 180754.1268 251563.4965 1.159228863 1.264923565 1.316067403 0.980572258 0.882145754 0.420962932 1.169836025 0.757782477 0.718522875 1 17.94056307 3.507781752 2.834236451 0.81532007 1.247622787 0.504456636 0.186359446 0.2101282 3.375641492 0.051709664 0.081216189 3219.450503 -3.507781752 0.432302717 FCADHPFLFFIQHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 FCADHPFLFFIQHSK 15 0 A0A2R8YD12;A0A024QZX5;A0A087X1N8;P35237 A0A2R8YD12 SERPINB6 Serpin B6 0 210.34 1.12E-09 390160000 754350 787220 646500 580720 527460 140350 823770 337660 733760 748490 FALSE TRUE 724869.168 764769.2564 763336.9313 610691.0288 544426.2299 143187.9732 833851.5437 330687.203 650466.641 697794.1056 1.038800933 1.09598125 1.093928603 0.875173671 0.780210417 0.205200892 1.194982212 0.473903692 0.932175603 1 19.41244189 3.50783398 2.680650996 0.725753456 1.078284606 0.21484662 0.260307244 0.361854624 5.182955431 0.070432725 0.111637264 3219.837695 -3.50783398 0.35253115 APPHELTEEEKQQILHSEEFLSFFDHSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 APPHELTEEEKQQILHSEEFLSFFDHSTR 29 1 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5;E7EV09 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ; 248.73 1.81E-46 306410000 163915 195131 148096 151453 143301 112361 186054 120704 174630 183480 FALSE TRUE 157509.0206 189566.0549 174860.2416 159269.5075 147910.4068 114633.0164 188330.9845 118211.4202 154806.7345 171052.7362 0.920821403 1.108231643 1.022259249 0.931113474 0.864706465 0.67016184 1.101011236 0.691081726 0.905023433 1 17.38408166 3.507934003 2.720814921 0.852549113 1.025870864 0.195207452 0.127899529 0.358754126 5.297235698 0.034611138 0.05472401 3220.579346 -3.507934003 0.173321751 RS(ph)NSSEALLVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSNSSEALLVDR 12 1 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 RS(0.573)NS(0.42)S(0.007)EALLVDR 81.317 0.0056501 0 71515 66649 102330 68240 73014 69040 70617 70281 60193 83379 TRUE FALSE 68720.11474 64748.23578 120823.3073 71761.87458 75362.56162 70436.0361 71481.23197 68829.67279 53360.14299 77731.66606 0.884068465 0.832971156 1.554364051 0.923200006 0.969522016 0.906143399 0.919589603 0.885477905 0.686465963 1 16.24621482 3.508781607 24.96108847 0.895564068 1.093728814 0.168369136 0.19622089 1137.581206 896868.6015 0.052094356 0.080614754 3226.871025 -3.508781607 0.198164746 VQTT(ph)PPPAVQGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 VQTTPPPAVQGQK 13 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 VQTT(1)PPPAVQGQK;VQT(0.072)T(0.928)PPPAVQGQK 160.78 2.83E-06 267090000 937630 923930 798870 960480 905360 998990 1046960 1107170 1126850 1074130 TRUE FALSE 900986.383 897580.421 943243.5798 1010050.488 934481.7266 1019190.262 1059773.01 1084306.553 998934.7121 1001378.218 0.899746336 0.896345062 0.941945373 1.008660334 0.933195579 1.017787529 1.058314421 1.082814198 0.997559857 1 19.93355555 3.508941862 0.694263822 1.046338378 0.88308172 0.651979552 0.03569307 0.543032423 0.51006785 0.020581262 0.055561814 3228.061961 -3.508941862 -0.163256658 FNPFVTSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FNPFVTSDR 9 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KSS0;E5RHH1;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ;;; 168.25 0.00013811 2262850000 1524030 1482190 1471280 1439320 1480220 1370860 1591690 1563460 1597910 1631750 FALSE TRUE 1464469.223 1439919.392 1737173.024 1513603.478 1527832.621 1398579.728 1611169.578 1531174.005 1416521.956 1521230.119 0.962687502 0.946549358 1.14195282 0.99498653 1.004340238 0.919374203 1.059122849 1.00653674 0.931168755 1 20.53680698 3.509254196 24.87703735 0.991056423 1.019754785 0.043657877 0.061157231 2349.946312 1819301.099 0.016438497 0.025440543 3230.384342 -3.509254196 0.028698363 ELFEMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELFEMAR 7 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 143 0.005702 316630000 453490 466580 428180 381360 373750 182213 503580 375570 370910 470730 FALSE TRUE 435767.1094 453273.5952 505561.6508 401042.0353 385772.0082 185897.4717 509742.9627 367814.3483 328805.8518 438847.0378 0.992981772 1.032873772 1.152022475 0.913853805 0.87905802 0.423604253 1.161550424 0.838137931 0.749249336 1 18.74335864 3.509423912 3.87428282 0.839307203 1.056363263 0.222980606 0.180717028 0.338776756 10.92605416 0.049619273 0.07555952 3231.646974 -3.509423912 0.21705606 GMLPHK ddPTM_BT-474_Pertuzumab_2h_R1 2 GMLPHK 6 0 P40429;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 93.595 0.04544 1831160000 2725000 2980400 2872400 2463700 2377600 1337920 3123300 2666000 2994900 3311500 FALSE TRUE 2618503.987 2895401.91 3391506.576 2590851.852 2454077.663 1364973.659 3161523.88 2610946.168 2654931.508 3087209.155 0.848178356 0.937870343 1.098567154 0.839221356 0.79491785 0.442138381 1.024071814 0.845730249 0.859977855 1 21.5578718 3.509502379 23.28361215 0.817800782 0.960792296 0.12541431 0.158788648 560.2463063 402841.9564 0.042653643 0.065992247 3232.230909 -3.509502379 0.142991514 S(ph)SSVEEKPLSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSVEEKPLSHR 12 1 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(0.333)S(0.333)S(0.333)VEEKPLSHR;S(0.333)S(0.333)S(0.333)VEEKPLSHR 97.417 0.0029793 237890000 234560 205503 113606 224170 249300 201510 235660 286100 266580 232400 TRUE FALSE 225393.1359 199642.2556 134137.1314 235739.4406 257318.9609 205584.6703 238544.0776 280191.935 236318.956 216659.341 1.040311185 0.92145695 0.619115385 1.088064976 1.187666129 0.948884407 1.101009892 1.293237272 1.090739753 1 17.72506891 3.509965128 24.21730797 1.123909849 0.864273876 0.406635358 0.132178131 407.1749386 300227.6473 0.036148464 0.05594477 3235.676748 -3.509965128 -0.259635973 GS(ph)SQPNLSTSHSEQEYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSSQPNLSTSHSEQEYGK 18 0 I3L2B2;O95208-3;O95208-2;F6PQP6;O95208;E9PBC1 I3L2B2 EPN2 Epsin-2 1 GS(0.391)S(0.391)QPNLS(0.07)T(0.119)S(0.03)HSEQEYGK;GS(0.55)S(0.449)QPNLS(0.001)TSHSEQEYGK 147.39 4.96E-08 414500000 417348 449050 387386 390770 368955 394442 380179 446270 494600 422250 TRUE FALSE 401037.5788 436243.5337 457395.2676 410937.6865 380822.7727 402417.8875 384831.7443 437054.3685 438455.0815 393650.6314 1.018765237 1.108199756 1.161932005 1.043914715 0.967413087 1.022271668 0.977597173 1.110259539 1.113817803 1 18.58655627 3.510027427 24.50172741 1.035405076 1.098394811 0.207723357 0.05622846 848.3302214 631658.571 0.01593464 0.02466105 3236.140933 -3.510027427 0.062989735 LRPENVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRPENVR 7 1 A0A3B3ISG5;P14735 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 132.08 0.0031038 354850000 386660 417140 376920 330820 299060 137795 430430 323250 332080 404070 FALSE TRUE 371548.8997 405243.5756 445037.8285 347893.6598 308679.5365 140581.3093 435697.7311 316574.7745 294383.6706 376701.979 0.986320541 1.075767047 1.181405603 0.923524906 0.819426373 0.373189729 1.156611208 0.840385217 0.781476305 1 18.52306409 3.510401748 4.39334624 0.825817071 1.079742815 0.257794771 0.191413596 0.289012453 12.83152948 0.05290247 0.080170378 3238.931384 -3.510401748 0.253925744 EVAYLGNEVSDEECLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVAYLGNEVSDEECLKR 17 1 Q8NFW8 Q8NFW8 CMAS N-acylneuraminate cytidylyltransferase 0 ; 156.13 1.49E-08 256660000 188246 237550 146077 211300 219886 251580 204829 245340 232370 215610 FALSE TRUE 180889.1382 230775.3066 172476.3634 222205.2183 226958.8329 256667.12 207335.7586 240273.6433 205992.3318 201006.5427 0.899916668 1.148098482 0.85806343 1.105462615 1.129111669 1.276909282 1.031487611 1.195352351 1.024804114 1 17.61688294 3.510602969 22.96112572 1.125837145 0.985821562 0.256718979 0.106134802 292.326903 200470.7143 0.026094487 0.040380223 3240.432421 -3.510602969 -0.140015582 VEFNIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEFNIR 6 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 135.82 0.031258 1007360000 616730 689810 751750 554680 603270 513820 582830 574190 545510 624440 FALSE TRUE 592627.5098 670137.2942 887607.9476 583307.1013 622674.7274 524209.7924 589962.8479 562332.7758 483585.9918 582146.1226 1.018004736 1.151149631 1.524716756 1.001994308 1.069619299 0.900478028 1.013427428 0.965964994 0.830695203 1 19.1510218 3.510835385 24.76350636 0.968654114 1.229956244 0.454491371 0.132244749 497.6139278 365503.1588 0.034904472 0.054033969 3242.167026 -3.510835385 0.26130213 YIQHTYR ddPTM_BT-474_Pertuzumab_2h_R1 6 YIQHTYR 7 0 P52565;J3KTF8;J3QQX2;J3KRY1;P52565-2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;; 159.2 0.0013924 8173190000 3471040 3818510 3254670 2948730 2705960 1203366 3921160 2791340 2924470 3487070 FALSE TRUE 3335387.919 3709609.834 3842861.269 3100914.309 2792999.661 1227698.885 3969148.329 2733697.854 2592496.426 3250887.643 1.025992986 1.14110675 1.182095997 0.953866959 0.859149859 0.377650359 1.220942944 0.840908132 0.797473401 1 21.63240226 3.511309263 3.555498874 0.847248508 1.117231148 0.262122569 0.199996642 0.321273426 8.418997339 0.055729133 0.085490923 3245.706632 -3.511309263 0.26998264 IPMFIVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 IPMFIVHK 8 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 94.887 0.010621 0 191180 211610 195140 170070 157240 82305 222060 160540 180620 209490 FALSE TRUE 183708.4742 205575.09 230406.1389 178847.3331 162297.7674 83969.26349 224777.6367 157224.7929 160116.7748 195301.0557 0.940642505 1.052606138 1.179748558 0.915752004 0.831013262 0.429947822 1.150928938 0.805038111 0.819845926 1 17.57534022 3.511340922 5.204794698 0.833293222 1.057631321 0.227889003 0.179217485 0.278520533 19.7480443 0.048227971 0.072936233 3245.943245 -3.511340922 0.224338099 HS(ph)SADNLANEMTYITETEDVFYTYK ddPTM_BT-474_Pertuzumab_2h_R1 4 HSSADNLANEMTYITETEDVFYTYK 25 0 J3KN34;P26045-2;P26045;P26045-3 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.43)S(0.43)ADNLANEMT(0.073)Y(0.065)ITET(0.001)EDVFYTYK 283.85 1.18E-53 349702000 175808 166813 147774 152808 148792 162046 176989 103526 228492 193757 TRUE FALSE 168937.229 162055.6566 174480.049 160694.4392 153578.0298 165322.6811 179155.0443 101388.1519 202554.5461 180633.6658 0.935247747 0.897150904 0.965933168 0.889615114 0.850218198 0.91523737 0.991814253 0.561291559 1.121355453 1 17.46270728 3.511981549 8.346496485 0.869381621 0.929103366 0 0.139766533 1.328458415 293.2969658 0.037763766 0.057535654 3250.734865 -3.511981549 0.059721745 NIIGSS(ph)PVADFSAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 NIIGSSPVADFSAIK 15 0 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 NIIGS(0.126)S(0.874)PVADFSAIK;NIIGS(0.163)S(0.837)PVADFSAIK 140.84 5.11E-06 38106000 147372 144039 126240 129434 124744 124440 121521 138712 149340 167291 TRUE FALSE 141612.5393 139931.1487 149054.3762 136114.1043 128756.504 126956.2621 123008.2103 135847.5487 132387.5493 155960.2316 0.908004162 0.897223269 0.955720408 0.872748796 0.825572665 0.81402971 0.788715233 0.871039671 0.848854531 1 17.25081868 3.512432863 6.625989669 0.846474616 0.917756895 0.183611416 0.055648193 0.271539984 37.07006023 0.014051075 0.021314014 3254.114745 -3.512432863 0.071282279 MYPPRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 MYPPRSPK 8 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 MYPPRS(1)PK;MYPPRS(1)PK;MYPPRS(1)PK 64.103 0.041849 2265760000 1641120 1529140 1275590 1201880 1370910 922530 1162990 1244740 1344750 1258380 TRUE FALSE 1576983.216 1485530.424 1506117.488 1263909.171 1415006.565 941184.1887 1177223.02 1219035.684 1192099.618 1173148.802 1.344231195 1.266276215 1.283824768 1.077364755 1.206161199 0.80227179 1.003472891 1.03911429 1.016153804 1 20.16195459 3.512439388 1.193455061 0.990145341 1.319283248 0.69684474 0.087303053 0.273392999 0.785534937 0.030254527 0.06415288 3254.163639 -3.512439388 0.329137907 SSS(ph)QIPEGFGLTSGGSNYSLAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSQIPEGFGLTSGGSNYSLAR 22 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 S(0.127)S(0.127)S(0.746)QIPEGFGLTSGGSNYSLAR;S(0.138)S(0.138)S(0.724)QIPEGFGLTSGGSNYSLAR;S(0.013)S(0.013)S(0.974)QIPEGFGLTSGGSNYSLAR 284.63 6.62E-46 538303000 304873 323278 268177 278452 260529 291848 251218 325442 291704 291497 TRUE FALSE 292958.2261 314058.428 316642.5495 292822.9411 268909.1519 297749.3665 254292.481 318721.509 258590.9848 271753.6486 1.078028677 1.155673271 1.16518233 1.077530854 0.989532812 1.095659131 0.935746336 1.172832492 0.951563985 1 18.05193988 3.512689833 5.822967429 1.038841908 1.133836338 0.320289044 0.069257116 0.245049972 23.59433458 0.017997415 0.02726224 3256.040764 -3.512689833 0.09499443 TQDHDENVALEACEFWLTLAEQPICK ddPTM_BT-474_Pertuzumab_2h_R1 5 TQDHDENVALEACEFWLTLAEQPICK 26 0 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ;;;; 151.47 1.18E-07 330806000 279899 267328 220737 258290 276104 299533 270041 247523 332854 326865 FALSE TRUE 268960.2376 259704.0672 260629.0862 271620.3779 284985.1359 305589.7625 273345.8425 242411.5636 295069.8094 304726.1424 0.882629352 0.852253978 0.855289553 0.891358962 0.93521722 1.002834086 0.897021307 0.795506292 0.968311439 1 18.21715375 3.512832248 4.411536765 0.915193865 0.863047105 0.195167416 0.057735879 0.471990948 20.95829875 0.017683949 0.026851852 3257.108664 -3.512832248 -0.05214676 TIVAVGS(ph)MEEAVILPFR ddPTM_BT-474_Pertuzumab_2h_R1 4 TIVAVGSMEEAVILPFR 17 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 TIVAVGS(1)MEEAVILPFR;TIVAVGS(1)MEEAVILPFR;TIVAVGS(1)MEEAVILPFR;TIVAVGS(1)MEEAVILPFR 188.27 4.41E-10 106349000 108675 109458 69023.8 119927 156245 115860 141264 172056 145537 138455 TRUE FALSE 104427.8609 106336.365 81497.93609 126116.4468 161270.7623 118202.7686 142992.8311 168502.9835 129016.2499 129077.3195 0.809033386 0.823819129 0.631388507 0.977061248 1.24941208 0.915751652 1.107807565 1.305442227 0.999526876 1 16.977876 3.513700087 5.554399434 1.117409881 0.765117691 0.613677935 0.120340298 0.122433135 10.2007273 0.033221424 0.050360443 3263.623769 -3.513700087 -0.35229219 KPLTSSSAAPQRPISTQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPLTSSSAAPQRPISTQR 18 2 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 177 5.40E-14 3373700000 1398130 1477160 1187860 1379900 1475690 1499750 1548720 1551780 1479510 1733100 FALSE TRUE 1343489.534 1435032.843 1402532.726 1451116.804 1523156.909 1530075.973 1567673.699 1519735.201 1311562.227 1615715.593 0.831513627 0.888171686 0.868056687 0.898126385 0.942713504 0.946995857 0.970265872 0.940595738 0.811753153 1 20.62374184 3.513750781 2.336965344 0.936049456 0.863732227 0.320521025 0.047564527 0.370778121 4.019925882 0.013684137 0.022395636 3264.004744 -3.513750781 -0.07231723 HNKS(ph)PTLSCR ddPTM_BT-474_Pertuzumab_2h_R1 3 HNKSPTLSCR 10 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 HNKS(0.918)PT(0.082)LSCR;HNKS(0.967)PT(0.033)LSCR;HNKS(0.966)PT(0.034)LSCR 137.09 6.08E-05 649490000 1021250 977700 784960 822110 784930 714190 860420 590230 1017870 944830 TRUE FALSE 981338.4209 949816.9533 926819.7333 864539.1956 810177.9863 728631.4111 870950.0773 578041.5442 902325.6649 880835.8225 1.114099127 1.078313267 1.05220486 0.981498678 0.919783194 0.827204562 0.988776858 0.656242094 1.024397103 1 19.74851362 3.514212568 1.222523132 0.864801777 1.102317744 0.362321325 0.102458291 0.429257849 1.293018822 0.034796671 0.073035264 3267.477217 -3.514212568 0.237515967 AFELLHLHLDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFELLHLHLDLR 12 0 Q9H4A4;A6NKB8;A0A087WU27 Q9H4A4 RNPEP Aminopeptidase B 0 ; 208.27 3.98E-08 363640000 386020 419440 347580 270120 273560 68061 404580 141151 289960 274660 FALSE TRUE 370933.9116 407477.9819 410395.4379 284060.9256 282359.3058 69437.24005 409531.3711 138236.1825 257044.9564 256057.0336 1.448637854 1.591356333 1.602750107 1.109365838 1.102720366 0.271178804 1.599375598 0.539864813 1.003858214 1 17.96610566 3.51480366 2.209398785 0.885858898 1.556701136 0.416390644 0.331053353 0.275945446 2.674516856 0.091469795 0.151895726 3271.927412 -3.51480366 0.670842238 SVSTPSEAGS(ph)QDSGDGAVGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSTPSEAGSQDSGDGAVGSR 21 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5;E7EV09;E7EQU2;E7ETL8;E9PGG1;E7EMU4;E7ESD3;E7ET01;E7ERR6;E7EUM4;E7ERH4 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 1 SVSTPS(0.001)EAGS(0.989)QDS(0.01)GDGAVGSR 290.49 1.09E-54 128140000 39401 41209 27356 39398 44124 40550 40395 44409 45263 39658 TRUE FALSE 37861.16536 40033.75967 32299.83773 41431.3355 45543.28853 41369.94878 40889.36609 43491.93863 40124.934 36971.92834 1.024051681 1.082815029 0.873631406 1.120616029 1.231834275 1.118955668 1.105957085 1.17635029 1.085281071 1 15.17414267 3.514975623 24.71098804 1.13443136 1.00154634 0.362859897 0.075003779 459.4973252 299954.4843 0.018868313 0.029221935 3273.223216 -3.514975623 -0.13288502 SPDVGLYGVIPECGETYHSDLAEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPDVGLYGVIPECGETYHSDLAEAK 25 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 70.091 0.039405 181700000 177070 163160 128320 143910 124310 113460 125270 126810 175750 155480 FALSE TRUE 170149.9086 158506.8366 151510.2785 151337.2123 128308.544 115754.2389 126803.0917 124191.3292 155799.5968 144949.2011 1.173858892 1.093533702 1.045264667 1.044070689 0.885196628 0.79858487 0.87481056 0.856792092 1.07485654 1 17.14518786 3.515033099 1.843082472 0.896690346 1.114757405 0.531045929 0.079907057 0.25183071 1.704239453 0.024388852 0.042782615 3273.656437 -3.515033099 0.218067059 QRQEELCLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QRQEELCLAR 10 1 Q5VY30;P02753 Q5VY30 RBP4 Retinol-binding protein 4;Plasma retinol-binding protein(1-182);Plasma retinol-binding protein(1-181);Plasma retinol-binding protein(1-179);Plasma retinol-binding protein(1-176) 0 155.26 1.19E-05 460640000 320510 353500 370680 288620 284910 302260 296070 302780 309510 326390 FALSE TRUE 307984.1149 343418.5261 437670.1217 303515.7128 294074.3889 308371.9043 299693.3932 296527.4872 274375.7224 304283.3146 1.01216235 1.128614386 1.438363856 0.997477345 0.966449275 1.013436786 0.984915632 0.974511164 0.901711363 1 18.2150557 3.515065527 24.99201725 0.975586923 1.191823183 0.484830486 0.102329643 459.4599156 302622.3316 0.026956282 0.041749336 3273.900881 -3.515065527 0.21623626 ERVEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERVEEK 6 1 Q15843;F8VSA6;E9PS38;S4R3E9;E9PL57 Q15843 NEDD8;NEDD8-MDP1 NEDD8 0 80.462 0.058778 236150000 285540 269820 265750 305290 372220 407640 393620 388590 428950 475440 FALSE TRUE 274380.7811 262124.9978 313776.9366 321046.0535 384192.7943 415882.7601 398437.2393 380565.4807 380257.3943 443238.0253 0.619037098 0.59138653 0.707919715 0.724319745 0.86678663 0.938283126 0.898923866 0.85860296 0.857907879 1 18.75772213 3.515100315 1.352913158 0.901018935 0.610125963 0.878569423 0.045465599 0.142231047 0.523282033 0.015101926 0.030164857 3274.163144 -3.515100315 -0.290892972 DFDCCCLSLQPCHDPVVTPDGYLYER ddPTM_BT-474_Pertuzumab_2h_R1 1 DFDCCCLSLQPCHDPVVTPDGYLYER 26 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2;M0QX85 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 0 145.52 2.25E-07 267520000 102770 107540 73693 99588 113430 105640 97515 98495 123450 121230 FALSE TRUE 98753.63478 104473.0645 87010.96439 104727.7486 117078.579 107776.1132 98708.41774 96461.04383 109436.4735 113018.9841 0.873779176 0.924385096 0.769879194 0.926638559 1.035919584 0.953610705 0.873379092 0.853494168 0.968301692 1 16.7862056 3.515512067 24.97267409 0.93392038 0.860419416 0.286657847 0.062403032 882.1301253 573810.7609 0.018000622 0.027879797 3277.268827 -3.515512067 -0.073500964 HLFNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLFNLK 6 0 Q7LBR1 Q7LBR1 CHMP1B Charged multivesicular body protein 1b 0 ; 136.29 0.01323 1292950000 2507240 2611120 2209120 2048300 2099780 1620920 2250970 1757930 2552150 2381570 FALSE TRUE 2409254.289 2536653.414 2608357.126 2154013.008 2167321.331 1653696.113 2278518.044 1721628.131 2262440.631 2220264.143 1.085120569 1.142500735 1.174795861 0.970160697 0.976154724 0.744819538 1.026237374 0.775415906 1.018996158 1 21.08229989 3.516178009 2.389318143 0.901042853 1.135288275 0.484121983 0.095132485 0.213653572 2.419803596 0.025834929 0.042144917 3282.298004 -3.516178009 0.234245422 GDYPLEAVR ddPTM_BT-474_Pertuzumab_2h_R1 6 GDYPLEAVR 9 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 256.45 1.28E-14 13476090000 6058210 6421580 5357540 4687100 4263470 1726540 5808210 4297740 4384750 4983010 FALSE TRUE 5821448.455 6238442.826 6325766.656 4929001.793 4400608.385 1761451.822 5879292.611 4208990.167 3887011.562 4645506.294 1.253135414 1.342898369 1.361695853 1.061025748 0.947282838 0.379173272 1.265587051 0.906034757 0.836725066 1 22.14740441 3.51619498 2.790651531 0.889830831 1.321304367 0.463071868 0.206986294 0.244229599 3.784681679 0.059241218 0.093819893 3282.426274 -3.51619498 0.431473536 WFCHIQHYPGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 WFCHIQHYPGIR 12 0 O43324 O43324 EEF1E1 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 94.363 0.0038467 359350000 462030 453330 424100 299100 285720 152418 385830 102098 339020 382160 FALSE TRUE 443973.3568 440401.4723 500744.3041 314536.5868 294910.4433 155499.9964 390551.903 99989.64062 300535.8709 356275.9628 1.246150185 1.236124573 1.405495617 0.882845377 0.827758463 0.43645941 1.096206154 0.280652222 0.843547986 1 18.44263563 3.517370616 2.536895957 0.690701092 1.291043986 0.506909857 0.236827955 0.203303511 2.595671715 0.06510369 0.10496269 3291.323847 -3.517370616 0.600342894 LQLKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQLKPR 6 1 Q15056;K7EJP0;Q15056-2 Q15056;Q15056-2 EIF4H;TNNI3 Eukaryotic translation initiation factor 4H 0 136.19 0.012106 1667800000 2364700 2347400 2176000 1808100 1571000 558350 2249100 1699600 1863200 2130900 FALSE TRUE 2272284.91 2280454.45 2569251.605 1901416.258 1621532.642 569640.2196 2276625.159 1664502.666 1651697.347 1986572.245 1.143821935 1.147934316 1.29330892 0.957134211 0.8162465 0.286745282 1.146006728 0.837876735 0.831430798 1 20.92184983 3.517790168 3.769438993 0.814112318 1.18829651 0.38916719 0.20969166 0.238589711 7.064758134 0.058772806 0.090212813 3294.504979 -3.517790168 0.374184192 QVKPYVEEGLHPQIIIR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVKPYVEEGLHPQIIIR 17 1 Q99832-3;Q99832;Q99832-4;F8WAM2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 181.41 4.84E-10 3211600000 3035970 2945680 2637770 2671430 2509930 2762840 2839740 2668910 3339170 3445630 FALSE TRUE 2917320.936 2861672.091 3114473.716 2809302.822 2590664.178 2818706.518 2874493.588 2613796.076 2960121.421 3212254.411 0.908184895 0.890860973 0.969560102 0.874558009 0.806494084 0.877485453 0.894852406 0.813695225 0.921509022 1 21.61515473 3.517872646 24.24764935 0.869881779 0.92006645 0.0534599 0.055584308 660.171584 392809.0384 0.013918776 0.021559083 3295.130702 -3.517872646 0.050184671 VIQYLAYVASSHK ddPTM_BT-474_Pertuzumab_2h_R1 2 VIQYLAYVASSHK 13 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 180.84 1.26E-05 572340000 1226860 1630780 1259600 1142530 962310 420480 1446400 985200 1224900 1507220 FALSE TRUE 1178912.955 1584271.751 1487237.74 1201496.11 993263.5751 428982.3937 1464101.476 964855.2757 1085854.487 1405134.647 0.839003548 1.127487501 1.058430765 0.855075428 0.70688142 0.305296289 1.041965252 0.686663928 0.772776111 1 20.42227695 3.518004254 3.625645716 0.734430234 1.017793172 0.243072397 0.200034562 0.298017801 8.068841527 0.054476126 0.083847894 3296.129408 -3.518004254 0.283362938 RPYTVILIER ddPTM_BT-474_Pertuzumab_2h_R1 1 RPYTVILIER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 71.268 0.082566 557050000 631360 656790 510210 530470 597110 500690 530110 564060 591700 662890 FALSE TRUE 606685.7532 638058.9923 602416.2966 557847.6203 616316.5854 510814.2948 536597.6448 552411.9639 524532.6966 617991.8699 0.981705072 1.032471499 0.974796475 0.902677927 0.997289148 0.826571222 0.868292401 0.893882251 0.848769575 1 19.23722833 3.518318766 1.057245994 0.88572791 1.009750047 0.366708965 0.054957811 0.512258207 1.154062316 0.019575945 0.044514391 3298.517299 -3.518318766 0.124022138 SRDPGMVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDPGMVR 8 1 P33993;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 91.069 0.011627 344050000 125130 129350 126640 109180 106360 85799 126390 106120 116130 119490 FALSE TRUE 120239.7813 125661.0646 149526.6651 114814.7929 109781.166 87533.91457 127936.7986 103928.5849 102947.4093 111396.8359 1.079382375 1.128048779 1.342288261 1.030682712 0.985496268 0.785784568 1.148477851 0.932958141 0.92415021 1 16.76534873 3.518669128 8.343088107 0.965975627 1.179620219 0.470368427 0.104561538 0.28932209 54.06229961 0.027440158 0.042069739 3301.179415 -3.518669128 0.213644592 VFVHYTGWLLDGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFVHYTGWLLDGTK 14 0 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 252.08 3.40E-24 3081700000 4473000 5341400 4937100 4258700 4225100 2529000 5527100 4170100 5476900 6160500 FALSE TRUE 4298190.215 5189068.502 5829343.795 4478492.017 4361004.179 2580138.113 5594742.303 4083985.978 4855185.273 5743243.848 0.748390688 0.903508303 1.014991519 0.77978441 0.759327706 0.44924753 0.974143263 0.711093954 0.845373347 1 22.45343439 3.518900272 23.8710022 0.768536087 0.891579751 0.070985079 0.155871504 627.7533929 358672.9465 0.039984127 0.061933748 3302.93686 -3.518900272 0.123043665 MFGIDR ddPTM_BT-474_Pertuzumab_2h_R1 5 MFGIDR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;; 148.37 0.025066 1939476000 2566450 2741790 2186030 1784280 1949360 496229 2069490 1681490 1623500 1813740 FALSE TRUE 2466150.297 2663596.834 2581094.249 1876366.905 2012062.935 506263.0904 2094817.038 1646766.644 1439207.086 1690893.774 1.458489193 1.575259708 1.526467415 1.109689404 1.189940471 0.299405615 1.238881513 0.973903074 0.851151686 1 20.6893546 3.519979479 1.894880131 0.9137883 1.536881456 0.555606354 0.239200598 0.253555346 1.810867747 0.0711901 0.124236828 3311.154758 -3.519979479 0.623093156 YIQELWR ddPTM_BT-474_Pertuzumab_2h_R1 3 YIQELWR 7 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;; 166.05 0.002647 3808890000 4697300 5415690 4837600 3980160 3832080 1773420 4718880 3769610 4155830 4925760 FALSE TRUE 4513724.323 5261239.824 5711861.932 4185576.535 3955342.333 1809279.767 4776631.065 3691766.236 3684077.601 4592133.888 0.982925244 1.145706975 1.243836106 0.911466572 0.861329924 0.39399543 1.040176785 0.803932622 0.802258316 1 22.13073328 3.520303041 3.697780332 0.806011836 1.125212157 0.382148222 0.173663221 0.229233858 6.458470243 0.047569905 0.073237022 3313.622579 -3.520303041 0.319200321 QKFDNLYCCR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKFDNLYCCR 10 1 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 72.2 0.042319 0 230750 290350 207040 214450 157480 124560 243710 204260 238900 233420 FALSE TRUE 221732.0349 282069.5023 244456.7336 225517.7902 162545.4872 127078.6885 246692.5959 200041.9596 211781.0736 217610.2555 1.018941108 1.296214196 1.123369544 1.036338061 0.746956925 0.583973803 1.133644163 0.919267151 0.973212743 1 17.73138702 3.520584371 3.760990258 0.892778521 1.157007461 0.354969737 0.153233477 0.255137503 7.465573559 0.044189785 0.067973228 3315.769796 -3.520584371 0.26422894 FYEEEENGGVWEGFGDFSPTDVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FYEEEENGGVWEGFGDFSPTDVHR 24 0 P19838;P19838-2;P19838-3;A0A494C1E9;D6RF93 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 0 ; 214.49 1.49E-32 155575000 88652 87339 75577 89808 89633 100368 109078 93395 108035 119648 FALSE TRUE 85187.38183 84848.17723 89235.4451 94443.00164 92516.12685 102397.5097 110412.9292 91466.36061 95771.31972 111544.1344 0.763710098 0.760669108 0.800001234 0.846687297 0.829412746 0.917999949 0.989858676 0.820001528 0.85859575 1 16.76725513 3.520827062 1.019240763 0.903539272 0.756763073 0.557220692 0.053756064 0.484915067 1.014055634 0.021337845 0.049603827 3317.623218 -3.520827062 -0.146776199 AEVVETTQVYTEEETRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEVVETTQVYTEEETRR 17 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 289.98 9.36E-46 342350000 114200 122120 125200 97219 90998 72920 107650 79652 122710 146950 FALSE TRUE 109736.9377 118637.2572 147826.4251 102236.4842 93925.03331 74394.49236 108967.4529 78007.15837 108780.4752 136996.9456 0.801017404 0.865984688 1.079049058 0.746268348 0.68559947 0.543037599 0.795400601 0.569408011 0.79403577 1 17.0637842 3.52205079 11.8513622 0.698069057 0.910881229 0.246303306 0.138908454 1.431199475 375.6437388 0.034738984 0.05365751 3326.984598 -3.52205079 0.212812172 EPEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 3 EPEQLRK 7 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646;P51991;P51991-2 F8W6I7;P51991;P51991-2 HNRNPA1;HNRNPA1L2;HNRNPA3 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoprotein A3" 0 ;; 113.5 0.0098046 6137800000 1978350 1969990 1797140 2191150 2176750 2167160 2482770 2772230 2760160 2745110 FALSE TRUE 1901033.895 1913807.814 2121923.175 2304235.514 2246767.141 2210981.46 2513154.882 2714982.482 2446838.208 2559181.255 0.742828939 0.747820347 0.829141418 0.900379959 0.877924194 0.863940941 0.982015196 1.060879325 0.956101958 1 21.2872509 3.522536453 0.451183661 1.028891857 0.677326169 0.827669122 0.04156965 0.749102545 0.250142771 0.039393154 0.127542256 3330.707181 -3.522536453 -0.351565688 CIVHSPTNPGFMTCSDDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 CIVHSPTNPGFMTCSDDFR 19 0 Q05048 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 ; 211.09 1.45E-16 341450000 160978 174133 135766 137175 119303 72636 177196 116621 145848 165947 FALSE TRUE 154686.8018 169166.8973 160301.9363 144254.6182 123140.4893 74104.74969 179364.5777 114212.7356 129291.9465 154707.2619 0.99986775 1.093464491 1.036162972 0.932435985 0.795958043 0.478999814 1.159380468 0.738250643 0.835719959 1 17.23918139 3.522813179 3.046488916 0.823300083 1.047556491 0.23807022 0.16610999 0.347253416 6.420110099 0.04571899 0.071823257 3332.830135 -3.522813179 0.224256408 GYFEHREDR ddPTM_BT-474_Pertuzumab_2h_R1 4 GYFEHREDR 9 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8;M0QZV6 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ;;; 130.41 0.00021745 831937000 770033 904745 566058 619592 697713 607305 659544 547460 636683 600924 FALSE TRUE 739939.259 878942.5584 668357.2725 651569.2174 720155.5723 619585.1232 667615.6968 536154.7597 564409.415 560222.8822 1.320794424 1.568915848 1.193020303 1.16305356 1.285480467 1.105961828 1.191696587 0.957038309 1.007472977 1 19.09564139 3.523086137 0.385467101 0.962439907 1.54718003 0.658595476 0.101229255 1.368794053 0.310034669 0.097307757 0.342044903 3334.925505 -3.523086137 0.584740123 SGAQASST(ph)PLS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 SGAQAS(0.012)S(0.419)T(0.569)PLS(0.829)PT(0.171)R;SGAQAS(0.063)S(0.167)T(0.77)PLS(0.98)PT(0.02)R;SGAQAS(0.206)S(0.307)T(0.487)PLS(0.991)PT(0.009)R;SGAQASS(0.086)T(0.913)PLS(0.939)PT(0.061)R 188.77 4.22E-06 2559680000 2284420 2264560 2345530 2094100 1941810 2397990 2092030 2419420 2099010 2362780 TRUE FALSE 2195142.341 2199976.966 2769419.447 2202176.752 2004270.082 2446479.001 2117632.889 2369458.132 1860739.185 2202746.806 0.996547735 0.998742552 1.257257275 0.999741208 0.909895807 1.11064921 0.9613601 1.075683381 0.844735845 1 21.07087224 3.524186188 24.99966885 0.994104254 1.084448642 0.171546126 0.097817039 760.1063535 403746.5902 0.02529499 0.039185645 3343.383446 -3.524186188 0.090344388 YHGNVMLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YHGNVMLLR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 187.78 4.01E-05 1832560000 813020 960340 830190 594650 393480 159002 811890 255170 532860 706150 FALSE TRUE 781246.2796 932952.0435 980223.8005 625339.9578 406136.6415 162217.1294 821826.1527 249900.6503 472371.9667 658321.8315 1.186723943 1.417167104 1.488973559 0.949900076 0.616927196 0.246410071 1.248365333 0.379602557 0.717539574 1 19.32843352 3.524743709 3.549680677 0.670955964 1.365429238 0.531237281 0.276886117 0.167809363 4.279187388 0.073904767 0.114460561 3347.678239 -3.524743709 0.694473274 YWPQEAGEYAVHVLCNSEDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 YWPQEAGEYAVHVLCNSEDIR 21 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 206.86 3.98E-22 81647000 72473 92549 54032 63153 46637 31805 47500 42854 63696 64163 FALSE TRUE 69640.67504 89909.59313 63796.78434 66412.3339 48137.12146 32448.11889 48081.31921 41969.04992 56465.49712 59817.18286 1.164225256 1.503073011 1.066529403 1.110255126 0.804737354 0.542454815 0.803804474 0.701621974 0.943967844 1 15.86827235 3.525079836 1.669965887 0.765722704 1.301706733 0.626132812 0.157304682 0.209302862 1.163753892 0.046663437 0.08570421 3350.270214 -3.525079836 0.535984028 NFQLLVITHDEDFVELLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NFQLLVITHDEDFVELLGR 19 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494BZX8 Q92878-2 RAD50 DNA repair protein RAD50 0 112.55 0.00019445 8607600 16857 17249 12473 13123 11720 10495 8403.1 11723 14655 12449 FALSE TRUE 16198.2098 16757.07541 14727.14856 13800.2796 12096.98444 10707.21609 8505.939651 11480.91595 12991.42584 11605.81814 1.395697365 1.443851283 1.268945315 1.189082875 1.042320696 0.92257314 0.732903062 0.989237968 1.119389058 1 13.50256061 3.525104159 1.311752383 0.938310531 1.417035166 0.787981936 0.095845154 0.199954696 0.690570907 0.034010544 0.069745013 3350.45785 -3.525104159 0.478724635 SPS(ph)PQFAPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPQFAPQK 10 0 Q13796;C9IZC6;F5H3B6 Q13796 SHROOM2 Protein Shroom2 1 S(0.079)PS(0.921)PQFAPQK;S(0.365)PS(0.635)PQFAPQK 132.86 0.0002228 795380000 1124240 1272860 1144570 1043190 1002100 846700 1128660 1073250 1212790 1292960 TRUE FALSE 1080303.458 1236559.279 1351419.26 1097029.161 1034333.457 863820.8541 1142472.879 1051087.012 1075119.164 1205386.668 0.896229805 1.025861089 1.121149998 0.910105604 0.858092664 0.716633822 0.947806135 0.87199157 0.891928866 1 20.20106458 3.525248744 9.305796868 0.872705646 1.015806902 0.328393715 0.085020068 0.506891589 94.85100108 0.022362572 0.034480178 3351.573472 -3.525248744 0.143101256 TPHTATLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPHTATLR 8 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 104.06 0.0046536 427070000 124002 112135 95890 118983 115034 143076 125145 132856 137553 122843 FALSE TRUE 119155.8647 108937.0196 113219.4561 125123.7269 118734.1731 145969.0947 126676.5619 130112.4772 121938.5601 114522.7342 1.04045599 0.951226151 0.988619918 1.09256671 1.036773824 1.274586184 1.106125896 1.136127932 1.064754182 1 16.80527449 3.525387876 1.874695998 1.121331587 0.987969728 0.300876076 0.072733939 0.355147002 2.480864133 0.021153965 0.037223733 3352.647359 -3.525387876 -0.133361859 SLGTRPPHVFAIADK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGTRPPHVFAIADK 15 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71;A0A590UJW9 Q9UM54-1 MYO6 Unconventional myosin-VI 0 84.874 0.0049031 502940000 668030 727220 605120 594050 575610 273150 719260 623220 706450 802780 FALSE TRUE 641922.6491 706480.3976 714478.6448 624708.9917 594125.0184 278673.2801 728062.519 610350.2892 626256.7577 748406.9956 0.857718665 0.94397888 0.954665909 0.834718269 0.793852839 0.372355258 0.972816293 0.815532582 0.836786349 1 19.51346352 3.525730996 3.748058176 0.785037276 0.920392423 0.095712828 0.161643366 0.512756529 14.70040204 0.045158647 0.069724235 3355.297213 -3.525730996 0.135355147 DGWSLWYSEYR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGWSLWYSEYR 11 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;; 231.38 2.58E-12 447506000 553400 539790 504166 405997 280175 221917 309261 336939 461907 761630 FALSE TRUE 531772.5162 524395.7177 595280.0113 426950.5538 289187.0833 226404.3138 313045.8286 329981.0919 409473.2538 710044.1217 0.748928834 0.738539623 0.838370452 0.601301441 0.407280441 0.3188595 0.44088222 0.464733221 0.576687056 1 19.43754915 3.527083909 4.468852225 0.489695078 0.768748297 0.247242559 0.177107767 0.231806633 9.879626047 0.045274011 0.069480094 3365.765922 -3.527083909 0.279053219 KAIVER ddPTM_BT-474_Pertuzumab_2h_R1 5 KAIVER 6 1 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;;; 94.262 0.071645 2187840000 3996920 4162480 3582940 3669830 3585400 3896970 3605440 4038380 4249440 4473830 FALSE TRUE 3840715.948 4043770.146 4230456.96 3859230.366 3700727.647 3975769.403 3649564.453 3954986.042 3767061.386 4170813.509 0.920855353 0.969539908 1.014300196 0.925294396 0.887291565 0.953235956 0.875024607 0.948252909 0.903195834 1 21.99189738 3.528519124 24.51960179 0.922916393 0.96860179 0.174680844 0.039779009 402.8834054 192196.0715 0.009849385 0.015258367 3376.907182 -3.528519124 0.045685397 DCEAEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCEAEVR 7 0 P30153;B3KQV6;C9J9C1;P30154-4;P30154;P30154-2;P30154-3;P30154-5;H0YDG7 P30153 PPP2R1A;PPP2R1B Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform;Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform 0 ; 171.47 0.0021788 727310000 1670880 1711060 1389000 1605010 1680460 1778360 1657220 1721110 1997870 1883100 FALSE TRUE 1605580.162 1662262.244 1640023.198 1687844.758 1734513.522 1814319.658 1677501.554 1685568.477 1771080.173 1755555.96 0.914570768 0.946858022 0.934190214 0.961430337 0.988013804 1.033472985 0.95553864 0.960133722 1.008842904 1 20.74349655 3.528943354 2.586219172 0.986472384 0.932805643 0.576143837 0.022582221 0.242850695 3.210337177 0.006990917 0.011321765 3380.207447 -3.528943354 -0.053666741 IDHILDAL ddPTM_BT-474_Pertuzumab_2h_R1 2 IDHILDAL 8 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 97.602 0.01888 33237000 168776 294370 164197 169053 100599 19528.1 200230 128604 139013 124707 FALSE TRUE 162180.0473 285974.8558 193871.0504 177777.8456 103834.8582 19922.97156 202680.4746 125948.2825 123232.827 116260.4838 1.394971378 2.459776929 1.667557575 1.529133888 0.893122536 0.171364946 1.743330734 1.083328387 1.059971738 1 16.82700129 3.528961575 2.546428341 1.02059709 1.911002541 0.435286965 0.436383881 0.266192284 3.411568551 0.126065265 0.204790728 3380.349265 -3.528961575 0.890405451 LWDFQGFECIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LWDFQGFECIR 11 0 P43034;I3L3N5;P43034-2 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 118.28 0.0017258 107400000 90473 93638 78363 80363 75293 67059 95830 74950 83903 112280 FALSE TRUE 86937.21514 90967.53592 92524.93728 84510.54406 77714.86772 68414.97893 97002.79621 73402.25631 74378.68319 104675.1756 0.830542816 0.869045936 0.883924357 0.807359946 0.742438379 0.653593161 0.926702971 0.701238435 0.710566596 1 16.67555981 3.529517426 4.684057034 0.772706998 0.86095057 0.079796576 0.100508199 0.414700441 19.43034927 0.025833147 0.039677613 3384.678525 -3.529517426 0.088243571 NIIIALIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 NIIIALIDR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 114.84 0.0036589 69948000 193407 186324 157003 149307 141964 120704 126322 142368 179241 178685 FALSE TRUE 185848.4406 181010.222 185376.9346 157012.7522 146530.401 123144.7176 127867.9664 139428.051 158894.3131 166582.5058 1.11565401 1.086610032 1.112823545 0.942552469 0.879626587 0.739241597 0.767595408 0.836990958 0.953847539 1 17.34587737 3.530407908 2.239700113 0.840450387 1.107024557 0.670944607 0.074831381 0.166459095 1.652126495 0.021955701 0.036772005 3391.62563 -3.530407908 0.26657417 NGPLNES(ph)QEDEEDSEHGTSLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGPLNESQEDEEDSEHGTSLNR 22 0 Q9H2K8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 1 NGPLNES(1)QEDEEDSEHGTSLNR;NGPLNES(1)QEDEEDSEHGTSLNR 394.05 3.18E-132 1216110000 294900 378150 192684 363220 401010 351940 430320 452520 486700 453040 TRUE FALSE 283374.982 367365.5322 227506.285 381965.8277 413908.8508 359056.4679 435586.3849 443175.3039 431451.8564 422355.1973 0.670939967 0.869802324 0.538661029 0.904371084 0.980001794 0.850129157 1.031327157 1.049295254 1.021537936 1 18.68809728 3.53095589 6.11671415 0.988246024 0.710367523 0.677995272 0.090873494 0.128714468 10.83600897 0.024303294 0.037367598 3395.907793 -3.53095589 -0.277878501 QPYPSRPPFDNQHS(ph)QDLDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 QPYPSRPPFDNQHSQDLDSR 20 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 QPYPSRPPFDNQHS(1)QDLDSR;QPYPSRPPFDNQHS(1)QDLDSR;QPYPSRPPFDNQHS(1)QDLDSR;QPYPSRPPFDNQHS(1)QDLDSR 218.11 6.13E-25 1123400000 459681 417676 303240 466651 621320 419327 526600 622360 531988 524215 TRUE FALSE 441716.1583 405764.2894 358042.2135 490734.914 641305.3221 427806.0792 533044.6883 609508.0485 471598.9525 488709.4511 0.903842063 0.830277148 0.732627971 1.004144513 1.312242521 0.875379181 1.090719009 1.247178763 0.964988402 1 18.89861748 3.530991678 6.206956344 1.100518388 0.82776474 0.451646182 0.12675194 0.183421034 15.91092266 0.033648786 0.051745106 3396.187647 -3.530991678 -0.272753648 ASSHSS(ph)QTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ASS(0.008)HS(0.086)S(0.904)QT(0.001)QGGGSVTK 246.49 3.50E-20 7423600000 1447600 1944700 1163600 957800 1017100 823180 531020 769100 712520 820520 TRUE FALSE 1391026.192 1889239.06 1373888.404 1007232.173 1049815.945 839825.2636 537518.7816 753217.8162 631637.7167 764945.4496 1.818464562 2.469769656 1.796060628 1.316737257 1.372406288 1.09788909 0.702689037 0.984668667 0.825729099 1 19.54499734 3.531167809 0.982740384 0.894106993 2.205194805 0.837584684 0.208864775 0.210348824 0.407091582 0.079844471 0.191728956 3397.565274 -3.531167809 1.311087812 LETHMTPEMFR ddPTM_BT-474_Pertuzumab_2h_R1 4 LETHMTPEMFR 11 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 218.18 1.08E-11 1722290000 1886620 2357560 1810720 1499800 1482260 480428 1834160 1251620 1436160 1784000 FALSE TRUE 1812888.805 2290324.697 2137957.383 1577204.858 1529938.239 490142.5833 1856606.999 1225773.61 1273133.138 1663168.091 1.090021396 1.377085521 1.285472824 0.948313563 0.919893935 0.294704177 1.116307491 0.73701126 0.765486751 1 20.66550255 3.531549217 2.414329269 0.786720634 1.265419276 0.460758798 0.214635855 0.24269569 2.795258074 0.059939264 0.098665627 3400.550405 -3.531549217 0.478698642 TTAGS(ph)VDWTDQLGLR ddPTM_BT-474_Pertuzumab_2h_R1 7 TTAGSVDWTDQLGLR 15 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;T(0.003)T(0.015)AGS(0.983)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR 328 9.14E-69 1992250000 1715696 1727923 1139861 1594220 1744393 1491417 1604131 1870707 1822051 1696657 TRUE FALSE 1648644.704 1678644.328 1345859.239 1676497.885 1800502.985 1521574.474 1623762.835 1832076.247 1615219.409 1581740.91 1.042297568 1.061263774 0.850872118 1.059906761 1.13830462 0.961961889 1.026566882 1.158265703 1.021165602 1 20.59308187 3.531584121 24.9998719 1.063103809 0.986278571 0.129015925 0.076884526 552.2045792 253474.2902 0.020671253 0.032023584 3400.823721 -3.531584121 -0.076825237 LAMQEFMILPVGAANFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAMQEFMILPVGAANFR 17 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ; 185.59 1.33E-09 263620000 326000 388520 279210 292560 251570 264120 275960 253084 320350 288420 FALSE TRUE 313259.5596 377439.79 329669.458 307659.0567 259661.9775 269460.6874 279337.281 247857.727 283985.211 268885.0565 1.165031496 1.403721705 1.226060913 1.144202882 0.965698804 1.002140806 1.038872463 0.921798073 1.0561584 1 18.03663005 3.531604269 2.20735581 0.991161397 1.284746693 0.765510311 0.06653107 0.127530844 1.229464058 0.018363077 0.03090139 3400.981492 -3.531604269 0.293585296 RPGQAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPGQAAK 7 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 72.138 0.084047 79488000 221210 188140 176660 147700 114930 71285 158830 145800 121410 144460 FALSE TRUE 212564.8686 182774.4314 208586.3918 155322.8147 118626.8278 72726.43154 160773.8091 142789.179 107628.0458 134675.5955 1.578347345 1.357145893 1.548806159 1.153310769 0.880833884 0.540011954 1.193785767 1.060245388 0.799165174 1 17.03912892 3.532067144 3.310327842 0.929407062 1.479371967 0.695094556 0.172017083 0.152046425 3.306289782 0.050931131 0.079746373 3404.608223 -3.532067144 0.549964905 STTSVS(ph)EEDVSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 STTSVSEEDVSSR 13 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 STTSVS(1)EEDVSSR 281.68 1.90E-32 119650000 149440 143680 104910 134320 149510 133820 132390 148950 161360 137700 TRUE FALSE 143599.7196 139582.3871 123869.5707 141252.2713 154319.1249 136525.9321 134010.2284 145874.1304 143043.0893 128373.4563 1.118609124 1.087315019 0.964915756 1.100323037 1.202110852 1.06350593 1.043909171 1.136326267 1.114273101 1 16.9699874 3.532156877 24.99966775 1.102208444 1.055422793 0.059101631 0.063114562 714.4892226 324551.3316 0.016660822 0.025810606 3405.311751 -3.532156877 -0.046785651 HELQVEMK ddPTM_BT-474_Pertuzumab_2h_R1 1 HELQVEMK 8 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 103.55 0.008118 0 448410 391430 371460 367340 363830 320980 427510 297330 502010 513690 FALSE TRUE 430885.6415 380266.7997 438591.0851 386298.4614 375532.9224 327470.4355 432741.9953 291190.0316 445023.9294 478897.3188 0.899745362 0.794046625 0.915835332 0.806641521 0.784161672 0.683800937 0.903621671 0.608042727 0.929267949 1 18.86935683 3.532319972 7.817224367 0.786479393 0.862408281 0 0.114461164 0.776171555 99.74109588 0.028656356 0.044207413 3406.590824 -3.532319972 0.075928888 GFAFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFAFVR 6 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 ; 110.43 0.066786 1555580000 1338580 1532490 1313850 1212340 1136650 620780 1516470 1304600 1251600 1486910 FALSE TRUE 1286266.814 1488784.886 1551291.921 1274909.013 1173211.38 633332.5969 1535029.013 1277659.554 1109523.615 1386200.261 0.927908362 1.074004188 1.119096544 0.919714884 0.846350569 0.456883911 1.107364539 0.921699115 0.800406439 1 20.40270426 3.532562387 4.775701915 0.856927269 1.042726926 0.201010811 0.164592117 0.351287007 16.84216953 0.045928092 0.070659957 3408.492846 -3.532562387 0.185799657 LCYSSDHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LCYSSDHEK 9 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 142.98 0.00010303 280180000 319650 311130 288810 248220 188830 97491 340850 202520 251430 406840 FALSE TRUE 307157.7246 302256.877 341004.3915 261030.6639 194903.8884 99462.33482 345021.4243 198337.8912 222888.7205 379284.3644 0.809834924 0.796913623 0.899073159 0.688218889 0.513872721 0.262236844 0.909664243 0.522926621 0.587655968 1 18.53292037 3.532635105 5.102261668 0.604924026 0.828822112 0.165795675 0.197044268 0.322432514 17.9160668 0.051190933 0.078724704 3409.063614 -3.532635105 0.223898086 DGIVLGADTR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGIVLGADTR 10 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 ;; 145.89 6.89E-05 948120000 2144440 2263080 1961520 1822460 1736240 973810 2216810 1873840 1970230 2220840 FALSE TRUE 2060632.914 2198539.174 2316010.298 1916517.379 1792087.736 993501.1054 2243939.984 1835144.549 1746577.75 2070420.529 0.995272644 1.061880494 1.118618303 0.925665754 0.865567024 0.47985474 1.083808798 0.886363192 0.843585989 1 20.9814924 3.53309281 3.904448937 0.856182001 1.0578123 0.260117499 0.149432238 0.314444548 9.653284263 0.041674654 0.06450603 3412.658333 -3.53309281 0.201630299 HVVLGAIENK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVVLGAIENK 10 0 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 0 107.21 0.0023148 881470000 508450 496680 500190 422160 435420 268020 510490 335270 520410 613570 FALSE TRUE 488579.2119 482515.1727 590585.4597 443947.7282 449425.6797 273439.548 516737.5293 328346.5573 461335.2385 572012.3574 0.854141009 0.843539771 1.032469757 0.776115625 0.785692256 0.478030841 0.903367773 0.574020042 0.806512714 1 19.12568679 3.533199145 6.276029788 0.727464027 0.90475591 0.156692242 0.149438372 0.319861371 27.49568604 0.037472509 0.057695596 3413.494011 -3.533199145 0.177291883 LFVCDVLPLIINNHDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFVCDVLPLIINNHDVR 17 0 Q9NVR2 Q9NVR2 INTS10 Integrator complex subunit 10 0 ; 168.41 2.10E-09 127401000 217939 206575 199552 187431 189993 196091 185845 203516 220031 217210 FALSE TRUE 209421.7029 200683.6833 235615.4854 197104.3364 196104.2974 200056.0944 188119.4267 199313.3235 195054.0033 202498.1732 1.034190579 0.991039475 1.163543758 0.973363528 0.96842502 0.987940243 0.928993204 0.984272205 0.963238336 1 17.62754937 3.533656846 24.99991448 0.970104249 1.057855766 0.469739447 0.043985336 239.5994137 105949.5886 0.011125604 0.017235633 3417.093374 -3.533656846 0.087751517 TSGHVDK ddPTM_BT-474_Pertuzumab_2h_R1 5 TSGHVDK 7 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;;; 66.258 0.068362 1109890000 2285087 2261430 1868458 2014620 1880959 1806904 2393800 2104669 1973910 2456660 FALSE TRUE 2195783.274 2196936.231 2206129.924 2118594.78 1941461.754 1843440.837 2423096.04 2061206.85 1749840.012 2290268.23 0.958745026 0.959248442 0.963262685 0.925042208 0.847700601 0.80490172 1.057996617 0.899984911 0.764032784 1 21.12708514 3.533755711 4.791894107 0.897544535 0.959024881 0.113276123 0.080756096 0.514288583 24.63095987 0.02219772 0.034173956 3417.871343 -3.533755711 0.061480345 NSRPEANEALER ddPTM_BT-474_Pertuzumab_2h_R1 2 NSRPEANEALER 12 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 ; 228.38 9.76E-12 1766770000 1567820 1510120 1272920 1346800 1361350 1358560 1301810 1421880 1623890 1495880 FALSE TRUE 1506547.861 1467052.856 1502964.96 1416308.509 1405139.059 1386031.014 1317741.94 1392517.681 1439552.815 1394562.715 1.080301262 1.051980553 1.077732069 1.015593271 1.007583986 0.993882167 0.944914077 0.998533566 1.03226108 1 20.41138138 3.53395261 1.974872489 0.991618704 1.069799797 0.689299522 0.02194221 0.188243033 1.455245321 0.006756634 0.011770625 3419.421276 -3.53395261 0.078181093 IETLDPALIRPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 IETLDPALIRPGR 13 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 177.1 1.43E-05 2700370000 3299590 3570390 2695880 3314310 3656840 3469890 3530230 3797230 3625190 3746440 FALSE TRUE 3170638.375 3468565.973 3183085.486 3485361.936 3774465.58 3540053.553 3573434.011 3718815.874 3213673.629 3492690.282 0.907792595 0.993092915 0.911356355 0.997901805 1.080675718 1.013560685 1.023117918 1.064742526 0.920114115 1 21.73590729 3.533979599 6.328483118 1.024764466 0.944130855 0.365368253 0.046070253 0.223199277 19.28797856 0.0117767 0.018140278 3419.633784 -3.533979599 -0.080633611 AGAHLQGGAK ddPTM_BT-474_Pertuzumab_2h_R1 19 AGAHLQGGAK 10 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;; 157.58 2.08E-05 56367534800 97731931.1 100543321.1 80737291.7 82436984.2 80856511.6 62671460 88443140.1 84135450.6 93624792.3 85036444.4 FALSE TRUE 93912459.18 97675924.02 95328316.3 86691566.83 83457334.73 63938719.86 89525533.7 82398024.14 82996898.39 79276850.28 1.184613905 1.232086336 1.202473559 1.093529404 1.052732726 0.806524473 1.129277127 1.039370558 1.046924772 1 26.24039631 3.534447175 2.313389781 1.014797187 1.211352005 0.555453765 0.077854037 0.234254918 2.476994846 0.023166293 0.038602722 3423.317459 -3.534447175 0.196554818 TYYYNNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TYYYNNR 7 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 168.74 0.0024144 579580000 244110 246580 222420 201858 205310 116874 223230 227810 219600 232180 FALSE TRUE 234569.9113 239547.7798 262616.2417 212275.9156 211913.9826 119237.2724 225961.9555 223105.6439 194671.9286 216454.2418 1.083692837 1.106690162 1.213264473 0.980696492 0.979024393 0.550865954 1.043924821 1.030728906 0.899367585 1 17.72370255 3.534524106 3.67041501 0.920769008 1.131142192 0.336141669 0.135887978 0.294213864 7.893742081 0.039524771 0.061454154 3423.923921 -3.534524106 0.210373184 NCLTNFHGMDLTR ddPTM_BT-474_Pertuzumab_2h_R1 5 NCLTNFHGMDLTR 13 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;; 190.24 4.58E-06 4243490000 3049780 2862290 2617090 2107000 2082360 1007847 2150490 2010410 2192070 2544810 FALSE TRUE 2930591.226 2780660.292 3090056.38 2215742.523 2149341.001 1028226.357 2176808.34 1968894.331 1943235.404 2372447.752 1.235260597 1.172063869 1.302476051 0.933947869 0.905959256 0.433403162 0.917536893 0.829899975 0.819084594 1 21.17794488 3.534578055 2.634401678 0.800387186 1.231247117 0.619915903 0.145744914 0.176675515 2.418246271 0.04114316 0.066660934 3424.349275 -3.534578055 0.43085993 ELSDFLR ddPTM_BT-474_Pertuzumab_2h_R1 6 ELSDFLR 7 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;;;;; 139.27 0.0062933 1011160000 1962898 2209975 2029588 1803221 1822806 1188479 2158112 1890831 2066699 2339773 FALSE TRUE 1886185.776 2146948.677 2396379.7 1896285.452 1881438.21 1212510.86 2184523.62 1851784.679 1832095.994 2181298.091 0.864707939 0.984252765 1.098602575 0.869338061 0.862531452 0.555866649 1.00147872 0.84893701 0.839910878 1 21.05675551 3.534897974 11.01543013 0.843253786 0.983034889 0.177624816 0.126479197 1.398917302 263.7226593 0.033202919 0.051386134 3426.87272 -3.534897974 0.139781103 TFHIFYYLLSGAGEHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TFHIFYYLLSGAGEHLK 17 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 221.49 2.12E-15 358360000 793910 715720 688450 498560 719740 580410 809460 327510 860140 714970 FALSE TRUE 762883.1195 695308.3664 812868.2295 524290.7413 742891.0908 592146.2879 819366.4136 320746.804 762500.5132 666544.4451 1.144534509 1.043153793 1.219525923 0.786580318 1.114540968 0.888382301 1.229274986 0.481208427 1.143960495 1 19.34634155 3.534990648 0.609234023 0.885157437 1.158879471 0.063302858 0.212976693 2.382079454 1.640482568 0.131896339 0.386549211 3427.604056 -3.534990648 0.273722034 GRYPDHSVDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 GRYPDHSVDRR 11 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;; 162.93 1.38E-05 220913000 221746 239548 187980 176694 172193 147965 199233 152223 167020 177392 FALSE TRUE 213079.9212 232716.3256 221952.1676 185813.1985 177731.7442 150956.9537 201671.2731 149079.5419 148060.5898 165377.0818 1.288448912 1.407186068 1.342097497 1.123572846 1.074706013 0.912804556 1.219463246 0.901452246 0.89529086 1 17.33539979 3.535460817 1.803068166 0.994741071 1.36223361 0.731120263 0.09385366 0.177796918 1.147925464 0.028368117 0.051066307 3431.316806 -3.535460817 0.367492538 QPAQSQNLS(ph)PLSGFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPAQSQNLSPLSGFSR 16 0 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 QPAQS(0.01)QNLS(0.987)PLS(0.002)GFSR 113.33 0.0016763 0 159230 143220 123440 93923 104820 103240 81235 75912 79610 71902 TRUE FALSE 153007.1156 139135.5058 145748.3539 98770.37729 108191.6305 105327.5835 82229.17823 74344.39067 70573.00655 67032.0135 2.282597636 2.075657564 2.174309652 1.473480687 1.61402925 1.571302696 1.226715027 1.109087834 1.052825402 1 16.03256265 3.535504288 0.410558293 0.945386308 2.614701193 0.91829451 0.12977169 0.552545764 0.145150804 0.12057215 0.415218177 3431.660283 -3.535504288 1.669314885 up NS(ph)PNNISGISNPPGTPR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPNNISGISNPPGTPR 17 0 Q9BWW4-2;Q9BWW4;Q9NW25;A0A087WVT6;Q9BWW4-3 Q9BWW4-2 SSBP3 Single-stranded DNA-binding protein 3 1 NS(0.991)PNNIS(0.009)GISNPPGTPR 268.49 5.86E-28 262770000 93359 80921 77153 95611 94953 87414 104280 124670 101860 102090 TRUE FALSE 89710.42707 78613.21231 91096.26336 100545.4952 98007.24948 89181.57097 105556.2098 122095.5209 90297.27983 95175.35337 0.942580446 0.825982878 0.95714132 1.05642366 1.029754511 0.937023797 1.109070848 1.282848097 0.948746463 1 16.5383004 3.535914382 0.727762842 1.107351603 0.865761632 0.256266904 0.101005699 0.99441048 1.021893903 0.055892787 0.154335383 3434.902244 -3.535914382 -0.24158997 KWQVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KWQVSR 6 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 170.17 0.0093336 1632870000 2187300 2348600 1999670 1855840 1719220 1386930 1687610 1867630 2176000 2523100 FALSE TRUE 2101817.898 2281620.228 2361054.851 1951620.125 1774520.273 1414974.675 1708263.476 1829062.788 1928989.603 2352208.19 0.893550965 0.969990768 1.003761003 0.82969702 0.754406128 0.601551632 0.726238215 0.77759392 0.820076051 1 21.16558433 3.536119804 3.756708224 0.759122884 0.956047692 0.383195063 0.097351828 0.207272672 5.814447254 0.026296039 0.040864991 3436.527345 -3.536119804 0.196924807 LEYGGLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEYGGLGR 8 0 Q96DG6 Q96DG6 CMBL Carboxymethylenebutenolidase homolog 0 77.282 0.078204 336230000 388850 345730 323800 380030 447450 525610 391950 465770 481540 452050 FALSE TRUE 373653.3121 335870.1189 382317.8629 399643.3938 461842.6356 536238.1943 396746.8013 456151.6867 426877.598 421432.2509 0.886627237 0.796972985 0.907187008 0.948298079 1.095888211 1.272418504 0.941424869 1.082384383 1.01292105 1 18.6849412 3.536774573 2.382816018 1.071892952 0.852743917 0.531960525 0.086222623 0.224537652 2.516227077 0.025148441 0.041682495 3441.712375 -3.536774573 -0.219149035 EHTLAWK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHTLAWK 7 0 P22102;P22102-2;F8WD69;C9JBJ1;C9JTV6;C9JZG2;C9JKQ7 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 120.65 0.0045151 339730000 829250 897650 931550 721660 753150 729110 895530 555250 906020 948000 FALSE TRUE 796841.9932 872049.9009 1099901.807 758904.9591 777375.7537 743853.1038 906489.764 543783.8935 803172.4079 883791.1156 0.901618017 0.986714944 1.244526889 0.858692677 0.87959218 0.841661667 1.025683273 0.61528554 0.908780812 1 19.7533459 3.537016701 24.99760356 0.852903718 1.040709757 0.241911168 0.132558203 310.5719755 129617.4171 0.035367414 0.05479086 3443.631732 -3.537016701 0.187806039 NTCEHIYEFPQLSEDVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 NTCEHIYEFPQLSEDVIR 18 0 A6NIH7 A6NIH7 UNC119B Protein unc-119 homolog B 0 178.72 8.73E-14 156610000 135430 144120 102580 140280 160400 154190 151720 153350 168060 170780 FALSE TRUE 130137.2459 140009.8387 121118.4879 147519.8676 165559.4117 157307.8274 153576.7947 150183.2689 148982.5334 159212.9185 0.817378685 0.879387427 0.760732791 0.926557148 1.039861672 0.988034319 0.964600085 0.943285698 0.935744001 1 17.28059787 3.537330454 5.994427698 0.973981401 0.826620536 0.771299712 0.038690649 0.106559042 7.910240154 0.010541398 0.016255364 3446.120458 -3.537330454 -0.147360864 HEMLPEFYK ddPTM_BT-474_Pertuzumab_2h_R1 3 HEMLPEFYK 9 0 Q86VP6;Q86VP6-2;A0A0C4DGH5;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 114.84 0.0015728 1156780000 2095980 2240330 2094530 1834870 1836650 1332150 2172710 1444780 2486190 2403170 FALSE TRUE 2014066.784 2176437.982 2473058.164 1929567.861 1895727.515 1359086.986 2199300.275 1414944.788 2203968.134 2240401.155 0.898975962 0.971450125 1.103846138 0.861259983 0.846155391 0.606626622 0.981654678 0.631558676 0.983738171 1 21.09532565 3.538169836 5.995551942 0.812575507 0.989886689 0.175141576 0.13820168 0.294175591 21.61493511 0.03491759 0.053863653 3452.787382 -3.538169836 0.177311182 YSS(ph)QDADEQDWEFQKR ddPTM_BT-474_Pertuzumab_2h_R1 3 YSSQDADEQDWEFQKR 16 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YS(0.355)S(0.645)QDADEQDWEFQKR;YS(0.013)S(0.987)QDADEQDWEFQKR;YS(0.148)S(0.852)QDADEQDWEFQKR 200.1 2.23E-11 1039560000 470120 484900 365729 477070 577540 494280 502260 540540 574300 536110 TRUE FALSE 451747.1907 471071.1268 431824.3659 501691.6399 596117.0986 504274.6803 508406.8081 529377.6601 509107.8717 499798.7922 0.903858108 0.942521539 0.863996417 1.003787219 1.192714164 1.00895538 1.017222963 1.059181551 1.018625654 1 18.93098789 3.538615498 6.206120456 1.052649964 0.910101598 0.5849287 0.054823295 0.155645056 12.15046128 0.014505464 0.02238385 3456.332367 -3.538615498 -0.142548366 GLGSS(ph)PDLELLLR ddPTM_BT-474_Pertuzumab_2h_R1 7 GLGSSPDLELLLR 13 0 Q9NQQ7-2;Q9NQQ7;Q9NQQ7-3 Q9NQQ7-2 SLC35C2 Solute carrier family 35 member C2 1 GLGS(0.108)S(0.892)PDLELLLR;GLGS(0.324)S(0.676)PDLELLLR;GLGS(0.171)S(0.829)PDLELLLR;GLGS(0.073)S(0.927)PDLELLLR;GLGS(0.025)S(0.975)PDLELLLR;GLGS(0.36)S(0.64)PDLELLLR;GLGS(0.048)S(0.952)PDLELLLR 229.63 5.70E-12 263123400 329138 456753 259095 502727 397082 372676 499403 631222 477309 404398 TRUE FALSE 316274.9231 443726.8516 305919.23 528672.8007 409854.5032 380211.7641 505514.8433 618187.0451 423126.8834 377007.7633 0.83890825 1.176970065 0.811440134 1.402286245 1.087124837 1.008498501 1.340860567 1.63971967 1.122329365 1 18.52423471 3.538859623 0.670632568 1.321863943 0.911870146 0.15359665 0.22511956 1.471295029 1.259431417 0.131409279 0.375110548 3458.27578 -3.538859623 -0.409993797 (ac)AAAITDMADLEELSRLS(ph)PLPPGS(ph)PGSAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAAITDMADLEELSRLSPLPPGSPGSAAR 29 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 2 AAAIT(0.067)DMADLEELS(0.151)RLS(0.778)PLPPGS(0.645)PGS(0.359)AAR;AAAITDMADLEELS(0.045)RLS(0.952)PLPPGS(0.843)PGS(0.159)AAR 63.282 2.57E-06 44995000 1358.4 1141.3 0 1296.9 2557.98 976.78 993.21 1378.8 1265.2 1010.6 TRUE FALSE 1305.312226 1108.751241 0 1363.833164 2640.25975 996.5311608 1005.365201 1350.327298 1121.5798 942.1511619 1.385459445 1.176829458 0 1.447573616 2.802373819 1.057718975 1.067095432 1.433238479 1.190445701 1 9.879814739 3.538875911 24.99997532 1.464338258 0.859271922 0.162587287 0.593391856 407.9275819 165138.7337 0.161415235 0.250063082 3458.405482 -3.538875911 -0.605066336 SSFSQHAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 121.67 0.0014233 793214000 1095170 1610360 1295000 951990 768502 588243 1197790 639720 584298 1078470 FALSE TRUE 1052369.546 1564434.11 1529035.307 1001122.318 793221.5648 600137.6765 1212448.912 626509.5584 517970.9406 1005424.266 1.046692009 1.555993984 1.520786158 0.995721261 0.788942133 0.596899932 1.205907748 0.623129538 0.515176486 1 19.93937298 3.539018411 3.559813859 0.783145485 1.389422361 0.565439534 0.229003047 0.165112201 4.119343187 0.062791243 0.098113227 3459.540439 -3.539018411 0.606276876 AFLLDPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFLLDPDR 8 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 84.498 0.040502 88197000 258950 286830 252660 216890 189700 90481 267640 211080 230400 290990 FALSE TRUE 248829.9477 278649.8892 298321.2824 228083.7189 195801.8728 92310.58781 270915.4584 206721.1242 204245.9579 271280.9881 0.917240642 1.027163353 1.099676334 0.840765586 0.721767766 0.340276657 0.998652579 0.762018473 0.752894478 1 18.04942842 3.539840261 4.436980512 0.75015876 1.014061945 0.28822009 0.176204889 0.267067599 10.44198204 0.048022137 0.074280268 3466.0934 -3.539840261 0.263903184 ASS(ph)HSSQTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.165)S(0.825)HS(0.003)S(0.007)QTQGGGSVTK;AS(0.001)S(0.333)HS(0.333)S(0.333)QT(0.002)QGGGSVTK;AS(0.116)S(0.88)HS(0.003)SQTQGGGSVTK;AS(0.049)S(0.95)HS(0.001)SQTQGGGSVTK 270.08 1.33E-28 24556920000 3012630 4355000 2802900 2051854 2086803 1668396 1164174 1646686 1554917 1869462 TRUE FALSE 2894893.089 4230799.664 3309446.38 2157750.431 2153926.914 1702132.11 1178421.51 1612681.359 1378409.341 1742841.674 1.661018974 2.42752955 1.898879531 1.238064515 1.235870674 0.976641846 0.676149491 0.925317189 0.790897625 1 20.73301008 3.540007492 1.415964006 0.873500422 2.095595513 0.829125354 0.21672205 0.150162088 0.601202958 0.068023903 0.136507461 3467.428323 -3.540007492 1.222095091 SFSQPEAGGS(ph)HHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SFSQPEAGGSHHK 13 0 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;B7WPG3;Q8WVV9-5;Q8WVV9-3;Q8WVV9-2 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 1 SFSQPEAGGS(1)HHK 109.54 0.0007272 193780000 183240 184640 158700 145640 126680 139510 153250 102940 170330 173010 TRUE FALSE 176078.7782 179374.248 187380.6203 153156.4979 130754.7772 142330.9878 155125.5193 100814.253 150994.8525 161291.8786 1.091677893 1.112109609 1.161748638 0.949561126 0.810671798 0.882443611 0.961768941 0.625042339 0.936159054 1 17.29931427 3.540634738 3.466096376 0.843359246 1.1197514 0.548477069 0.100455828 0.16681809 3.932004866 0.028533894 0.044725649 3472.439902 -3.540634738 0.276392154 LWTFLEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LWTFLEDR 8 0 Q86TU7 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 0 87.251 0.035959 47085000 94738 98502 85780 73783 66380 54252 74521 69320 67683 89707 FALSE TRUE 91035.53422 95692.8194 101282.3542 77590.94947 68515.17298 55349.01261 75433.01029 67888.51778 59999.90959 83631.06499 1.088537307 1.144225766 1.211061394 0.927776652 0.819255058 0.661823601 0.90197357 0.811761967 0.717435675 1 16.35175131 3.540852443 3.343077465 0.809859377 1.146472507 0.718767894 0.091704857 0.12018469 2.634180635 0.024612581 0.038712849 3474.181017 -3.540852443 0.33661313 VHSDFTAAATR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHSDFTAAATR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 143.97 3.69E-05 441510000 224922 232510 216880 197426 196859 176625 255646 153714 238380 254790 FALSE TRUE 216131.7996 225879.0425 256075.0405 207615.1795 203191.1485 180196.4785 258774.6722 150539.7522 211320.1018 237532.8464 0.90990279 0.950938137 1.0780616 0.874048296 0.855423373 0.758617098 1.089426899 0.633763938 0.889645811 1 17.8577675 3.541136701 9.634146494 0.849442485 0.976904263 0.124799198 0.12331906 0.876311072 127.8396519 0.031794203 0.049211538 3476.455711 -3.541136701 0.127461779 ERPS(ph)SREDTPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 ERPS(0.54)S(0.443)REDT(0.013)PS(0.003)R;ERPS(0.812)S(0.187)REDTPSR;ERPS(0.889)S(0.111)REDTPSR 125.98 0.00023288 1907190000 514799 570326 403769 536286 580725 662996 599062 571133 570187 568844 TRUE FALSE 494680.0859 554060.8609 476739.0401 563963.7847 599404.547 676402.2334 606393.5 559338.904 505461.7622 530315.6892 0.932803038 1.044775541 0.898972159 1.06344918 1.130278736 1.275470908 1.14345759 1.054728184 0.953133713 1 19.01649191 3.541169748 5.840158431 1.104051023 0.968156802 0.305749858 0.089225576 0.276075649 18.59104805 0.025229896 0.038962353 3476.720255 -3.541169748 -0.135894222 DRNVATPR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRNVATPR 8 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;; 145.84 0.00051341 506886000 406128 413981 319246 353554 364665 292882 380867 359170 367530 411994 FALSE TRUE 390256.0688 402174.6672 376940.8538 371800.9643 376394.7809 298804.2747 385528.1643 351753.014 325809.5352 384089.2794 1.016055614 1.047086417 0.981388635 0.968006618 0.979966901 0.777955259 1.003746225 0.915810549 0.848265111 1 18.55108217 3.542744884 1.368551299 0.914206834 1.027390556 0.312212377 0.065489229 0.508088203 1.900638859 0.020796352 0.042570066 3489.352813 -3.542744884 0.113183722 NSNSPPS(ph)PSSMNQR ddPTM_BT-474_Pertuzumab_2h_R1 5 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 NSNSPPS(1)PSSMNQR;NSNSPPS(1)PSSMNQR;NSNSPPS(1)PSSMNQR;NSNSPPS(0.852)PS(0.133)S(0.014)MNQR;NSNS(0.001)PPS(0.987)PS(0.012)S(0.001)MNQR 386.13 6.96E-114 2413040000 1367561 1407799 1145273 1209396 1095710 1204618 1144692 1256338 1428389 1408758 TRUE FALSE 1314115.204 1367649.951 1352249.308 1271813.072 1130954.507 1228976.201 1158701.083 1230394.181 1266244.269 1313341.566 1.000589061 1.041351303 1.029624998 0.968379518 0.861127476 0.935762815 0.882254178 0.936842489 0.964139339 1 20.32481074 3.543123229 4.241825805 0.923851394 1.02419634 0.544085351 0.038018902 0.148159839 5.201376956 0.009947356 0.015433063 3492.393964 -3.543123229 0.100344946 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIK ddPTM_BT-474_Pertuzumab_2h_R1 3 MESEGGADDSAEEGDLLDDDDNEDRGDDQLELIK 34 1 P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIK 362 5.12E-133 732750000 212912 239926 314836 380864 235422 333950 431650 452560 527900 602860 TRUE FALSE 204591.1637 233083.5454 371733.8687 400520.4367 242994.5624 340702.6978 436932.6618 443214.4779 467975.0051 562027.7552 0.364023239 0.414718923 0.6614155 0.712634622 0.432353314 0.60620262 0.777421858 0.788598915 0.832654617 1 19.10028185 3.543517519 0.160773406 1.136312648 4.83E-20 0.76250028 0.095122348 6.945201808 0.317523321 0.509583562 1.835734741 3495.566099 -3.543517519 -1.136312648 down FWTHWNR ddPTM_BT-474_Pertuzumab_2h_R1 1 FWTHWNR 7 0 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 141.78 0.0025335 319200000 188420 238650 192570 138050 118790 63766 124840 102720 133030 159590 FALSE TRUE 181056.3381 231843.9357 227371.6827 145174.777 122610.9882 65055.39221 126367.8293 100598.7961 117928.9921 148780.8272 1.216933267 1.558291751 1.528232414 0.975762669 0.824104763 0.437256557 0.849355604 0.6761543 0.79263568 1 17.1828291 3.543669956 2.817474576 0.735198313 1.447392699 0.770821815 0.162665283 0.111725643 1.7402464 0.044388467 0.071517662 3496.793256 -3.543669956 0.712194386 YGTCPHGGYGLGLER ddPTM_BT-474_Pertuzumab_2h_R1 5 YGTCPHGGYGLGLER 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;; 256.52 9.31E-25 6815890000 4497910 4709740 4243050 4049190 4255150 3413720 4430250 4156410 4640570 4899330 FALSE TRUE 4322126.704 4575422.827 5009863.521 4258169.181 4392020.764 3482747.757 4484468.725 4070578.681 4113791.948 4567494.015 0.946279665 1.001735922 1.096851688 0.932276904 0.961582161 0.76250735 0.981822573 0.891206133 0.900667179 1 22.12297141 3.544386707 8.017599005 0.910317536 1.014215046 0.281841042 0.070494737 0.379664357 41.47422111 0.018096208 0.028002076 3502.569061 -3.544386707 0.10389751 IHFPLATYAPVISAEK ddPTM_BT-474_Pertuzumab_2h_R1 3 IHFPLATYAPVISAEK 16 0 P68363;P68363-2;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;; 255.31 1.58E-26 11973450000 4285940 4141930 3572120 3428110 2813220 3202110 3842190 2664840 3931060 4199960 FALSE TRUE 4118440.726 4023806.212 4217681.545 3605035.168 2903709.776 3266858.858 3889211.871 2609810.123 3484822.549 3915492.968 1.051831981 1.027662735 1.077177658 0.920710418 0.741594941 0.834341649 0.993287921 0.666534238 0.890008634 1 21.90076253 3.545261695 4.186182775 0.834270076 1.047516769 0.443730896 0.097175245 0.183537532 6.218943474 0.026003824 0.040407418 3509.632922 -3.545261695 0.213246693 HYTEAIKR ddPTM_BT-474_Pertuzumab_2h_R1 5 HYTEAIKR 8 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 194.2 0.00010818 5623800000 5519760 6115010 5030000 5165770 5154090 5242390 5932380 4317900 6351170 6406710 FALSE TRUE 5304041.677 5940615.902 5939032.892 5432376.009 5319875.986 5348394.718 6004982.241 4228733.856 5630211.808 5972777.825 0.888035991 0.994615249 0.994350211 0.909522532 0.890687071 0.895461856 1.005391866 0.708001198 0.942645444 1 22.50997063 3.545443452 4.680224209 0.887137455 0.962230802 0.043368268 0.083425816 0.44926956 18.91980368 0.023023098 0.035670371 3511.102046 -3.545443452 0.075093347 RPSDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSDIK 6 1 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 89.369 0.080564 245320000 352420 359420 288590 383000 363320 441800 396590 450780 453370 405310 FALSE TRUE 338647.0368 349169.6935 340744.6326 402766.6759 375006.5178 450733.4987 401443.5871 441471.2355 401905.3383 377857.9927 0.896228327 0.924076506 0.901779608 1.065920752 0.99245358 1.1928648 1.062419202 1.168352249 1.063641225 1 18.52748461 3.545723877 1.329713682 1.105452001 0.897570508 0.60269513 0.06204746 0.259556666 0.916525222 0.019095221 0.03979661 3513.369909 -3.545723877 -0.207881493 TTAAHGLELR ddPTM_BT-474_Pertuzumab_2h_R1 3 TTAAHGLELR 10 0 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ;; 125.74 0.00040106 834020000 836050 911260 727980 692720 665450 365520 768180 700580 795510 793070 FALSE TRUE 803376.2417 885271.757 859542.1798 728471.3622 686854.8036 372911.0648 777581.2166 686112.7782 705207.0399 739354.6625 1.086591162 1.197357374 1.162557327 0.98528 0.928992321 0.504373724 1.051702594 0.927988708 0.953814286 1 19.49590705 3.547056596 2.721945517 0.887776822 1.154507796 0.390848044 0.141720346 0.282553031 4.105527422 0.041230514 0.066977453 3524.167942 -3.547056596 0.266730974 KHELLNSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KHELLNSTR 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 137.46 0.00010651 871450000 1995830 2098330 1869860 1284110 1358770 379010 1804090 603610 1478610 1645270 FALSE TRUE 1917830.757 2038487.683 2207785.297 1350383.071 1402476.071 386673.8419 1826168.993 591145.2426 1310764.392 1533834.397 1.250350599 1.329014192 1.439389611 0.880396915 0.914359512 0.252096212 1.190590716 0.385403563 0.854567086 1 20.5487113 3.547244854 2.508591314 0.717132892 1.340723761 0.471794577 0.267510171 0.219576656 2.716653071 0.071692973 0.118369343 3525.695927 -3.547244854 0.623590869 KFIQTFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFIQTFGK 8 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 109.44 0.009851 0 728140 761560 666360 659900 642430 504020 788780 720940 779690 785820 FALSE TRUE 699683.4838 739841.0544 786786.0751 693957.5181 663094.3444 514211.6297 798433.3256 706052.3371 691182.8599 732595.7115 0.955074501 1.009889961 1.073970353 0.947258505 0.905129984 0.701903685 1.089868959 0.963768046 0.94347107 1 19.48265773 3.547407888 9.811075532 0.933790648 1.012503272 0.121310629 0.095610118 1.197918162 161.9916476 0.026326152 0.040769551 3527.019721 -3.547407888 0.078712624 IFHLWR ddPTM_BT-474_Pertuzumab_2h_R1 1 IFHLWR 6 0 E9PDF6;O43795;O43795-2 E9PDF6 MYO1B Unconventional myosin-Ib 0 123.07 0.052231 0 146210 170020 147240 128210 108890 71156 155860 123710 145890 167490 FALSE TRUE 140495.9516 165171.1961 173849.5433 134826.9335 112392.5457 72594.82307 157767.4613 121155.3453 129329.1788 156145.7531 0.899774402 1.057801399 1.113379902 0.863468463 0.719792524 0.464917051 1.010385862 0.775911883 0.828259343 1 17.25253381 3.547942649 5.116077019 0.787208836 1.024957542 0.300799068 0.151710383 0.251851668 12.34303971 0.040885422 0.063331012 3531.365331 -3.547942649 0.237748705 KGDRSPEPGQTWT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 KGDRSPEPGQTWTR 14 2 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 KGDRS(0.036)PEPGQT(0.08)WT(0.884)R 85.443 0.012436 874230000 286680 288230 275920 236600 222810 249040 240260 227470 256630 222030 TRUE FALSE 275476.2287 280009.9626 325784.8818 248810.9544 229976.886 254075.7594 243200.3737 222772.665 227498.4383 206991.7103 1.330856333 1.352759307 1.573903038 1.202033424 1.111043943 1.227468284 1.174928085 1.076239549 1.099070286 1 17.65921347 3.548537728 6.077285258 1.127047658 1.411618376 0.728573514 0.082846089 0.120103766 7.979550292 0.022125538 0.034248511 3536.207398 -3.548537728 0.284570718 YSGTLNLDR ddPTM_BT-474_Pertuzumab_2h_R1 5 YSGTLNLDR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 200.88 5.21E-05 5168650000 2930710 3283890 2945710 2351020 1875260 586705 3276530 2132980 2410250 3130180 FALSE TRUE 2816174.613 3190236.672 3478065.324 2472356.424 1935579.441 598568.5771 3316629.154 2088933.218 2136648.525 2918170.121 0.965048128 1.093231902 1.191865169 0.847228339 0.663285333 0.20511778 1.136544141 0.715836682 0.732187788 1 21.47663256 3.549014924 4.612451573 0.731044416 1.081492038 0.29805415 0.233427269 0.267432164 10.71597623 0.063430069 0.098457094 3540.09506 -3.549014924 0.350447622 VNSSLSDELRR ddPTM_BT-474_Pertuzumab_2h_R1 1 VNSSLSDELRR 11 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 147.72 0.0028375 0 206390 227290 159170 215260 238400 225310 226320 242330 266560 237960 FALSE TRUE 198324.0506 220807.9117 187935.5597 226369.5944 246068.3525 229865.9226 229089.7719 237325.8008 236301.2263 221842.7572 0.893984789 0.99533523 0.847156617 1.020405612 1.109201651 1.036166001 1.032667348 1.069792874 1.065174402 1 17.75917793 3.549602714 6.604709011 1.055355428 0.921395502 0.673822543 0.043483528 0.132359404 9.980898618 0.010752538 0.0166471 3544.889601 -3.549602714 -0.133959925 EFEPLLNWMK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFEPLLNWMK 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 156.92 2.35E-05 216406000 330870 399900 355980 291470 269220 190479 339930 268130 313490 355480 FALSE TRUE 317939.2346 388495.2435 420313.5047 306512.8016 277879.7058 194330.6159 344090.165 262593.0218 277903.9295 331403.023 0.959373369 1.17227429 1.268285066 0.924894405 0.838494783 0.586387578 1.038283121 0.792367612 0.838567877 1 18.33822724 3.549869052 4.994046639 0.839394634 1.135763199 0.46921484 0.134925133 0.176123442 8.13246944 0.035530828 0.055092067 3547.064226 -3.549869052 0.296368565 NFPNAIEHTLQWAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFPNAIEHTLQWAR 14 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 232.8 3.23E-14 8780000000 3059600 2939300 2623660 2389830 2208090 1585300 2218260 2611130 2837900 2832300 FALSE TRUE 2940027.449 2855474.042 3097813.725 2513169.413 2279115.22 1617355.852 2245407.729 2557209.253 2515753.489 2640465.798 1.113450305 1.081428149 1.173207291 0.951790178 0.863148927 0.612526719 0.85038319 0.968468993 0.952768822 1 21.33236102 3.550133017 3.700349222 0.867492649 1.117399969 0.536708334 0.102678936 0.195308037 5.133945476 0.030847374 0.048367812 3549.220795 -3.550133017 0.24990732 KVGTLWR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVGTLWR 7 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C0V6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 117.04 0.0085324 865140000 1255410 1390970 1219760 1101180 1020490 527520 1302040 1155380 1312840 1539850 FALSE TRUE 1206347.189 1351300.898 1440197.765 1158012.032 1053314.988 538186.8158 1317974.755 1131520.999 1163811.907 1435554.588 0.840335296 0.941309309 1.003234414 0.806665272 0.733733845 0.374898189 0.918094488 0.788211754 0.810705435 1 20.45317676 3.550161724 5.182120119 0.75543464 0.928479444 0.161989782 0.157902736 0.365259673 17.99838773 0.042942138 0.066560625 3549.455406 -3.550161724 0.173044805 ASNIFGT(ph)PEENQASWAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASNIFGTPEENQASWAK 17 0 Q9UK76-3;J3KSH8 Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 ASNIFGT(1)PEENQASWAK 229.75 1.13E-14 40204000 60323 69113 34561 85093 96721 158410 80903 101790 97186 89616 TRUE FALSE 57965.51047 67141.96491 40806.94151 89484.65993 99832.1188 161613.1587 81893.11511 99688.00093 86153.85272 83546.2285 0.693813611 0.803650459 0.488435471 1.071079587 1.194932681 1.934415971 0.98021319 1.193207673 1.031211753 1 16.35028708 3.550285191 4.078893268 1.239708495 0.678674623 0.46734913 0.266522212 0.201746265 6.376301774 0.074132531 0.115603988 3550.464632 -3.550285191 -0.561033872 RVTYVVLDEADR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVTYVVLDEADR 12 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 73.156 0.064068 127760000 99583 119850 105050 78932 73550 49441 97040 57076 71090 94344 FALSE TRUE 95691.18627 116431.9953 124034.8718 83005.68998 75915.80255 50440.73089 98227.60455 55897.36065 63020.16123 87953.99685 1.087968594 1.323782881 1.410224393 0.943739829 0.863130787 0.573489923 1.116806604 0.635529512 0.716512762 1 16.42446152 3.550287515 3.631984201 0.801780979 1.276971735 0.588830005 0.169737427 0.15208945 3.856794983 0.045322248 0.07116603 3550.483637 -3.550287515 0.475190755 HFELGGDK ddPTM_BT-474_Pertuzumab_2h_R1 4 HFELGGDK 8 0 H0Y5B4;H7BZ11;J3KQN4;P83881;R4GN19;Q969Q0 H0Y5B4;Q969Q0 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a;60S ribosomal protein L36a-like 0 ;;; 149.82 0.00049914 5661670000 10765300 9833000 9586500 8865780 9255230 7242200 10724100 7886150 11807500 11337300 FALSE TRUE 10344580.17 9552572.468 11318993.8 9323343.968 9552932.878 7388642.246 10855344.74 7723298.247 10467162.1 10569414.57 0.978727829 0.903793905 1.070919654 0.882105996 0.903828004 0.699058798 1.027052602 0.730721479 0.990325626 1 23.33339213 3.550581456 12.65012105 0.871051002 0.976501203 0.117022579 0.109428059 2.270093982 388.0889255 0.026988461 0.041807838 3552.887499 -3.550581456 0.105450201 HMGGILAVANIR ddPTM_BT-474_Pertuzumab_2h_R1 1 HMGGILAVANIR 12 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 76.143 0.031912 147810000 152910 158730 146960 128100 122550 76196 157760 130090 143730 146420 FALSE TRUE 146934.1081 154203.1758 173518.9411 134711.2564 126491.932 77736.73533 159690.7141 127403.596 127414.373 136502.843 1.076417933 1.129670067 1.271174558 0.986875097 0.926661521 0.569488031 1.169870975 0.933340239 0.933419189 1 17.05857147 3.550717319 5.336469441 0.923064535 1.155240069 0.345451978 0.145809993 0.251918109 13.0232792 0.039554736 0.061303797 3553.999147 -3.550717319 0.232175535 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK ddPTM_BT-474_Pertuzumab_2h_R1 4 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK 32 0 P35637-2;P35637 P35637-2 FUS RNA-binding protein FUS 0 ;;; 261.94 1.22E-59 332840000 102847 144209 118142 165907 181062 190684 189734 330159 139793 211864 FALSE TRUE 98827.62554 140096.3005 139492.8875 174469.4802 186886.0237 194539.7611 192056.0214 323341.1013 123924.2847 197514.2626 0.500356907 0.709297135 0.706242099 0.883325983 0.946190018 0.984940321 0.972365332 1.637051912 0.627419423 1 17.59159731 3.550755577 0.723237762 1.151217764 0.524511089 0.337672345 0.240862964 0.893135603 0.898400716 0.127278412 0.360063014 3554.31224 -3.550755577 -0.626706675 WVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 WVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGR 39 1 Q99447-3;Q99447;Q99447-4;I3L1R7;Q99447-2;I3L2Q1;I3L1C4 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 ; 200.11 7.91E-31 278800000 159986 154610 122416 156324 172678 191349 166356 151412 202245 197404 FALSE TRUE 153733.5702 150200.6742 144539.2943 164391.9004 178232.3447 195218.2079 168391.9145 148285.2893 179286.9955 184033.6513 0.835355758 0.816158747 0.785396004 0.893270873 0.968476925 1.060774519 0.915006105 0.80575095 0.974207675 1 17.48961007 3.55093541 4.28695439 0.937102402 0.813757323 0.485609048 0.063845461 0.245489141 8.494712168 0.020112375 0.031310576 3555.784313 -3.55093541 -0.123345079 DKDPILR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDPILR 7 1 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 84.476 0.019624 2481100000 1960850 2968800 1735100 2794300 3357300 3117800 3378700 3856700 3890000 4061000 FALSE TRUE 1884217.814 2884132.731 2048671.167 2938514.158 3465290.604 3180844.052 3420049.541 3777057.797 3448423.508 3785944.853 0.497687602 0.761799985 0.541125465 0.776164015 0.915304036 0.840171787 0.903354294 0.997652619 0.910848848 1 21.85222197 3.550995658 0.615077906 0.975194223 0.521061991 0.776975979 0.07835783 0.517915088 0.361513285 0.047013248 0.14054587 3556.277633 -3.550995658 -0.454132233 QAHLYR ddPTM_BT-474_Pertuzumab_2h_R1 4 QAHLYR 6 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 114.6 0.058509 845350000 820480 817230 698140 642580 657520 491289 704060 621980 677620 761330 FALSE TRUE 788414.7345 793923.4006 824309.428 675743.6308 678669.7279 501223.2002 712676.4969 609135.8956 600699.4184 709764.441 1.110811826 1.118573085 1.161384511 0.952067463 0.956190095 0.706182462 1.004102848 0.858222617 0.846336311 1 19.43698077 3.551128559 2.443985239 0.884660321 1.130666027 0.611553899 0.083262828 0.179575982 2.108275774 0.02276624 0.03791361 3557.366075 -3.551128559 0.246005706 ILRPWQSSETR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILRPWQSSETR 11 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 ; 191.79 1.53E-06 3245200000 3755100 3885700 3553600 2609200 2416700 506200 3220800 2283000 2608500 3210900 FALSE TRUE 3608346.541 3774883.64 4195814.569 2743861.125 2494435.35 516435.7108 3260217.114 2235855.252 2312394.016 2993422.883 1.20542492 1.261059258 1.401677856 0.916629969 0.833305366 0.172523473 1.089126809 0.746922617 0.772491594 1 21.51336467 3.551592159 3.317168474 0.754502372 1.285109583 0.497504342 0.232829049 0.200432407 4.264253049 0.064038516 0.101451605 3561.165514 -3.551592159 0.530607211 RPDLLTMVVDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPDLLTMVVDYR 12 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 153.39 9.71E-05 594610000 1022030 1186250 1024590 849780 805880 305690 1127700 779150 872170 1112500 FALSE TRUE 982087.9377 1152419.311 1209756.205 893637.2476 831801.8621 311871.2612 1141501.13 763060.2802 773164.918 1037149.384 0.946910785 1.111141104 1.166424262 0.861628287 0.802007767 0.300700426 1.100613998 0.735728422 0.745471125 1 19.98419227 3.552158458 3.850505821 0.768578194 1.076887467 0.293313682 0.203124759 0.276918434 7.807502053 0.054703653 0.085642717 3565.812131 -3.552158458 0.308309273 TQDLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQDLFR 6 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 97.075 0.096511 346120000 324610 357840 302150 282280 280200 162010 348430 282470 318400 345730 FALSE TRUE 311923.8823 347634.7536 356755.2263 296848.5046 289212.8875 165285.9532 352694.1906 276636.8958 282256.5668 322313.3992 0.967765793 1.078561284 1.106858192 0.920993373 0.897303333 0.5128113 1.094258543 0.858285434 0.875720859 1 18.29810464 3.552389854 3.748145927 0.866260352 1.052900186 0.232509549 0.14393261 0.3313045 8.875255248 0.039207448 0.06149472 3567.712535 -3.552389854 0.186639834 RDSASYR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSASYR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 111.74 0.01044 62980000 39183 42796 37989 31833 24884 15497 39404 33826 33484 32977 FALSE TRUE 37651.68504 41575.49998 44854.45736 33475.90494 25684.41646 15810.35996 39886.23794 33127.48128 29683.0367 30743.43842 1.224706376 1.352337348 1.458992867 1.088879666 0.835443847 0.514267784 1.297390272 1.077546396 0.965508031 1 14.90799091 3.553244717 4.854381722 0.964123105 1.342350507 0.456354845 0.193036856 0.220319178 9.439150018 0.056355768 0.087528594 3574.74212 -3.553244717 0.378227402 STS(ph)YGYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 S(0.001)T(0.009)S(0.99)YGYSR 137.85 0.00076622 1207700000 2766900 2782300 2213600 2437500 2236500 2525800 2255800 2596600 2628400 2589800 TRUE FALSE 2658766.489 2702951.528 2613646.761 2563299.667 2308439.054 2576873.407 2283407.155 2542979.303 2330035.051 2414390.539 1.101216413 1.119517114 1.08252858 1.061675659 0.956116675 1.067297674 0.945748883 1.053259306 0.965061374 1 21.20322763 3.553370153 2.691121209 1.003711833 1.104448305 0.590912947 0.038471247 0.183481412 2.600613695 0.010024982 0.016389817 3575.774744 -3.553370153 0.100736472 LQQWYR ddPTM_BT-474_Pertuzumab_2h_R1 3 LQQWYR 6 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ;; 148.53 0.025017 7907780000 4869110 5602360 4487650 3325000 2634910 983790 3140480 2891730 2942920 3175280 FALSE TRUE 4678819.798 5442586.178 5298668.182 3496603.648 2719664.273 1003682.908 3178914.134 2832014.765 2608852.059 2960215.457 1.580567315 1.838577717 1.789960312 1.181199037 0.918738623 0.339057384 1.07387931 0.956692108 0.881304789 1 21.49727075 3.55392946 2.737281122 0.859045708 1.750817005 0.794613438 0.198511179 0.120021993 1.758187847 0.058559613 0.095475717 3580.38278 -3.55392946 0.891771297 EVCGFAPYER ddPTM_BT-474_Pertuzumab_2h_R1 6 EVCGFAPYER 10 0 Q9Y3U8;J3QSB5 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;;;;; 139.38 9.58E-05 4244390000 2083550 2295070 1945340 1829550 1745220 1430310 2098350 1883980 1858980 2081400 FALSE TRUE 2002122.563 2229616.851 2296906.212 1923973.295 1801356.586 1459231.848 2124030.235 1845075.155 1647956.384 1940424.924 1.031795942 1.14903536 1.183713002 0.991521636 0.928330988 0.752016649 1.094621188 0.950861397 0.849276034 1 20.88794119 3.554300111 4.303463649 0.933069835 1.123068185 0.467882302 0.091485608 0.200131667 6.87184155 0.02517989 0.039251613 3583.439784 -3.554300111 0.18999835 SLS(ph)LSLADSGHLPDVHGFNSYGSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.434)LS(0.552)LS(0.014)LADSGHLPDVHGFNSYGSHR;S(0.149)LS(0.85)LS(0.002)LADSGHLPDVHGFNSYGSHR 300.3 5.76E-63 765580000 346580 314927 185721 227748 173542 156448 151492 20110.6 166587 148045 TRUE FALSE 333035.2704 305945.5903 219284.916 239502.1016 179124.136 159611.4858 153346.0044 19695.30908 147676.7421 138017.7803 2.412988165 2.216711424 1.588816423 1.735298895 1.297833769 1.156455968 1.111059779 0.142701245 1.06998346 1 17.07449461 3.554576055 0.57141021 0.649027659 2.587956933 0.779461494 0.290896177 0.562425826 0.329604318 0.203205449 0.625325227 3585.71737 -3.554576055 1.938929274 up AVQALCAVYEHWVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVQALCAVYEHWVPR 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 143.38 4.42E-06 1057950000 581210 648730 444510 546930 505730 550770 550950 480140 583790 626530 FALSE TRUE 558495.6706 630228.8556 524842.8451 575157.1228 521997.2647 561906.9468 557692.6909 470224.9412 517520.6066 584094.565 0.956173373 1.078984283 0.898558002 0.984698638 0.893686221 0.962013654 0.954798631 0.805049335 0.886021952 1 19.15584244 3.554996365 0.697446262 0.893940714 1.01452844 0.149912387 0.065732699 1.326294024 1.228532625 0.035194552 0.101501539 3589.189308 -3.554996365 0.120587726 NIIHGSDSVK ddPTM_BT-474_Pertuzumab_2h_R1 4 NIIHGSDSVK 10 0 Q32Q12;P22392-2;P22392;O60361 Q32Q12;O60361 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 ;;; 184.24 1.58E-06 3737600000 6061300 9763200 6269100 5654200 4697200 3992610 4948720 4314230 5313200 6460400 FALSE TRUE 5824417.695 9484763.095 7402065.825 5946013.94 4848289.704 4073343.31 5009283.916 4225139.643 4710067.811 6022831.354 0.967056415 1.574801375 1.229001011 0.987245631 0.804985134 0.676317013 0.831715786 0.701520497 0.78203548 1 22.52201043 3.555570509 2.328734061 0.775331724 1.295472517 0.616610798 0.160507871 0.166610633 1.776766682 0.043397149 0.073360331 3593.937404 -3.555570509 0.520140793 TGHSGTLDPK ddPTM_BT-474_Pertuzumab_2h_R1 3 TGHSGTLDPK 10 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ;; 140.07 3.99E-05 609400000 856520 753970 665500 666320 675710 604490 717960 513710 916600 855800 FALSE TRUE 823046.2515 732467.5138 785770.654 700708.8551 697444.8258 616713.202 726746.6092 503101.709 812551.4107 797835.9037 1.031598412 0.918067876 0.98487753 0.878261873 0.874170769 0.772982513 0.910897348 0.630582939 1.018444278 1 19.60573252 3.555773023 1.525827264 0.830399788 0.980808416 0.121765986 0.110414086 0.581688699 2.690862363 0.033793532 0.066517408 3595.613672 -3.555773023 0.150408628 RGS(ph)DASDFDISEIQSVCSDVETVPQTHRPTPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RGSDASDFDISEIQSVCSDVETVPQTHRPTPR 32 2 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073;H0YC65;A0A494C1U5 F6QMI7 DST Dystonin 1 RGS(1)DASDFDISEIQSVCSDVETVPQTHRPTPR;RGS(1)DASDFDISEIQSVCSDVETVPQTHRPTPR;RGS(0.994)DAS(0.006)DFDISEIQSVCSDVETVPQTHRPTPR;RGS(0.982)DAS(0.018)DFDISEIQSVCSDVETVPQTHRPTPR 331.58 2.78E-117 1663290000 68191.8 70177.7 56554.8 66951.8 72484.1 72525.7 71380.8 76872.7 78181 73486.7 TRUE FALSE 65526.78907 68176.30071 66775.51041 70407.19042 74815.6169 73992.21935 72254.37958 75285.25188 69306.22064 68509.38035 0.956464483 0.995138189 0.974691496 1.027701463 1.092049242 1.080030486 1.054664036 1.098904289 1.011631112 1 16.06401392 3.556625282 3.405267311 1.064562749 0.977557996 0.552377127 0.031824532 0.158582596 3.521668933 0.008381834 0.013281051 3602.676629 -3.556625282 -0.087004752 HSLSGRPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSLSGRPLK 9 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 123.86 0.00032793 2950000000 3811700 4274800 3334100 3316600 3120200 2946300 3857400 2522700 4000500 3774400 FALSE TRUE 3662734.55 4152886.889 3936646.037 3487770.123 3220564.067 3005876.205 3904608.015 2470605.363 3546380.011 3518756.526 1.040917302 1.180214334 1.118760564 0.991193934 0.915256297 0.854243873 1.109655637 0.702124556 1.007850354 1 21.74663426 3.55672145 2.641377232 0.911234779 1.121403394 0.357222622 0.106645275 0.262921691 3.589038562 0.029636393 0.048739199 3603.474478 -3.55672145 0.210168615 HCKDDVNR ddPTM_BT-474_Pertuzumab_2h_R1 3 HCKDDVNR 8 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 ;; 128.36 0.00068304 217664000 526420 544412 443944 440877 415049 323179 492013 397433 540350 537137 FALSE TRUE 505846.9244 528885.9028 524174.5563 463630.7148 428399.428 329713.9008 498034.4023 389225.8697 479011.7333 500756.2326 1.010166008 1.056174379 1.046765916 0.925861097 0.855504935 0.658431946 0.99456456 0.777276136 0.956576678 1 18.93374895 3.55688919 2.972469908 0.856328248 1.039909525 0.348361591 0.098324927 0.251272066 4.311101541 0.026287891 0.042363804 3604.866532 -3.55688919 0.183581277 FTGS(ph)FDDDPDPHRDPYGEEVDR ddPTM_BT-474_Pertuzumab_2h_R1 5 FTGSFDDDPDPHRDPYGEEVDR 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.023)GS(0.977)FDDDPDPHRDPYGEEVDR;FT(0.236)GS(0.764)FDDDPDPHRDPYGEEVDR;FT(0.068)GS(0.932)FDDDPDPHRDPYGEEVDR;FT(0.188)GS(0.812)FDDDPDPHRDPYGEEVDR;FT(0.173)GS(0.827)FDDDPDPHRDPYGEEVDR 215.37 8.64E-26 1740920000 1066272 988512 807508 1178500 1569652 1096339 1466140 1610621 1380039 1555157 TRUE FALSE 1024600.911 960320.6056 953442.6585 1239322.526 1620141.282 1118507.726 1484083.06 1577361.114 1223382.758 1449824.831 0.706706693 0.662370091 0.657626106 0.854808457 1.117473813 0.771477838 1.023629219 1.087966684 0.843814185 1 20.46744717 3.557508026 3.812507889 0.980915045 0.676415041 0.643385364 0.098973687 0.139676965 3.812687936 0.027031432 0.042457133 3610.006848 -3.557508026 -0.304500003 S(ph)RTS(ph)VQT(ph)EDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 3 S(0.871)RT(0.133)S(0.994)VQT(0.999)EDDQLIAGQS(0.002)AR;S(0.597)RT(0.405)S(0.998)VQT(1)EDDQLIAGQS(0.001)AR 187.92 1.25E-13 478030000 1092290 1112990 806970 824090 671100 714860 500550 845830 659030 537190 TRUE FALSE 1049602.099 1081248.615 952807.43 866621.3837 692686.541 729314.959 506675.8806 828363.3149 584219.6773 500805.6428 2.095827222 2.159018434 1.90254931 1.730454511 1.383144441 1.456283429 1.011721589 1.654061464 1.166559694 1 18.93389129 3.557911472 1.1375098 1.293387776 2.158194352 0.784130179 0.186545845 0.237172348 0.611473594 0.064417392 0.14814245 3613.361989 -3.557911472 0.864806576 LCDSYEIRPGK ddPTM_BT-474_Pertuzumab_2h_R1 5 LCDSYEIRPGK 11 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;; 178.67 6.79E-06 6417450000 8119830 7844780 6599800 7119150 7304970 7392280 7184800 7778080 8014500 7890010 FALSE TRUE 7802498.067 7621054.555 7792530.672 7486570.185 7539940.994 7541756.966 7272729.732 7617459.93 7104727.56 7355612.595 1.060754351 1.036086996 1.059399278 1.017803764 1.025059558 1.02530644 0.988732024 1.035598304 0.965892027 1 22.81041407 3.558144408 0.381203833 0.994126613 1.072793149 0.564618415 0.018730291 1.923340189 0.417520644 0.017525369 0.06427071 3615.300559 -3.558144408 0.078666537 TT(ph)PTLGLEEVLSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPTLGLEEVLSSR 14 0 O43474-4;O43474-1;O43474 O43474-4 KLF4 Krueppel-like factor 4 1 T(0.14)T(0.86)PTLGLEEVLSSR 84.468 0.024246 0 25472 28329 23233 23511 22460 25156 20979 25541 25900 27678 TRUE FALSE 24476.52608 27521.08466 27431.71992 24724.40553 23182.4463 25664.67156 21235.74728 25013.56942 22959.94058 25803.34441 0.948579599 1.06657045 1.063107149 0.958186084 0.898427969 0.99462578 0.822984298 0.969392534 0.889804834 1 14.65527045 3.558606035 4.84335609 0.926304558 1.029231675 0.355004544 0.058184286 0.212534989 8.764574831 0.014681757 0.022844557 3619.145429 -3.558606035 0.102927117 KQS(ph)SSEISLAVER ddPTM_BT-474_Pertuzumab_2h_R1 2 KQSSSEISLAVER 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KQS(0.739)S(0.221)S(0.04)EISLAVER;KQS(0.765)S(0.227)S(0.008)EISLAVER 197.51 8.16E-08 816080000 793620 795460 601480 653100 635280 512210 511380 778840 634820 606760 TRUE FALSE 762604.453 772774.2596 710180.8159 686806.5693 655714.3581 522567.2371 517638.4214 762756.6818 562757.895 565663.6048 1.348158953 1.366137494 1.255482605 1.21416079 1.159194887 0.923812727 0.915099393 1.348428068 0.994863184 1 19.10958482 3.558772111 1.453771568 1.073779571 1.349651018 0.513526787 0.119495836 0.406045946 1.705962056 0.041810525 0.084493585 3620.529671 -3.558772111 0.275871447 NVFIIGATNRPDIIDPAILRPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVFIIGATNRPDIIDPAILRPGR 23 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 284.88 1.71E-52 19400800000 3001900 2909100 2340190 2370850 1928050 1813930 1756530 2435600 2894200 3081100 FALSE TRUE 2884582.429 2826135.316 2763114.39 2493209.853 1990067.479 1850608.907 1778026.94 2385304.009 2565662.549 2872414.353 1.004236184 0.983888454 0.9619484 0.867984053 0.692820476 0.644269482 0.619000855 0.830417801 0.893207676 1 21.45383245 3.559524669 2.911900585 0.759066437 0.985094056 0.397751968 0.109670409 0.247647607 4.078004055 0.031537766 0.051070336 3626.808867 -3.559524669 0.226027619 QWDYYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QWDYYAR 7 0 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 0 ; 113.41 0.014274 669510000 1159660 1301720 1006430 995710 1015560 619350 1185870 979280 1106650 1133890 FALSE TRUE 1114339.205 1264596.22 1188314.289 1047098.712 1048226.41 631873.6814 1200383.032 959057.5258 981027.7315 1057090.62 1.054156743 1.196298781 1.124136631 0.990547728 0.991614522 0.597747884 1.135553574 0.907261409 0.928045063 1 20.01166763 3.559562984 2.328451518 0.921040449 1.134325234 0.314142363 0.131059115 0.348158235 3.708981719 0.037125064 0.062950485 3627.12885 -3.559562984 0.213284785 AAAIASSLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAIASSLIR 10 0 P61328;Q92913 P61328 FGF12;FGF13 Fibroblast growth factor 12;Fibroblast growth factor 13 0 69.954 0.055433 11175000000 4504000 4417300 3790700 3504800 3268400 2875700 2873500 3716900 3925100 4330800 FALSE TRUE 4327978.701 4291322.929 4475763.814 3685683.148 3373531.054 2933848.624 2908666.753 3640144.716 3479539.103 4037471.059 1.071952873 1.062873979 1.108556259 0.912869243 0.835555477 0.726655023 0.720417982 0.901590293 0.861811528 1 21.94502049 3.560478176 3.051921771 0.828168092 1.079652459 0.654675665 0.077421249 0.152331097 2.741789725 0.022080239 0.03552624 3634.78039 -3.560478176 0.251484367 DKANMQHR ddPTM_BT-474_Pertuzumab_2h_R1 16 DKANMQHR 8 1 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7;H0YBK1;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;;;;;;;;;;;; 164.96 0.00019653 4745973000 6316386 6223101 5287421 4853186 4362850 2384357 5700844 4546738 5483658 6094961 FALSE TRUE 6069534.652 6045624.253 6242975.593 5103659.511 4503185.032 2432570.332 5770612.634 4452846.271 4861176.133 5682143.863 1.068176871 1.063968882 1.098700727 0.89819259 0.792515139 0.428107839 1.015569611 0.783656025 0.855517961 1 22.43800393 3.561808135 3.18939993 0.798588631 1.075629566 0.374924969 0.151616874 0.257700513 5.033923483 0.041992684 0.067223354 3645.928394 -3.561808135 0.277040935 GFAFVQYVNER ddPTM_BT-474_Pertuzumab_2h_R1 2 GFAFVQYVNER 11 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;B4DSU6;G3V4M8;P07910;G3V2Q1;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 188.04 7.73E-06 1728590000 577330 726520 735480 475320 371732 113076 713190 468080 461610 592990 FALSE TRUE 554767.3053 705800.3609 868397.5967 499851.3222 383689.0974 115362.4742 721918.2326 458413.9844 409209.968 552826.2591 1.003511132 1.2767128 1.570832757 0.904174348 0.694050058 0.208677631 1.305868201 0.829218904 0.740214419 1 19.07646662 3.562201926 6.664378698 0.798723821 1.28070112 0.367180745 0.286803379 0.270286174 17.80161931 0.077933299 0.120878309 3649.235793 -3.562201926 0.4819773 TTPSYVAFTDTER ddPTM_BT-474_Pertuzumab_2h_R1 8 TTPSYVAFTDTER 13 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65;P54652;P17066;P48741 A0A0G2JIW1;Q53FA3;P11142;P54652;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA2;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;; 302.64 1.10E-40 8220840000 2794922 2917742 2443556 2294345 2138563 1893299 2351585 2179808 2593598 2674237 FALSE TRUE 2685693.358 2834530.855 2885160.926 2412756.42 2207351.821 1931582.803 2380364.401 2134794.203 2299183.628 2493108.546 1.077246862 1.136946428 1.157254437 0.967770306 0.885381354 0.774768835 0.954777683 0.856278082 0.922215614 1 21.24951427 3.562292036 3.346820059 0.888776469 1.124641766 0.735270142 0.059993655 0.112973322 2.411710151 0.016014956 0.025500529 3649.993034 -3.562292036 0.235865297 FVFSFK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVFSFK 6 0 P61081;M0QYI6 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 103.28 0.080999 152350000 593020 605210 541390 510270 490720 430260 538790 548110 573170 621190 FALSE TRUE 569844.1228 587950.0034 639231.2162 536605.0959 506504.4545 438960.152 545383.8732 536791.337 508106.1445 579116.248 0.983989181 1.015253855 1.103804665 0.926593059 0.874616204 0.757982794 0.94175198 0.926914655 0.877381953 1 19.14349345 3.562380753 5.837781529 0.892565382 1.031680364 0.477921914 0.064507001 0.194567756 10.50338174 0.017560706 0.027267941 3650.73873 -3.562380753 0.139114982 TTIENIQLPHTLLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTIENIQLPHTLLSR 15 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 142.54 4.57E-06 296320000 283430 318340 223680 294550 304830 337010 298810 317370 318540 388100 FALSE TRUE 272353.2423 309261.2549 264103.9517 309751.7608 314635.1338 343824.5731 302466.9262 310816.1986 282380.6746 361813.6413 0.752744538 0.854752888 0.729944705 0.856108575 0.869605504 0.950280846 0.835974357 0.859050525 0.780458895 1 18.46488728 3.562755194 6.854753108 0.873560886 0.78690008 0.335145174 0.064190506 0.322361929 21.9785422 0.016299038 0.025277885 3653.887686 -3.562755194 -0.086660805 VTEQEWR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTEQEWR 7 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;;; 138.26 0.0065205 3339190000 2557150 2853340 2207500 2649720 2784500 2897160 2947390 2908420 3203940 3042180 FALSE TRUE 2457213.751 2771965.537 2606444.356 2786472.367 2874065.971 2955742.56 2983461.04 2848360.111 2840242.163 2836130.439 0.866396593 0.977375899 0.919014274 0.982490907 1.013375807 1.042174408 1.051947752 1.004312098 1.001449766 1 21.43549246 3.562848905 1.755229101 1.022442479 0.921340555 0.684172245 0.02968575 0.206019948 1.255315176 0.008781046 0.016374577 3654.676202 -3.562848905 -0.101101923 LLELLGHYQESGSVIIFVDK ddPTM_BT-474_Pertuzumab_2h_R1 3 LLELLGHYQESGSVIIFVDK 20 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;; 158.74 2.65E-11 58542000 89725 90045 80676 85279 93299 98897 100556 99028 122425 108066 FALSE TRUE 86218.4478 87477.00476 95255.94783 89680.25941 96300.04707 100896.7651 101786.6344 96983.03719 108527.8272 100746.5936 0.855795166 0.868287469 0.945500433 0.890156741 0.955864051 1.001490587 1.010323335 0.962643339 1.0772357 1 16.62037153 3.563192869 0.523449352 1.020681097 0.832373811 0.751487529 0.033019828 0.753095806 0.355731026 0.023992303 0.076952933 3657.571874 -3.563192869 -0.188307286 DYLHYIR ddPTM_BT-474_Pertuzumab_2h_R1 6 DYLHYIR 7 0 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;;;; 148.21 0.0020996 4575220000 4055190 4111580 3839460 3217700 2982090 1530670 4117810 3267050 3460840 3888320 FALSE TRUE 3896708.692 3994321.764 4533335.83 3383765.883 3078011.633 1561621.196 4168204.991 3199584.276 3067979.952 3624960.623 1.074965799 1.101893835 1.250588986 0.933462797 0.849115881 0.430796734 1.149862143 0.882653526 0.846348491 1 21.78953389 3.563271824 4.922683673 0.858441049 1.136769614 0.342013996 0.175247023 0.257390537 10.59445077 0.047843114 0.074515431 3658.236882 -3.563271824 0.278328565 VQFHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VQFHLK 6 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 90.285 0.049203 719740000 1784960 1985360 1734190 1492010 1388690 832880 1753470 1450090 1734800 1833400 FALSE TRUE 1715201.79 1928739.477 2047596.71 1569012.815 1433358.475 849721.4043 1774929.49 1420145.135 1537872.777 1709222.185 1.003498436 1.128431104 1.197969888 0.917968903 0.838602779 0.497139232 1.038442811 0.830872164 0.899750068 1 20.70490852 3.563400347 4.386144436 0.840628264 1.110149886 0.392997444 0.143569846 0.218846911 7.470172773 0.038854403 0.060736352 3659.319645 -3.563400347 0.269521622 FVFLLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVFLLDR 7 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 95.62 0.031016 50395000 127250 140730 124200 98963 96887 47693 110970 96209 94604 136280 FALSE TRUE 122276.9293 136716.5182 146645.7028 104070.4923 100003.4583 48657.38514 112328.0841 94222.25053 83864.95053 127049.6342 0.962434328 1.07608746 1.154239473 0.819132561 0.787121183 0.382979341 0.884127568 0.741617645 0.660095962 1 16.9550327 3.56394917 3.6357661 0.727395659 1.064157817 0.454143761 0.156850296 0.200993926 4.970612325 0.042068519 0.066514425 3663.946888 -3.56394917 0.336762159 ICGDIHGQYYDLLR ddPTM_BT-474_Pertuzumab_2h_R1 5 ICGDIHGQYYDLLR 14 0 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;A0A087WYY5;F5H1L6;F5H037;P62136;P62136-2;E9PMD7 F8W0W8;P62136 PPP1CC;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ;;;; 150.34 7.24E-06 2164890000 3319160 3400320 2810080 2626870 2523000 1437790 2996160 2711150 2770410 3024440 FALSE TRUE 3189443.558 3303346.203 3317923.966 2762443.076 2604154.586 1466863.099 3032827.902 2655163.805 2455924.671 2819591.985 1.131172019 1.171568873 1.17673904 0.979731497 0.923592704 0.520239491 1.075626516 0.941683697 0.871021298 1 21.42705498 3.56399667 2.794931861 0.887055304 1.162287788 0.436437101 0.137545843 0.262920368 3.993557248 0.03986054 0.065182759 3664.347649 -3.56399667 0.275232484 KYAVLYQPLFDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KYAVLYQPLFDKR 13 2 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;H0YHC3;H0YH88;F8W020;F8VRJ2;F8VVB5 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 71.548 0.023605 499770000 164010 161370 134380 116940 126920 83480 115390 106550 134820 147820 FALSE TRUE 157600.3079 156767.8856 158665.4553 122975.2874 131002.4971 85168.0228 116802.1773 104349.7053 119515.7988 137808.0197 1.143622179 1.137581731 1.151351391 0.892366697 0.950615917 0.61801935 0.847571698 0.757210687 0.867263016 1 17.07230032 3.564259779 1.73730857 0.808280231 1.15495672 0.644477236 0.100119818 0.197410684 1.178421153 0.028645299 0.053709195 3666.568294 -3.564259779 0.346676489 LSLEEETLWLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSLEEETLWLR 11 0 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 ;; 200.6 8.25E-05 78364000 77925 85236 65597 80712 89098 88566 87711 86321 96071 99447 FALSE TRUE 74879.60485 82805.15273 77451.8371 84877.55599 91963.91809 90356.8652 88784.43346 84538.44118 85165.42284 92711.36611 0.807663699 0.893149958 0.835408217 0.915503239 0.991937903 0.974603967 0.95764346 0.911845491 0.918608218 1 16.5004586 3.564475188 4.071626647 0.952710955 0.850898769 0.69534261 0.03337151 0.143709134 4.316724042 0.009451051 0.014831299 3668.38736 -3.564475188 -0.101812186 LEYDAYR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEYDAYR 7 0 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 ;; 105.12 0.018609 641800000 1265670 1378030 1279290 1033340 954880 488230 1319420 1024280 1108620 1292330 FALSE TRUE 1216206.217 1338729.934 1510486.161 1086670.801 985594.5824 498102.3451 1335567.457 1003128.26 982774.1053 1204799.338 1.009467866 1.111164234 1.253724262 0.901951692 0.818057042 0.413431789 1.108539335 0.832610235 0.815716007 1 20.20036145 3.564789843 5.178528985 0.826112752 1.121745848 0.356284672 0.176380731 0.241533054 10.65619001 0.04753094 0.073974383 3671.046143 -3.564789843 0.295633096 KLGQSESQGPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLGQSESQGPPR 12 1 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ; 198.74 2.88E-07 332660000 290550 279420 235010 287730 291320 294530 307120 322160 350980 333840 FALSE TRUE 279194.9848 271451.2152 277481.5348 302579.7798 300690.5724 300485.5984 310878.6264 315507.2834 311138.2218 311228.7194 0.897073333 0.872192051 0.891567897 0.972210342 0.966140184 0.965481588 0.998875126 1.01374733 0.999709225 1 18.24761567 3.564872988 0.902143965 1.002172751 0.870696261 0.891034838 0.016203024 0.205578757 0.329177956 0.007113026 0.018685486 3671.749026 -3.564872988 -0.13147649 EHCPAGQPVK ddPTM_BT-474_Pertuzumab_2h_R1 3 EHCPAGQPVK 10 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;; 127.76 0.00034743 262428000 828900 841160 691920 632160 636820 331158 782830 486770 817480 784200 FALSE TRUE 796505.6716 817170.9404 816965.3357 664785.8534 657303.8936 337854.2417 792410.5077 476718.0294 724683.0976 731085.4355 1.089483709 1.117750267 1.117469034 0.909313496 0.899079453 0.462126894 1.083882224 0.652068837 0.991242695 1 19.47968049 3.56501426 2.354119927 0.817775822 1.113049353 0.306473449 0.17181272 0.313782872 3.412028872 0.046510491 0.078971119 3672.9436 -3.56501426 0.295273532 LQTVLEAVHDLLRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQTVLEAVHDLLRPR 15 1 B0QYP8;A0A087WZB5;Q9HBI1-3;Q9HBI1;Q9HBI1-2 B0QYP8 PARVB Beta-parvin 0 64.675 0.038341 11125000 9384.1 11986 9084 9133.5 8795.6 9617 9048.2 8197.8 10434 11203 FALSE TRUE 9017.358997 11644.17102 10725.68087 9604.88103 9078.518462 9811.462329 9158.934578 8028.512565 9249.576063 10444.21083 0.863383471 1.114892375 1.026949862 0.919636838 0.869239295 0.939416342 0.876938883 0.768704567 0.885617517 1 13.35041587 3.565260049 3.367862133 0.873190801 1.012452423 0.260635982 0.080427103 0.26681678 5.741223879 0.022359891 0.035636531 3675.022899 -3.565260049 0.139261621 NGYGFINR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGYGFINR 8 0 P67809;C9J5V9;P16989;P16989-3;P16989-2;Q9Y2T7 P67809;P16989;P16989-2;Q9Y2T7 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3;Y-box-binding protein 2 0 ; 113.1 0.0067774 459990000 473560 500740 432080 390250 340070 175322 477260 413820 438430 501630 FALSE TRUE 455052.7517 486459.3855 510166.4676 410390.8493 351008.6604 178867.131 483100.8506 405274.4724 388661.2644 467654.1533 0.973054015 1.040211836 1.090905456 0.877552025 0.75057317 0.382477371 1.033030172 0.866611511 0.831086951 1 18.83508247 3.565304235 4.418458593 0.804476218 1.033404599 0.260413939 0.168364578 0.314561484 10.78196454 0.047422455 0.074156238 3675.39682 -3.565304235 0.228928381 (ac)S(ph)GEDEQQEQTIAEDLVVTK ddPTM_BT-474_Pertuzumab_2h_R1 13 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 S(0.991)GEDEQQEQT(0.009)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.999)GEDEQQEQT(0.001)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.985)GEDEQQEQT(0.015)IAEDLVVTK;S(0.977)GEDEQQEQT(0.023)IAEDLVVTK;S(0.999)GEDEQQEQT(0.001)IAEDLVVTK;S(0.998)GEDEQQEQT(0.002)IAEDLVVTK;S(0.969)GEDEQQEQT(0.031)IAEDLVVTK;S(0.974)GEDEQQEQT(0.026)IAEDLVVTK 147.52 5.54E-108 5809143000 2483352.1 2344538.7 2075351.3 2394507.5 2395783.9 2584354 2553579.9 2773680.8 2983840.2 3047338.3 TRUE FALSE 2386299.954 2277674.752 2450413.446 2518088.319 2472846.465 2636611.409 2584831.375 2716403.322 2645127.17 2840939.363 0.839968634 0.80173297 0.862536342 0.886357644 0.870432681 0.928077327 0.909850949 0.956163781 0.931074843 1 21.43793661 3.565338014 0.230092626 1.010786687 0.726375193 0.881345303 0.019089081 1.835335727 0.140895588 0.03443986 0.150896691 3675.682696 -3.565338014 -0.284411494 NVTFHGVLLDAFFNESSADWR ddPTM_BT-474_Pertuzumab_2h_R1 4 NVTFHGVLLDAFFNESSADWR 21 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 261.82 1.16E-36 1488395000 1657641 1541238 1317236.7 1130944 915080 924486 662087 995921 1330870 1485010 FALSE TRUE 1592858.557 1497283.401 1555290.673 1189312.155 944514.3793 943179.7403 670189.8188 975354.8833 1179795.217 1384428.95 1.150552766 1.081516969 1.123416751 0.859063338 0.682241136 0.6812771 0.484091162 0.704517833 0.852189068 1 20.40085958 3.565362332 2.613481186 0.69924578 1.119778706 0.635010223 0.128375605 0.160678234 2.142877284 0.035915433 0.059549235 3675.888524 -3.565362332 0.420532927 IQNGAQGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQNGAQGIR 9 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;E7EN40;D6R9T0;D6RFM3;D6RDU3;D6RJ04;D6RIH9;D6RAM1;D6RDL0;D6RF17;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ; 155.82 0.00016845 81731000 112677 118839 102362 92005 86951 49015 109638 96921 95508 112281 FALSE TRUE 108273.4583 115449.8281 120861.0904 96753.38908 89747.85788 50006.11688 110979.7826 94919.54748 84666.33224 104676.1079 1.03436649 1.102924349 1.154619644 0.924312062 0.857386272 0.477722356 1.06022076 0.906792862 0.808841043 1 16.67557266 3.565989784 3.852182247 0.850483318 1.096626418 0.354793884 0.147699444 0.265440154 7.228946277 0.041422388 0.065266883 3681.203139 -3.565989784 0.2461431 KLYELIITR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLYELIITR 9 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 151.15 0.00013397 483500000 556240 607000 551190 476120 469970 237840 572890 504410 541910 636780 FALSE TRUE 534501.5258 589688.9543 650802.2942 500692.6103 485087.0119 242649.2878 579901.1992 493993.7572 480394.6487 593650.3234 0.900364246 0.9933271 1.096272113 0.843413354 0.817125828 0.408741103 0.976839692 0.832129181 0.809221573 1 19.17925387 3.566834464 5.443840814 0.797311083 0.995489645 0.225728488 0.156662826 0.323057889 15.14969284 0.042236622 0.065700178 3688.36986 -3.566834464 0.198178563 HLTASEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 HLTASEAK 8 0 P39748;P39748-2 P39748 FEN1 Flap endonuclease 1 0 ;;; 122.18 0.0014016 1340050000 2004290 2106530 1782290 1533790 1465510 790480 1889690 1357790 1694760 1729760 FALSE TRUE 1925960.131 2046453.827 2104389.45 1612949.086 1512649.46 806464.0472 1912816.591 1329751.162 1502377.95 1612601.814 1.194318469 1.269038524 1.304965324 1.000215348 0.938017957 0.500101166 1.186167952 0.824599818 0.931648431 1 20.62095882 3.566985256 3.052402511 0.887719554 1.257656177 0.488547401 0.163825977 0.209482723 3.754906405 0.04454551 0.071952865 3689.650725 -3.566985256 0.369936623 IPDWFLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 IPDWFLNR 8 0 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ; 120.62 0.0034157 1366690000 1340300 1494420 1441900 1103290 987320 634000 1551270 975230 1124340 1374520 FALSE TRUE 1287919.594 1451800.605 1702483.405 1160230.929 1019078.044 646819.9144 1570254.906 955091.1597 996709.6368 1281422.536 1.005070192 1.1329601 1.328588625 0.905424164 0.795270893 0.504767082 1.22539979 0.745336634 0.777814974 1 20.28931484 3.567012068 6.182433091 0.83531909 1.151693533 0.358440043 0.188398781 0.247927923 13.96330346 0.04939442 0.076701554 3689.878516 -3.567012068 0.316374443 YSDFEWLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSDFEWLR 8 0 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 0 ; 161.9 0.00080229 411230000 769330 844530 750500 645830 621000 307500 831710 655810 655250 860870 FALSE TRUE 739263.7331 820444.8313 886132.0448 679161.3637 640975.029 313717.8607 841888.7158 642267.2943 580868.767 802562.5081 0.921129165 1.022281533 1.104128384 0.84624108 0.798660568 0.390895236 1.049000803 0.800270743 0.723767633 1 19.61425424 3.567115157 4.697842574 0.786553042 1.015200512 0.251701497 0.171009991 0.302663969 11.33931511 0.045910162 0.071673459 3690.754489 -3.567115157 0.22864747 AAS(ph)LTEDRDR ddPTM_BT-474_Pertuzumab_2h_R1 4 AASLTEDRDR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 AAS(0.849)LT(0.151)EDRDR;AAS(1)LTEDRDR;AAS(0.997)LT(0.003)EDRDR;AAS(1)LTEDRDR 182.1 1.10E-06 3605090000 2291960 1976910 1440550 2128750 2373750 1943930 2378890 2660460 2240220 2299890 TRUE FALSE 2202387.669 1920530.462 1700889.43 2238615.043 2450103.825 1983237.596 2408003.567 2605520.571 1985919.617 2144116.402 1.027177287 0.895721175 0.793282225 1.044073466 1.142710266 0.924967317 1.123075018 1.215195485 0.926218192 1 21.0319518 3.567124863 7.339113618 1.076245736 0.905232193 0.294493452 0.102297387 0.29841057 21.31118055 0.027840196 0.043174759 3690.836977 -3.567124863 -0.171013543 ASS(ph)PAQCVTPVQTVV ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSPAQCVTPVQTVV 15 0 Q13614;Q13614-2 Q13614 MTMR2 Myotubularin-related protein 2 1 AS(0.125)S(0.875)PAQCVTPVQTVV;AS(0.026)S(0.974)PAQCVTPVQTVV 139.78 5.30E-06 195364000 270306 282680 228293 264520 278830 293370 281794 287420 298059 332630 TRUE FALSE 259742.1427 274618.2432 269550.6235 278171.9089 287798.8202 299302.1424 285242.6793 281484.6766 264224.5919 310100.6738 0.837605864 0.885577705 0.869235852 0.897037422 0.928081892 0.965177336 0.919838953 0.9077203 0.852060683 1 18.24237714 3.567572524 2.311853799 0.924108235 0.864617346 0.369665606 0.037622604 0.365276412 3.831248172 0.010787035 0.018437398 3694.643367 -3.567572524 -0.059490889 PLTS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 4 PLTSPLR 7 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 PLT(0.015)S(0.985)PLR;PLT(0.138)S(0.862)PLR;PLT(0.023)S(0.977)PLR;PLT(0.026)S(0.974)PLR 121.67 0.0046315 1801260000 3180540 2778840 3028310 2120440 2296290 754480 2671940 1943850 2168090 2582500 TRUE FALSE 3056240.981 2699590.204 3575592.981 2229876.163 2370152.253 769736.1025 2704640.001 1903708.818 1921977.513 2407584.975 1.269421853 1.121285534 1.485136774 0.926187938 0.98445217 0.319712953 1.123382987 0.790713033 0.798301008 1 21.19915529 3.567609712 4.628392965 0.828040798 1.273731634 0.468140068 0.217267948 0.192123137 7.017073222 0.056687256 0.088554613 3694.959748 -3.567609712 0.445690836 GIPLATGDT(ph)SPEPELLPGAPLPPPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GIPLATGDTSPEPELLPGAPLPPPK 25 0 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 GIPLAT(0.02)GDT(0.49)S(0.49)PEPELLPGAPLPPPK;GIPLAT(0.105)GDT(0.498)S(0.397)PEPELLPGAPLPPPK;GIPLAT(0.101)GDT(0.507)S(0.392)PEPELLPGAPLPPPK 186.82 5.43E-17 379086000 670590 655190 573040 689750 676090 728410 733860 814970 850400 835960 TRUE FALSE 644382.6014 636504.6227 676601.0752 725348.0802 697837.0489 743138.9493 742841.1982 798140.5847 753866.1572 779339.6846 0.826831501 0.816722971 0.868172234 0.930721346 0.895420909 0.953549478 0.953167422 1.024124141 0.967313961 1 19.57189276 3.567707256 0.474441789 1.007659456 0.775089854 0.881223468 0.02294587 0.532543454 0.197106615 0.018720391 0.0626563 3695.789743 -3.567707256 -0.232569602 VLVWDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLVWDLR 7 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ; 105.12 0.018609 860240000 1538700 1751900 1507470 1166230 1094610 334820 1440600 1078290 1135080 1563340 FALSE TRUE 1478565.903 1701937.527 1779903.362 1226419.27 1129819.125 341590.2898 1458230.494 1056022.935 1006230.477 1457453.589 1.014485754 1.167747323 1.221241881 0.84148084 0.775200756 0.234374729 1.000533056 0.72456711 0.690403101 1 20.47501851 3.56805453 3.489010992 0.722610392 1.136501341 0.425623179 0.205323708 0.221299744 5.055205914 0.055869138 0.088846026 3698.746179 -3.56805453 0.413890949 KNS(ph)SRDS(ph)GRGDSVSDSGSDALR ddPTM_BT-474_Pertuzumab_2h_R1 1 KNSSRDSGRGDSVSDSGSDALR 22 3 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 2 KNS(0.848)S(0.209)RDS(0.848)GRGDS(0.062)VS(0.009)DS(0.012)GS(0.012)DALR 59.038 0.094758 440580000 138090 156680 99005 132120 124430 106080 112380 130670 138740 128580 TRUE FALSE 132693.2901 152211.6398 116897.4059 138938.729 128432.404 108225.0103 113755.3401 127971.6188 122990.8168 119871.1621 1.106965911 1.269793645 0.975192063 1.159067174 1.071420363 0.902844424 0.948980039 1.06757636 1.026025065 1 16.8711251 3.570328179 1.01841081 0.999600902 1.165837356 0.353981761 0.082230979 0.65797957 1.350181095 0.031326043 0.077825031 3718.160896 -3.570328179 0.166236454 QWADDWLVHLISPNVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 QWADDWLVHLISPNVYR 17 0 Q9H7Z7;A6NHH0;X6RJ95 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 108.56 0.0006498 172258000 254667 289224 200371 198687 169739 148728 179803 149495 177910 215273 FALSE TRUE 244714.3321 280975.6147 236582.4969 208941.2599 175198.8091 151735.3821 182003.4829 146407.876 157714.4027 200692.368 1.219350464 1.400031389 1.178831559 1.04110217 0.872971956 0.756059553 0.906877948 0.72951392 0.785851521 1 17.61462623 3.570401026 1.563043382 0.815652681 1.310330062 0.826790848 0.087690468 0.133485089 0.645829922 0.025716996 0.05080169 3718.784616 -3.570401026 0.494677382 DLMHGLITLMLDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLMHGLITLMLDSR 14 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 147.39 8.05E-06 57669000 84715 89942 86969 71142 76554 39484 93129 63595 78495 101720 FALSE TRUE 81404.24414 87376.94222 102686.2329 74813.64715 79016.42893 40282.39353 94268.74056 62281.74103 69584.57668 94830.4138 0.85841916 0.921402098 1.082840713 0.788920391 0.833239314 0.424783484 0.994077077 0.656769685 0.73377911 1 16.53306221 3.570942932 6.613212546 0.754154801 0.950778182 0.193125391 0.164181562 0.349176652 20.82143274 0.041429244 0.064313482 3723.42776 -3.570942932 0.196623381 NSMFHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSMFHNR 7 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;Q99873-5;H0YDE4;E9PNR9;E9PMW9;E9PMZ2 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 82.716 0.023735 206114000 364480 451770 371310 332360 302250 210300 387130 324520 362160 468470 FALSE TRUE 350235.7186 438885.9619 438413.9767 349513.1394 311972.1457 214552.4101 391867.8127 317818.5486 321049.1151 436740.1096 0.801931654 1.004913339 1.003832639 0.800277171 0.714319887 0.491258772 0.897256295 0.727706344 0.735103344 1 18.73641551 3.571403258 4.639341136 0.744102209 0.942185468 0.248685309 0.134834741 0.270038296 9.733107515 0.035310877 0.055214311 3727.376459 -3.571403258 0.198083259 HVFGESDELIGQK ddPTM_BT-474_Pertuzumab_2h_R1 3 HVFGESDELIGQK 13 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;; 128.85 0.00016055 3609220000 8914400 8923000 6488400 7130400 7386400 7448600 6566000 5747400 8539500 7991800 FALSE TRUE 8566015.393 8668524.777 7660998.214 7498400.799 7623990.264 7599215.795 6646356.672 5628714.182 7570131.761 7450508.268 1.149722285 1.163480996 1.028251757 1.006428089 1.023284585 1.01995938 0.892067552 0.755480563 1.016055749 1 22.82890742 3.571672229 0.632264808 0.889805613 1.186111283 0.49164929 0.078855297 0.861742882 0.633663237 0.050874697 0.155352895 3729.685643 -3.571672229 0.29630567 LKPGYLEATVDWFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKPGYLEATVDWFR 14 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 212.24 2.48E-09 5498100000 5865600 5863000 5009900 4733400 4436500 3206400 5286800 4813800 5143600 5894800 FALSE TRUE 5636365.867 5695792.98 5915300.375 4977691.341 4579204.052 3271235.605 5351501.44 4714393.348 4559720.092 5495539.945 1.025625493 1.036439192 1.076382018 0.905769295 0.83325826 0.595252812 0.973789927 0.85785808 0.829712847 1 22.3898298 3.571766016 3.580953484 0.840736586 1.044547119 0.423226381 0.10280182 0.226186742 5.378589798 0.028360802 0.04506942 3730.491169 -3.571766016 0.203810533 YIELLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIELLTR 7 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 113.89 0.014024 730320000 735920 893070 744590 704750 701960 697530 761570 733600 760030 718390 FALSE TRUE 707159.4328 867600.518 879153.9763 741122.232 724539.1809 711634.5345 770890.3215 718450.9036 673754.5807 669732.8054 1.055882924 1.295442766 1.312693613 1.106593892 1.081833195 1.062564845 1.151041602 1.072742589 1.006005044 1 19.35322611 3.571863818 5.916908651 1.074037565 1.228073998 0.462363781 0.075933111 0.202116717 10.27725669 0.019981625 0.031063155 3731.331361 -3.571863818 0.154036432 KLEEQAR ddPTM_BT-474_Pertuzumab_2h_R1 6 KLEEQAR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 127.46 0.0061773 4445610000 6136150 5949460 5325040 4913960 4383660 2050960 6007060 5509190 5694620 6628650 FALSE TRUE 5896342.474 5779787.226 6287393.183 5167570.064 4524664.405 2092431.816 6080576.197 5395423.301 5048190.611 6179685.631 0.95414926 0.935288228 1.017429293 0.836218923 0.732183589 0.338598424 0.983962059 0.873090255 0.816900877 1 22.55910202 3.572788148 4.721413606 0.783190055 0.964108542 0.173130958 0.173443904 0.410374916 15.08985791 0.049048773 0.076674148 3739.281391 -3.572788148 0.180918487 VLS(ph)PLMSR ddPTM_BT-474_Pertuzumab_2h_R1 15 VLSPLMSR 8 0 A0A087WXR4;Q8NG45;Q8NG42;P06401-5;P06401;Q8NG44 A0A087WXR4 PGR;PR Progesterone receptor 1 VLS(1)PLMSR;VLS(1)PLMSR;VLS(1)PLMSR;VLS(1)PLMSR;VLS(1)PLMSR;VLS(1)PLMSR;VLS(1)PLMSR;VLS(1)PLMSR;VLS(1)PLMSR;VLS(0.999)PLMS(0.001)R;VLS(1)PLMSR;VLS(1)PLMSR;VLS(0.998)PLMS(0.002)R;VLS(1)PLMSR;VLS(1)PLMSR 213.03 1.91E-05 5344788000 6585060 5952620 5620060 5039130 4220620 5318920 4795330 4219750 5971330 7576680 TRUE FALSE 6327708.575 5782857.106 6635729.86 5299200.103 4356380.075 5426472.207 4854016.683 4132610.688 5293489.652 7063504.715 0.895831295 0.818695158 0.939438724 0.750222491 0.616744839 0.768240757 0.687196637 0.585065184 0.749414047 1 22.75195276 3.573275037 5.298211079 0.702165934 0.876459709 0.241161518 0.111539225 0.245963224 10.63484983 0.028269924 0.044048711 3743.475864 -3.573275037 0.174293774 KQQMAR ddPTM_BT-474_Pertuzumab_2h_R1 5 KQQMAR 6 1 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;; 138.53 0.019664 2440600000 5627471 5894837 5068176 3853404 3424292 1052646 4717105 3436267 3471520 4619016 FALSE TRUE 5407543.212 5726722.02 5984108.144 4052278.642 3534437.462 1073931.223 4774834.342 3365306.886 3077447.603 4306165.932 1.255767496 1.329888841 1.38966037 0.941040988 0.820785246 0.249393832 1.108836589 0.781508873 0.71466071 1 22.03797248 3.573722565 3.104481411 0.770970344 1.326288735 0.564623114 0.213748685 0.184961244 3.406282798 0.05935688 0.096025507 3747.335396 -3.573722565 0.555318391 VVDLAPLHLDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VVDLAPLHLDAR 12 0 A0A494C1S7;Q9Y5Q9;H7C0C0 A0A494C1S7 GTF3C3 General transcription factor 3C polypeptide 3 0 142.91 6.18E-05 69391000 89433 101310 78769 82501 85199 71847 91451 84516 91915 99911 FALSE TRUE 85937.85949 98420.73799 93004.31051 86758.8865 87939.50321 73299.79557 92570.20469 82770.71507 81481.19454 93143.93898 0.922635014 1.056652092 0.998500939 0.931449619 0.944124805 0.786951855 0.993840348 0.888632325 0.87478794 1 16.50717427 3.574019032 2.490174799 0.907825876 0.999323955 0.21721996 0.065156742 0.374320126 4.535352095 0.017677896 0.029807238 3749.894352 -3.574019032 0.091498079 DLGYIYFYQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGYIYFYQR 10 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 160.88 1.69E-05 1092870000 992400 1169610 943050 831730 702370 391470 1040200 747560 887030 1144920 FALSE TRUE 953615.9108 1136253.868 1113480.113 874655.685 724962.3689 399385.7916 1052930.279 732122.6248 786338.0731 1067373.549 0.893422843 1.064532534 1.043196278 0.819446656 0.679202112 0.374176212 0.986468402 0.685910407 0.736703729 1 20.02563373 3.574311789 3.806036126 0.726287754 1.005311655 0.308868277 0.169953699 0.259741637 6.813957855 0.045535808 0.072065236 3752.422997 -3.574311789 0.279023901 HVFAIFNTEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVFAIFNTEQR 11 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ; 194.17 6.33E-07 2091340000 1984370 2115300 1795720 1625390 1626520 1434340 1829830 1468120 1738580 1784440 FALSE TRUE 1906818.627 2054973.715 2120246.55 1709276.573 1678838.493 1463343.338 1852224.007 1437802.809 1541223.687 1663578.289 1.146215143 1.235273223 1.27450963 1.027469872 1.00917312 0.879635991 1.113397559 0.864283225 0.92645095 1 20.66585833 3.574439575 3.335220555 0.96055531 1.219877994 0.702155569 0.073505444 0.129401573 2.710060202 0.02002465 0.032105569 3753.527266 -3.574439575 0.259322685 TAHSLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 TAHSLFK 7 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 105.12 0.0079989 2018380000 2680480 2773200 2453590 2140490 1988030 1061130 2751020 1870340 2659580 2847190 FALSE TRUE 2575723.878 2694111.051 2897008.293 2250960.945 2051976.79 1082586.776 2784687.806 1831716.825 2357675.628 2654347.285 0.970379382 1.014980619 1.091420218 0.848028047 0.773062667 0.407854233 1.049104547 0.690081827 0.888231785 1 21.33992571 3.574489014 4.268649129 0.780444452 1.023090664 0.254616964 0.169436093 0.281603971 8.852652682 0.044364988 0.069692915 3753.954585 -3.574489014 0.242646212 TQQHYYER ddPTM_BT-474_Pertuzumab_2h_R1 5 TQQHYYER 8 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;; 142.43 0.00061765 2299130000 1533590 1595830 1385445 1156459 1223386 509218 1444669 1167570 1201316 1350986 FALSE TRUE 1473655.607 1550318.491 1635825.731 1216143.988 1262737.322 519514.7369 1462349.291 1143459.271 1064947.644 1259482.515 1.170048484 1.230917041 1.298807813 0.965590211 1.002584241 0.412482691 1.161071531 0.907880227 0.84554381 1 20.26439966 3.574667499 2.975410453 0.884947279 1.233190238 0.410536781 0.184291898 0.259358027 4.41399684 0.051126708 0.08329218 3755.49769 -3.574667499 0.348242958 IRFQESEERPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IRFQESEERPK 11 2 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 91.961 0.0058218 112740000 49442 54106 46485 56011 49244 63969 59774 67189 75622 81089 FALSE TRUE 47509.75198 52562.94986 54885.87355 58901.73442 50827.97798 65262.49701 60505.53209 65801.52367 67037.70759 75596.7698 0.628462725 0.695306823 0.72603464 0.779156763 0.672356479 0.863297429 0.800371924 0.870427716 0.886780054 1 16.20603697 3.575420057 0.142452796 1.104721791 0.366801871 0.858201615 0.040987453 5.802916059 0.223757995 0.28030109 0.929509877 3762.010968 -3.575420057 -0.73791992 LVNHFVEEFKR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVNHFVEEFKR 11 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 227.36 2.63E-12 7443600000 7132400 7582400 6200600 6081400 4892600 3995800 6900700 6000200 7731800 8051700 FALSE TRUE 6853657.923 7366157.376 7321186.352 6395261.783 5049974.922 4076597.814 6985152.831 5876293.773 6854118.478 7506351.187 0.913047865 0.981323308 0.975332245 0.851980093 0.672760279 0.543086476 0.930565685 0.782842906 0.91310922 1 22.83968036 3.575623908 4.412887394 0.789968805 0.957282667 0.212817777 0.12535324 0.315096283 10.3764509 0.034440026 0.054029567 3763.777209 -3.575623908 0.167313863 SDYMFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDYMFQR 7 0 A0A2R8Y430;P48637;A0A2R8YF34 A0A2R8Y430 GSS Glutathione synthetase 0 ; 107.32 0.017459 618410000 788520 909550 694620 686290 581450 330020 910030 654770 710940 833510 FALSE TRUE 757703.7666 883610.5245 820153.2857 721709.5091 600152.8673 336693.2305 921167.2194 641248.7707 630237.0717 777055.6253 0.975095916 1.137126476 1.055462774 0.928774576 0.772342221 0.433293602 1.18545853 0.825228915 0.811057859 1 19.56765835 3.57628456 3.345356987 0.835102116 1.063832308 0.222244093 0.181687506 0.371532946 7.809740765 0.05073988 0.081400356 3769.50705 -3.57628456 0.228730192 DCQLNAHK ddPTM_BT-474_Pertuzumab_2h_R1 8 DCQLNAHK 8 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;;;; 149.19 0.00050922 15502630000 12855720 12531960 11678850 10664670 10273060 7256990 12320230 11545380 12942430 13361720 FALSE TRUE 12353304.25 12174560.77 13789477.99 11215074.9 10603502.3 7403731.31 12471008.66 11306963.87 11473259.61 12456718.8 0.99169809 0.977348928 1.106991191 0.900323358 0.851227556 0.594356462 1.001147161 0.907700017 0.9210499 1 23.57042077 3.577582491 6.50523169 0.872609771 1.019857108 0.256678297 0.111557193 0.339132019 18.69114576 0.030561813 0.047473895 3780.789434 -3.577582491 0.147247336 RDVYLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDVYLSPR 8 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 RDVYLS(1)PR;RDVYLS(1)PR 116.24 0.0014148 1201100000 1002380 1044920 843830 729430 728940 313140 864690 687170 726700 839840 TRUE FALSE 963205.8814 1015119.905 996328.8519 767075.9697 752387.0171 319471.9053 875272.3349 672979.6994 644208.0626 782956.8887 1.230215731 1.296520816 1.272520705 0.979716739 0.960955869 0.408032562 1.117906168 0.859536086 0.822788677 1 19.57857335 3.578815754 2.326281576 0.852309491 1.276330533 0.51828746 0.174526945 0.235927178 2.500315057 0.049622484 0.0854114 3791.540981 -3.578815754 0.424021042 S(ph)PPSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPSLR 6 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.999)PPS(0.001)LR 69.432 0.098096 1110500000 74409 62932 70041 71481 83040 96705 96304 82317 104260 106240 TRUE FALSE 71501.01402 61137.24098 82698.96675 75170.14298 85711.05702 98660.44136 97482.59716 80617.12518 92424.84189 99044.27017 0.721909646 0.617271861 0.834969722 0.758954989 0.865381277 0.996124674 0.984232576 0.813950419 0.933166974 1 16.5957859 3.578862808 1.112216305 0.927536671 0.677712346 0.668725235 0.070336962 0.343989523 0.842112877 0.02609628 0.062412919 3791.951795 -3.578862808 -0.249824325 DVYLSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVYLSPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 120.62 0.01051 590060000 666750 693870 605630 495130 488710 260920 619670 447230 480710 601840 FALSE TRUE 640692.6729 674081.507 715080.8132 520683.7186 504429.801 266195.9812 627253.7068 437994.5442 426141.8161 561076.8407 1.141898268 1.201406756 1.274479289 0.928007861 0.899038713 0.474437656 1.117946173 0.780632014 0.75950705 1 19.09783884 3.579221205 3.301912611 0.830162812 1.205155899 0.506578779 0.161658475 0.195093501 3.998298467 0.04338593 0.069821332 3795.082359 -3.579221205 0.374993087 DQLIYNLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQLIYNLLK 9 0 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8;F5GXC7;F5H8H6;F5GXU1;F5GWW2 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ; 156.92 0.00016235 1289010000 2669900 2578200 2262000 2106260 2050590 1498920 2440300 2274000 2345800 1916250 FALSE TRUE 2565557.356 2504672.26 2670793.718 2214964.331 2116549.09 1529229.189 2470165.121 2227041.105 2079514.618 1786460.681 1.436111852 1.402030443 1.495019592 1.239861786 1.184772278 0.85601055 1.382714519 1.246621954 1.164041639 1 20.76867273 3.579752314 3.606676247 1.163489654 1.439494586 0.499696455 0.134952496 0.225974758 5.381631834 0.038339503 0.06110901 3799.726289 -3.579752314 0.276004932 QRPGQQVATCVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QRPGQQVATCVR 12 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 161.25 6.01E-05 148330000 112890 103970 90281 80238 70426 40634 96676 63836 98727 99832 FALSE TRUE 108478.134 101004.8774 106596.785 84379.0928 72691.31625 41455.64732 97859.14981 62517.76429 87519.92486 93070.28972 1.165550621 1.085253712 1.14533634 0.906616849 0.781036746 0.445422996 1.05145423 0.671726332 0.940363731 1 16.50603308 3.580939206 3.020927026 0.791113551 1.129152651 0.419509456 0.164968892 0.229283003 4.001883889 0.044099009 0.071941935 3810.124841 -3.580939206 0.3380391 NFRPDDPTR ddPTM_BT-474_Pertuzumab_2h_R1 3 NFRPDDPTR 9 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ;; 117.7 0.0010118 3329170000 2381010 2343540 1968680 2412980 2163050 2224550 2393690 2461560 2498930 2581210 FALSE TRUE 2287957.497 2276704.534 2324464.269 2537514.187 2232626.468 2269531.925 2422984.694 2410727.926 2215261.943 2406382.348 0.950787184 0.946110886 0.965957996 1.054493352 0.927793736 0.943130225 1.006899297 1.001805855 0.920577707 1 21.19843446 3.58104936 0.003990257 1.93935922 1.51E-05 0.032223173 0.03969741 97282.04609 93.06994471 22196.70322 23039.24629 3811.091359 -3.58104936 -1.939344138 VAGHPLAQNER ddPTM_BT-474_Pertuzumab_2h_R1 1 VAGHPLAQNER 11 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 61.577 0.086427 224720000 89275 103740 88129 62632 51567 20008 76366 53887 51379 75376 FALSE TRUE 85786.0343 100781.4368 104055.8707 65864.44503 53225.69939 20412.57547 77300.58995 52774.21462 45546.67132 70270.71638 1.220793507 1.434188264 1.480785683 0.937295767 0.757437837 0.290484807 1.100039873 0.751012902 0.648160054 1 16.10063599 3.581658368 3.557015992 0.752188457 1.38262456 0.63050564 0.211965849 0.150572645 3.496916418 0.057999765 0.092655392 3816.439376 -3.581658368 0.630436103 AQNTWGCGNSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQNTWGCGNSLR 12 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 327.29 1.08E-57 893130000 185848 213737 181987 159223 158642 118403 173496 170012 154453 187982 FALSE TRUE 178584.8547 207641.43 214876.0992 167440.5181 163744.864 120797.1898 175619.2959 166501.1928 136920.143 175249.8117 1.019030223 1.184831116 1.226113153 0.955439076 0.934351155 0.689285704 1.002108329 0.950079154 0.781285535 1 17.41905337 3.581770305 4.261281837 0.895709277 1.14620662 0.538965824 0.103464622 0.173932487 5.348856762 0.028167668 0.04435132 3817.423166 -3.581770305 0.250497344 LQQHSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQQHSDK 7 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 0 ; 70.919 0.055723 88539000 93836 101265 67884 96570 95340 97533 107902 121854 84512 105744 FALSE TRUE 90168.78538 98377.02135 80152.14887 101553.9893 98406.69769 99505.18409 109222.537 119337.6723 74918.55206 98581.86469 0.914658955 0.997922099 0.813051661 1.030148797 0.998223132 1.009366017 1.107937421 1.210543873 0.759962822 1 16.58903465 3.582153553 9.583244113 1.041025486 0.917534861 0.130981969 0.115808916 0.662537157 56.196847 0.031295013 0.048499034 3820.793386 -3.582153553 -0.123490625 AIHSWLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIHSWLTR 8 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ; 164.77 0.00032814 3600700000 2186800 2361400 1919600 1595600 1626350 424820 2096200 1458810 1643590 1951730 FALSE TRUE 2101337.438 2294055.184 2266514.421 1677949.107 1678663.025 433410.1515 2121853.923 1428685.064 1457016.554 1819537.589 1.154874432 1.260790213 1.24565408 0.92218436 0.922576722 0.238197965 1.16615009 0.785191288 0.800761997 1 20.79514042 3.58236062 2.572489813 0.805857423 1.2283782 0.385613649 0.226201513 0.28483294 3.669944019 0.063037157 0.106137737 3822.615531 -3.58236062 0.422520777 S(ph)PLPTKR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPLPTKR 7 1 D6R9T3;Q96FZ2;E7EMP6 D6R9T3 HMCES Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein 1 S(1)PLPTKR;S(1)PLPTKR;S(1)PLPTKR 80.239 0.018653 1172080000 1223220 1278510 973750 984860 1010890 992820 1005250 940020 1031760 1015840 TRUE FALSE 1175415.21 1242048.147 1149728.286 1035688.743 1043406.195 1012895.501 1017552.55 920608.2585 914638.9303 947036.252 1.241151231 1.311510667 1.214027746 1.093610451 1.101759508 1.069542479 1.074459978 0.972094 0.965790833 1 19.85306013 3.583413447 0.533796134 0.97864951 1.343116382 0.886924775 0.03736428 0.451730893 0.221332853 0.027718706 0.090767592 3831.893644 -3.583413447 0.364466872 KHPS(ph)SPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.659)S(0.341)PAR;KHPS(0.614)S(0.386)PAR 73.885 0.025975 190390000 97855 127420 93497 64085 51494 6379.8 83188 39036 40218 68634 TRUE FALSE 94030.71842 123786.1064 110393.9877 67392.43453 53150.35128 6508.803927 84206.07963 38229.89296 35652.62125 63985.35805 1.469566183 1.934600511 1.725300773 1.053247752 0.830664278 0.101723334 1.316021074 0.597478769 0.557199683 1 15.96545419 3.583413733 2.559126162 0.719576294 1.744375789 0.658783427 0.313594833 0.161678453 2.061927363 0.086510123 0.145940705 3831.896174 -3.583413733 1.024799495 EHPWEVMPDLYFYRDPEEIEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHPWEVMPDLYFYRDPEEIEK 21 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 224.05 2.00E-25 619830000 739980 636400 791410 834590 817990 777340 929700 953530 1272590 1293240 FALSE TRUE 711060.7635 618250.4951 934435.3918 877663.2899 844301.3912 793058.3474 941077.9467 933839.2723 1128130.918 1205647.703 0.589774908 0.512795316 0.775048457 0.72795999 0.700288641 0.657786139 0.780557989 0.774554018 0.935705277 1 20.20137697 3.58467785 0.084015511 1.348636243 2.10E-17 0.751418056 0.069146726 26.79343284 0.561264906 2.917443474 6.261387482 3843.066062 -3.58467785 -1.348636243 S(ph)PAPGLASGDRPPSVSSVHSEGDCNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPAPGLASGDRPPSVSSVHSEGDCNR 26 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(1)PAPGLASGDRPPSVSSVHSEGDCNR 191.99 3.01E-18 664260000 57649 63900 49789 65947 88961 70058 69534 76139 77635 93077 TRUE FALSE 55396.01335 62077.63456 58786.97985 69350.53257 91822.51136 71474.62076 70384.97789 74566.70304 68822.20027 86772.81189 0.638402884 0.715404206 0.677481559 0.799219607 1.058194489 0.823698336 0.811140913 0.859332565 0.793130922 1 16.40495546 3.585407041 4.233441125 0.877400178 0.682542219 0.573822997 0.081563959 0.175774082 5.312402777 0.022077169 0.034812648 3849.52408 -3.585407041 -0.19485796 LLAAVEAFYSPPSHDRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 150.28 3.37E-08 1192450000 635790 696390 602530 496770 475210 433190 531590 422140 510770 577180 FALSE TRUE 610942.6239 676529.639 711420.5742 522408.3592 490495.5612 441949.3986 538095.7574 413422.6615 452789.5309 538087.0845 1.135397302 1.257286522 1.322129066 0.970862104 0.911554236 0.821334337 1.000016118 0.768319243 0.841480021 1 19.03748015 3.585731193 3.827080535 0.879056452 1.238876099 0.782709178 0.081756644 0.098624274 2.563894489 0.022228721 0.035322934 3852.398394 -3.585731193 0.359819647 GIVEFASKPAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIVEFASKPAAR 12 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 190.66 5.80E-06 5187600000 4213200 4287900 3536900 4119000 4139900 4337100 4529400 4687800 4680500 4652900 FALSE TRUE 4048543.486 4165613.29 4176096.508 4331582.084 4273063.643 4424799.134 4584832.152 4590995.292 4149189.262 4337754.939 0.933326927 0.960315497 0.962732235 0.998576947 0.985086457 1.020066646 1.056959698 1.058380512 0.9565292 1 22.04851712 3.585874113 0.926640668 1.027262476 0.939870157 0.466078378 0.029333558 0.536079667 0.899548478 0.012303485 0.032849377 3853.666372 -3.585874113 -0.087392319 HTNFVEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 HTNFVEFR 8 0 M0R0N4;M0QYZ2;P53680;M0QZ21 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 ;;; 122.44 0.0013902 754691000 419372 461680 444068 299040 327462 132699 392169 226924 315932 349794 FALSE TRUE 402982.4786 448513.3384 524320.9658 314473.4902 337995.1126 135382.2647 396968.4815 222237.9401 280068.7239 326102.1408 1.235755391 1.37537686 1.607842759 0.964340465 1.036470082 0.415152947 1.217313326 0.681497949 0.858837428 1 18.31496439 3.586294725 4.379853538 0.853804326 1.400981958 0.545583731 0.219864592 0.159776622 5.056160875 0.056739247 0.089306743 3857.400435 -3.586294725 0.547177632 YAWQGVALLPFVDER ddPTM_BT-474_Pertuzumab_2h_R1 2 YAWQGVALLPFVDER 15 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 169.23 2.81E-06 131088000 231020 281390 212811 200953 172628 165341 203129 193234 192819 245230 FALSE TRUE 221991.483 273365.0327 251270.6817 211324.2084 178180.7364 168684.3083 205614.9535 189243.6504 170930.9955 228620.3537 0.971004897 1.195716078 1.099073978 0.924345558 0.779373899 0.737835917 0.899372913 0.82776379 0.74766307 1 17.80259432 3.586540905 3.20310101 0.825044374 1.099852197 0.624360047 0.088534725 0.145984914 2.823790261 0.023414844 0.037984544 3859.587626 -3.586540905 0.274807823 LMIWDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LMIWDTR 7 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;Q16576;E9PC52;Q16576-2;Q5JP01;Q5JP02 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 ; 117.17 0.01231 2072160000 6109500 6877700 5656700 4280200 3778200 1832040 3992000 3992400 4334300 5677800 FALSE TRUE 5870733.986 6681554.73 6678991.523 4501101.635 3899729.234 1869085.104 4040855.29 3909955.545 3842288.435 5293237.549 1.109100797 1.262281292 1.26179705 0.850349449 0.736737998 0.35310811 0.763399574 0.738669956 0.725886265 1 22.33571897 3.587625808 3.086127734 0.698202655 1.217685834 0.668829095 0.153893339 0.142959473 2.586998471 0.042593286 0.069524817 3869.241242 -3.587625808 0.519483179 EQIYDVYR ddPTM_BT-474_Pertuzumab_2h_R1 6 EQIYDVYR 8 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;;;; 152.63 0.0010562 2823790000 3082430 3511430 2923300 2412060 2270860 809858 3183300 2353760 2401500 2966630 FALSE TRUE 2961965.228 3411287.454 3451605.338 2536546.706 2343904.274 826233.8836 3222258.178 2305154.033 2128891.788 2765697.508 1.070964999 1.233427533 1.248005369 0.917145385 0.847491191 0.298743402 1.165079756 0.833480172 0.769748601 1 21.39921194 3.587919494 3.552633742 0.815570032 1.188254252 0.372160317 0.211573876 0.256405782 5.908730192 0.058235161 0.093308263 3871.858648 -3.587919494 0.37268422 SQASMVINS(ph)DTDDEEEVSAALTLAHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQASMVINSDTDDEEEVSAALTLAHLK 27 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQASMVINS(0.983)DT(0.017)DDEEEVSAALTLAHLK 177.99 1.36E-17 65867000 82236 70440 79017 96688 95488 118550 128900 126190 124020 117110 TRUE FALSE 79022.1262 68431.12017 93297.12962 101678.0793 98559.45824 120947.1622 130477.5168 123584.1324 109941.7695 109178.0354 0.723791429 0.626784682 0.854541202 0.931305266 0.90274072 1.107797569 1.195089436 1.131950506 1.006995309 1 16.73632312 3.588706362 0.918907277 1.107061569 0.655745219 0.794541925 0.07733897 0.274534951 0.452123586 0.032235037 0.086788106 3878.880159 -3.588706362 -0.45131635 KPGYHAPVALLNDIPQSTEQYDPFAEHRPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPGYHAPVALLNDIPQSTEQYDPFAEHRPPK 31 2 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 0 162.91 5.58E-13 586150000 795550 731830 668200 748950 862360 906720 909700 667640 1112400 969650 FALSE TRUE 764459.0265 710958.9249 788958.604 787603.3993 890098.5926 925054.4996 920833.1807 653853.0007 986125.0156 903974.7418 0.845664144 0.786480962 0.872766204 0.871267042 0.984649848 1.023318968 1.018649237 0.723308927 1.090876736 1 19.78592294 3.588914162 2.200446549 0.948129126 0.824774517 0.28762177 0.095042826 0.499979477 4.743298756 0.029515981 0.052021875 3880.736556 -3.588914162 -0.123354608 AGSIS(ph)TLDSLDFAR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.332)IS(0.668)TLDSLDFAR;AGS(0.031)IS(0.968)T(0.001)LDSLDFAR;AGS(0.143)IS(0.857)TLDSLDFAR;AGS(0.016)IS(0.983)TLDSLDFAR 347.99 8.36E-82 2208670000 735591 773225 829366 1227916 1146238 1215696 1851960 1616210 1818910 1892490 TRUE FALSE 706843.2905 751173.3801 979250.8853 1291288.892 1183107.786 1240278.206 1874624.84 1582834.699 1612434.962 1764309.967 0.400634414 0.425760436 0.555033358 0.731894574 0.670578191 0.702982032 1.06252579 0.897140938 0.913918185 1 20.75067262 3.589053265 0.452282548 1.005055988 0.245869013 0.869321533 0.079264765 0.644470558 0.209655175 0.068266789 0.239167267 3881.979742 -3.589053265 -0.759186974 down MFLQYYLNEQGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 MFLQYYLNEQGDR 13 0 Q9NPE3;H0YM60 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 ; 184.88 2.12E-05 494440000 215829 241708 181063 224417 269650 246854 214775 260884 217180 263440 FALSE TRUE 207394.1641 234814.7245 213785.1118 235999.1883 278323.5371 251845.557 217403.4807 255496.6542 192526.6369 245596.9742 0.844449183 0.956097791 0.870471277 0.960920586 1.13325312 1.025442426 0.885204231 1.04030864 0.783912903 1 17.90593326 3.58934339 5.89550314 0.985019844 0.898011723 0.150381794 0.091867544 0.435068432 19.80436862 0.024296549 0.037835696 3884.573923 -3.58934339 -0.087008121 HFILDECDK ddPTM_BT-474_Pertuzumab_2h_R1 8 HFILDECDK 9 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;;;;;; 182.65 4.61E-05 8894430000 11284950 10401660 8859280 9301920 9323340 8862920 10335080 7151970 12799550 11844370 FALSE TRUE 10843921.68 10105014.84 10460348.97 9781993.206 9623233.698 9042134.315 10461563.8 7004279.32 11346598.74 11042140.27 0.982048897 0.915131903 0.947311727 0.885878368 0.871500766 0.818875154 0.947421745 0.634322618 1.027572415 1 23.3965165 3.589874349 1.360551597 0.848761783 0.95380879 0.016795049 0.10670748 0.929209942 3.399883447 0.034134893 0.073857701 3889.326019 -3.589874349 0.105047007 ISSDLDGHPVPK ddPTM_BT-474_Pertuzumab_2h_R1 4 ISSDLDGHPVPK 12 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;; 121.02 0.00038366 5927160000 14056800 14490000 12444500 11319800 11780400 6513790 12480600 12348900 13184200 14063900 FALSE TRUE 13507444.72 14076759.39 14693497.98 11904016.23 12159327.26 6645503.297 12633341.32 12093890.9 11687584.89 13111339.53 1.030210886 1.073632435 1.120671 0.907917624 0.92739016 0.506851591 0.963543145 0.922399338 0.891410436 1 23.64431175 3.590368118 3.433567179 0.861300073 1.074408726 0.333621939 0.130088493 0.286638619 6.233898158 0.036697169 0.059100945 3893.75048 -3.590368118 0.213108654 YVIYIER ddPTM_BT-474_Pertuzumab_2h_R1 4 YVIYIER 7 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KS10;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ;;; 141.98 0.0058623 2099460000 1570690 1674260 1548210 1352770 1440020 1339020 1242090 1453310 1467890 1657250 FALSE TRUE 1509305.698 1626511.744 1828005.987 1422586.622 1486339.551 1366095.902 1257291.069 1423298.641 1301261.281 1545002.981 0.976895007 1.052756379 1.183173113 0.920766263 0.962030215 0.884202761 0.813779057 0.921227116 0.842238686 1 20.55917819 3.590650385 6.985508625 0.898236101 1.068718453 0.546241853 0.06874557 0.180418291 9.910776529 0.018132169 0.028158374 3896.282027 -3.590650385 0.170482352 QHYIDLK ddPTM_BT-474_Pertuzumab_2h_R1 7 QHYIDLK 7 0 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72;O60361 Q32Q12;O60361 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 ;;;;;; 145.63 0.0022734 19179120000 26407800 26200410 22136100 20952930 20643450 20798900 21446810 15440570 27773730 27998960 FALSE TRUE 25375753.98 25453199.96 26136585.68 22034313.23 21307465.32 21219468.01 21709282.48 15121716.83 24620972.61 26102565.5 0.972155552 0.97512254 1.001303327 0.844143585 0.816297743 0.81292653 0.831691524 0.57931918 0.943239568 1 24.63768827 3.59094904 2.788679837 0.793900918 0.983533639 0.254530969 0.106861284 0.29541224 4.432533183 0.030530934 0.05084023 3898.962337 -3.59094904 0.189632721 KQELELVVSELEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQELELVVSELEAR 14 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 169.92 5.22E-06 160780000 328820 354950 301270 331500 337380 383380 357490 404390 444940 414090 FALSE TRUE 315969.3509 344827.1735 355716.1907 348608.7547 348232.1341 391132.2063 361865.0696 396039.2052 394432.2765 386043.3155 0.818481601 0.893234411 0.921441135 0.903030154 0.902054563 1.013182176 0.937369085 1.025893182 1.021730621 1 18.55840321 3.592337997 0.404324177 1.025139612 0.802553558 0.762234878 0.031971958 1.087373852 0.268001721 0.029284434 0.1081913 3911.451927 -3.592337997 -0.222586054 AWNPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AWNPFR 6 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 119.23 0.049289 914240000 562660 663960 533480 447410 385310 177670 588750 422290 423660 547930 FALSE TRUE 540670.6251 645024.5109 629891.7032 470500.8837 397703.8461 181262.6091 595955.2986 413569.5639 375567.8929 510818.2131 1.058440383 1.262728099 1.233103455 0.921073039 0.778562385 0.354847585 1.16666807 0.809621805 0.735228078 1 18.96245044 3.592721473 3.584087459 0.805018916 1.191866527 0.412522567 0.200778426 0.234188354 5.455741983 0.055325144 0.088747419 3914.907214 -3.592721473 0.386847611 QRS(ph)PIALPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QRSPIALPVK 10 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 QRS(1)PIALPVK 73.781 0.026622 462550000 1251400 1332200 1132500 1100900 1075400 689220 1253100 1228900 1352000 1417500 TRUE FALSE 1202493.905 1294206.96 1337167.942 1157717.581 1109991.218 703156.5006 1268435.813 1203522.786 1198526.628 1321491.462 0.90995208 0.979353251 1.011862718 0.876068907 0.839953378 0.532093109 0.959851689 0.910730655 0.906949959 1 20.33373567 3.592984148 5.116319851 0.85047546 0.967531141 0.137032872 0.121709074 0.44327679 16.86311544 0.03407068 0.05330098 3917.275783 -3.592984148 0.117055681 S(ph)MSAPSDLEMIGNEDLEFTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.499)MS(0.499)APS(0.003)DLEMIGNEDLEFTR 182.76 1.80E-16 38275000 32402 33435 24903 34274 36460 31532 40374 44988 36802 33224 TRUE FALSE 31135.69402 32481.46654 29403.52606 36042.88525 37632.76901 32169.59864 40868.10909 44058.98208 32624.39125 30973.70889 1.005229762 1.048678628 0.949305948 1.163660619 1.214990725 1.038609834 1.319445122 1.422463879 1.053293016 1 14.91875653 3.593630999 4.322763536 1.213102255 1.006803553 0.246523551 0.127289239 0.274908029 8.434083733 0.036636579 0.057822464 3923.114638 -3.593630999 -0.206298702 AEDS(ph)DS(ph)EPEPEDNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEDSDSEPEPEDNVR 15 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 2 AEDS(1)DS(1)EPEPEDNVR;AEDS(1)DS(1)EPEPEDNVR 248.94 5.97E-16 0 607340 589240 487270 607010 595940 704530 600690 682510 689710 737990 TRUE FALSE 583604.4814 572435.4521 575330.5283 638337.8588 615108.9513 718776.0793 608041.4239 668415.93 611417.0123 688005.28 0.848255818 0.832021888 0.836229815 0.927809535 0.894046847 1.044724656 0.883774357 0.971527326 0.888680698 1 19.39206011 3.5939124 1.858584379 0.948866309 0.834794345 0.501483408 0.048411019 0.273966728 1.860199239 0.013470216 0.025267069 3925.657442 -3.5939124 -0.114071964 HVEVSQAPLPPAPAYLSS(ph)PLALPSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 HVEVSQAPLPPAPAYLSSPLALPSQR 26 0 A0A087X0G7;A0A087WUW6;A0A087X1B1;Q9Y6K9;Q9Y6K9-2;Q9Y6K9-3 A0A087X0G7 IKBKG NF-kappa-B essential modulator 1 HVEVSQAPLPPAPAY(0.001)LS(0.26)S(0.739)PLALPSQR 114.76 0.00085646 73004000 50156 47275 46460 50866 52268 63214 54631 39410 52806 61713 TRUE FALSE 48195.84807 45926.76329 54856.3555 53491.20036 53949.24769 64492.23039 55299.59052 38596.16973 46811.68426 57533.12354 0.837706092 0.798266467 0.953474314 0.929746154 0.937707609 1.120958266 0.961178311 0.670851283 0.813647537 1 15.81210518 3.594067374 0.001595342 1.782619507 7.39E-05 0.001408708 0.119026222 5250251.426 2013.344907 1116482.523 1133132.503 3927.058529 -3.594067374 -1.782545606 RLSELLR ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSELLR 7 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;; 179.21 0.0011295 6333250000 2716196 3076999 2710470 2071035 1830131 581877 2866752 1960898 2134126 2705228 FALSE TRUE 2610044.057 2989246.001 3200312.223 2177921.365 1888998.826 593642.9516 2901836.169 1920404.771 1891868.963 2522000.498 1.034910207 1.185267808 1.268957808 0.863568967 0.74900811 0.235385739 1.15060888 0.761460901 0.75014615 1 21.26613713 3.594662215 4.410446364 0.766503718 1.163051825 0.369700196 0.226787302 0.238409513 7.502651771 0.061301726 0.096649157 3932.440992 -3.594662215 0.396548107 RGAGAELK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGAGAELK 8 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 72.042 0.075649 113380000 142660 166760 143910 128950 128140 94599 145990 138820 145840 159670 FALSE TRUE 137084.6895 162004.1681 169917.7383 135605.125 132261.7395 96511.85659 147776.6693 135953.3185 129284.8546 148855.4087 0.920925149 1.088332426 1.141495225 0.910985541 0.888524916 0.648359757 0.992753106 0.91332468 0.868526416 1 17.18355212 3.594847831 5.918034802 0.881354764 1.053185528 0.33600005 0.104239759 0.254548235 11.40095887 0.028065628 0.043718944 3934.12207 -3.594847831 0.171830764 FYFHDGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FYFHDGVR 8 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 157.86 0.00037013 723060000 463460 524090 474250 373590 363550 189710 458070 326750 443810 569710 FALSE TRUE 445347.4708 509143.4663 559957.5246 392871.0247 375243.9159 193546.0662 463675.9977 320002.4983 393430.5494 531123.0343 0.838501519 0.958616805 1.054289663 0.739698713 0.706510341 0.364409099 0.873010523 0.602501638 0.740752187 1 19.01868657 3.595238478 5.068013612 0.68654124 0.949808163 0.286282116 0.164639019 0.242899191 9.089022711 0.041988529 0.065733354 3937.662394 -3.595238478 0.263266923 KCDSWWAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KCDSWWAK 8 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 71.349 0.078523 355330000 516440 464190 458430 430030 448670 317100 531880 480350 509500 495850 FALSE TRUE 496256.9538 450951.7557 541278.4987 452223.8998 463101.878 323511.9793 538389.3065 470430.6046 451663.696 462265.6378 1.073531998 0.97552515 1.170925231 0.978277126 1.001809004 0.69983999 1.164675162 1.017662933 0.977065261 1 18.8183626 3.595463138 17.47449523 0.981134553 1.065423772 0.124890988 0.115861482 5.448236637 783.5928054 0.031024653 0.048063191 3939.699873 -3.595463138 0.084289219 RGDTVATLSER ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDTVATLSER 11 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 177.16 1.30E-05 816720000 180250 183438 145914 141036 134280 90790 143158 148768 134750 180995 FALSE TRUE 173205.6307 178206.5278 172283.9056 148314.8849 138599.2381 92625.83601 144910.0104 145695.8888 119453.7449 168736.0474 1.02648861 1.056126006 1.021026083 0.878975697 0.821396733 0.54893923 0.858796995 0.863454437 0.707932577 1 17.36440869 3.595954981 2.339059312 0.791533821 1.042558934 0.477602341 0.109638961 0.25368684 2.711464251 0.031488937 0.054841904 3944.164151 -3.595954981 0.251025114 EKAHEGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKAHEGAR 8 1 Q9BR76;A0A087WW53;F5H390;Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0;F8VV53 Q9BR76;Q9ULV4 CORO1B;CORO1C Coronin-1B;Coronin;Coronin-1C 0 65.347 0.058831 40953000 14460 14382 11172 9298.7 11734 13293 13958 11880 9062 10303 FALSE TRUE 13894.88721 13971.83944 13191.02892 9778.607021 12111.43477 13561.79357 14128.82218 11634.67385 8033.319751 9605.168633 1.446605234 1.454616777 1.373326115 1.018056777 1.260928905 1.41192665 1.470960346 1.211293033 0.836353848 1 13.22959523 3.596470752 0.042597101 7.03E-06 2.658780007 0.37032539 0.170148198 265.739854 2.725206649 68.72753566 102.2905003 3948.851043 -3.596470752 2.658772974 DKASGDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKASGDVK 8 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 67.113 0.054662 123850000 175150 170730 170590 137110 141160 116410 157140 138260 132260 175710 FALSE TRUE 168304.9444 165860.9476 201419.4078 144186.2635 145700.5396 118763.89 159063.1263 135404.8827 117246.3993 163809.0052 1.027446227 1.012526432 1.229599115 0.880209628 0.889453784 0.725014414 0.971027973 0.826602192 0.715750634 1 17.32165514 3.596808943 6.902361044 0.849975619 1.081373429 0.523403636 0.101305496 0.187347348 9.873099949 0.025904279 0.040241885 3951.927268 -3.596808943 0.23139781 HTTEAAAGALQNITAGDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTTEAAAGALQNITAGDRR 19 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 149.47 5.53E-08 144090000 673720 640340 510710 506570 481080 273360 569750 503290 504220 529490 FALSE TRUE 647390.2776 622078.1302 603006.6577 532714.1384 496554.3751 278887.5265 576722.7709 492896.8856 446983.0595 493627.1707 1.311496441 1.260218576 1.221583198 1.079183177 1.00592999 0.564976045 1.168336763 0.998520574 0.905507407 1 18.91306228 3.596826364 1.944104627 0.943527124 1.279424989 0.509128863 0.143595392 0.292756007 2.172118937 0.043540719 0.080504489 3952.085793 -3.596826364 0.335897865 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 9 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHS(0.001)NIAT(0.002)EHIPS(0.997)PAK;RPTPNDDTLDEGVGLVHSNIAT(0.002)EHIPS(0.998)PAK;RPTPNDDTLDEGVGLVHS(0.001)NIAT(0.209)EHIPS(0.79)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIAT(0.099)EHIPS(0.901)PAK;RPTPNDDTLDEGVGLVHSNIAT(0.003)EHIPS(0.997)PAK 233.04 1.40E-45 44802359000 3184450 2564457 2559979 2753936 2881302 3177944 3836268 1839764 3894093 4194920 TRUE FALSE 3059998.173 2491321.197 3022624.152 2896066.967 2973981.696 3242204.205 3883217.395 1801772.23 3452051.888 3910794.332 0.782449271 0.63703713 0.772892639 0.740531647 0.76045464 0.829039814 0.992948508 0.460717716 0.882698397 1 21.89903024 3.597385222 1.608151831 0.783529126 0.716231856 0.044311679 0.148494236 1.781798176 9.076328501 0.046940233 0.094022033 3957.174684 -3.597385222 -0.06729727 ALFDFNGNDEEDLPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALFDFNGNDEEDLPFK 16 0 P46108-2;P46108 P46108-2 CRK Adapter molecule crk 0 198.46 9.46E-11 21689000 28118 27270 20313 26882 28266 27743 26645 29825 33079 30493 FALSE TRUE 27019.11747 26492.2863 23984.01096 28269.38324 29175.20156 28303.98247 26971.08948 29209.10333 29324.0106 28427.68195 0.950450956 0.931918626 0.843685074 0.99443153 1.026295482 0.995648626 0.948761476 1.027488044 1.031530135 1 14.79500884 3.598175087 8.032365157 1.004023231 0.911249837 0.62237774 0.033882596 0.187169738 11.54761619 0.009132679 0.014166084 3964.378273 -3.598175087 -0.092773393 LTELMFEHYNIPAFFLCK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTELMFEHYNIPAFFLCK 18 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 144.73 9.61E-08 188540000 664400 645630 561360 567100 568960 536050 641180 538020 671780 703220 FALSE TRUE 638434.5135 627217.2645 662810.2394 596368.099 587261.1151 546889.2983 649026.9526 526909.699 595522.3507 655590.283 0.973831568 0.956721417 1.011012909 0.909665861 0.895774587 0.834193722 0.98998867 0.803717982 0.908375804 1 19.32243495 3.598423365 5.10626443 0.892805791 0.977672776 0.23800015 0.058458337 0.267003199 10.02139269 0.014875482 0.023290619 3966.645278 -3.598423365 0.084866985 TVS(ph)PSTIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSPSTIR 8 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 T(0.008)VS(0.915)PS(0.071)T(0.006)IR;T(0.029)VS(0.971)PSTIR 160.16 0.00037232 1253460000 1308770 1217220 1070290 1311890 1301970 1344870 1416140 1473340 1560990 1588980 TRUE FALSE 1257621.821 1182506.077 1263715.211 1379596.8 1343849.047 1372064.193 1433471.145 1442915.014 1383792.959 1481356.969 0.848966081 0.798258692 0.853079465 0.931306112 0.907174351 0.926221175 0.967674352 0.974049499 0.934138758 1 20.4984879 3.598579744 0.636297022 0.972213393 0.797325678 0.818129936 0.025630557 0.442730049 0.325282654 0.014976436 0.047483512 3968.073834 -3.598579744 -0.174887714 YRDYYR ddPTM_BT-474_Pertuzumab_2h_R1 2 YRDYYR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 90.986 0.044147 512480000 425330 451000 367170 265430 221350 97614 254190 227100 252850 300890 FALSE TRUE 408707.6334 438137.9216 433525.7867 279128.8741 228469.9238 99587.82196 257300.8533 222410.3056 224147.528 280510.4523 1.457013919 1.561930823 1.545488887 0.995074771 0.814479182 0.355023569 0.917259415 0.79287707 0.799070146 1 18.097695 3.598847899 2.750583297 0.763897439 1.533960396 0.807110031 0.161791405 0.110165992 1.609071698 0.045796461 0.076877309 3970.524669 -3.598847899 0.770062957 GPPASS(ph)PAPAPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPAS(0.015)S(0.985)PAPAPK;GPPAS(0.034)S(0.966)PAPAPK;GPPAS(0.016)S(0.984)PAPAPK;GPPAS(0.113)S(0.887)PAPAPK 182.23 1.80E-05 2652130000 5324040 5475540 4849530 4493300 4183160 4708710 4034300 4944880 5212440 5111050 TRUE FALSE 5115970.631 5319382.96 5725947.948 4725199.751 4317715.14 4803923.342 4083672.97 4842766.5 4620745.664 4764874.031 1.07368434 1.11637431 1.201699753 0.991673593 0.90615515 1.008195245 0.857036921 1.016347225 0.969751904 1 22.18400664 3.599734555 5.68535379 0.958684825 1.128076042 0.667086845 0.054197816 0.126734156 5.362981035 0.013926986 0.021725818 3978.639183 -3.599734555 0.169391217 LASYLDR ddPTM_BT-474_Pertuzumab_2h_R1 8 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 189.31 0.0012958 13554590000 12046360 13798200 11115690 8237210 6736071 4044567 7212200 7130590 8858130 10727930 FALSE TRUE 11575574.93 13404688.85 13124542.45 8662333.395 6952742.841 4126350.916 7300465.061 6983340.825 7852592.219 10001317.75 1.157404977 1.340292268 1.31228132 0.866119207 0.695182677 0.412580724 0.729950317 0.698242072 0.785155758 1 23.25368676 3.60019854 3.155545522 0.69452266 1.279414115 0.744715762 0.143227341 0.115850878 2.174007347 0.039135451 0.064113563 3982.892093 -3.60019854 0.584891454 EACPELDYFVVFSSVSCGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EACPELDYFVVFSSVSCGR 19 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 113.76 0.00039741 80111000 55510 48712 43468 54582 64544 60422 63878 63006 62707 68035 FALSE TRUE 53340.60783 47322.78145 51323.63454 57398.98356 66620.11638 61643.77424 64659.75807 61704.90408 55588.76425 63426.92885 0.840977307 0.746099209 0.809177355 0.904962365 1.05034435 0.971886474 1.019437 0.972850258 0.876422133 1 15.95280787 3.600280347 3.081144977 0.982043542 0.791898247 0.742022294 0.048091124 0.121318222 2.182524007 0.01317455 0.02166892 3983.64241 -3.600280347 -0.190145295 KYSCDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KYSCDR 6 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q03001-3;Q03001-9;Q6P0N6;Q15149-4;Q15149-5;Q15149-8;F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;E7ETB9 Q15149-3;Q15149-4;Q15149-5;Q15149-8;F6QMI7 PLEC;DST Plectin;Dystonin 0 88.029 0.083007 443910000 248050 273770 218190 223350 225740 187260 267310 226370 237390 256370 FALSE TRUE 238355.9318 265962.3476 257621.7866 234877.1203 233001.1321 191046.5255 270581.4197 221695.3804 210442.4824 239005.8315 0.99728082 1.112786018 1.077889125 0.982725479 0.974876348 0.799338344 1.132112208 0.927573101 0.880490995 1 17.86668629 3.600501724 3.238978701 0.953776263 1.067731976 0.252329367 0.084566522 0.344343094 6.761461601 0.022933301 0.03742405 3985.673549 -3.600501724 0.113955713 LWTLSANDMEDDS(ph)MDLIDSDELLDPEDLKKPDPASLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LWTLSANDMEDDSMDLIDSDELLDPEDLKKPDPASLR 37 2 Q6FI81-3;Q6FI81 Q6FI81-3 CIAPIN1 Anamorsin 1 LWT(0.001)LS(0.026)ANDMEDDS(0.509)MDLIDS(0.463)DELLDPEDLKKPDPASLR 43.896 0.051009 239470000 50191 55988 52704 45394 63050 50789 71001 62561 73788 71053 TRUE FALSE 48229.48023 54391.27706 62228.78519 47736.78978 65078.06051 51815.98838 71869.93148 61269.09349 65411.89558 66240.51702 0.728096374 0.821117943 0.939436888 0.720658472 0.982450975 0.782240096 1.084984458 0.924948902 0.987490716 1 16.01542631 3.600644291 0.337267415 1.017494175 0.693561083 0.411945312 0.091564295 3.074527572 0.492037163 0.094308822 0.38396465 3986.982143 -3.600644291 -0.323933092 ALHSVLQAVPLNELR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALHSVLQAVPLNELR 15 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 182.35 5.50E-07 1299460000 1216850 1350460 1108490 1033890 995240 731420 1246740 1003100 1105910 1302080 FALSE TRUE 1169294.157 1311946.203 1308818.801 1087249.187 1027252.798 746209.8135 1261997.977 982385.6345 980371.7332 1213888.962 0.963262863 1.080779416 1.078203067 0.895674333 0.846249394 0.614726583 1.039632138 0.809287888 0.807628839 1 20.21120503 3.601201032 3.876770778 0.844696034 1.044116835 0.35534537 0.112736457 0.238693277 6.245383854 0.029837522 0.047626604 3992.096514 -3.601201032 0.199420801 RHT(ph)MDKDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 RHTMDKDSR 9 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 RHT(1)MDKDSR;RHT(1)MDKDSR;RHT(1)MDKDSR;RHT(1)MDKDSR 162.22 0.0030472 1329740000 3930700 3702730 2923280 2687690 2727340 1982200 2904200 1605750 3222650 2916620 TRUE FALSE 3777083.898 3597131.766 3451581.724 2826402.003 2815067.368 2022281.442 2939742.468 1572590.701 2856828.282 2719074.73 1.389106323 1.322924937 1.269395683 1.039471984 1.03530342 0.743738824 1.081155452 0.578355087 1.050661922 1 21.37468437 3.601680286 1.067643177 0.853930431 1.39233683 0.616449001 0.146248587 0.32743859 0.731919035 0.050871839 0.128331985 3996.504316 -3.601680286 0.538406399 LELQGPR ddPTM_BT-474_Pertuzumab_2h_R1 4 LELQGPR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 163.34 0.0028812 965900000 1798630 1938580 1687390 1467610 1444420 1198974 1685330 1414850 1544740 1701860 FALSE TRUE 1728337.551 1883293.596 1992338.909 1543353.528 1490881.081 1223218.076 1705955.573 1385632.853 1369387.591 1586591.506 1.089339975 1.187005974 1.255735267 0.972747882 0.939675446 0.770972283 1.075233017 0.873339387 0.863100291 1 20.5974993 3.602113363 4.545584111 0.917918634 1.17701692 0.644150202 0.085526795 0.133192091 4.32461793 0.022475347 0.035426387 4000.491605 -3.602113363 0.259098287 KLSAS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSASSPR 8 1 A0A0A0MRY2;B0QZE2;B7Z2J6;E7ENI9;J3QKD2;Q15326-5;Q15326-2;Q15326;Q15326-4;Q15326-6;Q15326-3 A0A0A0MRY2 ZMYND11 Zinc finger MYND domain-containing protein 11 1 KLS(0.062)AS(0.469)S(0.469)PR;KLS(0.052)AS(0.474)S(0.474)PR 82.749 0.011923 407830000 1253560 1298230 1014330 1050550 1159450 844950 1143090 1190120 1099760 1116750 TRUE FALSE 1204569.489 1261205.752 1197641.995 1104769.011 1196744.762 862035.4679 1157079.477 1165543.606 974919.8554 1041111.528 1.157003315 1.211403119 1.150349374 1.06114377 1.149487572 0.827995315 1.111388594 1.119518491 0.936422112 1 19.98969319 3.603020104 1.438419895 1.03008259 1.186874219 0.368373115 0.089150393 0.509495084 2.077077875 0.028844651 0.061463467 4008.852748 -3.603020104 0.156791629 GSDALS(ph)ETSSVSHIEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALS(0.984)ET(0.013)S(0.002)SVSHIEDLEK;GSDALS(0.992)ET(0.007)S(0.001)SVSHIEDLEK;GSDALS(0.482)ET(0.482)S(0.032)S(0.003)VSHIEDLEK 348.19 1.18E-90 1003714000 835134 892433 766785 894365 1029176 860092 1008877 1287854 1104724 1046415 TRUE FALSE 802496.04 866981.6846 905360.1065 940523.2848 1062280.381 877483.6495 1021223.939 1261259.365 979320.3629 975540.38 0.822616938 0.888719424 0.928060104 0.964104925 1.088914824 0.899484704 1.046828978 1.292882787 1.003874758 1 19.89584207 3.603844093 0.578547028 1.115773174 0.801851268 0.397178589 0.096941095 1.218721496 0.715468436 0.067727139 0.22262337 4016.465983 -3.603844093 -0.313921905 QQEGFKPNYMENR ddPTM_BT-474_Pertuzumab_2h_R1 4 QQEGFKPNYMENR 13 1 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;;; 218.68 2.17E-11 1436280000 1632130 1569460 1333240 1330330 1251460 1022930 1433640 1400360 1543080 1670650 FALSE TRUE 1568344.555 1524700.537 1574186.126 1398988.491 1291714.347 1043614.345 1451185.315 1371442.077 1367916.028 1557495.387 1.006965778 0.978943854 1.010716397 0.89822962 0.829353562 0.670059349 0.93174293 0.880543267 0.878279344 1 20.57079646 3.604347856 3.722906214 0.856665345 0.996787601 0.356819359 0.079771137 0.255620255 6.290798284 0.022138545 0.035532387 4021.127618 -3.604347856 0.140122256 DLDFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLDFEK 6 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 Q04637-9;A0A0A0MSA7 EIF4G1;EIF4G3 Eukaryotic translation initiation factor 4 gamma 1;Eukaryotic translation initiation factor 4 gamma 3 0 97.068 0.09653 459520000 1103900 1124100 958060 1105400 1273900 1182500 1364500 1301500 1523200 1464700 FALSE TRUE 1060758.368 1092041.769 1131202.754 1162449.826 1314876.15 1206410.96 1381199.159 1274623.57 1350292.722 1365494.564 0.776830897 0.799740839 0.828419815 0.851303152 0.962930344 0.883497446 1.011501031 0.933451955 0.988867153 1 20.38099214 3.605243865 0.578043035 0.983889329 0.741616635 0.836418598 0.033417021 0.474930987 0.278017679 0.020316349 0.066932224 4029.432315 -3.605243865 -0.242272693 GYPHWPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GYPHWPAR 8 0 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;M0R0J3;H3BPQ6;P51858;O75475;O75475-3;O75475-2;Q9Y3E1 Q7Z4V5-2;P51858;O75475;Q9Y3E1 HDGFRP2;HDGFRP3;HDGF;PSIP1 Hepatoma-derived growth factor-related protein 2;Hepatoma-derived growth factor;PC4 and SFRS1-interacting protein;Hepatoma-derived growth factor-related protein 3 0 ;;; 138.85 0.00068775 1436190000 1297550 1460360 1360240 835700 759560 172415 1144270 658240 784730 1083250 FALSE TRUE 1246840.311 1418711.963 1606065.626 878830.5772 783991.9372 175901.3494 1158273.919 644647.114 695650.7403 1009880.513 1.234641421 1.404831507 1.590352132 0.870232237 0.776321483 0.174180358 1.146941548 0.638339988 0.688844602 1 19.94575318 3.605356234 4.377559412 0.723460172 1.406348156 0.587325479 0.252334324 0.150247664 4.642812778 0.066389035 0.104993615 4030.47502 -3.605356234 0.682887983 DYPVVSIEDPFDQDDWGAWQK ddPTM_BT-474_Pertuzumab_2h_R1 6 DYPVVSIEDPFDQDDWGAWQK 21 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 284.07 3.27E-45 1916886300 3694565 3489239 2756186 3023885 2490424 2597527 2859739 2971614 3312106 3342101 FALSE TRUE 3550177.315 3389729.32 3254290.121 3179948.067 2570530.75 2650050.776 2894737.341 2910249.132 2936129.612 3115737.522 1.139434015 1.087938023 1.044468636 1.020608458 0.825015179 0.850537234 0.929069705 0.934048235 0.942354608 1 21.57114227 3.605423697 2.328512244 0.91105247 1.098367715 0.697833684 0.052180147 0.167105202 1.768724009 0.015385817 0.027029665 4031.101158 -3.605423697 0.187315245 GNEFLFSHLWPLIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNEFLFSHLWPLIEK 15 0 H7C5G1;Q2TAA2-2;Q2TAA2 H7C5G1 IAH1 Isoamyl acetate-hydrolyzing esterase 1 homolog 0 127.75 7.62E-05 136700000 454950 443720 361580 374910 394110 271480 398250 406250 438140 442630 FALSE TRUE 437170.051 431065.54 426925.5493 394259.15 406786.9061 276969.5116 403123.9026 397860.7955 388404.184 412650.2758 1.059420232 1.044626807 1.034594121 0.955431689 0.985790947 0.67119672 0.976914172 0.964159771 0.941243001 1 18.65456008 3.605783015 1.905971912 0.91689163 1.05171072 0.283764671 0.088295222 0.457285918 3.258386696 0.026859553 0.050434639 4034.437716 -3.605783015 0.134819091 VNMSKYDAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VNMSKYDAAR 10 1 Q86UK0-2;Q86UK0 Q86UK0-2 ABCA12 ATP-binding cassette sub-family A member 12 0 72.607 0.049826 117550000 124450 112690 109400 79709 82515 36926 93790 83019 76738 83677 FALSE TRUE 119586.3564 109476.1915 129171.0136 83822.79104 85169.16991 37672.66902 94937.83008 81304.62864 68027.02395 78009.48226 1.532972056 1.403370313 1.65583734 1.074520541 1.09177971 0.482924228 1.21700372 1.042240331 0.872035322 1 16.25136188 3.606110021 3.965103857 0.963189223 1.516643145 0.648224781 0.190816024 0.149486052 4.036815704 0.052210071 0.083293437 4037.476623 -3.606110021 0.553453922 VYLLYRPGHYDILYK ddPTM_BT-474_Pertuzumab_2h_R1 2 VYLLYRPGHYDILYK 15 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 141.29 2.88E-06 3128400000 7380600 7976600 6507200 5087600 4721900 1995870 6053300 4099700 5752800 6227800 FALSE TRUE 7092157.992 7749115.178 7683195.792 5350171.646 4873784.202 2036227.859 6127382.096 4015039.762 5099766.262 5805985.559 1.221525255 1.334676964 1.323323269 0.921492414 0.839441324 0.350711837 1.055356069 0.691534576 0.87836358 1 22.46910955 3.606189705 2.918620889 0.780507569 1.301472492 0.584539155 0.184285753 0.171253165 2.792203823 0.04954888 0.082592305 4038.217489 -3.606189705 0.520964923 RVDIIPGFEFDR ddPTM_BT-474_Pertuzumab_2h_R1 5 RVDIIPGFEFDR 12 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;; 141.54 9.72E-05 2648590000 806863 900219 683800 716118 689482 722075 745528 708687 716800 775399 FALSE TRUE 775329.9019 874545.6355 807377.871 753076.9358 711659.8147 736675.8512 754651.9947 694052.3658 635431.8691 722880.5351 1.072556065 1.209806591 1.116889765 1.041772325 0.984477767 1.019083812 1.04395119 0.960120424 0.879027499 1 19.46339772 3.6062616 2.120789067 0.98324095 1.145744482 0.636386745 0.051420018 0.201174069 1.771022327 0.015205947 0.02750246 4038.886043 -3.6062616 0.162503532 HLSNVSST(ph)GSIDMVDSPQLATLADEVSASLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLSNVSSTGSIDMVDSPQLATLADEVSASLAK 32 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 HLS(0.03)NVS(0.148)S(0.116)T(0.336)GS(0.336)IDMVDS(0.035)PQLATLADEVSASLAK 71.05 0.012048 86795000 19519 24736 15275 15153 17278 19479 12686 16374 15548 16841 TRUE FALSE 18756.1759 24030.5535 18035.53229 15935.04815 17833.76256 19872.87873 12841.25506 16035.87118 13783.05622 15700.34407 1.194634705 1.53057496 1.148734844 1.014948977 1.13588355 1.265760714 0.817896411 1.021370685 0.877882431 1 13.93850856 3.606650396 0.508761595 0.935141118 1.423059543 0.454344433 0.143582364 1.402563989 0.603855645 0.106636071 0.366002276 4042.503419 -3.606650396 0.487918425 QHYNCEHSK ddPTM_BT-474_Pertuzumab_2h_R1 4 QHYNCEHSK 9 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1 P50454 SERPINH1 Serpin H1 0 ;;; 185.08 2.50E-05 1171670000 1754470 2071930 1668800 975190 915930 156981 1444780 104313 1200160 1195840 FALSE TRUE 1685903.373 2012840.585 1970389.282 1025519.673 945391.7203 160155.2634 1462461.65 102158.9001 1063922.868 1114844.692 1.512231601 1.80548968 1.767411458 0.919876715 0.848003069 0.143657017 1.31180752 0.091635096 0.954323841 1 20.08841131 3.606767627 2.762791995 0.658159337 1.716204856 0.584953134 0.363002158 0.168330285 2.478132437 0.096149159 0.162118834 4043.594782 -3.606767627 1.058045519 AVGIWHCGSCMK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVGIWHCGSCMK 12 0 Q6P4E4;E9PEL3;P61513;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 191.53 5.25E-06 1254560000 2255700 2559600 2374400 1829730 1677410 794550 2421000 1970580 2013980 2409200 FALSE TRUE 2167544.75 2486602.714 2803506.898 1924162.585 1731365.416 810616.3454 2450628.922 1929886.834 1785361.434 2246022.738 0.96505913 1.107113776 1.248209491 0.856697731 0.770858365 0.360911905 1.091097112 0.859246348 0.794899091 1 21.0989411 3.606955255 5.96856754 0.808659849 1.10523382 0.326071759 0.190144397 0.27250938 12.06300731 0.051884041 0.08086847 4045.342103 -3.606955255 0.296573971 DSGYLHLLYK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSGYLHLLYK 10 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 85.377 0.014281 367560000 648060 683900 607240 562270 561490 461170 637150 610960 605590 705660 FALSE TRUE 622733.0987 664395.8416 716981.776 591288.8221 579550.8358 470495.1734 644947.6323 598343.4625 536845.962 657865.0197 0.946597068 1.009927298 1.089861529 0.898799608 0.880957063 0.715184969 0.980364684 0.909523146 0.816042723 1 19.32743208 3.608068305 6.538487872 0.881100441 1.014345439 0.345817337 0.081809492 0.263186969 12.83129158 0.021731866 0.033802895 4055.723177 -3.608068305 0.133244998 QEESVDPDYWEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QEESVDPDYWEK 12 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 142.91 0.00014368 242570000 327470 318280 304130 355320 387350 355730 369950 457350 516480 484880 FALSE TRUE 314672.1104 309202.966 359093.0563 373658.1078 399809.4645 362923.1043 374477.5588 447905.5627 457851.3557 452038.6457 0.696117718 0.684018875 0.794385745 0.826606555 0.884458593 0.802858578 0.828419345 0.990856793 1.012858878 1 18.78608659 3.608917575 0.277381857 1.039459125 0.544039043 0.814384761 0.048660323 1.999501576 0.211027645 0.07370308 0.32739183 4063.661973 -3.608917575 -0.495420081 HHPDLIFCR ddPTM_BT-474_Pertuzumab_2h_R1 2 HHPDLIFCR 9 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ; 116.52 0.0013002 193720000 482760 460030 356120 297450 270150 102842 357160 160518 296630 334830 FALSE TRUE 463893.2055 446910.3948 420478.8058 312801.4301 278839.6201 104921.5357 361531.0309 157203.2472 262957.806 312151.6659 1.486114784 1.431709146 1.347033676 1.002081566 0.893282499 0.336123581 1.158190298 0.503611752 0.842403981 1 18.25188764 3.609108413 1.706115333 0.746298355 1.464802604 0.624635467 0.22017791 0.215002926 1.229197729 0.062556077 0.1233702 4065.448023 -3.609108413 0.718504249 VLWLADCDVSDSSCSSLAATLLANHSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLWLADCDVSDSSCSSLAATLLANHSLR 28 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 304.06 8.07E-72 431230000 151077 155750 125476 158106 165147 201412 170718 163758 179717 189381 FALSE TRUE 145172.7438 151308.1625 148152.3044 166265.8696 170459.1032 205484.6886 172807.298 160376.3401 159316.2796 176554.0562 0.822256633 0.857007569 0.839132828 0.941727838 0.965478262 1.163862746 0.978778407 0.908369615 0.902365446 1 17.42975044 3.609941411 2.622657055 0.983838562 0.838774655 0.483678983 0.067852468 0.280816639 3.744408768 0.021369734 0.036534112 4073.253237 -3.609941411 -0.145063906 S(ph)PGNTSQPPAFFSK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPGNTSQPPAFFSK 14 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK 261.59 1.71E-24 8109730000 5837510 5817960 4890010 5554460 5815890 5596120 6025010 6526700 6375230 6430680 TRUE FALSE 5609373.655 5652037.477 5773743.585 5841126.346 6002963.384 5709277.381 6098745.875 6391921.364 5651540.618 5995124.316 0.935655936 0.942772356 0.963073204 0.974312798 1.001307574 0.952320099 1.017284305 1.066186626 0.942689479 1 22.51535824 3.610765397 0.638135769 1.013099838 0.926888573 0.313051323 0.032630545 1.215063768 0.892266866 0.019987581 0.064468333 4080.988743 -3.610765397 -0.086211265 TPLRPLDPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPLRPLDPTR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 108.47 0.0019581 318540000 956840 1040900 953070 673420 646520 249980 863160 630970 669580 888840 FALSE TRUE 919445.635 1011214.551 1125310.95 708175.2869 667315.903 255034.7669 873723.6103 617940.249 593572.0855 828638.0751 1.109586516 1.220333197 1.358024672 0.85462557 0.805316486 0.307775825 1.054409201 0.745729973 0.716322485 1 19.66038259 3.61104817 4.534783393 0.761523123 1.226311701 0.521597346 0.196425509 0.171922405 5.560452229 0.052064558 0.082235309 4083.646775 -3.61104817 0.464788578 KEEAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEEAIR 6 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 81.784 0.097755 1597430000 3828500 3746300 3190500 3386900 3217300 3255700 3626000 3819600 4074400 3665700 FALSE TRUE 3678877.987 3639459.192 3767094.322 3561698.315 3320787.376 3321532.485 3670376.073 3740723.925 3611891.193 3417418.874 1.076507775 1.064973106 1.102321507 1.042218834 0.971723836 0.971941868 1.074019957 1.094605041 1.056906199 1 21.70447566 3.612192131 6.810458745 1.035195196 1.079372383 0.255522338 0.039406828 0.463781821 23.65709514 0.012436348 0.01933254 4094.417559 -3.612192131 0.044177188 GS(ph)SGEGLPFAEEGNLTIK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSSGEGLPFAEEGNLTIK 18 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 GS(0.959)S(0.041)GEGLPFAEEGNLTIK;GS(0.579)S(0.421)GEGLPFAEEGNLTIK 305.9 4.13E-50 186770000 326880 363770 311520 444620 393390 416010 544570 563820 521320 585420 TRUE FALSE 314105.1682 353395.6358 367818.5937 467566.8915 406043.7466 424422.0072 551234.6106 552176.92 462141.9392 545768.982 0.575527702 0.647518726 0.673945581 0.856712102 0.743984653 0.777658719 1.010014546 1.011741118 0.846772086 1 19.05793088 3.612218451 0.427072174 1.00429966 0.48322318 0.765941905 0.072640122 1.02646394 0.286571407 0.067893347 0.250398191 4094.665703 -3.612218451 -0.52107648 HVLVTLGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HVLVTLGEK 9 0 F8VPF3;H0YI43;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ; 131.44 0.00033308 1724690000 3648530 3415990 2989520 2658580 2637840 1388160 3435230 2276860 3378400 3324170 FALSE TRUE 3505941.414 3318569.31 3529792.766 2795789.632 2722688.519 1416229.546 3477271.372 2229842.045 2994898.195 3099021.005 1.131306115 1.070844407 1.13900253 0.902152527 0.878564074 0.456992561 1.122054793 0.719531117 0.966401386 1 21.5633811 3.612747042 3.198579201 0.83711666 1.110798572 0.310285947 0.169764376 0.281584027 5.411912709 0.044683894 0.073556709 4099.65246 -3.612747042 0.273681911 VANILHDDCAFLSAFGDVSKPER ddPTM_BT-474_Pertuzumab_2h_R1 1 VANILHDDCAFLSAFGDVSKPER 23 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 190.24 9.50E-18 455930000 357320 358220 295710 307660 324240 289340 307970 308220 390560 406580 FALSE TRUE 343355.5394 348003.9163 349151.375 323538.3695 334669.4741 295190.653 311739.029 301855.1493 346225.2662 379041.9745 0.905850968 0.918114456 0.921141717 0.853568711 0.882935128 0.778780908 0.822439334 0.796363384 0.913421968 1 18.53199809 3.613129346 2.204952986 0.844559057 0.916571339 0.0675085 0.06151922 0.496935159 4.72142026 0.016991653 0.030526872 4103.26292 -3.613129346 0.072012282 ALLFVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALLFVPR 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 166.66 0.0025941 2370300000 1131530 1248980 1131390 974420 1092090 767430 1103570 1052050 987900 1116220 FALSE TRUE 1087308.557 1213360.313 1335857.341 1024709.933 1127218.067 782947.9604 1117075.82 1030324.8 875757.7336 1040617.425 1.044868681 1.16600038 1.283716098 0.98471341 1.083220441 0.752387901 1.073474067 0.990109117 0.841575119 1 19.98900834 3.613277052 6.589053268 0.963477122 1.164344198 0.429431978 0.107962802 0.227641049 11.23177072 0.028269981 0.043974664 4104.658706 -3.613277052 0.200867076 ETLQQHK ddPTM_BT-474_Pertuzumab_2h_R1 3 ETLQQHK 7 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 133.7 0.003246 2768620000 4409400 5097000 4106900 3552770 3125380 1544570 4498300 3336830 4358400 4448400 FALSE TRUE 4237075.773 4951638.55 4849108.187 3736128.885 3225910.686 1575802.264 4553351.541 3267923.294 3863652.704 4147105.906 1.021694615 1.193998577 1.169275224 0.900900283 0.777870341 0.379976374 1.097958828 0.788000926 0.931650359 1 21.98367346 3.613658309 3.837495551 0.81613811 1.134416043 0.344433602 0.18374332 0.251446053 6.485808027 0.049982414 0.080233149 4108.263672 -3.613658309 0.318277932 FYTQQWEDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FYTQQWEDYR 10 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJA0 A0A590UJ56 CUL1 Cullin-1 0 ; 115.57 0.0055881 0 257880 301270 256990 193100 217437 96725 248250 169395 192737 240600 FALSE TRUE 247801.7645 292678.0746 303433.8097 203065.9141 224431.0586 98680.84577 251288.1578 165896.9341 170858.3038 224303.9477 1.10475882 1.304828014 1.352779623 0.905315828 1.00056669 0.439942528 1.120301985 0.739607732 0.761726691 1 17.77509549 3.61370635 3.693853492 0.832011176 1.258554583 0.494925055 0.185695851 0.184281678 4.487482623 0.048428348 0.078097308 4108.718148 -3.61370635 0.426543407 NNSNGHQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NNSNGHQLK 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;X6R960 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 63.076 0.078441 33742000 50782 52831 43955 44317 40808 37237 50861 41890 56102 59918 FALSE TRUE 48797.3833 51324.31161 51898.64627 46604.20568 42120.62638 37989.95765 51483.45213 41024.95686 49733.53616 55859.70049 0.873570443 0.918807497 0.929089233 0.834308191 0.754043183 0.680095978 0.92165643 0.734428515 0.890329445 1 15.76952022 3.614166971 4.822097164 0.809817401 0.907710618 0.105097897 0.090910023 0.359366379 12.55895744 0.023107533 0.036371618 4113.078237 -3.614166971 0.097893217 ATVWDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATVWDLR 7 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-5;H0Y9T9 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 92.47 0.036399 311370000 926860 1077980 929480 670900 624490 121924 984630 611930 650090 873900 FALSE TRUE 890637.2865 1047237.066 1097457.712 705525.2294 644577.288 124389.3868 996680.1965 599293.4317 576294.5086 814709.9746 1.09319551 1.285410881 1.347053241 0.865983296 0.791173925 0.152679347 1.223355829 0.735591131 0.707361548 1 19.63592705 3.6143722 4.184959999 0.76172656 1.244612224 0.396698148 0.261311996 0.226213183 6.60113842 0.070027307 0.111430088 4115.022366 -3.6143722 0.482885664 LRIDYER ddPTM_BT-474_Pertuzumab_2h_R1 2 LRIDYER 7 1 P15924 P15924 DSP Desmoplakin 0 ; 149.91 0.0018096 1072220000 724310 802050 611110 586990 468240 519710 489000 615040 625580 634400 FALSE TRUE 696003.1644 779176.3193 721551.1711 617284.6242 483301.3648 530218.8923 494984.5283 602339.2091 554566.781 591431.5229 1.176811072 1.317441308 1.220007969 1.043712755 0.817172143 0.896500899 0.836926185 1.018442856 0.937668622 1 19.17385161 3.614461975 3.022686721 0.919293357 1.249838529 0.814153576 0.068203118 0.103659399 1.802521521 0.019329463 0.032172572 4115.873088 -3.614461975 0.330545172 HIAFTPESQR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIAFTPESQR 10 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 125.75 0.00040089 284420000 237650 301070 247060 155630 146480 37665 208460 95188 151650 214140 FALSE TRUE 228362.3753 292483.7784 291709.2378 163662.083 151191.6622 38426.61211 211011.1958 93222.33454 134435.3278 199636.1071 1.14389315 1.465084562 1.4612048 0.819802016 0.757336258 0.192483277 1.056979115 0.466961292 0.67340187 1 17.60701315 3.615210276 3.547908126 0.660506829 1.367932401 0.59007566 0.247513489 0.149949087 3.42971459 0.064338606 0.104377718 4122.970964 -3.615210276 0.707425572 VLDFEHFLPMLQTVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLDFEHFLPMLQTVAK 16 0 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 266.45 3.40E-27 784070000 1338000 1386400 1197400 1169100 1164400 864270 1505500 1185700 1321100 1444300 FALSE TRUE 1285709.481 1346861.229 1413796.816 1229437.391 1201853.983 881746.1316 1523924.759 1161214.881 1171134.267 1346476.275 0.954869763 1.000285898 1.04999757 0.913077649 0.892592024 0.654854562 1.131787309 0.862410206 0.869777128 1 20.36075738 3.615263558 6.007325796 0.897912861 1.001061989 0.133810653 0.114393533 0.452282139 20.28591903 0.029965631 0.046721225 4123.476823 -3.615263558 0.103149129 LWSWGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LWSWGR 6 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 158.08 0.022184 1563930000 941450 1061580 932520 670800 591570 523300 491390 667130 778100 928340 FALSE TRUE 904657.0932 1031304.778 1101047.108 705420.0684 610598.3863 533881.4845 497403.7778 653353.5324 689773.3501 865462.7049 1.045287207 1.191622437 1.272206303 0.815078529 0.705516694 0.616874051 0.574725837 0.754918183 0.796999508 1 19.72311213 3.615749688 4.368063123 0.717368393 1.17011578 0.71347871 0.121143432 0.109837504 3.3971018 0.032209195 0.051078087 4128.095049 -3.615749688 0.452747387 ALWFER ddPTM_BT-474_Pertuzumab_2h_R1 3 ALWFER 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;; 126.68 0.040453 1266433000 1153685 1341884 1068667 861980 845386 255414 1119373 793853 918822 1117867 FALSE TRUE 1108597.715 1303614.782 1261798.899 906466.8911 872578.6084 260578.6461 1133072.222 777459.6581 814521.1786 1042152.872 1.063757289 1.25088633 1.210761811 0.869802229 0.837284655 0.250038793 1.087241854 0.746013065 0.781575525 1 19.99113549 3.615957761 3.142770443 0.769474198 1.184799239 0.403849467 0.212245859 0.241453751 4.502610452 0.057638248 0.095343986 4130.073314 -3.615957761 0.415325041 CLQDNNWDYTR ddPTM_BT-474_Pertuzumab_2h_R1 4 CLQDNNWDYTR 11 0 Q9UBU9;H0YDU0 Q9UBU9 NXF1 Nuclear RNA export factor 1 0 ;;; 215.56 2.96E-11 433670000 460535 481826 408030 435890 467630 438898 471256 465502 510341 521139 FALSE TRUE 442536.7831 468084.7942 481770.0976 458386.3351 482671.7436 447772.8183 477023.3719 455889.221 452409.2292 485841.7913 0.910866029 0.963451071 0.991619301 0.943488896 0.993475144 0.921643272 0.981849195 0.938349128 0.931186319 1 18.89012707 3.615981309 0.002640255 1.908098906 1.15E-05 0.083595786 0.029673998 245451.8675 152.9145486 54563.85954 55948.60553 4130.297261 -3.615981309 -1.908087414 LAAFGQLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAAFGQLHK 9 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 125.31 0.00050504 1587210000 1996100 2106290 1909430 1449570 1241360 460850 1901090 1440930 1654100 2042250 FALSE TRUE 1918090.205 2046220.671 2254506.476 1524382.481 1281289.472 470168.7028 1924356.108 1411174.292 1466333.503 1903926.588 1.007439161 1.074737169 1.184135192 0.800651921 0.672972099 0.246946865 1.010730203 0.741191546 0.770162837 1 20.86054642 3.616100449 4.792077536 0.725716504 1.085524504 0.373473006 0.201946335 0.231514471 8.047164373 0.054719479 0.086192174 4131.430475 -3.616100449 0.359808001 ALQLLHCFPLDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALQLLHCFPLDIR 13 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 132.47 0.00011842 390340000 624040 663870 545300 415730 418770 175985 489460 354670 428850 527560 FALSE TRUE 599651.8269 644937.0776 643847.8401 437185.8751 432240.1174 179543.5373 495450.1579 347345.9406 380168.7459 491827.8913 1.219231031 1.311306433 1.309091761 0.888900127 0.878844256 0.36505359 1.007364907 0.706234735 0.772971099 1 18.90779403 3.616367178 2.739383066 0.767623916 1.289100352 0.617369683 0.17268183 0.166002566 2.405498484 0.046404391 0.078906656 4133.968644 -3.616367178 0.521476436 KSLDFYTR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSLDFYTR 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 107.95 0.0062601 394190000 900020 892850 906970 598380 662220 346260 694820 586340 571440 672830 FALSE TRUE 864846.2234 867386.7922 1070879.654 629262.4635 683520.9077 353261.6144 703323.415 574231.8741 506572.5269 627258.6248 1.378771354 1.382821627 1.707237832 1.003194597 1.089695511 0.563183351 1.121265435 0.9154627 0.807597547 1 19.25870088 3.616460837 5.354672809 0.920753851 1.476401644 0.696573973 0.170137687 0.121803009 4.821900847 0.044477701 0.069645726 4134.860264 -3.616460837 0.555647794 KADPQEAINCLMR ddPTM_BT-474_Pertuzumab_2h_R1 1 KADPQEAINCLMR 13 1 P54920;M0R2M1;M0R058;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 82.55 0.019313 701630000 151030 152080 124970 116130 127470 111570 114300 126000 125440 131830 FALSE TRUE 145127.5806 147742.8273 147554.8589 122123.4832 131570.1883 113826.0218 115698.8376 123398.056 111200.5771 122901.0367 1.180849117 1.202128406 1.200598977 0.993673337 1.070537661 0.926159981 0.941398386 1.004044061 0.904797714 1 16.90713756 3.618223634 1.550623605 0.965852654 1.206874163 0.816095005 0.046739911 0.152708363 0.720938028 0.013897962 0.028950526 4151.677722 -3.618223634 0.24102151 FFPASADR ddPTM_BT-474_Pertuzumab_2h_R1 3 FFPASADR 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;; 152.31 0.001068 940600000 917560 1134060 950470 651790 573550 344238 904400 444520 625710 767150 FALSE TRUE 881700.7408 1101717.719 1122241.072 685428.96 591998.7566 351198.7282 915468.3177 435340.5067 554682.024 715190.2472 1.232819861 1.540454059 1.569150413 0.958386895 0.827750041 0.491056372 1.280034678 0.608705877 0.77557269 1 19.44796754 3.618923398 4.086547017 0.817880684 1.455155015 0.616688579 0.217530223 0.140204937 3.974462264 0.056958089 0.090972407 4158.372577 -3.618923398 0.637274331 SVETLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVETLK 6 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 126.24 0.040887 979730000 1781160 1801650 1473040 1687910 1735140 1804210 1825480 1780170 1976180 1987020 FALSE TRUE 1711550.298 1750268.706 1739251.096 1775023.237 1790952.354 1840692.362 1847820.77 1743408.867 1751852.331 1852437.366 0.92394503 0.944846362 0.938898733 0.958209584 0.966808588 0.993659703 0.997507827 0.94114322 0.94570125 1 20.82099333 3.618969315 1.841726116 0.971769295 0.934668771 0.43645295 0.01944984 0.398895862 2.650816958 0.006272288 0.012084294 4158.812251 -3.618969315 -0.037100524 TQAVFNHTEDYVLLPDER ddPTM_BT-474_Pertuzumab_2h_R1 3 TQAVFNHTEDYVLLPDER 18 0 Q05048 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 ;; 207.13 7.77E-16 1081184000 734015 732231 623416 592648 577289 332394 782463 582000 670944 777990 FALSE TRUE 705328.8823 711348.4888 736081.139 623234.6343 595858.025 339115.2344 792039.0163 569981.4966 594781.2499 725296.0443 0.972470328 0.980769845 1.014869921 0.859283101 0.821537674 0.467554231 1.092021696 0.785860479 0.820053073 1 19.46821046 3.619147355 3.97188389 0.820893431 0.988256099 0.17571047 0.152636459 0.384397392 10.4662399 0.040662194 0.065148483 4160.517519 -3.619147355 0.167362668 GHQQLYWSHPR ddPTM_BT-474_Pertuzumab_2h_R1 5 GHQQLYWSHPR 11 0 A0A2R8Y851;P62273;P62273-2 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ;;;; 233.54 1.03E-15 5100650000 3149272 2945960 2517952 2229465 2358349 1327685 3009780 1720605 2664912 2745012 FALSE TRUE 3026194.969 2861944.105 2973001.938 2344527.956 2434207.437 1354531.7 3046614.588 1685073.905 2362402.362 2559089.892 1.182527811 1.1183445 1.161741894 0.916156936 0.951200442 0.529302118 1.190507062 0.658466086 0.92314161 1 21.28719939 3.620196162 2.226537316 0.850709752 1.158633304 0.340950477 0.172156847 0.315886708 3.057994384 0.046332743 0.083474265 4170.577179 -3.620196162 0.307923552 S(ph)PVPAQIAITVPK ddPTM_BT-474_Pertuzumab_2h_R1 5 SPVPAQIAITVPK 13 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK 203.04 9.34E-08 1522140000 642871 643915 565699 689630 645525 870337 676710 811466 947850 850930 TRUE FALSE 617746.8906 625551.1747 667933.3932 725221.8869 666288.8979 887935.8105 684991.7794 794708.9435 840254.0417 793295.7532 0.778709439 0.788547237 0.841972733 0.914188541 0.839899741 1.119299841 0.863475919 1.001781417 1.059193924 1 19.5974993 3.620597439 0.605281996 1.009251983 0.737530261 0.593195219 0.071353655 0.866013213 0.559633276 0.04240017 0.140937517 4174.432462 -3.620597439 -0.271721723 CAPSAGS(ph)PAAAVGRES(ph)PGAAATSSSGPQAQQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 CAPSAGSPAAAVGRESPGAAATSSSGPQAQQHR 33 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 CAPS(0.027)AGS(0.973)PAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPS(0.025)AGS(0.975)PAAAVGRES(1)PGAAATSSSGPQAQQHR 172.03 2.13E-14 1207580000 127819 145567 95467 144361 158095 190069 158105 140663 141219 158974 TRUE FALSE 122823.6922 141415.5717 112720.0106 151811.4885 163180.2693 193912.3254 160039.9363 137758.2599 125188.4112 148206.5494 0.828733229 0.954178964 0.760560252 1.024323751 1.101032781 1.308392417 1.079843886 0.929501837 0.844688792 1 17.17724968 3.621018018 6.541533898 1.048392468 0.859277472 0.343723124 0.122132541 0.306189402 15.30068527 0.035980419 0.055994053 4178.477019 -3.621018018 -0.189114996 FVSFLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVSFLGR 7 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 0 124.37 0.009661 220090000 139910 159930 139650 116610 107610 74656 143110 120920 122250 161400 FALSE TRUE 134442.1625 155368.953 164887.8615 122628.2561 111071.3734 76165.59547 144861.423 118422.9597 108372.6925 150468.2342 0.893491993 1.03256979 1.095831704 0.814977704 0.738171574 0.506190532 0.962737575 0.787029637 0.720236355 1 17.19909942 3.621304335 5.511388688 0.775836942 1.00857999 0.34938754 0.13577467 0.235404817 9.731411115 0.035957139 0.056261753 4181.232666 -3.621304335 0.232743047 YLNFFTK ddPTM_BT-474_Pertuzumab_2h_R1 2 YLNFFTK 7 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 114.93 0.013479 366490000 1156090 1192080 1046170 922900 866160 498590 1137490 989750 1057550 1212310 FALSE TRUE 1110908.725 1158083.046 1235236.191 970530.9796 894020.823 508671.8314 1151410.943 969311.3166 937501.3576 1130199.164 0.982931823 1.024671653 1.092936741 0.858725622 0.79102945 0.450072737 1.018768178 0.857646464 0.829501019 1 20.1081456 3.621461678 4.925968526 0.817306591 1.031571584 0.287140543 0.147609334 0.286516638 10.38852058 0.040487704 0.063722791 4182.747786 -3.621461678 0.214264992 TDLFYER ddPTM_BT-474_Pertuzumab_2h_R1 4 TDLFYER 7 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ;;; 158.03 0.0033409 1072940000 1359580 1422960 1131740 1085160 1051710 613786 1282180 1112880 1202540 1272370 FALSE TRUE 1306446.111 1382378.574 1336270.593 1141165.238 1085539.207 626197.1735 1297871.702 1089898.639 1066032.701 1186191.247 1.101378984 1.165392662 1.126522049 0.962041527 0.915146871 0.527905745 1.094150464 0.918822022 0.898702215 1 20.1779052 3.621589031 2.714732362 0.889359627 1.138512068 0.376436731 0.137333511 0.294864437 4.201822653 0.039138572 0.066932876 4183.974517 -3.621589031 0.249152442 LGFHLPLEVAYQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGFHLPLEVAYQR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 113.24 0.00083752 1748180000 1407790 1501060 1248250 1199220 1244370 1075680 1389420 1097930 1385140 1443000 FALSE TRUE 1352772.01 1458251.238 1473836.542 1261111.888 1284396.291 1097430.987 1406424.138 1075257.362 1227904.714 1345264.325 1.005580826 1.083988635 1.095573944 0.937445426 0.954753848 0.8157735 1.045463045 0.799290773 0.912760929 1 20.35945824 3.621892767 3.947059354 0.909866239 1.063658799 0.417011328 0.073978484 0.19850171 5.370721745 0.019266576 0.030920974 4186.90172 -3.621892767 0.15379256 LLS(ph)GDSTEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLSGDSTEKR 10 1 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;E7ERL6 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 LLS(0.946)GDS(0.049)T(0.005)EKR 58.781 0.066682 123680000 127570 156350 128760 128560 134040 136120 123850 157700 143660 131160 TRUE FALSE 122584.4234 151891.0511 152029.7963 135194.997 138351.5183 138872.4397 125365.7133 154443.4399 127352.3191 122276.4164 1.00251894 1.242194166 1.243328851 1.105650632 1.131465269 1.135725464 1.025264864 1.263068092 1.041511706 1 16.89978665 3.62190534 20.11858918 1.118105678 1.171309571 0.060582509 0.09423188 13.86932984 2343.289891 0.024395473 0.037793323 4187.022932 -3.62190534 0.053203892 GDKHDDLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDKHDDLQR 9 1 Q9BY42;A2A2L6;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 126.39 0.00028535 831930000 1004400 1089800 873580 870430 846510 703360 898800 901250 1114200 1014300 FALSE TRUE 965146.9376 1058719.971 1031455.339 915352.9966 873738.7629 717582.4211 909799.7833 882638.8726 987720.6871 945600.5576 1.020670863 1.119627059 1.09079392 0.968012328 0.924004069 0.758864211 0.962139643 0.933416193 1.044543258 1 19.85087136 3.622752761 3.528859022 0.928455219 1.081624713 0.417036697 0.073477308 0.222411076 5.064821522 0.020618347 0.033594672 4195.200882 -3.622752761 0.153169493 SRS(ph)PFSTTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPFSTTR 9 1 Q8NG27-3;Q8NG27;K7EPI8;Q8NG27-2 Q8NG27-3 PJA1 E3 ubiquitin-protein ligase Praja-1 1 S(0.006)RS(0.974)PFS(0.012)T(0.004)T(0.003)R 72.2 0.051308 0 105440 116220 87770 108330 120700 109760 112030 131700 114310 104160 TRUE FALSE 101319.2882 112905.5194 103631.9914 113920.9243 124582.4251 111979.4224 113401.0567 128980.349 101334.008 97105.15042 1.043397675 1.162714016 1.067214159 1.173170772 1.282964133 1.153176962 1.167817115 1.328254458 1.043549262 1 16.5672602 3.622877456 5.704350974 1.191645908 1.098831928 0.058603329 0.097955077 0.414881488 17.92000978 0.02513577 0.039280829 4196.405581 -3.622877456 -0.09281398 SMS(ph)AEDLLER ddPTM_BT-474_Pertuzumab_2h_R1 6 SMSAEDLLER 10 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SMS(1)AEDLLER;SMS(1)AEDLLER;SMS(1)AEDLLER;SMS(1)AEDLLER;S(0.009)MS(0.991)AEDLLER;SMS(1)AEDLLER 244.71 1.82E-12 5144180000 5072300 4734750 3797720 3903630 3595200 3047080 3273370 5051660 3125670 3126140 TRUE FALSE 4874068.908 4599719.566 4484052.484 4105096.812 3710842.873 3108694.045 3313430.481 4947341.456 2770857.045 2914403.753 1.672406887 1.578271219 1.538583142 1.4085546 1.273276865 1.066665537 1.13691539 1.697548409 0.950745772 1 21.47476933 3.622981858 1.693228128 1.244164969 1.621885029 0.448489488 0.200123372 0.425718824 2.3924671 0.064355207 0.129103649 4197.414492 -3.622981858 0.37772006 ETDLQELFRPFGS(ph)ISR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 ETDLQELFRPFGS(1)ISR;ETDLQELFRPFGS(0.998)IS(0.002)R 143.4 8.58E-07 70810000 61684 65172 51801 60715 68157 60899 64953 66931 71854 63826 TRUE FALSE 59273.32108 63313.35837 61162.59301 63848.50843 70349.3318 62130.41951 65747.91424 65548.85146 63697.43516 59503.00817 0.996139908 1.064036262 1.027890772 1.073029926 1.182281938 1.044155941 1.104951099 1.101605675 1.070491007 1 15.86067499 3.623409116 4.807101972 1.092011428 1.033154968 0.198170402 0.046995053 0.306166863 10.82026555 0.011874804 0.018725857 4201.545938 -3.623409116 -0.05885646 YHSDFNR ddPTM_BT-474_Pertuzumab_2h_R1 2 YHSDFNR 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 158.12 0.0014326 608940000 264700 278420 256900 156810 150310 72033 190573 105407 165737 198705 FALSE TRUE 254355.2314 270479.7342 303327.5447 164902.9829 155144.8577 73489.55661 192905.2894 103230.3086 146923.2306 185246.5334 1.373063381 1.46010686 1.637426295 0.890181208 0.837504783 0.396712183 1.041343586 0.557259058 0.793122699 1 17.49908702 3.623589436 4.148479133 0.745801393 1.485584535 0.741139125 0.190377416 0.103316511 3.008559279 0.048990494 0.078241221 4203.290786 -3.623589436 0.739783141 VLSAPPHFHFGQTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSAPPHFHFGQTNR 15 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 113.65 0.00038626 4292900000 2183120 2011810 2183170 1178710 1771700 1927130 1752620 1462710 1794450 1675850 FALSE TRUE 2097801.257 1954435.149 2577717.383 1239543.364 1828688.34 1966097.889 1774069.088 1432504.527 1590751.559 1562343.187 1.342727561 1.250964042 1.649904711 0.793387378 1.170478007 1.258428945 1.135518177 0.916894917 1.018183183 1 20.57527996 3.62365871 0.447552008 0.978091635 1.474236635 0.309725615 0.191429832 2.464214147 0.767636612 0.162094702 0.594794 4203.961304 -3.62365871 0.496145 LQLQGLDLS(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 3 LQLQGLDLSSR 11 0 P49454 P49454 CENPF Centromere protein F 1 LQLQGLDLS(0.92)S(0.08)R;LQLQGLDLS(0.934)S(0.066)R;LQLQGLDLS(0.893)S(0.107)R 133.88 0.00016 138459000 334763 308732 274187 270322 278906 272971 254899 333738 232923 300963 TRUE FALSE 321680.0919 299927.2656 323738.6902 284273.3508 287877.2648 278490.6606 258018.5302 326846.1937 206482.5575 280578.5079 1.146488711 1.068960227 1.153825689 1.01316866 1.026013243 0.992558777 0.919594776 1.164901033 0.735917227 1 18.09804498 3.623820741 4.570438883 0.992962005 1.117281129 0.284221752 0.103367653 0.330275028 10.95998048 0.026891868 0.042570014 4205.530058 -3.623820741 0.124319125 NISSSPS(ph)VESLPGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NISSSPSVESLPGGR 15 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 NISSSPS(1)VESLPGGR;NISSS(0.002)PS(0.998)VESLPGGR 237.86 9.92E-18 487030000 343095 336330 247780 331341 365031 319702 330159 393930 351255 369404 TRUE FALSE 329686.4681 326738.1977 292559.3578 348441.5487 376772.5536 326166.5935 334199.5846 385795.2078 311382.005 344383.938 0.957322429 0.94876143 0.849515107 1.01178223 1.094047985 0.947101643 0.970427327 1.12024739 0.904171103 1 18.39365833 3.623873716 9.034981177 1.017292347 0.921708027 0.262019494 0.066278771 0.404795207 29.2789031 0.017537466 0.027189209 4206.043073 -3.623873716 -0.09558432 EKHFQQQEQER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKHFQQQEQER 11 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 0 138.45 3.44E-05 35430000 92275 90437 82928 68947 76753 41280 92344 63081 69014 88532 FALSE TRUE 88668.79098 87857.82531 97914.93432 72505.36293 79221.82995 42114.70988 93474.1335 61778.35531 61179.82005 82535.64878 1.074309008 1.064483367 1.186335066 0.87847329 0.959849848 0.510260845 1.132530426 0.748505115 0.741253276 1 16.33272976 3.623993171 4.605967957 0.84039582 1.103080111 0.34210122 0.16198413 0.241192514 8.086877812 0.041549158 0.065734735 4207.200129 -3.623993171 0.262684292 GFGHIGIAVPDVYSACK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFGHIGIAVPDVYSACK 17 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 173.36 1.49E-09 561240000 1469500 1384000 1068200 996860 863290 712940 797930 839490 998050 992500 FALSE TRUE 1412070.315 1344529.675 1261247.502 1048308.064 891058.5069 727356.1353 807695.306 822154.2381 884755.5482 925277.091 1.526105346 1.453110304 1.363102485 1.132966626 0.963018014 0.786095476 0.872922624 0.888549221 0.956206046 1 19.81952595 3.624940693 1.481855878 0.888569154 1.499966452 0.948522715 0.056516003 0.080353907 0.346118977 0.017893692 0.038436898 4216.389208 -3.624940693 0.611397298 RQPS(ph)MSETMPLYTLCK ddPTM_BT-474_Pertuzumab_2h_R1 4 RQPSMSETMPLYTLCK 16 1 A0A0A0MR03;Q9Y5B0;K7EJD2 A0A0A0MR03 CTDP1 RNA polymerase II subunit A C-terminal domain phosphatase 1 RQPS(0.988)MS(0.012)ETMPLYTLCK;RQPS(0.982)MS(0.018)ETMPLYTLCK;RQPS(0.968)MS(0.026)ET(0.006)MPLYTLCK;RQPS(0.731)MS(0.21)ET(0.059)MPLYTLCK 271.66 2.27E-35 1142110000 1620590 1640430 1386220 1312070 1280610 1289060 1300970 1388440 1396590 1423690 TRUE FALSE 1557255.551 1593646.543 1636740.79 1379786.09 1321801.984 1315125.676 1316891.66 1359768.229 1238054.958 1327262.208 1.173284029 1.200702117 1.233170643 1.039573101 0.9958861 0.990855965 0.992186511 1.024491032 0.932788526 1 20.34002198 3.625975846 3.942303148 0.994601418 1.202089832 0.927926088 0.026514367 0.054924969 1.491011971 0.007196271 0.011568412 4226.451075 -3.625975846 0.207488415 RPSS(ph)EDFVFL ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSSEDFVFL 10 1 Q86TL0;K7EQ67;K7EN30;Q86TL0-2 Q86TL0 ATG4D "Cysteine protease ATG4D;Cysteine protease ATG4D, mitochondrial" 1 RPS(0.394)S(0.606)EDFVFL 61.435 0.097039 14813000 26788 27637 18117 36475 46108 31025 45542 47313 41029 45579 TRUE FALSE 25741.09534 26848.81982 21391.14491 38357.47912 47591.10569 31652.34676 46099.35662 46335.97002 36371.55993 42491.89373 0.605788377 0.631857455 0.503417076 0.902701098 1.120004347 0.74490318 1.084897673 1.090466109 0.855964673 1 15.37490002 3.626336445 4.63536351 0.9914773 0.587077528 0.720851625 0.112009968 0.112818049 3.834032585 0.029980995 0.047433792 4229.9618 -3.626336445 -0.404399773 YIQQTKPLTLER ddPTM_BT-474_Pertuzumab_2h_R1 2 YIQQTKPLTLER 12 1 O43809 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ; 135.58 0.00011411 2896100000 1512980 1654710 1270180 1312720 1229380 941120 1438140 1356170 1466910 1625650 FALSE TRUE 1453851.069 1607519.291 1499729.781 1380469.637 1268924.124 960150.0912 1455740.388 1328164.616 1300392.527 1515543.278 0.959293667 1.060688477 0.98956579 0.910874442 0.837273434 0.633535251 0.960540295 0.876362051 0.858037211 1 20.53140362 3.626480709 2.772355973 0.853824082 1.011802809 0.313063462 0.093644186 0.310636909 4.610261126 0.026409086 0.045103749 4231.367139 -3.626480709 0.157978727 HIMGQNVADYMR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIMGQNVADYMR 12 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ; 190.66 6.36E-06 718410000 1398570 1685570 1689800 938490 1140550 791108 1168450 722308 593410 944630 FALSE TRUE 1343912.338 1637499.194 1995184.449 986925.5814 1177236.827 807104.7458 1182749.841 707392.0874 526048.5846 880649.3687 1.526047013 1.859422435 2.265583239 1.120679372 1.336782684 0.91648819 1.343042853 0.803261903 0.597341693 1 19.7482082 3.626623727 5.835967576 1.015662186 1.877671656 0.687821278 0.268188424 0.13170019 5.922179373 0.073825907 0.115309243 4232.760803 -3.626623727 0.86200947 SNYNFEKPFLWLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNYNFEKPFLWLAR 14 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 220.21 4.31E-12 6693800000 5702900 6252600 5292300 4281800 4235100 1393800 5248900 4120800 5526000 5927300 FALSE TRUE 5480024.363 6074281.97 6248736.337 4502784.211 4371325.838 1421983.591 5313137.608 4035704.04 4898711.647 5525838.692 0.991709072 1.099250686 1.130821344 0.814859872 0.791070113 0.257333533 0.961507909 0.730333306 0.88651007 1 22.39776202 3.626846932 3.990054838 0.749319911 1.076070654 0.322677824 0.1956146 0.253532789 7.015017795 0.052531321 0.084353329 4234.936781 -3.626846932 0.326750742 TNTNVNCPIECFMPLDVQADREDS(ph)RE ddPTM_BT-474_Pertuzumab_2h_R1 4 TNTNVNCPIECFMPLDVQADREDSRE 26 2 H0Y7Z1;P02751-12;P02751-10;P02751-6;P02751-5;P02751-9;P02751-14;P02751-13;P02751-8;P02751-17;P02751-3;P02751-11;P02751-1;P02751-7;P02751 H0Y7Z1 FN1 Fibronectin;Anastellin;Ugl-Y1;Ugl-Y2;Ugl-Y3 1 TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE 170.6 5.42E-12 465068000 217276 231601 195143 126633 169760 182094 136215 147045 140530 135817 TRUE FALSE 208784.6137 224995.9662 230409.681 133168.5443 175220.4846 185776.0654 137882.0399 144008.4694 124577.6235 126617.9936 1.648933203 1.776966763 1.819723046 1.051734754 1.383851375 1.467216942 1.088960865 1.137346006 0.983885623 1 16.95012291 3.627993303 0.396544537 0.979904486 2.003115408 0.675875852 0.176769047 1.453044921 0.335913449 0.169232666 0.65609532 4246.130164 -3.627993303 1.023210923 MLVDLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 MLVDLAK 7 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4 P06744 GPI Glucose-6-phosphate isomerase 0 91.041 0.038841 111080000 557730 472830 466240 412810 431110 358130 445550 435110 500740 432870 FALSE TRUE 535933.295 459345.3513 550499.9395 434115.1736 444977.0447 365371.634 451002.7742 426124.8264 443898.0945 403551.3293 1.328042447 1.13825756 1.364138585 1.075737191 1.102652903 0.905390733 1.117584657 1.055937115 1.099979265 1 18.62239266 3.628990775 6.226400988 1.051917242 1.262147969 0.626337495 0.079802178 0.150548732 7.38171045 0.020150802 0.031411963 4255.893731 -3.628990775 0.210230728 YLGQDYEQLR ddPTM_BT-474_Pertuzumab_2h_R1 5 YLGQDYEQLR 10 0 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0;E9PIA9 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;;; 258.83 6.97E-17 2969480000 2240607 2602986 2161308 1666335 1633116 416422 2371353 1630482 1644084 2111233 FALSE TRUE 2153041.601 2528751.388 2551904.434 1752334.749 1685646.659 424842.3382 2400374.327 1596811.977 1457454.477 1968237.308 1.093893298 1.284779725 1.296543066 0.890306642 0.856424503 0.215849144 1.219555344 0.811290371 0.740487171 1 20.90847274 3.629178662 3.960942913 0.804808028 1.230683469 0.371587076 0.243257107 0.243660519 6.693534077 0.065688932 0.105666321 4257.735339 -3.629178662 0.425875441 AVFWDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVFWDIK 7 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 119.89 0.028715 0 251130 278350 213450 231970 230460 157770 297650 231550 272250 273150 FALSE TRUE 241315.562 270411.7305 252025.1632 243941.9995 237872.9552 160960.2175 301292.7297 226768.4116 241345.3214 254649.3072 0.947638792 1.061898552 0.989695067 0.957952732 0.934119781 0.632085825 1.183167286 0.89051258 0.947755657 1 17.95815227 3.629631435 2.758001595 0.928249952 1.007347776 0.052595322 0.129017979 0.836607157 12.30115694 0.035485738 0.060812496 4262.176549 -3.629631435 0.079097824 QLDMILDEQRR ddPTM_BT-474_Pertuzumab_2h_R1 4 QLDMILDEQRR 11 1 P49257 P49257 LMAN1 Protein ERGIC-53 0 ;;; 150.49 5.43E-05 1905580000 1821400 2310740 1584140 1440190 1356530 1139120 1405830 1264690 1512460 1288890 FALSE TRUE 1750217.674 2244839.958 1870429.337 1514518.378 1400164.019 1162153.787 1423034.968 1238573.71 1340771.882 1201592.332 1.456581927 1.868220941 1.55662556 1.260426134 1.165257119 0.967178098 1.184290986 1.030776975 1.115829259 1 20.19651608 3.629746217 1.983406361 1.07539087 1.675575068 0.827715172 0.112754733 0.115885749 0.89119836 0.030761496 0.058136966 4263.303165 -3.629746217 0.600184198 EGSQGELT(ph)PANSQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGSQGELTPANSQSR 15 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 EGSQGELT(1)PANSQSR;EGSQGELT(1)PANSQSR 239.75 9.12E-17 369370000 662140 628400 523540 537600 526400 529870 523870 606330 503610 587300 TRUE FALSE 636262.8368 610478.6473 618155.3241 565345.6004 543332.1341 540584.3344 530281.2778 593809.0736 446442.3041 547521.6479 1.162077955 1.114985407 1.12900618 1.032553877 0.992348223 0.987329609 0.968511985 1.084539901 0.815387493 1 19.06255648 3.62986197 1.901996899 0.984971347 1.141007806 0.558568735 0.063522826 0.273218206 1.93308822 0.018359724 0.035269448 4264.439626 -3.62986197 0.156036459 HFVALSTNTTK ddPTM_BT-474_Pertuzumab_2h_R1 2 HFVALSTNTTK 11 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90 P06744 GPI Glucose-6-phosphate isomerase 0 ; 218.11 1.09E-11 6517700000 8700200 8867700 6409400 6486800 6032900 5016200 6544200 4774700 6936800 5530800 FALSE TRUE 8360186.565 8614801.878 7567721.156 6821584.525 6226953.707 5117631.001 6624289.877 4676100.776 6149363.545 5156193.99 1.621387128 1.670767604 1.467695198 1.32298834 1.207664746 0.992521036 1.28472472 0.906890002 1.192616794 1 22.29787511 3.630179992 0.999643279 1.062450095 1.68661283 0.823918952 0.104291061 0.221234349 0.42695529 0.036801551 0.100286139 4267.563498 -3.630179992 0.624162735 (ac)SGEDEQQEQT(ph)IAEDLVVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 S(0.41)GEDEQQEQT(0.59)IAEDLVVTK 49.12 0.0018488 32917000 27967 24927 24027 29272 28268 32404 32628 33669 36936 37547 TRUE FALSE 26874.01872 24216.10637 28369.21338 30782.73143 29177.26589 33059.23108 33027.31122 32973.72338 32743.18013 35003.90825 0.767743377 0.691811503 0.810458454 0.879408414 0.833543091 0.944443999 0.943532105 0.942001195 0.93541498 1 15.09522839 3.630820358 0.578843421 0.966269962 0.685497495 0.851555003 0.035364246 0.461971067 0.267282132 0.022179284 0.075776419 4273.860655 -3.630820358 -0.280772467 LLDAESEDRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDAESEDRPK 11 1 O95239;O95239-2;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 0 ; 171.05 1.37E-05 412110000 322780 335150 302120 321160 373110 409020 385700 433450 494150 500090 FALSE TRUE 310165.4007 325591.8501 356719.8046 337735.1061 385111.422 417290.6646 390420.312 424499.106 438056.1636 466218.4589 0.665279109 0.698367566 0.765134451 0.724413844 0.82603212 0.895053932 0.83741925 0.910515442 0.939594208 1 18.8306466 3.631269375 0.257873211 1.017288146 0.511265725 0.930913949 0.027737845 1.248394861 0.113540123 0.043018301 0.197627175 4278.281685 -3.631269375 -0.506022421 VLDLDLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLDLDLFR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 191.63 0.00041919 492950000 854580 988720 850830 631050 617370 169756 911740 624550 617390 784170 FALSE TRUE 821182.0688 960522.6737 1004593.908 663618.5661 637228.2667 173188.5826 922898.1469 611652.8242 547306.4755 731057.4674 1.123279777 1.313881215 1.374165442 0.907751573 0.87165277 0.236901462 1.26241532 0.836668595 0.748650414 1 19.47962529 3.631273955 4.509293796 0.827314632 1.273398685 0.393303296 0.247442354 0.227326376 7.545461688 0.066510221 0.105599148 4278.326798 -3.631273955 0.446084053 ATVTPS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 7 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.109)PS(0.891)PVK;ATVT(0.011)PS(0.989)PVK;ATVT(0.482)PS(0.518)PVK;ATVT(0.057)PS(0.943)PVK;ATVT(0.058)PS(0.942)PVK;ATVT(0.108)PS(0.892)PVK;ATVT(0.061)PS(0.939)PVK 179.19 5.25E-05 61406300000 49981200 43477220 42764860 33284430 30839880 10639350 43119900 37286700 36174100 45699950 TRUE FALSE 48027879.45 42237292.25 50493421.5 35002243.42 31831872.75 10854484.95 43647614.23 36516716.61 32067767.82 42604651.68 1.127291917 0.991377481 1.185162171 0.821559197 0.747145476 0.254772296 1.024480016 0.857106329 0.752682314 1 25.34450762 3.631320802 5.09900109 0.76734317 1.088941671 0.345276804 0.203178478 0.262177661 10.21697369 0.055960289 0.088028798 4278.788323 -3.631320802 0.321598501 QEARPEPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 QEARPEPAR 9 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;; 118.4 0.00090745 514482000 1277510 1361010 1128810 860912 870815 260437 1120370 768962 925350 1104120 FALSE TRUE 1227583.497 1322195.327 1332811.077 905343.7715 898825.5553 265703.2146 1134081.423 753082.666 820308.1474 1029336.969 1.192596335 1.284511649 1.294824841 0.879540713 0.873208271 0.25813045 1.101759149 0.731619177 0.796928676 1 19.97328392 3.631751984 3.159564812 0.778018075 1.263585971 0.491632358 0.210919674 0.20273335 3.841409353 0.056628196 0.094467493 4283.038559 -3.631751984 0.485567897 KAALSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAALSSPR 8 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 KAALS(0.217)S(0.783)PR 70.908 0.030695 329370000 821480 848630 643410 629830 626480 295750 743750 615390 626500 750750 TRUE FALSE 789375.6534 824427.9033 759688.4996 662335.6018 646631.2982 301730.2676 752852.235 602681.9814 555382.3465 699901.0338 1.127838959 1.177920682 1.085422742 0.946327509 0.923889617 0.431104189 1.075655269 0.861096001 0.79351554 1 19.41679141 3.631877185 1.93830084 0.839864755 1.150779457 0.38711382 0.160811975 0.346830222 2.547401299 0.046963372 0.089714264 4284.273475 -3.631877185 0.310914702 ARFEELCSDLFR ddPTM_BT-474_Pertuzumab_2h_R1 8 ARFEELCSDLFR 12 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P17066;P48741 A0A0G2JIW1;P17066 HSPA1B;HSPA1A;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;; 209.21 5.28E-08 14442300000 7931843 9058370 6063414 6922156 4930048 3494885 7184694 6009512 7630336 8731096 FALSE TRUE 7621857.806 8800034.157 7159207.79 7279409.301 5088627.471 3565553.969 7272622.434 5885413.477 6764172.246 8139731.091 0.936377102 1.081120993 0.879538612 0.894305871 0.625159162 0.438043214 0.893472076 0.723047655 0.831006844 1 22.9565497 3.632244708 2.280217011 0.73569791 0.990372785 0.278601927 0.152156098 0.354066046 3.590969743 0.043376291 0.078350905 4287.90059 -3.632244708 0.254674875 LLEVQGSRPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEVQGSRPGK 11 1 P62136;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 ; 123.95 0.0003277 6729400000 3126530 3291600 2617350 3183100 3322360 3526020 3062000 3686400 3721500 3786700 FALSE TRUE 3004341.751 3197726.791 3090363.368 3347380.172 3429226.727 3597318.54 3099473.672 3610274.552 3299050.922 3530223.436 0.851034447 0.905814277 0.875401635 0.94820632 0.971390845 1.019005909 0.877982294 1.022675935 0.93451618 1 21.75132807 3.633075174 3.001051287 0.971046574 0.879028441 0.500856366 0.041712938 0.211189896 3.64459443 0.010890225 0.018367426 4296.107832 -3.633075174 -0.092018133 KHPSS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.146)S(0.854)PAR;KHPS(0.14)S(0.86)PAR;KHPS(0.035)S(0.965)PAR;KHPS(0.147)S(0.853)PAR 148.28 0.00032082 2691790000 2275190 2743100 2067320 1341743 1181555 113495.8 1923080 885330 911244 1611974 TRUE FALSE 2186273.059 2664869.474 2440930.711 1410990.517 1219560.79 115790.7628 1946615.228 867047.6261 807803.4014 1502793.565 1.454805976 1.773277139 1.624262153 0.938911737 0.811529153 0.077050345 1.295331091 0.576957239 0.537534509 1 20.51921541 3.633100934 2.764060192 0.7026823 1.647652974 0.632972582 0.306817845 0.163845298 2.420982396 0.083059626 0.142621445 4296.362667 -3.633100934 0.944970674 AGS(ph)ISTLDSLDFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.887)IS(0.112)TLDSLDFAR;AGS(0.991)IS(0.009)TLDSLDFAR 219.35 5.29E-12 357334000 134891 133547 144783 224476 203890 224149 330310 286180 323250 345520 TRUE FALSE 129619.3106 129738.3703 170948.5088 236061.2333 210448.307 228681.4464 334352.4326 280270.283 286556.0152 322117.6226 0.402397452 0.402767068 0.530702131 0.732841722 0.653327518 0.709931498 1.03798243 0.870086774 0.889600553 1 18.29722807 3.633286602 0.44574974 0.987032697 0.223553089 0.870901832 0.078123985 0.674984543 0.207172586 0.067271425 0.25014205 4298.199821 -3.633286602 -0.763479608 down LGDNGEAFFVQETDNDQEVIPMHLATS(ph)PILSEGASR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGDNGEAFFVQETDNDQEVIPMHLATSPILSEGASR 36 0 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 1 LGDNGEAFFVQETDNDQEVIPMHLAT(0.429)S(0.479)PILS(0.042)EGAS(0.05)R 69.625 0.0085074 19557000 4575.4 3850.8 3489.6 4574.9 5178.8 5184.3 3930.1 5830.3 6409.5 5437.4 TRUE FALSE 4396.58831 3740.978954 4120.248346 4811.011137 5345.380805 5289.130098 3978.197739 5709.902268 5681.920431 5069.120055 0.867327714 0.737993757 0.812813329 0.949082106 1.054498759 1.043402019 0.784790594 1.126408964 1.120888906 1 12.30751962 3.633349323 2.976179842 1.018820949 0.796175402 0.512641794 0.093755692 0.214760844 3.649743912 0.026678961 0.045082125 4298.820617 -3.633349323 -0.222645547 SMQHSPNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMQHSPNLR 9 0 O76041-2;O76041 O76041-2 NEBL Nebulette 0 63.076 0.095193 0 102330 111080 88124 91638 90019 76459 95284 114200 86257 102020 FALSE TRUE 98330.83047 107912.1072 104049.9671 96367.44816 92914.54289 78005.05337 96450.11409 111841.7301 76465.46698 95110.09453 1.03386324 1.134602039 1.093994992 1.013219981 0.976915682 0.820155355 1.014089141 1.175918609 0.803967942 1 16.53731085 3.633772887 3.508574145 0.984934671 1.092626195 0.210767312 0.101400968 0.459614963 10.47420068 0.0299093 0.049046655 4303.015264 -3.633772887 0.107691524 NFAFLEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFAFLEFR 8 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 136.27 0.001857 463900000 1221940 1159690 1053040 724100 687880 303720 717220 692580 807850 1009210 FALSE TRUE 1174185.234 1126616.777 1243347.753 761470.8878 710006.2849 309861.4265 725997.5529 678277.981 716146.2548 940855.3078 1.247997672 1.197438934 1.321507933 0.809338993 0.754639187 0.329340148 0.771635709 0.720916357 0.761165132 1 19.84361335 3.635514686 3.776809307 0.700523331 1.250831213 0.693924229 0.158359093 0.124280911 3.205058674 0.042632926 0.069194487 4320.307766 -3.635514686 0.550307882 RFEELGVK ddPTM_BT-474_Pertuzumab_2h_R1 4 RFEELGVK 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;;; 146.79 0.00087828 2936380000 4139140 3880890 3082810 3073190 3242230 2414380 2861340 2994410 3354800 3227170 FALSE TRUE 3977377.833 3770210.817 3639942.344 3231797.704 3346519.272 2463200.418 2896357.935 2932574.387 2973977.168 3008590.901 1.322006867 1.253148381 1.209849549 1.074189815 1.112321144 0.818722285 0.962695837 0.974733516 0.988495035 1 21.52065652 3.636237551 1.08573846 0.954880257 1.308676791 0.820613014 0.06191014 0.219834105 0.502587273 0.022055781 0.057681883 4327.504732 -3.636237551 0.353796534 ITITNDQNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ITITNDQNR 9 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 125.82 0.0011421 165800000 179110 193420 173990 131420 128860 74704 145030 146770 130920 171800 FALSE TRUE 172110.1832 187903.851 205433.8634 138202.6019 133004.8989 76214.56606 146804.9205 143739.1482 116058.5105 160163.833 1.074588314 1.173197766 1.282648271 0.862882708 0.830430294 0.475853785 0.916592203 0.897450726 0.724623708 1 17.28918888 3.636493736 5.082814871 0.805172034 1.175020433 0.58281638 0.140475947 0.155904634 6.186879013 0.038415113 0.060495677 4330.058221 -3.636493736 0.369848398 VIGSGCNLDSAR ddPTM_BT-474_Pertuzumab_2h_R1 4 VIGSGCNLDSAR 12 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5;Q6ZMR3;A0A087WUM2;F5H5G7;F5H155;P07864;G3XAP5;F5H245;A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50 P00338;A0A5F9ZHM4 LDHA;LDHAL6A;LDHC;LDHB L-lactate dehydrogenase A chain;L-lactate dehydrogenase A-like 6A;L-lactate dehydrogenase;L-lactate dehydrogenase C chain;L-lactate dehydrogenase B chain 0 ;;; 168.69 0.0001067 1407480000 491611 540691 441302 317345 324839 121933 387840 314621 288886 319388 FALSE TRUE 472398.2986 525271.0221 521055.0881 333723.2135 335287.7414 124398.5688 392586.5019 308123.9664 256092.8724 297755.5663 1.586530538 1.764101436 1.749942393 1.120795885 1.126050289 0.417787551 1.318485853 1.034821852 0.860077531 1 18.18376895 3.636872975 3.072818434 0.97193963 1.713370866 0.689505798 0.222223615 0.146509401 2.646455957 0.061590245 0.103638047 4333.841008 -3.636872975 0.741431236 FPSS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FPSSPLR 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 FPS(0.039)S(0.961)PLR;FPS(0.112)S(0.888)PLR 115.49 0.0059452 216460000 624650 795820 673170 478290 474410 124366 759630 379910 449610 731380 TRUE FALSE 600237.9874 773123.9928 794826.7936 502974.6042 489669.8285 126880.7657 768926.5792 372064.7257 398572.1577 681842.9812 0.880317029 1.133873948 1.165703565 0.737669255 0.718156294 0.186085021 1.127717965 0.545675084 0.584551236 1 19.37908002 3.637406678 4.839307242 0.674189438 1.065968366 0.300978496 0.250404027 0.247566828 9.238246522 0.064519682 0.101983945 4339.170122 -3.637406678 0.391778928 NLLSVAYK ddPTM_BT-474_Pertuzumab_2h_R1 2 NLLSVAYK 8 0 P27348;E9PG15;P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;A0A0J9YWZ2;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1;P31947-2;P31947;P61981;P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4;Q04917;A2IDB2 P27348;P31946-2;P63104;P31947-2;P61981;P62258;Q04917 YWHAQ;YWHAB;YWHAZ;SFN;YWHAG;YWHAE;YWHAH "14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein zeta/delta;14-3-3 protein sigma;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein epsilon;14-3-3 protein eta" 0 ; 124.23 0.0030562 1706830000 3209700 3112400 2754500 2172700 1778470 1058390 2290300 2352700 2588200 2870500 FALSE TRUE 3084261.375 3023637.399 3252299.424 2284833.307 1835676.103 1079791.371 2318329.377 2304115.923 2294398.387 2676078.478 1.152530242 1.129876207 1.215322888 0.853799067 0.6859575 0.403497648 0.866315915 0.861004616 0.857373356 1 21.35168899 3.637436035 4.249562473 0.767651068 1.161960877 0.570432422 0.150161749 0.168246917 5.224860197 0.0430688 0.06891774 4339.463452 -3.637436035 0.394309808 LSFFFDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSFFFDFR 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 106.36 0.0097971 544220000 728300 989250 858380 531610 466680 208010 698990 422950 552510 864940 FALSE TRUE 699837.2308 961037.5586 1013508.361 559046.4558 481691.186 212216.1047 707544.4487 414215.9347 489791.3811 806356.8434 0.867900157 1.191826629 1.25689807 0.693299078 0.59736727 0.263178897 0.87745823 0.513688125 0.607412692 1 19.6210589 3.637770439 5.196198857 0.614296263 1.112131377 0.493747929 0.209970786 0.161702901 6.647505751 0.053664897 0.084409849 4342.806097 -3.637770439 0.497835114 VSTNGSDDPEDAGAGENRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSTNGSDDPEDAGAGENRR 19 1 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;A0A590UK95 A0A590UJQ1 ITCH E3 ubiquitin-protein ligase Itchy homolog 0 ; 78.794 0.015443 1011240000 204972 235930 187936 227380 247340 279150 260540 250580 296580 277650 FALSE TRUE 196961.4676 229201.5074 221900.2158 239115.109 255295.9157 284794.6043 263728.5665 245405.4354 262913.4818 258844.5182 0.760925783 0.885479472 0.857272224 0.923778918 0.986290602 1.100253566 1.018868656 0.948080481 1.015719721 1 17.98172624 3.639245292 1.415955328 1.010628707 0.819151044 0.76523448 0.044580516 0.228066271 0.894327894 0.015250902 0.034125993 4357.579227 -3.639245292 -0.191477663 TFTAWCNSHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TFTAWCNSHLR 11 0 O43707;F5GXS2;O43707-3;K7EP19;P12814-3;P12814;P12814-2;P12814-4;P35609-2;P35609;G3V2N5;A0A494C1A0;Q08043;A0A494C166;A0A494C033;A0A494C0Q3 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ; 167.2 1.95E-05 952310000 1144020 1293680 1180760 908280 825560 460480 1289470 867960 1050490 1261890 FALSE TRUE 1099310.434 1256785.513 1394149.598 955156.4396 852114.8872 469791.2211 1305250.92 850036.3227 931242.7792 1176421.066 0.934453203 1.068312655 1.185077042 0.81191715 0.724328144 0.399339348 1.109509985 0.72256129 0.791589683 1 20.16597309 3.639253691 6.293924544 0.777578992 1.06206088 0.305829666 0.184580408 0.267827456 14.23837818 0.048414741 0.075498981 4357.663502 -3.639253691 0.284481888 YLDLHDCYLK ddPTM_BT-474_Pertuzumab_2h_R1 4 YLDLHDCYLK 10 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;;; 140.16 3.98E-05 1871380000 4719470 4939630 3991100 4164370 4320470 3325710 4866720 4313470 4802860 5135880 FALSE TRUE 4535027.895 4798756.589 4712380.552 4379293.635 4459441.841 3392958.135 4926280.375 4224395.337 4257659.468 4788022.273 0.947160986 1.00224191 0.984201886 0.914635184 0.931374498 0.708634576 1.028875827 0.882283978 0.889231341 1 22.19099843 3.640019588 3.091876169 0.900132603 0.980926237 0.13103365 0.08142307 0.47360938 8.670030234 0.021758503 0.036642579 4365.355208 -3.640019588 0.080793634 FVLKPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FVLKPQR 7 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7 A0A2R8Y430 GSS Glutathione synthetase 0 ; 114.54 0.0053646 542060000 847370 912100 799570 615400 499040 197927 947540 569140 633030 883730 FALSE TRUE 814253.8436 886087.801 944070.0853 647160.8677 515092.0748 201929.2196 959136.278 557387.0601 561171.0883 823874.18 0.988323051 1.075513498 1.145891094 0.785509345 0.625207207 0.245097157 1.164178101 0.676543911 0.68113688 1 19.6520645 3.640183753 4.908677839 0.720298722 1.069278372 0.303112876 0.229634796 0.263532435 10.15379599 0.061387791 0.09698656 4367.005638 -3.640183753 0.348979651 LTGMAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTGMAFR 7 0 P04406;E7EUT5;P04406-2;O14556 P04406;P04406-2;O14556 GAPDH;GAPDHS "Glyceraldehyde-3-phosphate dehydrogenase;Glyceraldehyde-3-phosphate dehydrogenase, testis-specific" 0 ; 128.48 0.0087314 6611000000 6844600 7730700 6556700 4358300 3734000 1407580 5990000 3934300 4009000 4756700 FALSE TRUE 6577105.465 7510228.005 7741641.543 4583232.385 3854107.501 1436042.232 6063307.412 3853055.33 3553915.127 4434524.472 1.483159132 1.693581364 1.745765886 1.033534128 0.869114045 0.323832294 1.367295964 0.868876777 0.801419667 1 22.08034798 3.640227022 4.086354185 0.879861119 1.646143396 0.659207307 0.247458418 0.13669692 4.031634963 0.067306615 0.108313593 4367.440755 -3.640227022 0.766282276 GLYGIKDDVFLSVPCILGQNGISDLVK ddPTM_BT-474_Pertuzumab_2h_R1 3 GLYGIKDDVFLSVPCILGQNGISDLVK 27 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 272.18 8.06E-61 1253209000 1939060 1854930 1359330 1346360 1496690 1652740 1452080 1638730 1777860 1275700 FALSE TRUE 1863279.391 1802029.213 1604991.169 1415845.801 1544832.393 1686159.535 1469850.989 1604889.653 1576044.786 1189295.703 1.566708252 1.515207033 1.34953079 1.190490975 1.298947259 1.417779894 1.235900362 1.349445432 1.325191693 1 20.18167604 3.640807358 0.036065372 4.63E-16 2.784194227 0.617832236 0.09511887 241.7325987 2.050589165 65.94268224 93.07591643 4373.280748 -3.640807358 2.784194227 IASHYYITNDTVQTYNQLLKPTLSEIELFR ddPTM_BT-474_Pertuzumab_2h_R1 1 IASHYYITNDTVQTYNQLLKPTLSEIELFR 30 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 307.68 1.56E-83 363360000 112500 100030 94582 102790 111260 108470 122810 111370 131910 126670 FALSE TRUE 108103.3756 97177.24234 111675.0714 108095.0042 114838.7789 110663.3377 124312.9855 109070.1706 116936.1298 118090.5281 0.915427997 0.82290463 0.945673401 0.915357108 0.972463929 0.93710596 1.052692265 0.923614894 0.990224464 1 16.84953373 3.641079054 1.055262372 0.978615451 0.870919808 0.46941518 0.042808027 0.491975348 1.058419021 0.014611191 0.039135578 4376.017543 -3.641079054 -0.107695643 TAVAHRPGAFK ddPTM_BT-474_Pertuzumab_2h_R1 2 TAVAHRPGAFK 11 1 Q969H8 Q969H8 MYDGF Myeloid-derived growth factor 0 ; 118.9 0.0003952 916810000 1335510 1320920 1109780 1010320 956870 611680 1180220 1033360 1182860 1236970 FALSE TRUE 1283316.793 1283248.655 1310341.933 1062462.736 987648.5926 624048.5887 1194663.885 1012020.755 1048586.692 1153188.92 1.112841765 1.112782678 1.136276901 0.921325828 0.85644995 0.541150351 1.035965456 0.877584529 0.909293069 1 20.13719745 3.6413636 3.572920933 0.862909307 1.121179374 0.446537309 0.124761302 0.219238896 5.205175271 0.034533971 0.056690424 4378.885609 -3.6413636 0.258270068 NVEELVIVLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NVEELVIVLKK 11 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 90.731 0.010895 0 285040 298050 213870 240220 230080 239670 235860 200580 265490 253970 FALSE TRUE 273900.3217 289549.9058 252521.0665 252617.783 237480.7322 244516.2916 238746.5252 196437.9529 235352.6882 236768.3857 1.1568281 1.222924695 1.066532028 1.066940513 1.003008622 1.032723566 1.008354745 0.829662931 0.99402075 1 17.85311693 3.641540846 0.621243262 0.93382816 1.226659318 0.655818239 0.058338247 0.688254579 0.466501446 0.036103904 0.122861863 4380.673102 -3.641540846 0.292831158 IDKELINR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDKELINR 8 1 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423;G3V3P2;G3V227;G3V3X0;G3V2Y7 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 135.71 0.00074973 1016100000 1160680 1263800 1004250 1178870 1170890 1290810 1310420 1335810 1538670 1513540 FALSE TRUE 1115319.342 1227757.661 1185740.314 1239711.622 1208552.74 1316911.063 1326457.312 1308225.057 1364006.632 1411026.588 0.790431132 0.870116603 0.840338747 0.878588421 0.856506001 0.933299963 0.940065427 0.927144157 0.966676776 1 20.42831374 3.64174765 0.224852124 1.016720448 0.715924736 0.881154635 0.020885563 2.192474249 0.156275732 0.040466516 0.186903994 4382.759601 -3.64174765 -0.300795712 HNTTSQNVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HNTTSQNVSK 10 0 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 0 89.548 0.011438 13315000 32187 40189 29246 30662 29874 26955 36840 26208 34406 39963 FALSE TRUE 30929.09646 39042.84907 34531.40277 32244.46949 30834.92434 27500.04857 37290.85894 25666.79564 30500.37512 37256.27041 0.830171569 1.047953771 0.926861502 0.865477653 0.827643884 0.738132085 1.000928395 0.688925525 0.818664208 1 15.18519564 3.642108817 2.807382652 0.827495241 0.948208562 0.109590643 0.105480782 0.429314685 6.552212847 0.027984218 0.048190612 4386.405904 -3.642108817 0.120713321 QQRPLEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQRPLEFR 8 1 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 0 83.783 0.01634 188680000 298570 275460 233290 236250 228510 170740 273320 240470 259980 316930 FALSE TRUE 286901.5543 267604.1505 275450.6925 248442.8908 235860.2317 174192.4798 276664.9719 235504.2105 230468.1603 295464.0488 0.971020182 0.905707993 0.932264665 0.840856584 0.798270492 0.589555584 0.936374402 0.797065536 0.780020992 1 18.17262307 3.643162015 2.926666088 0.804721256 0.935631927 0.209764822 0.102328245 0.381407223 6.307437967 0.027572121 0.047072914 4397.056181 -3.643162015 0.130910671 RLGDSSLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 69.672 0.090163 0 131890 130780 107950 113010 94189 93907 128560 122210 141890 133300 FALSE TRUE 126735.593 127050.2824 127458.9663 118842.4596 97218.67473 95805.86388 130133.3557 119686.3208 125783.2421 124271.4723 1.019828531 1.022360805 1.025649443 0.956313283 0.782308867 0.770940121 1.047169985 0.963103749 1.012165059 1 16.92313562 3.643254827 4.669749716 0.926609726 1.022383402 0.187767073 0.085991191 0.399850165 14.55947819 0.025489246 0.040471469 4397.995967 -3.643254827 0.095773676 GDVVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDVVPK 6 0 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A0A1W2PQM2;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ; 100.82 0.086601 1574250000 3571600 3563600 3221900 3384500 3549600 3942200 3931000 4031300 4509600 4415400 FALSE TRUE 3432017.923 3461969.617 3804169.001 3559174.451 3663776.108 4021913.985 3979108.754 3948052.246 3997689.114 4116341.025 0.833754517 0.841030808 0.92416274 0.864645186 0.890056505 0.977060443 0.966661588 0.959116901 0.971175393 1 21.97293108 3.644487562 0.36315006 0.999020815 0.783895294 0.813295308 0.02503094 1.222266028 0.22733557 0.026316058 0.108014624 4410.497314 -3.644487562 -0.215125521 RYESQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 RYESQLR 7 1 O15212 O15212 PFDN6 Prefoldin subunit 6 0 ; 192.58 0.00081639 165375000 203912 244550 212818 140696 124163 44836 213479 117902 136231 192392 FALSE TRUE 195942.8936 237575.6734 251278.9467 147957.3374 128156.8157 45742.61464 216091.6199 115467.2825 120766.628 179361.1185 1.092449106 1.324566191 1.400966658 0.824913106 0.714518379 0.255030828 1.204785194 0.643769862 0.673315538 1 17.45250765 3.645613139 4.949428244 0.737435253 1.276237372 0.485361394 0.24247308 0.175692668 7.044288267 0.063548272 0.100461454 4421.942986 -3.645613139 0.538802118 DRVDCGYPHVTPK ddPTM_BT-474_Pertuzumab_2h_R1 5 DRVDCGYPHVTPK 13 1 X6R3S7;Q07654 X6R3S7 TFF3 Trefoil factor 3 0 ;;;; 138.77 2.72E-05 3509940000 1688110 1658750 1608350 1284023 1118430 1338490 1281106 1308243 1598796 1610280 FALSE TRUE 1622136.795 1611444.074 1899014.623 1350291.581 1154405.317 1365555.185 1296784.558 1281227.325 1417307.381 1501214.301 1.080549788 1.073427073 1.264985699 0.899466239 0.768981028 0.909633744 0.863823744 0.853460644 0.9441073 1 20.51769851 3.646383864 7.283197952 0.876755383 1.13232663 0.691520642 0.075587739 0.13244797 9.110204368 0.019231579 0.029894909 4429.7974 -3.646383864 0.255571247 ADEASELACPT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 8 ADEASELACPTPK 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK 278.51 2.90E-31 18740094000 24982991 20446701 16708236 15880693 17184264 14285773 9797550 13232050 12638205 11253766 TRUE FALSE 24006628.09 19863581.11 19727785.92 16700297.47 17737011.46 14574641.12 9917455.348 12958803.54 11203568.95 10491538.41 2.288189507 1.893295372 1.880352066 1.591787288 1.690601585 1.389180552 0.945281327 1.235167145 1.067867125 1 23.3227229 3.647447095 0.420188836 0.962610959 2.497949397 0.907886447 0.128485085 0.628044886 0.165598339 0.115538653 0.446936453 4440.655631 -3.647447095 1.535338437 up GICFIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GICFIR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 119.58 0.048604 193660000 647390 654730 577520 462990 457060 386120 535490 446200 449600 518090 FALSE TRUE 622089.2831 636057.7414 681890.7109 486884.9694 471761.75 393927.611 542043.4868 436985.8141 398563.2929 482999.3028 1.287971389 1.316891635 1.411784048 1.00804487 0.976733811 0.815586293 1.122244864 0.90473384 0.825183992 1 18.88166158 3.647608602 4.578051832 0.944751202 1.336072031 0.803437434 0.088374207 0.090252947 3.254831876 0.023519843 0.03746515 4442.307343 -3.647608602 0.39132083 TVS(ph)FEALPIMR ddPTM_BT-474_Pertuzumab_2h_R1 8 TVSFEALPIMR 11 0 O15084-2;O15084;O15084-4;O15084-1 O15084-2 ANKRD28 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit A 1 T(0.006)VS(0.994)FEALPIMR;T(0.002)VS(0.998)FEALPIMR;T(0.067)VS(0.933)FEALPIMR;T(0.005)VS(0.995)FEALPIMR;T(0.008)VS(0.992)FEALPIMR;TVS(1)FEALPIMR;T(0.001)VS(0.999)FEALPIMR;TVS(1)FEALPIMR 201.66 4.48E-08 1156753700 658738 693677 494724 739264 834899 683370 784701 876857 838427 918726 TRUE FALSE 632993.7907 673894.0111 584131.6319 777417.5036 861754.2846 697188.2096 794304.4056 858749.5965 743252.2819 856499.8697 0.739047154 0.786799899 0.681998506 0.907667977 1.006134753 0.813996866 0.927384152 1.002626652 0.867778628 1 19.7080935 3.648354171 5.681289295 0.936066699 0.74172523 0.675424698 0.062455766 0.127540445 6.349911024 0.016479268 0.025832456 4449.940162 -3.648354171 -0.19434147 AAPFSLEYR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAPFSLEYR 9 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 95.605 0.018453 322460000 409840 479690 422080 265640 240810 73733 404540 217760 238390 370080 FALSE TRUE 393822.9997 466009.7109 498359.2451 279349.7122 248555.8723 75223.93178 409490.8815 213263.1799 211328.9666 345014.152 1.141469118 1.350697379 1.444460299 0.809676098 0.720422252 0.218031438 1.186881405 0.618128789 0.612522604 1 18.39629601 3.648821076 4.866870557 0.714654929 1.314595477 0.527275177 0.249487722 0.161458142 6.430151236 0.065168616 0.103252034 4454.726813 -3.648821076 0.599940548 DFVNYLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFVNYLVR 8 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 132.08 0.0022738 1425280000 1778130 2008140 1688360 1365190 1231420 560010 1898780 1439100 1385210 1746490 FALSE TRUE 1708638.714 1950869.813 1993484.209 1435647.62 1271029.743 571333.7859 1922017.838 1409382.082 1227966.768 1628198.677 1.049404313 1.198176759 1.224349484 0.881739827 0.780635534 0.350899306 1.180456578 0.865608173 0.754187303 1 20.63484532 3.649001744 4.781080817 0.823123025 1.160650198 0.355859214 0.20232085 0.244557608 9.490342455 0.055437093 0.087976769 4456.580384 -3.649001744 0.337527173 GKHDELADSLPCAEGEFIFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKHDELADSLPCAEGEFIFLR 21 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 215.37 3.96E-25 185366000 435760 419120 358210 382120 383190 381170 402800 387940 477120 472540 FALSE TRUE 418730.0174 407167.108 422946.5153 401841.259 395515.6544 388877.5186 407729.5869 379928.9034 422959.3379 440534.4449 0.950504602 0.924257144 0.960075926 0.912167626 0.897808693 0.882740324 0.925533955 0.862427235 0.960105033 1 18.7488953 3.649517966 7.369214801 0.909367669 0.94279315 0.031205251 0.038473184 0.513162412 37.14053836 0.009589211 0.014905057 4461.880824 -3.649517966 0.033425481 NSS(ph)GPQSGWMK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSGPQSGWMK 11 0 F8VXG7;Q99590-2;Q99590 F8VXG7 SCAF11 Protein SCAF11 1 NS(0.017)S(0.983)GPQSGWMK 124.07 0.00037431 109490000 201790 207670 166490 166430 176480 149080 168910 186490 186950 175340 TRUE FALSE 193903.8237 201747.4549 196578.4466 175019.4722 182156.6395 152094.4997 170977.1711 182638.9163 165728.2198 163464.0656 1.186216818 1.234200643 1.202578963 1.070690806 1.114352802 0.930446084 1.045961817 1.117303155 1.013851082 1 17.318614 3.649659759 1.991875922 1.042673201 1.216890169 0.68165878 0.052234467 0.207083934 1.603270731 0.015870833 0.030491311 4463.337821 -3.649659759 0.174216968 KIQNDAGVR ddPTM_BT-474_Pertuzumab_2h_R1 4 KIQNDAGVR 9 1 A0A087WTP3;Q92945;M0R0I5;Q96AE4;E9PEB5;Q96AE4-2;Q96I24;Q96I24-2 A0A087WTP3;Q96AE4;Q96I24 KHSRP;FUBP1;FUBP3 Far upstream element-binding protein 2;Far upstream element-binding protein 1;Far upstream element-binding protein 3 0 ;;; 163.64 0.0001008 1616230000 2338140 2446320 2030690 1947950 1923600 1325840 2374510 2012670 2256680 2457660 FALSE TRUE 2246762.904 2376553.349 2397680.855 2048483.933 1985474.341 1352649.393 2403569.964 1971107.661 2000511.147 2291200.499 0.980605104 1.037252458 1.046473609 0.894065768 0.866565079 0.5903671 1.049043925 0.860294707 0.873127929 1 21.12767228 3.649799645 4.413587836 0.866382869 1.022917905 0.253037149 0.114141253 0.294511986 10.13063734 0.03050864 0.048825845 4464.775695 -3.649799645 0.156535036 DTSGPTPGTPS(ph)PAMAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTSGPTPGTPSPAMAR 16 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 DTSGPT(0.001)PGT(0.152)PS(0.847)PAMAR 305.43 5.91E-37 0 161440 191490 146110 145650 142580 137350 132390 174510 157090 145690 TRUE FALSE 155130.7463 186028.8927 172515.3272 153167.014 147166.2152 140127.3111 134010.2284 170906.3075 139257.8018 135822.2865 1.142159732 1.369649249 1.270154785 1.12770163 1.083520378 1.03169601 0.98665861 1.258308278 1.025294194 1 17.0513607 3.650063682 3.417697728 1.083774899 1.272869805 0.482500315 0.089249712 0.221145701 4.916268857 0.025015435 0.041588989 4467.490954 -3.650063682 0.189094906 ARPEYMLPVHFYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ARPEYMLPVHFYGR 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 118.33 0.00015105 4391400000 3344300 3426500 2550500 2294900 1773830 1496820 2295700 2074500 1896490 2269590 FALSE TRUE 3213601.059 3328779.575 3011432.086 2413340.064 1830886.853 1527086.726 2323795.463 2031660.85 1681208.406 2115868.648 1.518809337 1.573244907 1.423260413 1.140590682 0.865312152 0.7217304 1.098270191 0.960201784 0.794571255 1 21.01281864 3.650278573 2.177372397 0.914006823 1.54031311 0.872735858 0.102502374 0.10546445 0.975321037 0.030706966 0.057162813 4469.702037 -3.650278573 0.626306287 VREFNFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VREFNFEK 8 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 78.939 0.026748 292710000 263640 292980 235150 197430 187120 109160 241590 187010 234160 226490 FALSE TRUE 253336.6573 284624.4973 277646.8359 207619.386 193138.8847 111367.29 244546.6507 183148.1781 207579.1385 211149.6306 1.19979683 1.34797535 1.3149293 0.983280839 0.914701504 0.527433033 1.158167552 0.867385738 0.983090228 1 17.6879062 3.650594543 3.621007435 0.90229784 1.295724485 0.548728635 0.153942309 0.171238462 4.229067651 0.041433102 0.068210901 4472.955145 -3.650594543 0.393426644 RGQAALDR ddPTM_BT-474_Pertuzumab_2h_R1 5 RGQAALDR 8 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;; 155.42 0.00065629 2051974000 2045300 2344080 1973200 1717000 1645760 971333 2225900 1780610 2012430 2219200 FALSE TRUE 1965367.415 2277229.133 2329801.134 1805614.576 1698697.365 990974.0188 2253141.23 1743839.781 1783987.383 2068891.607 0.949961519 1.100700068 1.126110776 0.872744889 0.821066391 0.478987887 1.089057166 0.842886005 0.862291372 1 20.98042663 3.650783842 5.527067977 0.841981603 1.062363584 0.273429003 0.154017905 0.27897196 13.60849931 0.041242071 0.064775064 4474.905232 -3.650783842 0.220381981 ALSSQHQAR ddPTM_BT-474_Pertuzumab_2h_R1 8 ALSSQHQAR 9 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;;;; 149.72 8.70E-05 525661000 638526 1066165 859866 428556 321657 113231.6 647214 305149 334230 550088 FALSE TRUE 613571.698 1035759.018 1015262.914 450673.8265 332003.3895 115521.2205 655134.7985 298847.5665 296289.6116 512830.0498 1.196442561 2.019692525 1.979725865 0.878797619 0.64739457 0.225262191 1.2774891 0.582741917 0.577753998 1 18.96812128 3.651345977 4.968900156 0.712194613 1.75803733 0.648455531 0.334982875 0.124142336 5.180788212 0.087741043 0.138866214 4480.701135 -3.651345977 1.045842717 PGMYPDPHSPFAVS(ph)PIPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 PGMYPDPHSPFAVSPIPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 PGMYPDPHS(0.018)PFAVS(0.982)PIPGR 50.858 0.076877 0 105780 96844 99540 188120 235090 258260 296710 232020 228590 182620 TRUE FALSE 101646.0007 94082.10394 117529.0923 197828.8957 242651.8834 263482.1941 300341.2257 227228.7059 202641.4215 170250.9847 0.597036198 0.552608281 0.690328414 1.161983856 1.425259794 1.547610397 1.764108596 1.334668967 1.190251098 1 17.37730362 3.651487489 2.213093081 1.42368965 0.572697863 0.755066469 0.194072266 0.140462373 1.34182898 0.056097862 0.103972063 4482.161377 -3.651487489 -0.850991787 DISQNKR ddPTM_BT-474_Pertuzumab_2h_R1 9 DISQNKR 7 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ;;;;;;;; 147.34 0.0034608 21283300000 10059660 10646860 7810250 8324240 6253700 4737820 9110010 7740190 9985150 10425800 FALSE TRUE 9666517.366 10343221.98 9221735.913 8753855.024 6454855.94 4833621.967 9221501.027 7580352.372 8851677.633 9719651.28 0.994533352 1.064155666 0.948772301 0.90063468 0.664103655 0.497304052 0.948748135 0.779899623 0.910699096 1 23.21247312 3.651633509 2.621748391 0.786173876 1.017240474 0.289685901 0.139638739 0.332449361 4.449848276 0.039833128 0.070259174 4483.668638 -3.651633509 0.231066599 YAYYDTER ddPTM_BT-474_Pertuzumab_2h_R1 1 YAYYDTER 8 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 129.55 0.0025258 442490000 537200 566250 435180 365530 344750 162930 402900 339320 350020 498170 FALSE TRUE 516205.6301 550101.1044 513826.7065 384395.0471 355839.1968 166224.5562 407830.8107 332312.9234 310287.197 464428.5022 1.111485681 1.184468873 1.106363421 0.827673249 0.76618725 0.357912048 0.878134759 0.715530855 0.668105415 1 18.82509699 3.652205037 2.391779674 0.711560089 1.153002284 0.572131969 0.155997705 0.197838853 2.206703905 0.042927276 0.077701719 4489.572998 -3.652205037 0.441442195 LMLDWAEDNLIHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LMLDWAEDNLIHK 13 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ; 205.8 6.70E-08 876920000 633990 630330 514730 639590 681000 654280 717560 683760 760450 785920 FALSE TRUE 609212.9699 612353.6056 607753.1611 672599.3165 702904.9835 667509.9899 726341.7139 669640.1171 674126.9041 732688.9384 0.831475594 0.835762045 0.829483194 0.917987541 0.959349796 0.911041446 0.991337082 0.91394872 0.920072447 1 19.48284131 3.652399057 3.474581762 0.943867866 0.831616778 0.765899439 0.028820925 0.11008946 2.531477331 0.00745542 0.012375511 4491.579151 -3.652399057 -0.112251088 (ac)SHHWGYGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHHWGYGK 8 0 E5RID5;E5RK37;P00918 E5RID5 CA2 Carbonic anhydrase 2 0 41.029 0.040038 85377000 169050 246430 191860 131360 127000 120410 158640 76434 134140 174470 FALSE TRUE 162443.3391 239402.0577 226533.3699 138139.5053 131085.0703 122844.7727 160581.4838 74855.61119 118912.9896 162652.9915 0.998711045 1.471857698 1.392740261 0.849289669 0.805918595 0.755256768 0.987264251 0.460216627 0.731083938 1 17.31143783 3.653190939 4.524731577 0.760751395 1.305577536 0.597975618 0.182782205 0.13638446 4.960800061 0.049636601 0.079317953 4499.77646 -3.653190939 0.54482614 KVTHAVVTVPAYFNDAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVTHAVVTVPAYFNDAQR 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 193.06 9.27E-15 1361960000 2118700 2529600 1722540 1777890 1411930 1553070 1677140 1517750 1828030 1808930 FALSE TRUE 2035898.862 2457458.285 2033841.296 1869647.116 1457346.011 1584474.139 1697665.341 1486407.932 1620519.698 1686409.56 1.207238686 1.457213208 1.2060186 1.10865543 0.864170867 0.939554766 1.006674405 0.881403882 0.960928909 1 20.68552352 3.653373977 2.108632728 0.937887257 1.327132548 0.802934359 0.077407387 0.117050644 1.015159385 0.020742569 0.039151281 4501.673331 -3.653373977 0.389245292 EEASLLSHS(ph)PGTSNQS(ph)QPCSPKPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 2 EEASLLSHS(1)PGT(0.001)S(0.044)NQS(0.733)QPCS(0.222)PKPIR 153.32 1.40E-07 682430000 187950 190860 128360 186630 185900 180520 203280 193790 187710 219650 TRUE FALSE 180604.7062 185416.8597 151557.5074 196261.9967 191879.6423 184170.2381 205767.8014 189788.1688 166401.9477 204772.9099 0.881975581 0.905475533 0.740124792 0.958437309 0.937036264 0.899387708 1.004858512 0.926822639 0.812617 1 17.64366534 3.653536879 24.99999992 0.933778816 0.84879227 0.293868635 0.064877154 103.6581183 30477.44344 0.016807379 0.026037878 4503.362211 -3.653536879 -0.084986546 FEDEELQQILDDIQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 FEDEELQQILDDIQTK 16 0 O15514;E9PHV4;E9PB93 O15514 POLR2D DNA-directed RNA polymerase II subunit RPB4 0 ; 186.95 3.30E-09 17725900 33597 32209 29886.4 35066 29044 34814 33803 33052 42348 39010 FALSE TRUE 32283.9921 31290.43086 35287.5373 36875.76046 29978.22664 35517.96293 34216.69123 32369.46465 37540.83258 36367.81795 0.887707702 0.860387909 0.970295698 1.013966813 0.824306442 0.976631674 0.940850817 0.890057927 1.032254193 1 15.15037475 3.654122594 0.013161412 1.839023494 4.88E-05 0.199498248 0.059880533 4364.854395 13.34807499 873.9180807 992.3260864 4509.439804 -3.654122594 -1.838974702 NLVLTGFSHIDLIDLDTIDVSNLNR ddPTM_BT-474_Pertuzumab_2h_R1 3 NLVLTGFSHIDLIDLDTIDVSNLNR 25 0 Q9UBT2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;; 215.28 1.74E-33 323110000 244967 262975 198558 168434 147112 142158 106920 161241 191085 214240 FALSE TRUE 235393.4188 255475.2105 234441.8475 177126.8989 151843.9911 145032.5322 108228.5189 157911.317 169393.8319 199729.334 1.178562078 1.279107107 1.173797773 0.886834675 0.760248823 0.726145375 0.541875932 0.790626564 0.848116942 1 17.60768671 3.654304334 2.324701559 0.750832582 1.234264618 0.751538264 0.110977079 0.133493344 1.406941821 0.031167868 0.057002566 4511.327271 -3.654304334 0.483432036 SSFLSS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 SSFLSSPER 9 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 SS(0.002)FLS(0.062)S(0.937)PER 87.878 0.013807 137190000 339750 399030 331690 235160 250670 78994 302600 227000 231350 317050 TRUE FALSE 326472.1944 387650.0551 391633.7614 247296.6358 258733.0282 80591.3128 306303.3093 222312.3707 205088.1179 295575.9211 1.10452906 1.31150756 1.324985337 0.83666029 0.875352184 0.272658586 1.036293174 0.752132886 0.693859355 1 18.17316922 3.654621876 4.242587634 0.761793542 1.253683961 0.519615337 0.205438793 0.167280388 5.503316883 0.054056098 0.087097345 4514.627018 -3.654621876 0.491890419 NCVAIAADRR ddPTM_BT-474_Pertuzumab_2h_R1 5 NCVAIAADRR 10 1 P49720;A0A087WXQ8;A0A087WY10;A0A087WUL2 P49720 PSMB3 Proteasome subunit beta type-3 0 ;;;; 215.87 1.28E-08 3021070000 1732336 1615491 1449812 1235364 1180268 577999 1497352 1350566 1489622 1620349 FALSE TRUE 1664634.394 1569418.778 1711825.279 1299121.284 1218232.392 589686.5358 1515677.042 1322676.34 1320526.356 1510601.319 1.101968053 1.038936454 1.133207854 0.860002747 0.806455268 0.390365432 1.003360068 0.875595912 0.874172648 1 20.52669152 3.655678793 4.704216633 0.816917045 1.085877311 0.353170871 0.162012824 0.246941374 9.701422122 0.044843412 0.071428776 4525.627381 -3.655678793 0.268960266 HWMLDK ddPTM_BT-474_Pertuzumab_2h_R1 3 HWMLDK 6 0 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 ;; 132.8 0.014739 5444110000 9972500 9819700 8877700 7060500 7474600 5278900 7796800 6103100 9024600 9417800 FALSE TRUE 9582763.675 9539651.77 10482097.87 7424893.251 7715027.297 5385642.975 7892219.571 5977068.852 8000165.242 8779924.017 1.091440388 1.086530106 1.193871137 0.845667142 0.878712308 0.613404281 0.898893835 0.680765442 0.911188437 1 23.06577702 3.657826374 5.093442636 0.805770635 1.119581423 0.584086921 0.111238977 0.131478678 5.968383491 0.028151779 0.044544967 4548.061978 -3.657826374 0.313810788 MIKPFFHSLSEK ddPTM_BT-474_Pertuzumab_2h_R1 4 MIKPFFHSLSEK 12 1 P10599 P10599 TXN Thioredoxin 0 ;;; 193.23 1.85E-06 12560200000 26011600 25859700 20837500 20526900 19708600 12273960 22599500 21419700 25374000 26063800 FALSE TRUE 24995037.91 25122206.68 24603299.78 21586295.77 20342545.02 12522147.88 22876079.44 20977375.71 22493649.9 24298475.61 1.028666914 1.033900524 1.012544991 0.888380659 0.837194289 0.515347056 0.941461506 0.863320648 0.925722677 1 24.53436247 3.657856144 2.742074195 0.834636291 1.030727342 0.294965151 0.12245791 0.335527441 4.916807858 0.034948266 0.061241484 4548.373748 -3.657856144 0.196091051 GSGTAEVELK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSGTAEVELK 10 0 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 191.45 1.84E-06 571200000 655690 619220 537630 661300 621720 609370 716900 737870 734390 696940 FALSE TRUE 630064.9099 601560.4519 634791.7005 695429.7723 641718.1884 621691.8789 725673.6366 722632.7266 651025.126 649735.633 0.969725036 0.92585418 0.97699998 1.070327279 0.987660451 0.956838208 1.116875233 1.112195007 1.001984643 1 19.3094933 3.658835675 0.663186671 1.060416422 0.931844426 0.249218776 0.053939462 1.342792961 1.045786268 0.031881082 0.109238193 4558.643971 -3.658835675 -0.128571996 EAQLYAAQAHLK ddPTM_BT-474_Pertuzumab_2h_R1 5 EAQLYAAQAHLK 12 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;E9PI86 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;;; 221.8 2.63E-11 2488750000 3985100 3799840 3188180 3213230 3141530 2535610 3500600 3450840 3786480 3889060 FALSE TRUE 3829357.886 3691472.284 3764355.047 3379065.185 3242580.166 2586881.771 3543441.39 3379578.948 3356654.665 3625650.502 1.056185058 1.018154475 1.038256458 0.931988669 0.894344384 0.713494522 0.977325693 0.932130371 0.925807565 1 21.78980843 3.659277987 3.374107449 0.902360606 1.037142291 0.39028711 0.072916695 0.256902808 5.651858213 0.020604515 0.034541529 4563.289132 -3.659277987 0.134781685 STT(ph)PTSSPFR ddPTM_BT-474_Pertuzumab_2h_R1 3 STTPTSSPFR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.071)T(0.028)T(0.899)PT(0.002)SSPFR;S(0.004)T(0.066)T(0.927)PT(0.002)SSPFR;ST(0.001)T(0.997)PT(0.001)SSPFR 211.84 5.75E-07 4867290000 5518350 5871470 4692740 4519050 4388010 3063040 4986250 4945860 5242720 5485810 TRUE FALSE 5302686.781 5704021.424 5540822.507 4752278.712 4529154.327 3124976.767 5047273.219 4843726.263 4647588.405 5114251.202 1.036845194 1.115318978 1.08340836 0.929222778 0.885594811 0.6110331 0.986903658 0.947103705 0.908752469 1 22.28609159 3.659788323 3.44125819 0.886636969 1.084077393 0.401238173 0.103155705 0.248725766 5.686436203 0.02952454 0.049326609 4568.654575 -3.659788323 0.197440424 NWQWWR ddPTM_BT-474_Pertuzumab_2h_R1 2 NWQWWR 6 0 P35579;P35579-2;P35749;P35749-2;P35749-4;P35749-3 P35579;P35749 MYH9;MYH11 Myosin-9;Myosin-11 0 ; 122.51 0.044642 1147440000 1923850 1988230 1689480 1339550 1237690 893140 1341640 1395850 1519530 1806440 FALSE TRUE 1848663.815 1931527.627 1994806.618 1408684.336 1277501.423 911199.9027 1358059.392 1367025.21 1347039.325 1684088.21 1.097723863 1.146927825 1.184502455 0.836467073 0.758571561 0.541064237 0.806406329 0.811730171 0.799862689 1 20.68353628 3.659898961 4.279394892 0.772013598 1.14402242 0.691832094 0.106843725 0.117143347 4.002473205 0.028849481 0.046544157 4569.818601 -3.659898961 0.372008823 DAEGLQELALAPCHEWLSDEDLVPVLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DAEGLQELALAPCHEWLSDEDLVPVLAR 28 0 X6RJB2;X6RGT4;X6RHD7;A0A0C4DFV0;Q9H469 X6RJB2 FBXL15 F-box/LRR-repeat protein 15 0 95.794 0.0021405 17874000 14220 12240 10022 13108 13965 17099 14558 12010 12595 15628 FALSE TRUE 13664.26668 11890.92718 11833.19834 13784.50545 14414.19691 17444.7535 14736.16516 11761.9893 11165.2684 14569.50164 0.937867816 0.816151951 0.812189643 0.946120587 0.989340422 1.197347303 1.011439205 0.807302102 0.766345252 1 13.83066391 3.6603342 6.600626658 0.9572993 0.851768278 0.146713995 0.115190519 0.529851874 37.23365803 0.034806179 0.054301823 4574.400655 -3.6603342 -0.105531022 LPVDSVFNKFEDEDSDDVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPVDSVFNKFEDEDSDDVPR 20 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 213.03 1.04E-22 291090000 652070 637110 567050 653000 651510 662270 681580 747950 837160 824760 FALSE TRUE 626586.3835 618940.2466 669528.549 686701.4083 672466.4108 675661.5532 689921.3799 732504.5711 742129.1065 768898.2706 0.814914544 0.804970268 0.8707635 0.893097871 0.874584372 0.878739853 0.897285644 0.952667731 0.965185038 1 19.55243321 3.660949955 0.18677978 1.033541901 0.686324685 0.897143557 0.01899324 3.257703787 0.173012953 0.065292832 0.283073449 4580.890968 -3.660949955 -0.347217216 CPLLKPWALTFSYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 CPLLKPWALTFSYGR 15 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 198.74 7.09E-09 3503800000 1576260 1559030 1237540 1251290 1271390 996610 1261100 1295520 1470540 1367100 FALSE TRUE 1514658.017 1514567.991 1461191.007 1315869.227 1312285.414 1016762.137 1276533.719 1268767.059 1303610.464 1274505.099 1.188428369 1.188357733 1.146477176 1.032455051 1.029643126 0.79777016 1.001591692 0.995497829 1.022836601 1 20.28150571 3.661179339 1.752732891 0.968923039 1.190568675 0.683853919 0.061482265 0.212404079 1.272258189 0.018942461 0.038844701 4583.311123 -3.661179339 0.221645636 QQFVEYDKNSDDTVTWDEYNIQMYDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQFVEYDKNSDDTVTWDEYNIQMYDR 26 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 140.57 2.86E-07 160480000 131410 147720 116780 110390 97078 108730 102310 107090 135660 151380 FALSE TRUE 126274.3519 143507.1702 137884.7438 116087.2411 100200.602 110928.5951 103562.1004 104878.5541 120260.4455 141126.8978 0.894757512 1.016866186 0.977026676 0.822573464 0.710003576 0.786020219 0.733822553 0.743150709 0.852144045 1 17.10663346 3.661612219 4.208104777 0.781921873 0.968770424 0.407418467 0.083519646 0.170770682 5.705041154 0.02103369 0.034040283 4587.881784 -3.661612219 0.186848551 ALEHFTDLYDIK ddPTM_BT-474_Pertuzumab_2h_R1 4 ALEHFTDLYDIK 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 234.17 5.15E-16 9372880000 7858660 8259590 8120620 9504070 9227790 8524500 10690550 10401120 12723460 13917470 FALSE TRUE 7551534.879 8024034.58 9588196.676 9994576.192 9524610.246 8696871.231 10821384.15 10186333.24 11279146.16 12974827.36 0.582014286 0.618430932 0.738984528 0.770305139 0.734083775 0.670288011 0.834029143 0.785084299 0.869309922 1 23.62921201 3.662154246 0.070023796 1.392627703 1.72E-18 0.833438345 0.047707426 32.5403112 0.541393833 3.715909793 7.23851551 4593.611327 -3.662154246 -1.392627703 EFPDVLECTVSHAVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFPDVLECTVSHAVEK 16 0 P48507 P48507 GCLM Glutamate--cysteine ligase regulatory subunit 0 200.55 3.53E-11 33219000 60906 63270 53043 59674 64402 69511 65555 67325 70628 75205 FALSE TRUE 58525.72618 61465.60155 62629.05004 62753.78229 66473.54882 70916.56005 66357.2817 65934.71522 62610.60554 70111.29836 0.834754562 0.876686112 0.89328042 0.895059481 0.948114646 1.011485477 0.946456324 0.940429243 0.893017345 1 16.09735933 3.662617194 1.32738776 0.954388465 0.855290746 0.601432669 0.0332449 0.342059276 1.171337916 0.011090984 0.026489594 4598.510619 -3.662617194 -0.099097719 KVEDLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVEDLAR 7 1 Q9NVP1;H7C452 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 ; 101.64 0.014284 895050000 1294490 1287250 1101770 902570 869730 344860 1159400 957740 1027180 1148220 FALSE TRUE 1243899.9 1250538.89 1300884.348 949151.7459 897705.6553 351833.3055 1173589.084 937962.3343 910578.8327 1070450.037 1.162034525 1.16823658 1.215268628 0.886684771 0.838624527 0.328677933 1.096351108 0.876231774 0.850650475 1 20.02978603 3.662776498 4.147636299 0.827249626 1.181486116 0.409381876 0.188880402 0.22376329 7.316652337 0.052021582 0.08441253 4600.197717 -3.662776498 0.35423649 YIMIFR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIMIFR 6 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 141.66 0.027043 312460000 676770 828580 669710 364110 303060 126656 346090 290020 358960 572760 FALSE TRUE 650321.0802 804949.7097 790741.4946 382901.7607 312808.2001 129217.0711 350325.5529 284030.9857 318212.3657 533966.455 1.217906245 1.507491158 1.480882342 0.717089542 0.585819947 0.241994736 0.656081575 0.531926646 0.595940742 1 19.02638959 3.6628305 4.048192156 0.569784565 1.415491312 0.781393938 0.189833914 0.089249746 2.790972852 0.049059388 0.079891252 4600.769762 -3.6628305 0.845706747 KEDMTYAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEDMTYAVR 9 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 141.88 0.00016942 3188500000 3016630 3144060 2880820 2539220 2566840 1787490 3154810 2752810 2950310 3230520 FALSE TRUE 2898736.765 3054394.487 3401448.257 2670269.449 2649404.74 1823634.273 3193419.508 2695963.512 2615403.178 3011714.003 0.962487395 1.014171493 1.12940613 0.886627829 0.879699977 0.605513761 1.060332922 0.895159205 0.868410206 1 21.52215335 3.662966972 9.574166273 0.880598242 1.033110278 0.25613066 0.117150872 0.628547585 76.47212889 0.031172208 0.04833265 4602.21573 -3.662966972 0.152512036 THILLFLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 THILLFLPK 9 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 77.677 0.025556 0 153690 184640 150380 95231 100530 53517 127170 39952 132670 123310 FALSE TRUE 147683.6249 179374.248 177557.0112 100145.8833 103763.6387 54599.15041 128726.3445 39126.97724 117609.8578 114958.1039 1.284673459 1.560344525 1.544536707 0.871151141 0.902621349 0.474948251 1.119767465 0.340358582 1.023067134 1 16.81074865 3.663598649 4.050331501 0.763265361 1.475041699 0.594244333 0.241874651 0.134966208 4.237111307 0.062490975 0.101799508 4608.914471 -3.663598649 0.711776338 GPSWDPFR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;; 110.81 0.0078046 4087890000 5238100 5501900 4342330 3461430 2754320 749920 5131200 2794320 3615770 4991400 FALSE TRUE 5033389.261 5344991.199 5127085.626 3640074.817 2842915.204 765083.8962 5193997.161 2736616.316 3205322.948 4653328.032 1.081675142 1.148638386 1.101810487 0.782251926 0.610942359 0.164416497 1.116189773 0.588098732 0.688823768 1 22.14983146 3.664724346 3.307442373 0.674719637 1.120623378 0.374444755 0.240059863 0.245035233 5.226996022 0.064368448 0.108738182 4620.876332 -3.664724346 0.44590374 LLEEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEEFR 6 0 Q6N069;Q6N069-5;Q6N069-4;Q6N069-3;Q6N069-2 Q6N069 NAA16 "N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 ; 112.66 0.062352 352000000 663650 1197710 709550 764640 764120 674740 759950 750510 807080 895050 FALSE TRUE 637713.8243 1163552.483 837781.4689 804103.162 788698.6138 688383.7051 769250.4954 735011.7062 715463.662 834427.4663 0.764253156 1.394432147 1.004019526 0.96365855 0.945197331 0.824977284 0.92189019 0.880857517 0.857430623 1 19.67042712 3.664937125 2.322974026 0.897652557 1.094214313 0.159401786 0.149840754 0.417137638 4.391431767 0.039441764 0.07280441 4623.140854 -3.664937125 0.196561756 RDDFCK ddPTM_BT-474_Pertuzumab_2h_R1 3 RDDFCK 6 1 P32456;H3BNS1;Q9H0R5-4;P32455;Q9H0R5 P32456 GBP2;GBP3;GBP1 Interferon-induced guanylate-binding protein 2;Guanylate-binding protein 3;Interferon-induced guanylate-binding protein 1 0 ;; 97.068 0.066531 793840000 943340 936010 762130 965210 970740 961420 981720 1109810 1144270 1096370 FALSE TRUE 906473.2299 909315.9112 899863.8445 1015024.604 1001964.734 980860.5711 993734.583 1086892.036 1014377.267 1022111.883 0.886863018 0.889644202 0.880396617 0.993066043 0.980288704 0.959641099 0.972236601 1.063378729 0.99243271 1 19.9631217 3.665049801 0.695827454 1.014701393 0.858539905 0.709737021 0.030284549 0.564422178 0.488096087 0.016779092 0.057152881 4624.340466 -3.665049801 -0.156161488 FFDQYR ddPTM_BT-474_Pertuzumab_2h_R1 1 FFDQYR 6 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 118.01 0.05172 81500000 275520 292760 259650 158610 150660 47307 219310 147070 148260 190500 FALSE TRUE 264752.3738 284410.7714 306574.5309 166795.8811 155506.1157 48263.57995 221993.9814 144032.9531 131430.1464 177597.2653 1.49074578 1.60143666 1.726234525 0.939180459 0.875610981 0.271758576 1.249985359 0.811008845 0.740046003 1 17.43824984 3.665190259 4.722939703 0.826904359 1.60561521 0.687676054 0.236802369 0.11819585 4.96486495 0.063003359 0.100685233 4625.836294 -3.665190259 0.778710851 MLQHIDYR ddPTM_BT-474_Pertuzumab_2h_R1 5 MLQHIDYR 8 0 P14678-2;P14678;P14678-3;J3QLE5;P63162;P63162-2;J3KRY3;S4R3P3 P14678-2;S4R3P3 SNRPB;SNRPN Small nuclear ribonucleoprotein-associated proteins B and B;Small nuclear ribonucleoprotein-associated protein N 0 ;;;; 146.58 0.00055098 3224640000 2742780 2937760 2570710 1785790 1829420 863780 2445510 1561410 1812340 2219300 FALSE TRUE 2635589.125 2853977.961 3035294.482 1877954.836 1888264.956 881246.2234 2475438.883 1529166.338 1606610.761 2068984.834 1.273856184 1.379409802 1.467045303 0.907669696 0.912652874 0.425931698 1.196450956 0.739090163 0.776521285 1 20.98049164 3.66569016 4.84870717 0.835276201 1.373749805 0.610981415 0.191102875 0.133126802 5.886194334 0.049332436 0.078634199 4631.163997 -3.66569016 0.538473603 S(ph)KSPASTSSVNGTPGSQLSTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSPASTSSVNGTPGSQLSTPR 22 1 O15075-2;O15075;Q5VZY9 O15075-2 DCLK1 Serine/threonine-protein kinase DCLK1 1 S(0.607)KS(0.383)PAS(0.004)T(0.006)SSVNGTPGSQLSTPR;S(0.498)KS(0.498)PAS(0.002)T(0.001)SSVNGTPGSQLSTPR 187.45 1.72E-17 2262700000 725415 791280 588811 753152 851540 675533 780174 924440 872400 681674 TRUE FALSE 697064.9798 768713.4691 695222.2457 792022.265 878930.5574 689192.7401 789722.0028 905349.9909 773368.8094 635503.6128 1.096870208 1.209613059 1.093970564 1.246290735 1.383045729 1.084482804 1.242671146 1.424618165 1.216938494 1 19.2775408 3.666623649 7.321263332 1.257601291 1.141332892 0.077788743 0.12280216 0.500396889 44.77237585 0.032432094 0.05048073 4641.129095 -3.666623649 -0.1162684 LPPS(ph)SPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPPSSPQK 8 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LPPS(0.751)S(0.249)PQK;LPPS(0.5)S(0.5)PQK 90.15 0.014056 1226730000 1056880 999870 889680 796990 820530 476570 920010 914350 923970 970220 TRUE FALSE 1015575.961 971354.6866 1050464.967 838122.7494 846923.0926 486206.5719 931269.3576 895468.353 819084.7992 904506.1352 1.1227961 1.073906134 1.161368537 0.926608142 0.936337588 0.537538169 1.029588768 0.990008048 0.905560247 1 19.78677076 3.667228396 5.28952084 0.900971107 1.114514443 0.362682756 0.131124495 0.247874478 12.99352758 0.036673318 0.058020769 4647.596289 -3.667228396 0.213543337 GGDLMAYDRR ddPTM_BT-474_Pertuzumab_2h_R1 7 GGDLMAYDRR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;; 145.25 4.93E-05 12449000000 4758800 5393260 3783100 3719250 3326720 2109434 4131860 3538320 3671840 3768910 FALSE TRUE 4572820.835 5239449.505 4466790.325 3911200.938 3433726.97 2152088.201 4182426.939 3465252.456 3255028.117 3513638.369 1.301448913 1.491174946 1.271272071 1.113148403 0.977256795 0.612495646 1.190340752 0.986229114 0.926398159 1 21.74453428 3.667643036 2.035108977 0.953907435 1.392946925 0.625738796 0.141552756 0.213550318 1.723787733 0.041514031 0.080417447 4652.035669 -3.667643036 0.43903949 NINDAWVCTNDMFR ddPTM_BT-474_Pertuzumab_2h_R1 4 NINDAWVCTNDMFR 14 0 P61970 P61970 NUTF2 Nuclear transport factor 2 0 ;;; 250.26 5.94E-18 1214170000 1210040 1238890 959880 889594 852301 726687 775125 910791 984620 1028359 FALSE TRUE 1162750.299 1203558.07 1133351.668 935506.0529 879716.0357 741381.109 784611.2116 891982.8476 872850.0655 958707.329 1.212831345 1.255396755 1.18216648 0.975799417 0.917606457 0.77331328 0.818405355 0.930401615 0.910444761 1 19.87073094 3.667932391 2.087627953 0.880420544 1.237732096 0.858620231 0.059243808 0.10956003 0.930723614 0.017613602 0.033804218 4655.136191 -3.667932391 0.357311552 KGDIIQLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGDIIQLQR 9 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 115.42 0.0023715 1470860000 1176550 1249060 1048230 928960 902670 372730 1282050 973120 1080130 1279770 FALSE TRUE 1130569.125 1213438.032 1237668.479 976903.7369 931705.2003 380266.856 1297740.111 953024.7319 957518.1707 1193090.038 0.94759749 1.017054869 1.037363853 0.818801353 0.78091776 0.318724358 1.087713475 0.798786933 0.802553152 1 20.18627149 3.668346494 4.993125018 0.788444961 1.002181829 0.187343483 0.189785504 0.343392496 16.35655637 0.050922563 0.08101806 4659.577012 -3.668346494 0.213736868 LHFFMPGFAPLTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 LHFFMPGFAPLTSR 14 0 Q5JP53;P07437;Q5ST81;A6NNZ2;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ;; 127.79 5.88E-05 1481870000 2337690 2589180 2346390 1091164 877112 205700 1688960 591344 1035276 1559201 FALSE TRUE 2246330.49 2515339.121 2770434.868 1147479.105 905325.1041 209859.3949 1709629.998 579132.5398 917755.8087 1453594.927 1.545362087 1.730426458 1.905919466 0.789407753 0.622818013 0.14437268 1.176139216 0.39841398 0.631369711 1 20.47119386 3.66845859 4.958208286 0.636593745 1.727049481 0.742327736 0.282575436 0.095853899 4.510588205 0.072484785 0.115409124 4660.779851 -3.66845859 1.090455736 MAQEVLTHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 MAQEVLTHLK 10 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;C9JF49;H7BZC5 O14980 XPO1 Exportin-1 0 92.445 0.0094629 231410000 1115900 1229200 1022600 960140 936890 611270 1198700 1003300 1205400 1230000 FALSE TRUE 1072289.394 1194144.42 1207406.568 1009692.94 967025.9177 623630.2982 1213370.049 982581.5044 1068568.045 1146691.004 0.935116252 1.041382914 1.052948495 0.88052748 0.843318657 0.543852089 1.058149096 0.856884288 0.931870959 1 20.12904525 3.66856478 5.977062159 0.86295831 1.012644452 0.18179677 0.131349162 0.348228323 23.00040397 0.035072035 0.055043657 4661.919608 -3.66856478 0.149686143 KKPPQQQHHK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKPPQQQHHK 10 2 O75179-6;O75179-2;O75179;O75179-4;H0YLQ3;A0A1W2PQ15;O75179-5;O75179-3 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 0 72.643 0.01524 58753000 78750 62317 70269 36172 39774 8038.5 55885 13955 52630 62344 FALSE TRUE 75672.36294 60539.78017 82968.17143 38038.84125 41053.36683 8201.043978 56568.93735 13666.82437 46655.66304 58121.38535 1.301971081 1.04160938 1.427498173 0.654472378 0.706338409 0.141102005 0.973289556 0.235142784 0.802727994 1 15.82678147 3.669053063 6.127150836 0.590060591 1.234156417 0.494479456 0.279851093 0.162171681 11.24905683 0.069433658 0.108838504 4667.16401 -3.669053063 0.644095827 GDLSRPEDADTSGPCCEHTQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDLSRPEDADTSGPCCEHTQEK 22 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 0 211.17 2.17E-23 536510000 308220 327440 248660 332680 351980 358150 353480 365230 393700 363120 FALSE TRUE 296174.4216 318101.7318 293598.3934 349849.6547 363301.7564 365392.0384 357805.994 357687.8729 349008.8265 338525.559 0.874895303 0.939668286 0.86728575 1.033451228 1.073188558 1.079363223 1.056954149 1.05660522 1.030967433 1 18.36890524 3.669234661 5.347861864 1.053946639 0.898706201 0.861131215 0.028151763 0.065619712 3.576889665 0.007081093 0.011200781 4669.115975 -3.669234661 -0.155240437 SNILSDNPDFS(ph)DEADIIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNILSDNPDFSDEADIIK 18 0 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 SNILSDNPDFS(1)DEADIIK 147.9 7.69E-08 19810000 55911 56423 45131 44974 45492 39303 40999 53256 50864 45176 TRUE FALSE 53725.93631 54813.87128 53287.17563 47295.11353 46955.29149 40097.73359 41500.75803 52156.24499 45090.13196 42116.18928 1.275659959 1.301491712 1.265242097 1.122967541 1.114898862 0.952074114 0.9853873 1.238389462 1.070612815 1 15.36208729 3.669244235 2.200835943 1.073366475 1.291814974 0.629625635 0.075490977 0.237042826 2.238909423 0.024065984 0.045384361 4669.218904 -3.669244235 0.218448499 NTIEMQAITALAHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 NTIEMQAITALAHLR 15 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 105.39 0.0013189 64275000 98575 104540 78183 87784 80978 82616 91292 85779 93479 92296 FALSE TRUE 94722.58002 101558.6216 92312.40727 92314.54276 83582.73091 84286.55212 92409.2588 84007.63367 82867.65582 86044.70971 1.100853037 1.180300589 1.072842335 1.072867153 0.971387215 0.97956693 1.07396793 0.976325377 0.963076709 1 16.39279887 3.66990414 1.70562726 0.997054333 1.136764453 0.681744258 0.0385205 0.206431832 1.169653875 0.011340681 0.023767808 4676.319109 -3.66990414 0.13971012 APPARPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 APPARPVK 8 1 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ; 67.981 0.052614 1448330000 2273500 1857700 1771020 1351430 1375300 1172530 1353370 1341740 1479580 1447710 FALSE TRUE 2184649.107 1804720.215 2091082.71 1421177.464 1419537.774 1196239.36 1369932.947 1314032.6 1311624.281 1349655.312 1.618671884 1.337171201 1.549345741 1.052992902 1.051778006 0.886329531 1.015024306 0.973606067 0.971821671 1 20.36415957 3.670034386 4.380858796 0.984615449 1.486518491 0.89815991 0.078567842 0.058861436 2.210345654 0.019937416 0.03223285 4677.721769 -3.670034386 0.501903042 MSCFSRPS(ph)MSPT(ph)PLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MSCFS(0.002)RPS(0.997)MS(0.058)PT(0.943)PLDR 152.94 1.25E-05 253640000 105450 101900 82318 75654 65099 60884 82251 72560 80186 82525 TRUE FALSE 101328.8974 98993.91177 97194.69375 79558.51201 67192.96846 62115.11619 83257.61234 71061.61064 71083.62145 76935.50824 1.31706282 1.286712911 1.263326856 1.034093539 0.873367447 0.807366034 1.082174073 0.92365167 0.923937764 1 16.23136198 3.67037368 2.829204466 0.935473989 1.298229247 0.840416447 0.069026047 0.100126404 1.570211771 0.019591181 0.034403184 4681.377678 -3.67037368 0.362755258 DCGATWVVLGHSER ddPTM_BT-474_Pertuzumab_2h_R1 6 DCGATWVVLGHSER 14 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;;;;; 196.33 2.50E-08 7689370000 5792150 6071190 4102570 4516000 3679200 3714600 3588140 3708030 4291820 4002700 FALSE TRUE 5565786.374 5898045.606 4843995.66 4749071.301 3797544.809 3789711.757 3632052.731 3631457.885 3804630.586 3731593.564 1.491530704 1.580570205 1.298103767 1.272665745 1.017673748 1.015574631 0.973324846 0.973165438 1.019572609 1 21.83136043 3.670458064 1.117809244 0.982671578 1.555730709 0.942069102 0.052433083 0.103818055 0.249154515 0.016771269 0.045089222 4682.28736 -3.670458064 0.573059131 NMGGPYGGGNYGPGGSGGS(ph)GGYGGR ddPTM_BT-474_Pertuzumab_2h_R1 7 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 NMGGPYGGGNYGPGGS(0.141)GGS(0.859)GGYGGR;NMGGPYGGGNYGPGGS(0.022)GGS(0.978)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGS(0.001)GGS(0.999)GGYGGR 502.26 7.91E-287 4921550000 2402952 2436008 1886890 1896090 1738962 1686854 1550972 2070038 2082399 2155826 TRUE FALSE 2309041.979 2366535.437 2227892.997 1993947.432 1794897.292 1720963.344 1569953.259 2027290.992 1846013.796 2009809.985 1.148885714 1.177492129 1.108509269 0.992107437 0.893068153 0.856281617 0.781145119 1.008697841 0.918501654 1 20.93862768 3.670686892 2.100083133 0.905803517 1.16183598 0.740854244 0.062530292 0.162995705 1.401142101 0.018827466 0.036145117 4684.755097 -3.670686892 0.256032463 AAGISLIVPGKSPT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGISLIVPGKSPTR 15 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 AAGISLIVPGKS(0.359)PT(0.641)R 153.21 4.35E-06 3220000000 1371100 1390400 1152900 1310100 1402900 1404900 1413300 1534500 1423600 1462100 TRUE FALSE 1317515.896 1350747.153 1361254.676 1377714.418 1448025.553 1433308.041 1430596.388 1502812.039 1261998.896 1363070.665 0.966579305 0.990959008 0.998667722 1.010743209 1.062326107 1.051528785 1.049539415 1.102519537 0.925849942 1 20.37842893 3.670722598 1.837851954 1.043236627 0.980690307 0.148233854 0.045023805 0.505935026 3.328675625 0.01309165 0.026523961 4685.140273 -3.670722598 -0.06254632 LKS(ph)IEER ddPTM_BT-474_Pertuzumab_2h_R1 4 LKSIEER 7 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 LKS(1)IEER;LKS(1)IEER;LKS(1)IEER;LKS(1)IEER 139.86 0.001613 2347250000 4967820 4955800 3858520 5111770 6348500 5430270 5128760 6038600 5135420 4682150 TRUE FALSE 4773672.102 4814465.436 4555840.396 5375589.062 6552705.268 5540073.78 5191527.299 5913900.8 4552468.651 4365023.81 1.0936188 1.102964301 1.043714902 1.231514259 1.501184313 1.269196692 1.189346846 1.354838154 1.042942456 1 22.05755809 3.670931045 6.053306422 1.259052181 1.08273301 0.169004329 0.137494045 0.29977389 20.84105784 0.035521171 0.055742834 4687.389523 -3.670931045 -0.17631917 YFQHLLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 YFQHLLGK 8 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 95.531 0.0095844 469960000 867810 1038600 776890 789190 741520 681600 799450 754380 1000800 1091900 FALSE TRUE 833895.0258 1008980.145 917291.3048 829920.1905 765371.6642 695382.419 809233.9082 738801.7894 887193.3797 1017944.64 0.819194868 0.991193533 0.901121012 0.815290103 0.751879458 0.683124004 0.794968485 0.725777965 0.871553663 1 19.95722767 3.671025621 3.41856213 0.780932453 0.914225089 0.162241526 0.09220102 0.295074018 6.788955731 0.02360904 0.039801831 4688.410403 -3.671025621 0.133292636 YNQLLR ddPTM_BT-474_Pertuzumab_2h_R1 4 YNQLLR 6 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 148.53 0.025017 3944520000 4637420 5039200 3970910 3010130 2871480 2308520 2725600 2947380 3186690 3388750 FALSE TRUE 4456184.499 4895486.95 4688541.769 3165483.17 2963843.762 2355199.856 2758956.708 2886515.573 2824950.311 3159226.944 1.410530037 1.549583818 1.484078812 1.001980303 0.938154749 0.745498787 0.873301208 0.913677816 0.89419037 1 21.59114015 3.671168891 3.143989182 0.887028675 1.497734234 0.935510048 0.069195204 0.054929479 1.067170957 0.019217361 0.032963481 4689.95733 -3.671168891 0.61070556 KRVPDHHPC ddPTM_BT-474_Pertuzumab_2h_R1 2 KRVPDHHPC 9 2 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 111.04 0.0012316 152242000 431060 470620 322870 284740 241320 129367 354890 75957 365020 404570 FALSE TRUE 414213.6986 457198.3784 381219.7912 299435.4655 249082.277 131982.8894 359233.25 74388.46141 323584.4599 377168.1135 1.098220353 1.21218725 1.010742365 0.793904508 0.660401206 0.349931197 0.952448622 0.197228925 0.857931644 1 18.52484819 3.671386938 1.781891414 0.604704496 1.156625142 0.386848852 0.241792434 0.30375833 1.87837508 0.067900849 0.139595151 4692.31261 -3.671386938 0.551920646 QTQT(ph)PDLLPEALEAQVLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 QTQTPDLLPEALEAQVLPR 19 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 QT(0.002)QT(0.998)PDLLPEALEAQVLPR;QT(0.066)QT(0.934)PDLLPEALEAQVLPR;QT(0.144)QT(0.856)PDLLPEALEAQVLPR;QTQT(1)PDLLPEALEAQVLPR 254.32 7.51E-30 132027000 62779.6 65925 53769.6 67153 72352 70307 70530.8 83056 79214 74873 TRUE FALSE 60326.10383 64044.88355 63486.96282 70618.77438 74679.26779 71728.65571 71393.97703 81340.86458 70221.95881 69801.78502 0.864248727 0.917525011 0.909532081 1.011704419 1.06987619 1.027604891 1.02281019 1.165312098 1.006019528 1 16.09097631 3.671403275 1.825354752 1.062851005 0.887726681 0.671042562 0.046974406 0.199310785 1.293434719 0.014369784 0.029221382 4692.489127 -3.671403275 -0.175124324 CSDVSELS(ph)SSPPGPYHQEPYVCKPEER ddPTM_BT-474_Pertuzumab_2h_R1 1 CSDVSELSSSPPGPYHQEPYVCKPEER 27 1 Q9Y478;F5H610;F5H2X8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 CSDVSELS(0.979)S(0.011)S(0.011)PPGPYHQEPYVCKPEER 380.01 9.59E-128 321110000 210150 191680 164820 200730 213330 214150 215470 216670 250300 223690 TRUE FALSE 201937.1057 186213.4741 194606.6404 211089.6994 220191.9532 218480.2597 218106.9863 212195.6888 221886.9933 208539.2771 0.968340873 0.892941976 0.933189388 1.012229937 1.055877609 1.047669594 1.045879651 1.017533444 1.064005767 1 17.66995961 3.671503206 3.360700373 1.038479124 0.926125366 0.793062962 0.024429139 0.094414243 2.100244209 0.006308248 0.010674605 4693.568988 -3.671503206 -0.112353758 LRPVNQNK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRPVNQNK 8 1 B4DXZ6;P51114;P51114-3;C9JZE0;C9JY20;C9J5B4;C9IZ22;C9JAJ4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 75.692 0.034412 690120000 748790 872090 638600 595710 508360 426880 651830 463500 784770 791480 FALSE TRUE 719526.459 847218.8471 754009.2256 626454.6645 524711.8611 435511.8061 659807.2905 453928.563 695686.1996 737872.3546 0.975136762 1.14819161 1.021869461 0.849001403 0.711114677 0.590226485 0.894202481 0.615185757 0.9428273 1 19.49301174 3.671837904 2.875711651 0.761470747 1.065822415 0.415923656 0.133023035 0.20911729 3.392175084 0.034644472 0.060669651 4697.18758 -3.671837904 0.304351668 EIHQFNR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIHQFNR 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 143.02 0.00245 1751050000 1999780 2257030 1739950 1750420 1650930 1734860 1665790 1755510 2050440 2259950 FALSE TRUE 1921626.387 2192661.714 2054397.67 1840759.386 1704033.663 1769940.058 1686176.436 1719258.105 1817682.647 2106881.574 0.912071381 1.040714268 0.975089296 0.873689062 0.808794231 0.840075721 0.800318564 0.816020286 0.862736031 1 21.00667779 3.672041493 3.501220124 0.839535204 0.984096238 0.426835294 0.061536383 0.176673897 4.274103718 0.015535214 0.026088835 4699.390052 -3.672041493 0.144561034 EAPSPLMIHSPQMS(ph)QFQSLTHQSPPQQNVQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 EAPS(0.001)PLMIHS(0.005)PQMS(0.263)QFQS(0.263)LT(0.263)HQS(0.204)PPQQNVQPK 45.47 0.047803 113810000 24608 19739 21596 22755 30139 26703 25357 30748 33326 29507 TRUE FALSE 23646.29215 19176.06305 25498.8776 23929.38828 31108.44831 27242.95296 25667.32655 30113.04305 29542.97219 27508.46461 0.859600581 0.697096814 0.926946595 0.869891818 1.130868216 0.990348002 0.933070126 1.0946828 1.073959329 1 14.747588 3.67290306 1.653912373 1.03448076 0.789134048 0.599331294 0.078019761 0.240391074 1.280069062 0.022658871 0.04837029 4708.722102 -3.67290306 -0.245346712 KMS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KMSPLR 6 1 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 KMS(1)PLR;KMS(1)PLR;KMS(1)PLR;KMS(1)PLR 85.731 0.033309 1421750000 2270520 2151390 1970480 1670610 1730110 906940 2077490 1725930 2019460 2298740 TRUE FALSE 2181785.568 2090034.464 2326589.569 1756830.382 1785760.559 925278.9482 2102914.944 1690288.942 1790219.367 2143044.292 1.018077683 0.97526424 1.085646982 0.819782582 0.833282152 0.431759134 0.981274606 0.788732621 0.835362747 1 21.03123024 3.673226793 6.260009209 0.798095949 1.020819784 0.301802842 0.147603547 0.26124155 19.86298861 0.038515317 0.060369013 4712.233398 -3.673226793 0.222723835 KLPEYNPR ddPTM_BT-474_Pertuzumab_2h_R1 3 KLPEYNPR 8 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 142.92 0.00097762 2138290000 1784420 1965070 1645310 1374800 1360300 933230 1494080 1459540 1661920 1746170 FALSE TRUE 1714682.894 1909028.128 1942654.117 1445753.593 1404055.285 952100.55 1512364.998 1429399.989 1473265.809 1627900.351 1.053309493 1.17269348 1.193349529 0.888109393 0.862494614 0.584864147 0.929027995 0.878063567 0.905009823 1 20.63458096 3.673266131 5.185195159 0.850676842 1.142895307 0.580243243 0.107307948 0.141679294 7.571764151 0.029074651 0.046187248 4712.66025 -3.673266131 0.292218465 YMHSGPVVAMVWEGLNVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 YMHSGPVVAMVWEGLNVVK 19 0 Q32Q12;P22392-2;J3KPD9;E7ERL0;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 186.68 2.00E-14 732300000 470380 491200 379280 342490 423480 374440 364470 317830 449080 446710 FALSE TRUE 451997.0296 477191.4569 447824.333 360165.9499 437101.6188 382011.4333 368930.4929 311266.6994 398102.3211 416453.9338 1.085347004 1.145844518 1.075327417 0.864839831 1.049579757 0.917295774 0.88588548 0.747421681 0.955933631 1 18.66779739 3.673573969 0.789838856 0.872405155 1.149365432 0.454764022 0.085197572 0.685079857 0.781052067 0.039593632 0.130102389 4716.001869 -3.673573969 0.276960277 YGEVEEMNVCDNLGDHLVGNVYVK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGEVEEMNVCDNLGDHLVGNVYVK 24 0 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ; 242.71 1.21E-37 549520000 291090 276014 242760 276997 278803 293600 305020 294390 352510 316200 FALSE TRUE 279713.881 268142.351 286632.1322 291292.8484 287770.9517 299536.7932 308752.926 288310.7436 312494.5426 294783.4924 0.948879053 0.909624718 0.972347976 0.988158618 0.976211217 1.016124718 1.047388792 0.978042364 1.060081554 1 18.16929621 3.674392614 0.878083718 1.01769832 0.923711961 0.616225238 0.026125995 0.485908636 0.697521674 0.010406246 0.032514712 4724.899918 -3.674392614 -0.093986359 STFSTNYR ddPTM_BT-474_Pertuzumab_2h_R1 8 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 183.74 0.00051576 12058250000 6719770 6932920 5554450 4722260 4568120 2656890 5444650 4569180 5567740 5848840 FALSE TRUE 6457153.959 6735199.91 6558262.673 4965976.405 4715057.728 2710614.136 5511283.255 4474824.836 4935713.497 5452692.857 1.184213769 1.235206179 1.202756664 0.910738333 0.864720947 0.497114766 1.010745223 0.820663286 0.905188249 1 22.37853746 3.67453245 3.098940854 0.836911354 1.216869984 0.588965574 0.134054498 0.168587699 3.191097614 0.036388694 0.062775692 4726.421513 -3.67453245 0.37995863 GFAYVQFEDVR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFAYVQFEDVR 11 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 ;; 163.64 5.52E-05 317639000 395553 445360 348926 259865 263272 100492 354607 231029 243059 336313 FALSE TRUE 380094.3515 432658.7689 411984.69 273276.6638 271740.383 102524.0171 358946.7865 226258.1704 215467.9613 313534.221 1.212289843 1.379941135 1.314002308 0.871600755 0.866700873 0.326994664 1.144840858 0.72163788 0.687223106 1 18.25826339 3.674651316 3.332558471 0.781706443 1.316686129 0.555182833 0.205454503 0.171367165 3.765494983 0.054280276 0.092223319 4727.715303 -3.674651316 0.534979686 TS(ph)PPCS(ph)PANLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 T(0.015)S(0.985)PPCS(1)PANLSR;T(0.385)S(0.615)PPCS(1)PANLSR;T(0.241)S(0.759)PPCS(1)PANLSR 218 5.17E-11 1423910000 874660 868560 713200 773680 740960 781010 788480 858260 869280 916100 TRUE FALSE 840477.3202 843789.5192 842091.105 813609.7175 764793.6513 796802.5573 798129.6541 840536.6311 770602.9787 854051.731 0.984105868 0.987984086 0.985995431 0.952646881 0.895488673 0.932967557 0.934521441 0.984175315 0.902290752 1 19.70396393 3.675464968 4.408144914 0.941668238 0.98643194 0.302218813 0.03010893 0.265447097 10.40673565 0.008094029 0.013115843 4736.580995 -3.675464968 0.044763702 APS(ph)PEPAAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 APSPEPAAPR 10 0 P20749 P20749 BCL3 B-cell lymphoma 3 protein 1 APS(1)PEPAAPR;APS(1)PEPAAPR 117.14 0.0010466 1318130000 1486750 1432400 1379080 1249440 1300110 1404290 1363360 1454050 1466860 1444550 TRUE FALSE 1428646.166 1391549.354 1628310.433 1313923.748 1341929.219 1432685.706 1380045.208 1424023.359 1300348.202 1346709.342 1.060842249 1.033295984 1.209103095 0.975655034 0.996450516 1.063841812 1.024753571 1.05740958 0.965574502 1 20.36100708 3.675484372 24.99996785 1.018923152 1.094305582 0.373882994 0.052090983 248.4561417 98474.03791 0.013622943 0.021104574 4736.79263 -3.675484372 0.07538243 SKAEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKAEMR 6 1 P22059 P22059 OSBP Oxysterol-binding protein 1 0 83.377 0.052036 92737000 333610 350980 277190 274600 269150 158540 345860 298450 292290 336080 FALSE TRUE 320572.1524 340970.394 327284.3991 288772.1389 277807.4542 161745.7874 350092.7381 292286.9032 259110.4646 313317.0023 1.023155941 1.088260106 1.044579122 0.921661247 0.886665748 0.516236866 1.117375488 0.932879164 0.826991394 1 18.25726353 3.675550158 3.070497889 0.88156025 1.059045591 0.219538178 0.145242736 0.407897906 7.583353929 0.040905288 0.070767617 4737.510203 -3.675550158 0.177485341 ALIQYFSPYVSADMHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALIQYFSPYVSADMHR 16 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 126.07 0.00057267 0 214090 282510 202040 180150 173660 160150 210440 152680 176180 214210 FALSE TRUE 205723.1261 274453.0914 238553.1224 189447.5631 179245.9316 163388.3427 213015.4277 149527.1046 156180.785 199701.3659 1.030153826 1.374317547 1.194549278 0.948654318 0.897569883 0.818163371 1.066669858 0.74875354 0.782071691 1 17.60748467 3.675669286 3.134620709 0.87657994 1.222734419 0.583650095 0.118661928 0.160059739 3.105153503 0.031679694 0.054563755 4738.809889 -3.675669286 0.346154479 DRCPLPCIPTLIGT(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRCPLPCIPTLIGTPVK 17 1 Q9H0H5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 DRCPLPCIPTLIGT(1)PVK;DRCPLPCIPTLIGT(1)PVK 152.88 8.95E-07 913750000 1250740 1081160 1005780 966110 882910 854450 915340 1210770 1122870 1224720 TRUE FALSE 1201859.698 1050326.375 1187546.819 1015971.053 911309.602 871727.5644 926542.2047 1185767.176 995406.5051 1141768.624 1.052629818 0.919911752 1.040094109 0.889822186 0.798156109 0.763488807 0.811497343 1.038535437 0.871811052 1 20.12283889 3.677733144 7.751479402 0.880307621 0.995626455 0.292098985 0.086947026 0.42817116 49.60628687 0.025177799 0.039191681 4761.383294 -3.677733144 0.115318834 EPFHSILSVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EPFHSILSVLK 11 0 Q8NCW5-2;Q8NCW5;Q5T3I4 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 108.7 0.0020282 275390000 412950 474220 368340 294260 275010 93708 403870 283530 316710 397140 FALSE TRUE 396811.4575 460695.7099 434907.2317 309446.7939 283855.9464 95602.83996 408812.6819 277675.0064 280758.4086 370241.3541 1.071764278 1.244311865 1.174658711 0.835797488 0.766678123 0.258217616 1.104178875 0.74998377 0.758311857 1 18.49810652 3.677887306 3.683017508 0.762057832 1.175610551 0.409159843 0.210704548 0.218568322 5.948578838 0.056622308 0.094597081 4763.073754 -3.677887306 0.413552719 SIEEAMNEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIEEAMNEIR 10 0 I3L0X5;O75391 I3L0X5 SPAG7 Sperm-associated antigen 7 0 81.972 0.045157 42015000 27711 40209 30348 29425 28814 33332 28459 32768 29384 35028 FALSE TRUE 26628.02348 39062.27869 35832.55869 30943.62778 29740.82848 34005.99588 28807.28976 32091.32935 26048.45151 32655.52236 0.815421759 1.196192125 1.097289405 0.94757718 0.910744227 1.041355134 0.882156759 0.982722891 0.797673705 1 14.99503937 3.678162159 7.912741389 0.93893657 1.052140248 0.142403421 0.109085916 0.494360552 59.46411757 0.027419443 0.042663142 4766.089123 -3.678162159 0.113203678 GKAEEQAVR ddPTM_BT-474_Pertuzumab_2h_R1 6 GKAEEQAVR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 146.11 8.72E-05 1962720000 2784020 2837640 2342780 2190800 2140920 1299423 2628390 2389060 2614300 2740280 FALSE TRUE 2675217.421 2756713.286 2766172.461 2303867.451 2209784.636 1325698.223 2660557.023 2339725.076 2317535.624 2554678.395 1.04718364 1.079084276 1.082786963 0.901822889 0.864995234 0.518929594 1.041444993 0.915858952 0.907173141 1 21.28471025 3.678248073 4.219039684 0.870190078 1.071589659 0.30622253 0.131958796 0.271201861 9.846634267 0.036661434 0.059891509 4767.03206 -3.678248073 0.201399582 QLS(ph)LEGSGLGVEDLK ddPTM_BT-474_Pertuzumab_2h_R1 4 QLSLEGSGLGVEDLK 15 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 QLS(1)LEGSGLGVEDLK;QLS(1)LEGSGLGVEDLK;QLS(0.858)LEGS(0.142)GLGVEDLK;QLS(1)LEGSGLGVEDLK 267.39 2.07E-25 466995000 506927 467484 437762 619041 720905 526650 731000 873119 772576 762601 TRUE FALSE 487115.7324 454151.814 516875.3314 650989.7802 744093.564 537299.2238 739946.1967 855088.7875 684876.4114 710949.355 0.685162352 0.638796295 0.72702131 0.915662664 1.046619648 0.755748943 1.040786086 1.202742195 0.963326581 1 19.43938727 3.678288198 0.654881763 1.065005106 0.576846214 0.625733324 0.10810934 0.735812189 0.550174978 0.063942683 0.226525337 4767.472518 -3.678288198 -0.488158892 GFCFITFK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFCFITFK 8 0 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 135.16 0.0019674 137700000 174330 206840 180160 166360 169640 137670 232760 166850 158070 211070 FALSE TRUE 167516.9909 200941.1257 212718.9196 174945.8595 175096.6247 140453.7817 235608.5865 163404.4892 140126.5563 196774.0409 0.851316516 1.021177005 1.081031414 0.889069812 0.889835996 0.713782067 1.197356041 0.830416901 0.712119117 1 17.58618038 3.678294751 24.50254338 0.89128585 0.98817537 0.084451863 0.141866058 481.9182987 195934.7972 0.037301033 0.05778653 4767.544449 -3.678294751 0.09688952 LNLKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNLKPR 6 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 91.26 0.043863 559170000 929770 1066400 897710 642660 553280 179650 950910 606240 735220 955410 FALSE TRUE 893433.5605 1035987.316 1059946.166 675827.7596 571076.7537 183282.6461 962547.521 593720.9321 651760.9079 890699.2297 1.00306987 1.163116888 1.190015811 0.758760912 0.641155549 0.205773891 1.080665043 0.666578473 0.731740734 1 19.76457882 3.678393097 5.350801484 0.704254719 1.123038472 0.388313913 0.224919284 0.199759001 11.96977287 0.059464757 0.094411792 4768.624179 -3.678393097 0.418783753 SATTTPSGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 1 SATTTPSGS(1)PR;SATTTPS(0.001)GS(0.999)PR;SATT(0.002)T(0.002)PS(0.091)GS(0.905)PR 158.06 3.18E-05 412626000 228332 270306 188109 304373 302098 324833 367817 343613 329573 342089 TRUE FALSE 219408.533 262597.1375 222104.4808 320081.727 311815.2565 331401.3458 372318.4545 336517.2715 292161.2547 318919.0073 0.687975718 0.823397576 0.696429111 1.003645815 0.977725533 1.039139525 1.167438898 1.055180982 0.916098596 1 18.28283056 3.678502352 5.115185405 1.036247558 0.744581131 0.777191686 0.070139833 0.094130226 5.143554927 0.019509263 0.03111025 4769.823968 -3.678502352 -0.291666428 EYYDHLPELK ddPTM_BT-474_Pertuzumab_2h_R1 6 EYYDHLPELK 10 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;;;; 143.96 3.31E-05 9203850000 7765270 7815880 6771350 7334140 7902180 7971840 8240590 8591360 9700500 9411200 FALSE TRUE 7461794.663 7592978.755 7995083.573 7712655.844 8156360.796 8133036.067 8341440.805 8413945.414 8599339.908 8773771.041 0.85046608 0.865417928 0.911248257 0.879058253 0.929630003 0.926971541 0.950724696 0.958988487 0.980119024 1 23.06476563 3.678640768 0.253837078 1.010713264 0.782402735 0.929295191 0.012446398 1.256174453 0.10860801 0.018555841 0.088616179 4771.344423 -3.678640768 -0.228310529 NKPYPK ddPTM_BT-474_Pertuzumab_2h_R1 2 NKPYPK 6 1 P27635;X1WI28;A0A087WV22;Q96L21;A6QRI9 P27635 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ; 80.377 0.058982 3601800000 2142520 2018520 1969550 1770710 1632180 1689450 1981410 2024900 2429600 2171200 FALSE TRUE 2058787.95 1960953.786 2325491.497 1862096.555 1684680.552 1723611.837 2005659.088 1983085.107 2153801.994 2024142.69 1.017116016 0.968782387 1.148877255 0.919943324 0.832293375 0.851526844 0.990868429 0.979716063 1.064056405 1 20.94887956 3.678794372 24.99986413 0.943639443 1.037312278 0.242374252 0.077591275 371.0299571 155199.3498 0.02203718 0.034139861 4773.032284 -3.678794372 0.093672835 KPLPTAAAQCS(ph)FEDPDSAVDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPLPTAAAQCSFEDPDSAVDDR 22 1 O14795;O14795-2;A0A1B0GUS7;A0A0U1RRL2 O14795 UNC13B Protein unc-13 homolog B 1 KPLPTAAAQCS(1)FEDPDSAVDDR;KPLPT(0.001)AAAQCS(0.999)FEDPDSAVDDR 120.18 2.61E-05 1215320000 289760 306570 235591 410210 462470 375930 454850 583620 487790 576690 TRUE FALSE 278435.8589 297826.9238 278167.5344 431380.9873 477345.7676 383531.5622 460416.5904 571568.0431 432418.1242 537630.2726 0.517894682 0.55396234 0.517395594 0.802374809 0.887869958 0.713374194 0.856381446 1.063124739 0.804303898 1 19.03625485 3.679370924 0.527654763 0.966130079 0.393342842 0.731895617 0.095421886 0.829474396 0.374195917 0.070049446 0.262758537 4779.372983 -3.679370924 -0.572787237 YISPDQLADLYK ddPTM_BT-474_Pertuzumab_2h_R1 1 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 106.62 0.004426 957970000 1379500 1240300 1165700 1072900 953200 966220 1080200 1224900 1406400 1367500 FALSE TRUE 1325587.615 1204927.858 1376367.921 1128272.498 983860.5437 985757.6304 1093419.811 1199605.387 1246751.368 1274878.007 1.039776047 0.945131889 1.079607549 0.885004284 0.771729168 0.773217222 0.857666227 0.940957002 0.97793778 1 20.28192777 3.679471058 9.170196679 0.876890932 1.013758025 0.378137597 0.07837717 0.476174703 71.33055518 0.02214302 0.034373355 4780.475074 -3.679471058 0.136867092 S(ph)LPNLSR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLPNLSR 7 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 S(1)LPNLSR;S(1)LPNLSR;S(1)LPNLSR;S(1)LPNLSR;S(1)LPNLSR;S(1)LPNLSR 105.35 0.0083367 2219630000 2075560 2203830 1755690 1840060 1908770 1491270 2102170 2023600 1989310 2245420 TRUE FALSE 1994444.821 2140978.926 2072982.238 1935025.717 1970167.321 1521424.501 2127896.985 1981811.953 1763491.869 2093335.703 0.952759186 1.022759476 0.990277018 0.924374296 0.941161667 0.726794321 1.016510148 0.946724383 0.842431468 1 20.99737226 3.67989953 3.23100936 0.912102854 0.993130523 0.158505517 0.078980691 0.458729811 9.52150425 0.02162531 0.037128712 4785.193789 -3.67989953 0.081027669 EKDFIILSCVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDFIILSCVR 11 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 119.69 0.00050383 274650000 315800 310120 273890 221560 200150 92837 294690 243280 258880 294150 FALSE TRUE 303458.1869 301275.6812 323388.0157 232994.7382 206588.0065 94714.22775 298296.5044 238256.183 229493.0277 274226.9585 1.106595021 1.098636264 1.179271423 0.849641988 0.753346818 0.345386275 1.087772355 0.868828449 0.8368726 1 18.06501088 3.679959406 5.519222765 0.810573477 1.125084008 0.36832348 0.184756809 0.227967831 14.81756998 0.051026847 0.080856244 4785.853565 -3.679959406 0.314510531 NFGIWLR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFGIWLR 7 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 123.99 0.009748 454110000 739130 772700 724440 428220 356570 181298 433140 457940 530810 728060 FALSE TRUE 710243.9824 750663.3526 855362.4231 450320.4855 368039.3979 184963.9698 438440.8969 448483.379 470554.6741 678747.8477 1.046403292 1.105953198 1.260206461 0.663457699 0.542232876 0.272507634 0.645955488 0.660751088 0.693268753 1 19.37251619 3.680143988 6.214087849 0.60790637 1.133696197 0.624862477 0.175684436 0.130381531 10.77159039 0.046534793 0.073124382 4787.888056 -3.680143988 0.525789827 GYNPGLLVHPDLAYLQAEGGGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GYNPGLLVHPDLAYLQAEGGGDR 23 0 P19838;P19838-2;A0A494C1E9;A0A494C157;D6RH30 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 0 179.58 4.81E-17 176580000 123430 137880 106700 141340 157060 157900 160720 149100 142870 176020 FALSE TRUE 118606.2191 133947.7974 125983.0635 148634.5743 162111.9775 161092.8462 162686.9394 146021.0329 126651.9966 164098.0086 0.722776712 0.81626705 0.767730606 0.905767081 0.987897287 0.981686783 0.991401058 0.889840371 0.771807029 1 17.32419821 3.680232412 4.103803786 0.935301099 0.772491439 0.55439189 0.067589903 0.175856791 6.073621542 0.019007 0.031226968 4788.86299 -3.680232412 -0.16280966 NVALLSQLYHSPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 ; 258.09 2.28E-24 1470490000 1420000 1439060 1082230 838550 681130 557390 468680 820560 904800 1080680 FALSE TRUE 1364504.83 1398019.418 1277813.035 881827.666 703039.165 568660.8077 474415.846 803615.1493 802090.8972 1007484.581 1.354367953 1.387633562 1.26832019 0.875276587 0.697816302 0.564436239 0.470891421 0.79764511 0.796132181 1 19.94232633 3.680268202 2.245473753 0.693192363 1.372855636 0.80602048 0.135383077 0.122216186 1.202079138 0.038934208 0.07363992 4789.257656 -3.680268202 0.679663273 IINDLLQSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IINDLLQSLR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 156.48 2.53E-05 63408000 110360 120320 97282 89244 80967 80091 110930 86883 95428 97395 FALSE TRUE 106047.0092 116888.5914 114863.0214 93849.89354 83571.37709 81710.49489 112287.5945 85088.83569 84595.41351 90798.3499 1.167939828 1.287342683 1.265034239 1.03360792 0.920406342 0.899911672 1.236669991 0.937118745 0.931684481 1 16.47037846 3.680382009 4.743487373 0.993680188 1.245361859 0.589546179 0.094360319 0.144960842 6.856196607 0.025671381 0.041328009 4790.51285 -3.680382009 0.251681671 GREDSLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GREDSLPK 8 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 0 90.601 0.013767 0 152750 153380 130710 155840 156510 174520 160620 190510 186060 164640 FALSE TRUE 146780.3611 149005.7526 154332.2046 163882.9211 161544.2863 178048.914 162585.7156 186575.9019 164939.2488 153488.7862 0.956293712 0.970792436 1.005494984 1.067719181 1.052482662 1.160012522 1.059267714 1.215566991 1.074601298 1 17.22777373 3.680449543 1.011831557 1.119111882 0.950478388 0.446770145 0.05745759 0.470191154 0.911807683 0.02030164 0.058940307 4791.257845 -3.680449543 -0.168633493 YLMGER ddPTM_BT-474_Pertuzumab_2h_R1 3 YLMGER 6 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 102.98 0.081604 7454600000 5657200 5996000 4830600 3070440 2979590 894810 4249700 2778890 2866790 2821570 FALSE TRUE 5436110.37 5824999.951 5703596.876 3228905.776 3075431.218 912903.6713 4301709.1 2721504.95 2541364.018 2630462.551 2.066598655 2.214439415 2.168286667 1.22750494 1.169159857 0.347050625 1.635343221 1.034610795 0.966128188 1 21.32688508 3.681121689 3.462736971 1.047247901 2.170447018 0.743516774 0.296339581 0.117579355 2.829422873 0.079982415 0.135528663 4798.678887 -3.681121689 1.123199117 up GDRYDALR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDRYDALR 8 1 A0AVT1 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 119.21 0.0015849 625400000 559950 693850 545250 378110 366740 118958 502670 363220 424170 473340 FALSE TRUE 538066.5349 674062.0774 643788.804 397624.3024 378536.5252 121363.4123 508821.8258 355719.3801 376019.9999 441280.2602 1.219330624 1.527514684 1.458911404 0.90106977 0.857814317 0.2750257 1.153058208 0.806107619 0.852111535 1 18.75133569 3.681839777 4.441454166 0.8174081 1.416588876 0.575518499 0.2233498 0.143697266 5.945871195 0.05935811 0.096482027 4806.619865 -3.681839777 0.599180775 NLGQNLWGPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLGQNLWGPHR 11 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 141.95 3.79E-05 823720000 1460470 1654030 1389440 961390 932870 513410 1090910 941460 1121310 1306280 FALSE TRUE 1403393.218 1606858.684 1640542.716 1011007.453 962876.6108 523791.502 1104260.883 922018.522 994023.5897 1217804.492 1.152396158 1.319471799 1.347131437 0.830188638 0.790666003 0.430111324 0.90676368 0.757115389 0.816242341 1 20.21585111 3.682217635 5.136597014 0.767978916 1.277967782 0.694408431 0.146511759 0.105029319 6.00220945 0.038443081 0.061401045 4810.803689 -3.682217635 0.509988866 ALNRPPTYPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALNRPPTYPTK 11 1 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54;H0YK11 P55010 EIF5 Eukaryotic translation initiation factor 5 0 71.268 0.040902 0 150790 176200 153950 142600 153440 110380 180700 154380 165220 159820 FALSE TRUE 144896.9601 171174.9485 181772.1896 149959.6031 158375.537 112611.9592 182911.4607 151191.9991 146464.9183 148995.249 0.972493828 1.14886179 1.219986481 1.006472381 1.06295696 0.755809061 1.227632839 1.014743759 0.983017373 1 17.1849068 3.682838781 24.95352117 1.013421942 1.117289078 0.136908033 0.121806536 557.6361897 249722.117 0.031852849 0.049346264 4817.689215 -3.682838781 0.103867135 LAFVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAFVIR 6 0 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 106.05 0.075504 166180000 165600 200820 153120 137070 128010 119580 120470 153270 156150 177120 FALSE TRUE 159128.1689 195092.8102 180792.1901 144144.1991 132127.5579 121997.9895 121944.3479 150104.9209 138424.5066 165123.5046 0.963691809 1.181496303 1.094890703 0.872947794 0.800174138 0.738828732 0.738503874 0.909046361 0.838308919 1 17.33318597 3.683138611 4.119854131 0.828094277 1.091814309 0.602703913 0.088248434 0.133395508 4.706976728 0.023463901 0.038607101 4821.016422 -3.683138611 0.263720031 HVEFDFLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVEFDFLIK 9 0 Q9GZL7 Q9GZL7 WDR12 Ribosome biogenesis protein WDR12 0 107.57 0.0034151 0 209250 225180 188090 174680 169580 187160 179150 146830 238000 230950 FALSE TRUE 201072.2787 218758.0869 222082.047 183695.2557 175034.6947 190944.5034 181342.4913 143797.9092 210983.2378 215307.5508 0.933884009 1.01602608 1.031464276 0.853176097 0.812951957 0.886845365 0.842248637 0.667872114 0.979915646 1 17.71603939 3.683273493 6.230729099 0.836273539 0.995843277 0.266303711 0.092008158 0.22623282 19.67380049 0.024739384 0.038915731 4822.513949 -3.683273493 0.159569737 AVCST(ph)YLQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVCSTYLQSR 10 0 Q5SQL3;J3KP92;Q86Z02;Q86Z02-2;H7BXX9;Q9H2X6-2;Q9H2X6-3;Q9H2X6 Q5SQL3 HIPK1;HIPK2 Homeodomain-interacting protein kinase 1;Homeodomain-interacting protein kinase 2 1 AVCS(0.006)T(0.69)Y(0.304)LQSR 129.38 0.0034041 887920000 143680 170520 117180 168780 181550 163150 183140 185130 200400 194580 TRUE FALSE 138064.8268 165656.9366 138357.0327 177490.756 187389.7206 166449.0048 185381.3221 181307.0008 177651.4321 181400.9233 0.76110322 0.913208894 0.762714049 0.978444612 1.03301415 0.91757529 1.02194255 0.999482238 0.979330364 1 17.46882227 3.683746358 7.815451401 0.991570831 0.822613829 0.732115193 0.049121768 0.141012558 18.38445036 0.012056073 0.018784017 4827.76762 -3.683746358 -0.168957002 QLEEPGAGTPS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLEEPGAGTPSPVR 14 0 Q96P11-2;Q63ZY6;Q96P11-5;Q96P11;Q96P11-4;Q63ZY6-5;Q63ZY6-4 Q96P11-2 NSUN5;NSUN5P2 Probable 28S rRNA (cytosine-C(5))-methyltransferase;Putative methyltransferase NSUN5C 1 QLEEPGAGTPS(1)PVR;QLEEPGAGTPS(1)PVR 245.71 1.18E-17 1990840000 1301440 1447850 1222740 1451280 1447140 1647660 1437300 1353350 1360500 1610620 TRUE FALSE 1250578.286 1406558.736 1443716.318 1526180.735 1493688.572 1680976.814 1454890.107 1325402.85 1206061.744 1501531.273 0.832868625 0.936749544 0.961496003 1.016416216 0.994776865 1.119508361 0.9689376 0.882700796 0.803221195 1 20.51800309 3.683967129 0.002531228 1.20904492 0.696737907 0.002289875 0.088262047 3351352.239 1966.747971 196603.9271 201464.3429 4830.222412 -3.683967129 -0.512307013 VGRPTASK ddPTM_BT-474_Pertuzumab_2h_R1 3 VGRPTASK 8 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;; 105.94 0.0039145 3700730000 4944540 4775580 3927530 3208920 3210050 947090 3992360 3363570 3730860 4152530 FALSE TRUE 4751301.91 4639385.134 4637322.038 3374532.746 3313304.174 966240.8087 4041219.696 3294111.104 3307348.414 3871275.444 1.227322101 1.198412565 1.197879641 0.871685003 0.855868879 0.249592369 1.043898775 0.850911063 0.85433043 1 21.88437753 3.683999053 2.974828337 0.798547974 1.21610236 0.438396632 0.202984316 0.245191424 4.297379621 0.056728641 0.099523836 4830.577491 -3.683999053 0.417554386 LDPDSIPS(ph)PIQVIENDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDPDSIPSPIQVIENDR 17 0 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 1 LDPDS(0.003)IPS(0.997)PIQVIENDR 62.378 0.065396 14716000 10724 12416 9913.7 12556 13980 15052 13911 14336 15043 16880 TRUE FALSE 10304.89422 12061.90784 11705.32612 13204.01666 14429.6794 15356.36175 14081.24698 14039.95659 13335.38171 15736.70256 0.654831861 0.766482545 0.743823305 0.839058666 0.91694428 0.975830972 0.894802893 0.892179066 0.847406352 1 13.94184565 3.684190858 1.60357285 0.915916583 0.706571493 0.782018966 0.04737639 0.18361327 0.917469411 0.014356821 0.031519413 4832.711366 -3.684190858 -0.20934509 EKPLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKPLIR 6 1 Q9H6H4 Q9H6H4 REEP4 Receptor expression-enhancing protein 4 0 87.989 0.047254 1127300000 1385200 1436500 1211700 1693100 1709900 2323700 1618100 2010500 1995600 1861300 FALSE TRUE 1331064.853 1395532.426 1430681.144 1780481.094 1764900.486 2370686.806 1637902.792 1968982.472 1769067.854 1735232.493 0.767081563 0.804233687 0.8244896 1.026076391 1.017097417 1.366207016 0.943909706 1.134708162 1.019499036 1 20.72669754 3.684515235 1.996135093 1.093866349 0.781891546 0.575719959 0.108838244 0.223814703 1.736201966 0.030331403 0.060138651 4836.322297 -3.684515235 -0.311974803 KQEVQAWDGEVR ddPTM_BT-474_Pertuzumab_2h_R1 6 KQEVQAWDGEVR 12 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;;;; 168.89 7.27E-05 8338640000 6218290 6171970 5084150 6082480 6033130 6420230 6220960 6904090 6983880 6603210 FALSE TRUE 5975272.352 5995951.459 6002969.001 6396397.522 6227191.106 6550051.449 6297093.969 6761518.129 6191099.221 6155968.705 0.970646967 0.974006163 0.975146121 1.039056212 1.01156965 1.064016366 1.022924948 1.098367853 1.005706741 1 22.55355447 3.68461308 1.458633048 1.045271258 0.967387096 0.447737562 0.029295669 0.327265153 1.350647259 0.00885872 0.020518319 4837.412032 -3.68461308 -0.077884162 SGVRGT(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SGVRGTPVR 9 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RFR3 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 SGVRGT(1)PVR;S(0.002)GVRGT(0.998)PVR;SGVRGT(1)PVR 100.38 0.0076013 2536150000 1158070 1239290 923460 962010 902180 899020 996180 959140 915430 1026610 TRUE FALSE 1112811.344 1203946.663 1090349.764 1011659.451 931199.439 917198.8004 1008371.549 939333.4238 811514.2242 957076.7903 1.162718974 1.257941552 1.139250032 1.057030597 0.972962095 0.958333552 1.053595238 0.981460875 0.847909209 1 19.86827516 3.685013951 1.807937233 0.973688837 1.211023964 0.76698527 0.054158011 0.165713708 1.053555175 0.015989083 0.033098923 4841.879212 -3.685013951 0.237335128 NVALLSQLYHS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 4 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR 216.3 3.98E-12 1155520000 1004080 917260 852070 602950 479539 528170 417095 683210 752640 975030 TRUE FALSE 964839.4435 891100.6429 1006058.003 634068.3218 494963.8074 538849.9593 422199.5334 669101.4747 667203.4625 908990.3496 1.0614408 0.980319146 1.106786231 0.697552314 0.544520421 0.592800528 0.464470864 0.736093045 0.734005001 1 19.79390545 3.685312985 5.702174194 0.650971348 1.042539626 0.588267978 0.139704109 0.127117369 9.456316855 0.035831561 0.05677609 4845.214244 -3.685312985 0.391568277 WAHDKFS(ph)GEEGEIEDDES(ph)GTENR ddPTM_BT-474_Pertuzumab_2h_R1 6 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.989)GT(0.011)ENR;WAHDKFS(1)GEEGEIEDDES(0.892)GT(0.108)ENR;WAHDKFS(1)GEEGEIEDDES(0.895)GT(0.105)ENR;WAHDKFS(1)GEEGEIEDDES(0.875)GT(0.125)ENR;WAHDKFS(1)GEEGEIEDDES(0.871)GT(0.129)ENR;WAHDKFS(1)GEEGEIEDDES(0.935)GT(0.065)ENR 265.46 6.53E-44 4361140000 4409520 3652540 4385520 4416880 4404630 4590370 4822150 4781970 6571890 6365460 TRUE FALSE 4237191.083 3548373.135 5178081.019 4644835.706 4546308.924 4683190.427 4881164.914 4683220.648 5825876.599 5934321.724 0.714014386 0.597940809 0.87256493 0.782707093 0.766104221 0.789170295 0.822531224 0.789175388 0.981725776 1 22.50065171 3.685643562 0.052810445 1.505090276 4.13E-14 0.6129557 0.070208936 97.95028251 1.201945677 12.97017106 21.65758823 4848.903728 -3.685643562 -1.505090276 KYDEVLHMVR ddPTM_BT-474_Pertuzumab_2h_R1 3 KYDEVLHMVR 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 135.47 9.31E-05 1141790000 2642154 2917474 2631247 2121023 2092279 860428 3144161 2181260 2559281 2855563 FALSE TRUE 2538895.701 2834270.498 3106771.865 2230489.251 2159579.054 877826.4437 3182640.183 2136216.219 2268762.15 2662153.175 0.953700082 1.064653426 1.167014691 0.837851583 0.811215175 0.329743026 1.195513546 0.802439258 0.852228253 1 21.34416215 3.685855241 9.313516105 0.823893596 1.061923431 0.200357775 0.209206611 0.724432566 124.4043747 0.055205576 0.08574405 4851.267702 -3.685855241 0.238029835 IKFPLPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKFPLPHR 8 1 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 87.616 0.0091315 1355190000 5615900 6243900 5855900 4264600 4020800 1598060 6023000 4672300 5156100 6094600 FALSE TRUE 5396424.419 6065830.085 6914191.394 4484696.517 4150132.684 1630373.868 6096711.276 4575815.372 4570801.144 5681807.313 0.949772515 1.067588137 1.216900013 0.789308097 0.730424749 0.28694635 1.073023237 0.805345046 0.80446254 1 22.43791848 3.69055861 10.42563523 0.773259449 1.076932306 0.301752715 0.204379418 0.854229996 183.5274593 0.054977753 0.085332765 4904.092017 -3.69055861 0.303672857 KPYCNAHYPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPYCNAHYPK 10 1 Q14847;Q14847-2;C9J9W2;F6S2S5;O76041-2 Q14847;O76041-2 LASP1;NEBL LIM and SH3 domain protein 1;Nebulette 0 ; 110.14 0.0012504 37714000000 48110000 47280000 41935000 33423000 29602000 13381300 45364000 35936000 39926000 48408000 FALSE TRUE 46229808.01 45931620.69 49513587.34 35147965.04 30554175.21 13651879.05 45919178.2 35193909.04 35393767.86 45129283.04 1.02438605 1.017778648 1.097149877 0.77882835 0.677036575 0.302506004 1.017502941 0.779846403 0.784274987 1 25.42756052 3.690566369 6.194235104 0.74781292 1.043473078 0.325845743 0.18617282 0.23995478 23.07983084 0.050430673 0.079639407 4904.179625 -3.690566369 0.295660158 KFMTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFMTNR 6 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 110.63 0.045756 2070000000 2206300 2277300 1949930 1572050 1548490 857240 2008570 1759820 1602990 1933820 FALSE TRUE 2120075.357 2212353.634 2302325.727 1653183.689 1598298.587 874573.9801 2033151.48 1723479.102 1421025.295 1802840.649 1.175963809 1.227148742 1.27705448 0.916988248 0.88654457 0.485108865 1.127748857 0.955979722 0.788214586 1 20.78184045 3.690894685 5.645026279 0.880244849 1.226930666 0.500743459 0.158748076 0.170181798 13.31160072 0.043527555 0.069259258 4907.888465 -3.690894685 0.346685817 GLEHVTVDDLVAEITPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GLEHVTVDDLVAEITPK 17 0 E5RHX8;Q9NPA8-2;Q9NPA8 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 ;;; 167.71 2.19E-09 653443000 654130 625998 554124 629912 644521 702090 693280 679810 798400 754310 FALSE TRUE 628565.8764 608145.15 654266.5332 662421.8338 665252.6033 716286.7408 701764.568 665771.6859 707768.9792 703219.9118 0.893839702 0.864800811 0.930386814 0.941983898 0.946009338 1.018581426 0.997930457 0.946747489 1.006468911 1 19.4236164 3.691000639 1.053810904 0.986421973 0.875187041 0.766516044 0.023353824 0.297733093 0.626610652 0.008699207 0.024983033 4909.085983 -3.691000639 -0.111234932 DYLLCDYNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYLLCDYNR 9 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 163.2 0.00014702 2088400000 1891410 2227200 1642930 1223670 1119200 228259 1710960 1128710 1238320 1566460 FALSE TRUE 1817491.606 2163682.437 1939843.998 1286823.755 1155200.084 232874.5534 1731899.24 1105401.744 1097751.105 1460362.269 1.244548455 1.481606641 1.328330675 0.88116749 0.791036655 0.159463551 1.18593809 0.756936664 0.7516978 1 20.47789487 3.691054801 3.1435504 0.765954037 1.377041333 0.516802828 0.250781379 0.194861284 3.8624463 0.068123123 0.118732848 4909.698245 -3.691054801 0.611087296 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GYDSEDDTWEPEQHLVNCEEYIHDFNRR 28 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GYDS(0.999)EDDT(0.001)WEPEQHLVNCEEYIHDFNRR;GYDS(0.999)EDDT(0.001)WEPEQHLVNCEEYIHDFNRR 141.84 4.62E-08 344530000 1395.2 0 1154 2468.8 2404.6 5323.2 1748.4 3010.3 3178.7 5303.5 TRUE FALSE 1340.674042 0 1362.553471 2596.215064 2481.946143 5430.838751 1769.797442 2948.136253 2817.867302 4944.289221 0.271156071 0 0.275581263 0.525093688 0.501982395 1.098406365 0.357947799 0.596270995 0.569923638 1 12.27154742 3.691170635 1.86961685 0.658833071 0.130056004 0.522091466 0.217728138 0.283183761 1.924888542 0.062112857 0.127418838 4911.007923 -3.691170635 -0.528777067 S(ph)RTPPSAPSQSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRTPPSAPSQSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.5)RT(0.5)PPSAPSQSR;S(0.5)RT(0.5)PPSAPSQSR;S(0.5)RT(0.5)PPSAPSQSR 56.956 0.070631 4770364000 518037 520739 385753 498347 477360 535249 514396 523993 525158 540823 TRUE FALSE 497791.5413 505888.0336 455467.1481 524066.7484 492714.7179 546072.1015 520691.3321 513172.3614 465544.2655 504192.5765 0.987304384 1.003362717 0.903359489 1.039417819 0.977235169 1.083062558 1.032723123 1.017810228 0.923346132 1 18.94361535 3.691386508 24.99994295 1.01441127 0.96854392 0.166175648 0.046239738 680.8949319 360840.2682 0.01215516 0.018830741 4913.449621 -3.691386508 -0.04586735 GSS(ph)QPNLSTSHSEQEYGK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSSQPNLSTSHSEQEYGK 18 0 I3L2B2;O95208-3;O95208-2;F6PQP6;O95208;E9PBC1 I3L2B2 EPN2 Epsin-2 1 GS(0.021)S(0.978)QPNLSTSHSEQEYGK;GS(0.037)S(0.963)QPNLSTSHSEQEYGK;GS(0.145)S(0.855)QPNLSTSHSEQEYGK 258.2 7.66E-31 3969580000 2115220 2225400 1706610 1951730 1954060 2009710 1834120 2152990 2239450 2133060 TRUE FALSE 2032554.864 2161933.771 2015032.39 2052459.019 2016914.115 2050347.713 1856566.509 2108530.004 1985237.025 1988585.946 1.022110645 1.087171402 1.01329912 1.032119845 1.014245383 1.031058133 0.9336114 1.060316255 0.998315928 1 20.92331149 3.691994744 1.197506003 1.007979094 1.05194028 0.185492704 0.034738914 0.869519785 2.391528762 0.011229553 0.029704569 4920.335813 -3.691994744 0.043961186 KFAYLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFAYLGR 7 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 107.43 0.011993 787250000 1114150 1249410 1050310 721320 639010 127484 1135290 711840 767470 1045520 FALSE TRUE 1070607.786 1213778.05 1240124.381 758547.4116 659564.337 130061.8138 1149184.019 697140.2552 680350.0231 974705.9991 1.098390476 1.245276064 1.272306092 0.778232013 0.676680289 0.133436969 1.179005792 0.715231317 0.698005372 1 19.8946076 3.692657528 5.623140266 0.724647887 1.209674594 0.409541058 0.255796351 0.188809483 14.9752246 0.068117293 0.108553801 4927.850549 -3.692657528 0.485026707 NINPDVLFEVHNYNITTVENFQHFMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NINPDVLFEVHNYNITTVENFQHFMDR 27 0 Q9GZZ9-2;Q9GZZ9;E7EWE1;E7EQ61;C9JRV9;C9J5W5 Q9GZZ9-2 UBA5 Ubiquitin-like modifier-activating enzyme 5 0 56.914 0.040944 115350000 56179 69758 52773 101770 127540 141210 144470 81083 117520 98989 FALSE TRUE 53983.46257 67768.57014 62310.25503 107022.3619 131642.4399 144065.363 146238.0671 79408.60772 104179.6223 92284.38686 0.584968535 0.734344914 0.675198234 1.159701717 1.426486586 1.561102239 1.584645811 0.860477166 1.128897594 1 16.49379897 3.692690321 3.88841582 1.264153612 0.664943302 0.597991304 0.219382301 0.169498969 5.437676085 0.066089908 0.110649586 4928.222658 -3.692690321 -0.59921031 APS(ph)PTKPLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPTKPLRR 10 2 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 APS(0.999)PT(0.001)KPLRR 83.226 0.0082169 334840000 356580 412150 280190 283850 266800 206150 260260 292270 268530 304990 TRUE FALSE 342644.4594 400395.8855 330826.5658 298499.5325 275381.8643 210318.4942 263445.1397 286234.5224 238047.6002 284332.7556 1.20508261 1.408194721 1.163519008 1.049824639 0.968519662 0.739691401 0.92653813 1.006688525 0.837214832 1 18.11722078 3.693370354 1.726416825 0.91271907 1.305851021 0.752625455 0.090252085 0.175390248 1.015506406 0.027039493 0.057709102 4935.945477 -3.693370354 0.393131951 KFYEQFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFYEQFSK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 98.943 0.011488 514800000 433600 432250 385250 323130 346140 200430 408330 308630 388000 441020 FALSE TRUE 416654.4326 419922.6532 454873.2448 339806.778 357273.9075 204482.8319 413327.2647 302256.6826 343955.8666 411149.3226 1.013389564 1.021338551 1.106345602 0.826480209 0.868963872 0.497344446 1.005297205 0.735150628 0.836571649 1 18.64930293 3.693970856 7.470090851 0.808016744 1.044298505 0.352799317 0.137034865 0.253133522 37.55018416 0.034496849 0.054016326 4942.775163 -3.693970856 0.236281761 ELPEQLQEHAIEDK ddPTM_BT-474_Pertuzumab_2h_R1 5 ELPEQLQEHAIEDK 14 0 Q15424;Q15424-3;Q15424-4 Q15424 SAFB Scaffold attachment factor B1 0 ;;;; 201.3 1.80E-08 1457830000 1894020 1712960 1845850 2181920 2105220 1954950 2454140 2548550 3129650 3065570 FALSE TRUE 1819999.604 1664108.058 2179436.156 2294529.153 2172936.313 1994480.428 2484174.499 2495921.552 2774385.253 2857936.213 0.636823032 0.582276137 0.762590902 0.802862269 0.760316589 0.697874368 0.869219714 0.873330042 0.970765281 1 21.44654229 3.694250223 0.198617962 1.062576884 0.375770468 0.800933686 0.05758492 4.105479279 0.234964397 0.15941011 0.732097786 4945.955708 -3.694250223 -0.686806417 KRLS(ph)VER ddPTM_BT-474_Pertuzumab_2h_R1 2 KRLSVER 7 2 P11388;P11388-2;P11388-3;P11388-4;J3KTB7 P11388 TOP2A DNA topoisomerase 2-alpha 1 KRLS(1)VER;KRLS(1)VER 70.028 0.045787 1142250000 2084380 2027980 1793020 1541970 1546620 896100 1971620 1780520 1542890 1942170 TRUE FALSE 2002920.125 1970143.996 2117058.6 1621551.256 1596368.437 914219.756 1995749.275 1743751.64 1367747.596 1810625.096 1.106203669 1.088101562 1.169241829 0.895575379 0.881667022 0.50491941 1.102243242 0.963066094 0.755400772 1 20.78805643 3.695743006 6.919567631 0.874573436 1.117770067 0.3617014 0.151770825 0.258878704 34.53171849 0.041532491 0.065334924 4962.9855 -3.695743006 0.243196631 ADVFHAYLSLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADVFHAYLSLLK 12 0 Q86VP6;Q86VP6-2;A0A0C4DGH5;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 216.06 4.00E-11 675160000 2575200 2915400 2516900 2007480 1906570 819730 2851500 1986160 2518100 2986100 FALSE TRUE 2474558.337 2832255.646 2971759.818 2111086.283 1967896.556 836305.5022 2886397.51 1945145.102 2232255.845 2783848.787 0.888898258 1.017388466 1.067500445 0.758333676 0.70689779 0.300413408 1.036837031 0.698725129 0.801859589 1 21.40864942 3.695867666 8.220546868 0.738812343 0.993730812 0.231175399 0.193179617 0.419285249 75.55349144 0.050370286 0.078661096 4964.410282 -3.695867666 0.254918469 VYNYNHLMPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYNYNHLMPTR 11 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 129.82 0.00023706 881200000 876440 1026250 852390 457950 418890 146894 746620 328970 408270 586310 FALSE TRUE 842187.7558 996982.3548 1006435.834 481584.8544 432363.9773 149864.2973 755757.3589 322176.6545 361924.9012 546598.7015 1.540778918 1.823974979 1.841270079 0.881057443 0.791008058 0.274176095 1.382654874 0.589420819 0.662140068 1 19.06012251 3.696325083 5.344068963 0.777185564 1.746025412 0.70283839 0.279615351 0.098669313 7.204838316 0.072167574 0.115913763 4969.641758 -3.696325083 0.968839848 HAYGDQYR ddPTM_BT-474_Pertuzumab_2h_R1 5 HAYGDQYR 8 0 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;; 143.73 0.00059669 1635233000 1697458 1877692 1531644 935475 971550 203879 1489098 669901 953822 1304984 FALSE TRUE 1631119.465 1824142.063 1808446.142 983754.9769 1002800.788 208001.5731 1507322.027 656067.3102 845548.1253 1216596.271 1.340723709 1.499381599 1.486480096 0.80861252 0.824267517 0.170970089 1.238966502 0.539264607 0.695011275 1 20.21441906 3.696358417 4.528236552 0.725821214 1.451817326 0.582848334 0.266584516 0.131459338 6.238968511 0.067941529 0.111396581 4970.023217 -3.696358417 0.725996113 QVNYEVDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVNYEVDRR 9 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 155.15 0.00011865 406940000 289640 387900 287040 255300 262000 117513 367910 229147 295320 369330 FALSE TRUE 278320.5486 376837.4718 338914.5132 268476.0636 270427.4679 119889.1934 372412.5926 224415.0344 261796.5117 344314.9501 0.808331292 1.094455735 0.984315415 0.77973978 0.785407279 0.348196305 1.08160448 0.651772554 0.76034024 1 18.3933693 3.696495915 4.619840248 0.752216443 0.976588847 0.158312004 0.196701249 0.310845587 15.54804497 0.050163173 0.08202655 4971.596975 -3.696495915 0.224372404 AYT(ph)PVVVTLWYR ddPTM_BT-474_Pertuzumab_2h_R1 3 AYTPVVVTLWYR 12 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12 P21127-2 CDK11B Cyclin-dependent kinase 11B 1 AYT(1)PVVVTLWYR;AYT(1)PVVVTLWYR;AYT(1)PVVVTLWYR 175.48 0.00030813 3105124000 746664 636560 586196 568682 585338 501587 612209 589924 721325 676037 TRUE FALSE 717483.5454 618405.9321 692134.6571 598031.7462 604165.9284 511729.4328 619701.3969 577741.8632 639443.21 630248.4118 1.138413889 0.981209822 1.098193417 0.948882591 0.958615551 0.811948786 0.983265305 0.916689122 1.014589165 1 19.26556105 3.696672463 8.121620913 0.939785289 1.063400857 0.432842601 0.064818925 0.271530214 48.95948415 0.01639722 0.025626313 4973.618419 -3.696672463 0.123615568 DRPFFPGLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRPFFPGLVK 10 1 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72;O60361 Q32Q12;O60361 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 ; 129.89 0.00026554 25855000000 14770300 15890100 15478800 12505400 11605300 8727100 16680700 13539900 17150100 17699900 FALSE TRUE 14193060.35 15436929.91 18276163.48 13150805.19 11978595.01 8903567.941 16884843.4 13260296.33 15203292.55 16501070.01 0.860129697 0.935510843 1.107574447 0.796966814 0.72592838 0.539575187 1.023257485 0.80360221 0.921351921 1 23.97605624 3.696812752 24.99000662 0.816978486 0.964515714 0.158300145 0.143166812 802.7524646 480522.4212 0.038300911 0.059336066 4975.225293 -3.696812752 0.147537229 KLELSDNR ddPTM_BT-474_Pertuzumab_2h_R1 4 KLELSDNR 8 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;; 130.66 0.0016652 8621400000 21994200 22682700 18520600 14882300 15535000 5639680 19335500 16033400 16821000 18224600 FALSE TRUE 21134642.35 22035811.6 21867684.41 15650377.29 16034697.38 5753718.194 19572133.63 15702304.69 14911550.6 16990231.61 1.243929031 1.296969465 1.287073944 0.921139726 0.943759788 0.338648603 1.15196391 0.924196035 0.877654345 1 24.01820218 3.697730005 3.999370521 0.872199166 1.282022536 0.459431334 0.197373974 0.197535542 6.89956586 0.053746271 0.089953813 4985.744344 -3.697730005 0.409823369 KTQYEEHIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTQYEEHIYR 10 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 ; 119.27 0.00046356 310680000 603490 605080 497480 483740 478000 404290 567690 495330 557640 566550 FALSE TRUE 579904.9436 587823.7108 587385.7024 508705.8794 493375.3041 412465.0208 574637.56 485101.2624 494339.045 528177.0639 1.097936626 1.112929264 1.11209998 0.963135119 0.934109672 0.780921871 1.087963865 0.918444392 0.935934327 1 19.01066213 3.697798062 4.281367403 0.940875697 1.109485562 0.516959913 0.071818755 0.162762859 6.746276534 0.018981645 0.031423758 4986.525699 -3.697798062 0.168609864 YGEAGEGPGWGGAHPR ddPTM_BT-474_Pertuzumab_2h_R1 4 YGEAGEGPGWGGAHPR 16 0 P26640;A0A140T954;A2ABF4;A0A0G2JJT9 P26640 VARS Valine--tRNA ligase 0 ;;; 220.21 1.17E-14 2473110000 1292440 1309990 1112950 1170310 1184070 1231710 1154560 1249880 1425100 1493320 FALSE TRUE 1241930.016 1272630.368 1314084.822 1230709.839 1222156.687 1256616.02 1168689.851 1224069.541 1263328.623 1392176.106 0.892078244 0.914130304 0.943907036 0.884018792 0.877875063 0.9026272 0.839469838 0.879249066 0.907448861 1 20.40891029 3.698157543 24.86691742 0.888842155 0.916447736 0.000401394 0.041132414 1129.950118 695451.3523 0.010248825 0.015877629 4990.654937 -3.698157543 0.02760558 DEALQNISADDLPDSASQAAHPQDSAFSYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEALQNISADDLPDSASQAAHPQDSAFSYR 30 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ; 248.82 3.43E-46 901730000 148082 152914 122999 164466 149358 182824 178109 167804 191730 187974 FALSE TRUE 142294.7917 148553.0424 145227.6554 172954.11 154162.2357 186520.8265 180288.7512 164338.7888 169965.6142 175242.3536 0.811988591 0.847700567 0.828724635 0.986942406 0.879708772 1.064359287 1.028796678 0.937780082 0.969888904 1 17.41899197 3.698444964 1.317469758 0.987059188 0.815781623 0.65775788 0.049218029 0.291698123 0.975476789 0.015847213 0.039721379 4993.958907 -3.698444964 -0.171277565 DTGIFLDLMHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 DTGIFLDLMHLK 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 164.81 5.63E-05 8222920000 5336030 5588310 4728920 4839910 4977630 4133860 5746940 4934620 5900930 5915920 FALSE TRUE 5127492.048 5428936.87 5583541.038 5089698.335 5137739.99 4217449.482 5817272.771 4832718.373 5231081.165 5515229.469 0.929696956 0.984353761 1.012385989 0.922844346 0.931555073 0.76469157 1.054765319 0.876249737 0.948479332 1 22.39498948 3.698625303 18.02153925 0.921721671 0.976366067 0.073390514 0.07409955 44.70607492 20173.63434 0.018761292 0.029070265 4996.033053 -3.698625303 0.054644396 LLGHLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLGHLVK 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 91.26 0.016535 707940000 1949360 2112420 1785200 1487000 1353990 666690 2011020 1668970 1764980 1966900 FALSE TRUE 1873176.856 2052175.85 2107825.352 1563744.248 1397542.318 680170.9286 2035631.464 1634505.186 1564626.87 1833680.111 1.021539605 1.119156955 1.149505488 0.852790102 0.762151648 0.370932162 1.110134451 0.891379678 0.853271441 1 20.80631055 3.698672466 6.916069864 0.828080287 1.09891652 0.300151302 0.183455009 0.277150181 39.21986079 0.050666142 0.079855051 4996.57564 -3.698672466 0.270836232 TIAQDYGVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TIAQDYGVLK 10 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 150.61 4.95E-05 266180000 221700 239280 199640 177610 178360 137870 212830 181080 205020 218860 FALSE TRUE 213035.7189 232455.9687 235719.389 186776.4734 184097.1114 140657.8259 215434.6772 177340.6347 181746.9891 204036.4173 1.04410635 1.139286662 1.155280965 0.915407533 0.90227575 0.689376082 1.055863851 0.869161678 0.890757599 1 17.63846715 3.698891296 6.770450325 0.896183264 1.115502303 0.5126985 0.093491252 0.158796221 21.56903822 0.024169087 0.038147192 4999.093918 -3.698891296 0.219319039 NIQVSHQEFSK ddPTM_BT-474_Pertuzumab_2h_R1 4 NIQVSHQEFSK 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 177.1 8.13E-06 741500000 2404290 2354860 1917300 1858840 1781990 1742600 1690410 1844590 2443680 2405740 FALSE TRUE 2310327.689 2287701.698 2263798.76 1954774.955 1839309.327 1777836.566 1711097.743 1806498.572 2166283.691 2242797.087 1.030109992 1.0200217 1.009364054 0.87157905 0.820096181 0.79268721 0.76293025 0.805466791 0.965884834 1 21.09686767 3.699544243 3.103181112 0.836295647 1.02444263 0.495315328 0.072258881 0.182212299 3.537697041 0.019437832 0.034223602 5006.615542 -3.699544243 0.188146982 ENDWYLAYK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENDWYLAYK 9 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 ; 143.86 0.00023481 325170000 600480 642220 550460 549620 562140 494920 612950 601460 664780 678940 FALSE TRUE 577012.5777 623904.5144 649940.3669 577985.9541 580221.7436 504927.6215 620451.4655 589039.6408 589316.9614 632954.7891 0.911617366 0.985701546 1.026835373 0.913155195 0.916687501 0.797730944 0.980246103 0.930618823 0.931056959 1 19.27174293 3.700512455 24.54484327 0.919993115 0.975816479 0.14007909 0.056652213 759.6368829 490041.0978 0.015017003 0.023264939 5017.789696 -3.700512455 0.055823365 DLFDSMDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLFDSMDK 8 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ; 175.38 0.00061997 452530000 1036450 961870 1016590 1209000 1158620 1055240 1380470 1475840 1632590 1686620 FALSE TRUE 995944.3881 934438.4094 1200310.427 1271396.635 1195888.065 1076577.676 1397364.605 1445363.388 1447265.228 1572383.725 0.633397797 0.594281405 0.763369913 0.808579111 0.760557392 0.68467872 0.888691852 0.919217978 0.920427504 1 20.58452191 3.700970769 0.216709969 1.048944864 0.397516967 0.78946938 0.058554515 3.619089249 0.2363736 0.135839507 0.649215956 5023.087795 -3.700970769 -0.651427897 AQLEPVAS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 7 AQLEPVASPAK 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK 185.67 4.58E-06 8167870000 15264240 13711320 14184180 11817690 12138820 9881370 14665180 14670500 14712830 16067770 TRUE FALSE 14667696.63 13320286.58 16747576.85 12427602.4 12529276.17 10081178.07 14844656.86 14367549.05 13042691.22 14979485.63 0.9791856 0.889235246 1.118034175 0.829641465 0.836428999 0.672998948 0.990999106 0.959148358 0.870703544 1 23.83648475 3.701271152 24.97182478 0.879752261 0.984860242 0.2050795 0.10357007 967.0944579 647639.1255 0.028697237 0.044458963 5026.563257 -3.701271152 0.105107981 NYYGYQGYR ddPTM_BT-474_Pertuzumab_2h_R1 4 NYYGYQGYR 9 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 157.34 0.00015999 657690000 486021 542923 380040 371542 308983 208400 370366 378689 391587 405482 FALSE TRUE 467026.762 527439.3676 448721.6819 390717.3271 318921.7188 212613.9908 374898.6499 370868.9398 347135.6854 378018.343 1.235460582 1.395274535 1.187036794 1.033593566 0.843667311 0.562443582 0.991747244 0.981087153 0.918303812 1 18.52809672 3.701362796 2.20379732 0.884188018 1.309939815 0.656881165 0.126798768 0.197259523 1.868170616 0.038615875 0.074921217 5027.624065 -3.701362796 0.425751797 ELLIFNK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLIFNK 7 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 110.35 0.015875 213052000 733340 717510 611260 578580 607280 486320 649410 604340 686530 664920 FALSE TRUE 704680.262 697047.3173 721728.2794 608440.5831 626813.7127 496153.7236 657357.6738 591860.1678 608597.9926 619884.3762 1.136793068 1.124479571 1.164294999 0.981538827 1.011178434 0.800397207 1.060452076 0.954791233 0.98179276 1 19.24163962 3.701532323 6.17684847 0.967051487 1.14023914 0.602287714 0.063967284 0.125088463 14.35534595 0.016505926 0.026276566 5029.586977 -3.701532323 0.173187653 QYSLQNWEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QYSLQNWEAR 10 0 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7 A0A2R8Y430 GSS Glutathione synthetase 0 ; 180.15 4.72E-06 1134820000 447480 526620 415380 280110 264300 82862 415310 236120 321430 401380 FALSE TRUE 429991.9869 511601.3132 490448.4061 294566.5107 272801.4495 84537.52641 420392.688 231244.0395 284942.6139 374194.1751 1.149114592 1.367208116 1.31067889 0.787202288 0.729037136 0.225918873 1.123461336 0.617978726 0.761483296 1 18.51342758 3.701719515 4.816219368 0.72369604 1.287511459 0.524808998 0.228989271 0.140857001 8.181969449 0.058942884 0.096318852 5031.755322 -3.701719515 0.563815419 HCPGGEGMFR ddPTM_BT-474_Pertuzumab_2h_R1 1 HCPGGEGMFR 10 0 E9PS41;Q6RFH5-2;Q6RFH5 E9PS41 WDR74 WD repeat-containing protein 74 0 78.655 0.029351 70344000 268160 261160 240300 177940 170340 83779 241720 179690 211730 248310 FALSE TRUE 257680.0107 253711.9725 283727.5554 187123.5047 175819.1408 85473.06878 244678.2417 175979.3387 187695.298 231491.7425 1.113128304 1.095987139 1.225648709 0.808337709 0.759505021 0.36922729 1.056963151 0.760197045 0.810807746 1 17.82060121 3.701753617 8.138421815 0.780661565 1.139913478 0.45497841 0.17499617 0.252110286 51.66686271 0.045854209 0.071857131 5032.150445 -3.701753617 0.359251913 SLSNS(ph)NPDISGTPTSPDDEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSNSNPDISGTPTSPDDEVR 21 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SLS(0.001)NS(0.999)NPDISGTPTSPDDEVR;SLS(0.001)NS(0.999)NPDISGTPTSPDDEVR 418.19 2.00E-152 763680000 296410 374820 303360 353710 291700 367650 385990 379650 410890 458540 TRUE FALSE 284825.9695 364130.5006 358183.9002 371965.0155 301082.7954 375084.1349 390713.8611 371810.0948 364247.4898 427482.6774 0.666286576 0.851801768 0.837891028 0.870128862 0.70431578 0.877425343 0.913987588 0.86976646 0.852075439 1 18.70550643 3.702110651 0.034290828 1.618623262 3.63E-10 0.506981384 0.063951414 305.3224226 2.39385476 47.28534299 66.26442931 5036.289086 -3.702110651 -1.618623262 AMHGELQK ddPTM_BT-474_Pertuzumab_2h_R1 2 AMHGELQK 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 105.04 0.0076861 0 568100 582110 514990 428910 497710 332900 513490 352970 563840 530590 FALSE TRUE 545898.0239 565508.7927 608060.1489 451046.0965 513719.2942 339631.4661 519774.2442 345681.0462 499835.247 494652.6667 1.103598668 1.143244201 1.229266897 0.911844061 1.038545486 0.686605954 1.050786298 0.698835909 1.010477211 1 18.91605633 3.702147609 8.849534862 0.89359106 1.157072299 0.434506551 0.126520238 0.304310316 71.09500927 0.031922155 0.04989005 5036.717687 -3.702147609 0.263481239 EGPEPPEEVPPPTT(ph)PPVPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGPEPPEEVPPPTTPPVPK 19 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 EGPEPPEEVPPPT(0.015)T(0.985)PPVPK;EGPEPPEEVPPPT(0.145)T(0.855)PPVPK;EGPEPPEEVPPPT(0.004)T(0.996)PPVPK 195.28 1.43E-14 934290000 1070560 1025800 940050 917180 975800 1031040 970620 1068470 1137330 1083970 TRUE FALSE 1028721.332 996545.1884 1109937.946 964515.7697 1007187.493 1051888.335 982498.7379 1046405.721 1008225.066 1010551.746 1.017979866 0.986139692 1.098348452 0.954444711 0.996670875 1.04090497 0.972239909 1.035479603 0.997697614 1 19.94671177 3.702611428 24.99993073 1.002959543 1.029354546 0.1572435 0.035535701 1292.360275 898740.497 0.00913428 0.01415263 5042.099689 -3.702611428 0.026395003 AAPPPPALT(ph)PDSQTVDSSCK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAPPPPALTPDSQTVDSSCK 20 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 AAPPPPALT(0.943)PDS(0.05)QT(0.007)VDSSCK 163.45 2.19E-10 94482000 133700 123610 111680 137670 136600 163030 161660 138010 168630 162700 TRUE FALSE 128474.8562 120084.7638 131863.0603 144775.1652 140993.8631 166326.5783 163638.4434 135160.0453 149487.8294 151680.1841 0.847011473 0.791697113 0.86934929 0.95447646 0.92954702 1.096561026 1.07883864 0.891085715 0.985546202 1 17.21067309 3.703347469 1.616287071 0.996030533 0.816332684 0.615155017 0.05806603 0.28634087 1.450030035 0.019137935 0.042713593 5050.652266 -3.703347469 -0.179697849 YELYSR ddPTM_BT-474_Pertuzumab_2h_R1 5 YELYSR 6 0 A0A0G2JQD6;Q8IXL6 A0A0G2JQD6 FAM20C Extracellular serine/threonine protein kinase FAM20C 0 ;;;; 109.88 0.067884 3630820000 2520910 2476360 3080950 1652460 2286960 1666880 2293040 2033240 1859080 2066490 FALSE TRUE 2422390.05 2405736.637 3637746.2 1737743.659 2360522.145 1700585.456 2321102.909 1991252.883 1648045.032 1926524.792 1.257388465 1.248744188 1.88824261 0.902009497 1.225274731 0.882721812 1.204813413 1.03359837 0.855449688 1 20.87756932 3.70338738 24.99649671 1.031185174 1.443187403 0.507873343 0.202190589 478.2080722 339847.2197 0.051622725 0.079976961 5051.116441 -3.70338738 0.412002229 TLFLGIPDENFEDHSAPPS(ph)PEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLFLGIPDENFEDHSAPPSPEEK 23 0 Q99683-2;Q99683 Q99683-2 MAP3K5 Mitogen-activated protein kinase kinase kinase 5 1 TLFLGIPDENFEDHSAPPS(1)PEEK;TLFLGIPDENFEDHSAPPS(1)PEEK 129.35 2.50E-05 228070000 201212 186878 187445 204795 241860 255990 289700 257330 346790 342980 TRUE FALSE 193348.4126 181548.4224 221320.4812 215364.4945 249639.6466 261166.2932 293245.4353 252016.0456 307423.8531 319749.6591 0.604686845 0.567783005 0.692167997 0.673540967 0.780734676 0.816783649 0.917109454 0.788166737 0.961451699 1 18.2865833 3.70340311 0.266442117 1.011093056 0.369963651 0.880911109 0.048357575 1.638675293 0.153306531 0.069582175 0.336761836 5051.299386 -3.70340311 -0.641129405 SWDSSSPVDRPEPEAAS(ph)PTTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SWDSSSPVDRPEPEAAS(0.978)PT(0.019)T(0.004)R 115.92 8.61E-05 308340000 138230 139910 109430 118940 118880 122930 113130 125650 128240 125900 TRUE FALSE 132827.8188 135919.9038 129206.4353 125078.5077 122703.8832 125415.7288 114514.5188 123055.2836 113682.7328 117372.6809 1.131675768 1.158019931 1.100822051 1.065652644 1.045421151 1.068525724 0.97564883 1.048415037 0.968562122 1 16.84073713 3.704728047 0.512297781 0.997398355 1.18409855 0.794131484 0.02714805 0.721008785 0.298521735 0.018677015 0.073094607 5066.733324 -3.704728047 0.186700195 YDNSLK ddPTM_BT-474_Pertuzumab_2h_R1 6 YDNSLK 6 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 134.66 0.032419 19718040000 11030390 10998920 9025110 9497200 9714410 9468150 9364190 10460590 11630560 10220690 FALSE TRUE 10599310.16 10685241.57 10656148.14 9987351.63 10026882.82 9659602.48 9478791.758 10244575.16 10310307.59 9528433.563 1.112387476 1.121405895 1.118352568 1.048163013 1.052311773 1.013766053 0.99479014 1.075158377 1.082056932 1 23.18380763 3.704872897 3.970652874 1.039369428 1.118677955 0.637863735 0.027439829 0.14893798 5.232124977 0.007838167 0.01322439 5068.423516 -3.704872897 0.079308527 RLIELYK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLIELYK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 141.39 0.004105 1068100000 1306630 1350130 1075100 1004800 922290 548020 1219540 1111030 1209590 1279070 FALSE TRUE 1255565.455 1311625.614 1269394.485 1056657.848 951956.2955 559101.3399 1234465.095 1088086.842 1072282.414 1192437.45 1.052940308 1.099953389 1.064537587 0.886132727 0.798328076 0.468872678 1.035245157 0.912489659 0.899235775 1 20.18548216 3.705191932 3.780931467 0.847392231 1.078674022 0.315766334 0.145770395 0.278016796 8.633142943 0.041321579 0.070328178 5072.148173 -3.705191932 0.231281791 KLAEQFPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLAEQFPR 8 1 Q96K17;Q96K17-2;E9PL10 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4;Transcription factor BTF3 0 113.71 0.0044847 434020000 468250 517620 421310 290760 302200 127980 390030 283470 292830 384990 FALSE TRUE 449950.2723 502857.9844 497450.089 305766.1584 311920.5375 130567.8433 394803.3038 277616.2454 259589.166 358914.2844 1.253642699 1.401053138 1.385985765 0.851919725 0.869066936 0.363785586 1.099993288 0.773488985 0.723262287 1 18.45327982 3.705468304 5.139613687 0.799139703 1.354424861 0.634408209 0.186184102 0.112516499 8.125827903 0.048277708 0.078563099 5075.376966 -3.705468304 0.555285158 IIDPLPPIDHSEIDYPPFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IIDPLPPIDHSEIDYPPFEK 20 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 148.26 2.37E-08 0 65388 62882 47959 61604 61214 61685 67181 63112 69962 65126 FALSE TRUE 62832.56467 61088.66693 56626.25814 64783.38982 63183.0039 62932.31296 68003.18117 61808.71515 62020.20706 60714.95801 1.034877841 1.006155138 0.932657454 1.067008723 1.040649718 1.036520736 1.120039993 1.018014624 1.021497982 1 15.88976437 3.705813322 24.99996037 1.04667163 0.992722596 0.27118603 0.038902853 777.833181 593813.9196 0.01021967 0.015833755 5079.410609 -3.705813322 -0.053949033 KQDAETPPPPDPPAPETLLAPPPLPS(ph)TPDPPRR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQDAETPPPPDPPAPETLLAPPPLPSTPDPPRR 33 2 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 KQDAETPPPPDPPAPET(0.006)LLAPPPLPS(0.497)T(0.497)PDPPRR;KQDAETPPPPDPPAPET(0.001)LLAPPPLPS(0.499)T(0.499)PDPPRR 85.097 0.00021996 990840000 793180 818200 759800 676120 689320 731070 646800 810460 856020 775040 TRUE FALSE 762181.6487 794865.7371 897112.7617 711014.6342 711492.6038 745852.7363 654715.7319 793723.7178 758848.1983 722545.8505 1.054855755 1.100090377 1.24159977 0.984040852 0.98470236 1.032256618 0.90612344 1.098509828 1.050242276 1 19.46272961 3.706594017 24.99214618 1.011155562 1.128972865 0.439353344 0.064192946 610.5791927 477363.5806 0.017274339 0.026763541 5088.549655 -3.706594017 0.117817303 DRYDS(ph)DRYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRYDSDRYR 9 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 DRYDS(1)DRYR 60.255 0.076332 277350000 148800 142140 118120 104270 91936 92670 108060 131540 94643 100910 TRUE FALSE 142984.7315 138086.3064 139466.9116 109651.3872 94893.20493 94543.85089 109382.4706 128823.653 83899.52342 94075.27582 1.519897021 1.467827813 1.48250335 1.165570722 1.008694411 1.004980853 1.162712197 1.369367795 0.891833935 1 16.52152799 3.706912044 4.148823322 1.111475203 1.492123563 0.689284495 0.123916705 0.140078091 5.561394999 0.03646693 0.061214638 5092.277288 -3.706912044 0.38064836 LSDFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSDFFK 6 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 113.25 0.061181 298200000 890780 879660 748430 732010 736860 561110 792450 831180 904360 903220 FALSE TRUE 855967.3328 854572.9581 883687.9497 769789.1238 760561.7711 572456.0286 802148.2401 814015.8425 801700.8442 842044.1049 1.016535034 1.014879094 1.049455657 0.914190978 0.903232701 0.679840908 0.95262022 0.966714021 0.952088898 1 19.68353628 3.70693227 8.109369927 0.905035468 1.025737418 0.293855161 0.082983532 0.357777579 84.08360742 0.023441635 0.036884466 5092.514446 -3.70693227 0.12070195 DVCLYPR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVCLYPR 7 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;; 118.69 0.011517 2345760000 2185070 2421190 2121580 1522530 1440820 536775 2158260 1653660 1726370 2088390 FALSE TRUE 2099675.049 2352140.032 2504996.7 1601107.956 1487165.284 547628.9583 2184673.431 1619511.343 1530399.715 1946941.485 1.078447948 1.208120557 1.286631735 0.822370866 0.763846934 0.281276537 1.122105337 0.831823327 0.786053267 1 20.89277809 3.706969533 9.048480323 0.793166415 1.192701137 0.421176364 0.209372956 0.362095698 100.1756006 0.056298099 0.088204472 5092.951415 -3.706969533 0.399534722 AAT(ph)PLPSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AATPLPSLR 9 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AAT(0.998)PLPS(0.002)LR;AAT(0.995)PLPS(0.005)LR;AAT(0.999)PLPS(0.001)LR 105.52 0.034474 2020710000 2493030 2684990 2442230 2151520 2037010 2122230 2029770 2662570 2510890 2614300 TRUE FALSE 2395599.631 2608416.714 2883595.288 2262560.205 2102532.277 2165142.945 2054610.932 2607586.999 2225864.294 2437231.132 0.982918526 1.07023773 1.183143958 0.928332227 0.862672501 0.888361763 0.843010294 1.069897296 0.913275833 1 21.21681164 3.707392739 24.06271252 0.931036226 1.077913833 0.443623221 0.076655614 395.4024637 305264.5746 0.021530902 0.033360608 5097.916752 -3.707392739 0.146877607 FSALQQAVPTESTDNRR ddPTM_BT-474_Pertuzumab_2h_R1 6 FSALQQAVPTESTDNRR 17 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;;; 234.04 6.42E-20 4236680000 1936060 2041380 1620830 2017750 2056050 2171930 2109780 2163480 2291090 2449020 FALSE TRUE 1860396.635 1983161.841 1913750.036 2121886.319 2122184.716 2215847.913 2135600.119 2118803.382 2031015.068 2283145.694 0.81483921 0.868609413 0.838207584 0.929369652 0.929500347 0.970524097 0.935376189 0.92801935 0.889568753 1 21.12259149 3.707440926 4.919189809 0.937904228 0.842854728 0.700072279 0.029909266 0.105950546 6.838496601 0.007663825 0.012564986 5098.482413 -3.707440926 -0.095049499 ASAPS(ph)PNAQVACDHCLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASAPSPNAQVACDHCLK 17 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 1 ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK 316.14 1.75E-58 5271000000 3013020 2903060 2977990 2302960 2397660 2596730 2397250 2448290 2625100 3129820 TRUE FALSE 2895267.847 2820267.571 3516179.038 2421816.042 2474782.911 2649237.66 2426588.263 2397731.956 2327109.653 2917834.504 0.992265957 0.966561869 1.205064589 0.830004594 0.848157395 0.907946512 0.831640129 0.821750498 0.797546828 1 21.47646663 3.707777552 24.86859521 0.852656834 1.04582395 0.544095891 0.080151656 425.5266481 343768.5875 0.020371937 0.031564146 5102.43584 -3.707777552 0.193167116 LNIWDWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNIWDWK 7 0 O60508 O60508 CDC40 Pre-mRNA-processing factor 17 0 84.476 0.050059 73080000 275560 283940 257650 238530 255660 262910 229080 270640 273400 308180 FALSE TRUE 264790.8106 275842.3092 304213.0864 250840.5619 263883.5361 268226.2203 231883.5496 265051.1894 242364.7782 287306.6941 0.921631191 0.960097049 1.058844408 0.87307594 0.91847333 0.933588482 0.807094141 0.922537466 0.843575117 1 18.13223208 3.707782926 24.86441638 0.894772307 0.978181541 0.278415097 0.058926265 717.2779445 579468.411 0.014851724 0.023010928 5102.498973 -3.707782926 0.083409234 TGSEPALS(ph)PAVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGSEPALSPAVVR 13 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 TGSEPALS(1)PAVVR;TGSEPALS(1)PAVVR 245.18 4.56E-17 555600000 678290 677780 635150 567800 533320 666870 563960 648670 723220 676410 TRUE FALSE 651781.6769 658450.378 749935.7338 597104.226 550474.7221 680354.5683 570861.9112 635274.7378 641123.0976 630596.1482 1.033596033 1.044171265 1.189248834 0.946888476 0.872943363 1.078906952 0.905273387 1.007419312 1.016693647 1 19.26635683 3.708175488 24.98538943 0.973564766 1.084522011 0.372421029 0.067447304 679.0215584 558352.7062 0.017457029 0.027047371 5107.11324 -3.708175488 0.110957245 NNWEVSALSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NNWEVSALSR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 120.36 0.0064045 0 363047 320497 395023 241891 295108 354642 311126 302912 358956 347137 FALSE TRUE 348858.7219 311356.7394 466412.4433 254375.0235 304600.4168 361813.1042 314933.6531 296656.7613 318208.8197 323625.1018 1.077971764 0.962090819 1.441212195 0.786017593 0.941213815 1.118000743 0.973143465 0.916667958 0.983263715 1 18.30396399 3.708366973 24.99855675 0.960212392 1.140591827 0.309597237 0.136358455 858.7974487 711033.6238 0.035498128 0.055001886 5109.36552 -3.708366973 0.180379434 MDRT(ph)PPPPTLSPAAITVGR ddPTM_BT-474_Pertuzumab_2h_R1 7 MDRTPPPPTLSPAAITVGR 19 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C4H9 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(0.99)PPPPT(0.001)LS(0.006)PAAIT(0.004)VGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR 182.23 4.80E-14 4684560000 1218108 1225073 952743 1160697 1150103 1220839 1156011 1324949 1272554 1317665 TRUE FALSE 1170502.993 1190135.118 1124924.854 1220600.711 1187097.107 1245525.201 1170158.608 1297588.34 1128099.005 1228418.376 0.952853698 0.968835326 0.915750591 0.993635992 0.966362219 1.013925895 0.952573351 1.056308148 0.918334524 1 20.22837057 3.708437841 24.43396391 0.990513041 0.948115412 0.189464514 0.037025103 733.3835037 594880.6205 0.009386708 0.01454416 5110.199338 -3.708437841 -0.042397628 MQAQWER ddPTM_BT-474_Pertuzumab_2h_R1 2 MQAQWER 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 107.67 0.019324 212120000 310250 328480 267162 221221 212103 134394 271849 252886 239735 252423 FALSE TRUE 298125.087 319112.072 315444.1164 232638.2423 218925.4856 137111.5388 275175.9694 247663.8157 212521.2879 235326.1654 1.26685907 1.356041609 1.340454921 0.988577883 0.930306603 0.582644682 1.169338603 1.052427873 0.90309247 1 17.84430221 3.708457409 5.117882252 0.950846487 1.326297527 0.5911484 0.142848468 0.138291668 10.14091373 0.040445255 0.06606876 5110.42959 -3.708457409 0.37545104 MQHLIAR ddPTM_BT-474_Pertuzumab_2h_R1 12 MQHLIAR 7 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;; 146.94 0.0021848 11021360000 13272920 14329590 12569200 6814421 6821062 1904675 10861560 5600688 6949544 8893260 FALSE TRUE 12754199.61 13920924.12 14840734.04 7166114.084 7040467.654 1943188.833 10994487.02 5485031.836 6160660.9 8290911.579 1.538335018 1.679058327 1.790000279 0.864333676 0.849178958 0.234375776 1.326089045 0.661571624 0.743061947 1 22.9830993 3.709393478 7.122218518 0.796802409 1.670515209 0.688841425 0.264135269 0.106248237 20.59152545 0.067561697 0.107310235 5121.456374 -3.709393478 0.8737128 VMDQHK ddPTM_BT-474_Pertuzumab_2h_R1 1 VMDQHK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 80.377 0.064673 340710000 813110 829520 735160 399010 354780 41041 662870 360990 399460 598270 FALSE TRUE 781332.7623 805862.9018 868019.7655 419602.9539 366191.8209 41870.87714 670982.4013 353535.4303 354114.9755 557748.64 1.400868969 1.444849604 1.556292034 0.752315512 0.656553499 0.075071231 1.203019341 0.633861573 0.634900652 1 19.08925557 3.709577408 6.728637328 0.689942186 1.465720198 0.613764917 0.275852665 0.119506981 20.14198211 0.072017568 0.11484391 5123.625853 -3.709577408 0.775778012 GFCYVEFDEVDSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFCYVEFDEVDSLK 14 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 217.83 1.31E-11 448750000 261810 260240 250740 257430 295640 270110 284930 341780 361040 369840 FALSE TRUE 251578.1758 252818.21 296054.2957 270715.9932 305149.5291 275571.8093 288417.0586 334722.1236 320056.2528 344790.4074 0.72965538 0.733251867 0.858650036 0.785161035 0.885029057 0.79924442 0.83649966 0.970798828 0.928263217 1 18.39536011 3.709664709 0.185069815 1.048379449 0.557524919 0.752690537 0.044347609 5.287716499 0.270924218 0.144285295 0.64274032 5124.655896 -3.709664709 -0.490854529 VDCGYPHVTPK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDCGYPHVTPK 11 0 X6R3S7;Q07654 X6R3S7 TFF3 Trefoil factor 3 0 ;;; 136.48 9.84E-05 1924240000 4325670 4392130 4341070 3398870 3324320 3760430 3360590 3649550 4071370 4509690 FALSE TRUE 4156618.034 4266870.753 5125597.916 3574286.088 3431249.772 3836468.471 3401717.906 3574185.517 3609205.146 4204244.679 0.988671771 1.014895915 1.219148338 0.850161292 0.81613941 0.912522644 0.809115112 0.850137371 0.858466959 1 22.0034152 3.709700307 24.79029482 0.85989638 1.068304406 0.592523313 0.076832114 378.6377892 325240.5327 0.019423311 0.030096556 5125.07596 -3.709700307 0.208408026 DTLYEAVR ddPTM_BT-474_Pertuzumab_2h_R1 3 DTLYEAVR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;; 98.009 0.018208 1131000000 2185320 2148660 1751610 1304350 1369450 394660 1810960 1330760 1287820 1727400 FALSE TRUE 2099915.278 2087382.321 2068164.891 1371667.66 1413499.603 402640.2956 1833123.07 1303279.341 1141632.073 1610401.659 1.303969892 1.296187388 1.284254074 0.851754997 0.877731089 0.250024764 1.138301777 0.809288374 0.708911386 1 20.61898913 3.709814986 3.492370482 0.792244626 1.304235237 0.517190717 0.217248278 0.186205286 4.796795569 0.058174713 0.100911293 5126.429459 -3.709814986 0.51199061 AYLLIEEDIRDLAASDDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYLLIEEDIRDLAASDDYR 19 1 H7C1J2 H7C1J2 DNTTIP1 0 156.11 1.75E-08 27503000 37226 43346 18302 48832 53259 74263 34465 46969 46363 31610 FALSE TRUE 35771.16676 42109.81452 21609.57853 51352.22537 54972.1241 75764.64874 34886.79298 45999.07374 41100.06661 29469.02654 1.21385641 1.428951664 0.73329801 1.742583023 1.865420428 2.570992585 1.183846128 1.560929529 1.394686945 1 14.84691178 3.709882124 24.64681755 1.656533964 1.15572686 0.208333462 0.433119433 883.7836294 759539.605 0.11651052 0.180535067 5127.22202 -3.709882124 -0.500807104 CVFS(ph)YNSNCQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 CVFSYNSNCQEK 12 0 Q6NT55 Q6NT55 CYP4F22 Cytochrome P450 4F22 1 CVFS(0.348)Y(0.305)NS(0.348)NCQEK 52.344 0.096178 3981700000 1924800 1374300 2508000 757540 1503200 1564700 1459700 1471200 1323500 1384000 TRUE FALSE 1849576.688 1335106.31 2961251.39 796636.7302 1551551.793 1596339.306 1477564.245 1440819.206 1173261.829 1290260.447 1.433490961 1.034757217 2.295080343 0.617423197 1.202510545 1.237222539 1.145167434 1.116688657 0.909321704 1 20.29923088 3.710051699 24.99964343 1.062854217 1.532474917 0.359655815 0.335350851 824.0700653 722632.1288 0.085191421 0.132004959 5129.224399 -3.710051699 0.4696207 QEQSYFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEQSYFVR 8 0 O60664-4;O60664;O60664-3;O60664-2 O60664-4 PLIN3 Perilipin-3 0 ; 140.35 0.0029436 0 280440 288590 258130 242040 257219 228619 264000 259420 289700 290240 FALSE TRUE 269480.0948 280359.6958 304779.8331 254531.7134 265492.6827 233241.8328 267230.911 254062.8863 256814.4705 270581.7863 0.995928434 1.036136614 1.126387098 0.9406831 0.981191995 0.862001231 0.987616035 0.938950437 0.949119577 1 18.0457052 3.711074267 24.94895981 0.948103086 1.051149311 0.496458553 0.046731448 523.9358864 475569.1593 0.011935306 0.018494665 5141.315633 -3.711074267 0.103046225 QGFDFLCMPVFHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGFDFLCMPVFHPR 14 0 O14744-2;O14744;G3V580;O14744-4;O14744-3;O14744-5;G3V2L6;C9JSX3 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 136.51 2.66E-05 145100000 151120 168970 127320 97208 85888 48413 119010 92301 105770 130050 FALSE TRUE 145214.0633 164151.141 150329.5562 102224.9165 88650.66552 49391.94403 120466.48 90394.95209 93763.43302 121241.5977 1.197724759 1.353917667 1.239917315 0.843150523 0.731190179 0.40738447 0.993606834 0.745577045 0.773360256 1 16.88752524 3.711286359 3.477635676 0.761530381 1.283198247 0.659612757 0.15818304 0.132841636 3.393849583 0.042165992 0.073304516 5143.827066 -3.711286359 0.521667866 APGASPGNPLS(ph)PSLSDKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 APGASPGNPLSPSLSDKDR 19 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 APGAS(0.002)PGNPLS(0.827)PS(0.077)LS(0.095)DKDR;APGASPGNPLS(0.793)PS(0.16)LS(0.047)DKDR 88.504 0.0015418 863420000 343040 335100 282850 343980 382180 390670 354770 380000 393400 364850 TRUE FALSE 329633.6175 325543.2761 333967.287 361732.849 394473.1668 398569.6151 359111.7814 372152.8672 348742.8813 340138.3845 0.969116197 0.957090675 0.981857097 1.063487291 1.159743166 1.171786641 1.055781405 1.094121934 1.025297047 1 18.3757623 3.711342461 3.430240677 1.09253524 0.96512463 0.507972795 0.050542362 0.181392432 4.483705215 0.013936809 0.024293849 5144.491578 -3.711342461 -0.127410611 SEGSMSTDKR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEGSMSTDKR 10 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;;; 152.54 2.86E-05 1044070000 873940 813890 782270 695972 715640 655800 780240 784510 818690 849800 FALSE TRUE 839785.4586 790678.6541 923643.5905 731891.1983 738659.2105 669060.7253 789788.8105 768309.5943 725755.7434 792242.2891 1.060010896 0.998026317 1.165859994 0.923822432 0.932365289 0.844515289 0.996903121 0.969791193 0.916078015 1 19.59558219 3.711399606 24.82946126 0.940274576 1.066971811 0.537850768 0.056845853 507.875749 464278.7896 0.014976046 0.02320804 5145.168541 -3.711399606 0.126697235 SPPAS(ph)PESWK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 SPPAS(1)PESWK;SPPAS(1)PESWK;SPPAS(1)PESWK;SPPAS(1)PESWK 137.4 9.68E-05 2038450000 3771190 3922870 3288900 3438680 3436990 3807050 3492390 3662220 3882440 4172660 TRUE FALSE 3623807.726 3810993.588 3883277.391 3616150.687 3547543.905 3884031.159 3535130.914 3586593.877 3441721.688 3890042.022 0.931560046 0.979679286 0.998261039 0.929591677 0.911955163 0.998454808 0.908764197 0.921993608 0.884751802 1 21.89135431 3.711640481 24.47708953 0.932502843 0.970818042 0.131403712 0.038292519 939.3063053 854062.7305 0.009902713 0.015347389 5148.023027 -3.711640481 0.038315199 RFELYFQGPSSNKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RFELYFQGPSSNKPR 15 2 P33993;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 143.14 2.51E-06 323040000 287790 285460 230030 215220 201020 236660 209830 208470 230730 258040 FALSE TRUE 276542.8486 277318.9603 271601.538 226327.53 207485.9909 241445.4273 212397.9623 204165.0216 204538.4977 240562.721 1.149566514 1.152792749 1.129025881 0.940825449 0.862502677 1.00366934 0.88292135 0.848697674 0.850250184 1 17.87605357 3.712173351 3.335170706 0.899600642 1.150440646 0.802801819 0.05265141 0.098073028 2.269273837 0.01456559 0.025550296 5154.343417 -3.712173351 0.250840004 LGQSDPAPLQHQMDIYQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGQSDPAPLQHQMDIYQK 18 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 215.75 9.34E-19 948250000 1582350 1491670 1275750 969430 1185230 336540 1213890 1057800 1101120 1205080 FALSE TRUE 1520510.013 1449129.032 1506306.404 1019462.398 1223353.999 343345.0694 1228745.949 1035956.06 976125.4739 1123458.858 1.353418509 1.289881709 1.34077576 0.907431893 1.088917489 0.305614279 1.093716908 0.922113038 0.868857339 1 20.09951586 3.712259108 4.432474534 0.877410766 1.32796964 0.485434812 0.209485966 0.170980034 8.350078477 0.05535685 0.092541913 5155.361305 -3.712259108 0.450558874 KAPDFVFYAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAPDFVFYAPR 11 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 122.34 0.00062972 1403530000 2891900 3100100 2326030 1773470 1408040 1128730 2001380 1705240 1770260 2012440 FALSE TRUE 2778881.351 3011688.183 2746395.363 1864998.999 1453330.885 1151553.694 2025873.487 1670026.198 1569307.506 1876135.646 1.48117294 1.605261426 1.463857567 0.99406405 0.774640623 0.613790211 1.079811841 0.8901415 0.83645738 1 20.83933271 3.712282148 3.133055354 0.866338806 1.54399744 0.854078838 0.121012446 0.088285091 1.767442815 0.034040801 0.060495781 5155.634816 -3.712282148 0.677658634 SIFQHIQSAQSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIFQHIQSAQSQR 13 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 137.93 5.49E-05 1264650000 1309900 1624920 1288930 930960 987890 349030 1295890 944250 1024250 1235500 FALSE TRUE 1258707.66 1578578.873 1521868.323 979006.9572 1019666.379 356087.6257 1311749.489 924750.9075 907981.434 1151818.485 1.092800365 1.370510105 1.32127444 0.849966353 0.885266553 0.309152554 1.138850875 0.802861666 0.788302537 1 20.13548195 3.712335473 6.805656693 0.815622731 1.272852676 0.472436292 0.211207724 0.150369986 27.87828577 0.054769354 0.087563177 5156.267898 -3.712335473 0.457229945 EIDDEANSYFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIDDEANSYFQR 12 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4;H3BR89;H3BMH0 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 179.2 4.89E-05 179660000 444690 500080 524870 346590 381930 456710 448800 435930 425450 441640 FALSE TRUE 427311.0232 485818.208 619725.6847 364477.5514 394215.1253 465944.9891 454292.5487 426927.8932 377154.6996 411727.3294 1.037849549 1.179951325 1.505184719 0.885240122 0.957466501 1.131683412 1.103382059 1.036919006 0.916030277 1 18.65132969 3.712401251 24.98586056 1.016487879 1.234890948 0.410473423 0.129311097 760.2948539 726188.2109 0.035004163 0.054244861 5157.048917 -3.712401251 0.218403069 GSLDQDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSLDQDRR 8 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 0 ;;; 113.62 0.0045108 1250720000 1739240 2240520 1526660 1214920 938350 155013 1955770 923090 1296200 1718070 FALSE TRUE 1671268.578 2176622.563 1802561.422 1277622.167 968532.8799 158147.4691 1979705.298 904027.8689 1149060.81 1601703.589 1.043431875 1.358942178 1.125402625 0.797664547 0.604689211 0.098737039 1.235999789 0.56441646 0.717399161 1 20.61117576 3.712593991 3.114881435 0.684673657 1.208903796 0.353284486 0.286590123 0.25704352 5.079334893 0.076385789 0.13595857 5159.338126 -3.712593991 0.524230139 IEDFGVHCK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEDFGVHCK 9 0 Q92905;E5RHH5 Q92905 COPS5 COP9 signalosome complex subunit 5 0 ; 114.5 0.0016287 961440000 1359510 1372790 1152950 1339660 1430760 1451930 1452020 1459580 1640060 1670970 FALSE TRUE 1306378.846 1333639.373 1361313.712 1408800.013 1476781.695 1481289.019 1469790.255 1429439.163 1453887.264 1557793.714 0.83860837 0.856107816 0.873872901 0.90435595 0.94799567 0.950889072 0.94350763 0.917604912 0.933298968 1 20.57107277 3.712616962 1.490693964 0.943255603 0.8450542 0.799856485 0.020906487 0.186499681 0.800567915 0.006367696 0.015036493 5159.611029 -3.712616962 -0.098201403 (ac)MESYHKPDQQK ddPTM_BT-474_Pertuzumab_2h_R1 9 MESYHKPDQQK 11 1 P29401;P29401-2;E9PFF2;F8W888;F8WAX4 P29401 TKT Transketolase 0 ;;;;;;;; 103.08 6.63E-08 8630650000 7221420 8075850 5981940 6027570 6255630 4098100 6663540 6325360 6903880 7404490 FALSE TRUE 6939198.923 7845534.665 7063009.626 6338653.61 6456848.02 4180966.39 6745090.396 6194739.106 6120180.486 6902977.297 1.005247247 1.1365436 1.023183088 0.918249233 0.93537147 0.605675813 0.97712771 0.897401054 0.886600118 1 22.71878731 3.712707261 2.226886781 0.875388851 1.073472073 0.349298025 0.10569924 0.325018359 3.144266131 0.029675482 0.057964853 5160.683933 -3.712707261 0.198083223 TQLWFHGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQLWFHGR 8 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 115.71 0.0024106 1598710000 1217290 1435610 1238500 753900 735770 170665 1243580 732100 763000 950030 FALSE TRUE 1169716.961 1394667.808 1462324.5 792808.8693 759436.7103 174115.9632 1258799.304 716981.8792 676387.4388 885683.6219 1.320693905 1.574679461 1.651068693 0.895137778 0.857458229 0.196589345 1.421274226 0.809523696 0.763689677 1 19.75643192 3.712794682 9.345887512 0.847330993 1.521380203 0.524033505 0.291017262 0.298009444 104.9554184 0.076355921 0.120141258 5161.722852 -3.712794682 0.67404921 NIELICQENEGENDPVLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NIELICQENEGENDPVLQR 19 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 260.5 9.59E-31 250770000 190720 201854 150653 169423 175042 164119 154865 177471 198909 204875 FALSE TRUE 183266.4515 196097.3216 177879.3484 178166.9413 180672.3849 167437.5986 156760.2842 173806.1618 176329.6842 190998.6338 0.959517081 1.026694891 0.931312151 0.932817884 0.945935483 0.876642913 0.820740343 0.909986414 0.923198668 1 17.54320279 3.71305061 1.179431516 0.898643928 0.991920867 0.24693675 0.04796006 0.597398729 1.58151125 0.015872186 0.043605542 5164.765524 -3.71305061 0.093276939 SIFDHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIFDHIK 7 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 79.116 0.033497 745000000 1285440 1395410 1149070 834780 743730 228875 1306750 821140 959760 1216080 FALSE TRUE 1235203.584 1355614.273 1356732.51 877863.0958 767652.7509 233503.0093 1322742.397 804183.172 850812.0684 1133713.818 1.089519739 1.195728808 1.196715157 0.774325126 0.677113341 0.205962921 1.166733946 0.709335248 0.750464583 1 20.11262508 3.713241612 6.278258296 0.739459255 1.164930544 0.385694678 0.234210647 0.173357827 25.75381651 0.06179289 0.099513807 5167.037478 -3.713241612 0.425471289 LRLPLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRLPLDK 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 102.46 0.0078384 668740000 699670 702090 571090 894700 873740 1185050 777030 1006570 1091940 1040170 FALSE TRUE 672326.1229 682067.0806 674298.6668 940875.5742 901844.6406 1209012.523 786539.5256 985783.9777 967987.549 969718.3594 0.693321021 0.703366162 0.695355162 0.970256534 0.930006771 1.246766663 0.811100994 1.016567303 0.998215141 1 19.88720627 3.713502106 4.222321871 0.996877627 0.694742102 0.647825111 0.101070083 0.125056963 5.336153422 0.026267007 0.044287246 5170.13765 -3.713502106 -0.302135525 EILWRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EILWRPK 7 1 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 77.282 0.035083 412880000 1310100 1280300 1334100 980930 1077000 1060800 1136900 1202800 1245900 1164000 FALSE TRUE 1258899.844 1243787.098 1575201.547 1031555.915 1111642.683 1082250.103 1150813.722 1177961.76 1104470.655 1085161.243 1.160103949 1.146177221 1.451582939 0.950601509 1.02440323 0.99731732 1.060500206 1.085517721 1.017794049 1 20.049478 3.713516088 24.99803387 1.02825643 1.241977021 0.611281885 0.084878888 508.5729052 507628.9539 0.022394145 0.03470961 5170.304109 -3.713516088 0.213720592 FPDELAHVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FPDELAHVEK 10 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 126.67 0.0003764 377880000 808380 759210 833510 931100 831130 795140 1027200 1060800 1130000 1300700 FALSE TRUE 776787.6159 737558.0741 984143.7983 979154.1826 857864.0513 811218.2756 1039771.181 1038894.109 1001727.137 1212602.43 0.640595463 0.608243935 0.811596426 0.807481626 0.707456978 0.668989485 0.857470804 0.856747507 0.826096924 1 20.20967519 3.713811768 0.061272423 1.441078539 1.90E-09 0.679274367 0.064736469 66.66523686 0.942172977 7.972093605 14.53317307 5173.825393 -3.713811768 -1.441078537 IYHPNVDK ddPTM_BT-474_Pertuzumab_2h_R1 5 IYHPNVDK 8 0 P61088;F8VSD4;F8VV71;F8VQQ8;Q5JXB2 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ;;;; 119.27 0.0017256 6156410000 10465570 10575550 9024640 9162740 8932770 7764230 10612270 9836550 11167330 11388580 FALSE TRUE 10056563.95 10273945.67 10655593.2 9635630.109 9220100.66 7921228.05 10742146.13 9633421.805 9899661.516 10617221.33 0.947193587 0.967668032 1.003614116 0.907547258 0.868409951 0.746073554 1.011766243 0.907339265 0.932415479 1 23.33990291 3.713835138 19.55233404 0.90465895 0.972309423 0.137994047 0.070316065 89.50829827 70780.74875 0.01889998 0.029327633 5174.103812 -3.713835138 0.067650473 GISTKPVYIPEVELNHK ddPTM_BT-474_Pertuzumab_2h_R1 1 GISTKPVYIPEVELNHK 17 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 109.38 0.00036634 722670000 734040 642330 599610 586240 575400 611370 624510 603600 748630 675110 FALSE TRUE 705352.9053 624011.3773 707972.8653 616495.9167 593908.2636 623732.3203 632152.9402 591135.4491 663648.6609 629384.1984 1.120703232 0.991463368 1.124865968 0.979522394 0.943633897 0.991019987 1.004399128 0.939228297 1.05444125 1 19.26358143 3.714235084 24.29327928 0.981771457 1.070256105 0.446916203 0.046060422 445.5757662 444985.0806 0.011412131 0.017688679 5178.870889 -3.714235084 0.088484648 VSDILHSIFSSYK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSDILHSIFSSYK 13 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 159.08 4.62E-05 194648000 940190 1138570 1072160 724350 678300 262150 1092900 663140 924230 1289640 FALSE TRUE 903446.3354 1106099.098 1265923.162 761733.7903 700118.1355 267450.8526 1106275.237 649445.9273 819315.2851 1202291.534 0.751436993 0.91999242 1.05292529 0.633568289 0.582319775 0.222450916 0.920138923 0.540173418 0.681461411 1 20.19735534 3.71471966 21.685549 0.625990251 0.909305537 0.224738896 0.211499453 177.3282845 161296.2102 0.05389667 0.083597074 5184.65258 -3.71471966 0.283315287 RGILTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGILTLK 7 1 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38;P0CG39 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ; 157.34 0.0023769 15211900000 6230100 6924200 5880300 4310300 3873600 1281930 6201500 4927700 5026000 5833200 FALSE TRUE 5986620.804 6726728.596 6943001.017 4532755.1 3998197.862 1307851.503 6277395.812 4825941.273 4455469.551 5438112.168 1.100863796 1.236960252 1.276730012 0.833516294 0.735217983 0.240497338 1.15433364 0.88742952 0.819304459 1 22.37467448 3.714743395 9.231896568 0.805018684 1.208078747 0.391513005 0.22548499 0.370374635 138.4958031 0.062005163 0.097836358 5184.935939 -3.714743395 0.403060063 HLAGEVAK ddPTM_BT-474_Pertuzumab_2h_R1 3 HLAGEVAK 8 0 Q13200;Q13200-3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;; 111.74 0.0031755 685260000 1816380 1742440 1563900 1527870 1629930 1433630 1844880 1311250 2034980 2088710 FALSE TRUE 1745393.861 1692747.317 1846531.519 1606723.554 1682358.179 1462618.981 1867458.193 1284172.229 1803977.602 1947239.811 0.896342531 0.869306034 0.948281515 0.825128751 0.863970718 0.751124218 0.959028355 0.659483348 0.926428061 1 20.89299914 3.714769604 24.02291078 0.832993692 0.901109634 0.018209187 0.096744556 1084.263031 1094831.525 0.024394301 0.037818238 5185.248857 -3.714769604 0.068115941 AS(ph)PGLLPVANGNSLNK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPGLLPVANGNSLNK 16 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK 276.3 2.85E-35 942040000 2090740 2026970 1787260 1800360 1698850 1890660 1875190 2088080 2112610 2163590 TRUE FALSE 2009031.569 1969162.8 2110257.639 1893276.795 1753495.053 1928890.441 1898139.136 2044960.418 1872795.37 2017048.122 0.996025602 0.976259703 1.046210854 0.938637395 0.869337243 0.956293714 0.941048017 1.01383819 0.928483237 1 20.94381407 3.714864494 24.91286769 0.950565838 1.003174826 0.288849556 0.040529218 1034.959536 1088102.884 0.011438093 0.017733181 5186.381912 -3.714864494 0.052608988 VTMLFLGLHNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTMLFLGLHNVR 12 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 105.17 0.0020589 184620000 154650 148350 149350 110890 110610 68674 148780 109970 141800 148930 FALSE TRUE 148606.107 144119.2032 176340.8673 116613.0462 114167.8711 70062.63533 150600.8141 107699.0811 125703.4585 138842.8384 1.070318849 1.038002427 1.270075355 0.83989241 0.82228131 0.504618287 1.084685504 0.775690574 0.905365087 1 17.08309324 3.71496241 23.26844067 0.834259694 1.117319189 0.403003835 0.154707 291.3524157 287280.8263 0.03978439 0.061689633 5187.551363 -3.71496241 0.283059495 GSPQQIDHAK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSPQQIDHAK 10 0 A0A087WTP3;Q92945;M0R3J3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;; 142.07 3.64E-05 2919180000 2554100 2451070 2037190 2366670 2401830 2512300 2466320 2554650 2757300 2632380 FALSE TRUE 2454282.948 2381167.883 2405355.55 2488814.122 2479087.043 2563100.427 2496503.562 2501895.585 2444302.864 2454086.558 1.000080026 0.970286837 0.980142914 1.014150913 1.010187288 1.044421363 1.017284233 1.019481394 0.996013305 1 21.2267547 3.715041811 5.938904222 1.016805149 0.982091901 0.497121666 0.014143246 0.125625643 16.04208298 0.003706368 0.006012061 5188.499876 -3.715041811 -0.034713248 QLRDELR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLRDELR 7 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 ; 130.27 0.007481 206160000 247240 296650 227230 199135 194678 111794 263220 216361 215436 252840 FALSE TRUE 237577.5875 288189.8325 268295.5157 209412.3812 200939.9947 114054.5513 266441.3651 211893.0697 190980.6085 235714.9216 1.007902198 1.222620233 1.138220329 0.888413766 0.852470405 0.483866488 1.130354257 0.898937871 0.810218577 1 17.84668356 3.715048164 5.207913916 0.862947572 1.134249091 0.345100705 0.161934966 0.199204099 16.36823054 0.043422905 0.071368831 5188.57578 -3.715048164 0.27130152 SHKDEVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHKDEVVK 8 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 123.86 0.00079885 779120000 2418500 2297400 1808500 1778960 1859920 1383440 2234300 1021340 2465900 2097440 FALSE TRUE 2323982.346 2231880.401 2135336.18 1870772.339 1919746.016 1411414.105 2261644.032 1000248.972 2185981.37 1955378.521 1.188507658 1.141405809 1.092032135 0.956731558 0.981777183 0.721811194 1.156627225 0.511537261 1.117932588 1 20.89901648 3.715242344 1.04135606 0.862045751 1.194061437 0.231420427 0.179431252 0.731207027 1.48590348 0.061593031 0.184460244 5190.896188 -3.715242344 0.332015686 EKINIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKINIR 6 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 99.919 0.034885 2014540000 3146430 3404860 2509310 2305070 2705780 912340 2749090 2577770 2482690 2763090 FALSE TRUE 3023464.037 3307756.727 2962798.136 2424034.939 2792813.871 930788.1399 2782734.186 2524538.149 2200865.439 2575943.453 1.173730748 1.28409524 1.150179804 0.941028009 1.084190675 0.361338732 1.080277668 0.980044087 0.854391985 1 21.29666949 3.715311243 1.83367046 0.887739631 1.234929515 0.344119866 0.194893429 0.40709659 2.656163388 0.057244122 0.121372719 5191.719774 -3.715311243 0.347189884 MSCFSRPS(ph)MS(ph)PTPLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MS(0.004)CFS(0.02)RPS(0.975)MS(0.57)PT(0.431)PLDR;MSCFS(0.004)RPS(0.996)MS(0.996)PT(0.004)PLDR;MSCFSRPS(1)MS(0.994)PT(0.006)PLDR;MSCFS(0.01)RPS(0.99)MS(0.999)PT(0.001)PLDR 192.96 5.38E-09 1845060000 1380190 1349470 1081280 922050 858910 728870 974660 935290 1055370 1035430 TRUE FALSE 1326250.649 1310984.437 1276691.349 969637.111 886537.6202 743608.2508 986588.1806 915975.9347 935568.8221 965299.4038 1.373926725 1.358111723 1.322585867 1.004493639 0.918406887 0.77033949 1.022054066 0.94890345 0.969200663 1 19.88061696 3.715354656 3.08512007 0.93551013 1.364252755 0.894798999 0.063910093 0.074885933 1.450135222 0.01807892 0.032327411 5192.238769 -3.715354656 0.428742625 HVDFLEAISSALR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVDFLEAISSALR 13 0 Q7Z4Q2;Q7Z4Q2-2 Q7Z4Q2 HEATR3 HEAT repeat-containing protein 3 0 ; 151.78 4.49E-05 154834000 348400 307020 343930 233818 287270 237530 316270 224898 310480 326010 FALSE TRUE 334784.1428 298264.0902 406085.8017 245885.375 296510.3004 242333.0193 320140.6069 220253.7777 275235.612 303929.0523 1.101520701 0.981360906 1.336120383 0.80902228 0.975590514 0.797334172 1.053339931 0.724688134 0.90559165 1 18.21337506 3.715852312 24.99738704 0.883129031 1.123836731 0.443397946 0.124700488 654.608684 720595.7226 0.031251504 0.048451865 5198.191946 -3.715852312 0.240707701 LFVGNLPTDITEEDFKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFVGNLPTDITEEDFKR 17 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 100.77 0.0020077 907120000 141910 176410 134330 128700 112520 131740 130170 144340 162380 136890 FALSE TRUE 136364.0003 171378.9595 158606.4192 135342.2224 116139.308 134403.8731 131763.0594 141359.3286 143947.3032 127618.3184 1.068529989 1.342902506 1.242818595 1.060523475 0.910052017 1.053170695 1.032477634 1.10767271 1.127951731 1 16.9614759 3.716325312 6.754864071 1.044077826 1.230828819 0.479406563 0.083935533 0.14142465 28.21137864 0.022355034 0.035957882 5203.856502 -3.716325312 0.186750994 AGLNEMVEYITHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGLNEMVEYITHSR 14 0 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 0 ; 249.82 3.40E-18 535660000 694880 775970 609210 749130 812280 822420 832300 769960 816880 841660 FALSE TRUE 667723.3214 753840.0954 719307.7988 787792.6891 838407.7239 839049.8959 842485.9364 754060.0569 724151.207 784653.6185 0.850978452 0.960729776 0.91672017 1.004000581 1.068506796 1.069325211 1.073704265 0.961010106 0.922892841 1 19.5816964 3.71643848 4.058449439 1.018176344 0.913032475 0.460109481 0.052026548 0.212576663 8.185225107 0.01512388 0.025738682 5205.212696 -3.71643848 -0.105143869 YCQVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 YCQVIR 6 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 97.64 0.095015 223570000 145050 161260 148680 122210 122950 120790 120880 154690 150960 166900 FALSE TRUE 139381.2856 156661.0227 175549.7834 128517.2727 126904.7984 123232.4566 122359.3656 151495.5974 133823.6537 155595.7143 0.89579129 1.006846643 1.12824305 0.825969232 0.815606001 0.792004183 0.786392904 0.973648909 0.860072877 1 17.2474428 3.716580315 24.97331183 0.860861692 1.009948978 0.378923733 0.08524592 784.0064803 890762.9268 0.023241745 0.036040343 5206.912929 -3.716580315 0.149087286 AMASVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AMASVAR 7 0 H7C2G2;Q93070 H7C2G2 ART4 NAD(P)(+)--arginine ADP-ribosyltransferase;Ecto-ADP-ribosyltransferase 4 0 95.793 0.046926 220290000 193180 202240 231520 113570 121470 75294 172390 124690 140680 155270 FALSE TRUE 185630.312 196472.3132 273360.8141 119431.3613 125377.1929 76816.49627 174499.7604 122115.1079 124710.5962 144753.4246 1.282389778 1.357289568 1.888458355 0.825067605 0.866143189 0.530671357 1.205496594 0.84360773 0.86153814 1 17.14323795 3.716601938 24.87171996 0.873525056 1.494170277 0.643480282 0.215926267 432.7240354 490129.2588 0.05633902 0.087361953 5207.172181 -3.716601938 0.620645221 YSSNLGNFNYER ddPTM_BT-474_Pertuzumab_2h_R1 1 YSSNLGNFNYER 12 0 Q9BZZ5-2;Q9BZZ5-5 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 142.19 0.00014227 180770000 116190 109510 130140 70547 89161 79081 93078 82147 91661 98178 FALSE TRUE 111649.1663 106386.882 153659.1929 74187.93912 92028.94454 80680.072 94217.11641 80450.63574 81256.02755 91528.31661 1.219831965 1.162338454 1.678815897 0.810546308 1.005469651 0.881476629 1.029376699 0.878969905 0.887769278 1 16.48193053 3.716632571 24.99510195 0.927279277 1.334529801 0.652047137 0.142402148 450.7648253 513812.8899 0.036121332 0.056010056 5207.539474 -3.716632571 0.407250524 VEAMNKR ddPTM_BT-474_Pertuzumab_2h_R1 3 VEAMNKR 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 91.9 0.025758 2402640000 1038150 1153450 806750 874230 839590 598610 948340 793660 970740 1049810 FALSE TRUE 997577.9503 1120554.735 952547.6711 919349.1151 866596.1748 610714.3043 959946.0686 777270.6437 860545.6649 978705.4336 1.019283143 1.144935643 0.9732731 0.939352213 0.88545148 0.62400216 0.980832471 0.794182414 0.879269324 1 19.90051518 3.716826365 1.691570175 0.845876995 1.078580164 0.395140843 0.104313735 0.332008297 1.840392523 0.029517075 0.065242195 5209.863748 -3.716826365 0.232703169 CSSVAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 CSSVAAK 7 0 F5H3V4;F5GZH5;Q9ULI2-2;Q9ULI2 F5H3V4 RIMKLB Beta-citrylglutamate synthase B 0 82.386 0.057303 359640000 203650 173230 228550 113340 143810 150150 169340 169850 152180 148280 FALSE TRUE 195691.1329 168289.65 269854.0691 119189.491 148435.7793 153186.1359 171412.4336 166342.5381 134905.1644 138236.8635 1.415621911 1.217400668 1.952113656 0.862212061 1.073778553 1.108142445 1.239990761 1.203315338 0.97589862 1 17.07678286 3.716914484 24.99996522 1.093854194 1.497281065 0.522633547 0.200549044 664.60252 767575.5628 0.052440963 0.081319868 5210.920938 -3.716914484 0.40342687 KASDSELER ddPTM_BT-474_Pertuzumab_2h_R1 2 KASDSELER 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 119.27 0.0013689 2076200000 3046400 3278100 2487400 3025300 2958300 3135600 3265800 3216600 3269600 3415200 FALSE TRUE 2927343.32 3184611.798 2936928.512 3181436.096 3053456.406 3199003.98 3305767.837 3150176.086 2898448.715 3183885.462 0.919424821 1.000228129 0.922435354 0.999230699 0.959034627 1.004748449 1.038281018 0.989412504 0.910349556 1 21.60235701 3.717216562 24.69609286 0.988381017 0.952649297 0.173270673 0.037738968 1224.325351 1416603.149 0.009969881 0.015462191 5214.546708 -3.717216562 -0.03573172 MLPDKDCR ddPTM_BT-474_Pertuzumab_2h_R1 15 MLPDKDCR 8 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;;;;;; 104.2 0.0042189 1.1054E+11 221997270 224917800 175397420 153716880 151338820 68086480 196360720 158586080 169328400 187685800 FALSE TRUE 213321371.3 218503364.6 207095635.5 161650226.6 156206770.6 69463235.28 198763841.2 155311222 150106949.9 174973673.6 1.219162671 1.248778517 1.183581685 0.923854562 0.892744419 0.396992495 1.135964269 0.887626229 0.857883057 1 27.38256263 3.717391865 2.716892787 0.858069646 1.234384647 0.451261885 0.176768374 0.251689685 3.686814871 0.049278428 0.09099174 5216.651985 -3.717391865 0.376315001 RLEAAYLDLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEAAYLDLQR 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 151.7 5.34E-05 613290000 767300 872540 693440 403800 389330 138747 629850 345140 390330 543600 FALSE TRUE 737313.0677 847656.0135 818760.0335 424640.1664 401853.153 141552.5594 637558.2927 338012.7384 346021.3748 506781.4878 1.454893451 1.672626238 1.61560762 0.837915703 0.792951524 0.279316753 1.258053635 0.666979253 0.682782191 1 18.9510043 3.717413534 5.441080166 0.772699133 1.593883236 0.695187718 0.240537068 0.090556672 8.816985154 0.06182264 0.101464677 5216.912275 -3.717413534 0.821184103 LEDEFDMFALTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDEFDMFALTR 12 0 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 0 ; 178.08 5.22E-05 88452000 154139 174015 119261 166488 173951 165339 161811 181371 167962 184796 FALSE TRUE 148115.0775 169052.2626 140814.1156 175080.4656 179546.2919 168682.2679 163791.2914 177625.6255 148895.6579 172279.6023 0.859736588 0.981266849 0.817358026 1.016257661 1.042179628 0.979119208 0.950729449 1.031031086 0.864267481 1 17.39439237 3.717464181 24.82687692 0.987527858 0.895635109 0.34337754 0.061013981 788.1714229 927542.2032 0.015414804 0.023906681 5217.520709 -3.717464181 -0.091892749 KLPVESIQIVLEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPVESIQIVLEELR 15 1 K7ENE3;Q9BRG1;K7EKV4 K7ENE3 VPS25 Vacuolar protein-sorting-associated protein 25 0 ; 199.49 1.19E-08 339180000 507940 553770 485870 438280 472020 273880 553670 504230 520730 548520 FALSE TRUE 488089.1432 537977.0218 573677.5171 460899.6833 487202.952 279418.0412 560445.9791 493817.4743 461618.9135 511368.2518 0.954476821 1.052034458 1.12184813 0.901306801 0.95274384 0.546412571 1.095973356 0.965678789 0.902713283 1 18.96400307 3.717489363 23.78458595 0.909684573 1.043711268 0.161708359 0.139309947 771.402905 870736.0053 0.037586343 0.058312158 5217.82324 -3.717489363 0.134026695 HQPTAIIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 HQPTAIIAK 9 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 130.98 0.00034591 517830000 2145400 2032690 1699120 1367770 1437660 775820 1806460 1236610 1665300 1787650 FALSE TRUE 2061555.396 1974719.671 2006188.781 1438360.774 1483903.64 791507.612 1828567.998 1211073.571 1476262.126 1666570.873 1.237004336 1.184899906 1.203782457 0.86306607 0.89039336 0.474931864 1.097203862 0.72668591 0.885808188 1 20.66845124 3.71773284 4.074689966 0.829115326 1.211155286 0.52451211 0.156714044 0.153445501 5.994246736 0.039793929 0.067780514 5220.749308 -3.71773284 0.38203996 NIHLNLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 NIHLNLDR 8 0 Q9Y5S9;Q9Y5S9-2;A0A0J9YW13 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;; 141.48 0.00063284 909430000 1807660 1807970 1524990 717363 689680 104116 943670 622012 841048 1145750 FALSE TRUE 1737014.649 1756408.466 1800589.616 754386.1904 711864.1836 106221.2969 955218.9157 609167.2348 745575.757 1068147.332 1.626193875 1.644350375 1.685712787 0.706256682 0.66644756 0.099444425 0.894276367 0.570302632 0.69800835 1 20.02667922 3.717786998 5.456389713 0.627918802 1.655940679 0.80293098 0.224449354 0.067154321 6.626502196 0.057574513 0.09451583 5221.400397 -3.717786998 1.028021876 DWSNDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DWSNDVR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 113.5 0.014228 1905840000 3741200 4205400 3099700 3885400 4095600 3959100 4106600 4123100 4341700 4341900 FALSE TRUE 3594989.768 4085466.11 3659884.742 4085925.96 4227338.694 4039155.715 4156857.799 4037956.544 3848848.418 4047819.246 0.888130015 1.00930053 0.904162098 1.009414134 1.04434967 0.997859704 1.026937604 0.997563453 0.950844933 1 21.94871344 3.717805801 24.35948404 1.006055118 0.941407847 0.419119855 0.037380646 536.6658025 629873.305 0.009430007 0.014627314 5221.626463 -3.717805801 -0.064647271 EEADKLVR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEADKLVR 8 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ;; 89.247 0.012805 1027880000 1190060 1339400 973990 1060470 809160 1116180 989280 1058280 1197080 1204290 FALSE TRUE 1143551.14 1301201.623 1150011.659 1115200.984 835187.3663 1138749.924 1001387.105 1036426.148 1061192.497 1122722.366 1.018552025 1.158970074 1.02430636 0.993300764 0.743894833 1.014275621 0.891927635 0.923136636 0.945195829 1 20.09856978 3.718206698 2.828297685 0.917284855 1.084344562 0.406584808 0.078721738 0.227809173 3.640415105 0.020289297 0.037112134 5226.448773 -3.718206698 0.167059707 DGAWGAFR ddPTM_BT-474_Pertuzumab_2h_R1 8 DGAWGAFR 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 158.36 0.0008502 10121910000 5882500 7065720 6487230 4321400 3606400 1313849 7359390 4131170 4967410 6664340 FALSE TRUE 5652605.397 6864212.584 7659616.769 4544427.972 3722403.131 1340415.927 7449456.416 4045859.896 4403530.442 6212958.316 0.909809001 1.104821928 1.23284535 0.731443499 0.599135378 0.215745199 1.199019217 0.651197013 0.708765489 1 22.56684894 3.71852914 20.84895351 0.713742748 1.084724847 0.290417698 0.252143231 110.3318075 114834.3777 0.066469473 0.103280774 5230.330591 -3.71852914 0.370982099 DADAGDEDEESEEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DADAGDEDEESEEPR 15 0 Q9NZT2-2;Q9NZT2;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 ; 331.57 1.61E-68 753370000 441610 446790 352450 418730 423130 454180 409810 445490 498470 439000 FALSE TRUE 424351.393 434047.9867 416145.5552 440340.7055 436740.3607 463363.8308 414825.3774 436290.4758 441885.7754 409266.139 1.036859277 1.060551913 1.016809151 1.075927529 1.067130454 1.132182183 1.013583431 1.066031206 1.079702749 1 18.64267978 3.718930951 24.82174186 1.06493994 1.040321288 0.08225392 0.03562997 1736.285921 2195536.726 0.009102328 0.014111759 5235.171949 -3.718930951 -0.024618652 SCFGFEGLLGAEDLSGVS(ph)PVVCSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SCFGFEGLLGAEDLSGVSPVVCSK 24 0 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 SCFGFEGLLGAEDLSGVS(1)PVVCSK;SCFGFEGLLGAEDLS(0.002)GVS(0.998)PVVCSK 133.38 2.74E-05 30097000 64338 70343 65715 53946 55248 63362 60418 69720 59291 67402 TRUE FALSE 61823.59983 68336.88651 77591.16232 56730.15952 57025.10209 64643.22305 61157.41356 68280.25764 52560.53425 62836.8025 0.983875649 1.087529661 1.234804434 0.902817414 0.907511201 1.028747811 0.9732738 1.086628455 0.836460993 1 15.93932215 3.719545495 24.99207477 0.973809997 1.100615915 0.343972311 0.087486408 963.0786996 1265799.42 0.023599938 0.036630624 5242.585177 -3.719545495 0.126805918 FGQLGLNDENDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FGQLGLNDENDR 12 0 Q5GLZ8-6;Q5GLZ8-3;Q5GLZ8-2;Q5GLZ8;H0Y6K7 Q5GLZ8-6 HERC4 Probable E3 ubiquitin-protein ligase HERC4 0 105.13 0.002064 0 74497 65524 49439 73463 81595 67138 71945 91603 75863 77558 FALSE TRUE 71585.57488 63655.31967 58373.72706 77254.43423 84219.57728 68495.57636 72825.48443 89711.36604 67251.35028 72304.92758 0.990051125 0.880373189 0.807327094 1.068453241 1.164783371 0.947315469 1.007199466 1.240736545 0.930107429 1 16.14180635 3.719624469 23.80110248 1.069251022 0.891362755 0.339639304 0.099162408 422.4148564 530938.9577 0.026802665 0.041611977 5243.538593 -3.719624469 -0.177888267 IPDHDPAPNVTVLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IPDHDPAPNVTVLLR 15 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 77.562 0.025519 405510000 215160 179440 149290 191360 193430 192160 218680 190850 241830 190720 FALSE TRUE 206751.3093 174322.5469 176270.0239 201236.1125 199651.8516 196045.6069 221356.2713 186908.8808 214378.4722 177802.3645 1.162815297 0.980428733 0.991381776 1.131796605 1.12288637 1.102604048 1.244956848 1.051217071 1.205712156 1 17.43991498 3.719891903 24.10391466 1.126864918 1.038430617 0.164001145 0.079785963 739.28656 954522.2504 0.019866395 0.030842614 5246.768504 -3.719891903 -0.088434301 AT(ph)PTKAPAPVVLGSPVVLGPPVGQAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATPTKAPAPVVLGSPVVLGPPVGQAR 26 1 A0A0C4DFM2;Q6ZN55;Q6ZN55-2 A0A0C4DFM2 ZNF574 Zinc finger protein 574 1 AT(0.953)PT(0.047)KAPAPVVLGSPVVLGPPVGQAR 81.967 1.14E-05 0 84791 80272 81196 65144 73230 66979 78851 81474 87610 83921 TRUE FALSE 81477.27398 77982.72115 95869.9234 68506.08965 75585.50946 68333.36127 79816.00212 79791.53343 77664.88009 78236.95592 1.041416719 0.996750452 1.225379007 0.875623148 0.966110051 0.873415389 1.020182869 1.019870118 0.992687908 1 16.25556262 3.719896191 24.99957676 0.967813217 1.078738933 0.370526243 0.073578863 928.0561195 1243060.972 0.019798555 0.030730534 5246.820306 -3.719896191 0.110925716 GKNDGTVQGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GKNDGTVQGR 10 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q6AWB1;C9J1B7;C9JZA4;C9JTE5;C9JJN7;C9JJD0;C9JKG6;E9PCY0 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ;;; 172.56 3.36E-06 669760000 750880 762980 647090 748960 792380 866270 871300 828000 827790 858280 FALSE TRUE 721534.7795 741220.5574 764033.5574 787613.9154 817867.6223 883786.5729 881963.23 810901.5107 733822.7496 800147.9311 0.901751728 0.926354401 0.954865379 0.984335377 1.022145519 1.104528973 1.102250216 1.013439489 0.917108851 1 19.60990722 3.720262447 1.532808461 1.03457072 0.913266029 0.439567985 0.050633617 0.386562081 1.754061131 0.016592481 0.038881179 5251.247007 -3.720262447 -0.121304691 FKPEELVDYK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKPEELVDYK 10 1 O60361 O60361 NME2P1 Putative nucleoside diphosphate kinase 0 96.229 0.0062769 183510000 427790 428950 459430 305570 336840 310650 388530 406250 456930 477290 FALSE TRUE 411071.4939 416716.766 542459.221 321340.5043 347674.7645 316931.5558 393284.9464 397860.7955 405061.222 444962.7232 0.923833554 0.936520621 1.219111608 0.722173988 0.781357058 0.712265409 0.883860436 0.894144104 0.910326193 1 18.76332495 3.720375889 24.99869316 0.837198273 1.017491836 0.358075047 0.111896432 869.1248672 1194793.055 0.030108823 0.046743791 5252.618864 -3.720375889 0.180293563 WLHNEDQMAVEK ddPTM_BT-474_Pertuzumab_2h_R1 11 WLHNEDQMAVEK 12 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;;;; 217.88 3.56E-11 10014620000 12759091 12674589 10900245 11231152 11860242 10824428 12549680 11657750 13835038 14201440 FALSE TRUE 12260451.62 12313122.13 12870161.75 11810793.1 12241737.46 11043305.35 12703266.74 11417013.39 12264542.49 13239563.82 0.926046491 0.930024758 0.972098622 0.892083248 0.924632988 0.834113986 0.959492844 0.862340599 0.926355479 1 23.65835226 3.72038471 24.66709862 0.90580366 0.941453442 0.054897804 0.04588705 1380.249293 1873181.21 0.011208563 0.017406557 5252.725546 -3.72038471 0.035649782 IKYPENFFLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKYPENFFLLR 11 1 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;A0A087WYY5;P62140;E7ETD8;C9JP48;C9J9S3;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 125.28 0.00030234 1464290000 2271300 2353100 2307800 1462750 1275880 456650 2249800 1598870 1655720 2082200 FALSE TRUE 2182535.085 2285991.892 2724870.797 1538242.703 1316919.839 465883.7759 2277333.725 1565852.776 1467769.607 1941170.739 1.124339575 1.177635664 1.403725464 0.792430399 0.678415253 0.240001442 1.173175383 0.806653812 0.756125969 1 20.88849559 3.720553718 22.0256708 0.77058525 1.229473672 0.443131446 0.234694636 154.3162262 188756.4761 0.063522235 0.098760498 5254.77007 -3.720553718 0.458888422 GYHYATCLEGALK ddPTM_BT-474_Pertuzumab_2h_R1 1 GYHYATCLEGALK 13 0 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 145.31 4.17E-05 243360000 401190 414830 352100 349890 385380 264690 439640 340840 423190 439660 FALSE TRUE 385511.0513 402999.4546 415732.3024 367947.8648 397776.0977 270042.2132 445020.4458 333801.5349 375151.2454 409881.4366 0.940542842 0.983209823 1.014274532 0.897693411 0.970466243 0.658830064 1.085729692 0.814385588 0.915267714 1 18.64484713 3.720670545 22.1031914 0.89696047 0.979729127 0.082978102 0.108745356 378.5449013 467692.6413 0.027033035 0.042031973 5256.183826 -3.720670545 0.082768657 LGS(ph)YSGPTSVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGSYSGPTSVSR 12 0 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 LGS(0.993)YS(0.007)GPTSVSR;LGS(0.993)YS(0.007)GPTSVSR 179.59 2.15E-05 1354350000 1303470 1213650 1024000 1043210 1029620 919940 1056970 1207480 1359940 1073470 TRUE FALSE 1252528.951 1179037.89 1209059.579 1097050.193 1062738.662 938541.8171 1069905.515 1182545.116 1205565.313 1000762.921 1.251574099 1.178139064 1.208137865 1.096213869 1.061928495 0.93782633 1.069089884 1.181643616 1.204646263 1 19.93266881 3.720767405 4.445811861 1.084210765 1.21056878 0.401252081 0.074833986 0.243340988 12.40028429 0.022297058 0.037643391 5257.356223 -3.720767405 0.126358015 TPS(ph)FELPDASERPPTYCELVPR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSFELPDASERPPTYCELVPR 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 T(0.006)PS(0.994)FELPDASERPPTYCELVPR;T(0.002)PS(0.998)FELPDASERPPTYCELVPR;T(0.001)PS(0.999)FELPDASERPPTYCELVPR 173.36 2.33E-12 776220000 148632 165499 108198 166404 168447 159984 161902 190336 160455 159911 TRUE FALSE 142823.2971 160779.1306 127751.7855 174992.1304 173865.2507 163218.9861 163883.4051 186405.4951 142240.8211 149080.0855 0.958030689 1.078474901 0.856933943 1.173812919 1.166254031 1.094840974 1.099297767 1.250371533 0.954123554 1 17.18572803 3.720808418 24.9939118 1.125079726 0.975879337 0.297969526 0.095504331 848.352908 1194424.038 0.024318138 0.037762667 5257.85273 -3.720808418 -0.14920039 ENTEFTDHELQEWYK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENTEFTDHELQEWYK 15 0 P37235;E9PC71 P37235 HPCAL1 Hippocalcin-like protein 1 0 ; 142.01 4.66E-06 476640000 650540 768710 541070 833630 707380 700170 909210 930470 956430 743580 FALSE TRUE 625116.1776 746787.1434 638853.385 876653.7442 730133.5201 714327.9171 920337.184 911255.4693 847860.0761 693216.6643 0.901761613 1.077278118 0.921578228 1.264617239 1.053254426 1.030454047 1.327632804 1.314531973 1.223080921 1 19.40294681 3.720826164 0.647223348 1.228564218 0.913023442 0.292830865 0.126826417 1.354680595 0.959640319 0.071072222 0.269619094 5258.06758 -3.720826164 -0.315540776 DNSEEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNSEEFR 7 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 0 94.874 0.05235 0 246730 255250 198370 239830 233640 262400 232500 270540 257660 274160 FALSE TRUE 237087.5188 247970.5199 234219.8717 252207.655 241155.2428 267705.9078 235345.4045 264953.2545 228411.517 255590.899 0.927605481 0.970185249 0.916385805 0.98676305 0.943520461 1.047400001 0.920789455 1.036630238 0.893660603 1 17.96347694 3.720843225 23.85864828 0.978845066 0.941271482 0.114109656 0.046974322 873.368144 1176097.329 0.011451938 0.017791652 5258.274144 -3.720843225 -0.037573584 (ac)SDVEENNFEGRES(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 SDVEENNFEGRESR 14 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 1 SDVEENNFEGRES(1)R;SDVEENNFEGRES(1)R 79.804 1.55E-05 631700000 79460 91194 96020 54740 68772 81829 64924 63116 65884 70665 TRUE FALSE 76354.61535 88593.23641 113372.95 57565.13796 70984.11384 83483.63845 65718.55933 61812.63254 58405.12453 65878.79661 1.159016547 1.344791359 1.720932315 0.873803726 1.077495605 1.267230774 0.997567696 0.938278107 0.886554211 1 16.00752658 3.721107032 24.99717338 1.011906286 1.401901238 0.553428786 0.165554199 605.6795826 867459.5374 0.045348208 0.070430165 5261.469198 -3.721107032 0.389994952 KVVDYSQFQESDDADEDYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;; 304.91 4.97E-55 2828270000 1682430 1721390 1282040 1690950 1658780 1726340 1794570 1852220 1827000 1737810 FALSE TRUE 1616678.776 1672297.643 1513733.147 1778220.132 1712136.165 1761247.778 1816532.484 1813971.01 1619606.619 1620106.581 0.99788421 1.032214585 0.934341706 1.097594537 1.056804648 1.087118464 1.121242581 1.119661528 0.999691402 1 20.6276573 3.721158179 24.97518644 1.079664629 0.992553605 0.368450018 0.046861824 722.1519562 1036399.171 0.012220009 0.018982512 5262.088881 -3.721158179 -0.087111024 RCQYVTEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RCQYVTEK 8 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;;; 181.53 0.00037416 3336890000 3250570 3290290 2629270 2490780 2353360 1782843 2701680 2889450 2981120 2831590 FALSE TRUE 3123534.131 3196454.151 3104437.577 2619329.454 2429057.962 1818893.307 2734743.968 2829781.848 2642715.755 2639803.887 1.183244765 1.210868037 1.176010685 0.992243957 0.920166067 0.689025922 1.035964823 1.071966695 1.001103062 1 21.33199932 3.721244518 3.643123853 0.957980828 1.196930772 0.539983251 0.098465438 0.200024293 5.811278901 0.029969438 0.052181565 5263.135098 -3.721244518 0.238949943 LYEIAR ddPTM_BT-474_Pertuzumab_2h_R1 5 LYEIAR 6 0 Q7Z5M8-2;Q7Z5M8 Q7Z5M8-2 ABHD12B Abhydrolase domain-containing protein 12B 0 ;;;; 120.76 0.046406 3070950000 2303420 2516360 3015370 1138320 1832060 1740640 1491950 1364950 1384190 1379280 FALSE TRUE 2213399.8 2444595.877 3560314.436 1197068.832 1890989.874 1775836.933 1510208.93 1336763.306 1227062.554 1285860.137 1.721337909 1.901136684 2.768819355 0.930947929 1.470603077 1.381049838 1.174473714 1.039586863 0.954273734 1 20.2943023 3.721357039 24.99994821 1.156351361 2.107501901 0.695302634 0.301387494 442.7423419 643385.7565 0.080639528 0.125253506 5264.498902 -3.721357039 0.95115054 YQEDS(ph)DPERSDYEEQQLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 YQEDSDPERSDYEEQQLQK 19 1 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 YQEDS(0.904)DPERS(0.095)DY(0.001)EEQQLQK;YQEDS(0.997)DPERS(0.003)DYEEQQLQK 192.99 3.80E-15 1604490000 431740 397770 414250 469650 422150 422350 541110 509420 623780 628810 TRUE FALSE 414867.1235 386425.9891 489114.1899 493888.6928 435728.8381 430890.2064 547732.266 498900.299 552971.1095 586220.1386 0.707698518 0.659182385 0.834352418 0.842496974 0.743285345 0.735031395 0.9343457 0.851045991 0.943282349 1 19.161083 3.721373601 0.137888648 1.100383275 0.432925651 0.671822151 0.061077224 12.24485713 0.423445291 0.485815979 1.700957996 5264.699667 -3.721373601 -0.667457625 IGAEVYHNLK ddPTM_BT-474_Pertuzumab_2h_R1 5 IGAEVYHNLK 10 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;; 161.63 7.01E-06 13191020000 14280510 14954960 10925100 10025400 8123880 5944420 10763920 9453460 11428970 11117860 FALSE TRUE 13722411.88 14528459.18 12899508.6 10542812.1 8385191.978 6064620.245 10895652.07 9258242.747 10131601.24 10364837.44 1.323938939 1.40170642 1.244545192 1.017171003 0.809003713 0.585114844 1.051213021 0.893235692 0.977497361 1 23.30519415 3.721454496 2.382705428 0.880786091 1.35744169 0.716937458 0.123672042 0.156970219 1.74527695 0.035866538 0.06903591 5265.680394 -3.721454496 0.476655599 VTTHPLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTTHPLAK 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 92.439 0.011777 3496700000 6147100 6172500 5080700 5199400 5292100 4292900 5674400 5728200 6357900 6407700 FALSE TRUE 5906864.536 5996466.344 5998895.51 5467741.657 5462325.203 4379705.379 5743845.005 5609910.668 5636177.846 5973700.772 0.988811586 1.003810966 1.00421761 0.915302233 0.914395517 0.733164507 0.961522049 0.939101385 0.943498522 1 22.51019354 3.721705784 6.628713589 0.909755721 0.999617209 0.246840293 0.066490723 0.219322397 46.3459675 0.018086574 0.029386563 5268.728066 -3.721705784 0.089861489 DLPEHAVLK ddPTM_BT-474_Pertuzumab_2h_R1 10 DLPEHAVLK 9 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;;; 133.23 0.00031705 27042550000 22331140 20411980 19483410 17234554 18213800 15834141 20079510 20175890 20181250 20592930 FALSE TRUE 21458414.36 19829850.32 23004495.59 18124031.4 18799663.42 16154318.18 20325249.05 19759250.82 17890359.11 19198152.51 1.1177333 1.032904094 1.198266113 0.944050808 0.979243363 0.841451706 1.058708594 1.029226683 0.931879205 1 24.19446415 3.721769648 24.99041433 0.974442525 1.107961468 0.499687421 0.067144764 707.9937557 1053724.345 0.018215559 0.028302009 5269.502904 -3.721769648 0.133518943 ETDLQELFRPFGSISR ddPTM_BT-474_Pertuzumab_2h_R1 4 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;;; 227.4 4.62E-15 4965261000 1664205 1857770 1391285 1727957 1696022 2040767 1675012 1838371 1898653 2074771 FALSE TRUE 1599166.029 1804788.219 1642721.148 1817137.068 1750576.088 2082032.707 1695511.298 1800407.996 1683125.871 1934244.912 0.826765018 0.933071199 0.84928291 0.939455524 0.905043657 1.076405937 0.876575292 0.930806634 0.870172056 1 20.88333905 3.721869004 23.26184747 0.939181026 0.876042863 0.220152096 0.062324585 534.5787343 745002.2291 0.016085663 0.025017304 5270.708568 -3.721869004 -0.063138163 LKQEYFVVAATLQDIIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKQEYFVVAATLQDIIR 17 1 P11216;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 183.56 6.24E-10 1453330000 2146360 2173260 1838350 1731960 1778460 1506510 1992210 1838220 2001290 1910570 FALSE TRUE 2062477.878 2111280.753 2170580.739 1821346.663 1835665.781 1536972.664 2016591.262 1800260.115 1774111.949 1781165.392 1.157937319 1.185336725 1.218629527 1.022558978 1.030598163 0.862902834 1.132175188 1.010720353 0.996039984 1 20.76439006 3.722006061 13.16597455 1.010895862 1.187104114 0.632085775 0.062707205 1.119205369 889.9849025 0.016427328 0.0258865 5272.372192 -3.722006061 0.176208252 ADSEPES(ph)PLNASYVYK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADSEPESPLNASYVYK 16 0 Q5T1V6;Q5T1V6-2 Q5T1V6 DDX59 Probable ATP-dependent RNA helicase DDX59 1 ADSEPES(1)PLNASYVYK 166.9 6.83E-09 40158000 107890 115190 99548 94539 95067 100650 100790 112010 107350 104710 TRUE FALSE 103673.5395 111904.894 117538.538 99418.16912 98124.91639 102685.212 102023.4982 109696.9544 95164.07805 97617.89843 1.062034127 1.146356311 1.204067491 1.018442014 1.005193904 1.051909676 1.045131065 1.123738127 0.974863007 1 16.57485807 3.722267241 24.9912264 1.041999185 1.138373014 0.475960736 0.050176863 745.2031713 1143013.074 0.013842513 0.021517051 5275.543899 -3.722267241 0.096373829 DRVGVGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRVGVGIR 8 1 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 90.601 0.01193 403420000 198580 211919 165839 207806 201900 196269 192278 207838 212696 234540 FALSE TRUE 190819.2741 205875.2776 195809.7964 218530.8926 208394.2969 200237.6937 194631.1557 203546.0727 188551.6418 218654.3969 0.872698088 0.941555626 0.895521879 0.999435162 0.953076178 0.915772546 0.890131451 0.930903177 0.862327236 1 17.73829283 3.722356071 0.00402983 1.840984625 5.83E-08 0.083911587 0.043947618 116263.7766 105.601883 23638.70984 24607.85421 5276.623057 -3.722356071 -1.840984567 VKLDGSR ddPTM_BT-474_Pertuzumab_2h_R1 6 VKLDGSR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;;;;; 117.04 0.0048531 4701340000 7090110 7059040 6345460 5844930 6115520 4355780 6923730 6791840 7345720 7657420 FALSE TRUE 6813020.663 6857723.091 7492225.776 6146587.538 6312231.255 4443856.856 7008464.679 6651586.131 6511864.661 7138776.123 0.954368164 0.960630082 1.049511239 0.86101419 0.884217567 0.622495618 0.981745969 0.931754409 0.912182221 1 22.76724533 3.72242109 24.48633486 0.880344153 0.985415857 0.181067225 0.100407949 1037.269734 1573710.179 0.027458312 0.042691017 5277.413092 -3.72242109 0.105071704 S(ph)MGETESGDAFLDLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SMGETESGDAFLDLK 15 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5;B1AKL6 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(1)MGETESGDAFLDLK;S(1)MGETESGDAFLDLK;S(1)MGETESGDAFLDLK;S(1)MGETESGDAFLDLK 226.65 8.78E-13 132063000 224277 202526 192470 179429 198297 195523 189509 201186 231850 229399 TRUE FALSE 215512.0069 196750.1568 227253.6105 188689.3522 204675.4031 199476.609 191828.2678 197031.4388 205531.36 213861.6014 1.007717166 0.919988233 1.062619979 0.882296546 0.95704606 0.932736909 0.896973868 0.921303486 0.961048447 1 17.70631795 3.72244885 24.93942404 0.930489174 0.989096449 0.264782101 0.045315029 953.7928101 1476377.077 0.01118353 0.017383951 5277.750438 -3.72244885 0.058607275 VAQLEQVYIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VAQLEQVYIR 10 0 P62318;P62318-2 P62318 SNRPD3 Small nuclear ribonucleoprotein Sm D3 0 84.054 0.035322 52404000 71622 73059 57960 43039 42135 20705 57318 44056 45703 50348 FALSE TRUE 68822.93306 70975.42885 68434.66131 45260.24795 43490.31054 21123.66929 58019.47483 43146.2282 40514.98704 46937.88511 1.466255518 1.512113907 1.457983485 0.964258356 0.926550279 0.450034535 1.23609052 0.91921969 0.86316175 1 15.51846522 3.723090691 3.840006516 0.902425591 1.492139611 0.67610977 0.181423028 0.127652929 4.273905465 0.048966726 0.084686048 5285.556149 -3.723090691 0.58971402 ERPTPSLNNNCTTSEDSLVLYNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 287.1 1.29E-52 1495250000 234337 261930 189640 249530 260890 290580 271570 242340 244633 259410 FALSE TRUE 225178.851 254460.0129 223912.1665 262408.2732 269281.7638 296455.7267 274893.5549 237335.5943 216863.2874 241839.9296 0.931106998 1.052183621 0.925869301 1.085049411 1.113471064 1.225834489 1.136675632 0.981374724 0.896722422 1 17.88369294 3.723220479 24.07540012 1.069813045 0.977966336 0.173290101 0.091665226 915.9558967 1437537.21 0.026561482 0.041337098 5287.13596 -3.723220479 -0.091846709 IAIYELLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 IAIYELLFK 9 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3 P46783 RPS10 40S ribosomal protein S10 0 ; 152.59 0.00018634 186416000 516360 460420 420310 391920 379580 260990 484550 432340 471450 515740 FALSE TRUE 496180.0803 447289.2724 496269.3667 412147.0382 391789.5354 266267.3966 490480.0678 423412.0279 417932.9725 480808.4704 1.031970339 0.930285758 1.03215604 0.857195876 0.814855726 0.553790985 1.020115281 0.880625143 0.869229638 1 18.87510279 3.723374627 20.36063003 0.84953143 0.991352147 0.218496027 0.122008993 104.6432401 140301.1864 0.03290625 0.051376028 5289.012904 -3.723374627 0.141820717 RYLSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RYLSPK 6 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 89.427 0.080459 245950000 657250 680860 626760 494520 453650 228390 686630 546070 659560 802270 FALSE TRUE 631563.9434 661442.5394 740029.4742 520042.2365 468242.0642 233008.2023 695033.1833 534793.4637 584689.5139 747931.5383 0.844414109 0.884362412 0.989434776 0.695307271 0.626049364 0.311536806 0.929273801 0.715029968 0.781742023 1 19.51254669 3.723584026 23.5653231 0.703688035 0.903899624 0.177202797 0.177771729 568.8356261 895050.0516 0.047251307 0.073587461 5291.563669 -3.723584026 0.200211589 ATS(ph)FEESER ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSFEESER 9 0 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 AT(0.033)S(0.967)FEESER 63.624 0.082775 0 259170 318620 192290 334880 383510 311190 326650 393680 321890 298110 TRUE FALSE 249041.3499 309533.2696 227041.0805 352163.1969 395845.9474 317482.475 330647.6404 385550.3704 285350.3967 277918.7442 0.896094111 1.113754563 0.816933313 1.26714446 1.424322597 1.142357188 1.189727744 1.387277319 1.026740379 1 18.08430361 3.723675105 24.87337628 1.235852849 0.959410051 0.387849425 0.14757497 647.5282283 1082006.269 0.037458593 0.058294629 5292.67352 -3.723675105 -0.276442798 AERPGLQNMELAPVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 AERPGLQNMELAPVQR 16 1 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 86.411 0.0052283 0 140500 140200 127730 117380 133810 126930 118820 146840 129620 138300 FALSE TRUE 135009.1047 136201.6333 150813.6523 123437.9959 138114.1202 129496.6116 120274.1547 143807.7027 114906.081 128932.8178 1.047127543 1.056376767 1.169707254 0.957382286 1.071209972 1.004372772 0.932843606 1.115369268 0.891208949 1 16.97626 3.723685542 24.98284727 1.00693969 1.087601155 0.279518356 0.068291036 1106.064395 1857647.531 0.017507596 0.027250906 5292.80071 -3.723685542 0.080661466 SPTPTLPLSTSS(ph)FDEQN ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTPTLPLSTSSFDEQN 17 0 Q96HE9 Q96HE9 PRR11 Proline-rich protein 11 1 SPTPTLPLST(0.002)S(0.412)S(0.586)FDEQN;SPTPTLPLS(0.001)T(0.009)S(0.262)S(0.727)FDEQN 191.96 2.24E-10 197030000 311210 326160 202940 371510 401700 312250 386430 429520 361300 372740 TRUE FALSE 299047.5691 316858.2361 239615.7724 390683.6756 414621.0453 318563.9089 391159.2459 420650.2619 320286.7387 347493.9878 0.860583433 0.911838038 0.689553721 1.124289022 1.193174731 0.916746534 1.125657593 1.210525294 0.921704403 1 18.40662849 3.723688875 24.99758388 1.088500534 0.829776359 0.514637744 0.110002967 576.7374195 969425.3157 0.029088252 0.04526333 5292.841331 -3.723688875 -0.258724175 GKDYYQTLGLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKDYYQTLGLAR 12 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 115.37 0.00087256 2191480000 1484350 1648810 1405810 1220870 1157940 848760 1418610 1399620 1483910 1629240 FALSE TRUE 1426339.961 1601787.553 1659871.139 1283879.247 1195186.192 865922.5087 1435971.374 1370717.358 1315462.758 1518890.124 0.939067243 1.054577634 1.092818442 0.845274604 0.786881271 0.570102139 0.945408329 0.902446686 0.866068412 1 20.53458608 3.724076362 22.34027113 0.837682908 1.031396732 0.351309793 0.114028207 204.4142907 315285.5075 0.031616869 0.049315974 5297.565833 -3.724076362 0.193713825 AEENLLMVLGTDMSDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEENLLMVLGTDMSDRR 17 1 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-2;Q9H9E3-3 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 ; 193.8 1.77E-10 114020000 90367 90145 69205 89471 95516 100142 81371 92311 104348 102307 FALSE TRUE 86835.35773 87574.15286 81711.88296 94088.60903 98588.35889 102166.9399 82366.84264 90404.74559 92502.8525 95377.65576 0.910437115 0.918183113 0.856719347 0.986484814 1.033663053 1.071183172 0.863586361 0.947860847 0.969858734 1 16.5413637 3.724082587 24.56499421 0.97645342 0.897420183 0.351181889 0.053627266 800.438395 1358110.25 0.015598344 0.024293997 5297.641766 -3.724082587 -0.079033237 SQSQNLFSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSQNLFSVK 10 0 Q86W26 Q86W26 NLRP10 "NACHT, LRR and PYD domains-containing protein 10" 0 60.518 0.097569 425660000 786710 746630 875530 432340 632490 586880 650970 421190 620660 622300 FALSE TRUE 755964.5034 725336.8434 1033757.747 454653.1192 652834.6153 598747.1157 658936.7656 412492.2793 550205.2788 580151.0667 1.303047683 1.250255123 1.781876836 0.783680571 1.125283832 1.032053805 1.135802041 0.711008396 0.948382775 1 19.14606909 3.724144892 24.97071723 0.955661379 1.425579431 0.59566559 0.181991825 521.2014214 902817.8919 0.048775125 0.075942626 5298.401826 -3.724144892 0.469918052 KVS(ph)GDSSHTETTAEEVPEDPLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVSGDSSHTETTAEEVPEDPLLK 23 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;H7C2V9;H7C231 H7BYY2 BCOR BCL-6 corepressor 1 KVS(0.167)GDS(0.167)S(0.167)HT(0.167)ET(0.167)T(0.167)AEEVPEDPLLK 49.25 0.066655 305150000 315860 292840 297080 246070 283700 303760 297400 292630 323410 337860 TRUE FALSE 303515.842 284488.4899 350768.9645 258769.7022 292825.4681 309902.2353 301039.6702 286587.0882 286697.8526 314976.4413 0.963614424 0.903205614 1.113635557 0.821552562 0.929674191 0.983890205 0.955752973 0.909868329 0.910219988 1 18.2648844 3.724190413 24.99965452 0.929028449 0.98445726 0.154431685 0.06690039 1574.549395 2739222.448 0.017245562 0.026848252 5298.957219 -3.724190413 0.055428811 RES(ph)PPAGQK ddPTM_BT-474_Pertuzumab_2h_R1 3 RESPPAGQK 9 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RES(1)PPAGQK;RES(1)PPAGQK;RES(1)PPAGQK 84.352 0.0095248 913940000 1021210 1038770 920080 1174890 1160890 1230840 1363480 1435200 1502440 1520140 TRUE FALSE 981299.9842 1009145.297 1086358.923 1235526.214 1198231.081 1255728.428 1380166.676 1405562.618 1331889.31 1417179.564 0.69243165 0.712080051 0.766564062 0.871820513 0.845504064 0.886075738 0.973882711 0.991802771 0.939816904 1 20.43459114 3.724231415 0.461742865 1.001206594 0.602706194 0.938630684 0.026611125 0.465264559 0.148269371 0.022633147 0.093280155 5299.457518 -3.724231415 -0.3985004 QTVTSTPCWIELHLNGPLQWLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTVTSTPCWIELHLNGPLQWLDK 23 0 Q15796-2;Q15796;P84022-3;P84022-2;P84022;H3BQ00;P84022-4 Q15796-2 SMAD2;SMAD3 Mothers against decapentaplegic homolog 2;Mothers against decapentaplegic homolog 3 0 63.165 0.040011 59383000 63438 59392 60858 60259 73031 80630 75198 73934 82986 89268 FALSE TRUE 60958.77283 57698.19831 71856.39438 63368.97421 75380.10844 82260.39384 76118.29562 72407.23706 73565.77719 83221.79885 0.732485643 0.69330631 0.863432362 0.761446821 0.905773601 0.988447678 0.914643719 0.870051333 0.883972447 1 16.34467385 3.724315171 1.00721816 0.920537383 0.709109541 0.65985293 0.057027141 0.410334281 0.773254591 0.021141169 0.065554796 5300.47964 -3.724315171 -0.211427841 QIEEELWEEEFIER ddPTM_BT-474_Pertuzumab_2h_R1 2 QIEEELWEEEFIER 14 0 Q9BPZ3;D6RA77 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 0 ; 175.28 5.60E-06 486380000 126325 134942 98349 143063 148167 146660 135804 185402 149050 150738 FALSE TRUE 121388.0793 131093.5863 116122.8521 150446.4986 152932.9261 149625.5657 137466.01 181573.3839 132130.4689 140528.381 0.863797608 0.932861998 0.826330249 1.070577328 1.088270747 1.064735569 0.978208167 1.292076253 0.940240455 1 17.100502 3.724555415 20.99140373 1.082801456 0.880183201 0.444986289 0.094002566 75.27419809 112823.5904 0.025054522 0.039162137 5303.412583 -3.724555415 -0.202618256 TTS(ph)PSS(ph)DTDLLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSPSSDTDLLDR 13 0 K7ENU0;K7ERZ4;K7EJ43;Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3 K7ENU0;Q96QT6 PHF12 PHD finger protein 12 2 TT(0.001)S(0.998)PS(0.299)S(0.701)DTDLLDR 232.5 9.40E-13 112520000 178550 170670 132020 169800 172010 173830 166530 178350 192360 169170 TRUE FALSE 171572.0686 165802.6587 155878.9508 178563.3983 177542.8579 177344.9617 168568.044 174667.0102 170524.0992 157711.9652 1.087882383 1.051300442 0.988377455 1.132212119 1.125741206 1.124486411 1.068834845 1.107506396 1.081237552 1 17.26693259 3.724716961 24.99814229 1.097780824 1.043398123 0.203791489 0.043030552 1002.841291 1810880.249 0.01093426 0.017043451 5305.385688 -3.724716961 -0.054382701 EQLQDLHDQIAGQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQLQDLHDQIAGQK 14 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 125.28 0.00045893 0 141240 172780 113000 171510 160720 186740 166290 190150 184490 192660 FALSE TRUE 135720.1847 167852.4836 133421.6137 180361.6517 165889.7048 190516.0107 168325.1068 186223.3361 163547.4686 179610.9666 0.755634175 0.934533602 0.742836678 1.004179506 0.923605657 1.060714801 0.937164974 1.036814954 0.910565049 1 17.45451591 3.72472454 24.98021369 0.984663088 0.823354696 0.579995404 0.066350862 494.5997682 892970.311 0.01601487 0.024952603 5305.478263 -3.72472454 -0.161308392 AGPGSS(ph)PLFSLLPGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGPGSSPLFSLLPGYR 16 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 1 AGPGS(0.023)S(0.977)PLFSLLPGYR;AGPGS(0.07)S(0.93)PLFSLLPGYR 220.52 1.20E-14 839930000 796820 855560 721180 706390 659110 814460 744850 759120 822490 868150 TRUE FALSE 765679.3935 831160.2665 851513.2686 742846.8726 680310.8717 830928.9392 753965.6971 743443.9067 729124.3834 809349.4272 0.946043041 1.026948607 1.052095967 0.917832085 0.840565087 1.026662788 0.931570063 0.918569757 0.900877123 1 19.62640318 3.724789059 24.75739693 0.929586077 1.010221146 0.281364136 0.05435673 780.7431333 1403557.209 0.01421095 0.022144353 5306.266517 -3.724789059 0.080635069 RVDHCPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVDHCPIK 8 1 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 51.727 0.095691 43622000 62201 69040 68543 37411 31734 15033 59204 46317 40584 65491 FALSE TRUE 59770.11615 67071.0468 80930.24483 39341.78619 32754.75293 15336.97756 59928.55626 45360.53776 35977.07446 61055.23624 0.978951517 1.098530625 1.325525046 0.644363835 0.536477376 0.251198398 0.981546546 0.74294263 0.589254529 1 15.89782741 3.724821692 24.59334187 0.667488516 1.130755214 0.479428774 0.21772103 517.3710605 926119.4772 0.059015554 0.091985159 5306.665247 -3.724821692 0.463266697 KIEFPLPDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIEFPLPDRR 10 2 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 127.17 0.00020421 1913950000 1685870 1817380 1607940 1479360 1703010 1314940 1922320 1618340 1815220 1913640 FALSE TRUE 1619984.337 1765550.102 1898530.526 1555709.947 1757788.863 1341528.988 1945845.927 1584920.713 1609163.836 1784027.458 0.908048993 0.989642897 1.064182346 0.872021302 0.985292494 0.751966558 1.090704024 0.888394798 0.901983783 1 20.76670639 3.724841063 24.79147994 0.925591964 0.98752657 0.083069869 0.091387391 1668.488759 3014989.404 0.02294389 0.035762406 5306.901946 -3.724841063 0.061934606 KPSQTASYER ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 77.867 0.040363 0 99751 108830 96531 71819 73546 37117 101330 72017 82682 89672 FALSE TRUE 95852.62064 105726.275 113976.299 75525.5872 75911.67388 37867.53117 102570.1069 70529.82378 73296.28599 83598.43557 1.146583904 1.264692027 1.363378372 0.903433021 0.908051369 0.452969376 1.226938114 0.843673967 0.87676624 1 16.35118832 3.724885325 22.00493531 0.882542536 1.258865447 0.456829 0.185238488 131.6619908 211857.951 0.048166229 0.075246351 5307.442836 -3.724885325 0.376322911 NLVTEDVMR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLVTEDVMR 9 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ; 155.58 0.00016974 694060000 976310 1003660 751210 550590 556210 197253 627690 545070 604210 594510 FALSE TRUE 938154.7258 975036.5995 886970.3576 579006.0159 574100.9998 201241.5908 635371.858 533814.114 535622.6139 554243.3082 1.692676686 1.759221239 1.600326688 1.044678406 1.035828473 0.363092504 1.146377139 0.963140386 0.966403394 1 19.08015992 3.725062481 2.389479435 0.907677842 1.731835728 0.758702153 0.196636628 0.140881857 1.575786421 0.055687181 0.107442465 5309.608268 -3.725062481 0.824157886 DAASVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DAASVEK 7 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 109.01 0.016573 346350000 248350 269160 182520 280940 282440 304280 266710 312050 263140 310220 FALSE TRUE 238644.2074 261483.8203 215505.4241 295439.3471 291524.9391 310432.7501 269974.0768 305606.0585 233269.4504 289208.5231 0.825163121 0.904135942 0.745155854 1.0215444 1.008009501 1.07338728 0.93349281 1.056697967 0.806578755 1 18.14175054 3.725073767 24.95343968 0.993173584 0.832750067 0.461400999 0.079212927 608.1517826 1125205.85 0.019904462 0.031026536 5309.746255 -3.725073767 -0.160423517 VVTTSAR ddPTM_BT-474_Pertuzumab_2h_R1 3 VVTTSAR 7 0 F8VTQ9;F8VXU8;Q8IUR5 F8VTQ9 TMTC1 Transmembrane and TPR repeat-containing protein 1 0 ;; 122.15 0.010163 972440000 849460 871350 911350 458960 559770 289651 683780 492620 505310 584380 FALSE TRUE 816262.1641 846499.9511 1076051.218 482646.9806 577775.5104 295507.9417 692148.3042 482447.2249 447949.3272 544799.4221 1.498280158 1.553782763 1.975132818 0.885916837 1.060528861 0.542416034 1.270464461 0.885550177 0.822227978 1 19.05536565 3.725123374 24.84996482 0.927839583 1.663536993 0.729533282 0.209738955 336.7182808 622705.0026 0.053586459 0.083539822 5310.352792 -3.725123374 0.73569741 KPGTNLTEEDLVDIVDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPGTNLTEEDLVDIVDTR 18 1 Q49AR2;Q49AR2-2 Q49AR2 C5orf22 UPF0489 protein C5orf22 0 ; 242.98 7.34E-24 680230000 746720 682290 685720 776540 755180 794310 906180 951930 935040 961970 FALSE TRUE 717537.3569 662831.7572 809644.8578 816617.3225 779471.0505 810371.4924 917270.1019 932272.3128 828898.1792 896814.9151 0.800095254 0.739095376 0.902800393 0.910575091 0.86915487 0.903610632 1.022808705 1.03953703 0.924268949 1 19.77445075 3.725239198 0.481999156 1.012558762 0.715247078 0.688782289 0.050159747 1.080249351 0.381660352 0.040910597 0.167029742 5311.769222 -3.725239198 -0.297311685 KLSELLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSELLR 7 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 167.24 0.0017534 10207300000 12304700 13988400 11950200 9654800 9891000 4639300 12710700 10547000 11482400 13183900 FALSE TRUE 11823818.72 13589464.53 14109866.97 10153085.39 10209153 4733109.825 12866257.35 10329200.76 10178966.09 12290942.71 0.961994454 1.105648676 1.147988995 0.82606238 0.830624081 0.385089243 1.046808016 0.840391255 0.828168053 1 23.55109224 3.725276573 22.05387222 0.813781943 1.075254466 0.307369713 0.171215417 181.4586818 301254.2539 0.045430973 0.071017167 5312.226367 -3.725276573 0.261472523 YLAFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YLAFLR 6 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 118.11 0.051516 174360000 227240 252080 269800 104270 74780 20056 250770 106480 100050 205960 FALSE TRUE 218359.2096 244890.9252 318558.8617 109651.3872 77185.36661 20461.54606 253838.9983 104281.1508 88692.74344 192010.1457 1.137227456 1.275406173 1.659073068 0.571070798 0.401985876 0.106564921 1.322008258 0.543102295 0.461916963 1 17.55082302 3.725309029 24.69097659 0.618048665 1.349052623 0.496119 0.335909537 518.3303633 965777.4232 0.089557154 0.139658961 5312.62338 -3.725309029 0.731003957 KGHYAER ddPTM_BT-474_Pertuzumab_2h_R1 2 KGHYAER 7 1 P16104 P16104 H2AFX Histone H2AX 0 ; 86.011 0.032694 69530000 181053 194084 126652 109557 93665 29002 136027 70348 83739 114319 FALSE TRUE 173977.2486 188548.9143 149540.8338 115211.2499 96677.81979 29588.44031 137691.7391 68895.28922 74233.29978 106576.0723 1.632423159 1.769148649 1.403137032 1.081023605 0.907125002 0.277627423 1.291957342 0.646442374 0.696528763 1 16.70152405 3.725353159 1.636316539 0.784860184 1.709906904 0.680144329 0.249337062 0.209315041 1.083846397 0.071856141 0.163177055 5313.163233 -3.725353159 0.92504672 PIT(ph)PVYTVAPNVQR ddPTM_BT-474_Pertuzumab_2h_R1 3 PITPVYTVAPNVQR 14 0 B7Z8Z7;A0AV96;A0AV96-2 B7Z8Z7 RBM47 RNA-binding protein 47 1 PIT(0.998)PVYT(0.002)VAPNVQR;PIT(1)PVYTVAPNVQR;PIT(1)PVYTVAPNVQR 196.74 2.73E-07 660550000 407333 351527 336924 311616 321082 297985 284941 413977 415329 372983 TRUE FALSE 391413.976 341501.7941 397813.6616 327698.5391 331409.8941 304010.4609 288428.1932 405428.2303 368182.5931 347720.5292 1.125656794 0.982115709 1.144061475 0.942419304 0.953092689 0.874295405 0.829482786 1.165960006 1.058846292 1 18.40756872 3.725354808 24.37923073 0.979184682 1.07376177 0.208542697 0.09651079 1064.166629 1964559.09 0.028218259 0.043995702 5313.183412 -3.725354808 0.094577089 YLQEEVNINR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLQEEVNINR 10 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52 Q9UHD8 9-Sep Septin-9 0 ; 204.07 4.51E-07 909630000 347210 357570 278110 343480 356030 371730 338640 400750 339820 360600 FALSE TRUE 333640.6493 347372.4537 328370.6635 361207.044 367482.0283 379246.6353 342784.3776 392474.3725 301245.0582 336176.2408 0.992457553 1.033304593 0.976781294 1.074457383 1.093123141 1.128118496 1.019656763 1.167466123 0.896092649 1 18.35885824 3.725453578 23.57272908 1.069466766 1.004093492 0.075142415 0.072614271 649.249473 1167661.919 0.018292656 0.028558591 5314.391906 -3.725453578 -0.065373274 QGCDCECLGGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QGCDCECLGGGR 12 0 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ; 195.51 5.06E-07 434780000 190073 185633 120064 198728 177545 189408 205090 168160 197734 207423 FALSE TRUE 182644.737 180338.9286 141762.2356 208984.3759 183255.8962 193237.9595 207599.9528 164687.4372 175288.0653 193374.0555 0.944515212 0.932591128 0.733098529 1.080726033 0.947675714 0.999296204 1.073566732 0.851652187 0.906471475 1 17.56103472 3.725517452 24.99325204 0.971716051 0.876320559 0.257422725 0.084496723 1199.580856 2298632.125 0.023056299 0.035962505 5315.173575 -3.725517452 -0.095395492 KLDLEAWFPGSGAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDLEAWFPGSGAFR 15 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 140.81 7.81E-06 881440000 1979510 2035320 1743740 1716740 1693720 1703930 1857390 1964200 2053690 2033940 FALSE TRUE 1902148.561 1977274.666 2058872.607 1805341.157 1748200.042 1738384.632 1880121.294 1923638.584 1820563.721 1896179.432 1.003147977 1.042767701 1.085800517 0.952094051 0.921959184 0.91678277 0.99153132 1.014481304 0.96012207 1 20.85466406 3.725542714 24.8248287 0.966659778 1.04379163 0.515763956 0.034893449 615.6970943 1174120.615 0.010477162 0.016334943 5315.482763 -3.725542714 0.077131851 FLFENQTPAHVYYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLFENQTPAHVYYR 14 0 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 140.1 1.00E-05 892260000 504040 528440 420850 399400 440770 349970 487850 399550 414570 438430 FALSE TRUE 484341.5596 513369.4086 496906.9568 420013.0819 454947.7673 357046.6332 493820.4542 391299.1529 367509.7516 408734.7456 1.184977702 1.255996497 1.215719882 1.02759329 1.1130636 0.873541183 1.208168524 0.957342524 0.899139982 1 18.64080536 3.725555838 3.542467687 1.014170592 1.226727575 0.5109308 0.093052743 0.186398958 5.060094363 0.024347203 0.042789973 5315.643396 -3.725555838 0.212556983 RDHHSTHYR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDHHSTHYR 9 1 P05060 P05060 CHGB Secretogranin-1;PE-11;GAWK peptide;CCB peptide 0 ;;; 104.2 0.0052892 3697640000 3247080 3432880 3673510 1829810 2474620 2014300 2595360 2150240 2076200 2227480 FALSE TRUE 3120180.524 3334977.624 4337394.974 1924246.713 2554218.4 2055030.526 2627122.792 2105836.793 1840518.48 2076610.796 1.502535059 1.605971437 2.088689408 0.926628484 1.229993798 0.989607937 1.265101192 1.014073892 0.886308828 1 20.98579942 3.725624656 24.99866373 1.061060777 1.719755926 0.752476342 0.180573182 351.71221 679681.6585 0.046798231 0.073003839 5316.48577 -3.725624656 0.658695149 NDRGDQVPNR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDRGDQVPNR 10 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 133.12 0.00018738 629690000 285250 272620 247065 227363 204422 242598 246167 263333 274010 283120 FALSE TRUE 274102.1146 264845.1445 291715.1414 239097.2317 210997.4193 247503.4978 249179.6654 257895.0815 242905.5335 263944.0302 1.038485752 1.003414036 1.10521591 0.905863381 0.799402127 0.93771205 0.944062516 0.977082457 0.920291826 1 18.00987251 3.725813505 24.77621619 0.924967579 1.044476114 0.508869914 0.055170359 568.1255765 1104250.368 0.015520945 0.024218654 5318.798105 -3.725813505 0.119508535 LPPSS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LPPSSPQK 8 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LPPS(0.195)S(0.805)PQK;LPPS(0.227)S(0.773)PQK;LPPS(0.06)S(0.94)PQK 91.095 0.013353 1646530000 2059320 1987420 1772790 1549110 1612320 935840 1880410 1781580 1813960 1913300 TRUE FALSE 1978839.498 1930740.727 2093172.589 1629059.753 1664181.737 954763.326 1903423.02 1744789.75 1608046.866 1783710.487 1.109395001 1.082429431 1.173493459 0.913298299 0.932988705 0.535268102 1.067114329 0.978179903 0.901517863 1 20.76645004 3.725833696 21.44662454 0.903826052 1.117838283 0.352651112 0.135145864 128.5472292 216620.7427 0.037000056 0.057937908 5319.045384 -3.725833696 0.214012231 MYSYPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 MYSYPAR 7 0 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 81.635 0.062041 126580000 99701 125330 111230 68467 56811 46582 108360 67762 70099 86384 FALSE TRUE 95804.57469 121755.7111 131331.7353 72000.59008 58638.37741 47523.91996 109686.1421 66362.69102 62141.6554 80533.13474 1.189629275 1.511871002 1.63077888 0.894049267 0.728127343 0.590116355 1.362000156 0.82404207 0.771628419 1 16.29729487 3.725841865 23.9862325 0.881970715 1.450870832 0.584142104 0.217535764 294.9397669 556225.7218 0.058520031 0.091388972 5319.145435 -3.725841865 0.568900117 LLLAS(ph)PPNER ddPTM_BT-474_Pertuzumab_2h_R1 2 LLLASPPNER 10 0 Q52LW3 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 LLLAS(1)PPNER;LLLAS(1)PPNER 126.34 0.00040392 276650000 198319 230960 171112 241360 244570 240525 261150 312260 245950 283150 TRUE FALSE 190568.4742 224373.2469 202035.7448 253816.6185 252436.8162 245388.5803 264346.0318 305811.7219 218030.7871 263971.9983 0.721926854 0.849988818 0.765368092 0.961528572 0.956301493 0.929600798 1.001416944 1.158500613 0.825961801 1 18.01002537 3.725875548 0.809417876 1.016444474 0.731914596 0.503025824 0.08629638 0.670130437 0.782231503 0.037986061 0.133780424 5319.557993 -3.725875548 -0.284529878 S(ph)PVSPLAAQGIPLPAQLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 S(0.978)PVS(0.022)PLAAQGIPLPAQLTK;S(0.775)PVS(0.225)PLAAQGIPLPAQLTK 307.97 2.00E-61 1727250000 1315030 1260610 1114320 1099580 1161300 1062180 1097310 1328760 1329730 1267980 TRUE FALSE 1263637.174 1224658.637 1315702.412 1156329.456 1198654.269 1083658.007 1110739.208 1301320.642 1178784.625 1182098.585 1.068977824 1.036003809 1.113022576 0.978200524 1.014005333 0.916723885 0.939633311 1.100856272 0.997196545 1 20.17291893 3.725927366 24.86953558 0.997391056 1.069001645 0.354807978 0.049219974 924.0852419 1819134.255 0.014415312 0.022484047 5320.192735 -3.725927366 0.07161059 NYNECIR ddPTM_BT-474_Pertuzumab_2h_R1 2 NYNECIR 7 0 Q9H832-2;Q9H832;D6RB11 Q9H832-2 UBE2Z Ubiquitin-conjugating enzyme E2 Z 0 ; 135.77 0.0070847 1746770000 704321 654298 582775 589577 642778 574810 648678 643831 719337 691968 FALSE TRUE 676795.3567 635638.0617 688095.4063 620005.1396 663453.5381 586433.052 656616.7154 630535.6649 637680.8795 645100.391 1.049131834 0.985332005 1.066648565 0.961098688 1.028450064 0.90905704 1.017851988 0.977422543 0.988498671 1 19.29916417 3.725941616 24.98773812 0.982883786 1.028866924 0.284233617 0.036485294 941.1090406 1863551.484 0.008932563 0.013942086 5320.3673 -3.725941616 0.045983138 ALIVLAHSER ddPTM_BT-474_Pertuzumab_2h_R1 2 ALIVLAHSER 10 0 P15559-2;P15559;B4DLR8;P15559-3;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 168.83 4.82E-06 1595470000 1539040 1673890 1565920 709700 718910 107046 1259120 535940 632230 963960 FALSE TRUE 1478892.615 1626152.296 1848916.578 746327.7021 742034.393 109210.5435 1274529.487 524872.6517 560461.9009 898670.1306 1.645645677 1.809509675 2.057391822 0.830480147 0.825702744 0.121524617 1.418239512 0.584054854 0.623656981 1 19.77743213 3.725961195 19.3194703 0.759448428 1.834714763 0.695502481 0.323020501 18.48113579 28338.76015 0.082559756 0.129663853 5320.607167 -3.725961195 1.075266335 TVLSSAR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVLSSAR 7 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 0 ;;; 126.24 0.0092382 2301170000 1360840 1280500 1464600 576216 708060 317103 1001050 655820 660010 838570 FALSE TRUE 1307656.868 1243981.394 1729285.8 605954.5768 730835.3929 323515.0399 1013301.149 642277.0878 585088.4318 781772.907 1.672681231 1.59123114 2.212005282 0.775103066 0.934843593 0.413822271 1.296157926 0.821564782 0.748412265 1 19.57639006 3.726001863 24.99391491 0.858327903 1.80189841 0.747923842 0.257843169 342.4835933 681596.8193 0.066124057 0.103210256 5321.105419 -3.726001863 0.943570507 KVIQYLAYVASSHK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVIQYLAYVASSHK 14 1 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 111.74 0.00041158 236680000 413040 466680 434890 312840 363510 319020 370810 327750 422650 432410 FALSE TRUE 396897.9402 453370.7433 513484.2971 328985.7099 375202.6293 325470.803 375348.0837 320981.848 374672.5439 403122.4855 0.984559171 1.124647618 1.273767442 0.816093673 0.93074101 0.80737447 0.931101829 0.796239008 0.929426061 1 18.62085873 3.726024114 24.9979818 0.875318991 1.127357036 0.598079658 0.089926971 442.3347436 882022.4291 0.022781305 0.035561125 5321.378046 -3.726024114 0.252038046 YKDAIHFYNK ddPTM_BT-474_Pertuzumab_2h_R1 2 YKDAIHFYNK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 126.67 0.00022616 7339700000 10178000 10254800 9578400 7374700 7162000 4239700 10359700 8203800 9768100 10245000 FALSE TRUE 9780232.508 9962343.144 11309429.95 7755309.151 7392372.234 4325429.639 10486485.11 8034388.663 8659266.239 9551097.025 1.023990488 1.043057475 1.184097483 0.811980983 0.773981482 0.452872547 1.097935146 0.841200612 0.906625304 1 23.18723502 3.7260443 24.65540289 0.831944085 1.07964938 0.315859751 0.163541042 722.333243 1422896.19 0.043968303 0.068661075 5321.625389 -3.7260443 0.247705295 VQIYHNPTANSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQIYHNPTANSFR 13 0 P50552;K7ENR7;K7ENL7 P50552 VASP Vasodilator-stimulated phosphoprotein 0 99.941 0.0026295 476290000 305440 317690 281390 232620 244960 106160 340000 258490 252300 305710 FALSE TRUE 293503.0671 308629.7923 332243.4325 244625.5461 252839.3609 108306.6279 344161.0217 253152.0912 223659.9617 285003.9894 1.029820908 1.082896393 1.165750112 0.858323235 0.887143234 0.380017936 1.207565629 0.888240518 0.784760811 1 18.12062259 3.726404194 23.41538583 0.858356319 1.091829857 0.230131419 0.19681079 464.7057512 895104.9826 0.052216839 0.081665705 5326.037183 -3.726404194 0.233473538 KY(ph)NTMLGYK ddPTM_BT-474_Pertuzumab_2h_R1 1 KYNTMLGYK 9 1 A0A0D9SEQ4;A0A0D9SFM8;A0A0D9SGF7;A0A0D9SFI7;A0A3B3IRN7;Q9UM63-2;Q9UM63 A0A0D9SEQ4 PLAGL1 Zinc finger protein PLAGL1 1 KY(0.998)NT(0.001)MLGY(0.001)K 47.198 0.060525 427400000 740080 541200 499840 431920 498000 477710 530470 70165 661440 524130 TRUE FALSE 711156.8554 525765.5059 590172.2069 454211.443 514018.6223 487369.6235 536962.0505 68716.06823 586356.1042 488630.2083 1.455409108 1.075998776 1.207809499 0.929560709 1.051958339 0.997420166 1.098912923 0.140630004 1.199999702 1 18.89838353 3.726506325 0.527579369 0.746611603 1.434513136 0.206104808 0.288697526 2.192702271 0.961158986 0.209073634 0.838008537 5327.289831 -3.726506325 0.687901534 VLEALLPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLEALLPLK 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 107.66 0.0069498 0 96736 115770 85966 67003 66424 41399 92330 60898 70660 82730 FALSE TRUE 92955.45017 112468.353 101501.9685 70461.03286 68560.58828 42236.11614 93459.96216 59640.43502 62638.97303 77126.62341 1.205231683 1.45822996 1.316043203 0.91357601 0.888935432 0.547620449 1.21177303 0.773279477 0.812157596 1 16.23494133 3.726631474 4.14183884 0.866632748 1.346545228 0.598771639 0.168347815 0.130898722 5.460222919 0.043196299 0.074171394 5328.825195 -3.726631474 0.47991248 IYKPLLFMDLLDER ddPTM_BT-474_Pertuzumab_2h_R1 2 IYKPLLFMDLLDER 14 1 A0A0J9YWM9;H3BSH7;Q969X6;A0A0J9YXV4;Q969X6-2 A0A0J9YWM9 CIRH1A Cirhin 0 ; 149.3 6.86E-06 169112000 532670 515190 439150 440530 445160 419430 469770 445320 520690 591180 FALSE TRUE 511852.6675 500497.2856 518514.1738 463265.8061 459478.9757 427911.162 475519.1858 436123.9864 461583.4541 551138.852 0.928718173 0.908114686 0.940804975 0.840560966 0.833690047 0.776412623 0.862793802 0.791314176 0.837508465 1 19.07205631 3.726901506 19.03051502 0.834977508 0.924102803 0.246115013 0.058256008 31.40309654 51258.79639 0.014137466 0.02226298 5332.139532 -3.726901506 0.089125295 ALHSLLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALHSLLLR 8 0 M0R1K3;Q15102 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 172.15 0.00028527 334030000 226730 282860 217810 109930 101260 25602 183690 94096 115270 161170 FALSE TRUE 217869.1409 274793.1097 257173.1122 115603.5005 104517.1199 26119.68998 185938.0532 92152.88472 102185.0329 150253.8123 1.450007408 1.828859484 1.711591261 0.769388135 0.69560378 0.17383712 1.237493081 0.613314786 0.680082796 1 17.19704207 3.727115357 6.934477537 0.720319489 1.682026626 0.709028398 0.271320768 0.072357394 20.507237 0.069306287 0.113442956 5334.765787 -3.727115357 0.961707138 QATS(ph)PASK ddPTM_BT-474_Pertuzumab_2h_R1 1 QATSPASK 8 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 1 QAT(0.023)S(0.976)PAS(0.001)K 98.04 0.008721 0 473260 470340 378300 457740 474830 475550 538980 482750 415860 554780 TRUE FALSE 454764.476 456926.3637 446667.2252 481364.0163 490103.3382 485165.9468 545576.1985 472781.0438 368653.3162 517204.2565 0.879274427 0.883454376 0.863618618 0.930703896 0.947601131 0.938054822 1.054856358 0.914108958 0.712780902 1 18.98037462 3.727139292 20.05010858 0.932597397 0.876249673 0.077116472 0.082843565 132.6383678 232849.5114 0.022286028 0.035061131 5335.059803 -3.727139292 -0.056347724 IHLAQSLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 IHLAQSLHK 9 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 117.31 0.00067779 199870000 369770 494950 492620 122130 98979 22840 327220 30686 130010 238860 FALSE TRUE 355318.9796 480834.5106 581647.3923 128433.1439 102162.7494 23301.84045 331224.6162 30052.32338 115251.8098 222681.7994 1.595635478 2.159289676 2.612011371 0.576756359 0.458783563 0.104641872 1.487434613 0.134956352 0.517562774 1 17.76462412 3.727205648 24.86707808 0.575860495 2.126009913 0.709088316 0.443059119 323.9897602 709529.0652 0.114207812 0.178684447 5335.87501 -3.727205648 1.550149418 AVCMLSNTTAIAEAWAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVCMLSNTTAIAEAWAR 17 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ; 185.12 1.39E-09 692620000 84690 84979 63677 88842 84861 98069 111303 84351 89556 93469 FALSE TRUE 81380.22117 82555.48212 75184.85039 93427.14627 87590.63113 100052.0224 112665.1594 82609.12237 79389.97833 87138.26138 0.933920644 0.947407956 0.862822475 1.072171338 1.005191402 1.148198516 1.292947066 0.948023533 0.911080587 1 16.41101871 3.727216882 24.49310653 1.061373341 0.917986119 0.272051801 0.103828403 740.5951219 1599074.969 0.029383714 0.045998764 5336.013037 -3.727216882 -0.143387222 IVATKPLYVALAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 IVATKPLYVALAQR 14 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YB86 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 112.96 0.00051349 302400000 443320 405240 407000 207820 175890 51721 338910 188140 208440 348510 FALSE TRUE 425994.5643 393682.952 480553.9537 218545.6151 181547.6616 52766.83406 343057.682 184254.8433 184778.7651 324905.1073 1.311135328 1.211685945 1.479059402 0.672644444 0.558771338 0.162406909 1.055870389 0.567103561 0.568716099 1 18.3096589 3.727305539 22.63220971 0.63381836 1.321732771 0.621496559 0.24233214 119.7231187 240745.0853 0.062445551 0.097949764 5337.102449 -3.727305539 0.68791441 LYANMFER ddPTM_BT-474_Pertuzumab_2h_R1 2 LYANMFER 8 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 116.25 0.0053682 567340000 896870 1086740 1028500 575040 678200 446160 968950 595690 566140 743580 FALSE TRUE 861819.3289 1055747.239 1214372.829 604717.8833 700014.9189 455181.6609 980808.2999 583388.7933 501874.1607 693216.6643 1.243217847 1.522968638 1.751794051 0.872336045 1.009806825 0.656622503 1.414865439 0.841567757 0.723978788 1 19.40294681 3.727408706 24.99435969 0.94039148 1.507691028 0.578440356 0.2247265 483.1644121 1082898.354 0.058552795 0.091619725 5338.370421 -3.727408706 0.567299548 LQNAT(ph)PTNFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQNATPTNFK 10 0 Q9NXF1-2;Q9NXF1 Q9NXF1-2 TEX10 Testis-expressed sequence 10 protein 1 LQNAT(0.637)PT(0.363)NFK 97.86 0.014678 0 226940 224560 194610 192370 182740 194480 201680 237080 211050 231340 TRUE FALSE 218070.9339 218155.7687 229780.3561 202298.2388 188617.9981 198412.5188 204148.2202 232184.2152 187092.4888 215671.1357 1.011127118 1.01152047 1.065420068 0.937994035 0.874563012 0.91997716 0.946571823 1.076566015 0.8674897 1 17.71847358 3.727418941 24.75114549 0.952896082 1.027572345 0.293183793 0.058523188 935.9461444 2079198.481 0.017020377 0.026646667 5338.496235 -3.727418941 0.074676263 KLDYGQHVVAGTPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDYGQHVVAGTPGR 15 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 153.94 1.67E-06 2379700000 2753900 2773600 2187600 2663300 2711700 2908500 2772100 2694400 3040200 2957700 FALSE TRUE 2646274.543 2694499.644 2582947.983 2800753.232 2798924.293 2967311.863 2806025.789 2638759.698 2695089.242 2757372.345 0.959708814 0.977198328 0.936742543 1.015732691 1.015069401 1.076137529 1.017644858 0.95698345 0.977412154 1 21.39486267 3.727479976 24.84535853 1.00719512 0.959814738 0.36508075 0.030482259 857.4456711 1922592.152 0.009319718 0.014597525 5339.246552 -3.727479976 -0.047380382 WYNHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 WYNHIK 6 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ; 97.306 0.041221 3426600000 5877500 6186000 5595100 3850800 3791800 1649620 4934800 4135300 4796700 5940900 FALSE TRUE 5647800.802 6009581.337 6606259.032 4049540.249 3913766.691 1682976.447 4995193.559 4049904.61 4252198.725 5538517.551 1.019731498 1.085052323 1.192784707 0.731159595 0.706645173 0.303867674 0.901900827 0.731225382 0.767750339 1 22.40106844 3.727543998 23.39737015 0.716118203 1.097775782 0.476829701 0.174225185 235.9026327 501016.5158 0.045763294 0.071754064 5340.033701 -3.727543998 0.381657578 EMLQQSK ddPTM_BT-474_Pertuzumab_2h_R1 3 EMLQQSK 7 0 P08238;Q58FF7;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha 0 ;; 155 0.0038174 1080040000 1568110 1565150 1379490 1261160 1316460 868650 1563550 1417310 1571560 1662880 FALSE TRUE 1506826.528 1520513.454 1628794.53 1326248.619 1358805.131 886214.6982 1582685.193 1388042.053 1393163.097 1550251.656 0.971988336 0.980817178 1.050664596 0.855505371 0.876506163 0.571658604 1.020921465 0.895365631 0.898668994 1 20.564071 3.727670509 24.38345768 0.868224599 0.99912275 0.200428874 0.115868148 787.6554807 1763598.062 0.030950202 0.048487649 5341.58949 -3.727670509 0.13089815 AGDTETLK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGDTETLK 8 0 C9JNG9;P12111 C9JNG9 COL6A3 Collagen alpha-3(VI) chain 0 ; 75.311 0.090077 4022700000 2550400 2319600 2819800 1203300 1847140 1660960 1872430 1703580 1638750 1635830 FALSE TRUE 2450727.548 2253447.279 3329400.586 1265402.457 1906554.936 1694545.749 1895345.358 1668400.478 1452725.97 1525033.777 1.606998865 1.477637619 2.183165144 0.829753725 1.250172268 1.11115293 1.242821888 1.094008869 0.952586095 1 20.54040977 3.727703917 24.99997887 1.092387211 1.728104269 0.696550819 0.207224113 384.4244254 885223.1499 0.052788709 0.082662778 5342.00041 -3.727703917 0.635717058 GQDGIGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQDGIGSK 8 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 76.943 0.080248 284570000 364260 340920 264450 342180 341780 353430 340850 335480 359060 389150 FALSE TRUE 350024.3165 331197.2954 312241.9977 359839.9508 352773.6641 360576.5968 345021.4243 328552.2208 318301.0141 362792.5239 0.964805759 0.912911027 0.860662712 0.991861538 0.972384051 0.993892026 0.951015805 0.905620152 0.877363763 1 18.4687852 3.727787866 24.99651175 0.951279312 0.912804949 0.163625224 0.043878381 1475.901657 3424605.409 0.012506052 0.019592737 5343.033118 -3.727787866 -0.038474363 QGFGELLQAVPLADSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 QGFGELLQAVPLADSFR 17 0 P27695;G3V3M6;G3V5Q1 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 118.51 0.00038468 205881000 296650 322300 258500 239250 256710 206206 270100 256250 257710 283220 FALSE TRUE 285056.59 313108.3196 305216.7003 251597.7212 264967.3103 210375.6266 273405.5646 250958.348 228455.8412 264037.2571 1.079607451 1.185849008 1.155960729 0.952887194 1.003522432 0.79676493 1.035481006 0.950465668 0.865240927 1 18.01038199 3.72779018 8.390240946 0.943812687 1.145164948 0.623761554 0.070082458 0.09867927 58.75242393 0.017833323 0.028957895 5343.06158 -3.72779018 0.201352261 EKELAEDIMSVEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKELAEDIMSVEEK 14 1 Q6DKK2 Q6DKK2 TTC19 "Tetratricopeptide repeat protein 19, mitochondrial" 0 ; 188.47 7.57E-07 188242000 532890 495570 463570 411590 386300 411250 452240 539800 538670 426480 FALSE TRUE 512064.0697 481436.8288 547347.4111 432832.2092 398725.6903 419565.7568 457774.6484 528652.9414 477522.4399 397594.1297 1.287906514 1.210875093 1.376648623 1.088628269 1.002846019 1.055261447 1.151361688 1.329629644 1.201029905 1 18.60093693 3.727891143 24.97833367 1.138288269 1.283716581 0.372227398 0.100750474 959.5007129 2246290.091 0.030883053 0.048408008 5344.303868 -3.727891143 0.145428312 FPGQLNADLR ddPTM_BT-474_Pertuzumab_2h_R1 4 FPGQLNADLR 10 0 Q13509;A0A0B4J269;Q13509-2;G3V2A3;Q5JP53;P07437;Q5ST81;A6NNZ2;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;P68371;M0R2D3;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB1;TUBB4B;TUBB4A;TUBB2A;TUBB8;TUBB2B;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-1 chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ;;; 139.98 9.33E-05 1315380000 1163080 1285580 1181690 631200 497585 126481 1124660 589800 670320 997870 FALSE TRUE 1117625.548 1248916.517 1395247.67 663776.3076 513590.2734 129038.5325 1138423.926 577620.4239 594228.0838 930283.3761 1.201381833 1.342511915 1.499809311 0.713520552 0.552079384 0.138708845 1.223738868 0.620908036 0.638760295 1 19.82731072 3.727939503 23.17909684 0.682377391 1.347362098 0.538608843 0.275269724 187.4273222 409034.5871 0.072539189 0.113888751 5344.899005 -3.727939503 0.664984706 KAEAAASALADADADLEER ddPTM_BT-474_Pertuzumab_2h_R1 4 KAEAAASALADADADLEER 19 1 O43633;M0R1T5 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;;; 213.72 3.47E-17 1713180000 2046230 2068140 1737450 1847380 1924710 2005320 1846350 2058200 2146330 2250670 FALSE TRUE 1966261.069 2009158.672 2051445.864 1942723.503 1986620.045 2045868.944 1868946.184 2015697.451 1902687.617 2098230.116 0.937104588 0.957549249 0.977702993 0.925886769 0.946807516 0.975045077 0.890725078 0.96066558 0.90680598 1 21.00074148 3.727987162 24.76216148 0.94143893 0.957461975 0.035538841 0.031296315 1998.736835 4680885.294 0.00771218 0.01214457 5345.485582 -3.727987162 0.016023045 YPS(ph)CESVTDEYAGHLIQILK ddPTM_BT-474_Pertuzumab_2h_R1 4 YPSCESVTDEYAGHLIQILK 20 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 YPS(0.996)CES(0.002)VT(0.003)DEYAGHLIQILK;YPS(0.989)CES(0.01)VT(0.002)DEYAGHLIQILK;YPS(1)CESVTDEYAGHLIQILK;YPS(0.98)CES(0.018)VT(0.002)DEYAGHLIQILK 230.55 1.03E-25 914110000 606448 621717 493674 615805 600304 635418 659250 692468 738137 759530 TRUE FALSE 582747.3417 603986.2399 582891.8735 647586.7698 619613.3233 648266.5873 667318.0987 678168.2938 654346.7823 708086.3566 0.822989084 0.852983869 0.8231932 0.914559028 0.875053329 0.915519105 0.942424737 0.957748003 0.924105903 1 19.43356579 3.728036887 0.246293271 1.004712571 0.733281935 0.851523587 0.021367294 2.060637443 0.164988059 0.033978666 0.168825366 5346.09765 -3.728036887 -0.271430636 NYSEVIEVDES(ph)DVEEDIFPTTSK ddPTM_BT-474_Pertuzumab_2h_R1 2 NYSEVIEVDESDVEEDIFPTTSK 23 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 1 NYSEVIEVDES(0.995)DVEEDIFPT(0.004)T(0.001)SK;NYSEVIEVDES(1)DVEEDIFPTTSK 110.94 0.00064923 119832000 456230 428740 394420 353310 390420 390140 324840 419800 432690 407550 TRUE FALSE 438400.0272 416512.755 465700.4678 371544.3714 402978.2139 398028.8981 328815.4891 411130.9833 383572.8452 379946.2755 1.153847413 1.096241184 1.225700837 0.9778866 1.060618934 1.047592578 0.865426273 1.082076625 1.009544954 1 18.53543591 3.728062952 24.99509255 1.009268473 1.152360951 0.550462058 0.063006666 520.1734523 1238540.432 0.016345038 0.025619669 5346.418515 -3.728062952 0.143092478 FKMPDLHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKMPDLHLK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 102.53 0.0021447 1139320000 4761500 5106300 4101300 4039600 3600100 3536100 4507200 4599200 5051700 4779400 FALSE TRUE 4575415.316 4960673.324 4842496.143 4248084.24 3715900.486 3607602.365 4562360.462 4504224.913 4478252.194 4455686.981 1.026870904 1.113335238 1.086812463 0.953407243 0.833968028 0.809662434 1.023940973 1.010893479 1.005064362 1 22.08721645 3.728134992 9.077230567 0.9467683 1.079504869 0.396852903 0.071994428 0.213218008 161.1520702 0.021525791 0.034872024 5347.305446 -3.728134992 0.132736569 EANEILQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EANEILQR 8 0 P12268;H0Y4R1;E7ETK5;P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9 P12268;P20839-3 IMPDH2;IMPDH1 Inosine-5-monophosphate dehydrogenase 2;Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 103.87 0.010909 264890000 360790 389590 293210 369270 363170 370280 402820 380620 421810 399660 FALSE TRUE 346689.9279 378479.2746 346199.5694 388328.069 374851.6929 377767.3153 407749.8317 372760.064 373927.8972 372590.6722 0.930484722 1.015804482 0.929168643 1.042237764 1.006068377 1.013893646 1.094364036 1.000454632 1.003588992 1 18.50723203 3.728146987 24.95286244 1.024787193 0.964217801 0.411602985 0.035068385 654.4328189 1568133.651 0.008967443 0.014059726 5347.453131 -3.728146987 -0.060569392 YAPLHLVPLIER ddPTM_BT-474_Pertuzumab_2h_R1 2 YAPLHLVPLIER 12 0 Q7L576;Q7L576-2;Q7L576-3;Q96F07;Q96F07-2;E7EVJ5;H7C229;H0YL50;E7EW33 Q7L576 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 ; 84.289 0.01232 558700000 942090 1163760 809650 744500 720210 470210 864850 735310 810830 870690 FALSE TRUE 905272.0813 1130570.704 955971.7656 782923.7342 743376.2087 479717.9684 875434.293 720125.5915 718787.9777 811717.3908 1.11525525 1.392813209 1.177715023 0.964527486 0.91580668 0.590991365 1.078496411 0.887162946 0.885515065 1 19.630618 3.728187083 2.675044453 0.889113454 1.260539721 0.562708472 0.133375044 0.188562389 2.675325034 0.035968229 0.067337867 5347.946854 -3.728187083 0.371426267 VEHES(ph)FEK ddPTM_BT-474_Pertuzumab_2h_R1 7 VEHESFEK 8 0 K7EMC6;A0A0A0MSA9;A0A0C4DG49;P15151-3;P15151-2;P15151-4;P15151 K7EMC6 PVR Poliovirus receptor 1 VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK 95.62 0.0099869 16426050000 4766293 4325238 5205852 2617336 3529040 3559295 3915017 3870762 4184741 3949544 TRUE FALSE 4580021 4201886.447 6146665.26 2752417.025 3642554.777 3631266.384 3962930.149 3790829.412 3709706.746 3682037.867 1.243882102 1.141185017 1.669365032 0.747525453 0.989276837 0.986211037 1.076287179 1.029546558 1.007514556 1 21.81207303 3.728237596 24.99979083 0.987418082 1.330448163 0.564533122 0.150322012 515.1139512 1247478.052 0.038961356 0.061100099 5348.568916 -3.728237596 0.343030081 S(ph)SGPYGGGGQYFAKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-2;P09651;P09651-3;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 S(0.991)S(0.009)GPYGGGGQYFAKPR;S(0.978)S(0.022)GPYGGGGQYFAKPR 237 5.78E-20 1145110000 466800 463330 415850 326240 326640 310500 318570 393750 345440 344230 TRUE FALSE 448556.9399 450116.282 491003.3455 343077.2855 337146.6722 316778.5227 322468.755 385618.9249 306227.0994 320914.9955 1.397743783 1.402602834 1.530010602 1.06905969 1.050579365 0.987110379 1.004841654 1.201623266 0.954231194 1 18.29183168 3.728306485 24.19231107 1.051974857 1.439367445 0.86704342 0.07257616 150.52415 355127.8852 0.020023702 0.031429664 5349.417382 -3.728306485 0.387392588 LLEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEEER 6 0 Q8NE71;Q8NE71-2;H0YGW7;A0A087WZF6;Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065;Q5JSZ5-5;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;A0A087WW94;Q9UMZ2-9;Q9UMZ2-6;Q14789;Q14789-2;Q14789-4;Q14789-3 Q8NE71;Q5JSZ5;Q5JSZ5-5;Q9UMZ2-4;Q9UMZ2-9;Q14789 ABCF1;SYNRG;PRRC2B;GOLGB1 ATP-binding cassette sub-family F member 1;Protein PRRC2B;Synergin gamma;Golgin subfamily B member 1 0 111.28 0.065105 158330000 381470 381150 387730 411090 373240 392690 400850 388460 462160 453000 FALSE TRUE 366561.7307 370279.9752 457801.436 432306.4042 385245.6036 400630.4609 405755.7222 380438.1653 409697.5343 422317.9065 0.867975819 0.876780192 1.084020897 1.023651608 0.912217071 0.948646635 0.960782661 0.900833612 0.970116417 1 18.68796989 3.728307209 0.004262127 1.893892816 9.49E-08 0.047433709 0.063357184 148403.1053 141.9834556 30875.22317 32220.87907 5349.426304 -3.728307209 -1.893892721 VTNLFCFEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTNLFCFEHR 10 0 O95159;E9PQ47;E9PNY1;E9PJX1;E9PJ47;E9PMQ3;E9PQA5 O95159 ZFPL1 Zinc finger protein-like 1 0 73.435 0.044998 337620000 283190 333530 249420 182390 167560 76936 257840 168550 226920 244290 FALSE TRUE 272122.6217 324018.051 294495.7423 191803.1698 172949.7196 78491.69863 260995.523 165069.3836 201160.9929 227744.0207 1.194861761 1.422729123 1.293099777 0.84218751 0.759403997 0.344648779 1.146003843 0.724802272 0.883276726 1 17.79705365 3.728320812 4.447512171 0.794185997 1.32188067 0.551106926 0.202156343 0.136954484 7.130853452 0.05254206 0.089574351 5349.593864 -3.728320812 0.527694673 RQEQIAK ddPTM_BT-474_Pertuzumab_2h_R1 4 RQEQIAK 7 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;; 139.88 0.0042686 3189380000 1867050 1784070 1584930 1455340 1622830 1307710 1564650 1580530 1676570 1716360 FALSE TRUE 1794083.622 1733190.07 1871362.108 1530450.272 1675029.801 1334152.792 1583798.655 1547891.503 1486252.802 1600109.408 1.121225594 1.083169727 1.169521345 0.956466016 1.046822044 0.83378848 0.989806476 0.967366041 0.928844487 1 20.60973912 3.72832253 24.83733916 0.959731376 1.120491972 0.647498253 0.055491254 362.6840579 879862.1785 0.014150998 0.022198007 5349.615022 -3.72832253 0.160760596 VSITEAMHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSITEAMHR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 135.71 0.00021314 254400000 216000 239380 239220 117580 130180 98062 197290 119370 136100 180460 FALSE TRUE 207558.4812 232553.1168 282452.3754 123648.3179 134367.3579 100044.8808 199704.494 116904.9678 120650.4986 168237.2835 1.233724635 1.382292391 1.678892868 0.734963828 0.798677648 0.594665337 1.187040648 0.694881452 0.717144833 1 17.36013793 3.728346943 24.99935454 0.811278013 1.42670221 0.689949871 0.188398312 355.9350152 871199.3399 0.048686277 0.076373706 5349.915756 -3.728346943 0.615424197 RCDIIIISGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RCDIIIISGR 10 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ; 212.09 7.52E-08 875020000 97356 97326 72043 101345 98432 100643 111543 105192 101191 115763 FALSE TRUE 93551.21989 94550.35777 85062.77269 106575.4276 101598.1547 102678.0704 112908.0966 103019.7484 89704.22191 107922.2689 0.866838891 0.876096831 0.788185548 0.987520265 0.941401211 0.951407633 1.046198322 0.954573597 0.831192884 1 16.71963306 3.72839331 24.81167956 0.960977774 0.846946063 0.46845557 0.056167639 532.2486804 1298868.035 0.014952809 0.023457011 5350.486959 -3.72839331 -0.114031711 TYSYLTPDLWK ddPTM_BT-474_Pertuzumab_2h_R1 1 TYSYLTPDLWK 11 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 133.81 0.00035823 92058000 340310 334090 312120 230990 235480 147060 316260 267470 262370 300230 FALSE TRUE 327010.309 324562.0803 368527.0271 242911.4216 243054.4281 150033.654 320130.4845 261946.651 232586.8575 279895.1547 1.168331439 1.15958449 1.316660974 0.867865762 0.86837669 0.536035195 1.143751434 0.935874189 0.830978506 1 18.09452699 3.728420878 24.47911227 0.884937285 1.20933152 0.507793317 0.149567402 421.2547882 1016983.524 0.040485146 0.063546984 5350.826613 -3.728420878 0.324394235 WCNEHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 WCNEHLK 7 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 Q60FE5;O75369-8;Q14315-2 FLNA;FLNB;FLNC Filamin-A;Filamin-B;Filamin-C 0 ;;; 122.18 0.0043663 2736780000 4375340 4428580 3721770 2926000 2723710 1164870 4051840 3034690 3870340 4332060 FALSE TRUE 4204346.876 4302281.234 4394376.629 3077011.211 2811320.606 1188424.47 4101427.63 2972022.591 3430995.229 4038645.718 1.041028892 1.065278199 1.088081732 0.761891838 0.696104784 0.294263115 1.015545288 0.735895842 0.849541027 1 21.94544016 3.728424562 10.55310775 0.746596152 1.064901745 0.344241742 0.188614494 0.363310131 368.7506557 0.04956666 0.079924463 5350.871992 -3.728424562 0.318305593 HFVGMLPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HFVGMLPEK 9 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 83.783 0.015936 459670000 2127600 2072900 2004300 1011200 952600 253930 1815100 641710 1210100 1685300 FALSE TRUE 2044451.04 2013782.922 2366521.595 1063388.153 983241.2441 259064.6386 1837313.737 628458.4643 1072734.521 1571153.13 1.301242381 1.281722884 1.506232302 0.676820186 0.625808666 0.164888217 1.169404625 0.399998226 0.682768917 1 20.58339237 3.728429124 22.86612875 0.642456264 1.354931542 0.57651286 0.269552661 134.0622178 302570.533 0.067532868 0.106213545 5350.928206 -3.728429124 0.712475278 TVYCNVHK ddPTM_BT-474_Pertuzumab_2h_R1 4 TVYCNVHK 8 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 109.71 0.0035651 1554340000 3644570 3644710 3420080 2515560 2518190 1468740 3409240 2832620 3395280 3871180 FALSE TRUE 3502136.175 3540766.439 4038164.535 2645388.353 2599189.868 1498438.929 3450963.299 2774125.407 3009862.049 3608981.531 0.970394596 0.98109852 1.118920809 0.733001355 0.72020038 0.415197173 0.956215284 0.768672653 0.83399209 1 21.78316033 3.728436355 24.58484371 0.760509179 1.01923403 0.350645399 0.153792736 560.8719587 1361971.301 0.040588816 0.063698186 5351.017296 -3.728436355 0.258724851 EAHS(ph)PGPLVKPFETASVK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAHSPGPLVKPFETASVK 18 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 EAHS(1)PGPLVKPFETASVK;EAHS(1)PGPLVKPFETASVK;EAHS(1)PGPLVKPFETASVK 208.46 3.81E-16 2368920000 2194680 1930710 1866070 1544550 1610310 1802970 1644750 1422260 2101030 2189410 TRUE FALSE 2108909.479 1875648.041 2203310.36 1624264.411 1662107.084 1839427.289 1664878.943 1392889.834 1862529.883 2041119.311 1.033212252 0.918931114 1.079461817 0.795771419 0.814311576 0.901185579 0.815669586 0.682414706 0.91250417 1 20.96092908 3.728438209 24.98128059 0.823484972 1.001374667 0.399292668 0.089354146 588.2076085 1451648.734 0.023621474 0.037068853 5351.040138 -3.728438209 0.177889695 VGATAAVYSAAILEYLTAEVLELAGNASK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGATAAVYSAAILEYLTAEVLELAGNASK 29 0 Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-4;Q71UI9-2 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z;Histone H2A 0 206.94 1.81E-25 433510000 225340 234590 226600 183640 215870 238180 184970 259700 221830 232960 FALSE TRUE 216533.4637 227899.7229 267551.6607 193117.6824 222813.6546 242996.1628 187233.7182 254337.1042 196648.7884 217181.4117 0.997016559 1.049351881 1.231927072 0.889199867 1.025933356 1.118862618 0.862107474 1.171081366 0.905458653 1 17.7285411 3.728520867 24.99876551 1.010907339 1.088423849 0.134337445 0.107797702 1593.247978 3967151.96 0.027596322 0.043284099 5352.058684 -3.728520867 0.07751651 LRLEGPGDEDADGAGS(ph)PSDWASPLEDPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRLEGPGDEDADGAGSPSDWASPLEDPLR 29 1 O60347 O60347 TBC1D12 TBC1 domain family member 12 1 LRLEGPGDEDADGAGS(0.826)PS(0.147)DWAS(0.027)PLEDPLR 60.746 0.018743 26430000 15424 17407 11356 17753 20621 19766 13023 17473 15670 19897 TRUE FALSE 14821.21303 16910.5694 13408.28181 18669.23446 21284.29319 20165.68206 13182.37937 17112.17644 13891.20729 18549.35847 0.799014858 0.911652521 0.722843425 1.006462541 1.147440933 1.087136361 0.710664975 0.922521201 0.748878044 1 14.17908167 3.728547385 24.68504431 0.941391918 0.821218489 0.173273903 0.134301278 1188.750958 2930560.665 0.038217174 0.060002503 5352.385498 -3.728547385 -0.120173429 QNSS(ph)SSDSGGSIVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QNSSSSDSGGSIVR 14 0 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 QNS(0.016)S(0.471)S(0.471)S(0.041)DSGGSIVR 180.56 1.82E-06 113860000 185110 174140 125840 194850 217720 164500 191700 222530 190260 183310 TRUE FALSE 177875.6966 169173.6977 148582.0873 204906.2319 224723.1615 167826.3027 194046.0819 217934.6777 168662.4824 170894.2504 1.040852434 0.989932062 0.869438772 1.199023556 1.314983746 0.982047683 1.135474608 1.275260444 0.986940649 1 17.38274433 3.728744428 24.97107795 1.148830253 0.969060184 0.270802655 0.117464307 747.0028991 1900275.665 0.03093687 0.048569401 5354.81447 -3.728744428 -0.179770068 GPWALEEESLVGREPEER ddPTM_BT-474_Pertuzumab_2h_R1 4 GPWALEEESLVGREPEER 18 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63 O00515 LAD1 Ladinin-1 0 ;;; 235.24 7.93E-24 413431000 529556 585750 444124 554358 588125 634679 562548 571150 595790 604555 FALSE TRUE 508860.3661 569044.9835 524387.0863 582968.4828 607042.5747 647512.6442 569432.6307 559355.5529 528158.417 563607.9514 0.902862291 1.009646834 0.930411086 1.034351062 1.077065313 1.148870669 1.010334629 0.992455042 0.937102494 1 19.10433244 3.728798496 24.2965211 1.031658203 0.953840747 0.285424895 0.058313376 647.365475 1611200.998 0.016667289 0.026204411 5355.481163 -3.728798496 -0.077817456 FGEENIEVYHSYFWPLEWTIPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 FGEENIEVYHSYFWPLEWTIPSR 23 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 116.65 0.0004557 48311000 35369 34161 31084 24596 29306 25950 21245 21560 31288 38052 FALSE TRUE 33986.74038 33186.76173 36701.57026 25865.40251 30248.65411 26474.72678 21505.00267 21114.77847 27736.31741 35474.70415 0.95805564 0.935504961 1.034584252 0.72912243 0.85268235 0.746298734 0.606206681 0.595206612 0.781861839 1 15.11450303 3.728829943 23.83349973 0.728093964 0.971993951 0.414559512 0.114296741 299.7915521 734285.1877 0.031326347 0.04926095 5355.868961 -3.728829943 0.243899988 ELQTLHNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELQTLHNLR 9 0 P33176;O60282;O60282-2;Q12840;J3KNA1;A0A0G2JMZ6 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ;;; 174.41 5.47E-05 1205370000 873145 1058466 853874 779050 810954 443608 1010378 880818 954349 1055180 FALSE TRUE 839021.5281 1028279.586 1008188.026 819256.8639 837039.0719 452578.0577 1022743.308 862628.8005 846015.3025 983711.7187 0.852914032 1.045305821 1.024881586 0.832822105 0.85089875 0.460071837 1.039677874 0.876912193 0.860023609 1 19.90787606 3.728899316 23.8490251 0.839384106 0.981461009 0.12767296 0.153064917 673.394959 1662284.606 0.0407518 0.06412317 5356.724569 -3.728899316 0.142076903 RRNDLDDPER ddPTM_BT-474_Pertuzumab_2h_R1 4 RRNDLDDPER 10 2 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;;; 129.82 0.00016481 527857000 132478.3 134882 104403.6 140051 144549.2 163685 135831 170987.2 126243.5 142722.1 FALSE TRUE 127300.9016 131035.2974 123271.653 147279.0489 149198.7563 166994.8228 137493.3404 167456.2546 111912.8671 133055.405 0.956751073 0.984817546 0.926468586 1.106900158 1.121328038 1.255077333 1.03335404 1.258545299 0.841099744 1 17.02166759 3.728959378 22.8090222 1.112373621 0.958892916 0.192552 0.116631945 254.7095468 605097.9609 0.029328587 0.046200315 5357.465438 -3.728959378 -0.153480705 MKETIMNQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MKETIMNQEK 10 1 P20290-2;D6RDG3 P20290-2 BTF3 Transcription factor BTF3 0 ; 137.16 8.99E-05 660150000 979400 988580 899840 773230 755700 615370 964600 897000 1101970 1091660 FALSE TRUE 941123.9652 960386.6663 1062461.105 813136.493 780007.7768 627813.203 976405.0633 878476.6365 976878.9854 1017720.896 0.924736801 0.943664093 1.043961178 0.798977889 0.766426021 0.61688151 0.959403573 0.863180308 0.959869243 1 19.95691053 3.729111818 24.914155 0.841329971 0.968075033 0.193688868 0.109389567 970.9019551 2560029.773 0.029903197 0.047001605 5359.346268 -3.729111818 0.126745061 MKGDYFR ddPTM_BT-474_Pertuzumab_2h_R1 6 MKGDYFR 7 1 P27348;E9PG15;P31946-2;P31946 P27348;P31946-2 YWHAQ;YWHAB "14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;; 106.04 0.0071055 24867600000 16314830 16695620 15609100 8930620 9111630 1735698 14094090 9242980 10318460 13652730 FALSE TRUE 15677228.41 16219477.26 18430011.59 9391530.368 9404713.854 1770795.003 14266577.69 9052109.233 9147151.679 12728018.44 1.231710064 1.274312836 1.4479875 0.737862725 0.73889851 0.139125741 1.120879716 0.711195484 0.718662667 1 23.60150449 3.729147367 23.63758511 0.724507908 1.3136344 0.539120818 0.245475904 223.829972 562059.6775 0.064035685 0.100835926 5359.78498 -3.729147367 0.589126492 ALWFQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALWFQGR 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 169.6 0.0023398 1214820000 1113360 1204610 1080330 738420 750120 572170 918350 766260 875660 961500 FALSE TRUE 1069848.66 1170255.702 1275569.663 776529.9447 774248.291 583739.6694 929589.042 750436.4632 776258.7479 896376.7486 1.193525671 1.305540002 1.423028503 0.866298625 0.863753207 0.651221342 1.037051712 0.837188676 0.865996077 1 19.7737457 3.729172225 24.86621504 0.866463547 1.307182253 0.765397007 0.109757465 257.4245474 681818.1954 0.028287337 0.044488558 5360.091772 -3.729172225 0.440718706 IGFPWSEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGFPWSEIR 9 0 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 148.38 0.00020972 467010000 698320 764330 760460 453930 555040 538760 708910 439950 729810 473720 FALSE TRUE 671028.8824 742532.0568 897892.0383 477357.3817 572893.3657 549654.0963 717585.8526 430864.8788 646965.0284 441634.5225 1.51942126 1.681327023 2.033111074 1.080887832 1.297211465 1.244590421 1.62484094 0.975614126 1.464933096 1 18.75249343 3.729357451 24.96087548 1.249320468 1.738290517 0.518722312 0.222111154 481.7550195 1306618.841 0.056596378 0.089040388 5362.378321 -3.729357451 0.488970049 DELPYTFAAPESYEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 DELPYTFAAPESYEELR 17 0 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 0 195.88 3.84E-11 20283000 16617 14094 12166 14926 15583 13556 17176 17900 15359 14453 FALSE TRUE 15967.58927 13692.05292 14364.66683 15696.33265 16084.24135 13830.11161 17386.20503 17530.35874 13615.51071 13474.08544 1.185059227 1.016176792 1.06609587 1.164927499 1.19371674 1.026423031 1.29034398 1.30104257 1.010496094 1 13.71789973 3.729473725 21.2080856 1.168042799 1.081817252 0.003042385 0.110293073 186.7504767 435865.1373 0.029728469 0.047020062 5363.814197 -3.729473725 -0.086225547 FKMPEMHFK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKMPEMHFK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 100.15 0.0029172 2087800000 4841700 5131800 3960700 3045700 2839700 1175470 4093000 3145400 3674800 3754500 FALSE TRUE 4652481.011 4985446.089 4676486.595 3202888.942 2931041.529 1199238.809 4143091.358 3080446.391 3257652.11 3500204.371 1.329202675 1.424329999 1.336061012 0.915057695 0.83739154 0.342619654 1.183671272 0.880076151 0.9307034 1 21.73900773 3.729520321 3.792264069 0.85771599 1.379400877 0.560749192 0.200684306 0.163045405 5.312519715 0.054753648 0.095559394 5364.389714 -3.729520321 0.521684888 YDGFDCVYGLELNKDER ddPTM_BT-474_Pertuzumab_2h_R1 1 YDGFDCVYGLELNKDER 17 1 Q9Y657 Q9Y657 SPIN1 Spindlin-1 0 97.352 0.0019113 151960000 128680 130870 119010 103360 107800 113030 114320 132540 116710 119520 FALSE TRUE 123651.0433 127137.7157 140517.7544 108694.422 111267.4849 115315.544 115719.0824 129803.0027 103461.5701 111424.8039 1.109726371 1.141018079 1.261099409 0.975495744 0.998588115 1.034918079 1.038539699 1.164938129 0.928532664 1 16.7657109 3.729602789 24.99683301 1.035642245 1.167654968 0.492384865 0.068743661 608.1802473 1697127.897 0.019207662 0.030236922 5365.408455 -3.729602789 0.132012723 WRPDEEILK ddPTM_BT-474_Pertuzumab_2h_R1 4 WRPDEEILK 9 1 P10155-3;P10155-5;P10155-4;P10155;G5E9R9 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;; 145.99 8.74E-05 2014730000 2174110 2211650 1944760 1762670 1864540 1398160 2153580 2013530 2198070 2218580 FALSE TRUE 2089143.378 2148575.907 2296221.393 1853641.61 1924514.622 1426431.753 2179936.156 1971949.902 1948554.309 2068313.6 1.010070899 1.038805676 1.110190153 0.896209167 0.930475254 0.689659321 1.053967907 0.953409532 0.942098098 1 20.98002351 3.729614535 24.88324172 0.922387232 1.051600587 0.292500249 0.092153282 755.1673494 2100474.066 0.0248321 0.039093076 5365.553563 -3.729614535 0.129213355 RLQVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLQVLK 6 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 95.957 0.068555 760270000 1165090 1252580 1062090 1019530 1144880 920760 1123660 1166070 1239070 1236150 FALSE TRUE 1119556.995 1216857.645 1254033.289 1072148.065 1181706.105 939378.3981 1137411.687 1141990.247 1098415.968 1152424.459 0.971479723 1.055910984 1.088169623 0.930341296 1.025408733 0.815132298 0.98697288 0.99094586 0.953134897 1 20.13624076 3.729664022 24.68017408 0.957852803 1.040259199 0.273281725 0.06058268 671.0000495 1861432.856 0.015857381 0.025017578 5366.164999 -3.729664022 0.082406396 MVQEAEK ddPTM_BT-474_Pertuzumab_2h_R1 3 MVQEAEK 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 A0A0G2JIW1;P11142 HSPA1B;HSPA1A;HSPA8 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock cognate 71 kDa protein 0 ;; 157.58 0.0034116 1156360000 1987860 1875120 1753960 1273930 1294180 610680 1767680 1348930 1705430 1798950 FALSE TRUE 1910172.234 1821643.414 2070939.589 1339677.68 1335808.475 623028.368 1789313.397 1321074.124 1511836.736 1677105.514 1.138969622 1.086182949 1.234829634 0.798803456 0.796496382 0.371490263 1.066905679 0.787710799 0.901455945 1 20.67754203 3.729699053 24.21327425 0.804084969 1.146612958 0.426931883 0.177742149 369.1693974 1008716.581 0.046510334 0.073325027 5366.597862 -3.729699053 0.342527989 GNKPWISLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNKPWISLPR 10 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 134.2 0.0001615 2266500000 3738900 4008400 3869500 1723990 1602450 218726 3234800 1908310 1874280 2790900 FALSE TRUE 3592779.654 3894084.357 4568804.727 1812965.331 1653994.26 223148.7896 3274388.45 1868902.732 1661519.592 2601869.857 1.380845258 1.496648399 1.755969736 0.696793241 0.635694462 0.085764778 1.258475108 0.718292165 0.638586741 1 21.31111737 3.729711832 24.353053 0.711758485 1.539703861 0.62473715 0.293107099 275.4026088 757945.8136 0.077901696 0.122777178 5366.755769 -3.729711832 0.827945376 QAEILQESR ddPTM_BT-474_Pertuzumab_2h_R1 1 QAEILQESR 9 0 E5RJD8;O75347;E5RIW3;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 122.44 0.0013625 179800000 110530 114480 90032 109060 123560 99614 110570 128460 105010 123740 FALSE TRUE 106210.3654 111215.1425 106302.7852 114688.5997 127534.4196 101628.2633 111923.1887 125807.2561 93089.70504 115358.9796 0.920694391 0.964078764 0.92149554 0.99418875 1.10554393 0.880974014 0.970216529 1.090571853 0.806956731 1 16.81577078 3.72974687 22.93135317 0.988985689 0.938288485 0.041532619 0.083942837 582.21242 1514787.856 0.021846732 0.034490024 5367.188771 -3.72974687 -0.050697204 VLQLYPNNK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLQLYPNNK 9 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 130.34 0.0027504 0 221440 215480 212610 163120 181430 153670 214970 200390 222750 243620 FALSE TRUE 212785.88 209334.7214 251033.3565 171538.6427 187265.8607 156777.3127 217600.8672 196251.8765 197464.3538 227119.4004 0.936889934 0.921694584 1.105292441 0.755279569 0.824526044 0.690285869 0.95809018 0.864091205 0.869429707 1 17.79309142 3.729845117 24.95935195 0.846049346 0.98133255 0.298151421 0.095387983 742.3153996 2125834.907 0.024910805 0.03925087 5368.403078 -3.729845117 0.135283204 TVSLPLSS(ph)PNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSLPLSSPNIK 12 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;H0Y785;H0Y472;H0Y4P6;H0Y7Y3;A0A0A0MQZ8 Q8IWZ3-6;A0A0A0MQZ8 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 TVSLPLS(0.043)S(0.957)PNIK;TVSLPLS(0.011)S(0.989)PNIK 225.72 1.78E-11 747430000 2784200 2606400 2493600 2134800 2021700 2353600 2430700 2735200 2681800 2892700 TRUE FALSE 2675390.386 2532068.024 2944248.99 2244977.284 2086729.817 2401191.405 2460447.634 2678717.164 2377373.307 2696774.852 0.992070355 0.938924516 1.091766703 0.83246745 0.773787183 0.890393724 0.912366723 0.993303969 0.881561657 1 21.36280365 3.729925469 24.92073773 0.898755119 1.000720926 0.326787083 0.072065822 795.7408753 2296481.416 0.020585239 0.032465554 5369.396418 -3.729925469 0.101965808 HSEVQQANLK ddPTM_BT-474_Pertuzumab_2h_R1 4 HSEVQQANLK 10 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;; 164.33 6.19E-06 2787150000 4913960 5045500 4054530 3949200 4167730 3106660 4947500 3316170 5328500 5304200 FALSE TRUE 4721917.011 4901607.28 4787273.764 4153018.685 4301788.82 3169478.794 5008048.985 3247689.931 4723631.019 4944941.81 0.954898398 0.991236595 0.968115288 0.839851882 0.869937198 0.640953709 1.012761965 0.656770101 0.955245016 1 22.23752211 3.730012465 4.043431047 0.829571355 0.975663653 0.146918903 0.120891461 0.305000438 11.90965053 0.030064701 0.052008268 5370.472102 -3.730012465 0.146092298 KSHEAEVLK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSHEAEVLK 9 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ;; 98.048 0.0040753 1628110000 2927010 2780990 2594270 2106110 2250830 1379550 2817980 2172560 3046690 3145880 FALSE TRUE 2812619.213 2701678.888 3063112.298 2214806.589 2323229.991 1407445.446 2852467.282 2127695.877 2700842.524 2932806.746 0.959019621 0.921192265 1.044430324 0.75518327 0.79215243 0.479897098 0.972606629 0.725481104 0.920907089 1 21.48385058 3.730182646 24.57365796 0.787820961 0.96951189 0.21751808 0.143081308 636.0557814 1865633.812 0.03618614 0.057110135 5372.576969 -3.730182646 0.18169093 KHEEEEAK ddPTM_BT-474_Pertuzumab_2h_R1 3 KHEEEEAK 8 1 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 ;; 135.79 0.00053144 1596710000 3468660 2680770 2661280 2470060 2695290 2370860 3221740 1957200 3416220 3728460 FALSE TRUE 3333100.932 2604317.064 3142232.496 2597540.093 2781986.451 2418800.414 3261168.618 1916783.136 3028425.028 3475928.083 0.958909636 0.749243656 0.903998132 0.747293969 0.800357885 0.695871823 0.938215216 0.551444993 0.871256526 1 21.7289668 3.730187435 24.43159437 0.772903317 0.858569793 0.02586585 0.130017515 1125.964763 3285387.133 0.03257733 0.051448625 5372.636216 -3.730187435 0.085666476 VAHFLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAHFLEK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 100.07 0.010067 1914840000 3812000 4092800 3453400 3079500 3167400 1842000 3963700 3271700 3972400 4313900 FALSE TRUE 3663022.826 3976077.351 4077506.2 3238433.364 3269282.298 1879246.502 4012208.946 3204138.252 3521469.806 4021715.711 0.910810979 0.988652018 1.013872311 0.805236769 0.812907359 0.467274824 0.997636142 0.796709286 0.875613807 1 21.93937967 3.730208235 24.04332183 0.809020919 0.972865795 0.185396414 0.141151076 533.3403406 1535285.645 0.036717885 0.057991107 5372.893536 -3.730208235 0.163844876 HCDLQVR ddPTM_BT-474_Pertuzumab_2h_R1 4 HCDLQVR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 143.11 0.002444 1107100000 445436 521874 412166 404705 421218 357841 460390 395353 513158 504801 FALSE TRUE 428027.8687 506990.6645 486653.5648 425591.8735 434766.8595 365076.7902 466024.3905 387188.8224 454906.4552 470610.3786 0.909516424 1.07730447 1.034090166 0.904340178 0.923836106 0.775751676 0.990255234 0.822737534 0.966630733 1 18.84417361 3.730222478 22.88854494 0.899710324 1.014003768 0.228636802 0.077431799 212.080875 582173.0113 0.019110199 0.030233903 5373.069747 -3.730222478 0.114293444 KKLEEELEGMR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKLEEELEGMR 11 2 P15924 P15924 DSP Desmoplakin 0 ; 125.53 0.00018361 206460000 365880 379630 333080 364310 442630 400040 411810 489710 520560 469070 FALSE TRUE 351581.0051 368803.3241 393274.9653 383112.0828 456867.5959 408129.0829 416849.854 479597.3174 461468.2112 437299.4711 0.803982233 0.843365585 0.899326414 0.876086316 1.044747653 0.933294252 0.953236584 1.096725126 1.055268167 1 18.73826208 3.730354093 0.501582379 1.049880955 0.755398927 0.713378983 0.049386486 0.964259317 0.373784983 0.037360546 0.152199153 5374.698328 -3.730354093 -0.294482027 ECS(ph)PTSSLER ddPTM_BT-474_Pertuzumab_2h_R1 2 ECSPTSSLER 10 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 ECS(0.95)PT(0.041)S(0.008)S(0.002)LER;ECS(0.951)PT(0.046)S(0.003)SLER 76.068 0.038921 710250000 634990 591730 483030 604310 608050 614720 623580 659070 697020 691590 TRUE FALSE 610173.8888 574854.4398 570324.2659 635498.5115 627608.4805 627150.0596 631211.5586 645459.9742 617897.2117 644747.9933 0.946375786 0.891595547 0.884569276 0.985654113 0.973416726 0.972705718 0.979005077 1.001104278 0.95835461 1 19.29837585 3.730382154 24.99782606 0.981850476 0.905921737 0.754829221 0.019305923 263.4653291 805293.7353 0.005029286 0.007942855 5375.04561 -3.730382154 -0.075928739 HSQFIGYPITLFVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSQFIGYPITLFVEK 15 0 P07900;P07900-2;G3V2J8;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ; 173.34 9.75E-07 4108500000 4199500 4338300 3834200 2606600 2988800 1236820 3371800 2193150 3692900 3750400 FALSE TRUE 4035378.897 4214575.932 4527125.231 2741126.938 3084937.466 1261829.348 3413065.097 2147860.686 3273697.474 3496382.067 1.154158447 1.205410579 1.294802783 0.783989531 0.882322757 0.360895727 0.976170519 0.61430949 0.936309994 1 21.73743141 3.730390538 23.05186497 0.765586174 1.216852606 0.523951673 0.184175206 138.877746 391844.4569 0.04577664 0.072450927 5375.149377 -3.730390538 0.451266432 LTLHGLQQYYVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTLHGLQQYYVK 12 0 O00148;O00148-2;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0Y400;H0YCC6 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 129.34 0.00023591 782940000 1216700 1312000 1203300 677400 643340 299160 1103000 675780 759720 1062900 FALSE TRUE 1169150.019 1274583.045 1420763.077 712360.6952 664033.6154 305209.2202 1116498.844 661824.9068 673479.7706 990908.8363 1.179876469 1.286276798 1.433797969 0.718896299 0.670125839 0.308009384 1.126742242 0.667896867 0.679658659 1 19.91839281 3.730440868 24.4784499 0.725076072 1.298613053 0.593687602 0.212550932 285.6340444 861096.2043 0.055125867 0.087094043 5375.772341 -3.730440868 0.573536981 FCIWTESAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 FCIWTESAFR 10 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 189.7 2.28E-06 838020000 602280 703760 614790 321052 272491 113418 547210 277324 347830 500880 FALSE TRUE 578742.2317 683689.4539 725896.2289 337621.5322 281255.9205 115711.3897 553906.9197 271597.1625 308345.7966 466954.9515 1.239396284 1.46414435 1.554531602 0.723028059 0.602319174 0.247799899 1.186210614 0.581634613 0.66033307 1 18.83292385 3.730491139 23.74091953 0.69567293 1.423836117 0.630393283 0.247037135 173.3252079 509934.7458 0.06379504 0.100924764 5376.394633 -3.730491139 0.728163186 EIPS(ph)ATQS(ph)PISK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIPSATQSPISK 12 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 2 EIPS(0.999)AT(0.37)QS(0.631)PISK 137.21 0.00014077 166420000 352110 330030 307900 268000 268130 280000 285140 371220 283730 308770 TRUE FALSE 338349.1519 320617.8675 363544.3792 281831.5121 276754.645 285661.7918 288629.6286 363554.1773 251522.1599 287856.7329 1.175408157 1.113810555 1.262935126 0.979068682 0.961431898 0.992374884 1.002685001 1.262969164 0.873775497 1 18.13499143 3.730513874 24.97680268 1.032006636 1.177027209 0.372438457 0.100497767 761.7626578 2364484.057 0.028661668 0.045259031 5376.676086 -3.730513874 0.145020572 DITYFIQQLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DITYFIQQLLR 11 0 B4DXW1;P61158;Q9P1U1-2;Q9P1U1;A0A0A0MTI9;H7C4J1;C9IZN3;Q9C0K3;Q9P1U1-3 B4DXW1 ACTR3;ACTR3B;ACTR3C Actin-related protein 3;Actin-related protein 3B;Actin-related protein 3C 0 88.681 0.029773 179950000 36167 38114 30575 31720 29834 31613 35973 33990 37325 34918 FALSE TRUE 34753.55366 37027.02604 36100.58264 33357.073 30793.6377 32252.23652 36413.24833 33288.09462 33088.02248 32552.97276 1.067599998 1.137439161 1.108979598 1.024701285 0.945954704 0.990761635 1.118584426 1.022582327 1.016436278 1 14.99050168 3.73060027 7.242077376 1.020203234 1.108125273 0.457740628 0.043591299 0.130607227 48.40784649 0.012260095 0.020174045 5377.745802 -3.73060027 0.087922039 YVGSMVADVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 YVGSMVADVHR 11 0 P09467;A0A3B3IUC7;O00757 P09467 FBP1;FBP2 "Fructose-1,6-bisphosphatase 1;Fructose-1,6-bisphosphatase isozyme 2" 0 ; 139.86 3.89E-05 590490000 766810 876330 836260 299420 276950 68511 622380 286120 287590 518810 FALSE TRUE 736842.2174 851337.9264 987390.7845 314873.1021 285858.3483 69896.33936 629996.8726 280211.522 254943.9889 483670.5366 1.523438295 1.760160816 2.041453241 0.651007407 0.591018734 0.144512295 1.302533078 0.57934379 0.527102582 1 18.88366513 3.730616846 24.77122872 0.674009332 1.773531796 0.72327812 0.308892604 251.8786669 785438.9829 0.080582117 0.127348888 5377.951067 -3.730616846 1.099522464 (ac)S(ph)DVEENNFEGRES(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 SDVEENNFEGRESR 14 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 2 S(1)DVEENNFEGRES(1)R;S(1)DVEENNFEGRES(1)R 97.095 3.51E-06 13707100000 28921 12547 0 36867 21900 33712 36797 19083 28113 35546 TRUE FALSE 27790.73535 12189.17184 0 38769.71029 22604.43339 34393.67974 37247.33269 18688.92938 24921.7301 33138.43776 0.838625392 0.367825784 0 1.169931744 0.682121274 1.037878731 1.123991812 0.563965312 0.752049034 1 15.01621797 3.730736645 24.99402956 0.877142867 0.398717924 0.43077113 0.26321109 566.2208186 1808818.172 0.070529042 0.111497986 5379.434758 -3.730736645 -0.478424942 YTRPTPVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 YTRPTPVQK 9 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8Y4D2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523;O15523-3;C9J8G5;C9J081 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 82.417 0.016884 477580000 606990 606710 488690 499620 463990 420990 549710 546530 616870 583190 FALSE TRUE 583268.1597 589407.2248 577007.1539 525405.4481 478914.6597 429502.7062 556437.5154 535243.9645 546845.5037 543690.0218 1.07279541 1.08408689 1.061279646 0.966369488 0.880859756 0.789977173 1.023446253 0.984465307 1.005803825 1 19.05242483 3.730791173 3.780855973 0.945731287 1.076680268 0.427638142 0.065374856 0.229278881 7.416319287 0.019276848 0.033706375 5380.110218 -3.730791173 0.130948981 RKVDWLTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RKVDWLTEK 9 2 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3QL52;Q14240;Q14240-2;E7EQG2;P38919;I3L3H2;J3KTN0 P60842;Q14240;P38919;J3KTN0 EIF4A1;EIF4A2;EIF4A3 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed;Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 150.1 4.84E-05 4335900000 3278300 3217700 2965200 2185280 1862610 958020 3107400 2600900 3113200 3493000 FALSE TRUE 3150180.412 3125934.346 3501077.601 2298062.563 1922522.542 977391.8208 3145429.291 2547190.506 2759802.588 3256415.999 0.967376531 0.959930902 1.07513217 0.705703007 0.590379897 0.300143416 0.965917528 0.782206729 0.847496938 1 21.63485358 3.73084898 24.63057045 0.725786873 0.996724973 0.279306952 0.189506125 601.8619569 1922317.26 0.052143602 0.082507402 5380.82639 -3.73084898 0.2709381 TGHYLTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGHYLTVK 8 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 95.099 0.0098907 351510000 1110100 1119900 1015800 663600 736210 370730 925740 541050 887480 1006900 FALSE TRUE 1066716.065 1087961.548 1199377.656 697848.4755 759890.8633 378226.4146 937069.483 529877.1284 786736.991 938701.7661 1.13637377 1.159006606 1.277698306 0.743418731 0.809512553 0.402925006 0.998261127 0.564478674 0.838111762 1 19.84030735 3.730931821 24.46535012 0.738121111 1.187824271 0.551463682 0.17476825 270.3754622 867087.6674 0.042966085 0.068011744 5381.852872 -3.730931821 0.44970316 LWDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LWDLEK 6 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 96.964 0.096803 478180000 824260 745590 672380 648720 702100 672920 632840 729080 775730 814820 FALSE TRUE 792047.0079 724326.5032 793894.023 682200.5169 724683.6841 686526.9035 640584.8852 714024.2432 687672.3825 759631.5156 1.042672653 0.953523502 1.045104115 0.898067685 0.953993705 0.903763061 0.843283713 0.939961321 0.905271001 1 19.53494024 3.730959302 24.98070383 0.915600271 1.007742432 0.466262426 0.045310519 463.0671084 1521808.033 0.011338639 0.017936995 5382.193432 -3.730959302 0.092142161 QLS(ph)ESESSLEMDDER ddPTM_BT-474_Pertuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.995)ES(0.005)ESSLEMDDER;QLS(0.999)ES(0.001)ESSLEMDDER 246.48 5.08E-16 247980000 262022 276623 192602 284964 306538 253312 251295 336635 246409 283569 TRUE FALSE 251781.8906 268733.9829 227409.4658 299671.0262 316398.0732 258434.1422 254370.4234 329683.3696 218437.6834 264362.6191 0.952411091 1.016535484 0.860217933 1.133560513 1.196833631 0.977574451 0.962202691 1.247087696 0.826280524 1 18.01215867 3.731169532 24.91396759 1.067924994 0.9504029 0.124123188 0.121606704 952.0350553 3209133.031 0.03168216 0.05018416 5384.79944 -3.731169532 -0.117522093 MKGDYYR ddPTM_BT-474_Pertuzumab_2h_R1 8 MKGDYYR 7 1 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6;E7ESK7;P31947-2;P31947;P61981;Q04917;A2IDB2 B7Z2E6;P63104;P31947-2;P61981;Q04917 YWHAZ;SFN;YWHAG;YWHAH "14-3-3 protein zeta/delta;14-3-3 protein sigma;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein eta" 0 ;;;;;;; 95.909 0.011965 18292950000 16322370 18235200 15656430 8644582 8489010 1947625 13861940 8323023 9162410 11712740 FALSE TRUE 15684473.74 17715149.95 18485895.18 9090729.913 8762066.716 1987007.312 14031586.57 8151149.667 8122331.629 10919425.69 1.436382662 1.622351803 1.69293658 0.832528209 0.802429264 0.181969947 1.285011407 0.746481537 0.743842383 1 23.38039364 3.731185655 21.9924899 0.79057321 1.587736556 0.648887164 0.264561632 61.72375972 184064.7249 0.068774573 0.109380902 5384.999347 -3.731185655 0.797163346 LHQNICR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHQNICR 7 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 92.467 0.015648 91004000 148860 169600 140060 106270 106770 59461 152900 92240 123320 167610 FALSE TRUE 143042.3866 164763.1741 165371.9576 111754.6074 110204.354 60663.34216 154771.2359 90335.21177 109321.2306 156257.6254 0.915426599 1.054432855 1.05832888 0.715194584 0.705273447 0.388226443 0.990487572 0.578117142 0.699621732 1 17.25356707 3.73123564 22.11933182 0.70212635 1.013899805 0.356364692 0.173000911 105.1779819 317609.8324 0.043029449 0.06843261 5385.619167 -3.73123564 0.311773455 TCNS(ph)PQNS(ph)TDSVSDIVPDSPFPGALGSDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 2 T(0.435)CNS(0.534)PQNS(0.53)T(0.475)DS(0.026)VSDIVPDSPFPGALGSDTR 92.93 0.00048394 27474000 19851 20176 18263 23490 21632 24510 27394 26135 33237 28344 TRUE FALSE 19075.20097 19600.60023 21563.53036 24702.32172 22327.81293 25005.60899 27729.25597 25595.30312 29464.0751 26424.23563 0.721882791 0.741766025 0.816051244 0.93483581 0.844974789 0.946313428 1.04938725 0.968629839 1.115039826 1 14.68957412 3.73126934 0.471608667 1.048503557 0.633614722 0.830607892 0.050664804 0.757872309 0.253175881 0.03889247 0.160906218 5386.037094 -3.73126934 -0.414888835 HQNVQLPR ddPTM_BT-474_Pertuzumab_2h_R1 5 HQNVQLPR 8 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45;A0A087WUW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;; 129.56 0.0010853 2990470000 1042732 1078925 931255 741179 773956 484024 857710 797142 978529 987335 FALSE TRUE 1001980.881 1048155.115 1099553.494 779431.337 798850.9976 493811.2969 868206.9115 780680.7391 867450.4902 920461.921 1.088563098 1.138727297 1.194567064 0.846782815 0.867880549 0.536482048 0.94322958 0.84814018 0.942407796 1 19.81199851 3.731286723 23.85924307 0.842089452 1.140429973 0.539967419 0.120404505 208.8270379 684978.9087 0.031720202 0.050345516 5386.252677 -3.731286723 0.298340521 MIYASSK ddPTM_BT-474_Pertuzumab_2h_R1 1 MIYASSK 7 0 P60981;P60981-2;F6RFD5;G3V1A4;E9PQB7;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 P60981;G3V1A4;P23528;Q9Y281 DSTN;CFL1;CFL2 Destrin;Cofilin-1;Cofilin-2 0 148.07 0.0049062 400700000 696460 760990 707480 402370 438570 113450 731950 448140 489440 603290 FALSE TRUE 669241.5732 739287.3103 835337.3738 423136.3639 452677.0023 115744.0367 740907.8231 438885.7524 433880.8231 562428.6309 1.189913771 1.314455328 1.485232664 0.75233788 0.804861235 0.205793287 1.317336605 0.780340346 0.771441565 1 19.10131051 3.731312038 24.89366957 0.80130164 1.328326065 0.449991809 0.266104217 456.9425308 1569270.456 0.069680938 0.110414178 5386.566657 -3.731312038 0.527024425 KDS(ph)ESAPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSESAPVK 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 KDS(0.994)ES(0.006)APVK 79.875 0.015745 188980000 137930 126100 117620 109950 128320 120320 107740 115380 150270 163080 TRUE FALSE 132539.5431 122503.7515 138876.5504 115624.5327 132447.5293 122752.9528 109058.5543 112997.3627 133211.9796 152034.4463 0.871773117 0.805763131 0.913454508 0.760515366 0.8711679 0.807402242 0.717327928 0.743235269 0.876196038 1 17.21403871 3.731359258 24.95005809 0.805391711 0.85787354 0.004385762 0.081759812 1446.871453 5012873.83 0.021059719 0.033366278 5387.152354 -3.731359258 0.052481829 CDPDAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 CDPDAAR 7 0 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 81.297 0.064172 275530000 326310 340950 269180 321560 319970 348820 336060 332780 372170 371470 FALSE TRUE 313557.4444 331226.4398 317826.8139 338155.7501 330262.1256 355873.3794 340172.8028 325907.9767 329922.8219 346310.006 0.905424155 0.956444902 0.917752327 0.976453883 0.953660362 1.027615065 0.982278297 0.941087381 0.952680593 1 18.40170455 3.731405909 24.49968961 0.973413004 0.929530905 0.420354729 0.026536299 468.1908217 1603215.626 0.007332818 0.011630712 5387.731067 -3.731405909 -0.0438821 IYIDSNNNPER ddPTM_BT-474_Pertuzumab_2h_R1 4 IYIDSNNNPER 11 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 244.28 1.68E-15 4977070000 929129 964550 740689 935794 945650 913096 1025964 982443 1006492 1011697 FALSE TRUE 892817.6115 937041.9784 874547.9788 984090.4405 976067.6911 931559.4267 1038520.054 962155.2087 892239.2477 943173.8611 0.946609791 0.993498672 0.927239415 1.0433818 1.03487568 0.987685797 1.101090793 1.020124972 0.945996581 1 19.84716421 3.731425494 24.76421537 1.023999115 0.95955423 0.327588811 0.040981907 523.9493726 1818497.69 0.010739512 0.017034444 5387.974032 -3.731425494 -0.064444885 DFPYEEDSRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFPYEEDSRPR 11 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 172.13 1.25E-05 351250000 156190 163930 127590 159870 176060 172120 155600 175870 160770 181050 FALSE TRUE 150085.9221 159254.8769 150648.3512 168120.9099 181723.1298 175600.3843 157504.2793 172238.223 142520.0636 168787.3222 0.889201393 0.943523926 0.89253357 0.996051763 1.076639687 1.040364774 0.933152308 1.020445261 0.84437659 1 17.36484702 3.731476594 24.22584141 0.992343743 0.911930059 0.254857138 0.061288484 475.9387364 1627610.381 0.016204661 0.025740058 5388.608035 -3.731476594 -0.080413684 LWNDVTEELMS(ph)DEEDSLNEPGVWVARPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LWNDVTEELMSDEEDSLNEPGVWVARPPR 29 1 A0A0C4DFZ6;Q9H972 A0A0C4DFZ6 C14orf93 Uncharacterized protein C14orf93 1 LWNDVTEELMS(1)DEEDSLNEPGVWVARPPR 109.11 0.00023609 19589000 3482 3781.9 2349.4 4169.2 4250.6 3729.5 3871 4056.4 4538.6 3324.6 TRUE FALSE 3345.91959 3674.043915 2773.988842 4384.372912 4387.324409 3804.913045 3918.374456 3972.633922 4023.397155 3099.421881 1.079530222 1.185396521 0.895002019 1.414577647 1.415529921 1.227620244 1.264227526 1.281733844 1.298112135 1 11.59778343 3.731607506 24.99984067 1.286508844 1.066518279 0.375713334 0.127662191 519.9765182 1869571.124 0.032110265 0.050929499 5390.232595 -3.731607506 -0.219990565 EKGTWVQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKGTWVQLK 9 1 P46778 P46778 RPL21 60S ribosomal protein L21 0 ; 120.09 0.00065789 942740000 1893330 1931650 1831250 1100330 1131510 430010 1750130 1250970 1528170 1848480 FALSE TRUE 1819336.57 1876561.233 2162197.611 1157118.163 1167906.047 438705.0968 1771548.614 1225137.032 1354698.548 1723280.803 1.055740055 1.088946868 1.254698368 0.671462342 0.677722426 0.254575514 1.028009255 0.710932908 0.786115963 1 20.71672637 3.731639495 24.87961087 0.716849962 1.128710278 0.442543002 0.205400663 434.8660389 1563229.464 0.053793406 0.08537896 5390.629642 -3.731639495 0.411860315 LMHNAS(ph)DS(ph)EVDQDDVVEWK ddPTM_BT-474_Pertuzumab_2h_R1 5 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 2 LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK 169.6 7.30E-12 944172000 749621 709034 607430 620512 641688 659486 636081 618620 793133 713112 TRUE FALSE 720324.9826 688813.0445 717206.1132 652536.6987 662328.4773 672821.2588 643865.5496 605845.2808 703099.8669 664812.2891 1.083501305 1.036101552 1.078809951 0.981535254 0.99626389 1.012046964 0.96849225 0.91130277 1.057591562 1 19.34258753 3.731654506 24.4105374 0.981577081 1.063133999 0.462075578 0.037098155 323.4444885 1143256.609 0.010300554 0.01635326 5390.815972 -3.731654506 0.081556917 VVFQEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVFQEFR 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 79.469 0.075704 139811000 349790 399790 379960 114104 97353 45414 228910 107253 123166 204136 FALSE TRUE 336119.8201 388388.3806 448627.2242 119992.9211 100484.4477 46332.3022 231711.4691 105038.1881 109184.712 190309.6869 1.766172945 2.040822971 2.357353593 0.630513996 0.528004902 0.243457403 1.217549526 0.551932956 0.573721253 1 17.53798947 3.731664275 24.98448601 0.662044534 2.053387167 0.830543584 0.28494682 187.319458 678632.5267 0.074332677 0.117969513 5390.937225 -3.731664275 1.391342633 TQLS(ph)QGR ddPTM_BT-474_Pertuzumab_2h_R1 3 TQLSQGR 7 0 Q8ND56-2;Q8ND56 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 TQLS(1)QGR;TQLS(1)QGR;T(0.001)QLS(0.999)QGR 96.665 0.01318 675250000 633850 574050 458580 684480 758820 604110 685360 828130 758210 758380 TRUE FALSE 609078.4412 557678.6561 541455.6071 719806.0948 783228.1344 616325.5181 693747.6407 811028.8261 672141.1795 707014.2471 0.861479728 0.788779941 0.765834082 1.018092772 1.10779682 0.871729984 0.98123573 1.147118081 0.95067558 1 19.43137976 3.731733465 24.22166216 1.021120109 0.803706115 0.604010795 0.07596647 220.9768017 783992.0059 0.020994554 0.033371818 5391.796162 -3.731733465 -0.217413994 RLLAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLLAEK 6 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;B5MCA1;Q96G28;Q96G28-2;P02545-2;Q3BDU5;Q5TCI8;A0A3B3ISJ8 P02545;P02545-2;A0A3B3ISJ8 LMNA;CFAP36 Prelamin-A/C;Lamin-A/C;Cilia- and flagella-associated protein 36 0 ; 128.48 0.026627 2800100000 4618700 4946100 3941200 3173000 3475600 1407480 3906500 3737000 3704700 4033300 FALSE TRUE 4438196.098 4805042.071 4653462.512 3336758.91 3587395.83 1435940.21 3954308.916 3659829.644 3284157.987 3760120.999 1.180333319 1.277895598 1.237583182 0.887407323 0.954063934 0.381886703 1.051644061 0.973327626 0.873418166 1 21.84234766 3.731736557 6.009592733 0.872646514 1.238176285 0.463187731 0.176316948 0.138203098 22.41922144 0.047740754 0.079576835 5391.834545 -3.731736557 0.365529771 LSSSDRYS(ph)DAS(ph)DDS(ph)FSEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 3 LS(0.007)S(0.007)S(0.007)DRY(0.001)S(0.978)DAS(1)DDS(0.992)FS(0.008)EPR;LSS(0.002)S(0.02)DRY(0.052)S(0.971)DAS(0.956)DDS(0.998)FS(0.002)EPR 220.48 2.36E-19 655090000 918240 944240 714830 941040 931340 975520 930450 992710 1062690 997220 TRUE FALSE 882354.1656 917311.1997 844015.6823 989607.1872 961297.3969 995245.6828 941837.1254 972210.1916 942057.8864 929677.4012 0.949097143 0.986698395 0.907858663 1.064462991 1.034011793 1.070527993 1.013079509 1.045750053 1.013316969 1 19.82637066 3.731772605 24.99998443 1.036999313 0.951766099 0.672446438 0.027606415 279.2512755 1028472.593 0.006798775 0.010800783 5392.282108 -3.731772605 -0.085233214 LSSLRAS(ph)TSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 LSSLRAS(0.986)T(0.013)SK 79.875 0.022397 0 124390 279640 202220 142290 201180 111760 198570 107650 232700 199800 TRUE FALSE 119528.7013 271664.941 238765.6524 149633.604 207651.1374 114019.8638 201000.1591 105426.9899 206284.8716 186267.368 0.641704999 1.458467706 1.281843701 0.803326989 1.114801479 0.612130106 1.079094858 0.565998172 1.107466508 1 17.50701543 3.731856931 24.86170352 0.869577828 1.160451695 0.125271443 0.267041164 737.2067398 2734052.529 0.066747831 0.1060991 5393.329219 -3.731856931 0.290873867 VWDVRPFAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VWDVRPFAPK 10 1 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 74.841 0.037195 486610000 1128900 1194800 1022600 781590 790080 461090 936210 902430 956170 1047100 FALSE TRUE 1084781.34 1160725.474 1207406.568 821927.9536 815493.6407 470413.5557 947667.618 883794.5051 847629.5902 976178.9843 1.111252503 1.189049849 1.236870069 0.841984889 0.835393564 0.48189273 0.970792891 0.905361127 0.868313705 1 19.89678617 3.731867242 23.80529392 0.836465173 1.180056721 0.561727876 0.135773508 193.9035721 689628.4608 0.037043495 0.05894862 5393.45726 -3.731867242 0.343591548 AAS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 2 AASPFR 6 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 AAS(1)PFR;AAS(1)PFR 107.01 0.033184 1183660000 704700 760420 640170 571540 608360 456760 663520 617700 703500 780340 TRUE FALSE 677159.5449 738733.5661 755862.9595 601037.2479 627928.4519 465996.0002 671640.3562 604944.2791 623641.6293 727486.8767 0.930820289 1.015459646 1.039005628 0.826182942 0.863147463 0.640555885 0.923233639 0.831553528 0.857254817 1 19.4725617 3.73188423 24.7333877 0.838200858 0.997131636 0.355029159 0.089517385 428.4110597 1587095.541 0.022725943 0.036127309 5393.668246 -3.73188423 0.158930778 TSYAQHQQVR ddPTM_BT-474_Pertuzumab_2h_R1 6 TSYAQHQQVR 10 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;; 210.08 8.38E-08 678728000 1244335 1369701 1329649 412288 422432 119581.1 849992 428290 484250 746532 FALSE TRUE 1195705.013 1330638.469 1569946.152 433566.2331 436019.9089 121999.1118 860394.4564 419445.6618 429279.9701 695968.7227 1.718044179 1.911922799 2.25577113 0.622967985 0.62649354 0.175293958 1.236254487 0.602678897 0.616809285 1 19.40866295 3.731990075 24.92354063 0.684783071 1.956913729 0.80179342 0.288104272 192.2694861 729321.7619 0.074715506 0.118800456 5394.982934 -3.731990075 1.272130658 DKLPLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKLPLEK 7 1 Q92831 Q92831 KAT2B Histone acetyltransferase KAT2B 0 ; 95.099 0.012508 1416080000 2090080 1810120 2283150 1017580 1621100 1498250 1527000 1792110 1705030 1617300 FALSE TRUE 2008397.363 1758497.15 2695765.993 1070097.426 1673244.154 1528545.642 1545687.883 1755102.302 1511482.142 1507758.83 1.332041519 1.166298691 1.787929169 0.709727182 1.109755831 1.013786562 1.025155915 1.164047105 1.002469435 1 20.52397425 3.732017374 24.99839633 1.024854632 1.402510683 0.526713244 0.18342276 421.655159 1610930.666 0.046810638 0.074419224 5395.322063 -3.732017374 0.377656052 FKMPEMNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKMPEMNIK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 133.23 0.000258 3067000000 5094500 5064720 4418300 3578270 3562630 1813230 4627050 4160140 4550890 4745380 FALSE TRUE 4895401.308 4920279.144 5216785.095 3762944.944 3677225.229 1849894.753 4683677.222 4074231.655 4034292.046 4423971.186 1.106562657 1.112186074 1.179208651 0.850580798 0.831204607 0.418152532 1.058704278 0.920944437 0.911916438 1 22.07691056 3.732114552 23.63680529 0.85054936 1.130605829 0.377335582 0.162790109 254.1906896 932083.7797 0.044671636 0.071180906 5396.529451 -3.732114552 0.280056469 LLPYPTLASPAS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 3 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.007)PAS(0.993)D;LLPYPTLASPAS(1)D;LLPYPTLASPAS(1)D 231.52 2.39E-12 139724000 207641 223251 174194 211268 216624 238257 215588 220445 229446 245125 TRUE FALSE 199526.1602 216884.1001 205674.7307 222171.5668 223591.9077 243074.7198 218226.4304 215892.7337 203400.252 228522.4654 0.873113984 0.949071242 0.900019744 0.972208865 0.978424188 1.063679754 0.954945196 0.944733085 0.890066767 1 17.80197647 3.732160865 24.04376445 0.971097235 0.911568614 0.303294448 0.044723918 412.8854955 1551208.823 0.012398737 0.019754478 5397.104977 -3.732160865 -0.059528621 KGPELPLVPVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGPELPLVPVKR 12 2 Q96DI7;Q96DI7-2 Q96DI7 SNRNP40 U5 small nuclear ribonucleoprotein 40 kDa protein 0 70.412 0.026632 437460000 652490 665930 573350 420460 383790 291090 596040 380090 489950 579400 FALSE TRUE 626989.9694 646938.3284 676967.0991 442159.991 396134.9539 296976.0392 603334.5158 372241.0087 434332.93 540156.7219 1.160755655 1.197686342 1.253279042 0.818577226 0.733370405 0.549796063 1.116961969 0.689135196 0.804086874 1 19.04301853 3.732172654 23.15395207 0.800662671 1.203284965 0.583540059 0.149784331 114.7971068 416097.879 0.038159906 0.060876081 5397.251483 -3.732172654 0.402622295 LGDTALHAAAWK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGDTALHAAAWK 12 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 0 ; 88.187 0.0071554 0 791690 841380 695460 630540 640470 409750 819890 662260 746990 839780 FALSE TRUE 760749.8795 817384.6662 821145.0924 663082.245 661071.2992 418035.4257 829924.0591 648584.0996 662194.8268 782900.9526 0.971706417 1.044046074 1.04884927 0.846955471 0.844386888 0.533956977 1.060062651 0.828436978 0.845821971 1 19.57847027 3.732387971 22.7700093 0.843015095 1.023785145 0.260406839 0.13086617 178.8624125 659801.6774 0.033903079 0.05415984 5399.928027 -3.732387971 0.18077005 KVNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_BT-474_Pertuzumab_2h_R1 1 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 KVNVTVDYIRPAS(0.998)PAT(0.002)ETVPAFSER 168.96 5.51E-12 380910000 163700 147260 117380 157260 161730 164250 134080 176450 179440 161120 TRUE FALSE 157302.423 143060.289 138593.1771 165376.2074 166932.1923 167571.2475 135720.9111 172806.2458 159070.7235 150207.1989 1.047236246 0.952419658 0.922679992 1.100987227 1.111346151 1.115600642 0.903557966 1.150452489 1.059008654 1 17.19659443 3.732431421 24.88474482 1.068510553 0.971942734 0.238331852 0.07231321 592.2940363 2404733.854 0.01881541 0.029996454 5400.468302 -3.732431421 -0.096567819 VKVDGPR ddPTM_BT-474_Pertuzumab_2h_R1 6 VKVDGPR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 90.657 0.015484 2750020000 9894360 10087000 9034610 5890430 5763300 2235290 8894490 6480960 7325660 8689030 FALSE TRUE 9507677.472 9799328.636 10667365 6194435.798 5948681.779 2280489.095 9003343.429 6347125.911 6494081.788 8100514.259 1.173712825 1.209716855 1.316875035 0.764696611 0.734358534 0.28152399 1.111453315 0.783546045 0.801687594 1 22.94958207 3.732451151 24.53749352 0.77206636 1.23106311 0.502916905 0.205271257 296.130806 1189353.686 0.054387957 0.086715641 5400.713643 -3.732451151 0.458996749 IHPQTIIAGWR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHPQTIIAGWR 11 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 158.05 3.03E-05 848790000 442590 436370 436860 226900 261910 109460 439260 240190 313680 363720 FALSE TRUE 425293.0935 423925.1549 515810.3199 238610.3362 270334.573 111673.3562 444635.7953 235229.9926 278072.3615 339084.9204 1.254237708 1.250203502 1.521183305 0.703689022 0.797247405 0.32933743 1.311281536 0.693720005 0.820067024 1 18.3712871 3.732474837 24.99796697 0.799762851 1.332707711 0.502357631 0.243398404 375.3414269 1541753.832 0.062186165 0.099144563 5401.008199 -3.732474837 0.53294486 GTAFVTLLNGEQAEAAINAFHQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTAFVTLLNGEQAEAAINAFHQSR 24 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 187.95 5.15E-28 0 90073 127580 76361 121260 114820 137110 130690 109450 84255 126010 FALSE TRUE 86552.84758 123941.5433 90161.13134 127518.2431 118513.2896 139882.4581 132289.4233 107189.8193 74690.72563 117475.2305 0.736775295 1.055044053 0.767490568 1.08549047 1.008836408 1.190740019 1.126104821 0.912446129 0.63579978 1 16.84199707 3.732478386 24.87171387 1.001850069 0.873297381 0.13250952 0.162178209 1031.735681 4219021.704 0.044076076 0.070287513 5401.052338 -3.732478386 -0.128552688 KAAALEFLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAAALEFLNR 10 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 137.78 0.00013173 4307100000 4277700 4342300 3610900 3571600 3761600 2603300 4401800 3867300 4198100 4290500 FALSE TRUE 4110522.755 4218461.856 4263469.954 3755930.704 3882595.28 2655940.51 4455670.545 3787438.904 3721549.288 3999900.613 1.027656222 1.054641668 1.065893972 0.939006007 0.970672938 0.664001626 1.113945314 0.946883253 0.93041044 1 21.93153272 3.732540602 22.91788143 0.93721381 1.049921729 0.189356048 0.10576232 249.4622329 949696.0433 0.027717243 0.044302516 5401.826143 -3.732540602 0.112707919 HSQFLGYPITLYLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSQFLGYPITLYLEK 15 0 Q58FF8 Q58FF8 HSP90AB2P Putative heat shock protein HSP 90-beta 2 0 ; 161.14 1.67E-06 8143700000 1942400 1911870 1705790 1000010 959250 272570 1655210 840470 1254060 1516610 FALSE TRUE 1866488.861 1857345.34 2014064.198 1051620.636 990105.1474 278081.5522 1675466.955 823114.0008 1111704.366 1413888.654 1.320110219 1.313643288 1.424485721 0.743778962 0.700270948 0.196678537 1.185006295 0.582163241 0.786274339 1 20.43123708 3.73258877 23.25001673 0.719707012 1.348836131 0.564837022 0.245095835 119.5599587 465481.3404 0.062105067 0.099278855 5402.42529 -3.73258877 0.629129119 S(ph)RSPLGFYVHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.559)RS(0.441)PLGFYVHLK;S(0.589)RS(0.411)PLGFYVHLK 102.08 0.0014488 1140550000 1302440 1326490 1069890 1009840 953580 865590 1241080 1002020 1231210 1212140 TRUE FALSE 1251539.205 1288659.804 1263242.923 1061957.963 984252.7667 883092.8229 1256268.708 981327.9368 1091448.202 1130040.678 1.10751695 1.140365855 1.117873849 0.939751979 0.870988793 0.781469942 1.1117022 0.868400542 0.965848596 1 20.10794328 3.732630429 5.160843021 0.926358421 1.125419562 0.516010253 0.083258225 0.131351749 11.56957538 0.021577308 0.036445508 5402.943543 -3.732630429 0.199061141 KREELSNVLAAMR ddPTM_BT-474_Pertuzumab_2h_R1 2 KREELSNVLAAMR 13 2 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ; 148.52 2.44E-05 1561200000 5057000 5122300 4676200 2662100 2904300 588130 4178800 2933500 3346700 4036000 FALSE TRUE 4859366.849 4976217.019 5521293.362 2799491.3 2997719.447 600022.3916 4229941.404 2872922.2 2966796.647 3762638.125 1.291478661 1.322534045 1.467399515 0.74402353 0.796706818 0.159468536 1.124195648 0.763539332 0.788488435 1 21.84331311 3.732805343 24.83195002 0.75694552 1.356677081 0.562983112 0.239037514 292.8859658 1263699.102 0.06240261 0.099631286 5405.120039 -3.732805343 0.599731562 GEEVDVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEEVDVAR 8 0 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 117.72 0.0047089 107270000 281650 292010 217590 281870 253020 301210 281600 294370 285710 311110 FALSE TRUE 270642.8066 283682.1607 256913.3533 296417.3445 261158.6181 307300.6726 285046.305 288291.1566 253277.3986 290038.2426 0.933128005 0.978085366 0.885791305 1.021994003 0.900428219 1.059517772 0.982788692 0.99397636 0.873255183 1 18.14588361 3.732832189 24.9633731 0.977498098 0.93690994 0.113528629 0.05535536 1036.586385 4517248.767 0.013925239 0.022246263 5405.45416 -3.732832189 -0.040588158 KYEMFAQTLQQSR ddPTM_BT-474_Pertuzumab_2h_R1 3 KYEMFAQTLQQSR 13 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 254.58 1.31E-23 8399320000 5463950 5491650 5252220 2249820 2266050 391480 4376990 2350940 2677250 3902830 FALSE TRUE 5250412.793 5335033.519 6201412.989 2365933.48 2338939.556 399395.9938 4430556.913 2302392.267 2373339.804 3638487.848 1.443020566 1.46627768 1.704392937 0.650251857 0.642832862 0.109769775 1.217691826 0.632788225 0.652287407 1 21.79490756 3.732858963 24.84406312 0.687614465 1.530735138 0.65858662 0.276067424 238.895719 1040951.442 0.071613964 0.114410634 5405.787419 -3.732858963 0.843120673 KLELSENR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLELSENR 8 1 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 ; 98.044 0.01251 2626200000 3475700 3571300 3189300 1829120 2001740 362050 2855600 1917810 2213600 2774600 FALSE TRUE 3339865.801 3469450.021 3765677.456 1923521.102 2066127.785 369370.8991 2890547.687 1878206.553 1962321.408 2586673.871 1.291181637 1.341278489 1.455799086 0.743627221 0.798758517 0.14279763 1.117476664 0.726108759 0.758627298 1 21.30266674 3.732973935 24.5051108 0.742124254 1.360605625 0.569573018 0.241779928 231.8108097 1016803.66 0.062500475 0.099946774 5407.218695 -3.732973935 0.618481371 KLIEFLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLIEFLLK 8 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PNN8;E9PKG4 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 93.111 0.018101 0 122940 120980 110570 97516 110200 83747 121510 105160 145570 127390 FALSE TRUE 118135.3689 117529.7689 130552.4586 102548.8124 113744.6831 85440.42172 122997.0757 102988.4093 129045.5039 118761.7618 0.994725634 0.98962635 1.099280245 0.863483421 0.9577551 0.719427031 1.035662269 0.867184923 1.086591356 1 16.85771088 3.732980317 24.85997786 0.92265193 1.024052303 0.150712525 0.10121499 695.0926338 3096606.23 0.025310726 0.040460422 5407.29815 -3.732980317 0.101400373 LKGPDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKGPDVK 7 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 61.962 0.080551 489340000 558580 572710 556100 280580 318390 234510 420300 329630 381850 407570 FALSE TRUE 536750.0761 556376.8715 656599.6404 295060.7674 328631.3035 239251.9529 425443.7571 322823.0253 338503.9888 379964.9209 1.412630605 1.464284835 1.728053313 0.77654739 0.864899062 0.629668529 1.119692197 0.849612708 0.890882211 1 18.53550671 3.732997437 24.974291 0.872770906 1.527919119 0.817327491 0.142771129 167.5580961 752204.1344 0.036949912 0.059043401 5407.511315 -3.732997437 0.655148213 ESYPVFYLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESYPVFYLFR 10 0 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 146.81 6.51E-05 225730000 244210 242460 219560 139750 146930 77135 225540 144560 144990 173070 FALSE TRUE 234666.0032 235545.2782 259239.3761 146962.5142 151656.1369 78694.72255 228300.226 141574.7855 128531.343 161347.8147 1.454410793 1.459860356 1.606711417 0.910842917 0.939933008 0.487733427 1.414957038 0.877450901 0.796610374 1 17.29981451 3.733005681 24.86484936 0.924088913 1.502280815 0.607080699 0.217018274 272.1882995 1218362.906 0.056509908 0.090324932 5407.61397 -3.733005681 0.578191902 HNMNIGTWDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HNMNIGTWDEK 11 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 186.02 4.21E-06 149510000 263830 253880 226530 220620 226820 248580 257450 216600 296150 285920 FALSE TRUE 253519.2319 246639.591 267469.0101 232006.2246 234115.8713 253606.4579 260600.7501 212127.1343 262532.2936 266554.3837 0.95109759 0.925288069 1.003431294 0.87038983 0.878304337 0.951424825 0.977664469 0.795811839 0.984910808 1 18.02407038 3.733049726 24.98419956 0.910048993 0.956473892 0.043717843 0.062302847 1039.882498 4714413.52 0.016392531 0.02624301 5408.162421 -3.733049726 0.046424899 DKGFGFIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKGFGFIR 8 1 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 118.18 0.0017663 2619100000 4819600 4966700 4480800 3380800 3461500 1731450 4993800 4133900 4372600 4894000 FALSE TRUE 4631244.704 4825054.579 5290580.235 3555283.493 3572842.291 1766461.105 5054915.618 4048533.52 3876240.779 4562525.021 1.015061766 1.057540409 1.15957287 0.779235944 0.783084427 0.387167434 1.107920635 0.887344946 0.849582361 1 22.12140104 3.733089352 24.88556454 0.824365473 1.075406557 0.288959729 0.179382532 542.5740218 2467852.069 0.04879657 0.078078218 5408.655898 -3.733089352 0.251041084 QRT(ph)LEDEEEQER ddPTM_BT-474_Pertuzumab_2h_R1 2 QRTLEDEEEQER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQER;QRT(1)LEDEEEQER 231.37 5.82E-12 1341550000 376330 357500 284560 392750 445370 328810 358430 565930 338530 352380 TRUE FALSE 361622.6075 347304.45 335986.322 413019.8746 459695.7305 335458.7635 362816.5736 554243.3477 300101.4936 328512.9887 1.100786331 1.057201578 1.022748973 1.257240623 1.399322847 1.021143075 1.104420787 1.687127653 0.91351485 1 18.32559089 3.733124719 23.77703281 1.247816385 1.05994122 0.045028565 0.21545535 463.4317809 2027093.184 0.05812429 0.093093042 5409.096371 -3.733124719 -0.187875165 FLGEVHCGTNVR ddPTM_BT-474_Pertuzumab_2h_R1 4 FLGEVHCGTNVR 12 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;;; 148.78 6.54E-05 1605890000 1646200 1808100 1355760 1829950 1875610 1884230 1956040 1962390 1909840 2015090 FALSE TRUE 1581864.684 1756534.758 1600775.991 1924393.939 1935940.699 1922330.422 1979978.603 1921865.961 1693042.97 1878606.159 0.842041679 0.935020227 0.852108348 1.024373272 1.030519723 1.023274842 1.05396152 1.023027605 0.901222942 1 20.84123121 3.733304555 24.88153584 1.013901757 0.882253096 0.639130284 0.045123764 237.9746993 1126543.557 0.011704986 0.018749058 5411.336675 -3.733304555 -0.13164866 HLWDYTFGPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLWDYTFGPEK 11 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 122.7 0.00038533 430390000 742540 754500 592690 393210 375770 154500 592200 335350 450280 507530 FALSE TRUE 713520.7159 732982.3987 699802.2673 413503.6152 387856.9833 157624.0959 599447.5207 328424.9053 399166.1021 473154.541 1.508007752 1.54913952 1.479014163 0.873929297 0.819725797 0.333134488 1.266916977 0.694117623 0.84362733 1 18.85195195 3.733406673 4.026330794 0.813193075 1.528044234 0.665770067 0.220745072 0.118642099 4.588942016 0.05697121 0.099012764 5412.609224 -3.733406673 0.714851158 LLPLEEHYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPLEEHYR 9 0 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1;Q9NZN3-2;Q9NZN3;Q9NZN4 A0A024R571;Q9NZN3;Q9NZN4 EHD1;EHD3;EHD2 EH domain-containing protein 1;EH domain-containing protein 3;EH domain-containing protein 2 0 ; 164.46 6.22E-05 475230000 218800 250760 216880 111466 116154 23874 217490 101876 108509 179044 FALSE TRUE 210249.0541 243608.5703 256075.0405 117218.7736 119890.1989 24356.74864 220151.7077 99772.225 96191.51323 166917.1904 1.259600965 1.459457649 1.534144206 0.702257049 0.718261544 0.145921152 1.31892771 0.597734869 0.576282844 1 17.34877302 3.733463273 24.74962432 0.712117934 1.421906627 0.545692457 0.290463965 255.1617652 1238912.937 0.074382993 0.119276924 5413.31467 -3.733463273 0.709788694 VPS(ph)PDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPSPDHR 7 0 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 1 VPS(1)PDHR;VPS(1)PDHR 88.496 0.011958 2093610000 807120 856040 658310 868160 879210 998370 891940 935670 851760 951730 TRUE FALSE 775576.8581 831626.5774 777281.261 912965.8416 907490.5881 1018557.725 902855.8285 916348.0875 755071.7757 887268.4794 0.874117447 0.93728854 0.876038402 1.02896233 1.02279142 1.147970146 1.017567793 1.032774305 0.8510071 1 19.75901119 3.733557257 24.77412579 1.022394938 0.899962168 0.374875001 0.069607711 370.3252073 1833665.131 0.018506452 0.029678631 5414.486278 -3.733557257 -0.12243277 EEHSKT(ph)PEER ddPTM_BT-474_Pertuzumab_2h_R1 6 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EEHS(0.001)KT(0.999)PEER;EEHS(0.001)KT(0.999)PEER;EEHS(0.021)KT(0.979)PEER;EEHS(0.024)KT(0.976)PEER;EEHS(0.002)KT(0.998)PEER;EEHS(0.017)KT(0.983)PEER 182.33 2.62E-06 1860293000 1972096 1776301 1594491 1576024 1681842 1647833 1668286 1672555 2094784 1793570 TRUE FALSE 1895024.308 1725642.635 1882650.993 1657362.788 1735939.975 1681153.312 1688702.983 1638016.155 1856992.902 1672089.906 1.133326803 1.032027422 1.125926893 0.991192388 1.038185787 1.005420406 1.009935516 0.979622058 1.11058197 1 20.67322099 3.733559609 24.97378059 1.01586073 1.090587078 0.406088983 0.042770064 388.6795782 1940970.41 0.010638032 0.017062381 5414.515597 -3.733559609 0.074726348 LRLPLDKEPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRLPLDKEPAR 11 2 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 137.55 4.28E-05 1271850000 1208840 1319790 1143990 810940 908440 352730 1192280 898840 1016800 1189990 FALSE TRUE 1161597.196 1282150.881 1350734.441 852792.7106 937660.7976 359862.4423 1206871.479 880278.6399 901377.1268 1109390.917 1.047058506 1.155725057 1.21754597 0.768703527 0.84520324 0.324378392 1.087868542 0.79347922 0.812497302 1 20.08133639 3.733561543 24.825196 0.795441266 1.141671372 0.390764348 0.19174207 358.4072807 1779837.241 0.049584773 0.079535508 5414.53971 -3.733561543 0.346230107 IAGYVTHLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 IAGYVTHLMK 10 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 125.48 0.00040796 289090000 688660 698930 698970 191910 189980 23685 498180 198830 259290 412280 FALSE TRUE 661746.4058 678997.2007 825289.4275 201814.4981 196090.8792 24163.92693 504276.8759 194724.091 229856.4862 384355.9084 1.721702181 1.766584527 2.147201095 0.525071929 0.510180473 0.062868624 1.312005006 0.506624425 0.598030318 1 18.55208332 3.733587118 24.99632008 0.628921506 1.867304818 0.748099922 0.327902436 187.8683917 944208.8394 0.084991973 0.136304817 5414.85857 -3.733587118 1.238383312 RYGEDYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RYGEDYSR 8 1 Q9H201;I6L9I8;Q9H201-2 Q9H201 EPN3 Epsin-3 0 104.01 0.0074751 143510000 189920 216780 164270 181510 173920 143560 230590 184000 214970 207960 FALSE TRUE 182497.7164 210597.6466 193957.2432 190877.7529 179514.2948 146462.8816 233412.0294 180200.3357 190567.5068 193874.684 0.941317931 1.086256557 1.000425838 0.984541916 0.925929529 0.755451298 1.203932482 0.929468108 0.982941676 1 17.5647649 3.733732752 3.437172623 0.966897845 1.018616447 0.028938434 0.107798278 0.928921983 23.45813252 0.028846171 0.051394755 5416.674669 -3.733732752 0.051718602 LHFFMPGFAPLTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHFFMPGFAPLTAR 14 0 Q13509;A0A0B4J269;Q13509-2 Q13509 TUBB3 Tubulin beta-3 chain 0 ; 78.763 0.020971 351470000 467370 515670 463560 138720 128819 46543 278726 96831 142790 241649 FALSE TRUE 449104.6637 500963.5965 547335.6038 145879.3558 132962.5801 47484.13135 282137.1322 94831.40601 126581.0778 225281.898 1.993523082 2.223718821 2.429558738 0.647541401 0.590205344 0.210776506 1.252373736 0.420945521 0.561878602 1 17.78137187 3.733753892 24.90949597 0.645502624 2.216412114 0.856826102 0.289584719 118.8299354 615803.0305 0.073560166 0.118128343 5416.938338 -3.733753892 1.57090949 VTCPNHPDAILVEDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTCPNHPDAILVEDYR 16 0 B1APE1;B1APE2;Q00403 B1APE1 GTF2B Transcription initiation factor IIB 0 ; 133.16 3.52E-05 588660000 293500 328260 230450 338790 353300 389240 299710 341500 340850 343520 FALSE TRUE 282029.6955 318898.3462 272097.4413 356274.9925 364664.2154 397110.6995 303377.9406 334447.9057 302158.137 320253.0844 0.880646305 0.995769789 0.849632539 1.112479504 1.138675108 1.239990241 0.94730685 1.044323761 0.943497976 1 18.28885294 3.733761459 24.99243115 1.064971361 0.917391568 0.366089436 0.091462479 455.1083719 2370056.127 0.02515846 0.040399043 5417.032723 -3.733761459 -0.147579793 RAPFDLFENK ddPTM_BT-474_Pertuzumab_2h_R1 2 RAPFDLFENK 10 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ; 189.66 1.58E-06 9709400000 10444700 10830100 9624700 6584100 6523300 2122580 10520300 7620400 8888500 9704800 FALSE TRUE 10036509.58 10521236.15 11364097.39 6923906.19 6733127.869 2165500.022 10649050.58 7463036.077 7879514.744 9047485.252 1.109314831 1.162890666 1.256050391 0.765285159 0.744198822 0.239348279 1.177017733 0.82487408 0.870906614 1 23.10908542 3.733765268 24.64561778 0.795236564 1.17476584 0.360351136 0.227559893 350.8988398 1803441.587 0.060959238 0.097940809 5417.080229 -3.733765268 0.379529276 QRPQATAEQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 QRPQATAEQIR 11 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 169.65 1.52E-05 88115000 65626 68667 68417 21255 24118 10902 45997 26325 27913 43162 FALSE TRUE 63061.26337 66708.68439 80781.47383 22351.9731 24893.77737 11122.44591 46559.92505 25781.37955 24744.43326 40238.5993 1.567183363 1.657828194 2.007561775 0.555485864 0.618654173 0.276412353 1.157096068 0.640712649 0.614942709 1 15.29629247 3.7338328 24.99983159 0.685477042 1.735554839 0.787084275 0.250080677 162.6665521 860151.6864 0.064968447 0.10437577 5417.922647 -3.7338328 1.050077797 LTFDEYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTFDEYR 7 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 86.472 0.07599 0 659050 716690 538480 333580 372150 166710 356590 326650 334300 456060 FALSE TRUE 633293.5974 696250.7029 635795.3144 350796.1038 384120.5427 170080.9904 360954.0551 319904.5634 296351.6655 425170.65 1.489504502 1.637579412 1.495388533 0.825071307 0.90345028 0.400029942 0.848962776 0.752414503 0.697018163 1 18.69768248 3.733861875 3.387429572 0.750022733 1.571230831 0.841512131 0.152484354 0.081172766 1.976859355 0.039636551 0.070812247 5418.28537 -3.733861875 0.821208098 RLPDAHSDYAR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLPDAHSDYAR 11 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;; 176.87 5.34E-06 4333970000 1045140 1227940 908750 835380 913180 537464 1038240 908380 838620 968030 FALSE TRUE 1004294.773 1192920.353 1072981.34 878494.0619 942553.264 548331.8903 1050946.292 889621.6356 743423.3734 902464.4659 1.112835808 1.321847451 1.188945804 0.97343895 1.04442147 0.607593884 1.164529277 0.985769157 0.823770244 1 19.7835106 3.733921813 3.129839728 0.944611694 1.227467243 0.41053928 0.146082846 0.245040967 4.935805321 0.039156984 0.071030394 5419.033216 -3.733921813 0.282855549 LRDTESGWDDTAVVNDLSSTSSGTESGPQSPLT(ph)PDGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRDTESGWDDTAVVNDLSSTSSGTESGPQSPLTPDGKR 38 2 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30 E9PP16 PPFIBP2 Liprin-beta-2 1 LRDTESGWDDTAVVNDLS(0.001)S(0.001)T(0.001)S(0.001)S(0.001)GT(0.003)ES(0.009)GPQS(0.031)PLT(0.951)PDGKR 80.475 0.069164 188240000 76989 60739 53217 70264 71699 76974 61079 88174 71745 67308 TRUE FALSE 73980.18476 59006.78319 62834.49571 73890.33346 74005.26345 78530.46702 61826.50307 86353.17609 63600.80838 62749.16921 1.178982697 0.940359593 1.001359803 1.177550785 1.179382363 1.251498116 0.985295963 1.376164452 1.013572119 1 15.93730874 3.734103829 24.20830623 1.165370272 1.030246585 0.090281 0.128860472 383.5854737 2083556.618 0.032119269 0.051726546 5421.30485 -3.734103829 -0.135123687 DISLSDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 DISLSDYK 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 198.07 0.00032315 5502000000 6674800 6253500 5506300 5071600 5076800 3000030 6222900 6273600 6503300 6620600 FALSE TRUE 6413941.437 6075156.303 6501410.897 5333345.884 5240099.883 3060692.662 6299057.712 6144047.968 5765072.648 6172180.865 1.039169392 0.984280344 1.053340957 0.864094232 0.848986768 0.495885122 1.020556243 0.995441984 0.934041431 1 22.55734891 3.734159928 24.20997072 0.878512632 1.021465244 0.18074227 0.142087011 451.7268561 2485139.782 0.040355669 0.065027895 5422.005182 -3.734159928 0.142952612 SMS(ph)APSDLEMIGNEDLEFTR ddPTM_BT-474_Pertuzumab_2h_R1 5 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.116)MS(0.884)APSDLEMIGNEDLEFTR;S(0.007)MS(0.993)APSDLEMIGNEDLEFTR;S(0.007)MS(0.993)APSDLEMIGNEDLEFTR;S(0.01)MS(0.987)APS(0.003)DLEMIGNEDLEFTR;S(0.012)MS(0.988)APSDLEMIGNEDLEFTR 365.74 5.84E-112 485023000 289162 315608 221672 333899 350137 311755 316105 390856 309044 301663 TRUE FALSE 277861.2294 306607.1689 261733.0615 351131.5674 361399.4746 318058.8997 319973.5875 382784.687 273962.6207 281231.0963 0.988017445 1.0902321 0.930668994 1.248551714 1.285062283 1.130952103 1.137760339 1.361103704 0.974154794 1 18.1013966 3.734160298 24.94773274 1.189929577 1.011698771 0.249957928 0.11996394 412.7205555 2339933.565 0.0305603 0.049236369 5422.009799 -3.734160298 -0.178230806 DRPFFAGLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRPFFAGLVK 10 1 Q32Q12;P22392-2;J3KPD9;E7ERL0;E5RHP0;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 143.24 3.13E-05 3519100000 3730000 3944600 3359000 2251200 1980250 745540 3677800 2333200 2797800 3469700 FALSE TRUE 3584227.476 3832103.87 3966046.021 2367384.702 2043946.54 760615.3296 3722810.017 2285018.605 2480205.473 3234694.129 1.10805762 1.184688171 1.226096151 0.731872816 0.631882477 0.235142891 1.150900168 0.706409482 0.766751159 1 21.62519787 3.734290815 24.01678704 0.731856758 1.174121416 0.426126889 0.226552501 188.5602093 1060617.686 0.059695434 0.096285537 5423.639495 -3.734290815 0.442264658 HILANFK ddPTM_BT-474_Pertuzumab_2h_R1 2 HILANFK 7 0 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2;H0YCX0;Q56UQ5 Q5W0H4 TPT1 Translationally-controlled tumor protein;TPT1-like protein 0 ; 158.53 0.0014171 1408700000 3026300 3324500 3050900 1416970 1537600 529250 2799900 1333190 1994010 2603900 FALSE TRUE 2908028.85 3229688.515 3602265.497 1490099.992 1587058.3 539951.7976 2834166.014 1305659.161 1767658.344 2427535.534 1.197934617 1.330439234 1.483918751 0.613832412 0.653773458 0.222427969 1.16750753 0.537853779 0.728169915 1 21.21106098 3.734364462 24.98746221 0.682415075 1.336731718 0.576779429 0.248444509 226.2939402 1347546.993 0.062689936 0.10108535 5424.559313 -3.734364462 0.654316643 FRPSLEER ddPTM_BT-474_Pertuzumab_2h_R1 1 FRPSLEER 8 1 P35221-2;P35221;G3XAM7;P26232;P26232-5;P26232-2;P26232-3;H0YBB8 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 0 129.63 0.00098741 146330000 299940 399800 278430 114760 84701 11727 210890 93022 77078 146850 FALSE TRUE 288218.0132 388398.0954 328748.4946 120682.7774 87425.48459 11964.12797 213470.9349 91101.06319 68328.42858 136903.7187 2.10526066 2.837016402 2.40131165 0.881515699 0.638591014 0.087390818 1.559277841 0.665438923 0.499098412 1 17.06280211 3.73437488 4.573413733 0.748987373 2.508401207 0.798520826 0.388663903 0.077841444 4.480475936 0.101751064 0.174352126 5424.689432 -3.73437488 1.759413834 KLDVLSNDLVMNMLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDVLSNDLVMNMLK 15 1 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 203.37 8.73E-09 294750000 1086920 1079380 958570 701260 709930 263350 1000740 796710 948960 1166170 FALSE TRUE 1044441.965 1048597.139 1131804.922 737452.1126 732765.5432 268675.1174 1012987.355 780257.6601 841238.0392 1087184.267 0.960685319 0.964507279 1.041042403 0.678313819 0.674003079 0.247129328 0.931753141 0.717686673 0.77377687 1 20.05216505 3.734412655 24.74694876 0.699267974 0.986321236 0.297042732 0.189740387 353.1409289 2106859.538 0.04970668 0.080163052 5425.161297 -3.734412655 0.287053262 MTEEEVEMLVAGHEDSNGCINYEAFVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MTEEEVEMLVAGHEDSNGCINYEAFVR 27 0 P60660;J3KND3;G3V1Y7 P60660 MYL6 Myosin light polypeptide 6 0 157.31 6.97E-09 34212000 11278 12260 9117.5 12850 12519 13767 11311 15220 13361 14814 FALSE TRUE 10837.24329 11910.3568 10765.23507 13513.19004 12921.685 14045.37817 11449.4274 14905.70168 11844.31529 13810.63459 0.784702776 0.862404745 0.779488806 0.978462645 0.935632966 1.016997306 0.829029784 1.079291584 0.857622814 1 13.75349199 3.734437116 24.87229435 0.960981358 0.814219369 0.467254948 0.072179755 262.2276491 1581716.236 0.017638901 0.028473683 5425.466872 -3.734437116 -0.146761988 GFSLEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFSLEELR 8 0 P26373;P26373-2;J3QSB4 P26373 RPL13 60S ribosomal protein L13 0 ;;; 152.34 0.0010671 987359000 2765260 3159580 2744500 1125212 1213971 202389 2282960 1039134 1155140 1795120 FALSE TRUE 2657190.582 3069471.872 3240492.201 1183284.326 1253019.48 206481.4442 2310899.547 1017675.52 1024013.35 1673534.923 1.587771217 1.834124779 1.936315852 0.707056847 0.748726221 0.123380421 1.380849312 0.608099362 0.611886454 1 20.67446723 3.734532676 24.84444038 0.730908616 1.790876062 0.705639072 0.309569574 156.8141498 967235.0294 0.079142685 0.127727681 5426.660801 -3.734532676 1.059967446 ITQSEFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ITQSEFDR 8 0 A0A087WW40;Q9Y371-2;Q9Y371;Q9Y371-3 A0A087WW40 SH3GLB1 Endophilin-B1 0 119.07 0.0041071 247630000 101210 116350 93039 112680 128370 136680 130820 119010 129580 132560 FALSE TRUE 97254.60131 113031.8119 109853.2169 118495.4283 132499.1376 139443.7632 132421.0143 116552.4019 114870.6216 123581.5931 0.786966723 0.91463307 0.888912452 0.95884367 1.072159164 1.128353825 1.071527004 0.94312105 0.929512387 1 16.91510435 3.734604943 1.938794211 1.023320363 0.853310652 0.562370828 0.063570995 0.29045761 2.118859239 0.020611848 0.043440153 5427.563869 -3.734604943 -0.170009711 LALLEEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LALLEEAR 8 0 Q5TZA2-2;Q5TZA2;B1AKD8 Q5TZA2-2 CROCC Rootletin 0 98.299 0.017729 34389000 86268 96881 81042 41152 39164 15711 67253 41733 37552 62338 FALSE TRUE 82896.55119 94118.04874 95688.09217 43275.85965 40423.74563 16028.68718 68076.06233 40871.19897 33289.25439 58115.79174 1.426403198 1.61949181 1.64650759 0.744648887 0.695572484 0.275806054 1.171386646 0.703271826 0.572809101 1 15.82664262 3.734623432 24.15787348 0.729889306 1.569670001 0.73022788 0.230165397 99.95477444 613307.1597 0.059721063 0.096529035 5427.794944 -3.734623432 0.839780696 FKGPEFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 FKGPEFVR 8 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 99.653 0.0060746 1027330000 1577990 1722810 1424370 1285790 1332380 796770 1689290 1518170 1500280 1684880 FALSE TRUE 1516320.406 1673677.146 1681785.344 1352149.776 1375237.213 812881.2353 1709964.036 1486819.259 1329974.504 1570761.577 0.965340908 1.065519535 1.070681489 0.860824326 0.87552257 0.517507716 1.088620999 0.946559478 0.846706797 1 20.58303278 3.734669554 24.61358175 0.876907155 1.037014537 0.204330108 0.14221454 432.1245776 2733482.838 0.038555436 0.062247558 5428.371403 -3.734669554 0.160107382 KLAVNMVPFPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLAVNMVPFPR 11 1 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;A6NNZ2;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB1;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-1 chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 152.07 5.31E-05 3490300000 4007700 4536800 3503700 1788890 1672150 407300 2866700 1804830 1905940 2525800 FALSE TRUE 3851074.653 4407414.906 4136896.529 1881214.827 1725936.223 415535.8851 2901783.532 1767559.63 1689585.682 2354725.316 1.63546662 1.871732077 1.756848878 0.79891052 0.732967116 0.176468942 1.23232358 0.75064366 0.717529841 1 21.16712735 3.734734912 6.129181692 0.761737277 1.771015466 0.7563094 0.255421246 0.068328933 12.27401807 0.066771567 0.111825154 5429.188399 -3.734734912 1.009278189 LLEPSVGSLFGDDEDDDLFSSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEPSVGSLFGDDEDDDLFSSAK 23 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 0 98.562 0.0029408 19639000 33583 35905 27779 37898 37270 40934 38119 41581 45239 41918 FALSE TRUE 32270.53923 34881.02455 32799.28324 39853.92032 38468.8234 41761.71353 38585.51172 40722.33782 40103.65838 39078.85652 0.825780028 0.892580481 0.839310209 1.019833328 0.984389688 1.068652393 0.987375659 1.042055511 1.026223947 1 15.25410063 3.734805612 24.97967762 1.020186002 0.856559259 0.875870825 0.028586076 90.61948953 602834.9578 0.00699428 0.01129882 5430.072302 -3.734805612 -0.163626744 LYAVHQEGNK ddPTM_BT-474_Pertuzumab_2h_R1 6 LYAVHQEGNK 10 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;; 126.31 0.00038589 2915090000 7960940 7808340 7027400 4696680 5023500 1528720 7002660 5259520 6466470 7587340 FALSE TRUE 7649817.664 7585653.788 8297407.504 4939076.218 5185085.44 1559631.766 7088360.648 5150909.074 5732423.435 7073442.704 1.081484361 1.072413266 1.173036646 0.698256341 0.733035617 0.220491185 1.002109008 0.728203972 0.81041491 1 22.75398113 3.734811238 24.95335975 0.725182042 1.105321618 0.400303493 0.205237248 293.7108206 1954745.317 0.053382938 0.086322081 5430.142635 -3.734811238 0.380139576 AKFENLCK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKFENLCK 8 1 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 ; 118.18 0.0017663 12627400000 9237300 9463700 8391000 5664900 5400300 1682960 9042300 6667500 8039500 8976200 FALSE TRUE 8876296.104 9193804.542 9907440.357 5957266.168 5574005.554 1716990.604 9152962.372 6529813.795 7126889.664 8368233.979 1.060713183 1.098655292 1.183934434 0.711890488 0.666091026 0.205179565 1.093774672 0.780309658 0.851659942 1 22.99649176 3.734939068 24.39947692 0.745747019 1.112856413 0.343810213 0.224912687 246.1071483 1658104.108 0.060383805 0.09780708 5431.741187 -3.734939068 0.367109395 SVWVAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVWVAR 6 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 139.01 0.028046 2913290000 2902090 2902940 2437610 2360450 2375830 1828400 2621530 2804600 2830080 3051090 FALSE TRUE 2788673.114 2820150.993 2878140.351 2482273.107 2452250.73 1865371.501 2653613.068 2746684.03 2508821.183 2844436.957 0.980395473 0.991461944 1.011848881 0.872676437 0.862121667 0.655796395 0.9329133 0.965633646 0.882009769 1 21.43971168 3.73495373 24.28478982 0.87864714 0.994258088 0.260971554 0.087022937 296.8414041 1998608.135 0.024525239 0.039731352 5431.924563 -3.73495373 0.115610948 IRTS(ph)PTFR ddPTM_BT-474_Pertuzumab_2h_R1 2 IRTSPTFR 8 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 IRT(0.344)S(0.655)PT(0.001)FR;IRT(0.058)S(0.941)PT(0.001)FR 91.752 0.0074274 938890000 98061 84005 67337 93634 86108 98804 91986 104198 89609 94189 TRUE FALSE 94228.66771 81609.25965 79506.2938 98466.46196 88877.74202 100801.8846 93111.75218 102046.2749 79436.96199 87809.49514 1.073103399 0.92938992 0.905440735 1.121364629 1.012165505 1.147961099 1.060383641 1.162132577 0.904651164 1 16.42208933 3.735010502 24.99201482 1.072384975 0.965319208 0.179190803 0.083548672 394.1228597 2774540.133 0.021072665 0.034111978 5432.634689 -3.735010502 -0.107065767 VYNWDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VYNWDVK 7 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ; 101.99 0.020244 488960000 727990 693550 598970 568110 638230 511730 596990 587890 757120 695510 FALSE TRUE 699539.346 673770.6331 707217.203 597430.2252 658759.2476 522077.5312 604296.1422 575749.8661 671174.9117 648402.4882 1.078865918 1.039124071 1.090707108 0.921387928 1.015972732 0.805175089 0.931976902 0.887951352 1.035120814 1 19.3065301 3.735026864 24.90121581 0.931990228 1.06652154 0.441096116 0.064758141 234.722682 1654017.528 0.016531457 0.026777346 5432.839359 -3.735026864 0.134531312 SIFGEDALANVSIEKPIHQGPDAAVTGHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIFGEDALANVSIEKPIHQGPDAAVTGHIR 30 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 161.05 2.73E-12 1681410000 670510 654750 524070 670710 724700 766180 794080 502700 830200 724240 FALSE TRUE 644305.7279 636077.1711 618781.1069 705325.4235 748010.6337 781672.6846 803798.1886 492319.0693 735959.1765 675186.5797 0.954263232 0.942076146 0.916459428 1.0446378 1.107857674 1.157713598 1.190483065 0.729160034 1.090008597 1 19.3649267 3.735050743 23.80171919 1.032068398 0.938047254 0.139223552 0.119861621 390.370995 2647265.155 0.035466073 0.057519401 5433.138086 -3.735050743 -0.094021144 LLLPWLEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLLPWLEAR 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 110.31 0.0053688 1176940000 1161120 1425330 1159970 672640 773680 166542 1031230 743580 761490 1077060 FALSE TRUE 1115742.147 1384680.984 1369602.382 707355.031 798566.1198 169909.5933 1043850.501 728224.8132 675048.8476 1004109.767 1.111175475 1.37901356 1.363996674 0.704459865 0.795297632 0.169214163 1.039578078 0.725244228 0.672285909 1 19.93748556 3.735063587 24.54060984 0.717508791 1.294157091 0.545688555 0.231957695 160.9815658 1129700.312 0.059462855 0.096377894 5433.298768 -3.735063587 0.5766483 RYPSSISSS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 4 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSIS(0.002)S(0.304)S(0.693)PQK;RYPSSISS(0.133)S(0.867)PQK;RYPSSISS(0.049)S(0.951)PQK;RYPSSIS(0.002)S(0.242)S(0.756)PQK 156.58 3.67E-05 10637950000 3874350 3555920 3379930 2151110 2147830 762489 3573950 2600920 2873710 3479050 TRUE FALSE 3722936.119 3454508.643 3990758.537 2262129.045 2216916.903 777907.05 3617689.069 2547210.093 2547498.488 3243410.845 1.147845986 1.065085124 1.230420298 0.697453746 0.683514056 0.239842279 1.115396489 0.785349194 0.785438111 1 21.62908035 3.735065089 24.97841107 0.749261749 1.139513943 0.398584489 0.219071551 299.0714314 2137113.264 0.058439339 0.094653823 5433.317567 -3.735065089 0.390252194 ALNEELHLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALNEELHLQR 10 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A6I8PUA5;A0A087WX84;Q99996-4 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 149.33 2.35E-05 142380000 108290 113580 85876 119400 129470 109610 127880 126940 129080 121800 FALSE TRUE 104057.9071 110340.8096 101395.7035 125562.2483 133634.5201 111826.3893 129445.0337 124318.6446 114427.3795 113550.3775 0.916403004 0.971734414 0.892957872 1.105784508 1.176874292 0.984817415 1.139978893 1.094832508 1.007723462 1 16.79297298 3.735086957 24.99554398 1.082260563 0.931502025 0.53552101 0.061761333 206.9703962 1489307.382 0.015636379 0.025303727 5433.59115 -3.735086957 -0.150758537 AICDHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 AICDHVR 7 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ; 143.23 0.0024359 768140000 567960 690290 566300 260392 233964 32624 518390 227294 271985 494390 FALSE TRUE 545763.4953 670603.6051 668643.0073 273830.8623 241489.6645 33283.67963 524734.2119 222600.2995 241110.4031 460904.5249 1.184113988 1.454972926 1.450719121 0.594116238 0.523947263 0.072213827 1.138487872 0.482964014 0.5231244 1 18.81410841 3.735096822 24.52424454 0.596763962 1.372439132 0.590556978 0.283426431 143.0356522 1012718.712 0.072242326 0.117098045 5433.714572 -3.735096822 0.77567517 RDGWPAMCIHGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDGWPAMCIHGDK 13 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 106.19 0.00090476 529180000 732510 682430 626270 537880 614790 430900 673590 598430 739030 683780 FALSE TRUE 703882.6994 662967.7646 739450.9203 565640.0513 634565.2787 439613.0932 681833.5959 586072.2114 655138.4127 637466.9716 1.104186932 1.040003316 1.15998311 0.887324483 0.995448089 0.689624895 1.069598311 0.919376591 1.027721344 1 19.28199107 3.735189435 24.97372397 0.936738194 1.095252341 0.338852352 0.102229712 312.5615545 2315460.986 0.025774237 0.041834255 5434.873443 -3.735189435 0.158514147 S(ph)GSDRLPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSDRLPSR 9 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.5)GS(0.5)DRLPSR 95.094 0.0058876 0 135320 141450 125050 113480 125400 138660 122130 127230 137120 146060 TRUE FALSE 130031.5448 137415.9845 147649.3167 119336.7164 129433.6049 141463.8002 123624.6635 124602.656 121554.7125 136167.2261 0.954940102 1.009170771 1.084323452 0.876398233 0.950548885 1.038897569 0.907888535 0.915070826 0.892686999 1 17.05501998 3.735215724 24.9998801 0.937824212 1.015447373 0.28744071 0.054692226 364.9210336 2727439.549 0.014661583 0.023760407 5435.202438 -3.735215724 0.077623161 KGPSGYGFNLHSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGPSGYGFNLHSDK 14 1 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 142.45 6.10E-06 5986900000 9540100 8943200 8675300 6249300 6246600 4270600 8598700 7646800 9858900 11288500 FALSE TRUE 9167262.345 8688148.692 10243119.69 6571827.122 6447527.562 4356954.458 8703933.463 7488890.908 8739759.004 10523919.84 0.871088196 0.825562036 0.973317913 0.624465714 0.612654568 0.414004907 0.827061931 0.711606609 0.830466132 1 23.32716883 3.735241901 24.98888731 0.696424941 0.883546648 0.205049994 0.15197183 406.6277934 3061785.781 0.039730211 0.064467428 5435.530054 -3.735241901 0.187121707 EKMLRAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKMLRAAR 8 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 0 ;;; 77.282 0.054069 10815630000 10140890 10430800 10317000 3588650 5264910 2484000 7000630 4998970 4504380 5353160 FALSE TRUE 9744572.807 10133323.8 12181511.4 3773860.657 5434260.612 2534228.182 7086305.804 4895739.523 3993061.666 4990585.705 1.952591015 2.030487882 2.440898147 0.756195942 1.088902372 0.507801755 1.419934698 0.98099498 0.800118844 1 22.25077771 3.735255259 24.99988331 0.955420725 2.130241927 0.826750168 0.252670182 106.1264834 802682.6611 0.064971588 0.105419099 5435.697239 -3.735255259 1.174821202 LRVEFPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRVEFPR 7 1 J3KTL2;Q07955;Q07955-3;Q07955-2;Q13242;S4R3G0 J3KTL2;Q13242 SRSF1;SRSF9 Serine/arginine-rich splicing factor 1;Serine/arginine-rich splicing factor 9 0 ; 160.75 0.0012174 863140000 1156780 1297630 1160070 203820 202750 26589.7 457750 203794 238220 505510 FALSE TRUE 1111571.759 1260622.863 1369720.455 214339.1746 209271.6379 27127.36195 463352.0814 199585.5827 211178.2643 471271.3574 2.358666066 2.674940548 2.906436882 0.454810527 0.444057621 0.057562085 0.983195932 0.423504589 0.448103329 1 18.84619848 3.73539439 24.99976328 0.518033687 2.649507173 0.917391674 0.289006195 63.58848256 502080.229 0.073392949 0.119174559 5437.438906 -3.73539439 2.131473486 RRQEIEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 RRQEIEQK 8 2 Q9H307 Q9H307 PNN Pinin 0 ;; 117.04 0.0012128 196212000 163945 162988 138449 112908 118406 66541 139765 130084 134333 151481 FALSE TRUE 157537.8481 158339.7418 163469.8141 118735.1954 122214.6365 67886.50461 141475.4859 127397.7199 119084.081 141221.0569 1.115540781 1.121219068 1.157545607 0.840775434 0.865413694 0.480710923 1.001801636 0.90211561 0.843245927 1 17.10759569 3.735397808 24.25083784 0.842550209 1.130413558 0.475563474 0.136453445 153.9110784 1180118.731 0.03650763 0.059310475 5437.481701 -3.735397808 0.287863348 MTFSEHPYNNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MTFSEHPYNNLR 12 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 0 64.199 0.080309 0 157390 168550 135190 142050 147020 125980 178420 148330 146780 169490 FALSE TRUE 151239.0248 163743.119 159621.8403 149381.2175 151749.0318 128527.4019 180603.5573 145266.9337 130118.1498 158010.2913 0.957146674 1.036281356 1.010199013 0.945389166 0.960374356 0.813411588 1.142986041 0.919351091 0.823478956 1 17.269659 3.735438272 22.14454923 0.946216006 1.004716253 0.080673763 0.088614169 146.036945 1035760.289 0.022954179 0.037373257 5437.988336 -3.735438272 0.058500247 RYPSSISS(ph)SPQK ddPTM_BT-474_Pertuzumab_2h_R1 3 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSISS(0.5)S(0.5)PQK;RYPSSISS(0.5)S(0.5)PQK;RYPSSIS(0.002)S(0.499)S(0.499)PQK 174.24 1.89E-05 10065000000 3435490 3026450 2889180 1871300 1876330 528984 3185610 2135570 2511640 3235280 TRUE FALSE 3301227.253 2940138.609 3411319.095 1967878.017 1936683.858 539680.4189 3224596.448 2091469.733 2226529.157 3016151.604 1.094516353 0.974798019 1.131017118 0.652446652 0.642104281 0.178930137 1.069109538 0.693423278 0.738202003 1 21.52427752 3.735622734 24.92764702 0.6954194 1.057579258 0.337488413 0.227883422 270.904715 2298605.309 0.059463537 0.096735889 5440.298559 -3.735622734 0.362159858 LKPPVHYNGPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKPPVHYNGPSK 12 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 85.258 0.0070749 505820000 828850 740170 701210 638420 766640 550320 760740 723670 876390 855280 FALSE TRUE 796457.6257 719061.0763 827934.2453 671368.9327 791299.6718 561447.8475 770050.1637 708725.9616 776905.8813 797351.1238 0.998879417 0.901812332 1.038355902 0.841999105 0.992410556 0.704141288 0.965760429 0.888850521 0.974358546 1 19.60485565 3.735654565 24.98276967 0.902687699 0.971895526 0.10894891 0.089435326 538.7947417 4631922.856 0.022057384 0.035878302 5440.69731 -3.735654565 0.069207826 DPIPEVDLDDLS ddPTM_BT-474_Pertuzumab_2h_R1 1 DPIPEVDLDDLS 12 0 Q92539 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 0 88.948 0.013284 0 28571 29100 22642 31013 33422 29992 30495 33850 36067 32674 FALSE TRUE 27454.41373 28270.09649 26733.91307 32613.58465 34497.04898 30598.45879 30868.20693 33150.98567 31972.82537 30460.96088 0.901298349 0.928076321 0.8776451 1.070668282 1.132500354 1.004513906 1.013369442 1.088310569 1.049632856 1 14.89467383 3.735665203 24.99387102 1.055955045 0.904913559 0.743100375 0.040057909 119.7463193 1033679.429 0.010667159 0.017353708 5440.830589 -3.735665203 -0.151041486 RFNDGSDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFNDGSDEK 9 1 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 89.9 0.018911 383470000 857260 836450 853190 505630 625250 700100 693240 644880 719700 657260 FALSE TRUE 823757.3314 812595.265 1007380.412 531725.6249 645361.7341 714256.5017 701724.0785 631563.0026 638002.6732 612743.1948 1.344376141 1.326159592 1.644049939 0.867778915 1.053233622 1.165670231 1.145217253 1.030714022 1.041223597 1 19.22492303 3.735751344 24.99993524 1.054808759 1.42699166 0.725547137 0.111050679 129.606148 1153377.23 0.02932773 0.047729361 5441.909867 -3.735751344 0.372182901 IIPTLEEYQHYK ddPTM_BT-474_Pertuzumab_2h_R1 1 IIPTLEEYQHYK 12 0 P61978-3;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 181.49 1.81E-05 1118100000 778470 810510 678590 641040 649550 697210 692070 662440 813260 784530 FALSE TRUE 748046.5318 787395.0484 801226.3082 674124.1512 670443.3657 711308.0639 700539.7597 648760.3825 720942.1343 731393.0843 1.02276949 1.0765689 1.095479743 0.921698832 0.916666263 0.972538679 0.957815674 0.887020121 0.985710898 1 19.48028746 3.735774188 24.99928618 0.941070388 1.066102333 0.674385705 0.036713352 126.6899941 1136641.075 0.009577562 0.01557981 5442.196115 -3.735774188 0.125031945 NFEVEADDLVTISELGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFEVEADDLVTISELGR 17 0 P46734-2;P46734;P46734-3;E9PRZ0;J3QR49 P46734-2 MAP2K3 Dual specificity mitogen-activated protein kinase kinase 3 0 ; 179.56 2.12E-09 34920000 22860 24609 19123.9 25175 26709 22801 25288 29544 30646 25587 FALSE TRUE 21966.60593 23907.17541 22580.01414 26474.28477 27568.11924 23262.05184 25597.48211 28933.90608 27167.19456 23853.9697 0.92087842 1.002230476 0.946593562 1.109848176 1.155703625 0.975185771 1.07309108 1.21295979 1.138896163 1 14.54194175 3.73579996 24.33919144 1.106537671 0.961133779 0.450081154 0.069313861 147.9828269 1304690.632 0.01928695 0.031433707 5442.519076 -3.73579996 -0.145403892 YKVEGFPTIYFAPSGDK ddPTM_BT-474_Pertuzumab_2h_R1 1 YKVEGFPTIYFAPSGDK 17 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 156.11 6.88E-08 736260000 1451000 1520200 1299600 1129500 1029800 1095400 1297500 1225600 1585300 1660800 FALSE TRUE 1394293.316 1476845.384 1534466.629 1187793.63 1062924.452 1117549.739 1313379.193 1200290.932 1405343.39 1548312.537 0.900524463 0.953841908 0.991057421 0.767153661 0.6865051 0.721785629 0.848264909 0.775225223 0.907661313 1 20.56226529 3.735900721 24.99365465 0.7976361 0.949011332 0.306932908 0.089048853 238.0364372 2236707.907 0.022850637 0.037259348 5443.781941 -3.735900721 0.151375232 RAPFDLFENR ddPTM_BT-474_Pertuzumab_2h_R1 6 RAPFDLFENR 10 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 214.67 1.37E-08 13941180000 6891670 7764030 6329330 2812700 3028080 461475 4798100 2590030 2946370 4080610 FALSE TRUE 6622335.917 7542607.466 7473180.726 2957863.784 3125480.943 470806.3407 4856820.583 2536544.975 2611910.43 3804226.65 1.740783746 1.982691401 1.964441505 0.777520389 0.82158116 0.123758752 1.276690647 0.666770203 0.686581182 1 21.85917177 3.735931706 24.14971806 0.75330796 1.90464421 0.773905251 0.280147226 59.56911856 547217.7609 0.071090207 0.115989584 5444.170354 -3.735931706 1.15133625 IAGHPLAQNER ddPTM_BT-474_Pertuzumab_2h_R1 1 IAGHPLAQNER 11 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 60.255 0.094806 128750000 126160 151310 134570 69596 77293 59330 113940 91198 81916 106540 FALSE TRUE 121229.5277 146994.7869 158889.7925 73187.8579 79779.19954 60529.69325 115334.4318 89314.72943 72617.2391 99323.9509 1.220546773 1.479953079 1.599712769 0.736860115 0.803222172 0.60941689 1.161194563 0.899226507 0.731115088 1 16.59985403 3.735953489 24.99983112 0.854830882 1.438059106 0.71629077 0.168587264 119.1811367 1142833.647 0.045187429 0.073680598 5444.443423 -3.735953489 0.583228224 DYFFALAHTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYFFALAHTVR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 193.28 1.02E-06 782100000 1291450 1460590 1195070 555550 529800 103390 1026090 486600 612410 888740 FALSE TRUE 1240978.706 1418935.403 1411045.733 584222.0021 546841.4982 105480.6166 1038647.596 476551.54 542891.7842 828544.8482 1.49778097 1.712563184 1.703040863 0.70511814 0.660002291 0.127308277 1.253580417 0.575166862 0.655235242 1 19.66022027 3.735981917 24.5493985 0.693647351 1.645271871 0.699379255 0.278300662 88.22482036 839909.5782 0.070885365 0.115644756 5444.799812 -3.735981917 0.95162452 IVDAVIQEHQPSVLLELGAYCGYSAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 IVDAVIQEHQPSVLLELGAYCGYSAVR 27 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 246.21 1.76E-45 2544400000 381610 372600 289680 408750 423680 455870 425980 376770 443160 454090 FALSE TRUE 366696.2593 361973.8128 342031.6199 429845.6365 437308.052 465088.0037 431193.2707 368989.5678 392854.3347 423334.0798 0.866210109 0.855054743 0.807947284 1.015381603 1.033009325 1.098631142 1.018564985 0.871627363 0.928000729 1 18.69143711 3.735990292 24.93422018 0.989776995 0.844269112 0.579810078 0.059160607 187.2694321 1816667.619 0.018599721 0.030329645 5444.904819 -3.735990292 -0.145507883 VACAEEWQESR ddPTM_BT-474_Pertuzumab_2h_R1 2 VACAEEWQESR 11 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 125.74 0.00074911 548160000 265350 261460 210490 268460 289840 251960 267260 309870 272960 322350 FALSE TRUE 254979.8286 254003.4168 248530.2253 282315.2528 299162.9668 257054.8038 270530.8078 303471.0762 241974.7251 300516.9474 0.848470713 0.845221606 0.827009017 0.939432053 0.995494495 0.855375399 0.900218141 1.009830157 0.805194939 1 18.19708683 3.736006734 24.86945595 0.932400312 0.840732559 0.304175237 0.061655108 243.7048301 2373180.349 0.015780058 0.025737888 5445.110959 -3.736006734 -0.091667753 VRVDSTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VRVDSTAK 8 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 102.07 0.0045933 747000000 1038560 1035150 904600 697670 714080 385820 1015780 758230 905100 1042360 FALSE TRUE 997971.927 1005628.536 1068081.343 733676.8323 737049.0317 393621.5447 1028211.419 742572.2855 802356.8425 971760.0288 1.026973633 1.034852747 1.099120473 0.754997953 0.75846815 0.40506044 1.058091904 0.764151914 0.825673848 1 19.89024057 3.736051484 24.85265577 0.783091489 1.051769339 0.338323176 0.165012929 217.3917267 2153244.418 0.042678158 0.069660316 5445.672058 -3.736051484 0.26867785 IKLEAER ddPTM_BT-474_Pertuzumab_2h_R1 2 IKLEAER 7 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 88.37 0.017016 574950000 835730 858700 731510 466830 502150 136250 740400 512540 561490 646730 FALSE TRUE 803068.7477 834210.7168 863710.1294 490923.1522 518302.1108 139005.0684 749461.2367 501955.8699 497752.0092 602926.4011 1.331951539 1.3836029 1.432529954 0.814233962 0.859644079 0.230550641 1.243039342 0.832532576 0.825560148 1 19.20162238 3.736107434 24.71930422 0.825106422 1.382785632 0.532142915 0.23773472 138.0422597 1390976.351 0.062001439 0.101277017 5446.373662 -3.736107434 0.55767921 LGLPLLTDCAQPSRPHGS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGLPLLTDCAQPSRPHGSPSR 21 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 LGLPLLTDCAQPS(0.045)RPHGS(0.933)PS(0.022)R;LGLPLLTDCAQPSRPHGS(0.995)PS(0.004)R;LGLPLLTDCAQPS(0.004)RPHGS(0.946)PS(0.05)R 151.06 3.97E-08 1172680000 282507 292957 226517 298195 289227 320117 314861 309847 325354 316653 TRUE FALSE 271466.3141 284602.1532 267453.6607 313584.8797 298530.2491 326589.9851 318714.3631 303448.5512 288421.1779 295205.8103 0.919583235 0.964080459 0.905990504 1.062258495 1.011261428 1.106312863 1.079634452 1.027922014 0.97701728 1 18.17136159 3.736209549 24.99947429 1.04230964 0.933304303 0.618080419 0.038721041 130.1946018 1384394.857 0.010316487 0.016847951 5447.654414 -3.736209549 -0.109005337 DKVNCSFYFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKVNCSFYFK 10 1 P0DN76;Q01081;Q8WU68-3;Q8WU68;A0A1B0GW87;M0QYK5;M0R2N4;Q01081-3;Q8WU68-2;Q01081-2 P0DN76;Q01081-2 U2AF1;U2AF1L4 Splicing factor U2AF 35 kDa subunit;Splicing factor U2AF 26 kDa subunit 0 ; 128.08 0.00030922 2396360000 4856300 4997400 4354500 3577400 3724100 2324300 4705200 4230700 4864700 5145400 FALSE TRUE 4666510.427 4854879.045 5141455.015 3762030.043 3843889.059 2371298.939 4762783.645 4143334.567 4312479.65 4796897.475 0.972818463 1.012087306 1.071829248 0.784263175 0.801328167 0.494340134 0.992888355 0.863752996 0.899014347 1 22.19367017 3.736251223 24.99399315 0.82504403 1.01822924 0.281846824 0.135023969 255.2726964 2762761.716 0.036159028 0.059046564 5448.177187 -3.736251223 0.19318521 KVEWTSDTVDNEHMGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVEWTSDTVDNEHMGR 16 1 O60927 O60927 PPP1R11 Protein phosphatase 1 regulatory subunit 11 0 ; 213.99 3.15E-13 626970000 703450 717020 567140 703360 764510 748410 716550 696050 796300 763580 FALSE TRUE 675958.3963 696571.2916 669634.814 739660.4939 789101.1585 763543.363 725319.3532 681676.3243 705907.3624 711862.0465 0.949563753 0.978520059 0.940680596 1.039050329 1.108502922 1.072600185 1.018904375 0.957596107 0.991635059 1 19.44123816 3.736253596 24.98668214 1.025704496 0.958481327 0.3873385 0.040666054 263.7596293 2856708.87 0.012797592 0.020946292 5448.206957 -3.736253596 -0.067223169 SPS(ph)PSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 S(0.017)PS(0.983)PSFR;S(0.038)PS(0.936)PS(0.026)FR;S(0.291)PS(0.709)PSFR;S(0.171)PS(0.829)PSFR 132.38 0.0035397 2234440000 2255460 2471800 1896800 2483640 2627490 2589630 2476670 2693910 2584310 2892430 TRUE FALSE 2167314.13 2401306.684 2239593.954 2611820.958 2712005.602 2641994.093 2506980.228 2638279.817 2290949.963 2696523.14 0.803743939 0.890519591 0.830548761 0.968588372 1.005741639 0.979778016 0.929708405 0.978400585 0.849594031 1 21.36266898 3.736287183 24.98785279 0.960058344 0.846495643 0.570950588 0.046501579 139.4032452 1532217.949 0.011824599 0.019344384 5448.628319 -3.736287183 -0.113562701 TQHIQQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQHIQQPR 8 0 P51397 P51397 DAP Death-associated protein 1 0 118.26 0.0044304 0 54124 56598 44892 29365 28374 11728 45537 29993 29452 40488 FALSE TRUE 52008.77424 54983.88046 53004.98302 30880.53117 29286.67548 11965.1482 46094.29543 29373.63407 26108.73243 37745.7117 1.377872397 1.456692111 1.404265031 0.818120252 0.775894113 0.316993578 1.221179661 0.778197913 0.691700627 1 15.20402513 3.736297819 5.636005203 0.793516948 1.421396609 0.628207393 0.216028234 0.100576335 12.63840483 0.056485128 0.095371201 5448.761757 -3.736297819 0.627879661 RDELTLEGIK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDELTLEGIK 10 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 196.24 5.40E-07 1603430000 1922030 1881530 1687020 1473260 1527190 1159850 1831870 1818460 1916030 2044190 FALSE TRUE 1846914.943 1827870.607 1991902.042 1549295.125 1576313.453 1183302.962 1854288.973 1780908.166 1698530.307 1905735.191 0.969135141 0.959141971 1.045214493 0.812964536 0.827141914 0.620916782 0.97300453 0.934499281 0.891272993 1 20.86191623 3.736400056 24.96585764 0.8624313 0.987961679 0.241245118 0.101814387 285.0866626 3294259.305 0.028214297 0.046192528 5450.044592 -3.736400056 0.125530379 AGFESER ddPTM_BT-474_Pertuzumab_2h_R1 4 AGFESER 7 0 Q13946-3;Q13946-2;Q13946;E5RG23 Q13946-3 PDE7A "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A" 0 ;;; 114.94 0.013473 1631250000 1778780 1820380 1434300 2066600 1946560 2628430 2017570 2203730 2286430 2063410 FALSE TRUE 1709263.311 1768464.545 1693509.916 2173257.474 2009172.87 2681578.655 2042261.625 2158222.205 2026884.052 1923653.403 0.888550561 0.919325977 0.880361251 1.12975522 1.044456796 1.394003021 1.061657793 1.121939224 1.053663851 1 20.87541745 3.736458577 24.3984745 1.12508548 0.898403923 0.489017579 0.102215554 104.0740216 1207999.122 0.026322346 0.043134632 5450.779039 -3.736458577 -0.226681557 RYPSS(ph)ISSS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RYPS(0.354)S(0.645)IS(0.001)S(0.003)S(0.997)PQK;RYPS(0.471)S(0.523)IS(0.008)S(0.073)S(0.925)PQK 224.07 1.40E-11 1266650000 2343700 2021500 1829600 1646530 1606640 1538950 1588740 2059900 2088190 2044010 TRUE FALSE 2252105.613 1963848.799 2160249.419 1731507.611 1658319.035 1570068.623 1608183.475 2017362.345 1851147.426 1905567.382 1.181855669 1.03058481 1.133651552 0.908657247 0.870249486 0.823937604 0.843939443 1.058667547 0.971441599 1 20.86178919 3.736475361 24.9375611 0.924517069 1.106886096 0.566672649 0.076065853 144.6107962 1729405.454 0.021967946 0.035995539 5450.989694 -3.736475361 0.182369027 LGPNYLHIPVNCPYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGPNYLHIPVNCPYR 15 0 P04040 P04040 CAT Catalase 0 66.533 0.058292 367170000 191200 225930 186210 114860 121850 45714 187640 136670 124520 175680 FALSE TRUE 183727.6926 219486.6976 219862.2892 120787.9384 125769.4159 46638.3684 189936.3944 133847.7167 110385.0116 163781.0371 1.121788553 1.340122773 1.342416027 0.73749648 0.767911952 0.28476049 1.159697104 0.817235738 0.673979195 1 17.3214088 3.73651714 24.91277525 0.775328847 1.2753105 0.510621884 0.220150048 134.7377459 1642642.004 0.057839488 0.094740203 5451.514098 -3.73651714 0.499981653 LDRLDLAR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDRLDLAR 8 1 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ;; 132.84 0.00086181 420210000 987230 1111130 835380 733810 762060 312490 1003570 790510 804350 895300 FALSE TRUE 948647.9602 1079441.66 986351.7489 771682.022 786572.352 318808.7619 1015851.99 774185.6923 713043.5601 834660.5335 1.136567409 1.293270278 1.181740012 0.924545957 0.942385941 0.381962186 1.217084011 0.927545584 0.854291693 1 19.67083003 3.7365546 3.423553613 0.889129486 1.221352343 0.341973183 0.19874946 0.270881483 6.776409046 0.053827627 0.096246167 5451.984339 -3.7365546 0.332222857 SCSSISTALPQVNEDLVSLPHQLPEASEPPQS(ph)PSEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SCSSISTALPQVNEDLVSLPHQLPEASEPPQSPSEKR 37 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 SCSSISTALPQVNEDLVSLPHQLPEAS(0.001)EPPQS(0.966)PS(0.033)EKR;SCSSISTALPQVNEDLVSLPHQLPEAS(0.03)EPPQS(0.967)PS(0.003)EKR 272.75 1.63E-76 379420000 221770 214938 190662 183287 185731 208181 193311 217093 233517 209482 TRUE FALSE 213102.9832 208808.1787 225118.8647 192746.464 191705.2063 212390.5625 195676.7978 212609.9537 207009.1291 195293.5976 1.09119288 1.069201353 1.152720148 0.986957414 0.981625658 1.087544933 1.001962175 1.088668325 1.059989328 1 17.57528513 3.736618652 24.99820574 1.03515493 1.100854448 0.396110763 0.041876573 193.3194246 2488542.263 0.011241673 0.018440804 5452.788485 -3.736618652 0.065699517 QPS(ph)DSVSDTVALGVPGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPSDSVSDTVALGVPGPR 18 0 F8VW41;Q86VP3-4;Q86VP3;Q86VP3-3;Q86VP3-2 F8VW41 PACS2 Phosphofurin acidic cluster sorting protein 2 1 QPS(1)DSVSDTVALGVPGPR 112.82 0.00027784 76336000 17142 16919 12259 20853 19181 20183 20000 24978 19786 19014 TRUE FALSE 16472.07169 16436.48669 14474.474 21929.22583 19797.97428 20591.11409 20244.76598 24462.19557 17539.97623 17726.16484 0.929251862 0.927244377 0.816559821 1.237110566 1.116878606 1.161622622 1.142083816 1.380004969 0.989496396 1 14.11359281 3.736700408 24.99973943 1.1739704 0.89464125 0.516783207 0.111139358 115.6012736 1553595.916 0.029032017 0.047626885 5453.815074 -3.736700408 -0.27932915 VNIVDLQQVINVDLIHIENR ddPTM_BT-474_Pertuzumab_2h_R1 1 VNIVDLQQVINVDLIHIENR 20 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 205.02 9.06E-22 477350000 102010 109300 83560 113100 115940 128100 118000 107660 130260 117170 FALSE TRUE 98023.33642 106182.871 98661.15078 118937.1046 119669.3154 130690.2698 119444.1193 105436.7834 115473.4309 109233.9715 0.897370434 0.972068208 0.903209408 1.088828895 1.095532037 1.196425141 1.093470443 0.965238029 1.057120136 1 16.73706208 3.736706311 24.98160648 1.070580847 0.929001232 0.548914573 0.060907079 140.2845487 1889947.477 0.017921829 0.029419413 5453.889204 -3.736706311 -0.141579616 IGKPHTVPCK ddPTM_BT-474_Pertuzumab_2h_R1 2 IGKPHTVPCK 10 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 110.14 0.0011573 4281100000 5737400 5410400 4889900 4444700 4496700 3719400 5433500 5647100 5619100 5548000 FALSE TRUE 5513176.065 5256100.689 5773613.705 4674091.5 4641340.439 3794608.816 5499996.798 5530485.412 4981243.325 5172229.018 1.065918784 1.016215769 1.11627186 0.903689973 0.897357875 0.733650579 1.063370701 1.069265377 0.96307478 1 22.30235473 3.736835615 24.99112116 0.953479069 1.061143501 0.252779726 0.093151741 264.5658451 3832942.367 0.027667937 0.045431378 5455.513253 -3.736835615 0.107664431 FSGDLDDQTCR ddPTM_BT-474_Pertuzumab_2h_R1 4 FSGDLDDQTCR 11 0 P05455 P05455 SSB Lupus La protein 0 ;;; 270.54 1.19E-26 7628900000 9219900 9720100 7407900 9141700 9066100 9486600 8707000 9462700 10316300 10242900 FALSE TRUE 8859576.115 9442892.265 8746672.318 9613504.233 9357719.34 9678425.552 8813558.871 9267291.938 9145236.873 9549139.26 0.927787927 0.988873657 0.915964474 1.006740395 0.979954223 1.013539052 0.922968933 0.970484531 0.957702744 1 23.18693927 3.736876113 24.99419532 0.975320293 0.948675185 0.203195405 0.030455002 302.850154 4493635.414 0.00785951 0.012899905 5456.022002 -3.736876113 -0.026645107 T(ph)S(ph)NLS(ph)VLRT(ph)ALRY(ph)IQSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSNLSVLRTALRYIQSLK 18 2 Q99583 Q99583 MNT Max-binding protein MNT 5 T(0.994)S(0.994)NLS(0.993)VLRT(0.972)ALRY(0.97)IQS(0.077)LK 42.338 0.07773 70849000 37363 65456 38962 77365 100800 77881 78544 76895 57600 76525 TRUE FALSE 35902.81265 63589.25897 46003.30011 81357.81692 104042.3235 79455.80718 79505.24497 75307.09138 51061.48948 71341.89359 0.503250066 0.891331247 0.644828694 1.140393292 1.458362237 1.113732804 1.114425774 1.055580215 0.715729383 1 16.12246189 3.736933709 24.86388291 1.102975215 0.700956111 0.48091187 0.192155429 116.6686833 1783045.221 0.051657909 0.08492386 5456.745626 -3.736933709 -0.402019103 HTQLEQMFR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTQLEQMFR 9 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 101.38 0.0040217 327190000 310260 311710 267310 249270 273700 241560 286690 259400 315860 321560 FALSE TRUE 298134.6962 302820.336 315618.8633 262134.8546 282503.8091 246444.5087 290198.598 254043.2994 280004.897 299780.4548 0.99451012 1.010140358 1.052833359 0.874422766 0.942369006 0.822083311 0.968037086 0.847431163 0.934033198 1 18.1935468 3.736997792 24.99899767 0.903854439 1.01825919 0.451318318 0.053215739 105.0987268 1681170.266 0.012760825 0.020992712 5457.550868 -3.736997792 0.114404751 S(ph)MDELNHDFQALALEGR ddPTM_BT-474_Pertuzumab_2h_R1 7 SMDELNHDFQALALEGR 17 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 1 S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR 282.75 3.01E-36 1265407000 551944 543632 460559 451363 461890.8 467608 435236 532673 562164 516831 TRUE FALSE 530373.4183 528128.1476 543792.2564 474657.8985 476747.9371 477063.3541 440562.5484 521673.1164 498349.4995 481825.576 1.100758126 1.096098202 1.128608118 0.985123916 0.989461666 0.990116295 0.914361068 1.082701173 1.034294409 1 18.87815145 3.737007556 24.9998226 1.001771078 1.107249157 0.602643651 0.040544127 103.2177023 1661520.195 0.011398067 0.018749309 5457.67357 -3.737007556 0.105478079 VGIDT(ph)PDIDIHGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VGIDT(1)PDIDIHGPEGK 147.16 3.88E-06 527860000 296430 290730 249600 158370 186560 220440 129370 155570 195280 157550 TRUE FALSE 284845.1879 282438.6651 294708.2723 166543.4947 192560.8718 224897.4478 130953.2688 152357.4251 173112.6331 146878.9982 1.939318701 1.92293431 2.006469788 1.133882289 1.311017056 1.531174985 0.891572453 1.037298913 1.17860712 1 17.1642686 3.737136151 24.9903498 1.154748306 1.952910306 0.829077099 0.166756251 50.78014931 890873.9956 0.047559977 0.078287709 5459.289831 -3.737136151 0.798162 NALLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 NALLHK 6 0 A0A1B0GVP4;A8MVM7 A0A1B0GVP4 Putative uncharacterized protein ENSP00000382790 0 91.584 0.047726 676630000 1834300 1749600 1623700 1430000 1540600 1533000 1611700 1646200 2012700 1995800 FALSE TRUE 1762613.528 1699703.121 1917138.709 1503802.471 1590154.798 1563998.31 1631424.467 1612205.395 1784226.734 1860622.688 0.947324538 0.913513058 1.030374789 0.808225376 0.854635821 0.840577899 0.876816389 0.866487013 0.958940652 1 20.82735409 3.737202893 24.99999221 0.876680974 0.958715018 0.24702691 0.059884766 149.1163839 2745723.513 0.014943724 0.024620173 5460.128873 -3.737202893 0.082034044 VAYVSFGPHAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAYVSFGPHAGK 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 174.42 3.04E-05 1790600000 4783100 4847800 4479400 2607090 3573600 1538130 3685000 3346300 3487100 4096500 FALSE TRUE 4596171.164 4709545.49 5288927.224 2741642.227 3688548.089 1569232.042 3730098.132 3277197.736 3091259.027 3819040.406 1.203488488 1.233175088 1.384883809 0.717887725 0.965831124 0.410896947 0.976710832 0.858120729 0.809433444 1 21.86477875 3.737224061 24.99296328 0.815528399 1.269781736 0.609945552 0.16634164 74.53764915 1393825.119 0.042073809 0.069333986 5460.395013 -3.737224061 0.454253337 HNTPS(ph)LLEAALTQEASTPDSQVWPTAPDITR ddPTM_BT-474_Pertuzumab_2h_R1 1 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNT(0.4)PS(0.599)LLEAALTQEASTPDSQVWPTAPDITR 199.04 7.50E-26 63469000 32267 33504 28415 24598 25318 32437 30614 13502 41021 33136 TRUE FALSE 31005.96997 32548.49872 33550.22259 25867.50573 26132.37646 33092.89836 30988.66329 13223.17898 36364.46805 30891.66921 1.003700051 1.053633538 1.086060529 0.837361865 0.845936045 1.071256401 1.003139814 0.428049999 1.177160995 1 14.91493021 3.737285114 24.7964139 0.868490095 1.048381593 0.072511317 0.192542506 204.039747 3966661.682 0.053171393 0.087610472 5461.162679 -3.737285114 0.179891498 GGHFYSAKPEILR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGHFYSAKPEILR 13 1 P52701;P52701-2;A0A087WWJ1;A0A494C0M1;C9J7Y7;C9J8Y8;C9JH55 P52701 MSH6 DNA mismatch repair protein Msh6 0 ; 113.99 0.00046779 652480000 775240 830960 661170 574150 627270 452690 664880 567530 722090 745720 FALSE TRUE 744942.7637 807261.8344 780658.1266 603781.9503 647446.7092 461843.702 673017.0003 555810.3072 640121.3704 695211.7202 1.071533667 1.161174087 1.122907028 0.868486438 0.931294296 0.664320938 0.968074877 0.799483511 0.92075745 1 19.40709288 3.737294651 8.130330043 0.865370095 1.123170085 0.583918265 0.092175689 0.068445164 52.76289238 0.022564124 0.037615654 5461.282611 -3.737294651 0.25779999 LFPDIPIGYSGHETGIAISVAAVALGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFPDIPIGYSGHETGIAISVAAVALGAK 28 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 148.28 7.94E-14 0 19894 20194 14915 22255 20244 22117 23994 23949 20065 23205 FALSE TRUE 19116.52049 19618.08689 17610.47228 23403.58322 20895.16665 22564.22089 24287.64575 23454.44478 17787.30532 21633.30468 0.883661593 0.906846512 0.814044481 1.081831166 0.965879553 1.043031623 1.122696976 1.084182242 0.822218592 1 14.40096645 3.737340899 24.99327255 1.029343566 0.872050425 0.403808311 0.081953778 100.6231177 2061884.325 0.021625626 0.035645412 5461.864208 -3.737340899 -0.157293141 SSS(ph)YSEANEPDLQMANGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSYSEANEPDLQMANGGK 19 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 S(0.108)S(0.108)S(0.777)YS(0.008)EANEPDLQMANGGK 329.08 3.41E-75 164910000 146910 152470 122410 161630 169960 177560 149880 180580 185790 183470 TRUE FALSE 141168.5948 148121.7049 144532.21 169971.7437 175426.9178 181150.3849 151714.2763 176850.9599 164699.8981 171043.4135 0.825337801 0.865988943 0.845003073 0.993734516 1.025628021 1.059090094 0.8869928 1.03395364 0.962912834 1 17.38400302 3.737359629 21.49982179 0.995654912 0.847497804 0.698828142 0.044867003 7.965389185 142610.0699 0.011444511 0.01890426 5462.099778 -3.737359629 -0.148157108 ICSWNVDGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ICSWNVDGLR 10 0 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 131.52 0.00057706 134232000 319170 363640 293370 135249 144343 24939.9 259770 126764 147084 212070 FALSE TRUE 306696.4835 353269.3432 346388.485 142229.2171 148985.9237 25444.20187 262949.143 124146.2791 130387.6409 197706.31 1.551273116 1.78683899 1.752035557 0.719396448 0.75357192 0.128696964 1.329998739 0.627932812 0.659501667 1 17.59299939 3.737442256 24.74018021 0.734784384 1.705728251 0.692724992 0.290209522 44.47314291 983835.0129 0.073614293 0.121520133 5463.139067 -3.737442256 0.970943867 AIGVKPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIGVKPPR 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 112.17 0.0028202 9810100000 3020200 3565000 2564000 3376900 3378400 3845300 3865400 4025300 4367000 4564200 FALSE TRUE 2902167.245 3463329.691 3027371.836 3551182.214 3487069.304 3923054.601 3912705.921 3942176.148 3871276.468 4255062.669 0.682050412 0.813931535 0.711475264 0.834578123 0.819510681 0.921973401 0.919541315 0.926467236 0.909804807 1 22.02074895 3.737472152 0.317774673 0.992182307 0.60140978 0.840522524 0.03823099 1.385145362 0.182639426 0.042159446 0.200019422 5463.515148 -3.737472152 -0.390772528 QKEGESEDLASR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKEGESEDLASR 12 1 Q08379;B7ZC06;H0Y7B8 Q08379 GOLGA2 Golgin subfamily A member 2 0 135.02 0.00012315 306430000 472760 484180 398640 485430 480620 502880 512110 552990 601890 572920 FALSE TRUE 454284.0165 470371.6605 470683.1157 510483.1005 496079.5788 513048.5782 518377.3554 541570.5633 533565.9705 534115.6181 0.85053498 0.880655133 0.881238256 0.955753929 0.928786881 0.960557154 0.970533978 1.013957549 0.99897092 1 19.02679255 3.73750735 0.437380486 1.012455166 0.809374584 0.917662388 0.015475604 0.573710743 0.159198601 0.013216534 0.056205743 5463.957975 -3.73750735 -0.203080583 EKEEDSSGHTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEEDSSGHTR 11 1 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 94.191 0.00522 282770000 445030 443630 347970 433170 450180 477990 405790 403280 516640 507030 FALSE TRUE 427637.7356 430978.1068 410855.9196 455525.9556 464660.4485 487655.2853 410756.1794 394952.1271 457993.1931 472688.4065 0.904692668 0.911759419 0.869189754 0.96369183 0.983016385 1.031663308 0.868978747 0.835544349 0.968911416 1 18.85052995 3.737692154 24.99767028 0.937016415 0.896868495 0.135380507 0.057222905 235.6993263 6784351.379 0.017417537 0.028825388 5466.283522 -3.737692154 -0.04014792 LLHEMILVCDAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLHEMILVCDAYR 13 0 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 114.56 0.00073315 158510000 317210 383820 303370 158080 178650 45525 325460 119690 179470 239780 FALSE TRUE 304813.0825 372873.8294 358195.7074 166238.5277 184396.4395 46445.54669 329443.0768 117218.3597 159097.318 223539.487 1.363576013 1.668044578 1.602382256 0.743665157 0.824894259 0.207773344 1.473757864 0.524374289 0.71171908 1 17.77017017 3.737705524 24.92706046 0.769722755 1.557005349 0.55244717 0.313618732 49.5423238 1444235.639 0.078174932 0.129360541 5466.451815 -3.737705524 0.787282594 YIS(ph)PDQLADLYK ddPTM_BT-474_Pertuzumab_2h_R1 1 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 1 YIS(1)PDQLADLYK 127.36 0.00021276 0 24506 31794 24825 22606 26356 23016 24710 25203 27819 25853 TRUE FALSE 23548.27843 30887.26625 29311.42973 23772.69837 27203.76468 23481.39929 25012.40837 24682.54924 24661.10375 24101.95328 0.977027801 1.281525439 1.21614333 0.986339078 1.128695436 0.974252958 1.037775158 1.024089166 1.023199384 1 14.55686245 3.737741173 24.99988961 1.028572598 1.170561518 0.352509349 0.082191806 71.23888872 2173403.83 0.020388589 0.033723068 5466.900544 -3.737741173 0.141988919 LVEHFCAEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEHFCAEFK 10 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 121.6 0.00051065 1422260000 3388400 3457200 2949900 2464500 2627500 1263150 3447400 2521700 3530000 4075900 FALSE TRUE 3255977.582 3358604.041 3483012.55 2591693.14 2712015.924 1288691.758 3489590.312 2469626.014 3129289.199 3799835.663 0.856873263 0.883881394 0.916621891 0.682054007 0.713719267 0.339144077 0.918352956 0.64992969 0.823532773 1 21.85750559 3.737769174 24.99591562 0.709054432 0.88560111 0.138182696 0.168650887 115.6681809 3653151.554 0.042203751 0.069849543 5467.253034 -3.737769174 0.176546678 IIYIVHDEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 IIYIVHDEVK 10 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;; 187.64 1.21E-06 2688890000 6819050 6377050 5765260 4314300 4914900 2006433 6362650 5015540 5777120 6385440 FALSE TRUE 6552553.987 6195182.778 6807170.73 4536961.54 5072992.222 2047004.45 6440518.014 4911967.346 5121325.557 5952948.461 1.100724125 1.040691486 1.14349566 0.762136875 0.852181445 0.343863963 1.081903876 0.825131845 0.860300671 1 22.50517297 3.73779542 24.99414869 0.809934106 1.089542539 0.321143387 0.184275219 79.4782494 2596077.636 0.047641122 0.078896648 5467.583446 -3.73779542 0.279608433 LIKDDFLQQNGYTPYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIKDDFLQQNGYTPYDR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 223.65 2.71E-15 2465400000 1375560 1588250 1284930 1220450 1112360 1294610 1416940 1369850 1429370 1707870 FALSE TRUE 1321801.594 1542954.665 1517145.434 1283437.571 1148140.07 1320787.901 1434280.936 1341562.119 1267113.91 1592194.444 0.830175987 0.969074268 0.952864419 0.806080926 0.721105437 0.829539323 0.900820212 0.842586861 0.795828622 1 20.6025851 3.73779781 24.99885778 0.834470244 0.922541831 0.161930888 0.076589489 103.6964874 3398391.197 0.019707048 0.032641353 5467.613538 -3.73779781 0.088071586 LDPHLVLDQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDPHLVLDQLR 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;; 114.82 0.0012066 665028000 3682080 4087940 3269050 1340423 1272245 153566 2744020 1148860 1463641 2239720 FALSE TRUE 3538180.243 3971355.954 3859840.055 1409602.392 1313167.916 156671.2097 2777602.138 1125135.64 1297494.61 2088021.769 1.694513101 1.901970569 1.848563129 0.675089892 0.62890528 0.075033322 1.330255354 0.538852447 0.621398986 1 20.99370532 3.737920976 24.78492274 0.679040687 1.823711158 0.73645168 0.306734268 23.54847522 912474.9472 0.077945526 0.129194479 5469.164371 -3.737920976 1.144670471 KLDPDSIPSPIQVIENDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLDPDSIPSPIQVIENDR 18 1 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 0 104.89 0.0007914 18629000 13461 15921 10348 18108 15464 16548 20605 17651 17758 17553 FALSE TRUE 12934.92924 15466.94867 12218.11379 19042.55605 15961.4136 16882.6119 20857.17015 17286.50068 15742.18629 16364.11968 0.790444552 0.945174502 0.746640457 1.163677389 0.975390911 1.0316847 1.274567197 1.056366063 0.961994082 1 13.99824837 3.73798435 24.99998362 1.075033947 0.839195301 0.541979482 0.100204947 39.07268302 1695100.929 0.026045416 0.043205509 5469.962517 -3.73798435 -0.235838647 WYHPGCFVK ddPTM_BT-474_Pertuzumab_2h_R1 2 WYHPGCFVK 9 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 100.15 0.0048555 1139560000 3356800 3849600 3049500 1398650 1467560 329060 2504890 1239360 1723400 2340880 FALSE TRUE 3225612.545 3739813.177 3600612.486 1470834.494 1514765.4 335713.8187 2535545.593 1213766.783 1527766.857 2182330.113 1.478058945 1.713678951 1.6498936 0.673974339 0.694104614 0.153832739 1.161852452 0.556179276 0.700062217 1 21.05743792 3.73798976 24.86044591 0.684660791 1.623857393 0.724936796 0.256101584 21.92743858 954941.4244 0.064009495 0.106152238 5470.030654 -3.73798976 0.939196602 QKVDLQSLPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKVDLQSLPTR 11 1 Q9C005 Q9C005 DPY30 Protein dpy-30 homolog 0 ; 160.69 2.48E-05 1200050000 1643800 1754760 1434760 1408300 1477430 1241240 1556780 1586370 1719260 1826510 FALSE TRUE 1579558.479 1704715.963 1694053.048 1480982.532 1524952.878 1266338.723 1575832.339 1553610.905 1524096.813 1702798.851 0.927624821 1.001125859 0.994863866 0.86973428 0.895556675 0.743680748 0.925436577 0.91238663 0.895053935 1 20.69947659 3.737996558 24.99958209 0.885919437 0.977196953 0.264907096 0.062680716 61.58569974 2729581.071 0.016257417 0.026972696 5470.116274 -3.737996558 0.091277516 (ac)MMEGLDDGPDFLSEEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 MMEGLDDGPDFLSEEDR 17 0 G3V5X9;Q9UNH7;G3V2U1;H0YJF8;G3V4Z5 G3V5X9 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ; 142.12 1.50E-71 239510000 2130.1 2678.5 0 8973.5 6347.6 4347.4 9965 12642.1 2465 6765 FALSE TRUE 2046.853337 2602.111803 0 9436.62341 6551.776319 4435.307407 10086.95465 12381.03622 2185.183534 6306.800524 0.324547023 0.412588252 0 1.496261595 1.038843118 0.703257918 1.599377468 1.963124752 0.346480521 1 12.62269259 3.738004818 24.99997613 1.249654443 0.262399382 0.46104959 0.448160124 42.50850055 1912071.968 0.123844884 0.205356136 5470.220315 -3.738004818 -0.987255061 KLTAT(ph)PTPLGGMTGFHMQTEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLTATPTPLGGMTGFHMQTEDR 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLT(0.032)AT(0.937)PT(0.031)PLGGMTGFHMQTEDR;KLT(0.464)AT(0.523)PT(0.012)PLGGMTGFHMQTEDR 207.99 5.66E-23 1464700000 631550 654740 551280 512380 551580 541860 565530 537620 670770 598290 TRUE FALSE 606868.3278 636067.4563 650908.5592 538823.9932 569322.0716 552816.7805 572451.1253 526517.9591 594627.0017 557767.2854 1.088031413 1.140381433 1.166989489 0.966037283 1.020716142 0.991124426 1.026326105 0.943974258 1.0660844 1 19.08930379 3.738008743 24.99998258 0.998232814 1.132658848 0.728157149 0.036280312 23.02803712 1043193.104 0.009121373 0.015124721 5470.269752 -3.738008743 0.134426033 (ac)MDVHDLFR ddPTM_BT-474_Pertuzumab_2h_R1 3 MDVHDLFR 8 0 Q9Y2R4;A0A087X1P7;A0A087WTD6;A0A087X069 Q9Y2R4 DDX52 Probable ATP-dependent RNA helicase DDX52 0 ;; 60.682 0.011805 73428000 15503.7 16259.4 14703 10274.3 12535.6 12891.5 11129.5 13989 11385.6 11632 FALSE TRUE 14897.79826 15795.69783 17360.15917 10804.55785 12938.81896 13152.17496 11265.70615 13700.12226 10093.15442 10844.15428 1.37380914 1.456609471 1.600877184 0.996348593 1.193160723 1.212835471 1.038873651 1.26336475 0.930746111 1 13.40462992 3.738009471 24.99910002 1.116488707 1.475049691 0.701042317 0.114753581 27.03565045 1226307.542 0.028943835 0.048019325 5470.278924 -3.738009471 0.358560985 TPASTPVSGT(ph)PQASPMIER ddPTM_BT-474_Pertuzumab_2h_R1 2 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVS(0.418)GT(0.568)PQAS(0.014)PMIER;TPASTPVS(0.185)GT(0.561)PQAS(0.254)PMIER 130.27 3.39E-06 0 161447 172713 134303 177565 188135 188929 178316 185318 186441 203646 TRUE FALSE 155137.4728 167787.3943 158574.5397 186729.1509 194186.5331 192749.2738 180498.2845 181491.1185 165276.9993 189852.875 0.817145765 0.883775894 0.835249609 0.983546606 1.022826402 1.015256018 0.950727159 0.955956651 0.870553049 1 17.53452232 3.73810132 24.99994256 0.971179327 0.849228964 0.638820145 0.043344747 27.23897586 1482667.187 0.011882836 0.019716819 5471.435952 -3.73810132 -0.121950362 VIVPNMEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIVPNMEFR 9 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 82.452 0.040824 0 227300 246490 206450 145060 177800 104840 211560 145470 164440 203600 FALSE TRUE 218416.8647 239460.3465 243760.1075 152546.564 183519.0985 106959.9366 214149.1346 142465.9937 145773.4606 189809.9907 1.150713216 1.261579255 1.284232229 0.803680372 0.966856896 0.563510573 1.128228993 0.750571628 0.767996775 1 17.53419641 3.7381085 24.99989899 0.847756752 1.235115352 0.571107787 0.149936418 26.25489495 1451793.629 0.036746297 0.061005142 5471.526411 -3.7381085 0.387358599 RIVSQLLTLMDGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RIVSQLLTLMDGLK 14 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 125.53 0.00014542 59775000 138530 150790 128440 52958 57196 21888 104300 54668 63918 101760 FALSE TRUE 133116.0944 146489.6168 151651.9651 55691.16873 59035.76128 22330.59036 105576.4546 53539.0867 56662.29661 94867.70456 1.403176087 1.54414632 1.598562607 0.587040331 0.622295665 0.235386641 1.112880881 0.564355245 0.597276986 1 16.53362942 3.738160904 24.9953967 0.657523022 1.518180175 0.732544784 0.232748914 16.62094897 1039387.611 0.058717775 0.097550402 5472.186678 -3.738160904 0.860657153 LNSNDEDIHTANER ddPTM_BT-474_Pertuzumab_2h_R1 1 LNSNDEDIHTANER 14 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424;F8W943 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 188.19 8.61E-07 339750000 180650 201010 141160 204140 190530 202520 213870 198040 195650 224160 FALSE TRUE 173589.9983 195277.3916 166670.7521 214675.6899 196658.5705 206615.0932 216487.405 193950.4048 173440.6322 208977.4435 0.830663804 0.934442437 0.79755379 1.027267279 0.941051662 0.988695668 1.035936709 0.928092532 0.829949057 1 17.6729877 3.738168043 24.99998959 0.963725478 0.862242255 0.380162006 0.064238605 39.65056472 2525098.766 0.01671724 0.027750106 5472.276624 -3.738168043 -0.101483224 AGGSAALS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 6 AGGSAALSPSK 11 0 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.981)PS(0.019)K;AGGSAALS(0.994)PS(0.005)K;AGGSAALS(0.966)PS(0.034)K;AGGSAALS(0.992)PS(0.008)K;AGGSAALS(0.998)PS(0.002)K;AGGSAALS(0.99)PS(0.01)K 211.25 1.05E-08 19138100000 25983360 19942980 21369540 9427060 15020950 3624590 15612230 14271460 13733830 14729230 TRUE FALSE 24967901.57 19374225.74 25231491.24 9913591.696 15504112.5 3697881.693 15803297.14 13976749.36 12174823.2 13731606.13 1.818279764 1.41092204 1.837475602 0.721954271 1.129082232 0.269297099 1.150870262 1.017852481 0.886627761 1 23.71099705 3.738281995 24.99999975 0.892167999 1.66109545 0.665320747 0.261888309 14.80915392 1328821.599 0.066592298 0.110709697 5473.712651 -3.738281995 0.76892745 KTYVTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTYVTPR 7 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ; 120.15 0.0074091 2240020000 2544300 2793300 2230940 1867450 2054660 2083010 1671490 2033240 2174110 2355630 FALSE TRUE 2444865.943 2713637.819 2634120.485 1963829.318 2120750.005 2125129.889 1691946.195 1991252.883 1927314.147 2196081.082 1.113285827 1.235672873 1.19946413 0.894242628 0.965697497 0.967691907 0.770438855 0.906730129 0.877615204 1 21.06649989 3.738359301 24.99991921 0.903966212 1.188094151 0.778644794 0.066113253 7.477891139 928652.2632 0.01732718 0.028823455 5474.687075 -3.738359301 0.284127939 SNFLVLCYLHDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNFLVLCYLHDVK 13 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 132.84 0.00011418 404400000 629610 661870 565920 406950 474050 235970 573320 437860 569830 624690 FALSE TRUE 605004.1451 642994.1156 668194.3328 427952.7383 489298.2488 240741.4751 580336.4617 428818.038 505145.2873 582379.1899 1.038849182 1.104081545 1.147352695 0.734835217 0.840171245 0.41337582 0.996492443 0.736321018 0.867382104 1 19.15159928 3.738359984 24.99987923 0.782877757 1.097493192 0.425513531 0.158168468 15.31579461 1908488.128 0.039419111 0.065584406 5474.695688 -3.738359984 0.314615435 GIAYIEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 GIAYIEFK 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 129.4 0.0025415 676640000 1264050 1311940 1182380 669340 817120 233439 1071820 885110 987660 1180550 FALSE TRUE 1214649.529 1274524.756 1396062.368 703884.7176 843403.4069 238159.2965 1084937.254 866832.1692 875544.9774 1100590.297 1.103634597 1.158037427 1.268466905 0.639551993 0.766319137 0.216392328 0.985777593 0.787606589 0.795523075 1 20.06984608 3.738384218 24.99957816 0.730919474 1.174845435 0.478057472 0.208135029 13.25750764 1878962.565 0.054346158 0.090436555 5475.001191 -3.738384218 0.443925962 QKQPER ddPTM_BT-474_Pertuzumab_2h_R1 1 QKQPER 6 1 Q9Y5P6;Q9Y5P6-2 Q9Y5P6 GMPPB Mannose-1-phosphate guanyltransferase beta 0 71.949 0.079239 85196000 93484 108030 76184 116920 114630 116650 124870 116410 109640 128090 FALSE TRUE 89830.54193 104949.0902 89952.1435 122954.2552 118317.1781 119008.7429 126398.1964 114006.0928 97194.12685 119414.3502 0.752259186 0.878864977 0.753277503 1.029643883 0.990812058 0.996603362 1.058484145 0.954710155 0.813923341 1 16.86561669 3.738395812 24.99999999 0.980555689 0.803206993 0.590908046 0.069620688 10.40741504 1578832.893 0.018230706 0.030337538 5475.147351 -3.738395812 -0.177348695 IRELESQISELQEDLESER ddPTM_BT-474_Pertuzumab_2h_R1 8 IRELESQISELQEDLESER 19 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 266.78 1.35E-31 1658268000 425050.7 402344.2 328413.3 430960 415655.2 415474.4 464859.8 456927.9 496733 495939.4 FALSE TRUE 408439.2487 390869.7374 387764.8888 453201.8972 429025.127 423875.577 470548.8933 447492.1792 440345.9523 462348.9827 0.88340034 0.8453998 0.838684421 0.980216058 0.927924886 0.916787087 1.017735327 0.967866689 0.952410341 1 18.81862269 3.738404765 24.99998145 0.964607804 0.854785344 0.733493942 0.030457779 7.12662005 1143191.249 0.008184905 0.013624322 5475.260223 -3.738404765 -0.10982246 YLDLILNDFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLDLILNDFVR 11 0 Q15046;Q15046-2;J3KRL2;H3BPV7 Q15046 KARS Lysine--tRNA ligase 0 ; 131.28 0.0004805 37155000 215011 235780 186569 143232 148055 97862 196759 149242 161990 178460 FALSE TRUE 206608.1324 229055.7853 220286.1685 150624.2207 152817.3235 99840.83669 199166.9955 146160.1005 143601.5743 166372.7452 1.241838813 1.376762672 1.324052015 0.90534192 0.918523784 0.600103319 1.197113116 0.878509881 0.863131603 1 17.34405959 3.738452716 24.9115789 0.907643927 1.320472341 0.633771839 0.141145932 5.49529194 1268808.432 0.036103812 0.060115951 5475.864785 -3.738452716 0.412828414 SSPPAPPLPPGS(ph)GSPGTPQALPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 SSPPAPPLPPGS(0.982)GS(0.017)PGTPQALPR;S(0.1)S(0.1)PPAPPLPPGS(0.615)GS(0.185)PGTPQALPR 205.92 1.53E-24 386820000 112830 115685 93668 119504 112148 126849 131283 123452 134510 139009 TRUE FALSE 108420.4789 112385.7771 110595.8912 125671.6158 115755.3423 129413.9737 132889.6806 120902.6731 119240.9887 129593.7966 0.836617814 0.867215716 0.853404207 0.96973481 0.893216692 0.998612411 1.025432421 0.932935651 0.920113399 1 16.98363714 3.73850313 1.229214216 0.96736332 0.839408034 0.611617467 0.039553302 0.354727763 1.016428308 0.013141806 0.036309345 5476.500476 -3.73850313 -0.127955287 VGTEGLVDS(ph)FSQGLER ddPTM_BT-474_Pertuzumab_2h_R1 3 VGTEGLVDSFSQGLER 16 0 O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170;T1ECW5 O75170-6 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 1 VGTEGLVDS(1)FSQGLER;VGTEGLVDS(0.999)FS(0.001)QGLER;VGTEGLVDS(0.978)FS(0.022)QGLER 252.51 1.65E-26 143060000 142004 122575 106064 130899 149026 120754 121750 162247 134650 132216 TRUE FALSE 136454.3267 119079.281 125232.1242 137654.7131 153819.5566 123195.7286 123240.0129 158896.5428 119365.0965 123260.8926 1.107036659 0.966075116 1.015992352 1.116775242 1.247918569 0.999471333 0.999830606 1.289107514 0.9683939 1 16.91135562 3.738729852 24.74133116 1.109015235 1.023338747 0.035597658 0.108492326 29.81159228 4358048.612 0.028321955 0.047207894 5479.360211 -3.738729852 -0.085676488 S(ph)LDNFFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDNFFAK 8 0 Q9UKY7;Q9UKY7-2 Q9UKY7 CDV3 Protein CDV3 homolog 1 S(1)LDNFFAK 116.77 0.0023164 14177000 55067 52938 44046 35476 36949 38260 31527 41589 43362 36235 TRUE FALSE 52914.92076 51428.26007 52006.092 37306.92061 38137.49814 39033.64341 31912.83686 40730.17262 38439.72755 33780.77118 1.566421337 1.522412257 1.539517607 1.104383332 1.128970619 1.155498885 0.944704213 1.205720627 1.137917407 1 15.04391464 3.738816916 19.54581894 1.105669542 1.540747082 0.888895438 0.072215259 0.320421417 24366.36806 0.018409216 0.030736278 5480.458784 -3.738816916 0.43507754 AHIAQLCEK ddPTM_BT-474_Pertuzumab_2h_R1 4 AHIAQLCEK 9 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;; 127.94 0.00043119 1615830000 3975050 4378810 3697000 1981810 2092730 972870 3696320 1846050 2808180 3704700 FALSE TRUE 3819700.651 4253930.626 4365130.139 2084091.452 2160044.561 992542.098 3741556.67 1807928.422 2489407.179 3453777.369 1.105948717 1.231674822 1.263871313 0.603423796 0.625415112 0.287378714 1.08332306 0.523464088 0.720778126 1 21.71974366 3.738865546 24.99997993 0.668376427 1.203615963 0.533684594 0.217044037 18.88017792 1547868.071 0.053883076 0.090058897 5481.072497 -3.738865546 0.535239536 TSRPENAIIYNNNEDFQVGQAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSRPENAIIYNNNEDFQVGQAK 22 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 325.06 2.79E-68 2902310000 1842720 1611000 1412750 1063150 1248620 416770 1358510 1284120 1378480 1329070 FALSE TRUE 1770704.465 1565055.857 1668065.351 1118019.299 1288782.996 425197.375 1375135.852 1257602.473 1222000.729 1239050.905 1.429081289 1.263108603 1.346244407 0.902319101 1.040137246 0.343163766 1.109829989 1.014972402 0.986239326 1 20.24080403 3.738870573 24.59697441 0.914440855 1.337841178 0.484720675 0.204216371 19.52219031 1549148.377 0.054303862 0.090720708 5481.13593 -3.738870573 0.423400322 KEQEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 KEQEEER 7 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 0 99.802 0.016452 239330000 345890 319850 265420 322280 317140 317040 357190 347720 326310 375340 FALSE TRUE 332372.2364 310728.1912 313387.2982 338912.9094 327341.0961 323450.766 361561.3981 340539.4605 289268.6568 349917.8875 0.949857805 0.888003164 0.895602395 0.968549827 0.935479745 0.924361908 1.03327498 0.973198206 0.826675821 1 18.41665689 3.738872961 24.99178164 0.954898889 0.908839325 0.104489228 0.053610427 57.59582621 4608277.255 0.014030832 0.023453314 5481.166079 -3.738872961 -0.046059564 TQRPADVIFATVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQRPADVIFATVR 13 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 164.88 3.31E-05 560850000 535600 470200 439050 392120 465240 368430 461890 436430 504510 508320 FALSE TRUE 514668.1599 456790.3564 518396.1016 412357.3602 480204.8671 375879.907 467542.748 427417.568 447240.1399 473891.0336 1.086047474 0.963914326 1.093914138 0.870152273 1.013323387 0.793177926 0.986603913 0.901932169 0.943761557 1 18.85419584 3.738921818 24.99999494 0.925695818 1.039554214 0.370132766 0.07020305 32.03730568 2217369.59 0.016672109 0.027916515 5481.782729 -3.738921818 0.113858396 (ac)MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDT(ph)PLPEEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVK 40 1 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLSPPHLS(0.001)S(0.001)S(0.001)PEDLCPAPGT(0.429)PPGT(0.085)PRPPDT(0.483)PLPEEVK 63.227 0.074356 222580000 41684 64760 41279 63878 78466 69628 55467 68798 49231 53509 TRUE FALSE 40054.9432 62913.10821 48739.03355 67174.75124 80989.93015 71035.92587 56145.82174 67377.29726 43642.50327 49884.78777 0.802949055 1.261168204 0.977031992 1.346597916 1.623539635 1.423999761 1.125509885 1.350658192 0.874865971 1 15.60631232 3.738924116 24.99484144 1.282613993 1.038461591 0.169358065 0.229039955 53.8924847 3705654.809 0.059468711 0.09944598 5481.811734 -3.738924116 -0.244152402 VRDALTAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VRDALTAEK 9 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 100.69 0.0046488 375750000 841170 876320 747020 485910 467490 193786 726930 625020 687780 806250 FALSE TRUE 808296.1464 851328.2116 882023.1314 510987.8733 482527.2404 197704.4857 735826.3868 612113.1186 609706.0978 751641.9694 1.075373887 1.132624636 1.173461791 0.67982882 0.641964206 0.263030131 0.978958622 0.814367935 0.811165585 1 19.5196861 3.738938272 24.98996824 0.729896124 1.127700438 0.449457858 0.195393832 30.84206007 2040815.064 0.053086941 0.088782893 5481.990412 -3.738938272 0.397804314 EATSDPS(ph)RTPEEEPLNLEGLVAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EAT(0.101)S(0.087)DPS(0.406)RT(0.406)PEEEPLNLEGLVAHR;EAT(0.014)S(0.094)DPS(0.534)RT(0.358)PEEEPLNLEGLVAHR 176.26 3.70E-13 808610000 210788 229858 177515 222680 216929 279970 242600 187598 249340 255420 TRUE FALSE 202550.1719 223302.6749 209595.9093 234172.5415 223906.7183 285631.1852 245569.0114 183724.0357 221035.9685 238120.1759 0.850621629 0.937773013 0.880210627 0.983421672 0.94030973 1.199525341 1.031281833 0.771560138 0.928253844 1 17.86133034 3.738972333 24.50039931 0.968412148 0.894358882 0.133605365 0.101852855 77.77788972 4628204.736 0.030318346 0.050674533 5482.420382 -3.738972333 -0.074053266 LRQPFFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRQPFFQK 8 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ; 146.54 0.00050311 3727600000 6146800 6732900 5545800 1922700 2068990 120440 4108000 2131500 2625900 3679300 FALSE TRUE 5906576.26 6540884.284 6548049.426 2021930.777 2135540.942 122875.3793 4158274.933 2087483.78 2327818.841 3430097.734 1.721984829 1.906909013 1.908997916 0.589467395 0.622588949 0.035822705 1.212290511 0.608578514 0.678645048 1 21.70981825 3.73904853 24.98929499 0.663095096 1.852058494 0.772671061 0.290178693 18.65928939 955650.457 0.074329566 0.124425347 5483.382349 -3.73904853 1.188963399 TKPQMQEER ddPTM_BT-474_Pertuzumab_2h_R1 3 TKPQMQEER 9 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 68.657 0.052395 234310000 789070 831540 699040 377460 400600 230977 612280 426850 463040 565950 FALSE TRUE 758232.272 807825.2934 825372.0781 396940.7558 413485.6628 235647.5132 619773.2658 418035.3983 410477.6404 527617.7024 1.43708649 1.531080723 1.564337349 0.752326455 0.783684211 0.446625487 1.174663517 0.792307378 0.777983071 1 19.00913344 3.739051823 24.99423689 0.813686287 1.512859477 0.761839192 0.177446189 19.7553316 1005199.434 0.045863482 0.076784054 5483.423933 -3.739051823 0.69917319 DAFMDHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAFMDHLK 8 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 ; 105.78 0.007471 371100000 526470 550660 461590 338560 366830 117533 518890 376800 475310 540160 FALSE TRUE 505894.9704 534955.716 545009.581 356033.1222 378629.4201 119909.5978 525240.331 369018.9483 421354.8015 503574.4821 1.004608034 1.062316966 1.082281967 0.707011842 0.751883651 0.238116906 1.04302412 0.732799142 0.836727865 1 18.94184565 3.739078763 24.99290061 0.742893271 1.050993801 0.293546673 0.206037743 54.67714878 2637321.144 0.05296197 0.088628294 5483.764085 -3.739078763 0.30810053 TVDVPASLPT(ph)PPHNNQEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVDVPASLPTPPHNNQEELR 20 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765;H7C2V8 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 TVDVPASLPT(1)PPHNNQEELR;TVDVPASLPT(1)PPHNNQEELR;TVDVPASLPT(1)PPHNNQEELR;TVDVPASLPT(1)PPHNNQEELR 257.2 1.20E-35 1063940000 645645 619284 498828 617645 590945 629218 664203 633914 672268 704440 TRUE FALSE 620412.4796 601622.6267 588977.316 649521.7325 609953.2826 641941.2191 672331.715 620823.4544 595954.955 656727.6513 0.944702843 0.916091511 0.896836481 0.989027538 0.928776611 0.977484681 1.023760327 0.945328635 0.907461341 1 19.32493568 3.739136222 24.99999494 0.966182337 0.918898402 0.296443003 0.033987061 66.9730018 2908777.717 0.009001029 0.015087988 5484.489661 -3.739136222 -0.047283936 S(ph)LGGAVGSVASGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLGGAVGSVASGAR 14 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 S(1)LGGAVGSVASGAR;S(1)LGGAVGSVASGAR;S(1)LGGAVGSVASGAR;S(1)LGGAVGSVASGAR 187.49 9.88E-07 3309060000 498685 417172 362574 454191 464042 453773 435651 561352 465253 426193 TRUE FALSE 479195.8389 405274.663 428099.1872 477631.8519 478968.3324 462948.601 440982.6273 549759.885 412439.4299 397326.5685 1.20605033 1.020003934 1.077449185 1.202114054 1.205477736 1.165158934 1.109874502 1.383647429 1.038036373 1 18.59996574 3.739169322 24.98217318 1.184903619 1.093051425 0.011252431 0.109701993 114.2423621 4688635.68 0.027998237 0.046942654 5484.907678 -3.739169322 -0.091852195 YAYDKR ddPTM_BT-474_Pertuzumab_2h_R1 3 YAYDKR 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 84.566 0.08932 1929850000 3121950 3260920 2619950 1690700 1697600 440630 2654550 1876620 2141440 2526910 FALSE TRUE 2999940.743 3167921.754 3093433.245 1777957.23 1752204.846 449539.8405 2687037.177 1837867.141 1898352.709 2355760.135 1.27344915 1.344755651 1.313135917 0.754727616 0.743795949 0.190825812 1.140624267 0.78015886 0.805834465 1 21.16776122 3.739176155 23.63083592 0.763225223 1.313877834 0.532103511 0.230493795 19.21942591 737800.6971 0.060276882 0.100966344 5484.993982 -3.739176155 0.550652611 LQEAGILSAEELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQEAGILSAEELQR 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 209.25 1.61E-08 117425000 92088 102783 74458 107605 105092 108456 105632 122557 98188 100860 FALSE TRUE 88489.09915 99851.72948 87914.21691 113158.5069 108472.3796 110649.0546 106924.756 120026.1551 87042.10988 94028.66236 0.94108644 1.061928639 0.934972536 1.20344695 1.153609728 1.176758787 1.137150666 1.276484767 0.92569763 1 16.52081297 3.739184304 24.99997553 1.147952002 0.987589145 0.283178966 0.101154857 60.04657787 2406864.292 0.025154861 0.042108064 5485.096892 -3.739184304 -0.160362856 NQPTVYIAAS(ph)PPNTDELMSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQPTVYIAASPPNTDELMSR 20 0 A0A1B0GV57;Q9NYJ8;Q9NYJ8-2 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 NQPTVYIAAS(1)PPNTDELMSR;NQPTVYIAAS(1)PPNTDELMSR 278.27 1.36E-44 243140000 272780 287240 220160 281490 272280 300250 270860 288260 328490 306640 TRUE FALSE 262119.456 279048.1964 259947.8094 296017.7326 281038.1335 306321.2607 274174.8657 282307.3303 291201.1923 285870.9997 0.916915169 0.97613328 0.909318573 1.035494097 0.983094241 1.071536676 0.959085972 0.987533995 1.018645447 1 18.12500475 3.739372339 24.99999333 1.004933313 0.938323434 0.502805869 0.033456198 63.18715534 1946060.05 0.008493965 0.014244806 5487.472276 -3.739372339 -0.066609879 SVEFEEMDILDQGALQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEFEEMDILDQGALQR 17 0 Q14376;Q5QPP1 Q14376 GALE UDP-glucose 4-epimerase 0 144.27 1.21E-06 52066000 63505 56439 48730 63389 61652 69234 72254 67745 60583 73376 FALSE TRUE 61023.15439 54829.41498 57536.59499 66660.51389 63635.09257 70633.95892 73138.26607 66346.04208 53705.87182 68406.17816 0.892070805 0.801527237 0.841102318 0.974480897 0.930253586 1.032566952 1.069176323 0.969883772 0.785102651 1 16.06183901 3.739393402 22.75737335 0.972141813 0.840562812 0.357170395 0.07400605 21.97019361 600326.9022 0.019817616 0.033248066 5487.73842 -3.739393402 -0.131579001 SS(ph)PEQPIGQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPEQPIGQGR 11 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 S(0.072)S(0.928)PEQPIGQGR;S(0.161)S(0.839)PEQPIGQGR 117.21 0.00092866 977410000 635030 661990 534580 641220 667720 689770 665190 625000 844440 721940 TRUE FALSE 610212.3255 643110.6934 631190.4977 674313.441 689197.8202 703717.622 673330.7942 612093.5316 748582.7114 673042.3608 0.906647725 0.955527811 0.937816896 1.001888559 1.024003629 1.045577014 1.000428552 0.909442804 1.112237141 1 19.36033778 3.739419312 4.980662767 1.005053081 0.934805487 0.351967558 0.048887978 0.241532357 18.76486299 0.013510869 0.023140872 5488.065825 -3.739419312 -0.070247594 NILFVITKPDVYK ddPTM_BT-474_Pertuzumab_2h_R1 2 NILFVITKPDVYK 13 1 F8VZJ2;H0YHX9;Q13765;E9PAV3-2;E9PAV3;F8W0W4;F8W1N5;F8VZ58;F8VNW4;Q9BZK3 F8VZJ2 NACA;NACAP1 "Nascent polypeptide-associated complex subunit alpha;Nascent polypeptide-associated complex subunit alpha, muscle-specific form;Putative nascent polypeptide-associated complex subunit alpha-like protein" 0 ; 173.68 1.94E-05 926970000 1344180 1281680 1067090 726520 662360 548650 515600 935090 1123330 1303240 FALSE TRUE 1291647.96 1245127.741 1259936.9 764015.7843 683665.4109 559744.0789 521910.067 915780.0647 995814.2878 1214970.394 1.063110645 1.024821467 1.037010372 0.628834898 0.562701292 0.460705941 0.429566078 0.753746815 0.819620209 1 20.21248973 3.739424254 23.34070883 0.635294184 1.039964938 0.528798511 0.161216556 22.06889702 596405.1249 0.042553416 0.071404283 5488.128276 -3.739424254 0.404670754 QTS(ph)IETDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QTSIETDR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 QT(0.013)S(0.987)IETDR;QT(0.072)S(0.928)IETDR 167.18 0.00032954 530440000 651880 646520 525470 821990 934350 820500 854320 868570 832120 867900 TRUE FALSE 626403.8089 628081.8826 620434.118 864413.0024 964404.2163 837091.0722 864775.4237 850633.726 737661.2261 809116.36 0.774182602 0.77625656 0.766804564 1.068342015 1.191922774 1.034574399 1.068789937 1.051311984 0.911687444 1 19.62598767 3.73942752 24.99512537 1.05530184 0.772798757 0.784683738 0.065723659 32.87517297 947867.2772 0.017539121 0.029445218 5488.169549 -3.73942752 -0.282503083 AVEHINK ddPTM_BT-474_Pertuzumab_2h_R1 7 AVEHINK 7 0 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;;; 138.62 0.0027684 31679300000 40253250 40658690 29707370 32409550 27175770 27138380 31007870 28655040 36324050 33995930 FALSE TRUE 38680108.49 39499143.97 35076152.6 34082210.76 28049903.32 27687136.64 31387353.59 28063303.41 32200696.13 31693355.38 1.220448514 1.246291013 1.106735219 1.075374013 0.885040507 0.873594364 0.990344923 0.885463312 1.016007795 1 24.91767707 3.739465141 1.597239836 0.934251771 1.232474418 0.802915481 0.056160793 0.150538391 0.740919716 0.016231735 0.037956134 5488.644993 -3.739465141 0.298222647 SATRPS(ph)PS(ph)PERSS(ph)TGPEPPAPTPLLAER ddPTM_BT-474_Pertuzumab_2h_R1 1 SATRPSPSPERSSTGPEPPAPTPLLAER 28 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.008)AT(0.152)RPS(0.918)PS(0.921)PERS(0.317)S(0.579)T(0.104)GPEPPAPTPLLAER 125.77 2.45E-05 617020000 178240 170990 140300 177830 166980 189520 182340 194680 205490 188890 TRUE FALSE 171274.1837 166113.5326 165655.331 187007.8276 172351.0633 193352.2243 184571.5315 190659.79 182163.6367 176096.3121 0.972616529 0.943310684 0.94070869 1.061963339 0.978731816 1.097991332 1.048128319 1.082701777 1.034454581 1 17.42600517 3.739487114 24.99434463 1.048753215 0.951321835 0.592732957 0.034447643 50.90546644 1373271.346 0.008805475 0.014760399 5488.922688 -3.739487114 -0.097431381 AADIS(ph)LDNLVEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AADISLDNLVEGK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK 190.11 4.92E-06 68006000 203275 168251 168498 139915 155005 159708 148417 188826 176463 183587 TRUE FALSE 195330.7883 163452.6462 198949.3368 147136.0299 159990.8766 162937.4052 150233.3716 184926.6771 156431.66 171152.489 1.141267588 0.955011798 1.162409837 0.859678003 0.934785568 0.952001377 0.877774975 1.080479041 0.91398998 1 17.38492275 3.739526783 24.99999177 0.952337457 1.073107943 0.399662833 0.078219761 98.102587 2538431.323 0.020026888 0.033715866 5489.424083 -3.739526783 0.120770486 MSSYAFFVQTCR ddPTM_BT-474_Pertuzumab_2h_R1 2 MSSYAFFVQTCR 12 0 P26583;D6R9A6;P09429;Q5T7C4;B2RPK0 P26583;P09429 HMGB2;HMGB1;HMGB1P1 High mobility group protein B2;High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ; 119.76 0.00092398 282190000 338400 344350 293741 145011 166379 98412 238110 166031 175357 210570 FALSE TRUE 325174.9539 334529.4752 346826.5329 152495.0351 171730.7316 100401.9581 241024.0614 162602.4018 155451.2085 196307.9063 1.65645368 1.70410597 1.766747654 0.776815554 0.87480293 0.511451423 1.227785808 0.828302868 0.791874415 1 17.58275875 3.739540387 24.99997723 0.858914956 1.708602834 0.837227917 0.17182739 31.16298854 795152.7289 0.043893787 0.07377565 5489.596037 -3.739540387 0.849687878 YCLHGEAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 YCLHGEAGK 9 0 Q29RF7;Q29RF7-3;H0Y9L9 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 ; 112.84 0.001897 273050000 969690 996510 865480 730820 825120 503260 940060 855630 996550 1101700 FALSE TRUE 931793.4428 968090.5105 1021891.488 768537.7078 851660.7342 513436.262 951564.7355 837960.9415 883425.8219 1027080.878 0.907224994 0.942565022 0.994947439 0.748273797 0.829205131 0.49989857 0.92647498 0.815866559 0.860132674 1 19.97011836 3.739591259 24.99566472 0.799924526 0.947677741 0.196148315 0.125444054 136.8166571 3318117.04 0.032060931 0.053884069 5490.239102 -3.739591259 0.147753215 IWHHTFYNELR ddPTM_BT-474_Pertuzumab_2h_R1 2 IWHHTFYNELR 11 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;Q9BYX7;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;A6NL76;Q6S8J3;A5A3E0;P0CG38;P0CG39 P60709;P63261;P68133;Q6S8J3 ACTB;POTEKP;ACTG1;ACTA1;ACTC1;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ; 166.97 1.14E-05 8970500000 6632700 10100800 6986200 1162540 1311080 295260 3635100 361760 1090790 2069170 FALSE TRUE 6373486.751 9812735.074 8248761.747 1222538.829 1353252.079 301230.3595 3679587.441 354289.5296 966968.0922 1929023.273 3.303996816 5.086893047 4.276133867 0.633760539 0.701521904 0.156156934 1.907487324 0.183662652 0.501273419 1 20.87943912 3.739625433 24.41886722 0.708832777 4.308796753 0.871892651 0.61381587 20.02549181 459226.1351 0.152467446 0.256450136 5490.671147 -3.739625433 3.599963976 ICLTDHFKPLWAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ICLTDHFKPLWAR 13 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ; 243.85 3.16E-17 1996400000 1825160 2056900 1642770 1052790 1124890 556950 1480460 1163000 1410210 1730920 FALSE TRUE 1753830.729 1998239.226 1939655.082 1107124.618 1161073.108 568211.9106 1498578.312 1138983.644 1250128.873 1613683.247 1.086849438 1.238309458 1.202004846 0.686085463 0.719517359 0.352121094 0.928669437 0.705828511 0.774705244 1 20.62192599 3.739637654 24.94662726 0.720384423 1.181980096 0.593216208 0.165574466 58.31127705 1350609.427 0.041830196 0.070365673 5490.825651 -3.739637654 0.461595672 RVEVNGEHATVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVEVNGEHATVR 12 1 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8YFL4;A0A2R8YER9;A0A2R8Y897;A0A2R8Y6L2;A0A2R8Y809;A0A2R8Y4V6;A0A2R8Y784;A0A2R8YFM3;A0A2R8YH53;A0A2R8Y4P2;A0A2R8Y6G3;A0A2R8Y787;A0A2R8Y5H6;A0A2R8YF12;A0A2R8Y597;A0A2R8Y3S1 Q15813-2 TBCE Tubulin-specific chaperone E 0 ; 139.19 3.96E-05 233357000 215715 238040 178539 233640 226880 277010 243640 219490 240220 242240 FALSE TRUE 207284.6193 231251.3323 210804.9689 245698.1884 234177.8012 282611.332 246621.7392 214957.4548 212951.2327 225832.869 0.91786736 1.023993244 0.933455656 1.087964695 1.036951805 1.251418065 1.092054227 0.951843085 0.942959427 1 17.78489595 3.739638447 24.97472868 1.053678186 0.964994202 0.19677104 0.086160319 181.2269443 4199226.682 0.024590744 0.04136253 5490.835681 -3.739638447 -0.088683984 LSLS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 6 LSLSPLR 7 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR 148.62 0.002173 1147629000 2014640 2294820 1691630 762455 690795 298474 1294650 566120 589932 976490 TRUE FALSE 1935905.641 2229373.98 1997345.171 801805.3939 713015.0485 304509.3488 1310494.314 554429.4242 522965.3926 910351.4625 2.126547516 2.44891569 2.194037417 0.880764657 0.783230519 0.334496468 1.439547656 0.609027883 0.574465373 1 19.79606411 3.739688589 4.454682181 0.786652316 2.297290981 0.846729593 0.283767731 0.066951221 3.540447619 0.073252835 0.126799643 5491.469668 -3.739688589 1.510638665 up QMNMS(ph)PPPGNAGPVIMSIEEK ddPTM_BT-474_Pertuzumab_2h_R1 3 QMNMSPPPGNAGPVIMSIEEK 21 0 Q92843-2;Q86U42-2;Q86U42;B4DEH8;G3V4T2 Q92843-2 PABPN1 Polyadenylate-binding protein 2 1 QMNMS(1)PPPGNAGPVIMSIEEK;QMNMS(1)PPPGNAGPVIMSIEEK;QMNMS(1)PPPGNAGPVIMSIEEK 201.35 4.49E-22 377741000 626740 568264 546654 430625 500910 505385 451199 528894 596165 632752 TRUE FALSE 602246.3079 552057.6671 645446.5381 452849.6079 517022.2251 515604.231 456720.9083 517972.1541 528490.8485 589895.1434 1.020937898 0.935857285 1.094171643 0.767678142 0.876464624 0.874060817 0.774240835 0.878074959 0.895906424 1 19.17009901 3.739703376 24.99910227 0.857936597 1.008875774 0.480528717 0.07108918 80.48166479 1760609.832 0.017297024 0.029093464 5491.656645 -3.739703376 0.150939178 QRWDEAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 QRWDEAFR 8 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 177.3 0.00023309 1760030000 932790 969620 785570 324930 344060 98989 678180 276220 363150 574200 FALSE TRUE 896335.5355 941967.387 927539.9739 341699.6762 355127.0024 100990.6254 686479.7697 270515.9605 321926.7344 535308.9226 1.674426668 1.759670626 1.732719062 0.6383224 0.663405722 0.188658588 1.282399267 0.50534551 0.601384959 1 19.03001217 3.739726202 24.85094685 0.679906761 1.72601204 0.746385215 0.273726046 43.12528632 919446.8118 0.068493361 0.115292213 5491.945284 -3.739726202 1.046105279 ALS(ph)PVTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALSPVTSR 8 0 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80;A0A0A0MR72 Q96L91-4 EP400 E1A-binding protein p400 1 ALS(0.992)PVT(0.007)SR;ALS(0.961)PVT(0.035)S(0.003)R;ALS(0.921)PVT(0.079)SR 142.92 0.00063962 2708700000 3247700 3552450 2679630 3585150 3607280 3629310 3640160 3779090 3655510 3932670 TRUE FALSE 3120776.293 3451137.604 3163898.749 3770180.021 3723311.437 3702697.135 3684709.367 3701050.471 3240551.83 3666306.758 0.851204359 0.941311743 0.862966183 1.028331853 1.015548257 1.009925622 1.005019386 1.009476488 0.883873621 1 21.80589607 3.739827933 24.99511071 0.996662303 0.890775857 0.556303683 0.044039967 81.92205778 1615721.259 0.011141947 0.018786672 5493.231897 -3.739827933 -0.105886446 FCLESER ddPTM_BT-474_Pertuzumab_2h_R1 4 FCLESER 7 0 Q9H074;Q9H074-3;Q9H074-2 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ;;; 127.31 0.0089977 776700000 1340310 1545150 1175160 747360 795820 280945 1160480 724790 799890 1075760 FALSE TRUE 1287929.203 1501083.835 1387537.553 785931.3392 821418.273 286625.9004 1174682.301 709822.8332 709089.8406 1002897.817 1.284207804 1.496746537 1.383528341 0.783660435 0.819044831 0.285797711 1.171288123 0.70777184 0.707040965 1 19.93574319 3.739847497 6.084403128 0.770112971 1.402382156 0.615357574 0.219429484 0.091775186 16.03405314 0.055544433 0.094031055 5493.479359 -3.739847497 0.632269186 IQEQSTS(ph)PDTSLGSTTPSSHTLELVALDSEVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IQEQSTSPDTSLGSTTPSSHTLELVALDSEVLR 33 0 A0A494C0H4;H0Y9M2;Q17R98-2;Q17R98;A0A5F9ZGW8 A0A494C0H4 ZNF827 Zinc finger protein 827 1 IQEQS(0.184)T(0.18)S(0.541)PDT(0.022)S(0.022)LGS(0.013)T(0.013)T(0.013)PS(0.004)S(0.004)HT(0.002)LELVALDSEVLR 53.987 0.036059 46193000 10363 11657 8781.7 12127 13915 11086 11512 14403 10665 12751 TRUE FALSE 9958.002503 11324.55377 10368.74854 12752.87592 14362.58861 11310.16652 11652.8873 14105.57302 9454.353911 11887.36341 0.837696481 0.952654797 0.872249647 1.07280946 1.208223229 0.951444498 0.980275179 1.186602321 0.795328079 1 13.53714114 3.739850312 24.94767393 1.045409025 0.89404575 0.228261446 0.11487138 148.9619548 2881476.773 0.029312786 0.049375122 5493.514972 -3.739850312 -0.151363275 MTSSDKDFR ddPTM_BT-474_Pertuzumab_2h_R1 8 MTSSDKDFR 9 1 Q86VP6;Q86VP6-2;O75155-2;O75155;A0A3B3ISC4;F8WBB8 Q86VP6 CAND1;CAND2 Cullin-associated NEDD8-dissociated protein 1;Cullin-associated NEDD8-dissociated protein 2 0 ;;;;;;; 96.342 0.006779 5655580000 15510450 16138720 13270780 12623210 12857230 8975220 15542250 14626900 16090790 16597800 FALSE TRUE 14904284.47 15678459.51 15669105.15 13274695.38 13270794.48 9156705.098 15732460.7 14324849.4 14264230.98 15473616.22 0.963206289 1.01323823 1.012633694 0.857892246 0.857640146 0.591762453 1.016728118 0.925759641 0.921842107 1 23.88330706 3.739883026 24.92474452 0.877067999 0.998047292 0.182816118 0.110812749 191.305946 3605692.008 0.029928376 0.05042369 5493.928786 -3.739883026 0.120979293 ILLDHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILLDHEK 7 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 104.21 0.0082028 98761000 293420 297590 260200 156740 166650 60952 265430 179110 231970 298600 FALSE TRUE 281952.822 289103.0246 307223.9281 164829.3702 172010.4486 62184.4912 268678.4117 175411.3159 205637.7381 278375.556 1.012850503 1.038535957 1.103631125 0.592111508 0.617907876 0.223383447 0.965165245 0.630124708 0.73870616 1 18.08667301 3.739885525 24.99844549 0.660251833 1.050358889 0.40625138 0.204239676 108.3431163 2044207.649 0.051874951 0.087438303 5493.960409 -3.739885525 0.390107056 RLS(ph)QPAGGLLDSITNIFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSQPAGGLLDSITNIFGR 19 1 Q676U5-3;Q676U5;Q676U5-4 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 RLS(1)QPAGGLLDSITNIFGR;RLS(1)QPAGGLLDSITNIFGR 171.73 5.94E-12 105456000 47705 56658 48319 41312 48850 52074 39074 51968 58956 44938 TRUE FALSE 45840.63586 55042.16931 57051.31815 43444.11727 50421.30461 53126.97196 39552.1993 50894.84264 52263.56204 41894.30923 1.0941972 1.313834034 1.361791594 1.036993283 1.203535887 1.268119058 0.944094795 1.214839045 1.247509817 1 15.35446667 3.739910607 24.99997122 1.141160402 1.262330246 0.180500431 0.1213152 212.7425985 3939693.831 0.030859588 0.052023357 5494.277702 -3.739910607 0.121169844 TSDDEVGS(ph)PKEESR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSDDEVGSPKEESR 14 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 1 TSDDEVGS(1)PKEESR 70.335 0.026947 197440000 274270 228640 217660 191010 218240 216560 194950 215740 264380 228080 TRUE FALSE 263551.2252 222119.4111 256996.0038 200868.049 225259.8878 220938.9916 197335.8564 211284.8936 234368.6908 212631.9384 1.239471488 1.044619226 1.208642529 0.944674871 1.05938877 1.039067758 0.928063102 0.993664899 1.102227128 1 17.69799879 3.739930099 24.99999073 1.006768192 1.152281897 0.521955023 0.067499614 97.32284032 1776628.721 0.016856944 0.028414918 5494.524312 -3.739930099 0.145513705 TFVLEVMGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TFVLEVMGR 9 0 Q01813;Q01813-2;Q5VSR5;P17858;P17858-2;A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 Q01813;P17858;A0A2R8Y891 PFKP;PFKL;PFKM "ATP-dependent 6-phosphofructokinase, platelet type;ATP-dependent 6-phosphofructokinase, liver type;ATP-dependent 6-phosphofructokinase, muscle type" 0 90.709 0.026165 42626000 161400 176140 138550 120520 134470 96222 144720 131110 134040 130660 FALSE TRUE 155092.3096 171116.6597 163589.067 126740.0516 138795.3497 98167.67477 146491.1267 128402.5327 118824.3411 121810.2818 1.273228395 1.404780098 1.34298242 1.040470884 1.139438704 0.80590631 1.20261709 1.054119002 0.975486957 1 16.89427639 3.739969946 7.710783516 1.039729409 1.347394701 0.654000349 0.102888441 0.070494584 39.98203882 0.026028573 0.04375578 5495.028456 -3.739969946 0.307665292 KIQEESLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIQEESLR 8 1 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ; 166.33 0.00051168 610840000 461270 559450 434050 300040 356280 126912 465910 312060 370270 473540 FALSE TRUE 443243.0584 543495.0338 512492.4904 315525.1004 367740.0698 129478.2476 471611.9459 305615.8519 328238.5019 441466.714 1.004023734 1.231112146 1.160885915 0.714720024 0.832996142 0.293291076 1.068284269 0.692273828 0.743518121 1 18.75194514 3.739988604 24.99788548 0.74979417 1.141917776 0.407983793 0.202796677 112.3843706 1967350.009 0.050237382 0.08481444 5495.26454 -3.739988604 0.392123607 RSQS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSQSPVK 7 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RS(0.145)QS(0.855)PVK 54.608 0.08124 90093000 225480 226820 179640 113130 129940 45162 162140 106680 114420 149830 TRUE FALSE 216667.9923 220351.3157 212104.9441 118968.6529 134119.6381 46075.20658 164124.3178 104477.0207 101431.5213 139681.8806 1.551153173 1.577522544 1.518485741 0.85171142 0.960179212 0.329858149 1.174986455 0.747964018 0.726160908 1 17.09178536 3.740212242 4.298803702 0.814661478 1.563457644 0.716644619 0.208128895 0.100509579 4.744513752 0.052953283 0.092073707 5498.095028 -3.740212242 0.748796166 VVPTTDHIDTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVPTTDHIDTEK 12 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 84.365 0.012278 531800000 1193100 1251800 921050 1246400 1142400 1199700 1298600 1180700 1467900 1318100 FALSE TRUE 1146472.333 1216099.89 1087504.224 1310726.853 1179146.334 1223958.756 1314492.655 1156318.132 1301270.146 1228823.913 0.932983417 0.989645365 0.88499598 1.066651486 0.959573069 0.996040802 1.069716044 0.940995793 1.058955748 1 20.22884677 3.740218274 24.99999346 1.007249086 0.941251969 0.351484404 0.047455297 177.9638457 2683946.545 0.011692302 0.019767763 5498.171396 -3.740218274 -0.065997117 HLDVDLDRQS(ph)LSS(ph)IDKNPSER ddPTM_BT-474_Pertuzumab_2h_R1 3 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 HLDVDLDRQS(1)LS(0.209)S(0.791)IDKNPSER;HLDVDLDRQS(0.996)LS(0.465)S(0.539)IDKNPSER;HLDVDLDRQS(0.999)LS(0.227)S(0.774)IDKNPSER 168.26 5.92E-12 2673220000 1416490 1360840 1188990 1027450 1159720 1227460 1150420 795450 1637580 1423190 TRUE FALSE 1361132.005 1322030.176 1403866.942 1080476.818 1197023.447 1252280.082 1164499.184 779023.6795 1451688.784 1326796.074 1.025878831 0.996407965 1.058087953 0.814350328 0.902190978 0.943837645 0.877677593 0.587146507 1.094131052 1 20.33951522 3.740352502 24.94124123 0.857246675 1.023753226 0.169592921 0.12773155 222.6994299 3099736.948 0.034613445 0.058529625 5499.870983 -3.740352502 0.166506551 KAVEEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAVEEAR 7 1 Q96DT6 Q96DT6 ATG4C Cysteine protease ATG4C 0 ; 111.04 0.010693 462000000 1897430 1973560 1626970 1503890 1552470 1045720 1891410 1783060 1829770 2018070 FALSE TRUE 1823276.338 1917276.001 1920999.671 1581505.943 1602406.607 1066865.175 1914557.641 1746239.188 1622062.181 1881384.321 0.969114241 1.019077272 1.02105649 0.840607592 0.851716786 0.567063923 1.0176324 0.928167184 0.862164185 1 20.84336316 3.740354788 24.68541816 0.86414244 1.004682136 0.221669872 0.116971738 207.1338478 2849861.827 0.03151506 0.053304422 5499.899929 -3.740354788 0.140539696 KLTATEGPGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 KLTATEGPGSPR 12 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR 157.84 4.55E-05 5782760000 6221840 6179600 4905440 5969370 6139660 6064900 5987280 6375620 6552200 6071220 TRUE FALSE 5978683.614 6003363.858 5791962.129 6277449.901 6337147.74 6187536.433 6060554.124 6243961.219 5808421.725 5660010.862 1.056302498 1.060662957 1.0233129 1.10908796 1.119635261 1.093202219 1.070767225 1.103171243 1.02622095 1 22.43237339 3.740408673 24.99617594 1.082429654 1.048149804 0.080557654 0.036839084 291.7398883 3945973.959 0.00914721 0.015589825 5500.582379 -3.740408673 -0.03427985 YNHIDESEMK ddPTM_BT-474_Pertuzumab_2h_R1 4 YNHIDESEMK 10 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 189.58 9.95E-07 4272880000 7404230 7151180 6280220 5925400 6419200 5511980 7290300 5380450 9082090 8591400 FALSE TRUE 7114864.506 6947235.348 7415195.457 6231210.604 6625679.398 5623436.012 7379520.872 5269341.827 8051129.218 8009496.826 0.888303555 0.867374755 0.925800411 0.777977786 0.82722792 0.702096041 0.921346376 0.657886749 1.005197879 1 22.93328018 3.740425417 24.92567467 0.816586872 0.89118109 0.010426424 0.110390369 393.1902295 5255504.225 0.026747208 0.045215225 5500.794455 -3.740425417 0.074594218 TGGS(ph)PSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGGSPSVR 8 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 T(0.076)GGS(0.902)PS(0.022)VR 83.647 0.018895 252380000 335820 340100 276930 348120 342470 377470 355330 376530 397130 379290 TRUE FALSE 322695.7831 330400.681 326977.4113 366086.5149 353485.8586 385102.702 359678.6348 368754.5239 352049.4673 353600.3505 0.912600292 0.93439014 0.924708957 1.035311516 0.999676211 1.089090272 1.017189701 1.042856783 0.995614023 1 18.43176018 3.74051922 24.70788956 1.029265714 0.924948822 0.754379048 0.02655601 64.93429669 819142.6581 0.006582519 0.011168113 5501.98269 -3.74051922 -0.104316892 QAS(ph)VHDS(ph)GEEGEA ddPTM_BT-474_Pertuzumab_2h_R1 2 QASVHDSGEEGEA 13 0 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 QAS(1)VHDS(1)GEEGEA;QAS(1)VHDS(1)GEEGEA 160.5 6.40E-05 1805200000 1123000 1278930 995230 1373700 1470910 1483590 1399520 1411880 1515220 1481630 TRUE FALSE 1079111.918 1242456.169 1175090.2 1444596.822 1518223.156 1513589.206 1416647.744 1382724.185 1343218.578 1381277.88 0.781241728 0.899497622 0.850726864 1.045840842 1.0991439 1.095789072 1.025606624 1.001047077 0.97244631 1 20.39757215 3.740540973 24.42879034 1.036753161 0.849389608 0.779534533 0.046370789 60.91587351 751424.1374 0.012977858 0.021976173 5502.258284 -3.740540973 -0.187363553 HWGGNVLGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 HWGGNVLGPK 10 0 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 72.79 0.046931 422850000 1814300 1875400 1588900 610290 674580 403300 1403200 515770 850380 1110000 FALSE TRUE 1743395.15 1821915.428 1876049.575 641787.14 696278.4783 411455.0023 1420372.781 505119.1693 753848.4275 1034818.711 1.684734854 1.760613147 1.812925834 0.620192825 0.672850685 0.39761071 1.37258127 0.488123343 0.728483568 1 19.98094662 3.740563451 24.99783884 0.738044942 1.753543526 0.755723897 0.260029783 78.94255191 985294.8846 0.065325427 0.110786601 5502.543073 -3.740563451 1.015498584 SLDLFNCEVTNLNDYR ddPTM_BT-474_Pertuzumab_2h_R1 7 SLDLFNCEVTNLNDYR 16 0 Q92688;Q92688-2;P39687;H0YN26 Q92688;P39687 ANP32B;ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member B;Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;;;; 375.79 3.42E-104 1432727000 555553 582080.1 454055.8 586627.6 581794.2 584254 553482.2 681245 601862.5 665323 FALSE TRUE 533841.3746 565479.7455 536113.7835 616903.5207 600508.1388 596068.0162 560255.8807 667177.0527 533541.5922 620260.0806 0.860673436 0.911681669 0.864337074 0.994588464 0.968155388 0.960996902 0.903259614 1.075640805 0.860190118 1 19.24251375 3.740564737 24.97801689 0.971601447 0.882175817 0.336533166 0.055693502 189.9352057 2367213.232 0.013982123 0.023693852 5502.559374 -3.740564737 -0.08942563 MLNS(ph)SFEDDPFFSESILAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLNSSFEDDPFFSESILAHR 20 0 A0A494C175;A0A0S2Z4A4;P58340 A0A494C175 MLF1 Myeloid leukemia factor 1 1 MLNS(0.605)S(0.395)FEDDPFFSESILAHR 167.72 8.58E-12 63579000 27920 31851 24541 38745 46651 36798 37736 45379 31525 39946 TRUE FALSE 26828.85553 30942.64067 28976.10461 40744.63409 48151.57178 37542.08077 38197.82446 44441.90779 27946.41416 37240.42184 0.720422976 0.830888565 0.778082073 1.094097008 1.292992115 1.008100309 1.025708694 1.193378206 0.750432266 1 15.18458179 3.740575527 24.44555132 1.073739497 0.781906914 0.456998854 0.136225626 107.3317392 1302171.843 0.034740301 0.058877188 5502.696076 -3.740575527 -0.291832583 VTKS(ph)PAPVHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTKSPAPVHR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 VT(0.069)KS(0.931)PAPVHR;VT(0.002)KS(0.998)PAPVHR;VT(0.022)KS(0.978)PAPVHR;VT(0.005)KS(0.995)PAPVHR 124.47 0.00026328 2537910000 4277890 4206410 3477930 3062790 3067370 3448220 2728360 3635240 3888940 3465150 TRUE FALSE 4110705.329 4086447.305 4106469.317 3220860.959 3166034.742 3517945.371 2761750.486 3560171.024 3447483.835 3230452.304 1.272486 1.264976827 1.271174724 0.997030959 0.980059275 1.088994679 0.854911395 1.102065806 1.067183017 1 21.62330474 3.740678556 24.83176039 1.01451234 1.269088967 0.762014185 0.065723598 77.5606702 909354.8476 0.016765667 0.028436094 5504.001656 -3.740678556 0.254576627 NQGGYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQGGYDR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 125.08 0.0095001 167873000 277720 258770 201365 268400 250430 250090 273830 280260 268870 306750 FALSE TRUE 266866.3954 251390.133 237756.1348 282252.1562 258485.3084 255146.9912 277181.2135 274472.5331 238349.0048 285973.5493 0.93318559 0.87906778 0.831392048 0.986986932 0.90387838 0.892204862 0.969254724 0.959782937 0.833465212 1 18.12552219 3.740721641 24.98986601 0.934082376 0.881000408 0.183843438 0.051980266 328.5030469 3798770.749 0.013206979 0.022409742 5504.547715 -3.740721641 -0.053081969 YQVFFFGTHETAFLGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 YQVFFFGTHETAFLGPK 17 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 231.91 3.13E-16 1928930000 1070900 1123480 915020 865090 910260 914650 948470 884940 1091240 1052780 FALSE TRUE 1029048.044 1091439.45 1080384.469 909737.3986 939539.3396 933144.8497 960077.6596 866665.6798 967367.0101 981474.2729 1.048471746 1.112040815 1.100777166 0.926909063 0.957273528 0.950758339 0.978199517 0.883024348 0.985626457 1 19.90459093 3.740796124 24.99779038 0.947240989 1.089591008 0.749745705 0.03490773 84.98317998 950292.8629 0.008915752 0.015169325 5505.491843 -3.740796124 0.142350018 LFDIHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFDIHK 6 0 A0A2R8Y430;P48637;A0A2R8Y5T7;A0A2R8YF34;A0A2R8Y790;A0A2R8Y446;A0A0S2Z4J7 A0A2R8Y430 GSS Glutathione synthetase 0 ; 92.279 0.046937 894390000 1694790 1997390 1567690 820980 711950 44446 1823910 754750 1217620 1810100 FALSE TRUE 1628555.733 1940426.393 1851006.456 863350.8762 734850.5183 45344.72857 1846231.556 739164.1487 1079400.882 1687500.315 0.965069884 1.149882092 1.09689251 0.511615239 0.435466893 0.026870945 1.09406294 0.438023118 0.639644848 1 20.68645634 3.740826919 24.51512687 0.562905452 1.078541599 0.366715095 0.2862116 148.1052758 1602077.101 0.072201443 0.122653772 5505.882247 -3.740826919 0.515636147 ILTTEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILTTEGR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 128.75 0.0086702 201440000 141660 156500 113920 176330 197930 175720 162610 164170 191580 184420 FALSE TRUE 136123.7706 152036.7732 134507.8781 185430.4124 204296.5982 179273.1788 164600.0698 160779.8321 169832.6416 171929.0691 0.791743777 0.884299403 0.782345178 1.078528566 1.188260945 1.042715928 0.95737196 0.935152112 0.987806439 1 17.39145397 3.74083731 24.99864185 1.022093192 0.82594644 0.638448766 0.071490715 153.80534 1688809.974 0.021714148 0.03691908 5506.013988 -3.74083731 -0.196146751 KDISQNKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDISQNKR 8 2 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 66.435 0.034698 332020000 434560 429920 369820 274030 272310 148050 412520 296810 415740 460800 FALSE TRUE 417576.9148 417659.1025 436654.7006 288172.7211 281069.0985 151043.6724 417568.5432 290680.7698 368546.9381 429589.6056 0.972036822 0.972228139 1.01644615 0.670809343 0.654273509 0.351599923 0.972017334 0.676647586 0.857904692 1 18.71259956 3.740884742 24.78362425 0.719433672 0.985436162 0.288589683 0.175142316 210.3533425 2243116.841 0.044571894 0.075739926 5506.615361 -3.740884742 0.26600249 STSTLEIQPSRAS(ph)PTSDIESVER ddPTM_BT-474_Pertuzumab_2h_R1 3 STSTLEIQPSRASPTSDIESVER 23 1 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 STSTLEIQPS(0.013)RAS(0.874)PT(0.057)S(0.057)DIESVER;STSTLEIQPS(0.017)RAS(0.955)PT(0.013)S(0.013)DIESVER;STSTLEIQPSRAS(0.972)PT(0.014)S(0.014)DIESVER 262.19 4.98E-44 2758000000 1144162 1091133 813070 1240180 1186790 1230260 1253200 1199087 1190780 1243493 TRUE FALSE 1099446.884 1060014.955 960009.8356 1304185.838 1224964.178 1255136.7 1268537.036 1174325.434 1055607.647 1159270.112 0.948395782 0.914381338 0.828115748 1.125006006 1.056668473 1.082695644 1.094254932 1.012986898 0.910579541 1 20.14478532 3.740899863 24.99994926 1.04460724 0.898705994 0.523351419 0.062590668 165.6989618 1770845.419 0.016715613 0.028463347 5506.807096 -3.740899863 -0.145901246 KVEDMMK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEDMMK 7 1 P13639 P13639 EEF2 Elongation factor 2 0 76.827 0.063663 963930000 2030500 1852000 1661500 1053300 1097900 523420 1636400 1304200 1546700 1701400 FALSE TRUE 1951145.815 1799182.773 1961770.01 1107660.939 1133214.951 534003.911 1656426.753 1277267.814 1371125.1 1586162.663 1.230104491 1.134299032 1.23680254 0.698327457 0.714438044 0.336664028 1.044298162 0.805256513 0.864429061 1 20.5971093 3.74091722 24.99908569 0.770035779 1.193791746 0.519979624 0.184663534 165.2250053 1752714.696 0.048753504 0.082926166 5507.027183 -3.74091722 0.423755966 ERDQLLHILFNLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDQLLHILFNLIK 14 1 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 0 105.78 0.00058863 15089000 50563 50756 42391 36068 38432 18601 52923 37216 49279 54573 FALSE TRUE 48586.94206 49308.48858 50051.99668 37929.4738 39668.20018 18977.12496 53570.68751 36447.47659 43685.05451 50876.7221 0.954993562 0.969175814 0.98378973 0.745517247 0.77969253 0.373002115 1.052950845 0.716388067 0.858645225 1 15.6347181 3.740953647 24.33386379 0.773141504 0.969305328 0.179695724 0.173672703 223.4146923 2271803.416 0.043535276 0.074022677 5507.489108 -3.740953647 0.196163824 VKTDDIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKTDDIAR 8 1 Q52LJ0;Q52LJ0-1 Q52LJ0 FAM98B Protein FAM98B 0 ; 102.07 0.0045933 238430000 670120 646300 547050 361340 405580 138480 548750 418880 489580 569920 FALSE TRUE 643930.9695 627868.1568 645914.1041 379988.8007 418625.849 141280.1605 555465.7666 410229.9816 434004.9309 531318.8108 1.211948375 1.181716408 1.215680851 0.715180402 0.787899545 0.265904684 1.045447207 0.772097606 0.816844655 1 19.01921827 3.740972357 24.70545657 0.760090045 1.200975364 0.499620939 0.197501332 143.4230479 1469191.73 0.050707785 0.086243228 5507.726379 -3.740972357 0.440885319 ADWWTNTAHYNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADWWTNTAHYNR 12 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 153.54 7.07E-05 290020000 307200 323640 262490 188980 225170 94284 288040 204890 226470 259580 FALSE TRUE 295194.2844 314410.1041 309927.7821 198733.2804 232412.7975 96190.48708 291565.1197 200658.9499 200762.075 241998.4154 1.21981908 1.299223813 1.2807017 0.82121728 0.96038975 0.397483954 1.204822433 0.829174644 0.829600784 1 17.88463808 3.740989485 24.62086027 0.860235013 1.269845792 0.480437564 0.192185703 141.1273096 1430565.029 0.048102836 0.081819299 5507.943604 -3.740989485 0.40961078 GNRES(ph)DGFREEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNRESDGFREEK 12 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 GNRES(1)DGFREEK 78.069 0.021045 570910000 382400 359030 306040 320890 336110 310140 348910 365580 347860 395710 TRUE FALSE 367455.3852 348790.8159 361348.2358 337451.1714 346921.2834 316411.2433 353180.065 358030.6452 308372.3911 368908.2092 0.996061828 0.945467754 0.979507169 0.914729363 0.940400009 0.857696401 0.957365697 0.970514172 0.835905473 1 18.49290237 3.741060595 24.89272052 0.926548605 0.970857802 0.17592695 0.047875715 399.1105375 3974005.471 0.01211692 0.020612954 5508.845532 -3.741060595 0.044309197 KGVTSILPVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGVTSILPVLR 11 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 100.55 0.0043449 0 350360 357210 295020 219700 235760 227590 268060 231790 267560 285070 FALSE TRUE 336667.5439 347022.7205 348336.6767 231038.7433 243343.4345 232192.0257 271340.5985 227003.4555 237187.7105 265761.955 1.266801126 1.305765231 1.31070934 0.869344686 0.915644357 0.873684218 1.020991129 0.854160843 0.89248181 1 18.01977507 3.741143476 24.99976524 0.912889937 1.295559257 0.914653835 0.052669937 53.71614712 519921.9206 0.013093581 0.022317061 5509.896938 -3.741143476 0.38266932 QQSHFAMMHGGTGFAGIDSSS(ph)PEVK ddPTM_BT-474_Pertuzumab_2h_R1 3 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.003)S(0.109)S(0.888)PEVK;QQSHFAMMHGGTGFAGIDS(0.011)S(0.443)S(0.546)PEVK;QQSHFAMMHGGTGFAGIDS(0.028)S(0.205)S(0.767)PEVK 173.81 2.56E-12 972270000 391150 360900 305258 268631 300704 292755 291213 190556 400180 408120 TRUE FALSE 375863.4256 350607.4854 360424.911 282495.0781 310376.4173 298674.7067 294776.9518 186620.952 354753.2441 380477.6689 0.987872499 0.921492939 0.947295835 0.742474792 0.815754623 0.784999308 0.774754935 0.49049121 0.932389134 1 18.53745226 3.741164418 23.44662989 0.754296391 0.949147711 0.208083906 0.130087038 118.4346994 1066459.609 0.034651433 0.05897729 5510.162637 -3.741164418 0.19485132 DWVLNEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DWVLNEFK 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 105.52 0.010171 581960000 1067900 989160 888850 520890 612700 170850 848490 669650 745040 956600 FALSE TRUE 1026165.287 960950.1253 1049484.967 547773.1953 632408.0519 174304.7041 858874.0744 655821.4935 660466.1827 891808.6299 1.150656377 1.07752952 1.176805126 0.614227287 0.709129774 0.195450793 0.96306993 0.735383659 0.740591827 1 19.76637463 3.74119902 24.95401797 0.694661704 1.129250283 0.469611449 0.207443393 192.5900463 1821508.432 0.053416686 0.091038386 5510.60167 -3.74119902 0.434588579 WQDEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 WQDEHK 6 0 Q96BX8 Q96BX8 MOB3A MOB kinase activator 3A 0 71.029 0.08931 75613000 132470 136060 114420 113110 124170 102230 130680 125810 143000 139960 FALSE TRUE 127292.9259 132179.702 135098.2393 118947.6207 128164.0408 104297.1606 132279.3009 123211.9795 126767.2395 130480.3845 0.975571358 1.013023547 1.03539118 0.911613045 0.982247571 0.799332107 1.013786872 0.944295037 0.971542504 1 16.99347341 3.741246643 24.98752379 0.943517269 1.008498181 0.190113501 0.05835178 365.2592569 3397911.107 0.01464035 0.024910962 5511.205981 -3.741246643 0.064980912 LKSDTAAAAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKSDTAAAAVR 11 1 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 154.94 2.90E-05 986560000 2050880 2267340 1842580 1407930 1519710 651920 2076850 1699680 1906910 2078810 FALSE TRUE 1970729.342 2202677.683 2175575.194 1480593.436 1568592.852 665102.2691 2102267.112 1664581.014 1690445.571 1938010.347 1.016882776 1.136566524 1.122581826 0.763976022 0.809383115 0.343188193 1.08475536 0.858912346 0.87225828 1 20.88614484 3.741341457 24.67136417 0.812477118 1.09646601 0.310958232 0.186077378 243.2718187 2158273.924 0.048940285 0.083488609 5512.409303 -3.741341457 0.283988892 KVIIWR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVIIWR 6 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ; 126.04 0.028323 944620000 706600 767210 559220 418100 525150 538190 244559 419850 532950 602450 FALSE TRUE 678985.2908 745329.922 660283.4938 439678.1911 542041.9267 549072.5705 247551.9862 411179.9508 472451.7503 561645.5249 1.208921394 1.327046845 1.175623172 0.782839303 0.965096137 0.977614075 0.440761967 0.732098686 0.84119205 1 19.09930035 3.741353216 1.132251707 0.761839466 1.315116267 0.556712378 0.164433204 0.386154829 0.928907863 0.057163594 0.167829444 5512.558564 -3.741353216 0.553276801 LFVGNLPPDITEEEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFVGNLPPDITEEEMR 16 0 Q15233;C9JYS8;C9IZL7;C9J4X2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 166.86 1.52E-08 54886000 170300 170990 130010 171330 171790 163120 165170 175330 182680 190910 FALSE TRUE 163644.4877 166113.5326 153505.6991 180172.3618 177315.7814 166418.3982 167191.3999 171709.3742 161942.9323 177979.4957 0.91945697 0.933329606 0.862490921 1.012320892 0.996270838 0.935042531 0.939385738 0.964770541 0.909896568 1 17.44135152 3.741354881 24.99612091 0.962514601 0.907916213 0.387617625 0.03454157 277.6747018 2483928.282 0.009062089 0.015471891 5512.579689 -3.741354881 -0.054598389 QNLNDR ddPTM_BT-474_Pertuzumab_2h_R1 4 QNLNDR 6 0 K7EMD9 K7EMD9 KRT13 0 ;;; 110.63 0.066388 1727860000 1211550 1132100 887890 1826380 1712140 3030440 1232060 1658880 1723150 1455650 FALSE TRUE 1164201.287 1099813.616 1048351.474 1920639.691 1767212.538 3091717.573 1247138.319 1624623.548 1527545.236 1357057.529 0.857886465 0.810439936 0.772518078 1.415297178 1.302238483 2.278250927 0.919001805 1.197166306 1.12563042 1 20.37205045 3.741360853 24.6633297 1.333256285 0.813297301 0.300519422 0.353364195 255.5614711 2250865.991 0.09418567 0.160742067 5512.655504 -3.741360853 -0.519958984 YSGSYNDYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YSGSYNDYLR 10 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 137.05 0.0098092 0 304560 354130 268820 137720 146750 37024 241070 135870 133490 221990 FALSE TRUE 292657.4585 344030.5591 317401.7539 144827.7457 151470.347 37772.65065 244020.2868 133064.237 118336.7748 206954.4196 1.414115529 1.662349419 1.533679515 0.699805039 0.731901968 0.182516763 1.179101598 0.642963979 0.571801149 1 17.65895353 3.741407954 8.074128388 0.703956337 1.550726428 0.689034968 0.252705944 0.062138737 44.21353017 0.063816191 0.107628621 5513.253401 -3.741407954 0.846770091 S(ph)FLESNYFTKPNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFLESNYFTKPNLK 14 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 S(1)FLESNYFTKPNLK;S(1)FLESNYFTKPNLK 138.55 8.95E-06 761460000 771980 697110 600420 597490 646360 555600 568500 798520 642900 605840 TRUE FALSE 741810.1681 677229.1053 708929.2503 628326.5305 667150.7564 566834.6127 575457.4731 782030.283 569920.6873 564805.9172 1.313389512 1.199047469 1.2551732 1.112464497 1.181203554 1.003591845 1.018858789 1.384600018 1.009055801 1 19.10739568 3.741416675 23.7955462 1.12707335 1.250187815 0.254289662 0.115382832 224.1213093 1867265.798 0.031433713 0.053618401 5513.364117 -3.741416675 0.123114465 NREELGFRPEYSASQLK ddPTM_BT-474_Pertuzumab_2h_R1 4 NREELGFRPEYSASQLK 17 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 195.97 9.23E-12 5286010000 1709010 1572570 1439580 1249540 1415790 1210870 1428770 1535800 1643420 1580390 FALSE TRUE 1642220 1527721.843 1699744.129 1314028.909 1461330.171 1235354.621 1446255.715 1504085.193 1456865.851 1473348.778 1.114617275 1.036904409 1.153660393 0.891865476 0.99184266 0.838467198 0.981611236 1.020861602 0.988812611 1 20.49066756 3.74144126 24.99981955 0.961356272 1.095245065 0.55419553 0.058523266 202.6283672 1758511.848 0.015551731 0.026547668 5513.676227 -3.74144126 0.133888793 SS(ph)GPYGGGGQYFAKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-2;P09651;P09651-3;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 S(0.271)S(0.729)GPYGGGGQYFAKPR;S(0.153)S(0.847)GPYGGGGQYFAKPR 93.342 0.0027037 760110000 199850 187282 161492 136070 137693 142592 145230 168629 161993 162854 TRUE FALSE 192039.6411 181940.9007 190677.1968 143092.589 142122.0204 145475.3079 147007.3682 165146.7522 143604.2338 151823.7535 1.264885346 1.198369139 1.255911492 0.942491446 0.936098714 0.958185426 0.96827647 1.087753058 0.945861438 1 17.212038 3.741481923 24.99963851 0.983926195 1.235586722 0.878202211 0.044783681 92.17210774 788776.8647 0.01308763 0.022373678 5514.192498 -3.741481923 0.251660527 ASFAYAWVLDETGEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ASFAYAWVLDETGEER 16 0 Q9Y450;Q9Y450-4;J3QT46;B7Z524;H0YDX7;E9PHZ9 Q9Y450 HBS1L HBS1-like protein 0 77.644 0.015757 0 38557 37633 33349 30502 33893 33148 34083 33477 36723 45271 FALSE TRUE 37050.14981 36559.74369 39375.90614 32076.21188 34983.19913 33818.27527 34500.11795 32785.68825 32554.359 42204.75485 0.877866723 0.866247034 0.932973223 0.760014174 0.828892367 0.801290646 0.817446235 0.776824516 0.771343398 1 15.36511792 3.741621724 24.99881994 0.81022491 0.889750796 0.173602979 0.0664871 366.9085684 2996383.27 0.015745631 0.026911481 5515.967822 -3.741621724 0.079525886 LSTIQNS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSTIQNSPTK 10 0 Q5VYV7 Q5VYV7 SLX4IP Protein SLX4IP 1 LSTIQNS(1)PTK;LSTIQNS(0.999)PT(0.001)K 193.34 6.13E-07 669450000 1112610 1016710 876950 691420 735070 391730 926830 832730 891730 992680 TRUE FALSE 1069127.971 987714.4263 1035434.373 727104.2691 758714.1941 399651.049 938172.8228 815533.8345 790504.5488 925444.8994 1.155258376 1.067286045 1.118850375 0.785680779 0.819837242 0.431847481 1.013753302 0.88123435 0.854188671 1 19.81978757 3.741668846 24.45926959 0.820577919 1.10914707 0.428382903 0.151861901 193.0090669 1518815.979 0.040196655 0.068746856 5516.566347 -3.741668846 0.28856915 GGET(ph)PGSEQWK ddPTM_BT-474_Pertuzumab_2h_R1 3 GGETPGSEQWK 11 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 GGET(1)PGSEQWK;GGET(1)PGSEQWK;GGET(0.999)PGS(0.001)EQWK 196.7 6.46E-06 1040330000 1539440 1555440 1376720 1195900 1172640 1433930 1175740 1463940 1721140 1706810 TRUE FALSE 1479276.983 1511080.374 1625523.929 1257620.542 1210359.031 1462925.047 1190129.058 1433709.127 1525763.403 1591206.238 0.929657606 0.949644576 1.021567091 0.790356719 0.760655031 0.919381166 0.747941423 0.901020303 0.958872185 1 20.60168941 3.741977516 24.98821994 0.857276138 0.965225238 0.226283886 0.08180012 394.079427 2881942.075 0.020784857 0.035663781 5520.488585 -3.741977516 0.107949101 RLQTQVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLQTQVFK 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ; 133.13 0.0014951 1072620000 1615810 1514500 1370040 786470 1038520 342930 1320040 1078750 1015080 1261400 FALSE TRUE 1552662.359 1471307.943 1617636.704 827059.811 1071924.939 349864.2796 1336195.044 1056473.436 899852.374 1175964.254 1.320331254 1.251150226 1.375583227 0.70330353 0.911528505 0.297512682 1.136254813 0.898389072 0.765203849 1 20.16541278 3.742076082 24.99822482 0.819075897 1.309234461 0.541141229 0.210809585 233.8943411 1663199.906 0.054353128 0.09331546 5521.741636 -3.742076082 0.490158564 QPS(ph)VDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPSVDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR 38 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 QPS(1)VDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR 244.49 1.73E-50 132400000 76421 97105 64907 100530 106620 100830 100300 88466 95054 104310 TRUE FALSE 73434.38283 94335.66048 76637.13875 105718.3653 110049.5291 102868.8517 101527.5014 86639.14619 84263.86842 97244.99079 0.755148232 0.970082466 0.788083151 1.087134304 1.131672986 1.057831883 1.044038367 0.890936854 0.866511146 1 16.56933632 3.74208787 24.90105153 1.008356968 0.8510024 0.419847705 0.092972107 335.2791974 2366932.429 0.026348505 0.04518349 5521.891511 -3.74208787 -0.157354568 KQQLAEEEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQQLAEEEAR 10 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 109.72 0.0031765 466440000 403400 409160 333890 433460 482660 397210 412940 488100 492160 491990 FALSE TRUE 387634.682 397491.1574 394231.3503 455830.9225 498185.1972 405241.8583 417993.6832 478020.5644 436292.0601 458667.0791 0.845132994 0.866622384 0.859515253 0.993816525 1.08615861 0.883520699 0.911322618 1.042195061 0.951217299 1 18.80708784 3.742314013 23.70558387 0.9825709 0.858043407 0.511793331 0.055523369 131.2778978 829111.2158 0.014945707 0.025662085 5524.767589 -3.742314013 -0.124527493 RQQEGFK ddPTM_BT-474_Pertuzumab_2h_R1 4 RQQEGFK 7 1 Q15233;Q15233-2;H7C367;Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q15233;Q8WXF1 NONO;PSPC1 Non-POU domain-containing octamer-binding protein;Paraspeckle component 1 0 ;;; 169.06 0.001645 3371150000 3347580 3497270 2918970 2308580 2588600 1275830 3083390 2908170 3172030 3343540 FALSE TRUE 3216752.873 3397531.284 3446492.811 2427726.09 2671864.67 1301628.157 3121125.449 2848115.273 2811954.453 3117079.058 1.031976672 1.089972766 1.105680269 0.778846492 0.857169363 0.417579449 1.001298136 0.913712877 0.90211201 1 21.57176332 3.742341991 24.92432732 0.833582044 1.077286203 0.323610267 0.157025975 374.9563363 2471455.502 0.041867353 0.071977257 5525.123512 -3.742341991 0.243704159 EIVQQLIDEYHAATRPDYISWGTQEQ ddPTM_BT-474_Pertuzumab_2h_R1 2 EIVQQLIDEYHAATRPDYISWGTQEQ 26 1 P23258 P23258 TUBG1 Tubulin gamma-1 chain 0 ; 206.56 2.70E-25 424180000 229885 253148 192415 255279 259196 266831 265736 252363 259786 284723 FALSE TRUE 220900.84 245928.4669 227188.6707 268453.9798 267533.2747 272226.5056 268988.1567 247151.6159 230296.1824 265438.4576 0.832211135 0.926499005 0.855899604 1.011360532 1.007891913 1.025572964 1.013372964 0.931107037 0.867606693 1 18.01801788 3.742433677 24.98059941 0.978924163 0.87703282 0.491268178 0.050278056 314.5759507 2028956.399 0.013886808 0.023893982 5526.290072 -3.742433677 -0.101891343 ASAS(ph)PGENDSGTGGEEPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASASPGENDSGTGGEEPQR 19 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 AS(0.015)AS(0.985)PGENDSGTGGEEPQR 130.85 1.76E-05 70233000 46734 47674 38564 55625 58644 59666 61747 52492 53361 62847 TRUE FALSE 44907.58361 46314.3842 45533.37265 58495.81292 60530.33752 60872.4874 62502.67826 51408.02186 47303.68299 58590.31671 0.766467671 0.790478475 0.77714843 0.998387041 1.033111629 1.038951329 1.066774883 0.877414985 0.807363497 1 15.83837463 3.742535101 24.71346838 0.974298958 0.779276203 0.59601651 0.074148141 221.1670628 1375217.909 0.021350656 0.036735946 5527.580813 -3.742535101 -0.195022755 LINQVLELQHTLEDLSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LINQVLELQHTLEDLSAR 18 0 A0A0C4DGB0;Q9UIL1-3;Q9UIL1-2;Q9UIL1 A0A0C4DGB0 SCOC Short coiled-coil protein 0 245.3 3.35E-24 468610000 212600 239490 174880 239270 231690 246980 241420 234290 246050 258200 FALSE TRUE 204291.357 232659.9797 206484.7062 251618.7534 239142.5193 251974.1048 244374.5702 229451.8296 218119.4355 240711.884 0.848696598 0.966549619 0.857808525 1.045310889 0.993480319 1.046787141 1.015216059 0.953221859 0.906143194 1 17.87694784 3.742692411 24.99999999 0.993331715 0.898571384 0.480160925 0.049054581 337.3337958 2041079.124 0.012954639 0.022314348 5529.583377 -3.742692411 -0.094760331 VGELKDDDFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGELKDDDFEK 11 1 Q02750;Q02750-2 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 0 60.364 0.085837 1035800000 1309800 1060000 1047800 627530 890470 861860 799620 634570 961500 821130 FALSE TRUE 1258611.568 1029769.838 1237160.768 659916.8985 919112.7763 879287.3997 809405.9888 621465.9077 852354.5509 765514.1337 1.644138903 1.345200294 1.616117474 0.862057106 1.20064769 1.148623338 1.05733644 0.81182813 1.113440645 1 19.54606949 3.742721021 24.99960878 1.021024845 1.516157052 0.746169648 0.135454321 180.9984069 1087604.12 0.036138908 0.062340585 5529.947663 -3.742721021 0.495132207 VLPQGPPT(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLPQGPPTPAK 11 0 Q8IWY9;Q8IWY9-1;H3BPZ6 Q8IWY9 CDAN1 Codanin-1 1 VLPQGPPT(1)PAK 110.98 0.019238 161360000 419420 395670 350740 316150 359430 349670 329750 372890 386360 394500 TRUE FALSE 403028.6027 384385.879 414126.5202 332466.5394 370991.3924 356740.567 333785.5791 365189.6912 342502.0326 367780.1636 1.095841056 1.045151199 1.126016466 0.903981705 1.008731381 0.969983165 0.907568195 0.992956465 0.931268367 1 18.48848414 3.742727575 24.99994444 0.960227916 1.084617739 0.69805736 0.039081323 187.4634522 1124694.76 0.009464452 0.016319908 5530.031115 -3.742727575 0.124389823 AALS(ph)EEELEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AALSEEELEKK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 AALS(1)EEELEKK 67.234 0.037075 598160000 967360 847930 912210 495660 754620 729760 627220 759060 812160 703210 TRUE FALSE 929554.5017 823747.8666 1077066.639 521241.072 778893.0376 744516.2472 634896.106 743385.1457 719967.0017 655580.9603 1.417909546 1.256515848 1.64291934 0.795082688 1.188095879 1.13565874 0.968448055 1.133933398 1.098212189 1 19.32241443 3.742746323 24.99982927 1.060367425 1.420854995 0.632282822 0.1369765 231.5312739 1382854.616 0.033609346 0.05796733 5530.269848 -3.742746323 0.360487569 QES(ph)DEESRPQNANYPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QESDEESRPQNANYPR 16 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 QES(1)DEESRPQNANYPR 146.89 6.54E-07 83414000 56048 56528 45970 57009 61849 58351 56184 60383 66879 57788 TRUE FALSE 53857.5822 54915.87679 54277.8016 59951.24132 63838.42925 59530.8972 56871.5966 59136.06995 59287.1763 53873.96729 0.999695863 1.019339758 1.007495908 1.112805393 1.184958756 1.105003032 1.055641518 1.097674311 1.100479123 1 15.71730069 3.742855332 24.71251047 1.099511395 1.009893427 0.43303129 0.044202384 280.0814899 1611630.524 0.011481556 0.01985042 5531.658135 -3.742855332 -0.089617968 DPSQQELPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPSQQELPR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 125.04 0.001193 1061690000 587230 543640 474330 398490 446800 484180 424920 456650 431040 490100 FALSE TRUE 564280.4024 528135.9195 560051.9824 419056.1167 461171.7278 493970.4513 430120.2981 447220.0179 382110.1463 456905.0905 1.235005725 1.155898524 1.225751243 0.917162285 1.009338126 1.08112267 0.941377776 0.978802879 0.836300917 1 18.80153499 3.742894956 24.99982591 0.97084033 1.200586513 0.748936761 0.063421734 184.8428075 1066142.201 0.016483517 0.028459013 5532.162856 -3.742894956 0.229746184 KLGSSLDWDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLGSSLDWDR 10 1 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 119.74 0.0010452 229160000 437720 516010 398310 327830 354230 198980 471040 344950 419920 505950 FALSE TRUE 420613.4185 501293.9 470293.4774 344749.3456 365624.1297 203003.5119 476804.7284 337826.662 372252.442 471681.5558 0.891731748 1.062780373 0.99705717 0.730894268 0.775150364 0.430382552 1.010861507 0.716217664 0.789202879 1 18.84745366 3.742971377 24.40186037 0.764249883 0.991748849 0.259210475 0.157194482 319.8912798 1769740.44 0.038872484 0.067131336 5533.136407 -3.742971377 0.227498966 AFELMHSGK ddPTM_BT-474_Pertuzumab_2h_R1 4 AFELMHSGK 9 0 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 ;;; 144.77 9.88E-05 3829430000 7711650 6908120 6167200 5805390 6491770 5070980 6885060 6443280 7696580 7323550 FALSE TRUE 7410270.192 6711107.181 7281750.229 6105006.874 6700583.678 5173518.69 6969321.424 6310224.016 6822896.505 6827519.435 1.085353218 0.982949554 1.066529403 0.894176418 0.981408217 0.757744996 1.020769181 0.924233768 0.999322898 1 22.70293009 3.743019239 24.93250601 0.935148378 1.038744611 0.287217876 0.075579254 460.2730125 2573824.196 0.018621024 0.032205308 5533.746228 -3.743019239 0.103596233 AVQGMLDFDYVCSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AVQGMLDFDYVCSR 14 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 179.67 4.28E-06 78524000 108178 114606 92458 124306 137120 124742 127271 128423 137051 133435 FALSE TRUE 103950.2842 111337.5491 109167.2173 130721.4476 141530.5893 127264.3687 128828.5806 125771.0202 121493.545 124397.3286 0.835631161 0.895015595 0.877568824 1.050838061 1.137730134 1.023047441 1.035621762 1.011042774 0.976657187 1 16.92459598 3.743118747 23.32876078 1.036408821 0.871966195 0.757665124 0.042515355 75.42227914 386010.5597 0.011695884 0.020172639 5535.014295 -3.743118747 -0.164442626 CDSVCVNPYHYER ddPTM_BT-474_Pertuzumab_2h_R1 2 CDSVCVNPYHYER 13 0 K7EIU8;Q13485;K7EIJ2;K7ES96 K7EIU8 SMAD4 Mothers against decapentaplegic homolog;Mothers against decapentaplegic homolog 4 0 ; 114.88 0.00070784 405380000 763550 721770 622720 578000 596080 603530 591690 706340 703090 725380 FALSE TRUE 733709.6219 701185.8263 735259.3563 607830.6493 615253.4545 615733.7901 598931.2792 691753.8322 623278.1708 676249.3665 1.084969034 1.036874652 1.087260695 0.898826201 0.909802634 0.910512927 0.885666307 1.022927143 0.921669138 1 19.36719581 3.743155949 24.97072753 0.936705612 1.066418786 0.667687149 0.04332144 241.0333274 1309754.103 0.011754931 0.020356183 5535.488451 -3.743155949 0.129713174 RPST(ph)SSASGQWSPTPEWVLSWK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 RPS(0.167)T(0.274)S(0.274)S(0.274)AS(0.011)GQWSPTPEWVLSWK 196.8 1.22E-22 2821200000 244500 241590 198460 193980 173740 197860 213740 229550 230660 227920 TRUE FALSE 234944.6697 234700.0897 234326.1367 203991.331 179328.5049 201860.8648 216355.8141 224809.7123 204476.4438 212482.7754 1.105711601 1.104560543 1.102800621 0.960037023 0.843967256 0.950010486 1.018227542 1.058013817 0.962320091 1 17.69698637 3.743157074 23.91066253 0.974772392 1.104377904 0.576877053 0.052491471 183.8715194 956488.4566 0.016147602 0.027898215 5535.502788 -3.743157074 0.129605513 TLTTGSSAYLWKPPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 TLTTGSSAYLWKPPSR 16 1 Q9BQS8;Q9BQS8-4;Q9BQS8-3;Q9BQS8-2 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 1 TLTTGSSAYLWKPPS(1)R 160.67 5.27E-09 1166000000 603420 597360 520400 363080 396440 371600 455370 415220 582870 511310 TRUE FALSE 579837.6793 580323.8777 614447.8562 381818.6023 409191.8526 379114.0066 460942.9543 406645.5619 516705.0412 476678.5183 1.21641244 1.217432411 1.289019397 0.800998131 0.858423103 0.795324295 0.966989148 0.853081367 1.083969639 1 18.86265709 3.743185544 24.99986642 0.896665059 1.238602534 0.750282033 0.087734345 175.7994511 950273.88 0.022075022 0.038195965 5535.865678 -3.743185544 0.341937475 EGSRPMMGDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGSRPMMGDHR 11 1 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 72.958 0.026961 70634000 88494 101800 75960 58484 62600 30206 82781 54943 63778 76447 FALSE TRUE 85035.55664 98896.76367 89687.66172 61502.36625 64613.58585 30816.78602 83794.09864 53808.40785 56538.18882 71269.1766 1.193160363 1.387651274 1.258435498 0.862958844 0.906613335 0.432399917 1.17574108 0.755002519 0.793304925 1 16.12099064 3.743328395 4.13457417 0.834270196 1.298816938 0.538519962 0.183815144 0.147777418 6.183633887 0.046739333 0.081948546 5537.686867 -3.743328395 0.464546742 AGASCVCCSQPQQSST(ph)SPPPSDALQWVVVEVSGTPNQLETHR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGASCVCCSQPQQSSTSPPPSDALQWVVVEVSGTPNQLETHR 42 0 Q13952-3;Q13952 Q13952-3 NFYC Nuclear transcription factor Y subunit gamma 1 AGASCVCCSQPQQS(0.063)S(0.227)T(0.254)S(0.254)PPPS(0.197)DALQWVVVEVS(0.003)GT(0.001)PNQLETHR 59.53 0.022352 70927000 22109 22886 17082 27025 27544 27490 26166 23465 29779 29075 TRUE FALSE 21244.95584 22233.31369 20169.09739 28419.76349 28429.97777 28045.86663 26486.22734 22980.43955 26398.61276 27105.72435 0.783781151 0.820244218 0.744089961 1.048478289 1.04885512 1.034684271 0.977145159 0.847807616 0.973912832 1 14.72630994 3.743425523 24.99858359 0.979285618 0.786459013 0.728263275 0.057783485 266.018487 1366945.978 0.018038221 0.031278114 5538.925491 -3.743425523 -0.192826604 S(ph)LGDEGLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGDEGLNR 9 0 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 S(1)LGDEGLNR;S(1)LGDEGLNR 90.653 0.011837 1049470000 531100 549060 386080 661240 639910 587140 636040 725000 526730 568920 TRUE FALSE 510344.0248 533401.3464 455853.2443 695366.6756 660493.2863 599012.3731 643824.0478 710028.4966 466937.8186 530386.5417 0.962211491 1.005684165 0.859473626 1.311056411 1.245305517 1.129388335 1.213877045 1.338700063 0.880372675 1 19.01668464 3.743430219 24.98891844 1.188398451 0.948779199 0.333303212 0.136665024 407.7517693 2092418.224 0.034327964 0.059530403 5538.985377 -3.743430219 -0.239619252 FYTLIPHDFGMK ddPTM_BT-474_Pertuzumab_2h_R1 2 FYTLIPHDFGMK 12 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 174.84 2.93E-05 1802560000 7810300 7931000 6254400 4715200 4973700 1941250 6340600 4632600 5892700 6700800 FALSE TRUE 7505064.841 7704815.645 7384709.208 4958552.037 5133683.577 1980503.405 6418198.159 4536935.191 5223785.4 6246948.848 1.201396878 1.233372617 1.182130571 0.793755825 0.821790558 0.317035317 1.027413273 0.726264181 0.836213891 1 22.57472029 3.743505394 4.142772616 0.768882406 1.216404319 0.520884708 0.182789913 0.154520097 6.503476091 0.047143628 0.082656834 5539.944248 -3.743505394 0.447521913 NYLPAINGIVFLVDCADHER ddPTM_BT-474_Pertuzumab_2h_R1 2 NYLPAINGIVFLVDCADHER 20 0 Q9Y6B6;D6RD69;D6RDB2;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ; 184.15 4.11E-17 299090000 253730 282640 217208 219974 230595 222869 175362 260718 248566 285277 FALSE TRUE 243813.9511 274579.3839 256462.3174 231326.8845 238012.2976 227375.5639 177508.1326 255334.0822 220349.8298 265954.9347 0.916749115 1.032428235 0.964307422 0.869797301 0.894934692 0.854940196 0.667436883 0.960065217 0.828523186 1 18.02082228 3.743540173 3.594508381 0.859550623 0.980189638 0.224773681 0.087033909 0.30595262 8.663414379 0.02273049 0.040613049 5540.387916 -3.743540173 0.120639016 ITITNDKGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ITITNDKGR 9 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13;P54652;P17066 A0A0G2JIW1;Q53FA3;P11142;P54652;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA2;HSPA6 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6 0 104.05 0.003031 957430000 632930 607170 496960 518380 455500 449920 613880 518190 673810 627680 FALSE TRUE 608194.3959 589854.1061 586771.7268 545133.6539 470151.5712 459017.6907 621392.8471 507489.1954 597321.9136 585166.6745 1.039352414 1.008010421 1.002742898 0.931586978 0.803448986 0.784422132 1.061907443 0.867255805 1.020772268 1 19.15848808 3.743551234 3.806635101 0.912945118 1.018572711 0.194220241 0.085255104 0.338726627 11.18211739 0.022927091 0.040626746 5540.529025 -3.743551234 0.105627593 RRDEDMLYS(ph)PELAQR ddPTM_BT-474_Pertuzumab_2h_R1 4 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR 223.36 6.67E-13 3532870000 1574430 1716220 1310670 1677770 1675160 1743120 1774990 1690510 1702940 1820740 TRUE FALSE 1512899.535 1667275.086 1547537.225 1764359.911 1729043.043 1778367.081 1796712.859 1655600.378 1509629.391 1697419.658 0.891293752 0.982240943 0.911699836 1.039436478 1.018630269 1.047688515 1.058496554 0.975363028 0.889367213 1 20.69491186 3.743562871 24.96987816 1.006900668 0.933794452 0.322373338 0.050019844 525.5863164 2623574.75 0.01341156 0.023236884 5540.677478 -3.743562871 -0.073106216 SGEQAEGS(ph)PGGPGDSQGR ddPTM_BT-474_Pertuzumab_2h_R1 5 SGEQAEGSPGGPGDSQGR 18 0 P38936 P38936 CDKN1A Cyclin-dependent kinase inhibitor 1 1 SGEQAEGS(1)PGGPGDSQGR;SGEQAEGS(1)PGGPGDSQGR;SGEQAEGS(1)PGGPGDSQGR;SGEQAEGS(1)PGGPGDSQGR;SGEQAEGS(1)PGGPGDSQGR 319.85 4.82E-52 409560000 162182.7 184123.2 142495.1 337161 353291 288835.3 356910 352606 275581.7 342641 TRUE FALSE 155844.4208 178872.1866 168247.1344 354561.9196 364654.9259 294675.7477 361277.9713 345324.5629 244298.8207 319433.6199 0.487877328 0.559966689 0.526704529 1.109970578 1.141567146 0.922494469 1.130995452 1.081052655 0.764787441 1 18.28515664 3.743624157 24.90954484 1.035222683 0.528361189 0.814238064 0.108578692 153.8920477 757052.7538 0.027801808 0.048230583 5541.45942 -3.743624157 -0.506861494 AQPSMS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQPSMSPK 8 0 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 1 AQPS(0.028)MS(0.972)PK 94.584 0.010758 306180000 612470 520330 465840 296140 304250 128060 439430 411440 427330 502590 TRUE FALSE 588533.9953 505490.6979 550027.6506 311423.8209 314036.4776 130649.4609 444807.8758 402943.6202 378821.2899 468549.1316 1.256077443 1.07884246 1.173895358 0.664655636 0.670231693 0.278838338 0.949330275 0.859981575 0.808498542 1 18.83784081 3.743685723 24.75505511 0.739139518 1.160528862 0.502616321 0.192300811 322.8365565 1559344.568 0.052146669 0.090472358 5542.245031 -3.743685723 0.421389344 QSMDMS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 2 QSMDMSPIK 9 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 1 QSMDMS(1)PIK;QSMDMS(1)PIK 115.75 0.0014952 926620000 2631500 2478800 2117120 1226970 1322530 444940 2216500 1556220 1727990 2083310 TRUE FALSE 2528658.071 2408107.051 2499730.679 1290294.069 1365070.379 453936.9917 2243626.19 1524083.513 1531835.82 1942205.558 1.301951825 1.23988269 1.287057731 0.664344751 0.70284547 0.233722424 1.155195021 0.784717924 0.78870942 1 20.88926447 3.743740769 24.73068842 0.75460616 1.27265599 0.523237928 0.225176654 293.7558988 1402421.059 0.058816265 0.102131369 5542.947548 -3.743740769 0.51804983 KEDMEYALR ddPTM_BT-474_Pertuzumab_2h_R1 6 KEDMEYALR 9 1 Q13242;H0YIB4 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;;;; 154.24 0.00012213 11179480000 11684890 11524700 9589570 9908420 10112280 8738240 11496070 11314510 11622790 12092820 FALSE TRUE 11228231.58 11196026.84 11322618.62 10419794.74 10437550.67 8914933.2 11636762.34 11080861.41 10303419.61 11273762.53 0.995961335 0.993104725 1.00433361 0.92425175 0.925826727 0.790768226 1.032198639 0.982889376 0.913929097 1 23.42646575 3.743873479 24.05601301 0.939681069 0.997330379 0.164464618 0.061157023 523.5723247 2370658.886 0.016635947 0.028877098 5544.641597 -3.743873479 0.05764931 IHWWENVYGFDMSCIK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHWWENVYGFDMSCIK 16 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 120.29 0.0001282 289070000 430850 423740 345620 274000 322580 160314 375820 238060 360900 380530 FALSE TRUE 414011.9057 411655.3501 408081.2223 288141.1728 332956.0787 163555.6589 380419.3976 233143.9778 319932.145 354756.3642 1.167031652 1.160388908 1.150314028 0.812222703 0.938548571 0.461036575 1.072339882 0.657194631 0.901836238 1 18.43646904 3.743882872 6.574260189 0.814195284 1.160868047 0.443522174 0.165466048 0.115403104 28.09056765 0.040139865 0.068349082 5544.76152 -3.743882872 0.346672763 NINTFVET(ph)PVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 NINTFVETPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NINTFVET(1)PVQK;NINTFVET(1)PVQK 195.2 6.21E-06 247360000 540940 418250 394040 309610 292340 336150 277000 475690 360720 399560 TRUE FALSE 519799.4668 406321.9195 465251.7934 325589.0092 301743.3816 342947.1833 280390.0089 465866.8353 319772.5779 372497.4453 1.39544438 1.09080458 1.249006669 0.874070449 0.810054902 0.920669894 0.752730018 1.250657799 0.858455761 1 18.50687101 3.743935351 24.852037 0.937937721 1.229657169 0.505314736 0.14496066 384.6099063 1778377.378 0.03907764 0.067957794 5545.431571 -3.743935351 0.291719448 KEVDMMK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEVDMMK 7 1 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 71.223 0.088026 977590000 1750200 1698100 1529500 830190 974770 552540 1452100 1049700 1412300 1568700 FALSE TRUE 1681800.249 1649671.851 1805914.674 873036.2054 1006124.362 563712.7374 1469871.234 1028023.328 1251981.625 1462450.552 1.14998777 1.128018892 1.234855203 0.596968017 0.687971543 0.385457639 1.005074142 0.702945701 0.856084757 1 20.47995641 3.743986429 24.97859522 0.732381153 1.166660472 0.547614721 0.175851334 316.7723449 1458308.05 0.04442868 0.077284764 5546.083815 -3.743986429 0.434279319 FKMPFLSIS(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKMPFLSISSPK 12 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FKMPFLS(0.009)IS(0.799)S(0.192)PK 81.656 0.010331 208130000 533210 563730 508860 354920 414750 491240 377100 469130 589300 408140 TRUE FALSE 512371.5637 547652.9723 600822.3215 373237.4637 428090.8104 501173.2094 381715.0626 459442.3016 522405.1345 380496.3143 1.346587456 1.439312161 1.579048992 0.980922678 1.125085301 1.317156542 1.003203049 1.207481608 1.372957148 1 18.53752295 3.744018408 24.99999161 1.153314208 1.453415801 0.526916367 0.134896521 360.1520956 1649709.158 0.034280976 0.059624507 5546.492213 -3.744018408 0.300101593 RDS(ph)LDSSTEASGSDVVLGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSLDSSTEASGSDVVLGGR 20 1 Q9Y2I9 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 RDS(0.983)LDS(0.015)S(0.001)TEASGSDVVLGGR 109.5 0.00012035 328640000 81293 68207 51552 82958 66511 74021 82082 79897 93809 77293 TRUE FALSE 78115.97969 66261.80314 60868.59317 87239.47232 68650.38672 75517.75534 83086.54407 78247.09903 83160.1956 72057.87626 1.084072745 0.919563642 0.844718112 1.210686143 0.952711768 1.04801528 1.153052912 1.085892384 1.154075028 1 16.13686851 3.744072025 24.99531654 1.086859151 0.946462721 0.326033459 0.090163512 512.5611241 2324557.476 0.022718537 0.039517674 5547.177014 -3.744072025 -0.140396429 QQPQPSQTES(ph)PQEAQIIQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQPQPSQTESPQEAQIIQAK 20 0 O96020-2;O96020;E5RHN2;E5RK20;Q8WUE3 O96020-2 CCNE2 G1/S-specific cyclin-E2 1 QQPQPS(0.015)QT(0.066)ES(0.919)PQEAQIIQAK 126.97 1.44E-05 147350000 146950 152520 104320 123350 106490 91061 103340 118500 131150 118950 TRUE FALSE 141207.0315 148170.2789 123172.9446 129716.1083 109915.3476 92902.31581 104604.7058 116052.9336 116262.4018 110893.4106 1.273358181 1.336150437 1.110732766 1.169736846 0.991180152 0.837762274 0.943290546 1.046526868 1.048415783 1 16.75881412 3.744142244 1.28591456 0.977609217 1.304677433 0.734970086 0.073815582 0.258678292 0.813518345 0.025407294 0.068564333 5548.073984 -3.744142244 0.327068216 RRS(ph)PSLSSK ddPTM_BT-474_Pertuzumab_2h_R1 11 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RRS(1)PSLSSK;RRS(0.994)PS(0.006)LSSK;RRS(0.987)PS(0.013)LSSK;RRS(1)PSLSSK;RRS(1)PSLSSK;RRS(0.98)PS(0.02)LSSK;RRS(0.902)PS(0.098)LSSK;RRS(0.987)PS(0.013)LSSK;RRS(0.832)PS(0.168)LSSK;RRS(0.985)PS(0.015)LSSK;RRS(1)PSLSSK 160.84 5.12E-05 25908784000 5398221 5837651 4622441 4518419 4567321 3606957 5627919 4772751 5996496 5775850 TRUE FALSE 5187252.555 5671166.909 5457818.914 4751615.146 4714233.028 3679892.142 5696795.156 4674192.024 5315798.913 5384646.535 0.96334133 1.053210619 1.013589078 0.882437708 0.875495355 0.683404587 1.057970123 0.868059211 0.987214087 1 22.36042021 3.744327861 23.12793163 0.899221013 1.014363398 0.182790362 0.097778218 250.5915568 1004915.407 0.024719113 0.042987852 5550.445731 -3.744327861 0.115142385 TTIESHTK ddPTM_BT-474_Pertuzumab_2h_R1 4 TTIESHTK 8 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 ;;; 103.74 0.0047148 476221000 581280 594900 477950 575610 559030 632670 599030 582850 663430 632690 FALSE TRUE 558562.935 577934.0345 564326.1969 605317.3011 577011.7076 645463.0209 606361.1083 570813.9438 588120.2077 589837.3428 0.946977911 0.979819338 0.956748846 1.026244453 0.978255641 1.09430681 1.028014106 0.967748059 0.997088799 1 19.16995764 3.744387792 24.84595672 1.011881822 0.963045759 0.33331056 0.033582905 591.3938563 2521579.713 0.009236549 0.016124077 5551.211732 -3.744387792 -0.048836063 TSLPLS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSLPLSPVK 9 0 Q86XL3;Q86XL3-2 Q86XL3 ANKLE2 Ankyrin repeat and LEM domain-containing protein 2 1 TSLPLS(1)PVK 113.38 0.0018986 103170000 274750 316940 233050 173350 170620 42563 239100 202260 184200 228680 TRUE FALSE 264012.4662 307901.1815 275167.3192 182296.6143 176108.1473 43423.65302 242026.1773 198083.2603 163290.3882 213191.2999 1.238382928 1.444248342 1.290706137 0.855084679 0.826056914 0.203683983 1.135253537 0.929133883 0.765933639 1 17.70178904 3.744443584 3.901620146 0.811482387 1.347774505 0.49894711 0.233962367 0.184157501 6.508195079 0.064366463 0.113801544 5551.924919 -3.744443584 0.536292118 GLTLAPGLS(ph)PARPLFGSDFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLTLAPGLSPARPLFGSDFEK 21 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 GLTLAPGLS(1)PARPLFGSDFEK;GLTLAPGLS(0.998)PARPLFGS(0.002)DFEK 202.2 3.95E-22 809170000 1312880 1265680 1146850 1033250 1083810 1119800 1175380 1317920 1317910 1302380 TRUE FALSE 1261571.198 1229584.046 1354111.307 1086576.156 1118671.733 1142443.123 1189764.652 1290704.491 1168306.382 1214168.643 1.039041163 1.012696262 1.115258012 0.894913703 0.921347903 0.94092623 0.979900658 1.0630356 0.962227438 1 20.21153739 3.744489554 24.99359153 0.972183412 1.051368251 0.403622498 0.049444733 617.118722 2601471.088 0.014486904 0.02527084 5552.512611 -3.744489554 0.079184839 KKAEGGGGGGRPGAPAAGDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KKAEGGGGGGRPGAPAAGDGK 21 3 Q00839 Q00839 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 181.69 2.16E-17 1238670000 1785740 1506900 1568210 1084110 1313650 1303680 1254030 1558150 1619350 1803990 FALSE TRUE 1715951.307 1463924.687 1851620.432 1140061.047 1355904.745 1330041.303 1269377.194 1525973.658 1435528.177 1681804.15 1.020303884 0.870448968 1.100972685 0.677879792 0.806220359 0.790841967 0.754771115 0.907343258 0.853564416 1 20.68157828 3.74451594 24.99999523 0.821901533 0.98456255 0.388836416 0.097124631 501.4393109 2104997.531 0.024074363 0.042030167 5552.849979 -3.74451594 0.162661016 DRDLEVDTTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRDLEVDTTLK 11 1 P02452 P02452 COL1A1 Collagen alpha-1(I) chain 0 ; 171.29 1.34E-05 163280000 1151210 986730 1085290 568360 857770 935230 786530 882940 897040 862320 FALSE TRUE 1106219.44 958589.4265 1281426.045 597693.1277 885360.9511 954140.9914 796155.7894 864706.9805 795211.7799 803914.2983 1.376041504 1.192402509 1.593983398 0.743478663 1.101312606 1.18686904 0.990349085 1.075620849 0.989174818 1 19.61668218 3.744577012 24.99967522 1.02781433 1.36796846 0.594646994 0.141235391 351.6403514 1461152.043 0.035121555 0.061346096 5553.630894 -3.744577012 0.34015413 LDNLVAILDINR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDNLVAILDINR 12 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 176.8 5.60E-05 185646000 308670 322150 258340 165036 223566 138911 236350 192422 186331 208674 FALSE TRUE 296606.8351 312962.5974 305027.7847 173553.5277 230757.2034 141719.8756 239242.522 188448.4185 165179.486 194540.3241 1.52465478 1.608728673 1.567941177 0.892121099 1.186166439 0.728485861 1.229783712 0.96868564 0.849075824 1 17.5697097 3.744714386 24.874195 0.990153754 1.571270312 0.785499137 0.140702534 190.7169106 770895.5248 0.034073762 0.059509572 5555.387872 -3.744714386 0.581116558 FVHLLDQSDQDFQEELDLMK ddPTM_BT-474_Pertuzumab_2h_R1 3 FVHLLDQSDQDFQEELDLMK 20 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 246.68 4.66E-30 198255000 143558 145071 119570.8 158157.9 141214.6 144509 162315.6 174305.1 182603.8 172083 FALSE TRUE 137947.5946 140933.7171 141179.9034 166320.4482 145756.8959 147431.071 164302.0669 170705.6388 161875.3822 160427.6651 0.859874103 0.878487616 0.880022179 1.036731714 0.908552124 0.918987825 1.024150459 1.064066093 1.009024111 1 17.29156342 3.744730506 0.441314933 1.03677738 0.809682822 0.568540001 0.04745327 1.645974535 0.464912291 0.042453741 0.181731131 5555.594072 -3.744730506 -0.227094558 ACFHCETCK ddPTM_BT-474_Pertuzumab_2h_R1 6 ACFHCETCK 9 0 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;; 169.09 5.87E-05 7238430000 15021100 15650300 12209000 4513870 3894280 792748 9520680 3579280 5252290 8657520 FALSE TRUE 14434058.81 15203968.77 14415437.89 4746831.372 4019543.053 808777.9077 9637196.93 3505366.617 4656072.059 8071138.459 1.788354751 1.883745254 1.786047651 0.588124141 0.498014385 0.100206174 1.194031917 0.43430882 0.57687922 1 22.94434075 3.744782611 7.101449999 0.600832817 1.829909209 0.78691152 0.284036505 0.055719423 19.22122959 0.071647896 0.122069174 5556.260655 -3.744782611 1.229076393 FQPQLNPDVVAPLPTHTAHEDFTFGES(ph)RPELGSEGLGSAAHGSQPDLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLRR 49 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPT(0.004)HT(0.004)AHEDFT(0.06)FGES(0.233)RPELGS(0.233)EGLGS(0.233)AAHGS(0.233)QPDLRR 123.54 5.71E-11 1771600000 0 0 0 5737.9 5154.9 5052.5 4321.1 5797.8 5093.8 4541.1 TRUE FALSE 0 0 0 6034.033707 5320.71204 5154.665012 4373.982914 5678.073404 4515.573179 4233.527252 0 0 0 1.425297003 1.256803541 1.21758163 1.033176983 1.341215744 1.06662197 1 12.04764446 3.744890903 24.99989357 1.207664646 8.97E-08 0.948683107 0.126955271 92.95512717 367102.1019 0.031507817 0.055108304 5557.646294 -3.744890903 -1.207664557 SRLDQELK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRLDQELK 8 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ; 92.732 0.010551 1719830000 1595520 1552450 1383960 1121200 1381790 903820 1518110 1328060 1485260 1597320 FALSE TRUE 1533165.314 1508175.646 1634072.358 1179065.266 1426236.53 922095.8597 1536689.084 1300635.097 1316659.512 1489132.094 1.029569721 1.012788357 1.09733204 0.791780173 0.95776361 0.619216968 1.031936046 0.873418216 0.884179125 1 20.5060403 3.744954672 24.98335163 0.876281253 1.043185875 0.320715403 0.111134333 576.6621077 2253172.073 0.027185232 0.047539488 5558.462393 -3.744954672 0.166904621 YKDIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 YKDIIR 6 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 68.915 0.086532 242820000 1038700 1101600 883460 908410 940040 796980 1108500 929310 1118400 1174400 FALSE TRUE 998106.4557 1070183.447 1043120.874 955293.149 970277.2403 813095.4817 1122066.155 910119.4237 991443.9207 1094856.842 0.91163193 0.977464273 0.952746363 0.872527907 0.886213798 0.742650044 1.024851936 0.831267969 0.905546627 1 20.06231081 3.74504446 22.9535803 0.885903327 0.950299214 0.08187944 0.07657365 338.7003553 1199024.075 0.018590815 0.032458291 5559.611701 -3.74504446 0.064395888 SPDKPGGSPSASR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 68.83 0.045018 40017000 108950 98475 83763 66622 71184 72358 67896 82744 90369 71891 FALSE TRUE 104692.1135 95666.58942 98900.8374 70060.3694 73473.69801 73821.12834 68726.93156 81035.30748 80110.68998 67021.75854 1.562061573 1.427395991 1.475652677 1.045337677 1.096266341 1.101450185 1.025442081 1.209089544 1.195293763 1 16.03234192 3.745058473 24.51654903 1.106817008 1.482272718 0.866447639 0.070470518 137.7763824 519830.8967 0.0186119 0.032555754 5559.791087 -3.745058473 0.37545571 YLYYTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLYYTGR 7 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 133.47 0.01366 282510000 721580 724820 608870 568670 634450 560640 631770 654000 683070 737520 FALSE TRUE 693379.8559 704148.8433 718906.3532 598019.1268 654857.6604 571976.5249 639501.7902 640494.6715 605530.7573 687567.1135 1.008454073 1.024116525 1.045579899 0.869761097 0.952427258 0.831884646 0.930093627 0.931537677 0.880686038 1 19.39114102 3.745314918 24.9883445 0.91144106 1.025856808 0.569528273 0.044700725 348.58219 1289617.743 0.010766693 0.018879978 5563.075034 -3.745314918 0.114415748 LRS(ph)PS(ph)NDSAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 LRS(1)PS(1)NDSAHR;LRS(1)PS(0.998)NDS(0.002)AHR 118.33 0.00041781 776170000 488330 515990 413630 648090 588070 684440 663300 685710 655900 641260 TRUE FALSE 469245.5237 501274.4704 488382.1421 681538.0026 606985.8056 698279.8457 671417.6638 671549.8489 581444.9818 597826.889 0.784918732 0.838494353 0.816929033 1.140025675 1.015320349 1.168030175 1.123097131 1.12331824 0.972597574 1 19.18936826 3.745323269 24.99999194 1.088594588 0.815952045 0.786522013 0.062846584 215.6386406 797165.0086 0.015665616 0.027451568 5563.182015 -3.745323269 -0.272642542 SKFEDMAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKFEDMAK 8 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 111.06 0.0030158 5524700000 14366400 12307100 10622400 5988900 7600700 2580500 9321800 8076100 8654400 8941000 FALSE TRUE 13804945.21 11956113.56 12542103.97 6297987.847 7845183.418 2632679.478 9435882.977 7909325.713 7671988.794 8335418.106 1.656179094 1.434374785 1.504676048 0.755569519 0.941186551 0.315842522 1.132022756 0.948881701 0.920408394 1 22.99082314 3.745371965 23.80607745 0.860346216 1.522006586 0.681077818 0.210887858 161.655792 564992.9427 0.054838381 0.095987321 5563.805828 -3.745371965 0.66166037 VVWVEESDKR ddPTM_BT-474_Pertuzumab_2h_R1 6 VVWVEESDKR 10 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;;;;; 218.52 1.08E-08 5567600000 3044430 3002930 2571073 2141650 2192964 1088994 3064260 2712280 3105900 3302150 FALSE TRUE 2925450.31 2917289.377 3035723.084 2252180.813 2263502.679 1111014.205 3101761.331 2656270.47 2753331.253 3078492.439 0.950286664 0.947635713 0.986107046 0.731585624 0.735263355 0.360895544 1.007558534 0.862847814 0.894376487 1 21.55379259 3.745411942 24.44940092 0.79008455 0.959972411 0.154942157 0.17294232 763.0393401 2722942.93 0.046399351 0.081308636 5564.318002 -3.745411942 0.169887862 DFSALESQLQDTQELLQEENR ddPTM_BT-474_Pertuzumab_2h_R1 3 DFSALESQLQDTQELLQEENR 21 0 P35579 P35579 MYH9 Myosin-9 0 ;; 314.58 1.20E-66 181472000 115246 123042 101203 118805 128897 138487 125359 136099 133009 152833 FALSE TRUE 110742.0589 119532.9626 119492.6333 124936.5403 133043.0891 141287.302 126893.1809 133288.5081 117910.3759 142481.4848 0.777238243 0.838936812 0.838653763 0.876861583 0.933757037 0.991618681 0.890594179 0.9354795 0.827548759 1 17.12041493 3.745470803 1.506619623 0.927082838 0.804638141 0.52669455 0.047877227 0.337594101 1.473427607 0.014215227 0.034653777 5565.072201 -3.745470803 -0.122444697 EPPTVPS(ph)ER ddPTM_BT-474_Pertuzumab_2h_R1 1 EPPTVPSER 9 0 P27815 P27815 PDE4A "cAMP-specific 3,5-cyclic phosphodiesterase 4A" 1 EPPTVPS(1)ER 63.32 0.049493 273760000 0 3704.6 0 7501.2 5274.8 3927.8 6830.7 6237.1 4315.9 4615 TRUE FALSE 0 3598.948435 0 7888.337831 5444.468732 4007.222807 6914.29615 6108.301705 3825.977126 4302.421939 0 0.836493604 0 1.833464486 1.265442769 0.931387684 1.60707068 1.419735626 0.889261253 1 12.0709333 3.745483433 24.99963229 1.307533197 0.334597421 0.621505502 0.356021358 343.9598415 1242102.322 0.087701762 0.153830762 5565.234036 -3.745483433 -0.972935776 GCLDEETSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GCLDEETSR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 147.19 0.00021636 195030000 249800 278410 214310 279050 288420 294980 284510 270050 302490 305730 FALSE TRUE 240037.5398 270470.0194 253040.5843 293451.8039 297697.2912 300944.6977 287991.9185 264473.3731 268152.6033 285022.6348 0.842170096 0.948942247 0.887791191 1.029573683 1.044468947 1.055862451 1.010417712 0.927903053 0.940811608 1 18.12071697 3.745724148 24.86987815 0.998570307 0.898565277 0.542505652 0.045449924 481.4861745 1671586.418 0.013285258 0.023313377 5568.319524 -3.745724148 -0.100005029 AIEEGTLEEIEEEVR ddPTM_BT-474_Pertuzumab_2h_R1 5 AIEEGTLEEIEEEVR 15 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ;;;; 234.79 2.69E-17 155974000 179286 187249 146114 204018 181863 205127 212276 226966 200330 199681 FALSE TRUE 172279.3049 181908.8419 172520.0501 214547.3934 187712.7886 209274.8085 214873.8972 222279.0728 177589.3783 186156.428 0.925454505 0.977182705 0.926747746 1.152511335 1.008360499 1.124187925 1.154265257 1.194044574 0.953979297 1 17.50615591 3.745971287 24.96998404 1.100427093 0.946533747 0.411563609 0.075315421 499.934015 1684504.298 0.01948601 0.034263517 5571.489117 -3.745971287 -0.153893346 KVVNPLFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVVNPLFEK 9 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 125.75 0.0024342 0 2327600 2380800 2058700 1127900 1502500 458990 1960800 1719800 1752900 2027500 FALSE TRUE 2236634.819 2312901.915 2430752.886 1186111.054 1550829.277 468271.0923 1984796.857 1684285.529 1553918.141 1890175.619 1.183294714 1.223643926 1.285993143 0.627513678 0.820468353 0.247739463 1.050059495 0.891073566 0.822102521 1 20.85008885 3.746037876 24.94836893 0.778763545 1.230243959 0.487661732 0.21189551 484.697697 1617221.153 0.055678855 0.097942274 5572.34345 -3.746037876 0.451480414 GIDVEQVSVVINFDLPVDKDGNPDNETYLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIDVEQVSVVINFDLPVDKDGNPDNETYLHR 31 1 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ; 165.37 8.57E-13 457870000 190494 185288 155291 203076 205531 209660 200239 211121 224960 244330 FALSE TRUE 183049.2839 180003.7677 183355.5381 213556.7767 212142.0913 213899.4688 202689.5848 206761.2776 199423.4839 227781.3115 0.803618535 0.790248184 0.804963045 0.937551792 0.931341074 0.939056271 0.889842909 0.907718356 0.875504152 1 17.79728986 3.746074896 23.12706372 0.919903896 0.798673709 0.761879407 0.032222572 96.12936291 295859.0216 0.008032121 0.01409519 5572.818458 -3.746074896 -0.121230187 (ac)GS(ph)ASPGLSSVS(ph)PSHLLLPPDTVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 2 GS(0.448)AS(0.532)PGLS(0.116)S(0.085)VS(0.728)PS(0.091)HLLLPPDTVSR;GS(0.498)AS(0.498)PGLS(0.12)S(0.12)VS(0.645)PS(0.119)HLLLPPDTVSR 84.046 9.10E-19 210557000 6852.2 6816.8 5330.1 7614.2 7292.7 7511 7322 8746.7 5408.5 9095.6 TRUE FALSE 6584.408448 6622.391538 6293.367637 8007.169774 7527.276319 7662.877566 7411.608826 8566.077588 4794.549754 8479.54691 0.776504749 0.780984127 0.742182065 0.944292173 0.887697939 0.903689507 0.874057176 1.010204635 0.565425229 1 13.04977146 3.746301469 24.68216813 0.891695569 0.767999688 0.171945006 0.116778175 804.8376711 2566262.359 0.028627673 0.050388089 5575.726586 -3.746301469 -0.123695881 RWEYENELSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RWEYENELSK 10 1 P15924;P15924-3 P15924 DSP Desmoplakin 0 ; 174.77 4.82E-06 767140000 1007600 1001130 815330 774590 799730 711650 897230 882960 989000 865630 FALSE TRUE 968221.878 972578.7526 962678.2679 814566.6827 825454.0417 726040.0506 908210.5691 864726.5674 876732.8662 807000.1091 1.199779117 1.205177969 1.192909712 1.009376174 1.022867324 0.89967776 1.125415671 1.071532157 1.086409848 1 19.62220934 3.746318143 23.25806771 1.035974452 1.199877885 0.645626599 0.057126775 152.8027961 458118.1183 0.015694826 0.027574449 5575.94065 -3.746318143 0.163903433 GASPPIS(ph)AIEEFSIIPEAPMR ddPTM_BT-474_Pertuzumab_2h_R1 1 GASPPISAIEEFSIIPEAPMR 21 0 A0A2R8YF49;C9J591;A0A2R8YFR7;Q12774;A0A5F9ZH52 A0A2R8YF49;A0A2R8YFR7;A0A5F9ZH52 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 GAS(0.445)PPIS(0.555)AIEEFSIIPEAPMR 139.04 4.10E-07 14589000 10075 11589 8585.1 13166 14049 13166 13089 12051 11740 15280 TRUE FALSE 9681.257861 11258.49307 10136.61854 13845.49884 14500.89884 13432.22554 13249.1871 11802.14264 10407.32442 14245.07199 0.679621547 0.790343009 0.711587737 0.971950078 1.017958972 0.942938411 0.930089164 0.828507055 0.730591213 1 13.79817529 3.746350471 24.70070244 0.911284748 0.733499975 0.517882874 0.083905959 463.3614743 1469258.923 0.023341107 0.041099699 5576.355732 -3.746350471 -0.177784774 RGS(ph)DELTVPR ddPTM_BT-474_Pertuzumab_2h_R1 6 RGSDELTVPR 10 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RGS(0.95)DELT(0.05)VPR;RGS(1)DELTVPR;RGS(0.971)DELT(0.029)VPR;RGS(1)DELTVPR;RGS(0.999)DELT(0.001)VPR;RGS(0.921)DELT(0.079)VPR 156.08 1.23E-05 8992180000 2561930 2590780 2066220 2689100 2656700 2665420 2711340 2902640 2806410 2844810 TRUE FALSE 2461806.943 2516893.491 2439631.917 2827884.773 2742155.168 2719316.619 2744522.19 2842699.47 2487838.102 2652128.485 0.92823819 0.949008883 0.919876971 1.0662699 1.033945069 1.025333665 1.034837568 1.071855864 0.938053385 1 21.33871924 3.74635049 24.89208434 1.030848504 0.934038095 0.572830601 0.036073621 367.0453724 1172868.323 0.009003337 0.015851946 5576.355979 -3.74635049 -0.096810409 EHGAFDAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHGAFDAVK 9 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 70.908 0.051079 369250000 636370 612870 524540 464940 528470 391960 613750 463090 631130 700370 FALSE TRUE 611499.9569 595391.5477 619336.0463 488935.6091 545468.7175 399885.6998 621261.2561 453527.0297 559486.7683 652933.3161 0.93654274 0.911871906 0.948544103 0.748829317 0.835412597 0.612444931 0.951492658 0.694599308 0.856881943 1 19.31657613 3.746474116 24.5872041 0.796560655 0.930274826 0.186889955 0.108546924 644.245958 2001661.598 0.025582217 0.04506916 5577.943564 -3.746474116 0.133714171 QVDFWFGDANLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 QVDFWFGDANLHK 13 0 Q4G0J3;Q4G0J3-3;D6RFF0;D6RF22;D6RF49;D6RAF3 Q4G0J3 LARP7 La-related protein 7 0 141 3.96E-05 253090000 326210 296030 268300 238600 263620 257580 283490 285540 297310 286480 FALSE TRUE 313461.3526 287587.5142 316787.7783 250914.1746 272099.5767 262788.4441 286959.4354 279643.4992 263560.6152 267076.4544 1.173676479 1.076798458 1.186131436 0.939484445 1.018807807 0.983944634 1.074446776 1.04705411 0.986835832 1 18.02689327 3.746497284 24.98635985 1.014760718 1.138661759 0.669761611 0.044206302 386.8504547 1217885.467 0.011415706 0.020120084 5578.241138 -3.746497284 0.12390104 ENS(ph)REALAEAALESPRPALVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSREALAEAALESPRPALVR 21 2 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 ENS(1)REALAEAALESPRPALVR 123.68 2.05E-05 981130000 221480 203650 205250 146420 163600 193940 176840 232110 201780 183910 TRUE FALSE 212824.3167 197842.1014 242343.2408 153976.7537 168862.3426 197861.5997 179004.2208 227316.8474 178874.7803 171453.6119 1.241293866 1.153910374 1.413462441 0.89806655 0.98488647 1.154024097 1.044038786 1.325821281 1.043283827 1 17.38745877 3.746530073 24.99898695 1.091149421 1.257991023 0.347783611 0.124779259 873.9009899 2741288.688 0.034373549 0.060594249 5578.662301 -3.746530073 0.166841602 FKMPFLSISS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 FKMPFLSISSPK 12 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FKMPFLSIS(0.213)S(0.787)PK 97.129 0.0030857 216470000 701190 727020 652900 467570 518920 654210 497140 616270 759870 607960 TRUE FALSE 673786.7196 706286.1014 770893.5537 491701.3437 535611.5331 667438.5744 503224.148 603543.8091 673612.7432 566782.3277 1.188792746 1.246132893 1.360122777 0.867531184 0.945003941 1.177592423 0.887861395 1.064859964 1.188485791 1 19.11243525 3.746569829 24.97795664 1.019636247 1.263127816 0.520747056 0.108251661 479.1536678 1494310.376 0.027822763 0.04902059 5579.173006 -3.746569829 0.243491569 T(ph)RSPDVISSASTALSQDIPEIASEALSR ddPTM_BT-474_Pertuzumab_2h_R1 12 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.485)RS(0.485)PDVIS(0.008)S(0.008)AS(0.008)T(0.008)ALSQDIPEIASEALSR;T(0.479)RS(0.479)PDVIS(0.01)S(0.01)AS(0.01)T(0.01)ALSQDIPEIASEALSR;T(0.496)RS(0.496)PDVIS(0.002)S(0.002)AS(0.002)T(0.002)ALSQDIPEIASEALSR;T(0.423)RS(0.423)PDVIS(0.036)S(0.036)AS(0.041)T(0.041)ALSQDIPEIASEALSR;T(0.495)RS(0.495)PDVIS(0.002)S(0.002)AS(0.003)T(0.003)ALSQDIPEIASEALSR;T(0.498)RS(0.498)PDVIS(0.001)S(0.001)AS(0.002)T(0.002)ALSQDIPEIASEALSR;T(0.498)RS(0.498)PDVIS(0.002)S(0.002)ASTALSQDIPEIASEALSR;T(0.58)RS(0.42)PDVISSASTALSQDIPEIASEALSR;T(0.499)RS(0.499)PDVISSAST(0.002)ALSQDIPEIASEALSR;T(0.424)RS(0.424)PDVIS(0.038)S(0.038)AS(0.038)T(0.038)ALS(0.001)QDIPEIASEALSR;T(0.481)RS(0.481)PDVIS(0.009)S(0.009)AS(0.009)T(0.009)ALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR 177.6 2.59E-17 32731415000 345063.7 374145.9 294026.6 386386.3 376971.8 393108.8 381102.4 407394.7 420966.9 439832.2 TRUE FALSE 331578.2291 363475.6253 347163.7472 406327.7432 389097.4403 401057.7293 385766.4452 398981.8571 373180.5023 410041.9733 0.808644604 0.886435167 0.846654171 0.99094183 0.948921002 0.978089453 0.940797456 0.973026868 0.910103176 1 18.64541207 3.746633149 24.86586151 0.961400506 0.851163689 0.756399492 0.030100218 256.3620637 789670.8516 0.007139751 0.012597649 5579.986506 -3.746633149 -0.110236817 SKLPKPVQDLIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKLPKPVQDLIK 12 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 128.14 0.00014468 2120000000 3253490 2876660 2540680 1764160 1829840 963900 2474380 2426860 2858210 2895880 FALSE TRUE 3126340.014 2794620.473 2999837.393 1855208.509 1888698.465 983390.7184 2504662.203 2376744.493 2533757.983 2699739.468 1.15801545 1.035144504 1.111158106 0.687180571 0.699585455 0.364253933 0.927742188 0.880360687 0.938519444 1 21.36438876 3.746674036 24.3226434 0.774972354 1.094809909 0.409088667 0.173704578 438.0324181 1313140.291 0.047434039 0.083606364 5580.511872 -3.746674036 0.319837555 GNKHDDGTQS(ph)DSENAGAHR ddPTM_BT-474_Pertuzumab_2h_R1 6 GNKHDDGTQSDSENAGAHR 19 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGT(0.001)QS(0.999)DSENAGAHR;GNKHDDGTQS(1)DSENAGAHR;GNKHDDGTQS(1)DSENAGAHR;GNKHDDGT(0.021)QS(0.979)DSENAGAHR;GNKHDDGT(0.003)QS(0.997)DSENAGAHR;GNKHDDGT(0.022)QS(0.974)DS(0.004)ENAGAHR 327.66 2.14E-75 2253029900 785855.2 764389.9 683609.6 610373.9 668038.2 787939.2 689449.1 553033.1 974127.8 834407.8 TRUE FALSE 755143.11 742590.2485 807153.0615 641875.3701 689526.2554 803871.8705 697886.7843 541612.7732 863548.896 777892.6165 0.970754953 0.954617942 1.037615018 0.8251465 0.88640288 1.033396967 0.897150544 0.696256478 1.110113244 1 19.56921149 3.746689348 24.89568225 0.89813718 0.984358163 0.042666497 0.111235358 1385.623904 4243706.412 0.029518947 0.052061413 5580.708628 -3.746689348 0.086220983 EQVANSAFVER ddPTM_BT-474_Pertuzumab_2h_R1 7 EQVANSAFVER 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;;;; 267.85 7.03E-21 14796270000 2415334 2611098 1972374 2715680 2667909 2558335 2786118 2746241 2833522 2859504 FALSE TRUE 2320940.077 2536632.042 2328825.857 2855836.57 2753724.716 2610066.287 2820215.346 2689530.164 2511872.462 2665827.247 0.870626587 0.951536542 0.873584685 1.071275933 1.03297193 0.979083056 1.057913767 1.008891393 0.942248776 1 21.34615186 3.746709643 24.99360749 1.015319565 0.903877995 0.625038255 0.040595696 391.6735876 1201285.887 0.010189154 0.0179864 5580.969424 -3.746709643 -0.111441571 S(ph)PPVQPHT(ph)PVTISLGTAPSLQNNQPVEFNHAINYVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 37 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 2 S(1)PPVQPHT(0.997)PVT(0.003)ISLGTAPSLQNNQPVEFNHAINYVNK 100.89 0.00016422 106170000 43139 39479 30403 44858 48841 41852 41294 41295 44113 46465 TRUE FALSE 41453.08019 38353.09757 35897.49841 47173.12676 50412.01512 42698.27612 41799.36832 40442.24382 39105.47718 43317.88416 0.956950714 0.88538714 0.828699257 1.088998867 1.163769101 0.985696253 0.964944829 0.933615402 0.902755939 1 15.40267516 3.746748535 24.97849507 1.001933165 0.889849851 0.323647372 0.076270639 851.175234 2596633.086 0.022224519 0.039246716 5581.46923 -3.746748535 -0.112083314 LGEMWSEQSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGEMWSEQSAK 11 0 P26583 P26583 HMGB2 High mobility group protein B2 0 ; 178.08 1.79E-05 177627000 190465 179909 157736 144624 171186 141695 164703 175458 169365 174883 FALSE TRUE 183021.4172 174778.1715 186242.404 152088.062 176692.3532 144560.17 166718.6846 171834.731 150139.3952 163038.0186 1.122568949 1.072008682 1.142324996 0.932838017 1.083749389 0.8866654 1.022575507 1.053954976 0.920885794 1 17.3148489 3.746944278 24.92633162 0.993891259 1.10827166 0.480529306 0.059813017 552.861673 1643765.605 0.014848006 0.026200882 5583.985451 -3.746944278 0.114380401 HLQLAIR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLQLAIR 7 0 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;H0YFX9;P16104;Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-4;Q71UI9-2;Q71UI9-3;C9J386 A0A0U1RR32;Q7L7L0;Q99878;P16104;Q71UI9 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;H2AFX;H2AFV;H2AFZ Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A;Histone H2AX;Histone H2A.V;Histone H2A.Z 0 ;;; 170.31 0.00097941 8921840000 4661700 5128150 3863760 915140 813332 242665 2578080 552883 886550 1541310 FALSE TRUE 4479515.61 4981900.183 4562027.381 962370.4851 839493.5624 247571.8526 2609631.314 541465.7728 785912.5607 1436915.701 3.11745192 3.467078953 3.174874753 0.669747352 0.584232994 0.17229393 1.816133899 0.37682501 0.546944097 1 20.454544 3.747134572 7.166365906 0.725770708 3.283213071 0.879633596 0.426335648 0.042516813 14.54061658 0.109078768 0.186849507 5586.432711 -3.747134572 2.557442363 ELDALDANDELTPLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELDALDANDELTPLGR 16 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 239.87 1.78E-19 894370000 1041130 1107190 874300 1160400 1147460 1203430 1118900 1225030 1222170 1282930 FALSE TRUE 1000441.489 1075614.025 1032305.459 1220288.383 1184369.093 1227764.179 1132593.433 1199732.702 1083434.385 1196036.008 0.836464355 0.899315754 0.863105669 1.020277295 0.990245348 1.026527772 0.946955965 1.003090788 0.90585432 1 20.18982939 3.747247638 24.8694107 0.985530327 0.869597298 0.688781411 0.036452002 322.5962657 923533.5636 0.008946815 0.015804373 5587.887293 -3.747247638 -0.115933029 IIKNEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 IIKNEVK 7 1 P50914 P50914 RPL14 60S ribosomal protein L14 0 84.476 0.037389 0 660670 431480 544150 263460 411380 390220 350690 491290 491900 453380 FALSE TRUE 634850.286 419174.6129 642490.0096 277057.2022 424612.4113 398110.5158 354981.8491 481144.6898 436061.5742 422672.1688 1.501992165 0.991725133 1.520066986 0.655489579 1.004590419 0.94188959 0.839851486 1.138340126 1.031677992 1 18.68917959 3.747268218 24.99990819 0.957216348 1.303307784 0.491734005 0.181938852 581.1895378 1668616.693 0.044741662 0.079105616 5588.152098 -3.747268218 0.346091436 LKDYAFIHFDER ddPTM_BT-474_Pertuzumab_2h_R1 4 LKDYAFIHFDER 12 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;; 152.99 3.71E-05 4934085000 7846880 8616920 6197650 6381940 7175280 6299570 7150790 6328460 7094240 7097130 FALSE TRUE 7540215.254 8371173.878 7317703.221 6711312.688 7406079.398 6426951.622 7238303.507 6197775.089 6288931.617 6616435.064 1.139619022 1.265209104 1.105988822 1.01433969 1.11934589 0.971361702 1.093988445 0.936724237 0.950501525 1 22.65762267 3.747398609 0.544504883 0.971672885 1.250135226 0.592561243 0.062531404 1.057986342 0.49329016 0.040844653 0.167617329 5589.83012 -3.747398609 0.278462341 NSSYFVEWIPNNVK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSSYFVEWIPNNVK 14 0 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB2B;TUBB4A;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 262.07 3.58E-24 1147840000 1046530 1059130 857300 774030 781270 749860 835290 915940 1027810 1012360 FALSE TRUE 1005630.451 1028924.649 1012233.181 813977.7811 806400.2591 765022.683 845512.5289 897025.5189 911137.3177 943791.9555 1.06552132 1.090202818 1.07251728 0.862454672 0.854425866 0.810584026 0.895867489 0.950448363 0.965400597 1 19.84810935 3.747459022 23.91573051 0.900095195 1.077492744 0.679822096 0.053519572 210.6415679 566125.8692 0.014827867 0.026205351 5590.607747 -3.747459022 0.177397549 KNTLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KNTLAR 6 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 114.59 0.04034 3465200000 6866900 6765300 5566800 4690400 5283900 3729600 5510300 5790600 5900000 6802800 FALSE TRUE 6598533.956 6572360.268 6572844.593 4932472.106 5453861.442 3805015.067 5577736.7 5671022.086 5230256.735 6342040.297 1.040443398 1.036316384 1.036392751 0.777742158 0.859953767 0.599967028 0.879486165 0.894195215 0.824696232 1 22.59651561 3.747482864 24.26733227 0.827798453 1.037577432 0.485906538 0.096021411 360.2600729 979855.2993 0.024741783 0.043746483 5590.91467 -3.747482864 0.209778979 QKYNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKYNVR 6 1 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KSS0;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ; 124.12 0.016864 1525100000 2389080 2337000 2058670 1301410 1773350 1127870 1584650 1855670 1981780 2300800 FALSE TRUE 2295712.112 2270351.048 2430717.464 1368575.926 1830391.413 1150676.304 1604043.421 1817349.766 1756816.643 2144964.767 1.070279637 1.058456103 1.133220229 0.638041215 0.853343347 0.536454641 0.747818074 0.847263225 0.819042191 1 21.03252252 3.747608315 24.99399301 0.76752197 1.084432422 0.58218317 0.120093844 437.6963545 1209119.639 0.030065693 0.053242383 5592.52991 -3.747608315 0.316910452 AIS(ph)PTSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AISPTSSSR 9 0 O14795;O14795-2;A0A0U1RRL2;B1AM27 O14795 UNC13B Protein unc-13 homolog B 1 AIS(0.984)PT(0.016)SSSR 136.84 0.00019032 612480000 573170 680390 510110 765170 770610 889530 761320 654000 758610 810940 TRUE FALSE 550769.8827 660985.9434 602298.2243 804660.5154 795397.3705 907516.9061 770637.2619 640494.6715 672495.7732 756014.3115 0.7285178 0.87430348 0.796675691 1.064345612 1.052093007 1.200396464 1.019342161 0.847199136 0.889527834 1 19.52805402 3.747613169 24.44264228 1.004546662 0.807279415 0.498623694 0.096555131 494.9409507 1336376.193 0.028756595 0.050894587 5592.59241 -3.747613169 -0.197267246 EISLWFKPEELVDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 EISLWFKPEELVDYK 15 1 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ; 184.99 4.03E-07 11829500000 7160700 6354600 5597400 3833500 4506100 4774200 4247700 4538100 5966300 5397000 FALSE TRUE 6880851.927 6173373.03 6608974.693 4031347.394 4651042.799 4870737.595 4299684.623 4444386.649 5289030.637 5031456.383 1.367566645 1.22695549 1.313531151 0.801228727 0.924392948 0.968057203 0.854560647 0.883320119 1.051192783 1 22.26254463 3.747661714 24.99227459 0.916571103 1.29511157 0.840679051 0.075022968 226.5419829 622098.9296 0.018658059 0.033036131 5593.217576 -3.747661714 0.378540466 NVIHPFLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NVIHPFLSR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 91.584 0.010654 239790000 361960 374830 289750 166360 165160 78244 174310 183630 210870 296860 FALSE TRUE 347814.203 364140.2154 342114.2705 174945.8595 170472.5214 79826.14729 176443.2579 179837.9763 186932.9216 276753.4078 1.256765746 1.315756934 1.236170037 0.632136243 0.615972619 0.288437812 0.63754683 0.649813051 0.675449394 1 18.07824156 3.747766402 4.83669338 0.612294835 1.282767322 0.757079318 0.162242935 0.081119957 5.596271656 0.041614388 0.07235407 5594.566008 -3.747766402 0.670472487 (ac)AEEQPQVELFVK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEEQPQVELFVK 12 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 58.223 0.0033736 14421000 44018 31753 27898 38227 35641 43268 28735 39756 43398 38368 FALSE TRUE 42297.7279 30847.43553 32939.78919 40199.90005 36787.42513 44142.90861 29086.66753 38935.02471 38471.64098 35769.30119 1.182514796 0.862399726 0.920895519 1.123865961 1.028463624 1.234100392 0.81317405 1.088503924 1.075549136 1 15.12643431 3.747783767 24.78385481 1.049790623 0.975982992 0.047391275 0.126147532 1750.031143 4702559.478 0.031222884 0.055304329 5594.789702 -3.747783767 -0.073807631 AIS(ph)ETEENSDELSGER ddPTM_BT-474_Pertuzumab_2h_R1 2 AISETEENSDELSGER 16 0 Q00987-8;A7UKX8;F5GWH7;J3KN53;E7EPE2;Q00987-9;Q00987;Q00987-11 Q00987-8 MDM2;mdm2 E3 ubiquitin-protein ligase Mdm2 1 AIS(0.961)ET(0.039)EENSDELSGER;AIS(0.886)ET(0.114)EENSDELSGER 479.83 5.65E-231 948020000 335950 427960 301070 584050 603980 519740 527410 607790 472640 520040 TRUE FALSE 322820.7026 415754.9998 355480.0463 614192.8905 623407.5652 530249.4989 533864.6013 595238.9241 418987.8887 484817.2276 0.665860626 0.857549972 0.733224865 1.266854508 1.285861 1.093710101 1.10116673 1.227759432 0.864218235 1 18.88708144 3.747844823 24.96113724 1.139208839 0.762745603 0.632337506 0.127829504 391.1657637 1051669.391 0.03219879 0.057052714 5595.576317 -3.747844823 -0.376463236 ELNYFAK ddPTM_BT-474_Pertuzumab_2h_R1 6 ELNYFAK 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;; 117.02 0.012389 3004501000 4044090 4388860 2896170 3362730 2764470 2518130 3036470 3113200 3480540 2826890 FALSE TRUE 3886042.492 4263694.01 3419572.344 3536280.898 2853391.688 2569048.314 3073631.228 3048911.332 3085443.691 2635422.222 1.474542659 1.617840957 1.297542502 1.341827077 1.082707607 0.974814697 1.166276584 1.156896723 1.170758774 1 21.32960268 3.747846879 1.392179498 1.105094038 1.544254467 0.778292956 0.091773753 0.202844481 0.75198652 0.028619931 0.073573772 5595.602802 -3.747846879 0.439160429 EYWNDPELDEGER ddPTM_BT-474_Pertuzumab_2h_R1 2 EYWNDPELDEGER 13 0 A0A494C108;Q8N9T8;H0YFD2;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 0 ; 182.08 2.68E-05 283170000 300620 330280 259960 326070 323700 370370 333910 335440 323790 354050 FALSE TRUE 288871.438 320860.7378 306940.5548 342898.5118 334112.1045 377859.1352 337996.4905 328513.0468 287034.7166 330069.8781 0.875182672 0.972099422 0.92992598 1.038866417 1.012246577 1.144785272 1.024014952 0.995283328 0.869618028 1 18.33241196 3.748118291 23.28346651 1.016757935 0.93037234 0.259355229 0.066432063 384.3235008 936243.4028 0.017698437 0.031325783 5599.100858 -3.748118291 -0.086385595 AADEDWDS(ph)ELEDDLLGEDLLSGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AADEDWDSELEDDLLGEDLLSGKK 24 1 Q96EV2;A8MTF7;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 1 AADEDWDS(1)ELEDDLLGEDLLSGKK 66.045 0.022845 16660000 6236.9 5675.1 5785.6 4142.4 5764.5 4847.4 6161.8 4730.2 6291.5 6230.3 TRUE FALSE 5993.155053 5513.251705 6831.18662 4356.18976 5949.920378 4945.417749 6237.209952 4632.519717 5577.315296 5808.316232 1.031823133 0.949199645 1.176104459 0.749991837 1.024379552 0.851437414 1.073841317 0.797566719 0.960229277 1 12.50390429 3.748120425 24.93926341 0.917416693 1.042058115 0.228378054 0.10863098 944.7149309 2464528.121 0.025824067 0.045832329 5599.128381 -3.748120425 0.124641422 GSFMLGLETHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSFMLGLETHDR 12 0 Q92905 Q92905 COPS5 COP9 signalosome complex subunit 5 0 135.6 0.00012484 231180000 251290 282730 213570 295210 309810 334970 302290 242830 309690 308900 FALSE TRUE 241469.309 274666.8172 252166.8498 310445.8235 319775.32 341743.3229 305989.5154 237815.4756 274535.2895 287977.9279 0.838499363 0.953777323 0.875646449 1.078019506 1.110416074 1.186699708 1.062545028 0.825811469 0.953320595 1 18.13559871 3.748319177 24.76986994 1.023303813 0.895754663 0.315403237 0.095033433 971.658019 2466323.604 0.029223315 0.051816267 5601.69136 -3.748319177 -0.12754915 KPIDSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPIDSLR 7 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 81.594 0.042935 388650000 546450 659330 520710 636690 713390 769650 774020 818560 888140 882200 FALSE TRUE 525094.1299 640526.554 614813.8801 669549.6472 736336.8372 785212.8503 783492.6883 801656.4499 787322.0706 822447.8082 0.638452829 0.778805108 0.747541514 0.814093783 0.895299167 0.954726662 0.952635147 0.974720149 0.957291226 1 19.6495646 3.748349654 0.563850663 0.990447382 0.616136026 0.943729975 0.027063822 0.321448258 0.162582232 0.01716894 0.070079012 5602.084483 -3.748349654 -0.374311356 KQLQDEMLR ddPTM_BT-474_Pertuzumab_2h_R1 3 KQLQDEMLR 9 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;; 204.34 2.68E-05 5004300000 5003500 5386700 4231000 3877560 4253500 2986330 4620500 4280220 4503330 4683600 FALSE TRUE 4807957.688 5233076.59 4995635.818 4077681.336 4390317.69 3046715.639 4677047.061 4191831.961 3992130.858 4366375.6 1.10113241 1.198494374 1.144115 0.933882403 1.005483287 0.697767649 1.071150879 0.96002551 0.914289384 1 22.05800481 3.748562924 7.218310525 0.940534676 1.153693782 0.501831631 0.094715511 0.116729005 39.70246324 0.024184888 0.041562565 5604.836186 -3.748562924 0.213159106 NVSKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 NVSKPR 6 1 Q9Y3U8;J3QSB5;J3KTD3 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;; 106.42 0.03544 225240000 2770640 2455770 2152280 1877710 2042720 1970120 1859070 2377930 2384300 2657060 FALSE TRUE 2662360.326 2385733.844 2541244.873 1974618.838 2108425.944 2009957.176 1881821.855 2328824.915 2113644.26 2477094.96 1.074791386 0.963117637 1.025897236 0.797151046 0.8511688 0.811417087 0.759689025 0.940143576 0.853275427 1 21.24021774 3.748712565 24.93416996 0.85350051 1.015453657 0.528381639 0.070064669 512.9889565 1259947.409 0.017483945 0.031074056 5606.767729 -3.748712565 0.161953148 QQNELAELHANLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQNELAELHANLAR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 120.7 0.00011884 622440000 1157230 1013550 986570 607530 820380 892280 784660 825310 934810 796680 FALSE TRUE 1112004.172 984644.5464 1164865.145 638884.6961 846768.2678 910322.5129 794262.9038 808267.0601 828694.2878 742720.154 1.49720479 1.325727518 1.568376917 0.860195718 1.140090602 1.225660174 1.069397268 1.088252494 1.115755757 1 19.5024592 3.748880861 24.99977012 1.08417438 1.44996553 0.739501457 0.106450438 359.683927 871296.2626 0.026513574 0.047136909 5608.940865 -3.748880861 0.365791149 SLTVS(ph)DDAESSEPER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLTVSDDAESSEPER 15 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 SLTVS(0.989)DDAES(0.002)S(0.008)EPER 288.22 1.02E-34 108610000 225800 223310 197220 175890 175170 180450 198950 244740 236700 203650 TRUE FALSE 216975.4864 216941.4174 232862.0411 184967.704 180804.5021 184098.8226 201384.8096 239686.0335 209830.8083 189856.6041 1.142838762 1.142659316 1.22651536 0.974249512 0.952321374 0.969672999 1.060720593 1.262458236 1.105206792 1 17.53455066 3.748928252 24.96652197 1.063196513 1.16786996 0.277828063 0.088951093 1288.443193 3102716.514 0.027765943 0.049379548 5609.552949 -3.748928252 0.104673447 NFEATLGWLQEHACSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NFEATLGWLQEHACSR 16 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 228.39 4.15E-15 1207980000 1040200 1090670 881260 899940 942290 971880 874310 956640 1196910 1178480 FALSE TRUE 999547.834 1059565.159 1040523.286 946386.0112 972599.6136 991532.0795 885010.0673 936885.0497 1061041.795 1098660.5 0.909787722 0.964415449 0.947083549 0.861399869 0.885259472 0.902491788 0.805535529 0.852752101 0.965759481 1 20.06731421 3.74899575 24.0574538 0.88259729 0.94282757 0.08565632 0.054732612 687.9880282 1586099.261 0.013738295 0.024403629 5610.424853 -3.74899575 0.060230281 KLCVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLCVFK 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 103.71 0.05524 1687720000 2634100 2662900 2191410 2132560 2316410 1924010 2392000 2523200 2576000 2727800 FALSE TRUE 2531156.46 2586956.699 2587446.535 2242621.677 2390919.431 1962914.8 2421274.012 2471095.038 2283583.279 2543043.676 0.995325595 1.0172679 1.017460517 0.881865183 0.940180247 0.771876165 0.952116566 0.971707667 0.897972497 1 21.27812481 3.749049781 24.6987624 0.916025208 1.010743004 0.3463233 0.058851938 698.7597447 1645359.63 0.015468938 0.027498674 5611.122896 -3.749049781 0.094717796 EMTLDEWK ddPTM_BT-474_Pertuzumab_2h_R1 4 EMTLDEWK 8 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 160.54 0.0008207 1203620000 2416630 2332240 1987280 1751050 1950190 1136950 2332820 2148780 2384120 2473170 FALSE TRUE 2322185.428 2265726.799 2346425.703 1841421.9 2012919.632 1159939.908 2361369.749 2104406.942 2113484.693 2305659.993 1.007167334 0.982680363 1.017680712 0.798652839 0.873034029 0.503083677 1.024162173 0.912713474 0.916650633 1 21.13674835 3.749088301 24.2684455 0.856885967 1.000526575 0.184603465 0.135880925 836.865701 1929137.064 0.035596832 0.063287555 5611.620601 -3.749088301 0.143640609 APALS(ph)PTRPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 APALSPTRPPK 11 1 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-5;O94875-4 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 APALS(0.998)PT(0.002)RPPK;APALS(0.926)PT(0.074)RPPK;APALS(0.979)PT(0.021)RPPK;APALS(0.994)PT(0.006)RPPK 102.9 0.0016993 1109890000 1942710 2009410 1548300 1959310 1856120 1945720 1916840 2073380 2160140 2089380 TRUE FALSE 1866786.745 1952103.594 1828112.252 2060430.224 1915823.785 1985063.792 1940298.861 2030563.978 1914929.963 1947864.432 0.958376114 1.002176313 0.938521297 1.057789336 0.983550885 1.01909751 0.996115967 1.042456521 0.983092012 1 20.89346184 3.749220091 24.99323373 1.013433475 0.969939752 0.368867815 0.027010783 736.7971573 1727561.881 0.00641705 0.011432374 5613.323755 -3.749220091 -0.043493724 RAS(ph)ISEPSDTDPEPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RASISEPSDTDPEPR 15 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 RAS(0.98)IS(0.02)EPSDTDPEPR;RAS(0.996)IS(0.003)EPSDTDPEPR;RAS(0.96)IS(0.036)EPS(0.004)DTDPEPR 208.82 2.86E-09 1367640000 763320 841800 666040 866200 849810 917310 915860 863730 884290 993420 TRUE FALSE 733488.6105 817792.6882 786408.244 910904.6858 877144.9104 935858.6367 927068.5686 845893.6737 783909.1064 926134.7786 0.791989058 0.883016929 0.849129373 0.983555209 0.947102874 1.010499399 1.001008266 0.91335915 0.846430913 1 19.82086264 3.749304582 23.72739859 0.955706922 0.845542273 0.521451715 0.050877899 314.021042 693492.4019 0.013579969 0.024142014 5614.41591 -3.749304582 -0.110164649 RQLHGES(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 RQLHGESPTR 10 1 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;Q9UQ26-2;A0A0J9YXG4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 RQLHGES(0.974)PT(0.026)R 54.524 0.083636 191000000 186540 179460 143560 205710 193670 206070 209250 203470 191830 228720 TRUE FALSE 179249.8106 174341.9765 169504.4855 216326.7178 199899.5714 210236.8766 211810.8641 199268.2734 170054.2626 213228.5907 0.840646229 0.817629456 0.794942578 1.014529604 0.937489531 0.985969451 0.993351142 0.934528868 0.797520924 1 17.70204137 3.74934559 24.96976164 0.951537555 0.817728415 0.522829763 0.058739033 567.120764 1313014.914 0.015144154 0.026955952 5614.946077 -3.74934559 -0.133809141 MALLQEFASRPLGAAPQAEHQGLPVPGS(ph)PGGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 MALLQEFASRPLGAAPQAEHQGLPVPGSPGGQK 33 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 MALLQEFASRPLGAAPQAEHQGLPVPGS(1)PGGQK;MALLQEFASRPLGAAPQAEHQGLPVPGS(1)PGGQK 233.04 7.05E-47 1871450000 2152310 2110790 1866500 1627750 1839630 1795550 1889410 1898040 2267500 2133940 TRUE FALSE 2068195.346 2050592.336 2203818.07 1711758.373 1898803.37 1831857.251 1912533.165 1858844.811 2010102.906 1989406.343 1.039604278 1.030755905 1.107776738 0.860436772 0.954457281 0.920805977 0.961358735 0.934371612 1.010403386 1 20.92390655 3.749412987 24.99829921 0.945335832 1.056516666 0.572650639 0.043667975 483.5108477 1113758.239 0.010649754 0.018960545 5615.817518 -3.749412987 0.111180834 IYDDDFFQNLDGVANALDNVDAR ddPTM_BT-474_Pertuzumab_2h_R1 6 IYDDDFFQNLDGVANALDNVDAR 23 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 338.91 6.78E-87 1308242000 705922 800996 629134 813428 862196 887816 838981 862912 888503 886158 FALSE TRUE 678333.7878 778152.3783 742832.5088 855409.1166 889929.3174 905768.2478 849248.7004 845092.5657 787643.8643 826137.7294 0.821090435 0.94191604 0.899163036 1.035431607 1.07721665 1.096388914 1.027974719 1.022943918 0.953405027 1 19.65602279 3.749454823 5.547381336 1.03541331 0.891552729 0.669020846 0.046021011 0.101599022 11.51646797 0.012383524 0.02142963 5616.358515 -3.749454823 -0.143860581 GLLAQGLRPES(ph)PPPAGPLLNGAPAGESPQPK ddPTM_BT-474_Pertuzumab_2h_R1 7 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK 306.01 2.11E-82 20585150000 5224820 5267750 4331200 5409530 5775910 5579440 5405740 5988010 6075370 5586970 TRUE FALSE 5020628.258 5117518.928 5113944.187 5688716.492 5961697.391 5692260.1 5471897.063 5864355.501 5385719.468 5208559.546 0.96391876 0.982520961 0.98183464 1.09218613 1.144596186 1.092866473 1.050558607 1.125907355 1.034013228 1 22.31245301 3.749488177 8.368558014 1.086511843 0.976532536 0.554368688 0.040930252 0.111333929 63.14894424 0.010166094 0.017522938 5616.789872 -3.749488177 -0.109979307 ISHGEVLEWQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISHGEVLEWQK 11 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 119.27 0.00060815 380880000 918620 978630 742140 629750 673610 288460 850460 617860 718060 824180 FALSE TRUE 882719.3148 950720.4306 876261.2068 662251.473 695277.2774 294292.8588 860868.1839 605100.9751 636548.8392 768357.5545 1.148839248 1.237341164 1.140434166 0.861905332 0.90488767 0.383015508 1.120400494 0.78752525 0.828453935 1 19.5514183 3.74981043 2.986503276 0.825777836 1.195629805 0.421368594 0.18026339 0.235775127 4.261125279 0.047535761 0.088394394 5620.959156 -3.74981043 0.369851969 LIVAYVDDLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LIVAYVDDLDR 11 0 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 96.143 0.016825 17902000 20510 22655 17449 23312 24900 20925 23657 23649 24781 24916 FALSE TRUE 19708.44652 22008.90158 20602.42245 24515.13511 25700.93111 21348.11784 23946.52144 23160.63989 21967.96477 23228.41713 0.848462744 0.947498982 0.886949048 1.055394131 1.106443499 0.919051768 1.030914905 0.997082141 0.945736623 1 14.50360323 3.749830133 24.77833644 1.008786238 0.89962312 0.477423902 0.054323793 588.2079259 1293291.655 0.013936869 0.024833913 5621.214183 -3.749830133 -0.109163118 KFDQLLAEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFDQLLAEEK 10 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;A0A0C4DFM8;A1L2Z2 P35579;P35580;P35749;Q7Z406 MYH9;MYH10;MYH11;MYH14 Myosin-9;Myosin-10;Myosin-11;Myosin-14 0 ; 132.56 0.0003532 4204300000 13719600 12899100 11211000 8213500 9367400 4333900 12079800 11322400 12854000 13006800 FALSE TRUE 13183422.86 12531230.3 13237077.09 8637399.719 9668710.928 4421534.427 12227636.21 11088588.48 11394867.81 12125837.85 1.087217479 1.033432118 1.091642264 0.712313642 0.797364359 0.364637436 1.008395161 0.914459571 0.939717976 1 23.5315811 3.749871599 24.28119884 0.814284919 1.067030804 0.297116082 0.176903 662.64091 1422480.104 0.047505249 0.084607175 5621.75091 -3.749871599 0.252745885 EMVYAS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 EMVYASR 7 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 EMVYAS(1)R;EMVYAS(1)R 93.467 0.015644 548380000 767410 750200 563820 556990 581550 494060 462440 597130 534910 519100 TRUE FALSE 737418.7688 728805.0305 665714.8161 585736.3206 600256.0839 504050.2317 468099.4791 584799.0568 474189.2593 483940.8946 1.523778579 1.505979426 1.375611823 1.210346815 1.24034999 1.041553292 0.967265805 1.208410083 0.979849532 1 18.88447133 3.749913522 0.820702875 1.053461855 1.585193313 0.863387859 0.073788586 0.310119571 0.368009894 0.032237876 0.117076719 5622.293612 -3.749913522 0.531731458 RS(ph)SLDAEIDSLTSILADLECSSPYKPRPPQS(ph)STGSTASPPVSTPVTGHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 2 RS(0.408)S(0.408)LDAEIDS(0.061)LT(0.061)S(0.061)ILADLECS(0.101)S(0.101)PY(0.106)KPRPPQS(0.111)S(0.111)T(0.111)GS(0.111)T(0.111)AS(0.111)PPVS(0.02)T(0.004)PVTGHK 58.106 0.0025298 63649000 40094 33445 34589 25247 31832 33067 32428 31072 39540 36679 TRUE FALSE 38527.08215 32491.18135 40840.00173 26550.0007 32855.90519 33735.6374 32824.86356 30430.35234 35051.58497 34194.69866 1.126697519 0.95018183 1.194337231 0.776436165 0.960847923 0.986575075 0.959940133 0.88991433 1.02505904 1 15.06148506 3.750188506 24.99417629 0.938786035 1.076383141 0.374043277 0.086905477 798.1765873 1715678.276 0.02104603 0.037538685 5625.854628 -3.750188506 0.137597106 GFGFVS(ph)FER ddPTM_BT-474_Pertuzumab_2h_R1 3 GFGFVSFER 9 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 1 GFGFVS(1)FER;GFGFVS(1)FER;GFGFVS(1)FER 123.75 0.00057588 111306000 105814 113480 73866 134865 127473 103791 109200 164314 86905 91492 TRUE FALSE 101678.6719 110243.6615 87215.22934 141825.3988 131573.2848 105889.7251 110536.4223 160920.8585 77039.90874 85295.16535 1.192080131 1.292496017 1.022510819 1.662760113 1.542564391 1.241450494 1.295928343 1.886635167 0.903215422 1 16.38017635 3.750319756 24.94651345 1.424698357 1.181375714 0.057065613 0.287076033 1528.758297 3243185.726 0.072285409 0.128996899 5627.555101 -3.750319756 -0.243322643 SRS(ph)YS(ph)PAHNR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSYSPAHNR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(0.416)RS(0.593)Y(0.286)S(0.706)PAHNR 62.759 0.047228 273750000 195480 239210 182860 300580 291360 347560 301050 236410 307190 319200 TRUE FALSE 187840.4255 232387.965 215906.8697 316092.9698 300731.859 354587.9013 304734.34 231528.0509 272319.079 297580.2997 0.631226011 0.780925233 0.725541543 1.062210671 1.010590618 1.191570483 1.024040705 0.778035546 0.915111247 1 18.1829195 3.750420751 23.50839138 0.985691875 0.71940028 0.605560701 0.104993787 279.5637368 554129.374 0.031340005 0.055848443 5628.863933 -3.750420751 -0.266291596 ASS(ph)ASVPAVGASAEGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSASVPAVGASAEGTR 17 0 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 ASS(1)ASVPAVGASAEGTR 319.53 1.91E-58 925790000 314250 329650 250490 328000 320760 325410 305720 374760 301220 321280 TRUE FALSE 301968.7626 320248.7048 295759.1151 344928.1193 331077.5367 331990.0132 309461.4928 367021.075 267026.7684 299519.4194 1.008177577 1.069208485 0.987445541 1.151605195 1.105362508 1.108408977 1.033193418 1.225366541 0.891517381 1 18.19229002 3.750533661 24.83937872 1.09128231 1.026370334 0.042508716 0.087978998 1599.421614 3318164.234 0.021487834 0.038366021 5630.327544 -3.750533661 -0.064911976 ETNCESDRER ddPTM_BT-474_Pertuzumab_2h_R1 1 ETNCESDRER 10 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 67.385 0.066527 0 13441 16540 12865 9193.2 12619 12016 11002 9383 13856 12785 FALSE TRUE 12915.71086 16068.29539 15189.99168 9667.662154 13024.9016 12258.97175 11136.64577 9189.237771 12283.12497 11919.06056 1.083618192 1.348117606 1.274428601 0.811109408 1.092779211 1.028518287 0.934356001 0.770969971 1.030544723 1 13.54098291 3.750623363 24.86979552 0.940580355 1.246661112 0.569780762 0.112133169 483.8694166 997592.0556 0.029867386 0.053325956 5631.490592 -3.750623363 0.306080757 SRNS(ph)PLLER ddPTM_BT-474_Pertuzumab_2h_R1 7 SRNSPLLER 9 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 S(0.002)RNS(0.998)PLLER;S(0.002)RNS(0.998)PLLER;S(0.003)RNS(0.997)PLLER;S(0.009)RNS(0.991)PLLER;S(0.229)RNS(0.771)PLLER;S(0.245)RNS(0.755)PLLER;S(0.2)RNS(0.8)PLLER 137.62 9.65E-05 31053960000 1941466 2017137 1628084 2116727 2123675 2086520 2197326 2319872 2218231 1945149 TRUE FALSE 1865591.362 1959610.228 1922314.995 2225971.534 2191984.935 2128710.864 2224217.533 2271965.833 1966426.716 1813402.326 1.028779624 1.08062629 1.060059849 1.227511128 1.208769231 1.17387677 1.226543885 1.252874666 1.08438524 1 20.79026761 3.750690781 23.70719445 1.187558892 1.058902324 0.295841589 0.0743122 375.5708951 734011.2619 0.018031903 0.032160821 5632.364866 -3.750690781 -0.128656568 AAEINGEVDDDDAGGEWR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAEINGEVDDDDAGGEWR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 311.33 8.48E-61 214680000 139629 141222 115317 161737 153631 171390 161808 164834 151291 180847 FALSE TRUE 134172.1443 137194.4868 136157.3471 170084.266 158572.6806 174855.6232 163788.2547 161430.1203 134117.0799 168598.0716 0.79581067 0.813736987 0.807585436 1.008815014 0.94053674 1.037115203 0.971471697 0.957484975 0.795484068 1 17.36322851 3.750707562 24.08151304 0.960049807 0.806513594 0.565983296 0.061384608 333.5233662 661212.3803 0.015688226 0.027990907 5632.582512 -3.750707562 -0.153536213 SHSTKS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSTKSPAR 9 1 Q4LE39-2;Q4LE39;H7C5R6 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 1 S(0.012)HS(0.34)T(0.087)KS(0.562)PAR;S(0.003)HS(0.101)T(0.083)KS(0.813)PAR 54.023 0.08343 160078000 401850 407950 294180 141480 144186 16829.2 244050 35159 138204 187660 TRUE FALSE 386145.2577 396315.6654 347344.87 148781.7998 148823.8736 17169.49795 247036.7569 34432.95436 122515.6613 174949.621 2.207179732 2.265313083 1.985399385 0.850426533 0.850667025 0.098139669 1.41204511 0.196816399 0.700291093 1 17.41658001 3.750751263 2.618496157 0.661878999 2.239896561 0.774393991 0.353747703 0.116070108 1.573199785 0.092105883 0.177038783 5633.149315 -3.750751263 1.578017562 NGGCNHMQCSK ddPTM_BT-474_Pertuzumab_2h_R1 1 NGGCNHMQCSK 11 0 O95376 O95376 ARIH2 E3 ubiquitin-protein ligase ARIH2 0 66.289 0.063117 10887000 39007 37464 31285 22964 27047 14356 35065 28841 34483 32839 FALSE TRUE 37482.56332 36395.5634 36938.89543 24149.17479 27916.99132 14646.28816 35494.13596 28245.42327 30568.6344 30614.78528 1.2243288 1.188823082 1.206570456 0.788807583 0.911879377 0.478405712 1.159378896 0.922607264 0.99849253 1 14.90194094 3.750790488 24.18240456 0.892868682 1.20479907 0.424125746 0.166779814 478.0267654 945208.9649 0.043032805 0.076811494 5633.658122 -3.750790488 0.311930388 DDEVQVVR ddPTM_BT-474_Pertuzumab_2h_R1 3 DDEVQVVR 8 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ;; 187.8 0.00046603 516180000 727290 692310 627570 586970 647890 682690 608890 718450 762030 748140 FALSE TRUE 698866.7027 672565.9966 740985.8592 617263.592 668729.9702 696494.4595 616341.778 703613.7564 675527.5491 697467.8114 1.002005672 0.964296826 1.062394346 0.885006565 0.958796893 0.998604449 0.883684907 1.008811797 0.968542975 1 19.41176711 3.750880811 24.99928139 0.958280803 1.005038725 0.203468637 0.046816538 1309.783767 2657715.243 0.01156665 0.020648255 5634.829913 -3.750880811 0.046757922 SKDDQVTVIGAGVTLHEALAAAELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKDDQVTVIGAGVTLHEALAAAELLK 26 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 221.31 1.67E-34 701400000 1381700 1017500 1006400 647570 964580 237530 1017400 972190 1003900 1063200 FALSE TRUE 1327701.636 988481.8962 1188278.867 680991.1653 995606.5917 242333.0193 1029851.246 952113.9368 889941.4807 991188.517 1.339504659 0.997269318 1.198842447 0.687045051 1.004457351 0.244487315 1.039006433 0.960578054 0.897852896 1 19.91879995 3.750888589 24.66476815 0.83496849 1.160411894 0.312600793 0.234102881 823.3675282 1647318.922 0.059687551 0.106593339 5634.930819 -3.750888589 0.325443404 QLTQPETHFGR ddPTM_BT-474_Pertuzumab_2h_R1 6 QLTQPETHFGR 11 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;;;; 185.25 4.55E-06 4435270000 2691060 3176190 2445330 3488000 3308790 3635810 3336770 3529460 3659740 3752270 FALSE TRUE 2585890.4 3085608.171 2887255.527 3668016.098 3415220.235 3709328.569 3377606.389 3456575.418 3244301.658 3498125.411 0.739221753 0.882074771 0.825372217 1.048566208 0.976300113 1.060376097 0.965547541 0.988122212 0.927440065 1 21.73815058 3.750904086 24.35791625 0.994398451 0.822208068 0.742268722 0.048458312 264.200774 521356.9344 0.011939554 0.021319936 5635.131904 -3.750904086 -0.172190383 LGFYGLDESDLDKVFHLPTTTFIGGQESALPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGFYGLDESDLDKVFHLPTTTFIGGQESALPLR 33 1 Q02218;A0A0D9SFS3;Q02218-3;C9J4G7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 66.083 0.0029877 33695000 58635 79008 39321 87080 62687 60275 91105 73417 75317 53140 FALSE TRUE 56343.47938 76754.7692 46427.17939 91574.20924 64703.38429 61493.8018 92219.97024 71900.91329 66767.32991 49540.78047 1.137315134 1.54932499 0.937150746 1.848461174 1.306063079 1.241276403 1.861496112 1.451348013 1.347724628 1 15.59632898 3.75091984 24.99803444 1.466810088 1.24206982 0.10998982 0.284398798 1657.726131 3352943.459 0.069009669 0.123297402 5635.336325 -3.75091984 -0.224740268 NYGS(ph)PLISGSTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 NYGSPLISGSTPK 13 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NYGS(0.997)PLIS(0.003)GSTPK;NYGS(0.778)PLIS(0.222)GSTPK 183.76 5.59E-06 464160000 1916570 1751120 1567860 1192990 1379960 1479280 1373630 1417360 1782900 1742360 TRUE FALSE 1841668.326 1701179.772 1851207.179 1254560.357 1424347.667 1509192.055 1390440.895 1388091.021 1580512.667 1624348.405 1.133788982 1.047299807 1.139661401 0.772346839 0.876873251 0.929106127 0.855999175 0.854552519 0.97301334 1 20.63142968 3.75097797 24.99855085 0.885078199 1.100955054 0.686629236 0.065487637 398.7504991 802760.1074 0.016007723 0.028599403 5636.090654 -3.75097797 0.215876855 ETCAWFTDNYEQAR ddPTM_BT-474_Pertuzumab_2h_R1 6 ETCAWFTDNYEQAR 14 0 Q13630 Q13630 TSTA3 GDP-L-fucose synthase 0 ;;;;; 396.84 4.54E-114 2360240000 1017630 1143941 867994 1228757 1199740 1175067 1188494 1223092 1275976 1360816 FALSE TRUE 977859.8946 1111316.923 1024859.824 1292173.296 1238330.727 1198827.66 1203039.145 1197834.723 1131132.554 1268646.72 0.770789755 0.875986124 0.80783705 1.018544624 0.976103676 0.944965719 0.948285386 0.944183045 0.891605627 1 20.27485895 3.751021667 24.9987403 0.956731512 0.823982479 0.719908822 0.040585027 415.0333615 832617.1772 0.010231299 0.018284915 5636.657768 -3.751021667 -0.132749033 LTIAEER ddPTM_BT-474_Pertuzumab_2h_R1 1 LTIAEER 7 0 P62701;Q8TD47 P62701 RPS4X;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2" 0 133.79 0.0075314 1238600000 636050 629740 508480 658570 637390 645690 639260 732830 687160 677150 FALSE TRUE 611192.4628 611780.4318 600373.6471 692558.8766 657892.2282 658746.2942 647083.4551 717696.8044 609156.4776 631286.0274 0.968170427 0.96910181 0.951032687 1.09706036 1.042146032 1.04349893 1.0250242 1.136880547 0.964945288 1 19.26793429 3.751044371 24.98704539 1.053617258 0.963401651 0.390078714 0.045626052 685.9001591 1372869.956 0.011442975 0.020465721 5636.952443 -3.751044371 -0.090215607 YRQDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 YRQDYK 6 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 77.748 0.065301 1637180000 497770 491780 401990 347500 358740 391230 346730 410970 484970 494370 FALSE TRUE 478316.5981 477754.9159 474638.5352 365434.5166 370279.1979 399140.9387 350973.3855 402483.3259 429918.2388 460885.8796 1.037820032 1.03660133 1.029839612 0.792895883 0.803407556 0.866029871 0.761519068 0.873281964 0.932808441 1 18.81405004 3.751083008 23.94443982 0.849413436 1.03493847 0.587726796 0.065992513 270.9167689 518025.3433 0.016310975 0.029124754 5637.453965 -3.751083008 0.185525034 VLDPFTIKPLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLDPFTIKPLDR 12 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 170.95 3.63E-05 8236300000 12585500 11598500 9187600 7363600 8744600 2191220 8733800 8236500 7524300 8493300 FALSE TRUE 12093644.75 11267722.14 10848003.7 7743636.278 9025878.001 2235527.97 8840686.857 8066413.397 6670173.008 7918041.226 1.527353092 1.423044136 1.370036274 0.977973726 1.139912984 0.282333459 1.116524479 1.018738494 0.842401904 1 22.91671215 3.751180425 1.681525597 0.893569861 1.494313204 0.541000847 0.22664219 0.300738679 1.641577254 0.06754636 0.155471572 5638.718645 -3.751180425 0.600743342 KREDSAPPSSVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KREDSAPPSSVAR 13 2 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ; 115.06 0.00039011 191610000 300170 291490 241990 226430 233290 246620 248230 276120 261340 275450 FALSE TRUE 288439.0245 283176.9906 285722.976 238116.0794 240793.9847 251606.8254 251267.913 270418.0255 231673.7788 256793.5262 1.123233241 1.102741938 1.112656461 0.927266676 0.937694919 0.979802058 0.978482272 1.053056242 0.902179203 1 17.97024931 3.751216185 24.63053469 0.97512712 1.111863706 0.731866926 0.039938721 355.7584157 692382.2498 0.010945197 0.019565912 5639.182954 -3.751216185 0.136736586 TPAAPAS(ph)PAAVPSEGSGGSTTGWR ddPTM_BT-474_Pertuzumab_2h_R1 5 TPAAPASPAAVPSEGSGGSTTGWR 24 0 P07199 P07199 CENPB Major centromere autoantigen B 1 TPAAPAS(1)PAAVPSEGSGGSTTGWR;TPAAPAS(1)PAAVPSEGSGGSTTGWR;TPAAPAS(1)PAAVPSEGSGGSTTGWR;TPAAPAS(1)PAAVPSEGSGGSTTGWR;TPAAPAS(1)PAAVPSEGSGGSTTGWR 388.85 2.83E-137 4213900000 1117768 1185016 871234 1259574 1211403 1257334 1200070 1189003 1243039 1274842 TRUE FALSE 1074084.391 1151220.504 1028685.364 1324580.765 1250368.878 1282758.155 1214756.816 1164449.673 1101934.424 1188495.816 0.903734264 0.968636564 0.865535537 1.114501833 1.052059974 1.079312302 1.022095997 0.979767583 0.927167273 1 20.18070539 3.751299176 24.93518255 1.024563468 0.918235568 0.47262236 0.054288485 733.8640782 1436503.558 0.01478031 0.026434766 5640.260671 -3.751299176 -0.1063279 YDDIKK ddPTM_BT-474_Pertuzumab_2h_R1 3 YDDIKK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;; 83.614 0.091054 28742700000 12030100 10671500 9620300 8484600 8933900 8256000 9558200 11427200 11940200 9894400 FALSE TRUE 11559950.39 10367159.27 11358902.21 8922491.223 9221267.007 8422941.977 9675176.111 11191224.33 10584798.55 9224243.475 1.253213927 1.123903472 1.231418299 0.967287046 0.999677321 0.913130925 1.048885596 1.213240344 1.147497741 1 23.13699916 3.751388761 24.79980941 1.053399784 1.194951065 0.410095479 0.087763544 901.9379542 1743651.275 0.026190987 0.046850471 5641.424252 -3.751388761 0.141551281 NLQYYDISAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NLQYYDISAK 10 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 162.36 1.58E-05 604840000 1261200 1088640 998550 861690 937000 906330 896540 1163310 1134360 1203910 FALSE TRUE 1211910.91 1057593.053 1179010.198 906161.9242 967139.456 924656.6136 907512.1247 1139287.242 1005592.208 1122368.103 1.079780249 0.94228716 1.050466593 0.80736607 0.861695422 0.823844344 0.808569062 1.015074501 0.895955797 1 20.09811448 3.751467171 24.95936327 0.887445968 1.015988923 0.406160084 0.075539714 840.1017356 1624627.603 0.020089786 0.035938349 5642.442871 -3.751467171 0.128542955 QAHLTNQYMQR ddPTM_BT-474_Pertuzumab_2h_R1 1 QAHLTNQYMQR 11 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YB86 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 98.156 0.004347 63931000 76195 87342 69441 43964 49020 48425 64676 59965 66691 69958 FALSE TRUE 73217.21516 84851.09168 81990.53341 46232.98731 50596.77282 49404.18668 65467.52423 58726.70179 59120.51727 65219.68235 1.122624529 1.301004369 1.257144016 0.708880903 0.77578993 0.757504252 1.003800109 0.900444462 0.906482754 1 15.99301979 3.751478822 24.96540337 0.863415875 1.234332353 0.73006704 0.100900772 392.2448045 758040.4463 0.027055358 0.048382084 5642.594254 -3.751478822 0.370916478 HSLECTLILTEGDSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSLECTLILTEGDSAK 16 0 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 163.99 7.53E-09 396540000 261920 242180 167980 284020 271990 243730 276290 200050 305740 288450 FALSE TRUE 251683.8768 235273.2635 198337.7227 298678.3062 280738.8054 248658.3876 279671.3197 195918.8976 271033.677 268913.0246 0.935930408 0.874904679 0.737553426 1.110687393 1.043976229 0.924679598 1.040006597 0.728558603 1.007886016 1 18.03678011 3.751505869 24.98520005 0.958363296 0.852007043 0.218009646 0.107701355 1530.610603 2954172.94 0.029856672 0.053412555 5642.945669 -3.751505869 -0.106356253 RGNVCGDSK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGNVCGDSK 9 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 141.91 0.0001693 5388700000 4115300 4032600 3280810 2698440 2777940 1472650 3841800 3491370 3643920 4145810 FALSE TRUE 3954469.526 3917594.196 3873725.348 2837706.812 2867294.963 1502427.992 3888817.098 3419271.989 3230277.478 3865010.596 1.023145843 1.013605034 1.002254781 0.734204148 0.741859535 0.388725452 1.006159492 0.88467338 0.835774547 1 21.88204094 3.751596161 21.95298535 0.793296061 1.013062383 0.263915559 0.163775861 216.5553746 364691.9297 0.043989519 0.078444824 5644.118987 -3.751596161 0.219766321 FVMEEGRK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVMEEGRK 8 1 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 103.56 0.0076141 449130000 495170 538520 420950 406310 381450 290300 512800 454680 505720 539620 FALSE TRUE 475818.209 523161.9369 497025.029 427279.7078 393719.6857 296170.0649 519075.7998 445290.6991 448312.7858 503071.0568 0.945827041 1.039936466 0.987981762 0.849342657 0.782632355 0.588724119 1.03181408 0.885144739 0.891152015 1 18.94040266 3.751835736 7.071415017 0.854457098 0.996689038 0.206007982 0.116293152 0.242862126 69.70071689 0.031256812 0.054101654 5647.233382 -3.751835736 0.14223194 TPPDTTFPEPTCLSAS(ph)PPNAPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPDTTFPEPTCLSASPPNAPPR 23 0 A1A4S6;H0Y8W5 A1A4S6 ARHGAP10 Rho GTPase-activating protein 10 1 TPPDTTFPEPTCLS(0.073)AS(0.927)PPNAPPR 120.27 6.78E-05 196450000 106000 118610 90009 129360 128370 130210 110700 135600 129770 135540 TRUE FALSE 101857.4028 115227.3589 106275.6285 136036.2851 132499.1376 132842.9354 112054.7797 132799.8126 115039.0536 126359.7551 0.806090537 0.911899195 0.841055987 1.076579208 1.048586534 1.05130732 0.886791682 1.05096605 0.910408963 1 16.94717752 3.751967752 24.95969357 1.005054453 0.858903621 0.541694988 0.063359081 589.6559348 1097743.275 0.015887032 0.028424626 5648.950281 -3.751967752 -0.146150832 VGDAIPAVEVFEGEPGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGDAIPAVEVFEGEPGNK 18 0 P30044-2;P30044;P30044-3 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 227.34 7.04E-19 72296000 77677 72287 60221 88857 76079 79818 86065 101200 89854 90493 FALSE TRUE 74641.29696 70225.44554 71104.27431 93442.92042 78526.15013 81431.97465 87118.28921 99110.18464 79654.15062 84363.82851 0.884754738 0.83241179 0.842828918 1.107618301 0.930803539 0.965247501 1.032649783 1.174794772 0.944174204 1 16.36433695 3.752194746 24.53761401 1.032610651 0.851239785 0.535914946 0.071538738 479.0403901 862135.1956 0.019916235 0.035658637 5651.903606 -3.752194746 -0.181370866 YEEGLVHNGWDDLEFLSDITEEDLEEAGVQDPAHKR ddPTM_BT-474_Pertuzumab_2h_R1 3 YEEGLVHNGWDDLEFLSDITEEDLEEAGVQDPAHKR 36 1 O15357;O15357-2 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 0 ;; 133.46 3.56E-09 75865700 23613.1 27814.3 22780.8 20825.1 21977.8 26514.9 23337.8 22016.7 29228 27829.2 FALSE TRUE 22690.27395 27021.0634 26897.79732 21899.88591 22684.7359 27051.04944 23623.41498 21562.04745 25910.15997 25944.3035 0.874576338 1.041502748 1.036751567 0.844111537 0.874362879 1.042658534 0.910543425 0.831089856 0.998683968 1 14.66313019 3.752256864 24.97315847 0.91788122 0.989999465 0.082097429 0.078692569 1551.266327 2828505.395 0.020368059 0.036490064 5652.712061 -3.752256864 0.072118246 RRS(ph)TPAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSTPAPK 8 2 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RRS(0.5)T(0.5)PAPK 48.741 0.086774 29084000 25647 26554 20477 30045 31331 23576 28886 31362 29176 32850 TRUE FALSE 24644.68689 25796.70592 24177.64941 31595.62605 32338.79007 24052.72287 29239.51551 30714.36374 25864.0628 30625.04024 0.804723412 0.842340311 0.789473229 1.031692556 1.055959105 0.785394001 0.954758436 1.002916682 0.844539716 1 14.90242412 3.752270298 24.86075553 0.954098614 0.815195106 0.400398458 0.079283981 769.0215895 1394517.997 0.020551995 0.036804607 5652.886924 -3.752270298 -0.138903508 AQDGSHPLSLQDLIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQDGSHPLSLQDLIEK 16 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3;H0Y9K1 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 185.33 1.68E-09 608830000 776290 780280 663630 763690 822720 797520 846540 896640 998230 957190 FALSE TRUE 745951.7286 758027.1784 783562.7034 803104.1324 849183.536 813646.4008 856900.2097 878124.0707 884915.1153 892358.6687 0.83593263 0.849464688 0.878080452 0.899979079 0.951616839 0.911793015 0.960264342 0.984048345 0.991658563 1 19.76726417 3.752371686 0.352478339 1.008115353 0.769762456 0.934979361 0.014454015 0.730505942 0.120578278 0.015142674 0.070236848 5654.206772 -3.752371686 -0.238352896 GAPVGGHILSYLLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GAPVGGHILSYLLEK 15 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 103.21 0.0014902 182400000 328860 367090 279680 430860 399500 392180 469560 399010 413320 445260 FALSE TRUE 316007.7876 356620.9526 330224.3974 453096.7362 412350.2803 400110.1483 475306.6157 390770.3041 366401.6464 415102.1436 0.761277176 0.859116143 0.795525638 1.091530707 0.993370636 0.963883599 1.14503532 0.941383489 0.882678281 1 18.66310686 3.752507639 24.94606198 1.003150462 0.810687279 0.60657708 0.072756539 529.6694393 947380.0535 0.018712041 0.033513249 5655.977056 -3.752507639 -0.192463183 DKLCGPYEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DKLCGPYEK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;; 80.245 0.022489 1271860000 1239740 1385000 1063610 838648 914170 549404 1125940 1000700 1315440 1336410 FALSE TRUE 1191289.59 1345501.156 1255827.987 881930.7238 943575.1083 560513.3253 1139719.591 980035.1953 1166116.766 1245893.76 0.956172692 1.079948547 1.007973574 0.707869926 0.757347968 0.44988854 0.91478072 0.786612171 0.93596806 1 20.24874962 3.752630636 21.67657342 0.777051571 1.021223546 0.320686208 0.14631711 147.4069464 227093.9484 0.037303234 0.066632083 5657.579117 -3.752630636 0.244171975 TVAISDAAQLPHDYCTTPGGTLFSTT(ph)PGGTR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCTTPGGTLFS(0.008)T(0.249)T(0.742)PGGTR;TVAISDAAQLPHDYCTTPGGTLFST(0.003)T(0.997)PGGTR;TVAISDAAQLPHDYCTTPGGTLFS(0.035)T(0.087)T(0.877)PGGTR;TVAISDAAQLPHDYCTTPGGTLFST(0.01)T(0.985)PGGT(0.005)R 320.81 1.87E-92 15262800000 2869210 3059430 2304180 3372620 3458160 3107810 3232070 3404030 3261830 3010990 TRUE FALSE 2757078.101 2972178.052 2720596.582 3546681.322 3569394.857 3170652.048 3271625.039 3333735.591 2891560.733 2807052.965 0.982196679 1.05882507 0.969200302 1.263489277 1.271580872 1.129530538 1.165501713 1.187628318 1.030105512 1 21.42062486 3.752720175 24.97193873 1.163920905 1.008949114 0.373607578 0.085329756 763.8472705 1347124.54 0.021383503 0.03830984 5658.745673 -3.752720175 -0.15497179 VREEEIEVDSR ddPTM_BT-474_Pertuzumab_2h_R1 6 VREEEIEVDSR 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 ;;;;; 139.46 3.56E-05 3284610000 4330770 4222780 3390210 4229190 3994540 4637810 4291410 4198150 4367640 4759910 FALSE TRUE 4161518.72 4102350.449 4002896.362 4447459.003 4123028.007 4731589.696 4343929.559 4111456.735 3871843.818 4437517.056 0.937803431 0.924469787 0.902057685 1.00224043 0.929129501 1.066269636 0.978909941 0.9265219 0.872524831 1 22.08132123 3.752781997 24.79360245 0.965648367 0.92174625 0.152592664 0.050008915 1533.988086 2674351.727 0.01335295 0.023939244 5659.551256 -3.752781997 -0.043902117 SLS(ph)YSPVER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.003)LS(0.995)YS(0.002)PVER 126.33 0.00049987 101950000 158250 144250 102420 186250 158850 162750 147920 193930 154860 168850 TRUE FALSE 152065.415 140136.1312 120929.5723 195862.3848 163959.5545 166040.9165 149730.2892 189925.2777 137280.942 157413.6391 0.966024392 0.890241354 0.768228046 1.24425295 1.041584169 1.054806416 0.951190062 1.206536351 0.872103223 1 17.26420102 3.752789235 24.99688066 1.063497548 0.876372282 0.341537843 0.112645509 832.4258701 1462404.687 0.02769603 0.049649896 5659.64557 -3.752789235 -0.187125266 SLLGLDSGELQSGPESS(ph)SSPGVHVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLGLDSGELQSGPESSSSPGVHVR 25 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 SLLGLDSGELQSGPES(0.077)S(0.411)S(0.288)S(0.223)PGVHVR 116.65 0.00078789 111830000 51435 65396 49751 79368 72179 81002 79764 71724 71312 103220 TRUE FALSE 49424.86334 63530.97011 58742.11241 83464.19199 74500.70309 82639.91594 80740.17569 70242.87434 63216.96072 96228.81746 0.51361811 0.660207324 0.610442006 0.867351322 0.774203664 0.858785529 0.839043624 0.729956745 0.656944171 1 16.55418138 3.752809233 22.96557014 0.803665442 0.601300866 0.54537615 0.092716175 219.5296756 353829.339 0.023201045 0.04151162 5659.906187 -3.752809233 -0.202364575 VYYS(ph)PPVAR ddPTM_BT-474_Pertuzumab_2h_R1 3 VYYSPPVAR 9 0 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 VYYS(1)PPVAR;VYYS(1)PPVAR;VYY(0.001)S(0.999)PPVAR 105.17 0.0035613 572720000 491990 541540 417470 576030 555970 571220 564200 612670 546370 578280 TRUE FALSE 472762.4869 526095.8094 492916.1156 605758.9773 573853.28 582770.4598 571104.8484 600018.1504 484348.3682 539112.5805 0.876927202 0.975855189 0.914310171 1.123622411 1.064440528 1.080981006 1.059342462 1.11297375 0.898417855 1 19.04022705 3.75294435 24.812587 1.059084755 0.927713273 0.437000166 0.064775541 617.1165634 1064550.629 0.015881521 0.028462528 5661.667368 -3.75294435 -0.131371483 NLRPGDSQTAAQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 NLRPGDSQTAAQAR 14 1 Q8WZA9;M0QZP8 Q8WZA9 IRGQ Immunity-related GTPase family Q protein 0 ;;; 278.16 3.31E-33 993150000 762350 729420 600935 573351 586679 530802 583429 618003 722040 733210 FALSE TRUE 732556.5192 708617.6558 709537.3222 602941.7138 605550.0628 541535.1801 590569.1786 605241.0221 640077.0462 683549.0336 1.07169564 1.036674212 1.038019641 0.882075293 0.885891184 0.79224043 0.863974857 0.885439072 0.936402533 1 19.38268531 3.753129852 4.994771316 0.88127331 1.049715297 0.660145047 0.051081458 0.10105377 7.634417348 0.013150135 0.022999994 5664.086169 -3.753129852 0.168441987 EALQYFYFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EALQYFYFLR 10 0 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 78.655 0.068283 103590000 283950 302690 264590 163480 230740 243960 246480 203430 244360 212000 FALSE TRUE 272852.9201 294057.5776 312407.2988 171917.2224 238161.9617 248893.0384 249496.496 199229.0994 216621.2772 197641.0512 1.380547809 1.487836539 1.580680213 0.86984572 1.205022743 1.259318532 1.262371833 1.008035012 1.096033825 1 17.59252311 3.753287461 24.9925364 1.114610362 1.483503043 0.663019464 0.124803444 501.8253845 851632.019 0.032721319 0.058667673 5666.142094 -3.753287461 0.368892681 YDSYESCDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDSYESCDSR 10 0 Q9ULX6;V9GZ50;M0R1Y5;M0R010;M0QYT7 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 ; 214.96 1.96E-08 753950000 389580 436480 323250 433410 421430 407590 412050 449880 441360 477440 FALSE TRUE 374354.7829 424032.0178 381668.4657 455778.342 434985.6787 415831.7491 417092.7912 440589.8208 391258.6631 445102.5635 0.841052857 0.95266137 0.857484312 1.023984985 0.977270666 0.934238046 0.937071195 0.989861342 0.879030352 1 18.76377828 3.753323497 24.99522193 0.96215918 0.890625699 0.37293228 0.046876188 908.0206923 1537376.792 0.011436142 0.020508845 5666.612266 -3.753323497 -0.07153348 ISKEEAMR ddPTM_BT-474_Pertuzumab_2h_R1 6 ISKEEAMR 8 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;;;; 95.642 0.0086688 5113450000 3469290 3692880 2879870 2332890 2470220 1187340 3227060 2562490 2954080 3080880 FALSE TRUE 3333706.311 3587562.678 3400326.571 2453290.732 2549676.87 1211348.828 3266553.726 2509573.686 2618745.223 2872209.253 1.160676684 1.249060344 1.183871463 0.854147632 0.88770582 0.421748111 1.137296568 0.873743333 0.911752937 1 21.45372943 3.753361202 6.140431653 0.863372433 1.205317788 0.433104001 0.172064973 0.149647658 24.20250726 0.044696112 0.077668359 5667.104247 -3.753361202 0.341945354 TVALWDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVALWDLR 8 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5;Q16576;E9PC52;Q16576-2;Q5JP02 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 79.474 0.065008 208370000 539480 605560 447840 188580 198370 134980 354460 139220 171170 270280 FALSE TRUE 518396.5252 588290.0217 528774.6501 198312.6364 204750.7512 137709.3881 358797.9875 136345.0583 151739.4992 251973.6949 2.057343825 2.334727925 2.09853116 0.787037062 0.812587803 0.546522875 1.423950177 0.541108303 0.602203731 1 17.9429136 3.753488447 5.67976033 0.804777628 2.192845787 0.855908561 0.253367214 0.05548355 6.658713554 0.064707306 0.11265499 5668.764915 -3.753488447 1.38806816 up (ac)MEVS(ph)PLQPVNENMQVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 MEVSPLQPVNENMQVNK 17 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK 120.7 3.15E-12 268720000 585090 590310 486550 604760 606870 666890 638490 655400 631130 702190 TRUE FALSE 562224.0359 573474.9368 574480.4082 635971.7361 626390.5247 680374.9727 646304.0316 641865.761 559486.7683 654630.0459 0.858842394 0.876029049 0.877564988 0.971497932 0.956861862 1.039327445 0.987281344 0.980501529 0.854660998 1 19.32032029 3.753547217 4.381906516 0.973494648 0.869508136 0.509759014 0.044546213 0.162500187 7.986045249 0.01185413 0.020931283 5669.532083 -3.753547217 -0.103986511 TQTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.066)QT(0.19)PPVS(0.755)PAPQPT(0.256)EERLPS(0.322)S(0.322)PVY(0.088)EDAASFK 59.372 0.047262 218660000 138180 126050 109120 107090 112000 112300 112010 138700 126780 112340 TRUE FALSE 132779.7728 122455.1774 128840.4114 112616.9277 115602.5817 114570.7829 113380.8119 135835.7965 112388.4659 104731.1117 1.26781594 1.169234007 1.230201888 1.07529583 1.103803634 1.09395175 1.082589595 1.296995652 1.073114417 1 16.67633055 3.753584402 23.97054977 1.12466852 1.217098966 0.311199192 0.076497598 742.7424881 1185044.601 0.020792048 0.037278305 5670.017533 -3.753584402 0.092430446 DLEGSDIDTR ddPTM_BT-474_Pertuzumab_2h_R1 5 DLEGSDIDTR 10 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;;; 267.53 1.69E-17 13170810000 11783400 12610380 10047390 12832550 12200290 12959600 12841400 12986200 14839340 14564480 FALSE TRUE 11322891.7 12250744.31 11863176.88 13494839.44 12592723.41 13221651.99 12998556.89 12718030.43 13154840.33 13578014.8 0.833913637 0.902248561 0.873704813 0.993874263 0.927434798 0.973754425 0.957323813 0.936663468 0.968833849 1 23.69476923 3.753655123 24.43575239 0.959711055 0.873184942 0.728450963 0.026526615 312.9283516 506582.1615 0.006386287 0.011454835 5670.940918 -3.753655123 -0.086526113 GPPDFS(ph)SDEEREPTPVLGSGAAAAGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 GPPDFS(0.988)S(0.012)DEEREPTPVLGSGAAAAGR;GPPDFS(0.99)S(0.01)DEEREPTPVLGSGAAAAGR;GPPDFS(0.988)S(0.012)DEEREPTPVLGSGAAAAGR;GPPDFS(0.937)S(0.063)DEEREPTPVLGSGAAAAGR;GPPDFS(0.923)S(0.077)DEEREPTPVLGSGAAAAGR;GPPDFS(0.988)S(0.012)DEEREPTPVLGSGAAAAGR 298.5 1.03E-70 20221240000 1864173 1980730 1385631 2153810 1954350 1950370 2005400 2101830 2019030 1999600 TRUE FALSE 1791319.058 1924241.52 1636045.345 2264968.392 2017213.443 1989807.818 2029942.685 2058426.476 1789838.179 1864165.311 0.960922858 1.032226868 0.877628897 1.215004044 1.082100086 1.067398801 1.088928473 1.104208121 0.960128465 1 20.83009837 3.753658441 24.99962678 1.080642925 0.964456285 0.352192433 0.072128896 865.6063909 1433304.203 0.017684969 0.031709295 5670.984247 -3.753658441 -0.116186639 SVS(ph)VDESRPELIFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVSVDESRPELIFR 14 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 S(0.003)VS(0.997)VDESRPELIFR;S(0.006)VS(0.994)VDESRPELIFR 228.9 9.00E-13 392340000 447610 504570 366500 640970 743960 387950 612570 614720 573150 631570 TRUE FALSE 430116.9063 490180.1576 432734.7027 674050.5385 767890.149 395794.6148 620066.8149 602025.8172 508088.4148 588793.2014 0.730505898 0.832516674 0.734951935 1.144800139 1.304176317 0.67221329 1.053114767 1.022474131 0.862931864 1 19.16740149 3.753737378 24.3810307 1.011206872 0.772643991 0.330944264 0.157914622 705.6244486 1133560.829 0.040788112 0.073144577 5672.015101 -3.753737378 -0.238562881 HRNWYIQATCATSGDGLYEGLDWLANQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HRNWYIQATCATSGDGLYEGLDWLANQLK 29 1 P61204;P61204-2;H0YGG7 P61204 ARF3 ADP-ribosylation factor 3 0 62.605 0.012477 111610000 65142 65738 58642 41483 48842 61474 50114 58288 56000 53067 FALSE TRUE 62596.17862 63863.2166 69239.91388 43623.9426 50413.04729 62717.0464 50727.31012 57084.33243 49643.11477 49472.72482 1.265266444 1.290877283 1.399557314 0.881777641 1.019006886 1.267709564 1.025359131 1.153854627 1.003444119 1 15.59434574 3.753828376 24.94388095 1.067801826 1.315798049 0.586554068 0.102510809 594.5665749 971377.0566 0.026502982 0.047539883 5673.203684 -3.753828376 0.247996223 SNS(ph)LSTPRPTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SNSLSTPRPTR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.08)NS(0.915)LS(0.005)TPRPTR;SNS(0.632)LS(0.153)T(0.153)PRPT(0.062)R;SNS(0.588)LS(0.132)T(0.132)PRPT(0.147)R 92.295 0.01449 110490000 1074170 956750 817408 545300 742850 725594 672827 738430 675610 655780 TRUE FALSE 1032190.249 929464.4268 965131.8087 573442.9983 766744.4449 740266.0078 681061.2581 723181.1625 598917.5852 611363.4365 1.688341479 1.520314058 1.578654776 0.937973984 1.254154892 1.210844424 1.114003909 1.182898942 0.979642467 1 19.22167075 3.75389822 24.70759911 1.120454174 1.588224584 0.821841127 0.105995391 275.022458 443036.7605 0.026191231 0.046987615 5674.116122 -3.75389822 0.467770409 TDAASKPFAEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDAASKPFAEVR 12 1 Q13427;E9PG73;C9JM79;Q13427-2;C9JN15 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G;Peptidyl-prolyl cis-trans isomerase 0 83.204 0.011793 547650000 583070 609750 514510 452570 510200 433620 532730 582170 580140 637720 FALSE TRUE 560282.9798 592360.527 607493.4022 475927.1919 526611.0464 442388.0935 539249.7091 570147.9861 514284.9393 594526.6564 0.942401781 0.996356548 1.021810201 0.800514471 0.88576524 0.74410136 0.907023602 0.958994824 0.8650326 1 19.18138197 3.754041528 24.97738865 0.879699434 0.987806218 0.324534904 0.070502873 979.1896443 1579851.185 0.018594474 0.033369988 5675.98878 -3.754041528 0.108106784 SLS(ph)PILPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSPILPGR 9 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 S(0.081)LS(0.919)PILPGR 122.57 0.00061059 193810000 192060 205860 166650 208860 226170 209270 201600 241430 245120 244970 TRUE FALSE 184554.0829 199989.0744 196767.3621 219639.2896 233444.9635 213501.5828 204067.2411 236444.3861 217295.0052 228377.9637 0.808108102 0.875693395 0.861586464 0.961735914 1.022186903 0.934860699 0.893550489 1.035320494 0.951470981 1 17.80106393 3.754088493 3.611495123 0.973340576 0.847528593 0.644818059 0.041972768 0.148407291 4.226578863 0.011451619 0.020673934 5676.602616 -3.754088493 -0.125811983 EREQQIEEHRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EREQQIEEHRR 11 2 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 114.93 0.00066972 401540000 220170 234190 171750 262130 228470 254310 267930 232230 259260 269850 FALSE TRUE 211565.513 227511.1305 202789.0456 275658.5607 235818.945 259452.3224 271209.0075 227434.3693 229829.8917 251572.8191 0.840971269 0.904354975 0.806084879 1.095740635 0.937378473 1.031320964 1.078053696 0.90404985 0.913572033 1 17.94061653 3.754248985 24.97700371 0.989471218 0.855858832 0.508051551 0.064671807 718.9830282 1144669.132 0.016875611 0.030285687 5678.700768 -3.754248985 -0.133612386 VGGTNPNGGS(ph)FEEVLSSTAHASAQSLAGGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGGTNPNGGSFEEVLSSTAHASAQSLAGGSR 31 0 Q16890-5;E9PPQ1;J3KNE7;Q16890 Q16890-5 TPD52L1 Tumor protein D53 1 VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR;VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR;VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR;VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR 323.64 1.63E-93 1428690000 175683 292176 177333 371943 322361 322730 349617 277556 327893 428348 TRUE FALSE 168817.1141 283843.4266 209381.0179 391139.0228 332730.0343 329255.8217 353895.7174 271824.3716 290671.9613 399335.6084 0.422744956 0.710789172 0.524323435 0.979474443 0.833209028 0.824509046 0.886211272 0.680691543 0.727888911 1 18.6072422 3.754274925 24.93030025 0.826335255 0.568436162 0.575849362 0.114711297 630.5819133 1000397.202 0.029290443 0.052575866 5679.039967 -3.754274925 -0.257899093 ERESSANNSVS(ph)PSESLR ddPTM_BT-474_Pertuzumab_2h_R1 5 ERESSANNSVSPSESLR 17 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 ERESSANNSVS(0.997)PS(0.003)ESLR;ERESSANNS(0.004)VS(0.592)PS(0.403)ES(0.001)LR;ERESSANNS(0.001)VS(0.489)PS(0.489)ES(0.022)LR;ERESSANNS(0.001)VS(0.968)PS(0.031)ESLR;ERESSANNS(0.003)VS(0.679)PS(0.318)ESLR 389.49 1.90E-121 2278340000 703014 756834 565583 818675 798806 778989 801200 799400 800295 768297 TRUE FALSE 675539.4357 735249.8353 667796.4294 860926.9149 824500.3204 794740.6913 811005.3253 782892.1106 709448.8667 716259.5599 0.943148927 1.02651312 0.932338592 1.201976159 1.151119464 1.109570798 1.132278535 1.093028498 0.990491306 1 19.45012296 3.75440149 24.99887047 1.104887449 0.973251498 0.452647701 0.064792865 716.6911202 1131024.109 0.016389275 0.02941627 5680.695237 -3.75440149 -0.131635951 (ac)MEDSMDMDMSPLRPQNYLFGCELK ddPTM_BT-474_Pertuzumab_2h_R1 5 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;; 76.693 5.18E-43 270909000 246680 270469 212631 231307 233797 242785 235591 253089 279317 260283 FALSE TRUE 237039.4729 262755.4889 251058.1517 243244.782 241317.2928 247694.279 238474.2331 247862.6237 247610.1052 242653.8006 0.976862808 1.08284102 1.034635151 1.002435492 0.994492121 1.020772304 0.982775595 1.021466069 1.020425415 1 17.88853993 3.754542338 11.21893057 1.006545231 1.036598182 0.152055178 0.026642557 1.060179265 733.9953858 0.006446425 0.011331048 5682.537866 -3.754542338 0.03005295 AGPPPEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGPPPEKR 8 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 117.04 0.0034575 312080000 199981 192231 157544 166724 148870 167750 185874 169532 195276 209011 FALSE TRUE 192165.5214 186748.7601 186015.7053 175328.6456 153658.5388 171142.0199 188148.7816 166031.105 173109.0871 194854.4988 0.986200075 0.95840107 0.954639008 0.899792649 0.788580914 0.878306742 0.965586028 0.85207735 0.888401798 1 17.57203772 3.75466236 3.813909735 0.886556405 0.967949049 0.247009232 0.055213842 0.280039088 9.20252586 0.014488733 0.025984925 5684.108516 -3.75466236 0.081392644 RGVTIKPTVDDD ddPTM_BT-474_Pertuzumab_2h_R1 3 RGVTIKPTVDDD 12 2 P41091;Q2VIR3 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ;; 133.15 0.00066885 2333990000 1620710 1538590 1327990 1231570 1302820 1412190 1395390 1437020 1501230 1627670 FALSE TRUE 1557370.861 1494710.92 1567987.334 1295131.475 1344726.388 1440745.449 1412467.2 1407345.035 1330816.664 1517426.461 1.02632378 0.985030219 1.033320147 0.853505266 0.886188835 0.949466407 0.930830743 0.927455182 0.877022181 1 20.53319517 3.754671363 24.98698274 0.916305581 1.011905273 0.549177874 0.04027721 601.7467155 933276.8636 0.010012868 0.017979057 5684.226349 -3.754671363 0.095599691 HNLITEMVALNPDFKPPADYKPPATR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNLITEMVALNPDFKPPADYKPPATR 26 2 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 ; 215.68 2.49E-34 2560610000 1879350 1702750 1585730 1442280 1676010 1731680 1640360 1320690 2417400 2024560 FALSE TRUE 1805902.924 1654189.237 1872306.685 1516716.244 1729920.384 1766695.756 1660435.216 1293417.29 2142986.887 1887434.748 0.956802838 0.876421947 0.991984855 0.803586055 0.916545796 0.936030111 0.87973119 0.685277884 1.135396542 1 20.84799534 3.754680822 24.80640259 0.882887306 0.935205069 0 0.115726985 2980.95746 4587198.807 0.029587977 0.053138657 5684.350146 -3.754680822 0.052317763 (ac)MDPLS(ph)PPLCTLPPGPEPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDPLSPPLCTLPPGPEPPR 19 0 Q9BUH6;Q9BUH6-2 Q9BUH6 C9orf142 Protein PAXX 1 MDPLS(0.98)PPLCT(0.02)LPPGPEPPR;MDPLS(0.85)PPLCT(0.15)LPPGPEPPR 53.3 0.00037417 39136000 10139 13677.3 8073.4 14769.5 10934.4 14019.8 12630.6 13160.8 14886.8 12645.6 TRUE FALSE 9742.756671 13287.2368 9532.442972 15531.75566 11286.11491 14303.28996 12785.17706 12889.02488 13196.91287 11789.10225 0.826420576 1.127077916 0.808580906 1.317467211 0.957334551 1.213263713 1.084491151 1.093299948 1.119416271 1 13.52516624 3.754753264 24.95535355 1.111015528 0.941331633 0.32755674 0.124674082 957.9088237 1476279.965 0.028776557 0.051666416 5685.2984 -3.754753264 -0.169683895 LSEEEILENPDLFLTSEATDYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSEEEILENPDLFLTSEATDYGR 23 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 154.75 3.64E-08 15299000 12512 13797 10643 14558 14255 12585 14042 16468 13261 16592 FALSE TRUE 12023.01721 13403.52307 12566.42685 15309.34012 14713.52502 12839.47732 14213.8502 16127.93005 11755.66687 15468.20906 0.777272738 0.866520682 0.812403479 0.989729326 0.951210639 0.830055844 0.918907298 1.042650121 0.75998888 1 13.91701855 3.754911981 24.02293631 0.932456887 0.823511116 0.275028594 0.080537215 649.1544099 953713.6124 0.020438565 0.036694204 5687.376518 -3.754911981 -0.108945771 Y(ph)EEFIS(ph)MIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 YEEFISMIFR 10 0 Q6P093 Q6P093 AADACL2 Arylacetamide deacetylase-like 2 2 Y(1)EEFIS(1)MIFR 54.776 0.097442 291550000 28594 30888 23885 19448 21150 20948 18375 19494 28301 20569 TRUE FALSE 27476.51487 30007.10448 28201.55082 20451.71361 21830.30896 21371.58291 18599.87875 19091.44209 25088.38913 19175.84331 1.432871265 1.564838844 1.470681125 1.06653529 1.138427583 1.114505504 0.969964056 0.995598565 1.308333027 1 14.22700241 3.75542114 5.657484023 1.075307743 1.500883552 0.788252091 0.096036896 0.071737378 8.323624624 0.025257174 0.044116586 5694.04821 -3.75542114 0.425575809 KQQEEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQQEEYK 7 1 Q9GZZ9-2;Q9GZZ9;E7EWE1;E7EQ61 Q9GZZ9-2 UBA5 Ubiquitin-like modifier-activating enzyme 5 0 ; 96.027 0.020898 263730000 815130 787020 656430 557810 619030 355890 744090 697360 799990 907160 FALSE TRUE 783273.8184 764574.9602 775061.5032 586598.6409 638941.6621 363086.3396 753196.396 682959.2723 709178.489 845717.2452 0.926165125 0.904055066 0.916454652 0.693610831 0.7555027 0.429323561 0.89060073 0.807550368 0.838552711 1 19.68981587 3.755498856 23.30628666 0.760962541 0.914408021 0.173024948 0.140333785 562.1960136 773551.6287 0.036067336 0.064749544 5695.067241 -3.755498856 0.15344548 SNPKS(ph)PQKPIVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNPKSPQKPIVR 12 2 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y467;A0A2R8YES9;H7C5K3 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.048)NPKS(0.952)PQKPIVR;S(0.029)NPKS(0.971)PQKPIVR 83.54 0.0066484 2722500000 4037600 3522700 3304100 2748100 2874500 3395900 3379200 3343200 4048900 3594500 TRUE FALSE 3879806.128 3422236.045 3901224.369 2889929.77 2966960.903 3464567.425 3420555.66 3274161.752 3589285.846 3351041.313 1.157791195 1.021245555 1.164182714 0.862397536 0.885384758 1.033877861 1.020744103 0.977058008 1.071095672 1 21.67617804 3.755511125 24.96468982 0.97864221 1.105090393 0.437928795 0.07024164 829.3134122 1221407.799 0.018415365 0.033087469 5695.22813 -3.755511125 0.126448183 GPELLTMWFGESEANVR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPELLTMWFGESEANVR 17 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 189.3 8.44E-10 713670000 618816 717703 562975 790177 767742 839332 793602 766570 793225 846389 FALSE TRUE 594631.9866 697234.8131 664717.1058 830958.1297 792437.1187 856303.8681 803314.3387 750740.0616 703181.4235 789062.3191 0.753593185 0.88362452 0.842413951 1.053095693 1.004276975 1.085217032 1.018061969 0.951433167 0.89116082 1 19.58977972 3.755609938 20.11692569 1.000188688 0.832251464 0.653966105 0.057930084 42.53745662 50188.77624 0.015659104 0.028042259 5696.524091 -3.755609938 -0.167937223 KS(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSSLESLQTAVAEVTLNGDIPFHRPRPR 29 3 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 KS(0.297)S(0.297)S(0.297)LES(0.109)LQTAVAEVTLNGDIPFHRPRPR 108.13 0.0003001 339410000 77629 110700 81902 64305 70735 97704 71601 70708 96944 84801 TRUE FALSE 74595.17286 107542.9444 96703.5133 67623.78876 73010.25551 99679.64182 72477.27446 69247.85509 85939.32354 79057.35274 0.943557687 1.360315526 1.223207076 0.855376336 0.923509996 1.260852259 0.916768295 0.875919224 1.087050357 1 16.27061203 3.755721365 24.75587354 0.981067005 1.194155665 0.250971118 0.146773465 900.5758362 1299154.58 0.037606514 0.067585129 5697.985835 -3.755721365 0.213088661 EAARS(ph)PDKPGGS(ph)PSASR ddPTM_BT-474_Pertuzumab_2h_R1 3 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 2 EAARS(1)PDKPGGS(0.748)PS(0.245)AS(0.007)R;EAARS(0.997)PDKPGGS(0.449)PS(0.132)AS(0.422)R;EAARS(1)PDKPGGS(0.608)PS(0.377)AS(0.015)R 129.43 1.80E-05 2820670000 1324210 1178640 1030470 960250 1016190 1023890 1142910 1132520 1186950 1177140 TRUE FALSE 1272458.409 1145026.341 1216698.852 1009808.618 1048876.674 1044593.757 1156897.274 1109133.066 1052212.412 1097411.259 1.159509162 1.043388549 1.108699078 0.920173371 0.955773567 0.951870822 1.054205763 1.010681326 0.95881321 1 20.06567285 3.756028405 24.62672536 0.983469635 1.097817909 0.628252659 0.043913566 493.0047364 695053.568 0.011767642 0.021149086 5702.015651 -3.756028405 0.114348274 ILNLLS(ph)PSDGER ddPTM_BT-474_Pertuzumab_2h_R1 1 ILNLLSPSDGER 12 0 A0A494C1S7;Q9Y5Q9;Q9Y5Q9-2 A0A494C1S7 GTF3C3 General transcription factor 3C polypeptide 3 1 ILNLLS(0.979)PS(0.021)DGER 96.464 0.0057373 19805000 36989 39178 30181 42096 43360 38466 37161 42298 44842 45977 TRUE FALSE 35543.42899 38060.6818 35635.37807 44268.5796 44754.71378 39243.80888 37615.78743 41424.53152 39751.72415 42862.93684 0.82923457 0.887962529 0.831379758 1.032793898 1.044135495 0.915565096 0.877583064 0.966441746 0.92741485 1 15.38744308 3.756041353 24.94978381 0.960922386 0.853369301 0.521536973 0.051025153 740.7741099 1057283.627 0.014081464 0.025315277 5702.185658 -3.756041353 -0.107553086 FYVVTYTGDKDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 FYVVTYTGDKDSR 13 1 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 0 98.167 0.0031408 263820000 365230 369620 292260 298360 323750 241070 363660 272270 400530 337840 FALSE TRUE 350956.4078 359078.7995 345077.8833 313758.3954 334163.7128 245944.6006 368110.5799 266647.5294 355063.5136 314957.7959 1.114296621 1.140085447 1.095632138 0.996191869 1.060979335 0.780881133 1.168761608 0.846613524 1.127336799 1 18.264799 3.75628639 1.867831654 0.982159635 1.130690078 0.193891719 0.110276815 0.49304078 3.330939284 0.029508468 0.064691003 5705.403839 -3.75628639 0.148530442 SLDSDES(ph)EDEEDDYQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 SLDSDES(1)EDEEDDYQQK 261.64 2.79E-27 109890000 80650 82480 70496 64684 65716 74574 74642 80386 87031 74376 TRUE FALSE 77498.10884 80127.75116 83236.19538 68022.34899 67829.81482 76081.93737 75555.49112 78726.00101 77151.60574 69338.44727 1.117678747 1.155603483 1.200433506 0.981019213 0.978242483 1.097254703 1.089662288 1.135387424 1.112681474 1 16.08136791 3.756294366 24.97901528 1.066584685 1.157675068 0.400581972 0.055967456 1013.886557 1428114.512 0.016024027 0.028815995 5705.508621 -3.756294366 0.091090383 VKAEAEAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 VKAEAEAAR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 118.28 0.00092591 1331560000 1624860 1667820 1288210 820940 840410 157889 1318230 822750 1048890 1271940 FALSE TRUE 1561358.675 1620255.407 1521018.203 863308.8118 867442.5509 161081.6238 1334362.893 805759.925 929824.4045 1185790.371 1.316724029 1.366392784 1.282704128 0.728045052 0.731531114 0.135843255 1.125294087 0.67951296 0.78413894 1 20.17741756 3.756346179 4.771447212 0.721370182 1.335561694 0.545142603 0.243176119 0.137769866 8.785214687 0.062665806 0.110383548 5706.189349 -3.756346179 0.614191512 EVFEDAAEIR ddPTM_BT-474_Pertuzumab_2h_R1 5 EVFEDAAEIR 10 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;; 238.54 7.67E-12 12102430000 4785020 4919470 3986010 4760660 4912550 4782170 4995900 4990170 5024330 5366080 FALSE TRUE 4598016.128 4779171.532 4706370.675 5006358.233 5070566.632 4878868.754 5057041.319 4887121.246 4453989.122 5002630.622 0.919119654 0.955331683 0.940779168 1.00074513 1.013580057 0.975260642 1.010876417 0.976910273 0.8903294 1 22.2542555 3.756420789 22.9091347 0.982712951 0.940102296 0.245708007 0.034156336 405.6113187 520270.5635 0.008815482 0.015836178 5707.169738 -3.756420789 -0.042610655 EKS(ph)PSLGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EKSPSLGK 8 1 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 EKS(0.844)PS(0.156)LGK;EKS(0.965)PS(0.035)LGK;EKS(0.961)PS(0.039)LGK;EKS(0.986)PS(0.014)LGK 91.469 0.0075489 6978930000 4992900 4229200 4320440 2860920 3499450 3560780 4005210 4347140 4671600 4376780 TRUE FALSE 4797771.948 4108587.357 5101239.616 3008572.424 3612012.987 3632781.411 4054226.958 4257370.04 4141299.553 4080336.792 1.175827436 1.006923586 1.250200627 0.737334337 0.885224228 0.890314108 0.993601059 1.04338692 1.01494062 1 21.96025681 3.756470066 24.99108536 0.944954256 1.130577839 0.46663247 0.100643149 849.1950715 1184974.474 0.027183612 0.048877086 5707.81733 -3.756470066 0.185623583 FVLDEADEMLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVLDEADEMLSR 12 0 J3KTN0 J3KTN0 EIF4A1 0 114.83 0.0023612 16780000 23807 28068 19620 33014 26653 41684 25874 28558 31330 27456 FALSE TRUE 22876.59612 27267.52812 23165.77044 34717.8565 27510.31795 42526.87904 26190.65375 27968.26732 27773.54975 25596.38066 0.893743394 1.065288428 0.905040863 1.356358032 1.074773747 1.661441108 1.023217075 1.092664923 1.085057693 1 14.64365221 3.757128446 24.80343363 1.187816951 0.965750635 0.232176441 0.191380492 1153.890053 1541394.004 0.048776206 0.087729758 5716.476809 -3.757128446 -0.222066315 ES(ph)HTPVS(ph)IQEEIVGDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESHTPVSIQEEIVGDFK 17 0 Q12830-4;Q12830;E7ETD6;E9PE19;A0A2R8Y7Q1;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 2 ES(0.533)HT(0.533)PVS(0.934)IQEEIVGDFK 66.673 0.021457 6476100 19103 21792 17114 17095 18136 18228 20119 15454 26172 21458 TRUE FALSE 18356.43364 21170.5135 20206.8805 17977.275 18719.36091 18596.58265 20365.22234 15134.8695 23201.06428 20004.63055 0.91760923 1.058280654 1.010110157 0.898655687 0.935751393 0.929613901 1.018025416 0.756568309 1.159784692 1 14.28804636 3.757462522 23.84105017 0.937654706 1.001628089 0.003667119 0.102181325 1258.949194 1587908.991 0.025212127 0.045330486 5720.875834 -3.757462522 0.063973383 IFASIAPSIYGHEDIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFASIAPSIYGHEDIKR 17 1 P49736 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 164.41 1.69E-09 976380000 1941840 2117400 1635960 1710380 1528670 1831520 1832040 1728060 2009880 2120900 FALSE TRUE 1865950.746 2057013.825 1931614.364 1798652.917 1577841.059 1868554.589 1854461.054 1692374.957 1781726.849 1977249.554 0.943710288 1.040341024 0.976919863 0.909674205 0.797997934 0.94502719 0.937899341 0.855923803 0.901113795 1 20.91506354 3.7575079 4.205457544 0.89691987 0.994551154 0.295446091 0.055617695 0.214888682 9.239124463 0.014204038 0.025291825 5721.473622 -3.7575079 0.097631283 S(ph)PVPTTLPGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPVPTTLPGLR 11 0 F8VV64;Q63HR2-5;Q63HR2-2;Q63HR2-6;Q63HR2;Q63HR2-4 F8VV64 TNS2 Tensin-2 1 S(0.999)PVPTT(0.001)LPGLR;S(1)PVPTTLPGLR 107.06 0.0023587 406370000 93524 87612 71722 98223 96649 91250 75190 140903 67759 80478 TRUE FALSE 89868.97868 85113.39154 84683.76085 103292.3008 99757.80286 93095.13752 76110.19771 137993.3038 60067.28239 75027.15338 1.197819385 1.134434504 1.128708168 1.376732238 1.329622655 1.240819268 1.014435365 1.839244828 0.800607243 1 16.1951252 3.757640688 23.77491418 1.288253536 1.151732039 0 0.267245217 1520.646382 1894805.328 0.067375696 0.121166259 5723.223261 -3.757640688 -0.136521497 KESVS(ph)PEDSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KESVSPEDSEK 11 1 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 KES(0.025)VS(0.975)PEDSEK 88.19 0.0080629 272120000 581190 537280 499390 400850 503270 415600 499310 581620 539510 457870 TRUE FALSE 558476.4523 521957.3005 589640.8819 421537.9165 519458.1366 424003.7167 505420.7051 569609.3437 478267.0866 426858.0571 1.3083423 1.222788915 1.381351182 0.987536511 1.216934126 0.993313139 1.184048647 1.334423315 1.120435889 1 18.70339689 3.757737234 24.97235133 1.147402041 1.296023602 0.344108141 0.11211844 1153.813039 1502524.699 0.029990738 0.05395829 5724.495707 -3.757737234 0.14862156 LFELLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFELLEK 7 0 O60264;A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 O60264 SMARCA5;SMARCA1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5;Probable global transcription activator SNF2L1 0 101.99 0.020244 25377000 140860 136570 115090 116000 125000 120400 123480 141900 135700 130730 FALSE TRUE 135355.0355 132675.1573 135889.3232 121986.7739 129020.7385 122834.5705 124991.1852 138969.7154 120295.9049 121875.5407 1.110600492 1.088611846 1.114984372 1.000912679 1.058627004 1.007868928 1.025564149 1.140259273 0.987038944 1 16.89504909 3.75783804 24.81417409 1.04293474 1.103120204 0.359985217 0.042884092 1009.470676 1299400.586 0.01157564 0.020827719 5725.824602 -3.75783804 0.060185464 AAAYDIS(ph)EDEED ddPTM_BT-474_Pertuzumab_2h_R1 2 AAAYDISEDEED 12 0 P49585 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 AAAYDIS(1)EDEED;AAAYDIS(1)EDEED 296.65 2.80E-36 889430000 1003270 1101950 818710 1112890 1071420 1100830 1095460 1086010 1045590 1209800 TRUE FALSE 964061.0992 1070523.465 966669.1091 1170326.386 1105883.197 1123089.537 1108866.567 1063583.514 926899.0067 1127859.168 0.854770814 0.949164129 0.857083168 1.037652944 0.980515323 0.995771075 0.983160485 0.943010922 0.821821583 1 20.1051555 3.757895863 24.98844541 0.965167368 0.893221848 0.271005584 0.059090035 1220.127064 1576860.153 0.015222544 0.027391421 5726.586999 -3.757895863 -0.07194552 KPLVLCGDLNVAHEEIDLR ddPTM_BT-474_Pertuzumab_2h_R1 5 KPLVLCGDLNVAHEEIDLR 19 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;; 232.54 5.21E-21 11568190000 11468450 11744060 9440410 11403250 11535120 11989390 11435900 11537370 12725910 12468660 FALSE TRUE 11020250.29 11409130.91 11146502.09 11991773.1 11906157.61 12231823.68 11575855.97 11299119.28 11281318.05 11624146.55 0.948048121 0.981502673 0.958909287 1.031626111 1.024260797 1.052277139 0.995845666 0.972038612 0.970507211 1 23.47062146 3.757907121 24.82438262 1.005387292 0.964688286 0.389665043 0.025070259 959.5832547 1231280.822 0.007387584 0.013288808 5726.735444 -3.757907121 -0.040699006 IGGELR ddPTM_BT-474_Pertuzumab_2h_R1 1 IGGELR 6 0 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 98.513 0.092707 829220000 1311700 1384400 1108100 1394500 1415200 1448100 1358800 1445600 1467700 1475400 FALSE TRUE 1260437.314 1344918.267 1308358.32 1466470.312 1460721.193 1477381.574 1375429.401 1415747.855 1301092.849 1375469.844 0.916368555 0.977788262 0.951208291 1.066159552 1.061979803 1.074092304 0.999970597 1.029283093 0.945926117 1 20.39149308 3.757920472 23.79586967 1.02851808 0.951388331 0.451140025 0.038713317 408.9458291 502646.631 0.010131044 0.018219354 5726.911507 -3.757920472 -0.077129749 GPS(ph)WDPFR ddPTM_BT-474_Pertuzumab_2h_R1 8 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR 131.52 0.0010507 9558862000 11837460 11489950 8483320 16498670 15310390 10909280 14581320 16806910 13289680 14601060 TRUE FALSE 11374838.98 11162267.88 10016444.63 17350168.34 15802862.6 11129873.12 14759770.56 16459841.44 11781091.24 13612117.2 0.835640688 0.820024373 0.735847663 1.27461203 1.160940827 0.817644526 1.084311157 1.209205092 0.865485587 1 23.69838814 3.758201952 24.98014078 1.071717796 0.799456232 0.433825845 0.136453295 752.3640969 956864.7158 0.035701599 0.064240902 5730.624491 -3.758201952 -0.272261564 SLTNDWEDHLAVK ddPTM_BT-474_Pertuzumab_2h_R1 12 SLTNDWEDHLAVK 13 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;; 227.63 8.79E-12 1.7408E+11 77837215 76543486 67379204 74405655 79930575 81030912 84637926 84932623 98336123 92019472 FALSE TRUE 74795250.58 74360540.72 79556125.01 78245739.77 82501614.54 82669412.56 85673750.26 83178734.65 87173418.58 85786911.2 0.871872522 0.8668052 0.927369034 0.912094149 0.961703987 0.963659973 0.998680907 0.969597034 1.016162225 1 26.35425421 3.758221712 0.493128087 1.002401383 0.831248423 0.901089968 0.015698118 0.513199196 0.187863899 0.01097189 0.04660244 5730.885246 -3.758221712 -0.17115296 IDKEACR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDKEACR 7 1 Q14019 Q14019 COTL1 Coactosin-like protein 0 ; 86.833 0.018045 637330000 629150 644280 504350 480600 521930 337310 574240 498270 588250 548820 FALSE TRUE 604562.1224 625905.7652 595497.2642 505403.8236 538718.3525 344130.6393 581267.7209 487980.5504 521474.3261 511647.9326 1.1815979 1.223313387 1.163880916 0.987796083 1.052908295 0.672592651 1.136069715 0.953742836 1.019205381 1 18.9647919 3.758560556 2.55665241 0.968342794 1.204922478 0.434536636 0.112939852 0.259418812 3.340314662 0.030328153 0.059110987 5735.358327 -3.758560556 0.236579684 TVAISDAAQLPHDYCT(ph)TPGGTLFSTT(ph)PGGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.545)T(0.454)PGGTLFS(0.091)T(0.056)T(0.849)PGGT(0.004)R 181.56 5.27E-18 4695400000 861740 878390 671950 926320 847110 1105300 774540 860290 1008000 893570 TRUE FALSE 828062.2481 853339.1772 793386.3124 974127.4862 874358.0625 1127649.923 784019.0522 842524.7109 893576.0659 833047.708 0.994015397 1.024358112 0.952390007 1.16935378 1.049589422 1.35364387 0.941145441 1.011376303 1.072658933 1 19.66803959 3.758584349 24.91306702 1.082180601 0.993664867 0.139340847 0.108049967 1775.125377 2208563.687 0.028380154 0.051085442 5735.672546 -3.758584349 -0.088515735 ALSQTVPSSGTNGVSLPADCTGAVPAAS(ph)PDTAAWR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALSQTVPSSGTNGVSLPADCTGAVPAASPDTAAWR 35 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EN31 Q9H6Z4 RANBP3 Ran-binding protein 3 1 ALSQTVPSSGTNGVSLPADCTGAVPAAS(0.976)PDT(0.024)AAWR 240.41 1.36E-47 298410000 337010 366050 276670 420100 382810 405930 395790 398010 419460 398710 TRUE FALSE 323839.2766 355610.6124 326670.4235 441781.4113 395123.4313 414138.1827 400633.7964 389790.9544 371844.6593 371705.0166 0.871226543 0.956701138 0.878843193 1.188526901 1.063002687 1.114158175 1.077827252 1.048656696 1.000375682 1 18.50379863 3.758874357 24.99814017 1.072814836 0.907701357 0.656979054 0.055603237 484.2189892 595879.2269 0.013847636 0.024922757 5739.503924 -3.758874357 -0.16511348 LLQIIDRDGEEEEEEEEPLDESSVK ddPTM_BT-474_Pertuzumab_2h_R1 3 LLQIIDRDGEEEEEEEEPLDESSVK 25 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;A2A2P1 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 ;; 188.3 1.12E-17 301237000 174985 155153 136019 170057 169935 170096 167645 198475 198456 190391 FALSE TRUE 168146.3927 150728.1884 160600.659 178833.6621 175401.1136 173535.4577 169696.6897 194376.4219 175928.1069 177495.648 0.947326848 0.849193713 0.90481463 1.007538293 0.988199517 0.977688522 0.956061129 1.095105283 0.991168566 1 17.43742413 3.758942694 5.081302983 1.007402725 0.893838467 0.561806577 0.040978229 0.130797853 10.11558002 0.011353331 0.020006249 5740.407109 -3.758942694 -0.113564258 SIEEVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIEEVLR 7 0 A0A2R8YF87;Q96AX1;H3BMM5;A0A2R8Y5U3 A0A2R8YF87 VPS33A Vacuolar protein sorting-associated protein 33A 0 94.262 0.033338 113360000 125240 123620 101180 130790 123610 153010 124980 127340 133980 137520 FALSE TRUE 120345.4823 120094.4786 119465.4767 137540.0876 127586.0279 156103.967 126509.5426 124710.3845 118771.1521 128205.6479 0.938690957 0.936733136 0.931826941 1.072808334 0.995166984 1.217606007 0.986770432 0.972737056 0.926411231 1 16.96810029 3.758953635 23.28590764 1.024587361 0.935848585 0.231744067 0.074049796 537.1611833 613356.5084 0.019962891 0.035913107 5740.551728 -3.758953635 -0.088738775 RNQKPEVR ddPTM_BT-474_Pertuzumab_2h_R1 3 RNQKPEVR 8 2 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;; 143.04 0.00034189 1419400000 1970580 1888580 1617630 1498210 1779950 1615210 1571290 1896330 1810930 1826480 FALSE TRUE 1893567.555 1834719.548 1909971.725 1575532.798 1837203.708 1647870.653 1590519.917 1857170.123 1605360.818 1702770.883 1.112050702 1.077490557 1.121684511 0.925275863 1.07894945 0.967758299 0.934077469 1.090675288 0.942793205 1 20.69945289 3.759248467 24.86878485 0.999734647 1.101116798 0.466333452 0.054558072 723.8930614 870185.9579 0.01357202 0.024429325 5744.450182 -3.759248467 0.101382151 SQS(ph)GTLDGESAAWSASGEDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSGTLDGESAAWSASGEDSR 21 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4 P49815 TSC2 Tuberin 1 S(0.047)QS(0.951)GT(0.001)LDGESAAWSASGEDSR;S(0.011)QS(0.988)GTLDGESAAWSASGEDSR 237.14 7.89E-30 450000000 233630 270530 200118 296030 266340 288120 267540 289660 311980 289510 TRUE FALSE 224499.4813 262814.7493 236283.7742 311308.1438 274907.068 293945.9838 270814.2346 283678.4198 276565.3383 269901.2298 0.83178384 0.973744171 0.875445341 1.153415062 1.018546926 1.089087234 1.003382736 1.051045303 1.024690916 1 18.04207203 3.759360591 24.99442763 1.048493313 0.901666406 0.631701927 0.054110248 501.2281222 602302.1895 0.01279488 0.023035582 5745.933448 -3.759360591 -0.146826908 AQS(ph)PVSGPNVAHLTDGATLNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQSPVSGPNVAHLTDGATLNDR 22 0 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 AQS(0.995)PVS(0.005)GPNVAHLTDGATLNDR;AQS(0.586)PVS(0.414)GPNVAHLTDGATLNDR 233.33 1.33E-30 1893450000 471680 533020 390220 551590 509610 582480 554530 480250 551920 555240 TRUE FALSE 453246.2241 517818.7915 460741.4344 580057.626 526002.0685 594258.1447 561316.504 470332.6697 489268.3554 517633.1002 0.875612908 1.000358731 0.890092682 1.120596086 1.016167761 1.148029646 1.084390669 0.908621704 0.945202993 1 18.98157035 3.759373841 24.99524232 1.028129401 0.929855168 0.302824481 0.075946527 1232.020543 1479567.148 0.021159351 0.038087814 5746.108749 -3.759373841 -0.098274234 REPHPAEAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 REPHPAEAEK 10 1 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 ;;; 152.85 1.12E-05 445946000 720083 752097 590906 490261 549372 281484 629139 552884 652079 662905 FALSE TRUE 691941.3603 730647.9299 697695.8588 515563.429 567043.0493 287175.7993 636838.5913 541466.7522 578057.7257 618005.8539 1.119635608 1.182267005 1.128947007 0.834237129 0.917536696 0.464681358 1.030473396 0.876151494 0.935359628 1 19.23726098 3.759388391 6.893693964 0.857295174 1.148960918 0.426859535 0.147455422 0.165027246 35.6014797 0.037905214 0.066535989 5746.301258 -3.759388391 0.291665743 NKHEAMITDLEER ddPTM_BT-474_Pertuzumab_2h_R1 8 NKHEAMITDLEER 13 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 223.72 9.20E-12 13467290000 10151000 9818760 8343510 8659360 8964690 9766810 9768010 8364270 11587480 10816290 FALSE TRUE 9754287.697 9538738.578 9851367.857 9106270.607 9253047.395 9964301.59 9887553.828 8191544.902 10272117.85 10083693.04 0.967332867 0.945956857 0.976960308 0.903069001 0.917624858 0.988159948 0.980548871 0.812355639 1.018686091 1 23.26552077 3.759551018 24.58465701 0.933416551 0.961670691 0 0.057672697 2496.931477 2924480.736 0.015150634 0.027273606 5748.453438 -3.759551018 0.028254141 ERDFYFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERDFYFGK 8 1 Q15691;Q15555-4;Q15555-5;Q15555-3;Q15555 Q15691;Q15555-4 MAPRE1;MAPRE2 Microtubule-associated protein RP/EB family member 1;Microtubule-associated protein RP/EB family member 2 0 ; 138.98 0.00062227 958290000 829100 872720 688870 893930 830960 839770 897090 941950 995880 927260 FALSE TRUE 796697.8554 847830.8801 813364.1328 940065.8344 857688.5831 856750.7248 908068.8558 922498.4033 882831.8775 864455.8543 0.921617745 0.980768279 0.940897246 1.087465404 0.99217164 0.991086729 1.050451392 1.067143451 1.02125733 1 19.72143277 3.759673291 24.99821552 1.03290469 0.951061797 0.562971101 0.033069777 603.7655018 714879.2637 0.008665833 0.015601608 5750.072115 -3.759673291 -0.081842893 NKPLS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 3 NKPLSPIK 8 1 P35251-2;P35251;A0A1W2PP02;D6RAD2 P35251-2 RFC1 Replication factor C subunit 1 1 NKPLS(1)PIK;NKPLS(1)PIK;NKPLS(1)PIK 90.913 0.0077877 1803290000 4871380 3621550 3272170 1949740 2531920 723430 2901660 2751930 2448500 2770260 TRUE FALSE 4681001.084 3518266.94 3863523.908 2050366.315 2613361.506 738058.2503 2937171.383 2695101.684 2170556.545 2582627.823 1.812495414 1.362281824 1.495966192 0.793907003 1.01190016 0.285778014 1.13728016 1.043550162 0.840444963 1 21.30040832 3.759840584 8.648061788 0.882676811 1.538762975 0.622193109 0.24392827 0.192320404 70.84467666 0.063572202 0.112072119 5752.287504 -3.759840584 0.656086163 RDS(ph)SGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSSGNK 7 1 Q9BW91-2;Q9BW91;D6RAW2;H7C386 Q9BW91-2 NUDT9 "ADP-ribose pyrophosphatase, mitochondrial" 1 RDS(0.993)S(0.007)GNK 61.691 0.095288 411330000 163130 185730 140770 195160 192630 185250 179740 202960 189620 200440 TRUE FALSE 156754.6993 180433.1622 166210.2704 205232.231 198826.1189 188995.8819 181939.7119 198768.8051 168095.1326 186864.0203 0.83887042 0.96558536 0.889471768 1.098297204 1.064014991 1.011408626 0.973647638 1.063708277 0.899558579 1 17.51162929 3.759866379 24.81530083 1.020271991 0.904736783 0.449295941 0.059495478 668.7977844 778961.0152 0.014792214 0.026634011 5752.629166 -3.759866379 -0.115535208 SDIYVCMISFAHNVAAQGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDIYVCMISFAHNVAAQGK 19 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 221.85 2.57E-19 400400000 286260 281150 252800 206670 266990 235150 254080 268840 253340 286810 FALSE TRUE 275072.6427 273131.8773 298486.5835 217336.2635 275577.9758 239904.8941 257189.507 263288.3601 224581.9053 267384.1032 1.028754662 1.021496319 1.116321352 0.812824176 1.030644576 0.897229458 0.961872841 0.984682174 0.839922428 1 18.02855417 3.759937716 24.99914731 0.938996744 1.052121325 0.396936823 0.06914947 840.400751 982791.6463 0.016542102 0.029786248 5753.574172 -3.759937716 0.113124581 AEDEGEGGREETER ddPTM_BT-474_Pertuzumab_2h_R1 1 AEDEGEGGREETER 14 1 Q9BTK6 Q9BTK6 PAGR1 PAXIP1-associated glutamate-rich protein 1 0 111.43 0.0005945 140110000 164680 164540 132690 179270 162950 171410 192030 173580 183320 193420 FALSE TRUE 158244.1235 159847.4803 156670.0347 188522.1462 168191.4347 174876.0276 194380.1206 169995.5123 162510.2821 180319.4911 0.877576365 0.88646812 0.868846921 1.045489564 0.93274129 0.969812118 1.077976204 0.942746185 0.901235253 1 17.46019582 3.759939739 24.90902214 0.980245579 0.878514217 0.481303558 0.049366228 682.5465722 795238.8358 0.012718426 0.022900877 5753.600972 -3.759939739 -0.101731362 QVHPDTGISSK ddPTM_BT-474_Pertuzumab_2h_R1 33 QVHPDTGISSK 11 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 179.93 6.89E-06 1.88458E+11 125018245.3 139025256.7 97721920.3 144539617.8 115028643.2 137915772.2 144982040.4 134783712.5 147193005.8 146107014.1 FALSE TRUE 120132394.1 135060392.5 115382445.1 151999324.8 118728644 140704523.6 146756374 132000381.7 130484272.9 136211055.9 0.881957733 0.991552349 0.847085755 1.115910333 0.871652034 1.032989009 1.077418958 0.969087134 0.957956548 1 27.02126857 3.760046809 24.99186673 1.000712683 0.915334 0.274212633 0.071597893 1162.248091 1351875.524 0.01740164 0.03133421 5755.01962 -3.760046809 -0.085378682 EIYLEVIHNLPDFELLSANTLEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIYLEVIHNLPDFELLSANTLEDR 24 0 Q8IXB1-2;Q8IXB1 Q8IXB1-2 DNAJC10 DnaJ homolog subfamily C member 10 0 119.02 0.00042012 91557000 42500 48196 36926 52701 52583 55692 50714 47693 51453 50668 FALSE TRUE 40839.05301 46821.49727 43599.34961 55420.90493 54274.37995 56818.1304 51334.6531 46708.12288 45612.27115 47236.21123 0.864570886 0.991220423 0.923006915 1.173271596 1.148999434 1.202851137 1.086764831 0.988820265 0.965620865 1 15.52760563 3.760105714 24.23496112 1.082808956 0.932761471 0.436706822 0.080359973 587.7397023 661114.7928 0.022862833 0.041162396 5755.800259 -3.760105714 -0.150047485 LHTLEEEKEELAQYQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHTLEEEKEELAQYQK 16 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 255.91 7.62E-27 191300000 368730 323640 304050 268300 321430 321170 355920 209670 459470 392360 FALSE TRUE 354319.6239 314410.1041 358998.5986 282146.9952 331769.0879 327664.2775 360275.8554 205340.2412 407312.8919 365785.1077 0.968655138 0.859548673 0.981446732 0.771346316 0.907005454 0.895783537 0.984938555 0.561368511 1.113530549 1 18.48063681 3.76012681 24.65619232 0.860982171 0.928850011 0 0.144484457 2594.298092 2965997.545 0.036754723 0.066184665 5756.079853 -3.76012681 0.06786784 LLGLELALS(ph)SDAESAAGGPAGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLGLELALSSDAESAAGGPAGVR 23 0 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 LLGLELALS(0.971)S(0.029)DAESAAGGPAGVR;LLGLELALS(0.969)S(0.031)DAESAAGGPAGVR 231.93 1.55E-33 28849000 25221 30539 23944 37163 35332 34050 41194 36422 39612 44729 TRUE FALSE 24235.33544 29668.05762 28271.21343 39080.98688 36468.48587 34738.51433 41698.14449 35669.87297 35115.41183 41699.46499 0.581190561 0.71147334 0.677975447 0.937205954 0.874555246 0.833068586 0.999968333 0.855403612 0.842107011 1 15.34774125 3.760566229 9.434435586 0.898967639 0.662024932 0.759388503 0.064166208 0.184283067 75.3879574 0.015845634 0.028026644 5761.906799 -3.760566229 -0.236942707 KWQIFK ddPTM_BT-474_Pertuzumab_2h_R1 2 KWQIFK 6 1 B4DZG7;F8VYN9;P40616-2;P40616;F8W1Z8 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 95.957 0.068555 1065950000 2449870 2945900 2085670 1735620 1702540 1673240 1340350 1687620 2280780 2535010 FALSE TRUE 2354126.372 2861885.816 2462596.964 1825195.556 1757303.745 1707074.059 1356753.604 1652770.057 2021875.416 2363311.515 0.996113444 1.210964276 1.042011156 0.772304262 0.743576856 0.722322914 0.574090041 0.699344986 0.85552641 1 21.17237838 3.760665609 3.322693709 0.733961367 1.108828435 0.601973002 0.116703223 0.139623039 3.216840556 0.030305922 0.055781319 5763.225446 -3.760665609 0.374867067 CEDCGKPLSIEADDNGCFPLDGHVLCR ddPTM_BT-474_Pertuzumab_2h_R1 1 CEDCGKPLSIEADDNGCFPLDGHVLCR 27 1 Q15942;Q15942-2;H0Y2Y8 Q15942 ZYX Zyxin 0 134.76 1.47E-05 227390000 214770 182600 144930 224320 184930 218310 197820 196460 250640 237190 FALSE TRUE 206376.551 177392.4268 171122.075 235897.1821 190878.4414 222724.3778 200240.9803 192403.0323 222188.398 221124.91 0.933303041 0.802227242 0.773870637 1.066805101 0.863215462 1.007233322 0.905555961 0.870110167 1.004809444 1 17.75450203 3.760868551 24.9989933 0.944509495 0.833043005 0.359906885 0.073328168 927.2119672 1039060.336 0.018291494 0.032943072 5765.91918 -3.760868551 -0.11146649 TQATGLTKPTLPPS(ph)PLMAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQATGLTKPTLPPSPLMAAR 20 1 B1AHC3;B1AHC4;H0Y9T8;P85298-4;P85298-3;P85298 B1AHC3 PRR5-ARHGAP8;ARHGAP8 Rho GTPase-activating protein 8 1 TQATGLTKPTLPPS(1)PLMAAR;TQATGLTKPT(0.001)LPPS(0.999)PLMAAR 152.14 4.11E-08 1472440000 1553560 1590010 1340910 1290580 1358980 1513080 1341860 1598920 1583710 1568130 TRUE FALSE 1492845.158 1544664.472 1583242.265 1357186.988 1402692.826 1543675.514 1358282.084 1565901.743 1403933.88 1461919.158 1.021154384 1.056600471 1.08298893 0.928359808 0.959487273 1.055923992 0.929108888 1.071127452 0.960336194 1 20.4794321 3.760906443 24.92606507 0.992304764 1.053883181 0.291934436 0.047357153 1063.458431 1186250.247 0.011980227 0.021574187 5766.422278 -3.760906443 0.061578417 TGADTTAAGPLFQQRPYPS(ph)PGAVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGADTTAAGPLFQQRPYPSPGAVLR 25 1 O60828-2;O60828;O60828-5;O60828-4;H7C053 O60828-2 PQBP1 Polyglutamine-binding protein 1 1 TGADTTAAGPLFQQRPYPS(1)PGAVLR;TGADTTAAGPLFQQRPY(0.042)PS(0.958)PGAVLR 169.57 5.89E-12 366380000 222086 216579 179247 170755 171058 197958 171972 235572 186359 187521 TRUE FALSE 213406.6336 210402.379 211640.9202 179567.686 176560.2359 201960.8464 174076.6448 230707.3559 165204.3076 174820.0356 1.220721829 1.203536987 1.210621651 1.027157358 1.009954238 1.155250001 0.995747679 1.319684869 0.944996419 1 17.41551101 3.760980573 21.82152211 1.08909269 1.210817989 0.281251508 0.102573926 246.7937837 240202.3905 0.026750358 0.048140176 5767.406643 -3.760980573 0.121725299 KKEPPRAS(ph)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAET(ph)PEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR 47 3 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 2 KKEPPRAS(0.982)PPGGLAEPPGS(0.013)AGPQAGPT(0.005)VVPGS(0.005)AT(0.016)PMET(0.058)GIAET(0.921)PEGR 42.885 0.032957 139270000 37817 37260 31190 31045 28577 37289 31240 39889 34887 39042 TRUE FALSE 36339.06983 36197.38128 36826.72682 32647.23617 29496.20516 38043.00913 31622.32446 39065.27821 30926.77402 36397.65056 0.998390535 0.994497741 1.01178857 0.896959987 0.810387613 1.045205076 0.868801254 1.073291204 0.849691492 1 15.15155771 3.761208283 24.38841605 0.941347399 1.000852837 0.12275494 0.080365547 1416.020918 1524853.171 0.020329829 0.036613227 5770.431401 -3.761208283 0.059505438 CLPIESNPHSFDSPHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 CLPIESNPHSFDSPHTK 17 0 Q8N3C0 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 0 185.26 3.41E-10 131530000 38205 41512 32959 42556 38055 57383 52168 20454 53498 54255 FALSE TRUE 36711.90636 40328.1184 38915.42447 44752.32026 39279.07364 58543.32358 52806.44759 20031.61775 47425.13132 50580.26052 0.725814893 0.797309424 0.769379676 0.884778366 0.776569223 1.157434204 1.044012962 0.396036271 0.937621334 1 15.62628685 3.761321736 18.89564303 0.849210351 0.767481601 0.054196664 0.194433026 173.8748896 144333.7914 0.055080682 0.098994951 5771.93904 -3.761321736 -0.08172875 IAGDYVSEEVWYR ddPTM_BT-474_Pertuzumab_2h_R1 4 IAGDYVSEEVWYR 13 0 O95782-2;O95782;O94973-3;O94973;O94973-2;A0A0G2JQM1;A0A0G2JS82 O95782-2;O94973-3 AP2A1;AP2A2 AP-2 complex subunit alpha-1;AP-2 complex subunit alpha-2 0 ;;; 250.16 2.28E-17 1025850000 421110 465804 359487 526757 493798 456167 509348 538206 512220 533160 FALSE TRUE 404652.5556 452519.726 424454.2976 553942.9919 509681.4611 465391.0093 515581.5532 527091.858 454074.933 497048.5983 0.814110646 0.910413444 0.85394929 1.114464448 1.02541575 0.936308866 1.037286002 1.060443304 0.913542327 1 18.92302739 3.76136285 24.89217682 1.016582461 0.864583328 0.589424506 0.058402396 519.7187309 567351.6032 0.014819045 0.02669199 5772.485489 -3.76136285 -0.151999133 LLS(ph)WSDNWR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 1 LLS(0.923)WS(0.077)DNWR;LLS(0.983)WS(0.017)DNWR;LLS(0.971)WS(0.029)DNWR;LLS(0.987)WS(0.013)DNWR 124.42 0.00055603 221952000 247269 263968 209060 285547 279068 254972 279496 306763 271846 298642 TRUE FALSE 237605.4541 256439.8911 246841.7925 300284.1149 288044.4757 260127.7085 282916.5557 300428.2368 240987.1818 278414.7113 0.85342277 0.921071627 0.88659752 1.078549741 1.034587843 0.934317398 1.016169563 1.079067393 0.865569138 1 18.08687592 3.76138506 24.28002225 1.008292741 0.890434702 0.409277061 0.062396277 523.607757 556997.1052 0.015854195 0.028552532 5772.780705 -3.76138506 -0.117858039 IEELAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IEELAR 6 0 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3;H7C5Q9 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 0 ; 126.16 0.040975 207280000 298570 321570 248580 371310 320650 329730 375130 368350 376120 350800 FALSE TRUE 286901.5543 312399.1384 293503.9356 390473.3536 330963.9985 336397.3665 379720.9532 360743.4438 333424.4344 327040.0035 0.877267463 0.955232189 0.897455762 1.193962052 1.011998517 1.028612289 1.161084115 1.103056017 1.019521865 1 18.31910759 3.761594752 24.99348717 1.080560833 0.914509815 0.579179882 0.063875871 536.8389116 582502.0682 0.015964475 0.028757739 5775.568672 -3.761594752 -0.166051018 TATAVAHCK ddPTM_BT-474_Pertuzumab_2h_R1 1 TATAVAHCK 9 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 93.467 0.006984 0 1166700 1148100 925360 781090 885790 639330 871170 956240 931680 838830 FALSE TRUE 1121104.074 1115357.312 1092593.137 821402.1485 914282.2398 652257.6906 881831.6391 936493.3098 825919.5923 782015.2969 1.43360888 1.426260223 1.397150594 1.050365833 1.169136005 0.834072803 1.127639884 1.197538352 1.056142502 1 19.5768373 3.762075324 6.315559853 1.076401905 1.422214956 0.742651933 0.096028414 0.095546546 14.75054192 0.026121146 0.046035262 5781.96321 -3.762075324 0.345813051 RPTPNDDTLDEGVGLVHSNIAT(ph)EHIPSPAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPTPNDDTLDEGVGLVHSNIATEHIPSPAKK 31 2 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHS(0.004)NIAT(0.82)EHIPS(0.176)PAKK 103.94 0.0078341 148360000 90738 73100 68616 84533 83092 92630 111130 57747 123070 110170 TRUE FALSE 87191.85864 71015.25957 81016.43755 88895.75826 85764.72964 94503.04207 112490.0422 56554.50427 109099.6096 102708.0878 0.848928848 0.691428115 0.788802901 0.86551858 0.835033847 0.920112954 1.095240352 0.550633407 1.062229975 1 16.64819027 3.762126025 3.274838659 0.876653885 0.763977849 0.116983652 0.148305066 0.623152986 13.85702069 0.040258335 0.074386181 5782.638259 -3.762126025 -0.112676036 SILHDVVEVAGLTSFSFGEDDDCR ddPTM_BT-474_Pertuzumab_2h_R1 1 SILHDVVEVAGLTSFSFGEDDDCR 24 0 I3L0X5;O75391;I3L4C3 I3L0X5 SPAG7 Sperm-associated antigen 7 0 142.99 2.53E-07 9457200 4695.4 3450.3 3207.4 5093.3 3872.9 6512.4 4740.6 4263.3 4850.3 4299 FALSE TRUE 4511.898577 3351.900822 3787.048528 5356.165823 3997.475346 6644.08519 4798.616881 4175.261365 4299.714278 4007.824901 1.12577238 0.836339138 0.944913668 1.336427103 0.997417663 1.65777831 1.197312008 1.04177739 1.072829873 1 11.96860376 3.762221805 23.88240577 1.191009018 0.955741381 0.200416932 0.198126945 683.9107897 690300.8466 0.051042731 0.09193402 5783.91371 -3.762221805 -0.235267637 VLLESEQFLTELTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLLESEQFLTELTR 14 0 P37108;H0YLA2 P37108 SRP14 Signal recognition particle 14 kDa protein 0 ; 165.7 9.13E-06 263500000 72522 69717 52861 74035 72242 60165 73936 71949 76462 75527 FALSE TRUE 69687.76006 67728.73942 62414.15859 77855.95522 74565.72954 61381.57752 74840.85088 70463.22801 67782.35431 70411.48902 0.989721437 0.961898979 0.886420092 1.105728004 1.05899947 0.871755141 1.062906806 1.000734809 0.96266043 1 16.10352323 3.762518425 24.99663258 1.008281012 0.947602068 0.166471287 0.064513575 1505.482586 1570756.432 0.01653546 0.029789492 5787.865434 -3.762518425 -0.060678944 GSYWTLHPDSGNMFENGCYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSYWTLHPDSGNMFENGCYLR 21 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 0 115.42 0.0001541 508600000 447940 479280 361500 375850 346900 371790 383490 403370 376860 424870 FALSE TRUE 430434.0096 465611.4037 426831.0915 395247.6635 358058.3535 379307.8485 388183.2653 395040.2685 334080.4327 396093.1765 1.086698876 1.175509782 1.077602738 0.997865369 0.903975061 0.957622779 0.980030176 0.997341767 0.843439 1 18.59548032 3.762617565 2.562187233 0.953248515 1.13017586 0.696941781 0.049312852 0.151860169 1.963456257 0.013274983 0.025953803 5789.186829 -3.762617565 0.176927345 LLDWLVDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDWLVDRR 9 1 J3QQY1;Q96JB5;J3KRI2;J3KRK4;J3KS63;J3QS62;Q96JB5-4;J3QL95 J3QQY1 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 0 90.108 0.018685 42264000 51972 78283 52301 50719 55753 39557 62980 52099 52071 56029 FALSE TRUE 49940.87678 76050.44549 61752.95413 53336.61367 57546.34588 40356.86964 63750.76808 51023.13744 46160.11838 52234.10592 0.956097092 1.455953809 1.182234347 1.021107047 1.101700601 0.772615304 1.220481656 0.976816517 0.883716062 1 15.67270449 3.762619168 3.81762721 1.001220883 1.229858009 0.250511189 0.158601728 0.276339683 8.986518936 0.039857312 0.072078989 5789.208192 -3.762619168 0.228637126 DFPGIYTTINAHQWSETVQPIMEALR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFPGIYTTINAHQWSETVQPIMEALR 26 0 E9PGT6;Q99627-2;Q99627 E9PGT6 COPS8 COP9 signalosome complex subunit 8 0 ; 249.39 8.87E-46 610250000 107715 95201 82339 110932 125912 94665 104426 106185 124112 114552 FALSE TRUE 103505.3787 92485.96069 97219.48892 116657.2138 129962.0738 96579.19116 105703.9966 103992.2426 110023.3261 106793.291 0.96921237 0.866027817 0.910352027 1.09236463 1.216949797 0.904356353 0.989799974 0.973771308 1.030245674 1 16.70446149 3.76340163 23.21467676 1.025496055 0.910280371 0.293150526 0.081150671 426.0300376 398134.6298 0.022101086 0.039810649 5799.647927 -3.76340163 -0.115215684 NHACEMCGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NHACEMCGK 9 0 I3L2Z5;A0A087WWR2;P56270-3;P56270;P56270-2;J3QSH4;Q14119 I3L2Z5 MAZ;VEZF1 Myc-associated zinc finger protein;Vascular endothelial zinc finger 1 0 108.43 0.0026124 60548000 273520 214530 165750 164700 156120 119890 141490 50936 143580 116290 FALSE TRUE 262830.536 208411.8144 195704.7121 173200.1867 161141.7416 122314.2579 143221.5969 49884.1538 127281.4003 108413.5747 2.424332347 1.922377479 1.805167965 1.597587638 1.486361297 1.128219028 1.32106701 0.4601283 1.174035638 1 16.72618589 3.763782995 0.48136996 0.8105912 2.640926027 0.816723399 0.222332669 0.776736751 0.267504785 0.172318368 0.741032208 5804.742983 -3.763782995 1.830334827 up IWNSSLQTNKEPVGILTSNHR ddPTM_BT-474_Pertuzumab_2h_R1 1 IWNSSLQTNKEPVGILTSNHR 21 1 P43155-2;P43155;P43155-3 P43155-2 CRAT Carnitine O-acetyltransferase 0 194.24 2.63E-18 384190000 86398 140480 82008 158280 116320 146020 153370 140970 115430 118580 FALSE TRUE 83021.47064 136473.6479 96828.66986 166448.8498 120061.5384 148972.6244 155246.9879 138058.9202 102326.8703 110548.471 0.750996101 1.234514116 0.875893343 1.505663971 1.086053361 1.34757743 1.404334104 1.248854181 0.925628997 1 16.75431955 3.763994372 24.99837706 1.239100173 0.981872474 0.250491704 0.20431366 1039.33366 1021538.676 0.049541902 0.089267479 5807.568921 -3.763994372 -0.257227699 VTYHPDGPEGQAYDVDFTPPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTYHPDGPEGQAYDVDFTPPFR 22 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ; 191.65 1.35E-17 2048160000 979220 1078320 828521 1230181 997547 1187181 1193830 1187190 1257840 1264900 FALSE TRUE 940950.9998 1047567.369 978253.1751 1293670.789 1029634.005 1211186.613 1208440.449 1162674.112 1115055.276 1179227.196 0.797938686 0.888350754 0.829571416 1.097049655 0.873143028 1.027102001 1.024773218 0.985962769 0.945581377 1 20.16941027 3.764175341 24.89041346 0.990890308 0.843593301 0.595808208 0.058342033 484.286572 470590.5733 0.013972784 0.025178523 5809.98941 -3.764175341 -0.147297007 VASGNDHLVMLTADGDLYTLGCGEQGQLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VASGNDHLVMLTADGDLYTLGCGEQGQLGR 30 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 ; 214.29 1.95E-34 315560000 99798 106094 85337 123035 119395 126647 114612 122794 106882 124681 FALSE TRUE 95897.78383 103068.303 100759.2942 129384.8511 123235.4486 129207.8891 116014.6559 120258.261 94749.20345 116236.2448 0.825024793 0.886713978 0.866849186 1.113119675 1.06021533 1.111597242 0.998093634 1.034602083 0.815143363 1 16.82670047 3.7642496 21.80819328 1.025145058 0.862247531 0.453417664 0.080001848 137.6061014 116816.1628 0.020605232 0.037111336 5810.98294 -3.7642496 -0.162897527 LAES(ph)PQLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAESPQLSK 9 0 Q96A19 Q96A19 CCDC102A Coiled-coil domain-containing protein 102A 1 LAES(1)PQLSK 160.16 6.87E-05 340380000 387610 341330 308120 354410 361010 382730 370800 403090 400220 401860 TRUE FALSE 372461.7727 331595.6026 363804.1381 372701.1426 372622.2145 390469.0628 375337.9613 394766.0506 354788.7035 374641.6643 0.994181396 0.885100709 0.971072288 0.994820326 0.99460965 1.042246766 1.001858568 1.05371636 0.947008134 1 18.51515183 3.765045832 2.267432285 1.012585713 0.938504285 0.318307966 0.037180538 0.291053717 2.918992582 0.009863139 0.020106883 5821.646518 -3.765045832 -0.074081428 SFKPDFGAESIYGGFLLGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFKPDFGAESIYGGFLLGVR 20 1 P35606;P35606-2;H0Y938 P35606 COPB2 Coatomer subunit beta 0 ; 202.22 1.08E-21 860910000 751620 843730 675090 597750 659440 697310 699560 753900 739980 786770 FALSE TRUE 722245.8594 819667.6465 797093.7803 628599.9491 680651.4865 711410.086 708121.4245 738331.7015 655980.5726 733481.3671 0.984681945 1.117503025 1.086726693 0.857008749 0.927973793 0.969908873 0.96542524 1.006612758 0.894338428 1 19.48440079 3.765210432 24.97527073 0.951013684 1.068423823 0.501048114 0.053284105 608.7310295 570479.1124 0.013741172 0.024763114 5823.853364 -3.765210432 0.117410139 SEALKDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SEALKDR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 92.439 0.01429 665400000 1458050 1476770 1271640 1058080 1323140 1166670 1275540 1343430 1501310 1408560 FALSE TRUE 1401067.794 1434653.966 1501453.635 1112687.636 1365700 1190260.867 1291150.44 1315687.701 1330887.583 1313156.977 1.06694616 1.092522822 1.143392346 0.84733787 1.040012751 0.906411715 0.983241504 1.001927206 1.013502275 1 20.32460796 3.765547373 24.9978667 0.973207855 1.100110689 0.535140494 0.055736511 559.2290765 518012.6456 0.013517093 0.024359718 5828.37347 -3.765547373 0.126902835 (ac)AAHEWDWFQR ddPTM_BT-474_Pertuzumab_2h_R1 3 AAHEWDWFQR 10 0 Q96JQ2;G3V3D8 Q96JQ2 CLMN Calmin 0 ;; 57.96 0.0052949 155041000 19144.7 18221.8 15713.4 20423.8 23891.5 20585.2 21329 22191.7 21165.2 21968.5 FALSE TRUE 18396.50396 17702.13211 18553.16092 21477.87477 24659.9918 21001.44685 21590.03068 21733.43364 18762.61523 20480.55393 0.8982425 0.864338541 0.905891559 1.048695989 1.204068595 1.025433537 1.054172204 1.061174113 0.916118543 1 14.32196712 3.765551198 4.718962473 1.054005617 0.883877829 0.520376709 0.067835237 0.147704634 8.652543979 0.017972969 0.032047369 5828.424807 -3.765551198 -0.170127787 FDIYDPFHPTDEAYS(ph)PPPAPEQK ddPTM_BT-474_Pertuzumab_2h_R1 10 FDIYDPFHPTDEAYSPPPAPEQK 23 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 FDIYDPFHPT(0.001)DEAYS(0.999)PPPAPEQK;FDIYDPFHPT(0.001)DEAY(0.461)S(0.538)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPT(0.008)DEAYS(0.992)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK 240.09 1.97E-37 14980899000 8657214 7976925 6828989 6760973 7075774 7366296 7551686 7694056 8710125 8205386 TRUE FALSE 8318880.506 7749430.909 8063139.222 7109907.627 7303372.697 7515247.552 7644105.792 7535171.055 7721388.126 7649627.898 1.087488257 1.01304678 1.054056397 0.929444899 0.954735681 0.982433087 0.999278121 0.985037593 1.009380878 1 22.86695814 3.765689064 24.95681522 0.979985025 1.047682123 0.581700984 0.027721945 548.95492 505009.1683 0.007195718 0.012967513 5830.27533 -3.765689064 0.067697098 RRES(ph)QEEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RRESQEEPR 9 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;H0YD62;H0YF37 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 RRES(1)QEEPR;RRES(1)QEEPR 107.17 0.004239 171910000 206775 223873 165583 244279 242424 223245 227866 245610 211891 207028 TRUE FALSE 198694.0044 217488.3612 195507.5315 256886.2685 250221.7881 227759.1669 230654.6923 240538.0677 187838.022 193005.8092 1.029471627 1.126848783 1.012961902 1.330976874 1.296446927 1.180063791 1.195066062 1.24627372 0.973224707 1 17.55828475 3.76609041 24.96033291 1.194267345 1.063469566 0.17310757 0.112410268 1081.879309 980899.9367 0.027943946 0.05036187 5835.665765 -3.76609041 -0.130797779 RGGPNYQEGLR ddPTM_BT-474_Pertuzumab_2h_R1 6 RGGPNYQEGLR 11 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 152.55 5.27E-05 1140240000 805798 867948 652628 721668 729210 615592 822901 745025 783205 815083 FALSE TRUE 774306.5233 843194.9728 770572.3972 758913.372 752665.7019 628039.692 832971.9086 729639.9734 694298.8519 759876.7024 1.018989687 1.109647092 1.014075566 0.998732254 0.990510302 0.826502102 1.096193509 0.960208375 0.913699354 1 19.53540582 3.76615881 1.89475838 0.966526842 1.063128773 0.239755728 0.067846556 0.489335541 3.401881496 0.019159601 0.042147526 5836.584939 -3.76615881 0.096601932 VGCYDANDAS(ph)DEEEFDREGDCISLPGALPGPIRPLSEDDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGCYDANDASDEEEFDREGDCISLPGALPGPIRPLSEDDPR 41 2 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 VGCYDANDAS(0.994)DEEEFDREGDCIS(0.006)LPGALPGPIRPLSEDDPR 63.92 0.0023732 83065000 53217 59166 45423 68762 65203 64054 58513 68099 64566 69557 TRUE FALSE 51137.22081 57478.64361 53631.94653 72310.81506 67300.31371 65349.21577 59229.0996 66692.73185 57236.73836 64845.84244 0.788596753 0.886389034 0.82706839 1.115118755 1.037850866 1.007762615 0.913383146 1.028481231 0.882658567 1 15.98472646 3.766401261 24.91012836 0.997794497 0.839255116 0.574353138 0.064601359 511.8689746 457987.7301 0.016449104 0.029645861 5839.844203 -3.766401261 -0.158539381 QINQEAAHRR ddPTM_BT-474_Pertuzumab_2h_R1 2 QINQEAAHRR 10 1 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;K7ERN1;K7ENS6;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 0 ; 74.162 0.027796 19654500 10872.3 14145.7 9551.4 10790.2 8645.9 10290.9 11431.3 11150.4 11675.6 11140.8 FALSE TRUE 10447.3985 13742.27849 11277.55045 11347.08352 8924.003226 10498.98905 11571.19967 10920.14034 10350.23484 10386.22369 1.005889995 1.323125603 1.085818174 1.092512914 0.859215389 1.010857205 1.114091128 1.051406234 0.996534943 1 13.34238358 3.766477451 2.802467249 1.01824396 1.166303349 0.263935852 0.096638309 0.335367286 5.245043599 0.02586185 0.049546281 5840.868797 -3.766477451 0.148059389 QLPDKWQHDLFDSGFGGGAGVETGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLPDKWQHDLFDSGFGGGAGVETGGK 26 1 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ; 268.68 8.79E-54 3300800000 3136100 2770000 2384130 1836740 2372770 2315190 2114190 2434460 2581100 2399960 FALSE TRUE 3013537.745 2691002.312 2814995.326 1931534.372 2449092.302 2362004.728 2140064.09 2384187.55 2288104.349 2237408.572 1.346887548 1.202731743 1.25814988 0.863290861 1.09461112 1.055687709 0.956492308 1.065602224 1.022658257 1 21.0933973 3.766884193 23.2179823 1.016310414 1.262604125 0.747419084 0.069367869 144.4941914 118446.7152 0.016880193 0.030419546 5846.34167 -3.766884193 0.246293712 AYNADFDGDEMNAHFPQSELGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYNADFDGDEMNAHFPQSELGR 22 0 B9ZVN9;O95602 B9ZVN9 POLR1A DNA-directed RNA polymerase;DNA-directed RNA polymerase I subunit RPA1 0 181.83 4.83E-17 143030000 66653 73083 57826 76074 70301 91111 71362 69973 77411 84252 FALSE TRUE 64048.12707 70998.7444 68276.44453 80000.18826 72562.29551 92953.32685 72235.3495 68528.0331 68623.62781 78545.537 0.815426688 0.903918251 0.869259377 1.018519846 0.923824552 1.183432317 0.919662049 0.872462469 0.87367953 1 16.26124168 3.766976202 21.13174874 0.963178754 0.866972881 0.237002742 0.087543867 187.969998 139783.6467 0.023968587 0.043181869 5847.580397 -3.766976202 -0.096205874 TPEELDDSDFETEDFDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPEELDDSDFETEDFDVR 18 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 151.74 4.92E-09 0 69919 74031 54356 82497 62403 71795 90507 82148 78832 66353 FALSE TRUE 67186.48818 71919.70836 64179.33834 86754.68006 64410.24917 73246.74409 91614.65174 80451.61509 69883.32185 61858.85221 1.086125684 1.162642141 1.037512596 1.402461846 1.041245462 1.184094782 1.481027346 1.300567538 1.129722252 1 15.91669244 3.767010118 24.99191711 1.242909949 1.102148341 0.120377048 0.144747926 1332.244596 1170326.801 0.037120889 0.066904959 5848.037082 -3.767010118 -0.140761609 VYNLLT(ph)PDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VYNLLTPDSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 VYNLLT(1)PDSK;VYNLLT(0.957)PDS(0.043)K 105.65 0.028178 546080000 1003350 949020 814910 786800 822820 826450 849200 1020340 977560 960800 TRUE FALSE 964137.9727 921954.8788 962182.3646 827406.8423 849286.7526 843161.3852 859592.7636 999269.6224 866591.4871 895724.1602 1.076378215 1.029284371 1.074194945 0.923729513 0.948156576 0.941318123 0.959662362 1.11559972 0.967475843 1 19.77269499 3.767354869 24.99106475 0.987915143 1.056885706 0.326623458 0.051940934 1122.133802 973917.0585 0.015393774 0.027744932 5852.681213 -3.767354869 0.068970563 TQTPQLHFLDT(ph)DDEVSPTSWGDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQTPQLHFLDTDDEVSPTSWGDSR 24 0 Q86US8 Q86US8 SMG6 Telomerase-binding protein EST1A 1 TQTPQLHFLDT(1)DDEVSPTSWGDSR;TQTPQLHFLDT(1)DDEVSPTSWGDSR 187.72 6.71E-17 243450000 111769 121745 106214 79161 101952 106966 93274 103856 127706 117238 TRUE FALSE 107400.9439 118272.9518 125409.2325 83246.5087 105231.3787 109128.9258 94415.51511 101711.3373 113209.3503 109297.3658 0.98264897 1.082120789 1.147413129 0.761651555 0.962798855 0.998458883 0.863840719 0.93059276 1.03579212 1 16.73789911 3.767551929 24.99921623 0.932419395 1.071866937 0.357434796 0.082569643 741.1453975 639087.4972 0.020631158 0.037184899 5855.337452 -3.767551929 0.139447542 AEPVEVVAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEPVEVVAPR 10 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 88.37 0.027515 0 128130 181180 127370 225860 240620 257390 209020 162460 145690 156080 FALSE TRUE 123122.5379 176012.9238 150388.5923 237516.6617 248359.7608 262594.6022 211578.0493 159105.1442 129151.882 145508.5626 0.846153214 1.20963963 1.03353775 1.632320858 1.706839491 1.804667694 1.454059098 1.093441798 0.887589567 1 17.15074453 3.767637786 23.79852132 1.39088292 1.047762959 0.208897197 0.29915677 679.8439107 556421.9234 0.084297413 0.151926403 5856.495129 -3.767637786 -0.343119962 KTGQIWPNDGEGAFHGDADGSFGT(ph)PPGYGCAADR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 34 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 KTGQIWPNDGEGAFHGDADGS(0.002)FGT(0.998)PPGYGCAADR;KTGQIWPNDGEGAFHGDADGSFGT(1)PPGYGCAADR 239.79 3.65E-47 787920000 452710 396760 333750 267743 286618 305442 279626 260416 298486 340420 TRUE FALSE 435017.5927 385444.7933 394066.0492 281561.2483 295837.3283 311618.2465 283048.1466 255038.3186 264603.1206 317363.0502 1.370725396 1.214523219 1.241688498 0.88718976 0.932173194 0.981898322 0.891874925 0.803616925 0.833755286 1 18.27577464 3.767865938 4.351680784 0.893003455 1.277617621 0.863729606 0.067559254 0.073007347 3.338604056 0.01905833 0.034240007 5859.572581 -3.767865938 0.384614166 GKFEDMAK ddPTM_BT-474_Pertuzumab_2h_R1 5 GKFEDMAK 8 1 P09429;Q5T7C4;B2RPK0;P23497 P09429;P23497 HMGB1;HMGB1P1;SP100 High mobility group protein B1;Putative high mobility group protein B1-like 1;Nuclear autoantigen Sp-100 0 ;;;; 109.66 0.0032602 14117380000 20587920 21366280 17407280 11234340 14654450 4619990 21800720 17622400 19081430 20737640 FALSE TRUE 19783321.33 20756934.61 20553162.72 11814145.63 15125823.69 4713409.363 22067523.73 17258491.28 16915386.06 19333061.17 1.023289646 1.073649663 1.063109589 0.611085101 0.782381205 0.243800468 1.14143971 0.89269315 0.874946079 1 24.20456675 3.768328658 23.22063455 0.792658127 1.055379841 0.216681664 0.227411525 468.2980226 365293.8166 0.059907824 0.107970093 5865.819001 -3.768328658 0.262721714 VYFQS(ph)PPGAAGEGPGGADDEGPVRR ddPTM_BT-474_Pertuzumab_2h_R1 4 VYFQSPPGAAGEGPGGADDEGPVRR 25 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 1 VYFQS(1)PPGAAGEGPGGADDEGPVRR;VYFQS(1)PPGAAGEGPGGADDEGPVRR;VY(0.004)FQS(0.996)PPGAAGEGPGGADDEGPVRR;VYFQS(1)PPGAAGEGPGGADDEGPVRR 152.98 6.90E-08 2595390000 2487000 2644570 2110710 1878430 2164200 2228100 1945690 2485710 2383380 2281920 TRUE FALSE 2389805.29 2569149.453 2492162.249 1975375.997 2233813.458 2273153.709 1969501.936 2434379.22 2112828.694 2127363.526 1.123364795 1.207668281 1.17147926 0.928555921 1.050038431 1.068530921 0.925794728 1.144317457 0.993167679 1 21.02063515 3.768344159 24.19294056 1.026895023 1.171520601 0.533743335 0.064370458 369.5279902 300162.9241 0.016158043 0.029123285 5866.028375 -3.768344159 0.144625578 IESLIDRDYMER ddPTM_BT-474_Pertuzumab_2h_R1 2 IESLIDRDYMER 12 1 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ; 154.67 6.54E-05 665970000 752630 826150 637520 598000 655840 595870 725370 591590 667340 672560 FALSE TRUE 723216.3875 802589.0109 752734.0456 628862.8517 676935.6892 607918.8997 734247.295 579373.4598 591586.3609 627006.9121 1.153442448 1.280032158 1.200519533 1.002959998 1.079630346 0.969556935 1.171035408 0.924030419 0.943508516 1 19.25812182 3.768669626 5.439534442 1.014644536 1.220749357 0.610622779 0.072540401 0.121188448 10.64877999 0.018669657 0.033243755 5870.426104 -3.768669626 0.206104821 KLDELYGTWR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDELYGTWR 10 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 170.04 7.13E-06 8057800000 10886600 12726700 9506400 9212500 9278600 6315500 11666300 9417900 12036500 11786000 FALSE TRUE 10461139.64 12363746.98 11224417.95 9687958.229 9577054.596 6443203.737 11809075.67 9223417.074 10670166.98 10987723.72 0.952075234 1.125232786 1.021541698 0.881707483 0.87161407 0.586400232 1.074751784 0.839429286 0.971098951 1 23.3893892 3.768715783 4.515624548 0.878053638 1.045540565 0.205529958 0.128076869 0.28243389 14.28284812 0.032725009 0.058704456 5871.050057 -3.768715783 0.167486927 SS(ph)SPVQVEEEPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVQVEEEPVR 13 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 S(0.004)S(0.498)S(0.498)PVQVEEEPVR 281.1 2.05E-32 677280000 485920 553790 401560 562770 505090 531320 469400 612520 548580 586420 TRUE FALSE 466929.7092 537996.4514 474130.8247 591814.6271 521336.6786 542063.6544 475144.6576 599871.248 486307.4982 546701.2511 0.854085679 0.984077593 0.867257618 1.082519248 0.953604327 0.991517128 0.869112073 1.097256037 0.889530612 1 19.06039315 3.768819197 24.99807888 0.986251872 0.910034032 0.195532522 0.07509405 1159.721007 958097.563 0.018119952 0.032660862 5872.448228 -3.768819197 -0.07621784 MMS(ph)PNKLHTNFHIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 MMSPNKLHTNFHIPK 15 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 MMS(0.997)PNKLHT(0.003)NFHIPK 78.78 0.013224 350140000 1086100 969350 651460 733070 721300 646660 796200 208310 748800 709040 TRUE FALSE 1043654.011 941705.0871 769193.3136 770903.8306 744501.2696 659735.9083 805944.1338 204008.3257 663799.3632 661016.0893 1.57886325 1.424632626 1.163652937 1.166240645 1.126298258 0.998063313 1.219250404 0.308628381 1.004210599 1 19.33432586 3.769070622 0.477974913 0.759107775 1.715742574 0.490190845 0.227350394 1.594021863 0.538079127 0.182348757 0.790882718 5875.848941 -3.769070622 0.956634799 GDNRLDLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDNRLDLLK 9 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 112.13 0.0018355 480360000 1057390 1054180 828990 642860 678530 285680 923000 726640 771350 852140 FALSE TRUE 1016066.03 1024115.819 978806.9338 676038.0816 700355.5337 291456.6453 934295.9501 711634.6301 683789.5818 794423.7988 1.278997471 1.289130336 1.232096691 0.850979141 0.881589316 0.366878039 1.176067423 0.895787149 0.860736527 1 19.59954932 3.769536602 4.612319873 0.858402203 1.276920091 0.485904787 0.191161653 0.173090515 9.257303857 0.050577148 0.090698624 5882.156871 -3.769536602 0.418517888 GDHSPVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDHSPVTR 8 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 95.502 0.0096049 54632000 23368 22619 17777 27992 28336 27471 26492 21324 26734 24794 FALSE TRUE 22454.75273 21973.92827 20989.69935 29436.67047 29247.45317 28026.48244 26816.21702 20883.65195 23699.2684 23114.6803 0.971449851 0.950648159 0.908067907 1.273505413 1.26531939 1.212497083 1.160137916 0.903480026 1.025290772 1 14.49652179 3.769692241 24.96444165 1.115285227 0.944114559 0.339194352 0.112847777 926.4192794 742892.2641 0.033854083 0.061022825 5884.265245 -3.769692241 -0.171170668 VINDKHDDVMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VINDKHDDVMAK 12 1 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 102.73 0.0013954 295420000 1015000 917050 932380 616310 887810 853080 932320 763640 1166300 928970 FALSE TRUE 975332.6779 890896.6319 1100881.807 648117.833 916367.2149 870329.8621 943730.011 747870.5671 1033906.514 866050.0345 1.126185138 1.028689563 1.271152662 0.748360726 1.058099623 1.004941779 1.08969456 0.863541986 1.193818454 1 19.72409085 3.769755174 24.99993322 0.989684875 1.130677106 0.220130473 0.126884464 1035.261511 829675.851 0.030659291 0.05526437 5885.117985 -3.769755174 0.140992232 SLIEEGGDWDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLIEEGGDWDRR 12 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;; 240.52 5.25E-16 5917600000 2878120 3032040 2358010 3262990 3159580 3115820 3147470 3209060 3152390 3146420 FALSE TRUE 2765639.888 2945569.188 2784154.861 3431393.305 3261210.76 3178824.015 3185989.679 3142791.79 2794543.903 2933310.171 0.942839225 1.004179243 0.949151197 1.169802409 1.111785174 1.083698562 1.086141422 1.071414752 0.952692944 1 21.4840982 3.77003145 24.99162277 1.074224574 0.969268802 0.394580691 0.057781309 663.2335202 526684.7463 0.014753929 0.026595686 5888.862989 -3.77003145 -0.104955772 EIGDVENWAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIGDVENWAR 10 0 G8JLQ3;P78537-2;P78537 G8JLQ3 BLOC1S1 Biogenesis of lysosome-related organelles complex 1 subunit 1 0 ;;; 168.83 1.12E-05 460495000 516152 561062 435226 603970 595600 593020 533914 610250 593940 581210 FALSE TRUE 495980.2092 545061.0611 513881.0198 635140.9641 614758.0149 605011.2707 540448.1992 597648.1242 526518.4212 541844.129 0.915355879 1.005937006 0.948392706 1.1721839 1.134566164 1.116578068 0.997423743 1.102989019 0.971715652 1 19.04751837 3.770052802 24.85356532 1.076581626 0.961499345 0.390926736 0.064963352 632.1969379 498926.0538 0.016543316 0.029820036 5889.152519 -3.770052802 -0.115082281 REGGDGEEQDVGDAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 REGGDGEEQDVGDAGR 16 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 218.83 2.08E-14 896320000 503480 538760 417870 563510 502060 581820 533950 546650 581210 612240 FALSE TRUE 483803.445 523395.0923 493388.4045 592592.8186 518209.2159 593584.799 540484.6398 535361.4865 515233.4774 570772.4395 0.847629303 0.916994333 0.864422264 1.03822956 0.907908617 1.039967521 0.94693542 0.937959596 0.902695088 1 19.12255615 3.770203401 24.93039908 0.962856384 0.880413185 0.427315218 0.048153438 650.9064679 512827.5205 0.011810562 0.021289478 5891.195032 -3.770203401 -0.082443198 EEVTELLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEVTELLAR 9 0 P19388;A0A087WVZ9;A0A0A0MQR7;A0A087WWX0 P19388 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" 0 ;;; 151.27 0.0001937 388079000 339802 347943 278021 365079 325459 366273 346091 385667 375032 386847 FALSE TRUE 326522.1622 338020.0063 328265.5792 383920.7709 335927.6843 373679.291 350326.5652 377702.8417 332459.9396 360645.5081 0.905382584 0.937263875 0.910216742 1.064537787 0.931462272 1.03614015 0.971387574 1.047296675 0.921846889 1 18.46022193 3.77028765 24.74383394 0.998497681 0.919585324 0.393316172 0.044573446 549.4982361 428550.3424 0.010459753 0.018854766 5892.337988 -3.77028765 -0.078912357 IEREEEEEEEALPLDMMDEDDLQLMK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEREEEEEEEALPLDMMDEDDLQLMK 26 1 Q8WTT2 Q8WTT2 NOC3L Nucleolar complex protein 3 homolog 0 130.23 6.67E-05 23324000 9056.6 11124 9322.7 6518.7 9075.5 8122.7 9526.4 9817.3 8082.5 9580.2 FALSE TRUE 8702.658059 10806.75441 11007.51927 6855.130888 9367.4217 8286.946559 9642.986933 9614.569324 7165.008485 8931.324521 0.974397251 1.2099834 1.232462133 0.767537992 1.048827828 0.927851915 1.079681621 1.07649983 0.802233584 1 13.12465843 3.770479042 24.99945744 0.976744161 1.146051168 0.315669963 0.119964631 836.9411155 655514.5245 0.030367182 0.054739333 5894.935294 -3.770479042 0.169307007 VPAFLSAAEVEEHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPAFLSAAEVEEHLR 15 0 Q14894;I3NI53;I3L2W5;I3L3J9 Q14894 CRYM Ketimine reductase mu-crystallin 0 ; 186.56 3.76E-07 141084000 81150 107160 74484 135856 119921 101833 135947 120531 95488 128236 FALSE TRUE 77978.56828 104103.9017 87944.91569 142867.5444 123778.3679 103892.133 137610.7601 118041.9927 84648.60256 119550.4615 0.652264887 0.870794645 0.735630081 1.195039673 1.035365036 0.86902327 1.151068414 0.987382159 0.708057514 1 16.86726017 3.770685535 24.71202956 0.997586737 0.764686276 0.387572938 0.137542369 602.8449932 463735.1702 0.034735128 0.062612833 5897.738811 -3.770685535 -0.232900461 IAQLSESPVILT(ph)PNAK ddPTM_BT-474_Pertuzumab_2h_R1 1 IAQLSESPVILTPNAK 16 0 Q6P4F7-3;Q6P4F7;H3BQ41;H3BR51;Q6P4F7-2 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 IAQLS(0.003)ES(0.367)PVILT(0.63)PNAK 111.06 0.0094548 64282000 77850 68779 56508 73676 70715 62266 74993 88053 58639 73066 TRUE FALSE 74807.53593 66817.49026 66720.25261 77478.42719 72989.6122 63525.06118 75910.78677 86234.67478 51982.54655 68117.17474 1.098218419 0.980919871 0.979492365 1.137428666 1.071530234 0.932585085 1.114414787 1.265975506 0.763134213 1 16.05573098 3.770839885 24.8038696 1.065226264 1.015681205 0 0.1305415 2882.499985 2214946.208 0.033910489 0.061126226 5899.835261 -3.770839885 -0.049545059 YVVLCRGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YVVLCRGAK 9 1 O75426-2;O75426-4;O75426;O75426-3 O75426-2 FBXO24 F-box only protein 24 0 ; 71.501 0.029683 811670000 2382000 2440400 1876930 1615770 1765080 1178460 1833490 1677290 1978270 1820180 FALSE TRUE 2288908.807 2370802.181 2216133.003 1699160.083 1821855.401 1202289.269 1855928.799 1642653.375 1753705.083 1696897.587 1.348878579 1.397139226 1.305991015 1.001333313 1.073638984 0.708521998 1.093718804 0.968033302 1.033477268 1 20.69446807 3.770970315 2.828510401 0.97501362 1.37413249 0.740880523 0.100236476 0.127415321 2.030083283 0.026584042 0.051023378 5901.607398 -3.770970315 0.39911887 VS(ph)PGQAAPAMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPGQAAPAMAR 12 0 Q96HA7-2;Q96HA7 Q96HA7-2 TONSL Tonsoku-like protein 1 VS(1)PGQAAPAMAR;VS(1)PGQAAPAMAR 169.17 4.67E-05 626870000 257300 244164 195994 221238 216718 182944 251210 216847 207209 262810 TRUE FALSE 247244.4315 237200.6818 231414.4757 232656.1197 223688.9313 186643.253 254284.3831 212369.0337 183687.503 245009.6446 1.00912122 0.968127937 0.944511699 0.949579434 0.912980106 0.761779208 1.037854585 0.866778261 0.749715397 1 17.90247902 3.771049803 1.028346446 0.884994641 0.998198462 0.182822869 0.085250894 1.113184447 2.149309842 0.029813087 0.097634948 5902.68766 -3.771049803 0.113203821 FPSNLEVEAS(ph)PQAS(ph)SAEVNASPLWNLAHVK ddPTM_BT-474_Pertuzumab_2h_R1 1 FPSNLEVEASPQASSAEVNASPLWNLAHVK 30 0 O94864;O94864-2;O94864-4 O94864 SUPT7L STAGA complex 65 subunit gamma 2 FPS(0.031)NLEVEAS(0.918)PQAS(0.389)S(0.372)AEVNAS(0.289)PLWNLAHVK 44.107 0.066669 16823000 29603 27309 23120 29724 27088 31667 31735 25896 35374 30719 TRUE FALSE 28446.08203 26530.17406 27298.2983 31258.0592 27959.31012 32307.32844 32123.38242 25361.23855 31358.49182 28638.37477 0.993285487 0.926385463 0.953206965 1.091474619 0.976288297 1.128113194 1.121690134 0.885568359 1.094981544 1 14.805662 3.771256135 22.90921418 1.034430999 0.954501832 0.218873178 0.072341819 399.630962 280011.8655 0.019222614 0.03464851 5905.492668 -3.771256135 -0.079929167 LQTLS(ph)PSHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQTLSPSHK 9 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 LQT(0.001)LS(0.998)PS(0.001)HK;LQT(0.002)LS(0.966)PS(0.032)HK 159.44 0.0011091 0 338010 319120 288620 231300 294470 269650 279810 331710 292420 312720 TRUE FALSE 324800.1955 310019.0101 340780.0543 243237.4207 303941.895 275102.5078 283234.3985 324860.0726 259225.7075 291539.1959 1.114087574 1.063387066 1.168899617 0.834321505 1.042542133 0.943621001 0.971513959 1.114292957 0.889162456 1 18.15333033 3.771408752 24.99904605 0.98521258 1.110250983 0.415261782 0.077284527 717.8753275 546336.1868 0.019685536 0.035485855 5907.568314 -3.771408752 0.125038403 PVVDPSRITR ddPTM_BT-474_Pertuzumab_2h_R1 1 PVVDPSRITR 10 1 Q9NQU5-2;Q9NQU5;H0YL16;H0YL47;H0YK38;H0YM99;H0YK74;H0YK91;H0YLZ9;H0YMS4 Q9NQU5-2 PAK6 Serine/threonine-protein kinase PAK 6 0 68.847 0.05358 394430000 44774 45346 35510 33739 28655 37882 38658 30985 40856 39520 FALSE TRUE 43024.18258 44052.77648 41927.44692 35480.27383 29576.7141 38647.99999 39131.10817 30345.14892 36218.19816 36843.2752 1.167762159 1.195680249 1.137994565 0.963005423 0.802771033 1.048983832 1.062096352 0.823627888 0.983034162 1 15.1691137 3.771613654 3.82232766 0.943208625 1.177193776 0.594789271 0.080513031 0.15044621 4.811156332 0.02199502 0.040129434 5910.356187 -3.771613654 0.233985151 SNEDS(ph)LILEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SNEDSLILEK 10 0 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 SNEDS(1)LILEK;SNEDS(1)LILEK;SNEDS(1)LILEK 106.14 0.0025763 351424000 516810 464590 432980 342670 410070 411800 403920 525890 421430 482700 TRUE FALSE 496612.4938 451340.3481 511229.1176 360355.2398 423260.274 420126.8781 408863.2938 515030.1877 373591.0332 450006.2991 1.103567872 1.002964512 1.136048803 0.800778212 0.940565221 0.933602216 0.908572379 1.144495508 0.830190675 1 18.77958567 3.771667341 24.95914598 0.952802916 1.073070801 0.317412522 0.094554153 922.915909 695782.9249 0.025018523 0.045099247 5911.086861 -3.771667341 0.120267885 TKFEECR ddPTM_BT-474_Pertuzumab_2h_R1 4 TKFEECR 7 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;; 107.57 0.0067915 6994470000 5825960 5420150 4525130 4384310 4638950 3245470 5102920 5189310 5528850 6064270 FALSE TRUE 5598275.042 5265572.629 5342921.652 4610584.765 4788166.04 3311095.627 5165371.061 5082148.935 4901238.127 5653531.591 0.990226189 0.93137759 0.945059131 0.815522951 0.846933631 0.585668546 0.913653878 0.898933499 0.866933889 1 22.43072093 3.771691886 8.176510935 0.839752604 0.953504081 0.192778435 0.101235752 0.500352631 112.3353014 0.026597747 0.047530575 5911.420945 -3.771691886 0.113751476 KFPVTENSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFPVTENSK 9 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 106.4 0.0047173 345310000 640130 717740 532300 379040 380650 117940 601750 432790 472060 566710 FALSE TRUE 615113.0119 697270.7579 628498.4509 398602.2998 392893.9529 120324.8276 609114.3965 423852.7353 418473.7278 528326.2269 1.164267418 1.31977313 1.189602974 0.75446245 0.743657863 0.227747217 1.152913419 0.802255716 0.792074492 1 19.0110695 3.771697096 5.073986803 0.773291125 1.241379933 0.447154398 0.225584159 0.175232351 12.14964015 0.059247756 0.106054703 5911.491861 -3.771697096 0.468088808 DCISWVGDEGEFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DCISWVGDEGEFK 13 0 Q06546 Q06546 GABPA GA-binding protein alpha chain 0 ; 156.51 0.00010983 136971000 90364 87597 74408 91253 92203 99753 90353 104321 98968 107565 FALSE TRUE 86832.47498 85098.81933 87855.1808 95962.57827 95168.79323 101770.074 91458.76704 102166.7349 87733.56755 100279.5267 0.865904316 0.848616084 0.876102866 0.956950849 0.949035125 1.014863924 0.91203828 1.018819476 0.874890124 1 16.61366757 3.771868385 2.987494693 0.964969231 0.857283036 0.528052267 0.042374213 0.182794399 3.279313237 0.010625541 0.020160771 5913.823857 -3.771868385 -0.107686195 KSADTLWGIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSADTLWGIQK 11 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 108.3 0.0033368 2407700000 5724200 5890200 4501900 3372700 3520700 2117100 4298800 3831500 4022100 3602800 FALSE TRUE 5500491.936 5722217.263 5315493.474 3546765.451 3633946.513 2159909.213 4351410 3752378.186 3565528.07 3358779.147 1.637646209 1.703659875 1.58256713 1.055968641 1.081924817 0.643063779 1.295533231 1.11718515 1.061554783 1 21.67950551 3.772004051 3.945001153 1.044234731 1.664368399 0.765630204 0.153731066 0.106316319 3.68040041 0.041946861 0.076308568 5915.671525 -3.772004051 0.620133668 RRPESAPAESS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRPESAPAESSPSK 14 2 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 RRPESAPAES(0.035)S(0.965)PSK 78.078 0.01194 145590000 115660 136820 110020 81941 93786 116770 117790 106940 112340 112240 TRUE FALSE 111139.8793 132918.0276 129903.0614 86169.98483 96802.71186 119131.1694 119231.5493 104731.6516 99587.63417 104637.8848 1.062138054 1.270266766 1.241453433 0.823506562 0.925121069 1.13850896 1.139468267 1.000896108 0.951735926 1 16.67504576 3.772018813 24.99825489 1.008183936 1.199184192 0.428788039 0.102055341 648.859889 484792.8383 0.027703203 0.049939198 5915.872599 -3.772018813 0.191000257 RKEEKE ddPTM_BT-474_Pertuzumab_2h_R1 1 RKEEKE 6 3 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 80.462 0.078812 48520000 103210 95274 83968 75783 80922 79531 98223 91206 100230 104510 FALSE TRUE 99176.4391 92556.8788 99142.88546 79694.16971 83524.92962 81139.17131 99425.08246 89322.56423 88852.3106 97431.44461 1.017909972 0.949969275 1.01756559 0.817951227 0.857268718 0.832782185 1.020461955 0.916773477 0.911946969 1 16.57209984 3.772030291 24.92584328 0.907085784 0.990630389 0.279994413 0.063777301 868.7326956 646967.8242 0.016784807 0.030256626 5916.028958 -3.772030291 0.083544604 EVLYDS(ph)EGLSGEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLYDSEGLSGEER 14 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 EVLYDS(0.525)EGLS(0.475)GEER 159.34 5.17E-06 84418000 55863 54680 45039 62444 53874 57380 66045 60811 62271 65349 TRUE FALSE 53679.8122 53120.57994 53178.54919 65666.74232 55606.90614 58540.26291 66853.27847 59555.2316 55202.25714 60922.85402 0.881111252 0.871931901 0.87288342 1.077867138 0.91274296 0.96089167 1.097343182 0.97755157 0.90610097 1 15.89469591 3.772497439 23.96464317 0.990808492 0.874971084 0.454156778 0.057797046 342.4835442 241844.7028 0.014792946 0.026665969 5922.39595 -3.772497439 -0.115837408 EVDILNHVFDDVESFVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVDILNHVFDDVESFVSR 18 0 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 124.63 3.14E-05 162120000 43665 41952 36078 41590 47728 44416 50645 43302 39339 47528 FALSE TRUE 41958.52353 40755.57004 42598.09715 43736.46488 49263.21447 45314.12195 51264.80866 42407.79857 34873.40164 44308.88623 0.946955049 0.919805789 0.961389481 0.987081116 1.111813423 1.022687001 1.156987075 0.957094664 0.787052093 1 15.43530844 3.772786784 2.993839921 1.013571205 0.93603754 0.081400583 0.092690222 0.625420114 11.26682755 0.026196623 0.049723871 5926.343003 -3.772786784 -0.077533665 QFCQEGQPHVLEALS(ph)PPQTSGLSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 QFCQEGQPHVLEALS(0.653)PPQT(0.304)S(0.043)GLSPSR 113.41 0.0010314 2969500000 277790 273920 222560 283570 290410 285530 262370 282160 306460 298930 TRUE FALSE 266933.6597 266108.0698 262781.5428 298205.0817 299751.3014 291303.6122 265580.9625 276333.2974 271671.9456 278683.2048 0.957839063 0.954876595 0.942940006 1.070050425 1.075598731 1.045285856 0.952985174 0.991567818 0.974841472 1 18.08826653 3.773471878 24.86053313 1.013856562 0.952184339 0.378978579 0.037414738 716.9940437 510573.543 0.010996492 0.019823123 5935.699116 -3.773471878 -0.061672222 RPLDS(ph)PEAEELPAMK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPLDSPEAEELPAMK 15 1 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 1 RPLDS(1)PEAEELPAMK;RPLDS(1)PEAEELPAMK;RPLDS(1)PEAEELPAMK;RPLDS(1)PEAEELPAMK 227 8.36E-13 1143970000 1579310 1536950 1332040 1483020 1562290 1585120 1565340 1729760 1756670 1762250 TRUE FALSE 1517588.819 1493117.691 1572769.259 1559558.84 1612542.477 1617172.212 1584497.099 1694039.852 1557260.186 1642891.238 0.923730545 0.908835385 0.957317942 0.949276984 0.981527224 0.984345266 0.964456479 1.031133293 0.947877833 1 20.64780554 3.773708696 0.738916999 0.992944138 0.905328177 0.573037767 0.022353481 0.671894103 0.620813147 0.010153757 0.040102038 5938.936689 -3.773708696 -0.087615961 HNGVGGS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 1 HNGVGGSPPK 10 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 HNGVGGS(1)PPK 76.073 0.023892 236670000 159490 147400 133880 110870 141110 137000 151380 92920 208060 156040 TRUE FALSE 153256.9545 143196.2963 158075.0941 116592.014 145648.9313 139770.2339 153232.6337 91001.16953 184441.9011 145471.2718 1.053520414 0.984361342 1.086641315 0.801477931 1.001221269 0.960809871 1.053353228 0.625561105 1.26789227 1 17.15037475 3.774305881 24.8421364 0.932188801 1.035793051 0.035812199 0.159440137 1504.190462 1045372.578 0.040008397 0.072122697 5947.108763 -3.774305881 0.103604249 KS(ph)ST(ph)KR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSTKR 6 2 A0A0U1RR16;Q8NEY4-2;Q8NEY4 A0A0U1RR16 ATP6V1C2 V-type proton ATPase subunit C 2 2 KS(0.682)S(0.318)T(1)KR 71.692 0.096635 345410000 182780 219450 152780 242390 218530 238630 228730 176210 247540 242610 TRUE FALSE 175636.7555 213191.5009 180390.7446 254899.7769 225559.2159 243455.2621 231529.2662 172571.2019 219440.297 226177.8086 0.77654283 0.942583634 0.797561643 1.126988446 0.997265016 1.076388809 1.023660401 0.762989097 0.970211438 1 17.78709786 3.774556327 24.99955032 0.976504946 0.849264787 0.328600833 0.09905931 926.0866681 643177.8979 0.028288857 0.050996242 5950.53929 -3.774556327 -0.127240159 QQDLHLES(ph)PQRQPEYSPESPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 QQDLHLES(1)PQRQPEYSPESPR;QQDLHLES(1)PQRQPEYSPESPR 183.47 2.60E-17 507020000 268330 294530 219501 343910 303430 323750 312640 292670 317690 374810 TRUE FALSE 257843.3669 286130.2928 259169.7135 361659.2363 313190.1015 330296.4468 316466.1818 286626.2622 281627.1631 349423.7849 0.737910177 0.818863241 0.741705988 1.035016081 0.896304474 0.945260343 0.905680138 0.820282633 0.805975939 1 18.41461829 3.774738866 24.99507075 0.902936596 0.771430114 0.481280982 0.07014213 585.3944119 404439.3676 0.018606281 0.033541884 5953.0409 -3.774738866 -0.131506481 EKFS(ph)FEPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKFSFEPK 8 1 P23443-5;P23443;P23443-3;P23443-2;P23443-4;K7ERJ3 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 EKFS(1)FEPK;EKFS(1)FEPK;EKFS(1)FEPK 99.752 0.0039912 2665360000 4811000 4021850 3713420 2765900 3469430 3594830 3005760 4173600 4360300 3924970 TRUE FALSE 4622980.801 3907150.776 4384517.599 2908648.43 3581027.367 3667519.926 3042545.39 4087413.702 3865337.024 3659128.286 1.263410419 1.067781851 1.198241017 0.79490201 0.978655867 1.002293344 0.831494594 1.11704575 1.056354607 1 21.80306857 3.774859607 24.91250536 0.975501646 1.16560823 0.470083642 0.100724529 540.549199 370984.7023 0.025952557 0.046784706 5954.696173 -3.774859607 0.190106584 NAASFPLRS(ph)PQPVCSPAGSEGTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 NAASFPLRSPQPVCSPAGSEGTPK 24 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 NAASFPLRS(1)PQPVCSPAGSEGTPK 195.27 2.71E-19 86285000 82960 80852 65577 62902 70686 56473 61435 66928 79984 82246 TRUE FALSE 79717.83148 78546.18012 77428.22265 66148.37976 72959.67939 57614.92275 62186.85991 65545.91341 70904.55164 76675.40516 1.039679299 1.024398632 1.009818239 0.862706622 0.951539535 0.751413346 0.811040513 0.854849261 0.924736576 1 16.22647626 3.775482818 1.926327259 0.862080801 1.038063186 0.471116332 0.068390468 0.267444069 1.922113162 0.019223875 0.042368035 5963.247274 -3.775482818 0.175982385 LTATEGPGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTATEGPGSPR 11 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 LTATEGPGS(1)PR;LTATEGPGS(1)PR 126.5 0.00032118 1369720000 1362200 1446710 1124920 1480510 1334240 1483500 1351850 1577660 1563380 1467690 TRUE FALSE 1308963.718 1405451.247 1328218.068 1556919.299 1377157.041 1513497.386 1368394.345 1545080.77 1385911.657 1368282.049 0.956647585 1.027164866 0.970719501 1.137864302 1.00648623 1.106129681 1.000082071 1.12921219 1.012884484 1 20.38393422 3.775606545 24.93135264 1.062067197 0.989076055 0.268363207 0.053138652 663.0945352 446250.5589 0.012374796 0.022308261 5964.946393 -3.775606545 -0.072991142 EGPLGWSSDGSLGSVLLDSPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGPLGWSSDGSLGSVLLDSPSSPR 24 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 EGPLGWSSDGSLGSVLLDS(0.031)PS(0.811)S(0.159)PR;EGPLGWSSDGSLGSVLLDS(0.017)PS(0.492)S(0.492)PR 150.83 7.79E-08 50236000 90204 86127 71174 97443 100087 96511 85426 96159 94572 95233 TRUE FALSE 86678.72795 83670.74229 84036.72506 102472.0449 103306.3893 98462.51854 86471.46894 94173.28305 83836.58304 88782.78409 0.97630108 0.942420799 0.946543025 1.154188236 1.163585827 1.109027156 0.973966629 1.060715588 0.944288737 1 16.43799233 3.776031509 24.88798533 1.061641104 0.953821502 0.319401121 0.068666075 658.3336284 437259.9914 0.018766923 0.033831248 5970.786037 -3.776031509 -0.107819602 S(ph)RTS(ph)PVTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.987)RT(0.015)S(0.998)PVTR;S(0.596)RT(0.405)S(0.998)PVT(0.001)R;S(0.943)RT(0.099)S(0.958)PVTR;S(0.697)RT(0.335)S(0.968)PVTR 93.772 0.0061634 5867820000 265692 305061 228109 344384 323111 307793 292499 355586 322442 293734 TRUE FALSE 255308.4629 296360.959 269333.3706 362157.6995 333504.1588 314016.7853 296078.6903 348243.0248 285839.7359 273839.1345 0.932330082 1.082244725 0.983545946 1.322519881 1.217883482 1.146719901 1.081213942 1.271706564 1.043823544 1 18.06296911 3.776089864 24.92796172 1.16989591 1.007660641 0.326623798 0.100469793 582.9589511 387215.537 0.024604651 0.044355158 5971.588381 -3.776089864 -0.162235269 AAVVESHK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAVVESHK 8 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390;A0A2R8YF59;H0YC68 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ; 141.39 0.0006343 1170140000 2146100 2046810 1574230 1545610 1367110 356300 2499500 1233620 1704980 2192100 FALSE TRUE 2062228.039 1988436.983 1858728.38 1625379.117 1411084.335 363504.6301 2530089.629 1208145.316 1511437.818 2043627.114 1.009101917 0.97299403 0.909524231 0.795340356 0.690480335 0.177872288 1.238038784 0.591176985 0.73958591 1 20.96270055 3.776197965 2.219223621 0.721466068 0.986587011 0.133790848 0.256965169 0.588447824 5.644158956 0.070096884 0.145586115 5973.074964 -3.776197965 0.265120943 GQGPRS(ph)PHK ddPTM_BT-474_Pertuzumab_2h_R1 3 GQGPRSPHK 9 1 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 1 GQGPRS(1)PHK;GQGPRS(1)PHK;GQGPRS(1)PHK 75.416 0.023144 566918000 674980 652940 485650 369703 359145 160331 484870 310734 398121 439770 TRUE FALSE 648601.0354 634318.7905 573417.7582 388783.4161 370697.2251 163573.0027 490803.9841 304317.2343 352927.9731 409983.9862 1.582015535 1.547179431 1.398634526 0.948289273 0.904174889 0.398974126 1.197129646 0.742266148 0.860833557 1 18.64520803 3.776494332 2.160219852 0.835141353 1.568827781 0.712656413 0.190368819 0.159142266 1.444580869 0.051541499 0.108200632 5977.152434 -3.776494332 0.733686428 ELVHYQQSPGEDTSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELVHYQQSPGEDTSLR 16 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q9ULV0 MYO5B Unconventional myosin-Vb 0 226.74 5.67E-15 357420000 259880 281190 213720 322500 280210 300060 294460 296440 303810 346830 FALSE TRUE 249723.6023 273170.7365 252343.9582 339144.2636 289223.2091 306127.4188 298063.6896 290318.4104 269322.7625 323338.8952 0.772327753 0.844843415 0.780431807 1.048881742 0.894489384 0.946769545 0.921830606 0.897876546 0.832942669 1 18.30268754 3.776973646 24.99586963 0.926810337 0.803765195 0.523787448 0.05881706 457.2013217 297505.4571 0.014568897 0.026263687 5983.752836 -3.776973646 -0.123045142 QVS(ph)ASELHTSGILGPETLR ddPTM_BT-474_Pertuzumab_2h_R1 9 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 QVS(0.982)AS(0.018)ELHTSGILGPETLR;QVS(0.87)AS(0.129)ELHT(0.001)SGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.967)AS(0.033)ELHTSGILGPETLR;QVS(0.993)AS(0.007)ELHTSGILGPETLR;QVS(0.993)AS(0.007)ELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.908)AS(0.092)ELHTSGILGPETLR 260.33 4.40E-31 19648190000 2034945 3485624 1997169 4299809 3992850 3589813 3661450 3521941 2225068 2833852 TRUE FALSE 1955417.1 3386217.416 2358101.865 4521722.658 4121283.646 3662401.478 3706259.92 3449211.688 1972487.609 2641912.68 0.740152055 1.281729499 0.892573734 1.711533728 1.559962098 1.386268935 1.402869954 1.305573691 0.746613476 1 21.33315135 3.778121544 24.98765401 1.332805453 1.002509481 0.211861185 0.285798184 818.4249036 516934.6737 0.072814005 0.13126518 5999.589602 -3.778121544 -0.330295972 GSESDKHFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSESDKHFR 9 1 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YGE5;A0A2R8YD53;A0A2R8Y4Q3;A0A2R8YE54;A0A2R8Y4G4;A0A2R8Y5G3;C9JY58 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 118.18 0.00061987 88193000 127260 163940 104070 168210 127280 171090 169050 134780 155870 142170 FALSE TRUE 122286.5385 159264.5917 122877.764 176891.3383 131374.0768 174549.557 171118.8845 131996.7459 138176.2911 132540.6993 0.922633872 1.201627821 0.927094581 1.334619021 0.991198006 1.316950627 1.291066709 0.995895952 1.042519708 1 17.01607591 3.778467946 24.99986604 1.140432492 1.035569736 0.122256129 0.147011698 1296.623636 812263.1427 0.036851752 0.066434004 6004.376912 -3.778467946 -0.104862756 NAPWTLTPEFLAEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 NAPWTLTPEFLAEHR 15 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;H7BZN1 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 106.6 0.0012233 353120000 621720 623170 502590 517130 521760 468330 542280 607310 609970 598480 FALSE TRUE 597422.4951 605397.8017 593419.1931 543819.1413 538542.8843 477799.9535 548916.5849 594768.8363 540728.7628 557944.4165 1.070756293 1.085050381 1.063581202 0.974683365 0.965226765 0.856357622 0.983819478 1.066000158 0.9691445 1 19.08976188 3.778624152 4.514244969 0.976996656 1.076531042 0.470414135 0.048390186 0.218402532 10.42420136 0.014660468 0.026560703 6006.536938 -3.778624152 0.099534386 EELGLIEQAYDNPHEALSR ddPTM_BT-474_Pertuzumab_2h_R1 6 EELGLIEQAYDNPHEALSR 19 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;;; 327.42 3.59E-75 2511870000 1816280 1977380 1584580 2038490 2017980 2047590 2116020 2111500 2297320 2229350 FALSE TRUE 1745297.77 1920987.058 1870948.855 2143696.713 2082890.159 2088993.673 2141916.486 2067896.787 2036537.865 2078354.139 0.839749943 0.924282836 0.900206957 1.031439577 1.002182506 1.005119211 1.03058302 0.994968446 0.979880102 1 20.98701007 3.778867608 7.158948039 1.006642477 0.890996844 0.83206898 0.024331669 0.091237207 13.53911317 0.006075899 0.010907041 6009.905008 -3.778867608 -0.115645633 GADFLVTEVENGGSLGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 GADFLVTEVENGGSLGSK 18 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 297.72 5.00E-49 685070000 1041380 967400 849300 1030630 1023610 1106570 1057710 1156570 1262820 1099810 FALSE TRUE 1000681.718 939810.6992 1002787.403 1083820.938 1056535.345 1128945.604 1070654.571 1132686.425 1119469.968 1025318.889 0.975971211 0.916603321 0.978024899 1.057057418 1.030445607 1.10106779 1.044216178 1.104716237 1.091826143 1 19.96764125 3.778880901 2.262948969 1.069785391 0.944279597 0.665295384 0.034113724 0.15939429 1.590958411 0.009093203 0.018797693 6010.088964 -3.778880901 -0.125505793 KQLDKEQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQLDKEQVR 9 2 O76021;J3QSV6;I3L3U9;I3L1A3 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 78.655 0.016399 351430000 464390 449450 355510 233780 278580 108240 348260 295140 301310 326320 FALSE TRUE 446241.1254 436632.1261 419758.5653 245845.4138 287540.7787 110428.687 352522.1101 289045.2559 267106.552 304218.0557 1.466846287 1.435260392 1.379795043 0.808122362 0.945179858 0.36299189 1.158781024 0.950125249 0.878010187 1 18.21474626 3.779007332 5.678404968 0.874000799 1.435173342 0.632676661 0.194036997 0.128961314 11.2120932 0.050807555 0.091346514 6011.838871 -3.779007332 0.561172543 NEFISEYCGELISQDEADRR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEFISEYCGELISQDEADRR 20 1 A0A0A0MSY9;Q92800-5;Q92800-4;Q92800-3;Q92800;Q92800-2 A0A0A0MSY9 EZH1 Histone-lysine N-methyltransferase EZH1 0 78.708 0.013573 48334000 29737 29657 24257 34173 34483 32028 28870 32651 34292 37388 FALSE TRUE 28574.84516 28811.2114 28640.77949 35936.67263 35592.17701 32675.6281 29223.3197 31976.74544 30399.31592 34855.67746 0.819804613 0.826585896 0.821696251 1.03101346 1.021129974 0.937454971 0.838409173 0.917404216 0.872148188 1 15.08910605 3.779665834 23.99051911 0.93701497 0.823084504 0.476224267 0.058496743 321.3601018 187556.1117 0.016513413 0.029769431 6020.961275 -3.779665834 -0.113930466 RRHT(ph)MDKDSR ddPTM_BT-474_Pertuzumab_2h_R1 5 RRHTMDKDSR 10 3 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 RRHT(1)MDKDSR;RRHT(1)MDKDSR;RRHT(1)MDKDSR;RRHT(1)MDKDSR;RRHT(1)MDKDSR 162.41 3.59E-06 1033250000 445631 441475 315445 224661 237598 117148 243997 189993 231579 241404 TRUE FALSE 428215.2478 428884.5652 372452.9285 236255.7811 245240.5555 119516.8128 246983.1083 186069.5782 205291.1228 225053.4921 1.90272652 1.905700557 1.654952896 1.049776118 1.089698956 0.531059579 1.097441795 0.826779342 0.912188124 1 17.77990843 3.779850526 1.785484529 0.887274539 1.93027753 0.885071593 0.149841074 0.10224206 0.62935777 0.041136179 0.094606768 6023.522354 -3.779850526 1.043002991 S(ph)PDPYR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPDPYR 6 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-6 P18583-7 SON Protein SON 1 S(1)PDPYR;S(1)PDPYR 97.033 0.043565 1013600000 703060 723640 566930 750240 671360 707570 730200 756730 806450 800370 TRUE FALSE 675583.6379 703002.4957 669386.8623 788959.9763 692954.9041 721877.5502 739136.406 741103.2611 714905.1769 746160.227 0.905413628 0.942160236 0.897108742 1.057359998 0.928694507 0.967456485 0.990586712 0.993222681 0.958112147 1 19.50912594 3.77992158 24.99999949 0.982745642 0.917620791 0.483744678 0.033121459 433.3393361 261923.933 0.008027023 0.014470758 6024.507921 -3.77992158 -0.065124851 DKEVEFGGPAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKEVEFGGPAPR 12 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 66.215 0.053495 324780000 493270 500910 436810 405010 461610 446520 491350 486930 518880 506970 FALSE TRUE 473992.4631 486624.5372 515751.2838 425912.6146 476458.1049 455548.9403 497363.2883 476874.7253 459978.9177 472632.4703 1.002877485 1.02960454 1.09123117 0.901149712 1.008094312 0.963854515 1.052325685 1.008975801 0.9732275 1 18.85035922 3.77996228 24.99997834 0.992144461 1.040074375 0.253008951 0.042154071 788.8631072 476344.3472 0.01078968 0.019451144 6025.072537 -3.77996228 0.047929914 STELDSNWSWFQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 STELDSNWSWFQLR 14 0 Q9NP61;Q9NP61-2;B0QYV9;B0QYV8 Q9NP61 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 0 104.41 0.0053312 0 59930 73433 55855 47418 54433 44396 65875 67633 56357 62886 FALSE TRUE 57587.86934 71338.76274 65949.24099 49865.24866 56183.88688 45293.71754 66681.19796 66236.35492 49959.58963 58626.67521 0.982281003 1.216831118 1.124901604 0.85055563 0.958333159 0.772578649 1.137386654 1.12979893 0.852164812 1 15.83926962 3.78131747 24.12921886 0.975536233 1.118887367 0.229451924 0.122967418 527.5776632 297728.489 0.033702125 0.060756608 6043.902788 -3.78131747 0.143351135 YTIENPR ddPTM_BT-474_Pertuzumab_2h_R1 1 YTIENPR 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 94.262 0.033338 162010000 185460 193140 150980 232120 213840 210400 183830 224890 219780 240480 FALSE TRUE 178212.0182 187631.8363 178265.4445 244099.741 220718.3578 214654.4322 186079.7665 220245.9429 194831.4958 224192.0754 0.79490775 0.836924481 0.795146056 1.088797365 0.984505618 0.957457715 0.830001534 0.98239843 0.869038281 1 17.77437576 3.781359679 24.99277991 0.953059993 0.811785861 0.505537044 0.067744862 414.000479 241756.8346 0.017508688 0.031563983 6044.490216 -3.781359679 -0.141274132 GCRLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 GCRLSPR 7 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR 55.064 0.078661 1168990000 910870 927020 701330 409193 498650 155371 646260 461300 478330 575590 TRUE FALSE 875272.1934 900582.2972 828075.932 430311.4998 514689.5301 158512.7081 654169.1232 451773.9938 424031.9837 536604.7766 1.631130082 1.678297206 1.543176595 0.80191515 0.959159427 0.295399361 1.219089266 0.841911987 0.790212839 1 19.03350037 3.781414125 4.561149727 0.841041351 1.641187862 0.720279607 0.22125008 0.10486524 5.05044006 0.056428493 0.102425963 6045.248035 -3.781414125 0.800146511 DFQQLLQGISEDVPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFQQLLQGISEDVPHR 16 0 G5E9X1;B3KQH5;Q9UL03-3;Q9UL03 G5E9X1 INTS6 Integrator complex subunit 6 0 ; 125.45 7.70E-05 40859000 48136 49215 39832 53849 53985 54387 49898 48690 53975 59361 FALSE TRUE 46254.7919 47811.43639 47030.52846 56628.15334 55721.47655 55486.7424 50508.66665 47684.53448 47847.98428 55340.4266 0.835822829 0.863951352 0.849840367 1.023269187 1.006885562 1.002643923 0.912690229 0.861658238 0.864611772 1 15.75604614 3.781982144 24.18309068 0.944153356 0.851279404 0.411025411 0.055909241 406.6208903 226460.7774 0.016771878 0.030235616 6053.159868 -3.781982144 -0.092873952 LKDEIAEVANEIENLGSTEER ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDEIAEVANEIENLGSTEER 21 1 K7ENQ8;Q15438-2;Q15438;K7ERV8 K7ENQ8 CYTH1 Cytohesin-1 0 64.87 0.022352 11559000 16631 16341 13564 15870 15651 17886 16587 16032 19005 17449 FALSE TRUE 15981.04213 15874.97068 16015.31653 16689.0526 16154.42863 18247.66717 16789.99667 15700.9336 16847.63208 16267.16369 0.982411098 0.975890511 0.984518066 1.025935001 0.993069778 1.121748544 1.03214039 0.965191837 1.035683442 1 13.98967511 3.782667063 4.415398256 1.023087587 0.97942613 0.213891259 0.03847629 0.376638497 16.58898465 0.010880401 0.019808997 6062.713741 -3.782667063 -0.043661457 T(ph)HT(ph)GQY(ph)S(ph)ALSVACGPSGEAGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 THTGQYSALSVACGPSGEAGPR 22 0 Q8N9L1-2 Q8N9L1-2 4 T(0.659)HT(0.695)GQY(0.689)S(0.708)ALS(0.686)VACGPS(0.563)GEAGPR 46.307 0.060061 381230000 6944.4 9599.7 7037.6 12316 9472.1 19654 11398 13084 11669 11444 TRUE FALSE 6673.005171 9325.925955 8309.450871 12951.63024 9776.778699 20051.41735 11537.49213 12813.81083 10344.38404 10668.88769 0.625464 0.874123548 0.778848847 1.213962563 0.916382193 1.87942904 1.081414715 1.201044683 0.969584116 1 13.38112215 3.782668395 1.668007867 1.214252642 0.723375914 0.340594976 0.263128033 0.423914491 2.269860819 0.076068482 0.182217325 6062.732343 -3.782668395 -0.490876727 LKPGGVGAPSSSSPS(ph)PSPSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPSSSS(0.005)PS(0.994)PSPSAR 142.2 1.21E-08 0 137620 121720 117900 134570 151150 145160 144010 160600 171210 170000 TRUE FALSE 132241.6583 118248.6648 139207.1527 141515.1738 156011.877 148095.2347 145772.4375 157283.5539 151774.9586 158485.7486 0.834407254 0.746115445 0.878357543 0.8929205 0.984390574 0.934438812 0.919782623 0.992414493 0.957656824 1 17.27399359 3.783000551 1.592696755 0.961799745 0.790169171 0.77659773 0.035713325 0.166817218 0.812273878 0.010082245 0.024830602 6067.370993 -3.783000551 -0.171630574 KYEPPVPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYEPPVPTR 9 1 P62191 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 120.06 0.0011641 191170000 696120 733240 579120 739790 705500 705960 723540 767830 776980 780720 FALSE TRUE 668914.8608 712328.7131 683779.8665 777970.6506 728193.0482 720234.9949 732394.899 751974.0422 688780.4878 727841.139 0.919039643 0.978687072 0.939463064 1.068874249 1.000483497 0.989549719 1.00625653 1.033156828 0.946333548 1 19.47326407 3.783508842 24.99370359 1.008318237 0.949025611 0.422365978 0.032378356 417.4679365 232133.7523 0.007963911 0.014357118 6074.476305 -3.783508842 -0.059292626 DLLDLLVEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLDLLVEAK 10 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ; 175.73 6.31E-06 106482000 438520 473710 364890 408880 478440 468350 463240 504810 547250 559670 FALSE TRUE 421382.1536 460200.2546 430833.7399 429982.3458 493829.4571 477820.3579 468909.2697 494385.4971 485128.4743 521763.0524 0.807612098 0.882010047 0.825726808 0.824095044 0.946463064 0.915780364 0.898701561 0.947528758 0.929786945 1 18.99303526 3.784013465 0.183513318 1.022282991 0.703643135 0.729057841 0.031076149 6.025083492 0.29480703 0.100846332 0.469671006 6081.538567 -3.784013465 -0.318639855 IMFNRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IMFNRPK 7 1 A0A0C4DGA2;O75521-2;O75521;F1LLU7;F8WAW4;C9JB63 A0A0C4DGA2 ECI2 "Enoyl-CoA delta isomerase 2, mitochondrial" 0 86.113 0.018528 263310000 200660 255360 188740 320330 271550 380400 319770 369660 343510 325940 FALSE TRUE 192817.9854 248077.3828 222849.5165 336862.2697 280284.6524 388091.9486 323683.4409 362026.3918 304516.1849 303863.7935 0.634553999 0.816409813 0.733386212 1.108596275 0.922402268 1.277190494 1.065225433 1.191410098 1.002146986 1 18.21306526 3.784328262 1.359382702 1.111313782 0.685880759 0.672613373 0.109717979 0.242479914 0.848894778 0.031623659 0.086524023 6085.948352 -3.784328262 -0.425433023 RKEDQDRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 RKEDQDRSPR 10 3 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 RKEDQDRS(1)PR;RKEDQDRS(1)PR 109 0.011478 780200000 606670 609350 496640 521090 534600 550560 537300 598040 613840 639070 TRUE FALSE 582960.6657 591971.9346 586393.8957 547983.5173 551795.8945 561692.7004 543875.6381 585690.265 544159.4566 595785.2197 0.978474535 0.993599564 0.984237065 0.919766888 0.9261658 0.942777165 0.912871988 0.983056051 0.913348366 1 19.18443281 3.78477468 11.58821753 0.941920622 0.986284923 0.336945468 0.027538963 1.275320033 317.5345062 0.006735395 0.012135929 6092.207402 -3.78477468 0.044364301 MEITIRNS(ph)PYR ddPTM_BT-474_Pertuzumab_2h_R1 4 MEITIRNSPYR 11 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;Q9UQ88-9;A0A087X1I0;A0A087WYI9 P21127-2 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 MEITIRNS(1)PYR;MEITIRNS(1)PYR;MEIT(0.055)IRNS(0.944)PYR;MEIT(0.047)IRNS(0.952)PYR 183.28 3.28E-06 1328370000 2204350 2472710 1686730 1295010 1519610 684417 1652610 1200920 1259190 1394870 TRUE FALSE 2118201.565 2402190.732 1991559.632 1361845.621 1568489.636 698256.3807 1672835.136 1176120.582 1116252.03 1300394.212 1.628891873 1.847278855 1.531504534 1.047255985 1.206164731 0.536957466 1.286406168 0.904433879 0.858395108 1 20.31051761 3.785055949 2.047598097 0.960369828 1.750971502 0.728092745 0.196841664 0.157664784 1.282730813 0.052910658 0.114546115 6096.154268 -3.785055949 0.790601674 NDLNHSTQFVQGLALCTLGCMGSSEMCR ddPTM_BT-474_Pertuzumab_2h_R1 1 NDLNHSTQFVQGLALCTLGCMGSSEMCR 28 0 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9;H3BN71;B4DGE1;H3BRM7 O43747 AP1G1 AP-1 complex subunit gamma-1 0 145.67 9.35E-08 64016000 70342 101570 78063 119320 142710 135080 186780 96617 105200 140940 FALSE TRUE 67592.95687 98673.32305 92170.7206 125478.1195 147300.3968 137811.4102 189065.8695 94621.82519 93258.13703 131394.0083 0.514429522 0.750972775 0.701483438 0.954975962 1.121058705 1.048840902 1.438923068 0.720138052 0.709759435 1 17.00353996 3.785905984 2.47631305 1.008877895 0.640070247 0.387289953 0.200047877 0.331912792 3.984615235 0.058730193 0.118520403 6108.097822 -3.785905984 -0.368807648 NDHSAYKR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDHSAYKR 8 1 Q7L576;Q96F07;Q96F07-2;E7EVJ5;A0A087WTQ3;A0A087WWZ1;A0A0G2JR96;A0A0G2JQT1 Q7L576;A0A0G2JR96 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 ; 108.98 0.0024063 181831000 280630 311990 215526 216168 201824 193867 248020 145555 280370 243120 FALSE TRUE 269662.6693 303092.3507 254476.3425 227324.4564 208315.8523 197787.1236 251055.343 142549.2384 248543.573 226653.2659 1.189758587 1.337251195 1.122756125 1.00296131 0.919094863 0.872641843 1.107662588 0.628930882 1.096580594 1 17.79012742 3.786398278 1.804339067 0.908399091 1.266185389 0.472966296 0.133565484 0.273532982 1.719642739 0.037933277 0.087382901 6115.02558 -3.786398278 0.357786298 RKDDSYFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RKDDSYFDR 9 2 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 ; 208.63 5.48E-06 778960000 391390 400940 316150 332130 331550 269970 381600 373640 358100 398680 FALSE TRUE 376094.0461 389505.5838 373285.3377 349271.2691 342214.6069 275428.9784 386270.1349 365924.2034 317449.9893 371677.0485 1.011883967 1.047967813 1.004327115 0.939717076 0.920731071 0.741043816 1.039262813 0.984521925 0.854101674 1 18.50369008 3.78677543 2.945990375 0.92663187 1.029492069 0.242195334 0.078670248 0.405640243 6.999603996 0.022184038 0.04277854 6120.338323 -3.78677543 0.102860199 QHIIPLENVTIDSIKDEGDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QHIIPLENVTIDSIKDEGDLR 21 1 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 0 132.83 6.55E-06 136640000 192160 166640 132950 135670 126710 122160 116730 88229 157860 161130 FALSE TRUE 184650.1748 161887.5904 156977.0225 142671.945 130785.7422 124630.1589 118158.5767 86407.04032 139940.3946 150216.5216 1.229226804 1.077694974 1.045005042 0.949775321 0.870648187 0.829670116 0.786588422 0.575216623 0.931591233 1 17.19668397 3.787434367 0.802238289 0.770506734 1.225591868 0.572533908 0.111319485 0.586202903 0.646078055 0.048601302 0.189354665 6129.631512 -3.787434367 0.455085134 AMQHAEVYYK ddPTM_BT-474_Pertuzumab_2h_R1 1 AMQHAEVYYK 10 0 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 93.258 0.0089085 288770000 427330 406980 306390 335050 308560 185370 347490 329010 369600 389200 FALSE TRUE 410629.4712 395373.3289 361761.4886 352341.9707 318485.1126 189118.3084 351742.6866 322215.8285 327644.5575 362839.1373 1.13171218 1.089665607 0.997029955 0.971069365 0.877758433 0.521218052 0.969417713 0.888040444 0.90300225 1 18.46897055 3.787555872 1.51710522 0.852872663 1.113277106 0.382292502 0.124491214 0.439493758 1.934273649 0.038590598 0.098505658 6131.346676 -3.787555872 0.260404443 RLDINEGAARPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLDINEGAARPR 12 2 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ;;; 194.06 1.13E-06 5511060000 1596440 1627790 1304670 1627050 1604880 1641770 1688240 1643010 1594030 1684190 FALSE TRUE 1534049.36 1581367.023 1540452.891 1711022.245 1656502.423 1674967.714 1708901.186 1609081.269 1413082.397 1570118.311 0.977027877 1.007164245 0.981106252 1.089740966 1.055017581 1.066778027 1.088390075 1.024815301 0.899984662 1 20.58244184 3.787630588 24.99794855 1.038100012 0.990305909 0.119592527 0.052491526 770.5597502 392547.6854 0.013757043 0.02480081 6132.401601 -3.787630588 -0.047794104 KCGHTNNLRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KCGHTNNLRPK 11 2 M0R2S1;P62987 M0R2S1 UBA52 Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40 0 ; 177.44 4.79E-06 547940000 812370 720360 650910 558720 685570 632260 645030 731070 787680 741480 FALSE TRUE 780621.6823 699816.0381 768543.9164 587555.6062 707621.9817 645044.7304 652924.0701 715973.149 698265.8686 691258.8992 1.129275418 1.012379065 1.111803287 0.849979084 1.023671424 0.93314492 0.944543457 1.035752523 1.010136534 1 19.39886662 3.78764314 24.99983458 0.975180423 1.077275268 0.437865381 0.058606341 382.0978572 194617.4522 0.014562521 0.026252911 6132.578836 -3.78764314 0.102094845 AKVEEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AKVEEAR 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 114.89 0.0052918 487310000 1796130 1812350 1450670 1470610 1496910 1021230 1748290 1653100 1867840 1897070 FALSE TRUE 1725935.254 1760663.552 1712838.339 1546508.358 1545059.47 1041879.97 1769686.096 1618962.907 1655810.634 1768579.759 0.975887712 0.995523975 0.968482383 0.874435179 0.87361594 0.589105447 1.000625551 0.915402825 0.936237467 1 20.75415985 3.787892579 4.273350732 0.877447822 0.984423265 0.138537447 0.108867825 0.425250405 16.82071396 0.029372904 0.053824442 6136.102123 -3.787892579 0.106975443 WGDIEFPPPFGR ddPTM_BT-474_Pertuzumab_2h_R1 1 WGDIEFPPPFGR 12 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 99.653 0.0085501 286260000 301190 301820 260730 340170 365110 354590 401020 335910 389870 427950 FALSE TRUE 289419.1618 293212.3891 307849.7109 357726.2145 376854.0947 361760.0527 405927.8027 328973.3411 345613.5921 398964.5653 0.725425732 0.734933412 0.771621687 0.896636558 0.944580365 0.906747326 1.017453273 0.824567818 0.866276412 1 18.60590109 3.787995054 2.758081177 0.917733293 0.732380304 0.701486867 0.053852628 0.158784488 2.383136102 0.015052132 0.029514816 6137.550151 -3.787995054 -0.185352988 RAS(ph)WASENGETDAEGTQMTPAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RASWASENGETDAEGTQMTPAK 22 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 RAS(0.945)WAS(0.054)ENGET(0.001)DAEGTQMTPAK;RAS(1)WASENGETDAEGTQMTPAK 254.27 2.92E-37 1134210000 487510 499110 446250 540940 585010 636530 625940 609890 690050 664290 TRUE FALSE 468457.5702 484875.8715 526897.3018 568857.9782 603827.3779 649401.0727 633600.441 597295.5584 611718.4169 619297.0466 0.756434368 0.782945558 0.85079899 0.918554321 0.9750206 1.048609995 1.023096177 0.964473449 0.987762529 1 19.24027204 3.788653232 1.264100217 1.00189854 0.755419845 0.944922015 0.022551323 0.117605541 0.352563477 0.008270295 0.023960352 6146.858728 -3.788653232 -0.246478696 LSYLSAPGS(ph)EYSMYSTDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSYLSAPGSEYSMYSTDSR 19 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 LSYLSAPGS(0.988)EYS(0.012)MYSTDSR;LSYLS(0.001)APGS(0.411)EY(0.338)S(0.071)MY(0.086)S(0.031)T(0.031)DS(0.031)R 138.66 1.56E-06 191202000 131332 137647 112225 144319 135923 149103 153663 156754 146381 158695 TRUE FALSE 126199.4002 133721.4423 132506.5539 151767.3209 140295.0867 152117.9648 155543.5738 153516.9751 129764.4426 147946.4463 0.85300731 0.903850317 0.89563864 1.025826065 0.948282911 1.028196139 1.051350523 1.037652333 0.877104154 1 17.17471552 3.788755107 6.113780846 1.002014741 0.884786917 0.508148025 0.04992035 0.172055784 15.44665446 0.012997304 0.023496307 6148.300803 -3.788755107 -0.117227824 YDQDLCYTDILFTEQER ddPTM_BT-474_Pertuzumab_2h_R1 3 YDQDLCYTDILFTEQER 17 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;; 190.86 6.40E-10 164813000 107828 110030 87768 123082 112799 123986 115581 116405 115748 120451 FALSE TRUE 103613.9625 106892.0521 103629.63 129434.2768 116427.2823 126493.0819 116995.5149 114001.1961 102608.7723 112292.7465 0.922712871 0.951905225 0.922852395 1.152650379 1.03681926 1.126458171 1.041879538 1.015214247 0.913761356 1 16.77690521 3.789518386 24.9986075 1.043249367 0.934431577 0.387802915 0.06239862 373.0746837 183019.7636 0.016271409 0.029333662 6159.116039 -3.789518386 -0.10881779 KEEVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEEVSR 6 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 117.02 0.037006 339650000 604000 545330 469890 546300 539830 573450 602980 582270 594670 588390 FALSE TRUE 580395.0122 529777.7223 554809.5756 574494.6085 557194.1222 585045.5519 610359.4496 570245.921 527165.5547 548537.8212 1.058076562 0.965799808 1.011433586 1.047319959 1.015780682 1.066554628 1.112702581 1.039574481 0.961037752 1 19.06523157 3.79055181 6.06492937 1.04150523 1.006745586 0.036380087 0.043495782 0.510242704 43.86205483 0.011393234 0.020618498 6173.789386 -3.79055181 -0.034759644 NAFMMLIHADQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 NAFMMLIHADQDR 13 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 103.21 0.0016283 1552370000 1507500 1485020 1107450 1067950 1158510 697660 1114520 961240 1277000 1409820 FALSE TRUE 1448585.233 1442668.684 1307590.85 1123067.027 1195774.526 711767.1632 1128159.829 941390.0581 1132040.314 1314331.636 1.102145908 1.097644342 0.994871321 0.854477665 0.909796655 0.54154305 0.858352488 0.716250018 0.861304927 1 20.32589792 3.790557141 1.395089859 0.78346144 1.114324831 0.493209122 0.116144917 0.327709996 1.210063597 0.03388498 0.091799349 6173.865174 -3.790557141 0.330863391 LETLGSASTST(ph)PGRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LETLGSASTSTPGRR 15 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 LETLGSASTS(0.003)T(0.997)PGRR;LETLGSASTS(0.014)T(0.985)PGRR 186.97 2.11E-07 917180000 423490 389860 315600 276950 266540 268860 238699 420070 216491 245580 TRUE FALSE 406939.5426 378741.5745 372635.9405 291243.4227 275113.5012 274296.5334 241620.2698 411395.4077 191915.8493 228946.6479 1.777442677 1.65427875 1.62761038 1.272101712 1.201648959 1.198080583 1.055356224 1.796905137 0.838255773 1 17.80465192 3.791454152 3.074522867 1.248935759 1.70559989 0.458643839 0.241106033 0.267620098 5.039014594 0.066426164 0.127458287 6186.630131 -3.791454152 0.456664131 VPAFEGDDGFCVFESNAIAYYVSNEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPAFEGDDGFCVFESNAIAYYVSNEELR 28 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 176.68 4.20E-14 42737000 23102.2 19633.9 17808.9 23959.6 21884.7 25211 23431.7 26118 27387 26282.8 FALSE TRUE 22199.34048 19073.9604 21027.36439 25196.15783 22588.64125 25720.78369 23718.46415 25578.65417 24278.14258 24502.64255 0.90599781 0.778445033 0.85816721 1.028303693 0.921885923 1.049714685 0.967996171 1.043914105 0.990837724 1 14.58064973 3.793045903 5.625218127 1.001590212 0.838122551 0.701415771 0.04564299 0.102278534 7.251107631 0.011007554 0.019980607 6209.346602 -3.793045903 -0.163467661 ELTPAS(ph)PTCTNSVSK ddPTM_BT-474_Pertuzumab_2h_R1 6 ELTPASPTCTNSVSK 15 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 ELTPAS(0.87)PT(0.129)CT(0.001)NSVSK;ELTPAS(0.966)PT(0.034)CTNSVSK;ELTPAS(1)PTCTNSVSK;ELTPAS(0.998)PT(0.002)CTNSVSK;ELTPAS(0.995)PT(0.005)CTNSVSK;ELTPAS(0.998)PT(0.002)CTNSVSK 321.25 1.31E-56 4635640000 4591690 4435690 3765800 4580170 4556640 4801390 4789260 4977580 5286640 5240410 TRUE FALSE 4412241.678 4309188.464 4446363.83 4816553.123 4703208.464 4898477.395 4847872.397 4874791.234 4686522.791 4885472.363 0.903135122 0.882041314 0.910119534 0.985893024 0.962692676 1.002661981 0.992303719 0.997813696 0.959277311 1 22.22006663 3.793217229 3.302673236 0.987189001 0.892711779 0.880860404 0.014793598 0.072818424 1.593705091 0.003886046 0.007369863 6211.796632 -3.793217229 -0.094477222 TDVSNFDEEFTGEAPTLS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDVSNFDEEFTGEAPTLSPPR 21 0 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFTGEAPT(0.002)LS(0.998)PPR;TDVSNFDEEFTGEAPT(0.004)LS(0.996)PPR 214.02 5.84E-24 352370000 166382 171093 140361 174899 174156 174461 174930 189719 203539 194844 TRUE FALSE 159879.6075 166213.5952 165727.355 183925.5583 179757.8859 177988.721 177070.8457 185801.2364 180434.106 181647.0423 0.880166313 0.915036067 0.912359226 1.012543645 0.98959985 0.979860276 0.974807205 1.022869594 0.993322565 1 17.47077835 3.793275352 5.519190211 0.996452721 0.902261862 0.880967544 0.015783781 0.069031276 4.685517188 0.004299125 0.007808901 6212.628033 -3.793275352 -0.094190859 QLVEILTTHCDSYWVEMASLQVFEK ddPTM_BT-474_Pertuzumab_2h_R1 3 QLVEILTTHCDSYWVEMASLQVFEK 25 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;A0A0G2JLQ8;F5H5B1;K7ELX1;K7EJ90;F5H7Q5 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;; 179.47 2.73E-17 213369000 141248 146441 120715 117642 132124 130912 138303 120223 161438 158416 FALSE TRUE 135727.872 142264.6461 142530.8858 123713.5177 136373.8885 133559.1303 139995.5935 117740.353 143112.235 147686.3432 0.919027914 0.96328911 0.965091847 0.837677439 0.923402161 0.904343133 0.947925112 0.797232503 0.969028225 1 17.1721769 3.793360119 24.99978971 0.899289818 0.950551601 0.055365157 0.057928849 603.1590519 275161.6423 0.014364582 0.025896113 6213.840751 -3.793360119 0.051261783 ESAEQSSGPGPSLRPQNSTTWR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESAEQSSGPGPSLRPQNSTTWR 22 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 0 217.02 1.18E-25 253220000 90821 105890 89116 75038 94031 88120 93201 90386 109560 106650 FALSE TRUE 87271.61491 102870.1209 105221.2436 78910.72017 97055.59251 89901.84678 94341.62172 88519.49751 97123.20811 99426.50051 0.877750041 1.034634834 1.058281676 0.793658831 0.976154164 0.904204074 0.948857913 0.890300846 0.97683422 1 16.60134281 3.793376378 24.99986059 0.923054114 0.994663368 0.141111264 0.070557392 509.3412516 232293.7235 0.016970188 0.030593426 6214.073383 -3.793376378 0.071609254 NLKPIKPMQFLGDEETVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLKPIKPMQFLGDEETVR 18 2 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ; 219.95 3.96E-19 13170400000 9189900 8519800 6884800 5746300 5955900 5789800 4398200 7048500 7878700 7108100 FALSE TRUE 8830748.548 8276823.646 8129036.512 6042867.232 6147476.933 5906873.723 4452026.487 6902946.012 6984343.006 6626662.056 1.332608857 1.249018522 1.226716625 0.911902128 0.927688311 0.891379955 0.67183545 1.041692779 1.053976036 1 22.65985092 3.793514637 3.712314505 0.918835712 1.28048155 0.697802362 0.103102065 0.13185127 3.712552587 0.028620308 0.053389044 6216.05197 -3.793514637 0.361645838 GLPGDVTNQEVHDLLSDYELK ddPTM_BT-474_Pertuzumab_2h_R1 3 GLPGDVTNQEVHDLLSDYELK 21 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 ;; 288.25 5.15E-46 341659000 508571 428275 423281 474079 529130 503718 533225 522582 627420 593134 FALSE TRUE 488695.4831 416061.0163 499777.2925 498546.274 546149.947 513903.5231 539750.7671 511790.4991 556197.912 552960.5059 0.883780085 0.752424471 0.903820955 0.901594723 0.987683462 0.9293675 0.976110882 0.925546207 1.005854679 1 19.07681692 3.794458951 1.808882828 0.96165047 0.820477269 0.625452163 0.043780668 0.211985018 1.339043329 0.01157785 0.026871706 6229.582631 -3.794458951 -0.141173201 REDS(ph)FESLDSLGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 REDSFESLDSLGSR 14 1 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 REDS(0.715)FES(0.273)LDS(0.012)LGSR;REDS(0.954)FES(0.045)LDSLGS(0.001)R 175.38 2.53E-06 1167430000 835910 884160 729800 969040 964700 967370 1023580 1087160 1029360 1124180 TRUE FALSE 803241.7131 858944.6225 861691.0943 1019052.271 995730.4516 986930.8842 1036106.878 1064709.766 912511.3682 1048038.287 0.766424016 0.819573705 0.822194289 0.972342597 0.950089766 0.941693539 0.988615484 1.015907318 0.870685145 1 19.99925999 3.794541194 3.66332142 0.967314702 0.798177297 0.772753098 0.039831377 0.105270591 2.872014851 0.010605914 0.019832564 6230.762449 -3.794541194 -0.169137405 DVDREDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVDREDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 101.54 0.0081925 476270000 725540 732050 599070 730240 716240 805870 738190 652990 886160 856650 FALSE TRUE 697185.0947 711172.6508 707335.2752 767927.7739 739278.5101 822165.2435 747224.19 639505.5283 785566.8319 798628.3325 0.872978163 0.890492638 0.88568768 0.96155839 0.925685303 1.029471671 0.935634462 0.800754872 0.983645082 1 19.60716473 3.79537256 10.8141612 0.933483289 0.883730882 0.175182608 0.058983062 1.984836152 372.656058 0.016807799 0.030313172 6242.701361 -3.79537256 -0.049752407 KAMEAVAAQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAMEAVAAQGK 11 1 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 ; 102.66 0.0038046 346630000 1819120 1767040 1438660 1400670 1460790 1334000 1551730 1597960 1802820 1496690 FALSE TRUE 1748026.779 1716645.749 1698657.865 1472958.747 1507777.637 1360974.394 1570720.536 1564961.568 1598171.432 1395317.853 1.252780343 1.230290106 1.217398502 1.055643876 1.080597968 0.975386641 1.125708047 1.121580695 1.145381626 1 20.41216237 3.795553947 5.255341873 1.079268601 1.236084343 0.673053411 0.05145029 0.134795735 8.033585889 0.013974189 0.025455404 6245.309229 -3.795553947 0.156815742 (ac)VDYIVEYDYDAVHDDELTIR ddPTM_BT-474_Pertuzumab_2h_R1 3 VDYIVEYDYDAVHDDELTIR 20 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ;; 82.102 1.10E-06 0 14765.4 13395 11708.5 15353.1 12662.3 17456.6 16122.2 17116 14515.6 17722.9 FALSE TRUE 14188.35184 13012.98772 13824.4864 16145.47533 13069.59438 17809.58441 16319.50831 16762.54862 12867.84994 16522.5122 0.858728484 0.787591352 0.83670608 0.977180415 0.791017384 1.077898094 0.987713497 1.01452784 0.778807108 1 14.01214544 3.796291767 5.563382768 0.952625658 0.821559735 0.263074012 0.090894245 0.271181609 18.06848368 0.023211706 0.042213816 6255.928365 -3.796291767 -0.131065923 AVAHCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVAHCPK 7 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 61.837 0.089078 63555000 209850 223910 182530 186820 211200 187300 215610 198650 233480 242090 FALSE TRUE 201648.83 217524.306 215517.2314 196461.8026 217993.4398 191087.3343 218248.6997 194547.8081 206976.3292 225693.0287 0.893465036 0.963806048 0.954913108 0.87048237 0.965884685 0.846669192 0.967015689 0.862001849 0.917070104 1 17.78400233 3.796854589 24.9997777 0.911747945 0.940035859 0.016373671 0.050169741 774.9820618 332353.6759 0.011728054 0.02114305 6264.040966 -3.796854589 0.028287914 LSEVLQAVTDHDIPQQLVER ddPTM_BT-474_Pertuzumab_2h_R1 4 LSEVLQAVTDHDIPQQLVER 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;;; 246.22 5.09E-30 1822547000 1038230 1065263 855458 1146052 1153405 1118315 1135204 1019772 1164818 1167916 FALSE TRUE 997654.8238 1034882.742 1010058.29 1205199.881 1190505.319 1140928.096 1149096.966 998713.3518 1032592.744 1088812.009 0.916278307 0.950469625 0.927670049 1.106894368 1.09339841 1.047865092 1.055367645 0.917250493 0.948366417 1 20.05432345 3.796980122 24.99881102 1.020187355 0.93337223 0.36144201 0.05626766 360.2801789 154169.2393 0.016806782 0.030298849 6265.851853 -3.796980122 -0.086815124 QPNQPLRPADKEPEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPNQPLRPADKEPEPR 16 2 P78332;E9PGM9;F8WCA5;P78332-2;C9JSL1;F8WF63 P78332 RBM6 RNA-binding protein 6 0 76.85 0.014376 208120000 219630 201380 178470 218390 231040 234310 245540 223050 245950 252470 FALSE TRUE 211046.6168 195636.8396 210723.499 229661.1341 238471.6114 239047.9087 248544.992 218443.9396 218030.7871 235369.982 0.896659017 0.831188573 0.89528621 0.975745217 1.013177676 1.01562615 1.055975744 0.928087506 0.926332174 1 17.84457081 3.797125102 3.201039953 0.988526425 0.863837771 0.636290502 0.039795379 0.166931341 3.402597726 0.011533032 0.022062494 6267.943921 -3.797125102 -0.124688654 ANPHNYDAWFDYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ANPHNYDAWFDYLR 14 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 150.05 7.32E-06 186860000 133290 148140 113860 112550 111760 98015 154970 118490 128930 129580 FALSE TRUE 128080.8794 143915.1922 134437.0348 118358.719 115354.8619 99996.93046 156866.5692 116043.1401 114294.4069 120803.4312 1.060242066 1.191317091 1.112857752 0.979762891 0.954897231 0.827765648 1.298527432 0.960594736 0.946118879 1 16.88230191 3.797754271 5.637689373 1.001383571 1.130570658 0.197037232 0.1160152 0.359786321 24.20891596 0.030090896 0.054737052 6277.030959 -3.797754271 0.129187086 S(ph)YENLAAEIMPVEYR ddPTM_BT-474_Pertuzumab_2h_R1 5 SYENLAAEIMPVEYR 15 0 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 1 S(0.921)Y(0.079)ENLAAEIMPVEYR;S(0.999)Y(0.001)ENLAAEIMPVEYR;S(0.996)Y(0.004)ENLAAEIMPVEYR;S(0.992)Y(0.008)ENLAAEIMPVEYR;S(0.999)Y(0.001)ENLAAEIMPVEYR 181.63 6.09E-07 202961500 142388.3 143616 117982.8 151808.1 158988 149536.3 138267.5 160405.9 162197 157897.5 TRUE FALSE 136823.6078 139520.2123 139304.9165 159642.9342 164101.9934 152560.0264 139959.659 157093.4621 143785.0765 147202.9617 0.929489504 0.947808459 0.946345881 1.084508983 1.114800895 1.036392371 0.950793771 1.067189548 0.976781139 1 17.16744717 3.798129189 9.543160524 1.036004742 0.941630211 0.446591334 0.046696189 0.490177287 76.03480105 0.012454321 0.022476422 6282.452146 -3.798129189 -0.094374531 LQASLS(ph)SSDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQASLSSSDVR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 LQAS(0.006)LS(0.925)S(0.06)S(0.009)DVR;LQAS(0.001)LS(0.479)S(0.479)S(0.041)DVR;LQAS(0.031)LS(0.831)S(0.119)S(0.019)DVR;LQAS(0.007)LS(0.948)S(0.04)S(0.004)DVR 188.09 3.46E-06 2205810000 3017160 2922450 2202000 2239170 2280780 2056570 1578460 2742830 2093770 1888580 TRUE FALSE 2899246.052 2839104.587 2599950.383 2354733.832 2354143.36 2098155.254 1597777.666 2686189.602 1856094.007 1760664.794 1.646676903 1.612518519 1.476686756 1.337411777 1.337076409 1.19168354 0.90748544 1.525667811 1.054200671 1 20.74768884 3.798145942 0.850623768 1.177120484 1.700259922 0.592025748 0.158809727 0.660984816 0.825530524 0.065639762 0.252424295 6282.694497 -3.798145942 0.523139438 EGLELLK ddPTM_BT-474_Pertuzumab_2h_R1 5 EGLELLK 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;; 103.92 0.019235 954265000 2306290 2393200 1758410 1951924 1563476 1699256 1880184 2017831 2227920 2075320 FALSE TRUE 2216157.637 2324948.279 2076193.803 2052663.032 1613766.625 1733616.121 1903194.254 1976162.085 1975015.862 1934756.728 1.145445112 1.201674735 1.073103286 1.060941152 0.834092784 0.896038295 0.983686593 1.021400808 1.02080837 1 20.88372075 3.79984218 2.090805594 0.96493938 1.168296276 0.634544562 0.061871798 0.218275016 1.852148951 0.019000997 0.041380596 6307.280996 -3.79984218 0.203356896 LQTTDNLLPMSPEEFDEVS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 LQTTDNLLPMSPEEFDEVSR 20 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta 1 LQTTDNLLPMS(0.429)PEEFDEVS(0.571)R 50.531 0.089189 20151000 35293 35792 29224 40369 41304 40529 41216 35555 38142 38110 TRUE FALSE 33913.71054 34771.2472 34505.42688 42452.44893 42632.58067 41348.52415 41720.41374 34820.77683 33812.28006 35528.77576 0.954542053 0.97867845 0.971196619 1.194875084 1.199945108 1.163803798 1.174271076 0.980072521 0.95168717 1 15.11670036 3.800514715 13.88587959 1.098815355 0.969147593 0.309248448 0.086712808 3.381917188 756.0666726 0.02479282 0.044701808 6317.055833 -3.800514715 -0.129667762 KIQSLGDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KIQSLGDSK 9 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 122.51 0.00093603 898790000 1869220 1794470 1443180 1287140 1290910 704200 1734780 1428350 1787970 1896610 FALSE TRUE 1796168.816 1743293.473 1703994.729 1353569.45 1332433.293 718439.4065 1756010.757 1398854.073 1585007.141 1768150.915 1.015845876 0.98594156 0.963715662 0.765528235 0.753574415 0.406322447 0.99313398 0.791139524 0.896420734 1 20.75380999 3.80260315 4.54012296 0.786226242 0.993938486 0.227548337 0.157293033 0.308871862 12.80576852 0.041115488 0.075756563 6347.506443 -3.80260315 0.207712243 ERFS(ph)PPRHELSPPQK ddPTM_BT-474_Pertuzumab_2h_R1 4 ERFSPPRHELSPPQK 15 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPRHELSPPQK;ERFS(1)PPRHELSPPQK;ERFS(1)PPRHELSPPQK;ERFS(1)PPRHELSPPQK 142.3 2.41E-06 4217740000 1864490 1900350 1569520 1864500 1998570 1875580 1971470 1989810 2201010 2089130 TRUE FALSE 1791623.669 1846153.879 1853167.178 1960727.068 2062855.819 1913505.513 1995597.44 1948719.728 1951160.572 1947631.364 0.919898756 0.947896975 0.951497913 1.006723913 1.059161326 0.98247828 1.024627902 1.000558814 1.001812051 1 20.89328921 3.802862539 3.254049667 1.012140876 0.936767162 0.726933276 0.02012768 0.126005988 2.638605217 0.005291689 0.010139012 6351.298717 -3.802862539 -0.075373714 AVS(ph)MDNSNK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVSMDNSNK 9 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 AVS(1)MDNSNK;AVS(1)MDNSNK;AVS(1)MDNSNK 218.55 5.51E-07 3350730000 3472050 2954870 2308240 1858210 1562860 1263510 1314050 1820370 2017690 1909820 TRUE FALSE 3336358.447 2870600.001 2725390.315 1954112.441 1613130.811 1289059.038 1330131.737 1782778.723 1788650.29 1780466.19 1.873867904 1.612274367 1.530717252 1.09752853 0.906015975 0.724000852 0.74706936 1.001298836 1.004596605 1 20.76382361 3.803297148 1.537823121 0.881568291 1.784598446 0.917396326 0.105776158 0.112266338 0.507191198 0.034253429 0.088357816 6357.657788 -3.803297148 0.903030155 YSS(ph)QDADEQDWEFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSSQDADEQDWEFQK 15 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YS(0.246)S(0.754)QDADEQDWEFQK;YS(0.024)S(0.976)QDADEQDWEFQK 247.82 2.73E-18 159085000 164266 164299 147597 202532 243152 185720 212986 241030 230269 229825 TRUE FALSE 157846.3031 159613.3534 174271.0612 212984.7008 250973.2049 189475.3856 215592.5864 236052.6463 204129.8285 214258.748 0.73670879 0.744956063 0.813367308 0.994053698 1.171355696 0.884329753 1.006225362 1.101717659 0.95272576 1 17.70899458 3.803318302 3.033459878 1.026981305 0.74706881 0.714595227 0.073493265 0.131752186 2.387990983 0.019782013 0.038439404 6357.96748 -3.803318302 -0.279912495 ELSLKAS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELSLKASPLR 10 1 Q86W50 Q86W50 METTL16 Methyltransferase-like protein 16 1 ELS(0.008)LKAS(0.992)PLR;ELSLKAS(1)PLR;ELSLKAS(1)PLR 117.7 0.00055859 866730000 1981830 2006770 1553530 1270440 1434880 744590 1662510 1490030 1643620 1622600 TRUE FALSE 1904377.893 1949538.884 1834287.429 1336007.561 1481034.218 759646.12 1682856.295 1459260.36 1457043.148 1512699.857 1.258926471 1.288781033 1.212591791 0.883194082 0.979066807 0.502179012 1.112485261 0.964672769 0.963207038 1 20.52869433 3.803907666 4.32056514 0.913984193 1.267643816 0.514549694 0.151061285 0.178826682 6.656762859 0.039897545 0.073839066 6366.601485 -3.803907666 0.353659622 KLES(ph)TESR ddPTM_BT-474_Pertuzumab_2h_R1 4 KLESTESR 8 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 KLES(0.7)T(0.3)ESR;KLES(0.896)T(0.103)ES(0.001)R;KLES(0.487)T(0.487)ES(0.026)R;KLES(0.943)T(0.056)ESR 119.34 0.0018155 1691980000 3532660 3072970 2362300 2336480 2726830 2272310 1621810 2149940 2063660 1861420 TRUE FALSE 3394599.742 2985331.904 2789220.159 2457066.013 2814540.963 2318257.665 1641658.196 2105542.988 1829401.968 1735344.365 1.956153378 1.720310945 1.607300669 1.415895347 1.621891896 1.335906412 0.946012923 1.213328622 1.054201117 1 20.72679055 3.804174059 0.354721697 0.957173948 2.236077388 0.859023123 0.120345781 1.19315356 0.1949844 0.127128661 0.62075396 6370.507902 -3.804174059 1.278903439 SPHSPS(ph)PIATPPSQSSSCSDAPMLSTVHSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPHSPSPIATPPSQSSSCSDAPMLSTVHSAK 31 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.027)PHS(0.477)PS(0.496)PIATPPSQSSSCSDAPMLSTVHSAK 170.11 1.39E-12 452110000 210380 210580 176360 220580 230810 249830 239400 202290 244370 256880 TRUE FALSE 202158.117 204574.4646 208232.1751 231964.1602 238234.2133 254881.7338 242329.8488 198112.6408 216630.1421 239481.2888 0.844149946 0.854239868 0.869513339 0.96861079 0.994792597 1.064307508 1.011894708 0.827257285 0.904580659 1 17.86955341 3.804677212 4.374884344 0.960075398 0.852547741 0.409160364 0.06108315 0.278497861 10.58565213 0.018939869 0.035032572 6377.892749 -3.804677212 -0.107527657 DYVFIEFCVEDSKDVNVNFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DYVFIEFCVEDSKDVNVNFEK 21 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 79.467 0.0068858 110490000 33858 39788 31489 26557 27717 34424 31035 35581 40258 35086 FALSE TRUE 32534.79193 38653.2852 37179.76277 27927.60995 28608.54248 35120.07687 31414.81561 34846.23992 35688.08062 32709.59397 0.99465594 1.181710945 1.136662314 0.853804849 0.874622366 1.073693452 0.960415945 1.06532169 1.091058503 1 14.99742623 3.80468958 24.99989116 0.992652514 1.112080036 0.271052583 0.086646639 263.0233239 99433.95633 0.023224971 0.041869411 6378.074386 -3.80468958 0.119427522 RLS(ph)PSAS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(1)PS(0.001)AS(0.999)PPR 96.707 0.022946 1774000000 379290 399800 316370 477380 436810 396930 430360 441490 470920 480830 TRUE FALSE 364466.9275 388398.0954 373545.0966 502017.639 450860.3904 404956.1966 435626.8744 432373.0772 417463.1359 448262.9558 0.813065016 0.866451466 0.8333169 1.119917746 1.005794444 0.903389832 0.971811007 0.964552327 0.931290731 1 18.77398576 3.805140634 24.99999057 0.97955995 0.840494827 0.597225906 0.055408597 139.0455824 52209.22502 0.0145737 0.02627311 6384.702027 -3.805140634 -0.139065124 NAADKER ddPTM_BT-474_Pertuzumab_2h_R1 1 NAADKER 7 1 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 82.671 0.021757 103290000 183330 177460 138240 128190 124630 71553 168020 142540 133750 155060 FALSE TRUE 176165.2609 172399.0146 163223.0431 134805.9013 128638.8371 72999.85068 170076.279 139596.4992 118567.2607 144557.6481 1.218650575 1.19259698 1.129120771 0.932540776 0.889879151 0.504987814 1.176529096 0.965680481 0.820207456 1 17.14128541 3.80540402 2.558929977 0.898066474 1.202825585 0.403439589 0.159242032 0.304622025 3.898118459 0.045123126 0.091761896 6388.575325 -3.80540402 0.304759111 LRRES(ph)PESEGPIYEGLIL ddPTM_BT-474_Pertuzumab_2h_R1 4 LRRESPESEGPIYEGLIL 18 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 1 LRRES(0.95)PES(0.05)EGPIYEGLIL;LRRES(1)PESEGPIYEGLIL;LRRES(0.997)PES(0.003)EGPIYEGLIL;LRRES(0.993)PES(0.007)EGPIYEGLIL 178.22 7.08E-14 382668000 436197 466828 383448 466568 489633 547071 484898 509729 545612 567060 TRUE FALSE 419149.939 453514.5225 452745.5834 490647.6304 505382.4901 558133.1504 490832.3268 499202.918 483676.4132 528652.5211 0.792864731 0.857868835 0.856414309 0.928109885 0.95598237 1.055765608 0.928459257 0.944293081 0.914923118 1 19.01196024 3.805693904 1.573784657 0.964023901 0.818918024 0.692814592 0.03951361 0.245185976 1.16189471 0.01224316 0.031210182 6392.841018 -3.805693904 -0.145105877 WQDIQNDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 WQDIQNDPR 9 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 85.731 0.034005 525840000 565010 585110 475120 589750 606670 611600 592610 621980 547520 667940 FALSE TRUE 542928.7845 568423.2357 560984.753 620187.0682 626184.0915 623966.971 599862.5384 609135.8956 485367.825 622699.8289 0.871894867 0.912836666 0.900891131 0.995964732 1.005595413 1.002034917 0.963325363 0.978217541 0.779457136 1 19.24817736 3.80591181 8.083937659 0.964268795 0.896574723 0.179616914 0.063761857 0.56930176 62.77369369 0.016275926 0.029436983 6396.049405 -3.80591181 -0.067694071 KTEAAATTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTEAAATTR 9 1 E7EVA0;P27816-4;B5MEG9;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 ; 110.66 0.0036088 464110000 565160 672270 487382 527700 470900 604460 583520 486890 567170 625440 FALSE TRUE 543072.9224 653097.5178 575462.7692 554934.6602 486046.9262 616682.5953 590661.2923 476835.5514 502787.2394 583078.3917 0.93138921 1.12008527 0.986938939 0.951732508 0.833587615 1.057632394 1.013004942 0.817789783 0.862297843 1 19.15333033 3.806206642 3.274508704 0.924743254 1.029505511 0.152350355 0.085808977 0.403666366 8.52354035 0.023594558 0.045273793 6400.39301 -3.806206642 0.104762257 GKPVDSQTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GKPVDSQTSR 10 1 Q9Y450;Q9Y450-4;E9PN23 Q9Y450 HBS1L HBS1-like protein 0 ;; 153.95 1.40E-05 271298000 214647 254302 185624 268450 269410 274114 307840 311021 323356 338599 FALSE TRUE 206258.3579 247049.5559 219170.386 282304.7367 278075.8173 279656.7729 311607.438 304598.3077 286649.9825 315665.3881 0.653408215 0.782631119 0.694312377 0.89431641 0.880919568 0.885927895 0.987144773 0.964940469 0.908081764 1 18.26803656 3.807951484 0.599754833 0.971467882 0.624367572 0.831982343 0.046234971 0.547273266 0.3070738 0.026234337 0.115828458 6426.15926 -3.807951484 -0.34710031 S(ph)KHEEEEWTDDDLVESL ddPTM_BT-474_Pertuzumab_2h_R1 1 SKHEEEEWTDDDLVESL 17 1 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 S(0.793)KHEEEEWT(0.207)DDDLVESL 141.83 3.69E-07 98013000 317980 322960 244880 280740 254110 304360 257500 252040 325270 338330 TRUE FALSE 305552.9901 313749.497 289135.2633 295229.025 262283.6789 310514.3677 260651.362 246835.2859 288346.7132 315414.6077 0.968734429 0.994720883 0.916683173 0.936003019 0.831552098 0.984464131 0.826376952 0.782574047 0.91418313 1 18.26688995 3.808593599 0.938498822 0.868783019 0.991776696 0.147219362 0.067916245 1.011559012 1.565752577 0.025706378 0.094752864 6435.667513 -3.808593599 0.122993677 RVVFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVVFLK 6 1 Q02878;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 116 0.038405 634680000 777900 884640 645280 558050 586110 507990 554440 596760 717910 829660 FALSE TRUE 747498.808 859410.9334 761896.4502 586851.0274 604962.7604 518261.9059 561225.4026 584436.6975 636415.8665 773466.3892 0.966427008 1.111116068 0.985041446 0.758728544 0.78214486 0.670050972 0.725597661 0.755607103 0.822809983 1 19.56097908 3.808972055 3.96953727 0.767623282 1.040039965 0.584492971 0.089391117 0.132227141 4.069924564 0.021918334 0.041010899 6441.278176 -3.808972055 0.272416682 S(ph)LQLPASPAPDPSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLQLPASPAPDPSPR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR 220.64 1.72E-12 373490000 413480 409030 295170 278950 248030 205065 239990 309570 273970 289000 TRUE FALSE 397320.7445 397364.8649 348513.785 293346.6429 256008.1102 209211.5548 242927.0694 303177.2713 242870.0742 269425.7726 1.474694647 1.474858404 1.293542862 1.08878464 0.950199039 0.776509065 0.901647482 1.125271975 0.901435939 1 18.03952834 3.809054237 1.735736754 0.95100501 1.484247403 0.866790617 0.084418161 0.140696218 0.816024814 0.027919879 0.067375869 6442.497184 -3.809054237 0.533242393 HAS(ph)SSPESPKPAPAPGSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HAS(0.333)S(0.333)S(0.333)PESPKPAPAPGSHR;HAS(0.333)S(0.333)S(0.333)PESPKPAPAPGSHR 103.02 0.00023 131448000 99474 87944 65289 71358 70517 73343 59974 41149 88939 69613 TRUE FALSE 95586.44611 85435.92323 77088.17465 75040.79493 72785.24335 74826.04571 60707.97975 40299.25877 78843.01758 64898.04951 1.472870862 1.316463651 1.187835 1.156287369 1.121532063 1.152978345 0.935436122 0.620962557 1.214874995 1 15.9858875 3.809359235 0.516010682 0.88811749 1.546357014 0.511083978 0.152646578 1.437440138 0.567796448 0.115127706 0.521247317 6447.023229 -3.809359235 0.658239524 RTQAPTKAS(ph)E ddPTM_BT-474_Pertuzumab_2h_R1 3 RTQAPTKASE 10 2 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 RTQAPTKAS(1)E;RTQAPTKAS(1)E;RTQAPTKAS(1)E 157.33 7.37E-06 2077040000 1171640 1106900 915640 811930 919740 968470 841930 950720 1059900 1079680 TRUE FALSE 1125851.013 1075332.296 1081116.516 853833.8046 949324.2724 988053.127 852233.7912 931087.2998 939584.5955 1006552.312 1.118522108 1.06833225 1.074078817 0.848275638 0.943144495 0.981621238 0.84668604 0.925026239 0.933468221 1 19.94099072 3.810171768 7.447236516 0.920966001 1.086487366 0.705119723 0.047818541 0.145531474 13.39192875 0.011819405 0.021414194 6459.096432 -3.810171768 0.165521366 KVQEFEHVNGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVQEFEHVNGR 11 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 117.2 0.00057555 198680000 173300 167270 149670 177070 179900 186060 196010 200350 223900 208050 FALSE TRUE 166527.2444 162499.6234 176718.6984 186208.6039 185686.6469 189822.2607 198408.829 196212.7025 198483.8107 193958.5882 0.858571131 0.837805765 0.911115615 0.960043098 0.957352024 0.978674172 1.022944283 1.011621627 1.023330869 1 17.56538913 3.81022435 0.690703893 1.016379334 0.814315355 0.93167659 0.016542688 0.265655644 0.205561706 0.008297052 0.035553419 6459.878509 -3.81022435 -0.202063979 EKHPNS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 5 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.839)S(0.161)PR;EKHPNS(0.818)S(0.182)PR;EKHPNS(0.5)S(0.5)PR;EKHPNS(0.902)S(0.098)PR;EKHPNS(0.686)S(0.314)PR 116.71 0.00076858 662775000 1164936 1080194 844991 929059 938547 762509 946450 820785 965728 960608 TRUE FALSE 1119409.013 1049387.925 997699.6704 977007.8463 968736.2166 777927.4544 958032.9382 803835.5029 856102.6061 895545.1645 1.24997494 1.171786713 1.11406963 1.090964348 1.08172793 0.868663564 1.069776239 0.897593482 0.95595693 1 19.77240667 3.810478159 0.644207341 0.947612479 1.276343549 0.724941257 0.059672779 0.642166613 0.423825754 0.030783104 0.134451643 6463.654873 -3.810478159 0.32873107 VSLEPHQGPGT(ph)PESK ddPTM_BT-474_Pertuzumab_2h_R1 6 VSLEPHQGPGTPESK 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(0.999)PES(0.001)K;VSLEPHQGPGT(0.999)PES(0.001)K;VSLEPHQGPGT(0.999)PES(0.001)K 215.62 8.52E-12 8057990000 1551599 1526370 1214688 1318802 1200985 1189987 1438888 1400146 1434957 1630430 TRUE FALSE 1490960.796 1482839.422 1434209.142 1386865.529 1239615.773 1214049.352 1456497.542 1371232.496 1272066.697 1519999.524 0.980895568 0.975552557 0.943558942 0.912411818 0.815536948 0.798716929 0.958222367 0.902126925 0.836886247 1 20.53563944 3.810699386 2.423182744 0.882566787 0.975800984 0.283767398 0.058351119 0.371987572 4.257642816 0.016275212 0.033847336 6466.948259 -3.810699386 0.093234197 ASEEHLK ddPTM_BT-474_Pertuzumab_2h_R1 6 ASEEHLK 7 0 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ;;;;; 110.61 0.0067645 23816000000 23633800 25990300 18851800 17857200 18627200 19625500 17706700 16343000 20618700 20982800 FALSE TRUE 22710164.97 25249082.09 22258739.62 18778812.23 19226360.8 20022341.06 17923399.89 16005511.34 18278151.62 19561616.27 1.160955448 1.290746212 1.137878349 0.959982651 0.982861566 1.023552491 0.916253527 0.818210066 0.934388619 1 24.22152224 3.811464018 2.422709022 0.931406967 1.228354227 0.77703761 0.061784869 0.137164558 1.569170598 0.019106323 0.039766151 6478.344194 -3.811464018 0.296947259 AKNWEDEDFYDS(ph)DDDTFLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AKNWEDEDFYDSDDDTFLDR 20 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR 207.83 3.80E-22 534340000 906140 875910 615900 615290 770270 866720 710980 838770 898580 777050 TRUE FALSE 870727.047 850929.9044 727206.8306 647045.1906 795046.4341 884245.6722 719681.1859 821449.1064 796576.9656 724419.7114 1.201964874 1.174636597 1.003847382 0.893191033 1.097494203 1.22062619 0.993458867 1.133940854 1.099606972 1 19.46646628 3.812682116 0.007959088 7.07E-07 2.190147611 0.065433709 0.097519164 30927.67526 53.32925338 7036.754824 7643.28149 6496.539994 -3.812682116 2.190146903 KFGDPVVQSDMK ddPTM_BT-474_Pertuzumab_2h_R1 4 KFGDPVVQSDMK 12 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;; 138.21 0.00012572 7043780000 11972740 12033800 9374960 8651360 7090680 6068090 10360000 9666690 12913710 12601790 FALSE TRUE 11504832.08 11690607.81 11069223.82 9097857.726 7318758.162 6190790.937 10486788.78 9467069.473 11447799.78 11748259.54 0.979279701 0.995092743 0.942201164 0.774400472 0.622965311 0.526953879 0.892624882 0.805827403 0.974425168 1 23.48594371 3.813292424 4.075131529 0.780385261 0.982115749 0.244204707 0.137352991 0.304990723 9.708778992 0.037630272 0.070385504 6505.675903 -3.813292424 0.201730488 GS(ph)PTPGFSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPTPGFSTR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(1)PTPGFSTR 115.15 0.00242 0 406820 445130 335730 485610 404270 442290 454600 481800 441210 515770 TRUE FALSE 390921.0246 432435.3282 396403.8793 510672.3903 417273.7117 451233.4068 460163.5308 471850.6616 391125.6905 480836.4385 0.81300208 0.899339762 0.824404824 1.062050106 0.867808008 0.938434301 0.957006362 0.981312197 0.813427725 1 18.8751867 3.813307328 25 0.944432032 0.850957804 0.313035326 0.067820374 162.7021109 54416.55275 0.016338568 0.02945477 6505.899168 -3.813307328 -0.093474228 HDPDLTLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 HDPDLTLIR 9 0 C9JQB7;P46091 C9JQB7 GPR1 G-protein coupled receptor 1 0 ;;; 99.442 0.0053345 5106180000 1429810 1594430 1686240 3826830 4149440 4473950 3758330 3488910 4599030 3973240 FALSE TRUE 1373931.444 1548958.418 1990981.078 4024333.155 4282910.506 4564416.334 3804325.567 3416862.789 4076967.395 3704128.916 0.370918906 0.418170764 0.537503182 1.08644522 1.15625309 1.232250939 1.02704999 0.922447049 1.100654834 1 21.82070288 3.813610027 3.590910208 1.07165475 0.410111888 0.926179136 0.082366627 0.067207151 1.68138465 0.025828254 0.049085989 6510.435295 -3.813610027 -0.661542863 down IGGIGTVPVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGGIGTVPVGR 11 0 A0A2U3TZH3;Q05639;P68104;A0A087WVQ9;Q5VTE0 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ; 130.31 0.00052766 283070000 284930 282900 243530 295240 304060 316050 308390 336340 341160 350460 FALSE TRUE 273794.6206 274831.969 287541.2883 310477.3718 313840.366 322440.7475 312164.1691 329394.4615 302432.9471 326723.032 0.838002203 0.841177211 0.880076579 0.950276967 0.960570071 0.986893227 0.955439741 1.008176434 0.925655425 1 18.31770863 3.814002265 1.57541228 0.976157412 0.833851166 0.860998617 0.022022638 0.12611359 0.598380579 0.006151033 0.015828888 6516.317924 -3.814002265 -0.142306246 VVYAFS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVYAFSPK 8 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 VVYAFS(1)PK;VVYAFS(1)PK 125.75 0.0013099 1588240000 2961100 2546670 2098480 1495110 1679360 610510 2162170 1836520 2141660 2223400 TRUE FALSE 2845376.938 2474041.465 2477722.016 1572272.806 1733378.14 622854.9305 2188631.283 1798595.22 1898547.735 2072807.138 1.372716683 1.193570506 1.195346143 0.758523443 0.836246705 0.300488608 1.055877917 0.867709874 0.915930721 1 20.98315446 3.814213395 4.176916412 0.810900402 1.26350185 0.503708611 0.19817299 0.188709064 6.264263136 0.052614012 0.098212302 6519.486567 -3.814213395 0.452601449 LTGVFAPRPSTGPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTGVFAPRPSTGPHK 15 1 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 143.97 2.59E-06 530480000 578470 690900 436880 328840 326830 125920 379300 332450 324780 421220 FALSE TRUE 555862.7529 671196.2085 515833.9343 345811.4718 337342.7838 128466.1887 383941.9869 325584.7913 287912.336 392690.3942 1.415524192 1.709224922 1.313589387 0.880621163 0.859055349 0.3271437 0.977721871 0.829113205 0.733178963 1 18.58303278 3.814504512 2.433704307 0.778860606 1.564077138 0.740470063 0.187978755 0.137990859 1.592566552 0.050917037 0.10611106 6523.858194 -3.814504512 0.785216532 DVEDEILWVTER ddPTM_BT-474_Pertuzumab_2h_R1 2 DVEDEILWVTER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ; 232.88 2.45E-14 123355000 95661 92177 77685 100770 96838 90382 99213 112817 114034 100969 FALSE TRUE 91922.46236 89548.20221 91724.40759 105970.7518 99952.88222 92209.58597 100427.1984 110487.2895 101089.3384 94130.2797 0.976545089 0.95132196 0.974441039 1.125788132 1.061856849 0.979595368 1.066895782 1.173769906 1.073930076 1 16.52237126 3.814824186 7.08639511 1.077660048 0.96464772 0.429507116 0.052881516 0.251081618 20.14409499 0.014933929 0.027098823 6528.662022 -3.814824186 -0.113012329 LAYIAHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAYIAHPK 8 0 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 84.244 0.022325 0 1091100 1216600 835180 409780 412990 56664 817530 417540 600230 814870 FALSE TRUE 1048458.606 1181903.759 986115.6045 430928.7949 426274.1984 57809.7849 827535.1767 408917.6531 532094.4068 759678.1291 1.380135304 1.555795427 1.298070284 0.567251812 0.561124748 0.076097735 1.089323419 0.538277512 0.700420858 1 19.53502876 3.81544493 4.059534442 0.622509682 1.457155476 0.63763361 0.264763369 0.132460277 4.151988054 0.067383069 0.126232805 6538.000211 -3.81544493 0.834645794 RS(ph)ET(ph)PPHWR ddPTM_BT-474_Pertuzumab_2h_R1 3 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 RS(1)ET(1)PPHWR;RS(1)ET(1)PPHWR;RS(1)ET(1)PPHWR 85.271 0.012921 1395660000 701780 767680 680619 732940 755009 712841 689152 753067 876574 821039 TRUE FALSE 674353.6617 745786.518 803621.9936 770767.1212 779294.5502 727255.1334 697586.0483 737515.9033 777068.9944 765429.2972 0.881013654 0.974337566 1.049897092 1.006973634 1.018114348 0.95012712 0.911365754 0.963532368 1.015206757 1 19.5459096 3.815731299 0.001850892 1.947126127 3.44E-06 0.027207121 0.048643191 1375979.431 545.3301695 284060.9795 289632.7835 6542.31271 -3.815731299 -1.947122688 WKPPMIDNPSYQGIWKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 WKPPMIDNPSYQGIWKPR 18 2 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 222.7 3.12E-19 1471620000 1483000 2320000 1178920 1398970 885830 760910 1314770 1445900 1310960 997160 FALSE TRUE 1425042.72 2253835.872 1391977.069 1471171.009 914323.5264 776296.1215 1330860.549 1416041.66 1162145.317 929621.465 1.532927943 2.424466255 1.497359002 1.582548451 0.983543906 0.835066907 1.431615554 1.523245442 1.250127456 1 19.82628386 3.815791365 2.118256884 1.234512529 1.961080799 0.473595336 0.307893753 0.280739308 2.445115514 0.087556673 0.192707419 6543.217625 -3.815791365 0.72656827 RFDAQTGADR ddPTM_BT-474_Pertuzumab_2h_R1 4 RFDAQTGADR 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 190.36 1.46E-06 2269900000 1290580 1353730 1020770 1164040 1142280 907300 1362250 1209110 1223030 1324190 FALSE TRUE 1240142.707 1315122.946 1205245.846 1224116.244 1179022.474 925646.2276 1378921.623 1184141.456 1084196.762 1234501.432 1.004569679 1.065306942 0.976301699 0.991587545 0.955059624 0.749813815 1.116986653 0.959206223 0.878246662 1 20.23549708 3.815964964 1.776717418 0.94809414 1.032301862 0.12263084 0.089121918 0.814734741 4.955782713 0.02591323 0.062206672 6545.833643 -3.815964964 0.084207722 RGEELIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGEELIGR 8 1 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 119.75 0.0026212 165790000 66196 56427 51188 59206 66734 54474 67565 63040 65908 69984 FALSE TRUE 63608.98714 54817.75721 60438.81027 62261.62876 68880.55972 55575.5016 68391.88068 61738.20197 58426.40015 65243.92134 0.974941203 0.840197157 0.92635159 0.954290108 1.055739114 0.85181118 1.048249082 0.946267494 0.895507182 1 15.99355587 3.815965275 3.828696447 0.965580642 0.903494955 0.111060901 0.066139804 0.442917961 12.43739418 0.016390506 0.030924899 6545.83833 -3.815965275 -0.062085688 TGSQGQCTQVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGSQGQCTQVR 11 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ; 134.13 0.0003426 29545000 23627 20808.9 16503.2 12670.6 11806.1 3464.7 17902.3 11918 18591.5 18828.6 FALSE TRUE 22703.63072 20215.45055 19485.69535 13324.53118 12185.85393 3534.758608 18121.3937 11671.88914 16481.07086 17553.32215 1.293409334 1.151659519 1.110085896 0.759088853 0.694219238 0.201372628 1.032362623 0.664939037 0.938914624 1 14.09945648 3.816003236 2.633405647 0.725430311 1.216134304 0.435774043 0.224647688 0.249655282 3.377180153 0.060348332 0.122831379 6546.410518 -3.816003236 0.490703994 VGDSTPVSEKPVSAAVDANASES(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 4 VGDSTPVSEKPVSAAVDANASESP 24 1 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 VGDSTPVSEKPVSAAVDANAS(0.001)ES(0.999)P;VGDSTPVSEKPVSAAVDANAS(0.001)ES(0.999)P;VGDSTPVSEKPVSAAVDANASES(1)P;VGDSTPVSEKPVSAAVDANASES(1)P 301.9 1.75E-62 2958680000 4353290 4389800 3918450 4382930 4942570 4918620 4965790 5393050 5538930 5445530 TRUE FALSE 4183158.614 4264607.202 4626601.08 4609133.543 5101552.253 5018077.866 5026562.823 5281681.633 4910173.887 5076699.403 0.823991787 0.840035398 0.911340364 0.907899637 1.004895474 0.988452825 0.990124178 1.040377067 0.967198075 1 22.27545941 3.816648738 0.879604932 1.007859785 0.807436756 0.884866664 0.023566307 0.233582757 0.311124679 0.008966511 0.034840418 6556.147843 -3.816648738 -0.200423029 DLIDWTDGIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLIDWTDGIAR 11 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A0A0MSJ3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 0 173.37 2.85E-05 46368000 86467 94869 76918 98277 105620 96876 103930 103700 104300 124780 FALSE TRUE 83087.77405 92163.42901 90818.79363 103349.0877 109017.3632 98834.89909 105201.9264 101558.5588 92460.30126 116328.5395 0.714250986 0.792268427 0.780709481 0.888424184 0.937150623 0.849618671 0.90435182 0.873032183 0.794820443 1 16.82784556 3.81678078 3.251669437 0.887702168 0.758579738 0.553584654 0.053677805 0.19127915 3.928815704 0.013655204 0.026442689 6558.141458 -3.81678078 -0.12912243 KELNYFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KELNYFAK 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 123.35 0.0021665 2231700000 5932300 6464500 4284500 3780000 3161700 1991900 4194500 3733300 4100100 3695100 FALSE TRUE 5700459.157 6280138.789 5058804.458 3975086.253 3263398.952 2032177.583 4245833.546 3656206.05 3634673.837 3444827.586 1.654787944 1.823063312 1.468521815 1.153928942 0.947333029 0.58992142 1.232524253 1.061361116 1.055110523 1 21.71600035 3.817055915 2.131860238 0.991849651 1.738826892 0.783703653 0.160202313 0.146453669 1.292200336 0.047140827 0.103602714 6562.297491 -3.817055915 0.746977241 RTFEDISEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTFEDISEK 9 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 0 ; 157.77 0.00010864 1616600000 1780370 2119930 1492060 1481300 1442630 619440 2081480 1417560 1866480 2180450 FALSE TRUE 1710791.172 2059471.672 1761708.433 1557750.071 1489033.504 631965.5012 2106953.775 1388286.891 1654605.015 2032766.179 0.841607456 1.013137513 0.866655718 0.76632034 0.732515879 0.310889421 1.036495882 0.68295454 0.81396721 1 20.95501285 3.818538048 3.072794914 0.742224793 0.929289799 0.104660992 0.190641805 0.493340979 9.057993186 0.049515942 0.097116351 6584.731161 -3.818538048 0.187065006 ASSHS(ph)SQTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.197)S(0.197)HS(0.301)S(0.301)QT(0.004)QGGGSVTK;AS(0.178)S(0.178)HS(0.322)S(0.322)QTQGGGSVTK 182.15 1.41E-09 180497000 573296 554850 405969 241409 309341 232904 192868 271601 272546 269007 TRUE FALSE 550890.9585 539026.2213 479336.629 253868.1474 319291.2342 237613.4785 195228.3763 265992.3444 241607.7207 250786.9163 2.196649517 2.149339484 1.911330288 1.012286252 1.273157463 0.947471591 0.778463164 1.060630867 0.963398427 1 17.93610256 3.818965922 2.507791137 0.992165681 2.177508016 0.945182122 0.120091519 0.060109356 0.736529867 0.034052533 0.070551841 6591.221735 -3.818965922 1.185342336 up NYDYYASR ddPTM_BT-474_Pertuzumab_2h_R1 4 NYDYYASR 8 0 O95861-3;O95861-4;O95861 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ;;; 110.76 0.010762 1376670000 877225 872552 672771 700977 628524 551550 719771 721489 872124 929773 FALSE TRUE 842942.0772 847667.6713 794355.6854 737154.507 648741.0453 562702.7189 728579.7728 706590 773124.1398 866798.6466 0.97247738 0.977929159 0.916424695 0.850433385 0.748433385 0.649173509 0.840540967 0.815172016 0.891930488 1 19.72533738 3.819374724 2.323473286 0.808531974 0.973008112 0.318071133 0.086351553 0.318443133 3.344838466 0.023865223 0.050794623 6597.42899 -3.819374724 0.164476137 SRS(ph)WPASPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRSWPASPR 9 1 Q86YD1 Q86YD1 PTOV1 Prostate tumor-overexpressed gene 1 protein 1 SRS(1)WPASPR;SRS(1)WPASPR;SRS(1)WPASPR;S(0.021)RS(0.942)WPAS(0.037)PR 137.6 9.70E-05 2390740000 412711 446484 342856 359561 381082 273337 444428 411556 369053 406839 TRUE FALSE 396581.7978 433750.7135 404817.706 378117.9863 393339.8486 278864.0614 449867.0428 403057.2248 327159.6506 379283.4322 1.045608018 1.143605749 1.067322408 0.996927243 1.037060455 0.735239237 1.186097268 1.06268081 0.862573007 1 18.53291683 3.820005617 3.32314332 0.993626904 1.096815136 0.140364143 0.115164038 0.541362493 11.5462859 0.031170954 0.060256411 6607.019932 -3.820005617 0.103188232 IKPNLSS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 3 IKPNLSSSPR 10 1 A0A1P0AZG4;Q96JN0-3 A0A1P0AZG4 1 IKPNLS(0.114)S(0.443)S(0.443)PR;IKPNLS(0.108)S(0.446)S(0.446)PR;IKPNLS(0.094)S(0.453)S(0.453)PR 58.274 0.067928 1321610000 3669190 3631710 2836640 2638740 2903700 1835540 3101780 3060640 2957530 3079880 TRUE FALSE 3525793.998 3528137.187 3349283.949 2774925.688 2997100.148 1872655.876 3139740.511 2997436.714 2621803.593 2871276.984 1.227953283 1.228769361 1.166478876 0.966443051 1.043821325 0.652203144 1.093499697 1.043938544 0.913114133 1 21.45326108 3.820553611 2.63037392 0.962116069 1.228258532 0.501940959 0.114437563 0.244347338 3.29388269 0.031964261 0.065342606 6615.361947 -3.820553611 0.266142463 ESFESQFLADTER ddPTM_BT-474_Pertuzumab_2h_R1 2 ESFESQFLADTER 13 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UJ50 A0A590UJ56 CUL1 Cullin-1 0 ; 168.58 6.97E-05 101338000 113174 118053 95730 132252 119975 134315 132503 127926 123401 141167 FALSE TRUE 108751.035 114686.244 113030.5405 139077.5416 123834.1048 137030.9413 134124.6114 125284.2834 109393.0358 131605.6334 0.826340273 0.871438715 0.85885792 1.056774988 0.94094836 1.04122398 1.019140351 0.951967482 0.83121849 1 17.00586172 3.821035164 9.095301479 0.977432839 0.853532955 0.470122513 0.06087062 0.365822374 37.98305232 0.015726153 0.028419327 6622.701248 -3.821035164 -0.123899884 ASGS(ph)ENEGDYNPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASGSENEGDYNPGR 14 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 AS(0.002)GS(0.998)ENEGDYNPGR;ASGS(1)ENEGDYNPGR 247.7 7.82E-18 984790000 488090 520090 422370 608350 539680 563810 614730 656110 569900 560570 TRUE FALSE 469014.9032 505257.5424 498701.6546 639747.0164 557039.2973 575210.6245 622253.2496 642561.0992 505207.3412 522602.0946 0.897460818 0.96681117 0.954266467 1.224157008 1.065895646 1.100666512 1.190682655 1.22954176 0.96671511 1 18.99535338 3.821908154 7.427190917 1.129045927 0.940372807 0.448222689 0.0856793 0.231219411 18.14592975 0.021807126 0.039546397 6636.027145 -3.821908154 -0.18867312 YEPFSFADDIGSNNCGYYDLQAVLTHQGR ddPTM_BT-474_Pertuzumab_2h_R1 3 YEPFSFADDIGSNNCGYYDLQAVLTHQGR 29 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ;; 318.41 2.49E-92 1985894000 509999 499698 416624 520325 488029 572790 503718 508285 600841 605347 FALSE TRUE 490067.6752 485447.1023 491917.2246 547179.0356 503726.896 584372.2062 509882.6516 497788.7371 532636.0486 564346.3085 0.868381113 0.860193635 0.871658443 0.969580251 0.892584728 1.035485122 0.90349249 0.882062538 0.943810636 1 19.10622121 3.822109494 6.935145418 0.937215754 0.865208511 0.379737782 0.045739473 0.307149069 21.82118902 0.011973153 0.021752246 6639.104335 -3.822109494 -0.072007243 NISFTVWDVGGQDK ddPTM_BT-474_Pertuzumab_2h_R1 2 NISFTVWDVGGQDK 14 0 P61204;F5H423;F5H0C7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 225.86 6.09E-12 365830000 896080 891070 676610 468960 465550 403300 362650 693020 748690 789880 FALSE TRUE 861060.2029 865657.556 798888.4781 493163.0818 480524.8386 411455.0023 367088.2192 678708.8948 663701.85 736380.724 1.169313882 1.175557056 1.084885104 0.669712101 0.652549453 0.558753086 0.498503298 0.921682049 0.901302585 1 19.49009234 3.822341733 4.38115779 0.725792556 1.161612739 0.589573584 0.153153889 0.157087112 5.467263148 0.042366298 0.079008092 6642.655546 -3.822341733 0.435820183 VEISAPSNFEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEISAPSNFEHR 12 0 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 160.18 0.00025897 0 178600 204570 156580 252180 224250 246490 221450 210930 197770 247050 FALSE TRUE 171620.1145 198735.8639 184877.4891 265195.04 231463.2049 251474.1967 224160.1713 206574.2218 175319.9787 230317.0835 0.745147134 0.862879387 0.802708537 1.151434518 1.004976276 1.091860807 0.973267671 0.896912286 0.761211353 1 17.8132619 3.822351833 24.99994964 0.97838728 0.809507332 0.390616541 0.102402421 102.2546612 30507.02074 0.027855211 0.050216692 6642.810035 -3.822351833 -0.168879948 ARSDEGQLS(ph)PATR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSDEGQLSPATR 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 ARSDEGQLS(1)PATR 142.4 2.44E-05 283760000 237170 231960 198080 226700 218410 265720 229950 253600 251010 245030 TRUE FALSE 227901.1342 225344.7279 233877.4623 238400.0142 225435.356 271093.0405 232764.1969 248363.0714 222516.3971 228433.8998 0.997667747 0.986476736 1.023829924 1.043628001 0.986873473 1.186746103 1.018956455 1.087242618 0.974095339 1 17.80141724 3.824775378 1.289133739 1.054071058 0.990039344 0.089295209 0.058059025 0.974648986 3.01792661 0.017617491 0.052864396 6679.983323 -3.824775378 -0.064031714 SSDEENGPPSS(ph)PDLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 SSDEENGPPSS(1)PDLDR;SSDEENGPPSS(1)PDLDR 314.11 9.77E-58 1161440000 1257730 1343650 1097440 1406050 1408580 1527190 1482430 1516190 1589460 1661350 TRUE FALSE 1208576.521 1305330.418 1295771.82 1478616.409 1453888.255 1558070.828 1500572.422 1484880.147 1409031.164 1548825.285 0.780318176 0.842787389 0.836615875 0.954669596 0.938703848 1.005969391 0.968845509 0.958713782 0.90974184 1 20.56274298 3.825007013 1.775294365 0.965109134 0.804651178 0.830159984 0.029648571 0.138441492 0.840380233 0.008348033 0.020256655 6683.5471 -3.825007013 -0.160457957 KQSLGELIGT(ph)LNAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQSLGELIGTLNAAK 15 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 KQS(0.095)LGELIGT(0.905)LNAAK 238.21 1.78E-17 12569000000 2682900 2546200 2019900 1874200 1836500 1584400 1886500 2250900 2341200 2000700 TRUE FALSE 2578049.302 2473584.869 2384940.862 1970927.687 1895572.69 1616437.654 1909587.551 2204418.128 2075436.791 1865190.807 1.382190654 1.326183284 1.278657848 1.056689578 1.016288888 0.866633938 1.02380279 1.181872718 1.112720899 1 20.83089179 3.82508262 2.748682645 1.041776811 1.350126482 0.7534617 0.077355954 0.159257463 2.339983115 0.024724146 0.050102861 6684.710749 -3.82508262 0.308349671 HGFEAASIKEER ddPTM_BT-474_Pertuzumab_2h_R1 3 HGFEAASIKEER 12 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4;E7ERA5 P35580 MYH10 Myosin-10 0 ;; 147.87 3.96E-05 405116000 742608 739690 586344 640940 640343 689780 660450 595638 795170 742350 FALSE TRUE 713586.0584 718594.7654 692309.404 674018.9902 660940.2141 703727.8242 668532.7847 583337.8672 704905.6352 692069.9733 1.031089465 1.038326749 1.000345963 0.973917402 0.955019347 1.016844902 0.965990161 0.842888566 1.018546769 1 19.40055839 3.825677991 0.671732888 0.943691271 1.053893852 0.181953634 0.048825481 1.64462373 1.18172183 0.026760352 0.118487314 6693.881056 -3.825677991 0.110202581 NQEEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NQEEKR 6 1 H7BXC7;Q9H7P9-3;Q9H7P9;E7ESZ3;Q9H7P9-2 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 0 87.582 0.083822 84483000 183220 170400 134760 128580 136830 79561 163720 124570 123170 167280 FALSE TRUE 176059.5598 165540.3588 159114.1297 135216.0292 141231.2612 81169.77793 165723.6543 121997.586 109188.258 155949.9766 1.128948934 1.061496529 1.020289539 0.867047448 0.905618996 0.52048599 1.062671877 0.782286658 0.700149242 1 17.25072381 3.82605469 1.526196149 0.817109225 1.109698953 0.375992774 0.143093995 0.424596711 1.882667615 0.041110161 0.109627782 6699.689721 -3.82605469 0.292589728 GIPDDRDGLFDTIQR ddPTM_BT-474_Pertuzumab_2h_R1 3 GIPDDRDGLFDTIQR 15 1 Q93008;Q93008-3;O00507;H7C2M9 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ;; 146.16 3.59E-06 1176120000 269489 298665 237806 320094 309980 349459 302226 325826 313643 308628 FALSE TRUE 258957.0719 290147.3666 280782.8342 336614.0897 319950.7882 356525.3004 305924.7322 319097.5792 278039.5615 287724.3507 0.900017921 1.00842131 0.975874421 1.16991867 1.112004554 1.239121053 1.063256313 1.109039185 0.966340044 1 18.1343278 3.826147358 6.91388575 1.103608771 0.964334334 0.377010288 0.077607056 0.258694977 17.48149623 0.019627622 0.035671782 6701.119432 -3.826147358 -0.139274436 MSS(ph)PEDDSDTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 MS(0.143)S(0.857)PEDDSDTKR 102.5 0.0014375 637780000 488030 419660 402490 331130 364400 468090 395310 439220 486910 420680 TRUE FALSE 468957.2481 407691.7077 475228.8963 348219.659 376121.2569 477555.1005 400147.922 430149.9535 431638.0181 392186.9689 1.195749184 1.039534049 1.21174066 0.887891966 0.959035579 1.217672025 1.020298872 1.09679818 1.100592453 1 18.58118207 3.826574198 24.99995333 1.049805685 1.138060027 0.210654442 0.094465901 140.6924743 39959.37771 0.024314912 0.04383433 6707.708763 -3.826574198 0.088254342 DLSIEEQSECAQDFYHNVAER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSIEEQSECAQDFYHNVAER 21 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 0 ; 270.68 1.21E-44 401480000 155166 157753 129611 172770 164268 180566 170805 162535 171865 199666 FALSE TRUE 149101.9412 153254.0389 153034.5909 181686.6804 169551.8294 184217.1682 172895.3627 159178.5955 152355.6057 186142.444 0.801009904 0.823315927 0.822137002 0.976062614 0.910871405 0.989656976 0.928833634 0.855144007 0.818489338 1 17.50604753 3.827044671 7.815222568 0.917950025 0.815332666 0.458895142 0.054363116 0.3046823 24.08801098 0.014745629 0.026716019 6714.979196 -3.827044671 -0.102617359 EMTGIWR ddPTM_BT-474_Pertuzumab_2h_R1 1 EMTGIWR 7 0 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 81.297 0.064172 592470000 316010 383550 379370 556350 670240 679090 802230 663990 684230 611200 FALSE TRUE 303659.9798 372611.5295 447930.598 585063.2902 691798.8783 692821.6651 812047.9307 650278.3745 606559.0789 569802.8796 0.532921104 0.653930583 0.786115013 1.026781912 1.21410211 1.215897093 1.425138341 1.141233921 1.064506868 1 19.12010339 3.827147542 1.461737546 1.202427028 0.560963923 0.824213906 0.109438342 0.163979004 0.66379703 0.033448545 0.091978245 6716.569955 -3.827147542 -0.641463105 SRS(ph)FDYNYR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRSFDYNYR 9 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.003)RS(0.997)FDYNYR;S(0.003)RS(0.997)FDYNYR;S(0.004)RS(0.996)FDYNYR;S(0.016)RS(0.984)FDYNYR 160.86 3.94E-05 3274400000 1505520 1728080 1478700 2660340 2247210 2662150 3462200 2383440 3023300 3394070 TRUE FALSE 1446682.614 1678796.85 1745933.984 2797640.466 2319493.551 2715980.497 3504571.439 2334221.131 2680107.659 3164186.616 0.457205212 0.530561896 0.551779713 0.88415786 0.73304575 0.858350289 1.107574194 0.73770021 0.847013146 1 21.59340326 3.82726578 1.377808611 0.8838615 0.458004108 0.704573291 0.108545861 0.260810502 0.931071821 0.033402265 0.095787108 6718.398807 -3.82726578 -0.425857392 ELLS(ph)PLS(ph)EPDDRYPLIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 2 ELLS(1)PLS(1)EPDDRYPLIVK 88.755 0.0017173 17372000 113480 108610 100520 110960 107090 114420 118220 130110 132030 132130 TRUE FALSE 109045.0761 105512.5491 118686.2001 116686.6589 110534.6471 116733.6508 119666.8117 127423.183 117042.5079 123180.7174 0.885244691 0.856567094 0.963512817 0.947280235 0.897337257 0.947661722 0.971473573 1.034440988 0.950169072 1 16.91041691 3.827941589 0.340409603 1.01052036 0.824741178 0.5553518 0.033849691 2.648232901 0.389825316 0.038205917 0.193499383 6728.8615 -3.827941589 -0.185779182 LGVADIIDCVVLTS(ph)SPEATETSQQLQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.04)S(0.442)S(0.442)PEAT(0.067)ET(0.008)S(0.001)QQLQLR;LGVADIIDCVVLT(0.068)S(0.519)S(0.413)PEATETSQQLQLR;LGVADIIDCVVLT(0.007)S(0.661)S(0.333)PEATETSQQLQLR 226.39 8.66E-35 358683000 210439 210670 169257 223498 217080 227925 200880 204656 248689 238570 TRUE FALSE 202214.8112 204661.8979 199845.505 235032.7586 224062.5753 232533.7997 203338.4295 200429.7821 220458.8673 222411.4414 0.909192486 0.920195007 0.898539678 1.056747607 1.007423781 1.045511859 0.914244466 0.901166688 0.991220892 1 17.76287148 3.828028543 24.99998202 0.977936715 0.910397204 0.353456405 0.047432869 100.1818362 27990.36675 0.014169636 0.025544671 6730.208882 -3.828028543 -0.067539511 KPELVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPELVR 6 1 P43155-2;P43155;P43155-3 P43155-2 CRAT Carnitine O-acetyltransferase 0 86.872 0.085115 1280500000 1140100 1456000 1111500 1951400 1574700 1443000 1957100 1996800 1712400 1668000 FALSE TRUE 1095543.632 1414476.306 1312372.775 2052111.988 1625351.656 1472178.449 1981051.575 1955565.382 1518015.531 1555024.874 0.704518397 0.909616514 0.84395613 1.319665056 1.045225502 0.946723408 1.273967772 1.2575782 0.97620016 1 20.56850623 3.828743023 8.053045075 1.134583946 0.825759565 0.509322523 0.133123452 0.248745763 20.05254961 0.034837377 0.063082944 6741.290197 -3.828743023 -0.308824381 EDQLDTVLAVLEDSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDQLDTVLAVLEDSSR 16 0 Q96HW7-2;Q96HW7-3;Q96HW7 Q96HW7-2 INTS4 Integrator complex subunit 4 0 ;; 168.5 1.39E-08 26680200 31947.2 30956 28388.5 28879.9 37235.8 32065.4 31177.4 36572 38003 38346.7 FALSE TRUE 30698.6681 30073.16519 33518.93345 30370.3951 38433.52332 32713.78436 31558.95835 35816.77542 33689.05876 35749.44385 0.858717362 0.841220504 0.93760713 0.849534757 1.075080314 0.915085127 0.882781799 1.00188343 0.942365954 1 15.12563318 3.828890451 1.364032394 0.960117245 0.851224198 0.321381134 0.060093373 0.557147514 1.946006239 0.01804698 0.052244485 6743.579019 -3.828890451 -0.108893048 AFLASLS(ph)PAMVVPEDQLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 AFLASLSPAMVVPEDQLTR 19 0 Q9H211;H3BSY1 Q9H211 CDT1 DNA replication factor Cdt1 1 AFLASLS(1)PAMVVPEDQLTR;AFLAS(0.099)LS(0.901)PAMVVPEDQLTR;AFLASLS(1)PAMVVPEDQLTR;AFLAS(0.002)LS(0.998)PAMVVPEDQLTR 200.48 6.76E-16 119897000 92262 92822 80413 106346 104444 126308 110339 117782 106459 113551 TRUE FALSE 88656.29904 90174.80744 94945.41788 111834.5298 107803.5361 128862.0343 111689.3617 115349.7605 94374.22063 105860.0896 0.837485585 0.851830069 0.89689531 1.056437135 1.018358633 1.217286276 1.055065815 1.089643519 0.891499535 1 16.69179926 3.829198693 2.593412877 1.060792363 0.845079393 0.545912061 0.077374008 0.19992808 2.615052085 0.020961976 0.043366228 6748.366999 -3.829198693 -0.21571297 LKQQSELQSQVR ddPTM_BT-474_Pertuzumab_2h_R1 5 LKQQSELQSQVR 12 1 Q14847;Q14847-2;C9J9W2 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;; 243.88 2.08E-16 10213640000 5659340 6220410 4278920 3563780 3720300 1638090 4841560 3680300 3791760 4033220 FALSE TRUE 5438166.736 6043009.997 5052216.028 3747707.113 3839966.828 1671213.302 4900812.46 3604300.519 3361335.301 3760046.417 1.446303086 1.60716367 1.343657888 0.996718311 1.021255166 0.444466136 1.303391479 0.95857873 0.893961119 1 21.84231904 3.829938483 2.501310378 0.94197083 1.527184139 0.592936794 0.201444962 0.19637113 2.389764229 0.054639829 0.114441343 6759.872164 -3.829938483 0.58521331 T(ph)PPGEVVWVER ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPGEVVWVER 11 0 A0A494C030 A0A494C030 1 T(1)PPGEVVWVER 101.72 0.03436 153680000 14608 11783 11320 17954 17776 20681 14325 19100 15320 15130 TRUE FALSE 14037.10321 11446.96038 13365.77581 18880.60809 18347.78118 21099.18399 14500.31364 18705.57833 13580.93783 14105.23162 0.99516999 0.81154005 0.947575777 1.338553566 1.30077844 1.495841015 1.028009608 1.326144712 0.962829834 1 13.78394274 3.83213336 5.721550499 1.230668164 0.899940147 0.38129428 0.167269452 0.204406712 10.0352455 0.041324003 0.07574494 6794.1223 -3.83213336 -0.330728017 LDHKFDLMYAK ddPTM_BT-474_Pertuzumab_2h_R1 3 LDHKFDLMYAK 11 1 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ;; 155.02 1.91E-05 15900100000 33328400 34009400 24247800 14350300 15697130 5032650 25282800 13730310 20521300 22232700 FALSE TRUE 32025889.28 33039485.21 28629916.85 15090920.7 16202042.44 5134413.631 25592218.47 13446774.3 18191808.06 20726859.43 1.545139503 1.594042037 1.381295461 0.728085254 0.781693073 0.247717878 1.234736915 0.648760819 0.877692451 1 24.3049982 3.832849509 3.552476973 0.769771712 1.556152897 0.655751407 0.240217916 0.135582078 3.20425488 0.060976995 0.117466134 6805.335012 -3.832849509 0.786381186 KWNTTLYEGTWR ddPTM_BT-474_Pertuzumab_2h_R1 2 KWNTTLYEGTWR 12 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 214.23 7.10E-11 1843140000 1331360 1545690 1146600 1177340 1214590 1160360 1354470 1154930 1414920 1438110 FALSE TRUE 1279328.979 1501608.435 1353816.126 1238102.658 1253658.39 1183823.274 1371046.409 1131080.292 1254304.213 1340705.529 0.954220708 1.120013607 1.009778879 0.923470987 0.935073634 0.882985301 1.022630533 0.843645579 0.935555337 1 20.35456097 3.833113485 4.047943031 0.92647923 1.042426741 0.323435807 0.061325055 0.216274675 6.355740411 0.015061471 0.028462718 6809.472728 -3.833113485 0.115947511 LLGIFENQDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLGIFENQDR 10 0 Q9NZJ9;F8VRL4;F8VRR0;A0A0C4DGJ4 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ;; 123.88 0.0025107 254556000 182531 198810 167228 203591 230918 216871 252948 238647 227829 223896 FALSE TRUE 175397.4867 193140.1335 197449.8196 214098.3559 238345.6872 221256.2802 256043.6533 233718.8561 201966.8071 208731.3245 0.840302658 0.925304977 0.945952027 1.02571263 1.141877903 1.060005156 1.226666165 1.11971146 0.967592227 1 17.6712876 3.833454961 1.409759084 1.103004109 0.86794888 0.5643059 0.071928474 0.304817283 1.141347069 0.021925009 0.062359596 6814.82897 -3.833454961 -0.235055229 SEWMNHINK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEWMNHINK 9 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 0 138.4 0.00013778 339990000 311560 333390 256030 245290 239490 198500 301920 267940 323610 345830 FALSE TRUE 299383.8908 323882.0436 302300.3164 257949.4463 247193.4133 202513.806 305614.9873 262406.9454 286875.1495 322406.6261 0.928590998 1.004576263 0.937636797 0.800074891 0.766713192 0.62813165 0.947917824 0.813900597 0.88979297 1 18.29852187 3.834675348 4.606025645 0.822877744 0.966868826 0.239787535 0.098125329 0.282712982 10.06555815 0.025174709 0.046918878 6834.005882 -3.834675348 0.143991082 SSSSSGVPYS(ph)PAIPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSSSGVPYSPAIPNK 16 0 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5;Q9UPT5-4 A0A0A0MRE1 EXOC7 Exocyst complex component 7 1 SSSSSGVPYS(1)PAIPNK;SSSSSGVPYS(1)PAIPNK 291.06 1.65E-45 1702030000 2060760 2126260 1657120 1509600 1527540 1555160 1513700 1909870 2028470 1770790 TRUE FALSE 1980223.221 2065621.147 1956598.446 1587510.637 1576674.711 1586606.401 1532225.113 1870430.517 1798206.59 1650852.816 1.199515306 1.251244888 1.185204658 0.961630632 0.955066797 0.961082893 0.928141563 1.133008648 1.089259183 1 20.65478007 3.834675394 4.893583961 1.008943191 1.222708891 0.707704741 0.061393112 0.137314119 5.333890607 0.018256362 0.033839623 6834.006595 -3.834675394 0.2137657 S(ph)NPSIQATLNK ddPTM_BT-474_Pertuzumab_2h_R1 3 SNPSIQATLNK 11 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 S(0.991)NPS(0.009)IQATLNK;S(1)NPSIQATLNK;S(1)NPSIQATLNK 188.12 3.45E-06 1353420000 1190570 1150470 903670 923990 873650 849240 846560 1027950 1139000 1006070 TRUE FALSE 1144041.208 1117659.722 1066983.271 971677.2346 901751.7457 866412.2147 856920.4545 1006722.473 1009705.495 937927.9828 1.219753786 1.191626375 1.137596159 1.035982775 0.961429622 0.923751323 0.913631398 1.073347306 1.076527744 1 19.83911763 3.834860069 1.995799631 0.991993995 1.2077441 0.74497461 0.051192044 0.187376593 1.445326698 0.016519633 0.038113905 6836.913245 -3.834860069 0.215750104 RS(ph)AS(ph)PERMD ddPTM_BT-474_Pertuzumab_2h_R1 3 RSASPERMD 9 2 Q16629;Q16629-4;C9JAB2;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 2 RS(1)AS(1)PERMD;RS(1)AS(1)PERMD;RS(1)AS(1)PERMD 79.744 0.014787 835858000 1132760 1159560 911030 1179950 1091890 1188240 1118300 1183210 1258590 1186610 TRUE FALSE 1088490.487 1126490.484 1075673.387 1240847.361 1127011.633 1212267.027 1131986.09 1158776.3 1115720.14 1106239.848 0.983955233 1.018305828 0.972369047 1.121680225 1.018776928 1.095844657 1.023273653 1.047491014 1.008569834 1 20.07723278 3.835260975 24.357672 1.046773962 0.994219442 0.296828377 0.037637778 46.54496119 11718.76022 0.008929769 0.016098369 6843.227443 -3.835260975 -0.052554519 RIDFIPVSPAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RIDFIPVSPAPS(0.972)PT(0.028)R 158.44 1.12E-06 238880000 110550 130500 102790 150230 130810 150730 171290 127140 150010 164160 TRUE FALSE 106229.5838 126778.2678 121366.4396 157983.3883 135017.6224 153777.8639 173386.2983 124514.5146 132981.4937 153041.297 0.694123651 0.828392534 0.793030652 1.032292534 0.882229994 1.004812864 1.132937983 0.813600754 0.868925554 1 17.22356148 3.83550521 6.139920249 0.954557821 0.773967618 0.473101333 0.09187304 0.228406029 12.01556575 0.024521922 0.044801658 6847.076966 -3.83550521 -0.180590203 DGVLEEQIER ddPTM_BT-474_Pertuzumab_2h_R1 1 DGVLEEQIER 10 0 Q09161;X6R941 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 107.24 0.0075547 0 101350 85176 77705 94282 101630 93580 95337 112990 91572 91714 FALSE TRUE 97389.12995 82746.86388 91748.02204 99147.90532 104899.0212 95472.25172 96503.76272 110656.717 81177.13046 85502.12909 1.139025788 0.967775478 1.07304956 1.159595748 1.226858587 1.116606718 1.128670873 1.294198381 0.94941648 1 16.38367272 3.835826033 4.623845528 1.149801116 1.046873566 0.041573873 0.102938129 0.404284016 14.4041437 0.025729474 0.047950466 6852.136931 -3.835826033 -0.10292755 KIHSQEEALR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIHSQEEALR 10 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ; 199.68 1.78E-07 523810000 393140 416760 293480 265600 293570 154110 338240 265790 286770 282390 FALSE TRUE 377775.6542 404874.4129 346518.3644 279307.6478 303012.9457 157226.2098 342379.4823 260301.3436 254217.0718 263263.4738 1.434971775 1.537905761 1.316241708 1.060943411 1.150987417 0.597219992 1.300520264 0.98874842 0.965637459 1 18.00614784 3.836418884 1.927430466 1.003133179 1.494537616 0.580694142 0.168335816 0.236325333 1.69764438 0.046228379 0.108709774 6861.497103 -3.836418884 0.491404437 SVACS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVACSPK 7 0 J3KRA9;Q96Q15-2;Q96Q15;Q96Q15-4;Q96Q15-3 J3KRA9 SMG1 Serine/threonine-protein kinase SMG1 1 SVACS(1)PK 65.933 0.072634 147010000 321500 270830 257420 187810 241350 201850 284450 271370 297420 302840 TRUE FALSE 308935.4246 263106.1936 303941.5203 197502.8966 249113.2419 205931.5453 287931.1842 265766.1147 263658.1285 282328.3771 1.094241492 0.93191551 1.076553209 0.699550285 0.882352828 0.729404346 1.019845002 0.941336884 0.93387045 1 18.10701462 3.836902582 24.47224101 0.888893427 1.024005229 0.288885953 0.105722748 53.28494177 13252.2717 0.027263964 0.049150805 6869.143391 -3.836902582 0.135111802 NNQITNNQR ddPTM_BT-474_Pertuzumab_2h_R1 3 NNQITNNQR 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;; 214.6 1.56E-06 593553000 538933 547574 353560 428228 332752 305102 349735 353919 452943 345066 FALSE TRUE 517870.9025 531957.7257 417456.1569 450328.8984 343455.2703 311271.3715 354015.1615 346610.449 401526.8095 321694.3725 1.609822698 1.653612159 1.29767939 1.399865639 1.067644633 0.967599679 1.100470483 1.077452634 1.248162367 1 18.29533117 3.837214721 1.102542006 1.076356951 1.666136698 0.804372404 0.103174319 0.245280793 0.536674078 0.034294613 0.117879024 6874.082204 -3.837214721 0.589779747 NGIS(ph)FTIWDR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGISFTIWDR 10 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 1 NGIS(0.938)FT(0.062)IWDR;NGIS(0.905)FT(0.095)IWDR 128.31 0.00034921 84214000 135399 127191 105294 97114 119295 88616 88908 130147 103066 103925 TRUE FALSE 130107.4574 123563.6372 124322.9681 102126.0652 123132.232 90407.87624 89996.0827 127459.419 91366.37977 96886.06718 1.342891307 1.275349912 1.28318727 1.054084123 1.270897205 0.93313599 0.928885704 1.315559839 0.94302909 1 16.56400159 3.837417513 1.053185877 1.070643443 1.34625019 0.414441905 0.128228832 0.72892365 1.439720721 0.045324464 0.161239252 6877.292768 -3.837417513 0.275606747 VSVS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSVSPGR 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VSVS(1)PGR;VS(0.005)VS(0.995)PGR;VS(0.004)VS(0.996)PGR 96.027 0.013672 4351540000 1808980 1922150 1564640 2016610 1920420 2023470 2152910 2065940 2114600 2188640 TRUE FALSE 1738283.062 1867332.164 1847405.253 2120687.484 1982192.053 2064385.95 2179257.957 2023277.617 1874559.473 2040401.463 0.851931883 0.915178801 0.905412629 1.039348149 0.97147159 1.011754788 1.068053516 0.991607609 0.918720902 1 20.96042161 3.83872609 5.274555033 1.002425585 0.890142807 0.610934976 0.040042837 0.15081543 6.354488324 0.010490469 0.019346559 6898.046067 -3.83872609 -0.112282778 SFLEDIRK ddPTM_BT-474_Pertuzumab_2h_R1 3 SFLEDIRK 8 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 103.74 0.0075598 3800695000 5573610 5758590 4420310 3793200 4115930 2102861 5327400 4380790 5330440 5455880 FALSE TRUE 5355787.159 5594360.651 5219158.346 3988967.507 4248322.626 2145382.29 5392598.315 4290325.156 4725350.798 5086348.388 1.052972929 1.099877599 1.026111062 0.784249761 0.835240196 0.421792242 1.060210175 0.843498091 0.929026177 1 22.27819885 3.839293597 4.531208667 0.83015135 1.072800908 0.281106215 0.161975838 0.2818356 9.623073567 0.042075423 0.078651024 6907.065866 -3.839293597 0.242649558 DIRPEYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIRPEYR 7 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UK73;B1AKN7;B1AKN6;S4R3K4;A0A590UJ82 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 0 70.525 0.051795 324320000 35811 50126 55777 98613 103200 123220 150900 107540 145100 110310 FALSE TRUE 34411.46653 48696.45556 65857.14465 103702.4287 106519.5217 125711.5928 152746.7593 105319.2614 128628.8563 102838.6054 0.334616231 0.473523103 0.64039321 1.008399796 1.035793137 1.222416351 1.485305627 1.024121836 1.250783748 1 16.65002243 3.839642218 1.17321149 1.201111541 0.3216984 0.854372249 0.13061626 0.190657437 0.478324381 0.042373463 0.139447733 6912.612595 -3.839642218 -0.879413141 down EYFSWEGAFQHVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EYFSWEGAFQHVGK 14 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 234.82 3.20E-17 6820600000 3855400 3797800 2533680 2125970 1428260 1270020 1338070 1690080 2766800 3583000 FALSE TRUE 3704726.706 3689490.462 2991572.337 2235691.566 1474201.28 1295700.675 1354445.701 1655179.257 2452724.463 3340320.219 1.109093279 1.104531967 0.895594476 0.669304564 0.441335316 0.387897145 0.40548379 0.495515145 0.734278244 1 21.67155498 3.839933705 1.926855566 0.529704507 1.112599091 0.580920069 0.177091668 0.208325208 1.495528662 0.048253671 0.113929336 6917.253713 -3.839933705 0.582894584 KIHPQTIIAGWR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIHPQTIIAGWR 12 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 145.31 4.14E-05 1243620000 2025200 2205600 1605600 1409990 1537670 1102970 1745420 1480720 1676200 1730630 FALSE TRUE 1946052.945 2142698.448 1895767.636 1482759.753 1587130.552 1125272.809 1766780.972 1450142.615 1485924.803 1613412.889 1.206171687 1.328053385 1.175004644 0.919020645 0.983710099 0.697448754 1.095058174 0.898804407 0.920982356 1 20.62168426 3.840788684 3.325092321 0.926358584 1.265876738 0.669668493 0.099482998 0.133588162 2.783159956 0.025103128 0.049198458 6930.884864 -3.840788684 0.339518153 YYRPTEVDFLQGDCTK ddPTM_BT-474_Pertuzumab_2h_R1 2 YYRPTEVDFLQGDCTK 16 1 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 ; 151.48 5.83E-07 789500000 227570 236818 200285 254440 270050 256480 281810 296580 317900 293790 FALSE TRUE 218676.3128 230064.1825 236480.9548 267571.6789 278736.4035 261666.2013 285258.8751 290455.5194 281813.3247 273891.3416 0.798405351 0.839983408 0.863411576 0.976926387 1.017689723 0.955364999 1.041503807 1.060477186 1.028923817 1 18.06324413 3.841594388 0.976924388 1.030936646 0.784263984 0.899571339 0.027725328 0.207473083 0.34532547 0.010596824 0.040038602 6943.754983 -3.841594388 -0.246672662 FSFWDKDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSFWDKDAR 9 1 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 68.846 0.051906 307840000 2481300 2896000 1891200 1184100 1198500 397710 1910800 1258200 1492300 1725100 FALSE TRUE 2384328.053 2813408.915 2232981.91 1245211.543 1237050.841 405751.9687 1934184.942 1232217.73 1322900.36 1608257.44 1.482553721 1.749352339 1.388448052 0.774261329 0.769187078 0.252292922 1.202658787 0.766181893 0.822567536 1 20.61706693 3.842048609 3.377415595 0.786238445 1.610164273 0.683443594 0.23411876 0.133230004 2.849256229 0.061174233 0.119611066 6951.021135 -3.842048609 0.823925827 LKATVTPS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKATVT(0.007)PS(0.993)PVK;LKATVT(0.299)PS(0.701)PVK 171.51 3.80E-05 13495000000 15055000 12565500 10147900 6146600 6411800 2919700 9769700 8792500 8025100 9412500 TRUE FALSE 14466633.96 12207144.24 11981851.27 6463826.763 6618041.37 2978738.334 9889264.511 8610931.802 7114124.292 8774982.991 1.64862245 1.391130246 1.365455783 0.736619862 0.754194211 0.339458018 1.126983895 0.981304672 0.810727986 1 23.0649649 3.842796114 3.810025432 0.826167063 1.493450101 0.671601272 0.208460958 0.149770826 3.910198643 0.058539953 0.112076391 6962.995486 -3.842796114 0.667283038 AQLADSFHLQQFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQLADSFHLQQFFR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 211.51 3.74E-09 611780000 691690 860610 793110 980730 783970 748850 912320 843800 908650 988270 FALSE TRUE 664657.9901 836066.2454 936442.6196 1031345.593 809187.107 763992.2601 923485.2451 826375.2351 805503.8614 921333.5926 0.721408614 0.907452254 1.016399084 1.119405176 0.878278089 0.829224361 1.002335367 0.896933794 0.874280356 1 19.81336409 3.84339754 0.008490749 1.833083151 2.14E-05 0.052097827 0.104054658 32436.44618 58.9060614 6077.139036 6645.438518 6972.644765 -3.84339754 -1.833061758 S(ph)WHEESPFEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SWHEESPFEK 10 0 Q9BY84 Q9BY84 DUSP16 Dual specificity protein phosphatase 16 1 S(1)WHEESPFEK;S(1)WHEESPFEK;S(1)WHEESPFEK 240.6 1.79E-12 930840000 1968980 1972570 1593180 1670060 1714590 1786500 1885240 1666000 2122380 1921600 TRUE FALSE 1892030.085 1916314.235 1881103.066 1756251.997 1769741.345 1822624.254 1908312.131 1631596.518 1881456.32 1791448.32 1.056145502 1.069701098 1.050045957 0.980353146 0.987883002 1.017402642 1.065234263 0.910769515 1.050243146 1 20.77269499 3.845182486 4.885044158 0.996861832 1.062008041 0.297397776 0.039818879 0.258288832 9.557504268 0.010415663 0.019353179 7001.361244 -3.845182486 0.065146209 AATAARPPAPPPAPQPPS(ph)PTPS(ph)PPRPTLAR ddPTM_BT-474_Pertuzumab_2h_R1 5 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 AATAARPPAPPPAPQPPS(0.805)PT(0.24)PS(0.935)PPRPT(0.02)LAR;AAT(0.001)AARPPAPPPAPQPPS(0.989)PT(0.014)PS(0.976)PPRPT(0.02)LAR;AAT(0.001)AARPPAPPPAPQPPS(0.957)PT(0.047)PS(0.962)PPRPT(0.033)LAR;AATAARPPAPPPAPQPPS(0.996)PT(0.016)PS(0.987)PPRPT(0.001)LAR;AAT(0.002)AARPPAPPPAPQPPS(0.753)PT(0.248)PS(0.993)PPRPT(0.004)LAR 137.57 9.87E-07 22736060000 841630 882050 719810 932690 939320 926780 905230 939550 966940 1069750 TRUE FALSE 808738.1691 856894.7976 849895.6791 980826.2427 969534.0809 945520.1266 916308.4755 920147.9642 857177.0249 997294.8797 0.810931837 0.859219089 0.852200985 0.983486693 0.972163901 0.94808481 0.918793924 0.922643827 0.859502082 1 19.92766062 3.845713752 6.076284411 0.939037047 0.840392572 0.593411556 0.03892402 0.173810459 8.411899382 0.010264809 0.018778883 7009.931144 -3.845713752 -0.098644475 KDVLIEFYAPWCGHCK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDVLIEFYAPWCGHCK 16 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 165.02 4.66E-09 188000000 404970 453860 292200 217550 208010 245380 221390 174210 260790 159900 FALSE TRUE 389143.3247 440916.3572 345007.04 228777.7816 214700.8306 250341.7517 224099.437 170612.5026 231186.2125 149069.8306 2.610476735 2.957783983 2.31439882 1.534702097 1.440270172 1.679358934 1.50331852 1.144513963 1.550858491 1 17.18562878 3.846143667 2.384982142 1.398418252 2.788307484 0.887201877 0.203989745 0.086961 0.961024411 0.055502145 0.120019528 7016.873814 -3.846143667 1.389889232 RNEFLGELQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNEFLGELQK 10 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141 D6RGI3;B1AMS2 SEPT11;SEPT6 Septin-11;Septin-6 0 ; 205.56 2.67E-07 1513620000 1996420 2077600 1636000 1549240 1655400 1179090 1984740 1843640 1997510 2124800 FALSE TRUE 1918397.699 2018348.882 1931661.593 1629196.462 1708647.444 1202932.008 2009029.842 1805568.19 1770761.039 1980885.403 0.96845466 1.018912492 0.975150601 0.822458714 0.862567537 0.607269863 1.014208009 0.91149553 0.893924018 1 20.91771399 3.84649123 5.731837142 0.869677343 0.993901581 0.196144172 0.106174536 0.367809092 16.52109335 0.027871345 0.051163586 7022.491631 -3.84649123 0.124224237 LVFVHSAEGNEFWSALLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 LVFVHSAEGNEFWSALLEK 19 0 P07384;E9PRM1;E9PL37 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;; 286.6 3.47E-40 2053808100 1598384 1658191 1363635 1592193.7 1609917 1764048 1746465 1664957 1999797 1903730 FALSE TRUE 1535917.386 1610901.016 1610074.178 1674367.008 1661701.442 1799718.259 1767838.761 1630575.056 1772788.428 1774788.671 0.865408604 0.907657933 0.907192053 0.943417678 0.936281299 1.014046511 0.996084091 0.918743218 0.998872968 1 20.75921582 3.846500013 0.883486712 0.975738385 0.86884841 0.662622277 0.027909902 0.584851804 0.77289568 0.011568032 0.047024772 7022.633642 -3.846500013 -0.106889975 VQEAPIDEHWIIECNDGVFQR ddPTM_BT-474_Pertuzumab_2h_R1 3 VQEAPIDEHWIIECNDGVFQR 21 0 A0A1W2PR36;Q14353;Q14353-2 A0A1W2PR36 GAMT Guanidinoacetate N-methyltransferase 0 ;; 259.6 1.47E-36 2210331000 1084689 1142070 917003 1228649 1216295 1225151 1198598 1137599 1208959 1239893 FALSE TRUE 1042298.155 1109499.282 1082725.841 1292059.722 1255418.233 1249924.393 1213266.801 1114107.183 1071723.043 1155913.943 0.901709129 0.95984592 0.93668378 1.117781934 1.086082784 1.081329973 1.049616893 0.963832291 0.92716508 1 20.14060256 3.84655473 12.13036038 1.031869884 0.93519232 0.398074816 0.056052279 0.799213934 86.0899002 0.016109878 0.029057336 7023.518494 -3.84655473 -0.096677563 FGSTGST(ph)PPVS(ph)PTPSER ddPTM_BT-474_Pertuzumab_2h_R1 1 FGSTGSTPPVSPTPSER 17 0 E7ER32;A0A087X287;A0A087WU73;A0A494BZX7;W0Z7M9;B0QY83;A0A499FIJ6;Q969V6 E7ER32 MKL1;mkl1 MKL/myocardin-like protein 1 2 FGS(0.031)T(0.038)GS(0.046)T(0.885)PPVS(0.997)PT(0.003)PSER 109.07 0.0033137 262730000 199850 213200 172160 244260 193420 237880 249290 237260 249520 258130 TRUE FALSE 192039.6411 207119.7447 203273.1417 256866.2879 199641.53 242690.0966 252340.8856 232360.4981 221195.5357 240646.6252 0.798015102 0.860680031 0.844695584 1.067400333 0.829604528 1.008491586 1.048595156 0.965567242 0.919171567 1 17.87655667 3.846618118 8.005631336 0.974557868 0.835468846 0.503138633 0.064906752 0.241013347 16.07805111 0.016254266 0.029446373 7024.543687 -3.846618118 -0.139089021 QPGVDSLS(ph)PVASLPK ddPTM_BT-474_Pertuzumab_2h_R1 5 QPGVDSLSPVASLPK 15 0 Q9UBW7;Q9UBW7-2;A0A087X151 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 QPGVDS(0.01)LS(0.99)PVASLPK;QPGVDS(0.442)LS(0.558)PVASLPK;QPGVDSLS(1)PVASLPK;QPGVDSLS(1)PVASLPK;QPGVDS(0.079)LS(0.921)PVASLPK 233.57 1.30E-17 1110111000 753546 710219 631292 725046 792746 744502 783440 830986 812066 875644 TRUE FALSE 724096.5892 689964.2495 745380.5074 762465.7109 818245.395 759556.3405 793027.9731 813825.8487 719883.6721 816335.8519 0.887008193 0.845196555 0.913080695 0.934009831 1.002339164 0.930445893 0.971448174 0.996925281 0.881847429 1 19.63880329 3.847073517 2.107929178 0.964591811 0.866691738 0.51230836 0.036690184 0.236166502 2.035702713 0.009774718 0.022265837 7031.91345 -3.847073517 -0.097900074 RPAEATS(ph)SPTS(ph)PERPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.362)S(0.479)S(0.16)PT(0.322)S(0.677)PERPR 132.86 0.00018122 7162700000 870030 906400 744660 943990 950780 1041600 902030 991270 949060 1020500 TRUE FALSE 836028.2657 880550.3595 879236.6269 992709.437 981362.7022 1062661.866 913069.313 970799.9281 841326.6876 951380.626 0.87875267 0.925550022 0.924169153 1.043440879 1.031514281 1.116968158 0.959730825 1.020411706 0.884321863 1 19.85966312 3.848100032 4.966018869 1.011683866 0.907543744 0.383900659 0.05732978 0.231642302 8.663071621 0.014932454 0.02771949 7048.554019 -3.848100032 -0.104140121 EFEDAFPADFIAEGIDQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFEDAFPADFIAEGIDQTR 19 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 136.6 1.28E-05 58605000 110365 85910 93458 123212 110521 96707 133546 138314 140342 144078 FALSE TRUE 106051.8138 83459.93091 110347.9396 129570.9861 114076.0083 98662.4818 135180.3759 135457.7676 124410.9645 134319.4687 0.789549086 0.621353939 0.821533472 0.964647845 0.84928871 0.734535974 1.0064094 1.008474563 0.926231809 1 17.0353089 3.848202266 0.34366525 1.0142379 0.59228907 0.478972059 0.090207655 3.073626086 0.457808929 0.09983962 0.514810522 7050.21346 -3.848202266 -0.42194883 KFGEEIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFGEEIAR 8 1 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 118.18 0.0031054 1021240000 1270150 1289440 1143550 1366640 1377210 1528230 1576240 1559130 1626740 1679960 FALSE TRUE 1220511.134 1252666.434 1350214.923 1437172.454 1421509.21 1559131.858 1595530.497 1526933.421 1442079.295 1566174.813 0.779294319 0.799825424 0.862109971 0.91763221 0.907631255 0.995503085 1.018743555 0.974944437 0.920765219 1 20.57881382 3.848480777 0.848382721 0.982671013 0.756758583 0.86727493 0.028816538 0.30304665 0.364747401 0.012122056 0.050609828 7054.736167 -3.848480777 -0.22591243 NIVHNYSEAEIK ddPTM_BT-474_Pertuzumab_2h_R1 2 NIVHNYSEAEIK 12 0 Q9H201;I6L9I8;Q9H201-2;D6RFG3;D6REL6;D6RBR6;D6R907;D6RBI9;Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9H201;Q9Y6I3 EPN3;EPN1 Epsin-3;Epsin-1 0 ; 202.32 1.38E-07 778580000 1427800 1306370 1092160 1015120 1089340 873810 1075080 1234470 1503850 1549050 FALSE TRUE 1371999.997 1269113.607 1289537.607 1067510.465 1124379.61 891479.0369 1088237.151 1208977.763 1333139.253 1444131.464 0.950052008 0.878807531 0.892950288 0.739205877 0.778585356 0.617311553 0.753558231 0.837166001 0.923142585 1 20.46177065 3.848579203 5.948035465 0.791192363 0.907254411 0.162674699 0.100176595 0.371034662 17.23770411 0.026000777 0.047633322 7056.335203 -3.848579203 0.116062048 GVEPS(ph)PSPIKPGDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GVEPSPSPIKPGDIK 15 1 Q92890;Q92890-1;Q92890-3;C9JNP9 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPS(0.621)PS(0.379)PIKPGDIK 61.648 0.053035 257680000 168760 146190 156590 171090 170830 183000 185320 210890 230910 221510 TRUE FALSE 162164.6726 142020.8043 184889.2963 179919.9754 176324.9021 186700.3854 187588.0016 206535.0478 204698.0649 206506.9304 0.785274723 0.687728998 0.895317634 0.871253933 0.853844962 0.904087747 0.908385986 1.000136157 0.991240655 1 17.65583067 3.848766975 0.325900831 1.021232511 0.629545724 0.762134699 0.045903024 1.792263516 0.237259746 0.050896284 0.266322111 7059.386737 -3.848766975 -0.391686786 WVESLK ddPTM_BT-474_Pertuzumab_2h_R1 4 WVESLK 6 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 132.94 0.034151 4471150000 5700100 5675070 5289630 5557720 5934130 6206910 6798140 6940510 7359320 7670490 FALSE TRUE 5477333.79 5513222.56 6245583.808 5844554.595 6125006.681 6332417.973 6881337.671 6797186.043 6523920.846 7150960.88 0.765957734 0.770976468 0.873390851 0.817310386 0.856529183 0.885533857 0.962295527 0.95052765 0.912313877 1 22.76970568 3.84891917 0.277941275 1.003816495 0.651011628 0.849216345 0.029222691 1.87053513 0.177859598 0.040422488 0.219123845 7061.861076 -3.84891917 -0.352804867 EKASATR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKASATR 7 1 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ; 73.665 0.04403 74821000 179219 186405 139702 137787 146313 162918 172916 125966 131707 176328 FALSE TRUE 172214.9233 181088.9119 164949.2591 144898.2036 151019.2905 166212.3136 175032.1977 123364.7581 116756.1735 164385.1475 1.047630677 1.101613587 1.003431645 0.881455568 0.918691821 1.011115153 1.064768931 0.750461705 0.71025987 1 17.32672043 3.850079464 0.441679908 0.85244382 1.144827626 0.269938445 0.107312098 3.231368877 0.862382988 0.094689337 0.463269377 7080.753303 -3.850079464 0.292383806 S(ph)PSPAVPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSPAVPLR 9 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 S(0.739)PS(0.261)PAVPLR;S(0.737)PS(0.263)PAVPLR;S(0.937)PS(0.063)PAVPLR;S(0.894)PS(0.106)PAVPLR 147.2 9.75E-05 1806080000 1219790 1290900 1013040 1348380 1200100 1299740 1215790 1419170 1336680 1421540 TRUE FALSE 1172119.258 1254084.796 1196118.863 1417970.053 1238702.306 1326021.633 1230669.202 1389863.644 1184945.69 1325257.83 0.884446205 0.946294953 0.90255559 1.069957877 0.934687786 1.000576343 0.928626245 1.048749619 0.894124648 1 20.33784163 3.852021026 19.26016324 0.98405681 0.914605795 0.276664167 0.052678512 5.194207915 869.1917024 0.012448555 0.022442165 7112.479474 -3.852021026 -0.069451014 T(ph)AMRVSPHHPAPTPNPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TAMRVSPHHPAPTPNPR 17 1 A8MZI9;Q01196-7;Q01196-3;Q01196-4;Q01196;Q01196-9;Q01196-10;Q01196-2;Q01196-8;Q01196-11 A8MZI9 RUNX1 Runt-related transcription factor 1 1 T(0.64)AMRVS(0.36)PHHPAPTPNPR 77.681 0.025315 253930000 283390 253100 176200 189020 168580 177850 169100 61943 208290 185750 TRUE FALSE 272314.8055 245881.8358 208043.2595 198775.3449 174002.5288 181446.2489 171169.4964 60663.8554 184645.7924 173168.9871 1.572537959 1.419895329 1.201388673 1.14786919 1.004813459 1.047798754 0.988453529 0.350315934 1.066275178 1 17.40182105 3.852320427 0.556932334 0.76132338 1.712720097 0.577602134 0.198365749 1.150318987 0.527815205 0.133660684 0.638498058 7117.384487 -3.852320427 0.951396717 QSPS(ph)PSTRPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QS(0.169)PS(0.308)PS(0.308)T(0.216)RPIR;QS(0.104)PS(0.478)PS(0.156)T(0.262)RPIR 76.073 0.069668 64579000 222400 211141 181472 215799 220992 243080 221906 223514 239870 239090 TRUE FALSE 213708.3621 205119.4654 214268.0272 226936.4123 228100.4084 247995.2441 224621.752 218898.3578 212640.9632 222896.2213 0.958779655 0.92024649 0.961290532 1.018125883 1.023348027 1.112604075 1.007741408 0.982064014 0.953990884 1 17.76601263 3.852507741 3.611909309 1.015323525 0.939649449 0.385447701 0.039374985 0.262530643 6.21607836 0.011368234 0.022073561 7120.454924 -3.852507741 -0.075674077 ELDLSELDDPDSAYLQEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDLSELDDPDSAYLQEAR 19 0 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 0 155.98 4.77E-08 105040000 139910 147290 121130 155110 154150 178360 150740 148140 169650 176060 FALSE TRUE 134442.1625 143089.4334 143020.8855 163115.2457 159108.3747 181966.5614 152584.8012 145080.8572 150392.0432 164135.2994 0.819093535 0.871777332 0.871359702 0.993785288 0.969373287 1.108637582 0.92962819 0.883910151 0.916268736 1 17.32452602 3.853331797 4.471871604 0.964731493 0.851085369 0.456142947 0.058749991 0.247997922 7.995239323 0.017224548 0.032372526 7133.978513 -3.853331797 -0.113646125 ETGEPYRLS(ph)PEPTPLAEPILEVEVTLSK ddPTM_BT-474_Pertuzumab_2h_R1 5 ETGEPYRLSPEPTPLAEPILEVEVTLSK 28 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 ET(0.022)GEPYRLS(0.978)PEPTPLAEPILEVEVTLSK;ET(0.01)GEPY(0.005)RLS(0.917)PEPT(0.068)PLAEPILEVEVTLSK;ETGEPYRLS(1)PEPTPLAEPILEVEVTLSK;ET(0.152)GEPY(0.017)RLS(0.824)PEPT(0.007)PLAEPILEVEVTLSK;ETGEPYRLS(1)PEPTPLAEPILEVEVTLSK 314.34 5.36E-83 1667895900 321287 310433.3 347491.8 420576.4 374569.8 360853.2 488457 473790.6 550804.2 644499.9 TRUE FALSE 308730.7488 301580.0462 410291.2982 442282.3984 386618.1778 368149.8989 494434.8829 464006.6585 488279.2164 600847.3477 0.5138256 0.501924569 0.682854472 0.736097779 0.643454913 0.612717856 0.822896006 0.772253818 0.812651031 1 19.19663898 3.853618476 0.105028569 1.232914688 2.78E-22 0.821709015 0.060947975 15.78730611 0.374414066 1.196690107 3.454631179 7138.689228 -3.853618476 -1.232914688 S(ph)PSPMTALQPGSTGPLPPADDKLEELIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPMTALQPGSTGPLPPADDKLEELIR 28 1 A0A5H1ZRP3;O43151;O43151-3;O43151-2 A0A5H1ZRP3 TET3 Methylcytosine dioxygenase TET3 1 S(0.489)PS(0.489)PMT(0.02)ALQPGS(0.002)TGPLPPADDKLEELIR 62.302 0.016615 42789000 22623 23584 18343 17392 13618 19976 17329 21206 24392 24652 TRUE FALSE 21738.86815 22911.40741 21657.98814 18289.6032 14056.03534 20379.92841 17541.07749 20768.08869 21623.12242 22982.29808 0.945896188 0.996915423 0.942376957 0.795812635 0.61160269 0.886766342 0.763242972 0.903655875 0.940859889 1 14.48823544 3.853664857 4.977872198 0.831416773 0.970397373 0.217125189 0.102175295 0.311973177 11.50607588 0.026824189 0.04983419 7139.451648 -3.853664857 0.1389806 RAS(ph)DTSLTQGIVAFR ddPTM_BT-474_Pertuzumab_2h_R1 3 RASDTSLTQGIVAFR 15 1 Q9H0K1 Q9H0K1 SIK2 Serine/threonine-protein kinase SIK2 1 RAS(0.992)DT(0.008)SLTQGIVAFR;RAS(0.995)DT(0.005)SLTQGIVAFR;RAS(0.439)DT(0.439)S(0.108)LT(0.013)QGIVAFR 238.72 5.43E-18 874280000 329798 379885 273811 274462 294527 280977 277101 304867 281767 307672 TRUE FALSE 316909.1295 369051.0517 323294.7386 288627.0167 304000.7284 286658.5475 280492.2449 298571.3899 249781.9914 286833.1014 1.1048555 1.286640384 1.127117955 1.006254213 1.059852322 0.999391444 0.977893568 1.040923758 0.870826938 1 18.129852 3.853674001 3.158537798 0.998775955 1.198392065 0.637855369 0.062926866 0.147163956 2.775144291 0.015805894 0.031602084 7139.601978 -3.853674001 0.19961611 QSST(ph)PSAPELGQQPDVNISEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSSTPSAPELGQQPDVNISEWK 22 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 QS(0.062)S(0.361)T(0.551)PS(0.026)APELGQQPDVNISEWK 182.54 1.68E-16 166270000 175950 176720 156000 182010 191610 183540 186670 214470 251260 234150 TRUE FALSE 169073.6795 171680.1186 184192.6702 191403.5579 197773.3097 187251.3046 188954.5233 210041.1196 222738.0182 218290.8119 0.774534109 0.786474323 0.843794883 0.876828283 0.906008402 0.857806625 0.865609146 0.962207789 1.020372851 1 17.73589188 3.853740797 0.223048446 1.034927565 0.63483544 0.816356075 0.033893165 3.503210654 0.223758495 0.072672577 0.391613541 7140.700149 -3.853740797 -0.400092124 TAALESNLPGS(ph)PNTSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TAALESNLPGSPNTSR 16 0 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 TAALESNLPGS(1)PNTSR;TAALESNLPGS(1)PNTSR;TAALESNLPGS(1)PNTSR;TAALESNLPGS(0.982)PNT(0.009)S(0.009)R 439.59 7.05E-182 3221710000 1923330 2110420 1699130 2244590 2138850 2147830 2244200 2467140 2314780 2166790 TRUE FALSE 1848164.137 2050232.888 2006200.588 2360433.559 2207648.053 2191260.594 2271665.191 2416192.697 2052015.879 2020031.383 0.914918527 1.014951008 0.993153178 1.16851331 1.092878096 1.084765619 1.124569257 1.196116415 1.015833663 1 20.94594628 3.853768572 5.532801023 1.111414317 0.974364225 0.443884135 0.062061853 0.186135707 7.778377079 0.015685658 0.028884983 7141.156848 -3.853768572 -0.137050092 SYQNS(ph)PSSDDGIRPLPEYSTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.002)YQNS(0.84)PS(0.079)S(0.079)DDGIRPLPEYSTEK 131.57 7.21E-06 259350000 177730 159340 144820 182140 171550 199310 177730 201630 210950 212350 TRUE FALSE 170784.1151 154795.7792 170992.1955 191540.2672 177068.0615 203340.1848 179905.1129 197466.27 187003.8404 197967.3454 0.862688313 0.781925822 0.863739397 0.967534655 0.894430651 1.027140029 0.908761557 0.997468899 0.944619629 1 17.59490295 3.853848689 3.300117801 0.961964501 0.821559847 0.655243903 0.042668013 0.134661528 2.741595571 0.01039232 0.02057146 7142.474344 -3.853848689 -0.140404654 ALENDFFNS(ph)PPRK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALENDFFNSPPRK 13 1 F5H148;H3BMT1;Q9NYV6-3;Q9NYV6;Q9NYV6-2;A6NIE6 F5H148 RRN3;RRN3P2 RNA polymerase I-specific transcription initiation factor RRN3;Putative RRN3-like protein RRN3P2 1 ALENDFFNS(1)PPRK 146.3 2.59E-05 258250000 192870 193350 195010 178610 201560 235870 234960 222850 295580 281690 TRUE FALSE 185332.4272 187835.8473 230252.645 187828.0835 208043.3605 240639.453 237835.5108 218248.0696 262026.9976 262610.8854 0.705730179 0.715262991 0.876782562 0.715233427 0.792211489 0.916334647 0.905657473 0.831070156 0.997776605 1 18.00256719 3.854239716 0.184907404 1.045726403 0.510799991 0.683186043 0.059882812 6.996273986 0.33532369 0.186375831 0.914985612 7148.908135 -3.854239716 -0.534926412 AS(ph)PEPPGPESSSR ddPTM_BT-474_Pertuzumab_2h_R1 13 ASPEPPGPESSSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(0.985)PEPPGPES(0.013)S(0.002)SR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR 241.76 6.99E-17 32309140000 5823856 5773755 4893474 5619980 5648200 5718922 5916780 6581673 6380510 6106522 TRUE FALSE 5596253.269 5609093.16 5777833.607 5910027.841 5829879.483 5834562.521 5989191.324 6445759.153 5656221.254 5692921.826 0.983019518 0.985274931 1.014915325 1.038136132 1.024057533 1.024880141 1.05204173 1.132240939 0.993553298 1 22.44073786 3.854897483 0.712162522 1.05726357 0.96951695 0.187115929 0.037674639 1.450353221 1.166569034 0.018927703 0.086333408 7159.743821 -3.854897483 -0.087746619 KPALGFYDTSEENYQALDADFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPALGFYDTSEENYQALDADFR 22 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 219.04 1.81E-25 189580000 85879 79979 72807 88650 113090 75169 100910 97304 92765 111860 FALSE TRUE 82522.75374 77698.07723 85964.84448 93225.23712 116727.6426 76688.96868 102144.9668 95294.6384 82234.7061 104283.6226 0.791329949 0.745065 0.824336961 0.893958561 1.119328613 0.735388422 0.97949193 0.913802532 0.788567793 1 16.67015308 3.855192753 3.091534669 0.919550988 0.771122404 0.272318145 0.101417853 0.328872352 5.964900356 0.025972126 0.052257213 7164.613265 -3.855192753 -0.148428584 GSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GS(0.009)VPLS(0.092)S(0.477)S(0.416)PPAT(0.005)HFPDETEITNPVPK;GS(0.001)VPLS(0.011)S(0.494)S(0.494)PPATHFPDETEITNPVPK;GS(0.004)VPLS(0.071)S(0.462)S(0.462)PPATHFPDETEITNPVPK 211.92 5.65E-26 1492010000 666360 664370 569290 796990 703740 764060 860490 769960 865470 892720 TRUE FALSE 640317.9145 645422.8181 672173.3668 838122.7494 726376.4362 779509.8167 871020.934 754060.0569 767225.4739 832255.2792 0.769376813 0.775510633 0.807652872 1.007050085 0.872780809 0.936623457 1.046579043 0.906044186 0.921863151 1 19.66666659 3.856136561 5.034115257 0.950358375 0.77707872 0.719646939 0.049227977 0.117752768 4.375373226 0.012626831 0.023443381 7180.200328 -3.856136561 -0.173279655 TLTELILDAQEHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTELILDAQEHVK 14 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 ; 150.12 7.30E-06 220070000 268230 260296 220368 276564 289455 297109 262439 272357 307974 301642 FALSE TRUE 257747.2751 252872.6129 260193.3997 290837.5012 298765.583 303116.7475 265650.807 266732.7328 273014.0827 281211.5187 0.916560162 0.899225658 0.925258684 1.034230399 1.062422992 1.077895916 0.944665454 0.948512828 0.970849572 1 18.10129616 3.856748737 5.365967687 1.001505725 0.909198211 0.498796544 0.042208735 0.228463869 9.135132909 0.013021645 0.02404404 7190.328583 -3.856748737 -0.092307514 SPSSESS(ph)PQHPTPPARPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSSESSPQHPTPPARPR 18 1 O14733;O14733-4;O14733-2;O14733-3 O14733 MAP2K7 Dual specificity mitogen-activated protein kinase kinase 7 1 S(0.001)PS(0.001)S(0.003)ES(0.173)S(0.821)PQHPTPPARPR 69.122 0.016523 317810000 11430 11013 9922.2 14968 13954 14650 15387 14723 15316 16074 TRUE FALSE 10983.30296 10698.92002 11715.36226 15740.50027 14402.84308 14946.23304 15575.31071 14418.9649 13577.39189 14985.29366 0.732938787 0.713961319 0.781790636 1.050396517 0.961131854 0.997393403 1.039373072 0.962207697 0.906047769 1 13.87125974 3.857376456 4.558974378 0.987010209 0.728961519 0.890121065 0.039716318 0.065957998 2.164203719 0.010434026 0.019585062 7200.728826 -3.857376456 -0.258048691 QLEEEQAVRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLEEEQAVRPK 11 1 E9PC90;P14635-2;P14635 E9PC90 CCNB1 G2/mitotic-specific cyclin-B1 0 99.011 0.0046454 371400000 139800 143290 121330 172830 164220 156020 178330 176670 159590 201220 FALSE TRUE 134336.4614 139203.5095 143257.03 181749.777 169502.2854 159174.8313 180512.4559 173021.7028 141474.0123 187591.1902 0.716112848 0.742057819 0.763666086 0.968860941 0.903572739 0.848519758 0.962265103 0.92233384 0.754161281 1 17.51723255 3.857695842 5.251207992 0.906609267 0.734914219 0.580201978 0.06572032 0.155113697 6.035367037 0.016471808 0.030473283 7206.026284 -3.857695842 -0.171695048 ELVFDIDMTDYDDVRR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELVFDIDMTDYDDVRR 16 1 A0A5F9ZHB6;P49642;F8VSB2;F8VNY2 A0A5F9ZHB6 PRIM1 DNA primase small subunit;DNA primase 0 ; 256.37 1.97E-26 130126000 92474 98110 78131 102703 102474 108122 92243 98512 98576 107595 FALSE TRUE 88860.01384 95311.99886 92251.00971 108003.5141 105770.1693 110308.3009 93371.89743 96477.69277 87386.06574 100307.4948 0.885876115 0.950198178 0.919682122 1.07672427 1.054459285 1.099701484 0.930856638 0.961819383 0.871181819 1 16.61406988 3.858107773 23.75740735 0.997708741 0.921740637 0.237416934 0.066135185 20.22173207 3961.763196 0.018436435 0.033236896 7212.864484 -3.858107773 -0.075968104 LVPLLDTGDIIIDGGNSEYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVPLLDTGDIIIDGGNSEYR 20 0 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 233.97 3.89E-29 150230000 49866 55461 45767 62765 64041 70283 53467 68069 65497 72189 FALSE TRUE 47917.18159 53879.30658 54038.11498 66004.30917 66100.93693 71704.17041 54121.34514 66663.35136 58062.05515 67299.57473 0.711998282 0.800589109 0.802948833 0.980753733 0.982189519 1.065447601 0.804185544 0.990546398 0.862740298 1 16.03830977 3.858589113 3.57114114 0.953406532 0.763589737 0.575592815 0.072562381 0.172700141 3.996620549 0.018651131 0.036412626 7220.863129 -3.858589113 -0.189816795 GGPGKLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 GGPGKLSPR 9 1 Q12888;Q12888-2;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GGPGKLS(1)PR;GGPGKLS(1)PR;GGPGKLS(1)PR 77.358 0.06171 8344360000 7565160 7649180 5829430 5783330 6316360 3558190 6922710 6519040 6602280 7048190 TRUE FALSE 7269505.183 7431032.876 6882937.676 6081808.354 6519531.456 3630139.04 7007432.196 6384419.546 5852816.853 6570809.813 1.106333221 1.130915836 1.047502191 0.925579727 0.992196037 0.552464482 1.066448793 0.971633593 0.890729913 1 22.64763975 3.858736472 2.129091937 0.910990374 1.121040759 0.295359792 0.131056144 0.414934701 3.650019791 0.036943992 0.084800184 7223.313631 -3.858736472 0.210050386 RGADDDRPSWR ddPTM_BT-474_Pertuzumab_2h_R1 5 RGADDDRPSWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 136.7 5.27E-05 924531000 472929 470007 390278 522048 493220 557826 500085 525418 472592 518707 FALSE TRUE 454446.4118 456602.8605 460809.9163 548990.9598 509084.8692 569105.6239 506205.1898 514567.9347 418945.3374 483574.5129 0.93976502 0.944224413 0.952924325 1.135276871 1.052753724 1.176872661 1.046798738 1.064092339 0.866351154 1 18.88337868 3.859174921 7.903488575 1.057069077 0.94381982 0.267007365 0.077657919 0.345778417 20.98258678 0.019833901 0.035948561 7230.60972 -3.859174921 -0.113249256 IREPLTAQQLETTTER ddPTM_BT-474_Pertuzumab_2h_R1 2 IREPLTAQQLETTTER 16 1 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 0 ; 211.17 7.11E-12 965780000 161840 162354 138845 188984 220756 165872 176811 207771 183009 181605 FALSE TRUE 155515.1139 157723.8229 163937.3801 198737.4869 227856.8172 169226.0455 178974.8659 203480.4562 162234.5856 169304.7316 0.918551492 0.931597253 0.968297688 1.173844848 1.345838448 0.99953524 1.05711674 1.201859241 0.958240115 1 17.36926277 3.860409936 4.847136357 1.120522677 0.931061103 0.321265354 0.109640134 0.243773248 8.587597024 0.028533528 0.053221206 7251.200869 -3.860409936 -0.189461574 VLGS(ph)EGEEEDEALSPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLGSEGEEEDEALSPAK 17 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK 373.42 7.27E-105 2528040000 1529890 1538570 1351340 1485260 1573520 1707690 1635990 1662620 2089190 1694630 TRUE FALSE 1470100.207 1494691.49 1595557.198 1561914.447 1624133.7 1742220.662 1656011.735 1628286.316 1852033.91 1579851.201 0.930530804 0.946096372 1.009941441 0.988646555 1.028029538 1.102775161 1.04820741 1.030658024 1.172283763 1 20.59135725 3.861562567 0.727116638 1.070031597 0.912665586 0.537681769 0.045934789 0.882354747 0.740684774 0.020831292 0.095370951 7270.471345 -3.861562567 -0.157366011 YKEALLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YKEALLGR 8 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 126.07 0.0011263 2313300000 1843230 1974850 1543270 1532370 1717770 1560540 1756470 1710430 1838070 1829610 FALSE TRUE 1771194.534 1918529.212 1822173.219 1611455.799 1773023.632 1592095.188 1777966.205 1675109.023 1629419.999 1705688.885 1.038404219 1.124782619 1.068291665 0.94475365 1.03947657 0.933403038 1.042374269 0.982071841 0.955285582 1 20.70192309 3.865956918 5.932569208 0.988049165 1.08486834 0.532865391 0.039388041 0.158253644 6.954908761 0.009319087 0.017098875 7344.41008 -3.865956918 0.096819175 VEGELEEMER ddPTM_BT-474_Pertuzumab_2h_R1 2 VEGELEEMER 10 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 166.33 1.30E-05 306970000 307530 287410 255880 309870 317100 324530 303580 352020 360620 364180 FALSE TRUE 295511.3876 279213.3482 302123.208 325862.4278 327299.8095 331092.219 307295.3029 344750.664 319683.9294 339513.7642 0.870395898 0.822391837 0.889870279 0.959791508 0.964025156 0.975195276 0.905104108 1.015424705 0.941593429 1 18.37311054 3.865997927 2.768852132 0.966881777 0.846606528 0.722744444 0.030517339 0.12994651 1.918841071 0.007813786 0.01635019 7345.103623 -3.865997927 -0.120275248 QLQTFFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLQTFFHK 8 0 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753;P49753-2 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ; 112.84 0.0033424 376440000 442140 468630 326490 368400 345360 233223 415180 360000 402460 399400 FALSE TRUE 424860.68 455265.1312 385494.0057 387413.1681 356468.818 237938.9289 420261.097 352565.8742 356774.428 372348.2823 1.141030321 1.222686267 1.035304912 1.040459126 0.957353196 0.639022496 1.128677416 0.946871225 0.95817396 1 18.50629318 3.867374316 1.608974122 0.940566013 1.182935445 0.367578335 0.119322255 0.428701134 2.11496036 0.035126753 0.095289779 7368.419043 -3.867374316 0.242369432 VEGNAVACPVSSAQS(ph)PPHSAGAPAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 VEGNAVACPVSSAQSPPHSAGAPAAK 26 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 VEGNAVACPVSSAQS(1)PPHSAGAPAAK;VEGNAVACPVSSAQS(0.999)PPHS(0.001)AGAPAAK;VEGNAVACPVSSAQS(1)PPHSAGAPAAK 317.84 3.40E-82 726402000 455147 428895 384792 493566 500853 440131 533862 585048 593786 516542 TRUE FALSE 437359.352 416663.3345 454332.4741 519039.0004 516963.3916 449030.7504 540395.5629 572966.5544 526381.9026 481556.1503 0.908220883 0.865243512 0.943467286 1.077836925 1.073526714 0.932457721 1.122185985 1.18982294 1.093085204 1 18.8773445 3.868035055 0.746021566 1.103583647 0.839806437 0.509125173 0.070479875 0.85357318 0.756325287 0.034249732 0.156962859 7379.637933 -3.868035055 -0.26377721 MENALTGSQSSHASLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MENALTGSQSSHASLR 16 0 O95772-2 O95772-2 STARD3NL MLN64 N-terminal domain homolog 0 72.531 0.08746 76645000 52635 55630 53716 79478 78868 151590 65768 72059 77998 79708 FALSE TRUE 50577.96601 54043.48687 63423.67611 83579.8691 81404.86085 154655.2537 66572.88846 70570.95647 69143.99403 74309.30616 0.680641075 0.727277506 0.853509195 1.124756419 1.095486757 2.08123668 0.895888979 0.949692039 0.930489028 1 16.18125528 3.869409222 2.228923686 1.163966629 0.701076795 0.251960402 0.323415921 0.470794146 4.543466472 0.094986541 0.215996655 7403.025111 -3.869409222 -0.462889834 AEASS(ph)PVPYLSPETNPASSTSAVNHNVNLTNVR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEASSPVPYLSPETNPASSTSAVNHNVNLTNVR 33 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 AEAS(0.003)S(0.997)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.001)S(0.999)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.001)S(0.999)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.003)S(0.997)PVPYLSPETNPASSTSAVNHNVNLTNVR 407.98 1.95E-186 3781580000 686090 810820 647970 927000 961220 941380 912910 872480 832180 985620 TRUE FALSE 659276.8443 787696.2075 765072.593 974842.5811 992138.5143 960415.3486 924082.4657 854462.9831 737714.4152 918863.0795 0.71749193 0.857250906 0.832629594 1.060922571 1.07974576 1.045221394 1.005680265 0.929913283 0.80285565 1 19.80949037 3.869535745 4.956541119 0.989293197 0.80023023 0.530348452 0.080932396 0.193263197 6.939096123 0.022649269 0.042219135 7405.182146 -3.869535745 -0.189062967 IVEAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 IVEAFR 6 0 E7ET76;B5MCK8;P19440-2;P36268-2;A6NGU5;P36268;P19440;P36268-3 E7ET76 GGT1;GGT2;GGT3P Gamma-glutamyltranspeptidase 1;Gamma-glutamyltranspeptidase 1 heavy chain;Gamma-glutamyltranspeptidase 1 light chain;Inactive gamma-glutamyltranspeptidase 2;Putative gamma-glutamyltranspeptidase 3;Putative gamma-glutamyltranspeptidase 3 heavy chain;Putative gamma-glutamyltranspeptidase 3 light chain 0 97.306 0.095899 57180000 30703 34009 53423 104800 142830 121580 161210 107490 98857 91243 FALSE TRUE 29503.09282 33039.09662 63077.72449 110208.7406 147424.2567 124038.4309 163182.9362 105270.2939 87635.1678 85063.03034 0.346838018 0.388407237 0.741540999 1.295612678 1.733117855 1.458194358 1.918376709 1.237556357 1.030238018 1 16.37624463 3.869594852 2.306398093 1.440421858 0.36693336 0.706174953 0.269440609 0.157113707 1.623730391 0.075220687 0.168623833 7406.19005 -3.869594852 -1.073488498 LPHLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPHLLK 6 0 Q5XPI4;Q5XPI4-2;C9JI97 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 0 89.775 0.049783 562760000 629650 627670 542760 675860 686100 762310 729290 781650 864960 872560 FALSE TRUE 605042.5819 609769.4662 640848.8056 710741.2156 708169.0296 777724.4305 738215.2692 765508.6543 766773.367 813460.734 0.743788307 0.749599139 0.787805457 0.87372529 0.870563261 0.956068803 0.907499574 0.941051759 0.94260649 1 19.63371318 3.871371209 0.510546856 0.964453092 0.665244183 0.926279639 0.023150746 0.47678911 0.176546929 0.015814557 0.078372261 7436.54497 -3.871371209 -0.299208909 DLDEVLQTHSVFVNVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDEVLQTHSVFVNVSK 17 0 Q9Y3A5;A0A087X020;F8WE72 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 124.84 4.89E-05 2383700000 3478900 3994600 2645000 2265600 2205780 2176130 1956460 2306060 3067700 2922800 FALSE TRUE 3342940.742 3880677.919 3123010.338 2382527.888 2276730.917 2220132.84 1980403.743 2258439.055 2719467.557 2724836.153 1.226841012 1.424187621 1.146127753 0.874374734 0.835547824 0.814776638 0.726797368 0.82883481 0.998029755 1 21.37773805 3.872977152 2.796146592 0.845265206 1.324306792 0.803150449 0.092245486 0.100418281 1.510297061 0.024151326 0.050676791 7464.094896 -3.872977152 0.479041586 SQSDLDDQHDYDSVAS(ph)DEDTDQEPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SQSDLDDQHDYDSVAS(0.999)DEDTDQEPLR;SQSDLDDQHDYDS(0.001)VAS(0.867)DEDT(0.132)DQEPLR;SQSDLDDQHDYDSVAS(1)DEDTDQEPLR;SQSDLDDQHDYDSVAS(1)DEDTDQEPLR 204.51 2.42E-25 2315880000 945648 1004862 824395 1116198 995364 1120871 1173000 1046955 1158210 1244612 TRUE FALSE 908691.0307 976204.3196 973381.5151 1173805.113 1027380.787 1143535.78 1187355.525 1025335.013 1026734.856 1160313.321 0.783142807 0.841328202 0.838895407 1.011627714 0.885433933 0.985540508 1.02330595 0.883670811 0.884877247 1 20.146083 3.873437001 5.81450451 0.947408708 0.818869618 0.570135459 0.052705525 0.174541144 7.502243356 0.013759609 0.025297934 7472.002375 -3.873437001 -0.12853909 DGWGGYGSDKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGWGGYGSDKR 11 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;;; 160.15 4.46E-05 4131930000 3555710 3728730 2912390 2858610 2991420 2539310 3397960 3367760 3448720 3766880 FALSE TRUE 3416748.922 3622390.271 3438723.659 3006143.205 3087641.741 2590656.588 3439545.251 3298214.579 3057235.764 3511745.862 0.9729488 1.031506952 0.979206296 0.856025271 0.879232684 0.737711865 0.979440252 0.939195121 0.870574319 1 21.74375701 3.873626403 5.146027276 0.893378752 1.002794754 0.302182027 0.070020896 0.272549375 10.22951966 0.018532735 0.034435067 7475.261727 -3.873626403 0.109416003 DEATAAVIDLNDRPIGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEATAAVIDLNDRPIGSR 18 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 275.37 4.17E-39 2820100000 767660 733260 637350 787430 843060 749370 805730 903990 800970 850960 FALSE TRUE 737658.9985 712348.1427 752533.3228 828069.3567 870177.7905 764522.7748 815590.7648 885322.2906 710047.2435 793323.7212 0.929833533 0.897928706 0.948582908 1.04379755 1.096876051 0.963695846 1.028068042 1.115965988 0.895028378 1 19.59755016 3.873871292 3.826160939 1.031499054 0.91543975 0.340048269 0.060366657 0.230693516 5.90856774 0.015651888 0.0303772 7479.47805 -3.873871292 -0.116059304 GGPEVQQVPAGERPLWFICSGMGTQWR ddPTM_BT-474_Pertuzumab_2h_R1 4 GGPEVQQVPAGERPLWFICSGMGTQWR 27 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 219.95 2.64E-34 9365040000 1669900 1664150 1423540 1793510 1823540 1827470 1959270 1599050 2294690 2168940 FALSE TRUE 1604638.462 1616690.071 1680805.344 1886073.266 1882195.82 1864422.695 1983248.132 1566029.059 2034206.411 2022035.762 0.793575708 0.799535845 0.831244123 0.932759599 0.930842004 0.922052285 0.980817535 0.774481386 1.006019008 1 20.94737708 3.874021218 3.458700697 0.919306334 0.799058334 0.454953407 0.062688651 0.24992328 5.472231822 0.016845603 0.033406196 7482.060548 -3.874021218 -0.120248001 ATGDWK ddPTM_BT-474_Pertuzumab_2h_R1 3 ATGDWK 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;; 128.75 0.038361 1412030000 2140730 2108720 1825260 2142000 2137370 2190220 2293020 2430610 2629040 2465280 FALSE TRUE 2057067.905 2048581.37 2155125.085 2252548.877 2206120.447 2234507.749 2321082.665 2380417.054 2330602.401 2298304.39 0.895037191 0.891344671 0.937702201 0.980091622 0.959890455 0.972241866 1.009910904 1.035727498 1.014052974 1 21.13213845 3.874938628 0.511136774 1.022780786 0.851311127 0.87123176 0.016758521 0.677792948 0.25107 0.012833133 0.06391994 7497.882467 -3.874938628 -0.171469659 TQTPQLHFLDTDDEVS(ph)PTSWGDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQTPQLHFLDTDDEVSPTSWGDSR 24 0 Q86US8 Q86US8 SMG6 Telomerase-binding protein EST1A 1 TQTPQLHFLDTDDEVS(0.996)PT(0.004)SWGDSR;TQTPQLHFLDTDDEVS(0.989)PT(0.009)S(0.002)WGDSR 265.38 1.66E-44 223730000 88032 82683 69370 148667 117945 122957 135938 105819 96794 97863 TRUE FALSE 84591.61212 80324.9618 81906.70213 156339.7217 121738.808 125443.2748 137601.6499 103633.8007 85806.35091 91234.65184 0.927187318 0.88042164 0.897758697 1.713600244 1.33434836 1.374952085 1.508216967 1.135903942 0.940501763 1 16.47729426 3.875213426 23.29606998 1.301636781 0.899554129 0.397805188 0.216527129 8.383690818 1527.887931 0.056200626 0.10131723 7502.628211 -3.875213426 -0.402082652 RRDS(ph)GIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRDSGIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK 49 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RRDS(0.31)GIGEET(0.31)AT(0.31)GLGS(0.057)HVEVT(0.01)PHT(0.002)APPGVSAGPDAISEVLSTLSLEVNK 237.92 2.73E-61 1036800000 240030 288800 250860 252360 333180 329810 299210 177700 340580 328660 TRUE FALSE 230649.3622 280563.7068 296195.9824 265384.3298 343897.0373 336478.9842 302871.8215 174030.4329 301918.7862 306399.5655 0.752773138 0.915679193 0.966698441 0.866138075 1.122380956 1.098170566 0.988486459 0.567985247 0.985376026 1 18.22505473 3.875893773 0.004071156 0.92822546 0.895948042 0 0.157030058 26550067.54 22946.5944 89010.01965 92935.84735 7514.390715 -3.875893773 -0.032277417 GDS(ph)PENR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDSPENR 7 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 GDS(1)PENR;GDS(1)PENR;GDS(1)PENR 132.13 0.0035647 229331000 589482 619298 511173 654098 647347 686901 738356 663158 535165 743430 TRUE FALSE 566444.3917 601636.2274 603553.3321 687856.0762 668169.5042 700790.6089 747392.2216 649463.5556 474415.3128 693076.8239 0.817289472 0.868065713 0.870831791 0.992467289 0.964062686 1.011129769 1.07836851 0.937072967 0.684506099 1 19.40265575 3.875933095 4.38170805 0.958970234 0.848021287 0.179511734 0.098535362 0.388480889 12.01224975 0.026282712 0.049862794 7515.07112 -3.875933095 -0.110948947 VLPSFWIPSLT(ph)PEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLPSFWIPSLTPEAK 15 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 1 VLPSFWIPS(0.025)LT(0.975)PEAK 124.78 0.0016187 0 174400 161240 134740 101610 120550 126220 135880 144280 148880 155110 TRUE FALSE 167584.2552 156641.5931 159090.5153 106854.1043 124427.6002 128772.2549 137542.9401 141300.5676 131979.7666 144604.2615 1.158916434 1.08324327 1.100178609 0.738941599 0.860469802 0.890514937 0.951167957 0.97715355 0.912696245 1 17.14175054 3.876051361 9.357367149 0.908292914 1.113711982 0.652195033 0.070197784 0.223004382 15.90169647 0.019118162 0.034550594 7517.117889 -3.876051361 0.205419068 LVSPET(ph)EASEESLQFNLEKPATGER ddPTM_BT-474_Pertuzumab_2h_R1 1 LVSPETEASEESLQFNLEKPATGER 25 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LVS(0.429)PET(0.556)EAS(0.015)EESLQFNLEKPATGER 91.086 0.021304 82478000 38123 40985 33859 45137 39189 43222 46516 53369 51792 52389 TRUE FALSE 36633.11101 39816.14793 39978.07449 47466.52598 40449.54978 44095.97845 47085.27672 52266.9115 45912.78929 48840.64637 0.750053772 0.815225655 0.818541061 0.971865229 0.828194399 0.902854113 0.964059246 1.07015192 0.94005286 1 15.57579467 3.877084473 0.37681074 1.026582317 0.668771712 0.675489498 0.054318738 1.850217078 0.335266476 0.054753246 0.284834397 7535.02111 -3.877084473 -0.357810605 KEGDLIAAQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEGDLIAAQAR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 157.03 4.94E-05 2903360000 6086850 5858590 4740930 4279320 4927630 3794880 5309240 5388930 5181260 5983440 FALSE TRUE 5848969.173 5691508.749 5597721.512 4500176.218 5086131.694 3871615.074 5374216.067 5277646.712 4593105.086 5578176.279 1.048545058 1.020317119 1.003503875 0.806746864 0.911791137 0.694064669 0.96343604 0.946124046 0.823406227 1 22.4113621 3.877352692 5.734233451 0.879254813 1.02908101 0.391599894 0.083924539 0.234491913 9.976078649 0.021651015 0.039864143 7539.676155 -3.877352692 0.149826197 GAGATS(ph)GSPPAGRN ddPTM_BT-474_Pertuzumab_2h_R1 3 GAGATSGSPPAGRN 14 1 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGAT(0.091)S(0.454)GS(0.454)PPAGRN;GAGAT(0.026)S(0.582)GS(0.392)PPAGRN;GAGAT(0.043)S(0.479)GS(0.479)PPAGRN 100.73 0.0017682 433945000 706172 759385 507878 538267 605204 659086 551364 518340 580955 567601 TRUE FALSE 678574.0175 737728.0833 599662.8523 566047.0244 624670.9363 672413.1705 558111.7576 507636.0979 515007.424 529156.8787 1.28236832 1.394157599 1.1332421 1.069714951 1.180502345 1.270725559 1.054718893 0.959330056 0.973260378 1 19.01333597 3.877433889 0.301433861 0.943430988 1.49214239 0.595418868 0.088873055 3.314900064 0.366669605 0.118072489 0.646651254 7541.085924 -3.877433889 0.548711402 APSS(ph)PVAKPGPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 APSSPVAKPGPVK 13 1 Q9GZR2;A0A0C4DG31;Q9GZR2-2 Q9GZR2 REXO4 RNA exonuclease 4 1 APS(0.165)S(0.835)PVAKPGPVK 60.209 0.096422 0 249420 239740 194450 181800 207610 193650 214610 181050 249390 260540 TRUE FALSE 239672.3907 232902.8499 229591.4405 191182.7198 214287.9642 197565.7357 217236.4614 177311.2542 221080.2927 242893.3937 0.986739026 0.958868606 0.945235426 0.787105474 0.882230516 0.813384558 0.894369575 0.729996199 0.910194754 1 17.88996373 3.878621591 5.440664444 0.843096421 0.968016908 0.294967617 0.071144398 0.223339167 8.980847662 0.017335355 0.03206355 7561.737392 -3.878621591 0.124920487 TFIAIKPDGVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TFIAIKPDGVQR 12 1 Q32Q12;P22392-2;J3KPD9;P22392;E7ERL0;E5RHP0;F6XY72;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 139.19 5.57E-05 22572000000 10760500 11031700 8203700 7916900 8297100 8709900 7913400 7627100 9272800 9361300 FALSE TRUE 10339967.76 10717086.72 9686291.08 8325492.158 8563983.757 8886020.146 8010246.556 7469597.72 8220190.619 8727250.813 1.184790948 1.228002603 1.109890307 0.953965039 0.98129227 1.018192365 0.917843056 0.855893555 0.941899207 1 23.05709583 3.878675857 2.174213263 0.939719847 1.209992126 0.839289855 0.045394733 0.124986135 1.147654471 0.014425885 0.033490342 7562.6823 -3.878675857 0.270272279 ALYDYAGQEADELSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALYDYAGQEADELSFR 16 0 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ; 182.02 5.15E-09 184707000 108290 112353 90829 131709 128761 117932 114861 134286 118321 111853 FALSE TRUE 104057.9071 109148.8024 107243.8208 138506.5173 132902.7145 120316.6658 116266.7033 131512.9472 104889.6961 104277.0967 0.997898008 1.046718847 1.02845039 1.328254446 1.27451491 1.153816798 1.114978332 1.261187273 1.005874727 1 16.67006279 3.878758395 14.96368485 1.179599396 1.026128203 0.264211115 0.103083292 1.284316098 152.0286797 0.02569092 0.046320149 7564.119731 -3.878758395 -0.153471193 IKPS(ph)IR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKPSIR 6 1 H7C201 H7C201 GLS 1 IKPS(1)IR;IKPS(1)IR 75.38 0.047143 383830000 798010 789470 633790 655500 662990 535070 749410 789910 797840 770940 TRUE FALSE 766822.887 766955.0886 748329.9516 689330.4336 684315.6755 545889.482 758581.5038 773598.0825 707272.548 718723.5471 1.066923284 1.067107223 1.041193035 0.959103728 0.952126417 0.759526363 1.055456589 1.07634999 0.984067589 1 19.45507743 3.880326008 3.899829042 0.974964213 1.064865081 0.205392694 0.080466012 0.446663177 11.79521345 0.023666174 0.0458989 7591.472229 -3.880326008 0.089900867 QHAAVSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QHAAVSEK 8 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 ; 92.838 0.011494 121463000 272350 259860 187657 213380 204876 160872 203640 171956 232690 242940 FALSE TRUE 261706.2609 252449.0472 221570.7943 224392.5674 211466.0226 164124.9421 206132.2072 168405.0485 206276.0067 226485.4574 1.155510221 1.114636896 0.978300315 0.990759274 0.933684772 0.724659958 0.910134406 0.743557889 0.910769323 1 17.78905889 3.880837397 0.898991074 0.840062649 1.177613644 0.594573473 0.083250899 0.497127181 0.669473048 0.030221161 0.128510555 7600.416592 -3.880837397 0.337550995 KAPS(ph)SPPPPPPPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPSSPPPPPPPLR 14 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 KAPS(0.5)S(0.5)PPPPPPPLR 54.974 0.083548 1196300000 508340 503910 429480 535840 502440 568530 531490 581150 608180 610330 TRUE FALSE 488473.5108 489538.9802 507096.5897 563494.7666 518601.4389 580026.0661 537994.5336 569149.0494 539141.9561 568991.8055 0.858489536 0.860362092 0.891219495 0.990338984 0.911439205 1.019392653 0.945522463 1.000276355 0.947539052 1 19.11804835 3.881010594 3.319786906 0.972978849 0.860951351 0.711594722 0.030511257 0.121323802 2.484850189 0.007472762 0.015032704 7603.448235 -3.881010594 -0.112027498 NPWGEVEWTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 NPWGEVEWTGR 11 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 188.99 7.47E-05 910630000 336616 351683 294351 389378 349165 399745 406524 405137 404852 423384 FALSE TRUE 323460.6746 341653.3452 347546.7735 409473.8452 360396.2093 407828.1178 411499.1623 396770.7794 358894.8982 394707.8246 0.819493951 0.865585438 0.880516554 1.037410002 0.913070851 1.03324052 1.042541183 1.005226536 0.90926725 1 18.59042559 3.882529922 4.205612924 0.993863648 0.848102528 0.653417438 0.045862117 0.135581066 3.991859572 0.011948445 0.022873156 7630.094596 -3.882529922 -0.145761119 RGS(ph)MSYLAAVEEEVEESSVK ddPTM_BT-474_Pertuzumab_2h_R1 4 RGSMSYLAAVEEEVEESSVK 20 1 Q8WXH0;Q8WXH0-2;G3V5X4;A0A0A0MRE3;A0A0C4DGK3;Q8WXH0-7 Q8WXH0 SYNE2 Nesprin-2 1 RGS(0.392)MS(0.392)Y(0.215)LAAVEEEVEESSVK;RGS(0.703)MS(0.274)Y(0.024)LAAVEEEVEESSVK;RGS(0.989)MS(0.011)YLAAVEEEVEESSVK;RGS(0.912)MS(0.088)YLAAVEEEVEESSVK 227.03 2.46E-25 231837000 326488 294611 235497 196940 216545 202941 178531 248658 225292 181193 TRUE FALSE 313728.488 286208.9827 278056.5465 207104.097 223510.3666 207044.6061 180715.9158 243523.1254 199717.7967 168920.6367 1.857253762 1.694339947 1.646078016 1.226043786 1.323167914 1.225691603 1.069827342 1.441642242 1.182317333 1 17.36598606 3.882856573 1.892271252 1.229064791 1.79886344 0.792720906 0.122994577 0.15539923 1.074726168 0.03403551 0.085187377 7635.835654 -3.882856573 0.569798648 LIESAEELIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LIESAEELIR 10 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 97.431 0.012148 0 19470 18957 16384 20827 22272 22282 20484 20064 22723 23896 FALSE TRUE 18709.09087 18416.36492 19344.95326 21901.88397 22988.39911 22732.55731 20734.68932 19649.67139 20143.5803 22277.50264 0.839819938 0.826679957 0.868362741 0.983139103 1.031910959 1.020426646 0.930745679 0.882041031 0.90421178 1 14.44329989 3.884770361 4.163611218 0.957835059 0.835835839 0.586821282 0.046282129 0.197840515 5.75991696 0.014561717 0.027949993 7669.558435 -3.884770361 -0.12199922 IAIS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IAISPLK 7 0 Q6MZP7-3;Q6MZP7 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 IAIS(1)PLK 102.55 0.0089963 29015000 77648 75207 65277 81746 79217 90574 81669 85527 87394 95509 TRUE FALSE 74613.43032 73062.17 77074.00598 85964.92086 81765.08675 92405.46834 82668.48965 83760.83756 77473.39951 89040.09036 0.837975681 0.820553637 0.86561015 0.965463091 0.918295191 1.03779621 0.928441215 0.940709261 0.870095697 1 16.44216744 3.885203356 3.521514642 0.949352304 0.830825154 0.582734041 0.043279143 0.167091558 3.780563404 0.011200317 0.022267101 7677.208863 -3.885203356 -0.11852715 TKIDWNK ddPTM_BT-474_Pertuzumab_2h_R1 2 TKIDWNK 7 1 P47755;P52907 P47755;P52907 CAPZA2;CAPZA1 F-actin-capping protein subunit alpha-2;F-actin-capping protein subunit alpha-1 0 ; 112.84 0.0057124 3358200000 10026600 9738500 7688400 6409300 7133600 3672800 9213600 8836400 9236800 9087800 FALSE TRUE 9634749.387 9460767.515 9077864.908 6740084.741 7363058.723 3747066.532 9326358.793 8653925.252 8188277.188 8472275.211 1.137209208 1.116673772 1.071478992 0.79554601 0.869076905 0.442273939 1.100809235 1.021440526 0.966479131 1 23.01431802 3.885422121 5.142419564 0.889099145 1.119708088 0.268102977 0.170319433 0.326982611 12.50338808 0.047152378 0.08780865 7681.077039 -3.885422121 0.230608943 RRDYYDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRDYYDR 7 2 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 89.298 0.071416 33530000 31852 38427 25773 23695 22655 23611 22705 27026 28529 28777 FALSE TRUE 30607.18863 37331.09958 30430.75442 24917.90179 23383.71865 24088.4306 22982.87058 26467.90366 25290.50752 26827.90816 1.140871232 1.391502437 1.134294714 0.928805244 0.871619155 0.897887023 0.856677697 0.98658097 0.94269398 1 14.71144695 3.885586106 3.323120684 0.921713352 1.267145972 0.789749776 0.071750662 0.094802038 1.948066341 0.018015809 0.036343556 7683.977875 -3.885586106 0.34543262 ELESQISELQEDLESER ddPTM_BT-474_Pertuzumab_2h_R1 6 ELESQISELQEDLESER 17 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 536.99 0 1848099000 663188 686509 575750 903117 811401 639642 856627 847201 942306 982022 FALSE TRUE 637269.8798 666930.4355 679800.8325 949726.9766 837500.4501 652575.9995 867110.6575 829706.0033 835339.3733 915508.7752 0.696082765 0.728480659 0.742538849 1.037376159 0.914792379 0.712801469 0.947135277 0.906278591 0.912431859 1 19.80421419 3.885752995 7.329783677 0.907727575 0.718019871 0.551323899 0.080985584 0.20192586 11.57818652 0.021031581 0.03822837 7686.931218 -3.885752995 -0.189707703 MAPTPIPTRSPS(ph)DSSTASTPVAEQIER ddPTM_BT-474_Pertuzumab_2h_R1 1 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.253)RS(0.184)PS(0.445)DS(0.017)S(0.049)T(0.049)AS(0.001)TPVAEQIER 194.55 6.68E-19 10786000000 1389900 1247800 1102600 1619100 1582900 1684300 1431400 1375900 1461000 1774300 TRUE FALSE 1335581.171 1212213.966 1301864.347 1702661.945 1633815.416 1718357.7 1448917.901 1347487.184 1295153.405 1654125.081 0.807424533 0.732842987 0.787041054 1.029342923 0.987721808 1.038831779 0.875942163 0.814622304 0.782983959 1 20.6576369 3.886203051 7.662805703 0.921556817 0.767727712 0.416724683 0.084521687 0.303503232 18.33527383 0.024646127 0.044732731 7694.901249 -3.886203051 -0.153829105 KPTAEAS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPTAEASPVK 10 1 Q6ZRI6;H3BMJ2;Q6ZRI6-2 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 1 KPT(0.001)AEAS(0.999)PVK;KPTAEAS(1)PVK 98.676 0.0031939 869640000 1319600 1144710 954690 724050 839970 525500 1045470 1017070 1214830 1158160 TRUE FALSE 1268028.573 1112063.992 1127223.72 761418.3073 866988.3979 536125.97 1058264.775 996067.1491 1076927.591 1079716.792 1.174408496 1.029958967 1.043999435 0.705201876 0.8029776 0.496543144 0.980131811 0.922526311 0.99741673 1 20.04222151 3.887813736 5.831193064 0.838496193 1.08705115 0.35018507 0.150191028 0.264528218 11.82238437 0.040608821 0.074762773 7723.492629 -3.887813736 0.248554956 SES(ph)PPAELPSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SESPPAELPSLR 12 0 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 SES(1)PPAELPSLR;SES(1)PPAELPSLR;SES(1)PPAELPSLR;SES(1)PPAELPSLR 322.06 8.15E-47 4097730000 2563700 2482990 2057270 2705010 2754280 2294270 2538830 2900380 2491510 2586260 TRUE FALSE 2463507.77 2412177.556 2429064.453 2844615.89 2842873.918 2340661.711 2569900.961 2840486.139 2208684.23 2411090.307 1.021740149 1.000450937 1.007454779 1.179804789 1.179082306 0.970789731 1.065866738 1.178091974 0.916052055 1 21.20125426 3.888330929 17.76595246 1.083945202 1.0087931 0.075717405 0.087012247 5.567733134 868.064088 0.022247851 0.040108864 7732.695854 -3.888330929 -0.075152102 KATQAS(ph)QEY ddPTM_BT-474_Pertuzumab_2h_R1 1 KATQASQEY 9 1 P16104 P16104 H2AFX Histone H2AX 1 KAT(0.005)QAS(0.995)QEY 62.705 0.085664 291560000 690590 760260 438580 524460 416050 441980 383180 429570 488770 434320 TRUE FALSE 663600.9793 738578.1292 517841.1622 551527.4435 429432.6261 450917.1384 387869.4715 420699.2294 433286.8787 404903.1195 1.638912983 1.824086043 1.278926087 1.362121991 1.060581175 1.113642046 0.957931546 1.039012072 1.070100125 1 18.62721723 3.888749368 0.962358561 1.02362261 1.801947362 0.860473298 0.103718425 0.229382556 0.359543189 0.034299466 0.141198231 7740.149839 -3.888749368 0.778324751 VDKWWGNRK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDKWWGNRK 9 2 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 120.09 0.00040573 2648200000 3654200 3895000 2943200 2430970 2370140 1899760 3511100 3172300 3616000 3660900 FALSE TRUE 3511389.824 3783918.414 3475101.711 2556432.653 2446377.706 1938174.449 3554069.892 3106790.896 3205526.84 3412943.982 1.028844845 1.108696314 1.01821235 0.74904032 0.716793981 0.567889323 1.041350198 0.910296481 0.939226327 1 21.7025853 3.888988943 5.403683538 0.842762846 1.067565978 0.331367878 0.134798679 0.266474675 10.93609232 0.037481901 0.069484793 7744.420809 -3.888988943 0.224803132 DVITLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVITLR 6 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17;A6NJU9;F8W1W9;A0A1B0GW90;C9JGN3;E9PS57;I3L0I5;E9PKP1;F6SDX0;F8W0I5;E7EUG2;A0A087WT63;F8VUA1;A0A087WUS9;E7EQW1;A0A087WWP6;C9JB18;A0A087WV59;A0A494C1T1;H0YIQ3;F8VY45;A6NJ64;Q92617-3;Q92617-2;A6NHN6;E9PQR5;E9PJ23;O75200;Q92617-6;Q92617-5;Q92617;H0YDQ7;F5H4N5;C9JG80;C9K082;A8MRT5;E5RHQ5 Q9Y365 STARD10;NPIPB9;NPIPB3;NPIPB6;NPIPB7;NPIPB5;NPIPB4;NPIPB11;NPIPB15;NPIPB8 PCTP-like protein;Putative NPIP-like protein LOC613037;Nuclear pore complex-interacting protein family member B9;Putative NPIP-like protein LOC729978;Nuclear pore complex-interacting protein family member B3;Nuclear pore complex-interacting protein family member B15;Nuclear pore complex-interacting protein family member B8;Nuclear pore complex-interacting protein family member B6;Nuclear pore complex-interacting protein family member B7;Nuclear pore complex-interacting protein family member B4;Nuclear pore complex-interacting protein family member B5;Nuclear pore complex-interacting protein family member B11 0 ;;;;; 137.83 0.029234 2980650000 2518140 2553480 2102280 2955850 2665260 2816650 2736970 2816170 2978940 2987700 FALSE TRUE 2419728.305 2480657.251 2482208.761 3108401.773 2750990.508 2873604.593 2770465.858 2758015.105 2640783.22 2785340.418 0.868737009 0.890611874 0.891168902 1.115986309 0.987667608 1.031688829 0.994659698 0.990189597 0.948100707 1 21.40942223 3.8901988 10.26932395 1.007343616 0.882475623 0.662615375 0.041301772 0.246323233 21.40349007 0.010404011 0.018784734 7766.025275 -3.8901988 -0.124867993 VEERDPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEERDPPR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 113.62 0.0025657 1636650000 1540130 1602430 1346640 1809810 1688860 1751820 1793310 1844780 1908730 2062500 FALSE TRUE 1479940.017 1556730.265 1590007.804 1903214.511 1743183.716 1787243.001 1815257.064 1806684.648 1692058.972 1922805.038 0.769677626 0.809614201 0.826920968 0.989811486 0.906583705 0.929497773 0.944067146 0.939608859 0.87999508 1 20.87478106 3.890275649 4.717266753 0.93702116 0.795462991 0.773833736 0.034746786 0.096483704 3.356807623 0.008508641 0.01603765 7767.399611 -3.890275649 -0.141558169 SAEPPRS(ph)PLLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEPPRSPLLKR 12 2 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;Q9Y2H9;O15021-2;H7C1I9;O15021-3;O15021-6;O15021 Q6P0Q8;O15021-2 MAST2;MAST1;MAST4 Microtubule-associated serine/threonine-protein kinase 2;Microtubule-associated serine/threonine-protein kinase 1;Microtubule-associated serine/threonine-protein kinase 4 1 S(0.006)AEPPRS(0.994)PLLKR 82.85 0.0072219 85373000 179270 205260 155040 146550 132950 179460 154930 177590 217390 173110 TRUE FALSE 172263.9302 199406.1858 183059.1768 154113.4631 137226.4575 183088.8042 156826.0797 173922.7044 192712.7986 161385.1055 1.0674091 1.235592251 1.13430032 0.954942295 0.850304352 1.134483902 0.971750641 1.07768746 1.194117623 1 17.30014791 3.890819546 6.499187556 1.026750003 1.159383579 0.23731867 0.098267004 0.325117338 16.73363506 0.025623746 0.046845855 7777.133358 -3.890819546 0.132633576 KFTFGLDWVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFTFGLDWVPK 11 1 P45974-2;P45974;H7C5J3;Q92995-2;Q92995 P45974-2;Q92995-2 USP5;USP13 Ubiquitin carboxyl-terminal hydrolase 5;Ubiquitin carboxyl-terminal hydrolase 13 0 84.365 0.025681 163290000 745480 691970 518770 407920 413690 391920 409480 458450 481520 528380 FALSE TRUE 716345.8174 672235.6931 612523.279 428972.8001 426996.7146 399844.8909 414491.3387 448982.8473 426859.8683 492592.352 1.45423658 1.364689668 1.243468918 0.870847463 0.866835859 0.811715589 0.841448993 0.911469383 0.866558051 1 18.9100347 3.890857468 2.393739278 0.870490594 1.412798149 0.944674887 0.05332152 0.057908827 0.645187827 0.014263885 0.032164369 7777.812476 -3.890857468 0.542307556 LLTSHDCEILESEVTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLTSHDCEILESEVTGR 17 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 143.67 5.40E-07 100893000 62861 64622 52809 62813 65870 64697 64410 58939 69669 81359 FALSE TRUE 60404.32262 62779.04383 62352.76103 66054.78646 67988.76837 66005.21767 65198.26885 57721.88905 61760.4672 75848.48246 0.796381426 0.827690176 0.822069987 0.870878155 0.896376119 0.870224631 0.859585673 0.761015741 0.814261079 1 16.2108327 3.891387773 5.221302684 0.852836948 0.814874318 0.109011819 0.058873506 0.659085652 26.17376391 0.015710727 0.029243455 7787.315555 -3.891387773 -0.03796263 ERSDYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERSDYDR 7 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A087X0F4 C9JUL9;Q9BXP5-4;REV__Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 0 ; 102.46 0.0078384 267000000 250371 254528 206221 279575 234485 251298 268597 256669 292450 293086 FALSE TRUE 240586.2245 247269.1106 243489.7221 294003.8993 242027.423 256379.4177 271884.1704 251368.6955 259252.3021 273235.0242 0.880510195 0.904968576 0.891136569 1.076011028 0.88578477 0.93831096 0.995056074 0.919972453 0.948825294 1 18.0597829 3.891633295 21.49857987 0.959844991 0.893424431 0.315894723 0.049308689 11.36207984 2238.413115 0.012147149 0.021898628 7791.719229 -3.891633295 -0.06642056 AAGMAS(ph)PWGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGMASPWGK 10 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3 M0QXA7 WIZ Protein Wiz 1 AAGMAS(1)PWGK 81.676 0.021289 61030000 74370 83129 60462 60578 59234 57605 54804 78231 70276 68901 TRUE FALSE 71463.53818 80758.24231 71388.82837 63704.43784 61139.3154 58769.81257 55474.70775 76615.50251 62298.5631 64234.2739 1.112545279 1.257245352 1.111382196 0.991751505 0.951817646 0.914929196 0.863630962 1.192751126 0.969864829 1 15.97105567 3.891884689 3.467087956 0.992282598 1.185603359 0.472749447 0.087177454 0.229191677 5.077318393 0.024898272 0.04989678 7796.230824 -3.891884689 0.193320761 CYYYHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 CYYYHAR 7 0 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 103.28 0.0084106 271060000 227540 228950 243500 261320 312110 277340 475090 291790 338580 303190 FALSE TRUE 218647.4852 222420.5702 287505.8666 274806.7565 322149.3016 282948.0048 480904.2935 285764.4345 300145.8178 282654.6712 0.773549874 0.786898618 1.017162976 0.972234972 1.139727499 1.001037781 1.70138456 1.011001988 1.061881682 1 18.10868101 3.892175036 0.930033665 1.182717753 0.729444903 0.331890779 0.198803348 0.875076525 1.265418744 0.07303111 0.30947374 7801.444721 -3.892175036 -0.453272851 DRENYDR ddPTM_BT-474_Pertuzumab_2h_R1 5 DRENYDR 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;; 157.91 0.001317 2001872000 1685506 1589221 1398035 1742263 1647990 1874715 1794097 1781243 1935400 2094444 FALSE TRUE 1619634.562 1543897.973 1650691.024 1832181.402 1700999.095 1912623.022 1816053.696 1744459.71 1715701.506 1952585.442 0.829482043 0.790694194 0.845387345 0.938336097 0.871152196 0.979533587 0.930076429 0.893410179 0.87868191 1 20.89695425 3.893075454 3.709602959 0.921193661 0.810837228 0.598148649 0.039964956 0.158425841 3.923039884 0.01013454 0.019998077 7817.636161 -3.893075454 -0.110356433 FLTAVNLEHPEMLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLTAVNLEHPEMLEK 15 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;E9PFN5;Q9Y2Q3-4;C9JNT3 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 109.36 0.0010061 302910000 672650 725380 597120 871840 830320 754250 872740 794160 838140 923000 FALSE TRUE 646362.0943 704692.8726 705032.8669 916835.7669 857027.9969 769501.4518 883420.8532 777760.3185 742997.861 860484.3879 0.751160746 0.818949051 0.81934417 1.065487974 0.995983203 0.894265442 1.026655295 0.90386337 0.863464662 1 19.71478949 3.893574744 6.757951356 0.958996947 0.793234964 0.611481171 0.061488489 0.166911573 9.157157427 0.016086553 0.029354308 7826.628938 -3.893574744 -0.165761983 LSSPCIMVVNHDASSIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSPCIMVVNHDASSIPR 18 0 Q08J23;Q08J23-2 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 131.45 1.69E-05 1088400000 121310 120580 102270 142840 134820 118900 135770 152310 141020 147050 FALSE TRUE 116569.0711 117141.1765 120752.464 150211.9895 139156.6077 121304.2395 137431.5939 149164.7453 125012.0008 137090.1725 0.850309464 0.854482669 0.880825093 1.095716686 1.015073547 0.884850002 1.002490487 1.088077595 0.911896152 1 17.06476563 3.893767146 6.648625209 1.004319557 0.856054624 0.511601603 0.061970366 0.190609857 10.26886665 0.016595945 0.030310038 7830.097077 -3.893767146 -0.148264932 RPAEPGPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPAEPGPAR 9 1 A0A0A0MTR2;Q8N543;H3BR79;H3BR02 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 78.098 0.04928 34274000 95992 100600 63281 65326 56116 57423 70105 24475 78458 58598 FALSE TRUE 92240.52652 97730.9865 74717.28438 68697.48269 57921.0221 58584.1324 70962.96596 23969.5827 69551.77676 54629.10527 1.688486862 1.788991162 1.367719351 1.257525313 1.060259395 1.072397802 1.298995574 0.438769454 1.273163388 1 15.73738217 3.894259671 0.699358941 0.918051292 1.920761593 0.58357854 0.230992678 0.80807389 0.606456413 0.111917435 0.547658093 7838.982072 -3.894259671 1.002710301 SMSSIPPYPASSLASSS(ph)PPGSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPASSLASS(0.006)S(0.994)PPGSGR;SMSSIPPYPASSLAS(0.004)S(0.016)S(0.98)PPGSGR 259.16 2.69E-40 391780000 110738 123315 100565 139800 131710 127681 133241 152015 134226 136814 TRUE FALSE 106410.2365 119798.1769 118739.3326 147015.0948 135946.5718 130262.7973 134871.6432 148875.8371 118989.2272 127547.4659 0.834279503 0.939243881 0.93094231 1.152630463 1.065850825 1.021288791 1.05742315 1.16721909 0.932901539 1 16.96067471 3.894337359 5.351040541 1.068306652 0.897451593 0.512492265 0.069378759 0.16451943 6.820285729 0.017673367 0.032829313 7840.384454 -3.894337359 -0.170855058 ASHSSERPPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ;; 115.18 0.00069605 482170000 12564.5 16114.2 11351.5 23375.1 17458.9 23290.2 21445.1 30360.4 17918.6 28217.4 FALSE TRUE 12073.46545 15654.63879 13402.96856 24581.49171 18020.48137 23761.1438 21707.55155 29733.44713 15884.55565 26306.21036 0.458958751 0.595092892 0.509498266 0.934436826 0.685027646 0.903252254 0.825187332 1.130282421 0.603832914 1 14.68311581 3.894615496 0.703986775 0.923757346 0.397423453 0.495031813 0.152455577 0.957790693 0.729545735 0.069996673 0.342036934 7845.407317 -3.894615496 -0.526333893 SRTS(ph)PITR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.323)RT(0.184)S(0.493)PITR;S(0.333)RT(0.21)S(0.456)PITR 80.014 0.016076 9445400000 314660 324530 290660 427550 404600 527090 461620 333530 437770 457780 TRUE FALSE 302362.7393 315274.7221 343188.7277 449615.9067 417614.3264 537748.1209 467269.4436 326642.4889 388076.1849 426774.1529 0.708484188 0.738739026 0.804145999 1.053521877 0.978537064 1.260029731 1.094886934 0.765375519 0.909324481 1 18.70311328 3.89472081 3.695592503 0.998911699 0.730278298 0.496698078 0.120316491 0.234004006 5.771031942 0.036396286 0.071951019 7847.310006 -3.89472081 -0.268633401 FDLDGDAPDEIATYMVEHDFILQAER ddPTM_BT-474_Pertuzumab_2h_R1 2 FDLDGDAPDEIATYMVEHDFILQAER 26 0 Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;H0Y7R3;H0Y493 Q9Y3S1 WNK2 Serine/threonine-protein kinase WNK2 0 ; 185.14 1.48E-17 57577000 45026 48638 40064 50356 56005 51185 53828 47258 55226 67032 FALSE TRUE 43266.33414 47250.89186 47304.45602 52954.87919 57806.45169 52219.99577 54486.76317 46282.10579 48956.97601 62491.86293 0.692351486 0.75611271 0.756969849 0.847388391 0.925023659 0.835628725 0.871901726 0.740610115 0.783413611 1 15.93138073 3.895253963 2.765270856 0.843574164 0.726139515 0.388717929 0.069535525 0.32921294 4.861819297 0.019211585 0.041235164 7856.949528 -3.895253963 -0.11743465 SRT(ph)SVQTEDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 S(0.142)RT(0.593)S(0.265)VQTEDDQLIAGQSAR;S(0.161)RT(0.61)S(0.229)VQTEDDQLIAGQSAR 364.17 1.37E-107 3436100000 289600 425970 334630 646170 421250 596930 689870 485300 571260 594870 TRUE FALSE 278282.1118 413821.7527 395105.0848 679518.9111 434799.8888 609000.3336 698312.8354 475278.3854 506412.9597 554578.925 0.501789915 0.74619091 0.712441579 1.225288017 0.784018053 1.098131043 1.259176654 0.857007657 0.913148583 1 19.08103327 3.895411948 6.06983457 1.012015898 0.648468095 0.551502773 0.152128093 0.174419217 8.504461498 0.038885101 0.071438758 7859.808198 -3.895411948 -0.363547803 MPGGPKPGGGPGLS(ph)TPGGHPKPPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 MPGGPKPGGGPGLS(0.918)T(0.082)PGGHPKPPHR;MPGGPKPGGGPGLS(0.92)T(0.08)PGGHPKPPHR 122.47 8.18E-05 2357100000 4479600 3594100 2963400 2304130 2146250 1859070 2060020 1826560 2494330 2732700 TRUE FALSE 4304532.28 3491599.787 3498952.3 2423046.425 2215286.08 1896661.669 2085231.141 1788840.898 2211184.115 2547611.795 1.689634303 1.370538398 1.373424439 0.951105043 0.869554021 0.744486139 0.818504273 0.702163847 0.867943899 1 21.28071403 3.895980645 1.164771523 0.792615623 1.638348844 0.89861766 0.098711784 0.149001693 0.360069388 0.029844272 0.107502841 7870.107149 -3.895980645 0.845733222 DDGLFSGDPNWFPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDGLFSGDPNWFPK 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 127.37 0.00062783 0 39632 43938 32979 34953 31790 36126 31631 40002 44799 46130 FALSE TRUE 38083.13762 42684.93126 38939.03891 36756.92852 32812.55422 36856.49247 32018.10964 39175.94472 39713.60533 43005.57401 0.885539572 0.992544158 0.905441674 0.854701498 0.762983752 0.857016638 0.744510691 0.910950397 0.923452512 1 15.39223604 3.896055844 3.861837864 0.853139204 0.94098975 0.125202303 0.074631727 0.366693426 9.713862704 0.01900932 0.037236538 7871.469987 -3.896055844 0.087850546 DGLKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGLKPR 6 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 71.378 0.080612 227130000 479540 448540 419080 548340 520360 730450 558280 487290 645240 636190 FALSE TRUE 460799.0466 435748.0784 494817.0784 576639.8931 537097.852 745220.1995 565112.3976 477227.2912 571995.0603 593100.2846 0.776932769 0.734695446 0.834289059 0.972246866 0.90557679 1.25648262 0.952810869 0.804631702 0.96441542 1 19.17791654 3.896542763 2.68544843 0.969264222 0.755904049 0.421567965 0.107844784 0.307173034 4.289758684 0.031987139 0.069432226 7880.300214 -3.896542763 -0.213360172 IGDPLLEDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGDPLLEDTR 10 0 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 137.13 0.00023109 459190000 702780 776240 621590 876730 786810 729690 863700 879400 858310 912900 FALSE TRUE 675314.5806 754102.3952 733925.1402 921978.1404 812118.4582 744444.8317 874270.219 861240.0827 760878.2471 851068.4699 0.793490306 0.886065483 0.862357338 1.083318409 0.954233986 0.874717908 1.027261907 1.01195158 0.894027066 1 19.69891568 3.897365532 8.827248373 0.978281464 0.848284897 0.487459198 0.061542559 0.28195199 22.06138656 0.015835509 0.028650492 7895.243557 -3.897365532 -0.129996567 EVPENETPVDTNLIELDTNDDDIVFEDFAR ddPTM_BT-474_Pertuzumab_2h_R1 3 EVPENETPVDTNLIELDTNDDDIVFEDFAR 30 0 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 261.86 2.32E-58 337835000 159447 158182 133502 180275 167539 176523 174218 168830 185569 208648 FALSE TRUE 153215.635 153670.8042 157628.7811 189579.0144 172928.0441 180092.416 176350.132 165343.6015 164503.9851 194516.0851 0.787675913 0.790015922 0.810363734 0.974618702 0.889016679 0.925848451 0.906609507 0.850025341 0.845708904 1 17.56952994 3.899058233 6.888086223 0.902750771 0.791555842 0.569220291 0.046293066 0.187158591 10.96687236 0.011940124 0.021776093 7926.07602 -3.899058233 -0.11119493 GAILSEEELAAMS(ph)PTAAAVAK ddPTM_BT-474_Pertuzumab_2h_R1 6 GAILSEEELAAMSPTAAAVAK 21 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 GAILSEEELAAMS(0.999)PT(0.001)AAAVAK;GAILSEEELAAMS(0.998)PT(0.002)AAAVAK;GAILSEEELAAMS(1)PTAAAVAK;GAILSEEELAAMS(0.979)PT(0.021)AAAVAK;GAILSEEELAAMS(1)PTAAAVAK;GAILSEEELAAMS(1)PTAAAVAK 375.69 1.31E-112 637696000 1077235 1021339 925693 985468 1049962 1084282 1086242 1163495 1148973 1129550 TRUE FALSE 1035135.465 992211.4117 1092986.317 1036328.122 1083734.981 1106206.925 1099535.755 1139468.422 1018546.402 1053044.572 0.982993021 0.942231163 1.037929776 0.9841256 1.029144454 1.050484428 1.044149301 1.082070457 0.967239591 1 20.00613507 3.899487832 0.979455175 1.038130243 0.960419994 0.230768177 0.036187933 0.839523806 1.362064888 0.012612218 0.052179415 7933.920264 -3.899487832 -0.077710249 HSLS(ph)STK ddPTM_BT-474_Pertuzumab_2h_R1 3 HSLSSTK 7 0 P42858;A0A3B3IU44 P42858 HTT Huntingtin 1 HSLS(0.992)S(0.008)TK;HSLS(0.958)S(0.042)TK;HS(0.002)LS(0.795)S(0.151)T(0.053)K 137.69 0.002998 382077000 1103410 974350 802560 720940 789840 589160 835420 584350 967360 929220 TRUE FALSE 1060287.517 946562.492 947600.4449 758147.7998 815245.9209 601073.2189 845644.1199 572282.9683 857549.3483 866283.1017 1.223950364 1.09267108 1.093869248 0.875173253 0.941084871 0.693853104 0.976175246 0.660618875 0.98991813 1 19.72447905 3.899773301 1.225383141 0.839628196 1.201593274 0.50674578 0.11661232 0.381638522 1.032788449 0.034513226 0.1200732 7939.137085 -3.899773301 0.361965078 RIVDGK ddPTM_BT-474_Pertuzumab_2h_R1 6 RIVDGK 6 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 104.8 0.05375 14199050000 26303750 27491010 22287120 25809660 25458840 29521610 26879690 28601940 29491900 28974930 FALSE TRUE 25275770.37 26706993.31 26314898.36 27141699.65 26277746.71 30118557.18 27208651.69 28011299.94 26144103.15 27012432.18 0.935708795 0.988692656 0.974177304 1.00478548 0.97280195 1.11498872 1.007264044 1.036978076 0.967854467 1 24.68712021 3.899982333 0.990581424 1.02382985 0.949596998 0.262798945 0.039687103 0.945879911 1.57466954 0.013741635 0.056435678 7942.95923 -3.899982333 -0.074232852 LFPEFDDS(ph)DYDEVPEEGPGAPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFPEFDDSDYDEVPEEGPGAPAR 23 0 Q96P48-3;Q96P48 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 LFPEFDDS(0.977)DY(0.023)DEVPEEGPGAPAR;LFPEFDDS(0.793)DY(0.207)DEVPEEGPGAPAR 90.968 0.0034467 64850000 28491 23925 22126 31389 29022 29416 25966 33517 30209 35164 TRUE FALSE 27377.54022 23242.68243 26124.66039 33008.99005 29955.51899 30010.81167 26283.77968 32824.86224 26779.80097 32782.31096 0.835131491 0.709000731 0.796913324 1.006914677 0.913770815 0.915457477 0.801767139 1.001297995 0.8168979 1 15.00062994 3.900210948 6.624678763 0.919023211 0.767490763 0.443909508 0.073018008 0.197815392 11.14142997 0.017658888 0.032275808 7947.141549 -3.900210948 -0.151532448 RWLPAGDALLQMITIHLPSPVTAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RWLPAGDALLQMITIHLPSPVTAQK 25 1 P13639 P13639 EEF2 Elongation factor 2 0 165.24 1.01E-11 67024000 88239 79678 65318 47483 65729 69241 62528 55641 74711 66126 FALSE TRUE 84790.52233 77405.66145 77122.41559 49933.60332 67843.23298 70641.10046 63293.23637 54491.99391 66230.12049 61647.22712 1.375415023 1.25562276 1.251028135 0.809989446 1.100507454 1.145892585 1.026700459 0.883932602 1.074340625 1 15.91174838 3.900493526 6.849504099 1.004922289 1.300677366 0.650755853 0.09732593 0.152295012 8.971382129 0.025944101 0.047334963 7952.314113 -3.900493526 0.295755076 RQS(ph)PEPSPVTLGR ddPTM_BT-474_Pertuzumab_2h_R1 3 RQSPEPSPVTLGR 13 1 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 RQS(1)PEPSPVTLGR;RQS(1)PEPSPVTLGR;RQS(1)PEPSPVTLGR 158.17 2.92E-05 5268300000 1125000 1166970 941030 1402220 1262810 1254800 1262470 1292610 1219130 1296180 TRUE FALSE 1081033.756 1133689.158 1111095.054 1474588.742 1303429.431 1280172.916 1277920.486 1265917.152 1080739.473 1208388.574 0.894607728 0.93818262 0.919484906 1.220293516 1.078650906 1.059405015 1.05754102 1.047607681 0.894364194 1 20.20465302 3.900858962 24.67035152 1.055599048 0.919404186 0.39279359 0.076021948 36.17756102 8995.512294 0.019519295 0.035188935 7959.008375 -3.900858962 -0.136194862 GS(ph)LAS(ph)LDSLRK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSLASLDSLRK 11 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 2 GS(1)LAS(1)LDSLRK;GS(1)LAS(0.999)LDS(0.001)LRK;GS(1)LAS(0.996)LDS(0.004)LRK;GS(1)LAS(0.998)LDS(0.002)LRK 130.72 0.00076408 770860000 2763850 2833550 1928280 1848100 1801940 1786790 1245920 2422810 1712090 1405420 TRUE FALSE 2655835.686 2752739.928 2276763.09 1943480.662 1859901.037 1822920.118 1261167.942 2372778.127 1517740.721 1310229.652 2.027000139 2.100959878 1.737682465 1.48331299 1.419522932 1.391298171 0.962554877 1.810963539 1.158377632 1 20.32138827 3.901351784 1.465873179 1.340582407 2.10415834 0.636705162 0.23072855 0.294706136 1.185774181 0.068019816 0.206205066 7968.045108 -3.901351784 0.763575933 HTDNVIQWLNAMDEIGLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 HTDNVIQWLNAMDEIGLPK 19 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 147.9 1.01E-07 562470000 796030 764330 640980 761620 779120 790990 784830 688800 945710 885450 FALSE TRUE 764920.2675 742532.0568 756819.3445 800927.2995 804181.1024 806984.3597 794434.9843 674576.0393 838356.9655 825477.6828 0.926639549 0.899518027 0.91682593 0.97025918 0.974200901 0.977596822 0.962394261 0.817194763 1.015602218 1 19.65486969 3.901789446 8.028246158 0.945731111 0.911877522 0.097516733 0.052369172 0.887481298 64.73893103 0.014718949 0.026691954 7976.078987 -3.901789446 -0.033853589 DAEDAIYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DAEDAIYGR 9 0 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;; 210.05 1.73E-05 3340300000 3805290 3922410 3119970 3663210 3821880 3701280 3817050 4164560 4278650 4213610 FALSE TRUE 3656575.06 3810546.707 3683817.982 3852268.707 3944814.241 3776122.418 3863764.2 4078560.381 3792955.59 3928218.442 0.930848199 0.970044503 0.937783384 0.980665603 1.004224765 0.961281169 0.983591991 1.038272296 0.965566362 1 21.90544373 3.902267448 0.521427149 1.003222815 0.923447347 0.416693023 0.023134015 1.869482137 0.712352288 0.016112528 0.083409393 7984.862603 -3.902267448 -0.079775468 RS(ph)PDVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSPDVLK 7 1 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 1 RS(1)PDVLK;RS(1)PDVLK 98.943 0.0066715 239740000 545500 538240 474480 556230 544240 602060 595270 632740 685750 649630 TRUE FALSE 524181.2569 522889.9222 560229.0908 584937.097 561745.9739 614234.0657 602555.0923 619673.6979 607906.5349 605629.9815 0.865514048 0.863381831 0.925035266 0.965832463 0.927539902 1.014206833 0.994922825 1.023188608 1.003758984 1 19.2080771 3.902877507 0.589954335 1.015010203 0.821463079 0.875083629 0.02005908 0.500030882 0.252910718 0.011492017 0.058973651 7996.086924 -3.902877507 -0.193547124 QTLPSS(ph)PTTTK ddPTM_BT-474_Pertuzumab_2h_R1 3 QTLPSSPTTTK 11 0 F8VW64;F8VWX1;F8W659;J3KQU3;P51513-2;P51513 F8VW64 NOVA1 RNA-binding protein Nova-1 1 QTLPS(0.055)S(0.918)PT(0.025)T(0.002)TK;QTLPS(0.35)S(0.547)PT(0.076)T(0.021)T(0.006)K;QTLPS(0.154)S(0.829)PT(0.015)T(0.001)TK 170.79 1.80E-05 361570000 1031610 985590 855870 999590 1031510 989940 1044500 1112160 1181510 1152010 TRUE FALSE 991293.5407 957481.9382 1010544.748 1051178.96 1064689.456 1009957.265 1057282.903 1089193.507 1047389.938 1073983.337 0.923006444 0.891524017 0.940931496 0.978766545 0.991346346 0.940384483 0.984450007 1.01416239 0.975238537 1 20.03454018 3.902993953 2.644715453 0.984928526 0.907359466 0.714521041 0.01951903 0.149205431 2.025663621 0.005588781 0.012270188 7998.231177 -3.902993953 -0.07756906 VNIGEVLDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VNIGEVLDKR 10 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ; 116.74 0.0016846 947850000 1140090 1120240 886600 866230 908310 954710 838200 940550 1117000 1235220 FALSE TRUE 1095534.022 1088291.852 1046828.342 910936.2341 937526.6161 974014.8903 848458.1423 921127.3138 990202.8428 1151557.449 0.951349864 0.945060842 0.909054379 0.791047146 0.814137946 0.845823967 0.736791849 0.79989697 0.85988141 1 20.13515496 3.903217455 3.853094832 0.81973883 0.945141261 0.317190888 0.065668754 0.217227567 5.807932264 0.016110121 0.031702159 8002.348384 -3.903217455 0.125402431 LQFIADHCPTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQFIADHCPTLR 12 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3KSA5;J3KRJ4;J3QLT0;J3QS84;J3KRE8;J3QLE8;J3KTB0;J3QS88;J3QL53 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ; 123.99 0.00033093 1311130000 662290 693230 571570 760450 745290 714470 747320 696520 815930 885290 FALSE TRUE 636406.9746 673459.7591 674865.4135 799696.9156 769262.9297 728917.0729 756465.9257 682136.6186 723309.0471 825328.5198 0.771095339 0.815989928 0.817693073 0.968943756 0.93206876 0.883184157 0.916563414 0.826503147 0.876389256 1 19.65460897 3.903756838 6.641720885 0.902484413 0.799046072 0.533085907 0.04786919 0.211074195 12.30132425 0.012849798 0.023491083 8012.293277 -3.903756838 -0.103438341 RGESLDNLDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGESLDNLDSPR 12 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RGES(0.492)LDNLDS(0.508)PR 102.66 0.0024681 1267400000 667640 683420 511210 577930 534080 419580 508080 762120 590130 635650 TRUE FALSE 641547.8907 663929.5307 603597.0188 607757.0366 551259.1682 428064.1951 514298.035 746381.9557 523140.9164 592596.8593 1.082604271 1.120373016 1.018562635 1.025582615 0.930243149 0.722353128 0.867871685 1.259510482 0.88279394 1 19.17669145 3.903839434 1.887585271 0.965308904 1.101016876 0.166307964 0.129769626 0.809732152 5.572243755 0.041736027 0.107232686 8013.81725 -3.903839434 0.135707972 IEEEEQEPEPPEPFEYIDD ddPTM_BT-474_Pertuzumab_2h_R1 7 IEEEEQEPEPPEPFEYIDD 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;;; 203.87 1.13E-15 1730842000 4045700 4210010 3471360 4182400 4267330 4476490 4442010 4662420 4960890 4959870 FALSE TRUE 3887589.571 4089944.637 4098711.972 4398254.165 4404592.545 4567007.695 4496372.647 4566139.398 4397750.565 4623933.587 0.840753765 0.884516302 0.886412379 0.951193196 0.952563972 0.98768886 0.972412895 0.987501077 0.951084284 1 22.14068925 3.904153067 0.923433956 0.980384668 0.837564512 0.910338288 0.015081308 0.201716142 0.284882579 0.005179797 0.022492811 8019.606637 -3.904153067 -0.142820156 LGNDFHTNKR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGNDFHTNKR 10 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;; 187.42 8.00E-07 5656650000 5344420 5426520 4197330 4111700 4186210 3870730 4824650 4598410 5058750 5034320 FALSE TRUE 5135554.158 5271760.963 4955880.9 4323905.33 4320863.246 3948998.813 4883695.51 4503451.227 4484501.908 4693341.022 1.094221394 1.123242683 1.055938803 0.921285138 0.920636968 0.841404619 1.040558418 0.959540593 0.955503103 1 22.16218386 3.904159024 3.761985544 0.947919697 1.10629076 0.639662298 0.049984353 0.146156301 3.764154137 0.013553208 0.026834224 8019.716654 -3.904159024 0.158371064 DANDPVDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DANDPVDDR 9 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 160.36 0.00015204 281110000 899290 882530 747790 870490 900480 964740 903620 883140 1024320 999590 FALSE TRUE 864144.7526 857361.1085 882932.2875 915416.0932 929444.757 984247.7038 914678.7719 864902.8504 908043.4879 931886.879 0.927306492 0.92002702 0.947467238 0.982325338 0.997379379 1.056187962 0.981534124 0.92812 0.974413857 1 19.82979531 3.904229666 2.702810328 0.985058675 0.924008343 0.444495946 0.029759082 0.31651059 4.483364024 0.009455847 0.020622347 8021.021241 -3.904229666 -0.061050332 LWS(ph)LER ddPTM_BT-474_Pertuzumab_2h_R1 2 LWSLER 6 0 O60437;K7EKI8;K7EQ71;M0QZ12;Q96CP6-2;Q96CP6-3;Q96CP6 O60437;M0QZ12 PPL;GRAMD1A Periplakin;GRAM domain-containing protein 1A 1 LWS(1)LER;LWS(1)LER 84.743 0.058221 30571000 57562 60128 50363 63261 68456 56011 62551 76842 66676 62940 TRUE FALSE 55312.4134 58413.20831 59464.71442 66525.90779 70657.94941 57143.5808 63316.51785 75255.18585 59107.22001 58677.01774 0.942658907 0.995504042 1.013424279 1.133764297 1.2041844 0.973866481 1.079068438 1.282532561 1.0073317 1 15.84050793 3.904326841 3.122717015 1.116997391 0.972364321 0.230309934 0.091972661 0.326614207 6.076297772 0.025168292 0.052376984 8022.816167 -3.904326841 -0.14463307 RQVEEEILALK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQVEEEILALK 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 96.306 0.011402 441050000 1002040 1039300 863290 1144510 1093760 1184150 1097730 1115970 1161680 1189650 FALSE TRUE 962879.169 1009660.182 1019305.707 1203578.298 1128941.784 1208094.324 1111164.348 1092924.83 1029810.957 1109073.946 0.868183021 0.910363268 0.919060186 1.085210146 1.017913898 1.089282035 1.001884818 0.985439099 0.928532277 1 20.08092413 3.904536826 6.103901036 1.015162796 0.895113945 0.588309592 0.04494587 0.165148568 8.659715731 0.012208184 0.022447868 8026.6962 -3.904536826 -0.120048851 ELAVQIYEEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELAVQIYEEAR 11 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523;O15523-3 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;; 159.94 6.53E-05 494020000 307163 332651 273714 403614 393826 378645 358874 374914 359482 416540 FALSE TRUE 295158.7304 323164.1192 323180.2085 424444.5669 406493.771 386301.4613 363266.0074 367171.8949 318675.1104 388327.3748 0.760077063 0.83219505 0.832236483 1.093007072 1.046781137 0.994782975 0.9354633 0.945521533 0.820635194 1 18.56691389 3.90507883 7.371771766 0.973623497 0.804838603 0.550381713 0.070128003 0.211357918 14.31074275 0.019221428 0.034964485 8036.719853 -3.90507883 -0.168784894 RGAT(ph)PPAPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGATPPAPPR 10 1 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 RGAT(1)PPAPPR;RGAT(1)PPAPPR 56.951 0.070768 672540000 168278 153624 134473 163731 148643 180720 154648 175680 197943 171695 TRUE FALSE 161701.5097 149242.7939 158775.2624 172181.1765 153424.2371 184374.2822 156540.6285 172052.1466 175473.3405 160065.9447 1.01021807 0.932383176 0.991936559 1.075689003 0.958506429 1.151864518 0.977975851 1.074882898 1.096256551 1 17.28830687 3.905491067 5.107095865 1.048585118 0.969131612 0.240650533 0.057366199 0.271661326 11.20846478 0.013734064 0.02572487 8044.352016 -3.905491067 -0.079453506 LNNDDNVDGLLVQLPLPEHIDER ddPTM_BT-474_Pertuzumab_2h_R1 6 LNNDDNVDGLLVQLPLPEHIDER 23 0 P13995-2;P13995 P13995-2 MTHFD2 "Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial;NAD-dependent methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase" 0 ;;;;; 242.67 2.37E-37 653517000 326355 495664 345372 724917 344562 422101 625686 529071 447244 427122 FALSE TRUE 313600.6858 481528.148 407788.4032 762330.0532 355645.1497 430636.1714 633343.3324 518145.499 396474.7361 398192.6465 0.787560214 1.209284381 1.024098277 1.914475468 0.893148462 1.081476956 1.590545024 1.301243264 0.995685731 1 18.60310705 3.905914731 21.37582495 1.281492375 1.026739568 0.114472565 0.306409396 31.09657399 7057.916731 0.076484657 0.137885204 8052.203286 -3.905914731 -0.254752807 KELQAAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KELQAAGK 8 1 P06744;A0A2U3TZU2;P06744-2 P06744 GPI Glucose-6-phosphate isomerase 0 ; 87.258 0.024776 2687900000 5908200 6429500 4608300 4434600 4591800 2962000 4870800 5481600 5869900 4900500 FALSE TRUE 5677301.012 6246136.955 5441122.321 4663470.237 4739499.417 3021893.669 4930410.307 5368403.044 5203573.561 4568584.77 1.242682646 1.367192964 1.190986398 1.020769116 1.037410852 0.661450716 1.079198604 1.175069155 1.138990261 1 22.12331589 3.907748628 3.093113949 1.022450104 1.303853685 0.436460337 0.134160747 0.263109181 4.820418834 0.039239085 0.082120709 8086.277256 -3.907748628 0.28140358 FEMDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FEMDLR 6 0 Q9BX97 Q9BX97 PLVAP Plasmalemma vesicle-associated protein 0 ; 102.98 0.081604 289065000 436320 494460 596040 1152100 1274930 1190320 1064240 1271350 1230740 1140400 FALSE TRUE 419268.132 480358.4849 703757.6868 1211560.019 1315939.281 1214389.086 1077264.487 1245096.178 1091031.555 1063159.692 0.394360448 0.451821573 0.66194918 1.13958423 1.237762578 1.142245229 1.013266864 1.171128089 1.026216064 1 20.01992688 3.908136306 2.740148629 1.117707976 0.426944991 0.932894899 0.075522629 0.060920403 0.887124517 0.020755408 0.045208067 8093.498789 -3.908136306 -0.690762985 down RAS(ph)PS(ph)PPPKR ddPTM_BT-474_Pertuzumab_2h_R1 4 RASPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RAS(1)PS(1)PPPKR;RAS(1)PS(1)PPPKR;RAS(1)PS(1)PPPKR;RAS(1)PS(1)PPPKR 66.533 0.035229 2592780000 922821 830102 711906 924665 871730 806901 882460 855501 949312 956514 TRUE FALSE 886756.1351 806428.3037 840563.2505 972387.0715 899769.9871 823217.0911 893259.8095 837834.6054 841550.0816 891728.4548 0.994423953 0.904342908 0.942622438 1.090451994 1.009017916 0.92317015 1.001717288 0.939562488 0.943729088 1 19.76624493 3.908920449 23.20873398 0.983560208 0.942790288 0.116904967 0.048977176 70.39766336 17932.6918 0.013078741 0.023578062 8108.125254 -3.908920449 -0.04076992 S(ph)PEIMSTISGTR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPEIMSTISGTR 12 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(1)PEIMSTISGTR;S(1)PEIMSTISGTR;S(1)PEIMSTISGTR;S(1)PEIMSTISGTR 156.73 7.70E-05 1053356000 442133 445465 403674 483712 487203 498816 491062 635338 595022 584727 TRUE FALSE 424853.9536 432760.7744 476626.8715 508676.4343 502874.327 508902.4013 497071.7636 622218.0483 527477.5971 545122.9195 0.779372759 0.793877415 0.874347518 0.933140795 0.922497127 0.93355532 0.911852622 1.141427054 0.967630562 1 19.05622205 3.908945958 0.42588357 1.042164742 0.684802762 0.66662074 0.056443173 1.572198297 0.372490789 0.050661975 0.268513858 8108.601511 -3.908945958 -0.35736198 WESPAQNTAHLDQFER ddPTM_BT-474_Pertuzumab_2h_R1 2 WESPAQNTAHLDQFER 16 0 P17612-2;P17612;Q15136 P17612-2 PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit alpha 0 ; 255.21 1.33E-26 959880000 246760 258850 220800 282460 291910 273800 332610 313050 278410 328020 FALSE TRUE 237116.3464 251467.8514 260703.4717 297037.7945 301299.5503 279336.4236 336680.5807 306585.4081 246806.064 305802.9132 0.775389429 0.822319999 0.852521217 0.97133736 0.985273643 0.913452461 1.100972444 1.002558821 0.807075581 1 18.22224263 3.909000832 1.895120144 0.979148193 0.791428881 0.494105304 0.071328502 0.284886752 1.976866744 0.020326769 0.052428665 8109.62612 -3.909000832 -0.187719311 VDENENCSSLGS(ph)PSEPPQTLDLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDENENCSSLGSPSEPPQTLDLVR 24 0 Q96P16;A0A0C4DGQ6;Q96P16-3 Q96P16 RPRD1A Regulation of nuclear pre-mRNA domain-containing protein 1A 1 VDENENCSSLGS(0.987)PS(0.013)EPPQTLDLVR;VDENENCS(0.028)S(0.025)LGS(0.87)PS(0.076)EPPQT(0.001)LDLVR 90.71 0.0061386 112875000 43080 45849 36585 58017 42011 48677 44649 56073 47889 51241 TRUE FALSE 41396.38597 44541.43141 43196.72333 61011.26432 43362.32197 49661.28229 45195.42782 54915.07295 42452.84149 47770.40143 0.866569774 0.932406471 0.904257072 1.277177133 0.907723625 1.039582687 0.946096881 1.149562727 0.888685048 1 15.54382938 3.909426521 24.71261238 1.037438573 0.904058717 0.221330034 0.109981302 75.68790339 20647.57383 0.026535199 0.047837044 8117.578952 -3.909426521 -0.133379856 RLNKHEENLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLNKHEENLK 10 2 P42766 P42766 RPL35 60S ribosomal protein L35 0 62.303 0.05163 337750000 756690 692390 497950 224500 374690 106040 456120 344970 429100 453080 FALSE TRUE 727117.7182 672643.7151 587940.6418 236086.4719 386742.2441 108184.2015 461702.133 337846.2489 380390.3669 422392.488 1.721426727 1.592461358 1.391929683 0.558926777 0.915599247 0.256122456 1.093064262 0.799839624 0.900561392 1 18.68822465 3.909584255 3.861000746 0.78530938 1.633353022 0.716207971 0.228103357 0.11463993 3.11789838 0.057732267 0.113997188 8120.527749 -3.909584255 0.848043642 AKQTLENER ddPTM_BT-474_Pertuzumab_2h_R1 2 AKQTLENER 9 1 P35579 P35579 MYH9 Myosin-9 0 ; 89.9 0.010756 280920000 699210 802940 509930 359160 407370 243044 534430 398570 429070 447770 FALSE TRUE 671884.1002 780040.9374 602085.6943 377696.2906 420473.426 247958.5162 540970.5142 390339.3902 380363.7724 417442.1391 1.609526297 1.868620497 1.442321314 0.904787168 1.007261574 0.593994935 1.295917359 0.935074238 0.911177231 1 18.67121672 3.909997322 3.240824852 0.954668557 1.733954489 0.779607604 0.172441073 0.104056197 2.081224519 0.044117406 0.091224881 8128.255046 -3.909997322 0.779285932 DEGLHCDFACLMFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DEGLHCDFACLMFK 14 0 P31350;P31350-2;A0A286YFD6;C9JXC1 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 0 ; 166.38 3.81E-06 301934000 669720 659981 433770 537881 432225 248729 553983 463698 443589 607803 FALSE TRUE 643546.602 641158.9881 512161.8882 565641.1029 446127.9097 253758.4708 560762.8097 454122.4743 393234.6364 566635.9614 1.135732015 1.13151835 0.903864073 0.998244272 0.787327208 0.447833332 0.989635053 0.801436028 0.69398108 1 19.11206264 3.910069306 1.222016809 0.784918321 1.154964586 0.405533675 0.155156533 0.537583601 1.440535825 0.049037967 0.173690371 8129.602396 -3.910069306 0.370046264 GAYGGGYGGYDDYNGYNDGYGFGSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAYGGGYGGYDDYNGYNDGYGFGSDR 26 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ; 346.42 8.30E-110 122110000 200424 204835 170910 225804 218279 237460 209456 221102 231485 226371 FALSE TRUE 192591.2085 198993.3064 201797.2389 237457.7715 225300.1423 242261.6039 212019.3852 216536.1664 205207.7933 211038.6905 0.912587204 0.942923337 0.956209681 1.125185959 1.067577427 1.147948764 1.00464699 1.026049611 0.972370482 1 17.68714799 3.910120375 6.583830863 1.050605676 0.932843177 0.495091966 0.052210594 0.201344346 12.33036388 0.01406553 0.025747506 8130.55843 -3.910120375 -0.117762499 RYS(ph)PPIQR ddPTM_BT-474_Pertuzumab_2h_R1 12 RYSPPIQR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RY(0.011)S(0.989)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RY(0.024)S(0.976)PPIQR;RY(0.004)S(0.996)PPIQR;RY(0.004)S(0.996)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RY(0.013)S(0.987)PPIQR;RYS(1)PPIQR;RY(0.001)S(0.999)PPIQR 115.18 0.0015401 1.22359E+11 3821248 3940402 3435267 4744074 4833993 4600892 5217832 4549433 4908006 4478665 TRUE FALSE 3671909.404 3828025.593 4056096.164 4988916.228 4989482.775 4693925.189 5281689.389 4455485.619 4350869.735 4175321.03 0.879431636 0.91682186 0.971445341 1.194858118 1.194993807 1.124207014 1.264978034 1.067100131 1.042044361 1 21.9934557 3.910347271 3.878381842 1.136038124 0.904898524 0.611528304 0.075608154 0.143965347 3.952336995 0.019807661 0.0390899 8134.807331 -3.910347271 -0.231139599 KGNYAER ddPTM_BT-474_Pertuzumab_2h_R1 19 KGNYAER 7 1 Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;Q8IUE6 Q99878 HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;HIST2H2AB Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A type 2-B 0 ;;;;;;;;;;;;;;;;;; 141.52 0.004091 1.21963E+11 61125368 62674756 40564731 40890116 36515567 12243539 50199063 40307905 39357001 43329180 FALSE TRUE 58736521.04 60887333.32 47895680.25 43000459.79 37690123.38 12491111.75 50813414.15 39475532.68 34889359.24 40394456.04 1.454073821 1.507319055 1.185699349 1.064513896 0.933051885 0.309228369 1.257930397 0.97725125 0.863716526 1 25.26765397 3.911265785 1.665711157 0.900732284 1.498061399 0.506818943 0.226356202 0.330864071 1.750644561 0.067103613 0.188219748 8152.030302 -3.911265785 0.597329115 RMS(ph)PKPELTEEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RMSPKPELTEEQK 13 2 P41208 P41208 CETN2 Centrin-2 1 RMS(1)PKPELTEEQK;RMS(1)PKPELTEEQK 204.07 4.22E-08 1250190000 1268870 1057150 874650 557740 792510 862410 773210 716160 1001080 862330 TRUE FALSE 1219281.158 1027001.117 1032718.711 586525.0282 818001.8039 879848.5211 782672.7753 701371.0457 887441.5953 803923.621 1.516662934 1.277485933 1.284598044 0.729578051 1.017511841 1.094442927 0.973566089 0.872434927 1.103887947 1 19.61669892 3.91155083 5.864187841 0.966789701 1.370976607 0.707153592 0.115980329 0.116935292 6.151202734 0.029737801 0.054941257 8157.382557 -3.91155083 0.404186906 MGPSGGEGMEPER ddPTM_BT-474_Pertuzumab_2h_R1 2 MGPSGGEGMEPER 13 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 117.94 0.0010851 1745710000 620650 598830 542980 761070 710100 669810 784250 809270 785880 832980 FALSE TRUE 596394.3118 581751.9547 641108.5645 800348.9139 732941.0114 683354.0171 793847.8861 792558.2917 696670.1971 776561.5227 0.767993642 0.749138269 0.825573436 1.030631689 0.943828647 0.879974087 1.022260134 1.020599487 0.897121705 1 19.5667407 3.911834166 4.162060213 0.972309849 0.762935309 0.760450118 0.049607592 0.104941346 3.254958266 0.013471985 0.026198491 8162.706206 -3.911834166 -0.209374541 YTYEHDPITK ddPTM_BT-474_Pertuzumab_2h_R1 4 YTYEHDPITK 10 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ;;; 147.12 2.75E-05 1857030000 3312510 3417090 2949680 3344740 3412660 3627840 3911760 3918960 4457360 4518370 FALSE TRUE 3183053.447 3319637.939 3482752.791 3517362.432 3522431.308 3701197.41 3959633.289 3838032.106 3951379.18 4212336.775 0.755650276 0.788075151 0.826798278 0.835014535 0.836217875 0.878656577 0.940008717 0.911140849 0.938049209 1 22.00618935 3.911913978 0.20975326 1.022258119 0.608096519 0.955031796 0.015322401 1.784530645 0.100671125 0.035811021 0.196899 8164.206445 -3.911913978 -0.4141616 RLDQELDFILSQQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDQELDFILSQQK 14 1 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 ; 187.37 1.53E-06 309950000 446680 461990 359650 340720 379370 329920 415530 402680 428220 423510 FALSE TRUE 429223.2518 448814.4975 424646.7554 358304.6 391572.7806 336591.2084 420615.3804 394364.5173 379610.2608 394825.2905 1.087121981 1.136742018 1.075530787 0.907501644 0.991762154 0.852506708 1.065320258 0.998832969 0.961463893 1 18.59085488 3.912563672 5.558059315 0.972328057 1.110882688 0.548688555 0.055208149 0.16130836 7.904682215 0.014267343 0.026509523 8176.429043 -3.912563672 0.13855463 EKDSPHMQDPNQADEEAMTQIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDSPHMQDPNQADEEAMTQIIR 23 1 P23511-2;P23511 P23511-2 NFYA Nuclear transcription factor Y subunit alpha 0 201.87 1.31E-24 260240000 170150 164520 142200 164420 167340 194700 156440 168050 205530 199010 FALSE TRUE 163500.3499 159828.0507 167898.7032 172905.7359 172722.6431 198636.9674 158354.5595 164579.7088 182199.0961 185530.8754 0.881256823 0.861463356 0.904963677 0.931951275 0.930964416 1.070641029 0.85352133 0.887074501 0.982041914 1 17.50129977 3.913471826 2.210451011 0.941883101 0.870970611 0.232822507 0.057290666 0.546695356 5.202708149 0.016547751 0.039564108 8193.544679 -3.913471826 -0.07091249 VEPQLAEDQPVHGDLDLVMNLMDAHK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEPQLAEDQPVHGDLDLVMNLMDAHK 26 0 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 ; 128.4 5.08E-05 21983400 14332.1 14035.6 12546.5 19142.4 18904.4 18944.9 18816.1 13547.6 22244 18125.3 FALSE TRUE 13771.98569 13635.31843 14813.93165 20130.34156 19512.47719 19327.97886 19046.37706 13267.83733 19718.95437 16897.65729 0.815023376 0.806935435 0.876685531 1.191309613 1.154744522 1.143825948 1.127160809 0.785187976 1.166963801 1 14.04453562 3.913804689 5.745236128 1.063368112 0.817607141 0.504335197 0.113009883 0.210982671 10.98108187 0.032916434 0.060968754 8199.826986 -3.913804689 -0.245760971 LRECLPLIIFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRECLPLIIFLR 12 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 168.61 4.20E-05 671300000 546600 534080 387960 341390 365190 341600 337530 362800 371500 365270 FALSE TRUE 525238.2677 518848.5613 458073.0021 359009.1788 376936.668 348507.386 341660.7931 355308.0532 329328.8775 340529.9376 1.542414366 1.523650358 1.345176889 1.054266128 1.106911982 1.02342657 1.00332087 1.043397405 0.967106974 1 18.37742211 3.91416723 1.749704257 1.022725838 1.556424723 0.972859166 0.034806242 0.051693807 0.303517548 0.009773886 0.026639925 8206.674909 -3.91416723 0.533698885 NIGRDT(ph)PTSAGPNSFNK ddPTM_BT-474_Pertuzumab_2h_R1 4 NIGRDTPTSAGPNSFNK 17 1 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 NIGRDT(0.95)PT(0.049)S(0.001)AGPNSFNK;NIGRDT(0.987)PT(0.013)SAGPNSFNK;NIGRDT(0.998)PT(0.002)SAGPNSFNK;NIGRDT(0.913)PT(0.087)S(0.001)AGPNSFNK 212.06 3.09E-12 3680920000 1349600 1290480 1040840 1034520 1036260 1137460 946460 1297150 1311200 1213100 TRUE FALSE 1296856.14 1253676.774 1228942.941 1087911.701 1069592.244 1160460.221 958043.0606 1270363.399 1162358.073 1130935.656 1.146710808 1.108530593 1.086660354 0.961957203 0.945758707 1.026106316 0.847124286 1.123285301 1.027784442 1 20.10908542 3.914571458 3.701183108 0.994353999 1.123550165 0.423103552 0.066961273 0.23890935 6.106831433 0.018018484 0.036065837 8214.316983 -3.914571458 0.129196166 NFLHLTDKDGEQPQILLEDSSAGEDSVHDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NFLHLTDKDGEQPQILLEDSSAGEDSVHDR 30 1 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 0 202.03 1.27E-25 183670000 163970 215460 146970 141280 145140 166290 154960 128390 198920 183910 FALSE TRUE 157561.8711 209315.2918 173530.7483 148571.4777 149808.5599 169652.4977 156856.4468 125738.7016 176339.4355 171453.6119 0.918976681 1.220827543 1.01211486 0.866540378 0.873755637 0.989495035 0.914862307 0.733368637 1.028496476 1 17.38745877 3.914661869 4.749488985 0.896663567 1.08019672 0.252690177 0.105518868 0.229304752 8.928495551 0.026872765 0.051055644 8216.027205 -3.914661869 0.183533154 S(ph)PPVRPNESLSGSWK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPVRPNESLSGSWK 15 1 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 S(1)PPVRPNESLSGSWK 108.92 0.00063054 103680000 122300 125400 116030 143390 159690 157030 166510 156150 183130 173050 TRUE FALSE 117520.3808 121823.7148 136999.2021 150790.3751 164826.5739 160205.2542 168547.7992 152925.4479 162341.8501 161329.1694 0.728450913 0.75512516 0.849190525 0.934675209 1.021678687 0.993033404 1.044744728 0.947909473 1.006277109 1 17.29964779 3.915471478 1.495012814 0.999220329 0.725292712 0.945414582 0.024978543 0.090788389 0.380405355 0.007586383 0.023114461 8231.357767 -3.915471478 -0.273927617 NPLPSKET(ph)IEQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NPLPSKETIEQEK 13 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 NPLPS(0.011)KET(0.989)IEQEK 163.18 6.33E-05 319880000 293500 285360 208770 154010 229460 159400 129570 155090 292750 182320 TRUE FALSE 282029.6955 277221.8122 246499.3831 161958.4746 236840.7893 162623.1772 131155.7164 151887.3373 259518.2473 169971.304 1.659278295 1.630991854 1.450241172 0.952857752 1.393416322 0.956768427 0.771634466 0.893605766 1.526835655 1 17.37493167 3.915501388 2.782893082 1.045174945 1.645284866 0.539770289 0.218315496 0.202081262 3.040148291 0.060327558 0.131575204 8231.924671 -3.915501388 0.600109922 EKQLAAENR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKQLAAENR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 149.33 8.01E-05 2676230000 5206500 5368600 3896810 3234750 3506220 2165620 4484800 3972810 4337180 4194250 FALSE TRUE 5003024.224 5215492.784 4601050.251 3401695.835 3619000.751 2209410.32 4539686.324 3890770.085 3844841.509 3910169.712 1.279490302 1.333827728 1.176688121 0.869961175 0.925535467 0.565042053 1.160994703 0.995038674 0.983292745 1 21.89879979 3.915537521 3.60976269 0.932077579 1.301131445 0.544114463 0.143268004 0.183147428 4.485914354 0.03898564 0.078589432 8232.609601 -3.915537521 0.369053866 DVYDYFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVYDYFR 7 0 P49354;E9PQP6;H0YCW1 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 97.602 0.02763 132450000 399640 492340 329110 263070 266710 152560 393790 394530 264710 396700 FALSE TRUE 384021.627 478298.9453 388587.498 276647.0742 275288.9694 155644.8677 398609.3198 386382.8176 234661.2306 369831.1557 1.038370135 1.293290027 1.050715961 0.748036151 0.744363922 0.420853855 1.077814332 1.044754645 0.634509091 1 18.49650724 3.916240816 4.44609604 0.824517375 1.168493443 0.359312021 0.197077265 0.252448385 8.89106189 0.054666044 0.105171169 8245.952252 -3.916240816 0.343976069 SPALKS(ph)PLQSVVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPALKSPLQSVVVR 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 SPALKS(1)PLQSVVVR;SPALKS(1)PLQSVVVR 191.07 3.21E-07 2757700000 1586210 1625220 1390910 1829380 1911020 1718420 1857920 1912820 1884690 1852040 TRUE FALSE 1524219.16 1578870.317 1642278.378 1923794.521 1972489.694 1753167.63 1880657.781 1873319.599 1670747.892 1726599.681 0.882786656 0.914439134 0.951163374 1.114209936 1.142412868 1.01538744 1.089226299 1.084976222 0.967652149 1 20.7195022 3.916548415 4.032445608 1.066772324 0.903919155 0.623854614 0.0515334 0.135102133 4.033341267 0.013371295 0.026257701 8251.79471 -3.916548415 -0.16285317 IHTADKPYK ddPTM_BT-474_Pertuzumab_2h_R1 1 IHTADKPYK 9 1 A0A0G2JMG9;Q6ZN08 A0A0G2JMG9 ZNF66 Putative zinc finger protein 66 0 101.11 0.0025285 736430000 1131400 1156300 879170 1025800 827560 995120 1125700 1030800 1137400 1009500 FALSE TRUE 1087183.637 1123323.456 1038055.576 1078741.661 854179.219 1015242.008 1139476.653 1009513.62 1008287.12 941125.6658 1.155194972 1.193595603 1.102993589 1.146224888 0.907614413 1.078752865 1.210759301 1.072666124 1.071362898 1 19.84402785 3.916588928 2.067392872 1.073700738 1.172101161 0.225862206 0.076136722 0.546543003 4.53931476 0.021818736 0.054121924 8252.564505 -3.916588928 0.098400423 HGGPKDEER ddPTM_BT-474_Pertuzumab_2h_R1 5 HGGPKDEER 9 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;; 167.67 3.59E-05 3138550000 4123319 3731471 3161046 3000288 3336194 2928377 3471544 2334056 4207179 3706124 FALSE TRUE 3962175.135 3625053.101 3732317.329 3155133.223 3443505.71 2987590.789 3514029.794 2285856.928 3729597.678 3455104.92 1.146759715 1.04918756 1.080232704 0.913180148 0.996642877 0.864688876 1.017054438 0.661588282 1.079445564 1 21.72029809 3.91729008 0.800032724 0.890583291 1.156402112 0.258936343 0.113463111 1.150837662 1.156795618 0.046333049 0.223513243 8265.898724 -3.91729008 0.265818821 IACDEEFS(ph)DSEDEGEGGRR ddPTM_BT-474_Pertuzumab_2h_R1 2 IACDEEFSDSEDEGEGGRR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 1 IACDEEFS(0.997)DS(0.003)EDEGEGGRR;IACDEEFS(0.999)DS(0.001)EDEGEGGRR 311.16 9.65E-62 1282100000 531370 516640 484740 699210 586000 734680 732910 791880 789270 821280 TRUE FALSE 510603.4729 501905.933 572343.301 735296.3119 604849.2222 749535.733 741879.5718 775527.4013 699675.3785 765653.9741 0.666885421 0.655525799 0.747522145 0.960350676 0.789977252 0.9789484 0.968948895 1.012895417 0.913827136 1 19.54633301 3.917492901 0.707799517 0.982629841 0.578279991 0.797575177 0.059979173 0.505543436 0.383484782 0.027559377 0.139642665 8269.75991 -3.917492901 -0.404349849 FRELAEEAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FRELAEEAAR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 173.04 3.22E-06 964670000 446880 496730 346460 290050 320520 195296 407060 339770 365520 419140 FALSE TRUE 429415.4355 482563.7467 409073.029 305019.5153 330829.8169 199245.0189 412041.722 332753.6308 324027.702 390751.2745 1.098948266 1.234963974 1.046888534 0.780597621 0.846650641 0.509902416 1.054485933 0.851574013 0.829242854 1 18.57589105 3.917942176 3.834776169 0.834763081 1.164596808 0.483480332 0.139626446 0.183069327 5.022649523 0.035915226 0.071430084 8278.31935 -3.917942176 0.329833727 LLDTVDDMLANDIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLDTVDDMLANDIAR 15 0 A0A024R571;Q9H4M9;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ;;; 263.74 1.03E-24 133669000 159627 178911 145904 204490 186345 184884 199038 200094 193265 225950 FALSE TRUE 153388.6004 173808.6335 172272.0984 215043.7534 192338.9562 188622.4812 201473.8866 195961.989 171326.3674 210646.2052 0.728181171 0.825121123 0.817826736 1.020876465 0.91309006 0.895446851 0.956456283 0.930289671 0.81333707 1 17.6844624 3.918891423 6.28569634 0.929114037 0.786942698 0.560912727 0.058263776 0.165798347 10.41394639 0.014508443 0.02668965 8296.433239 -3.918891423 -0.14217134 DAELAWIDGVLDMR ddPTM_BT-474_Pertuzumab_2h_R1 3 DAELAWIDGVLDMR 14 0 Q9P2I0;H0YJF4 Q9P2I0 CPSF2 Cleavage and polyadenylation specificity factor subunit 2 0 ;; 202.05 3.95E-08 86153000 120248 122318 106916 138436 150388 132137 140565 147769 152721 153462 FALSE TRUE 115548.5752 118829.6104 126238.0995 145580.6986 155225.3666 134808.9007 142285.2765 144717.5185 135384.7523 143067.8821 0.807648604 0.83058202 0.882365054 1.017563806 1.084977036 0.942272289 0.994529831 1.011530446 0.946297313 1 17.12634031 3.919652863 3.064546923 1.001391041 0.821726779 0.793044783 0.038114183 0.109171804 1.982399944 0.010341451 0.021924649 8310.991973 -3.919652863 -0.179664262 YWGSGLHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 YWGSGLHDK 9 0 Q99986 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 ; 71.889 0.048304 675370000 460920 451180 348710 381610 389540 338330 408530 373000 426170 426840 FALSE TRUE 442906.7368 438312.7882 411729.654 401304.9378 402069.9079 345171.2644 413529.7123 365297.4197 377792.9683 397929.7466 1.113027464 1.101482842 1.034679256 1.008481877 1.010404252 0.867417597 1.039202814 0.917994754 0.949396147 1 18.60215422 3.920068756 0.96197821 0.954829406 1.130196623 0.606272114 0.045543038 0.476388914 0.73265855 0.015406442 0.066783194 8318.954634 -3.920068756 0.175367217 ALES(ph)PERPFLAILGGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 1 ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK 217.73 2.95E-15 2860190000 1212320 1224210 812050 815060 690700 741920 690120 753840 918420 710760 TRUE FALSE 1164941.194 1189296.729 958805.499 857125.3443 712916.9928 756922.1307 698565.895 738272.9406 814164.8119 662619.5921 1.758084439 1.794840876 1.446992377 1.293540599 1.075906902 1.142317764 1.054248778 1.114173123 1.228706216 1 19.33782134 3.920265291 1.430560789 1.105761772 1.81729385 0.935386928 0.069176173 0.094387639 0.358738589 0.019502829 0.061867544 8322.720131 -3.920265291 0.711532077 ITDFENRR ddPTM_BT-474_Pertuzumab_2h_R1 4 ITDFENRR 8 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;;; 126.24 0.0019682 2194840000 2796840 3032490 2068990 2149790 2212940 1921840 1959100 2223940 2487720 2543410 FALSE TRUE 2687536.401 2946006.354 2442902.517 2260740.92 2284121.225 1960700.922 1983076.052 2178014.862 2205324.455 2371142.575 1.133435175 1.242441676 1.030263866 0.95343947 0.963299824 0.826901318 0.836337752 0.91855078 0.930068262 1 21.17715098 3.920854577 1.782498245 0.902241328 1.193620233 0.764650589 0.05872965 0.157494814 0.961449899 0.016462285 0.044719481 8334.020746 -3.920854577 0.291378905 CDPAPFYLFDEIDQALDAQHR ddPTM_BT-474_Pertuzumab_2h_R1 6 CDPAPFYLFDEIDQALDAQHR 21 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;;;;; 234.11 9.10E-30 522144000 281593 262119 231362.9 302954 295715 300953 297843 288293 329859 337748 FALSE TRUE 270588.0342 254643.6228 273175.3227 318589.4922 305226.9415 307038.4759 301488.0917 282339.6488 292414.7892 314872.0271 0.859358758 0.808721007 0.867575711 1.011806273 0.969368236 0.975121476 0.957494048 0.896680634 0.928678206 1 18.26440607 3.920987954 5.61785147 0.955067353 0.834685151 0.721800595 0.033598777 0.122383959 6.565429652 0.009509478 0.017695581 8336.580606 -3.920987954 -0.120382202 QGAIYHGLATLLNQPS(ph)PMMQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QGAIYHGLATLLNQPSPMMQR 21 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 QGAIYHGLATLLNQPS(1)PMMQR;QGAIYHGLATLLNQPS(1)PMMQR 255.12 1.34E-36 2551000000 1189510 1216890 850870 1024440 830910 959060 922800 928040 918750 977270 TRUE FALSE 1143022.634 1182185.489 1004641.137 1077311.471 857636.9748 978452.8503 934093.5024 908875.6497 814457.3517 911078.6324 1.25458176 1.297566913 1.102694214 1.182457181 0.941342431 1.073949948 1.025261124 0.997582006 0.893948472 1 19.79721605 3.921651617 0.664483664 0.977151551 1.345815442 0.742570874 0.063937207 0.657593628 0.430493587 0.030767211 0.159637851 8349.329823 -3.921651617 0.368663891 RMEELHNQEMQK ddPTM_BT-474_Pertuzumab_2h_R1 10 RMEELHNQEMQK 12 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;;;;;; 174.9 1.89E-05 6403261000 5218992 5480627 4229610 4118433 4604875 3956712 4818563 4563012 5484413 5155621 FALSE TRUE 5015028.023 5324324.884 4993994.614 4330985.821 4752994.986 4036719.428 4877534.015 4468784.208 4861845.429 4806426.198 1.043400609 1.107751303 1.039024508 0.901082352 0.988883381 0.839858819 1.014794322 0.929751966 1.011530237 1 22.19653315 3.921746991 5.252190805 0.951638485 1.075477712 0.466642547 0.053826253 0.159482682 7.69713681 0.012863073 0.024146538 8351.163581 -3.921746991 0.123839227 S(ph)LTS(ph)SLENIFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 2 S(0.996)LT(0.004)S(0.751)S(0.249)LENIFSR 121.76 0.00054171 34988000 98942 96701 77721 80638 81995 69643 88949 97123 99342 93481 TRUE FALSE 95075.23725 93943.18216 91766.91359 84799.73684 84632.44364 71051.22918 90037.58447 95117.37611 88065.11264 87149.44861 1.090944794 1.07795498 1.052983296 0.973038134 0.971118521 0.815280307 1.033140036 1.091428318 1.010506825 1 16.41120392 3.922127566 3.425900663 0.990453906 1.082503693 0.278170394 0.066383842 0.38832672 8.735802047 0.020095878 0.041298574 8358.484975 -3.922127566 0.092049786 VLDNYLTSPLPEEVDET(ph)SAEDEGVSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLDNYLTSPLPEEVDETSAEDEGVSQR 27 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 1 VLDNYLTSPLPEEVDET(0.548)S(0.452)AEDEGVSQR 91.389 0.023361 21188000 47338 50691 41446 54818 55430 50049 50869 58625 50526 55439 TRUE FALSE 45487.97863 49245.34231 48936.21416 57647.16355 57212.95629 51061.02507 51491.55004 57414.37326 44790.5003 51684.06715 0.880116081 0.952814765 0.946833654 1.115375912 1.10697473 0.987945181 0.996275117 1.110871811 0.866621045 1 15.65743198 3.922189837 7.32419464 1.035366364 0.924433669 0.279686354 0.073152612 0.311279933 25.66647226 0.018521173 0.033761257 8359.683542 -3.922189837 -0.110932695 TAS(ph)FSESR ddPTM_BT-474_Pertuzumab_2h_R1 11 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 TAS(0.979)FS(0.021)ESR;TAS(1)FSESR;TAS(0.989)FS(0.011)ESR;TAS(0.977)FS(0.023)ESR;TAS(0.994)FS(0.006)ESR;T(0.002)AS(0.994)FS(0.004)ESR;T(0.012)AS(0.984)FS(0.004)ESR;TAS(0.998)FS(0.001)ESR;T(0.015)AS(0.97)FS(0.015)ESR;TAS(1)FSESR;TAS(1)FSESR 213.63 1.40E-05 36087520000 12751970 12289880 10620990 13202140 13047930 12184150 12690440 15313070 14447040 13951310 TRUE FALSE 12253608.91 11939384.66 12540439.16 13883504.03 13467628.52 12430521.86 12845749.4 14996849.75 12807072.59 13006375.35 0.942123273 0.917964024 0.964176323 1.067438364 1.035463621 0.955725291 0.987650214 1.153038364 0.984676533 1 23.63271563 3.922585851 4.482340061 1.034615701 0.931724237 0.357114656 0.052534848 0.226516494 8.346088287 0.014818879 0.028569851 8367.309846 -3.922585851 -0.102891464 HT(ph)GEKHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 HTGEKHFK 8 1 D6RGC2;D6RIY0;A0A087WTY0;Q15928;B4DXR9;Q8TF20;Q8TF20-2 D6RGC2 ZNF721;ZNF141;ZNF732 Zinc finger protein 141;Zinc finger protein 732;Zinc finger protein 721 1 HT(1)GEKHFK 72.485 0.074421 275270000 598240 569380 398920 191690 322170 356600 264410 248120 302060 283840 TRUE FALSE 574860.1194 553141.8399 471013.7179 201583.1439 332532.8906 363810.6963 267645.9287 242996.2353 267771.4151 264615.264 2.172437488 2.090362557 1.779994513 0.761797112 1.256665567 1.37486663 1.011453099 0.918300145 1.011927321 1 18.01353676 3.923081714 3.877643232 1.057541485 2.105302442 0.881992288 0.164784364 0.073842533 2.096466778 0.046410691 0.092396366 8376.868803 -3.923081714 1.047760957 up AQGVRS(ph)PLLR ddPTM_BT-474_Pertuzumab_2h_R1 5 AQGVRSPLLR 10 1 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 AQGVRS(1)PLLR;AQGVRS(1)PLLR;AQGVRS(1)PLLR;AQGVRS(1)PLLR;AQGVRS(1)PLLR 134.18 0.00010745 2089200000 2214780 2423820 1483590 1471430 1559280 734473 1746420 1346410 1435720 1581470 TRUE FALSE 2128223.949 2354695.027 1751707.715 1547370.679 1609435.657 749324.5473 1767793.21 1318606.163 1272743.085 1474355.628 1.443494302 1.597101121 1.188117495 1.049523364 1.091619706 0.508238672 1.199027681 0.894360992 0.86325379 1 20.49165313 3.923785446 1.522629577 0.921689306 1.544217041 0.625511579 0.177474598 0.261242336 1.137713433 0.050219916 0.152707235 8390.453715 -3.923785446 0.622527735 EALNVFGNDYDTEDGTGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EALNVFGNDYDTEDGTGVR 19 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ; 260.49 9.59E-31 242040000 226520 216690 197600 245840 254950 264600 260750 266620 277120 260640 FALSE TRUE 217667.348 210510.2134 233310.7156 258527.8319 263150.6983 269950.3933 263941.1365 261114.2038 245662.4994 242986.6206 0.895799725 0.866344874 0.960179268 1.063959123 1.082984312 1.110968137 1.086237324 1.074603215 1.011012453 1 17.89051735 3.924104814 2.582587994 1.069978621 0.880962786 0.82494783 0.033578137 0.099590901 1.297215388 0.008914853 0.020153628 8396.626098 -3.924104814 -0.189015835 ALSAAVADSLTNS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALSAAVADSLTNSPR 15 0 Q14687;Q14687-2;Q14687-3;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 1 ALSAAVADSLTNS(1)PR;ALSAAVADSLTNS(1)PR 298.47 3.80E-44 671870000 1140890 1164870 1000130 1250590 1285410 1318960 1260210 1395430 1362550 1340340 TRUE FALSE 1096302.757 1131649.048 1180875.739 1315133.1 1326756.38 1345630.275 1275632.827 1366613.883 1207879.036 1249557.578 0.877352734 0.905639779 0.945035075 1.052478992 1.061780908 1.07688537 1.020867585 1.0936782 0.966645361 1 20.25298595 3.924270763 2.462716789 1.047533429 0.890424043 0.732498566 0.03648891 0.130517301 1.546337256 0.009407509 0.021682661 8399.835144 -3.924270763 -0.157109386 LTLEDLEDSWDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LTLEDLEDSWDR 12 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;;; 305.82 1.07E-36 1369190000 1632970 1785787 1477059 1984904 1963878 1808432 1923400 2095890 1961007 2108839 FALSE TRUE 1569151.727 1734858.103 1743996.418 2087345.133 2027047.919 1844999.734 1946939.145 2052609.139 1738401.707 1966005.456 0.798142102 0.882427919 0.887076083 1.061718891 1.03104898 0.938450973 0.990302005 1.044050581 0.884230357 1 20.90683589 3.924581644 4.381039438 0.996527277 0.848109769 0.59354338 0.052586236 0.144450133 5.159082262 0.013561042 0.026297219 8405.850155 -3.924581644 -0.148417508 RLVELLMHNDYK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLVELLMHNDYK 12 1 C9JYI4;P52294;Q5TFJ7;O60684;O15131 C9JYI4;O60684;O15131 KPNA1;KPNA6;KPNA5 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed;Importin subunit alpha-7;Importin subunit alpha-6" 0 136.27 7.33E-05 370180000 314640 294900 242330 238910 270710 228870 274300 259600 337090 307510 FALSE TRUE 302343.5209 286489.7407 286124.4216 251240.1737 279417.633 233497.9082 277656.9655 254239.1693 298824.9564 286682.0738 1.054630019 0.999329107 0.998054806 0.876372109 0.974660289 0.814483812 0.968518756 0.88683316 1.042356616 1 18.12909217 3.924779605 5.367761341 0.928816809 1.021019015 0.244898547 0.06392579 0.255171644 13.1230101 0.015394066 0.028851677 8409.682596 -3.924779605 0.092202206 FAQSAPGS(ph)PLSSQPVLITVQR ddPTM_BT-474_Pertuzumab_2h_R1 4 FAQSAPGSPLSSQPVLITVQR 21 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 FAQSAPGS(1)PLSSQPVLITVQR;FAQSAPGS(0.863)PLS(0.131)S(0.006)QPVLITVQR;FAQSAPGS(0.989)PLS(0.008)S(0.003)QPVLITVQR;FAQSAPGS(0.991)PLS(0.009)SQPVLITVQR 336.84 2.66E-80 1334690000 845410 876310 736840 929020 908510 950790 975100 1012900 956180 1062500 TRUE FALSE 812370.4425 851318.4968 870003.3789 976966.8335 937733.0492 970015.6252 987033.5655 991983.261 847638.455 990535.9286 0.820132233 0.859452416 0.878315823 0.986301259 0.946692616 0.979283635 0.996464174 1.001461161 0.855737213 1 19.91784978 3.925878969 2.410771595 0.970610158 0.837919895 0.611094681 0.042055853 0.186599652 2.118908943 0.011190423 0.026068758 8430.997662 -3.925878969 -0.132690263 IRVESLLVTAISK ddPTM_BT-474_Pertuzumab_2h_R1 1 IRVESLLVTAISK 13 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 90.476 0.0041961 0 367680 380460 295880 306320 304260 305260 364790 340990 387610 390310 FALSE TRUE 353310.6591 369609.6533 349352.0978 322129.2119 314046.7992 311432.5664 369254.4091 333948.4373 343610.1378 363873.956 0.970969901 1.015762868 0.960090966 0.885276911 0.863064789 0.855880343 1.014786585 0.917758558 0.944310886 1 18.47307927 3.927426577 0.001254581 1.165187422 0.71189077 0 0.057260013 15366106.28 4362.317576 783250.3282 792920.8437 8461.09511 -3.927426577 -0.453296652 RS(ph)PLPIDRPDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RSPLPIDRPDLR 12 2 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;Q9UQ26-2;D6RDY0;Q9UQ26-5;Q9UQ26-4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 RS(1)PLPIDRPDLR;RS(1)PLPIDRPDLR;RS(1)PLPIDRPDLR;RS(1)PLPIDRPDLR 93.51 0.0039296 846000000 559769 582830 483920 615738 574412 590198 603646 650076 678053 660501 TRUE FALSE 537892.6086 566208.2591 571375.1087 647516.312 592888.4836 602132.2079 611033.6003 636651.7034 601083.2661 615764.679 0.87353599 0.919520522 0.927911471 1.051564557 0.962849127 0.977860908 0.992316742 1.033920465 0.976157429 1 19.23201959 3.927776014 5.084331472 0.999868473 0.901974818 0.711031103 0.027351078 0.110790542 5.304693938 0.007136547 0.013500397 8467.905721 -3.927776014 -0.097893655 HTDTDVLEACSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HTDTDVLEACSK 12 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 0 106.01 0.0019685 216940000 276450 277750 221790 224410 239540 264400 245410 201490 320800 315920 FALSE TRUE 265646.0284 269828.8419 261872.3867 235991.827 247245.0216 269746.3492 248413.401 197329.1611 284384.1289 294522.457 0.901955087 0.916157106 0.88914234 0.801269382 0.839477655 0.915877016 0.843444685 0.669996995 0.965577063 1 18.16801812 3.927864595 5.974969246 0.838675066 0.907739706 0 0.088363036 0.524584541 33.57187861 0.023240571 0.04306898 8469.633047 -3.927864595 0.069064639 LDYVPSSAS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 6 LDYVPSSASR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LDYVPSSAS(1)R;LDYVPSS(0.004)AS(0.996)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSS(0.001)AS(0.999)R;LDYVPSSAS(1)R 177.83 2.39E-06 9443650000 9314760 8933610 6681280 6528770 6407330 5952040 5381860 7144840 5594110 5647450 TRUE FALSE 8950728.881 8678832.19 7888735.92 6865720.602 6613427.588 6072394.327 5447724.813 6997296.557 4959090.085 5264943.181 1.700061819 1.648418965 1.498351577 1.304044577 1.256125159 1.153363696 1.034716734 1.329035531 0.941907617 1 22.32798653 3.927916945 0.694286078 1.101735515 1.834177021 0.846962402 0.09833731 0.498866783 0.359361682 0.04768 0.24722991 8470.654057 -3.927916945 0.732441507 SFPLHFDENSFFAGDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SFPLHFDENSFFAGDKK 17 1 Q96HE7;G3V2H0 Q96HE7 ERO1L ERO1-like protein alpha 0 156.49 3.97E-08 295410000 489780 574130 413410 421080 413380 432440 431510 456100 599200 456930 FALSE TRUE 470638.8561 557756.3745 488122.3833 442811.9893 426676.7431 441184.2331 436790.9485 446681.3756 531181.3281 425981.7241 1.104833446 1.309343437 1.14587635 1.03950936 1.00163157 1.035688172 1.025374855 1.048592816 1.246958022 1 18.70043201 3.928663638 4.351426635 1.0542891 1.211882417 0.36330152 0.08100283 0.2034704 7.321271592 0.020332025 0.039592787 8485.230367 -3.928663638 0.157593317 VPSPLEGSEGDGDT(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 1 VPSPLEGSEGDGDTD 15 0 Q9Y606-2;Q9Y606;F5H168;F5H1S9 Q9Y606-2 PUS1 "tRNA pseudouridine synthase A, mitochondrial;tRNA pseudouridine synthase" 1 VPSPLEGSEGDGDT(1)D 139.46 5.71E-05 63778000 50740 52653 44825 65676 55161 65667 61911 60898 58393 69142 TRUE FALSE 48757.0247 51151.38799 52925.87463 69065.54623 56935.30366 66994.83173 62668.68534 59640.43502 51764.47144 64458.95075 0.756404256 0.793549808 0.821078749 1.071465567 0.883280025 1.039341022 0.972226271 0.925246755 0.803061031 1 15.97609308 3.928803142 7.299454899 0.952988792 0.782602318 0.527118172 0.072806711 0.199449604 17.94764518 0.018321714 0.03344477 8487.95643 -3.928803142 -0.170386474 TQLWASEPGT(ph)PPLPTSLPSQNPILK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQLWASEPGTPPLPTSLPSQNPILK 25 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 TQLWASEPGT(1)PPLPTSLPSQNPILK;TQLWASEPGT(1)PPLPTSLPSQNPILK 213.41 1.37E-25 3496100000 2981100 2747700 2794100 3068900 3112600 3524100 3330400 3845000 4151500 3875600 TRUE FALSE 2864595.316 2669338.286 3299056.024 3227286.297 3212719.606 3595359.717 3371158.431 3765599.406 3680239.125 3613102.16 0.792835406 0.738794025 0.913081302 0.89321756 0.88918593 0.995089416 0.933037119 1.042206735 1.01858153 1 21.78480662 3.928872427 0.452811491 1.026445073 0.679178491 0.801262261 0.04171427 0.991087135 0.267743165 0.031981336 0.173121397 8489.31067 -3.928872427 -0.347266582 ALYHTEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ALYHTEER 8 0 A0A0C4DGB9 A0A0C4DGB9 PPA2 0 93.374 0.011114 191910000 423490 592430 490420 886110 713610 853150 832080 773900 622300 773140 FALSE TRUE 406939.5426 575534.4764 579049.8033 931842.2433 736563.9137 870401.2775 842263.2439 757918.6946 551659.1129 720774.5392 0.564586456 0.79849446 0.803371612 1.292834573 1.021906121 1.207591598 1.168552992 1.051533667 0.765369867 1 19.45918852 3.929090017 5.167237734 1.082066148 0.705915988 0.55948908 0.144451661 0.149571115 7.460261775 0.037155457 0.070165676 8493.565037 -3.929090017 -0.37615016 YQQGDFGYCPR ddPTM_BT-474_Pertuzumab_2h_R1 4 YQQGDFGYCPR 11 0 P67870;Q5SRQ3;Q5SRQ6;N0E472;A0A0G2JM12 P67870 CSNK2B;CSNK2B-LY6G5B-1181;CSNK2B-LY6G5B--991 Casein kinase II subunit beta 0 ;;; 271.26 1.14E-26 1616680000 1532840 1469640 1092050 1256570 1078690 806290 1278690 1264360 1318090 1469260 FALSE TRUE 1472934.918 1427727.306 1289407.728 1321421.728 1113387.043 822593.7362 1294338.991 1238250.524 1168465.949 1369745.712 1.075334572 1.042330189 0.941348249 0.964720471 0.812842146 0.600544852 0.94494838 0.904000293 0.85305319 1 20.38547666 3.929094217 1.442220114 0.852242119 1.069709764 0.362347725 0.103030115 0.508355796 1.963523147 0.032145254 0.102635607 8493.64718 -3.929094217 0.217467645 RFIGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 RFIGSPR 7 1 P23443-5;P23443;P23443-3;P23443-2;P23443-4;K7ERJ3 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 RFIGS(1)PR;RFIGS(1)PR;RFIGS(1)PR;RFIGS(1)PR 69.375 0.035082 1911370000 233152 327874 271826 499559 439590 874630 366804 190656 361503 369973 TRUE FALSE 224040.1621 318523.3545 320951.0049 525341.2999 453729.8116 892315.6179 371293.0571 186718.887 320466.695 344914.3992 0.64955294 0.923485234 0.930523648 1.523106316 1.31548527 2.587063979 1.076478854 0.541348484 0.929119503 1 18.39587883 3.929547443 5.478735248 1.261129578 0.816327567 0.141399054 0.509951115 0.506768122 28.28379389 0.148670752 0.278518617 8502.515709 -3.929547443 -0.444802011 GDVHDIGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDVHDIGK 8 0 Q99707-2;Q99707;B1ANE3 Q99707-2 MTR Methionine synthase 0 81.594 0.025474 0 89473 80983 75206 96796 88793 100220 106870 96313 104000 114220 FALSE TRUE 85976.29624 78673.44413 88797.39715 101791.6532 91649.10748 102246.5171 108177.907 94324.10289 92194.356 106483.7777 0.807412154 0.738830326 0.833905399 0.955935781 0.860686102 0.960207454 1.015909741 0.885807256 0.865806586 1 16.70027413 3.929928718 3.727251969 0.930184867 0.773975185 0.616936281 0.052316867 0.148645728 3.989067492 0.013707631 0.027711102 8509.9835 -3.929928718 -0.156209682 ILDSEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILDSEVR 7 0 A4FU01-3;A4FU01-2;A4FU01-6;A4FU01-4;A4FU01 A4FU01-3 MTMR11 Myotubularin-related protein 11 0 ; 116 0.012922 788060000 421470 541260 687080 1395650 1311930 1499470 1348790 1516840 1581640 1505540 FALSE TRUE 404998.4864 525823.7947 811250.64 1467679.664 1354129.42 1529790.311 1365296.895 1485516.724 1402098.858 1403568.435 0.288549155 0.374633528 0.577991511 1.045677309 0.964776199 1.089929264 0.972732687 1.058385674 0.998952971 1 20.42066798 3.929957107 2.275722031 1.025551403 0.319503111 0.974223267 0.046135683 0.038598397 0.390380677 0.011812501 0.028361346 8510.539791 -3.929957107 -0.706048291 down NENEEILERPAQLANAR ddPTM_BT-474_Pertuzumab_2h_R1 4 NENEEILERPAQLANAR 17 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 269.59 2.03E-28 3361400000 1384590 1397830 1170910 1389300 1426990 1444280 1408250 1556850 1537280 1521030 FALSE TRUE 1330478.692 1357965.257 1382519.484 1461001.939 1472890.429 1473484.331 1425484.585 1524700.503 1362774.419 1418009.283 0.938272202 0.957656112 0.974972096 1.030319023 1.038702953 1.03912178 1.005271687 1.075240142 0.9610476 1 20.43543555 3.930666353 2.367250638 1.028108957 0.946948966 0.509939748 0.029151649 0.209759066 2.29799756 0.00758695 0.017905251 8524.449717 -3.930666353 -0.081159991 LKDRDPEFYK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKDRDPEFYK 10 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 ; 100.55 0.0022129 574700000 823570 786780 640310 634290 683700 708720 657510 716210 865540 805130 FALSE TRUE 791383.9739 764341.8047 756028.2606 667025.7829 705691.8314 723050.804 665556.8041 701420.0132 767287.5278 750597.828 1.054338215 1.018310707 1.00723481 0.888659357 0.940173026 0.963299888 0.886702278 0.934481805 1.022235209 1 19.51768059 3.932234736 5.672945197 0.941409928 1.031289562 0.436969832 0.041227718 0.17620884 10.79053171 0.010446409 0.0195103 8555.290013 -3.932234736 0.089879633 LDLFEISQPTEDLEFHGVMR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDLFEISQPTEDLEFHGVMR 20 0 P55196-5;P55196;J3KN01;P55196-3;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ; 161.65 2.22E-11 63013000 43134 44510 37474 51282 48132 46813 47882 53022 49522 50958 FALSE TRUE 41448.27559 43240.61838 44246.3854 53928.67017 49680.20949 47759.59093 48467.99424 51927.07717 43900.47017 47506.56927 0.872474612 0.910202927 0.931374041 1.135183428 1.045754519 1.005326035 1.020237727 1.093050455 0.924092622 1 15.5358394 3.932610489 7.257140726 1.037920726 0.89826724 0.543591295 0.053993139 0.178252687 16.82014006 0.013568946 0.024800487 8562.695276 -3.932610489 -0.139653486 NKGNECFQK ddPTM_BT-474_Pertuzumab_2h_R1 6 NKGNECFQK 9 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;;; 140.49 9.94E-05 5755850000 8648520 8400490 6735110 6464617 6896730 6791384 7161060 7728240 9073790 8012350 FALSE TRUE 8310526.277 8160916.25 7952294.199 6798256.658 7118569.584 6928710.438 7248699.194 7568649.143 8043771.4 7469666.398 1.112569937 1.092540927 1.064611694 0.910115164 0.952996989 0.927579636 0.970418063 1.013251294 1.076858185 1 22.83261238 3.932671863 5.776381113 0.97789215 1.097458813 0.577360831 0.044302272 0.157621324 10.03285486 0.012383203 0.023082492 8563.905433 -3.932671863 0.119566663 DLSKY(ph)NFENK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLSKYNFENK 10 1 K7ES28;Q9Y2G9-3;Q9Y2G9 K7ES28 SBNO2 Protein strawberry notch homolog 2 1 DLS(0.001)KY(0.999)NFENK 80.219 0.087604 76865000 69554 102800 121690 242310 258880 259950 319210 248460 216560 179730 TRUE FALSE 66835.75278 99868.24465 143682.09 254815.6481 267207.1103 265206.3671 323116.5875 243329.2142 191977.0167 167556.727 0.39888433 0.596026471 0.857513109 1.520772414 1.594726246 1.582785555 1.928401164 1.452219905 1.145743415 1 17.35429008 3.933276171 2.232492082 1.520296195 0.477464212 0.716212102 0.247907102 0.1511033 1.470425023 0.067279768 0.163610235 8575.830151 -3.933276171 -1.042831984 RRLS(ph)DK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRLSDK 6 2 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 RRLS(1)DK 74.301 0.063545 269390000 121680 121120 89445 88837 92256 88822 77712 97856 89968 87223 TRUE FALSE 116924.6111 117665.7762 105609.7012 93421.88822 95223.49802 90618.0417 78663.0627 95835.2394 79755.20982 81315.30852 1.437916343 1.447031049 1.298767761 1.148884385 1.171040235 1.114403221 0.967383192 1.178563313 0.980814207 1 16.31123936 3.933337601 0.793215537 1.055906776 1.527859296 0.848483184 0.064463391 0.381019423 0.371316912 0.026374194 0.131261689 8577.043277 -3.933337601 0.47195252 VEDMAELTCLNEASVLHNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEDMAELTCLNEASVLHNLK 20 0 P35579;Q5BKV1;B1AH99;P35580;P35580-5;P35580-2;P35580-3;P35580-4;E7ERA5 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 227.95 3.38E-25 86875000 95803 92815 82064 100480 98756 109750 100250 112930 134640 116170 FALSE TRUE 92058.91284 90168.00708 96894.7903 105665.7848 101932.5764 111969.2202 101476.8895 110597.956 119356.2317 108301.7024 0.850022768 0.832563155 0.894674674 0.975661347 0.941190897 1.033863898 0.936983327 1.021202378 1.102071611 1 16.7246964 3.933706938 0.534871535 1.030199555 0.775082974 0.73244667 0.041607246 1.008395786 0.398877093 0.027111492 0.146925415 8584.340549 -3.933706938 -0.255116581 QQAISEKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQAISEKDR 9 1 Q9H6T3;Q9H6T3-3;Q9H6T3-2 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 0 ; 115.18 0.0013849 152563000 177021 178091 134971 136579 127607 130250 155504 147522 149298 173675 FALSE TRUE 170102.8236 173012.019 159363.2621 143627.8586 131711.595 132883.7442 157407.1045 144475.6191 132350.3169 161911.8376 1.050589174 1.068556948 0.984259487 0.887074477 0.813477242 0.820716671 0.972177864 0.892310416 0.817422117 1 17.30484894 3.934641266 2.730353502 0.881800402 1.058888001 0.585012493 0.059327475 0.183499108 2.679890812 0.015928284 0.035622605 8602.828506 -3.934641266 0.177087599 KKTDELR ddPTM_BT-474_Pertuzumab_2h_R1 4 KKTDELR 7 2 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;A0A494C198;D6RDA2;D6R9L5 H0Y993 DEK Protein DEK 0 ;;; 110.41 0.0038304 1375740000 3502230 3325390 2718790 2711190 3017180 2460330 3109930 3296790 3558180 3202040 FALSE TRUE 3365358.98 3230553.133 3210135.832 2851114.841 3114230.335 2510079.558 3147990.254 3228710.134 3154270.324 2985162.979 1.127361891 1.082203269 1.075363675 0.955095203 1.043236285 0.840851765 1.054545523 1.081585882 1.056649284 1 21.50937827 3.934755967 5.795666408 1.010174559 1.099149688 0.287337543 0.065755348 0.308030234 20.21465075 0.018090085 0.03374309 8605.100894 -3.934755967 0.088975129 EEGDLGPVYGFQWR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEGDLGPVYGFQWR 14 0 P04818;P04818-2 P04818 TYMS Thymidylate synthase 0 ;;; 248.09 1.56E-17 396773000 384674 389062 317675 417384 369022 370522 421692 419195 383178 461275 FALSE TRUE 369640.5148 377966.3327 375085.9391 438925.2383 380891.9278 378014.2087 426852.7928 410538.4768 339681.2399 430032.4334 0.85956427 0.878925177 0.872227093 1.020679382 0.885728373 0.879036508 0.992606045 0.954668636 0.789896793 1 18.71408595 3.9348494 24.99982318 0.932182144 0.870825684 0.159286704 0.064813322 346.5244267 132969.2362 0.016251261 0.029297416 8606.952386 -3.9348494 -0.06135646 VFDMLNRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFDMLNRR 8 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 143.01 0.00097537 1489770000 3682200 4689100 2682700 1976230 1926810 914610 2976200 2098500 2447400 2781200 FALSE TRUE 3538295.553 4555371.459 3167523.566 2078223.467 1988787.594 933104.0408 3012623.626 2055165.242 2169581.412 2592826.847 1.364647839 1.756913102 1.221648708 0.801528058 0.767034481 0.359879042 1.161906986 0.792634975 0.836762939 1 21.30609443 3.934872046 3.223286874 0.808576185 1.558333635 0.666550568 0.212474955 0.13445958 2.734042164 0.054833896 0.116000411 8607.401195 -3.934872046 0.74975745 DAAAVGNHVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAAAVGNHVAK 11 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ; 110.08 0.0018429 645620000 656734 735417 654610 862550 1077020 1037800 952530 870480 879980 927680 FALSE TRUE 631068.1092 714443.6272 772912.5887 907066.3089 1111663.326 1058785.027 964187.3471 852504.2838 780088.3596 864847.4073 0.72968723 0.826092119 0.89369822 1.04881659 1.285386667 1.224244899 1.114864124 0.985727975 0.901995373 1 19.72208608 3.935061713 2.203479057 1.090762717 0.772876936 0.573842062 0.107608124 0.24767548 2.347237499 0.033272399 0.081591479 8611.16108 -3.935061713 -0.317885781 ALGSNDPMQSILNSLEQQHEEEKR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALGSNDPMQSILNSLEQQHEEEKR 24 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ;; 165.66 9.07E-12 269394000 196091 194469 172112 212282 215978 216080 225941 230991 250577 241613 FALSE TRUE 188427.5469 188922.9345 203216.467 223237.8995 222925.1285 220449.2856 228706.1335 226220.9551 222132.5495 225248.3363 0.836532469 0.838731764 0.902188537 0.991074576 0.989686016 0.978694401 1.015351045 1.004317985 0.986167326 1 17.78115692 3.935094204 2.072187428 0.997686035 0.833614893 0.975715358 0.010156048 0.045450448 0.379756722 0.003007616 0.007612217 8611.805336 -3.935094204 -0.164071142 SFFDNISCDDNR ddPTM_BT-474_Pertuzumab_2h_R1 6 SFFDNISCDDNR 12 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;;;; 191.33 1.28E-05 2205970000 2001750 2024080 1682980 2078250 2149660 1999390 2074200 2131970 2129600 2236070 FALSE TRUE 1923519.397 1966355.22 1987131.924 2185508.732 2218805.766 2039819.036 2099584.68 2087944.074 1887856.736 2084618.987 0.922719887 0.943268402 0.953235069 1.048397211 1.06436993 0.978509285 1.007179102 1.001595058 0.905612367 1 20.99135229 3.935776716 7.009426603 1.002904742 0.936546561 0.332122318 0.040220978 0.279946366 26.21499975 0.010652291 0.019532229 8625.349782 -3.935776716 -0.066358181 S(ph)PPPVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPPVSK 7 0 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(1)PPPVSK;S(1)PPPVSK 74.173 0.049197 9649200000 5581500 5077300 5566900 6231800 5393800 5755800 6918200 7347500 7903500 7989500 TRUE FALSE 5363368.809 4932500.375 6572962.665 6553423.945 5567296.476 5872186.22 7002867.001 7195771.557 7006327.814 7448364.049 0.720073398 0.662226006 0.88247065 0.879847427 0.747452251 0.788386038 0.940188605 0.966087521 0.940653245 1 22.82849216 3.935940375 0.231601717 1.036678049 0.523979327 0.646437639 0.065312783 5.040801987 0.330621821 0.128218308 0.741847472 8628.600753 -3.935940375 -0.512698722 AIEQADLLQEEDESPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIEQADLLQEEDESPR 16 0 A0A2R8YGH5;H7C1E4;P61966 A0A2R8YGH5 AP1S1 AP-1 complex subunit sigma-1A 0 ; 295.29 1.07E-28 69560000 140879 137159 119007 149605 153685 158914 149654 153266 147733 158230 FALSE TRUE 135373.2929 133247.3596 140514.2122 157326.132 158628.4176 162127.35 151485.5104 150101.0035 130962.9692 147512.9412 0.91770452 0.903292678 0.952555153 1.066524271 1.075352551 1.099072045 1.02693031 1.017544646 0.887806644 1 17.170482 3.936019896 4.31745585 1.029627496 0.913035729 0.425967295 0.054441118 0.199704395 7.34042357 0.014851994 0.029132625 8630.180839 -3.936019896 -0.116591767 LKEDLEIEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEDLEIEHR 10 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A087WX84;Q99996-4 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 165.66 3.48E-06 134030000 280340 287190 245920 279250 294200 295470 327750 317490 363690 348130 FALSE TRUE 269384.0029 278999.6224 290363.2145 293662.126 303663.2102 301444.6058 331761.1025 310933.7206 322405.4359 324550.845 0.830020957 0.859648424 0.894661711 0.904826256 0.93564141 0.928805488 1.022216111 0.958043171 0.993389606 1 18.30808499 3.936031626 0.41109537 1.00231671 0.772999997 0.880407249 0.020457669 0.890886503 0.191488392 0.017260458 0.094983371 8630.413933 -3.936031626 -0.229316713 VLDGLHNELQTIGFQIETIGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLDGLHNELQTIGFQIETIGK 21 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 170.91 1.41E-17 0 288649 282770 253961 301310 318090 325620 330010 326580 352560 356440 FALSE TRUE 277368.278 274705.6765 299857.402 316860.6452 328321.6537 332204.2595 334048.7611 319836.0089 312538.8669 332298.0013 0.834697401 0.826684709 0.902374979 0.953543638 0.98803379 0.999717898 1.005268644 0.96249754 0.940537908 1 18.34211809 3.936722443 1.766937764 0.981579629 0.825235203 0.904909797 0.019441829 0.106817759 0.639839948 0.005890943 0.016424628 8644.152958 -3.936722443 -0.156344426 KGNYSER ddPTM_BT-474_Pertuzumab_2h_R1 5 KGNYSER 7 1 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q7L7L0;P04908 A0A0U1RR32;Q7L7L0 HIST1H2AD;HIST3H2A;HIST1H2AB Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E 0 ;;;; 127.46 0.0061773 21133300000 8564780 9031900 5775740 5999170 5702280 2007330 7427820 6135560 5744070 6532620 FALSE TRUE 8230058.929 8774319.055 6819544.699 6308787.883 5885699.015 2047919.588 7518723.883 6008858.542 5092027.255 6090159.829 1.351369941 1.440737075 1.119764487 1.035898574 0.966427677 0.336266969 1.234569222 0.986650385 0.836107327 1 22.53804866 3.9370433 1.689437082 0.904322116 1.41042042 0.440029521 0.217860149 0.371863036 2.024399213 0.063700999 0.183104606 8650.54162 -3.9370433 0.506098304 AS(ph)PPPQGPLPGPPGALHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPPPQGPLPGPPGALHR 18 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR 187.07 2.89E-14 3539590000 768160 758400 645082 754080 772770 864290 711600 813860 819290 944930 TRUE FALSE 738139.458 736771.1746 761662.6672 792998.1592 797626.8489 881766.536 720308.7737 797053.5066 726287.6339 880929.0494 0.837910225 0.836356997 0.864612953 0.900183913 0.905438241 1.000950686 0.817669453 0.904787403 0.824456447 1 19.7486663 3.939111655 2.448255882 0.902399041 0.836759139 0.201259631 0.05703606 0.498990117 5.860745633 0.014907763 0.034980475 8691.838635 -3.939111655 -0.065639901 ATSSS(ph)NPSS(ph)PAPDWYK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSSSNPSSPAPDWYK 16 0 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 2 AT(0.002)S(0.016)S(0.113)S(0.869)NPS(0.079)S(0.921)PAPDWYK;ATSS(0.032)S(0.968)NPS(0.008)S(0.992)PAPDWYK 254.58 2.03E-26 790960000 2057210 1979340 2047780 2465400 2210540 2051090 2572900 3008100 3092300 3172300 TRUE FALSE 1976811.959 1922891.161 2417859.399 2592639.589 2281644.027 2092564.445 2604387.92 2945981.684 2741275.068 2957437.295 0.668420582 0.650188311 0.817552211 0.876650739 0.771493627 0.707560038 0.880623208 0.996126507 0.92690894 1 21.49591615 3.939701813 0.217240211 1.050019109 0.448234213 0.671429616 0.06964827 5.595079294 0.329661644 0.161636619 0.920010162 8703.657903 -3.939701813 -0.601784897 LGS(ph)PLAVDEALRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSPLAVDEALRR 13 1 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LGS(1)PLAVDEALRR 82.349 0.0077123 122120000 45207 42140 34934 31499 37068 34722 29300 34448 41004 38322 TRUE FALSE 43440.26046 40938.20846 41247.3509 33124.66716 38260.32588 35424.10263 29658.58216 33736.63676 36349.39782 35726.41681 1.215914283 1.145880615 1.154533664 0.927175746 1.070925363 0.991538077 0.83015832 0.944305077 1.017437545 1 15.12470361 3.941320964 0.951607535 0.948225848 1.233824513 0.646528693 0.066621243 0.480591292 0.711576677 0.024298974 0.109973113 8736.167745 -3.941320964 0.285598665 AGVDYAPNLPPFPS(ph)PADVK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGVDYAPNLPPFPSPADVK 19 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 AGVDYAPNLPPFPS(1)PADVK 71.558 0.020883 15120000 33942 31977 30508 42848 41299 40965 41384 47163 41826 46053 TRUE FALSE 32615.50912 31065.04727 36021.47425 45059.39041 42627.41984 41793.34037 41890.46977 46189.06757 37078.08783 42933.78929 0.75966994 0.723557081 0.839000583 1.049508817 0.992864141 0.973437031 0.975699338 1.075820894 0.863610886 1 15.38982589 3.94151307 3.67821046 0.99610404 0.745411357 0.780642963 0.053906354 0.092991756 2.501434771 0.013741671 0.028162151 8740.032947 -3.94151307 -0.250692683 GSVPLSSS(ph)PPATHFPDETEITNPVPK ddPTM_BT-474_Pertuzumab_2h_R1 5 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GSVPLS(0.031)S(0.156)S(0.808)PPAT(0.005)HFPDETEITNPVPK;GSVPLS(0.001)S(0.098)S(0.902)PPATHFPDETEITNPVPK;GSVPLS(0.001)S(0.031)S(0.968)PPATHFPDETEITNPVPK;GSVPLS(0.002)S(0.015)S(0.983)PPAT(0.001)HFPDETEITNPVPK;GSVPLS(0.001)S(0.037)S(0.961)PPAT(0.001)HFPDETEITNPVPK 311.55 5.89E-82 56358440000 4211460 4202160 3629720 5218220 4632630 4671100 4881750 4803980 5282680 5601220 TRUE FALSE 4046871.487 4082318.511 4285691.147 5487532.96 4781642.751 4765552.842 4941494.317 4704776.134 4683012.313 5221844.38 0.774988911 0.78177713 0.820723644 1.050880218 0.915699972 0.912618702 0.946312061 0.900979767 0.896811925 1 22.31612803 3.942085116 8.528064523 0.937397772 0.783896769 0.704799431 0.045850717 0.189200801 26.43605827 0.011628307 0.021146386 8751.552766 -3.942085116 -0.153501004 ASS(ph)ESQIFELNK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSESQIFELNK 12 0 Q9BV36;Q9BV36-4 Q9BV36 MLPH Melanophilin 1 ASS(1)ESQIFELNK;ASS(1)ESQIFELNK 328.14 4.63E-58 267360000 1007950 1045220 794860 747400 829350 783390 714690 911830 1045300 1051110 TRUE FALSE 968558.1997 1015411.349 938508.8836 785973.4036 856026.7959 799230.6825 723436.59 893000.3919 926641.9263 979917.3835 0.988408019 1.036221386 0.957742866 0.802081295 0.873570375 0.815610271 0.73826284 0.911301715 0.945632705 1 19.9023006 3.943003069 4.83637426 0.859398562 1.010038084 0.397165033 0.071586973 0.181193477 8.862855832 0.018376967 0.035438399 8770.07018 -3.943003069 0.150639522 DLS(ph)LEVDRDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLSLEVDRDR 10 1 E7EMW7;O95071-2;O95071;E5RFK7 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 DLS(1)LEVDRDR 71.176 0.031352 148790000 50810 47201 39765 33598 50023 34439 44531 47775 44335 47600 TRUE FALSE 48824.28903 45854.87369 46951.42007 35331.99681 51632.03522 35135.38018 45075.9837 46788.42955 39302.27667 44376.0096 1.100240636 1.033325757 1.058036099 0.796195898 1.16351235 0.791765201 1.015773705 1.054363156 0.885664958 1 15.43749232 3.943408731 24.99988949 0.967532273 1.061509632 0.161504046 0.108892643 521.426364 230346.4347 0.026344082 0.047492641 8778.265878 -3.943408731 0.093977359 DKPSVEPVEEYDYEDLKESSNS(ph)VSNHQLSGFDQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKPSVEPVEEYDYEDLKESSNSVSNHQLSGFDQAR 35 2 Q9Y450;E9PN23;G5E991;E9PLR4;E9PMN1;Q9Y450-2 Q9Y450;Q9Y450-2 HBS1L HBS1-like protein 1 DKPSVEPVEEYDYEDLKES(0.011)S(0.071)NS(0.906)VS(0.011)NHQLSGFDQAR;DKPSVEPVEEYDYEDLKES(0.129)S(0.129)NS(0.705)VS(0.035)NHQLSGFDQAR 187.2 9.99E-21 376770000 273230 260465 189221 124494 152913 180073 116958 206295 184971 160779 TRUE FALSE 262551.8695 253036.7932 223417.4439 130919.1503 157831.5855 183714.1994 118389.367 202034.9362 163973.8675 149889.2951 1.751638563 1.68815787 1.4905497 0.873438961 1.052987709 1.225665911 0.789845378 1.347894364 1.0939665 1 17.19353783 3.944221179 3.938978663 1.077457143 1.703380119 0.764037058 0.152640791 0.103421664 3.242543456 0.039754982 0.080250621 8794.703032 -3.944221179 0.625922976 AAESTEEVSSLRPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAESTEEVSSLRPPR 15 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 94.532 0.0040445 123200000 138550 133490 117740 141180 149780 137100 137410 161910 165810 160740 FALSE TRUE 133135.3128 129682.9959 139018.2371 148466.3167 154597.8097 139872.2559 139091.6647 158566.5019 146987.9439 149852.9366 0.888439799 0.865401765 0.927697783 0.990746795 1.031663531 0.933396829 0.928187781 1.058147444 0.980881304 1 17.19318783 3.94475836 2.877835487 0.991249296 0.877445075 0.594620283 0.037441073 0.183746812 2.998537421 0.010592068 0.023476097 8805.587971 -3.94475836 -0.113804221 LRS(ph)PSNDS(ph)AHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 LRS(1)PS(0.123)NDS(0.877)AHR 128.74 0.00014765 330430000 275850 299760 258160 405900 326810 392620 336000 395560 348330 371820 TRUE FALSE 265069.477 291211.1383 304815.2547 426848.5476 337322.1405 400559.0454 340112.0685 387391.5478 308789.0387 346636.3002 0.764690475 0.840105719 0.879351801 1.231401753 0.973129878 1.155560007 0.981178452 1.117573513 0.890815643 1 18.40306322 3.945185487 7.803449044 1.055883161 0.816057118 0.540868179 0.095176431 0.190394222 24.80962499 0.022480038 0.041101371 8814.252495 -3.945185487 -0.239826044 LGLDPTQEDCVATHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGLDPTQEDCVATHR 15 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ;; 163.8 1.52E-06 1920620000 353782 397132 347633 539830 507036 538945 489310 528070 446327 417174 FALSE TRUE 339955.8083 385806.1842 410458.0162 567690.691 523345.2734 549842.8372 495298.3221 517165.17 395661.8301 388918.4334 0.874105671 0.991997681 1.055383291 1.459665169 1.345642758 1.413774175 1.273527505 1.329752271 1.017338846 1 18.56910809 3.947276111 4.668261615 1.288890862 0.948859754 0.454029784 0.146783747 0.160650324 7.482765037 0.036651368 0.071437894 8856.785171 -3.947276111 -0.340031108 TLEEILLER ddPTM_BT-474_Pertuzumab_2h_R1 2 TLEEILLER 9 0 O75152;E9PBY7;E9PQ61 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 0 ; 93.649 0.021534 40644000 61572 66622 56948 63461 75379 75702 68206 80712 74406 80897 FALSE TRUE 59165.69817 64722.00579 67239.7704 66736.22982 77803.63399 77232.74631 69040.72543 79045.26899 65959.74282 75417.77413 0.784506025 0.85817974 0.891563974 0.884887291 1.031635246 1.024065576 0.91544369 1.048098673 0.874591482 1 16.20261695 3.947481968 1.093604814 0.984609415 0.795846592 0.562548897 0.055781487 0.455144404 0.929681388 0.017821936 0.073310177 8860.984311 -3.947481968 -0.188762824 AESTFLFLVGQDDHNWK ddPTM_BT-474_Pertuzumab_2h_R1 2 AESTFLFLVGQDDHNWK 17 0 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753;P49753-2 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ; 267.22 9.48E-28 1671170000 1596190 1795370 1414430 2142380 1642980 1744540 2217030 1964760 2165180 1923010 FALSE TRUE 1533809.13 1744167.805 1670048.965 2252948.489 1695827.944 1779815.794 2244162.676 1924187.019 1919397.844 1792762.82 0.85555608 0.972893785 0.931550424 1.25669077 0.945929894 0.992778171 1.251790059 1.073308191 1.070636797 1 20.7737532 3.947527078 24.78387332 1.087903874 0.923724001 0.36227807 0.099927983 303.9323837 143552.5882 0.02510895 0.045266335 8861.90476 -3.947527078 -0.164179872 SESSEKPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SESSEKPAR 9 1 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 68.893 0.051785 115560000 224690 228950 173300 154260 184200 129350 199130 179040 213170 235300 FALSE TRUE 215908.8664 222420.5702 204619.165 162221.3771 190124.9603 131965.5456 201567.0125 175342.7614 188971.8353 219362.9214 0.984254153 1.013938767 0.932788293 0.739511382 0.866714206 0.601585467 0.918874581 0.799327253 0.861457506 1 17.74296016 3.948475016 4.889861551 0.815979735 0.994898062 0.326263351 0.100903953 0.199060348 10.42847342 0.024366529 0.047128383 8881.268821 -3.948475016 0.178918327 YCVHYLEDVGSFEYTR ddPTM_BT-474_Pertuzumab_2h_R1 3 YCVHYLEDVGSFEYTR 16 0 O95749-2;O95749 O95749-2 GGPS1 Geranylgeranyl pyrophosphate synthase 0 ;; 250.31 8.44E-21 979280000 588821 574324 507724 694560 727080 626910 638908 646975 713850 760420 FALSE TRUE 565809.2243 557944.8418 599481.0211 730406.3248 750467.1885 639586.5497 646727.1472 633614.7402 632816.7407 708916.0761 0.798132873 0.787039342 0.845630451 1.030314235 1.058612174 0.902203478 0.912276035 0.893779619 0.892653957 1 19.43525532 3.948571466 5.827523228 0.947349505 0.797382406 0.593350121 0.05596641 0.156394776 12.35581309 0.016220036 0.030521369 8883.241435 -3.948571466 -0.149967099 REPEEHQVEEEHRK ddPTM_BT-474_Pertuzumab_2h_R1 1 REPEEHQVEEEHRK 14 2 F8W785;O00461 F8W785 GOLIM4 Golgi integral membrane protein 4 0 91.207 0.0017525 312770000 68451 79658 65224 108790 96933 111870 86228 75828 105570 105990 FALSE TRUE 65775.85924 77386.23183 77011.4277 114404.6649 100050.938 114132.088 87283.28406 74262.1253 93586.13619 98811.20289 0.665672083 0.783172652 0.779379518 1.157810669 1.012546503 1.155052106 0.883333888 0.751555726 0.947120705 1 16.592387 3.949156887 12.94138183 0.965419887 0.738606063 0.474941929 0.116836538 2.001874548 508.9754977 0.0349224 0.063061696 8895.223951 -3.949156887 -0.226813824 ESADPLGAWLQDAR ddPTM_BT-474_Pertuzumab_2h_R1 6 ESADPLGAWLQDAR 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 190.78 1.31E-06 584880000 444941 457767 384176 485140 464603 492046 496775 489294 504933 513310 FALSE TRUE 427552.2138 444711.9334 453605.1491 510178.1335 479547.3774 501995.5072 502854.6811 479189.9079 447615.1227 478543.0565 0.893445653 0.92930391 0.94788785 1.066107065 1.002098706 1.049008026 1.050803421 1.00135171 0.935370635 1 18.86828921 3.949520873 4.426870403 1.017088076 0.915764535 0.588299698 0.035753996 0.14158769 5.908717378 0.009433767 0.018631554 8902.682248 -3.949520873 -0.101323541 S(ph)GNSDSIER ddPTM_BT-474_Pertuzumab_2h_R1 2 SGNSDSIER 9 0 C9J8U3;A0A0A0MRW7;Q7Z2E3-4;Q7Z2E3-5;Q7Z2E3-10;Q7Z2E3-8;Q7Z2E3-7;Q7Z2E3;A0A5F9ZI51;A0A5F9ZGW5;Q7Z2E3-13;Q7Z2E3-9;Q7Z2E3-11 C9J8U3 APTX Aprataxin 1 S(1)GNSDSIER;S(0.979)GNS(0.021)DSIER 187.93 4.19E-05 239627000 315000 296050 260360 315780 319170 297400 326400 340660 350570 364380 TRUE FALSE 302689.4517 287606.9439 307412.8437 332077.4436 329436.3929 303413.6318 330394.5808 333625.252 310774.7633 339700.218 0.891048741 0.846649277 0.90495333 0.97756029 0.969785639 0.893180562 0.972606325 0.982116685 0.914850055 1 18.37390262 3.949559047 4.222062029 0.957659962 0.869397659 0.569256807 0.031934153 0.144495715 5.402310055 0.008181524 0.01632953 8903.464825 -3.949559047 -0.088262302 QGTQYTFSSIER ddPTM_BT-474_Pertuzumab_2h_R1 2 QGTQYTFSSIER 12 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 235.49 1.11E-15 314880000 62157 65902 51350 54482 57809 47781 56523 74676 49949 64453 FALSE TRUE 59727.83572 64022.53948 60630.08727 57293.82255 59668.47899 48747.16456 57214.74538 73133.9145 44278.99892 60087.5409 0.994013648 1.065487762 1.009029266 0.953505863 0.99302581 0.811269089 0.95218983 1.217122775 0.736908155 1 15.87477826 3.949590137 5.543852405 0.972160911 1.031677367 0.051768763 0.120735241 0.778150865 55.49593249 0.032419486 0.061482837 8904.10222 -3.949590137 0.059516456 KKVENTR ddPTM_BT-474_Pertuzumab_2h_R1 3 KKVENTR 7 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;; 98.458 0.0063262 6367450000 5764193 5466952 4379556 4166847 4372799 3377842 5382478 5257917 5150112 5647815 FALSE TRUE 5538921.965 5311039.882 5171039.192 4381898.473 4513454.051 3446144.28 5448350.376 5149339.177 4565492.877 5265283.459 1.051970327 1.008690211 0.982100818 0.83222461 0.857210079 0.654503087 1.034768673 0.977979479 0.867093465 1 22.32807977 3.949648109 4.283767485 0.891655074 1.024983609 0.250069963 0.10119958 0.325222428 12.57949488 0.028038625 0.055783907 8905.290865 -3.949648109 0.133328535 HGCHTVIAS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 HGCHTVIASR 10 0 G3V0I9;A0A0J9YXZ6;A0A0J9YWI0;Q9NUI1-2;Q9NUI1-3;Q9NUI1 G3V0I9 DECR2 "Peroxisomal 2,4-dienoyl-CoA reductase" 1 HGCHT(0.099)VIAS(0.901)R;HGCHT(0.106)VIAS(0.894)R 56.432 0.079965 2007110000 267840 292390 351270 667900 660690 722750 667470 448010 806790 761640 TRUE FALSE 257372.5167 284051.3235 414752.303 702370.399 681941.6939 737364.5002 675638.6975 438758.4369 715206.5815 710053.4444 0.362469218 0.400042174 0.584114205 0.989179624 0.960408965 1.03846338 0.951532174 0.617923116 1.007257393 1 19.43756809 3.950449678 3.053199073 0.909770072 0.385674739 0.795049588 0.115834355 0.127313302 2.354942862 0.035101832 0.076683207 8921.742368 -3.950449678 -0.524095333 down RAPSS(ph)PVAKPGPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RAPSSPVAKPGPVK 14 2 Q9GZR2;A0A0C4DG31;Q9GZR2-2 Q9GZR2 REXO4 RNA exonuclease 4 1 RAPS(0.403)S(0.597)PVAKPGPVK 71.685 0.021251 1255600000 1234900 1220400 913650 771530 837740 664080 1013800 954720 1080000 1162100 TRUE FALSE 1186638.743 1185595.387 1078766.879 811348.7558 864686.6679 677508.1526 1026207.188 935004.6984 957402.9277 1083389.932 1.095301616 1.094338568 0.99573279 0.748898187 0.798130611 0.625359469 0.947218686 0.863036171 0.883710379 1 20.04712116 3.951216132 4.003243055 0.831325715 1.088703202 0.533787909 0.09830982 0.161367451 5.374797532 0.025889264 0.052414263 8937.501595 -3.951216132 0.257377487 TVAYTEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAYTEQK 8 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 140.5 0.0029262 0 57162 70627 46550 48350 43008 31017 59504 52901 54511 64804 FALSE TRUE 54928.04584 68612.78711 54962.6205 50845.34929 44391.39138 31644.18499 60232.22775 51808.57586 48323.13981 60414.76736 0.909182444 1.135695627 0.909754732 0.841604653 0.734777163 0.523782287 0.99697856 0.857548214 0.799856425 1 15.88261361 3.951372933 3.481619215 0.81466708 1.02408382 0.248747304 0.137252654 0.303229003 7.409596077 0.036328603 0.076315265 8940.729026 -3.951372933 0.209416739 (ac)AVPETRPNHTIYINNLNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVPETRPNHTIYINNLNEK 19 1 P09012;M0R221;M0R2B8;M0R268;M0QXK2;M0R0G9 P09012 SNRPA U1 small nuclear ribonucleoprotein A 0 ; 136.36 3.91E-39 1784670000 976060 987470 766160 696050 821790 822570 786170 912030 821830 835640 FALSE TRUE 937914.4961 959308.3224 904622.1551 731973.2239 848223.6217 839202.929 795791.3836 893196.2618 728539.3038 779041.3585 1.20393415 1.231395884 1.16119914 0.939581982 1.088804352 1.07722513 1.021500816 1.146532533 0.935174103 1 19.5713404 3.951707858 6.963477215 1.045770074 1.212938943 0.603315254 0.062950323 0.153893448 18.64499282 0.015791985 0.029227799 8947.626721 -3.951707858 0.167168868 GAAVDEYFR ddPTM_BT-474_Pertuzumab_2h_R1 3 GAAVDEYFR 9 0 K7EQA8;Q86X55-2;Q86X55-1;Q86X55 K7EQA8 CARM1 Histone-arginine methyltransferase CARM1 0 ;; 138.54 0.00031079 371490000 1640510 1888470 1273770 1365490 1291230 1259770 1436100 1454840 1470520 1358900 FALSE TRUE 1576397.056 1834612.685 1503968.574 1435963.103 1332763.586 1285243.413 1453675.421 1424797.046 1303592.735 1266860.493 1.244333583 1.448156838 1.187161951 1.133481635 1.052020797 1.014510611 1.147462905 1.124667676 1.028994702 1 20.27282623 3.951992422 2.711899634 1.079874381 1.345544455 0.712402659 0.068630741 0.136625945 1.98256597 0.017660635 0.040295555 8953.49142 -3.951992422 0.265670074 VLVPEHEKDVLEWIACVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLVPEHEKDVLEWIACVR 18 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 162.15 2.18E-11 263240000 143460 149710 119690 97034 128680 143780 144280 120640 144160 141280 FALSE TRUE 137853.4246 145440.4174 141320.6455 102041.9364 132819.1091 146687.3301 146045.7418 118148.7418 127795.5612 131710.9798 1.046635784 1.104239128 1.072960248 0.774741305 1.00841334 1.113706165 1.108834981 0.897030316 0.970272648 1 17.00701609 3.952093941 24.99905654 0.981951637 1.078729083 0.172724875 0.092978222 678.3586259 353991.4031 0.025305977 0.045622253 8955.5846 -3.952093941 0.096777446 ELISDNQYR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELISDNQYR 9 0 P25205;P25205-2 P25205 MCM3 DNA replication licensing factor MCM3 0 ;;; 175.51 0.0001253 1260540000 1329720 1398110 1129970 1465510 1426640 1395190 1431340 1466600 1417290 1587050 FALSE TRUE 1277753.072 1358237.272 1334180.715 1541145.147 1472529.171 1423401.698 1448857.167 1436314.197 1256405.181 1479557.69 0.863604766 0.918002239 0.901742949 1.041625587 0.995249581 0.962045419 0.979250202 0.970772689 0.849176203 1 20.49673452 3.952491954 22.09468442 0.971101146 0.895570689 0.350810019 0.047886528 115.4098465 53673.94646 0.012239227 0.022066623 8963.795799 -3.952491954 -0.075530457 THS(ph)EGSLLQEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 THSEGSLLQEPR 12 0 P49796-1;P49796-4;P49796-6;P49796;C9J582 P49796-1 RGS3 Regulator of G-protein signaling 3 1 T(0.052)HS(0.948)EGSLLQEPR 175.27 1.81E-05 364680000 241590 212020 154350 152960 172590 129290 107290 117090 148850 122230 TRUE FALSE 232148.3957 205973.3972 182244.4785 160854.2839 178141.5141 131904.3324 108603.0471 114672.0506 131953.172 113951.2532 2.037260575 1.807557103 1.599319651 1.411606098 1.563313338 1.15755052 0.953065842 1.006325489 1.157979121 1 16.79805727 3.952564875 0.464831001 0.959641814 2.324053494 0.906374164 0.108676185 0.710941881 0.201144442 0.089344809 0.499018552 8965.30099 -3.952564875 1.364411681 up SLEPSPS(ph)PGPQEEDGEVALVLLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLEPSPSPGPQEEDGEVALVLLGR 24 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 SLEPS(0.088)PS(0.912)PGPQEEDGEVALVLLGR;SLEPS(0.017)PS(0.983)PGPQEEDGEVALVLLGR;SLEPS(0.001)PS(0.999)PGPQEEDGEVALVLLGR;SLEPS(0.002)PS(0.998)PGPQEEDGEVALVLLGR 232.54 1.83E-34 287028000 154374 190441 146760 302053 212919 175997 240097 254669 191958 165104 TRUE FALSE 148340.8934 185009.8091 173282.7967 317641.9915 219767.733 179555.7799 243035.3789 249409.9962 170167.7326 153921.359 0.963744696 1.201976193 1.125787855 2.063664156 1.427792312 1.166542324 1.578958115 1.620372882 1.105549832 1 17.23183392 3.952877156 24.99870533 1.467564134 1.103113683 0.195857954 0.293625336 536.6304521 284683.191 0.073257688 0.132072101 8971.749852 -3.952877156 -0.364450451 ATS(ph)LPSIPNPFPELCS(ph)PPSQSPILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.456)S(0.514)LPS(0.03)IPNPFPELCS(0.594)PPS(0.341)QS(0.065)PILGGPSSAR;AT(0.453)S(0.504)LPS(0.042)IPNPFPELCS(0.632)PPS(0.302)QS(0.066)PILGGPSSAR 107.45 6.95E-05 1040110000 49259 49964 42192 51443 55735 52480 48433 61493 49275 48503 TRUE FALSE 47333.90382 48539.07564 49817.03296 54097.97939 57527.76689 53541.18156 49025.73754 60223.14806 43681.50858 45217.84861 1.046796902 1.07344947 1.101711702 1.196385522 1.272235824 1.184071848 1.084212077 1.331844613 0.966023593 1 15.46460473 3.953281259 3.328961249 1.173406845 1.062282222 0.062915775 0.108195224 0.438988982 9.769976348 0.027132874 0.057856589 8980.101777 -3.953281259 -0.111124623 T(ph)PSPARPALR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPSPARPALR 10 1 Q9H211 Q9H211 CDT1 DNA replication factor Cdt1 1 T(0.5)PS(0.5)PARPALR;T(0.627)PS(0.373)PARPALR 81.709 0.032653 994120000 864860 887480 827810 1157490 1071410 1312280 1120810 1176320 1273520 1387500 TRUE FALSE 831060.315 862169.9393 977413.6815 1217228.198 1105872.876 1338815.201 1134526.808 1152028.581 1128955.349 1293523.389 0.642477996 0.666528295 0.755621189 0.94101754 0.854930715 1.035014297 0.877082562 0.890612872 0.872775365 1 20.30287471 3.953282799 2.410256944 0.91825862 0.650548367 0.800832876 0.055282176 0.120945489 1.380219381 0.01451691 0.034823021 8980.13363 -3.953282799 -0.267710254 NSTFSEIFKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSTFSEIFKK 10 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 171.62 6.36E-06 1740730000 3750320 3444060 2523190 1776140 2262610 775640 2332110 2464620 2869500 2676700 FALSE TRUE 3603753.348 3345838.781 2979186.561 1867806.798 2335388.906 791323.9722 2360651.06 2413724.736 2543766.39 2495404.725 1.444155857 1.34080005 1.193869087 0.748498542 0.935875805 0.317112477 0.945999275 0.967267839 1.019380289 1 21.25084239 3.953614435 2.79405892 0.841747385 1.392561951 0.565293222 0.196508116 0.198449904 3.06346669 0.054241391 0.122590943 8986.993645 -3.953614435 0.550814567 (ac)ADHSFSDGVPS(ph)DSVEAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADHSFSDGVPSDSVEAAK 18 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;E9PKT8;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 ADHS(0.012)FS(0.066)DGVPS(0.784)DS(0.139)VEAAK;ADHSFS(0.008)DGVPS(0.807)DS(0.184)VEAAK 63.918 1.91E-19 67002000 210552 218505 170624 158068 168268 197323 169829 195310 204346 219241 TRUE FALSE 202323.3951 212273.4513 201459.5523 166225.9084 173680.493 201313.0063 171907.4181 191276.7802 181149.4988 204391.6118 0.989881108 1.038562441 0.985654698 0.813271675 0.849743742 0.984937711 0.841068851 0.935834786 0.886286366 1 17.64097646 3.953851452 10.6234991 0.898823168 1.013722677 0.405648316 0.057817407 0.647211249 147.9914327 0.014124039 0.025618825 8991.899651 -3.953851452 0.114899509 EESAEQPEFYYDEFGFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EESAEQPEFYYDEFGFR 17 0 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 148.52 8.36E-07 40676000 20243 20658 18107 25568 22249 24030 29216 29088 26432 29156 FALSE TRUE 19451.88118 20068.85407 21379.33769 26887.56754 22964.65929 24515.90306 29573.55415 28487.32264 23431.55017 27181.23815 0.715636318 0.738334801 0.786547602 0.989195834 0.844871715 0.901942102 1.088013503 1.048050956 0.862048669 1 14.73032355 3.95386344 0.659503941 1.002299782 0.641541616 0.629352401 0.075216788 0.91938562 0.57781597 0.039835833 0.218354532 8992.147861 -3.95386344 -0.360758166 SGELAQEYDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGELAQEYDKR 11 1 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 167.71 3.03E-05 957190000 593530 572000 458430 439810 494600 429010 500160 543010 589910 582530 FALSE TRUE 570334.1914 555687.12 541278.4987 462508.6468 510509.2582 437684.8761 506281.1077 531796.6537 522945.8899 543074.7242 1.05019469 1.023224052 0.996692489 0.851648265 0.940035018 0.805938587 0.93224944 0.979232931 0.962935424 1 19.05079119 3.953990899 6.350462908 0.923184345 1.030838991 0.41460787 0.055048683 0.200432378 20.85571912 0.014729079 0.027566223 8994.787323 -3.953990899 0.107654646 DEAGHFLWPGFGENAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEAGHFLWPGFGENAR 16 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ; 148.7 9.06E-07 564250000 514770 720520 532100 1177220 584960 628310 963580 866330 811250 623660 FALSE TRUE 494652.2193 699971.4751 628262.3065 1237976.465 603775.7696 641014.8587 975372.5803 848439.9828 719160.301 581418.9527 0.850767277 1.20390206 1.080567298 2.129233076 1.038452164 1.102500797 1.677572731 1.459257526 1.236905501 1 19.14921857 3.954933849 24.99956973 1.408822185 1.056057058 0.172201807 0.329463525 669.4605917 371370.6477 0.08220619 0.14820856 9014.338231 -3.954933849 -0.352765127 TAVIPINGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 TAVIPINGSPR 11 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR 202.8 4.07E-08 8782630000 4476470 4563170 3820720 4721380 4414110 4437940 5202410 4941690 4705580 5432210 TRUE FALSE 4301524.603 4433032.859 4511209.095 4965050.988 4556093.857 4527678.187 5266078.65 4839642.375 4171422.286 5064281.578 0.84938496 0.87535276 0.890789548 0.980405791 0.899652554 0.894041557 1.039847127 0.955642434 0.823694777 1 22.27192619 3.954939692 4.232458212 0.943174026 0.86539122 0.244901804 0.057555642 0.298445082 11.50069738 0.015005538 0.030102731 9014.459508 -3.954939692 -0.077782806 VIFWSALAGAIPLNGDS(ph)EEEANRDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIFWSALAGAIPLNGDSEEEANRDDR 26 1 Q9H089 Q9H089 LSG1 Large subunit GTPase 1 homolog 1 VIFWSALAGAIPLNGDS(1)EEEANRDDR;VIFWSALAGAIPLNGDS(1)EEEANRDDR 221.31 1.69E-34 1310310000 208998 216796 184907 268263 239389 254143 253610 236472 262140 258801 TRUE FALSE 200830.1271 210613.1903 218323.8081 282108.0856 247089.1646 259281.9456 256713.755 231588.7706 232382.9662 241272.1778 0.832379966 0.872927796 0.904885968 1.169252453 1.024109646 1.074645025 1.064000655 0.959865214 0.963156914 1 17.88030204 3.955507692 10.54261647 1.033402844 0.861619447 0.639803672 0.057982722 0.465430199 109.5368049 0.015661077 0.028434941 9026.256933 -3.955507692 -0.171783397 S(ph)PPGS(ph)GASTPVGPWDQAVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(1)PPGS(1)GASTPVGPWDQAVQR;S(1)PPGS(1)GASTPVGPWDQAVQR 144.17 2.33E-07 404050000 236090 225078 196663 252610 261880 228382 245440 255040 253660 280810 TRUE FALSE 226863.3418 218658.9958 232204.3788 265647.2324 270303.608 233000.0405 248443.7681 249773.3349 224865.5802 261790.4886 0.866583591 0.835244233 0.886985544 1.014732177 1.032518826 0.890024851 0.94901755 0.954096294 0.858952445 1 17.99805316 3.95584752 6.611260601 0.954935123 0.853020409 0.431350293 0.050593802 0.193905266 22.78814672 0.013211261 0.024665079 9033.322605 -3.95584752 -0.101914714 KISSDLDGHPVPK ddPTM_BT-474_Pertuzumab_2h_R1 3 KISSDLDGHPVPK 13 1 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;; 95.508 0.0030278 2804700000 3474870 3201040 2569540 2337280 2747770 2038520 2684910 2657370 3141040 3031710 FALSE TRUE 3339068.239 3109749.473 3033913.037 2457907.301 2836154.518 2079740.271 2717768.732 2602494.381 2784482.308 2826369.581 1.181398307 1.100262858 1.07343111 0.869634077 1.003462016 0.735834508 0.96157585 0.920790543 0.985179831 1 21.4305187 3.956059198 2.529680867 0.919345209 1.14413965 0.568802461 0.07777264 0.191600656 2.415144986 0.019965048 0.047038978 9037.726566 -3.956059198 0.224794442 ELNS(ph)NHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_BT-474_Pertuzumab_2h_R1 6 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDRLNEQAS(0.001)EEILK;ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.357)NHDGADET(0.322)S(0.322)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 100.72 8.32E-06 831972000 782363 694082 560683 435801 634008 623531 560856 492779 698646 600494 TRUE FALSE 751787.389 674287.4609 662010.8904 458292.7418 654401.4431 636139.224 567719.9235 482602.9414 619338.635 559822.0065 1.342904316 1.204467586 1.182538169 0.818640097 1.16894555 1.136324076 1.014107907 0.86206497 1.106313485 1 19.09460867 3.956269694 8.173091704 1.010549773 1.254396251 0.488147777 0.109280899 0.25752526 45.07066453 0.029184476 0.053589875 9042.108079 -3.956269694 0.243846478 YITEPEMVFEEHEVNEDIQPMTAFESEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YITEPEMVFEEHEVNEDIQPMTAFESEK 28 0 H0Y8R1;F5H5I6;H0YAK1;Q12849;Q12849-5 H0Y8R1 GRSF1 G-rich sequence factor 1 0 115.55 0.00034897 62877000 27338 27756 26698 48106 31516 34180 51615 39116 46350 40244 FALSE TRUE 26269.60074 26964.42606 31522.92249 50588.75643 32529.74076 34871.14302 52246.67981 38308.24093 41088.54232 37518.23803 0.700182154 0.718701823 0.840202636 1.348377724 0.867038072 0.929445114 1.392567523 1.021056503 1.095161832 1 15.19530446 3.956297792 7.480093863 1.092956627 0.725677811 0.506696281 0.157275237 0.191394573 29.01381794 0.039699868 0.073341012 9042.693116 -3.956297792 -0.367278816 GGREDMDISK ddPTM_BT-474_Pertuzumab_2h_R1 3 GGREDMDISK 10 1 P49321;P49321-3;P49321-4;E9PPR5;E9PNB5 P49321 NASP Nuclear autoantigenic sperm protein 0 ;; 152.67 1.61E-05 2771650000 3877120 3784930 3021940 3046210 3385590 2705390 3637710 3385620 3919760 3742490 FALSE TRUE 3725597.864 3676987.502 3568071.781 3203425.263 3494490.577 2760094.839 3682229.383 3315705.764 3474805.278 3489007.819 1.067810122 1.05387769 1.022660873 0.918147918 1.001571438 0.791083019 1.055380089 0.95032913 0.995929347 1 21.7343854 3.956302818 4.013139185 0.95735928 1.058034048 0.283447487 0.066579272 0.26229309 8.946346704 0.016552732 0.03367287 9042.797767 -3.956302818 0.100674768 EDVFVHQTAIK ddPTM_BT-474_Pertuzumab_2h_R1 5 EDVFVHQTAIK 11 0 P67809;H0Y449;A0A0D9SEI8;P16989;P16989-3;P16989-2;Q9Y2T7 P67809;P16989;P16989-2;Q9Y2T7 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3;Y-box-binding protein 2 0 ;;;; 195.25 1.57E-07 5108820000 5600230 6294840 7027670 8416580 6847570 6550730 8881680 8682640 9541230 11576600 FALSE TRUE 5381366.82 6115317.326 8297726.299 8850960.702 7067828.308 6683190.249 8990376.657 8503340.45 8458149.57 10792506.57 0.498620667 0.566626231 0.768841441 0.820102415 0.654882928 0.619243565 0.833020263 0.787893007 0.783705761 1 23.36352664 3.956453191 0.080098568 1.30384401 1.14E-17 0.65038463 0.083075689 48.03452437 0.811449273 4.088569587 9.694859787 9045.929337 -3.956453191 -1.30384401 YDIFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 YDIFLR 6 0 Q70JA7 Q70JA7 CHSY3 Chondroitin sulfate synthase 3 0 ;;; 126.05 0.041086 949050000 323618 414685 551107 1016010 1083370 745731 1747670 1012920 961430 903201 FALSE TRUE 310970.6508 402858.5898 650704.2942 1068446.398 1118217.58 760810.1918 1769058.508 992002.848 852292.497 842026.3918 0.369312237 0.478439386 0.772783728 1.268898942 1.328007757 0.903546729 2.100953753 1.178113724 1.012192142 1 19.68350593 3.956750204 1.899978654 1.305940865 0.385074433 0.533957492 0.315628053 0.255261054 1.782109804 0.087400895 0.238769383 9052.117954 -3.956750204 -0.920866432 KLNVTEQEK ddPTM_BT-474_Pertuzumab_2h_R1 6 KLNVTEQEK 9 1 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;; 215.06 1.05E-06 10034760000 16476140 14650790 11909260 11726870 9886120 9469240 12644830 13328700 14961750 14002360 FALSE TRUE 15832234.23 14232963.81 14061528.2 12332095.17 10204116.03 9660714.521 12799581.21 13053457.69 13263354.86 13053967.69 1.21282928 1.090317071 1.077184236 0.944700911 0.781686938 0.740059632 0.980512709 0.999960932 1.016040118 1 23.63798504 3.957516398 2.021297309 0.917860286 1.161286562 0.52132007 0.091755168 0.301903425 2.39934772 0.028771195 0.075833809 9068.102028 -3.957516398 0.243426275 TPLAVELEVLDGHDPDPGR ddPTM_BT-474_Pertuzumab_2h_R1 6 TPLAVELEVLDGHDPDPGR 19 0 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ;;;;; 199.49 6.91E-16 2495560000 898606 1054200 822439 1373220 967192 1069900 1251800 1099290 1066870 1093100 FALSE TRUE 863487.4841 1024135.248 971072.0224 1444092.049 998302.6091 1091534.111 1267119.903 1076589.277 945763.3903 1019063.363 0.84733444 1.004977006 0.952906421 1.41707778 0.979627612 1.071115056 1.243416208 1.056449791 0.928071231 1 19.95881233 3.957689602 24.99134541 1.10765174 0.939351458 0.227704895 0.138251623 644.3928567 380622.011 0.034450269 0.062113098 9071.719273 -3.957689602 -0.168300282 DRVTSAVEALLSADSASR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRVTSAVEALLSADSASR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 265.29 4.50E-31 1699035000 1129518 1145562 966343 1207123 1099110 1250796 1133149 1277317 1331065 1353472 FALSE TRUE 1085375.188 1112891.693 1140982.676 1269422.763 1134463.871 1276087.952 1147016.816 1250939.958 1179968.081 1261800.136 0.860179958 0.881987299 0.904249923 1.006041073 0.89908365 1.011323359 0.909032091 0.991393107 0.93514658 1 20.26705198 3.958463716 4.503611204 0.961901803 0.874551533 0.506170387 0.038077953 0.150637765 6.896771869 0.008855361 0.017596155 9087.903687 -3.958463716 -0.08735027 T(ph)SPQPESGIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPQPESGIK 10 0 A0A1B0GVV3;Q5EBL4-2;Q5EBL4;Q5EBL4-3 A0A1B0GVV3 RILPL1 RILP-like protein 1 1 T(0.739)S(0.261)PQPESGIK 96.82 0.072436 277340000 420710 400800 358140 399730 423850 415630 409990 462740 513690 439730 TRUE FALSE 404268.1881 389369.5764 422863.8648 420360.1132 437483.5202 424034.3234 415007.5803 453184.2573 455378.0648 409946.6954 0.986148181 0.949805379 1.031509388 1.025401882 1.06717172 1.034364536 1.012345227 1.10547118 1.110822626 1 18.64507681 3.958529329 0.93558678 1.062444555 0.956256737 0.417255562 0.036741493 0.751620017 1.058084418 0.013529572 0.063794345 9089.276788 -3.958529329 -0.106187818 RSSAGS(ph)LESNVEGSIISS(ph)PHMR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSAGSLESNVEGSIISSPHMR 22 1 A0A3B3IRZ4;Q6DN90-3 A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 2 RS(0.266)S(0.28)AGS(0.343)LES(0.109)NVEGS(0.002)IIS(0.489)S(0.51)PHMR 71.903 0.016188 45621000 25098 21714 19789 25287 25326 24867 23863 27638 24174 24900 TRUE FALSE 24117.14241 21094.73798 23365.3125 26592.0651 26140.63379 25369.82778 24155.04253 27067.26564 21429.86887 23213.50082 1.038927415 0.90872713 1.006539801 1.145543074 1.126096145 1.092891071 1.040560091 1.166013944 0.923164026 1 14.50267649 3.958670286 8.039270184 1.083358964 0.969739347 0.21284527 0.074546467 0.323316795 58.30319085 0.018099041 0.033342084 9092.227346 -3.958670286 -0.113619617 GT(ph)PSQSPVVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 GT(0.705)PS(0.295)QSPVVGR;GT(0.988)PS(0.012)QSPVVGR;GT(0.976)PS(0.021)QS(0.003)PVVGR 126.56 0.0034078 761000000 199191 203538 183799 270217 237359 233495 259671 260579 277741 272922 TRUE FALSE 191406.3955 197733.2955 217015.5679 284162.9318 244993.8678 238216.4289 262848.9314 255197.9526 246213.0061 254436.7498 0.752274959 0.777141257 0.852925405 1.116831322 0.962887114 0.936250086 1.033061975 1.002991717 0.967678632 1 17.95694754 3.958704534 4.902928939 1.000616198 0.773396631 0.814075043 0.046868411 0.075579117 4.327934176 0.012069659 0.0235931 9092.944361 -3.958704534 -0.227219567 GIPLATGDTS(ph)PEPELLPGAPLPPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GIPLATGDTSPEPELLPGAPLPPPK 25 0 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 GIPLATGDT(0.126)S(0.874)PEPELLPGAPLPPPK;GIPLAT(0.033)GDT(0.128)S(0.84)PEPELLPGAPLPPPK 218.93 8.90E-34 694750000 757700 710850 656190 753490 762460 774880 836710 826270 915240 883780 TRUE FALSE 728088.2463 690577.254 774778.1299 792377.7092 786985.2183 790548.6045 846949.9073 809207.2358 811345.7922 823920.7934 0.883687185 0.838159759 0.940355112 0.961715878 0.955170964 0.959495877 1.02795064 0.982142024 0.984737609 1 19.65214613 3.959644917 0.905794414 0.991502874 0.842621647 0.787274974 0.024386909 0.367148081 0.478692636 0.00891006 0.043018313 9112.654761 -3.959644917 -0.148881227 EGEEDGRDQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGEEDGRDQSR 11 1 E7ESY4;Q13330-3;Q13330;Q13330-2 E7ESY4 MTA1 Metastasis-associated protein MTA1 0 ; 110.08 0.0016808 96446000 118304 115222 94870 95190 108945 103309 106035 103026 127122 117836 FALSE TRUE 113680.5489 111935.9814 112015.1194 100102.7673 112449.3149 105397.9788 107332.688 100898.4771 112691.6435 109854.8628 1.034824914 1.018944256 1.019664643 0.911227458 1.023617089 0.959429343 0.977040846 0.91847074 1.025822987 1 16.74523921 3.960274279 24.70116184 0.968660775 1.024989582 0.282871993 0.036573504 476.4810628 296272.9599 0.008961014 0.016158236 9125.870018 -3.960274279 0.056328806 RGDDSFGDKYR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDDSFGDKYR 11 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 196.15 3.46E-08 2205560000 1536700 1592170 1117240 1092020 1071340 840250 1232360 1190910 1288570 1306200 FALSE TRUE 1476644.065 1546762.87 1319150.121 1148379.283 1105800.624 857240.4307 1247441.99 1166317.292 1142296.936 1217729.911 1.212620346 1.27020192 1.083286293 0.943049253 0.908083652 0.703965981 1.024399565 0.95777995 0.938054429 1 20.21576275 3.960995472 2.409532253 0.920371285 1.243910568 0.700533049 0.083087007 0.16078423 1.836586681 0.023263727 0.056286836 9141.037105 -3.960995472 0.323539283 HTPS(ph)PGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPATSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.003)PS(0.997)PGLPAEGAPEAPRPS(0.44)S(0.56)PPPEVLEPHSLDQPPATSPR 312.29 1.71E-110 676410000 51097 54934 44555 61884 53815 57175 79966 35558 70792 70037 TRUE FALSE 49100.07275 53367.33611 52607.07962 65077.84066 55546.00835 58331.11767 80944.64783 34823.71487 62755.98894 65293.33161 0.751992149 0.81734742 0.805703712 0.996699648 0.850714874 0.893370215 1.239707729 0.533342594 0.961139329 1 15.99464804 3.96100046 20.80773924 0.898726202 0.791383434 0.105209708 0.166758429 199.7890173 106595.7509 0.043364176 0.078230124 9141.142092 -3.96100046 -0.107342768 GMQELGVHPDQETYTDYVIPCFDSVNSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GMQELGVHPDQETYTDYVIPCFDSVNSAR 29 0 P42704;B8ZZ38;A0A0C4DG06 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 177.14 1.35E-17 677450000 301210 436980 321780 697920 331070 409690 610820 500860 423770 404120 FALSE TRUE 289438.3802 424517.7582 379932.804 733939.7348 341719.1672 417974.2125 618295.3979 490517.066 375665.4062 376748.5924 0.768253382 1.126793216 1.008451821 1.948088857 0.907021749 1.109424749 1.641135256 1.301974515 0.99712491 1 18.5232426 3.961004077 24.99741286 1.300140575 0.977546879 0.162800559 0.312252101 850.7892947 545379.2214 0.077866394 0.140409522 9141.218225 -3.961004077 -0.322593696 VDSGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDSGYR 6 0 Q14697;F5H6X6;K7EKT3;Q14697-2;E9PKU7;Q92947-2;Q92947;K7EKH1 Q14697;Q14697-2;Q92947-2 GANAB;GCDH "Neutral alpha-glucosidase AB;Glutaryl-CoA dehydrogenase, mitochondrial" 0 103.29 0.080996 509030000 181130 200850 161060 256730 240230 202040 225810 215960 226980 202580 FALSE TRUE 174051.2394 195121.9547 190167.1248 269979.8661 247957.2161 206125.3872 228573.5303 211500.3505 201214.182 188859.0762 0.921593195 1.03316165 1.006926056 1.429530799 1.312921895 1.091424312 1.210286183 1.119884492 1.065419709 1 17.52695059 3.96105601 24.94349391 1.183726658 0.988043783 0.339834949 0.120256127 554.3911943 355086.2828 0.031529127 0.056853842 9142.311399 -3.96105601 -0.195682875 VWDAVSGDELMTLAHK ddPTM_BT-474_Pertuzumab_2h_R1 2 VWDAVSGDELMTLAHK 16 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 309.87 1.25E-57 3127600000 2765040 2736810 2494780 2714250 3000860 3198210 3016630 3012070 3563230 3601140 FALSE TRUE 2656979.18 2658758.858 2945642.242 2854332.768 3097385.387 3262879.997 3053548.42 2949869.702 3158747.069 3357231.58 0.791419691 0.791949794 0.877402161 0.850204313 0.922601052 0.971896016 0.909543577 0.878661371 0.940878516 1 21.67884063 3.961504648 0.944096823 0.928240599 0.771119642 0.697561708 0.036447564 0.505712501 0.725861434 0.013557868 0.063849915 9151.760548 -3.961504648 -0.157120957 DPSVDITQDLVDES(ph)EEERFDDMSSPGLELPSCELSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPSVDITQDLVDESEEERFDDMSSPGLELPSCELSR 36 1 Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 DPS(0.004)VDIT(0.013)QDLVDES(0.973)EEERFDDMS(0.007)S(0.003)PGLELPSCELSR 69.241 0.0031415 19842000 14589 13718 11819 17232 15597 17419 14583 15429 17363 16640 TRUE FALSE 14018.84575 13326.77607 13954.95621 18121.34559 16098.69167 17771.22411 14761.47112 15110.38576 15392.02503 15512.95798 0.903686181 0.85907382 0.899567718 1.168142504 1.037757705 1.145572891 0.951557475 0.974049293 0.992204392 1 13.92118618 3.96185944 22.36504714 1.032905574 0.880865152 0.516603886 0.066950052 125.3162026 73483.7807 0.0182529 0.032924328 9159.240012 -3.96185944 -0.152040422 KVT(ph)SPLQS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVTSPLQSPTK 11 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 2 KVT(0.563)S(0.437)PLQS(1)PTK 101.53 0.0027841 758190000 1690200 1559400 1254500 1211000 1243600 1019000 1208400 1467600 1602000 1518500 TRUE FALSE 1624145.115 1514927.439 1481216.056 1273499.855 1283601.523 1039604.878 1223188.761 1437293.547 1420147.676 1415650.642 1.147278196 1.070128034 1.046314685 0.899586252 0.906721959 0.73436542 0.864047049 1.015288309 1.003176655 1 20.43303385 3.96200829 2.170896814 0.912633561 1.11543497 0.495817912 0.080026879 0.289874087 2.67228865 0.024312209 0.061958926 9162.379802 -3.96200829 0.202801409 KLDPGSEETQTLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDPGSEETQTLVR 14 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 131.4 9.06E-05 1305240000 1349150 1328650 847980 775650 583350 500520 547970 735070 1016490 1248030 FALSE TRUE 1296423.726 1290758.203 1001228.849 815681.3895 602113.9825 510640.8573 554676.2208 719890.5476 901102.3167 1163499.816 1.114244891 1.109375511 0.860532022 0.70105846 0.51750243 0.438883488 0.476730819 0.618728544 0.774475684 1 20.15003955 3.962434499 1.852795847 0.601034446 1.130208431 0.580744486 0.156079556 0.222741521 1.474689456 0.042739548 0.119492571 9171.376013 -3.962434499 0.529173985 TIQTIALITYLMEHKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TIQTIALITYLMEHKR 16 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8YFV8;A0A2R8YCY3;A0A0U1RQE1;F6VDE0;P51531-2;P51531;A0A0U1RQZ9 A0A2R8Y4P4;F6VDE0 SMARCA4;SMARCA2 Transcription activator BRG1;Probable global transcription activator SNF2L2 0 ; 133.71 2.09E-05 125688000 99920 111049 79676 76403 85820 86288 85542 70380 111060 91993 FALSE TRUE 96015.01593 107881.9912 94075.22558 80346.16799 88580.47824 88032.80248 86588.88858 68926.62841 98452.9344 85762.23217 1.119548938 1.257919582 1.096930702 0.93684791 1.032861156 1.026475177 1.009638933 0.803694431 1.147975419 1 16.38805484 3.962449368 4.341623166 0.979945993 1.188548428 0.43902427 0.087938216 0.167339374 7.113142423 0.023118746 0.04651789 9171.690011 -3.962449368 0.208602435 RRNDS(ph)YTEEEPEWFSAGPTSQSETIELTGFDDK ddPTM_BT-474_Pertuzumab_2h_R1 3 RRNDSYTEEEPEWFSAGPTSQSETIELTGFDDK 33 2 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RRNDS(0.338)Y(0.314)T(0.338)EEEPEWFS(0.006)AGPT(0.001)S(0.001)QS(0.001)ET(0.001)IELTGFDDK;RRNDS(0.356)Y(0.288)T(0.356)EEEPEWFSAGPTSQSETIELTGFDDK;RRNDS(0.462)Y(0.076)T(0.462)EEEPEWFSAGPTSQSETIELTGFDDK 205.11 1.98E-27 910900000 106782 107055 85269 87822 94446 91920 76332 120359 108735 94854 TRUE FALSE 102608.8414 104001.8962 100679.0051 92354.50394 97483.94136 93778.68538 77266.17385 117873.5446 96391.85865 88429.45409 1.160346883 1.176100173 1.138523427 1.044386227 1.10239221 1.060491511 0.873760611 1.332967005 1.090042448 1 16.43223936 3.962491125 6.240538362 1.089121297 1.166012896 0.10806498 0.108131108 0.515981478 59.33758146 0.028987244 0.054899675 9172.571911 -3.962491125 0.076891599 EVTYELDHPGFQIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVTYELDHPGFQIR 14 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ;;; 218.11 5.51E-12 1820250000 1062320 1130450 933820 1187840 1194880 1272220 1227730 1130750 1174190 1299380 FALSE TRUE 1020803.36 1098210.673 1102582.047 1249144.565 1233314.4 1297945.16 1242755.327 1107399.617 1040900.874 1211371.835 0.842683749 0.906584288 0.910192902 1.03118178 1.018113815 1.071467177 1.025907398 0.914169857 0.859274455 1 20.20821034 3.962576252 3.371717947 0.987320937 0.877246752 0.38530687 0.059768212 0.282999243 6.558425923 0.017488426 0.037511097 9174.370014 -3.962576252 -0.110074185 SLETENR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLETENR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 148.33 0.0048655 2184300000 2274180 2306630 1887930 2288420 2167790 2462560 2183380 2296230 2558160 2557020 FALSE TRUE 2185302.531 2240847.171 2229120.948 2406525.63 2237518.934 2512354.65 2210100.858 2248812.048 2267768.401 2383830.758 0.916718825 0.940019405 0.935100338 1.009520337 0.938623234 1.053914856 0.927121546 0.943360614 0.951312669 1 21.18485038 3.96280033 24.06095426 0.969921524 0.930666778 0.224472624 0.036976844 576.7485812 373045.0476 0.009477335 0.017092629 9179.104846 -3.96280033 -0.039254746 IDLENTLEQEQEALVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDLENTLEQEQEALVNR 17 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 157.86 2.27E-08 41176000 26656 29425 23551 33948 27296 30187 31312 36184 30326 29608 FALSE TRUE 25614.25405 28585.82781 27807.18959 35700.06035 28174.00063 30797.40182 31695.20562 35436.78776 26883.51962 27602.62379 0.927964466 1.035619948 1.0074111 1.293357495 1.020700092 1.115741824 1.148267855 1.283819539 0.973947978 1 14.75251779 3.962881427 24.83457483 1.138452362 0.991722952 0.226181413 0.105748648 622.6268721 416575.8986 0.026486271 0.047766796 9180.819042 -3.962881427 -0.14672941 LEEWLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEEWLGR 7 0 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 146.21 0.0051989 391607000 595900 624000 532017 705220 654060 693800 683740 700900 741130 807120 FALSE TRUE 572611.5692 606204.131 628164.3066 741616.4887 675098.4339 707829.1114 692107.8146 686426.1701 657000.0295 752453.0435 0.760993093 0.805637157 0.834821936 0.985598364 0.897196762 0.940695393 0.919802 0.912251171 0.873144225 1 19.52124203 3.963812011 3.825030581 0.926257978 0.787447053 0.724392694 0.037945026 0.110258976 3.428005479 0.009345052 0.019398429 9200.512314 -3.963812011 -0.138810925 GDYDAFFEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDYDAFFEAR 10 0 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 ;;; 203.29 4.84E-07 4691300000 1406320 1553360 1240560 1750910 1660510 1372220 1647390 1686170 1643780 1766560 FALSE TRUE 1351359.46 1509059.694 1464756.788 1841274.675 1713921.812 1399967.229 1667551.252 1651350 1457184.986 1646909.318 0.820542725 0.916297988 0.889397353 1.118018251 1.040689851 0.850057264 1.01253374 1.002696373 0.88479977 1 20.65132969 3.963957645 24.95112909 0.987503227 0.877027094 0.32311811 0.074194741 655.7095524 453930.5465 0.019220879 0.0346675 9203.598079 -3.963957645 -0.110476134 DKEDQWIR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKEDQWIR 8 1 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ;; 79.489 0.025449 852780000 581170 626470 545260 654890 696390 888530 569990 803340 788640 717140 FALSE TRUE 558457.2339 608603.689 643800.6112 688688.9514 718790.0168 906496.6854 576965.7081 786750.7483 699116.8934 668567.469 0.835304228 0.910310054 0.962955335 1.030096413 1.07511964 1.355879141 0.862988008 1.176770909 1.045693854 1 19.35071363 3.964048515 1.376805814 1.09499651 0.849539843 0.338404313 0.119359877 0.523985798 1.808970527 0.034459992 0.120316703 9205.524006 -3.964048515 -0.245456668 QQS(ph)LFS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQSLFSSPR 9 0 Q5T7B8-4;Q5T7B8-2;Q5T7B8 Q5T7B8-4 KIF24 Kinesin-like protein KIF24 2 QQS(0.731)LFS(0.906)S(0.363)PR 66.92 0.091174 319350000 20930 22438 19680 28946 26413 39918 23846 17580 27152 33095 TRUE FALSE 20112.03246 21798.09021 23236.61378 30439.90653 27262.59813 40725.16931 24137.83448 17216.96686 24069.81879 30853.44617 0.651856922 0.706504229 0.753128634 0.986596647 0.883615982 1.319955284 0.78233836 0.558024111 0.780133884 1 14.91314402 3.964265477 5.18999692 0.873660841 0.688646274 0.187398449 0.186162014 0.405630685 28.50619881 0.054937613 0.107082904 9210.123992 -3.964265477 -0.185014567 DLKPSNIFLVDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLKPSNIFLVDTK 13 1 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 107.07 0.0012073 288490000 616520 605330 585780 658400 629470 689470 723510 792150 880000 850620 FALSE TRUE 592425.7168 588066.5811 691643.4766 692380.1029 649717.4742 703411.5558 732364.5318 775791.8257 780106.0893 793006.7497 0.747062641 0.741565669 0.872178549 0.873107452 0.819308883 0.887018372 0.923528749 0.978291579 0.983731966 1 19.59697362 3.964281371 0.275300172 1.026139629 0.601144951 0.861536341 0.032721633 2.039663839 0.180833959 0.047810094 0.286304423 9210.461061 -3.964281371 -0.424994678 WVEENIPSSFTDVALPVLVDS(ph)DEEIMTR ddPTM_BT-474_Pertuzumab_2h_R1 1 WVEENIPSSFTDVALPVLVDSDEEIMTR 28 0 A0A3B3IU29;A0A494BZZ8;Q96K49-2;Q96K49 A0A3B3IU29 TMEM87B Transmembrane protein 87B 1 WVEENIPSSFTDVALPVLVDS(0.938)DEEIMT(0.061)R 58.16 0.032765 34977000 11460 14288 12603 25277 15789 15925 19494 23471 23644 22685 TRUE FALSE 11012.13053 13880.52023 14880.64245 26581.549 16296.86752 16247.01441 19732.5734 22986.31565 20960.03224 21148.52474 0.52070443 0.656335153 0.703625555 1.256898499 0.770591222 0.768233936 0.933047276 1.086899248 0.991087203 1 14.36826941 3.964588036 12.75325492 0.965616284 0.61131498 0.576455488 0.137723801 1.342816787 483.6448726 0.036702463 0.066720165 9216.967077 -3.964588036 -0.354301304 QEVPHDGPMCDLLWSDPEDTTGWGVSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEVPHDGPMCDLLWSDPEDTTGWGVSPR 28 0 P60510;H3BTA2;H3BV22 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit;Serine/threonine-protein phosphatase 0 ; 169.84 4.14E-12 129081000 43096 43315.2 35767.6 48980 44177 41900 42227 45170 47964 52528 FALSE TRUE 41411.76067 42079.89291 42231.60097 51507.86367 45597.99333 42747.24671 42743.78666 44237.22372 42519.3278 48970.23177 0.845651719 0.859295359 0.862393324 1.051819887 0.931136972 0.872923104 0.872852447 0.903349282 0.86826887 1 15.5796174 3.965037847 24.99898432 0.920963457 0.854566086 0.256422599 0.055933028 893.738985 639051.6772 0.014887821 0.026854938 9226.518289 -3.965037847 -0.066397371 KLTDTSKDEENHEESESLQEDMLGNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLTDTSKDEENHEESESLQEDMLGNR 26 2 Q8IX12-2;Q8IX12;A0A0C4DGG8 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 138.93 2.09E-06 175460000 146100 129980 100450 95534 116600 136500 121040 115410 149050 118310 FALSE TRUE 140390.2505 126273.0977 118603.5495 100464.5212 120350.5449 139260.1235 122521.3237 113026.7432 132130.4689 110296.7583 1.27284113 1.144848675 1.075313104 0.910856518 1.091152149 1.262594891 1.110833406 1.02475127 1.197954236 1 16.75103086 3.965169752 0.011710004 7.86E-07 2.249541943 0.093404816 0.104011348 10656.26691 25.40131357 2283.997148 2600.646958 9229.321008 -3.965169752 2.249541157 ILKEQER ddPTM_BT-474_Pertuzumab_2h_R1 4 ILKEQER 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 93.429 0.013627 2462980000 3614720 4113980 2771970 2088130 2626530 1651150 3325040 2784440 3081930 2817620 FALSE TRUE 3473452.746 3996653.318 3272926.641 2195898.64 2711014.723 1684537.384 3365732.834 2726940.341 2732082.227 2626780.088 1.322323388 1.521502823 1.245984259 0.835965923 1.032067639 0.641293648 1.28131504 1.03813043 1.040087916 1 21.32486399 3.965214197 4.978125427 0.993366594 1.417215075 0.557661539 0.160624046 0.134872538 8.477753067 0.041181663 0.080952071 9230.265584 -3.965214197 0.423848481 SLVGS(ph)WLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLVGSWLK 8 0 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 SLVGS(1)WLK;SLVGS(1)WLK 159.83 0.00037437 559400000 883000 839060 666970 622140 763110 567320 703300 822910 790580 729530 TRUE FALSE 848491.3838 815130.8303 787506.3157 654248.72 787656.1262 578791.5991 711907.1958 805916.6209 700836.6728 680118.2833 1.247564438 1.198513333 1.157896112 0.961963141 1.158116383 0.851016085 1.04674027 1.184965381 1.030462921 1 19.37542615 3.965502466 4.274602846 1.04762691 1.216698476 0.425864509 0.090132933 0.217853033 9.009871391 0.0242365 0.049116106 9236.394332 -3.965502466 0.169071566 DSNYHLLMSVQESLER ddPTM_BT-474_Pertuzumab_2h_R1 4 DSNYHLLMSVQESLER 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;;; 198.51 4.05E-11 956860000 417357 682840 492740 1149380 514510 618330 983490 785080 653620 618580 FALSE TRUE 401046.227 663366.0718 581789.0789 1208699.64 531059.6814 630833.0563 995526.2448 768867.8236 579423.7978 576683.0256 0.695436157 1.150313157 1.008854177 2.095951477 0.920886619 1.093899123 1.726297117 1.333258982 1.004752649 1 19.13741903 3.965917978 24.99569552 1.341690073 0.962051045 0.170752029 0.359469732 963.1217921 706353.2673 0.089701133 0.161829486 9245.235504 -3.965917978 -0.379639028 TKDIVNGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKDIVNGLR 9 1 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 112.36 0.0018018 1387310000 2788950 2822600 2077620 2212480 2058360 1833730 2460140 2338300 2544870 2438480 FALSE TRUE 2679954.751 2742102.212 2453092.15 2326666.358 2124569.019 1870809.277 2490247.929 2290013.288 2255987.027 2273319.578 1.178872859 1.206210618 1.079079323 1.023466468 0.934566807 0.822941612 1.095423606 1.007343319 0.992375665 1 21.11636908 3.966063336 2.066974742 0.980625083 1.196400358 0.62011753 0.065978504 0.225709576 1.880211973 0.019340116 0.050862758 9248.330396 -3.966063336 0.215775274 SGTNS(ph)PPPPFSDWGR ddPTM_BT-474_Pertuzumab_2h_R1 5 SGTNSPPPPFSDWGR 15 0 D6RAU6;D6REP2;D6RAJ6;Q9UKT5-2;Q9UKT5 D6RAU6 FBXO4 F-box only protein 4 1 S(0.001)GT(0.006)NS(0.993)PPPPFSDWGR;SGTNS(1)PPPPFSDWGR;S(0.002)GT(0.022)NS(0.975)PPPPFS(0.001)DWGR;S(0.003)GT(0.25)NS(0.747)PPPPFSDWGR;SGT(0.002)NS(0.997)PPPPFSDWGR 140.27 5.21E-06 2122548000 1406862 1435694 1220864 1516018 1508635 1454510 1563714 1664928 1624066 1714780 TRUE FALSE 1351880.278 1394749.413 1441501.283 1594259.871 1557161.615 1483921.189 1582851.2 1630546.655 1439708.836 1598636.423 0.845645863 0.872461926 0.901706768 0.997262321 0.974056134 0.928241824 0.99012582 1.019960906 0.900585534 1 20.60841043 3.966078524 2.761226758 0.975688721 0.858677219 0.650336608 0.034213606 0.160118827 2.425767055 0.00920319 0.021164829 9248.653829 -3.966078524 -0.117011502 DRYDSDRYR ddPTM_BT-474_Pertuzumab_2h_R1 3 DRYDSDRYR 9 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 148.91 5.00E-05 493840000 290806 356845 210049 199675 190640 123487 247472 181453 243430 243620 FALSE TRUE 279440.98 346668.13 248009.5268 209980.2507 196772.1087 125983.9917 250500.6364 177705.9321 215796.8469 227119.4004 1.230370367 1.526369519 1.091978608 0.924536831 0.866381773 0.554703788 1.10294689 0.782433961 0.950147132 1 17.79309142 3.966117539 2.839886157 0.867592652 1.377586252 0.615226595 0.15454858 0.152028801 2.442463256 0.038817767 0.088353917 9249.484706 -3.966117539 0.5099936 VT(ph)KSPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTKSPQK 7 1 Q9NVP1 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 1 VT(0.597)KS(0.403)PQK 72.607 0.082687 796960000 2730500 2275400 1769700 1248100 1368500 662860 1756600 1536600 1386100 1701800 TRUE FALSE 2623789.041 2210507.82 2089524.157 1312514.591 1412519.045 676263.4834 1778097.796 1504868.673 1228755.739 1586535.57 1.653785197 1.393292317 1.317035808 0.827283431 0.890316657 0.4262517 1.120742472 0.948525013 0.774489877 1 20.59744844 3.966259962 1.937680583 0.854440821 1.560332243 0.703298347 0.181426797 0.192927509 1.404019956 0.051242122 0.139994449 9252.518505 -3.966259962 0.705891423 QASEGPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 QASEGPLK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 99.139 0.016344 772610000 677970 737710 491730 480880 489580 306600 617040 487670 525170 605470 FALSE TRUE 651474.1829 716671.2331 580596.5495 505698.2744 505327.7853 312799.6621 624591.5201 477599.4441 465554.9033 564460.9776 1.154152738 1.26965594 1.028585806 0.895895898 0.895239539 0.554156398 1.106527368 0.846115964 0.824777835 1 19.10651432 3.96679798 2.524815133 0.867493372 1.21319179 0.492393472 0.136220887 0.222550401 2.802075669 0.035512457 0.084715029 9263.987908 -3.96679798 0.345698417 LDYFLLSHSLLPALCDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDYFLLSHSLLPALCDSK 18 0 P27695 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 268.17 2.10E-31 3152900000 8138800 7753200 6139200 5469800 6794100 6136200 6553300 6858200 7577200 7180800 FALSE TRUE 7820726.698 7532086.327 7248690.006 5752097.034 7012638.397 6260278.168 6633501.246 6716575.773 6717068.022 6694438.02 1.168242454 1.125126008 1.082792907 0.859235236 1.047532052 0.935146184 0.990897403 1.003306887 1.003380419 1 22.67453152 3.966905284 7.833890885 0.979785756 1.136606214 0.670604683 0.048885558 0.131859863 28.00925979 0.011841671 0.022084682 9266.277114 -3.966905284 0.156820458 LTGS(ph)T(ph)SSLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LT(0.039)GS(0.952)T(0.58)S(0.306)S(0.125)LNK 97.779 0.030909 562260000 2848200 2543100 2062900 1798300 1891300 2022700 1775000 2534300 2588500 2119600 TRUE FALSE 2736889.195 2470573.278 2435711.919 1891110.479 1952135.382 2063600.38 1796722.981 2481965.819 2294664.332 1976037.604 1.385039024 1.250266327 1.232624275 0.957021503 0.987903964 1.044312302 0.90925546 1.256031674 1.161245275 1 20.91417897 3.967977846 3.344355838 1.057396112 1.312368358 0.55674738 0.100668563 0.202193764 4.63241351 0.02879592 0.062271729 9289.190003 -3.967977846 0.254972246 SSGPYGGGGQYFAKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-2;P09651;P09651-3;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ; 290.71 1.46E-45 11983000000 3450200 3419700 2510900 2390360 2380790 2105780 2677900 2707500 2880700 2815000 FALSE TRUE 3315362.37 3322173.504 2964675.485 2513726.766 2457370.273 2148360.314 2710672.941 2651589.179 2553695.013 2624337.543 1.263314004 1.265909377 1.129685277 0.957851925 0.936377365 0.81862957 1.032897978 1.010384196 0.973081767 1 21.32352186 3.968049165 2.499783116 0.961534445 1.26741525 0.830823737 0.055554315 0.117222138 1.446359669 0.016428359 0.039411942 9290.715588 -3.968049165 0.305880805 MDTDLETMDLDQGGEALAPR ddPTM_BT-474_Pertuzumab_2h_R1 3 MDTDLETMDLDQGGEALAPR 20 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 288 2.87E-45 414231000 360365 377860 305179 365240 369000 395960 368424 403010 414830 413740 FALSE TRUE 346281.5374 367083.8028 360331.634 384090.0802 380869.2201 403966.5825 372932.8831 394687.7027 367740.2375 385717.0213 0.897760582 0.951691998 0.9341865 0.995782034 0.987431716 1.047313342 0.966856173 1.023257157 0.953393854 1 18.55718329 3.968206254 1.309343868 1.00042137 0.911946372 0.562554376 0.027645754 0.354026043 1.088380898 0.007885306 0.028888913 9294.076729 -3.968206254 -0.088474998 GLAAGS(ph)AETLPANFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLAAGSAETLPANFR 15 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 GLAAGS(1)AETLPANFR 128.73 0.00024525 0 65183 69184 56672 83711 73475 74952 72977 73667 77182 87670 TRUE FALSE 62635.5763 67210.94006 66913.89106 88031.33474 75838.3901 76467.58079 73870.11436 72145.75071 68420.62293 81732.03281 0.76635285 0.822332906 0.81869848 1.07707262 0.927890663 0.935588877 0.903808603 0.882710832 0.837133503 1 16.318614 3.968221577 24.92818805 0.929084152 0.800886013 0.489418624 0.063142813 542.9116903 425881.3616 0.016620288 0.03000107 9294.404672 -3.968221577 -0.128198139 ALGNNFYEYYVDDPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALGNNFYEYYVDDPPR 16 0 P30047;H0YNX7;P30047-2 P30047 GCHFR GTP cyclohydrolase 1 feedback regulatory protein 0 112.08 0.0017832 83129000 40767 50933 40890 80821 62102 54619 60839 72560 66770 60711 FALSE TRUE 39173.78057 49480.44071 48279.73259 84992.1815 64099.56723 55723.4336 61583.56588 71061.61064 59190.54952 56598.98989 0.692128616 0.874228335 0.853014032 1.501655447 1.132521399 0.984530531 1.088068285 1.255527895 1.04578809 1 15.78848869 3.968391696 24.66547119 1.152389992 0.803289024 0.52608875 0.147413814 399.000495 311359.9998 0.03757981 0.067841976 9298.046126 -3.968391696 -0.349100968 AEDEDIVLT(ph)PDGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEDEDIVLTPDGTR 14 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 AEDEDIVLT(0.995)PDGT(0.005)R 96.435 0.0095557 0 171410 173580 144360 207740 189920 175910 175760 197430 190610 187620 TRUE FALSE 164711.1077 168629.6684 170449.0633 218461.4863 196028.9493 179467.0207 177911.0035 193353.0015 168972.7519 174912.3303 0.941678082 0.96408108 0.974482834 1.24897705 1.120726875 1.026039848 1.017143864 1.10542808 0.96604254 1 17.41627247 3.969375563 24.85114366 1.075449554 0.956980065 0.305489941 0.075397956 687.3044949 557735.797 0.019612007 0.035414931 9319.134135 -3.969375563 -0.118469489 S(ph)RTSPVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.564)RT(0.285)S(0.15)PVT(0.001)R;S(0.567)RT(0.216)S(0.216)PVTR 80.706 0.014992 7525600000 336247 310867 284716 394948 377285 363015 343357 366712 422574 432510 TRUE FALSE 323106.0955 302001.3775 336170.5147 415331.3136 389420.7147 370355.412 347559.1057 359139.2691 374605.1711 403215.7125 0.801323176 0.748982166 0.833723747 1.030047443 0.965787549 0.918504415 0.86196816 0.890687684 0.929044081 1 18.62119233 3.969965287 7.990829459 0.93070516 0.778832731 0.66437841 0.048765485 0.155158359 37.27226659 0.013505802 0.025281821 9331.79709 -3.969965287 -0.151872429 GAES(ph)ENEEESPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GAESENEEESPR 12 0 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 GAES(1)ENEEESPR 132 0.00019792 118550000 44611 41479 35619 49244 44673 36382 48022 47980 46872 44316 TRUE FALSE 42867.5528 40296.05953 42056.14564 51785.48874 46109.94762 37117.66897 48609.7076 46989.19623 41551.28706 41314.43785 1.037592547 0.975350546 1.01795275 1.25344774 1.11607346 0.898418831 1.176579185 1.137355333 1.005732844 1 15.33435842 3.970198537 24.8968407 1.094891859 1.004016467 0.103981455 0.095691759 1182.548997 987931.6448 0.024743616 0.044701678 9336.810332 -3.970198537 -0.090875392 NLSTVMDEIHTVLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NLSTVMDEIHTVLKK 15 1 Q8IX12-2;Q8IX12 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 172.24 6.74E-07 148847000 215696 213506 164576 165934 170328 171437 165833 170473 235361 204969 FALSE TRUE 207266.3619 207417.0179 194318.5442 174497.8736 175806.7548 174903.5736 167862.5139 166952.673 208643.806 191086.2671 1.084674294 1.085462713 1.016915277 0.913188982 0.920038669 0.915312106 0.878464562 0.873703148 1.091882788 1 17.54386457 3.970347136 2.778900798 0.927472696 1.085321687 0.454634796 0.06186145 0.209494898 3.22213088 0.01630069 0.037567697 9340.005597 -3.970347136 0.15784899 VLISDSLDPCCR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLISDSLDPCCR 12 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YFM8;A0A286YER3;A0A286YFC8;A0A286YFB2;A0A286YF34;A0A286YFF3;A0A286YFK5 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 145.25 0.00014827 131070000 161660 174920 146470 205290 193910 193950 180240 186710 203770 208880 FALSE TRUE 155342.1485 169931.4529 172940.3872 215885.0415 200147.2913 197871.8019 182445.831 182854.3733 180638.8839 194732.3715 0.797721238 0.872641007 0.888092646 1.108624312 1.027806983 1.016121769 0.936905506 0.939003473 0.927626375 1 17.57113321 3.970480209 12.80744708 0.987929225 0.846445074 0.599362603 0.053658094 1.397418265 606.6526517 0.015292538 0.02799564 9342.86791 -3.970480209 -0.141484152 RPAPAVSPGSWKPGPPGS(ph)PRPWK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 RPAPAVSPGSWKPGPPGS(1)PRPWK 128.06 3.13E-05 922420000 1101600 1124400 828590 797840 885000 857170 872160 877000 898100 886900 TRUE FALSE 1058548.254 1092333.213 978334.6449 839016.618 913466.8287 874502.5647 882833.755 858889.6435 796151.4531 826829.473 1.280249784 1.321110638 1.183236298 1.014739611 1.104782617 1.057657707 1.067733776 1.038774828 0.962896799 1 19.65723029 3.970737526 2.968276729 1.042318893 1.300205955 0.882540317 0.039209016 0.078029949 1.380017036 0.010372556 0.023359241 9348.40516 -3.970737526 0.257887062 KTLDSVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTLDSVAK 8 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 111.06 0.0053021 1213230000 3604800 3714000 2964300 2835600 3199800 2974200 3463100 3555800 3690700 3560000 FALSE TRUE 3463920.431 3608080.356 3500014.95 2981945.656 3302724.473 3034340.362 3505482.454 3482371.487 3271747.209 3318878.029 1.043702239 1.087138583 1.054577758 0.898480037 0.995132826 0.91426691 1.056225153 1.049261665 0.985799171 1 21.66226418 3.971449203 24.9409139 0.991694521 1.066779885 0.340881427 0.04819208 810.827908 708310.827 0.013354537 0.024140401 9363.736915 -3.971449203 0.075085364 GKDIGKPIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKDIGKPIEK 10 2 O60869 O60869 EDF1 Endothelial differentiation-related factor 1 0 51.841 0.086613 385520000 388000 366220 299720 229650 284960 323610 304740 325620 424940 360010 FALSE TRUE 372836.531 355775.7642 353886.0712 241502.264 294125.9972 330153.6159 308469.4993 318895.8332 376702.5927 335626.202 1.110868367 1.060035724 1.054405374 0.719557241 0.876349926 0.983694401 0.919086464 0.95015178 1.122387318 1 18.35649582 3.971711851 24.9947377 0.932203477 1.078394275 0.295559206 0.096768496 814.4984856 719673.4411 0.025358857 0.045841006 9369.401521 -3.971711851 0.146190798 EREQPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EREQPPR 7 1 Q15233;Q15233-2;H7C367;Q8WXF1;Q8WXF1-2 Q15233;Q8WXF1 NONO;PSPC1 Non-POU domain-containing octamer-binding protein;Paraspeckle component 1 0 ;; 157.58 0.0013374 456801000 250847 246839.3 206857 268145 249400 261074 253888.7 278392.4 264194 259885 FALSE TRUE 241043.6219 239799.6848 244240.6614 281983.9956 257422.1775 266353.0952 256995.8659 272643.4997 234203.8047 242282.7575 0.994885581 0.989751344 1.00808107 1.163863242 1.062486576 1.099348125 1.060727014 1.125311196 0.966654859 1 17.88633221 3.971719164 24.48939814 1.0776186 0.993967869 0.257473406 0.053903078 565.0751234 489320.6082 0.012936222 0.02339012 9369.559295 -3.971719164 -0.083650732 GGTLGGGTLGPPS(ph)PPGAPSPPEPGGEIELVFRPHPLLVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 GGTLGGGTLGPPS(1)PPGAPSPPEPGGEIELVFRPHPLLVEK;GGTLGGGTLGPPS(1)PPGAPSPPEPGGEIELVFRPHPLLVEK 193.17 5.50E-25 2670200000 1358370 1389730 1178230 1391070 1496830 1429730 1443910 1523490 1686030 1610930 TRUE FALSE 1305283.399 1350096.261 1391162.371 1462863.289 1544976.896 1458640.12 1461581.003 1492029.399 1494638.943 1501820.276 0.869134223 0.898973254 0.926317478 0.974060154 1.028736208 0.97124812 0.973206332 0.99348066 0.995218247 1 20.51828074 3.971743954 1.740592419 0.991642097 0.877197189 0.883562627 0.016080429 0.120906921 0.700267895 0.004710727 0.01390353 9370.094144 -3.971743954 -0.114444908 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_BT-474_Pertuzumab_2h_R1 5 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HT(0.002)PS(0.012)PGLPAEGAPEAPRPS(0.492)S(0.492)PPPEVLEPHS(0.001)LDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.488)S(0.488)PPPEVLEPHS(0.022)LDQPPAT(0.001)S(0.001)PR;HTPSPGLPAEGAPEAPRPS(0.497)S(0.497)PPPEVLEPHS(0.004)LDQPPAT(0.001)S(0.001)PR 215.55 3.13E-40 7294200000 1645851 1572872 1364786 1969198 1890695 1729679 2097470 1332708 2255947 2043488 TRUE FALSE 1581529.323 1528015.231 1611433.19 2070828.545 1951510.922 1764654.294 2123139.465 1305187.114 1999861.354 1905080.738 0.830163936 0.802073739 0.845860838 1.087003036 1.024371767 0.926288456 1.114461673 0.685108556 1.049751496 1 20.86142071 3.971866969 22.04519138 0.961748028 0.818080848 0.275130544 0.114161656 233.3776694 182877.6835 0.030713002 0.055617659 9372.748605 -3.971866969 -0.14366718 AEIEKS(ph)PGGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEIEKSPGGGR 11 1 Q86US8 Q86US8 SMG6 Telomerase-binding protein EST1A 1 AEIEKS(1)PGGGR 94.007 0.0053447 234280000 300910 309960 246180 223890 262240 298980 274290 248810 318580 277960 TRUE FALSE 289150.1045 301120.2443 290670.2022 235444.9897 270675.1878 305025.5804 277646.8431 243671.9866 282416.134 259133.5216 1.115834427 1.162027369 1.121700506 0.908585614 1.044539456 1.177098117 1.071443175 0.940333713 1.089847937 1 17.98333613 3.971927216 24.81950611 1.032338091 1.139664198 0.290473496 0.071995924 786.5425672 695394.3131 0.019517207 0.035295229 9374.048928 -3.971927216 0.107326107 IWDPTPSHTPAGAATPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IWDPTPSHTPAGAATPGR 18 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 157.42 4.49E-09 286820000 54252 52001 45373 73567 59126 55403 61052 68527 64771 73184 FALSE TRUE 52131.77186 50517.98239 53572.91042 77363.80169 61027.84149 56523.28662 61799.17264 67111.8935 57418.46762 68227.18249 0.764090938 0.740437763 0.785213583 1.133914649 0.894479872 0.828456995 0.905785207 0.983653304 0.841577587 1 16.05805902 3.971976478 24.92103015 0.936552836 0.754904623 0.492997756 0.08301274 531.2602998 472445.6771 0.02116 0.03825849 9375.112292 -3.971976478 -0.181648213 LQEDKEQMAQQLAEETQGFQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LQEDKEQMAQQLAEETQGFQR 21 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 290.54 9.45E-55 1408250000 961630 941990 803050 985110 971210 982440 1012560 1109290 1193950 1124720 FALSE TRUE 924048.4365 915125.3675 948178.9988 1035951.645 1002449.852 1002305.61 1024952.012 1086382.774 1058417.801 1048541.713 0.881270078 0.872760098 0.904283528 0.987992783 0.956041939 0.955904374 0.977502373 1.036089228 1.00941888 1 19.99995282 3.972370043 0.47346238 1.016680985 0.818601139 0.8154307 0.022665041 1.017641088 0.296667008 0.018351699 0.105356415 9383.612014 -3.972370043 -0.198079846 YFDS(ph)GDYNMAK ddPTM_BT-474_Pertuzumab_2h_R1 14 YFDSGDYNMAK 11 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;O43768-6;O43768-5;O43768-7;P56211;H3BMD8;P56211-2;H3BQ52;H3BTD3 A6NMQ3;P56211 ENSA;ARPP19 Alpha-endosulfine;cAMP-regulated phosphoprotein 19 1 YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK 249.75 1.91E-16 27391060000 28191440 28266480 20623430 16226400 20851660 17839110 16912920 24583190 24873750 20864410 TRUE FALSE 27089687.36 27460347.67 24350542.57 17063846.45 21522372.58 18199829.03 17119905.37 24075538.54 22050186.18 19451244.93 1.392696841 1.411752706 1.251875788 0.877262433 1.106477897 0.935663969 0.880144455 1.237737668 1.133613106 1 24.21335916 3.973054137 4.58653001 1.0373999 1.392182003 0.66985409 0.10839123 0.121080081 6.29487313 0.029912644 0.060357493 9398.404581 -3.973054137 0.354782102 IGIIGGTGLDDPEILEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGIIGGTGLDDPEILEGR 18 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2;J3QSB7;Q13126-7;Q13126-6;Q13126-5;F2Z2F3;F8WES2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase;Purine nucleoside phosphorylase 0 ; 89.548 0.006679 29467000 83786 82382 72013 93113 93159 96372 88329 87315 97226 98469 FALSE TRUE 80511.55049 80032.54602 85027.35102 97918.57309 96155.54384 98320.70787 89409.99672 85511.91474 86189.31208 91799.60692 0.877035896 0.87181796 0.926227833 1.06665569 1.047450496 1.071036262 0.973969276 0.931506328 0.938885415 1 16.48620036 3.973919573 5.269593582 1.000030378 0.878740157 0.57341785 0.045770942 0.151321775 12.13317501 0.014005037 0.027631967 9417.151852 -3.973919573 -0.121290221 AAVEELLER ddPTM_BT-474_Pertuzumab_2h_R1 1 AAVEELLER 9 0 Q15814 Q15814 TBCC Tubulin-specific chaperone C 0 117.81 0.0025383 55324000 57856 56714 48709 59332 60103 59101 65494 57701 66122 59874 FALSE TRUE 55594.92356 55096.57225 57511.79983 62394.13163 62036.26758 60296.06271 66295.53516 56509.45419 58616.10777 55818.68065 0.995991358 0.98706332 1.030332483 1.117800186 1.111388998 1.080212968 1.187694413 1.012375311 1.050116325 1 15.7684604 3.973961653 4.30037479 1.083821213 0.993644987 0.328984444 0.051081357 0.219878868 9.544401272 0.013206384 0.027024974 9418.064348 -3.973961653 -0.090176226 LDSQNAQGYEWIFIAWSPDHSHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDSQNAQGYEWIFIAWSPDHSHVR 24 0 Q12792;Q12792-3;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 ; 142.32 1.53E-07 692230000 120422 124575 101992 136026 139350 102486 132967 108329 144786 155398 FALSE TRUE 115715.7751 121022.243 120424.2232 143046.3182 143832.3193 104558.3371 134594.2899 106091.9683 128350.5003 144872.755 0.798740764 0.835369238 0.831241341 0.98739282 0.992818279 0.721725331 0.929051773 0.732311388 0.885953334 1 17.14442678 3.974185553 24.69598794 0.87518902 0.821117498 0.086738763 0.094704875 1963.970907 1878884.073 0.025006124 0.045304913 9422.921066 -3.974185553 -0.054071522 VSHEQFR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSHEQFR 7 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;; 89.046 0.018161 246530000 1993840 2046210 1587410 1759440 1659450 1616730 1970200 1976410 1940790 1911080 FALSE TRUE 1915918.528 1987854.094 1874290.299 1850244.909 1712827.716 1649421.388 1994311.897 1935596.443 1720479.656 1781640.849 1.075367423 1.115743442 1.052002315 1.038506111 0.961376541 0.925787815 1.11936808 1.086412249 0.965671424 1 20.76477511 3.974240079 2.83159093 1.022140091 1.095195104 0.243334279 0.056091969 0.455127747 7.294461424 0.01658883 0.038126278 9424.104199 -3.974240079 0.073055013 ASEAGEVPFNHEILR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASEAGEVPFNHEILR 15 0 Q7L5N1;E7EM64 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 ;; 146.78 3.82E-06 4644580000 1393590 1441140 1183610 1557120 1435190 1432810 1516610 1489430 1498950 1596540 FALSE TRUE 1339126.962 1400040.098 1397514.656 1637483.15 1481354.19 1461782.4 1535170.727 1458672.75 1328795.48 1488404.924 0.899706082 0.940631192 0.938934449 1.100159724 0.995262893 0.982113386 1.031420081 0.980024136 0.89276477 1 20.50533564 3.974632039 24.96790177 0.998531998 0.925072143 0.30848653 0.049098882 841.5940796 828324.2628 0.012661155 0.022944411 9432.613491 -3.974632039 -0.073459855 SGSTS(ph)PLGFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSTSPLGFAR 11 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 SGS(0.001)T(0.042)S(0.958)PLGFAR 119.55 0.0005991 579370000 790300 783860 664680 938690 846620 869150 860720 841380 928650 950660 TRUE FALSE 759414.2023 761505.0803 784802.4617 987135.9034 873852.3012 886724.8085 871253.7488 824005.209 823233.5452 886270.9514 0.856864598 0.859223784 0.885510758 1.113808257 0.98598775 1.000512097 0.983055743 0.929744124 0.928873437 1 19.7573883 3.974633761 24.61508587 0.986096689 0.861624923 0.585822022 0.048165494 430.6268412 417876.4423 0.013118376 0.023779797 9432.650893 -3.974633761 -0.124471766 STEEAFEVFWR ddPTM_BT-474_Pertuzumab_2h_R1 2 STEEAFEVFWR 11 0 Q02241;H7BYN4;A0A2U3TZL8;A0A2R8Y531;H0YME6;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 0 ; 127.76 0.00065101 45875000 49315 54031 43935 64380 58760 56559 56822 53513 56725 64362 FALSE TRUE 47387.71528 52490.08878 51875.03183 67702.65952 60650.06876 57702.66173 57517.40463 52407.93785 50285.81581 60002.70441 0.789759657 0.874795383 0.864544896 1.128326801 1.01078892 0.961667683 0.958580204 0.873426262 0.838059156 1 15.87273991 3.974884991 24.79426308 0.960689694 0.841625599 0.357619595 0.076554755 812.7490212 802371.9621 0.021535749 0.039051536 9438.109053 -3.974884991 -0.119064095 LIAVDISPVESTGVSHFATYVAAMR ddPTM_BT-474_Pertuzumab_2h_R1 1 LIAVDISPVESTGVSHFATYVAAMR 25 0 Q8NFV4;Q8NFV4-4 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 223.15 9.64E-34 116760000 51256 55490 48277 94356 65205 66864 78259 86143 70154 55895 FALSE TRUE 49252.85885 53907.47953 57001.72782 99225.72447 67302.37804 68216.03589 79216.75705 84364.11695 62190.41203 52109.18186 0.945185802 1.034510188 1.093890285 1.904188876 1.291564665 1.309098194 1.520207269 1.618987555 1.193463605 1 15.66924998 3.97517582 24.68467509 1.4442519 1.008435911 0.35152203 0.235448226 563.4876526 560322.9971 0.057478585 0.104273643 9444.431476 -3.97517582 -0.435815989 MGVMS(ph)SPTENSFTLDADF ddPTM_BT-474_Pertuzumab_2h_R1 2 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.4)S(0.4)PT(0.2)ENSFTLDADF;MGVMS(0.532)S(0.407)PT(0.061)ENSFTLDADF 110.98 0.00099283 33706000 94486.8 97456 80612.4 109885 107843 96597.3 97593 108380 102309.5 99161 TRUE FALSE 90794.1514 94676.6503 95180.85389 115556.178 111311.868 98550.56359 98787.37233 106141.9151 90695.75448 92444.73715 0.982145163 1.024143215 1.029597323 1.250002776 1.204090914 1.066048394 1.068610019 1.14816612 0.981080776 1 16.49630357 3.975453445 24.90712239 1.113466673 1.00907566 0.208828946 0.079795062 944.6325171 958511.2219 0.020589077 0.03734827 9450.4708 -3.975453445 -0.104391013 DLATVAFCDAQSTQEIHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLATVAFCDAQSTQEIHEK 19 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 ; 364.77 8.17E-108 431870000 387110 398280 331847 442180 413520 420330 399480 422410 491760 460250 FALSE TRUE 371981.3132 386921.4444 391819.1348 465000.9628 426821.2463 428829.3606 404368.9557 413687.0859 435937.4664 429076.8576 0.866933993 0.901753235 0.913167718 1.083724173 0.994743107 0.999423187 0.94241614 0.964132832 1.015989231 1 18.71087657 3.975496748 22.11755589 0.99343934 0.890122724 0.649167335 0.035882617 110.884481 100089.6692 0.009772597 0.017778483 9451.413157 -3.975496748 -0.103316616 DLLQFFKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLQFFKPR 9 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 214.93 6.00E-07 1075000000 868740 830330 717970 823540 804870 810720 897370 871440 951620 925230 FALSE TRUE 834788.6804 806649.8014 847723.1502 866042.9981 830759.3745 827113.3139 908352.2825 853444.4595 843596.0871 862563.348 0.967799852 0.935177461 0.982795237 1.004034081 0.963128536 0.95890153 1.053084721 0.989428152 0.978010588 1 19.71827089 3.97607075 0.589145652 0.999716679 0.941578334 0.224906618 0.026707517 2.561558987 1.225558052 0.015841274 0.09134234 9463.913234 -3.97607075 -0.058138345 LFGDEAAEQWR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFGDEAAEQWR 11 0 Q2T9J0-2;Q2T9J0 Q2T9J0-2 TYSND1 "Peroxisomal leader peptide-processing protease;Peroxisomal leader peptide-processing protease, 15 kDa form;Peroxisomal leader peptide-processing protease, 45 kDa form" 0 112.89 0.0034077 58808000 56024 63136 51710 82812 54772 61111 76476 74742 73322 82461 FALSE TRUE 53834.52014 61335.4231 61055.14728 87085.93724 56533.79112 62346.70629 77411.93616 73198.55158 64998.79395 76875.84302 0.700278762 0.797850413 0.794204589 1.132812777 0.735390845 0.811005172 1.006973493 0.952165839 0.845503495 1 16.23024271 3.976220113 24.5057121 0.921994402 0.760805218 0.32495746 0.108021839 673.8002541 694369.1896 0.027512435 0.049996292 9467.168624 -3.976220113 -0.161189184 AVT(ph)PVSQGSNSSSADPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVTPVSQGSNSSSADPK 17 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 AVT(1)PVSQGSNSSSADPK 200.58 1.37E-10 273240000 153880 149200 121140 112450 118100 137120 131120 139040 155640 155000 TRUE FALSE 147866.1995 144944.9621 143032.6927 118253.558 121898.7938 139892.6603 132724.6858 136168.7754 137972.3997 144501.7119 1.023283375 1.003067439 0.989833898 0.818354028 0.843580274 0.968103827 0.918499054 0.942333302 0.954814983 1 17.14072706 3.976376456 24.41647996 0.917518218 1.008994261 0.362116848 0.051874473 566.7081296 585732.5809 0.013762264 0.025019269 9470.57736 -3.976376456 0.091476043 GKELNEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 GKELNEFR 8 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 ;;; 103.55 0.0043337 2932700000 4031580 4532200 3219210 3162650 3342860 2759090 3859680 3624440 3826860 3713900 FALSE TRUE 3874021.396 4402946.093 3800992.858 3325874.746 3450386.128 2814880.69 3906915.918 3549594.047 3392450.896 3462354.245 1.118898045 1.271662511 1.097805883 0.960581879 0.996543359 0.812996156 1.128398668 1.025196671 0.979810457 1 21.72332191 3.976769824 4.370731635 0.992457984 1.195467055 0.522602579 0.080638911 0.152507621 6.997791911 0.020913619 0.042822118 9479.159349 -3.976769824 0.203009071 DPDEGVSPEHLEQLLGQLGQTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPDEGVSPEHLEQLLGQLGQTLR 23 0 Q8IWY9;Q8IWY9-1 Q8IWY9 CDAN1 Codanin-1 0 ; 170.18 7.63E-12 23203000 24613 25526 21518.9 28878 26805 26289 28553 23766 33914 32492 FALSE TRUE 23651.09675 24798.02347 25407.84392 30368.39704 27667.20717 26820.58159 28902.44016 23275.22379 30064.2249 30291.2879 0.780788748 0.818652002 0.838783877 1.002545588 0.913371768 0.885422293 0.954150258 0.768380132 0.992504016 1 14.8866153 3.976808452 15.64120649 0.912194687 0.806964742 0.375011018 0.068048119 7.866351023 5307.560344 0.01780431 0.032814145 9480.002503 -3.976808452 -0.105229945 EVLYDSEGLS(ph)GEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLYDSEGLSGEER 14 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 EVLYDS(0.031)EGLS(0.969)GEER 184.87 1.30E-06 109620000 57793 56553 50880 84713 63036 58909 79844 78061 80522 83338 TRUE FALSE 55534.38567 54940.16381 60075.14782 89085.04808 65063.61019 60100.18034 80821.15476 76449.01307 71381.48014 77693.44303 0.714788578 0.70714029 0.773233177 1.146622477 0.837440171 0.773555373 1.040257087 0.983982819 0.9187581 1 16.24550523 3.976970789 22.22970699 0.951894431 0.718269837 0.533934808 0.097575294 135.9164028 131199.4183 0.025429445 0.046390863 9483.546743 -3.976970789 -0.233624594 ELHGQNPVVTPCNK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELHGQNPVVTPCNK 14 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 115.68 0.00040533 239070000 208230 198900 168310 212180 192800 214310 195390 201920 233700 234860 FALSE TRUE 200092.1414 193227.5667 198727.361 223130.6352 199001.5871 218643.495 197781.2413 197750.2814 207171.3558 218952.723 0.913860027 0.882508169 0.907626808 1.019081344 0.908879252 0.998587695 0.903305693 0.903164294 0.946192187 1 17.74025987 3.977021658 24.94210087 0.945881278 0.897404923 0.247243274 0.04069939 1067.404711 1158630.439 0.010454654 0.019015042 9484.657605 -3.977021658 -0.048476355 QYPEFPWTDVQAEIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 QYPEFPWTDVQAEIFR 16 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 133.71 7.50E-05 39550000 28459 31950 23899 24828 28562 23123 23643 31550 28565 27828 FALSE TRUE 27346.79082 31038.81728 28218.08093 26109.37606 29480.72267 23590.5629 23932.35011 30898.48147 25322.42095 25943.18477 1.054103074 1.196415072 1.087687621 1.006405971 1.136357118 0.909316382 0.922490832 1.191005721 0.976072181 1 14.66306797 3.977342544 6.857827365 1.032850133 1.129549538 0.184694706 0.088511576 0.292770747 58.87510424 0.023113476 0.044479766 9491.6681 -3.977342544 0.096699406 IAIWTTECENR ddPTM_BT-474_Pertuzumab_2h_R1 4 IAIWTTECENR 11 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;; 219.97 2.21E-11 1474310000 528890 503100 442678 528150 566630 535750 535310 565130 570520 583740 FALSE TRUE 508220.3941 488752.0806 522679.7619 555407.8848 584856.1686 546583.2321 541861.2839 553459.868 505756.9614 544202.7699 0.933880572 0.898106566 0.960450389 1.020589963 1.074702668 1.004374219 0.995697402 1.017010384 0.929353891 1 19.05378477 3.977642891 3.731792216 1.008869599 0.916852405 0.523559548 0.034436626 0.164172256 4.941504688 0.009105728 0.019330742 9498.234575 -3.977642891 -0.092017194 ALFARPDLLLLDEPTNMLDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALFARPDLLLLDEPTNMLDVR 21 1 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ; 131.82 1.15E-05 221410000 228230 205215 177792 212150 201530 225240 210109 227460 238530 201519 FALSE TRUE 219310.5193 199362.4691 209922.9694 223099.0869 208012.3955 229794.5071 212680.3768 222762.8715 211453.0744 187869.9386 1.167352908 1.061172802 1.117384563 1.187518815 1.107214901 1.223157408 1.132061778 1.185729197 1.125529054 1 17.51937471 3.977872708 24.0701568 1.149333033 1.108016818 0 0.062359622 1115.469847 1213419.208 0.014467644 0.02641474 9503.262108 -3.977872708 -0.041316215 SAQSLEYCAELLGLDQDDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SAQSLEYCAELLGLDQDDLR 20 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;; 270.26 3.13E-38 427820000 304137 311791 260561 357760 331727 339592 332557 324691 336144 365391 FALSE TRUE 292250.9898 302899.026 307650.1688 376224.0365 342397.3002 346458.7829 336626.932 317986.0174 297986.3424 340642.7421 0.85793987 0.889198531 0.903146114 1.104453405 1.005150728 1.017073726 0.98821108 0.933488309 0.874776725 1 18.37789994 3.977912461 24.48454384 0.986261552 0.879219939 0.43329244 0.055887697 567.7052172 629316.9271 0.015388563 0.028057946 9504.132032 -3.977912461 -0.107041614 HDGGS(ph)PSIK ddPTM_BT-474_Pertuzumab_2h_R1 6 HDGGSPSIK 9 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HDGGS(1)PSIK;HDGGS(1)PSIK;HDGGS(1)PSIK;HDGGS(1)PSIK;HDGGS(0.685)PS(0.315)IK;HDGGS(0.997)PS(0.003)IK 132.03 0.0002039 3710200000 4410620 3911330 3411380 3305270 3337860 3494030 3969410 2354493 4568440 4669110 TRUE FALSE 4238248.094 3799782.698 4027892.252 3475855.381 3445225.298 3564681.681 4017988.827 2305871.897 4049849.844 4352867.021 0.973668176 0.872937923 0.925342362 0.798520921 0.79148416 0.81892731 0.923067212 0.529736352 0.93038676 1 22.05353452 3.978562059 1.064637526 0.791223524 0.957389639 0.05703231 0.124733808 1.3015932 2.455916772 0.041755573 0.184868822 9518.358524 -3.978562059 0.166166115 LFLLPHKDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFLLPHKDQR 10 1 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 116.77 0.00062895 747820000 1012500 1182510 702110 481170 631300 480210 706120 570520 581520 551390 FALSE TRUE 972930.3806 1148785.973 828996.8954 506003.2414 651606.3378 489920.1752 714761.7078 558738.5626 515508.2875 514043.8642 1.892699142 2.234801449 1.612696801 0.9843581 1.267608434 0.953070758 1.390468319 1.086947246 1.00284883 1 18.97153195 3.978604669 3.594156419 1.121042908 2.056488049 0.863897326 0.154671365 0.068629542 1.885457261 0.03768998 0.080867618 9519.292451 -3.978604669 0.935445141 VGLVEDSPSTAGDGDDSPVVSLTVPS(ph)TSPPSSSGLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGLVEDSPSTAGDGDDSPVVSLTVPSTSPPSSSGLSR 37 0 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VGLVEDSPSTAGDGDDSPVVSLTVPS(0.275)T(0.275)S(0.209)PPS(0.06)S(0.06)S(0.06)GLS(0.06)R;VGLVEDSPSTAGDGDDSPVVSLT(0.001)VPS(0.276)T(0.276)S(0.221)PPS(0.056)S(0.056)S(0.056)GLS(0.056)R 110.91 8.96E-06 299700000 144600 156999 129040 181632 168912 170670 162075 165530 170705 165244 TRUE FALSE 138948.8721 152521.5422 152360.3985 191006.0493 174345.2079 174121.0643 164058.5223 162111.7477 151327.2841 154051.8767 0.901961567 0.99006611 0.989020074 1.239881353 1.131730503 1.130275515 1.064956337 1.0523192 0.982313798 1 17.23305673 3.979465543 24.24928226 1.09012751 0.956896083 0.396664426 0.071900457 505.2414074 596646.3566 0.019139191 0.035070164 9538.180628 -3.979465543 -0.133231427 QLEEAEEEAQR ddPTM_BT-474_Pertuzumab_2h_R1 4 QLEEAEEEAQR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 271.39 1.13E-26 1886080000 832317 835610 723964 951652 838741 916985 960776 933565 960137 926451 FALSE TRUE 799789.1315 811779.2209 854800.3993 1000766.874 865719.866 935527.065 972534.2641 914286.5565 851146.273 863701.6486 0.926001627 0.939883839 0.989694069 1.158695107 1.002336707 1.083159985 1.126007187 1.058567571 0.985463296 1 19.72017352 3.979808555 6.662147273 1.064847221 0.939849702 0.485459009 0.052487022 0.121677433 23.41144549 0.01297795 0.025179269 9545.717002 -3.979808555 -0.124997519 RKPQEESER ddPTM_BT-474_Pertuzumab_2h_R1 3 RKPQEESER 9 2 P26358;P26358-2;K7EJL0;K7ENQ6;K7ERQ1;K7ELB1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;; 258.52 2.64E-15 498054000 325852 338881 266207 263077 293620 247578 315276 322508 311815 340246 FALSE TRUE 313117.3436 329216.4457 314316.5266 276654.4355 303064.554 252584.1968 319134.442 315848.0971 276419.0684 317200.8354 0.987126479 1.037880135 0.990906995 0.87217436 0.955434287 0.796291083 1.006095843 0.995735389 0.871432347 1 18.27503704 3.979983023 21.1846298 0.932313489 1.012975936 0.233272688 0.064572397 150.2863642 159057.3368 0.016767013 0.03090874 9549.552549 -3.979983023 0.080662448 DQDLTQEIAMEHFVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQDLTQEIAMEHFVK 15 0 Q9ULX6;Q9ULX6-2 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 ; 223.76 1.22E-12 1987320000 1702640 1667550 1419830 1664090 1655060 1712630 1673360 1753920 2045860 1871300 FALSE TRUE 1636098.946 1619993.107 1676424.865 1749973.884 1708296.508 1747260.552 1693839.08 1717700.939 1813622.55 1744555.184 0.937831581 0.92859952 0.960946882 1.003106064 0.979216091 1.001550749 0.97092892 0.984606824 1.039590244 1 20.7344278 3.979994903 3.211816159 0.993606181 0.933564175 0.674693141 0.017884649 0.142713575 3.018621456 0.004654234 0.010321703 9549.813772 -3.979994903 -0.060042006 LSFS(ph)PENILIQNQDIVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSFSPENILIQNQDIVR 17 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LS(0.114)FS(0.886)PENILIQNQDIVR;LS(0.001)FS(0.999)PENILIQNQDIVR;LSFS(1)PENILIQNQDIVR 248.7 6.94E-21 491981000 258044 280976 211226 271228 275483 278683 264589 310994 339074 306955 TRUE FALSE 247959.3552 272962.8396 249399.2369 285226.1096 284344.1609 284318.1612 267827.1193 304571.8652 300583.741 286164.6644 0.86649187 0.953866335 0.871523524 0.996720228 0.993638266 0.99354741 0.935919604 1.064323807 1.050387341 1 18.12648601 3.980030877 0.456681209 1.031310787 0.836352014 0.572104697 0.041293538 1.887604813 0.504127866 0.032241335 0.187035949 9550.604864 -3.980030877 -0.194958773 CVELVHEEMQR ddPTM_BT-474_Pertuzumab_2h_R1 1 CVELVHEEMQR 11 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 110.74 0.0017539 257640000 308140 313040 263650 353170 359040 307860 316990 318840 399270 365880 FALSE TRUE 296097.5481 304112.4057 311297.4199 371397.146 370588.8477 314085.1401 320869.4184 312255.8426 353946.5435 341098.6217 0.868070198 0.891567384 0.912631714 1.088826288 1.086456597 0.920804483 0.940693975 0.915441525 1.037666296 1 18.3798294 3.980759625 23.1169059 0.988501132 0.885388904 0.412000192 0.058952545 320.600992 385199.3982 0.017006507 0.031357498 9566.644255 -3.980759625 -0.103112228 SRS(ph)PRPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPRPSK 8 2 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 S(0.166)RS(0.834)PRPSK 60.255 0.048761 104620000 73595 76500 66368 87263 79480 93157 100140 82897 104460 102950 TRUE FALSE 70718.82604 74318.2949 78362.17395 91766.65389 82036.54638 95040.69837 101365.5433 81185.14798 92602.13873 95977.1048 0.736830166 0.774333577 0.816467366 0.956130674 0.854751209 0.990243439 1.056142957 0.84588036 0.964835717 1 16.55040267 3.980822217 1.165337616 0.951886814 0.724359119 0.652548693 0.060183808 0.400308498 0.933788744 0.019627138 0.080967407 9568.02315 -3.980822217 -0.227527695 RQKEELER ddPTM_BT-474_Pertuzumab_2h_R1 1 RQKEELER 8 2 H3BST1;Q9UL45;H3BMT8;H3BRA4;H3BNE3;H3BR42 H3BST1 BLOC1S6 Biogenesis of lysosome-related organelles complex 1 subunit 6 0 81.594 0.01263 32931000 28538 28982 23058 22142 25507 23266 23458 31869 25917 27480 FALSE TRUE 27422.70341 28155.46174 27225.09352 23284.75127 26327.45582 23736.45446 23745.08602 31210.89401 22975.01081 25618.75512 1.070415142 1.09901756 1.062701657 0.90889472 1.027663354 0.926526459 0.926863382 1.218283006 0.896804341 1 14.64491275 3.980880105 23.77288596 1.00274623 1.083752207 0.166740875 0.088935294 814.72452 1013002.384 0.02421295 0.044651485 9569.298572 -3.980880105 0.081005976 QMNPHIR ddPTM_BT-474_Pertuzumab_2h_R1 3 QMNPHIR 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 117.17 0.0052914 572690000 386080 475570 292225 276288 310558 237033 315542 268451 319935 316954 FALSE TRUE 370991.5668 462007.2092 345036.558 290547.2568 320547.3801 241825.9697 319403.6974 262907.393 283617.3201 295486.4233 1.2555283 1.563548011 1.167690056 0.983284625 1.084812549 0.818399597 1.080942041 0.889744409 0.959831985 1 18.17273232 3.980910311 3.416004835 0.97062004 1.409241056 0.735928366 0.103692482 0.100758439 2.457599515 0.025042471 0.054611553 9569.964154 -3.980910311 0.438621015 EGAS(ph)PVTEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGASPVTEVR 10 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 EGAS(1)PVTEVR;EGAS(1)PVTEVR 175.74 2.84E-06 634640000 509010 523580 456220 630810 576030 475880 612510 651660 584440 617420 TRUE FALSE 489117.3265 508648.011 538669.1026 663366.1797 594558.5281 485502.6197 620006.0806 638202.9933 518096.8214 575601.5935 0.849749778 0.883680686 0.935836712 1.152474537 1.032934125 0.843469902 1.077144483 1.108758211 0.900096225 1 19.13471106 3.98118617 8.623384098 1.024934858 0.877026434 0.322290265 0.087184072 0.250854243 104.3822705 0.022964905 0.04393065 9576.044825 -3.98118617 -0.147908424 RQGS(ph)FSEDVISHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQGSFSEDVISHK 13 1 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5;E9PNZ4 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 RQGS(0.672)FS(0.328)EDVISHK 64.275 0.038409 348310000 312510 316140 287570 229860 284370 314140 297280 289710 303630 301330 TRUE FALSE 300296.7637 307123.9967 339540.296 241723.1021 293517.0193 320492.126 300918.2016 283727.3873 269163.1953 280920.6507 1.068973616 1.093276681 1.208669762 0.860467543 1.044839596 1.140863533 1.071185763 1.009991208 0.958146703 1 18.09980316 3.981424514 0.200829998 0.977630715 1.169693625 0.113433 0.086507768 24.85210042 1.2722581 0.217303351 1.228032476 9581.301672 -3.981424514 0.19206291 RTEEPDRDER ddPTM_BT-474_Pertuzumab_2h_R1 4 RTEEPDRDER 10 2 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 157.68 4.92E-06 452469000 226502 243656 201298.1 279521 250734 262493.1 269626 230706 271039 303456 FALSE TRUE 217650.0514 236707.1694 237677.1445 293947.1123 258799.0868 267800.8903 272925.7636 225941.8405 240271.789 282902.6548 0.76934609 0.836708901 0.840137554 1.03903978 0.914799075 0.946618513 0.964733837 0.79865578 0.849309064 1 18.10994619 3.981491013 23.9901193 0.918707265 0.811876363 0.376717681 0.067568579 528.8368327 685447.7948 0.018629639 0.034426915 9582.768855 -3.981491013 -0.106830902 LVDTGDKFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVDTGDKFR 9 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 63.216 0.070699 52462000 61616 72243 53547 50676 57141 48426 64945 57942 68064 68105 FALSE TRUE 59207.9786 70182.70037 63224.13405 53291.39443 58978.99216 49405.2069 65739.81634 56745.47745 60337.66007 63492.18769 0.932523839 1.105375369 0.995778163 0.83933782 0.928917309 0.778130487 1.035400082 0.893739522 0.950316287 1 15.95429147 3.982375503 23.67550533 0.9145406 1.026856388 0.225707855 0.079471149 431.1219491 579143.7178 0.019017227 0.035300711 9602.305156 -3.982375503 0.112315788 FVVDLSDQVAPTDIEEGMR ddPTM_BT-474_Pertuzumab_2h_R1 2 FVVDLSDQVAPTDIEEGMR 19 0 P35998 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 290.65 3.65E-49 84691000 172907 169628 143811 189515 177589 187679 165754 183813 180176 190842 FALSE TRUE 166149.6033 164790.3755 169800.8468 199295.8919 183301.3115 191473.998 167782.547 180017.1973 159723.1758 177916.1014 0.933864906 0.926225194 0.954387183 1.120167823 1.030268256 1.076203876 0.943043073 1.011809476 0.897744356 1 17.44083755 3.98241596 24.43545547 1.012958074 0.932610299 0.253507592 0.058452961 708.831927 985026.0037 0.015166258 0.028133703 9603.199705 -3.98241596 -0.080347774 LAS(ph)PSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_BT-474_Pertuzumab_2h_R1 3 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.347)PS(0.347)GS(0.111)T(0.135)S(0.029)S(0.029)GLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.785)PS(0.206)GS(0.007)T(0.002)SSGLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.79)PS(0.167)GS(0.037)T(0.004)S(0.001)SGLEVVAPEGTSAPGGGPGTLDDSATICR 239.22 3.86E-50 4178910000 913060 893610 750690 941140 909690 932750 871740 926940 917980 1035460 TRUE FALSE 877376.6058 868125.1177 886356.382 989712.3482 938951.005 951610.8441 882408.6149 907798.3651 813774.7589 965327.3719 0.908890218 0.899306435 0.91819253 1.025260836 0.972676247 0.985790802 0.914102967 0.940404666 0.84300392 1 19.88065876 3.982890496 24.70632866 0.952421601 0.905261095 0.16466415 0.047672418 1144.174607 1652210.35 0.012472394 0.023179433 9613.698464 -3.982890496 -0.047160507 RLS(ph)GSSLCSGSWVSADGFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSGSSLCSGSWVSADGFLR 20 1 O75400-3;O75400;F5H578;H0YG38 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 RLS(0.952)GS(0.036)S(0.012)LCSGSWVSADGFLR 170.55 5.59E-12 360550000 150030 110070 111390 166110 146280 152990 150590 143070 168700 150210 TRUE FALSE 144166.6617 106930.9114 131520.6509 174682.957 150985.229 156083.5626 152432.9655 140115.5545 149549.8832 140036.1429 1.029496091 0.763595092 0.939190756 1.24741337 1.078187573 1.114594842 1.088525878 1.000567079 1.067937749 1 17.0954397 3.982953485 24.86751096 1.082331173 0.885257414 0.455289195 0.088105673 518.9873991 757104.2436 0.021760372 0.040462207 9615.0929 -3.982953485 -0.197073758 AS(ph)SHSSQTQGGGSVTKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.493)S(0.493)HS(0.014)SQTQGGGSVTKK;AS(0.582)S(0.415)HS(0.002)S(0.001)QTQGGGSVTKK 231.06 2.76E-16 462600000 1032960 1543390 712370 499290 596980 568800 343510 524110 527660 544660 TRUE FALSE 992590.7812 1499374.028 841111.1056 525058.4167 616182.4039 580301.5257 347713.9781 513286.9453 467762.2489 507769.6931 1.954805091 2.952862388 1.656481505 1.034048357 1.213507644 1.142843958 0.68478679 1.010865659 0.921209468 1 18.95381476 3.983147627 3.470909199 1.002705321 2.452214255 0.82438838 0.266807871 0.079479176 2.017412131 0.065999203 0.143675476 9619.392079 -3.983147627 1.449508934 RQSPEPS(ph)PVTLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQSPEPSPVTLGR 13 1 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 RQS(0.027)PEPS(0.732)PVT(0.242)LGR;RQS(0.004)PEPS(0.947)PVT(0.049)LGR 147.36 4.53E-05 1528800000 931370 956350 804910 1125260 999110 1028920 1028400 1032350 977830 1087610 TRUE FALSE 894971.0307 929075.8344 950375.1421 1183334.803 1031247.281 1049725.467 1040985.867 1011031.612 866830.8378 1013945.206 0.882662126 0.916297872 0.937304241 1.167059913 1.017064112 1.035288161 1.02666876 0.997126478 0.854908956 1 19.95154826 3.983288635 24.63469699 1.017281605 0.906310214 0.308884509 0.071115884 688.3254846 1014686.181 0.018372902 0.034263599 9622.515846 -3.983288635 -0.110971391 FVINYDYPNSSEDYVHR ddPTM_BT-474_Pertuzumab_2h_R1 4 FVINYDYPNSSEDYVHR 17 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 208.43 5.18E-12 11316210000 4473320 4707260 3914620 5241310 5053460 5278900 4833260 4696500 5064030 5113370 FALSE TRUE 4298497.709 4573013.554 4622078.914 5511814.637 5216009.13 5385642.975 4892410.882 4599515.634 4489182.545 4767036.895 0.9017127 0.959298964 0.969591597 1.156234944 1.094182664 1.12976742 1.026300192 0.964858409 0.941713405 1 22.18466136 3.983335089 23.26148694 1.044305152 0.938990604 0.340975658 0.065761609 361.2811114 504295.1671 0.019004651 0.035494118 9623.545177 -3.983335089 -0.105314547 FQS(ph)VESGANNVVFIR ddPTM_BT-474_Pertuzumab_2h_R1 1 FQSVESGANNVVFIR 15 0 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 1 FQS(1)VESGANNVVFIR 84.842 0.0072545 0 12381 12959 11206 16267 14744 14207 12200 21508 8522 11585 TRUE FALSE 11897.13683 12589.42201 13231.17348 17106.54182 15218.25415 14494.27527 12349.30725 21063.85228 7554.618287 10800.33763 1.101552307 1.165650782 1.225070357 1.583889542 1.409053556 1.342020571 1.143418629 1.950295723 0.699479826 1 13.39878879 3.983380655 17.95098554 1.376263731 1.149037717 0.009308428 0.321127314 44.13734779 47683.84977 0.07901382 0.148814773 9624.554913 -3.983380655 -0.227226014 AADPPAENSS(ph)APEAEQGGAE ddPTM_BT-474_Pertuzumab_2h_R1 2 AADPPAENSSAPEAEQGGAE 20 0 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 AADPPAENS(0.128)S(0.872)APEAEQGGAE;AADPPAENS(0.08)S(0.92)APEAEQGGAE 294.12 2.20E-44 337040000 443070 439140 381620 469270 460310 527500 491140 480510 474020 495630 TRUE FALSE 425754.3346 426616.1572 450587.2231 493489.0809 475116.2892 538166.4114 497150.7182 470587.3006 420211.2369 462060.5386 0.921425439 0.923290611 0.975169237 1.068018235 1.028255498 1.164709743 1.075942818 1.018453777 0.909428964 1 18.81772236 3.983412115 3.110478471 1.043998224 0.922954094 0.365787397 0.0610787 0.26178992 5.165206552 0.016830187 0.037838846 9625.252147 -3.983412115 -0.12104413 MNGFIDQIDGIVHFETR ddPTM_BT-474_Pertuzumab_2h_R1 3 MNGFIDQIDGIVHFETR 17 0 D6RFN0;Q9BT78;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ;; 185.96 5.50E-10 412447000 361223 388943.8 313236.9 426345.7 382423.8 433613.4 452708.6 439490.9 489578.1 451753 FALSE TRUE 347106.0058 377851.5036 369845.7757 448349.4527 394724.8088 442381.36 458248.9833 430415.2593 434003.2466 421155.3669 0.824175668 0.897178413 0.878169447 1.064570199 0.937242737 1.050399436 1.088075849 1.02198688 1.030506271 1 18.68399303 3.983707683 1.059421746 1.036357001 0.821080765 0.71497792 0.04524874 0.353063695 0.656611443 0.014487418 0.064961366 9631.80504 -3.983707683 -0.215276236 VVGYAFDQVDDHLQTPYHETVYSLLDTLSPAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VVGYAFDQVDDHLQTPYHETVYSLLDTLSPAYR 33 0 Q9P0R6 Q9P0R6 GSKIP GSK3-beta interaction protein 0 58.861 0.018774 132070000 23430 24097 19234 18684 19464 22756 26642 20195 28730 18995 FALSE TRUE 22514.3297 23409.77715 22710.01166 19648.28348 20090.07724 23216.14191 26968.05277 19777.96619 25468.69085 17708.45173 1.271388941 1.321955048 1.282439143 1.109542707 1.134490894 1.311020425 1.522891621 1.116865918 1.438222338 1 14.11215046 3.983717701 24.49302084 1.243324901 1.298053306 0.02845462 0.150648241 2635.927951 3965180.479 0.037789252 0.070632903 9632.027221 -3.983717701 0.054728405 MTNNEDS(ph)LSPTSSTLSNLELDAAEKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 MT(0.03)NNEDS(0.533)LS(0.361)PT(0.072)S(0.003)S(0.001)TLSNLELDAAEKDR 70.213 0.032155 229310000 146290 130730 114660 146330 147850 151710 132320 129930 144930 150920 TRUE FALSE 140572.8251 127001.7084 135381.6126 153882.1088 152605.7295 154777.6801 133939.3717 127246.9001 128478.154 140698.054 0.999109946 0.902654335 0.962213824 1.0937046 1.084632838 1.1000698 0.951963215 0.904397015 0.913148053 1 17.10224285 3.983722006 24.80846409 1.002618035 0.946270113 0.102348982 0.070313179 1679.528244 2559697.696 0.021129846 0.03946111 9632.122702 -3.983722006 -0.056347922 IKGEHPGLSIGDVAK ddPTM_BT-474_Pertuzumab_2h_R1 3 IKGEHPGLSIGDVAK 15 1 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ;; 160.48 1.03E-06 14849980000 24916400 23461590 19236500 18412480 21013500 21336980 20405670 23663130 24006450 23246530 FALSE TRUE 23942639.54 22792488.42 22712963.46 19362750.3 21689418.31 21768428.35 20655400.69 23174478.1 21281338.44 21672021.82 1.104771846 1.051701065 1.048031589 0.893444574 1.000802717 1.004448433 0.953090619 1.069327001 0.981972915 1 24.36933042 3.983735403 23.93384456 0.991390695 1.071143977 0.430988677 0.043663683 407.8486661 600167.0043 0.011511671 0.021543767 9632.41983 -3.983735403 0.079753282 KPESFFTQFDAVCLTCCSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPESFFTQFDAVCLTCCSR 19 1 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054;M0R286;M0QYP2 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 149.94 1.29E-07 220590000 269600 255620 228310 296280 312930 268870 296080 274470 313610 289050 FALSE TRUE 259063.7339 248329.9679 269570.6957 311571.0463 322995.6776 274306.7356 299703.5156 268802.0986 278010.3076 269472.386 0.961373957 0.92154143 1.000364823 1.15622625 1.198622547 1.017940056 1.112186373 0.997512593 1.031683846 1 18.03977792 3.98411881 6.824647346 1.074353384 0.945502046 0.413269343 0.063915475 0.148293079 33.8741439 0.017275236 0.033798479 9640.927347 -3.98411881 -0.128851337 S(ph)GTPDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGTPDPR 7 0 Q2YD98 Q2YD98 UVSSA UV-stimulated scaffold protein A 1 S(0.89)GT(0.11)PDPR 81.548 0.02822 390560000 302580 301290 256550 358580 334700 308240 329030 320680 311200 344710 TRUE FALSE 290754.8391 292697.5042 302914.2919 377086.3568 345465.9295 314472.824 333056.7676 314057.8459 275873.8807 321362.4847 0.904756631 0.910801721 0.94259382 1.173398809 1.075003916 0.978561092 1.036389695 0.977269784 0.858450796 1 18.293842 3.984145446 24.65259238 1.016590675 0.912508779 0.256601624 0.07532049 800.0526978 1244027.348 0.02021893 0.037929662 9641.518664 -3.984145446 -0.104081897 IKDEFQFLQAQYHSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKDEFQFLQAQYHSLK 16 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 0 165.71 4.16E-09 613570000 649750 615900 499190 456480 532310 527340 560330 543740 689360 622860 FALSE TRUE 624357.0517 598335.135 589404.7374 480038.9875 549432.2346 538003.1761 567187.4862 532511.579 611106.7428 580673.1374 1.075229783 1.030416419 1.015037031 0.826693981 0.946198815 0.926516385 0.976775831 0.91705909 1.052410906 1 19.14736677 3.984495467 24.21932043 0.943186522 1.04529906 0.359155485 0.05651853 436.0937005 681218.4406 0.013889237 0.026134373 9649.292402 -3.984495467 0.102112538 GSKS(ph)PLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSKSPLKR 8 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 GS(0.065)KS(0.935)PLKR 91.215 0.006598 1569900000 2286100 2179400 1720300 1571800 1676400 1673100 2061900 2102100 1970100 2137600 TRUE FALSE 2196756.685 2117245.646 2031196.478 1652920.786 1730322.928 1706931.228 2087134.149 2058690.9 1746462.507 1992818.448 1.102336586 1.062437799 1.019258167 0.829438722 0.868279261 0.856541262 1.047327794 1.033054919 0.876378131 1 20.92637885 3.984524235 5.94860487 0.937716997 1.073966542 0.419388476 0.072719946 0.18058554 24.39924809 0.021157864 0.041938676 9649.931604 -3.984524235 0.136249545 ELDELKPWIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDELKPWIEK 11 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 102.62 0.0025937 513670000 469210 492830 375810 380530 441050 343750 404420 467540 473680 449310 FALSE TRUE 450872.7545 478774.9709 443727.2268 400169.1989 455236.7738 350700.8605 409369.4129 457885.1356 419909.8322 418877.8335 1.076382464 1.142994288 1.059323725 0.955336298 1.086800822 0.837239005 0.977300254 1.093123338 1.002463722 1 18.67617002 3.984751563 5.548476102 0.999449157 1.108664377 0.319571139 0.068856673 0.203819891 21.21950132 0.018248625 0.03646744 9654.984096 -3.984751563 0.10921522 GREFGVTTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GREFGVTTGR 10 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 143 3.17E-05 466510000 541120 583280 440330 387510 422650 490640 498790 469630 523630 526200 FALSE TRUE 519972.4322 566645.4255 519907.4261 407509.4375 436244.9211 500561.077 504894.3412 459931.9764 464189.7176 490560.0053 1.059956838 1.15509911 1.059824324 0.83070253 0.889279428 1.020387051 1.029220352 0.937565173 0.946244522 1 18.90407009 3.984872216 23.49591087 0.951719054 1.107511459 0.543839215 0.060293308 224.0553218 347998.4871 0.016089943 0.030363648 9657.666769 -3.984872216 0.155792405 SS(ph)RSS(ph)PELTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.43)S(0.562)RS(0.103)S(0.904)PELT(0.001)R;S(0.422)S(0.57)RS(0.035)S(0.973)PELTR;S(0.409)S(0.59)RS(0.001)S(0.999)PELTR 136.39 6.76E-05 2379020000 1080020 1073020 898110 1146800 1088660 1057280 1034420 1159560 1149750 1143380 TRUE FALSE 1037811.624 1042418.52 1060418.455 1205986.485 1123677.738 1078658.926 1047079.541 1135614.681 1019235.2 1065937.854 0.973613631 0.977935549 0.994822026 1.131385362 1.054168152 1.011934159 0.982308244 1.065366687 0.956186326 1 20.0236919 3.984994477 24.71047114 1.033329841 0.978425612 0.179734542 0.046067184 887.4066699 1461354.197 0.011832499 0.022300979 9660.385942 -3.984994477 -0.054904228 TDRLEVCR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDRLEVCR 8 1 H7C4T5;C9JP00;A0A0A0MQX8;Q9NR56-7;Q9NR56-6;Q9NR56-2;Q9NR56-5;Q9NR56;C9JCX1;H7C4Y1;Q86VM6 H7C4T5 MBNL1 Muscleblind-like protein 1 0 119.68 0.0015025 357300000 283940 283760 203380 181540 206160 133370 209450 238060 214640 221020 FALSE TRUE 272843.3109 275667.4426 240135.2902 190909.3012 212791.3236 136066.8328 212013.3118 233143.9778 190274.967 206050.1185 1.324159932 1.337865974 1.165421752 0.926518764 1.032716337 0.660357945 1.028940499 1.131491598 0.923440221 1 17.65263577 3.985236204 2.80458523 0.968214035 1.332215193 0.627288109 0.116512408 0.184827026 2.914927004 0.0332657 0.077644785 9665.764373 -3.985236204 0.364001158 RSNATNSSYS(ph)PTTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSNATNSSYSPTTGR 15 1 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 RSNATNS(0.004)S(0.049)Y(0.003)S(0.929)PT(0.011)T(0.003)GR;RS(0.001)NAT(0.001)NS(0.015)S(0.148)Y(0.001)S(0.797)PT(0.018)T(0.021)GR 58.693 0.068489 164135000 30836 45286 30624 26304.2 29798 37102 33954 33080 32946 40468 TRUE FALSE 29630.89503 43994.48762 36158.43803 27661.76291 30756.47973 37852.22786 34369.53921 32396.88644 29206.1082 37727.06631 0.785401515 1.166125329 0.958421673 0.733207366 0.815236453 1.003317553 0.911004819 0.858717351 0.774142043 1 15.2033123 3.98537783 24.92376321 0.868227153 0.99739093 0.123671004 0.118673939 1020.782728 1739953.963 0.029044564 0.054930496 9668.91696 -3.98537783 0.129163777 ASS(ph)PGHPAFLEDGSPS(ph)PVLAFAAS(ph)PRPNHSYIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSPGHPAFLEDGSPSPVLAFAASPRPNHSYIFK 34 1 Q9C073;D6RJ87;Q9C073-2 Q9C073 FAM117A Protein FAM117A 3 AS(0.463)S(0.537)PGHPAFLEDGSPS(1)PVLAFAAS(0.998)PRPNHS(0.001)Y(0.001)IFK 165.87 1.07E-13 92938000 29797 27032 23835 30302 27570 33314 29635 24739 31463 40746 TRUE FALSE 28632.5003 26261.07383 28142.51471 31865.88985 28456.81409 33987.63191 29997.68199 24228.131 27891.45214 37986.23713 0.753759847 0.691331277 0.740860818 0.838879875 0.749134851 0.894735422 0.789698698 0.637813399 0.734251515 1 15.21318919 3.985633148 22.94357984 0.783436928 0.72093316 0.09373607 0.094422435 616.786822 985013.4977 0.024590177 0.046708794 9674.602901 -3.985633148 -0.062503767 LDYEDIIDDLPCR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDYEDIIDDLPCR 13 0 A0A494C108;Q8N9T8;H0YH26 A0A494C108 KRI1 Protein KRI1 homolog 0 159.94 0.00010399 52507000 56072 54698 50463 72719 64648 57591 61455 73244 73489 74357 FALSE TRUE 53880.64425 53138.06659 59582.78664 76472.0363 66727.46163 58755.52948 62207.10467 71731.4858 65146.83681 69320.73416 0.777265921 0.766553719 0.859523307 1.103162528 0.962590233 0.847589544 0.897380927 1.034776776 0.939788616 1 16.08099931 3.985770355 6.757184623 0.966657018 0.780707489 0.59180214 0.066595068 0.10471083 23.7220003 0.017976736 0.035344734 9677.659879 -3.985770355 -0.185949529 SLAALDALNT(ph)DDENDEEEYEAWK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLAALDALNTDDENDEEEYEAWK 23 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;S(0.003)LAALDALNT(0.996)DDENDEEEY(0.001)EAWK 252.91 6.49E-43 884140000 288364.7 284471.9 229668.3 225765.9 249971.2 250834.3 237887.2 311788.8 291095.6 258046.6 TRUE FALSE 277095.0887 276359.0399 271174.4708 237417.7052 258011.7507 255906.3414 240798.5347 305350.2523 258051.6479 240568.8739 1.151832671 1.148773054 1.127221765 0.986901178 1.07250679 1.063754995 1.000954657 1.269284124 1.072672635 1 17.87609047 3.985849906 24.35779135 1.082973222 1.147226536 0.154079026 0.076263875 1079.080302 1857530.765 0.021184959 0.040251853 9679.43274 -3.985849906 0.064253314 SQLSCVVVDDIER ddPTM_BT-474_Pertuzumab_2h_R1 2 SQLSCVVVDDIER 13 0 I3L0N3;P46459;P46459-2;K7EQD6;I3L2G1 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 141.32 9.26E-05 143605000 130739 129306 114141 176703 152537 142080 143468 155891 144164 165754 FALSE TRUE 125629.5753 125618.3195 134768.8178 185822.663 157443.4911 144952.9549 145223.8043 152671.7964 127799.1071 154527.3339 0.812992576 0.812919736 0.872135785 1.202522934 1.018871465 0.938040871 0.939793631 0.987992173 0.827032369 1 17.23750253 3.985928495 24.75827315 0.98764294 0.820348999 0.403448675 0.088292944 559.0585944 983648.7744 0.023056245 0.043815669 9681.184464 -3.985928495 -0.167293941 TKGDFILVGDLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKGDFILVGDLMR 13 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 160.8 3.94E-05 866880000 1476900 1507620 1084190 999190 1084470 762870 1268460 1110660 1343900 1319580 FALSE TRUE 1419181.115 1464624.154 1280127.251 1050758.316 1119352.962 778295.7541 1283983.793 1087724.483 1191346.106 1230203.671 1.153614762 1.190554205 1.040581556 0.85413362 0.909892393 0.632656016 1.043716437 0.884182439 0.968413714 1 20.23046576 3.986523516 3.150131146 0.892632719 1.170762438 0.520580892 0.105424945 0.181950143 3.699254126 0.02709811 0.060892475 9694.457613 -3.986523516 0.278129719 FCADSDGFSQELR ddPTM_BT-474_Pertuzumab_2h_R1 3 FCADSDGFSQELR 13 0 P52732 P52732 KIF11 Kinesin-like protein KIF11 0 ;; 212.09 3.88E-08 372415000 442012 440282 387464 506572 486539 490957 517132 491867 508517 536783 FALSE TRUE 424737.6824 427725.5884 457487.3639 532716.2416 502188.9688 500884.4869 523460.8161 481709.7746 450792.282 500426.2093 0.848751873 0.854722595 0.914195451 1.064525062 1.003522516 1.000915775 1.046029977 0.962599012 0.900816691 1 18.93279783 3.986992616 4.360684078 0.996839372 0.855863705 0.663400637 0.042061607 0.117909806 5.522793986 0.01127443 0.023440461 9704.934674 -3.986992616 -0.140975667 LLDLSDSTSVAS(ph)FPSADETDGNLPESR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDLSDSTSVASFPSADETDGNLPESR 27 0 Q13464 Q13464 ROCK1 Rho-associated protein kinase 1 1 LLDLS(0.011)DS(0.011)T(0.011)S(0.011)VAS(0.931)FPS(0.022)ADET(0.003)DGNLPESR 44.289 0.096682 35486000 26033 24936 21464 27189 24040 26718 24839 28804 29950 28211 TRUE FALSE 25015.60158 24224.84969 25343.02226 28592.22755 24813.26843 27258.25627 25142.98711 28209.18733 26550.20156 26300.24384 0.951154739 0.921088407 0.96360408 1.087146861 0.943461535 1.03642599 0.955998251 1.07258273 1.009504008 1 14.68278856 3.987014472 23.83381567 1.01648039 0.937677709 0.368798365 0.042785512 303.4145638 556898.2529 0.010223289 0.019621538 9705.423086 -3.987014472 -0.07880268 GEVQVSDKER ddPTM_BT-474_Pertuzumab_2h_R1 4 GEVQVSDKER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;; 178.67 2.00E-06 4263260000 3578210 3436320 2768270 2809000 2984290 2729730 3129450 3216390 3488400 3579650 FALSE TRUE 3438369.597 3338319.518 3268557.969 2953972.827 3080282.398 2784927.011 3167749.145 3149970.423 3092411.457 3337197.117 1.030316603 1.00033633 0.979432097 0.885165821 0.923014821 0.834510792 0.949224464 0.943897023 0.926649325 1 21.67020547 3.98734679 3.30143155 0.920408187 1.014169345 0.453369134 0.041249823 0.206523008 4.674943777 0.010708414 0.02375121 9712.852425 -3.98734679 0.093761158 VMEMADGIEVEDLPQFTTR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMEMADGIEVEDLPQFTTR 19 0 Q96HQ2 Q96HQ2 CDKN2AIPNL CDKN2AIP N-terminal-like protein 0 113.76 0.00011667 0 28832 26957 23764 32532 28799 29314 25747 32499 34238 32236 FALSE TRUE 27705.21356 26188.21275 28058.68343 34210.98042 29725.34599 29906.74916 26062.09949 31827.88429 30351.44578 30052.62701 0.921889909 0.871411765 0.933651605 1.138369049 0.989109737 0.99514592 0.867215351 1.059071617 1.009943183 1 14.87520349 3.987368774 24.67390194 1.006476535 0.898121017 0.343730392 0.064278963 549.7642241 1073920.821 0.016442999 0.031688739 9713.344105 -3.987368774 -0.108355519 SPFNSPSPQDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPFNSPSPQDSPR 13 0 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 SPFNSPSPQDS(1)PR;SPFNSPSPQDS(1)PR 227.63 9.22E-12 702700000 409900 393500 345190 496420 404380 401880 457590 440570 465070 504290 TRUE FALSE 393880.6548 382277.7653 407573.5117 522040.2957 417387.2499 410006.2889 463190.1233 431472.0755 412277.2033 470133.9891 0.837805102 0.813125139 0.866930537 1.110407475 0.88780488 0.872105184 0.985230028 0.917764053 0.876935539 1 18.84271246 3.987381832 24.94426407 0.945008741 0.829105764 0.36578667 0.068038985 614.8968109 1215569.115 0.017064062 0.032838658 9713.636149 -3.987381832 -0.115902976 HLVYESDQNKDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLVYESDQNKDGK 13 1 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 226.04 6.87E-12 786250000 862740 844880 674010 627210 700860 803820 786410 611060 1056530 882360 FALSE TRUE 829023.167 820784.8496 795818.6003 659580.3833 723403.7984 820073.7911 796034.3208 598441.3975 936597.1437 822596.9713 1.007812083 0.997797072 0.967446548 0.801826905 0.879414615 0.996932665 0.967708791 0.727502554 1.138585694 1 19.64982623 3.987563439 22.92805883 0.908994784 0.99775898 0.043580895 0.108431904 431.2716572 795109.6032 0.027238254 0.052583491 9717.698907 -3.987563439 0.088764197 DREEDEEDAYERR ddPTM_BT-474_Pertuzumab_2h_R1 1 DREEDEEDAYERR 13 2 P49756 P49756 RBM25 RNA-binding protein 25 0 123.29 0.00012662 101190000 81983 89486 64640 61897 67864 71982 67181 65457 81389 81967 FALSE TRUE 78779.01372 86933.9469 76321.88591 65091.51159 70046.90719 73437.52536 68003.18117 64105.29008 72150.06193 76415.30208 1.030932439 1.137651027 0.99877752 0.851812527 0.916660738 0.96103167 0.889915754 0.838906454 0.944183429 1 16.22157394 3.987748382 4.883888929 0.905152636 1.082888017 0.629102787 0.052039009 0.099518779 6.6868457 0.013155997 0.026883895 9721.838056 -3.987748382 0.177735381 VLS(ph)TSTDLEAAVADALLLGDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLSTSTDLEAAVADALLLGDSR 22 0 Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460-4 CLASP1 CLIP-associating protein 1 1 VLS(0.316)T(0.316)S(0.316)T(0.052)DLEAAVADALLLGDSR 85.231 0.0033257 498950000 36558 39014 35317 55880 53639 40069 43196 48435 48521 52736 TRUE FALSE 35129.27294 37901.35892 41699.56752 58763.9735 55364.34715 40879.22263 43724.64557 47434.80032 43013.0995 49164.14375 0.714530352 0.770914655 0.84817032 1.195260794 1.126112303 0.831484483 0.889360461 0.964825108 0.874887595 1 15.5853189 3.987824675 13.53548167 0.978320891 0.759381688 0.45966599 0.105771152 1.404930072 1565.999811 0.029192637 0.056659834 9723.546045 -3.987824675 -0.218939203 KTQMAEVLPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTQMAEVLPSPR 12 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR 117.18 0.0004667 473170000 691810 682050 587320 765060 665380 715280 778160 795430 670780 802260 TRUE FALSE 664773.3004 662598.6018 693461.7889 804544.8383 686782.552 729743.4517 787683.3549 779004.0925 594635.8665 747922.2156 0.888826788 0.885919134 0.927184371 1.075706566 0.918253981 0.975694312 1.053162132 1.041557633 0.795050413 1 19.51252871 3.988596347 20.90368248 0.987812579 0.892167396 0.19397461 0.07564766 88.45996534 162164.5404 0.018895507 0.036816009 9740.83859 -3.988596347 -0.095645183 KVGYTPDWIFLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVGYTPDWIFLLR 13 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 86.641 0.014003 883240000 174320 192520 123670 88529 120940 129940 117260 97477 113170 115140 FALSE TRUE 167507.3817 187029.5181 146019.92 93097.9923 124830.1449 132567.4758 118695.063 95464.06589 100323.416 107341.4652 1.560509551 1.74237903 1.360330975 0.867306889 1.162925666 1.235007138 1.105770847 0.889349383 0.934619402 1 16.71184796 3.988761499 4.054166047 1.034745761 1.643094129 0.817625915 0.119034553 0.085508007 3.255857843 0.033355113 0.070501732 9744.543497 -3.988761499 0.608348368 DLEAEHVEVEDTTLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEAEHVEVEDTTLNR 16 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ; 179.25 2.17E-12 559830000 465470 464470 403360 516020 536480 531450 514630 427060 572660 599040 FALSE TRUE 447278.9178 451223.7704 476256.1247 542651.854 553736.3664 542196.2831 520928.1959 418241.0618 507654.0376 558466.4872 0.800905566 0.807969289 0.852792666 0.971682037 0.991530162 0.970866284 0.93278327 0.748909865 0.909014326 1 19.09111118 3.988879663 4.528371682 0.915852469 0.807977773 0.352253872 0.068774736 0.277267776 14.62443148 0.020920143 0.04333503 9747.195196 -3.988879663 -0.107874696 S(ph)PSSLSANIISSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSSLSANIISSPK 14 0 K7EQL6;Q8NFA0 K7EQL6 USP32 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 32 1 S(0.799)PS(0.173)S(0.027)LSANIISSPK 120.32 0.00014311 22553000 48099 40797 37739 51537 48194 53060 43357 44746 49430 51022 TRUE FALSE 46219.2379 39633.5095 44559.2768 54196.83075 49744.20378 54132.90955 43887.61594 43821.97946 43818.91363 47566.23449 0.971681664 0.833227812 0.936783777 1.139397123 1.045788137 1.138053288 0.922663238 0.921283342 0.921218888 1 15.5376502 3.989428121 24.82135115 1.007587058 0.898092484 0.237219561 0.082252573 700.9077744 1645653.337 0.022919082 0.045009587 9759.512409 -3.989428121 -0.109494573 KPPPGER ddPTM_BT-474_Pertuzumab_2h_R1 3 KPPPGER 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;; 77.282 0.061682 586730000 895230 871510 750610 957980 887900 986160 911320 933990 911730 1071320 FALSE TRUE 860243.4219 846655.3881 886261.9242 1007421.463 916460.1099 1006100.831 922473.0068 914702.7801 808234.2327 998758.5422 0.861312705 0.847707782 0.887363549 1.008673688 0.917599271 1.007351415 0.923619642 0.915839757 0.809238869 1 19.92977641 3.989557384 21.71077907 0.937249464 0.857766466 0.282621125 0.056110673 112.4403376 233781.4813 0.014103775 0.027716098 9762.417671 -3.989557384 -0.079482998 MPLDDLDREDEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MPLDDLDREDEVR 13 1 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 ; 132.31 0.00010972 954730000 1143880 1165860 972820 1236310 1116080 1212730 1180500 1260120 1191890 1200790 FALSE TRUE 1099175.905 1132610.814 1148630.214 1300116.107 1151979.727 1237252.232 1194947.312 1234098.082 1056591.644 1119459.424 0.98188097 1.011747983 1.026057926 1.161378501 1.029050006 1.105222936 1.067432447 1.102405371 0.943840948 1 20.09437081 3.98965137 24.01875035 1.068102217 1.002336551 0.141951052 0.057763677 449.865752 1044134.032 0.013790735 0.02716521 9764.530574 -3.98965137 -0.065765666 AEEWHGRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 AEEWHGRPK 9 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 0 ; 102.06 0.0021904 370060000 602580 596080 517370 687650 643910 640320 653470 628290 716450 693950 FALSE TRUE 579030.5074 579080.382 610870.2678 723139.6989 664621.9499 653267.7091 661467.3613 615315.5919 635121.5996 646948.1484 0.895018417 0.895095509 0.944233737 1.117770722 1.02731873 1.009768265 1.022442622 0.951104959 0.98171948 1 19.30329056 3.989836393 19.51740379 1.012174765 0.901208185 0.597317002 0.040462346 19.65834019 37756.86353 0.011227702 0.02209786 9768.691461 -3.989836393 -0.110966579 SCELFSIIDVDADQEPSQS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCELFSIIDVDADQEPSQSPPR 22 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 SCELFSIIDVDADQEPS(0.111)QS(0.889)PPR 92.833 0.0012967 13686000 6479.3 8058 7359.4 15890 9265.9 9715 11911 10557 8120.3 12886 TRUE FALSE 6226.081793 7828.19373 8689.407289 16710.0848 9563.946089 9911.443956 12056.77038 10338.99426 7198.517587 12013.21974 0.518269201 0.651631611 0.723320432 1.390974706 0.796118467 0.825044756 1.003625226 0.860634741 0.599216342 1 13.55233525 3.989874266 24.32731637 0.922118772 0.610581624 0.339048431 0.193929644 388.0016221 932195.0135 0.048792849 0.096284305 9769.543395 -3.989874266 -0.311537148 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.068)NHDGADET(0.466)S(0.466)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.123)NHDGADET(0.438)S(0.438)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 193.13 1.04E-28 2179690000 631322 588825 467161 389792 518760 549148 495259 489849 611846 525256 TRUE FALSE 606649.2383 572032.2875 551587.3846 409909.2118 535446.3865 560252.1488 501320.1278 479733.447 542391.8071 489679.9433 1.238868871 1.168175857 1.126424295 0.837096184 1.093461952 1.144119045 1.023771005 0.97968776 1.107645544 1 18.90147958 3.990034468 20.04533754 1.026547212 1.189467833 0.436793398 0.081591317 32.31192153 65003.0059 0.020920573 0.04125292 9773.147829 -3.990034468 0.162920621 SPDEATAADQES(ph)EDDLSASR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPDEATAADQESEDDLSASR 20 0 C9JME2;Q9Y4F1;Q9Y4F1-2;M0QXT1 C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 SPDEATAADQES(1)EDDLSASR 90.654 0.0019993 138390000 44788 48738 42297 68606 42087 50229 61649 58520 64376 54905 TRUE FALSE 43037.63544 47348.03996 49941.00879 72146.76388 43440.76658 51244.66479 62403.4789 57311.54155 57068.30637 51186.23545 0.840804858 0.925015086 0.975672627 1.409495409 0.848680631 1.001141505 1.219145701 1.119667056 1.114915091 1 15.64346829 3.990164547 24.27597972 1.107214728 0.89976831 0.285944367 0.140647433 394.903185 974717.8321 0.034964167 0.069206674 9776.075499 -3.990164547 -0.207446418 EMLMEDVGS(ph)EEEQEEEDEAPFQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EMLMEDVGSEEEQEEEDEAPFQEK 24 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK 157.08 1.03E-08 208134000 172574 156692 173767 220619 179182 189985 241614 250680 295640 266210 TRUE FALSE 165829.6173 152223.2976 205170.5623 232005.173 184945.5518 193826.6269 244570.9444 245503.3704 262080.1866 248179.3596 0.668184564 0.613360022 0.826702763 0.934828639 0.745209239 0.780994145 0.985460454 0.989217519 1.056011213 1 17.92102361 3.990569551 0.30874429 1.057057209 0.448367595 0.69289387 0.081107928 2.778718849 0.306903498 0.101703951 0.616584366 9785.19649 -3.990569551 -0.608689614 IKEWVDKYDPGALVIPFSGALELK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKEWVDKYDPGALVIPFSGALELK 24 2 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 146.64 1.08E-07 131490000 313140 289610 229800 182960 214610 254210 247070 272010 307330 276640 FALSE TRUE 300902.1426 281350.6064 271329.9719 192402.5875 221513.1256 259350.3004 250093.7166 266392.8984 272443.1868 257902.9264 1.16672636 1.090916688 1.052062401 0.746027159 0.858901171 1.005612088 0.969720352 1.032919254 1.056378811 1 17.97646862 3.991235284 22.44482375 0.953862791 1.114488808 0.397633891 0.08792913 119.9686028 307230.4729 0.024465386 0.04886327 9800.207799 -3.991235284 0.160626017 EWDRDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EWDRDK 6 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 94.163 0.040853 1592590000 1310260 1278860 957860 832980 893810 779600 1105750 1047590 1162500 1108520 FALSE TRUE 1259053.591 1242388.165 1130966.609 875970.1976 922560.2104 795364.0461 1119282.499 1025956.9 1030537.874 1033438.953 1.218314432 1.202188249 1.094371957 0.847626456 0.892708957 0.769628476 1.083065909 0.992760044 0.997192791 1 19.97902174 3.991689503 3.761717756 0.943257891 1.205225602 0.628902398 0.084245147 0.148858719 4.64997255 0.023642755 0.050977096 9810.46298 -3.991689503 0.26196771 IEALQNHENESVYK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEALQNHENESVYK 14 0 P52292 P52292 KPNA2 Importin subunit alpha-1 0 171.08 3.07E-06 590480000 283230 272610 371310 391570 378640 340690 419930 461420 613780 623560 FALSE TRUE 272161.0585 264835.4297 438413.9767 411778.9746 390819.2995 347578.9852 425069.229 451891.5158 544106.2676 581325.7258 0.468173085 0.455571495 0.754162352 0.708344662 0.672289703 0.597907455 0.731206637 0.777346496 0.935974865 1 19.14898723 3.991775239 0.123923034 1.186342043 6.44E-16 0.753250405 0.083016925 15.08257336 0.407796416 0.924176832 3.369980066 9812.399884 -3.991775239 -1.186342043 down SAEDWWWDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEDWWWDR 9 0 Q8N531-2;Q8N531 Q8N531-2 FBXL6 F-box/LRR-repeat protein 6 0 108.98 0.0058716 51996000 68600 67789 56916 67750 65506 61967 74609 69544 71713 76564 FALSE TRUE 65919.03616 65855.72409 67201.98729 71246.58562 67613.05998 63220.0152 75522.08726 68107.8921 63572.44089 71378.25208 0.923517097 0.922630103 0.941491075 0.99815537 0.94725015 0.885704166 1.05805459 0.954182683 0.890641603 1 16.12319695 3.991800592 13.43993492 0.962396943 0.925312511 0.096372933 0.04814662 2.240115669 3685.691099 0.012061489 0.023930948 9812.972726 -3.991800592 -0.037084432 LISKPVASDSTYFAWCPDGEHILTATCAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LISKPVASDSTYFAWCPDGEHILTATCAPR 30 1 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;Q9BY44-2;H7C5R5 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 0 ; 258.11 2.01E-58 567370000 519610 487110 430090 557690 533240 534310 507590 523160 605840 606900 FALSE TRUE 499303.0667 473218.0997 507816.8303 586472.4477 550392.1489 545114.1143 513802.0383 512356.5632 537067.5831 565794.1224 0.88248189 0.836378607 0.897529349 1.036547437 0.972778131 0.963449588 0.908107769 0.905552997 0.949227929 1 19.10991766 3.992112934 24.1544095 0.953690724 0.861311145 0.539222587 0.038670588 204.0732529 624992.9778 0.010727153 0.02164202 9820.032693 -3.992112934 -0.092379579 NIYAFMGT(ph)PVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 NIYAFMGTPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NIYAFMGT(1)PVQK;NIYAFMGT(1)PVQK 117.08 0.0086322 166447000 569380 438680 377390 279700 277430 257470 183510 425660 283910 257906 TRUE FALSE 547128.0001 426169.2759 445592.768 294135.3505 286353.7879 262676.2198 185755.8503 416869.9723 251681.727 240437.7969 2.275549049 1.772472055 1.85325591 1.223332414 1.190968274 1.092491377 0.772573417 1.733795508 1.046764403 1 17.87530418 3.992225618 1.375314849 1.174928537 2.154816738 0.687971858 0.254141488 0.308774941 1.05473231 0.078778972 0.28774914 9822.580983 -3.992225618 0.979888201 IFYYFSNS(ph)PSKR ddPTM_BT-474_Pertuzumab_2h_R1 1 IFYYFSNSPSKR 12 1 Q08999;Q08999-2 Q08999 RBL2 Retinoblastoma-like protein 2 1 IFYYFSNS(0.969)PS(0.031)KR 113.53 0.00070811 198000000 132270 134270 101610 100360 102490 101730 121130 117270 114640 117370 TRUE FALSE 127100.7422 130440.7511 119973.1873 105539.5916 105786.6839 103787.0503 122612.4252 114848.3335 101626.5478 109420.4254 1.161581503 1.19210605 1.096442341 0.964532822 0.966791013 0.948516239 1.120562498 1.049605987 0.928771274 1 16.73952254 3.992423289 3.761712191 1.006437063 1.174558719 0.649500228 0.053282398 0.148180749 4.631255451 0.015102332 0.032592907 9827.052785 -3.992423289 0.168121657 SPPVRPNESLSGS(ph)WK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPVRPNESLSGSWK 15 1 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 SPPVRPNESLSGS(1)WK;SPPVRPNESLS(0.008)GS(0.992)WK 136.68 1.29E-05 945140000 526660 565680 425590 449410 442900 509010 461290 465310 595450 496240 TRUE FALSE 506077.5449 549547.3603 502503.5802 472604.104 457146.2807 519302.531 466935.405 455701.1859 527857.0123 462629.2228 1.093916078 1.187878615 1.086190745 1.021561286 0.988148302 1.122502655 1.009308064 0.985024645 1.140993665 1 18.81949687 3.992435936 4.724186145 1.034982816 1.14131719 0.358103209 0.054903501 0.17761074 10.79248011 0.013692531 0.028339764 9827.338954 -3.992435936 0.106334374 RPPSAFFLFCSEYRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPPSAFFLFCSEYRPK 16 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 236.02 5.73E-20 8781700000 5843900 5570200 3636000 2504000 2616400 2875400 2728600 3005000 3014600 3083500 FALSE TRUE 5615513.927 5411343.35 4293106.082 2633231.74 2700558.882 2933542.558 2761993.423 2942945.7 2672395.246 2874651.799 1.953458826 1.882434371 1.493435165 0.916017634 0.939438607 1.020486224 0.960809732 1.023757278 0.929641373 1 21.45495578 3.993030103 2.42186784 0.97247515 1.935874784 0.985326905 0.046917941 0.031583061 0.366722712 0.01351496 0.033826889 9840.79314 -3.993030103 0.963399634 NS(ph)PQALRR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSPQALRR 8 1 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 NS(1)PQALRR;NS(1)PQALRR 108.9 0.0022792 486370000 225916 272879 182575 177979 179528 180389 193414 209291 218568 192449 TRUE FALSE 217086.953 265096.7581 215570.3639 187164.5175 185302.6812 184036.5892 195781.0584 204969.0677 193757.077 179414.2578 1.209976039 1.477567955 1.201523037 1.043197569 1.032820264 1.025763456 1.091223522 1.142434666 1.079942471 1 17.45293502 3.993520579 4.82269804 1.071324163 1.345888145 0.716886884 0.071628242 0.088265099 5.752567388 0.017883793 0.036975206 9851.913251 -3.993520579 0.274563982 KHDNEGSGSK ddPTM_BT-474_Pertuzumab_2h_R1 5 KHDNEGSGSK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 139.86 2.62E-05 386900000 321911.6 333497.5 255724.4 230818.6 292489.1 288563.6 340614.2 216115.5 372212.7 298582.8 FALSE TRUE 309330.9388 323986.4778 301939.4876 242731.1756 301897.2775 294398.5537 344782.7385 211652.6394 329960.6747 278359.521 1.111264086 1.163913764 1.084710473 0.872006011 1.084558834 1.057619846 1.238623839 0.760357105 1.185375925 1 18.0865899 3.994140949 24.00696133 1.016191014 1.134269788 0.096553978 0.131301517 322.9283176 1323208.277 0.03247621 0.066731695 9865.996324 -3.994140949 0.118078774 LFDANKDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LFDANKDR 8 1 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ;;;;; 117.01 0.0019704 4812390000 20316810 20961500 13634740 11177240 12087290 9536480 13328270 13378000 14497020 11522830 FALSE TRUE 19522806.6 20363698.54 16098840.82 11754098.7 12476088.66 9729314.16 13491385.36 13101739.62 12851379.07 10742378.46 1.817363508 1.895641512 1.498629087 1.094180282 1.16138979 0.9056946 1.255903002 1.219631171 1.196325294 1 23.35681012 3.994825742 2.738278807 1.13439601 1.860292288 0.890846374 0.103843153 0.081289164 1.221720569 0.028621936 0.068130061 9881.565234 -3.994825742 0.725896278 RGS(ph)ISSMSSVSSVLDEKDDDRIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGSISSMSSVSSVLDEKDDDRIR 23 3 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 1 RGS(0.997)IS(0.002)SMSSVSSVLDEKDDDRIR;RGS(0.939)IS(0.055)S(0.005)MSSVSSVLDEKDDDRIR 173.4 2.15E-11 991220000 150823 143706 107065 63885 119136 113804 103569 118820 148286 102367 TRUE FALSE 144928.6704 139607.6456 126414.0271 67182.11251 122968.1176 116105.1949 104836.5084 116366.3255 131453.1949 95433.59191 1.518633717 1.462877408 1.324628201 0.703967137 1.28852027 1.216607198 1.098528372 1.219343453 1.377431073 1 16.54220955 3.994904695 22.05876506 1.140823843 1.466505629 0.411439868 0.174613919 47.87055844 207263.3482 0.043458775 0.08941395 9883.361826 -3.994904695 0.325681786 DVDGLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVDGLDR 7 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 ; 82.305 0.057811 1112680000 1112190 1233970 1013670 1272360 1064470 1292520 1273200 1484130 1477340 1497440 FALSE TRUE 1068724.385 1198778.384 1196862.718 1338026.652 1098709.644 1318655.64 1288781.802 1453482.197 1309638.557 1396017.055 0.765552528 0.85871328 0.857341043 0.958460104 0.787031677 0.944584191 0.923184855 1.041163639 0.938125041 1 20.41288514 3.995053974 0.284795708 1.02218638 0.687925206 0.567314273 0.055479301 3.869831757 0.361741512 0.071696823 0.440045416 9886.759601 -3.995053974 -0.334261174 (ac)MEDSMDMDMS(ph)PLRPQNYLFGCELK ddPTM_BT-474_Pertuzumab_2h_R1 21 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.002)MDMDMS(0.998)PLRPQNYLFGCELK;MEDS(0.001)MDMDMS(0.998)PLRPQNY(0.001)LFGCELK;MEDS(0.001)MDMDMS(0.999)PLRPQNYLFGCELK;MEDS(0.003)MDMDMS(0.997)PLRPQNYLFGCELK;MEDS(0.091)MDMDMS(0.908)PLRPQNY(0.001)LFGCELK;MEDS(0.431)MDMDMS(0.569)PLRPQNYLFGCELK;MEDS(0.182)MDMDMS(0.795)PLRPQNY(0.023)LFGCELK;MEDS(0.158)MDMDMS(0.84)PLRPQNY(0.002)LFGCELK;MEDS(0.065)MDMDMS(0.93)PLRPQNY(0.004)LFGCELK;MEDSMDMDMS(1)PLRPQNYLFGCELK;MEDS(0.002)MDMDMS(0.934)PLRPQNY(0.064)LFGCELK;MEDS(0.201)MDMDMS(0.721)PLRPQNY(0.078)LFGCELK;MEDS(0.008)MDMDMS(0.991)PLRPQNY(0.001)LFGCELK;MEDS(0.398)MDMDMS(0.594)PLRPQNY(0.008)LFGCELK;MEDS(0.02)MDMDMS(0.979)PLRPQNYLFGCELK;MEDS(0.028)MDMDMS(0.972)PLRPQNYLFGCELK;MEDS(0.001)MDMDMS(0.998)PLRPQNY(0.001)LFGCELK;MEDS(0.001)MDMDMS(0.999)PLRPQNY(0.001)LFGCELK;MEDSMDMDMS(0.998)PLRPQNY(0.001)LFGCELK;MEDSMDMDMS(1)PLRPQNYLFGCELK;MEDSMDMDMS(1)PLRPQNYLFGCELK 120.85 2.50E-44 8453816000 3623261 3671974 2920461 3057771 3307940 3376113 3109899 3557662 3844299 3600089 TRUE FALSE 3481659.954 3567252.897 3448253.268 3215582.928 3414342.894 3444380.318 3147958.874 3484195.036 3407910.294 3356251.765 1.037365549 1.062868088 1.027411979 0.958087519 1.017308335 1.026258028 0.937938836 1.03812088 1.015391732 1 21.67841951 3.995448707 22.00998657 1.000378296 1.048872699 0.333150594 0.029363101 45.95814177 222278.6694 0.007197972 0.014859754 9895.749806 -3.995448707 0.048494403 LKGELESSDQVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKGELESSDQVR 12 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 147.73 5.53E-05 1983620000 2126810 2555390 1807980 2636980 2467320 2455880 2713410 3152100 2939670 2683970 FALSE TRUE 2043691.914 2482512.779 2134722.204 2773074.854 2546683.589 2505539.576 2746617.523 3087008.033 2605970.986 2502182.321 0.816763789 0.992139045 0.853144148 1.108262508 1.017784982 1.001341731 1.097688805 1.233726259 1.041479257 1 21.25475548 3.995762334 0.609280222 1.114038396 0.80032641 0.455461013 0.084298253 1.423727724 0.724549129 0.047278513 0.280810759 9902.898643 -3.995762334 -0.313711986 AQQELVPPQQQAS(ph)PPQLPK ddPTM_BT-474_Pertuzumab_2h_R1 4 AQQELVPPQQQASPPQLPK 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AQQELVPPQQQAS(1)PPQLPK;AQQELVPPQQQAS(1)PPQLPK;AQQELVPPQQQAS(1)PPQLPK;AQQELVPPQQQAS(1)PPQLPK 151.91 3.93E-08 2996360000 2390100 2350750 2216030 2478250 2601620 2847430 2868230 3085710 3225440 3295530 TRUE FALSE 2296692.25 2283708.912 2616515.916 2606152.779 2685303.47 2905006.986 2903332.257 3021989.01 2859301.573 3072320.818 0.747543107 0.743317201 0.851641502 0.848268437 0.874030946 0.945541549 0.944996447 0.983617659 0.930665039 1 21.55089744 3.995944958 0.431203593 0.989723494 0.640619298 0.922505361 0.023916726 0.667137682 0.154707989 0.019087967 0.11311015 9907.063749 -3.995944958 -0.349104196 LTVNYEQCASGVHGPEGFHYK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTVNYEQCASGVHGPEGFHYK 21 0 P19525-2;P19525;C9JZT2 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 122 1.66E-05 304840000 151700 131210 126740 156410 134750 225230 189870 96153 199630 168500 FALSE TRUE 145771.3963 127468.0193 149644.7373 164482.3388 139084.3561 229784.3049 192193.6859 94167.40695 176968.8393 157087.3449 0.92796397 0.811446774 0.952621215 1.047075682 0.885395041 1.4627805 1.223482935 0.5994589 1.12656331 1 17.26120744 3.996038669 4.332236897 1.026680565 0.869865907 0.098757204 0.212015739 0.561953405 26.09797114 0.059473698 0.125467564 9909.201717 -3.996038669 -0.156814657 TDGALLVNAMFFKPHWDEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TDGALLVNAMFFKPHWDEK 19 1 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5 P50454 SERPINH1 Serpin H1 0 ;; 227.95 6.91E-20 3944950000 3937340 3998460 3064450 2760090 3217870 3371340 3265190 3369600 4583810 3895230 FALSE TRUE 3783464.4 3884427.836 3618264.283 2902538.576 3321375.711 3439510.805 3305150.372 3300016.582 4063475.106 3631402.603 1.041874122 1.069676998 0.996382026 0.799288565 0.914626131 0.947157664 0.910158067 0.908744346 1.118982264 1 21.79209546 3.996175317 20.85550281 0.931836568 1.050089512 0.249873893 0.076957159 22.41886694 122279.2061 0.018964778 0.039261349 9912.32007 -3.996175317 0.118252944 ELEELLLEASQESGQETL ddPTM_BT-474_Pertuzumab_2h_R1 3 ELEELLLEASQESGQETL 18 0 O75864 O75864 PPP1R37 Protein phosphatase 1 regulatory subunit 37 0 ;; 157.52 8.85E-09 41446700 86272 87556 78723.7 99908 97328 101299 103462 111191 112289 120966 FALSE TRUE 82900.39486 85058.98861 92950.82379 105064.2639 100458.6435 103347.3352 104728.1989 108894.867 99542.42347 112772.8651 0.735109415 0.754250489 0.824230401 0.931644893 0.890805101 0.916420232 0.928664877 0.965612312 0.882680629 1 16.78306045 3.997444052 1.562541431 0.932855625 0.728237433 0.84665258 0.03230257 0.146640118 0.668259421 0.008982211 0.029805097 9941.319968 -3.997444052 -0.204618192 AAPTRGS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAPTRGSPTK 10 1 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 AAPTRGS(0.813)PT(0.187)K 79.089 0.016988 73310000 174250 175280 124150 107700 117230 116360 124110 134360 132270 118410 TRUE FALSE 167440.1174 170281.186 146586.6667 113258.4099 121000.8094 118712.8789 125628.8953 131585.419 117255.2641 110389.9852 1.516805324 1.542541977 1.327898236 1.025984465 1.096121257 1.075395369 1.138046128 1.192005043 1.062191139 1 16.75224977 3.997501073 3.166174894 1.101777754 1.527833449 0.914143446 0.055090914 0.067324534 1.390976616 0.01537794 0.034929184 9942.625305 -3.997501073 0.426055695 PLS(ph)MS(ph)YS(ph)FDLSDVTTPESTK ddPTM_BT-474_Pertuzumab_2h_R1 1 PLSMSYSFDLSDVTTPESTK 20 0 Q08AE8 Q08AE8 SPIRE1 Protein spire homolog 1 3 PLS(0.587)MS(0.587)Y(0.549)S(0.587)FDLS(0.587)DVT(0.05)T(0.05)PES(0.001)TK 48.883 0.086165 47669000 5268.4 8253.8 9763.5 18714 17144 19858 27088 10560 20976 28925 TRUE FALSE 5062.505103 8018.409705 11527.98164 19679.83178 17695.45233 20259.54237 27419.51105 10341.93231 18594.89242 26965.88399 0.187737406 0.297353861 0.427502456 0.729804808 0.656216289 0.751302734 1.016822258 0.383519128 0.689571031 1 14.71884771 3.997943302 1.790683252 0.719230944 0.209229134 0.594880131 0.170893206 0.27910087 1.715996324 0.048940907 0.146859158 9952.754746 -3.997943302 -0.510001809 SGS(ph)MDNTSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSMDNTSAR 10 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.005)GS(0.995)MDNTSAR 131.17 0.00026975 103930000 167470 162820 126350 125650 125640 136180 124620 149520 150910 154650 TRUE FALSE 160925.0873 158176.533 149184.2556 132134.8116 129681.3247 138933.6529 126145.1368 146432.3597 133779.3295 144175.4178 1.116175627 1.097111668 1.034741275 0.916486414 0.899469041 0.963643144 0.874942059 1.015654139 0.927892782 1 17.13746568 3.998068243 2.857558874 0.942900779 1.107231411 0.723932275 0.041121805 0.131484907 2.166606432 0.010788397 0.025365924 9955.618435 -3.998068243 0.164330631 RGS(ph)EDFETR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSEDFETR 9 1 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 1 RGS(0.99)EDFET(0.01)R 53.08 0.076387 0 58240 57419 50509 66475 68958 60838 58722 62514 65513 67011 TRUE FALSE 55963.91641 55781.46634 59637.09987 69905.78272 71176.0967 62068.18604 59440.6574 61223.06405 58076.23889 62472.28528 0.895819901 0.892899405 0.954616909 1.118988723 1.139322763 0.993531544 0.951472435 0.980003593 0.929632054 1 15.93092869 3.998828816 7.202957554 1.015104952 0.900807107 0.377672879 0.062930316 0.146638024 50.79022216 0.018067461 0.036705786 9973.068816 -3.998828816 -0.114297845 AKDPFAHLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKDPFAHLPK 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 80.763 0.013839 4421600000 16405800 15129400 10309400 8090100 7034300 6195600 6342200 8032600 13691600 16052300 FALSE TRUE 15764643.2 14697924.33 12172537.91 8507631.031 7260564.648 6320879.277 6419817.741 7866724.003 12137386.97 14965063.42 1.053429762 0.98214915 0.813397015 0.568499497 0.48516765 0.422375709 0.428987005 0.525672614 0.811048148 1 23.83509506 3.998930226 2.133808547 0.559411249 1.034283043 0.463845565 0.173777814 0.239528209 2.137234493 0.045659537 0.122837468 9975.397853 -3.998930226 0.474871793 LLNTWTNRYPDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLNTWTNRYPDAK 13 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 88.768 0.0070745 280240000 274010 292540 196280 132020 205790 181780 178800 201390 221120 195020 FALSE TRUE 263301.3863 284197.0456 231752.1622 138833.568 212409.4222 185455.7161 180988.2079 197231.2261 196019.3846 181811.1217 1.44821386 1.563144449 1.274686389 0.763614276 1.168297188 1.020046048 0.995473798 1.084813868 1.078148481 1 17.47208093 3.999020327 5.359077228 1.026347583 1.492068235 0.789056436 0.102329173 0.065491449 6.230337008 0.024692853 0.050960609 9977.467613 -3.999020327 0.465720652 ENSSPSVTSANLDHTKPCWYWDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSSPSVTSANLDHTKPCWYWDKK 24 2 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 0 144.22 1.39E-07 536660000 237770 246980 190160 165430 221800 241710 186660 236260 250940 219880 FALSE TRUE 228477.6855 239936.3722 224526.1421 173967.8621 228934.3984 246597.5418 188944.4009 231381.1484 222454.3432 204987.3318 1.114594173 1.17049366 1.09531716 0.848676163 1.116822179 1.202989178 0.921736964 1.128758282 1.0852102 1 17.64517523 3.999547602 24.99805959 1.049317316 1.140134327 0.141103667 0.098138126 33.95409642 1876698.205 0.024381006 0.051782045 9989.588578 -3.999547602 0.090817011 S(ph)QS(ph)T(ph)PHQEKVITESK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSTPHQEKVITESK 15 1 Q9ULI3-2;Q9ULI3 Q9ULI3-2 HEG1 Protein HEG homolog 1 3 S(1)QS(1)T(1)PHQEKVIT(0.001)ESK;S(1)QS(1)T(1)PHQEKVITESK 110.37 0.00077585 1121690000 569690 521420 581960 589720 653980 689040 768390 742580 865780 755390 TRUE FALSE 547425.885 506549.6121 687133.1176 620155.5199 675015.8606 702972.8609 777793.7867 727245.4635 767500.284 704226.7625 0.7773432 0.719299009 0.975727073 0.880619075 0.958520602 0.998219463 1.104464965 1.03268649 1.089848221 1 19.42568053 3.999591094 0.5867424 1.063230286 0.664606161 0.766123369 0.057937308 0.783615824 0.365157127 0.03197272 0.191516039 9990.589012 -3.999591094 -0.398624125 SATLSGS(ph)ATNLASLTAALAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SATLSGS(0.994)AT(0.006)NLASLTAALAK;S(0.211)AT(0.211)LS(0.136)GS(0.437)AT(0.006)NLASLTAALAK;SATLSGS(1)ATNLASLTAALAK 408.69 2.26E-151 564460000 920549 838514 602208 535020 531414 460902 356760 713516 560938 506106 TRUE FALSE 884572.9274 814600.4017 711040.3816 562632.4463 548507.4139 470221.7542 361126.1356 698781.6453 497262.6699 471826.9898 1.874782381 1.726481145 1.506993871 1.192454986 1.162518096 0.99659783 0.765378292 1.481012448 1.053908913 1 18.84789842 3.999663347 1.415855598 1.09755804 1.878272605 0.751170198 0.168499218 0.25458158 0.927582482 0.053150566 0.191731112 9992.251277 -3.999663347 0.780714565 ENPLLPEEEEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENPLLPEEEEQR 12 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 194.96 1.99E-06 90606000 78613 83838 69562 88796 85729 96265 88028 95698 89560 103150 FALSE TRUE 75540.71705 81447.02233 82133.4008 93378.7722 88486.55114 98211.54426 89105.313 93721.80286 79393.52427 96163.55862 0.78554411 0.846963481 0.854101096 0.971041146 0.920167186 1.021296899 0.926601659 0.974608305 0.825609258 1 16.55320266 4.000074396 1.884281039 0.950139797 0.805974146 0.522341785 0.052819717 0.267478722 1.834777509 0.01388822 0.040377514 10001.71317 -4.000074396 -0.144165651 S(ph)APELPEGILK ddPTM_BT-474_Pertuzumab_2h_R1 4 SAPELPEGILK 11 0 Q3KR16-2;Q3KR16;Q3KR16-3 Q3KR16-2 PLEKHG6 Pleckstrin homology domain-containing family G member 6 1 S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK 150.68 3.54E-05 218348000 1088500 1077950 787573 664164 742782 825550 722330 871760 884890 906840 TRUE FALSE 1045960.217 1047207.921 929904.9606 698441.5836 766674.2576 842243.1866 731170.0906 853757.8514 784440.997 845418.9191 1.23720938 1.238685222 1.099933938 0.826148514 0.906857228 0.996243599 0.864861283 1.009863669 0.927872537 1 19.68930687 4.000344919 3.821299505 0.935640843 1.232652561 0.825223714 0.056792296 0.080191023 2.620362596 0.014578131 0.031671263 10007.94521 -4.000344919 0.297011718 DSEAWVPDSEER ddPTM_BT-474_Pertuzumab_2h_R1 2 DSEAWVPDSEER 12 0 Q96F63;M0QXS4 Q96F63 CCDC97 Coiled-coil domain-containing protein 97 0 ; 185.61 2.98E-05 124732000 178167 184483 160168 213504 195224 218972 191993 201667 240050 243760 FALSE TRUE 171204.0367 179221.7255 189113.9205 224522.967 201503.5573 223399.7639 194342.6678 197502.506 212800.5304 227249.9181 0.75337337 0.788654742 0.832184769 0.988000211 0.886704642 0.983057621 0.855193566 0.869098249 0.936416313 1 17.79392025 4.000727037 3.682123048 0.918605761 0.773858254 0.632630542 0.049409095 0.149225921 4.429816045 0.012866268 0.02819217 10016.75466 -4.000727037 -0.144747506 QIEAQEKPR ddPTM_BT-474_Pertuzumab_2h_R1 3 QIEAQEKPR 9 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;; 130.98 0.00031547 962680000 780360 731480 725710 795800 851230 877170 917400 999700 1058430 1043230 FALSE TRUE 749862.6685 710618.9066 856861.9403 836871.3334 878610.586 894906.9784 928627.4156 979055.8456 938281.4637 972571.1029 0.77101064 0.730660108 0.881027554 0.860473163 0.903389565 0.920145556 0.954816993 1.006667628 0.964743309 1 19.8914442 4.001177828 0.415721312 1.006443941 0.64609064 0.887814301 0.029242412 0.857118072 0.182254979 0.024392895 0.145575632 10027.15729 -4.001177828 -0.360353301 YDDPPDWQEILTYFR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDDPPDWQEILTYFR 15 0 P61221;D6R9I9;D6RGF4;H0Y990 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ; 150.69 7.30E-06 566400000 107231 103308 93485 121346 121879 106547 120943 124452 133260 118734 FALSE TRUE 103040.294 100361.757 110379.8191 127608.6816 125799.3487 108701.4533 122423.1366 121882.0227 118132.8835 110692.0404 0.930873562 0.906675463 0.997179369 1.152826175 1.13648053 0.982016891 1.105979582 1.10109112 1.067221121 1 16.75619196 4.00134276 4.421925142 1.083376667 0.922467876 0.606817478 0.051442606 0.11858181 5.862389873 0.013064098 0.027689837 10030.96605 -4.00134276 -0.160908791 EEFYVHYVGFNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEFYVHYVGFNR 12 0 Q9H7Z6;Q9H7Z6-2 Q9H7Z6 KAT8 Histone acetyltransferase KAT8 0 111.63 0.0013611 83447000 164190 156560 144920 181980 183580 175970 198040 178920 210360 210140 FALSE TRUE 157773.2733 152095.0621 171110.2677 191372.0096 189485.0174 179528.234 200463.6728 175225.2395 186480.8147 195907.0306 0.805347683 0.77636347 0.873425865 0.976851157 0.967219077 0.916395054 1.023259207 0.894430582 0.951884239 1 17.57980965 4.001460932 3.233254361 0.955206185 0.791622811 0.780568539 0.036324519 0.103570129 2.247054773 0.009206365 0.020875109 10033.69585 -4.001460932 -0.163583374 LEPVSPPS(ph)PPHTDPELELVPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEPVSPPSPPHTDPELELVPPR 22 0 C9J0Q5;C9JE98;C9J330;H7C1Y3;H0YGK8;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LEPVSPPS(1)PPHTDPELELVPPR;LEPVSPPS(1)PPHTDPELELVPPR;LEPVS(0.001)PPS(0.999)PPHTDPELELVPPR;LEPVSPPS(1)PPHTDPELELVPPR 247.34 3.10E-31 392688000 537535 513577 464612 563218 554571 579133 601609 579782 639570 669731 TRUE FALSE 516527.5379 498930.2868 548577.7236 592285.7485 572409.2799 590843.4661 608971.6709 567809.2991 566968.6949 624369.5228 0.827278589 0.799094556 0.878610668 0.948614125 0.916779662 0.946304143 0.975338559 0.90941226 0.908065936 1 19.25204059 4.001492707 3.021317169 0.938833571 0.81324236 0.769848973 0.028522317 0.111965435 2.085210077 0.007291087 0.016881874 10034.42999 -4.001492707 -0.125591211 LDVGNFSWGSECCTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDVGNFSWGSECCTR 15 0 P62241 P62241 RPS8 40S ribosomal protein S8 0 ;;; 319.58 3.83E-56 1045680000 217248 227931 200636 272622 237280 281152 281004 332227 222049 284239 FALSE TRUE 208757.708 221430.631 236895.3883 286692.0541 244912.3267 286837.0861 284443.011 325366.3964 196842.9284 264987.2394 0.787802871 0.835627525 0.89398791 1.081908905 0.924241965 1.082456222 1.073421542 1.227856848 0.742839274 1 18.01556336 4.002056138 1.708724692 1.04482594 0.792112203 0.309905678 0.121447899 0.415635552 2.307101634 0.034392919 0.107346234 10047.45658 -4.002056138 -0.252713737 GIS(ph)PVVSEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GISPVVSEHR 10 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 GIS(1)PVVSEHR 69.03 0.030294 0 168900 172150 162170 240880 201750 272730 198030 225030 220440 230280 TRUE FALSE 162299.2013 167240.4506 191477.7265 253311.8457 208239.472 278244.7875 200453.5504 220383.0519 195416.5754 214682.9305 0.755994903 0.779011401 0.891909413 1.17993473 0.969986163 1.296073176 0.933719089 1.026551349 0.910256698 1 17.71184796 4.002253313 4.069516519 1.045875574 0.77414356 0.511147631 0.110010161 0.158367578 6.13925828 0.027591007 0.059360514 10052.01929 -4.002253313 -0.271732014 DMLLANKVPAAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DMLLANKVPAAAR 13 1 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;Q8NHW5;F8VWV4;F8VPE8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ; 129.76 0.00013673 2710000000 3856200 4048000 2955400 2711300 2996700 2505900 3360100 3504900 3618200 3792000 FALSE TRUE 3705495.441 3932555.003 3489506.523 2851230.518 3093091.577 2556571.015 3401221.909 3432522.59 3207477.105 3535164.462 1.048181911 1.112410765 0.987084635 0.806534052 0.874949839 0.723183049 0.962111366 0.97096546 0.907306333 1 21.7533459 4.002613368 5.080362762 0.892287458 1.076213825 0.483406628 0.078343588 0.14976221 11.67277659 0.021179471 0.044223213 10060.35644 -4.002613368 0.183926367 SGPPS(ph)PPSTATSFGGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGPPSPPSTATSFGGPR 17 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 SGPPS(0.993)PPS(0.006)T(0.001)ATSFGGPR;SGPPS(0.981)PPS(0.016)T(0.002)ATSFGGPR 161.19 3.14E-09 192225000 134550 132622 123056 167248 169911 149021 163516 165639 170040 182809 TRUE FALSE 129291.6372 128839.7504 145294.9566 175879.6893 175376.3416 152034.3067 165517.1577 162218.4968 150737.7721 170427.1836 0.758632716 0.755981221 0.85253393 1.031993169 1.029039722 0.892077798 0.97118989 0.951834639 0.88447024 1 17.37879594 4.003123523 3.751702999 0.962801474 0.760590466 0.760717061 0.047294813 0.103135158 3.212674272 0.012581592 0.027536794 10072.18103 -4.003123523 -0.202211009 NGESAS(ph)PERDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NGESASPERDR 11 1 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 NGES(0.002)AS(0.998)PERDR 73.156 0.026846 33867000 26548 25423 23452 32477 27302 25472 31727 31816 31653 35196 TRUE FALSE 25510.47481 24697.96093 27690.29809 34153.14186 28180.19363 25987.06129 32115.28452 31158.98848 28059.88414 32812.14357 0.777470535 0.752707938 0.843903966 1.040868963 0.858834278 0.791995233 0.97876216 0.949617583 0.855167663 1 15.00194223 4.003212859 6.425857474 0.921612732 0.771657478 0.453260696 0.070715611 0.126782375 25.02703891 0.018070323 0.03722517 10074.25313 -4.003212859 -0.149955254 DLIIEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLIIEQR 7 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 83.265 0.052128 113230000 47612 49051 43799 56349 55353 53669 59145 66065 57441 64370 FALSE TRUE 45751.2704 47652.11351 51714.4536 59257.17864 57133.47952 54754.22395 59868.8342 64700.73466 50920.53849 60010.16257 0.762392042 0.794067396 0.861761598 0.987452393 0.952063402 0.912415858 0.997644926 1.078162963 0.848531921 1 15.87291922 4.003293409 1.893405255 0.978101135 0.766452916 0.6369101 0.057882843 0.21948727 1.521124998 0.016772559 0.048820984 10076.12181 -4.003293409 -0.211648219 TGENFR ddPTM_BT-474_Pertuzumab_2h_R1 4 TGENFR 6 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ;;; 132.96 0.034132 2046280000 2244880 2207160 1893810 2157210 2139100 2234240 2313190 2421160 2472220 2408990 FALSE TRUE 2157147.608 2144213.958 2236063.595 2268543.867 2207906.094 2279417.864 2341499.511 2371162.2 2191583.95 2245826.962 0.960513719 0.954754749 0.995652663 1.010115163 0.983114965 1.01495703 1.042600143 1.055808057 0.975847199 1 21.09881534 4.003766413 0.717881241 1.024709756 0.941738622 0.416623662 0.02384275 1.147406463 0.843570659 0.011393637 0.066530028 10087.10202 -4.003766413 -0.082971134 S(ph)PAPGLASGDRPPSVSSVHSEGDCNRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPAPGLASGDRPPSVSSVHSEGDCNRR 27 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.957)PAPGLAS(0.043)GDRPPSVSSVHSEGDCNRR 87.749 0.0040064 433510000 20817 16688 17460 24116 20171 23907 20739 24905 25897 22459 TRUE FALSE 20003.44863 16212.07458 20615.4104 25360.62965 20819.81853 24390.41592 20992.81009 24390.70305 22957.28113 20937.83193 0.955373445 0.774295765 0.984601007 1.211234752 0.994363629 1.16489692 1.002625781 1.164910633 1.096449776 1 14.35382444 4.003856631 7.442336954 1.095678225 0.867369408 0.548441783 0.082123682 0.075856934 29.40434123 0.018573852 0.038238251 10089.19767 -4.003856631 -0.228308816 IGTTPDIILDDLLETDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IGTTPDIILDDLLETDR 17 0 Q10570;A0A087X101 Q10570 CPSF1 Cleavage and polyadenylation specificity factor subunit 1 0 ;;; 236.92 7.79E-20 59369600 26707.9 25297.5 23494 30929.2 30705.3 28232.5 31265.9 31168.8 30073.5 33549.1 FALSE TRUE 25664.12574 24576.04007 27739.88842 32525.45972 31692.96386 28803.38049 31648.54144 30525.15339 26659.68236 31276.78957 0.820548595 0.785759677 0.886916106 1.03992322 1.01330617 0.920918703 1.01188587 0.975968244 0.85237912 1 14.93280481 4.004771168 4.346013355 0.974342378 0.806500699 0.640026743 0.051431844 0.115963579 5.429243692 0.013113268 0.028007072 10110.46587 -4.004771168 -0.167841679 LKAEGSEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 LKAEGSEIR 9 1 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 ;;; 140.07 0.00010029 4948800000 6720190 8106120 5625310 5884660 5933660 5213870 7007850 6387190 7068260 6748810 FALSE TRUE 6457557.545 7874941.394 6641928.651 6188368.008 6124521.563 5319298.024 7093614.165 6255292.294 6265900.757 6291707.087 1.026360168 1.251638273 1.055663997 0.983575351 0.973427637 0.84544591 1.127454611 0.994212256 0.995898358 1 22.58502008 4.005733578 24.45715611 0.992673843 1.142662256 0.354232909 0.0810947 116.5819978 497275.1091 0.019498462 0.041916639 10132.89582 -4.005733578 0.149988413 TDLQGSASPSKVEGVHT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 TDLQGSAS(0.002)PS(0.315)KVEGVHT(0.683)PR 100.62 0.00088985 325830000 114290 129230 85866 80617 75783 94995 81886 95031 108340 81504 TRUE FALSE 109823.4204 125544.4869 101383.8963 84777.65303 78220.62902 96915.86399 82888.14536 93068.57664 96041.6974 75983.66148 1.445355729 1.652256347 1.334285481 1.115735296 1.029440112 1.275482941 1.090868007 1.224849854 1.263978275 1 16.21340161 4.006208476 3.938461078 1.15599624 1.54615735 0.724551536 0.099937832 0.101430642 3.589319612 0.024707032 0.053758426 10143.98215 -4.006208476 0.390161109 DRDYSVLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DRDYSVLEK 9 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 0 ; 82.914 0.015601 587060000 640460 656230 484580 502180 459790 283710 674480 543990 668620 680260 FALSE TRUE 615430.1151 637514.9629 572154.3854 528097.57 474579.5629 289446.8106 682734.488 532756.4164 592721.0607 634185.3843 0.970426204 1.005250166 0.902187908 0.832717977 0.748329392 0.456407255 1.076553489 0.840064167 0.934617977 1 19.2745451 4.007311232 2.987443035 0.830671309 0.987649944 0.117779002 0.157410414 0.52281581 9.507082298 0.042152607 0.098602898 10169.77236 -4.007311232 0.156978634 SSSFSDT(ph)LEESSPIAAIFDTENLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.179)S(0.179)S(0.179)FS(0.179)DT(0.285)LEESSPIAAIFDTENLEK;S(0.18)S(0.18)S(0.18)FS(0.18)DT(0.279)LEESSPIAAIFDTENLEK 206.86 1.31E-24 1793063000 69322 70642 59020 66691 72486 70820 69337 78584 78166 71371 TRUE FALSE 66612.8196 68627.35933 69686.22689 70132.9305 74817.57802 72252.02892 70185.56695 76961.21294 69292.92338 66536.9786 1.001139832 1.031416827 1.047330798 1.054044412 1.124451089 1.085892844 1.054835498 1.156668285 1.041419746 1 16.02186874 4.007343845 1.289078557 1.087904583 1.006152652 0.20872702 0.042304625 0.645364855 1.886738749 0.012501212 0.049453543 10170.53609 -4.007343845 -0.081751931 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.575)PPRDLPT(0.422)IPGVT(0.003)SPSSDEPPMEAS(0.344)QS(0.232)HLRNS(0.424)PEDKR;T(0.924)PPRDLPT(0.076)IPGVTSPSSDEPPMEAS(0.055)QS(0.158)HLRNS(0.787)PEDKR;T(1)PPRDLPTIPGVTSPSSDEPPMEAS(0.025)QS(0.349)HLRNS(0.626)PEDKR 203.42 1.53E-30 1859680000 247658 257536 200052 186041 223584 294191 222045 217401 249115 258880 TRUE FALSE 237979.2516 250191.3254 236205.8465 195642.5983 230775.7824 300139.7436 224762.4531 212911.5934 220836.5096 241345.827 0.986050824 1.03665072 0.978702841 0.810631784 0.95620374 1.24360859 0.93128792 0.882184689 0.91502104 1 17.88074236 4.007463122 23.27019455 0.957441223 1.010432344 0.029692836 0.10709175 319.5284333 996244.2784 0.028589666 0.061504119 10173.32977 -4.007463122 0.052991121 VVDYSQFQESDDADEDYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;; 370.98 1.24E-107 1266620000 402928 393611 372433 547301 469940 436280 538983 511407 465652 531839 FALSE TRUE 387181.1283 382385.5997 439739.9278 575547.2702 485056.0469 445101.8805 545579.2352 500846.2667 412793.1371 495817.0708 0.780895115 0.771223143 0.886899532 1.160805676 0.978296383 0.897713908 1.100363959 1.010143249 0.83255128 1 18.91944842 4.007565278 5.389858454 1.001564188 0.78475762 0.510759428 0.086906198 0.126334512 11.99706745 0.02195864 0.046032979 10175.72304 -4.007565278 -0.216806568 LGIAVIHGEAQDAESDLVDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGIAVIHGEAQDAESDLVDGR 21 0 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 0 121.63 2.94E-05 41525000 22904 24579 22868 32782 30548 29467 35531 31010 37942 36657 FALSE TRUE 22008.88636 23878.03099 27000.7563 34473.88295 31530.60416 30062.84293 35965.83901 30369.63266 33634.98323 34174.18874 0.644020741 0.698715372 0.790092093 1.008769607 0.922643823 0.879694414 1.052427002 0.888671649 0.984221849 1 15.06061947 4.007699024 2.571318085 0.954374428 0.665973858 0.828120047 0.053995143 0.103029781 1.358905516 0.013723602 0.034007189 10178.85725 -4.007699024 -0.28840057 NHET(ph)DGGSAHGDDDDDGPHFEPVVPLPDKIEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NHETDGGSAHGDDDDDGPHFEPVVPLPDKIEVK 33 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.5)DGGS(0.5)AHGDDDDDGPHFEPVVPLPDKIEVK 92.991 0.00012737 39193000 77194 63138 64968 42314 60828 61332 59661 30554 78674 58617 TRUE FALSE 74177.17314 61337.36606 76709.16281 44497.83061 62784.58786 62572.17506 60391.14916 29923.04922 69743.25735 54646.81838 1.357392348 1.12243252 1.403726055 0.814280354 1.148915705 1.145028694 1.105117388 0.547571663 1.276254673 1 15.73784988 4.007704163 0.505984644 0.925027375 1.429018206 0.181145429 0.21993122 3.355664349 1.112293864 0.154060404 0.932681698 10178.9777 -4.007704163 0.50399083 VIFLEDDDVAAVVDGR ddPTM_BT-474_Pertuzumab_2h_R1 6 VIFLEDDDVAAVVDGR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;;;; 262.07 1.69E-26 959098000 425018 447439 391557 525259 508136 531532 526757 504088 529165 600967 FALSE TRUE 408407.8267 434678.4778 462320.06 552367.6799 524480.6559 542279.9412 533203.6097 493678.4066 469096.4076 560262.9698 0.72895738 0.775847238 0.825184038 0.985907886 0.936133002 0.967902522 0.951702394 0.881154803 0.83727898 1 19.09574462 4.008308378 2.966071279 0.931121069 0.751796033 0.715592531 0.047495668 0.142223629 2.546138868 0.013030359 0.030588007 10193.14913 -4.008308378 -0.179325036 LDAENAIVHMGGQWLGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDAENAIVHMGGQWLGGR 18 0 E7ETJ9;Q01085;Q01085-2 E7ETJ9 TIAL1 Nucleolysin TIAR 0 ; 155.11 2.12E-08 1074200000 711880 704080 606260 739470 694120 774560 798340 763760 738740 795540 FALSE TRUE 684058.9426 684000.3278 715824.6682 777634.1353 716447.0002 790222.1339 808110.3237 747988.0891 654881.3323 741657.3672 0.922338229 0.922259197 0.965168958 1.04850861 0.966008068 1.065481405 1.089600615 1.008535912 0.882997138 1 19.50039332 4.008657613 3.684599435 1.014243886 0.923561735 0.287227822 0.054196263 0.266492542 7.918906264 0.014357236 0.031761199 10201.34917 -4.008657613 -0.090682152 RLDPNKYPVPENWLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDPNKYPVPENWLHK 16 2 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 104.28 0.00082505 3832800000 3872500 3877600 2883700 2831200 2823200 3069600 2893500 3251600 3646000 3268300 FALSE TRUE 3721158.419 3767014.645 3404848.738 2977318.571 2914010.792 3131669.415 2928911.519 3184453.324 3232121.365 3046935.13 1.221279174 1.236329125 1.117466763 0.977151939 0.956374412 1.027809678 0.96126481 1.045133286 1.060777873 1 21.53892735 4.009055398 3.029174429 1.005221624 1.228765419 0.881350152 0.033148866 0.079571808 1.492177854 0.009219264 0.021509205 10210.69722 -4.009055398 0.223543795 ALTAHLYSLLQTQHALGDAFADLSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALTAHLYSLLQTQHALGDAFADLSQK 26 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 172.61 2.68E-12 300140000 561510 476170 441710 527590 551050 547690 541860 456050 636660 595230 FALSE TRUE 539565.5684 462590.0978 521536.8228 554818.9831 568775.0237 558764.6671 548491.4448 446632.4081 564389.0259 554914.5419 0.972339933 0.833624032 0.939850704 0.999827795 1.024977687 1.006938231 0.98842507 0.80486701 1.017073771 1 19.08190608 4.009240946 24.74127683 0.964026013 0.898920814 0.142473652 0.068211043 394.478008 1056134.491 0.018664298 0.040233091 10215.06058 -4.009240946 -0.065105199 S(ph)PLTGYVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLTGYVR 8 0 Q9NP66;H0YNS8;H0YKM5 Q9NP66 HMG20A High mobility group protein 20A 1 S(0.999)PLT(0.001)GYVR 72.638 0.047871 136130000 124340 122950 137050 225190 211370 201630 201310 205100 229920 218380 TRUE FALSE 119480.6553 119443.5864 161817.9837 236812.0829 218168.908 205707.0967 203773.692 200864.6133 203820.4455 203588.9281 0.586872068 0.586689991 0.794827033 1.163187434 1.071614798 1.010404145 1.000907534 0.986618551 1.001137181 1 17.63529958 4.009406489 3.526423593 1.028322105 0.591623528 0.923899921 0.051756741 0.058310773 1.553843681 0.014661598 0.032790147 10218.95506 -4.009406489 -0.436698578 LMDVGLIAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LMDVGLIAIR 10 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 76.221 0.085254 72578000 219760 234240 175840 174680 199540 165580 228950 195120 222370 230730 FALSE TRUE 211171.5362 227559.7045 207618.1995 183695.2557 205958.3853 168928.141 231751.9586 191090.7038 197127.4899 215102.4516 0.981725381 1.057913115 0.965206105 0.853989596 0.957489716 0.785338055 1.077402684 0.888370646 0.916435347 1 17.71466444 4.009510935 10.20583092 0.92271508 1.017886731 0.192943429 0.076704025 0.309824854 292.957939 0.017888222 0.037629598 10221.41298 -4.009510935 0.095171652 FLSHLVDGVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLSHLVDGVKR 11 1 E7ESC6;Q9UIA9 E7ESC6 XPO7 Exportin-7 0 118.28 0.00048156 114470000 217630 229190 171300 164050 168840 221780 167290 209070 228170 192190 FALSE TRUE 209124.779 222653.7256 202257.7205 172516.6402 174270.8919 226264.5436 169337.3451 204752.6314 202269.0982 179172.8001 1.167168113 1.242675928 1.128841657 0.962850612 0.972641449 1.26282864 0.945106316 1.142766264 1.128905158 1 17.45099212 4.009743981 7.882434318 1.065947281 1.200828114 0.273936759 0.094764921 0.179545262 76.06689316 0.023186444 0.048448123 10226.89933 -4.009743981 0.134880833 KRVS(ph)VELTNSLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRVSVELTNSLFK 13 2 P14923 P14923 JUP Junction plakoglobin 1 KRVS(1)VELTNSLFK 147.37 3.37E-05 1454200000 597730 668840 439810 470280 320620 398540 431320 631800 526530 467200 TRUE FALSE 574370.0508 649765.3381 519293.4505 494551.2072 330933.0335 406598.7519 436598.6232 618753.1092 466760.5218 435556.1279 1.318705016 1.491806214 1.192253805 1.135447708 0.759794232 0.933516316 1.002393481 1.420604762 1.071642647 1 18.73249912 4.00999792 3.000601885 1.067437267 1.404242922 0.424832692 0.163899648 0.286476086 5.261477322 0.049667076 0.116359663 10232.88092 -4.00999792 0.336805655 TVWDWELMNDIKPIWQRPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVWDWELMNDIKPIWQRPSK 20 2 P14625 P14625 HSP90B1 Endoplasmin 0 ; 268.25 2.89E-37 4940400000 3256400 3726000 2743720 2889500 2869890 3168900 3131090 3192150 3710600 3710700 FALSE TRUE 3129136.288 3619738.128 3239571.238 3038627.441 2962202.618 3232977.329 3169409.216 3126230.987 3289388.244 3459370.984 0.904539092 1.046357313 0.936462511 0.878375709 0.856283594 0.93455641 0.916180783 0.903699257 0.950863108 1 21.72207831 4.010388315 24.99008201 0.912824072 0.979438648 0.154684615 0.049076473 279.3890241 672085.1654 0.011354896 0.024492339 10242.08357 -4.010388315 0.066614575 MVNHFIAEFKR ddPTM_BT-474_Pertuzumab_2h_R1 2 MVNHFIAEFKR 11 1 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 170.52 1.01E-05 539950000 1094350 1286420 712270 529510 544910 298870 808720 575630 753650 733870 FALSE TRUE 1051581.592 1249732.561 840993.0334 556838.0746 562437.525 304913.3562 818617.3573 563743.0393 668098.8116 684164.3312 1.537030716 1.826655533 1.229226656 0.813895214 0.822079578 0.445672687 1.196521537 0.823987767 0.97651804 1 19.38398337 4.010410012 3.351329282 0.862620585 1.678180346 0.737480887 0.19327313 0.108908549 2.569600821 0.04934001 0.111904092 10242.59527 -4.010410012 0.815559761 RPS(ph)TSSASGQWSPTPEWVLSWK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 RPS(0.421)T(0.056)S(0.079)S(0.112)AS(0.332)GQWS(0.001)PTPEWVLSWK 177.73 3.85E-17 2755400000 306360 326630 247380 262230 246920 262400 299230 303140 307040 303640 TRUE FALSE 294387.1125 317314.8322 292087.0689 275763.7217 254862.406 267705.9078 302892.0662 296880.0531 272186.1064 283074.1923 1.039964506 1.120959949 1.031839273 0.974174719 0.900337837 0.945709341 1.070009469 1.048771174 0.961536282 1 18.1108207 4.010551538 5.598239185 0.991914375 1.080484868 0.367642434 0.049455393 0.197152085 21.14828491 0.014293732 0.030057168 10245.93362 -4.010551538 0.088570493 QSPS(ph)PS(ph)TRPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 QS(0.128)PS(0.882)PS(0.976)T(0.014)RPIR;QS(0.435)PS(0.612)PS(0.923)T(0.03)RPIR 122.1 0.0047574 2942700000 1509630 1506620 1286250 1550730 1558650 1593010 1644790 1632670 1628370 1591860 TRUE FALSE 1450631.991 1463652.673 1518703.987 1630763.361 1608785.393 1625221.754 1664919.432 1598954.794 1443524.264 1484041.904 0.977487217 0.986261014 1.023356539 1.098866114 1.084056581 1.095131983 1.121881685 1.077432375 0.972697779 1 20.5011004 4.010667117 3.231557765 1.073167752 0.982311801 0.349858841 0.043879805 0.231320668 5.016866608 0.011383973 0.026087298 10248.66073 -4.010667117 -0.090855952 QWIQISDAVYHMVYEQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 QWIQISDAVYHMVYEQAK 18 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 205.95 9.07E-16 245370000 296630 298790 193566 205945 203340 167294 171555 177657 243870 250260 FALSE TRUE 285037.3717 290268.8017 228547.6821 216573.8461 209880.6158 170676.7993 173654.5414 173988.3209 216186.9 233309.6673 1.221712649 1.244135338 0.979589422 0.928267777 0.899579594 0.731546195 0.744309241 0.74573987 0.926609268 1 17.83188656 4.010825464 1.143736866 0.808821192 1.286597531 0.732044668 0.089421726 0.290605402 0.639069596 0.028163425 0.124189274 10252.39815 -4.010825464 0.477776339 MMDKVEFVHMLNATMCATTR ddPTM_BT-474_Pertuzumab_2h_R1 1 MMDKVEFVHMLNATMCATTR 20 1 P49591 P49591 SARS "Serine--tRNA ligase, cytoplasmic" 0 134.32 5.52E-06 264960000 207160 196130 202490 250070 251870 273020 255770 273760 342050 295210 FALSE TRUE 199063.9582 190536.5644 239084.4474 262976.1427 259971.6273 278540.6515 258900.1898 268106.7603 303221.918 275215.1638 0.723303017 0.692318555 0.868718293 0.955529263 0.944612294 1.012083228 0.940719204 0.974171469 1.101763122 1 18.07020044 4.011086365 1.71205406 0.989096352 0.692392044 0.860823358 0.045122219 0.130324944 0.725824857 0.012602376 0.039796853 10258.55911 -4.011086365 -0.296704309 QNLFQEAEEFLYR ddPTM_BT-474_Pertuzumab_2h_R1 6 QNLFQEAEEFLYR 13 0 A0A087X1Z3;Q9UL46 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;; 292.08 3.37E-40 750094000 399979 399786 295379 299897 288821 299099 299663 323641 345974 423609 FALSE TRUE 384347.3785 388384.4947 348760.556 315374.7201 298111.1898 305146.9867 303330.3654 316957.7003 306700.482 394917.5851 0.973234399 0.983457079 0.883122376 0.798583634 0.754869373 0.772685234 0.768085233 0.802592015 0.776618954 1 18.59119208 4.011214982 2.522614514 0.79629801 0.980852303 0.488393021 0.067322715 0.194612643 2.466884601 0.016337215 0.040991208 10261.59764 -4.011214982 0.184554293 HFNALGGWGELQNSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HFNALGGWGELQNSVK 16 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 127.83 6.41E-05 223600000 1035700 1052400 829360 909770 882030 974380 954010 990170 1040300 1043500 FALSE TRUE 995223.699 1022386.582 979243.801 956723.3387 910401.296 994082.6312 965685.4598 969722.6435 922209.5053 972822.8155 1.023026684 1.050948401 1.006600365 0.983450761 0.935834647 1.021853739 0.992663252 0.99681322 0.947972735 1 19.89181754 4.011686732 3.709751491 0.983951704 1.036679439 0.438911031 0.024436138 0.199394669 6.019894951 0.006267262 0.013895082 10272.75031 -4.011686732 0.052727735 RDYDDMS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 11 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 RDYDDMS(1)PR;RDY(0.001)DDMS(0.999)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDY(0.001)DDMS(0.999)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR 167.18 6.38E-05 6938450000 6152069 6561805 5055265 5471811 5707732 5779817 5823501 6249424 6118068 6415502 TRUE FALSE 5911639.342 6374668.746 5968863.839 5754211.821 5891326.383 5896688.86 5894770.747 6120371.211 5423570.57 5980974.335 0.988407408 1.065824461 0.997975163 0.962086025 0.985011146 0.985907735 0.985587033 1.023306717 0.906803853 1 22.5119491 4.011895146 24.8915989 0.982633389 1.028311925 0.24574547 0.033395945 282.7678245 591705.4568 0.00788068 0.017005019 10277.68129 -4.011895146 0.045678536 KPEMFETAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPEMFETAIK 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 98.803 0.008223 565270000 704670 698230 550440 558820 595280 578730 653860 632000 679250 729430 FALSE TRUE 677130.7173 678317.164 649916.7525 587660.7672 614427.7218 590432.3171 661862.1343 618948.9791 602144.3876 680025.0564 0.995743776 0.997488486 0.955724714 0.864175168 0.903536886 0.868250826 0.973290805 0.910185549 0.885473825 1 19.37522838 4.012334632 4.562136754 0.912046727 0.994224727 0.39246065 0.040683872 0.174288128 9.327782096 0.009944145 0.021333274 10288.08708 -4.012334632 0.082178 LQEKEDLQELNDR ddPTM_BT-474_Pertuzumab_2h_R1 10 LQEKEDLQELNDR 13 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;; 254.58 7.47E-24 48009030000 25403960 24775250 19676600 19572130 20964010 22353750 21617390 23954740 24982790 22026420 FALSE TRUE 24411145.16 24068684.13 23232599.32 20582249.97 21638336.42 22805758.14 21881950.09 23460066.25 22146848.42 20534550.95 1.188783977 1.172106669 1.131390668 1.002322867 1.053752598 1.110604181 1.065616197 1.142467946 1.078516324 1 24.29155006 4.013684145 4.596044291 1.075358452 1.176772677 0.548275263 0.041978521 0.158679143 8.653200535 0.011213892 0.024083108 10320.1057 -4.013684145 0.101414225 FFDDDLLVSTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 FFDDDLLVSTSR 12 0 O43924 O43924 PDE6D "Retinal rod rhodopsin-sensitive cGMP 3,5-cyclic phosphodiesterase subunit delta" 0 ; 285.28 5.09E-28 114521000 198035 208000 177509 229220 234010 236420 220970 235350 238870 226320 FALSE TRUE 190295.5733 202068.0437 209588.825 241050.0717 241537.1442 241200.5744 223674.297 230489.9403 211754.479 210991.1448 0.901912606 0.957708646 0.993353655 1.142465348 1.144773845 1.143178661 1.060112249 1.092415231 1.00361785 1 17.68682293 4.014793568 2.921294723 1.090796379 0.928768401 0.587826241 0.052179703 0.16907348 2.92954587 0.013820856 0.032850106 10346.50252 -4.014793568 -0.162027978 ALLLVGDVAQAADVAIEHR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALLLVGDVAQAADVAIEHR 19 0 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 ;; 155.92 2.11E-08 83167800 46559.3 54955.1 42768.1 56016.9 55933.2 63043.3 65439.5 59828.5 61616.6 61567.8 FALSE TRUE 44739.71108 53387.83435 50497.24704 58907.93892 57732.34218 64318.07872 66240.36818 58593.02057 54622.14189 57397.75807 0.77946792 0.930137973 0.879777342 1.026310799 1.005829219 1.120567787 1.154058458 1.020824202 0.951642429 1 15.80870677 4.015573412 1.073750667 1.055641702 0.80405253 0.624514005 0.063684183 0.464233568 0.875562448 0.021710751 0.101748181 10365.09798 -4.015573412 -0.251589171 LREAIAELER ddPTM_BT-474_Pertuzumab_2h_R1 2 LREAIAELER 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 193.73 4.93E-07 277010000 168036 199598 138180 142033 148771 157862 152036 156756 156571 156377 FALSE TRUE 161468.9673 193905.6605 163152.1998 149363.3402 153556.3543 161054.0778 153896.662 153518.9338 138797.7165 145785.4465 1.107579468 1.330075567 1.119125425 1.024542187 1.053303728 1.104733577 1.055638033 1.053047046 0.952068398 1 17.15348718 4.015872818 7.404839109 1.044380403 1.221076495 0.575746526 0.062920191 0.098290437 27.14453351 0.014750786 0.031170876 10372.24624 -4.015872818 0.176696092 KPSLVSDLPWEGAAPQSPSFSGSEDS(ph)GSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSLVSDLPWEGAAPQSPSFSGSEDSGSPK 30 1 Q13425;Q13425-2;H7BY41;H0YCS0 Q13425 SNTB2 Beta-2-syntrophin 1 KPSLVSDLPWEGAAPQS(0.011)PS(0.065)FS(0.065)GS(0.065)EDS(0.397)GS(0.397)PK 43.31 0.082699 74906000 15600 16514 14554 19619 17269 21906 17160 20089 26351 19731 TRUE FALSE 14990.33475 16043.03689 17184.23155 20631.53894 17824.47307 22348.95433 17370.00921 19674.15513 23359.74495 18394.6018 0.814931191 0.872160054 0.934199704 1.121608349 0.96900565 1.214973533 0.944299279 1.06956135 1.269923927 1 14.16699482 4.016455885 1.985263231 1.080084602 0.829022787 0.503374812 0.097965322 0.275104544 2.109136254 0.025828931 0.074220865 10386.18095 -4.016455885 -0.251061815 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR 31 2 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 282.46 3.06E-72 1094110000 92969 95226 82552 108446 116563 91070 90178 121787 103755 108519 FALSE TRUE 89335.6687 92510.24772 97470.98276 114042.9111 120312.3548 92911.4978 91281.62534 119272.0559 91977.16738 101168.9115 0.883034792 0.914413789 0.963447974 1.127252526 1.189222588 0.91837993 0.902269521 1.178939796 0.909144578 1 16.6264065 4.016569517 4.100665195 1.042210085 0.902565634 0.214238895 0.101382457 0.29901417 11.67498036 0.026650856 0.058353725 10388.89884 -4.016569517 -0.139644451 KLVWVPSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLVWVPSDK 9 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 113.93 0.0033898 0 9277800 9041400 7189100 7216400 7494200 7590400 7721100 8839100 9463100 9189400 FALSE TRUE 8915213.319 8783548.124 8488330.291 7588839.269 7735257.749 7743883.089 7815593.131 8656569.496 8388888.561 8566993.753 1.040646646 1.025277755 0.990817845 0.885822902 0.902913901 0.903920712 0.912291214 1.010455913 0.979210304 1 23.03035761 4.016614843 4.205420586 0.941344551 1.030446847 0.445996845 0.040868163 0.202357379 8.46569542 0.011719115 0.025562251 10389.98314 -4.016614843 0.089102296 TTSS(ph)YQNLVWSDHSQELHSPTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSSYQNLVWSDHSQELHSPTLK 23 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 T(0.019)T(0.019)S(0.11)S(0.851)YQNLVWSDHSQELHSPTLK 233.44 8.05E-37 156380000 289070 289650 165230 159750 154540 154000 116170 44308 165960 139510 TRUE FALSE 277772.8248 281389.4656 195090.7365 167994.7166 159510.9194 157113.9855 117591.7232 43393.02432 147120.9166 130060.8634 2.135714138 2.163521433 1.499995705 1.29166232 1.226432881 1.208003556 0.904128422 0.333636293 1.131169767 1 16.98882738 4.016734812 0.574858949 0.749076858 2.622836951 0.791291778 0.237647268 0.812351984 0.356968782 0.149609508 0.921699235 10392.85367 -4.016734812 1.873760093 up STFVLDEFKR ddPTM_BT-474_Pertuzumab_2h_R1 2 STFVLDEFKR 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 175.15 4.63E-06 4075800000 8555900 8016800 4897900 3752900 2799000 2043600 2891100 3809500 5663500 6944000 FALSE TRUE 8221525.969 7788168.713 5783059.483 3946587.619 2889032.377 2084922.992 2926482.147 3730832.494 5020603.223 6473676.695 1.269993291 1.203051848 0.893319169 0.609636194 0.446273812 0.322061649 0.452058743 0.576308127 0.775541236 1 22.62615389 4.017830164 1.989393863 0.550900563 1.268264662 0.663049545 0.181079123 0.182661677 1.406617513 0.049054556 0.141035319 10419.09898 -4.017830164 0.717364099 AKQEQEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 AKQEQEAK 8 1 P05455 P05455 SSB Lupus La protein 0 ;;; 138.08 0.00065725 460426000 946200 876210 684020 584900 693570 486500 868570 731230 780020 873900 FALSE TRUE 909221.4579 851221.3487 807637.6299 615086.7591 715879.3089 496337.3633 879199.8195 716129.845 691475.3997 814709.9746 1.116006292 1.04481518 0.991319187 0.754976345 0.878692211 0.609219696 1.079156813 0.878999727 0.848738105 1 19.63592705 4.017884307 3.412949993 0.863409361 1.07827944 0.3459482 0.120796123 0.255851653 6.288329936 0.030831402 0.07019167 10420.39801 -4.017884307 0.214870079 IIKPVLTQESATYIAEEYSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IIKPVLTQESATYIAEEYSR 20 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 221.51 7.10E-25 1374590000 592160 577210 526630 669080 679720 704770 638750 690420 697970 728540 FALSE TRUE 569017.7325 560748.5359 621803.7558 703611.299 701583.8111 719020.9323 646567.2136 676162.5857 618739.3717 679195.3369 0.837782154 0.825607164 0.915500626 1.035948365 1.032963233 1.058636438 0.951960619 0.995534788 0.910988839 1 19.37346703 4.017947862 3.387885442 0.998358084 0.83278006 0.730754519 0.040528551 0.11910368 2.877219919 0.011004016 0.025100919 10421.92304 -4.017947862 -0.165578024 LGLAVIHGEAQCTELDMDDGRHS(ph)PPMVK ddPTM_BT-474_Pertuzumab_2h_R1 19 LGLAVIHGEAQCTELDMDDGRHSPPMVK 28 1 C9J168;B4DP31;Q14558;Q14558-2;C9JUN4 C9J168 PRPSAP1 Phosphoribosyl pyrophosphate synthase-associated protein 1 1 LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK 285.51 2.00E-62 9208361000 3975320.8 4033443.7 3366258.9 3925998.6 4062186 4315031.4 4371600.3 3456914.4 4982250.3 4822317.2 TRUE FALSE 3819960.868 3918413.835 3974616.765 4128619.858 4192849.902 4402284.291 4425101.252 3385527.91 4416686.133 4495697.361 0.84969262 0.871591996 0.884093489 0.918349152 0.932636155 0.979221673 0.984296962 0.753059567 0.982425145 1 22.10011349 4.0179909 1.940620619 0.920215245 0.856815662 0.151596366 0.067902537 0.874020393 6.383372197 0.020282833 0.059266295 10422.9559 -4.0179909 -0.063399583 (ac)GSAS(ph)PGLSSVSPSHLLLPPDTVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 1 GS(0.025)AS(0.967)PGLS(0.003)S(0.004)VSPSHLLLPPDTVSR 119.06 7.58E-45 443370000 3461 0 2549 2697.5 4310.4 5071.8 3268.3 2102.5 4682.6 3353.4 TRUE FALSE 3325.740294 0 3009.661002 2836.718298 4449.047931 5174.355271 3308.298433 2059.08264 4151.050879 3126.271231 1.063804145 0 0.9626999 0.907380738 1.423116423 1.655120394 1.058225019 0.658638515 1.327796142 1 11.61022723 4.018769863 24.44091276 1.11689587 0.519263507 0.315903123 0.35568216 216.957442 282502.8583 0.091251003 0.197071022 10441.66757 -4.018769863 -0.597632362 VEETVKHDWDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VEETVKHDWDR 11 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3;A0A0B4J225 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ;; 185.59 2.64E-06 1129440000 1052300 1097140 732210 578280 763030 807320 619210 624890 834990 817340 FALSE TRUE 1011174.953 1065850.641 864536.6349 608125.1001 787573.5529 823644.5635 626788.0772 611985.8031 740205.4358 761980.8338 1.327034628 1.398789306 1.134591051 0.79808451 1.03358709 1.080925565 0.822577222 0.803151177 0.971422643 1 19.53939518 4.01893654 3.677658537 0.919343843 1.358406137 0.767624694 0.095184347 0.102681587 3.017782336 0.026603343 0.059599692 10445.67574 -4.01893654 0.439062294 EGPYSISVLYGDEEVPR ddPTM_BT-474_Pertuzumab_2h_R1 5 EGPYSISVLYGDEEVPR 17 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;;; 273.74 2.65E-35 597963000 394907 411651 342942 436594 405912 464933 430206 471603 496289 487467 FALSE TRUE 379473.5978 399911.1165 404919.2481 459126.6687 418968.5281 474334.2638 435470.9897 461864.2332 439952.3533 454450.4259 0.835016486 0.879988429 0.891008623 1.010289885 0.921923502 1.043753591 0.958236509 1.016313787 0.968097571 1 18.7937634 4.019546048 1.251458234 0.992143987 0.834022782 0.715478015 0.034588381 0.271558752 0.736668118 0.009667216 0.040047907 10460.34596 -4.019546048 -0.158121206 IINEPTAAAIAYGLDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 IINEPTAAAIAYGLDKR 17 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 269.49 4.03E-28 6344700000 1391380 1699070 1144690 1298050 1061650 1084150 1446490 1292450 1566200 1641180 FALSE TRUE 1337003.331 1650614.187 1351560.946 1365042.516 1095798.936 1106072.256 1464192.577 1265760.456 1388411.542 1530021.417 0.873846154 1.078817701 0.883360802 0.892172162 0.71619843 0.722912924 0.956975217 0.827282835 0.907445822 1 20.54512042 4.019780575 22.48301709 0.849545565 0.977521613 0.17493859 0.097298276 105.9578736 120428.0922 0.023648889 0.051068116 10465.99625 -4.019780575 0.127976048 QGPEECDAVALLSLINSCDHFVVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGPEECDAVALLSLINSCDHFVVDR 25 0 Q8TB03-2;Q8TB03 Q8TB03-2 CXorf38 Uncharacterized protein CXorf38 0 89.829 0.014121 22460000 20361 23851 17035 17553 20226 18261 18712 21793 22713 19545 FALSE TRUE 19565.26961 23170.79283 20113.60344 18458.91243 20876.58766 18630.24993 18941.00305 21342.96693 20134.71546 18221.19974 1.073764071 1.271639253 1.10385725 1.013045941 1.145730685 1.022449136 1.039503618 1.171326106 1.105015902 1 14.15333033 4.020057466 24.88573712 1.080852414 1.176463372 0.240606746 0.069885366 304.9662866 378372.7396 0.016788044 0.036258761 10472.67114 -4.020057466 0.095610958 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPK ddPTM_BT-474_Pertuzumab_2h_R1 5 RADDFPVRDDPSDVTDEDEGPAEPPPPPK 29 2 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 2 RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK 150.12 4.25E-08 3834181000 2358306 2239562 2097673 2645495 2455997 2461146 2767759 3121643 3233462 3229316 TRUE FALSE 2266140.794 2175691.885 2476769.174 2782029.314 2534996.374 2510912.058 2801631.663 3057179.981 2866412.95 3010591.551 0.752722764 0.722679197 0.82268522 0.924080622 0.842026004 0.834026143 0.930591751 1.015474843 0.952109544 1 21.52161556 4.020862464 0.299113638 1.02215545 0.586274308 0.773904016 0.045170692 2.431500042 0.248045805 0.060139989 0.376410583 10492.10104 -4.020862464 -0.435881142 RYLLS(ph)SAYVDSHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RYLLSSAYVDSHK 13 1 Q92552;Q92552-2;E5RJ73 Q92552 MRPS27 "28S ribosomal protein S27, mitochondrial" 1 RY(0.06)LLS(0.468)S(0.468)AY(0.004)VDSHK 46.156 0.094113 480830000 428140 451240 257050 342800 306180 357110 300840 297270 205110 299130 TRUE FALSE 411407.8155 438371.077 303504.653 360491.9491 316028.5578 364331.0089 304521.7699 291131.2706 181826.7727 278869.6587 1.47526919 1.571956874 1.08833874 1.292689749 1.133248268 1.306456251 1.091986024 1.043968971 0.652013466 1 18.08923145 4.021218988 0.301947876 0.869404164 1.811192836 0.596321178 0.15761941 3.468910909 0.360739896 0.186992792 1.169810985 10500.71783 -4.021218988 0.941788672 SDPEGENIHAGLLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDPEGENIHAGLLK 14 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;; 162.72 4.39E-06 1893260000 3166310 3139470 2917550 3407330 3431480 3233860 3806610 4191280 4307480 4400770 FALSE TRUE 3042567.105 3049935.389 3444816.186 3583182.71 3541856.671 3299250.865 3853196.432 4104728.603 3818512.929 4102701.928 0.741600818 0.743396777 0.839645737 0.873371445 0.863298561 0.804165382 0.939185078 1.000493985 0.930731259 1 21.96814291 4.021396956 0.266818823 1.021939688 0.584531316 0.790500052 0.04096489 2.843186538 0.231499178 0.06368077 0.400641743 10505.02175 -4.021396956 -0.437408372 EHYVDLK ddPTM_BT-474_Pertuzumab_2h_R1 6 EHYVDLK 7 0 Q32Q12;P22392-2;J3KPD9;E7ERL0;E5RHP0;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ;;;;; 127.12 0.003886 22446990000 16167400 16226000 11920300 11662500 12509900 14102200 11442200 9158830 15023700 15025100 FALSE TRUE 15535560.13 15763250.37 14074563.38 12264403.02 12912292.29 14387356.15 11582233.07 8969696.96 13318272.56 14007436.59 1.109093732 1.125348686 1.004792225 0.875563701 0.921816937 1.027122704 0.826863144 0.640352494 0.950800132 1 23.73968963 4.021644954 0.650933825 0.832629817 1.204321773 0.372090316 0.107736752 1.483907897 0.860520492 0.059035155 0.363380846 10511.02222 -4.021644954 0.371691956 FCLDNGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 FCLDNGAK 8 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 145.63 0.0013173 1174950000 2458370 2565460 1713480 2037680 1649600 1715360 1879730 2095000 2277080 1790800 FALSE TRUE 2362294.183 2492295.593 2023143.952 2142844.909 1702660.882 1750045.754 1902734.698 2051737.518 2018595.425 1669507.521 1.414964684 1.492832803 1.211820808 1.283519171 1.019858168 1.048240713 1.139698189 1.228947754 1.209096335 1 20.67099116 4.02165531 1.624593924 1.133015411 1.466977645 0.658396775 0.090333006 0.260321158 1.288896115 0.026599055 0.088812605 10511.27285 -4.02165531 0.333962234 ERSDS(ph)GGSSSEPFDR ddPTM_BT-474_Pertuzumab_2h_R1 3 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERS(0.003)DS(0.811)GGS(0.04)S(0.073)S(0.073)EPFDR;ERSDS(1)GGSSSEPFDR;ERSDS(0.644)GGS(0.014)S(0.34)S(0.002)EPFDR 280.69 2.67E-33 1913230000 558723 641191 539838 723354 767779 823270 742481 714913 765170 843675 TRUE FALSE 536887.4875 622904.8605 637398.7352 760686.3866 792475.3088 839917.0835 751567.7046 700149.7967 678311.1095 786532.1408 0.682600824 0.791963644 0.810391212 0.967139608 1.007556167 1.067873822 0.955546081 0.890173154 0.862407363 1 19.5851462 4.022141906 1.84298198 0.961630603 0.718244411 0.716627273 0.059680008 0.22139757 1.446729053 0.018742501 0.057035521 10523.0566 -4.022141906 -0.243386192 EDLDVLGLTFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDLDVLGLTFR 11 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 110.47 0.0041634 55082000 27076 26073 24667 30021 32339 32645 35537 26488 32399 40363 FALSE TRUE 26017.83999 25329.42357 29124.87561 31570.38741 33379.2133 33305.10427 35971.91244 25941.01354 28721.20135 37629.17806 0.691427273 0.673132523 0.773997124 0.838986899 0.887056668 0.885087211 0.955957964 0.689385601 0.763269432 1 15.19956416 4.023852116 2.561790377 0.84573442 0.680150149 0.410308525 0.084225774 0.312372814 4.09448452 0.02368704 0.059900632 10564.57707 -4.023852116 -0.16558427 RRDS(ph)GDNSAPSGQER ddPTM_BT-474_Pertuzumab_2h_R1 1 RRDSGDNSAPSGQER 15 2 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RRDS(0.986)GDNS(0.014)APSGQER 156.67 1.64E-06 138490000 41431 35389 34670 45179 44541 48507 39858 41567 46562 38899 TRUE FALSE 39811.83072 34379.74037 40935.64023 47510.6936 45973.70172 49487.84477 40345.79413 40708.62692 41276.47696 36264.33608 1.097823234 0.948031705 1.12881262 1.310121699 1.267738684 1.364642239 1.112547436 1.12255266 1.138211296 1 15.14626382 4.023993027 8.150094796 1.196224143 1.025929399 0.274272558 0.105827725 0.249442957 68.83706667 0.027209921 0.058220467 10568.00541 -4.023993027 -0.170294743 MFGIDRDAIAQAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MFGIDRDAIAQAVR 14 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 271.56 5.33E-33 1692920000 1260440 1070300 1335640 1896050 2318700 2294600 2131100 1403870 2180700 1309050 FALSE TRUE 1211180.611 1039776.092 1577019.859 1993905.368 2393283.091 2340998.384 2157181.039 1374879.594 1933156.078 1220386.878 0.992456272 0.852005303 1.292229446 1.633830554 1.961085567 1.918242835 1.767620645 1.12659323 1.58405184 1 20.21890714 4.025410464 3.250042555 1.586854337 0.924253764 0.436291704 0.292544717 0.227237818 4.976751413 0.081412748 0.189354175 10602.5533 -4.025410464 -0.662600573 TPVSGSLKS(ph)PVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPVSGSLKSPVPR 13 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 TPVSGSLKS(1)PVPR;TPVSGSLKS(1)PVPR 140.22 2.38E-05 845240000 880480 826420 732800 834940 907790 864080 854880 953740 910820 930890 TRUE FALSE 846069.8682 802851.3107 865233.261 878031.3535 936989.8898 881552.2896 865342.2772 934044.9357 807427.5321 867839.9911 0.974914589 0.925114444 0.996996301 1.011743366 1.07968047 1.015800492 0.997121919 1.076287041 0.93038756 1 19.72706954 4.025581701 3.609080712 1.023070836 0.950240981 0.265692721 0.041673061 0.24455155 6.822856751 0.010334056 0.023421533 10606.73457 -4.025581701 -0.072829855 HGEAQVK ddPTM_BT-474_Pertuzumab_2h_R1 6 HGEAQVK 7 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;;;;; 135.87 0.0030357 10918430000 21845900 19194500 14855300 16412100 16336100 16327100 16717800 11643620 17529100 15858200 FALSE TRUE 20992138.08 18647091.65 17539983.16 17259130.45 16861565.49 16657245.15 16922397.44 11403175.18 15539270.06 14784109.99 1.419912196 1.261292811 1.186407784 1.167410853 1.140519484 1.126699217 1.144634168 0.771312929 1.05107917 1 23.81754406 4.026004649 0.365832079 0.921778054 1.557246781 0.658551872 0.093839004 2.242228297 0.352130642 0.097601268 0.603157727 10617.06924 -4.026004649 0.635468727 MSCFSRPSMS(ph)PTPLDR ddPTM_BT-474_Pertuzumab_2h_R1 6 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPS(0.016)MS(0.858)PT(0.126)PLDR;MSCFS(0.027)RPS(0.02)MS(0.905)PT(0.047)PLDR;MSCFSRPSMS(0.914)PT(0.086)PLDR;MSCFSRPS(0.001)MS(0.997)PT(0.002)PLDR;MSCFSRPSMS(0.983)PT(0.016)PLDR;MSCFSRPS(0.024)MS(0.973)PT(0.002)PLDR 190.63 5.01E-10 5096890000 3554060 3923090 2679840 2830010 2772970 2979330 2856080 3005910 3006880 3057770 TRUE FALSE 3415163.406 3811207.314 3164146.701 2976067.155 2862165.098 3039574.094 2891033.561 2943836.908 2665551.588 2850664.514 1.198023615 1.336953996 1.109968109 1.04399067 1.004034352 1.066268612 1.014161276 1.032684447 0.935063237 1 21.44286683 4.026137942 3.350650631 1.019020219 1.266846818 0.821855435 0.046570188 0.08351892 1.95916272 0.011420574 0.026365269 10620.32831 -4.026137942 0.247826599 EQVEPTPEDEDDDIELR ddPTM_BT-474_Pertuzumab_2h_R1 5 EQVEPTPEDEDDDIELR 17 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ;;;; 492.5 6.88E-232 5755920000 1000827 1001336 877086 1121678 1058341 1091408 1101774 1191950 1119652 1104125 FALSE TRUE 961713.5744 972778.8777 1035594.951 1179567.936 1092383.499 1113477.018 1115257.84 1167335.816 992553.7989 1029341.63 0.934299698 0.945049582 1.006075068 1.145944069 1.061244846 1.081737088 1.083467147 1.134060628 0.964260815 1 19.97329045 4.026298103 3.853496419 1.077796843 0.94195756 0.47924164 0.05235584 0.15596459 5.096502862 0.012839679 0.028743673 10624.24564 -4.026298103 -0.135839283 SVDFEMPPPS(ph)PPLNLHELSGPAEGASLT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVDFEMPPPSPPLNLHELSGPAEGASLTPK 30 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 SVDFEMPPPS(0.999)PPLNLHELS(0.258)GPAEGAS(0.186)LT(0.556)PK 70.835 0.010843 96139000 71617 61508 68129 69161 85891 83424 86468 80255 86920 89621 TRUE FALSE 68818.12846 59753.85206 80441.42582 72730.4075 88653.76202 85110.89044 87526.22125 78597.7062 77053.206 83550.88984 0.823667212 0.715179122 0.962783592 0.870492315 1.061075019 1.018671262 1.047579761 0.940716566 0.922230824 1 16.35036757 4.027573651 1.692660204 0.989170555 0.7656175 0.600518854 0.064957748 0.252899584 1.370774574 0.017982208 0.058691455 10655.49552 -4.027573651 -0.223553055 DTSLYRPALEELRR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTSLYRPALEELRR 14 2 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 233.97 1.89E-17 2745250000 1050050 1085160 771010 846850 945100 706990 908350 902620 874210 958130 FALSE TRUE 1009012.885 1054212.299 910348.658 890556.03 975499.9998 721285.8222 919466.659 883980.5816 774973.3458 893235.0017 1.129616376 1.180218305 1.019159187 0.997000821 1.092097822 0.807498386 1.029367028 0.989639434 0.867602976 1 19.76868026 4.028244908 0.933623907 0.95775037 1.185410362 0.466208418 0.077470146 0.77169219 1.032565167 0.026887956 0.143388516 10671.97767 -4.028244908 0.227659992 YIKNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIKNPR 6 1 P49368;P49368-2;B4DUR8;Q5SZX6 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 113.07 0.024125 2337640000 3132400 3391800 2537000 2838400 2853000 2858300 3205700 3089300 3216900 3468800 FALSE TRUE 3009982.345 3295069.185 2995492.335 2984890.164 2944769.336 2916096.784 3244932.316 3025504.875 2851730.998 3233855.086 0.930772179 1.018929141 0.926291456 0.923012963 0.910606461 0.901740092 1.003425394 0.935572187 0.88183636 1 21.6248236 4.028348402 0.000898587 1.763558309 0.119430275 0.009396182 0.04455641 7727178.796 1454.191744 1324150.318 1336570.668 10674.52115 -4.028348402 -1.644128034 FGYTVSEENYMCR ddPTM_BT-474_Pertuzumab_2h_R1 1 FGYTVSEENYMCR 13 0 Q96EK6;G3V5E4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 271.62 1.20E-16 0 43497 51381 36440 40582 37880 36613 45045 47336 45027 47662 FALSE TRUE 41797.08915 49915.66419 43025.5186 42676.44188 39098.4446 37353.33995 45596.27418 46358.49506 39915.72373 44433.81029 0.940659576 1.123371232 0.968305854 0.960449748 0.879925542 0.84065129 1.026161697 1.043315771 0.898318723 1 15.43937024 4.028447192 24.85218752 0.955119001 1.035471273 0.161100018 0.073189686 360.0754514 314566.0365 0.019282882 0.041654726 10676.94958 -4.028447192 0.080352272 AGSSPCLGSSSAAS(ph)SPPPPASR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGSSPCLGSSSAASSPPPPASR 22 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGSSPCLGSSSAAS(0.744)S(0.256)PPPPASR 194.19 4.74E-18 270150000 100650 100840 88629 116450 109520 113830 104330 109980 119230 129850 TRUE FALSE 96716.48673 97964.14193 104646.2318 122459.9985 113042.8103 116131.7206 105606.8217 107708.8746 105695.5103 121055.1438 0.798945701 0.809252204 0.864450931 1.01160508 0.933812531 0.959329087 0.872386075 0.889750498 0.873118704 1 16.88530486 4.029393595 4.460502621 0.925816359 0.80755158 0.560991001 0.046097483 0.156770276 7.395208962 0.012318977 0.027084842 10700.24189 -4.029393595 -0.118264779 YREDIINVR ddPTM_BT-474_Pertuzumab_2h_R1 3 YREDIINVR 9 1 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;; 202.2 1.84E-05 843470000 271210 283230 246626 323682 317143 362464 274228 330121 321167 365850 FALSE TRUE 260610.8134 275152.5577 291196.8044 340387.2668 327344.1926 369793.2704 277584.0843 323303.886 284709.4686 341070.6536 0.764096267 0.806731845 0.853772675 0.997996348 0.959754787 1.084213099 0.813860944 0.947908835 0.834752171 1 18.3797111 4.030447626 2.955242215 0.944032339 0.784044367 0.437534835 0.074993402 0.241608076 4.288584634 0.019550796 0.047097326 10726.24287 -4.030447626 -0.159987972 S(ph)IQFVDWCPTGFK ddPTM_BT-474_Pertuzumab_2h_R1 3 SIQFVDWCPTGFK 13 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 1 S(1)IQFVDWCPTGFK;S(1)IQFVDWCPTGFK;S(1)IQFVDWCPTGFK 214.82 3.17E-11 1139700000 1964170 1854450 1288930 1193811 1204410 568900 1601310 1236010 1348930 1518060 TRUE FALSE 1887408.065 1801562.902 1521868.323 1255423.729 1243150.941 580403.5478 1620907.311 1210485.962 1195805.122 1415240.444 1.333630672 1.27297302 1.075342589 0.887074514 0.878402639 0.410109498 1.145322915 0.85532177 0.844948381 1 20.43261575 4.032866159 1.821801702 0.849982649 1.333128368 0.512306461 0.174488063 0.292974012 1.865574412 0.048325182 0.150561328 10786.14263 -4.032866159 0.483145718 S(ph)VS(ph)PYSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVSPYSR 7 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(1)VS(1)PYSR;S(1)VS(0.999)PYS(0.001)R 120.45 0.0066575 1373220000 1316740 1275370 1106420 1299760 1282930 1336720 1315310 1379820 1548640 1429420 TRUE FALSE 1265280.345 1238997.696 1306374.706 1366840.769 1324196.609 1363749.394 1331407.157 1351326.235 1372844.88 1332604.11 0.949479546 0.929756772 0.980317182 1.025691546 0.993690923 1.023371745 0.999101794 1.014049277 1.030197092 1 20.34581682 4.033450493 3.688691115 1.011700746 0.940162358 0.844126687 0.012444071 0.071188405 2.069950212 0.002982128 0.006785661 10800.66493 -4.033450493 -0.071538388 TWESVKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TWESVKR 7 1 A6NFX8;Q9UKK9;A6NCQ0;A6NJU6;C9JYY9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ; 104.37 0.013096 1552370000 2123310 2229600 1623350 1524080 1658400 1699580 1896070 1841370 2045730 1963620 FALSE TRUE 2040328.698 2166013.991 1916725.456 1602737.951 1711743.942 1733946.672 1919274.672 1803345.066 1813507.307 1830622.268 1.114554724 1.183211866 1.047034929 0.87551538 0.935061248 0.947189763 1.048427469 0.985099492 0.990650741 1 20.8039027 4.033788571 5.14031889 0.970779651 1.144988445 0.711063783 0.045753774 0.099502967 6.682731646 0.012293693 0.026818795 10809.07602 -4.033788571 0.174208794 TAS(ph)LNQRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TASLNQRPR 9 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 T(0.004)AS(0.996)LNQRPR;T(0.002)AS(0.998)LNQRPR 116.55 0.00078499 737880000 524240 485130 365050 341380 359140 313300 316120 467450 350280 289570 TRUE FALSE 503752.1212 471294.5674 431022.6555 358998.6627 370692.0643 319635.1407 319988.7711 457796.9941 310517.6829 269957.166 1.866044635 1.745812398 1.596633503 1.329835648 1.373151414 1.184021693 1.185331643 1.695813454 1.150247973 1 18.04237099 4.03525026 1.583679149 1.313532649 1.857021601 0.602190391 0.176387114 0.327654766 1.527867879 0.052358424 0.182214503 10845.51701 -4.03525026 0.543488952 SRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLR 37 1 P60842;J3KT12;P60842-2;J3QS69;J3QL43;J3QQP0 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 58.16 0.03976 8017200 3217.1 3340.3 2213 1962.6 1126.6 1572.6 3329.6 2487.2 2567.1 2060.7 FALSE TRUE 3091.372175 3245.037914 2612.938328 2063.890021 1162.838112 1604.399049 3370.348641 2435.838451 2275.69357 1921.126954 1.609145179 1.689132469 1.360107058 1.074312147 0.605289572 0.835134319 1.754360187 1.267921647 1.184561783 1 10.90773714 4.036685346 3.362531563 1.133138812 1.647096375 0.370410201 0.283059715 0.291632342 6.845162938 0.082468753 0.192386326 10881.41429 -4.036685346 0.513957563 RAVDLIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RAVDLIQK 8 1 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 104.2 0.0074175 816500000 878450 850140 659880 686730 710380 518220 814680 753650 809140 871190 FALSE TRUE 844119.2028 825894.8396 779134.995 722172.2176 733230.0179 528698.7635 824650.2975 738086.8641 717289.8194 812183.5253 1.039320765 1.016882039 0.959309036 0.889173684 0.902788588 0.650959724 1.015349698 0.908768574 0.883162237 1 19.63144624 4.037293151 2.030244157 0.887797781 1.03549725 0.256347475 0.092613985 0.454273328 3.652653913 0.025293098 0.073701739 10896.65375 -4.037293151 0.147699469 RDS(ph)SESQLASTESDKPTTGR ddPTM_BT-474_Pertuzumab_2h_R1 5 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RDS(0.827)S(0.173)ESQLASTESDKPTTGR;RDS(0.622)S(0.044)ES(0.325)QLAS(0.007)T(0.002)ESDKPTTGR;RDS(0.932)S(0.067)ES(0.001)QLASTESDKPTTGR;RDS(0.953)S(0.046)ESQLASTESDKPTTGR;RDS(0.821)S(0.179)ESQLASTESDKPTTGR 297.95 5.60E-55 10006430000 1929138 1941093 1654440 1988362 2034845 1999499 1981474 2179747 2108308 2172595 TRUE FALSE 1853745.154 1885734.928 1953434.111 2090981.601 2100297.637 2039930.24 2005723.872 2134734.463 1868981.715 2025443.206 0.915229392 0.931023355 0.964447734 1.032357558 1.036957063 1.007152526 0.990264188 1.053959181 0.922751973 1 20.9498062 4.037612329 2.854085285 1.011170263 0.922017342 0.486281557 0.034011634 0.196317677 3.2315613 0.008617944 0.021187517 10904.66501 -4.037612329 -0.08915292 ESGGSGFRS(ph)PHLWK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.027)GGS(0.021)GFRS(0.952)PHLWK;ES(0.027)GGS(0.035)GFRS(0.938)PHLWK 98.227 0.0016073 425680000 1320340 1532690 1081030 1078040 1206200 1302520 1267740 1314870 1486380 1332540 TRUE FALSE 1268739.653 1488979.182 1276396.168 1133677.774 1244998.518 1328857.847 1283254.981 1287717.475 1317652.374 1242285.879 1.021294434 1.198580139 1.027457681 0.912573984 1.002183587 1.069687637 1.032978804 1.036570967 1.060667594 1 20.24456578 4.037991635 24.55555606 1.017742349 1.110707953 0.296578723 0.056974648 154.6526276 99956.13639 0.014042969 0.03033616 10914.19315 -4.037991635 0.092965604 KRQEEIER ddPTM_BT-474_Pertuzumab_2h_R1 4 KRQEEIER 8 2 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;H0YFJ7 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;;; 195.48 8.99E-05 914700000 711970 747040 568195 594478 613827 579802 686310 679440 743660 740440 FALSE TRUE 684145.4253 725735.1506 670880.4759 625159.0808 633571.3029 591525.9937 694709.2671 665409.3266 659242.8345 690289.3393 0.991099509 1.051349209 0.971883003 0.905647886 0.917834402 0.856924713 1.006403007 0.963957124 0.955023925 1 19.39684168 4.038246921 6.205319144 0.942431325 1.020022961 0.330323907 0.043735395 0.205326534 21.28082886 0.011316714 0.024570302 10920.6106 -4.038246921 0.077591636 DLNWIHVQDAEEAWK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLNWIHVQDAEEAWK 15 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 0 172.24 1.04E-06 54905000 83838 74747 74593 88946 90496 94454 97204 93542 104210 106760 FALSE TRUE 80561.51827 72615.28874 88073.61441 93536.51372 93406.88603 96363.9246 98393.61163 91610.32501 92380.51768 99529.05011 0.809427179 0.729588886 0.884903597 0.939791082 0.938488672 0.968198978 0.988591889 0.920438052 0.928176423 1 16.60283005 4.038352491 3.277027467 0.9508154 0.769795003 0.846729876 0.031096164 0.080784717 1.789341177 0.007904506 0.018600626 10923.26553 -4.038352491 -0.181020397 VANPSGNLTETYVQDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VANPSGNLTETYVQDR 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;; 261.35 1.84E-26 399264000 79872 103123 88969 141533 145597 159050 139362 102150 140709 151286 FALSE TRUE 76750.51394 100182.033 105047.6774 148837.5351 150280.2597 162266.1 141067.5538 100040.5668 124736.3042 141039.2645 0.544178348 0.710313071 0.74481158 1.055291487 1.065520728 1.150503022 1.000200578 0.709310043 0.884408357 1 17.10573733 4.03888883 2.393987491 0.963784496 0.612190262 0.595048563 0.120025416 0.251300097 2.86007866 0.038201701 0.10155589 10936.76374 -4.03888883 -0.351594234 IAESHLQSISNLNENQAS(ph)EEEDELGELR ddPTM_BT-474_Pertuzumab_2h_R1 2 IAESHLQSISNLNENQASEEEDELGELR 28 0 Q9UD71;J3KSJ8;Q9UD71-2;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR 287.61 1.04E-62 807390000 86844 83725 77179 107096 92357 104638 97695 94646 99016 93652 TRUE FALSE 83450.04047 81337.24498 91126.96214 112623.2374 95327.74678 106753.8521 98890.62063 92691.52703 87776.11879 87308.86662 0.955802586 0.931603491 1.043730902 1.289940435 1.091844969 1.222714899 1.132652667 1.061650788 1.005351715 1 16.41384055 4.039204307 5.389201835 1.121702562 0.949840535 0.389180106 0.084900708 0.177334708 12.78355789 0.02151876 0.047042675 10944.71121 -4.039204307 -0.171862026 TDTS(ph)PVLETAGTVAAMAATPSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDTSPVLETAGTVAAMAATPSAR 23 0 Q8WWH5 Q8WWH5 TRUB1 Probable tRNA pseudouridine synthase 1 1 TDT(0.023)S(0.977)PVLETAGTVAAMAATPSAR;T(0.025)DT(0.118)S(0.857)PVLETAGTVAAMAATPSAR 249.52 5.78E-38 103435000 105730 101725 94406 105615 111352 115333 111438 125445 121915 126373 TRUE FALSE 101597.9547 98823.9026 111467.2643 111065.8028 114933.7382 117665.1123 112801.8116 122854.5169 108075.7203 117813.6441 0.862361532 0.83881543 0.946132047 0.942724449 0.975555412 0.998739264 0.957459659 1.042786833 0.917344685 1 16.8461471 4.039539899 1.179196012 0.987531028 0.834904687 0.667235764 0.034291587 0.330278798 0.769988139 0.010254531 0.04630934 10953.17179 -4.039539899 -0.152626341 ISGETIFVTAPHEATAGIIGVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISGETIFVTAPHEATAGIIGVNR 23 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 348.88 1.45E-101 3058600000 950750 938120 855320 990850 1058060 1137020 1114770 1031500 1071890 1221210 FALSE TRUE 913593.6389 911365.7361 1009895.35 1041987.887 1092093.461 1160011.323 1128412.889 1010199.165 950213.5409 1138496.359 0.802456355 0.800499474 0.88704311 0.915231638 0.959241944 1.018897702 0.991143169 0.887309965 0.834621502 1 20.11869825 4.039840184 1.821130377 0.94396261 0.793647836 0.542834332 0.052055588 0.309187737 1.966074049 0.015782408 0.049686972 10960.74776 -4.039840184 -0.150314774 KQVEEIFNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQVEEIFNLK 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 137.01 0.0073498 0 2475300 2601100 1994400 2040100 2235300 2279800 2321900 2429800 2680500 2453900 FALSE TRUE 2378562.539 2526919.175 2354832.445 2145389.805 2307200.455 2325899.118 2350316.107 2379623.781 2376220.878 2287695.167 1.039720052 1.104569879 1.029347126 0.937795313 1.008526174 1.016699756 1.027372939 1.040183944 1.038696463 1 21.1254634 4.040597745 9.812334252 1.012216146 1.07104042 0.386712167 0.030887021 0.417700503 96.29433301 0.008120719 0.017548525 10979.88383 -4.040597745 0.058824275 QSGT(ph)PPGMGAPGVPGAAGVGGAGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSGTPPGMGAPGVPGAAGVGGAGGR 25 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 QS(0.002)GT(0.998)PPGMGAPGVPGAAGVGGAGGR;QS(0.005)GT(0.995)PPGMGAPGVPGAAGVGGAGGR 162.32 2.18E-10 492850000 73691 63324 67833 100657 74284 73113 107382 85533 101538 98328 TRUE FALSE 70811.07425 61518.06152 80091.93204 105851.9198 76673.41232 74591.39495 108696.173 83766.71366 90011.83192 91668.15698 0.772471888 0.671095215 0.873715963 1.154729443 0.836423627 0.813711079 1.185757155 0.913803838 0.981931293 1 16.48413305 4.040617344 5.462249883 0.978562845 0.728192995 0.452230605 0.11469148 0.160774524 11.80316966 0.028343271 0.061985748 10980.37933 -4.040617344 -0.25036985 SQS(ph)FSHQQPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SQSFSHQQPSR 11 0 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 S(0.035)QS(0.687)FS(0.279)HQQPSR;S(0.151)QS(0.597)FS(0.252)HQQPSR;S(0.134)QS(0.831)FS(0.035)HQQPSR 113.59 0.0008836 746150000 845310 838150 614070 658710 670980 552890 637130 827680 656820 629630 TRUE FALSE 812274.3507 814246.7826 725046.1089 692706.102 692562.6811 564069.8146 644927.3875 810588.1188 582260.5472 586984.5993 1.383808624 1.387168903 1.235204654 1.1801095 1.179865165 0.960961864 1.098712621 1.380935922 0.991952 1 19.16296313 4.041107485 1.562052002 1.13411801 1.405681916 0.464271211 0.115781601 0.45621976 2.059286601 0.035674027 0.126724225 10992.7787 -4.041107485 0.271563906 HQQYDCK ddPTM_BT-474_Pertuzumab_2h_R1 2 HQQYDCK 7 0 B7Z683;A0A0G2JQ41;A0A1C7CYZ0;Q12979-4;Q12979-2;Q12979;I3L1U8;I3L0R7 B7Z683 ABR Active breakpoint cluster region-related protein 0 ; 100.39 0.0098288 115980000 265404 293795 189803 218448 249923 227497 231020 190023 275559 241650 FALSE TRUE 255031.7183 285416.2543 224104.6242 229722.1275 257962.0003 232097.1452 233847.2919 186098.9586 244278.6976 225282.8303 1.132051288 1.266924132 0.994770103 1.01970544 1.145058414 1.030247822 1.038016486 0.826068096 1.084320085 1 17.78137784 4.041782109 0.444224575 0.957615766 1.266463843 0.299778097 0.092051645 3.079974303 0.743617471 0.0753033 0.474840341 11009.86791 -4.041782109 0.308848077 RLSEDYGVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 183.85 2.60E-06 756790000 2022500 2014800 1434100 1247900 1432500 1010300 1784500 1517700 1754300 1678800 FALSE TRUE 1943458.464 1957339.877 1693273.771 1312304.269 1478577.663 1030728.958 1806339.245 1486358.965 1555159.219 1565093.381 1.241752401 1.250621785 1.081899516 0.838483048 0.94472169 0.658573457 1.154141515 0.949693471 0.993652671 1 20.57781731 4.042938811 3.468729186 0.935881778 1.244765949 0.521436939 0.119564369 0.178290344 4.453960172 0.030810893 0.071780967 11039.23075 -4.042938811 0.30888417 TRLS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 7 TRLSPPR 7 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 T(0.001)RLS(0.999)PPR;T(0.003)RLS(0.997)PPR;T(0.02)RLS(0.98)PPR;T(0.044)RLS(0.956)PPR;T(0.003)RLS(0.997)PPR;T(0.029)RLS(0.971)PPR;T(0.002)RLS(0.998)PPR 84.213 0.013148 17338758000 807610.2 761206.5 674207 801609.8 803366 856255.4 781756.2 858679.4 823765.5 853036.3 TRUE FALSE 776047.9005 739497.6359 796051.2026 842980.9778 829206.997 873569.4709 791323.5662 840947.3703 730255.0939 795259.3916 0.975842485 0.929882305 1.000995664 1.060007573 1.042687462 1.098471115 0.995050891 1.057450411 0.918260258 1 19.60106598 4.044367848 5.25777027 1.030595955 0.954058649 0.258760567 0.047163102 0.216107791 13.92870137 0.011403726 0.025070175 11075.61493 -4.044367848 -0.076537306 EFAPSDEELDSYR ddPTM_BT-474_Pertuzumab_2h_R1 3 EFAPSDEELDSYR 13 0 I3L0X5;O75391;I3L4C3 I3L0X5 SPAG7 Sperm-associated antigen 7 0 ;; 237.68 2.19E-16 360440000 314747 589175 277050 334061 312545 336180 288861 330801 304978 334269 FALSE TRUE 302446.3393 572372.3059 327119.0979 351301.9282 322598.2938 342977.7899 292396.1673 323969.8437 270358.176 311628.6629 0.970534406 1.836712646 1.049707992 1.127309423 1.035200969 1.100597701 0.938283933 1.039602201 0.867565177 1 18.24946841 4.045385913 24.99998761 1.02303263 1.413521442 0.357452012 0.206039775 113.173452 62338.08328 0.045839714 0.099025045 11101.60864 -4.045385913 0.390488812 QESCLGNS(ph)PPFEK ddPTM_BT-474_Pertuzumab_2h_R1 3 QESCLGNSPPFEK 13 0 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 QES(0.001)CLGNS(0.999)PPFEK;QES(0.001)CLGNS(0.999)PPFEK;QESCLGNS(1)PPFEK 247.02 3.26E-17 612480000 1632980 1718220 1739430 1975300 1857820 2124810 2473360 2360630 3108850 3072950 TRUE FALSE 1569161.336 1669218.048 2053783.694 2077245.47 1917578.468 2167775.114 2503629.72 2311882.166 2755946.381 2864816.359 0.547735401 0.582661448 0.716898899 0.725088525 0.66935476 0.756689031 0.873923284 0.8069914 0.961997572 1 21.45001123 4.045894734 0.184943444 1.071439491 0.221297971 0.888173223 0.047436998 3.891124455 0.171705491 0.142891144 0.798942185 11114.62295 -4.045894734 -0.85014152 WPS(ph)DSWIR ddPTM_BT-474_Pertuzumab_2h_R1 1 WPSDSWIR 8 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 WPS(1)DSWIR 71.349 0.04868 0 85864 90416 65055 62167 72258 79726 58421 78864 78726 70179 TRUE FALSE 82508.33995 87837.42421 76811.88564 65375.44632 74582.24419 81338.11434 59135.97367 77235.43084 69789.35453 65425.71382 1.261099576 1.342552019 1.174032061 0.999231686 1.139953083 1.24321325 0.903864402 1.180505742 1.066696112 1 15.99757014 4.046955291 4.673359693 1.087686394 1.298318182 0.473448617 0.094306231 0.164194154 7.900243626 0.022761021 0.050643721 11141.79827 -4.046955291 0.210631788 RLEEEGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEEEGDR 8 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 125.97 0.001987 409760000 172848 189104 154523 201027 198026 201523 198568 214074 207648 230020 FALSE TRUE 166092.9091 183710.9391 182448.7434 211402.0276 204395.6861 205597.9331 200998.1346 209653.2971 184076.6696 214440.5405 0.774540619 0.856698732 0.850812738 0.985830511 0.953157857 0.958764293 0.937314064 0.977675661 0.858404242 1 17.71021815 4.047009806 1.890983574 0.952845763 0.801740139 0.657585449 0.041579203 0.20300751 1.400412968 0.010755212 0.033312305 11143.19694 -4.047009806 -0.151105624 VYSLDDIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYSLDDIRR 9 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ; 162.88 0.00014363 194040000 304290 351250 188350 162223 188152 106699 202740 155238 183278 199098 FALSE TRUE 292398.0104 341232.6939 222389.0348 170595.3485 194204.08 108856.5269 205221.1928 152032.2811 162473.0498 185612.9151 1.575310695 1.838410294 1.198133409 0.919092017 1.046285383 0.586470649 1.105640697 0.819082449 0.875332677 1 17.50193757 4.047450412 3.1382455 0.902357879 1.708000162 0.81546513 0.150008263 0.086920505 1.74425435 0.036635509 0.08814788 11154.50781 -4.047450412 0.805642283 EEIVELMR ddPTM_BT-474_Pertuzumab_2h_R1 5 EEIVELMR 8 0 P42574;A8MVM1;C9JXR7 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 ;;;; 174.27 0.00063491 726059000 776595 835963 686552 869089 870878 872136 916980 930171 928921 987116 FALSE TRUE 746244.8088 812122.1537 810627.2187 913942.7874 898890.5818 889771.1875 928202.2755 910962.6438 823473.7824 920257.7541 0.810908472 0.882494225 0.880869751 0.993137828 0.976781318 0.966871709 1.008632931 0.989899449 0.894829496 1 19.81167848 4.048362464 1.591632687 0.978600094 0.828553987 0.715089719 0.034263435 0.217545557 1.023135037 0.009537317 0.033752043 11177.95776 -4.048362464 -0.150046107 MPLLELGGETT(ph)PPLSTERS(ph)PEAVGSECPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.487)T(0.512)PPLS(0.148)T(0.141)ERS(0.706)PEAVGS(0.004)ECPS(0.001)R 50.706 0.04171 73546000 33608 33533 29855 34645 38248 41594 36594 35079 39253 38839 TRUE FALSE 32294.5622 32576.67167 35250.46262 36433.0326 39478.28166 42435.05918 37041.84832 34354.60639 34797.164 36208.39994 0.891908018 0.899699289 0.973543782 1.006203883 1.090307269 1.171967258 1.023018095 0.948802114 0.961024626 1 15.1440368 4.049621752 2.08731626 1.030065636 0.890034714 0.436090471 0.060434694 0.357014788 3.04472479 0.019180343 0.055851641 11210.4166 -4.049621752 -0.140030922 ERTESEVPPRPAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERTESEVPPRPASPK 15 2 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 ERTESEVPPRPAS(1)PK 85.231 0.0041859 99237000 98367 96542 90025 93656 108040 98433 107670 118690 127160 122100 TRUE FALSE 94522.70889 93788.71668 106294.5201 98489.59738 111515.2047 100423.3827 108987.6977 116239.01 112725.3299 113830.0582 0.830384438 0.823936297 0.933800103 0.865233655 0.979663952 0.882222009 0.957459737 1.021162704 0.990294933 1 16.79652204 4.05005155 0.323732957 1.019480269 0.731672193 0.689819636 0.03846755 2.436187375 0.289331601 0.041760405 0.267137451 11221.51643 -4.05005155 -0.287808076 FVDGLMIHSGDPVNYYVDTAVR ddPTM_BT-474_Pertuzumab_2h_R1 9 FVDGLMIHSGDPVNYYVDTAVR 22 0 P23396;P23396-2;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ;;;;;;;; 328.51 1.10E-80 8242440000 5209279 5483759 4691159 5985846 6099250 6477124 6011653 5747304 6185720 6628249 FALSE TRUE 5005694.618 5327367.562 5538955.786 6294776.229 6295437.915 6608095.885 6085225.408 5628620.164 5483542.998 6179311.791 0.810073158 0.862129593 0.896370983 1.018685647 1.018792728 1.069390267 0.98477397 0.910881398 0.887403514 1 22.55901474 4.050905106 2.515315792 0.980897388 0.830851198 0.579609089 0.0514087 0.233669235 2.949005327 0.015667274 0.041251756 11243.59274 -4.050905106 -0.150046189 SIS(ph)LGDSEGPIVATLAQPLR ddPTM_BT-474_Pertuzumab_2h_R1 5 SISLGDSEGPIVATLAQPLR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 S(0.004)IS(0.996)LGDSEGPIVATLAQPLR;SIS(1)LGDSEGPIVATLAQPLR;S(0.002)IS(0.998)LGDSEGPIVATLAQPLR;S(0.007)IS(0.993)LGDSEGPIVATLAQPLR;S(0.039)IS(0.96)LGDS(0.001)EGPIVATLAQPLR 355.97 2.65E-95 733795000 312772.3 299217 273415.9 351242 345366 352031 333975.4 334433 347017 369367 TRUE FALSE 300548.8127 290683.6241 322828.2352 369369.6417 356475.011 359149.308 338062.6908 327526.8417 307625.085 344349.4441 0.872801794 0.844153023 0.937501834 1.072659323 1.035212971 1.042979201 0.9817431 0.951146712 0.893351478 1 18.39351382 4.050914535 4.55630417 0.995411538 0.861108903 0.568246748 0.047952617 0.155173753 6.892808981 0.013468113 0.030142428 11243.83684 -4.050914535 -0.134302636 EEPCLLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEPCLLKR 8 1 Q60FE5;P21333-2;P21333;H0Y5F3;H7C2E7 Q60FE5 FLNA Filamin-A 0 ; 126.52 0.0019491 805390000 628580 683150 469800 418360 487580 523130 525720 512450 569710 555410 FALSE TRUE 604014.3987 663667.2309 554703.3106 439951.6097 503263.4535 533708.047 532153.9186 501867.7284 505038.9092 517791.586 1.166520305 1.281726565 1.071286838 0.849669291 0.971942123 1.030739126 1.027737671 0.969246589 0.975371024 1 18.982012 4.051121842 5.151352995 0.977137923 1.21950085 0.769168415 0.054140438 0.084115877 4.864625785 0.013722371 0.030351185 11249.20528 -4.051121842 0.242362927 ICANHYITPMMELKPNAGSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ICANHYITPMMELKPNAGSDR 21 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 186.11 2.01E-17 5345300000 3532800 3593500 2951900 3014900 3065500 3393800 3581900 3263800 3718600 3800500 FALSE TRUE 3394734.27 3491016.898 3485373.995 3170499.35 3164104.592 3462424.961 3625736.364 3196401.389 3296480.118 3543088.75 0.958128489 0.985303261 0.98371061 0.894840512 0.893035658 0.977233483 1.023326431 0.902151093 0.930397275 1 21.75657617 4.051185979 0.000962166 1.763294471 0.137812876 0.005739566 0.044365833 4975892.625 974.5578299 819178.6013 827251.2195 11250.8667 -4.051185979 -1.625481595 LSSSDRYS(ph)DAS(ph)DDSFSEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 2 LSSS(0.001)DRY(0.144)S(0.863)DAS(0.861)DDS(0.126)FS(0.005)EPR;LS(0.054)S(0.058)S(0.063)DRY(0.043)S(0.79)DAS(0.977)DDS(0.011)FS(0.004)EPR 154.34 4.40E-07 825610000 642070 708620 592390 802730 737140 813120 843160 797830 847810 906680 TRUE FALSE 616977.1946 688410.8514 699448.0506 844158.9915 760850.7776 829561.8435 853478.8443 781354.5317 751570.1631 845269.756 0.729917509 0.814427402 0.827485008 0.998685905 0.900127766 0.981416687 1.009711797 0.924384821 0.889148296 1 19.68905231 4.051327539 1.794763506 0.955291224 0.752721536 0.74319784 0.045342311 0.183950919 1.131524409 0.012363152 0.040016025 11254.53456 -4.051327539 -0.202569688 RSSKDEEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSKDEEPR 9 2 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 83.948 0.0089 21496000 29062 32764 22937 24326 23634 25571 24965 25446 31710 29218 FALSE TRUE 27926.22491 31829.6028 27082.22613 25581.46778 24394.20907 26088.06314 25270.52914 24920.53121 28110.41374 27239.03884 1.025227985 1.168528853 0.99424309 0.939147227 0.895560567 0.957745363 0.927732043 0.914882913 1.031989928 1 14.73338818 4.051363179 5.728173419 0.944966502 1.096024715 0.563927391 0.049793699 0.114506227 8.277177618 0.011737259 0.025775949 11255.45819 -4.051363179 0.151058213 QYYTLLNQAPDMLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 QYYTLLNQAPDMLHR 15 0 Q13283;E5RH42;E5RJU8;Q13283-2;E5RIF8;E5RI46;E5RH00 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 166.9 1.34E-06 1315210000 1312620 1356330 933000 1011370 1017820 1020250 1002750 971720 1117820 1163980 FALSE TRUE 1261321.359 1317648.796 1101613.854 1063566.927 1050559.105 1040880.154 1015021.954 951653.6424 990929.7599 1085142.598 1.162355401 1.214263267 1.015178887 0.980117202 0.968130001 0.959210482 0.935381172 0.876984872 0.913179302 1 20.04945321 4.051491605 1.828975592 0.93559331 1.200034396 0.850784782 0.039081136 0.127736748 0.819025844 0.011422765 0.036471166 11258.78704 -4.051491605 0.264441086 DDEDSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDEDSFR 7 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 149.4 0.004697 180520000 351100 297000 287930 331600 317440 375130 315050 377240 397690 380470 FALSE TRUE 337378.6238 288529.8508 339965.356 348713.9157 327650.7459 382715.3856 318905.6761 369449.8622 352545.8985 354700.428 0.951164975 0.813446582 0.958457699 0.983122343 0.923739359 1.078982024 0.899084554 1.041582792 0.993925777 1 18.43624155 4.051906034 7.78371661 0.987845748 0.882331645 0.348833109 0.057340344 0.228987398 29.43976857 0.013136951 0.028526901 11269.53596 -4.051906034 -0.105514104 NGS(ph)YGESSLEAHIWQEEEEVVQANRR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGSYGESSLEAHIWQEEEEVVQANRR 26 1 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 NGS(0.997)Y(0.001)GES(0.001)SLEAHIWQEEEEVVQANRR;NGS(1)YGESSLEAHIWQEEEEVVQANRR 150.82 6.09E-08 123679000 6851.7 7992.4 4453 5624.7 6722.5 5454.5 5559.5 6675.1 6317 5128.7 TRUE FALSE 6583.927989 7764.464577 5257.756156 5914.991441 6938.735318 5564.793727 5627.538824 6537.256852 5599.920643 4781.328581 1.377008059 1.623913614 1.099643345 1.237102061 1.451214908 1.163859298 1.17698224 1.367246936 1.171205984 1 12.22319584 4.052023544 0.033958903 7.02E-12 2.713939868 0.368231725 0.140302436 483.5899701 3.246735886 105.8543726 156.1398144 11272.58567 -4.052023544 2.713939868 NMPGLSAATLASLGGT(ph)SSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NMPGLSAATLASLGGTSSR 19 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NMPGLSAATLASLGGT(0.333)S(0.333)S(0.333)R 198.14 8.44E-15 87756000 258050 224690 165360 143840 141800 128470 98571 181170 142700 147320 TRUE FALSE 247965.1207 218282.0612 195244.2304 151263.5996 146361.1258 131067.7514 99777.34138 177428.7762 126501.2942 137341.8852 1.80545884 1.589333515 1.421592766 1.101365395 1.065669993 0.954317405 0.7264888 1.291876662 0.921068573 1 17.06741215 4.052189359 1.22271496 0.999954631 1.8207653 0.823771374 0.133039277 0.246808034 0.623842414 0.042522678 0.190250655 11276.89039 -4.052189359 0.820810669 IDIS(ph)PSTFR ddPTM_BT-474_Pertuzumab_2h_R1 8 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.832)PS(0.162)T(0.007)FR;IDIS(0.522)PS(0.478)TFR;IDIS(0.664)PS(0.334)T(0.002)FR;IDIS(0.751)PS(0.248)T(0.001)FR;IDIS(1)PSTFR;IDIS(0.995)PS(0.005)TFR;IDIS(0.975)PS(0.021)T(0.004)FR;IDIS(0.494)PS(0.253)T(0.253)FR 192.5 3.64E-05 59182720000 5954207 6018920 5473564 7030650 7108640 6737030 7272160 7232010 7265570 7631570 TRUE FALSE 5721510.008 5847266.295 6462758.774 7393502.689 7337295.862 6873257.363 7361158.869 7082666.466 6440812.953 7114676.966 0.804184088 0.821859702 0.908369952 1.039190215 1.031290092 0.966067384 1.034644145 0.99550078 0.905285368 1 22.76236682 4.052611072 2.908556257 0.997927822 0.810653327 0.789381741 0.037835199 0.106987304 1.826696437 0.009937669 0.024667441 11287.84591 -4.052611072 -0.187274495 NKDLPESALR ddPTM_BT-474_Pertuzumab_2h_R1 1 NKDLPESALR 10 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 73.466 0.040953 147620000 308840 329090 241930 239130 257470 250920 283340 311210 292170 289840 FALSE TRUE 296770.1914 319704.6754 285652.1327 251471.528 265751.7564 255993.7743 286807.5997 304783.4047 259004.0865 270208.8786 1.098299186 1.183176056 1.057153022 0.930656051 0.983504901 0.947392164 1.061429221 1.127954811 0.95853285 1 18.04371555 4.05279754 6.002104283 1.012860812 1.138262651 0.464821968 0.058560886 0.198466361 15.51405351 0.016687584 0.036577767 11292.69347 -4.05279754 0.125401839 ETWYLSWALDTNQEER ddPTM_BT-474_Pertuzumab_2h_R1 4 ETWYLSWALDTNQEER 16 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1;H3BSV8 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ;;; 242.48 1.39E-19 434684000 393845 394245 353255 452433 413170 440836 445383 475604 474890 501738 FALSE TRUE 378453.102 383001.5186 417096.0366 475783.1213 426459.9883 449750.006 450833.7304 465782.6112 420982.4781 467754.8384 0.809084313 0.818808246 0.891697963 1.017163442 0.911716894 0.961507972 0.963824836 0.995783631 0.900006678 1 18.83539305 4.053154005 3.25729004 0.963803373 0.813532401 0.745923862 0.03512341 0.107494142 2.323932973 0.00863595 0.020669674 11301.96623 -4.053154005 -0.150270972 GGPS(ph)PGDVEAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGPSPGDVEAIK 12 0 P09661;H0YLR3;H0YMA0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 1 GGPS(1)PGDVEAIK 121.56 0.00039244 64360000 110650 116330 100680 113240 135450 122060 112520 156690 128510 113720 TRUE FALSE 106325.6757 113012.3823 118875.1156 119084.33 139806.8723 124528.1368 113897.0534 153454.2967 113922.0836 106017.6431 1.002905484 1.065977124 1.121276725 1.123250116 1.318713265 1.174598238 1.074321689 1.447441126 1.074557783 1 16.69394485 4.053465813 1.252436388 1.210737475 1.005724317 0.137681825 0.124847693 0.852241581 2.280882075 0.037787405 0.165896062 11310.08354 -4.053465813 -0.205013158 AFWMAIGGDRDEIEGLSS(ph)DEEH ddPTM_BT-474_Pertuzumab_2h_R1 1 AFWMAIGGDRDEIEGLSSDEEH 22 1 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 1 AFWMAIGGDRDEIEGLS(0.114)S(0.886)DEEH 117.36 8.08E-05 39971000 31856 35948 30867 42263 40436 44224 48506 41135 41560 51107 TRUE FALSE 30611.0323 34922.79824 36445.35353 44444.19849 41736.66066 45118.23958 49099.63094 40285.54788 36842.28303 47645.47737 0.642475089 0.732971945 0.76492787 0.932810436 0.875983681 0.946957446 1.030520285 0.845527217 0.773258766 1 15.54005166 4.053638924 1.600402793 0.913558123 0.659551998 0.629610921 0.072451882 0.285509491 1.358073727 0.021218123 0.075388434 11314.59268 -4.053638924 -0.254006125 LTPS(ph)PDIIVLSDNEAS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 LTPS(1)PDIIVLS(0.003)DNEAS(0.558)S(0.438)PR;LT(0.024)PS(0.976)PDIIVLS(0.002)DNEAS(0.56)S(0.438)PR 132.14 9.06E-07 20450000 80080 76309 70610 89553 91189 83632 96941 88735 82981 92280 TRUE FALSE 76950.38507 74132.74203 83370.79771 94174.84106 94122.177 85323.09634 98127.39296 86902.59124 73561.34476 86029.79341 0.894462046 0.861710102 0.969092153 1.094677057 1.094064896 0.991785438 1.140621046 1.010145297 0.855068248 1 16.39254875 4.053949656 4.148985014 1.03405419 0.880119877 0.383769347 0.074139634 0.200572191 7.194222358 0.019004847 0.043179372 11322.69102 -4.053949656 -0.153934313 SLQELFLAHILSPWGAEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLQELFLAHILSPWGAEVK 19 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 231.6 2.99E-20 1040130000 3088200 3005400 2291800 2332210 2410500 2667500 2484600 2286900 2818000 2861500 FALSE TRUE 2967509.73 2919688.935 2705979.241 2452575.638 2488035.922 2721438.678 2515007.278 2239674.716 2498112.454 2667688.056 1.11239008 1.094464148 1.014353696 0.919363728 0.932656244 1.020148766 0.94276663 0.839556451 0.936433496 1 21.34715855 4.054409231 2.260950925 0.931920387 1.110582551 0.656249924 0.046437748 0.189594718 1.914478511 0.013883978 0.038802565 11334.67916 -4.054409231 0.178662164 FQGEDTVVIASKPYAFDR ddPTM_BT-474_Pertuzumab_2h_R1 3 FQGEDTVVIASKPYAFDR 18 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;; 178.77 7.94E-14 1960000000 778800 787270 679840 740820 785580 835510 849520 816030 889030 912250 FALSE TRUE 748363.635 764817.8304 802702.211 779053.809 810848.8941 852404.5847 859916.6799 799178.6953 788111.0415 850462.495 0.879949015 0.899296365 0.943841987 0.916035467 0.953421108 1.002283569 1.011116522 0.939698929 0.92668524 1 19.69788809 4.054505577 0.831135815 0.971352431 0.869804238 0.553143251 0.028536169 0.920180695 0.916126901 0.011985488 0.071991458 11337.19397 -4.054505577 -0.101548193 TDQVIQSLIALVNDPQPEHPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDQVIQSLIALVNDPQPEHPLR 22 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 238.87 1.44E-30 2431400000 319898 266241 277020 384470 339890 299990 330710 353670 378430 404590 FALSE TRUE 307396.0325 258648.0674 327083.6763 404312.5428 350822.8705 306056.0033 334757.3279 346366.5909 335472.2129 377186.7589 0.81497037 0.685729446 0.86716638 1.071916055 0.930103887 0.811417676 0.887510815 0.918289369 0.889406123 1 18.52491951 4.055631759 6.602128696 0.922504157 0.753936106 0.4930378 0.071770709 0.169531187 15.31896863 0.018230531 0.039823944 11366.63092 -4.055631759 -0.168568051 (ac)AESSESFTMASS(ph)PAQR ddPTM_BT-474_Pertuzumab_2h_R1 3 AESSESFTMASSPAQR 16 0 P49736;F8WDM3 P49736 MCM2 DNA replication licensing factor MCM2 1 AESSESFTMASS(1)PAQR;AESSESFT(0.001)MAS(0.061)S(0.938)PAQR;AESSESFTMAS(0.047)S(0.953)PAQR 129.92 3.23E-122 967890000 896124 961363.4 732300.8 786731 850861 894303 784237 887473 999837 978438.9 TRUE FALSE 861102.4834 933946.2571 864643.8445 827334.2812 878229.7168 912386.4194 793834.727 869146.3724 886339.6954 912168.3618 0.944017047 1.023874864 0.947899402 0.906997344 0.962793442 1.000239054 0.870272156 0.952835473 0.971684321 1 19.79894061 4.055767126 24.98947792 0.946424625 0.984431485 0.078168733 0.041540605 169.8652048 76114.68623 0.009946761 0.021487458 11370.17439 -4.055767126 0.038006861 GQYILTLSEDIVDGHER ddPTM_BT-474_Pertuzumab_2h_R1 2 GQYILTLSEDIVDGHER 17 0 Q92993-2;Q92993-4;Q92993;Q92993-3;H0YEG3;E9PJI1 Q92993-2 KAT5 Histone acetyltransferase KAT5;Histone acetyltransferase 0 ; 98.573 0.0017944 82838000 33302 32565 30369 40630 38199 37438 39203 41280 37626 41164 FALSE TRUE 32000.52102 31636.27808 35857.35385 42726.91917 39427.70553 38195.02201 39682.77804 40427.55357 33354.85422 38375.92561 0.833869685 0.824378242 0.934371049 1.113378205 1.027407285 0.995286013 1.034053965 1.053461328 0.869160905 1 15.22791393 4.056397855 3.954422785 1.019278366 0.831370045 0.608397469 0.058574851 0.12997354 4.184561707 0.014622834 0.033559594 11386.69938 -4.056397855 -0.187908321 DDGTVIHFNNPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDGTVIHFNNPK 12 0 Q96K17;Q96K17-2;E9PL10 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4;Transcription factor BTF3 0 167.3 4.96E-05 1053500000 1193100 1036600 1261200 1456000 1315700 1250000 1542100 1509300 1897700 2053500 FALSE TRUE 1146472.333 1007037.183 1489126.895 1531144.334 1358020.685 1275275.856 1560972.681 1478132.428 1682281.052 1914414.616 0.598863132 0.526028779 0.777849732 0.799797662 0.709366025 0.666144024 0.815378585 0.77210674 0.878744363 1 20.86847189 4.05752923 0.07744032 1.326850048 8.19E-13 0.714096465 0.069425726 44.42775006 0.695147542 3.682960842 8.803042877 11416.40139 -4.05752923 -1.326850048 NNSGEEFDCAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNSGEEFDCAFR 12 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 196.11 4.89E-07 345300000 336380 330280 285510 310170 365900 313830 335770 343980 386390 365100 FALSE TRUE 323233.8977 320860.7378 337108.0081 326177.9109 377669.5058 320175.8576 339879.2537 336876.6928 342528.6271 340371.4518 0.949650436 0.942678171 0.990412111 0.958299849 1.109580442 0.940666016 0.998553938 0.989732514 1.006337709 1 18.37675051 4.059467932 1.88407888 1.00143867 0.944323384 0.205729445 0.041826692 0.561607605 3.83955351 0.011108433 0.035128194 11467.47844 -4.059467932 -0.057115286 YAAVTQFEATDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 YAAVTQFEATDAR 13 0 E9PLK3;P55786;A6NEC2;E9PP11 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 125.54 0.00046287 99393000 77919 85465 72264 99887 93681 87210 86798 106420 102200 102310 FALSE TRUE 74873.83934 83027.62188 85323.7123 105042.18 96694.33444 88973.44595 87860.25989 104222.3898 90598.68446 95380.45257 0.78500193 0.870488865 0.894561831 1.101296725 1.013775169 0.932826838 0.921155829 1.092701775 0.949866372 1 16.54140601 4.059623125 2.853225631 1.00359288 0.823267832 0.573434897 0.060984745 0.185320247 3.034997019 0.016310626 0.041093727 11471.57701 -4.059623125 -0.180325048 EQISDIDDAVR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;;; 234.39 3.95E-15 9833480000 3278730 3746180 3074260 4349740 4162410 4166740 4869640 5247860 4444430 4649470 FALSE TRUE 3150593.607 3639342.614 3629847.169 4574230.603 4296297.698 4250994.338 4929236.111 5139489.857 3939916.939 4334557.256 0.726854768 0.839611153 0.837420515 1.055293617 0.991173364 0.980721695 1.137194832 1.185701227 0.908954873 1 22.04745321 4.060815232 0.847257821 1.073210622 0.69005721 0.626079031 0.082155472 0.655820032 0.680131563 0.032613405 0.196077402 11503.10891 -4.060815232 -0.383153412 LKNGFPHPEPDCNPSEAAS(ph)EESNSEIEQEIPVEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPS(0.087)EAAS(0.304)EES(0.304)NS(0.304)EIEQEIPVEQK 71.183 0.0026398 198640000 126350 123420 91294 82048 98416 98083 90051 92834 119440 115610 TRUE FALSE 121412.1023 119900.1824 107792.8566 86282.50711 101581.64 100066.3055 91153.07108 90916.94546 105881.6719 107779.6317 1.126484665 1.112456784 1.000122703 0.800545574 0.94249385 0.928434286 0.845735596 0.843544777 0.982390367 1 16.71772504 4.061120841 3.443630308 0.895053112 1.11934571 0.658566705 0.060720816 0.123166921 2.961925494 0.015230248 0.03617879 11511.20639 -4.061120841 0.224292598 AES(ph)GPDLR ddPTM_BT-474_Pertuzumab_2h_R1 5 AESGPDLR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 AES(1)GPDLR;AES(1)GPDLR;AES(1)GPDLR;AES(1)GPDLR;AES(1)GPDLR 162.34 0.00035906 14364170000 26524400 26809200 19138600 20385900 20019600 20383700 18716500 24207000 22562900 19648900 TRUE FALSE 25487797.12 26044627.86 22597370.76 21438018.74 20663548.62 20795872.38 18945558.13 23707116.99 20001654.18 18318062.5 1.391402454 1.42180036 1.233611402 1.170321301 1.12804226 1.135265936 1.034255567 1.294193476 1.091908829 1 24.12676358 4.061193257 2.1878179 1.137660086 1.415792541 0.679750203 0.076815914 0.186215975 1.754323921 0.02057155 0.05912348 11513.12598 -4.061193257 0.278132456 KYVSQYYPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KYVSQYYPK 9 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK4;Q5SSJ5-3 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 0 74.533 0.048869 0 281100 228850 185310 126050 173240 87507 175500 149230 133680 153710 FALSE TRUE 270114.3012 222323.4221 218799.6392 132555.4556 178812.4219 89276.4515 177647.8215 146148.3484 118505.2068 143299.0848 1.884968781 1.551464354 1.526873947 0.925026533 1.247826685 0.623007827 1.239699624 1.019883334 0.826978114 1 17.12866987 4.061334235 1.267347319 0.981193254 1.86323492 0.732557756 0.187971607 0.281258495 0.771591047 0.053958012 0.237704297 11516.86391 -4.061334235 0.882041666 ASS(ph)PGHPAFLEDGSPS(ph)PVLAFAASPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSPGHPAFLEDGSPSPVLAFAASPR 26 0 Q9C073;D6RJ87;Q9C073-2 Q9C073 FAM117A Protein FAM117A 2 AS(0.451)S(0.549)PGHPAFLEDGSPS(1)PVLAFAASPR 159.42 1.02E-11 58498000 23790 23967 26716 38803 40950 30879 42127 39372 38595 39670 TRUE FALSE 22860.2605 23283.48463 31544.17549 40805.62748 42267.19394 31503.39454 42642.56283 38558.95444 34213.8574 36983.11557 0.618126952 0.629570664 0.852934508 1.103358299 1.142878129 0.851831817 1.153027866 1.042609684 0.925121015 1 15.17457915 4.061593696 2.902809189 1.037132553 0.618278261 0.769181789 0.088880614 0.110296147 1.870509144 0.022800978 0.057193774 11523.74649 -4.061593696 -0.418854291 NHSGSRT(ph)PPVALNSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.185)GS(0.286)RT(0.528)PPVALNSSR 120.9 0.00014904 203360000 108660 131320 57664 57443 73641 103630 58272 18682 59012 38237 TRUE FALSE 104413.4471 127574.8822 68085.16753 60407.64011 76009.72964 105725.4696 58985.15017 18296.21017 52313.20516 35647.17393 2.929080641 3.578821772 1.90997378 1.694598294 2.13227926 2.965886435 1.654693589 0.513258364 1.467527419 1 15.12150009 4.061632208 0.268725111 0.707683952 4.500524075 0.542232026 0.605854843 4.902963283 0.397556496 0.926478564 6.03294749 11524.76843 -4.061632208 3.792840123 NVNHSWIER ddPTM_BT-474_Pertuzumab_2h_R1 2 NVNHSWIER 9 0 Q4G0J3;Q4G0J3-3;D6RFF0 Q4G0J3 LARP7 La-related protein 7 0 ; 134.68 0.00024221 518700000 284720 281460 192542 185383 198425 156223 188266 203159 233098 238040 FALSE TRUE 273592.8276 273433.0364 227338.6225 194950.6388 204807.5203 159381.9361 190570.0556 198963.6957 206637.6923 221917.3388 1.232859177 1.232139128 1.024429293 0.878483132 0.922900038 0.718204071 0.858743425 0.896566698 0.931147126 1 17.75966287 4.061987416 2.206187206 0.875160793 1.247040474 0.79874889 0.068762933 0.124292068 1.19179423 0.0184833 0.052914979 11534.19835 -4.061987416 0.371879681 SDS(ph)ENVYEVIQDLHVPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDSENVYEVIQDLHVPPR 18 0 A0A0G2JRG8;A0A0G2JNY3;A0A0G2JP16 A0A0G2JRG8 1 S(0.166)DS(0.657)ENVY(0.177)EVIQDLHVPPR;S(0.149)DS(0.847)ENVY(0.004)EVIQDLHVPPR 129.85 1.31E-05 70023000 76089 72947 72479 99021 97638 75214 87569 108100 106741 106194 TRUE FALSE 73115.35776 70866.62298 85577.56759 104131.4857 100778.6149 76734.87861 88640.69562 105867.6972 94624.20917 99001.38579 0.738528629 0.715814455 0.864407775 1.051818465 1.017951558 0.775088934 0.895348029 1.06935571 0.955786714 1 16.5951611 4.062011325 3.753438643 0.965671639 0.728795403 0.584534032 0.080231361 0.162089763 4.628850597 0.022242888 0.051813105 11534.83336 -4.062011325 -0.236876237 DDKESRPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDKESRPPR 9 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2;G3XAL2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 0 75.294 0.021749 47934000 78843 76954 71025 69122 85803 75345 81916 87846 94202 87664 FALSE TRUE 75761.72839 74759.34727 83860.79744 72689.3947 88562.93142 76868.52752 82918.51251 86031.9494 83508.58389 81726.4392 0.927016142 0.914751065 1.026115884 0.889423244 1.083650925 0.940558873 1.01458614 1.052681975 1.02180622 1 16.31851526 4.06248412 0.490957382 1.028179275 0.886231909 0.2749909 0.052366025 2.970414435 0.886719837 0.034831612 0.228200799 11547.3976 -4.06248412 -0.141947366 SLS(ph)RS(ph)PLPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSRSPLPSR 10 1 Q9NYV4;Q9NYV4-2 Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.435)LS(0.566)RS(0.999)PLPSR;S(0.451)LS(0.561)RS(0.984)PLPS(0.004)R 94.09 0.0047463 1257640000 817070 830630 747750 990430 952690 1011700 970590 900400 988090 1064630 TRUE FALSE 785138.0011 806941.2457 882885.0586 1041546.211 983334.1391 1032157.267 982468.3708 881806.4253 875926.1656 992521.6618 0.791053769 0.813021294 0.88953732 1.049393934 0.990743252 1.039934247 0.989870961 0.888450559 0.882525993 1 19.92073906 4.062508447 3.406822873 0.971728642 0.801920069 0.639081837 0.052717884 0.165851604 3.895995374 0.015414569 0.036768196 11548.04447 -4.062508447 -0.169808573 GLVGEIIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLVGEIIKR 9 1 Q32Q12;P22392-2;J3KPD9;P22392;E7ERL0;E5RHP0;F6XY72;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 191.17 5.80E-05 8692500000 8374900 9107100 6596600 6055600 6636000 8227300 6150200 6068300 7172400 7414400 FALSE TRUE 8047599.649 8847374.425 7788752.361 6368130.242 6849452.967 8393661.643 6225467.987 5942987.484 6358219.221 6912216.084 1.164257534 1.279962073 1.126809733 0.921286338 0.990919972 1.214322808 0.900647189 0.859780338 0.919852496 1 22.72071689 4.063842062 0.52721317 0.922933069 1.333126075 0.453307176 0.103337743 2.023397079 0.707847973 0.071716833 0.474199355 11583.56024 -4.063842062 0.410193006 ELLGPDFGYVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLGPDFGYVTR 12 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 155 0.00016743 127267000 197920 213260 182325 237220 233160 254660 240380 257730 212232 254260 FALSE TRUE 190185.0676 207178.0336 215275.1833 249462.9526 240659.8032 259809.3997 243321.8423 252407.7854 188140.3131 237038.7437 0.802337477 0.874026036 0.908185641 1.052414254 1.015276234 1.096063013 1.026506631 1.064837678 0.793711231 1 17.85476336 4.06415775 2.072788485 1.017657161 0.824816131 0.424602554 0.079411652 0.289162847 2.42858094 0.021076764 0.062890249 11591.98338 -4.06415775 -0.19284103 GELSEEELPYYVELPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GELSEEELPYYVELPDR 17 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 ; 184.21 1.51E-09 139793000 72320 87994 70110 100201 96178 101377 108292 133824 103493 108230 FALSE TRUE 69493.65445 85484.49728 82780.43659 105372.3856 99271.65272 103426.9124 109617.3099 131060.4876 91744.90852 100899.4857 0.688741414 0.847224311 0.820424762 1.044330255 0.983866786 1.025048955 1.086401077 1.298921265 0.909270329 1 16.6225593 4.06419666 0.686569683 1.109367781 0.630487884 0.57513994 0.103395154 0.99604109 0.63129078 0.049892002 0.327299255 11593.022 -4.06419666 -0.478879897 QIYYSDKYFDEHYEYR ddPTM_BT-474_Pertuzumab_2h_R1 1 QIYYSDKYFDEHYEYR 16 1 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 186.97 8.50E-10 120030000 224930 212790 157620 157250 150960 176360 145140 148190 181860 214560 FALSE TRUE 216139.4869 206721.4375 186105.4402 165365.6913 155815.7655 179926.12 146916.2667 145129.8247 161216.0152 200027.6601 1.080547994 1.033464259 0.930398527 0.826714122 0.778971095 0.899506198 0.734479755 0.72554878 0.80596861 1 17.60983999 4.06452008 1.50258669 0.800053538 1.087386317 0.58223881 0.077729512 0.285152703 1.169742326 0.022027573 0.084007141 11601.65856 -4.06452008 0.287332779 LDNARQS(ph)AER ddPTM_BT-474_Pertuzumab_2h_R1 3 LDNARQSAER 10 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 LDNARQS(1)AER;LDNARQS(1)AER;LDNARQS(1)AER 93.348 0.0053578 469780000 506010 513223 338147 314766 350102 275025 309116 282931 312773 286904 TRUE FALSE 486234.5698 498586.3825 399257.6849 331011.111 361363.3488 280586.1939 312899.0541 277088.376 277268.3203 267471.7365 1.817891401 1.864071281 1.49270981 1.237555471 1.351033771 1.04903119 1.169839693 1.035953853 1.036626613 1 18.02902693 4.064666422 0.666715355 1.042983102 2.099070288 0.922499938 0.085295129 0.368261321 0.21822384 0.039664107 0.261827396 11605.56858 -4.064666422 1.056087185 VCTLAIIDPGDSDIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VCTLAIIDPGDSDIIR 16 0 E5RI99;P62888;A0A0C4DH44;A0A0B4J213 E5RI99 RPL30 60S ribosomal protein L30 0 133.71 7.50E-05 92816000 238210 246910 219140 279530 269580 269710 289850 305180 305610 291530 FALSE TRUE 228900.4898 239868.3686 258743.4727 293956.5768 278251.2855 275163.721 293397.271 298877.9264 270918.434 271784.4134 0.842213455 0.882568524 0.952017334 1.081579967 1.023794124 1.01243378 1.079522064 1.099687515 0.996813727 1 18.0521032 4.065777812 2.242528203 1.049707521 0.85260839 0.801517008 0.035794069 0.124617483 1.236703256 0.009939474 0.028326369 11635.30606 -4.065777812 -0.19709913 FQAWVDKWTK ddPTM_BT-474_Pertuzumab_2h_R1 1 FQAWVDKWTK 10 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 78.692 0.026668 74706000 324260 322900 247880 243250 256930 283550 280330 279860 325800 317070 FALSE TRUE 311587.5607 313691.2082 292677.4301 255804.1617 265194.3868 289283.5753 283760.7624 274080.7932 288816.5499 295594.5665 1.054104493 1.061221158 0.990131292 0.865388578 0.897155824 0.97864984 0.959966097 0.927218644 0.977069888 1 18.17326023 4.066015072 4.207046054 0.939550843 1.055947505 0.580483559 0.038315102 0.138761326 4.888498455 0.009881053 0.022597564 11641.6643 -4.066015072 0.116396662 GLLASDLNTDGDMRVT(ph)PEPGAGPTQGLLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLLASDLNTDGDMRVTPEPGAGPTQGLLR 29 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4;V9GYX5;C9JVY3;V9GY85;H7C3H1 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR 191.02 5.29E-18 1987310000 869570 915820 794750 1031180 941190 1057770 1084550 1052770 1110620 1149330 TRUE FALSE 835586.243 889701.7103 938379.0041 1084399.323 971464.2311 1079158.834 1097823.047 1031029.932 984547.0737 1071484.855 0.779839527 0.830344644 0.875774398 1.01205287 0.906652321 1.007162004 1.024581021 0.962244055 0.918862333 1 20.03118003 4.066285014 1.929525369 0.975851583 0.790759105 0.761766621 0.03893434 0.161644071 1.163298907 0.010555627 0.033151864 11648.90261 -4.066285014 -0.185092478 SEDIY(ph)ADPAAYVMR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEDIYADPAAYVMR 14 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 SEDIY(1)ADPAAYVMR;SEDIY(1)ADPAAYVMR 141.08 0.0001007 212850000 503120 543990 304050 370260 308590 260830 306540 294870 419530 457750 TRUE FALSE 483457.5142 528475.9378 358998.5986 389369.163 318516.0776 266104.1613 310291.5282 288780.8315 371906.7132 426746.1848 1.132892411 1.238384681 0.841246182 0.912413929 0.746382953 0.623565414 0.727110257 0.676703956 0.871493938 1 18.70301873 4.066574442 1.533936774 0.751619156 1.213272169 0.605087616 0.118844104 0.256312411 1.102395021 0.032540786 0.122352436 11656.66841 -4.066574442 0.461653013 RSPTGSTTS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPTGSTTSR 10 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 RS(0.007)PT(0.004)GS(0.131)T(0.09)T(0.09)S(0.678)R 101.56 0.0034445 243920000 215200 221140 187450 235670 235850 261510 222480 216220 251250 243030 TRUE FALSE 206789.7461 214833.3037 221326.3848 247832.9569 243436.3294 266797.9114 225202.7768 211754.9814 222729.1533 226569.3616 0.912699513 0.948201037 0.976859286 1.093850268 1.074445052 1.177555118 0.99396836 0.934614371 0.983050628 1 17.78959326 4.066962513 3.240446983 1.032970016 0.929594029 0.30408924 0.06483693 0.356879148 7.547412944 0.019535269 0.047470154 11667.08906 -4.066962513 -0.103375987 LQAKES(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 6 LQAKESPQR 9 1 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR 102.4 0.0043364 3011540000 5262130 5286730 3077190 2211705 2864560 1163961 3378630 2495370 3354750 3277770 TRUE FALSE 5056480.142 5135957.637 3633306.685 2325851.36 2956701.174 1187497.089 3419978.685 2443839.737 2973932.844 3055763.718 1.654735316 1.68074436 1.189001186 0.761135865 0.967581739 0.388608937 1.119189505 0.799747612 0.973220811 1 21.54310156 4.067026567 2.789609302 0.849438078 1.68172711 0.74426362 0.188284286 0.117444469 1.833172142 0.046820683 0.120002655 11668.80996 -4.067026567 0.832289033 MFIGGLSWDTSKK ddPTM_BT-474_Pertuzumab_2h_R1 2 MFIGGLSWDTSKK 13 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ; 130.07 0.00023467 898460000 1754500 1766460 1304340 1238890 1410720 1408780 1370270 1417490 1745240 1668810 FALSE TRUE 1685932.2 1716082.29 1540063.253 1302829.261 1456097.09 1437266.497 1387039.774 1388218.336 1547127.672 1555780.012 1.083657193 1.103036597 0.989897827 0.837412263 0.935927367 0.923823732 0.891539783 0.89229732 0.994438584 1 20.56920665 4.06793518 3.959595981 0.916993993 1.091718167 0.671731483 0.046315321 0.10796319 3.37105251 0.011192941 0.025910752 11693.24853 -4.06793518 0.174724174 RFPELESLVPNALDYIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RFPELESLVPNALDYIR 17 1 Q8WWY3-4;Q8WWY3;E7EVX8;Q8WWY3-3;Q8WWY3-2;E7EU94;E7ESX0;E7EN72 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 105.38 0.0012902 180120000 161850 184660 123080 123360 130530 158660 123750 132350 155360 140780 FALSE TRUE 155524.7231 179393.6776 145323.2939 129726.6244 134728.616 161868.2139 125264.4895 129616.9262 137724.1841 131244.8452 1.184996811 1.366862655 1.107268584 0.988432149 1.026544058 1.233330068 0.954433596 0.987596321 1.049368331 1 17.00190123 4.068537102 5.439527456 1.034585841 1.273220555 0.569986469 0.082811466 0.13383252 7.359678372 0.020845556 0.046263028 11709.46632 -4.068537102 0.238634714 NQQFHK ddPTM_BT-474_Pertuzumab_2h_R1 5 NQQFHK 6 0 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;; 148.53 0.010753 5086300000 7835600 7287470 5961930 6114500 5897850 5815550 6391540 6919560 7861600 7870320 FALSE TRUE 7529376.089 7079638.491 7039383.373 6430070.078 6087559.702 5933144.406 6469761.578 6776668.668 6969184.127 7337256.216 1.026184158 0.964889092 0.959402693 0.87635894 0.829677951 0.808632577 0.881768523 0.923597114 0.949835186 1 22.80680923 4.068610127 2.004525016 0.888169193 1.005225148 0.360636815 0.054250099 0.360615706 2.81801562 0.01542359 0.047345004 11711.43538 -4.068610127 0.117055955 EAPS(ph)PLMIHS(ph)PQMSQFQSLTHQS(ph)PPQQNVQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 3 EAPS(0.998)PLMIHS(0.925)PQMS(0.122)QFQS(0.129)LT(0.333)HQS(0.493)PPQQNVQPK 85.416 9.31E-05 273770000 97544 110390 77316 71510 91676 89431 98463 72504 113480 108260 TRUE FALSE 93731.87264 107241.7853 91288.72109 75200.63967 94624.8418 91239.35609 99668.01965 71006.76706 100598.2261 100927.4538 0.928705413 1.062563072 0.904498406 0.745095976 0.937553047 0.904009293 0.987521392 0.703542638 0.996737978 1 16.62295914 4.069726799 7.916168611 0.877030161 0.994031454 0.111565663 0.101258538 0.39760105 39.26831303 0.024486192 0.053259402 11741.58697 -4.069726799 0.117001294 QAEATRAS(ph)PPRS(ph)PAEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAEATRASPPRSPAEPK 17 2 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 2 QAEAT(0.062)RAS(0.939)PPRS(1)PAEPK;QAEAT(0.024)RAS(0.976)PPRS(1)PAEPK 93.73 0.0016035 1074590000 908270 971360 660930 628030 706170 773220 500760 616280 591730 480530 TRUE FALSE 872773.8043 943657.7639 780374.7533 660442.7036 728884.5994 788855.0382 506888.4507 603553.6026 524559.2911 447983.2751 1.948228545 2.106457576 1.741972964 1.474257501 1.627035293 1.760902877 1.131489676 1.34726816 1.170934989 1 18.77308535 4.070010241 0.230648326 0.917071734 2.728344833 0.798055771 0.156963174 3.495933838 0.214887364 0.28266305 1.809769751 11749.25259 -4.070010241 1.811273099 KS(ph)PSSDSWTCADTSTER ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPSSDSWTCADTSTER 17 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 KS(0.357)PS(0.326)S(0.089)DS(0.13)WT(0.093)CADT(0.002)S(0.002)T(0.002)ER 70.335 0.034801 124140000 65860 63568 66749 76200 84303 84288 91390 85058 96725 93454 TRUE FALSE 63286.11839 61755.10288 78812.02912 80132.69113 87014.68256 85992.36111 92508.45816 83301.52258 85745.1835 87124.27734 0.726389019 0.708816242 0.904593203 0.919751573 0.998742087 0.987008027 1.061798858 0.956122967 0.984170958 1 16.41078716 4.070038029 1.400530049 0.995496079 0.689017943 0.901706411 0.035012644 0.132628945 0.460304914 0.009955808 0.040753333 11750.0044 -4.070038029 -0.306478136 SQIYGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQIYGSR 7 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 95.605 0.031042 272067000 261463 253217 189063 193529 194765 153550 222993 215300 227264 242734 FALSE TRUE 251244.7369 245995.4991 223230.8898 203517.0549 201029.7931 156654.8862 225722.055 210853.9798 201465.9435 226293.41 1.110260952 1.087064352 0.986466596 0.899350339 0.888359025 0.692264464 0.997475159 0.931772515 0.890286392 1 17.78783505 4.070102777 2.112773608 0.895801133 1.109528517 0.495812505 0.080088083 0.270793279 2.368338388 0.022176988 0.065912981 11751.7563 -4.070102777 0.213727384 YGVQADRVDK ddPTM_BT-474_Pertuzumab_2h_R1 4 YGVQADRVDK 10 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 147.37 2.46E-05 7302900000 4653730 4694700 3304870 3223700 3536930 2642830 3729350 3817800 4015370 3896470 FALSE TRUE 4471857.087 4560811.753 3902133.525 3390075.543 3650698.566 2696269.833 3774990.901 3738961.096 3559562.031 3632558.616 1.231048844 1.255537001 1.074210753 0.933247306 1.004993711 0.742250881 1.039209907 1.029291332 0.979904912 1 21.79255465 4.071179354 3.007129301 0.96461649 1.246220719 0.659910966 0.080281424 0.152963509 2.777277516 0.021691844 0.054261177 11780.92399 -4.071179354 0.281604228 KDGADFAK ddPTM_BT-474_Pertuzumab_2h_R1 6 KDGADFAK 8 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78;P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;;; 111.06 0.0053021 16136100000 17823880 16962400 13430510 13802640 14074030 11376590 15333740 16709690 17912000 14734180 FALSE TRUE 17127303.06 16478648.96 15857701.92 14514995.9 14526733.96 11606632.44 15521398.9 16364629.06 15878704.85 13736220.86 1.246871555 1.199649388 1.154444303 1.056695 1.057549533 0.844965479 1.129961366 1.191348714 1.155973321 1 23.71148181 4.07133281 2.14297968 1.072607075 1.232914646 0.338412978 0.091091434 0.444727554 4.008628394 0.02764739 0.081580718 11785.08746 -4.07133281 0.160307571 SKS(ph)PASTSSVNGTPGSQLSTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSPASTSSVNGTPGSQLSTPR 22 1 O15075-2;O15075;Q5VZY9 O15075-2 DCLK1 Serine/threonine-protein kinase DCLK1 1 S(0.192)KS(0.674)PAS(0.034)T(0.06)S(0.017)S(0.023)VNGTPGSQLSTPR;S(0.095)KS(0.724)PAS(0.064)T(0.111)S(0.006)SVNGTPGSQLSTPR 171.25 3.78E-12 2317420000 461600 481200 399520 488930 489090 452800 522510 615530 541820 465250 TRUE FALSE 443560.1617 467476.6471 471722.1513 514163.7359 504822.024 461955.9262 528904.6337 602819.0904 480314.8651 433738.2031 1.022644901 1.077785272 1.087573444 1.185424139 1.163886465 1.065057039 1.219409842 1.389822446 1.107384274 1 18.72646499 4.071860678 0.685410937 1.205718239 0.991654497 0.104883601 0.102497145 2.304306082 1.446251087 0.050895608 0.338502249 11799.42048 -4.071860678 -0.214063742 GEVDS(ph)NGSDGGEASR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEVDSNGSDGGEASR 15 0 Q7LBC6 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 GEVDS(0.582)NGS(0.418)DGGEASR 95.767 0.0041523 58547000 103540 102330 93921 127010 112670 119570 112060 126740 123060 123880 TRUE FALSE 99493.54233 99411.64859 110894.614 133565.0013 116294.1329 121987.7873 113431.4238 124122.7747 109090.7447 115489.4973 0.861494289 0.860785188 0.960213843 1.156512103 1.006967176 1.056267368 0.982179562 1.074753788 0.944594507 1 16.81740213 4.072569699 4.119869716 1.035643269 0.863294382 0.600706721 0.055053944 0.127098626 4.210746874 0.013199073 0.030423735 11818.69972 -4.072569699 -0.172348888 EEVDTGAVNLIESGACGAFVHGLEDEMYEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEVDTGAVNLIESGACGAFVHGLEDEMYEVR 31 0 Q96HW7-2;Q96HW7-3;Q96HW7 Q96HW7-2 INTS4 Integrator complex subunit 4 0 ; 95.741 0.00037747 42195000 9156.3 10097.1 9237.5 12873.5 10959 14889 14842.8 12623.5 12363.1 12846.3 FALSE TRUE 8798.461673 9809.140594 10906.92174 13537.90288 11311.50619 15190.06578 15024.45063 12362.82031 10959.69272 11976.20866 0.734661688 0.819052245 0.910715741 1.130399717 0.944498089 1.268353468 1.254524788 1.03228164 0.915122058 1 13.54788364 4.073263601 1.612031726 1.09268348 0.739340117 0.537071118 0.113083054 0.325887135 1.568713911 0.033347036 0.121596752 11837.59838 -4.073263601 -0.353343363 DYVDLFR ddPTM_BT-474_Pertuzumab_2h_R1 8 DYVDLFR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;;;; 160.91 0.003091 3838196000 3660951 3833870 3524474 4861960 4643040 3915961 4713700 4995550 4986160 5190680 FALSE TRUE 3517876.988 3724531.781 4161424.853 5112886.338 4792387.598 3995144.414 4771387.671 4892390.147 4420152.02 4839110.62 0.726967673 0.769672792 0.859956546 1.056575627 0.990344709 0.825594769 0.986005083 1.01101019 0.913422397 1 22.20631049 4.07377511 3.062657918 0.968124077 0.745093959 0.681669286 0.060424537 0.142139522 2.673759175 0.016142396 0.040225754 11851.54883 -4.07377511 -0.223030118 AS(ph)PAPAPS(ph)RSPSAQCPFPGGTVLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPAPAPSRSPSAQCPFPGGTVLSR 25 1 P78411-3;P78411-2;P78411;H0YML8 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 2 AS(0.999)PAPAPS(0.448)RS(0.448)PS(0.104)AQCPFPGGTVLSR 56.383 0.056579 115900000 72448 74204 53719 51283 54414 63825 56237 64768 59031 65898 TRUE FALSE 69616.65206 72087.77457 63427.21827 53929.72178 56164.27573 65115.58523 56925.24523 63430.51817 52330.04836 61434.66976 1.133181839 1.173405422 1.032433616 0.877838556 0.914211404 1.059915932 0.92659805 1.03248733 0.851799946 1 15.90676543 4.074579366 4.155579351 0.958541806 1.15130293 0.616255935 0.062911516 0.133986501 4.478348056 0.015598381 0.035942707 11873.51666 -4.074579366 0.192761124 GVLTNPNCEFEANYVAIHTLATWYK ddPTM_BT-474_Pertuzumab_2h_R1 2 GVLTNPNCEFEANYVAIHTLATWYK 25 0 O60502;O60502-3;O60502-2;O60502-4;H7C3X0 O60502 MGEA5 Protein O-GlcNAcase 0 ; 196.1 8.76E-25 181214000 138270 118712 114467 143815 143375 130650 129857 138674 150547 138400 FALSE TRUE 132866.2555 115326.45 135153.7332 151237.3094 147986.7871 133291.8325 131446.2288 135810.3334 133457.5357 129026.0447 1.029763067 0.893823028 1.047491873 1.17214559 1.14695283 1.033061447 1.01875733 1.052580769 1.034345709 1 16.97730279 4.075012613 8.319327676 1.068979137 0.962824442 0.315828096 0.060010054 0.294905551 29.0125184 0.015540885 0.033764888 11885.36745 -4.075012613 -0.106154695 AAKPGPAEAPSPTASPSGDAS(ph)PPATAPYDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPSPTAS(0.002)PS(0.023)GDAS(0.732)PPAT(0.206)APY(0.036)DPR;AAKPGPAEAPSPTASPS(0.001)GDAS(0.996)PPAT(0.004)APYDPR;AAKPGPAEAPSPTASPS(0.005)GDAS(0.994)PPATAPYDPR;AAKPGPAEAPSPTASPSGDAS(0.999)PPATAPYDPR 185.23 1.38E-18 3197150000 1021490 1066720 861110 987140 1042650 1047890 1049100 1130410 1134780 1141880 TRUE FALSE 981569.0415 1036298.19 1016731.732 1038086.414 1076187.784 1069079.054 1061939.2 1107066.638 1005964.532 1064539.451 0.922059808 0.973470912 0.955090703 0.975150722 1.010942134 1.004264382 0.997557394 1.039948907 0.944976282 1 20.02179798 4.076428874 0.822443084 1.005126412 0.925055672 0.443157725 0.024820729 0.968626052 0.925249658 0.00949837 0.059692376 11924.18964 -4.076428874 -0.08007074 DDFNSGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDFNSGFR 8 0 Q15056 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 ; 240.53 2.19E-08 697820000 630820 649910 593650 762070 730190 662830 846930 809450 819640 897990 FALSE TRUE 606166.857 631375.2031 700935.7607 801400.524 753677.2245 676232.8767 857294.9827 792734.5746 726597.9034 837168.3375 0.724068064 0.754179506 0.837269793 0.957275243 0.900269624 0.807762127 1.024041336 0.946923742 0.867923297 1 19.67515822 4.076452307 2.29684911 0.928100746 0.729878271 0.623436823 0.059275213 0.196802447 2.053162263 0.016017593 0.045660934 11924.83304 -4.076452307 -0.198222475 GYSYDLEVEQAYDLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GYSYDLEVEQAYDLAR 16 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 321.79 8.19E-58 1437370000 826490 841000 738230 932870 919350 854060 970910 954050 994840 982680 FALSE TRUE 794189.8571 817015.5034 871644.5828 981015.5325 948921.7277 871329.6784 982792.287 934348.5341 881909.9339 916122.2083 0.866903836 0.89181934 0.951450118 1.07083479 1.035802559 0.951106381 1.07277422 1.019895081 0.962655338 1 19.80518054 4.076663538 3.03163353 1.01861077 0.877111143 0.671485572 0.038203237 0.137141939 2.524454388 0.009804008 0.024591488 11930.6344 -4.076663538 -0.141499627 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;; 186.43 1.75E-18 5700700000 781660 737550 728920 992660 973870 1018750 1068140 590080 1134580 1094170 FALSE TRUE 751111.863 716515.7961 860652.0587 1043891.302 1005195.413 1039349.823 1081212.217 577894.6418 1005787.235 1020060.891 0.736340222 0.702424534 0.84372616 1.023361753 0.985426872 1.018909588 1.059948701 0.566529554 0.986007055 1 19.96022384 4.077324797 4.21226337 0.921370102 0.721618145 0.303480034 0.134371706 0.316168777 10.72166592 0.038287702 0.08815226 11948.81389 -4.077324797 -0.199751957 DGADFAK ddPTM_BT-474_Pertuzumab_2h_R1 5 DGADFAK 7 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78;P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;; 134.06 0.0074714 12491650000 11434660 10848800 8768280 9112580 9461820 8713210 9944900 10306090 11257550 9646130 FALSE TRUE 10987780.85 10539402.85 10352903.25 9582881.346 9766168.033 8889397.076 10066608.66 10093265.64 9979640.12 8992789.023 1.221843503 1.171983777 1.151244983 1.065618388 1.085999906 0.988502794 1.119408966 1.122373227 1.109738046 1 23.10033719 4.077993153 1.779648705 1.077875239 1.210038313 0.573700916 0.044904562 0.304979408 1.834263128 0.01297561 0.04403389 11967.21664 -4.077993153 0.132163074 S(ph)WS(ph)LGVCK ddPTM_BT-474_Pertuzumab_2h_R1 2 SWSLGVCK 8 0 Q6ZWI9 Q6ZWI9 RFPL4B Ret finger protein-like 4B 2 S(1)WS(1)LGVCK;S(1)WS(1)LGVCK 53.17 0.073038 1387960000 2520500 2469100 1787020 1745930 2324100 1263870 2150400 1552570 2056150 1989610 TRUE FALSE 2421996.073 2398683.686 2109974.266 1836037.657 2398856.787 1289426.317 2176717.238 1520508.887 1822744.472 1854851.943 1.30576248 1.293194152 1.137543228 0.989856718 1.293287476 0.695164012 1.173526139 0.819746769 0.982690009 1 20.8228726 4.078086572 0.593578488 0.935630985 1.431690118 0.403327569 0.153053996 1.747635722 0.788760093 0.079335544 0.54029857 11969.79113 -4.078086572 0.496059133 RLEAGAMVLADR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEAGAMVLADR 12 1 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 136.14 0.00018488 433850000 381540 378320 321690 381780 384610 348120 408310 406020 402520 427970 FALSE TRUE 366628.995 367530.684 379826.539 401483.7116 396981.3299 355159.2249 413307.0199 397635.5451 356827.6171 398983.2107 0.918908328 0.921168295 0.951986271 1.006267183 0.994982544 0.890160827 1.035900782 0.99662225 0.894342437 1 18.60596851 4.078265907 3.716067605 0.976568748 0.920229087 0.184955707 0.04469072 0.35242921 9.55738357 0.011328323 0.026788206 11974.73489 -4.078265907 -0.056339661 NVPHEDICEDS(ph)DIDGDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 NVPHEDICEDSDIDGDYR 18 0 O00629 O00629 KPNA4 Importin subunit alpha-3 1 NVPHEDICEDS(1)DIDGDYR 160.92 2.54E-11 242190000 106120 107300 84605 64773 79398 90971 59525 75607 76386 74353 TRUE FALSE 101972.7131 104239.9091 99895.00553 68115.94229 81951.90878 92810.49595 60253.48476 74045.68903 67714.98152 69317.00508 1.471106736 1.503814381 1.441132741 0.982672898 1.182277115 1.338928245 0.869245356 1.068218238 0.976888448 1 16.0809217 4.079062034 0.520843311 0.993915059 1.714763558 0.642000238 0.134403657 1.474953749 0.496841655 0.089143785 0.602748193 11996.70651 -4.079062034 0.7208485 LKGNKHDDGT(ph)QSDSENAGAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKGNKHDDGTQSDSENAGAHR 21 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 LKGNKHDDGT(0.5)QS(0.5)DSENAGAHR 86.791 0.002713 80050000 81436 84644 54559 32131 55819 74040 51374 44478 78661 58990 TRUE FALSE 78253.39109 82230.036 64419.02496 33789.28476 57614.46883 75537.13953 52002.73038 43559.51376 69731.73305 54994.55476 1.422929805 1.495239599 1.17137097 0.614411461 1.047639518 1.373538523 0.945597807 0.792069578 1.267975227 1 15.74700116 4.079962067 4.593058922 0.991291991 1.451427381 0.434085922 0.203825581 0.184908929 7.16130775 0.053146274 0.120796885 12021.59428 -4.079962067 0.46013539 AVFDETYPDPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVFDETYPDPVR 12 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 221.52 6.28E-11 840120000 849800 841925 749282 959387 948470 878272 917845 964260 922189 1029020 FALSE TRUE 816588.8765 817914.1233 884693.9251 1008901.078 978978.3989 896031.2616 929077.8617 944347.694 817505.9709 959323.5588 0.8512132 0.852594639 0.922205982 1.051679664 1.020488228 0.934024035 0.96847185 0.984389141 0.85216918 1 19.87165796 4.080316079 3.971215157 0.974002603 0.852885654 0.473204338 0.050693587 0.181958053 5.528220734 0.012987013 0.030299901 12031.3976 -4.080316079 -0.121116949 AS(ph)SPGHPAFLEDGSPSPVLAFAASPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSPGHPAFLEDGSPSPVLAFAASPR 26 0 Q9C073;D6RJ87;Q9C073-2 Q9C073 FAM117A Protein FAM117A 1 AS(0.552)S(0.448)PGHPAFLEDGSPSPVLAFAASPR;AS(0.5)S(0.5)PGHPAFLEDGSPSPVLAFAASPR 232.73 2.49E-36 159646000 81582 79249 88612 143287 107897 111077 138560 116522 132256 131663 TRUE FALSE 78393.68525 76988.89611 104626.1596 150682.0592 111367.605 113323.053 140255.7387 114115.78 117242.8533 122745.3477 0.638669299 0.627224555 0.852383911 1.227598944 0.907306118 0.923237052 1.14265625 0.929695358 0.955171463 1 16.90530882 4.080410779 3.966272064 1.007136226 0.635773959 0.704848229 0.097416763 0.110538299 3.35035312 0.024174827 0.05642029 12034.02138 -4.080410779 -0.371362266 VVLEHEEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVLEHEEVR 9 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 211.52 5.01E-06 1389690000 870800 911440 823270 1033980 1058620 1084000 1176150 1041270 1074870 1177680 FALSE TRUE 836768.1733 885446.6236 972053.2025 1087343.832 1092671.474 1105919.223 1190544.076 1019767.411 952855.2638 1097914.685 0.762143166 0.806480354 0.885363149 0.990371881 0.995224391 1.007290674 1.084368478 0.928822089 0.867877329 1 20.06633452 4.081087117 1.953920226 0.984239901 0.76890335 0.692566998 0.053127741 0.203036781 1.499598382 0.015452524 0.049165108 12052.77689 -4.081087117 -0.215336551 WNTEDKVSHVSTGGGASLELLEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 WNTEDKVSHVSTGGGASLELLEGK 24 1 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 132.48 2.94E-05 913890000 1402700 1996200 950700 980100 940560 1251300 800000 820680 1055400 766790 FALSE TRUE 1347880.933 1939270.33 1122512.638 1030683.078 970813.9666 1276602.143 809790.6393 803732.6712 935595.4166 714854.6303 1.885531514 2.712817751 1.570267003 1.441807935 1.358057884 1.785820626 1.132804636 1.12433023 1.308791154 1 19.44729037 4.081498924 5.441078898 1.324031391 2.291311281 0.667835293 0.275317526 0.109818299 5.458844441 0.068277088 0.152056219 12064.21099 -4.081498924 0.96727989 TLMELLNQMDGFDTLHR ddPTM_BT-474_Pertuzumab_2h_R1 3 TLMELLNQMDGFDTLHR 17 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;; 218.12 4.75E-15 2168731000 723626 743330 649991 815687 818008 822245 863158 782127 886393 885787 FALSE TRUE 695345.8959 722130.9562 767458.8327 857784.7038 844319.9702 838871.3573 873721.5858 765975.8041 785773.3827 825791.8575 0.842035302 0.874470909 0.929361104 1.038742022 1.022436783 1.015838737 1.058040931 0.927565218 0.951539272 1 19.65541867 4.081790611 2.677915162 0.999275068 0.853611565 0.704599755 0.037404016 0.161484679 2.312970119 0.010873198 0.028844136 12072.31645 -4.081790611 -0.145663503 KTKFENLCK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTKFENLCK 9 2 P07900;P07900-2;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ; 113.47 0.0010095 819860000 3766900 4368500 2129120 1271420 1913730 1161790 2227320 1872090 2193820 1879840 FALSE TRUE 3619685.383 4243914.657 2513899.346 1337038.139 1975286.863 1185282.19 2254578.608 1833430.687 1944786.751 1752516.762 2.065421262 2.421611449 1.434450956 0.762924594 1.127114391 0.676331442 1.286480482 1.046170129 1.109710784 1 20.74099681 4.081895591 3.999566793 1.017207236 2.235911071 0.871624623 0.188219078 0.063243822 1.937599216 0.0455318 0.106177837 12075.23498 -4.081895591 1.218703836 up EFEVYGPIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFEVYGPIKR 10 1 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 117.67 0.0014855 2487900000 2259300 2260700 1759720 1824060 1847800 1783860 2105210 2237800 2255100 2170320 FALSE TRUE 2171004.058 2196227.049 2077740.549 1918199.955 1907236.165 1819930.871 2130974.19 2191588.648 1999110.502 2023322.293 1.072989738 1.085455865 1.026895495 0.948044689 0.942625983 0.899476508 1.053205511 1.083163397 0.988033646 1 20.94829471 4.081915301 4.231302694 0.994630134 1.078311047 0.336527427 0.050436977 0.302777186 10.19338297 0.01534117 0.035381924 12075.78303 -4.081915301 0.083680913 S(ph)LPSHMEEAPNVFQLYQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLPSHMEEAPNVFQLYQR 18 0 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(1)LPSHMEEAPNVFQLYQR;S(1)LPSHMEEAPNVFQLYQR;S(0.999)LPS(0.001)HMEEAPNVFQLYQR;S(1)LPSHMEEAPNVFQLYQR 301.92 8.04E-50 914730000 526590 481340 476250 672160 597960 494835 597770 643980 617690 615390 TRUE FALSE 506010.2806 467612.6545 562318.9691 706850.2582 617193.9265 504840.9027 605085.6881 630681.588 547572.4208 573709.0872 0.881998023 0.815069283 0.980146527 1.232070877 1.075795974 0.879959746 1.054690786 1.099305558 0.954442649 1 19.12995984 4.082242923 5.125408274 1.049087409 0.85234144 0.422007822 0.089111638 0.183090646 8.294466919 0.023028234 0.051627046 12084.89617 -4.082242923 -0.19674597 ESVDSRDS(ph)S(ph)HSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESVDSRDSSHSR 12 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 ES(0.021)VDS(0.03)RDS(0.963)S(0.975)HS(0.01)R 49.595 0.096052 37759000 52017 52266 51269 65269 60518 69740 77740 58565 77945 75839 TRUE FALSE 49984.11813 50775.42485 60534.44877 68637.54091 62464.61643 71150.19058 78691.40537 57355.61228 69097.01037 70702.35698 0.706965372 0.718157456 0.856187139 0.970795654 0.883487045 1.006334069 1.112995503 0.811226312 0.977294299 1 16.10947069 4.082405292 2.202154545 0.957608082 0.700482562 0.643584907 0.075012406 0.204858821 1.955321763 0.02079006 0.061245267 12089.41517 -4.082405292 -0.257125521 FDLLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDLLKR 6 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;H0Y9G8;O15519-11;C9JV51;F8WBH9;C9J408;O15519-5;E9PAP3;O15519-14;O15519-8;O15519-6;O15519-10;O15519-12;O15519-9;O15519-2;O15519-13;O15519 D6RGI3 SEPT11;CFLAR Septin-11;CASP8 and FADD-like apoptosis regulator;CASP8 and FADD-like apoptosis regulator subunit p43;CASP8 and FADD-like apoptosis regulator subunit p12 0 ; 103.71 0.05524 602770000 995910 1083920 709210 628900 738960 565670 847650 806330 915320 895040 FALSE TRUE 956988.7362 1053007.663 837380.0233 661357.6044 762729.3195 577108.235 858023.7943 789679.0037 811416.7109 834418.1436 1.146893489 1.261966403 1.003549635 0.792597344 0.914085253 0.691629538 1.028289954 0.94638283 0.972434165 1 19.670411 4.082482949 4.597929707 0.905100647 1.200863347 0.589481106 0.098068826 0.134665832 5.167705766 0.024839236 0.056508871 12091.57708 -4.082482949 0.2957627 VMMEGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMMEGGR 7 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YB86 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 106.42 0.01793 129170000 139380 149410 97345 100140 99974 50518 144700 104540 110160 131410 FALSE TRUE 133932.8755 145148.9731 114937.4069 105308.2374 103189.7545 51539.50857 146470.8819 102381.2125 97655.09863 122509.4837 1.09324496 1.184797852 0.938191914 0.859592533 0.842300134 0.420698113 1.195588109 0.835700302 0.797122767 1 16.90253391 4.082506156 3.473667079 0.847826602 1.139175833 0.278173946 0.182990088 0.289607845 6.897022027 0.046282726 0.111759314 12092.22322 -4.082506156 0.291349231 SMGTGDTPGLEVPS(ph)SPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMGTGDTPGLEVPSSPLR 18 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.83)S(0.17)PLR 98.508 0.0047254 168580000 137990 132220 115500 131280 137430 140540 140630 142310 146950 136970 TRUE FALSE 132597.1982 128449.2151 136373.4193 138055.3765 141850.5608 143381.8151 142351.072 139371.2488 130268.8521 127692.8999 1.038406978 1.005922923 1.067979656 1.081151549 1.110872734 1.122864429 1.114792382 1.091456525 1.020173026 1 16.96231878 4.083190598 4.170676644 1.086266437 1.022555941 0.213785503 0.038986038 0.251736857 8.244674119 0.009645487 0.022321754 12111.29543 -4.083190598 -0.063710496 LPFPIIDDR ddPTM_BT-474_Pertuzumab_2h_R1 8 LPFPIIDDR 9 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;; 182.68 0.00010713 3301359000 914512 950152 892647 1029070 942268 858451 1011029 1001579 1001587 1095969 FALSE TRUE 878771.86 923054.5953 1053968.17 1082180.426 972576.906 875809.4674 1023402.275 980896.0436 887891.0428 1021738.043 0.860075501 0.903416097 1.031544412 1.059156437 0.951884793 0.857176135 1.001628824 0.960026936 0.869000668 1 19.96259393 4.083779001 0.003600764 1.893165469 0.000215936 0.021508259 0.069429524 305763.591 213.6316352 54982.39792 57338.47176 12127.71552 -4.083779001 -1.892949533 KPS(ph)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPSLIGLDPEQGHLNPMSYTQHCITTMAAPSWK 33 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 KPS(0.999)LIGLDPEQGHLNPMS(0.001)YT(0.001)QHCITTMAAPSWK;KPS(1)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK 153.33 6.10E-11 1989110000 824120 759100 573410 480680 544820 755440 526740 413690 858560 724060 TRUE FALSE 791912.4793 737451.2112 677037.9424 505487.9524 562344.6301 770715.5144 533186.4017 405147.1569 761099.8682 675018.7713 1.173171048 1.092489932 1.002991281 0.748850216 0.833079988 1.14176901 0.789883814 0.600201319 1.127524005 1 19.3645681 4.084830418 2.788514823 0.861088691 1.141357292 0.247498572 0.161317595 0.33081055 5.139643 0.044082224 0.115269971 12157.112 -4.084830418 0.2802686 DALQPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DALQPGR 7 0 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 83.614 0.051531 210700000 178370 199080 138600 147000 148600 165130 149580 159590 173550 183690 FALSE TRUE 171399.1032 193402.4333 163648.1031 154586.6876 153379.854 168469.0417 151410.6048 156294.4107 153849.3316 171248.5127 1.000879368 1.129367083 0.955617661 0.902703826 0.895656561 0.983769372 0.884157196 0.912676018 0.89839806 1 17.38573193 4.084960512 5.955645106 0.920573542 1.063667923 0.584021854 0.046336365 0.116763966 6.43330476 0.010643343 0.023526505 12160.75424 -4.084960512 0.143094381 NISFNDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NISFNDKK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 140.75 0.0010334 1580000000 1610200 1342800 1061800 900770 815690 823340 738770 1104600 1278700 1191000 FALSE TRUE 1547271.604 1304504.659 1253690.88 947258.8476 841927.4096 839988.4989 747811.2883 1081789.624 1133547.337 1110332.509 1.393520942 1.174877479 1.129113008 0.853130787 0.758266017 0.756519774 0.67350211 0.97429339 1.020907996 1 20.08256035 4.085377803 1.601253668 0.846987973 1.34655241 0.695263129 0.116061523 0.246366943 1.164093597 0.034944992 0.130747175 12172.4445 -4.085377803 0.499564438 S(ph)PSVAAMASPQLCR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPSVAAMASPQLCR 14 0 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 S(0.999)PS(0.001)VAAMASPQLCR;S(0.999)PS(0.001)VAAMASPQLCR;S(0.994)PS(0.006)VAAMASPQLCR;S(1)PSVAAMASPQLCR;S(0.999)PS(0.001)VAAMASPQLCR;S(0.999)PS(0.001)VAAMASPQLCR 275.66 4.69E-33 3304390000 819822 771592 723596 821169 803910 809369 855185 994643 963057 902942 TRUE FALSE 787782.4499 749586.9516 854365.8935 863549.6305 829768.4952 825734.9957 865651.0098 974103.2745 853734.8068 841784.9341 0.935847647 0.890473233 1.014945574 1.025855412 0.985725049 0.980933445 1.02835175 1.157187822 1.014195874 1 19.68309216 4.085484408 0.504031486 1.064191205 0.863574666 0.369922228 0.052155171 2.362428888 0.736376135 0.038552266 0.262223036 12175.43279 -4.085484408 -0.200616538 S(ph)PPAS(ph)PESWK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 S(1)PPAS(0.975)PES(0.025)WK;S(1)PPAS(0.992)PES(0.008)WK;S(1)PPAS(1)PESWK;S(1)PPAS(0.999)PES(0.001)WK 122.34 0.00071785 1682610000 1907440 1657200 1668660 1937580 1940880 1734560 2114790 2300710 2274480 2326680 TRUE FALSE 1832895.136 1609938.279 1970223.981 2037578.736 2003310.168 1769633.992 2140671.433 2253199.535 2016290.566 2169091.891 0.845005757 0.742217647 0.908317434 0.939369486 0.923570908 0.815840951 0.986897531 1.03877551 0.929555163 1 21.04865974 4.0856399 0.332973416 1.011838903 0.695867274 0.47678002 0.061879189 3.717095649 0.46098866 0.069360626 0.459543994 12179.79279 -4.0856399 -0.315971629 LMQQLLESDKYAER ddPTM_BT-474_Pertuzumab_2h_R1 2 LMQQLLESDKYAER 14 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 168.1 3.23E-06 1116550000 600700 578810 536710 683790 620960 682000 655530 623810 792490 802580 FALSE TRUE 577223.9799 562302.9055 633705.436 719080.4838 640933.7423 695790.5073 663552.5722 610928.1055 702529.8576 748220.5417 0.771462353 0.751520273 0.846950064 0.961054186 0.856610727 0.929927031 0.886840891 0.816508063 0.938934202 1 19.51310405 4.086138175 4.052533169 0.89773459 0.762466229 0.571657704 0.051023748 0.160142388 4.964301143 0.012845338 0.029948978 12193.77494 -4.086138175 -0.135268361 TCEESSFCKR ddPTM_BT-474_Pertuzumab_2h_R1 3 TCEESSFCKR 10 1 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 96.171 0.011099 1558920000 918610 1165400 734310 798420 799230 880020 874340 780540 1004170 908160 FALSE TRUE 882709.7056 1132163.933 867016.1516 839626.5519 824937.9588 897814.6073 885040.4345 764421.5762 890180.8314 846649.5143 1.04259164 1.337228586 1.024055571 0.991704994 0.974355911 1.060432437 1.045344525 0.902878421 1.051415983 1 19.69140534 4.086843347 9.354168548 0.998364771 1.189371222 0.465852614 0.078761494 0.221429586 21.77760706 0.018310461 0.039690547 12213.59028 -4.086843347 0.191006451 DSEEAEIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSEEAEIIR 9 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 88.948 0.025182 0 504730 576160 466750 639000 634800 558290 628410 679160 699810 741730 FALSE TRUE 485004.5936 559728.4809 551102.1078 671978.8666 655218.9185 569579.0063 636100.6696 665135.1087 620370.5026 691491.9664 0.701388616 0.809450446 0.796975431 0.971781162 0.94754379 0.823695768 0.919895965 0.961884072 0.897147809 1 19.39935297 4.087173799 1.726985746 0.927548299 0.73073192 0.664183406 0.052740775 0.240608641 1.350451284 0.014636673 0.051609033 12222.88708 -4.087173799 -0.196816379 IQRPNTTQEGEEMETDMDVADVAMES(ph)SPGSSISMEHR ddPTM_BT-474_Pertuzumab_2h_R1 3 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 1 IQRPNTTQEGEEMETDMDVADVAMES(0.558)S(0.436)PGS(0.005)S(0.001)ISMEHR;IQRPNTTQEGEEMETDMDVADVAMES(0.47)S(0.47)PGS(0.047)S(0.011)IS(0.002)MEHR;IQRPNTTQEGEEMET(0.001)DMDVADVAMES(0.359)S(0.359)PGS(0.114)S(0.13)IS(0.036)MEHR 159.22 9.18E-18 438130000 86557 91327 79737 104543 99888 118414 101440 91445 105828 121949 TRUE FALSE 83174.25675 88722.44338 94147.24964 109938.4768 103100.9882 120808.4122 102681.4531 89556.62879 93814.84911 113689.2856 0.731592747 0.780394062 0.828110135 0.967008247 0.906866357 1.062619152 0.903176166 0.787731476 0.825186372 1 16.79473677 4.087546111 2.643202098 0.909495183 0.749863209 0.430343681 0.076499034 0.307909772 4.291355357 0.022445851 0.060308915 12233.36998 -4.087546111 -0.159631974 RTETVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTETVQK 7 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 127.02 0.0062459 239540000 481950 449030 312040 311450 262030 136166 455130 264750 379620 452810 FALSE TRUE 463114.8612 436224.104 368432.5693 327523.9718 270458.4329 138919.3698 460700.0171 259282.82 336527.1291 422140.7754 1.097062611 1.033361688 0.872771812 0.775864335 0.640683034 0.32908304 1.09134214 0.614209371 0.797191716 1 18.68736466 4.088010102 1.845730501 0.724886062 1.093269793 0.28412867 0.198210321 0.433046525 2.819940111 0.052934668 0.177450626 12246.44685 -4.088010102 0.368383731 ALS(ph)SDSILSPAPDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.498)S(0.498)DS(0.004)ILSPAPDAR;ALS(0.892)S(0.106)DS(0.002)ILSPAPDAR;ALS(0.835)S(0.141)DS(0.024)ILSPAPDAR 439.77 5.54E-175 3860990000 1186020 1197130 845090 1039240 853180 754430 822720 1387630 945310 950720 TRUE FALSE 1139669.027 1162989.025 997816.5619 1092875.301 880623.3095 769685.0915 832788.6935 1358974.956 838002.3719 886326.8876 1.285833752 1.312144583 1.125788438 1.233038641 0.993564927 0.868398671 0.93959543 1.533266083 0.945477773 1 19.75747935 4.088162476 1.5690793 1.097752854 1.312321321 0.18164145 0.181958219 0.972811307 4.382044855 0.057685794 0.220626675 12250.74433 -4.088162476 0.214568466 DETNYGIPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DETNYGIPQR 10 0 P63244;D6RHH4;D6R9L0;D6RAC2;D6R9Z1;D6RFX4;D6REE5;E9PD14;D6RFZ9;D6RAU2;D6RBD0;D6R909;D6RGK8 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;; 181.55 4.36E-06 3042190000 1711710 1682270 1548460 1776400 1847220 1894960 1882210 1961800 2182220 2113380 FALSE TRUE 1644814.481 1634293.307 1828301.167 1868080.217 1906637.509 1933277.39 1905245.049 1921288.144 1934503.534 1970238.89 0.834829974 0.829489924 0.92795913 0.948149093 0.967718949 0.981240092 0.967012203 0.975154919 0.981862425 1 20.90993914 4.088227679 1.533231176 0.975959746 0.818268453 0.946878905 0.013290868 0.083365742 0.35582129 0.003532396 0.013783449 12252.58372 -4.088227679 -0.157691293 VEELGDLAQAHIQQLSEAAGEDDHFLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEELGDLAQAHIQQLSEAAGEDDHFLIR 28 0 A6NDU8;A0A0C4DGW6 A6NDU8 C5orf51 UPF0600 protein C5orf51 0 193.57 1.08E-18 21677000 16332 17671 16443 23578 23058 20143 23762 19729 26307 23780 FALSE TRUE 15693.72738 17167.04038 19414.61587 24794.86341 23799.68151 20550.30526 24052.80646 19321.58926 23320.73965 22169.35942 0.707901707 0.774358882 0.87574095 1.118429402 1.073539432 0.926968834 1.084957215 0.87154477 1.051935656 1 14.43627946 4.08824978 2.944552675 1.007189292 0.73470839 0.698826333 0.072883098 0.144011201 2.491173825 0.019354717 0.049675818 12253.20727 -4.08824978 -0.272480902 KDEVYLNLVLDYVPETVYR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDEVYLNLVLDYVPETVYR 19 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 0 122.77 5.22E-05 176000000 155160 149370 139790 166910 167260 156600 175890 195080 182660 182790 FALSE TRUE 149096.1757 145110.1138 165053.1626 175524.2451 172640.0698 159766.5593 178042.5944 191051.5298 161925.2026 170409.4705 0.87492893 0.851537848 0.968568015 1.030014615 1.013089644 0.937545072 1.044792839 1.121132114 0.950212462 1 17.37864599 4.088271212 3.100653789 1.023009787 0.861611329 0.590049863 0.048958505 0.169288023 3.238445889 0.013948222 0.035111295 12253.81196 -4.088271212 -0.161398458 ILYEEVDESEVEVIHVPSPALEER ddPTM_BT-474_Pertuzumab_2h_R1 2 ILYEEVDESEVEVIHVPSPALEER 24 0 Q86TI2;Q86TI2-4;Q86TI2-2;M0R2A8;M0R162 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 ; 209.67 5.02E-25 87140000 36567 39969 34307 48205 38234 51270 46490 41403 49745 52839 FALSE TRUE 35137.92121 38829.12325 40507.03806 50692.86583 39463.83133 52306.71453 47058.95853 40548.01358 44098.15615 49260.16747 0.713313069 0.788245864 0.822308168 1.029084318 0.801130677 1.061846056 0.955314627 0.823139986 0.895209221 1 15.58813391 4.08933565 2.666524 0.9252697 0.742919453 0.461882066 0.081613935 0.2541458 3.604913585 0.02128653 0.057079027 12283.88241 -4.08933565 -0.182350246 LGTQEYLQQLESHMK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGTQEYLQQLESHMK 15 0 Q6P2E9;Q6P2E9-2;I3L2F4 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ; 184.99 4.42E-07 831910000 373350 418450 302270 346770 342360 308820 359780 342870 421820 435390 FALSE TRUE 358759.0692 406516.2157 356896.913 364666.8413 353372.3203 315064.552 364183.0953 335789.6147 373936.762 405900.6475 0.883859317 1.001516549 0.879271603 0.898414042 0.870588215 0.776211011 0.897222257 0.827270458 0.921251948 1 18.63076712 4.089450422 10.37740087 0.871831291 0.942604644 0.104474031 0.061865847 0.559600509 60.5791458 0.01433625 0.031030676 12287.12912 -4.089450422 0.070773353 NS(ph)MDIQCEVDALLER ddPTM_BT-474_Pertuzumab_2h_R1 1 NSMDIQCEVDALLER 15 0 Q02241;H7BYN4;A0A2U3TZL8;A0A2R8Y531;H0YME6;Q02241-2 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 NS(1)MDIQCEVDALLER 87.287 0.0075832 4716900 8008.5 5478.2 6617.6 7124.8 7631.5 8564.4 7942 8928 7680.3 7776.1 TRUE FALSE 7695.518966 5321.9671 7813.547528 7492.511782 7876.974128 8737.578036 8039.196572 8743.63368 6808.464542 7249.417821 1.061536134 0.734123378 1.077817243 1.033532894 1.086566442 1.205279962 1.108943748 1.20611529 0.939173974 1 12.82364943 4.09044487 9.868005239 1.100751577 0.898161601 0.308809308 0.108019672 0.312459037 31.43058062 0.025475637 0.055176955 12315.29644 -4.09044487 -0.202589976 KLEPLSQDEDQHADLTQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLEPLSQDEDQHADLTQSR 19 1 M0R0J4;M0QYZ7;M0R253;M0QX43;A0A3B3IU31;B4E3M2;M0R264;Q5J8M5;A0A087WZK0;P49366-2;P49366-3;P49366 M0R0J4 DHPS Deoxyhypusine synthase 0 ; 179.03 2.38E-14 303770000 390390 392970 330220 399090 374150 430790 376390 409800 437560 420660 FALSE TRUE 375133.1272 381762.8804 389898.0997 419687.0827 386184.8745 439500.869 380996.3734 401337.4868 387890.0232 392168.3235 0.956561519 0.973466895 0.994211098 1.070170785 0.984742651 1.120694464 0.97151236 1.023380683 0.989090653 1 18.58111348 4.092211095 3.441015068 1.023550968 0.964481242 0.229595415 0.042206482 0.31847471 7.381228693 0.010225631 0.024960233 12365.48328 -4.092211095 -0.059069726 YQDEVFGGFVTEPQEES(ph)EEEVEEPEER ddPTM_BT-474_Pertuzumab_2h_R1 7 YQDEVFGGFVTEPQEESEEEVEEPEER 27 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER 201.7 2.86E-25 5060720000 1939319 1961260 1719885 2190092 2061037 2242791 2046979 2154599 2234173 2398347 TRUE FALSE 1863528.269 1905326.785 2030706.478 2303122.911 2127332.127 2288141.771 2072030.541 2110105.778 1980559.047 2235904.821 0.833455991 0.85215022 0.908225815 1.030063037 0.951441272 1.023362779 0.926707846 0.943736852 0.885797565 1 21.09242735 4.092215538 3.416012815 0.962299511 0.841834062 0.574953976 0.04214878 0.166765399 3.814502539 0.010873569 0.026600871 12365.60979 -4.092215538 -0.120465449 YGLDTEQVWR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGLDTEQVWR 10 0 Q9NXC5;Q9NXC5-2 Q9NXC5 MIOS WD repeat-containing protein mio 0 93.178 0.020852 57945000 63995 58277 56763 76286 66024 67341 69094 76235 67172 73720 FALSE TRUE 61494.00465 56614.99702 67021.33679 80223.1296 68147.72192 68702.68116 69939.59304 74660.72061 59546.91617 68726.87874 0.894759165 0.823767907 0.975183771 1.16727445 0.991573067 0.999647917 1.017645415 1.086339464 0.86642835 1 16.06858682 4.092263019 5.221934943 1.026891174 0.861966244 0.414636976 0.073886474 0.170380558 7.51103981 0.01789807 0.040139223 12366.9618 -4.092263019 -0.164924929 GAPVNISSS(ph)DLTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNISS(0.002)S(0.997)DLT(0.001)GR;GAPVNISS(0.03)S(0.97)DLTGR;GAPVNIS(0.003)S(0.039)S(0.958)DLTGR;GAPVNIS(0.001)S(0.068)S(0.931)DLTGR 251.07 1.06E-18 894700000 1647250 1635260 1190810 1280320 1235550 1208160 840930 1377890 1131440 1041160 TRUE FALSE 1582873.649 1588623.986 1406015.856 1346397.469 1275292.588 1232589.823 851221.5529 1349436.09 1003003.675 970641.3058 1.63075035 1.636674615 1.448543193 1.387121546 1.313865977 1.269871595 0.876968194 1.390252075 1.033341224 1 19.88857873 4.092785392 0.390331112 1.056789898 1.94352842 0.714064183 0.131166164 1.96989422 0.345161882 0.117486215 0.785257736 12381.84581 -4.092785392 0.886738522 VEYEKR ddPTM_BT-474_Pertuzumab_2h_R1 3 VEYEKR 6 1 P63279 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 ;; 115.3 0.039363 562750000 1089750 1129390 675610 535020 742370 650980 628580 708930 653350 518730 FALSE TRUE 1047161.365 1097180.903 797707.7559 562632.4463 766249.0053 664143.2616 636272.7501 694290.3478 579184.4471 483595.9551 2.165364194 2.268796692 1.649533557 1.163434972 1.584481833 1.373343293 1.315711481 1.435682703 1.197661893 1 18.88344265 4.092821016 3.433189777 1.337364158 2.221272508 0.840843169 0.158060069 0.078836097 1.818711245 0.037819816 0.092426713 12382.86153 -4.092821016 0.88390835 ATCAPQHGAPGPGPADASK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATCAPQHGAPGPGPADASK 19 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 120.56 3.77E-05 116500000 58128 53960 43867 61440 59948 62259 60585 64560 81651 78747 FALSE TRUE 55856.2935 52421.11363 51794.74272 64610.92576 61876.28186 63517.91964 61326.45735 63226.81344 72382.32079 73413.39555 0.76084607 0.714053794 0.705521688 0.880097226 0.842847295 0.865208851 0.835357865 0.861243551 0.985955223 1 16.16375571 4.093228472 0.15915924 1.058489774 0.476548548 0.757316114 0.046625224 8.807875561 0.310674887 0.220595263 1.111421809 12394.48459 -4.093228472 -0.581941226 VQPSGGPAADQDVLGEES(ph)PLGKPAMLHLPSEQGAPETLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQPSGGPAADQDVLGEESPLGKPAMLHLPSEQGAPETLQR 40 1 C9J2V2 C9J2V2 IKBKG 1 VQPSGGPAADQDVLGEES(1)PLGKPAMLHLPSEQGAPETLQR 173.81 2.04E-19 163660000 43898 42434 39162 44028 46556 55664 42512 46411 51656 55504 TRUE FALSE 42182.41763 41223.82387 46239.44455 46300.29036 48053.51602 56789.56422 43032.27457 45452.59663 45792.22744 51744.66464 0.815203228 0.796677767 0.893607967 0.894783852 0.928666102 1.097496034 0.831627277 0.878401608 0.884965199 1 15.65912249 4.093553148 2.152354372 0.924333687 0.801394026 0.3234657 0.070315306 0.418748451 3.804738529 0.01977317 0.060011309 12403.75409 -4.093553148 -0.12293966 NSWGEPWGER ddPTM_BT-474_Pertuzumab_2h_R1 2 NSWGEPWGER 10 0 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ; 135.55 0.00032865 436440000 639320 655360 557310 682410 684800 653660 722740 722130 719990 702010 FALSE TRUE 614334.6676 636669.7745 658028.3143 717629.2619 706827.2139 666877.4531 731585.1083 707217.7631 638259.7536 654462.2374 0.938686195 0.972813614 1.005448866 1.096517447 1.08001222 1.018970102 1.11784159 1.080608968 0.975243058 1 19.31995043 4.093725939 2.559329783 1.060776391 0.950854663 0.437499261 0.043354462 0.229235169 2.989540041 0.011196169 0.030785684 12408.69012 -4.093725939 -0.109921728 QLS(ph)ESES(ph)SLEMDDER ddPTM_BT-474_Pertuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 QLS(1)ESES(0.589)S(0.411)LEMDDER;QLS(0.916)ES(0.085)ES(0.68)S(0.319)LEMDDER 246.31 5.33E-18 584060000 370410 374970 412770 558650 522680 512150 622310 607310 579360 612800 TRUE FALSE 355933.9677 364276.2227 487366.721 587481.9934 539492.4769 522506.0239 629926.0159 594768.8363 513593.4817 571294.5102 0.623030611 0.637632983 0.853091903 1.028334743 0.944333382 0.914600114 1.102629213 1.041089711 0.898999505 1 19.12387514 4.094785356 2.524654171 0.996402923 0.617283466 0.855798119 0.058481302 0.098005471 1.242800301 0.016326081 0.045262471 12438.99681 -4.094785356 -0.379119456 MS(ph)GFIYQGK ddPTM_BT-474_Pertuzumab_2h_R1 5 MSGFIYQGK 9 0 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;E7EUY6;F6SJA5;Q15052-2;Q15052 B1ALK7;Q15052-2 ARHGEF7;ARHGEF6 Rho guanine nucleotide exchange factor 7;Rho guanine nucleotide exchange factor 6 1 MS(1)GFIYQGK;MS(1)GFIYQGK;MS(1)GFIYQGK;MS(1)GFIYQGK;MS(1)GFIYQGK 158.94 6.97E-05 4994310000 8620110 8214770 5648870 4146670 6023890 5357550 4347340 7305240 5929900 5157560 TRUE FALSE 8283226.571 7980492.803 6669746.467 4360680.136 6217653.893 5465883.332 4400544.047 7154384.241 5256762.612 4808233.867 1.722717072 1.659755541 1.38715101 0.906919309 1.293126346 1.136775682 0.915210069 1.487944314 1.093283471 1 22.19707564 4.095144092 3.283655273 1.153583899 1.697763975 0.645392268 0.168141052 0.150901637 3.204316434 0.043364589 0.107709382 12449.27591 -4.095144092 0.544180076 NPEISHMLNNPELMR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPEISHMLNNPELMR 15 0 Q9NRR5 Q9NRR5 UBQLN4 Ubiquilin-4 0 83.292 0.0087098 0 66681 67749 53807 71842 61869 64238 80417 72006 70902 80268 FALSE TRUE 64075.0328 65816.86485 63531.12183 75549.77423 63859.07257 65536.93637 81401.1673 70519.05094 62853.50221 74831.37686 0.856258905 0.879535666 0.848990417 1.009600216 0.853372947 0.875794875 1.087794595 0.942372757 0.839935129 1 16.1913557 4.095310045 0.526080355 0.957364869 0.820186636 0.162939439 0.07467933 4.340313451 1.478022285 0.049055074 0.340558881 12454.03394 -4.095310045 -0.137178232 GEASEDLCEMALDPELLLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEASEDLCEMALDPELLLLR 20 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 202.13 2.77E-21 122803000 252568 268634 240068 320660 305920 301120 310310 326000 343480 339330 FALSE TRUE 242697.3633 260972.8213 283453.6279 337209.301 315760.1946 307208.8527 314107.6666 319267.9861 304489.5904 316346.8769 0.76718748 0.824957793 0.896021578 1.065947938 0.998145446 0.971113911 0.992921662 1.00923388 0.962518086 1 18.27114783 4.095736388 2.566603481 0.999077778 0.7868724 0.883018194 0.029850602 0.0813427 1.066773717 0.007679574 0.021137984 12466.26595 -4.095736388 -0.212205378 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR ddPTM_BT-474_Pertuzumab_2h_R1 14 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR 34 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;;;;; 202.76 3.09E-27 16537417800 3682526.8 3765061.9 3283372.1 4068815.5 3939097.9 4332474.1 3958152 4236715.1 4278616.2 4525486.8 FALSE TRUE 3538609.581 3657686.021 3876750.477 4278807.556 4065802.561 4420079.695 4006593.048 4149225.453 3792925.626 4218971.548 0.838737484 0.866961528 0.918885191 1.014182605 0.963695184 1.047667576 0.949661073 0.98346846 0.89901664 1 22.00845993 4.095790609 2.56344241 0.979440718 0.847446111 0.641504858 0.037998793 0.16459344 2.15313468 0.009656151 0.026596741 12467.82245 -4.095790609 -0.131994607 LES(ph)PSFTGTGDTEIAHATEDLENNGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LESPSFTGTGDTEIAHATEDLENNGSK 27 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 LES(0.848)PS(0.151)FTGT(0.001)GDTEIAHATEDLENNGSK;LES(0.842)PS(0.157)FTGT(0.001)GDTEIAHATEDLENNGSK 322.07 9.55E-83 222990000 116663 100679 157659 196773 152083 156379 197101 200812 217320 282210 TRUE FALSE 112103.681 97807.7335 186151.4884 206928.4781 156974.8878 159541.0905 199513.181 196665.162 192650.7447 263095.6653 0.426094747 0.371757297 0.70754297 0.786514205 0.596645664 0.60639954 0.758329411 0.747504379 0.732245985 1 18.00522795 4.096078357 0.132878418 1.106435489 1.23E-16 0.68145617 0.09764618 16.57616786 0.466394743 0.852290268 3.545309165 12476.08593 -4.096078357 -1.106435489 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_BT-474_Pertuzumab_2h_R1 7 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 0 ;;;;;; 95.571 1.78E-05 2446767000 1088004.3 1093334.4 785057.2 641618.3 881281.1 1035696.8 845173.2 735781.3 1090040.9 853372.5 FALSE TRUE 1045483.889 1062153.573 926934.4995 674732.2974 909628.3069 1056639.299 855516.6824 720587.159 966304.0269 795572.8205 1.314127208 1.335080267 1.165115846 0.848108784 1.143362724 1.328149067 1.075346795 0.905746326 1.214601608 1 19.60163446 4.096533904 4.401208549 1.06891428 1.321820726 0.358012477 0.132470261 0.228410908 7.838480368 0.035259368 0.081291639 12489.17941 -4.096533904 0.252906446 EALEALVPVTIEVEVPFDLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EALEALVPVTIEVEVPFDLHR 21 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ; 189.55 2.12E-17 1654020000 1363030 1417160 1226030 1590920 1525300 1552390 1508280 1539390 1656170 1736230 FALSE TRUE 1309761.281 1376743.984 1447600.894 1673027.572 1574362.66 1583780.389 1526738.782 1507601.059 1468168.525 1618633.596 0.809177126 0.850559378 0.894335134 1.033604873 0.972649193 0.978467513 0.94322692 0.931403539 0.90704192 1 20.62634501 4.097819967 2.985841216 0.961484282 0.826264791 0.705430594 0.035442828 0.143979045 2.551379128 0.009660233 0.024905189 12526.21805 -4.097819967 -0.135219491 LALLNVATQGVHLWDLQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LALLNVATQGVHLWDLQDR 19 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ; 286.6 3.47E-40 632330000 201530 191553 169937 190594 225505 206482 188617 208623 212509 208213 FALSE TRUE 193653.9848 186090.096 200648.3961 200430.5792 232758.5731 210657.2075 190925.3513 204314.8621 188385.8692 194110.5481 0.997647921 0.958681009 1.033681055 1.032558927 1.199103168 1.085243484 0.98359081 1.052569601 0.970508152 1 17.56651899 4.097962409 4.245617215 1.051338937 0.978555022 0.154967982 0.061586672 0.372390636 12.08710849 0.016314946 0.03790834 12530.32711 -4.097962409 -0.072783915 AQTAPNKDVQR ddPTM_BT-474_Pertuzumab_2h_R1 4 AQTAPNKDVQR 11 1 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 114.72 0.0011122 713675000 1299030 1532770 834480 690280 839740 710710 1004910 828720 935710 896260 FALSE TRUE 1248262.471 1489056.9 985289.0989 725905.4335 866750.9997 725081.0431 1017208.389 811606.6424 829492.1236 835555.5119 1.493931227 1.782116064 1.179202441 0.868769846 1.037335027 0.867783209 1.217403721 0.971337788 0.992743285 1 19.67237615 4.098536578 4.665133433 1.002144009 1.632096717 0.832129085 0.113916794 0.068662223 2.543168828 0.026881867 0.061382586 12546.90407 -4.098536578 0.629952708 RGS(ph)MNNELLSPEFGPVRDPLADGVEGLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RGS(0.568)MNNELLS(0.432)PEFGPVRDPLADGVEGLGR 109.71 0.00029235 156510000 40989 42526 43049 47991 51906 58952 56257 65745 55563 61616 TRUE FALSE 39387.10456 41313.20012 50828.91192 50467.82126 53575.60363 60144.04983 56945.48999 64387.34278 49255.72118 57442.69344 0.685676493 0.719207225 0.884862963 0.878576861 0.93267917 1.04702698 0.991344357 1.120897 0.857475829 1 15.80983578 4.099851795 0.741937912 1.020869138 0.605529265 0.725706161 0.068196631 0.652912319 0.481117544 0.028740837 0.196781047 12584.9587 -4.099851795 -0.415339873 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDIT(ph)TPPNK ddPTM_BT-474_Pertuzumab_2h_R1 3 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDITTPPNK 40 3 P27816-6;P27816 P27816-6 MAP4 Microtubule-associated protein 4 1 KPCNSQPSELSSETSGIARPEEGRPVVS(0.012)GT(0.012)GNDIT(0.592)T(0.385)PPNK;KPCNSQPSELSSETSGIARPEEGRPVVS(0.003)GT(0.035)GNDIT(0.536)T(0.427)PPNK;KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDIT(0.5)T(0.5)PPNK 161.66 1.79E-18 4835980000 1540940 1291780 1732540 1713230 1732380 1951530 2082540 2318380 2769690 2722790 TRUE FALSE 1480718.361 1254939.699 2045648.518 1801650.006 1788103.576 1990991.274 2108026.747 2270504.643 2455286.403 2538373.008 0.583333638 0.494387427 0.805889643 0.709765665 0.704429006 0.784357251 0.830463742 0.894472418 0.967267771 1 21.27547265 4.099933516 0.225297693 1.050510898 0.242955182 0.815524332 0.065228326 3.482716528 0.203259119 0.121331965 0.788661372 12587.32703 -4.099933516 -0.807555716 RTIQEVLEEQS(ph)EDEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RTIQEVLEEQSEDEDR 16 1 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 RTIQEVLEEQS(1)EDEDR;RTIQEVLEEQS(1)EDEDR 127.5 4.03E-05 443520000 143021 143753 129727 168166 156860 144215 168006 177117 162116 179358 TRUE FALSE 137431.5812 139653.3052 153171.5547 176845.0674 161905.5444 147131.1261 170062.1077 173459.4721 143713.2713 167209.9229 0.821910439 0.835197474 0.91604345 1.057623043 0.968277131 0.879918629 1.017057509 1.037375468 0.859478127 1 17.35130094 4.100021213 3.505255457 0.978521269 0.827495528 0.478557631 0.060089645 0.187932569 4.471002823 0.015555084 0.037996085 12589.86906 -4.100021213 -0.151025741 LGSS(ph)SNLQFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.087)S(0.825)S(0.087)NLQFK 128.36 0.0034085 0 124700 111780 84484 61035 77936 79365 66260 109710 108140 83361 TRUE FALSE 119826.5861 108592.1438 99752.13814 64185.02366 80442.88222 80969.81468 67070.9097 107444.4502 95864.40056 77714.88522 1.541874324 1.397314601 1.283565405 0.82590386 1.035102632 1.04188296 0.863038136 1.382546598 1.233539756 1 16.24590333 4.100694971 3.005265425 1.074974818 1.481027686 0.525817802 0.158126104 0.219776315 3.940088452 0.044430526 0.114591627 12609.41594 -4.100694971 0.406052868 DGGS(ph)GNSTIIVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 DGGS(0.991)GNS(0.008)TIIVSR;DGGS(1)GNSTIIVSR;DGGS(0.682)GNS(0.159)T(0.159)IIVSR;DGGS(0.917)GNS(0.042)T(0.042)IIVSR 269.55 4.18E-25 2698110000 747385 766337 804052 1062570 929967 1126222 1156800 1034380 1252380 1317450 TRUE FALSE 718176.3679 744481.8191 949362.0824 1117409.365 959880.2331 1148994.98 1170957.264 1013019.692 1110215.073 1228217.938 0.584730401 0.606147978 0.772958978 0.909781017 0.781522728 0.935497638 0.953379061 0.824788224 0.903923513 1 20.22813515 4.101193155 2.088841676 0.891367771 0.576629351 0.807177989 0.059387002 0.133377043 1.135894692 0.015602885 0.048828866 12623.88864 -4.101193155 -0.31473842 KLGDTYPSISNAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLGDTYPSISNAR 13 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 84.759 0.015388 329000000 299680 346000 243230 240180 253410 287460 313300 310310 313860 301640 FALSE TRUE 287968.1743 336132.4188 287187.0716 252575.7186 261561.1628 293272.6382 317134.2591 303901.9901 278231.9286 281209.6541 1.024033742 1.195308958 1.021256089 0.898175845 0.930128674 1.042896764 1.127750255 1.080695437 0.989411012 1 18.1012866 4.101391895 13.71806361 1.017610372 1.109623102 0.218038608 0.073783888 1.091876782 141.7212749 0.020408169 0.044100783 12629.66684 -4.101391895 0.09201273 RDS(ph)LEEGELR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSLEEGELR 10 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;A0A087X1I0;A0A087WYI9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 RDS(1)LEEGELR;RDS(1)LEEGELR 158.25 8.52E-06 568610000 417310 440250 416940 593420 525670 498690 585260 605740 493060 613740 TRUE FALSE 401001.0638 427694.501 492290.3328 624046.4773 542578.653 508773.8535 592422.587 593231.2573 437089.8959 572170.8431 0.700841486 0.7474944 0.860390456 1.090664589 0.948280849 0.889199196 1.035394575 1.036807912 0.763915011 1 19.12608646 4.101805999 3.124721987 0.972572947 0.719143391 0.549018951 0.08712744 0.17133403 3.306565538 0.022175524 0.056404119 12641.7151 -4.101805999 -0.253429555 FRNS(ph)VEGLNQEIEIIIK ddPTM_BT-474_Pertuzumab_2h_R1 3 FRNSVEGLNQEIEIIIK 17 1 Q6P1L5 Q6P1L5 FAM117B Protein FAM117B 1 FRNS(1)VEGLNQEIEIIIK;FRNS(1)VEGLNQEIEIIIK;FRNS(1)VEGLNQEIEIIIK 282.75 2.83E-36 350693000 517610 502080 435550 492780 492020 522010 503900 550310 595380 559670 TRUE FALSE 497381.229 487761.17 514263.5738 518212.4349 507846.2701 532565.3999 510066.8789 538945.9062 527794.9584 521763.0524 0.953270314 0.934832713 0.985626658 0.993194962 0.97332739 1.02070355 0.977583362 1.032932293 1.011560623 1 18.99303526 4.102465861 0.555132751 1.012965733 0.920421026 0.603675361 0.018000907 1.336894663 0.510381623 0.010432765 0.073687189 12660.93738 -4.102465861 -0.092544708 EEEMGEEEEVER ddPTM_BT-474_Pertuzumab_2h_R1 4 EEEMGEEEEVER 12 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 335.87 5.61E-58 1813530000 802024 764481 679774 821133 825510 824781 751733 858210 855321 875134 FALSE TRUE 770680.0154 742678.7504 802624.2833 863511.7725 852063.2789 841458.6369 760932.9333 840487.6636 758228.5459 815860.3947 0.944622414 0.910301266 0.9837765 1.058406289 1.044373871 1.031375763 0.932675416 1.030185641 0.929360649 1 19.63796278 4.103191076 5.113984253 1.005989714 0.928472267 0.340335671 0.041694923 0.213339376 8.784672247 0.010480674 0.023627955 12682.09717 -4.103191076 -0.077517447 GEAAAERPGEAAVASSPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 0 ; 193.27 5.16E-15 710570000 546400 569930 509620 570290 585530 675360 624400 705620 698530 663800 FALSE TRUE 525046.0839 553676.1544 601719.6704 599722.7352 604364.1042 689016.2419 632041.594 691048.7004 619235.8029 618840.2347 0.848435597 0.894699671 0.972334436 0.969107536 0.976607645 1.113399232 1.021332419 1.116683534 1.000639209 1 19.23920747 4.103449517 0.693845541 1.059505295 0.807001415 0.680286875 0.04470275 0.7987368 0.502991511 0.019989356 0.140213143 12689.64629 -4.103449517 -0.25250388 AAS(ph)LTEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AASLTEDR 8 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 AAS(0.999)LT(0.001)EDR;AAS(0.996)LT(0.004)EDR 162.8 0.00035623 637250000 589320 545530 652860 868140 864220 613160 911150 1031700 916050 1043400 TRUE FALSE 566288.7229 529972.0185 770846.3248 912944.8094 892018.4212 625558.5153 922300.9263 1010395.034 812063.8444 972729.5886 0.582164591 0.54482975 0.792456952 0.938539158 0.9170261 0.643096008 0.948157573 1.038721394 0.834830002 1 19.89167928 4.103837298 3.266819163 0.904340021 0.56002522 0.629365113 0.102691837 0.156098041 3.268172927 0.028218266 0.070763475 12700.98194 -4.103837298 -0.344314801 FS(ph)PPEPGDTPTDEPDALYVACQGQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 FSPPEPGDTPTDEPDALYVACQGQPK 26 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 FS(0.998)PPEPGDT(0.002)PTDEPDALYVACQGQPK 114.68 0.00086691 87695000 63038 60844 55185 70273 63538 59844 66657 74211 72889 73052 TRUE FALSE 60574.40527 59108.78869 65158.15708 73899.79795 65581.75747 61054.08668 67472.76831 72678.51692 64614.9463 68104.12297 0.889438152 0.867917919 0.956743208 1.085100207 0.962963101 0.896481505 0.990729568 1.067167651 0.948767027 1 16.05545452 4.10394406 4.51634491 0.996461287 0.879834684 0.430079249 0.051695413 0.193927357 6.788616943 0.013904575 0.031997062 12704.10457 -4.10394406 -0.116626603 ALPNNTSSS(ph)PQPK ddPTM_BT-474_Pertuzumab_2h_R1 6 ALPNNTSSSPQPK 13 0 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1;A0A087WT22;J3KP33;A0A087WXZ1;E7ESS1;P04637-5;P04637-9;P04637-8;P04637-6;P04637-2;P04637-3 P04637-7 TP53 Cellular tumor antigen p53 1 ALPNNT(0.043)S(0.033)S(0.313)S(0.61)PQPK;ALPNNTSS(0.007)S(0.992)PQPK;ALPNNTSS(0.009)S(0.99)PQPK;ALPNNTS(0.001)S(0.066)S(0.933)PQPK;ALPNNTS(0.016)S(0.115)S(0.869)PQPK;ALPNNTSS(0.006)S(0.994)PQPK 306.65 1.06E-41 17971880000 7059850 6698940 5030620 4912720 4841000 5094190 5497680 5624600 5882840 6344400 TRUE FALSE 6783943.257 6507892.79 5939764.94 5166266.068 4996715.161 5197198.012 5564962.252 5508450.044 5215044.666 5914688.137 1.146965503 1.100293479 1.004239751 0.873463816 0.844797738 0.878693499 0.940871627 0.931317073 0.881710843 1 22.49587067 4.104062605 2.395383549 0.90482475 1.135193572 0.806804852 0.042361134 0.118806326 1.35078481 0.01147068 0.033106163 12707.57275 -4.104062605 0.230368822 VLELNASDER ddPTM_BT-474_Pertuzumab_2h_R1 1 VLELNASDER 10 0 P35249;C9J8M3;C9JZI1;P35249-2;C9JXZ7;C9JTT7 P35249 RFC4 Replication factor C subunit 4 0 92.538 0.021866 85678000 82396 83619 74547 95285 99357 97785 92746 90544 89328 98352 FALSE TRUE 79175.87323 81234.26799 88019.30119 100202.6703 102552.9081 99762.2797 93881.05329 88674.23476 79187.85993 91690.53144 0.86351199 0.885961361 0.959960639 1.092835527 1.118467813 1.088032517 1.023890382 0.96710351 0.86364272 1 16.48448514 4.104075544 3.285579897 1.024141544 0.872548966 0.416326151 0.069190341 0.247848619 5.242824437 0.019794797 0.049551407 12707.95137 -4.104075544 -0.151592578 AGFAGDDAPRAVFPSIVGRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGFAGDDAPRAVFPSIVGRPR 21 2 C9JTX5;F8WCH0;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63267-2;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I" 0 97.776 0.00060828 576060000 405110 357030 366030 464640 374500 562340 369950 444640 552590 522680 FALSE TRUE 389277.8533 346847.854 432179.7633 488620.1261 386546.1326 573710.9001 374477.5588 435458.0286 489862.2998 487278.418 0.798881787 0.711806313 0.886925723 1.002753473 0.793275709 1.177378022 0.768508403 0.893653428 1.005302681 1 18.8943868 4.104356176 4.995980491 0.934544088 0.757279489 0.310314227 0.112335271 0.239810788 9.562336038 0.026830841 0.060709465 12716.16561 -4.104356176 -0.177264599 AHHAACKEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHHAACKEEK 10 1 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 85.958 0.0083427 8480200 37316 35456 22190 21615 23452 19044 26177 934.37 28897 20852 FALSE TRUE 35857.64946 34444.8296 26200.22661 22730.55274 24206.35488 19429.08273 26497.36196 915.074933 25616.73371 19439.67547 1.844560087 1.771882954 1.347770782 1.169286636 1.245203652 0.999455097 1.363055777 0.047072542 1.317755214 1 14.24671651 4.104380527 0.499679725 0.770105731 2.25848508 0.451617117 0.348608962 2.075798864 0.626532446 0.243276972 1.700685926 12716.87863 -4.104380527 1.488379349 IFDSEEILAGYKR ddPTM_BT-474_Pertuzumab_2h_R1 1 IFDSEEILAGYKR 13 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 151.78 7.20E-05 1425500000 960470 1038200 749220 731880 802810 805970 891240 979200 963160 909730 FALSE TRUE 922933.7705 1008591.553 884620.7203 769652.4145 828633.1127 822267.2656 902147.2617 958979.1778 853826.1147 848113.1768 1.088220058 1.189218114 1.043045603 0.907487863 0.977031292 0.969525398 1.063710937 1.130720762 1.006736056 1 19.69389727 4.105472905 6.383941886 1.017529924 1.137193505 0.414636293 0.060501004 0.233615702 12.37955536 0.017579321 0.038730702 12748.90559 -4.105472905 0.119663581 LLRPLS(ph)PVT(ph)PPPPNSGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLRPLSPVTPPPPNSGSK 18 1 E7EWN3;Q9C0A6;Q9C0A6-2;Q9C0A6-3;H0Y3R4;H7C1F2 E7EWN3 SETD5 SET domain-containing protein 5 2 LLRPLS(1)PVT(0.999)PPPPNSGSK 86.08 0.0080532 151380000 261580 250930 239220 260420 298990 284330 278920 300930 334300 298270 TRUE FALSE 251357.1644 243773.7221 282452.3754 273860.3074 308607.2849 290079.3474 282333.5064 294715.6903 296351.6655 278067.9072 0.903941656 0.876669748 1.015767617 0.984868445 1.109827049 1.043196068 1.015340135 1.059869488 1.065752853 1 18.08507772 4.106059046 1.918981803 1.046121109 0.882418625 0.720027444 0.036050468 0.16789474 1.188190745 0.009359398 0.03133862 12766.12364 -4.106059046 -0.163702484 FIDFFKR ddPTM_BT-474_Pertuzumab_2h_R1 2 FIDFFKR 7 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 81.297 0.044229 342890000 1139560 1315240 683330 573530 585590 370370 891170 693180 791810 818390 FALSE TRUE 1095024.735 1277730.643 806822.9316 603129.952 604426.0342 377859.1352 902076.405 678865.5908 701927.0483 762959.7164 1.435232702 1.674702629 1.057490867 0.790513495 0.792212251 0.495254372 1.182338183 0.889779075 0.920005386 1 19.54124736 4.106350534 4.246695697 0.868190841 1.551404311 0.7067325 0.174300574 0.108529639 3.474362558 0.044566912 0.103961068 12774.69482 -4.106350534 0.68321347 DCDPGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 7 DCDPGSPR 8 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 1 DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR 114.4 0.0027937 1756810000 3986370 3911410 3786109 4400415 4398844 5012443 4700028 4718126 5453992 5631035 TRUE FALSE 3830578.253 3799860.416 4470343.118 4627520.945 4540336.812 5113798.032 4757548.349 4620695.049 4834877.693 5249639.984 0.729683991 0.723832573 0.851552322 0.881493009 0.864885369 0.974123568 0.906261832 0.880192749 0.920992241 1 22.32378706 4.106618241 1.173015074 0.918155889 0.695583497 0.786967631 0.039490222 0.292846002 0.649269786 0.012015495 0.061603536 12782.5718 -4.106618241 -0.222572392 IVGELEQMVSEDVPLDHR ddPTM_BT-474_Pertuzumab_2h_R1 15 IVGELEQMVSEDVPLDHR 18 0 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 ;;;;;;;;;;;;;; 254.59 1.54E-30 3105231000 1111536.7 1202052 1023595.2 1260870.6 1303671.8 1396104.3 1343390.7 1360049.6 1405393.5 1483659.6 FALSE TRUE 1068096.617 1167770.654 1208581.622 1325944.283 1345605.587 1424334.485 1359831.517 1331964.1 1245859.122 1383170.014 0.772209205 0.844271234 0.873776622 0.958627117 0.972841787 1.029760963 0.983126806 0.962979306 0.900727394 1 20.39954707 4.107951219 1.310106692 0.976332935 0.77507292 0.817118362 0.032479276 0.234931687 0.68267268 0.010121657 0.047099234 12821.86557 -4.107951219 -0.201260015 GIQYLQEQGMLGTTPEDIAQFLHQEER ddPTM_BT-474_Pertuzumab_2h_R1 1 GIQYLQEQGMLGTTPEDIAQFLHQEER 27 0 Q9Y6D6;E5RIF2 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 159.7 1.46E-11 75897000 40382 46931 41252 58539 59895 62004 50648 50331 71489 65760 FALSE TRUE 38803.8268 45592.57383 48707.15405 61560.20481 61821.57707 63257.76336 51267.84537 49291.64726 63373.86843 61306.01663 0.632952994 0.743688407 0.794492233 1.004146219 1.008409622 1.031836137 0.836261238 0.80402626 1.033729998 1 15.90374105 4.108018984 2.166336666 0.939922339 0.666951205 0.649024627 0.080969704 0.23593788 2.170816574 0.024654844 0.076060981 12823.86638 -4.108018984 -0.272971134 SGGLQT(ph)PECLS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R 166.04 0.00028114 508170000 1051570 1021630 702290 700220 758470 698340 546490 896140 802130 669290 TRUE FALSE 1010473.482 992494.1127 829209.4254 736358.4381 782866.8764 712460.9133 553178.1081 877634.3958 711075.5652 623958.3922 1.619456513 1.5906415 1.328949872 1.18014029 1.254678014 1.141840421 0.886562494 1.406559166 1.139620164 1 19.2510903 4.10805697 1.735443526 1.159117882 1.646700539 0.660806079 0.131062178 0.247630432 1.398801009 0.036804985 0.133761945 12824.98808 -4.10805697 0.487582656 HKELAPYDENWFYTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HKELAPYDENWFYTR 15 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 196.22 5.43E-09 1682990000 4048000 4110600 2304800 2014030 1941370 2739700 2387400 1581210 2365320 2281600 FALSE TRUE 3889799.685 3993369.713 2721328.63 2117974.33 2003815.929 2795098.611 2416617.715 1548557.461 2096818.79 2127065.2 1.828716715 1.87740823 1.279381859 0.995726097 0.942056656 1.314063439 1.13612771 0.728025385 0.985780215 1 21.02043283 4.109049032 2.83337511 1.005393723 1.872904107 0.843801673 0.142153155 0.100755015 1.608181629 0.041640187 0.111083965 12854.31777 -4.109049032 0.867510384 SANTS(ph)PESSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 SANTSPESSSR 11 0 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 S(0.001)ANT(0.283)S(0.716)PESSSR;SANT(0.289)S(0.711)PESSSR;SANT(0.001)S(0.999)PESSSR;SANT(0.194)S(0.806)PESSSR;SANT(0.349)S(0.647)PES(0.004)SSR 124.42 0.00036668 255334000 476414 501803 442917 601188 530280 555302 596270 561251 605842 617117 TRUE FALSE 457795.2142 487492.0698 522961.9545 632215.3847 547336.9378 566530.5869 603567.3306 549660.9707 537069.3561 575319.1159 0.795723976 0.847342034 0.908994574 1.098895147 0.951362336 0.98472408 1.04910008 0.95540189 0.933515576 1 19.13400288 4.109259885 3.039874267 0.993538424 0.816589429 0.678039969 0.048132573 0.137819308 2.519496612 0.012200988 0.031599547 12860.56015 -4.109259885 -0.176948995 DVTGPDEESFLYFAYGSNLLTER ddPTM_BT-474_Pertuzumab_2h_R1 2 DVTGPDEESFLYFAYGSNLLTER 23 0 O75223;O75223-3;B8ZZK2;O75223-2;O75223-4;A0A0B4J1Y4 O75223 GGCT Gamma-glutamylcyclotransferase 0 ; 287.84 8.67E-53 80300000 78504 83542 70338 85284 91748 85125 89554 94625 101391 104265 FALSE TRUE 75435.97689 81159.46396 83049.64126 89685.51746 94699.15774 86846.28582 90649.98864 92670.96068 89881.51875 97203.03868 0.776066036 0.834947807 0.854393467 0.922661664 0.974240713 0.893452376 0.932583897 0.953375141 0.924678076 1 16.56871379 4.109326474 1.191517535 0.943553169 0.773865713 0.803138879 0.028692126 0.268959658 0.618756452 0.008563407 0.043521604 12862.53216 -4.109326474 -0.169687456 SRS(ph)APPNLWAAQR ddPTM_BT-474_Pertuzumab_2h_R1 6 SRSAPPNLWAAQR 13 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 S(0.012)RS(0.988)APPNLWAAQR;S(0.054)RS(0.946)APPNLWAAQR;S(0.012)RS(0.988)APPNLWAAQR;S(0.038)RS(0.962)APPNLWAAQR;S(0.011)RS(0.989)APPNLWAAQR;S(0.018)RS(0.982)APPNLWAAQR 209.54 2.25E-08 5386590000 1738240 1736040 1211800 1327000 1273220 1174520 1359950 1478160 1410390 1341380 TRUE FALSE 1670307.659 1686529.839 1430799.216 1395486.629 1314174.278 1198269.599 1376593.475 1447635.479 1250288.44 1250527.138 1.335682856 1.348655129 1.14415687 1.115918709 1.050896248 0.958211592 1.100810557 1.157620203 0.999809122 1 20.25410494 4.109615689 1.985173452 1.063646654 1.359049219 0.790985405 0.058004166 0.163456282 1.245472303 0.016973517 0.055739306 12871.10074 -4.109615689 0.295402565 LEDFLDNER ddPTM_BT-474_Pertuzumab_2h_R1 4 LEDFLDNER 9 0 Q16512;Q16512-2;Q16512-3 Q16512 PKN1 Serine/threonine-protein kinase N1 0 ;;; 193.1 7.90E-05 295879000 528300 555750 540430 713800 662840 657500 747200 784700 777400 789120 FALSE TRUE 507653.4519 539900.5541 638097.7228 750639.3035 684160.8506 670795.1005 756344.4571 768495.6708 689152.8111 735672.1995 0.690053875 0.733887395 0.86736691 1.0203448 0.929980569 0.911812491 1.028099822 1.044616979 0.936766146 1 19.48870355 4.109660219 2.188763992 0.985603408 0.694082919 0.861301502 0.043155671 0.112722584 1.059957304 0.012685813 0.03896663 12872.42051 -4.109660219 -0.291520489 IVQMTEAEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 IVQMTEAEVR 10 0 P62140;C9JP48;C9J9S3 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase 0 99.815 0.010325 62865000 54824 64368 43068 45933 57616 32637 52859 56459 50340 54630 FALSE TRUE 52681.41747 62532.28766 50851.34564 48303.60763 59469.27097 33296.9425 53505.90425 55293.10192 44625.61424 50929.86144 1.034391533 1.227811855 0.998458354 0.94843391 1.167669993 0.653780347 1.050580205 1.085671556 0.876217075 1 15.63622417 4.110428525 7.820923362 0.978829486 1.130169018 0.175848232 0.137306971 0.384624134 24.97949556 0.033370287 0.0727113 12895.21315 -4.110428525 0.151339532 FLEVQYLTGGLIEPDTPGRVPLDEALQR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLEVQYLTGGLIEPDTPGRVPLDEALQR 28 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 151.31 4.64E-08 226440000 24837 27052 25916 38202 36352 31653 36555 36318 36438 31154 FALSE TRUE 23866.34258 26280.50345 30599.5977 40173.6098 37521.29509 32293.04535 37002.37102 35568.02061 32301.711 29043.91183 0.821733061 0.904854126 1.053563235 1.383202443 1.291881593 1.111869694 1.274014714 1.224629135 1.112168057 1 14.82594816 4.110568896 3.028579182 1.214639368 0.853686062 0.615709283 0.105134936 0.145062772 2.632477049 0.026119838 0.067840456 12899.38175 -4.110568896 -0.360953305 ANFDKESER ddPTM_BT-474_Pertuzumab_2h_R1 4 ANFDKESER 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 137.98 0.0001364 2949120000 4525070 5007090 3228670 2980420 3512960 3089120 3790180 3640310 4321510 3951420 FALSE TRUE 4348225.262 4864292.696 3812162.49 3134239.833 3625957.549 3151584.123 3836565.357 3565136.326 3830950.302 3683786.804 1.180368326 1.320459884 1.034848837 0.850820094 0.984301682 0.855528371 1.041473234 0.967791166 1.039948973 1 21.81275814 4.110642257 5.052150221 0.961893373 1.247453467 0.724458991 0.069752357 0.092545704 3.692974478 0.016721646 0.037832234 12901.56091 -4.110642257 0.285560094 EVDEDS(ph)EPER ddPTM_BT-474_Pertuzumab_2h_R1 2 EVDEDSEPER 10 0 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EVDEDS(1)EPER;EVDEDS(1)EPER 175.48 2.92E-06 1276220000 814670 806030 723990 901630 841410 831350 903350 969840 933260 947260 TRUE FALSE 782831.7957 783042.8136 854831.0981 948163.2324 868474.7168 848160.4666 914405.4675 949812.4651 827320.2373 883101.2365 0.886457592 0.886696543 0.967987658 1.073674448 0.983437324 0.960434015 1.035448066 1.075541994 0.936835102 1 19.75221931 4.111416275 3.621963415 1.015121803 0.885768762 0.562101701 0.042491305 0.155249366 3.87502905 0.011181219 0.027277026 12924.57513 -4.111416275 -0.12935304 HFFHEDEEPFNPDYVEVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HFFHEDEEPFNPDYVEVDR 19 0 Q9HCK8-2;Q9HCK8;A0A2R8Y840;A0A2R8Y4P3 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 0 48.824 0.090607 122310000 78110 69087 84693 117800 108850 98268 118510 112740 120780 128940 FALSE TRUE 75057.37484 67116.7064 99998.90909 123879.6721 112351.2591 100255.0463 119960.3608 110411.8796 107069.5608 120206.779 0.62440218 0.558343772 0.831890763 1.030554792 0.934649943 0.834021568 0.997950048 0.918516248 0.890711503 1 16.87515873 4.111622701 3.969619205 0.937617992 0.591733973 0.853830257 0.057422435 0.070125489 2.023016893 0.014151435 0.033643336 12930.71981 -4.111622701 -0.345884019 CFSIDNPGYEPEVVAVHPGGDTVAIGGVDGNVR ddPTM_BT-474_Pertuzumab_2h_R1 3 CFSIDNPGYEPEVVAVHPGGDTVAIGGVDGNVR 33 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ;; 304.71 3.08E-90 787750000 326713 318208 297308 372462 359838 392752 340377 368700 420995 389070 FALSE TRUE 313944.6948 309133.0194 351038.1692 391684.8085 371412.5161 400693.7145 344542.6355 361086.2162 373205.4126 362717.9424 0.865533954 0.852268342 0.967799296 1.079860582 1.023970619 1.104697804 0.949891349 0.995501391 1.028913569 1 18.46848859 4.112219295 3.728954462 1.022920911 0.858326303 0.719486664 0.041193492 0.117449981 3.072760392 0.010932043 0.026452932 12948.49503 -4.112219295 -0.164594608 DGQYLLTGGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGQYLLTGGDR 11 0 A0A494C1L5;P50851-2;P50851;A0A494BZW2;H0YAC6;A0A3B3IS13 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 90.697 0.026274 847060000 426630 445240 382970 491320 509610 526500 452900 465640 491130 490380 FALSE TRUE 409956.8279 432542.1911 452181.1981 516677.0841 526002.0685 537146.1907 458442.7257 456024.3713 435378.9814 457166.1258 0.896734917 0.946137884 0.989096026 1.130173595 1.15057096 1.174947487 1.00279242 0.997502539 0.952343047 1 18.80235898 4.112230668 2.867591496 1.059503411 0.91615346 0.37416912 0.070942264 0.303070849 4.949843932 0.020851635 0.05552516 12948.83414 -4.112230668 -0.143349951 APS(ph)RQDVYGPQPQVR ddPTM_BT-474_Pertuzumab_2h_R1 6 APSRQDVYGPQPQVR 15 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR 258.8 4.71E-25 14884180000 2566860 2431020 1228900 1086044 890678 1003118 510659 1261971 676155 616694 TRUE FALSE 2466544.273 2361689.69 1450989.567 1142094.861 919327.4668 1023401.733 516908.5976 1235910.858 599400.7191 574924.7661 4.290203552 4.107823891 2.523790333 1.986511851 1.599039598 1.780062007 0.899089112 2.149691457 1.042572445 1 19.13301365 4.11252152 1.329392741 1.488300335 4.601169612 0.888334958 0.382942995 0.159331067 0.478675514 0.107638563 0.498470716 12957.50902 -4.11252152 3.112869277 up GTVLLADNVICPGAPDFLAHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTVLLADNVICPGAPDFLAHVR 22 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ; 150.94 5.23E-08 1914790000 401400 408190 372010 479450 436180 459570 523180 461550 478280 514480 FALSE TRUE 385712.8442 396548.8209 439240.4823 504194.472 450210.1258 468862.8203 529582.8333 452018.8312 423987.6595 479633.8113 0.80418193 0.826774117 0.915782983 1.051207108 0.938653855 0.977543303 1.10413991 0.942424868 0.883982008 1 18.87157384 4.113277097 3.062652805 0.985655737 0.811380542 0.57544609 0.057956584 0.172974008 3.20419377 0.015138832 0.039250302 12980.07186 -4.113277097 -0.174275195 SQPPGEDSDT(ph)DVDDDSRPPGRPAEVHLER ddPTM_BT-474_Pertuzumab_2h_R1 2 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQPPGEDS(0.369)DT(0.631)DVDDDSRPPGRPAEVHLER;SQPPGEDS(0.392)DT(0.608)DVDDDSRPPGRPAEVHLER 221.5 8.74E-33 3821700000 38605 0 41283 47341 41460 61872 58233 60484 51991 63606 TRUE FALSE 37096.27392 0 48743.75644 49784.27468 42793.59855 63123.09423 58945.67287 59234.98426 46089.19964 59297.90897 0.625591603 0 0.82201476 0.839562061 0.721671292 1.064507928 0.99405989 0.998938838 0.777248312 1 15.85569361 4.11337233 6.71639346 0.915085714 0.317434532 0.650378836 0.173789831 0.11081506 6.055830362 0.04124423 0.090591959 12982.91847 -4.11337233 -0.597651182 LRLSPS(ph)PTSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 LRLS(0.262)PS(0.738)PTSQR;LRLS(0.089)PS(0.428)PT(0.241)S(0.241)QR 172.92 3.37E-05 1989590000 807100 810720 711070 904860 842130 876220 872140 905500 894910 917440 TRUE FALSE 775557.6397 787599.0594 839576.1667 951559.933 869217.8763 893937.7687 882813.5102 886801.1086 793323.5686 855300.9716 0.906765765 0.920844341 0.981614887 1.112543964 1.016271354 1.045173335 1.032167084 1.036829301 0.927537317 1 19.70607265 4.113742295 3.69312439 1.028497749 0.913041452 0.499829296 0.043521061 0.166045576 4.27384067 0.010783886 0.026197193 12993.98304 -4.113742295 -0.115456297 LEDTYFDR ddPTM_BT-474_Pertuzumab_2h_R1 5 LEDTYFDR 8 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;;;; 180.93 0.00055023 5843830000 3906760 3564860 4620550 6398260 5467870 6082330 6471580 6490860 6805510 7458840 FALSE TRUE 3754079.5 3463193.683 5455586.169 6728474.965 5643749.004 6205318.88 6550781.132 6356821.473 6032977.036 6953646.123 0.539872095 0.498039967 0.784564827 0.96761826 0.81162442 0.892383473 0.942064209 0.914170977 0.867599088 1 22.72933822 4.113812786 3.448267352 0.906386122 0.515598487 0.899794381 0.051907654 0.059964056 1.376053198 0.012681855 0.03148902 12996.09226 -4.113812786 -0.390787635 SRENLS(ph)AVMLYNPGLEFER ddPTM_BT-474_Pertuzumab_2h_R1 3 SRENLSAVMLYNPGLEFER 19 1 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(0.183)RENLS(0.817)AVMLYNPGLEFER;S(0.387)RENLS(0.613)AVMLYNPGLEFER;S(0.341)RENLS(0.659)AVMLYNPGLEFER 239.51 1.66E-24 1929740000 574110 578540 417290 472220 454700 394561 436903 582880 506450 470090 TRUE FALSE 551673.1465 562040.6056 492703.5856 496591.3308 469325.8384 402539.2938 442249.9496 570843.3243 448959.9192 438250.3856 1.258808126 1.2824646 1.124251345 1.133122405 1.070907987 0.918514409 1.009126208 1.302550649 1.02443702 1 18.74139583 4.114520878 2.041051508 1.080864532 1.280362151 0.398611933 0.097303215 0.408702918 3.305925084 0.029355908 0.095212943 13017.29893 -4.114520878 0.199497619 RMSDEFVDS(ph)FK ddPTM_BT-474_Pertuzumab_2h_R1 1 RMSDEFVDSFK 11 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(0.109)DEFVDS(0.891)FK 193.11 1.16E-06 284990000 647930 604520 584020 723990 667880 689060 703530 780820 770570 780820 TRUE FALSE 622608.1793 587279.6815 689565.4055 761355.2107 689362.9668 702993.2653 712140.0106 764695.7941 683098.1241 727934.3659 0.855308127 0.806775595 0.947290632 1.045911893 0.947012532 0.965737157 0.978302501 1.05050102 0.938406203 1 19.47344885 4.114766015 4.449347242 0.992007721 0.832011353 0.739731274 0.036913726 0.09501156 3.214718937 0.009298312 0.021553393 13024.6486 -4.114766015 -0.159996369 AILQNHTDFKDK ddPTM_BT-474_Pertuzumab_2h_R1 1 AILQNHTDFKDK 12 1 K7EQA8;Q86X55-2;Q86X55-1;Q86X55 K7EQA8 CARM1 Histone-arginine methyltransferase CARM1 0 99.671 0.0022021 156380000 404780 399940 304940 291130 347780 337670 348480 311980 452840 393460 FALSE TRUE 388960.7501 388534.1028 360049.4414 306155.2542 358966.6595 344497.9188 352744.8025 305537.504 401435.5017 366810.6037 1.060385785 1.059222658 0.981567702 0.834641232 0.978615819 0.939171101 0.961653777 0.83295712 1.094394485 1 18.48467582 4.114946289 4.07297163 0.935535939 1.059643541 0.25081826 0.072754634 0.240722116 7.199470134 0.017635732 0.041729617 13030.05621 -4.114946289 0.124107602 LEQLDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEQLDHR 7 0 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 150.88 0.0019188 334200000 793180 863030 758170 1101300 921370 1067000 942220 1010100 1074600 908860 FALSE TRUE 762181.6487 838417.2294 895188.1844 1158138.225 951006.7028 1088575.471 953751.1702 989241.082 952615.9131 847302.1027 0.899539428 0.989513925 1.056515948 1.366853949 1.12239389 1.284754833 1.125632956 1.167518738 1.124293106 1 19.69251692 4.11522747 3.128535839 1.178001088 0.937592125 0.462457707 0.096728237 0.189526101 3.651790975 0.023195623 0.059748074 13038.49515 -4.11522747 -0.240408962 DTEAMKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTEAMKR 7 1 P18206;P18206-2 P18206 VCL Vinculin 0 ; 72.138 0.084047 199085000 193027 187624 175171 259452 218364 226319 279656 302680 319651 332822 FALSE TRUE 185483.2914 182273.1472 206828.2964 272842.3488 225387.8764 230895.3252 283078.5138 296429.5522 283365.5586 310279.6695 0.597793893 0.587447922 0.666586685 0.879343301 0.726402335 0.744152286 0.912333426 0.955362473 0.913258542 1 18.24320964 4.116324105 0.276119247 1.024585735 0.318327447 0.813869559 0.062258799 2.557476408 0.213243342 0.087878974 0.60077101 13071.4602 -4.116324105 -0.706258288 FKEANNFLWPFK ddPTM_BT-474_Pertuzumab_2h_R1 2 FKEANNFLWPFK 12 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 110.31 0.0013718 930350000 2891100 3058000 1978310 1794350 2036530 2013740 2190490 2348800 2347420 2186450 FALSE TRUE 2778112.616 2970788.834 2335834.624 1886956.619 2102036.837 2054459.203 2217297.872 2300296.459 2080950.723 2038359.794 1.362915725 1.457440852 1.145938333 0.925723037 1.031239354 1.007898217 1.087785325 1.128503646 1.020894706 1 20.9589773 4.116640577 4.29749582 1.041788158 1.40862929 0.873462662 0.057022809 0.070193557 2.263447061 0.015550196 0.036352125 13080.98891 -4.116640577 0.366841132 SEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEISR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEISR 36 2 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 162.38 5.23E-18 1081900000 181590 214880 138370 119630 133240 181370 131160 79098 192320 129010 FALSE TRUE 174493.262 208751.8328 163376.537 125804.1186 137525.7856 185037.4257 132765.1753 77464.59866 170488.6399 120272.0378 1.450821531 1.735663889 1.358391693 1.045996401 1.14345602 1.538490817 1.103873999 0.644078209 1.417525162 1 16.87594174 4.117181173 0.465097161 0.998680396 1.837004183 0.307531377 0.250035108 3.186067756 0.813172915 0.197488299 1.39112453 13097.28182 -4.117181173 0.838323787 ADTLDPALLRPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 ADTLDPALLRPGR 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 179.67 1.24E-05 2496690000 2186430 2370060 1979520 2589090 2499400 2512740 2653280 2612820 2614560 2846640 FALSE TRUE 2100981.898 2302468.209 2337263.298 2722713.245 2579795.471 2563549.324 2685751.634 2558864.354 2317766.11 2653834.537 0.791677804 0.867600514 0.880711765 1.025954409 0.972101099 0.965979336 1.012026785 0.964213977 0.873364966 1 21.33964699 4.117408491 2.044888515 0.972933595 0.814068579 0.652512995 0.043096295 0.199805319 1.622156907 0.01142504 0.037168687 13104.139 -4.117408491 -0.158865016 DVEPEDPMFLMDPFAIHR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVEPEDPMFLMDPFAIHR 18 0 Q15773;F5H7L5;F5H800;F5H0Y3 Q15773 MLF2 Myeloid leukemia factor 2 0 ;;;;; 206.97 7.94E-16 630943000 590077 647255 511115 648042 661276 645981 674957 682897 748752 755158 FALSE TRUE 567016.1385 628795.9211 603484.8502 681487.5253 682546.5431 659043.1784 683217.3257 668794.9383 663756.812 704010.476 0.805408666 0.893162733 0.857210043 0.968007648 0.969511913 0.936126948 0.970464715 0.949978674 0.942822351 1 19.42523737 4.117689188 1.166492096 0.961022132 0.815770409 0.770804135 0.027215784 0.306188169 0.665041343 0.008005791 0.042124287 13112.61132 -4.117689188 -0.145251723 IDTIEIITDR ddPTM_BT-474_Pertuzumab_2h_R1 9 IDTIEIITDR 10 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;; 251.75 1.13E-16 17345856000 6268539 6374515 5671684 7372792 6858591 6482301 6844851 7564550 7598430 7936030 FALSE TRUE 6023557.566 6192720.074 6696683.465 7753302.679 7079203.808 6613377.568 6928620.334 7408339.399 6735888.082 7398515.619 0.814157579 0.837021964 0.905138789 1.047953816 0.956841098 0.893878976 0.936487897 1.001327804 0.910437773 1 22.81880442 4.118133837 3.416934246 0.96231574 0.823461441 0.61366254 0.04352349 0.151534512 3.418927022 0.011317025 0.028290209 13126.04344 -4.118133837 -0.138854299 KT(ph)NHRLSLPMPASGTSLSAAIHR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTNHRLSLPMPASGTSLSAAIHR 23 2 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 KT(0.866)NHRLS(0.134)LPMPASGTSLSAAIHR 202.49 2.08E-24 549260000 931420 955420 573800 510460 561660 626580 536100 659410 563430 504930 TRUE FALSE 895019.0767 928172.3571 677498.4241 536804.9018 579726.304 639249.8769 542660.9522 645792.9531 499471.7885 470730.6414 1.901340168 1.971769576 1.439248616 1.140365327 1.231545714 1.357995042 1.15280567 1.371894872 1.061056461 1 18.84454224 4.118409835 3.370427346 1.221225235 1.944594605 0.865147266 0.116143245 0.072945461 1.606832821 0.02814428 0.070711797 13134.38779 -4.118409835 0.72336937 S(ph)RADLTAEMISAPLGDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRADLTAEMISAPLGDFR 18 1 Q9H3Q1;Q9H3Q1-2;J3KRZ9;J3QQS6;J3QR93 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.614)RADLT(0.386)AEMISAPLGDFR;S(0.991)RADLT(0.009)AEMISAPLGDFR 190.33 1.71E-14 90473000 248340 203263 100735 33098 43898 29135 18181.3 44126 34821 38188 TRUE FALSE 238634.5982 197466.1383 118940.0553 34806.19175 45310.01904 29724.12966 18403.80819 43214.78268 30868.26606 35601.49275 6.702937991 5.546569063 3.340872704 0.977661021 1.272699978 0.834912454 0.516939228 1.213847492 0.867049769 1 15.11965011 4.118420039 1.626006833 0.908622896 6.782611655 0.987434122 0.235163334 0.039953541 0.193708496 0.065579353 0.256257056 13134.69641 -4.118420039 5.873988759 up EASRPPEEPSAPS(ph)PTLPAQFK ddPTM_BT-474_Pertuzumab_2h_R1 5 EASRPPEEPSAPSPTLPAQFK 21 1 A0A0C4DFX9;Q9H3P2;H0Y3X6;Q9H3P2-7 A0A0C4DFX9 NELFA Negative elongation factor A 1 EASRPPEEPSAPS(0.923)PT(0.077)LPAQFK;EASRPPEEPSAPS(0.975)PT(0.025)LPAQFK;EASRPPEEPSAPS(0.991)PT(0.008)LPAQFK;EASRPPEEPSAPS(0.992)PT(0.008)LPAQFK;EASRPPEEPSAPS(0.977)PT(0.023)LPAQFK 223.64 2.11E-25 8130650000 5575530 5510110 4654480 5147500 5554460 5818800 5585680 6128120 6516620 6653450 TRUE FALSE 5357632.124 5352967.058 5495648.074 5413163.092 5733124.25 5936460.123 5654039.223 6001572.18 5776880.617 6202805.905 0.863743313 0.862991224 0.885993881 0.872695869 0.924279163 0.957060436 0.911529284 0.96755763 0.931333449 1 22.56448955 4.118512674 0.190796683 1.01223788 0.747270251 0.814450309 0.01926903 4.689612745 0.209952388 0.050873928 0.306024649 13137.49833 -4.118512674 -0.264967629 NTDDDRPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 NTDDDRPPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 135.43 0.00020163 532893000 1154090 1169540 1073320 1394600 1264330 1240510 1354790 1395780 1516550 1598210 FALSE TRUE 1108986.887 1136185.864 1267292.8 1466575.473 1304998.323 1265593.962 1371370.325 1366956.655 1344397.602 1489961.813 0.744305577 0.762560392 0.850553879 0.984304068 0.875860248 0.84941369 0.920406358 0.917444087 0.902303395 1 20.50684393 4.118525547 3.243120341 0.913776279 0.750317928 0.703202244 0.043183504 0.126482733 2.601421223 0.010764776 0.027433457 13137.88776 -4.118525547 -0.163458351 ACRPPGS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ACRPPGSPGR 10 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 ACRPPGS(1)PGR;ACRPPGS(1)PGR 82.543 0.010718 1003560000 481310 500800 430380 607300 494530 468120 562420 583250 518030 569070 TRUE FALSE 462499.8731 486517.6743 508159.2398 638642.8258 510437.0066 477585.7071 569303.0642 571205.6837 459225.4062 530526.382 0.871775446 0.917047089 0.957839717 1.20379089 0.962133126 0.900211042 1.073090959 1.076677246 0.865603336 1 19.01706497 4.118663083 3.892604376 1.01919353 0.893720856 0.200052855 0.091366224 0.32185204 8.983263667 0.023334909 0.056010965 13142.04904 -4.118663083 -0.125472674 RFS(ph)LDER ddPTM_BT-474_Pertuzumab_2h_R1 1 RFSLDER 7 1 Q7LBC6;Q7LBC6-2 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 RFS(1)LDER 99.568 0.0099881 0 54474 56815 51892 61439 72738 69491 66911 69606 57972 63159 TRUE FALSE 52345.09586 55194.69183 61270.03873 64609.87415 75077.68383 70896.15563 67729.87683 68168.61178 51391.2616 58881.18467 0.88899529 0.937390987 1.040570754 1.097292361 1.275070878 1.204054504 1.150280471 1.157731662 0.872795985 1 15.84551908 4.118829534 1.969363091 1.129495843 0.894737435 0.340866751 0.105649206 0.355681538 2.659401955 0.028905421 0.096847478 13147.08693 -4.118829534 -0.234758407 S(ph)LPSS(ph)PERR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.357)S(0.643)PERR 87.831 0.046177 320900000 294680 249400 259220 317430 309020 282940 300300 363310 330590 308740 TRUE FALSE 283163.5798 242287.3562 306066.8203 333812.6003 318959.9089 288661.2407 303975.1612 355807.5215 293062.8091 287828.7648 0.983791804 0.841776034 1.063364256 1.159761084 1.108158558 1.002892261 1.05609723 1.236177773 1.018184577 1 18.13485125 4.119247341 6.00708132 1.0981191 0.914613961 0.420181949 0.077538389 0.166979459 8.038308542 0.019617422 0.043507261 13159.74097 -4.119247341 -0.18350514 RLEEPSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLEEPSLR 8 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ;;; 172.94 0.00045002 1469080000 454197 478085 421137 540551 533803 546440 532436 557386 536780 589706 FALSE TRUE 436446.4791 464450.4839 497245.824 568448.9019 550973.2583 557489.3912 538952.111 545875.7843 475846.9848 549764.6874 0.793878707 0.844816873 0.904470286 1.03398584 1.002198342 1.014050928 0.980332356 0.992926241 0.865546652 1 19.06845472 4.119388211 2.419625278 0.98574869 0.808930965 0.691067588 0.044230801 0.155906169 1.807690901 0.011555835 0.033837846 13164.01022 -4.119388211 -0.176817724 AFEDWLNDDLGSYQGAQGNR ddPTM_BT-474_Pertuzumab_2h_R1 3 AFEDWLNDDLGSYQGAQGNR 20 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 ;; 305.69 5.23E-55 256297000 153011 148114 151870 184643 195906 178340 198241 204912 199920 208401 FALSE TRUE 147031.161 143889.9337 179316.2873 194172.4474 202207.4944 181946.157 200667.1327 200680.4956 177225.9197 194285.8146 0.756777643 0.74060957 0.922951002 0.999416492 1.040773331 0.936487089 1.032845002 1.032913782 0.912191763 1 17.56782104 4.119793571 2.974922023 0.998088659 0.743344199 0.851669611 0.040187209 0.082383885 1.4428338 0.010310714 0.027241421 13176.30292 -4.119793571 -0.25474446 SSFQITSVTTDYEGPGS(ph)PGASDPPTPQPPTGPPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSFQITSVTTDYEGPGSPGASDPPTPQPPTGPPPR 35 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 SSFQITSVTTDYEGPGS(1)PGASDPPTPQPPTGPPPR 163.5 8.69E-15 83637000 13142 14184 13329 18902 16674 18758 18459 18603 15266 18247 TRUE FALSE 12628.39611 13779.48621 15737.8468 19877.53449 17210.33435 19137.29961 18684.90676 18218.84155 13533.06768 17011.11444 0.742361481 0.810028423 0.925150839 1.168502778 1.011711162 1.124988 1.098394043 1.070996355 0.795542687 1 14.05419004 4.120002559 2.835913239 1.049148603 0.765637226 0.534398073 0.097071243 0.18337732 2.927872466 0.024681802 0.066630507 13182.64507 -4.120002559 -0.283511376 LEEEVDDVFLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEEEVDDVFLIR 12 0 H0Y8R1;F5H5I6;H0YAK1;Q12849 H0Y8R1 GRSF1 G-rich sequence factor 1 0 ;;; 156.48 0.00013856 21262000 51451.7 69805.4 62364.2 124235 67687 69348.8 116093 101343 89046 97136 FALSE TRUE 49440.91068 67814.61834 73634.79822 130646.7832 69864.21383 70751.08025 117513.7809 99250.23164 78937.87139 90556.8922 0.545965188 0.748862032 0.813133009 1.442703919 0.771495268 0.78128874 1.297679039 1.09599865 0.871693689 1 16.46653683 4.120111411 3.042896918 1.042800752 0.631738554 0.361943888 0.207472574 0.261475026 4.779656407 0.053631227 0.140394514 13185.9496 -4.120111411 -0.411062198 ARS(ph)PVRLPHEGSPSPGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARSPVRLPHEGSPSPGEK 18 2 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 ARS(0.999)PVRLPHEGS(0.001)PSPGEK;ARS(1)PVRLPHEGSPSPGEK 125.78 1.51E-05 371330000 230980 240120 208418 234680 255910 274070 255140 244760 315080 301310 TRUE FALSE 221953.0462 233272.0127 246083.7688 246791.8629 264141.5776 279611.8832 258262.4796 239705.6205 279313.4393 280902.0053 0.790144043 0.830439115 0.876048459 0.878569246 0.940333542 0.995407216 0.919404186 0.853342504 0.994344768 1 18.0997074 4.120773167 0.991543051 0.936455056 0.777477833 0.604850386 0.044233192 0.707410546 1.026430667 0.016140312 0.097740287 13206.057 -4.120773167 -0.158977223 KPNFEVGSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPNFEVGSSR 10 1 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7;H3BUG4 Q6FI81-3 CIAPIN1 Anamorsin 0 ; 101.35 0.0054391 1619510000 1058010 1026430 934580 1084390 1078040 1092360 1171890 1200380 1185560 1275870 FALSE TRUE 1016661.8 997157.2214 1103479.396 1140355.498 1112716.136 1114448.268 1186231.94 1175591.734 1050980.199 1189454.188 0.854729681 0.838331758 0.927719122 0.958721663 0.93548465 0.936940891 0.997290986 0.988345533 0.883581906 1 20.18186828 4.120822297 3.29708953 0.958741775 0.845169778 0.63184646 0.033188687 0.144067936 3.051185509 0.008604764 0.021839902 13207.55103 -4.120822297 -0.113571998 SKGQESFK ddPTM_BT-474_Pertuzumab_2h_R1 4 SKGQESFK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;; 104.22 0.0042152 17424700000 13462500 12779300 9468970 8319780 9439680 6430010 11555400 11364600 12830000 12088000 FALSE TRUE 12936370.62 12414846.88 11180223.52 8749164.843 9743315.88 6560029.208 11696818.44 11129917.04 11373592.19 11269268.99 1.147933431 1.10165503 0.99209838 0.776373769 0.864591651 0.582116658 1.037939413 0.987634339 1.009257317 1 23.4258906 4.121164618 3.150007449 0.893518706 1.130634155 0.333790804 0.129541814 0.29378792 5.727366188 0.035567724 0.091903499 13217.96562 -4.121164618 0.237115449 EAEDTQVFGDLPRPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAEDTQVFGDLPRPR 15 1 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 ;;; 163.8 1.38E-06 918920000 400792 412591 351681 396774 418978 436432 441557 448311 474330 478822 FALSE TRUE 385128.6055 400824.3086 415237.5798 417251.5537 432454.8079 445256.9541 446960.9067 439053.2212 420486.047 446390.9594 0.862760765 0.897922102 0.93021055 0.934722231 0.96878039 0.997459614 1.001276789 0.983562081 0.941968107 1 18.76794828 4.121165348 0.778472407 0.986098552 0.84425153 0.839596138 0.017838574 0.495862594 0.401926884 0.007554439 0.052847729 13217.98785 -4.121165348 -0.141847022 RLDYITAEIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLDYITAEIKR 11 2 O15212 O15212 PFDN6 Prefoldin subunit 6 0 79.492 0.015184 407580000 576180 485680 410710 377590 386950 257000 498130 396500 489510 417620 FALSE TRUE 553662.2486 471828.8819 484934.4332 397077.4652 399396.5982 262196.7161 504226.2639 388312.1364 433942.877 389334.2254 1.422074435 1.211886475 1.245547916 1.019888413 1.025845076 0.673448926 1.295098738 0.997374777 1.114576753 1 18.57064965 4.121781557 1.377508017 1.017991092 1.384403955 0.423375746 0.149980756 0.527920925 1.721517482 0.043509582 0.198444855 13236.75582 -4.121781557 0.366412863 EQVALYVDLDDVAEDDPELVDSICENAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQVALYVDLDDVAEDDPELVDSICENAR 28 0 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ;;; 230.07 5.82E-35 264173000 237422 245322 214301 285519 257373 267338 263202 257116 298310 309145 FALSE TRUE 228143.2858 238325.6568 253029.9578 300254.6698 265651.6363 272743.7575 266423.1448 251806.4647 264447.0994 288206.3338 0.791597057 0.8269272 0.877947249 1.04180455 0.921741146 0.946348937 0.924418077 0.87370205 0.91756172 1 18.13674252 4.122031433 3.392521465 0.936411801 0.806739924 0.584125199 0.045788211 0.176385118 3.927956472 0.01224072 0.030779728 13244.3739 -4.122031433 -0.129671876 EYKPKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EYKPKPR 7 2 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 ; 58.604 0.061055 349590000 564200 639970 536430 611900 621120 633430 686950 788240 764600 804100 FALSE TRUE 542150.4402 621718.6822 633374.8338 643480.2323 641098.8889 646238.3886 695357.0996 771962.5685 677805.8135 749637.5908 0.723216721 0.829358999 0.844908048 0.858388427 0.855211767 0.862067747 0.927591023 1.029781028 0.904177995 1 19.51583377 4.12247533 0.265481605 1.019704758 0.612655823 0.761818121 0.040640317 3.230727914 0.249321519 0.061703499 0.422927001 13257.91806 -4.12247533 -0.407048935 RNS(ph)LDGGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RNSLDGGGR 9 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 RNS(1)LDGGGR;RNS(1)LDGGGR;RNS(1)LDGGGR;RNS(1)LDGGGR 159.93 4.02E-05 998355000 611041 626261 537596 680666 667525 664019 652481 673733 673474 721849 TRUE FALSE 587160.8422 608400.6495 634751.556 715795.2538 688996.5479 677445.9191 660466.2577 659820.1781 597024.055 672957.5243 0.872508028 0.904069912 0.943226776 1.063655919 1.023833634 1.006669656 0.981438254 0.980478194 0.887164544 1 19.36015592 4.122650896 3.168181652 0.992189787 0.88536491 0.480358092 0.042918955 0.209461385 4.126242106 0.011463798 0.029596789 13263.27873 -4.122650896 -0.106824877 GIPVELWAHYVEELNSTQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GIPVELWAHYVEELNSTQR 19 0 Q5T3Q7;Q9H583 Q5T3Q7 HEATR1 "HEAT repeat-containing protein 1;HEAT repeat-containing protein 1, N-terminally processed" 0 159.8 3.27E-11 102710000 71202 71399 68678 75723 100120 98172 101140 62948 86344 81649 FALSE TRUE 68419.34712 69362.77043 81089.64233 79631.0731 103340.4507 100157.1051 102377.7816 61648.1018 76542.5911 76118.8405 0.898849045 0.911243129 1.065303173 1.046141436 1.357619875 1.315799143 1.344972951 0.809892812 1.005566961 1 16.21596597 4.123458021 2.061645401 1.128817349 0.890805443 0.217481538 0.165550563 0.588590012 4.859804644 0.050602324 0.16518176 13287.95109 -4.123458021 -0.238011906 VQCCLYFIAPSGHGLKPLDIEFMK ddPTM_BT-474_Pertuzumab_2h_R1 2 VQCCLYFIAPSGHGLKPLDIEFMK 24 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1 E7EPK1 7-Sep Septin-7 0 ; 170.28 4.90E-12 677470000 1003120 1141060 720050 752560 751550 798110 778530 811080 942930 936870 FALSE TRUE 963916.9614 1108518.086 850179.0524 791399.7118 775724.2883 814248.331 788057.883 794330.9146 835892.5395 873414.9604 1.103618561 1.269176893 0.973396485 0.906098187 0.888150906 0.932258283 0.902272023 0.909454212 0.957039411 1 19.73630772 4.123653716 5.434015941 0.921943479 1.184113677 0.813613866 0.048633549 0.065838878 2.838956999 0.011083615 0.024886814 13293.94007 -4.123653716 0.262170198 GFESPSDNSSAMLLQWHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFESPSDNSSAMLLQWHEK 19 0 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 ; 295.37 1.13E-49 1407700000 1286560 1220050 1128670 1319500 1287120 1359040 1333010 1419930 1532230 1539700 FALSE TRUE 1236279.813 1185255.369 1332645.776 1387599.553 1328521.384 1386520.72 1349323.775 1390607.949 1358297.674 1435414.748 0.861270107 0.825723277 0.928404685 0.966688935 0.925531374 0.965937352 0.940023626 0.968784772 0.946275407 1 20.45303622 4.124665561 4.320532546 0.955777527 0.843827409 0.824840282 0.020903061 0.070686074 2.294555407 0.004796056 0.011240603 13324.94916 -4.124665561 -0.111950118 HAVSEGTK ddPTM_BT-474_Pertuzumab_2h_R1 15 HAVSEGTK 8 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;A0A2R8Y619;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 0 ;;;;;;;;;;;;;; 163.99 0.00033272 2.08907E+11 108390020 107899860 74837180 94419440 80834130 70783150 103025010 74761540 103568010 104227740 FALSE TRUE 104154018.2 104822661.6 88361923.17 99292438.61 83434233.2 72214433.79 104285860.9 73217688.07 91811403.7 97168302.33 1.07189295 1.078774241 0.909369836 1.021860383 0.858656899 0.743189209 1.073249798 0.753514123 0.944869896 1 26.53398243 4.125478594 1.059706834 0.885624838 1.107658821 0.257141476 0.103962268 0.930600069 1.585483355 0.032194923 0.186660558 13349.91788 -4.125478594 0.222033983 S(ph)PSYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSYGR 6 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 S(1)PSYGR;S(0.997)PS(0.003)YGR;S(1)PSYGR;S(1)PSYGR 157.21 0.010126 26882100000 2349970 2560510 2329610 3079910 3044770 3236380 3459780 2735960 3230230 3396310 TRUE FALSE 2258130.574 2487486.762 2750622.349 3238864.524 3142707.792 3301821.821 3502121.823 2679461.47 2863547.833 3166274.899 0.713182098 0.785619329 0.868725059 1.022925876 0.992556835 1.042809588 1.106070046 0.846250422 0.904390151 1 21.59435509 4.126231063 2.107308044 0.982763743 0.728964724 0.659068295 0.069191998 0.220008758 1.903906084 0.020564419 0.066381611 13373.06832 -4.126231063 -0.253799019 KLELDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLELDR 6 1 Q9NRR4-3;Q9NRR4-2;Q9NRR4-4;Q9NRR4 Q9NRR4-3 DROSHA Ribonuclease 3 0 ; 86.866 0.085126 2379200000 4257400 4050500 3623100 4075300 4233700 4421500 4363100 4497600 4555000 4543800 FALSE TRUE 4091016.101 3934983.706 4277874.765 4285626.721 4369880.805 4510905.759 4416496.923 4404722.988 4037935.496 4236044.379 0.965763277 0.92892882 1.00987487 1.011704869 1.031594671 1.064886332 1.042599304 1.03981984 0.953232576 1 22.01428627 4.126838164 4.676598225 1.025603006 0.947753447 0.476966965 0.029835778 0.155761476 5.621416232 0.007565811 0.017439559 13391.77561 -4.126838164 -0.077849559 PIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 PISPGLSYASHTVGFTPPTSLTR 23 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 PIS(1)PGLSYASHTVGFTPPTSLTR;PIS(0.995)PGLS(0.005)YASHTVGFTPPTSLTR 273.92 7.14E-52 2725000000 647550 490170 600500 755020 735150 694210 685210 751810 844760 861330 TRUE FALSE 622243.0301 476190.8315 709023.7081 793986.6727 758796.7674 708247.4018 693595.8049 736284.8608 748866.3863 802991.3519 0.774906266 0.593021121 0.882978013 0.988786082 0.944962565 0.882011245 0.863764975 0.91692751 0.93259583 1 19.61502492 4.127960949 6.082738779 0.923792686 0.686103883 0.743511602 0.057347671 0.089830617 4.416973284 0.013734038 0.030453972 13426.44228 -4.127960949 -0.237688803 EDGFTAEHLAAEAMAADMDPWLVFDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDGFTAEHLAAEAMAADMDPWLVFDAR 27 0 Q9H3H3-1;Q9H3H3;Q9H3H3-3 Q9H3H3-1 C11orf68 UPF0696 protein C11orf68 0 ; 194.37 1.32E-18 94759000 86593 87205 79627 98620 108154 93744 99223 96011 101107 115377 FALSE TRUE 83208.84983 84717.99878 94017.37019 103709.79 111632.8716 95639.56791 100437.3208 94028.3393 89629.75724 107562.413 0.773586679 0.787617128 0.874072713 0.964182442 1.03784276 0.889154168 0.933758531 0.874174692 0.833281392 1 16.7148145 4.128104153 3.093782241 0.927090024 0.776871999 0.530032101 0.056810528 0.20496242 3.862661413 0.015503156 0.040636361 13430.87023 -4.128104153 -0.150218025 DCPDSAEEYER ddPTM_BT-474_Pertuzumab_2h_R1 2 DCPDSAEEYER 11 0 Q7L576;A0A0G2JR96;A0A0G2JQT1 Q7L576;A0A0G2JR96 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ; 195.58 1.48E-07 472000000 220036 221209 207501 287220 253720 197032 267050 284820 288540 298110 FALSE TRUE 211436.7499 214900.3359 245001.0465 302043.4586 261881.1342 201016.122 270318.2378 278938.3675 255786.1489 277918.7442 0.760786216 0.773248802 0.881556396 1.08680492 0.942293889 0.723290984 0.972652056 1.003668782 0.920363071 1 18.08430361 4.128392414 3.866332771 0.947541476 0.765839547 0.401418404 0.088117926 0.224745603 6.210220953 0.023529067 0.056949713 13439.78786 -4.128392414 -0.181701929 CLEELVFGDVENDEDALLR ddPTM_BT-474_Pertuzumab_2h_R1 1 CLEELVFGDVENDEDALLR 19 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 106.17 0.00074253 10680000 14568 13869 13483 17345 16641 16975 15879 15797 19665 18034 FALSE TRUE 13998.66645 13473.4697 15919.67803 18240.17753 17176.27288 17318.24613 16073.33195 15470.78643 17432.71164 16812.54112 0.8326324 0.801394007 0.946893032 1.084914969 1.02163455 1.030079035 0.956032276 0.920193225 1.036887376 1 14.03725018 4.128411143 4.285921758 0.998574998 0.817305329 0.7423781 0.043921733 0.115322669 3.708420863 0.01264156 0.029742047 13440.36749 -4.128411143 -0.181269669 LLEYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEYYR 6 0 Q6UX06 Q6UX06 OLFM4 Olfactomedin-4 0 97.596 0.095131 98655000 61214 73190 73135 113320 97431 96011 115450 113270 101460 106280 FALSE TRUE 58821.6892 71102.69286 86352.12138 119168.4588 100564.9566 97952.4082 116862.9116 110930.9349 89942.68616 99081.56094 0.593669384 0.717617811 0.871525646 1.202730939 1.01497146 0.988603806 1.179461754 1.119592121 0.907764122 1 16.59632898 4.128799556 2.394991166 1.069471529 0.6276502 0.761874575 0.090176631 0.128896417 1.461935032 0.023540943 0.070228524 13452.3933 -4.128799556 -0.441821328 TT(ph)PPPGRPPAPSSEEEDGEAVAH ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 T(0.47)T(0.529)PPPGRPPAPSSEEEDGEAVAH 83.362 0.012553 642250000 68827 71622 61254 74420 74718 81704 81889 83640 68641 67411 TRUE FALSE 66137.16475 69579.41069 72323.96039 78260.82512 77121.37233 83356.11086 82891.18208 81912.80477 60849.16145 62845.19293 1.052382237 1.107155654 1.150827247 1.245295328 1.227164223 1.326372105 1.318974105 1.303406052 0.968238916 1 15.93951478 4.12880815 1.851469871 1.229355942 1.062196194 0.099551936 0.120456081 0.601627502 3.914697491 0.032325519 0.1153979 13452.6595 -4.12880815 -0.167159748 ELDPSLVSANDS(ph)PSGMQTR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELDPSLVSANDSPSGMQTR 19 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 ELDPSLVSANDS(0.997)PS(0.003)GMQTR;ELDPSLVS(0.001)ANDS(0.999)PSGMQTR;ELDPSLVSANDS(1)PSGMQTR;ELDPSLVSANDS(1)PSGMQTR 377.17 2.61E-108 1763910000 1093500 1056280 966260 1232230 1124800 1151340 1197850 1243750 1123700 1252490 TRUE FALSE 1050764.811 1026155.929 1140884.676 1295825.538 1160980.214 1174620.884 1212509.647 1218066.128 996142.2869 1167657.737 0.899891105 0.878815681 0.97707114 1.109764871 0.994281267 1.005963346 1.038411864 1.04317052 0.853111537 1 20.15518602 4.128986962 4.548583564 1.013418272 0.889909596 0.355915813 0.061269929 0.196648081 6.857934655 0.015029994 0.034879934 13458.19952 -4.128986962 -0.123508676 KWDTCAPEVILHAVGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KWDTCAPEVILHAVGGK 17 1 O95861-3;O95861-4;O95861;A6NF51;O95861-2 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ; 119.4 7.91E-05 838910000 1608470 1595060 1241060 1383300 1210120 1276390 1394240 1425770 1786740 1704470 FALSE TRUE 1545609.214 1549570.451 1465347.149 1454692.279 1249044.609 1302199.48 1411303.126 1396327.351 1583916.766 1589024.729 0.972677886 0.975170759 0.922167618 0.915462329 0.78604479 0.819496045 0.888156805 0.878732298 0.996785473 1 20.59971015 4.129066118 0.001004644 1.808046049 1.24E-07 0 0.070126984 12795508.04 2454.47984 2195631.591 2221712.369 13460.65267 -4.129066118 -1.808045926 RVS(ph)SDEEHTVDSCISDMK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVSSDEEHTVDSCISDMK 18 1 Q70CQ2-3;Q70CQ2-2;Q70CQ2;H7C150;H7C183 Q70CQ2-3 USP34 Ubiquitin carboxyl-terminal hydrolase 34 1 RVS(0.747)S(0.042)DEEHT(0.212)VDSCISDMK;RVS(0.328)S(0.328)DEEHT(0.328)VDS(0.016)CISDMK 161.53 4.35E-10 219900000 249240 237330 215246 253080 274550 262740 248550 246850 299590 265540 TRUE FALSE 239499.4253 230561.5808 254145.7403 266141.4891 283381.1501 268052.7828 251591.8292 241752.4612 265581.7992 247554.7393 0.967460473 0.931355956 1.026624419 1.075081374 1.144721167 1.082802065 1.016307868 0.976561636 1.0728205 1 17.91738804 4.130145179 4.733452721 1.049939993 0.949961616 0.438953517 0.045811871 0.211834177 7.789115225 0.013284576 0.030584582 13494.139 -4.130145179 -0.099978377 LDPAQS(ph)ASRENLLEEQGSIALR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDPAQSASRENLLEEQGSIALR 22 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 LDPAQS(0.513)AS(0.487)RENLLEEQGSIALR;LDPAQS(0.897)AS(0.103)RENLLEEQGSIALR;LDPAQS(0.643)AS(0.357)RENLLEEQGSIALR 296.02 9.28E-56 2165190000 108648 96236 103547 145056 110292 121363 121060 147991 129438 141284 TRUE FALSE 104401.916 93491.4435 122260.2463 152542.3575 113839.6423 123817.043 122541.5685 144934.9341 114744.7409 131714.7088 0.79263673 0.709802605 0.928220146 1.158126977 0.864289519 0.940039606 0.930355991 1.100370152 0.871161178 1 17.00705694 4.130408654 5.052052008 0.986153662 0.753074268 0.502331816 0.089569284 0.148304825 5.916376528 0.022050081 0.050152386 13502.32801 -4.130408654 -0.233079394 SPT(ph)PPPTLHLVPEPAAPPPPPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTPPPTLHLVPEPAAPPPPPPR 23 0 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 S(0.216)PT(0.781)PPPT(0.003)LHLVPEPAAPPPPPPR;S(0.059)PT(0.939)PPPT(0.001)LHLVPEPAAPPPPPPR 124.1 0.00021753 611710000 303320 311530 287560 387120 369610 354850 367220 343560 406040 395300 TRUE FALSE 291465.9191 302645.4694 339528.4887 407099.3096 381498.8413 362025.3101 371714.1482 336465.3659 359948.0415 368525.9789 0.790896533 0.821232387 0.921314936 1.104669231 1.03520203 0.982360351 1.008651139 0.913003113 0.976723656 1 18.4914068 4.130596951 3.362157739 0.996108285 0.80216097 0.734691553 0.046834913 0.130508224 2.861050003 0.013454297 0.034202708 13508.18349 -4.130596951 -0.193947315 SCWVCFATDEDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCWVCFATDEDDR 13 0 Q9NX47 Q9NX47 5-Mar E3 ubiquitin-protein ligase MARCH5 0 74.162 0.081098 74571000 23436 28000 23216 34594 30057 31732 33523 36284 30999 39693 FALSE TRUE 22520.09521 27201.46741 27411.64764 36379.40049 31023.8107 32373.64278 33933.2645 35534.72272 27480.12348 37004.55776 0.608576256 0.735084245 0.740764092 0.983105939 0.838378097 0.874855551 0.917002298 0.960279622 0.742614563 1 15.17541535 4.130646407 1.70363099 0.901598725 0.634754373 0.603713583 0.077506633 0.262537518 1.412822331 0.020436846 0.078377916 13509.72183 -4.130646407 -0.266844352 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAK ddPTM_BT-474_Pertuzumab_2h_R1 4 HAPSPEPAVQGTGVAGVPEESGDAAAIPAK 30 0 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK 209.56 4.81E-26 6189500000 2464330 2329350 1763110 1841400 1803650 1933940 1955050 1206100 2398930 2579440 TRUE FALSE 2368021.259 2262919.219 2081743.197 1936434.875 1861666.04 1973045.592 1978976.487 1181193.614 2126613.524 2404732.231 0.984733863 0.941027524 0.865686071 0.805260082 0.774167708 0.820484529 0.822950872 0.491195485 0.884345249 1 21.19744483 4.130740251 0.828488108 0.748749452 1.030581201 0.160706406 0.125361659 1.541832477 1.436914892 0.049145239 0.340259289 13512.64139 -4.130740251 0.281831748 TS(ph)PENVQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 T(0.462)S(0.538)PENVQDR 168.85 6.18E-05 324980000 250520 238120 238120 272360 296180 282500 293340 284140 359690 335410 TRUE FALSE 240729.4014 231329.0507 281153.581 286416.5322 305706.8987 288212.3436 296929.9827 278272.4097 318859.4991 312692.3819 0.769860142 0.739797527 0.89913793 0.915969012 0.977660206 0.921712073 0.949591355 0.889923854 1.019722633 1 18.25438455 4.131311358 3.161338639 0.943880321 0.751752941 0.798124331 0.039055681 0.098690752 1.935995561 0.009680665 0.025230409 13530.42249 -4.131311358 -0.19212738 STSAPQMS(ph)PGSSDNQSSSPQPAQQK ddPTM_BT-474_Pertuzumab_2h_R1 6 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 STSAPQMS(0.808)PGS(0.19)S(0.002)DNQSSSPQPAQQK;STSAPQMS(0.786)PGS(0.207)S(0.007)DNQSSSPQPAQQK;STSAPQMS(0.99)PGS(0.008)S(0.001)DNQSSSPQPAQQK;STSAPQMS(0.95)PGS(0.049)SDNQSSSPQPAQQK;STSAPQMS(0.998)PGS(0.001)SDNQSSSPQPAQQK;STSAPQMS(0.992)PGS(0.006)S(0.001)DNQSSSPQPAQQK 258.09 3.84E-45 6689212000 3816740 3760110 3440267 3928739 3991880 4179840 4104580 4366650 4750210 4620560 TRUE FALSE 3667577.581 3652875.344 4061999.775 4131501.691 4120282.446 4264359.229 4154813.078 4276477.152 4210986.075 4307605.356 0.851419125 0.848006036 0.942983268 0.959117967 0.956513447 0.989960518 0.964529648 0.992773664 0.977570071 1 22.03845465 4.131358188 1.707777323 0.978616387 0.837714362 0.918415333 0.014886812 0.096874845 0.524142438 0.00399046 0.015291197 13531.88155 -4.131358188 -0.140902025 EQALQEAMEQLEQLELER ddPTM_BT-474_Pertuzumab_2h_R1 2 EQALQEAMEQLEQLELER 18 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 ; 247.38 5.22E-24 74767000 42456 42379 39149 50104 47784 46554 48614 50078 49958 55406 FALSE TRUE 40796.77258 41170.39241 46224.09516 52689.87344 49321.01576 47495.35378 49208.95267 49043.8718 44286.97728 51653.30227 0.789819252 0.797052475 0.894891384 1.020067859 0.954847291 0.919502756 0.952677767 0.949481827 0.857389079 1 15.65657297 4.131444363 3.552044265 0.948232788 0.791347059 0.690086808 0.041572293 0.120317864 2.900512859 0.010375884 0.025875495 13534.5669 -4.131444363 -0.156885729 DLGQPAAAAGHFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLGQPAAAAGHFQR 14 0 P23610 P23610 F8A1 Factor VIII intron 22 protein 0 137.21 2.26E-05 630220000 233400 258140 206940 259460 239690 287100 275880 294340 302510 280090 FALSE TRUE 224278.47 250778.0999 244338.6614 272850.7617 247399.8465 292905.3587 279256.302 288261.7761 268170.333 261119.2548 0.858912033 0.960396812 0.935735902 1.044927774 0.947459224 1.121730218 1.069458865 1.10394684 1.027003287 1 17.99434932 4.131498661 0.673872807 1.07022918 0.83528883 0.593151947 0.049848434 1.038324776 0.598434185 0.022543227 0.167050429 13536.25916 -4.131498661 -0.23494035 KEKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 KEKPELSEPSHLNGPSSDPEAAFLSR 26 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 KEKPELSEPSHLNGPS(0.002)S(0.998)DPEAAFLSR;KEKPELSEPSHLNGPS(0.029)S(0.971)DPEAAFLSR;KEKPELSEPSHLNGPS(0.307)S(0.693)DPEAAFLSR 222.34 1.32E-34 1652490000 1218350 1269200 885780 771310 955270 1170350 979120 949600 1184080 1072210 TRUE FALSE 1170735.535 1233003.659 1045860.15 811117.4015 985997.1271 1194015.279 991102.7634 929990.4282 1049668.202 999588.2617 1.17121777 1.233511543 1.046290948 0.811451507 0.986403267 1.194507103 0.991511007 0.930373499 1.050100569 1 19.93097443 4.131564095 4.973716094 0.991585514 1.200799112 0.442781708 0.091341714 0.181000428 7.096981501 0.024090449 0.054964726 13538.29878 -4.131564095 0.209213598 IEEGERPDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IEEGERPDR 9 1 Q5JR04;Q9HCE1;Q9HCE1-2 Q5JR04 MOV10 Putative helicase MOV-10 0 ;;; 123.86 0.00049775 883459000 775520 840150 696680 887690 871970 916330 934910 931320 955250 934670 FALSE TRUE 745211.821 816189.7446 822585.5736 933503.7873 900017.707 934858.8204 946351.7082 912087.9165 846814.0247 871363.9684 0.855224508 0.936680623 0.944020643 1.071313276 1.032883777 1.072868347 1.086057885 1.046735864 0.971825845 1 19.73291593 4.132128615 1.541187497 1.046549564 0.868239531 0.716314254 0.037636665 0.229681732 0.976825745 0.01053994 0.044245886 13555.90806 -4.132128615 -0.178310033 REEEEFNTGPLSVLTQSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 REEEEFNTGPLSVLTQSVK 19 1 P62316;P62316-2;K7ERG4 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 ; 243.06 3.11E-24 75056000 340810 337170 259670 280260 296630 219537 341450 310990 330210 330780 FALSE TRUE 327490.7684 327554.2417 306598.1453 294724.2522 306171.3733 223976.1886 345628.7672 304567.9478 292725.9452 308375.976 1.061985349 1.06219118 0.99423486 0.955730262 0.992850926 0.726308811 1.120803156 0.987651346 0.949250162 1 18.23433085 4.132415794 2.949728958 0.964316909 1.064795534 0.156661536 0.091724329 0.484376461 8.339691206 0.023670589 0.063637853 13564.87493 -4.132415794 0.100478625 RPDS(ph)PTRPTLR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPDSPTRPTLR 11 2 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 RPDS(0.984)PT(0.013)RPT(0.003)LR;RPDS(0.99)PT(0.009)RPT(0.001)LR;RPDS(0.999)PT(0.001)RPTLR;RPDS(0.998)PT(0.002)RPTLR;RPDS(0.994)PT(0.005)RPT(0.001)LR;RPDS(0.985)PT(0.009)RPT(0.006)LR 133.48 0.0001267 5785710000 2167190 2184850 1947480 2418470 2358150 2383480 2398010 2448980 2498140 2669790 TRUE FALSE 2082493.819 2122540.217 2299432.957 2543287.527 2434002.036 2431675.599 2427357.564 2398407.707 2214561.62 2488962.745 0.836691438 0.852781031 0.923851898 1.021826273 0.977918228 0.976983526 0.975248653 0.963617359 0.889752819 1 21.24711321 4.132463274 3.177870002 0.97107952 0.841510729 0.709107193 0.032330041 0.124992863 2.475774437 0.008295373 0.021598681 13566.35803 -4.132463274 -0.12956879 LHYGTDPCTGQPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHYGTDPCTGQPFR 14 0 Q8NFF5-2;Q8NFF5;Q8NFF5-3;Q5T196;Q8NFF5-4;Q8NFF5-5 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 0 116.63 0.00035003 150820000 191150 173050 174940 209870 205370 216690 226570 198630 238800 247590 FALSE TRUE 183679.6467 168114.7834 206555.5495 220701.4159 211975.9126 221071.6203 229342.8314 194528.2211 211692.4251 230820.5088 0.795768312 0.728335555 0.894875202 0.956160339 0.918358224 0.957764201 0.993598154 0.842768358 0.917130052 1 17.81641189 4.132481997 4.806409993 0.93145741 0.762973456 0.702580645 0.045469609 0.110259892 4.147761728 0.011720593 0.026924601 13566.94291 -4.132481997 -0.168483953 LWSLDSDEPVADIEGHTVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LWSLDSDEPVADIEGHTVR 19 0 O43172-2;O43172 O43172-2 PRPF4 U4/U6 small nuclear ribonucleoprotein Prp4 0 ;; 355.49 6.03E-91 564066000 411908 405035 359964 397226 433256 458512 430362 421819 454399 477172 FALSE TRUE 395810.18 393483.7984 425017.5022 417726.8815 447192.0727 467783.4268 435628.8989 413108.2902 402817.5305 444852.7154 0.889755567 0.884526012 0.955411729 0.939022888 1.005258723 1.051546749 0.97926546 0.928640595 0.905507636 1 18.76296823 4.132562819 1.883036926 0.97275188 0.881174024 0.414044375 0.039828336 0.407259239 2.749978893 0.012170559 0.043134984 13569.46792 -4.132562819 -0.091577856 DTDIVDEAIYYFK ddPTM_BT-474_Pertuzumab_2h_R1 4 DTDIVDEAIYYFK 13 0 O15145;C9JZD1;F8VR50 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ;;; 218.71 5.51E-11 280335000 508370 475940 468890 515480 537240 527000 595270 637110 666950 678880 FALSE TRUE 488502.3384 462366.6572 553628.8534 542083.9846 554520.8125 537656.3011 602555.0923 623953.4559 591240.6321 632898.8529 0.771848987 0.730553792 0.874750919 0.856509665 0.876160243 0.849513787 0.952055908 0.985865993 0.934178707 1 19.27161543 4.132703721 0.286586601 1.011786095 0.604890164 0.812215766 0.036045637 2.328403954 0.207254332 0.046873897 0.325680344 13573.87111 -4.132703721 -0.406895931 RQS(ph)LTSPDSQSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RQSLTSPDSQSAR 13 1 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RQS(0.835)LT(0.082)S(0.082)PDS(0.001)QS(0.001)AR 75.316 0.0063868 0 108540 106370 95993 117410 111340 122890 107450 120190 127320 131530 TRUE FALSE 104298.1368 103336.4317 113341.0705 123469.5442 114921.3522 125374.92 108765.0052 117708.0345 112867.1674 122621.3559 0.850570735 0.842727851 0.924317543 1.006917133 0.937205035 1.022455828 0.886998879 0.959930948 0.920452775 1 16.90385074 4.133033004 3.923276036 0.957859472 0.84607774 0.572087546 0.039218502 0.145460121 4.120210156 0.00944579 0.022833561 13584.16676 -4.133033004 -0.111781733 SKPIPIMPAS(ph)PQKGHAVNLLDVPVPVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKPIPIMPASPQKGHAVNLLDVPVPVAR 28 2 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 1 S(0.127)KPIPIMPAS(0.873)PQKGHAVNLLDVPVPVAR;SKPIPIMPAS(1)PQKGHAVNLLDVPVPVAR 184.78 5.52E-18 3654700000 2167400 2227900 1618360 1496530 1761330 2172800 1844050 1830120 2013600 1836110 TRUE FALSE 2082695.612 2164362.473 1910833.652 1573766.093 1817984.779 2216735.505 1866618.036 1792327.382 1785024.57 1711748.634 1.216706455 1.264416066 1.116305054 0.919390886 1.062062935 1.295012282 1.090474383 1.047073937 1.042807649 1 20.70703943 4.133191867 4.986268813 1.072622012 1.239348414 0.365943774 0.090396189 0.225605847 8.89972663 0.023969827 0.054693285 13589.13669 -4.133191867 0.166726402 AVHADFFNDFEDLFDDDDIQ ddPTM_BT-474_Pertuzumab_2h_R1 4 AVHADFFNDFEDLFDDDDIQ 20 0 Q8WXC6 Q8WXC6 MYEOV2 Myeloma-overexpressed gene 2 protein 0 ;;; 127.17 2.20E-05 74139500 100689 98005 86621 107564 104556 110881 103250 98191 106101 115393 FALSE TRUE 96753.96256 95209.99336 102275.3416 113115.3909 107919.1387 113123.0898 104513.6044 96163.32154 94056.85929 107577.3293 0.899389892 0.885037711 0.950714637 1.05147982 1.003177336 1.051551386 0.971520719 0.893899506 0.874318594 1 16.71501455 4.13355273 4.705750738 0.974199772 0.892626742 0.272918475 0.054865326 0.309598392 11.35268366 0.01584328 0.03656821 13600.43285 -4.13355273 -0.08157303 SFELPPYT(ph)PPPILS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 2 SFELPPY(0.003)T(0.997)PPPILS(1)PVR;SFELPPY(0.316)T(0.685)PPPILS(0.999)PVR 130.38 0.0001617 191315000 160777 228780 205450 358260 427480 349360 275930 291640 239350 265950 TRUE FALSE 154493.6571 222255.4184 242579.3852 376749.8415 441230.2824 356424.2986 279306.9139 285617.5321 212179.9914 247936.9696 0.623116663 0.896419032 0.978391345 1.519538785 1.77960666 1.437560115 1.126523867 1.151976377 0.855781983 1 17.91961388 4.134681223 2.446521643 1.281848508 0.718368734 0.383862057 0.25973412 0.316114557 3.744990149 0.074738623 0.221936099 13635.81884 -4.134681223 -0.563479774 AAAAAATAPPS(ph)PGPAQPGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAAAATAPPSPGPAQPGPR 20 0 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 AAAAAAT(0.003)APPS(0.997)PGPAQPGPR 64.534 0.021514 0 226650 218380 221190 267250 274440 256010 290050 276390 291650 339430 TRUE FALSE 217792.2674 212152.0162 261163.9533 281042.8045 283267.6118 261186.6976 293599.7187 270682.4499 258543.1147 316440.1038 0.688257477 0.670433405 0.825318758 0.888139023 0.89516976 0.825390633 0.927820827 0.855398689 0.8170365 1 18.27157292 4.135179031 3.359687616 0.879087745 0.67630744 0.725383115 0.050165796 0.1105045 2.421188707 0.011898455 0.030383639 13651.45781 -4.135179031 -0.202780306 HQKEECQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 HQKEECQDR 9 1 E9PQ42;E9PJD7;Q6ZMK1-4;Q6ZMK1-2;Q6ZMK1 E9PQ42 CYHR1 Cysteine and histidine-rich protein 1 0 109.42 0.0014734 66907000 33419 37434 25345 20750 27732 34228 28455 26897 38289 36119 FALSE TRUE 32112.94853 36366.41897 29925.4053 21820.90999 28624.02497 34920.11361 28803.2408 26341.56755 33942.59324 33672.62796 0.95368109 1.079999429 0.888716061 0.648031096 0.850068043 1.037047469 0.855390344 0.782284281 1.008017351 1 15.0392887 4.135579381 6.795620963 0.864903666 1.01549721 0.165680059 0.114311985 0.30352694 17.32372229 0.028823485 0.063359225 13664.04805 -4.135579381 0.150593544 ERPGLGSENMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPGLGSENMDR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 147.73 6.00E-05 1012850000 616770 698870 570060 722820 775260 782570 763220 747060 853260 816010 FALSE TRUE 592665.9465 678938.9119 673082.5229 760124.8268 800196.942 798394.1016 772560.5147 731632.9499 756401.502 760740.9159 0.779064113 0.892470613 0.884772343 0.999190146 1.051865261 1.049495413 1.015536957 0.961737347 0.994295806 1 19.53704568 4.135613011 1.353816533 1.010545347 0.795248237 0.833506976 0.033330411 0.235901216 0.732203601 0.010953618 0.052102308 13665.10619 -4.135613011 -0.21529711 GNDTFVTLDEILR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNDTFVTLDEILR 13 0 F8W7U8;P49959-2;P49959;P49959-3;F5GXT0;F5H742;F5H256 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 104.24 0.0035989 43096000 56513 50545 49682 52892 69270 61694 53259 62198 63031 60512 FALSE TRUE 54304.40948 49103.50609 58660.64257 55621.76246 71498.13246 62941.49495 53910.79957 60913.58956 55875.98513 56413.46834 0.962614267 0.870421684 1.039834002 0.985966013 1.26739473 1.115717519 0.955637034 1.079770334 0.990472431 1 15.78375202 4.136255765 5.351413453 1.061853953 0.917434872 0.284885457 0.087110158 0.238471928 10.33622952 0.022283007 0.05028945 13685.34546 -4.136255765 -0.144419081 KREQSNDIAR ddPTM_BT-474_Pertuzumab_2h_R1 3 KREQSNDIAR 10 2 P45973 P45973 CBX5 Chromobox protein homolog 5 0 ;; 150.46 1.21E-05 95279000 200856 225145 122316 112101 126184 98068 153473 129026 141069 137087 FALSE TRUE 193006.3255 218724.085 144421.2221 117886.546 130242.823 100051.0022 155351.2485 126361.568 125055.4385 127801.9754 1.510198296 1.711429611 1.130039044 0.92241568 1.019098669 0.782859591 1.215562185 0.988729381 0.978509433 1 16.96355061 4.136763476 4.573839825 0.995326125 1.608951547 0.82884387 0.111430692 0.070665013 2.508888149 0.026994794 0.062784496 13701.35364 -4.136763476 0.613625422 IRLDETDDPDDYGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 IRLDETDDPDDYGDR 15 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;;;; 222.45 1.28E-12 16877380000 7210730 7395560 6970600 9126510 8047770 8617470 9044380 9187070 9505500 10015270 FALSE TRUE 6928926.7 7184645.87 8230342.48 9597530.275 8306633.831 8791721.148 9155067.828 8997353.794 8426475.49 9336926.842 0.742099281 0.769487219 0.881483021 1.02791105 0.889653948 0.941607586 0.980522605 0.963631176 0.902489184 1 23.15451635 4.137737465 3.023134236 0.955213393 0.749299997 0.801407783 0.039876347 0.096314918 1.738247157 0.009800653 0.026211919 13732.11605 -4.137737465 -0.205913396 FPSLLTHNENMVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 FPSLLTHNENMVAK 14 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 165.64 3.93E-06 2160900000 1590340 1511120 1391770 1674770 1648500 1531070 1876410 1676750 1706570 1804380 FALSE TRUE 1528187.755 1468024.337 1643293.799 1761205.08 1701525.5 1562029.284 1899374.067 1642124.527 1512847.328 1682167.735 0.908463361 0.872697952 0.976890571 1.046985413 1.01150763 0.92858117 1.129122873 0.976195472 0.899343922 1 20.68189014 4.138010238 4.804898181 1.00244907 0.891095728 0.335317075 0.059727296 0.210148988 7.988873347 0.014817989 0.034114489 13740.74367 -4.138010238 -0.111353342 MEVGPFSTGQES(ph)PTAENAR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 MEVGPFSTGQES(0.978)PT(0.022)AENAR;MEVGPFSTGQES(0.999)PT(0.001)AENAR;MEVGPFSTGQES(0.732)PT(0.268)AENAR 376.58 2.89E-108 858980000 354570 372698 423844 656030 464505 474210 621730 583020 668190 756480 TRUE FALSE 340713.0124 362069.0179 500442.0392 689887.7869 479446.2252 483798.8511 629338.9177 570980.4333 592339.8725 705242.9358 0.483114392 0.513396164 0.709602342 0.97822715 0.679831305 0.686003115 0.892371814 0.809622336 0.839908977 1 19.42776078 4.138137504 3.38555485 0.823844412 0.49158327 0.642661205 0.100652167 0.14156848 3.146709027 0.025091176 0.064059685 13744.77086 -4.138137504 -0.332261142 CIDVHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 CIDVHLK 7 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 83.614 0.02215 1584500000 2343450 2221990 2034260 2268190 2345680 2425100 2446220 2446040 2903130 2646310 FALSE TRUE 2251865.383 2158621.021 2401896.034 2385251.558 2421130.927 2474137.184 2476157.572 2395528.419 2573578.853 2467073.067 0.912768014 0.874972472 0.973581231 0.966834582 0.981377877 1.002863359 1.003682301 0.971000191 1.043170909 1 21.23436901 4.138178312 4.441240076 0.991825512 0.894056123 0.761772801 0.022279367 0.091748949 3.13580445 0.005526971 0.012953704 13746.06244 -4.138178312 -0.097769389 QEITDKDHTVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEITDKDHTVSR 12 1 Q13464;A0A0U1RQV4 Q13464 ROCK1 Rho-associated protein kinase 1 0 187.97 5.89E-06 194320000 112290 108140 107130 125290 127570 123760 131810 135440 160880 149680 FALSE TRUE 107901.5827 105055.9531 126490.7741 131756.2319 131673.4049 126262.512 133423.1302 132643.1167 142617.5769 139542.0403 0.773255016 0.752862384 0.906470723 0.944204568 0.943611005 0.904834928 0.95615006 0.95056025 1.022040215 1 17.09034031 4.138456263 3.231242461 0.953768526 0.759614055 0.856592651 0.031653432 0.080998934 1.655398957 0.008135935 0.021165895 13754.86281 -4.138456263 -0.194154471 ELNDLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELNDLAR 7 0 A0A0A0MQU3;P62837 A0A0A0MQU3 UBE2D2 Ubiquitin-conjugating enzyme E2 D2 0 97.033 0.050203 0 272830 313950 276350 422050 337400 326010 407070 357380 423990 465750 FALSE TRUE 262167.502 304996.4534 326292.5924 443832.0511 348252.7774 332602.1456 412051.8444 349999.9781 375860.4327 434204.3377 0.603788307 0.702426086 0.751472438 1.022173232 0.802048131 0.766003738 0.94898141 0.806072044 0.865630304 1 18.72801461 4.138723098 2.644716655 0.871181976 0.638780028 0.550847692 0.08483133 0.204144322 2.834294767 0.02118565 0.060548836 13763.31654 -4.138723098 -0.232401947 KLYGAQFHPEVGLTENGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLYGAQFHPEVGLTENGK 18 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 141 7.99E-08 336820000 513740 479020 377280 358740 398370 422880 371620 449670 449630 427440 FALSE TRUE 493662.4728 465358.8186 445462.8885 377254.6144 411183.9328 431430.9233 376167.9967 440384.1574 398589.8874 398489.1081 1.238835549 1.167808126 1.11787971 0.946712487 1.031857395 1.08266679 0.943985643 1.105134741 1.000252904 1 18.60418077 4.138987652 2.383297571 1.024252517 1.217445326 0.682649478 0.051519294 0.165795168 1.859589627 0.013105621 0.039764711 13771.70311 -4.138987652 0.193192809 LQPSSS(ph)PENSLDPFPPR ddPTM_BT-474_Pertuzumab_2h_R1 6 LQPSSSPENSLDPFPPR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 LQPS(0.02)S(0.147)S(0.833)PENSLDPFPPR;LQPS(0.091)S(0.091)S(0.818)PENSLDPFPPR;LQPS(0.005)S(0.08)S(0.915)PENSLDPFPPR;LQPS(0.006)S(0.025)S(0.97)PENSLDPFPPR;LQPSS(0.001)S(0.999)PENSLDPFPPR;LQPS(0.01)S(0.03)S(0.959)PENSLDPFPPR 302.11 3.98E-41 2021180000 1329820 1397510 1167530 1432840 1353320 1548290 1522670 1531580 1687330 1913270 TRUE FALSE 1277849.164 1357654.383 1378528.643 1506789.044 1396850.767 1579597.485 1541304.891 1499952.338 1495791.372 1783682.519 0.716410656 0.761152486 0.772855387 0.844763027 0.783127464 0.885582198 0.864113919 0.840930111 0.838597316 1 20.76642742 4.139480665 0.038908174 1.548788625 2.87E-13 0.822646927 0.03170096 133.1717403 0.992398064 15.50524377 24.56964993 13787.34569 -4.139480665 -1.548788625 ATSSSNPSS(ph)PAPDWYK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSSSNPSSPAPDWYK 16 0 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 ATSSS(0.001)NPS(0.124)S(0.875)PAPDWYK;ATSSSNPSS(1)PAPDWYK 284.44 1.03E-35 458294000 1192830 1198070 1254450 1519830 1388870 1441430 1754310 1497840 1919530 2213690 TRUE FALSE 1146212.885 1163902.217 1481157.02 1598268.608 1433544.265 1470576.702 1775779.771 1466909.081 1701633.002 2063754.805 0.55540168 0.563973111 0.717700095 0.774446947 0.694629159 0.712573363 0.860460635 0.710796204 0.824532545 1 20.97684014 4.140396031 0.079424013 1.292074078 3.00E-13 0.778107178 0.059518118 37.4895269 0.583369645 2.855353514 7.17884454 13816.43606 -4.140396031 -1.292074078 TSELLSGMGVSALEKEEPDSENIPQELLSNLGHPES(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSELLSGMGVSALEKEEPDSENIPQELLSNLGHPESPPR 39 1 D6RF40;D6RAG5;D6R9R7;A0A0A0MTL5;Q13309-2;Q13309 D6RF40 SKP2 S-phase kinase-associated protein 2 1 TSELLSGMGVSALEKEEPDSENIPQELLSNLGHPES(1)PPR 108.5 7.11E-06 87964000 65283 70124 42937 39180 44676 57334 51112 39491 52315 42804 TRUE FALSE 62731.66819 68124.13218 50696.67103 41202.0845 46113.04411 58493.33276 51737.52395 38675.49705 46376.42052 39904.84695 1.572031294 1.707164352 1.270438929 1.03250827 1.155575015 1.465820251 1.2965223 0.969192968 1.162175126 1 15.28427637 4.140479601 4.604314058 1.162451105 1.638399099 0.642220784 0.142230762 0.128585769 4.641919671 0.038282297 0.089055978 13819.09495 -4.140479601 0.475947994 FDEILEASDGIMVAR ddPTM_BT-474_Pertuzumab_2h_R1 9 FDEILEASDGIMVAR 15 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;; 251.34 4.14E-19 1231571000 848053 819780 843504 1123243 944548 935590 1111888 1159379 1144210 1194228 FALSE TRUE 814910.1512 796400.677 995943.9364 1181213.706 974930.2442 954508.2708 1125495.618 1135437.418 1014324.078 1113341.874 0.731949611 0.715324462 0.89455356 1.060962256 0.875679131 0.857336181 1.010916453 1.019846145 0.911062542 1 20.08646524 4.140566314 3.925588074 0.96270889 0.721982303 0.694681491 0.062240878 0.118062289 3.368672971 0.016543006 0.040192945 13821.8544 -4.140566314 -0.240726587 AKPVVSDFDS(ph)DEEQDER ddPTM_BT-474_Pertuzumab_2h_R1 1 AKPVVSDFDSDEEQDER 17 1 F6VDE0;P51531-2;P51531;B1ALG1;F6T8Q0;B1ALG2;A0A0U1RR26;A0A1W2PS06;B4DNT1;B1ALF6 F6VDE0 SMARCA2 Probable global transcription activator SNF2L2 1 AKPVVSDFDS(1)DEEQDER 122.87 3.36E-05 212230000 112060 121820 122880 175940 162590 142710 182630 132610 209120 218460 TRUE FALSE 107680.5713 118345.8129 145087.1495 185020.2845 167819.855 145595.694 184865.0806 129871.5572 185381.5743 203663.5096 0.528718038 0.581085012 0.712386572 0.908460651 0.824005514 0.714883556 0.90769859 0.637677105 0.910234605 1 17.63582799 4.140617843 2.839793404 0.815608437 0.543710123 0.552063117 0.101793127 0.198500923 3.174818914 0.025451108 0.070311089 13823.49446 -4.140617843 -0.271898314 ALASNTSFFSGCS(ph)PIEEEAH ddPTM_BT-474_Pertuzumab_2h_R1 4 ALASNTSFFSGCSPIEEEAH 20 0 O95239;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 1 ALASNTSFFSGCS(1)PIEEEAH;ALASNTSFFSGCS(1)PIEEEAH;ALASNTSFFSGCS(1)PIEEEAH;ALASNTSFFSGCS(1)PIEEEAH 262.54 2.03E-36 820290000 775290 767480 742940 965720 872430 1054530 935420 848150 959440 1067640 TRUE FALSE 744990.8097 745592.2218 877205.7846 1015560.925 900492.5033 1075853.319 946867.9498 830635.4061 850528.3935 995327.7918 0.748487901 0.749092136 0.881323512 1.02032811 0.904719541 1.080903525 0.951312681 0.834534525 0.854520893 1 19.9248122 4.140652373 3.663005412 0.940572565 0.746348543 0.554408028 0.070716442 0.17999152 4.588359835 0.019572767 0.048658266 13824.59358 -4.140652373 -0.194224022 EDTESLEIFQNEVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDTESLEIFQNEVAR 15 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 107.65 0.0050669 0 23494 25292 24206 33411 34728 30887 31390 31962 31628 31929 FALSE TRUE 22575.82851 24570.69692 28580.56266 35135.34571 35845.05766 31511.5563 31774.16021 31301.97353 28037.72204 29766.42039 0.758432764 0.825450175 0.960161225 1.180368524 1.204211228 1.058627671 1.067449824 1.051586758 0.941924547 1 14.86139812 4.141561189 2.823975669 1.076990649 0.779038593 0.693216347 0.073986648 0.144971952 2.293393297 0.020275579 0.056229132 13853.5536 -4.141561189 -0.297952056 IACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IACDEEFSDSEDEGEGGR 18 0 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 IACDEEFS(1)DS(1)EDEGEGGR 176.85 1.42E-13 243670000 390320 421840 384430 522820 480080 445860 480950 533760 594210 572970 TRUE FALSE 375065.8629 409809.5362 453905.0526 549802.8029 495522.2092 454875.5947 486836.01 522737.6695 526757.7719 534162.2316 0.702157211 0.76720051 0.849751304 1.029280564 0.927662384 0.851568246 0.911401034 0.978612187 0.986138182 1 19.02691845 4.141613408 2.510936438 0.947918057 0.720702039 0.75603446 0.050092973 0.141862981 1.771981141 0.013773382 0.040663306 13855.21942 -4.141613408 -0.227216018 KYAEAVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYAEAVTR 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 117.7 0.0032532 3580500000 5941800 6304200 3826900 4029300 4027800 3509500 4062200 4490400 4884500 4167100 FALSE TRUE 5709587.887 6124410.388 4518505.959 4237252.656 4157357.845 3580464.495 4111914.419 4397671.671 4330032.037 3884858.605 1.469702882 1.576482187 1.163106928 1.090709621 1.070143927 0.921646026 1.058446352 1.132003019 1.114591927 1 21.88943066 4.141880429 4.014736137 1.064114259 1.524844794 0.89300069 0.063582552 0.06389779 1.891520246 0.017345659 0.04189107 13863.74075 -4.141880429 0.460730535 DLLPSDMAVALLEAQAGTGHIIDPATSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLPSDMAVALLEAQAGTGHIIDPATSAR 29 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 222.05 1.75E-34 363050000 156065 158889 138907 163361 175218 169317 166299 174146 185228 187689 FALSE TRUE 149965.8073 154357.6413 164010.5849 171792.0808 180854.0461 172740.7057 168334.2169 170549.8242 164201.694 174976.6569 0.857061793 0.882161335 0.937328372 0.981799995 1.033589562 0.987221432 0.962038137 0.974700439 0.93842057 1 17.41680294 4.141964518 2.130618441 0.981914691 0.860288895 0.788350306 0.023403179 0.150225702 1.328165741 0.006723153 0.02205454 13866.42534 -4.141964518 -0.121625796 FNSLPQYS(ph)PVTFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FNSLPQYSPVTFDR 14 0 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 FNS(0.001)LPQYS(0.953)PVT(0.046)FDR 76.82 0.027687 55239000 67205 53987 57841 75793 62124 66005 71971 72829 67137 69814 TRUE FALSE 64578.5543 52447.34362 68294.15537 79704.68581 64122.27488 67339.66632 72851.80263 71325.0557 59515.88922 65085.4356 0.992212063 0.805823041 1.04930012 1.224616308 0.985201594 1.034634949 1.119325729 1.095868147 0.914427148 1 15.99004712 4.142063425 7.96961308 1.065244667 0.899904197 0.312495646 0.090037924 0.227182014 16.30895922 0.0216031 0.04708251 13869.58367 -4.142063425 -0.16534047 MCINTEWGAFGDDGSLEDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 MCINTEWGAFGDDGSLEDIR 20 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 341.27 5.02E-80 518860000 284220 319270 290240 460860 327450 366710 386500 420330 385930 415670 FALSE TRUE 273112.3682 310164.7322 342692.8244 484645.0398 337982.7266 374125.1275 391230.1026 411650.0386 342120.8444 387516.3007 0.704776464 0.800391446 0.884331379 1.250644267 0.872176799 0.965443587 1.009583602 1.062277994 0.882855363 1 18.56389747 4.142217232 3.183618802 1.008015054 0.743072251 0.492867136 0.102264989 0.186149081 3.704538811 0.025240784 0.066323853 13874.49651 -4.142217232 -0.264942803 LPNFGFVVFDDSEPVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPNFGFVVFDDSEPVQR 17 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 141.38 1.46E-06 235870000 97293 103453 93055 109697 125527 112244 120424 136795 118645 108452 FALSE TRUE 93490.682 100502.6217 109872.1085 115358.4753 129564.69 114513.6506 121897.7849 133970.1354 105176.917 101106.4494 0.92467575 0.994027802 1.086697328 1.140960601 1.281468103 1.132604806 1.205638074 1.325040452 1.040259228 1 16.6255155 4.142563564 1.463853359 1.191460892 0.921041772 0.400276636 0.095307832 0.415967658 1.556484987 0.0267175 0.119822406 13885.56526 -4.142563564 -0.270419121 SDS(ph)YSQSLK ddPTM_BT-474_Pertuzumab_2h_R1 8 SDSYSQSLK 9 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 1 SDS(0.983)YS(0.017)QSLK;SDS(0.997)YS(0.003)QSLK;SDS(1)YSQSLK;S(0.002)DS(0.99)YS(0.008)QSLK;SDS(1)YSQSLK;SDS(1)YSQSLK;SDS(0.999)YS(0.001)QSLK;SDS(0.928)YS(0.072)QSLK 278.37 2.82E-21 18234190000 10060630 9458560 6849850 5978040 7283530 6769500 6054600 9587780 7428070 6179170 TRUE FALSE 9667449.457 9188811.13 8087770.269 6286567.361 7517811.357 6906383.928 6128698.006 9389788.992 6584866.635 5760649.312 1.678187463 1.595099898 1.403968517 1.091294925 1.30502847 1.198889839 1.06389014 1.629987955 1.143077156 1 22.4578 4.142763796 2.862826378 1.248431484 1.653498194 0.498713738 0.169450047 0.234620458 3.812539628 0.045053165 0.1242886 13891.96871 -4.142763796 0.40506671 EVADIFNAPS(ph)DDEEFVGFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVADIFNAPSDDEEFVGFR 19 0 Q96GN5-5;Q96GN5-2;Q96GN5 Q96GN5-5 CDCA7L Cell division cycle-associated 7-like protein 1 EVADIFNAPS(1)DDEEFVGFR;EVADIFNAPS(1)DDEEFVGFR;EVADIFNAPS(1)DDEEFVGFR;EVADIFNAPS(1)DDEEFVGFR 205.24 4.41E-16 142672000 174909 187150 180732 260577 213745 215499 250564 250342 240520 265131 TRUE FALSE 168073.3629 181812.6652 213394.2928 274025.4102 220620.302 219856.5374 253630.4772 245172.3502 213217.1779 247173.4412 0.679981482 0.735567156 0.863338277 1.108636142 0.892572847 0.889482852 1.026123502 0.991904102 0.862621716 1 17.91516421 4.143335053 3.096641338 0.967012444 0.698756812 0.67948118 0.070707613 0.133070271 2.514950449 0.017915835 0.047697255 13910.25376 -4.143335053 -0.268255632 DLIEAIRR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLIEAIRR 8 1 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;;;; 179.68 0.00038977 4555250000 4217820 4699460 3296130 3693150 3578590 3820750 3853380 4041390 4243740 3985290 FALSE TRUE 4052982.931 4565436.002 3891814.013 3883753.914 3693698.597 3898008.183 3900538.817 3957933.884 3762008.426 3715362.759 1.090871389 1.228799527 1.047492335 1.045322938 0.994169032 1.049159513 1.04984064 1.065288679 1.012554808 1 21.82507165 4.143523094 7.872349333 1.036675618 1.159224273 0.639148015 0.038098634 0.124139736 8.894965887 0.008834718 0.019266199 13916.27795 -4.143523094 0.122548655 SDYAQLLEDMQNAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDYAQLLEDMQNAFR 15 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 267.86 3.85E-25 435220000 428910 422290 397820 481470 481070 449420 502700 494280 542140 578910 FALSE TRUE 412147.723 410246.7027 469714.9235 506318.7244 496544.0534 458507.5803 508852.193 484072.9453 480598.54 539699.9101 0.763660907 0.760138542 0.87032611 0.938148617 0.92003731 0.849560231 0.942842834 0.896929824 0.890492163 1 19.04179792 4.1437987 3.394704543 0.912808567 0.759132835 0.73118697 0.037584242 0.109244595 2.445133861 0.008966437 0.022990173 13925.11211 -4.1437987 -0.153675732 YSYYDESQGEIYR ddPTM_BT-474_Pertuzumab_2h_R1 4 YSYYDESQGEIYR 13 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ;;; 231.92 3.77E-12 513980000 126830 130625 113629 146945 133971 132627 144052 139854 158616 157213 FALSE TRUE 121873.3434 126899.7029 134164.288 154528.8491 138280.2989 135308.8088 145814.9515 136965.966 140610.5767 146564.8235 0.831532018 0.865826464 0.915392144 1.054337906 0.943475355 0.923201117 0.994883684 0.934507768 0.959374653 1 17.16117936 4.144124257 3.158595678 0.967172129 0.844453521 0.635374578 0.037324579 0.151237304 2.967090268 0.009443172 0.024946286 13935.5546 -4.144124257 -0.122718607 SDLFQDDLYPDTAGPEAALEAEEWVSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDLFQDDLYPDTAGPEAALEAEEWVSGR 28 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;; 133.75 1.53E-05 120692000 162688 180089 187026 268758 230356 196845 272040 288889 267061 307393 FALSE TRUE 156329.9731 174953.038 220825.7586 282628.6326 237765.6099 200825.3408 275369.3069 282923.3412 236745.3549 286572.9983 0.545515363 0.610500777 0.770574199 0.986236087 0.829686018 0.700782495 0.960904581 0.987264477 0.826125826 1 18.12854316 4.144189038 2.585770024 0.896734815 0.560125822 0.667802321 0.090004261 0.168588806 2.235596933 0.024815115 0.072300985 13937.63344 -4.144189038 -0.336608993 VTLVFEHVDQDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTLVFEHVDQDLR 13 0 F8W1L8;F8VYH9;F8VTV8;F8VWX7;P11802;F8VXD2;F8VZZ0;F8VZ51 F8W1L8 CDK4 Cyclin-dependent kinase 4 0 ;;; 192.18 2.94E-06 694990000 953010 1009010 902920 1151810 1144970 1132750 1168790 1107490 1265580 1416890 FALSE TRUE 915765.3156 980234.0227 1066097.729 1211255.052 1181799 1155654.981 1183094.002 1084619.944 1121916.664 1320922.778 0.693276951 0.742082761 0.807085582 0.916976429 0.894676827 0.874884588 0.895657204 0.821107761 0.849343113 1 20.3331147 4.14421066 2.235703217 0.881504414 0.70398148 0.696506068 0.046278579 0.177017796 1.734442023 0.012090922 0.038503519 13938.32735 -4.14421066 -0.177522934 EGDKHTLSK ddPTM_BT-474_Pertuzumab_2h_R1 6 EGDKHTLSK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;; 121.83 0.00036223 13548230000 22554270 22566180 13628410 8576170 14510050 19868510 13776960 13066610 14184890 10201450 FALSE TRUE 21672824.19 21922614.64 16091366.85 9018787.161 14976778.94 20270264.89 13945566.56 12796779.94 12574680.76 9510496.705 2.278831996 2.305096707 1.691958617 0.948298227 1.574763064 2.131357122 1.466334198 1.345542755 1.322189697 1 23.18108926 4.144306564 4.008230194 1.440407444 2.297995278 0.560221183 0.310589096 0.160645034 4.758984405 0.081169567 0.196462802 13941.40565 -4.144306564 0.857587834 FGKPNKR ddPTM_BT-474_Pertuzumab_2h_R1 1 FGKPNKR 7 2 P51858;P51858-2;P51858-3;Q5TGJ6 P51858 HDGF;HDGFL1 Hepatoma-derived growth factor;Hepatoma-derived growth factor-like protein 1 0 59.205 0.059019 1611100000 2022200 2585500 1518100 1626000 1744300 982940 2097300 1817500 2235600 2170300 FALSE TRUE 1943170.188 2511764.071 1792454.44 1709918.055 1800406.994 1002815.72 2122967.385 1779967.99 1981824.06 2023303.648 0.960394744 1.24141726 0.885904813 0.845111932 0.889835293 0.495632834 1.049257924 0.879733495 0.979499079 1 20.94828142 4.144827182 8.402833953 0.868364995 1.099943437 0.245655732 0.155587215 0.298341647 23.44284508 0.03770959 0.082028894 13958.12817 -4.144827182 0.231578443 LVTFYEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVTFYEDR 8 0 Q14894;I3NI53;I3L2W5;I3L325 Q14894 CRYM Ketimine reductase mu-crystallin 0 85.212 0.039324 156000000 239760 219850 107890 97353 78270 55253 83810 72410 86895 95856 FALSE TRUE 230389.9141 213580.0933 127388.123 102377.4 80787.62563 56370.25352 84835.69185 70914.7082 77031.04389 89363.58774 2.578118448 2.390012517 1.425503678 1.145627683 0.904032925 0.630796669 0.949331758 0.793552609 0.861995874 1 16.44739949 4.145087272 1.401301254 0.843948118 2.737247577 0.96581132 0.118638945 0.078299338 0.263131683 0.033086289 0.155226167 13966.4899 -4.145087272 1.893299459 up GDS(ph)RS(ph)PSHKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GDS(0.994)RS(0.916)PS(0.09)HKR 70.889 0.028227 801960000 185220 189580 150100 152620 155620 190760 147070 159070 197620 173260 TRUE FALSE 177981.3976 184173.364 177226.409 160496.7365 160625.6586 194617.2979 148869.8867 155785.1489 175187.0061 161524.9459 1.101881797 1.140216225 1.097207667 0.993634362 0.994432518 1.204874559 0.921652602 0.96446495 1.084581735 1 17.30139747 4.145621483 0.527926829 1.003209445 1.17316093 0.184506151 0.075981913 3.825244417 1.266703018 0.049818971 0.374539409 13983.68019 -4.145621483 0.169951485 FVIFPIEYHDIWQMYK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVIFPIEYHDIWQMYK 16 0 P31350;P31350-2;A0A286YFD6;C9JXC1 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 0 ; 212.24 5.02E-12 252540000 978320 1033230 587770 616640 617050 504900 731450 565810 620130 752390 FALSE TRUE 940086.1728 1003763.292 693993.1139 648464.8643 636897.9736 515109.4239 740401.7039 554125.8258 549735.4422 701429.9551 1.340242409 1.431024274 0.9893976 0.924489836 0.907999393 0.734370439 1.055560428 0.789994527 0.783735337 1 19.41993952 4.145693231 3.738203229 0.880464971 1.390115764 0.805103728 0.09673721 0.082429882 2.183325858 0.023817999 0.059041519 13985.99055 -4.145693231 0.509650793 LHDINAQLVEDQGFLDTLK ddPTM_BT-474_Pertuzumab_2h_R1 3 LHDINAQLVEDQGFLDTLK 19 0 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 ;; 221.85 2.57E-19 620320000 491010 502493 491561 620797 633263 582485 715562 473758 804820 802402 FALSE TRUE 471820.7864 488162.3916 580397.0074 652836.4076 653632.4795 594263.2458 724319.2618 463974.7317 713460.2077 748054.5978 0.630730414 0.652575886 0.775875196 0.872712245 0.873776435 0.794411594 0.968270583 0.620241802 0.953754191 1 19.51278405 4.145808576 2.772455321 0.842793517 0.633123139 0.4196685 0.103326853 0.272254668 4.153135818 0.026373325 0.074194747 13989.70562 -4.145808576 -0.209670378 GGSSVEAPCPSDVT(ph)PEDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSSVEAPCPSDVTPEDDR 19 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 GGSSVEAPCPSDVT(1)PEDDR 282.67 2.05E-39 0 53892 56262 50079 68926 61132 64231 61449 59617 70128 69320 TRUE FALSE 51785.84106 54657.46285 59129.3893 72483.27912 63098.3663 65529.79483 62201.03124 58385.88812 62167.36344 64624.89466 0.801329601 0.845764827 0.914963028 1.121599958 0.976378633 1.014002347 0.962493348 0.903458155 0.961972376 1 15.9798024 4.145817461 3.367137317 0.983012127 0.818961388 0.601113483 0.054109143 0.172745521 3.81367695 0.0150525 0.038794603 13989.99182 -4.145817461 -0.164050739 LDIDPETITWQR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDIDPETITWQR 12 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;; 227.27 3.10E-11 720771000 1106780 1170830 992010 1269220 1174900 1299610 1248340 1282530 1317540 1407390 FALSE TRUE 1063525.814 1137439.075 1171288.274 1334724.596 1212691.726 1325889.005 1263617.558 1256045.307 1167978.383 1312066.222 0.810573275 0.866906758 0.892705151 1.017269231 0.924261067 1.010535126 0.963074529 0.957303287 0.890182495 1 20.32340911 4.146076512 2.128810005 0.96373633 0.825344632 0.637992199 0.038986385 0.195066895 1.720324339 0.009894255 0.032681416 13998.33919 -4.146076512 -0.138391698 SELPDSIESALQGDER ddPTM_BT-474_Pertuzumab_2h_R1 1 SELPDSIESALQGDER 16 0 A0A087X2H1;Q9ULT8;G3V4V5;A0A087WVU6 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 0 101.61 0.0062521 0 12882 12066 12363 17599 15917 14469 14017 15101 15248 18399 FALSE TRUE 12378.5572 11721.88949 14597.26911 18507.2865 16428.98476 14761.57309 14188.54424 14789.15907 13517.11096 17152.81934 0.721663124 0.683379756 0.851012817 1.078964696 0.957800839 0.86059165 0.82718438 0.862199897 0.788040187 1 14.06615811 4.146242503 4.800660867 0.90168361 0.703076747 0.496816648 0.082018121 0.174296448 6.775630872 0.022063638 0.05098514 14003.69049 -4.146242503 -0.198606864 YPGSTFMDHVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YPGSTFMDHVLR 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 127.37 0.00027088 437040000 213880 202060 218040 319120 258880 227870 290890 273140 303320 320830 FALSE TRUE 205521.3331 196297.4466 257444.6783 335589.8214 267207.1103 232477.6875 294449.9988 267499.5635 268888.3852 299099.8983 0.687132742 0.656293926 0.860731414 1.121999116 0.893370783 0.777257661 0.984453691 0.894348561 0.898991898 1 18.19026789 4.146372103 4.465392847 0.930453301 0.671513048 0.600521475 0.085436787 0.134979212 4.732069071 0.021694053 0.051000482 14007.87001 -4.146372103 -0.258940253 QGYGEGFR ddPTM_BT-474_Pertuzumab_2h_R1 5 QGYGEGFR 8 0 Q9Y6B6;Q9H029;Q9NR31;Q9NR31-2;H0Y5E8 Q9Y6B6;Q9NR31 SAR1B;DKFZp434B2017;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 ;;;; 185.05 0.00049972 3432830000 2861660 2927600 2613550 3294790 3089900 2960170 3477750 3479560 3330680 3361390 FALSE TRUE 2749823.163 2844107.714 3085876.623 3464834.507 3189289.44 3020026.666 3520311.745 3407705.87 2952595.17 3133720.061 0.877494834 0.907581934 0.984732702 1.105661782 1.017732719 0.963719352 1.123365098 1.087431488 0.942201317 1 21.57944488 4.146707531 2.933060934 1.042778141 0.886337791 0.492654297 0.056432749 0.196860413 3.354526406 0.014845896 0.0406682 14018.6932 -4.146707531 -0.156440351 VGIGAFPTEQDNEIGELLQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGIGAFPTEQDNEIGELLQTR 21 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 151.38 1.45E-07 54245000 79407 75305 72066 86946 88346 94002 83244 86585 85683 103416 FALSE TRUE 76303.68665 73157.37513 85089.9293 91433.29348 91187.72932 95902.78485 84262.76497 84796.98949 75956.62505 96411.54221 0.791437258 0.75880308 0.882569943 0.948364598 0.945817557 0.994723066 0.873990427 0.879531512 0.787837465 1 16.55691825 4.147129709 4.505760637 0.913175497 0.775141041 0.470427866 0.05967197 0.180534174 6.426233066 0.015533334 0.036449549 14032.3274 -4.147129709 -0.138034456 GTQEVAPPTPLTPTSHTANT(ph)SPRPVSGMER ddPTM_BT-474_Pertuzumab_2h_R1 4 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPTSHT(0.009)ANT(0.78)S(0.207)PRPVS(0.003)GMER;GTQEVAPPTPLTPT(0.002)S(0.002)HT(0.119)ANT(0.438)S(0.438)PRPVS(0.002)GMER;GTQEVAPPTPLTPTSHT(0.004)ANT(0.886)S(0.11)PRPVS(0.001)GMER;GTQEVAPPTPLTPT(0.034)S(0.034)HT(0.158)ANT(0.357)S(0.357)PRPVS(0.06)GMER 198.72 4.05E-25 6099590000 454027 485157 438944 578436 519565 530550 604607 574684 606350 695330 TRUE FALSE 436283.1229 471320.7974 518270.9451 608289.1513 536277.2801 541278.0845 612006.3613 562816.5746 537519.69 648234.6798 0.673032679 0.727083589 0.79951129 0.938377983 0.827288784 0.835003281 0.944112341 0.868229658 0.829205389 1 19.30615668 4.147147495 2.236715486 0.883822776 0.684366153 0.660569144 0.055058676 0.180852645 1.773016618 0.013856725 0.044305051 14032.90208 -4.147147495 -0.199456623 MEIYRPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEIYRPHK 8 1 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 70.816 0.030253 327400000 205480 216320 201890 257140 248190 262620 280090 239480 290770 295340 FALSE TRUE 197449.6144 210150.7654 238376.014 270411.0262 256173.2568 267930.3563 283517.8252 234534.6543 257763.0086 275336.3587 0.71712147 0.763251052 0.865762935 0.98211158 0.930401121 0.973101982 1.029714443 0.851811419 0.936174974 1 18.07083561 4.148435495 2.249847026 0.949587992 0.72381756 0.778244333 0.046268979 0.147789424 1.466763211 0.012876673 0.041088509 14074.58166 -4.148435495 -0.225770433 EAGELPTS(ph)PLHLLS(ph)PGTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 2 EAGELPT(0.259)S(0.741)PLHLLS(0.999)PGT(0.001)PR;EAGELPT(0.445)S(0.555)PLHLLS(0.999)PGT(0.001)PR 147 5.80E-08 66618000 81435 83434 80657 108191 109887 98631 109665 97447 94295 112650 TRUE FALSE 78252.43017 81054.54401 95233.51411 113774.7505 113421.6152 100625.3864 111007.1131 95434.6854 83591.02692 105020.1152 0.745118495 0.771800182 0.906812128 1.083361509 1.07999896 0.958153457 1.057008107 0.908727678 0.795952535 1 16.68030616 4.148625681 3.3503542 0.983183837 0.752845072 0.540179034 0.08193682 0.182303194 3.993694993 0.022224291 0.057552077 14080.74655 -4.148625681 -0.230338765 RKLESTESR ddPTM_BT-474_Pertuzumab_2h_R1 3 RKLESTESR 9 2 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;; 164.66 3.49E-05 720630000 1088400 1031610 774440 837300 818510 634180 920100 919270 933690 925240 FALSE TRUE 1045864.125 1002189.493 914398.5353 880513.1533 844838.1175 647003.5541 931360.459 900286.7533 827701.4255 862572.6707 1.212493927 1.161860939 1.060082897 1.020798807 0.979439932 0.750085849 1.079747238 1.043722789 0.959572977 1 19.71828648 4.148636009 1.476284358 0.976316989 1.220285213 0.516509739 0.082568948 0.435594713 1.658874512 0.025328216 0.114010148 14081.08139 -4.148636009 0.243968224 FLEVDER ddPTM_BT-474_Pertuzumab_2h_R1 2 FLEVDER 7 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ; 102.72 0.019862 377990000 531960 608070 491910 666500 656650 665000 658390 677380 683730 766400 FALSE TRUE 511170.4151 590728.439 580809.0795 700898.1449 677771.7436 678446.7556 666447.5738 663391.8663 606115.8368 714491.0454 0.71543292 0.826782145 0.812899032 0.980975408 0.948607751 0.949552496 0.932758469 0.928481708 0.848318311 1 19.4465564 4.148723413 1.608422061 0.937335241 0.738335252 0.707324868 0.046104417 0.236047125 1.103634159 0.012515992 0.052124366 14083.91557 -4.148723413 -0.198999989 MGFCTDREDINSLCMTVVQNLMER ddPTM_BT-474_Pertuzumab_2h_R1 2 MGFCTDREDINSLCMTVVQNLMER 24 1 Q01581;D6RIW1 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ; 319.93 7.06E-74 1089620000 147407 147594 141441 181504 179538 196167 174262 168635 173897 184110 FALSE TRUE 141646.1715 143384.7636 167002.535 190871.4432 185313.0028 200133.6311 176394.6705 165152.6283 154156.9416 171640.0657 0.825251207 0.835380498 0.972981071 1.112044804 1.079660521 1.166007659 1.027701019 0.962203246 0.898140775 1 17.38902683 4.14908696 3.485015533 1.036199821 0.826252077 0.561909076 0.071269067 0.178031442 4.188309279 0.020299836 0.051781295 14095.71014 -4.14908696 -0.209947744 EALQDVEDENQ ddPTM_BT-474_Pertuzumab_2h_R1 3 EALQDVEDENQ 11 0 P62258;P62258-2;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;; 285.88 2.02E-27 5045400000 5178660 5430840 5349690 7230250 6276730 5986690 7215460 7750190 7022280 8145190 FALSE TRUE 4976272.242 5275957.761 6316497.986 7603404.069 6478626.721 6107744.974 7303764.958 7590145.868 6225140.214 7593509.026 0.655332367 0.694798379 0.8318286 1.001303092 0.853179564 0.804337619 0.961843192 0.999557101 0.819797566 1 22.85633529 4.149153789 2.888898431 0.920209079 0.664788662 0.653509413 0.070661051 0.154926392 2.563469774 0.01884367 0.052146034 14097.87932 -4.149153789 -0.255420418 AS(ph)LSDLSSLDDVEGMSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASLSDLSSLDDVEGMSVR 18 0 A0A087WTM5;H7BYJ1;Q969K3;Q969K3-2 A0A087WTM5 RNF34 E3 ubiquitin-protein ligase RNF34 1 AS(1)LSDLSSLDDVEGMSVR;AS(0.989)LS(0.011)DLSSLDDVEGMSVR 207.53 7.68E-16 271020000 153899 151871 143749 186662 174934 173732 169218 190582 180431 184384 TRUE FALSE 147884.4569 147539.7878 169727.642 196295.6482 180560.911 177244.9801 171288.9405 186646.4151 159949.2293 171895.5074 0.860316009 0.8583109 0.987388469 1.141947519 1.050410878 1.031120491 0.996471304 1.085813224 0.930502674 1 17.39117231 4.149425854 3.96072924 1.03988766 0.857610376 0.620844325 0.053424933 0.122826144 3.597376743 0.01313001 0.03202087 14106.71375 -4.149425854 -0.182277284 CELVLIHTYPVGEDSLVSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 CELVLIHTYPVGEDSLVSDR 20 0 Q9NVM9-2;Q9NVM9;F8VRX9;F5H457 Q9NVM9-2 ASUN Protein asunder homolog 0 131.67 1.39E-05 134430000 123790 118160 107050 125900 118160 128290 122680 144060 154770 140330 FALSE TRUE 118952.1499 114790.1925 126396.3163 132397.7141 121960.7237 130884.1117 124181.3945 141085.1107 137201.1584 130825.3241 0.909244068 0.877430981 0.966145639 1.012019003 0.932240945 1.000449359 0.949215264 1.078423552 1.048735475 1 16.99728231 4.150215163 0.390678255 1.038909907 0.826137786 0.528938272 0.040682288 2.806691475 0.477376774 0.037585949 0.26969511 14132.37534 -4.150215163 -0.212772121 YEKDIAAYR ddPTM_BT-474_Pertuzumab_2h_R1 4 YEKDIAAYR 9 1 P26583;P09429 P26583;P09429 HMGB2;HMGB1 High mobility group protein B2;High mobility group protein B1 0 ;;; 131.82 0.00029406 3269250000 6162700 6662000 3513440 2992640 3795060 3721720 3721670 3724600 3638550 3230850 FALSE TRUE 5921854.871 6472006.283 4148396.764 3147090.509 3917131.551 3796975.728 3767216.911 3647685.708 3225517.058 3012021.652 1.966073141 2.14872502 1.377279862 1.044843256 1.300499135 1.26060705 1.250727035 1.211042326 1.070881099 1 21.52230071 4.150467492 4.355324107 1.189531779 2.059269989 0.91328357 0.108184687 0.048337691 1.64965321 0.025884698 0.061407749 14140.58875 -4.150467492 0.869738209 TATPQQAQEVHEK ddPTM_BT-474_Pertuzumab_2h_R1 6 TATPQQAQEVHEK 13 0 P60174;P60174-3;P60174-4;U3KPZ0 P60174 TPI1 Triosephosphate isomerase 0 ;;;;; 249.32 1.54E-17 6323920000 6091420 5698910 3983550 3936720 3973540 4075650 3718070 4050560 5045530 4278070 FALSE TRUE 5853360.572 5536382.667 4703466.099 4139894.591 4101352.523 4158062.435 3763572.853 3966914.521 4472782.587 3988312.508 1.467628367 1.388151669 1.179312325 1.038006571 1.028342818 1.042561842 0.94365044 0.994634827 1.121472447 1 21.92734703 4.150666568 1.60568491 1.014039003 1.484904105 0.934538453 0.042705927 0.098164228 0.456767934 0.012261029 0.051322935 14147.07215 -4.150666568 0.470865101 ELLVSQHTVQLVGGLS(ph)PLS(ph)SPSDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLVSQHTVQLVGGLSPLSSPSDTK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 ELLVSQHTVQLVGGLS(1)PLS(0.644)S(0.354)PS(0.002)DTK 162.87 9.93E-12 72103000 84123 81762 89690 114560 107240 104090 114730 116640 137230 131850 TRUE FALSE 80835.38016 79430.22781 105898.9781 120472.4553 110689.472 106194.7711 116134.1001 114231.3432 121652.2257 122919.6821 0.657627638 0.64619617 0.861529874 0.980090847 0.900502427 0.863936266 0.944796619 0.929316944 0.989688744 1 16.90735641 4.150949504 3.524221495 0.935225957 0.647114118 0.89017575 0.04033592 0.064806652 1.557452352 0.010213936 0.025988188 14156.29172 -4.150949504 -0.288111838 KAPAGQEEPGT(ph)PPSSPLSAEQLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 1 KAPAGQEEPGT(0.997)PPS(0.003)SPLSAEQLDR 191.22 5.85E-18 773910000 890250 945220 646830 681390 683670 718890 725840 818100 742630 845280 TRUE FALSE 855458.0458 918263.2511 763726.5697 716556.6196 705660.8664 733426.4484 734723.047 801205.9491 658329.7558 788028.4327 1.085567488 1.165266649 0.969161185 0.909303002 0.895476403 0.930710642 0.932356012 1.016722133 0.835413709 1 19.58788816 4.151286529 5.24786827 0.936122804 1.124568794 0.685221973 0.051641319 0.103090911 4.637253165 0.012734885 0.028972965 14167.28168 -4.151286529 0.18844599 VTAVDWHFEEAVDGECPPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTAVDWHFEEAVDGECPPQR 20 0 F8VPD4;P27708;H7C3Z5 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 177.64 6.48E-17 172647000 160001 171787 147170 209578 174012 201645 200180 153053 196975 229544 FALSE TRUE 153747.984 166887.803 173766.8928 220394.3457 179609.254 205722.4001 202629.8627 149892.4021 174615.2238 213996.7804 0.718459333 0.779861279 0.812007043 1.029895615 0.839308207 0.961334089 0.946882763 0.700442323 0.815971266 1 17.70722957 4.151433558 3.142145054 0.880742411 0.743103598 0.279862255 0.09406352 0.371973205 7.239993442 0.02591203 0.0691466 14172.07879 -4.151433558 -0.137638813 QINIHNLSAFYDSELFR ddPTM_BT-474_Pertuzumab_2h_R1 2 QINIHNLSAFYDSELFR 17 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 89.982 0.0039149 127863000 165533 147522 103900 92692 92113 92797 77243 77943 102098 105372 FALSE TRUE 159063.7874 143314.817 122677.0412 97475.84523 95075.8983 94673.41892 78188.32294 76333.44981 90508.26307 98235.06058 1.619216056 1.458896815 1.248811173 0.992271442 0.967840787 0.963743681 0.795930928 0.777048941 0.92134379 1 16.5839504 4.151668881 0.876496327 0.857876496 1.7574377 0.934440269 0.067760453 0.244908595 0.256963372 0.025705432 0.179592685 14179.76001 -4.151668881 0.899561204 IVHKGDECILK ddPTM_BT-474_Pertuzumab_2h_R1 2 IVHKGDECILK 11 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 164.04 1.40E-05 2059790000 2295460 2253700 1699880 1569010 1790310 2160180 1898890 1916470 2364100 1914350 FALSE TRUE 2205750.885 2189426.683 2007086.13 1649986.794 1847896.947 2203860.32 1922129.184 1876894.225 2095737.279 1784689.369 1.235929862 1.226783058 1.124613708 0.924523238 1.035416571 1.234870537 1.077010497 1.051664372 1.174286862 1 20.76724156 4.15172915 4.102242077 1.074285669 1.232742043 0.374816918 0.081394154 0.222341244 6.923740375 0.021076311 0.050923821 14181.72794 -4.15172915 0.158456375 LGSTVFVANLDYK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSTVFVANLDYK 13 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 173.76 1.37E-06 0 215630 235130 166190 170120 190380 193400 214560 163060 244960 226360 FALSE TRUE 207202.9412 228424.3226 196224.2299 178899.9136 196503.7456 197310.6805 217185.8495 159692.754 217153.1678 211028.4356 0.981872138 1.082433853 0.929847342 0.847752641 0.931171882 0.934995703 1.029178124 0.756735715 1.029023255 1 17.68707789 4.151884505 7.182664887 0.916894087 1.031470812 0.171631562 0.082571408 0.281633807 19.46938385 0.02002706 0.043921907 14186.80193 -4.151884505 0.114576725 GLIVYQLENQPSEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLIVYQLENQPSEFR 15 0 P78406;E9PQ57;E9PPG9 P78406 RAE1 mRNA export factor 0 ; 167.3 3.07E-06 218655000 167135 164242 156501 217470 192180 190892 174704 202116 205283 192204 FALSE TRUE 160603.1794 159557.979 184784.212 228693.6528 198361.6442 194751.967 176842.0798 197942.234 181980.1345 179185.8519 0.896293863 0.890460811 1.031243316 1.276293024 1.107016219 1.08687134 0.986919882 1.104675575 1.015594326 1 17.4510972 4.1521781 4.389367739 1.087474048 0.892635395 0.478141497 0.07740333 0.165100456 5.729670469 0.019900294 0.047161918 14196.39584 -4.1521781 -0.194838653 DFQYVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFQYVDR 7 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 0 ; 166.68 0.0025927 821240000 853080 881520 770010 953110 917520 947030 984860 998500 987520 1035630 FALSE TRUE 819740.6905 856379.9127 909167.9358 1002300.121 947032.8641 966179.5955 996913.0113 977880.6261 875420.8696 965485.8577 0.849044742 0.886993741 0.941668828 1.038130298 0.98088735 1.000718538 1.03255061 1.012837856 0.906715373 1 19.8808956 4.15246581 2.361349354 0.999125154 0.857819792 0.678199755 0.035164071 0.160264947 1.760629799 0.00911363 0.028344439 14205.80374 -4.15246581 -0.141305362 RPPS(ph)PDVIVLS(ph)DNEQPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 3 RPPS(1)PDVIVLS(1)DNEQPS(0.242)S(0.758)PR 166.28 6.28E-12 912310000 170400 167560 156500 204830 184400 186680 205200 201040 188900 174050 TRUE FALSE 163740.5796 162781.3529 184783.0313 215401.3008 190331.3935 190454.7975 207711.299 196888.4537 167456.8639 162261.4385 1.00911579 1.003204177 1.138798183 1.327495324 1.172992149 1.173752675 1.28010266 1.213402615 1.032018855 1 17.30796066 4.152497254 4.215356278 1.190978967 1.005020074 0.304244372 0.094834239 0.20260785 6.602651942 0.022865803 0.05482753 14206.83231 -4.152497254 -0.185958893 RPLEQQQPHHIPTSAPVY(ph)QQPQQQPVAQSYGGYKEPAAPVSIQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPLEQQQPHHIPTSAPVYQQPQQQPVAQSYGGYKEPAAPVSIQR 44 2 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 RPLEQQQPHHIPT(0.009)S(0.01)APVY(0.98)QQPQQQPVAQSYGGYKEPAAPVSIQR 159.74 2.20E-20 344540000 290070 373440 119650 171670 140420 172390 84426 16124 191740 121260 TRUE FALSE 278733.7437 362789.8568 141273.4166 180529.9093 144936.7368 175875.8439 85459.23064 15791.03377 169974.479 113046.9522 2.465645807 3.209196266 1.249687974 1.596946276 1.282093272 1.555776963 0.75596227 0.139685621 1.503574185 1 16.78656257 4.152687327 0.621047054 0.779935693 3.463744831 0.601971068 0.513500133 1.198757486 0.565517253 0.270107293 2.088480628 14213.05142 -4.152687327 2.683809138 VCSTNDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VCSTNDLK 8 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 93.162 0.024005 0 171520 173310 151750 178490 176280 187460 174830 198180 203850 211920 FALSE TRUE 164816.8088 168367.3685 179174.6007 187701.8903 181950.2063 191250.5696 176969.6218 194087.5137 180709.8026 197566.4696 0.834234721 0.852206191 0.906907943 0.950069567 0.920956915 0.968031519 0.89574725 0.98239096 0.914678503 1 17.59197859 4.152999634 1.824329915 0.946262543 0.831697286 0.659042652 0.029877269 0.210677821 1.317633558 0.007455232 0.028056873 14223.2759 -4.152999634 -0.114565257 GPAAS(ph)PPQEPSSRPPS(ph)PPAGLSTEPAGPGTAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPAASPPQEPSSRPPSPPAGLSTEPAGPGTAPR 33 1 A6NHQ4 A6NHQ4 C17orf96 Uncharacterized protein C17orf96 2 GPAAS(0.997)PPQEPS(0.05)S(0.046)RPPS(0.906)PPAGLS(0.001)T(0.001)EPAGPGTAPR 126.73 5.39E-08 207890000 22371 26654 30678 45183 48487 43751 45599 37974 49550 41883 TRUE FALSE 21496.71659 25893.85402 36222.19703 47514.90004 50046.62839 44635.6752 46157.0542 37189.82363 43925.29173 39046.2271 0.550545294 0.663158926 0.9276747 1.21688838 1.281727637 1.143149505 1.182113039 0.952456265 1.124956109 1 15.25289553 4.153006751 2.492515496 1.125355464 0.573593003 0.832906516 0.093076175 0.115827728 1.423780952 0.026967037 0.081194595 14223.50897 -4.153006751 -0.551762461 ALEEELEDLELGL ddPTM_BT-474_Pertuzumab_2h_R1 1 ALEEELEDLELGL 13 0 Q9BRP8-2;Q9BRP8 Q9BRP8-2 WIBG Partner of Y14 and mago 0 128.36 0.00013232 0 644230 664740 565170 675810 732370 743410 659940 691700 714360 745330 FALSE TRUE 619052.7794 645782.266 667308.7911 710688.6351 755927.3462 758442.2596 668016.5431 677416.1533 633268.8476 694848.1352 0.890918098 0.929386197 0.960366384 1.022797068 1.087902964 1.091522336 0.961384955 0.97491253 0.911377344 1 19.40633817 4.1531581 2.218645549 1.007455543 0.900950842 0.363482684 0.051817018 0.382035432 3.677942349 0.015443765 0.050098963 14228.46666 -4.1531581 -0.106504701 DPS(ph)PEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DPSPEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK 41 2 O15234 O15234 CASC3 Protein CASC3 1 DPS(1)PEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK 61.373 0.0049657 220970000 36763 45509 39525 72047 62861 59233 46280 49873 50000 54875 TRUE FALSE 35326.26132 44211.12788 46668.04673 75765.3543 64882.98115 60430.73184 46846.38848 48843.10512 44324.20962 51158.26737 0.690528885 0.864202995 0.912228837 1.480999224 1.268279488 1.181250557 0.915714915 0.9547451 0.866413424 1 15.64267978 4.153234045 3.114300602 1.089395262 0.761280283 0.334933124 0.179282853 0.310773632 5.950369304 0.051258891 0.137598915 14230.95498 -4.153234045 -0.32811498 LKDENGALIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDENGALIR 10 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;E1CKY7;O60237-4;O60237;O60237-6 O14974 PPP1R12A;sm-M20;PPP1R12B Protein phosphatase 1 regulatory subunit 12A;Protein phosphatase 1 regulatory subunit 12B 0 86.014 0.012628 126900000 176630 168610 151440 178880 164310 174610 184290 197700 191740 185620 FALSE TRUE 169727.1043 163801.4079 178808.5768 188112.0182 169595.1804 178140.7338 186545.3961 193617.4259 169974.479 173047.7921 0.980810574 0.946567454 1.033290137 1.087052403 0.980048219 1.029430839 1.077999285 1.11886678 0.982240091 1 17.40081101 4.153393639 5.377944515 1.048764215 0.964090724 0.295936579 0.044494009 0.208792766 9.837741787 0.011667601 0.026451909 14236.18552 -4.153393639 -0.084673491 AS(ph)SPCPEFEQFQIVPAVETPYLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSPCPEFEQFQIVPAVETPYLAR 24 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 AS(0.543)S(0.457)PCPEFEQFQIVPAVETPYLAR;AS(0.5)S(0.5)PCPEFEQFQIVPAVETPYLAR 133.58 2.64E-05 120951000 132748 133690 123379 157738 137413 153341 153997 158653 159036 172412 TRUE FALSE 127560.0614 129877.2921 145676.3299 165878.8771 141833.0139 156441.6601 155881.6614 155376.7601 140982.9 160734.3817 0.793607815 0.808024336 0.90631717 1.032006192 0.882406194 0.973293072 0.969809071 0.966667856 0.877117257 1 17.29431903 4.15408653 3.468739124 0.955828386 0.797261012 0.652910624 0.045017919 0.125512331 2.938786467 0.010775336 0.027669241 14258.91664 -4.15408653 -0.158567373 TPNTEQQTPLFQVIS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TPNTEQQTPLFQVISPQR 18 0 Q8IZD4;Q8IZD4-2 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 TPNTEQQTPLFQVIS(1)PQR;TPNTEQQTPLFQVIS(1)PQR;TPNTEQQTPLFQVIS(1)PQR;TPNTEQQTPLFQVIS(1)PQR 247 2.57E-24 412057000 341434 312658 331354 426910 398926 358428 434710 425052 408760 460434 TRUE FALSE 328090.3818 303741.3 391237.0387 448942.8763 411757.8171 365675.6597 440030.111 416274.5277 362359.2785 429248.3951 0.764336886 0.707611964 0.911446713 1.045881316 0.959253015 0.851897558 1.025117662 0.969775385 0.844171539 1 18.71145321 4.154327205 4.809381654 0.957386344 0.736233935 0.649902185 0.063634324 0.110774545 4.454091665 0.015751032 0.036529451 14266.82074 -4.154327205 -0.221152408 SESELIDELSEDFDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;;; 407.37 1.29E-132 1004937000 618469 652125 644765 881706 757194 744700 868193 892057 873903 1005281 FALSE TRUE 594298.5477 633527.0335 761288.3782 927210.9523 781549.8327 759758.3442 878818.2056 873635.7112 774701.1951 937192.4225 0.634126497 0.675983948 0.812307441 0.989349604 0.833926752 0.810674869 0.937713734 0.932183925 0.826619141 1 19.83798576 4.154441511 2.945032564 0.899346266 0.644805431 0.712966235 0.062662626 0.129620319 2.228329033 0.015911481 0.043896085 14270.57626 -4.154441511 -0.254540835 GGGSCSGSAGGGGS(ph)GSLPSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGGSCSGSAGGGGSGSLPSQR 21 0 O15234 O15234 CASC3 Protein CASC3 1 GGGSCSGSAGGGGS(1)GSLPSQR;GGGSCSGSAGGGGS(0.976)GS(0.024)LPSQR 236.43 4.80E-32 190570000 130952 130013 135367 165276 150178 171559 173422 184651 176683 201246 TRUE FALSE 125834.2511 126305.1565 159830.8281 173805.9142 155008.6118 175028.0405 175544.3903 180837.8923 156626.6866 187615.4292 0.670703106 0.673213057 0.851906631 0.926394566 0.826203967 0.932908564 0.935660735 0.963875376 0.834828389 1 17.51741895 4.154681921 2.933744075 0.916119716 0.663537145 0.78780757 0.050118746 0.105116178 1.793602617 0.012766117 0.035294095 14278.47814 -4.154681921 -0.252582571 TSS(ph)VVTLEVAK ddPTM_BT-474_Pertuzumab_2h_R1 4 TSSVVTLEVAK 11 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TSS(1)VVTLEVAK;TSS(1)VVTLEVAK;TS(0.001)S(0.999)VVTLEVAK;TS(0.002)S(0.998)VVTLEVAK 252.21 2.33E-20 1908280000 3980510 3555480 2801800 2527080 2800540 2413090 2588140 3370720 3498490 2981200 TRUE FALSE 3824947.269 3454081.192 3308147.586 2657502.902 2890621.912 2461884.333 2619814.432 3301113.454 3101356.082 2779280.669 1.376236417 1.242796825 1.190289136 0.95618371 1.040061173 0.885799107 0.942623198 1.187758218 1.115884451 1 21.4062801 4.154745769 1.864344281 1.027158807 1.348986122 0.653582855 0.086769932 0.260305882 1.709316569 0.026479175 0.098178154 14280.57744 -4.154745769 0.321827315 FSDAGQPMSFVLEFHFEPNEYFTNEVLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSDAGQPMSFVLEFHFEPNEYFTNEVLTK 29 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;P55209-3;B7Z4K9 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 295.01 8.82E-81 393580000 170109 173021 145398 167646 165443 198471 167516 163971 206624 215180 FALSE TRUE 163460.9522 168086.6105 171674.653 176298.2302 170764.6243 202484.2196 169566.1109 160584.9415 183168.9098 200605.6669 0.814837161 0.837895624 0.855781671 0.87882976 0.851245266 1.009364405 0.845270792 0.800500524 0.913079439 1 17.61400284 4.154762359 1.211340996 0.88713924 0.812265494 0.175950816 0.062355883 1.475961967 3.439049774 0.019842172 0.108484849 14281.12299 -4.154762359 -0.074873746 ISAIHILDVLVLNGTDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISAIHILDVLVLNGTDVR 18 0 Q8N1G2;H0YCQ1;H0Y4T0 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 ; 263.2 6.99E-31 198944000 151233 157576 145647 188041 187312 180602 184621 182878 193592 205638 FALSE TRUE 145322.6472 153082.0868 171968.6528 197745.8185 193337.0606 184253.8962 186880.447 179101.5054 171616.2478 191709.9551 0.758033912 0.798508803 0.897025158 1.031484351 1.008487329 0.961107607 0.974808256 0.934231638 0.895186938 1 17.54856573 4.155074928 2.803583316 0.968576327 0.76881235 0.808632405 0.037464491 0.112121274 1.749191021 0.010398304 0.029419127 14291.40503 -4.155074928 -0.199763977 AENGERS(ph)DLEEDNER ddPTM_BT-474_Pertuzumab_2h_R1 2 AENGERSDLEEDNER 15 1 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 1 AENGERS(1)DLEEDNER;AENGERS(1)DLEEDNER 189.44 6.78E-07 493390000 512000 497460 475360 528170 570680 569020 577810 641520 654310 633120 TRUE FALSE 491990.474 483272.9279 561268.1263 555428.917 589036.4405 580525.9743 584881.4116 628272.3878 580035.4719 590238.2185 0.833545607 0.818776068 0.950917966 0.941024996 0.99796391 0.983545213 0.990924331 1.064438676 0.982714189 1 19.17093781 4.155106546 0.771595422 1.015971673 0.769667221 0.832591109 0.029567622 0.481097668 0.371739231 0.011923538 0.08915066 14292.44553 -4.155106546 -0.246304452 SKEINQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKEINQTR 8 1 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;H7C0P8 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 78.655 0.027417 186162000 433870 416710 319730 311880 343750 335520 334480 426260 383940 359680 FALSE TRUE 416913.8807 404825.8388 377512.3234 327976.1642 354807.0309 342304.4443 338573.4663 417457.582 340356.7408 335318.5532 1.243336752 1.207287324 1.125831898 0.978103242 1.058119294 1.020833595 1.009706928 1.244958199 1.015025078 1 18.35517278 4.155460475 3.089915498 1.064229404 1.231640667 0.481678505 0.072372567 0.243401958 4.593634734 0.020355966 0.054974091 14304.09793 -4.155460475 0.167411263 SPAEGSERLS(ph)LS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPAEGSERLSLSPLR 15 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(0.001)PAEGS(0.015)ERLS(0.984)LS(1)PLR 61.181 0.052013 74374000 63275 67385 80460 115120 99992 111220 111320 112810 102970 122930 TRUE FALSE 60802.14305 65463.24578 95000.91182 121061.357 103208.3335 113468.9446 112682.3675 110480.4341 91281.27729 114603.8416 0.530541928 0.571213363 0.8289505 1.056346413 0.90056609 0.990097217 0.983233772 0.964020338 0.796494044 1 16.80629588 4.155646866 3.041848141 0.955678322 0.536496364 0.854016851 0.066135928 0.078689487 1.440920941 0.01628902 0.04431803 14310.23831 -4.155646866 -0.419181958 KFDVNTSAVQVLIEHIGNLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFDVNTSAVQVLIEHIGNLDR 21 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 295.73 4.69E-55 13898800000 4076100 4436500 3698700 4469600 4825400 4895800 4931800 4463300 5247600 5561800 FALSE TRUE 3916801.506 4309975.364 4367137.367 4700276.592 4980613.373 4994796.43 4992156.844 4371131.295 4651914.448 5185094.332 0.755396383 0.831224099 0.842248393 0.906497797 0.960563696 0.963299047 0.962789975 0.843018664 0.897170649 1 22.30593881 4.155778143 1.315528912 0.927281967 0.761383407 0.650921744 0.043315088 0.422756125 1.208888379 0.014128394 0.071755938 14314.56462 -4.155778143 -0.165898559 TVSS(ph)PIPYTPSPSSSR ddPTM_BT-474_Pertuzumab_2h_R1 6 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.05)S(0.95)PIPYTPSPSSSR;TVS(0.002)S(0.998)PIPYTPSPSSSR;TVS(0.001)S(0.999)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVS(0.005)S(0.995)PIPYTPSPSSSR 350.79 3.43E-87 4300410000 1709904 1709845 1919646 2513770 2275296 2016290 2717610 2652260 2740690 2925580 TRUE FALSE 1643079.061 1661081.895 2266568.734 2643505.971 2348482.962 2057060.765 2750868.924 2597489.904 2429578.361 2727427.861 0.602428055 0.609028718 0.831027932 0.969230391 0.86106144 0.754212713 1.008594568 0.952358793 0.890794729 1 21.37910961 4.15592085 3.275129571 0.915684868 0.597757614 0.752907786 0.070820207 0.113633965 2.395745689 0.018809582 0.049540089 14319.26908 -4.15592085 -0.317927254 EREVDEDS(ph)EPER ddPTM_BT-474_Pertuzumab_2h_R1 3 EREVDEDSEPER 12 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREVDEDS(1)EPER;EREVDEDS(1)EPER;EREVDEDS(1)EPER 274.6 5.10E-28 1769930000 872696 821170 759313 906590 916680 842200 871780 1001080 949460 933690 TRUE FALSE 838590.0755 797751.0356 896537.7499 953379.2185 946165.8447 859229.861 882449.1044 980407.3482 841681.2813 870450.3447 0.963397948 0.916480808 1.02997001 1.095271229 1.086984284 0.987109565 1.013784542 1.126321971 0.966949219 1 19.73140248 4.156116944 5.544949576 1.048494509 0.940462383 0.373688829 0.049922349 0.173854465 8.710892994 0.012486683 0.028193754 14325.73603 -4.156116944 -0.108032126 DTPDEPWAFPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 DTPDEPWAFPAR 12 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 147.75 0.00014297 1842330000 873100 949450 772620 982380 955690 953670 971150 1314860 1006370 1179590 FALSE TRUE 838978.2867 922372.6156 912249.6208 1033080.75 986430.6368 972953.8608 983035.2242 1287707.682 892131.0966 1099695.319 0.762918849 0.83875288 0.829547608 0.939424522 0.897003579 0.88474857 0.893915985 1.170967685 0.811252973 1 20.06867244 4.156356859 0.37352389 1.010699963 0.669019353 0.324454767 0.090245057 4.20399057 0.645780696 0.086777027 0.624253174 14333.65208 -4.156356859 -0.34168061 (ac)S(ph)SSPVNVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.333)S(0.333)S(0.333)PVNVKK 42.821 0.07944 34042000000 28201000 26246000 21166000 18016000 22103000 23623000 24037000 26033000 26191000 24358000 TRUE FALSE 27098873.74 25497489.78 24991167.04 18945807.92 22813963.07 24100673.25 24331172 25495409.45 23217907.48 22708210.96 1.193351329 1.122831289 1.100534387 0.834315303 1.004656998 1.06131977 1.071470229 1.122739677 1.022445472 1 24.43671071 4.156743615 3.303404733 1.029072045 1.163829945 0.363722615 0.073977038 0.29488068 6.32074154 0.020810772 0.054659653 14346.42246 -4.156743615 0.134757899 VTKS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTKSPQK 7 1 Q9NVP1 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 1 VT(0.001)KS(0.999)PQK;VT(0.004)KS(0.996)PQK 79.986 0.018858 1756020000 6090200 4912800 3654640 2678130 2938420 1306260 3923020 3320650 3077810 3925100 TRUE FALSE 5852188.251 4772691.754 4315114.745 2816348.61 3032936.948 1332673.472 3971031.092 3252077.417 2728429.912 3659249.481 1.599286488 1.304281596 1.179234913 0.769651981 0.828841259 0.364193116 1.085203704 0.888727985 0.745625551 1 21.80311635 4.156956198 1.562189319 0.808623438 1.567763682 0.664033061 0.187756943 0.277858123 1.207904757 0.05359837 0.232693882 14353.44659 -4.156956198 0.759140244 DFSVDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFSVDR 6 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ;;; 160.77 0.020256 2394490000 2558280 2628430 2396580 3086480 2965270 2650520 3153700 3246370 2987380 3032190 FALSE TRUE 2458299.589 2553469.75 2829695.318 3245773.603 3060650.603 2704115.33 3192295.924 3179331.325 2648265.147 2826817.071 0.869635186 0.903302084 1.001018194 1.148207868 1.082719725 0.956593675 1.129289885 1.124703596 0.936836407 1 21.4307471 4.157411427 3.111628671 1.0651523 0.879745336 0.471226522 0.069358084 0.191502668 3.66526643 0.01781875 0.048074799 14368.49982 -4.157411427 -0.185406964 TKFEECRK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKFEECRK 8 2 P43487;F6WQW2;P43487-2;C9JXG8;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 70.028 0.029467 455650000 513020 512740 276240 224750 268920 180800 313720 258870 370520 334730 FALSE TRUE 492970.6112 498117.1572 326162.7129 236349.3744 277570.056 184455.8999 317559.3992 253524.244 328460.1229 312058.439 1.579738119 1.596230369 1.045197541 0.757388184 0.889481012 0.591094093 1.017627981 0.812425534 1.052559655 1 18.2514567 4.157621308 3.498803533 0.863027551 1.602176769 0.821979563 0.13062555 0.078500245 1.872698813 0.031593932 0.081136388 14375.44533 -4.157621308 0.739149218 EIVRPDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIVRPDPK 8 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 71.692 0.043853 242690000 824200 847160 501260 419240 470220 673630 510180 501810 603290 570060 FALSE TRUE 791989.3528 822999.8263 591848.8325 440877.0266 485345.0533 687251.2601 516423.7355 491447.4481 534807.0484 531449.3284 1.490244338 1.548595101 1.113650542 0.829574906 0.913248032 1.293164227 0.971727139 0.924730585 1.006318043 1 19.01957262 4.157642154 4.166195748 0.991031082 1.523118157 0.764367971 0.115296046 0.094057074 3.04581172 0.030280541 0.073142353 14376.13538 -4.157642154 0.532087075 RRDS(ph)LDSSTEASGSDVVLGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RRDSLDSSTEASGSDVVLGGR 21 2 Q9Y2I9 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 RRDS(0.453)LDS(0.453)S(0.086)T(0.009)EASGSDVVLGGR;RRDS(0.491)LDS(0.491)S(0.014)T(0.004)EASGSDVVLGGR 149.44 6.36E-08 1654600000 237559 243485 231338 273620 312500 367170 314280 235809 260230 290300 TRUE FALSE 228274.9316 236541.0462 273145.9227 287741.561 322551.8463 374594.429 318126.2527 230939.4617 230689.7814 270637.7224 0.843470487 0.874013586 1.009267741 1.06319828 1.191821463 1.384117578 1.175468999 0.853315863 0.8523933 1 18.04600342 4.158081431 2.352388245 1.077610363 0.844052805 0.245741601 0.149617008 0.490118841 5.337995975 0.045741291 0.143762587 14390.68381 -4.158081431 -0.233557558 RDELSEEINNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDELSEEINNLR 12 1 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;A0A087WYS2;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ;;; 313.87 3.57E-46 1430690000 598590 587930 605920 873740 758650 663460 763440 792230 762730 832390 FALSE TRUE 575196.441 571162.812 715423.2226 918833.8261 783052.6662 676875.6158 772783.2071 775870.1737 676148.088 776011.4839 0.741221558 0.736023659 0.921923499 1.184046686 1.009073554 0.872249483 0.995839911 0.999817902 0.871311961 1 19.56571848 4.158328756 4.238554336 0.991089718 0.736720174 0.593224499 0.081903517 0.136478021 4.55671261 0.021204675 0.0509792 14398.88145 -4.158328756 -0.254369544 SSATS(ph)GDIWPGLSAYDNS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSATSGDIWPGLSAYDNSPR 20 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 S(0.001)S(0.002)AT(0.086)S(0.911)GDIWPGLSAYDNS(1)PR;SSAT(0.019)S(0.981)GDIWPGLSAYDNS(1)PR 277.17 2.09E-44 158682000 116867 124371 132774 178549 153464 155687 187511 195194 174774 209796 TRUE FALSE 112299.7084 120824.0609 156769.2153 187763.9353 158400.3089 158835.0978 189805.8157 191163.1757 154934.3882 195586.3301 0.574169516 0.617753096 0.801534623 0.960005412 0.80987413 0.812097133 0.970445203 0.977385156 0.792153461 1 17.57744602 4.15845272 2.625375058 0.90341234 0.579076235 0.7373194 0.07260692 0.136840826 1.870385223 0.019510777 0.057428014 14402.99202 -4.15845272 -0.324336105 HLYPNTPYAYTFWTYMMNAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLYPNTPYAYTFWTYMMNAR 20 0 P27695 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 110.37 0.00018382 183390000 365460 370480 249620 243220 269500 298350 277260 258500 346480 280300 FALSE TRUE 351177.4192 359914.2731 294731.8868 255772.6133 278168.7123 304382.8414 280653.1908 253161.8847 307149.043 261315.0313 1.343885261 1.377319442 1.127879576 0.978790283 1.064495643 1.164811836 1.074003242 0.96879955 1.175397532 1 17.99543059 4.158473871 4.134615305 1.05903844 1.362885695 0.757359777 0.066691554 0.092636802 2.968011063 0.016969035 0.041112342 14403.69349 -4.158473871 0.303847255 ITS(ph)PLMEPSSIEK ddPTM_BT-474_Pertuzumab_2h_R1 6 ITSPLMEPSSIEK 13 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 IT(0.053)S(0.947)PLMEPSSIEK;IT(0.197)S(0.803)PLMEPSSIEK;ITS(1)PLMEPSSIEK;IT(0.026)S(0.974)PLMEPSSIEK;IT(0.032)S(0.968)PLMEPSSIEK;IT(0.002)S(0.998)PLMEPSSIEK 187.63 7.13E-06 1665521000 2460340 2377220 2062780 2363430 2428790 2316540 2420440 2551150 2703260 2628180 TRUE FALSE 2364187.193 2309424.013 2435570.232 2485406.906 2506914.236 2363382.026 2450062.069 2498467.861 2396397.258 2450171.028 0.964907007 0.942556249 0.994040908 1.014380987 1.023158877 0.96457839 0.99995553 1.019711617 0.978053055 1 21.22445103 4.158498148 5.680051093 1.001503834 0.953958416 0.511557257 0.017765395 0.140630143 7.428367378 0.004467962 0.010058858 14404.49868 -4.158498148 -0.047545418 ITHQEVDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITHQEVDSR 9 0 Q8WTS6;D6RJA0 Q8WTS6 SETD7 Histone-lysine N-methyltransferase SETD7 0 ; 120.09 0.00072136 887700000 730490 825880 714120 955180 1023580 960670 1004000 875800 1019780 954170 FALSE TRUE 701941.6432 802326.711 843177.3695 1004476.954 1056504.38 980095.4056 1016287.252 857714.4239 904018.8497 889543.216 0.789103475 0.901953606 0.947876792 1.129205345 1.187693146 1.101796279 1.142482157 0.964218948 1.016273109 1 19.76270517 4.158703329 2.006956165 1.077195221 0.816393276 0.650332801 0.069383813 0.231302398 1.789108764 0.020598483 0.072507982 14411.30563 -4.158703329 -0.260801945 AEQDASIPPGTHEALLQTALSPPPPPT(ph)RPVSPPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 AEQDASIPPGTHEALLQTALSPPPPPTRPVSPPQK 35 1 Q5JQP0;Q5JQP1;Q5JQN9;Q5JQP2;Q5JQP8;Q9UGP5 Q5JQP0 POLL DNA polymerase lambda 1 AEQDASIPPGTHEALLQTALS(0.031)PPPPPT(0.558)RPVS(0.411)PPQK;AEQDASIPPGTHEALLQTALS(0.001)PPPPPT(0.553)RPVS(0.447)PPQK 74.841 0.0048782 197903000 194902 189681 173638 199415 200870 206560 204775 228807 235173 200500 TRUE FALSE 187285.0144 184271.4836 205018.2492 209706.832 207331.166 210736.7847 207281.0977 224082.0555 208477.147 186919.9564 1.001953018 0.985830979 1.096823759 1.121907131 1.109197594 1.127417258 1.108929735 1.198812903 1.115328459 1 17.51206108 4.158817843 3.813137181 1.12388289 0.992369014 0.48466583 0.046668341 0.152347168 4.247866748 0.011527321 0.028700234 14415.10608 -4.158817843 -0.131513876 GRPITMFIPSDVDNYDDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GRPITMFIPSDVDNYDDIR 19 1 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 78.987 0.008534 201530000 38722 36307 36834 49331 40695 44933 49668 38271 54502 50610 FALSE TRUE 37208.70143 35271.55991 43490.72317 51876.97882 42003.99163 45841.57605 50275.85184 37480.69048 48315.16145 47182.13962 0.788618357 0.747561687 0.921762419 1.099504585 0.890251946 0.971587478 1.065569562 0.794383018 1.024013787 1 15.52595322 4.159896491 4.898792594 0.963764541 0.768166565 0.49071328 0.083190789 0.165039687 7.010858218 0.02102257 0.048700854 14450.95307 -4.159896491 -0.195597976 VGLVEDSPSTAGDGDDSPVVSLTVPSTS(ph)PPSSSGLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGLVEDSPSTAGDGDDSPVVSLTVPSTSPPSSSGLSR 37 0 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VGLVEDSPSTAGDGDDSPVVSLT(0.011)VPS(0.118)T(0.118)S(0.278)PPS(0.119)S(0.119)S(0.119)GLS(0.119)R;VGLVEDSPSTAGDGDDSPVVSLT(0.001)VPS(0.084)T(0.084)S(0.323)PPS(0.088)S(0.116)S(0.153)GLS(0.153)R 114.76 5.41E-06 316190000 136593 144350 132066 177573 176587 165704 181039 162002 149996 181147 TRUE FALSE 131254.7945 140233.2793 155933.264 186737.5638 182267.0812 169054.6484 183254.6094 158656.6021 132969.0829 168877.7523 0.777217796 0.830383383 0.923349949 1.105755857 1.079284149 1.00104748 1.085131741 0.93947604 0.787368857 1 17.36561976 4.160238619 2.96279841 1.002472951 0.794320951 0.444937285 0.086784485 0.233259562 4.061412604 0.023475377 0.06502011 14462.34173 -4.160238619 -0.208151999 (ac)S(ph)QGDSNPAAIPHAAEDIQGDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQGDSNPAAIPHAAEDIQGDDR 22 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1 S(0.973)QGDS(0.027)NPAAIPHAAEDIQGDDR;S(0.855)QGDS(0.145)NPAAIPHAAEDIQGDDR 100.41 4.67E-31 895080000 0 5862.6 0 0 3881.2 0 4149 0 0 3345.1 TRUE FALSE 0 5695.404388 0 0 4006.042323 0 4199.776703 0 0 3118.533397 0 1.826308608 0 0 1.284591765 0 1.34671532 0 0 1 11.60665199 4.160442685 24.93435959 0.439955605 0.914454962 0.069666726 0.669688322 72.47806734 23129.96574 0.155432825 0.335773527 14469.13888 -4.160442685 0.474499357 MVSDINNGWQHLEQAEK ddPTM_BT-474_Pertuzumab_2h_R1 5 MVSDINNGWQHLEQAEK 17 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;; 365.61 1.28E-104 2925820000 2321230 2259290 2521710 3387060 2643410 2291770 3261780 3385890 3952320 4369750 FALSE TRUE 2230513.765 2194857.261 2977439.092 3561866.573 2728437.683 2338111.16 3301698.639 3315970.188 3503669.203 4073782.94 0.547528869 0.538776192 0.730878188 0.874338821 0.669755292 0.573941026 0.810474855 0.813978122 0.860052991 1 21.95793768 4.16057501 0.087610431 1.281322977 6.08E-17 0.616674105 0.091955237 45.78057284 0.785050457 3.261691482 9.031605746 14473.54813 -4.16057501 -1.281322977 AKPAMPQDSVPSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 0 77.746 0.012631 0 106650 105230 109290 139260 139920 140580 135900 142760 140680 128660 FALSE TRUE 102482.0001 102228.9434 129041.1341 146447.2253 144420.6539 143422.6239 137563.1849 139811.9561 124710.5962 119945.7436 0.854402974 0.852293215 1.075829206 1.220945578 1.204049844 1.195729166 1.14687842 1.165626657 1.039725066 1 16.87202244 4.160617707 3.615640893 1.151949974 0.847836795 0.731698228 0.067741924 0.097785956 2.48477092 0.01654863 0.042086046 14474.97116 -4.160617707 -0.304113179 TDTGEPMGR ddPTM_BT-474_Pertuzumab_2h_R1 3 TDTGEPMGR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 145.65 0.00022489 874635000 1324600 1358180 1145270 1339870 1370270 1443580 1361250 1487070 1500590 1490470 FALSE TRUE 1272833.168 1319446.036 1352245.765 1409020.851 1414345.979 1472770.177 1377909.385 1456361.485 1330249.314 1389519.139 0.916024207 0.94957025 0.973175343 1.014034864 1.017867217 1.059913559 0.991644768 1.04810466 0.957345082 1 20.40615428 4.160708627 1.446645142 1.01820147 0.916360433 0.581569769 0.027520757 0.322751797 1.163032134 0.007501269 0.035209011 14478.00184 -4.160708627 -0.101841037 SKGHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_BT-474_Pertuzumab_2h_R1 3 SKGHYEVTGSDDETGKLQGSGVSLASK 27 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVT(0.003)GS(0.996)DDET(0.002)GKLQGSGVSLASK;S(0.007)KGHYEVT(0.162)GS(0.825)DDET(0.007)GKLQGSGVSLASK;SKGHYEVT(0.053)GS(0.947)DDETGKLQGSGVSLASK 148.02 6.02E-08 2118440000 1125230 1220460 780550 652340 790710 1043810 795590 952850 1094570 907510 TRUE FALSE 1081254.768 1185653.676 921612.7482 686007.3456 816143.9053 1064916.553 805326.6684 933173.3145 970319.0024 846043.5394 1.278013149 1.401409763 1.089320709 0.810841657 0.964659462 1.258701832 0.951873788 1.102984978 1.146890151 1 19.69037238 4.160902464 5.685973927 1.037309747 1.338369532 0.509643619 0.117990957 0.149016266 8.035322451 0.030101846 0.067818481 14484.46517 -4.160902464 0.301059785 TENWLSEWWLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TENWLSEWWLK 11 0 P43155-2;P43155;P43155-3 P43155-2 CRAT Carnitine O-acetyltransferase 0 137.89 0.00016018 268820000 204190 195700 207510 255900 221100 222750 314520 292890 245490 249640 FALSE TRUE 196210.0291 190118.8276 245011.673 269107.0297 228211.8823 227254.1576 318369.1898 286841.7191 217623.0044 232731.6604 0.843074074 0.816901436 1.052764684 1.156297468 0.980579444 0.976464299 1.367966822 1.232499775 0.935081217 1 17.82830796 4.161078418 3.899210792 1.116143775 0.826629648 0.386368973 0.127972838 0.20624469 6.005959533 0.034846809 0.086261784 14490.33473 -4.161078418 -0.289514127 TIETSPS(ph)LSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TIETSPSLSR 10 0 F8W7R3;Q9NVI1-2;Q9NVI1-1;Q9NVI1;H3BP78 F8W7R3 FANCI Fanconi anemia group I protein 1 TIET(0.032)S(0.321)PS(0.647)LSR 193.3 6.17E-07 287420000 382600 417460 380600 480110 497110 526740 517580 488030 473520 594190 TRUE FALSE 367647.569 405554.4495 449382.8864 504888.5346 513099.9946 537391.0437 523914.2989 477952.01 419767.9948 553944.9821 0.663689682 0.73212045 0.811241009 0.911441661 0.926265263 0.970116277 0.945787607 0.862814946 0.757779217 1 19.07938317 4.161115391 1.731261726 0.908155862 0.668227852 0.651867603 0.062945913 0.261042384 1.443681436 0.018027452 0.071955865 14491.56839 -4.161115391 -0.23992801 LTLDKLDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTLDKLDVK 9 1 P00558 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 115.18 0.0019963 0 34939000 33190000 19868800 19462300 17966900 13615400 21197400 22315700 25765700 18344200 FALSE TRUE 33573545.25 32243453.7 23459534.14 20466751.64 18544821.66 13890712.72 21456820.12 21854873 22840885.75 17101730.99 1.963166493 1.885391234 1.371763721 1.196764915 1.084382725 0.81224016 1.254657796 1.277933386 1.335589114 1 24.02763902 4.162148859 2.246349467 1.147923681 1.98052346 0.824731192 0.143395315 0.130963253 1.292877697 0.041610576 0.135666491 14526.09429 -4.162148859 0.832599779 KPANDITSQLEINFGDLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPANDITSQLEINFGDLGR 19 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 252.55 1.20E-30 6753900000 2865300 2873100 2861300 3468100 3493200 3325100 3745600 3684000 3780200 4102200 FALSE TRUE 2753320.908 2791162.001 3378400.559 3647089.057 3605561.95 3392335.8 3791439.773 3607924.113 3351087.544 3824354.34 0.719943986 0.729838753 0.883391093 0.953648311 0.942789718 0.887034908 0.991393432 0.943407381 0.87624923 1 21.86678477 4.162522192 2.964542575 0.94021221 0.716867986 0.844647255 0.036722752 0.084584315 1.47509524 0.009130814 0.025351702 14538.58673 -4.162522192 -0.223344224 VLDPFTIKPLDRK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLDPFTIKPLDRK 13 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 137.84 3.15E-05 1072090000 1040770 937740 607240 479280 636200 344790 606130 613370 723010 656720 FALSE TRUE 1000095.558 910996.5733 716981.776 504015.6982 656663.9508 351761.89 613548.0003 600703.6952 640936.9359 612239.7695 1.633503094 1.487973534 1.171080044 0.823232536 1.072560104 0.574549233 1.002136795 0.981157587 1.046872431 1 19.22373724 4.162656853 2.209170609 0.92648 1.616045571 0.769027906 0.13811535 0.139253977 1.326396036 0.036042941 0.118972106 14543.09541 -4.162656853 0.689565571 LMEEIMSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMEEIMSEK 9 0 P17844;P17844-2;J3KTA4;J3QSF1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 130.96 0.00080597 34441000 44541 45893 38952 48822 44011 49627 47040 47593 52447 55586 FALSE TRUE 42800.28848 44584.17657 45991.49288 51341.70927 45426.65378 50630.49194 47615.68959 46610.18792 46493.43644 51821.11071 0.825923796 0.860347761 0.887504962 0.990748916 0.876605174 0.977024445 0.918847337 0.899444016 0.897191044 1 15.66125232 4.163459537 2.691684886 0.929592424 0.837080509 0.457225617 0.040693159 0.242048465 3.480143258 0.01002344 0.029288924 14569.99952 -4.163459537 -0.092511915 RS(ph)PPGAGGSPPGAAVAPSALQLSPAAAAAAAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPPGAGGSPPGAAVAPSALQLSPAAAAAAAHR 33 1 P78415 P78415 IRX3 Iroquois-class homeodomain protein IRX-3 1 RS(0.717)PPGAGGS(0.278)PPGAAVAPS(0.004)ALQLSPAAAAAAAHR 61.725 0.0087694 67687000 34238 32448 28917 33046 32266 37167 33403 34265 36629 38332 TRUE FALSE 32899.94111 31522.61481 34142.94516 34751.50802 33303.86519 37918.54221 33811.79591 33557.41578 32471.02948 35735.7395 0.920645314 0.88210333 0.955428533 0.972458063 0.931948398 1.061081784 0.94616192 0.939043553 0.908642998 1 15.12508002 4.163461348 6.465792188 0.962925215 0.901677326 0.276498942 0.040779507 0.25318265 17.04471652 0.010258879 0.022748403 14570.06028 -4.163461348 -0.061247889 DCMEHAVLPVDGATLAEVMR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCMEHAVLPVDGATLAEVMR 20 0 K7EIG1;A0A494C0R8;O75153 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 219.66 5.91E-26 398620000 512830 505070 488310 559450 553930 627350 610510 576240 679540 702040 FALSE TRUE 492788.0366 490665.8981 576558.4794 588323.2815 571747.6615 640035.4468 617981.604 564340.4426 602401.4681 654490.2055 0.752934165 0.749691736 0.88092759 0.898903111 0.873577109 0.977914477 0.944218262 0.862259569 0.920413267 1 19.32001208 4.163612882 2.757553814 0.917085506 0.744540977 0.733474982 0.0410466 0.13614167 2.055479084 0.010722998 0.030931878 14575.14494 -4.163612882 -0.172544529 EVVESEGER ddPTM_BT-474_Pertuzumab_2h_R1 2 EVVESEGER 9 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 ; 159.58 0.00015341 264720000 163507 160376 150695 218129 171283 171197 179478 192666 186344 191328 FALSE TRUE 157116.9657 155802.2335 177928.9387 229386.6638 176792.4733 174658.7206 181674.5055 188687.3798 165191.0103 178369.1841 0.880852634 0.873481786 0.99753183 1.286021826 0.991160408 0.979197844 1.018530787 1.057847412 0.926118551 1 17.44450686 4.164167687 4.795285585 1.041864924 0.876749017 0.320796969 0.09090394 0.215289009 9.032298937 0.023099982 0.053924513 14593.77637 -4.164167687 -0.165115907 TS(ph)PPCSPANLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.007)S(0.992)PPCS(0.001)PANLSR 162.13 6.66E-05 1461700000 547210 479990 498790 607300 566590 527780 652410 621170 653080 645410 TRUE FALSE 525824.4282 466301.1552 588932.4485 638642.8258 584814.8819 538452.0732 660394.3887 608342.6224 578945.0963 601695.8058 0.873904094 0.774978238 0.978787691 1.061404816 0.971944421 0.894890853 1.097555247 1.011046806 0.962189018 1 19.19867477 4.164632607 6.25625026 1.00233497 0.82528291 0.600085013 0.056464898 0.118486562 7.67512609 0.014041701 0.031263555 14609.40764 -4.164632607 -0.177052059 EAESSPFVER ddPTM_BT-474_Pertuzumab_2h_R1 1 EAESSPFVER 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 154.75 3.24E-05 245750000 136690 137390 116080 148710 120790 150300 132900 142770 153130 144870 FALSE TRUE 131348.0037 133471.7717 137058.2382 156384.9409 124675.32 153339.169 134526.47 139821.7496 135747.3244 135057.8259 0.972531601 0.988256481 1.014811525 1.157910991 0.923125478 1.135359377 0.996065716 1.035273215 1.00510521 1 17.04321771 4.165050144 4.214506547 1.03760222 0.979555145 0.102204876 0.064505771 0.422307565 14.24526984 0.014994987 0.036308383 14623.46007 -4.165050144 -0.058047075 TS(ph)PDTLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.468)S(0.532)PDTLRR 63.426 0.044949 188660000 147570 157080 109170 110400 121210 137680 116630 127010 151530 133850 TRUE FALSE 141802.8013 152600.2322 128899.4475 116097.7572 125108.8297 140463.9839 118057.3528 124387.1991 134328.9497 124784.2203 1.136384079 1.222912896 1.032978747 0.930388129 1.002601366 1.12565502 0.946092002 0.996818338 1.076489875 1 16.92907598 4.165238323 6.10335861 1.008936629 1.178882136 0.574957167 0.057084776 0.123683324 7.752897877 0.014155891 0.031621894 14629.79777 -4.165238323 0.169945507 TEKYEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 TEKYEHK 7 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 0 98.933 0.0065485 166920000 631900 615270 423200 380810 478770 501940 454420 466500 502960 436990 FALSE TRUE 607204.6494 597723.102 499681.654 400463.6497 494170.0719 512089.5707 459981.3279 456866.612 445866.0894 407392.2781 1.490466762 1.467193008 1.226536881 0.982992735 1.213007949 1.256993807 1.129087007 1.121441511 1.094439226 1 18.63605911 4.16531637 3.55212359 1.127880963 1.487017676 0.764326666 0.079664331 0.102282528 2.529237248 0.020208587 0.051994645 14632.42713 -4.16531637 0.359136713 S(ph)RGSDSPAADVEIEYVTEEPEIYEPNFIFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRGSDSPAADVEIEYVTEEPEIYEPNFIFFK 31 1 Q13435;E9PPJ0;H0YCG1 Q13435 SF3B2 Splicing factor 3B subunit 2 1 S(0.333)RGS(0.333)DS(0.333)PAADVEIEYVTEEPEIYEPNFIFFK 147.28 9.39E-09 15157000 32371 32629 21639 18813 24220 30224 21063 23732 25501 24531 TRUE FALSE 31105.90553 31698.45287 25549.64866 19783.94118 24999.0583 30835.14999 21320.77529 23241.92591 22606.23339 22869.49352 1.360148422 1.386058368 1.117193463 0.865079988 1.093118143 1.348309265 0.932280169 1.016285117 0.988488589 1 14.48113679 4.165469686 4.331621221 1.039885304 1.375561891 0.546924319 0.120995584 0.151361732 5.365299544 0.031552449 0.075790068 14637.59363 -4.165469686 0.335676587 TTQVPQFILDDFIQNDR ddPTM_BT-474_Pertuzumab_2h_R1 6 TTQVPQFILDDFIQNDR 17 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 296.22 8.81E-46 498533000 213250 211309 183662 223366 211710 220635 197185 234526 245234 243356 FALSE TRUE 204915.9542 205282.6742 216853.8089 234893.946 218519.8444 225096.3909 199598.209 229682.9561 217396.0644 226873.2814 0.90321766 0.904834069 0.955836702 1.03535306 0.963180164 0.992167916 0.879778385 1.012384335 0.958226827 1 17.79152719 4.165737192 4.189269917 0.975416591 0.903246415 0.348169456 0.039377426 0.2196764 7.347244582 0.009669931 0.023472411 14646.6125 -4.165737192 -0.072170176 RPAPAVS(ph)PGSWKPGPPGS(ph)PRPWK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 RPAPAVS(1)PGSWKPGPPGS(1)PRPWK;RPAPAVS(0.999)PGS(0.001)WKPGPPGS(1)PRPWK 117.88 0.00048335 4039500000 2383580 2278120 1649630 1536050 1620940 1826500 1768600 1933410 2039170 2076820 TRUE FALSE 2290427.058 2213150.248 1947754.837 1615325.725 1673079.007 1863433.081 1790244.656 1893484.408 1807691.97 1936155.132 1.182977036 1.143064526 1.005991103 0.834295609 0.86412446 0.962439967 0.924639057 0.977961103 0.933650378 1 20.88476312 4.16595584 3.123039121 0.928334016 1.172205779 0.791669598 0.047644808 0.104967868 2.029485137 0.012852981 0.034959809 14653.98827 -4.16595584 0.243871764 TVS(ph)PPIR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVSPPIR 7 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 TVS(1)PPIR;TVS(1)PPIR;T(0.001)VS(0.999)PPIR;T(0.005)VS(0.995)PPIR 132.38 0.0035397 7527100000 412784 415670 387459 484949 442891 490624 479246 487151 496600 537851 TRUE FALSE 396651.9449 403815.4986 457481.4603 509977.276 457136.9912 500544.7534 485111.1559 477091.1616 440228.0499 501421.8727 0.791054333 0.805340813 0.912368377 1.017062286 0.911681393 0.998250736 0.96747107 0.951476566 0.877959407 1 18.9356654 4.166318983 3.37395421 0.958565167 0.793599717 0.722420952 0.039689702 0.110072886 2.47153075 0.00964041 0.025356142 14666.24659 -4.166318983 -0.16496545 HEAPS(ph)SPISGQPCGDDQNASPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEAPSSPISGQPCGDDQNASPSK 23 0 O75376;O75376-2;A0A088AWL3;E7EVU5;E7EW50;J3KS51;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 HEAPS(0.463)S(0.463)PIS(0.074)GQPCGDDQNASPSK 93.166 3.26E-05 0 75792 77781 55134 63501 56899 71114 73728 36962 95643 70461 TRUE FALSE 72829.96485 75562.76204 65097.94025 66778.29422 58729.20801 72551.9738 74630.30532 36198.72178 84786.00761 65688.61371 1.108715205 1.150317502 0.991007978 1.016588575 0.894054611 1.104483254 1.136122398 0.551065394 1.290726091 1 16.0033557 4.167235444 4.499672413 0.966425277 1.130118945 0.056283364 0.183188928 0.451763573 17.24003912 0.046896882 0.111569642 14697.22842 -4.167235444 0.163693667 AEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEQGSEEEGEGEEEEEEGGESKADDPYAHLSK 32 1 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK 221.63 3.58E-36 251280000 66260 68674 40989 35770 38254 58291 37501 47495 50640 42592 TRUE FALSE 63670.48595 66715.48476 48396.6241 37616.09399 39484.47465 59469.68396 37959.94846 46514.21165 44891.5595 39707.2059 1.603499529 1.680185831 1.218837312 0.947336715 0.994390659 1.497705079 0.955996464 1.171429986 1.130564553 1 15.27711323 4.167310898 4.488379505 1.111987329 1.6446159 0.657543588 0.153681533 0.111988999 4.256150518 0.037783008 0.089956471 14699.78213 -4.167310898 0.532628571 MKEIAEAYLGYPVTNAVITVPAYFNDSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 MKEIAEAYLGYPVTNAVITVPAYFNDSQR 29 1 A0A0G2JIW1;P0DMV9;P0DMV8 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 192.87 1.75E-18 1075020000 1457470 1584630 944600 1006680 950030 1052490 1075690 1019430 1258620 1139070 FALSE TRUE 1400510.461 1539437.904 1115310.233 1058634.875 980588.5777 1073772.069 1088854.616 998378.4143 1115746.734 1061919.774 1.318847709 1.449674393 1.050277299 0.996906641 0.923411167 1.011161196 1.025364291 0.940163691 1.050688349 1 20.01824335 4.167465886 5.18648665 0.990190085 1.383845055 0.913563874 0.047446237 0.043188754 2.110692424 0.011388919 0.026173117 14705.02904 -4.167465886 0.39365497 LEDLVCDVVDR ddPTM_BT-474_Pertuzumab_2h_R1 8 LEDLVCDVVDR 11 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;;;;; 218.6 2.44E-11 1473447000 903199 943482 876379 1099385 1047359 1034881 1129082 1156839 1232064 1274347 FALSE TRUE 867900.9845 916574.8171 1034760.18 1156124.392 1081048.253 1055807.003 1142900.043 1132949.87 1092205.26 1188034.343 0.730535266 0.771505321 0.870985074 0.973140548 0.909946973 0.888700743 0.962009264 0.953633939 0.919338121 1 20.18014511 4.167542654 2.306795199 0.940351944 0.735646149 0.857283576 0.031312803 0.102294583 1.067664711 0.00816391 0.026355119 14707.6286 -4.167542654 -0.204705795 AGSISTLDS(ph)LDFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGSIS(0.007)T(0.119)LDS(0.874)LDFAR;AGSISTLDS(1)LDFAR 148.18 8.21E-06 49227000 39905 33853 47130 59123 46309 64051 68575 54924 60903 80518 TRUE FALSE 38345.46848 32887.54559 55647.4394 62174.34512 47798.57104 65346.1551 69414.24136 53789.80021 53989.54677 75064.44414 0.510833976 0.438124147 0.741328868 0.828279565 0.636767135 0.870534057 0.92472864 0.71658161 0.719242611 1 16.19584209 4.167569728 4.712901568 0.797740867 0.473670934 0.625306557 0.102760482 0.119552401 4.956232863 0.025108232 0.059007467 14708.54548 -4.167569728 -0.324069932 RT(ph)SEEDTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSEEDTPK 9 1 A0A1B0GW41;Q8WYH8-2;Q8WYH8 A0A1B0GW41 ING5 Inhibitor of growth protein 5 1 RT(0.629)S(0.291)EEDT(0.08)PK 101.72 0.004301 0 321470 299350 286250 315240 330710 378450 332040 323250 421020 365200 TRUE FALSE 308906.597 290812.8311 337981.7426 331509.5742 341347.5875 386102.5183 336103.6048 316574.7745 373227.5747 340464.6787 0.907308794 0.854164468 0.992707214 0.973697405 1.002593246 1.134045739 0.987190818 0.929831475 1.096229941 1 18.37714561 4.167679909 5.459014688 1.009878082 0.881042454 0.465723722 0.057290899 0.172425104 9.206503377 0.015041834 0.034227341 14712.27755 -4.167679909 -0.128835628 EELMS(ph)SDLEETAGSTSIPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EELMSSDLEETAGSTSIPKR 20 1 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.5)S(0.5)DLEETAGSTSIPKR 188.98 1.44E-17 190660000 217000 227760 126440 88766 140450 167160 121160 152340 134420 104230 TRUE FALSE 208519.4001 221264.5078 149290.5206 93347.2239 144967.7018 170540.0897 122642.7923 149194.1258 119161.2051 97170.40926 2.145914602 2.277077039 1.536378428 0.960654839 1.49189144 1.755061968 1.262141358 1.535386409 1.226311652 1 16.56822942 4.168482597 4.68430194 1.365309674 2.214562414 0.692573757 0.232442994 0.104244712 4.295762656 0.057286626 0.134935548 14739.49477 -4.168482597 0.849252739 ERDHS(ph)PTPSVFNS(ph)DEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(1)PTPSVFNS(1)DEER 219.18 2.51E-15 710030000 392260 391310 381780 499950 466800 434590 486600 447640 533770 559340 TRUE FALSE 376930.0455 380150.2219 450776.1387 525752.4794 481815.0459 443377.7076 492555.1564 438396.0776 473178.6673 521455.4036 0.722842343 0.729017706 0.8644577 1.008240543 0.923981308 0.850269658 0.94457772 0.840716338 0.907419243 1 18.99218435 4.168913902 3.864817268 0.913558346 0.722710401 0.69077684 0.052122596 0.119832133 3.488472892 0.013308085 0.033291638 14754.14007 -4.168913902 -0.190847945 LNMGEIETLDDY ddPTM_BT-474_Pertuzumab_2h_R1 2 LNMGEIETLDDY 12 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 ; 197.21 4.60E-07 81876000 210132 208376 183580 217857 218762 224224 213088 227488 234606 234960 FALSE TRUE 201919.8091 202433.3205 216756.9897 229100.6259 225798.6784 228757.9629 215695.8347 222790.2933 207974.5104 219045.9499 0.921814848 0.924159157 0.989550319 1.045902131 1.030827908 1.044337788 0.984705879 1.017093872 0.949456087 1 17.74087401 4.168951307 3.748161018 1.012307889 0.921282012 0.613047106 0.027277501 0.134318696 3.692513425 0.006974707 0.017645157 14755.41088 -4.168951307 -0.091025877 AGMSS(ph)NQSIS(ph)SPVLDAVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.156)S(0.836)NQS(0.204)IS(0.513)S(0.292)PVLDAVPR 90.755 0.0031954 218190000 92451 100100 103210 154470 98785 128030 133590 157510 144740 155090 TRUE FALSE 88837.91271 97245.24601 121862.3429 162442.2152 101962.5092 130618.8543 135224.9144 154257.3635 128309.722 144585.6162 0.614431194 0.672578978 0.842838632 1.123501905 0.705205068 0.903401443 0.935258416 1.066892873 0.887430751 1 17.14156451 4.169240714 3.22449122 0.946053662 0.63194658 0.554983707 0.107053356 0.171026542 3.525062075 0.0275942 0.07425917 14765.24693 -4.169240714 -0.314107082 GPPS(ph)PPAPVMHSPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 1 GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR;GPPS(0.989)PPAPVMHS(0.005)PS(0.005)R;GPPS(0.976)PPAPVMHS(0.01)PS(0.013)R 113.67 0.0015126 819070000 947040 949490 843100 1001080 962900 1082340 1043060 1055620 1030660 1067960 TRUE FALSE 910028.6298 922411.4748 995466.9247 1052745.859 993872.553 1104225.656 1055825.28 1033821.078 913663.7977 995626.118 0.914026474 0.926463718 0.999840107 1.057370673 0.998238731 1.109076627 1.060463623 1.038362754 0.917677611 1 19.92524455 4.169464274 3.006535975 1.032225997 0.915610473 0.428733888 0.047712322 0.215626333 3.872653444 0.012255622 0.034080832 14772.84952 -4.169464274 -0.116615524 KVS(ph)SAEGAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVSSAEGAAK 10 1 P05114;A6NL93;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 KVS(0.808)S(0.192)AEGAAK;KVS(0.901)S(0.099)AEGAAK 116.19 0.00119 107800000 280140 223107 203869 184394 206522 151206 168360 207787 200810 197164 TRUE FALSE 269191.8191 216744.2068 240712.6633 193910.5964 213164.9677 154263.4889 170420.44 203496.1258 178014.8907 183809.9067 1.464512028 1.179175871 1.309573938 1.054951825 1.159703367 0.839255575 0.927155903 1.107100969 0.968472777 1 17.487855 4.169483625 0.73413017 0.98556009 1.493088611 0.692444452 0.098248691 0.888062654 0.60411889 0.042169927 0.329060099 14773.50776 -4.169483625 0.507528521 PGFAFCQPLEHDLLS(ph)PVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 PGFAFCQPLEHDLLSPVEK 19 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 PGFAFCQPLEHDLLS(1)PVEK 107.9 0.00018381 32022000 55470 40169 53005 71098 79431 66891 60306 52917 61002 62993 TRUE FALSE 53302.17107 39023.41945 62584.18259 74767.3763 81985.97025 68243.58185 61044.04287 51824.24546 54077.3087 58726.428 0.907635163 0.664495029 1.065690264 1.273147011 1.396066014 1.16205913 1.039464598 0.882468885 0.920834291 1 15.84172227 4.169632608 7.57940109 1.094991437 0.787285523 0.380853147 0.156397641 0.244000374 22.75888965 0.045154164 0.098925182 14778.57662 -4.169632608 -0.307705915 SRS(ph)PQWR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.036)RS(0.964)PQWR;S(0.138)RS(0.862)PQWR 99.815 0.0062082 1166080000 180099 186772 194055 245630 228560 255250 272410 238420 269140 270970 TRUE FALSE 173060.532 181445.4454 229125.0552 258306.9937 235911.84 260411.3299 275743.8351 233496.5437 238588.3555 252616.9605 0.685070914 0.718263117 0.907005827 1.022524351 0.933871738 1.030854497 1.091549176 0.924310637 0.944466892 1 17.94659198 4.169715556 2.694269086 0.990404523 0.686213369 0.851740456 0.047962677 0.095651777 1.378007425 0.012994147 0.038262923 14781.39954 -4.169715556 -0.304191154 LDDLVRPYVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDDLVRPYVHK 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 151.79 2.00E-05 2322400000 3709700 3739300 3301700 3619400 3747200 3844100 4185400 4143200 4723600 4546000 FALSE TRUE 3564720.823 3632658.825 3898390.636 3806197.668 3867732.091 3921830.336 4236622.177 4057641.472 4187396.731 4238095.371 0.841113876 0.85714419 0.919844953 0.898091556 0.912610914 0.925375668 0.999652393 0.957420992 0.9880374 1 22.01498462 4.169920033 0.290497698 1.008709076 0.750987391 0.865900257 0.019558245 1.950936492 0.175432653 0.024345943 0.175182259 14788.36062 -4.169920033 -0.257721685 AQHEDQVEQYK ddPTM_BT-474_Pertuzumab_2h_R1 4 AQHEDQVEQYK 11 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 191.29 1.90E-06 4540810000 6135200 5676370 5680900 6493800 6363000 6616600 7089300 7055700 7702000 7829300 FALSE TRUE 5895429.601 5514485.485 6707565.001 6828945.796 6567671.674 6750392.185 7176060.974 6909997.329 6827701.249 7299014.537 0.807702132 0.755510961 0.918968577 0.935598328 0.89980252 0.924836106 0.983154772 0.946702777 0.935427819 1 22.79927026 4.170685329 5.234394078 0.942575084 0.781710163 0.826577623 0.029690422 0.068289072 3.472809765 0.007419117 0.017051041 14814.44307 -4.170685329 -0.160864921 MDDPDYWR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDDPDYWR 8 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 103.92 0.010888 232570000 750160 787100 705750 900370 844490 893750 900600 891380 909780 1055800 FALSE TRUE 720842.9179 764652.6787 833294.7243 946838.2036 871653.7878 911822.2374 911621.8122 872972.6915 806505.5885 984289.7256 0.732348311 0.77685732 0.846594964 0.961950713 0.885566277 0.926375856 0.926172232 0.886906232 0.819378246 1 19.90872351 4.170925422 2.477298753 0.90917313 0.742633989 0.655043183 0.046456397 0.168390691 2.040686346 0.011645302 0.036082079 14822.63527 -4.170925422 -0.166539141 TTDEELS(ph)ELEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTDEELSELEDR 12 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 TTDEELS(1)ELEDR;TTDEELS(1)ELEDR 273.5 9.52E-28 545490000 705370 667720 483540 487610 534010 478920 414530 652580 485860 491310 TRUE FALSE 677803.3606 648677.2794 570926.4343 512775.6105 551186.9166 488604.0905 419603.1421 639103.995 430707.2097 458033.1361 1.479812937 1.416223474 1.246474085 1.119516406 1.20337782 1.06674398 0.916097787 1.395322619 0.940340722 1 18.80509245 4.171532741 1.439642624 1.111955363 1.506234181 0.541574558 0.130756939 0.428869232 1.518456722 0.037766397 0.181865658 14843.37778 -4.171532741 0.394278817 SPVPSPGSSS(ph)PQLQVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SPVPSPGS(0.024)S(0.346)S(0.63)PQLQVK;SPVPSPGS(0.009)S(0.243)S(0.748)PQLQVK 233.2 1.26E-19 572620000 578600 577410 510600 587810 611440 602860 642250 633390 657000 622110 TRUE FALSE 555987.6723 560942.8321 602876.7782 618146.9445 631107.5229 615050.2423 650110.0476 620310.2752 582420.1144 579973.9356 0.958642515 0.967186278 1.039489434 1.06581849 1.088165319 1.060479109 1.120929766 1.069548538 1.004217739 1 19.14562854 4.171651268 2.695231284 1.066338738 0.957572245 0.538919785 0.03433295 0.179639427 2.589905592 0.008719818 0.025737576 14847.42936 -4.171651268 -0.108766492 NQSFCPTVNLDKLWTLVSEQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQSFCPTVNLDKLWTLVSEQTR 22 1 P46776;E9PLL6;E9PJD9 P46776 RPL27A 60S ribosomal protein L27a 0 ; 234.51 1.76E-30 637270000 180641 189608 115168 104345 118257 159269 103709 134875 149073 125935 FALSE TRUE 173581.35 184200.5655 135981.4195 109730.258 122060.8438 162489.5283 104978.2218 132089.7841 132150.858 117405.3103 1.478479547 1.56892874 1.158222053 0.934627724 1.039653517 1.384004931 0.894152245 1.12507504 1.125595237 1 16.84113814 4.171669142 4.875516967 1.078748968 1.524768159 0.654917705 0.128916043 0.106804413 4.813905938 0.031484883 0.07358693 14848.04044 -4.171669142 0.446019191 ATLGETHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATLGETHR 8 0 P04062-4;P04062-5;P04062-2;P04062;A0A0G2JNZ5;A0A0G2JNZ0;A0A0G2JLB3;P04062-3 P04062-4 GBA Glucosylceramidase 0 ; 150.4 0.0004898 536880000 388620 457350 407100 491800 402290 417140 494410 421450 473960 515270 FALSE TRUE 373432.3008 444306.8258 480672.0259 517181.8569 415230.0232 425574.8566 500460.7375 412746.9102 420158.0478 480370.3039 0.777384234 0.924925671 1.000628103 1.076631617 0.864395696 0.885930819 1.041822805 0.859226532 0.8746545 1 18.87378744 4.171896985 0.005317785 1.844823727 0.000147025 0.039079276 0.088509742 124567.1046 124.4912569 20907.12604 22289.81897 14855.8322 -4.171896985 -1.844676702 AALAPAKES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 10 AALAPAKESPR 11 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR 128.35 0.00016203 43289670000 32796310 31137650 23627410 24114260 23619870 23717750 27147320 28018530 28289480 30931560 TRUE FALSE 31514593.95 30249634.71 27897408.58 25358799.85 24379624.57 24197339.16 27479557.02 27439937.56 25078176.83 28836537.89 1.092870235 1.049003692 0.967432661 0.879398212 0.845442149 0.839120814 0.95294231 0.951568377 0.869666703 1 24.78139463 4.172651501 2.343125779 0.904481328 1.084886185 0.646360354 0.048827592 0.191018117 2.059246966 0.013585119 0.043732826 14881.66422 -4.172651501 0.180404857 GS(ph)PLNAAPYGIESMSQDTEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSPLNAAPYGIESMSQDTEVR 21 0 P18031;B4DSN5 P18031 PTPN1 Tyrosine-protein phosphatase non-receptor type 1;Tyrosine-protein phosphatase non-receptor type 1 GS(1)PLNAAPYGIESMSQDTEVR;GS(1)PLNAAPYGIESMSQDTEVR 177.87 6.62E-17 137060000 35791.7 41629 37934 64035 39416.6 44676.5 52928 65034 44947 41531 TRUE FALSE 34392.92079 40441.78168 44789.51764 67339.85402 40684.47074 45579.88944 53575.7487 63691.02517 39844.80499 38718.06838 0.888291235 1.04451961 1.156811781 1.739235888 1.050787719 1.177225294 1.383740226 1.644994904 1.029101054 1 15.24071936 4.172968653 3.086270576 1.331840247 0.945950896 0.201336269 0.242520362 0.323244121 6.121970689 0.061951203 0.170855993 14892.53582 -4.172968653 -0.385889351 YVTAFNGELEDYMSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YVTAFNGELEDYMSDR 16 0 F5H8D7 F5H8D7 XRCC1 0 ;; 191.06 1.76E-09 171314000 144751 142993 128288 149983 162963 156951 149435 151382 165998 164935 FALSE TRUE 139093.9709 138914.9796 151472.4954 157723.6406 168204.8529 160124.6568 151263.8302 148255.9088 147154.603 153763.8055 0.904595008 0.903430942 0.985098508 1.025752712 1.093917078 1.041367676 0.983741458 0.964179498 0.957017176 1 17.23035642 4.17329535 3.742896464 1.008264772 0.902012024 0.550753079 0.037471214 0.184477468 5.096398513 0.011180622 0.028428826 14903.74289 -4.17329535 -0.106252748 TEQELPRPQS(ph)PSDLDSLDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 1 TEQELPRPQS(0.976)PS(0.024)DLDSLDGR;TEQELPRPQS(0.862)PS(0.138)DLDSLDGR 189.39 1.34E-17 471640000 332470 338830 325210 392310 401430 404190 449250 462250 438170 481000 TRUE FALSE 319476.7048 329166.9001 383982.6813 412557.1661 414342.3605 412362.9987 454748.0559 452704.376 388430.7786 448421.4416 0.712447433 0.734057004 0.856298664 0.920021051 0.924002115 0.919588049 1.014108635 1.009551136 0.866218121 1 18.77449574 4.173482693 0.869277749 0.970637398 0.647280905 0.813498935 0.043606058 0.451620549 0.456480802 0.016265155 0.119108303 14910.17338 -4.173482693 -0.323356492 ERDHSPTPS(ph)VFNS(ph)DEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(0.134)PT(0.333)PS(0.532)VFNS(1)DEER 160.77 4.05E-09 241810000 103580 118160 110350 144010 159730 146680 138380 149430 148270 188330 TRUE FALSE 99531.97909 114790.1925 130292.6997 151442.3734 164867.8605 149645.9701 140073.5358 146344.2183 131439.0112 175574.2414 0.566893972 0.653798596 0.742094619 0.862554622 0.939020777 0.852323034 0.797802313 0.833517589 0.748623546 1 17.42172168 4.173821845 1.854687589 0.852588067 0.57746542 0.695304575 0.067336384 0.214328659 1.383058179 0.018173627 0.069950568 14921.82165 -4.173821845 -0.275122647 PSTQPRPDSWGEDNWEGLETDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 PSTQPRPDSWGEDNWEGLETDSR 23 1 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PPN3;H0YDH0 E9PS17 SCYL1 N-terminal kinase-like protein 0 ;;; 221.6 1.60E-32 1697380000 879940 831500 759360 824330 953710 846890 947200 1000200 1115680 1125890 FALSE TRUE 845550.972 807786.4341 896593.2439 866873.7701 984386.9483 864014.696 958792.1169 979545.5205 989032.6837 1049632.467 0.805568614 0.769589794 0.854197323 0.825883151 0.937839652 0.82315927 0.913455087 0.933227154 0.942265711 1 20.00145282 4.173869017 0.172145126 1.035505065 0.604788535 0.753447513 0.035155578 6.874526183 0.260369376 0.117729178 0.674285043 14923.4425 -4.173869017 -0.43071653 TSPDTLRR ddPTM_BT-474_Pertuzumab_2h_R1 6 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 168.27 0.00049359 2095880000 3338890 3579100 2391150 2459770 2626440 2680060 2889580 2886330 3026660 2757910 FALSE TRUE 3208402.487 3477027.572 2823283.996 2586719.024 2710921.828 2734252.649 2924943.544 2826726.277 2683086.246 2571114.299 1.247864589 1.352342668 1.09807798 1.006069246 1.05437624 1.063450446 1.137617081 1.099416808 1.043549968 1 21.29396232 4.17423066 6.122090369 1.068144914 1.299408195 0.81081583 0.045893374 0.073158519 5.090467262 0.011626438 0.026055676 14935.87464 -4.17423066 0.231263281 NTTSS(ph)PCK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTTSSPCK 8 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 NTTS(0.153)S(0.846)PCK 84.479 0.019801 0 226730 210690 153780 152720 163100 102420 190600 188410 153580 189910 TRUE FALSE 217869.1409 204681.3275 181571.4668 160601.8975 168346.2596 104491.0026 192932.6198 184519.2677 136146.2423 177047.2265 1.230570765 1.156083218 1.025553861 0.90711332 0.950855107 0.590187176 1.089724045 1.042203661 0.768982632 1 17.43377472 4.175451455 1.849837772 0.915600878 1.228667532 0.418788122 0.135236617 0.397849933 2.550677688 0.038204985 0.147801554 14977.91822 -4.175451455 0.313066654 LQVLQT(ph)PT(ph)VS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 LQVLQTPTVSK 11 0 Q96N23;Q96N23-2 Q96N23 CFAP54 Cilia- and flagella-associated protein 54 3 LQVLQT(1)PT(1)VS(1)K 41.052 0.084846 0 417700 390900 441600 535090 492510 533930 510360 594980 617010 658490 TRUE FALSE 401375.8222 379751.9147 521406.9433 562706.059 508352.0314 544726.4304 516605.9383 582693.4551 546969.6115 613889.8858 0.653823807 0.6185994 0.849349298 0.916623766 0.828083412 0.887335731 0.841528669 0.949182367 0.890989776 1 19.22762038 4.175520502 4.407963243 0.894836966 0.63415333 0.825376126 0.04801406 0.070128579 2.670070535 0.011562585 0.027872757 14980.29971 -4.175520502 -0.260683637 NSGTQS(ph)DGEEKQPGLVMER ddPTM_BT-474_Pertuzumab_2h_R1 2 NSGTQSDGEEKQPGLVMER 19 1 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 NSGT(0.008)QS(0.992)DGEEKQPGLVMER;NSGT(0.002)QS(0.998)DGEEKQPGLVMER 141.48 9.97E-08 709840000 494190 495140 364700 376710 371020 394210 413120 472280 510400 424780 TRUE FALSE 474876.5084 481019.092 430609.4027 396152.0482 382954.1953 402181.1963 418175.8861 462527.253 452461.5318 396009.2722 1.199155024 1.214666236 1.087372021 1.000360537 0.967033406 1.015585302 1.055974987 1.167970766 1.142552873 1 18.59517468 4.175681991 4.522100446 1.058261532 1.208005538 0.508683978 0.060302208 0.186794752 7.475739399 0.017943057 0.042934262 14985.87103 -4.175681991 0.149744006 NS(ph)LESISSIDR ddPTM_BT-474_Pertuzumab_2h_R1 3 NSLESISSIDR 11 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 NS(1)LESISSIDR;NS(0.998)LES(0.002)ISSIDR;NS(0.888)LES(0.112)ISSIDR 197.17 1.35E-06 1662780000 901270 981070 735530 1239670 952740 851110 1236730 1394740 1192810 965610 TRUE FALSE 866047.372 953090.8442 868456.6328 1303649.517 983385.7474 868320.0273 1251865.472 1365938.132 1057407.209 900208.3746 0.962052116 1.058744698 0.964728453 1.448164174 1.09239791 0.964576704 1.390639664 1.517357725 1.174624942 1 19.77989946 4.176196737 0.638149907 1.282847761 0.867894367 0.146144612 0.189374168 2.924632982 1.439351219 0.100003735 0.805606792 15003.64354 -4.176196737 -0.414953394 KYIEIDS(ph)DEEPRGELLSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYIEIDSDEEPRGELLSLR 19 2 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR 128.17 1.15E-05 218030000 159287 188191 99571 91621 128899 139530 97183 103047 106327 117043 TRUE FALSE 153061.8879 182823.9769 117565.6946 96349.57079 133045.1534 142351.3922 98372.35462 100919.0434 94257.20472 109115.5734 1.40275016 1.675507641 1.077441936 0.883004761 1.219304901 1.304592808 0.901542755 0.924882126 0.863829074 1 16.7354975 4.176242024 6.562862138 1.017241782 1.537433694 0.654560726 0.150533839 0.113280914 9.154877937 0.039878699 0.088659006 15005.20815 -4.176242024 0.520191912 ASAFNSWFENAEEDLTDPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASAFNSWFENAEEDLTDPVR 20 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 91.657 0.0041027 28042000 12114 12249 11237 13920 12612 14216 11879 15351 16018 14395 FALSE TRUE 11640.57149 11899.67051 13267.77587 14638.41287 13017.67643 14503.45726 12024.37876 15033.99649 14199.70379 13420.01383 0.867403837 0.886710749 0.988655901 1.090789701 0.970019599 1.080733407 0.896003455 1.12026684 1.058099043 1 13.71209854 4.176356209 3.273239214 1.032903396 0.871466663 0.492472662 0.061568236 0.17955712 3.828537079 0.015032865 0.040521656 15009.15382 -4.176356209 -0.161436733 SQSFT(ph)HSPSGDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 SQS(0.253)FT(0.746)HSPSGDPK 220.97 2.23E-10 405940000 517810 505070 375190 393380 403070 397200 363170 516010 470360 444170 TRUE FALSE 497573.4127 490665.8981 442995.1791 413682.3889 416035.1126 405231.6561 367614.5831 505354.2132 416966.7047 414085.9703 1.201618621 1.184937267 1.069814509 0.999025368 1.004707096 0.978617208 0.887773577 1.220408923 1.006956851 1 18.6595708 4.176688522 3.060389153 1.025529668 1.200168763 0.445597207 0.078359457 0.252315151 4.705253758 0.021718254 0.060412044 15020.64291 -4.176688522 0.174639095 VKAEPAKIEAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKAEPAKIEAFR 12 2 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 136.3 6.32E-05 1474710000 5374000 5385000 2917800 2444000 3417000 3527400 2665100 3097600 3248200 2156280 FALSE TRUE 5163978.139 5231425.072 3445111.366 2570135.133 3526910.908 3598726.445 2697716.291 3033633.478 2879477.954 2010233.235 2.568845271 2.602397066 1.713786891 1.278525839 1.754478459 1.790203436 1.341991687 1.509095275 1.432409883 1 20.93893147 4.177387805 3.915309013 1.487243657 2.60416681 0.808010454 0.218396686 0.080702242 2.454335306 0.053045668 0.13324117 15044.84802 -4.177387805 1.116923153 RVS(ph)GPDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVSGPDPK 8 1 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(1)GPDPK 57.003 0.069843 944200000 1977800 1859900 1871900 2204300 2257000 1998500 2166100 2498900 2504800 2563000 TRUE FALSE 1900505.389 1806857.473 2210193.97 2318064.187 2329598.455 2038911.039 2192609.38 2447296.842 2220465.605 2389405.727 0.795388313 0.756195339 0.924997352 0.970142559 0.974969813 0.853313029 0.917637953 1.024228248 0.929296176 1 21.18822042 4.177741696 4.995552506 0.952219742 0.775313439 0.699447326 0.045682091 0.101421875 4.982524931 0.012093236 0.02823209 15057.11253 -4.177741696 -0.176906303 RNS(ph)LPQIPMLNLEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSLPQIPMLNLEAR 15 1 Q14289;Q14289-2;H0YB74 Q14289 PTK2B Protein-tyrosine kinase 2-beta 1 RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR 116.65 0.00026474 122317000 55706 65156 59152 77770 83906 80119 91936 78867 81025 80583 TRUE FALSE 53528.94793 63297.81467 69842.08223 81783.71902 86604.91269 81739.06107 93061.14027 77238.36889 71827.38168 75125.04163 0.712531358 0.842566118 0.929677784 1.088634592 1.152810179 1.088040143 1.238749933 1.028130796 0.956104384 1 16.19700626 4.177815021 1.573809311 1.09054154 0.720305882 0.715764712 0.077425758 0.241231357 1.057385643 0.022316299 0.100115439 15059.65495 -4.177815021 -0.370235657 QLSESES(ph)SLEMDDER ddPTM_BT-474_Pertuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLSESES(0.949)S(0.051)LEMDDER;QLSESES(0.692)S(0.308)LEMDDER 305.33 9.87E-45 271610000 209095 223810 272050 348470 301230 349140 413730 359470 379380 439960 TRUE FALSE 200923.3362 217427.1579 321215.4867 366454.5785 310919.3365 356199.85 418793.3515 352046.8189 336314.3729 410161.1173 0.489864416 0.530101828 0.783144655 0.89344056 0.758041958 0.868438852 1.021045959 0.858313487 0.819956741 1 18.64583121 4.178016984 2.398573299 0.883574888 0.483745228 0.806212269 0.073279157 0.121450812 1.37451724 0.019492452 0.06228423 15066.65986 -4.178016984 -0.399829661 TYIPPKGETK ddPTM_BT-474_Pertuzumab_2h_R1 2 TYIPPKGETK 10 1 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ; 88.187 0.011278 2460500000 1822480 1706280 1341940 1214380 1441150 1226090 1488870 1703410 1790270 1618490 FALSE TRUE 1751255.467 1657618.565 1584458.409 1277054.297 1487505.899 1250882.38 1507091.236 1668233.988 1587046.055 1508868.231 1.160641752 1.098584046 1.05009727 0.846365687 0.985842149 0.829020291 0.9988223 1.1056194 1.051812228 1 20.52503539 4.178133033 2.935710626 0.980634327 1.139184018 0.372147997 0.080536146 0.306556894 5.259656637 0.023178118 0.065928682 15070.68641 -4.178133033 0.158549691 ILKLPSFELLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILKLPSFELLHK 12 1 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 83.314 0.0077322 83102000 181420 194590 112070 104100 116100 119640 128230 108420 164420 168240 FALSE TRUE 174329.9058 189040.4837 132323.542 109472.6135 119834.4619 122059.2028 129799.3171 106181.0891 145755.7309 156844.9549 1.111479205 1.205269776 0.843658261 0.697967069 0.764031345 0.778215677 0.827564502 0.676981221 0.929298178 1 17.2589796 4.178945814 5.289670478 0.787963049 1.158783438 0.664771938 0.096593344 0.087849671 4.874331166 0.022439743 0.051756584 15098.91755 -4.178945814 0.370820389 TCNSPQNS(ph)TDSVSDIVPDSPFPGALGSDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.067)CNS(0.285)PQNS(0.536)T(0.108)DS(0.005)VSDIVPDSPFPGALGSDTR;T(0.081)CNS(0.336)PQNS(0.565)T(0.018)DSVSDIVPDSPFPGALGSDTR 155.8 4.51E-09 762060000 152079 154111 136085 170828 150564 168219 176387 162001 171294 187486 TRUE FALSE 146135.5845 149715.9052 160678.5867 179644.4536 155407.0278 171620.5034 178545.6769 158655.6227 151849.4232 174787.4062 0.836076166 0.856560026 0.919280114 1.027788314 0.889120281 0.981881402 1.021501953 0.90770626 0.868766386 1 17.41524171 4.179202992 3.422946931 0.953512798 0.84251567 0.41411062 0.051782653 0.22158788 5.176807511 0.013175982 0.034952245 15107.86139 -4.179202992 -0.110997129 S(ph)PDPGIVPQEAPVGNSLSELSEENFDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPDPGIVPQEAPVGNSLSELSEENFDGK 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 S(1)PDPGIVPQEAPVGNSLSELSEENFDGK;S(1)PDPGIVPQEAPVGNSLSELSEENFDGK;S(1)PDPGIVPQEAPVGNSLSELSEENFDGK 226.07 9.09E-35 652760000 695140 674620 619600 695420 779530 761320 740890 756310 767550 731810 TRUE FALSE 667973.1603 655380.4981 731575.5029 731310.7095 804604.2904 776714.412 749957.2334 740691.9342 680420.9418 682243.8569 0.979082704 0.96062499 1.072307937 1.071919816 1.179349997 1.138470364 1.099250988 1.085670361 0.997328059 1 19.37992797 4.179238212 4.377284422 1.090859238 0.968795683 0.405073475 0.052777541 0.174615022 6.662778329 0.013473086 0.032665764 15109.08667 -4.179238212 -0.122063555 KAAS(ph)PSPQSVR ddPTM_BT-474_Pertuzumab_2h_R1 6 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAAS(0.775)PS(0.221)PQS(0.004)VR;KAAS(0.824)PS(0.176)PQSVR;KAAS(0.982)PS(0.018)PQSVR;KAAS(0.851)PS(0.149)PQSVR;KAAS(0.5)PS(0.5)PQSVR;KAAS(0.756)PS(0.244)PQSVR 181.77 6.44E-06 20646350000 3760670 3725940 2827951 2922836 3141333 3114223 3368730 3406630 3746090 3397840 TRUE FALSE 3613698.859 3619679.839 3339024.653 3073683.916 3242376.829 3177194.723 3409957.525 3336281.9 3320849.568 3167701.27 1.140795343 1.142683457 1.054084451 0.970320006 1.023574053 1.002996953 1.076476989 1.053218601 1.048346825 1 21.59500486 4.179781233 4.257347197 1.029708965 1.143190803 0.714869337 0.028906679 0.111676734 4.03964591 0.007881139 0.019287158 15127.99016 -4.179781233 0.113481838 EESHSNDQSPQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EESHSNDQSPQIR 13 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 196.5 1.41E-07 204950000 335620 344780 299910 387810 341670 376120 378910 353530 394520 406390 FALSE TRUE 322503.5994 334947.212 354110.4085 407824.9206 352660.1258 383725.4041 383547.2139 346229.482 349735.7436 378864.8433 0.851236543 0.884081006 0.934661568 1.076439073 0.9308336 1.012829274 1.012358947 0.913860148 0.923114799 1 18.53132375 4.179829798 3.272235626 0.976652634 0.862731486 0.470852539 0.04764424 0.211094202 4.508771731 0.01245935 0.033729028 15129.68194 -4.179829798 -0.113921148 LELLAAYEEVIR ddPTM_BT-474_Pertuzumab_2h_R1 3 LELLAAYEEVIR 12 0 Q16643;Q16643-3;D6R9W4;D6RFI1 Q16643 DBN1 Drebrin 0 ;; 134.75 0.00032552 102904500 127971.1 125528.5 111558.7 124429 129854.4 145527 145112.1 113904 150907 147043 FALSE TRUE 122969.8479 121948.5501 131719.8387 130850.7956 134031.2847 148469.6556 146888.0253 111551.8426 133776.67 137083.6466 0.897042433 0.889592253 0.960872007 0.954532498 0.977733581 1.083058842 1.07152114 0.813750183 0.975876214 1 17.06469695 4.179898766 3.723127797 0.973425354 0.891828469 0.195151307 0.069509067 0.425322312 11.7655617 0.019744486 0.050671859 15132.08477 -4.179898766 -0.081596886 LSPS(ph)PSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 LSPSPSSR 8 0 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LS(0.003)PS(0.994)PS(0.003)SR;LS(0.013)PS(0.859)PS(0.122)S(0.005)R;LSPS(0.928)PS(0.066)S(0.005)R;LS(0.006)PS(0.994)PSSR;LS(0.003)PS(0.641)PS(0.354)S(0.002)R 173.14 0.00029318 6853600000 4145700 4715430 4191620 6430350 4770020 5287810 5702050 5642540 6212800 5982130 TRUE FALSE 3983681.461 4580950.553 4949138.976 6762221.134 4923452.025 5394733.141 5771833.394 5526019.577 5507548.99 5576955.007 0.714311207 0.821407121 0.887426736 1.212529261 0.882820826 0.967325922 1.034943511 0.990866803 0.987554854 1 22.4110462 4.180022407 2.735807549 1.005701386 0.749303719 0.582257245 0.082399217 0.176784695 2.628256786 0.020394504 0.060370386 15136.39341 -4.180022407 -0.256397667 EYATEVDVDFVRK ddPTM_BT-474_Pertuzumab_2h_R1 1 EYATEVDVDFVRK 13 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 89.231 0.012097 420510000 255290 248590 187560 182440 191640 225020 205940 238690 234100 221490 FALSE TRUE 245312.9846 241500.4566 221456.2642 191855.7503 197804.2746 229570.0586 208460.3553 233760.9681 207525.9494 206488.285 1.18802374 1.169560087 1.072488273 0.929136247 0.957944295 1.111782485 1.009550519 1.132078597 1.005025294 1 17.65570041 4.180160149 3.753986655 1.031012071 1.182513937 0.522545193 0.059067632 0.18588341 5.230239761 0.016115131 0.041239513 15141.19487 -4.180160149 0.151501866 AGSNEDPILAPS(ph)GTPPPTIPPDETFGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.552)GT(0.447)PPPT(0.001)IPPDETFGGR;AGSNEDPILAPS(0.497)GT(0.497)PPPT(0.005)IPPDETFGGR 75.954 0.0057609 278608000 557860 598910 509760 624780 652300 678590 628670 648450 706550 731030 TRUE FALSE 536058.2145 581829.6732 601884.9715 657024.9707 673281.8219 692311.5547 636363.8515 635059.2809 626345.4061 681516.687 0.786566528 0.853727699 0.883155149 0.964062925 0.987916855 1.015839477 0.933746545 0.931832328 0.919046324 1 19.37838946 4.180308057 1.564825885 0.961431128 0.79279262 0.781530787 0.031510087 0.234192722 1.011253951 0.009761522 0.04423717 15146.35238 -4.180308057 -0.168638508 EADVDQDGR ddPTM_BT-474_Pertuzumab_2h_R1 8 EADVDQDGR 9 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ;;;;;;; 186.41 9.71E-05 4879771000 3019769 3250043 2911494 3941426 3636823 3528900 3786308 3963753 3729852 3751167 FALSE TRUE 2901753.089 3157354.956 3437665.732 4144843.468 3753804.715 3600256.776 3832645.97 3881900.115 3306454.838 3497097.118 0.82976051 0.902850235 0.983005509 1.18522401 1.07340591 1.029498654 1.095950682 1.110034976 0.945485563 1 21.73772643 4.180508811 2.662595737 1.071223104 0.850829874 0.599682088 0.063634 0.165520001 2.327469077 0.016038824 0.048241873 15153.35548 -4.180508811 -0.22039323 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.598)S(0.402)PEQLAAGAEEGGGPR 198.49 5.79E-27 474973000 65200 66212 69564 82712 81264 101581 84557 82386 101998 92170 TRUE FALSE 62651.91192 64323.69859 82135.76224 86980.77623 83877.93036 103635.0374 85591.83386 80684.70031 90419.61465 85927.2438 0.729127447 0.748583287 0.955875676 1.01226075 0.976150597 1.20607892 0.996096582 0.938988576 1.0522811 1 16.390828 4.180556953 2.689631521 1.02139654 0.723633037 0.738516029 0.067335854 0.140240714 2.013415403 0.018517277 0.055379762 15155.03533 -4.180556953 -0.297763503 QPGTCS(ph)PDLAAPLDENGAVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPGTCSPDLAAPLDENGAVDR 21 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 QPGT(0.002)CS(0.998)PDLAAPLDENGAVDR;QPGT(0.001)CS(0.999)PDLAAPLDENGAVDR 188.19 2.74E-17 675200000 296320 323450 313320 409140 372180 409380 422130 430050 428350 485850 TRUE FALSE 284739.4868 314225.5227 369943.8938 430255.7644 384151.5077 417657.9441 427296.1532 421169.3172 379725.5038 452942.9467 0.628643163 0.693741949 0.816756054 0.949911611 0.848123391 0.922098351 0.94337743 0.929850702 0.838351732 1 18.78896981 4.181615473 1.92047212 0.916561034 0.629869016 0.836417555 0.045567676 0.128146902 0.892846461 0.011693763 0.044320764 15192.01822 -4.181615473 -0.286692018 LLNGNHENGDLDPT(ph)SPLENMDYIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLNGNHENGDLDPTSPLENMDYIK 24 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73;F8WE35;F5H8I0;F5H2W9;F5H2H9;F5GZ10;F5H502;F5H1K9;F5H6X8;F5H221;F5H592 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 LLNGNHENGDLDPT(0.624)S(0.376)PLENMDYIK;LLNGNHENGDLDPT(0.651)S(0.349)PLENMDYIK 204.89 3.81E-24 566371000 361227 337163 380057 436096 432958 440682 494619 468393 547588 549108 TRUE FALSE 347109.8495 327547.4414 448741.7542 458602.9668 446884.4873 449592.892 500672.2953 458720.5209 485428.1059 511916.4261 0.678059605 0.639845539 0.876591825 0.89585515 0.872963758 0.878254475 0.978035222 0.896084786 0.948256554 1 18.96554877 4.181809827 4.512564126 0.915726088 0.656870644 0.862245095 0.041636603 0.061062121 2.507170318 0.010196223 0.024558145 15198.81844 -4.181809827 -0.258855444 AFDQDGDGHITVDELR ddPTM_BT-474_Pertuzumab_2h_R1 4 AFDQDGDGHITVDELR 16 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ;;; 244.88 4.39E-20 9082100000 5996300 6578200 6171600 8795800 7861300 7240900 8726700 8163900 7778300 8381100 FALSE TRUE 5761957.967 6390596.177 7286945.407 9249752.292 8114165.854 7387315.959 8833499.965 7995312.612 6895339.993 7813440.632 0.737441831 0.817897835 0.932616724 1.18382576 1.038488194 0.945462608 1.130551876 1.023276811 0.882497266 1 22.89752655 4.181876334 2.850024547 1.033729699 0.76137647 0.597165359 0.081970193 0.165392841 2.673617586 0.02094226 0.060782881 15201.14612 -4.181876334 -0.27235323 GS(ph)LSNAGDPEIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSLSNAGDPEIVK 13 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 GS(0.999)LS(0.001)NAGDPEIVK 129.29 0.00016297 144710000 188530 195150 207350 233030 218680 241540 261130 291250 318940 373540 TRUE FALSE 181162.0392 189584.5131 244822.7575 245056.7062 225714.0408 246424.1043 264325.7871 285235.5857 282735.2683 348239.8031 0.520222093 0.544407938 0.703029221 0.703701025 0.648156927 0.707627624 0.759033817 0.81907807 0.811898197 1 18.40972158 4.182069189 0.10515486 1.216059254 9.07E-21 0.91618861 0.038272106 11.84547639 0.245981642 0.718516282 2.413848156 15207.89793 -4.182069189 -1.216059254 GPVEGYEENEEFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPVEGYEENEEFLR 14 0 F5GYQ2;Q9UI30;Q9UI30-2;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;; 337.75 2.44E-68 2094890000 749611 778184 733326 885730 855934 1004327 888672 953282 976406 1032394 FALSE TRUE 720315.3734 755990.9542 865854.3209 931442.6314 883465.8944 1024635.18 899547.8338 933596.3936 865568.4843 962469.0348 0.748403686 0.785470417 0.899617847 0.967763739 0.917916174 1.064590281 0.93462522 0.970001486 0.899320864 1 19.8763806 4.182595469 1.890750851 0.965382613 0.743614947 0.767824267 0.043279757 0.162636658 1.093449572 0.011264436 0.043326483 15226.33811 -4.182595469 -0.221767666 GIAPAS(ph)PMLGNASNPNKADIPER ddPTM_BT-474_Pertuzumab_2h_R1 3 GIAPASPMLGNASNPNKADIPER 23 1 H0YIY6;P27448-6;P27448-7;H0YKP9;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 GIAPAS(1)PMLGNASNPNKADIPER;GIAPAS(1)PMLGNASNPNKADIPER;GIAPAS(1)PMLGNASNPNKADIPER 229.56 3.12E-33 2901400000 2422250 2454920 1716800 1744090 1840850 2025230 1875020 2210870 2141080 1899700 TRUE FALSE 2327585.792 2384908.085 2027063.95 1834102.694 1900062.612 2066181.538 1897967.056 2165214.762 1898033.575 1771031.627 1.314254221 1.346620833 1.144566771 1.035612615 1.072856398 1.16665423 1.071673157 1.222572612 1.071710717 1 20.75615855 4.183359784 4.872973082 1.107867637 1.331676511 0.693076994 0.061872062 0.104090834 5.056707451 0.015685883 0.037036244 15253.15854 -4.183359784 0.223808874 DKNESLTMR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKNESLTMR 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 99.973 0.0045369 633290000 651630 647490 468600 495680 521260 516540 526170 559030 612880 572890 FALSE TRUE 626163.5792 629024.2192 553286.444 521262.1042 538026.8013 526984.7927 532609.4259 547485.8351 543308.4318 534087.65 1.172398536 1.177754661 1.035946897 0.975986066 1.007375477 0.986700952 0.997232244 1.025086117 1.017264548 1 19.026717 4.183692586 4.015708394 1.003357839 1.177981645 0.960045658 0.013947916 0.03588856 1.167382605 0.003760264 0.00942586 15264.85157 -4.183692586 0.174623806 AIEQADLLQEEDES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 AIEQADLLQEEDESPR 16 0 A0A2R8YGH5;H7C1E4;P61966 A0A2R8YGH5 AP1S1 AP-1 complex subunit sigma-1A 1 AIEQADLLQEEDES(1)PR;AIEQADLLQEEDES(1)PR;AIEQADLLQEEDES(1)PR 437.81 3.16E-161 765830000 496875 517050 473521 619620 600250 562441 609270 608340 589700 583783 TRUE FALSE 477456.5757 502304.2402 559096.7781 651598.6625 619557.5864 573813.9424 616726.4285 595777.5664 522759.7282 544242.8574 0.877285883 0.922941355 1.027292817 1.197257168 1.138384414 1.054334356 1.133182402 1.094690648 0.960526576 1 19.05389104 4.183768913 3.11385742 1.091935697 0.890721005 0.543505401 0.065694488 0.165790165 3.21033305 0.016624164 0.046267557 15267.53462 -4.183768913 -0.201214691 SMYEEEINETR ddPTM_BT-474_Pertuzumab_2h_R1 4 SMYEEEINETR 11 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;;; 261.03 2.65E-20 1508350000 610939 679200 600886 959070 685358 711285 777950 790420 839480 834400 FALSE TRUE 587062.8285 659829.881 709479.4668 1008567.718 707403.1625 725667.67 787470.7848 774097.5508 744185.7498 777885.3448 0.754690691 0.848235393 0.912061747 1.296550609 0.909392582 0.932872273 1.012322433 0.995130653 0.956677941 1 19.569198 4.184035069 3.24334993 1.010598257 0.789958714 0.3999507 0.103654244 0.231579877 4.871861174 0.026269411 0.07176648 15276.89414 -4.184035069 -0.220639543 CAPSAGS(ph)PAAAVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 CAPSAGSPAAAVGR 14 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPSAGS(1)PAAAVGR;CAPSAGS(1)PAAAVGR 241.07 2.11E-17 3153200000 464810 490460 413930 528680 494530 475740 508080 548320 580550 598410 TRUE FALSE 446644.7113 476472.561 488736.3588 555965.2382 510437.0066 485359.7888 514298.035 536997.0004 514648.3979 557879.1577 0.800611934 0.854078441 0.876061334 0.996569294 0.914959807 0.870008822 0.921880712 0.962568673 0.922508738 1 19.08959313 4.184099124 2.19378075 0.936003393 0.813996094 0.582452935 0.039032077 0.231943809 2.167460393 0.01037186 0.03558142 15279.14752 -4.184099124 -0.122007299 CVPAPGAGASGGTS(ph)PSATQPNPAVFIFEHK ddPTM_BT-474_Pertuzumab_2h_R1 2 CVPAPGAGASGGTSPSATQPNPAVFIFEHK 30 0 O60343-2;O60343-3;O60343 O60343-2 TBC1D4 TBC1 domain family member 4 1 CVPAPGAGAS(0.003)GGT(0.125)S(0.713)PS(0.125)AT(0.033)QPNPAVFIFEHK;CVPAPGAGASGGT(0.017)S(0.886)PS(0.097)AT(0.001)QPNPAVFIFEHK 224.93 5.38E-35 517280000 244901 224456 207832 237729 233144 260910 248096 246284 264850 254990 TRUE FALSE 235329.9982 218054.7346 245391.8656 249998.2222 240643.2885 266185.779 251132.2731 241198.1493 234785.3383 237719.3002 0.989949062 0.917278212 1.032275736 1.051653029 1.012300172 1.119748286 1.056423576 1.014634273 0.987657873 1 17.85889951 4.184568155 9.241219893 1.037754915 0.953760033 0.407142686 0.038794099 0.268004503 43.24011218 0.009747728 0.02120715 15295.65767 -4.184568155 -0.083994882 INETDTFGPGDDDEIQFDDIGDDDEDIDDI ddPTM_BT-474_Pertuzumab_2h_R1 1 INETDTFGPGDDDEIQFDDIGDDDEDIDDI 30 0 P47813;O14602;X6RAC9;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 215.53 1.82E-34 82391000 198810 211240 179270 224380 223920 228150 220460 220950 260360 255370 FALSE TRUE 191040.2854 205215.642 211668.0768 235960.2787 231122.5902 232763.3493 223158.0554 216387.3053 230805.0243 238073.5624 0.802442251 0.86198417 0.889086863 0.9911234 0.970803258 0.977695074 0.937349167 0.908909427 0.96946936 1 17.8610479 4.184722862 1.902661923 0.957039526 0.813418288 0.783495194 0.028377858 0.185597708 1.264882618 0.008367265 0.032134632 15301.10734 -4.184722862 -0.143621238 WRS(ph)LQQLAEER ddPTM_BT-474_Pertuzumab_2h_R1 5 WRSLQQLAEER 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 WRS(1)LQQLAEER;WRS(1)LQQLAEER;WRS(1)LQQLAEER;WRS(1)LQQLAEER;WRS(1)LQQLAEER 244.17 4.44E-16 470521000 916122 864186 511613 493869 543828 441623 481196 626260 515313 461938 TRUE FALSE 880318.9394 839540.2614 604072.8499 519357.6383 561320.7215 450552.9196 487085.0206 613327.5121 456816.8286 430650.5278 2.044160828 1.949469946 1.402698501 1.205983982 1.303425133 1.046214716 1.131044755 1.42418846 1.060759941 1 18.71615807 4.184957194 2.396299844 1.196777781 2.055457575 0.877748878 0.122042353 0.094950685 1.071447087 0.032542764 0.105127412 15309.36559 -4.184957194 0.858679794 NPEFFEHR ddPTM_BT-474_Pertuzumab_2h_R1 6 NPEFFEHR 8 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;;;; 97.565 0.0081413 2176910000 1570230 1576780 1349216 1647810 1627070 1447540 1742740 1569470 1715310 1867040 FALSE TRUE 1508863.676 1531811.778 1593049.344 1732853.672 1679406.184 1476810.251 1764068.173 1537059.896 1520595.2 1740583.718 0.866872222 0.880056364 0.915238565 0.995558935 0.964852289 0.848456891 1.013492287 0.883071512 0.873612217 1 20.73113978 4.184998394 3.69267962 0.934934286 0.871548258 0.188184828 0.053884891 0.372721848 10.22983631 0.013369404 0.034625001 15310.81798 -4.184998394 -0.063386027 ACLISLGYDVENDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ACLISLGYDVENDR 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 241.92 4.30E-17 2017580000 1273236 1346280 1405700 2105090 1594970 1387380 1851720 1861950 1974980 2380820 FALSE TRUE 1223476.529 1307885.413 1659741.26 2213733.947 1646273.659 1415433.774 1874381.903 1823500.082 1750788.55 2219564.941 0.551223579 0.589253051 0.747777742 0.997372911 0.741710066 0.637707754 0.844481668 0.821557436 0.788798074 1 21.08184549 4.185218188 3.664809805 0.818282803 0.562856565 0.499950425 0.103069637 0.180159373 4.869986595 0.02589906 0.06729223 15318.56869 -4.185218188 -0.255426238 WGQPPS(ph)PTPVPRPPDADPNTPSPK ddPTM_BT-474_Pertuzumab_2h_R1 2 WGQPPSPTPVPRPPDADPNTPSPK 24 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.972)PT(0.028)PVPRPPDADPNTPSPK;WGQPPS(0.5)PT(0.5)PVPRPPDADPNTPSPK 206.95 4.88E-25 662630000 472520 426590 427190 523840 470070 456860 530180 600280 636410 610430 TRUE FALSE 454053.396 414424.0709 504392.7358 550875.4452 485190.2285 466098.0222 536668.5014 587884.0082 564167.4048 569085.0324 0.797865644 0.728228731 0.886322267 0.968001992 0.852579493 0.819030541 0.943037456 1.033033685 0.991358712 1 19.11828471 4.185474985 0.275461668 1.034515194 0.614602116 0.591292455 0.06112334 4.657236041 0.374976943 0.089536993 0.65071083 15327.62918 -4.185474985 -0.419913077 S(ph)SPPAPPLPPGSGSPGTPQALPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 S(0.5)S(0.5)PPAPPLPPGS(0.001)GSPGTPQALPR 170.64 7.44E-12 209990000 32349 30575 30097 40651 35102 36436 34670 34383 39109 40450 TRUE FALSE 31084.76532 29703.03094 35536.1974 42749.00298 36231.08771 37172.76088 35094.30183 33672.97903 34669.51028 37710.28547 0.824304694 0.787663911 0.94234761 1.133616531 0.960774687 0.985745942 0.930629439 0.892938852 0.919364832 1 15.20267045 4.185544731 5.693352619 0.967864151 0.805841854 0.527086903 0.062608233 0.149448328 10.29354255 0.017235576 0.039375186 15330.09095 -4.185544731 -0.162022297 GTGNAS(ph)PDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTGNASPDAR 10 0 O14795;O14795-2;A0A1B0GUS7;B1AM27;I6L9J0;F8W8M9;A0A1B0GVW8;A0A0U1RRB5 O14795 UNC13B Protein unc-13 homolog B 1 GT(0.004)GNAS(0.996)PDAR 97.716 0.0061561 63040000 157650 164940 141290 187000 179300 167850 184600 175620 164420 180270 TRUE FALSE 151488.8637 160236.0727 166824.246 196651.0924 185067.3473 171244.042 186859.19 171993.3856 145755.7309 168060.1523 0.901396682 0.953444766 0.992646048 1.170123255 1.10119707 1.018944941 1.111858983 1.023403723 0.867283106 1 17.35861817 4.185582473 3.018594341 1.048456218 0.919642869 0.251886084 0.077454667 0.323297489 5.880231386 0.020241246 0.057321844 15331.42325 -4.185582473 -0.128813349 DPGVLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DPGVLDR 7 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;; 123.69 0.0098156 14319500000 3095530 3276970 2872770 3767860 3515610 3347040 3768210 3690030 3835970 3849000 FALSE TRUE 2974553.265 3183514.024 3391943.443 3962319.706 3628692.788 3414719.442 3814326.481 3613829.591 3400526.767 3588303.802 0.828958034 0.887191888 0.945277666 1.104231951 1.011255732 0.951624955 1.062988724 1.007113609 0.947669694 1 21.77487061 4.185608571 2.63836048 1.013048618 0.845600378 0.645060429 0.045617159 0.160628583 2.216187314 0.011699705 0.035628473 15332.34459 -4.185608571 -0.16744824 KYNRFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYNRFEK 7 2 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ; 65.676 0.039337 2502700000 2103150 1967030 1370380 1325330 1524920 1294430 1454570 1477630 1408220 1401090 FALSE TRUE 2020956.573 1910932.23 1618038.15 1393730.44 1573970.437 1320604.261 1472371.463 1447116.424 1248364.769 1306192.926 1.54721139 1.462978548 1.238743617 1.067017293 1.205006094 1.011033083 1.127223577 1.107888731 0.955727706 1 20.31693657 4.186294732 1.520489643 1.074748862 1.577536366 0.870448927 0.067375588 0.154777518 0.621451729 0.018354602 0.086445378 15356.58796 -4.186294732 0.502787504 ADEVVWVR ddPTM_BT-474_Pertuzumab_2h_R1 5 ADEVVWVR 8 0 P14868;C9J7S3;H7C278;C9JLC1;C9JQM9 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;; 146.54 0.0012834 2651270000 1853332 1709792 1700231 1952903 1935103 1947307 2044724 2119852 2320576 2251146 FALSE TRUE 1780901.736 1661030.406 2007500.563 2053692.558 1997347.345 1986682.882 2069747.944 2076076.315 2057153.941 2098673.876 0.848584316 0.791466661 0.956556703 0.97856679 0.951718782 0.946637257 0.986217043 0.989232457 0.980216109 1 21.00104657 4.186473404 6.205244381 0.974003617 0.820177319 0.900349585 0.020471154 0.046846741 3.916295439 0.005137848 0.011575067 15362.90708 -4.186473404 -0.153826298 SWEDS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 SWEDSPER 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SWEDS(1)PER;SWEDS(1)PER 185.33 0.00022379 2794700000 3125200 2992400 2730300 3486400 3189600 3163600 3525800 2812200 3545800 3725600 TRUE FALSE 3003063.729 2907059.682 3223725.945 3666333.522 3292196.381 3227570.16 3568949.795 2754127.087 3143295.649 3473261.794 0.864623489 0.836982599 0.928155186 1.055588015 0.947868769 0.929261988 1.027549896 0.792951194 0.904998194 1 21.72785973 4.186765434 6.208858407 0.940981717 0.850870599 0.236412852 0.069265344 0.290881693 24.44599495 0.018707336 0.042151092 15373.24096 -4.186765434 -0.090111118 NPDVDTSFLPDRDREEEENR ddPTM_BT-474_Pertuzumab_2h_R1 2 NPDVDTSFLPDRDREEEENR 20 2 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 ; 274.75 9.67E-45 1492860000 555250 553290 522140 608090 624890 651840 611780 654420 669440 711850 FALSE TRUE 533550.2161 537510.7109 616502.3129 639473.5978 644990.1544 665020.6514 619267.1466 640905.9983 593447.9777 663635.7654 0.803980502 0.809948377 0.928976925 0.963591221 0.971903848 1.002086816 0.933143117 0.965749635 0.894237485 1 19.34003211 4.186777223 3.31178663 0.960214493 0.801770812 0.810685216 0.029437049 0.088278015 1.941614748 0.007301024 0.019827611 15373.65827 -4.186777223 -0.158443681 AEGDVAALNRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEGDVAALNRR 11 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 149.33 5.52E-05 253200000 309200 345360 218960 232170 216560 307150 245220 255840 268660 259660 FALSE TRUE 297116.1222 335510.6709 258530.9427 244152.3215 223525.8491 313360.7834 248221.0757 250556.8146 238162.8431 242072.9969 1.227382343 1.385989661 1.067987533 1.008589659 0.923382004 1.294488801 1.025397623 1.035046526 0.983847212 1 17.88508263 4.18683705 7.705072759 1.044908241 1.306110854 0.533967824 0.098801159 0.151672698 19.36897531 0.024211206 0.053245163 15375.77623 -4.18683705 0.261202613 YLGS(ph)PITTVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 YLGSPITTVPK 11 0 P30307-4;P30307-3;P30307-2;P30307;D6RJC2;A0A3B3IT42 P30307-4 CDC25C M-phase inducer phosphatase 3 1 YLGS(1)PITTVPK;YLGS(0.997)PIT(0.003)TVPK 169.89 1.72E-05 318370000 603560 622750 615630 793940 846820 922530 709840 731310 680550 750340 TRUE FALSE 579972.2079 604989.7797 726888.0356 834915.3385 874058.7344 941184.1887 718527.2343 716208.1929 603296.8171 699518.8035 0.82910167 0.864865643 1.039125799 1.193556677 1.24951428 1.345473751 1.027173581 1.023858386 0.862445461 1 19.41600331 4.186968458 3.302136209 1.108250129 0.836840911 0.369270016 0.130345203 0.258428574 5.650847146 0.036529085 0.099355412 15380.42932 -4.186968458 -0.271409218 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK 30 2 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 188.26 2.06E-18 15535530000 11451600 11902040 7270480 8066470 7495330 8138850 7728250 8021670 10759960 7938730 FALSE TRUE 11004058.81 11562605.47 8584417.467 8482781.483 7736424.097 8303423.123 7822830.635 7856019.711 9538534.45 7401032.746 1.486827472 1.562296219 1.159894539 1.146161863 1.045316831 1.121927629 1.056991761 1.061476145 1.288811275 1 22.81929517 4.187198794 4.914628345 1.102949316 1.52692923 0.824460613 0.076695311 0.06409511 3.256348072 0.018496301 0.043745231 15388.58878 -4.187198794 0.423979914 LQQELDDLLVDLDHQR ddPTM_BT-474_Pertuzumab_2h_R1 20 LQQELDDLLVDLDHQR 16 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;;;;;;;;;; 308.29 1.37E-57 30149770900 2083806.2 2255601.8 1961128 2512678.3 2482749.24 2470335.1 2598624.1 2488862.4 2694541.3 2887944.9 FALSE TRUE 2002368.75 2191274.245 2315547.455 2642357.928 2562609.124 2520286.968 2630426.839 2437466.522 2388668.268 2692341.82 0.743727537 0.813891546 0.860049581 0.98143479 0.951814181 0.936094722 0.977003299 0.905333232 0.887208396 1 21.36043016 4.187282693 1.888076653 0.943368608 0.754472979 0.792159676 0.035270093 0.163389884 1.093294324 0.009576055 0.037184188 15391.5619 -4.187282693 -0.188895629 LEELILEDTSLSPEER ddPTM_BT-474_Pertuzumab_2h_R1 1 LEELILEDTSLSPEER 16 0 Q14CX7 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 215.51 2.26E-12 0 25675 27567 25000 34075 28979 31283 30566 33740 34453 35342 FALSE TRUE 24671.59261 26780.81615 29518.05612 35833.61483 29911.13585 31915.56369 30940.07585 33043.25721 30542.03988 32948.25486 0.74879816 0.812814404 0.895891338 1.087572467 0.907821552 0.968657182 0.93905052 1.00288338 0.926969881 1 15.00791443 4.187453912 2.739988029 0.973522601 0.766796631 0.713522859 0.049299613 0.129151645 1.926576784 0.01198164 0.035795744 15397.63115 -4.187453912 -0.206725971 QGSITS(ph)PQANEQSVTPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSIT(0.002)S(0.998)PQANEQSVTPQR;QGSIT(0.002)S(0.998)PQANEQSVTPQR;QGSITS(1)PQANEQSVTPQR;QGSIT(0.015)S(0.985)PQANEQSVTPQR 397.5 4.55E-127 2291770000 1004630 1048980 1119090 1490850 1398920 1358790 1487340 1407250 1482580 1571090 TRUE FALSE 965367.9489 1019064.117 1321334.457 1567792.947 1443917.532 1386265.665 1505542.512 1378189.796 1314283.734 1464678.675 0.659098794 0.69575951 0.902132652 1.07040061 0.985825463 0.946464019 1.027899523 0.940950271 0.897318816 1 20.48215277 4.18771178 3.307965041 0.978777777 0.665902754 0.872579033 0.045820744 0.072515409 1.592249575 0.011829828 0.032180605 15406.77641 -4.18771178 -0.312875024 EIDLLLGQTDDTR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIDLLLGQTDDTR 13 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 220.45 4.84E-11 286421000 284608 305832 263656 351744 333956 319158 321398 341637 361549 377202 FALSE TRUE 273485.2047 297109.9708 311304.5042 369897.55 344697.998 325611.5934 325331.3649 334582.0766 320507.4733 351653.7726 0.777711562 0.844893455 0.885258537 1.051879942 0.980219821 0.925943695 0.925146807 0.951453113 0.911429077 1 18.42379617 4.187826755 2.500192773 0.958189049 0.797129 0.677561811 0.042244272 0.16929885 2.08802204 0.011294727 0.0356517 15410.85573 -4.187826755 -0.16106005 GSLLGDFLTAYHGLEKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSLLGDFLTAYHGLEKPR 18 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 0 ; 212.59 1.06E-16 136786000 330040 310710 296690 340430 351850 353510 356030 355040 388570 384520 FALSE TRUE 317141.6719 301848.855 350308.4828 357999.6331 363167.5748 360658.2144 360387.2016 347708.2999 344461.1626 358476.1179 0.884694004 0.842033374 0.977215679 0.998670805 1.013087223 1.006087146 1.005331133 0.969962245 0.960904075 1 18.45151748 4.187885798 6.041968366 0.992168132 0.86339702 0.884716008 0.018516317 0.053095162 4.275386386 0.004917087 0.011136914 15412.95102 -4.187885798 -0.128771113 EEVGNISILQENDFGDFGMDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEVGNISILQENDFGDFGMDDR 22 0 O60216;E5RFV8;E5RIN7 O60216 RAD21 Double-strand-break repair protein rad21 homolog 0 ; 241.76 1.11E-30 67689000 55240 56433 49804 59088 59719 62128 59614 65169 58500 69211 FALSE TRUE 53081.15973 54823.58609 58804.69068 62137.53876 61639.91587 63384.27073 60343.57396 63823.23738 51859.32525 64523.27732 0.822666826 0.849671442 0.911371727 0.963025149 0.955312849 0.982347354 0.935221775 0.989150583 0.803730489 1 15.9775321 4.188170325 2.260848806 0.949954142 0.825511742 0.417525067 0.051985178 0.27755593 2.765440283 0.013004211 0.043936239 15423.05207 -4.188170325 -0.124442399 SRAS(ph)PVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.278)RAS(0.698)PVS(0.025)R;S(0.262)RAS(0.736)PVS(0.002)R;S(0.037)RAS(0.963)PVSR 70.488 0.031007 5345704000 998236 980165 955664 1134763 1233186 1163489 1359942 842875 1355528 1369031 TRUE FALSE 959223.8335 952211.6539 1128373.743 1193328.254 1272852.548 1187015.545 1376585.377 825469.3367 1201654.144 1276305.311 0.751562988 0.746068864 0.884093903 0.934986515 0.99729472 0.930040434 1.078570594 0.64676479 0.941509946 1 20.28354205 4.18841321 4.123406588 0.913126278 0.746105133 0.30288531 0.107092667 0.282084685 9.838939005 0.028846827 0.072044349 15431.68004 -4.18841321 -0.167021145 IS(ph)MSEVDLNVAAPK ddPTM_BT-474_Pertuzumab_2h_R1 6 ISMSEVDLNVAAPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(0.996)MS(0.004)EVDLNVAAPK;IS(0.999)MS(0.001)EVDLNVAAPK;IS(0.861)MS(0.139)EVDLNVAAPK;IS(0.979)MS(0.021)EVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(0.975)MS(0.025)EVDLNVAAPK 362.97 4.79E-83 828695000 1499826 1323212 1030013 959929 924013 1032004 773835 1064646 1069907 862506 TRUE FALSE 1441211.142 1285475.289 1216159.262 1009471.051 953734.7173 1052871.828 783305.4242 1042660.688 948455.6428 804087.7004 1.792355661 1.598675479 1.512470917 1.255424067 1.18610783 1.309399245 0.974154217 1.296700208 1.179542533 1 19.61699334 4.188710627 0.855832963 1.15575378 1.899857264 0.826191375 0.10223997 0.454261118 0.436804908 0.036014748 0.274034741 15442.25169 -4.188710627 0.744103484 DSIPVTELSASGPFESHDLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSIPVTELSASGPFESHDLLR 21 0 Q9Y244 Q9Y244 POMP Proteasome maturation protein 0 263.52 9.30E-37 91212000 65258 63283 64006 80640 76389 71186 81980 77758 84684 84348 FALSE TRUE 62707.64521 61478.2308 75573.30801 84801.84006 78846.12156 72625.42969 82983.29576 76152.27013 75071.02734 78635.03483 0.797451738 0.781817302 0.961064088 1.078423126 1.002684385 0.923575984 1.055296738 0.968426736 0.954676596 1 16.26288461 4.188731121 4.65380561 0.99664109 0.787637411 0.783359622 0.043047923 0.077586093 3.529083439 0.010738476 0.025824114 15442.98042 -4.188731121 -0.209003679 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR 33 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 296.43 1.05E-89 792360000 149680 162834 133024 178349 165140 175117 166382 181613 159913 183473 FALSE TRUE 143830.3401 158190.1338 157064.3959 187553.6133 170451.8781 178657.9857 168418.2327 177862.6281 141760.3466 171046.2103 0.840885863 0.924838577 0.918257093 1.09650844 0.996525312 1.044501281 0.984635862 1.039851323 0.828783908 1 17.38402661 4.188788865 2.133794959 1.002804406 0.864640091 0.321287682 0.068689481 0.356143284 3.129937092 0.017457366 0.061604054 15445.03388 -4.188788865 -0.138164315 FMFNIADGGFTELHSLWQNEER ddPTM_BT-474_Pertuzumab_2h_R1 2 FMFNIADGGFTELHSLWQNEER 22 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 302.42 6.96E-56 401730000 206124 206139 180359 220160 214925 210120 230450 213688 225335 222020 FALSE TRUE 198068.4462 200260.1176 212953.8834 231522.484 221838.2578 214368.7704 233270.316 209275.2681 199755.9155 206982.3876 0.956933817 0.967522502 1.02885026 1.118561278 1.071773596 1.035686045 1.127005629 1.01107766 0.965086536 1 17.65914849 4.189229741 3.895673245 1.051796376 0.95999627 0.325525559 0.047686492 0.226835324 7.022020484 0.012253254 0.031256529 15460.72092 -4.189229741 -0.091800106 RGERPDYKGEEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 RGERPDYKGEEELR 14 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 181.58 7.10E-07 1979520000 910320 906090 646158 658940 731400 738560 710400 781330 829650 770780 FALSE TRUE 874743.688 880249.2004 762933.1243 692947.9724 754926.1452 753494.1892 719094.0877 765195.2625 735471.6102 718574.3841 1.217332133 1.224993849 1.061731591 0.964337148 1.050588724 1.04859595 1.000723243 1.064879683 1.02351493 1 19.45477798 4.189352628 4.379486458 1.026979395 1.223758817 0.883547034 0.028448353 0.055817906 2.227056506 0.007007702 0.017176967 15465.09627 -4.189352628 0.196779422 S(ph)PSFGDPQLS(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSFGDPQLSPEAR 14 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 2 S(0.999)PS(0.001)FGDPQLS(1)PEAR;S(0.994)PS(0.006)FGDPQLS(1)PEAR 143.57 1.33E-05 242577000 152184 146380 177216 229283 210387 241700 211970 233436 208012 230149 TRUE FALSE 146236.481 142205.3857 209242.8733 241116.3231 217154.2889 246587.3396 214564.1523 228615.465 184399.3498 214560.8032 0.681561957 0.662774298 0.975214812 1.123766874 1.012087416 1.14926555 1.000015609 1.065504331 0.859427011 1 17.71102702 4.190341839 4.403550145 1.037196913 0.667398489 0.777255029 0.07542609 0.07631092 3.095165326 0.018084393 0.044303467 15500.36193 -4.190341839 -0.369798424 GRLT(ph)PSPDIIVLS(ph)DNEASSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PSPDIIVLS(1)DNEASSPR;GRLT(1)PSPDIIVLS(1)DNEASSPR 200.79 1.67E-21 272790000 350580 358670 301438 368220 347500 375370 332740 407650 401960 360320 TRUE FALSE 336878.946 348441.0828 355914.5521 387223.8783 358677.6531 382960.2386 336812.1717 399231.885 356331.186 335915.2055 1.002868999 1.037288807 1.05953689 1.15274293 1.067762481 1.140050323 1.002670216 1.188490067 1.060777185 1 18.35773758 4.190633646 2.547568845 1.097186951 1.012819537 0.158474912 0.058730198 0.400055722 5.130252369 0.01419309 0.044459194 15510.78028 -4.190633646 -0.084367414 EEQNGEDEDGGWR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEQNGEDEDGGWR 13 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9IYH5;C9JH78;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 ; 270.74 1.05E-31 571710000 415200 423070 413990 527200 465720 464580 523570 531190 572250 611630 FALSE TRUE 398973.525 411004.4578 488807.2022 554408.8552 480700.3068 473974.1259 529977.6063 520220.7409 507290.5791 570203.7553 0.699703433 0.72080279 0.857250058 0.972299551 0.843032516 0.831236416 0.929453027 0.912341836 0.889665447 1 19.12111802 4.190709385 3.471013011 0.903899965 0.703603258 0.722065919 0.049042433 0.112560856 2.737921981 0.012184294 0.032584902 15513.48552 -4.190709385 -0.200296707 DSLGDFIEHYAQLGPSS(ph)PEQLAAGAEEGGGPR ddPTM_BT-474_Pertuzumab_2h_R1 5 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.155)S(0.845)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.068)S(0.932)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.085)S(0.915)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.035)S(0.965)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.246)S(0.754)PEQLAAGAEEGGGPR 389.42 2.10E-166 12303870000 929511 885150 963990 1062370 1092830 1291760 1157240 1116560 1415350 1375540 TRUE FALSE 893184.6825 859906.3887 1138204.437 1117199.043 1127981.869 1317880.272 1171402.649 1093502.646 1254685.402 1282373.451 0.696509026 0.670558478 0.88757642 0.871196329 0.879604821 1.027688363 0.913464521 0.852717783 0.978408748 1 20.29038503 4.19084637 4.389093948 0.919424142 0.680699439 0.754054256 0.055530884 0.093597849 3.776972051 0.014294236 0.035075921 15518.37957 -4.19084637 -0.238724704 MILIQDGSQNTNVDKPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MILIQDGSQNTNVDKPLR 18 1 A0A087WTP3;Q92945;M0R0I5;M0QYH3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 181.94 6.47E-14 632400000 234760 227950 211520 268330 257730 234860 249690 257230 253990 289250 FALSE TRUE 225585.3197 221449.0892 249746.3692 282178.5435 266020.1195 239609.0301 252745.7809 251918.1106 225158.12 269658.8399 0.836558222 0.821219469 0.926156804 1.046427937 0.986506208 0.888563602 0.93727979 0.934210467 0.834973999 1 18.0407758 4.191075685 5.322672809 0.94499211 0.828367899 0.411537528 0.055460298 0.17249347 10.83135942 0.014304198 0.033315171 15526.57569 -4.191075685 -0.116624211 AVS(ph)MDNSNKYTK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVSMDNSNKYTK 12 1 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 AVS(1)MDNSNKYTK;AVS(1)MDNSNKYTK 144.29 3.81E-05 708510000 1880630 1762340 751520 552090 681180 671110 455830 718340 818480 660350 TRUE FALSE 1807132.9 1712079.789 887336.3815 580583.4311 703090.7733 684680.304 461408.5839 703506.028 725569.5817 615623.9063 2.93544952 2.781048252 1.44136115 0.94308136 1.142078412 1.112173028 0.749497508 1.142752939 1.178592277 1 19.23168973 4.191218058 3.068945344 1.044130934 2.93898265 0.972165872 0.121514915 0.034111713 0.642991484 0.031759539 0.089866106 15531.66655 -4.191218058 1.894851716 up QVQEFLKDGDDVIIIGVFK ddPTM_BT-474_Pertuzumab_2h_R1 1 QVQEFLKDGDDVIIIGVFK 19 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 167.82 1.57E-11 234950000 866090 864000 556340 511580 617420 697660 590260 588470 763760 648660 FALSE TRUE 832242.2453 839359.5659 656883.0137 537982.7051 637279.875 711767.1632 597483.7784 576317.8889 677061.1667 604725.6804 1.376231029 1.388000532 1.086249576 0.889630989 1.053832995 1.17700833 0.988024484 0.953023673 1.119617024 1 19.20592132 4.191563029 4.433348309 1.022653088 1.386946651 0.768266602 0.077048861 0.085204896 3.527732194 0.020001756 0.048969786 15544.00865 -4.191563029 0.364293564 NETDEDGWTTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 NETDEDGWTTVR 12 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 174.42 0.00031706 0 115710 113490 108520 128240 118800 135770 131640 132880 138800 154560 FALSE TRUE 111187.9253 110253.3763 128131.978 134858.4818 122621.3099 138515.3624 133251.0497 130135.9816 123044.0059 144091.5135 0.771647979 0.765162178 0.889240281 0.935922446 0.850996057 0.961301322 0.924766813 0.903148134 0.853929582 1 17.13662584 4.191645883 4.302224344 0.913214082 0.766273853 0.657361553 0.042572693 0.108176685 4.188567919 0.010039162 0.024817142 15546.97439 -4.191645883 -0.146940229 S(ph)LPSTSSTSSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPSTSSTSSTK 12 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2;A0A590UK73;B1AKN7 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.999)LPS(0.001)T(0.001)SSTSSTK 75.479 0.016428 0 108040 109690 104960 136750 123000 135670 116480 138640 123450 146770 TRUE FALSE 103817.6774 106561.7486 123928.6068 143807.6839 126956.4067 138413.3404 117905.5171 135777.0356 109436.4735 136829.1372 0.758739546 0.778794274 0.905717959 1.051001905 0.927846286 1.011577967 0.861698901 0.992310836 0.799803871 1 17.06201595 4.19188142 3.759652268 0.949578892 0.76366791 0.505521117 0.070307492 0.156004956 4.500714913 0.016636 0.043148378 15555.40847 -4.19188142 -0.185910981 NFVFHTLS(ph)PVKAEAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 NFVFHTLSPVKAEAAK 16 1 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 NFVFHT(0.005)LS(0.995)PVKAEAAK 89.028 0.0035809 275760000 576010 538140 416880 445000 417550 455440 442320 433820 501580 509820 TRUE FALSE 553498.8924 522792.7741 492219.4894 467966.5033 430980.875 464649.3088 447733.2445 424861.4654 444642.7412 475289.4373 1.164551216 1.099946123 1.03562051 0.984592685 0.906775622 0.977613371 0.942022291 0.893900499 0.93551993 1 18.85844681 4.191956033 1.039849926 0.93382043 1.191363858 0.856441434 0.030824882 0.283075551 0.438127242 0.009935207 0.066739001 15558.08115 -4.191956033 0.257543428 LNFSHGTHE ddPTM_BT-474_Pertuzumab_2h_R1 1 LNFSHGTHE 9 0 H3BU13 H3BU13 PKM 0 95.642 0.0079067 187040000 256400 251670 281250 374120 338280 572900 329130 153410 450170 364510 FALSE TRUE 246379.6045 244492.618 332078.1314 393428.378 349161.0834 584484.4305 333157.9914 150242.0299 399068.5889 339821.413 0.72502672 0.719473843 0.977213674 1.157750403 1.027484055 1.719975281 0.980391402 0.44212055 1.174347977 1 18.37441724 4.192007628 4.37565607 1.033811691 0.717716846 0.172623888 0.293374512 0.414992922 16.71494887 0.083826659 0.206190829 15559.92963 -4.192007628 -0.316094845 KSDIYVCMISFAHNVAAQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSDIYVCMISFAHNVAAQGK 20 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 217.42 6.88E-25 653140000 526400 517710 362042 315380 405260 466590 360961 453910 457510 403500 FALSE TRUE 505827.706 502945.4177 427471.043 331656.7996 418295.5559 476024.7695 365378.5487 444536.5999 405575.3828 376170.5856 1.344676393 1.337014208 1.136375515 0.881665958 1.11198369 1.265449208 0.97131079 1.181742052 1.078168784 1 18.52102752 4.192098946 4.404603694 1.082364588 1.344807888 0.519052079 0.102103329 0.151761077 6.206667158 0.025566701 0.062763261 15563.20171 -4.192098946 0.262443299 ALIEHEMK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALIEHEMK 8 0 O95372;Q5QPQ1;Q5QPQ3;Q5QPQ2;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ;; 103.92 0.0046803 1616020000 2632699 2698194 2378395 2954046 2755038 2948969 2973640 2828510 3230790 3196840 FALSE TRUE 2529810.212 2621244.149 2808223.884 3106504.668 2843656.299 3008599.174 3010032.296 2770100.28 2864044.264 2980315.179 0.848839824 0.879519108 0.94225735 1.042340988 0.954146165 1.00949027 1.009971132 0.929465548 0.96098704 1 21.50703348 4.19243589 2.93165856 0.982121666 0.857017131 0.704106404 0.031432181 0.141412468 2.426138084 0.008374921 0.024287874 15575.28099 -4.19243589 -0.125104535 DSYCSYMGHFDLLNYFAIAENESK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSYCSYMGHFDLLNYFAIAENESK 24 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 210.88 3.67E-25 260960000 297820 314270 254690 271800 316620 298810 314330 312000 373010 343750 FALSE TRUE 286180.8651 305307.3273 300718.1485 285827.6306 326804.3698 304852.1429 318176.8646 305557.091 330667.4686 320467.5063 0.893010553 0.952693553 0.938373291 0.891908306 1.01977381 0.951273177 0.992852187 0.953472926 1.031828382 1 18.28981856 4.192612166 0.288557181 1.007216556 0.855407551 0.464215401 0.033632535 5.640797542 0.495493904 0.040416282 0.296893592 15581.60412 -4.192612166 -0.151809005 AGMSSNQSISS(ph)PVLDAVPR ddPTM_BT-474_Pertuzumab_2h_R1 16 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQSIS(0.083)S(0.917)PVLDAVPR;AGMSSNQS(0.004)IS(0.169)S(0.827)PVLDAVPR;AGMSSNQS(0.001)IS(0.054)S(0.946)PVLDAVPR;AGMSSNQS(0.003)IS(0.048)S(0.949)PVLDAVPR;AGMSSNQSIS(0.05)S(0.95)PVLDAVPR;AGMSSNQS(0.002)IS(0.263)S(0.735)PVLDAVPR;AGMSSNQSIS(0.04)S(0.96)PVLDAVPR;AGMSSNQS(0.001)IS(0.108)S(0.892)PVLDAVPR;AGMSS(0.001)NQS(0.042)IS(0.18)S(0.777)PVLDAVPR;AGMS(0.007)S(0.007)NQS(0.013)IS(0.124)S(0.848)PVLDAVPR;AGMSSNQS(0.031)IS(0.158)S(0.81)PVLDAVPR;AGMSSNQS(0.001)IS(0.059)S(0.94)PVLDAVPR;AGMSSNQSIS(0.228)S(0.772)PVLDAVPR;AGMSSNQSIS(0.003)S(0.997)PVLDAVPR;AGMSSNQSIS(0.347)S(0.653)PVLDAVPR;AGMSSNQSIS(0.123)S(0.877)PVLDAVPR 391.06 5.24E-127 46720340000 4541880 4857500 4514820 5991860 5347290 5509720 5902770 5941290 5959370 6374770 TRUE FALSE 4364378.308 4718968.856 5330748.406 6301100.613 5519290.439 5621130.313 5975009.865 5818600.285 5282887.301 5943001.15 0.734372785 0.794038018 0.896979198 1.060255661 0.928704252 0.945840354 1.005385951 0.979067669 0.888925842 1 22.50276023 4.193700974 2.66705347 0.971786214 0.748493147 0.769498558 0.045369766 0.116352837 1.641332315 0.01135376 0.034748895 15620.71734 -4.193700974 -0.223293067 GYFEYIEENKYSR ddPTM_BT-474_Pertuzumab_2h_R1 5 GYFEYIEENKYSR 13 1 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;; 262.64 3.65E-24 12695600000 5771580 5614390 4347750 4395060 4918530 5217580 4794200 5258630 5637830 5002060 FALSE TRUE 5546020.273 5454273.094 5133485.14 4621889.573 5076738.984 5323083.042 4852872.854 5150037.453 4997847.174 4663266.021 1.18929957 1.169625123 1.100834719 0.991127153 1.088665961 1.141492469 1.040659665 1.10438423 1.071748245 1 22.1529093 4.193843098 3.59721854 1.070397347 1.183306614 0.525329007 0.043476331 0.172651154 4.545748367 0.010818232 0.028622315 15625.83012 -4.193843098 0.112909267 QDPGTELLHCENEDLICFK ddPTM_BT-474_Pertuzumab_2h_R1 1 QDPGTELLHCENEDLICFK 19 0 Q9NQE9 Q9NQE9 HINT3 Histidine triad nucleotide-binding protein 3 0 207.56 3.12E-16 188650000 101750 123300 80013 86946 96582 98436 104200 97879 110590 123140 FALSE TRUE 97773.49751 119783.6047 94473.12898 91433.29348 99688.64774 100426.4434 105475.2308 95857.76445 98036.28683 114799.6181 0.851688352 1.043414662 0.822939401 0.79645991 0.8683709 0.874797713 0.918776844 0.835000726 0.853977465 1 16.80875832 4.19386474 0.004216635 1.748400559 8.66E-08 0.042976226 0.073260232 214844.4468 169.1768641 34184.19221 35976.83436 15626.60879 -4.19386474 -1.748400473 NADGFIDLEEYIGDMYSHDGNTDEPEWVK ddPTM_BT-474_Pertuzumab_2h_R1 4 NADGFIDLEEYIGDMYSHDGNTDEPEWVK 29 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;; 338.44 1.83E-105 584048800 115302.7 120860.6 128998.7 182971.4 147305.7 125282.7 172214.8 154841.5 216294 206468.2 FALSE TRUE 110796.543 117413.774 152311.6347 192414.5759 152043.9216 127816.002 174322.4162 151643.9689 191741.2119 192483.9249 0.575614525 0.609992622 0.79129535 0.999639715 0.789904516 0.664034683 0.905646621 0.787826666 0.996141428 1 17.55437844 4.194046213 3.644619312 0.856552655 0.58432887 0.529060333 0.10482135 0.171337362 4.640752181 0.026140328 0.068816656 15633.13987 -4.194046213 -0.272223785 GEVDSNGS(ph)DGGEASR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEVDSNGSDGGEASR 15 0 Q7LBC6 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 GEVDS(0.012)NGS(0.988)DGGEASR 168.29 1.32E-06 46436000 108090 113150 110590 141330 129290 119040 156420 152450 144180 135070 TRUE FALSE 103865.7233 109923.0728 130576.0731 148624.0582 133448.7303 121447.0704 158334.3148 149301.8542 127813.2909 125921.5886 0.824844449 0.872948587 1.036963356 1.180290528 1.059776419 0.964465837 1.257404044 1.185673211 1.015022859 1 16.94216612 4.194277139 2.88305395 1.11040156 0.833616228 0.543484857 0.088274701 0.182855162 3.031429372 0.02361275 0.069252194 15641.45463 -4.194277139 -0.276785332 RALPNNTSSS(ph)PQPK ddPTM_BT-474_Pertuzumab_2h_R1 4 RALPNNTSSSPQPK 14 1 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1;A0A087WT22;J3KP33;A0A087WXZ1;E7ESS1;P04637-5;P04637-9;P04637-8;P04637-6;P04637-2;P04637-3 P04637-7 TP53 Cellular tumor antigen p53 1 RALPNNTS(0.001)S(0.024)S(0.975)PQPK;RALPNNTSS(0.017)S(0.982)PQPK;RALPNNTSS(0.036)S(0.964)PQPK;RALPNNT(0.004)S(0.015)S(0.181)S(0.8)PQPK 222.45 4.12E-12 1227178000 1714500 1641780 1072701 962840 1117789 1289425 1038071 1217245 1337050 1288080 TRUE FALSE 1647495.445 1594958.042 1266561.933 1012532.288 1153743.698 1315498.057 1050775.223 1192108.465 1185273.689 1200837.194 1.371955709 1.328205063 1.054732431 0.843188646 0.96078278 1.095484103 0.875035541 0.99273113 0.987039455 1 20.19560914 4.194389222 3.450051339 0.964857725 1.364016063 0.842290484 0.065762928 0.076430614 1.842467042 0.016400476 0.044179317 15645.4919 -4.194389222 0.399158338 VYSLFLDESR ddPTM_BT-474_Pertuzumab_2h_R1 1 VYSLFLDESR 10 0 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 79.128 0.050655 0 213340 215070 187880 222270 234310 229170 243410 191840 263080 253310 FALSE TRUE 205002.4369 208936.4142 221834.0954 233741.3813 241846.7939 233803.9744 246388.9244 187878.437 233216.2613 236153.0881 0.868091282 0.884749871 0.939365634 0.989787528 1.024110233 0.990052581 1.043344071 0.795578997 0.987563886 1 17.84936288 4.194482872 3.04409953 0.963888213 0.871831649 0.259946439 0.064478481 0.409411551 7.596422094 0.018374657 0.052424863 15648.86599 -4.194482872 -0.092056564 EYIPGQPPLSQSSDSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 7 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQSSDS(0.108)S(0.888)PT(0.004)R;EYIPGQPPLSQSSDS(0.026)S(0.974)PT(0.001)R;EYIPGQPPLSQSSDS(0.04)S(0.948)PT(0.013)R;EYIPGQPPLSQSSDS(0.081)S(0.915)PT(0.004)R;EYIPGQPPLSQSSDS(0.034)S(0.963)PT(0.004)R;EYIPGQPPLSQSSDS(0.134)S(0.863)PT(0.003)R;EYIPGQPPLSQSSDS(0.062)S(0.726)PT(0.212)R 340.46 9.96E-76 32946560000 3208800 3279640 3129550 3836090 3736050 4036340 3819420 3813390 4121910 4258550 TRUE FALSE 3083396.548 3186107.878 3695129.301 4034071.065 3856223.441 4117957.56 3866163.204 3734642.164 3654008.057 3970114.615 0.776651771 0.802522896 0.930736178 1.016109472 0.971312875 1.037238961 0.973816521 0.940688752 0.920378481 1 21.92074923 4.194563944 3.092303322 0.976953072 0.780613808 0.844317978 0.032280368 0.091744116 1.75873398 0.008892308 0.025178962 15651.78754 -4.194563944 -0.196339263 MFNGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MFNGEK 6 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9 P06744 GPI Glucose-6-phosphate isomerase 0 ; 100.74 0.086812 657150000 959390 1079140 776900 898030 943660 856010 997790 1055290 1079000 856570 FALSE TRUE 921895.9781 1048363.984 917303.112 944377.4359 974013.6809 873319.1087 1010001.252 1033497.893 956516.4435 798553.7509 1.154457013 1.312828326 1.148705533 1.18260973 1.219722129 1.093625955 1.264788064 1.294212057 1.197810971 1 19.60702999 4.194574372 24.9993709 1.194436498 1.233645295 0.030973284 0.088484774 503.0704581 285917.3332 0.02174133 0.046967136 15652.16335 -4.194574372 0.039208798 SFIKDYPVVSIEDPFDQDDWGAWQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFIKDYPVVSIEDPFDQDDWGAWQK 25 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 303.8 1.66E-63 1902830000 2028430 2098310 1104090 911410 1219840 1566010 1141730 1023570 1431180 1144810 FALSE TRUE 1949156.713 2038468.253 1303623.623 958447.9793 1259077.261 1597675.795 1155702.833 1002432.922 1268718.446 1067270.999 1.826299707 1.909981865 1.221455117 0.898036188 1.179716551 1.496972931 1.082857901 0.939248722 1.188750043 1 20.02549512 4.195003861 5.008522516 1.113245159 1.873854712 0.776531557 0.159831228 0.080505643 4.524414336 0.042714313 0.101428831 15667.64999 -4.195003861 0.760609553 LDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_BT-474_Pertuzumab_2h_R1 4 LDNTPASPPRSPAEPNDIPIAK 22 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 2 LDNT(0.001)PAS(0.999)PPRS(1)PAEPNDIPIAK;LDNT(0.001)PAS(0.999)PPRS(1)PAEPNDIPIAK;LDNTPAS(1)PPRS(1)PAEPNDIPIAK;LDNT(0.014)PAS(0.986)PPRS(1)PAEPNDIPIAK 229.65 1.50E-26 3572620000 3907950 3740970 3760130 4560800 4142310 4045530 4717560 4877760 5007690 5011450 TRUE FALSE 3755222.994 3634281.198 4439669.135 4796183.435 4275551.163 4127333.388 4775294.91 4777032.551 4439238.025 4672020.028 0.803768599 0.777882196 0.950267573 1.026575958 0.915139733 0.883415175 1.022104974 1.022476899 0.950175299 1 22.15561503 4.19507515 5.212975832 0.975441957 0.789744256 0.714072768 0.045773176 0.093859323 5.817301838 0.012410869 0.029180103 15670.22204 -4.19507515 -0.185697701 MEANKENR ddPTM_BT-474_Pertuzumab_2h_R1 12 MEANKENR 8 1 P16949;P16949-2 P16949 STMN1 Stathmin 0 ;;;;;;;;;;; 161.27 0.00031786 16163540000 19350530 19260690 13835910 14125300 14601480 15228190 16838680 16543200 18418890 16938090 FALSE TRUE 18594289.89 18711393.98 16336366.72 14854308.43 15071149.86 15536114.44 17044756.8 16201577.14 16328054.83 15790858.08 1.177535116 1.184951058 1.034545851 0.940690389 0.954422476 0.98386765 1.079406624 1.026009927 1.034019478 1 23.91258623 4.195401053 4.6044079 1.005830119 1.183404684 0.776243635 0.0377398 0.091466784 4.212063088 0.010772709 0.026198555 15681.9857 -4.195401053 0.177574565 RS(ph)S(ph)VKRSDSGDEQLPT(ph)ICR ddPTM_BT-474_Pertuzumab_2h_R1 4 RSSVKRSDSGDEQLPTICR 19 3 Q01668-3 Q01668-3 3 RS(0.5)S(0.5)VKRS(0.5)DS(0.5)GDEQLPT(1)ICR;RS(0.5)S(0.5)VKRS(0.5)DS(0.5)GDEQLPT(1)ICR;RS(0.5)S(0.5)VKRS(0.5)DS(0.5)GDEQLPT(1)ICR;RS(0.5)S(0.5)VKRS(0.5)DS(0.5)GDEQLPT(1)ICR 72.819 0.014313 8053280000 1376220 1419780 1574610 2369400 1770750 1828210 2029210 1827470 2183040 2545550 TRUE FALSE 1322435.801 1379289.265 1859177.054 2491685.018 1827707.782 1865177.659 2054044.079 1789732.106 1935230.451 2373137.631 0.557252046 0.581209133 0.783425719 1.049953861 0.7701651 0.785954272 0.865539382 0.754162794 0.815473332 1 21.17836434 4.195491476 4.110433799 0.845255272 0.563155374 0.607082077 0.092366796 0.13346727 4.726265707 0.023073019 0.058199128 15685.25112 -4.195491476 -0.282099898 QKLYTLQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKLYTLQDK 9 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 92.866 0.0089251 630900000 1267800 1331800 760220 660950 741720 768030 927340 854610 1152000 996790 FALSE TRUE 1218252.974 1293818.368 897608.665 695061.7087 765578.0974 783560.0928 938689.0643 836962.0049 1021229.79 929276.5255 1.310969277 1.392285646 0.965922027 0.747960042 0.823843147 0.84319368 1.010128889 0.900659795 1.098951455 1 19.82574844 4.195731059 5.597177693 0.909202328 1.353192965 0.75096031 0.098523866 0.077256788 5.740122261 0.025161625 0.058265212 15693.90645 -4.195731059 0.443990637 TCEERPAEDGS(ph)DEEDPDSMEAPTR ddPTM_BT-474_Pertuzumab_2h_R1 5 TCEERPAEDGSDEEDPDSMEAPTR 24 1 Q9H6Y2;D6RGJ8 Q9H6Y2 WDR55 WD repeat-containing protein 55 1 TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR 297.1 3.19E-62 7972040000 2744220 2674510 2384580 2876750 2695530 2918730 2797170 2745580 3101640 3228090 TRUE FALSE 2636972.849 2598235.593 2815526.651 3025219.412 2782234.17 2977748.72 2831402.603 2688882.814 2749554.83 3009448.589 0.876231233 0.863359355 0.935562302 1.005240436 0.924499651 0.989466553 0.940837672 0.893480229 0.913640738 1 21.52106774 4.19580722 5.666729495 0.946182543 0.869534458 0.447265161 0.035678661 0.166799577 12.7877602 0.0094135 0.02174455 15696.65885 -4.19580722 -0.076648085 GS(ph)GSALGGPLDPQFVGPSDTSLGAAPGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSGSALGGPLDPQFVGPSDTSLGAAPGHR 29 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 GS(0.819)GS(0.181)ALGGPLDPQFVGPSDTSLGAAPGHR;GS(0.848)GS(0.152)ALGGPLDPQFVGPSDTSLGAAPGHR 117.54 1.13E-10 374560000 82089 85440 87339 115455 110762 94015 117143 108975 119640 118943 TRUE FALSE 78880.87113 83003.33485 103123.1001 121413.6464 114324.7603 95916.04771 118576.6311 106724.6282 106058.9688 110886.8847 0.711363399 0.748540597 0.929984646 1.094932433 1.031003447 0.864990012 1.069347664 0.962463942 0.956460893 1 16.75872921 4.19621115 3.407300939 0.995034833 0.719582349 0.751104454 0.060683832 0.104217559 2.450893624 0.015278928 0.041475792 15711.26484 -4.19621115 -0.275452484 VKVDGPRS(ph)PS(ph)YGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 VKVDGPRS(1)PS(0.997)Y(0.003)GR;VKVDGPRS(0.999)PS(0.968)Y(0.033)GR 92.211 0.0033129 8643230000 3137440 3130630 1987310 1937600 2254420 2568540 1979860 2343670 2431590 1955650 TRUE FALSE 3014825.376 3041347.498 2346461.124 2037599.768 2326935.467 2620477.639 2004090.119 2295272.395 2155566.097 1823192.084 1.653597228 1.668144309 1.287007083 1.117600162 1.276297483 1.437302006 1.099220503 1.25893065 1.182303344 1 20.79803513 4.196253992 4.417828173 1.215861366 1.667439362 0.724093527 0.112562689 0.093055219 3.902587027 0.027122759 0.066873591 15712.81481 -4.196253992 0.451577996 EYEEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EYEEEER 7 0 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 180.7 0.001588 1291710000 1232650 1245910 1218710 1395650 1454170 1387810 1518240 1609120 1614300 1647050 FALSE TRUE 1184476.675 1210377.867 1438958.007 1467679.664 1500944.699 1415872.469 1536820.675 1575891.11 1431051.432 1535493.836 0.77139787 0.788266184 0.937130435 0.955835594 0.977499657 0.922095834 1.000864112 1.026308978 0.931981228 1 20.55027129 4.196846242 2.544644688 0.97702777 0.766681075 0.863994184 0.030292034 0.09649343 1.233726765 0.008492209 0.026862383 15734.25709 -4.196846242 -0.210346695 NKAS(ph)PQSEFMPSK ddPTM_BT-474_Pertuzumab_2h_R1 2 NKASPQSEFMPSK 13 1 Q9NQW6;Q9NQW6-2;H7C1K5 Q9NQW6 ANLN Actin-binding protein anillin 1 NKAS(0.783)PQS(0.217)EFMPSK;NKAS(0.997)PQS(0.003)EFMPSK 141.53 2.42E-05 673260000 757250 668170 545070 535390 518460 508690 566450 613040 616700 580230 TRUE FALSE 727655.8328 649114.4458 643576.274 563021.5421 535136.7368 518976.0603 573382.3845 600380.5098 546694.8014 540930.5053 1.345192822 1.199996006 1.189757774 1.040838955 0.989289255 0.959413557 1.059992696 1.10990322 1.01065626 1 19.04508373 4.196999276 1.309131442 1.030139658 1.338912708 0.832533227 0.047101278 0.272009717 0.748823176 0.015787193 0.087511373 15739.8024 -4.196999276 0.308773049 LLDSVEQDFHLEIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDSVEQDFHLEIAK 15 0 Q6IBS0;H0Y858;H7C5I2;Q9NR96-4 Q6IBS0 TWF2 Twinfilin-2 0 ; 188.47 2.98E-07 121312000 231850 225880 203996 229450 238030 238230 254940 248270 286520 272740 FALSE TRUE 222789.0457 219438.1236 240862.6151 241291.942 245686.4511 243047.1738 258060.032 243143.1377 253995.4508 254267.0769 0.876200916 0.863022167 0.94728196 0.948970449 0.966253493 0.955873552 1.014917209 0.956250965 0.998931729 1 17.95598514 4.197586905 0.787115761 0.984005384 0.834064761 0.803911826 0.020953063 0.545214818 0.426462863 0.007816494 0.062878076 15761.11381 -4.197586905 -0.149940623 FYHDAK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYHDAK 6 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 126.05 0.01766 252010000 551130 586010 494780 639890 572840 621890 652530 600350 681500 748570 FALSE TRUE 529591.2303 569297.5686 584197.7523 672914.7996 591265.9188 634465.0419 660515.8573 587952.5627 604138.9771 697868.6871 0.758869455 0.81576603 0.837117015 0.964242718 0.847245234 0.90914674 0.946475848 0.842497412 0.865691481 1 19.41259608 4.197979481 2.076050983 0.900236661 0.771166898 0.49361383 0.050353634 0.292318011 2.412729917 0.012890952 0.047186447 15775.36736 -4.197979481 -0.129069763 LSGS(ph)RQDLIPSYSLGSNK ddPTM_BT-474_Pertuzumab_2h_R1 4 LSGSRQDLIPSYSLGSNK 18 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 LS(0.164)GS(0.836)RQDLIPSYSLGSNK;LS(0.195)GS(0.805)RQDLIPSYSLGSNK;LS(0.183)GS(0.817)RQDLIPSYSLGSNK;LS(0.232)GS(0.768)RQDLIPSYSLGSNK 267.24 1.83E-31 3758120000 5962700 5584610 3616230 3682570 3606750 3563170 3303780 4662700 3996090 3573890 TRUE FALSE 5729671.092 5425342.391 4269763.204 3872627.879 3722764.389 3635219.739 3344212.648 4566413.616 3542470.616 3331827.247 1.719678323 1.628338443 1.28150798 1.162313527 1.117334157 1.09105889 1.0037173 1.370543332 1.063221576 1 21.66788217 4.198672452 2.109177851 1.136161075 1.728958861 0.830329746 0.099837617 0.134384051 1.148424898 0.027669962 0.100151136 15800.55901 -4.198672452 0.592797785 TDALTSS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 3 TDALTSSPGR 10 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 TDALTS(0.001)S(0.999)PGR;TDALTS(0.048)S(0.952)PGR;TDALTS(0.004)S(0.996)PGR 130.01 0.00030216 4127160000 2034070 2310430 2544440 3561290 2883280 3157000 3496860 3112990 4265400 4433500 TRUE FALSE 1954576.296 2244538.799 3004276.909 3745088.604 2976023.32 3220836.703 3539655.619 3048705.669 3781209.674 4133215.096 0.472894889 0.543049115 0.72686198 0.906095743 0.720026239 0.779256977 0.856392793 0.737611181 0.914834962 1 21.97883301 4.198868345 2.64050279 0.822357133 0.484663452 0.718254265 0.08307433 0.138382215 1.911370647 0.020180991 0.062591171 15807.68762 -4.198868345 -0.337693681 LQGDANNLHGFEVDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQGDANNLHGFEVDSR 16 0 C9JLU1;P52434;P52434-3;P52434-2;P52434-5 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ;;; 227.22 5.23E-15 6304800000 5724700 6081500 5161190 6773400 6318500 6684800 6673200 6116200 6760000 7121000 FALSE TRUE 5500972.395 5908061.574 6093931.843 7122975.986 6521740.291 6819971.236 6754868.618 5989898.333 5992633.14 6638688.327 0.828623385 0.88994411 0.917942151 1.072949299 0.982383864 1.027307037 1.017500489 0.902271358 0.902683308 1 22.66246679 4.198913332 2.486564942 0.981220974 0.846261173 0.494676724 0.051706733 0.266013706 3.239178189 0.014686977 0.047289211 15809.32516 -4.198913332 -0.1349598 ERS(ph)PS(ph)PSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 ERS(1)PS(0.944)PS(0.056)FR;ERS(1)PS(0.98)PS(0.02)FR 63.662 0.042446 1129020000 521770 555130 501220 633610 619400 624120 621360 656060 665120 717610 TRUE FALSE 501378.6516 539298.2359 591801.6036 666310.688 639323.5635 636740.134 628964.3895 642512.1317 589618.366 669005.6355 0.749438607 0.806119123 0.884598832 0.995971712 0.955632553 0.951770957 0.940148119 0.960398684 0.881335425 1 19.35165884 4.199548676 2.224334397 0.952766315 0.758538692 0.829040021 0.03222457 0.113757987 1.091661892 0.008107667 0.028226535 15832.47007 -4.199548676 -0.194227623 VGHFDPVTR ddPTM_BT-474_Pertuzumab_2h_R1 3 VGHFDPVTR 9 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;; 147.2 9.30E-05 1893390000 581492 598454 525487 694319 644810 651118 681037 556760 689010 710079 FALSE TRUE 558766.6498 581386.6779 620454.1903 730152.8868 665550.8993 664284.0521 689371.7345 545262.7114 610796.4734 661984.7169 0.84407787 0.878247886 0.937263617 1.102975444 1.005387107 1.003473396 1.041371072 0.823678701 0.922674584 1 19.33643838 4.199705515 3.492561142 0.976556129 0.855932819 0.325519594 0.070198565 0.309779977 7.706831276 0.020253746 0.054656979 15838.18876 -4.199705515 -0.120623311 DGLLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGLLLR 6 0 O14746-3;O14746 REV__O43296 TERT Telomerase reverse transcriptase 0 ;; 122.51 0.044642 2296680000 1658370 1662390 1473780 1638720 1785160 1809800 1732740 1838320 1841410 1924610 FALSE TRUE 1593559.067 1614980.265 1740124.83 1723294.536 1842581.293 1846395.396 1753945.79 1800358.05 1632380.857 1794254.45 0.888145528 0.900084302 0.969831692 0.960451588 1.026934219 1.029059951 0.977534591 1.003401747 0.909782253 1 20.77495307 4.199722841 1.742905044 0.991135396 0.881600458 0.554508341 0.032689353 0.294368727 1.628843766 0.008946775 0.038123843 15838.82066 -4.199722841 -0.109534938 KTAPTLS(ph)PEHWK ddPTM_BT-474_Pertuzumab_2h_R1 3 KTAPTLSPEHWK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KTAPT(0.03)LS(0.97)PEHWK;KTAPT(0.013)LS(0.987)PEHWK;KTAPT(0.002)LS(0.998)PEHWK 160.81 3.15E-05 1558510000 2310720 2321060 1722860 1890560 1917230 1919380 2088890 2065930 2167450 2169040 TRUE FALSE 2220414.508 2254865.641 2034219.127 1988132.028 1978899.444 1958191.179 2114454.461 2023267.824 1921410.163 2022128.989 1.098057799 1.11509486 1.005978915 0.983187541 0.978621767 0.968380944 1.045657558 1.000563186 0.950191691 1 20.9474436 4.200146179 5.418067037 0.992581438 1.107213689 0.784444757 0.024160064 0.074236332 5.320045112 0.006254753 0.014668687 15854.26739 -4.200146179 0.114632251 PNSSPS(ph)PSPGQASETPHPRPS ddPTM_BT-474_Pertuzumab_2h_R1 1 PNSSPSPSPGQASETPHPRPS 21 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 PNS(0.077)S(0.218)PS(0.699)PS(0.007)PGQASETPHPRPS 145.77 6.97E-08 419900000 49520 49064 50659 53455 63848 59719 58662 64716 73848 68789 TRUE FALSE 47584.70365 47664.74276 59814.2082 56213.81896 65901.72891 60926.5591 59379.9231 63379.59198 65465.08464 64129.85976 0.742005422 0.743253501 0.932704491 0.876562325 1.027629394 0.950049779 0.925932527 0.988300804 1.020820642 1 15.96870863 4.200344508 1.187741643 0.977175401 0.695723782 0.803919928 0.043995824 0.281572058 0.605115534 0.012866727 0.078544422 15861.50922 -4.200344508 -0.281451619 VEELEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VEELEHR 7 0 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 0 ;;; 162.31 0.0014236 1374160000 1925200 1972010 1722690 2102840 2053540 2111310 2145080 2075730 2270160 2255030 FALSE TRUE 1849961.056 1915770.206 2034018.404 2211367.824 2119593.979 2154002.135 2171332.131 2032865.45 2012460.954 2102294.81 0.879972232 0.911275715 0.967522916 1.051882835 1.008228708 1.024595659 1.032839029 0.966974489 0.957268669 1 21.00353357 4.200359583 2.742124048 1.005046803 0.887497962 0.720174816 0.027341591 0.145444582 2.173553999 0.007622708 0.023174818 15862.05981 -4.200359583 -0.117548841 DAEDAMDAMDGAVLDGR ddPTM_BT-474_Pertuzumab_2h_R1 10 DAEDAMDAMDGAVLDGR 17 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;;;;;; 405.5 6.48E-140 7900901000 3192353 2996807 2607698 2794848 3074250 2991035 2953034 3097133 3415627 3346444 FALSE TRUE 3067592.315 2911340.999 3078967.037 2939090.44 3173136.043 3051515.777 2989174.113 3033176.121 3027899.342 3119786.367 0.983269992 0.933186012 0.986915985 0.942080673 1.017100426 0.978116902 0.958134232 0.972238405 0.970547014 1 21.57301581 4.200877824 24.99910575 0.976016539 0.958227709 0.103980767 0.022707087 335.9090352 222844.944 0.005355023 0.011568636 15880.99921 -4.200877824 -0.01778883 SYS(ph)LSELSVLQAK ddPTM_BT-474_Pertuzumab_2h_R1 5 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 SYS(0.859)LS(0.141)ELSVLQAK;SYS(0.999)LS(0.001)ELSVLQAK;SYS(0.997)LS(0.003)ELSVLQAK;SYS(0.878)LS(0.122)ELSVLQAK;SYS(0.87)LS(0.13)ELSVLQAK 385.97 5.60E-108 1989765000 2677830 2474610 2040520 2218380 1935990 1980830 2071870 3019830 2270110 2152420 TRUE FALSE 2573177.443 2404036.546 2409287.355 2332870.858 1998262.877 2020883.74 2097226.165 2957469.455 2012416.63 2006634.676 1.282334784 1.198043956 1.20066068 1.162578762 0.99582794 1.007100975 1.04514598 1.473845484 1.002881418 1 20.93634656 4.201091067 1.534220248 1.128984751 1.267110938 0.135906024 0.139440378 1.36300612 5.549666381 0.044038275 0.211797327 15888.79887 -4.201091067 0.138126187 SGILPILVHCLER ddPTM_BT-474_Pertuzumab_2h_R1 2 SGILPILVHCLER 13 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ; 140.08 3.92E-05 441840000 706100 753290 503950 569800 581150 576360 580200 563680 658010 643350 FALSE TRUE 678504.8314 731806.9067 595024.9753 599207.4463 599843.2175 588014.3941 587300.6612 552039.811 583315.4634 599775.3315 1.131264985 1.220135055 0.992079774 0.99905317 1.000113186 0.980391095 0.979201095 0.920410997 0.97255661 1 19.19406266 4.201407561 8.01665741 0.975652543 1.175559586 0.870702104 0.030051888 0.06371446 11.95060232 0.007986055 0.017673377 15900.38209 -4.201407561 0.199907043 INFDKYHPGYFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 INFDKYHPGYFGK 13 1 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 95.631 0.0027684 1180200000 1378000 1533400 817580 700800 891770 1148100 961200 853240 1001300 954960 FALSE TRUE 1324146.237 1489668.933 965334.893 736968.372 920454.5919 1171315.369 972963.4531 835620.2958 887636.6218 890279.7086 1.487337321 1.673259448 1.084305172 0.827794192 1.033893711 1.315671196 1.092873895 0.938604225 0.997031173 1 19.76389915 4.201825063 7.215565365 1.032994459 1.580292046 0.751972396 0.125029303 0.083826876 12.76556549 0.033092938 0.074066791 15915.67504 -4.201825063 0.547297587 GLDYLHSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDYLHSEK 9 0 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;Q9P289-2;Q8NBY1;B4E0Y9;Q9P289-3;Q9P289 B4DR80;Q8NBY1 STK24;STK26 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit;Serine/threonine-protein kinase 26 0 ; 104.17 0.0033041 371240000 669580 759720 701990 960830 903460 802970 968380 929250 1080350 1125610 FALSE TRUE 643412.0733 738053.5294 828855.2087 1010418.551 932520.6114 819206.6036 980231.3241 910060.6628 957713.1972 1049371.432 0.613140451 0.703329161 0.789858751 0.962879797 0.888646844 0.780664099 0.934112836 0.867243604 0.912654155 1 20.00109399 4.201981531 2.053437231 0.895145539 0.626823277 0.744355218 0.058495578 0.166606346 1.340550366 0.015033743 0.055894466 15921.41018 -4.201981531 -0.268322262 RIDT(ph)PSLEEPSDLEELEQFAK ddPTM_BT-474_Pertuzumab_2h_R1 3 RIDTPSLEEPSDLEELEQFAK 21 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 RIDT(0.983)PS(0.017)LEEPSDLEELEQFAK;RIDT(0.996)PS(0.004)LEEPSDLEELEQFAK;RIDT(0.956)PS(0.044)LEEPSDLEELEQFAK 277.1 4.62E-45 292723000 539110 470090 322801 254152 293328 327120 239991 386150 352860 302310 TRUE FALSE 518040.9852 456683.4935 381138.3214 267268.8152 302763.1615 333734.5905 242928.0816 378175.8676 312804.8121 281834.2744 1.838104986 1.620397286 1.352349079 0.948319063 1.074259552 1.184151896 0.86195365 1.341837746 1.109889181 1 18.10448755 4.202251617 2.123479451 1.095307298 1.806403252 0.803587476 0.129821069 0.139172588 1.206009481 0.034510257 0.125006229 15931.31471 -4.202251617 0.711095954 CDSLLHFTENLFPS(ph)PNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 CDSLLHFTENLFPSPNKK 18 1 E5RFP7;E5RIE3;E5RFE4;Q56NI9 E5RFP7 ESCO2 N-acetyltransferase ESCO2 1 CDSLLHFTENLFPS(1)PNKK 148.89 3.11E-08 225170000 639150 601570 412440 404660 409570 401610 505480 465390 465010 499170 TRUE FALSE 614171.3114 584413.8126 486977.0827 425544.5511 422744.191 409730.8294 511666.2154 455779.5339 412224.0143 465360.7713 1.319774569 1.25582956 1.046450652 0.914440102 0.908422491 0.880458463 1.0995044 0.979411162 0.885815994 1 18.82799007 4.202363343 2.655815721 0.957634433 1.311578766 0.821233691 0.061967809 0.110966618 1.55103477 0.01701117 0.052843189 15935.41372 -4.202363343 0.353944333 NDRGPGGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDRGPGGPR 9 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 144.65 9.03E-05 168391000 237950 255360 165099 179693 178222 210659 176577 191240 225840 193126 FALSE TRUE 228650.6509 248077.3828 194936.0619 188966.9773 183954.6725 214918.6693 178738.0021 187290.8272 200203.59 180045.404 1.269961053 1.377860125 1.082705015 1.049551797 1.021712681 1.193691505 0.992738488 1.0402422 1.11196168 1 17.45800125 4.202556767 7.874232875 1.060566302 1.323776796 0.748865902 0.060778001 0.084361954 15.72906287 0.014489617 0.032155108 15942.51255 -4.202556767 0.263210494 EELSGS(ph)LLQSVQEALEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EELSGSLLQSVQEALEER 18 0 Q12851;Q12851-2 Q12851 MAP4K2 Mitogen-activated protein kinase kinase kinase kinase 2 1 EELS(0.001)GS(0.999)LLQSVQEALEER;EELS(0.001)GS(0.999)LLQSVQEALEER 150.59 5.65E-08 26431000 17185 21536 13470.4 14555.5 15608.2 15516.8 13620 19126 18759.7 15362.3 TRUE FALSE 16513.3912 20921.81437 15904.80093 15306.7111 16110.25193 15830.56033 13786.68563 18731.04142 16630.1775 14321.79774 1.153025025 1.460837162 1.110531039 1.068770233 1.124876375 1.105347291 0.962636527 1.307869428 1.16117947 1 13.80592498 4.202641505 24.98682752 1.117875012 1.306931201 0.336293224 0.112255077 170.6946223 118742.2306 0.027512227 0.059436406 15945.62348 -4.202641505 0.189056189 VIPSQEHLNGPLPVPFTNGEIQKENS(ph)REALAEAALESPRPALVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVR 44 3 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 VIPSQEHLNGPLPVPFT(0.196)NGEIQKENS(0.773)REALAEAALES(0.031)PRPALVR 116.53 5.86E-07 559550000 59112 69502 37976 42813 42718 55995 32916 42556 44439 47310 TRUE FALSE 56801.83769 67519.87101 44839.10797 45022.58406 44092.06327 57127.25727 33318.83585 41677.20373 39394.47102 44105.65156 1.287858487 1.530866649 1.016629534 1.020789456 0.999691915 1.29523667 0.755432347 0.944940212 0.893184198 1 15.42867591 4.202677502 9.506916148 0.985907827 1.409066338 0.59451713 0.138249588 0.193271829 49.15167917 0.034565866 0.075678058 15946.94522 -4.202677502 0.423158511 S(ph)QLDLFDDVGTFASGPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQLDLFDDVGTFASGPPK 18 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3;H0YDN9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 S(1)QLDLFDDVGTFASGPPK 130.36 2.02E-05 14965000 35928 35188 24539 29873 28459 25168 22165 33797 30657 27217 TRUE FALSE 34523.89404 34184.47269 28973.74317 31414.74911 29374.40958 25676.9142 22436.2619 33099.08014 27176.94588 25373.56835 1.360624315 1.347247349 1.141886816 1.238089522 1.157677516 1.011955191 0.88423755 1.304470845 1.071073075 1 14.6310388 4.202880174 0.803791674 1.084192829 1.437687107 0.477202694 0.110463209 1.320961041 1.080933862 0.045241749 0.364614146 15954.3889 -4.202880174 0.353494278 SVAVS(ph)DEEEVEEEAERR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVAVSDEEEVEEEAERR 17 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 SVAVS(1)DEEEVEEEAERR 234.04 2.45E-20 256250000 65427 67533 58684 75615 68301 74664 64088 75946 80070 73613 TRUE FALSE 62870.04051 65607.02496 69289.50422 79517.49921 70497.96369 76173.75724 64872.32811 74377.68856 70980.78928 68627.12594 0.916110643 0.955992606 1.009651843 1.158689048 1.027260908 1.10996572 0.945286973 1.083794309 1.0342964 1 16.06649132 4.202904663 3.121139716 1.053135135 0.928783164 0.396810175 0.05625556 0.22130407 4.338288149 0.013638612 0.038875596 15955.28854 -4.202904663 -0.12435197 SS(ph)SPELVTHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.117)S(0.455)S(0.429)PELVTHLK 213.99 4.15E-10 1518800000 1228800 1344000 1147100 1475100 1480100 1470400 1559900 1418000 1617800 1598500 TRUE FALSE 1180777.137 1305670.436 1354406.487 1551230.088 1527708.761 1500132.495 1578990.523 1388717.804 1434154.126 1490232.171 0.792344415 0.876152361 0.908856025 1.040931821 1.025148155 1.006643478 1.059560083 0.931880167 0.962369592 1 20.50710568 4.203031118 1.794842555 1.000627393 0.80477113 0.764601191 0.038519504 0.200363218 1.185950261 0.011252928 0.046996478 15959.93498 -4.203031118 -0.195856263 DSYLILETLPTEYDSR ddPTM_BT-474_Pertuzumab_2h_R1 6 DSYLILETLPTEYDSR 16 0 P17980;E9PM69;E9PKD5;E9PLG2;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;;;; 211.26 1.76E-11 616903000 676474 668750 608866 712119 700694 703453 714595 755609 808040 816458 FALSE TRUE 650036.6482 649677.9048 718901.6304 748871.5469 723232.4589 717677.3016 723340.4274 740005.4101 716314.6868 761158.5724 0.854009495 0.853538183 0.944483392 0.983857469 0.950173177 0.942874885 0.950315024 0.972209257 0.9410847 1 19.53783752 4.203238888 4.403026175 0.960556997 0.851918474 0.853062343 0.017842017 0.060239898 2.580114344 0.004234677 0.010553374 15967.57217 -4.203238888 -0.108638523 KLDPAQSAS(ph)RENLLEEQGSIALR ddPTM_BT-474_Pertuzumab_2h_R1 3 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.026)AS(0.974)RENLLEEQGSIALR;KLDPAQS(0.024)AS(0.976)RENLLEEQGSIALR;KLDPAQS(0.211)AS(0.789)RENLLEEQGSIALR 163.16 1.24E-11 7493260000 1400220 1472760 897560 937900 1136050 1039080 829970 1149900 1064840 1015130 TRUE FALSE 1345497.854 1430758.327 1059769.058 986305.1314 1172592.08 1060090.91 840127.4211 1126154.163 943963.8274 946374.3409 1.421739576 1.511831275 1.119820152 1.042193442 1.239036214 1.120160241 0.887732671 1.189966924 0.997452896 1 19.85205143 4.203321769 6.371987386 1.081773453 1.467532605 0.719398773 0.097987495 0.079628081 9.166655066 0.023747852 0.054193263 15970.61974 -4.203321769 0.385759152 LS(ph)YASAESLETMSEAELPLGFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSYASAESLETMSEAELPLGFSR 23 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LS(0.476)Y(0.281)AS(0.217)AES(0.026)LETMSEAELPLGFSR 183.54 2.33E-17 62745000 30148 33726 28122 35912 38498 36753 34313 41399 35650 38016 TRUE FALSE 28969.78283 32764.1675 33204.27097 37765.42262 39736.32313 37496.17084 34732.93276 40544.09618 31603.16146 35441.14246 0.817405445 0.924467024 0.936884893 1.065581412 1.121191936 1.057984259 0.9800173 1.143983895 0.891708316 1 15.11313749 4.203566486 1.571259765 1.048864176 0.831051515 0.477703131 0.071495739 0.368724859 1.589066372 0.019343166 0.091407145 15979.62142 -4.203566486 -0.217812662 TSS(ph)FTEQLDEGTPNR ddPTM_BT-474_Pertuzumab_2h_R1 7 TSSFTEQLDEGTPNR 15 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71;C9JHJ5;C9J0Y3 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 TSS(0.794)FT(0.206)EQLDEGTPNR;TSS(0.814)FT(0.186)EQLDEGTPNR;TSS(0.967)FT(0.033)EQLDEGTPNR;TSS(0.5)FT(0.5)EQLDEGTPNR;T(0.001)S(0.023)S(0.876)FT(0.1)EQLDEGTPNR;TSS(0.861)FT(0.139)EQLDEGTPNR;TS(0.006)S(0.981)FT(0.012)EQLDEGTPNR 369.39 1.67E-97 5726680000 4216640 4103060 3575190 4110950 4233310 4007030 3973640 4648570 4591110 4353100 TRUE FALSE 4051849.047 3986044.746 4221306.363 4323116.622 4369478.261 4088054.892 4022270.595 4552575.405 4069946.44 4058260.66 0.998420108 0.982205206 1.040176252 1.065263418 1.076687435 1.007341626 0.991131653 1.121804583 1.002879505 1 21.9524301 4.203881611 7.025160424 1.045366918 0.990279031 0.17233898 0.039526179 0.24102204 36.00833345 0.00995317 0.022406513 15991.22048 -4.203881611 -0.055087887 GGS(ph)LPKVEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGSLPKVEAK 10 1 P06748;P06748-2 P06748 NPM1 Nucleophosmin 1 GGS(1)LPKVEAK;GGS(1)LPKVEAK 105 0.0015788 579110000 1434040 1253800 899070 655060 899760 992420 813150 926690 1087030 849230 TRUE FALSE 1377996.131 1218042.852 1061551.949 688867.7251 928701.5975 1012487.412 823101.5729 907553.5277 963634.9116 791710.8957 1.740529452 1.538494491 1.340832815 0.870100094 1.17303122 1.278860021 1.039649167 1.146319361 1.217155046 1 19.59461418 4.203944071 2.387441025 1.117086724 1.694892659 0.769542045 0.117526818 0.132442551 1.478330485 0.03001789 0.10006937 15993.52049 -4.203944071 0.577805935 MKEIAEAYLGK ddPTM_BT-474_Pertuzumab_2h_R1 4 MKEIAEAYLGK 11 1 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 132.47 0.00016579 13211600000 26397500 27929600 18608400 18463200 19761500 17668250 23729900 22507900 27320900 25744000 FALSE TRUE 25365856.52 27133075.15 21971351.82 19416087.96 20397146.59 18025514.12 24020313.61 22043104 24219545.97 24000335.95 1.056895894 1.130528973 0.915460178 0.808992341 0.849869212 0.751052575 1.000832391 0.91844981 1.009133623 1 24.51655126 4.204366103 7.868097768 0.898582287 1.093660379 0.447394467 0.082755444 0.163255304 31.80507061 0.021187117 0.047114969 16009.06999 -4.204366103 0.195078092 RPHTPT(ph)PGIYMGR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.385)PT(0.615)PGIYMGR;RPHT(0.408)PT(0.592)PGIYMGR;RPHT(0.139)PT(0.861)PGIYMGR 97.121 0.0029908 1320690000 638810 620570 616530 874410 697950 635010 710530 758400 838220 821460 TRUE FALSE 613844.599 602871.9512 727950.6856 919538.4049 720400.1956 647850.3373 719225.6787 742738.775 743068.7797 765821.7825 0.801550195 0.787222256 0.95054842 1.200721141 0.94068909 0.84595444 0.939155421 0.969858513 0.970289429 1 19.54664917 4.20440601 5.62254656 0.976710895 0.79324975 0.43118692 0.084270273 0.16084329 13.32672509 0.02236382 0.052337001 16010.54111 -4.20440601 -0.183461145 DVEDMFSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVEDMFSR 8 0 Q15717;Q15717-2;M0QZR9;M0R055 Q15717 ELAVL1 ELAV-like protein 1 0 ;;; 221.33 1.29E-05 3736910000 3198830 3245710 2761120 3223860 3287320 3299930 3367360 3430700 3616070 3512960 FALSE TRUE 3073816.187 3153145.529 3260115.805 3390243.801 3393059.633 3366656.846 3408570.759 3359854.846 3205588.893 3275024.09 0.938562924 0.962785446 0.995447885 1.035181332 1.036041122 1.027979261 1.040777309 1.02590233 0.978798569 1 21.64307409 4.204520732 2.078021265 1.023920072 0.941514927 0.700644445 0.018237608 0.173002666 1.428244532 0.004845625 0.01792319 16014.77098 -4.204520732 -0.082405145 IDISPS(ph)TLR ddPTM_BT-474_Pertuzumab_2h_R1 3 IDISPSTLR 9 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 IDIS(0.035)PS(0.96)T(0.004)LR;IDIS(0.101)PS(0.899)TLR;IDIS(0.179)PS(0.82)T(0.001)LR 201.09 2.31E-05 61425800000 2632460 2573900 2403690 3139100 2844600 2515610 2863140 2970470 2943880 3257770 TRUE FALSE 2529580.553 2500494.892 2838090.253 3301109.327 2936099.142 2566477.358 2898179.964 2909128.756 2609703.084 3037118.336 0.832888374 0.823311645 0.934468117 1.086921536 0.966738473 0.845036997 0.954253224 0.957858218 0.859269477 1 21.53427169 4.204601357 5.565700141 0.951947279 0.827284115 0.370886799 0.064015398 0.17529573 14.1473911 0.016497686 0.03870506 16017.74431 -4.204601357 -0.124663164 DKMMNGGHYTYSENR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKMMNGGHYTYSENR 15 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 61.097 0.055335 148690000 70609 90008 55416 59137 68262 70493 72003 68466 73138 74920 FALSE TRUE 67849.52222 87441.05997 65430.90392 62189.06766 70457.70922 71918.41676 72884.19425 67052.15317 64835.68086 69845.60167 0.971421544 1.251919346 0.936793475 0.890379153 1.008763724 1.029677103 1.043504423 0.960005377 0.928271492 1 16.09188165 4.205202987 24.99996763 0.976209118 1.111671055 0.334022251 0.077352336 173.1419349 129761.6445 0.018472919 0.03990996 16039.94915 -4.205202987 0.135461937 EIEDFDSLEALR ddPTM_BT-474_Pertuzumab_2h_R1 6 EIEDFDSLEALR 12 0 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;;;; 262.61 4.66E-21 1156090000 1471940 1498330 1491750 1760100 1732510 1736330 1879570 1929050 1938280 2112470 FALSE TRUE 1414414.957 1455599.095 1761342.409 1850938.972 1788237.758 1771439.782 1902572.74 1889214.443 1718254.58 1969390.525 0.718199331 0.739111454 0.894359136 0.9398537 0.908015822 0.899486293 0.966071846 0.959288886 0.872480373 1 20.90931779 4.205644259 3.112148187 0.93375631 0.718671833 0.849475062 0.034308 0.08122468 1.583954449 0.008627448 0.024717861 16056.25507 -4.205644259 -0.215084478 NRTPSDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 NRTPSDVK 8 1 P39687;H0YN26;H7BZ09;O95626 P39687 ANP32A;ANP32D Acidic leucine-rich nuclear phosphoprotein 32 family member A;Acidic leucine-rich nuclear phosphoprotein 32 family member D 0 ; 143.03 0.00055443 683880000 759350 686290 440740 360540 450790 308330 465940 504930 579300 462430 FALSE TRUE 729673.7625 666717.6811 520391.5222 379147.5126 465290.0697 314564.6439 471642.3131 494503.019 513540.2926 431109.2042 1.692549719 1.546516926 1.207099076 0.87946977 1.079285864 0.729663484 1.094020514 1.147048159 1.191206979 1 18.71769384 4.205741146 2.583534979 1.025825953 1.667938791 0.777085656 0.128140865 0.129607737 1.709211973 0.035093102 0.111409247 16059.83746 -4.205741146 0.642112837 FSELTAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FSELTAEK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 99.802 0.018836 0 194740 199530 121040 116470 138230 144620 142540 132380 154060 142960 FALSE TRUE 187129.3455 193839.5998 142914.6205 122481.0307 142676.2935 147544.3155 144284.4472 129646.3067 136571.7547 133277.1919 1.404061287 1.454409393 1.072311162 0.918994683 1.070522957 1.107048501 1.08258919 0.972756891 1.02471963 1 17.02407038 4.206360167 5.672980291 1.027982335 1.431562919 0.897520315 0.05390223 0.045329368 3.937214153 0.014021591 0.03285044 16082.74467 -4.206360167 0.403580584 TCNVLVALEQQS(ph)PDIAQGVHLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 1 TCNVLVALEQQS(1)PDIAQGVHLDR;TCNVLVALEQQS(1)PDIAQGVHLDR 207.18 7.98E-25 176915000 121759 125470 105128 130383 130532 119803 128469 130861 137655 137754 TRUE FALSE 117000.5237 121891.7184 124126.9682 137112.0823 134730.6803 122225.4987 130041.2421 128158.6746 122028.9815 128423.7989 0.911050169 0.949136527 0.966541788 1.067653219 1.049109912 0.95173558 1.012594575 0.997935552 0.950205356 1 16.97055305 4.206367396 2.621655912 1.004186981 0.922545335 0.410812364 0.035595229 0.272416704 3.704638365 0.009498592 0.029911478 16083.01237 -4.206367396 -0.081641646 TPT(ph)PEPAEVETR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 T(0.151)PT(0.849)PEPAEVETR;T(0.066)PT(0.934)PEPAEVETR;T(0.338)PT(0.662)PEPAEVETR 220.37 3.32E-10 3364130000 1063920 1159950 1014490 1361640 1306700 1220340 1271940 1377140 1352860 1353870 TRUE FALSE 1022340.83 1126869.362 1197830.91 1431914.404 1348731.192 1245016.111 1287506.382 1348701.578 1199289.004 1262171.179 0.809985878 0.892802324 0.949024134 1.134485106 1.068580249 0.986408287 1.020072716 1.068556785 0.950179361 1 20.26747616 4.206455994 2.359044777 1.036053498 0.830155898 0.666878997 0.051402422 0.168178197 1.828998181 0.013399987 0.045219495 16086.2937 -4.206455994 -0.2058976 QDAKDPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_BT-474_Pertuzumab_2h_R1 4 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 QDAKDPTSLLGVLQAEADS(0.788)T(0.178)S(0.034)EGLEDAVHSR;QDAKDPTSLLGVLQAEADS(0.915)T(0.068)S(0.016)EGLEDAVHSR;QDAKDPTSLLGVLQAEADS(0.967)T(0.033)SEGLEDAVHSR;QDAKDPTSLLGVLQAEADS(0.462)T(0.462)S(0.076)EGLEDAVHSR 201.99 5.66E-26 144360800 199213 201635 114834 110729 131219 146316 104363 135653 147005 126170 TRUE FALSE 191427.5357 195884.5672 135587.0583 116443.737 135439.7783 149274.6098 105640.2256 132851.7181 130317.6087 117624.3935 1.62744759 1.665339658 1.152712071 0.989962485 1.15145995 1.269078677 0.898114944 1.1294572 1.107913119 1 16.84382776 4.206894092 5.094825093 1.085686032 1.652106339 0.841912889 0.097174047 0.057997726 3.727859614 0.023706569 0.0569952 16102.52906 -4.206894092 0.566420308 SSDELDAWTDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSDELDAWTDFR 12 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 0 ; 185.77 2.94E-05 179525000 169638 188740 174161 225975 214753 252580 245230 201123 256280 255730 FALSE TRUE 163008.3594 183357.32 205635.7669 237637.5968 221660.7253 257687.3407 248231.1981 196969.7398 227188.1688 238409.1793 0.68373357 0.769086662 0.862532925 0.996763621 0.929749123 1.080861657 1.041198157 0.82618354 0.952933815 1 17.86308026 4.206927795 1.761851809 0.966827798 0.686900354 0.698497108 0.065985796 0.256777969 1.45283491 0.02004199 0.085740198 16103.77874 -4.206927795 -0.279927444 GNS(ph)RPGTPSAEGGST(ph)SSTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.81)RPGT(0.19)PS(0.252)AEGGS(0.12)T(0.58)S(0.027)S(0.018)T(0.002)LR 188.96 5.93E-16 726600000 798520 811530 766090 961620 843090 915930 921020 1000000 959660 1065400 TRUE FALSE 767312.9556 788385.959 904539.5046 1011249.323 870208.7555 934450.7322 932291.7183 979349.6505 850723.42 993239.509 0.772535676 0.793752113 0.910696258 1.018132398 0.876131837 0.940811077 0.938637368 0.9860156 0.856513874 1 19.92178212 4.20709996 3.672747161 0.944975347 0.777376339 0.641544548 0.047804829 0.121016332 3.394848552 0.011413135 0.030484108 16110.16395 -4.20709996 -0.167599008 LPAYLATS(ph)PIPTEDQFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPAYLATSPIPTEDQFFK 18 0 Q92539;J3KTK1 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 LPAYLATS(0.999)PIPTEDQFFK;LPAYLATS(1)PIPTEDQFFK 250.19 7.84E-25 468770000 715330 685020 808480 1064950 883630 791990 1043690 1125140 1015920 1081930 TRUE FALSE 687374.1128 665483.9003 954590.3205 1119912.197 912052.7614 808004.5804 1056462.99 1101905.466 900597.0207 1008649.917 0.681479372 0.659776885 0.946404004 1.110308124 0.904231236 0.801075345 1.047403041 1.092455813 0.892873737 1 19.9439941 4.207141262 5.269547586 0.985255936 0.667795864 0.645516068 0.090022039 0.102894515 7.288791457 0.024107238 0.057500021 16111.69613 -4.207141262 -0.317460072 MDVAQSELDIYLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDVAQSELDIYLSR 14 0 Q9NTJ3;E9PD53;Q9NTJ3-2 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 114.56 0.0025348 0 26673 22104 22200 24183 26765 22468 27122 24790 27756 29011 FALSE TRUE 25630.58967 21473.61556 26212.03384 25431.08753 27625.92053 22922.31835 27453.92715 24278.07784 24605.25524 27046.05913 0.947664484 0.793964676 0.969162779 0.940288099 1.021439774 0.84752896 1.015080497 0.897656761 0.909753806 1 14.72313077 4.207463992 24.99987735 0.945958395 0.87081431 0.202375944 0.062538315 256.5321317 206236.9686 0.014310028 0.030917923 16123.67338 -4.207463992 -0.075144085 DTNIDHGQPRPPSNR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTNIDHGQPRPPSNR 15 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 0 87.647 0.0042602 59453000 33851 34043 30722 33302 36195 38485 36675 38238 39372 41639 FALSE TRUE 32528.0655 33072.12697 36274.14881 35020.72021 37359.24505 39263.19307 37123.83962 37448.37194 34902.65562 38818.75344 0.837947193 0.851962622 0.934449089 0.902159835 0.962401977 1.011449096 0.956337758 0.964697952 0.899118404 1 15.24446617 4.207708188 0.985677858 0.963952883 0.81276343 0.656128389 0.032518528 0.580151012 0.776064769 0.01081502 0.078148626 16132.74197 -4.207708188 -0.151189453 KTESHHK ddPTM_BT-474_Pertuzumab_2h_R1 3 KTESHHK 7 1 A0A0U1RR32;A0A0U1RRH7;P20671;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8 A0A0U1RR32;Q7L7L0;Q99878 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1 0 ;; 73.248 0.032073 116358000 302459 371876 229353 267269 275309 251010 354836 100430 500371 274401 FALSE TRUE 290638.5679 361270.4606 270802.189 281062.7851 284164.564 256085.5942 359178.5891 98356.0854 443570.9818 255815.5759 1.136125378 1.412230117 1.058583662 1.09869301 1.110818069 1.001055519 1.404052853 0.384480441 1.733948296 1 17.96474458 4.207717337 21.63661983 1.055090938 1.27417707 0.030249903 0.328851154 112.8014065 79130.46142 0.078823737 0.170353048 16133.08186 -4.207717337 0.219086132 DPSEEIEILLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPSEEIEILLR 11 0 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;Q5SVM6;B7Z3B5;F2Z2J1;Q15349;Q15349-3;Q15349-2 E9PGT3 RPS6KA1;RPS6KA2 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-2 0 ; 150.61 7.87E-05 39625000 42374 43700 38795 47154 45043 44672 46988 52668 51488 50187 FALSE TRUE 40717.97723 42453.71879 45806.11949 49587.62359 46491.849 45575.29845 47563.0532 51580.38739 45643.2981 46787.78979 0.870269304 0.907367477 0.979018665 1.059841121 0.993674829 0.974085304 1.016569781 1.102432657 0.975538667 1 15.51384446 4.208019149 2.410660548 1.023804402 0.875906714 0.646687359 0.037611998 0.182263793 2.075308766 0.010639716 0.035459299 16144.29738 -4.208019149 -0.147897688 DIPSFER ddPTM_BT-474_Pertuzumab_2h_R1 2 DIPSFER 7 0 K7EJR3;R4GMR5;P48556 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ; 200.12 3.18E-05 0 536600 577780 474370 580770 561210 584590 652080 680230 640780 624510 FALSE TRUE 515629.0788 561302.2801 560099.2113 610743.6093 579261.8293 596410.8103 660060.3501 666183.0128 568041.3408 582211.3814 0.885638954 0.964086753 0.962020375 1.049006647 0.994933881 1.024388786 1.13371255 1.14422877 0.975661691 1 19.15118352 4.208238985 0.641255316 1.076257766 0.848090565 0.453651579 0.055470598 1.604531563 0.778324548 0.028727784 0.24498769 16152.47157 -4.208238985 -0.228167201 DGVPEGAQLQGPVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGVPEGAQLQGPVHR 15 0 P16989;P16989-3;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 0 ; 189.1 2.72E-07 1436100000 915370 933870 884020 1082470 1026380 938220 1090010 1165480 1184940 1248030 FALSE TRUE 879596.3284 907236.942 1043782.079 1138336.406 1059394.445 957191.4512 1103349.868 1141412.431 1050430.579 1163499.816 0.755991807 0.779748247 0.897105495 0.978372657 0.910523947 0.822682941 0.948302572 0.981016425 0.90281972 1 20.15003955 4.208285206 3.340277616 0.932683715 0.760427775 0.655950527 0.047755996 0.141204314 3.209626426 0.012696084 0.035331523 16154.19071 -4.208285206 -0.17225594 SPDTNYLFMGDYVDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPDTNYLFMGDYVDR 15 0 P67775;P62714;P67775-2;E7ESG8;E5RHC1;E5RFI3;E5RHP4 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform;Serine/threonine-protein phosphatase 0 ;; 127.02 0.00018785 563735000 186647 188039 183577 219958 230642 228687 203312 232984 234298 238214 FALSE TRUE 179352.6289 182676.3118 216753.4475 231310.0587 238060.8094 233311.2078 205800.1931 228172.799 207701.4733 222079.5536 0.80760532 0.822571501 0.976017126 1.041563958 1.071961851 1.050574914 0.926695816 1.027437219 0.935257073 1 17.76071705 4.208435006 3.757754023 1.009292455 0.808910088 0.748158887 0.044113838 0.099840233 2.957491905 0.011458799 0.030394693 16159.76369 -4.208435006 -0.200382367 RPQYSNPPVQGEVMEGADNQGAGEQGR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPQYSNPPVQGEVMEGADNQGAGEQGR 27 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;; 296.86 1.77E-70 2056890000 414620 456280 479650 672070 584540 515020 657010 631750 646510 740680 FALSE TRUE 398416.192 443267.3411 566333.4248 706755.6132 603342.26 525434.0573 665050.6849 618704.1417 573120.8952 690513.0839 0.576985725 0.641939091 0.820163206 1.023522406 0.873759345 0.760932804 0.963125392 0.896006399 0.829992811 1 19.39730923 4.208635547 3.067379451 0.899806182 0.592322859 0.713706443 0.074496642 0.125102346 2.367523594 0.018747856 0.054317943 16167.22739 -4.208635547 -0.307483323 TGLFEWDNDFEDIR ddPTM_BT-474_Pertuzumab_2h_R1 5 TGLFEWDNDFEDIR 14 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 0 ;;;; 279.86 7.13E-33 349040600 403098 407899 411341 494582 480148 480561 495390 518427 548347 601238 FALSE TRUE 387344.4845 396266.1199 485679.4689 520107.4363 495592.3965 490278.2727 501452.731 507721.3013 486100.9474 560515.6147 0.691050301 0.706967138 0.866486956 0.927908916 0.884172329 0.874691551 0.894627585 0.905811164 0.867238904 1 19.09639504 4.208777981 3.671029995 0.900961644 0.692179792 0.84101797 0.035736819 0.070117704 1.968972378 0.008231416 0.0220418 16172.53058 -4.208777981 -0.208781851 NS(ph)PVTKT(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 3 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.996)PVT(0.434)KT(0.57)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;NS(0.996)PVT(0.428)KT(0.575)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.995)PVT(0.189)KT(0.811)PPRDLPT(0.005)IPGVTSPSSDEPPMEASQSHLR 191.08 3.54E-23 2357030000 322580 296714 186595 141308 201150 250331 176629 177508 229123 192469 TRUE FALSE 309973.217 288252.0072 220316.8673 148600.9228 207620.1724 255392.8643 178790.6385 173842.3978 203113.9176 179432.9032 1.727516032 1.606461257 1.227850987 0.828169863 1.157090861 1.423333512 0.996420586 0.968843477 1.13197699 1 17.45308494 4.208893282 3.163502401 1.074678186 1.699238839 0.715981145 0.148198211 0.127348357 2.574269214 0.039740319 0.113471452 16176.8248 -4.208893282 0.624560653 VTSAHKGPDETLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTSAHKGPDETLR 13 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 192.65 1.52E-06 4462150000 2868420 3435440 2251540 2422840 2524660 3283150 2575540 2708650 3006710 3085050 FALSE TRUE 2756318.975 3337464.615 2658443.363 2547883.063 2605867.982 3349537.542 2607060.229 2652715.431 2665400.886 2876096.816 0.95835403 1.160414558 0.924323322 0.885882231 0.906043207 1.164612236 0.906457743 0.922331758 0.926742407 1 21.45568081 4.209363049 24.99265621 0.95104106 1.059384532 0.181586428 0.088775295 285.0363081 243986.6131 0.021963743 0.047458967 16194.3324 -4.209363049 0.108343472 AELDDTPMR ddPTM_BT-474_Pertuzumab_2h_R1 2 AELDDTPMR 9 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 185.47 9.96E-05 787790000 1894180 1929210 1688700 2071100 2061800 2016890 2051400 2134800 2038330 2074400 FALSE TRUE 1820153.351 1874190.82 1993885.655 2177989.719 2128119.669 2057672.898 2076505.647 2090715.634 1806947.324 1933899.04 0.941183233 0.969125472 1.031018483 1.126216867 1.10042956 1.064002233 1.073740461 1.081088304 0.934354527 1 20.88308105 4.209374892 3.15577943 1.062998719 0.948876646 0.35741383 0.051637836 0.22795703 4.584637026 0.012969782 0.037100552 16194.77402 -4.209374892 -0.114122073 AKEAAEQDVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 AKEAAEQDVEK 11 1 P26373;P26373-2;J3KS98 P26373 RPL13 60S ribosomal protein L13 0 ;;; 207.66 2.03E-08 2461140000 3814350 3611760 2651730 2300660 2835590 2431460 2989880 3277510 3941700 3378600 FALSE TRUE 3665280.985 3508756.141 3130956.598 2419397.338 2926799.328 2480625.787 3026471.046 3209828.273 3494254.741 3149764.413 1.163668295 1.113974152 0.994028819 0.768120095 0.929212139 0.787559151 0.960856321 1.019069318 1.109370189 1 21.5868125 4.209388313 3.479009725 0.936455427 1.14831533 0.40014564 0.096488591 0.229189328 5.70315218 0.026164129 0.071659523 16195.27448 -4.209388313 0.211859904 SVSSSPWLPQDGFDPS(ph)DYAEPMDAVVKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVSSSPWLPQDGFDPSDYAEPMDAVVKPR 29 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 SVSSSPWLPQDGFDPS(0.612)DY(0.387)AEPMDAVVKPR 46.54 0.065878 57016000 17009 18617 18671 24412 22404 24215 24281 26786 23606 22673 TRUE FALSE 16344.26948 18086.06139 22045.26503 25671.90625 23124.64501 24704.64389 24578.15814 26232.85974 20926.34584 21137.33751 0.773241638 0.8556452 1.042953731 1.214528851 1.094018818 1.168768009 1.162784013 1.241067363 0.990018058 1 14.36750604 4.209415525 2.471876216 1.143402132 0.784855952 0.701457344 0.079681572 0.136976254 1.644652015 0.019831874 0.065130224 16196.28929 -4.209415525 -0.35854618 SSS(ph)PIPLT(ph)PSKEGSAVFAGFEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPIPLTPSKEGSAVFAGFEGR 23 1 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 2 S(0.11)S(0.13)S(0.76)PIPLT(0.971)PS(0.029)KEGSAVFAGFEGR 106.88 0.0032104 123840000 152780 142620 92888 83985 100420 111480 82752 113770 106050 88586 TRUE FALSE 146809.1887 138552.6172 109674.9279 88319.47591 103650.1005 113734.202 83764.74373 111420.6097 94011.6486 82585.99132 1.777652437 1.677676989 1.328008856 1.069424421 1.255056685 1.377160947 1.014273031 1.349146604 1.138348612 1 16.33360946 4.209431747 2.950769481 1.196919291 1.760255143 0.758677017 0.123583756 0.11240668 1.959847914 0.029882009 0.088396399 16196.89427 -4.209431747 0.563335852 SEGTYLNSVIESHTEFIFTTIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEGTYLNSVIESHTEFIFTTIK 22 0 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 308.37 3.98E-67 176640000 145820 154680 158240 205250 208530 212520 199880 189170 205630 185140 FALSE TRUE 140121.1932 150268.6778 186837.488 215842.9771 215237.5568 216817.3 202326.1912 185263.5734 182287.7445 172600.3029 0.811824724 0.870616536 1.082486444 1.250536491 1.247028848 1.256181457 1.172223848 1.073367603 1.056126446 1 17.39707547 4.210115801 3.133704275 1.158751854 0.823874707 0.682195758 0.083476442 0.13758577 2.726385561 0.022832451 0.065599783 16222.42596 -4.210115801 -0.334877147 NTADHDES(ph)PPRTPTGNAPSSESDIDISSPNVSHDESIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTADHDESPPRTPTGNAPSSESDIDISSPNVSHDESIAK 39 1 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 1 NT(0.294)ADHDES(0.589)PPRT(0.051)PT(0.066)GNAPSSESDIDISSPNVSHDESIAK 160.24 2.97E-18 644610000 225730 223750 158380 146360 186310 215250 187570 148920 247990 177310 TRUE FALSE 216908.222 217368.8691 187002.7891 153913.6571 192302.8304 219602.5025 189865.5378 145844.75 219839.2149 165300.6358 1.312204403 1.314991125 1.131288989 0.931113522 1.163352031 1.328503677 1.148607426 0.882299994 1.329935689 1 17.33473275 4.210121421 5.167458532 1.101962708 1.315993628 0.241621147 0.140473924 0.231645728 15.87814452 0.036353797 0.087556672 16222.63589 -4.210121421 0.21403092 ASSDLCDLVSNQS(ph)AEGLLEDCDLFGPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSDLCDLVSNQSAEGLLEDCDLFGPAR 28 0 A6NHN7;A6NHB5;Q14202-2;Q14202 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 AS(0.013)S(0.013)DLCDLVS(0.227)NQS(0.748)AEGLLEDCDLFGPAR 60.876 0.022867 36035000 19610 20101 20575 27842 23120 23437 27401 26436 24193 26984 TRUE FALSE 18843.61952 19527.73916 24293.36019 29278.92896 23863.6758 23910.9122 27736.34163 25890.08736 21446.71207 25156.34965 0.749060169 0.776254879 0.965694965 1.16387828 0.948614411 0.950492124 1.102558282 1.029167098 0.85253673 1 14.61863497 4.21023333 4.063391287 1.013469978 0.755673718 0.585646178 0.080899636 0.128555024 4.606918211 0.020188256 0.052196338 16226.81668 -4.21023333 -0.25779626 DLIHTGVANDHEEDFELR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLIHTGVANDHEEDFELR 18 0 E9PFH4;C9J7E5;Q9Y5L0-5;Q9Y5L0-3;Q9Y5L0;Q9Y5L0-1 E9PFH4 TNPO3 Transportin-3 0 ; 204.05 6.45E-16 148416000 39603 45930 42953 65696 62209 63508 65489 38503 56580 59409 FALSE TRUE 38055.27098 44620.12137 50715.56258 69086.57843 64210.00898 64792.17527 66290.47397 37707.89959 50157.2756 55385.17551 0.68710211 0.805632933 0.915688397 1.24738394 1.15933566 1.169846889 1.196899231 0.68083019 0.905608317 1 15.75721225 4.210490148 2.755591902 1.036331227 0.721059195 0.366414395 0.159674639 0.340644306 5.142389616 0.047796701 0.147012158 16236.41517 -4.210490148 -0.315272032 ATEDGEEDEEMIESIENLEDLKGHSVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATEDGEEDEEMIESIENLEDLKGHSVR 27 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ;;; 344.33 1.11E-96 517143000 577600 569660 367483 332131 427629 526250 390423 388430 460145 403803 FALSE TRUE 555026.7534 553413.8546 433895.3527 349272.3207 441384.0751 536891.1356 395201.1135 380408.7848 407911.2687 376453.0631 1.474358447 1.470073985 1.152588185 0.927797792 1.17248103 1.426183469 1.049801827 1.010507875 1.083564749 1 18.52211047 4.210651882 4.74281971 1.100535496 1.478085796 0.57545417 0.127528827 0.131244164 7.065913909 0.034114991 0.084117425 16242.46284 -4.210651882 0.3775503 VENMSSNQDGNDS(ph)DEFM ddPTM_BT-474_Pertuzumab_2h_R1 3 VENMSSNQDGNDSDEFM 17 0 Q86WR0;Q86WR0-2 Q86WR0 CCDC25 Coiled-coil domain-containing protein 25 1 VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM 274.17 1.16E-35 593590000 668877 679730 582015 702967 684850 725270 675621 739680 724260 729300 TRUE FALSE 642736.5474 660344.7659 687198.0574 739247.2111 706878.8222 739935.4563 683889.4519 724405.3495 642045.0411 679903.8614 0.945334457 0.971232557 1.010728276 1.087281972 1.039674669 1.08829424 1.005861991 1.065452619 0.944317392 1 19.37497124 4.210699222 2.871569385 1.038653866 0.952259619 0.33068231 0.041584247 0.254288451 4.186684531 0.010126732 0.030447837 16244.23344 -4.210699222 -0.086394247 DVYFEDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVYFEDVR 8 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 0 75.213 0.090667 52821000 111560 115420 112820 151790 129410 115780 144850 151100 141390 157490 FALSE TRUE 107200.1119 112128.3346 133209.0837 159623.9001 133572.5902 118121.1509 146622.7176 147979.7322 125340 146823.062 0.730131291 0.763697018 0.907276295 1.087185473 0.909752108 0.804513605 0.998635471 1.007877987 0.853680602 1 17.16371907 4.210746953 3.750236636 0.953287329 0.739392991 0.522859141 0.077184232 0.163630204 4.839898378 0.020004439 0.053278665 16246.01884 -4.210746953 -0.213894338 QAATMSEVEWR ddPTM_BT-474_Pertuzumab_2h_R1 1 QAATMSEVEWR 11 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 110.66 0.0023402 0 54058 75658 40962 48552 43266 54203 53459 60570 48038 63395 FALSE TRUE 51945.3536 73500.30792 48364.74459 51057.77454 44657.69018 55299.0218 54113.24723 59319.20833 42584.92763 59101.20018 0.878922144 1.243634777 0.818337774 0.863904191 0.755613931 0.935666647 0.915603187 1.003688726 0.720542519 1 15.85089981 4.210959325 24.99993646 0.882596063 1.061278939 0.271274757 0.120716689 234.2239278 212149.1188 0.028629512 0.061867696 16253.96519 -4.210959325 0.178682877 TQTGDS(ph)SSISSFSYR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQTGDSSSISSFSYR 15 0 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 TQTGDS(0.949)S(0.025)S(0.025)ISSFSYR 112.82 0.00076973 151300000 91828 120540 93887 130450 137540 152370 142610 133120 148730 183800 TRUE FALSE 88239.26024 117102.3172 110854.4694 137182.5401 141964.099 155451.0258 144355.3038 130371.0255 131846.7939 171351.0623 0.514961851 0.683405843 0.646943578 0.800593462 0.828498505 0.907207832 0.84245351 0.760841653 0.769454196 1 17.38659561 4.210962918 0.959982502 0.839506672 0.500377487 0.693840015 0.071890391 0.611621529 0.764299245 0.024551889 0.181980781 16254.09964 -4.210962918 -0.339129185 VTDDLVCLVYK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTDDLVCLVYK 11 0 P49458 P49458 SRP9 Signal recognition particle 9 kDa protein 0 136.63 0.0029253 0 113120 116230 86445 95681 99708 89382 100420 114190 109850 102950 FALSE TRUE 108699.1453 112915.2342 102067.5345 100619.1079 102915.1984 91189.36528 101648.97 111831.9366 97380.28853 95977.1048 1.132552868 1.176480937 1.06345711 1.048365734 1.072289048 0.950115816 1.059096023 1.165193895 1.014619984 1 16.55040267 4.210998214 9.951416232 1.05633165 1.154493253 0.37813204 0.054209366 0.373181208 130.9557076 0.014640211 0.032241101 16255.42071 -4.210998214 0.098161602 SQTTTERDS(ph)DTDVEEEELPVENR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQTTTERDS(0.999)DT(0.001)DVEEEELPVENR;SQTTTERDS(1)DTDVEEEELPVENR 334.63 6.92E-87 2135100000 290080 326890 309410 453440 372510 472510 481380 475850 531220 486970 TRUE FALSE 278743.3529 317567.4173 365327.2698 476842.0927 384492.1225 482064.4759 487271.2724 466023.5312 470918.1327 453987.0882 0.613989605 0.699507597 0.804708502 1.050342852 0.846923035 1.061846225 1.073315266 1.026512743 1.03729411 1 18.79229174 4.211199647 0.872905512 1.034559828 0.519379177 0.843015107 0.063020176 0.409257571 0.405185734 0.022124792 0.174126684 16262.96198 -4.211199647 -0.515180651 TAST(ph)PTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_BT-474_Pertuzumab_2h_R1 7 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 TAS(0.021)T(0.976)PT(0.003)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.006)AS(0.023)T(0.969)PT(0.003)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.002)AS(0.062)T(0.929)PT(0.006)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.001)AS(0.036)T(0.518)PT(0.442)PPQT(0.003)GGGLEPQANGETPQVAVIVRPDDR;T(0.005)AS(0.13)T(0.453)PT(0.37)PPQT(0.042)GGGLEPQANGETPQVAVIVRPDDR;T(0.012)AS(0.389)T(0.596)PT(0.002)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.036)AS(0.132)T(0.563)PT(0.115)PPQT(0.153)GGGLEPQANGETPQVAVIVRPDDR 229.34 1.43E-36 10682390000 122199.2 95758.6 104810 120532.2 109456 127441 131030 121560.9 128171.7 140364.3 TRUE FALSE 117423.5202 93027.65849 123751.4985 126752.8813 112976.7516 130017.9443 132633.5843 119050.6249 113622.186 130857.3009 0.897340227 0.710909195 0.945698082 0.968634386 0.863358413 0.993585711 1.013574202 0.909774419 0.868290765 1 16.99763489 4.211395013 24.97722955 0.943637507 0.804124732 0.432562996 0.064682789 161.5565316 148542.2104 0.015426295 0.033337657 16270.27947 -4.211395013 -0.139512775 EELMSS(ph)DLEETAGSTSIPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EELMSSDLEETAGSTSIPKR 20 1 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.105)S(0.895)DLEETAGSTSIPKR;EELMS(0.148)S(0.852)DLEETAGSTSIPKR 195.39 1.54E-19 311740000 251110 273210 154299 118666 193393 243930 146145 184535 186563 153634 TRUE FALSE 241296.3436 265418.3183 182184.2617 124790.3665 199613.6615 248862.4317 147933.5662 180724.2878 165385.1504 143228.2323 1.684698189 1.853114529 1.271985688 0.871269333 1.393675382 1.737523585 1.032852 1.261792349 1.154696582 1 17.12795637 4.211402632 8.286148625 1.228502577 1.769060495 0.481237522 0.229558372 0.160613399 42.43926247 0.057912632 0.129394696 16270.56493 -4.211402632 0.540557919 NPEAALS(ph)PTFR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPEAALSPTFR 11 0 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 NPEAALS(0.811)PT(0.189)FR 154.72 3.34E-05 282850000 287990 278130 271890 339520 336120 335750 321480 318960 304190 345490 TRUE FALSE 276735.0324 270198.0047 321026.5712 357042.6679 346931.6051 342539.095 325414.3684 312373.3645 269659.6265 322089.6546 0.859186343 0.838890666 0.996699418 1.108519516 1.07712744 1.063489902 1.010322324 0.969833585 0.837219149 1 18.2971028 4.211702822 6.181718324 1.013231816 0.848273247 0.450538017 0.070074291 0.140516976 16.91154113 0.018833627 0.043786662 16281.81523 -4.211702822 -0.164958569 KQS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 4 KQSPPR 6 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KQS(1)PPR;KQS(1)PPR;KQS(1)PPR;KQS(1)PPR 64.563 0.065141 2061034000 485884 458094 397491 442271 456248 454711 454856 477044 483014 508612 TRUE FALSE 466895.1161 445029.6076 469326.4658 465096.6593 470923.6313 463905.568 460422.6638 467192.8747 428184.2757 474163.2562 0.984671651 0.938557768 0.989799314 0.980878744 0.993167701 0.978366758 0.971021389 0.985299617 0.90303133 1 18.85502434 4.212166456 24.99980703 0.975896291 0.961614615 0.036953894 0.027546778 680.631926 644675.211 0.00652655 0.014105535 16299.20626 -4.212166456 -0.014281676 GNLELRPGGAHPGTCSPS(ph)RPGS ddPTM_BT-474_Pertuzumab_2h_R1 1 GNLELRPGGAHPGTCSPSRPGS 22 2 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 GNLELRPGGAHPGT(0.002)CS(0.409)PS(0.589)RPGS 102.53 0.00031989 580080000 333270 349690 304810 395050 366920 417140 396120 354240 348430 412020 TRUE FALSE 320245.44 339717.1836 359895.9475 415438.5778 378722.315 425574.8566 400967.8351 346924.8202 308877.6871 384113.5184 0.833726033 0.884418713 0.936952047 1.081551567 0.985964557 1.107940325 1.043878478 0.903183053 0.804131259 1 18.55117321 4.212171182 2.747991141 0.989116744 0.847743339 0.282805129 0.082824775 0.367549324 5.516063988 0.023046461 0.071171064 16299.38366 -4.212171182 -0.141373405 NAGEIGEMKDGVPEGAQLQGPVHR ddPTM_BT-474_Pertuzumab_2h_R1 1 NAGEIGEMKDGVPEGAQLQGPVHR 24 1 P16989-2 P16989-2 YBX3 Y-box-binding protein 3 0 105.16 0.0017549 279070000 298350 271800 212660 189470 206270 237870 211570 232090 295930 274610 FALSE TRUE 286690.1522 264048.5301 251092.3926 199248.5694 212904.8619 242679.8944 214159.2569 227297.2604 262337.267 256010.4201 1.119837826 1.031397589 0.980789737 0.778283045 0.831625767 0.947929753 0.836525548 0.887843785 1.02471324 1 17.96584301 4.212372256 2.401264744 0.891437691 1.097291313 0.46335475 0.074839992 0.238156034 2.687035744 0.019213001 0.064641962 16306.93184 -4.212372256 0.205853622 ES(ph)GGSGFRSPHLWK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.546)GGS(0.356)GFRS(0.098)PHLWK;ES(0.441)GGS(0.393)GFRS(0.166)PHLWK 71.085 0.025607 467740000 1145190 1351140 880910 952760 941370 1038400 1007010 1149840 1191860 1100490 TRUE FALSE 1100434.709 1312606.81 1040110.033 1001932.058 971650.021 1059397.159 1019334.09 1126095.402 1056565.049 1025952.832 1.072597759 1.279402687 1.013799076 0.976586863 0.94707085 1.032598309 0.993548687 1.097609332 1.029837841 1 19.96853297 4.212429647 24.85200124 1.015458453 1.176000191 0.548768605 0.059618016 129.8055574 123452.4048 0.014780083 0.031944875 16309.0869 -4.212429647 0.160541737 DLESAEERR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLESAEERR 9 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 93.143 0.015391 363770000 232020 288230 181275 192922 232990 248190 219460 214705 269450 273370 FALSE TRUE 222952.4019 280009.9626 214035.4249 202878.7275 240484.3349 253208.5718 222145.8171 210271.2667 238863.1656 254854.4064 0.874822629 1.098705596 0.839834115 0.796057366 0.943614585 0.99354206 0.871657745 0.825064278 0.937253426 1 17.95931377 4.212493659 24.99995571 0.890814407 0.986764438 0.137847261 0.082914832 319.8250205 306733.9083 0.020366166 0.044018425 16311.49093 -4.212493659 0.09595003 RDS(ph)PPPPAR ddPTM_BT-474_Pertuzumab_2h_R1 6 RDSPPPPAR 9 1 O96013;O96013-4;O96013-2;M0R2X4 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RDS(1)PPPPAR;RDS(1)PPPPAR;RDS(1)PPPPAR;RDS(1)PPPPAR;RDS(1)PPPPAR;RDS(1)PPPPAR 136.38 0.00011912 4059403000 1571432 1656661 1408397 1748154 1733912 1692823 1772133 1851542 1875273 1831378 TRUE FALSE 1510018.7 1609414.65 1662925.668 1838376.437 1789684.854 1727053.041 1793820.894 1813307.011 1662399.871 1707337.137 0.884429131 0.942646075 0.973987874 1.076750688 1.048231668 1.011547751 1.050654177 1.06206734 0.973679911 1 20.70331654 4.21318671 1.944506559 1.036560653 0.893777054 0.697338064 0.031472274 0.184801937 1.310355676 0.008241777 0.032703491 16337.54175 -4.21318671 -0.142783599 FDENYAFLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 FDENYAFLHR 10 0 B0QYD3;Q9UH17-2;Q9UH17-3;Q9UH17 B0QYD3 APOBEC3B DNA dC->dU-editing enzyme APOBEC-3B 0 113.69 0.0014551 264220000 89627 95040 98600 132090 118000 103790 140100 121410 128600 142680 FALSE TRUE 86124.27775 92329.55225 116419.2133 138907.1807 121795.5772 105888.7049 141814.5857 118902.8411 114001.8671 133016.1565 0.647472307 0.694122839 0.875226111 1.044288035 0.915644989 0.796058973 1.066145568 0.893897735 0.857052783 1 17.02124196 4.213259625 3.393178398 0.934785446 0.658358571 0.646459984 0.078366538 0.13348006 3.149953684 0.019461849 0.054163249 16340.28493 -4.213259625 -0.276426875 RLNNLS(ph)PAPHLAS(ph)GSPPPGLPSGLPSGLQS(ph)GSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 35 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 3 RLNNLS(0.966)PAPHLAS(0.516)GS(0.516)PPPGLPS(0.005)GLPS(0.032)GLQS(0.517)GS(0.374)PS(0.075)R 47.382 0.03896 102970000 17173 20750 16286 20354 19809 24298 21429 26911 20946 23768 TRUE FALSE 16501.86017 20158.23032 19229.24248 21404.47238 20446.17448 24789.32221 21691.25451 26355.27845 18568.29789 22158.17219 0.744730208 0.909742471 0.867817179 0.96598547 0.922737413 1.118744001 0.97892797 1.189415725 0.837988699 1 14.43555126 4.213260624 0.647712936 1.044132308 0.707780345 0.402340795 0.095642954 1.699511267 0.839679296 0.044807852 0.385554863 16340.32252 -4.213260624 -0.336351963 SPPYT(ph)AFLGNLPYDVTEESIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.331)PPY(0.291)T(0.377)AFLGNLPYDVTEESIK;S(0.264)PPY(0.309)T(0.426)AFLGNLPYDVTEESIK 100.21 0.0026609 57184000 85858 76785 86827 84939 94871 84847 93977 102851 123327 126459 TRUE FALSE 82502.57444 74595.16698 102518.5704 89322.71197 97922.61187 86562.66447 95127.11864 100727.0909 109327.436 117893.8193 0.699804069 0.632731787 0.869583927 0.7576539 0.830600047 0.734242601 0.80688809 0.854388224 0.927338148 1 16.84712856 4.213393296 0.053639944 1.46680569 4.55E-12 0.675648625 0.059145481 101.2663935 1.018461214 9.842369014 18.8425721 16345.31506 -4.213393296 -1.46680569 NPNKDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NPNKDVR 7 1 Q29RF7;Q29RF7-3;H0Y9L9 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 ; 66.994 0.060527 96756000 642560 664290 428020 427800 465290 522680 498970 505290 576100 501210 FALSE TRUE 617448.0448 645345.0996 505372.7353 449878.8093 480256.4754 533248.9477 505076.5441 494855.5849 510703.5432 467262.6003 1.321415505 1.381118667 1.081560422 0.962796528 1.027808507 1.141218979 1.080926536 1.059052414 1.092969013 1 18.83387404 4.213416206 7.192201647 1.057337202 1.351825523 0.852273124 0.049221407 0.052468089 10.33679158 0.012612507 0.028736506 16346.17732 -4.213416206 0.294488321 GDGPPDRDPTLS(ph)PSAFILR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDGPPDRDPTLSPSAFILR 19 1 Q9H7N4;M0R3G4;M0R2L3;M0R232 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GDGPPDRDPT(0.017)LS(0.982)PS(0.001)AFILR;GDGPPDRDPT(0.001)LS(0.988)PS(0.011)AFILR;GDGPPDRDPTLS(0.992)PS(0.008)AFILR;GDGPPDRDPT(0.201)LS(0.763)PS(0.036)AFILR 225.98 9.74E-20 575191000 344568 353373 344277 478323 442194 390059 447532 413480 351613 454517 TRUE FALSE 331101.9016 343295.148 406495.5123 503009.3074 456417.5716 397946.2602 453009.0305 404941.4935 311699.3663 423732.1587 0.781394319 0.810170153 0.959321836 1.187092594 1.077136965 0.93914576 1.069092872 0.95565438 0.735604697 1 18.6927931 4.213423989 4.182493762 1.000748421 0.790069697 0.335053909 0.110377499 0.218174568 8.471122 0.0286545 0.073731788 16346.47027 -4.213423989 -0.210678724 S(ph)QSFTHSPSGDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.496)QS(0.496)FT(0.008)HSPSGDPK;S(0.497)QS(0.497)FT(0.007)HSPSGDPK 120.9 0.0001629 1438040000 2471300 2334000 1705190 1685870 1876080 1782730 1624820 2263200 2194100 1795880 TRUE FALSE 2374718.864 2267436.605 2013355.765 1772877.953 1936425.817 1818778.022 1644705.033 2216464.129 1945034.966 1674243.448 1.41838325 1.354305199 1.202546599 1.058912881 1.156597518 1.08632829 0.982357157 1.323860118 1.161739632 1 20.67507789 4.213731808 2.655046696 1.128000035 1.407299893 0.581677305 0.092353813 0.208125101 2.904792128 0.024987193 0.078932525 16358.06042 -4.213731808 0.279299859 GPSQEEEDNHS(ph)DEEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSQEEEDNHSDEEDR 16 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPSQEEEDNHS(1)DEEDR;GPSQEEEDNHS(1)DEEDR 274.75 1.97E-35 287090000 127182 135630 159937 230837 187208 184068 218428 193195 205810 228320 TRUE FALSE 122211.5868 131761.9652 188841.1737 242750.5252 193229.7153 187789.9811 221101.1872 189205.4557 182447.3116 212855.683 0.574152332 0.619020189 0.887179384 1.140446531 0.907796835 0.882240861 1.038737534 0.888890788 0.8571409 1 17.69951608 4.214229293 3.92516157 0.954298607 0.585039556 0.757229725 0.081038452 0.093566716 3.102609139 0.020462161 0.053870432 16376.80934 -4.214229293 -0.36925905 SMNLRPEEDDIPWEDLR ddPTM_BT-474_Pertuzumab_2h_R1 5 SMNLRPEEDDIPWEDLR 17 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 ;;;; 195.96 1.50E-11 967850000 771916 797272 757350 904756 880326 987392 908546 931512 1003936 1073293 FALSE TRUE 741748.6693 774534.5832 894219.9922 951450.5656 908642.4853 1007357.743 919665.0577 912275.9517 889973.3941 1000597.909 0.741305436 0.774071759 0.893685649 0.950882025 0.908099524 1.006755794 0.91911551 0.91173082 0.889441589 1 19.93243091 4.214326886 2.62130166 0.93575855 0.743876813 0.79845014 0.036401841 0.11406972 1.54958479 0.009297493 0.029627128 16380.48987 -4.214326886 -0.191881738 ALSSGGSITS(ph)PPLSPALPK ddPTM_BT-474_Pertuzumab_2h_R1 5 ALSSGGSITSPPLSPALPK 19 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9JW88;C9JRZ2;C9J0V6;C9JXQ0;C9JPV7;F8WCD5;C9JHT0;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 ALSSGGSITS(1)PPLSPALPK;ALSSGGSIT(0.016)S(0.984)PPLSPALPK;ALSSGGSIT(0.028)S(0.972)PPLSPALPK;ALSSGGSIT(0.001)S(0.999)PPLSPALPK;ALSSGGSIT(0.003)S(0.997)PPLSPALPK 274.81 2.13E-39 3613690000 4743868 4477084 3975139 4674016 4447128 4902592 4681586 4811620 4742126 4960456 TRUE FALSE 4558472.394 4349401.948 4693535.044 4915242.526 4590173.911 5001725.769 4738880.65 4712258.366 4203819.737 4624479.897 0.985726502 0.940516998 1.014932522 1.062874666 0.992581655 1.081575849 1.02473808 1.018981263 0.909036223 1 22.14085969 4.214417837 18.18728406 1.017858972 0.963122602 0.160353511 0.044682912 14.73348509 11099.88779 0.010915919 0.023664626 16383.92069 -4.214417837 -0.05473637 QGLAETAS(ph)PVAVSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 QGLAETASPVAVSLR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 QGLAET(0.001)AS(0.999)PVAVSLR;QGLAETAS(1)PVAVSLR;QGLAET(0.016)AS(0.984)PVAVSLR 292.19 6.37E-44 1408640000 663420 709820 843470 1135920 853060 946570 1231690 1042750 1152840 1383470 TRUE FALSE 637492.813 689576.6286 995903.7919 1194544.967 880499.4496 965710.2939 1246763.791 1021216.848 1021974.436 1289766.345 0.494270001 0.534652367 0.772158303 0.926171606 0.682681366 0.74874825 0.966658648 0.791784382 0.792371766 1 20.2986783 4.21442846 3.598437626 0.831442245 0.50192901 0.656538674 0.093847016 0.126310503 3.407521806 0.022993895 0.062560924 16384.32144 -4.21442846 -0.329513235 LKLS(ph)PSPSSR ddPTM_BT-474_Pertuzumab_2h_R1 5 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LKLS(0.763)PS(0.237)PSSR;LKLS(0.877)PS(0.123)PSSR;LKLS(0.5)PS(0.5)PSSR;LKLS(0.5)PS(0.5)PSSR;LKLS(0.816)PS(0.184)PSSR 190.37 5.51E-07 14416300000 9476480 9885270 9179160 12950900 9617380 11142300 13771100 13945700 16309600 15521700 TRUE FALSE 9106128.685 9603351.778 10838038.4 13619297.5 9926731.762 11367604.94 13939634.84 13657716.42 14458202.58 14470401.43 0.629293439 0.663654828 0.748979802 0.941183115 0.686002514 0.785576336 0.963320534 0.943838116 0.999156979 1 23.78660161 4.214536367 0.258910077 1.044281709 0.383691459 0.703095474 0.076568881 4.111656871 0.291103783 0.116019561 0.857064993 16388.39288 -4.214536367 -0.66059025 RS(ph)PTGSTTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPTGSTTSR 10 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 RS(0.369)PT(0.208)GS(0.14)T(0.095)T(0.095)S(0.095)R 83.182 0.016717 209200000 183640 188520 175100 211210 213840 237860 208920 213050 213740 215110 TRUE FALSE 176463.1458 183143.5942 206744.4651 222110.5734 220718.3578 242669.6922 211476.8255 208650.443 189477.1313 200540.4081 0.8799381 0.913250332 1.030936693 1.107560195 1.100617875 1.210078779 1.054534732 1.040440902 0.94483268 1 17.61353344 4.214581109 2.973107457 1.07191514 0.885647249 0.50268844 0.066309163 0.202950901 3.59740009 0.017901013 0.053129756 16390.08134 -4.214581109 -0.186267891 AKAPQQEEGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKAPQQEEGPK 11 1 P35269;M0QXD6;M0R0R9 P35269 GTF2F1 General transcription factor IIF subunit 1 0 116.03 0.00095239 43282000 48842 47205 32731 29133 36176 36138 33026 44470 40437 42075 FALSE TRUE 46933.20064 45858.75962 38646.2198 30636.55762 37339.63389 36868.73512 33430.18207 43551.67896 35846.76129 39225.22277 1.196505649 1.169114064 0.985239014 0.781042285 0.951929173 0.939924174 0.852262389 1.11029781 0.913870177 1 15.25949402 4.215124915 4.18638821 0.942186229 1.189399621 0.586175074 0.081804004 0.139721861 5.459752044 0.021547874 0.055578042 16410.61718 -4.215124915 0.247213393 IRIDSLSAQLSQLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 IRIDSLSAQLSQLQK 15 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 159.31 1.62E-06 559640000 683410 694190 434460 436380 492550 502470 514880 492260 594690 494750 FALSE TRUE 656701.5817 674392.3809 512976.5865 458901.6241 508393.3181 512630.2877 521181.2555 482094.659 527183.2843 461240.1418 1.423773696 1.462128552 1.112168131 0.994929935 1.102231293 1.111417332 1.129956411 1.045214012 1.142969218 1 18.81515855 4.215137824 6.132387211 1.079815549 1.444982257 0.897461287 0.049139911 0.038712502 4.766716959 0.011683593 0.02738382 16411.10501 -4.215137824 0.365166709 RAS(ph)QEANLLTLAQK ddPTM_BT-474_Pertuzumab_2h_R1 4 RASQEANLLTLAQK 14 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2;H7C1L3 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK 263.14 8.19E-25 3744390000 5091530 5085060 4656620 5709700 5755950 4986920 5444140 6081900 5827050 5479090 TRUE FALSE 4892547.379 4940039.068 5498174.82 6004378.301 5941095.359 5087758.939 5510767.014 5956306.64 5165587.713 5107986.354 0.957823111 0.967120647 1.076387923 1.175488321 1.163099301 0.996040041 1.07885312 1.166077242 1.011276725 1 22.28432324 4.215745515 4.505339954 1.096683341 0.959599967 0.344446757 0.065261399 0.180227802 8.589756001 0.016368697 0.041312854 16434.08447 -4.215745515 -0.137083374 AHS(ph)DDEKWGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHSDDEKWGR 10 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 AHS(1)DDEKWGR 139.46 2.48E-05 190980000 302680 291360 174380 138480 191650 254580 197040 147720 254080 191360 TRUE FALSE 290850.931 283050.6981 205894.3451 145626.9694 197814.5963 259727.782 199451.4345 144669.5304 225237.9036 178399.0168 1.630339316 1.586615797 1.154122645 0.816299171 1.108832324 1.455881242 1.118007476 0.81093233 1.262551261 1 17.44474814 4.216211632 4.292351622 1.070993881 1.621862428 0.569546679 0.180808565 0.138027063 5.774911949 0.048410285 0.124089276 16451.7322 -4.216211632 0.550868546 GRLT(ph)PS(ph)PDIIVLSDNEASSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PS(1)PDIIVLSDNEASSPR;GRLT(1)PS(1)PDIIVLSDNEASSPR 213.05 1.42E-22 422320000 228330 249270 221731 289710 257930 315090 283520 288450 294730 315770 TRUE FALSE 219406.6112 242161.0637 261802.7241 304661.9678 266226.5527 321461.3357 286989.8026 282493.4067 261273.486 294382.6166 0.74531103 0.822606533 0.889328069 1.034918336 0.904355548 1.091984776 0.974887056 0.959613071 0.887530279 1 18.16733296 4.216478742 1.891445609 0.977850711 0.752959921 0.655112128 0.057175795 0.221681077 1.473496747 0.015009068 0.061370834 16461.85385 -4.216478742 -0.22489079 RDS(ph)LGTYSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 RDSLGTYSSR 10 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(0.758)LGT(0.241)YSSR 136.92 6.43E-05 2399100000 860320 840340 769290 871360 920670 858220 936040 969930 940540 958180 TRUE FALSE 826697.7433 816374.326 908317.8158 916330.994 950284.1867 875573.7964 947495.5375 949900.6066 833773.8423 893281.6151 0.9254615 0.913904767 1.016832542 1.025803037 1.063812543 0.980176667 1.06069074 1.063383137 0.933382965 1 19.76875554 4.216629539 6.232992638 1.025400931 0.919111549 0.493770629 0.039289723 0.107358312 14.24820084 0.009582172 0.022463014 16467.57077 -4.216629539 -0.106289381 IENFDVSFGDR ddPTM_BT-474_Pertuzumab_2h_R1 3 IENFDVSFGDR 11 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ;; 194.17 1.47E-06 698020000 378255 410641 376889 486418 450019 463445 504750 490620 499550 571680 FALSE TRUE 363472.3764 398929.9207 445001.2262 511522.0913 464494.2698 472816.1754 510927.2815 480488.5255 442843.1783 532959.6044 0.681988604 0.748518119 0.834962392 0.959776477 0.871537479 0.887151993 0.958660426 0.901547738 0.830913215 1 19.02366666 4.216780403 2.071409488 0.910930864 0.689146474 0.742598476 0.047298187 0.161402267 1.318057998 0.011978353 0.045377496 16473.29225 -4.216780403 -0.221784391 PRPPGRPVS(ph)GHGMDSR ddPTM_BT-474_Pertuzumab_2h_R1 8 PRPPGRPVSGHGMDSR 16 2 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(0.999)GHGMDS(0.001)R;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR 148.91 4.62E-07 2290850000 1200044 997392 1044036 1088232 1294452 1409380 1146188 1173484 1439360 1226781 TRUE FALSE 1153144.954 968947.3567 1232716.53 1144395.784 1336089.224 1437878.629 1160215.392 1149251.145 1275969.887 1143690.03 1.008267033 0.847211509 1.077841458 1.000617085 1.168226695 1.257227563 1.014449161 1.004862432 1.115660584 1 20.12526467 4.216855459 24.21633946 1.079218595 0.927739331 0.327314294 0.087227692 169.1851233 188759.6147 0.022790866 0.049312217 16476.13943 -4.216855459 -0.151479264 DS(ph)LGTYSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DSLGTYSSR 9 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DS(0.953)LGT(0.047)YSSR;DS(1)LGTYSSR;DS(0.995)LGT(0.005)YSSR;DS(1)LGTYSSR 213.81 1.35E-06 2160970000 1340950 1334420 1310580 1501090 1511700 1507420 1584410 1707050 1632210 1749640 TRUE FALSE 1288544.192 1296363.648 1547430.96 1578561.435 1560325.203 1537901.065 1603800.484 1671798.821 1446928.364 1631135.324 0.789967682 0.794761556 0.948683372 0.96776853 0.956588445 0.94284088 0.983241831 1.024929567 0.887068254 1 20.63744505 4.216893818 4.334519049 0.96934668 0.788352343 0.798701474 0.034501452 0.075487771 3.247864058 0.008769187 0.022434984 16477.59476 -4.216893818 -0.180994337 EGPLPAARPAGAT(ph)LERPK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGPLPAARPAGATLERPK 18 2 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 EGPLPAARPAGAT(1)LERPK;EGPLPAARPAGAT(1)LERPK;EGPLPAARPAGAT(1)LERPK 160.57 1.92E-09 3812700000 2198458 4225800 1408395 2307050 1468957 1830038 1956935 3262180 2320810 1278366 TRUE FALSE 2112539.831 4105284.321 1662923.306 2426117.127 1516207.336 1867042.622 1980884.556 3194814.843 2057361.378 1191781.132 1.772590431 3.444662959 1.395326089 2.035706944 1.272219617 1.566598574 1.662121091 2.680706009 1.726291282 1 20.18468788 4.217057565 24.99991685 1.769546021 2.608627921 0.285830758 0.577333887 274.6230853 319283.4212 0.142686964 0.308672429 16483.80865 -4.217057565 0.8390819 TEPTS(ph)PTPSAFK ddPTM_BT-474_Pertuzumab_2h_R1 4 TEPTSPTPSAFK 12 0 Q86XN7-2;Q86XN7 Q86XN7-2 PROSER1 Proline and serine-rich protein 1 1 TEPT(0.052)S(0.849)PT(0.099)PSAFK;TEPT(0.005)S(0.948)PT(0.048)PSAFK;TEPT(0.011)S(0.976)PT(0.011)PS(0.002)AFK;TEPT(0.256)S(0.713)PT(0.032)PSAFK 264.84 1.49E-21 2212930000 4529500 4358790 4072950 4643580 4813590 4515390 4665160 5199260 5378360 5161360 TRUE FALSE 4352482.132 4234481.577 4809022.667 4883235.72 4968423.494 4606694.28 4722253.624 5091893.464 4767831.121 4811776.49 0.904547861 0.880024578 0.999427691 1.014850904 1.032554921 0.957379107 0.981395049 1.058214877 0.990867122 1 22.1981382 4.21711993 7.908878715 1.007721102 0.892134351 0.736624687 0.026742827 0.076370773 21.75097774 0.007033584 0.015966191 16486.17592 -4.21711993 -0.115586752 TPRPAS(ph)PGPSLPAR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPRPASPGPSLPAR 14 1 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 1 T(0.004)PRPAS(0.995)PGPS(0.001)LPAR;TPRPAS(0.997)PGPS(0.003)LPAR;TPRPAS(0.999)PGPS(0.001)LPAR 136.04 1.78E-05 2451160000 1024430 1021950 964260 1220160 1047050 1051970 1197600 1234290 1217300 1247860 TRUE FALSE 984394.143 992804.9866 1138523.232 1283132.604 1080729.314 1073241.554 1212256.587 1208801.48 1079117.207 1163341.331 0.84617826 0.853408162 0.978666537 1.102971733 0.928987293 0.922550868 1.042047209 1.039077224 0.927601538 1 20.14984302 4.217493132 4.829158989 0.998986829 0.847186356 0.520305678 0.054944274 0.132476394 7.759164723 0.014121339 0.035064166 16500.34908 -4.217493132 -0.151800473 YQADIPEMLLEGESDER ddPTM_BT-474_Pertuzumab_2h_R1 2 YQADIPEMLLEGESDER 17 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8 Q9BTC8 MTA3 Metastasis-associated protein MTA3 0 ; 218.4 1.08E-14 79027000 60992 60114 66671 90216 81570 76670 82979 76986 77522 90977 FALSE TRUE 58608.36521 58399.60758 78719.93279 94872.05857 84193.77313 78220.31993 83994.52182 75396.2122 68722.02756 84815.04676 0.69101377 0.688552442 0.928136407 1.118575798 0.99267496 0.922245792 0.990325715 0.888948543 0.810257498 1 16.37203261 4.217639881 5.368061606 0.957813987 0.686693027 0.663709099 0.076114951 0.097528741 7.943600586 0.020236967 0.048978731 16505.92552 -4.217639881 -0.27112096 KKANEVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKANEVDR 8 2 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;P11908;P11908-2 B1ALA9;P11908 PRPS1;PRPS2 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2 0 ; 138.66 0.00039137 999340000 1623400 1589170 1101080 1157140 1145360 1254810 1321570 1348090 1379690 1272880 FALSE TRUE 1559955.733 1543848.428 1300069.649 1216860.134 1182201.545 1280183.118 1337743.769 1320251.47 1223073.375 1186666.704 1.314569397 1.300995825 1.095564277 1.025443901 0.996237225 1.078805964 1.12731213 1.112571429 1.030679778 1 20.17848335 4.217974326 4.258407308 1.063732937 1.313886295 0.848617852 0.042312626 0.074835577 3.07835219 0.011839864 0.030513001 16518.64143 -4.217974326 0.250153358 WDLLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 WDLLSR 6 0 F8VNY0 F8VNY0 AVIL 0 138.07 0.028989 186180000 366900 320260 340370 437720 403740 376630 395810 408210 417480 452380 FALSE TRUE 352561.1424 311126.4984 401882.4305 460310.7817 416726.6638 384245.7166 400654.0412 399780.3208 370089.4206 421739.8997 0.835968194 0.737721279 0.952915365 1.091456564 0.988112967 0.911096429 0.950002695 0.947930991 0.877530015 1 18.68599399 4.218259644 15.30904343 0.964760971 0.786850399 0.600101054 0.058133977 1.698094578 1281.163349 0.014995612 0.032759959 16529.49725 -4.218259644 -0.177910572 EQELQQTLQQEQSVLDQLRGEAEAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQELQQTLQQEQSVLDQLRGEAEAAR 26 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 142.94 2.47E-07 120782000 50598 55715 28033 24713 32676 43829 29379 30172 31578 29698 FALSE TRUE 48620.57422 54126.06275 33099.18669 25988.44089 33727.05322 44715.25241 29738.54899 29548.93766 27993.39783 27686.52801 1.756109477 1.954960287 1.195497922 0.938667387 1.218175613 1.615054527 1.074116227 1.067267721 1.011083723 1 14.75689653 4.218350105 9.489556813 1.146551253 1.855760113 0.705822441 0.184748139 0.122958652 54.30082418 0.048045242 0.107564236 16532.94059 -4.218350105 0.70920886 VDKGVVPLAGTDGETTTQGLDGLSER ddPTM_BT-474_Pertuzumab_2h_R1 1 VDKGVVPLAGTDGETTTQGLDGLSER 26 1 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 210.21 1.41E-25 340830000 139850 137370 82079 89418 102780 87544 83180 96698 104560 82782 FALSE TRUE 134384.5074 133452.3421 96912.50114 94032.8737 106086.012 89314.19966 84197.98172 94701.15251 92690.78715 77175.10141 1.741293564 1.729214989 1.255748284 1.218435376 1.374614482 1.157292936 1.090999301 1.22709463 1.201045227 1 16.23584785 4.218408385 4.430673408 1.196950542 1.746901692 0.848934042 0.092164941 0.063513791 2.913438921 0.022830843 0.058172198 16535.15937 -4.218408385 0.54995115 SVVS(ph)FDKVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SVVSFDKVK 9 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 SVVS(1)FDKVK;SVVS(1)FDKVK;SVVS(1)FDKVK 152.85 0.00020908 1464630000 2722910 2305980 1917550 1407690 1736510 1457170 1634530 2383620 2609590 2414310 TRUE FALSE 2616495.667 2240215.708 2264093.941 1480341.05 1792366.421 1486634.976 1654533.867 2334397.414 2313360.283 2250786.633 1.162480543 0.995303453 1.005912292 0.657699414 0.79632889 0.660495737 0.735091387 1.03714736 1.027800792 1 21.10199787 4.218420765 2.110214728 0.843817626 1.119606648 0.320491929 0.139829201 0.428893447 3.648226451 0.040339542 0.150975133 16535.63072 -4.218420765 0.275789022 EQCCYNCGKPGHLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQCCYNCGKPGHLAR 15 1 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ;;; 174.83 5.35E-07 5266480000 1788080 1824900 1429938 1594610 1570500 1752330 1667660 1685380 1916860 1830250 FALSE TRUE 1718199.857 1772855.639 1688359.605 1676908.013 1621016.559 1787763.313 1688069.322 1650576.314 1699266.089 1706285.537 1.006982606 1.039014632 0.989494178 0.982782762 0.950026548 1.047751548 0.989324052 0.967350586 0.995886123 1 20.70242766 4.218439115 23.43291074 0.988359007 1.022998596 0.213520952 0.024852999 141.7447301 165072.7356 0.006197916 0.013423535 16536.32941 -4.218439115 0.034639588 LEKHELIEFR ddPTM_BT-474_Pertuzumab_2h_R1 6 LEKHELIEFR 10 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 199.68 1.65E-07 5333480000 4210960 4582050 3270060 3197330 3660490 4169660 4184700 3818230 4303220 4215390 FALSE TRUE 4046391.028 4451374.42 3861032.584 3362344.584 3778232.985 4253973.382 4235913.61 3739382.216 3814736.506 3929877.881 1.029648032 1.132700444 0.982481568 0.855585005 0.961412314 1.082469611 1.077874107 0.951526315 0.97070103 1 21.90605305 4.218804479 24.80327841 0.984708101 1.081174224 0.258135387 0.065037389 271.4907959 340850.2084 0.017504223 0.037899597 16550.24697 -4.218804479 0.096466123 SSS(ph)PVTELASR ddPTM_BT-474_Pertuzumab_2h_R1 7 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SS(0.006)S(0.994)PVTELASR;S(0.003)S(0.162)S(0.836)PVTELASR;SS(0.005)S(0.995)PVTELASR;SS(0.001)S(0.999)PVTELASR;SS(0.001)S(0.999)PVTELASR;SS(0.002)S(0.998)PVTELASR;S(0.001)S(0.046)S(0.951)PVT(0.001)ELASR 281.36 2.22E-27 16679360000 3765979 3760321 3483847 4356785 3920269 3746263 4110916 4568263 4448395 4440403 TRUE FALSE 3618800.377 3653080.327 4113455.651 4581639.196 4046368.013 3822015.005 4161226.62 4473926.773 3943431.849 4139650.55 0.874180159 0.882461039 0.993672196 1.106769555 0.977466084 0.923269962 1.005212051 1.080749865 0.952600178 1 21.98107756 4.21893184 4.764029475 1.01208186 0.875793577 0.490510467 0.051535835 0.143579897 8.125101666 0.013595381 0.033970256 16555.10121 -4.21893184 -0.136288283 VKPAPDETSFSEALLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKPAPDETSFSEALLKR 17 2 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 209.25 2.50E-12 2475600000 1592390 1550540 1044070 976300 1071960 1444510 1118630 1240030 1349230 1175800 FALSE TRUE 1530157.638 1506320.117 1232756.674 1026686.96 1106440.567 1473718.982 1132320.129 1214422.947 1196071.067 1096162.019 1.395922877 1.374176528 1.124611739 0.936619717 1.009376851 1.344435363 1.0329861 1.107886358 1.091144417 1 20.06402962 4.219529604 4.497962311 1.082816461 1.391880699 0.586719035 0.102704769 0.127388619 6.114493385 0.026061918 0.066241038 16577.90338 -4.219529604 0.309064238 DQGELER ddPTM_BT-474_Pertuzumab_2h_R1 3 DQGELER 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 126.04 0.0092852 1924730000 3129900 3049780 2610150 2965350 2879670 3144630 3075690 3202300 3275520 3355300 FALSE TRUE 3007580.048 2962803.26 3081862.167 3118392.069 2972297.201 3208216.573 3113331.214 3136171.386 2903696.702 3128042.542 0.961489496 0.947174861 0.985236654 0.996914852 0.950209967 1.025630735 0.995296954 1.0025987 0.928279159 1 21.5768287 4.219744364 13.54312837 0.987492833 0.954333772 0.179066732 0.026443542 1.72514143 1242.666891 0.006356777 0.013987992 16586.10321 -4.219744364 -0.03315906 EEEWDPEYTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEWDPEYTPK 11 0 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4;Q9Y2W1;A0A3B3ITZ9 Q9NYF8;Q9NYF8-4;Q9Y2W1 BCLAF1;THRAP3 Bcl-2-associated transcription factor 1;Thyroid hormone receptor-associated protein 3 0 107.24 0.0051723 135760000 108240 88800 95421 102790 115160 107900 108390 120210 117850 121400 FALSE TRUE 104009.8611 86267.51094 112665.6973 108095.0042 118864.226 110081.8119 109716.5092 117727.6215 104472.1621 113177.4699 0.918997935 0.762232192 0.995478141 0.955092956 1.050246362 0.972647755 0.969420057 1.040203687 0.923082679 1 16.78822727 4.219759208 24.99717758 0.991704741 0.840615081 0.581290478 0.050059232 124.4227238 165425.1794 0.011437371 0.02477309 16586.67015 -4.219759208 -0.15108966 VIHVESGK ddPTM_BT-474_Pertuzumab_2h_R1 4 VIHVESGK 8 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ;;; 151.27 0.00047585 626130000 1429890 1472800 1143650 1283140 1371380 1212570 1412940 1375790 1509830 1483540 FALSE TRUE 1374008.318 1430797.186 1350332.995 1349363.009 1415491.683 1237088.996 1430231.982 1347379.456 1338440.428 1383058.514 0.993456389 1.03451674 0.976338298 0.975636963 1.023450323 0.894458899 1.034108078 0.974202784 0.967739553 1 20.39943076 4.220045383 24.97908591 0.98060066 1.01398657 0.115144265 0.036861904 418.1222869 564095.3919 0.008567107 0.018563366 16597.6034 -4.220045383 0.033385909 EDLTEIR ddPTM_BT-474_Pertuzumab_2h_R1 5 EDLTEIR 7 0 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;Q8NHW5;F8VWV4;F8VPE8;F8VZS0;F8VS58 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;;; 133.81 0.0075265 2827950000 4098670 4247570 3780930 4566620 4392210 4461680 4599180 4928140 5017870 5423910 FALSE TRUE 3938489.445 4126433.462 4464228.157 4802303.805 4533489.424 4551898.227 4655466.141 4826372.187 4448262.434 5056543.745 0.778889622 0.816058096 0.882861572 0.949720609 0.896558925 0.900199515 0.920681473 0.954480458 0.879704134 1 22.26972018 4.220178745 2.130320289 0.925911076 0.781581133 0.717559849 0.032871016 0.165942301 1.440716907 0.008239441 0.030697737 16602.70092 -4.220178745 -0.144329943 RLDLPIER ddPTM_BT-474_Pertuzumab_2h_R1 4 RLDLPIER 8 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8;A0A3B3ISY3 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;; 143.39 0.0009655 741430000 298140 317928 285101 397368 315104 357811 365636 347038 380460 396099 FALSE TRUE 286488.3592 308861.0047 336625.0927 417876.2101 325239.6063 365046.1836 370110.7627 339871.544 337271.7758 369270.8619 0.775821731 0.836407734 0.911593975 1.131625192 0.88076163 0.988559405 1.002274484 0.920385492 0.913345218 1 18.4943199 4.220422453 3.067745243 0.971114423 0.793966959 0.511420954 0.066126883 0.19208342 3.643168829 0.016482324 0.048547043 16612.0203 -4.220422453 -0.177147464 TEEDSEEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEEDSEEVR 9 0 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 256.36 1.29E-14 900190000 1299840 1342940 1320220 1650840 1439010 1395090 1736790 1738010 1724140 1896160 FALSE TRUE 1249040.816 1304640.666 1558813.122 1736040.05 1485297.064 1423299.676 1758045.356 1702119.486 1528422.855 1767731.394 0.706578397 0.738031055 0.881815601 0.982072308 0.840227802 0.805156078 0.994520639 0.962883553 0.864623924 1 20.75346764 4.220481919 3.453695785 0.919798548 0.713033625 0.60506502 0.063593127 0.151881657 3.743946983 0.016744263 0.046730921 16614.29507 -4.220481919 -0.206764923 VEYSEEELKTHISK ddPTM_BT-474_Pertuzumab_2h_R1 4 VEYSEEELKTHISK 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 261.35 1.01E-24 2651470000 5061640 6132110 3860120 4187010 4627880 5745600 4679640 4739870 5483690 5169350 FALSE TRUE 4863825.513 5957228.227 4557729.552 4403102.088 4776739.963 5861779.969 4736910.834 4641990.028 4861204.501 4819225.32 1.009254639 1.236138141 0.945739045 0.913653501 0.991184194 1.216332414 0.982919561 0.963223282 1.008710774 1 22.20036982 4.220729241 24.99944608 1.002296534 1.122696497 0.213814036 0.092020593 320.0737572 448742.0182 0.023340508 0.05058449 16623.75927 -4.220729241 0.120399963 EEVPHAEEFLDDSTVWGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEVPHAEEFLDDSTVWGIR 19 0 A0A590UJ99;O43683-2;O43683-3;O43683 A0A590UJ99 BUB1 Mitotic checkpoint serine/threonine-protein kinase BUB1 0 141.13 1.68E-07 26327000 18094 19658 17140 22109 21363 19907 23214 25235 18064 24606 FALSE TRUE 17386.86648 19097.37309 20237.57928 23250.04814 22050.1603 20309.53318 23498.09988 24713.88843 16013.45045 22939.4137 0.757947291 0.832513565 0.88221868 1.013541516 0.961234693 0.885355373 1.024354858 1.077354842 0.698075838 1 14.4855409 4.220935349 1.888990329 0.963510849 0.766964212 0.281048683 0.099548908 0.453100397 2.997271785 0.026630543 0.109927611 16631.65048 -4.220935349 -0.196546636 RSGS(ph)FGK ddPTM_BT-474_Pertuzumab_2h_R1 3 RSGSFGK 7 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.241)GS(0.759)FGK;RS(0.106)GS(0.894)FGK;RS(0.323)GS(0.677)FGK 63.32 0.07113 1039632000 1358870 1262300 1007920 996270 1093230 1074470 860880 1453950 1001000 1209480 TRUE FALSE 1305763.858 1226300.44 1190073.565 1047687.614 1128394.736 1096196.52 871415.707 1423925.424 887370.6765 1127560.842 1.158042927 1.087569197 1.055440665 0.929162822 1.000739555 0.97218392 0.772832538 1.262836887 0.786982523 1 20.10477385 4.221056277 1.849071503 0.979630737 1.148524475 0.20178763 0.128700057 0.699051977 4.400853398 0.034383314 0.144680568 16636.28213 -4.221056277 0.168893737 KTTHFVEGGDAGNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTTHFVEGGDAGNR 14 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 133.66 2.81E-05 119010000 89190 93234 92288 106760 111980 118560 111750 112860 141450 128920 FALSE TRUE 85704.3562 90575.05761 108966.4945 112269.8964 115581.9384 120957.3644 113117.6299 110529.4016 125393.189 120188.1336 0.713085008 0.753610651 0.906632721 0.934117979 0.961675125 1.006400223 0.941171367 0.919636559 1.043307565 1 16.87493494 4.221068261 1.649312799 0.967657358 0.695931141 0.878670299 0.035194649 0.145351824 0.697896388 0.00991591 0.046360341 16636.74122 -4.221068261 -0.271726217 AEKEEENR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEKEEENR 8 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 93.111 0.010306 186040000 317260 312540 238540 264360 252140 269210 284330 309710 290220 287900 FALSE TRUE 304861.1285 303626.6652 281649.4843 278003.6513 260250.3121 274653.6107 287809.7156 303314.3803 257275.4423 268400.2766 1.135845061 1.131245724 1.049363614 1.035780048 0.969635037 1.023298538 1.072315272 1.13008222 0.958551331 1 18.03402663 4.221297858 4.332816057 1.038585049 1.135878439 0.427150781 0.047335788 0.209637311 9.104224999 0.013080363 0.033718887 16645.53884 -4.221297858 0.09729339 RGSMS(ph)YLAAVEEEVEESSVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSMSYLAAVEEEVEESSVK 20 1 Q8WXH0;Q8WXH0-2;G3V5X4;A0A0A0MRE3;A0A0C4DGK3;Q8WXH0-7 Q8WXH0 SYNE2 Nesprin-2 1 RGS(0.338)MS(0.384)Y(0.278)LAAVEEEVEESSVK 147.28 7.58E-08 127650000 89621 77016 57287 48714 54726 51324 50072 64064 59973 43799 TRUE FALSE 86118.51224 74819.57909 67640.03524 51228.13538 56486.31149 52361.80644 50684.79611 62741.05601 53165.11647 40832.45472 2.109070171 1.83235565 1.656526303 1.254593576 1.383368007 1.282357546 1.241287022 1.53654872 1.302030868 1 15.31742868 4.221326244 1.448912024 1.317344241 2.123337187 0.808983732 0.13600976 0.225487235 0.787592127 0.038068133 0.201552913 16646.62684 -4.221326244 0.805992947 DGTGVVEFVR ddPTM_BT-474_Pertuzumab_2h_R1 6 DGTGVVEFVR 10 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 195.32 8.53E-07 3393700000 2671140 2648080 2258570 2639640 2650560 2570930 2542960 2806280 2983780 2800570 FALSE TRUE 2566748.896 2572559.351 2666743.841 2775872.137 2735817.67 2622915.966 2574081.505 2748329.337 2645073.803 2610884.899 0.983095385 0.985320859 1.02139464 1.063192076 1.047850738 1.004608042 0.985903862 1.052642856 1.013094757 1 21.31610743 4.22181391 5.083827823 1.02663273 0.983526451 0.30628123 0.02346414 0.19191963 13.43969473 0.006084685 0.015039629 16665.32969 -4.22181391 -0.043106279 SEADSDKNATILELR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEADSDKNATILELR 15 1 P15924 P15924 DSP Desmoplakin 0 ; 174.87 8.10E-07 2220800000 3022400 3175400 2317700 2272300 2513400 3018300 2672000 2819800 3280200 2729600 FALSE TRUE 2904281.267 3084840.701 2736559.947 2389573.675 2594245.794 3079332.094 2704700.735 2761570.145 2907845.448 2544721.761 1.141296196 1.212250686 1.075386704 0.939031415 1.019461473 1.210085968 1.062866981 1.085214968 1.142696814 1 21.27907649 4.221918216 21.27819813 1.069338164 1.176773269 0.269352385 0.072328803 49.77112949 63637.00638 0.018625733 0.040538223 16669.33277 -4.221918216 0.107435105 DSIVQLCTARPERPMAFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSIVQLCTARPERPMAFLR 19 2 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6;K7EQK3;X6RAV4 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ; 206.63 2.00E-16 2875700000 787590 921340 593190 702150 738850 741560 681240 699400 827530 817670 FALSE TRUE 756810.1121 895064.2853 700392.6284 738388.0456 762615.7813 756554.8513 689577.2189 684957.1456 733592.2637 762288.4826 0.992813258 1.174180518 0.918802585 0.968646467 1.000429363 0.992478397 0.904614506 0.898553712 0.962355172 1 19.53997755 4.22192674 24.99987021 0.95008335 1.083496926 0.467414527 0.0542837 166.1761448 249755.2174 0.01346047 0.029199714 16669.65991 -4.22192674 0.133413575 SGSIVELIAGGGS(ph)SCSPVLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 1 SGSIVELIAGGGS(0.365)S(0.312)CS(0.312)PVLS(0.012)R 76.704 0.011286 115640000 40249 48654 43782 61564 58645 66729 60644 52744 67815 74385 TRUE FALSE 38676.02458 47266.43556 51694.38133 64741.32542 60531.36969 68078.3061 61386.17941 51654.81797 60116.9255 69346.83769 0.557718648 0.681594679 0.745446844 0.933587278 0.872878587 0.981707434 0.885205172 0.74487633 0.866902191 1 16.08154247 4.222138483 1.703718687 0.880562384 0.568179291 0.71409608 0.07160976 0.261417138 1.35616502 0.021379696 0.097165732 16677.78929 -4.222138483 -0.312383092 GEQVSQNGLPAEQGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 GEQVSQNGLPAEQGSPR 17 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR 337.14 3.12E-72 3685710000 1048780 1106540 1267140 1577770 1467070 1536180 1641020 1622610 1579160 1839210 TRUE FALSE 1007792.518 1074982.563 1496140.385 1659198.899 1514259.639 1567242.612 1661103.294 1589102.536 1399900.377 1714638.669 0.587757955 0.62694408 0.872568905 0.967666791 0.883136294 0.914036666 0.96877746 0.926785664 0.816440456 1 20.70947315 4.222188467 3.551463289 0.923066838 0.593780103 0.87205672 0.048162038 0.065063888 1.711900903 0.011672371 0.032287404 16679.7089 -4.222188467 -0.329286735 EETVSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EETVSLR 7 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 143.85 0.0055686 286850000 171800 171280 161960 209170 175120 160150 202810 211840 198520 221100 FALSE TRUE 165085.8661 166395.2621 191229.7748 219965.2888 180752.8938 163388.3427 205292.0494 207465.43 175984.8419 206124.7001 0.800902881 0.807255327 0.92773828 1.067146677 0.876910403 0.792667461 0.995960452 1.00650446 0.853778522 1 17.65315787 4.222246623 5.184825461 0.944344011 0.801962621 0.329108289 0.077795365 0.189659767 14.18638392 0.020208172 0.049764026 16681.94263 -4.222246623 -0.142381391 DYIWNTLNSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYIWNTLNSGR 11 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 86.014 0.034399 762380000 184760 210720 201290 325690 201710 200370 340720 286390 234300 231770 FALSE TRUE 177539.3749 204710.4719 237667.5807 342498.8999 208198.1853 204421.6187 344889.8333 280475.9464 207703.2463 216072.0115 0.821667618 0.94741781 1.099946166 1.5851146 0.96355925 0.946080972 1.596180046 1.298066994 0.961268629 1 17.72115268 4.222294362 3.130874079 1.221510227 0.860207091 0.207344891 0.233570004 0.33811034 6.703616869 0.06010799 0.175754045 16683.77643 -4.222294362 -0.361303136 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR 31 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ; 157.16 6.06E-09 812650000 105773 78238 92222 86806 100253 102679 94403 111124 116525 99742 FALSE TRUE 101639.2742 76006.72884 108888.5669 91286.06806 103477.7288 104755.2397 95558.33215 108829.2506 103297.5705 92986.3855 1.093055437 0.817396315 1.171016233 0.98171434 1.11282666 1.126565348 1.027659389 1.17037833 1.11088919 1 16.50473188 4.222395673 24.99958596 1.093056317 0.955225763 0.264823179 0.08787235 239.065031 369722.8864 0.020058492 0.043538999 16687.66886 -4.222395673 -0.137830554 IEYEPFRK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEYEPFRK 8 1 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 76.827 0.055792 309900000 295530 320330 226120 255040 248910 267430 303980 248730 266540 336010 FALSE TRUE 283980.3609 311194.502 266984.914 268202.645 256916.4162 272837.6178 307700.1982 243593.6386 236283.4966 313251.7434 0.906556362 0.993432626 0.852301446 0.856188834 0.820159573 0.870985154 0.982277688 0.777628996 0.754292679 1 18.25696301 4.222943879 24.72116408 0.856877506 0.949994487 0.162667522 0.076390853 286.8899866 454146.6537 0.018669244 0.040562371 16708.74685 -4.222943879 0.093116982 LLFAIEETEGFGQE ddPTM_BT-474_Pertuzumab_2h_R1 6 LLFAIEETEGFGQE 14 0 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;Q9H0M0-3;Q9H0M0;Q9H0M0-6 A0A590UJQ1;Q9H0M0-3 ITCH;WWP1 E3 ubiquitin-protein ligase Itchy homolog;NEDD4-like E3 ubiquitin-protein ligase WWP1 0 ;;;;; 289.22 4.61E-43 322939000 308814.8 350783 283807 354659 369041 399112 383881 381576 383409 427198 FALSE TRUE 296745.9762 340779.0123 335097.2382 372962.9935 380911.5389 407182.3181 388579.0505 373696.3223 339886.0177 398263.499 0.745099606 0.855662176 0.841395807 0.936472949 0.956430956 1.022394267 0.975683314 0.938314265 0.853419956 1 18.60336374 4.223003127 1.073682846 0.958340862 0.741195751 0.676880535 0.046422752 0.520882942 0.852512198 0.015284135 0.106711593 16711.02646 -4.223003127 -0.217145111 QIDSS(ph)PVGGETDETTVSQNYR ddPTM_BT-474_Pertuzumab_2h_R1 8 QIDSSPVGGETDETTVSQNYR 21 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QIDSS(1)PVGGETDETTVSQNYR;QIDS(0.03)S(0.97)PVGGETDETTVSQNYR;QIDS(0.021)S(0.979)PVGGETDETTVSQNYR;QIDS(0.08)S(0.92)PVGGETDETTVSQNYR;QIDS(0.133)S(0.867)PVGGETDETTVSQNYR;QIDS(0.1)S(0.9)PVGGETDETTVSQNYR;QIDS(0.009)S(0.991)PVGGETDETTVSQNYR;QIDS(0.001)S(0.999)PVGGETDETTVSQNYR 402.82 1.88E-151 6923500000 1639527 1757162 1621096 2013270 2070233 2055148 2127648 1996738 2093585 2223509 TRUE FALSE 1575452.472 1707049.46 1914064.108 2117175.106 2136823.925 2096704.501 2153686.793 1955504.663 1855930.008 2072908.755 0.760020174 0.82350439 0.923371134 1.021354703 1.030833566 1.011479399 1.038968448 0.943362634 0.895326436 1 20.98322518 4.2230147 2.173718396 0.99145212 0.767027442 0.785481119 0.041784379 0.152682353 1.384746841 0.01201665 0.044278493 16711.47177 -4.2230147 -0.224424678 GASFLFPPAESLS(ph)PEEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GASFLFPPAESLSPEEPR 18 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 GASFLFPPAES(0.037)LS(0.963)PEEPR;GASFLFPPAES(0.377)LS(0.623)PEEPR 142.39 1.19E-07 183066000 220320 248190 228650 319070 336100 306500 299400 286450 260650 280470 TRUE FALSE 211709.6508 241111.8642 269972.1413 335537.2409 346910.9617 312697.64 303064.1468 280534.7074 231062.1047 261473.5171 0.809679134 0.922127284 1.032502811 1.283255164 1.326753721 1.195905587 1.159062494 1.072899124 0.883692189 1 17.99630531 4.223072257 2.54015182 1.142690428 0.836612886 0.420659709 0.124097526 0.273990185 3.477830291 0.034393434 0.113301275 16713.68671 -4.223072257 -0.306077542 FVINYDYPNSSEDYIHR ddPTM_BT-474_Pertuzumab_2h_R1 6 FVINYDYPNSSEDYIHR 17 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;; 264 1.94E-27 14430010000 4093020 4402430 3692100 4896220 4505040 4960080 4592860 4441810 4928090 5319050 FALSE TRUE 3933060.253 4276877.007 4359344.6 5148914.501 4649948.703 5060376.216 4649068.795 4350085.071 4368673.883 4958786.006 0.793149825 0.862484689 0.879115291 1.038341742 0.937719171 1.020486912 0.937541727 0.877247993 0.880996655 1 22.24155554 4.223212287 2.247432744 0.947306447 0.810194387 0.484396429 0.053479582 0.301992914 2.946342267 0.015042343 0.05403795 16719.07657 -4.223212287 -0.13711206 HRSNS(ph)FSDER ddPTM_BT-474_Pertuzumab_2h_R1 2 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 HRS(0.003)NS(0.988)FS(0.009)DER;HRS(0.109)NS(0.876)FS(0.016)DER 112.44 0.00098159 417890000 630760 963310 385060 510560 415580 736120 512110 424290 572030 536040 TRUE FALSE 606109.2019 935837.342 454648.9076 536910.0628 428947.5081 751004.8508 518377.3554 415528.2632 507095.5525 499733.5333 1.21286478 1.872672694 0.909782669 1.074392705 0.858352461 1.502810599 1.037307526 0.83149966 1.01473189 1 18.9307995 4.223242782 24.99991364 1.025229912 1.54276884 0.444832504 0.229733365 175.8985075 287081.4122 0.055824395 0.121294134 16720.25059 -4.223242782 0.517538927 NPYYGGESASITPLEDLYKR ddPTM_BT-474_Pertuzumab_2h_R1 2 NPYYGGESASITPLEDLYKR 20 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 256.11 5.67E-36 971760000 646050 652770 444640 447080 498250 538330 467100 546520 643810 564150 FALSE TRUE 620801.6518 634153.6387 524996.339 470153.8524 514276.6637 549215.4014 472816.5095 535234.171 570727.3879 525939.618 1.180366777 1.205753697 0.998206488 0.893931235 0.977824538 1.044255619 0.898993902 1.017672282 1.085157627 1 19.00453765 4.223305048 7.708337604 0.984926479 1.193582987 0.680553289 0.055724741 0.072250092 23.15132646 0.013902027 0.032153238 16722.64798 -4.223305048 0.208656508 KIEPELDGSAQVTSHDASTNGLINFIK ddPTM_BT-474_Pertuzumab_2h_R1 3 KIEPELDGSAQVTSHDASTNGLINFIK 27 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48 P06744 GPI Glucose-6-phosphate isomerase 0 ;; 255.58 4.73E-53 6796850000 2697910 2569090 1734190 1677680 2049560 2144530 1657049 2061720 2251900 1741757 FALSE TRUE 2592472.695 2495822.069 2047596.71 1764265.266 2115485.959 2187893.866 1677328.461 2019144.762 1996273.753 1623786.247 1.596560323 1.537038556 1.261001387 1.086513246 1.302810615 1.347402634 1.032973684 1.243479408 1.229394421 1 20.6309303 4.223332426 3.460676389 1.192331475 1.584660285 0.673109931 0.106933709 0.124590133 3.089236899 0.026066713 0.072989227 16723.70224 -4.223332426 0.39232881 LKGNKHDDGTQS(ph)DSENAGAHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKGNKHDDGTQSDSENAGAHR 21 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 LKGNKHDDGT(0.137)QS(0.863)DSENAGAHR;LKGNKHDDGT(0.097)QS(0.903)DSENAGAHR;LKGNKHDDGT(0.002)QS(0.998)DSENAGAHR 222.72 1.82E-25 490689000 635050 608350 377519 322560 401411 548132 370774 344963 610880 469933 TRUE FALSE 610231.5439 591000.4536 445745.0812 339207.3603 414322.7494 559215.6046 375311.6431 337839.3935 541535.4634 438104.0193 1.392891909 1.348995735 1.017441205 0.774262151 0.945717754 1.276444817 0.856672449 0.771139681 1.236088781 1 18.74091393 4.223669511 4.232970908 0.958122188 1.382858646 0.476842054 0.161256653 0.156135369 6.389937399 0.041674691 0.108635588 16736.68765 -4.223669511 0.424736457 LISPESTVMLLEAQAATGGIIDPHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LISPESTVMLLEAQAATGGIIDPHR 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 183.01 2.13E-17 289770000 415850 545460 316175 220914 481710 819080 393519 401090 317165 239055 FALSE TRUE 399598.1223 529904.0149 373314.8558 232315.398 497204.6396 835642.3588 398335.0032 392807.3513 281161.7589 222863.5919 1.793016611 2.377705619 1.675082289 1.042410723 2.230981899 3.749568746 1.787348933 1.762546085 1.261586769 1 17.76580142 4.223699721 24.93536508 1.887964275 2.085361415 0.012761671 0.756381203 1574.574382 2642018.031 0.197731417 0.429894766 16737.85191 -4.223699721 0.197397141 CDSWWAK ddPTM_BT-474_Pertuzumab_2h_R1 2 CDSWWAK 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 117.17 0.01231 516420000 1365770 1367600 1254610 1364340 1513140 1523230 1461280 1575860 1660590 1569960 FALSE TRUE 1312394.198 1328597.387 1481345.936 1434753.751 1561811.522 1554030.754 1479163.582 1543317.94 1472086.785 1463625.211 0.896673676 0.907744262 1.01210742 0.980274008 1.067084326 1.061768233 1.010616359 1.054448864 1.005781244 1 20.48111474 4.223720792 1.450158137 1.033915261 0.879390274 0.747173524 0.028062661 0.237159879 0.828858746 0.007657267 0.040711866 16738.66402 -4.223720792 -0.154524987 DSLEEGELR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSLEEGELR 9 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;A0A087X1I0;A0A087WYI9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 0 95.502 0.012633 0 79182 79241 73513 81040 90402 90949 84442 91848 90319 93871 FALSE TRUE 76087.4799 76981.12427 86798.43439 85222.48411 93309.86243 92788.05109 85475.42646 89951.3067 80066.36577 87513.03356 0.869441691 0.879653249 0.991834369 0.973826191 1.066239606 1.060276936 0.97671653 1.027861829 0.9149079 1 16.41721028 4.223775511 3.272463323 1.00737724 0.868174828 0.596555333 0.041717355 0.149570995 3.269240629 0.010611313 0.03045852 16740.77315 -4.223775511 -0.139202413 NNSQIASGQNQPQAAAGSHQLS(ph)MGQPHNAAGPSPHTLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHTLRR 39 1 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 NNSQIASGQNQPQAAAGS(0.088)HQLS(0.423)MGQPHNAAGPS(0.423)PHT(0.066)LRR 133.47 2.34E-09 219770000 66482 92809 46758 57379 49165 74674 64741 62116 81030 62941 TRUE FALSE 63883.80994 90162.17819 55208.21073 60340.33707 50746.43688 76183.95944 65533.31972 60833.28289 71831.81411 58677.95001 1.088719186 1.536559784 0.94086809 1.028330694 0.864829751 1.298340508 1.116830423 1.036731564 1.224170478 1 15.84053085 4.223849482 24.99999428 1.066296008 1.312639619 0.288203955 0.156408098 244.0634581 414761.5604 0.037142012 0.080767832 16743.62476 -4.223849482 0.246343612 AHQCGDDDKTRPLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHQCGDDDKTRPLVK 15 2 Q9BQ61;K7EN60 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 ; 234.22 7.19E-18 1523370000 1391310 1353210 926760 979670 1046920 1173250 1130390 741460 1445670 1288850 FALSE TRUE 1336936.067 1314617.776 1094246.148 1030230.886 1080595.133 1196973.919 1144224.051 726148.5919 1281563.602 1201555.042 1.112671514 1.094097008 0.910691654 0.857414642 0.89933053 0.996187338 0.952286006 0.604340681 1.066587512 1 20.19647131 4.224389303 4.08325512 0.883224385 1.110148651 0.273715098 0.119802736 0.228428487 8.499180528 0.031600987 0.083416739 16764.44973 -4.224389303 0.226924267 GSYGS(ph)DAEEEEYR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSYGSDAEEEEYR 13 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 GSYGS(1)DAEEEEYR;GSYGS(1)DAEEEEYR 344.55 9.02E-64 6748900000 4047900 4222700 4178800 5490800 4623200 4813800 5299900 5310500 5341500 5859300 TRUE FALSE 3889703.593 4102272.73 4934002.117 5774180.846 4771909.427 4911138.334 5364761.762 5200836.319 4735155.313 5462444.392 0.712081133 0.750995788 0.903259011 1.057069039 0.873584989 0.899073378 0.982117414 0.952107874 0.866856479 1 22.38111526 4.224604319 3.636149271 0.945192149 0.721967564 0.703242753 0.055407658 0.110408342 3.074803511 0.013667228 0.037593336 16772.75176 -4.224604319 -0.223224585 LGDDIDLIVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGDDIDLIVR 10 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 116.37 0.0025569 66766000 146440 145913 145829 164615 170949 159096 175734 182281 197406 204439 FALSE TRUE 140716.9629 141751.7041 172183.5442 173110.7999 176447.7298 162313.0301 177884.6853 178516.8337 174997.2985 190592.1644 0.738314523 0.743743608 0.903413552 0.908278682 0.925786904 0.851624885 0.933326329 0.936643089 0.918176773 1 17.54012928 4.224674013 4.674331506 0.919747176 0.737368805 0.817724632 0.034274283 0.066110057 3.600741231 0.008246209 0.02093366 16775.4436 -4.224674013 -0.182378371 CIACQAAKLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 CIACQAAKLSPR 12 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 CIACQAAKLS(1)PR 150.37 4.12E-05 210010000 691320 657370 398470 377600 423620 314290 528470 419920 548330 574410 TRUE FALSE 664302.4501 638622.4512 470482.3929 397087.9813 437246.122 320645.1591 534937.5739 411248.5053 486085.8772 535504.6991 1.240516566 1.192561806 0.878577525 0.741521002 0.816512204 0.598771887 0.998940952 0.767964326 0.907715428 1 19.03053971 4.224842547 3.773205909 0.819538608 1.231829454 0.638206175 0.11413511 0.114764768 3.495619447 0.027032106 0.073363411 16781.95478 -4.224842547 0.412290846 IILLFDAHKLDISDEFSEVIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IILLFDAHKLDISDEFSEVIK 21 1 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9NZN3 A0A024R571;Q9NZN3 EHD1;EHD3 EH domain-containing protein 1;EH domain-containing protein 3 0 122.01 1.73E-05 143600000 319790 323810 183750 159490 203800 269810 186840 197610 273120 223450 FALSE TRUE 307292.2533 314575.2558 216957.7125 167721.298 210355.4121 275265.7431 189126.6038 193529.2844 242116.5626 208315.5325 1.475128857 1.510090256 1.041486009 0.805131024 1.009792259 1.321388472 0.907885272 0.929019945 1.162258809 1 17.66841089 4.225076252 7.026162151 1.010782346 1.494749171 0.662097886 0.134303417 0.075209902 17.75385874 0.034392333 0.080840287 16790.98802 -4.225076252 0.483966826 KVTGTEGSSSTLVDYTSTSSTGGS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 4 KVTGTEGSSSTLVDYTSTSSTGGSPVR 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 KVTGTEGSSSTLVDYTSTS(0.002)S(0.002)T(0.005)GGS(0.991)PVR;KVTGTEGSSSTLVDYTSTSSTGGS(1)PVR;KVTGTEGSSSTLVDYTSTSSTGGS(1)PVR;KVTGTEGSSSTLVDYTSTSSTGGS(1)PVR 224.01 1.21E-34 3011690000 2257430 2202700 2059270 2435940 2350920 2453920 2379630 2482410 2745110 2502920 TRUE FALSE 2169207.14 2139881.153 2431425.897 2561659.155 2426539.477 2503539.944 2408752.624 2431147.366 2433496.621 2333394.999 0.929635634 0.917067686 1.042012132 1.09782491 1.039918007 1.072917335 1.032295271 1.041892764 1.042899561 1 21.15399912 4.225693033 7.788423971 1.049269244 0.923008876 0.80223468 0.024368526 0.047466314 16.98591737 0.005783444 0.013457596 16814.85136 -4.225693033 -0.126260368 EIADYLAAGKDER ddPTM_BT-474_Pertuzumab_2h_R1 4 EIADYLAAGKDER 13 1 P53990-2;P53990;P53990-4;P53990-5;H3BQF7;H3BMU1;H3BUI0;P53990-3;F5GXM3;H3BPP6;H3BRE2 P53990-2 IST1 IST1 homolog 0 ;;; 170.95 2.36E-05 1391010000 2917130 2995000 2272510 2410220 2613980 2449470 2688630 2954180 2993170 2779030 FALSE TRUE 2803125.335 2909585.532 2683203.109 2534611.743 2698061.041 2498999.962 2721534.258 2893175.151 2653397.89 2590803.823 1.081951983 1.123043554 1.035664331 0.978310948 1.041399205 0.964565491 1.050459411 1.116709465 1.024160095 1 21.30496835 4.225861822 23.86205505 1.032851487 1.102497752 0.34362628 0.041303563 149.8754332 281630.9576 0.011593995 0.025340281 16821.38776 -4.225861822 0.069646265 DQMEYMLQNHVFPLFSSELGYMR ddPTM_BT-474_Pertuzumab_2h_R1 2 DQMEYMLQNHVFPLFSSELGYMR 23 0 O95373 O95373 IPO7 Importin-7 0 ; 122.39 6.58E-05 392710000 114747 93724 101548 123399 112138 111795 112363 107652 108028 153466 FALSE TRUE 110262.5604 91051.08329 119899.9825 129767.6372 115745.0206 114055.5715 113738.132 105428.9486 95765.11433 143071.6111 0.770680916 0.636402166 0.838041744 0.907011784 0.80900061 0.797192193 0.794973448 0.736896354 0.669350919 1 17.12637791 4.225945743 24.99928889 0.806843565 0.703541523 0.19854339 0.090203859 334.713856 663316.5893 0.022219007 0.048505539 16824.63856 -4.225945743 -0.103302042 SLSSS(ph)PDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSSSPDKR 9 1 Q9BVI0;Q5JWZ0;Q5JXL1;B0QYY0;Q9BVI0-2 Q9BVI0 PHF20 PHD finger protein 20 1 SLS(0.001)S(0.113)S(0.886)PDKR 93.843 0.0055891 343650000 221170 220240 163320 173940 181000 182470 185070 205480 224530 213410 TRUE FALSE 212526.4319 213958.9708 192835.557 182917.0642 186822.0294 186159.6684 187334.942 201236.7662 199042.2957 198955.5506 1.068210619 1.075410916 0.969239393 0.919386585 0.939013909 0.935684719 0.941591936 1.011465956 1.000436002 1 17.60208662 4.226178832 7.087609295 0.962651992 1.072297898 0.674581234 0.029770669 0.078793771 19.66147086 0.008290274 0.019527859 16833.67089 -4.226178832 0.109645906 AAEEEDEADPKR ddPTM_BT-474_Pertuzumab_2h_R1 5 AAEEEDEADPKR 12 1 P20962 P20962 PTMS Parathymosin 0 ;;;; 192.68 6.05E-06 8964670000 4165300 3982950 2893560 2777270 3259370 3288690 3037310 3777770 3781730 2993570 FALSE TRUE 4002515.471 3869360.166 3416490.659 2920605.238 3364210.596 3355189.565 3074481.508 3699757.729 3352443.865 2790812.838 1.434175527 1.386463511 1.224191968 1.046507024 1.205459052 1.202226649 1.101643746 1.325691813 1.201242813 1 21.41225394 4.226308258 3.535032775 1.17535836 1.421878856 0.559381235 0.088469354 0.167935435 4.379214977 0.022421558 0.06251556 16838.6883 -4.226308258 0.246520496 NS(ph)PVT(ph)KTPPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.997)PVT(0.577)KT(0.426)PPRDLPTIPGVTSPSSDEPPMEASQSHLR 157.33 4.52E-13 1641200000 275410 286060 141790 127550 132120 205070 136300 175630 205680 168090 TRUE FALSE 264646.6727 277901.8489 167414.6071 134132.8708 136369.7598 209216.6559 137968.0802 172003.1791 182332.0687 156705.1146 1.688819624 1.773406373 1.068341691 0.855957198 0.87023171 1.335097814 0.880431252 1.097623263 1.163536169 1 17.25769274 4.226329561 8.55333842 1.030703748 1.732289121 0.795877683 0.141238101 0.053651123 27.41191511 0.034655079 0.080089047 16839.51431 -4.226329561 0.701585373 YLNEYGAPDAGGLEHVPLGWSYWYALEK ddPTM_BT-474_Pertuzumab_2h_R1 2 YLNEYGAPDAGGLEHVPLGWSYWYALEK 28 0 H7C3P4;F6S8M0;P15586-2;P15586;F5H4C6 H7C3P4 GNS N-acetylglucosamine-6-sulfatase 0 ; 116.34 0.00030254 390840000 320990 337560 293290 355510 362780 339830 364880 379240 412610 410590 FALSE TRUE 308445.3559 327933.1193 346294.0272 373857.9137 374449.1482 346701.5954 369345.5106 371408.5615 365772.2426 382780.3736 0.805802432 0.856713515 0.904680728 0.976690394 0.978234972 0.905745486 0.964901902 0.970291549 0.955566868 1 18.54615733 4.226369823 1.713180168 0.962162456 0.806902843 0.834200183 0.024052351 0.161470555 0.846991364 0.006574403 0.029976281 16841.07549 -4.226369823 -0.155259614 EGILPER ddPTM_BT-474_Pertuzumab_2h_R1 2 EGILPER 7 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7;O43768-8 A6NMQ3 ENSA Alpha-endosulfine 0 ; 113.14 0.014418 390450000 435230 419510 435530 516820 484710 500200 497570 571850 544340 560190 FALSE TRUE 418220.7304 407545.9855 514239.9593 543493.1421 500301.1374 510314.3867 503659.4105 560041.0977 482548.8053 522247.8323 0.800808935 0.780368937 0.984666527 1.040680513 0.957976475 0.977149842 0.964406895 1.072366534 0.923984314 1 18.99437507 4.226423437 7.950498702 0.995811928 0.790069796 0.797357498 0.040166507 0.049352377 19.53971435 0.009899804 0.023041569 16843.15468 -4.226423437 -0.205742131 ELNS(ph)NHDGADETSEKEQQEAIEHIDEVQNEIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDR;ELNS(0.405)NHDGADET(0.298)S(0.298)EKEQQEAIEHIDEVQNEIDR;ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDR;ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDR 152.98 6.99E-11 8186410000 1565889 1134486 1505116 1567277 2133589 1709767 1834695 1271307 1792619 1939142 TRUE FALSE 1504692.327 1102131.57 1777123.942 1648164.354 2202217.828 1744339.66 1857148.546 1245054.066 1589128.406 1807802.185 0.832332397 0.609652748 0.983030089 0.911695078 1.218174115 0.964895205 1.027296328 0.688711451 0.879038879 1 20.78580539 4.22665011 24.98952892 0.945867053 0.72099256 0.329177091 0.134911567 247.4970143 519278.7277 0.03669814 0.080265915 16851.94799 -4.22665011 -0.224874493 RPQS(ph)PGAS(ph)PSQAER ddPTM_BT-474_Pertuzumab_2h_R1 1 RPQSPGASPSQAER 14 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 2 RPQS(1)PGAS(0.845)PS(0.155)QAER 88.945 0.022204 685250000 260830 246970 229500 287520 275750 266450 261910 262510 296100 289910 TRUE FALSE 250636.4752 239926.6574 270975.7552 302358.9417 284619.7492 271837.8016 265115.3329 257089.0768 262487.9694 270274.1375 0.927341689 0.88771593 1.002595948 1.118712077 1.053078004 1.005785474 0.980912696 0.951215973 0.97119159 1 18.04406394 4.226870451 19.78034519 1.009248932 0.90752895 0.452965167 0.045220789 15.9040889 26914.03907 0.013124205 0.028976699 16860.50006 -4.226870451 -0.101719982 VFDKEGNGTVMGAELR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFDKEGNGTVMGAELR 16 1 P08590;P05976-2;P05976 P08590 MYL3;MYL1 "Myosin light chain 3;Myosin light chain 1/3, skeletal muscle isoform" 0 ; 112.3 0.00068378 944250000 1295370 1447030 977940 1018570 1141130 1263330 1168070 1294930 1310080 1267730 FALSE TRUE 1244745.508 1405762.121 1154675.512 1071138.52 1177835.483 1288875.398 1182365.19 1268189.243 1161365.211 1181865.518 1.053204015 1.189443384 0.976993994 0.906311677 0.996590107 1.090543195 1.000422783 1.073040226 0.982654281 1 20.17263445 4.226873273 24.99996028 1.008544944 1.121323714 0.403873483 0.057064257 198.2933174 424164.4652 0.01480972 0.03241565 16860.60961 -4.226873273 0.11277877 SKGGVVGIKVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKGGVVGIKVDK 12 2 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 115.82 0.00051117 1912790000 1845240 1860490 994350 822090 1157370 1810320 900590 1113520 1201940 878690 FALSE TRUE 1773125.981 1807430.647 1174051.164 864518.1634 1194597.857 1846925.911 911611.6898 1090525.423 1065500.81 819175.5436 2.164525045 2.206402109 1.433210712 1.05535153 1.458292873 2.25461554 1.112840461 1.331247535 1.300699 1 19.64381312 4.226942005 6.928763523 1.385244414 2.189561943 0.491249124 0.332415279 0.109252319 25.17497904 0.083943081 0.198742958 16863.27822 -4.226942005 0.804317529 RLEDLSESIVNDFAYMK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLEDLSESIVNDFAYMK 17 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 125.18 7.66E-05 113150000 166440 213580 104710 126070 139810 123580 138040 129390 142660 117070 FALSE TRUE 159935.3408 207488.9075 123633.4263 132576.4878 144307.1156 126078.8723 139729.3748 126718.0513 126465.8349 109140.7446 1.465404523 1.901113175 1.13278892 1.214729552 1.322211206 1.155195273 1.280267743 1.161051738 1.15874081 1 16.73583027 4.226978179 25 1.193004039 1.683258863 0.712272457 0.128141931 88.63537773 191315.4295 0.028808122 0.063067667 16864.68287 -4.226978179 0.490254824 GGAGGSPGS(ph)SSGSGSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGAGGSPGSSSGSGSSR 17 0 Q8TAE6 Q8TAE6 PPP1R14C Protein phosphatase 1 regulatory subunit 14C 1 GGAGGS(0.204)PGS(0.643)S(0.135)S(0.017)GS(0.001)GSSR 84.842 0.0054373 11133000 13131 13371 13077 17805 16223 15719 14914 15032 15868 17327 TRUE FALSE 12617.826 12989.67217 15440.3048 18723.91818 16744.82753 16036.84895 15096.52199 14721.58395 14066.73116 16153.42686 0.78112379 0.804143436 0.955853203 1.159129784 1.036611468 0.992783085 0.934570858 0.911359805 0.870820247 1 13.97955264 4.227003551 4.619596742 0.982943305 0.787959713 0.517706247 0.073858837 0.1585073 8.378107796 0.020907598 0.053478246 16865.66815 -4.227003551 -0.194983592 LVASMEEARR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVASMEEARR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 107.79 0.0054758 0 46877 61479 26500 34529 34278 33356 33782 27320 28928 37836 FALSE TRUE 45044.99501 59725.67911 31289.13949 36311.04583 35380.583 34030.48117 34195.43422 26755.83245 25644.21472 35273.33402 1.277026861 1.693224663 0.887047974 1.029419159 1.003040512 0.964765087 0.969441511 0.758528594 0.7270142 1 15.10629032 4.227063445 24.99991014 0.912182578 1.48512575 0.740230028 0.13449688 89.18022958 193918.3374 0.033976946 0.074394244 16867.99427 -4.227063445 0.572943172 VLLS(ph)LLSIKMPITDADQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLLSLLSIKMPITDADQIR 19 1 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 VLLS(0.498)LLS(0.498)IKMPIT(0.004)DADQIR 47.392 0.084589 116020000 191220 209710 134860 140230 152220 171550 151350 166280 163680 171760 TRUE FALSE 183746.911 203729.2761 159232.2019 147467.2871 157116.2945 175018.8585 153202.2666 162846.2599 145099.7326 160126.5422 1.14751064 1.272301727 0.994414791 0.920942182 0.98120082 1.093003422 0.956757477 1.016984802 0.90615666 1 17.28885294 4.227114048 24.83998526 0.986037465 1.209906166 0.719216967 0.056524377 84.33665262 183018.7263 0.013595807 0.029777351 16869.95982 -4.227114048 0.223868701 DMPGGFLFEGLS(ph)DDEDDFHPNTR ddPTM_BT-474_Pertuzumab_2h_R1 7 DMPGGFLFEGLSDDEDDFHPNTR 23 0 H3BUV9;Q96S82 H3BUV9 UBL7 Ubiquitin-like protein 7 1 DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR 349.24 9.09E-102 3323530000 1698630 1823970 1551184.4 1961204 1973563 2068317 1956932 1822078 2135484 2206437 TRUE FALSE 1632245.662 1771952.161 1831517.927 2062421.973 2037044.446 2110139.787 1980881.519 1784451.453 1893072.809 2056993.057 0.793510535 0.861428363 0.890386052 1.002639249 0.990302053 1.025837097 0.962998642 0.86750485 0.920310743 1 20.97210549 4.227295799 1.952997265 0.958496689 0.804856921 0.606099706 0.045675713 0.302341736 2.153489276 0.014356238 0.058246798 16877.02132 -4.227295799 -0.153639768 GGNLPPVS(ph)PNDSGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGNLPPVSPNDSGAK 15 0 Q9UK61-3;Q9UK61;Q9UK61-2;A0A087X0F1;Q9UK61-4 Q9UK61-3 FAM208A Protein FAM208A 1 GGNLPPVS(1)PNDSGAK;GGNLPPVS(1)PNDSGAK 158.91 1.88E-06 278100000 323670 302591 275604 303289 318120 317193 303908 344785 358615 347656 TRUE FALSE 311020.6186 293961.4009 325411.7736 318941.7816 328352.6187 323606.8598 307627.317 337665.0693 317906.5286 324108.9495 0.959617496 0.906983289 1.00401971 0.984057312 1.013093342 0.998450861 0.949147864 1.041825811 0.980863161 1 18.30611933 4.227296715 24.98305146 0.997942075 0.933300392 0.496543146 0.025391552 138.9731442 308241.1071 0.006053419 0.013267949 16877.05692 -4.227296715 -0.064641683 ERPQDRPEDLDVPPALADFIHQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPQDRPEDLDVPPALADFIHQQR 24 2 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 ; 185.28 1.44E-17 121694000 78254 77611 71642 89643 84158 88712 87368 79395 86915 88699 FALSE TRUE 75195.74717 75397.61027 84589.30307 94269.48597 86865.0185 90505.81742 88437.23572 77755.4655 77048.77358 82691.33773 0.909354586 0.91179575 1.022952408 1.140016458 1.050473011 1.094501793 1.069486093 0.940309682 0.93176354 1 16.33544859 4.227313917 5.829819475 1.03336497 0.909236907 0.387709782 0.060689329 0.163780557 19.04823591 0.016969816 0.041281664 16877.72541 -4.227313917 -0.124128063 QPASAQSTPS(ph)TTPHSSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPASAQSTPSTTPHSSPK 18 0 A0A087WT18;Q96A73-2;Q96A73 A0A087WT18 KIAA1191 Putative monooxygenase p33MONOX 1 QPASAQS(0.001)T(0.038)PS(0.192)T(0.192)T(0.192)PHS(0.192)S(0.192)PK 65.225 0.056526 36495000 9724.1 9411 12498 14573 12732 17239 19851 11372 14303 18513 TRUE FALSE 9344.071421 9142.607494 14756.66662 15325.11428 13141.53634 17587.58439 20093.94248 11137.16423 12679.3834 17259.09802 0.541399754 0.529726842 0.855007985 0.887944101 0.761426601 1.01903265 1.164252179 0.645292368 0.734649249 1 14.07506945 4.227314958 6.372436194 0.875233224 0.533068203 0.48432282 0.143460583 0.122108321 20.08811103 0.037664399 0.090307222 16877.76586 -4.227314958 -0.342165021 AFYPEEISSMVLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 AFYPEEISSMVLTK 14 0 A0A0G2JIW1;P0DMV9;P0DMV8;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 138.45 3.05E-05 0 56839 67019 40805 48657 51012 50860 44981 55530 53932 54547 FALSE TRUE 54617.66904 65107.68374 48179.3712 51168.1936 52652.84731 51888.42405 45531.49093 54383.28609 47809.86546 50852.4831 1.074041339 1.280324573 0.947433995 1.006208359 1.035403664 1.020371492 0.895364162 1.069432263 0.940167766 1 15.6340306 4.227476571 24.99999936 0.994058506 1.177182975 0.559303073 0.066604048 123.5307525 278624.8465 0.015263198 0.033459144 16884.04773 -4.227476571 0.183124469 AS(ph)PNPVAMETR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPNPVAMETR 11 0 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 AS(1)PNPVAMETR;AS(1)PNPVAMETR 176.56 8.93E-06 570250000 229690 259310 159485 177858 195457 190796 188853 190393 201355 199421 TRUE FALSE 220713.4609 251914.7327 188307.4872 187037.2727 201744.0519 194654.0258 191164.2395 186461.318 178498.0245 185914.038 1.187180178 1.355006515 1.012873956 1.006041688 1.085146953 1.047010908 1.028239941 1.002943726 0.960110524 1 17.50427618 4.227637555 24.99986808 1.020500696 1.271093342 0.812556281 0.048649179 68.29030957 156298.7341 0.011620017 0.025489307 16890.30746 -4.227637555 0.250592646 S(ph)PDEVTLTSIVPTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPDEVTLTSIVPTR 14 0 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 S(1)PDEVTLTSIVPTR;S(0.999)PDEVT(0.001)LTSIVPTR;S(1)PDEVTLTSIVPTR 248.61 5.98E-18 398867000 76742 73325 81857 105768 81501 89567 97924 103158 102406 121787 TRUE FALSE 73742.8378 71233.84279 96650.3808 111226.6992 84122.55368 91378.10611 99122.4232 101027.7513 90781.3002 113538.258 0.649497703 0.627399469 0.851258267 0.979640705 0.740918129 0.80482216 0.873031038 0.889812412 0.79956573 1 16.79281899 4.227703828 8.461533846 0.862753631 0.638011894 0.599597483 0.074761275 0.081809895 42.86159629 0.017943914 0.041706244 16892.88509 -4.227703828 -0.224741737 TIPWLEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 TIPWLEDR 8 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;; 188.98 0.00045163 364120000 238328 224590 300918 470790 302057 241165 351422 393273 392044 452970 FALSE TRUE 229013.8783 218184.9131 355300.5765 495087.5283 311772.9377 246041.5215 355722.8076 385151.7751 347540.8087 422289.9384 0.542314314 0.516670878 0.841366427 1.172387697 0.738291182 0.582636476 0.842366287 0.912055297 0.822990976 1 18.68787435 4.227728465 7.947830157 0.859490279 0.528581492 0.455430167 0.146276495 0.114355387 47.18659457 0.038030984 0.088903844 16893.84343 -4.227728465 -0.330908786 VPLAPITDPQQLQLS(ph)PLKGLSLVDKENTPPALSGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPLAPITDPQQLQLSPLKGLSLVDKENTPPALSGTR 36 2 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 VPLAPITDPQQLQLS(1)PLKGLSLVDKENTPPALSGTR 138.18 8.87E-10 210340000 213080 226400 74674 65908 96295 133630 66338 78972 57758 48111 TRUE FALSE 204752.598 219943.2937 88169.25291 69309.51978 99392.41613 136332.0902 67149.86429 77341.2006 51201.55398 44852.39912 4.565031126 4.903713023 1.965764477 1.5452801 2.215988845 3.039571859 1.497129822 1.724349246 1.141556639 1 15.45289754 4.227803633 9.029963847 1.822937099 4.738293902 0.822051028 0.551904494 0.052813258 34.57741368 0.139153152 0.321850386 16896.7677 -4.227803633 2.915356803 RKHSPS(ph)PPPPTPTESR ddPTM_BT-474_Pertuzumab_2h_R1 1 RKHSPSPPPPTPTESR 16 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 RKHS(0.44)PS(0.56)PPPPTPTESR 92.977 0.0023942 64378000 42173 46225 30067 30070 34886 41514 31549 35458 43067 38056 TRUE FALSE 40524.83254 44906.70826 35500.77574 31621.9163 36008.13987 42353.44152 31935.1061 34725.77991 38178.21471 35478.43322 1.142238505 1.265746657 1.000629749 0.891299684 1.014930384 1.19377993 0.900127294 0.97878561 1.076096412 1 15.11465468 4.227864074 24.99703929 1.002137044 1.203992576 0.458201158 0.085575019 155.6455787 363735.1008 0.021523631 0.047261807 16899.11937 -4.227864074 0.201855532 IFDSEEILAGYK ddPTM_BT-474_Pertuzumab_2h_R1 2 IFDSEEILAGYK 12 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 96.113 0.0040214 56052000 250820 241410 242880 292380 245300 293640 315380 282630 312560 315160 FALSE TRUE 241017.6771 234525.2232 286773.8188 307469.7668 253190.2973 299577.602 319239.7148 276793.5917 277079.4992 293813.9325 0.820307176 0.798210014 0.976038871 1.046477831 0.861736866 1.019616733 1.08653702 0.942071022 0.943044112 1 18.16454328 4.227916226 9.508152248 0.984737383 0.809083237 0.58642689 0.058847143 0.102046629 77.7734564 0.014633811 0.03373361 16901.14881 -4.227916226 -0.175654146 DDLYAEQMER ddPTM_BT-474_Pertuzumab_2h_R1 1 DDLYAEQMER 10 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 145.25 7.16E-05 697510000 153090 154340 150240 171680 174420 182220 180870 192790 185650 187210 FALSE TRUE 147107.0736 149938.3743 177391.7101 180540.4254 180030.3777 185904.6132 183083.5412 188808.8191 164575.7903 174530.1 0.842875089 0.85909751 1.016396084 1.034437185 1.03151478 1.065172216 1.049008402 1.081812359 0.942965084 1 17.41311634 4.228060655 3.973995418 1.037376038 0.84467231 0.789659244 0.036401569 0.078313644 2.724741118 0.008978814 0.02405647 16906.7704 -4.228060655 -0.192703728 DQGTYEDYVEGLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DQGTYEDYVEGLR 13 0 F8VPF3;H0YI43;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;; 260.22 1.22E-23 5572670000 3047050 3124850 3159090 3936840 3483540 3350660 3899920 4176800 4157350 4401080 FALSE TRUE 2927967.917 3035732.338 3730007.837 4140020.784 3595591.228 3418412.641 3947648.388 4090547.62 3685425.057 4102990.932 0.713617935 0.73988278 0.909094828 1.009025088 0.876334188 0.833151401 0.962139194 0.996967258 0.898228906 1 21.96824453 4.228071677 4.02195294 0.938766828 0.71940829 0.706607749 0.054236581 0.109397022 3.926934615 0.014419467 0.03848258 16907.19948 -4.228071677 -0.219358539 AGSNEDPILAPSGT(ph)PPPTIPPDETFGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.02)GT(0.979)PPPT(0.001)IPPDETFGGR;AGSNEDPILAPS(0.226)GT(0.773)PPPT(0.001)IPPDETFGGR 107.6 0.003008 353260000 490320 496760 429330 543620 495110 491680 511710 514760 557680 572180 TRUE FALSE 471157.7523 482592.8912 506919.4814 571676.2933 511035.6628 501622.1065 517972.46 504130.0261 494374.5044 533425.739 0.88326775 0.904704921 0.950309376 1.071707365 0.95802588 0.940378519 0.971030121 0.945080054 0.926791619 1 19.02492791 4.228128677 3.793193695 0.970077126 0.890397774 0.394409813 0.038688653 0.221935165 6.863009747 0.010127644 0.02757402 16909.41866 -4.228128677 -0.079679352 FASEAEDKIR ddPTM_BT-474_Pertuzumab_2h_R1 1 FASEAEDKIR 10 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 86.014 0.012628 704150000 541560 613480 416050 470070 525510 502530 511980 547100 572150 557770 FALSE TRUE 520395.2365 595984.1511 491239.49 494330.369 542413.5064 512691.5009 518245.7644 535802.1938 507201.9306 519991.7411 1.000775965 1.146141571 0.944706331 0.950650424 1.043119464 0.985960854 0.996642299 1.0304052 0.97540382 1 18.98812918 4.228150683 24.99996595 0.994379084 1.073458788 0.361727553 0.043687904 189.8127913 455848.0355 0.010419357 0.022888839 16910.27548 -4.228150683 0.079079705 STGVVNIPAAECLDEYEDDEAGQKER ddPTM_BT-474_Pertuzumab_2h_R1 2 STGVVNIPAAECLDEYEDDEAGQKER 26 1 Q96IZ0;H0YI16 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 0 ; 141.5 2.71E-07 254785000 150893 160570 112370 110452 138264 140613 121632 137979 166683 131930 FALSE TRUE 144995.9347 155990.7008 132677.7587 116152.441 142711.3871 143456.2912 123120.5688 135129.6854 147761.8446 122994.2636 1.178883718 1.268276229 1.078731274 0.944372831 1.160309294 1.166365707 1.00102692 1.098666568 1.201371839 1 16.9082315 4.228159671 24.99189928 1.082392913 1.223579972 0.335758032 0.080006685 200.5457791 481885.0609 0.019741753 0.043393536 16910.62547 -4.228159671 0.141187059 EEEELNLPIS(ph)PEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EEEELNLPISPEEER 15 0 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 EEEELNLPIS(1)PEEER;EEEELNLPIS(1)PEEER 263.47 4.84E-25 185585000 207750 232350 242470 316420 279710 267800 268790 473000 247450 263110 TRUE FALSE 199630.9003 225723.6055 286289.7227 332750.4741 288707.1262 273215.0995 272079.5324 463232.3847 219360.5134 245289.3253 0.813858899 0.920234116 1.167151169 1.356563208 1.177006483 1.113848306 1.109218805 1.888514244 0.894292946 1 17.90412493 4.228171719 2.399707056 1.281124768 0.824322532 0.203760572 0.259446922 0.400508609 4.497383548 0.070748861 0.244220445 16911.09459 -4.228171719 -0.456802236 TTTELFHSNEESGFFNELEALR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTTELFHSNEESGFFNELEALR 22 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ; 251.12 5.35E-32 264750000 109362 117597 98366 129333 127131 128569 120807 115338 129060 148376 FALSE TRUE 105088.0121 114243.2487 116142.9243 136007.8916 131220.2841 131168.7533 122285.4722 112956.23 114409.6499 138326.3614 0.759710666 0.825896435 0.839629722 0.983239133 0.948628177 0.948255647 0.884035921 0.816592216 0.827099396 1 17.0777166 4.228201448 2.250180694 0.902983205 0.776069639 0.402116705 0.059983491 0.379741053 3.709627687 0.017450947 0.063161817 16912.25227 -4.228201448 -0.126913566 NRQEITDKDHTVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NRQEITDKDHTVSR 14 2 Q13464;A0A0U1RQV4 Q13464 ROCK1 Rho-associated protein kinase 1 0 ; 103.21 0.00067794 263440000 121463 136571 88317 102701 99439 114813 109737 107992 115361 109056 FALSE TRUE 116716.0917 132676.1288 104277.8465 108001.4109 102637.5457 117134.5975 111079.9942 105761.9275 102265.7029 101669.54 1.147994686 1.304974222 1.025654749 1.062278938 1.009521099 1.152111021 1.092559229 1.040251854 1.005863732 1 16.63352799 4.228202278 24.99993746 1.054270032 1.226484463 0.61367935 0.056329925 113.0807586 272923.4428 0.013535131 0.029758478 16912.28459 -4.228202278 0.172214431 IKIGDPLLEDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKIGDPLLEDTR 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 101.75 0.0022739 458990000 1242980 1432050 856410 917640 972970 978200 1106550 1128920 1175330 1029000 FALSE TRUE 1194402.967 1391209.336 1011182.338 964999.5104 1004266.464 997979.8742 1120092.29 1105607.407 1041911.466 959304.9135 1.24507125 1.450226426 1.054078139 1.00593617 1.046868883 1.040315608 1.167608207 1.152508855 1.08611084 1 19.87162992 4.228276854 24.99997024 1.079536145 1.347648844 0.714783829 0.070118314 97.61945009 237316.0993 0.018256389 0.040137514 16915.18899 -4.228276854 0.268112698 GTLTLCPYHSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 GTLTLCPYHSDR 12 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 147.24 6.54E-05 1515950000 1020970 1263500 625330 850410 785730 697310 782120 691830 786210 884550 FALSE TRUE 981069.3637 1227466.217 738341.0414 894299.762 811003.719 711410.086 791691.8185 677543.4687 696962.7369 824638.6406 1.189696087 1.488489814 0.895351012 1.084474724 0.98346558 0.862693125 0.960046958 0.821624692 0.845173513 1 19.65340254 4.228290664 24.99992851 0.926108433 1.339092956 0.722290595 0.101022431 87.06989622 211954.049 0.02508606 0.055148883 16915.72688 -4.228290664 0.412984522 FSFSPEPTLEDIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSFSPEPTLEDIRR 14 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ; 203.85 2.32E-08 1357620000 345540 375930 265590 318920 306230 316750 334660 323620 346580 351300 FALSE TRUE 332035.9148 365208.8445 313588.021 335379.4994 316080.1661 323154.902 338755.6692 316937.1339 307237.6914 327506.1381 1.01383112 1.11512061 0.957502729 1.024040347 0.96511219 0.986714032 1.034349069 0.967728836 0.938112773 1 18.32116242 4.228337359 24.9999637 0.985579738 1.064475875 0.442442002 0.036021795 153.6280709 375684.9727 0.008464069 0.01860276 16917.54574 -4.228337359 0.078896137 KQDPPVTHDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQDPPVTHDLR 11 1 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 139.46 2.54E-05 1608630000 813760 690540 747330 854280 867440 747220 871980 849860 1000820 1030340 FALSE TRUE 781957.3595 670846.4753 882389.1553 898369.4932 895341.9954 762329.3004 882651.5521 832310.094 887211.1094 960554.1541 0.814069 0.698395267 0.918625099 0.935261681 0.932109857 0.7936349 0.918898272 0.866489506 0.923645071 1 19.87350743 4.228390736 24.99861024 0.902385707 0.75623213 0.539074609 0.05682143 131.252855 322635.5479 0.013462287 0.02961574 16919.62512 -4.228390736 -0.146153578 NDTKEDVFVHQTAIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDTKEDVFVHQTAIKK 16 2 P67809;P16989;P16989-3;P16989-2 P67809;P16989;P16989-2 YBX1;YBX3 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3 0 143.14 8.65E-07 1006400000 1163700 1172500 745790 645530 813130 1081600 861780 787070 1127600 932120 FALSE TRUE 1118221.317 1139061.448 880570.843 678845.8807 839285.0649 1103470.693 872326.7214 770816.7295 999599.5753 868986.6822 1.28681065 1.310792756 1.013330654 0.781192502 0.9658204 1.269836139 1.003843602 0.887029393 1.150304827 1 19.72897454 4.22852642 8.211621998 0.998177822 1.299526995 0.458181214 0.125675222 0.106473722 51.45245923 0.032659259 0.076329015 16924.91201 -4.22852642 0.301349173 NLAPDEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLAPDEKR 8 1 O95232;J3KPP4;D6RDI2;C9JL41;O95232-2;E7EN55 O95232 LUC7L3 Luc7-like protein 3 0 ; 97.741 0.012854 1071160000 1136150 1263880 853830 921720 916220 1128980 1029740 1080270 1271510 1146020 FALSE TRUE 1091748.002 1227835.38 1008136.074 969290.0797 945691.0484 1151808.749 1042342.266 1057962.047 1127173.515 1068399.045 1.021854154 1.1492292 0.943595073 0.907236004 0.885147786 1.078069804 0.97561138 0.99023118 1.055011722 1 20.02701916 4.228638096 24.99973303 0.977138578 1.085541688 0.312844063 0.062875908 206.8526543 521168.5831 0.015916447 0.035044401 16929.26471 -4.228638096 0.108403111 DSFDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSFDDR 6 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 99.279 0.090682 343620000 632390 629220 676100 841070 744900 676280 825600 860460 898980 978050 FALSE TRUE 607675.4997 611275.2617 798286.3098 884477.7235 768860.385 689954.845 835703.9398 842691.2003 796931.5592 911805.8023 0.666452767 0.670400715 0.875500362 0.970028619 0.843228221 0.756690562 0.916537203 0.924200305 0.874014573 1 19.79836706 4.228724531 5.661863397 0.89199609 0.665694004 0.670498678 0.063600984 0.087553668 9.200290496 0.016127059 0.039577412 16932.6344 -4.228724531 -0.226302086 LMFNSPGFVEYVVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LMFNSPGFVEYVVDR 15 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 151.54 6.95E-06 213424000 115731 137176 87804 102198 118994 94195 121339 126680 104505 121095 FALSE TRUE 111208.1046 133263.8748 103672.136 107472.451 122821.5501 96099.68744 122823.983 124064.0137 92642.03052 112893.1278 0.985074174 1.180442755 0.918321053 0.951983997 1.08794532 0.851244795 1.087966871 1.098950983 0.820617095 1 16.78459814 4.228764172 24.99975257 0.99071975 1.082758488 0.134992433 0.10243272 381.2157259 972840.5724 0.025049773 0.055195503 16934.18 -4.228764172 0.092038738 LPT(ph)PTSSVPAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPTPTSSVPAQK 12 0 Q9BTA9-2;Q9BTA9;Q9BTA9-3 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 LPT(0.969)PT(0.025)S(0.003)S(0.003)VPAQK 94.122 0.005472 0 191410 193620 167740 196750 191090 208150 190100 214880 214200 218140 TRUE FALSE 183929.4856 188098.1472 198054.3494 206904.2911 197236.5834 212358.9356 192426.5007 210442.6529 189884.914 203365.1835 0.904429571 0.924927974 0.973885234 1.017402721 0.969864064 1.04422464 0.946211625 1.034801775 0.933713976 1 17.63371318 4.228767656 2.704472564 0.994758678 0.907835229 0.454650248 0.033711812 0.208616634 3.022325154 0.007843946 0.02505885 16934.31584 -4.228767656 -0.086923449 IMSS(ph)IGEGIDFSQER ddPTM_BT-474_Pertuzumab_2h_R1 6 IMSSIGEGIDFSQER 15 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 IMS(0.005)S(0.995)IGEGIDFSQER;IMS(0.003)S(0.997)IGEGIDFSQER;IMSS(1)IGEGIDFSQER;IMSS(1)IGEGIDFSQER;IMS(0.016)S(0.984)IGEGIDFSQER;IMS(0.001)S(0.999)IGEGIDFSQER 366.02 2.10E-97 935584000 1568230 1499870 1080778 1070876 1170055 1036195 802941 1066339 939919 927842 TRUE FALSE 1506941.838 1457095.176 1276098.626 1126144.039 1207690.882 1057147.573 812767.6321 1044318.727 833223.3356 864998.4349 1.742132444 1.684506142 1.475261197 1.301902978 1.396176956 1.222138134 0.93961746 1.207307071 0.963265715 1 19.722338 4.228805523 0.386059397 0.982657638 2.155635741 0.884865508 0.091725377 1.225488381 0.194422707 0.081790794 0.646037301 16935.79246 -4.228805523 1.172978103 YDLDFKSPDDPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDLDFKSPDDPSR 13 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 74.678 0.030511 789700000 3110900 3041800 1516260 1410810 1623910 2159280 1494390 1655300 2104620 1509270 FALSE TRUE 2989322.589 2955050.842 1790281.911 1483622.073 1676144.54 2202942.121 1512678.792 1621117.477 1865712.361 1407045.799 2.124538229 2.100180993 1.272369324 1.054423441 1.191250876 1.565650616 1.075074311 1.152142651 1.325978417 1 20.42423786 4.228856116 5.340295762 1.203341013 2.125853541 0.85209927 0.151531407 0.052760301 4.49132289 0.037521787 0.093154153 16937.76552 -4.228856116 0.922512528 S(ph)SSPAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.259)S(0.259)S(0.224)PAGET(0.259)EGDREPQARPGEGTAPLPPPGQK;S(0.328)S(0.328)S(0.328)PAGET(0.016)EGDREPQARPGEGTAPLPPPGQK;S(0.328)S(0.328)S(0.328)PAGET(0.015)EGDREPQARPGEGTAPLPPPGQK;S(0.333)S(0.333)S(0.333)PAGET(0.001)EGDREPQARPGEGTAPLPPPGQK 156.7 1.01E-09 4817840000 1229944 1279040 912504 939429 995645 1198554 1009424 1148407 1132864 1149383 TRUE FALSE 1181876.429 1242563.032 1077413.771 987913.0433 1027670.826 1222789.583 1021777.633 1124691.994 1004266.028 1071534.266 1.10297586 1.159611103 1.005486997 0.921961224 0.959064828 1.141157705 0.953565057 1.049608986 0.937222504 1 20.03124655 4.228886846 23.99626733 0.99935849 1.131293474 0.435468949 0.06151887 97.36473622 241521.6306 0.015108902 0.033350784 16938.96403 -4.228886846 0.131934983 GPLS(ph)PFNSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPLSPFNSR 9 0 A1L390-3;A1L390;A0A0U1RR71;G3V3I3;G3V278 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 GPLS(1)PFNSR;GPLS(1)PFNSR 105.94 0.0031637 876770000 1394590 1326070 1208210 1341630 1364080 1409210 1378040 1581590 1498160 1538050 TRUE FALSE 1340087.881 1288251.782 1426560.423 1410871.685 1407956.872 1437705.192 1394904.866 1548929.614 1328095.158 1433876.504 0.934590864 0.898439844 0.994897692 0.983956207 0.981923386 1.002670166 0.972820785 1.080239205 0.926227018 1 20.45148934 4.228894622 24.38364454 0.998552761 0.916515357 0.397352627 0.037069225 115.7902516 292098.5362 0.009243966 0.020393863 16939.26733 -4.228894622 -0.082037403 LEETDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEETDRR 7 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQL2;A0A0U1RQJ6;A0A0U1RRJ7 P47897 QARS Glutamine--tRNA ligase 0 ; 152.41 0.0029109 1601320000 1415290 1537340 1303740 1667120 1622490 1685070 1709050 1618460 1787440 1951810 FALSE TRUE 1359978.902 1493496.568 1539354.82 1753160.263 1674678.864 1719143.27 1729965.865 1585038.235 1584537.305 1819612.17 0.747400421 0.820777412 0.845979624 0.963480181 0.920349342 0.944785542 0.95073329 0.871085752 0.870810457 1 20.79519956 4.228896464 1.707971717 0.924003691 0.754938364 0.690740803 0.040399549 0.256185579 1.332317067 0.011274037 0.051812366 16939.33918 -4.228896464 -0.169065327 KSLS(ph)PGVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSLSPGVSR 9 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KS(0.001)LS(0.995)PGVS(0.004)R 97.957 0.0038829 209960000 407800 428070 303970 306200 341250 418770 356030 351490 404310 369670 TRUE FALSE 391862.7252 415861.8627 358904.1408 322003.0187 352226.6162 427237.8163 360387.2016 344231.6087 358414.4238 344631.9216 1.137047094 1.206684107 1.041412934 0.934338924 1.022037119 1.239693103 1.045716253 0.998838433 1.039991949 1 18.39469681 4.228910282 24.88279015 1.040927506 1.171865599 0.326658342 0.075578431 199.7323421 515002.0136 0.019956905 0.044008633 16939.87814 -4.228910282 0.130938093 QGSITS(ph)PQANEQSVT(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 4 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGSITS(1)PQANEQSVT(1)PQR;QGSIT(0.007)S(0.993)PQANEQSVT(1)PQR;QGSIT(0.001)S(0.999)PQANEQSVT(1)PQR;QGSIT(0.01)S(0.99)PQANEQS(0.174)VT(0.826)PQR 271.42 3.67E-27 320818000 625766 648155 698770 906042 789747 718417 868607 930320 887315 990527 TRUE FALSE 601310.3729 629670.254 825053.2831 952802.9362 815149.9295 732943.884 879237.2723 911108.5669 786590.7211 923437.724 0.651165051 0.681876252 0.893458499 1.031799884 0.882734058 0.793712304 0.952134886 0.986648632 0.851807004 1 19.81665514 4.228914273 4.211226036 0.927988846 0.658359338 0.700167429 0.06784355 0.104140748 4.231798841 0.017524043 0.046166881 16940.03383 -4.228914273 -0.269629508 GPGGSQGSQGPS(ph)PQGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPGGSQGSQGPSPQGAR 17 0 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 1 GPGGSQGSQGPS(1)PQGAR;GPGGSQGSQGPS(1)PQGAR;GPGGSQGS(0.005)QGPS(0.995)PQGAR;GPGGSQGS(0.006)QGPS(0.994)PQGAR 338.82 2.47E-72 641488000 478542 512109 470467 599387 549920 658415 583050 567902 633561 640654 TRUE FALSE 459840.0496 497504.1527 555490.8524 630321.4349 567608.6762 671728.6024 590185.5403 556174.6252 561641.8114 597261.9339 0.76991354 0.832974821 0.930062374 1.055351763 0.950351335 1.124680085 0.988151943 0.93120722 0.94036097 1 19.18800425 4.228950192 2.36721128 0.994667126 0.779612497 0.669749268 0.055265724 0.185170576 2.018799859 0.015181217 0.052984433 16941.43493 -4.228950192 -0.215054629 ERFS(ph)PPRHELS(ph)PPQKR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERFSPPRHELSPPQKR 16 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR 139.95 2.51E-06 13386600000 1564080 1658310 1125830 1133180 1259360 1562560 1309300 1306670 1415220 1346500 TRUE FALSE 1502954.024 1611016.622 1329292.525 1191663.556 1299868.458 1594156.034 1325323.605 1279686.808 1254570.159 1255300.356 1.197286385 1.283371438 1.058943797 0.949305519 1.035503935 1.26993992 1.055782068 1.019426787 0.999418309 1 20.25960117 4.228957078 24.69645372 1.05173165 1.240328907 0.46141876 0.082824814 137.394101 353326.2039 0.021708859 0.047883734 16941.70354 -4.228957078 0.188597258 EAVVDLHADDSRIS(ph)EDETER ddPTM_BT-474_Pertuzumab_2h_R1 3 EAVVDLHADDSRISEDETER 20 1 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.004)RIS(0.996)EDETER;EAVVDLHADDS(0.064)RIS(0.936)EDETER;EAVVDLHADDS(0.009)RIS(0.991)EDETER 284.9 3.01E-45 3430130000 959160 982810 947640 1194130 1173960 1152690 1140660 1094510 1182090 1271470 TRUE FALSE 921674.9668 954781.2211 1118899.628 1255759.192 1211721.49 1175998.182 1154619.738 1071907.986 1047904.099 1185352.204 0.777553678 0.805483145 0.943938539 1.059397526 1.022245949 0.992108655 0.974073135 0.904294928 0.884044502 1 20.17688436 4.228966686 3.928008831 0.972815042 0.784603286 0.692155305 0.048770682 0.126671965 4.279875574 0.014041911 0.037823296 16942.07835 -4.228966686 -0.188211755 MPARAS(ph)PPHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 MPARASPPHSK 11 1 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 MPARAS(0.999)PPHS(0.001)K;MPARAS(1)PPHSK 107.35 0.001338 602800000 382940 425790 257140 235120 305660 342020 303320 311180 340000 314500 TRUE FALSE 367974.2814 413646.8861 303610.918 247254.5714 315491.8315 348935.8787 307032.1209 304754.0243 301404.6254 293198.6349 1.255034088 1.410807681 1.035512727 0.843300555 1.076034449 1.190100625 1.047181277 1.039411471 1.02798782 1 18.16151886 4.229219728 24.99958844 1.035244061 1.332920886 0.65494892 0.087220519 103.5309102 277088.5979 0.022577708 0.049830414 16951.95255 -4.229219728 0.297676825 DCVGPEVEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DCVGPEVEK 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;; 124.92 0.0012006 3971800000 5595790 5461840 3410880 3901980 3430080 3631570 3796830 4262010 4869600 3667330 FALSE TRUE 5377100.34 5306073.671 4027301.891 4103361.655 3540411.638 3705002.834 3843296.741 4173998.004 4316823.423 3418938.473 1.572739721 1.551965241 1.177939271 1.200185873 1.035529497 1.08367052 1.12411989 1.220846189 1.262620974 1 21.70511703 4.229334646 4.55000249 1.143122888 1.572327346 0.829078886 0.077203991 0.070173251 3.55925119 0.020082849 0.051804774 16956.43879 -4.229334646 0.429204458 KQQMGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQQMGK 6 1 P31946-2;P31946;Q4VY19;A0A0J9YWE8;A0A0J9YWZ2 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ; 110.54 0.04589 3616300000 3600000 3760800 2647000 2856800 3078600 2574200 3722000 3209800 2845800 3732100 FALSE TRUE 3459308.02 3653545.666 3125371.782 3004239.79 3177625.965 2626252.088 3767550.949 3143516.508 2522756.715 3479321.543 0.994247866 1.050074166 0.898270466 0.863455635 0.913288963 0.754817299 1.082840693 0.903485484 0.72507145 1 21.73037458 4.229370568 23.89193028 0.894607522 1.022161013 0.215130944 0.09889037 147.5379124 383570.072 0.023966476 0.053041405 16957.84134 -4.229370568 0.127553491 LLKGEGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLKGEGPK 8 1 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 86.624 0.018173 0 1575700 1430000 1103500 1022300 1260300 881970 1225600 1274700 1382700 1138400 FALSE TRUE 1514119.902 1389217.8 1302926.997 1075061.026 1300838.694 899804.0377 1240599.259 1248377 1225741.693 1061295.154 1.426671832 1.308983457 1.227676384 1.012970823 1.225708691 0.847835811 1.168948388 1.176276924 1.154948921 1 20.01739451 4.229520166 1.776007683 1.096735128 1.418424073 0.535573102 0.107102727 0.327273801 1.867204376 0.028823109 0.127890265 16963.6837 -4.229520166 0.321688945 SAS(ph)LETK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASLETK 7 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 SAS(0.999)LETK;S(0.01)AS(0.99)LETK 64.841 0.07574 472330000 797930 845300 560120 521880 694830 673730 698480 602530 776100 722170 TRUE FALSE 766746.0134 821192.8716 661346.1438 548814.2893 717179.838 687353.2822 707028.2072 590087.5449 688000.3817 673256.7827 1.138861179 1.219732044 0.982308921 0.815163402 1.065239677 1.020937776 1.050161284 0.876467286 1.021898924 1 19.36079733 4.229602497 24.17289334 0.972142714 1.179296611 0.5257135 0.075865873 81.50427687 219937.2966 0.0190117 0.042093903 16966.89989 -4.229602497 0.207153896 TLDS(ph)DEERPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLDSDEERPR 10 1 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 TLDS(1)DEERPR;TLDS(1)DEERPR 212.9 1.94E-08 1316220000 999610 928600 938740 1226000 1005400 950410 1139070 1141110 1219240 1344200 TRUE FALSE 960544.1361 902117.2372 1108391.2 1289274.007 1037739.604 969627.9414 1153010.279 1117545.68 1080836.987 1253156.137 0.766499966 0.719876168 0.884479729 1.028821524 0.828100804 0.773748708 0.920085092 0.891784868 0.862491876 1 20.25713475 4.229613099 21.27698349 0.893626781 0.743188049 0.429581725 0.071484728 25.60391319 60890.5337 0.017864106 0.039786182 16967.31409 -4.229613099 -0.150438732 EQGVTFPSGDIQEQLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQGVTFPSGDIQEQLIR 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 290.87 1.29E-45 691100000 446827 483330 498004 643760 577030 595590 669280 629950 648700 702600 FALSE TRUE 429364.5068 469545.9016 588004.4008 676984.5307 595590.694 607633.2379 677470.8488 616941.3124 575062.2956 655012.2762 0.655506045 0.716850537 0.897699818 1.033544798 0.909281727 0.927666946 1.034287255 0.94187748 0.877941249 1 19.32116242 4.229693146 2.956820051 0.959048016 0.666660183 0.832922033 0.048756843 0.089657909 1.571057393 0.012245368 0.037247499 16970.44168 -4.229693146 -0.292387833 ATGEGFVEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATGEGFVEFR 10 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 77.533 0.076106 169360000 212840 236660 244880 307160 284710 436340 269650 315620 338200 261030 FALSE TRUE 204521.9775 229910.6885 289135.2633 323012.5644 293867.9557 445163.0938 272950.0574 309102.3367 299808.9539 243350.2056 0.840443003 0.944772937 1.188144726 1.327356858 1.207592798 1.829310531 1.121634792 1.270195503 1.232006166 1 17.89267447 4.229722668 2.117824377 1.302951392 0.841510711 0.36520249 0.204503021 0.338921873 2.895447827 0.05294721 0.201548652 16971.59534 -4.229722668 -0.461440681 QDTVSEPVTPASLAALQSDVQPVGHDYVEEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDTVSEPVTPASLAALQSDVQPVGHDYVEEVR 32 0 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ; 172.03 2.19E-14 157756000 246528 246618 228285 293682 265871 269604 247994 271173 295793 305691 FALSE TRUE 236893.4132 239584.6961 269541.1777 308838.9632 274422.9822 275055.5776 251029.0248 265573.1828 262215.8187 284986.2763 0.831244986 0.840688538 0.945804062 1.083697669 0.962934025 0.965153765 0.880846011 0.931880602 0.92009981 1 18.12053292 4.229979663 5.292399046 0.958320988 0.833932349 0.495059737 0.050722092 0.144404401 11.95509594 0.013730438 0.034239273 16981.6413 -4.229979663 -0.124388639 LEAMCFDGVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEAMCFDGVKR 11 1 P47813;X6RAC9 P47813 EIF1AX "Eukaryotic translation initiation factor 1A, X-chromosomal" 0 141.08 6.14E-05 1024500000 586100 677220 413220 417590 497810 605090 435710 540980 608080 577150 FALSE TRUE 563194.564 657906.3487 487898.046 439141.8699 513822.5107 617325.3344 441042.3493 529808.574 539053.3077 538059.1164 1.04671503 1.222739897 0.906774054 0.816159148 0.954955497 1.14731879 0.819691249 0.984666104 1.001847736 1 19.03740516 4.229985519 24.99962282 0.950129099 1.134727476 0.348417358 0.098790619 171.5827521 500233.063 0.024338015 0.053917192 16981.8703 -4.229985519 0.184598377 DVLS(ph)PLRPSR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVLSPLRPSR 10 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 DVLS(1)PLRPSR;DVLS(1)PLRPSR;DVLS(1)PLRPSR;DVLS(1)PLRPSR;DVLS(1)PLRPSR;DVLS(1)PLRPSR 179.93 1.24E-06 4766890000 1279211 1274491 1183294 1509197 1354139 1371272 1458589 1402116 1319150 1570724 TRUE FALSE 1229218.02 1238143.765 1397141.548 1587086.838 1397696.111 1399000.059 1476439.648 1373161.815 1169405.622 1464337.464 0.839436298 0.845531713 0.954111728 1.083825878 0.95449044 0.95538091 1.008264614 0.937735903 0.79859025 1 20.48181664 4.230035881 5.652630603 0.964685309 0.840877492 0.331132457 0.06772787 0.169623211 17.82151986 0.017078013 0.042060848 16983.83965 -4.230035881 -0.123807817 KLYGDVPFIEER ddPTM_BT-474_Pertuzumab_2h_R1 1 KLYGDVPFIEER 12 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 110.77 0.0023305 142720000 222750 245690 166150 184180 191520 204000 198600 222440 221310 220590 FALSE TRUE 214044.6837 238683.1618 196177.001 193685.5519 197680.4147 208125.0198 201030.5262 217846.5363 196187.8166 205649.2428 1.040824079 1.160632339 0.953939817 0.941824775 0.961250389 1.012038833 0.977540804 1.059311152 0.953992409 1 17.64982623 4.230197337 24.99983957 0.986979916 1.100728217 0.54991741 0.042633587 122.5646074 366378.6733 0.010896094 0.024164571 16990.15484 -4.230197337 0.113748301 CGLGQENS(ph)DNEHLVENEVSLLLEESDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 CGLGQENSDNEHLVENEVSLLLEESDLR 28 0 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 CGLGQENS(1)DNEHLVENEVSLLLEESDLR;CGLGQENS(1)DNEHLVENEVSLLLEESDLR;CGLGQENS(0.999)DNEHLVENEVS(0.001)LLLEESDLR 166.74 3.86E-12 285809400 52659.4 48636.5 48181.1 60145.3 57765.5 50164.5 56756.7 59008.8 59212 60093.9 TRUE FALSE 50601.41243 47249.43464 56888.49655 63249.40614 59623.57977 51178.86056 57451.30547 57790.24766 52490.502 56023.68663 0.903214613 0.843383174 1.015436505 1.128976152 1.064256627 0.913521827 1.025482415 1.031532395 0.936934093 1 15.7737493 4.230331715 24.73857346 1.01907433 0.873298889 0.480115705 0.058627158 115.3023466 346638.2131 0.015068363 0.033457921 16995.41271 -4.230331715 -0.145775441 LLLDTS(ph)PPGGVVLSSFR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLLDTSPPGGVVLSSFR 17 0 O15211;A2AB89 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 LLLDT(0.006)S(0.994)PPGGVVLSSFR;LLLDT(0.001)S(0.999)PPGGVVLSSFR;LLLDT(0.022)S(0.978)PPGGVVLSSFR 168.42 2.20E-09 1128579000 1497197 1513385 1464191 1836784 1694981 1607453 1906652 1706135 1672848 2189398 TRUE FALSE 1438684.886 1470224.742 1728802.884 1931580.642 1749501.603 1639956.801 1929986.178 1670902.716 1482953.308 2041108.123 0.704854814 0.720307134 0.84699231 0.946339207 0.857133232 0.803463953 0.945558031 0.818625283 0.72654324 1 20.96092118 4.230471627 4.615280794 0.864441302 0.70878913 0.407670874 0.075233634 0.173390194 9.194609126 0.018209569 0.046901185 17000.8888 -4.230471627 -0.155652173 FPGQLNADLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 FPGQLNADLRK 11 1 Q13509;A0A0B4J269;Q13509-2;G3V2A3;Q5JP53;P07437;Q5ST81;A6NNZ2;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;P68371;M0R2D3;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB1;TUBB4B;TUBB4A;TUBB2A;TUBB8;TUBB2B;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-1 chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 147.63 5.65E-05 5177400000 2140600 2279600 1481090 1468240 1640340 1088520 2169790 1944730 2104670 1936030 FALSE TRUE 2056942.985 2214588.04 1748755.91 1544016.042 1693103.026 1110530.62 2196344.539 1904570.646 1865756.685 1804900.964 1.139643131 1.226985904 0.968893 0.855457487 0.938058686 0.615286181 1.216878146 1.05522169 1.033716931 1 20.78348825 4.230479101 24.16444781 0.964090295 1.183314531 0.268421178 0.147079743 146.031195 436653.8213 0.03855178 0.085749297 17001.18139 -4.230479101 0.219224236 QKGYNHGQGSYSYSNSYNS(ph)PGGGGGSDYNYESK ddPTM_BT-474_Pertuzumab_2h_R1 1 QKGYNHGQGSYSYSNSYNSPGGGGGSDYNYESK 33 1 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 QKGYNHGQGSYS(0.007)YS(0.032)NS(0.24)YNS(0.721)PGGGGGSDYNYESK 255.15 1.69E-59 434290000 133320 133290 79953 68728 94655 134970 85323 79449 100510 98877 TRUE FALSE 128109.707 129488.6997 94402.28564 72275.06032 97699.66404 137699.1859 86367.2084 77808.35039 89100.52617 92179.97272 1.389778096 1.404737883 1.024108414 0.784064675 1.059879507 1.493808056 0.936941136 0.844091706 0.966593106 1 16.49216572 4.230513678 7.46602418 1.005522532 1.398906362 0.42108061 0.179741763 0.118980826 40.22436776 0.048452094 0.115051829 17002.53504 -4.230513678 0.39338383 KQVENERR ddPTM_BT-474_Pertuzumab_2h_R1 6 KQVENERR 8 2 Q9H307 Q9H307 PNN Pinin 0 ;;;;; 125.16 0.00071647 361462000 627761 695777 370564 370710 421857 423482 454273 423340 476057 433243 FALSE TRUE 603227.4061 675934.1212 437533.158 389842.3875 435426.4135 432045.0962 459832.5289 414597.8811 422017.0052 403899.0657 1.493510278 1.673522369 1.083273508 0.965197547 1.078057491 1.069685802 1.138483765 1.026488834 1.044857592 1 18.62363528 4.230570904 25 1.053500667 1.583516344 0.925333619 0.060530849 33.33453579 104305.7279 0.014201667 0.031560853 17004.77556 -4.230570904 0.530015676 ASDVHEVRK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASDVHEVRK 9 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 142.98 6.69E-05 1196120000 3417060 3765580 2434960 2816990 2718160 3213900 2957670 2834730 3333650 3162290 FALSE TRUE 3283517.517 3658189.345 2875011.437 2962375.191 2805592.085 3278887.26 2993866.85 2776191.835 2955228.028 2948105.282 1.113772136 1.240861162 0.975206501 1.004840366 0.951659394 1.112201549 1.015522366 0.941686802 1.002416042 1 21.49135662 4.230613231 24.9999886 0.998560015 1.177316659 0.646838346 0.052262761 90.24245442 283877.574 0.013003509 0.028901803 17006.43296 -4.230613231 0.178756644 RPS(ph)QNAISFFNVGHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSQNAISFFNVGHSK 16 1 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 RPS(1)QNAISFFNVGHSK;RPS(1)QNAISFFNVGHSK 252.37 9.68E-27 2320000000 1976290 2078400 1413050 1374230 1505670 1878920 1491550 1772530 2028580 1855250 TRUE FALSE 1899054.402 2019126.067 1668419.568 1445154.175 1554101.243 1916913.05 1509804.035 1735926.636 1798304.103 1729592.265 1.097978084 1.167400033 0.964631724 0.83554616 0.898536189 1.108303436 0.872924831 1.003662349 1.039727188 1 20.72200055 4.230631868 24.86852514 0.961030795 1.132689066 0.422204006 0.078138152 132.0883576 414300.2249 0.019518994 0.043409879 17007.16275 -4.230631868 0.171658271 HLFSS(ph)TENLAAGSWKEPAEGGGLSSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.088)S(0.456)T(0.456)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.003)S(0.911)T(0.086)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.213)S(0.412)T(0.375)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.117)S(0.766)T(0.117)ENLAAGSWKEPAEGGGLSSDR 314.78 2.38E-82 2489500000 2200870 2735160 1264338 1685590 1484891 1838330 1558260 1478560 1769190 1385579 TRUE FALSE 2114857.567 2657155.915 1492832.002 1772583.502 1532653.868 1875502.292 1577330.452 1448027.219 1568358.968 1291732.5 1.637225638 2.057048123 1.155682002 1.37225277 1.186510262 1.451927773 1.221096823 1.120996196 1.214151512 1 20.30087591 4.230666635 24.99998989 1.227089229 1.847136915 0.735299498 0.15150076 70.8986355 224536.2322 0.035555602 0.079054941 17008.5243 -4.230666635 0.620047686 FKYDDAERR ddPTM_BT-474_Pertuzumab_2h_R1 2 FKYDDAERR 9 2 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ; 99.973 0.0027979 653570000 670870 724800 487780 531540 554320 634100 581520 509040 755180 719560 FALSE TRUE 644651.6587 704129.4137 575932.6966 558972.8431 572150.2062 646921.9365 588636.8157 498528.1461 669455.1324 670823.5603 0.960985417 1.0496492 0.85854572 0.833263583 0.852907143 0.964369731 0.877483813 0.743158374 0.997960078 1 19.35557383 4.230694934 24.9683318 0.873590903 1.005317316 0.227292933 0.079326328 180.670686 573516.319 0.019629716 0.043649198 17009.63262 -4.230694934 0.131726413 (ac)MEVKPPPGRPQPDSGRR ddPTM_BT-474_Pertuzumab_2h_R1 4 MEVKPPPGRPQPDSGRR 17 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 78.285 2.14E-05 3194730000 1807349 2004050 1371481 1576120 1635341 1832150 1469204 1891754 1845270 1728353 FALSE TRUE 1736715.803 1946896.456 1619338.125 1657463.742 1687943.228 1869197.328 1487184.558 1852688.619 1635802.686 1611290.112 1.07784178 1.208284245 1.004994764 1.028656311 1.047572511 1.160062558 0.922977524 1.149816911 1.015213011 1 20.61978484 4.230720103 24.99994978 1.049439358 1.14306302 0.23315911 0.072691001 222.1278849 708275.7792 0.016874057 0.037545459 17010.61842 -4.230720103 0.093623663 S(ph)PVPSAFSDQSR ddPTM_BT-474_Pertuzumab_2h_R1 10 SPVPSAFSDQSR 12 0 Q9UQ35;Q9UQ35-2;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.998)PVPS(0.002)AFSDQSR;S(0.999)PVPS(0.001)AFSDQSR;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(0.999)PVPS(0.001)AFSDQSR;S(1)PVPSAFSDQSR;S(0.999)PVPS(0.001)AFSDQSR 170.89 4.19E-05 47661090000 4334920 4325937 4454900 5565037 5054603 4839836 5017995 5645561 5919569 6082763 TRUE FALSE 4165506.534 4202565.512 5259999.529 5852249.226 5217188.896 4937700.8 5079406.724 5528978.192 5247604.344 5670772.044 0.734557218 0.741092303 0.927563211 1.0320022 0.920013863 0.870728141 0.895716965 0.974995671 0.925377409 1 22.43511373 4.230782205 5.663159394 0.942139284 0.73519091 0.767185102 0.045341154 0.069547425 7.380166513 0.011726739 0.028926191 17013.05105 -4.230782205 -0.206948374 KLFEELVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLFEELVR 8 1 P14618-2;H3BTN5;H3BR70 P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 140.75 0.0010334 1269430000 1869260 1995380 1446890 1745340 1728490 1579290 1823230 1801930 1939220 1837650 FALSE TRUE 1796207.253 1938473.716 1708375.209 1835417.207 1784088.451 1611224.326 1845543.234 1764719.516 1719087.875 1713184.329 1.048461174 1.131503297 0.997192877 1.071348352 1.041387328 0.940485095 1.077258998 1.030081519 1.00344595 1 20.70824895 4.230794466 24.99991578 1.02426378 1.08998224 0.303749691 0.041921753 187.7617741 604428.4328 0.010031851 0.022315281 17013.53136 -4.230794466 0.06571846 DQKLPHLER ddPTM_BT-474_Pertuzumab_2h_R1 3 DQKLPHLER 9 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;; 104.79 0.0019241 446563000 1119770 1178670 775160 767780 844730 980060 921020 863510 1101830 1031190 FALSE TRUE 1076008.15 1145055.486 915248.6553 807405.2178 871901.5076 999877.4847 932291.7183 845678.2167 976754.8776 961346.5828 1.119271831 1.191095393 0.952048587 0.839869026 0.906958555 1.040080136 0.96977691 0.879680889 1.016027825 1 19.87469712 4.230802158 24.60593419 0.941803334 1.155183625 0.639110204 0.061225174 73.19598342 232144.3746 0.015549725 0.034627484 17013.83268 -4.230802158 0.21338029 SLES(ph)VLSLGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLESVLSLGPR 11 0 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 1 S(0.241)LES(0.759)VLSLGPR 245.78 6.03E-16 361950000 30697 24406 34388 38229 40005 33584 38911 46681 45665 47419 TRUE FALSE 29497.3273 23709.96478 40602.67656 40202.00327 41291.79716 34263.09149 39387.20446 45717.02104 40481.30064 44207.26889 0.667250614 0.536336339 0.918461547 0.909398031 0.934049947 0.775055604 0.890966699 1.034151672 0.915715937 1 15.43199599 4.230913371 24.99696354 0.922457743 0.60179346 0.766150709 0.07081177 70.06185049 229017.6552 0.018570166 0.041349032 17018.19011 -4.230913371 -0.320664283 GLEPS(ph)PAAVAALPPEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLEPSPAAVAALPPEVR 17 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 GLEPS(1)PAAVAALPPEVR;GLEPS(1)PAAVAALPPEVR 107.5 0.00073582 50129000 34549 31194 33447 41880 37522 45044 37053 39963 35785 42497 TRUE FALSE 33198.78688 30304.37766 39491.61692 44041.43182 38728.92921 45954.82054 37506.4657 39137.75008 31722.83682 39618.64034 0.837958764 0.764902011 0.996793847 1.111634106 0.977543118 1.159929269 0.946687352 0.98786202 0.800704834 1 15.27389175 4.230942444 24.42308962 1.002741909 0.801430376 0.42197739 0.091703005 102.2744171 327886.8287 0.022702216 0.050615607 17019.32939 -4.230942444 -0.201311533 MHNYNYGGNLQENPSGPS(ph)LMHGQTWTSPAQGPGYSQGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 MHNYNYGGNLQENPSGPSLMHGQTWTSPAQGPGYSQGYR 39 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 MHNYNYGGNLQENPS(0.012)GPS(0.269)LMHGQT(0.269)WT(0.224)S(0.224)PAQGPGY(0.001)SQGYR 82.784 0.0012186 131140000 5779.8 5047.1 5816.2 9057 3718.9 6323.8 9297.4 4691 9817.2 6794.4 TRUE FALSE 5553.919026 4903.16165 6867.316721 9524.432855 3838.521796 6451.671569 9411.184362 4594.129211 8702.792613 6334.209236 0.876813319 0.774076363 1.084163226 1.503649864 0.605998579 1.018544119 1.485770995 0.725288515 1.373935134 1 12.62894881 4.231185809 24.16829105 1.085404103 0.82544482 0.129897816 0.281962647 203.9613304 668423.8813 0.067773345 0.151388457 17028.86916 -4.231185809 -0.259959283 RELGSIDGVQQISLEDALSSQEVEVAYICSESSSHEDYIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RELGSIDGVQQISLEDALSSQEVEVAYICSESSSHEDYIR 40 1 P53004;C9J1E1 P53004 BLVRA Biliverdin reductase A 0 46.898 0.028082 60868000 13608 12720 12687 14802 15741 14130 16694 14696 15287 14457 FALSE TRUE 13076.18432 12357.23805 14979.82312 15565.93299 16247.32356 14415.71828 16898.30617 14392.52246 13551.68385 13477.81451 0.970200644 0.916857703 1.111443039 1.15493005 1.205486509 1.069588713 1.253786818 1.067867676 1.00548081 1 13.71829896 4.231249672 23.77909563 1.119536895 0.943529152 0.412857956 0.077854795 68.73266556 223561.154 0.018841171 0.042142551 17031.37346 -4.231249672 -0.176007743 SKDDQVTVIGAGVTLHEALAAAELLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SKDDQVTVIGAGVTLHEALAAAELLKK 27 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 224.21 1.16E-34 878120000 698860 578750 414670 294029 401100 197589 433630 431810 468670 417420 FALSE TRUE 671547.7786 562244.6167 489610.0933 309203.8719 414001.7458 201584.385 438936.8937 422892.9726 415468.5464 389147.7716 1.725688357 1.444810064 1.258159828 0.794566729 1.063867703 0.518015005 1.127943999 1.086715648 1.067636967 1 18.56995857 4.231301846 1.829262485 0.960745724 1.698787507 0.676480763 0.17805291 0.234772737 1.434682692 0.049158562 0.213031913 17033.41963 -4.231301846 0.738041783 S(ph)PTVLCQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPTVLCQK 8 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 S(0.999)PT(0.001)VLCQK;S(1)PTVLCQK;S(1)PTVLCQK;S(0.593)PT(0.407)VLCQK 157.34 0.00039692 1229610000 1531200 1371860 1381620 1606650 1544530 1425800 1568120 1687010 1737400 1821920 TRUE FALSE 1471359.011 1332735.896 1631309.468 1689569.399 1594211.21 1454630.653 1587311.122 1652172.654 1540177.636 1698519.736 0.866259591 0.784645517 0.960430093 0.994730508 0.93858857 0.856410804 0.934526157 0.972713251 0.906776414 1 20.69584655 4.231346776 24.99995007 0.943860997 0.825452546 0.544029754 0.043948225 109.0047049 377766.4864 0.011071407 0.024718395 17035.18192 -4.231346776 -0.118408451 DAQAGKEPGGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAQAGKEPGGSR 12 1 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1 P04637-7 TP53 Cellular tumor antigen p53 0 ; 84.734 0.011008 406570000 598150 618370 425410 421320 476190 579900 479860 494210 546320 550520 FALSE TRUE 574773.6367 600734.693 502291.0502 443064.3757 491507.0838 591625.9753 485732.6702 484004.3908 484304.044 513232.79 1.119908252 1.170491646 0.978680747 0.863281506 0.957668905 1.152743914 0.946417843 0.943050406 0.94363426 1 18.96925382 4.231386539 23.63382746 0.970245948 1.145199971 0.490237844 0.070111649 61.61367723 202982.1443 0.018273697 0.040915205 17036.74171 -4.231386539 0.174954024 S(ph)ASPHDVDLCLVSPCEFEHRK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.536)AS(0.464)PHDVDLCLVSPCEFEHRK;S(0.551)AS(0.449)PHDVDLCLVSPCEFEHRK 126.27 1.02E-05 594449000 299194 327394 205644 229233 242263 279988 234805 246910 254410 262717 TRUE FALSE 287501.1677 318057.0437 242808.4453 241063.7426 250055.6094 285649.5492 237678.6138 241811.2222 225530.4434 244922.9436 1.173843346 1.298600446 0.99136668 0.984243203 1.020956248 1.166283342 0.970422004 0.987295101 0.920822035 1 17.9019684 4.231414597 24.99999783 1.007317291 1.236221911 0.663381886 0.065819742 84.40426042 295287.916 0.016713143 0.037323089 17037.8424 -4.231414597 0.228904621 LTADFREDPDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTADFREDPDPR 12 1 P17174 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 64.878 0.056781 282540000 859370 946800 520000 595830 608250 421950 681340 603670 751880 690050 FALSE TRUE 825784.8703 919798.191 613975.5673 626580.8577 627814.9136 430482.1181 689678.4427 591204.0035 666529.7345 643312.2989 1.283645396 1.429784869 0.954397372 0.973991728 0.975910013 0.669165068 1.072074083 0.919000001 1.036090458 1 19.29515974 4.231450179 24.99646056 0.944218753 1.356715161 0.693397901 0.108102836 72.30710914 254196.0565 0.025929145 0.057929927 17039.2384 -4.231450179 0.412496408 RALS(ph)SDSILSPAPDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.785)S(0.133)DS(0.076)ILS(0.005)PAPDAR;RALS(0.844)S(0.144)DS(0.01)ILS(0.002)PAPDAR;RALS(0.495)S(0.495)DS(0.01)ILS(0.001)PAPDAR 210.26 1.08E-11 586250000 416455 470030 232371 279045 252810 271033 241548 343042 237505 216846 TRUE FALSE 400179.4782 456625.2046 274365.6088 293446.5459 260941.8632 276513.473 244504.1367 335958.0628 210544.4281 202158.8273 1.979530073 2.258744823 1.357178474 1.451564346 1.290776499 1.367803111 1.209465547 1.661852056 1.041480261 1 17.62512967 4.231485495 24.96162169 1.340644347 2.119137502 0.736706661 0.195115753 66.13376444 233328.5551 0.045637183 0.101987347 17040.62404 -4.231485495 0.778493155 GDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDSESEEDEDLEVPVPSR 18 0 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 2 GDS(1)ES(1)EEDEDLEVPVPSR;GDS(1)ES(1)EEDEDLEVPVPSR 357.93 1.46E-90 1059650000 572680 593060 632370 830510 678060 658150 808200 809860 838890 888960 TRUE FALSE 550299.0325 576146.5095 746653.326 873372.7206 699870.4157 671458.2439 818090.9934 793136.108 743662.7241 828749.9474 0.664010941 0.695199452 0.900939214 1.05384347 0.844489243 0.810206077 0.987138516 0.957027039 0.897330644 1 19.66057735 4.231489919 4.318394114 0.932925785 0.671897263 0.686294045 0.068527872 0.10583131 4.623877699 0.017581742 0.046189932 17040.79762 -4.231489919 -0.261028522 EVYPHVSTIINICLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVYPHVSTIINICLK 15 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 61.409 0.089534 194250000 166410 188750 111730 133800 138430 126630 122690 144760 157390 158300 FALSE TRUE 159906.5132 183367.0348 131922.0964 140705.434 142882.7267 129190.5454 124191.5169 141770.6554 139523.747 147578.2 1.083537496 1.242507598 0.893913169 0.953429667 0.968183151 0.875403992 0.841530232 0.96064768 0.945422475 1 17.1711201 4.231503778 25 0.925884063 1.163022563 0.725036756 0.057404832 66.56658442 235826.1283 0.01376435 0.030765263 17041.34144 -4.231503778 0.2371385 ALPNNTSS(ph)SPQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALPNNTSSSPQPK 13 0 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1;A0A087WT22;J3KP33;A0A087WXZ1;E7ESS1;P04637-5;P04637-9;P04637-8;P04637-6;P04637-2;P04637-3 P04637-7 TP53 Cellular tumor antigen p53 1 ALPNNT(0.002)S(0.076)S(0.896)S(0.027)PQPK;ALPNNTSS(0.5)S(0.5)PQPK 273.02 4.15E-32 4637600000 4838700 4560300 3385000 3366000 3549200 3543600 3804400 3954600 4272800 4662200 TRUE FALSE 4649598.255 4430244.709 3996744.799 3539719.663 3663363.241 3615254.02 3850959.385 3872936.128 3787769.657 4346425.041 1.069752316 1.019284738 0.919547619 0.814397955 0.842845144 0.831776457 0.886006166 0.891062446 0.871467843 1 22.05139783 4.231646801 2.685301475 0.870624126 1.06027713 0.654490833 0.048339105 0.145828074 2.080084145 0.01186284 0.038227948 17046.95447 -4.231646801 0.189653004 MGFCTDR ddPTM_BT-474_Pertuzumab_2h_R1 3 MGFCTDR 7 0 Q01581;D6RIW1 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;; 110.34 0.015881 938280000 592390 563460 740890 952840 730690 733060 989010 898600 959780 1107870 FALSE TRUE 569238.7439 547390.6725 874785.304 1002016.187 754193.3074 747882.9755 1001113.8 880043.596 850829.7981 1032832.978 0.551143075 0.529989538 0.846976542 0.970162851 0.730218073 0.724108342 0.969289151 0.852067677 0.823782563 1 19.97817554 4.231680896 9.125539963 0.858793753 0.540054686 0.674741357 0.089914859 0.064181412 55.05496061 0.022114348 0.051909123 17048.29281 -4.231680896 -0.318739066 LQATLDMQSGIIHAAEEKDWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQATLDMQSGIIHAAEEKDWK 21 1 O00231;O00231-2;J3QS13 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 198.84 5.01E-22 221920000 255690 285920 160790 130960 211540 224270 189170 177590 236390 222510 FALSE TRUE 245697.3521 277765.8415 189848.3298 137718.8613 218344.3762 228804.8931 191485.119 173922.7044 209555.9982 207439.1995 1.18443068 1.339022915 0.915199876 0.663899888 1.052570472 1.102997378 0.92309033 0.838427379 1.01020443 1 17.66232902 4.231681374 24.93027609 0.927311328 1.261726823 0.52908156 0.121700546 102.0767715 369929.8573 0.031382831 0.07024234 17048.31156 -4.231681374 0.334415495 YADLTEDQLPSCESLK ddPTM_BT-474_Pertuzumab_2h_R1 3 YADLTEDQLPSCESLK 16 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;; 184.21 2.97E-12 0 173805 149884 155857 184961 161257 151766 179235 193713 184923 190748 FALSE TRUE 167012.5084 145609.4551 184023.8269 194506.8594 166443.9779 154834.8125 181428.5315 189712.7589 163931.3163 177828.4681 0.93917757 0.818819712 1.03483896 1.093789209 0.935980497 0.870697556 1.020244585 1.06683008 0.921850804 1 17.44012677 4.231733216 24.99887916 0.997686818 0.878998634 0.296977758 0.06988492 172.5041226 631641.5983 0.018259178 0.040873973 17050.34675 -4.231733216 -0.118688184 RSNVSSPATPTASSSSST(ph)TPTRK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSNVSSPATPTASSSSSTTPTRK 23 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RSNVSSPATPTASSS(0.001)S(0.015)S(0.098)T(0.442)T(0.442)PT(0.003)RK 140.57 9.20E-06 132920000 20722 24879 14483 18875 16373 19772 17647 19622 19271 21641 TRUE FALSE 19912.16133 24169.47528 17100.40027 19849.14101 16899.65241 20171.80339 17862.96926 19216.79884 17083.43687 20175.23579 0.986960526 1.197977338 0.847593577 0.983836879 0.837643366 0.99982987 0.885390855 0.952494387 0.846752774 1 14.30029791 4.231759437 24.99999348 0.919708582 1.092468942 0.44982748 0.076650587 108.9033797 400316.0325 0.016833887 0.037705503 17051.37622 -4.231759437 0.17276036 AVIPGDEDASFPPLKSEDSGIGLSAS(ph)SPELSEHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVIPGDEDASFPPLKSEDSGIGLSASSPELSEHLR 35 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 AVIPGDEDASFPPLKSEDS(0.002)GIGLS(0.057)AS(0.514)S(0.423)PELS(0.005)EHLR 81.939 0.00078725 81192000 37473 49212 24153 25582 29749 41672 32289 35510 36824 30253 TRUE FALSE 36008.51373 47808.52194 28517.98438 26902.29009 30705.9036 42514.63639 32684.16244 34776.70609 32643.8939 28203.93736 1.276719391 1.695100983 1.011134864 0.953848739 1.088709821 1.507400752 1.15885105 1.233044367 1.157423287 1 14.78360896 4.231763568 24.99999593 1.156736181 1.485910204 0.381874229 0.175462883 150.2743999 552726.8207 0.044209195 0.098986642 17051.53843 -4.231763568 0.329174023 TLNDELEIIEGMKFDR ddPTM_BT-474_Pertuzumab_2h_R1 3 TLNDELEIIEGMKFDR 16 1 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 103.61 0.0013003 234973000 154419 229942 94750 135232 100540 157016 162898 171699 142872 114230 FALSE TRUE 148384.1348 223384.2793 111873.4327 142211.3397 103773.9604 160190.9711 164891.5945 168153.3556 126653.7695 106493.1004 1.393368531 2.097640866 1.050522826 1.335404259 0.974466515 1.504238026 1.548378194 1.579007044 1.189314323 1 16.70040044 4.231788895 24.99990281 1.320939597 1.745504715 0.32210077 0.26713878 174.1470658 642926.5598 0.066329614 0.148538342 17052.53284 -4.231788895 0.424565118 KSYESSEDCSEAAGS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSYESSEDCSEAAGSPAR 18 1 Q6P6C2-3;Q6P6C2;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 KSYESSEDCSEAAGS(1)PAR;KSYESSEDCSEAAGS(1)PAR 231.07 6.06E-20 1824030000 1203240 1247120 882690 913630 970710 1109500 1082980 1061970 1163630 1089860 TRUE FALSE 1156216.051 1211553.359 1042211.718 960782.5538 1001933.769 1131934.85 1096233.833 1040039.948 1031539.601 1016042.811 1.137959973 1.192423533 1.025755713 0.945612274 0.986113732 1.114062161 1.078924845 1.023618234 1.015252103 1 19.95452976 4.231807061 24.96526181 1.026374591 1.165191764 0.604772873 0.04572153 97.3873866 360008.2251 0.012383965 0.027741607 17053.24614 -4.231807061 0.138817173 KKNEGVNWLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKNEGVNWLR 10 2 F8VUA2;F8VVT7;Q9HD42 F8VUA2 CHMP1A Charged multivesicular body protein 1a 0 ; 117.25 0.00055258 1351350000 1471740 1494330 1088580 1158060 1242010 1137580 1292480 1294250 1605540 1449270 FALSE TRUE 1414222.774 1451713.172 1285310.621 1217827.615 1281960.38 1160582.647 1308297.757 1267523.285 1423285.83 1351109.652 1.046712065 1.074459922 0.951300007 0.901353649 0.948820385 0.858984795 0.96831353 0.938135024 1.053419926 1 20.36571333 4.23183801 22.21015704 0.945598223 1.060586042 0.422101171 0.050044073 29.33898434 96936.9423 0.012121236 0.027306066 17054.46148 -4.23183801 0.11498782 S(ph)FDYNYRR ddPTM_BT-474_Pertuzumab_2h_R1 3 SFDYNYRR 8 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR 128.51 0.00069231 1717180000 2683640 3211430 1417680 1202140 1664470 2204900 1542650 2116890 1765220 1560860 TRUE FALSE 2578760.382 3119843.161 1673886.312 1264182.589 1718009.189 2249484.589 1561529.412 2073175.482 1564839.626 1455141.562 1.772171484 2.144013505 1.150325409 0.868769488 1.18064746 1.545887113 1.073111684 1.424724258 1.075386524 1 20.47272808 4.231893091 24.99953485 1.190777858 1.958092555 0.705032627 0.204683207 73.31897146 274909.5044 0.051015527 0.114330996 17056.62461 -4.231893091 0.767314697 IQPFDDDEDEDIWEDSDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQPFDDDEDEDIWEDSDTR 19 0 O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170;T1ECW5;A0A0A0MSJ8 O75170-6 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 0 ; 206.1 8.85E-16 199197000 161311 164949 151303 173405 191113 165747 178608 198203 199682 193446 FALSE TRUE 155006.7878 160244.816 178646.8178 182354.4528 197260.3232 169098.5179 180793.8581 194110.0388 177014.9365 180343.7301 0.859507495 0.888552188 0.990590678 1.011149391 1.093801947 0.937645671 1.002495945 1.076333725 0.98154195 1 17.46038974 4.23191741 2.497692355 1.020232183 0.860556096 0.636677211 0.042074292 0.172173092 2.104712446 0.011021112 0.037227233 17057.57974 -4.23191741 -0.159676087 EKEQFRK ddPTM_BT-474_Pertuzumab_2h_R1 3 EKEQFRK 7 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;; 113.5 0.0034398 9057800000 4623670 4984330 3168400 3035140 3626050 4238820 3853530 3998770 4157720 3746880 FALSE TRUE 4442971.865 4842181.789 3741000.361 3191783.939 3742685.191 4324531.845 3900690.653 3916194.002 3685753.056 3493100.48 1.271927873 1.386213141 1.070968437 0.913739515 1.071450768 1.238021027 1.116684354 1.121122631 1.055152314 1 21.73607671 4.232009181 24.99995425 1.082082027 1.329070528 0.599029456 0.083431084 97.06212498 370389.5463 0.022030395 0.049405679 17061.18457 -4.232009181 0.246988501 TLHPAVHAGILAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLHPAVHAGILAR 13 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 102.97 0.00095269 1530500000 3365100 2979100 3460300 3909700 3971200 4357800 4656500 3828100 3754500 4589500 FALSE TRUE 3233588.172 2894138.985 4085653.184 4111480.086 4098937.255 4445917.702 4713487.64 3749048.397 3328304.9 4278649.077 0.755749797 0.676414198 0.954893264 0.960929492 0.957997999 1.039093794 1.101629873 0.876222455 0.777886861 1 22.02872393 4.232075105 24.97415064 0.960232811 0.716081975 0.568900621 0.084428945 96.89796867 373136.4211 0.022173601 0.04975557 17063.77458 -4.232075105 -0.244150835 DDFLGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDFLGGR 7 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 180.49 0.0015951 593110000 352370 322650 356240 409370 403180 393840 437090 461080 448700 457490 FALSE TRUE 338598.9908 313448.3379 420620.4925 430497.6348 416148.6509 401803.7146 442439.2382 451558.5369 397765.4571 426503.7948 0.793894439 0.734925086 0.986205745 1.009364137 0.975720863 0.94208708 1.037362958 1.058744476 0.9326188 1 18.70219905 4.232090238 24.24018998 0.998546374 0.764409729 0.845509519 0.038981742 32.39773914 121375.495 0.010266706 0.023074534 17064.36916 -4.232090238 -0.234136645 VQIPVSRPDPEPVS(ph)DNEEDSYDEEIHDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 VQIPVSRPDPEPVS(1)DNEEDSYDEEIHDPR 144.18 4.07E-08 1293500000 523950 621580 604230 878580 697520 717170 881010 816780 943100 923080 TRUE FALSE 503473.4547 603853.147 713427.802 923923.6191 719956.3643 731671.6688 891792.0639 799913.2076 836043.2418 860558.9694 0.585053985 0.701698743 0.829028373 1.073631967 0.836614793 0.850228392 1.036293962 0.929527477 0.971511856 1 19.71491453 4.23216098 2.212378083 0.948885444 0.602637221 0.747692853 0.073012176 0.154467 1.452300198 0.018949698 0.069961754 17067.14899 -4.23216098 -0.346248223 EDFSGYDFENR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDFSGYDFENR 11 0 G3V1P2;Q8N584-2;Q8N584 G3V1P2 TTC39C Tetratricopeptide repeat protein 39C 0 80.706 0.055081 309640000 535140 535560 487130 577880 519820 644710 636570 523320 590370 653530 FALSE TRUE 514226.1372 520286.3532 575165.2271 607704.4561 536540.4824 657746.4779 644360.5341 512513.2591 523353.6726 609265.831 0.84400948 0.853956232 0.944030008 0.997437285 0.880634454 1.07957224 1.057601627 0.841198099 0.858990684 1 19.21671231 4.232329542 4.662890612 0.954785769 0.846380414 0.247188418 0.075893548 0.275348911 15.1030141 0.020296186 0.052331601 17073.77454 -4.232329542 -0.108405355 RGPNYTSGYGTNSELSNPSETESER ddPTM_BT-474_Pertuzumab_2h_R1 4 RGPNYTSGYGTNSELSNPSETESER 25 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ;;; 271.73 9.79E-53 3044310000 576065 572090 559490 696590 678740 698360 628640 622540 717120 705180 FALSE TRUE 553551.7429 555774.5533 660602.2888 732541.0934 700572.2885 712481.3177 636333.4844 609684.3314 635715.544 657417.5305 0.842009404 0.845390528 1.004844346 1.114270702 1.065642846 1.08375771 0.967928987 0.927392872 0.966989036 1 19.3264504 4.232454777 6.241199047 1.014641157 0.842077676 0.617326762 0.054408004 0.105083361 16.49141445 0.016233021 0.039613412 17078.69869 -4.232454777 -0.172563481 DLDKADSMIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDKADSMIR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 117.98 0.00080835 1898890000 2957200 3210100 2095800 2061500 2394300 2560100 2682600 2653800 3048500 2709400 FALSE TRUE 2841629.355 3118551.091 2474557.681 2167894.262 2471314.834 2611866.976 2715430.461 2598998.103 2702447.06 2525889.925 1.125001263 1.234634598 0.979677561 0.858269492 0.978393718 1.034038321 1.075039112 1.028943533 1.069898982 1 21.26836034 4.232520287 24.99990063 1.004280026 1.179817945 0.55906485 0.062792579 100.3060986 415156.884 0.017129826 0.038569866 17081.27509 -4.232520287 0.175537919 KPGGEREER ddPTM_BT-474_Pertuzumab_2h_R1 2 KPGGEREER 9 2 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 0 ; 76.85 0.019272 64715000 194738 234754 107485 111806 136205 153629 144669 136645 138948 131000 FALSE TRUE 187127.4237 228059.0458 126909.9305 117576.3211 140586.1575 156735.4836 146439.5025 133823.233 123175.2056 122127.2533 1.53223313 1.867388642 1.039161424 0.962736145 1.15114484 1.283378438 1.199073086 1.095768793 1.008580822 1 16.89802566 4.232566933 24.99995563 1.105160674 1.69981094 0.803539753 0.119989928 51.71659076 215716.0053 0.030169978 0.067951695 17083.10983 -4.232566933 0.594650265 S(ph)LPGSPEFLHQEACPFVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPGSPEFLHQEACPFVGR 19 0 Q96S53-3;Q96S53-2;Q96S53 Q96S53-3 TESK2 Dual specificity testis-specific protein kinase 2 1 S(0.991)LPGS(0.009)PEFLHQEACPFVGR;S(0.953)LPGS(0.047)PEFLHQEACPFVGR 308.39 1.20E-61 1654660000 83773 90526 77628 100639 91891 96022 99832 102743 109093 110400 TRUE FALSE 80499.05854 87944.28711 91657.10643 105832.9909 94846.75747 97963.63063 101053.7739 100621.3211 96709.22 102922.5097 0.782132682 0.854470877 0.890544806 1.028278374 0.921535607 0.951819295 0.981843274 0.977641543 0.939631382 1 16.65119902 4.232610108 1.81280582 0.968925616 0.789630003 0.790428709 0.032112183 0.165008909 0.986589052 0.008283635 0.036287852 17084.8082 -4.232610108 -0.179295613 TEVS(ph)PVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEVSPVPR 8 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 TEVS(1)PVPR;TEVS(1)PVPR 107.21 0.004246 351700000 582230 532400 525480 591870 543130 673250 615140 593950 627200 719900 TRUE FALSE 559475.8079 517216.4733 620445.9252 622416.4816 560600.2697 686863.5763 622668.2673 581684.7249 556002.8854 671140.5318 0.83361946 0.770653013 0.92446499 0.927401121 0.835294909 1.023427351 0.927776282 0.866710767 0.828444803 1 19.35625536 4.232619014 24.99900867 0.911504188 0.802136227 0.355106856 0.061432354 140.1233879 589572.3327 0.015109819 0.034061735 17085.15858 -4.232619014 -0.109367961 IQFTSLYHKEEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 2 IQFT(0.001)S(0.001)LYHKEEAPAS(0.999)PLRPLYPQIS(1)PLK 87.347 0.0018809 251630000 244570 238260 152460 144420 168370 206420 168270 177310 201460 176510 TRUE FALSE 235011.934 231465.0581 180012.9135 151873.5335 173785.774 210593.9538 170329.3386 173648.4865 178591.1054 164554.8205 1.428168031 1.406613659 1.093938864 0.922935792 1.056096524 1.279779913 1.035091759 1.055262228 1.085298534 1 17.32820876 4.232650676 5.238360512 1.066359722 1.423491505 0.733266697 0.084955037 0.080990233 6.512100968 0.021869909 0.054988089 17086.40422 -4.232650676 0.357131783 DVLLQVDDER ddPTM_BT-474_Pertuzumab_2h_R1 2 DVLLQVDDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 158.79 1.83E-05 179787000 210416 217498 226220 284600 247300 220277 296950 297320 285260 339480 FALSE TRUE 202192.7101 211295.17 267102.9862 299288.2401 255254.6291 224731.1519 300584.1629 291180.2381 252878.4807 316486.7172 0.638866338 0.667627292 0.843962706 0.945658139 0.806525567 0.710080833 0.949752854 0.920039364 0.799017674 1 18.27178543 4.232689982 4.082277175 0.872115849 0.645529338 0.539989582 0.081296706 0.150576646 5.640047962 0.020692515 0.055389752 17087.9507 -4.232689982 -0.226586511 ESLCDSPHQNLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ESLCDSPHQNLSR 13 0 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1;U3KPT1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ;; 217.2 2.62E-11 174630000 506370 516870 526750 677510 614910 576400 649350 658030 635000 702430 FALSE TRUE 486580.5006 502129.3737 621945.4425 712476.3723 634689.1386 588055.2029 657296.9395 644441.4505 562917.4621 654853.7904 0.743036854 0.766780892 0.94974703 1.087993049 0.969207398 0.897994654 1.003730831 0.984099749 0.859607855 1 19.32081331 4.232696219 4.603887627 0.973894054 0.749222672 0.687301415 0.058001225 0.096341549 5.084529661 0.014548592 0.037658327 17088.19608 -4.232696219 -0.224671383 YRVDFQGMEYQGGDDEFFDLDDY ddPTM_BT-474_Pertuzumab_2h_R1 1 YRVDFQGMEYQGGDDEFFDLDDY 23 1 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 85.945 0.006334 16224000 21388 22220 19678 25923 20291 21493 27243 24201 24778 28656 FALSE TRUE 20552.13331 21586.30736 23234.25233 27260.88914 20943.67844 21927.60319 27576.40798 23701.24089 21965.30532 26715.1036 0.769307641 0.808018853 0.869704744 1.020429849 0.783963961 0.820794241 1.032240354 0.887185064 0.822205508 1 14.70536799 4.232833741 3.226125278 0.904945341 0.780500949 0.251524999 0.082501693 0.333068274 7.059133232 0.020768743 0.060793346 17093.60803 -4.232833741 -0.124444393 GPSWDPFRDWYPHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;; 211.7 7.50E-10 7376020000 5612000 6369310 2404920 2901100 2361210 2802340 3079960 2332200 2973870 3113350 FALSE TRUE 5392676.836 6187663.515 2839542.541 3050826.119 2437160.464 2859005.235 3117653.472 2284039.255 2636288.745 2902480.031 1.857954845 2.131853948 0.978315961 1.051110115 0.839682078 0.9850215 1.07413434 0.786926777 0.908288332 1 21.46885471 4.232852018 25 0.944158861 1.994904525 0.941079631 0.104269549 23.91832128 104748.6983 0.025572157 0.057731356 17094.32742 -4.232852018 1.050745664 RPES(ph)PPSILTPPVVPTADK ddPTM_BT-474_Pertuzumab_2h_R1 6 RPESPPSILTPPVVPTADK 19 1 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 1 RPES(0.879)PPS(0.111)ILT(0.01)PPVVPTADK;RPES(0.681)PPS(0.319)ILTPPVVPTADK;RPES(0.988)PPS(0.012)ILTPPVVPTADK;RPES(0.987)PPS(0.013)ILTPPVVPTADK;RPES(0.993)PPS(0.007)ILTPPVVPTADK;RPES(0.996)PPS(0.004)ILTPPVVPTADK 234.73 2.35E-24 5360256000 3622170 3414250 3405950 3960350 3891850 3468780 4001430 4425990 4461790 4480860 TRUE FALSE 3480611.592 3316878.933 4021480.93 4164744.138 4017034.89 3538921.108 4050400.697 4334591.76 3955306.305 4177367.361 0.833206968 0.794011789 0.962683093 0.996978187 0.961618776 0.847165404 0.969606057 1.037637197 0.946841865 1 21.99416259 4.232972062 24.77556631 0.967395226 0.813609358 0.619686188 0.047516735 72.16262599 319922.8151 0.012854605 0.0290625 17099.05313 -4.232972062 -0.153785868 EEAS(ph)PVPLTSNVGSTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEASPVPLTSNVGSTVK 17 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 EEAS(1)PVPLTSNVGSTVK;EEAS(0.94)PVPLT(0.055)S(0.005)NVGSTVK 200.67 1.28E-11 347340000 468760 409390 526900 660800 551090 531380 626660 680370 689680 749030 TRUE FALSE 450440.341 397714.598 622122.5508 694903.9672 568816.3103 542124.8677 634329.2525 666320.1217 611390.4178 698297.5309 0.645055039 0.569548911 0.89091329 0.995140232 0.814575858 0.776352262 0.90839395 0.954206613 0.875544293 1 19.41348235 4.23299433 24.87424019 0.899318545 0.607301935 0.742236514 0.069427736 55.18492405 246611.3261 0.017805204 0.040258157 17099.9299 -4.23299433 -0.29201661 VADKIQLINNMLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VADKIQLINNMLDK 14 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 186.42 9.72E-07 1025330000 2546600 2505230 1463750 1549730 1554040 1730110 1575150 1807170 2137940 1596350 FALSE TRUE 2447076.057 2433783.293 1728282.186 1629711.751 1604027.108 1765094.01 1594427.157 1769851.308 1895250.014 1488227.793 1.644288642 1.635356701 1.161302184 1.095068752 1.077810209 1.186037526 1.071359616 1.189234146 1.273494571 1 20.50516394 4.233002354 5.998648301 1.13532836 1.645321022 0.888300901 0.072106231 0.039633439 5.30289621 0.017409657 0.042794876 17100.24582 -4.233002354 0.509992662 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_BT-474_Pertuzumab_2h_R1 15 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.284)NHDGADET(0.358)S(0.358)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.594)S(0.406)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNS(0.004)NHDGADET(0.498)S(0.498)EKEQQEAIEHIDEVQNEIDR;ELNS(0.067)NHDGADET(0.467)S(0.467)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNS(0.001)NHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.945)S(0.055)EKEQQEAIEHIDEVQNEIDR;ELNS(0.003)NHDGADET(0.531)S(0.466)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNS(0.125)NHDGADET(0.438)S(0.438)EKEQQEAIEHIDEVQNEIDR;ELNS(0.003)NHDGADET(0.533)S(0.463)EKEQQEAIEHIDEVQNEIDR 418.47 5.68E-187 35622505000 3143370 2760298.8 3027051 3518784 3393690 3002580 3880012 3205920 3948887 4303284 TRUE FALSE 3020523.625 2681577.781 3574106.452 3700388.864 3502851.121 3063294.225 3927496.747 3139716.632 3500625.903 4011818.742 0.752906305 0.668419476 0.890894301 0.922371897 0.873132947 0.763567455 0.978981604 0.782616772 0.872578281 1 21.93582499 4.233022671 24.99590528 0.87455056 0.710662874 0.472487909 0.073171993 100.0733681 451696.3703 0.017135935 0.038745391 17101.04582 -4.233022671 -0.163887687 LPLQES(ph)EEEEREER ddPTM_BT-474_Pertuzumab_2h_R1 2 LPLQESEEEEREER 14 1 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5;C9JBL0 P23497 SP100 Nuclear autoantigen Sp-100 1 LPLQES(1)EEEEREER;LPLQES(1)EEEEREER 153.04 3.94E-06 664630000 135766 125325 131619 176332 151799 155607 147590 148686 158673 163705 TRUE FALSE 130460.1146 121750.8537 155405.4811 185432.5157 156681.7527 158753.4802 149396.2506 145615.5821 140661.1063 152617.1145 0.854819691 0.797753608 1.01827034 1.215017832 1.026632912 1.040207585 0.978895788 0.954123544 0.921660108 1 17.21955723 4.233078267 24.95340396 1.019997861 0.826286626 0.514757234 0.074977024 98.32762769 447555.2405 0.020490673 0.046356705 17103.23516 -4.233078267 -0.193711235 EKEPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEPPK 6 1 Q5STZ8;H7C5Z1;Q8NE71;Q8NE71-2;E9PFR3;Q14738;Q14738-2 Q5STZ8;Q8NE71;E9PFR3 ABCF1;PPP2R5D ATP-binding cassette sub-family F member 1;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 0 ; 94.407 0.0406 869640000 972760 931550 855940 931360 968620 992870 1028850 1040570 1069110 1153460 FALSE TRUE 934743.4638 904983.1061 1010627.398 979427.6012 999776.542 1012946.512 1041441.374 1019081.866 947749.1149 1075335.127 0.869257816 0.84158239 0.939825523 0.910811501 0.929734849 0.941982166 0.968480754 0.947687693 0.881352326 1 20.03635491 4.233177797 24.99837997 0.938803119 0.855420093 0.552314425 0.030438844 81.69733958 379418.1544 0.00727074 0.016454711 17107.15526 -4.233177797 -0.083383026 ADKQHVLDMLFSAFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADKQHVLDMLFSAFEK 16 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 0 87.932 0.0037864 19993000 70882 70154 38922 35479 47253 57218 42466 40526 54640 41584 FALSE TRUE 68111.85308 68153.27661 45956.07122 37310.07544 48772.93566 58374.98716 42985.71161 39689.12394 48437.49627 38767.47864 1.756932756 1.758001268 1.185428427 0.962406552 1.258088928 1.505772086 1.108808546 1.023773671 1.249436331 1 15.24255929 4.233240701 6.866136697 1.159952008 1.761423993 0.717979451 0.149405023 0.066204664 15.79285265 0.039131801 0.09460108 17109.63326 -4.233240701 0.601471985 ESIPSLPQS(ph)PMR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESIPSLPQSPMR 12 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 ESIPSLPQS(1)PMR;ESIPSLPQS(1)PMR;ESIPSLPQS(1)PMR;ESIPSLPQS(1)PMR 213.67 6.22E-09 1890590000 2478570 2251320 2322200 2813600 2703060 2505350 2773160 2765550 2639880 2822120 TRUE FALSE 2381704.744 2187114.558 2741873.197 2958810.233 2790006.38 2556009.894 2807098.762 2708440.426 2340211.89 2630975.299 0.905255456 0.83129422 1.04215087 1.124605858 1.060445676 0.97150661 1.066942272 1.029443502 0.889484554 1 21.32716627 4.233281383 24.99932664 1.029477292 0.86827482 0.499186536 0.06175383 88.42285729 418726.2334 0.015438185 0.034985836 17111.23608 -4.233281383 -0.161202472 DDYVHEFCR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDYVHEFCR 9 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ; 142.55 0.00010406 986130000 886430 932960 679010 819930 827330 725350 852840 779180 949310 948920 FALSE TRUE 851787.3356 906352.8943 801722.2115 862246.6856 853941.8208 740017.074 863277.311 763089.6607 841548.3086 884648.8032 0.962853657 1.024534133 0.906260438 0.974676824 0.96528907 0.836509439 0.975841835 0.862590508 0.951279542 1 19.75474531 4.233319285 24.99989493 0.927135242 0.993693899 0.165833711 0.051669656 168.8151704 805222.4452 0.012199711 0.027639927 17112.72946 -4.233319285 0.066558657 EGQEEVLKEVVESEGER ddPTM_BT-474_Pertuzumab_2h_R1 2 EGQEEVLKEVVESEGER 17 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 ; 89.049 0.0037804 183699000 122120 134341 82210 79350 98873 120068 95877 106384 110921 94435 FALSE TRUE 117347.4154 130509.7262 97067.17575 83445.26301 102053.3398 122495.8572 97050.37141 104187.1332 98329.7131 88038.83334 1.332905162 1.482410901 1.102549546 0.947823362 1.159185509 1.391384376 1.102358672 1.183422466 1.116890233 1 16.42585241 4.23339004 24.99720932 1.137377644 1.407658059 0.481568538 0.116599174 99.6901436 481962.5681 0.029697159 0.067366587 17115.51771 -4.23339004 0.270280415 RIDIS(ph)PSTFRK ddPTM_BT-474_Pertuzumab_2h_R1 2 RIDISPSTFRK 11 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.991)PS(0.007)T(0.002)FRK;RIDIS(0.987)PS(0.009)T(0.003)FRK 82.651 0.009577 1315930000 1584580 1720560 1098940 1121080 1215360 1614570 1235260 1395320 1548450 1362470 TRUE FALSE 1522652.862 1671491.313 1297542.904 1178939.073 1254453.158 1647217.712 1250377.481 1366506.154 1372676.448 1270188.693 1.198761152 1.315939374 1.021535549 0.928160579 0.987611655 1.296829141 0.984402938 1.075829254 1.080687031 1 20.2766114 4.233496219 24.99986478 1.050131564 1.257350284 0.425049644 0.097854956 105.7290698 521930.5989 0.024519774 0.05565426 17119.70273 -4.233496219 0.20721872 GDMS(ph)DEDDENEFFDAPEIITMPENLGHKR ddPTM_BT-474_Pertuzumab_2h_R1 7 GDMSDEDDENEFFDAPEIITMPENLGHKR 29 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR 175.48 2.50E-13 663341000 409065 448552 200095.7 163047 250130 351366 209648.4 198816.6 253979 200830.9 TRUE FALSE 393078.2876 435759.7361 236257.4441 171461.8752 258175.6586 358470.8613 212214.1398 194710.9677 225148.3687 187228.4443 2.099458173 2.327422726 1.261867261 0.91578967 1.378933952 1.914617529 1.133450319 1.039964673 1.202532925 1 17.5144401 4.233497145 24.86194885 1.235029795 2.213440602 0.68330686 0.267550047 60.25271583 295850.8744 0.070689806 0.160542429 17119.73922 -4.233497145 0.978410807 S(ph)PGPPALKHPATK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPGPPALKHPATK 13 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 S(1)PGPPALKHPATK;S(1)PGPPALKHPATK;S(1)PGPPALKHPATK;S(1)PGPPALKHPATK 144.3 2.49E-05 1675670000 3005570 3131000 1874000 1731370 2075560 2763890 2009450 2178190 2501560 2193290 TRUE FALSE 2888109.002 3041706.946 2212673.487 1820726.213 2142322.272 2819777.749 2034042.25 2133209.615 2217593.396 2044736.515 1.412460227 1.487578925 1.082131351 0.890445395 1.047725346 1.379042106 0.994769857 1.043268705 1.084537485 1 20.96348352 4.233497177 24.09695773 1.066109933 1.450019665 0.624353508 0.119382536 45.16985695 214971.0988 0.030515313 0.069389348 17119.7405 -4.233497177 0.383909731 YGVFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGVFLR 6 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ; 118.11 0.051518 725320000 640640 606860 551700 652120 636640 642350 622280 655690 669630 664250 FALSE TRUE 615603.0805 589552.947 651404.4625 685775.9914 657118.1038 655338.7571 629895.6488 642149.7724 593616.4097 619259.7558 0.994095086 0.952028517 1.051908277 1.107412495 1.061134843 1.058261498 1.017175172 1.036963514 0.958590324 1 19.24018517 4.233502573 24.99753881 1.040643963 0.973061796 0.29315883 0.038921767 132.0032565 652391.1364 0.00994779 0.022609741 17119.95318 -4.233502573 -0.067582167 VEAQHILASAPTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEAQHILASAPTDR 14 0 A0A0A0MQS1;Q53H96-2;Q53H96 A0A0A0MQS1 PYCRL Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 3 0 95.428 0.003772 385360000 194900 180320 194780 232420 231790 254020 208050 220700 231120 277600 FALSE TRUE 187283.0925 175177.4502 229981.0789 244415.2241 239245.7359 259156.4584 210596.1781 216142.4679 204884.2265 258797.9047 0.723665413 0.676888981 0.88865124 0.94442505 0.92445005 1.001385458 0.813747616 0.835178585 0.791676527 1 17.98146641 4.233545552 24.7696971 0.892579091 0.700277165 0.569533313 0.069196703 74.68377338 368875.9872 0.018173206 0.041293536 17121.64753 -4.233545552 -0.192301925 RFGFPEGSVELYAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RFGFPEGSVELYAEK 15 1 P23396;E9PPU1;F2Z2S8;H0YCJ7;H0YF32 P23396 RPS3 40S ribosomal protein S3 0 95.197 0.0066994 256050000 233290 240050 167560 190960 191670 156710 196480 216580 232070 232380 FALSE TRUE 224172.7689 233204.009 197841.8194 200815.4685 197835.2396 159878.7836 198884.581 212107.5473 205726.3865 216640.6956 1.034767583 1.076455226 0.913225554 0.926951734 0.913195183 0.737990538 0.918038877 0.979075269 0.949620227 1 17.72494475 4.23358203 24.99460759 0.913905855 1.055611425 0.40457854 0.067035922 109.6685607 550593.7062 0.017675397 0.040157717 17123.08571 -4.23358203 0.141705569 SADGVIVSGVKDVDDFFEHER ddPTM_BT-474_Pertuzumab_2h_R1 1 SADGVIVSGVKDVDDFFEHER 21 1 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 160.77 1.25E-11 34635000 77645 88298 32654 26749 43154 64283 28314 37330 38324 23859 FALSE TRUE 74610.54756 85779.82749 38555.30418 28129.5191 44542.0876 65582.8463 28660.5152 36559.12245 33973.62019 22243.00868 3.354337025 3.856484918 1.733367313 1.264645422 2.002520803 2.948470113 1.288517917 1.643623081 1.527384208 1 14.44106433 4.233589739 24.98659125 1.716101717 3.605411238 0.690206579 0.516473872 59.94682917 301334.6273 0.129495885 0.294235395 17123.38963 -4.233589739 1.889309521 QLFHPEQLITGKEDAANNYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLFHPEQLITGKEDAANNYAR 21 1 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ; 170.91 4.56E-12 1914410000 2156480 2607700 946720 874660 1178920 2001470 1056470 1079110 1281970 931910 FALSE TRUE 2072202.377 2533330.949 1117813.364 919801.3074 1216841.032 2041941.095 1069399.396 1056826.001 1136446.14 868790.9056 2.385156617 2.915927104 1.28663106 1.058714245 1.400614376 2.350325126 1.230905375 1.216433085 1.30807785 1 19.72864948 4.23370926 24.99910396 1.375073153 2.650542022 0.657928298 0.373048592 64.55956972 332683.2752 0.095419779 0.217057534 17128.10275 -4.23370926 1.275468869 QLNVNAKPFVPNVHAAEFVPSFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLNVNAKPFVPNVHAAEFVPSFLR 24 1 P15170-2;P15170-3 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 95.357 0.0042232 461170000 654240 760970 390890 421710 489360 500090 529180 465850 597060 524770 FALSE TRUE 628671.5775 739267.8807 461532.5183 443474.5036 505100.7088 510202.1624 535656.2631 456230.0347 529284.2519 489226.8605 1.285030787 1.511094219 0.943391616 0.906480284 1.032446805 1.042874387 1.094903625 0.932553119 1.08187897 1 18.90014409 4.233753837 24.99999996 1.001970844 1.398062546 0.803771308 0.077813142 40.39595247 210103.2711 0.018688942 0.042516244 17129.86094 -4.233753837 0.396091702 LSAQAQVAEDILDKYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSAQAQVAEDILDKYR 16 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ; 202.35 1.77E-12 440460000 371190 356120 334020 386870 382930 402570 375310 410050 419510 419630 FALSE TRUE 356683.4844 345963.8063 394384.8442 406836.4071 395247.2912 410710.2412 379903.156 401582.3242 371888.9835 391208.0863 0.911748752 0.884347278 1.008120379 1.039948869 1.010324952 1.049851104 0.971102514 1.026518465 0.950616811 1 18.57757667 4.233761767 24.99997992 1.009750816 0.898047998 0.696371117 0.028749122 51.55140939 268566.736 0.006752104 0.015360946 17130.17369 -4.233761767 -0.111702819 LSLPGLLSQVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSLPGLLSQVSPR 13 0 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 LSLPGLLS(0.072)QVS(0.928)PR;LSLPGLLS(0.03)QVS(0.97)PR 89.911 0.0075867 229090000 339890 360460 259536 287594 306670 324700 305390 326530 356980 338710 TRUE FALSE 326606.723 350180.0337 306439.9285 302436.7608 316534.3191 331265.6565 309127.4542 319787.0414 316457.127 315768.87 1.034322107 1.108975795 0.970456424 0.957778899 1.00242408 1.049076359 0.978967478 1.01272504 1.002179623 1 18.26850942 4.233784739 24.99963705 0.997678894 1.071648954 0.517097355 0.028958648 83.03131027 434641.3394 0.007197649 0.016375209 17131.07985 -4.233784739 0.07397006 DRLGS(ph)YSGPTSVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRLGSYSGPTSVSR 14 1 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 DRLGS(0.97)YS(0.03)GPTSVSR;DRLGS(1)YSGPTSVSR;DRLGS(0.999)YS(0.001)GPTSVSR;DRLGS(0.999)YS(0.001)GPTSVSR 188.96 4.68E-07 2547450000 759780 767510 554437 617440 621130 628350 568320 773490 726300 626440 TRUE FALSE 730086.9576 745621.3663 654636.0993 649306.1524 641109.2105 641055.6675 575275.2702 757517.1612 643853.4689 584010.6608 1.250126079 1.276725608 1.120931762 1.111805308 1.097769704 1.097678023 0.985042412 1.297094748 1.102468691 1 19.15563518 4.23384957 23.43538822 1.115530811 1.263425897 0.384670671 0.080337831 53.08859124 264106.5324 0.020439997 0.046677424 17133.63735 -4.23384957 0.147895086 EAARS(ph)PDKPGGS(ph)PSASRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAARSPDKPGGSPSASRR 18 3 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 2 EAARS(0.999)PDKPGGS(0.472)PS(0.294)AS(0.234)RR 64.152 0.054049 86379000 119660 113000 73009 60054 85010 92479 84836 78490 88341 90152 TRUE FALSE 114983.5549 109777.3506 86203.35038 63153.39414 87744.42385 94348.98874 85874.24835 76869.15407 78312.90004 84045.92474 1.36810387 1.306159115 1.025669604 0.751415305 1.044005692 1.122588502 1.021753864 0.914608939 0.931787 1 16.35889025 4.233893328 4.009449785 0.969441216 1.351382368 0.712742536 0.09243491 0.107546877 3.842300921 0.024521864 0.066143728 17135.36374 -4.233893328 0.381941152 SYDLTPVDKFWQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SYDLTPVDKFWQK 13 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 98.592 0.0029627 360810000 408110 422150 271420 286210 297410 398850 306270 285000 364540 340210 FALSE TRUE 392160.61 410110.6953 320471.6317 300981.3324 306976.4628 406915.0203 310018.2239 279114.6504 323158.9475 317167.2737 1.236447271 1.293042282 1.010418345 0.948967177 0.967869286 1.282966605 0.977459686 0.880023488 1.018891211 1 18.27488439 4.233909452 24.88875759 1.004194594 1.26474482 0.506699632 0.100045227 80.96193427 433244.0591 0.026727837 0.060914131 17135.99994 -4.233909452 0.260550225 EAAHLLNDALAIR ddPTM_BT-474_Pertuzumab_2h_R1 3 EAAHLLNDALAIR 13 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ;; 203.82 5.60E-07 0 110688 110609 104728 127635 117697 121505 117164 129556 133929 144347 FALSE TRUE 106362.1906 107454.5396 123654.6793 134222.2576 121482.8309 123961.9143 118597.8881 126880.6233 118725.9414 134570.2491 0.79038414 0.798501454 0.918885713 0.997414053 0.902746571 0.921168796 0.881308379 0.942857906 0.882259951 1 17.03799997 4.233938362 5.455135448 0.928500669 0.792333131 0.663009598 0.038939153 0.086454288 8.055623425 0.009240671 0.023127945 17137.14067 -4.233938362 -0.136167538 NSKYEYDPDIS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSKYEYDPDISPPR 14 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 NSKYEYDPDIS(1)PPR;NSKYEYDPDIS(1)PPR 89.028 0.0038224 565100000 1071010 1060680 581770 546490 686890 832450 584070 697710 775730 615550 TRUE FALSE 1029153.745 1030430.445 686908.7804 574694.4144 708984.4407 849282.7094 591218.0234 683302.0447 687672.3825 573858.2502 1.793393656 1.795618421 1.197000793 1.001457092 1.235469631 1.479952077 1.030250978 1.190715729 1.198331439 1 19.13033489 4.233945741 7.103870394 1.173672816 1.798157277 0.778810639 0.133835168 0.052022924 14.59103009 0.033041006 0.079784381 17137.43184 -4.233945741 0.624484461 LGGSPTSLGTWGSWIGPDHDKFSAMK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGGSPTSLGTWGSWIGPDHDKFSAMK 26 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 362.41 4.18E-111 4976300000 2351060 2528360 1612880 1677940 1829710 2077860 2145710 1754900 2376330 2219080 FALSE TRUE 2259177.976 2456253.648 1904363.294 1764538.684 1888564.284 2119875.753 2171969.841 1718660.702 2106578.981 2068779.735 1.092034081 1.187295876 0.920524917 0.852936953 0.912888043 1.024698626 1.049879697 0.830760604 1.018271276 1 20.98034862 4.233998934 24.99993587 0.942404153 1.139665003 0.511032183 0.073316077 77.28861658 423583.582 0.018601784 0.042432128 17139.53099 -4.233998934 0.19726085 KIADDKYNDTFWK ddPTM_BT-474_Pertuzumab_2h_R1 1 KIADDKYNDTFWK 13 2 P14625 P14625 HSP90B1 Endoplasmin 0 139.3 2.20E-05 255420000 612660 641820 375270 323610 426070 550690 372040 430070 631870 424360 FALSE TRUE 588716.5699 623515.922 443089.6368 340311.5509 439774.9285 561825.3291 376593.1368 421188.9042 560142.7666 395617.7192 1.488094545 1.576056612 1.119994417 0.860203005 1.111615853 1.420121753 0.951911703 1.064636096 1.415868753 1 18.59374752 4.234077328 24.7158173 1.11048172 1.532075661 0.481219451 0.171811109 70.90848574 390920.6469 0.042679875 0.09746593 17142.62511 -4.234077328 0.421593941 MSVDAVEIETLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSVDAVEIETLR 12 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 0 84.658 0.028179 26544000 39652 39552 36904 46789 42928 44413 42782 44548 36796 53437 FALSE TRUE 38102.356 38424.01569 43573.37373 49203.7859 44308.81811 45311.06129 43305.57891 43628.06823 32619.07234 49817.66439 0.764836258 0.771292997 0.874657097 0.987677493 0.88941982 0.909538049 0.869281598 0.875754991 0.654769202 1 15.60436976 4.234193131 5.869662112 0.882440672 0.766624852 0.21323092 0.088172564 0.219574401 27.04061435 0.021428779 0.053021022 17147.19677 -4.234193131 -0.11581582 LSCS(ph)LEDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSCSLEDLR 9 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.032)CS(0.968)LEDLR;LS(0.018)CS(0.982)LEDLR;LSCS(1)LEDLR;LSCS(1)LEDLR 160.91 6.81E-05 9216500000 5443800 5706100 5602900 7047300 6281500 6105300 7102600 7775600 6978200 7209400 TRUE FALSE 5231050.278 5543367.615 6615468.666 7411011.998 6483550.152 6228753.349 7189523.743 7615031.143 6186063.991 6721100.917 0.778302594 0.824770775 0.98428349 1.102648523 0.964655974 0.926745994 1.06969436 1.133003542 0.920394451 1 22.68026614 4.234196857 3.292960343 1.027285374 0.78809637 0.615313788 0.067204615 0.149377261 3.314582113 0.018187755 0.052853582 17147.34387 -4.234196857 -0.239189004 LSQSVIDGVTVLGGQFHDYGLLTTPQLHYMVYCR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSQSVIDGVTVLGGQFHDYGLLTTPQLHYMVYCR 34 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 133.79 1.73E-08 47040000 20978 42258 9539.5 19853 23055 23735 25137 15024 23704 24585 FALSE TRUE 20158.15657 41052.84321 11263.49986 20877.61571 23796.58501 24214.93796 25444.63413 14713.74915 21013.2213 22919.83605 0.879507014 1.791149078 0.49143021 0.910897253 1.038252846 1.056505723 1.110157772 0.641965724 0.91681377 1 14.4843091 4.234240338 24.99999824 0.892462599 1.335327987 0.292615037 0.273345087 113.7068513 657999.2296 0.064348329 0.147101043 17149.06071 -4.234240338 0.442865388 GDLETLQPGDDVEFTIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDLETLQPGDDVEFTIK 17 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0;E9PNG3 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 171.87 3.89E-09 56921000 82953 74019 91403 101740 100130 95087 103880 128290 108560 125210 FALSE TRUE 79711.10505 71908.05059 107921.5553 106990.8136 103350.7724 97009.72429 105151.3145 125640.7667 96236.72392 116729.4152 0.682870765 0.616023395 0.924544642 0.916571144 0.885387563 0.831064939 0.900812485 1.076341953 0.824442783 1 16.83280863 4.234255908 24.99071728 0.925086487 0.649447034 0.692245354 0.072063718 53.54442758 310856.5777 0.018977199 0.043400353 17149.67554 -4.234255908 -0.275639452 GRDWNVDLIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GRDWNVDLIPK 11 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86;G5E9U5;P31150 P50395;Q5SX86;G5E9U5;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 105.17 0.0022815 459730000 709100 694320 505520 497990 574510 591360 565700 632880 691080 647840 FALSE TRUE 681387.588 674518.6734 596878.7092 523691.3236 592989.6359 603317.7044 572623.2058 619810.8068 612631.4956 603961.2198 1.128197582 1.116824477 0.988273236 0.867094288 0.98183396 0.998934509 0.948112539 1.026242723 1.014355683 1 19.20409639 4.234336757 5.355151679 0.976447948 1.125006532 0.653169065 0.042186855 0.096958497 8.454254041 0.0111041 0.027912658 17152.86845 -4.234336757 0.148558584 GLFIIDDKGILR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLFIIDDKGILR 12 1 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ; 140.31 5.43E-05 583170000 1089310 1359660 492900 551720 658080 972620 658200 562810 705110 536720 FALSE TRUE 1046738.561 1320883.828 581977.9945 580194.3353 679247.7409 992287.0428 666255.2485 551187.7768 625068.8689 500367.4763 2.091939645 2.639827508 1.163101165 1.159536466 1.357497785 1.983116589 1.331531884 1.101565955 1.24921962 1 18.93262849 4.234348212 24.9999915 1.309602326 2.365883707 0.698630552 0.28164676 52.58845997 312112.4306 0.072451321 0.165812734 17153.32089 -4.234348212 1.056281381 KGAVAEDGDELR ddPTM_BT-474_Pertuzumab_2h_R1 5 KGAVAEDGDELR 12 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9;G3V2D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;; 165.51 8.73E-05 11025000000 12734500 12575100 12494500 14161600 14286500 13417800 14776300 15822400 16611200 16478100 FALSE TRUE 12236821.66 12216470.46 14752534.09 14892481.87 14746038.25 13689117.11 14957136.78 15495661.91 14725566.22 15362023.61 0.796563133 0.79523836 0.96032492 0.969434903 0.959902069 0.891101163 0.973643653 1.008699264 0.95856943 1 23.87286494 4.234425221 7.298237444 0.965820276 0.794999042 0.83958285 0.029607276 0.044730448 14.31236433 0.007985828 0.019267054 17156.36276 -4.234425221 -0.170821234 KAEGAQNQGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAEGAQNQGQK 11 1 Q9P2E9 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 157.68 4.89E-05 92548000 112302 113990 84810 99748 87882 90916 108666 112428 100679 103863 FALSE TRUE 107913.1137 110739.1168 100137.0536 104896.0062 90708.80434 92754.38381 109995.887 110106.3225 89250.342 96828.2665 1.114479455 1.14366518 1.034171706 1.083320089 0.93680087 0.957926721 1.135989427 1.137129957 0.921738509 1 16.56314065 4.23449764 24.95932473 1.038202944 1.129072331 0.227991755 0.073196002 157.4005478 966955.056 0.019690988 0.045072444 17159.22385 -4.23449764 0.090869388 EGQLLHVYPVLFNVGINEQQTLAER ddPTM_BT-474_Pertuzumab_2h_R1 1 EGQLLHVYPVLFNVGINEQQTLAER 25 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 195.63 8.99E-25 144680000 90800 89745 79208 94591 88256 89492 105760 88176 88660 113330 FALSE TRUE 87251.43562 87185.56047 93522.64757 99472.85285 91094.83439 91301.58956 107054.3225 86355.13479 78595.68849 105654.0582 0.825821905 0.825198407 0.885177997 0.941495808 0.862199105 0.864156012 1.013253295 0.817338551 0.743896542 1 16.68898866 4.2345752 7.940825704 0.887180227 0.825280042 0.103866918 0.076247921 0.267162745 130.0603193 0.018694566 0.044823559 17162.28856 -4.2345752 -0.061900184 ELS(ph)PQHKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSPQHKR 8 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHKR;ELS(1)PQHKR 87.363 0.0094187 1147944000 1519737 1665937 1113057 1106944 1259073 1600412 1379916 1396330 1580297 1556560 TRUE FALSE 1460343.998 1618426.108 1314211.16 1164073.512 1299572.227 1632773.427 1396803.825 1367495.298 1400908.31 1451132.805 1.006347588 1.115284626 0.905644994 0.802182618 0.895557059 1.125171605 0.962560987 0.942363988 0.965389457 1 20.46874813 4.234624591 24.99999884 0.94730916 1.060816112 0.228310263 0.081489203 136.881226 869437.8336 0.021460964 0.049258028 17164.2405 -4.234624591 0.113506953 FIQENIFGICPHMTEDNKDLIQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 FIQENIFGICPHMTEDNKDLIQGK 24 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 223.85 4.39E-33 3320500000 1790130 1933400 1102150 1039600 1347450 1665450 1217570 1346600 1510190 1278760 FALSE TRUE 1720169.741 1878261.325 1301333.022 1093253.881 1390791.953 1699126.54 1232470.986 1318792.239 1338759.562 1192148.446 1.442915726 1.575526379 1.091586393 0.917045091 1.166626486 1.425264232 1.033823422 1.106231563 1.122980587 1 20.18513246 4.234675382 24.99990494 1.113864073 1.509221117 0.606042988 0.129342066 59.93082117 385641.0924 0.033099153 0.076029867 17166.24797 -4.234675382 0.395357044 HYLFYDGESVSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 HYLFYDGESVSGK 13 0 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 232.42 7.86E-13 2685400000 3646100 3697800 3130700 3922400 3619800 3756300 3860000 3091500 4797400 4433600 FALSE TRUE 3503606.381 3592342.365 3696487.132 4124835.534 3736234.154 3832254.96 3907239.835 3027659.445 4252819.264 4133308.323 0.847651834 0.869120347 0.894316814 0.997950119 0.903933088 0.927164068 0.94530568 0.732502685 1.028914112 1 21.97886555 4.234702817 3.446100927 0.912935477 0.854739238 0.091143055 0.078985702 0.678380928 16.6983896 0.020839722 0.059442924 17167.33244 -4.234702817 -0.058196239 EAEAAIYHLQLFEELR ddPTM_BT-474_Pertuzumab_2h_R1 28 EAEAAIYHLQLFEELR 16 0 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;; 277 2.57E-35 21136333900 9141695.5 8519677.5 9513777.2 12220348.7 10933091.3 10156204.5 11305538.6 11290811.1 11603502.8 12660449.3 FALSE TRUE 8784427.933 8276704.639 11233128.37 12851042.36 11284764.11 10361569.91 11443899.16 11057651.91 10286321.81 11802945.79 0.744257246 0.701240587 0.95172244 1.088799575 0.956097258 0.877879988 0.969579914 0.936855265 0.871504622 1 23.49264364 4.234717599 24.98978778 0.955886758 0.722748872 0.718244053 0.058574316 45.36206866 294981.635 0.015039144 0.034552568 17167.91677 -4.234717599 -0.233137886 FLEIGKFDLSQNHPLGMAIFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLEIGKFDLSQNHPLGMAIFLK 22 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 195.56 1.34E-22 439650000 708170 853060 459420 433510 615260 829920 601820 541740 684150 606670 FALSE TRUE 680493.9335 828731.564 542447.4137 455883.5031 635050.3967 846701.551 609185.2532 530552.8797 606488.1602 565579.7005 1.203179557 1.465278127 0.959099864 0.806046438 1.122830957 1.497050814 1.077098864 0.938069169 1.072330141 1 19.10937082 4.234741722 24.99900008 1.060144267 1.334228853 0.272805913 0.179693131 123.0827812 805739.337 0.047978875 0.110247313 17168.87039 -4.234741722 0.274084586 KASTAPGAEASPS(ph)PCITER ddPTM_BT-474_Pertuzumab_2h_R1 1 KASTAPGAEASPSPCITER 19 1 Q66PJ3 Q66PJ3 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 KASTAPGAEAS(0.137)PS(0.847)PCIT(0.016)ER 111.65 5.70E-05 0 201840 214330 129850 134630 158060 183040 137370 163780 156480 169410 TRUE FALSE 193951.8697 208217.5183 153316.7835 141578.2704 163144.1434 186741.1942 139051.1752 160397.8858 138717.0464 157935.7098 1.22804317 1.318368838 0.970754389 0.89642976 1.032978189 1.182387406 0.880428975 1.015589736 0.878313376 1 17.26897788 4.234790244 24.9995335 0.984735264 1.273206053 0.638117022 0.087668069 52.22800901 346308.7044 0.021648717 0.049766697 17170.7887 -4.234790244 0.288470789 RGDDWNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDDWNDR 8 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A087X0F4 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 128.28 0.0018283 1699280000 496930 572930 569900 797460 733360 748140 728170 762690 708220 831400 FALSE TRUE 477509.4262 556590.5974 672893.6074 838617.0062 756949.1904 763267.9034 737081.5623 746940.185 627825.8347 775088.5375 0.616070814 0.718099379 0.868150637 1.081962854 0.976597065 0.984749311 0.950964344 0.963683694 0.810005315 1 19.56400159 4.234811419 2.515106406 0.965908273 0.635086033 0.771751831 0.065076543 0.125835715 1.560303764 0.016761696 0.056612175 17171.62591 -4.234811419 -0.33082224 VLEALLPLKGLEER ddPTM_BT-474_Pertuzumab_2h_R1 2 VLEALLPLKGLEER 14 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 138.39 1.43E-05 621830000 1094600 1383980 534210 521070 749850 1180270 661750 677110 770450 584290 FALSE TRUE 1051821.822 1344510.245 630753.6304 547962.4851 773969.6062 1204135.868 669848.6945 663127.4419 682991.746 544715.5179 1.930956228 2.468279682 1.157950544 1.00596085 1.420869391 2.210577501 1.22972207 1.217383056 1.253850356 1 19.05514344 4.234822364 24.99999661 1.333812947 2.199618052 0.511268583 0.346595511 71.07368517 475327.0407 0.089154856 0.205019217 17172.05867 -4.234822364 0.865805105 GHYTIGKEIIDLVLDRIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHYTIGKEIIDLVLDRIR 18 2 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ; 150.59 3.23E-08 92252000 139120 155876 77487 88914 89051 114649 95573 87603 105755 101579 FALSE TRUE 133683.0366 151430.5691 91490.62459 93502.8622 91915.40629 116967.2813 96742.65096 85793.96744 93750.13576 94698.96385 1.411663139 1.599073136 0.966120651 0.987369432 0.970606251 1.235148481 1.021580881 0.905965218 0.989980586 1 16.53106102 4.234886553 24.99999647 1.007357396 1.505368217 0.8244316 0.091509327 32.38511018 220369.4241 0.023709925 0.054567806 17174.5969 -4.234886553 0.498010822 LRS(ph)PPEALVQGR ddPTM_BT-474_Pertuzumab_2h_R1 6 LRSPPEALVQGR 12 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR 143.88 3.79E-05 12798300000 1862780 1880490 1861980 2153380 2106120 2331780 2243160 2177900 2431690 2514230 TRUE FALSE 1789980.498 1826860.266 2198481.206 2264516.2 2173865.263 2378930.189 2270612.463 2132925.604 2155654.746 2343938.963 0.763663443 0.779397542 0.937943027 0.966115686 0.927441071 1.014928386 0.968716549 0.909974892 0.919671877 1 21.16050357 4.234927969 4.525134254 0.953441092 0.766634159 0.844225645 0.031718513 0.067292171 3.377250859 0.008305726 0.021686371 17176.23483 -4.234927969 -0.186806933 GDVDMSEVEHFMPILMEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDVDMSEVEHFMPILMEK 18 0 E7ENJ6;Q9BXS5;Q9BXS5-2;K7ENA7 E7ENJ6 AP1M1 AP-1 complex subunit mu-1 0 ; 154.82 2.32E-08 45438000 112229 106514 111334 120885 128466 135303 131783 124249 152051 160445 FALSE TRUE 107842.9666 103476.325 131454.5304 127123.8893 132598.2256 138038.9194 133395.7998 121683.2147 134790.8079 149577.9172 0.720981871 0.691788781 0.878836481 0.849884072 0.886482631 0.922856274 0.891814796 0.813510557 0.901141094 1 17.19053767 4.235004895 24.96991078 0.882143327 0.706385289 0.711621785 0.047126632 42.23763874 296621.302 0.011403787 0.026282972 17179.27752 -4.235004895 -0.175758037 LDKSQIHDIVLVGGSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDKSQIHDIVLVGGSTR 17 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 173.27 9.00E-10 1958630000 3846000 4867700 2291790 2410600 2866700 4306000 3127800 3118500 3520400 2818600 FALSE TRUE 3695694.068 4728877.962 2705967.434 2535011.355 2958910.009 4393070.27 3166078.952 3054101.885 3120778.951 2627693.711 1.4064402 1.799630582 1.029787993 0.96472863 1.126048289 1.671834983 1.204888887 1.162274687 1.187649435 1 21.32536569 4.235027504 24.9991629 1.183909014 1.603035409 0.413909963 0.20621768 82.50029609 583763.0021 0.052600597 0.12122057 17180.17187 -4.235027504 0.419126395 ADGAPSAAPPDGLLAS(ph)PDLGLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADGAPSAAPPDGLLASPDLGLLK 23 0 P17535 P17535 JUND Transcription factor jun-D 1 ADGAPSAAPPDGLLAS(1)PDLGLLK 107.23 0.0008803 16356000 29511 28007 28708 33761 35430 36469 33364 31468 35164 34417 TRUE FALSE 28357.67749 27208.26778 33896.17421 35503.40926 36569.63813 37206.42817 33772.31861 30818.1748 31172.33014 32085.90593 0.883804794 0.847981909 1.056419422 1.106511043 1.139741487 1.159587896 1.052559298 0.960489471 0.971527193 1 14.9696521 4.2350731 24.82231994 1.057547036 0.865893311 0.588442991 0.063533282 57.05966984 406134.7634 0.018434389 0.042527124 17181.97568 -4.2350731 -0.191653725 VFPEPTES(ph)GDEGEELGLPLLSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 VFPEPTESGDEGEELGLPLLSTR 23 0 Q9BUR4;E9PMG4 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 VFPEPT(0.174)ES(0.826)GDEGEELGLPLLSTR;VFPEPT(0.047)ES(0.953)GDEGEELGLPLLSTR;VFPEPT(0.105)ES(0.895)GDEGEELGLPLLSTR;VFPEPT(0.156)ES(0.844)GDEGEELGLPLLSTR 150.06 5.68E-08 217129000 175416 178369 156554 188348 188631 182365 189011 195185 192885 198865 TRUE FALSE 168560.5488 173282.0908 184846.7903 198068.6629 194698.4874 186052.5452 191324.1732 191154.3615 170989.5034 185395.6964 0.909193428 0.934660804 0.997039273 1.068356314 1.050178031 1.003542956 1.031977424 1.031061482 0.92229489 1 17.50024823 4.235097535 3.175238403 1.020014191 0.915287678 0.494918394 0.037258779 0.182329773 3.730216974 0.009430832 0.027902074 17182.94244 -4.235097535 -0.104726513 GKGAYQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKGAYQDR 8 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 98.033 0.0090527 363050000 1529790 1691680 943040 1072370 1157460 1271160 1148990 1152540 1295100 1159460 FALSE TRUE 1470004.116 1643434.943 1113468.306 1127715.144 1194690.752 1296863.726 1163051.683 1128739.646 1148085.678 1080928.741 1.359945442 1.520391567 1.030103339 1.043283522 1.10524469 1.199768011 1.075974427 1.04423132 1.062128921 1 20.04383999 4.235203562 24.99999629 1.075167937 1.44016856 0.848376092 0.062551385 26.80880287 199651.6688 0.015569546 0.035952241 17187.13791 -4.235203562 0.365000623 FLPLNIRNS(ph)PFTR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLPLNIRNSPFTR 13 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 FLPLNIRNS(1)PFTR 193.32 1.19E-06 459990000 634920 678560 317220 314090 413220 504550 318940 377480 349620 323480 TRUE FALSE 610106.6245 659208.1332 374548.7105 330300.2225 426511.5966 514752.3467 322843.2831 369684.9061 309932.6033 301570.4115 2.023098425 2.185917809 1.241994228 1.09526734 1.414301869 1.706906006 1.070540314 1.225865974 1.027728821 1 18.20213536 4.235240689 24.99936696 1.241158729 2.104508296 0.749639509 0.203591169 37.15849689 279816.1825 0.051591478 0.119194479 17188.60728 -4.235240689 0.863349566 LAIRES(ph)IESEIR ddPTM_BT-474_Pertuzumab_2h_R1 3 LAIRESIESEIR 12 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 LAIRES(1)IESEIR;LAIRES(1)IESEIR;LAIRES(1)IESEIR 169.02 2.72E-05 322897000 381426 374363 396625 482065 472952 436358 453127 473851 503884 534274 TRUE FALSE 366519.4502 363686.5338 468303.9604 506944.4324 488164.9306 445181.4577 458672.5038 464065.8113 446685.2008 498087.1461 0.735854063 0.730166471 0.94020487 1.017782604 0.980079358 0.893782265 0.920867979 0.931696019 0.896801301 1 18.92603865 4.235253406 9.356432605 0.944955078 0.73265245 0.828046422 0.039110286 0.03769375 44.50097946 0.010214476 0.024333235 17189.11059 -4.235253406 -0.212302628 ASKSS(ph)PAGNSPAPL ddPTM_BT-474_Pertuzumab_2h_R1 1 ASKSSPAGNSPAPL 14 1 B4DSP0;A0A087WZG9;Q86TG7-2 B4DSP0 PEG10 Retrotransposon-derived protein PEG10 1 AS(0.007)KS(0.215)S(0.778)PAGNSPAPL 134.88 9.51E-05 409070000 797420 907110 485360 468300 649090 836360 570850 566610 666240 593750 TRUE FALSE 766255.9448 881240.111 573075.3488 492469.0191 669968.5693 853271.7722 577836.2331 554909.3055 590611.2283 553534.7836 1.384295924 1.592023007 1.035301422 0.889680348 1.210345924 1.541496212 1.043902299 1.002483172 1.066981237 1 19.07831445 4.235272581 24.99945022 1.102805168 1.488159516 0.446181715 0.173480693 73.53229594 559096.0841 0.04606343 0.106444467 17189.86955 -4.235272581 0.385354347 GDVVIVLTGWRPGSGFTNTMR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDVVIVLTGWRPGSGFTNTMR 21 1 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 186.15 3.04E-17 1044180000 565570 631140 587230 897240 789620 775110 815820 633300 667670 750480 FALSE TRUE 543466.8991 613140.5052 693355.5239 943546.6639 815018.8444 790783.2553 825804.2492 620222.1337 591878.9007 699649.3211 0.776770423 0.876354034 0.991004354 1.348599413 1.164896213 1.130256589 1.180311656 0.886475717 0.84596509 1 19.41627247 4.235314466 3.103127148 1.079492155 0.806171555 0.340929027 0.139668402 0.296429539 5.76564939 0.039261347 0.117483768 17191.52749 -4.235314466 -0.273320599 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGKR ddPTM_BT-474_Pertuzumab_2h_R1 3 TGDLGIPPNPEDRSPSPEPIYNSEGKR 27 2 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 TGDLGIPPNPEDRS(1)PS(0.996)PEPIYNS(0.004)EGKR;TGDLGIPPNPEDRS(1)PS(0.999)PEPIYNS(0.001)EGKR;TGDLGIPPNPEDRS(0.999)PS(0.998)PEPIY(0.001)NS(0.001)EGKR 119.5 0.00013008 1797330000 1624390 1693650 887870 756330 1062000 1376300 894520 1068820 1253190 894850 TRUE FALSE 1560907.043 1645348.76 1048327.86 795364.2819 1096160.194 1404129.729 905467.4033 1046748.493 1110933.125 834241.0125 1.871050475 1.972270286 1.256624697 0.953398682 1.313961047 1.683122393 1.085378673 1.25473152 1.331669276 1 19.67010471 4.235357844 24.9888736 1.245067862 1.92166053 0.664797651 0.194965988 43.02072878 335670.6197 0.048609414 0.112451411 17193.2447 -4.235357844 0.676592668 EQLMFPFHFVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQLMFPFHFVDR 12 0 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 105.19 0.001002 0 439210 453710 318930 374530 337890 368610 373160 418640 444580 375500 FALSE TRUE 422045.1876 440770.635 376567.7456 393859.5382 348758.5387 376063.5468 377726.8437 409994.9377 394113.1422 350067.0505 1.20561243 1.259103461 1.075701769 1.125097428 0.996262111 1.074261477 1.079012844 1.171189739 1.125821872 1 18.41727175 4.235396856 24.99997156 1.089471868 1.23235797 0.563924545 0.052841847 57.08103172 451068.7407 0.013714047 0.03170694 17194.78921 -4.235396856 0.142886102 QQQQEALRR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQQQEALRR 9 1 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 84.817 0.02635 0 32808 31458 27867 29553 35295 32010 31453 33300 32482 36637 FALSE TRUE 31525.82709 30560.84864 32903.1868 31078.23387 36430.29573 32657.26413 31837.93122 32612.34336 28794.77954 34155.54336 0.923007629 0.894755159 0.963333725 0.909903073 1.0665998 0.956133644 0.932145359 0.954818462 0.843048498 1 15.05983212 4.235423076 24.97681324 0.953194948 0.90888139 0.094965512 0.054785085 175.9804989 1400969.315 0.013342305 0.030895039 17195.82734 -4.235423076 -0.044313558 VADEDDVDNEEAALLHEEATMTIEELLTR ddPTM_BT-474_Pertuzumab_2h_R1 16 VADEDDVDNEEAALLHEEATMTIEELLTR 29 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;;;;;;;;;;;;;; 341.13 1.10E-105 2176165000 615277.1 645872.8 627293.7 754298.4 726180.4 731106.1 788742.3 763932.1 860108.4 972375.4 FALSE TRUE 591231.3907 627453.1401 740659.6257 793227.8308 749538.6521 745889.5663 798395.1642 748156.6352 762472.5003 906515.5481 0.652202151 0.69215927 0.817040179 0.875029482 0.826834855 0.822809457 0.880729697 0.825310318 0.841102507 1 19.78997224 4.235448519 2.665752915 0.855811185 0.656271366 0.702984022 0.049961877 0.138333725 1.94148941 0.01172926 0.038188924 17196.83479 -4.235448519 -0.199539819 EEVVGGDDSDGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEVVGGDDSDGLR 13 0 P25490 P25490 YY1 Transcriptional repressor protein YY1 0 122.51 0.00036958 0 77293 77033 79882 97593 91771 85791 90584 100990 105560 104600 FALSE TRUE 74272.30411 74836.09426 94318.45437 102629.7864 94722.89756 87525.7528 91692.59409 98904.52121 93577.27134 97515.34883 0.76164732 0.767428873 0.9672165 1.052447514 0.971363982 0.897558732 0.940288838 1.014245679 0.959615819 1 16.5733417 4.235461166 6.392682499 0.976308096 0.762564359 0.820158429 0.039508204 0.053648523 9.424135593 0.010508014 0.025793769 17197.3356 -4.235461166 -0.213743737 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 SFREPAPAEALPQQYPEPAPAALCGPPPRAPSR 33 2 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R 98.987 4.39E-05 126980000 88048 87040 30584 28369 39700 51250 24105 37576 33296 21615 TRUE FALSE 84606.98682 84557.70442 36111.20914 29833.12749 40976.98655 52286.31011 24400.0042 36800.04247 29516.37767 20150.9968 4.198650204 4.196204549 1.79203091 1.480478995 2.033496753 2.594725742 1.210858423 1.826214496 1.464760179 1 14.29856359 4.235494131 7.33773894 1.720070102 4.210767584 0.851238774 0.42148107 0.038824516 12.84518369 0.101828942 0.246512738 17198.64099 -4.235494131 2.490697481 KIDKYTEVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KIDKYTEVLK 10 2 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 122.33 0.00027645 725570000 2298400 2450500 1242020 898770 1475560 1823420 1461610 1546820 1844570 1519210 FALSE TRUE 2208575.987 2380614.139 1466480.643 945155.6274 1523022.727 1860290.802 1479497.62 1514877.626 1635182.147 1416312.554 1.559384602 1.68085366 1.035421623 0.667335487 1.075343662 1.313474767 1.044612375 1.069592741 1.154534811 1 20.43370825 4.235513484 24.99672977 1.045933308 1.620119252 0.689996694 0.154186031 40.55266421 332680.306 0.04050397 0.093864839 17199.40741 -4.235513484 0.574185944 TPS(ph)PARPALR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSPARPALR 10 1 Q9H211 Q9H211 CDT1 DNA replication factor Cdt1 1 T(0.105)PS(0.895)PARPALR 81.918 0.011852 450680000 150540 167070 149530 197360 176150 214770 204880 176440 206510 224760 TRUE FALSE 144656.7304 162305.3272 176553.3973 207545.7733 181816.0247 219112.7966 207387.3827 172796.4523 183067.8506 209536.805 0.690364303 0.774591018 0.842588954 0.990497938 0.867704481 1.045700761 0.98974203 0.824659192 0.873678734 1 17.67684415 4.235554853 1.861366383 0.932293449 0.697177509 0.610476534 0.067464071 0.28446902 1.806943153 0.019294638 0.082986721 17201.04581 -4.235554853 -0.235115941 DLDLDAFAEELER ddPTM_BT-474_Pertuzumab_2h_R1 4 DLDLDAFAEELER 13 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 201.6 2.34E-07 247894000 279756 280971 283837 334913 317053 314983 319458 368368 357551 416743 FALSE TRUE 268822.8262 272957.9822 335132.6598 352197.9001 327251.2977 321352.1721 323367.6226 360761.0721 316963.3095 388516.6254 0.691921037 0.702564483 0.862595415 0.906519508 0.842309637 0.827125922 0.832313475 0.928560191 0.815829462 1 18.56761681 4.235556223 5.301737518 0.873731956 0.694165175 0.646728739 0.053161434 0.091021632 7.668857976 0.012463 0.031478646 17201.10011 -4.235556223 -0.179566781 LEIEPEWAYGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEIEPEWAYGKK 12 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 119.69 0.00078634 814750000 788160 802180 567040 611520 604300 678290 645190 706850 818730 751350 FALSE TRUE 757357.8358 779302.6118 669516.7417 643080.6205 623737.8583 692005.4885 653086.0282 692253.3005 725791.2028 700460.3953 1.081228633 1.112557708 0.955823836 0.918082771 0.890468416 0.987929501 0.932366816 0.988283285 1.036163083 1 19.41794396 4.235584135 24.99968293 0.95976973 1.096893199 0.626608474 0.041058665 43.374636 364320.1904 0.010561557 0.024491747 17202.20562 -4.235584135 0.137123469 KEVEVVEIIQATIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEVEVVEIIQATIIR 15 1 Q14764;H3BQK6;I3L155 Q14764 MVP Major vault protein 0 120.24 0.00023901 112710000 134500 131910 112850 128140 136390 127920 133260 128200 151260 143890 FALSE TRUE 129243.5913 128148.056 133244.5053 134753.3208 140777.1082 130506.63 134890.8757 125552.6252 134089.5989 134144.2021 0.963467591 0.955300743 0.993293062 1.004540775 1.049446088 0.972883121 1.005566201 0.935952678 0.999592951 1 17.03342518 4.235606617 24.91571613 0.99196419 0.959384161 0.21203144 0.027030756 120.3258098 1014935.831 0.007329681 0.016993555 17203.09617 -4.235606617 -0.032580029 YGIICMEDLIHEIYTVGKR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGIICMEDLIHEIYTVGKR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 248.97 3.87E-25 940080000 907400 1011050 525090 504730 648650 961330 582970 616100 710340 595870 FALSE TRUE 871937.8048 982215.8439 619985.4436 530779.1758 669514.4163 980768.7513 590104.5612 603377.3197 629705.1812 555511.1942 1.569613383 1.768129705 1.116062917 0.955478812 1.205222187 1.76552473 1.062273033 1.086165906 1.133559841 1 19.08345646 4.235626688 24.99952039 1.173597044 1.668871626 0.460783193 0.217656829 63.23910661 538870.4927 0.05635693 0.130770793 17203.89121 -4.235626688 0.495274582 SQPERDWVLNEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQPERDWVLNEFR 13 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 183.96 9.04E-06 1037410000 653620 836690 270240 332380 438210 524910 381170 337220 388460 323950 FALSE TRUE 628075.8078 812828.4204 319078.3795 349534.1716 452305.4226 535524.0398 385834.8725 330256.2892 344363.6494 302008.578 2.079662147 2.691408389 1.056520916 1.157365046 1.497657536 1.773208044 1.277562628 1.093532811 1.140244597 1 18.20423 4.235644476 24.99999993 1.268889318 2.385535419 0.75446983 0.259037508 32.94628948 282458.4682 0.066571354 0.154527565 17204.59589 -4.235644476 1.116646101 LWSDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LWSDFK 6 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 99.919 0.088987 242430000 702340 659490 669530 764760 770750 665710 791000 825600 884580 871970 FALSE TRUE 674891.7763 640681.9909 790528.9646 804229.3552 795541.8737 679171.1123 800680.4946 808551.0715 784166.1869 812910.6952 0.830216382 0.788133303 0.972467172 0.989320672 0.978633789 0.835480596 0.98495505 0.99463702 0.964640017 1 19.63273734 4.235678314 24.99994589 0.964262117 0.809174811 0.649145623 0.045825923 41.46117028 359631.4879 0.011751296 0.027282881 17205.93644 -4.235678314 -0.155087306 KGGQLS(ph)PVCNGGIMTPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGGQLSPVCNGGIMTPPK 18 1 O96020-2;O96020 O96020-2 CCNE2 G1/S-specific cyclin-E2 1 KGGQLS(1)PVCNGGIMTPPK 165.62 1.70E-11 263350000 373820 367810 253260 282200 278620 288250 270170 334340 319270 324040 TRUE FALSE 359210.7011 357320.4189 299029.7157 296764.3758 287582.0653 294078.6125 273476.4213 327435.7622 283027.8081 302092.4822 1.189075274 1.182817978 0.989861494 0.982362665 0.951966971 0.973472131 0.90527384 1.083892455 0.936891266 1 18.20463076 4.235678907 5.988444819 0.981010251 1.18833607 0.77992717 0.044197864 0.062441874 8.355625411 0.011109455 0.027520746 17205.95994 -4.235678907 0.20732582 EMDT(ph)ARTPLSEAEFEEIMNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EMDTARTPLSEAEFEEIMNR 20 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 EMDT(0.534)ART(0.466)PLSEAEFEEIMNR 78.236 0.024989 73349000 59661 51513 55639 67822 59698 60526 62648 57716 66382 72650 TRUE FALSE 57329.38216 50043.89968 65694.20498 71322.30155 61618.24039 61749.87719 63414.70496 56524.14443 58846.59366 67729.35079 0.846448128 0.738880546 0.969951789 1.053048652 0.909771608 0.911715179 0.936295775 0.834559076 0.868849221 1 16.04749355 4.235689724 24.99999766 0.927265027 0.792664326 0.437063314 0.064308357 69.88043203 608549.155 0.017252939 0.040061079 17206.38848 -4.235689724 -0.134600701 KFMNPFNMPNLYQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFMNPFNMPNLYQK 14 1 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 176.51 3.55E-06 489290000 767090 808940 420390 461340 489880 433950 549850 504550 577290 541320 FALSE TRUE 737111.2747 785869.8232 496363.8245 485149.8127 505637.4351 442724.7663 556579.2288 494130.8662 511758.4594 504655.9142 1.460621493 1.557238905 0.983568825 0.96134772 1.001944931 0.877280448 1.102888549 0.97914411 1.014074035 1 18.94494054 4.235757961 24.99999995 0.990117023 1.508930315 0.9310191 0.05649734 13.66855883 121929.8844 0.013309123 0.030926478 17209.09219 -4.235757961 0.518813291 RNPS(ph)PDHSYKR ddPTM_BT-474_Pertuzumab_2h_R1 5 RNPSPDHSYKR 11 2 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 RNPS(1)PDHSYKR;RNPS(1)PDHSYKR;RNPS(0.999)PDHS(0.001)YKR;RNPS(1)PDHSYKR;RNPS(0.997)PDHS(0.002)Y(0.001)KR 138.55 2.88E-05 2430390000 1142465 1182406 823074 878320 939332 1100663 962707 973897 1137658 1057665 TRUE FALSE 1097816.205 1148684.939 971821.781 923650.2005 969546.4669 1122919.16 974488.8962 953785.6866 1008515.833 986028.4075 1.113371782 1.164961303 0.985592072 0.936737921 0.983284517 1.138830435 0.988296979 0.967300414 1.022806063 1 19.91126969 4.235928907 24.99958047 1.000936477 1.139166567 0.525804806 0.05175354 49.04182675 465885.5154 0.013490205 0.031438431 17215.86731 -4.235928907 0.138230091 MEGGGAEVHAQLPSLEGDLRGPDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 MEGGGAEVHAQLPSLEGDLRGPDVK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 128.97 6.36E-05 629850000 478080 492930 348950 380670 361290 468680 414440 439210 475900 416360 FALSE TRUE 459396.1051 478872.119 412013.0274 400316.4243 372911.221 478157.0307 419512.0407 430140.16 421877.8271 388159.5663 1.183523852 1.233699129 1.06145272 1.031319228 0.960716296 1.231856876 1.080772128 1.108152928 1.08686701 1 18.56629032 4.235945871 24.99487657 1.07662814 1.208611514 0.386995328 0.069326177 64.92118654 620621.5073 0.017236796 0.040119314 17216.53982 -4.235945871 0.131983373 LFSLS(ph)NPSLSTTNLSGPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFSLSNPSLSTTNLSGPSR 19 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LFSLS(1)NPSLSTTNLSGPSR;LFSLS(0.936)NPS(0.064)LSTTNLSGPSR;LFSLS(1)NPSLSTTNLSGPSR;LFSLS(1)NPSLSTTNLSGPSR 370.35 5.89E-108 1111633000 665716 622646 464761 493671 515226 418170 449685 623129 528744 432073 TRUE FALSE 639699.0827 604888.7457 548753.6513 519149.4195 531798.7122 426625.6839 455188.3795 610261.1684 468723.1978 402808.3109 1.588098025 1.501678911 1.362319586 1.288824996 1.320227756 1.059128306 1.130037209 1.515016329 1.163638349 1 18.61973392 4.236012956 1.089395215 1.231938137 1.638234401 0.496570554 0.136355101 0.831583124 1.397084941 0.045555669 0.323090534 17219.19945 -4.236012956 0.406296264 HLTGEFEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLTGEFEKK 9 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 234.71 2.28E-10 2269400000 5697500 5837200 3877500 3947200 4400900 5558000 4803900 3660400 6007700 5070600 FALSE TRUE 5474835.401 5670728.771 4578250.505 4150915.465 4542458.945 5670386.568 4862691.565 3584811.461 5325731.082 4727163.746 1.158164958 1.199604896 0.968498396 0.878098515 0.96092693 1.199532505 1.028670007 0.758342984 1.126622933 1 22.17254341 4.236076407 24.98273991 0.974649891 1.178884973 0.290822715 0.115941558 70.7187168 711224.0804 0.030595946 0.071384508 17221.71534 -4.236076407 0.204235082 EFNAEVHRK ddPTM_BT-474_Pertuzumab_2h_R1 4 EFNAEVHRK 9 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;; 140.05 7.14E-05 3581410000 4236280 4766970 2862484 2968212 3673387 4442510 3313133 3545326 4212310 3700890 FALSE TRUE 4070721.494 4631020.683 3379798.534 3121401.777 3791544.829 4532340.596 3353680.113 3472113.779 3734146.228 3450225.424 1.179842182 1.342237134 0.979587743 0.904695025 1.098926697 1.313636079 0.97201768 1.006344036 1.082290508 1 21.71825919 4.236085785 24.99999486 1.045454584 1.261039677 0.379466024 0.110663464 63.17765218 638231.2364 0.028656905 0.066858152 17222.08725 -4.236085785 0.215585093 LNDYIFSFDK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNDYIFSFDK 10 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 100.55 0.0091532 121040000 209040 216810 158560 170040 206430 165070 200850 183620 241480 205830 FALSE TRUE 200870.4857 210626.7911 187215.3191 178815.7848 213070.0084 168407.8285 203308.0624 179828.1828 214068.2028 191888.9508 1.046805899 1.097649397 0.975644082 0.931871189 1.110381851 0.877631713 1.059508959 0.937147147 1.115583789 1 17.54991212 4.23618174 24.99941345 0.995844072 1.072227656 0.126309364 0.073986209 99.5098051 1045788.592 0.016683394 0.038996872 17225.89278 -4.23618174 0.076383584 LGHEEQQKR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGHEEQQKR 9 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ;; 146.69 6.11E-05 604352000 707030 751000 527608 602894 558760 691720 719920 547790 803110 760430 FALSE TRUE 679398.4859 729582.2153 622958.5022 634009.4316 576733.0229 705707.0523 728730.5963 536477.9451 711944.3197 708925.3988 0.95834976 1.029138209 0.878736329 0.894324611 0.81353133 0.995460247 1.027936928 0.756748095 1.004258447 1 19.43527429 4.236196926 24.96916985 0.908335991 0.993743989 0.085540627 0.086627487 111.516833 1178083.288 0.02130426 0.049799105 17226.49513 -4.236196926 0.085407998 DMLLELEEQLAESR ddPTM_BT-474_Pertuzumab_2h_R1 5 DMLLELEEQLAESR 14 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;;; 207.47 2.19E-08 269736400 189751 202828.3 193825 238798 230136 225358 241481 264843 253379 274632 FALSE TRUE 182335.3211 197043.8355 228853.4891 251122.3934 237538.5334 229914.8932 244436.3167 259373.8995 224616.4782 256030.93 0.712161305 0.769609498 0.893850946 0.980828345 0.927772802 0.897996555 0.954714013 1.013056897 0.877302122 1 17.96595858 4.23622707 2.278774788 0.951965632 0.716221491 0.810154581 0.040370507 0.125450674 1.256851079 0.010771887 0.039144057 17227.69086 -4.23622707 -0.235744141 SVVS(ph)DLEADDVKGSVPLSSSPPATHFPDETEITNPVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 S(0.004)VVS(0.996)DLEADDVKGSVPLSSSPPATHFPDETEITNPVPK;S(0.021)VVS(0.979)DLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 280.87 7.33E-77 140913000 142926 148573 88511 82322 114879 124374 104473 107949 112233 92181 TRUE FALSE 137340.2939 144335.8435 104506.9066 86570.64829 118574.1874 126888.9275 105751.5718 105719.8154 99492.78036 85937.49876 1.598141625 1.679544385 1.216080385 1.007367558 1.379772382 1.476525723 1.230563763 1.230194234 1.157734188 1 16.39100017 4.23622748 24.99871294 1.229323687 1.638843099 0.597917776 0.139360511 38.58359783 413429.34 0.035209107 0.082268017 17227.70712 -4.23622748 0.409519412 VS(ph)LERLDLDLTADSQPPVFK ddPTM_BT-474_Pertuzumab_2h_R1 4 VSLERLDLDLTADSQPPVFK 20 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 VS(1)LERLDLDLTADSQPPVFK;VS(1)LERLDLDLTADSQPPVFK;VS(1)LERLDLDLTADSQPPVFK;VS(1)LERLDLDLTADSQPPVFK 244.21 4.24E-30 861389000 1460360 1462060 969370 905450 1180300 1370430 1076400 1158970 1210620 1111350 TRUE FALSE 1403287.517 1420363.48 1144556.723 952180.383 1218265.421 1398141.034 1089573.305 1135036.864 1073195.493 1036077.275 1.354423604 1.370904965 1.104702082 0.919024484 1.175844168 1.349456327 1.051633244 1.095513715 1.035825724 1 19.98270018 4.236295203 20.90750709 1.098551726 1.362664954 0.500131871 0.108253631 5.868870203 54191.45288 0.027863995 0.065461613 17230.39378 -4.236295203 0.264113229 VAHALAEGLGVIACIGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAHALAEGLGVIACIGEK 18 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 ; 220.59 6.70E-19 598920000 1347110 1326670 779910 913560 908960 973440 814490 847400 1098140 953090 FALSE TRUE 1294463.452 1288834.671 920857.086 960708.9411 938197.5239 993123.6238 824457.9723 829900.8939 973483.751 888536.3654 1.456849154 1.450514262 1.036375237 1.081226361 1.055890969 1.117707347 0.927883207 0.934008923 1.095603724 1 19.7610713 4.236314087 6.71334161 1.02349716 1.457048229 0.887519448 0.060146707 0.040300171 8.803061178 0.016807052 0.04114251 17231.14301 -4.236314087 0.433551069 RSDS(ph)PENKYSDSTGHSK ddPTM_BT-474_Pertuzumab_2h_R1 4 RSDSPENKYSDSTGHSK 17 2 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 RSDS(1)PENKYSDSTGHSK;RS(0.002)DS(0.997)PENKYS(0.001)DSTGHSK;RS(0.001)DS(0.999)PENKYSDSTGHSK;RSDS(1)PENKYSDSTGHSK 226.81 1.02E-15 1137680000 1041730 1165970 508243 464897 641160 947010 567756 591397 791250 540723 TRUE FALSE 1001018.04 1132717.677 600093.8159 488890.3899 661783.4937 966159.191 574704.3678 579184.4453 701430.6172 504099.3496 1.985755468 2.247012773 1.190427673 0.96982944 1.312803705 1.916604717 1.140061713 1.148949003 1.391453129 1 18.94334857 4.23632354 24.99993675 1.266402977 2.116384296 0.637419135 0.258676852 33.63211091 375867.4565 0.066186179 0.154821188 17231.51809 -4.23632354 0.849981319 YDLSGRPLNIKEDPDGENARR ddPTM_BT-474_Pertuzumab_2h_R1 1 YDLSGRPLNIKEDPDGENARR 21 3 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 82.36 0.0018351 44464000 478350 549400 282640 278790 350300 510350 321400 380700 393390 323430 FALSE TRUE 459655.5532 533731.6499 333719.3353 293178.3853 361567.7176 520669.6267 325333.3893 372838.412 348734.0164 301523.798 1.524442038 1.77011451 1.106776107 0.97232254 1.199134927 1.726794469 1.078964219 1.236514048 1.156572114 1 18.20191235 4.236352545 24.99999963 1.201307267 1.647278337 0.443792525 0.20650001 49.63629753 562016.3098 0.051888396 0.121454171 17232.66896 -4.236352545 0.44597107 S(ph)STGPEPPAPTPLLAER ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTGPEPPAPTPLLAER 17 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.932)S(0.068)TGPEPPAPTPLLAER 249.41 5.23E-21 102440000 160380 144060 166590 202380 178270 152350 203420 199040 203160 232760 TRUE FALSE 154112.1723 139951.5498 196696.5188 212824.8561 184004.2165 155430.6214 205909.5148 194929.7544 180098.1285 216994.9579 0.710210845 0.644953004 0.906456632 0.980782494 0.847965401 0.716286788 0.948913822 0.898314672 0.829964577 1 17.72730199 4.23642321 24.99999694 0.886674856 0.677581881 0.540085015 0.078724339 38.78575499 453678.9938 0.019595484 0.045896987 17235.47314 -4.23642321 -0.209092976 MYEEHLKR ddPTM_BT-474_Pertuzumab_2h_R1 4 MYEEHLKR 8 1 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;; 199.29 8.38E-05 4175020000 3520170 3560860 2522110 2755995 3081143 3050694 2922780 2866670 3468870 3235520 FALSE TRUE 3382597.865 3459307.759 2977911.381 2898232.232 3180250.763 3112381.123 2958549.856 2807472.263 3075098.42 3016375.348 1.121411454 1.146842604 0.987248282 0.960832754 1.054328588 1.031828192 0.980829477 0.93074367 1.019468092 1 21.52438453 4.236465233 24.99973942 0.991364325 1.134127064 0.725957905 0.033947845 26.73150829 318947.965 0.00937264 0.021956212 17237.14095 -4.236465233 0.142762739 YRDPTTVTTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YRDPTTVTTLR 11 1 P63151;P63151-2;A0A590UJY3 P63151 PPP2R2A Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform 0 ; 144.28 3.36E-05 1198100000 486060 410490 419680 434370 470860 419710 454240 510780 446460 492120 FALSE TRUE 467064.2378 398783.2271 495525.5117 456787.8878 486005.6395 428196.8238 459799.125 500232.2145 395779.7325 458788.2741 1.018038743 0.86920972 1.080074491 0.995639849 1.059324457 0.933321203 1.002203306 1.090333478 0.862663139 1 18.80746899 4.23648163 24.9999983 1.009603457 0.943624253 0.090866915 0.072652014 103.4559878 1244137.014 0.016967705 0.039754858 17237.79177 -4.23648163 -0.065979205 IQVLQQQADDAEERAER ddPTM_BT-474_Pertuzumab_2h_R1 2 IQVLQQQADDAEERAER 17 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;Q5VU61;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ; 152.11 2.05E-07 451850000 332220 454620 98299 94854 214340 344250 143943 116539 143332 122990 FALSE TRUE 319236.4751 441654.6827 116063.8159 99749.42631 221234.4408 351210.9709 145704.6175 114132.4289 127061.5523 114659.7778 2.784206296 3.851871087 1.012245255 0.869960053 1.929486042 3.063070396 1.270756148 0.995400751 1.108161508 1 16.80699986 4.236482311 24.99999621 1.433479684 3.318038954 0.566074524 0.669228481 37.93976989 456403.8479 0.177600729 0.416284578 17237.8188 -4.236482311 1.884559271 QQASKS(ph)PYNGVR ddPTM_BT-474_Pertuzumab_2h_R1 5 QQASKSPYNGVR 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 QQAS(0.33)KS(0.67)PYNGVR;QQAS(0.001)KS(0.999)PYNGVR;QQAS(0.114)KS(0.886)PYNGVR;QQAS(0.076)KS(0.924)PYNGVR;QQAS(0.002)KS(0.998)PYNGVR 228.9 5.74E-12 3142530000 3473180 3442130 2306688 2351212 2596170 2774960 2559190 3032850 3104340 2699130 TRUE FALSE 3337444.286 3343963.823 2723557.834 2472558.333 2679678.166 2831071.592 2590510.133 2970220.588 2751948.338 2516315.521 1.326321861 1.328912767 1.08235943 0.982610612 1.064921368 1.125086091 1.029485417 1.180384798 1.093641999 1 21.2628814 4.236493702 9.086784472 1.077986894 1.328137148 0.775306607 0.055377143 0.044273656 46.27046051 0.014365624 0.034467041 17238.27091 -4.236493702 0.250150254 EEVVGGDDS(ph)DGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEVVGGDDSDGLR 13 0 P25490 P25490 YY1 Transcriptional repressor protein YY1 1 EEVVGGDDS(1)DGLR;EEVVGGDDS(1)DGLR 254.38 8.71E-24 738990000 716920 671350 778230 999380 810620 762620 969050 975420 912600 1038220 TRUE FALSE 688901.9738 652203.7553 918873.4726 1050958.122 836694.3285 778040.6989 980909.5238 955277.2361 809005.4739 967900.4346 0.711748801 0.673833518 0.949347102 1.085812222 0.864442559 0.803843733 1.013440524 0.986958164 0.835835428 1 19.88449912 4.236499256 24.99941472 0.945356484 0.692791096 0.593084308 0.082693633 33.22672298 402983.9205 0.021015635 0.049269162 17238.49137 -4.236499256 -0.252565389 RRSS(ph)PSARPPDVPGQQPQAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RRS(0.127)S(0.656)PS(0.218)ARPPDVPGQQPQAAK 198.55 4.70E-21 723090000 166250 174350 104940 98144 119460 166850 115580 131690 137310 125660 TRUE FALSE 159752.7662 169377.7087 123904.9924 103209.2236 123302.5394 170223.8213 116994.5026 128970.5555 121723.1445 117148.9363 1.363672358 1.445832238 1.057670657 0.881008628 1.052528032 1.453054776 0.998681732 1.100911025 1.039046092 1 16.83798433 4.236503725 24.99824949 1.07951979 1.404752371 0.469837006 0.140879405 43.90456533 533620.7135 0.035863641 0.084084063 17238.66875 -4.236503725 0.32523258 AQQNNVEHKVETFSGVYK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQQNNVEHKVETFSGVYK 18 1 P62081;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 181.4 4.43E-14 638850000 574190 575800 351920 316620 362160 528280 422690 394500 488990 426270 FALSE TRUE 551750.02 559378.7478 415519.7724 332960.7961 373809.2053 538962.1836 427863.0067 386353.4371 433481.9052 397398.3532 1.388405401 1.407602078 1.045600137 0.837851474 0.940641053 1.356226515 1.076660241 0.97220694 1.09079945 1 18.60022637 4.236522472 20.33966398 1.038005767 1.398004825 0.559995703 0.126926464 3.503935626 34994.47358 0.033318848 0.07851479 17239.41293 -4.236522472 0.359999058 FSEAEHWLDYFPPLAIQDLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSEAEHWLDYFPPLAIQDLKR 21 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 116.44 8.44E-05 84401000 143130 145710 96720 93643 118210 143410 104740 105510 135620 122340 FALSE TRUE 137536.3214 141554.4935 114199.4555 98475.92645 122012.332 146309.8485 106021.8395 103331.1816 120224.9862 114053.8028 1.205889834 1.241120331 1.001277052 0.863416423 1.069778727 1.282814293 0.929577417 0.905986289 1.054107651 1 16.79935502 4.236579815 24.99057774 1.006540478 1.223505136 0.369733979 0.109452716 51.60264484 651078.0001 0.029224228 0.068630232 17241.6893 -4.236579815 0.216964659 GITGVEDKESWHGKPLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GITGVEDKESWHGKPLPK 18 2 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 223.5 3.07E-19 960640000 2113700 2240200 1180700 1209900 1471100 1426100 1390600 1456000 1719300 1580000 FALSE TRUE 2031094.267 2176311.689 1394078.755 1272343.084 1518419.268 1454936.719 1407618.579 1425933.091 1524132.272 1472985.193 1.378896595 1.477483752 0.946430936 0.863785387 1.030844896 0.987747009 0.955623034 0.968056636 1.034723417 1 20.4903115 4.236602162 24.99999595 0.969919545 1.428190283 0.927090748 0.051007756 10.34155954 132019.5286 0.012472316 0.02928179 17242.5765 -4.236602162 0.458270738 ALSS(ph)DSILSPAPDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.309)S(0.687)DS(0.005)ILSPAPDAR;ALS(0.278)S(0.718)DS(0.004)ILSPAPDAR;ALS(0.301)S(0.698)DS(0.001)ILSPAPDAR 393.84 1.22E-114 4044590000 1213880 1216230 875160 1061080 887480 839330 909780 1453680 954260 986240 TRUE FALSE 1166440.228 1181544.311 1033320.88 1115842.466 916026.6002 856301.8277 920914.1598 1423661 845936.4054 919441.0863 1.268640531 1.285067993 1.12385763 1.213609531 0.996286346 0.931328652 1.00160214 1.548398284 0.92005504 1 19.81039761 4.236629937 23.74695116 1.124001188 1.27685432 0.129083106 0.177105377 61.7887714 760082.388 0.047504636 0.11171862 17243.67928 -4.236629937 0.152853132 KLEEELEGMR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLEEELEGMR 10 1 P15924 P15924 DSP Desmoplakin 0 ; 179.19 3.42E-06 498290000 1039460 989570 987800 1128470 1063650 1037700 1145880 1266560 1308150 1248270 FALSE TRUE 998836.754 961348.4325 1166317.433 1186710.472 1097863.268 1058683.005 1159903.622 1240405.093 1159654.296 1163723.561 0.858311018 0.826096905 1.002228942 1.019752896 0.943405552 0.909737536 0.996717486 1.065893254 0.996503238 1 20.15031696 4.236644335 24.99999783 0.99451408 0.842203925 0.688766882 0.040185118 28.22096729 368195.7337 0.011533622 0.027085541 17244.25097 -4.236644335 -0.152310155 VTKS(ph)PGETSKPRPFAGGGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTKSPGETSKPRPFAGGGYR 20 3 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 VT(0.095)KS(0.898)PGET(0.006)S(0.001)KPRPFAGGGYR 83.202 0.016386 1452400000 686880 720380 452500 419300 485900 708440 506080 584080 573390 628150 TRUE FALSE 660035.9702 699835.4677 534276.8158 440940.1232 501529.4148 722765.1422 512273.5584 572018.5439 508301.171 585604.841 1.127101287 1.195064348 0.912350408 0.752965297 0.856429762 1.23421989 0.87477685 0.976799548 0.867993458 1 19.15956795 4.236692088 24.98447155 0.934146143 1.161082866 0.360560123 0.120727831 48.60221895 649910.2857 0.030545114 0.071778559 17246.14718 -4.236692088 0.226936723 KVVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVVDYSQFQESDDADEDYGRDSGPPTKK 28 3 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGRDSGPPTKK 227.51 6.15E-34 349800000 209050 240850 60430 41475 85906 150650 68523 72920 92203 59743 TRUE FALSE 200880.0949 233981.1938 71351.04526 43615.52972 88669.24451 153696.2462 69361.60497 71414.17652 81736.50199 55696.5534 3.606688074 4.200999515 1.281067515 0.783092078 1.592005952 2.759528855 1.245348244 1.282201001 1.467532495 1 15.76530043 4.236716799 24.99996433 1.448015829 3.903844367 0.786993093 0.51546757 19.47255995 264041.3213 0.133169001 0.313057481 17247.1285 -4.236716799 2.455828537 LSDFLITGGGKGS(ph)GFSLDVIDGPISQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSDFLITGGGKGSGFSLDVIDGPISQR 27 1 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LSDFLIT(0.002)GGGKGS(0.997)GFS(0.001)LDVIDGPISQR;LSDFLIT(0.001)GGGKGS(0.999)GFSLDVIDGPISQR 159.42 8.97E-12 825580000 1134420 1172800 774340 789260 902400 935030 902140 1060390 1014590 938430 TRUE FALSE 1090085.612 1139352.892 914280.4631 829993.8032 931426.5155 953936.9472 913180.6592 1038492.576 899417.9967 874869.3002 1.245998244 1.302312119 1.045048058 0.948706056 1.064646474 1.090376525 1.043790951 1.187025966 1.028059844 1 19.73870798 4.236723515 24.99835234 1.061998053 1.274155229 0.683371897 0.060398191 27.40604951 372951.1751 0.016289879 0.038296817 17247.39519 -4.236723515 0.212157177 EEHGGLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEHGGLIR 8 0 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;; 153.04 0.0004475 3342840000 3226810 3076480 3247080 3991500 3450020 3547660 3891910 3883250 4025960 4387230 FALSE TRUE 3100702.698 2988741.803 3833899.587 4197501.793 3560993.027 3619396.116 3939540.359 3803059.53 3568949.899 4090079.004 0.758103375 0.730729602 0.937365655 1.026264233 0.870641624 0.884920832 0.963194196 0.929825445 0.872587032 1 21.96369728 4.236750661 24.99502148 0.933519303 0.744416439 0.706051125 0.049328661 22.48266995 310499.6098 0.012081047 0.028417953 17248.4733 -4.236750661 -0.189102864 EYDSISR ddPTM_BT-474_Pertuzumab_2h_R1 2 EYDSISR 7 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 151.29 0.0062246 408250000 1148370 1124620 1104940 1274220 1203070 1217220 1300040 1456570 1385110 1396780 FALSE TRUE 1103490.431 1092546.939 1304627.237 1339982.647 1241767.839 1241833.022 1315950.278 1426491.32 1227878.12 1302174.846 0.847421092 0.839017081 1.001883304 1.02903435 0.953610679 0.953660736 1.010578788 1.095468342 0.942944124 1 20.31249175 4.236781861 22.33066829 1.005079585 0.84321889 0.679560572 0.042425575 6.434233851 80800.42486 0.011570974 0.027292799 17249.7125 -4.236781861 -0.161860696 TAPPALPTGYDS(ph)EEEEESRPMSYDEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TAPPALPTGYDSEEEEESRPMSYDEKR 27 2 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR 231.44 1.69E-35 1786100000 741520 769920 422170 421260 474990 638320 448450 522460 602320 454950 TRUE FALSE 712540.5786 747962.6354 498465.5101 443001.2791 490268.4847 651227.2677 453938.2652 511671.0184 533947.1587 424135.8313 1.679982039 1.763497871 1.175249704 1.044479731 1.155923288 1.535421485 1.070266249 1.206384796 1.258906038 1 18.69416684 4.236788388 24.99998281 1.189902616 1.721740093 0.699528977 0.141702828 22.50101224 317431.9966 0.034608898 0.081452129 17249.97175 -4.236788388 0.531837477 VNIEGGAIALGHPLGASGCR ddPTM_BT-474_Pertuzumab_2h_R1 2 VNIEGGAIALGHPLGASGCR 20 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 199.89 1.41E-21 1710190000 766500 740770 829850 1047080 890980 976420 1019430 929390 1038140 1127060 FALSE TRUE 736544.3326 719643.9649 979822.3549 1101119.924 919639.1809 996163.8814 1031906.089 910197.7717 920294.6994 1050723.222 0.700987964 0.684903455 0.932521842 1.047963822 0.875243986 0.948074488 0.982091256 0.866258357 0.875867859 1 20.00295126 4.236823966 24.64342034 0.936471022 0.692945629 0.759174765 0.055837879 16.3116743 231485.0546 0.014032209 0.033048953 17251.38494 -4.236823966 -0.243525393 TFFPEYTHQLFGDDETAFGYK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFFPEYTHQLFGDDETAFGYK 21 0 O14929 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 0 275.23 9.12E-45 288430000 478830 449510 461190 522220 513450 528960 556240 504270 591510 631670 FALSE TRUE 460116.7942 436690.4149 544537.2921 549171.8368 529965.5856 539655.9336 563047.4315 493856.6483 524364.2646 588886.4283 0.78133367 0.74155286 0.924689831 0.932559846 0.899945321 0.916400698 0.956122275 0.838628001 0.890433604 1 19.1676299 4.236927104 24.99997951 0.91186661 0.76144323 0.698662119 0.041347204 21.68318528 331872.135 0.010209593 0.024062417 17255.48237 -4.236927104 -0.15042338 SLIPDIKPLAGQEAVVDLHADDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLIPDIKPLAGQEAVVDLHADDSR 24 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 152.88 5.20E-08 91697000 152908 142883 152248 164245 166790 170450 194418 167295 197784 210447 FALSE TRUE 146932.1863 138808.1167 179762.6003 172721.7041 172154.9518 173896.6158 196797.3456 163840.2998 175332.3895 196193.2372 0.748915653 0.707507143 0.916252787 0.880365228 0.877476483 0.886353772 1.00307915 0.835096572 0.893671933 1 17.58191579 4.236930217 24.99999714 0.903781459 0.728211356 0.667930778 0.051473032 22.10443762 338966.0216 0.012169329 0.028679916 17255.60606 -4.236930217 -0.175570104 DWEDDS(ph)DEDMSNFDR ddPTM_BT-474_Pertuzumab_2h_R1 29 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR 521.99 3.19E-278 2.75041E+11 38277766.8 35784817.7 34603212.6 38553830.2 38363566.3 37142765.6 40607251.1 40196529.3 47302213.7 42615258.6 TRUE FALSE 36781829.36 34764269.74 40856782.86 40543598 39597565.25 37893817.77 41104214.79 39366456.92 41932664.71 39728889.18 0.925820734 0.875037547 1.028389761 1.02050671 0.996694498 0.953810151 1.034617772 0.990877362 1.055470354 1 25.24368512 4.236931293 24.99996063 1.008041047 0.900429122 0.699536872 0.028711994 20.22375875 310331.3766 0.006848354 0.016140792 17255.64879 -4.236931293 -0.107611924 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTRIIYDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.001)CT(0.464)T(0.528)PGGT(0.117)LFS(0.336)T(0.295)T(0.259)PGGTRIIYDRK 129.09 2.60E-08 125950000 57619 71589 18606 16511 33877 55527 22996 21617 25930 17167 TRUE FALSE 55367.18578 69547.35181 21968.51809 17363.13469 34966.68447 56649.79398 23277.43193 21170.6014 22986.53511 16004.2638 3.459527191 4.345551453 1.372666582 1.084906804 2.184835548 3.539668847 1.454451902 1.322810075 1.436275695 1 13.96616869 4.236978173 24.99999971 1.716165232 3.90253974 0.600808217 0.725828628 27.01342395 426799.8391 0.190411684 0.449170768 17257.51158 -4.236978173 2.186374508 LFIGGLSFETTDESLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LFIGGLSFETTDESLR 16 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;; 263.44 1.41E-26 858972000 338244 326976 286465 329180 317642 340570 339040 330270 337830 392862 FALSE TRUE 325025.0505 317650.9646 338235.5979 346169.0192 327859.2434 347456.5587 343189.2729 323449.8091 299480.9547 366253.1068 0.887432883 0.867299031 0.923502331 0.945163366 0.895171228 0.948678802 0.937027609 0.883131919 0.817688503 1 18.48248147 4.237012755 24.99638528 0.915115864 0.877365951 0.112068413 0.045717214 89.47216091 1445000.116 0.011141459 0.026311301 17258.8858 -4.237012755 -0.037749913 LEVS(ph)PEAQPTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEVSPEAQPTAR 12 0 Q6WKZ4 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 LEVS(1)PEAQPTAR;LEVS(1)PEAQPTAR 150.22 7.13E-05 221410000 216970 242500 230060 281880 291570 319870 309310 332100 314220 320150 TRUE FALSE 208490.5725 235584.1374 271636.9597 296427.8606 300948.6138 326337.9906 313095.4283 325242.0189 278551.0629 298465.9553 0.69854055 0.789316615 0.910110365 0.993171433 1.008318063 1.093384303 1.04901555 1.089712288 0.933275832 1 18.18720685 4.237055016 1.104217261 1.043242868 0.6536843 0.868024363 0.044217684 0.255484388 0.443769166 0.01365628 0.095985286 17260.56534 -4.237055016 -0.389558568 (ac)AKPLTDSEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 AKPLTDSEKR 10 2 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 57.532 0.0036345 405890000 337530 355950 240030 256840 305280 298410 270310 308010 335950 309010 FALSE TRUE 324338.9544 345798.6545 283408.7604 270095.5432 315099.6084 304444.0547 273618.1346 301649.4859 297814.3644 288080.4775 1.125862319 1.200354351 0.983783292 0.937569757 1.093790219 1.056802104 0.94979756 1.047101451 1.033788777 1 18.13611237 4.237059367 24.99983524 1.014617044 1.163108359 0.60527842 0.048525812 23.95577998 398960.2778 0.012064231 0.028481559 17260.73824 -4.237059367 0.148491315 AEGGGGGGRPGAPAAGDGKTEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 AEGGGGGGRPGAPAAGDGKTEQK 23 2 Q00839 Q00839 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 128.38 2.39E-05 446444000 566268 509475 378645 295043 382716 432932 370571 452097 484335 421520 FALSE TRUE 544137.6205 494945.2718 447074.5744 310270.2046 395026.4077 441686.1817 375106.1587 442761.039 429355.3213 392970.0749 1.384679535 1.259498632 1.137680966 0.789551735 1.005232797 1.123968999 0.954541281 1.126704213 1.092590374 1 18.58405993 4.237059695 2.719689863 1.022959387 1.352925539 0.621869837 0.096090533 0.178994887 2.620881681 0.025526349 0.082298264 17260.75128 -4.237059695 0.329966152 ADEDPIMGFHQMFLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADEDPIMGFHQMFLLK 16 0 P61970;H3BRV9 P61970 NUTF2 Nuclear transport factor 2 0 ; 211.7 6.42E-12 3566630000 4478020 4041540 3366760 3241480 3601040 3264910 3427270 3721270 3934780 3988080 FALSE TRUE 4303014.028 3926279.236 3975208.425 3408773.171 3716870.722 3330928.717 3469213.955 3644424.474 3488120.27 3717963.789 1.157357702 1.056029445 1.069189656 0.916838723 0.999706004 0.895901334 0.933095143 0.98022054 0.93818027 1 21.82608129 4.237103786 1.200738119 0.949929791 1.160807769 0.734034092 0.039560546 0.345359863 0.74204412 0.011287846 0.07376315 17262.50374 -4.237103786 0.210877978 IDASKNEEDEGHSNSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHS(0.012)NS(0.029)S(0.959)PR;IDASKNEEDEGHSNS(0.363)S(0.637)PR;IDASKNEEDEGHSNS(0.194)S(0.806)PR;IDASKNEEDEGHSNS(0.357)S(0.643)PR;IDASKNEEDEGHS(0.001)NS(0.247)S(0.753)PR;IDASKNEEDEGHSNS(0.086)S(0.914)PR;IDASKNEEDEGHS(0.229)NS(0.195)S(0.576)PR;IDASKNEEDEGHSNS(0.068)S(0.932)PR 317.27 4.42E-43 25478230000 24722250 23405720 14329650 12809830 17142110 19830910 14485980 15324010 19452830 14346700 TRUE FALSE 23756077.14 22738211.78 16919336.52 13470946.86 17693501.54 20231904.59 14663263.76 15007563.84 17244626.29 13374985.23 1.776157261 1.700055095 1.26499852 1.007174709 1.32288008 1.512667434 1.096319996 1.122062087 1.289319277 1 23.67303396 4.237107401 4.131255572 1.200729327 1.757552414 0.683827478 0.146834116 0.110998748 4.29935441 0.037719855 0.1013677 17262.64746 -4.237107401 0.556823087 LNS(ph)GGGLSEELGSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNSGGGLSEELGSAR 15 0 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 LNS(0.999)GGGLS(0.001)EELGSAR;LNS(1)GGGLSEELGSAR 227.73 7.26E-13 296320000 250924 233593 217555 244539 235197 244215 234824 274630 261640 269347 TRUE FALSE 241117.6127 226931.1564 256872.028 257159.6871 242762.3251 249153.1946 237697.8464 268958.7945 231939.7241 251103.8878 0.960230504 0.903734141 1.022971131 1.024116709 0.966780432 0.992231529 0.946611574 1.071105656 0.923680339 1 17.93792484 4.237115915 24.99997061 0.99744341 0.931982319 0.253851821 0.041694085 42.82680405 741159.7266 0.009913357 0.023430093 17262.98589 -4.237115915 -0.065461092 DELLAQHAAGALGLPDLVAVLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 DELLAQHAAGALGLPDLVAVLTR 23 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 129.78 3.71E-05 176560000 159836 155845 150721 172975 155968 192154 166698 181539 202231 199855 FALSE TRUE 153589.4324 151400.4532 177959.6375 181902.2605 160984.8524 196039.4855 168738.1 177790.1562 179274.5847 186318.6428 0.824337437 0.812588858 0.955135969 0.976296616 0.864029761 1.052173215 0.905642599 0.954226338 0.962193487 1 17.50741251 4.237125351 24.82792268 0.954854122 0.818463104 0.579362131 0.047710724 20.66520114 357509.0475 0.010887211 0.025734009 17263.36095 -4.237125351 -0.136391018 VSGRT(ph)SPPLLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.061)GRT(0.571)S(0.368)PPLLDR;VS(0.045)GRT(0.512)S(0.443)PPLLDR;VS(0.016)GRT(0.712)S(0.273)PPLLDR;VS(0.015)GRT(0.619)S(0.366)PPLLDR 104.21 0.003497 5001390000 5389960 6532270 2070540 2075790 3227880 5216950 2593210 2478490 2867850 2114200 TRUE FALSE 5179314.404 6345976.055 2444732.637 2182921.771 3331707.692 5322440.303 2624946.48 2427308.315 2542303.691 1971003.351 2.627755251 3.219667817 1.240349305 1.107518041 1.690361252 2.700371007 1.331781845 1.231508975 1.289852546 1 20.9104988 4.237166301 24.9999552 1.478330737 2.923711812 0.606377944 0.474803156 23.47736906 420982.9547 0.123768957 0.292649659 17264.98882 -4.237166301 1.445381075 NEEDEGHSNSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHSNS(0.372)S(0.628)PR;NEEDEGHSNS(0.02)S(0.98)PR;NEEDEGHSNS(0.11)S(0.89)PR;NEEDEGHSNS(0.219)S(0.781)PR;NEEDEGHS(0.001)NS(0.052)S(0.948)PR;NEEDEGHSNS(0.031)S(0.969)PR;NEEDEGHSNS(0.022)S(0.977)PR;NEEDEGHSNS(0.037)S(0.963)PR 195.46 9.93E-08 44066556000 11185860 10459680 10008030 12135380 11121760 10865010 11764640 10613520 13608770 12506620 TRUE FALSE 10748704.22 10161380.17 11816703.65 12761688.42 11479501.51 11084707.95 11908619.18 10394347.1 12063959.48 11659535.49 0.921880999 0.871508147 1.013479796 1.094528031 0.984559078 0.950698933 1.021363089 0.891488955 1.034686115 1 23.47500698 4.237174027 24.99942516 0.992098839 0.896694559 0.378281497 0.051810478 39.15468451 705995.7108 0.013698379 0.03237777 17265.29596 -4.237174027 -0.09540428 SSELEGDTITLKPRPSADLTNSSAPS(ph)PSHK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSELEGDTITLKPRPSADLTNSSAPSPSHK 30 2 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 SSELEGDTITLKPRPSADLTNS(0.011)S(0.063)APS(0.916)PS(0.009)HK;SSELEGDTITLKPRPSADLTNS(0.001)S(0.003)APS(0.993)PS(0.003)HK;SSELEGDTITLKPRPSADLTNS(0.001)S(0.006)APS(0.965)PS(0.028)HK 134.19 2.51E-06 658010000 368033 374894 230952 208705 258734 305940 245043 286484 366349 317967 TRUE FALSE 353649.8635 364202.3902 272690.1639 219476.2901 267056.4141 312126.3164 248041.9095 280568.0053 324762.5974 296430.8119 1.193026667 1.228625283 0.919911672 0.740396346 0.900906395 1.05294829 0.836761563 0.946487322 1.095576385 1 18.17733589 4.237188293 24.99962228 0.926485832 1.210826054 0.558625679 0.097159495 23.18146906 422332.8857 0.024403448 0.057697018 17265.86309 -4.237188293 0.284340223 VAHHGENPVSCPELVQQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VAHHGENPVSCPELVQQLR 19 0 Q15648;Q15648-3 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 0 134.21 5.89E-06 288730000 377710 372450 240840 271250 297110 261130 258770 320220 286510 282660 FALSE TRUE 362948.6756 361828.0907 284365.1455 285249.245 306666.813 266410.2275 261936.9047 313607.3451 253986.5859 263515.1864 1.377334948 1.373082499 1.079122419 1.082477442 1.163753851 1.01098624 0.994010661 1.190092113 0.963840412 1 18.00752658 4.237206348 7.228572397 1.072147329 1.377037265 0.761883722 0.070139185 0.053901052 16.67406293 0.017023107 0.041519028 17266.58092 -4.237206348 0.304889936 SFSKEELMS(ph)SDLEETAGSTSIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 S(0.025)FS(0.021)KEELMS(0.845)S(0.11)DLEETAGSTSIPK;S(0.025)FS(0.032)KEELMS(0.471)S(0.471)DLEET(0.001)AGSTSIPK 180.06 2.83E-17 773790000 305910 294100 192771 169095 225748 287670 186051 242700 237970 186668 TRUE FALSE 293954.699 285712.556 227609.0079 177822.0132 233009.3894 293486.8845 188327.9478 237688.1602 210956.6433 174024.8101 1.689153971 1.641792086 1.307911256 1.021819895 1.338943506 1.686465765 1.082190222 1.36582916 1.212221655 1 17.40893348 4.237231168 4.747497026 1.269020957 1.675648145 0.43141588 0.189873774 0.166532723 9.695103517 0.046554126 0.120716629 17267.56773 -4.237231168 0.406627188 HVDSLSQRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 HVDSLSQRSPK 11 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 HVDSLS(0.004)QRS(0.996)PK;HVDSLS(0.001)QRS(0.999)PK;HVDS(0.006)LS(0.005)QRS(0.989)PK 141.54 2.31E-05 302156000 677457 805730 146715 140072 306327 468082 194816 121750 206150 131781 TRUE FALSE 650981.2315 782751.3693 173229.6642 147301.1327 316180.2862 477546.9387 197200.2165 119235.82 182748.7163 122855.3555 5.29876153 6.371324768 1.410029408 1.198980151 2.57359791 3.887066517 1.605141393 0.970538236 1.487511192 1 16.90660122 4.237270463 24.99994845 1.79640963 5.835044113 0.779152332 0.866291932 14.71770506 285218.5537 0.233673551 0.553309227 17269.13017 -4.237270463 4.038634483 S(ph)PSDSSTASTPVAEQIER ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSDSSTASTPVAEQIER 18 0 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 S(0.992)PS(0.008)DSSTASTPVAEQIER;S(0.999)PS(0.001)DSSTASTPVAEQIER;S(0.498)PS(0.498)DS(0.005)STASTPVAEQIER;S(1)PSDSSTASTPVAEQIER 400.72 6.93E-128 3870600000 240416 228966 283924 358493 290814 297965 331192 343995 360895 426314 TRUE FALSE 231020.2769 222436.1139 335235.3827 376994.8667 300168.2964 303990.0565 335245.2268 336891.383 319927.7126 397439.3731 0.581271743 0.55967307 0.843488103 0.948559434 0.75525556 0.764871518 0.843512871 0.847654777 0.804972366 1 18.60037528 4.237292515 24.96033243 0.842601244 0.570472324 0.709445798 0.071658238 15.4199067 303542.5268 0.017100407 0.040499018 17270.00705 -4.237292515 -0.272128919 IPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_BT-474_Pertuzumab_2h_R1 7 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 IPMTPTSSFVSPPPPT(0.076)AS(0.849)PHS(0.076)NR;IPMTPTSSFVSPPPPT(0.014)AS(0.984)PHS(0.001)NR;IPMTPTSSFVSPPPPT(0.096)AS(0.897)PHS(0.007)NR;IPMTPTSSFVSPPPPT(0.01)AS(0.961)PHS(0.029)NR;IPMTPTSSFVSPPPPT(0.231)AS(0.724)PHS(0.045)NR;IPMTPTSSFVSPPPPT(0.243)AS(0.713)PHS(0.044)NR;IPMTPTSSFVSPPPPT(0.052)AS(0.896)PHS(0.052)NR 179.86 3.04E-17 5472090000 936416 871617 936550 1175791 1051364 1006520 1000422 1100452 1179260 1216992 TRUE FALSE 899819.8275 846759.3366 1105805.418 1236473.714 1085182.078 1026872.524 1012665.464 1077727.282 1045395.349 1134564.048 0.793097427 0.746330133 0.974652264 1.089822753 0.956474938 0.905081142 0.892559098 0.949904312 0.921407082 1 20.11370662 4.237349592 25 0.95782278 0.769713734 0.668851202 0.053862231 18.45073098 380928.973 0.014523362 0.034416973 17272.27691 -4.237349592 -0.188109046 QYMEGFNDELEAFKER ddPTM_BT-474_Pertuzumab_2h_R1 2 QYMEGFNDELEAFKER 16 1 Q16543;K7EKQ2;K7EQA9;K7EL68 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 248.13 2.07E-20 357370000 379360 385390 208644 179680 260150 341650 207112 257850 278750 203779 FALSE TRUE 364534.1918 374399.0545 246350.6121 188953.3063 268517.961 348558.3971 209646.6986 252525.3074 247107.4686 189976.8668 1.918834634 1.970761287 1.296740051 0.994612184 1.413424516 1.834741266 1.103538037 1.329242405 1.300723992 1 17.53546423 4.237406647 24.99695438 1.301341896 1.944798153 0.57084837 0.228744847 20.14839088 436494.3142 0.056946478 0.135073168 17274.54619 -4.237406647 0.643456258 LKYALTGDEVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKYALTGDEVKK 12 2 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 55.314 0.072142 370180000 220440 255010 145910 156900 196600 202440 187790 185770 228490 209090 FALSE TRUE 211824.9611 247737.3645 172279.1828 164997.6278 202923.8175 206533.4755 190088.2302 181933.7846 202552.7731 194928.1481 1.086682263 1.270916319 0.883808647 0.846453575 1.041018547 1.059536437 0.97517076 0.933337675 1.039115054 1 17.57258291 4.237458411 24.99997751 0.96928103 1.178799301 0.532620813 0.077332177 20.22209242 458723.0819 0.019444705 0.04615344 17276.60527 -4.237458411 0.209518272 TPKDS(ph)PGIPPSAGAHQLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPKDSPGIPPSAGAHQLFR 19 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;Q5SVM6 E9PGT3 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 1 T(0.037)PKDS(0.963)PGIPPSAGAHQLFR;T(0.002)PKDS(0.998)PGIPPSAGAHQLFR 144.26 8.28E-08 901690000 583380 664500 415250 490920 511110 550610 514060 535340 642920 582770 TRUE FALSE 560580.8646 645549.1106 490294.9122 516256.44 527550.3173 561743.7115 520351.2201 524285.0419 569938.4169 543298.4688 1.031810132 1.188203442 0.902441182 0.950226201 0.971013812 1.033950478 0.95776309 0.965003717 1.049033726 1 19.05138546 4.237463634 25 0.976421369 1.110006781 0.495680576 0.052947685 20.16514908 459609.0248 0.01242122 0.029473203 17276.81305 -4.237463634 0.133585412 KLFVGGIKEDTEEHHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLFVGGIKEDTEEHHLR 17 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 136.35 3.41E-06 695880000 578800 626240 172520 132370 306150 430550 225470 71729 253270 151050 FALSE TRUE 556179.8561 608380.2484 203698.2017 139201.6316 315997.5928 439256.016 228229.3693 70247.77108 224519.8514 140819.249 3.949601068 4.320291813 1.446522426 0.988512811 2.243994306 3.11928958 1.620725654 0.49885063 1.594383247 1 17.10348503 4.237488951 24.99999675 1.55222807 4.134947169 0.689902314 0.689413312 15.73885743 367200.2127 0.191732086 0.455261354 17277.82023 -4.237488951 2.5827191 IWTVDDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 IWTVDDYR 8 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 0 ; 79.469 0.057327 214490000 396400 439700 378490 499320 496260 480730 475200 514860 491370 531230 FALSE TRUE 380908.2498 427160.1865 446891.5625 525089.965 512222.6536 490450.69 481015.6397 504227.9611 435591.7376 495249.3189 0.769124227 0.862515445 0.902356743 1.060253785 1.034272303 0.99031068 0.971259568 1.01812954 0.879540306 1 18.91779547 4.237503799 1.935805221 0.99487033 0.783330573 0.686996696 0.048794162 0.202002941 1.40394552 0.012911765 0.053818159 17278.41096 -4.237503799 -0.211539757 VMDS(ph)PERPVVNANVSVPLMFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMDSPERPVVNANVSVPLMFR 21 1 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 VMDS(1)PERPVVNANVSVPLMFR 154.69 1.90E-08 443630000 74423 64572 79960 90359 98746 79799 102170 85034 82444 97662 TRUE FALSE 71514.46688 62730.46978 94410.5507 95022.43882 101922.2548 81412.59045 103420.387 83278.01818 73085.30275 91047.26575 0.785465289 0.688987959 1.036939988 1.043660543 1.119443334 0.894179411 1.13589778 0.914667975 0.80271826 1 16.47432807 4.237535563 24.99999388 0.996344073 0.737226569 0.517709648 0.098885011 19.10649334 466042.5133 0.024381945 0.057921309 17279.67471 -4.237535563 -0.259117504 DLVIERPRPDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLVIERPRPDSR 12 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;;; 210.79 2.22E-08 1216570000 526454 522400 498924 587640 546751 539527 623270 595240 637760 690690 FALSE TRUE 505879.5957 507501.6635 589090.6653 617968.1708 564337.7425 550436.6056 630897.7647 582948.086 565364.1585 643908.9511 0.785638396 0.788157491 0.914866402 0.95971359 0.876424752 0.854836083 0.979793438 0.905326887 0.878018791 1 19.29649718 4.237598293 7.37937375 0.91785327 0.786157826 0.592566125 0.044462317 0.076310416 26.12710732 0.010622091 0.025903438 17282.17082 -4.237598293 -0.131695443 SS(ph)PPMLSADDAEYPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPPMLSADDAEYPR 15 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 S(0.004)S(0.996)PPMLSADDAEYPR;S(0.341)S(0.659)PPMLSADDAEYPR 350.55 2.51E-82 900070000 234220 225179 265300 324030 258930 266650 319220 356990 327370 358000 TRUE FALSE 225066.4235 218757.1154 313245.6116 340753.2271 267258.7186 272041.8457 323126.7098 349618.0317 290208.33 333752.3411 0.674351595 0.655447433 0.938557047 1.02097629 0.80076957 0.815100936 0.968163126 1.047537316 0.869531968 1 18.34841843 4.237635551 24.99198005 0.936328139 0.66489943 0.647622057 0.078941694 14.31082558 386678.2997 0.021260697 0.050563645 17283.65349 -4.237635551 -0.271428708 QHCS(ph)ILETQDPCLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QHCSILETQDPCLK 14 0 Q9ULE4 Q9ULE4 FAM184B Protein FAM184B 1 QHCS(0.978)ILET(0.022)QDPCLK 67.605 0.033569 466440000 238130 253830 240690 291820 290830 270870 315300 317980 317620 353480 TRUE FALSE 228823.6163 246591.0169 284188.0371 306880.8652 300184.8111 276347.177 319158.7357 311413.6019 281565.1092 329538.4848 0.694376004 0.748292015 0.862381938 0.93124439 0.910924899 0.83858848 0.968502164 0.944999192 0.85442254 1 18.33008743 4.237673865 1.998396275 0.920126855 0.693175772 0.754321934 0.045511279 0.167693603 1.253482178 0.011947535 0.048446737 17285.17835 -4.237673865 -0.226951082 DLEFTIYDDDDVSPFLEGLEERPQR ddPTM_BT-474_Pertuzumab_2h_R1 7 DLEFTIYDDDDVSPFLEGLEERPQR 25 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;;;;;; 337.57 3.61E-88 1632165000 249230 256888 227374.4 280589 255847 254676 275549 286350 325161 305459 FALSE TRUE 239489.8161 249561.8058 268466.012 295070.2319 264076.5511 259825.7232 278921.2511 280436.7724 288250.0865 284769.9899 0.840993871 0.87636273 0.942746854 1.036170392 0.927332797 0.912405564 0.979461534 0.984783448 1.012220728 1 18.11943759 4.23769192 2.876275321 0.974947327 0.848792639 0.647712575 0.035186141 0.163699294 2.701013728 0.009372065 0.029279139 17285.89695 -4.23769192 -0.126154688 LTWFVNEGLVDGWDDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTWFVNEGLVDGWDDPR 17 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 123.28 0.00012592 217830000 89652 87375 101470 124490 111870 94371 116980 135610 119330 155270 FALSE TRUE 86148.30072 84883.15055 119807.8862 130914.9438 115468.4001 96279.24628 118411.6362 132809.6061 105784.1587 144753.4246 0.595138256 0.58639822 0.827668751 0.904399631 0.797690282 0.665125862 0.818023039 0.917488526 0.730788643 1 17.14323795 4.23770684 24.54782137 0.829050884 0.59076815 0.53769841 0.08966289 12.48353389 358994.2273 0.022081818 0.052595407 17286.49081 -4.23770684 -0.238282735 TNYNDRYDEIRR ddPTM_BT-474_Pertuzumab_2h_R1 4 TNYNDRYDEIRR 12 2 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;; 152.16 3.91E-05 6248400000 3323850 3550070 1883360 1823730 2483290 2742890 2305300 2372600 2541580 2171600 FALSE TRUE 3193950.267 3448825.479 2223725.047 1917852.924 2563167.278 2798353.115 2333512.951 2323604.981 2253070.494 2024515.598 1.577636779 1.703531197 1.098398575 0.947314472 1.266064475 1.382233418 1.152627796 1.1477338 1.112893621 1 20.94914533 4.237793184 24.99939458 1.150522871 1.640584112 0.737684341 0.119607845 9.611976734 313163.4179 0.030890337 0.073621626 17289.92797 -4.237793184 0.49006124 TEEPDRDER ddPTM_BT-474_Pertuzumab_2h_R1 4 TEEPDRDER 9 1 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 159.4 6.03E-05 1346690000 1926230 2040960 1817390 2240980 2141930 2260490 2307330 2203970 2574490 2746840 FALSE TRUE 1850950.802 1982753.819 2145832.801 2356637.246 2210827.124 2306198.657 2335567.795 2158457.249 2282244.688 2560794.08 0.722803452 0.774273041 0.837956014 0.920275966 0.863336549 0.900579502 0.912048264 0.84288591 0.891225384 1 21.28815982 4.237804072 1.854464214 0.893821947 0.723947715 0.702217659 0.04050596 0.212853732 1.338959434 0.010353027 0.044875125 17290.36145 -4.237804072 -0.169874231 RKAEGDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 RKAEGDAK 8 2 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ;;; 91.867 0.0068522 193500000 557549 532630 348317 327119 429920 357395 452679 447830 329823 385557 FALSE TRUE 535759.3687 517439.9139 411265.6302 344001.6508 443748.7672 364621.7718 458219.021 438582.154 292382.8758 359442.881 1.490527138 1.439560891 1.1441752 0.957041213 1.23454599 1.014408105 1.27480344 1.220172042 0.813433486 1 18.455403 4.2378097 4.220411304 1.102337642 1.477642623 0.559397778 0.135725353 0.144305584 5.927652447 0.033622479 0.08991318 17290.58552 -4.2378097 0.375304982 DELRETLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DELRETLK 8 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 149.72 0.00045662 892760000 1011850 1078210 599950 588480 711060 634980 822730 801720 904700 861450 FALSE TRUE 972305.7833 1047460.506 708374.3108 618851.5233 733931.8907 647819.7307 832798.8158 785164.2018 802002.2488 803103.2242 1.210685942 1.304266344 0.882046404 0.770575319 0.913869934 0.80664566 1.036976058 0.977662868 0.998629099 1 19.61522591 4.237818458 24.99998847 0.921664254 1.257476226 0.716874916 0.083999352 9.777715487 329421.8358 0.022236942 0.053018432 17290.93421 -4.237818458 0.335811972 QDELGER ddPTM_BT-474_Pertuzumab_2h_R1 2 QDELGER 7 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 126.52 0.0091752 362930000 852410 898770 779380 948600 941490 979860 947940 1027820 1022790 1072440 FALSE TRUE 819096.8748 873137.9596 920231.3032 997557.3597 971773.8809 999673.4406 959541.1733 1006595.158 906687.1671 999802.6836 0.819258528 0.873310278 0.920412916 0.997754233 0.971965666 0.999870731 0.959730544 1.006793815 0.906866107 1 19.93128387 4.237819516 1.683442184 0.979393263 0.819732959 0.773126994 0.028810733 0.183488062 0.917197749 0.007387242 0.035044306 17290.97632 -4.237819516 -0.159660304 EPAAEIEALLGMDLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EPAAEIEALLGMDLVR 16 0 Q12765;Q12765-2;Q12765-3;C9K052;B8ZZP4;C9J7U9 Q12765 SCRN1 Secernin-1 0 158.58 2.19E-08 46818000 12964 12050 14039 14673 18765 17728 14478 15353 18703 15572 FALSE TRUE 12457.35255 11706.3458 16576.1596 15430.27529 19368.59327 18086.47231 14655.18609 15035.95518 16579.91385 14517.29457 0.858104276 0.806372409 1.141821537 1.062889178 1.334173745 1.245856948 1.009498431 1.035727085 1.142080142 1 13.825485 4.237825494 24.99982092 1.122087567 0.832238262 0.570060813 0.100484293 13.52903422 460167.7566 0.026830243 0.06399147 17291.21431 -4.237825494 -0.289849305 LDSSEMDHS(ph)ENEDYTMSSPLPGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDSSEMDHSENEDYTMSSPLPGKK 24 1 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LDS(0.019)S(0.019)EMDHS(0.962)ENEDYTMSSPLPGKK;LDS(0.002)S(0.002)EMDHS(0.996)ENEDY(0.001)TMSSPLPGKK 112.44 5.53E-07 199660000 178098 177273 126079 128321 130530 161116 144321 153928 183342 168064 TRUE FALSE 171137.7333 172217.3476 148864.2799 134943.6622 134728.616 164373.8759 146087.2436 150749.333 162529.7848 156680.8756 1.092269447 1.099159977 0.950111361 0.861264412 0.859891901 1.049099804 0.932387204 0.962142523 1.037330077 1 17.25746957 4.237953032 24.97117467 0.951029159 1.095714758 0.458491611 0.060268703 12.64096038 519636.4028 0.015316303 0.036574005 17296.29293 -4.237953032 0.1446856 GLKYELISETGGSHDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLKYELISETGGSHDKR 17 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6;Q96SI9;Q96SI9-2 Q12906;Q12906-7;Q96SI9 ILF3;STRBP Interleukin enhancer-binding factor 3;Spermatid perinuclear RNA-binding protein 0 82.865 0.0035258 767230000 322790 323700 226750 230790 270060 290720 265490 274910 304340 268300 FALSE TRUE 310175.0099 314468.3929 267728.769 242701.0996 278746.7252 296598.5576 268739.146 269233.0124 269792.5991 250127.802 1.240066108 1.257230865 1.070367895 0.970308369 1.114417202 1.185788046 1.074407338 1.076381795 1.078618998 1 17.9323059 4.237992911 24.99945693 1.076131589 1.24864854 0.620450654 0.055384711 9.321432639 410563.2297 0.01417682 0.033870945 17297.88122 -4.237992911 0.172516951 S(ph)PAMSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPAMSR 6 0 Q9BQI6 Q9BQI6 ANKRD32 Ankyrin repeat domain-containing protein 32 1 S(1)PAMSR 84.498 0.058514 39264000 22878 23089 23148 35682 23820 26905 26034 28126 24941 28310 TRUE FALSE 21983.90247 22430.52433 27331.35852 37523.5523 24586.19193 27449.03753 26352.61188 27545.18827 22109.80224 26392.53848 0.832959 0.849881278 1.035571419 1.421748511 0.931558438 1.040030217 0.998487201 1.04367332 0.837729279 1 14.6878425 4.237995179 6.241472053 1.048005606 0.839072468 0.233646485 0.142264308 0.190754492 30.34075189 0.035482039 0.088022736 17297.97157 -4.237995179 -0.208933138 IWDPTPSHTPAGAAT(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 3 IWDPTPSHTPAGAATPGR 18 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHTPAGAAT(1)PGR;IWDPTPSHT(0.239)PAGAAT(0.761)PGR;IWDPTPSHT(0.092)PAGAAT(0.908)PGR 121.46 0.00014046 1516400000 1854360 1840740 1905650 2571980 2061450 1922590 2182710 2446470 2240800 2522000 TRUE FALSE 1781889.561 1788243.897 2250043.346 2704720.196 2127758.411 1961466.087 2209422.658 2395949.54 1986433.778 2351182.694 0.757869461 0.760572074 0.956983629 1.150365815 0.904973662 0.834246566 0.939706924 1.019040139 0.844865771 1 21.16495521 4.237996869 8.467681329 0.960039985 0.758589388 0.456524106 0.085929269 0.089455925 63.21074373 0.021919424 0.053112994 17298.03886 -4.237996869 -0.201450598 TTFVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTFVKR 6 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 83.801 0.090714 587990000 1722000 2095200 1122000 1235000 1442400 1441100 1644000 1581600 1904200 1724500 FALSE TRUE 1654702.336 2035446.947 1324770.359 1298738.498 1488796.106 1470240.029 1664119.764 1548939.407 1688043.199 1607698.079 1.029236993 1.266062934 0.824016882 0.807824874 0.9260421 0.914500085 1.035094702 0.963451675 1.049975254 1 20.61656507 4.23800232 25 0.939078503 1.147649955 0.447403493 0.09225334 12.43012868 556729.1358 0.023307858 0.055713187 17298.25601 -4.23800232 0.208571453 AWRDPDEPVLLEEPVVLALAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 AWRDPDEPVLLEEPVVLALAEK 22 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 197.12 1.86E-22 411369000 500674 527588 351164 369103 424193 465727 408016 449875 493433 449399 FALSE TRUE 481107.1066 512541.7068 414627.1464 388152.4501 437837.5531 475144.319 413009.4219 440584.924 437420.5545 418960.8054 1.148334403 1.223364334 0.989656171 0.926464827 1.045056118 1.134102076 0.985794892 1.051613703 1.044060802 1 18.67645576 4.238046197 24.99999996 1.024786506 1.185849399 0.593865041 0.054131995 8.826133805 429040.3956 0.013856142 0.03313735 17300.00375 -4.238046197 0.161062893 S(ph)PAKSPNPSTPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPAKSPNPSTPR 12 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 S(1)PAKSPNPSTPR;S(1)PAKSPNPSTPR;S(1)PAKSPNPSTPR 124.2 0.00019822 907240000 1095410 1081820 647360 594800 766070 874230 744080 846190 766750 716590 TRUE FALSE 1052600.166 1050967.553 764352.3524 625497.6993 790711.3373 891907.5296 753186.2736 828715.8808 679711.7545 668054.721 1.575619681 1.573175849 1.144146323 0.936297102 1.183602649 1.335081546 1.127432005 1.240491018 1.017449219 1 19.34960675 4.238071052 9.171346999 1.139837075 1.575321271 0.719352701 0.112376744 0.049222935 55.25477161 0.028300645 0.068388765 17300.99388 -4.238071052 0.435484196 GDFIHVMDNSDPNWWK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDFIHVMDNSDPNWWK 16 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 208.51 1.47E-11 546600000 600750 562540 574330 679330 680050 596560 633890 622360 808760 750620 FALSE TRUE 577272.0258 546496.91 678124.2069 714390.3027 701924.4259 608622.8519 641647.7354 609508.0485 716952.9554 699779.8388 0.824933777 0.780955494 0.96905365 1.020878658 1.00306466 0.869734763 0.916928011 0.870999727 1.024540742 1 19.41654157 4.238083217 24.99993135 0.949072343 0.8029446 0.551554889 0.055811985 9.740422564 510205.0546 0.014913398 0.035685428 17301.47848 -4.238083217 -0.146127742 YVLINWVGEDVPDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 YVLINWVGEDVPDAR 15 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RFI1;D6RCR4 Q16643 DBN1 Drebrin 0 ;;; 200.44 1.61E-08 544495000 741190 738510 644297 691862 734936 802780 741331 793880 790450 845270 FALSE TRUE 712223.4754 717448.4179 760735.8002 727569.0807 758575.8839 819012.7616 750403.6305 777486.1006 700721.4298 788019.11 0.903814979 0.910445456 0.96537735 0.923288625 0.962636406 1.039331091 0.952265778 0.986633561 0.889218828 1 19.58787109 4.238177754 0.950717146 0.971393996 0.88907523 0.261764364 0.038635469 1.409839652 1.681713682 0.01292939 0.102037226 17305.24506 -4.238177754 -0.082318765 DAEDAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAEDAVR 7 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ; 104.76 0.018793 867330000 1203620 1165950 1229370 1447910 1330300 1277360 1442830 1507100 1643650 1639360 FALSE TRUE 1156581.2 1132698.248 1451544.506 1522636.809 1373090.308 1303189.094 1460487.785 1475977.858 1457069.743 1528324.687 0.756764063 0.741137179 0.949761866 0.996278357 0.898428403 0.852691254 0.955613554 0.965748882 0.95337709 1 20.54351964 4.238248783 24.99887775 0.943696306 0.748950558 0.784362796 0.041408974 3.457056668 277254.4169 0.010796459 0.025892477 17308.07559 -4.238248783 -0.194745748 EDFLVGRPPELGQGDADVAGYLQSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDFLVGRPPELGQGDADVAGYLQSAR 26 1 Q8N0W3-2;Q8N0W3 Q8N0W3-2 FUK L-fucose kinase 0 91.722 0.0089238 79413000 32736 32066 36002 37614 41855 47641 39204 42758 49158 43439 FALSE TRUE 31456.64093 31151.50908 42508.36226 39555.26305 43201.30409 48604.33366 39683.79028 41875.03236 43577.78993 40496.83784 0.776767832 0.769233124 1.049671148 0.976749424 1.066782159 1.200200713 0.979923184 1.034032151 1.076078831 1 15.30552164 4.238258104 24.99409732 1.048300363 0.773000383 0.767923198 0.06045551 3.339933951 276063.464 0.015225095 0.036516873 17308.44707 -4.238258104 -0.27529998 AKLTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 AKLTPGCEAEAETEAICFFVQQFTDMEHNR 30 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 248.73 2.13E-46 165347000 339040 354790 179601 168698 237770 316408 196845 209963 237280 181181 FALSE TRUE 325789.942 344671.7366 212058.8959 177404.524 245418.088 322805.9865 199254.048 205627.1907 210344.9692 168909.4495 1.928784582 2.040571073 1.255459044 1.05029366 1.452956532 1.911118576 1.179650094 1.217381214 1.245312028 1 17.36589052 4.238259239 24.99998005 1.305460303 1.984678028 0.569808628 0.24144263 5.523497649 458375.5583 0.06221017 0.149187472 17308.4923 -4.238259239 0.679217724 RDS(ph)SGGTKDGDRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSSGGTKDGDRPK 14 3 Q9Y478;F5H4Y8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 RDS(0.5)S(0.145)GGT(0.355)KDGDRPK;RDS(0.483)S(0.258)GGT(0.258)KDGDRPK 101.53 0.0074593 152017000 261693 278949 120108 102964 152927 221797 142342 145683 175604 120233 TRUE FALSE 251465.7482 270993.6476 141814.1874 108277.9844 157846.0358 226281.8873 144084.024 142674.5951 155670.1701 112089.5118 2.243436912 2.41765392 1.265186948 0.965995682 1.408214143 2.018760575 1.285437162 1.272863026 1.388802285 1 16.77429177 4.238267392 24.99999985 1.343968711 2.330545703 0.681878 0.27432177 4.192842495 357626.1574 0.070414385 0.168910794 17308.81723 -4.238267392 0.986576992 ECSEAMEVETSVISIDS(ph)PQKLAILDQELEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ECSEAMEVETSVISIDSPQKLAILDQELEHK 31 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVET(0.013)S(0.013)VIS(0.005)IDS(0.969)PQKLAILDQELEHK 93.29 0.00027461 23560000 32247 34761 15224 12771 22747 25562 16451 16823 26557 19120 TRUE FALSE 30986.75159 33769.65031 17975.31546 13430.11284 23478.67791 26078.88115 16652.33226 16475.59917 23542.3607 17824.98537 1.738388613 1.894512092 1.008433672 0.753443134 1.317177963 1.463052037 0.934212955 0.924298047 1.320750632 1 14.12161327 4.238269541 25 1.080328057 1.816450557 0.658781582 0.208982341 4.3052134 369923.0306 0.054321353 0.130309392 17308.9029 -4.238269541 0.736122501 TFDQLTPEESKER ddPTM_BT-474_Pertuzumab_2h_R1 6 TFDQLTPEESKER 13 1 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11;O43852-12;O43852-2;O43852-4;O43852-8;O43852-7 O43852;O43852-2 CALU Calumenin 0 ;;;;; 171.26 2.32E-05 4367530000 3726596 4143031 2395587 2552026 3013378 3430306 2977524 3130667 3600570 3039514 FALSE TRUE 3580956.508 4024875.812 2828522.86 2683736.368 3110306.04 3499669.138 3013963.829 3066017.632 3191848.388 2833645.009 1.263727989 1.420388157 0.998192382 0.947096887 1.09763433 1.235041484 1.063634936 1.082004846 1.126410816 1 21.4342276 4.238277754 24.99999998 1.0743428 1.342058112 0.633359952 0.083090048 4.490078213 397013.3117 0.021210855 0.050890486 17309.23021 -4.238277754 0.267715312 EKSTFREES(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKSTFREESPLR 12 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKST(0.015)FREES(0.984)PLR 202.82 6.90E-08 6728000000 7560900 8422900 3469820 3369880 5113450 6578200 4227160 4156910 4915670 3701720 TRUE FALSE 7265411.669 8182687.139 4096893.66 3543799.911 5277928.763 6711215.711 4278893.249 4071068.356 4357663.75 3450999.207 2.105306676 2.371106641 1.187161577 1.026890966 1.529391474 1.944716677 1.239899806 1.179678149 1.262725225 1 21.71858271 4.238334547 24.99999995 1.314047811 2.238206893 0.668448506 0.265106353 3.399932249 376187.1273 0.069319921 0.166443878 17311.49388 -4.238334547 0.924159082 VNCLDKFWHK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNCLDKFWHK 10 1 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 122.7 0.00028938 27310000000 16985100 17934200 9573300 10592000 12239900 11351500 13136000 11733500 13190400 11390600 FALSE TRUE 16321303.51 17422734.18 11303408.27 11138654.39 12633607.5 11581035.11 13296762.3 11491199.12 11693081.09 10619104.52 1.536975504 1.640697118 1.064440815 1.048925959 1.189705543 1.090584907 1.252154763 1.082125061 1.101136266 1 23.34015878 4.238343702 24.99999771 1.113332677 1.588836443 0.87949629 0.071768127 1.552649567 179048.7555 0.016994582 0.040809349 17311.85882 -4.238343702 0.475503766 DAEDVDLNHYR ddPTM_BT-474_Pertuzumab_2h_R1 4 DAEDVDLNHYR 11 0 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C003;H7C118;C9J177;Q15435-2;Q15435-5;Q15435-4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 ;;; 205.56 2.94E-08 2451480000 2425070 2461520 2398580 2871660 2661480 2597270 2942370 2904770 3320480 3372770 FALSE TRUE 2330295.583 2391319.86 2832056.762 3019866.717 2747088.921 2649788.579 2978379.604 2844785.484 2943553.031 3144329.284 0.741110543 0.760518268 0.90068708 0.960416815 0.873664516 0.842719811 0.947222551 0.904735232 0.936146556 1 21.58432088 4.238384211 4.435013223 0.916196423 0.745788475 0.723787771 0.042084839 0.092809275 4.392287056 0.010232291 0.027030397 17313.47368 -4.238384211 -0.170407948 MECCDVPAETLYDVLHDIEYRK ddPTM_BT-474_Pertuzumab_2h_R1 1 MECCDVPAETLYDVLHDIEYRK 22 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 99.86 0.00061248 6895800 20952 24957 8430.6 9654.6 11028 17938 11138 11129 14296 11967 FALSE TRUE 20133.17268 24245.2508 9954.196958 10152.87506 11382.72564 18300.71865 11274.31018 10899.18226 12673.17801 11156.46443 1.804619447 2.173201998 0.892235799 0.910044139 1.020280727 1.640369022 1.010563001 0.976938736 1.135949305 1 13.44559228 4.238550755 25 1.076267541 1.988910919 0.738748748 0.217791674 0.119654374 304270.032 0.055254546 0.133069374 17320.11433 -4.238550755 0.912643379 ASS(ph)PPDR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.001)S(0.999)PPDR;AS(0.043)S(0.957)PPDR;AS(0.002)S(0.998)PPDR 128 0.0039868 586190000 1438410 1448680 1332950 1752740 1547210 1540320 1616570 1568270 1526210 1668840 TRUE FALSE 1382195.347 1407365.065 1573843.716 1843199.121 1596977.415 1571466.326 1636354.067 1535884.676 1352961.039 1555807.98 0.888409987 0.904587894 1.011592521 1.184721473 1.026461771 1.010064446 1.051771226 0.98719424 0.869619552 1 20.56923258 4.238558775 5.197806299 1.023529798 0.893845706 0.308084685 0.072528786 0.194214966 15.27835875 0.018765295 0.047908352 17320.43421 -4.238558775 -0.129684092 VEGDLKGPEVDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEGDLKGPEVDIR 13 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 78.814 0.020252 863580000 2967000 3103600 1777080 1815260 2014850 2712400 2064630 2339300 2421200 1955510 FALSE TRUE 2851046.36 3015088.367 2098237.887 1908945.786 2079659.48 2767246.586 2089897.56 2290992.638 2146355.526 1823061.566 1.563878266 1.653859871 1.15094187 1.047109885 1.140751096 1.517911758 1.146366968 1.256673214 1.177335734 1 20.79793185 4.23856147 25 1.19594257 1.608869185 0.619410086 0.134097192 0.027286851 404137.3563 0.033161776 0.079864256 17320.54168 -4.23856147 0.412926615 MQFS(ph)FEEYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MQFSFEEYEK 10 0 A0A1W2PR28;Q5JU85-3;Q5JU85;A0A1W2PR18 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 MQFS(1)FEEYEK;MQFS(1)FEEYEK 86.729 0.014014 218326000 553030 552670 542280 650970 598380 649440 648460 628200 713090 701230 TRUE FALSE 531416.9762 536908.3927 640282.059 684566.6397 617627.4361 662572.1218 656396.0475 615227.4505 632143.0127 653735.0675 0.812893483 0.821293548 0.979421314 1.047162182 0.94476718 1.013517791 1.004070426 0.94109599 0.966971246 1 19.31834656 4.238641142 6.242527437 0.98554081 0.815242722 0.835418159 0.030202606 0.050692517 8.066296235 0.007672698 0.019070977 17323.71945 -4.238641142 -0.170298089 IYSFTDNAPS(ph)PSIGGSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IYSFTDNAPSPSIGGSSR 18 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 IYSFTDNAPS(1)PSIGGSSR;IYSFTDNAPS(0.99)PS(0.01)IGGSSR 331.07 6.99E-75 766780000 638700 613740 695760 801510 733160 744650 809570 866660 828350 1018440 TRUE FALSE 613738.8979 596236.7361 821499.3091 842876.0272 756742.7572 759707.3332 819477.7598 848763.1681 734319.1807 949460.1517 0.646408274 0.627974471 0.86522779 0.887742393 0.797024242 0.800146622 0.863098634 0.893942907 0.773407056 1 19.85674793 4.238688869 24.99999899 0.855206261 0.637191299 0.682044266 0.060798691 1.681054141 327337.0075 0.014157254 0.034154641 17325.62334 -4.238688869 -0.218014962 SPGSNS(ph)KVPEIEVTVEGPNNNNPQTSAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 S(0.025)PGS(0.125)NS(0.851)KVPEIEVTVEGPNNNNPQTSAVR 252.18 4.55E-58 832310000 435660 542610 152270 175030 230960 413250 229240 191180 274890 183850 TRUE FALSE 418633.9256 527135.2941 179788.5762 184063.3193 238389.0382 421606.1981 232045.5077 187232.0662 243685.6396 171397.6757 2.442471426 3.075510165 1.048955743 1.073896239 1.390853389 2.459812808 1.353842791 1.092383927 1.4217558 1 17.38698802 4.238766741 24.99999998 1.373692898 2.758991071 0.636755108 0.423926803 3.282005452 397805.1263 0.109376326 0.264136891 17328.73022 -4.238766741 1.385298173 YDGKWEVEEMKESK ddPTM_BT-474_Pertuzumab_2h_R1 1 YDGKWEVEEMKESK 14 2 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85 P27824 CANX Calnexin 0 104.41 0.00059569 305510000 289590 340110 143460 170890 153660 166790 218220 272080 243910 128110 FALSE TRUE 278272.5026 330410.3958 169386.4133 179709.6534 158602.6135 170162.6081 220890.6416 266461.4529 216222.3594 119432.9956 2.329946605 2.76649174 1.41825475 1.504690161 1.32796312 1.424753748 1.849494275 2.231053919 1.810407235 1 16.86584194 4.238833742 24.99999827 1.643637797 2.548219345 0.565358376 0.338004089 5.612551285 513484.5434 0.092258297 0.222997195 17331.40385 -4.238833742 0.904581548 LATPTYGDLNHLVSATMSGVTTSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LATPTYGDLNHLVSATMSGVTTSLR 25 0 Q13509;A0A0B4J269;Q13509-2;G3V2A3 Q13509 TUBB3 Tubulin beta-3 chain 0 ; 221.6 1.12E-33 1407860000 608530 614070 633670 736910 704920 777810 768150 747450 821530 833920 FALSE TRUE 584747.9748 596557.3248 748188.2649 774942.0134 727594.392 793537.8511 777550.8495 732014.8963 728273.3585 777437.8556 0.752147545 0.767337634 0.96237694 0.996789657 0.935887527 1.020709045 1.000145341 0.941573517 0.936760866 1 19.56836783 4.238834313 5.295643018 0.973789302 0.755779643 0.902594969 0.028234699 0.043532591 3.656906756 0.007191177 0.018310327 17331.42662 -4.238834313 -0.218009659 LRS(ph)PRGSPDGS(ph)LQTGKPSAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRSPRGSPDGSLQTGKPSAPK 21 3 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 2 LRS(1)PRGS(0.031)PDGS(0.963)LQT(0.006)GKPSAPK 144.74 1.79E-07 503650000 319640 330890 169670 124590 238640 293260 189730 197710 243700 197320 TRUE FALSE 307148.1154 321453.3412 200333.1433 131020.1048 246316.0723 299189.9181 192051.9725 193627.2194 216036.1977 183955.3406 1.669688493 1.747453159 1.089031406 0.712238657 1.3389993 1.62642692 1.044014117 1.05257732 1.174394812 1 17.48899604 4.238863974 24.9997556 1.132939197 1.70857101 0.516552951 0.223984065 6.234642424 513571.4427 0.058686974 0.141898591 17332.61036 -4.238863974 0.575631813 VPAAFPTKVPVPGPGS(ph)GGNGPER ddPTM_BT-474_Pertuzumab_2h_R1 2 VPAAFPTKVPVPGPGSGGNGPER 23 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 VPAAFPTKVPVPGPGS(1)GGNGPER;VPAAFPTKVPVPGPGS(1)GGNGPER 142.09 1.07E-07 3374000000 2158330 2402140 1473600 1578490 1645400 2247200 1773000 2018930 2061720 2125300 TRUE FALSE 2073980.077 2333633.319 1739912.3 1659956.058 1698325.785 2292639.924 1794698.504 1977238.39 1827682.189 1981351.538 1.046750179 1.177798727 0.878144169 0.837789774 0.857155206 1.157109115 0.905795095 0.99792407 0.922442158 1 20.91805344 4.239009992 24.99999851 0.945821187 1.112274466 0.345779337 0.092271794 12.5589357 698483.2291 0.023023754 0.055806934 17338.43888 -4.239009992 0.166453279 IDDDDDERENFEITDWDLQNEFNPNR ddPTM_BT-474_Pertuzumab_2h_R1 4 IDDDDDERENFEITDWDLQNEFNPNR 26 1 Q9UBB9;F6XM96;F6UKU9;F6SQZ1;F6UQ07 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 ;;; 288.46 4.93E-62 382983000 226528 214963.3 206602.7 206232 237309 243081 220156 242083 278998 260888 FALSE TRUE 217675.0353 208832.7572 243940.4037 216875.6582 244942.2595 247996.2644 222850.335 237083.9015 247327.3167 243217.8234 0.894979785 0.858624398 1.002970919 0.891693114 1.007090089 1.019646755 0.916258241 0.97478013 1.016896349 1 17.89188943 4.239026362 1.092420182 0.979271812 0.860283485 0.393089568 0.045246373 0.862231487 1.455185527 0.013814136 0.098381062 17339.09243 -4.239026362 -0.118988327 DQDNMQAELNR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDNMQAELNR 11 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 123.01 0.0021508 0 225380 222860 209870 229400 229210 247990 264310 265230 234000 266550 FALSE TRUE 216571.9004 216504.251 247798.1775 241239.3615 236582.7478 253004.5277 267544.7048 259752.9078 207437.301 248496.3311 0.871529569 0.871257334 0.997190487 0.970796472 0.952057307 1.018141904 1.076654547 1.045298764 0.834770075 1 17.92286503 4.239105271 24.75858132 0.995131778 0.871393404 0.354294611 0.061549673 12.29555422 558768.7924 0.015605473 0.037857028 17342.24317 -4.239105271 -0.123738373 IVTDRETGSSK ddPTM_BT-474_Pertuzumab_2h_R1 3 IVTDRETGSSK 11 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 153.34 2.97E-05 1402130000 3768940 4418690 1539980 1563180 2160770 3588340 2049990 2016120 2371420 1806870 FALSE TRUE 3621645.658 4292673.288 1818288.643 1643855.907 2230273.129 3660898.693 2075078.391 1974486.417 2102226.343 1684489.086 2.149996512 2.548353281 1.07943035 0.97587804 1.324005687 2.173299147 1.231874049 1.172157442 1.247990481 1 20.68387965 4.239117982 24.99978946 1.295509728 2.34917514 0.624199068 0.332922719 9.187776716 412005.1166 0.085977366 0.208634581 17342.75074 -4.239117982 1.053665412 ERELEEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERELEEAR 8 1 Q9Y490;Q9Y4G6;H0YMT1;A0A1B0GVU7 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 98.033 0.0071224 74607000 58524 57424 58080 70121 65512 58805 74093 70647 71052 67762 FALSE TRUE 56236.81738 55786.32374 68576.34798 73739.95321 67619.25298 59994.07739 74999.7723 69188.11476 62986.47483 63172.41938 0.89021155 0.883080374 1.08554253 1.167280815 1.07039201 0.949687822 1.187223365 1.095226611 0.997056555 1 15.94700721 4.239138818 24.97285014 1.078783057 0.886645892 0.514320852 0.070395061 10.39155541 448710.952 0.017298455 0.041987178 17343.58281 -4.239138818 -0.192137165 AVEEKIEWLESHQDADIEDFKAK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVEEKIEWLESHQDADIEDFKAK 23 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 136.62 6.41E-06 141720000 125210 137270 69759 75750 82099 106700 90122 88692 109970 88598 FALSE TRUE 120316.6548 133355.194 82366.00308 79659.46658 84739.7889 108857.5471 91224.93999 86860.47921 97486.66663 82597.17855 1.456667853 1.61452481 0.99720117 0.964433265 1.025940479 1.317932998 1.104455886 1.051615573 1.180266304 1 16.33380488 4.239165071 24.99998761 1.083985531 1.535596443 0.750642169 0.104964229 7.211223463 298187.5112 0.026675188 0.064750265 17344.63126 -4.239165071 0.451610911 KS(ph)PEIHR ddPTM_BT-474_Pertuzumab_2h_R1 6 KSPEIHR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(1)PEIHR;KS(1)PEIHR;KS(1)PEIHR;KS(1)PEIHR;KS(1)PEIHR;KS(1)PEIHR 113.93 0.0036873 4090130000 3439780 3419730 3342620 3706180 3775580 3919920 4041650 3899670 4467490 4475320 TRUE FALSE 3305349.595 3322202.649 3946705.79 3897456.394 3897024.96 3999183.468 4091112.922 3819140.452 3960359.264 4172202.59 0.792231327 0.796270693 0.945952577 0.934148405 0.934044998 0.958530508 0.980564302 0.915377518 0.949225063 1 21.99237778 4.239184641 7.337851986 0.948163816 0.793323666 0.8821699 0.02305978 0.034233542 11.36797202 0.005527673 0.013565474 17345.41282 -4.239184641 -0.15484015 FADDQLIIDFDNFVR ddPTM_BT-474_Pertuzumab_2h_R1 4 FADDQLIIDFDNFVR 15 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 134.98 7.41E-05 75421000 101935 113373 103440 134323 139056 128428 129775 137394 137020 143636 FALSE TRUE 97951.2675 110139.713 122133.909 141255.4261 143528.8625 131024.9022 131363.2253 134556.7659 121466.064 133907.4058 0.731485066 0.82250651 0.912077329 1.054873891 1.071851566 0.978473904 0.98100045 1.004849322 0.907089965 1 17.03087623 4.239198175 2.091566658 1.000539423 0.743426026 0.802291734 0.044526879 0.143590519 1.189020457 0.012202835 0.047736079 17345.95338 -4.239198175 -0.257113397 FLMECRNS(ph)PVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLMECRNSPVTK 12 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 FLMECRNS(1)PVTK;FLMECRNS(0.996)PVT(0.004)K 163.8 3.57E-05 712960000 965280 975930 374601 303729 522540 837500 375156 338938 523560 404130 TRUE FALSE 927555.7904 948097.4319 442299.7337 319404.4901 539347.9737 854434.8238 379747.2713 331938.8119 464127.6637 376757.9151 2.461941085 2.516463208 1.173962685 0.847771148 1.431550478 2.267861641 1.007934422 0.881040049 1.231898907 1 18.5232783 4.239249613 24.99326424 1.226258021 2.489202611 0.629477191 0.386344653 11.36168671 412064.1138 0.103299117 0.25114964 17348.00795 -4.239249613 1.26294459 ELQELVQYPVEHPDKFLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELQELVQYPVEHPDKFLK 18 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 204.29 6.54E-16 2629869000 8239570 8623730 4455769 3842383 5983540 7621270 5209922 5286863 6588877 4746451 FALSE TRUE 7917558.495 8377789.664 5261025.576 4040688.847 6176005.998 7775377.301 5273682.584 5177687.432 5840935.306 4424969.646 1.78929103 1.893298787 1.188940489 0.913156286 1.395717144 1.757159466 1.19180085 1.170106881 1.319994435 1 22.07723613 4.239271976 24.99991064 1.25298757 1.841295093 0.545063474 0.218783676 13.84279615 486397.8406 0.056609462 0.137633567 17348.90129 -4.239271976 0.588307523 EYTINIHK ddPTM_BT-474_Pertuzumab_2h_R1 6 EYTINIHK 8 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;;;; 150.4 0.0004898 7476710000 6486540 5954670 6016090 6476120 6608850 6472800 6724890 7220530 7331180 7794280 FALSE TRUE 6233038.846 5784848.642 7103331.29 6810353.329 6821429.662 6603684.451 6807191.215 7071423.532 6498975.181 7266366.473 0.857793076 0.796112977 0.977563039 0.937243305 0.938767634 0.908801459 0.936808134 0.973171881 0.894391331 1 22.7928027 4.239336723 24.99997296 0.944106492 0.826953005 0.67581003 0.032920162 10.20079771 328532.0052 0.007608283 0.018522116 17351.48794 -4.239336723 -0.117153487 EGPDLDRPGS(ph)DR ddPTM_BT-474_Pertuzumab_2h_R1 4 EGPDLDRPGSDR 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 EGPDLDRPGS(1)DR;EGPDLDRPGS(1)DR;EGPDLDRPGS(1)DR;EGPDLDRPGS(1)DR 147.7 3.74E-05 1986170000 2778520 2732770 2859470 3411770 3032420 3040280 3346620 3529770 3573300 3973290 TRUE FALSE 2669932.367 2654834.075 3376239.838 3587851.859 3129960.543 3101756.545 3387576.937 3456879.016 3167673.964 3704175.529 0.720789915 0.716713896 0.911468642 0.968596609 0.844981702 0.837367592 0.914529268 0.933238446 0.855163029 1 21.82072103 4.23937542 24.99909646 0.905062405 0.718751835 0.699184777 0.049663698 10.73884993 329425.9677 0.012122447 0.029524191 17353.03409 -4.23937542 -0.186310569 REPAEQPGDGER ddPTM_BT-474_Pertuzumab_2h_R1 4 REPAEQPGDGER 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;;; 145 0.00010186 993420000 818370 809670 716609 852076 840930 832730 781023 882770 906130 874540 FALSE TRUE 786387.1956 786579.0043 846116.1872 896051.7445 867979.2772 849568.3711 790581.3931 864540.491 803269.9212 815306.6268 0.96452938 0.96476464 1.037788924 1.099036504 1.064604713 1.04202314 0.9696737 1.06038693 0.98523659 1 19.63698322 4.239376312 24.68600661 1.036246463 0.964646978 0.344618515 0.037031155 18.18825516 550339.9643 0.009283674 0.022595578 17353.06972 -4.239376312 -0.071599484 LLDHLQLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDHLQLDK 9 0 H0YLT5;H0YKM6;H0YMB7;H0YKB0;Q9NZD8 H0YLT5 SPG21 Maspardin 0 84.268 0.017804 0 305040 300700 290090 323070 328760 345240 321290 340780 386920 398360 FALSE TRUE 293118.6996 292124.3304 342515.716 339743.6814 339334.864 352220.9893 325222.0431 333742.7739 342998.4637 371378.7224 0.789271657 0.78659415 0.922281475 0.914817304 0.913716494 0.948414565 0.875715337 0.898658846 0.923581355 1 18.50253163 4.239449868 24.99990299 0.917624162 0.787932854 0.748160002 0.03151789 10.22338687 287371.9066 0.007358783 0.017932 17356.00907 -4.239449868 -0.129691308 SLLGDSAPTLHLNKGT(ph)PSQS(ph)PVVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 SLLGDSAPTLHLNKGT(0.935)PS(0.074)QS(0.991)PVVGR;SLLGDSAPT(0.044)LHLNKGT(0.956)PS(0.325)QS(0.676)PVVGR 198.81 1.71E-24 996740000 958000 967970 564098 533106 657406 800300 628682 718710 786880 762420 TRUE FALSE 920560.3009 940364.4433 666043.0569 560619.6645 678552.061 816482.6143 636375.9984 703868.3873 697556.6813 710780.6143 1.295139854 1.323002379 0.937058557 0.788737978 0.954657524 1.148712553 0.895319858 0.990275161 0.981395197 1 19.43904481 4.239455072 24.99999599 0.959974854 1.309071241 0.725109085 0.085466266 11.33819984 316854.3833 0.021854656 0.05327704 17356.21705 -4.239455072 0.349096387 TTHFVEGGDAGNR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTHFVEGGDAGNR 13 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 164.53 3.69E-05 1361000000 704770 685360 774110 1001400 888150 874120 1021500 688140 1011600 981990 FALSE TRUE 677226.8092 665814.2038 914008.897 1053082.374 916718.1513 891795.3053 1034001.423 673929.6685 896767.409 915478.9426 0.739751378 0.72728511 0.998394233 1.150307588 1.001353618 0.974129785 1.129464998 0.736149831 0.979560935 1 19.80416718 4.239463042 24.99989423 0.985614883 0.733518151 0.496762072 0.105315516 20.50886557 568071.3756 0.028272165 0.068932661 17356.53556 -4.239463042 -0.252096732 SYSFDEIRK ddPTM_BT-474_Pertuzumab_2h_R1 4 SYSFDEIRK 9 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;; 147.95 0.00014621 2375930000 2907440 2925460 2154550 2216100 2706530 2348370 2908590 2294840 3334850 2708120 FALSE TRUE 2793814.03 2842028.745 2543925.113 2330473.187 2793587.995 2395855.65 2944186.194 2247450.752 2956291.809 2524696.62 1.10659396 1.125691191 1.00761616 0.923070585 1.10650443 0.948967742 1.166154448 0.890186462 1.170949327 1 21.26767861 4.239506221 24.99688092 1.019786264 1.116142605 0.129284373 0.091477438 41.01022208 1083949.76 0.020604897 0.050218932 17358.26125 -4.239506221 0.096356341 S(ph)PTPESSTIASYVTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTPESSTIASYVTLR 16 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 S(0.982)PT(0.018)PESSTIASYVTLR;S(0.994)PT(0.006)PESSTIASYVTLR 164.53 7.71E-09 325470000 54460 51537 51967 60576 54696 55253 50533 75183 63251 56835 TRUE FALSE 52331.64299 50067.21522 61358.5929 63702.33462 56455.34651 56370.25352 51151.43797 73630.44478 56071.01165 52985.51483 0.987659423 0.94492269 1.158025794 1.202259426 1.06548642 1.063880453 0.965385316 1.389633469 1.058232837 1 15.69331039 4.239519449 24.99974839 1.132083311 0.966291009 0.191530883 0.115159848 34.51115733 899682.3079 0.029344563 0.071624788 17358.79001 -4.239519449 -0.165792302 ETTSGTSTEPVKNSS(ph)PAPPQPAPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETTSGTSTEPVKNSSPAPPQPAPGK 25 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ETTSGTSTEPVKNS(0.259)S(0.741)PAPPQPAPGK;ETTSGTSTEPVKNS(0.054)S(0.946)PAPPQPAPGK 197 5.04E-25 1737560000 1116740 1155930 788190 795210 926680 1015130 924350 1048330 1160230 930590 TRUE FALSE 1073096.566 1122964.008 930633.4662 836250.8834 956487.5038 1035656.624 935662.4718 1026681.619 1028525.554 867560.3104 1.236912931 1.294393018 1.072701753 0.96391095 1.102502607 1.193757496 1.078498475 1.183412389 1.185537815 1 19.72660453 4.239533561 24.99999953 1.1059138 1.265653014 0.448277925 0.074137271 23.76200825 610483.8363 0.01921132 0.046930337 17359.35404 -4.239533561 0.159739214 TSS(ph)LDTLAAPYLAGHWPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 TS(0.009)S(0.958)LDT(0.032)LAAPYLAGHWPR 274.02 5.27E-39 88797000 114470 115300 83198 92871 91551 98094 105810 99703 120790 98230 TRUE FALSE 109996.3858 112011.7569 98233.72933 97664.08344 94495.82106 100077.5279 107104.9344 97644.09821 107078.4256 91576.79461 1.201138196 1.223145638 1.072692375 1.066471958 1.031875176 1.092826281 1.169564133 1.066253723 1.169274662 1 16.48269445 4.239554614 24.99998715 1.087267622 1.212141957 0.507527987 0.050538483 19.56860709 492102.7377 0.012098831 0.029554495 17360.1956 -4.239554614 0.124874335 KEWSGLLEELAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEWSGLLEELAR 12 1 Q01813;Q01813-2;Q5VSR5;V9GYV7 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 111.66 0.0021769 787840000 2999300 3117000 1847100 2365200 2048500 1956400 2559400 2121600 2709700 2674600 FALSE TRUE 2882084.04 3028106.212 2180912.059 2487268.255 2114391.863 1995959.748 2590722.703 2077788.219 2402106.216 2493446.96 1.155863384 1.214425757 0.87465749 0.997522023 0.847979483 0.800482136 1.039012558 0.833299546 0.963367681 1 21.24971008 4.239571976 24.99999967 0.911890456 1.185144654 0.653194398 0.077252868 13.43721435 332112.7031 0.017920389 0.043752823 17360.88963 -4.239571976 0.273254198 NEKPTQSVSS(ph)PEATSGSTGSVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NEKPTQSVSSPEATSGSTGSVEK 23 1 Q9BZ95-3;Q9BZ95-4;Q9BZ95-2;Q9BZ95-5;Q9BZ95;H0YE68 Q9BZ95-3 WHSC1L1 Histone-lysine N-methyltransferase NSD3 1 NEKPT(0.002)QS(0.01)VS(0.446)S(0.542)PEATSGSTGSVEK 119.28 0.00012207 212410000 138760 131830 125490 144860 147380 151510 130310 146960 151670 152020 TRUE FALSE 133337.1058 128070.3375 148168.8345 152336.242 152120.6115 154573.636 131904.7728 143925.2246 134453.0575 141723.55 0.940825331 0.903663064 1.045477865 1.074883052 1.073361566 1.090670083 0.930718803 1.015534995 0.948699475 1 17.11271998 4.239645494 24.99998267 1.023728934 0.922244173 0.384909491 0.050631323 28.7922535 663408.6301 0.013275731 0.032436157 17363.82877 -4.239645494 -0.101484762 QATENAKEEVRR ddPTM_BT-474_Pertuzumab_2h_R1 4 QATENAKEEVRR 12 2 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;; 249.04 4.25E-17 868840000 946040 1081020 388818 355381 583350 888630 501679 507554 567619 469759 FALSE TRUE 909067.7109 1050190.368 459086.0618 373722.256 602113.9825 906598.7074 507818.6977 497072.8325 503185.2708 437941.8045 2.075772857 2.39801352 1.048280975 0.853360543 1.374872132 2.070135114 1.159557486 1.135020287 1.14897748 1 18.74037965 4.239682453 24.99999679 1.241528852 2.236893452 0.614360276 0.320822966 19.2084663 428006.6833 0.083965899 0.205333872 17365.30649 -4.239682453 0.995364599 WGTLTDCVVMRDPQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 WGTLTDCVVMRDPQTK 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 202.41 2.78E-11 1735860000 2976000 3030400 1963340 1821890 2397900 3108400 2153700 2390300 2690700 2305000 FALSE TRUE 2859694.63 2943975.959 2318159.212 1915917.961 2475030.631 3171253.978 2180057.625 2340939.47 2385263.016 2148880.297 1.330783587 1.370004631 1.078775405 0.891588966 1.151776874 1.47577042 1.014508639 1.089376394 1.110002739 1 21.03515369 4.239740267 24.99934068 1.106657938 1.35039419 0.324143471 0.143616942 36.19692139 767003.1906 0.036848096 0.090184906 17367.61834 -4.239740267 0.243736252 ATFIKVPQNQNGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATFIKVPQNQNGK 13 1 P19338;H7BY16 P19338 NCL Nucleolin 0 127.37 7.85E-05 0 169430 186350 94501 108920 117190 135180 121130 134860 132410 114010 FALSE TRUE 162808.4883 181035.4805 111579.4329 114541.3743 120959.5228 137913.4322 122612.4252 132075.0939 117379.3719 106288.0012 1.531767335 1.703254163 1.049783905 1.077651033 1.13803554 1.297544697 1.153586706 1.242615276 1.10435205 1 16.69761921 4.239741293 25 1.151361887 1.617510864 0.813590673 0.092441827 11.70129737 247738.388 0.022757233 0.055694007 17367.65937 -4.239741293 0.466148977 AQVARPGGDTIFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQVARPGGDTIFGK 14 1 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 155.56 5.30E-06 9145900000 8345800 8691300 6173700 6849200 7197600 7995100 7439300 7859400 8196100 7904200 FALSE TRUE 8019636.909 8443432.634 7289424.923 7202688.033 7429117.341 8156766.4 7530344.379 7697100.643 7265713.089 7368841.494 1.088317196 1.145829048 0.989222652 0.977451888 1.008179827 1.106926565 1.021916998 1.044546914 0.986004801 1 22.81300639 4.239772962 24.99902178 1.021318331 1.117073136 0.526053651 0.037882778 24.8440269 512235.8239 0.009663582 0.023647184 17368.92587 -4.239772962 0.095754805 RGTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 RGT(0.464)GQS(0.68)DDS(0.857)DIWDDTALIK 110.14 0.00084546 30353000 48491 48265 31210 32377 35896 36217 34343 42538 46364 36720 TRUE FALSE 46595.91811 46888.52946 36850.34126 34047.98085 37050.62744 36949.33255 34763.29991 41659.57543 41100.95309 34232.92169 1.361143478 1.369691138 1.076459135 0.994597574 1.082309824 1.079350833 1.015493221 1.216944782 1.200626504 1 15.06309681 4.239814251 24.9924417 1.090640172 1.365417415 0.711158587 0.071813105 17.69399063 352709.4977 0.019158843 0.04693326 17370.57727 -4.239814251 0.274777243 ATLAENPNLFDDHEEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATLAENPNLFDDHEEGR 17 0 Q9BU68 Q9BU68 PRR15L Proline-rich protein 15-like protein 0 ; 256.45 4.26E-27 670270000 403940 426760 375050 470580 489050 492530 479360 442160 434240 488830 FALSE TRUE 388153.5782 414589.2226 442829.8779 494866.6902 504780.7374 502489.2941 485226.5511 433029.2415 384946.8957 455721.1087 0.851734912 0.909743294 0.971712456 1.085898109 1.107652746 1.102624576 1.064744515 0.95020668 0.844698409 1 18.79779167 4.239838136 2.449037485 1.024938657 0.863440276 0.356330217 0.076106217 0.347316739 4.062976032 0.021917356 0.076005306 17371.53262 -4.239838136 -0.16149838 EKKEESHSNDQSPQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKKEESHSNDQSPQIR 16 2 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 110.38 0.00053977 73942000 77166 77367 46591 38673 56345 73875 54046 58054 63865 51784 FALSE TRUE 74150.26741 75160.56891 55011.03011 40668.91816 58157.3881 75368.80312 54707.43111 56855.16461 56615.31294 48276.62356 1.535945597 1.556872941 1.139496221 0.842414303 1.204669751 1.561186296 1.133207484 1.177695548 1.17272727 1 15.55903716 4.239920664 24.99450059 1.164883681 1.546409415 0.456835439 0.170852099 31.86888051 585616.3877 0.044140505 0.108295468 17374.834 -4.239920664 0.381525734 ENSFGS(ph)PLEFR ddPTM_BT-474_Pertuzumab_2h_R1 6 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ENSFGS(1)PLEFR;ENS(0.008)FGS(0.992)PLEFR;ENS(0.001)FGS(0.999)PLEFR;ENS(0.008)FGS(0.992)PLEFR;ENSFGS(1)PLEFR;ENSFGS(1)PLEFR 211.39 9.95E-09 13884340000 7564410 7758920 8297730 10189120 9023580 8850870 9969300 10710560 10773500 11762800 TRUE FALSE 7268784.494 7537643.198 9797314.393 10714981.7 9313831.646 9029840.656 10091307.28 10489383.19 9550537.446 10966095.08 0.662841644 0.687358913 0.893418699 0.97710093 0.849329828 0.823432643 0.920227957 0.956528565 0.870915068 1 23.38654655 4.239961249 4.802112383 0.910928962 0.669158571 0.765156578 0.052519306 0.079700024 4.810536529 0.013331357 0.034677966 17376.45775 -4.239961249 -0.241770391 T(ph)ES(ph)KIRR ddPTM_BT-474_Pertuzumab_2h_R1 3 TESKIRR 7 2 Q6P6B7-2;Q6P6B7 Q6P6B7-2 ANKRD16 Ankyrin repeat domain-containing protein 16 2 T(1)ES(1)KIRR;T(1)ES(1)KIRR;T(1)ES(1)KIRR 80.18 0.033785 3197160000 3190370 3356700 2098900 2295150 2629700 2762170 2667930 2639500 2877000 2552590 TRUE FALSE 3065686.813 3260970.203 2478217.92 2413602.967 2714286.689 2818022.97 2700580.925 2584993.403 2550415.021 2379700.806 1.288265653 1.370327814 1.04139895 1.014246396 1.140599979 1.184192132 1.134840531 1.086268239 1.07173768 1 21.18234877 4.240048334 24.99999987 1.092560712 1.329296795 0.739615271 0.058008753 18.98601871 319016.5994 0.014860066 0.036505565 17379.94245 -4.240048334 0.236736083 VYEKMAS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 VYEKMASK 8 1 D6R9L8;D6RD98;D6RDG6;Q6ZTZ1 D6R9L8 MSANTD1 Myb/SANT-like DNA-binding domain-containing protein 1 1 VYEKMAS(1)K 76.847 0.035697 0 104420 99711 93110 112470 101710 108700 104240 108390 108950 117420 TRUE FALSE 100339.151 96867.33991 109937.0482 118274.5902 104981.5945 110897.9885 105515.7203 106151.7086 96582.45276 109467.0388 0.916615193 0.88489961 1.004293616 1.080458478 0.959024704 1.013071968 0.963904034 0.969713895 0.882297117 1 16.74013701 4.240108323 24.99601862 0.984699582 0.900757381 0.3266748 0.047852088 45.12880591 728781.6861 0.012041285 0.029598239 17382.34332 -4.240108323 -0.083942201 EVLLDEDDDLWIALR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVLLDEDDDLWIALR 15 0 A0A1B0GWF2;A0A1B0GVQ5;A0A2R8Y5D4;A0A0D9SG72;A0A1B0GTP9;P61764;P61764-2;A0A1B0GW76 A0A1B0GWF2 STXBP1 Syntaxin-binding protein 1 0 ; 171.05 2.57E-06 27016000 22105.2 22625.1 21705.1 27882 27630 29076 22990 25359.9 23603.3 28734 FALSE TRUE 21241.30435 21979.8543 25627.6944 29320.99336 28518.74404 29663.93664 23271.3585 24836.2092 20923.95234 26787.82059 0.792946342 0.820516706 0.956692028 1.094564348 1.064616061 1.107366557 0.868729071 0.927145571 0.781099465 1 14.70928959 4.240118664 4.356784418 0.977319068 0.800937971 0.333640367 0.095785375 0.232608507 10.45131429 0.026094209 0.069471599 17382.75719 -4.240118664 -0.176381097 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_BT-474_Pertuzumab_2h_R1 14 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;; 283.68 5.66E-77 4981595000 1165220.5 1150815.1 749140.4 749971.9 865773 1071453 835966.5 901518.7 1044192.2 866957.6 FALSE TRUE 1119682.395 1117994.98 884526.7348 788678.0396 893621.3748 1093118.514 846197.3081 882902.0238 925659.8791 808237.7895 1.385337841 1.383250071 1.094389233 0.975799511 1.105641664 1.352471424 1.04696578 1.092379044 1.145281613 1 19.62442028 4.240120147 24.92995515 1.105803107 1.384294076 0.575314068 0.097094576 26.80144471 428395.7739 0.0244212 0.060066632 17382.81656 -4.240120147 0.278490969 KDQEWSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDQEWSEK 8 1 Q92805;R4GNH1 Q92805 GOLGA1 Golgin subfamily A member 1 0 82.831 0.030876 320540000 259380 262060 147720 132550 177220 194660 176670 211630 193690 185810 FALSE TRUE 249243.1428 254586.3054 174416.29 139390.9214 182920.4422 198596.1586 178832.1403 207259.7665 171703.1232 173224.9232 1.438841122 1.469686352 1.006877572 0.804681675 1.055970693 1.146464117 1.032369575 1.196477751 0.99121489 1 17.40228699 4.240189877 24.99874934 1.041634447 1.454263893 0.747205172 0.098672715 21.40407187 328388.1471 0.026704161 0.065748055 17385.60775 -4.240189877 0.412629447 AAALEAMKDYTK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAALEAMKDYTK 12 1 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 126.76 0.00022026 0 258050 258360 155890 144820 181540 198670 200300 200770 217810 192340 FALSE TRUE 247965.1207 250991.8258 184062.7908 152294.1776 187379.399 202687.2435 202751.3313 196624.0293 193085.1219 179312.6405 1.3828647 1.399744185 1.026490884 0.84932204 1.044987116 1.130356694 1.130714102 1.096543048 1.076807086 1 17.45211767 4.240195278 24.98764232 1.050925233 1.391304576 0.763798853 0.077096358 20.68454708 316159.3509 0.021319634 0.052496924 17385.82395 -4.240195278 0.340379343 DTCVQS(ph)PISSFPCTDLK ddPTM_BT-474_Pertuzumab_2h_R1 5 DTCVQSPISSFPCTDLK 17 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 DTCVQS(0.998)PIS(0.001)S(0.001)FPCTDLK;DTCVQS(1)PISSFPCTDLK;DTCVQS(0.993)PIS(0.005)S(0.002)FPCTDLK;DTCVQS(0.976)PIS(0.007)S(0.018)FPCTDLK;DTCVQS(1)PISSFPCTDLK 259.29 3.55E-27 2756907000 2771580 2702350 2667630 3116300 3297190 3338570 2986890 2939650 3090590 3116300 TRUE FALSE 2663263.589 2625281.624 3149730.082 3277132.616 3403247.111 3406078.173 3023444.453 2878945.2 2739759.18 2905230.225 0.916713438 0.903639788 1.084158513 1.128011332 1.171420799 1.172395269 1.040690141 0.990952516 0.943043741 1 21.47022106 4.240202302 24.98839122 1.070075369 0.910176553 0.42538571 0.072492859 42.2760631 643438.074 0.020335507 0.050087832 17386.10514 -4.240202302 -0.159898817 T(ph)PTPEPAEVETR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 T(0.8)PT(0.2)PEPAEVETR 158.42 0.00082163 1838300000 690670 616150 691850 755800 771870 839350 810550 742380 729800 774640 TRUE FALSE 663677.8528 598578.0053 816882.6851 794806.9286 796697.8995 856322.2321 820469.7534 727049.5936 646956.1636 722172.9428 0.919001272 0.82885687 1.131145515 1.100576997 1.103195443 1.185757845 1.136112564 1.006752746 0.895846584 1 19.46198484 4.240241387 24.99999948 1.076291475 0.873929026 0.47651683 0.081953314 35.89547198 533870.1779 0.021254607 0.052370982 17387.6699 -4.240241387 -0.202362449 S(ph)IKMLVT(ph)LCQSDTEEIRNVASETLLS(ph)LGEDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIKMLVTLCQSDTEEIRNVASETLLSLGEDGR 32 2 H3BP45 H3BP45 FAM65B 3 S(0.955)IKMLVT(0.955)LCQS(0.044)DT(0.044)EEIRNVAS(0.045)ET(0.045)LLS(0.91)LGEDGR 50.757 0.045988 298950000 87207 80973 87732 110190 92405 95930 105300 79738 120580 121230 TRUE FALSE 83798.85403 78663.72932 103587.124 115876.9191 95377.29075 97869.77033 106588.6929 78091.38244 106892.2639 113018.9841 0.741458213 0.696022265 0.916546232 1.025287212 0.843905044 0.86595868 0.943104326 0.690958099 0.945790344 1 16.7862056 4.240247219 24.99997533 0.885728423 0.71874019 0.390570114 0.090272678 47.97244215 711021.5043 0.023399341 0.057648894 17387.9034 -4.240247219 -0.166988233 RINPPSSGGTSS(ph)SPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RINPPSSGGTSSSPIK 16 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 RINPPS(0.025)S(0.021)GGT(0.074)S(0.083)S(0.399)S(0.399)PIK 50.425 0.091062 0 158870 160500 117340 123950 143330 138180 128160 149240 171440 155180 TRUE FALSE 152661.1848 155922.6971 138545.9482 130347.0744 147940.3396 140974.0943 129728.4604 146158.1418 151978.8499 144669.5204 1.05524083 1.077785402 0.957671995 0.90099887 1.022608904 0.974456084 0.896722821 1.010289807 1.050524323 1 17.14240147 4.240312369 24.99619565 0.97362303 1.066513144 0.368082209 0.046958275 45.01186263 642233.5554 0.011728004 0.028927224 17390.51201 -4.240312369 0.092890114 DWTISR ddPTM_BT-474_Pertuzumab_2h_R1 5 DWTISR 6 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;;; 143.37 0.02654 1938410000 976850 966890 892916 1092890 963740 1002260 990420 1078170 1164230 1194020 FALSE TRUE 938673.622 939315.2439 1054285.784 1149294.184 994739.5723 1022526.384 1002541.056 1055905.413 1032071.491 1113147.962 0.843260424 0.843836827 0.947120976 1.032472073 0.893627448 0.918589818 0.900635936 0.948575975 0.927164696 1 20.08621394 4.240333417 24.90801883 0.942388137 0.843548582 0.504257512 0.040514272 34.82066018 489193.2117 0.010022821 0.024719895 17391.35485 -4.240333417 -0.098839555 APIRPDIVNFVHTNLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 APIRPDIVNFVHTNLRK 17 2 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 141.6 3.71E-07 565840000 643620 738710 372070 402330 496880 658830 517480 479830 534440 437580 FALSE TRUE 618466.6188 717642.7141 439311.3257 423094.2995 512862.5965 672151.994 523813.075 469921.3428 473772.6118 407942.3168 1.516063898 1.759176934 1.076895697 1.037142464 1.25719391 1.647664305 1.284037114 1.151930857 1.161371577 1 18.63800564 4.240344906 24.99999977 1.219886367 1.637620484 0.478345623 0.181186909 40.72066581 570500.5086 0.046972093 0.115862593 17391.81494 -4.240344906 0.417734117 EEGAAPS(ph)PTHVAELATMEVESAR ddPTM_BT-474_Pertuzumab_2h_R1 6 EEGAAPSPTHVAELATMEVESAR 23 0 Q9NRS6 Q9NRS6 SNX15 Sorting nexin-15 1 EEGAAPS(0.829)PT(0.171)HVAELATMEVESAR;EEGAAPS(0.5)PT(0.5)HVAELATMEVESAR;EEGAAPS(0.844)PT(0.156)HVAELATMEVESAR;EEGAAPS(0.7)PT(0.3)HVAELATMEVESAR;EEGAAPS(0.864)PT(0.136)HVAELATMEVESAR;EEGAAPS(0.83)PT(0.17)HVAELATMEVESAR 272.96 7.59E-52 907967000 735159 687105 828303 986868 859417 872288 930034 901290 1113460 1132792 TRUE FALSE 706428.1735 667509.4381 977995.7776 1037800.376 887060.9283 889926.261 941416.0343 882678.0465 987064.6888 1056066.989 0.668923639 0.632071114 0.926073618 0.982703168 0.839966534 0.842679745 0.891435907 0.835816341 0.934661058 1 20.01026992 4.240349176 24.99998365 0.895068454 0.650497291 0.769076294 0.055859873 20.59443172 287840.9896 0.013862354 0.034206238 17391.98594 -4.240349176 -0.244571163 KAASLTEDRDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KAASLTEDRDR 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 149.41 1.93E-05 1269140000 2244080 2465570 1642000 1920380 1954490 2245180 2138090 1994470 2289750 2344540 FALSE TRUE 2156378.873 2395254.358 1938745.926 2019491.042 2017357.946 2290579.078 2164256.585 1953283.498 2029827.179 2185742.218 0.986565962 1.095854003 0.886996605 0.923938343 0.922962429 1.047963964 0.990170098 0.893647696 0.928667234 1 21.05969183 4.24037418 24.99999974 0.946575942 1.041209974 0.318877707 0.053617115 52.79034462 727660.2452 0.013534443 0.033391803 17392.98729 -4.24037418 0.094634032 DSYVGDEAQSKR ddPTM_BT-474_Pertuzumab_2h_R1 13 DSYVGDEAQSKR 12 1 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 C9JTX5;P60709;P63261;P68133 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle" 0 ;;;;;;;;;;;; 199.15 2.81E-07 32939744000 24520964 25518440 15710277.7 16122589 17137326 22811112 18474009 20731880 23663988 19558661 FALSE TRUE 23562657.62 24790679.08 18549474.35 16954677.75 17688563.65 23272368.31 18700099.45 20303759.43 20977751.29 18233935.47 1.292242021 1.359590151 1.017305035 0.92984193 0.970090285 1.276321744 1.025565736 1.113514933 1.150478531 1 24.12012264 4.240418887 24.99999816 1.064924805 1.325916166 0.550676949 0.095869711 35.23195164 473952.9424 0.024395617 0.060248736 17394.77787 -4.240418887 0.26099136 AECLEKFPVIQHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AECLEKFPVIQHFK 14 1 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;Q68CR8;B7ZBQ0 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 169.04 2.04E-06 395690000 1046900 1124400 648620 670460 748160 857350 867830 867460 1012300 866690 FALSE TRUE 1005985.991 1092333.213 765840.0625 705062.5209 772225.2459 874686.2044 878450.7631 849546.6479 897387.9479 807988.3143 1.245050173 1.351917093 0.947835568 0.87261475 0.955738137 1.082548088 1.087207262 1.051434325 1.110644711 1 19.6239749 4.240436344 24.99995047 1.016478864 1.298483704 0.704260449 0.073849074 27.48588165 366308.2506 0.020321528 0.050207878 17395.47709 -4.240436344 0.28200484 YSYLTEPGMS(ph)PQSPCER ddPTM_BT-474_Pertuzumab_2h_R1 2 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.999)PQS(0.001)PCER;YSYLTEPGMS(1)PQSPCER 264.03 2.03E-27 3540900000 1901590 1968950 1767240 2279000 2148500 2118000 2135500 2225200 2095900 2143200 TRUE FALSE 1827273.76 1912797.474 2086619.58 2396619.463 2217608.454 2160827.411 2161634.888 2179248.842 1857982.219 1998039.155 0.914533509 0.957337332 1.044333678 1.199485734 1.10989239 1.081474007 1.081878142 1.090693762 0.929902807 1 20.93015342 4.240442208 3.354814249 1.080116751 0.926404422 0.383419213 0.066938169 0.213150337 4.931038236 0.016859465 0.049047216 17395.71198 -4.240442208 -0.15371233 ESQQQHGLR ddPTM_BT-474_Pertuzumab_2h_R1 3 ESQQQHGLR 9 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 166.34 6.08E-05 695434000 641620 666610 356535 366338 473215 588926 424239 419599 501463 381148 FALSE TRUE 616544.7811 647598.9355 420968.8056 385244.7481 488436.3902 600834.4872 429430.9638 410934.134 444539.0225 355332.5065 1.735120682 1.822515316 1.18471797 1.084180988 1.374589663 1.690907745 1.208532729 1.15647774 1.251050817 1 18.43881015 4.240454146 24.99996028 1.256834803 1.77881818 0.588324331 0.178750369 34.10142938 450202.2601 0.046201256 0.114189753 17396.19013 -4.240454146 0.521983377 SSS(ph)PATEQSWMENDFDELREEGFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 SS(0.001)S(0.999)PATEQSWMENDFDELREEGFR;S(0.013)S(0.013)S(0.973)PATEQSWMENDFDELREEGFR;S(0.006)S(0.006)S(0.986)PAT(0.001)EQSWMENDFDELREEGFR;S(0.128)S(0.128)S(0.743)PAT(0.001)EQSWMENDFDELREEGFR 399.83 1.93E-138 866603000 17144.9 16708 17045.3 16906.2 20920 18071.4 19170.2 21485.8 22298.5 21694.3 TRUE FALSE 16474.85835 16231.5042 20125.76488 17778.73101 21592.9108 18436.81609 19404.81064 21042.11072 19767.26776 20224.92574 0.814581896 0.802549508 0.995097097 0.879050496 1.06763857 0.911588815 0.959450279 1.040404845 0.977371587 1 14.30384678 4.240472425 24.99817619 0.979675691 0.808565635 0.629247553 0.052272766 28.41899218 371570.1897 0.012522582 0.030958557 17396.92233 -4.240472425 -0.171110056 GS(ph)LGILLGGDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSLGILLGGDYR 12 0 Q4VCS5;E7ERM3;Q4VCS5-2 Q4VCS5 AMOT Angiomotin 1 GS(1)LGILLGGDYR;GS(1)LGILLGGDYR 132.97 0.00017999 57212000 157269 126604 90090 67248 77709 57421 55233 90897 70127 64164 TRUE FALSE 151122.7536 122993.3779 106371.267 70718.67734 80208.58056 58582.09196 55908.95798 89019.94519 62166.47696 59818.11513 2.526371038 2.056122591 1.778245049 1.182228447 1.340874422 0.979336976 0.934649276 1.488177035 1.039258372 1 15.86829483 4.240487095 1.117994495 1.139925436 2.663833887 0.889237399 0.168851126 0.257440292 0.460149852 0.054468259 0.381665762 17397.51002 -4.240487095 1.52390845 up T(ph)PTQTNGSNVPFKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPTQTNGSNVPFKPR 15 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 T(0.982)PT(0.01)QT(0.007)NGSNVPFKPR 78.441 0.037031 330540000 125440 111120 133950 165700 130720 121440 156470 159410 142590 181960 TRUE FALSE 120537.6661 107950.9664 158157.7447 174251.7969 134924.7275 123895.6 158384.9267 156118.1278 126403.781 169635.6871 0.710567854 0.636369435 0.93233769 1.027211902 0.795379379 0.730362827 0.933676925 0.920314177 0.745148519 1 17.37208018 4.240489571 24.99999588 0.88358498 0.673468589 0.434592215 0.096742372 45.02800979 583538.4461 0.024149144 0.059683376 17397.60919 -4.240489571 -0.210116392 SSS(ph)LESLQTAVAEVTLNGDIPFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLESLQTAVAEVTLNGDIPFHR 24 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.304)S(0.304)S(0.392)LESLQTAVAEVTLNGDIPFHR 172.98 3.06E-12 30181000 4468 4498.2 5550.4 7501.1 5896.6 5663.3 6315.8 7433.6 7363.8 5241.8 TRUE FALSE 4293.38562 4369.91574 6553.480748 7888.23267 6086.269494 5777.815806 6393.09465 7280.093562 6527.892296 4886.768217 0.878573615 0.894234297 1.341066418 1.614202336 1.245459008 1.182338828 1.308245934 1.489756264 1.335830145 1 12.25466496 4.240494856 8.244238005 1.342954245 0.884638528 0.53509369 0.157913708 0.073087572 43.58688638 0.038484709 0.094375897 17397.82092 -4.240494856 -0.458315717 TPIS(ph)PLKTGVSKPIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPISPLKTGVSKPIVK 16 2 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 T(0.006)PIS(0.989)PLKT(0.005)GVSKPIVK 108.71 0.00081043 315020000 636110 650930 277440 234750 334540 540520 361650 354780 373010 263450 TRUE FALSE 611250.1179 632366.1137 327579.5796 246865.4756 345300.7829 551449.6847 366075.9809 347453.669 330667.4686 245606.2968 2.488739604 2.574714581 1.333758881 1.005126818 1.405911768 2.245258741 1.490499167 1.414677366 1.346331396 1 17.90598802 4.240524303 24.99029617 1.438447677 2.531727517 0.656366975 0.325333942 30.38061744 386602.5774 0.083646048 0.206827024 17399.0006 -4.240524303 1.09327984 AQLEEEAAAAEERPLVFLCSGCR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQLEEEAAAAEERPLVFLCSGCR 23 1 Q9NYP9 Q9NYP9 MIS18A Protein Mis18-alpha 0 ; 175.85 9.53E-13 120220000 21948.8 25584.6 23814.4 33774 29143 32733 32677 31345 34585 30555 FALSE TRUE 21091.01663 24854.95226 28118.19183 35517.08019 30080.41106 33394.88369 33076.9109 30697.7148 30659.05579 28485.48263 0.740412824 0.872548048 0.987106035 1.246848461 1.055990922 1.172347477 1.161184851 1.077661741 1.076304593 1 14.79793923 4.240533023 2.154100869 1.116756036 0.760572816 0.758858951 0.069474522 0.142116809 1.25621442 0.017273796 0.066111325 17399.34996 -4.240533023 -0.35618322 AKLNWLSVDFNNWKDWEDDS(ph)DEDMSNFDR ddPTM_BT-474_Pertuzumab_2h_R1 4 AKLNWLSVDFNNWKDWEDDSDEDMSNFDR 29 2 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR 379.51 2.22E-137 4344100000 2280330 2302350 811650 658960 1141880 1630350 887714 1046770 1266780 726304 TRUE FALSE 2191212.183 2236689.232 958333.2101 692969.0046 1178609.607 1663316.794 898578.1095 1025153.834 1122980.445 677110.7832 3.236120642 3.303284024 1.415327054 1.023420424 1.74064516 2.456491368 1.327076945 1.514011974 1.658488497 1 19.36903237 4.240535829 24.9998969 1.546752798 3.26970303 0.763623546 0.389791866 22.88535615 289634.994 0.09824351 0.24300294 17399.46237 -4.240535829 1.722950233 AAYEAELGDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAYEAELGDAR 11 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 185.6 1.02E-05 1404180000 694900 717570 622540 833520 732940 733370 738960 779450 735140 809040 FALSE TRUE 667742.5397 697105.6062 735046.8263 876538.0671 756515.6807 748199.2439 748003.6135 763354.0851 651689.9892 754243.0002 0.885314865 0.924245377 0.974549086 1.162142793 1.003013194 0.991986991 0.991727617 1.012079774 0.864031869 1 19.52466988 4.240540554 3.471705749 1.006911391 0.897865205 0.249008561 0.067661159 0.299087563 7.48718368 0.017248182 0.049479996 17399.65165 -4.240540554 -0.109046186 S(ph)PGSNSKVPEIEVTVEGPNNNNPQTSAVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 S(0.977)PGS(0.02)NS(0.004)KVPEIEVTVEGPNNNNPQTSAVR;S(0.468)PGS(0.395)NS(0.137)KVPEIEVTVEGPNNNNPQTSAVR;S(0.997)PGS(0.003)NSKVPEIEVTVEGPNNNNPQTSAVR 274.5 2.47E-71 1177020000 508153 540176 190989 178661 265582 425994 223664 256243 273081 187107 TRUE FALSE 488293.819 524770.7094 225504.9608 187881.7156 274124.6862 434607.8906 226401.2669 250951.4925 242081.9897 174434.0762 2.79930292 3.008418542 1.292780434 1.077092961 1.571508802 2.491530898 1.2979188 1.438660942 1.387813637 1 17.41232238 4.240541652 24.99972639 1.478519358 2.90386124 0.69038074 0.390353766 27.95766024 352787.3909 0.099029057 0.244962524 17399.69564 -4.240541652 1.425341882 S(ph)NPEGAEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNPEGAEDR 9 0 M0R3H9;M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R2I2 M0R3H9 BABAM1 BRISC and BRCA1-A complex member 1 1 S(1)NPEGAEDR;S(1)NPEGAEDR 99.498 0.0055557 81050000 89255 88006 83149 105321 90144 84056 96840 102810 106597 101921 TRUE FALSE 85766.81592 85496.15505 98175.87394 110756.6294 93043.56363 85755.66991 98025.15689 100686.9376 94496.55545 95017.79989 0.902639464 0.899790935 1.033236657 1.165640854 0.979222459 0.902522159 1.031650459 1.059663954 0.994514244 1 16.53591018 4.240542087 24.97785625 1.02477912 0.901215148 0.364164899 0.063034852 53.2370572 671044.3658 0.016484792 0.040800054 17399.71308 -4.240542087 -0.123563972 CAIKVEQSAER ddPTM_BT-474_Pertuzumab_2h_R1 2 CAIKVEQSAER 11 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 103.44 0.0024934 438100000 405220 429770 226026 218796 264335 332140 283140 304350 361640 305080 FALSE TRUE 389383.5544 417513.3804 266873.9261 230088.0878 272837.5753 338856.0984 286605.152 298065.0661 320588.1433 284416.6599 1.369060288 1.467963869 0.938320302 0.808982455 0.959288304 1.191407348 1.007694669 1.047987366 1.127177794 1 18.11764645 4.240554501 24.99993809 1.011125425 1.418512207 0.725037854 0.100600492 26.54175393 332765.2295 0.026683268 0.066038037 17400.21044 -4.240554501 0.407386782 TEAQDLCRAS(ph)PEPPGPESSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEAQDLCRASPEPPGPESSSR 21 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 TEAQDLCRAS(1)PEPPGPESSSR;TEAQDLCRAS(1)PEPPGPESSSR 224.41 1.93E-25 1609310000 918230 1010910 246457 265368 513750 664850 285966 325527 341032 225945 TRUE FALSE 882344.5564 982079.8366 290997.2623 279063.6743 530275.2353 678293.7225 289465.7375 318804.7537 302319.4771 210641.5439 4.188843948 4.662327376 1.381480865 1.32482733 2.517429494 3.220132695 1.374210102 1.513494194 1.435231966 1 17.68443048 4.240598509 24.99999952 1.773595223 4.425586575 0.742427693 0.636639889 25.92927705 318067.4531 0.166145139 0.411292021 17401.97374 -4.240598509 2.651991352 VFNPYTEFPEFSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VFNPYTEFPEFSR 13 0 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ;;; 210.95 5.99E-08 716489000 277175 252567 274202 312568 296656 285745 318554 325192 306042 326554 FALSE TRUE 266342.6946 245364.0364 323756.401 328699.6719 306198.2097 291522.9597 322452.5591 318476.6716 271301.3952 304436.2067 0.874871939 0.805962074 1.063462209 1.07969967 1.005787758 0.957583077 1.059179401 1.046119563 0.891160083 1 18.21578042 4.240605269 24.99999946 1.018537132 0.840416962 0.604294548 0.055670908 31.76111074 388317.2379 0.01363109 0.033747375 17402.2446 -4.240605269 -0.178120171 DNWEELYNR ddPTM_BT-474_Pertuzumab_2h_R1 4 DNWEELYNR 9 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 239.6 5.81E-10 1670960000 1069210 1059040 1047540 1273530 1188950 1045930 1223480 1230330 1349360 1468490 FALSE TRUE 1027424.091 1028837.216 1236853.78 1339257.036 1227193.657 1067079.421 1238453.314 1204923.256 1196186.31 1369027.864 0.750477122 0.751509332 0.903454059 0.978254038 0.896397866 0.779443172 0.904622431 0.880130556 0.873748695 1 20.38472038 4.240655518 24.8873035 0.895316926 0.750993161 0.529422261 0.056669357 38.88415378 461908.2585 0.013972253 0.034607892 17404.25823 -4.240655518 -0.144323765 ESQMTPSHGGS(ph)PVGPPQLPIMSSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESQMTPSHGGSPVGPPQLPIMSSLR 25 0 A0A5F9ZH11;P55201-3;P55201;P55201-2 A0A5F9ZH11 BRPF1 Peregrin 1 ESQMTPS(0.001)HGGS(0.998)PVGPPQLPIMSSLR 129.84 6.25E-05 179740000 90710 91387 63730 67546 82310 66307 66626 66459 75005 80086 TRUE FALSE 87164.95291 88780.73224 75247.42867 71032.05715 84957.5759 67647.77297 67441.38892 65086.59843 66490.74685 74661.70389 1.167465359 1.189106699 1.00784505 0.951385429 1.137900309 0.906057181 0.903292925 0.871753456 0.890560266 1 16.18808081 4.240676837 0.517977686 0.899341475 1.303532363 0.598007947 0.072784918 1.771913905 0.525957188 0.047113651 0.41039151 17405.1126 -4.240676837 0.404190889 RGLLYDS(ph)DEEDEERPARK ddPTM_BT-474_Pertuzumab_2h_R1 3 RGLLYDSDEEDEERPARK 18 3 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 RGLLYDS(1)DEEDEERPARK;RGLLYDS(1)DEEDEERPARK;RGLLYDS(1)DEEDEERPARK 124.08 0.00018021 981430000 458980 432798 302864 254910 307915 348999 333230 387576 416260 381024 TRUE FALSE 441042.5542 420455.0248 357598.262 268065.9356 317819.3656 356055.9989 337308.1684 379572.4202 369007.9099 355216.9051 1.241614765 1.183657137 1.006703951 0.754654218 0.894719145 1.002362201 0.949583659 1.068565191 1.038824179 1 18.43834072 4.24069607 3.808967817 0.960972023 1.224912077 0.595669015 0.082958011 0.15495081 4.852975223 0.023288072 0.064583683 17405.88341 -4.24069607 0.263940054 DQLIYNLLKEEQTPQNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQLIYNLLKEEQTPQNK 17 1 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8;F5GXC7;F5H8H6;F5GXU1;F5GWW2 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ; 234.48 3.56E-20 857310000 1676020 1667990 656320 629820 990050 1197360 726680 772310 959700 474840 FALSE TRUE 1610519.285 1620420.558 774931.6238 662325.0857 1021895.857 1221571.44 735573.3272 756361.5286 850758.8794 442678.6639 3.638122677 3.660489404 1.750551104 1.496175759 2.308437114 2.759499247 1.661641699 1.708601725 1.921842973 1 18.75590031 4.240711097 24.99693618 1.871610838 3.649306791 0.729354828 0.443611126 27.07563503 314703.3517 0.110350258 0.273573452 17406.48568 -4.240711097 1.777695953 VTQLTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTQLTDR 7 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 78.77 0.080109 167010000 87017 84249 77535 89918 86823 96580 82122 95868 93131 87106 FALSE TRUE 83616.27944 81846.30101 91547.29926 94558.67876 89615.74065 98532.91377 83127.0336 93888.2923 82559.15932 81206.23303 1.029678096 1.007882005 1.127343257 1.164426365 1.103557415 1.213366389 1.023653364 1.156171008 1.016660375 1 16.30930285 4.240711298 24.99577687 1.110759745 1.018780022 0.181252293 0.066891534 71.69561258 833208.3802 0.015158665 0.037523332 17406.49371 -4.240711298 -0.091979724 VFTTQELVQAFTHAPATLEADR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFTTQELVQAFTHAPATLEADR 22 0 O95433;O95433-2;G3V438;H0YJ63;H0YJG7 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ; 244.16 8.40E-31 2262600000 1377640 1458750 1300430 1422450 1370550 1531490 1339870 1333490 1712950 1693530 FALSE TRUE 1323800.306 1417147.878 1535446.629 1495862.815 1414634.985 1562457.777 1356267.73 1305952.966 1518503.097 1578825.705 0.838471468 0.897596153 0.972524468 0.947452788 0.896004531 0.989632847 0.859035754 0.827167281 0.961792738 1 20.59042048 4.240733681 0.005683147 1.803839271 1.23E-07 0.098334495 0.057412199 73841.83606 76.94989596 11787.71109 12645.05175 17407.39086 -4.240733681 -1.803839148 TDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 TDLLVNDNPDPAPLSPELQDFK 22 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 TDLLVNDNPDPAPLS(1)PELQDFK;TDLLVNDNPDPAPLS(1)PELQDFK 180.88 3.33E-17 124889000 187904 170915 211580 236050 231170 185427 225680 262950 279290 274790 TRUE FALSE 180560.5039 166040.6715 249817.2126 248232.5688 238605.793 189176.461 228441.9393 257519.9906 247586.1701 256178.2285 0.704823767 0.648145131 0.975169568 0.96898386 0.93140543 0.738456433 0.891730498 1.005237612 0.966460622 1 17.96678835 4.240763908 24.9999924 0.930728929 0.676484365 0.658866965 0.074270795 34.81466003 395004.4644 0.019784684 0.049075127 17408.60246 -4.240763908 -0.254244564 S(ph)LESVLSLGPR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLESVLSLGPR 11 0 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 1 S(1)LESVLSLGPR;S(1)LESVLSLGPR;S(1)LESVLSLGPR;S(0.999)LES(0.001)VLSLGPR;S(0.999)LES(0.001)VLSLGPR;S(0.999)LES(0.001)VLSLGPR 237.53 1.46E-15 628769000 115131.2 113943.1 125956.9 147490.8 136439.7 120061.1 150292.7 160930.8 155806.7 165633 TRUE FALSE 110631.7454 110693.5543 148720.1137 155102.8179 140828.4069 122488.8177 152132.027 157607.5227 138120.1766 154414.5294 0.716459428 0.716859707 0.96312254 1.004457408 0.912015258 0.793246712 0.985218345 1.020678063 0.894476557 1 17.23644898 4.240767509 24.96267319 0.948629568 0.716659466 0.674044243 0.063962891 31.98204602 361732.6742 0.01687021 0.041849724 17408.7468 -4.240767509 -0.231970102 GLQLTPGIGGMQQHFFDDEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLQLTPGIGGMQQHFFDDEDR 21 0 P12270 P12270 TPR Nucleoprotein TPR 0 223.97 3.35E-25 48746000 45733 37822 49324 53999 55882 52598 47259 60217 45678 56389 FALSE TRUE 43945.7038 36743.35359 58237.94401 56785.89486 57679.49528 53661.5676 47837.36978 58973.49791 40492.82494 52569.7228 0.835950837 0.698945165 1.107822924 1.080201527 1.097199913 1.020769461 0.909979494 1.121814892 0.770268945 1 15.68194451 4.240773505 24.99995573 1.023061634 0.767447954 0.461213207 0.105977499 43.59067968 492431.3413 0.024832796 0.061599769 17408.98714 -4.240773505 -0.25561368 EQQEAIEHIDEVQNEIDR ddPTM_BT-474_Pertuzumab_2h_R1 7 EQQEAIEHIDEVQNEIDR 18 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;;; 355.42 3.31E-90 18911950000 5534680 6003540 6718090 9120780 7514850 6762610 8731330 8263820 9195820 10613850 FALSE TRUE 5318378.587 5832324.917 7932198.306 9591504.549 7756571.975 6899354.608 8838186.628 8093169.229 8151949.066 9894964.486 0.537483343 0.589423532 0.801639896 0.969331882 0.783890835 0.697259158 0.89320044 0.81790786 0.823848239 1 23.2382631 4.240798672 3.807438194 0.842233906 0.550501653 0.655799777 0.083297918 0.123036332 3.849465857 0.020430276 0.056675172 17409.99604 -4.240798672 -0.291732254 MGIGGLDKEFSDIFR ddPTM_BT-474_Pertuzumab_2h_R1 2 MGIGGLDKEFSDIFR 15 1 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 192.4 1.24E-07 456420000 1091540 1199050 754370 797790 1007310 1020710 966800 1007420 1017640 997680 FALSE TRUE 1048881.41 1164854.268 890701.4399 838964.0375 1039711.041 1041349.456 978631.9876 986616.425 902121.7735 930106.245 1.127700643 1.252388396 0.957634082 0.902008821 1.117841157 1.119602692 1.052172258 1.060756693 0.969912608 1 19.827036 4.240811747 24.99992749 1.030312923 1.190044531 0.464971431 0.07150056 52.67102613 584901.6828 0.018457934 0.04583553 17410.52018 -4.240811747 0.159731608 DSGTDDQEEEPLER ddPTM_BT-474_Pertuzumab_2h_R1 2 DSGTDDQEEEPLER 14 0 E9PN81;Q8TDP1 E9PN81 RNASEH2C Ribonuclease H2 subunit C 0 ; 264.84 2.38E-24 226150000 221853 223210 205795 256524 229067 229886 242249 244481 274233 277194 FALSE TRUE 213182.7395 216844.2693 242986.7344 269763.2344 236435.1481 234534.4524 245213.7157 239432.3819 243103.2195 258419.4035 0.824948656 0.839117599 0.940280533 1.043896978 0.914928 0.907572919 0.948898235 0.926526332 0.940731293 1 17.97935487 4.240840015 5.076760996 0.949619979 0.829371922 0.608884168 0.038789947 0.112489001 8.150586418 0.009820713 0.025313703 17411.65346 -4.240840015 -0.120248056 QGSITSPQANEQSVT(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 3 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITSPQANEQSVT(1)PQR;QGSITSPQANEQS(0.005)VT(0.995)PQR;QGSITSPQANEQS(0.062)VT(0.938)PQR 395.75 7.08E-126 628640000 386841 387283 415536 514646 429166 453311 439103 532056 544690 533720 TRUE FALSE 371722.826 376238.068 490632.5987 541206.9417 442970.5141 462477.259 444476.8739 521068.8577 482859.0747 497570.669 0.747075439 0.756150013 0.986056111 1.087698644 0.890266532 0.929470501 0.893293961 1.047225832 0.970433156 1 18.92454192 4.240856818 24.70458644 0.975959193 0.751612608 0.698379736 0.058867844 26.87029992 289073.111 0.015034651 0.03732806 17412.32716 -4.240856818 -0.224346585 SPGETSKPRPFAGGGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 72.819 0.015514 572240000 429230 426290 314640 337210 399230 365020 353040 386680 406380 431620 FALSE TRUE 412455.2171 414132.6266 371502.4471 354613.4485 412071.5955 372400.9545 357360.6091 378694.9229 360249.4461 402385.993 1.025023794 1.029192452 0.923248954 0.881276821 1.024070427 0.925481903 0.888103998 0.941123522 0.895283266 1 18.61822056 4.2408902 24.9964991 0.931718683 1.027108162 0.414065328 0.043787122 51.52925497 552876.7552 0.010370219 0.025779546 17413.66558 -4.2408902 0.095389479 TAST(ph)PTPPQT(ph)GGGLEPQANGETPQVAVIVRPDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 2 T(0.079)AS(0.411)T(0.499)PT(0.329)PPQT(0.682)GGGLEPQANGETPQVAVIVRPDDR 70.835 0.020194 223360000 93934 92522 64966 69992 76464 74304 74009 82739 87560 86881 TRUE FALSE 90262.95543 89883.36315 76706.80136 73604.29551 78923.534 75806.47779 74914.74428 81030.41074 77620.55588 80996.47248 1.114406006 1.109719478 0.947038791 0.908734581 0.974407052 0.935923201 0.924913666 1.000419009 0.958320202 1 16.30557146 4.240897011 24.99702964 0.955225071 1.112062812 0.830035496 0.028205535 21.24785098 227316.6845 0.007049377 0.01753448 17413.93867 -4.240897011 0.156837742 AIPTVNHSGTFS(ph)PQAPVPTTVPVVDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIPTVNHSGTFSPQAPVPTTVPVVDVR 27 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 AIPTVNHS(0.068)GT(0.319)FS(0.612)PQAPVPTTVPVVDVR;AIPTVNHS(0.001)GT(0.078)FS(0.921)PQAPVPTTVPVVDVR 205.44 2.00E-25 456910000 158089 157710 157809 191693 166062 191910 199680 183966 180704 202833 TRUE FALSE 151910.7071 153212.2652 186328.5967 201586.2987 171403.535 195790.5517 202123.7436 180167.0378 160191.2395 189094.9402 0.803356805 0.810239899 0.985370611 1.06605866 0.906441679 1.035408729 1.068900856 0.952786138 0.847147149 1 17.52875123 4.24089808 7.967600395 0.986123835 0.805983561 0.536980543 0.065307645 0.081364268 40.34783942 0.016235909 0.039935874 17413.98154 -4.24089808 -0.180140274 DAELQDQEFGKRDS(ph)LGTYSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DAELQDQEFGKRDSLGTYSSR 21 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAELQDQEFGKRDS(0.999)LGT(0.001)YSSR;DAELQDQEFGKRDS(0.967)LGT(0.029)YS(0.003)S(0.001)R;DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(0.999)LGT(0.001)YSSR 201.6 3.57E-22 4776400000 2878580 2850000 1623210 1457910 1923300 2416480 1736670 2252300 2251090 1844740 TRUE FALSE 2766081.911 2768720.79 1916560.155 1533152.91 1985164.691 2465342.881 1757923.887 2205789.218 1995555.701 1719794.117 1.60837968 1.609914096 1.114412555 0.89147468 1.154303688 1.433510475 1.022171125 1.282589117 1.160345696 1 20.71380443 4.240917695 24.99799826 1.146514655 1.609147088 0.639500864 0.142877508 36.97749431 392140.965 0.035775941 0.088965382 17414.76809 -4.240917695 0.462632433 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR ddPTM_BT-474_Pertuzumab_2h_R1 4 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR 29 0 Q00577 Q00577 PURA Transcriptional activator protein Pur-alpha 0 ;;; 251.16 8.24E-47 568941000 212738 223238 205849 248579 234577 265502 255417 254481 283967 277350 FALSE TRUE 204423.9638 216871.4708 243050.4934 261408.192 242122.3822 270870.6323 258542.8696 249225.8784 251732.2566 258564.8375 0.790610068 0.838750825 0.939998245 1.010996679 0.936408773 1.047592685 0.999915039 0.963881558 0.973574981 1 17.98016657 4.240943559 2.164537505 0.988470019 0.792285415 0.859392092 0.028322796 0.110202874 0.984489582 0.007414515 0.028286865 17415.80523 -4.240943559 -0.196184603 DLLHPSPEEEKRK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 0 162.32 2.44E-05 180310000 412980 473790 161870 152810 227000 404670 226330 201080 284770 217570 FALSE TRUE 396840.285 460277.9731 191123.5098 160696.5424 234301.6612 412852.7047 229099.8942 196927.6277 252444.1035 202833.7901 1.956480155 2.269237156 0.94226662 0.792257258 1.155141168 2.035423705 1.129495702 0.970881763 1.244586039 1 17.62993849 4.240950176 24.99999816 1.163814197 2.112858923 0.577005847 0.326739246 43.6528088 456676.417 0.085470159 0.212494916 17416.07056 -4.240950176 0.949044726 LSDVDANTAIKHEEQSNEDIPIAEQSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSDVDANTAIKHEEQSNEDIPIAEQSSK 28 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 ; 116.35 0.00018133 267700000 364870 347800 257280 219726 292960 310930 279830 316100 369410 297790 FALSE TRUE 350610.477 337881.0845 303776.2192 231066.0852 302383.3245 317217.2176 283254.6432 309572.4245 327476.1255 277620.4181 1.262913151 1.217061363 1.094214256 0.832309406 1.089196993 1.142629277 1.020294708 1.115092423 1.179582279 1 18.08275415 4.240954527 3.988144188 1.058682988 1.248289128 0.394743874 0.090916005 0.209911712 7.397247026 0.023512874 0.064277165 17416.24506 -4.240954527 0.18960614 (ac)S(ph)GDEMIFDPTMSKK ddPTM_BT-474_Pertuzumab_2h_R1 6 SGDEMIFDPTMSKK 14 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 S(0.999)GDEMIFDPTMSKK;S(0.999)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK 126.67 2.62E-12 1417853000 3905150 3818180 2024660 1778260 2375270 3166500 2099190 2574480 2660850 2194890 TRUE FALSE 3752532.421 3709289.245 2390561.1 1870036.212 2451672.717 3230528.8 2124880.515 2521316.088 2358801.463 2046228.145 1.833877825 1.812744709 1.168276913 0.913894287 1.198142408 1.578772537 1.038437732 1.232177406 1.152755849 1 20.96453558 4.240962509 9.311172519 1.172307822 1.824746256 0.711707254 0.168654086 0.052267436 59.6750854 0.042043262 0.103008233 17416.56518 -4.240962509 0.652438434 VFLKNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFLKNEK 7 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 65.252 0.064833 620000000 1002100 1106000 619080 592430 782790 924030 843730 855570 926630 778370 FALSE TRUE 962936.8241 1074457.963 730961.5274 623005.3833 807969.1513 942714.5197 854055.8201 837902.1805 821442.8471 725650.3066 1.326998439 1.480682848 1.007319257 0.858547675 1.11344148 1.299130602 1.176952331 1.154691417 1.132009233 1 19.46891495 4.240985426 24.99990969 1.104985086 1.403840702 0.524568185 0.118002433 52.13467994 537479.4769 0.031703983 0.078895425 17417.48421 -4.240985426 0.298855616 DNLHQIDAVEGPAAFLDILAPPYDPDDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DNLHQIDAVEGPAAFLDILAPPYDPDDGR 29 0 Q96SZ5 Q96SZ5 ADO 2-aminoethanethiol dioxygenase 0 ;;; 182.72 9.39E-18 251471000 88976 86283 100350 116084 108931 86601 123421 123217 128931 133571 FALSE TRUE 85498.71955 83822.29332 118485.4773 122075.1092 112434.8645 88352.13156 124931.4631 120672.5259 114295.2934 124524.1172 0.6866037 0.673141037 0.951506262 0.980333062 0.902916375 0.709518233 1.003271221 0.969069515 0.917856685 1 16.92606566 4.24099461 24.9998191 0.927458756 0.679872266 0.607136874 0.080248632 41.00619745 421154.3655 0.020544625 0.051125884 17417.85257 -4.24099461 -0.24758649 RKVMDS(ph)DEDDDY ddPTM_BT-474_Pertuzumab_2h_R1 1 RKVMDSDEDDDY 12 2 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 RKVMDS(1)DEDDDY 106.54 0.022099 362220000 885920 870870 580170 515210 602020 840140 663250 761690 826980 710240 TRUE FALSE 851297.267 846033.6403 685019.6248 541800.0498 621384.52 857128.2064 671367.0519 745960.8353 733104.6974 662134.8122 1.285685711 1.277736232 1.034562165 0.818262444 0.9384562 1.294491984 1.013943142 1.126599631 1.107183437 1 19.33676546 4.241007599 23.73081834 1.046304025 1.281711183 0.398726926 0.11779042 34.05007955 330177.5098 0.030754014 0.076418382 17418.3735 -4.241007599 0.235407158 MDKEETKDWILPSDYDHAEAEAR ddPTM_BT-474_Pertuzumab_2h_R1 5 MDKEETKDWILPSDYDHAEAEAR 23 2 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;; 222.46 9.71E-33 6815890000 6016170 6205110 4167630 4217190 4973850 5310890 4973310 5189240 6442590 5679910 FALSE TRUE 5781051.425 6028146.338 4920813.449 4434839.681 5133838.402 5418279.835 5034174.855 5082080.381 5711254.193 5295204.637 1.091752221 1.138416124 0.929296182 0.83751998 0.969525968 1.023242765 0.950704496 0.95975146 1.078571006 1 22.33625501 4.241028604 24.99891622 0.963385318 1.115084217 0.483232664 0.060411868 50.6002942 512515.5208 0.015342448 0.038179017 17419.21597 -4.241028604 0.151698899 AFGFSHLEALLDDSKELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFGFSHLEALLDDSKELQR 19 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 193.8 2.71E-15 619610000 1519000 1674680 691360 778110 1056980 1316500 860780 790390 1141340 861220 FALSE TRUE 1459635.801 1626919.766 816304.1312 818268.3503 1090978.722 1343120.532 871314.4831 774068.1703 1011779.868 802888.8023 1.81798002 2.026332615 1.016708826 1.019155265 1.358816711 1.672859963 1.085224356 0.964103831 1.260174342 1 19.61484067 4.241031493 24.99999971 1.174001905 1.922156548 0.670109198 0.210494963 37.56377206 380043.381 0.056038874 0.139523504 17419.33184 -4.241031493 0.748154643 SLLGDSAPTLHLNKGT(ph)PS(ph)QSPVVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 SLLGDSAPTLHLNKGT(1)PS(0.983)QS(0.017)PVVGR 239.87 2.29E-37 2041900000 1165800 1168800 665490 523320 837230 998210 701530 923200 979180 861860 TRUE FALSE 1120239.247 1135466.968 785758.8467 550328.6079 864160.2633 1018394.49 710115.534 904135.5974 868027.5915 803485.4545 1.394224676 1.413176756 0.977937861 0.684926659 1.075514508 1.267470972 0.883793888 1.125266913 1.080327698 1 19.61591238 4.241038722 24.99800353 1.015082841 1.403700877 0.536900896 0.145525234 48.12777691 485462.5228 0.037216885 0.092663729 17419.62182 -4.241038722 0.388618036 NDEELNKLLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 NDEELNKLLGR 11 1 Q7L7L0;P04908 Q7L7L0 HIST3H2A;HIST1H2AB Histone H2A type 3;Histone H2A type 1-B/E 0 ;;; 165.66 1.95E-05 2110230000 6016200 6459900 1661960 1566880 2559160 4299020 2337950 2297480 2767340 1603800 FALSE TRUE 5781080.253 6275669.977 1962313.142 1647746.865 2641477.706 4385949.13 2366562.531 2250036.235 2453203.165 1495173.197 3.866495375 4.197286299 1.312431995 1.102044143 1.766670049 2.933405399 1.582801601 1.504866619 1.640748489 1 20.51188118 4.241059397 24.99961758 1.648913016 4.031891725 0.784934653 0.507647624 27.75503353 277665.5171 0.130472115 0.324931464 17420.45109 -4.241059397 2.382978709 ALEEALEAKEEFER ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEEALEAKEEFER 14 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 129.38 6.22E-05 105466000 165534 171438 77472 68578 112998 145471 96967 98019 101321 72191 FALSE TRUE 159064.7483 166548.7561 91472.91376 72117.3188 116632.6833 148412.5233 98153.71115 95994.8734 89819.46485 67301.43927 2.36346726 2.474668564 1.359152416 1.071556858 1.732989436 2.205190928 1.458419199 1.426342058 1.334584607 1 16.03834974 4.241148945 24.99985779 1.484264217 2.419068272 0.591285022 0.321667819 46.2602888 446788.7477 0.082480923 0.205706964 17424.04343 -4.241148945 0.934804055 VAIQLNDTHPALSIPELMR ddPTM_BT-474_Pertuzumab_2h_R1 2 VAIQLNDTHPALSIPELMR 19 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 181.14 3.21E-14 1390840000 604270 556730 599640 788720 624790 613690 697160 623740 732740 732580 FALSE TRUE 580654.4603 540852.6055 708008.2869 829425.9337 644886.9378 626099.2323 705692.0526 610859.551 649562.4271 682961.7041 0.850200614 0.791922303 1.036673481 1.214454528 0.944250511 0.916741347 1.033282025 0.894427239 0.951096413 1 19.38144516 4.241182319 24.99989544 0.99447381 0.821061409 0.405728936 0.08594346 69.66680723 664288.0032 0.022761535 0.056789491 17425.38248 -4.241182319 -0.173412401 S(ph)PEPDGPAPAFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPEPDGPAPAFLR 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR 236.08 1.10E-16 1432340000 596070 573090 630180 712420 640510 630090 719900 815650 779700 820960 TRUE FALSE 572774.9254 556746.0343 744067.5443 749188.0816 661112.5858 642830.8515 728710.3515 798806.5425 691191.7248 765355.648 0.748377473 0.72743441 0.972185344 0.978875747 0.86379788 0.839911293 0.952119911 1.04370634 0.903098744 1 19.54577077 4.241182555 24.99973721 0.946037223 0.737905859 0.66469424 0.058599818 41.00893037 390991.7434 0.016050426 0.040041201 17425.39191 -4.241182555 -0.208131363 GEAHLAVNDFELAR ddPTM_BT-474_Pertuzumab_2h_R1 6 GEAHLAVNDFELAR 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 241.42 1.94E-17 14354210000 5278970 5457460 6463730 7961630 7212610 7778940 8072560 7520200 7983040 8813570 FALSE TRUE 5072662.016 5301818.584 7631869.796 8372530.678 7444610.151 7936235.497 8171354.404 7364905.242 7076838.767 8216619.054 0.617366095 0.645255494 0.928833349 1.018975156 0.906042997 0.965876043 0.994491086 0.896342546 0.861283543 1 22.97011345 4.241199607 5.217490906 0.945782229 0.624923749 0.877334543 0.047228694 0.049712756 3.956196043 0.011863048 0.03045438 17426.07611 -4.241199607 -0.320858479 EQVHQGGVELQQLEAGLQEAGEEDTR ddPTM_BT-474_Pertuzumab_2h_R1 3 EQVHQGGVELQQLEAGLQEAGEEDTR 26 0 K7EJH0;K7EMX1;K7EJV2;K7ESQ2;Q8NBT2 K7EJH0 SPC24 Kinetochore protein Spc24 0 ;; 193.6 2.67E-18 266320000 135712 144211 121120 150268 150693 160527 152931 158990 154932 135017 FALSE TRUE 130408.225 140098.2435 143009.0783 158023.3495 155540.1772 163772.9659 154802.6153 155706.8009 137344.7689 125872.1783 1.036036928 1.113019933 1.136145256 1.255427145 1.235699416 1.30110536 1.229839806 1.237023169 1.091144769 1 16.94159991 4.241272027 1.825925132 1.211688557 1.04667889 0.220307239 0.08557201 0.475028833 2.87662089 0.0219058 0.096967993 17428.98222 -4.241272027 -0.165009666 AVPKEDIYSGGGGGGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVPKEDIYSGGGGGGSR 17 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;;; 157.54 1.99E-08 1576290000 874990 944890 596855 638419 748641 923350 702899 781522 804949 742198 FALSE TRUE 840794.4234 917942.6623 704719.9755 671367.8811 772721.7177 942020.7696 711501.2882 765383.2976 713574.5641 691928.2684 1.215146803 1.326644255 1.018487042 0.970285378 1.116765643 1.361442815 1.028287643 1.106159891 1.031284017 1 19.40026296 4.241279597 24.99999479 1.088482074 1.270895557 0.335033929 0.107438238 82.04361842 754319.3602 0.027169289 0.067855849 17429.28602 -4.241279597 0.182413483 NRDVITLR ddPTM_BT-474_Pertuzumab_2h_R1 3 NRDVITLR 8 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ;; 163.32 0.00030698 902160000 503613 511662 343075 390704 404856 471392 397971 396605 503159 418796 FALSE TRUE 483931.2472 497069.9007 405076.2842 410868.2803 417878.5609 480923.8692 402841.4881 388414.9682 446042.4997 390430.5739 1.239480921 1.273132623 1.037511689 1.052346583 1.070301838 1.231778199 1.031787762 0.99483748 1.142437426 1 18.57470651 4.24130083 24.9993653 1.069073489 1.256306839 0.549996878 0.067358095 50.73073043 462799.9359 0.017120671 0.042774643 17430.13818 -4.24130083 0.18723335 ERFS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 6 ERFSPPR 7 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR 81.335 0.02494 6150690000 1245245 1235403 1275512 1548528 1451672 1339461 1482805 1546943 1463669 1654036 TRUE FALSE 1196579.449 1200170.516 1506025.392 1628447.716 1498366.348 1366545.819 1500952.011 1514998.086 1297519.431 1542006.668 0.775988505 0.778317332 0.97666594 1.056057505 0.971699007 0.886212652 0.973375824 0.982484783 0.841448651 1 20.55637757 4.24131427 24.97453864 0.96313594 0.777152833 0.63206587 0.056086273 41.16063489 373290.2846 0.013914203 0.034766791 17430.67758 -4.24131427 -0.185983107 LSELEDLLPSRPEVPNIIGETEEVELQEFDSTRGS(ph)GGGQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSELEDLLPSRPEVPNIIGETEEVELQEFDSTRGSGGGQR 40 2 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 1 LSELEDLLPSRPEVPNIIGETEEVELQEFDS(0.018)T(0.014)RGS(0.968)GGGQR;LSELEDLLPSRPEVPNIIGETEEVELQEFDS(0.156)T(0.156)RGS(0.687)GGGQR 160.75 9.61E-19 71131000 23964 18684 25918.4 25375.5 25827.1 28202.1 26617.4 26950.3 30620.6 32255 TRUE FALSE 23027.46039 18151.15061 30602.43143 26685.1326 26657.85213 28772.36578 26943.1517 26393.76689 27144.67786 30070.34012 0.765786496 0.603623057 1.017694888 0.887423704 0.886516482 0.956835396 0.896004222 0.877734232 0.902706047 1 14.87605357 4.24131767 24.99999871 0.91812875 0.684704749 0.725507113 0.05963582 32.67155121 296238.6051 0.013676404 0.034175777 17430.81404 -4.24131767 -0.233424001 NS(ph)LESIS(ph)SIDRELSPEGPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLESISSIDRELSPEGPGK 20 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 2 NS(0.993)LES(0.04)IS(0.58)S(0.387)IDRELSPEGPGK 69.845 0.01101 36318000 90656 102350 61883 81139 73751 64812 77410 106000 93385 57026 TRUE FALSE 87113.06329 99431.07821 73066.63468 85326.59351 76123.26789 66122.54305 78357.36674 103811.063 82784.3263 53163.57823 1.638585404 1.870285664 1.374373906 1.604982139 1.43186878 1.243756445 1.473891889 1.952672608 1.557162423 1 15.69815059 4.241322354 24.99997418 1.50964171 1.754435533 0.168405836 0.243006324 142.620022 1290966.598 0.062368186 0.155909559 17431.00207 -4.241322354 0.244793823 SPPS(ph)TGSTYGSSQKEESAASGGAAYTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPSTGSTYGSSQKEESAASGGAAYTKR 28 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.216)PPS(0.776)T(0.006)GS(0.002)TYGSSQKEESAASGGAAYTKR 162.45 4.47E-12 739630000 861560 868380 438870 415740 467940 763520 484130 573970 690860 530000 TRUE FALSE 827889.2827 843614.6526 518183.5716 437196.3912 482991.7151 778958.8975 490054.9278 562117.3189 612436.4691 494102.6279 1.675541145 1.707367265 1.048736725 0.884829115 0.977512945 1.576512355 0.991807977 1.137652963 1.239492434 1 18.9144512 4.241363341 24.99985173 1.111344386 1.691454449 0.620690038 0.182709636 44.55046472 397362.3468 0.045530965 0.113842791 17432.64721 -4.241363341 0.580110063 RDESLKVDEHLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RDESLKVDEHLAK 13 2 P12429;D6RA82;D6RFJ9 P12429 ANXA3 Annexin A3;Annexin 0 72.496 0.023657 216110000 155030 156740 74377 64885 101080 124540 82600 90633 118900 95607 FALSE TRUE 148971.2562 152269.9287 87818.57841 68233.72263 104331.33 127058.2841 83610.88351 88761.39688 105402.9705 89131.45273 1.671365737 1.70837481 0.985270359 0.76554034 1.170533261 1.425515688 0.938062614 0.995848201 1.182556407 1 16.443647 4.241367196 24.99537717 1.054942783 1.689870541 0.698000515 0.166263494 38.49403337 342809.6603 0.043100749 0.107787924 17432.80194 -4.241367196 0.634927757 LFEELVR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFEELVR 7 0 P14618-2;H3BTN5;H3BR70 P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 160.68 0.0031111 299190000 456980 445313 447125 557980 465947 455902 527210 542140 525170 592820 FALSE TRUE 439120.7164 432613.1092 527930.4337 586777.4147 480934.6084 465120.6508 533662.1537 530944.6195 465554.9033 552667.7734 0.794547353 0.782772454 0.955240126 1.061718166 0.870205631 0.841591772 0.965611131 0.96069401 0.842377511 1 19.07605296 4.241416223 24.94256894 0.937199417 0.788659841 0.446091909 0.066198969 62.58995586 546669.4639 0.016576761 0.041481617 17434.77 -4.241416223 -0.148539577 TIQGDEEDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 TIQGDEEDLR 10 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;; 215.06 1.95E-08 2717130000 2432440 2546230 2178680 2678390 2542090 2683910 2773820 2881320 2919100 2980040 FALSE TRUE 2337377.556 2473614.013 2572415.94 2816622.029 2623858.634 2738180.499 2807766.839 2821819.735 2587736.006 2778199.236 0.841328269 0.890365954 0.925929252 1.013830107 0.944445812 0.98559544 1.010642722 1.015700997 0.931443639 1 21.40571863 4.241416584 1.399899023 0.9893699 0.83447712 0.747347393 0.028346892 0.272016797 0.859825594 0.0081304 0.046439444 17434.78453 -4.241416584 -0.15489278 GFKFDETEQALANER ddPTM_BT-474_Pertuzumab_2h_R1 2 GFKFDETEQALANER 15 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 178.51 6.46E-07 584460000 968130 1016080 651990 682970 796500 1004850 738990 827370 934010 772640 FALSE TRUE 930294.4093 987102.3932 769819.0964 718218.1635 822120.1459 1025168.755 748033.9807 810284.5204 827985.1005 720308.4046 1.291522358 1.370388554 1.068735408 0.99709813 1.141344653 1.423235865 1.038491257 1.124913322 1.149486935 1 19.45825521 4.241477948 24.99727999 1.12538718 1.33095551 0.347362693 0.116447342 83.57532767 716082.8129 0.029142785 0.073001989 17437.24814 -4.241477948 0.20556833 KLTGIKHELQANCYEEVKDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLTGIKHELQANCYEEVKDR 20 3 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 196.89 1.02E-21 4323800000 6834700 6691400 3082300 2356140 4159000 5519500 3624500 3800700 4556200 2886100 FALSE TRUE 6567592.368 6500567.824 3639340.175 2477740.668 4292778.012 5631108.072 3668857.715 3722214.217 4038999.277 2690621.876 2.440919858 2.416009429 1.352601868 0.920880295 1.595459418 2.092864895 1.363572395 1.383402941 1.501139685 1 21.35950823 4.241500223 24.96854832 1.424761123 2.428465117 0.645039934 0.304404998 45.14361624 383423.2025 0.07744066 0.19396524 17438.14253 -4.241500223 1.003703995 LPNGEPS(ph)PDPGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPNGEPSPDPGGK 13 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 LPNGEPS(1)PDPGGK;LPNGEPS(1)PDPGGK 130.72 0.00014561 627080000 1284010 1255010 1309890 1485640 1448900 1434320 1510370 1556760 1617770 1690120 TRUE FALSE 1233829.47 1219218.344 1546616.261 1562314.058 1495505.184 1463322.933 1528854.36 1524612.362 1434127.532 1575646.667 0.783062279 0.773789181 0.981575561 0.991538326 0.949137402 0.928712613 0.970302792 0.967610565 0.910183458 1 20.58751262 4.24152493 24.99999936 0.961368377 0.778425652 0.888281453 0.026093376 20.73005225 174821.4162 0.00633781 0.0158824 17439.1346 -4.24152493 -0.182942726 NSENKESIPSLPQS(ph)PMR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSENKESIPSLPQSPMR 17 1 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 NSENKESIPSLPQS(1)PMR 167.99 1.30E-09 232440000 336350 348640 202470 205450 258320 322520 240340 258170 280480 219410 TRUE FALSE 323205.0701 338697.1286 239060.8329 216053.2991 266629.0974 329041.5754 243281.3528 252838.6993 248641.0863 204549.1653 1.580085011 1.65582259 1.168720648 1.056241412 1.303496385 1.608618519 1.189353926 1.236077884 1.215556592 1 17.64208812 4.241562085 24.99999477 1.23922592 1.617953935 0.506144118 0.155624705 62.75799213 522701.9341 0.039174628 0.098205346 17440.62666 -4.241562085 0.378728015 PGHLQEGFGCVVTNR ddPTM_BT-474_Pertuzumab_2h_R1 3 PGHLQEGFGCVVTNR 15 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 244.57 4.84E-18 5275350000 1503440 1431270 1341640 1483670 1556410 1562930 1541790 1410910 1774870 1735280 FALSE TRUE 1444683.903 1390451.581 1584104.193 1560242.387 1606473.341 1594533.515 1560658.887 1381774.215 1573394.198 1617747.94 0.89302163 0.859498286 0.979203344 0.964453329 0.993030683 0.98565016 0.964710786 0.854134431 0.972583033 1 20.62555541 4.241582961 24.99808647 0.955561126 0.876259939 0.421833984 0.040180726 86.82189252 718078.1309 0.01128234 0.028300714 17441.46499 -4.241582961 -0.079301187 KAPAGQEEPGT(ph)PPS(ph)SPLSAEQLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 KAPAGQEEPGT(1)PPS(0.61)S(0.389)PLS(0.001)AEQLDR;KAPAGQEEPGT(1)PPS(0.54)S(0.46)PLSAEQLDR 126.88 8.69E-06 385090000 518390 540720 352590 369240 430830 458700 426890 446940 461340 570730 TRUE FALSE 498130.7457 525299.195 416310.8563 388296.5206 444688.0382 467975.2283 432114.4075 437710.5328 408970.6173 532073.9487 0.936205854 0.98726727 0.782430445 0.729779238 0.835763599 0.879530429 0.812132239 0.82264981 0.768634921 1 19.02126724 4.24163222 24.99999728 0.820421936 0.961736602 0.357711529 0.070495492 71.39779361 581083.6432 0.01627389 0.040844267 17443.44339 -4.24163222 0.141314666 LDVFARPAS(ph)PSLQLLPWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDVFARPASPSLQLLPWR 18 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 LDVFARPAS(0.972)PS(0.028)LQLLPWR;LDVFARPAS(0.984)PS(0.016)LQLLPWR 164.66 1.82E-11 1637390000 1052580 1203850 603800 742240 683450 1057560 752700 898120 938970 720720 TRUE FALSE 1011444.01 1169517.377 712920.0915 780547.0954 705433.7899 1078944.588 761911.7678 879573.5081 832382.0621 671904.9924 1.50533784 1.740599326 1.061043004 1.161692656 1.049901099 1.605799332 1.133957593 1.309074226 1.23883893 1 19.35789772 4.241730962 24.99996279 1.215731178 1.622968654 0.493964506 0.172235115 63.91626109 503992.2508 0.040674287 0.102193252 17447.40981 -4.241730962 0.407237475 RTIQEVLEEQS(ph)EDEDREAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTIQEVLEEQSEDEDREAK 19 2 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 RTIQEVLEEQS(1)EDEDREAK;RTIQEVLEEQS(1)EDEDREAK 249.12 2.94E-25 342250000 260858 270033 173056 169681 224132 246617 208257 213170 231048 242072 TRUE FALSE 250663.381 262331.9232 204331.0688 178438.2567 231341.4093 251603.7647 210805.7115 208767.965 204820.3997 225676.2478 1.110721148 1.162425934 0.905416812 0.790682486 1.025103047 1.114888107 0.934106772 0.92507726 0.907585099 1 17.78389506 4.241739878 24.99994106 0.948436851 1.136573602 0.453827686 0.081692261 73.25752658 576029.3327 0.021473806 0.053946407 17447.76801 -4.241739878 0.188136751 EPAITSQNS(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 6 EPAITSQNSPEAR 13 0 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR 289.2 1.80E-40 7457050000 1535800 1632300 1552002 2083030 1827540 1746340 1918380 1975720 2000040 2113230 TRUE FALSE 1475779.238 1585748.402 1832483.285 2190535.428 1886324.484 1781652.191 1941857.708 1934920.692 1773003.844 1970099.05 0.749088853 0.804907957 0.930147794 1.111891013 0.957476978 0.904346506 0.985665014 0.982143863 0.899956702 1 20.90983673 4.241741487 3.293006915 0.976439705 0.76350902 0.669255067 0.055885468 0.132853517 2.9459746 0.014327173 0.042098167 17447.83263 -4.241741487 -0.212930685 EEDNTYR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEDNTYR 7 0 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9;H3BN71;B4DGE1;H3BRM7;H3BN75;H3BS13;H3BV30 O43747 AP1G1 AP-1 complex subunit gamma-1 0 87.696 0.072232 0 324340 310340 341580 399560 399440 375250 376370 385610 413170 403940 FALSE TRUE 311664.4342 301489.4071 403311.1044 420181.3395 412288.3504 382837.8121 380976.1286 377647.0187 366268.6737 376580.784 0.827616404 0.800596897 1.070981637 1.115780086 1.094820468 1.016615367 1.011671718 1.002831357 0.972616472 1 18.52259986 4.241773593 24.99999999 1.036925115 0.814106561 0.806784441 0.043366512 35.08622845 272991.4474 0.012068337 0.0303355 17449.12257 -4.241773593 -0.222818554 NEEDEGHS(ph)NS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(1)NS(0.897)S(0.103)PR 136.01 0.00011295 46799000 123050 122470 115430 144390 131300 121720 139760 118750 167200 150290 TRUE FALSE 118241.07 118977.2755 136290.7687 151841.9852 135523.3837 124181.2618 141470.4247 116297.771 148220.157 140110.7244 0.843911631 0.849166086 0.972736165 1.0837285 0.967259175 0.886308042 1.009704469 0.830041893 1.057878742 1 17.09620786 4.241774621 23.70758011 0.964997614 0.846538744 0.338768472 0.071015279 51.01463301 376264.7928 0.017948714 0.045022941 17449.16385 -4.241774621 -0.118458871 RPEVDGVRK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPEVDGVRK 9 2 O95865;A0A140T971;Q5SSV3;Q5SRR8;H0Y7N1 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ; 56.548 0.068178 816870000 971910 973520 598280 611880 697580 808360 754250 686610 914280 810410 FALSE TRUE 933926.6827 945756.1628 706402.5047 643459.2001 720018.2942 824705.5931 763480.7371 672431.2636 810494.7674 755520.2089 1.236137262 1.25179466 0.934988232 0.85167702 0.953009974 1.091573175 1.010536486 0.890024192 1.072763849 1 19.52711082 4.241790309 24.99875421 0.968361461 1.24396608 0.696319305 0.070770574 43.07727565 333415.1028 0.01822202 0.045819456 17449.7942 -4.241790309 0.275604619 IGNSYFKEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IGNSYFKEEK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 67.153 0.05821 802660000 916860 941060 423690 348390 688810 765900 547960 467150 624330 476450 FALSE TRUE 881028.0976 914221.8902 500260.2079 366370.4497 710966.1992 781387.0228 554666.0984 457503.1893 553458.6758 444179.6171 1.983495108 2.05822567 1.126256561 0.824824993 1.600627701 1.759169022 1.248742799 1.029995911 1.246024479 1 18.76078367 4.241871017 24.99982858 1.237988307 2.020860713 0.592367271 0.262525551 59.50325359 449342.6532 0.069859641 0.175821134 17453.03731 -4.241871017 0.782872407 VEVNNLNNLNNHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEVNNLNNLNNHDR 14 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 0 ; 211.7 3.47E-09 1347520000 405140 407780 476520 606490 505550 457440 547830 630670 576830 640410 FALSE TRUE 389306.6809 396150.5137 562637.7641 637791.0216 521811.4749 466689.7502 554534.5074 617646.4441 511350.6767 597034.4603 0.652067354 0.663530399 0.942387419 1.068265006 0.874005622 0.781679754 0.928814908 1.034523943 0.856484358 1 19.18745468 4.241897516 9.520288367 0.938818305 0.657225192 0.653532517 0.080934933 0.064118482 78.06238253 0.021152393 0.052054491 17454.10227 -4.241897516 -0.281593113 FPQGPPSQMGS(ph)PMGSR ddPTM_BT-474_Pertuzumab_2h_R1 9 FPQGPPSQMGSPMGSR 16 0 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 1 FPQGPPS(0.065)QMGS(0.934)PMGS(0.001)R;FPQGPPS(0.206)QMGS(0.717)PMGS(0.078)R;FPQGPPS(0.006)QMGS(0.993)PMGS(0.001)R;FPQGPPS(0.001)QMGS(0.998)PMGS(0.001)R;FPQGPPSQMGS(1)PMGSR;FPQGPPSQMGS(1)PMGSR;FPQGPPSQMGS(0.999)PMGS(0.001)R;FPQGPPS(0.002)QMGS(0.998)PMGSR;FPQGPPSQMGS(1)PMGSR 277.32 2.63E-35 3281048000 913971 890179 954522 1123801 973676 924194 1124031 1173489 1171317 1339799 TRUE FALSE 878252.0029 864791.9665 1127025.359 1181800.504 1004995.173 942881.8359 1137787.228 1149256.042 1038354.005 1249053.22 0.703134173 0.692357982 0.902303713 0.946157045 0.804605566 0.754877231 0.910919734 0.920101741 0.83131286 1 20.25240352 4.241914024 24.99475214 0.879436922 0.697745998 0.547496343 0.06756002 62.71793874 467449.7714 0.016906983 0.042568501 17454.76573 -4.241914024 -0.181690924 S(ph)PQGPSPVLAEDS(ph)EGEG ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQGPSPVLAEDSEGEG 17 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 S(1)PQGPSPVLAEDS(1)EGEG;S(1)PQGPSPVLAEDS(1)EGEG 180.05 8.80E-14 0 155561 149698 144682 167924 170467 150762 160517 173415 169142 190335 TRUE FALSE 149481.5041 145428.7596 170829.2558 176590.5778 175950.2259 153810.5109 162481.4551 169833.9196 149941.7093 177443.4409 0.842417749 0.819578108 0.962725108 0.995193606 0.991584839 0.866814294 0.915680254 0.957115793 0.845011281 1 17.43699972 4.241915046 24.99978918 0.940742608 0.830997889 0.436506186 0.050330339 76.41819182 569501.2186 0.012423026 0.031278293 17454.80681 -4.241915046 -0.109744718 LFDVCGSQDFESDLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFDVCGSQDFESDLDR 16 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38 Q92878-2 RAD50 DNA repair protein RAD50 0 ;;; 292.03 3.45E-45 340920000 113168 114405 106143 135622 117066 109963 130047 134725 127387 144021 FALSE TRUE 108745.2694 111142.2814 125325.4012 142621.4677 120831.5342 112186.5272 131638.5541 131942.8817 112926.5618 134266.3294 0.809922115 0.827774781 0.933409007 1.062228098 0.899939209 0.835552202 0.980428635 0.982695232 0.841063894 1 17.03473803 4.241993491 4.899866233 0.944913503 0.815605633 0.35496291 0.066571473 0.185138068 11.90931633 0.016802081 0.043713796 17457.95988 -4.241993491 -0.12930787 HS(ph)PPMVR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSPPMVR 7 0 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7;I3L4G9 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 HS(1)PPMVR;HS(1)PPMVR 110.87 0.0043196 975920000 371110 365890 368890 493230 409290 386650 499580 236370 600540 561450 TRUE FALSE 356606.6109 355455.1754 435556.6289 518685.6594 422455.1846 394468.3279 505694.0095 231488.8769 532369.2169 523422.4914 0.681297836 0.679098016 0.832132046 0.99095027 0.807101704 0.753632743 0.96612969 0.442260088 1.017092742 1 18.99761639 4.242022605 24.15298628 0.81781425 0.680197834 0.122861186 0.164426122 135.4076944 944620.6092 0.041085759 0.103423629 17459.13027 -4.242022605 -0.137616416 T(ph)PESFLGPNAALVDLDSLVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPESFLGPNAALVDLDSLVSR 21 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.849)PES(0.151)FLGPNAALVDLDSLVSR;T(0.831)PES(0.169)FLGPNAALVDLDSLVSR;T(0.839)PES(0.161)FLGPNAALVDLDSLVSR 267.49 4.31E-36 1334530000 85461 85617 85968 111195 103316 90574 83679.1 113374 97891 101971 TRUE FALSE 82121.08964 83175.28699 101504.3299 116933.7873 106639.253 92405.46834 84703.18986 111032.7873 86778.82407 95064.41334 0.863846804 0.874936099 1.067742664 1.230047956 1.121757861 0.97203007 0.89100839 1.167974254 0.912842367 1 16.53661776 4.242026175 23.75474841 1.055683175 0.869391269 0.316602268 0.102569433 51.52854926 353172.3861 0.025885449 0.065127245 17459.27375 -4.242026175 -0.186291906 LIYGTVTEDNEEEDDDTLEELGGLFR ddPTM_BT-474_Pertuzumab_2h_R1 5 LIYGTVTEDNEEEDDDTLEELGGLFR 26 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 ;;;; 229.76 7.51E-35 76854900 54167 53112 54569.1 65554.1 59404.2 57732 62118.6 65247.9 67209.5 69444.5 FALSE TRUE 52050.09376 51597.29776 64430.95025 68937.35496 61314.99004 58899.3806 62878.82601 63900.50806 59580.15933 64740.96216 0.803974671 0.796980707 0.995211503 1.064818203 0.947081847 0.90976993 0.971237126 0.987018202 0.920285355 1 15.98239119 4.242028517 24.99979303 0.974411262 0.800477611 0.736632517 0.041604491 43.05692267 310379.989 0.0107254 0.027048368 17459.36792 -4.242028517 -0.173933651 GEHSIVYLKPSYAFGSVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEHSIVYLKPSYAFGSVGK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 250.04 2.13E-25 2670700000 972800 892860 1010800 1038900 1056800 1189100 1190400 993800 1341700 1375900 FALSE TRUE 934781.9005 867396.507 1193474.045 1092517.754 1090792.932 1213144.417 1204968.471 973277.6827 1189395.841 1282709.067 0.728755978 0.676222324 0.930432376 0.85172685 0.850382179 0.945767398 0.939393431 0.75876729 0.927253008 1 20.29076256 4.242116187 24.99999703 0.885501751 0.702489092 0.584960936 0.065744742 63.36235354 445495.5221 0.016222848 0.040952204 17462.89275 -4.242116187 -0.18301266 SATEYKNEEYQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SATEYKNEEYQR 12 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ; 130.1 0.00020292 728680000 621240 652870 418770 449450 522020 543440 513890 549840 602570 550930 FALSE TRUE 596961.254 634250.7868 494451.0545 472646.1684 538811.2474 554428.7291 520179.1395 538485.6119 534168.7798 513615.0204 1.162273746 1.234875854 0.962688073 0.920234319 1.04905664 1.07946362 1.012780232 1.048422633 1.040017832 1 18.97032787 4.242138894 24.99999872 1.017565714 1.198574848 0.714414857 0.046616795 48.73348047 340466.6472 0.012265962 0.030996688 17463.80581 -4.242138894 0.181009134 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLRK ddPTM_BT-474_Pertuzumab_2h_R1 3 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLRK 33 2 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ;; 359.41 1.88E-132 1321560000 463050 455100 326372 315240 367555 450940 378528 402227 430930 431110 FALSE TRUE 444953.4941 442120.9936 385354.6805 331509.5742 379377.7404 460058.3158 383160.5389 393920.8719 382012.633 401910.5357 1.10709587 1.10004828 0.958807113 0.824834247 0.943935793 1.144678417 0.953347835 0.98012079 0.950491712 1 18.61651487 4.242158822 24.17834736 0.968747323 1.103572179 0.347056114 0.073538069 67.37153151 452676.6227 0.019032002 0.047977505 17464.60721 -4.242158822 0.134824856 KVVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_BT-474_Pertuzumab_2h_R1 7 KVVDYSQFQESDDADEDYGRDSGPPTK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYS(0.001)QFQES(0.999)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK 344.74 4.93E-97 18737900000 8502800 8829990 3574320 3547432 5036278 6959240 4146417 4935245 5394610 3894996 TRUE FALSE 8170501.176 8578167.331 4220279.134 3730515.391 5198274.456 7099960.601 4197162.092 4833330.466 4782236.489 3631184.452 2.250092576 2.362360669 1.162232101 1.027354969 1.431564418 1.955274015 1.155865847 1.331061677 1.316990793 1 21.79200879 4.242175904 24.99852917 1.320555894 2.306227029 0.71020558 0.257396125 47.78542651 330406.6996 0.064912149 0.163985046 17465.29413 -4.242175904 0.985671135 TKDQPDGSSLS(ph)PAQS(ph)PSQSQPPAASSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKDQPDGSSLSPAQSPSQSQPPAASSLR 28 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 2 TKDQPDGS(0.001)S(0.005)LS(0.994)PAQS(0.998)PS(0.002)QSQPPAASSLR;TKDQPDGS(0.009)S(0.056)LS(0.935)PAQS(1)PSQSQPPAASSLR 151.18 2.95E-08 407820000 202292 187376 198044 220160 208679 213371 216959 235250 252950 230325 TRUE FALSE 194386.205 182032.2199 233834.9563 231522.484 215391.3496 217685.5078 219614.2091 230392.0053 224236.1765 214724.8826 0.905280295 0.847746278 1.088997947 1.078228481 1.003103818 1.013787993 1.022770191 1.072963704 1.044295257 1 17.71212986 4.242215059 25 1.042804238 0.876513237 0.80210927 0.032568838 36.1057207 246988.6071 0.008175854 0.020659136 17466.86884 -4.242215059 -0.166291001 CREMDEQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 CREMDEQIR 9 1 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 191.4 3.28E-05 792470000 403570 421140 188020 203100 226480 236520 285170 259530 303740 283710 FALSE TRUE 387798.0382 409129.4995 221999.3965 213582.0153 233764.9349 241302.5965 288659.9958 254170.6148 269260.7086 264494.069 1.466188031 1.546838086 0.83933601 0.807511549 0.883819194 0.912317608 1.091366611 0.960969052 1.018021726 1 18.01287585 4.242236742 24.99999975 0.939438186 1.506513285 0.883522141 0.082398658 28.98885725 197134.67 0.022272995 0.056315229 17467.74091 -4.242236742 0.567075099 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_BT-474_Pertuzumab_2h_R1 6 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK 35 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNY(0.032)EGS(0.968)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.467)EGS(0.513)PIKVT(0.02)LATLK;TVSLGAGAKDELHIVEAEAMNY(0.032)EGS(0.767)PIKVT(0.198)LAT(0.003)LK;TVSLGAGAKDELHIVEAEAMNY(0.465)EGS(0.535)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.004)EGS(0.995)PIKVT(0.001)LATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK 252.28 5.24E-60 12144013000 2865531 2791113 1536003 1259739 1936775 2293354 1753991 1865259 2582103 1851020 TRUE FALSE 2753542.881 2711513.19 1813592.91 1324754.281 1999073.127 2339727.189 1775456.867 1826740.75 2288993.492 1725648.767 1.595656621 1.571300743 1.050962945 0.767684772 1.158447284 1.355853656 1.028863405 1.058582016 1.326453874 1 20.71870742 4.242255779 24.70175108 1.090409301 1.583478972 0.606059176 0.158046003 51.70670795 345636.8222 0.040033841 0.101148805 17468.50664 -4.242255779 0.493069671 CTKEEHLCTQR ddPTM_BT-474_Pertuzumab_2h_R1 7 CTKEEHLCTQR 11 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;; 162.68 1.49E-05 4413613000 4091985 4317555 2349605 2509337 2913538 3703648 3103268 2862182 3579887 2905739 FALSE TRUE 3932065.702 4194422.559 2774230.89 2638844.183 3007254.596 3778538.3 3141246.722 2803076.941 3173513.236 2708930.709 1.451519483 1.548368345 1.024105519 0.974127605 1.110126068 1.394844943 1.159589173 1.03475402 1.171500336 1 21.36929206 4.242283183 24.99999313 1.113750336 1.499944047 0.643079243 0.116560625 58.85752403 395258.8016 0.030418001 0.076928557 17469.60895 -4.242283183 0.386193711 RTIPWLEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTIPWLEDR 9 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 107.03 0.0045543 222520000 182990 189190 116500 147520 131660 153000 138010 162280 134670 158180 FALSE TRUE 175838.5485 183794.4864 137554.1415 155133.5249 135894.9635 156093.7648 139699.0077 158928.8613 119382.8262 147466.3277 1.192397961 1.24634884 0.932783393 1.051992867 0.92153216 1.058504455 0.947328179 1.077729837 0.809559905 1 17.17002604 4.242292861 24.99983608 0.984854617 1.219373484 0.61602622 0.076876547 55.15815782 369452.714 0.017301585 0.043772446 17469.99823 -4.242292861 0.234518866 S(ph)PGNLTER ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGNLTER 8 0 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTER;S(1)PGNLTER 80.219 0.02729 683990000 1543110 1550890 965400 967760 1239770 1528930 1089890 1168870 1279770 1094850 TRUE FALSE 1482803.555 1506660.136 1139869.255 1017706.21 1279648.328 1559846.012 1103228.4 1144732.426 1134495.875 1020694.834 1.452739355 1.476112238 1.116758131 0.99707197 1.253703149 1.528219757 1.080860178 1.1215227 1.111493697 1 19.96112017 4.242316376 24.99436078 1.161099344 1.464425928 0.427793368 0.144539101 92.01806189 612349.8939 0.037149408 0.094009552 17470.94418 -4.242316376 0.303326584 FFDANYDGKDYDPVAAR ddPTM_BT-474_Pertuzumab_2h_R1 5 FFDANYDGKDYDPVAAR 17 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;;; 160.55 2.81E-09 4068150000 8066760 8143740 5460140 5682570 6736800 7279890 5930300 7299890 7544930 6689430 FALSE TRUE 7751502.101 7911488.509 6446908.758 5975848.119 6953495.29 7427094.364 6002876.785 7149144.721 6688461.177 6236348.948 1.242955159 1.268609017 1.033763314 0.958228632 1.114994582 1.190936304 0.962562685 1.146367014 1.072496301 1 22.57227022 4.242347548 24.98419652 1.06706558 1.255782165 0.536564007 0.072568315 70.82749671 467263.8131 0.017765139 0.044955891 17472.19823 -4.242347548 0.188716586 SVTQATQTS(ph)PGVPWPSQSANFPEFSFDFTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVTQATQTSPGVPWPSQSANFPEFSFDFTR 30 0 A0A0C4DGH6;A0JNW5;H0YHT7 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.004)VT(0.002)QAT(0.007)QT(0.18)S(0.807)PGVPWPSQSANFPEFSFDFTR 116.35 6.75E-05 94101000 68799 72850 67292 87480 85666 90619 84041 73330 84365 88034 TRUE FALSE 66110.25902 70772.38933 79453.1613 91994.85328 88421.52469 92451.37827 85069.5189 71815.70987 74788.23889 82071.37877 0.805521486 0.862327286 0.968098288 1.120912731 1.077373452 1.126475266 1.036530885 0.875039642 0.911258468 1 16.32459157 4.242379021 3.012072455 1.016416144 0.819086541 0.482180968 0.077011941 0.250542309 4.562582756 0.023260219 0.071387261 17473.46448 -4.242379021 -0.197329603 S(ph)NSDVTISDIDAEDVLDQNAVNPNTGAALHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSDVTISDIDAEDVLDQNAVNPNTGAALHR 31 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 S(0.494)NS(0.494)DVT(0.012)ISDIDAEDVLDQNAVNPNTGAALHR 147.37 9.93E-09 204290000 228980 227620 255350 266910 276940 303960 274860 308520 312920 354720 TRUE FALSE 220031.2084 221128.5005 301497.4252 280685.2571 285848.0266 310106.2795 278223.8189 302148.9542 277398.6335 330694.4984 0.665360958 0.668679103 0.911709831 0.848775103 0.864387004 0.937742481 0.841331864 0.913680015 0.838836554 1 18.33513952 4.242410848 24.99980728 0.888883041 0.667019923 0.783267159 0.047801837 36.70656524 238328.6132 0.010559381 0.02675794 17474.74505 -4.242410848 -0.221863118 GTQSIPNDS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTQSIPNDSPAR 12 0 Q9NQ92;H9KV77;J3QRX6 Q9NQ92 COPRS Coordinator of PRMT5 and differentiation stimulator 1 GTQSIPNDS(1)PAR;GTQSIPNDS(1)PAR 239.38 3.79E-16 2260400000 2186960 2366900 2303430 2967500 2607280 2610830 3179200 2905300 2944400 3492900 TRUE FALSE 2101491.185 2299398.329 2719711.041 3120653.031 2691145.529 2663622.771 3218108.001 2845304.54 2610164.056 3256322.772 0.645357151 0.706133418 0.835209293 0.958336519 0.826436971 0.817984874 0.98826444 0.873778412 0.801567977 1 21.63481228 4.2424275 2.688777824 0.889537678 0.655480615 0.631572205 0.066607841 0.166736889 2.380145458 0.016627394 0.054429507 17475.41507 -4.2424275 -0.234057063 NKEGLHNAK ddPTM_BT-474_Pertuzumab_2h_R1 1 NKEGLHNAK 9 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 132.91 0.00017527 353600000 898650 921180 581560 635990 625010 785200 752540 743280 885110 695560 FALSE TRUE 863529.7645 894908.8483 686660.8287 668813.5201 645114.0143 801077.282 761749.8096 727931.0083 784636.0235 648449.1017 1.331684726 1.380075701 1.058927874 1.031404806 0.994856825 1.235374187 1.174725677 1.122572314 1.210019447 1 19.30663381 4.24244681 24.99960921 1.110459943 1.355880306 0.608108958 0.080891339 65.39535925 420667.1565 0.020632537 0.052276418 17476.1921 -4.24244681 0.245420363 SPTPKS(ph)PPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTPKSPPSR 10 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 SPT(0.009)PKS(0.99)PPSR;SPT(0.058)PKS(0.942)PPSR 82.202 0.011337 149250000 204984 228460 97824 97066 139262 190601 136836 138347 147392 117478 TRUE FALSE 196972.9987 221944.5445 115502.9729 102075.5879 143741.4887 194455.0828 138510.6399 135490.0861 130660.6781 109521.1104 1.79849344 2.02650013 1.054618351 0.932017467 1.312454632 1.775503207 1.264693531 1.237113882 1.193018201 1 16.74084945 4.242491192 24.99999347 1.243935255 1.912496987 0.599083157 0.225601714 68.99909183 438843.9506 0.05862149 0.14865833 17477.97813 -4.242491192 0.668561732 EVS(ph)DSEAGGGPQGER ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSDSEAGGGPQGER 15 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EVS(0.5)DS(0.5)EAGGGPQGER;EVS(0.971)DS(0.029)EAGGGPQGER 340.52 2.47E-69 1355570000 444880 449670 532280 646170 526930 528940 647520 613660 674500 749950 TRUE FALSE 427493.5978 436845.8519 628474.8365 679518.9111 543879.182 539635.5292 655444.5435 600987.7066 597933.5877 699155.2185 0.611443048 0.624819554 0.898906022 0.971914238 0.777909065 0.771839378 0.937480728 0.859591248 0.855222949 1 19.41525326 4.24249444 24.95546759 0.876515103 0.618131166 0.692411803 0.070765159 51.28107586 325304.7259 0.017243537 0.043717174 17478.10887 -4.24249444 -0.258383936 DVYVPEASRPHQWQTDEEGVR ddPTM_BT-474_Pertuzumab_2h_R1 3 DVYVPEASRPHQWQTDEEGVR 21 1 P49757-3;P49757;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;G3V4S6;G3V433;G3V3R1;G3V3M5 P49757-3 NUMB Protein numb homolog 0 ;; 194.88 1.25E-18 1051830000 517432 517107 487394 587881 580745 598888 580776 527677 614300 612237 FALSE TRUE 497210.1854 502359.6147 575476.9378 618221.6089 599425.1903 610997.9257 587883.7104 516780.2856 544567.2394 570769.6427 0.871122338 0.880144242 1.008247277 1.083136808 1.050205101 1.070480768 1.029984194 0.90540955 0.954092858 1 19.12254908 4.242508618 6.583333477 1.010784032 0.874277839 0.544265595 0.050170131 0.118583519 23.42781957 0.014864373 0.037201764 17478.67945 -4.242508618 -0.136506192 FDLLWLIQDRPDRDNDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDLLWLIQDRPDRDNDLR 18 2 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 136.26 3.74E-06 398360000 968610 1024250 565620 582680 774660 943850 658260 684830 864620 702600 FALSE TRUE 930755.6503 995039.3928 667840.1161 612752.1846 799577.6424 962935.2937 666315.9828 670688.0212 766471.9624 655012.2762 1.420974361 1.51911564 1.019584121 0.935481985 1.220706346 1.470102666 1.017257244 1.023931987 1.170164271 1 19.32116242 4.242508898 24.99992985 1.109456414 1.470045122 0.492493366 0.147337579 84.3848758 534291.6142 0.038481128 0.097598157 17478.69071 -4.242508898 0.360588708 NGSGTLDLEEFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 NGSGTLDLEEFLR 13 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 150.21 0.00010268 32921000 54899 54772 57421 58554 65730 71971 62033 67082 76403 71358 FALSE TRUE 52753.48639 53209.95619 67798.25202 61575.97896 67844.26514 73426.30293 62792.17841 65696.73326 67730.05175 66524.8591 0.792989074 0.799850716 1.01914161 0.925608559 1.019833278 1.103742329 0.943890438 0.987551633 1.018116425 1 16.02160593 4.242510064 24.99124177 0.999585065 0.796419793 0.765651446 0.0455275 43.95232768 278109.855 0.01136442 0.028826293 17478.73766 -4.242510064 -0.203165272 EDMAALEKDYEEVGVDSVEGEGEEEGEEY ddPTM_BT-474_Pertuzumab_2h_R1 1 EDMAALEKDYEEVGVDSVEGEGEEEGEEY 29 1 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 147.11 4.85E-08 38341000 336340 333620 75485 71272 179290 223680 79477 82590 101850 55765 FALSE TRUE 323195.461 324105.4842 89126.81865 74950.35646 185057.0257 228202.9629 80449.6633 80884.48764 90288.41499 51987.98688 6.216733525 6.234238017 1.714373339 1.441686069 3.559611302 4.389532593 1.547466408 1.555830346 1.736716892 1 15.66589067 4.242515088 24.98829794 2.181241731 6.225487721 0.730878959 0.996356432 51.3654823 324565.6324 0.264147103 0.670016178 17478.93987 -4.242515088 4.04424599 EFDKHFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFDKHFGK 8 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 58.676 0.062152 598670000 1826100 1941900 997740 975650 1439200 1702600 1262400 1169300 1533800 1300900 FALSE TRUE 1754733.993 1886518.913 1178053.813 1026003.413 1485493.175 1737027.739 1277849.629 1145153.546 1359689.454 1212788.884 1.446858572 1.555521276 0.971359342 0.845986822 1.224857182 1.432258954 1.053645565 0.944231565 1.12112625 1 20.20989701 4.242520463 24.99991221 1.074151564 1.501190073 0.544056555 0.15636086 77.72292044 490673.2312 0.041864003 0.106225589 17479.15617 -4.242520463 0.427038509 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEKNESRR ddPTM_BT-474_Pertuzumab_2h_R1 1 KISENSYSLDDLEIGPGQLSSSTFDSEKNESRR 33 3 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.461)ENS(0.461)YS(0.078)LDDLEIGPGQLSSSTFDSEKNESRR 133.66 2.37E-07 68098000 56594 52645 26011 18884 28896 42369 24302 28020 33012 25705 TRUE FALSE 54382.24391 51143.61614 30711.76631 19858.6055 29825.46608 43225.73021 24599.41515 27441.37721 29264.61616 23963.97745 2.269332961 2.134187292 1.281580504 0.828685703 1.244595816 1.803779456 1.02651637 1.145109457 1.221191942 1 14.54857976 4.24253357 4.480641899 1.192246826 2.233619763 0.739350705 0.240474412 0.091403765 4.451644069 0.061793721 0.16410697 17479.68373 -4.24253357 1.041372937 up SKPAGSDGERR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 136.7 5.27E-05 788400000 1721620 1774560 1199370 1330110 1422530 1632160 1430770 1535480 1657250 1441700 FALSE TRUE 1654337.187 1723951.286 1416122.839 1398757.137 1468286.969 1665163.393 1448280.191 1503771.801 1469125.928 1344052.375 1.230857679 1.282651866 1.053621768 1.040701362 1.092432852 1.238912579 1.077547437 1.118834228 1.093057053 1 20.35815793 4.242547678 24.99997948 1.097692508 1.256754822 0.545242784 0.060762197 74.74908429 468679.96 0.014932523 0.037881846 17480.25154 -4.242547678 0.159062314 TAQVPS(ph)PPRGK ddPTM_BT-474_Pertuzumab_2h_R1 4 TAQVPSPPRGK 11 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 TAQVPS(1)PPRGK;TAQVPS(1)PPRGK;TAQVPS(1)PPRGK;TAQVPS(1)PPRGK 92.457 0.0060447 3766390000 2932160 3277520 1491920 1636500 2134570 3022200 1949260 1901330 2247380 1725730 TRUE FALSE 2817567.946 3184048.339 1761543.132 1720959.961 2203230.383 3083310.955 1973115.627 1862066.871 1992266.844 1608844.77 1.751298819 1.97908984 1.094911805 1.069686767 1.369448702 1.916475108 1.226417653 1.157393744 1.23832136 1 20.6175937 4.242599483 24.99990665 1.276889548 1.865194493 0.487767802 0.247913797 87.79126852 543392.2575 0.064060587 0.162649797 17482.33682 -4.242599483 0.588304945 SRSS(ph)SS(ph)PPPKQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.239)RS(0.344)S(0.416)S(0.063)S(0.938)PPPKQK;S(0.225)RS(0.345)S(0.43)S(0.033)S(0.967)PPPKQK 89.466 0.0050451 457660000 771790 786560 324160 295360 432340 634750 396420 419880 527000 380080 TRUE FALSE 741627.5935 764128.0789 382742.9229 310603.565 446246.6087 647585.0799 401271.5065 411209.3313 467177.1694 354336.8431 2.09300164 2.15650191 1.080166882 0.876577108 1.259385293 1.827597363 1.132457757 1.160504021 1.318454963 1 18.43476196 4.242629453 24.99165173 1.217631191 2.124752183 0.699351291 0.240640747 55.25116911 339351.2664 0.061994026 0.157469872 17483.54329 -4.242629453 0.907120992 DPLLDDHGDFIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPLLDDHGDFIR 12 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 167.44 4.92E-05 265130000 193822 198437 210466 261017 239718 208003 261620 256700 263048 323160 FALSE TRUE 186247.222 192777.7711 248501.888 274488.1187 247428.7472 212208.9632 264821.7838 251399.0553 233187.8938 301272.0854 0.618202718 0.6398793 0.824842062 0.911097085 0.82128003 0.704376454 0.879012018 0.834458509 0.774010953 1 18.20070748 4.242639653 5.098297904 0.837081062 0.624384977 0.569569066 0.074615324 0.114845491 8.424823528 0.017735203 0.045865306 17483.9539 -4.242639653 -0.212696085 EKRT(ph)PAPEPEPCEASELPAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKRTPAPEPEPCEASELPAKR 21 3 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 EKRT(1)PAPEPEPCEASELPAKR;EKRT(1)PAPEPEPCEASELPAKR 67.832 0.021668 443550000 296743 292520 166940 140310 210971 241818 189196 233506 234086 211682 TRUE FALSE 285145.9555 284177.616 197109.7716 147551.4159 217757.0738 246707.7256 191511.4372 228684.0195 207513.5386 197344.5896 1.444913976 1.44000713 0.998810112 0.747684121 1.103435743 1.250136759 0.970441792 1.15880562 1.051528897 1 17.59035744 4.242661817 24.97234059 1.043215402 1.442460752 0.62889481 0.125043734 65.50611388 398853.3763 0.032402898 0.08231412 17484.84622 -4.242661817 0.39924535 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_BT-474_Pertuzumab_2h_R1 4 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 278.45 4.01E-77 987124000 572760 558141 356785.4 348909 431470 524037 400279 421201 507773 429736.1 FALSE TRUE 550375.906 542223.3652 421264.4584 366916.2353 445348.6244 534633.3872 405177.7341 412503.0522 450132.7378 400629.6912 1.373777127 1.353427809 1.051505836 0.915848833 1.111621615 1.334482688 1.011352236 1.029636747 1.1235631 1 18.61190982 4.24267598 23.0120557 1.072903519 1.363602915 0.55522605 0.104305193 27.75606884 155186.8781 0.026834093 0.067930373 17485.41643 -4.24267598 0.290699396 SLSALIGQCIHIER ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSALIGQCIHIER 14 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ; 150.57 7.18E-06 955050000 977660 1013150 933020 1213590 1141330 1159400 1119710 1091170 1161010 1145450 FALSE TRUE 939451.9663 984255.954 1101637.469 1276223.525 1178041.916 1182843.862 1133413.346 1068636.958 1029217.012 1067867.651 0.879745693 0.921702191 1.031623598 1.195113949 1.103172209 1.107668971 1.06137998 1.000720414 0.963805778 1 20.02630142 4.24267604 3.610601441 1.064570431 0.891497235 0.509025842 0.062655408 0.183613204 5.040970383 0.017311448 0.049074447 17485.41884 -4.24267604 -0.173073196 TLDRS(ph)GDLGDMEPLKGTTPLMQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLDRSGDLGDMEPLKGTTPLMQK 23 2 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-27;O60716-29;O60716-32;O60716-31 O60716-13 CTNND1 Catenin delta-1 1 T(0.02)LDRS(0.98)GDLGDMEPLKGTTPLMQK 157.42 3.57E-09 277750000 316620 306170 147120 158870 190240 250330 151210 198210 185720 146710 TRUE FALSE 304246.1404 297438.3314 173707.8567 167069.2997 196359.2424 255391.8441 153060.5532 194116.8942 164637.8442 136773.201 2.224457263 2.174682826 1.270043074 1.221506103 1.435655822 1.867265241 1.11908292 1.419261177 1.203728822 1 17.06142605 4.24268056 24.84603227 1.345361098 2.199570526 0.713090508 0.223335121 47.70961109 287709.2312 0.053639394 0.136304001 17485.60084 -4.24268056 0.854209428 EDIIQGFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EDIIQGFR 8 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;; 117.39 0.004859 303980000 522450 512828 558560 652190 592943 545259 663640 647940 723070 748580 FALSE TRUE 502032.0764 498202.6476 659504.2171 685849.6041 612015.5501 556284.5106 671761.8248 634559.8126 640990.125 697878.0098 0.719369387 0.713882141 0.94501361 0.982764315 0.876966377 0.797108524 0.962577722 0.909270393 0.918484486 1 19.41261535 4.242703921 24.97832534 0.918347942 0.716625668 0.695680914 0.05476566 55.10968735 332221.6554 0.01360738 0.034581697 17486.54144 -4.242703921 -0.201722275 TPVS(ph)PVKFSPGDFWGR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 T(0.003)PVS(0.997)PVKFSPGDFWGR;T(0.03)PVS(0.97)PVKFSPGDFWGR;T(0.001)PVS(0.999)PVKFSPGDFWGR 194.92 8.23E-11 10660520000 5196600 5295060 2865618 3204154 3407540 3985850 3856470 3890662 3799778 3396924 TRUE FALSE 4993511.127 5144050.073 3383498.918 3369520.772 3517146.619 4066446.618 3903666.633 3810318.47 3368443.131 3166847.312 1.5768083 1.624344203 1.068412394 1.063998494 1.110614524 1.284067787 1.232666513 1.203189827 1.063658206 1 21.59461588 4.242738544 24.99855357 1.146515932 1.600576448 0.828697317 0.085565653 40.55267757 242637.1797 0.022142357 0.056315858 17487.93555 -4.242738544 0.454060516 EMVELPLRHPALFK ddPTM_BT-474_Pertuzumab_2h_R1 3 EMVELPLRHPALFK 14 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 148.72 4.62E-06 5478100000 5791050 6730980 3560420 3906150 5076310 5991160 4845740 4801670 5279410 4662780 FALSE TRUE 5564729.364 6539019.041 4203867.095 4107746.87 5239594.121 6112305.36 4905043.616 4702513.837 4680113.51 4346965.757 1.280141063 1.504272038 0.967080794 0.944968766 1.205345157 1.406108468 1.128383311 1.081792243 1.076639148 1 22.0515773 4.24276781 24.99999203 1.112814385 1.392206567 0.421552954 0.135776211 105.8695922 629075.6585 0.035259802 0.089717549 17489.11404 -4.24276781 0.279392182 QNVAYEYLCHLEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 QNVAYEYLCHLEEAKR 16 1 P46940;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 187.35 8.78E-10 1207570000 1460600 1568760 977940 1083870 1236870 1288830 1201230 1266100 1521520 1358560 FALSE TRUE 1403518.137 1524020.501 1154675.512 1139808.661 1276655.047 1314891.026 1215931.012 1239954.593 1348803.428 1266543.521 1.108148369 1.203291064 0.911674564 0.899936435 1.00798356 1.038172794 0.960038871 0.9790067 1.064948346 1 20.27246522 4.242825606 24.99999626 0.980631719 1.155719752 0.632832296 0.052690755 63.79947196 373958.41 0.013170659 0.03351785 17491.44167 -4.242825606 0.175088033 NLDDGIDDERLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NLDDGIDDERLR 12 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;; 249.28 6.26E-17 4355910000 7559830 8021900 4815050 5317490 6001320 7840660 5915350 5815710 6764460 6001660 FALSE TRUE 7264383.486 7793123.266 5685236.645 5591926.296 6194357.908 7999203.517 5987743.823 5695613.556 5996586.86 5595162.222 1.298332952 1.392832407 1.016098626 0.999421656 1.107091745 1.429664271 1.070164472 1.017953248 1.071744951 1 22.41574853 4.242829061 24.9999183 1.094090808 1.345582752 0.415268748 0.121659589 107.2062353 627874.863 0.031700145 0.080718602 17491.58082 -4.242829061 0.251491944 VDKGVVPLAGTNGETTTQGLDGLSER ddPTM_BT-474_Pertuzumab_2h_R1 1 VDKGVVPLAGTNGETTTQGLDGLSER 26 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 228.25 2.43E-34 907800000 270010 278180 152950 180480 194280 243650 157440 209170 214800 175890 FALSE TRUE 259457.7107 270246.5788 180591.4674 189794.5944 200529.1926 248576.7699 159366.7978 204850.5664 190416.8045 163976.8136 1.582282915 1.648077998 1.101323189 1.157447753 1.222911875 1.515926334 0.971886173 1.249265441 1.161242253 1 17.32313231 4.242887683 24.99996533 1.187242917 1.615180632 0.602515819 0.143422759 68.03429707 393059.0748 0.033851492 0.086245281 17493.94204 -4.242887683 0.427937715 ELPDVQGESDSIS(ph)PLLLHLEDDDFSENEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELPDVQGESDSISPLLLHLEDDDFSENEK 29 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 ELPDVQGES(0.005)DS(0.025)IS(0.97)PLLLHLEDDDFSENEK;ELPDVQGESDS(0.006)IS(0.994)PLLLHLEDDDFSENEK 224.71 8.48E-35 187483000 134794 130704 111104 122125 127901 127529 130203 127893 148709 138661 TRUE FALSE 129526.1015 126976.4499 131182.9643 128427.8859 132015.0518 130107.7238 131796.4633 125251.9649 131828.1778 129269.367 1.001986043 0.982262487 1.014803177 0.993490483 1.021240027 1.006485348 1.019549073 0.968922242 1.01979441 1 16.98002091 4.242905769 24.99681137 1.003523311 0.99212427 0.093491338 0.0157362 294.5314293 1694318.307 0.003898699 0.009947208 17494.67058 -4.242905769 -0.011399041 S(ph)CSPSPVS(ph)PQVQPQAADTISDSVAVPASLLGMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCSPSPVSPQVQPQAADTISDSVAVPASLLGMR 33 0 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 2 S(0.334)CS(0.335)PS(0.336)PVS(0.994)PQVQPQAADT(0.001)ISDSVAVPASLLGMR 78.159 0.00094637 27350000 31539 29924 31768 34752 34693 41004 37140 33926 36179 35043 TRUE FALSE 30306.42101 29070.59682 37509.18428 36545.55488 35808.93185 41833.12897 37594.53043 33225.41624 32072.11159 32669.5064 0.927666939 0.889838875 1.148140527 1.118644232 1.096096507 1.280494675 1.150752937 1.017016169 0.981713994 1 14.99565704 4.24292251 24.99927677 1.104749417 0.908752831 0.453079071 0.08347229 96.475383 552908.5848 0.021785067 0.055534809 17495.34496 -4.24292251 -0.195996586 ELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.111)NHDGADET(0.046)S(0.843)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.154)S(0.846)EKEQQEAIEHIDEVQNEIDR 163.92 2.63E-14 840100000 199785 186822 192346 218670 206175 189049 236070 204525 249160 254960 TRUE FALSE 191977.1813 181494.0195 227107.2009 229955.5849 212806.8061 192871.7003 238959.0953 200301.4873 220876.4014 237691.3321 0.807674304 0.763570206 0.95547111 0.967454652 0.89530739 0.811437668 1.005333653 0.8426958 0.929257283 1 17.85872977 4.242927463 24.99999032 0.916993748 0.785622214 0.454762997 0.060808184 95.0370926 544063.8187 0.014379366 0.03665465 17495.54447 -4.242927463 -0.131371534 HGFELVELSPEELPEEDDDFPESTGVK ddPTM_BT-474_Pertuzumab_2h_R1 4 HGFELVELSPEELPEEDDDFPESTGVK 27 0 Q6PD74;Q6PD74-2;H0YL49 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 0 ;;; 210.88 1.17E-25 541998000 274642 263174 256402 304556 299109 274672 308275 218406 386436 361113 FALSE TRUE 263908.687 255668.5352 302739.545 320274.1717 308730.1126 280226.056 312047.7617 213895.8398 342569.4054 336654.4949 0.783915531 0.759438947 0.899258883 0.951343816 0.917053292 0.832384716 0.926908051 0.635357148 1.017569676 1 18.3609092 4.24302352 24.96123302 0.873972119 0.771677202 0.163732901 0.103321567 223.0318388 1247382.278 0.026245188 0.066989071 17499.41456 -4.24302352 -0.102294918 RALSSDS(ph)ILSPAPDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.373)S(0.048)DS(0.514)ILS(0.065)PAPDAR 110.77 0.00092037 262510000 213350 204840 94573 115650 121510 126320 93909 149740 117280 103040 TRUE FALSE 205012.0461 198998.1638 111664.4449 121618.7104 125418.4795 128874.2769 95058.28643 146647.8167 103966.8661 96061.00902 2.134185849 2.071581027 1.162432562 1.266056974 1.305612764 1.341587792 0.989561607 1.526611246 1.082300375 1 16.55166334 4.243051131 24.8494365 1.241220568 2.102883941 0.834798489 0.158501456 35.00561366 193705.2603 0.036548937 0.093271454 17500.52715 -4.243051131 0.861663372 REEDEPEERS(ph)GDETPGSEVPGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 REEDEPEERSGDETPGSEVPGDK 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 REEDEPEERS(0.995)GDET(0.005)PGSEVPGDK;REEDEPEERS(0.991)GDET(0.005)PGS(0.005)EVPGDK 234.48 3.58E-37 1690420000 1627650 1600670 902970 821620 1221220 1346690 1036590 1214700 1252590 948500 TRUE FALSE 1564039.639 1555020.459 1066156.765 864023.9067 1260501.65 1373920.994 1049276.098 1189616.021 1110401.234 884257.2502 1.768760887 1.758561164 1.20570882 0.977118261 1.425492016 1.553757116 1.186618598 1.34532798 1.255744563 1 19.75410662 4.243072816 24.98072105 1.264963894 1.763661282 0.606341833 0.166876112 73.60250009 407468.1963 0.041421313 0.105747122 17501.40103 -4.243072816 0.498697388 RPHT(ph)PTPGIYMGR ddPTM_BT-474_Pertuzumab_2h_R1 14 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.991)PT(0.009)PGIYMGR;RPHT(0.984)PT(0.016)PGIYMGR;RPHT(0.999)PT(0.001)PGIYMGR;RPHT(0.982)PT(0.018)PGIYMGR;RPHT(0.992)PT(0.008)PGIYMGR;RPHT(0.582)PT(0.418)PGIYMGR;RPHT(0.971)PT(0.029)PGIYMGR;RPHT(0.986)PT(0.014)PGIYMGR;RPHT(0.959)PT(0.041)PGIYMGR;RPHT(0.989)PT(0.011)PGIYMGR;RPHT(0.995)PT(0.005)PGIYMGR;RPHT(0.998)PT(0.002)PGIYMGR;RPHT(0.999)PT(0.001)PGIYMGR;RPHT(0.991)PT(0.009)PGIYMGR 187.78 3.91E-06 1.03834E+11 3540160 3427888 3624780 4432490 3795180 3386860 4182765 4398220 4460130 4666910 TRUE FALSE 3401806.633 3330127.99 4279858.379 4661251.34 3917255.411 3455344.63 4233954.929 4307395.22 3953834.741 4350816.029 0.781877839 0.76540308 0.983690956 1.071351054 0.900349586 0.794183116 0.973140418 0.990020077 0.90875705 1 22.05285458 4.243119169 24.99159416 0.952170717 0.773640379 0.511296862 0.070016713 92.11606278 504995.116 0.0182891 0.046724825 17503.26907 -4.243119169 -0.178530337 RET(ph)DDEGEDD ddPTM_BT-474_Pertuzumab_2h_R1 2 RETDDEGEDD 10 1 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 RET(1)DDEGEDD;RET(1)DDEGEDD 140.57 7.56E-05 124851000 222400 208030 217020 265200 222240 239030 241370 242590 249060 278040 TRUE FALSE 213708.3621 202097.1881 256240.3416 278887.0038 229388.5514 243863.3504 244323.9583 237580.4317 220787.7529 259208.1031 0.824466363 0.779671567 0.988550661 1.075919311 0.88495903 0.940801416 0.942578397 0.916562518 0.851777974 1 17.98375129 4.243175525 24.99970443 0.947013389 0.802068917 0.492572496 0.060049155 95.26788957 516063.6902 0.015148526 0.038723366 17505.54051 -4.243175525 -0.144944471 IDASKNEEDEGHSNSSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;; 253.48 9.93E-31 8024400000 8681320 8581500 4898340 5037710 6168270 7387770 5809330 6017790 7030350 5785410 FALSE TRUE 8342044.417 8336764.022 5783579.001 5297706.817 6366678.006 7537155.771 5880426.318 5893520.534 6232294.142 5393559.028 1.546667863 1.545688845 1.072312173 0.982228393 1.180422421 1.397436411 1.090268279 1.092696029 1.155506802 1 22.36280614 4.243258643 24.98547831 1.127994696 1.546178567 0.707028654 0.109318442 61.99984009 329722.0163 0.028110111 0.071906972 17508.89117 -4.243258643 0.418183871 VKEDPDGEHARR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKEDPDGEHARR 12 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 113.24 0.00071298 365130000 835160 909820 445296 493507 594970 828770 539990 584950 692320 556390 FALSE TRUE 802521.0239 883872.8244 525770.8928 518976.9554 614107.7504 845528.2972 546598.5591 572870.5781 613730.736 518705.2097 1.547162066 1.703998356 1.01362177 1.000523892 1.183924393 1.630074812 1.053774955 1.104424184 1.183197555 1 18.98455533 4.243279436 24.99984054 1.15549568 1.625580361 0.533917268 0.178991267 90.11125707 477384.437 0.045455026 0.116302225 17509.72945 -4.243279436 0.470084681 AVVPGPAEHPLQYNYTFWYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVVPGPAEHPLQYNYTFWYSR 21 0 B9A044;B8ZZ50;O60573-2;O60573;C9JEL3 B9A044 EIF4E2 Eukaryotic translation initiation factor 4E type 2 0 187.06 3.01E-17 399550000 142610 140710 131140 165630 161090 126990 157740 137000 175810 165750 FALSE TRUE 137036.6435 136697.0886 154839.9152 174178.1841 166271.6061 129557.8248 159670.4693 134170.9021 155852.7859 154523.6049 0.886833074 0.884635643 1.002047003 1.127194672 1.076027228 0.838433875 1.03330795 0.86828742 1.008601799 1 17.23746771 4.243300619 24.42172362 0.987467873 0.885734291 0.216857331 0.081670943 145.6084851 750178.3503 0.021227438 0.054257623 17510.58352 -4.243300619 -0.101733582 KLDPAQS(ph)ASRENLLEEQGSIALR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.62)AS(0.38)RENLLEEQGSIALR;KLDPAQS(0.5)AS(0.5)RENLLEEQGSIALR 172.32 4.05E-12 3006100000 1252308 1261513 731985 752275 912417 1088891 868977 982978 905681 992331 TRUE FALSE 1203366.419 1225535.884 864270.9724 791100.0029 941765.7214 1110909.122 879611.8005 962679.1608 802871.8898 925119.5375 1.300768571 1.324732464 0.934226267 0.855132738 1.017993549 1.200827652 0.950808803 1.040599751 0.867857458 1 19.81928027 4.243320715 24.99974793 0.990133497 1.312750667 0.668295843 0.092708284 68.32636459 358833.8523 0.02351116 0.060186993 17511.39381 -4.243320715 0.32261717 KGPGQPSS(ph)PQRLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.008)S(0.992)PQRLDR;KGPGQPS(0.006)S(0.994)PQRLDR;KGPGQPS(0.02)S(0.98)PQRLDR;KGPGQPS(0.184)S(0.816)PQRLDR 148.97 3.97E-06 4974270000 2832610 2821920 1936900 1943240 2324870 2644490 2293530 2417280 2662350 2411410 TRUE FALSE 2721908.47 2741441.605 2286940.916 2043530.849 2399651.555 2697963.4 2321598.906 2367362.323 2360131.189 2248083.053 1.210768644 1.21945744 1.017284888 0.909010389 1.06742122 1.200117316 1.032701574 1.053058213 1.049841636 1 21.1002639 4.243337849 24.99564378 1.044885079 1.215113123 0.511512551 0.067912341 97.76609336 511518.3627 0.01771919 0.045394401 17512.0847 -4.243337849 0.170228044 VVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVDYSQFQESDDADEDYGRDSGPPTKK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGRDSGPPTKK 182.56 8.13E-18 1485100000 757920 742310 288220 286260 387990 532970 349450 392280 453530 318970 TRUE FALSE 728299.6485 721140.0456 340307.7654 301033.9129 400470.0507 543747.0186 353726.6736 384179.2809 402047.1758 297365.8778 2.449170207 2.42509346 1.144407583 1.012335091 1.346724963 1.828545436 1.189533501 1.291941375 1.352028615 1 18.18187958 4.2433634 24.99951059 1.289943594 2.437132428 0.816106746 0.221328122 46.12498472 240082.3508 0.055896573 0.143162811 17513.11502 -4.2433634 1.147188834 CDGETDKHWR ddPTM_BT-474_Pertuzumab_2h_R1 4 CDGETDKHWR 10 1 Q9NXV6;J3KNE1;D6RGD2 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 0 ;;; 215.56 4.89E-09 1244750000 1164720 1157870 845882 871925 1015698 1189860 988454 952000 1181590 1071340 FALSE TRUE 1119201.455 1124848.681 998751.6939 916925.1537 1048368.849 1213919.784 1000550.996 932340.8673 1047460.857 998777.1875 1.120571704 1.126225844 0.999974475 0.918047754 1.049652377 1.215405998 1.00177598 0.933482341 1.048743273 1 19.92980334 4.243367174 24.96306294 1.017357415 1.123398826 0.220728737 0.076818573 179.6408236 932941.7677 0.02053217 0.052578906 17513.26721 -4.243367174 0.10604141 ALGDEDDLAKREDEFVDLGDV ddPTM_BT-474_Pertuzumab_2h_R1 1 ALGDEDDLAKREDEFVDLGDV 21 2 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 0 72.207 0.025337 0 103490 104050 52789 47874 73523 90922 60670 65779 84282 59852 FALSE TRUE 99445.49639 101082.5959 62329.14658 50344.78288 75887.93407 92760.50514 61412.49761 64420.64066 74714.6607 55798.17073 1.782235781 1.811575443 1.117046415 0.902265831 1.360043404 1.662429143 1.100618476 1.154529617 1.33901631 1 15.76793021 4.243400411 24.90705065 1.212327907 1.796905907 0.57955257 0.201745212 80.29876376 413227.3943 0.051609246 0.132229973 17514.60757 -4.243400411 0.584577999 EGVKTENDHINLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGVKTENDHINLK 13 1 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 72.496 0.023668 213160000 351580 351760 199160 186300 259540 292770 224930 253080 324500 259130 FALSE TRUE 337839.8649 341728.1492 235152.6423 195914.9653 267888.3398 298690.01 227682.7606 247853.8096 287664.1204 241578.8943 1.398465979 1.414561277 0.973398951 0.810977159 1.108906225 1.23640772 0.942477865 1.025974601 1.190766773 1 17.88213489 4.243428961 24.99976133 1.033389066 1.406513809 0.620327806 0.115895321 75.61523551 388284.0218 0.029461341 0.07552374 17515.75898 -4.243428961 0.373124743 S(ph)KSPRDPDANWDSPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSPRDPDANWDSPSR 16 2 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.6)KS(0.4)PRDPDANWDSPSR;S(0.595)KS(0.405)PRDPDANWDSPSR 96.881 0.0025695 1446280000 889770 882120 625640 695710 754650 800300 718280 792510 808880 751670 TRUE FALSE 854996.8047 856962.8013 738707.0653 731615.6765 778924.0026 816482.6143 727070.5255 776144.3916 717059.3335 700758.7214 1.220101554 1.222907079 1.054153224 1.044033637 1.111543787 1.165140853 1.037547594 1.107577213 1.023261376 1 19.41855827 4.243435661 24.9994242 1.075858521 1.221504389 0.631544522 0.046612697 73.3228317 375990.4883 0.011143334 0.028547185 17516.02922 -4.243435661 0.145645868 KRTEEPDRDER ddPTM_BT-474_Pertuzumab_2h_R1 7 KRTEEPDRDER 11 3 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;;;;; 182.25 2.57E-06 1223917000 1087745 1203058 725251 784698 937045 1256831 921795 852273 1043251 968081 FALSE TRUE 1045234.723 1168747.964 856319.9888 825196.3578 967185.9034 1282244.984 933076.2029 834673.2647 924825.5201 902512.0116 1.158139404 1.294994359 0.948818384 0.914332826 1.071659868 1.420751156 1.033865689 0.924833414 1.02472378 1 19.78358661 4.24344245 24.99951687 1.042886041 1.226566898 0.218157914 0.139476236 193.8732626 992777.5004 0.037026476 0.09487534 17516.30304 -4.24344245 0.183680857 RPES(ph)SPEDSATRPPPFDAHVGKPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPESSPEDSATRPPPFDAHVGKPTR 25 3 Q13796 Q13796 SHROOM2 Protein Shroom2 1 RPES(0.5)S(0.5)PEDSATRPPPFDAHVGKPTR;RPES(0.496)S(0.496)PEDS(0.004)AT(0.004)RPPPFDAHVGKPTR 80.418 0.016694 1000170000 178036 179657 190124 209295 204496 213397 243000 214421 229370 279980 TRUE FALSE 171078.1563 174533.3583 224483.6361 220096.74 211073.7996 217712.0335 245973.9067 209993.1314 203332.8792 261016.7052 0.655429913 0.668667387 0.860035513 0.843228558 0.808660118 0.834092337 0.942368445 0.804519892 0.779003317 1 17.99378262 4.243553014 14.62260917 0.85088791 0.662021177 0.604748883 0.063415867 0.455563927 1317.573176 0.014706368 0.036835978 17520.76296 -4.243553014 -0.188866733 GFGFVTFDDHDPVDKIVLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVTFDDHDPVDKIVLQK 20 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 280.65 6.06E-45 5068500000 9925200 10733300 3807700 3678300 5906900 9507400 5130100 4956800 6488600 4174100 FALSE TRUE 9537312.211 10427196.79 4495836.092 3868137.504 6096900.803 9699646.142 5192883.698 4854440.348 5752041.33 3891384.489 2.450878919 2.679559633 1.155330732 0.994026037 1.566769056 2.49259516 1.334456596 1.247484118 1.478147777 1 21.8918521 4.243596139 24.9998911 1.43267377 2.565219728 0.561178374 0.408669856 92.29449939 458200.3545 0.105712838 0.271441479 17522.50284 -4.243596139 1.132545958 AVEES(ph)S(ph)DEER ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEESSDEER 10 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 AVEES(1)S(1)DEER;AVEES(1)S(1)DEER 101.89 0.004422 388500000 599440 569610 606000 704160 641760 634330 678580 693540 736120 787030 TRUE FALSE 576013.2221 553365.2805 715517.6804 740501.782 662402.7932 647156.5872 686884.665 679218.1566 652558.7437 733723.7571 0.785054616 0.754187492 0.975186742 1.009237843 0.902795891 0.882016673 0.936162498 0.925713731 0.88937933 1 19.48487747 4.243603284 24.99999754 0.935801891 0.769620986 0.72267346 0.042167537 63.19626447 313297.4814 0.010621953 0.027282054 17522.79113 -4.243603284 -0.166180905 ELNFVTDSVEQELPSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELNFVTDSVEQELPSSPK 18 0 B4DP81;Q8TAP6-2;Q8TAP6 B4DP81 CEP76 Centrosomal protein of 76 kDa 1 ELNFVTDSVEQELPS(0.045)S(0.955)PK;ELNFVTDSVEQELPS(0.001)S(0.999)PK 247.36 2.36E-24 99208000 129259 116876 136070 141929 139585 132638 153115 159791 169233 169169 TRUE FALSE 124207.4154 113542.8109 160660.8759 149253.9727 144074.8783 135320.0312 154988.8672 156491.26 150022.3793 157711.0329 0.787563261 0.719942091 1.0187041 0.946376229 0.913537091 0.858025141 0.982739535 0.992265773 0.951248473 1 17.26692406 4.24368307 24.99999996 0.955380045 0.753752611 0.754069535 0.046608235 59.7123517 291415.3508 0.01199038 0.030815226 17526.01059 -4.24368307 -0.201627434 S(ph)PHQLLS(ph)PS(ph)SFSPSATPSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPHQLLSPSSFSPSATPSQK 20 0 A0A3B3ITS5;Q14181;E9PIQ6 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 3 S(0.981)PHQLLS(0.767)PS(0.48)S(0.205)FS(0.54)PS(0.02)AT(0.005)PS(0.002)QK 50.144 0.066805 108490000 72942 70145 66074 72431 78262 70507 76317 79115 74736 84914 TRUE FALSE 70091.346 68144.53328 78015.04161 76169.17259 80779.36831 71932.69985 77250.99027 77481.2476 66252.2826 79162.69915 0.885408744 0.860816193 0.985502547 0.962185138 1.020422108 0.908669116 0.975850888 0.978759548 0.836912881 1 16.27253318 4.243780131 24.97627883 0.96022861 0.873112437 0.321413978 0.049601034 133.7267522 639884.9018 0.011561493 0.029734704 17529.92794 -4.243780131 -0.087116173 GS(ph)PLLGPVVPGPSPIPSVTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPLLGPVVPGPSPIPSVTEK 21 0 P49454 P49454 CENPF Centromere protein F 1 GS(1)PLLGPVVPGPSPIPSVTEK 156.11 1.90E-08 75357000 195890 191860 243420 276740 249970 232410 306870 282160 254030 326220 TRUE FALSE 188234.4022 186388.3407 287411.4088 291022.5846 258010.5121 237109.4894 310625.5669 276333.2974 225193.5794 304124.8288 0.618937964 0.612867885 0.945044211 0.956918203 0.848370431 0.779645287 1.02137523 0.908618012 0.740464303 1 18.21430408 4.243786711 24.99059576 0.899661635 0.61590278 0.639905319 0.085262562 73.99427812 353821.1463 0.020651295 0.053131429 17530.19355 -4.243786711 -0.283758855 GLLYDS(ph)DEEDEERPARK ddPTM_BT-474_Pertuzumab_2h_R1 7 GLLYDSDEEDEERPARK 17 2 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK 275.23 5.37E-36 6292090000 3172396 3332626 2132225 2239747 2556314 3370140 2486480 2785090 2920994 2717637 TRUE FALSE 3048415.257 3237582.769 2517565.489 2355340.611 2638540.161 3438286.54 2516910.286 2727576.918 2589415.007 2533569.025 1.20320987 1.27787431 0.993683402 0.929653223 1.04143212 1.357092112 0.993424794 1.076574939 1.022042416 1 21.2727397 4.243820199 24.99931096 1.058382031 1.240542141 0.316622428 0.110606922 156.7747883 745142.0442 0.027867776 0.071730142 17531.54532 -4.243820199 0.18216011 VAAETQS(ph)PSLFGSTK ddPTM_BT-474_Pertuzumab_2h_R1 3 VAAETQSPSLFGSTK 15 0 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 1 VAAETQS(0.994)PS(0.006)LFGSTK;VAAETQS(0.993)PS(0.007)LFGSTK;VAAETQS(0.994)PS(0.006)LFGSTK 295.22 5.13E-44 598020000 1146550 1156000 1223950 1419600 1648510 1481040 1347690 1330520 1230250 1414940 TRUE FALSE 1101741.558 1123032.012 1445144.992 1492865.726 1701535.821 1510987.644 1364183.433 1303044.297 1090597.178 1319104.854 0.835219092 0.851359169 1.095549749 1.131726354 1.289917035 1.145464395 1.034173614 0.987824655 0.82677065 1 20.33112782 4.243820334 24.03211306 1.070740315 0.843288916 0.37207388 0.114378628 85.5516325 390872.0284 0.03085336 0.079225559 17531.55077 -4.243820334 -0.227451399 ELKTDSS(ph)PNQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 ELKT(0.001)DS(0.098)S(0.901)PNQAR;ELKTDS(0.023)S(0.977)PNQAR;ELKT(0.001)DS(0.18)S(0.819)PNQAR 164.53 3.45E-05 1872080000 1554500 1616730 737220 749270 877130 1443120 868530 986330 1289790 931160 TRUE FALSE 1493748.421 1570622.443 870452.0534 787939.9145 905343.683 1472300.875 879159.3299 965961.9408 1143378.446 868091.7038 1.720726526 1.809281711 1.002719009 0.907668984 1.042912493 1.696019981 1.012749374 1.112741818 1.317117122 1 19.72748793 4.243826846 24.96873514 1.140778866 1.765004396 0.576980089 0.21524033 87.14839013 413182.9499 0.053783482 0.138425923 17531.81366 -4.243826846 0.62422553 AGAES(ph)PTMSVDGR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGAESPTMSVDGR 13 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 AGAES(0.977)PT(0.023)MSVDGR;AGAES(0.992)PT(0.008)MSVDGR;AGAES(0.997)PT(0.003)MSVDGR 306.67 1.04E-41 3172300000 1575750 1574680 1576680 1763420 1741920 1719600 1870990 1887630 1899060 2005300 TRUE FALSE 1514167.948 1529771.668 1861621.149 1854430.318 1797950.439 1754371.49 1893887.735 1848649.781 1683486.67 1869479.245 0.809941031 0.818287591 0.995796639 0.991950204 0.961738647 0.938427904 1.013056305 0.988858146 0.900511025 1 20.83420502 4.243955652 24.99942341 0.97516211 0.814114222 0.801726439 0.031757373 50.16429337 232443.4028 0.007694287 0.019830496 17537.01413 -4.243955652 -0.161047888 VPS(ph)PDHRR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPSPDHRR 8 1 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 1 VPS(1)PDHRR 60.518 0.056219 119130000 96778 104830 45550 55437 69585 82229 60001 65625 58630 55299 TRUE FALSE 92995.80877 101840.351 53781.89825 58298.11021 71823.26472 83891.72672 60735.31019 64269.82082 51974.5682 51553.54947 1.803868205 1.975428503 1.043223964 1.130826312 1.393177879 1.627273535 1.178101427 1.246661413 1.008166629 1 15.65378414 4.243958402 24.99952419 1.230579216 1.889648599 0.681588278 0.18687452 75.10073911 347813.9448 0.04712367 0.121492467 17537.1252 -4.243958402 0.659069383 SVVSDLEADDVKGSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 SVVSDLEADDVKGS(0.014)VPLS(0.329)S(0.329)S(0.329)PPATHFPDETEITNPVPK 241.05 3.09E-50 2049100000 310650 300070 160730 157090 198600 264540 176950 206500 233520 191960 TRUE FALSE 298509.4546 291512.2974 189777.4864 165197.4337 204988.1494 269889.1801 179115.567 202235.7028 207011.7886 178958.3782 1.668038443 1.628939088 1.060456003 0.923105335 1.145451537 1.508111454 1.000878354 1.130071164 1.156759413 1 17.44926456 4.244058245 24.73970088 1.12258877 1.648489113 0.668969119 0.149877958 67.03075861 301632.4609 0.037673188 0.097150366 17541.15736 -4.244058245 0.525900343 SRSHS(ph)DNDRPNCSWNTQYSSAYYTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.218)RS(0.218)HS(0.564)DNDRPNCS(0.001)WNTQYSSAYYTSR 211.73 4.97E-26 450570000 125780 140230 88289 98952 116540 134760 98132 120080 124180 129750 TRUE FALSE 120864.3785 136230.7777 104244.7863 104058.9246 120288.6149 137484.9395 99332.96877 117600.306 110083.607 120961.9169 0.999193644 1.126228661 0.861798398 0.860261868 0.994433769 1.136596898 0.821192085 0.972209345 0.910068307 1 16.88419338 4.244112828 24.99988393 0.944109534 1.06271114 0.214774667 0.09035447 199.9935846 900481.9607 0.022035502 0.056915206 17543.36214 -4.244112828 0.118601606 TPTSSPAS(ph)SPLVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 TPTS(0.002)S(0.108)PAS(0.574)S(0.316)PLVAK 125.61 9.46E-05 171590000 331950 299580 306170 334690 337520 344080 323560 341240 328630 415790 TRUE FALSE 318977.027 291036.2717 361501.7297 351963.391 348376.6373 351037.5333 327519.8241 334193.2748 291325.3001 387628.173 0.822894333 0.750813001 0.932599215 0.907992286 0.898739208 0.905603766 0.844932972 0.862149085 0.751558634 1 18.5643139 4.244124332 24.99692206 0.881527765 0.78685366 0.288962841 0.06278916 168.9924789 759234.3308 0.014871677 0.038407193 17543.82682 -4.244124332 -0.094674105 DVFHMVVEVPR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVFHMVVEVPR 11 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 166.14 2.08E-05 1960900000 1415010 1450560 1546460 1923680 1717160 1517460 1913680 1928660 2004410 2232470 FALSE TRUE 1359709.845 1409191.449 1825939.723 2022961.355 1772394.011 1548144.081 1937100.188 1888832.497 1776877.78 2081262.818 0.653310016 0.677084814 0.877322992 0.971987458 0.851595481 0.74384843 0.930733097 0.907541556 0.853749831 1 20.98902773 4.244132508 5.198075782 0.888872233 0.660337462 0.647044862 0.067141208 0.099518314 7.781471968 0.016738441 0.0432926 17544.15714 -4.244132508 -0.228534771 TGSELMEILDGMDQSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSELMEILDGMDQSHR 17 0 E9PQ42;E9PJD7;Q6ZMK1-4;Q6ZMK1-2;Q6ZMK1 E9PQ42 CYHR1 Cysteine and histidine-rich protein 1 0 108.56 0.0006498 35038000 48068 47875 50385 59366 52879 52094 59615 56519 62844 71238 FALSE TRUE 46189.44942 46509.65187 59490.69031 62429.88637 54579.90106 53147.37637 60344.5862 55351.8629 55710.21258 66412.98681 0.695488212 0.700309595 0.895768933 0.940025278 0.821825725 0.800255777 0.908626296 0.833449383 0.838845161 1 16.01917776 4.244140922 24.81994194 0.870835316 0.697898799 0.610808397 0.057737967 78.054294 347156.4668 0.013641609 0.035212957 17544.49702 -4.244140922 -0.172936517 VVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_BT-474_Pertuzumab_2h_R1 4 VVDYSQFQESDDADEDYGRDSGPPTK 26 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK 223.42 1.38E-34 12651700000 2572840 2603880 1368790 1553380 1805670 2071190 1601890 1816570 2018210 1681930 TRUE FALSE 2472290.568 2529619.892 1616160.802 1633550.128 1863751.015 2113070.881 1621494.409 1779057.195 1789111.262 1568011.383 1.576704478 1.613266281 1.030707314 1.041797366 1.18860809 1.347611952 1.034108825 1.134594566 1.141006552 1 20.5805046 4.244144576 24.99953914 1.124032358 1.594985607 0.796350822 0.097040428 55.60812773 248951.6499 0.024196202 0.062485648 17544.64464 -4.244144576 0.470953249 DRESRS(ph)PFLKPDER ddPTM_BT-474_Pertuzumab_2h_R1 1 DRESRSPFLKPDER 14 3 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 DRES(0.078)RS(0.922)PFLKPDER 104.2 0.005923 209500000 617000 591560 225610 185900 335490 419920 231320 256060 290310 185900 TRUE FALSE 592886.9579 574689.288 266382.7457 195494.3213 346281.3405 428411.0701 234150.9634 250772.2715 257355.2259 173308.8274 3.42098534 3.315983938 1.53704084 1.128011332 1.998059451 2.471951813 1.351061956 1.446967678 1.484951631 1 17.40298561 4.244147402 9.325620867 1.582659412 3.372857419 0.767289713 0.399819288 0.05618412 53.36473592 0.102157732 0.254227713 17544.75881 -4.244147402 1.790198007 EDLQELNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDLQELNDR 9 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 232.83 5.39E-09 2070410000 992990 923120 1004210 1231160 1026840 877720 1115910 1212190 1207030 1272840 FALSE TRUE 954182.853 896793.5214 1185693.086 1294700.315 1059869.241 895468.0998 1129566.84 1187157.853 1070013.015 1186629.413 0.804111918 0.755748603 0.999210935 1.091073844 0.893176277 0.75463164 0.951912053 1.000445328 0.901724669 1 20.17843802 4.244161595 24.99777653 0.94814625 0.7799302 0.387605341 0.085010695 144.1023038 643125.1101 0.022375373 0.057799999 17545.33218 -4.244161595 -0.16821605 DDDSNFHMDFIVAASNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DDDSNFHMDFIVAASNLR 18 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 235.24 8.69E-24 1094433000 478588 466572 564680 622870 559190 532758 676740 619010 786690 769450 FALSE TRUE 459884.2519 453265.8234 666730.2372 655016.3953 577176.8542 543530.7318 685022.1466 606227.2272 697388.2493 717334.4661 0.641101569 0.63187515 0.929455183 0.913125503 0.804613303 0.757708931 0.954955016 0.845110971 0.972193979 1 19.45228642 4.244168071 24.99705129 0.885071551 0.636488233 0.670812034 0.072645505 76.21836376 339757.9493 0.017470206 0.045120946 17545.5938 -4.244168071 -0.248583318 WPFSGKTS(ph)PPCS(ph)PANLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 WPFS(0.081)GKT(0.431)S(0.488)PPCS(0.997)PANLS(0.003)R;WPFS(0.031)GKT(0.179)S(0.8)PPCS(0.985)PANLS(0.004)R 63.63 0.023822 491460000 919050 925860 410800 420170 579340 773840 491650 544560 588520 508250 TRUE FALSE 883132.5099 899455.3793 485040.6982 441855.0241 597974.9972 789487.575 497666.9598 533314.6457 521713.6769 473825.7748 1.863833833 1.898282928 1.023668876 0.932526358 1.262014498 1.666198035 1.050316353 1.125550095 1.101066478 1 18.85399715 4.244226584 24.99953707 1.157803675 1.881058745 0.695171767 0.194775569 76.24061947 336380.982 0.05032272 0.130073307 17547.95792 -4.244226584 0.723255071 IGDELYLEPLEDGLSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 IGDELYLEPLEDGLSLR 17 0 Q99638;F5H492;F5H4F1 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 0 ;; 168.59 4.84E-09 39559000 48024 44592 46721 52283 49850 50844 51983 53119 54753 57713 FALSE TRUE 46147.16899 43320.27982 55164.524 54981.3319 51453.47052 51872.10052 52619.1835 52022.07409 48537.66898 53804.0471 0.857689551 0.805149095 1.025285773 1.021880971 0.956312272 0.964092913 0.97797817 0.966880316 0.902119294 1 15.71542707 4.244233391 24.99996146 0.975670113 0.831419277 0.729000264 0.035454818 66.87379883 294704.7738 0.008789561 0.022723481 17548.23295 -4.244233391 -0.144250836 DSDLMEAFHCNQTQVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDLMEAFHCNQTQVNR 17 0 O60671-2;O60671 O60671-2 RAD1 Cell cycle checkpoint protein RAD1 0 ; 209.67 4.06E-12 694100000 218386 196578 193499 216060 199758 200070 223613 222435 224171 238196 FALSE TRUE 209851.2337 190971.7879 228468.5737 227210.8825 206183.3975 204115.5525 226349.6428 217841.6395 198724.0479 222062.7728 0.945008617 0.859990108 1.028846802 1.023183128 0.928491502 0.919179518 1.019304767 0.980991261 0.894900327 1 17.76060803 4.244286908 24.99998374 0.974566046 0.902499374 0.263023271 0.048115476 180.4369259 787732.7605 0.011786071 0.030465313 17550.39549 -4.244286908 -0.072066672 ELASQPDVDGFLVGGASLKPEFVDIINAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELASQPDVDGFLVGGASLKPEFVDIINAK 29 1 P60174;P60174-3;P60174-4 P60174 TPI1 Triosephosphate isomerase 0 116.34 0.00014899 131310000 163020 153570 99110 101600 107180 102010 96944 125940 142060 118630 FALSE TRUE 156648.9982 149190.334 117021.3817 106843.5882 110627.542 104072.7121 98130.42967 123339.295 125933.9444 110595.0844 1.416419174 1.348977983 1.058106536 0.966078996 1.000293481 0.941024754 0.887294677 1.115233065 1.138693867 1 16.75492774 4.244294824 3.411335096 1.007665517 1.404373011 0.817279755 0.070543905 0.094573247 2.271409039 0.01951126 0.056688283 17550.71542 -4.244294824 0.396707494 NSSTYWEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 NSSTYWEGK 9 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 160.75 0.00015134 1331980000 1371680 1373740 877101 892800 995290 1239180 1039270 1173610 1239840 1144600 FALSE TRUE 1318073.229 1334562.28 1035612.662 938877.515 1027304.407 1264237.069 1051988.897 1149374.543 1099098.561 1067075.222 1.235220537 1.250673104 0.970515143 0.879860665 0.962729136 1.184768461 0.985861985 1.077126072 1.030010385 1 20.02523045 4.244343982 24.99991493 1.015719394 1.242946933 0.59994737 0.075577485 96.46156312 416965.0234 0.019694936 0.050943126 17552.7021 -4.244343982 0.227227539 S(ph)LEGLNQELEEVFVKEQGEEELLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLEGLNQELEEVFVKEQGEEELLR 24 1 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 S(1)LEGLNQELEEVFVKEQGEEELLR;S(1)LEGLNQELEEVFVKEQGEEELLR;S(1)LEGLNQELEEVFVKEQGEEELLR 122.09 7.43E-05 116329000 48826 53747 25284.8 27609.6 36588 47248 31448.8 35988.2 38983 30851.8 TRUE FALSE 46917.82594 52214.18818 29854.32582 29034.53476 37764.88625 48203.38693 31833.67982 35245.03109 34557.81327 28762.18011 1.631233299 1.815376581 1.03797159 1.009469194 1.313004999 1.675929528 1.106789531 1.225394979 1.201501873 1 14.81188541 4.244374325 24.99907625 1.214408677 1.723305102 0.543794411 0.192522173 107.024856 460195.9544 0.048639083 0.125890992 17553.9285 -4.244374325 0.508896425 LSTQVKPLIWIESVIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSTQVKPLIWIESVIEK 17 1 Q9Y6Q5;K7EJJ1;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 141.86 5.55E-07 102590000 288780 288620 206230 184320 259520 299540 247740 242180 273160 286540 FALSE TRUE 277494.1583 280388.8402 243500.3486 193832.7773 267867.6965 305596.904 250771.9162 237178.8984 242152.022 267132.3906 1.038788886 1.049625018 0.911534345 0.72560567 1.00275259 1.143990451 0.938755183 0.887870235 0.906486935 1 18.02719539 4.244420126 24.78258308 0.935038108 1.044207009 0.14772408 0.099996632 242.5328521 1025750.264 0.02624812 0.067962926 17555.77985 -4.244420126 0.109168901 S(ph)PVVELSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPVVELSK 8 0 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 1 S(1)PVVELSK;S(1)PVVELSK;S(0.995)PVVELS(0.005)K;S(0.999)PVVELS(0.001)K 104.22 0.0048482 1363110000 2161820 2187800 2321010 2692500 2533600 2368400 2483400 2921470 2918590 3018900 TRUE FALSE 2077333.684 2125406.086 2740468.138 2831460.248 2615095.545 2416290.671 2513792.592 2861140.624 2587283.899 2814427.214 0.738101762 0.755182467 0.973721446 1.006052043 0.929175049 0.858537275 0.893180886 1.016597839 0.919293235 1 21.42440991 4.244445824 24.63589191 0.948823459 0.746641969 0.734955872 0.048743296 59.43147862 248775.5475 0.012754106 0.033007288 17556.81867 -4.244445824 -0.202181491 RDS(ph)LTGSSDLYKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSLTGSSDLYKR 13 2 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(1)LTGSSDLYKR;RDS(1)LTGSSDLYKR 125.5 0.00010407 1028300000 596590 591650 391900 387320 472060 529710 438500 496360 601640 526640 TRUE FALSE 573274.6032 574776.7213 462725.0478 407309.6316 487244.2386 540421.0991 443866.4942 486109.9925 533344.3495 490970.2037 1.167636241 1.17069573 0.942470733 0.829601529 0.992411016 1.100720767 0.904059943 0.990100802 1.08630696 1 18.90527595 4.244455134 24.976353 0.976369679 1.169166089 0.500874716 0.075151232 110.2556142 467163.3998 0.018945332 0.049073346 17557.19504 -4.244455134 0.192796411 DTSSS(ph)PTTGSTVQSVDLIFTR ddPTM_BT-474_Pertuzumab_2h_R1 5 DTSSSPTTGSTVQSVDLIFTR 21 0 P57060 P57060 RWDD2B RWD domain-containing protein 2B 1 DT(0.024)S(0.024)S(0.169)S(0.775)PT(0.007)T(0.001)GSTVQSVDLIFTR;DTSS(0.017)S(0.979)PT(0.004)TGSTVQSVDLIFTR;DTS(0.002)S(0.022)S(0.909)PT(0.068)TGSTVQSVDLIFTR;DTSS(0.049)S(0.95)PT(0.001)TGSTVQSVDLIFTR;DTS(0.006)S(0.022)S(0.971)PT(0.001)TGSTVQSVDLIFTR 351.96 2.19E-95 515890000 421217 415571 407300 450565 451986 490697 440087 470662 521036 510019 TRUE FALSE 404755.374 403719.322 480908.1703 473818.7136 466524.5402 500619.2295 445472.9164 460942.6652 461890.1776 475474.9589 0.851265385 0.849086402 1.011426914 0.996516651 0.981175836 1.052882429 0.936900899 0.969436259 0.971429029 1 18.85900984 4.244455437 24.99995228 0.987294035 0.850175821 0.790319449 0.028776049 60.03517243 254602.048 0.007256198 0.018800779 17557.20732 -4.244455437 -0.137118214 DETEFYLGKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DETEFYLGKR 10 1 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ; 148.32 4.06E-05 999740000 1556120 1638610 788890 740400 1176450 1348040 983020 1093320 1252990 999400 FALSE TRUE 1495305.11 1591878.447 931459.9718 778612.1327 1214291.583 1375298.292 995050.4928 1070742.56 1110755.828 931709.7478 1.604904439 1.70855618 0.999731916 0.835680999 1.303293848 1.476101646 1.067983345 1.14922331 1.192169375 1 19.82952106 4.244465717 24.99998685 1.138755427 1.656730527 0.610587607 0.168716753 95.70619539 405172.6075 0.043666077 0.113143893 17557.6229 -4.244465717 0.5179751 GRPPAQALGPAAS(ph)PPPS(ph)PPLGPSLG ddPTM_BT-474_Pertuzumab_2h_R1 1 GRPPAQALGPAASPPPSPPLGPSLG 25 1 H7C0J3;H7C3H7 H7C0J3 CHD3 2 GRPPAQALGPAAS(1)PPPS(1)PPLGPSLG 61.345 0.038668 179800000 71723 72034 72786 84129 96849 88790 77242 87519 86829 79318 TRUE FALSE 68919.98587 69979.66085 85940.04932 88470.90777 99964.23604 90585.39463 78187.3107 85711.70207 76972.53594 73945.72121 0.932034805 0.946365249 1.162204491 1.196430386 1.35185964 1.225025507 1.057360851 1.159116453 1.040932926 1 16.17417905 4.244465976 7.199311348 1.161433265 0.937526322 0.427027053 0.096445556 0.112984601 32.64583584 0.024531296 0.061451138 17557.63336 -4.244465976 -0.223906943 AMKEYEEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 AMKEYEEEER 10 1 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 132.32 0.00020674 922570000 1806190 1857930 1026920 1026840 1363360 1685270 1231080 1348010 1512910 1246680 FALSE TRUE 1735602.098 1804943.656 1212507.288 1079835.335 1407213.713 1719347.314 1246146.325 1320173.122 1341170.799 1162241.253 1.493323433 1.552985364 1.043249226 0.929097408 1.210775911 1.47933771 1.072192475 1.135885617 1.153952156 1 20.14847814 4.244484036 24.96514372 1.138022835 1.523154574 0.554723891 0.141365782 105.4514129 444427.8131 0.036293964 0.094043956 17558.36349 -4.244484036 0.385131738 SAGGSSPEGGEDS(ph)DREDGNYCPPVKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 1 SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR 213.37 1.63E-26 869970000 370770 378690 246155 270580 289480 342980 292200 314450 350680 330630 TRUE FALSE 356279.8985 367890.132 290640.6842 284544.6662 298791.3871 349915.2906 295776.031 307956.4976 310872.2766 308236.1356 1.155866744 1.193533429 0.942915676 0.923138573 0.969358724 1.135218263 0.959576107 0.99909278 1.008552342 1 18.23367648 4.244507034 24.99968205 0.992612299 1.174700162 0.637240919 0.055068146 87.54935586 368061.0113 0.013937236 0.036123724 17559.29332 -4.244507034 0.182087864 S(ph)RTPSLPTPPTREPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTPSLPTPPTREPK 15 2 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 S(0.594)RT(0.405)PS(0.001)LPTPPTREPK 84.566 0.0043197 229730000 239810 235070 134320 115250 145960 208150 147700 189010 243730 153030 TRUE FALSE 230437.9601 228366.0338 158594.6119 121198.0663 150654.936 212358.9356 149507.5968 185106.8774 216062.7922 142665.1418 1.615236611 1.600713607 1.111656358 0.849528236 1.056003829 1.488513122 1.047961646 1.297491981 1.514475011 1 17.12227335 4.244527492 24.71387898 1.176886928 1.607975392 0.433328653 0.199917446 115.9792458 480352.1345 0.050438189 0.130655155 17560.12052 -4.244527492 0.431088464 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_BT-474_Pertuzumab_2h_R1 1 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTASPHSNR 40 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPT(0.085)AS(0.86)PHS(0.055)NR 121.58 9.87E-09 354320000 254120 269960 160280 182400 192390 265370 196180 189490 251990 210640 TRUE FALSE 244188.7095 262261.0051 189246.1614 191813.6859 198578.3991 270735.9632 198580.9095 185576.9653 223385.1516 196373.1652 1.243493271 1.335523644 0.963706835 0.976781556 1.011229813 1.378681058 1.011242597 0.94502202 1.137554367 1 17.58323827 4.244569212 24.99868799 1.050625533 1.289508532 0.374707935 0.122162919 150.3700618 625595.2079 0.031112708 0.080697998 17561.80749 -4.244569212 0.238882998 ISMPDVDLHLKGPNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISMPDVDLHLKGPNVK 16 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 183.6 1.18E-09 134960000 314710 335850 205220 228590 225930 352750 251940 247460 319170 268570 FALSE TRUE 302410.7853 326271.8868 242307.8191 240387.5573 233197.2436 359882.8467 255023.3171 242349.8645 282939.1597 250379.5147 1.207809615 1.303109351 0.967762157 0.960092752 0.931375092 1.437349406 1.018547054 0.967930083 1.13004117 1 17.933757 4.24457286 24.9999111 1.050525203 1.255459537 0.249306355 0.14146331 198.7199737 826287.1528 0.035357868 0.091697818 17561.95502 -4.24457286 0.204934333 ACTGLSGPGSGSKS(ph)PPATR ddPTM_BT-474_Pertuzumab_2h_R1 2 ACTGLSGPGSGSKSPPATR 19 1 I3L2J0;I3L2I4 I3L2J0 CIC 1 ACTGLSGPGSGS(0.025)KS(0.974)PPATR;ACTGLSGPGSGS(0.046)KS(0.954)PPATR 157.3 4.47E-09 819650000 910940 948050 462800 495110 684100 827730 587940 607650 624970 530440 TRUE FALSE 875339.4577 921012.5422 546438.2549 520662.6864 706104.6978 844467.2677 595135.3856 595101.8152 554026.0257 494512.8263 1.770104659 1.862464416 1.105003199 1.052880044 1.42787944 1.707675156 1.203478159 1.203410273 1.12034713 1 18.91564842 4.244598035 24.99834015 1.248806582 1.81628479 0.586452202 0.197099336 103.9185784 430269.7639 0.050952935 0.132193691 17562.97306 -4.244598035 0.567478208 RPSGRS(ph)PTSTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSGRSPTSTEK 12 2 A1L390-3;A1L390;A1L390-2;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RPS(0.117)GRS(0.754)PT(0.064)S(0.064)T(0.001)EK 97.223 0.0039712 39085000 44998 50448 20001 19860 32630 43141 31163 27037 31876 23809 TRUE FALSE 43239.42841 49009.27243 23615.62562 20884.97698 33679.57358 44013.34058 31544.38212 26478.6765 28257.57012 22196.39522 1.948038318 2.207983411 1.06393968 0.940917513 1.517344292 1.982904888 1.421148876 1.19292688 1.273070236 1 14.43803778 4.244637661 24.99993367 1.324398798 2.078011117 0.53068725 0.292242375 118.5968624 487873.7682 0.076846744 0.19944736 17564.57559 -4.244637661 0.753612318 ELIFEETAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELIFEETAR 9 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 164.96 0.00014393 219625000 187994 203827 181099 237718 228850 203815 219631 255300 229230 249400 FALSE TRUE 180646.9866 198014.0535 213827.6178 249986.6545 236211.1681 207936.2789 222318.9099 250027.9658 203208.7714 232507.9159 0.776949834 0.851644353 0.919657368 1.075174811 1.015927424 0.894319138 0.95617781 1.075352488 0.873986465 1 17.82692031 4.244641064 2.350228212 0.988781137 0.791065029 0.531837877 0.063935964 0.228723068 2.444776007 0.01687935 0.060788809 17564.71325 -4.244641064 -0.197716107 AIEALKEFNEDGALAVLQQFK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIEALKEFNEDGALAVLQQFK 21 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 308.59 1.65E-66 1553210000 2206900 2149100 1431800 1286100 1685890 2140900 1616050 1841440 2039500 1698220 FALSE TRUE 2120651.908 2087809.772 1690558.11 1352475.775 1740118.183 2184190.465 1635827.703 1803413.62 1807984.51 1583198.047 1.33947355 1.318729376 1.06781215 0.854268219 1.099115923 1.379606594 1.033242623 1.139095405 1.14198253 1 20.59441031 4.244651416 23.71077796 1.09586544 1.329101743 0.368472875 0.125299 83.43687209 324791.3628 0.031895972 0.082524442 17565.13194 -4.244651416 0.233236304 AIKVEQATKPSFESGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIKVEQATKPSFESGR 16 2 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ; 209.25 7.17E-12 5284100000 8839500 8962300 5319800 5239000 6599900 8424500 6374000 6963900 7665400 6444900 FALSE TRUE 8494042.567 8706703.979 6281206.198 5509385.418 6812191.777 8594849.162 6452006.919 6820093.031 6795255.928 6008381.182 1.413699016 1.449093144 1.045407408 0.916950049 1.133781558 1.430476679 1.073834486 1.135096597 1.130962854 1 22.51854491 4.244669991 24.96605518 1.117641007 1.431396233 0.508915554 0.126683954 119.1379979 486845.5332 0.032484949 0.084336097 17565.88322 -4.244669991 0.313755225 LSPS(ph)PTTEDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSPSPTTEDPR 11 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 LSPS(0.909)PT(0.076)T(0.016)EDPR;LSPS(0.971)PT(0.023)T(0.005)EDPR 165.58 2.25E-05 1684550000 838260 847400 803850 1023560 860210 922170 953160 987830 940400 1117530 TRUE FALSE 805499.8725 823232.9817 949123.5765 1076386.054 887879.4359 940816.9092 964825.0572 967430.9653 833649.7345 1041838.698 0.773152192 0.790173165 0.911008181 1.033159986 0.852223514 0.903035097 0.926079113 0.928580372 0.800171597 1 19.9907005 4.244794103 5.286145046 0.919173726 0.778715267 0.441011627 0.062141028 0.141802408 11.73736649 0.014849862 0.038364872 17570.90387 -4.244794103 -0.140458459 GVMAVTAVTATAAS(ph)DR ddPTM_BT-474_Pertuzumab_2h_R1 5 GVMAVTAVTATAASDR 16 0 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 GVMAVTAVTAT(0.008)AAS(0.992)DR;GVMAVTAVTATAAS(1)DR;GVMAVTAVTATAAS(1)DR;GVMAVTAVTATAAS(1)DR;GVMAVTAVTATAAS(1)DR 338.91 6.97E-72 1063266000 717911 729864 978442 1205762 886571 927929 1142213 1169318 1126089 1264788 TRUE FALSE 689854.2444 709048.9933 1155268.235 1267991.521 915088.3614 946692.3602 1156191.744 1145171.175 998260.0977 1179122.782 0.585057175 0.601336014 0.979769242 1.07536852 0.77607555 0.802878525 0.98055246 0.971206046 0.84661251 1 20.16928252 4.244816349 24.9380186 0.928351839 0.593196393 0.693679589 0.089273713 78.58788449 313275.8792 0.022794033 0.059247196 17571.80394 -4.244816349 -0.335155446 RRKEDEVEEWQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 RRKEDEVEEWQHR 13 3 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 235.73 6.45E-17 628530000 369610 388570 184598 196089 201366 357100 229655 284230 265180 239969 FALSE TRUE 355165.2326 377488.364 217958.965 206209.1768 207843.1203 364320.8067 232465.5866 278360.5512 235077.8781 223715.6859 1.587574117 1.687357605 0.974267692 0.921746618 0.929050278 1.628499161 1.0391117 1.244260321 1.050788536 1 17.77130689 4.244830116 24.99977307 1.117059569 1.637466086 0.535512571 0.200195874 114.0426268 454735.1471 0.049720536 0.12925887 17572.36096 -4.244830116 0.520406518 EIEQVYR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIEQVYR 7 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 0 101.41 0.02112 108730000 100440 98373 96924 120210 109440 98983 115520 102760 120080 125340 FALSE TRUE 96514.69376 95567.49836 114440.3229 126414.0525 112960.237 100984.5041 116933.7683 100637.9701 106449.0218 116850.6102 0.825966536 0.817860499 0.979372916 1.081843324 0.966706437 0.864218885 1.000711662 0.86125327 0.910983877 1 16.83430574 4.244834789 24.9915346 0.952074683 0.821913451 0.422689553 0.063364074 152.0147459 605494.7721 0.016635092 0.043256436 17572.55004 -4.244834789 -0.130161232 LVGEFLEVTCINPTFICDHPQIMSPLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVGEFLEVTCINPTFICDHPQIMSPLAK 28 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 65.155 0.014761 37649000 18157 13520 19687 21315 19060 19971 16946 21462 20490 21111 FALSE TRUE 17447.40437 13134.42284 23244.87883 22415.0697 19673.08221 20374.8273 17153.39022 21018.8022 18164.0611 19681.13317 0.886504055 0.667361108 1.181074211 1.138911541 0.99959093 1.035246656 0.871565172 1.067967074 0.922917443 1 14.26452567 4.244850595 24.99999468 1.026761124 0.776932578 0.504238311 0.099245055 115.2555244 458079.1786 0.024044357 0.062511218 17573.18962 -4.244850595 -0.249828546 T(ph)TSGDDACNLTSFRPATLTVTNFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSGDDACNLTSFRPATLTVTNFFK 25 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0U1RQT6 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 T(0.333)T(0.333)S(0.333)GDDACNLTSFRPATLTVTNFFK 62.683 0.096137 145570000 101310 122200 79661 83732 108060 123860 98023 111260 130180 96131 TRUE FALSE 97350.6932 118714.9756 94057.51475 88053.41855 111535.848 126364.5341 99222.6348 108962.4421 115402.5122 89619.96175 1.086261267 1.32464881 1.04951523 0.982520153 1.244542464 1.410004329 1.107148819 1.215827813 1.287687586 1 16.45153249 4.244867635 24.99874177 1.174303299 1.205454906 0.009448143 0.138104065 1307.9792 5184194.196 0.034041169 0.088673145 17573.87911 -4.244867635 0.031151607 ESVPEFPLS(ph)PPKKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESVPEFPLSPPKKK 14 2 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 ESVPEFPLS(1)PPKKK 110.22 0.00037697 1026100000 4916800 4690700 2413200 1856700 3227000 4342800 2986600 3023900 3290200 2584700 TRUE FALSE 4724646.02 4556925.829 2849318.921 1952524.51 3330799.386 4430614.391 3023150.904 2961455.408 2916710.29 2409635.967 1.960730204 1.89112625 1.182468622 0.810298542 1.382283229 1.838706947 1.254608972 1.229005314 1.21043607 1 21.20038378 4.244932225 22.47657193 1.256971223 1.925929833 0.544368306 0.251116798 33.30983498 117491.3353 0.065098843 0.168354144 17576.49297 -4.244932225 0.668958611 TLQRLSS(ph)GFDDIDLPSAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 T(0.006)LQRLS(0.408)S(0.586)GFDDIDLPSAVK;T(0.002)LQRLS(0.109)S(0.889)GFDDIDLPSAVK 155.39 1.60E-08 382710000 960010 942220 487890 484460 689890 866830 576670 588880 654340 579260 TRUE FALSE 922491.7479 915348.8081 576062.5761 509463.0387 712080.9384 884357.8965 583727.46 576719.4222 580062.0664 540026.2042 1.708235157 1.695008133 1.066730784 0.943404292 1.318604417 1.637620341 1.080924324 1.067947106 1.074136888 1 19.04266989 4.244939477 24.98135731 1.158632916 1.701621958 0.578101915 0.18879705 109.7096814 429641.196 0.049667572 0.12923723 17576.7865 -4.244939477 0.542989042 ERS(ph)PALKSPLQSVVVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(0.998)PALKSPLQS(0.002)VVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR 168.84 3.04E-09 11608110000 6893350 7182550 3649710 3774580 5046630 6398920 4397440 4969450 5519900 4303050 TRUE FALSE 6623950.261 6977710.706 4309293.784 3969386.526 5208959.437 6528310.547 4451257.186 4866829.121 4893304.093 4011600.591 1.651198845 1.739383208 1.074208084 0.989477002 1.298474093 1.627358058 1.109596303 1.213188853 1.219788457 1 21.93574654 4.244942952 24.98735773 1.206964935 1.695291244 0.568761463 0.175053251 109.4291922 428412.4405 0.044362569 0.115445432 17576.92713 -4.244942952 0.488326309 GKT(ph)PEEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKTPEEIR 8 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 1 GKT(1)PEEIR;GKT(1)PEEIR 100.82 0.0094309 618720000 1067190 1047920 925380 1000030 1079010 1006870 1027330 1201770 1175730 1087470 TRUE FALSE 1025483.035 1018034.348 1092616.751 1051641.668 1113717.337 1027229.601 1039902.772 1176953.03 1042266.059 1013814.688 1.011509349 1.00416216 1.077728271 1.037311533 1.098541331 1.013232115 1.025732596 1.160915346 1.02806368 1 19.95136254 4.245003727 24.92924823 1.063818229 1.007835727 0.125157499 0.045735386 240.9994417 932431.8008 0.011419436 0.02966145 17579.38701 -4.245003727 -0.055982502 SAPTAPT(ph)PPPPPPPATPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAPTAPTPPPPPPPATPR 18 0 A6NHN7;A6NHB5;Q14202-2;Q14202 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 SAPT(0.007)APT(0.993)PPPPPPPATPR;SAPTAPT(1)PPPPPPPATPR 226 4.19E-18 405630000 442920 450690 398040 468530 439220 479220 500370 478920 517070 539120 TRUE FALSE 425610.1967 437836.7625 469974.6824 492710.8894 453347.9102 488910.1567 506493.6777 469030.1346 458374.3813 502604.9222 0.846808652 0.871135047 0.935077755 0.980314493 0.901996559 0.972752425 1.007737201 0.933198451 0.911997398 1 18.93906527 4.245022882 2.792998302 0.955816827 0.850500058 0.587080336 0.033054439 0.182138678 2.818291892 0.008440664 0.027111602 17580.16239 -4.245022882 -0.105316769 SVVSDLEADDVKGSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 SVVSDLEADDVKGSVPLS(0.065)S(0.466)S(0.466)PPAT(0.003)HFPDETEITNPVPK 208.35 5.66E-31 1909500000 386000 413060 188950 207200 255700 355610 247180 249350 321250 250500 TRUE FALSE 370914.6933 401279.9332 223097.4682 217893.6168 263924.8227 362800.6778 250205.0628 244200.8354 284783.0468 233533.4119 1.588272489 1.718297737 0.955312845 0.933029733 1.130137314 1.55352793 1.071388718 1.045678361 1.219453116 1 17.83326945 4.245035236 24.99765488 1.118785258 1.653285329 0.615802271 0.170483704 100.2468206 387029.2154 0.043795129 0.114056355 17580.66248 -4.245035236 0.534500071 AT(ph)PPPS(ph)PLLSELLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATPPPSPLLSELLK 14 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128 BRD8 Bromodomain-containing protein 8 2 AT(1)PPPS(1)PLLSELLK 102.52 0.006202 113500000 150790 147050 136410 149470 169310 150940 151780 163970 164690 153180 TRUE FALSE 144896.9601 142856.278 161062.3214 157184.1646 174756.0099 153992.1102 153637.529 160583.9622 145995.0816 142804.9822 1.014649194 1.000359202 1.127848055 1.100691042 1.223738887 1.0783385 1.075855525 1.124498318 1.022338853 1 17.12368679 4.245112725 24.99194209 1.10292417 1.007504154 0.249950184 0.058493144 177.3858361 676590.9346 0.013746989 0.035814292 17583.79956 -4.245112725 -0.095420016 DVDFELIKVEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVDFELIKVEGK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 129.71 0.00020927 203000000 350880 347790 177180 156600 243950 316890 220390 208540 291020 220600 FALSE TRUE 337167.2217 337871.3697 209200.3673 164682.1448 251796.8733 323297.7329 223087.1987 204233.5761 257984.6297 205658.5655 1.639451393 1.642875262 1.017221757 0.800755098 1.224344207 1.572012 1.084745477 0.993071091 1.254431728 1 17.64989163 4.245242735 24.98320162 1.118221703 1.641163623 0.536746338 0.194291655 121.1700767 453020.4491 0.050824767 0.132616395 17589.06422 -4.245242735 0.522941921 GLLGLPEEETELDNLTEFNTAHNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLLGLPEEETELDNLTEFNTAHNK 24 0 Q12972;A0A0A0MT09;Q12972-2 Q12972 PPP1R8 Nuclear inhibitor of protein phosphatase 1;Activator of RNA decay 0 203.64 1.17E-24 64873000 33917 33134 36917 40698 38198 34296 42149 43413 48841 50051 FALSE TRUE 32591.48614 32189.05076 43588.72311 42798.42866 39426.67336 34989.48862 42664.83207 42516.50638 43296.77444 46661.00119 0.698473786 0.689849123 0.934157476 0.917220539 0.844959867 0.749865792 0.914357407 0.911178614 0.927900674 1 15.50992964 4.245286884 24.99855553 0.892015001 0.694161348 0.634853769 0.062196517 99.84074907 371054.0782 0.015627564 0.040791958 17590.85236 -4.245286884 -0.197853653 LQAKES(ph)PQRK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQAKESPQRK 10 2 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 LQAKES(1)PQRK 82.069 0.0099761 262700000 281570 303530 157510 150010 201610 284090 190580 207360 290970 221270 TRUE FALSE 270565.9331 294873.6216 185975.5608 157752.0341 208094.9687 289834.4944 192912.375 203077.9435 257940.3054 206283.1858 1.311623786 1.429460285 0.901554628 0.7647353 1.008782989 1.405032084 0.935182256 0.984461931 1.250418469 1 17.65426671 4.24530439 24.99776091 1.026432714 1.370542155 0.383605107 0.171938482 160.5833024 595233.2222 0.043626458 0.113926321 17591.56148 -4.24530439 0.344109441 TLEDPDLNVR ddPTM_BT-474_Pertuzumab_2h_R1 3 TLEDPDLNVR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 196.88 0.004696 821530000 682080 673690 634210 711280 696920 767730 737600 719380 779820 771740 FALSE TRUE 655423.5595 654477.0208 748825.8549 747989.246 719337.0647 783254.0266 746626.9694 704524.5516 691298.1029 719469.3624 0.91098189 0.909666283 1.040802978 1.039640164 0.999816118 1.08865515 1.037746718 0.979228009 0.960844393 1 19.45657373 4.245370043 24.99394861 1.019100072 0.910324025 0.612664559 0.034350511 105.7782556 388248.1698 0.009009757 0.023559355 17594.221 -4.245370043 -0.108776047 VTDKLTPIHDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTDKLTPIHDR 11 1 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;; 219.29 6.00E-12 2126530000 4555640 4992840 2789590 3110770 3756800 4624920 3515170 3638830 4309390 3631850 FALSE TRUE 4377600.552 4850449.092 3293730.967 3271317.212 3877640.884 4718439.051 3558189.702 3563686.889 3820206.114 3385861.565 1.292905947 1.432559778 0.972789615 0.966169806 1.145244958 1.393571167 1.050896392 1.052519963 1.128281839 1 21.69109156 4.245399178 24.99977664 1.094701718 1.362732926 0.449505089 0.121163745 148.9185521 544388.4774 0.031121072 0.081324812 17595.40136 -4.245399178 0.268031208 SSFVSDNSLNRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSFVSDNSLNRSPR 14 1 Q6UB98-2;Q6UB98 Q6UB98-2 ANKRD12 Ankyrin repeat domain-containing protein 12 1 SSFVSDNS(0.015)LNRS(0.985)PR;SSFVSDNS(0.03)LNRS(0.97)PR;SSFVSDNS(0.001)LNRS(0.999)PR 100.58 0.001047 1471070000 2113930 2117430 1469950 1858010 1669960 1646960 1780340 1916190 2096470 1747340 TRUE FALSE 2031315.279 2057042.97 1735602.664 1953902.119 1723675.78 1680262.66 1802128.333 1876620.007 1858487.515 1628991.105 1.246977514 1.262771149 1.065446372 1.199455364 1.058124734 1.031474422 1.106284944 1.152013661 1.140882543 1 20.6355473 4.245429247 24.99993695 1.102985405 1.254874408 0.556499605 0.056941643 117.4700743 427547.8632 0.01385156 0.036211001 17596.61963 -4.245429247 0.151889003 DINAYNCEEPTEKLPFPIIDDR ddPTM_BT-474_Pertuzumab_2h_R1 6 DINAYNCEEPTEKLPFPIIDDR 22 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;; 250.06 1.58E-31 8212430000 3752450 3776340 2318940 2376520 2927490 3544840 2764220 2950540 3372310 2745110 FALSE TRUE 3605800.105 3668642.481 2738024.043 2499172.482 3021655.375 3616519.094 2798049.351 2889610.318 2989499.507 2559181.255 1.408966285 1.433521941 1.069882814 0.976551574 1.180711749 1.413154729 1.093337702 1.129115147 1.168146844 1 21.2872509 4.245429368 25 1.137530467 1.421244259 0.510643769 0.114237081 131.5540634 478801.28 0.02905475 0.075942194 17596.62456 -4.245429368 0.283713792 IPGTPGAGGRLS(ph)PENNQVLTK ddPTM_BT-474_Pertuzumab_2h_R1 4 IPGTPGAGGRLSPENNQVLTK 21 1 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 IPGT(0.297)PGAGGRLS(0.703)PENNQVLTK;IPGT(0.006)PGAGGRLS(0.994)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK 175.46 1.02E-12 3570200000 2388230 2434330 1644187 1768130 2111020 2330600 1907800 2093630 2184820 2019140 TRUE FALSE 2294895.331 2364905.292 1941328.166 1859383.401 2178922.875 2377726.329 1931148.227 2050395.809 1936808.393 1882381.849 1.219144422 1.256336642 1.03131475 0.987782262 1.157535001 1.263147713 1.02590674 1.089256045 1.028913657 1 20.84412788 4.245471256 25 1.080734455 1.237740598 0.404514989 0.079516748 166.1285038 600972.3213 0.020191055 0.05277847 17598.32186 -4.245471256 0.157006143 CGLGQENSDNEHLVENEVSLLLEESDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 CGLGQENSDNEHLVENEVSLLLEESDLR 28 0 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 0 ; 87.489 0.0034841 26429000 14019 13968.1 13775.1 16495.1 15637.3 14346.1 14338.5 17097 18085.6 15517.8 FALSE TRUE 13471.12198 13569.74346 16264.567 17346.41409 16140.28796 14636.18797 14513.97885 16743.94098 16032.59851 14466.76558 0.93117718 0.937994287 1.124271137 1.199052683 1.115680479 1.011711145 1.003263568 1.157407361 1.108236559 1 13.82045479 4.245490966 24.80045008 1.096124231 0.934585625 0.485028922 0.063783284 119.0442925 425991.2885 0.016425144 0.042938432 17599.12055 -4.245490966 -0.161538605 ALLDSQFSYQHAIEESVVLIYDPIK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALLDSQFSYQHAIEESVVLIYDPIK 25 0 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;; 220.49 1.23E-33 639037000 614500 597565 566553 534489 640768 748266 608958 647134 717990 753964 FALSE TRUE 590484.6606 580523.0313 668941.73 562074.0413 661378.8847 763396.4512 616410.6102 633770.4568 636486.7853 702897.3467 0.840072399 0.82590016 0.951691926 0.799653099 0.940932396 1.086071038 0.876956803 0.901654359 0.905518833 1 19.42295448 4.245558668 24.96252413 0.926122101 0.832986236 0.232499302 0.071728655 245.7412854 876553.3607 0.017852378 0.046734987 17601.86427 -4.245558668 -0.093135865 ETDLQELFR ddPTM_BT-474_Pertuzumab_2h_R1 3 ETDLQELFR 9 0 O75821;K7ENA8;K7ER90;K7EL20;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;; 128.36 0.00097595 195757000 139719 149895 167638 210867 185885 172684 212935 215224 219406 261958 FALSE TRUE 134258.627 145620.1414 197933.9157 221749.8711 191864.1598 176175.7888 215540.9622 210779.5492 194499.9507 244215.3513 0.549755068 0.596277591 0.810489245 0.908009549 0.785635132 0.721395227 0.88258564 0.86308886 0.796428028 1 17.89779437 4.245624867 3.801473399 0.842142836 0.560224047 0.701941543 0.071674057 0.109567557 3.408816145 0.017483776 0.048898647 17604.54753 -4.245624867 -0.281918789 QQAS(ph)KSPYNGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQASKSPYNGVR 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 QQAS(0.623)KS(0.377)PYNGVR 91.812 0.0048977 453500000 340470 325320 218870 219690 251830 258620 228640 279740 292630 232590 TRUE FALSE 327164.056 316042.1921 258424.6777 231028.2272 259930.3407 263849.4736 231438.1647 273963.2712 259411.8692 216836.4721 1.508805473 1.457513992 1.191795251 1.065449115 1.198739023 1.216813163 1.067339652 1.263455675 1.196347951 1 17.72624791 4.245628568 4.10444294 1.159198798 1.496194782 0.749201325 0.077422198 0.092110052 3.495572329 0.018675733 0.051021388 17604.69755 -4.245628568 0.336995984 ALIQTCLNSPDS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALIQTCLNSPDSPPR 15 0 P11831 P11831 SRF Serum response factor 1 ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR 319.11 1.85E-56 3086010000 762799 771691 833583 1051480 957170 919488 912757 1014610 995543 1028280 TRUE FALSE 732987.9718 749683.1282 984229.9911 1105747.009 987958.2423 938080.6774 923927.5932 993657.9489 882533.1323 958633.6797 0.764617379 0.782032954 1.026700826 1.153461465 1.030589957 0.978560108 0.9637963 1.036535613 0.920615613 1 19.8706201 4.245631969 9.538759286 1.017741363 0.772762418 0.734714379 0.057757773 0.06846663 63.65141009 0.014887967 0.037322891 17604.8354 -4.245631969 -0.244978945 KKLGVSVS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KKLGVSVSPSR 11 2 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 KKLGVS(0.008)VS(0.897)PS(0.095)R 60.631 0.07279 362390000 492480 555840 241770 251310 308420 546400 346050 342060 394450 334230 TRUE FALSE 473233.3371 539987.9874 285463.2171 264280.1392 318340.6094 557448.5824 350285.0634 334996.3415 349673.6897 311592.3044 1.518758103 1.732995263 0.916143349 0.848160033 1.021657483 1.789031932 1.124177518 1.075111088 1.122215423 1 18.24930008 4.245637337 24.99992532 1.124079457 1.625876833 0.407393399 0.247541353 167.053932 590136.2913 0.063706438 0.166824431 17605.053 -4.245637337 0.501797375 S(ph)SPSKCPSLDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPSKCPSLDDR 12 1 P38398-7;P38398;P38398-4;P38398-8;P38398-6;E7EUM2;B7ZA85;H0Y8B8;P38398-5;P38398-3;A0A2R8Y7V5 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 S(0.583)S(0.417)PSKCPSLDDR;S(0.874)S(0.126)PSKCPSLDDR 125.22 0.00018723 676090000 967490 959470 567030 605560 733180 723880 711180 782720 792260 713200 TRUE FALSE 929679.4212 932106.855 669504.9345 636813.0242 756763.4006 738517.3496 719883.6336 766556.5585 702325.9662 664894.3287 1.398236353 1.401887209 1.006934344 0.957765763 1.138170936 1.110728905 1.082703826 1.15289983 1.056297123 1 19.34276555 4.245649544 24.99999963 1.074315765 1.400061967 0.835218947 0.05968884 63.2944439 223210.1846 0.015658273 0.040995283 17605.54784 -4.245649544 0.325746201 RT(ph)NSSSSSPVVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTNSSSSSPVVLK 13 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 RT(0.454)NS(0.454)S(0.053)S(0.014)S(0.02)S(0.005)PVVLK 101.67 0.0010764 126640000 248710 259830 172380 211600 212770 198300 203250 244030 242860 221140 TRUE FALSE 238990.1382 252419.9028 203532.9006 222520.7014 219613.9403 202309.7619 205737.4343 238990.6952 215291.551 206161.9908 1.159234723 1.224376529 0.987247454 1.079348819 1.065249416 0.981314553 0.997940665 1.159237424 1.04428343 1 17.65341885 4.245708775 24.99927921 1.048826086 1.191805666 0.558314722 0.053719145 128.7831498 450382.4932 0.013831618 0.036251388 17607.94914 -4.245708775 0.14297958 DTLRT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 7 DTLRTPPR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DT(0.003)LRT(0.997)PPR;DT(0.001)LRT(0.999)PPR;DTLRT(1)PPR;DT(0.047)LRT(0.953)PPR;DT(0.021)LRT(0.979)PPR;DTLRT(1)PPR;DT(0.004)LRT(0.996)PPR 119.53 0.0027108 11736770000 1658926 1665120 1638492 2072160 1737100 1674910 1980540 2041350 2029140 2090458 TRUE FALSE 1594093.338 1617632.408 1934603.952 2179104.426 1792975.399 1708777.828 2004778.441 1999195.409 1798800.534 1948869.418 0.817958003 0.830036324 0.992680133 1.11813773 0.920007971 0.876804681 1.028687927 1.025823173 0.922996953 1 20.894206 4.245712029 8.117684749 0.989360981 0.823194301 0.501057519 0.064443627 0.100154908 48.41369915 0.016546566 0.041495526 17608.08107 -4.245712029 -0.16616668 CDVDIRK ddPTM_BT-474_Pertuzumab_2h_R1 4 CDVDIRK 7 1 P60709;A0A2R8Y793;Q562R1;P63261 P60709;P63261 ACTB;ACTBL2;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;; 78.496 0.056405 66289510000 70474200 72271100 38320600 42143600 46362600 61457300 49540500 51166900 61111800 47994200 FALSE TRUE 67719990.35 70209998.99 45245984.86 44318636.25 47853895.13 62700008.71 50146791.46 50110285.63 54174644.67 44743510.09 1.513515373 1.569166095 1.011230115 0.990504235 1.069515893 1.401320741 1.120761231 1.11994534 1.21078218 1 25.4151751 4.245713381 24.99998553 1.123817503 1.541340939 0.682246338 0.116134246 93.5332532 326904.5645 0.02941894 0.077084382 17608.13589 -4.245713381 0.417523436 LGETYKDHENIVIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGETYKDHENIVIAK 15 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 150.74 1.88E-06 4650900000 10892100 11639900 7490700 7755900 9214400 10430500 9475300 9549300 12495800 9998100 FALSE TRUE 10466424.69 11307941.45 8844436.12 8156182.928 9510789.544 10641411.86 9591261.556 9352103.618 11077329.17 9320919.782 1.122896123 1.213178711 0.948880189 0.875040567 1.020370282 1.141669718 1.029003766 1.003345575 1.188437346 1 23.1520409 4.245789594 24.99998869 1.023639747 1.168037443 0.304375547 0.085933517 201.0973776 695438.4134 0.021726178 0.056979038 17611.22614 -4.245789594 0.144397695 EAEDSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAEDSLR 7 0 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776;REV__H7BZ55 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 155.51 0.0037367 346700000 933520 951840 949520 1203370 1114080 959970 1142950 1133910 1235050 1314050 FALSE TRUE 897037.0063 924694.4551 1121119.386 1265476.07 1149915.395 979381.2511 1156937.764 1110494.362 1094852.302 1225048.223 0.732246282 0.754822902 0.915163473 1.033001025 0.938669493 0.799463427 0.944401814 0.906490325 0.893721799 1 20.22440711 4.245802486 5.133774516 0.925529018 0.739279698 0.612028082 0.059130447 0.111158379 8.297692765 0.015004924 0.03903717 17611.74896 -4.245802486 -0.18624932 TAASGVEANSRPLDHAQPPSSLVIDK ddPTM_BT-474_Pertuzumab_2h_R1 1 TAASGVEANSRPLDHAQPPSSLVIDK 26 1 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 0 82.476 0.009369 145830000 131530 121140 141960 162450 123990 140670 159140 165910 173130 180090 FALSE TRUE 126389.6622 117685.2058 167615.3299 170834.064 127978.251 143514.4438 161087.6029 162483.9005 153477.0082 167892.3439 0.752801821 0.700956357 0.99835005 1.017521466 0.76226377 0.854800406 0.959469617 0.967786242 0.91413941 1 17.35717692 4.245810006 24.99809775 0.930541621 0.726879005 0.555988182 0.074080461 125.2290076 431816.845 0.019042937 0.04993639 17612.0539 -4.245810006 -0.203662616 GPIKFNVWDTAGQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPIKFNVWDTAGQEK 15 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 188.9 2.56E-07 2655800000 3406100 3458800 2120900 2033070 2689200 3486500 2640700 2604480 3098500 2512510 FALSE TRUE 3272985.846 3360158.411 2504193.809 2137996.986 2775700.56 3556999.419 2673017.677 2550696.578 2746771.27 2342335.46 1.397317294 1.434533383 1.069101268 0.912762934 1.185014106 1.518569599 1.141176284 1.088954431 1.172663488 1 21.15951628 4.245840019 24.97426635 1.143840779 1.415925473 0.355527206 0.150443674 191.0697211 655507.8382 0.039118684 0.102645289 17613.27107 -4.245840019 0.272084694 (ac)S(ph)REMQDVDLAEVKPLVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SREMQDVDLAEVKPLVEK 18 2 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RJ98 Q92597 NDRG1 Protein NDRG1 1 S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK 80.07 8.09E-08 306165000 726530 726920 216399 228826 441620 501570 321571 312137 363988 193913 TRUE FALSE 698136.4044 706188.9533 255507.1131 240635.7373 455825.1084 511712.0891 325506.4821 305691.2619 322669.6082 180779.0998 3.861820339 3.906363922 1.413366442 1.331103748 2.521448048 2.830593192 1.800575855 1.690965727 1.784883366 1 17.46386837 4.245904312 24.99912852 1.857674382 3.884093288 0.724884045 0.51330323 87.42341998 297596.119 0.130917851 0.343580148 17615.87872 -4.245904312 2.026418905 EDQTEYLEERR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDQTEYLEERR 11 1 P08238;Q58FF7;P07900;P07900-2;G3V2J8 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha 0 ;; 170.66 2.48E-05 1407720000 1318570 1346530 821730 706250 1022730 1265580 1012970 1138750 1235360 1050140 FALSE TRUE 1267038.827 1308128.283 970234.8903 742699.6471 1055627.039 1291170.895 1025367.03 1115234.415 1095127.112 979013.0824 1.294200097 1.33617038 0.991033631 0.758620758 1.078256316 1.31884948 1.047347628 1.139141483 1.118603144 1 19.90096861 4.245915279 24.99955275 1.064338631 1.315185358 0.374993183 0.133287497 190.3671483 647069.4093 0.035195321 0.092336417 17616.32358 -4.245915279 0.250846727 GDRSPEPGQTWT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 GDRSPEPGQTWTR 13 1 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GDRS(0.106)PEPGQT(0.17)WT(0.724)R 100.31 0.0063249 0 297270 277440 287750 326300 298100 375360 292180 314160 346870 305600 TRUE FALSE 285652.3598 269527.6828 339752.826 343140.3821 307688.6572 382950.0364 295755.7862 307672.4862 307494.7718 284901.4398 1.002635718 0.946038332 1.192527585 1.204417859 1.079982809 1.344149179 1.038098602 1.079926049 1.079302274 1 18.12010339 4.245947712 24.98447617 1.131357533 0.97433697 0.293247735 0.094819761 196.7280558 665353.4087 0.022905951 0.060122269 17617.63923 -4.245947712 -0.157020563 GDDALEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDDALEKR 8 1 Q9Y617 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 84.476 0.02794 427880000 263080 263460 168600 181640 212080 193100 205060 227430 237170 260700 FALSE TRUE 252798.5427 255946.3788 199069.7705 191014.4622 218901.7458 197004.6143 207569.5856 222733.491 210247.4559 243042.5568 1.04014106 1.05309285 0.819073717 0.785930105 0.900672494 0.81057662 0.854046256 0.916438232 0.865064368 1 17.89084943 4.246025353 24.99973595 0.864158317 1.046617054 0.598621457 0.058077254 102.8421795 344414.5701 0.013686188 0.035951724 17620.78909 -4.246025353 0.182458737 SVLTS(ph)PVANGVNLDYDGLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVLTSPVANGVNLDYDGLGK 20 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2 I3VM54 KDM2A Lysine-specific demethylase 2A 1 S(0.007)VLT(0.031)S(0.962)PVANGVNLDYDGLGK 133.95 1.03E-05 46338000 79045 80067 85333 88003 89235 95436 99674 102630 103120 112430 TRUE FALSE 75955.83401 77783.56755 100754.5713 92544.84538 92105.32482 97365.78131 100893.8402 100510.6546 91414.24991 104815.016 0.724665577 0.742103284 0.96126085 0.882934993 0.878741695 0.9289297 0.962589561 0.958933734 0.872148414 1 16.67748589 4.246028437 24.77161525 0.928948066 0.733384287 0.794149011 0.040174006 61.73569808 204778.6632 0.009859764 0.025886064 17620.91423 -4.246028437 -0.195563779 SSS(ph)PAGETEGDREPQAR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSSPAGETEGDREPQAR 17 1 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.002)S(0.002)S(0.996)PAGETEGDREPQAR;SS(0.021)S(0.978)PAGETEGDREPQAR;S(0.104)S(0.104)S(0.793)PAGETEGDREPQAR;S(0.007)S(0.136)S(0.857)PAGETEGDREPQAR;S(0.002)S(0.018)S(0.98)PAGETEGDREPQAR;SS(0.002)S(0.998)PAGETEGDREPQAR 248.91 3.71E-21 4357250000 1032380 1040792 1100737 1340242 1193231 1110053 1270196 1303640 1250919 1360763 TRUE FALSE 992033.4482 1011109.631 1299664.662 1409412.05 1231612.359 1132499.032 1285741.039 1276719.378 1108919.919 1268597.31 0.781992395 0.797029619 1.02448953 1.111000346 0.970845791 0.89271751 1.013513925 1.006402401 0.874130751 1 20.27480276 4.246058786 24.87764233 0.989671379 0.78951087 0.607602968 0.063328708 103.5065892 343408.235 0.015989331 0.041998023 17622.14562 -4.246058786 -0.200160509 ALQEGEGDLSIS(ph)ADRLSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALQEGEGDLSISADRLSEK 19 1 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 1 ALQEGEGDLS(0.219)IS(0.781)ADRLSEK 85.573 0.0018259 92858000 63289 63359 38621 45959 54482 43682 38395 62221 49626 45000 TRUE FALSE 60815.59591 61552.06335 45600.67382 48330.9495 56234.46301 44565.27997 38864.8895 60936.11461 43992.66453 41952.10992 1.44964332 1.467198276 1.086969735 1.152050507 1.340444214 1.062289359 0.926410843 1.452516089 1.048640095 1 15.35645575 4.246093422 24.95372487 1.1594551 1.458420967 0.420130144 0.150187079 165.5127801 548276.1262 0.0367113 0.096479598 17623.55111 -4.246093422 0.298965867 SKADVER ddPTM_BT-474_Pertuzumab_2h_R1 1 SKADVER 7 1 P49792;O14715;Q99666;F8W705;Q99666-2;F8WBP7;C9J1W9;C9JF75 P49792 RANBP2;RGPD8;RGPD5;RGPD6 E3 SUMO-protein ligase RanBP2;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 0 73.931 0.043371 150600000 301230 295980 220090 264790 254340 225830 253090 288430 292520 304940 FALSE TRUE 289457.5986 287538.9402 259865.1589 278455.8436 262521.0771 230396.4373 256187.3911 282473.8197 259314.3559 284286.1422 1.018191025 1.011441986 0.914097173 0.979491443 0.923439585 0.810438509 0.901160321 0.993625006 0.912159678 1 18.11698425 4.246140166 23.79870876 0.928413588 1.014816612 0.30094859 0.052118727 118.0854465 370754.097 0.013401853 0.035135579 17625.44807 -4.246140166 0.086403024 S(ph)LPGS(ph)PEFLHQEACPFVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPGSPEFLHQEACPFVGR 19 0 Q96S53-3;Q96S53-2;Q96S53 Q96S53-3 TESK2 Dual specificity testis-specific protein kinase 2 2 S(1)LPGS(1)PEFLHQEACPFVGR 94.542 0.00083445 30211000 65123 66071 62182 80360 75244 63540 73050 76515 78346 77409 TRUE FALSE 62577.92116 64186.71977 73419.67063 84507.38923 77664.29159 64824.82233 73944.00775 74934.93851 69452.49053 72166.01948 0.867138324 0.889431345 1.017371765 1.171013586 1.076189211 0.898273492 1.024637472 1.038368737 0.9623988 1 16.13903206 4.246176081 5.002780388 1.028670429 0.87440573 0.429471515 0.067036301 0.160758008 10.99718689 0.017562707 0.045929929 17626.90569 -4.246176081 -0.154264698 ILLDHEKEWK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILLDHEKEWK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 175.86 1.61E-06 492600000 621570 639220 308170 307030 466490 479570 393980 454720 504390 356360 FALSE TRUE 597278.3572 620990.0715 363863.1742 322875.8551 481495.0745 489267.234 398801.6451 445329.8731 447133.7618 332223.4198 1.79782135 1.869194146 1.095236376 0.971863619 1.449311053 1.472705429 1.200401962 1.34045298 1.345882726 1 18.34179425 4.246190453 24.99554499 1.255772591 1.833508045 0.672986245 0.16649821 100.5880933 329521.2258 0.041792003 0.109931172 17627.48904 -4.246190453 0.577735454 LDEIYVAGLVAHSDLDER ddPTM_BT-474_Pertuzumab_2h_R1 10 LDEIYVAGLVAHSDLDER 18 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;;;;; 272.31 5.60E-39 5547593000 3627850 3692547 4039405 4771189 4444979 4001188 4495082 4520261 5150056 5462804 FALSE TRUE 3486069.611 3587239.175 4769415.34 5017430.636 4587955.786 4082094.763 4550094.158 4426916.031 4565443.234 5092803.419 0.684508968 0.704374169 0.936500969 0.985200139 0.900870387 0.801541789 0.893436048 0.869249344 0.896449923 1 22.2800286 4.246228487 24.84839479 0.901687854 0.69444142 0.716916562 0.054061573 85.46415631 276946.7952 0.013656489 0.035919066 17629.03286 -4.246228487 -0.207246434 SDS(ph)ASSEPVGIYQGFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSASSEPVGIYQGFEK 17 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 S(0.438)DS(0.562)ASSEPVGIYQGFEK 392.82 5.44E-122 233800000 220160 218710 211240 220170 261190 234390 220840 261830 259070 257250 TRUE FALSE 211555.9038 212472.6049 249415.767 231533.0001 269591.4136 239129.5264 223542.706 256423.119 229661.4597 239826.2284 0.882121631 0.885943987 1.039985362 0.965419844 1.124111468 0.997094972 0.932102829 1.069203818 0.957616109 1 17.87162992 4.246242755 24.85936526 1.013813111 0.884032723 0.472462995 0.05345375 125.9559223 407582.1714 0.012537889 0.032976606 17629.61204 -4.246242755 -0.129780388 EQDFFFELDAMDHLQSFIADCDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQDFFFELDAMDHLQSFIADCDR 23 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 217.87 2.33E-32 29694000 22065.4 21938.1 21756.6 24418 25205.3 25598.1 25481 22478 26024.1 28731 FALSE TRUE 21203.05977 21312.44687 25688.50159 25678.21591 26016.05137 26115.71112 25792.8441 22013.82144 23069.95327 26785.02378 0.791601305 0.795685195 0.959062116 0.958678108 0.971290956 0.975011683 0.96295767 0.821870521 0.861300459 1 14.70913896 4.246257992 24.9779307 0.931153605 0.793643164 0.545840629 0.052586067 148.0934296 480550.559 0.014669937 0.038592516 17630.23056 -4.246257992 -0.137510441 DIISIAEDEDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DIISIAEDEDLR 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 240.1 7.91E-16 7021340000 2374860 2417890 2163680 2550060 2524380 2470260 2625490 2793990 2682090 2712020 FALSE TRUE 2282047.846 2348934.145 2554705.107 2681668.902 2605578.975 2520210.35 2657621.532 2736293.13 2377630.387 2528332.47 0.902590096 0.929044804 1.010430842 1.060647258 1.030552353 0.996787559 1.0511361 1.082252102 0.940394674 1 21.26975476 4.246275165 3.142844202 1.030979183 0.907623695 0.555074565 0.037842042 0.159980079 3.194180391 0.009591842 0.028987642 17630.92771 -4.246275165 -0.123355488 RRSSPS(ph)ARPPDVPGQQPQAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RRS(0.058)S(0.27)PS(0.672)ARPPDVPGQQPQAAK 155.87 1.13E-07 747350000 244360 249570 143730 142630 179490 230760 161730 214590 212290 165710 TRUE FALSE 234810.141 242452.508 169705.2083 149991.1514 185263.4589 235426.1253 163709.3001 210158.6415 188191.7292 154486.3141 1.519941377 1.569410918 1.098512896 0.970902518 1.199222468 1.523928684 1.059700991 1.360370611 1.218177353 1 17.23711951 4.24633816 24.97357958 1.199232605 1.544676323 0.453122331 0.159504668 159.2148595 511224.1692 0.039427018 0.103785111 17633.48531 -4.24633816 0.345443719 ANS(ph)LDNER ddPTM_BT-474_Pertuzumab_2h_R1 1 ANSLDNER 8 0 F8VW41;Q86VP3-4;Q86VP3;Q86VP3-3;Q86VP3-2 F8VW41 PACS2 Phosphofurin acidic cluster sorting protein 2 1 ANS(1)LDNER 82.505 0.021083 474650000 499890 491260 499230 531120 534210 605980 583750 584700 586420 533540 TRUE FALSE 480353.7461 477249.7458 589451.9663 558531.1668 551393.3498 618233.3308 590894.1071 572625.7407 519852.0601 497402.8606 0.965723731 0.959483315 1.185059462 1.122894963 1.10854479 1.242922749 1.187958804 1.151231298 1.045132832 1 18.92405528 4.246393147 24.96079587 1.142187123 0.962603417 0.492521518 0.067322165 122.7270617 391098.6129 0.015835522 0.041705999 17635.71805 -4.246393147 -0.179583706 DVYKEHFQDDVFNEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DVYKEHFQDDVFNEK 15 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;; 241.93 4.00E-18 1776040000 3449880 3398110 1777190 1762230 2370620 2932010 2252540 2263750 2795980 2164590 FALSE TRUE 3315054.876 3301199.23 2098367.766 1853178.901 2446873.145 2991297.251 2280107.258 2217002.771 2478592.072 2017980.391 1.642758716 1.63589262 1.039835558 0.918333453 1.21253564 1.482322258 1.129895646 1.098624536 1.228253794 1 20.94448073 4.246422599 24.99904118 1.14613329 1.63932597 0.654673234 0.145350392 108.6789364 345562.324 0.037646798 0.099177706 17636.91408 -4.246422599 0.49319268 WKGFSEEHNTWEPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 WKGFSEEHNTWEPEK 15 1 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 107.98 0.00067002 384760000 494610 533570 267830 344060 336070 328270 398880 410410 434030 375110 FALSE TRUE 475280.0944 518353.106 316232.8388 361816.9778 346879.9968 334907.8443 403761.6128 401934.8901 384760.734 349703.4656 1.359094608 1.48226471 0.904288547 1.034639383 0.991926106 0.95769095 1.154582818 1.149359185 1.100248559 1 18.41577257 4.246455556 24.99999983 1.048924505 1.420679799 0.779149197 0.081584412 84.19148354 266593.2259 0.021892419 0.057673916 17638.25253 -4.246455556 0.371755295 LLGSENDT(ph)GSPDFYTPR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLGSENDTGSPDFYTPR 17 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 LLGSENDT(0.753)GS(0.247)PDFYTPR;LLGSENDT(0.899)GS(0.101)PDFYTPR;LLGSENDT(0.568)GS(0.432)PDFYTPR 231.86 3.69E-15 266238000 331971 358016 310702 391571 366966 424997 397524 421608 418163 454040 TRUE FALSE 318997.2063 347805.7342 366852.7629 411780.0262 378769.7947 433590.7305 402389.0176 412901.6475 370694.8893 423287.4664 0.75361836 0.821677375 0.866675232 0.972814125 0.894828751 1.024341057 0.950628236 0.975463911 0.875752104 1 18.69127825 4.246465942 1.188396198 0.959747436 0.73488044 0.720875217 0.043071656 0.364437795 0.757084435 0.012306384 0.082834013 17638.67433 -4.246465942 -0.224866996 RDS(ph)LSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSLSGK 7 1 Q92845-2;Q92845-3;Q92845 Q92845-2 KIFAP3 Kinesin-associated protein 3 1 RDS(1)LSGK;RDS(1)LSGK 104.42 0.0049948 600050000 454980 450080 398920 439920 450970 430980 464500 508240 497070 475780 TRUE FALSE 437198.8786 437244.1591 471013.7179 462624.3239 465475.8596 439694.7109 470184.6899 497744.6664 440644.6975 443554.9968 0.985670056 0.985772141 1.061906012 1.042992024 1.049420845 0.99129694 1.060036959 1.122171253 0.993438696 1 18.75875347 4.246479407 24.78099941 1.048099386 0.985721056 0.22763596 0.037914994 200.4008562 627115.917 0.009734925 0.02564209 17639.22123 -4.246479407 -0.06237833 KQKPELLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQKPELLNK 9 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 71.016 0.028557 488520000 289630 245250 299130 329910 285830 383820 290300 297060 303160 354400 FALSE TRUE 278310.9394 238255.7101 353189.4451 346936.6946 295023.9815 391581.1034 293852.7782 290925.6072 268746.5478 330396.1723 0.842355217 0.721121278 1.068987702 1.050062693 0.892940071 1.185186561 0.889395226 0.880535646 0.813406965 1 18.33383745 4.246491063 24.9999652 0.966838865 0.781738219 0.333465751 0.107672192 209.5605581 660603.7777 0.027081097 0.071382119 17639.69465 -4.246491063 -0.185100646 RYPSS(ph)ISS(ph)SPQKDLTQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RYPS(0.151)S(0.774)IS(0.087)S(0.665)S(0.322)PQKDLTQAK;RY(0.002)PS(0.393)S(0.605)IS(0.003)S(0.583)S(0.415)PQKDLTQAK 149.74 3.22E-08 1200820000 2033600 1766730 1133360 867720 1129800 1243600 943240 1228600 1381560 1142610 TRUE FALSE 1954124.664 1716344.59 1338183.363 912503.1332 1166141.043 1268746.444 954783.6533 1203228.981 1224731.101 1065220.007 1.834479874 1.611258312 1.256250685 0.856633491 1.094741965 1.191065166 0.89632531 1.129559127 1.149744741 1 20.02272 4.246526414 2.388790594 1.053339179 1.803549573 0.868132439 0.105471239 0.094687664 1.047868158 0.026915218 0.096077054 17641.13053 -4.246526414 0.750210394 SS(ph)TGPEPPAPTPLLAER ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTGPEPPAPTPLLAER 17 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.272)S(0.728)TGPEPPAPTPLLAER 156.17 7.66E-08 111300000 165330 165620 198620 222940 198790 193510 211440 239740 240770 268390 TRUE FALSE 158868.7208 160896.6798 234515.0523 234445.9601 205184.2609 197422.9048 214027.666 234789.2852 213438.799 250211.7062 0.634937203 0.643042175 0.937266508 0.936990374 0.820042611 0.789023454 0.855386301 0.938362512 0.853032826 1 17.93278976 4.246585124 24.9356984 0.885511866 0.638989528 0.733921164 0.060680176 86.43115605 268573.3022 0.015206342 0.040109479 17643.51555 -4.246585124 -0.246522339 SELNEIKENQRS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 5 SELNEIKENQRSPVR 15 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR 234.38 6.19E-18 5509010000 5264490 5233880 2551430 2688220 3759010 4625370 3099560 3229510 3911330 2976170 TRUE FALSE 5058747.911 5084614.867 3012530.157 2826959.356 3879921.97 4718898.15 3137493.342 3162819.49 3467332.216 2774591.355 1.823240709 1.832563508 1.085756341 1.018874131 1.398376004 1.70075429 1.130794752 1.139922636 1.249673113 1 21.40384387 4.246664921 24.99778896 1.227881893 1.827902469 0.607935476 0.196512545 123.2290276 380091.9326 0.050826599 0.13414749 17646.75765 -4.246664921 0.600020575 AILILDNDGDRLFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AILILDNDGDRLFAK 15 1 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8VXB1;F8VUC5;F8W156;F8W651;F8VXR1 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 ; 224.16 1.07E-12 820470000 1093040 1148420 593370 638710 798770 1025150 704020 879950 884690 743240 FALSE TRUE 1050322.788 1115668.186 700605.1584 671673.8996 824463.1625 1045879.235 712636.0074 861778.725 784263.7001 692899.6928 1.515836707 1.61014386 1.011120608 0.969366716 1.18987376 1.509423725 1.028483653 1.243727965 1.13185748 1 19.40228699 4.246680721 24.968626 1.15240904 1.562990472 0.553413693 0.153011307 132.8146874 408384.1246 0.038018211 0.100347844 17647.39963 -4.246680721 0.410581432 SDYDMVDYLNELR ddPTM_BT-474_Pertuzumab_2h_R1 7 SDYDMVDYLNELR 13 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;;;; 330.93 4.64E-62 1765369000 1325438 1343248 1287417 1520749 1424635 1449818 1554504 1533297 1663846 1879607 FALSE TRUE 1273638.418 1304939.882 1520081.89 1599235.038 1470459.679 1479134.313 1573528.485 1501633.881 1474973.177 1752299.544 0.726838298 0.744701376 0.867478335 0.912649349 0.839159996 0.844110425 0.897979167 0.856950449 0.841735754 1 20.74081798 4.246687219 4.732703394 0.87613717 0.731727087 0.619020743 0.045965567 0.107919092 6.174571479 0.010519802 0.027828543 17647.66369 -4.246687219 -0.144410083 QESTTDHMDSMLLLETLQEELK ddPTM_BT-474_Pertuzumab_2h_R1 1 QESTTDHMDSMLLLETLQEELK 22 0 V9GY01;Q9Y448-2;Q9Y448 V9GY01 KNSTRN Small kinetochore-associated protein 0 151.82 4.58E-08 26429000 23154 22269 24787 25235 26628 28614 22125 31158 30174 32142 FALSE TRUE 22249.11608 21633.90992 29266.56228 26537.38137 27484.5138 29192.59468 22395.77237 30514.57641 26748.77402 29964.99371 0.742503613 0.721972784 0.976691755 0.88561278 0.917220743 0.974223288 0.747397866 1.018340825 0.892667433 1 14.87099045 4.246689371 24.98978604 0.922682326 0.732238095 0.527719653 0.073445459 127.6514784 392422.7939 0.016740447 0.044194036 17647.75115 -4.246689371 -0.190444231 TVSLGAGAKDELHIVEAEAMNYEGSPIK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 152.88 2.34E-08 283807000 290853 281375 162684 153720 212057 247711 192990 206075 247553 215200 FALSE TRUE 279486.1432 273350.4605 192084.6177 161653.5076 218878.006 252719.8861 195351.8693 201819.4792 219451.8213 200624.3123 1.393082124 1.362499177 0.957434398 0.805752333 1.090984455 1.259667302 0.97371982 1.005957239 1.093844603 1 17.61413692 4.246689432 24.83862871 1.02313191 1.377790911 0.624402607 0.109937514 108.3893756 331189.1538 0.028533814 0.07527911 17647.75364 -4.246689432 0.354659001 EEDAFHFVSYVPVNGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEDAFHFVSYVPVNGR 16 0 Q5LJB0;Q5LJA5;Q5LJA9;Q9Y5K5-2;Q9Y5K5-4;Q9Y5K5-3;Q9Y5K5;H0Y4E0;H0Y6Y4 Q5LJB0 UCHL5 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L5 0 ; 132.44 3.91E-05 484660000 686010 693730 716310 900720 777100 797270 812070 832160 910670 1038280 FALSE TRUE 659199.9708 673945.4996 845763.1512 947206.2671 802096.1272 813391.3457 822008.3556 814975.6052 807294.5594 967956.3708 0.6810224 0.696256071 0.873761645 0.978562976 0.82864905 0.84031819 0.849220461 0.841954896 0.834019573 1 19.8845825 4.246692112 7.061311785 0.872384956 0.687059326 0.635965726 0.057894438 0.081312545 20.88250189 0.013986392 0.035342644 17647.86252 -4.246692112 -0.185325631 (ac)MDPQRS(ph)PLLEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 MDPQRSPLLEVK 12 1 Q9BW19;A2AB20;A0A140T9E6 Q9BW19 KIFC1 Kinesin-like protein KIFC1 1 MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK 90.793 0.00021312 663780000 1432930 1379940 1267380 1457230 1440510 1327200 1492880 1572030 1350490 1520040 TRUE FALSE 1376929.511 1340585.462 1496423.759 1532437.815 1486845.312 1354036.893 1511150.312 1539567.031 1197188.037 1417086.337 0.9716624 0.946015375 1.055986301 1.081400459 1.049227047 0.955507691 1.066378436 1.086431356 0.84482364 1 20.43449623 4.246724363 24.97062601 1.027368202 0.958838863 0.08814074 0.069850486 351.6757895 1075653.062 0.016700142 0.044095047 17649.17311 -4.246724363 -0.068529339 GNS(ph)RPGTPSAEGGS(ph)TSSTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.489)RPGT(0.511)PS(0.078)AEGGS(0.743)T(0.1)S(0.071)S(0.007)T(0.002)LR;GNS(0.977)RPGT(0.023)PS(0.006)AEGGS(0.55)T(0.42)S(0.02)S(0.002)T(0.002)LR 170.5 1.10E-10 869790000 811494 825597 852987 1010215 940993 879653 968263 1194180 1045674 1082053 TRUE FALSE 779779.9173 802051.7819 1007140.725 1062352.317 971260.8944 897440.1864 980112.8922 1169519.766 926973.4713 1008764.587 0.773004849 0.795083206 0.998390248 1.053122137 0.962822156 0.889642835 0.971597244 1.159358468 0.918919522 1 19.9441581 4.246732991 5.527456595 1.00469761 0.779872413 0.584359678 0.070572006 0.110701266 10.67774484 0.019160681 0.049422789 17649.52374 -4.246732991 -0.224825197 KAPPLVENEEAEPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPPLVENEEAEPGR 15 1 O14908;K7ELJ2 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 94.203 0.0073141 385570000 218020 215510 207920 253250 220630 262740 227380 234470 220680 262990 FALSE TRUE 209499.5374 209363.8658 245495.7692 266320.2628 227726.7643 268052.7828 230162.7445 229628.1126 195629.3316 245177.4531 0.854481253 0.853927893 1.001298309 1.086234723 0.928824252 1.093301115 0.938759831 0.93657924 0.797909143 1 17.90346679 4.246743938 24.87171717 0.973555593 0.854204495 0.260515759 0.079959529 228.5570044 694640.0843 0.019804493 0.052282887 17649.96862 -4.246743938 -0.119351098 IDIS(ph)PSTLRK ddPTM_BT-474_Pertuzumab_2h_R1 5 IDISPSTLRK 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 IDIS(0.996)PS(0.003)T(0.001)LRK;IDIS(0.998)PS(0.002)TLRK;IDIS(0.333)PS(0.333)T(0.333)LRK;IDIS(0.964)PS(0.029)T(0.008)LRK;IDIS(0.493)PS(0.493)T(0.014)LRK 143.31 2.10E-05 4824830000 8318400 8682100 4595640 4813160 5936830 8025070 5795590 6146660 7049350 6352650 TRUE FALSE 7993307.732 8434495.009 5426174.377 5061567.764 6127793.529 8187342.414 5866518.164 6019729.323 6249137.341 5922379.357 1.34967844 1.424173377 0.916215266 0.854651055 1.034684399 1.382441401 0.990567779 1.016437644 1.05517343 1 22.49774547 4.246756147 24.99929119 1.034974515 1.386926072 0.537464044 0.131937586 142.3490957 434205.5162 0.034158437 0.090231258 17650.46483 -4.246756147 0.351951556 TAFDEAIAELDTLNEESYKDSTLIMQLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 TAFDEAIAELDTLNEESYKDSTLIMQLLR 29 1 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;; 193.19 1.53E-18 5986700000 822830 867103 485882 500914 593561 793938 660530 635790 728415 709053 FALSE TRUE 790672.8939 842374.0714 573691.6858 526766.2316 612653.4286 809991.9703 668613.7637 622660.7143 645728.383 661028.2088 1.196125798 1.274339068 0.867877767 0.796889187 0.926818887 1.225351596 1.011475388 0.941957856 0.976854504 1 19.33435231 4.246764543 24.99993492 0.968761429 1.235232543 0.499906146 0.106751235 156.0847964 475628.4233 0.028312726 0.074781982 17650.80606 -4.246764543 0.266471114 LEEDINSSMTNSTAASRPPVTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEDINSSMTNSTAASRPPVTLR 23 1 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 64.318 0.028806 209120000 58156 55120 52366 61233 50158 64682 52404 58670 75660 62272 FALSE TRUE 55883.19923 53548.03157 61829.70108 64393.24247 51771.37762 65989.91436 53045.33583 57458.444 67071.39399 58054.26197 0.962602871 0.922378991 1.065032936 1.109190614 0.891775657 1.136693709 0.913719924 0.989736878 1.155322481 1 15.82511436 4.246809681 24.98907057 1.025566623 0.942490909 0.151017532 0.08419768 347.8300725 1053664.787 0.019683958 0.051988039 17652.64066 -4.246809681 -0.083075713 VTAAMVLTSLSTS(ph)PLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTAAMVLTSLSTSPLVR 17 0 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 VTAAMVLTSLST(0.168)S(0.831)PLVR 217.91 5.05E-15 227810000 149410 144230 137690 173240 135290 142240 158460 166260 171400 155040 TRUE FALSE 143570.892 140116.7016 162573.6459 182180.9372 139641.7257 145116.1903 160399.2809 162826.6729 151943.3906 144539.0027 0.99330208 0.969404099 1.124773541 1.260427523 0.966117955 1.0039933 1.109730093 1.12652412 1.051227611 1 17.14109932 4.246819221 24.94605502 1.087994223 0.981353039 0.191245305 0.080208027 269.845397 815079.6306 0.02007591 0.053027224 17653.02846 -4.246819221 -0.106641183 ELDDISQEIAQLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELDDISQEIAQLQR 14 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 0 ; 234.79 7.46E-17 66843000 78605 76837 68224 77083 77114 81544 74295 80044 85064 86788 FALSE TRUE 75533.0297 74645.68399 80553.59443 81061.26287 79594.44184 83192.87555 75204.24443 78391.06343 75407.89134 80909.77146 0.933546447 0.922579345 0.995597849 1.00187235 0.983743254 1.028217903 0.929482843 0.968870163 0.931999806 1 16.30402633 4.246869555 24.99986055 0.978319523 0.928062873 0.334806233 0.029193412 215.2463235 647616.629 0.007321482 0.019345729 17655.07454 -4.246869555 -0.05025665 TFDQLTPDESKER ddPTM_BT-474_Pertuzumab_2h_R1 4 TFDQLTPDESKER 13 1 Q15293 Q15293 RCN1 Reticulocalbin-1 0 ;;; 143.64 3.73E-05 1591450000 1288746 1381520 882381 967971 1014033 1302318 1181958 1110874 1351247 1219430 FALSE TRUE 1238380.382 1342120.402 1041846.875 1017928.099 1046650.292 1328651.762 1196423.156 1087934.064 1197859.105 1136836.92 1.089321045 1.180574257 0.916443561 0.895403801 0.920668808 1.168726788 1.052414057 0.956983402 1.053677167 1 20.11659388 4.246879227 24.99999901 0.994961056 1.134947674 0.326387534 0.080106333 220.2373563 661866.3437 0.020770926 0.054894187 17655.46771 -4.246879227 0.139986618 SVEGWILFVTGVHEEATEEDIHDK ddPTM_BT-474_Pertuzumab_2h_R1 3 SVEGWILFVTGVHEEATEEDIHDK 24 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;; 248.18 2.70E-38 707911600 373485 330268 336645 357158 389016 371342 353847 292010 488231 447309 FALSE TRUE 358888.7933 320849.08 397484.2401 375590.9672 401529.0529 378850.7897 358177.4854 285979.8915 432809.0637 417012.363 0.860619073 0.769399443 0.953171357 0.90067106 0.962870861 0.908488149 0.858913349 0.685782765 1.037880653 1 18.66973063 4.246887578 24.99865621 0.889939721 0.815009277 0.109006096 0.095173215 490.3152407 1471957.935 0.024763972 0.065472453 17655.80721 -4.246887578 -0.074930445 LLVDVDESTLSPEEQKER ddPTM_BT-474_Pertuzumab_2h_R1 4 LLVDVDESTLSPEEQKER 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 288.96 1.85E-41 2014550000 2334100 2361520 1571860 1606500 2008510 2302890 1894050 1941270 2243280 1927960 FALSE TRUE 2242880.792 2294171.762 1855930.068 1689411.658 2073115.548 2349456.014 1917229.95 1901182.096 1988632.259 1797377.552 1.247862915 1.276399474 1.032576637 0.939931433 1.153411283 1.307157759 1.066681816 1.057753333 1.106407642 1 20.77746206 4.246910933 24.97126417 1.087888873 1.262131283 0.369854336 0.093357033 203.8575822 609613.5508 0.024252834 0.064094715 17656.7567 -4.246910933 0.17424241 LTTTGQVT(ph)SPVKGASFVTSTNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTTTGQVTSPVKGASFVTSTNPR 23 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.5)S(0.5)PVKGASFVTSTNPR;LTT(0.002)T(0.006)GQVT(0.579)S(0.413)PVKGASFVTSTNPR 180.71 7.22E-17 4086180000 3221220 3365670 2103380 2408330 2660910 3037200 2577240 2852690 2766620 2791460 TRUE FALSE 3095331.161 3269684.387 2483507.555 2532624.2 2746500.587 3098614.265 2608781.034 2793780.955 2452564.896 2602391.928 1.189417754 1.256415051 0.954317268 0.973190922 1.055375463 1.190679325 1.00245509 1.073543506 0.942427184 1 21.31140682 4.246930258 24.99999927 1.032758444 1.222916473 0.560249513 0.070150389 136.9603352 409089.1917 0.017450463 0.046157148 17657.54241 -4.246930258 0.190158029 GFGFVEFEDPRDADDAVYELDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVEFEDPRDADDAVYELDGK 23 1 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 172.61 4.38E-12 984380000 1695840 1756000 760110 821430 1297380 1456420 980610 1080460 1121720 834610 FALSE TRUE 1629564.698 1705920.599 897478.7856 863824.1007 1339111.406 1485869.81 992610.9985 1058148.123 994387.0482 778081.1213 2.094337792 2.192471392 1.153451435 1.110197995 1.721043435 1.90965925 1.275716595 1.359945762 1.277999197 1 19.56956105 4.246944192 24.99990639 1.382612693 2.143404995 0.589810143 0.263273732 131.4404272 391947.7913 0.067022306 0.177250263 17658.10893 -4.246944192 0.760792302 DTTS(ph)PMELAALEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DTTSPMELAALEK 13 0 Q6VY07-2;Q6VY07 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 DT(0.015)T(0.155)S(0.83)PMELAALEK;DTT(0.001)S(0.999)PMELAALEK;DTT(0.024)S(0.976)PMELAALEK;DTT(0.001)S(0.999)PMELAALEK 379.4 8.24E-92 483698000 1360200 1349550 1328720 1415200 1487630 1540800 1454490 1595480 1614020 1620200 TRUE FALSE 1307041.88 1311062.155 1568849.261 1488238.642 1535480.97 1571956.032 1472290.484 1562532.78 1430803.216 1510462.411 0.865325658 0.867987277 1.038654951 0.985286778 1.01656351 1.040711785 0.974728317 1.034473132 0.947261717 1 20.52655885 4.246948463 24.99982147 1.006795932 0.866656379 0.789693072 0.028481127 67.9051634 202385.4862 0.006388117 0.016890144 17658.2826 -4.246948463 -0.140139553 AHT(ph)SPAPAPRPTPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHTSPAPAPRPTPR 14 1 Q96P48-3;Q96P48 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 AHT(0.612)S(0.388)PAPAPRPTPR 82.349 0.017722 207330000 34909 35221 39940 47895 43807 46320 47959 35614 46204 54050 TRUE FALSE 33544.71769 34216.53156 47158.04646 50366.86669 45216.09194 47256.62214 48545.93659 34878.55845 40959.11562 50389.14536 0.66571317 0.679045682 0.935877085 0.999557868 0.897337941 0.937833373 0.963420519 0.692183966 0.81285593 1 15.62082537 4.246972381 24.86307584 0.890917332 0.67237927 0.518411711 0.088825472 156.0979153 461375.1428 0.024427376 0.064607429 17659.25515 -4.246972381 -0.218538062 IRIDS(ph)LSAQLSQLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 IRIDSLSAQLSQLQK 15 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 IRIDS(0.887)LS(0.113)AQLSQLQK 157.88 1.13E-06 229050000 415690 452010 217780 258840 338130 297710 320530 342760 305220 289630 TRUE FALSE 399444.3752 439119.1174 257137.6905 272198.7634 349006.2585 303729.9002 324452.742 335681.8862 270572.7052 270013.1021 1.479351824 1.626288183 0.952315604 1.008094649 1.292553049 1.12487097 1.201618512 1.243205917 1.002072503 1 18.04266989 4.246980654 24.99999812 1.127005157 1.552820165 0.704729261 0.115615921 101.0054729 299889.3258 0.028773087 0.076108998 17659.59153 -4.246980654 0.425815008 GES(ph)ENAGTNQETR ddPTM_BT-474_Pertuzumab_2h_R1 6 GESENAGTNQETR 13 0 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 GES(1)ENAGTNQETR;GES(1)ENAGTNQETR;GES(1)ENAGTNQETR;GES(1)ENAGTNQETR;GES(1)ENAGTNQETR;GES(1)ENAGTNQETR 285.04 1.03E-32 578998400 511533.6 499274.7 464369.7 554078 502466.5 505710 504872.3 559185.3 595955.5 541664.2 TRUE FALSE 491542.3014 485035.8744 548291.6346 582674.032 518628.7913 515935.8027 511051.0782 547637.9281 528305.1301 504976.8013 0.973395808 0.960511202 1.085775888 1.153862971 1.027034886 1.02170199 1.012028824 1.08448136 1.046196833 1 18.94585759 4.247106158 24.99688026 1.057503158 0.966953458 0.391793027 0.043136755 182.4426149 533657.7099 0.010925541 0.028937937 17664.69561 -4.247106158 -0.090549701 ETQS(ph)PEQVKSEK ddPTM_BT-474_Pertuzumab_2h_R1 4 ETQSPEQVKSEK 12 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 ETQS(1)PEQVKSEK;ET(0.004)QS(0.996)PEQVKSEK;ET(0.03)QS(0.97)PEQVKSEK;ET(0.137)QS(0.863)PEQVKSEK 143.67 3.78E-05 6788850000 5374730 5111900 2485060 2137120 3469870 4410610 3153900 3174560 4006520 2966540 TRUE FALSE 5164679.61 4966113.617 2934165.622 2247417.019 3581481.52 4499795.556 3192498.372 3109004.227 3551716.646 2765613.603 1.867462469 1.795664301 1.060945614 0.812628712 1.295004304 1.627051426 1.154354451 1.124164353 1.28424182 1 21.39916817 4.247157978 24.1701846 1.178393297 1.831564103 0.629759781 0.20287784 80.91299518 227466.6145 0.052591766 0.13902065 17666.80347 -4.247157978 0.653170806 DPGTPDQFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPGTPDQFLR 10 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 74.173 0.071173 0 94861 93724 94916 104490 101330 99271 112480 113640 106530 123620 FALSE TRUE 91153.72725 91051.08329 112069.4326 109882.7414 104589.3715 101278.3276 113856.5639 111293.2943 94437.16101 115247.1073 0.790941564 0.790050921 0.972427293 0.953453358 0.907522748 0.878792796 0.987934245 0.965692735 0.819431943 1 16.81437101 4.247221614 24.97058121 0.936388916 0.79049615 0.555430691 0.051944076 128.00745 369050.8895 0.012430259 0.032927969 17669.39233 -4.247221614 -0.145892766 IEEMLENAER ddPTM_BT-474_Pertuzumab_2h_R1 2 IEEMLENAER 10 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ; 166.34 1.30E-05 209580000 195850 193976 165742 179170 198171 196696 180593 205104 202276 217258 FALSE TRUE 188195.9655 188443.9944 195695.2663 188416.9852 204545.3502 200673.3279 182803.1512 200868.5307 179314.4765 202542.9221 0.929165845 0.93039042 0.966191582 0.930257069 1.009886438 0.990769392 0.902540307 0.991733153 0.885315935 1 17.62786815 4.247312615 23.55322527 0.959804595 0.929778091 0.082319161 0.039805116 227.721206 612808.9733 0.009149268 0.024176051 17673.09514 -4.247312615 -0.030026504 YKAEDEKQR ddPTM_BT-474_Pertuzumab_2h_R1 5 YKAEDEKQR 9 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;; 129.16 0.00022339 1669368000 2889550 2870770 1658470 1355370 1946040 2710820 2064100 2367250 2629560 2118830 FALSE TRUE 2776623.191 2788898.45 1958192.421 1425320.808 2008636.144 2765634.638 2089361.073 2318365.46 2331063.373 1975319.757 1.405657581 1.411871896 0.991329335 0.721564599 1.016866326 1.400094657 1.057733092 1.17366591 1.180094192 1 20.91365478 4.247349445 24.7710148 1.076111143 1.408764972 0.409289741 0.163659981 178.7986369 503925.0751 0.043250037 0.114653492 17674.59396 -4.247349445 0.332653829 GEASEDLCEMALDPELLLLRDDGEEEFAGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEASEDLCEMALDPELLLLRDDGEEEFAGAK 31 1 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 185.8 1.97E-18 79620000 165550 159500 98327 105880 126050 147340 110160 123650 137640 114080 FALSE TRUE 159080.123 154951.2162 116096.8762 111344.4795 130104.5127 150319.3158 111508.171 121096.5843 122015.6842 106353.26 1.495771009 1.456948439 1.091615586 1.046930574 1.223324163 1.413396409 1.048469704 1.138625974 1.147267928 1 16.69850473 4.24740715 22.97228184 1.147727054 1.476360428 0.598149053 0.110505885 47.53139117 123419.1468 0.027532499 0.072682776 17676.94254 -4.24740715 0.328633373 GDKSELNEIKENQRS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDKSELNEIKENQRSPVR 18 3 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 GDKSELNEIKENQRS(1)PVR;GDKSELNEIKENQRS(1)PVR 121.62 0.00020908 2325900000 1447270 1476440 701660 630510 1011040 1237350 889120 994900 1253140 949440 TRUE FALSE 1390709.088 1434333.377 828465.5703 663050.6967 1043561.02 1262370.065 900001.3165 974354.9673 1110888.801 885133.5831 1.571185542 1.620471084 0.935978011 0.749096757 1.178987036 1.426191582 1.016797163 1.100799909 1.255052144 1 19.75553568 4.247409671 24.98739079 1.087339287 1.595828602 0.581675089 0.173973057 136.0728623 384225.2803 0.045026954 0.119446747 17677.04514 -4.247409671 0.508489315 AKTQTPPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKTQTPPVSPAPQPTEERLPS(0.32)S(0.68)PVYEDAASFK 246.23 2.41E-47 826880000 1127900 1160300 488410 439520 618260 1016700 656070 791970 866770 620760 TRUE FALSE 1083820.421 1127209.38 576676.5516 462203.6799 638146.8944 1037258.371 664099.1809 775615.5427 768377.9034 578715.3723 1.872803926 1.947778535 0.996476989 0.798671855 1.1026956 1.792346325 1.147540246 1.340236634 1.327730246 1 19.14249444 4.247449414 24.99446608 1.209423643 1.910291624 0.562191986 0.254334471 144.8245113 407223.9344 0.065647552 0.174174376 17678.66288 -4.247449414 0.700867981 EYATEVDVDFVR ddPTM_BT-474_Pertuzumab_2h_R1 3 EYATEVDVDFVR 12 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ;; 318.19 3.41E-46 1505720000 769580 867470 787890 1080030 963620 947640 1055540 1063930 1062780 1134580 FALSE TRUE 739503.9628 842730.6049 930279.2495 1135770.478 994615.7124 966801.9301 1068458.014 1041959.474 942137.6699 1057733.886 0.6991399 0.796732161 0.879502171 1.07377715 0.940326982 0.914031348 1.010138777 0.985086596 0.890713328 1 20.01254528 4.24747508 2.185112411 0.972156813 0.714304875 0.754080031 0.051849347 0.150590088 1.370702844 0.013367716 0.051202667 17679.70766 -4.24747508 -0.257851939 ENLQPQSSGVQGQVPIS(ph)PEPLQRPEMLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENLQPQSSGVQGQVPISPEPLQRPEMLK 28 1 Q9H467 Q9H467 CUEDC2 CUE domain-containing protein 2 1 ENLQPQSSGVQGQVPIS(1)PEPLQRPEMLK;ENLQPQSSGVQGQVPIS(1)PEPLQRPEMLK 181.38 8.45E-18 531670000 170350 153797 220238 245390 233870 219860 235180 220640 210150 275130 TRUE FALSE 163692.5337 149410.8601 260039.9058 258054.6073 241392.6409 224305.7198 238058.2032 216083.7069 186294.653 256495.2 0.638189462 0.582509381 1.013819774 1.006079674 0.941119525 0.874502602 0.928119525 0.842447371 0.726308535 1 17.9685723 4.247478027 24.99971204 0.91057302 0.61034927 0.679984015 0.083943643 111.4309482 312386.6911 0.02152763 0.057132669 17679.82766 -4.247478027 -0.30022375 AMT(ph)PEQEETASLLSSVTQGMESAYVSPSGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AMTPEQEETASLLSSVTQGMESAYVSPSGYR 31 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AMT(0.997)PEQEET(0.002)AS(0.001)LLSSVTQGMESAYVSPSGYR 170.11 3.06E-12 45701000 24554 24310 25330 27028 27671 28112 26830 28536 33709 33017 TRUE FALSE 23594.40253 23616.7026 29907.69446 28422.91832 28561.06285 28680.4439 27158.35357 27946.72163 29882.49564 30780.72918 0.766531631 0.767256112 0.971636971 0.923399772 0.927887792 0.931766227 0.882316771 0.907929161 0.970818315 1 14.90973979 4.247488653 24.99993694 0.93078723 0.766893766 0.810536086 0.033162756 75.43970007 211238.6354 0.007950964 0.021099359 17680.26024 -4.247488653 -0.163893463 EDDRVAIHEAMEQQTISIAK ddPTM_BT-474_Pertuzumab_2h_R1 3 EDDRVAIHEAMEQQTISIAK 20 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;; 155.28 1.91E-08 1237530000 1511210 1474070 860650 926620 1094520 1366070 1098500 1024350 1249690 1025610 FALSE TRUE 1452150.242 1432030.967 1016188.6 974442.9692 1129726.23 1393692.871 1111943.772 1003196.815 1107830.43 956144.5212 1.518756015 1.497713928 1.062798121 1.019137743 1.181543381 1.457617379 1.162945294 1.049210441 1.158643286 1 19.86686917 4.247494193 24.80196557 1.143380983 1.508235248 0.591577201 0.123448034 124.4594785 345523.9115 0.032211076 0.085447794 17680.48576 -4.247494193 0.364854266 QSS(ph)SWTR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSSSWTR 7 0 Q92934;F5H1R6 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 QS(0.056)S(0.472)S(0.472)WTR 81.915 0.027175 502420000 790950 786070 715600 812030 789520 812900 806290 838680 916790 929320 TRUE FALSE 760038.7996 763652.0532 844924.8384 853938.9656 814915.6278 829337.395 816157.6182 821360.9649 812719.8427 866376.3286 0.877261733 0.881432269 0.975239986 0.985644387 0.94060237 0.957248447 0.942035916 0.948041789 0.938067922 1 19.7246343 4.247526172 24.9977351 0.957576534 0.879346948 0.729526715 0.019772426 95.20096715 265433.3646 0.004782124 0.012695816 17681.78771 -4.247526172 -0.078229586 T(ph)PRTPRT(ph)PQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPRTPRTPQLK 11 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(0.608)PRT(0.393)PRT(1)PQLK;T(0.937)PRT(0.065)PRT(0.999)PQLK 110.38 0.0020872 662090000 1192020 1136680 422970 448190 727820 912360 557820 564280 627970 484590 TRUE FALSE 1145434.541 1104262.999 499410.0879 471321.1396 751230.9913 930808.5443 564646.768 552627.4208 556685.4783 451768.2877 2.53544698 2.44431278 1.105456274 1.043280709 1.662867917 2.060367161 1.249859239 1.223254124 1.232236732 1 18.78522348 4.247560497 24.85632754 1.347713546 2.489880742 0.702428447 0.303648401 100.9708676 278859.8422 0.079190796 0.210227181 17683.18527 -4.247560497 1.142167196 TAAKGEAAAERPGEAAVASSPS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 TAAKGEAAAERPGEAAVASSPSK 23 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 TAAKGEAAAERPGEAAVAS(0.089)S(0.428)PS(0.483)K 123.21 3.26E-05 453900000 421180 415590 191170 145680 239340 375100 275460 282490 330870 202430 TRUE FALSE 404719.82 403737.7801 225718.6716 153198.5623 247038.5885 382684.779 278831.1619 276656.4828 293311.0247 188719.2358 2.144560507 2.139356799 1.196055456 0.811780323 1.309027071 2.027799537 1.477492004 1.465968647 1.554219015 1 17.52588196 4.247562801 24.99664948 1.385226422 2.141959142 0.501951755 0.312303776 167.6655757 465552.05 0.08130338 0.215851989 17683.27909 -4.247562801 0.756732721 DIYLS(ph)PDRTGSSFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIYLSPDRTGSSFGK 15 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 DIYLS(1)PDRTGSSFGK 130.09 3.75E-05 123870000 188880 200850 120650 125630 162420 184710 152820 161570 177400 159010 TRUE FALSE 181498.3608 195121.9547 142454.1388 132113.7794 167644.3868 188444.9628 154690.2569 158233.523 157262.2957 148240.1111 1.224353918 1.316256128 0.960968916 0.891214789 1.130897607 1.271214393 1.043511474 1.067413684 1.060861966 1 17.17757634 4.247563061 24.99990828 1.060179221 1.270305091 0.43829882 0.098032558 190.4086773 528755.6951 0.02559389 0.067958903 17683.28965 -4.247563061 0.210125871 NEEDEGHSNS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 5 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHS(0.01)NS(0.934)S(0.057)PR;NEEDEGHS(0.012)NS(0.494)S(0.494)PR;NEEDEGHS(0.023)NS(0.489)S(0.489)PR;NEEDEGHS(0.026)NS(0.487)S(0.487)PR;NEEDEGHS(0.068)NS(0.466)S(0.466)PR 158.98 2.99E-05 3178640000 842153 825855 784106 944160 898887 790811 901402 863313 1021270 968255 TRUE FALSE 809240.7297 802302.424 925811.3965 992888.2107 927800.5167 806801.7402 912433.6273 845485.2849 905339.7111 902674.2264 0.896492562 0.888806172 1.025631805 1.0999408 1.027835391 0.893790602 1.010811653 0.936644982 1.002952876 1 19.78384589 4.247564164 24.91450216 0.995740702 0.892649304 0.402846987 0.051955915 200.0547741 553576.4723 0.013743609 0.036473503 17683.33458 -4.247564164 -0.103091398 LSCS(ph)LEDLRSESVDK ddPTM_BT-474_Pertuzumab_2h_R1 4 LSCSLEDLRSESVDK 15 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LSCS(1)LEDLRSESVDK;LS(0.019)CS(0.981)LEDLRSESVDK;LS(0.031)CS(0.969)LEDLRSESVDK;LS(0.145)CS(0.855)LEDLRSESVDK 218.11 1.20E-12 1959980000 3344950 3338450 1943080 2060360 2677170 2931900 2316220 2622820 2806590 2221220 TRUE FALSE 3214225.656 3243240.675 2294237.78 2166695.427 2763283.604 2991185.027 2344566.593 2568657.85 2487997.669 2070774.791 1.552185042 1.566196715 1.107912743 1.046321134 1.334420149 1.444476261 1.132217083 1.240433224 1.201481533 1 20.98173923 4.247579762 24.999481 1.204880419 1.559191096 0.580549016 0.125443296 137.4307644 380925.5716 0.031119613 0.082641464 17683.96969 -4.247579762 0.354310677 NWDDVLTVDYTR ddPTM_BT-474_Pertuzumab_2h_R1 4 NWDDVLTVDYTR 12 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ;;; 280.38 1.17E-27 313199000 397328 413789 421665 523654 482010 475147 509329 519864 547390 579079 FALSE TRUE 381799.9825 401988.1429 497869.2454 550679.8457 497514.2894 484754.7979 515562.3207 509128.6267 485252.582 539857.4635 0.707223681 0.744619034 0.922223511 1.02004674 0.921566011 0.897931085 0.954997116 0.943079722 0.898853151 1 19.04221902 4.24762853 4.059170414 0.944987951 0.716625565 0.849325018 0.037140911 0.067452531 2.481122734 0.009164376 0.025200012 17685.95557 -4.24762853 -0.228362385 KNSAS(ph)AERDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KNSASAERDR 10 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 KNS(0.002)AS(0.998)AERDR 75.96 0.029477 123800000 316230 321560 177890 169510 242160 294070 211240 250330 262830 241150 TRUE FALSE 303871.382 312389.4236 210038.6801 178258.4314 249949.2963 300016.2969 213825.2183 245160.598 232994.6403 224816.6957 1.351640638 1.389529468 0.934266379 0.792905664 1.111791522 1.334492956 0.951109159 1.090491065 1.036376055 1 17.77838965 4.247659643 24.96741771 1.038212663 1.370585243 0.509708438 0.132920163 159.5964905 437917.5311 0.03423239 0.090945048 17687.22265 -4.247659643 0.332372579 GLSEDTTEETLKESFDGSVR ddPTM_BT-474_Pertuzumab_2h_R1 6 GLSEDTTEETLKESFDGSVR 20 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 284.46 5.01E-45 11375750000 9689870 9601510 6666540 6715800 8179080 9121470 7632480 8792660 9284190 8282310 FALSE TRUE 9311179.168 9327684.336 7871332.074 7062403.243 8442167.536 9305912.373 7725888.573 8611088.498 8230287.674 7721341.767 1.205901701 1.208039304 1.01942542 0.914660101 1.093354988 1.205219592 1.000588862 1.11523214 1.065914179 1 22.88042014 4.247678898 24.66334689 1.058179472 1.206970615 0.409970107 0.07414611 168.1148004 454709.1093 0.018762271 0.049830467 17688.00685 -4.247678898 0.148791143 ESSANNS(ph)VSPSESLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESSANNSVSPSESLR 15 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 ESSANNS(0.658)VS(0.342)PSESLR 366.63 2.02E-97 4270200000 542000 536640 511230 601700 539040 577350 610590 606260 598380 563880 TRUE FALSE 520818.0408 521335.5526 603620.6332 632753.8091 556378.7111 589024.4126 618062.5831 593740.5191 530454.411 525687.9053 0.990736206 0.991720653 1.148249041 1.203668189 1.05838218 1.120483098 1.17572152 1.129454403 1.009067178 1 19.00384702 4.247696049 24.6995483 1.116827619 0.991228333 0.327988116 0.06391185 163.0651993 440869.421 0.015045408 0.039967115 17688.70539 -4.247696049 -0.125599286 ELSDQATAS(ph)PIVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSDQATASPIVAR 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 ELSDQATAS(1)PIVAR 178 1.14E-07 0 621600 605220 407780 464570 483500 515370 446150 502520 619700 596000 TRUE FALSE 597307.1848 587959.7182 481474.917 488546.5134 499052.2166 525791.1345 451610.1172 492142.7864 549354.254 555632.3891 1.075004259 1.058181146 0.866535008 0.879262122 0.898169773 0.946293169 0.812785802 0.885734518 0.988700919 1 19.08377117 4.247721482 24.09476583 0.899656134 1.066592898 0.566152432 0.054378112 77.43313997 203656.1953 0.012772374 0.033880128 17689.74129 -4.247721482 0.166936765 GS(ph)PHSEGGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPHSEGGKR 10 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 GS(1)PHSEGGKR 73.848 0.020577 101190000 114380 112640 121110 149910 121980 127400 152380 118210 147170 146830 TRUE FALSE 109909.9031 109427.6175 142997.2711 157646.8731 125903.5975 129976.1153 154244.872 115768.9222 130463.8786 136885.0733 0.802935634 0.799412345 1.04465204 1.151673219 0.919775944 0.949527309 1.126820246 0.845738103 0.953090614 1 17.06260561 4.247748278 24.95807334 0.993312818 0.801173865 0.449496439 0.087355521 178.8927581 485947.3004 0.022164187 0.058909244 17690.8328 -4.247748278 -0.192138953 AS(ph)SPPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.748)S(0.252)PPDR 81.548 0.02822 24800000 95688 93087 89083 104810 104960 89991 102330 102460 102380 109350 TRUE FALSE 91948.40717 90432.2499 105182.2797 110219.2567 108336.1337 91810.67968 103582.3452 100344.1652 90758.25161 101943.6271 0.90195346 0.887080953 1.031769054 1.081178488 1.06270629 0.900602444 1.016074747 0.98431033 0.890278816 1 16.63741206 4.247749329 24.99914904 0.99767119 0.894517151 0.325800034 0.058270396 226.2958534 615655.6668 0.014744743 0.039184455 17690.87563 -4.247749329 -0.103154039 YLQLAEELIRPER ddPTM_BT-474_Pertuzumab_2h_R1 5 YLQLAEELIRPER 13 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;;;; 217.2 2.39E-11 1931256000 659221 671960 603860 712338 714481 755738 739053 722594 720850 777950 FALSE TRUE 633457.9145 652796.3587 712990.9348 749101.8495 737462.9302 771019.5402 748097.7517 707672.1814 639022.13 725258.7536 0.873423328 0.900087528 0.983084908 1.032875296 1.016827341 1.063095807 1.031490827 0.975751313 0.88109537 1 19.46813628 4.247751238 3.188453563 1.003107098 0.878610023 0.489124107 0.046035986 0.202038302 4.162674343 0.012357349 0.037172149 17690.95339 -4.247751238 -0.124497075 WSLELEDQER ddPTM_BT-474_Pertuzumab_2h_R1 4 WSLELEDQER 10 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ;;; 251.53 4.26E-14 1699210000 1100620 1112150 978000 1159730 1136330 1257870 1168900 1155220 1157560 1236630 FALSE TRUE 1057606.554 1080432.571 1154746.355 1219583.804 1172881.086 1283304.993 1183205.348 1131364.303 1026158.642 1152871.949 0.91736689 0.937166155 1.001625859 1.057865798 1.017355907 1.113137495 1.026311161 0.981344289 0.890089002 1 20.13680085 4.247834854 3.58433331 1.015615866 0.922225566 0.284147131 0.053521633 0.283468908 7.633478654 0.014277471 0.040902679 17694.35979 -4.247834854 -0.0933903 NTALETLHQNSITQVSIYEVDKQDCR ddPTM_BT-474_Pertuzumab_2h_R1 1 NTALETLHQNSITQVSIYEVDKQDCR 26 1 Q92747;Q92747-2 Q92747 ARPC1A Actin-related protein 2/3 complex subunit 1A 0 82.639 0.0092458 48597000 35636 40464 22985 28630 28411 30841 31555 38793 32257 27280 FALSE TRUE 34243.30572 39310.00634 27138.9008 30107.59773 29324.86562 31464.62615 31941.17953 37991.91099 28595.32059 25432.3013 1.346449357 1.545672406 1.067103621 1.183833007 1.153055922 1.237191467 1.255929581 1.493844798 1.124370156 1 14.63437439 4.247864843 24.99087661 1.224619075 1.446060877 0.339713601 0.1362224 251.4920077 675485.1768 0.035046248 0.093245015 17695.58168 -4.247864843 0.221441802 DLPTIPGVT(ph)SPSSDEPPMEASQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVT(0.553)S(0.324)PS(0.104)S(0.02)DEPPMEASQSHLR;DLPT(0.005)IPGVT(0.511)S(0.437)PS(0.038)S(0.009)DEPPMEASQSHLR 150.62 4.89E-07 1254860000 154228 150011 207226 238410 195325 208075 250520 202599 218474 265770 TRUE FALSE 148200.5993 145732.8332 244676.3479 250714.3687 201607.806 212282.4191 253585.9387 198415.2599 193673.7474 247769.1612 0.598139811 0.588179871 0.98751736 1.011886901 0.813692088 0.856774984 1.0234766 0.800806924 0.78167011 1 17.91863711 4.247901489 24.99824857 0.901568703 0.593159647 0.670534897 0.088551994 114.3138345 305922.5948 0.022056929 0.058678655 17697.0749 -4.247901489 -0.308409057 (ac)SSS(ph)PVNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVNVK 8 0 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.144)S(0.144)S(0.712)PVNVK 43.124 0.00087112 1014100000 597400 549190 584810 561460 621250 630910 648150 708150 653330 696300 TRUE FALSE 574052.9475 533527.6389 690498.176 590437.0179 641233.0705 643667.4325 656082.2536 693526.455 579166.7174 649138.9808 0.884329804 0.821900478 1.063713929 0.9095695 0.987820928 0.991571068 1.010696127 1.068379 0.892207577 1 19.30816787 4.24799046 24.9999967 0.994927588 0.853115095 0.498265592 0.054999055 148.8326 394570.1307 0.013095184 0.034863579 17700.70075 -4.24799046 -0.141812493 MGESDDSILR ddPTM_BT-474_Pertuzumab_2h_R1 2 MGESDDSILR 10 0 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ; 193.1 1.42E-06 3511800000 2589100 2610400 2331300 2703500 2698300 2442800 2912500 2963900 2877200 3115400 FALSE TRUE 2487915.11 2535953.948 2752617.769 2843027.959 2785093.27 2492195.09 2948144.046 2902694.429 2550592.318 2904391.183 0.85660469 0.873144762 0.947743467 0.978872259 0.958924984 0.858078314 1.015064384 0.999415797 0.878184844 1 21.46980435 4.248047181 3.78834661 0.958264598 0.860304889 0.355207524 0.048536309 0.223727562 6.891287556 0.012342639 0.034691154 17703.01271 -4.248047181 -0.09795971 VDVFREDLCTK ddPTM_BT-474_Pertuzumab_2h_R1 5 VDVFREDLCTK 11 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;; 184.31 4.52E-06 3110240000 4308490 4519530 2386350 2753560 3137310 4016110 3107270 3288930 3646600 3056340 FALSE TRUE 4140109.448 4390637.429 2817616.529 2895671.562 3238224.425 4097318.496 3145297.7 3221012.446 3232653.256 2849331.369 1.453010868 1.540936051 0.988869374 1.016263532 1.136485724 1.437992976 1.103872204 1.130445016 1.134530469 1 21.44219198 4.248062271 24.99993563 1.130601363 1.496973635 0.604188876 0.122203722 136.4406612 358983.3203 0.030926305 0.0823565 17703.62782 -4.248062271 0.366372272 QLKDSEER ddPTM_BT-474_Pertuzumab_2h_R1 1 QLKDSEER 8 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 0 94.692 0.0092837 227740000 391240 410930 230420 307140 290770 239840 337070 307100 365870 384820 FALSE TRUE 375949.9083 399210.6787 272062.0197 322991.5322 300122.8811 244689.7291 341195.1635 300758.2777 324337.9715 358755.7986 1.047927057 1.112764394 0.758348773 0.900310276 0.836565938 0.682050938 0.951051286 0.838337049 0.904063356 1 18.45264262 4.248066057 24.99999529 0.851784317 1.080345827 0.503678475 0.087728975 142.1133846 373760.4639 0.020094002 0.0535082 17703.78217 -4.248066057 0.22856151 DDSQNAIDHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDSQNAIDHK 10 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 91.961 0.0090474 0 380470 369890 237590 298760 293870 255480 335310 288290 318720 306560 FALSE TRUE 365600.8118 359341.0994 280527.7982 314179.0394 303322.5954 260645.9806 339413.6241 282336.7108 282540.2418 285796.4181 1.279235108 1.257332411 0.981565129 1.099310626 1.061323992 0.911998766 1.187606291 0.987894504 0.988606658 1 18.12462831 4.248069344 24.6150432 1.032623234 1.268283971 0.64200669 0.07189586 94.40173673 244369.4584 0.016610744 0.044199986 17703.91615 -4.248069344 0.235660737 LPLS(ph)PPLVEDSAFEPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPLSPPLVEDSAFEPSR 17 0 O96007 O96007 MOCS2 Molybdopterin synthase catalytic subunit 1 LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR 151.73 2.51E-07 61184000 30715 30771 35427 43623 41649 34241 36984 42016 35786 39007 TRUE FALSE 29514.62384 29893.44121 41829.44697 45874.38826 42988.67791 34933.37648 37436.62126 41148.35492 31723.72331 36365.02115 0.811621248 0.822038329 1.150265988 1.261497637 1.182143625 0.960631271 1.029467881 1.13153667 0.87236917 1 15.15026379 4.248076032 24.70301601 1.084701758 0.816829572 0.469402534 0.108628697 142.8167466 370758.0602 0.027381503 0.072852921 17704.18878 -4.248076032 -0.267872186 NQKDPGVLDR ddPTM_BT-474_Pertuzumab_2h_R1 6 NQKDPGVLDR 10 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;; 140.07 3.64E-05 16052780000 17502600 18596400 9221200 10113300 12296700 15432700 12288000 14139500 15004500 11831200 FALSE TRUE 16818579.04 18066048.88 10887675.96 10635248.62 12692234.52 15744759.77 12438384.22 13847514.38 13301252.06 11029862.29 1.524822215 1.637921527 0.987108967 0.964223156 1.150715593 1.427466578 1.127700772 1.255456689 1.205930928 1 23.39491144 4.2481399 24.99821846 1.157613539 1.581372066 0.627873217 0.13541804 133.1936267 347576.3919 0.034744239 0.092554462 17706.79256 -4.2481399 0.423758527 NDEELNKLLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDEELNKLLGK 11 1 A0A0U1RR32;A0A0U1RRH7;P20671;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;H0YFX9 A0A0U1RR32;Q99878 HIST1H2AD;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ Histone H2A type 1-D;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A 0 ; 147.87 3.20E-05 697470000 1866450 1744630 562410 563820 909460 1257860 808860 912920 977560 562820 FALSE TRUE 1793507.071 1694874.861 664049.9977 592918.8178 938713.6069 1283294.791 818759.0706 894067.883 866591.4871 524699.7001 3.41815913 3.230180731 1.265581051 1.130015545 1.789049254 2.445770011 1.560433655 1.703961109 1.651595164 1 19.00113244 4.24818036 24.34132759 1.620153526 3.324171744 0.767243367 0.386000331 66.99350285 169511.958 0.096945692 0.257979519 17708.44225 -4.24818036 1.704018217 SQT(ph)PPRR ddPTM_BT-474_Pertuzumab_2h_R1 6 SQTPPRR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.199)QT(0.801)PPRR;S(0.1)QT(0.9)PPRR;S(0.082)QT(0.918)PPRR;S(0.069)QT(0.931)PPRR;S(0.069)QT(0.931)PPRR;S(0.192)QT(0.808)PPRR 76.17 0.024311 2235480000 444633 430721 383507 438480 424236 438867 438973 444948 480059 466835 TRUE FALSE 427256.2508 418437.2588 452815.246 461110.0053 437881.9362 447741.1914 444345.2829 435759.6683 425564.7149 435215.8496 0.981711147 0.961447657 1.040438317 1.059497272 1.006125895 1.028779609 1.020976794 1.001249538 0.977824487 1 18.73137157 4.24822263 24.97548023 1.017788919 0.971579386 0.399939869 0.022163091 198.2135409 512353.3662 0.005683779 0.015149518 17710.16591 -4.24822263 -0.046209532 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPT(ph)SPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVPLFPHPPVPSLSTSESKPPPQPSPPTSPVR 32 1 E9PKC0;Q6IQ23;Q6IQ23-2;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 2 TVPLFPHPPVPSLSTSESKPPPQPS(0.999)PPT(0.599)S(0.401)PVR 119.97 6.19E-06 725870000 289900 293400 322420 364900 322100 342610 392270 358060 363490 414980 TRUE FALSE 278570.3875 285032.5193 380688.4662 383732.5327 332460.639 349537.8089 397070.7176 350665.9359 322228.1391 386873.035 0.720056355 0.73675985 0.984013957 0.991882344 0.859353351 0.903494887 1.026359249 0.9064109 0.832904105 1 18.56150065 4.248306448 24.94869985 0.935785102 0.728407948 0.659587322 0.060225805 113.6692439 290979.6063 0.014705387 0.039212291 17713.58427 -4.248306448 -0.207377154 KAERS(ph)PNQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAERSPNQGK 10 2 Q9P2E9;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAERS(1)PNQGK;KAERS(1)PNQGK 60.628 0.050538 131304000 262400 272290 107288 109587 175630 223180 162629 156745 187099 127315 TRUE FALSE 252145.1179 264524.5558 126677.3282 115242.7982 181279.2985 227692.8525 164619.3023 153508.161 165860.3059 118691.8416 2.124367727 2.228666706 1.067279153 0.970941192 1.527310521 1.918353017 1.386947073 1.293333719 1.39740275 1 16.85686125 4.24835663 24.98962657 1.347168728 2.176517694 0.621309425 0.266750369 136.5970404 348451.638 0.069087162 0.184287207 17715.63119 -4.24835663 0.829348966 ETEWLFGMDEGR ddPTM_BT-474_Pertuzumab_2h_R1 5 ETEWLFGMDEGR 12 0 Q8N6R0-3;Q8N6R0-4;Q8N6R0;Q8N6R0-1 Q8N6R0-3 METTL13 Methyltransferase-like protein 13 0 ;;;; 150.94 0.00014181 98695000 152761 160359 159535 190254 176693 184266 205722 206190 194040 227025 FALSE TRUE 146790.9312 155785.7183 188366.5233 200073.0317 182376.4908 187991.9848 208239.6874 201932.1044 172013.3927 211648.3945 0.693560334 0.73605906 0.889997412 0.945308525 0.861695602 0.888227785 0.983894481 0.954092304 0.812731857 1 17.69131002 4.24838374 3.114112714 0.921319183 0.700111879 0.70322305 0.053191888 0.126210751 2.468250143 0.01344743 0.040947342 17716.73707 -4.24838374 -0.221207304 DIIRQPS(ph)EEEIIK ddPTM_BT-474_Pertuzumab_2h_R1 4 DIIRQPSEEEIIK 13 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK 159.8 2.72E-05 977420000 566897 610200 301145 361355 450116 520124 387138 426469 458220 411310 TRUE FALSE 544742.0385 592797.6934 355568.6004 380004.5749 464594.3899 530641.2636 391875.9107 417662.2661 406204.7866 383451.6073 1.420627866 1.545951776 0.927284157 0.991010515 1.211611533 1.383854582 1.021969665 1.08921767 1.059337812 1 18.54868499 4.248387033 24.99999971 1.0965111 1.483289984 0.612193947 0.126388923 138.0212133 351140.9489 0.032338099 0.086293268 17716.87141 -4.248387033 0.386778885 YDEEFQR ddPTM_BT-474_Pertuzumab_2h_R1 4 YDEEFQR 7 0 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ;;; 199.65 0.00086569 7558040000 5556750 5769200 5398650 6426600 6422100 5971720 6931200 6465500 7260500 7647000 FALSE TRUE 5339586.067 5604668.065 6374306.147 6758277.596 6628672.679 6092472.27 7016026.099 6331985.166 6436318.478 7129061.879 0.748988599 0.786171892 0.894129726 0.947989751 0.929809951 0.854596632 0.984144368 0.888193324 0.902828253 1 22.76528081 4.248480355 2.870959548 0.923399881 0.754495642 0.711442767 0.040866916 0.129065143 2.116659146 0.009802192 0.031153299 17720.67884 -4.248480355 -0.168904239 S(ph)PIEPSALEPAYYQGVYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPIEPSALEPAYYQGVYSR 19 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 S(1)PIEPSALEPAYYQGVYSR;S(1)PIEPSALEPAYYQGVYSR;S(1)PIEPSALEPAYYQGVYSR;S(1)PIEPSALEPAYYQGVYSR 264.01 2.78E-31 1526240000 208706 193578 248707 313547 232397 211091 259382 270686 291056 311370 TRUE FALSE 200549.5388 188057.345 293653.8874 329729.1982 239872.2606 215359.4046 262556.3945 265096.2395 258016.5431 290280.6326 0.690881569 0.647846683 1.011620668 1.135898029 0.826346072 0.741900701 0.904491602 0.913241222 0.888852077 1 18.14708879 4.248486816 24.96734182 0.92036788 0.669363988 0.505658954 0.101997239 174.1032347 437912.062 0.026773758 0.071449465 17720.9425 -4.248486816 -0.251003892 DCSPS(ph)SPLKLDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DCSPSSPLKLDAR 13 1 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCS(0.017)PS(0.519)S(0.464)PLKLDAR 114.29 0.00045696 421210000 838760 834700 528340 510520 615780 766280 677230 721200 772840 679170 TRUE FALSE 805980.3319 810895.1733 623822.7909 536867.9984 635587.1229 781774.7066 685518.1433 706306.968 685110.4432 633169.211 1.272930392 1.280692679 0.985238669 0.84790604 1.003818745 1.234701077 1.082677634 1.115510602 1.08203373 1 19.27223158 4.248508781 24.99792714 1.051829277 1.276811682 0.488220704 0.095079843 190.3009914 478181.8781 0.025763795 0.068789155 17721.83877 -4.248508781 0.224982404 SQS(ph)FTHSPSGDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.001)QS(0.499)FT(0.499)HS(0.001)PSGDPK 189.32 5.63E-06 471340000 426620 407060 285750 320310 309180 318280 259280 401300 337590 326610 TRUE FALSE 409947.2187 395451.0474 337391.3815 336841.2375 319125.0555 324715.8397 262453.1462 393013.0148 299268.1985 304488.4138 1.346347513 1.298739228 1.108059835 1.106253053 1.048069618 1.066430856 0.861947891 1.290732248 0.982855783 1 18.21602781 4.248513008 2.173447205 1.065153762 1.353331093 0.520048063 0.102683085 0.274012918 2.463750854 0.026993663 0.104039181 17722.01125 -4.248513008 0.288177331 FNYSGS(ph)GGR ddPTM_BT-474_Pertuzumab_2h_R1 1 FNYSGSGGR 9 0 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 FNYS(0.001)GS(0.999)GGR 88.24 0.01355 224190000 235390 223010 221750 226230 261760 249200 202720 279610 275950 257620 TRUE FALSE 226190.6986 216649.9731 261825.1578 237905.7574 270179.7481 254238.9947 205200.948 273835.9558 244625.3129 240171.1679 0.94178956 0.902064869 1.090160655 0.990567517 1.124946639 1.05857417 0.854394596 1.14016998 1.01854571 1 17.87370344 4.248526523 24.97175294 1.037939434 0.921927166 0.253264726 0.07727325 257.9778204 646406.0572 0.018209967 0.048618588 17722.56275 -4.248526523 -0.116012268 QVVSASYNS(ph)PIGLYSTSNIQDALHGQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QVVSASYNSPIGLYSTSNIQDALHGQLR 28 0 Q53GG5-2;Q53GG5-3 Q53GG5-2 PDLIM3 PDZ and LIM domain protein 3 1 QVVS(0.115)AS(0.115)Y(0.135)NS(0.634)PIGLYSTSNIQDALHGQLR 94.594 0.0015038 71216000 14103 14158 15938 17525 15930 20938 19761 15383 17024 17982 TRUE FALSE 13551.83917 13754.2277 18818.35114 18429.46735 16442.40292 21361.38071 20002.84103 15065.33567 15091.50689 16764.06312 0.808386312 0.820459074 1.122541176 1.09934371 0.980812515 1.274236475 1.193197668 0.898668513 0.900229663 1 14.03308424 4.248576655 24.91096081 1.059931654 0.814422509 0.422146399 0.114278041 196.0046642 487473.925 0.030092615 0.080368291 17724.60867 -4.248576655 -0.245509145 ASS(ph)LPGSLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSLPGSLQR 10 0 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 AS(0.048)S(0.952)LPGS(0.001)LQR 72.187 0.040843 0 158950 157260 144530 173880 158270 156050 165990 159760 191000 184910 TRUE FALSE 152738.0583 152775.0988 170649.7861 182853.9676 163360.8983 159205.4379 168021.4353 156460.9002 169318.4807 172385.881 0.886024177 0.886239046 0.989929019 1.060724733 0.947646625 0.923541052 0.974682116 0.907620156 0.982206198 1 17.39528209 4.248628542 24.68090284 0.967401189 0.886131546 0.419454953 0.040545557 188.2517693 461476.433 0.010701498 0.028562358 17726.72643 -4.248628542 -0.081269643 ADTQTYQPYNKDWIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADTQTYQPYNKDWIK 15 1 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 196.45 8.14E-09 5741000000 4015000 3955900 2549270 2494390 3069600 3839900 3127970 3386700 3555790 3135000 FALSE TRUE 3858089.361 3843081.605 3009979.797 2623125.767 3168336.472 3917545.409 3166251.033 3316763.461 3152151.626 2922663.658 1.320059307 1.314924348 1.029875535 0.897512021 1.084057847 1.34040241 1.083344306 1.134842681 1.078520143 1 21.47885238 4.248632067 24.91982582 1.09099201 1.317491992 0.437758034 0.106701931 196.6382666 486532.4192 0.027684732 0.073917608 17726.87029 -4.248632067 0.226499982 LTVEDLEKER ddPTM_BT-474_Pertuzumab_2h_R1 2 LTVEDLEKER 10 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 88.021 0.011381 432040000 738480 811230 349520 370210 589400 668920 532460 520130 576750 429680 FALSE TRUE 709619.3852 788094.5147 412686.039 389316.5825 608358.5863 682446.0207 538976.4048 509389.1337 511279.7579 400577.3909 1.771491356 1.967396395 1.030227987 0.971888557 1.518704251 1.703655863 1.345498815 1.271637255 1.276357003 1 18.61172147 4.248654727 24.99999057 1.291516635 1.869444116 0.536936071 0.223521284 167.4611174 414740.8778 0.057718484 0.1542289 17727.79523 -4.248654727 0.577927481 RNS(ph)FIGTPYWMAPEVIDCDEDPRR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSFIGTPYWMAPEVIDCDEDPRR 24 2 Q7Z2Y5;F5H049 Q7Z2Y5 NRK Nik-related protein kinase 1 RNS(1)FIGTPYWMAPEVIDCDEDPRR 137.25 7.83E-06 94300000 14192 16674 7305.5 12582 8698.7 12293 10146 12213 12713 10679 TRUE FALSE 13637.36095 16198.47385 8625.76636 13231.35853 8978.501585 12541.57288 10270.16978 11960.79728 11269.87354 9955.701818 1.369804078 1.627054942 0.866414696 1.329023184 0.901845169 1.259737697 1.03158672 1.201401719 1.132001916 1 13.28130731 4.248773064 24.99997937 1.106917449 1.498429577 0.532233214 0.152424762 141.7300912 346946.8343 0.032868319 0.087861806 17732.62639 -4.248773064 0.391512128 EILKEQENR ddPTM_BT-474_Pertuzumab_2h_R1 1 EILKEQENR 9 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 74.944 0.036169 182410000 324100 347930 188530 199810 257260 307500 254240 266530 294450 251010 FALSE TRUE 311433.8137 338007.3771 222601.5648 210122.218 265535.0015 313717.8607 257351.4652 261026.0624 261025.2704 234008.8691 1.330863291 1.444421224 0.951252684 0.897924163 1.134721955 1.340623806 1.099750903 1.115453715 1.115450331 1 17.83620368 4.248801098 24.99989991 1.092568771 1.387642371 0.519892943 0.117166811 175.5190416 428482.7136 0.030660577 0.081971253 17733.77108 -4.248801098 0.2950736 DIELVMSQANVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIELVMSQANVSR 13 0 F8VZJ2;H0YHX9;Q13765;E9PAV3-2;E9PAV3;F8W0W4 F8VZJ2 NACA "Nascent polypeptide-associated complex subunit alpha;Nascent polypeptide-associated complex subunit alpha, muscle-specific form" 0 ; 169.89 6.45E-05 270460000 152585 145858 149316 159540 165706 153577 157580 183813 168306 188054 FALSE TRUE 146621.8095 141698.2726 176300.7227 167773.8785 171036.084 156682.4322 159508.5112 180017.1973 149200.6085 175316.9351 0.83632428 0.808240645 1.005611481 0.956974741 0.975582216 0.893709624 0.909829453 1.026810087 0.851033635 1 17.41960584 4.248802875 24.97823635 0.953889657 0.822282394 0.499585248 0.052091693 155.7996049 379947.3405 0.012246821 0.032741265 17733.84366 -4.248802875 -0.131607263 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK ddPTM_BT-474_Pertuzumab_2h_R1 2 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK 31 2 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ; 144.7 1.16E-08 586910000 614840 611790 395010 450990 490660 584860 496290 384991 664250 570750 FALSE TRUE 590811.3731 594342.3482 466397.0939 474265.6479 506442.5245 596686.2699 502363.7455 377040.8013 588847.1248 532092.5941 1.110354438 1.116990454 0.876533707 0.891321648 0.951793974 1.121395555 0.94412843 0.70859998 1.106662884 1 19.0213178 4.24889306 24.6878215 0.931783744 1.113672587 0.241323243 0.112367427 232.4827663 555469.2799 0.029068574 0.077700644 17737.52661 -4.24889306 0.181888843 GEVISSGSKPLS(ph)PGPCLDIPSILSNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEVISSGSKPLSPGPCLDIPSILSNK 26 1 Q8TEP8;H0Y966;A0A0A0MR42;K7ENP4;Q8TEP8-1;K7EPA2;Q8TEP8-2;C9JT09 Q8TEP8 CEP192 Centrosomal protein of 192 kDa 1 GEVISS(0.002)GS(0.01)KPLS(0.988)PGPCLDIPSILSNK 134.63 2.30E-05 161740000 140550 125390 131910 135470 133180 151010 148050 143650 148550 154560 TRUE FALSE 135057.1506 121814 155749.0713 142461.6229 137463.8557 154063.5257 149861.8802 140683.5773 131687.2268 144091.5135 0.937301214 0.845393299 1.080903847 0.988688504 0.954003829 1.069206103 1.040046541 0.976348807 0.913913828 1 17.13662584 4.248902172 24.99985102 1.002739158 0.891347253 0.421602741 0.052258419 192.5660463 465502.8131 0.012621164 0.033763854 17737.89876 -4.248902172 -0.111391905 SVPGYKVEEKS(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 2 SVPGYKVEEKSP 12 2 S5FZ81 S5FZ81 PHF10 1 SVPGYKVEEKS(1)P;SVPGYKVEEKS(1)P 69.729 0.03874 297490000 995870 947920 462090 377630 572590 649130 536700 588140 688090 463480 TRUE FALSE 956950.2994 920886.2497 545599.9421 397119.5296 591007.8774 662255.8534 543268.2951 575994.7035 609980.9079 432088.0868 2.21471114 2.131246563 1.262705358 0.919070768 1.367794891 1.532687139 1.257309127 1.333049258 1.411704989 1 18.72096593 4.248917845 6.861052522 1.275376095 2.181947484 0.814858907 0.173916682 0.054173328 11.92262316 0.043532646 0.110960518 17738.53892 -4.248917845 0.906571389 ESLCDS(ph)PHQNLSRPLLENK ddPTM_BT-474_Pertuzumab_2h_R1 4 ESLCDSPHQNLSRPLLENK 19 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1;U3KPT1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 ESLCDS(1)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK 299.19 4.74E-50 4283190000 3426840 3333580 2403120 2289840 2507470 3139410 2861110 2806730 3327030 3473770 TRUE FALSE 3292915.304 3238509.562 2837417.241 2408018.917 2588125.05 3202891.021 2896125.12 2748770.045 2949359.502 3238488.464 1.016806248 1.000006515 0.876154809 0.743562605 0.799176863 0.989008007 0.894282982 0.848781793 0.910721016 1 21.62688917 4.24894993 5.767326047 0.872374031 1.010828917 0.310678803 0.073761243 0.170037892 18.9530925 0.01857521 0.047946639 17739.84947 -4.24894993 0.138454886 DYFEEYGKIDTIEIITDR ddPTM_BT-474_Pertuzumab_2h_R1 22 DYFEEYGKIDTIEIITDR 18 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;;;;;;;;;;; 270.42 5.68E-39 7446736000 8661357 8315377 5058356.4 4854013.3 6584026 7997849 5773542.6 6243347 7437509 5959617 FALSE TRUE 8322861.593 8078230.59 5972513.924 5104529.508 6795807.176 8159570.987 5844200.941 6114419.703 6593234.159 5555966.832 1.49800419 1.453973869 1.074972926 0.918747297 1.223154742 1.468614056 1.051878299 1.100514076 1.186694298 1 22.40560656 4.249037025 19.94641382 1.133778258 1.47599298 0.492530841 0.141166473 15.3269196 29172.54694 0.03602034 0.095240326 17743.40744 -4.249037025 0.342214723 AFHNEAQVNPERK ddPTM_BT-474_Pertuzumab_2h_R1 4 AFHNEAQVNPERK 13 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 235.25 7.19E-17 3291850000 3273220 3271270 2149830 2140350 2564620 3359420 2651010 2546790 3224280 2943420 FALSE TRUE 3145298.944 3177976.583 2538352.104 2250813.72 2647113.331 3427349.774 2683453.853 2494197.897 2858273.252 2744059.542 1.146221099 1.158129601 0.925035359 0.820249592 0.964670515 1.249007072 0.977913858 0.908944525 1.041622169 1 21.38788036 4.249099483 24.9262878 0.981182952 1.152175464 0.285228076 0.105053081 265.4636761 627855.3162 0.027415902 0.073387781 17745.95936 -4.249099483 0.170992512 ALAEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 5 ALAEEAKR 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 140.5 0.0010399 1958580000 1772400 1840184 1266360 1503623 1540105 1487012 1647619 1645568 1805903 1681267 FALSE TRUE 1703132.649 1787703.754 1495219.422 1581225.163 1589643.876 1517080.401 1667783.054 1611586.446 1600904.462 1567393.289 1.086601979 1.14055851 0.953952931 1.008824763 1.014195919 0.967900279 1.064048868 1.028195321 1.021380195 1 20.57993579 4.249100137 24.99988958 1.011099245 1.113580273 0.643946622 0.031507326 129.2186338 306502.1 0.007727449 0.020681074 17745.98608 -4.249100137 0.102481028 VVPGQFDDADS(ph)SDSENRDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.726)S(0.274)DSENRDLK 205.38 5.27E-22 165470000 211740 204970 114870 105360 153450 180370 124100 154310 206140 158670 TRUE FALSE 203464.9667 199124.4563 135629.5643 110797.6422 158385.8586 184017.205 125618.7729 151123.4446 182739.8514 147923.1396 1.375477612 1.3461346 0.916892142 0.749021705 1.07073078 1.244005539 0.849216514 1.021634918 1.235370287 1 17.17448822 4.249116862 24.48833444 1.005076198 1.360806464 0.479040107 0.145875351 137.1272647 318098.7174 0.036491907 0.097612786 17746.66952 -4.249116862 0.355730266 LDPAQSAS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 LDPAQSASR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 LDPAQSAS(1)R 86.996 0.014434 300490000 406670 400270 512300 600090 468650 465160 530010 589860 583000 718790 TRUE FALSE 390776.8868 388854.6915 604884.0061 631060.7168 483724.5529 474565.8539 536496.4209 577679.1849 516820.2841 670105.7131 0.583157074 0.580288578 0.902669526 0.94173308 0.721863049 0.708195505 0.800614605 0.86207172 0.77125187 1 19.35402918 4.249133186 24.98458694 0.828436362 0.581722655 0.570688489 0.088755911 151.0411278 356925.8391 0.021831068 0.05845785 17747.33659 -4.249133186 -0.246713707 NSSLGSPSNLCGS(ph)PPGSIR ddPTM_BT-474_Pertuzumab_2h_R1 5 NSSLGSPSNLCGSPPGSIR 19 0 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR 404.02 1.72E-147 2207612000 725445 722143 555499 653512 600107 665953 625285 724733 772669 699330 TRUE FALSE 697093.8074 701548.1887 655890.0263 687239.8326 619409.9867 679419.0259 632937.4249 709767.0103 684958.8544 651963.7562 1.069221718 1.076053971 1.006022221 1.054107419 0.95006813 1.04211165 0.970816888 1.088660226 1.050608792 1 19.31443224 4.249134879 24.68004577 1.023711636 1.072637878 0.2187118 0.03914583 287.6663356 671390.1207 0.009536141 0.025515541 17747.40579 -4.249134879 0.048926242 NGSEADIDEGLYSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGSEADIDEGLYSR 14 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 299.66 2.01E-43 782990000 1230670 1211750 822080 944090 934530 1096860 1009190 1041700 1148370 1076610 FALSE TRUE 1182574.056 1177192.076 970648.1431 992814.598 964590.0062 1119039.261 1021540.769 1020188.531 1018011.852 1003690.246 1.178226112 1.17286392 0.967079382 0.989164339 0.961043519 1.114924914 1.017784893 1.016437626 1.01426895 1 19.93688267 4.249164062 24.90765113 1.012500503 1.17554514 0.732688733 0.039954268 100.5425672 236171.0399 0.00995927 0.026658641 17748.59838 -4.249164062 0.163044637 ENSFGSPLEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 127.93 0.00064306 55652000 49582 50249 50226 64566 52052 51106 53885 62640 56644 63881 FALSE TRUE 47644.28062 48815.94772 59302.95547 67898.259 53726.29985 52139.39834 54544.46075 61346.46211 50214.01059 59554.28297 0.800014344 0.819688279 0.995779859 1.140107069 0.902139983 0.87549368 0.915878053 1.030093203 0.843163717 1 15.86191765 4.249184628 21.32592321 0.965825239 0.809850434 0.359729313 0.081559444 37.59207165 75448.87197 0.02044165 0.054296418 17749.43887 -4.249184628 -0.155974805 ADDLGKGGNEESTK ddPTM_BT-474_Pertuzumab_2h_R1 5 ADDLGKGGNEESTK 14 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;; 201.3 1.65E-08 2920170000 4376100 4430970 1885685 1753251 2538730 3720130 2729800 3042790 3387060 2323892 FALSE TRUE 4205077.174 4304603.074 2226470.226 1843736.494 2620390.556 3795353.577 2763208.109 2979955.323 3002575.149 2166492.725 1.940960671 1.98689939 1.027684146 0.851023626 1.209508126 1.75184229 1.275429212 1.37547442 1.385915177 1 21.04692996 4.249203424 24.99924393 1.259827832 1.963930487 0.600116406 0.237424381 152.025634 357090.8488 0.062040754 0.16619109 17750.20708 -4.249203424 0.704102655 LLPQGTVIFEDISIEHFEGTVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPQGTVIFEDISIEHFEGTVTK 23 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 267.18 3.18E-44 183088000 78688 80301 75919 85441 90104 86998 91696 90686 103401 104482 FALSE TRUE 75612.78597 78010.8941 89639.25211 89850.62025 93002.27699 88757.15917 92818.20308 88813.30241 91663.35197 97405.34108 0.776269403 0.800889286 0.920270399 0.922440384 0.954796482 0.9112145 0.95290671 0.911790888 0.941050572 1 16.57171326 4.249321813 3.274540374 0.93627838 0.779289513 0.856825524 0.024800407 0.072837418 1.591665931 0.005733428 0.017078144 17755.04645 -4.249321813 -0.156988867 HVFEDPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVFEDPQR 8 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ; 140.5 0.00064854 1215020000 783600 783660 856160 1080700 1043210 810690 1037370 805690 935050 1038160 FALSE TRUE 752976.0457 761310.7841 1010887.157 1136475.057 1076765.797 827082.7072 1050065.644 789052.2199 828907.044 967844.4985 0.777992794 0.786604444 1.044472701 1.174233111 1.112540081 0.854561563 1.084952847 0.815267557 0.856446511 1 19.88441575 4.249386844 24.53804693 0.987811865 0.782298424 0.3559567 0.113104603 203.682753 461642.7415 0.030138459 0.080727503 17757.70527 -4.249386844 -0.205513441 FMQDPMEVFVDDETKLTLHGLQQYYVK ddPTM_BT-474_Pertuzumab_2h_R1 1 FMQDPMEVFVDDETKLTLHGLQQYYVK 27 1 O00148;O00148-2 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 265.1 1.55E-53 75236000 323960 320840 197150 187690 249170 340880 239470 246470 275100 253040 FALSE TRUE 311299.285 311689.9573 232779.3906 197376.7034 257184.7793 347772.8272 242400.7055 241380.3084 243871.8013 235901.3754 1.319616236 1.321272319 0.98676572 0.836691618 1.090221619 1.474229756 1.027551048 1.023225524 1.033787111 1 17.8478243 4.249395422 24.60168336 1.063931688 1.3204445 0.317473116 0.1531686 222.5880408 505399.6071 0.039860901 0.106787322 17758.05602 -4.249395422 0.256512812 NPPGFAFVEFEDPR ddPTM_BT-474_Pertuzumab_2h_R1 5 NPPGFAFVEFEDPR 14 0 P84103;P84103-2;A0A087X2D0;Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 P84103;Q16629 SRSF3;SRSF7 Serine/arginine-rich splicing factor 3;Serine/arginine-rich splicing factor 7 0 ;;;; 131.13 0.000135 3927260000 987390 933230 1006640 1110790 1015650 993510 1041300 1179380 1286430 1257460 FALSE TRUE 948801.7072 906615.1941 1188562.241 1168118.005 1048319.305 1013599.453 1054043.741 1155025.391 1140399.86 1172291.114 0.809356734 0.773370354 1.013879766 0.996440211 0.894248273 0.864631183 0.899131392 0.985271813 0.972795789 1 20.16089945 4.249466444 24.9972608 0.948213053 0.791363462 0.632556605 0.049246518 144.8728836 332056.7122 0.01301924 0.034911774 17760.9603 -4.249466444 -0.156849591 FVVDVDKNIDINDVTPNCR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVVDVDKNIDINDVTPNCR 19 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QLH6;J3QRW1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 154.49 3.22E-08 183560000 203190 213270 142540 145540 188560 193720 174530 199270 179010 206980 FALSE TRUE 195249.1102 207187.7484 168300.1488 153051.3368 194625.2036 197637.1511 176665.9503 195155.0049 158689.5353 192961.0602 1.011857573 1.073728286 0.872197471 0.793172139 1.008624245 1.02423334 0.915552341 1.011369883 0.822391497 1 17.55795021 4.249467679 24.98687984 0.935680187 1.042792955 0.240866361 0.079069928 317.5994549 727570.8411 0.019602873 0.052564036 17761.01082 -4.249467679 0.107112768 MVSDEYEQLSSEALEAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 MVSDEYEQLSSEALEAAR 18 0 F8W7C6 F8W7C6 RPL10 0 ;;; 290.71 8.50E-49 256187000 88828 92543 104352 136861 109067 114230 128814 121060 137511 141081 FALSE TRUE 85356.50356 89903.76425 123210.7277 143924.4126 112575.2391 116539.8089 130390.4643 118560.0687 121901.3278 131525.4582 0.648973246 0.683546482 0.936782349 1.094270376 0.855919764 0.886062747 0.991370538 0.901422966 0.926826863 1 17.00498255 4.249471558 5.410094254 0.945926718 0.660297541 0.756944615 0.064206064 0.074524564 6.580517386 0.01592394 0.041462731 17761.16948 -4.249471558 -0.285629178 EDGVFNISVDNTCSLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDGVFNISVDNTCSLFR 17 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 92.65 0.0075759 89334000 52544 52116 47929 53360 50304 52916 54095 59485 61081 59021 FALSE TRUE 50490.52239 50629.70271 56590.83647 56113.91599 51922.07384 53985.99778 54757.03079 58256.61396 54147.34095 55023.4551 0.917618174 0.920147646 1.028485695 1.01981811 0.943635287 0.98114518 0.995157987 1.058759648 0.984077442 1 15.74775911 4.249489797 24.93309568 1.003915757 0.918882845 0.560322418 0.029164096 156.1129289 356138.0731 0.007841067 0.021031862 17761.91539 -4.249489797 -0.085032911 KAAALEFLNRFEEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAAALEFLNRFEEAK 15 2 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 154.82 1.36E-06 259580000 555850 530710 282580 259090 380590 479410 329130 373020 473240 361210 FALSE TRUE 534126.7675 515574.6704 333648.492 272461.6659 392832.023 489103.9987 333157.9914 365317.0066 419519.7792 336744.925 1.586146451 1.531054018 0.990804812 0.809104001 1.166556625 1.452446533 0.989348218 1.084847846 1.245808765 1 18.36129668 4.24949282 23.14403263 1.094700001 1.558601241 0.562916217 0.164323116 63.7638216 134983.9969 0.041858645 0.111836142 17762.03901 -4.24949282 0.46390124 LATKSS(ph)PVKVGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LATKSSPVKVGEK 13 2 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 LAT(0.022)KS(0.155)S(0.822)PVKVGEK;LAT(0.012)KS(0.109)S(0.878)PVKVGEK 88.951 0.0040036 1326450000 3851800 3665300 1543550 1215310 2138670 3075100 2094330 2412100 2890100 1886220 TRUE FALSE 3701267.398 3560769.233 1822503.821 1278032.295 2207462.263 3137280.629 2119961.037 2362289.292 2562027.964 1758464.639 2.104829017 2.024930814 1.036417668 0.726788737 1.255335031 1.784102198 1.205575017 1.343381743 1.456968714 1 20.74588489 4.249615731 24.62971118 1.245291685 2.064880709 0.60854573 0.268748487 124.9160608 278294.0262 0.069716306 0.186953426 17767.06663 -4.249615731 0.819589023 GAVEKGEELSCEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GAVEKGEELSCEER 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ; 176.29 1.48E-06 813940000 1455450 1495750 842900 923650 1174380 1464410 1029680 1098510 1202430 1086320 FALSE TRUE 1398569.405 1453092.674 995230.7802 971319.6872 1212154.999 1494021.374 1042281.532 1075825.385 1065935.187 1012742.579 1.380972257 1.434809501 0.982708539 0.959098302 1.196903364 1.475223225 1.029167287 1.062289082 1.052523326 1 19.94983608 4.24963285 24.99994016 1.103481263 1.407891053 0.433398768 0.14294265 214.2932232 483842.017 0.037047206 0.099442994 17767.76697 -4.24963285 0.304409791 LLTDDGNKWLYK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLTDDGNKWLYK 12 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 143.86 5.71E-05 326570000 527430 520910 311500 305700 428500 447940 378910 382220 485480 505920 FALSE TRUE 506817.4525 506054.1568 367794.9793 321477.2136 442283.0917 456997.6537 383547.2139 374327.0234 430370.3457 471653.5878 1.074554431 1.072936091 0.779798964 0.681596031 0.93772867 0.968926487 0.813196854 0.793648205 0.912471265 1 18.84736812 4.249701059 24.85907919 0.848475549 1.073745437 0.452039298 0.09292301 168.9853097 377070.3319 0.023085798 0.061959673 17770.55775 -4.249701059 0.225269888 NLATTVTEEILEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLATTVTEEILEK 13 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 203.82 1.93E-07 16874000 23487 23216 15505 19742 20375 16149 18638 20383 21950 20444 FALSE TRUE 22569.10207 22553.90241 18307.09841 20760.88699 21030.38038 16475.54384 18866.09742 19962.08393 19458.32802 19059.30967 1.184151077 1.183353584 0.960533132 1.089278014 1.103417739 0.864435498 0.989862579 1.047366577 1.020935614 1 14.21820825 4.249719568 24.86889941 1.012927636 1.183752463 0.543335472 0.06384556 155.0275334 345487.9255 0.015964999 0.042851494 17771.31512 -4.249719568 0.170824828 DWEDDSDEDMSNFDR ddPTM_BT-474_Pertuzumab_2h_R1 6 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;;; 504.25 1.76E-249 2868430000 2413430 2343410 2333620 2458380 2385480 2624390 2589930 2646080 3100380 2924450 FALSE TRUE 2319110.487 2276578.241 2755357.045 2585257.286 2462211.131 2677456.964 2621626.338 2591437.523 2748437.86 2726374.397 0.850620696 0.835020401 1.010630473 0.94824001 0.903108221 0.982057698 0.961579723 0.950506844 1.008092602 1 21.37855226 4.24975765 24.99715944 0.964822978 0.842820473 0.722428864 0.031505423 108.9731972 243275.6536 0.007519782 0.02018871 17772.87352 -4.24975765 -0.122002505 SNTHEFVNLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNTHEFVNLVK 11 0 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 81.676 0.021022 800590000 1116530 1228210 1069270 1428950 1255760 1346110 1314870 1369930 1602980 1663310 FALSE TRUE 1072894.773 1193182.653 1262510.875 1502698.281 1296152.661 1373329.266 1330961.772 1341640.467 1421016.431 1550652.532 0.691898895 0.769471322 0.814180384 0.969074792 0.835875629 0.885646035 0.85832367 0.865210251 0.916399001 1 20.56444402 4.249832251 1.993077729 0.890859522 0.702161367 0.653715038 0.050790929 0.21830189 1.613607349 0.012709752 0.052857265 17775.92669 -4.249832251 -0.188698155 ELISNASDALDKIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELISNASDALDKIR 14 1 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ; 272.72 4.98E-33 8600400000 4223700 4589900 2324700 2523600 3150500 4212600 3342900 3327500 3787400 2955400 FALSE TRUE 4058633.134 4459000.546 2744825.003 2653843.298 3251838.694 4297781.658 3383811.41 3258785.962 3357470.23 2755228.126 1.473066095 1.618377986 0.996224224 0.963202747 1.180242995 1.559864179 1.228142011 1.18276448 1.218581575 1 21.39374034 4.249873128 24.99981022 1.182983354 1.545722183 0.455772436 0.165098942 209.1580324 462214.6466 0.04265898 0.114613091 17777.59992 -4.249873128 0.36273883 AAALEFLNRFEEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAALEFLNRFEEAK 14 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 216.15 5.69E-12 416600000 900970 882280 540980 540190 644410 860120 659930 700420 842740 686910 FALSE TRUE 865759.0963 857118.2382 638747.12 568069.2706 665138.0329 877512.2157 668006.4207 685956.0822 747075.6883 640384.9739 1.35193537 1.338442145 0.997442392 0.887074641 1.038653404 1.370288579 1.043132566 1.071162051 1.166604025 1 19.28857993 4.249916475 24.84981743 1.07538979 1.345188982 0.451759018 0.120418587 188.9636708 413496.9391 0.03077272 0.08267263 17779.37437 -4.249916475 0.269799193 RKDREDS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 6 RKDREDSPER 10 3 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER 161.21 3.95E-05 3262358000 1063096 1064873 710352 742732 878777 1012523 883871 895761 1034167 895811 TRUE FALSE 1021549.033 1034503.865 838728.4081 781064.4875 907043.6603 1032996.909 894688.0777 877263.2223 916772.6977 835136.9231 1.223211434 1.238723658 1.004300474 0.935253209 1.086101734 1.236919217 1.071307055 1.050442386 1.097751366 1 19.67165323 4.249933364 24.96526845 1.064585569 1.230967656 0.452825976 0.074939835 206.7036772 453743.5631 0.01957476 0.05260219 17780.06583 -4.249933364 0.166382087 S(ph)DERPVHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDERPVHIK 9 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 S(1)DERPVHIK;S(1)DERPVHIK 96.82 0.0043055 677340000 992370 977530 902160 1087860 1061350 957430 963800 1035380 1101780 1145220 TRUE FALSE 953587.0833 949651.8015 1065200.38 1144004.585 1095489.287 976789.8906 975595.2727 1013999.041 976710.5534 1067653.229 0.893161803 0.889475885 0.997702579 1.071513253 1.026072189 0.914894334 0.913775415 0.949745679 0.914820025 1 20.02601171 4.250013121 24.79831807 0.97076925 0.891318783 0.303136827 0.049736321 279.6612631 605542.5837 0.013705889 0.036829697 17783.33135 -4.250013121 -0.079450467 SWGNNYPQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SWGNNYPQHR 10 0 Q9BTL3;A0A3B3IU46 Q9BTL3 FAM103A1 RNMT-activating mini protein 0 ; 106.29 0.0024361 478170000 474910 478790 327090 371120 423260 402670 416260 400200 480200 421860 FALSE TRUE 456349.9922 465135.378 386202.4391 390273.5477 436874.5423 410812.2633 421354.3144 391935.7301 425689.7092 393287.0464 1.160348393 1.182686748 0.981986167 0.992337661 1.11082871 1.04456088 1.071365859 0.996564046 1.082389346 1 18.58522314 4.250013455 24.99982286 1.036209472 1.171517651 0.636748136 0.041235462 131.7017538 287479.4881 0.009986839 0.02683946 17783.34503 -4.250013455 0.135308179 SQEADVQDWEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQEADVQDWEFR 12 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;;; 253.16 1.04E-20 2631530000 2670080 2824940 2389700 3059710 2853070 2970470 2987000 3029660 3092190 3230760 FALSE TRUE 2565730.322 2744375.477 2821571.949 3217622 2944841.588 3030534.939 3023555.8 2967096.462 2741177.555 3011937.748 0.851853702 0.911166069 0.936796237 1.068289676 0.977723258 1.006174494 1.003857335 0.985112147 0.91010432 1 21.52226052 4.250022809 2.205628808 0.992501411 0.863546581 0.57931781 0.038467195 0.221852492 2.059753757 0.009925698 0.037904697 17783.72808 -4.250022809 -0.12895483 KGVNLPGAAVDLPAVSEKDIQDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGVNLPGAAVDLPAVSEKDIQDLK 24 2 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 106.11 0.0015458 3027400000 1904250 1803890 883720 910510 1342700 1642850 1167960 1089930 1212980 925080 FALSE TRUE 1829829.805 1752444.823 1043427.862 957501.5302 1385889.165 1676069.553 1182253.844 1067422.565 1075287.596 862423.5076 2.121729972 2.032000297 1.209878735 1.110245166 1.606970534 1.943441404 1.370850671 1.237701147 1.246820832 1 19.71803698 4.250024546 22.06607382 1.366297094 2.076867939 0.570014697 0.254966685 39.96635271 76921.10767 0.066034462 0.17643628 17783.79918 -4.250024546 0.710570845 GRLDSSEMDHS(ph)ENEDYTMSSPLPGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRLDSSEMDHSENEDYTMSSPLPGKK 26 2 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GRLDS(0.002)S(0.002)EMDHS(0.996)ENEDYTMSSPLPGKK 109.14 0.001284 59109000 70228 69816 45823 55843 51771 65260 54525 53643 70737 65677 TRUE FALSE 67483.41212 67824.91604 54104.23543 58725.06392 53436.26123 66579.60191 55192.29326 52535.2533 62707.23231 61228.63829 1.102154384 1.107731903 0.883642637 0.959111056 0.872733131 1.087393151 0.901413045 0.858017666 1.024148733 1 15.90191898 4.250025578 24.98376448 0.939192646 1.104943261 0.44153866 0.069864237 179.2150454 390527.0694 0.016770833 0.045079621 17783.84146 -4.250025578 0.165750616 NLKPIKPMQFLGDEETVRK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLKPIKPMQFLGDEETVRK 19 3 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 212.79 2.87E-17 4156900000 4712200 4075400 2813900 2602200 2287000 3029100 2203500 3136000 3546100 2694200 FALSE TRUE 4528042.014 3959173.582 3322434.325 2736499.854 2360563.432 3090350.477 2230467.092 3071240.504 3143561.594 2511719.434 1.802765847 1.576280188 1.32277287 1.089492647 0.939819711 1.230372483 0.888023981 1.22276416 1.251557619 1 21.26024389 4.250095148 1.679582964 1.092421609 1.810043607 0.807823351 0.118511144 0.181628882 0.896524952 0.032193287 0.156985345 17786.69051 -4.250095148 0.717621998 KGTVEGFEPADNK ddPTM_BT-474_Pertuzumab_2h_R1 4 KGTVEGFEPADNK 13 1 P37108;H0YLA2 P37108 SRP14 Signal recognition particle 14 kDa protein 0 ;;; 186.95 1.18E-05 3610480000 5282460 4547190 3362050 2554160 3578000 3519010 3032140 3681500 3716130 3099770 FALSE TRUE 5076015.623 4417508.593 3969647.223 2685980.504 3693089.619 3590166.793 3069248.236 3605475.738 3294290.502 2889819.817 1.756516304 1.528644993 1.373665998 0.929462968 1.277965359 1.242349704 1.062089829 1.247647247 1.139963981 1 21.46254811 4.250102785 2.030776585 1.151295993 1.726601171 0.764728454 0.115055936 0.160549085 1.238430329 0.029139022 0.119273769 17787.00329 -4.250102785 0.575305178 DVYEDELVPVFEAVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 DVYEDELVPVFEAVGR 16 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7;D6RBP6;D6RFL5;D6RA49 B7Z8Z7 RBM47 RNA-binding protein 47 0 ;; 156.14 4.46E-07 198755000 199579 208939 188952 223058 227609 233634 225214 255231 238881 249362 FALSE TRUE 191779.232 202980.2643 223099.8296 234570.0501 234930.2502 238358.2396 227970.2363 249960.3907 211764.2304 232472.4896 0.824954524 0.873136708 0.959682713 1.009022833 1.010572264 1.025318049 0.980633178 1.07522568 0.910921678 1 17.82670047 4.250134311 1.774348898 1.009468513 0.820631925 0.707366092 0.039098336 0.201780748 1.136507442 0.010136219 0.046911741 17788.29449 -4.250134311 -0.188836588 GRAS(ph)PGGVSTSSSDGKAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRASPGGVSTSSSDGKAEK 19 2 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGKAEK 88.239 0.0013506 146630000 286340 279340 129480 143280 172060 236140 171790 195270 205840 163530 TRUE FALSE 275149.5162 271373.4967 152879.9163 150674.698 177594.4662 240914.9126 173892.4174 191237.6063 182473.9062 152453.9674 1.804803908 1.780035648 1.00279395 0.988329136 1.164905506 1.580246921 1.140622447 1.254395733 1.196911495 1 17.21801417 4.250142735 24.9924819 1.185500679 1.792420248 0.698152194 0.16435183 122.9228186 265243.9241 0.041605918 0.11189587 17788.63956 -4.250142735 0.606919568 TILHYMGTSTFSEYTVVADISVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TILHYMGTSTFSEYTVVADISVAK 24 0 P11766;H0YAG8 P11766 ADH5 Alcohol dehydrogenase class-3 0 143.95 2.37E-07 178130000 119240 117320 120940 130290 137090 150740 121760 128520 146380 147730 FALSE TRUE 114579.969 113974.1485 142796.5483 137014.2825 141499.6244 153788.0661 123250.1353 125866.0171 129763.5561 137724.1155 0.83195284 0.827554042 1.036830389 0.994845979 1.027413564 1.116638618 0.894905985 0.913899622 0.942199234 1 17.07142167 4.250142893 24.93540703 0.984873544 0.829753326 0.525973377 0.060960399 187.4568775 403566.5942 0.016690814 0.044874344 17788.646 -4.250142893 -0.155120218 GNS(ph)PPSSGEACR ddPTM_BT-474_Pertuzumab_2h_R1 5 GNSPPSSGEACR 12 0 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(1)PPSSGEACR;GNS(1)PPSSGEACR;GNS(0.995)PPS(0.002)S(0.003)GEACR;GNS(1)PPSSGEACR;GNS(1)PPSSGEACR 187.08 1.15E-05 1318452000 849975 877665 799052 1000488 910746 1042256 935154 931123 1027711 1064419 TRUE FALSE 816757.0373 852634.8535 943458.4712 1052123.306 940040.9722 1063331.13 946598.6944 911894.9847 911049.5558 992324.953 0.82307417 0.85922948 0.950755565 1.060260857 0.947311633 1.071555368 0.953920076 0.918947953 0.918095986 1 19.92045311 4.250216529 3.388689958 0.97705102 0.832066563 0.553586922 0.049903903 0.17915227 4.228887902 0.013375644 0.039312164 17791.66239 -4.250216529 -0.144984458 LPSS(ph)PVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 13 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPS(0.056)S(0.944)PVYEDAASFK;LPS(0.008)S(0.992)PVYEDAASFK;LPS(0.027)S(0.973)PVYEDAASFK;LPS(0.016)S(0.984)PVYEDAASFK;LPS(0.002)S(0.998)PVYEDAASFK;LPS(0.009)S(0.991)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.013)S(0.987)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.007)S(0.993)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.001)S(0.999)PVYEDAASFK 346.5 9.14E-82 1.44047E+11 20847841 20107760 21933700 26337110 24479097 22000115 24100600 24173731 23748222 23578960 TRUE FALSE 20033084.33 19534306.37 25897607.5 27696371.4 25266489.39 22444972.4 24395550.35 23674535.01 21052423.4 21981936.04 0.911343036 0.88865268 1.178131328 1.259960513 1.149420567 1.021064403 1.109799897 1.07699954 0.957714706 1 24.38981512 4.250222027 24.99979493 1.101563901 0.899997728 0.455152678 0.084651637 193.9511987 415785.4733 0.021678907 0.058325194 17791.88765 -4.250222027 -0.201566173 IVDRIDNDGDGFVTTEELK ddPTM_BT-474_Pertuzumab_2h_R1 1 IVDRIDNDGDGFVTTEELK 19 1 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 182.15 2.73E-14 268820000 464400 454010 274050 263310 316160 426140 356340 344140 432480 410070 FALSE TRUE 446250.7346 441062.0793 323576.9312 276899.4607 326329.5735 434756.8428 360700.9955 337033.3887 383386.6835 382295.5936 1.167292383 1.153720018 0.846405077 0.724307225 0.853605375 1.137226926 0.943513348 0.881604168 1.002854048 1 18.54432905 4.250225008 24.40687017 0.916765621 1.160506464 0.446038697 0.105340549 151.5850847 317171.9888 0.027340297 0.073476383 17792.00974 -4.250225008 0.243740843 LRLS(ph)PS(ph)PTSQR ddPTM_BT-474_Pertuzumab_2h_R1 7 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 LRLS(0.921)PS(0.957)PT(0.122)S(0.001)QR;LRLS(0.997)PS(0.737)PT(0.144)S(0.122)QR;LRLS(0.994)PS(0.738)PT(0.145)S(0.124)QR;LRLS(0.999)PS(0.448)PT(0.303)S(0.25)QR;LRLS(0.993)PS(0.478)PT(0.295)S(0.234)QR;LRLS(0.989)PS(0.858)PT(0.084)S(0.07)QR;LRLS(0.896)PS(0.936)PT(0.153)S(0.015)QR 137.8 0.00084776 25104811000 2835252 2864075 2816657 3330040 3068450 3469679 3409781 3229719 3390929 3681028 TRUE FALSE 2724447.217 2782394.385 3325689.576 3501903.763 3167149.481 3539838.287 3451510.92 3163024.174 3006004.956 3431708.695 0.793903988 0.810789794 0.969106026 1.020454845 0.922907438 1.031508966 1.005770369 0.921705324 0.87594992 1 21.71049566 4.250232379 6.365109446 0.967907673 0.800165478 0.667812625 0.04687979 0.084937427 13.63109491 0.011943481 0.030686209 17792.31175 -4.250232379 -0.167742195 GAVAEDGDELRTEPEAK ddPTM_BT-474_Pertuzumab_2h_R1 4 GAVAEDGDELRTEPEAK 17 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;; 256.45 3.88E-27 3950020000 3596010 3568330 2490870 2573890 2977420 3402620 2892950 3316830 3477100 3249420 FALSE TRUE 3455473.954 3466564.722 2941025.618 2706728.771 3073191.418 3471423.308 2928354.787 3248336.301 3082394.185 3029333.889 1.14067121 1.144332335 0.970848948 0.893506253 1.014477615 1.145936181 0.966666236 1.072293917 1.017515499 1 21.53056917 4.250260435 24.98909765 1.014279606 1.142501865 0.412870371 0.062975947 226.6046255 483984.7338 0.016120596 0.043370427 17793.46116 -4.250260435 0.128222259 RS(ph)RSESETSTMAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSRSESETSTMAAK 14 2 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RS(0.569)RS(0.291)ES(0.087)ET(0.047)S(0.006)T(0.001)MAAK 57.173 0.093645 77387000 59792 56604 21066 26215 33141 44711 29767 33044 33668 21089 TRUE FALSE 57455.26254 54989.70934 24873.09481 27567.95929 34207.01036 45615.08705 30131.29745 32361.62985 29846.14979 19660.62325 2.922352044 2.796946397 1.265122397 1.402191525 1.73987416 2.320124163 1.532570818 1.64601241 1.518067327 1 14.26302144 4.250295771 24.61342991 1.60493221 2.859650493 0.716080415 0.327804677 95.69309945 200702.8947 0.080093585 0.215368778 17794.90899 -4.250295771 1.254718283 RGTQS(ph)PERK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGTQSPERK 9 2 A0A0C4DGC9;Q8TDR2 A0A0C4DGC9 STK35 Serine/threonine-protein kinase 35 1 RGT(0.039)QS(0.961)PERK 68.515 0.04556 40617000 38757 39732 24988 29178 32279 30633 30449 34571 38267 35583 TRUE FALSE 37242.33359 38598.88226 29503.88746 30683.88008 33317.28335 31252.42025 30821.64397 33857.09677 33923.09059 33172.93172 1.122672362 1.163565602 0.889396442 0.92496739 1.004351489 0.942106068 0.929120291 1.020624196 1.022613584 1 15.0177189 4.250319651 24.99989943 0.967206808 1.143119078 0.722532247 0.043742267 114.5078884 243440.9222 0.011135322 0.02996742 17795.88749 -4.250319651 0.17591227 NEDTTFDKEFLLELLVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NEDTTFDKEFLLELLVSR 18 1 O60306;H0YH15 O60306 AQR Intron-binding protein aquarius 0 ; 159.26 3.97E-11 171120000 474220 522260 324260 240250 491210 740890 409970 420790 326310 311250 FALSE TRUE 455686.9581 507365.6561 382860.9951 252649.3313 507010.2158 755871.3034 414987.3355 412100.5395 289268.6568 290168.7603 1.570420461 1.748519226 1.319442502 0.870697904 1.747294282 2.604936874 1.430158557 1.420209877 0.996898 1 18.14653268 4.250350923 24.57250154 1.469586841 1.659469798 0.031575582 0.47022881 935.917408 1950524.507 0.120550281 0.32412804 17797.16895 -4.250350923 0.189882957 RPKEEDPATGTGDPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPKEEDPATGTGDPPR 16 2 P45974-2;P45974;F5H571 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 101.39 0.00097448 588974000 1075410 1061060 599210 603600 821890 1060290 767700 756800 873640 701760 FALSE TRUE 1033381.788 1030799.608 707500.5764 634751.8683 848326.8383 1081729.79 777095.3422 741171.8155 774468.0498 654229.1701 1.579540986 1.57559408 1.081426217 0.970228625 1.296681464 1.653441698 1.187802956 1.132893257 1.183787097 1 19.31943656 4.250367401 24.84849845 1.201769116 1.57756784 0.424241349 0.180856516 210.4293014 442859.1045 0.046902127 0.126210247 17797.84421 -4.250367401 0.375798724 RPDVSVQGDEVTLYTPEER ddPTM_BT-474_Pertuzumab_2h_R1 2 RPDVSVQGDEVTLYTPEER 19 1 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2;D6RA17 D6RIY6 EXOSC9 Exosome complex component RRP45 0 ; 197.85 1.23E-15 519130000 478200 465830 458900 506940 515930 478630 512820 549000 525150 541770 FALSE TRUE 459511.4153 452544.9845 541833.4382 533103.2342 532525.357 488308.2265 519096.0446 537662.9581 465537.1736 505075.4353 0.909787693 0.895994841 1.072777253 1.055492302 1.054348162 0.966802565 1.027759436 1.06452011 0.921718106 1 18.94613935 4.250378875 24.99881805 1.025661208 0.902891188 0.516705183 0.045243023 159.927252 338282.9973 0.010822428 0.029137505 17798.31444 -4.250378875 -0.122770021 LS(ph)EGSQPAEEEEDQETPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 LS(1)EGSQPAEEEEDQETPSR 476.46 7.51E-240 1138300000 234460 220830 254960 295880 257850 271800 254700 259030 314210 319610 TRUE FALSE 225297.044 214532.1446 301036.9436 311150.4023 266143.9794 277295.9822 257817.0948 253680.94 278542.1981 297962.53 0.756125423 0.719997057 1.010318121 1.04426017 0.893212913 0.930640447 0.865266833 0.851385374 0.934822906 1 18.18477139 4.250395855 24.99461619 0.929473251 0.738061127 0.637652031 0.060748323 156.6531186 330826.3368 0.016550834 0.044554346 17799.01034 -4.250395855 -0.191412123 SGPKPFSAPKPQTS(ph)PSPKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFS(0.001)APKPQT(0.174)S(0.69)PS(0.135)PKR 53.355 0.08563 1534400000 1689800 1720500 704080 785670 955870 1370300 1002200 1131900 1389500 987890 TRUE FALSE 1623760.748 1671433.025 831322.9182 826218.5229 986616.4266 1398008.405 1014465.223 1108525.869 1231769.785 920979.3304 1.763080554 1.814843145 0.902651005 0.897108649 1.071268805 1.517958502 1.101507048 1.203638163 1.337456493 1 19.81280925 4.250431496 24.98242839 1.141415269 1.788962293 0.679186818 0.181282694 129.2618075 272027.9882 0.046405663 0.12491789 17800.47108 -4.250431496 0.647547025 IEWLESHQDADIEDFKAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEWLESHQDADIEDFKAK 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 203.56 7.03E-16 1470270000 3590300 3522200 1861600 1692020 2390940 2981100 2611680 2574790 3317000 2395120 FALSE TRUE 3449987.107 3421750.305 2198032.531 1779345.355 2467846.756 3041379.885 2643642.521 2521619.687 2940468.066 2232896.389 1.545072635 1.532426816 0.984386263 0.796877707 1.105222243 1.362078375 1.183952168 1.129304386 1.316885136 1 21.09048488 4.250432518 24.94489601 1.116649553 1.538750062 0.552002019 0.154461874 170.3965699 358025.2866 0.040609135 0.109332732 17800.51298 -4.250432518 0.422100509 CDEPILSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 CDEPILSNR 9 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 168.27 0.00013809 1074620000 699920 690160 753270 940740 758270 674720 847170 840660 873100 975940 FALSE TRUE 672566.3526 670477.3125 889402.6454 989291.7041 782660.4432 688363.3007 857537.9199 823300.0772 773989.3483 909838.7145 0.73921492 0.736918865 0.9775388 1.087326455 0.860218884 0.756577281 0.942516411 0.904885739 0.850688519 1 19.7952513 4.250464375 24.98234426 0.917312259 0.738066759 0.423755056 0.08584623 221.387154 464614.8852 0.021994452 0.059218795 17801.81874 -4.250464375 -0.179245501 NGYGFVEFEDSRDADDAVYELNGK ddPTM_BT-474_Pertuzumab_2h_R1 4 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 292.44 6.90E-62 1098594000 1259453 1259829 717708 749832 986538 1092839 934747 970382 1110240 892761 FALSE TRUE 1210232.184 1223899.91 847413.8009 788530.9194 1018270.891 1114936.953 946186.7134 950343.2726 984210.2097 832293.5023 1.454093035 1.470514797 1.018167027 0.94741929 1.223451689 1.339595888 1.136842605 1.141836708 1.182527807 1 19.66673285 4.250491804 24.99832534 1.134661522 1.462304148 0.604990783 0.109145979 156.6403185 328187.8868 0.028187792 0.075898378 17802.94312 -4.250491804 0.327642625 KMAVDALEYDESAEDANPAGALEEILENPER ddPTM_BT-474_Pertuzumab_2h_R1 1 KMAVDALEYDESAEDANPAGALEEILENPER 31 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 111.79 0.00014605 25741000 31808 35742 19439 25124 25465 33299 28404 25866 27319 27419 FALSE TRUE 30564.90819 34722.67316 22952.05972 26420.65265 26284.10485 33972.32859 28751.61665 25331.85806 24217.86165 25561.88671 1.195721918 1.358376772 0.897901629 1.033595562 1.02825371 1.329022735 1.124784605 0.991001108 0.947420741 1 14.6417067 4.25060922 24.9999862 1.053716389 1.277049373 0.385150007 0.117269583 244.7090727 507743.9798 0.029853701 0.08043504 17807.75698 -4.25060922 0.223332983 GFCYVEFDEVDSLKEALTYDGALLGDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFCYVEFDEVDSLKEALTYDGALLGDR 27 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 308.66 5.49E-82 1001478000 1274658 1235437 672915 727701 986175 1203702 760001 873769 958717 798912 FALSE TRUE 1224842.956 1200203.546 794525.7094 765257.7358 1017896.214 1228041.679 769302.1196 855725.3648 849887.4654 744800.9786 1.644523828 1.611441957 1.06676244 1.027466072 1.366668739 1.648818563 1.032896225 1.14893158 1.141093379 1 19.50649544 4.250636993 24.29140769 1.1920846 1.627983413 0.479060307 0.186852189 142.2165922 286058.0973 0.047736454 0.128464149 17808.89579 -4.250636993 0.435898813 GESAADS(ph)DGWDSAPSDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GESAADSDGWDSAPSDLR 18 0 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L0Y2;A0A087WVQ2;Q9BUL5-2 I3L4Q4 PHF23 PHD finger protein 23 1 GESAADS(1)DGWDSAPSDLR;GESAADS(1)DGWDSAPSDLR 406.71 3.35E-147 542650000 366830 455610 408920 610910 533280 499580 587220 608130 604640 664930 TRUE FALSE 352493.878 442616.4489 482820.9404 642439.1383 550433.4355 509681.8499 594406.574 595571.903 536003.8021 619893.6988 0.568636008 0.714019919 0.778876993 1.036369848 0.887948106 0.82220847 0.958884685 0.96076457 0.864670512 1 19.24166131 4.250668185 1.778382658 0.928172148 0.581226114 0.762566579 0.066391941 0.192847617 1.091770153 0.017839312 0.082475592 17810.17492 -4.250668185 -0.346946034 QGLAET(ph)ASPVAVSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGLAETASPVAVSLR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 QGLAET(0.731)AS(0.269)PVAVSLR 176.94 8.65E-06 778260000 242440 282560 358400 450320 409740 424600 502630 411740 492190 586550 TRUE FALSE 232965.1768 274501.6655 423170.8526 473561.0692 422919.6592 433185.7029 508781.3363 403237.4251 436318.6546 546822.4461 0.426034407 0.501994144 0.773872499 0.866023464 0.773413129 0.792187128 0.930432428 0.737419299 0.797916504 1 19.06071294 4.250766989 3.131517025 0.827114252 0.437971922 0.801748758 0.074417951 0.094889044 1.877214144 0.017836446 0.054355454 17814.22727 -4.250766989 -0.38914233 S(ph)YS(ph)PAHNR ddPTM_BT-474_Pertuzumab_2h_R1 4 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(0.977)Y(0.06)S(0.962)PAHNR;S(0.999)Y(0.001)S(1)PAHNR;S(0.997)Y(0.03)S(0.973)PAHNR;S(0.991)Y(0.208)S(0.801)PAHNR 126.67 0.00063867 1220300000 693951 648341 654490 703977 688515 693930 736360 706294 843335 787275 TRUE FALSE 666830.6277 629850.9495 772770.9021 740309.3373 710661.7103 707961.74 745371.794 691708.7821 747603.1463 733952.163 0.908547806 0.85816349 1.052890012 1.008661565 0.96826707 0.964588397 1.015559094 0.942443959 1.018599282 1 19.48532651 4.250834026 24.99991179 0.991133126 0.88335561 0.659936527 0.03227727 134.469858 273898.5814 0.007850587 0.021171281 17816.97728 -4.250834026 -0.107777516 QTTVSNSQQAYQEAFEISKK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTTVSNSQQAYQEAFEISKK 20 1 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 275.5 2.61E-44 807060000 222380 225400 122420 142410 157770 185670 150250 168120 201670 200760 FALSE TRUE 213689.1437 218971.8127 144544.0172 149759.7972 162844.8153 189424.3746 152088.8044 164648.2632 178777.2671 187162.3464 1.141731485 1.169956548 0.772292184 0.800159862 0.870072525 1.012085915 0.812603643 0.879708266 0.955198898 1 17.51393069 4.250879496 24.99992572 0.880228612 1.155844203 0.654391911 0.077774214 125.9012537 255499.126 0.018781283 0.050646877 17818.84277 -4.250879496 0.275615591 SLDLFNCEVTNLNDYRENVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDLFNCEVTNLNDYRENVFK 21 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 231.76 3.88E-26 563840000 627660 637590 333410 400410 460730 581990 441430 444690 496470 418860 FALSE TRUE 603130.3533 619406.5575 393664.6037 421075.2081 475549.7989 593758.2366 446832.3524 435506.9961 440112.807 390490.2391 1.544546554 1.586228017 1.008129178 1.078324542 1.217827621 1.520545655 1.144285587 1.115282669 1.127077614 1 18.57492696 4.250879786 24.99705808 1.165191718 1.565387555 0.58452882 0.1392118 164.2239764 333223.5962 0.03559552 0.095990258 17818.85468 -4.250879786 0.400195837 QQS(ph)LGGFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQSLGGFFK 9 0 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 QQS(1)LGGFFK 66.267 0.067358 123420000 230830 223400 127260 134210 167890 129290 106670 290330 141690 156390 TRUE FALSE 221808.9084 217028.8507 150258.7129 141136.5942 173290.3343 131904.3324 107975.4594 284334.584 125605.9452 145797.566 1.5213485 1.488562921 1.030598226 0.96803121 1.188568088 0.904708741 0.740584787 1.950201172 0.861509205 1 17.15360711 4.250891669 23.21194253 1.132676448 1.504956512 0.209348501 0.317234285 171.9489072 323660.3419 0.082347252 0.221342644 17819.34224 -4.250891669 0.372280064 TTS(ph)PLEEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 TTSPLEEEER 10 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 TT(0.001)S(0.999)PLEEEER;T(0.029)T(0.055)S(0.916)PLEEEER 333.87 3.55E-53 3167900000 1554100 1555300 1391200 1757000 1565800 1533020 1560790 1699530 1804460 1705450 TRUE FALSE 1493364.054 1510944.367 1642620.787 1847678.981 1616165.379 1564018.715 1579891.415 1664434.112 1599625.266 1589938.352 0.939259092 0.950316322 1.033134891 1.162107309 1.016495625 0.983697709 0.993680926 1.046854495 1.006092635 1 20.6005394 4.250968341 6.399067001 1.033325689 0.943594108 0.336241614 0.047931212 0.16631369 27.01529888 0.012460276 0.032071794 17822.48841 -4.250968341 -0.089731581 KEVGINGQT(ph)S(ph)NSSWMPFTLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEVGINGQTSNSSWMPFTLQK 21 1 Q8WY36-3 Q8WY36-3 BBX HMG box transcription factor BBX 2 KEVGINGQT(0.499)S(0.499)NS(0.499)S(0.499)WMPFT(0.003)LQK 61.648 0.040904 134250000 29926 34562 27040 38191 34600 37346 34537 37784 40553 43583 TRUE FALSE 28756.45884 33576.3256 31926.7295 40162.04209 35712.94042 38101.16171 34959.67414 37003.7472 35949.59345 40631.08459 0.707745292 0.826370399 0.785771038 0.988456067 0.878956119 0.937734301 0.860416956 0.910725066 0.884780552 1 15.31029626 4.250987094 1.410807851 0.91308734 0.718615347 0.611279631 0.052990957 0.375788706 1.203031566 0.014039847 0.081265392 17823.25802 -4.250987094 -0.194471994 LGS(ph)PLAVDEALR ddPTM_BT-474_Pertuzumab_2h_R1 4 LGSPLAVDEALR 12 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR 210.91 4.00E-08 291435000 379759 350729 362757 375276 411146 356829 386200 417471 445954 421719 TRUE FALSE 364917.5984 340726.5523 428315.2594 394644.0393 424370.8845 364044.3269 390926.4311 408850.078 395331.1715 393155.5965 0.928176024 0.866645561 1.089429384 1.003785887 1.079396779 0.925954838 0.994330068 1.039919263 1.005533623 1 18.58474087 4.251112649 24.99980465 1.01718268 0.897410754 0.523203589 0.045777 167.6948624 333990.6059 0.010785452 0.029108692 17828.41147 -4.251112649 -0.119771926 GNVVPS(ph)PLPTR ddPTM_BT-474_Pertuzumab_2h_R1 9 GNVVPSPLPTR 11 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 GNVVPS(0.971)PLPT(0.029)R;GNVVPS(0.999)PLPT(0.001)R;GNVVPS(1)PLPTR;GNVVPS(0.995)PLPT(0.005)R;GNVVPS(1)PLPTR;GNVVPS(0.998)PLPT(0.002)R;GNVVPS(0.987)PLPT(0.013)R;GNVVPS(1)PLPTR;GNVVPS(1)PLPTR 188.09 3.46E-06 1.34231E+11 4986811.7 4992929.6 5340632.4 6467531.8 5810097.8 5285199.2 5841213 6169909.7 5812651.7 6148549.3 TRUE FALSE 4791921.586 4850536.136 6305803.476 6801321.891 5996984.872 5392069.549 5912699.512 6042498.909 5152823.848 5732102.579 0.835979733 0.846205397 1.100085595 1.186531783 1.04621032 0.940679179 1.031506228 1.054150519 0.898941318 1 22.450633 4.25120737 24.58836176 1.037679053 0.841092363 0.507300262 0.075208407 149.2310698 290134.6453 0.019188802 0.051761772 17832.30035 -4.25120737 -0.19658669 VLDEEGS(ph)ER ddPTM_BT-474_Pertuzumab_2h_R1 2 VLDEEGSER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VLDEEGS(1)ER;VLDEEGS(1)ER 209.97 7.92E-06 6641400000 1643650 1738480 2318380 2843800 2122740 2212030 2910600 2839300 3040900 3601500 TRUE FALSE 1579414.341 1688900.253 2737362.838 2990568.859 2191019.86 2256758.762 2946220.793 2780667.463 2695709.78 3357567.197 0.470404387 0.503013091 0.815281624 0.890695162 0.65256173 0.672141056 0.87748677 0.828179244 0.802875899 1 21.67898484 4.251208196 6.794895386 0.807665425 0.483237822 0.65432901 0.095967974 0.085012276 17.36308704 0.023605305 0.060626816 17832.33425 -4.251208196 -0.324427603 KALVVPEPEPDSDS(ph)NQER ddPTM_BT-474_Pertuzumab_2h_R1 2 KALVVPEPEPDSDSNQER 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 KALVVPEPEPDS(0.013)DS(0.987)NQER;KALVVPEPEPDS(0.013)DS(0.987)NQER 180.66 4.74E-14 1149700000 1172920 1228400 823070 979930 984960 1157440 1009720 1007420 1141300 1321560 TRUE FALSE 1127080.99 1193367.235 971817.0581 1030504.305 1016642.133 1180844.23 1022077.255 986616.425 1011744.409 1232049.564 0.914801663 0.968603269 0.788780814 0.83641465 0.82516334 0.958438901 0.829574788 0.800792804 0.821188074 1 20.23262886 4.251209764 24.97391373 0.84824737 0.941702491 0.194170151 0.066453233 305.7914393 603729.394 0.015506048 0.041861438 17832.39865 -4.251209764 0.093455121 YEHANDDKSSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 YEHANDDKSSLK 12 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 145.6 3.85E-05 432780000 667210 678970 302170 327210 462870 571610 439910 424960 546300 409570 FALSE TRUE 641134.6956 659606.4404 356778.8407 344097.3473 477758.6339 583168.3458 445293.7502 416184.4275 484286.3143 381829.4591 1.679112704 1.727489655 0.934393175 0.901180721 1.251235656 1.527300558 1.166211091 1.089974641 1.268331457 1 18.54256889 4.251336868 24.97218979 1.152328407 1.703301574 0.62403276 0.174031436 152.1981667 297477.6382 0.045367047 0.122489125 17837.61836 -4.251336868 0.550973167 HT(ph)PS(ph)PGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPATSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 3 HT(1)PS(1)PGLPAEGAPEAPRPS(0.286)S(0.713)PPPEVLEPHS(0.001)LDQPPATSPR 138.93 3.57E-10 113030000 35621 33627 32002 36615 33731 34747 42053 27803 45576 38218 TRUE FALSE 34228.89194 32667.99088 37785.47328 38504.70454 34815.98825 35449.60815 42567.65719 27228.85833 40402.40355 35629.46082 0.960690708 0.916881427 1.060512071 1.080698491 0.977168541 0.994952136 1.194732006 0.764223137 1.133960566 1 15.12078303 4.251455138 24.97428303 1.012473865 0.938786049 0.08229378 0.109195445 664.0357533 1286089.153 0.026329064 0.071149802 17842.47669 -4.251455138 -0.073687816 QGPVSQSATQQPVTADKQQGHEPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 QGPVSQSATQQPVTADKQQGHEPVSPR 27 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVT(0.45)ADKQQGHEPVS(0.55)PR;QGPVSQSATQQPVT(0.053)ADKQQGHEPVS(0.947)PR 253.93 4.89E-53 6043700000 2789690 2840190 1558370 1784160 2116960 2800080 2112850 1905650 2333960 1993400 TRUE FALSE 2680665.831 2759190.562 1840002.125 1876240.711 2185053.941 2856699.536 2138707.69 1866297.662 2069018.646 1858385.242 1.442470468 1.484724749 0.990108016 1.009608056 1.175780937 1.53719448 1.150841947 1.004257685 1.113342163 1 20.82561817 4.251512827 24.99782618 1.13009635 1.463597835 0.439863215 0.153718716 228.6437804 441275.3225 0.040508245 0.109448668 17844.84695 -4.251512827 0.333501485 IAQPSMTAS(ph)PQTEEFFDLIASSQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 IAQPSMTASPQTEEFFDLIASSQSR 25 0 A0A0A0MSK4;A0A0A0MRC4;Q86YR5-4;Q86YR5;Q86YR5-2 A0A0A0MSK4 GPSM1 G-protein-signaling modulator 1 1 IAQPS(0.001)MT(0.022)AS(0.931)PQT(0.046)EEFFDLIASSQSR 168.69 7.04E-12 15625000 4544.2 4677.9 5259.7 7517.7 5761.6 6996.8 5321.2 5529 6070.8 5919.4 TRUE FALSE 4366.60764 4544.490872 6210.244791 7905.689398 5946.927097 7138.28009 5386.322437 5414.824218 5381.668235 5518.473766 0.791270889 0.823505024 1.125355498 1.432586207 1.077639824 1.293524332 0.976052921 0.981217715 0.975209535 1 12.4300536 4.251553537 7.964727376 1.110331263 0.805540064 0.413905409 0.142937202 0.148529398 54.58562967 0.037781207 0.09690217 17846.51974 -4.251553537 -0.304791199 LLVVDRETDEFFKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLVVDRETDEFFKK 14 2 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 127.76 4.37E-05 276400000 564630 571850 286140 261250 447670 581450 410680 360510 421860 366190 FALSE TRUE 542563.6354 555541.3979 337851.8631 274733.1438 462069.7121 593207.3174 415706.0247 353065.3425 373972.2214 341387.6251 1.589289111 1.627303853 0.98964297 0.804754255 1.353504574 1.737635678 1.21769506 1.034206622 1.095447503 1 18.38105124 4.251596058 24.99689557 1.166887125 1.608296799 0.362958893 0.240208006 273.3439353 524157.4073 0.063989294 0.172937596 17848.26716 -4.251596058 0.441409675 AILGSYDSELTPAEYS(ph)PQLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AILGSYDSELTPAEYSPQLTR 21 0 Q9Y6D9;Q9Y6D9-3;C9J9H5;C9JX80 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 1 AILGSYDSELTPAEY(0.009)S(0.99)PQLT(0.001)R 142.78 9.22E-08 60113000 30857 31362 35467 39435 36924 41395 35623 36607 45810 42086 TRUE FALSE 29651.07433 30467.58647 41876.67586 41470.24508 38111.69399 42232.03526 36058.96493 35851.05266 40609.84085 39235.47773 0.755720996 0.776531553 1.067316579 1.056957822 0.97135797 1.076373673 0.919039783 0.913740694 1.035028581 1 15.25987115 4.251627574 24.60503351 0.996234865 0.766126026 0.749638135 0.055028193 100.4913572 189220.5262 0.014815667 0.040020564 17849.5624 -4.251627574 -0.23010884 RNS(ph)RDGDPLPSSLSCK ddPTM_BT-474_Pertuzumab_2h_R1 4 RNSRDGDPLPSSLSCK 16 2 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 RNS(1)RDGDPLPSSLSCK;RNS(1)RDGDPLPSSLSCK;RNS(1)RDGDPLPSSLSCK;RNS(0.999)RDGDPLPS(0.001)SLSCK 185.67 8.48E-10 1447400000 1934080 2086270 746090 934290 1503450 1843560 1150610 1075480 1328300 988910 TRUE FALSE 1858494.015 2026771.622 880925.0597 982508.8189 1551809.835 1880838.046 1164691.509 1053270.962 1177516.953 921930.2449 2.015872704 2.198400187 0.955522465 1.065708414 1.683218273 2.040108844 1.263318473 1.142462749 1.277229985 1 19.81429807 4.251653099 24.9985412 1.327429254 2.107136899 0.505613298 0.317178488 201.608662 384940.6726 0.083255417 0.225034426 17850.61155 -4.251653099 0.779707645 KTES(ph)PIKLSPATPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTESPIKLSPATPSR 15 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KT(0.045)ES(0.955)PIKLSPATPSR;KT(0.005)ES(0.995)PIKLSPATPSR 111.66 0.00043052 1659140000 1339030 1293910 826770 789650 1048560 1097610 1050980 1042540 1243420 1259230 TRUE FALSE 1286699.227 1257008.954 976185.7304 830403.9311 1082287.885 1119804.426 1063842.208 1021011.185 1102272.174 1173941.23 1.096050802 1.070759695 0.831545656 0.707364142 0.921926802 0.95388457 0.906214195 0.869729385 0.938950048 1 20.16292876 4.251680223 22.20016031 0.883522179 1.083406045 0.503487467 0.076041645 46.83960326 79252.54558 0.019053497 0.051254461 17851.72646 -4.251680223 0.199883866 QDKPMDTSVLS(ph)EEGGEPFQK ddPTM_BT-474_Pertuzumab_2h_R1 3 QDKPMDTSVLSEEGGEPFQK 20 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 QDKPMDTSVLS(1)EEGGEPFQK;QDKPMDTSVLS(1)EEGGEPFQK;QDKPMDTSVLS(0.999)EEGGEPFQK 240.46 6.39E-30 1439150000 942590 875010 931650 966640 1047020 1091580 1197280 1290850 1407160 1521430 TRUE FALSE 905752.5407 850055.5715 1100019.879 1016528.406 1080698.349 1113652.496 1211932.671 1264193.496 1247425.096 1418382.191 0.638581439 0.599313483 0.775545468 0.716681592 0.761923236 0.785156852 0.854447185 0.891292562 0.87947036 1 20.4358149 4.251682398 0.181880027 1.051885034 0.302121775 0.907328569 0.035002085 3.660016916 0.14492028 0.102282218 0.648502164 17851.81585 -4.251682398 -0.749763259 ETEAAPTS(ph)PPIVPLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ETEAAPTSPPIVPLK 15 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A3B3IT55;Q7Z3B3-4;Q7Z3B3-2 A0A1W2PRB5;Q7Z3B3-4 KANSL1 KAT8 regulatory NSL complex subunit 1 1 ETEAAPT(0.152)S(0.848)PPIVPLK;ETEAAPT(0.072)S(0.928)PPIVPLK;ETEAAPT(0.005)S(0.995)PPIVPLK 295.98 4.82E-44 389419000 993220 1034320 912660 1016500 1128840 1132860 1104990 1230630 1141360 1228690 TRUE FALSE 954403.8643 1004822.206 1077597.964 1068961.687 1165150.164 1155767.205 1118513.198 1205217.06 1011797.598 1145469.732 0.833198676 0.877214106 0.940747655 0.933208148 1.017181102 1.008989739 0.97646683 1.052159675 0.883303652 1 20.12750791 4.251697757 0.984176716 0.995418936 0.807183331 0.584489866 0.043402269 0.649330113 0.834359185 0.013914504 0.110324008 17852.4472 -4.251697757 -0.188235605 AAIDWFDGKEFSGNPIK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAIDWFDGKEFSGNPIK 17 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ; 230.33 7.52E-16 2269500000 3039000 3081700 1731380 1700070 2212000 2968400 2315100 2439860 2635680 2246510 FALSE TRUE 2920232.52 2993812.933 2044278.88 1787810.816 2283150.989 3028423.082 2343432.886 2389476.038 2336488.656 2094351.877 1.394337099 1.429469884 0.976091412 0.853634404 1.090146796 1.445995353 1.118929876 1.140914316 1.115614182 1 20.99807242 4.251795154 24.88389175 1.104814541 1.411903719 0.435883557 0.144742177 222.0148817 417429.4542 0.038007924 0.102761591 17856.45131 -4.251795154 0.307089177 LLVDADNCLHR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLVDADNCLHR 11 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ;;; 221.59 8.30E-12 1315940000 761150 806480 673670 890540 867040 879010 812180 797930 836720 902170 FALSE TRUE 731403.4165 783479.98 795417.1547 936500.8761 894929.129 896784.1845 822119.7018 781452.4667 741739.0534 841065.2223 0.869615574 0.931532965 0.945725889 1.11346998 1.064042485 1.066248087 0.977474374 0.929122315 0.881904321 1 19.68185816 4.251817185 2.501943098 1.001119971 0.885906584 0.290976405 0.06554841 0.422905355 5.163479819 0.019247957 0.067056873 17857.35716 -4.251817185 -0.115213387 GIQFLQEQGMLGTSVEDIAQFLHQEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GIQFLQEQGMLGTSVEDIAQFLHQEER 27 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 ; 212.76 5.01E-26 252190000 113128 115498 112945 135312 128361 135431 136890 132743 137469 149379 FALSE TRUE 108706.8327 112204.1101 133356.6739 142295.4685 132489.8481 138169.5076 138565.3008 130001.8107 121864.0954 139261.4273 0.780595423 0.80570846 0.957599506 1.021786659 0.951375056 0.99215921 0.995001297 0.933509107 0.875074296 1 17.08743619 4.25197154 4.75876273 0.966392856 0.787844789 0.757123013 0.039245502 0.083882629 4.821317761 0.010036931 0.02680323 17863.70506 -4.25197154 -0.178548067 LGGSVLGQIPFLQNCEDEDS(ph)DEDDELDSVQHKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGGSVLGQIPFLQNCEDEDSDEDDELDSVQHKK 33 1 F5GYK2;Q9NRL3;Q9NRL3-3;R4GN16;Q9NRL3-2 F5GYK2 STRN4 Striatin-4 1 LGGSVLGQIPFLQNCEDEDS(1)DEDDELDSVQHKK;LGGSVLGQIPFLQNCEDEDS(1)DEDDELDSVQHKK 277.49 5.46E-74 553990000 977780 952950 546840 576070 696360 790480 688500 724550 964250 778550 TRUE FALSE 939567.2766 925772.799 645666.1524 605801.0417 718759.0518 806464.0472 696926.069 709587.7893 854792.3825 725818.115 1.294494112 1.275488693 0.889570182 0.834645801 0.990274336 1.111110388 0.960193821 0.977638577 1.177695024 1 19.46924854 4.252032913 24.59581475 0.988126745 1.284991724 0.614884509 0.092491819 123.4459254 225364.9788 0.023330941 0.063089373 17866.2297 -4.252032913 0.296864979 EGILPERAEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGILPERAEEAK 12 1 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7;O43768-8 A6NMQ3 ENSA Alpha-endosulfine 0 126.1 0.00026771 186200000 310850 300280 146090 157250 232500 267880 186200 193900 237200 178290 FALSE TRUE 298701.6383 291716.3084 172491.7128 165365.6913 239978.5737 273296.7171 188478.7713 189895.8972 210274.0504 166214.2595 1.797087923 1.755061866 1.037767237 0.994894733 1.443790529 1.644243508 1.133950672 1.142476571 1.265078285 1 17.34268463 4.252146795 24.66153443 1.220888379 1.776075486 0.576329949 0.194642125 147.3542345 267470.4953 0.050308507 0.136092995 17870.91524 -4.252146795 0.555187107 RNEQDFYAAVDDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNEQDFYAAVDDFR 14 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3 Q9H8V3-2 ECT2 Protein ECT2 0 95.428 0.0060481 47602000 44109 44801 48870 59915 58946 46642 51584 58392 42075 58514 FALSE TRUE 42385.17151 43523.31934 57701.89611 63007.22033 60842.05162 47585.1332 52215.30042 57186.18479 37298.82239 54550.79466 0.776985409 0.79784941 1.057764538 1.155019294 1.11532842 0.872308708 0.957186797 1.048310756 0.683744804 1 15.73531259 4.252229571 23.12495938 0.995606765 0.787416898 0.280262839 0.126712383 116.3572127 196841.9602 0.031104381 0.083963116 17874.32175 -4.252229571 -0.208189866 YIEIDS(ph)DEEPR ddPTM_BT-474_Pertuzumab_2h_R1 3 YIEIDSDEEPR 11 0 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 YIEIDS(1)DEEPR;YIEIDS(1)DEEPR;YIEIDS(1)DEEPR 234.87 1.73E-15 2042250000 1021810 1022990 1312420 1478640 1266200 1192990 1340560 1519700 1373570 1675410 TRUE FALSE 981876.5355 993815.3268 1549603.489 1554952.788 1306928.473 1217113.075 1356966.174 1488317.664 1217648.092 1561932.988 0.628629104 0.636272705 0.992106256 0.99553105 0.836737864 0.779235143 0.868773619 0.952869089 0.779577678 1 20.57490113 4.252253369 24.91332485 0.897044304 0.632450669 0.640224332 0.080371285 139.3352876 253509.2156 0.020034264 0.054231541 17875.30122 -4.252253369 -0.264593635 S(ph)NSGRELTDEEILASVMIK ddPTM_BT-474_Pertuzumab_2h_R1 9 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.494)NS(0.494)GRELT(0.011)DEEILASVMIK;S(0.387)NS(0.387)GRELT(0.225)DEEILASVMIK;S(0.648)NS(0.345)GRELT(0.007)DEEILASVMIK;S(0.479)NS(0.339)GRELT(0.182)DEEILASVMIK;S(0.633)NS(0.343)GRELT(0.024)DEEILASVMIK;S(0.484)NS(0.484)GRELT(0.032)DEEILASVMIK;S(0.333)NS(0.333)GRELT(0.333)DEEILAS(0.002)VMIK;S(0.442)NS(0.442)GRELT(0.117)DEEILASVMIK;S(0.497)NS(0.497)GRELT(0.006)DEEILASVMIK 214.16 7.34E-19 1423403000 1602879 1603132 980969 1062996 1289811 1550494 1215141 1233580 1463032 1320975 TRUE FALSE 1540236.717 1557412.245 1158251.92 1117857.351 1331298.942 1581846.051 1230012.259 1208106.142 1296954.741 1231504.187 1.250695477 1.264642266 0.940518053 0.907717053 1.081034849 1.284482885 0.998788532 0.981000434 1.053146839 1 20.2319901 4.252276219 24.98739241 1.032132823 1.257669046 0.463586346 0.097592144 216.6811915 394747.4524 0.025629265 0.069392023 17876.24175 -4.252276219 0.225536222 VISAFVEIIFDNSDNRLPIDKEEVSLRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VISAFVEIIFDNSDNRLPIDKEEVSLRR 28 3 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 126.46 1.54E-05 141339000 251340 249232 171972 180751 216516 254840 213887 201828 242990 215696 FALSE TRUE 241517.3549 242124.1474 203051.1659 190079.5808 223480.4338 259993.0394 216504.6131 197660.1813 215406.7939 201086.7178 1.201060704 1.20407827 1.009769159 0.94526174 1.111363477 1.292939893 1.076672868 0.982959906 1.071213436 1 17.61745827 4.252295396 24.66548405 1.063083858 1.202569621 0.27884905 0.090853708 283.4209992 508968.0937 0.024166401 0.065385339 17877.03112 -4.252295396 0.139485763 EIIKQEESVDPDYWEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIIKQEESVDPDYWEK 16 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 171.09 4.60E-09 417160000 908310 871730 584450 493660 715740 727130 698820 756390 750860 645820 FALSE TRUE 872812.241 846869.1139 690073.116 519137.8518 738762.4271 741833.0668 707372.3682 740770.2822 665625.5207 602078.0362 1.449666303 1.406576993 1.146152284 0.862243464 1.227021055 1.232121124 1.174884858 1.23035593 1.105546924 1 19.19959096 4.252322828 5.383134478 1.135730019 1.434843892 0.548425091 0.110723028 0.129372561 11.06739562 0.028497324 0.074742409 17878.16034 -4.252322828 0.299113872 (ac)AKS(ph)PENSTLEEILGQYQR ddPTM_BT-474_Pertuzumab_2h_R1 3 AKSPENSTLEEILGQYQR 18 1 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 AKS(0.995)PENS(0.002)T(0.003)LEEILGQYQR;AKS(1)PENSTLEEILGQYQR;AKS(1)PENSTLEEILGQYQR 138.42 1.31E-74 215212000 157025 153341 109535 109960 134439 156981 122285 136156 154187 143246 TRUE FALSE 150888.2894 148967.8648 129330.4111 115635.0488 138763.3525 160155.2634 123781.5604 133344.331 136684.3382 133543.8208 1.129878481 1.115497998 0.968449235 0.865895914 1.039084786 1.199271238 0.926898449 0.998506185 1.023516755 1 17.0269537 4.252346153 22.02630574 1.001857775 1.122688778 0.258185133 0.081342352 78.92241091 126089.9201 0.020644694 0.055629089 17879.12058 -4.252346153 0.120831003 QLNENKQER ddPTM_BT-474_Pertuzumab_2h_R1 4 QLNENKQER 9 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;; 160.36 5.96E-05 3161720000 4412080 4520640 2881420 3094030 3610560 4056510 3918230 3682760 4327470 3946950 FALSE TRUE 4239651.036 4391715.773 3402156.691 3253713.259 3726696.941 4138535.412 3966182.471 3606709.719 3836233.748 3679619.561 1.1521982 1.193524412 0.924594686 0.884252626 1.012794089 1.124718288 1.077878407 0.980185495 1.042562603 1 21.81112518 4.252372403 24.99654745 1.00766683 1.172861404 0.505186191 0.066086853 206.3456244 373437.132 0.017775631 0.048126924 17880.20126 -4.252372403 0.165194574 RES(ph)PSEER ddPTM_BT-474_Pertuzumab_2h_R1 2 RESPSEER 8 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RES(0.977)PS(0.023)EER;RES(0.982)PS(0.018)EER 149.49 0.00030892 235440000 115193 116260 119448 140723 129708 121409 136835 137304 131091 142119 TRUE FALSE 110691.1302 112944.3786 141034.9107 147985.7309 133880.1756 123863.9732 138509.6277 134468.6244 116210.0993 132493.1535 0.835447925 0.852454452 1.064469423 1.116931154 1.010468632 0.934870745 1.045409698 1.014909985 0.877102674 1 17.01555829 4.252395577 23.8633166 1.01200489 0.843950906 0.521983508 0.062710243 103.8720212 179158.3722 0.015671785 0.042368914 17881.15539 -4.252395577 -0.168053984 NKELEIAQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 NKELEIAQDR 10 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 101.39 0.0030683 362180000 726940 737350 505030 546570 595480 694540 623350 663980 751770 644950 FALSE TRUE 698530.3811 716321.4999 596300.1553 574778.5432 614634.155 708584.0747 630978.7438 650268.581 666432.2213 601266.962 1.161764117 1.1913535 0.991739432 0.955945661 1.02223171 1.178484965 1.049415291 1.081497275 1.10837991 1 19.19764616 4.252417142 24.99652759 1.053253706 1.176558883 0.413202589 0.060846663 246.1738142 444078.3103 0.015756876 0.042672344 17882.0433 -4.252417142 0.123305177 FGHEFLEFEFRPDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 FGHEFLEFEFRPDGK 15 1 P61326;Q96A72;F5H6N1;P61326-2 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;;; 191.06 1.15E-07 2855464000 3210470 2985370 2997590 2934720 3373370 3122830 3512060 2998800 4069680 3783650 FALSE TRUE 3085001.283 2900230.171 3539321.194 3086181.251 3481877.51 3185975.762 3555041.641 2936873.732 3607706.988 3527380.015 0.874587164 0.822205194 1.003385283 0.874921681 0.987100197 0.903213078 1.007841975 0.832593517 1.022772418 1 21.75016558 4.25241766 24.99985858 0.941798876 0.848396151 0.296995903 0.062777431 290.5501803 524179.885 0.014118091 0.038239975 17882.06462 -4.25241766 -0.093402725 YPEPERPSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 YPEPERPSSR 10 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 106.62 0.0021821 1939070000 901950 1030200 855020 1185500 1142030 1146620 1079690 1164900 1178230 1180230 FALSE TRUE 866700.7968 1000819.705 1009541.134 1246683.797 1178764.432 1169805.442 1092903.569 1140844.408 1044482.27 1100291.971 0.787700737 0.909594663 0.917521131 1.133048164 1.071319671 1.063177296 0.993285054 1.036856069 0.949277371 1 20.06945497 4.252421429 1.854214442 1.035302526 0.807509959 0.665869047 0.054499243 0.230510365 1.439220499 0.014752195 0.065824754 17882.21982 -4.252421429 -0.227792567 RIDIS(ph)PSTLRK ddPTM_BT-474_Pertuzumab_2h_R1 3 RIDISPSTLRK 11 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 RIDIS(0.846)PS(0.144)T(0.011)LRK;RIDIS(0.998)PS(0.001)TLRK;RIDIS(0.856)PS(0.126)T(0.019)LRK 122.2 0.00031171 2554850000 2193910 2190890 1179870 1305650 1531170 1997630 1471580 1708860 1900250 1562450 TRUE FALSE 2108169.572 2128407.962 1393098.755 1373034.753 1580421.474 2038023.447 1489589.636 1673571.444 1684541.586 1456623.87 1.44729852 1.461192561 0.9563888 0.942614481 1.08498941 1.399141872 1.022631626 1.148938637 1.156469849 1 20.47419696 4.252543138 24.95655147 1.098885466 1.454245831 0.576059293 0.125133441 167.6022887 299137.5984 0.031513327 0.085364995 17887.23191 -4.252543138 0.355360365 GLEYLYLNVHDEDRDDQTR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLEYLYLNVHDEDRDDQTR 19 1 Q9Y6G9;C9JGM7;C9JLW1 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;; 227.95 6.91E-20 1335410000 1024254 1087402 965275 1179610 1144798 1229550 1241140 1179607 1323680 1390270 FALSE TRUE 984225.0213 1056390.36 1139721.665 1240489.813 1181621.467 1254412.343 1256329.443 1155247.703 1173421.396 1296105.775 0.75937091 0.815049497 0.879343096 0.957089952 0.911670552 0.967831768 0.969310891 0.891322086 0.905343853 1 20.30575203 4.25258365 1.71175631 0.937819386 0.75732523 0.789555573 0.032440236 0.197398018 1.018645862 0.008999479 0.043315884 17888.90057 -4.25258365 -0.180494156 YFQFQEEGKEGENR ddPTM_BT-474_Pertuzumab_2h_R1 4 YFQFQEEGKEGENR 14 1 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 212.24 2.48E-09 2606230000 1024080 1035340 653720 702550 851540 962050 828690 866680 955280 832510 FALSE TRUE 984057.8214 1005813.117 771861.7459 738808.6897 878930.5574 981503.3102 838831.7561 848782.7551 846840.6193 776123.3562 1.267914196 1.295944915 0.994509107 0.951921732 1.13246245 1.264622824 1.08079695 1.093618364 1.091116009 1 19.56592645 4.252622098 24.99994699 1.084379689 1.281929695 0.49683215 0.082509249 210.103655 373537.1835 0.021451851 0.058130564 17890.48433 -4.252622098 0.197550006 IITVEKHPDADSLYVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 IITVEKHPDADSLYVEK 17 1 P54577 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 144.5 3.06E-07 329640000 706670 691030 438660 385130 559240 698390 521060 556690 693050 639500 FALSE TRUE 679052.5551 671322.501 517935.6199 405006.6055 577228.4625 712511.9243 527436.8881 545194.157 614377.8695 596186.0954 1.138994284 1.126028443 0.868748238 0.67932917 0.96820182 1.195116642 0.884684987 0.914469762 1.030513583 1 19.1854032 4.252626003 24.34456299 0.935968079 1.132511615 0.270268545 0.124416304 229.5347286 397271.6749 0.031976017 0.086565491 17890.6452 -4.252626003 0.196543536 NPDVDTSFLPDRDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPDVDTSFLPDRDR 14 1 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 180.27 1.62E-06 206040000 163750 169750 199120 264600 201110 173540 247050 238660 245040 262580 FALSE TRUE 157350.469 164908.8962 235105.4134 278256.0377 207578.8858 177049.0977 250073.4718 233731.5876 217224.0865 244795.2227 0.642784068 0.673660598 0.960416673 1.136689003 0.847969513 0.723253893 1.021561896 0.95480453 0.887370612 1 17.90121588 4.25263616 8.510964712 0.940867315 0.656878246 0.542635121 0.104036949 0.125482825 54.69047404 0.026577872 0.068487992 17891.06363 -4.25263616 -0.283989069 FDTQYPYGEKQDEFKR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDTQYPYGEKQDEFKR 16 2 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ; 113.29 0.00037843 661590000 788910 745950 383770 318016 461070 634110 423890 416450 564550 435400 FALSE TRUE 758078.525 724676.2364 453125.7759 334428.8439 475900.7353 646932.1387 429077.6926 407850.162 500464.6508 405909.9702 1.867602623 1.785312728 1.116320882 0.823899062 1.172429283 1.593782332 1.057076012 1.004779857 1.232944957 1 18.63080025 4.252783938 6.126101653 1.121942523 1.837460386 0.685720847 0.190060803 0.086266801 11.65199156 0.04947528 0.12833888 17897.15247 -4.252783938 0.715517863 EVQQGEEFER ddPTM_BT-474_Pertuzumab_2h_R1 2 EVQQGEEFER 10 0 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ; 213.25 5.97E-08 905310000 257620 259030 267120 324510 289060 248380 306550 298400 305680 341100 FALSE TRUE 247551.9256 251642.718 315394.5261 341258 298357.8774 253402.4138 310301.6506 292237.9357 270980.4879 317996.9932 0.778472536 0.791336784 0.991816064 1.073148512 0.93824119 0.796870471 0.975800581 0.918995909 0.852147957 1 18.2786536 4.252797359 23.87219554 0.94035042 0.784904399 0.426157349 0.073490283 135.6713909 227486.6055 0.018667514 0.05052382 17897.70554 -4.252797359 -0.155446021 TEPSS(ph)PLSDPSDIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 TEPSSPLSDPSDIIR 15 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 TEPS(0.184)S(0.815)PLS(0.001)DPSDIIR;TEPS(0.006)S(0.994)PLSDPSDIIR;TEPS(0.006)S(0.994)PLSDPSDIIR;TEPS(0.212)S(0.788)PLSDPSDIIR 290.17 7.20E-44 1400087000 1179055 1187932 1204354 1446816 1297386 1193903 1351917 1446373 1357879 1325923 TRUE FALSE 1132976.227 1154053.342 1422007.559 1521486.347 1339117.599 1218044.537 1368462.165 1416504.892 1203738.269 1236117.054 0.916560631 0.933611698 1.150382606 1.230859442 1.083325883 0.985379607 1.107065193 1.145931032 0.973806052 1 20.23738394 4.252902849 23.8548816 1.095174648 0.92508587 0.397657826 0.077656388 127.4101384 211909.4322 0.019274476 0.052187767 17902.05345 -4.252902849 -0.170088778 SDS(ph)PENKYSDSTGHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSPENKYSDSTGHSK 16 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.001)DS(0.99)PENKYS(0.009)DSTGHSK 175.85 2.04E-09 249250000 273570 273590 151530 145440 199860 251400 190670 214680 271960 198950 TRUE FALSE 262878.582 265787.4811 178914.8418 152946.1758 206288.6784 256483.4802 193003.4765 210246.783 241088.2409 185474.9393 1.417326691 1.433010207 0.964630815 0.824619091 1.112218606 1.382847091 1.04059059 1.13355898 1.299842673 1 17.50086474 4.252919532 24.95847411 1.099646395 1.425168717 0.432400819 0.151326986 226.9915634 394546.4491 0.038748629 0.105070831 17902.74112 -4.252919532 0.325522322 DTQS(ph)PSTCSEGLLGWSQK ddPTM_BT-474_Pertuzumab_2h_R1 6 DTQSPSTCSEGLLGWSQK 18 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DTQS(0.999)PS(0.001)TCSEGLLGWSQK;DTQS(0.997)PS(0.003)TCSEGLLGWSQK;DTQS(1)PSTCSEGLLGWSQK;DTQS(0.991)PS(0.009)TCSEGLLGWSQK;DTQS(0.952)PS(0.048)TCSEGLLGWSQK;DTQS(0.657)PS(0.34)T(0.002)CSEGLLGWSQK 348.99 2.63E-90 4073020000 2632810 2642450 2758140 3045550 3118730 2995030 3027380 3053690 3154280 3116090 TRUE FALSE 2529916.874 2567089.913 3256597.252 3202731.2 3219046.783 3055591.559 3064429.982 2990630.234 2796219.358 2905034.449 0.870873278 0.883669353 1.121018463 1.102476152 1.108092465 1.051826274 1.054868724 1.029464637 0.962542582 1 21.47012384 4.252975771 24.95498354 1.056974243 0.877271145 0.695229644 0.046709902 126.8304215 219560.1241 0.011960741 0.032435963 17905.05959 -4.252975771 -0.179703098 VPVLIS(ph)PTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VPVLISPTLK 10 0 P42684-2;P42684-6;P42684-3;P42684;P42684-4;P42684-7;P42684-10;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 VPVLIS(0.978)PT(0.022)LK 62.408 0.089461 43463000 180450 178620 173680 191060 196620 201660 187990 204760 195290 189470 TRUE FALSE 173397.8145 173525.9325 205067.8395 200920.6295 202944.4609 205737.7034 190290.6779 200531.6344 173121.4979 176637.0281 0.981661752 0.98238707 1.160956124 1.137477411 1.148934983 1.164748442 1.077297778 1.135275183 0.980097433 1 17.43042828 4.253065822 24.93278722 1.110655247 0.982024295 0.359425944 0.062169185 210.8632472 362443.0009 0.014379786 0.038993959 17908.77259 -4.253065822 -0.128630952 NVHS(ph)EDFENR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVHSEDFENR 10 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 NVHS(1)EDFENR;NVHS(1)EDFENR 192.46 4.38E-07 948100000 556730 521140 562710 590630 541580 694050 600670 549440 692680 707290 TRUE FALSE 534972.3761 506277.5974 664404.2144 621112.4851 559000.4126 708084.1665 608021.1791 538093.872 614049.8704 659384.6183 0.811320679 0.767803166 1.007612547 0.941957801 0.847760771 1.073856057 0.922103977 0.816054632 0.931246883 1 19.33076071 4.253071797 24.99195525 0.930288175 0.789561843 0.408646033 0.072430381 253.7300699 436980.0941 0.018392588 0.049890106 17909.01898 -4.253071797 -0.140726332 RPEVDGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPEVDGVR 8 1 O95865;A0A140T971;Q5SSV3;Q5SRR8;H0Y7N1 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ; 166.61 0.00050899 1669590000 1299960 1372070 1356550 1807390 1601650 1577790 1629110 1661920 1713330 1670490 FALSE TRUE 1249156.126 1332939.907 1601708.761 1900669.614 1653168.527 1609693.995 1649047.536 1627600.771 1518839.961 1557346.224 0.802105599 0.85590467 1.028485982 1.220454119 1.061529223 1.033613444 1.05888306 1.045111707 0.975274436 1 20.57065828 4.253157676 3.840284073 1.061237374 0.816758041 0.68255885 0.061643435 0.114467599 3.632370718 0.015844969 0.04469508 17912.56075 -4.253157676 -0.244479334 SLLLAGAAEYDNFFQHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLLAGAAEYDNFFQHLR 18 0 Q7Z460;C9J151;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 0 174.23 6.35E-12 106660000 119190 108140 111760 109720 118730 118290 119950 135880 123340 123610 FALSE TRUE 114531.923 105055.9531 131957.5181 115382.6623 122549.0583 120681.9048 121417.984 133074.0305 109338.9603 115237.7846 0.993874738 0.911645026 1.145088987 1.001257207 1.063445108 1.047242493 1.053629974 1.154777758 0.948811717 1 16.81425431 4.253297502 24.9999556 1.060736472 0.95275987 0.276696445 0.062716651 262.7105738 445659.3585 0.014495383 0.039338202 17918.32882 -4.253297502 -0.107976602 RKS(ph)EPAVGPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RKSEPAVGPPR 11 2 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-11;O94875-2;O94875-8;H7BZK1;H7BZX1;H7C1R7;O94875-7;O94875 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 RKS(1)EPAVGPPR;RKS(1)EPAVGPPR;RKS(1)EPAVGPPR 71.031 0.039491 647330000 1129600 900260 691300 489450 621010 522640 385370 907550 502310 404590 TRUE FALSE 1085453.983 874585.4662 816233.2879 514710.5732 640985.3506 533208.1389 390086.2733 888808.7754 445289.8747 377186.7589 2.877762693 2.318706703 2.164003027 1.364604035 1.69938455 1.413644902 1.034199277 2.356415633 1.180555425 1 18.52491951 4.253323308 1.317632673 1.518781256 2.922093381 0.60570282 0.386927512 0.470548686 1.264650248 0.114179696 0.709302864 17919.39355 -4.253323308 1.403312125 DQDS(ph)SDDERALEDWVSSETSALPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.5)S(0.5)DDERALEDWVSSETSALPRPR 144.43 1.27E-07 31948000 50192 49538 25881 31967 37577 43863 32820 37718 35899 31454 TRUE FALSE 48230.44115 48125.22474 30558.27242 33616.8207 38785.69833 44749.93991 33221.66098 36939.11012 31823.89602 29323.59256 1.644765765 1.64117765 1.042105341 1.146408668 1.32267894 1.526072899 1.132932839 1.259706158 1.085265932 1 14.83977424 4.253346562 24.99602338 1.212977927 1.642972088 0.602808251 0.146273332 163.1687102 275835.9549 0.035891219 0.097412527 17920.35307 -4.253346562 0.429994162 DYGRPLDEQESQFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYGRPLDEQESQFR 14 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 153.23 5.88E-06 445660000 149190 147950 174060 189140 164360 174750 192400 202760 188970 194100 FALSE TRUE 143359.4899 143730.6109 205516.5139 198901.5381 169646.7887 178283.5647 194754.6488 198572.9351 167518.9178 180953.4341 0.792245201 0.794296121 1.135742546 1.099186313 0.93751627 0.985245545 1.076269426 1.09737036 0.925757053 1 17.46525896 4.253370454 24.94980579 1.038368017 0.793270439 0.66785558 0.067265881 131.6708404 221818.8762 0.016871236 0.045788669 17921.33898 -4.253370454 -0.245097578 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_BT-474_Pertuzumab_2h_R1 6 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLREER 35 3 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 1 KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER 351.35 1.46E-131 3261550000 3615400 3268800 738173 403845 1362731 1869224 575501 612576 697648 331547 TRUE FALSE 3474106.171 3175577.024 871577.2817 424687.4888 1406564.48 1907020.99 582544.1534 599926.0915 618453.9238 309091.0264 11.23975099 10.27392177 2.819807782 1.373988413 4.550648062 6.16977145 1.884700958 1.940936618 2.000879583 1 18.23767224 4.253431596 5.604099159 2.782327552 10.91871538 0.824186534 1.486761751 0.063871473 6.233193772 0.391889128 1.025878113 17923.86219 -4.253431596 8.136387826 DEAEDYYDVITHPMDFQTVQNK ddPTM_BT-474_Pertuzumab_2h_R1 2 DEAEDYYDVITHPMDFQTVQNK 22 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 0 ; 238.79 1.45E-30 409250000 347740 338490 213480 268340 245720 259900 297690 287600 300690 281850 FALSE TRUE 334149.9364 328836.5966 252060.5848 282189.0596 253623.807 265155.3561 301333.2193 281660.9595 266556.9318 262760.0485 1.271692323 1.251471061 0.959280478 1.073942029 0.965229716 1.009115951 1.146799984 1.07193221 1.014450002 1 18.00338641 4.253511643 24.86893335 1.039018985 1.261581924 0.746183393 0.053802873 113.0927077 188110.2547 0.013628736 0.03699667 17927.16615 -4.253511643 0.222562939 MLQEDELR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLQEDELR 8 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 114.64 0.0060897 3375200000 3622800 3646400 3478200 3948400 4024400 3851500 4070900 3876800 4088900 4229000 FALSE TRUE 3481216.971 3542408.242 4106788.112 4152177.397 4153848.481 3929379.969 4120720.892 3796742.725 3624745.214 3942566.063 0.882982533 0.898503205 1.041653595 1.05316622 1.053590077 0.996655454 1.045187532 0.96301309 0.919387312 1 21.9107035 4.253530638 20.00580807 1.009889469 0.890741249 0.571166455 0.041010922 16.58518502 22158.89971 0.01076372 0.028990096 17927.95022 -4.253530638 -0.11914822 AADEEAFEDNSEEYIR ddPTM_BT-474_Pertuzumab_2h_R1 6 AADEEAFEDNSEEYIR 16 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;;;; 431.96 5.15E-160 4794410000 1598801 1718230 1589828 2029190 1839360 1860290 1961800 2076510 2140650 2327880 FALSE TRUE 1536318.089 1669227.763 1877145.285 2133916.739 1898524.685 1897906.338 1985809.095 2033629.343 1897652.386 2170210.614 0.707911978 0.769154732 0.86495996 0.983276335 0.874811261 0.874526337 0.915030588 0.93706543 0.87440932 1 21.04940363 4.253558023 2.472438459 0.917499242 0.717206787 0.752399187 0.042153312 0.133910597 1.59302453 0.010456155 0.036838186 17929.08075 -4.253558023 -0.200292455 ESAWS(ph)PPPIEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESAWSPPPIEIR 12 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 ESAWS(1)PPPIEIR;ESAWS(1)PPPIEIR;ESAWS(1)PPPIEIR;ESAWS(1)PPPIEIR 206.7 9.14E-08 354841000 721160 713320 676000 745240 781190 766380 777470 800510 685390 795860 TRUE FALSE 692976.2699 692976.812 798168.2375 783701.9257 806317.6858 781876.7287 786984.9104 783979.1888 607587.4006 741955.6933 0.933986054 0.933986784 1.07576267 1.056265128 1.08674641 1.053805147 1.0606899 1.056638821 0.818899843 1 19.50097351 4.253560106 24.58941675 1.035195741 0.933986308 0.192350114 0.073638166 279.4625017 458126.8459 0.017509312 0.047512434 17929.16675 -4.253560106 -0.101209433 RRPGGEGPQCEK ddPTM_BT-474_Pertuzumab_2h_R1 3 RRPGGEGPQCEK 12 2 Q9NWY4 Q9NWY4 C4orf27 UPF0609 protein C4orf27 0 ;; 96.64 0.0030205 118158000 171073 173951 121710 139368 149118 154939 152355 155177 175933 159157 FALSE TRUE 164387.278 168990.0878 143705.7044 146560.7992 153914.5159 158071.9727 154219.5661 151972.5407 155961.8234 148377.1546 1.107901539 1.138922553 0.968516378 0.987758524 1.0373195 1.065339022 1.039375411 1.024231399 1.051117497 1 17.17890945 4.253582692 24.99999865 1.024367727 1.123412103 0.664652471 0.028847448 147.1243673 244842.654 0.007421106 0.020153413 17930.09919 -4.253582692 0.099044376 GIVDQSQQAYQEAFEISK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIVDQSQQAYQEAFEISK 18 0 B7Z2E6;H0YB80;P63104-2;P63104;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 263.75 1.50E-30 106080000 52249 52589 60967 68499 60952 57329 65165 67466 71448 77144 FALSE TRUE 50207.05132 51089.21321 71985.0931 72034.2416 62912.57644 58488.23166 65962.50876 66072.80352 63337.52257 71918.96817 0.698105835 0.710371888 1.000919437 1.001602824 0.874770287 0.813251819 0.917178186 0.918711784 0.880678967 1 16.1340847 4.25370118 24.78743035 0.919450378 0.704238633 0.692648172 0.058934784 124.4212234 203692.5966 0.015049061 0.040860974 17934.9917 -4.25370118 -0.215211745 SS(ph)PLKLEFDFTEDTGNIEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPLKLEFDFTEDTGNIEAR 20 1 O75410-3;E7ET87;E7EVI4;O75410-2;O75410;O75410-9;O75410-7;H0YAY0;E5RFM9;R4GMT7 O75410-3 TACC1 Transforming acidic coiled-coil-containing protein 1 1 S(0.168)S(0.832)PLKLEFDFTEDTGNIEAR;S(0.197)S(0.803)PLKLEFDFTEDTGNIEAR;S(0.162)S(0.838)PLKLEFDFTEDTGNIEAR;S(0.417)S(0.583)PLKLEFDFTEDTGNIEAR 235.73 9.10E-30 521426000 297605 272627 310160 349281 347163 294181 325400 339330 313180 334796 TRUE FALSE 285974.2676 264851.9449 366212.8115 367307.4343 358329.8132 300129.5414 329382.3425 332322.7169 277629.1194 312119.9687 0.916231886 0.848558155 1.173307857 1.176814914 1.148051548 0.961583915 1.055306855 1.064727509 0.889494897 1 18.25174113 4.253722205 24.99923166 1.064636402 0.882394927 0.384257944 0.088994821 241.3491385 397942.1412 0.022333433 0.060656644 17935.85998 -4.253722205 -0.182241475 DCDLQEDACYNCGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DCDLQEDACYNCGR 14 0 P62633-2;P62633;P62633-7;P62633-3 P62633-2 CNBP Cellular nucleic acid-binding protein 0 ;;; 361.66 2.59E-82 2164190000 973608 934998 1030695 1159524 1022782 880573 1094440 1216250 1263511 1287540 FALSE TRUE 935558.323 908332.7725 1216964.514 1219367.173 1055680.712 898378.7894 1107834.084 1191134.012 1120082.528 1200333.769 0.779415149 0.756733499 1.013855101 1.015856759 0.879489305 0.748440819 0.922938363 0.992335668 0.933142562 1 20.19500419 4.253735463 24.99429778 0.93424031 0.768074198 0.440876823 0.076553563 239.8615421 395065.8341 0.020303315 0.055144976 17936.40755 -4.253735463 -0.166166112 FDVNTSAVQVLIEHIGNLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDVNTSAVQVLIEHIGNLDR 20 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 232.79 6.46E-27 1550230000 369440 404190 452190 512540 557290 520250 593590 555970 598410 704120 FALSE TRUE 355001.8764 392662.8969 533910.7919 538992.2508 575215.739 530769.8115 600854.532 544489.0252 530481.0055 656429.3252 0.54080746 0.598180005 0.813356094 0.821097154 0.876279771 0.808571146 0.915337735 0.829470903 0.808131181 1 19.32428017 4.253794297 2.390270884 0.857873007 0.538301839 0.815419758 0.055794185 0.110593902 1.222919773 0.013311938 0.04808273 17938.83754 -4.253794297 -0.319571168 KDPELWGSVLLESNPYR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDPELWGSVLLESNPYR 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 198.42 2.28E-11 6807100000 340870 317780 332520 362130 349960 302190 377680 365620 408760 412960 FALSE TRUE 327548.4235 308717.2255 392613.7609 380819.5727 361216.7812 308300.4888 382302.1608 358069.8192 362359.2785 384989.8514 0.850797553 0.801884061 1.019802884 0.989167822 0.938250138 0.8008016 0.993018802 0.930075995 0.941217742 1 18.55446089 4.253796311 24.9995566 0.945998094 0.826340751 0.414689398 0.059205263 239.5287167 393024.8259 0.01453423 0.039479149 17938.92072 -4.253796311 -0.119657343 SQSAAVT(ph)PSSTTSSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQSAAVTPSSTTSSTR 16 0 Q16186;A0A087WX59 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 1 SQSAAVT(0.821)PS(0.124)S(0.029)T(0.01)T(0.01)S(0.002)S(0.002)T(0.002)R;SQSAAVT(0.701)PS(0.262)S(0.022)T(0.004)T(0.002)S(0.003)S(0.003)T(0.003)R 92.613 0.052673 67112000 127500 124968 117433 132431 125748 136087 135962 132027 133332 144312 TRUE FALSE 122517.159 121404.035 138655.7554 139265.7798 129792.7986 138838.7724 137625.9436 129300.5963 118196.7103 134537.6197 0.910653536 0.902379834 1.030609548 1.035143777 0.964732384 1.031969888 1.022955096 0.961073911 0.878540222 1 17.03765011 4.2538011 24.96762394 0.991467931 0.906516616 0.35484972 0.045353916 260.0416113 426003.8412 0.011380272 0.030915492 17939.11853 -4.2538011 -0.084951314 QSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSAGPNSPTGGGGGGGSGGTR 21 0 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 QSAGPNS(0.97)PT(0.03)GGGGGGGSGGTR;QSAGPNS(0.987)PT(0.013)GGGGGGGSGGTR 253.18 2.46E-36 307200000 166790 172445 166779 216705 205381 201466 196758 193494 193358 205381 TRUE FALSE 160271.6624 167527.0374 196919.6753 227889.171 211987.2664 205539.7806 199165.9833 189498.2813 171408.8105 191470.3619 0.837057291 0.874950231 1.028460349 1.190205987 1.107154466 1.073480921 1.040192233 0.989700335 0.895223724 1 17.54676157 4.253863674 4.330778939 1.046930147 0.848258411 0.506380598 0.073225102 0.162159355 7.049996109 0.019988339 0.054623744 17941.70346 -4.253863674 -0.198671736 TPVEPEVAIHR ddPTM_BT-474_Pertuzumab_2h_R1 6 TPVEPEVAIHR 11 0 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;;;;; 203.02 3.80E-08 19567020000 8080050 8389910 7516060 9146300 8945360 9003190 9162250 9220640 9411900 10569000 FALSE TRUE 7764272.713 8150637.981 8874379.236 9618341.639 9233095.628 9185240.67 9274380.356 9030230.562 8343500.57 9853152.216 0.78799886 0.827211211 0.900663974 0.976168989 0.937070232 0.932213414 0.941260234 0.916481382 0.846784906 1 23.23215391 4.254131093 2.699786604 0.932042297 0.794861126 0.642866808 0.037997958 0.164234302 2.358361021 0.009549033 0.03175124 17952.75454 -4.254131093 -0.137181171 SWHEES(ph)PFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SWHEESPFEK 10 0 Q9BY84 Q9BY84 DUSP16 Dual specificity protein phosphatase 16 1 S(0.032)WHEES(0.968)PFEK 199.19 2.97E-07 105980000 149490 148370 103290 114190 129260 125800 131860 127900 155160 141950 TRUE FALSE 143647.7655 144138.6329 121956.8007 120083.3596 133417.7653 128343.7622 133473.7421 125258.8203 137546.8873 132335.6001 1.085480894 1.089190156 0.921572129 0.907415386 1.008177431 0.969835495 1.008600422 0.946523991 1.03937933 1 17.01384169 4.254324173 24.99818915 0.972305052 1.087335628 0.566750855 0.039156476 162.5591395 257785.2306 0.009442235 0.025672066 17960.73782 -4.254324173 0.115030576 GATQQILDEAER ddPTM_BT-474_Pertuzumab_2h_R1 3 GATQQILDEAER 12 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;; 302.09 3.17E-36 1324640000 1119350 1117270 1114170 1224170 1231530 1266630 1220390 1236910 1271980 1344410 FALSE TRUE 1075604.564 1085406.554 1315525.304 1287349.56 1271143.281 1292242.126 1235325.498 1211367.376 1127590.163 1253351.913 0.858182409 0.866003029 1.049605693 1.02712538 1.01419503 1.031028965 0.985617435 0.966502196 0.899659665 1 20.25736012 4.254438731 24.93022694 0.996274465 0.862092581 0.64868408 0.039628102 147.9827167 232343.3861 0.010327044 0.028080687 17965.4761 -4.254438731 -0.134181884 IERPGEGS(ph)PMVDNPMR ddPTM_BT-474_Pertuzumab_2h_R1 4 IERPGEGSPMVDNPMR 16 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 1 IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR 178.43 1.69E-09 2837160000 1071420 1059860 1065450 1254980 1160760 1210020 1121080 1159620 1245580 1202130 TRUE FALSE 1029547.722 1029633.831 1258000.516 1319749.668 1198096.9 1234487.433 1134800.112 1135673.442 1104186.98 1120708.664 0.91865777 0.918734604 1.122504497 1.177602806 1.069052946 1.101523949 1.012573694 1.01335296 0.985257824 1 20.09597986 4.254440131 24.9627568 1.061534285 0.918696051 0.491341934 0.057591778 211.826632 332987.7259 0.015507974 0.042172627 17965.53402 -4.254440131 -0.142838234 CPS(ph)QSSSRPAAMISQPPTPPTGQPVREDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.913)QS(0.056)S(0.015)S(0.015)RPAAMISQPPTPPTGQPVREDAK;CPS(0.998)QS(0.002)SSRPAAMISQPPTPPTGQPVREDAK 197.26 1.43E-25 886750000 318279 293174 182487 181226 212299 209032 173504 214905 235404 192226 TRUE FALSE 305840.3048 284812.9646 215466.4603 190579.0956 219127.7901 213258.7703 175627.3939 210467.1367 208681.9248 179206.3618 1.706637542 1.589301639 1.202337116 1.063461663 1.222767919 1.190017855 0.98002879 1.174440095 1.164478329 1 17.45126233 4.25448123 3.028057274 1.122671479 1.68915276 0.884919124 0.076549612 0.071506287 1.313169369 0.018977481 0.059134194 17967.23425 -4.25448123 0.566481281 QDDDWIVDDDGIGYVEDGR ddPTM_BT-474_Pertuzumab_2h_R1 3 QDDDWIVDDDGIGYVEDGR 19 0 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 0 ;; 313.87 3.02E-61 554770000 323354 346471 341366 432416 370293 394384 418130 447478 451649 500891 FALSE TRUE 310716.9682 336589.9863 403058.4298 454733.0416 382203.8106 402358.7147 423247.2 438237.4229 400379.699 466965.2064 0.665396402 0.720803138 0.863144458 0.973804976 0.818484558 0.861646027 0.90637845 0.93847982 0.85740799 1 18.83295553 4.254513799 3.023891452 0.90323444 0.675841122 0.730003218 0.051921635 0.120671906 2.209444829 0.012840481 0.040041559 17968.58172 -4.254513799 -0.227393317 LPSTSDDCPAIGT(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 6 LPSTSDDCPAIGTPLR 16 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR 411.69 5.12E-139 3422200000 1192054 1214343 1153748 1573267 1232764 1247817 1295582 1470801 1300456 1558696 TRUE FALSE 1145467.212 1179711.127 1362255.929 1654463.498 1272416.974 1273048.715 1311437.72 1440428.445 1152833.687 1453124.132 0.788278982 0.811844701 0.937467006 1.138556206 0.875642312 0.876077058 0.902495314 0.991263178 0.793348388 1 20.47072652 4.254539438 5.438592284 0.942556363 0.796718198 0.288076071 0.087734082 0.202395616 17.69142698 0.021681311 0.057083931 17969.64255 -4.254539438 -0.145838165 ALAAGADS(ph)PKTEEARPSPAPGPGTPTGTPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALAAGADSPKTEEARPSPAPGPGTPTGTPTR 31 2 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 ALAAGADS(0.994)PKT(0.006)EEARPSPAPGPGTPTGTPTR 109.59 5.83E-05 335570000 53896 55793 28877 30178 38820 59612 38594 41314 43568 38432 TRUE FALSE 51789.68473 54201.83827 34095.71627 31735.4902 40068.68056 60817.39548 39066.32492 40460.85146 38622.34329 35828.96641 1.445469684 1.512793801 0.951624333 0.885749531 1.118332025 1.697436504 1.0903559 1.129277663 1.077964205 1 15.1288388 4.25453996 24.98850423 1.133748884 1.479131993 0.31987383 0.209242555 307.0140732 480100.2551 0.053645313 0.14589637 17969.66412 -4.25453996 0.345383109 (ac)MEGHDPKEPEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEGHDPKEPEQLRK 14 2 P51991-2 P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 69.108 0.0015122 483870000 483890 462310 316210 274500 361530 408530 371610 368940 481460 346960 FALSE TRUE 464979.0438 449125.3714 373356.1811 288666.9779 373158.9408 416790.7565 376157.8743 361321.2601 426806.6792 323460.0902 1.437515966 1.388503204 1.154257333 0.892434605 1.153647551 1.288538429 1.162918968 1.117050514 1.319503371 1 18.30322819 4.25465847 4.814662503 1.136892504 1.421807093 0.47550967 0.116872383 0.153989069 9.092957774 0.029466782 0.07893973 17974.56835 -4.25465847 0.284914589 LDDPLHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDDPLHLR 8 0 O75146 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ; 123.92 0.0013271 395104000 709730 801950 636630 825930 836850 853160 921600 871730 978140 1006950 FALSE TRUE 681992.967 779079.1712 751683.2028 868556.3463 863768.0403 870411.4797 932878.8165 853728.4709 867105.6479 938748.3796 0.726491765 0.829912667 0.800729161 0.925228064 0.92012733 0.927204242 0.993747459 0.909432697 0.923682711 1 19.84037899 4.25475096 0.744580063 0.950022568 0.686740327 0.820945698 0.034351539 0.635890844 0.416673674 0.013726446 0.125473729 17978.39674 -4.25475096 -0.26328224 QNPQS(ph)PPQDSSVTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 QNPQSPPQDSSVTSK 15 0 Q9UBN7;C9JEF4;C9J172;Q9BRX7;A0A2R8YCS4;E7EP63;E7ER52;A6NDI8 Q9UBN7 HDAC6 Histone deacetylase 6 1 QNPQS(1)PPQDSSVTSK 224.32 1.21E-12 164850000 285170 281020 284830 298620 284310 301970 319240 327680 354200 361480 TRUE FALSE 274025.2411 273005.5847 336305.117 314031.814 293455.0894 308076.0403 323146.9546 320913.2935 313992.7009 336996.6376 0.813139392 0.810113676 0.99794799 0.931854443 0.870795304 0.914181348 0.958902608 0.952274467 0.931738379 1 18.36237467 4.254808934 24.99798118 0.94029849 0.811626415 0.683683548 0.036109878 137.9588361 212245.4907 0.008926083 0.02428653 17980.79682 -4.254808934 -0.128672075 SELEKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SELEKPR 7 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 ; 97.071 0.011187 354650000 349730 344920 253890 294450 301260 277560 322590 331590 329290 352850 FALSE TRUE 336062.165 335083.2193 299773.5708 309646.5998 310950.3015 283172.4534 326537.9529 324742.5506 291910.3797 328951.1552 1.021617221 1.01864126 0.911301164 0.941314827 0.945278035 0.860834348 0.992663949 0.987205989 0.887397339 1 18.32751385 4.254816938 24.28489257 0.942747506 1.020129351 0.351750286 0.043036289 193.4142611 288929.1297 0.010549919 0.028683892 17981.12824 -4.254816938 0.077381845 TASFS(ph)ESRADEVAPAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 TAS(0.35)FS(0.623)ES(0.027)RADEVAPAKK 155.86 6.66E-08 615710000 429750 442570 142090 149110 272720 398470 208140 272530 304820 223470 TRUE FALSE 412954.8949 429948.3369 167768.8238 156805.585 281492.2865 406527.3364 210687.2796 266902.1603 270218.1115 208334.1779 1.98217546 2.063743651 0.80528709 0.752663757 1.351157498 1.951323305 1.011294843 1.281125176 1.297041677 1 17.66854001 4.254853342 24.99855548 1.204152669 2.022960246 0.520708374 0.322422565 200.9174028 308269.9101 0.082579576 0.22469518 17982.63551 -4.254853342 0.818807577 HQEGEIFDTEKEKYEITEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 HQEGEIFDTEKEKYEITEQR 20 2 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 174.22 2.24E-12 1351050000 2667800 2463290 1110420 832740 1463650 2063570 1211240 764250 1829010 1126000 FALSE TRUE 2563539.427 2393039.381 1311097.595 875717.8112 1510729.632 2105296.799 1226063.517 748467.9704 1621388.453 1049735.017 2.442082416 2.279660431 1.248979575 0.834227493 1.439153317 2.005550701 1.167974296 0.713006576 1.544569273 1 20.00159377 4.254853381 5.105716247 1.219063138 2.391399434 0.618776833 0.351013336 0.114768509 8.135885874 0.094348038 0.250554679 17982.63714 -4.254853381 1.172336296 RAEPPKPEVVDSTESIPVS(ph)DEDSDAMVDDPNDEDFVPFRPR ddPTM_BT-474_Pertuzumab_2h_R1 5 RAEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 41 3 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 RAEPPKPEVVDS(0.005)T(0.004)ES(0.005)IPVS(0.749)DEDS(0.237)DAMVDDPNDEDFVPFRPR;RAEPPKPEVVDSTESIPVS(1)DEDSDAMVDDPNDEDFVPFRPR;RAEPPKPEVVDSTESIPVS(1)DEDSDAMVDDPNDEDFVPFRPR;RAEPPKPEVVDSTESIPVS(0.999)DEDS(0.001)DAMVDDPNDEDFVPFRPR;RAEPPKPEVVDS(0.002)T(0.002)ES(0.003)IPVS(0.991)DEDS(0.002)DAMVDDPNDEDFVPFRPR 205.4 1.06E-34 3433907000 348977 387402 358237 452709 431581 486468 542122 442232 455643 470154 TRUE FALSE 335338.593 376353.6743 422978.3948 476073.3657 445463.1948 496304.7163 548756.6512 433099.7547 403920.3169 438310.0508 0.765071648 0.858647146 0.96502098 1.086156626 1.016319827 1.13231425 1.251982815 0.988112761 0.921540166 1 18.74159224 4.254915765 1.585170502 1.066348616 0.756144898 0.566432094 0.086195855 0.360508965 1.539939193 0.025287109 0.131760751 17985.22045 -4.254915765 -0.310203718 EPVDFEQWIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EPVDFEQWIEK 11 0 Q9Y547;A6NIR2;X6R7Y7 Q9Y547 HSPB11 Intraflagellar transport protein 25 homolog 0 82.171 0.045758 26807000 17483 19353 23747 30869 23921 25487 24587 31349 37003 37599 FALSE TRUE 16799.74503 18801.07139 28038.61115 32462.15279 24690.44069 26002.3646 24887.90306 30701.63219 32802.57457 35052.38624 0.47927536 0.536370656 0.799905917 0.926103934 0.704386872 0.741814392 0.710020222 0.87587852 0.935815734 1 15.09722504 4.255127926 4.157021932 0.825424432 0.494018209 0.65760787 0.095193105 0.12057925 4.679747435 0.023981536 0.066339494 17994.00871 -4.255127926 -0.331406223 T(ph)PTAPAVNLAGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPTAPAVNLAGAR 13 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.999)PT(0.001)APAVNLAGAR;T(1)PTAPAVNLAGAR 118.24 0.0049541 687020000 56155 52634 70645 82246 60157 68638 76923 73741 73520 64218 TRUE FALSE 53960.40052 51132.92985 83412.12299 86490.72592 62092.00454 70025.90739 77864.40668 72218.22258 65174.31782 59868.45766 0.901316029 0.854087976 1.393256587 1.444679374 1.037140541 1.169662793 1.300591492 1.206281662 1.088625302 1 15.86950848 4.255217915 24.99987671 1.217959577 0.877701725 0.473049975 0.137649006 195.9777123 294125.3303 0.033380749 0.0908797 17997.73757 -4.255217915 -0.340257852 QRS(ph)PDIFQEAGWNSNGSWSPGPGER ddPTM_BT-474_Pertuzumab_2h_R1 2 QRSPDIFQEAGWNSNGSWSPGPGER 25 1 Q8TBB1-2;Q8TBB1 Q8TBB1-2 LNX1 E3 ubiquitin-protein ligase LNX 1 QRS(1)PDIFQEAGWNSNGSWSPGPGER;QRS(1)PDIFQEAGWNSNGSWSPGPGER 152.02 8.11E-08 214238000 162639 160215 149829 157301 176121 168710 162489 179457 181287 166215 TRUE FALSE 156282.8881 155645.8251 176906.4332 165419.3235 181786.0919 172121.4318 164477.589 175751.1502 160708.0598 154957.11 1.008555774 1.004444553 1.141647732 1.067516834 1.173138115 1.110768211 1.061439446 1.134192231 1.037113171 1 17.24150943 4.255274678 24.91982143 1.098550335 1.006500075 0.305626972 0.049674731 232.1973725 346188.2203 0.011106259 0.030238694 18000.09007 -4.255274678 -0.09205026 AKTQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKTQTPPVSPAPQPTEERLPS(0.611)S(0.389)PVYEDAASFK 253.17 2.26E-59 656720000 526640 503370 203380 193790 252620 459170 331570 354650 371250 267740 TRUE FALSE 506058.3266 489014.3805 240135.2902 203791.5251 260745.7517 468454.732 335627.8528 347326.3536 329107.2564 249605.7313 2.027430716 1.959147243 0.962058399 0.816453709 1.044630467 1.876778748 1.344631996 1.391499914 1.318508412 1 17.92929154 4.255317779 24.0388872 1.249908244 1.993290292 0.541759086 0.283612104 127.5969831 183038.2753 0.074710612 0.203227984 18001.87653 -4.255317779 0.743382048 LQDLQGEKDALHSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQDLQGEKDALHSEK 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 170.91 6.69E-07 166050000 263500 270780 150230 141950 199930 257030 186050 211350 276890 239850 FALSE TRUE 253202.1287 263057.6195 177379.9028 149276.0565 206360.93 262227.3227 188326.9356 206985.5486 245458.608 223604.7459 1.132364735 1.176440234 0.793274321 0.667588946 0.922882604 1.172727 0.842231388 0.925676009 1.09773434 1 17.77059128 4.255322336 24.99205831 0.920235981 1.154402664 0.302265467 0.137354346 297.2946185 443264.4503 0.034940012 0.095130849 18002.06544 -4.255322336 0.234166683 IDASKNEEDEGHSNS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 3 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHS(0.092)NS(0.454)S(0.454)PR;IDASKNEEDEGHS(0.063)NS(0.468)S(0.468)PR;IDASKNEEDEGHSNS(0.637)S(0.363)PR 221.48 3.75E-19 23953550000 8625000 8241510 5085500 4662586 5949414 7824976 5479823 5850482 7099589 5956179 TRUE FALSE 8287925.465 8006470.204 6004562.976 4903222.622 6140782.304 7983202.376 5546886.713 5729667.502 6293673.421 5552761.691 1.492577194 1.441889757 1.08136515 0.883024141 1.105896966 1.43769944 0.998941972 1.031859068 1.133431213 1 22.40477405 4.255347482 5.846767646 1.083373795 1.474441432 0.558526941 0.136439596 0.117335746 13.06892031 0.035135131 0.092048127 18003.10778 -4.255347482 0.391067637 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR ddPTM_BT-474_Pertuzumab_2h_R1 5 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR 32 1 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ;;;; 456.72 1.71E-232 6177200000 917340 988600 925690 1171040 1163420 1159460 1148360 1100650 1246540 1276730 FALSE TRUE 881489.3386 960406.0959 1092982.775 1231477.515 1200842.461 1182905.076 1162413.973 1077921.193 1105038.005 1190255.94 0.740588061 0.806890404 0.918275421 1.03463253 1.008894323 0.993824131 0.97660842 0.905621351 0.928403689 1 20.1828404 4.255492333 2.54794437 0.972463732 0.751092924 0.830538099 0.036835057 0.124921818 1.584436947 0.011085861 0.038368392 18009.11342 -4.255492333 -0.221370808 KGAVECCPNCR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGAVECCPNCR 11 1 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 193.22 1.68E-06 396230000 501480 495330 329630 370700 396680 467500 408250 410540 489460 476790 FALSE TRUE 481881.6072 481203.6734 389201.4736 389831.8714 409439.5725 476953.1703 413246.2856 402062.2055 433898.5528 444496.5886 1.084106424 1.082581252 0.875600586 0.877018815 0.921130967 1.073018742 0.929695067 0.904533839 0.976157217 1 18.76181282 4.255601437 24.96734502 0.939950385 1.083343984 0.485435355 0.0569563 197.9661792 290044.828 0.014400005 0.039217662 18013.63826 -4.255601437 0.143393598 SFEEKVENLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SFEEKVENLK 10 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 155.15 1.21E-05 882880000 1600000 1509700 1122900 1012400 1212200 1473700 1191800 1341300 1577000 1204900 FALSE TRUE 1537470.231 1466644.834 1325833.009 1064650.085 1251191.514 1503499.224 1206385.605 1313601.686 1397985.571 1123291.05 1.368719382 1.305667694 1.180311202 0.947795396 1.113862266 1.33847699 1.073974199 1.169422374 1.244544387 1 20.09930035 4.255612749 3.433050633 1.13608511 1.351482459 0.379368007 0.106399203 0.241493391 5.856164588 0.026944164 0.079401038 18014.10747 -4.255612749 0.21539735 AGVVNGTGAPGQS(ph)PGAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGVVNGTGAPGQSPGAGR 18 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;Q13330-2 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 AGVVNGTGAPGQS(1)PGAGR;AGVVNGTGAPGQS(1)PGAGR 334.98 5.05E-75 244260000 207669 206809 192752 206519 199092 251720 216217 225514 209751 234930 TRUE FALSE 199553.0659 200911.0098 227586.5741 217177.4703 205495.975 256809.9509 218863.1283 220857.0571 185940.9458 219017.9818 0.911126403 0.917326551 1.03912278 0.991596528 0.938260746 1.172551901 0.999292964 1.008396914 0.848975706 1 17.7406898 4.255649938 23.21082298 1.003897773 0.914226236 0.165823012 0.076302861 175.6693654 238584.7513 0.018269387 0.049683906 18015.6501 -4.255649938 -0.089671537 KQGGLGPMNIPLVSDPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQGGLGPMNIPLVSDPKR 18 2 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 206.59 4.70E-16 7326800000 5663300 5392400 3795000 3478200 4382900 5235400 3775200 4674700 4957600 4541600 FALSE TRUE 5441971.975 5238614.032 4480840.919 3657710.319 4523879.959 5341263.375 3821402.027 4578165.811 4394834.032 4233993.387 1.285304789 1.237274968 1.058301351 0.863891363 1.068466468 1.261519064 0.902552668 1.081287898 1.03798793 1 22.01358759 4.255669922 4.195301126 1.034527229 1.271386477 0.448826909 0.101467287 0.177470826 7.051323608 0.025382409 0.070114072 18016.47911 -4.255669922 0.236859248 ESRPS(ph)EEREWDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESRPSEEREWDR 12 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 ES(0.219)RPS(0.781)EEREWDR 85.362 0.011635 0 78477 82705 82068 104620 102300 104800 97617 93868 89416 117190 TRUE FALSE 75410.03208 80346.33438 96899.51319 110019.4507 105590.5724 106919.1278 98811.66605 91929.593 79265.87054 109252.6169 0.690235476 0.735417939 0.886930821 1.007018906 0.966480945 0.978641344 0.904432945 0.84144065 0.725528347 1 16.73730831 4.255698008 3.716840339 0.912988286 0.701512895 0.507330695 0.080104066 0.18587404 5.430708715 0.021647552 0.061957569 18017.64427 -4.255698008 -0.211475391 DYIYAVTPLLEDALMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYIYAVTPLLEDALMDR 17 0 O75533;H7C341 O75533 SF3B1 Splicing factor 3B subunit 1 0 167.14 5.25E-09 61119000 66050 66094 64128 72583 74615 60509 76406 73156 70206 83471 FALSE TRUE 63468.69298 64209.06383 75717.35612 76329.01733 77015.05924 61732.53344 77341.07948 71645.30304 62236.50921 77817.43482 0.815610192 0.825124395 0.973012748 0.980872956 0.989689 0.793299517 0.993878553 0.920684461 0.799775903 1 16.2478058 4.255706599 23.3827263 0.930334317 0.820367018 0.272071139 0.072630694 146.4846286 199759.5304 0.017214723 0.04682289 18018.00069 -4.255706599 -0.109967299 KPGPPLS(ph)PEIR ddPTM_BT-474_Pertuzumab_2h_R1 6 KPGPPLSPEIR 11 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR 131.24 0.0001271 9202790000 6792110 7312750 6236760 8307140 7982100 7260290 7884580 8217520 7724090 8226180 TRUE FALSE 6526666.832 7104197.53 7363881.268 8735872.491 8238851.496 7407098.038 7981073.849 8047825.34 6847283.685 7669013.501 0.851043857 0.926350896 0.960212323 1.139112937 1.07430395 0.965847568 1.040691068 1.04939512 0.892850649 1 22.87060958 4.25581554 2.377673503 1.02756981 0.867820001 0.417775129 0.06375254 0.277991427 3.037019987 0.01660481 0.060420767 18022.521 -4.25581554 -0.159749809 LEEPTPAPSTSYS(ph)PQADSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEEPTPAPSTSYSPQADSLR 20 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 LEEPTPAPSTSYS(1)PQADSLR;LEEPTPAPSTSYS(1)PQADSLR 222.13 3.39E-26 173610000 166280 169595 176200 192445 197384 207941 219305 204858 198199 231843 TRUE FALSE 159781.5938 164758.3167 208043.2595 202377.1095 203733.0356 212145.7095 221988.9202 200627.6107 175700.2804 216140.0671 0.739250227 0.76227568 0.962539072 0.936323895 0.942597263 0.981519587 1.027060476 0.928229612 0.812900092 1 17.72160701 4.255908179 7.318273002 0.949954686 0.748937404 0.681639118 0.05416872 0.084792081 20.56313112 0.013464349 0.035023136 18026.36577 -4.255908179 -0.201017283 LS(ph)PTPSMQDGLDLPSETDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSPTPSMQDGLDLPSETDLR 20 0 Q9UK58;Q9UK58-6;Q9UK58-5;Q9UK58-4 Q9UK58 CCNL1 Cyclin-L1 1 LS(1)PTPSMQDGLDLPSETDLR;LS(0.997)PT(0.003)PSMQDGLDLPSETDLR;LS(0.972)PT(0.028)PSMQDGLDLPSETDLR;LS(0.999)PT(0.001)PSMQDGLDLPSETDLR 291.7 1.85E-54 606475000 414708 412136 432587 457088 424830 433863 471287 514766 545770 504350 TRUE FALSE 398500.7529 400382.2848 510765.0937 480678.3665 438495.0428 442636.0071 477054.7513 504135.9022 483816.4777 470189.9253 0.847531458 0.8515331 1.086295274 1.022306818 0.932591319 0.941398323 1.014600113 1.072196309 1.028980954 1 18.8428841 4.255908272 24.86783444 1.013126484 0.849532098 0.668760127 0.045816909 144.4221549 207025.0513 0.012537756 0.034160684 18026.36965 -4.255908272 -0.163594386 DMDLWEQQEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 DMDLWEQQEEER 12 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 192.14 1.04E-05 77218000 48242 46184 52316 59007 44392 54082 55344 58848 57799 66724 FALSE TRUE 46356.64931 44866.87754 61770.66496 62052.35834 45819.909 55175.57509 56021.31643 57632.76824 51237.89983 62204.72405 0.745227151 0.721277656 0.993022088 0.997550577 0.736598541 0.886999757 0.900595852 0.926501469 0.823697888 1 15.92473653 4.255938791 24.96665818 0.902773161 0.733252258 0.441706854 0.07845443 221.0458569 317563.7931 0.018981246 0.051719513 18027.63644 -4.255938791 -0.169520902 DS(ph)QKPTSPLQSAGDHLEEELDLLLNLDAPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSQKPTSPLQSAGDHLEEELDLLLNLDAPIK 31 1 Q9NQS1 Q9NQS1 AVEN Cell death regulator Aven 1 DS(0.316)QKPT(0.316)S(0.316)PLQS(0.052)AGDHLEEELDLLLNLDAPIK 100.95 0.00012883 78554000 103150 84589 114200 109190 112820 104120 110220 115280 120760 135650 TRUE FALSE 99118.78396 82176.60454 134838.4804 114825.309 116448.9578 106225.3777 111568.9053 112899.4277 107051.8311 126462.3047 0.783781256 0.649811062 1.066234565 0.907980519 0.920819513 0.839976608 0.882230524 0.892751623 0.846511783 1 16.94834789 4.255996846 24.99999026 0.909783918 0.716796117 0.557335488 0.071861396 174.55121 250266.4391 0.016797035 0.045770836 18030.04646 -4.255996846 -0.1929878 AGSIST(ph)LDSLDFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGSIS(0.017)T(0.554)LDS(0.429)LDFAR 86.944 0.079799 18854000 19386 20410 22658 26538 28609 29497 32993 29469 36382 34710 TRUE FALSE 18628.37369 19827.92678 26752.80462 27907.62936 29529.23447 30093.44955 33396.7782 28860.45485 32252.06789 32359.06078 0.575677206 0.612747289 0.82674849 0.862436322 0.912549183 0.92998526 1.032068836 0.891881722 0.996693572 1 14.98188211 4.256041481 0.868234791 0.963297327 0.463561121 0.914730619 0.043261458 0.311068007 0.292750767 0.014975814 0.129433651 18031.89963 -4.256041481 -0.499736206 QKS(ph)PEIHRR ddPTM_BT-474_Pertuzumab_2h_R1 7 QKSPEIHRR 9 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR 126.71 0.00024309 20208420000 8922030 8653230 5251090 5588330 6637610 8222260 6543480 7024040 8043670 7020040 TRUE FALSE 8573347.204 8406448.353 6200078.773 5876744.381 6851114.754 8388519.731 6623561.066 6878991.119 7130586.303 6544566.438 1.309994678 1.284492782 0.947362798 0.897957785 1.046840126 1.281753316 1.012070261 1.051099593 1.089542962 1 22.64186619 4.25605245 23.33048275 1.045076235 1.297244402 0.531313408 0.096265736 90.06022944 120116.7745 0.024825645 0.067549699 18032.35507 -4.25605245 0.252168167 KQATS(ph)PASK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQATSPASK 9 1 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 1 KQAT(0.047)S(0.95)PAS(0.003)K 77.593 0.0197 104680000 521460 513270 368460 407280 432020 437300 530880 438820 434000 589450 TRUE FALSE 501080.7667 498632.0421 435048.9183 428299.7696 445916.3157 446142.5056 537377.0682 429758.2137 384734.1395 549526.0265 0.911841737 0.907385671 0.79168028 0.779398516 0.811456226 0.811867835 0.977891933 0.78205252 0.70011996 1 19.06782829 4.256091227 23.50447989 0.826269795 0.909613898 0.111971745 0.086527768 241.8544751 324258.6217 0.020304899 0.05526523 18033.9652 -4.256091227 0.083344103 FCSNSGRLS(ph)GPAELR ddPTM_BT-474_Pertuzumab_2h_R1 2 FCSNSGRLSGPAELR 15 1 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR 149.94 1.98E-06 2370290000 2199500 2452000 1647880 2222600 1823500 2152600 2188800 2183350 2711200 1911410 TRUE FALSE 2113541.108 2382071.361 1945688.573 2337308.652 1882154.534 2196127.047 2215587.189 2138263.06 2403435.942 1781948.498 1.186084284 1.336779016 1.091888219 1.311658925 1.056233968 1.232430145 1.243350855 1.199957834 1.348768466 1 20.76502421 4.256198074 24.9980775 1.197270274 1.261431537 0.063009506 0.109849892 758.7891722 1075434.755 0.024245425 0.06608126 18038.40254 -4.256198074 0.064161263 LPLS(ph)PIITLEEDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPLSPIITLEEDTK 14 0 A0A1W2PQQ1;Q5HYW2;A0A0J9YW69;A0A0J9YY72;Q5HYW2-2 A0A1W2PQQ1 NHSL2 NHS-like protein 2 1 LPLS(1)PIITLEEDTK 112.72 0.00060526 6368500 9682.3 11295 12793 16993 20038 15768 16365 15999 14099 12833 TRUE FALSE 9303.905012 10972.87766 15104.97968 17870.01077 20682.54047 16086.83976 16565.27977 15668.61506 12498.54063 11963.80948 0.777670777 0.917172551 1.26255602 1.493672295 1.728758762 1.344625204 1.384615811 1.309667718 1.044695726 1 13.54638922 4.256365165 2.987379781 1.360716908 0.803764789 0.48339043 0.19714116 0.197671304 3.523349909 0.050923936 0.160253332 18045.344 -4.256365165 -0.556952119 FSGEEGEIEDDES(ph)GTENR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSGEEGEIEDDESGTENR 18 0 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(1)GTENR;FSGEEGEIEDDES(1)GTENR 545.01 0 3073600000 1607090 1698270 2082450 2550570 2031030 1915720 2544080 2689100 2596500 3093900 TRUE FALSE 1544283.146 1649837.002 2458795.039 2682205.223 2096359.924 1954457.171 2575215.212 2633569.145 2301756.205 2884347.397 0.535401231 0.571996634 0.852461476 0.929917536 0.726805629 0.677608104 0.892824219 0.913055462 0.798016289 1 21.45981351 4.256404517 6.205494197 0.84465669 0.549058957 0.627108785 0.091051963 0.100467573 13.62622069 0.02320581 0.060716789 18046.97917 -4.256404517 -0.295597733 VEKIPGGIIEDSCVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEKIPGGIIEDSCVLR 16 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 130.11 4.72E-05 985780000 705360 718690 447360 499930 573640 712500 515600 629240 643050 640130 FALSE TRUE 677793.7514 698193.6649 528207.9035 525731.4472 592091.6516 726907.2382 521910.067 616245.9741 570053.6599 596773.4249 1.135763965 1.169947648 0.885106276 0.880956533 0.992154856 1.218062346 0.874553131 1.032629719 0.955226282 1 19.18682377 4.256683867 24.99013314 0.983354836 1.152855945 0.343822888 0.095510022 275.6784426 380126.1013 0.023432564 0.063895984 18058.59121 -4.256683867 0.169501108 QAQQERDELADEIANSSGK ddPTM_BT-474_Pertuzumab_2h_R1 4 QAQQERDELADEIANSSGK 19 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 279.96 1.18E-39 5628600000 3438900 3529350 2172910 2539260 2852950 3186960 2841360 2948180 3284460 2851860 FALSE TRUE 3304503.986 3428696.394 2565603.173 2670311.513 2944717.728 3251402.515 2876133.414 2887299.053 2911621.87 2658700.982 1.242901706 1.289613393 0.964983723 1.004366994 1.107577628 1.222928993 1.081781454 1.085981113 1.095129497 1 21.3422901 4.256814043 24.99183266 1.078691555 1.266257692 0.560542434 0.069071515 188.356185 257884.9496 0.017675181 0.048204399 18064.00491 -4.256814043 0.187566137 ERQTNPSAMEVEEDDPVPEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERQTNPSAMEVEEDDPVPEIR 21 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 158.37 2.18E-11 1135000000 968590 974380 610600 734180 723560 893780 755690 825830 922470 903200 FALSE TRUE 930736.432 946591.6364 720949.0027 772071.1178 746833.9645 911852.844 764938.3603 808776.3219 817755.0729 842025.4595 1.105354264 1.124184104 0.856208081 0.916921346 0.886949386 1.082927878 0.908450394 0.960512907 0.971176184 1 19.68350433 4.25682892 24.99998695 0.946673168 1.114769339 0.549795596 0.060394825 171.6459353 234891.6661 0.014382359 0.039223764 18064.62372 -4.25682892 0.168096171 ILTEAEIDAHLVALAER ddPTM_BT-474_Pertuzumab_2h_R1 4 ILTEAEIDAHLVALAER 17 0 G3V5Z7;P60900;P60900-2;P60900-3;H0YJC4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;; 208.26 5.34E-12 287230000 276853 292847 343197 433164 366961 347522 404850 419874 435203 502090 FALSE TRUE 266033.2787 284495.2903 405220.3323 455519.646 378764.6338 354549.1329 409804.6754 411203.4552 385800.58 468082.9971 0.568346384 0.607788132 0.865701884 0.973159993 0.809182637 0.757449288 0.875495752 0.878484067 0.824214044 1 18.83640484 4.256849458 5.428111384 0.86730778 0.581504864 0.735933835 0.068307745 0.080687956 6.899157375 0.01673143 0.044286601 18065.47803 -4.256849458 -0.285802916 GECLYCFVTLCDGHTFSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GECLYCFVTLCDGHTFSPK 19 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 188.96 1.50E-14 517350000 463530 487280 504250 622050 597670 624450 556480 561770 731950 685350 FALSE TRUE 445414.7351 473383.2515 595379.192 654154.075 616894.5983 637076.8068 563290.3687 550169.2532 648862.1046 638930.6341 0.697125339 0.740899287 0.931836979 1.023826438 0.965511067 0.997098547 0.881614277 0.86107822 1.015543895 1 19.28529979 4.256962212 4.07666358 0.95105653 0.708283642 0.77348722 0.052229044 0.102278877 3.759352969 0.014644997 0.040841914 18070.1689 -4.256962212 -0.242772888 TWYVQATCATQGTGLYDGLDWLSHELSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TWYVQATCATQGTGLYDGLDWLSHELSK 28 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 322.45 2.93E-83 1778620000 466530 472540 439680 499940 508150 478270 565060 529890 570900 539200 FALSE TRUE 448297.4918 459063.6219 519139.9566 525741.9633 524495.1062 487940.9471 571975.3733 518947.5863 506093.8254 502679.5037 0.891815736 0.91323322 1.032745423 1.045879053 1.043398631 0.970680013 1.137852984 1.032362733 1.006792244 1 18.93927934 4.256971211 4.37729033 1.039208164 0.897223813 0.615781021 0.041437869 0.113982251 5.068992737 0.010067576 0.027592866 18070.54333 -4.256971211 -0.141984352 AFEDDDITHVEGSVDPIR ddPTM_BT-474_Pertuzumab_2h_R1 4 AFEDDDITHVEGSVDPIR 18 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;; 227.22 3.09E-19 5069420000 2545860 2710870 2921780 3645550 3239750 3123900 3686950 3489020 3989940 4175410 FALSE TRUE 2446364.977 2633558.642 3449810.641 3833697.272 3343959.501 3187067.398 3732071.997 3416970.518 3537018.738 3892605.762 0.628464614 0.676554165 0.886247119 0.984866567 0.859054244 0.818749083 0.958759306 0.877810579 0.908650646 1 21.89230481 4.257039567 4.057721454 0.90743008 0.640612086 0.792406014 0.053384289 0.082731999 3.004045812 0.012972551 0.036227753 18073.38777 -4.257039567 -0.266817994 VHQFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHQFEK 6 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 155.73 0.0098399 744320000 1313290 1327580 1189010 1393300 1468900 1400760 1524580 1080090 1738960 1736240 FALSE TRUE 1261965.175 1289718.718 1403890.556 1465208.38 1516148.503 1429084.327 1543238.266 1057785.764 1541560.551 1618642.918 0.77964396 0.79679014 0.867325672 0.905207914 0.936678798 0.882890421 0.953414894 0.653501617 0.952378399 1 20.62635332 4.257081598 4.002963295 0.875295905 0.784007507 0.157857856 0.090297961 0.449238458 15.75153699 0.023854359 0.066871524 18075.13701 -4.257081598 -0.091288398 FEAWLAEVEGR ddPTM_BT-474_Pertuzumab_2h_R1 4 FEAWLAEVEGR 11 0 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 0 ;;; 123.88 0.00083909 67500100 70922 71342 73182 89957 79206 67049 79725 80834 80146 101317 FALSE TRUE 68150.28983 69307.39601 86407.61532 94599.69155 81753.73292 68404.77672 80700.6984 79164.74965 71048.16208 94454.70935 0.721512885 0.733763266 0.914804735 1.001534939 0.865533688 0.724207159 0.854385122 0.838123903 0.752192904 1 16.52733511 4.257105536 22.86822495 0.860683663 0.727637606 0.299938888 0.085568962 118.9706091 146698.3004 0.021343906 0.058130595 18076.13331 -4.257105536 -0.133046057 GS(ph)GGGGGGGGQGSTNYGK ddPTM_BT-474_Pertuzumab_2h_R1 5 GSGGGGGGGGQGSTNYGK 18 0 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 GS(1)GGGGGGGGQGSTNYGK;GS(1)GGGGGGGGQGSTNYGK;GS(1)GGGGGGGGQGSTNYGK;GS(1)GGGGGGGGQGSTNYGK;GS(1)GGGGGGGGQGSTNYGK 354.04 1.74E-90 2517540000 1225620 1188290 1261722 1325032 1314630 1351200 1389960 1404290 1336172 1518770 TRUE FALSE 1177721.415 1154401.133 1489743.232 1393417.06 1356916.268 1378522.19 1406970.746 1375290.921 1184495.356 1415902.355 0.831781522 0.81531126 1.052151108 0.984119459 0.958340286 0.973599758 0.993691932 0.971317631 0.836565708 1 20.43329035 4.257173048 24.99820139 0.97147497 0.823546251 0.56845641 0.051467478 165.6234526 222443.5984 0.012220487 0.033340208 18078.94353 -4.257173048 -0.147928719 LNLAQFLNEDLS(ph) ddPTM_BT-474_Pertuzumab_2h_R1 2 LNLAQFLNEDLS 12 0 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 1 LNLAQFLNEDLS(1);LNLAQFLNEDLS(1) 149.23 7.04E-05 32498000 69418 71553 69991 87894 79599 76222 89479 80226 85076 97881 TRUE FALSE 66705.06781 69512.3785 82639.93064 92430.21987 82159.37412 77763.26106 90574.07077 78569.30506 75418.52915 91251.43269 0.731002965 0.76176753 0.905628857 1.012918013 0.900362566 0.852186741 0.992576972 0.861019962 0.826491453 1 16.47755959 4.257413018 4.553314419 0.916049086 0.740105784 0.559560302 0.061471578 0.134952073 6.696614375 0.015195702 0.041337993 18088.93583 -4.257413018 -0.175943302 IGEWELIQESGVPLKPLFGPGYTGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 IGEWELIQESGVPLKPLFGPGYTGIR 26 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 172.2 4.65E-12 410080000 240990 220370 246370 242500 244720 245160 256640 273320 307560 274510 FALSE TRUE 231571.8444 214085.2634 290894.5395 255015.4541 252591.641 250117.3032 259780.8371 267675.8465 272647.0782 255917.1932 0.90487021 0.836541151 1.136674468 0.996476442 0.987005359 0.977336849 1.015097242 1.045947102 1.065372259 1 17.96531755 4.257454388 24.99998857 1.025668726 0.870705596 0.641473646 0.047008499 146.3886988 193696.2172 0.011313447 0.030873679 18090.65904 -4.257454388 -0.154963131 KGPGQPS(ph)SPQRLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.574)S(0.426)PQRLDR;KGPGQPS(0.552)S(0.448)PQRLDR 115.87 0.00031075 4196000000 2011920 1962250 1325600 1529940 1549530 1949670 1633200 1654220 1856070 1704860 TRUE FALSE 1933291.942 1906288.551 1565165.408 1608900.387 1599372.04 1989093.663 1653187.59 1620059.779 1645376.715 1589388.314 1.216374831 1.199385031 0.984759605 1.012276467 1.00628149 1.25148376 1.040140774 1.019297654 1.035226383 1 20.60004021 4.257467249 21.96581176 1.047563226 1.207880856 0.453250791 0.072034742 55.07219737 63977.94921 0.0180671 0.04918123 18091.19476 -4.257467249 0.16031763 SGGGENEERYS(ph)PTDNNANIFNFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGGGENEERYSPTDNNANIFNFFK 24 1 J3KR82;O00444-3;O00444-2;O00444 J3KR82 PLK4 Serine/threonine-protein kinase PLK;Serine/threonine-protein kinase PLK4 1 SGGGENEERYS(0.994)PT(0.006)DNNANIFNFFK 191.51 5.64E-18 44111000 28936 30223 34878 42323 37261 42468 37915 40397 45031 44220 TRUE FALSE 27805.14913 29361.06963 41181.23046 44507.2951 38459.5339 43326.73206 38379.01511 39562.78783 39919.26967 41224.94001 0.674473974 0.712216188 0.99893973 1.079620615 0.932919099 1.050983508 0.930965942 0.959680907 0.968328144 1 15.33122977 4.257521761 6.384225828 0.987772109 0.688951523 0.87232053 0.045444952 0.048136864 7.095705198 0.011213567 0.029383454 18093.46568 -4.257521761 -0.298820586 GFGFVTFENIDDAKDAMMAMNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVTFENIDDAKDAMMAMNGK 23 1 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;K7ENX8;K7ELV6;K7EJV5;K7ELT6;K7ER40 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ; 280.47 5.72E-52 812540000 1140570 1132190 757830 781570 964020 1022660 934930 1033570 1148320 1015490 FALSE TRUE 1095995.263 1099901.05 894786.7388 821906.9214 995028.5788 1043338.886 946371.953 1012226.418 1017967.528 946709.9578 1.157688534 1.161814176 0.945154037 0.868171835 1.051038463 1.102068144 0.999642969 1.069204364 1.075268639 1 19.85256297 4.257556462 24.76583291 1.01751331 1.159751526 0.444454985 0.065157061 218.481974 284840.411 0.017286858 0.047166502 18094.91146 -4.257556462 0.142238215 DPVQEAWAEDVDLR ddPTM_BT-474_Pertuzumab_2h_R1 11 DPVQEAWAEDVDLR 14 0 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;; 252.44 7.76E-24 29165260000 2043582 2110748 2265926 2747126 2435686 2274908 2681317 2935971 2786318 2910279 FALSE TRUE 1963716.556 2050551.534 2675429.233 2888905.502 2514032.052 2320908.198 2714131.76 2875342.173 2470026.862 2713163.211 0.72377384 0.75577891 0.986092257 1.064773947 0.926605536 0.855425206 1.000356981 1.059774864 0.91038639 1 21.37154441 4.257608525 6.00563393 0.980582841 0.735452765 0.70031628 0.061647167 0.087246373 10.41353909 0.016323608 0.042917008 18097.08078 -4.257608525 -0.245130076 KASSPS(ph)PLTIGTPESQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KASSPS(0.999)PLT(0.001)IGTPESQR;KASS(0.002)PS(0.998)PLTIGTPESQR 190.63 1.76E-10 1432340000 845190 925810 576260 681630 768450 880530 742411 771350 859530 825980 TRUE FALSE 812159.0404 899406.8053 680403.0008 716809.006 793167.8921 898334.9199 751496.8479 755421.3529 761959.7578 770035.6389 1.054703184 1.168006726 0.883599364 0.930877702 1.030040497 1.166614731 0.975924762 0.981021286 0.989512328 1 19.55456569 4.257609111 24.99822841 0.997224817 1.111354938 0.285797127 0.073678235 329.3575936 432223.9427 0.018769494 0.051221749 18097.1052 -4.257609111 0.114130121 RRDSGIGEETATGLGSHVEVTPHTAPPGVS(ph)AGPDAISEVLSTLSLEVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRDSGIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK 49 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RRDS(0.137)GIGEET(0.137)AT(0.137)GLGS(0.137)HVEVT(0.137)PHT(0.137)APPGVS(0.16)AGPDAIS(0.014)EVLS(0.002)T(0.002)LSLEVNK;RRDS(0.137)GIGEET(0.137)AT(0.137)GLGS(0.137)HVEVT(0.137)PHT(0.137)APPGVS(0.15)AGPDAIS(0.028)EVLSTLSLEVNK 55.331 0.0034931 1188340000 51952.4 48359.6 52164.1 50534.4 52685.3 66643.1 56936.7 47817.7 58751.6 68148.4 TRUE FALSE 49922.04277 46980.43156 61591.31325 53142.48644 54379.97052 67990.66914 57633.50837 46830.24778 52082.36467 63532.64817 0.785769903 0.739469122 0.969443507 0.836459489 0.855937413 1.070168978 0.9071479 0.737105239 0.819773237 1 15.95521053 4.257613909 24.9891186 0.885138612 0.762619434 0.248868776 0.092467229 392.1044502 514251.1447 0.02410833 0.06579455 18097.30513 -4.257613909 -0.122519177 EYFDDS(ph)TEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EYFDDSTEER 10 0 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 EYFDDS(0.972)T(0.028)EER 171.32 0.0024311 0 79452 82920 98023 113560 101240 89120 112870 119100 107890 129580 TRUE FALSE 76346.928 80555.20279 115737.9366 119420.8452 104496.4765 90922.06746 114251.3368 116640.5434 95642.77951 120803.4312 0.631993042 0.666828765 0.958068289 0.988555077 0.865012488 0.752644743 0.945762349 0.965539987 0.791722376 1 16.88230191 4.257696118 12.2673553 0.908019648 0.649198008 0.632705617 0.078934683 0.473494354 298.7482059 0.019665208 0.052362606 18100.73116 -4.257696118 -0.258821639 KDEKTDTLEDLFPTTK ddPTM_BT-474_Pertuzumab_2h_R1 2 KDEKTDTLEDLFPTTK 16 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 91.657 0.0028329 833930000 1099020 1021740 667250 507870 661630 868090 700750 854750 1031500 737580 FALSE TRUE 1056069.083 992600.9756 787836.9179 534081.2316 682911.9298 885643.3746 709325.9881 837099.1138 914408.4444 687623.0496 1.535825601 1.443524873 1.145739542 0.776706412 0.993148688 1.287978021 1.031562261 1.217380823 1.329810635 1 19.39125838 4.257711311 4.020106799 1.097500654 1.509418794 0.517728796 0.152871662 0.168386151 5.962986649 0.040441513 0.113348242 18101.3644 -4.257711311 0.411918139 EQSGTIYLQHADEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EQSGTIYLQHADEER 15 0 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 ; 191.44 1.75E-07 1696970000 841480 846770 881320 1076190 915420 995930 883080 938690 1018420 1034960 FALSE TRUE 808594.0313 822620.9487 1040594.129 1131732.295 944865.3157 1016068.387 893887.3972 919305.7235 902813.2312 964861.2374 0.838041783 0.852579539 1.078490967 1.172948245 0.979275858 1.053072035 0.926441402 0.952785424 0.935692301 1 19.87996195 4.257817098 22.89287419 1.009101319 0.845310071 0.470872913 0.070756808 87.44929265 103957.9874 0.019056558 0.051939858 18105.77414 -4.257817098 -0.163791249 FPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG ddPTM_BT-474_Pertuzumab_2h_R1 2 FPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG 34 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 234.17 7.07E-47 570680000 487630 503160 455170 531340 530540 566740 548690 582220 570140 569590 FALSE TRUE 468572.8805 488810.3694 537429.3442 558762.5211 547605.3009 578199.8711 555405.0324 570196.9535 505420.0974 531011.162 0.882416254 0.920527485 1.012086718 1.052261348 1.031250076 1.088865757 1.045938527 1.073794666 0.951806918 1 19.01838266 4.257867568 2.366277125 1.042608424 0.884522608 0.674703315 0.036708404 0.157000681 1.696289484 0.009216175 0.033775426 18107.87834 -4.257867568 -0.158085816 AESLQQEVEALKER ddPTM_BT-474_Pertuzumab_2h_R1 2 AESLQQEVEALKER 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 203.11 1.41E-08 329440000 233710 244540 175650 173910 229035 241750 215214 227230 256260 224356 FALSE TRUE 224576.3548 237565.9586 207393.8623 182885.5159 236402.1188 246638.3506 217847.8533 222537.6211 227170.4391 209160.1683 1.073705174 1.135808795 0.991555247 0.874380229 1.130244447 1.179184128 1.04153604 1.063957937 1.086107556 1 17.67424861 4.257967708 24.97920822 1.050230133 1.104756965 0.078436032 0.079624175 749.2365415 964339.3446 0.020524278 0.056016831 18112.05416 -4.257967708 0.054526832 GLPS(ph)PYNMSSAPGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPS(1)PYNMSSAPGSR;GLPS(1)PYNMSSAPGSR 173.19 1.03E-06 1433510000 258560 245120 272300 248410 295880 295180 319260 295510 282740 277720 TRUE FALSE 248455.1893 238129.4176 321510.6673 261230.4699 305397.2489 301148.7418 323167.1994 289407.6152 250644.5405 258909.777 0.95962073 0.919738993 1.241786506 1.008963326 1.179550855 1.163141637 1.248184611 1.117793304 0.96807677 1 17.98208992 4.258054302 24.99976839 1.126696905 0.9396797 0.356437725 0.093848216 234.7136932 301004.5131 0.021931646 0.05987352 18115.66587 -4.258054302 -0.187017205 VLVDSLVEDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLVDSLVEDDR 11 0 Q92621;U3KPX2 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ;;; 169.41 3.94E-05 209145000 132150 145091 135470 175902 157832 157807 171032 188560 172651 199109 FALSE TRUE 126985.4319 140953.1467 159952.4425 184980.3233 162908.8096 160997.9657 173125.1408 184666.1701 153052.3823 185623.1701 0.684103347 0.759351037 0.861705155 0.996536818 0.877631869 0.867337658 0.932669885 0.994844394 0.824532747 1 17.50201728 4.258068322 2.269150165 0.927765679 0.692978226 0.677449347 0.05692202 0.176814502 1.74286213 0.014738298 0.055813811 18116.25071 -4.258068322 -0.234787454 ELEEYRR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEEYRR 7 1 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;H0YG19 P35611 ADD1 Alpha-adducin 0 ; 112.17 0.010285 550390000 324890 337540 319340 407770 365220 363050 355160 443470 367810 394450 FALSE TRUE 312192.9396 327913.6897 377051.8417 428815.0586 376967.633 370391.1197 359506.5543 434312.1895 326057.7508 367733.5502 0.848965071 0.891715454 1.025339792 1.166102626 1.025110798 1.007226889 0.977627835 1.181051306 0.886668488 1 18.48830128 4.258318442 3.81521534 1.048727466 0.860380231 0.383678269 0.082175576 0.19089266 5.925945671 0.020141162 0.057384766 18126.68725 -4.258318442 -0.188347235 ASPSS(ph)PGRQDS(ph)DEDDGPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.012)PS(0.434)S(0.554)PGRQDS(1)DEDDGPQR;AS(0.061)PS(0.427)S(0.512)PGRQDS(1)DEDDGPQR 131.32 9.00E-06 301560000 257360 269010 314210 377060 315160 337110 359610 376490 397750 437770 TRUE FALSE 247302.0867 261338.0982 370994.7366 396520.1118 325297.4076 343926.5952 364011.0148 368715.3499 352599.0875 408119.448 0.605955163 0.640347083 0.909034692 0.971578575 0.797064215 0.842710625 0.891922736 0.903449595 0.863960513 1 18.63863193 4.258487337 6.986297328 0.891742959 0.620099679 0.794010217 0.055844456 0.064420409 12.63391592 0.013451344 0.03525403 18133.73801 -4.258487337 -0.27164328 LPS(ph)PTSPFSSLSQDQAATSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPSPTSPFSSLSQDQAATSK 20 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 LPS(0.969)PT(0.026)S(0.005)PFSSLSQDQAATSK;LPS(0.717)PT(0.039)S(0.244)PFSSLSQDQAATSK 123.41 3.01E-05 96020000 78392 81558 91232 107187 93474 94657 107988 119406 106427 127977 TRUE FALSE 75328.35397 79232.04569 107719.6518 112718.9339 96480.6761 96571.02939 109309.5894 116940.2244 94345.85314 119309.0038 0.631371913 0.664091084 0.902862721 0.944764689 0.808662155 0.80941946 0.916188938 0.980145845 0.790768929 1 16.8643434 4.258554575 6.05967142 0.895198403 0.643352055 0.672880028 0.068764342 0.090177413 10.97294917 0.0172633 0.04546506 18136.54572 -4.258554575 -0.251846349 YEPQS(ph)PGYEPR ddPTM_BT-474_Pertuzumab_2h_R1 4 YEPQSPGYEPR 11 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 YEPQS(1)PGYEPR;YEPQS(1)PGYEPR;YEPQS(1)PGYEPR;YEPQS(1)PGYEPR 209.22 1.77E-08 2497490000 1416810 1284810 1283860 1334220 1372940 1396990 1310990 1540590 1440890 1368900 TRUE FALSE 1361439.499 1248168.477 1515882.061 1403079.254 1417101.862 1425238.095 1327034.288 1508776.278 1277326.208 1276183.184 1.066805703 0.978048052 1.187824821 1.099434056 1.110421983 1.116797426 1.039846242 1.182256824 1.000895658 1 20.283404 4.25879259 24.99993855 1.101816556 1.022426903 0.142160789 0.065194449 363.9546949 449718.2734 0.014482766 0.039564828 18146.48817 -4.25879259 -0.079389653 TDQAQKAEGAGDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TDQAQKAEGAGDAK 14 1 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ; 103.04 0.0010386 168982000 367050 333660 80424 64026 138637 209400 88289 116479 119701 63318 FALSE TRUE 352705.2802 324144.3435 94958.40582 67330.38953 143096.385 213634.2115 89369.50719 114073.6679 106113.0443 59029.41546 5.97507662 5.491234175 1.608662479 1.140624365 2.424153854 3.619114467 1.513982588 1.932488524 1.797629935 1 15.84914644 4.258811265 7.657344922 1.945148133 5.764469009 0.825892395 0.707329011 0.06482215 16.71636412 0.178148469 0.467312589 18147.26852 -4.258811265 3.819320875 S(ph)KS(ph)EMLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSEMLSR 8 1 E9PR23;E9PRA4;E9PNU3;E9PQC8;Q71H61 E9PR23 ILDR2 Immunoglobulin-like domain-containing receptor 2 2 S(1)KS(1)EMLSR 104.39 0.0018292 0 9004.5 9425.6 11278 15009 10189 13948 12823 11734 11786 12870 TRUE FALSE 8652.594185 9156.791117 13316.18548 15783.61629 10516.73844 14230.03812 12979.93171 11491.6888 10448.10269 11998.30344 0.721151472 0.763173824 1.109839033 1.315487341 0.876518792 1.186004187 1.081813923 0.957776144 0.870798338 1 13.5505428 4.258869246 11.18225674 1.052995956 0.741708173 0.474257313 0.129518956 0.422210444 225.3315529 0.031914146 0.084864731 18149.69145 -4.258869246 -0.311287784 LDHKFDLMYAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDHKFDLMYAKR 12 2 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 141.37 3.63E-05 618790000 1648300 1460200 561590 622690 698100 688250 660210 378530 553130 554930 FALSE TRUE 1583882.614 1418556.526 663081.8055 654827.1055 720555.0205 702166.8866 668289.8475 370713.2232 490341.0013 517344.0968 3.061565066 2.741998091 1.281703627 1.265747709 1.392796448 1.357253114 1.291770509 0.71656993 0.947804381 1 18.98076464 4.258916254 3.508860716 1.135274769 3.008536853 0.926437595 0.197959195 0.060350093 1.535196766 0.059390641 0.174368005 18151.65607 -4.258916254 1.873262084 up T(ph)PRTPQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 T(0.512)PRT(0.488)PQLK 83.397 0.029408 1282400000 1466300 1452900 763330 727560 1175700 1429700 1051100 1142200 1157100 985930 TRUE FALSE 1408995.375 1411464.715 901280.7112 765109.4588 1213517.458 1458609.514 1063963.676 1118613.171 1025750.859 919152.0829 1.532929535 1.535616076 0.980556676 0.832407904 1.32025753 1.586907695 1.157549111 1.217005533 1.115975123 1 19.80994406 4.259239142 24.40476894 1.171679665 1.534273391 0.377799537 0.19518138 211.5370741 249649.9593 0.050851183 0.13888904 18165.15643 -4.259239142 0.362593727 SGGGPGPSGSET(ph)PPPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGGPGPSGSETPPPPR 17 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 SGGGPGPSGSET(1)PPPPR;SGGGPGPSGSET(1)PPPPR 240.61 2.80E-19 611130000 610940 620060 586730 718290 646400 638150 679030 743380 707500 769310 TRUE FALSE 587063.7894 602376.4959 692765.1627 755361.033 667192.043 651053.8302 687340.1723 728028.9432 627187.5661 717203.9485 0.818545116 0.839895677 0.965924915 1.053202558 0.930268224 0.907766656 0.958360831 1.015093328 0.87448984 1 19.45202391 4.259372 5.432378179 0.966346854 0.825854944 0.540822108 0.049391318 0.121750122 10.24402874 0.012263116 0.032631547 18170.71429 -4.259372 -0.140491911 FNEEHIPDSPFVVPVAS(ph)PSGDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 1 FNEEHIPDSPFVVPVAS(0.932)PS(0.068)GDAR;FNEEHIPDSPFVVPVAS(0.943)PS(0.057)GDAR;FNEEHIPDSPFVVPVAS(0.914)PS(0.086)GDAR;FNEEHIPDSPFVVPVAS(0.966)PS(0.034)GDAR 135.91 8.65E-06 792980000 369015 375309 378235 425736 395632 453887 413471 418835 516351 479983 TRUE FALSE 354593.4858 364605.5548 446590.4783 447708.286 408357.8626 463064.9061 418531.1818 410185.9109 457736.9992 447473.3239 0.792434916 0.814809588 0.998027043 1.000525086 0.912585937 1.034843602 0.935320967 0.916671205 1.022936955 1 18.77144215 4.259496013 10.26226174 0.970180702 0.803231969 0.736236866 0.041466753 0.177820818 82.26115695 0.010132055 0.026879761 18175.90371 -4.259496013 -0.166948734 GPS(ph)TPNVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSTPNVK 8 0 Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 GPS(0.5)T(0.5)PNVK;GPS(0.5)T(0.5)PNVK 110.38 0.0036049 686150000 2058100 2012730 1941870 2070800 1931500 2272100 2132100 2237000 2287000 2386700 TRUE FALSE 1977667.177 1955328.911 2292809.106 2177674.236 1993628.452 2318043.419 2158193.278 2190805.168 2027389.348 2225046.683 0.888820532 0.878781073 1.030454382 0.978709459 0.895993988 1.041795409 0.969954156 0.984610878 0.911167106 1 21.08540417 4.259614614 24.99340554 0.975700447 0.883800702 0.424750657 0.04318165 215.7655431 256132.9472 0.01005084 0.027464455 18180.86801 -4.259614614 -0.091899745 GPPS(ph)PPAPVMHS(ph)PSRK ddPTM_BT-474_Pertuzumab_2h_R1 8 GPPSPPAPVMHSPSRK 16 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.945)PS(0.055)RK;GPPS(1)PPAPVMHS(0.972)PS(0.028)RK;GPPS(1)PPAPVMHS(0.859)PS(0.141)RK;GPPS(1)PPAPVMHS(0.96)PS(0.04)RK;GPPS(1)PPAPVMHS(0.96)PS(0.04)RK;GPPS(1)PPAPVMHS(0.5)PS(0.5)RK;GPPS(1)PPAPVMHS(0.993)PS(0.007)RK;GPPS(1)PPAPVMHS(0.928)PS(0.072)RK 119.27 0.0002111 4937650000 2587560 2609380 1908550 2227030 2205180 2437360 2265960 2478350 2690500 2565720 TRUE FALSE 2486435.295 2534963.037 2253467.44 2341967.285 2276111.617 2486645.089 2293691.496 2427171.206 2385085.719 2391941.499 1.039505061 1.059793075 0.942108091 0.979107259 0.951574952 1.03959277 0.95892458 1.014728499 0.997133801 1 21.18975067 4.259665456 24.99988471 0.986499761 1.049649118 0.448140174 0.028499612 209.9840762 248733.6652 0.006691628 0.018285522 18182.99652 -4.259665456 0.063149358 MFVLDEADEMLSR ddPTM_BT-474_Pertuzumab_2h_R1 11 MFVLDEADEMLSR 13 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;Q14240;Q14240-2;E7EQG2;J3KTN0 P60842;Q14240;J3KTN0 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;;;;;;;;; 295.32 2.67E-40 3479789000 1959840 2118414 1817758 2285705 2319102 2331111 2270860 2268335 2407818 2607170 FALSE TRUE 1883247.286 2057998.907 2146267.306 2403670.509 2393698.022 2378247.662 2298651.464 2221493.09 2134492.595 2430584.054 0.774812656 0.846709623 0.883025338 0.988927129 0.984824211 0.978467565 0.9457198 0.913975012 0.878180942 1 21.2128716 4.259968027 1.842465116 0.950797643 0.781956103 0.711722684 0.037596802 0.234416187 1.436180333 0.010917998 0.049756626 18195.66897 -4.259968027 -0.168841539 YPNKYESIIATLCENLDSLDEPDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 YPNKYESIIATLCENLDSLDEPDAR 25 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01 P63010 AP2B1 AP-2 complex subunit beta 0 154.69 6.80E-08 146930000 55442 59569 67692 80574 65813 91038 73453 80448 94555 105950 FALSE TRUE 53275.26535 57870.15044 79925.4502 84732.4338 67929.93491 92878.85074 74351.93979 78786.72069 83821.51281 98773.91213 0.539365752 0.585884969 0.809175707 0.857842238 0.687731542 0.940317628 0.752748759 0.797647061 0.848619954 1 16.59184243 4.260194991 4.148506294 0.824434953 0.55077049 0.629545796 0.084081067 0.118510686 4.530266772 0.019287113 0.053821134 18205.18058 -4.260194991 -0.273664463 EEPLDPEEAEGPLSLVTT(ph)ANHSPDFDHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEPLDPEEAEGPLSLVTTANHSPDFDHDR 29 0 A0A3B3IUB6;Q9H334-8;C9J0F0;Q9H334-3;Q9H334-7;Q9H334-6;Q9H334;Q9H334-4;A0A3B3IRS5;A0A3B3IST0;H0Y882;A0A0B4J2F3;A0A3B3IRW5;A0A3B3IT66 A0A3B3IUB6 FOXP1 Forkhead box protein P1 1 EEPLDPEEAEGPLS(0.002)LVT(0.11)T(0.444)ANHS(0.444)PDFDHDR;EEPLDPEEAEGPLS(0.005)LVT(0.096)T(0.449)ANHS(0.449)PDFDHDR 129.59 2.90E-05 89419000 50807 51842 61827 76511 64057 60036 78620 33587 83873 88562 TRUE FALSE 48821.40627 50363.51692 73000.51423 80459.74188 66117.45158 61249.96905 79582.17508 32893.41671 74352.08866 82563.61686 0.591318648 0.609996495 0.88417292 0.974518135 0.800806143 0.741851815 0.963889157 0.398400869 0.900543018 1 16.33321855 4.26020183 21.03906879 0.798385131 0.600655541 0.215094021 0.167398471 69.67084846 67723.73026 0.042815099 0.116762583 18205.46725 -4.26020183 -0.19772959 (ac)ADEELEALRR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADEELEALRR 10 1 O14737;O14737-2;Q3HM38;X6R2P6;K7ESJ4 O14737 PDCD5 Programmed cell death protein 5 0 ; 95.741 4.74E-06 1807970000 87806 102414 52208 90527 70425 59154 65128 95206 102143 75191 FALSE TRUE 84374.44445 99493.25299 61643.14696 95199.10932 72690.28408 60350.13441 65925.05595 93239.96283 90548.15486 70098.2466 1.203659842 1.419340109 0.879382152 1.358081178 1.036977209 0.860936433 0.940466547 1.330132598 1.291732094 1 16.09709074 4.260248536 24.99997609 1.102838285 1.311499935 0.194384509 0.180410316 426.9089641 492095.5189 0.045253213 0.123698267 18207.42528 -4.260248536 0.208661649 ATMAQNENVVVQPVVAENIPVIPLS(ph)DSPPPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATMAQNENVVVQPVVAENIPVIPLSDSPPPSR 32 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ATMAQNENVVVQPVVAENIPVIPLS(0.477)DS(0.417)PPPS(0.106)R;ATMAQNENVVVQPVVAENIPVIPLS(0.487)DS(0.406)PPPS(0.107)R 106.49 3.31E-06 169517000 250473 264982 221403 285613 274999 296032 268022 261472 281209 304948 TRUE FALSE 240684.2382 257424.9728 261415.4472 300353.5212 283844.5926 302017.9699 271302.1334 256072.5118 249287.3332 284293.6003 0.846604489 0.905489862 0.919526317 1.056490617 0.99842062 1.062345299 0.95430264 0.900732593 0.876865793 1 18.1170221 4.260489492 2.277602853 0.972661349 0.859593114 0.342667103 0.057419909 0.419233382 4.162805748 0.016855893 0.063919629 18217.52994 -4.260489492 -0.113068235 LQEDTDKANK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQEDTDKANK 10 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 96.64 0.0056991 0 226380 235130 122130 150270 162320 167590 182460 208360 214830 181470 FALSE TRUE 217532.8193 228424.3226 144201.6078 158025.4527 167541.1702 170978.7846 184693.0001 204057.2932 190443.399 169178.8753 1.285815495 1.35019412 0.852361783 0.934073196 0.990319684 1.01063909 1.091702494 1.206162961 1.125692547 1 17.36818991 4.260703694 24.99918815 1.040694932 1.318005077 0.595782407 0.095505553 192.3165372 217118.5769 0.027250326 0.0744997 18226.51738 -4.260703694 0.277310145 IPS(ph)PLQPEMQGTPDDEPSEPEPSPSTLIYR ddPTM_BT-474_Pertuzumab_2h_R1 1 IPSPLQPEMQGTPDDEPSEPEPSPSTLIYR 30 0 Q96GY3;K7EMY4 Q96GY3 LIN37 Protein lin-37 homolog 1 IPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR 104.29 0.00022401 72695000 21058 21535 21079 26212 21914 23603 24536 29324 23446 22718 TRUE FALSE 20235.03008 20920.84288 24888.4442 27564.80446 22618.88371 24080.26883 24836.27891 28718.44915 20784.50837 21179.28962 0.955415901 0.987797195 1.175131208 1.301498065 1.067971783 1.136972451 1.172668175 1.35596848 0.981360033 1 14.37036658 4.260883454 5.431512454 1.174740632 0.966510655 0.258352695 0.113987229 0.187470504 15.57900997 0.027773696 0.074135708 18234.06312 -4.260883454 -0.208229977 ESFDGSVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESFDGSVR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 194.44 0.00038466 4096360000 4298690 4396920 4499790 5565280 4892860 4396330 5304840 5394600 5613260 5990260 FALSE TRUE 4130692.442 4271524.147 5313002.15 5852504.768 5050243.285 4485226.805 5369762.219 5283199.625 4976066.258 5584534.355 0.739666404 0.764884568 0.951377825 1.047984379 0.904326657 0.803151439 0.961541622 0.946041208 0.891044077 1 22.41300556 4.260885307 7.198665586 0.936060662 0.750297234 0.58901837 0.062114452 0.116572011 23.76302311 0.015792567 0.041637018 18234.14091 -4.260885307 -0.185763428 PAELWLT(ph)S(ph)YGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 PAELWLTSYGVR 12 0 Q8WU39-3 Q8WU39-3 MZB1 Marginal zone B- and B1-cell-specific protein 2 PAELWLT(0.999)S(0.999)Y(0.002)GVR 69.825 0.096757 0 38355 37521 41917 41650 43948 43201 40401 45473 50535 51913 TRUE FALSE 36856.0442 36450.93782 49492.33434 43799.56149 45361.62733 44074.55382 40895.43952 44533.96666 44798.47866 48396.88627 0.761537509 0.753167004 1.022634681 0.90500784 0.937284004 0.910689865 0.845001459 0.920182476 0.925647952 1 15.56262661 4.260887444 24.99965846 0.924009493 0.757352048 0.684523442 0.04744557 131.9257853 147716.5691 0.011250682 0.03076054 18234.23064 -4.260887444 -0.166657446 KEPAITSQNS(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KEPAITSQNSPEAR 14 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KEPAITSQNS(1)PEAR;KEPAIT(0.004)S(0.044)QNS(0.952)PEAR;KEPAITSQNS(1)PEAR;KEPAITSQNS(1)PEAR 228.94 9.00E-13 4267440000 1591940 1651510 1653220 1949750 1781610 1934210 1875350 2135710 2187390 2173080 TRUE FALSE 1529725.225 1604410.552 1951993.63 2050376.831 1838917.104 1973321.051 1898301.094 2091606.842 1939086.657 2025895.356 0.755086002 0.791951345 0.963521449 1.012084274 0.907705869 0.974048855 0.937018335 1.032435775 0.957150453 1 20.95012823 4.260899849 4.17048036 0.975454803 0.76436268 0.845788715 0.034242353 0.067954684 2.629577503 0.008554259 0.023866101 18234.75148 -4.260899849 -0.211092123 QNAVLQAAQDDLGHLR ddPTM_BT-474_Pertuzumab_2h_R1 3 QNAVLQAAQDDLGHLR 16 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;; 165.75 6.92E-09 354993000 330306 327007 328164 374281 327203 373111 348177 340609 369925 462006 FALSE TRUE 317397.2763 317681.0805 387470.5348 393597.6873 337727.7817 380655.5601 352438.0943 333575.3051 327932.6649 430713.9221 0.736909721 0.737568637 0.899600674 0.913826248 0.784111598 0.883778166 0.818264923 0.774470682 0.761370014 1 18.71637043 4.26107152 24.25786901 0.841718559 0.737238976 0.29169162 0.070865299 226.4849914 244055.3456 0.017043428 0.046589577 18241.96086 -4.26107152 -0.104479583 RHS(ph)WGPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RHSWGPGK 8 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 RHS(1)WGPGK;RHS(1)WGPGK 120.86 0.00089316 726900000 899260 859660 629820 703010 733780 686790 667900 587590 840100 736100 TRUE FALSE 864115.925 835143.3385 743642.4843 739292.4303 757382.7001 700677.3644 676073.96 575456.0612 744735.37 686243.2914 1.259197628 1.21697851 1.083642629 1.07730369 1.103664997 1.021033463 0.985181157 0.838559835 1.085235192 1 19.38836061 4.261181875 0.482928321 0.948959433 1.391053697 0.659550736 0.065748305 1.772499028 0.44623264 0.04835077 0.42567697 18246.5968 -4.261181875 0.442094264 KELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 34 2 Q01105-2 Q01105-2 SET Protein SET 1 KELNSNHDGADET(0.436)S(0.564)EKEQQEAIEHIDEVQNEIDR;KELNS(0.312)NHDGADET(0.312)S(0.375)EKEQQEAIEHIDEVQNEIDR;KELNSNHDGADET(0.449)S(0.551)EKEQQEAIEHIDEVQNEIDR;KELNSNHDGADET(0.181)S(0.819)EKEQQEAIEHIDEVQNEIDR 243.68 2.00E-47 3107410000 456138 410679 573303 500556 570470 488036 543251 592259 656401 652256 TRUE FALSE 438311.6227 398966.837 676911.6052 526389.7551 588819.6856 497904.4223 549899.4682 580028.6447 581889.1103 608078.1202 0.720814659 0.656111154 1.113198424 0.865661397 0.968329013 0.81881654 0.904323721 0.953871921 0.956931504 1 19.21389715 4.261212524 24.9999138 0.937912347 0.688462667 0.644962206 0.076646764 137.7022024 151973.1998 0.017646756 0.048254372 18247.88452 -4.261212524 -0.24944968 GFGFVEFEDPR ddPTM_BT-474_Pertuzumab_2h_R1 5 GFGFVEFEDPR 11 0 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;;; 123.35 0.00086469 2424160000 1297410 1397640 1379160 1772680 1638760 1565960 1755470 1788060 1633670 1828760 FALSE TRUE 1246705.783 1357780.676 1628404.891 1864168.227 1691472.204 1597624.784 1776953.967 1751135.936 1448222.631 1704896.456 0.731250146 0.796400667 0.955134187 1.093420202 0.99212606 0.937080242 1.042265036 1.027121577 0.849449024 1 20.70125269 4.261289254 3.145226631 0.997347314 0.744820657 0.682906844 0.061808556 0.1276796 2.539605808 0.015507025 0.047892377 18251.10879 -4.261289254 -0.252526657 CRELCEK ddPTM_BT-474_Pertuzumab_2h_R1 1 CRELCEK 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 81.642 0.024302 171210000 172930 179980 107110 131540 124160 182720 144240 145960 164030 154690 FALSE TRUE 166171.7044 174847.1466 126467.1596 138328.7952 128153.7192 186414.7236 146005.2523 142945.875 145410.0021 144212.7085 1.152268105 1.212425371 0.876948786 0.959199758 0.88864373 1.292637282 1.01242986 0.991215521 1.008302275 1 17.13783878 4.261315834 24.98429072 1.007509848 1.182346886 0.303478428 0.108149482 294.6750148 323535.358 0.026682372 0.072964212 18252.22584 -4.261315834 0.174837038 KPTDGASSSNCVTDISHLVR ddPTM_BT-474_Pertuzumab_2h_R1 4 KPTDGASSSNCVTDISHLVR 20 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;; 209.01 3.32E-22 6971400000 4098140 4133770 3685710 4415510 4324100 4473590 4290090 4215660 4528290 4911900 FALSE TRUE 3937980.158 4015878.927 4351799.785 4643395 4463188.604 4564049.055 4342593.405 4128605.148 4014257.503 4579212.638 0.859968835 0.876980224 0.950338001 1.014016026 0.974662886 0.996688605 0.948327529 0.901597168 0.876626141 1 22.12666813 4.261328308 4.554225758 0.955286464 0.865092395 0.434687931 0.040862826 0.198130708 9.709230972 0.011339033 0.031056036 18252.7501 -4.261328308 -0.090194069 S(ph)TSTPNVHMVSTTLPVDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.33)T(0.33)S(0.33)T(0.011)PNVHMVSTTLPVDSR;S(0.354)T(0.354)S(0.282)T(0.01)PNVHMVSTTLPVDSR;S(0.342)T(0.342)S(0.296)T(0.02)PNVHMVSTTLPVDSR;S(0.352)T(0.352)S(0.285)T(0.011)PNVHMVSTTLPVDSR 153.87 2.67E-08 468060000 460177 455745 347947 398536 383489 382892 386937 404969 375592 371642 TRUE FALSE 442192.7741 442747.5988 410828.7629 419104.4907 395824.272 390634.3386 391672.4508 396606.2486 332956.3708 346470.3563 1.27627881 1.277880173 1.185754439 1.209640257 1.14244773 1.127468285 1.130464536 1.14470471 0.960995262 1 18.4023724 4.261379893 0.181479503 0.95082757 1.525195205 0.811620098 0.042555811 6.030557323 0.23712174 0.128247678 0.816894194 18254.91827 -4.261379893 0.574367635 EHKLDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 EHKLDGK 7 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;; 80.438 0.017972 1150660000 2318250 2207390 1344930 1242250 1620030 2003220 1689150 1280390 2173120 1709240 FALSE TRUE 2227650.227 2144437.398 1587988.769 1306362.671 1672139.736 2043726.481 1709822.323 1253949.499 1926436.528 1593471.652 1.397985476 1.345764385 0.996559158 0.81982172 1.049368989 1.282562183 1.073017095 0.786929279 1.208955632 1 20.60374192 4.261424252 6.179715566 1.012286753 1.378215409 0.478094892 0.143534335 0.13716333 17.15301639 0.037421838 0.099107414 18256.78293 -4.261424252 0.365928656 VSKPSQLQAHTPASQQTPPLPPYAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSKPSQLQAHTPASQQTPPLPPYASPR 27 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 VSKPSQLQAHTPASQQT(0.001)PPLPPY(0.037)AS(0.962)PR 96.019 0.0028131 754100000 184860 177180 189610 217690 196550 183530 187330 197900 231170 237880 TRUE FALSE 177635.4668 172126.9999 223876.7449 228925.007 202872.2093 187241.1023 189622.6006 193813.2958 204928.5507 221768.1757 0.800996204 0.776157351 1.009507988 1.032271679 0.914794057 0.844310063 0.855048746 0.873945485 0.92406654 1 17.75869282 4.261494288 24.99313741 0.920688215 0.788576635 0.447313527 0.06269919 249.1939075 271566.9954 0.017021408 0.04654771 18259.72732 -4.261494288 -0.132111581 GQRPDFTDAIILR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQRPDFTDAIILR 13 1 A8MZF9;P55039 A8MZF9 DRG2 Developmentally-regulated GTP-binding protein 2 0 84.759 0.0087522 124990000 513200 535050 322510 407760 436500 512140 429450 421230 470110 450750 FALSE TRUE 493143.5766 519790.8979 380794.7312 428804.5425 450540.4189 522495.8217 434705.7376 412531.4533 416745.0837 420220.301 1.173535823 1.236948564 0.906178807 1.020427955 1.072152911 1.243385482 1.034471054 0.981702817 0.991730011 1 18.68078634 4.261778346 24.98048945 1.036402547 1.205242331 0.409067316 0.083462957 245.5289031 264165.5006 0.021642157 0.059190612 18271.67432 -4.261778346 0.168839784 CAAPRPPSS(ph)SPEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 CAAPRPPSSSPEQR 14 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 CAAPRPPS(0.141)S(0.43)S(0.43)PEQR;CAAPRPPS(0.021)S(0.651)S(0.328)PEQR;CAAPRPPS(0.113)S(0.444)S(0.444)PEQR;CAAPRPPS(0.056)S(0.472)S(0.472)PEQR 154.39 3.71E-06 3056892000 1410748 1579660 1399080 1844995 1704334 1794164 1949605 1779299 1954043 2026907 TRUE FALSE 1355614.408 1534609.643 1651924.878 1940215.413 1759155.451 1830443.225 1973464.849 1742555.854 1732228.231 1889622.784 0.717399483 0.812124863 0.874208807 1.026773931 0.930955885 0.968681814 1.044369737 0.922171276 0.916705835 1 20.84966683 4.261888396 1.735489698 0.969340839 0.720644585 0.790144881 0.043588575 0.18723319 0.993382368 0.011824814 0.057267604 18276.30494 -4.261888396 -0.248696254 NMPGLSAATLASLGGTS(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 3 NMPGLSAATLASLGGTSSR 19 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NMPGLSAATLASLGGT(0.144)S(0.428)S(0.428)R;NMPGLSAATLASLGGT(0.133)S(0.433)S(0.433)R;NMPGLSAATLASLGGT(0.12)S(0.44)S(0.44)R 222.24 2.60E-19 2257160000 2451830 2012110 1404810 1172150 1184040 1121080 810110 1666480 1255500 1228210 TRUE FALSE 2356009.773 1954726.593 1658690.417 1232644.802 1222125.722 1143749.006 820024.3685 1632066.606 1112980.903 1145022.243 2.057610486 1.707151634 1.448609778 1.076524766 1.067337975 0.998888024 0.716164576 1.425357993 0.972016841 1 20.12694419 4.26189667 1.28632477 1.046317832 2.126893663 0.814039488 0.166043559 0.286146191 0.71851382 0.050813719 0.329092672 18276.65314 -4.26189667 1.080575831 up SYS(ph)LDLDGQHFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSLDLDGQHFR 12 0 Q8TDW5;Q8TDW5-2 Q8TDW5 SYTL5 Synaptotagmin-like protein 5 1 S(0.131)YS(0.869)LDLDGQHFR;S(0.114)YS(0.886)LDLDGQHFR 131.96 0.00012205 227658000 406230 402660 159684 225884 374030 198376 187070 411090 220240 197802 TRUE FALSE 390354.0825 391176.531 188542.451 237541.9003 386061.0146 202387.2986 189359.4186 402600.8478 195239.2785 184404.6944 2.11683376 2.121293779 1.022438456 1.288155386 2.093553073 1.097517063 1.026868753 2.183246198 1.058754384 1 17.49251586 4.262145039 24.38507795 1.42630818 2.119065096 0.336258123 0.422476977 215.6711088 222987.5155 0.102836056 0.281232188 18287.10838 -4.262145039 0.692756916 GLS(ph)EDTTEETLKESFDGSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLSEDTTEETLKESFDGSVR 20 1 P19338;H7BY16 P19338 NCL Nucleolin 1 GLS(0.891)EDT(0.054)T(0.054)EETLKESFDGSVR;GLS(0.99)EDT(0.002)T(0.008)EETLKESFDGSVR 127.16 1.33E-05 65838000 211860 184792 137967 113699 140097 143639 127456 177540 136521 123995 TRUE FALSE 203580.277 179521.9131 162900.706 119567.019 144603.3472 146543.479 129015.8447 173873.737 121023.7084 115596.7082 1.76112521 1.553001949 1.409215786 1.034346227 1.250929628 1.267713253 1.116085801 1.504140902 1.046947706 1 16.81874079 4.262184837 2.021952081 1.216418647 1.736322351 0.629398927 0.148096526 0.242891798 1.845300968 0.039069184 0.164282109 18288.78426 -4.262184837 0.519903704 GEDLTEEEDGGIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 GEDLTEEEDGGIIR 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 335.81 3.08E-68 2471920000 1179350 1264400 1538780 1925370 1530520 1469030 1800690 1938580 2002080 2291300 FALSE TRUE 1133259.698 1228340.55 1816871.776 2024738.576 1579750.566 1498734.793 1822727.383 1898547.646 1774812.272 2136108.21 0.530525417 0.575036669 0.850552312 0.9478633 0.739546133 0.701619322 0.853293562 0.888788141 0.83086253 1 21.0265533 4.26219441 5.572306247 0.844788577 0.545867286 0.674000876 0.083130111 0.097639867 8.696354013 0.020890848 0.055782398 18289.18738 -4.26219441 -0.298921291 HEKEDGAISTIVLR ddPTM_BT-474_Pertuzumab_2h_R1 4 HEKEDGAISTIVLR 14 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 200.44 1.16E-08 4155140000 4574640 4449730 4123600 4391500 4448790 4954650 4890780 3447640 6174370 5787070 FALSE TRUE 4395858.011 4322828.057 4868826.249 4618145.841 4591889.371 5054836.418 4950634.829 3376445.029 5473481.403 5395106.594 0.814786128 0.801249796 0.90245228 0.855987877 0.851121158 0.936929851 0.917615758 0.625834721 1.014527018 1 22.36322003 4.262290552 24.5982586 0.863281849 0.808017893 0.047046209 0.103995828 748.8401346 776224.662 0.025897829 0.070836539 18293.23664 -4.262290552 -0.055263956 PVYAQVGQPDVDLPVS(ph)PSDGVLPNSTHEDGILRPSMK ddPTM_BT-474_Pertuzumab_2h_R1 3 PVYAQVGQPDVDLPVSPSDGVLPNSTHEDGILRPSMK 37 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 PVYAQVGQPDVDLPVS(0.999)PS(0.001)DGVLPNSTHEDGILRPSMK;PVYAQVGQPDVDLPVS(0.962)PS(0.038)DGVLPNSTHEDGILRPSMK;PVYAQVGQPDVDLPVS(0.99)PS(0.01)DGVLPNSTHEDGILRPSMK 193.97 6.12E-24 435474000 95315 94430 117556 126089 124743 114974 120700 110954 120637 128366 TRUE FALSE 91589.98442 91736.94886 138800.9842 132596.4684 128755.4719 117298.8531 122177.1627 108662.7611 106942.7935 119671.6565 0.765344001 0.766572065 1.159848441 1.108002281 1.075906156 0.980172386 1.020936505 0.908007496 0.893635107 1 16.86872197 4.262382374 24.9157969 1.013500968 0.765957659 0.624756103 0.078159016 159.6290332 166957.1139 0.021420458 0.05859148 18297.10475 -4.262382374 -0.247543309 SIYDDISS(ph)PGLGSTPLTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 SIYDDIS(0.005)S(0.992)PGLGS(0.002)T(0.001)PLTSR 139.88 3.69E-07 0 70778 78421 87714 101970 101440 117940 124270 98641 103520 123570 TRUE FALSE 68011.91751 76184.50986 103565.871 107232.6839 104702.9097 120324.8276 125790.8534 96604.02888 91768.84359 115200.4938 0.590378698 0.661321035 0.899005443 0.93083528 0.908875529 1.044481873 1.091929811 0.838573045 0.79660113 1 16.81378738 4.262491726 2.736149929 0.942858897 0.595765185 0.698011726 0.083409129 0.156070488 2.300504742 0.023090082 0.077141634 18301.71238 -4.262491726 -0.347093713 YIHILGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIHILGR 7 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 177.91 0.00072346 1739340000 1474570 1729390 1517740 2042260 2076100 1892930 2136600 2057490 2169400 2210300 FALSE TRUE 1416942.174 1680069.49 1792029.38 2147661.283 2142879.642 1931206.342 2162748.35 2015002.112 1923138.807 2060594.412 0.687637589 0.81533245 0.869666233 1.042253279 1.039932764 0.937208375 1.049574985 0.9778742 0.933293226 1 20.97462914 4.262593139 1.613470119 0.997045593 0.691578885 0.83717553 0.044476226 0.173673479 0.771060369 0.012156038 0.06328876 18305.98654 -4.262593139 -0.305466708 ADITGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADITGR 6 0 O95994;B5MC07;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 137.83 0.029234 2356700000 742740 802030 692750 934710 779100 855630 914520 903590 866050 948100 FALSE TRUE 713712.8997 779156.8897 817945.3351 982950.4951 804160.4591 872931.4248 925712.1693 884930.5507 767739.6348 883884.3425 0.807473179 0.881514529 0.925398602 1.112080447 0.909802811 0.9876082 1.047322738 1.001183648 0.868597392 1 19.75349808 4.262617331 2.3674866 0.991174691 0.822309057 0.447991609 0.064753622 0.261789579 2.827229451 0.016350252 0.060390869 18307.00628 -4.262617331 -0.168865634 APKPDGPGGGPGGSHMGGNYGDDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 APKPDGPGGGPGGSHMGGNYGDDRR 25 2 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ; 236.26 1.18E-38 335050000 341410 335890 337770 351120 343310 349800 372670 375990 427940 409220 FALSE TRUE 328067.3198 326310.7461 398812.5527 369241.3453 354352.8779 356873.1957 377230.8469 368225.6751 379362.0453 381503.1649 0.859933416 0.855329067 1.045371544 0.967859193 0.92883339 0.935439673 0.988801356 0.965196908 0.994387675 1 18.5413355 4.262641406 24.99932764 0.973533189 0.857631079 0.69593985 0.031765942 128.5575005 133458.8249 0.007810524 0.021366372 18308.02116 -4.262641406 -0.11590211 VQHQDALQISDVVMASLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQHQDALQISDVVMASLLR 19 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 226.32 1.53E-19 998750000 361160 373570 341978 392525 410683 396800 432030 408570 469490 462370 FALSE TRUE 347045.4679 362916.1494 403781.0319 412783.2623 423892.9917 404823.5679 437317.3124 400132.8867 416195.4635 431053.2681 0.805110397 0.841928774 0.936731169 0.957615434 0.983388883 0.939149748 1.014531949 0.928267842 0.965531396 1 18.71750664 4.262734404 2.083573749 0.966761141 0.802976317 0.849275178 0.024518688 0.116911884 0.950831209 0.0061381 0.025166359 18311.94198 -4.262734404 -0.163784824 DTEEPLPVKESDQTLAALLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 DTEEPLPVKESDQTLAALLSPK 22 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 DTEEPLPVKESDQTLAALLS(1)PK;DTEEPLPVKESDQTLAALLS(1)PK 194.73 1.56E-18 188882000 448980 412610 162255 111377 225330 327720 166059 219320 236300 141618 TRUE FALSE 431433.3652 400842.7668 191578.0878 117125.1803 232577.9441 334346.7229 168091.2797 214790.9654 209476.2147 132026.0867 3.267788783 3.036087615 1.451062382 0.88713665 1.761605982 2.532429244 1.273167174 1.626882768 1.58662746 1 17.01046349 4.262752921 6.40172236 1.549149651 3.177875669 0.696535642 0.432025016 0.090035101 12.34647414 0.108276307 0.287220585 18312.72277 -4.262752921 1.628726018 RNS(ph)CNVGGGGGGFKHPAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSCNVGGGGGGFKHPAFK 19 2 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RNS(1)CNVGGGGGGFKHPAFK 137.42 2.03E-06 483730000 1084200 943410 506130 423740 489940 462240 393350 738370 543120 479500 TRUE FALSE 1041828.265 916504.8705 597598.9498 445609.2722 505699.3651 471586.8095 398163.935 723122.4015 481467.2945 447023.0379 2.330591887 2.050240799 1.336841503 0.996837376 1.131260186 1.054949677 0.890701152 1.617640122 1.077052531 1 18.76998966 4.262891097 2.747924833 1.147537932 2.293773022 0.840239146 0.187103775 0.105473687 1.568807527 0.051717522 0.172432156 18318.5501 -4.262891097 1.14623509 up LDKDIVALMTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDKDIVALMTR 11 1 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 ; 109 0.001813 1001540000 2997000 3003500 2145300 2666900 2575500 1978860 2818200 2811200 2574900 2694000 FALSE TRUE 2879873.927 2917843.121 2533003.432 2804539.029 2658343.297 2018873.905 2852689.975 2753147.738 2282608.147 2511532.98 1.146659809 1.161777744 1.008548744 1.116664225 1.058454465 0.803841288 1.135836159 1.096202104 0.908850556 1 21.26013679 4.262901204 0.979619938 1.01734447 1.188090546 0.234216509 0.095938012 1.73649361 2.184679961 0.032869235 0.267769115 18318.97644 -4.262901204 0.170746077 GIS(ph)PIVFDR ddPTM_BT-474_Pertuzumab_2h_R1 9 GISPIVFDR 9 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR 213.13 2.50E-06 36538080000 11281210 11648420 12653930 15442210 13091750 12512970 14601960 15513500 15206070 15611310 TRUE FALSE 10840327.84 11316218.47 14940776.64 16239184.31 13512858.03 12765990.83 14780663.15 15193140.8 13479940.68 14553942.07 0.744837913 0.777536314 1.026579367 1.115792837 0.928467213 0.877150037 1.015577985 1.043919285 0.926205465 1 23.79490664 4.263023291 8.175884706 0.995218693 0.759547042 0.669127349 0.064811251 0.119267171 31.95013142 0.016808494 0.044616865 18324.12691 -4.263023291 -0.235671651 QQSHFAMMHGGTGFAGIDSS(ph)SPEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.025)S(0.699)S(0.276)PEVK 83.088 0.021928 1026600000 173480 166300 105420 117590 124550 127320 148780 101200 139440 174590 TRUE FALSE 166700.2098 161557.2868 124471.7391 123658.834 128556.2639 129894.4976 150600.8141 99110.18464 123611.3558 162764.8638 1.024178105 0.99258085 0.76473347 0.759739118 0.789828105 0.798049988 0.925266121 0.608916337 0.759447419 1 17.31242977 4.263133804 6.684328634 0.782379857 1.011588891 0.39898499 0.099972397 0.143014476 22.25189223 0.023956236 0.06353499 18328.79037 -4.263133804 0.229209034 ISMPDVDLHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 159.94 2.81E-05 8011230000 3015050 2971880 2819000 3229310 2725520 3040310 3214540 3297570 3475130 3186410 FALSE TRUE 2897218.513 2887124.892 3328456.008 3395975.076 2813188.826 3101787.151 3253880.502 3229474.027 3080647.811 2970591.613 0.975300173 0.971902324 1.120469066 1.143198231 0.947012984 1.044164785 1.095364468 1.087148437 1.037048579 1 21.50231885 4.263179038 24.82953804 1.063950445 0.973601107 0.279241891 0.054666757 261.5782276 263816.2271 0.013491839 0.03691042 18330.69948 -4.263179038 -0.090349338 EDVSNFDPDFIKEEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFR 34 1 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 EDVSNFDPDFIKEEPVLT(1)PIDEGHLPMINQDEFR;EDVS(0.001)NFDPDFIKEEPVLT(0.999)PIDEGHLPMINQDEFR 154.66 8.82E-11 63364000 34416 35891 34019 39878 40114 38517 42749 46212 49404 41580 TRUE FALSE 33070.98467 34867.42382 40166.99005 41936.10836 41404.30324 39295.84013 43272.17505 45257.70605 43795.86504 38763.74956 0.853142047 0.899485324 1.036199813 1.081838285 1.06811915 1.013726499 1.116305196 1.167526531 1.129814983 1 15.24242051 4.263186356 1.481553856 1.095760638 0.828960647 0.735028559 0.048709916 0.277901277 0.997447221 0.015000799 0.085028394 18331.00837 -4.263186356 -0.266799991 ESDGFREEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESDGFREEK 9 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 62.463 0.075199 1286300000 1672800 1654400 1091000 1244700 1467300 1463800 1439300 1391600 1618800 1504900 FALSE TRUE 1607425.127 1607218.132 1288167.969 1308939.116 1514497.037 1493399.039 1456914.584 1362862.974 1435040.611 1402971.783 1.145728764 1.145581224 0.918170975 0.932976082 1.079492158 1.064454081 1.038448957 0.971411536 1.022857785 1 20.42005456 4.263743276 24.81267979 1.004885318 1.145655234 0.56988667 0.049395181 158.5498894 156217.4404 0.012946349 0.035422713 18354.53035 -4.263743276 0.140769916 EEEELAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEELAR 7 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5;E7ESB6 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 80.294 0.070498 116640000 171860 180040 168350 200700 215950 205050 190030 204690 210840 237430 FALSE TRUE 165143.5212 174905.4355 198774.5899 211058.1511 222896.2279 209196.2515 192355.644 200463.08 186906.3271 221348.6546 0.746078721 0.790180703 0.898015803 0.953509979 1.006991564 0.945098365 0.869016549 0.905643996 0.844397846 1 17.75596108 4.263999094 2.833075817 0.926862251 0.752871788 0.643227293 0.048530813 0.172357818 2.735043676 0.013173223 0.043195415 18365.34514 -4.263999094 -0.173990463 VFGS(ph)LER ddPTM_BT-474_Pertuzumab_2h_R1 4 VFGSLER 7 0 Q14680-3;Q14680-4;Q14680-5;Q14680-2;Q14680-8;Q14680-6;Q14680;Q14680-7 Q14680-3 MELK Maternal embryonic leucine zipper kinase 1 VFGS(1)LER;VFGS(1)LER;VFGS(1)LER;VFGS(1)LER 139.78 0.0027993 1270250000 868710 891930 791030 970970 916670 925390 974180 1014190 906670 985510 TRUE FALSE 834759.8528 866493.0297 933986.7174 1021081.878 946155.523 944102.0198 986102.3063 993246.6221 803748.6227 918760.5299 0.908571739 0.943110856 1.016572531 1.111368898 1.029817338 1.027582258 1.073296331 1.081072368 0.874818406 1 19.80932935 4.264138004 3.249087087 1.038621153 0.916717592 0.302671284 0.060850857 0.250162487 5.334360571 0.015021505 0.045884647 18371.22026 -4.264138004 -0.12190356 ALKDFVASIDATYAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALKDFVASIDATYAK 15 1 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 163.7 1.39E-06 392740000 662250 620910 506920 455180 561610 606660 587250 559810 686370 584190 FALSE TRUE 636368.5378 603202.2547 598531.7204 478671.8943 579674.6957 618927.0809 594436.9412 548249.7279 608456.1551 544622.291 1.168458487 1.107560716 1.098984985 0.878906175 1.064360944 1.136433619 1.091466418 1.006660464 1.117207586 1 19.05489651 4.264335203 2.714806274 1.045592319 1.151205707 0.230105236 0.070424093 0.413530535 5.991111952 0.01845548 0.062140604 18379.56391 -4.264335203 0.105613389 GAGYTFGQDISETFNHANGLTLVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAGYTFGQDISETFNHANGLTLVSR 25 0 P67775;P62714;H0YC23 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 0 ; 349.52 6.67E-103 611430000 391760 392180 402200 425500 489510 440610 411410 423380 440310 473440 FALSE TRUE 376449.5861 380995.4104 474886.4869 447460.106 505255.5337 449519.4361 416444.9586 414637.055 390327.8547 441373.4871 0.852904846 0.863204115 1.075928892 1.013790178 1.144734671 1.018455909 0.943520558 0.939424472 0.884348213 1 18.75164045 4.264541835 21.68071088 1.00004764 0.858053202 0.412309389 0.068941935 54.7736063 45703.08608 0.018574148 0.050787815 18388.31076 -4.264541835 -0.141994438 EIEVGGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIEVGGGR 8 0 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;;; 227.47 6.08E-06 1568370000 1445750 1476000 1415730 1803330 1576990 1656160 1618480 1674100 1646990 1821580 FALSE TRUE 1389248.492 1433905.925 1671583.904 1896400.077 1627715.316 1689648.69 1638287.442 1639529.25 1460030.6 1698202.764 0.818069857 0.844366736 0.984325276 1.11671004 0.958492914 0.994962866 0.964718393 0.965449642 0.859750455 1 20.6955773 4.264633052 5.49060372 0.982387902 0.827304507 0.506364396 0.059086203 0.137191291 11.41472221 0.014927025 0.040098918 18392.17335 -4.264633052 -0.155083395 SRTS(ph)VQTEDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 S(0.117)RT(0.188)S(0.691)VQT(0.003)EDDQLIAGQSAR 237.39 8.49E-24 1951600000 389940 545610 423550 797610 499220 695500 756340 613710 653220 685230 TRUE FALSE 374700.7137 530049.737 500094.9068 838774.7477 515277.8647 709563.4865 765596.3152 601036.674 579069.2041 638818.7618 0.586552456 0.829734142 0.782843174 1.313008944 0.806610412 1.110743029 1.198456215 0.940856327 0.906468687 1 19.28504716 4.26469635 1.738058131 1.032369771 0.622161902 0.454640181 0.151131908 0.379554588 2.017576311 0.039457104 0.191946647 18394.85419 -4.26469635 -0.410207869 ALFAGDIEEMEER ddPTM_BT-474_Pertuzumab_2h_R1 2 ALFAGDIEEMEER 13 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 ; 205.13 1.68E-07 111869000 115936 125394 108550 135458 136150 128148 148726 141415 136266 155117 FALSE TRUE 111405.0929 121817.8859 128167.3997 142449.0036 140529.3884 130739.2404 150546.1533 138494.7308 120797.655 144610.7874 0.770378856 0.8423845 0.886292108 0.98505102 0.971776663 0.904076678 1.041043728 0.957706775 0.835329488 1 17.14181565 4.264782719 1.639370414 0.958300024 0.770882877 0.56411167 0.05377916 0.334133426 1.54049183 0.01462726 0.075331154 18398.5128 -4.264782719 -0.187417148 AADPPAENSSAPEAEQGGAE ddPTM_BT-474_Pertuzumab_2h_R1 2 AADPPAENSSAPEAEQGGAE 20 0 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ; 275.42 3.81E-44 775300000 852160 969140 759510 1027610 921770 1127530 1061770 992460 1091470 1099470 FALSE TRUE 818856.6451 941501.0761 896770.3522 1080645.075 951419.5692 1150329.429 1074764.259 971965.3542 967570.9014 1025001.918 0.798883037 0.918535917 0.874896268 1.054285906 0.928212477 1.122270514 1.048548535 0.948257108 0.943969845 1 19.96719518 4.264909533 1.171774794 1.005772537 0.798784696 0.510187911 0.062927608 0.658216585 1.299430049 0.019387919 0.137609536 18403.88593 -4.264909533 -0.206987841 AGELTEDEVER ddPTM_BT-474_Pertuzumab_2h_R1 4 AGELTEDEVER 11 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;; 286.53 1.60E-27 4807110000 1751680 1781000 1554480 1770070 1848540 1803490 1832970 1976030 2059230 2069770 FALSE TRUE 1683222.409 1730207.624 1835409.115 1861423.525 1907999.968 1839957.803 1855402.435 1935224.29 1825474.843 1929582.634 0.872324605 0.896674541 0.951194876 0.964676761 0.988814852 0.953552219 0.96155635 1.00292377 0.946046472 1 20.8798574 4.264951526 1.640849308 0.975434359 0.866460543 0.801480269 0.017777949 0.187972112 0.868453245 0.0047895 0.024653371 18405.66555 -4.264951526 -0.108973816 TLSVSPSVERPDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLSVSPSVERPDYR 14 1 Q99707-2;Q99707;A0A494C064;A0A494C1A2 Q99707-2 MTR Methionine synthase 0 62.287 0.071348 334510000 315260 325790 305980 347190 360670 364610 356990 380700 382210 452330 FALSE TRUE 302939.2907 316498.7882 361277.3925 365108.5175 372271.2781 371982.664 361358.9504 372838.412 338823.1232 421693.2862 0.718387749 0.75054263 0.856730245 0.865815344 0.882801055 0.882116638 0.856923651 0.884145952 0.803482375 1 18.68583453 4.264977523 2.644205223 0.876229555 0.720137522 0.616659168 0.046122807 0.166721443 2.282885346 0.010724202 0.036764686 18406.76734 -4.264977523 -0.156092034 TFLVGER ddPTM_BT-474_Pertuzumab_2h_R1 6 TFLVGER 7 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;; 126.67 0.0091423 1536580000 1836390 1883467 1788630 2081972 2128807 2050158 2160158 2141704 2214869 2334570 FALSE TRUE 1764621.849 1829752.365 2111875.229 2189422.824 2197282.01 2091613.599 2186594.66 2097477.064 1963446.357 2176447.494 0.810780804 0.840705953 0.970331347 1.005961701 1.009572717 0.961021851 1.004662261 0.963715904 0.902133574 1 21.05354379 4.264981725 4.095638313 0.978955529 0.818225589 0.799348797 0.030516958 0.082125801 3.005745446 0.007721802 0.021779448 18406.94545 -4.264981725 -0.160729941 RLQSIGTENTEENR ddPTM_BT-474_Pertuzumab_2h_R1 8 RLQSIGTENTEENR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;; 320.35 6.38E-56 29098060000 2998980 3022500 2957380 3867310 3270830 2633090 3329470 3460500 3491080 3364680 FALSE TRUE 2881776.546 2936301.259 3491844.353 4066902.333 3376039.217 2686332.884 3370217.05 3389039.466 3094787.234 3136787.227 0.918703227 0.93608557 1.113191332 1.296518392 1.076272942 0.856396271 1.07441685 1.080417389 0.986610506 1 21.58085624 4.265152829 13.85413526 1.066440891 0.927330431 0.202424773 0.105135134 2.749489133 1424.990562 0.027181227 0.073773331 18414.19885 -4.265152829 -0.13911046 LLEAQIATGGIIDPEESHR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLEAQIATGGIIDPEESHR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 215.75 3.99E-19 1685660000 544673 585199 592867 858560 701530 711140 740340 641420 660630 793700 FALSE TRUE 523386.577 568509.6975 700011.2552 902870.3845 724095.3496 725519.738 749400.5024 628174.4529 585638.052 739941.992 0.707334605 0.768316576 0.946035314 1.220190764 0.978583939 0.98050894 1.012782773 0.848950944 0.791464815 1 19.49705265 4.265350828 4.081403344 0.973075539 0.725305312 0.444233858 0.10606114 0.199109959 7.217671709 0.028772546 0.081271427 18422.59597 -4.265350828 -0.247770227 S(ph)PLDPDSGLLSCTLPNGFGGQSGPEGER ddPTM_BT-474_Pertuzumab_2h_R1 3 SPLDPDSGLLSCTLPNGFGGQSGPEGER 28 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 S(0.999)PLDPDS(0.001)GLLSCTLPNGFGGQSGPEGER;S(0.999)PLDPDS(0.001)GLLSCTLPNGFGGQSGPEGER;S(1)PLDPDSGLLSCTLPNGFGGQSGPEGER 232 1.18E-35 189943000 135458 137187 130967 167589 139163 149866 148634 155865 151126 158652 TRUE FALSE 130164.1516 133274.5611 154635.6502 176238.2884 143639.3043 152896.3932 150453.0274 152646.3333 133970.8101 147906.3587 0.880044325 0.901073911 1.045496972 1.191553155 0.971150297 1.033737795 1.017218115 1.032047132 0.905781274 1 17.17432455 4.265417536 7.321074217 1.029813012 0.889017021 0.380522349 0.068190148 0.177131679 33.93640155 0.016710787 0.044515629 18425.42593 -4.265417536 -0.140795991 GPS(ph)WDPFRDWYPHSR ddPTM_BT-474_Pertuzumab_2h_R1 5 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR 104.89 0.00082004 1012167000 1443580 1495896 562967 1012408 1153913 1091404 1049444 974490 889036 869568 TRUE FALSE 1387163.298 1453234.511 664707.66 1064658.498 1191029.66 1113472.937 1062287.41 954366.441 788116.3604 810671.3848 1.711128977 1.792630822 0.819947111 1.313304649 1.46918922 1.373519477 1.310379803 1.177254383 0.972177352 1 19.62875769 4.265613927 24.99964972 1.212401132 1.751880677 0.580171182 0.193152618 159.1914694 147104.2937 0.047460207 0.129903643 18433.75994 -4.265613927 0.539479545 SSEIEQAVQSLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSEIEQAVQSLDR 13 0 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 ;;; 228.12 1.85E-11 432087000 356001 364698 321276 376930 366648 358429 409551 412283 396929 424729 FALSE TRUE 342088.0873 354297.1701 379337.7199 396383.4025 378441.5659 365676.68 414563.2076 403769.212 351871.284 395961.7265 0.863942307 0.894776304 0.958016128 1.001064941 0.955752894 0.923515217 1.046977978 1.019717778 0.888649737 1 18.59500146 4.26568726 2.443686384 0.981227464 0.866881017 0.437819091 0.043794537 0.268908477 3.107702574 0.011718496 0.042492896 18436.87282 -4.26568726 -0.114346447 LICCDILDVLDKHLIPAANTGESK ddPTM_BT-474_Pertuzumab_2h_R1 1 LICCDILDVLDKHLIPAANTGESK 24 1 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 108.57 0.0013844 523220000 737740 677100 294300 287220 438330 533660 288590 309190 379180 292150 FALSE TRUE 708908.3052 657789.771 347486.5567 302043.4586 452429.2825 544450.9708 292121.8507 302805.1185 336137.0761 272362.4203 2.602812475 2.415126765 1.275824162 1.108976262 1.661129616 1.998994466 1.0725483 1.111772755 1.234153653 1 18.05516813 4.265716969 5.541608418 1.316365732 2.538909394 0.731635051 0.291334757 0.090511678 7.665354671 0.077481819 0.20840434 18438.13409 -4.265716969 1.222543662 up LQSFDS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 4 LQSFDSPER 9 0 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 LQSFDS(1)PER;LQS(0.002)FDS(0.998)PER;LQS(0.004)FDS(0.996)PER;LQS(0.007)FDS(0.993)PER 145.14 0.00010268 1833890000 1719710 1721310 1538550 1728430 1755010 1651300 1808350 1913680 1885040 1988640 TRUE FALSE 1652501.832 1672219.924 1816600.21 1817634.479 1811461.491 1684690.417 1830481.128 1874161.839 1671058.162 1853947.642 0.891342234 0.901977967 0.979855185 0.98041306 0.977083414 0.908704421 0.987342408 1.010903327 0.901351324 1 20.82216907 4.265969832 7.489326008 0.970395916 0.895905443 0.411468168 0.034154007 0.172494009 34.54001502 0.008330128 0.022219314 18448.8726 -4.265969832 -0.074490473 LSPQFPNEEDSFHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPQFPNEEDSFHK 14 0 P49770 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 75.376 0.030425 390320000 482830 403680 333750 206880 314120 290150 206640 134070 266570 239910 FALSE TRUE 463960.4698 392167.4416 394066.0492 217557.1016 324223.9551 296017.0318 209168.9221 131301.4076 236310.0912 223660.682 2.074394416 1.753403585 1.761892371 0.972710535 1.44962428 1.323509475 0.935206493 0.587056279 1.056556249 1 17.77095214 4.265984601 0.447907263 0.814862569 2.61767124 0.745099142 0.222292678 1.678964697 0.358663225 0.178894248 1.547150027 18449.49999 -4.265984601 1.802808671 up VHAELADVLTEAVVDSILAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHAELADVLTEAVVDSILAIK 21 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 127.78 1.92E-05 4103600000 321830 336680 344340 398560 424240 371900 444470 311610 557860 517710 FALSE TRUE 309252.5278 327078.216 406569.8978 419129.7294 437886.0649 379420.0728 449909.5568 305175.1446 494534.0715 482645.0406 0.640745272 0.677678601 0.842378692 0.868401608 0.90726316 0.786126534 0.932174826 0.632297276 1.024633074 1 18.88060303 4.26619802 4.093143896 0.851662465 0.649711058 0.381456429 0.106924785 0.220605131 8.038578657 0.026003309 0.073488876 18458.56861 -4.26619802 -0.201951407 RT(ph)SFDDRLEDDDFDLIEENLGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTSFDDRLEDDDFDLIEENLGVK 23 2 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 RT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK;RT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK 152.14 3.10E-06 223970000 236900 244070 219100 258760 282010 254330 247440 291430 261950 251850 TRUE FALSE 227641.6861 237109.3626 258696.2439 272114.6346 291081.1078 259472.7269 250468.2447 285411.8687 232214.5342 234791.9752 0.96954628 1.00986996 1.101810416 1.158960541 1.239740445 1.105117527 1.066766633 1.215594649 0.989022449 1 17.84102357 4.266329655 2.889484547 1.127573433 0.976489734 0.26248273 0.078190363 0.284794007 4.70947565 0.019196236 0.062453482 18464.16427 -4.266329655 -0.151083699 TGTRFER ddPTM_BT-474_Pertuzumab_2h_R1 1 TGTRFER 7 1 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 85.212 0.019131 59634000 36320 47580 24997 29571 30356 33504 28858 27729 31607 29741 FALSE TRUE 34900.57425 46223.06499 29514.51396 31097.16285 31332.42831 34181.47384 29211.17284 27156.38646 28019.10587 27726.61558 1.258739068 1.667100871 1.064483109 1.121563602 1.130048787 1.232803684 1.053542678 0.979433872 1.01054908 1 14.75898391 4.266357631 0.47271779 1.002343402 1.625421929 0.457944789 0.142554743 2.639662598 0.632638805 0.099721921 0.878607466 18465.3537 -4.266357631 0.623078527 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK 33 2 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 99.866 3.77E-05 97870000 59819 54150 28407 19946 37562 43827 28660 30607 39265 25914 FALSE TRUE 57481.20735 52605.69502 33540.77681 20975.41545 38770.21584 44713.21197 29010.74965 29974.95475 34807.80181 24158.8217 2.379305086 2.177494237 1.388344897 0.86823007 1.604805745 1.850802681 1.200834627 1.240745725 1.440790542 1 14.56026247 4.266481411 4.221499675 1.329395234 2.323888991 0.674962861 0.266542691 0.115182486 4.534314273 0.068274344 0.191585359 18470.61735 -4.266481411 0.994493757 GLDWVKEEAPDILCLQETK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLDWVKEEAPDILCLQETK 19 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 220.62 2.60E-19 224340000 973880 925210 500360 510400 678190 774860 674800 647780 765720 589010 FALSE TRUE 935819.6929 898823.9167 590786.1824 536741.8052 700004.5973 790528.2001 683058.4043 634403.1166 678798.6758 549115.8281 1.704230046 1.63685669 1.075886274 0.97746555 1.274784957 1.439638342 1.243924085 1.155317484 1.236166654 1 19.06675097 4.266779596 10.02624814 1.188546659 1.672037379 0.694469191 0.131139711 0.220666417 74.31128738 0.033759289 0.090865664 18483.30354 -4.266779596 0.48349072 ELDEETER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDEETER 8 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 109.11 0.0085645 98234000 60943 72999 71840 127920 70674 92915 103380 88224 73617 107970 FALSE TRUE 58561.28018 70917.13999 84823.08607 134521.9665 72947.29339 94793.80496 104645.1954 86402.14357 65260.30679 100657.0957 0.581789885 0.704541885 0.842693557 1.336437988 0.72471089 0.941749852 1.039620651 0.85838105 0.648342835 1 16.61908935 4.267046807 3.183860266 0.932491623 0.615654822 0.301262971 0.177302369 0.288921316 5.883630527 0.044264075 0.137060364 18494.6794 -4.267046807 -0.316836801 TFGETHPFTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFGETHPFTK 10 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 83 0.016328 311000000 769420 754340 672740 690910 762700 780020 777140 732990 851860 907030 FALSE TRUE 739350.2158 732826.9618 794319.083 726567.9479 787232.9382 795792.5388 786650.8718 717853.5004 755160.4241 845596.0502 0.874353914 0.866639528 0.939359973 0.859237632 0.930979914 0.941102479 0.930291564 0.848931946 0.893051031 1 19.68960911 4.267250788 24.91980876 0.909265034 0.870496662 0.146265177 0.04183454 436.6952393 379298.8125 0.010037739 0.027479367 18503.36809 -4.267250788 -0.038768372 HWPTFISDIVGASR ddPTM_BT-474_Pertuzumab_2h_R1 1 HWPTFISDIVGASR 14 0 O14980;C9JKM9 O14980 XPO1 Exportin-1 0 234.9 3.19E-17 386220000 158590 157850 184520 197860 189860 188190 220610 139110 213840 218530 FALSE TRUE 152392.1275 153348.2726 217866.8686 208071.5783 195967.0193 191995.3307 223309.8912 136237.3299 189565.7797 203728.7685 0.748014768 0.752707994 1.06939668 1.021316625 0.961901556 0.942406574 1.096113685 0.668719155 0.930481155 1 17.63629019 4.267342809 24.02310555 0.94375329 0.750360773 0.355967723 0.111508671 172.5403879 144006.8035 0.029483654 0.080705228 18507.28908 -4.267342809 -0.193392518 EPSTAS(ph)GGGQLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPSTASGGGQLNR 13 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 EPST(0.408)AS(0.591)GGGQLNR;EPST(0.374)AS(0.625)GGGQLNR 175.62 1.88E-05 833650000 167673 187029 174930 227370 201712 209255 221520 254430 243950 246760 TRUE FALSE 161120.1538 181695.116 206543.7423 239104.5929 208200.2497 213486.2795 224231.028 249175.9316 216257.8187 230046.7254 0.700380123 0.789818311 0.897833872 1.039374034 0.905034615 0.928012686 0.974719495 1.083153569 0.940060409 1 17.8115674 4.267393064 1.795264909 0.9861325 0.69775809 0.775921978 0.051045895 0.198009673 1.135873274 0.015062426 0.071433105 18509.43083 -4.267393064 -0.288374411 KAGTQIENIEEDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAGTQIENIEEDFR 14 1 P12814-3;P12814;P12814-2;P12814-4;P35609-2;P35609;G3V2N5;A0A494C1A0;Q08043;A0A494C166;A0A494C033;A0A087WSZ2;G3V5M4;A0A494C0Q3;G3V380 P12814-3 ACTN1;ACTN2;ACTN3 Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ; 178.03 3.25E-06 920060000 1050550 1107630 1119950 1343560 1210430 1245680 1307670 1457020 1491310 1542810 FALSE TRUE 1009493.345 1076041.477 1322349.878 1412901.293 1249364.58 1270868.503 1323673.657 1426932.028 1322022.741 1438314.105 0.701858754 0.748126903 0.919374895 0.982331528 0.868631251 0.883582035 0.920295263 0.992086515 0.91914745 1 20.45594734 4.267448008 3.753016536 0.9364148 0.712381557 0.806148533 0.041670284 0.089119122 2.625970871 0.010937587 0.031752038 18511.77266 -4.267448008 -0.224033243 KAEGDAKGDK ddPTM_BT-474_Pertuzumab_2h_R1 3 KAEGDAKGDK 10 2 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ;; 96.745 0.0036735 425484000 778030 694080 257444 192602 335707 440670 294765 320413 279297 210452 FALSE TRUE 747623.7274 674285.518 303969.8576 202542.2123 346505.3205 449580.6493 298372.4222 313796.3596 247592.3755 196197.8986 3.810559302 3.436762182 1.549302311 1.032336298 1.76610108 2.291465161 1.520772773 1.599386955 1.261952229 1 17.58195006 4.267773377 4.825429522 1.542100566 3.698449535 0.850040069 0.357085627 0.064778599 3.621328464 0.090470858 0.24805106 18525.64668 -4.267773377 2.156348969 DPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_BT-474_Pertuzumab_2h_R1 5 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;;;; 256.75 6.70E-53 545491000 272787 289115 280240 343829 342006 314526 350813 336291 355032 390071 FALSE TRUE 262126.1825 280869.7233 330885.6019 361574.0559 353006.9336 320885.9312 355106.3544 329346.4733 314730.2558 363651.1437 0.720817704 0.772360346 0.909898422 0.994288241 0.970729612 0.882400445 0.976502784 0.905665991 0.865473026 1 18.47219559 4.268116193 3.181780995 0.938290735 0.730865823 0.759704202 0.043783207 0.110314889 2.241868408 0.011049328 0.034277241 18540.27591 -4.268116193 -0.207424912 HYGFQLYQSDPSGNYGGWK ddPTM_BT-474_Pertuzumab_2h_R1 1 HYGFQLYQSDPSGNYGGWK 19 0 P25789;H0YN18;P25789-2;H0YMZ1;H0YL69;H0YLC2;H0YMI6;H0YMA1;H0YKT8;H0YMV3;H0YKS0 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type;Proteasome subunit beta type 0 236.16 3.50E-24 720060000 832460 766280 806550 852490 897240 769040 890420 719400 995020 1073600 FALSE TRUE 799926.5429 744426.4447 952311.5266 896487.1111 926100.5395 784590.5157 901317.2263 704544.1386 882069.5011 1000884.116 0.79921994 0.743768867 0.951470317 0.895695213 0.925282483 0.78389746 0.900521061 0.70392179 0.881290338 1 19.93284352 4.268262496 24.999775 0.861389961 0.771494344 0.1938858 0.081763282 387.1860373 325884.3646 0.020387404 0.055815876 18546.52273 -4.268262496 -0.089895617 SEVQQPVHPKPLSPDSR ddPTM_BT-474_Pertuzumab_2h_R1 5 SEVQQPVHPKPLSPDSR 17 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;;; 149.73 1.89E-07 3881040000 2768760 2840140 1981850 2435370 2430800 2552360 2496560 2662450 2683900 2724270 FALSE TRUE 2660553.798 2759141.988 2340014.381 2561059.738 2508988.89 2603970.468 2527113.648 2607469.477 2379234.924 2539752.766 1.047564091 1.086382117 0.921355185 1.008389388 0.987887058 1.025285021 0.995023485 1.026662718 0.936797847 1 21.27625663 4.268847698 24.99999913 0.992831813 1.066973171 0.460828903 0.03394491 178.9262134 147688.9799 0.007871904 0.021552486 18571.5306 -4.268847698 0.074141358 WTSQDSLLGMEFSGR ddPTM_BT-474_Pertuzumab_2h_R1 6 WTSQDSLLGMEFSGR 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 281.38 2.16E-33 3052510000 1116008 1256748 1221971 1582000 1498880 1579800 1504410 1487790 1798550 1775960 FALSE TRUE 1072393.174 1220906.778 1442808.342 1663647.21 1547092.836 1611744.638 1522821.42 1457066.617 1594386.144 1655672.647 0.647708456 0.737408315 0.871433338 1.004816509 0.934419518 0.97346818 0.919759967 0.88004511 0.962983925 1 20.65898603 4.268873491 2.273583472 0.943099024 0.656563071 0.885453605 0.037499829 0.103123757 1.01690362 0.010397575 0.040082365 18572.63358 -4.268873491 -0.286535952 KLGEMWSEQSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLGEMWSEQSAK 12 1 P26583 P26583 HMGB2 High mobility group protein B2 0 ; 244.58 3.33E-16 6313800000 7225500 6645100 4762000 4515600 5701600 4733000 5277400 5849400 5814400 4722900 FALSE TRUE 6943119.472 6455588.254 5622599.33 4748650.657 5884997.142 4828704.503 5341986.4 5728607.846 5154373.688 4403013.776 1.576901601 1.466174893 1.276988812 1.078500068 1.336583858 1.09668167 1.213256799 1.301065165 1.170646732 1 22.07005993 4.268914173 2.535699697 1.194668212 1.561478621 0.669273676 0.097505262 0.165446829 2.068441203 0.023934823 0.084973252 18574.37346 -4.268914173 0.366810409 EEILQPPEPHPVPPILTPS(ph)PPSAFPTVTTVWQDNDRYHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEILQPPEPHPVPPILTPSPPSAFPTVTTVWQDNDRYHPK 40 1 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 EEILQPPEPHPVPPILT(0.002)PS(0.983)PPS(0.013)AFPT(0.001)VT(0.001)T(0.001)VWQDNDRYHPK 73.337 0.0011806 238780000 107870 105030 127750 125050 118270 109310 134650 131850 147510 153690 TRUE FALSE 103654.3211 102034.6472 150837.2668 131503.8455 122074.262 111520.3231 136297.887 129127.2514 130765.2832 143280.4394 0.72343665 0.712132428 1.052741515 0.917807386 0.851995307 0.778335993 0.951266534 0.901220376 0.912652723 1 17.12848214 4.269069596 24.99985542 0.910871633 0.717784159 0.561121211 0.07137446 151.5326259 124167.3724 0.017474006 0.04784223 18581.02194 -4.269069596 -0.193087475 DFSESR ddPTM_BT-474_Pertuzumab_2h_R1 6 DFSESR 6 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;; 148.07 0.025152 8711540000 8465700 8727720 7500310 9002380 9025300 9059490 8973370 9358430 9666310 9589500 FALSE TRUE 8134851.085 8478813.971 8855782.86 9466993.911 9315606.971 9242679.095 9083188.786 9165175.15 8569031.013 8939994.624 0.909939147 0.948413766 0.990580334 1.058948502 1.042014829 1.033857344 1.016017254 1.025187994 0.958505164 1 23.09184253 4.269080203 2.333695082 1.021838198 0.915646749 0.656921994 0.026084846 0.178099547 1.859809499 0.006845455 0.025857686 18581.47576 -4.269080203 -0.106191449 RPGGS(ph)SPLNAVPCEGPPGSEPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPGGSSPLNAVPCEGPPGSEPPR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 RPGGS(0.5)S(0.5)PLNAVPCEGPPGSEPPR;RPGGS(0.5)S(0.5)PLNAVPCEGPPGSEPPR 114.13 0.00042832 1226680000 635830 666730 646900 769320 762070 780000 765700 780150 821690 885020 TRUE FALSE 610981.0607 647715.5132 763809.2202 809024.6974 786582.6736 795772.1344 775070.8656 764039.6299 728415.196 825076.8071 0.740514162 0.785036626 0.925743172 0.980544709 0.953344788 0.964482491 0.93939238 0.92602243 0.882845318 1 19.6541689 4.269173012 3.357096807 0.946232157 0.749212252 0.859350078 0.03008935 0.077463308 1.7687651 0.007680659 0.023296736 18585.44705 -4.269173012 -0.197019906 ISHSLYSGIEGLDES(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISHSLYSGIEGLDESPSR 18 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 ISHSLYSGIEGLDES(0.994)PS(0.006)R;ISHSLYSGIEGLDES(0.994)PS(0.006)R 259.93 6.57E-31 836210000 208030 232200 198145 260540 243620 279510 275650 236030 242710 322460 TRUE FALSE 199899.9576 225577.8833 233954.2092 273986.5006 251456.2586 285161.8837 279023.4872 231155.898 215158.5783 300619.497 0.664960056 0.750376757 0.778240306 0.911406291 0.836460247 0.948580803 0.928161646 0.768931824 0.715717312 1 18.19757905 4.269227475 1.663410536 0.862197573 0.669675386 0.405674141 0.081700626 0.508359696 2.421901496 0.023176189 0.118800787 18587.77791 -4.269227475 -0.192522187 SVNESLNNLFITEEDYQALR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVNESLNNLFITEEDYQALR 20 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 292.82 3.81E-54 309230000 60814 63430 59828 73766 67831 66067 71790 76852 74700 80657 FALSE TRUE 58437.32165 61621.0385 70640.25047 77573.0721 70012.84572 67402.92001 72668.58749 75264.97934 66220.36917 75194.02955 0.777153745 0.819493767 0.939439619 1.031638716 0.931095808 0.896386594 0.966414327 1.000943556 0.880659935 1 16.1983305 4.269665413 3.501817777 0.959594322 0.78687589 0.672745061 0.044494256 0.125317216 3.14149915 0.011242862 0.033550511 18606.53108 -4.269665413 -0.172718432 MGGDIANR ddPTM_BT-474_Pertuzumab_2h_R1 3 MGGDIANR 8 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;; 147.34 0.0012537 815570000 1334340 1354860 1173470 1394280 1369560 1381380 1351570 1440380 1492830 1589000 FALSE TRUE 1282192.518 1316220.719 1385542.133 1466238.958 1413613.141 1409312.45 1368110.918 1410635.65 1323370.197 1481375.615 0.865541801 0.888512479 0.935307777 0.989782026 0.954257062 0.951353888 0.923540866 0.952247111 0.893338721 1 20.49850606 4.269797904 3.117924484 0.949452203 0.870532586 0.522918586 0.028489548 0.186628307 3.626703852 0.006987225 0.021943416 18612.20829 -4.269797904 -0.078919617 RLDVTVQSFGWSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDVTVQSFGWSDR 14 1 Q52LJ0;Q52LJ0-1;Q8NCA5;E9PH82 Q52LJ0;Q8NCA5 FAM98B;FAM98A Protein FAM98B;Protein FAM98A 0 ; 192.78 5.36E-07 1504530000 543090 557280 569680 600060 673720 618190 685990 677830 672850 740340 FALSE TRUE 521865.4424 541386.92 672633.8485 631029.1685 695390.8157 630690.2254 694385.3508 663832.5736 596470.8888 690196.1124 0.756111825 0.784395783 0.974554676 0.914275171 1.007526416 0.913784088 1.006069635 0.961802829 0.864204938 1 19.39664682 4.269854109 6.383217751 0.955965589 0.76689963 0.735051199 0.044456571 0.07826505 9.47919889 0.010217825 0.027486513 18614.61716 -4.269854109 -0.189065959 T(ph)PPEDCEGPFRPAEILK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPEDCEGPFRPAEILK 17 1 P49790-3;P49790 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 T(1)PPEDCEGPFRPAEILK 66.045 0.06783 196850000 132030 145830 155480 208790 189380 227680 181020 160050 189500 198180 TRUE FALSE 126870.1216 141671.0712 183578.6946 219565.6769 195471.5797 232283.8456 183235.3769 156744.9116 167988.7544 184757.0921 0.686686071 0.76679639 0.99362191 1.188401887 1.057992294 1.257239129 0.991763698 0.848383734 0.909241169 1 17.49527022 4.269856049 3.602115227 1.030545989 0.706064792 0.542342368 0.113184724 0.190652327 5.092842069 0.03280769 0.096911346 18614.70033 -4.269856049 -0.324481197 YLAEFATGNDR ddPTM_BT-474_Pertuzumab_2h_R1 7 YLAEFATGNDR 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;;; 234.2 4.00E-15 6940900000 1569514 1666419 1678553 2145939 1897143 1696934 2061312 2183787 2002889 2352700 FALSE TRUE 1508175.658 1618894.362 1981904.866 2256691.169 1958166.328 1731247.168 2086538.953 2138691.035 1775529.438 2193349.533 0.687613002 0.738092282 0.903597368 1.028878952 0.892774406 0.789316587 0.951302527 0.975079896 0.809505923 1 21.06470431 4.269964989 3.883202683 0.922072502 0.700558653 0.568022377 0.072505085 0.147985343 4.705172363 0.018346146 0.052893036 18619.37028 -4.269964989 -0.221513849 EAEEGEDDRDSANGEDDS ddPTM_BT-474_Pertuzumab_2h_R1 2 EAEEGEDDRDSANGEDDS 18 1 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 221.66 4.99E-18 886050000 337640 394680 587240 719140 429650 636520 792100 700670 769930 896780 FALSE TRUE 324444.6555 383424.1128 693367.3311 756254.9016 443470.0824 649390.8705 801793.9567 686200.9196 682530.7742 836040.2918 0.38807299 0.45861918 0.829346788 0.90456753 0.530441041 0.776745902 0.959037459 0.820774939 0.816385025 1 19.67321295 4.27011269 5.072146657 0.821295623 0.410229877 0.644938315 0.120741301 0.110934043 7.014318951 0.030104099 0.082306188 18625.70371 -4.27011269 -0.411065746 KT(ph)PESFLGPNAALVDLDSLVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 KTPESFLGPNAALVDLDSLVSR 22 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KT(0.998)PES(0.002)FLGPNAALVDLDSLVSR;KT(0.999)PES(0.001)FLGPNAALVDLDSLVSR;KT(0.99)PES(0.01)FLGPNAALVDLDSLVSR 222.37 5.03E-26 778403000 246444 212506 235409 213601 246126 252577 248414 283875 272916 258294 TRUE FALSE 236812.696 206445.5369 277952.6429 224624.9732 254042.8663 257684.28 251454.1648 278012.882 241935.7198 240799.5173 0.9834434 0.857333683 1.154290698 0.932829832 1.054997407 1.070119587 1.044246964 1.154540861 1.004718458 1 17.87747297 4.270143807 0.743926534 1.068816184 0.897877175 0.151349415 0.080399734 2.313159605 1.493222132 0.031534185 0.297082118 18627.03826 -4.270143807 -0.170939009 VREELIDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VREELIDK 8 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 94.909 0.0091433 916230000 758980 743730 776640 778080 776040 805280 770740 898110 943770 895910 FALSE TRUE 729318.2225 722519.5486 916996.1243 818236.802 801002.0314 821563.3133 780172.5467 879563.7147 836637.1862 835229.2177 0.873195294 0.865055404 1.097897565 0.979655386 0.959020607 0.983638139 0.934081962 1.053080635 1.001685727 1 19.67181266 4.270406164 24.99844673 0.999443961 0.869125073 0.592550463 0.043767717 131.9420545 103571.1475 0.010632076 0.029111831 18638.29424 -4.270406164 -0.130318888 VMPNS(ph)PQNGVLVK ddPTM_BT-474_Pertuzumab_2h_R1 4 VMPNSPQNGVLVK 13 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 VMPNS(1)PQNGVLVK;VMPNS(1)PQNGVLVK;VMPNS(1)PQNGVLVK;VMPNS(1)PQNGVLVK 254.63 8.57E-24 822260000 1237210 1285710 1203350 1441030 1379330 1410980 1477070 1528780 1422060 1565730 TRUE FALSE 1188858.465 1249042.81 1420822.113 1515401.731 1423697.402 1439510.982 1495146.825 1497210.159 1260633.711 1459681.712 0.814464178 0.85569532 0.973378032 1.038172718 0.975347838 0.986181419 1.024296469 1.02571002 0.863636024 1 20.47722239 4.27079857 3.302719216 0.993419925 0.822731289 0.633807618 0.046253732 0.134601993 2.96139768 0.011401542 0.034907736 18655.14245 -4.27079857 -0.170688636 LYLEDDDPVQAEAYINR ddPTM_BT-474_Pertuzumab_2h_R1 4 LYLEDDDPVQAEAYINR 17 0 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ;;; 336.8 7.22E-72 441403000 273008 296151 270613 336718 339064 339739 336819 350649 341229 363253 FALSE TRUE 262338.5455 287705.0634 319518.7889 354096.0563 349970.3015 346608.7554 340941.0917 343407.9756 302494.1145 338649.5508 0.77466084 0.849565761 0.943508675 1.045612066 1.033429103 1.023502776 1.006766703 1.014051177 0.893236426 1 18.36943356 4.270828255 2.108197063 1.005730771 0.780483583 0.782001848 0.040357694 0.146934228 1.222930563 0.010657637 0.043925808 18656.41763 -4.270828255 -0.225247189 ERENMDTDDER ddPTM_BT-474_Pertuzumab_2h_R1 2 ERENMDTDDER 11 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ; 76.533 0.032003 249492000 187869 189030 172226 195208 194230 200458 198870 198427 222679 228109 FALSE TRUE 180526.8718 183639.0495 203351.0693 205282.7083 200477.5843 204511.3981 201303.8305 194329.4131 197401.4135 212658.9743 0.848903144 0.863537737 0.956230839 0.965314109 0.942718665 0.961687128 0.946603976 0.913807723 0.928253389 1 17.69818221 4.271105288 6.30497446 0.947315593 0.85447281 0.744087735 0.022317545 0.088230044 10.12710426 0.005613296 0.015137505 18668.32221 -4.271105288 -0.092842784 GSEEDPLLS(ph)PVETWK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSEEDPLLSPVETWK 15 0 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GSEEDPLLS(1)PVETWK;GSEEDPLLS(1)PVETWK;GSEEDPLLS(1)PVETWK;GSEEDPLLS(1)PVETWK 276.47 1.60E-33 169560000 492925 541838 554433 654900 678990 678660 716360 687600 723470 788890 TRUE FALSE 473660.946 526385.3108 654631.3764 688699.4675 700830.33 692382.9702 725127.028 673400.8197 641344.7186 735457.7776 0.644035539 0.715724718 0.890100555 0.936422849 0.952917151 0.941431298 0.985953307 0.915621318 0.872034722 1 19.48828299 4.271116029 2.216654321 0.94158236 0.643675054 0.908224457 0.033421014 0.085940631 0.800449399 0.008736138 0.034523848 18668.78391 -4.271116029 -0.297907306 GSPHSEGGKRS(ph)PEPNK ddPTM_BT-474_Pertuzumab_2h_R1 5 GSPHSEGGKRSPEPNK 16 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK 166.29 3.51E-09 3824922000 1826610 1760580 1093820 1163450 1520920 1538390 1401820 1373490 1643090 1268070 TRUE FALSE 1755224.062 1710369.982 1291497.606 1223495.794 1569841.773 1569497.3 1418975.892 1345126.952 1456573.312 1182182.489 1.484731907 1.446790151 1.092468902 1.034946639 1.32791831 1.327626922 1.200301904 1.137833595 1.232105301 1 20.17302133 4.271152588 10.68950918 1.179861819 1.466467024 0.558899078 0.105058977 0.387308176 123.0148517 0.026197397 0.071051303 18670.35555 -4.271152588 0.286605205 DFSWSPGGNIIAFWVPEDKDIPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFSWSPGGNIIAFWVPEDKDIPAR 24 1 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 163.71 1.50E-11 467700000 747020 792830 406340 511590 586680 776280 568870 593720 738010 681510 FALSE TRUE 717825.6325 770219.2647 479774.677 537993.2212 605551.095 791976.9135 575832.0012 581459.4745 654234.1988 635350.7207 1.129810055 1.212274165 0.7551336 0.846765737 0.953097361 1.246519265 0.906321473 0.915178744 1.029721345 1 19.27719367 4.271187335 24.99998442 0.955067355 1.171042412 0.326695501 0.123130245 228.5347453 175109.4865 0.031136263 0.085257027 18671.84936 -4.271187335 0.215975057 SAS(ph)PDDDLGSSNWEAADLGNEERK ddPTM_BT-474_Pertuzumab_2h_R1 4 SASPDDDLGSSNWEAADLGNEERK 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 S(0.004)AS(0.995)PDDDLGSSNWEAADLGNEERK;SAS(1)PDDDLGSSNWEAADLGNEERK;S(0.007)AS(0.775)PDDDLGS(0.165)S(0.054)NWEAADLGNEERK;SAS(1)PDDDLGSSNWEAADLGNEERK 261.93 2.68E-44 4512330000 2717280 2539210 1483990 1364340 1769280 2286100 1541330 1785060 2110060 1697180 TRUE FALSE 2611085.693 2466794.217 1752180.004 1434753.751 1826190.498 2332326.508 1560193.258 1748197.887 1870534.835 1582228.487 1.6502583 1.559063206 1.107412753 0.906793022 1.154188863 1.474076929 0.986073295 1.104895975 1.182215369 1 20.59352652 4.271361724 5.079324064 1.116490593 1.621072316 0.647485002 0.145067292 0.11053278 6.952549475 0.036676485 0.100457344 18679.34845 -4.271361724 0.504581724 VNS(ph)GDTEVGSSLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 VNSGDTEVGSSLLR 14 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 VNS(0.997)GDT(0.003)EVGSSLLR;VNS(1)GDTEVGSSLLR;VNS(0.941)GDT(0.059)EVGSSLLR 335.7 1.41E-68 759210000 701030 717131 690498 781511 869156 790355 808511 802577 852589 840831 TRUE FALSE 673632.9726 696679.126 815286.3486 821844.8764 897113.1921 806336.5196 818405.7995 786003.5045 755806.6711 783880.7674 0.859356423 0.888756498 1.040064232 1.048430974 1.144451082 1.028646898 1.044043729 1.002707985 0.964185757 1 19.5802747 4.271397173 4.881943636 1.037455567 0.868131604 0.673981941 0.044587799 0.107526759 6.073220509 0.011738669 0.032316515 18680.87322 -4.271397173 -0.169323962 EKGKFEDMAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKGKFEDMAK 10 2 P09429;Q5T7C4;B2RPK0;P23497 P09429;P23497 HMGB1;HMGB1P1;SP100 High mobility group protein B1;Putative high mobility group protein B1-like 1;Nuclear autoantigen Sp-100 0 ; 83.617 0.008707 3851900000 11903800 10854500 6696100 5127100 7433300 6872800 7681600 8854700 9646800 7879400 FALSE TRUE 11438586.34 10544940.29 7906234.224 5391710.245 7672398.845 7011772.725 7775609.719 8671847.351 8551735.707 7345721.22 1.557176755 1.435521438 1.076304693 0.733993312 1.044471825 0.954538365 1.0585223 1.180530419 1.16417918 1 22.80847271 4.271481266 3.801270852 1.027580095 1.52576279 0.724495798 0.117187224 0.118179418 3.563851614 0.032400537 0.094219147 18684.49076 -4.271481266 0.498182695 DVLDVYIEHR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVLDVYIEHR 10 0 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ;;;;; 182.28 1.79E-06 3522120000 2856450 2972940 2942370 3673550 3370920 3238950 3491590 3375940 3713060 4161260 FALSE TRUE 2744816.776 2888154.662 3474121.712 3863142.356 3479348.703 3304443.788 3534321.123 3306225.659 3291568.995 3879414.154 0.707533836 0.744482169 0.895527411 0.995805604 0.896874777 0.851789383 0.911045066 0.852248697 0.848470636 1 21.88740737 4.271552349 4.516652715 0.900457721 0.718341869 0.661913314 0.051695142 0.115845639 5.327229979 0.013009314 0.036272076 18687.54922 -4.271552349 -0.182115852 AS(ph)SHSS(ph)QTQGGGSVTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.5)S(0.5)HS(0.008)S(0.992)QTQGGGSVTKK 166.91 2.33E-09 307910000 760050 631560 266350 214010 270490 273810 149180 307830 243940 176630 TRUE FALSE 730346.4057 613548.5272 314485.3699 225055.0817 279190.5565 279346.6258 151005.7095 301473.2029 216248.9539 164666.6928 4.435301356 3.726002611 1.909829879 1.366731049 1.695488941 1.69643673 0.917038576 1.830808634 1.313252548 1 17.32918924 4.271767926 2.467785767 1.452064081 4.39536183 0.934554424 0.282284304 0.061969096 0.73004898 0.069817949 0.253972044 18696.82772 -4.271767926 2.943297749 up VAS(ph)DTEEADR ddPTM_BT-474_Pertuzumab_2h_R1 2 VASDTEEADR 10 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 VAS(0.997)DT(0.003)EEADR;VAS(0.998)DT(0.002)EEADR 211.43 6.18E-08 1032910000 699100 705880 630120 714780 770960 680910 741350 768330 803920 823570 TRUE FALSE 671778.3991 685748.9935 743996.7009 751669.8815 795758.6286 694678.4667 750422.8631 752463.717 712662.3719 767788.8703 0.874951989 0.893147869 0.969012094 0.979005962 1.036428971 0.904777985 0.977381793 0.980039886 0.928200967 1 19.55035012 4.271983193 4.056373906 0.972453432 0.879352 0.519230209 0.033986073 0.15360059 5.395819933 0.008224632 0.023495467 18706.09747 -4.271983193 -0.093101432 LVTSGAESGNLNTS(ph)PSSNQTR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVTSGAESGNLNTSPSSNQTR 21 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 LVTSGAESGNLNT(0.001)S(0.694)PS(0.305)SNQTR 406.46 1.49E-151 369340000 203950 223700 206900 253710 264020 281750 261090 239810 283450 297310 TRUE FALSE 195979.4085 217320.295 244291.4325 266804.0035 272512.4431 287447.178 264285.2975 234857.8397 251273.9443 277172.9289 0.707065475 0.784060319 0.881368298 0.962590411 0.983185639 1.037068011 0.953503283 0.847333254 0.906560195 1 18.08042683 4.27198725 1.90070901 0.947556582 0.708114332 0.743230386 0.049628937 0.232414512 1.522416827 0.015730049 0.071353243 18706.27222 -4.27198725 -0.23944225 IVDILYATDEGFVIPDEGGPQEEQEEY ddPTM_BT-474_Pertuzumab_2h_R1 4 IVDILYATDEGFVIPDEGGPQEEQEEY 27 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;; 165.85 9.32E-12 539017000 914120 961340 838260 1036290 997780 1062420 1031100 1048800 1066650 1081800 FALSE TRUE 878395.1798 933923.5245 989752.229 1089773.051 1029874.5 1083902.86 1043718.91 1027141.913 945568.3638 1008528.722 0.870966944 0.926025708 0.981382292 1.080557278 1.021165265 1.074736729 1.034892599 1.018455787 0.937572072 1 19.94382074 4.272274633 2.245918912 1.026892174 0.87831169 0.63214568 0.038432094 0.19645459 1.883028989 0.010095971 0.039552832 18718.65472 -4.272274633 -0.148580484 TVFPGAVPVLPAS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 TVFPGAVPVLPASPPPK 17 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 TVFPGAVPVLPAS(1)PPPK;TVFPGAVPVLPAS(1)PPPK;TVFPGAVPVLPAS(1)PPPK;TVFPGAVPVLPAS(1)PPPK 168.89 2.14E-09 1265070000 897969 850991 1085672 1113196 1047847 918417 1049771 1094253 1169064 1149628 TRUE FALSE 862875.3787 826721.5699 1281877.081 1170648.179 1081551.95 936988.021 1062618.412 1071656.293 1036356.756 1071762.672 0.805099302 0.771366266 1.19604565 1.09226437 1.009133812 0.874249538 0.991468018 0.999900744 0.96696478 1 20.03155404 4.272286211 24.99991605 1.011756123 0.78823231 0.570039183 0.079135834 140.714741 104306.0309 0.020446596 0.055988429 18719.15372 -4.272286211 -0.223523812 EDARPVPQGSCQSELHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDARPVPQGSCQSELHR 17 1 P22692-2;P22692 P22692-2 IGFBP4 Insulin-like growth factor-binding protein 4 0 63.691 0.031035 404770000 447340 439190 345810 490550 507890 394660 452180 603360 508050 556320 FALSE TRUE 429857.4582 426664.7312 408305.5595 515867.3443 524226.7431 402640.2956 457713.9141 590900.4052 450378.2939 518639.9509 0.828816711 0.82266075 0.787262067 0.994654082 1.010772005 0.776338759 0.882527297 1.139326818 0.868383342 1 18.98437382 4.272404418 0.332726923 1.007400306 0.689292542 0.222311118 0.099629886 7.119557043 0.804983825 0.110720615 0.895356021 18724.24942 -4.272404418 -0.318107764 YFDDEFTAQSITIT(ph)PPDR ddPTM_BT-474_Pertuzumab_2h_R1 5 YFDDEFTAQSITITPPDR 18 0 P31751;P31751-2;M0R0P9;M0R283 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSIT(0.006)IT(0.994)PPDR;YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSITIT(1)PPDR 233.65 1.07E-22 688456000 215258 247289 262341 359343 296687 280772 335775 337156 350146 415360 TRUE FALSE 206845.4794 240236.5598 309751.8544 377888.7353 306230.2068 286449.4022 339884.3149 330193.6108 310398.894 387227.2972 0.534170708 0.620401923 0.799922569 0.975883513 0.790828046 0.739744859 0.87773852 0.85271264 0.801593525 1 18.56282113 4.272606005 2.998636255 0.852085598 0.550926373 0.690432385 0.075960726 0.136154956 2.430354691 0.01879232 0.060466979 18732.94273 -4.272606005 -0.301159226 AGS(ph)PFSPPPSSSSLTGEAAISR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGSPFSPPPSSSSLTGEAAISR 22 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 AGS(1)PFSPPPSSSSLTGEAAISR;AGS(0.984)PFS(0.016)PPPSSSSLTGEAAISR;AGS(0.992)PFS(0.008)PPPSSSSLTGEAAISR;AGS(1)PFSPPPSSSSLTGEAAISR 238.8 1.52E-30 1320210000 526447 496293 372405 394075 395815 396370 381640 506711 470217 407237 TRUE FALSE 505872.8692 482139.2096 439706.8676 414413.258 408546.7489 404384.873 386310.6245 496247.2408 416839.9375 379654.4753 1.332455962 1.269942121 1.158176437 1.091553728 1.076101496 1.065139223 1.017532124 1.307102308 1.097945539 1 18.53432749 4.272641749 2.255870331 1.111620756 1.328343652 0.511202061 0.079883852 0.301152757 2.914576824 0.022677551 0.088582254 18734.48458 -4.272641749 0.216722896 IEQFVYSSPHDNK ddPTM_BT-474_Pertuzumab_2h_R1 4 IEQFVYSSPHDNK 13 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;;; 198.16 1.28E-07 2446480000 2208860 2168530 2094530 2536370 2582760 2581060 2847990 3056970 3298480 3074200 FALSE TRUE 2122535.309 2106685.648 2473058.164 2667272.36 2665836.821 2633250.802 2882844.554 2993842.501 2924050.379 2865981.696 0.740596254 0.735065981 0.862900893 0.930666223 0.930165334 0.918795401 1.005883798 1.044613267 1.020261359 1 21.45059796 4.27290541 0.47989898 1.030758286 0.578286072 0.911643708 0.031063436 0.853945191 0.210426501 0.023373703 0.209061092 18745.86174 -4.27290541 -0.452472214 SDDIYNQVSAYPLPEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDDIYNQVSAYPLPEHR 17 0 Q12768;E7EQI7;E5RFU6 Q12768 KIAA0196 WASH complex subunit strumpellin 0 131.45 2.69E-05 86988000 114070 121240 122160 137440 149980 142060 162680 141640 179020 172790 FALSE TRUE 109612.0183 117782.3539 144237.0294 144533.2949 154804.2429 144932.5505 164670.9265 138715.0845 158698.4001 161086.7794 0.680453223 0.731173311 0.895399548 0.897238715 0.960999056 0.899717227 1.022249791 0.86112023 0.985173338 1 17.29747857 4.272932495 1.666275931 0.941585842 0.660977876 0.801819145 0.047473751 0.183756989 0.877020694 0.012170374 0.0627801 18747.03088 -4.272932495 -0.280607966 RTSS(ph)KSEAGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RTSSKSEAGAR 11 2 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RT(0.135)S(0.135)S(0.594)KS(0.135)EAGAR;RTS(0.001)S(0.978)KS(0.02)EAGAR 119.17 0.00049015 137071000 224034 205056 89566 89092 115026 155603 97304 118245 125702 101028 TRUE FALSE 215278.5036 199208.0037 105752.5686 93690.0488 118725.9158 158749.3993 98494.83546 115803.1994 111432.8359 94185.28357 2.285691516 2.115065073 1.122814144 0.994741909 1.260556971 1.685501102 1.045756107 1.22952541 1.183123644 1 16.52321404 4.273753475 5.837517838 1.20417838 2.224818485 0.817938545 0.190761754 0.068985922 6.195015948 0.047629946 0.129412545 18782.50336 -4.273753475 1.020640105 up KKS(ph)EPDDELLFDFLNSSQKEPTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKSEPDDELLFDFLNSSQKEPTGR 24 3 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 KKS(1)EPDDELLFDFLNSSQKEPTGR;KKS(1)EPDDELLFDFLNSSQKEPTGR 194.25 1.58E-17 2365950000 1195920 1137900 821740 762760 985400 1006590 795180 1107680 1243450 825210 TRUE FALSE 1149182.124 1105448.206 970246.6975 802126.135 1017096.286 1026943.939 804911.6507 1084806.021 1102298.769 769317.7917 1.493767773 1.43692011 1.261178031 1.042646022 1.322075606 1.334876108 1.046266783 1.410088305 1.432826305 1 19.55322015 4.273774823 4.147659538 1.24388038 1.477494767 0.288049195 0.147374373 0.266568836 9.831290255 0.036247791 0.103235328 18783.42662 -4.273774823 0.233614387 SGKYDLDFK ddPTM_BT-474_Pertuzumab_2h_R1 4 SGKYDLDFK 9 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 107.06 0.0025861 31008760000 57789800 51350200 35794400 33938100 31761700 32110400 37983700 43986300 47885800 40308000 FALSE TRUE 55531310.73 49885742.57 42263244.32 35689649.41 32783343.93 32759694.29 38448555.88 43077967.53 42450004.74 37577903.26 1.477765014 1.327528634 1.124683409 0.949750952 0.872410142 0.871780793 1.023169271 1.146364321 1.129653362 1 25.16338123 4.273778148 2.124423873 1.00538526 1.466978161 0.773490631 0.087741868 0.186169583 1.574560509 0.027829443 0.114584422 18783.57047 -4.273778148 0.4615929 KS(ph)SSLVDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSSLVDIR 9 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 KS(0.333)S(0.333)S(0.333)LVDIR 66.498 0.038932 307500000 408750 461530 444830 598490 499580 549240 543600 587840 619010 678030 TRUE FALSE 392775.5981 448367.6163 525220.6762 629378.1406 515649.4444 560346.0091 550252.7394 575700.8986 548742.5799 632106.4242 0.621375742 0.709322986 0.830905455 0.995683822 0.815763651 0.886474156 0.870506482 0.910765777 0.868117391 1 19.26980795 4.273779708 2.427895935 0.898088394 0.63348516 0.756066574 0.054794264 0.133244109 1.514265012 0.013246004 0.048940245 18783.63791 -4.273779708 -0.264603234 LDSQPQETS(ph)PELPR ddPTM_BT-474_Pertuzumab_2h_R1 7 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LDSQPQET(0.079)S(0.921)PELPR;LDSQPQET(0.005)S(0.995)PELPR;LDSQPQET(0.025)S(0.975)PELPR;LDSQPQET(0.039)S(0.961)PELPR;LDSQPQET(0.019)S(0.981)PELPR;LDSQPQET(0.02)S(0.98)PELPR;LDSQPQET(0.001)S(0.999)PELPR 282.72 2.21E-33 30793890000 7289650 7467520 6218150 7644420 7204250 7511490 7625860 7676380 7545970 8446240 TRUE FALSE 7004762.419 7254553.641 7341908.027 8038949.432 7435981.244 7663377.474 7719187.556 7517860.07 6689383.121 7874168.642 0.889587554 0.921310423 0.932404214 1.020926754 0.944351281 0.973230042 0.980317784 0.95474969 0.849535161 1 22.90869618 4.274042055 2.443924554 0.959824986 0.896683751 0.206916366 0.043451856 0.461992206 5.325310768 0.01103177 0.04057729 18794.9881 -4.274042055 -0.063141235 VKADRDESSPYAAMLAAQDVAQR ddPTM_BT-474_Pertuzumab_2h_R1 4 VKADRDESSPYAAMLAAQDVAQR 23 2 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;; 149.71 5.18E-08 2243480000 1861470 1761490 1127400 1063430 1372980 1644830 1258000 1438390 1392280 1264070 FALSE TRUE 1788721.694 1711254.03 1331146.259 1118313.75 1417143.149 1678089.59 1273395.78 1408686.744 1234234.211 1178453.413 1.517855245 1.452118523 1.129570541 0.948967297 1.202544906 1.42397618 1.080565228 1.195369056 1.047333902 1 20.1684633 4.274072724 5.240505132 1.141809553 1.496119051 0.562915098 0.125498326 0.135032628 9.044327905 0.031544184 0.086464608 18796.31539 -4.274072724 0.354309498 DEDYKQR ddPTM_BT-474_Pertuzumab_2h_R1 5 DEDYKQR 7 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;; 140.98 0.0023598 4504990000 8617030 8021240 4370950 3891890 5391140 6747000 5108030 5667830 5970480 4753870 FALSE TRUE 8280266.941 7792482.089 5160877.896 4092750.909 5564550.914 6883428.963 5170543.599 5550787.33 5292736.141 4431886.151 1.868339271 1.758276685 1.164487922 0.92347835 1.255571719 1.553160151 1.166668868 1.252466138 1.194240096 1 22.07948939 4.274264376 5.615401975 1.204182253 1.830007728 0.710471787 0.159490651 0.096672409 7.776817322 0.040621799 0.110726638 18804.61195 -4.274264376 0.625825475 SLIEEGGDWDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLIEEGGDWDR 11 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;; 176.6 1.97E-05 1163330000 972590 1049880 921220 1162780 1120150 1107090 1139990 1243500 1199870 1285650 FALSE TRUE 934580.1075 1019938.45 1087704.946 1222791.215 1156180.642 1129476.118 1153941.539 1217821.29 1063665.788 1198571.78 0.779744795 0.850961509 0.907500881 1.020206912 0.964631957 0.94235167 0.962763814 1.016060373 0.887444378 1 20.19288488 4.274348125 1.912180984 0.971870319 0.784423479 0.731042309 0.038078116 0.185598786 1.231488187 0.009879422 0.044778073 18808.23857 -4.274348125 -0.18744684 ACANPAAGSVILLENLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ACANPAAGSVILLENLR 17 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 135.14 3.40E-05 435160000 464660 489420 516660 621890 629150 635710 553070 618330 616580 593820 FALSE TRUE 446500.5735 475462.2208 610031.955 653985.8174 649387.1811 648564.4918 559838.6361 605561.2694 546588.4233 553600.0425 0.806539991 0.858855102 1.10193625 1.181332672 1.173025887 1.171539816 1.011269135 1.093860591 0.987334504 1 19.07848453 4.274479563 4.82148351 1.098553552 0.822333646 0.688314095 0.069328154 0.101425088 5.438264964 0.017783728 0.049269721 18813.93169 -4.274479563 -0.276219906 S(ph)DSEATISR ddPTM_BT-474_Pertuzumab_2h_R1 3 SDSEATISR 9 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.862)DS(0.132)EAT(0.006)ISR;S(0.986)DS(0.014)EATISR;S(0.9)DS(0.1)EATISR 212.28 3.97E-06 1019840000 735710 629050 517180 502640 475360 468350 439750 682890 521040 469530 TRUE FALSE 706957.6398 611110.1099 610645.9306 528581.3106 490650.3861 477820.3579 445131.792 668788.0829 461893.7236 437728.3149 1.615060337 1.396094539 1.395034111 1.207555675 1.12090164 1.091591157 1.016913407 1.527861142 1.05520641 1 18.73967618 4.274508023 1.166961804 1.174709305 1.630778744 0.515168731 0.147813014 0.757882967 1.468651644 0.048038426 0.349593664 18815.16463 -4.274508023 0.456069439 GVDLLLEGVQGES(ph)SPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVDLLLEGVQGESSPTR 17 0 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 GVDLLLEGVQGES(0.499)S(0.499)PT(0.003)R 141.86 6.38E-07 48669000 81495 88557 91433 119500 103550 89289 112350 123720 112630 123540 TRUE FALSE 78310.0853 86031.44107 107956.977 125667.4093 106880.7798 91094.48476 113724.9729 121165.1388 99844.71458 115172.5258 0.679937205 0.746978852 0.937350087 1.091123152 0.928005868 0.790939368 0.98743144 1.052031619 0.866914344 1 16.81343708 4.274625141 3.624520354 0.964390689 0.695978787 0.591147965 0.081796657 0.151795881 4.085521983 0.021602292 0.06409749 18820.23931 -4.274625141 -0.268411902 GLQEVGLPLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLQEVGLPLHR 11 0 P11172-2;P11172-3;P11172 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 144.65 3.66E-05 154910000 230800 233540 219340 244240 239980 262560 274730 244820 261740 281490 FALSE TRUE 221780.0808 226879.6679 258979.6172 256845.2557 247699.1746 267869.1431 278092.2279 239764.3814 232028.3725 262424.4316 0.845119791 0.864552384 0.986873119 0.978739876 0.94388763 1.020747731 1.059704031 0.913651141 0.884172145 1 18.00154251 4.27489373 6.343785783 0.972721397 0.852493022 0.493172574 0.048136529 0.156188703 17.16157186 0.012476618 0.033836306 18831.88226 -4.27489373 -0.120228375 FIEEHATK ddPTM_BT-474_Pertuzumab_2h_R1 7 FIEEHATK 8 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;;; 157.68 0.00037306 13956797000 13192370 15241950 12084120 14187360 12975420 14315150 14604900 13546060 16302750 15852010 FALSE TRUE 12676797.6 14807264.51 14267989.29 14919571.35 13392786.17 14604612.14 14783639.14 13266329.13 14452130.17 14778339.24 0.857795818 1.001957274 0.965466353 1.009556697 0.906244332 0.988244477 1.000358626 0.897687413 0.97792654 1 23.81698082 4.275084485 0.004364553 1.901978474 1.25E-08 0.080079658 0.048726533 119017.9725 94.08324054 19944.5164 21063.98585 18840.15559 -4.275084485 -1.901978461 YYVGHK ddPTM_BT-474_Pertuzumab_2h_R1 4 YYVGHK 6 0 P61326;Q96A72;F5H6N1;P61326-2;F5H124 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;;; 105.82 0.032648 2870240000 3100570 3105310 2784740 2957860 3249260 3184160 3198280 3250570 3669900 3611700 FALSE TRUE 2979396.297 3016749.599 3288004.464 3110515.509 3353775.399 3248545.897 3237421.507 3183444.594 3253308.337 3367076.342 0.884861522 0.895955212 0.976516161 0.923803084 0.996049705 0.964797221 0.961493349 0.945462553 0.966211635 1 21.683065 4.275131845 7.361502193 0.963115897 0.889492625 0.669626567 0.02134082 0.112751104 17.53533165 0.004919695 0.013319118 18842.21025 -4.275131845 -0.073623272 ARLS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_BT-474_Pertuzumab_2h_R1 3 ARLSYSDKNLIDSMDQSAFAGFSFVNPK 28 2 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 ARLS(0.749)YS(0.251)DKNLIDSMDQSAFAGFSFVNPK;ARLS(0.5)YS(0.5)DKNLIDSMDQSAFAGFSFVNPK;ARLS(0.326)Y(0.282)S(0.326)DKNLIDS(0.053)MDQS(0.013)AFAGFS(0.001)FVNPK 319.12 2.80E-83 2421960000 1410460 1301750 776335 702121 889240 1028180 801348 1042520 1050790 804270 TRUE FALSE 1355337.664 1264625.365 916636.004 738357.549 917843.2122 1048970.504 811155.1365 1020991.598 931508.7245 749796.0765 1.80760837 1.686625743 1.222513738 0.984744482 1.224123786 1.399007726 1.081834331 1.361692372 1.242349425 1 19.51613875 4.27518073 4.268062152 1.204099209 1.774687605 0.745410709 0.130877927 0.096163599 3.78363039 0.032447651 0.091983848 18844.33128 -4.27518073 0.570588396 AGLS(ph)PAEPLLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGLSPAEPLLSR 12 0 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 AGLS(1)PAEPLLSR 108.72 0.0017579 59177000 78321 75873 72527 79570 76587 77895 79928 81825 81185 87210 TRUE FALSE 75260.12873 73709.17633 85634.24225 83676.61724 79050.49041 79470.09027 80906.18277 80135.28516 71969.21916 81303.18902 0.925672531 0.906596374 1.053270398 1.029192314 0.972292617 0.977453544 0.995116966 0.985635202 0.885195526 1 16.31102432 4.275207693 24.99727515 0.98767243 0.916134299 0.319229359 0.04154874 200.4973297 136757.8445 0.01015586 0.027811271 18845.50124 -4.275207693 -0.071538131 ETDLLLDDSLVSIFGNR ddPTM_BT-474_Pertuzumab_2h_R1 5 ETDLLLDDSLVSIFGNR 17 0 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;;; 336.5 7.48E-72 601791300 291893.1 301147 288071 348537 328987 336335 341924 338715 360568 364601 FALSE TRUE 280485.5949 292558.5824 340131.8378 366525.0363 339569.1656 343135.9241 346108.5682 331720.4169 319637.8323 339906.2495 0.825185166 0.860703746 1.000663678 1.078312143 0.999008303 1.009501663 1.018247145 0.975917381 0.940370566 1 18.37477736 4.275416302 4.404943198 1.004529946 0.835203877 0.792322706 0.032901671 0.084867008 3.603941265 0.008658604 0.024392065 18854.55566 -4.275416302 -0.169326069 (ac)AVTLDKDAYYR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVTLDKDAYYR 11 1 Q9Y5B9;G3V5A4;G3V401;G3V2X0 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 89.698 0.00017453 444990000 959280 928820 652470 656660 830460 810290 668300 938170 875380 811910 FALSE TRUE 921790.2771 902330.963 770385.8431 690550.3013 857172.5001 826674.619 676478.8553 918796.4617 776010.5323 756918.6125 1.217819541 1.192110946 1.017792178 0.912317771 1.132450023 1.092157869 0.893727336 1.213864273 1.025223214 1 19.52977866 4.275543005 7.263108349 1.045832382 1.207089986 0.352850832 0.09080568 0.230313739 34.48807283 0.022280282 0.060352514 18860.0572 -4.275543005 0.161257604 IYVEIER ddPTM_BT-474_Pertuzumab_2h_R1 6 IYVEIER 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ;;;;; 134.85 0.0072917 1044413000 1037013 1109441 1051185 1355408 1192979 1255860 1303949 1331782 1275111 1390871 FALSE TRUE 996485.3855 1077800.829 1241157.513 1425360.769 1231352.253 1281254.35 1319907.118 1304280.236 1130365.745 1296666.068 0.768498081 0.831209249 0.957191326 1.099250458 0.949629425 0.98811435 1.017923697 1.005872112 0.871747763 1 20.30637556 4.275560074 3.080982768 0.993573965 0.781530441 0.664033541 0.054120453 0.134884428 2.546837591 0.013376079 0.042618255 18860.79846 -4.275560074 -0.212043524 SRS(ph)SHKDSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSSHKDSPR 10 2 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(0.093)RS(0.86)S(0.046)HKDSPR 66.797 0.033861 31871000 68197 60874 24874 22812 33014 42354 26122 31858 28316 20309 TRUE FALSE 65531.78584 59137.93312 29369.28512 23989.33005 34075.92529 43210.4269 26441.68885 31200.12117 25101.68639 18933.45334 3.461163934 3.123462585 1.551184805 1.267034049 1.799773379 2.282226392 1.396559221 1.647883279 1.325784892 1 14.20864995 4.275593355 4.732388858 1.574980277 3.362437071 0.818563837 0.33178427 0.073021216 3.707614642 0.081817984 0.22766413 18862.24383 -4.275593355 1.787456795 FDFDSDEDFNAFFNSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 FDFDSDEDFNAFFNSSR 17 0 Q9HAV4 Q9HAV4 XPO5 Exportin-5 0 ;;; 297.16 8.10E-46 684208000 664085 692625 601612 701901 745038 744974 731217 733531 791375 836026 FALSE TRUE 638131.824 672872.0132 710336.6712 738126.1947 769002.8239 760037.8847 740165.8524 718383.3285 701541.4277 779401.2144 0.818746253 0.863319175 0.911387689 0.947042654 0.986658488 0.975156146 0.949659609 0.921711841 0.900103072 1 19.57200665 4.27580537 1.669065973 0.951239866 0.816520936 0.728255585 0.02801917 0.260445004 1.245775396 0.008264061 0.042825558 18871.45433 -4.27580537 -0.13471893 RGEEGHDPKEPEQLR ddPTM_BT-474_Pertuzumab_2h_R1 5 RGEEGHDPKEPEQLR 15 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;; 227.89 4.03E-13 8073810000 4473520 4285640 2923580 2808760 3562310 4128570 3393470 3313990 4266220 3659450 FALSE TRUE 4298689.893 4163417.743 3451935.941 2953720.44 3676894.936 4212052.514 3435000.301 3245554.948 3781936.591 3411592.192 1.260024543 1.220373805 1.01182549 0.865789424 1.077765081 1.234629545 1.006861344 0.95133145 1.108554709 1 21.70201377 4.275869189 5.728895187 1.027741386 1.245889923 0.446848599 0.092681098 0.166581302 13.87323829 0.024259893 0.066193076 18874.22766 -4.275869189 0.218148537 KNDKEAAGEGPALYEDPPDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KNDKEAAGEGPALYEDPPDQK 21 2 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5M0;G3V359;G3V5D9;G3V3Y6 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 163.42 9.75E-12 1264970000 1381700 1255510 581180 416120 727380 988890 645120 770750 873140 605220 FALSE TRUE 1327701.636 1219704.084 686212.1543 437596.0031 750776.8383 1008886.033 653015.1715 754833.7432 774024.8077 564227.9103 2.353130025 2.16172235 1.216196756 0.775566035 1.330626905 1.788082466 1.157360633 1.337817094 1.371830059 1 19.10591851 4.275959309 5.270995349 1.262230483 2.289916209 0.72287996 0.250650635 0.094976259 6.354178429 0.063998355 0.175802638 18878.14462 -4.275959309 1.027685726 up KAPSS(ph)PPPPPPPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPSSPPPPPPPLR 14 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 KAPS(0.387)S(0.613)PPPPPPPLR 62.94 0.044737 1013100000 470370 494220 449650 505210 558760 566360 567630 594010 613290 630800 TRUE FALSE 451987.4204 480125.3295 530911.7574 531283.9486 576733.0229 577812.1872 574576.8257 581743.4859 543671.8903 588075.3541 0.768587592 0.816435047 0.902795456 0.903428353 0.980712793 0.982547871 0.977046261 0.989232896 0.924493581 1 19.1656415 4.276050168 0.865031468 0.978391224 0.719010998 0.903141777 0.023306854 0.338421283 0.310274249 0.008121324 0.073286475 18882.09454 -4.276050168 -0.259380226 ILNDVQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ILNDVQDR 8 0 O00148;Q13838-2;Q13838;A0A0G2JJZ9;H0Y400 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;; 173.69 0.00064282 2193290000 1276210 1361050 1421180 1808240 1462880 1585570 1827100 1698040 1728870 1885160 FALSE TRUE 1226334.302 1322234.187 1678018.84 1901563.483 1509934.864 1617631.312 1849460.596 1662974.881 1532615.926 1757476.434 0.697781363 0.752348174 0.954788814 1.081985195 0.859149423 0.920428451 1.052338774 0.946228836 0.872054894 1 20.74507391 4.276363255 4.279705184 0.963071885 0.712843349 0.66667106 0.067117698 0.112458323 4.435114513 0.016634349 0.047204201 18895.71175 -4.276363255 -0.250228535 SPS(ph)PYYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPYYSR 8 0 P62995;P62995-3;H7BXF3;H7C2L4;Q13595;Q13595-3;Q13595-4 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 1 S(0.3)PS(0.7)PYYSR 128.87 0.0011696 3449300000 130470 157000 184260 245700 233340 203550 301230 153120 267460 287380 TRUE FALSE 125371.0882 152522.5137 217559.8808 258380.6064 240845.593 207665.9205 304916.5428 149958.0185 237099.0621 267915.4966 0.467950118 0.569293362 0.812046647 0.96441083 0.898961038 0.775117241 1.138107152 0.559721331 0.884977036 1 18.03141851 4.276411531 3.037710693 0.8651246 0.48610753 0.508662302 0.14362637 0.207971417 3.808617039 0.036410972 0.117012516 18897.8123 -4.276411531 -0.37901707 YYEVLGAAATTDYNNNHEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 YYEVLGAAATTDYNNNHEGR 20 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ;; 255.93 3.58E-36 2676510000 570330 613290 578900 728920 658460 673660 706990 724530 778430 857100 FALSE TRUE 548040.8731 595799.5697 683520.1076 766539.6486 679639.9639 687281.8668 715642.3551 709568.2023 690065.8898 799047.8536 0.685867399 0.745636906 0.855418239 0.959316323 0.85056228 0.860126041 0.895618894 0.888017156 0.863610217 1 19.60792238 4.276474265 2.699818172 0.894214727 0.695166162 0.734952453 0.044597229 0.129297773 1.843698437 0.010712346 0.036903246 18900.54229 -4.276474265 -0.199048565 TRTDST(ph)SDGRPAWMR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRTDSTSDGRPAWMR 15 2 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 T(0.002)RT(0.002)DS(0.42)T(0.567)S(0.01)DGRPAWMR 85.146 0.012951 595720000 177260 209410 100110 114800 129930 119450 88970 105500 92236 125160 TRUE FALSE 170332.4832 203437.8318 118202.1039 120724.8418 134109.3164 121865.3608 90058.84147 103321.3881 81765.75596 116682.8017 1.459790824 1.743511716 1.01302079 1.034641267 1.149349471 1.044415793 0.771826183 0.885489435 0.700752422 1 16.83223241 4.276553928 0.615497337 0.849696813 1.883616354 0.677516183 0.168472961 1.194406924 0.50129122 0.08425715 0.810057047 18904.00953 -4.276553928 1.033919541 GLLGLPEEETELDNLTEFNTAHNKR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLGLPEEETELDNLTEFNTAHNKR 25 1 Q12972;A0A0A0MT09;Q12972-2 Q12972 PPP1R8 Nuclear inhibitor of protein phosphatase 1;Activator of RNA decay 0 ; 146.6 1.65E-07 111080000 178241 175607 153465 159331 181338 177908 172235 175545 196557 188926 FALSE TRUE 171275.1447 170598.8603 181199.5393 167554.092 187170.9015 181505.4217 174342.8635 171919.9344 174244.6734 176129.8737 0.972436652 0.96859696 1.028783678 0.951309897 1.062686854 1.030520364 0.989854019 0.976097528 0.989296533 1 17.4262801 4.27664465 24.98677155 1.001839629 0.970516717 0.164146481 0.029628706 316.3584428 207556.5991 0.007374935 0.02019624 18907.95891 -4.27664465 -0.031322912 TASRPDDIPDSPSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 TASRPDDIPDSPSSPK 16 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TASRPDDIPDSPS(0.035)S(0.965)PK;TASRPDDIPDSPS(0.103)S(0.897)PK 203.26 1.71E-11 1892920000 1633330 1664520 1428980 1667260 1724480 1672580 1768710 1736750 1782210 1826330 TRUE FALSE 1569497.658 1617049.519 1687228.473 1753307.488 1779949.465 1706400.714 1790356.002 1700885.506 1579900.992 1702631.042 0.921807261 0.94973572 0.990953666 1.02976361 1.045411144 1.002214027 1.051523176 0.9989748 0.927917413 1 20.69933441 4.276659102 2.394892706 1.011145953 0.925253657 0.441495237 0.032454767 0.270466668 2.980582005 0.008579413 0.032191798 18908.58812 -4.276659102 -0.085892297 LATQSNEITIPVTFESR ddPTM_BT-474_Pertuzumab_2h_R1 4 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;;; 328.49 1.44E-71 1467720000 1226900 1225220 1066530 1242120 1148490 1309250 1180140 1249520 1388200 1405940 FALSE TRUE 1178951.392 1190277.925 1259275.696 1306225.962 1185432.224 1335723.932 1194582.906 1223716.975 1230617.356 1310714.432 0.899472351 0.908113847 0.960755192 0.996575555 0.904416855 1.019080816 0.911398301 0.933625926 0.938890521 1 20.32192197 4.276711494 6.562498804 0.953855875 0.902859374 0.258074523 0.036286792 0.258110803 29.93432063 0.008504293 0.023099888 18910.86936 -4.276711494 -0.050996501 MVQFEENGR ddPTM_BT-474_Pertuzumab_2h_R1 4 MVQFEENGR 9 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 293.09 1.78E-28 1867800000 1004200 1106390 1027860 1352100 1175800 1214110 1298010 1386050 1306010 1495380 FALSE TRUE 964954.7538 1074836.84 1213617.167 1421882.043 1213620.675 1238660.136 1313895.435 1357427.583 1157757.22 1394096.581 0.692172097 0.770991663 0.870540236 1.019930802 0.870542753 0.888503819 0.942470882 0.973696946 0.830471315 1 20.41089908 4.276875368 2.393566433 0.930890176 0.703006207 0.673504598 0.056036888 0.167444468 1.84289264 0.014080783 0.052876788 18918.00641 -4.276875368 -0.227883969 ITPLEIEVLEETVQTMDTS ddPTM_BT-474_Pertuzumab_2h_R1 13 ITPLEIEVLEETVQTMDTS 19 0 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ;;;;;;;;;;;; 309.04 4.17E-61 4829843000 1588088 1714799 1540997 1910500 1917625 1947655 1799737 2000294 2011576 2213809 FALSE TRUE 1526023.765 1665894.611 1819489.437 2009101.134 1979307.15 1987037.919 1821762.72 1958987.23 1783230.326 2063865.745 0.739400695 0.807171986 0.881592924 0.973465032 0.959029024 0.962774795 0.882694393 0.949183461 0.864024383 1 20.9769177 4.276970153 2.025804725 0.938017671 0.743810395 0.746818246 0.039474312 0.171375029 1.298589319 0.010135049 0.043793903 18922.1357 -4.276970153 -0.194207276 ERS(ph)DS(ph)GGSSSEPFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 2 ERS(0.92)DS(0.765)GGS(0.296)S(0.013)S(0.007)EPFDR;ERS(0.98)DS(0.825)GGS(0.174)S(0.019)S(0.003)EPFDR 152.02 3.47E-05 362430000 918880 896990 644510 683420 699580 676820 550990 698600 696150 656440 TRUE FALSE 882969.1537 871408.7234 760987.294 718691.3881 722082.626 690505.7641 557733.1804 684173.6659 617125.9705 611978.7341 1.44281019 1.423919942 1.2434865 1.174373141 1.179914572 1.128316599 0.911360394 1.117969674 1.008410809 1 19.223122 4.277059748 0.496171031 1.00933631 1.665006142 0.862404442 0.060983778 1.011672223 0.266903525 0.040499919 0.368765404 18926.03975 -4.277059748 0.655669832 SVEDRFDQQKNDYDQLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEDRFDQQKNDYDQLQK 18 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 87.429 0.0018358 510870000 289100 252940 164080 146370 154600 193330 151180 185320 205390 160870 FALSE TRUE 277801.6524 245726.3989 193732.9059 153924.1732 159572.8494 197239.2651 153030.1861 181493.0772 182074.9883 149974.1316 1.852330461 1.638458554 1.291775481 1.026338153 1.06400249 1.31515524 1.020377211 1.210162548 1.214042624 1 17.19435415 4.277072497 2.261691793 1.133704119 1.835826114 0.865845223 0.098325931 0.10249521 0.995907131 0.024958578 0.098081138 18926.59535 -4.277072497 0.702121994 IREYFGEFGEIEAIELPMDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IREYFGEFGEIEAIELPMDPK 21 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 143.98 1.20E-07 358190000 894050 845410 607660 540320 721850 824880 662700 717430 800750 739130 FALSE TRUE 859109.5376 821299.7345 717477.6793 568205.98 745068.9608 841559.6388 670810.3208 702614.8198 709852.217 689068.0668 1.246770209 1.191899283 1.041229037 0.824600656 1.081270482 1.221301174 0.973503712 1.019659528 1.030162695 1 19.39428698 4.277365463 4.006161202 1.022859213 1.231348642 0.422062044 0.092492241 0.203914425 6.858150907 0.02406725 0.069493657 18939.36714 -4.277365463 0.208489429 DFKPGDLIFAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFKPGDLIFAK 11 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 99.531 0.0042917 291640000 685370 663890 485640 546820 572720 527690 535330 635740 665480 626870 FALSE TRUE 658584.9827 644956.5072 573405.951 575041.4457 591142.0589 538360.2533 541881.5287 622611.7468 589937.5003 584411.5365 1.126919887 1.10359989 0.98116809 0.983966622 1.011516751 0.921200592 0.927225927 1.065365257 1.009455604 1 19.15662513 4.277574036 5.25852852 0.988853331 1.119436206 0.627724032 0.039425174 0.125147483 8.203252978 0.010640029 0.029300183 18948.46508 -4.277574036 0.130582875 GGAGGS(ph)PGSSSGSGSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGAGGSPGSSSGSGSSR 17 0 Q8TAE6 Q8TAE6 PPP1R14C Protein phosphatase 1 regulatory subunit 14C 1 GGAGGS(0.747)PGS(0.064)S(0.189)SGSGSSR;GGAGGS(0.997)PGS(0.003)SSGSGSSR 224.36 2.88E-15 85302000 73181 76033 73338 86079 82836 86681 86643 89408 85643 104810 TRUE FALSE 70321.00561 73864.61328 86591.80799 90521.54751 85500.49517 88433.74921 87703.36295 87561.69356 75921.16568 97711.12534 0.719682691 0.755948855 0.886202136 0.926420069 0.875033369 0.905053021 0.897578066 0.896128186 0.776996124 1 16.57623522 4.278188153 3.90715879 0.893544029 0.728335017 0.602164246 0.051599229 0.130712077 4.141947717 0.012012539 0.034966436 18975.27826 -4.278188153 -0.165209012 EMFEDTVEER ddPTM_BT-474_Pertuzumab_2h_R1 6 EMFEDTVEER 10 0 Q16576;E9PC52 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;;; 217.2 1.71E-08 5557820000 3027584 3266100 2656050 3423250 3246008 3452260 3377680 3492400 3501760 3528010 FALSE TRUE 2909262.67 3172954.026 3136057.319 3599924.343 3350418.795 3522067.063 3419017.058 3420280.72 3104254.885 3289054.74 0.884528504 0.964700887 0.953482859 1.094516397 1.018657049 1.070844769 1.039513577 1.039897779 0.943813688 1 21.64924159 4.278383865 1.637130801 1.032433482 0.893322374 0.512277909 0.042677327 0.35594297 1.62076039 0.011299616 0.060019004 18983.83127 -4.278383865 -0.139111108 SLTELQELEAVYER ddPTM_BT-474_Pertuzumab_2h_R1 3 SLTELQELEAVYER 14 0 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-2;E9PRT5;H3BSD2;H3BMV9;J3QLW1 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 ;; 218.85 1.22E-11 64372000 81112 86191 75619 91632 92122 93354 97479 92393 104538 101035 FALSE TRUE 77942.05337 83732.91707 89285.03544 96361.1385 95085.18779 95241.68184 98671.97716 90485.05226 92671.2845 94191.80946 0.827482281 0.888961764 0.947906574 1.023030973 1.009484671 1.011146111 1.047564302 0.960646714 0.983857142 1 16.52331399 4.278398075 1.742984644 1.003959641 0.826568658 0.870968098 0.022895711 0.150456101 0.798497685 0.00665368 0.033232678 18984.45244 -4.278398075 -0.177390983 DIWDIQMR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIWDIQMR 8 0 P32456 P32456 GBP2 Interferon-induced guanylate-binding protein 2 0 ; 119.41 0.0039554 144805000 297450 300830 280100 324790 329710 295160 318730 343470 331420 357840 FALSE TRUE 285825.3252 292250.6229 330720.3008 341552.4508 340315.4216 301128.3374 322630.7131 336377.2245 293798.591 333603.1781 0.856782381 0.876042682 0.991358364 1.023828528 1.020120442 0.902654283 0.967109231 1.008315408 0.88068283 1 18.34777351 4.278570029 6.310219427 0.976697668 0.864059187 0.471955601 0.045615234 0.152659278 15.63475875 0.01116142 0.030422935 18991.97058 -4.278570029 -0.112638481 ADYQAVDDEIEANLEEFDISEDDIDDGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADYQAVDDEIEANLEEFDISEDDIDDGFR 29 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 75.174 0.0057776 22251800 15710.9 17721 15981.4 20825 21537.7 17908.7 20613.4 20088.8 22634 25952 FALSE TRUE 15096.90066 17215.61443 18869.59448 21899.78075 22230.47968 18270.82618 20865.67296 19673.95926 20064.68321 24194.24792 0.623987185 0.711558156 0.779920688 0.905164765 0.918833259 0.755172314 0.862422879 0.813166804 0.82931626 1 14.56237647 4.278604893 1.956821328 0.855326938 0.631008502 0.610447624 0.064665333 0.25511027 1.78254208 0.01664635 0.074489413 18993.49529 -4.278604893 -0.224318435 KS(ph)PAKSPNPSTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPAKSPNPSTPR 13 2 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 KS(0.999)PAKS(0.001)PNPSTPR;KS(0.999)PAKS(0.001)PNPSTPR 93.152 0.0029977 656080000 1023750 949650 461520 388070 665320 725350 580710 678230 631830 526470 TRUE FALSE 983740.7182 922566.9118 544926.9305 408098.3392 686720.622 740017.074 587816.9027 664224.3135 560107.3072 490811.718 2.004313838 1.879675806 1.110256562 0.831476357 1.399152866 1.507741252 1.197642357 1.353317961 1.141185686 1 18.90481017 4.278654119 6.541991322 1.217958757 1.955974857 0.715127014 0.188785773 0.102618056 11.43434792 0.048341753 0.131637978 18995.64827 -4.278654119 0.7380161 DAEDALHNLDRK ddPTM_BT-474_Pertuzumab_2h_R1 6 DAEDALHNLDRK 12 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 ;;;;; 157.56 4.81E-05 2046940000 1597129 1533282 1045626 1065453 1280000 1332748 1283634 1150650 1641636 1387038 FALSE TRUE 1534711.433 1489554.299 1234593.878 1120441.157 1321172.362 1359697.078 1299343.497 1126888.675 1455284.364 1293092.681 1.186853391 1.151931583 0.954760549 0.86648171 1.021715135 1.051507829 1.004834005 0.871467832 1.125429279 1 20.30239425 4.279130651 6.052813065 0.977075231 1.174027853 0.487852479 0.074286039 0.142600371 13.09270495 0.018371079 0.050192972 19016.50279 -4.279130651 0.196952622 GVDLLLEGVQGESS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVDLLLEGVQGESSPTR 17 0 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 GVDLLLEGVQGES(0.02)S(0.979)PT(0.001)R 213.98 1.86E-13 55056000 68196 76547 74476 95760 85098 92239 98450 98546 94801 105950 TRUE FALSE 65530.82493 74363.95451 87935.46991 100702.1851 87835.25445 94104.13578 99654.86055 96510.99066 84039.58792 98773.91213 0.663442639 0.752870398 0.890270194 1.019522087 0.8892556 0.952722574 1.008918837 0.977089887 0.850827775 1 16.59184243 4.279147858 2.226061511 0.957998585 0.669822256 0.794975592 0.050645102 0.132565919 1.242376081 0.012983829 0.051898235 19017.25622 -4.279147858 -0.28817633 MKYNTEGRVS(ph)PSPSQESLSSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 MKYNTEGRVSPSPSQESLSSSK 22 2 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 MKYNT(0.012)EGRVS(0.977)PS(0.012)PSQESLSSSK;MKYNT(0.058)EGRVS(0.904)PS(0.038)PSQESLSSSK 146.53 4.43E-08 256450000 542560 516310 334780 272710 389360 556210 367840 429130 470810 405870 TRUE FALSE 521356.1554 501585.3443 395282.1931 286784.5958 401884.118 567456.9473 372341.736 420268.3155 417365.6226 378380.0634 1.377863703 1.325612507 1.044669715 0.757927342 1.062117582 1.499700968 0.984041634 1.110704173 1.103032805 1 18.52947655 4.279169932 6.060946713 1.075223745 1.358442786 0.297988633 0.172910753 0.238583307 21.9654136 0.044178651 0.120702134 19018.22287 -4.279169932 0.283219041 KHEEEEAKAER ddPTM_BT-474_Pertuzumab_2h_R1 4 KHEEEEAKAER 11 2 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 ;;; 238.13 7.98E-16 3986340000 2793540 2487550 1504820 1224160 1850730 2200880 1695850 1119920 2195220 1612890 FALSE TRUE 2684365.368 2416607.51 1776774.449 1287339.044 1910260.411 2245383.302 1716604.32 1096793.261 1946027.829 1503647.524 1.785235786 1.607163562 1.181642919 0.856144159 1.270417688 1.493290992 1.141626806 0.729421785 1.294204791 1 20.52003499 4.279510318 3.189495115 1.096510715 1.749793114 0.557097721 0.208195037 0.183996502 3.730418787 0.057629021 0.181528909 19033.13458 -4.279510318 0.653282399 GVESVFDIMEMEDEER ddPTM_BT-474_Pertuzumab_2h_R1 10 GVESVFDIMEMEDEER 16 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;;;;;;; 326.01 7.69E-59 1114014000 440943 488644 477283 632601 584052 573984 571552 611568 594973 649062 FALSE TRUE 423710.4601 474708.3516 563538.6552 665249.6134 602838.563 585590.3497 578546.8243 598938.9071 527434.1594 605100.4526 0.700231603 0.784511645 0.931314219 1.099403596 0.99626196 0.96775725 0.956116992 0.989817318 0.871647273 1 19.20681514 4.279648055 2.84716143 0.983230746 0.715781797 0.765259827 0.053303871 0.117989812 1.880850199 0.013751457 0.046056926 19039.1719 -4.279648055 -0.267448949 FWLADCHQVLETVGLATQLYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FWLADCHQVLETVGLATQLYR 21 0 Q12955;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 0 ; 230.29 9.75E-26 377640000 398360 409630 376310 441310 470570 458120 423050 432650 486680 485900 FALSE TRUE 382791.6508 397947.7535 444317.588 464086.062 485706.3114 467383.5003 428227.4124 423715.6263 431434.1267 452989.5602 0.845034156 0.878492108 0.980856132 1.024496153 1.072224073 1.031775434 0.945336162 0.93537614 0.952415165 1 18.78911828 4.280009656 3.586252483 0.991231169 0.852390446 0.633675876 0.040258987 0.168379465 4.392068459 0.012236146 0.036713607 19055.03086 -4.280009656 -0.138840723 S(ph)AEEGELAESK ddPTM_BT-474_Pertuzumab_2h_R1 2 SAEEGELAESK 11 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(1)AEEGELAESK;S(1)AEEGELAESK 220.53 9.52E-12 737130000 967660 1016410 1044320 1339190 1327250 1175820 1138260 1214790 1201220 1193900 TRUE FALSE 929842.7774 987422.982 1233051.855 1408305.756 1369942.202 1199595.886 1152190.366 1189704.162 1064862.542 1113036.09 0.835411166 0.887143724 1.10782738 1.265283102 1.230815617 1.077769083 1.035177904 1.068881929 0.956718791 1 20.08606894 4.280053364 4.937399284 1.101269152 0.85169638 0.513200678 0.090267092 0.154126113 8.456573518 0.024284959 0.067575732 19056.94867 -4.280053364 -0.249572772 YYITIIDAPGHR ddPTM_BT-474_Pertuzumab_2h_R1 4 YYITIIDAPGHR 12 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 189.13 8.31E-06 20177500000 13560700 14165900 13437600 16420400 15540400 15197100 16520300 15617300 16836300 19226700 FALSE TRUE 13030732.85 13761902.4 15866073.24 17267858.81 16040271.08 15504395.77 16722480.37 15294797.3 14925113.81 17924458.48 0.726980559 0.767772282 0.885163323 0.963368507 0.894881767 0.864985449 0.932942013 0.853292015 0.832667487 1 24.0954262 4.280091332 3.624075403 0.898846757 0.736446244 0.629684249 0.048294454 0.138487907 3.69587546 0.011858545 0.035450683 19058.61479 -4.280091332 -0.162400513 GSTIYTGYPLS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSTIYTGYPLSPTK 14 0 Q5SQL3;J3KP92;Q86Z02;H3BLW0;Q86Z02-4;Q86Z02-3 Q5SQL3 HIPK1 Homeodomain-interacting protein kinase 1 1 GSTIYTGYPLS(0.993)PT(0.007)K 142.91 9.73E-06 39881000 101440 95667 69753 75722 77692 73849 66898 85122 90162 90636 TRUE FALSE 97475.61265 92938.67083 82358.91875 79630.02149 80191.03374 75342.27738 67716.71774 83364.20095 79927.18775 84497.14299 1.15359655 1.099903116 0.974694716 0.942398982 0.949038404 0.891654732 0.801408371 0.986591949 0.945915861 1 16.36661494 4.280120259 1.578174569 0.923340694 1.170815404 0.690694437 0.052147379 0.277040806 1.150471893 0.014795569 0.081807401 19059.88425 -4.280120259 0.24747471 TEVSETARPS(ph)SPDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEVSETARPSSPDTR 15 1 O75132 O75132 ZBED4 Zinc finger BED domain-containing protein 4 1 TEVSET(0.001)ARPS(0.499)S(0.499)PDTR;T(0.025)EVS(0.022)ET(0.121)ARPS(0.416)S(0.416)PDTR 96.153 0.0023071 835540000 591420 657370 546200 808500 690320 651540 666640 716630 696040 833380 TRUE FALSE 568306.6526 638622.4512 644910.4902 850226.7819 712524.7697 664714.5852 674798.5397 701831.3401 617028.4572 776934.4303 0.731473121 0.821977282 0.830070679 1.094335312 0.917097688 0.855560726 0.868539884 0.903334069 0.794183438 1 19.56743332 4.280220806 2.410058888 0.909993174 0.752715687 0.336735182 0.080723584 0.36182005 4.037283176 0.021082785 0.079220414 19064.29749 -4.280220806 -0.157277487 VQAERPDTMLGVVCGALHVADVSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQAERPDTMLGVVCGALHVADVSLR 25 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 217.84 8.95E-34 2331900000 563030 651400 601170 757100 789550 831370 812710 779510 968650 949280 FALSE TRUE 541026.1651 632822.7098 709814.792 796174.0217 814946.5928 848180.871 822656.1881 763412.8461 858692.9129 884984.4201 0.611339762 0.715066498 0.802064732 0.899647501 0.920859819 0.958413337 0.929571379 0.862628572 0.970291559 1 19.75529253 4.280913397 1.110640425 0.931312877 0.569988542 0.91098391 0.034957059 0.245343996 0.416846244 0.011326753 0.087210223 19094.72453 -4.280913397 -0.361324335 STFS(ph)PAPRPEMPGTVEVESTFLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 STFSPAPRPEMPGTVEVESTFLAR 24 1 Q92576-2;Q92576;E7EVH3;E7ER40 Q92576-2 PHF3 PHD finger protein 3 1 STFS(1)PAPRPEMPGTVEVESTFLAR;ST(0.005)FS(0.995)PAPRPEMPGTVEVESTFLAR 213.44 4.94E-26 960610000 284530 289410 255890 314120 285400 310530 315220 281460 324530 345160 TRUE FALSE 273410.253 281156.3102 302135.0152 330331.7708 294580.1502 316809.1294 319077.7567 275647.7526 287690.7149 321782.0058 0.849675396 0.873747771 0.938943166 1.026570053 0.915464957 0.984545822 0.991596021 0.85662886 0.894054701 1 18.29572413 4.28115869 3.958772304 0.946329778 0.856267067 0.342691844 0.049634953 0.263651002 8.544297157 0.013272339 0.038641173 19105.51242 -4.28115869 -0.090062711 FELSENCSERPGLR ddPTM_BT-474_Pertuzumab_2h_R1 3 FELSENCSERPGLR 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ;; 244 1.32E-17 1157740000 661929 675683 608013 722750 656261 711302 715820 762730 762080 800360 FALSE TRUE 636060.0829 656413.1824 717894.4743 760051.2141 677370.2311 725685.0138 724580.4193 746979.359 675571.8733 746150.9043 0.852455018 0.879732476 0.962130408 1.018629355 0.907819353 0.972571379 0.971090989 1.001110304 0.905409173 1 19.50910791 4.281199692 3.781283685 0.969694403 0.859088305 0.575260339 0.035132146 0.140600658 4.112355446 0.008433558 0.024891812 19107.31627 -4.281199692 -0.110606098 CFSEENHEPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 CFSEENHEPLR 11 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 178.95 7.32E-06 3058770000 1796170 1906150 1650650 1988100 2061780 1981960 2064470 1993970 2353860 2361870 FALSE TRUE 1725973.691 1851788.468 1948959.174 2090706.079 2128099.026 2022036.589 2089735.601 1952793.823 2086659.681 2201898.441 0.783857084 0.840996312 0.885126733 0.949501594 0.966483733 0.918315101 0.949060848 0.886868252 0.947663908 1 21.0703165 4.281549279 1.663187913 0.937570355 0.782774998 0.77046222 0.02938333 0.226463206 1.069756463 0.00814148 0.042871519 19122.70297 -4.281549279 -0.154795357 VKPET(ph)PPRQSHSGSIS(ph)PYPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKPETPPRQSHSGSISPYPK 20 2 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKPET(0.978)PPRQS(0.016)HS(0.007)GSIS(0.999)PYPK;VKPET(0.998)PPRQS(0.002)HSGS(0.001)IS(0.999)PYPK 167.97 2.44E-11 1751410000 2876800 2579200 1210780 815350 1679540 2110100 1305560 1431050 1801760 1090750 TRUE FALSE 2764371.476 2505643.741 1429594.88 857430.3112 1733563.929 2152767.668 1321537.834 1401498.317 1597231.758 1016872.531 2.718503442 2.464068666 1.405874223 0.843203337 1.704799645 2.117047715 1.299610122 1.378243855 1.570729575 1 19.95570741 4.281816382 4.75819138 1.431725901 2.641993513 0.6633947 0.336376075 0.114412317 5.672660076 0.085646118 0.240087922 19134.46756 -4.281816382 1.210267613 VNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_BT-474_Pertuzumab_2h_R1 2 VNVTVDYIRPASPATETVPAFSER 24 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 VNVTVDYIRPAS(0.968)PAT(0.032)ETVPAFSER;VNVTVDYIRPAS(0.998)PAT(0.002)ETVPAFSER 268.13 6.89E-45 2215500000 950520 996130 929830 1091690 1064580 1142800 1169340 1080860 1217040 1286110 TRUE FALSE 913372.6275 967721.3477 1097870.965 1148032.252 1098823.183 1165908.199 1183650.733 1058539.863 1078886.721 1199000.624 0.761778275 0.807106625 0.91565504 0.957490954 0.916449216 0.972399993 0.987197762 0.882851803 0.899821651 1 20.19340098 4.281867945 2.69239349 0.93973175 0.766820134 0.76283941 0.035680056 0.132587279 1.875862966 0.009474542 0.032983576 19136.73948 -4.281867945 -0.172911617 AAGGATAGS(ph)RQPS(ph)VETLDSPTGSHVEWCK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGGATAGSRQPSVETLDSPTGSHVEWCK 29 1 F8WA39;Q13613;Q13613-2;E9PPP8;Q8NEC6 F8WA39 MTMR1 Myotubularin-related protein 1 2 AAGGAT(0.462)AGS(0.539)RQPS(0.799)VET(0.198)LDS(0.001)PT(0.001)GS(0.001)HVEWCK 63.282 0.022635 104350000 49406 49076 28293 36603 37559 36073 40674 51293 41778 37532 TRUE FALSE 47475.1589 47676.40053 33406.17447 38492.08522 38767.11935 36802.42078 41171.78058 50233.78163 37035.53659 34989.92421 1.356823713 1.36257513 0.954736977 1.100090557 1.107950938 1.051800528 1.176675329 1.435664202 1.058462898 1 15.09465192 4.282272527 24.95043629 1.142338643 1.359700391 0.361778372 0.126842357 175.3892917 100108.0752 0.034661172 0.094922402 19154.57527 -4.282272527 0.217361749 FSSSIENSDS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSSSIENSDSPVR 13 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 FSSSIENSDS(1)PVR;FSSSIENSDS(1)PVR 249.71 1.34E-17 744510000 363010 348950 340430 371400 323280 381460 396250 364830 361990 420590 TRUE FALSE 348823.1679 338998.2877 401953.2738 390567.9985 333678.5948 389173.3826 401099.426 357296.133 320898.4128 392103.0647 0.889621121 0.864564239 1.02512148 0.996085044 0.850997161 0.992528286 1.022943869 0.911230146 0.818403225 1 18.58087339 4.282857475 24.99277735 0.950134454 0.877092462 0.162424165 0.068064929 250.1752489 141147.6858 0.016666957 0.045643819 19180.39181 -4.282857475 -0.073041992 DGQYFEPVVPLPDLVEVSSGEENEQVVFSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGQYFEPVVPLPDLVEVSSGEENEQVVFSHR 31 0 P49792;J3KNE0;A6NKT7;O14715;Q99666;J3KQ37;F8VYC4;A0A286YES2;P0DJD0 P49792;F8VYC4 RANBP2;RGPD3;RGPD8;RGPD5;RGPD1 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 1 0 ; 177.34 4.05E-18 78586000 85583 89697 101516 116569 109685 108320 110122 114042 120462 127550 FALSE TRUE 82238.32174 87138.92938 119862.1994 122585.1401 113213.1176 110510.3046 111469.706 111686.9928 106787.6588 118910.9249 0.691596015 0.73280844 1.007999892 1.030898886 0.9520834 0.929353671 0.937421907 0.939249215 0.8980475 1 16.85952174 4.282908398 6.921350955 0.958345002 0.707942678 0.865322478 0.039401838 0.069210213 8.119803591 0.010338551 0.02824465 19182.64095 -4.282908398 -0.250402324 LPDNVTFEEGALIEPLSVGIHACR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPDNVTFEEGALIEPLSVGIHACR 24 0 Q00796;A0A6I8PIS1 Q00796 SORD Sorbitol dehydrogenase 0 194.97 1.16E-18 62462000 46322 47883 45749 58429 52465 52214 53235 53629 53591 57299 FALSE TRUE 44511.68503 46517.42372 54016.86198 61444.52769 54152.58437 53269.80285 53886.50585 52521.54241 47507.57435 53418.08769 0.833269908 0.87081784 1.011209205 1.15025697 1.013749962 0.997224071 1.008768905 0.983216447 0.889353708 1 15.70504071 4.283177624 4.692313062 1.010094211 0.844722118 0.521000803 0.059586704 0.153450211 7.300874326 0.015546244 0.043746964 19194.53628 -4.283177624 -0.165372093 NFGEDMDDERLK ddPTM_BT-474_Pertuzumab_2h_R1 6 NFGEDMDDERLK 12 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YBN4 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;;; 198.49 1.67E-07 4325590000 5196690 4901250 2513760 2380680 3442310 4175630 3199850 3531840 4171610 3323180 FALSE TRUE 4993597.61 4761471.149 2968052.35 2503547.18 3553035.027 4260064.1 3239010.721 3458906.27 3698066.322 3098098.059 1.611826842 1.536901369 0.958024018 0.808091653 1.146843954 1.375057864 1.045483603 1.116461198 1.193656964 1 21.56295138 4.283227432 7.817754063 1.087491658 1.580070857 0.655330329 0.14324189 0.147742219 21.81032584 0.037234592 0.101618105 19196.73777 -4.283227432 0.492579199 FLEFQYLTGGLVDPEVHGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLEFQYLTGGLVDPEVHGR 19 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 237.31 3.24E-24 2659100000 1813540 1845440 1566560 1891710 1818300 1995250 1815020 1808320 2125970 1965650 FALSE TRUE 1742664.852 1792809.858 1849672.24 1989341.38 1876787.271 2035595.322 1837232.758 1770977.56 1884638.798 1832514.775 0.95096906 0.978333099 1.009362798 1.085579995 1.024159421 1.110820688 1.002574595 0.966419253 1.028443986 1 20.8053934 4.283239886 2.835580069 1.028195056 0.956921037 0.310643719 0.039504871 0.360931094 5.695466437 0.011137314 0.037602033 19197.28827 -4.283239886 -0.071274019 YEWDVAEAR ddPTM_BT-474_Pertuzumab_2h_R1 6 YEWDVAEAR 9 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 236.82 7.15E-10 17487010000 8421080 8780800 9037530 10906860 9670680 8850020 10891190 10729180 11306820 12479400 FALSE TRUE 8091974.884 8530380.181 10670812.71 11469764.35 9981746.205 9028973.468 11024479.64 10507618.68 10023317.2 11634159.12 0.695535861 0.733218455 0.917196731 0.985869647 0.857968857 0.776074435 0.947595742 0.903169586 0.861542041 1 23.47186361 4.283433249 5.379962432 0.901729178 0.708013608 0.602844808 0.06232706 0.12415501 8.153358094 0.015401719 0.042631857 19205.83744 -4.283433249 -0.19371557 DNAGQVTLVPEEPEDMWHTYNLVQVGDSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNAGQVTLVPEEPEDMWHTYNLVQVGDSLR 30 0 Q9BRX2 Q9BRX2 PELO Protein pelota homolog 0 ; 379.12 3.06E-137 223103000 157620 168847 151500 186505 176038 186789 193414 186708 216700 222920 FALSE TRUE 151460.0361 164031.6489 178879.4201 196130.5454 181700.4221 190566.0016 195781.0584 182852.4146 192101.1245 207821.4298 0.728798932 0.789291311 0.860736163 0.94374553 0.874310326 0.916969928 0.94206386 0.87985351 0.924356668 1 17.6649849 4.283503054 1.688568779 0.917987976 0.723640796 0.790954323 0.034452763 0.192167807 0.940883887 0.008835487 0.046032003 19208.92471 -4.283503054 -0.19434718 KQPPVS(ph)PGTALVGSQKEPSEVPTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(0.999)PGT(0.001)ALVGSQKEPSEVPTPK 191.51 3.53E-18 520140000 752870 654050 479200 344220 527450 524450 445160 620690 520690 411210 TRUE FALSE 723447.0081 635397.1344 565802.0997 361985.2355 544415.9083 535054.7383 450608.0012 607872.5346 461583.4541 383358.3804 1.887129759 1.657449444 1.475909041 0.944247612 1.420122622 1.395703774 1.175422331 1.585650831 1.204052077 1 18.54833419 4.283552854 2.408944127 1.294234795 1.847281881 0.547925622 0.189494875 0.237118543 2.639914932 0.048400518 0.183010036 19211.1275 -4.283552854 0.553047087 QFCQEGQPHVLEALSPPQT(ph)SGLSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 QFCQEGQPHVLEALS(0.307)PPQT(0.583)S(0.108)GLS(0.002)PSR 122.09 0.00050908 2635200000 138120 153400 131510 171360 171200 168540 175900 172240 161830 175600 TRUE FALSE 132722.1177 149025.1822 155276.7824 180203.9101 176706.8035 171947.9943 178052.7168 168683.1838 143459.7368 163706.4556 0.810732339 0.910319521 0.948507387 1.100774612 1.079412555 1.050343395 1.087634059 1.030400317 0.876323028 1 17.32075169 4.283710623 1.8288728 1.037930975 0.819561569 0.554316879 0.062732062 0.296652754 1.761838947 0.017115483 0.082518222 19218.10772 -4.283710623 -0.218369407 NKPLS(ph)PIKLTPTSVLDYFGTGSVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NKPLSPIKLTPTSVLDYFGTGSVQR 25 2 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 NKPLS(0.999)PIKLT(0.001)PTSVLDYFGTGSVQR;NKPLS(0.911)PIKLT(0.086)PT(0.002)SVLDYFGTGSVQR 175.28 1.04E-12 1921560000 1128520 1001260 577580 543800 680930 669220 627770 654280 692940 558410 TRUE FALSE 1084416.191 972705.0451 681961.5542 571865.5832 702832.7319 682752.0869 635452.837 640768.8894 614280.3562 520588.3933 2.083058717 1.868472401 1.309982249 1.098498527 1.350073764 1.311500786 1.220643497 1.23085512 1.179973207 1 18.98978362 4.283879674 3.014868972 1.218222073 2.049536743 0.912498962 0.095966986 0.061606445 1.10579837 0.023370721 0.076246571 19225.5899 -4.283879674 0.83131467 DRPSAAHIVEALETDV ddPTM_BT-474_Pertuzumab_2h_R1 6 DRPSAAHIVEALETDV 16 1 Q96KB5;Q96KB5-2 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 0 ;;;;; 161.84 7.56E-09 1406680000 541605 590004 612027 803437 687665 693952 728220 711477 773653 894725 FALSE TRUE 520438.4778 573177.6636 722633.8934 844902.4799 709784.3692 707984.1849 737132.1742 696784.7513 685831.1549 834124.4788 0.623933826 0.687160823 0.866338193 1.012921334 0.850933389 0.848775216 0.883719628 0.835348643 0.822216794 1 19.66990317 4.283953411 3.766234507 0.884059592 0.639502134 0.696803501 0.062439783 0.118733448 3.423451078 0.01565779 0.046439123 19228.85439 -4.283953411 -0.244557459 CMIDQAHQEERPIR ddPTM_BT-474_Pertuzumab_2h_R1 4 CMIDQAHQEERPIR 14 1 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 ;;; 236.3 1.75E-17 2023310000 1061720 1090720 1025170 1182760 1206520 1260050 1199470 1127530 1326430 1355310 FALSE TRUE 1020226.809 1059613.734 1210441.024 1243802.385 1245328.812 1285529.074 1214149.473 1104246.111 1175859.227 1263513.647 0.807452149 0.838624685 0.957996004 0.984399645 0.985607726 1.017423973 0.960931032 0.873948702 0.930626456 1 20.26900982 4.283962975 4.240303667 0.958655207 0.815553494 0.684713138 0.03829752 0.136203278 5.110526828 0.011313662 0.032489905 19229.27787 -4.283962975 -0.143101713 EALTYDGALLGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 EALTYDGALLGDR 13 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;; 301.11 1.42E-40 4335700000 3733470 3943590 3668810 4602630 4060890 4164260 4532840 4714430 4668860 4755520 FALSE TRUE 3587561.865 3831122.674 4331845.579 4840172.286 4191512.215 4248464.19 4588314.252 4617075.373 4138870.586 4433424.395 0.80920786 0.86414526 0.977087956 1.09174576 0.945434464 0.95828051 1.034936844 1.041424182 0.933560656 1 22.07999004 4.284028976 3.100480152 1.00485451 0.820183152 0.673102441 0.045748289 0.135812982 2.585456432 0.011711918 0.037657606 19232.20039 -4.284028976 -0.184671358 RYPSSIS(ph)S(ph)SPQKDLTQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RYPS(0.175)S(0.283)IS(0.547)S(0.619)S(0.377)PQKDLTQAK 122.01 0.00018207 523630000 1073800 939100 562780 454650 594700 683220 516380 672200 737500 578270 TRUE FALSE 1031834.709 912317.7875 664486.865 478114.541 613829.0656 697035.1765 522699.6129 658318.8351 653782.0919 539103.2578 1.913983442 1.692287654 1.232578092 0.886870064 1.138611308 1.292953004 0.969572351 1.221136815 1.212721464 1 19.0402021 4.284042055 2.890496223 1.115274396 1.87700478 0.844810243 0.1198712 0.090564284 1.487541502 0.030358738 0.101455695 19232.77962 -4.284042055 0.761730384 YIEHNTR ddPTM_BT-474_Pertuzumab_2h_R1 1 YIEHNTR 7 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 0 73.26 0.049375 19580000 110200 110350 96998 118300 105060 122030 106840 117800 105570 122460 FALSE TRUE 105893.2622 107202.926 114527.6963 124405.4772 108439.3503 124497.5302 108147.5399 115367.3888 93586.13619 114165.6751 0.927540279 0.939011887 1.003171016 1.089692476 0.949841975 1.090498787 0.947285949 1.010526051 0.819739699 1 16.80076943 4.284135814 6.374372082 0.993644992 0.931910772 0.08203212 0.073064513 0.442620119 42.64075732 0.017103511 0.046887262 19236.93217 -4.284135814 -0.06173422 IRVDVADQAQDKDRDDR ddPTM_BT-474_Pertuzumab_2h_R1 6 IRVDVADQAQDKDRDDR 17 3 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 266.23 5.49E-28 10377390000 5632630 5490870 3446920 3663190 4360460 5392000 4263510 4604490 5543800 4607610 FALSE TRUE 5412500.592 5334275.764 4069855.12 3852247.675 4500718.156 5501029.934 4315688.111 4509405.672 4914491.066 4295532.471 1.260030189 1.241819448 0.947462311 0.896803295 1.047767229 1.280639821 1.004692233 1.049789683 1.144093567 1 22.03440555 4.284137449 11.89405578 1.049035744 1.251301964 0.399042982 0.100352529 0.842438362 216.4472303 0.025628668 0.070093203 19237.00462 -4.284137449 0.202266219 VSS(ph)PSPELGTTPASIFR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSSPSPELGTTPASIFR 17 0 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 VSS(0.5)PS(0.5)PELGTTPASIFR;VS(0.165)S(0.835)PSPELGTTPASIFR;VS(0.019)S(0.954)PS(0.027)PELGTTPASIFR;VSS(1)PSPELGTTPASIFR 247.9 2.89E-20 733817000 626560 641466 612115 699702 653698 698432 694508 766425 755497 810675 TRUE FALSE 602073.3425 623172.0177 722737.7969 735813.7041 674724.7898 712554.7736 703007.5967 750598.0559 669736.1479 755767.2602 0.796638561 0.824555456 0.956296779 0.973598279 0.892767953 0.942823024 0.930190594 0.993160323 0.886167188 1 19.5275825 4.284187536 5.08260803 0.947244611 0.805321549 0.698457815 0.035916496 0.094920246 5.412887617 0.008487776 0.023652817 19239.22334 -4.284187536 -0.141923062 GDDLLPAGTEDYIHIR ddPTM_BT-474_Pertuzumab_2h_R1 8 GDDLLPAGTEDYIHIR 16 0 K7EM18;P41567;O60739 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 ;;;;;;; 244.17 4.86E-20 6445066000 6392306 7070463 7291192 9516500 8607060 8352178 9121260 8479228 9508000 10072490 FALSE TRUE 6142487.614 6868820.318 8608872.586 10007647.71 8883913.902 8521064.762 9232888.708 8304128.979 8428691.701 9390271.281 0.654133137 0.731482628 0.916786356 1.065746389 0.946076384 0.90743542 0.983239827 0.884333235 0.897598317 1 23.16273541 4.284288257 3.318455215 0.948898618 0.670514253 0.804980996 0.051489351 0.099063314 2.176053007 0.013582625 0.042293089 19243.6858 -4.284288257 -0.278384365 VLNNMEIGTSLFDEEGAK ddPTM_BT-474_Pertuzumab_2h_R1 5 VLNNMEIGTSLFDEEGAK 18 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;; 313.31 7.37E-61 410721000 959412 909784 614100 743904 663264 680677 683833 767234 900258 690141 FALSE TRUE 921917.1184 883837.8511 725081.5306 782296.9746 684598.4889 694440.7553 692201.9528 751390.3498 798064.486 643397.1354 1.432889685 1.373704983 1.126957972 1.215885076 1.064037204 1.079334546 1.075854888 1.167848454 1.24039173 1 19.29534999 4.284743793 3.740976154 1.1253194 1.421748908 0.728404789 0.069166487 0.108201594 3.069656801 0.017203287 0.051186552 19263.88126 -4.284743793 0.296429509 KDSS(ph)SVVEWTQAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 KDS(0.249)S(0.375)S(0.375)VVEWTQAPK 134.37 2.40E-05 251450000 251270 227330 164400 136660 183100 182790 142250 214410 227520 195950 TRUE FALSE 241450.0906 220846.771 194110.7371 143713.039 188989.5778 186486.139 143990.8981 209982.3586 201692.8834 182678.132 1.321724106 1.208939289 1.062583326 0.786700835 1.034549542 1.020845446 0.788221866 1.149466312 1.104088822 1 17.47894442 4.284774972 2.777779598 0.987749369 1.299507641 0.502507909 0.112292574 0.221535719 3.344905562 0.029311888 0.100474359 19265.2643 -4.284774972 0.311758271 GADDDRPSWR ddPTM_BT-474_Pertuzumab_2h_R1 4 GADDDRPSWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 120.09 0.00055254 6271700000 4961470 5534800 4813780 6590200 5744300 6003660 6362600 6303080 6226070 6992100 FALSE TRUE 4767570.267 5376952.923 5683737.128 6930321.012 5929070.626 6125058.119 6440467.402 6172919.195 5519312.635 6518518.839 0.731388585 0.824873419 0.871936903 1.063174194 0.90957329 0.939639552 0.988026201 0.946981875 0.846712692 1 22.63611276 4.285002371 2.088910803 0.953099174 0.743881796 0.618659748 0.056748617 0.22068001 1.787059373 0.014455707 0.061739739 19275.35438 -4.285002371 -0.209217378 EQDLPLAEAVRPKT(ph)PPVVIK ddPTM_BT-474_Pertuzumab_2h_R1 4 EQDLPLAEAVRPKTPPVVIK 20 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK 121.3 0.0015495 12305870000 13143970 12591960 7294080 6665750 9703870 11165460 9222570 10491920 12041550 9150970 TRUE FALSE 12630289.12 12232849.63 8612282.512 7009770.156 10016003.79 11391233.25 9335438.57 10275258.19 10674643.73 8531166.651 1.480487914 1.433901145 1.009508179 0.821666068 1.174048545 1.335249177 1.094274553 1.204437635 1.251252515 1 23.02431162 4.285210731 8.62686811 1.121932842 1.460016651 0.499148384 0.138281974 0.253811677 42.31371024 0.036031091 0.098442844 19284.60424 -4.285210731 0.338083809 T(ph)TPDQELAPASEPVWERPWSVEEIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPDQELAPASEPVWERPWSVEEIRR 26 2 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.5)T(0.5)PDQELAPASEPVWERPWSVEEIRR;T(0.619)T(0.381)PDQELAPASEPVWERPWSVEEIRR 177.55 1.22E-15 605780000 179678 171363 132381 130333 146767 149808 164029 150394 181342 170278 TRUE FALSE 172655.9851 166475.895 156305.1915 137059.5017 151487.8938 152837.2204 166036.436 147288.3113 160756.8164 158744.9194 1.087631565 1.048700618 0.984631143 0.863394572 0.95428499 0.962784957 1.045932283 0.927830081 1.012673773 1 17.27635089 4.285220923 3.23309766 0.963263778 1.078368452 0.424883212 0.047143539 0.215542025 4.477507312 0.011967611 0.037759382 19285.05683 -4.285220923 0.115104674 LLPGPENHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPGPENHR 9 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 ; 141.02 0.00010771 397980000 564860 577800 496820 586410 584280 598560 622470 541180 691440 691380 FALSE TRUE 542784.6467 561321.7097 586606.4257 616674.6904 603073.8968 610663.2933 630087.9741 530004.4439 612950.63 644552.2168 0.842111209 0.870870808 0.910099152 0.956749002 0.935647852 0.947422532 0.977559238 0.822283176 0.950971254 1 19.29793771 4.285311078 2.429433003 0.930066498 0.845864416 0.345644883 0.045131597 0.394027072 4.465495303 0.012334217 0.046479075 19289.06061 -4.285311078 -0.084202082 YNTIETFNELFDAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 YNTIETFNELFDAHK 15 0 Q8N3C0 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 0 102.58 0.0031832 0 123560 124840 103830 125410 119090 129020 135790 125850 153570 142180 FALSE TRUE 118731.1386 121279.6854 122594.3907 131882.4251 122920.638 131628.8728 137451.8386 123251.1535 136137.3774 132550.022 0.895745899 0.914972956 0.924891515 0.994963435 0.92735283 0.993050554 1.036980882 0.929846346 1.027064163 1 17.01617738 4.285364847 0.596669075 0.991427655 0.857394306 0.5253829 0.033397449 1.975422488 0.769441075 0.017481265 0.169907477 19291.44891 -4.285364847 -0.13403335 MLGEDS(ph)DEEEEMDTSER ddPTM_BT-474_Pertuzumab_2h_R1 6 MLGEDSDEEEEMDTSER 17 0 A0A087X0M4;A0A087WWF4;Q9BWU0;H7C256 A0A087X0M4 SLC4A1AP Kanadaptin 1 MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER 306.37 4.72E-47 1380380000 1354580 1410470 1344600 1584530 1491370 1599910 1563770 1609330 1738280 1866910 TRUE FALSE 1301641.516 1370244.777 1587599.13 1666307.783 1539341.27 1632261.276 1582907.885 1576096.773 1540957.742 1740462.523 0.747871039 0.787287723 0.912170822 0.957393659 0.88444379 0.937831901 0.909475421 0.905562029 0.88537255 1 20.73103932 4.285688764 3.715663731 0.920279069 0.756739242 0.783063307 0.033187298 0.088352476 2.46555873 0.007707133 0.023011289 19305.84274 -4.285688764 -0.163539828 PMIHELLTEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 PMIHELLTEGR 11 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 124.42 0.00034944 510720000 304140 264140 276750 257290 294360 301600 306330 232290 358820 362080 FALSE TRUE 292253.8726 256606.9858 326764.8813 270568.7677 303828.3567 307698.5586 310078.9582 227493.1303 318088.2579 337555.9991 0.865793745 0.760190862 0.968031622 0.801552242 0.900082823 0.911548186 0.918600052 0.673941897 0.942327373 1 18.36476733 4.285755199 24.99999878 0.86747389 0.812992602 0.059756127 0.092883916 414.5862333 219608.5285 0.022774234 0.062369519 19308.79622 -4.285755199 -0.054481287 AEIDYSDAPDEFRDPLMDTLMTDPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEIDYSDAPDEFRDPLMDTLMTDPVR 26 1 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 0 ;;; 138.93 3.18E-06 159471000 74798 81180 80438 95076 96778 94008 95790 98389 112174 117753 FALSE TRUE 71874.81147 78864.82588 94974.93593 99982.88375 99890.95226 95908.90617 96962.30667 96357.23277 99440.47779 109777.4844 0.654731814 0.718406204 0.865158611 0.910777691 0.909940256 0.87366646 0.883262239 0.877750417 0.905836732 1 16.74422266 4.285776203 2.518919571 0.899651146 0.659571324 0.867739148 0.034506554 0.089880033 1.101325981 0.008324894 0.030555795 19309.73006 -4.285776203 -0.240079821 KPS(ph)PQPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(0.826)PQPS(0.182)S(0.992)PR;KPS(0.997)PQPS(0.004)S(0.998)PR;KPS(1)PQPS(0.171)S(0.829)PR;KPS(0.996)PQPS(0.165)S(0.839)PR 110.38 0.0012657 6539500000 3062170 2996590 2243330 2461950 2620840 2658080 2756130 2880220 3091120 2765750 TRUE FALSE 2942497.011 2911130.187 2648749.634 2589011.535 2705141.699 2711828.199 2789860.343 2820742.45 2740229.017 2578423.289 1.141200137 1.129035019 1.027274942 1.004106481 1.049145697 1.051738949 1.082002461 1.093979589 1.062753749 1 21.29805769 4.285970209 8.105392205 1.052561734 1.136006653 0.590820612 0.029185158 0.201001971 29.87750381 0.007961843 0.021764938 19318.35796 -4.285970209 0.083444919 NVSEELDR ddPTM_BT-474_Pertuzumab_2h_R1 4 NVSEELDR 8 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;;; 160.74 0.00127 202427000 1212026 1244700 1174164 1459930 1326264 1175662 1398280 1417656 1473067 1542070 FALSE TRUE 1164658.684 1209202.375 1386361.554 1535277.162 1368924.486 1199434.691 1415392.569 1388380.908 1305850.61 1437624.225 0.810127336 0.841111574 0.964342093 1.067926608 0.952213007 0.834317251 0.984535836 0.965746739 0.908339319 1 20.45525519 4.286128441 4.867246471 0.959447362 0.819725342 0.470475014 0.057141263 0.169594155 8.621553778 0.014634239 0.04109765 19325.39776 -4.286128441 -0.13972202 EWETIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EWETIR 6 0 Q9NRN7;E9PLW6;E9PNF3 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 ; 114.02 0.059648 231850000 297210 317290 317800 398890 329380 330440 392120 408420 392800 458610 FALSE TRUE 285594.7046 308241.1999 375233.5294 419476.7607 339974.8068 337121.7232 396918.8819 399985.9843 348210.9908 427547.9362 0.667982887 0.720951205 0.877640839 0.981122174 0.795173542 0.78850041 0.928361122 0.935534826 0.814437309 1 18.70572666 4.286539002 3.794611149 0.889535011 0.680781139 0.559374769 0.070168288 0.156785781 4.570201371 0.017687286 0.052505335 19343.67566 -4.286539002 -0.208753872 ASSPS(ph)PLTIGTPESQR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASSPSPLTIGTPESQR 16 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 ASS(0.001)PS(0.999)PLTIGTPESQR;ASSPS(0.957)PLT(0.043)IGTPESQR;ASSPS(1)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR 440.7 6.61E-182 2216800000 1118730 1154050 1116790 1366740 1268660 1233970 1282310 1320040 1348390 1426820 TRUE FALSE 1075008.795 1121137.624 1318618.796 1437277.615 1309467.601 1258921.719 1298003.293 1292780.713 1195326.42 1330180.211 0.808167785 0.842846417 0.991308385 1.080513455 0.984428719 0.946429445 0.975810107 0.971883886 0.898619909 1 20.34319028 4.287079213 5.027270298 0.98189269 0.819049762 0.674929919 0.043354391 0.110823546 6.023748608 0.011239664 0.031463257 19367.75189 -4.287079213 -0.162842928 GEIIDNDTEEEFYLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEIIDNDTEEEFYLRR 16 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 195.23 1.37E-10 163820000 101520 105860 96018 111120 113320 117780 112070 123180 128170 127160 FALSE TRUE 97552.48616 102840.9764 113370.5885 116854.9165 116965.0407 120161.5923 113441.5462 120636.29 113620.6789 118547.3399 0.822898989 0.867509777 0.956331779 0.985723649 0.986652596 1.013616943 0.956930339 1.017621231 0.958441404 1 16.85510377 4.287177332 1.858584536 0.990407704 0.817889792 0.901983039 0.018895417 0.100905985 0.62148441 0.004677002 0.022365591 19372.12807 -4.287177332 -0.172517912 EHQEDPEMLIDLMYR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHQEDPEMLIDLMYR 15 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0;K7ESB7;Q96HP0 Q96N67-2;K7ESB7;Q96HP0 DOCK7;DOCK6 Dedicator of cytokinesis protein 7;Dedicator of cytokinesis protein 6 0 ;;; 154.82 2.41E-06 115094000 159685 167319 167823 194928 201895 219986 197241 152247 236862 229179 FALSE TRUE 153444.3337 162547.2259 198152.3493 204988.2574 208389.136 224434.2676 199654.8944 149103.0462 209974.4188 213656.5022 0.718182373 0.760787639 0.92743421 0.959429062 0.975346567 1.05044436 0.934466737 0.697863368 0.98276634 1 17.7049337 4.287283075 4.399820574 0.924293462 0.729655952 0.439764994 0.089795447 0.225041791 9.049040694 0.025795881 0.073789217 19376.84544 -4.287283075 -0.194637511 TCLS(ph)PGSSEMSLQPDLVR ddPTM_BT-474_Pertuzumab_2h_R1 3 TCLSPGSSEMSLQPDLVR 18 0 Q6UB98-2;Q6UB98 Q6UB98-2 ANKRD12 Ankyrin repeat domain-containing protein 12 1 TCLS(1)PGSSEMSLQPDLVR;TCLS(0.999)PGS(0.001)SEMSLQPDLVR;TCLS(1)PGSSEMSLQPDLVR 387.62 1.64E-126 388480000 231976 236156 205829 247550 257708 232639 233646 264725 236853 250332 TRUE FALSE 222910.1215 229421.0621 243026.8789 260326.0852 265997.4119 237343.12 236505.4296 259258.3362 209966.4404 233376.7907 0.955151199 0.983050034 1.04134982 1.11547547 1.139776629 1.016995389 1.013405956 1.110900255 0.89968861 1 17.83230157 4.287426436 3.417076116 1.05330707 0.961733248 0.153447377 0.06641458 0.35786876 8.334700684 0.016454368 0.050810879 19383.24281 -4.287426436 -0.091573823 GSGNLEAIHIIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSGNLEAIHIIK 12 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 99.671 0.0015871 0 369150 380850 396890 434430 374660 446230 486620 441610 482700 553270 FALSE TRUE 354723.2099 369988.5309 468616.8518 456850.9844 386711.2792 455253.0763 492575.4011 432490.5992 427905.9196 515796.5301 0.687719264 0.717314889 0.908530446 0.885719383 0.749736101 0.88262144 0.95498006 0.838490711 0.829602168 1 18.97644254 4.287440605 6.634671763 0.873149202 0.698962743 0.540897566 0.065561196 0.149018436 14.85698921 0.015627416 0.042904536 19383.87521 -4.287440605 -0.174186459 EQYAQEHGLNFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQYAQEHGLNFQR 13 0 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 ; 142.45 3.92E-05 2156100000 1447090 1471810 1371550 1518970 1597440 1626830 1554200 1692000 1579210 1718180 FALSE TRUE 1390536.123 1429835.42 1619419.595 1597364.224 1648823.108 1659725.617 1573220.765 1657059.609 1399944.701 1601806.138 0.868105128 0.892639493 1.010995998 0.997226934 1.029352472 1.036158857 0.982154286 1.03449448 0.873978859 1 20.61126812 4.287665773 5.124985335 1.000626496 0.875659202 0.51484358 0.044628712 0.134174868 7.582454219 0.010481786 0.029292535 19393.92774 -4.287665773 -0.124967293 KRNEDEDSPNKLYTLVTYVPVTTFK ddPTM_BT-474_Pertuzumab_2h_R1 1 KRNEDEDSPNKLYTLVTYVPVTTFK 25 3 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 117.64 0.0004231 327180000 493760 435680 235730 170410 227970 358820 274820 282900 300640 250940 FALSE TRUE 474463.3133 423254.833 278331.6548 179204.8805 235302.8621 366075.5862 278183.3294 277058.0161 266512.6076 233943.6103 2.028109734 1.809217326 1.189738221 0.766017419 1.005810169 1.564802671 1.189104199 1.184294009 1.139217298 1 17.8358013 4.287749995 3.72114765 1.136044518 1.976113139 0.735557721 0.191267803 0.11397817 3.178200957 0.051015631 0.152642014 19397.68914 -4.287749995 0.840068621 FELINIDDLEDDPVVNGER ddPTM_BT-474_Pertuzumab_2h_R1 3 FELINIDDLEDDPVVNGER 19 0 Q9BQ70;H3BMJ8;Q9H7D3;H3BSP8;H3BTU3 Q9BQ70 TCF25 Transcription factor 25 0 ;; 222.16 5.81E-19 96749000 88738 94994 83773 105114 96205 98567 104011 115804 105230 117616 FALSE TRUE 85270.02085 92284.86413 98912.64462 110538.9461 99299.5212 100560.0923 105283.9177 113412.6069 93284.73156 109649.7636 0.777658046 0.841633043 0.902078048 1.008109298 0.905606341 0.917102682 0.960183719 1.034316931 0.85075178 1 16.74254318 4.287757356 1.932720061 0.957094263 0.780066671 0.556887381 0.051811129 0.276718659 1.868923454 0.013850838 0.0638911 19398.01791 -4.287757356 -0.177027592 SVCPGGS(ph)SPGSSSGGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVCPGGSSPGSSSGGGR 17 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 SVCPGGS(0.5)S(0.5)PGSSSGGGR 140.49 1.18E-05 0 138380 142410 135350 162340 162840 162190 156310 155570 152360 169420 TRUE FALSE 132971.9566 138348.6062 159810.7558 170718.3869 168077.8965 165469.5929 158222.9685 152357.4251 135064.7315 157945.0325 0.841887551 0.875928822 1.011812485 1.08087215 1.06415437 1.047640374 1.001759701 0.964623089 0.855137572 1 17.26906304 4.287768052 4.723916601 1.006400979 0.851954414 0.485641775 0.059632405 0.170609338 8.019904925 0.016022394 0.045278059 19398.49566 -4.287768052 -0.154446565 DYEEVGVDSVEGEGEEEGEEY ddPTM_BT-474_Pertuzumab_2h_R1 15 DYEEVGVDSVEGEGEEEGEEY 21 0 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 ;;;;;;;;;;;;;; 362.44 5.85E-96 7185720000 10767182 11291948 10090717 12110917 11402470 12149676 12555422 12786063 13965920 13923504 FALSE TRUE 10346388.62 10969912.7 11914334.03 12735962.88 11769240.8 12395350.77 12709079.01 12522026.33 12380567.31 12980452.67 0.797074562 0.84511018 0.917867376 0.981164771 0.906689551 0.954924384 0.979093667 0.964683332 0.953785482 1 23.62983736 4.287832355 1.74540259 0.960987006 0.791603168 0.854364476 0.023488823 0.15080324 0.798171538 0.006289284 0.032016321 19401.36808 -4.287832355 -0.169383838 VQLS(ph)ESPASLPSCPPVETALINQR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQLSESPASLPSCPPVETALINQR 24 0 H7C3T2;Q2TAZ0-3 H7C3T2 ATG2A Autophagy-related protein 2 homolog A 1 VQLS(0.372)ES(0.255)PAS(0.372)LPSCPPVETALINQR;VQLS(0.577)ES(0.415)PAS(0.008)LPSCPPVETALINQR 131.37 3.65E-05 212930000 104760 114565 97637 142790 103894 136609 121341 110148 134707 147964 TRUE FALSE 100665.8634 111297.7184 115282.1778 150159.409 107235.8449 139371.3276 122826.0075 107873.4053 119415.6261 137942.2665 0.729768083 0.806842755 0.835727734 1.088567071 0.77739657 1.010359849 0.890416046 0.782018507 0.865692794 1 17.07370505 4.287845777 2.58520388 0.899307349 0.747410036 0.272526903 0.095435319 0.407588567 5.276600158 0.024470436 0.088460928 19401.96769 -4.287845777 -0.151897312 ASS(ph)HS(ph)SQTQGGGSVTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.016)S(0.984)HS(0.602)S(0.392)QT(0.006)QGGGSVTKK 126.22 0.00015509 591650000 1434200 1166700 501160 382690 542590 510380 266860 619780 440550 292950 TRUE FALSE 1378149.878 1133426.858 591730.7602 402440.6768 560042.9001 520700.2333 270125.9125 606981.3264 390540.6109 273108.2356 5.046167413 4.150101354 2.166652935 1.473557456 2.050626188 1.906570969 0.989080069 2.222493676 1.429984746 1 18.05911329 4.287945169 2.402393666 1.657599663 5.000010333 0.904560461 0.391036596 0.07895673 0.872394986 0.096692368 0.369265521 19406.4085 -4.287945169 3.342410669 ESESVDKVMDQK ddPTM_BT-474_Pertuzumab_2h_R1 6 ESESVDKVMDQK 12 1 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4;D6RBQ9 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;;;; 202.29 1.26E-07 7360730000 20250150 19027700 10979980 9597910 13532910 16796360 12868790 15405580 16959910 13137470 FALSE TRUE 19458751.75 18485048.63 12964306.63 10093259.29 13968208.34 17135993.91 13026282.1 15087449.39 15034692.12 12247657.46 1.588773349 1.509272177 1.058513163 0.824097124 1.140479997 1.399124197 1.063573353 1.231864089 1.227556549 1 23.5460025 4.288000727 6.188324508 1.129204143 1.559743456 0.580245124 0.146529226 0.141324188 12.07912609 0.037856969 0.104274196 19408.89126 -4.288000727 0.430539313 (ac)S(ph)GDEMIFDPTMSK ddPTM_BT-474_Pertuzumab_2h_R1 16 SGDEMIFDPTMSK 13 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 S(0.996)GDEMIFDPT(0.003)MSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(0.999)GDEMIFDPT(0.001)MSK 84.658 3.27E-24 4720292000 9570430 9390180 8212360 8666300 9128420 9350800 8969460 10213500 10076380 10006070 TRUE FALSE 9196407.015 9122381.26 9696516.135 9113568.782 9422043.92 9539879.583 9079230.935 10002587.66 8932551.586 9328349.966 0.985855703 0.977920135 1.039467448 0.976975437 1.010044001 1.022675995 0.973294416 1.072278344 0.957570376 1 23.15319048 4.288085743 24.99827824 1.010241783 0.981887793 0.077686071 0.031999599 236.9602174 119603.7495 0.007388081 0.020233024 19412.69104 -4.288085743 -0.02835399 LDKDNLSYIEHIFEISR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDKDNLSYIEHIFEISR 17 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 206.98 3.90E-12 1898060000 1864770 1950100 1931290 2280180 2080480 2040910 2301240 2255160 2657430 2779520 FALSE TRUE 1791892.727 1894485.057 2280317.064 2397860.363 2147400.529 2082178.599 2329403.263 2208590.158 2355769.687 2591260.635 0.691513892 0.73110556 0.880002974 0.925364408 0.828708815 0.803538853 0.898945954 0.85232266 0.909121088 1 21.3052227 4.28814582 4.355095462 0.878124085 0.70215732 0.64282157 0.052374741 0.120659638 4.725326721 0.01242031 0.03563818 19415.37667 -4.28814582 -0.175966765 EYEELLASVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYEELLASVR 10 0 Q8WVV4-1;Q8WVV4 Q8WVV4-1 POF1B Protein POF1B 0 96.665 0.015321 131020000 53619 54619 51613 62042 57173 55783 62548 61678 58917 62661 FALSE TRUE 51523.5102 53061.3196 60940.61722 65243.99506 59012.02147 56910.97048 63313.48113 60404.32775 52228.98916 58416.91466 0.88199643 0.908321159 1.043201572 1.116868213 1.010187235 0.974220751 1.083821039 1.034021192 0.894073052 1 15.83409854 4.288223749 5.751089679 1.026059129 0.89112702 0.42470233 0.057636139 0.16635951 12.09558328 0.014169904 0.039206693 19418.86083 -4.288223749 -0.134932109 AKEVELVS(ph)E ddPTM_BT-474_Pertuzumab_2h_R1 2 AKEVELVSE 9 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AKEVELVS(1)E;AKEVELVS(1)E 118.77 0.0024626 3119500000 3789300 3666400 2849700 2948100 3105500 3693000 3282600 3491800 3662200 3425100 TRUE FALSE 3641209.967 3561837.862 3364704.181 3100251.794 3205391.228 3767674.99 3322773.441 3419693.11 3246482.409 3193114.926 1.140331636 1.11547437 1.053737263 0.970917698 1.003844616 1.17993717 1.040605652 1.070958355 1.016713299 1 21.60653305 4.288245172 3.830141342 1.046420859 1.133807874 0.290650488 0.05393434 0.292237264 8.658096486 0.013858604 0.041107063 19419.81873 -4.288245172 0.087387015 ESNTAGNDVFHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESNTAGNDVFHK 12 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 102.87 0.0023072 347160000 218690 245150 212370 276510 269650 270810 268210 291320 288750 299040 FALSE TRUE 210143.353 238158.562 250749.9831 290780.7142 278323.5371 276285.9637 271492.4342 285304.1402 255972.3105 278785.7544 0.753780814 0.854270917 0.899436141 1.043025727 0.998342034 0.991033291 0.973838978 1.023381344 0.918168545 1 18.08879732 4.288541467 1.646421001 0.99390705 0.7550313 0.826246573 0.035409976 0.172060817 0.788893134 0.009302704 0.050250988 19433.07232 -4.288541467 -0.238875751 YSAAVLS(ph)S(ph)AAATVSAVIATK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSAAVLSSAAATVSAVIATK 20 0 Q96HC4-6 Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 2 Y(0.004)S(0.004)AAVLS(0.494)S(0.513)AAAT(0.51)VS(0.472)AVIAT(0.003)K 42.325 0.095475 23617000 38487 25890 23740 11655 15405 14645 10603 15085 17901 13444 TRUE FALSE 36982.88549 25151.64255 28030.34609 12256.51595 15900.51582 14941.13193 10732.76269 14773.48948 15868.95353 12533.42591 2.950740346 2.006765169 2.236447266 0.977906284 1.268648806 1.192102786 0.856331123 1.178727156 1.266130557 1 13.6134932 4.288586873 0.961757813 1.078034699 3.144044861 0.856114948 0.244257975 0.362107269 0.425583464 0.077190499 0.672862651 19435.10419 -4.288586873 2.066010162 up AVSPPHLDGPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVSPPHLDGPPSPR 14 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BRN3;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 1 AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR 181.72 1.03E-06 1672270000 700300 723010 709450 818800 749010 839790 852230 819880 859470 925670 TRUE FALSE 672931.5018 702390.4627 837663.3966 861058.3661 773102.5869 856771.1292 862659.8457 802949.1915 761906.5688 862973.5464 0.779782306 0.81391888 0.970671002 0.99778072 0.895858964 0.992812738 0.999636489 0.930444734 0.882885196 1 19.71895681 4.288618148 5.105136048 0.957555918 0.790388921 0.712018649 0.041302977 0.09746329 5.417893785 0.010147852 0.028399847 19436.50383 -4.288618148 -0.167166997 IISVT(ph)PVKNIDPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 IISVTPVKNIDPVK 14 1 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 IIS(0.011)VT(0.989)PVKNIDPVK 178.51 3.19E-06 1285500000 2198700 2031900 1469200 1298200 1560800 1772900 1741900 1792100 1798900 1744300 TRUE FALSE 2112772.373 1973952.201 1734717.122 1365200.258 1611004.549 1808749.253 1763217.893 1755092.509 1594696.414 1626157.007 1.299242548 1.213875531 1.066758692 0.839525489 0.990682045 1.112284512 1.084285149 1.07928847 0.980653409 1 20.63303513 4.288699638 3.155575914 1.022273828 1.280376453 0.641001649 0.072773779 0.16646169 3.277503242 0.020275426 0.065047829 19440.15118 -4.288699638 0.258102625 ILS(ph)PDSFIK ddPTM_BT-474_Pertuzumab_2h_R1 4 ILSPDSFIK 9 0 Q8IZT6;Q8IZT6-2 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 ILS(1)PDSFIK;ILS(1)PDSFIK;ILS(1)PDSFIK;ILS(1)PDSFIK 218.11 5.68E-07 132201000 278111 309684 373593 415637 429131 387860 468482 434035 444561 515487 TRUE FALSE 267242.1147 300852.1155 441109.5656 437088.0754 442934.3883 395702.7949 474215.4229 425072.0256 394096.299 480572.6063 0.556091028 0.626028433 0.917883291 0.909515169 0.921680476 0.823398566 0.986771648 0.88451156 0.820055687 1 18.87439489 4.288997575 4.532119614 0.905240125 0.57511278 0.836922595 0.056180587 0.066652503 2.838056001 0.013106663 0.037350743 19453.4922 -4.288997575 -0.330127345 TQEDEEEISTS(ph)PGVSEFVSDAFDACNLNQEDLRK ddPTM_BT-474_Pertuzumab_2h_R1 4 TQEDEEEISTSPGVSEFVSDAFDACNLNQEDLRK 34 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 TQEDEEEIS(0.042)T(0.168)S(0.718)PGVS(0.071)EFVS(0.002)DAFDACNLNQEDLRK;TQEDEEEIS(0.01)T(0.036)S(0.952)PGVS(0.002)EFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.002)S(0.998)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.004)S(0.996)PGVSEFVSDAFDACNLNQEDLRK 239.38 2.33E-47 938752000 642291 607120 443920 414790 520218 625653 466908 484797 633317 557597 TRUE FALSE 617189.5576 589805.532 524146.2189 436197.3616 536951.2844 638304.1323 472622.1598 474785.7725 561425.5092 519830.4585 1.187290101 1.134611338 1.008302246 0.839114666 1.032935403 1.227908296 0.909185201 0.913347352 1.080016571 1 18.98768164 4.289530709 3.740233594 0.991869223 1.173831974 0.288709795 0.100947622 0.273704547 7.688464512 0.026577759 0.07956371 19477.38771 -4.289530709 0.181962751 THPYS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 THPYSPK 7 0 M0QZ39;M0R1C6;H0YD59;E9PME6;M0QXT0;B1AQP1;B4DLJ1;Q15853-4;P22415-2;Q15853-3;P22415;Q15853-2;Q15853 M0QZ39 USF2;USF1 Upstream stimulatory factor 2;Upstream stimulatory factor 1 1 THPYS(1)PK;THPYS(1)PK;THPYS(1)PK;THPYS(1)PK 131.5 0.003629 1897290000 5458550 4739380 4150610 3884130 4208710 3873950 4905220 2932190 5550410 5309060 TRUE FALSE 5245223.831 4604217.523 4900717.557 4084590.415 4344086.979 3952283.923 4965251.55 2871639.252 4920350.726 4949472.637 1.059754082 0.93024406 0.990149439 0.825257702 0.877686836 0.79852627 1.003187999 0.580190954 0.994116159 1 22.23884338 4.28991541 0.859450663 0.835379269 1.082833131 0.134689093 0.12562398 1.995769141 1.779858062 0.044216384 0.411982844 19494.64852 -4.28991541 0.247453862 EDGLAQQQTQLNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EDGLAQQQTQLNLR 14 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 370.17 9.75E-97 2149330000 560790 591288 507459 637180 566291 634418 708580 628769 678230 710220 FALSE TRUE 538873.7068 574425.0452 599168.1297 670064.9362 584506.2643 647246.3666 717251.814 615784.7004 601240.1738 662116.1668 0.813865805 0.867559311 0.904929014 1.012005098 0.882785066 0.977542007 1.083271864 0.93002517 0.90805844 1 19.33672483 4.290111994 1.347346494 0.97055075 0.801459683 0.48428466 0.054437105 0.565931034 1.563354643 0.01602627 0.105874034 19503.47482 -4.290111994 -0.169091067 GHSERS(ph)DTNEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHSERSDTNEKR 12 2 P30414 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 GHSERS(1)DTNEKR 112.72 0.00064856 89582000 120240 107480 60068 60408 77309 81579 68136 58234 68470 73248 TRUE FALSE 115540.8879 104414.7756 70923.62381 63525.66412 79795.7142 83228.58327 68969.86875 57031.44755 60697.57265 68286.84772 1.691993286 1.529061293 1.038613235 0.930276711 1.168537088 1.218808395 1.010002234 0.8351747 0.888861833 1 16.05932012 4.290266225 3.451974459 1.002550254 1.660371818 0.827253512 0.11067378 0.097561106 2.313101427 0.032384237 0.099959414 19510.40233 -4.290266225 0.657821565 WMDEAQALDTADR ddPTM_BT-474_Pertuzumab_2h_R1 2 WMDEAQALDTADR 13 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 200.93 2.46E-07 507770000 407710 420180 411600 464570 481220 506470 471800 474610 439910 536530 FALSE TRUE 391776.2425 408196.8778 485985.276 488546.5134 496698.8783 516711.1704 477574.0295 464809.1376 389973.2611 500190.3452 0.783254307 0.816083081 0.971600673 0.976721198 0.993019724 1.033029077 0.954784582 0.929264513 0.779649717 1 18.93211768 4.290716723 5.215280023 0.955844843 0.793543936 0.479136487 0.064849279 0.16280332 9.320543794 0.016440902 0.045994246 19530.65115 -4.290716723 -0.162300907 RS(ph)PPWEP ddPTM_BT-474_Pertuzumab_2h_R1 5 RSPPWEP 7 1 F5H8F7;Q9UBL3-2;Q9UBL3-3;Q9UBL3;H0YAQ0 F5H8F7 ASH2L Set1/Ash2 histone methyltransferase complex subunit ASH2 1 RS(1)PPWEP;RS(1)PPWEP;RS(1)PPWEP;RS(1)PPWEP;RS(1)PPWEP 125.16 0.0043178 9382400000 6312860 6448260 5448250 6529630 6669560 6727950 6257640 6743780 6642700 6894080 TRUE FALSE 6066146.452 6264361.938 6432869.971 6866624.987 6884092.455 6863993.759 6334222.87 6604518.586 5888648.544 6427137.821 0.943833262 0.974673659 1.000891867 1.068379919 1.071097687 1.067970526 0.985543339 1.027598718 0.916216317 1 22.61574498 4.290946783 2.532107882 1.023271679 0.949556682 0.224069595 0.044761756 0.417030836 5.157835824 0.011865312 0.043772073 19540.99993 -4.290946783 -0.073714997 TAS(ph)FSESRADEVAPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TASFSESRADEVAPAK 16 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.008)AS(0.945)FS(0.045)ES(0.002)RADEVAPAK;TAS(0.994)FS(0.006)ESRADEVAPAK;T(0.007)AS(0.649)FS(0.344)ESRADEVAPAK 247.36 1.68E-20 1527550000 1042320 998509 474539 520259 746041 862873 637003 763349 799246 651186 TRUE FALSE 1001584.982 970032.501 560298.7534 547109.6293 770038.0863 880320.8833 644798.8333 747585.5764 708518.9448 607080.5922 1.64983858 1.597864457 0.922939657 0.901214166 1.268428107 1.450088991 1.062130533 1.231443709 1.16709207 1 19.21152853 4.290984921 9.789267611 1.1435174 1.626522555 0.608797141 0.159301493 0.278660307 49.33949011 0.040888082 0.111938244 19542.71602 -4.290984921 0.483005155 ETGQTRS(ph)PS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETGQTRSPSPK 11 1 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 2 ET(0.002)GQT(0.014)RS(0.984)PS(1)PK;ET(0.002)GQT(0.02)RS(0.978)PS(1)PK 81.619 0.012051 462530000 2360600 2158900 1042580 964550 1506600 1773540 1207230 1369540 1594600 1089350 TRUE FALSE 2268345.142 2097330.286 1230997.398 1014330.541 1555061.157 1809402.194 1222004.442 1341258.52 1413587.693 1015567.354 2.2335743 2.065180883 1.212127776 0.998782146 1.53122405 1.781666363 1.20327267 1.320698735 1.391919194 1 19.95385449 4.291360732 5.62141256 1.324477986 2.177079049 0.693621871 0.224633947 0.106154688 7.096135423 0.056581492 0.157256824 19559.63437 -4.291360732 0.852601062 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHKVQGR ddPTM_BT-474_Pertuzumab_2h_R1 5 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHKVQGR 36 3 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR;MEFDLGAALEPT(0.005)S(0.016)QKPGVGAGHGGDPKLS(0.979)PHKVQGR;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR;MEFDLGAALEPT(0.12)S(0.12)QKPGVGAGHGGDPKLS(0.76)PHKVQGR;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR 124.59 1.86E-31 10967970000 4314610 3814050 2529750 1983310 2877300 3373550 2895780 2059650 3722050 2911180 TRUE FALSE 4145990.271 3705277.028 2986932.099 2085668.867 2969850.968 3441765.492 2931219.422 2017117.508 3299538.488 2714003.186 1.52762911 1.365244171 1.100563225 0.768484311 1.094269522 1.268150867 1.080035365 0.743225918 1.215745989 1 21.37199098 4.291370967 2.8368527 1.009133463 1.498618957 0.529015326 0.159455194 0.203858526 3.208377077 0.042932817 0.146758047 19560.09532 -4.291370967 0.489485495 RNPS(ph)NQSSLESDSNYPSISTSEIGDTEDALQQVEEIGLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNPSNQSSLESDSNYPSISTSEIGDTEDALQQVEEIGLEK 40 1 Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q9ULV0 MYO5B Unconventional myosin-Vb 1 RNPS(0.346)NQS(0.346)S(0.123)LES(0.144)DS(0.033)NY(0.007)PS(0.001)ISTSEIGDTEDALQQVEEIGLEK 66.419 0.0017238 25985000 13299 15869 12389 15779 17055 17853 16624 18635 15567 18312 TRUE FALSE 12779.26038 15416.43166 14627.96789 16593.35608 17603.58956 18213.99989 16827.44948 18250.18074 13799.89942 17071.71193 0.748563497 0.903039585 0.85685419 0.97197962 1.031155495 1.066911155 0.985691977 1.0690305 0.808348892 1 14.05932012 4.291467882 1.014433648 1.004591161 0.739324081 0.48156947 0.075468901 0.816512622 1.093307376 0.023876945 0.201911798 19564.46074 -4.291467882 -0.26526708 EGTETFADHR ddPTM_BT-474_Pertuzumab_2h_R1 3 EGTETFADHR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;; 131.52 0.00024805 1340690000 897431 914300 847115 1052030 889160 935030 1013880 1013940 1002730 1083100 FALSE TRUE 862358.4044 888225.0592 1000207.524 1106325.394 917760.6389 953936.9472 1026288.167 993001.7847 888904.2942 1009740.672 0.854039486 0.879656612 0.990558816 1.095652998 0.908907271 0.944734597 1.016387866 0.983422588 0.880329295 1 19.94555339 4.29198213 5.287242046 0.979788515 0.86240626 0.383576355 0.056246483 0.189815217 11.06864356 0.013847468 0.03872662 19587.64073 -4.29198213 -0.117382255 EFSIDVGYER ddPTM_BT-474_Pertuzumab_2h_R1 4 EFSIDVGYER 10 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 238.51 7.68E-12 1326480000 1861330 2060800 1696820 2260810 2099620 2153640 2246480 2308260 2254850 2306480 FALSE TRUE 1788587.166 2002028.002 2003473.12 2377490.675 2167156.184 2197188.076 2273973.094 2260593.624 1998888.881 2150260.055 0.831800396 0.931063197 0.931735264 1.105675878 1.007857714 1.021824347 1.057533989 1.051311733 0.929603318 1 21.03607972 4.292243204 1.632693776 1.028461804 0.838775185 0.601276627 0.04832763 0.303575289 1.35973805 0.012798443 0.070291642 19599.4193 -4.292243204 -0.189686619 DAQIGWIQTVEDLHER ddPTM_BT-474_Pertuzumab_2h_R1 2 DAQIGWIQTVEDLHER 16 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 224.19 8.03E-15 495330000 406250 424820 419790 455440 483470 495970 482120 477470 573750 603830 FALSE TRUE 390373.3009 412704.5495 495655.3912 478945.313 499021.2516 505998.8532 488020.3288 467610.0776 508620.3054 562932.0563 0.693464329 0.733133857 0.880488836 0.850804831 0.886467996 0.8988631 0.86692581 0.830668768 0.903519883 1 19.10260128 4.292784711 3.872253078 0.87956034 0.701961697 0.721362175 0.043731928 0.106687128 3.200238213 0.01030252 0.03062354 19623.87239 -4.292784711 -0.177598643 DATSLLAAGEGGLLDEVEPLRPDELER ddPTM_BT-474_Pertuzumab_2h_R1 4 DATSLLAAGEGGLLDEVEPLRPDELER 27 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 0 ;;; 284.33 2.24E-61 452765000 229713 245480 207275 259493 252491 268146 251675 274689 259502 273995 FALSE TRUE 220735.562 238479.1508 244734.2033 272885.4648 260612.6023 273568.0958 254755.0739 269016.5762 230044.4209 255437.0746 0.864148489 0.933612128 0.958099773 1.068307979 1.020261459 1.070980382 0.997330064 1.053161827 0.900591354 1 17.96260841 4.292833388 1.779558086 1.020680802 0.868862881 0.497383815 0.047908905 0.324162667 1.79241501 0.012354399 0.062380795 19626.07201 -4.292833388 -0.151817921 TLALLAFDSPEESPFGDLLHTMQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLALLAFDSPEESPFGDLLHTMQR 24 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 ; 273.51 5.85E-52 250790000 337694 353820 310230 340437 385689 412589 382932 362020 412070 407440 FALSE TRUE 324496.5451 343729.4 366295.462 358006.9944 398095.037 420931.8323 387618.4364 354544.1605 365293.5411 379843.7259 0.854289601 0.9049232 0.964332006 0.942511275 1.048049526 1.108171081 1.020468182 0.933394805 0.961694287 1 18.53504647 4.293070951 1.225480115 1.004377547 0.840255451 0.529140269 0.047692796 0.696787759 1.506082858 0.016511283 0.119993302 19636.81059 -4.293070951 -0.164122096 LEPAS(ph)PPEDTSAEVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEPASPPEDTSAEVSR 16 0 E9PFE2;Q9UHL9-2;Q9UHL9;Q9UHL9-3 E9PFE2 GTF2IRD1 General transcription factor II-I repeat domain-containing protein 1 1 LEPAS(1)PPEDTSAEVSR;LEPAS(0.995)PPEDT(0.002)S(0.003)AEVSR;LEPAS(0.999)PPEDTSAEVSR;LEPAS(1)PPEDTSAEVSR 238.12 9.24E-20 773830000 550561 583520 557260 732140 603652 636002 664880 671910 691750 754240 TRUE FALSE 529044.4674 566878.5809 657969.2782 769925.8331 623069.0148 648862.3962 673017.0003 658034.8237 613225.4401 703154.653 0.752387068 0.806193315 0.935739066 1.094959451 0.886105229 0.922787602 0.957139368 0.935832282 0.872106069 1 19.42348251 4.293666843 3.720187128 0.95052655 0.765776357 0.580147842 0.059120792 0.150800284 4.154460399 0.014755192 0.04447593 19663.77257 -4.293666843 -0.184750192 ATEETGQAQSGQANCQGLS(ph)PVSVASK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATEETGQAQSGQANCQGLSPVSVASK 26 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 ATEETGQAQSGQANCQGLS(0.997)PVS(0.003)VASK 154.33 4.29E-08 398320000 251770 215440 226580 221080 266120 239170 259790 280920 305830 305590 TRUE FALSE 241930.5501 209295.8621 267528.0462 232489.9653 274679.9915 244006.1813 262969.3877 275118.9038 271113.4605 284892.1171 0.849200576 0.734649538 0.939050364 0.816063174 0.964154411 0.856486251 0.923049014 0.965695038 0.951635529 1 18.12005618 4.293724047 0.223740272 1.013961317 0.657820156 0.504439491 0.055436276 7.1204998 0.378949322 0.094134496 0.707255162 19666.36283 -4.293724047 -0.356141161 DAEDALHNLDR ddPTM_BT-474_Pertuzumab_2h_R1 6 DAEDALHNLDR 11 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 ;;;;; 191.29 1.90E-06 6493420000 5956300 6084400 5826910 6497800 6471640 6029280 7181040 6473690 7793140 7842160 FALSE TRUE 5723521.211 5910878.869 6879962.256 6833152.237 6679806.178 6151196.173 7268923.716 6340006.039 6908495.419 7311003.518 0.782863966 0.808490771 0.941042121 0.93463944 0.913664747 0.841361402 0.994244319 0.86718684 0.94494489 1 22.80163802 4.2938575 5.622321143 0.92201283 0.791333032 0.561371377 0.047065608 0.132416988 8.624327033 0.010735964 0.029897888 19672.40697 -4.2938575 -0.130679798 TVSS(ph)PPTSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSSPPTSPR 10 0 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 TVS(0.002)S(0.985)PPT(0.01)S(0.003)PR 94.584 0.0083964 256600000 230520 243270 243230 289730 232920 276940 313040 287900 313180 331820 TRUE FALSE 221511.0235 236332.1778 287187.0716 304683 240412.0833 282539.9165 316871.0772 281954.7644 277629.1194 309345.5358 0.716063424 0.763974748 0.928369859 0.984927742 0.777163578 0.913347321 1.024327299 0.91145574 0.897472526 1 18.23885969 4.293940471 4.169747079 0.927240509 0.728299767 0.579660236 0.065004465 0.144134221 5.027403942 0.016253032 0.047401914 19676.1657 -4.293940471 -0.198940742 GDDGIFDDNFIEER ddPTM_BT-474_Pertuzumab_2h_R1 6 GDDGIFDDNFIEER 14 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ;;;;; 385.73 1.58E-113 5406280000 2238320 2395150 2147060 2669450 2607310 2652770 2658880 2629260 2753580 2952160 FALSE TRUE 2150843.98 2326842.667 2535081.503 2807220.634 2691176.494 2706410.827 2691420.169 2574964.862 2441005.142 2752207.574 0.781497733 0.845445921 0.921108396 1.019988703 0.977824681 0.983359995 0.977913219 0.935599802 0.88692625 1 21.39215785 4.294056339 2.286945446 0.966057091 0.788330345 0.757855221 0.035316349 0.157622062 1.558829825 0.009657392 0.038812245 19681.4159 -4.294056339 -0.177726746 DYVIEDDVNMAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYVIEDDVNMAIR 13 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 187.31 1.64E-05 125078000 198111 206279 180345 216630 224460 213200 217520 222830 223970 237490 FALSE TRUE 190368.6031 200396.1249 212937.3533 227810.3003 231679.9597 217511.0501 220182.0748 218228.4826 198545.8646 221404.5908 0.859822294 0.905112781 0.961756721 1.028932144 1.046409918 0.982414363 0.994478362 0.985654732 0.896755862 1 17.75632561 4.294063257 2.391125606 0.99197042 0.865476229 0.576739616 0.037283951 0.218011854 2.378500385 0.009989902 0.038718154 19681.72942 -4.294063257 -0.12649419 VEPPELPADLQHWISYNEASSQLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEPPELPADLQHWISYNEASSQLLR 25 0 Q8WUY1;H0YAR9 Q8WUY1 THEM6 Protein THEM6 0 147.39 2.37E-07 136260000 39603 45428 42976 56089 52859 46515 58548 71886 58746 41969 FALSE TRUE 38055.27098 44132.43792 50742.7192 58983.76001 54559.25774 47455.56517 59264.52794 70401.52898 52077.40036 39126.40225 0.972623824 1.127945208 1.296892029 1.507518111 1.394435844 1.212878324 1.514694031 1.799335613 1.331004063 1 15.25585484 4.294088302 1.544322552 1.451022678 0.947815092 0.293732588 0.202442488 0.572146248 2.227334573 0.058778838 0.342693218 19682.86448 -4.294088302 -0.503207586 VEVPQPLSWYPEELAWHTNLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEVPQPLSWYPEELAWHTNLSR 22 0 Q08J23;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 164.18 1.43E-11 215220000 97827 101930 93079 113960 106390 94252 116330 117710 124510 119580 FALSE TRUE 94003.81269 99023.0562 109900.4458 119841.4893 109812.131 96157.84002 117753.6813 115279.2474 110376.1468 111480.7401 0.843229177 0.888252591 0.985824509 1.074997252 0.98503231 0.862551145 1.056269282 1.034073215 0.990091622 1 16.76643496 4.294356218 3.260825564 1.002936654 0.852500301 0.498561061 0.054211789 0.198256653 4.159042982 0.014377308 0.045755262 19695.01054 -4.294356218 -0.150436352 S(ph)PEIHR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPEIHR 6 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;Q9Y2W1;A0A3B3ITZ9 E9PK91;Q9NYF8;Q9NYF8-4;Q9Y2W1 BCLAF1;THRAP3 Bcl-2-associated transcription factor 1;Thyroid hormone receptor-associated protein 3 1 S(1)PEIHR;S(1)PEIHR;S(1)PEIHR;S(1)PEIHR;S(1)PEIHR 91.516 0.050144 5039580000 750700 784286 787693 1047988 876673 848934 862081 908654 935906 980978 TRUE FALSE 721361.8141 761918.9312 930046.6472 1102074.786 904871.9832 866100.0271 872631.4052 889889.9774 829665.8745 914535.4863 0.788774 0.833121232 1.016960699 1.205065088 0.98943343 0.947038185 0.954179929 0.973051337 0.907199214 1 19.80267963 4.29450223 5.188457982 0.999537413 0.802993507 0.499397649 0.07565058 0.166545407 9.133644557 0.020149882 0.0565931 19701.63324 -4.29450223 -0.196543906 S(ph)FPLFDNSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SFPLFDNSK 9 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 S(1)FPLFDNSK;S(1)FPLFDNSK;S(1)FPLFDNSK;S(1)FPLFDNSK 133.05 0.00030196 233933000 821520 642129 488294 385806 379908 275772 365206 644908 411856 387898 TRUE FALSE 789414.0902 623816.1096 576539.5878 405717.4939 392128.0858 281348.2988 369675.5003 631590.4244 365103.8335 361625.323 2.182961314 1.725034366 1.594300928 1.121927775 1.084349079 0.778010501 1.0222611 1.746532625 1.009619101 1 18.46413618 4.294940276 1.375919568 1.15487288 2.21217156 0.667041027 0.247611051 0.446588772 1.296423794 0.080911928 0.529681063 19721.51508 -4.294940276 1.05729868 YSISLS(ph)PPEQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSISLSPPEQQK 12 0 Q15057;A0A0U1RQT1;A0A087X1H5;H7C3K3 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 YSISLS(1)PPEQQK 191.19 0.00011199 0 189090 202590 214520 251030 245450 222480 258450 257470 264260 280050 TRUE FALSE 181700.1537 196812.3316 253288.536 263985.6884 253345.1222 226978.698 261612.9884 252153.1545 234262.3127 261081.9641 0.695950616 0.753833503 0.970149496 1.011121888 0.970366234 0.869377166 1.002033937 0.965800742 0.897274975 1 17.99414327 4.295055907 4.413559511 0.96135958 0.711430802 0.8253966 0.043637415 0.074153861 2.897245999 0.01079312 0.03111385 19726.76662 -4.295055907 -0.249928777 DLDGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDGFR 6 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0;C9JTZ5;C9JUW1;F2Z3H1 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 134.12 0.032967 493930000 1104090 1190020 1056640 1348010 1296430 1230800 1280770 1383920 1369760 1438740 FALSE TRUE 1060940.942 1156081.795 1247598.353 1417580.958 1338130.848 1255687.619 1296444.446 1355341.568 1214270.587 1341292.858 0.790983815 0.861916015 0.930146124 1.056876542 0.997642566 0.936177071 0.966563296 1.010474006 0.90529863 1 20.35519284 4.295107066 2.291861702 0.982171716 0.799954279 0.706640844 0.040371824 0.167003775 1.658761571 0.010504106 0.042223047 19729.09055 -4.295107066 -0.182217438 T(ph)KGSPRT(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKGSPRTSPK 10 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 T(0.5)KGS(0.5)PRT(0.664)S(0.336)PK 86.467 0.02172 106980000 586260 515430 125650 106760 278290 339420 193730 192930 256740 155630 TRUE FALSE 563348.3111 500730.4411 148357.7501 112269.8964 287241.4506 346283.305 196100.9257 188945.9281 227595.9515 145089.0415 3.882776434 3.45119408 1.022528983 0.773799973 1.979759792 2.386695104 1.351590194 1.302275666 1.568663968 1 17.14657903 4.295411529 6.041658058 1.453398667 3.732537118 0.792315038 0.460012274 0.086238818 6.377514608 0.120037436 0.332886083 19742.92652 -4.295411529 2.279138451 ESNEEEQVWHFLGK ddPTM_BT-474_Pertuzumab_2h_R1 5 ESNEEEQVWHFLGK 14 0 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4;H0YAK2 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ;;;; 206.63 1.06E-08 2452215000 1076259 1397755 1163264 2143792 1213974 1248831 1961269 1859325 1736906 1565746 FALSE TRUE 1034197.608 1357892.396 1373491.681 2254433.362 1253022.576 1274083.218 1985271.597 1820929.289 1539739.713 1459696.629 0.708501745 0.930256582 0.940943244 1.544453359 0.85841301 0.872841105 1.360057671 1.247471052 1.054835424 1 20.47723713 4.29553033 2.140457368 1.143600557 0.747994572 0.274621541 0.20740923 0.438379715 3.733759062 0.055213842 0.235602618 19748.32792 -4.29553033 -0.395605985 KTETQEKNPLPSKETIEQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTETQEKNPLPSKETIEQEK 20 3 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ; 159.98 1.08E-11 4094500000 6375480 5778230 2543550 1891950 3384270 5060250 3055560 3704280 4326400 2720620 FALSE TRUE 6126319.193 5613440.538 3003226.066 1989593.766 3493128.118 5162571.722 3092954.857 3627785.324 3835285.21 2536349.984 2.415407665 2.213196354 1.184073998 0.784431872 1.377226384 2.035433499 1.219451131 1.430317325 1.512127756 1 21.2743224 4.295577356 5.720773262 1.341205814 2.347309257 0.613968387 0.316260217 0.130035382 8.613876721 0.080681626 0.224648256 19750.46643 -4.295577356 1.006103443 ELSNS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 6 ELSNSPLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELS(0.005)NS(0.995)PLR;ELS(0.005)NS(0.995)PLR;ELS(0.01)NS(0.99)PLR;ELS(0.007)NS(0.993)PLR;ELS(0.021)NS(0.979)PLR;ELS(0.002)NS(0.998)PLR 146.9 0.00057264 32044000000 20870100 21892300 21292800 26330400 24375000 22492200 25535400 26520400 25551200 25849700 TRUE FALSE 20054473.42 21267953.04 25140882.62 27689315.1 25159044.01 22947007.69 25847909.86 25972744.47 22650734.9 24098876.79 0.832174611 0.882528809 1.043238771 1.148987786 1.043992391 0.952202374 1.072577369 1.07775747 0.939908324 1 24.52246257 4.29611864 4.196095013 1.043268519 0.84546225 0.595572521 0.058690643 0.131828429 4.622010993 0.014788364 0.043163877 19775.09782 -4.29611864 -0.197806269 GDTNIKPILQVINIRPITTGNS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDTNIKPILQVINIRPITTGNSPPR 25 2 P27694;I3L524;I3L2M5 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 1 GDTNIKPILQVINIRPIT(0.27)T(0.2)GNS(0.53)PPR;GDTNIKPILQVINIRPIT(0.007)T(0.006)GNS(0.987)PPR 130.03 4.96E-05 495350000 409120 406030 346860 375480 407560 414340 369110 429750 456060 403550 TRUE FALSE 393131.1381 394450.4219 409545.3179 394858.5678 420669.5375 422718.2387 373627.2786 420875.5123 404289.9808 376217.1991 1.04495791 1.048464618 1.088587441 1.049549486 1.118156051 1.123601578 0.99311589 1.11870354 1.07461855 1 18.52120628 4.296175321 8.785244842 1.075878192 1.046435587 0.035900447 0.044009183 0.856994927 119.0111054 0.010079289 0.027642155 19777.67888 -4.296175321 -0.029442605 PSHLTNKFEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 PSHLTNKFEDK 11 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 184.03 3.06E-06 508180000 575040 555910 413960 396510 521910 513640 501700 459990 642750 519710 FALSE TRUE 552566.8011 540055.9911 488771.7805 416973.9286 538697.7091 524026.1527 507839.9547 450491.0458 569787.7146 484509.5788 1.140466206 1.114644611 1.00879694 0.860610289 1.111841195 1.081559944 1.048152559 0.929787698 1.176009184 1 18.88616566 4.296793086 5.280032828 1.020027172 1.132057717 0.181658679 0.084621189 0.301071051 16.7821963 0.02070473 0.058142958 19805.83179 -4.296793086 0.112030545 ASS(ph)HSS(ph)QTQGGGSVTKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.278)S(0.722)HS(0.001)S(0.998)QT(0.001)QGGGSVTKK;AS(0.036)S(0.806)HS(0.186)S(0.968)QT(0.004)QGGGSVTKK 147.08 4.21E-07 866680000 1730500 1395410 620080 478390 650250 597640 356820 738480 592700 423390 TRUE FALSE 1662870.147 1355614.273 732142.2496 503079.7652 671165.8818 609724.6903 361186.8699 723230.1299 525419.1808 394713.4182 4.212854365 3.434426626 1.854870435 1.274544371 1.700387803 1.544727547 0.915061037 1.832291725 1.331140915 1 18.59044604 4.296863786 2.282858549 1.418496486 4.192215092 0.928274425 0.272730367 0.072282152 0.711152545 0.068759482 0.278224394 19809.05631 -4.296863786 2.773718606 up NLLEENFEEHSMS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 NLLEENFEEHSMSPER 16 0 P38398-7;P38398;P38398-4;P38398-8;Q5YLB2 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 NLLEENFEEHS(0.099)MS(0.901)PER 158.33 6.13E-09 31479000 32340 33206 30174 37781 31193 34795 38816 35458 35491 38896 TRUE FALSE 31076.11705 32258.99739 35627.11302 39730.88194 32196.35117 35498.57874 39291.04182 34725.77991 31462.21047 36261.53928 0.85699939 0.889620188 0.982504155 1.095675549 0.887892567 0.978959511 1.083545889 0.957647706 0.867646854 1 15.14615255 4.296891131 4.168877302 0.985049223 0.865888982 0.292190088 0.06805494 0.250933469 8.657940407 0.016882988 0.049396352 19810.3036 -4.296891131 -0.119160241 AQSDGIWGEHEIDYILLVR ddPTM_BT-474_Pertuzumab_2h_R1 5 AQSDGIWGEHEIDYILLVR 19 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ;;;; 271.92 2.45E-39 1128699000 907183 987385 897318 1202029 1131895 1140683 1154468 1016209 1121185 1127667 FALSE TRUE 871729.2854 959225.7466 1059483.323 1264065.861 1168303.431 1163748.392 1168596.725 995223.929 993912.7792 1051289.11 0.829200338 0.912428121 1.007794444 1.202396038 1.111305558 1.106972745 1.111584543 0.946670064 0.945422881 1 20.00372804 4.296917811 2.716183777 1.060702027 0.84475836 0.496984973 0.076699961 0.246171107 3.527441461 0.021867905 0.077559692 19811.52064 -4.296917811 -0.215943667 HKPGGGDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HKPGGGDVK 9 1 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 96.113 0.004559 490220000 969030 884540 673930 589990 692000 799710 754550 686570 1042400 820640 FALSE TRUE 931159.2363 859313.7853 795724.1425 620439.4546 714258.8085 815880.6841 763784.4086 672392.0896 924071.1221 765057.3218 1.217110417 1.123201832 1.040084344 0.8109712 0.93360169 1.06643079 0.998336186 0.878878053 1.207845603 1 19.54520832 4.297037461 2.593854615 0.9743855 1.199640382 0.343813232 0.102049428 0.29282741 3.804773636 0.025938038 0.095012867 19816.97954 -4.297037461 0.225254882 NQYDNDVTVWSPQGR ddPTM_BT-474_Pertuzumab_2h_R1 4 NQYDNDVTVWSPQGR 15 0 P25786;P25786-2;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;; 340.14 5.93E-69 2296620000 763070 777980 663410 835470 747970 754110 745710 874080 847850 793480 FALSE TRUE 733248.3808 755792.7721 783302.9445 878588.7068 772029.1343 769358.6209 754836.222 856029.9425 751605.6225 739736.8928 0.991228622 1.021704851 1.058893983 1.187704325 1.043653685 1.0400436 1.020411756 1.157208665 1.016044528 1 19.4966527 4.297153138 3.289528109 1.076015595 0.998983772 0.132285557 0.058412333 0.39109194 8.331323909 0.014588193 0.04641137 19822.25863 -4.297153138 -0.077031822 GKDETDSPTVHLGLDS(ph)DSESELVIDLGEDHSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKDETDSPTVHLGLDSDSESELVIDLGEDHSGR 33 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 GKDETDSPTVHLGLDS(0.632)DS(0.248)ES(0.12)ELVIDLGEDHSGR;GKDETDSPTVHLGLDS(0.955)DS(0.045)ESELVIDLGEDHSGR 257.08 1.48E-59 236979000 123180 130798 125548 146279 151574 159599 172401 122025 157953 176775 TRUE FALSE 118365.9894 127067.7691 148237.3164 153828.4767 156449.5154 162826.2011 174510.895 119505.1411 140022.8376 164801.8718 0.718232069 0.771033531 0.899488063 0.933414621 0.949318801 0.988011843 1.058913307 0.725144319 0.849643491 1 17.3303731 4.297289133 2.926640951 0.917796634 0.725560394 0.417047885 0.086445812 0.286600134 4.799964754 0.024252209 0.082099115 19828.46675 -4.297289133 -0.19223624 ALLELQLEPEELYQTFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALLELQLEPEELYQTFQR 18 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 238.43 1.63E-23 518710000 860500 954230 845900 1090510 1003850 1150270 1061990 1090200 1108930 1247430 FALSE TRUE 826870.7087 927016.2947 998772.9469 1146791.352 1036139.747 1173529.248 1074986.951 1067686.989 983048.9154 1162940.455 0.711017237 0.79713135 0.858834124 0.98611356 0.890965434 1.009105189 0.924369727 0.918092568 0.845313198 1 20.1493458 4.297380696 1.749720884 0.934836895 0.71096326 0.698350788 0.049416692 0.23702024 1.254049163 0.012916928 0.066982797 19832.64765 -4.297380696 -0.223873635 TIETS(ph)PSLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TIETSPSLSR 10 0 F8W7R3;Q9NVI1-2;Q9NVI1-1;Q9NVI1;H3BP78 F8W7R3 FANCI Fanconi anemia group I protein 1 TIET(0.033)S(0.609)PS(0.358)LSR;TIET(0.188)S(0.809)PS(0.003)LSR 160.88 7.60E-06 471250000 637810 683010 731100 825670 801440 891080 869060 812180 881040 964220 TRUE FALSE 612883.6801 663531.2235 863226.0332 868282.9276 827219.0454 909098.2481 879695.8162 795408.1992 781028.0328 898912.5206 0.6818057 0.738148828 0.960300378 0.965925947 0.920244213 1.011331167 0.978622275 0.884856069 0.868858777 1 19.7778212 4.297563777 4.571130156 0.945274468 0.697169252 0.821620939 0.044689635 0.080254532 3.327462434 0.011728315 0.033659506 19841.01005 -4.297563777 -0.248105216 VSGTLDT(ph)PEKTVDSQGPTPVCTPTFLER ddPTM_BT-474_Pertuzumab_2h_R1 4 VSGTLDTPEKTVDSQGPTPVCTPTFLER 28 1 Q9BYG3;H7BZL0;C9J808 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 VSGTLDT(1)PEKTVDSQGPTPVCTPTFLER;VSGT(0.001)LDT(0.999)PEKTVDSQGPTPVCTPTFLER;VSGTLDT(0.974)PEKT(0.025)VDSQGPTPVCTPTFLER;VSGTLDT(0.978)PEKT(0.021)VDSQGPTPVCTPTFLER 369.41 2.83E-127 2101190000 2076850 1738820 1398812 1099176 1371660 1299491 1248950 1632050 1409530 1335200 TRUE FALSE 1995684.406 1689230.556 1651608.445 1155904.605 1415780.69 1325767.598 1264235.024 1598347.597 1249526.064 1244765.715 1.603261065 1.357067066 1.326842815 0.928612181 1.137387279 1.065074 1.015640943 1.284054966 1.003824293 1 20.2474428 4.297681451 1.57405994 1.087875165 1.596493448 0.724661013 0.106372547 0.277954416 1.131960163 0.029507567 0.170175808 19846.38679 -4.297681451 0.508618283 KVVGSMPTAGSAGS(ph)VPENLNLFPEPGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVVGSMPTAGSAGSVPENLNLFPEPGSK 28 1 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 KVVGSMPTAGS(0.001)AGS(0.999)VPENLNLFPEPGSK 137.69 2.81E-06 457640000 272560 256830 179540 161570 218510 218300 207540 244660 238520 189790 TRUE FALSE 261908.0539 249505.4599 211986.8718 169908.6471 225538.5726 222714.1756 210079.9366 239607.6855 211444.2096 176935.3543 1.48024715 1.410150396 1.198103526 0.960286585 1.274694781 1.258731905 1.187325944 1.354210336 1.195036517 1 17.43286282 4.297703218 4.300508986 1.197707103 1.460804432 0.463125789 0.114219299 0.193104224 7.073943596 0.029112719 0.084620648 19847.38152 -4.297703218 0.263097329 AVELLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVELLR 6 0 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 120.76 0.046406 344550000 311200 330170 337260 444970 394730 366900 393710 382210 385160 400060 FALSE TRUE 299037.96 320753.8749 398210.3843 467934.955 407426.8489 374318.9694 398528.3408 374317.2299 341438.2515 372963.5799 0.801788636 0.860013932 1.067692412 1.25463981 1.092403846 1.003634107 1.068544926 1.003629443 0.91547344 1 18.50867523 4.297783104 4.69080564 1.056243648 0.818883787 0.526522345 0.083782875 0.157526586 6.871978769 0.022235114 0.06353213 19851.03266 -4.297783104 -0.237359861 MS(ph)NELENYFK ddPTM_BT-474_Pertuzumab_2h_R1 2 MSNELENYFK 10 0 Q8TAP9 Q8TAP9 MPLKIP M-phase-specific PLK1-interacting protein 1 MS(1)NELENYFK;MS(1)NELENYFK 143.25 3.60E-05 108257000 148053 158578 171633 208940 204900 160125 193496 207100 199506 229150 TRUE FALSE 142266.9251 154055.5107 202650.9011 219723.4184 211490.7946 163362.8372 195864.0619 202823.3126 176858.9153 213629.4664 0.665951788 0.721134183 0.948609312 1.028525803 0.989988873 0.764701799 0.916840103 0.949416371 0.82787697 1 17.70475113 4.297963877 4.93982073 0.927141018 0.682411756 0.60655472 0.075917981 0.129788018 6.273356193 0.019193548 0.0544068 19859.29727 -4.297963877 -0.244729263 CKELGITALHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 CKELGITALHIK 12 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 87.498 0.0063175 225420000 631820 570740 347170 321690 412390 422240 415380 370530 508790 432250 FALSE TRUE 607127.7759 554463.054 409911.3418 338292.4595 425654.8989 430777.9821 420463.5447 362878.426 451034.2922 402973.3225 1.50662027 1.375929927 1.017217068 0.839490955 1.056285553 1.06899876 1.043402928 0.900502355 1.119265884 1 18.62032481 4.298096139 3.622055989 0.995119264 1.477948885 0.834353731 0.078490076 0.079328602 2.052615987 0.019850732 0.060731247 19865.34623 -4.298096139 0.48282962 NVGESVAAALS(ph)PLGIEVDIDVEHGGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NVGESVAAALSPLGIEVDIDVEHGGKR 27 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 NVGESVAAALS(1)PLGIEVDIDVEHGGKR 81.133 0.0052759 134150000 112890 113720 97194 78070 97695 115310 80124 92680 113550 96826 TRUE FALSE 108478.134 110476.8169 114759.1179 82099.20206 100837.4484 117641.6472 81104.58148 90766.12561 100660.28 90267.88878 1.201735584 1.223877266 1.271317181 0.909506173 1.117091025 1.303250234 0.89848763 1.005519536 1.11512833 1 16.46192524 4.298222457 0.374268438 1.007620634 1.361953731 0.233798778 0.121443151 6.310106887 0.901710427 0.115018614 0.982891817 19871.1251 -4.298222457 0.354333097 EREQQIEEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 EREQQIEEHR 10 1 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 ;;; 152.7 1.06E-05 1295380000 924360 963500 872510 1014630 1002040 1115460 1061280 993480 1159060 1242200 FALSE TRUE 888234.9893 936021.9234 1030191.966 1066995.176 1034271.527 1138015.365 1074268.262 972964.2908 1027488.368 1158064.688 0.766999459 0.808263937 0.889580675 0.9213606 0.893103414 0.982687217 0.92764098 0.840164026 0.887246092 1 20.14328441 4.298268887 2.27869902 0.912692909 0.768218659 0.595323708 0.04378445 0.242854614 2.37820865 0.011988876 0.048715436 19873.24961 -4.298268887 -0.14447425 IQEELEHLNQASEEINQVELQLDEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 IQEELEHLNQASEEINQVELQLDEAR 26 0 Q7L8J4 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 0 ;; 260.14 9.12E-53 139667000 80442 82661 74714 87345 89091 89784 88019 84191 98415 97302 FALSE TRUE 77298.23771 80303.58921 88216.4818 91852.88592 91956.69293 91599.494 89096.20285 82452.42643 87243.34179 90711.64887 0.852131327 0.885262149 0.972493422 1.012580932 1.013725294 1.009787554 0.982191416 0.908950807 0.961765582 1 16.46900021 4.298418905 3.480897083 0.979480767 0.858999007 0.702504096 0.029978374 0.151155485 3.607198639 0.009181883 0.0285426 19880.1156 -4.298418905 -0.12048176 NTADHDES(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NTADHDESPPR 11 0 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 1 NTADHDES(1)PPR;NTADHDES(1)PPR 136.39 6.45E-05 131655000 177118 191294 196104 255630 202555 194018 254460 218171 278280 266790 TRUE FALSE 170196.0327 185838.4824 231544.3551 268823.0949 209070.3655 197941.1769 257574.1576 213665.6926 246690.821 248720.0757 0.684287476 0.747179261 0.93094357 1.080825881 0.840585003 0.795839163 1.035598582 0.859060902 0.991841211 1 17.92416344 4.298611282 4.050312499 0.934677652 0.700448707 0.530289391 0.085684231 0.162550273 5.261234165 0.021121173 0.062376085 19888.92373 -4.298611282 -0.234228945 HQEGEIFDTEK ddPTM_BT-474_Pertuzumab_2h_R1 4 HQEGEIFDTEK 11 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 165.58 2.14E-05 10000090000 9448090 9329710 9177900 9631070 9625580 9632620 10760330 7395190 13458780 12136750 FALSE TRUE 9078848.197 9063635.806 10836550.69 10128130.68 9935195.522 9827398.176 10892018.14 7242476.742 11930995.72 11314717.11 0.802392858 0.801048379 0.957739428 0.895128935 0.878077236 0.868550056 0.962641667 0.640093488 1.054466992 1 23.43169718 4.298800903 24.8439125 0.881868245 0.801719649 0.099395398 0.107167978 182.6803724 75335.64402 0.025966743 0.071112822 19897.60946 -4.298800903 -0.080148596 QEDEVMR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEDEVMR 7 0 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ; 98.933 0.025355 347510000 633940 680450 616490 762580 726950 752660 772820 772300 794740 837480 FALSE TRUE 609164.9239 661044.2322 727903.4567 801936.8452 750333.0069 767879.3009 782278.0023 756351.7351 704524.447 780756.7337 0.780223721 0.846671189 0.932305064 1.027127671 0.961033027 0.983506472 1.001948454 0.968741866 0.902361026 1 19.57451358 4.298806064 2.24004912 0.977375295 0.78560106 0.811798903 0.031850663 0.127845127 1.204736028 0.008208012 0.033876135 19897.84594 -4.298806064 -0.191774236 GQSS(ph)PPPAPPICLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GQSSPPPAPPICLR 14 0 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 GQS(0.015)S(0.985)PPPAPPICLR;GQS(0.02)S(0.98)PPPAPPICLR;GQS(0.02)S(0.98)PPPAPPICLR;GQS(0.038)S(0.962)PPPAPPICLR 181.71 1.69E-06 883060000 971340 1026050 1026420 1308240 1140510 1122600 1211060 1163580 1220670 1416340 TRUE FALSE 933378.9589 996788.0586 1211916.927 1375758.423 1177195.54 1145299.741 1225881.315 1139551.666 1082104.659 1320410.03 0.706885693 0.754907972 0.917833778 1.04191758 0.891537865 0.867381885 0.928409575 0.863028635 0.81952169 1 20.33255457 4.298894315 4.482413737 0.911587133 0.720337792 0.588770063 0.062252762 0.142278689 5.633931436 0.015865086 0.045760611 19901.88968 -4.298894315 -0.191249341 IPEDDGNDLTHTFFNPDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IPEDDGNDLTHTFFNPDR 18 0 G5E9B7;A0A0D9SFG6;Q99418-2;Q99418;M0R2J0;Q15438-3;O43739-2;O43739;K7ENQ8;Q15438-2;Q15438 G5E9B7;K7ENQ8 CYTH2;CYTH1;CYTH3 Cytohesin-2;Cytohesin-1;Cytohesin-3 0 ;;; 226.74 3.35E-19 343301000 103263 116860 121515.4 148435 130714 136080 166995 151979 168008 170160 FALSE TRUE 99227.3678 113527.2672 143475.9359 156095.7481 134918.5345 138831.6308 169038.7348 148840.5805 148936.4362 158634.9116 0.625507757 0.715651215 0.904441112 0.983993665 0.850497114 0.875164423 1.065583439 0.938258666 0.938862919 1 17.27535078 4.299073179 2.514683385 0.948021142 0.632490124 0.791290004 0.057574288 0.12721188 1.545317281 0.01526337 0.057404967 19910.08798 -4.299073179 -0.315531018 MVHIDEEMGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 MVHIDEEMGPK 11 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 133.81 0.001322 0 142990 148070 133150 155880 155710 170050 162410 145990 179560 174430 FALSE TRUE 137401.7927 143847.1886 157213.1669 163924.9855 160718.5536 173488.5275 164397.6222 142975.2555 159177.1016 162615.7007 0.844947887 0.884583641 0.966777293 1.008051404 0.988333555 1.066862097 1.010957868 0.879221716 0.978854446 1 17.31110703 4.299171442 2.783976363 0.983797987 0.850273212 0.560568786 0.044219378 0.23390498 3.526659999 0.013123383 0.045960526 19914.5933 -4.299171442 -0.133524775 IS(ph)SKSPGHMVILDQTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISSKSPGHMVILDQTK 16 1 Q9NWH9;Q9NWH9-3 Q9NWH9 SLTM SAFB-like transcription modulator 1 IS(0.37)S(0.37)KS(0.26)PGHMVILDQTK;IS(0.342)S(0.342)KS(0.315)PGHMVILDQTK 206.74 1.16E-11 1348880000 3109800 2664130 1269010 1079630 1639760 1504360 1224570 1730150 1515850 1101020 TRUE FALSE 2988265.578 2588151.621 1498348.336 1135349.834 1692504.37 1534779.19 1239556.654 1694421.798 1343777.063 1026446.935 2.911271374 2.521466559 1.459742618 1.10609696 1.648896122 1.495234812 1.207618837 1.650764146 1.309153954 1 19.96922761 4.299253758 3.445375302 1.386542751 2.834202829 0.875512084 0.206849522 0.069138213 1.614305859 0.050063474 0.156458039 19918.3683 -4.299253758 1.447660079 up GVTIPYRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GVTIPYRPK 9 1 F8VZX2;Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 0 ; 142.92 9.41E-05 887440000 720450 795500 786180 972030 915360 859650 976580 974910 1053650 1208290 FALSE TRUE 692294.0175 772813.1189 928260.2145 1022196.585 944803.3857 877032.712 988531.6782 954777.7678 934044.0693 1126451.442 0.614579547 0.68605986 0.824057016 0.907448423 0.83874311 0.778580132 0.877562619 0.847597803 0.829191596 1 20.10335369 4.299409376 2.674377473 0.858176465 0.623383828 0.709780508 0.055576046 0.140473333 1.945986736 0.013337822 0.048005634 19925.50678 -4.299409376 -0.234792637 LSALGNVTTCNDYVALVHPDLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSALGNVTTCNDYVALVHPDLDR 23 0 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ;;; 254.25 1.63E-43 4109870000 1834384 1883510 1963237 2298380 1962476 1760033 2289478 2229111 2588470 2482580 FALSE TRUE 1762694.245 1829794.139 2318037.598 2416999.667 2025600.823 1795622.073 2317497.317 2183079.079 2294637.737 2314432.645 0.761609654 0.790601594 1.001557597 1.04431627 0.875204049 0.775836824 1.001324157 0.943245889 0.991447188 1 21.14222715 4.299610332 7.002877085 0.948355995 0.77247557 0.479413206 0.074061513 0.194329968 17.8229251 0.018982287 0.052368416 19934.72882 -4.299610332 -0.175880425 VTNDISPES(ph)SPGVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTNDISPESSPGVGR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 VTNDIS(0.079)PES(0.919)S(0.003)PGVGR 288 1.31E-34 4573000000 935710 996620 986530 1234000 1112700 1248300 1160300 1131600 1152900 1225100 TRUE FALSE 899141.4187 968197.3734 1164817.916 1297686.888 1148491.006 1273541.481 1174500.098 1108232.065 1022027.625 1142122.886 0.787254533 0.847717339 1.019870918 1.136206011 1.005575687 1.115065198 1.028348274 0.970326467 0.89484909 1 20.12328645 4.299636272 3.902358483 1.025208072 0.802012073 0.618354334 0.064679378 0.140715093 4.215684379 0.017036389 0.050913735 19935.91952 -4.299636272 -0.223195998 RPWEEDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPWEEDFR 8 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 0 ; 94.692 0.016322 455210000 531770 538170 541730 627310 634490 551190 608380 591640 589000 629190 FALSE TRUE 510987.8405 522821.9185 639632.6617 659685.5443 654898.9471 562335.4394 615825.5364 579422.4272 522139.1893 586574.4009 0.871139006 0.891313903 1.090454443 1.12464087 1.116480614 0.95867709 1.049867733 0.987807218 0.890149977 1 19.16195459 4.299791287 8.099131233 1.029855766 0.879231568 0.415367977 0.069270278 0.25631883 29.68707078 0.017942569 0.049304857 19943.03665 -4.299791287 -0.150624198 ETIFELEDEVEQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETIFELEDEVEQHR 14 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 0 ; 176.08 2.28E-06 84549000 128725 140032 131660 164334 156322 146675 161541 169672 172360 188867 FALSE TRUE 123694.2847 136038.4245 155453.8908 172815.2974 161350.2391 149640.869 163517.9871 166168.2139 152794.4154 176074.8699 0.70250959 0.772616925 0.882885166 0.981487577 0.9163729 0.849870678 0.928684413 0.943736117 0.867780936 1 17.42582949 4.299797575 2.500537973 0.923108348 0.710547991 0.755041052 0.043244671 0.136100389 1.63282883 0.010928484 0.041330391 19943.32536 -4.299797575 -0.212560357 LPS(ph)PDVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LPSPDVR 7 0 Q9H425;Q9H425-3;Q9H425-2;E5RFY9 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 LPS(1)PDVR;LPS(1)PDVR;LPS(1)PDVR 101.64 0.0093444 1108070000 1417570 1532810 1702850 2262630 1963850 1942120 1880920 1806420 1851840 2044420 TRUE FALSE 1362169.797 1489095.76 2010592.875 2379404.605 2027019.019 1981390.997 1903939.262 1769116.796 1641626.887 1905949.612 0.714693499 0.781288104 1.054903478 1.248408977 1.06352183 1.039582046 0.998945224 0.928207537 0.861317044 1 20.86207855 4.299908881 5.093470052 1.025231073 0.735222893 0.574795148 0.095477533 0.150382305 7.613075871 0.026440899 0.0747501 19948.43735 -4.299908881 -0.29000818 KLNVTEQEKIDK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLNVTEQEKIDK 12 2 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ; 180.48 1.09E-05 4314300000 3064410 2861620 2053850 1944770 2169390 2447440 2434360 2516670 2810230 2555970 FALSE TRUE 2944649.469 2780009.399 2425026.383 2045139.813 2239170.4 2496928.914 2464152.426 2464699.885 2491224.472 2382851.875 1.235766898 1.16667319 1.017699173 0.858274001 0.939701885 1.047874163 1.034119012 1.034348761 1.045480207 1 21.18425784 4.300103693 3.430812117 0.996046419 1.22043542 0.692309288 0.055378402 0.140072492 3.239294686 0.015663283 0.049092076 19957.38763 -4.300103693 0.224389001 DPS(ph)PESNKKGESPSLESR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPSPESNKKGESPSLESR 18 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(0.997)PES(0.003)NKKGESPSLESR 69.72 0.013759 257940000 408250 365160 154600 142890 219550 289930 162530 201240 288340 188210 TRUE FALSE 392295.1387 354745.9943 182539.6591 150264.57 226612.0251 295792.5832 164519.0908 197084.3237 255608.852 175462.3691 2.235779334 2.021778209 1.040335087 0.856392005 1.291513539 1.685789294 0.937631765 1.123228443 1.456773058 1 17.42080213 4.300315887 5.296931151 1.174082841 2.16909589 0.717869701 0.240184734 0.099871645 5.43591465 0.060552893 0.170417158 19967.14112 -4.300315887 0.995013049 RHPTGT(ph)TPPVK ddPTM_BT-474_Pertuzumab_2h_R1 3 RHPTGTTPPVK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 RHPT(0.115)GT(0.712)T(0.173)PPVK;RHPT(0.025)GT(0.488)T(0.488)PPVK;RHPT(0.143)GT(0.429)T(0.429)PPVK 73.887 0.024806 3448550000 2394580 2402850 2171790 2372050 2358840 2454500 2626040 2553560 2541270 2881030 TRUE FALSE 2300997.166 2334323.071 2564280.764 2494471.785 2434714.231 2504131.672 2658178.263 2500828.094 2252795.683 2685895.272 0.856696533 0.869104278 0.954721054 0.9287301 0.906481446 0.932326624 0.989680533 0.931096651 0.838750381 1 21.35697162 4.300400814 6.725868012 0.934123653 0.861206772 0.319800792 0.042205858 0.240101902 20.30361581 0.010021962 0.027703076 19971.04609 -4.300400814 -0.072916881 AKTQT(ph)PPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.125)QT(0.875)PPVS(0.709)PAPQPT(0.176)EERLPS(0.063)S(0.053)PVYEDAASFK 190.27 1.14E-19 6409900000 678460 598120 346380 299670 453680 517900 342750 387220 393970 310350 TRUE FALSE 651945.0331 581062.2032 408978.5712 315136.0046 468273.0292 528372.2928 346944.677 379223.7717 349248.1773 289329.7181 2.253294399 2.008304598 1.41353807 1.089193349 1.618475393 1.826194338 1.199132531 1.310697616 1.207094036 1 18.14235499 4.300437727 3.303361644 1.34840486 2.206148685 0.660664418 0.23184976 0.144132367 3.086840947 0.059902993 0.191041369 19972.74362 -4.300437727 0.857743825 TVLELQYVLDKLGDDEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVLELQYVLDKLGDDEVR 18 1 Q14444-2;Q14444;G3V153;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 286.7 7.09E-40 1440590000 1868130 1772020 1220230 1141380 1366340 1779980 1358220 1571730 1716120 1467600 FALSE TRUE 1795121.414 1721483.725 1440752.705 1200286.759 1410289.567 1815972.415 1374842.303 1539273.226 1521313.252 1368198.145 1.312033218 1.258212293 1.053029278 0.877275534 1.030764128 1.32727297 1.004856137 1.125036773 1.111910039 1 20.38384575 4.300767634 4.9099743 1.071430687 1.295838418 0.391572347 0.109497787 0.206781787 9.689668196 0.027850671 0.079193236 19987.92143 -4.300767634 0.224407731 EIIDLVLDR ddPTM_BT-474_Pertuzumab_2h_R1 12 EIIDLVLDR 9 0 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;;;;;;;;;; 214.29 1.59E-06 18624014000 4188772 4643356 4424397 5448683 5370231 4804487 6141977 5572727 5787375 6590715 FALSE TRUE 4025070.159 4510932.033 5223983.958 5729890.183 5542969.357 4901637.019 6217144.352 5457648.24 5130416.453 6144320.003 0.655087977 0.734162939 0.850213523 0.932550743 0.902129016 0.797750934 1.011852304 0.888242839 0.83498523 1 22.55082192 4.300776676 1.998246502 0.905785735 0.654346273 0.661021124 0.061866272 0.216284711 1.567918169 0.015773853 0.072449034 19988.33759 -4.300776676 -0.251439462 NSDDTVTWDEYNIQMYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSDDTVTWDEYNIQMYDR 18 0 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 201.3 3.30E-15 137530000 29642 33486 36535 46371 33360 38178 49982 48822 42176 50355 FALSE TRUE 28483.55787 32531.01207 43137.68722 48764.21287 34433.0547 38949.98532 50593.69467 47813.80864 37388.3573 46944.411 0.606750777 0.692968798 0.918909968 1.038765038 0.733485711 0.82970442 1.077736276 1.018519726 0.796438948 1 15.51866579 4.300827647 3.526123656 0.934945154 0.62492336 0.52431528 0.106687312 0.17923789 4.375322607 0.028214573 0.08751019 19990.68369 -4.300827647 -0.310021793 SGGPPPKR ddPTM_BT-474_Pertuzumab_2h_R1 6 SGGPPPKR 8 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ;;;;; 111.04 0.0053081 404298000 749563 727631 539896 606711 619661 679155 630377 683864 682954 706306 FALSE TRUE 720269.2493 706879.6763 637467.2171 638023.4274 639592.9588 692887.9794 638091.7423 669741.9694 605427.9251 658467.2655 1.093857337 1.073522882 0.968107681 0.968952385 0.971335999 1.052273994 0.969056133 1.017122649 0.9194503 1 19.3287522 4.300857208 5.705350917 0.986296281 1.087203917 0.589023052 0.033542133 0.128951331 8.040578501 0.007922484 0.022138472 19992.04441 -4.300857208 0.100907636 LNEADHNGDLALDLALSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNEADHNGDLALDLALSR 18 0 Q9P2R3;Q9P2R3-2;Q9P2R3-4 Q9P2R3 ANKFY1 Rabankyrin-5 0 ; 235.84 8.37E-24 460070000 473330 491710 452540 534960 468040 571440 542670 529200 627500 579010 FALSE TRUE 454831.7403 477686.9122 534324.0447 562569.3497 483094.9317 582994.9083 549311.3578 518271.8351 556268.8307 539793.137 0.842603785 0.884944397 0.98986817 1.042194336 0.894963086 1.08003394 1.01763309 0.960130464 1.030522236 1 19.04204711 4.300870264 3.298854365 1.000541075 0.850596802 0.586511966 0.047057477 0.157398906 3.360252229 0.011420113 0.036465066 19992.64542 -4.300870264 -0.149944274 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ;; 267.24 7.75E-60 721930000 248831 258644 252494 270129 304723 302497 313175 294802 288582 292961 FALSE TRUE 239106.4094 251267.7264 298125.2825 284070.3901 314524.692 308613.6966 317007.7293 288714.2357 255823.3812 273118.4905 0.875467673 0.919995295 1.091560231 1.040099444 1.151605266 1.129962662 1.160696695 1.057102487 0.936675436 1 18.05916746 4.30103521 4.296652305 1.080661068 0.886415454 0.521585104 0.066227686 0.151133676 5.453081343 0.016743005 0.04883344 20000.24014 -4.30103521 -0.194245614 HGDPGDAAQQEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGDPGDAAQQEAK 13 0 O14737;O14737-2;Q3HM38;X6R2P6;K7ESJ4 O14737 PDCD5 Programmed cell death protein 5 0 ; 164.68 3.66E-05 2408100000 3777200 3397500 2996000 2894800 3103500 3324400 3251800 2303100 4443100 3844000 FALSE TRUE 3629582.848 3300606.627 3537443.846 3044200.975 3203326.896 3391621.646 3291596.501 2255540.18 3938737.915 3583642.456 1.012819469 0.92102007 0.987108477 0.849471177 0.89387458 0.946417419 0.918505833 0.629398777 1.099087859 1 21.77299527 4.301512655 0.774363747 0.872779721 1.02808924 0.003659818 0.118972952 3.934286814 2.713594383 0.047895757 0.475389008 20022.23965 -4.301512655 0.155309518 VSNEEVTEELLHVNDDLNNVFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSNEEVTEELLHVNDDLNNVFLR 23 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6;B7Z2U2 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 ;;; 278.36 7.82E-52 938100000 292488 317305 264971 354267 309719 349455 331807 331372 360832 369085 FALSE TRUE 281057.2456 308255.7721 312857.1539 372550.7623 319681.3929 356521.2195 335867.7533 324529.0524 319871.8641 344086.5442 0.816821379 0.895866977 0.909239722 1.082724008 0.929072637 1.03613822 0.976114175 0.943161126 0.929626193 1 18.39241195 4.301616079 1.992639688 0.979638287 0.827317782 0.540324364 0.048612839 0.286323201 2.061086474 0.012589454 0.058078024 20027.00838 -4.301616079 -0.152320505 NFGEDMDDER ddPTM_BT-474_Pertuzumab_2h_R1 9 NFGEDMDDER 10 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YBN4 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;;;;;; 228.2 5.12E-09 11601220000 4846646 5110748 4923049 5607552 5396883 5433476 5990683 6178298 6577188 6621499 FALSE TRUE 4657233.716 4964994.471 5812753.467 5896958.431 5570478.643 5543344.607 6063998.771 6050713.987 5830573.192 6173018.975 0.754449927 0.80430572 0.941638685 0.955279492 0.902391304 0.897995718 0.98233924 0.980187168 0.944525396 1 22.5575448 4.302371471 3.200694315 0.950962498 0.762396993 0.83294066 0.031040056 0.095561121 1.916650108 0.00850932 0.027629321 20061.87275 -4.302371471 -0.188565505 KVEGNFNPFAS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVEGNFNPFASPQK 14 1 Q5TH58;Q9H6K1-2;Q9H6K1 Q5TH58 C6orf106 Uncharacterized protein C6orf106 1 KVEGNFNPFAS(1)PQK;KVEGNFNPFAS(1)PQK 149.36 4.60E-06 2257400000 3985300 3492000 2797900 2489100 2690500 2483000 3050300 3217900 3289300 3564500 TRUE FALSE 3829550.07 3392411.579 3303542.769 2617562.749 2777042.376 2533207.961 3087630.484 3151449.24 2915912.454 3323073.24 1.152412178 1.020865727 0.994122768 0.787693367 0.835684975 0.762308796 0.929149092 0.948353832 0.877474628 1 21.66408666 4.302538952 1.782923851 0.877974366 1.141482097 0.586076476 0.072530341 0.314509044 1.735796249 0.020548654 0.105791763 20069.61089 -4.302538952 0.263507731 AKTQT(ph)PPVSPAPQPTEERLPSSPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.048)QT(0.952)PPVSPAPQPTEERLPSSPVYEDAASFK 214.13 1.16E-27 870040000 344140 316330 179680 129010 215950 225230 205430 272450 329090 231480 TRUE FALSE 330690.6283 307308.5781 212152.173 135668.2216 222896.2279 229784.3049 207944.1138 266823.8123 291733.0829 215801.6534 1.532382274 1.424032547 0.983088728 0.628670909 1.032875441 1.064793996 0.963589067 1.236430806 1.351857496 1 17.71934639 4.3026262 5.114425027 1.034877322 1.499057498 0.500944109 0.178636771 0.17148319 8.572797841 0.048051706 0.136034497 20073.64317 -4.3026262 0.464180177 ISQRDPS(ph)PESNK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISQRDPSPESNK 12 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 ISQRDPS(0.998)PES(0.002)NK;ISQRDPS(0.982)PES(0.018)NK;IS(0.001)QRDPS(0.996)PES(0.003)NK 150.81 3.91E-05 1859000000 2341760 2226320 1291760 1390110 1738120 1964640 1556160 1819860 1947400 1639950 TRUE FALSE 2250241.43 2162827.533 1525209.767 1461853.744 1794028.208 2004366.367 1575204.752 1782279.255 1726339.316 1528874.726 1.471828523 1.414653207 0.997602839 0.956163196 1.173430483 1.311007588 1.03030335 1.165745777 1.129156815 1 20.54403877 4.303297835 6.93270744 1.106618939 1.450910005 0.651369225 0.101610164 0.1338711 11.4574953 0.025674074 0.070946476 20104.71102 -4.303297835 0.344291066 VLVTVEEDDTIMEELVDNHGKK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLVTVEEDDTIMEELVDNHGKK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 225.9 3.71E-26 317865000 419420 402530 268359 251736 349970 357030 321691 348690 415360 353550 FALSE TRUE 403028.6027 391050.2385 316857.4409 264728.1251 361227.1029 364249.3912 325627.9507 341489.4296 368210.0741 329603.7436 1.222767067 1.186425355 0.961328404 0.803170869 1.095943568 1.105113028 0.987937659 1.036060531 1.117129527 1 18.3303731 4.303404847 6.458818421 1.01336398 1.209898242 0.439977274 0.086440705 0.193097346 14.62934624 0.022142855 0.061406024 20109.66551 -4.303404847 0.196534262 RS(ph)SLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.454)S(0.454)LDAEIDS(0.023)LT(0.035)S(0.035)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.479)S(0.479)LDAEIDS(0.04)LT(0.001)S(0.001)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 134.64 1.94E-11 10088300000 197397 213942 179935 212951 223600 248759 218578 220617 260110 260762 TRUE FALSE 189682.507 207840.5836 212453.2571 223941.4266 230792.2971 253789.0774 221253.0229 216061.1819 230583.4033 243100.3575 0.780264204 0.854957951 0.873932311 0.921189212 0.949370455 1.043968343 0.910130389 0.888773608 0.948511165 1 17.89119249 4.303407201 1.108484461 0.946968209 0.765875142 0.640517319 0.042528333 0.657164458 1.08921912 0.014532102 0.117907722 20109.7745 -4.303407201 -0.181093067 ESNYFGLS(ph)PEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ESNYFGLSPEER 12 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 ESNYFGLS(1)PEER 125.67 0.00031584 181790000 165070 169140 175150 184520 179670 207010 174900 208870 210050 216820 TRUE FALSE 158618.8819 164316.2928 206803.5012 194043.0993 185449.2487 211195.884 177040.4785 204556.7615 186206.0046 202134.5883 0.784719148 0.812905373 1.023098041 0.959969795 0.917454308 1.044828032 0.875854449 1.011982973 0.921198129 1 17.62495668 4.303493698 6.962855912 0.96750767 0.795012367 0.645900008 0.050522882 0.116832221 10.04475081 0.011183877 0.03090112 20113.78011 -4.303493698 -0.172495303 SEEHS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEHSPPR 8 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 SEEHS(1)PPR;SEEHS(1)PPR 121.9 0.00091048 92850000 171876 189860 165107 225250 197465 224600 216490 186549 217560 240860 TRUE FALSE 165158.8959 184445.3787 194945.5077 236875.1795 203816.6411 229141.5659 219139.4694 182696.698 192863.5009 224546.3377 0.735522555 0.821413436 0.86817496 1.054905557 0.907681876 1.020464499 0.975920924 0.813625819 0.858902901 1 17.77665367 4.303554834 2.236832943 0.93581098 0.74795663 0.473999639 0.071577171 0.323858164 3.035419227 0.020220128 0.084328954 20116.61173 -4.303554834 -0.187854349 YVGFGNT(ph)PPPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 YVGFGNTPPPQK 12 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 YVGFGNT(1)PPPQK;YVGFGNT(1)PPPQK 176.43 0.00027961 534220000 1573230 1695010 1713500 1909950 1966940 1981430 2019170 2201980 2146950 2304470 TRUE FALSE 1511746.432 1646669.974 2023167.567 2008522.748 2030208.411 2021495.872 2043881.206 2156508.344 1903237.237 2148386.194 0.703666052 0.766468328 0.941715029 0.934898369 0.9449923 0.940936912 0.951356517 1.003780582 0.885891578 1 21.03482193 4.303680605 3.005714079 0.954115425 0.711521 0.88241469 0.031818309 0.072937278 1.286065582 0.007929675 0.026684115 20122.43832 -4.303680605 -0.242594425 GKLDDYQER ddPTM_BT-474_Pertuzumab_2h_R1 6 GKLDDYQER 9 1 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;;;;; 147.74 8.36E-05 4940440000 5803200 6052930 5290400 5681110 5949440 6085210 6608420 6853230 7287540 7391340 FALSE TRUE 5576404.528 5880306.363 6246492.964 5974312.768 6140809.141 6208257.116 6689295.821 6711708.406 6460289.011 6890717.958 0.809263209 0.853366282 0.906508292 0.867008751 0.891171164 0.9009594 0.970769064 0.97402164 0.937534964 1 22.71622288 4.303700304 0.233107301 1.012511822 0.697869848 0.836174507 0.023000036 3.577300517 0.202912184 0.042175648 0.325087827 20123.35109 -4.303700304 -0.314641974 NYKGYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 NYKGYEK 7 1 Q14847;Q14847-2;C9J9W2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 95.099 0.012508 2636400000 2984440 2817110 1489950 1507690 2084790 2423190 1847590 2199090 2547120 1850670 FALSE TRUE 2867804.785 2736768.781 1759217.109 1585502.062 2151849.164 2472188.562 1870201.359 2153678.023 2257981.616 1725322.472 1.662184798 1.586236095 1.019645392 0.918959839 1.247215635 1.432884925 1.083972063 1.248275645 1.308730195 1 20.7184346 4.303915186 7.012112855 1.171191311 1.63430227 0.607204111 0.149967372 0.148979085 12.88412806 0.038046418 0.105104534 20133.31023 -4.303915186 0.463110959 SYS(ph)PDGKESPSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSPDGKESPSDK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.005)YS(0.993)PDGKES(0.002)PSDK;S(0.001)YS(0.999)PDGKESPSDK 233.47 3.23E-16 527070000 591830 546810 261500 235700 367990 419480 346890 387360 467260 360180 TRUE FALSE 568700.6293 531215.5142 308758.867 247864.5052 379826.7325 427962.173 351135.3436 379360.8806 414218.6037 335784.6878 1.693646703 1.582012324 0.919514434 0.738165004 1.131161564 1.274513665 1.045715771 1.129774211 1.233583957 1 18.35717692 4.303942487 6.249843413 1.065568239 1.655138575 0.711404114 0.147649293 0.11152078 7.927404331 0.038905906 0.108132533 20134.57594 -4.303942487 0.589570335 VISFIENTST(ph)PVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VISFIENTSTPVDR 14 0 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 VISFIENTS(0.041)T(0.959)PVDR 149.31 8.41E-05 54662000 83471 86595 76524 91654 88016 88766 89573 103740 85484 103120 TRUE FALSE 80208.86104 84125.39539 90353.58907 96384.27392 90847.11457 90560.90934 90669.22117 101597.7327 75780.2147 96135.59055 0.834330559 0.875070251 0.939855766 1.002586798 0.944989406 0.942012306 0.943138963 1.056817066 0.788263891 1 16.55278301 4.303986277 2.624509716 0.961305263 0.839768846 0.265510555 0.065871588 0.337214744 4.480359794 0.016202086 0.059551518 20136.60622 -4.303986277 -0.121536417 ATENDIYNFFS(ph)PLNPVR ddPTM_BT-474_Pertuzumab_2h_R1 6 ATENDIYNFFSPLNPVR 17 0 P52597;P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7 P52597;P31943 HNRNPF;HNRNPH1 "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 1 ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR 248.46 7.51E-21 726796000 714362 725430 689019 765716 791916 790927 734762 779902 891575 866527 TRUE FALSE 686443.9433 704741.4467 813540.0604 805234.6945 817388.6973 806920.0858 743754.2371 763796.7512 790367.1438 807836.3545 0.849731433 0.872381446 1.007060472 0.996779472 1.011824601 0.998865774 0.920674383 0.945484499 0.97837531 1 19.62370355 4.304156478 6.19514222 0.977562514 0.857457013 0.749814605 0.027965394 0.111257774 7.768777125 0.007930548 0.022056465 20144.49931 -4.304156478 -0.1201055 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(ph)PVAPAPVPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR 42 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR 300.23 6.56E-97 8428660000 768676 805188 1042710 1109780 1068370 958450 1048450 1081910 1165770 1218870 TRUE FALSE 738635.2921 782224.8266 1231150.892 1167055.879 1102735.091 977830.5157 1061281.245 1059568.18 1033436.677 1136314.849 0.650026964 0.688387402 1.083459301 1.027053267 0.970448544 0.860527799 0.933967593 0.932460032 0.909463321 1 20.1159312 4.304298885 8.04872523 0.957883815 0.664967711 0.794075661 0.060128826 0.11419469 12.2040861 0.015734367 0.043281328 20151.10588 -4.304298885 -0.292916104 KPLHYAADCGQLEILEFLLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPLHYAADCGQLEILEFLLLK 21 1 P58546 P58546 MTPN Myotrophin 0 ; 128.78 1.14E-05 2973600000 2893300 2625900 2045160 2126400 2023400 2149500 2213700 2150900 2502900 2303200 FALSE TRUE 2780226.637 2551011.903 2414765.906 2236143.759 2088484.499 2192964.363 2240791.923 2106483.163 2218781.285 2147202.213 1.294813605 1.188063187 1.124610385 1.041422063 0.97265385 1.021312455 1.043586817 0.98103623 1.033335972 1 21.03402663 4.304697172 1.121790737 1.007000502 1.329464684 0.941965661 0.023478138 0.182960418 0.312238924 0.007311814 0.058921413 20169.59473 -4.304697172 0.322464182 TS(ph)VQTEDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 6 TSVQTEDDQLIAGQSAR 17 0 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 T(0.001)S(0.999)VQTEDDQLIAGQSAR;T(0.119)S(0.88)VQT(0.001)EDDQLIAGQSAR;T(0.024)S(0.976)VQTEDDQLIAGQSAR;T(0.298)S(0.702)VQTEDDQLIAGQSAR;T(0.018)S(0.982)VQTEDDQLIAGQSAR;T(0.007)S(0.993)VQTEDDQLIAGQSAR 432.59 7.35E-161 4828250000 2141050 2654200 2615300 3996950 2309730 3112400 3833990 3724900 3753890 3942340 TRUE FALSE 2057375.399 2578504.815 3087942.887 4203233.068 2384024.563 3175334.86 3880911.516 3647979.513 3327764.145 3675321.8 0.559781023 0.70157253 0.840182998 1.143636747 0.648657367 0.863961044 1.055937882 0.992560573 0.905434769 1 21.80943914 4.304720099 2.318789619 0.941098068 0.576547133 0.503599882 0.125469389 0.262354895 2.663157353 0.033097251 0.134166105 20170.65955 -4.304720099 -0.364550935 S(ph)PGYESESSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGYESESSR 10 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 S(0.997)PGYES(0.003)ESSR 112.94 0.0016306 257410000 38039 39710 39468 47988 33626 48238 53154 44648 44286 50104 TRUE FALSE 36552.39383 38577.50968 46600.74556 50464.66643 34707.61083 49213.40541 53804.51455 43726.0032 39258.83894 46710.41145 0.782532046 0.825886745 0.997652217 1.08037298 0.743038003 1.053585355 1.15187413 0.936108286 0.840472985 1 15.51145653 4.304734615 4.934232573 0.978519489 0.795280089 0.276529173 0.111207108 0.252699199 11.64287187 0.027644951 0.078777935 20171.33373 -4.304734615 -0.1832394 GLLSGQT(ph)SPTNAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLSGQTSPTNAK 13 0 G3V1P3;Q969J3 G3V1P3 LOH12CR1 Loss of heterozygosity 12 chromosomal region 1 protein 1 GLLSGQT(0.646)S(0.354)PTNAK;GLLSGQT(0.706)S(0.294)PTNAK 245.18 4.86E-16 268000000 982040 1017870 957240 1138040 1141670 1184920 1050980 1143420 1123070 1142240 TRUE FALSE 943660.7911 988841.3442 1130234.562 1196774.381 1178392.852 1208879.894 1063842.208 1119807.977 995583.8019 1064875.067 0.886170425 0.928598457 1.061377617 1.123863651 1.106601975 1.135231664 0.999030065 1.051586249 0.934930146 1 20.02225275 4.304895078 4.152354311 1.058009936 0.89688951 0.489509263 0.059152345 0.168939708 5.626674263 0.015197901 0.044865662 20178.788 -4.304895078 -0.161120426 LS(ph)PEVAPPAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSPEVAPPAHR 11 0 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 LS(1)PEVAPPAHR;LS(1)PEVAPPAHR 125.03 0.0002169 1095090000 853420 852020 909470 922460 867640 847950 924250 1084860 1097110 1105690 TRUE FALSE 820067.4029 827721.2238 1073831.46 970068.2711 895548.4286 865096.13 935561.248 1062457.262 972570.6723 1030800.631 0.795563543 0.802988666 1.041745055 0.941082341 0.868789173 0.839246799 0.907606398 1.030710721 0.943509969 1 19.9753339 4.305357444 11.64951091 0.943489534 0.798777662 0.475463505 0.061823256 0.586580717 99.73676545 0.01642527 0.04500386 20200.28252 -4.305357444 -0.144711873 FEIGEGENLDLPYGLER ddPTM_BT-474_Pertuzumab_2h_R1 8 FEIGEGENLDLPYGLER 17 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;;;; 357.57 1.28E-87 3671101000 1909990 1985881 1822431 2086294 2071988 2307876 2094946 2280435 2460363 2525045 FALSE TRUE 1835345.479 1929245.618 2151784.821 2193967.883 2138635.376 2354542.834 2120584.576 2233343.22 2181072.907 2354021.453 0.779663871 0.819553117 0.914088875 0.932008449 0.908502925 1.000221485 0.900834856 0.948735288 0.926530599 1 21.16669604 4.305380497 1.68983232 0.942887579 0.7684934 0.77179328 0.031571613 0.199771666 0.964999668 0.007964844 0.043534582 20201.35484 -4.305380497 -0.174394178 EAAFDDAVEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EAAFDDAVEER 11 0 Q09028-3;Q09028;E9PNS2;E9PIC4;E9PNS6 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ; 263.6 1.92E-20 408870000 492620 541780 603990 776090 621300 614150 707740 721040 705580 803840 FALSE TRUE 473367.8658 526328.9649 713144.4287 816144.0979 641284.6788 626568.5338 716401.5338 706150.272 625485.5164 749395.2008 0.63166653 0.702338318 0.951626629 1.089070356 0.855736303 0.836098941 0.955972941 0.942293561 0.834653752 1 19.51536721 4.305834365 4.593759887 0.932439418 0.651290523 0.672490641 0.074769913 0.115037378 4.614355268 0.018860212 0.054457207 20222.47767 -4.305834365 -0.281148895 KQS(ph)LGELIGTLNAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQSLGELIGTLNAAK 15 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 KQS(0.999)LGELIGT(0.001)LNAAK;KQS(1)LGELIGTLNAAK 258.38 8.53E-25 10393000000 252331 239847 161704 169990 185197 181033 196865 214682 243741 227532 TRUE FALSE 242469.6256 233006.7984 190927.5099 178763.2043 191154.0297 184693.6113 199274.2928 210248.7417 216072.5435 212121.055 1.143071939 1.098461435 0.900087499 0.842741444 0.901155379 0.870699098 0.939436648 0.991173374 1.01862846 1 17.6945283 4.305908828 5.273796346 0.929827798 1.12941423 0.65404459 0.054793344 0.123927487 6.39164349 0.014910977 0.042134834 20225.9453 -4.305908828 0.199586432 GYDVDFPR ddPTM_BT-474_Pertuzumab_2h_R1 6 GYDVDFPR 8 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9;O94808 Q06210-2 GFPT1;GFPT2 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1;Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2 0 ;;;;; 148.04 0.0012274 3365340000 6235990 6882330 6257490 7668740 7814430 7938320 8072060 8300620 7983140 8412640 FALSE TRUE 5992280.617 6686052.687 7388357.64 8064524.59 8065788.238 8098838.269 8170848.285 8129209.296 7076927.415 7842844.4 0.764044307 0.852503549 0.942050774 1.02826528 1.028426401 1.032640437 1.041822057 1.036512888 0.902341938 1 22.90294555 4.306102822 1.621594178 1.016840847 0.755133549 0.809989534 0.039541596 0.192101438 0.837306157 0.010808013 0.061674826 20234.98199 -4.306102822 -0.261707298 GYEEWLLNEIRR ddPTM_BT-474_Pertuzumab_2h_R1 4 GYEEWLLNEIRR 12 1 O43707;O43707-2;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;; 204.85 1.74E-07 1105200000 696130 749500 755810 983530 797940 702570 968460 922570 949240 1029610 FALSE TRUE 668924.47 728124.9938 892401.6799 1034290.101 823606.4648 716776.4468 980312.3032 903518.6071 841486.2547 959873.5976 0.696888082 0.758563415 0.929707497 1.077527399 0.858036378 0.746740455 1.021293122 0.941289154 0.876663612 1 19.87248491 4.306152301 4.015411674 0.931179584 0.712380961 0.467645574 0.087857962 0.187047262 5.822260866 0.022421931 0.066890471 20237.28746 -4.306152301 -0.218798624 S(ph)PSQDFSFIEDTEILDSAMYR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPSQDFSFIEDTEILDSAMYR 21 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(0.44)PS(0.44)QDFS(0.118)FIEDT(0.002)EILDSAMYR;S(0.491)PS(0.491)QDFS(0.019)FIEDTEILDSAMYR;S(0.47)PS(0.47)QDFS(0.06)FIEDTEILDSAMYR;S(0.45)PS(0.45)QDFS(0.099)FIEDTEILDSAMYR;S(0.499)PS(0.499)QDFS(0.002)FIEDTEILDSAMYR;S(0.5)PS(0.5)QDFSFIEDTEILDSAMYR 215.58 4.19E-25 133906000 83155.2 88097.7 79552.3 98085.6 107704.4 82484.7 96312.4 96898 102903.5 102341 TRUE FALSE 79905.40285 85585.23985 93929.17024 103147.8096 111168.8098 84152.59715 97491.09996 94897.02244 91222.32609 95409.35291 0.837500731 0.897031971 0.984485979 1.081107946 1.165177275 0.882016224 1.021819109 0.994630186 0.956115132 1 16.54184308 4.306279888 2.732075914 1.015100083 0.847013004 0.416160126 0.070121178 0.26636536 3.84895726 0.018370294 0.065901553 20243.23366 -4.306279888 -0.16808708 GELS(ph)EEELPYYVELPDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GELSEEELPYYVELPDR 17 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 GELS(1)EEELPYYVELPDR;GELS(1)EEELPYYVELPDR;GELS(1)EEELPYYVELPDR 262.36 4.47E-27 108217000 148122 173193 154793 186655 210710 204882 221744 234589 222213 226849 TRUE FALSE 142333.2285 168253.7052 182767.5385 196288.2869 217487.6785 209024.8544 224457.7694 229744.6552 196988.3118 211484.3152 0.673020259 0.795584793 0.864213208 0.928145838 1.028386802 0.988370481 1.061344758 1.086343708 0.931455894 1 17.69019114 4.306393022 0.775692571 1.034392932 0.585953065 0.872575736 0.043397064 0.492750502 0.339790998 0.017198307 0.172310355 20248.50771 -4.306393022 -0.448439867 PIRPGQHPAAS(ph)PTHPSAIR ddPTM_BT-474_Pertuzumab_2h_R1 4 PIRPGQHPAASPTHPSAIR 19 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 1 PIRPGQHPAAS(0.973)PT(0.027)HPSAIR;PIRPGQHPAAS(0.965)PT(0.035)HPSAIR;PIRPGQHPAAS(0.843)PT(0.157)HPSAIR;PIRPGQHPAAS(0.999)PT(0.001)HPSAIR 193.87 2.62E-15 5301440000 1326620 1420400 1928220 2368470 1787070 1954590 2154090 1416830 2157110 2695340 TRUE FALSE 1274774.224 1379891.583 2276692.247 2490707.021 1844552.73 1994113.149 2180452.398 1387571.965 1912243.916 2512782.221 0.50731584 0.549148896 0.906044395 0.991214837 0.734067885 0.793587734 0.867744279 0.552205421 0.761006625 1 21.26085421 4.306501367 7.395605004 0.80039856 0.522850353 0.460262239 0.126588559 0.22832593 20.75007279 0.033180732 0.091534374 20253.5598 -4.306501367 -0.277548207 SFS(ph)PEER ddPTM_BT-474_Pertuzumab_2h_R1 2 SFSPEER 7 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(0.007)FS(0.993)PEER;S(0.002)FS(0.998)PEER 106.94 0.0079608 802930000 949100 984640 869440 1093910 1032120 1053240 1026700 1033580 1071880 1087540 TRUE FALSE 912008.1227 956559.0313 1026567.149 1150366.826 1065319.077 1074537.234 1039265.062 1012236.212 950204.6761 1013879.947 0.899522794 0.943463804 1.012513515 1.134618383 1.050734932 1.059826893 1.025037594 0.998378767 0.937196439 1 19.9514554 4.306802657 3.167905334 1.031861093 0.908906277 0.44874228 0.048072744 0.226544399 4.434910546 0.013004038 0.042707534 20267.61554 -4.306802657 -0.122954817 VFLTDTDPNENFS(ph)AQGEDEWPPLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFLTDTDPNENFSAQGEDEWPPLRK 25 1 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 VFLTDT(0.001)DPNENFS(0.999)AQGEDEWPPLRK;VFLTDTDPNENFS(1)AQGEDEWPPLRK 131.09 5.17E-05 99934000 165780 154565 101415 119210 128853 119678 100959 128027 138090 122705 TRUE FALSE 159301.1343 150156.9575 119742.9465 125362.4424 132997.6738 122097.9712 102194.5664 125383.1977 122414.6021 114394.0811 1.392564483 1.312628732 1.046758236 1.095882245 1.162627232 1.067345181 0.893355369 1.096063682 1.070113077 1 16.80365288 4.307029396 3.868568843 1.055817023 1.375453179 0.760352836 0.067543724 0.102573443 2.967670814 0.017573657 0.053078756 20278.19971 -4.307029396 0.319636156 RPAS(ph)PSHNGSSGGGYGASK ddPTM_BT-474_Pertuzumab_2h_R1 3 RPASPSHNGSSGGGYGASK 19 1 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 RPAS(0.354)PS(0.354)HNGS(0.292)S(0.001)GGGYGASK;RPAS(0.956)PS(0.043)HNGS(0.002)SGGGYGASK;RPAS(0.634)PS(0.125)HNGS(0.239)S(0.001)GGGYGASK 158.67 2.14E-11 262156000 134902 151125 143151 182309 161982 172263 186458 182477 199249 211444 TRUE FALSE 129629.8807 146815.063 169021.5701 191717.9893 167192.2981 175746.2759 188739.9288 178708.7862 176631.0888 197122.7095 0.65761008 0.744790204 0.857443419 0.972581951 0.848163555 0.891557732 0.957474302 0.906586494 0.896046373 1 17.58873447 4.307036667 2.040653221 0.918299168 0.658976649 0.815873761 0.04266766 0.140399992 1.0650962 0.01075832 0.049085746 20278.53923 -4.307036667 -0.259322519 ILEPDDFLDDLDDEDYEEDT(ph)PKRR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILEPDDFLDDLDDEDYEEDTPKRR 24 2 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 1 ILEPDDFLDDLDDEDYEEDT(1)PKRR;ILEPDDFLDDLDDEDYEEDT(1)PKRR 280.32 1.56E-50 212840000 374220 316330 148655 122602 192865 209622 136126 189810 166537 126673 TRUE FALSE 359595.0687 307308.5781 175520.2653 128929.5039 199068.6779 213860.7005 137791.9507 185890.3572 147632.4179 118093.3249 3.045007574 2.602251892 1.48628439 1.091759454 1.685689501 1.81094656 1.166805582 1.574097074 1.250133469 1 16.84956789 4.307045937 3.342888789 1.407666799 2.96233532 0.843862436 0.251017747 0.081577526 1.777359818 0.061694187 0.197364807 20278.97208 -4.307045937 1.554668521 up GLLDKFPLFTAVYQICYESR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLDKFPLFTAVYQICYESR 20 1 Q8N335 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein 0 ; 202.43 1.06E-21 143712000 214742 224489 216927 230898 269615 234206 258871 271352 262862 278069 FALSE TRUE 206349.6452 218086.7935 256130.5344 242814.6735 278287.4113 238941.8058 262039.1407 265748.4864 233023.0078 259235.139 0.795994116 0.841270186 0.988023983 0.936658026 1.073494174 0.921718432 1.010816442 1.025125249 0.898886658 1 17.98390176 4.307304224 3.448193854 0.986713759 0.803513475 0.63780088 0.049505055 0.129072053 2.988463773 0.011761569 0.037116338 20291.03613 -4.307304224 -0.183200283 SDSAFFWEER ddPTM_BT-474_Pertuzumab_2h_R1 4 SDSAFFWEER 10 0 O75116;C9JFJ0;D6REE7;Q13464;A0A0U1RQV4 O75116;Q13464 ROCK2;ROCK1 Rho-associated protein kinase 2;Rho-associated protein kinase 1 0 ;;; 247.58 2.36E-12 728790000 498990 522980 495030 597070 558230 493200 631320 617570 598150 652180 FALSE TRUE 479488.9191 508065.1225 584492.9329 627884.8543 576185.9749 503172.8419 639046.283 604816.9637 530250.5196 608007.2677 0.788623664 0.835623436 0.96132557 1.032693008 0.947662973 0.827577019 1.051050402 0.994752852 0.87211214 1 19.21372904 4.307382887 3.744439766 0.96495273 0.799275225 0.462010655 0.06490671 0.188819502 5.128910553 0.016436046 0.050214516 20294.71172 -4.307382887 -0.165677505 TIQEVLEEQS(ph)EDEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 TIQEVLEEQSEDEDR 15 0 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR 425.67 3.09E-153 5536370000 1275720 1367770 1534390 1904310 1628090 1518300 1732810 1755700 1640950 2025400 TRUE FALSE 1225863.452 1328762.539 1811688.405 2002591.667 1680458.993 1549001.066 1754016.647 1719444.181 1454676.235 1888217.854 0.64921717 0.703712517 0.959470011 1.060572361 0.889970927 0.820350821 0.928927053 0.910617479 0.770396399 1 20.8485938 4.307543596 5.492076768 0.915263501 0.666333041 0.601458853 0.078728506 0.131589601 7.194272564 0.019735845 0.055555316 20302.22309 -4.307543596 -0.24893046 KEVLAS(ph)PDR ddPTM_BT-474_Pertuzumab_2h_R1 3 KEVLASPDR 9 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KEVLAS(1)PDR;KEVLAS(1)PDR;KEVLAS(1)PDR 106.17 0.0018244 1502930000 3491020 3537240 4100400 4373000 3831200 3202560 4666400 4686400 4375800 5086600 TRUE FALSE 3354587.079 3436361.379 4841433.493 4598691.054 3954434.027 3267317.957 4723508.799 4589624.202 3879077.529 4742080.051 0.707408361 0.724652756 1.020951448 0.969762426 0.833902841 0.68900523 0.996083733 0.967850427 0.818011819 1 22.17708859 4.307894513 9.510975604 0.909688795 0.714355618 0.3852225 0.098980615 0.368573428 47.07021791 0.025113296 0.068912249 20318.63428 -4.307894513 -0.195333177 LHPPS(ph)PVPQGVCPAHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LHPPSPVPQGVCPAHR 16 0 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 LHPPS(1)PVPQGVCPAHR;LHPPS(1)PVPQGVCPAHR;LHPPS(1)PVPQGVCPAHR 150.68 1.20E-06 1577840000 430580 456330 442900 572770 558700 461200 591120 418980 575850 567060 TRUE FALSE 413752.4576 443315.9152 522941.8823 602330.7283 576671.0929 470525.78 598354.3034 410327.9166 510481.9222 528652.5211 0.782654846 0.838577132 0.989197746 1.139369821 1.090832011 0.890047359 1.131848009 0.776176979 0.965628464 1 19.01196024 4.307992856 4.030504899 0.990636546 0.796845574 0.342209801 0.104553336 0.260080084 8.111013118 0.027622796 0.082462952 20323.23581 -4.307992856 -0.193790973 AS(ph)PHDVLETIFVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPHDVLETIFVR 13 0 H0YEM7;O75143-4;O75143-3;O75143-2;O75143;O75143-5;H0YCL5 H0YEM7 ATG13 Autophagy-related protein 13 1 AS(1)PHDVLETIFVR;AS(1)PHDVLETIFVR;AS(1)PHDVLETIFVR;AS(1)PHDVLETIFVR 166.04 2.21E-05 106571800 101644 111533 107586 135039 117181 123022 141465 123893 150824 161174 TRUE FALSE 97671.64011 108352.188 127029.1834 142008.379 120950.2333 125509.5891 143196.291 121334.5663 133703.0918 150257.5414 0.650028206 0.721109816 0.845409703 0.945099844 0.804952831 0.835296438 0.953005684 0.807510659 0.889826165 1 17.19707788 4.308067085 2.688668928 0.878059494 0.659271373 0.638868686 0.061338909 0.168492861 2.352283331 0.014869699 0.054097194 20326.70973 -4.308067085 -0.218788121 EDGNEEDKENQGDETQGQQPPQRR ddPTM_BT-474_Pertuzumab_2h_R1 6 EDGNEEDKENQGDETQGQQPPQRR 24 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;; 237.95 1.05E-37 1925394000 1389809.2 1292177.5 714244.5 600450 853565.6 1124545.1 878194.2 1038838.5 1215910.3 946486.1 FALSE TRUE 1335493.92 1255325.863 843324.3694 631439.2965 881021.3127 1147284.172 888941.8033 1017386.122 1077885.26 882379.7534 1.513513785 1.422659414 0.955738576 0.715609457 0.998460481 1.300215885 1.007436764 1.153002568 1.221566175 1 19.75104016 4.308111268 5.809251162 1.049124654 1.483933733 0.553798575 0.152604 0.155240739 9.301651016 0.040462183 0.113291929 20328.77776 -4.308111268 0.434809079 APIRPDIVNFVHTNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 APIRPDIVNFVHTNLR 16 1 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ; 270.51 2.38E-35 15680800000 11784600 12555300 11920500 14865300 13165100 14095200 14405100 14874200 14100300 15539600 FALSE TRUE 11324044.8 12197235.14 14074799.52 15632499.91 13588567.4 14380214.6 14581393.92 14567042.57 12499693.06 14487089.05 0.781664609 0.841938301 0.971540899 1.079064252 0.937977764 0.99262278 1.00650958 1.00551895 0.862816057 1 23.7882644 4.308159545 3.307840462 0.987717113 0.793690029 0.634968137 0.052473983 0.136921453 2.918363859 0.012811631 0.041249724 20331.03767 -4.308159545 -0.194027084 VKDTHEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKDTHEK 7 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 0 ; 71.223 0.032986 107341000 404900 389540 308189 330410 337900 356850 387790 345975 385540 447700 FALSE TRUE 389076.0604 378430.7006 363885.6079 347462.4997 348768.8604 364065.7515 392535.89 338830.4953 341775.1155 417376.8802 0.932193609 0.90668822 0.871839398 0.832491008 0.835620939 0.872271007 0.940483071 0.811809449 0.818864512 1 18.67099116 4.308216311 0.002986266 1.73884417 4.38E-07 0.027824034 0.057649231 494985.1388 264.6946406 75615.26788 78527.72685 20333.69528 -4.308216311 -1.738843732 RRET(ph)PS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 RRETPSPR 8 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RRET(1)PS(1)PR;RRET(1)PS(1)PR;RRET(1)PS(1)PR;RRET(1)PS(1)PR;RRET(1)PS(1)PR;RRET(1)PS(1)PR 83.182 0.020247 3679580000 1481214 1570058 1703067 2145970 1893117 1684728 1888875 1924260 1936070 2055410 TRUE FALSE 1423326.519 1525281.483 2010849.091 2256723.769 1954010.828 1718794.354 1911991.617 1884523.359 1716295.45 1916195.25 0.742787834 0.795994815 1.049396762 1.177710762 1.01973472 0.896982891 0.997806261 0.98347147 0.895678794 1 20.86981314 4.308324148 5.566923369 1.003589699 0.759643919 0.605751359 0.075493932 0.136288659 7.576418766 0.020002601 0.05624569 20338.74486 -4.308324148 -0.243945781 KSPS(ph)SDSWTCADTSTER ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPSSDSWTCADTSTER 17 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 KS(0.014)PS(0.315)S(0.315)DS(0.178)WT(0.178)CADTSTER 127.32 0.00010241 0 93280 92931 91364 97186 92936 91385 108840 97550 115950 109030 TRUE FALSE 89634.51447 90280.69887 107875.5072 102201.7811 95925.37084 93232.86731 110172.0165 95535.55841 102787.8421 101645.301 0.881836284 0.888193532 1.061293598 1.005474725 0.943726566 0.917237358 1.083886962 0.939891539 1.011240472 1 16.633184 4.308521928 10.87514649 0.990983305 0.884476216 0.440198176 0.049574826 0.446691274 66.78074557 0.011799438 0.032342312 20348.00932 -4.308521928 -0.106507089 S(ph)STVTEAPIAVVTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTVTEAPIAVVTSR 15 0 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 S(0.962)S(0.036)T(0.002)VTEAPIAVVTSR;S(0.973)S(0.025)T(0.001)VTEAPIAVVTSR 173.71 1.00E-06 183918000 732390 556230 539260 264790 338870 381590 242760 224650 290170 231670 TRUE FALSE 703767.3891 540366.865 636716.2778 278455.8436 349770.0613 389306.0112 245730.9695 220010.899 257231.1181 215978.7845 3.258502406 2.501944189 2.948050102 1.289274056 1.619464903 1.802519688 1.137755127 1.01866903 1.191001786 1 17.72053008 4.308612762 0.484250467 1.012713595 4.208650005 0.832451458 0.324529899 1.194675001 0.292853524 0.220239687 2.088023614 20352.26562 -4.308612762 3.195936409 up CS(ph)PTVAFVEFPSSPQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 CSPTVAFVEFPSSPQLK 17 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 CS(0.998)PT(0.002)VAFVEFPSSPQLK 156.49 6.41E-08 39122000 66974 64334 43772 53931 53184 52488 54629 56659 57922 53399 TRUE FALSE 64356.58204 62499.25731 51682.5741 56714.38537 54894.71166 53549.34332 55297.56604 55488.97185 51346.93739 49782.23817 1.292761925 1.255452941 1.038172971 1.139249408 1.102696738 1.075671671 1.11078907 1.114633932 1.031430873 1 15.60334347 4.308720203 6.042190172 1.087091495 1.280555872 0.774644785 0.042388097 0.084346611 5.367941926 0.009692879 0.027055483 20357.30122 -4.308720203 0.193464377 T(ph)SPADHGGSVGSESGGSAVDSVAGEHSVSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPADHGGSVGSESGGSAVDSVAGEHSVSGR 31 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR 281.83 1.11E-71 682210000 63752 70807 73289 87449 85625 90598 104800 66683 99977 103070 TRUE FALSE 61260.50136 68787.65369 86533.9526 91962.25337 88379.20589 92429.95363 106082.5737 65305.97275 88628.0301 96088.97709 0.637539323 0.715874555 0.90056066 0.9570531 0.919764249 0.961920466 1.10400357 0.679640628 0.922353768 1 16.55208332 4.308803683 3.086941036 0.919445694 0.649905839 0.508813051 0.100807956 0.219000972 4.063789753 0.02694578 0.089989934 20361.21466 -4.308803683 -0.269539855 S(ph)PVSSLQIR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPVSSLQIR 9 0 P55197-1;P55197;Q5JT35 P55197-1 MLLT10 Protein AF-10 1 S(1)PVSSLQIR;S(1)PVSSLQIR;S(1)PVSSLQIR 100.69 0.0047115 912130000 334465 340317 318661 351092 351349 363769 352046 374288 407648 422985 TRUE FALSE 321393.738 330611.4924 376250.1313 369211.9002 362650.4597 371124.6584 356354.4443 366558.822 361373.508 394335.8492 0.815025412 0.838400802 0.954136257 0.936287941 0.919648722 0.941138522 0.903682597 0.929559975 0.916410488 1 18.58906535 4.308821666 5.54396655 0.932577684 0.822281809 0.749624161 0.025571713 0.086843222 4.772869489 0.005759252 0.016205463 20362.05781 -4.308821666 -0.110295875 KVTEELLTDNR ddPTM_BT-474_Pertuzumab_2h_R1 3 KVTEELLTDNR 11 1 Q9UHB9;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 141.37 6.12E-05 1082290000 1813680 1832040 1606080 1787110 1876680 1927370 1971710 2026400 2101180 2078670 FALSE TRUE 1742799.38 1779792.013 1896334.383 1879342.961 1937045.117 1966342.742 1995840.377 1984554.132 1862662.855 1937879.829 0.899333052 0.918422281 0.978561392 0.969793345 0.999569265 1.014687656 1.029909258 1.024085241 0.961185945 1 20.88604768 4.308987427 0.868344237 1.010236852 0.868467779 0.770767893 0.019843667 0.581326491 0.522606457 0.007209708 0.069583201 20369.83106 -4.308987427 -0.141769073 S(ph)RS(ph)SS(ph)PVTELASR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSSSPVTELASR 13 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.765)RS(0.633)S(0.476)S(0.904)PVT(0.221)ELASR 85.421 0.0075769 224800000 136720 144040 128270 157070 141430 146790 142150 180890 182740 151330 TRUE FALSE 131376.8312 139932.1202 151451.2424 165176.4015 145979.2244 149758.1944 143889.6742 177154.5583 161996.1213 141080.2843 0.931220347 0.991861626 1.073511037 1.170797198 1.034724484 1.061510438 1.019913413 1.255700321 1.148254854 1 17.10615686 4.309289292 2.37120498 1.109961211 0.93699092 0.351465522 0.074183449 0.334766226 3.563238649 0.020446957 0.082066037 20383.99445 -4.309289292 -0.17297029 EALDLGITGPEGIEISRPEELEAEATHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EALDLGITGPEGIEISRPEELEAEATHR 28 1 Q9BPU6 Q9BPU6 DPYSL5 Dihydropyrimidinase-related protein 5 0 ; 180.88 8.68E-18 383570000 106308 117530 113917 147046 141274 138473 142533 127501 155519 140644 FALSE TRUE 102153.3658 114178.1595 134504.336 154635.0617 145818.2065 141273.0189 144277.3615 124868.0598 137865.1351 131118.0566 0.779094569 0.870804239 1.025826186 1.179357487 1.112113848 1.077449 1.100362263 0.952333058 1.051458042 1 17.00050685 4.309356117 2.87579105 1.065439613 0.794179042 0.733736169 0.058759935 0.143098901 2.297401868 0.016660605 0.058076117 20387.13117 -4.309356117 -0.271260571 (ac)ALVTVS(ph)RSPPGSGASTPVGPWDQAVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVT(0.015)VS(0.3)RS(0.3)PPGS(0.3)GAS(0.069)T(0.015)PVGPWDQAVQR 41.423 0.028099 28892000 3185.6 4165.4 4211.6 6910.4 4996 4877.2 6584.4 5549.6 5508 4610.5 TRUE FALSE 3061.10323 4046.60687 4972.729807 7267.046572 5156.700877 4975.820326 6664.981857 5434.998821 4882.754931 4298.226728 0.712178166 0.941459613 1.156925895 1.69070806 1.199727516 1.157644917 1.550635245 1.264474669 1.135992873 1 12.06952587 4.30955588 2.548586865 1.306505626 0.749416798 0.473122839 0.194341128 0.227079089 2.827326743 0.048280136 0.183106664 20396.51082 -4.30955588 -0.557088827 RIACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RIACDEEFSDSEDEGEGGR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 RIACDEEFS(1)DS(1)EDEGEGGR 133.95 3.74E-05 435460000 119530 128610 134140 169670 153870 142060 150370 152770 157100 187800 TRUE FALSE 114858.6355 124942.1687 158382.0819 178426.689 158819.3683 144932.5505 152210.273 149615.2461 139266.6666 175080.1387 0.656034638 0.713628454 0.904626208 1.019114391 0.907123843 0.827806921 0.869374871 0.854552933 0.795445261 1 17.41765591 4.3095834 4.462002671 0.891129197 0.671527336 0.622074608 0.066553974 0.136064349 5.085803796 0.017155032 0.049976707 20397.80331 -4.3095834 -0.219601861 APS(ph)APPGTGALPPAAPSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSAPPGTGALPPAAPSGR 19 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 APS(1)APPGTGALPPAAPSGR 118.24 8.72E-05 37656000 34722 27341 11843 8534.4 12527 11938 6725.9 12423 10871 9343.4 TRUE FALSE 33365.02585 26561.26145 13983.29355 8974.861407 12929.94233 12179.39454 6808.213576 12166.46071 9636.969655 8710.563196 3.830409711 3.049316198 1.605325997 1.030342264 1.484397971 1.398232728 0.781604292 1.396747884 1.10635437 1 13.08855029 4.309717994 2.21185226 1.192694812 3.822210995 0.950806373 0.207139444 0.06208758 0.565730684 0.05314373 0.226558378 20404.12587 -4.309717994 2.629516184 up HWELTAEGEEIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 HWELTAEGEEIAR 13 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 198.37 1.26E-07 480930000 1938910 2124800 2124800 2578700 2525900 2672500 2472300 2453900 2759200 2807600 FALSE TRUE 1863135.254 2064202.784 2508798.626 2711787.016 2607147.867 2726539.781 2502556.747 2403226.107 2445987.184 2617438.751 0.71181618 0.788634608 0.958493728 1.036046026 0.996068338 1.041682362 0.956109 0.918159444 0.934496436 1 21.31972435 4.309816779 3.084802109 0.979219336 0.724474754 0.858473366 0.038004382 0.096699357 1.790672814 0.011229813 0.037572711 20408.76755 -4.309816779 -0.254744582 TLRDPSLPLLELQDIMTSVSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLRDPSLPLLELQDIMTSVSGR 22 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 188.72 2.18E-17 483440000 209230 246410 282740 324240 298420 333060 378150 327400 388200 438110 FALSE TRUE 201053.0603 239382.6281 333837.4075 340974.0653 308018.9503 339794.7014 382777.9128 320639.0756 344133.1635 408436.4195 0.49225057 0.586095208 0.817354652 0.83482777 0.754141736 0.831940261 0.9371787 0.785040364 0.842562384 1 18.63975199 4.309897101 2.71441797 0.843186931 0.500190805 0.778265639 0.067346497 0.11784188 1.677235542 0.016428618 0.059554374 20412.54245 -4.309897101 -0.342996125 EDPDGEHAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDPDGEHAR 9 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 111.61 0.0020974 124310000 202770 207720 187990 229200 217120 206220 236050 199140 243990 255050 FALSE TRUE 194845.5242 201796.029 221963.9748 241029.0395 224103.862 210389.9097 238938.8505 195027.6894 216293.2781 237775.2363 0.819452552 0.848683959 0.93350333 1.013684365 0.942502951 0.884826835 1.004893757 0.820218676 0.90965435 1 17.85923894 4.310308911 4.226547639 0.931020807 0.827100588 0.349988805 0.056733648 0.250783017 8.4759067 0.014600277 0.043112037 20431.90738 -4.310308911 -0.103920219 S(ph)RSSS(ph)PVTELASR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSSSPVTELASR 13 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.98)RS(0.108)S(0.306)S(0.595)PVT(0.012)ELASR 94.569 0.030827 0 199950 198660 179110 207390 193420 179260 191360 224620 227420 215780 TRUE FALSE 192135.7329 192994.4113 211479.1613 218093.4228 199641.53 182884.76 193701.9209 219981.5185 201604.235 201165.0284 0.955114984 0.959383511 1.051271998 1.084151776 0.992426624 0.909128 0.962900572 1.093537581 1.002183315 1 17.61802 4.310348409 10.0672917 1.015003152 0.956828386 0.14819397 0.052053766 0.777800376 102.9498555 0.014016089 0.038442546 20433.76569 -4.310348409 -0.058174766 IQNS(ph)DDEER ddPTM_BT-474_Pertuzumab_2h_R1 1 IQNSDDEER 9 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 IQNS(1)DDEER 144.92 0.00010323 490170000 365110 436980 454620 630300 519890 500920 603370 584600 606820 627910 TRUE FALSE 350841.0975 424517.7582 536779.947 662829.8585 536612.734 511048.9456 610754.2225 572527.8057 537936.3376 585381.0964 0.599337935 0.725198953 0.916975198 1.132304857 0.91668955 0.873019216 1.043344628 0.978042867 0.918950648 1 19.15901663 4.310355957 2.701265762 0.979145682 0.617686627 0.771907457 0.069559853 0.122530357 1.725915777 0.017909715 0.065193406 20434.12084 -4.310355957 -0.361459055 GGPPFAFVEFEDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GGPPFAFVEFEDPR 14 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 116.77 0.00079665 997220000 604790 647880 683650 849110 745810 703860 767580 823380 788540 886420 FALSE TRUE 581154.1382 629403.0967 807200.7627 892932.6689 769799.656 718092.5315 776973.8736 806376.9153 699028.245 826381.9839 0.70325122 0.761637002 0.976788917 1.080532594 0.931530056 0.868959568 0.940211535 0.975791984 0.845889986 1 19.65644928 4.310659922 4.759164851 0.953042736 0.719659449 0.664872712 0.062851328 0.116723669 4.865158532 0.015978134 0.04598914 20448.42777 -4.310659922 -0.233383286 NMLAFSSPAAGGVCEPLKS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NMLAFSSPAAGGVCEPLKSPQR 22 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR 292.98 1.17E-55 1826190000 2354850 2092650 1497280 1532110 1348230 1501610 1156100 1807340 2350800 2053490 TRUE FALSE 2262819.859 2032969.671 1767871.803 1611182.381 1391597.042 1531973.583 1170248.698 1770017.797 2083947.039 1914405.293 1.18199624 1.061932746 0.923457436 0.841609865 0.726908271 0.80023472 0.611285762 0.924578408 1.088561052 1 20.86846486 4.310707096 1.774425053 0.836313068 1.188295756 0.410983596 0.127630447 0.414745839 2.249855859 0.035489561 0.186953899 20450.64906 -4.310707096 0.351982687 SQSFNTDTTTSGISSMSS(ph)SPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSFNTDTTTSGISSMSSSPSR 22 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 SQSFNTDTTTSGISSMS(0.001)S(0.701)S(0.231)PS(0.068)R 370.65 4.93E-113 232660000 307670 344250 334660 438150 376340 388300 433410 393480 467970 468890 TRUE FALSE 295645.9163 334432.3271 395140.5065 460762.974 388445.3179 396151.692 438714.2012 385354.5005 414848.0075 437131.6627 0.676331507 0.765060863 0.90393934 1.05405994 0.888623157 0.906252568 1.003620279 0.881552478 0.949023013 1 18.73770835 4.310808556 2.725809569 0.946380285 0.689345434 0.76076971 0.052577666 0.125937908 1.807609026 0.013199822 0.047783547 20455.4273 -4.310808556 -0.257034851 DIREEAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DIREEAEK 8 1 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;; 160.36 0.00032266 4841430000 8319300 7924000 5243400 5137600 6782600 5969900 6774500 7031000 7883900 6848600 FALSE TRUE 7994172.559 7698015.278 6190999.019 5402752.152 7000768.489 6090615.468 6857408.357 6885807.393 6988952.724 6384738.222 1.252075227 1.205690039 0.969655889 0.846197912 1.096484812 0.953933467 1.074031248 1.078479204 1.094634186 1 22.60619604 4.310834203 5.779564159 1.018317959 1.237184457 0.570196634 0.074699728 0.147229588 8.524047001 0.019258761 0.054008643 20456.6353 -4.310834203 0.218866498 VVPGQFDDADSS(ph)DSENRDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.021)S(0.979)DSENRDLK 196.02 1.09E-21 143220000 215600 197850 109130 99778 133900 174040 128040 139390 185780 140580 TRUE FALSE 207174.1136 192207.5117 128852.2186 104927.5545 138207.0151 177559.208 129606.9918 136511.5478 164691.0333 131058.3914 1.580777175 1.466579207 0.98316649 0.800616835 1.054545334 1.354809915 0.98892555 1.041608602 1.256623338 1 16.9998502 4.311082357 5.17277288 1.058122424 1.546801936 0.621468676 0.14536523 0.127377907 6.11196403 0.037163138 0.105582105 20468.32747 -4.311082357 0.488679511 FDPFGPIGT(ph)SPPGPRPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.547)S(0.453)PPGPRPDR;FDPFGPIGT(0.542)S(0.458)PPGPRPDR 81.144 0.012018 191881000 128233 130474 120518 141653 134257 132938 139520 139946 156369 142911 TRUE FALSE 123221.5126 126753.0093 142298.2835 148963.7283 138575.4983 135626.0974 141227.4875 137056.0662 138618.6467 133231.5107 0.924867638 0.951374105 1.068052766 1.118081808 1.040110539 1.017973126 1.060015658 1.028706088 1.040434398 1 17.02357581 4.311089312 5.309796205 1.048543317 0.93290843 0.669614309 0.030602347 0.111872366 5.610366007 0.007744997 0.021927445 20468.65529 -4.311089312 -0.115634887 AEPPKPEVVDSTESIPVS(ph)DEDSDAMVDDPNDEDFVPFRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 40 2 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 AEPPKPEVVDSTES(0.002)IPVS(0.973)DEDS(0.025)DAMVDDPNDEDFVPFRPR 121.35 8.64E-09 196620000 33220 36347 37993 42591 38740 44883 49911 40968 52744 55787 TRUE FALSE 31921.72567 35310.41915 44859.18025 44789.12661 39986.10728 45790.56501 50521.82575 40121.99648 46756.72224 52008.4968 0.613779048 0.678935584 0.862535605 0.86118864 0.768837973 0.880443924 0.971414843 0.7714508 0.899020835 1 15.66645972 4.311263867 3.401229466 0.86581742 0.625234959 0.635346244 0.070155807 0.14407916 3.232962201 0.017024593 0.054319858 20476.88387 -4.311263867 -0.240582461 DCQLNAHKDHQYQFLEDAVR ddPTM_BT-474_Pertuzumab_2h_R1 3 DCQLNAHKDHQYQFLEDAVR 20 1 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 180.04 3.62E-17 3245100000 4414160 4549910 2161160 2315240 3063700 3724540 2458920 108506.73 3018710 2010480 FALSE TRUE 4241649.747 4420151.022 2551729.687 2434729.814 3162246.693 3799852.751 2489012.999 106266.0281 2676038.696 1874308.399 2.263047933 2.35828374 1.361424666 1.299001709 1.687153883 2.027335925 1.327963424 0.056696128 1.427747268 1 20.83792692 4.311310692 0.314349212 0.72639162 3.215666761 0.420937792 0.484624755 5.351723858 0.528459487 0.601281827 5.016668467 20479.09178 -4.311310692 2.489275141 EYFYFELDETER ddPTM_BT-474_Pertuzumab_2h_R1 1 EYFYFELDETER 12 0 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 158.41 0.00017107 36106000 37358 38738 38089 44740 44527 45463 40210 43356 44059 47506 FALSE TRUE 35898.00806 37633.23017 44972.52959 47049.03676 45959.25139 46382.29301 40702.10201 42460.68345 39057.60703 44288.37631 0.81055146 0.849731539 1.015447694 1.062333747 1.03772717 1.047279148 0.91902448 0.958731997 0.881892954 1 15.43464049 4.311712413 5.149040785 0.989607917 0.822111932 0.58263035 0.054456073 0.14787165 7.009759605 0.01476608 0.041992085 20498.04363 -4.311712413 -0.167495985 GDQVLNFS(ph)DAEDLIDDSKLK ddPTM_BT-474_Pertuzumab_2h_R1 3 GDQVLNFSDAEDLIDDSKLK 20 1 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 GDQVLNFS(1)DAEDLIDDSKLK;GDQVLNFS(1)DAEDLIDDSKLK;GDQVLNFS(0.999)DAEDLIDDS(0.001)KLK 192.18 7.22E-18 115276000 103830 92965 49185 43008 60831 81672 52507 64168 73988 56753 TRUE FALSE 99772.20881 90313.72922 58073.82361 45227.64803 62787.68436 83323.4638 53149.59637 62842.90838 65589.19242 52909.06876 1.885729822 1.706961233 1.097615682 0.854818448 1.186709308 1.574842759 1.004546056 1.187753061 1.239658795 1 15.6912274 4.312136647 4.494117518 1.150578424 1.838203947 0.676024359 0.182044139 0.116982822 4.380028612 0.046192408 0.134616042 20518.07659 -4.312136647 0.687625523 SRPT(ph)SEGSDIES(ph)TEPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.057)RPT(0.878)S(0.065)EGS(0.044)DIES(0.948)T(0.008)EPQK 291.97 1.30E-44 819160000 1960700 1903500 1461900 1559000 1658200 1677300 1680300 1962900 1958200 1776200 TRUE FALSE 1884073.676 1849214.044 1726097.85 1639460.177 1711537.509 1711216.155 1700864.014 1922365.429 1735913.345 1655896.392 1.137796837 1.116745017 1.042394837 0.990074128 1.033601811 1.033407744 1.02715606 1.160921322 1.04832244 1 20.65918098 4.312274327 4.723028059 1.0502489 1.131888092 0.363360984 0.044329568 0.26177197 10.67635646 0.012483648 0.036019374 20524.58229 -4.312274327 0.081639192 GGQGDPAVPAQQPADPST(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 5 GGQGDPAVPAQQPADPSTPER 21 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 GGQGDPAVPAQQPADPST(1)PER;GGQGDPAVPAQQPADPS(0.002)T(0.998)PER;GGQGDPAVPAQQPADPS(0.18)T(0.82)PER;GGQGDPAVPAQQPADPS(0.082)T(0.918)PER;GGQGDPAVPAQQPADPS(0.119)T(0.881)PER 257.06 2.03E-35 4220820000 1910660 1964980 2005920 2307090 2066680 2295800 2285480 2154820 2280530 2542870 TRUE FALSE 1835989.295 1908940.694 2368434.365 2426159.191 2133156.639 2342222.649 2313450.388 2110322.214 2021653.795 2370639.15 0.774470166 0.805243048 0.999069962 1.023419862 0.899823425 0.988013148 0.975876226 0.890191244 0.852788496 1 21.17684465 4.312358613 6.37355088 0.949439438 0.784767221 0.602571124 0.053213124 0.142374664 9.508988271 0.013618691 0.037906528 20528.56597 -4.312358613 -0.164672217 LTDVILEADQNDSQSLELVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTDVILEADQNDSQSLELVHR 21 0 Q13572-2;Q13572;G3V588;G3V5A3 Q13572-2 ITPK1 Inositol-tetrakisphosphate 1-kinase 0 ; 184.95 3.77E-17 240090000 377730 397590 358170 463220 400680 464140 407830 396860 479050 497200 FALSE TRUE 362967.894 386251.1225 422899.2864 487126.8397 413568.2361 473525.2288 412821.1455 388664.7023 424670.2523 463524.2011 0.783061366 0.833292246 0.912356432 1.05091997 0.892225767 1.021576064 0.890614006 0.838499266 0.916177087 1 18.82228514 4.312380332 3.16362012 0.932913039 0.793482516 0.423769282 0.062644273 0.261535762 5.085029062 0.016936563 0.056093679 20529.59265 -4.312380332 -0.139430522 VLTANSNPSS(ph)PSAAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLTANSNPSSPSAAKR 16 1 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.454)S(0.536)PS(0.01)AAKR 98.882 0.001582 283690000 147150 137870 91944 100870 110430 118810 101160 113740 129020 113450 TRUE FALSE 141399.2153 133938.0826 108560.3261 106075.9128 113982.0812 121212.4196 102398.0263 111391.2293 114374.1905 105765.9304 1.336907024 1.266363204 1.026420565 1.002930834 1.077682395 1.146044091 0.968157004 1.053186303 1.081389726 1 16.69051545 4.312392135 4.340257369 1.045687349 1.319097639 0.819039694 0.048690303 0.07817826 2.750374502 0.01209692 0.035544061 20530.1506 -4.312392135 0.27341029 SGITS(ph)PVEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGITSPVEKR 10 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 S(0.001)GIT(0.159)S(0.84)PVEKR;S(0.01)GIT(0.183)S(0.807)PVEKR 84.605 0.014936 670801000 738800 681950 534520 514750 568440 656290 559200 599620 709500 631390 TRUE FALSE 709926.8792 662501.4537 631119.6543 541316.3092 586724.3888 669560.6335 566043.6569 587237.6375 628960.5345 588625.3929 1.206075864 1.125506072 1.072192369 0.919627858 0.996770435 1.137498724 0.96163649 0.997642379 1.068524298 1 19.16699025 4.31258814 2.178356129 1.011992438 1.196930492 0.546778905 0.056890273 0.255065967 2.241868769 0.0150194 0.065280835 20539.41831 -4.31258814 0.184938054 LKATVTPS(ph)PVKGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKAT(0.017)VT(0.098)PS(0.884)PVKGK;LKAT(0.004)VT(0.017)PS(0.979)PVKGK 142.01 2.09E-05 34701000000 16487380 15001260 8855330 8143210 10116810 11893400 10706340 12100050 12005960 11170740 TRUE FALSE 15843034.96 14573438.75 10455685.12 8563482.044 10442226.38 12133892.7 10837367.39 11850179.74 10643093.75 10414135.83 1.521300972 1.399390117 1.003989701 0.822294061 1.002697348 1.165136781 1.040640104 1.137893718 1.021985302 1 23.31203979 4.312597445 4.366262375 1.032254086 1.489629904 0.796908039 0.088642563 0.094069966 3.341920127 0.024408129 0.071626235 20539.8584 -4.312597445 0.457375818 EQQIEEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQQIEEHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 174.02 0.00027436 621220000 400420 429500 375520 472770 440820 484330 480120 453120 464090 536870 FALSE TRUE 384771.1437 417251.0805 443384.8174 497169.7164 454999.3756 494123.4844 485995.8522 443762.9137 411408.4488 500507.3167 0.768762276 0.833656306 0.885870801 0.993331565 0.909076372 0.987245277 0.971006489 0.886626227 0.821982886 1 18.93303163 4.312743289 2.078717488 0.933837632 0.773640833 0.520258527 0.053294785 0.298003011 2.352230521 0.014332797 0.065045254 20546.75719 -4.312743289 -0.1601968 GNRGS(ph)GGGGGGGGQGSTNYGK ddPTM_BT-474_Pertuzumab_2h_R1 3 GNRGSGGGGGGGGQGSTNYGK 21 1 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK 167.62 7.19E-12 1251350000 427970 453000 341226 339813 363150 419150 356330 373351 369780 363703 TRUE FALSE 411244.4593 440080.8835 402893.1287 357350.7897 374831.0496 427625.5002 360690.8731 365641.1714 327804.1246 339069.0719 1.212863376 1.297909246 1.188233201 1.053917385 1.10547107 1.261175187 1.063768132 1.078367807 0.966776836 1 18.37121967 4.312778082 0.203066996 0.958285604 1.464010213 0.547503311 0.071231244 9.281054614 0.42094558 0.167570872 1.207988817 20548.40336 -4.312778082 0.505724609 KGESVKR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGESVKR 7 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ; 101.6 0.0050281 3479800000 2136350 1959760 1440360 1446350 1501450 1525520 1628170 1803890 1802450 1660720 FALSE TRUE 2052859.08 1903869.564 1700665.093 1520996.297 1549745.503 1556367.06 1648096.032 1766639.041 1597843.432 1548237.955 1.325932537 1.229700872 1.098452009 0.982404734 1.000973718 1.005250552 1.064497887 1.141064289 1.032039957 1 20.56219579 4.312989593 2.319048728 1.043244733 1.318137324 0.830464584 0.044463956 0.145705749 1.473978632 0.013732329 0.056550386 20558.4133 -4.312989593 0.274892591 KEEAS(ph)SPGAGEGPAEEGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEEASSPGAGEGPAEEGTR 19 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KEEAS(0.553)S(0.447)PGAGEGPAEEGTR 69.152 0.008448 0 101430 101840 99674 106950 101680 110470 115140 110660 112890 126330 TRUE FALSE 97466.00346 98935.62291 117687.309 112469.7023 104950.6295 112703.7791 116549.1178 108374.8323 100075.2005 117773.5566 0.827571199 0.840049548 0.999267683 0.954965661 0.891122189 0.956953177 0.989603449 0.920196651 0.849725553 1 16.84565612 4.313076043 8.421909465 0.942373555 0.832226592 0.486361834 0.045742846 0.224039968 22.49214181 0.011030479 0.030341854 20562.50606 -4.313076043 -0.110146963 TIEKFEK ddPTM_BT-474_Pertuzumab_2h_R1 4 TIEKFEK 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;; 95.099 0.012508 28589120000 20332540 19270480 9567720 8806650 12813680 18026390 14050790 14652560 16770980 13359340 FALSE TRUE 19537921.86 18720904.78 11296819.84 9261162.262 13225843.65 18390895.96 14222747.77 14349979.52 14867208.66 12454500 1.568743976 1.503143825 0.907047239 0.743599684 1.061932928 1.47664667 1.141976616 1.152192341 1.19372184 1 23.57016377 4.313288654 7.458201708 1.097309145 1.545282216 0.494886596 0.182167151 0.208670325 17.53586819 0.048659658 0.13434812 20572.57499 -4.313288654 0.447973071 LGS(ph)LSAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LGSLSAR 7 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4;Q00G26 Q5SW79;Q00G26 CEP170;PLIN5 Centrosomal protein of 170 kDa;Perilipin-5 1 LGS(0.991)LS(0.009)AR;LGS(0.998)LS(0.002)AR;LGS(0.984)LS(0.016)AR;LGS(0.851)LS(0.149)AR 146.03 0.0023565 1654180000 1772060 1512940 1072470 1044480 964080 834510 833280 1456650 1318320 1077090 TRUE FALSE 1702805.936 1469792.433 1266289.186 1098385.738 995090.5088 851384.364 843477.9299 1426569.668 1168669.84 1004137.735 1.69578921 1.463735881 1.261071208 1.093859637 0.990990055 0.847876078 0.840002223 1.420691225 1.163854121 1 19.93752574 4.313431899 1.483754813 1.06466278 1.728703793 0.65288665 0.157286818 0.4125698 1.429341033 0.050887292 0.322930997 20579.36165 -4.313431899 0.664041013 TEAVS(ph)PTVSQLSAVFENTDSPSAIISEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEAVSPTVSQLSAVFENTDSPSAIISEK 28 0 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 T(0.001)EAVS(0.499)PT(0.499)VSQLSAVFENTDSPSAIISEK;T(0.016)EAVS(0.49)PT(0.49)VS(0.003)QLSAVFENTDSPSAIISEK 217.84 2.01E-34 120426000 105889 110080 91459 105277 110019 116176 105566 118425 127385 118824 TRUE FALSE 101750.7408 106940.6262 107987.6758 110710.3586 113557.8611 118525.1583 106857.9483 115979.4824 112924.7888 110775.9446 0.918527404 0.965377696 0.974829654 0.99940794 1.025113001 1.069953939 0.964631343 1.046973535 1.019398112 1 16.7572851 4.313465626 0.960225699 1.023076306 0.904688735 0.592565278 0.026932751 0.746428841 0.854627118 0.008682192 0.079996196 20580.9599 -4.313465626 -0.118387571 ENSS(ph)PENKNWLLAMAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSSPENKNWLLAMAAK 17 1 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ENS(0.294)S(0.706)PENKNWLLAMAAK 198.84 8.38E-12 375530000 712240 655640 420820 465210 505680 456170 495420 540540 542580 540600 TRUE FALSE 684404.8734 636941.7891 496871.5351 489219.5439 521945.6564 465394.0699 501483.0982 529377.6601 480988.5931 503984.6805 1.357987455 1.263811806 0.985886187 0.970703203 1.03563794 0.923429001 0.995036392 1.050384428 0.954371456 1 18.94302036 4.313473692 3.777905649 0.992191966 1.337955103 0.927260585 0.036357255 0.051320325 1.400990043 0.009330693 0.028600307 20581.3421 -4.313473692 0.345763137 TKDSGS(ph)ISLQETR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKDSGSISLQETR 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 T(0.001)KDS(0.101)GS(0.886)IS(0.013)LQETR 94.325 0.0018285 0 436760 367020 211570 197600 205400 209160 151340 248810 226950 173890 TRUE FALSE 419690.9363 356552.949 249805.4053 207798.1597 212006.8775 213389.3585 153192.1442 243671.9866 201187.5875 162112.2754 2.588890541 2.199419804 1.540940714 1.281816316 1.307778063 1.316305986 0.944975597 1.503106325 1.241038576 1 17.30663381 4.31372275 1.639937431 1.245659326 2.671295109 0.905871986 0.150908136 0.131025074 0.583905935 0.040298585 0.231390744 20593.14843 -4.31372275 1.425635783 up TLTDEVNS(ph)PDSDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(1)PDSDRR;TLTDEVNS(0.995)PDS(0.005)DRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR 260.44 1.13E-24 10458650000 3831360 4075180 3933340 4447170 4408520 4793670 4697100 4748630 5072130 5334550 TRUE FALSE 3681626.215 3958959.856 4644182.035 4676688.977 4550324.05 4890601.292 4754584.515 4650569.131 4496363.067 4973236.177 0.74028783 0.796053056 0.933835006 0.940371382 0.914962388 0.983384082 0.95603433 0.9351193 0.904112113 1 22.24575352 4.313761137 2.87835421 0.945355353 0.746553685 0.874540169 0.027337866 0.07938325 1.274134048 0.006754795 0.023695254 20594.96872 -4.313761137 -0.198801668 VT(ph)KSPAPVHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTKSPAPVHR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 VT(0.5)KS(0.5)PAPVHR 102.52 0.0047468 1368400000 2247600 2018200 1579700 1460300 1604200 1644600 1237500 1634600 1813900 1600200 TRUE FALSE 2159761.307 1960642.912 1865186.93 1535666.258 1655800.55 1677854.939 1252644.895 1600844.939 1607993.676 1491817.029 1.447738741 1.314265003 1.250278616 1.029393169 1.109922007 1.124705582 0.8396773 1.073083969 1.077875936 1 20.50863917 4.313918151 0.821225231 1.01738681 1.557371845 0.775674261 0.077386866 0.655738669 0.513655815 0.028831132 0.287945555 20602.41593 -4.313918151 0.539985035 DMSPLSETEMALGKDVT(ph)PPPETEVVLIK ddPTM_BT-474_Pertuzumab_2h_R1 5 DMSPLSETEMALGKDVTPPPETEVVLIK 28 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMS(0.002)PLS(0.002)ET(0.002)EMALGKDVT(0.985)PPPET(0.01)EVVLIK;DMSPLSET(0.001)EMALGKDVT(0.99)PPPET(0.008)EVVLIK;DMSPLSETEMALGKDVT(0.999)PPPET(0.001)EVVLIK;DMSPLSETEMALGKDVT(0.998)PPPET(0.001)EVVLIK;DMSPLSETEMALGKDVT(0.999)PPPET(0.001)EVVLIK 154.28 4.59E-08 1038159000 2094135 1946109 1234997 1126977 1511700 1717264 1383339 1672256 1844566 1417958 TRUE FALSE 2012293.889 1890607.877 1458188.43 1185140.418 1560325.203 1751988.255 1400268.716 1637723.329 1635178.601 1321918.442 1.522252679 1.430200092 1.10308502 0.896530664 1.18034907 1.32533763 1.059270128 1.23889892 1.236973893 1 20.33420174 4.314213463 4.731693167 1.140315284 1.496617179 0.573301311 0.119933502 0.14691786 5.951614045 0.030534306 0.088178887 20616.42997 -4.314213463 0.356301895 DLISLDS(ph)SPAKER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLIS(0.002)LDS(0.674)S(0.324)PAKER;DLISLDS(0.651)S(0.349)PAKER 86.772 0.0052526 1147740000 1210720 1138080 831310 761000 898140 955070 1006710 1089980 1066650 1138630 TRUE FALSE 1163403.724 1105623.073 981546.2094 800275.3012 927029.4888 974382.1698 1019030.418 1067471.532 945568.3638 1061509.576 1.095989853 1.041557323 0.924670141 0.753903045 0.873312413 0.917921225 0.959982313 1.005616488 0.890777045 1 20.01768596 4.314350882 3.716550802 0.915496692 1.08298539 0.456861586 0.067854172 0.216930566 5.735940299 0.018902104 0.058340269 20622.95442 -4.314350882 0.167488699 DWILPSDYDHAEAEAR ddPTM_BT-474_Pertuzumab_2h_R1 8 DWILPSDYDHAEAEAR 16 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;;;; 302.63 4.82E-46 9565300000 3484118 3879060 3892600 5185660 4304640 4197240 5004370 4475780 4969410 5648260 FALSE TRUE 3347954.817 3768433.007 4596079.41 5453292.534 4443102.655 4282111.069 5065614.977 4383353.579 4405303.41 5265698.319 0.635804525 0.715656838 0.872833788 1.035625705 0.843782227 0.813208583 0.962002506 0.83243538 0.836603835 1 22.32819344 4.314421437 3.281515551 0.894711405 0.651732685 0.61310489 0.072431577 0.156033627 3.255267237 0.018092759 0.05896177 20626.30509 -4.314421437 -0.24297872 GLNPDGTPALSTLGGFSPASKPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 GLNPDGTPALSTLGGFSPAS(0.096)KPS(0.335)S(0.569)PR;GLNPDGTPALSTLGGFSPAS(0.002)KPS(0.287)S(0.71)PR 234.72 4.10E-45 1266790000 1060170 1105450 1034120 1129820 1287690 1295530 1213740 1178010 1399770 1216570 TRUE FALSE 1018737.384 1073923.648 1221008.488 1188130.146 1329109.718 1321726.504 1228594.113 1153683.682 1240873.978 1134170.63 0.898222328 0.946880143 1.076565073 1.047576188 1.171878096 1.165368304 1.083253331 1.017204688 1.094080507 1 20.11320627 4.314493183 2.651583569 1.085820974 0.90087866 0.602077934 0.052463639 0.198037934 2.677781404 0.014486595 0.053811381 20629.71284 -4.314493183 -0.184942315 DYAFVHMEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DYAFVHMEK 9 0 Q96PK6;Q96PK6-2 Q96PK6 RBM14 RNA-binding protein 14 0 ;;; 127.76 0.00043624 2108560000 4728800 4462300 4255850 4304290 4669200 4267250 4730300 4686400 5399300 5065200 FALSE TRUE 4543993.268 4335039.573 5024976.766 4526434.923 4819389.058 4353536.719 4788190.826 4589624.202 4786394.1 4722129.492 0.962276294 0.918026407 1.064133623 0.958557983 1.020596548 0.921943527 1.013989734 0.971939505 1.013609243 1 22.17100617 4.314621261 24.99999997 0.991552105 0.940151186 0.248596955 0.038040546 49.66033542 16320.04389 0.008411762 0.023036555 20635.79766 -4.314621261 -0.051400919 IIDKNGIHDLDNISFPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IIDKNGIHDLDNISFPK 17 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 110.37 0.00033752 1478860000 2507190 2405830 1313200 1349410 1901700 2294610 1859010 1805080 2110110 1760060 FALSE TRUE 2409206.243 2337218.084 1550524.452 1419053.212 1962869.908 2341008.586 1881761.12 1767804.467 1870579.159 1640849.569 1.468267591 1.424395099 0.944952226 0.864828342 1.196252201 1.426705184 1.14682123 1.077371443 1.140006491 1 20.64601155 4.314629744 7.959090442 1.110021244 1.452354649 0.475734135 0.145345335 0.231811406 21.03851874 0.038490813 0.106051434 20636.20077 -4.314629744 0.342333406 IHCLENVDK ddPTM_BT-474_Pertuzumab_2h_R1 1 IHCLENVDK 9 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3;O15020;O15020-2;A4QPE4 Q01082;Q01082-3;O15020 SPTBN1;SPTB;SPTBN2 "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic;Spectrin beta chain, non-erythrocytic 2" 0 156.83 0.0013969 0 316870 307040 239700 252890 273980 249630 305740 197940 348800 307680 FALSE TRUE 304486.3701 298283.5198 283019.1221 265941.6832 282792.8155 254677.6896 309481.7376 193852.4698 309205.6863 286840.5595 1.061517836 1.039893104 0.986677486 0.927141139 0.985888523 0.887871959 1.078932973 0.675819592 1.077970587 1 18.12988951 4.314885018 0.682450322 0.914123765 1.118034466 0.084328628 0.110477017 3.477972066 1.777741176 0.048651712 0.505117764 20648.33409 -4.314885018 0.203910701 EAEMEEHR ddPTM_BT-474_Pertuzumab_2h_R1 6 EAEMEEHR 8 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;;; 176.44 0.00026027 1460720000 1104524 1201406 1264591 1507418 1338142 1333663 1496190 1438648 1668209 1839202 FALSE TRUE 1061357.981 1167143.077 1493130.724 1585216.024 1381184.553 1360630.58 1514500.821 1408939.416 1478840.908 1714631.21 0.619000736 0.680696275 0.870817419 0.924523019 0.805528643 0.793541242 0.883280796 0.821715718 0.862483372 1 20.70946688 4.315155876 4.140159828 0.859927947 0.633946135 0.697221884 0.05824787 0.110483092 3.543956869 0.013790953 0.04111848 20661.21588 -4.315155876 -0.225981811 DPTVHDDVLELEMDELNR ddPTM_BT-474_Pertuzumab_2h_R1 8 DPTVHDDVLELEMDELNR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;;;; 385.79 1.77E-126 5333890000 3162171 3511548 3127775 4054542 4079864 3697079 3908956 3908087 4262789 4376784 FALSE TRUE 3038589.861 3411402.089 3693033.519 4263797.399 4211096.531 3771836.47 3956794.973 3827383.638 3778895.064 4080340.521 0.744690264 0.836058185 0.905079735 1.044961168 1.032045367 0.924392572 0.969721755 0.938005938 0.926122475 1 21.96025813 4.315369364 2.092374966 0.97130909 0.752327837 0.768898229 0.041342561 0.176394731 1.411534607 0.011652915 0.052850513 20671.37493 -4.315369364 -0.218981253 VDDSPSTSGGS(ph)SDGDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDDSPSTSGGSSDGDQR 17 0 C9J180;Q96LR5;F8WF15;F8W8F0 C9J180 UBE2E2 Ubiquitin-conjugating enzyme E2 E2 1 VDDSPS(0.01)T(0.01)S(0.006)GGS(0.487)S(0.487)DGDQR 120.77 6.55E-05 126680000 137680 141970 121790 142410 150710 151080 139420 149790 162910 145500 TRUE FALSE 132299.3134 137921.1546 143800.1622 149759.7972 155557.724 154134.9411 141126.2637 146696.7842 144417.1398 135645.1554 0.975333863 1.016779067 1.060120148 1.104055628 1.146798966 1.13630996 1.040407696 1.081474556 1.064668615 1 17.049478 4.315567349 2.117561515 1.086976489 0.977935756 0.416256538 0.040955247 0.327151461 2.690883519 0.010923234 0.049015094 20680.80067 -4.315567349 -0.109040732 EYGS(ph)PLKAYT(ph)PVVVTLWYR ddPTM_BT-474_Pertuzumab_2h_R1 2 EYGSPLKAYTPVVVTLWYR 19 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12 P21127-2 CDK11B Cyclin-dependent kinase 11B 2 EYGS(1)PLKAY(0.267)T(0.733)PVVVT(0.001)LWYR;EYGS(1)PLKAY(0.001)T(0.998)PVVVT(0.001)LWYR 130.01 4.21E-05 649120000 1391180 1236200 611190 561980 850710 989110 670790 840040 891310 653220 TRUE FALSE 1336811.148 1200944.786 721645.6288 590983.8551 878073.8597 1009110.482 678999.3287 822692.8804 790132.2255 608976.8276 2.195175723 1.97206976 1.185013282 0.970453765 1.441883862 1.657058916 1.114983851 1.350942833 1.297475026 1 19.21602781 4.315600706 4.595586013 1.272180568 2.135673233 0.740269792 0.197963674 0.099508585 3.812861469 0.049584501 0.14415656 20682.3892 -4.315600706 0.863492665 RKSLVGT(ph)PYWMAPELISR ddPTM_BT-474_Pertuzumab_2h_R1 1 RKSLVGTPYWMAPELISR 18 2 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RKS(0.373)LVGT(0.623)PY(0.003)WMAPELISR 179.78 3.90E-12 372980000 560170 454660 161540 138770 188310 189290 166270 268170 164390 129900 TRUE FALSE 538277.9371 441693.542 190733.8714 145931.9363 194367.1622 193117.5735 168304.862 262632.1958 145729.1364 121101.7573 4.444840018 3.647292589 1.57498847 1.205035662 1.604990435 1.594671934 1.38978051 2.168690213 1.203361038 1 16.88586027 4.315827456 3.444131261 1.526566301 4.29536145 0.917071503 0.313565966 0.05898082 1.348924634 0.08067616 0.257384623 20693.1905 -4.315827456 2.768795149 QVTQLAIDTEER ddPTM_BT-474_Pertuzumab_2h_R1 1 QVTQLAIDTEER 12 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 172.13 0.00032991 0 104320 114210 109370 126530 137830 138420 131950 154350 133870 155080 FALSE TRUE 100243.0591 110952.8426 129135.5919 133060.2285 142263.4271 141218.9472 133564.8436 151162.6186 118673.6388 144576.2935 0.693357512 0.767434549 0.893200322 0.920346104 0.984002451 0.976778031 0.923836408 1.045556052 0.820837469 1 17.14147148 4.315958461 1.287569855 0.964266086 0.658419164 0.716618263 0.056247396 0.341973727 0.822371166 0.015576561 0.11410356 20699.43356 -4.315958461 -0.305846922 DRPMEESLLLFEAMR ddPTM_BT-474_Pertuzumab_2h_R1 8 DRPMEESLLLFEAMR 15 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 ;;;;;;; 233.92 1.11E-17 1321074000 374418 395513 353505 415529 426796 414821 444919 430599 467813 504482 FALSE TRUE 359785.3306 384233.3565 417391.2172 436974.5015 440524.2809 423208.9648 450364.0518 421706.9802 414708.8295 470312.9848 0.764991277 0.816973736 0.887475427 0.929114261 0.936661957 0.899845376 0.957583708 0.896651791 0.881772018 1 18.84326164 4.3160175 1.792370939 0.924093558 0.760526774 0.748705624 0.032116005 0.204606763 1.133225696 0.008183019 0.043188528 20702.24766 -4.3160175 -0.163566784 YGPEWAR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGPEWAR 7 0 Q9H425;Q9H425-3;E5RI90 Q9H425 C1orf198 Uncharacterized protein C1orf198 0 ; 107.22 0.017509 270950000 280530 293790 278820 328780 318350 306710 347360 334270 319800 364550 FALSE TRUE 269566.5775 285411.3969 329208.9763 345748.3752 328590.0169 312911.8863 351611.0956 327367.2077 283497.6447 339858.7038 0.793172499 0.839794284 0.96866425 1.017329765 0.966843024 0.920711704 1.034580229 0.963245031 0.834163261 1 18.37457555 4.316115529 3.847808327 0.966415084 0.8036623 0.554600758 0.053140826 0.151494271 4.254443431 0.013082647 0.039948544 20706.92112 -4.316115529 -0.162752785 NSHLINVLMWELEK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSHLINVLMWELEK 14 0 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 151.8 6.84E-06 309770000 667270 595030 506240 465760 545810 507610 521250 405080 738260 639580 FALSE TRUE 641192.3507 578060.327 597728.8292 489797.9294 563366.4743 517874.222 527629.2134 396714.9564 654455.8198 596260.6769 1.075355755 0.969475851 1.002462266 0.821449323 0.944832514 0.868536602 0.884896881 0.665338118 1.097600169 1 19.18558367 4.316377111 0.959585537 0.867541133 1.100692111 0.147008496 0.112622722 1.642137087 1.872136505 0.037376135 0.346745075 20719.39698 -4.316377111 0.233150978 NSATFKS(ph)FEDR ddPTM_BT-474_Pertuzumab_2h_R1 6 NSATFKSFEDR 11 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6 O43399 TPD52L2 Tumor protein D54 1 NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSAT(0.001)FKS(0.999)FEDR;NSAT(0.001)FKS(0.999)FEDR;NSAT(0.002)FKS(0.998)FEDR;NSATFKS(1)FEDR 169.92 9.88E-06 7846770000 13483600 12281300 3339880 3523400 9213820 7801450 5479130 7714430 7476580 4240740 TRUE FALSE 12956646.01 11931049.35 3943470.611 3705243.096 9510190.888 7959200.664 5546185.232 7555124.325 6627869.983 3953510.903 3.277250607 3.01783646 0.997460411 0.937203207 2.405505163 2.013198107 1.402850623 1.910991145 1.676451677 1 21.91470297 4.316555382 6.956367871 1.610617696 3.188964642 0.654839914 0.464480098 0.133196207 9.704656639 0.116199739 0.321997783 20727.90371 -4.316555382 1.578346946 GGNRFEPYANPTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGNRFEPYANPTKR 14 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 77.192 0.014262 539960000 1303700 1125600 825570 692660 866600 875520 561940 808830 1049600 807830 FALSE TRUE 1252749.963 1093498.99 974768.8637 728408.2656 894474.976 893223.6143 568817.1898 792127.3778 930453.8083 753114.9546 1.663424627 1.451968233 1.29431617 0.967194 1.187700457 1.186038876 0.755286011 1.051801419 1.235473818 1 19.52251057 4.316588099 1.213560475 1.041299421 1.740343122 0.700079657 0.133967957 0.429215902 0.886102398 0.040815412 0.316042372 20729.46524 -4.316588099 0.699043701 S(ph)PPGSGASTPVGPWDQAVQR ddPTM_BT-474_Pertuzumab_2h_R1 9 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.999)PPGS(0.001)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.989)PPGS(0.011)GASTPVGPWDQAVQR;S(0.81)PPGS(0.19)GASTPVGPWDQAVQR;S(0.887)PPGS(0.113)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR 321.6 9.40E-67 31277960000 414526 445473 433188 521995 481675 507819 492865 549904 547600 557819 TRUE FALSE 398325.8656 432768.5462 511474.7078 548935.2245 497168.5138 518087.4481 498896.8293 538548.2902 485438.7437 520037.4223 0.765956157 0.832187315 0.983534426 1.055568698 0.956024495 0.99625032 0.959347939 1.035595261 0.933468868 1 18.98825592 4.317116676 3.302047052 0.994180283 0.778114232 0.831762826 0.034888747 0.080981666 1.706091253 0.008374245 0.027301084 20754.7103 -4.317116676 -0.216066051 VVPPLDEDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VVPPLDEDGR 10 0 G3V5T9;P24941;P24941-2;E7ESI2 G3V5T9 CDK2 Cyclin-dependent kinase 2 0 93.178 0.020852 102350000 110970 117490 138740 151630 138360 122320 161710 144930 174460 172660 FALSE TRUE 106633.1697 114139.3002 163813.4043 159455.6425 142810.4751 124793.3942 163689.0554 141937.1449 154656.0322 160965.5844 0.662459433 0.709091329 1.017692104 0.990619473 0.887211236 0.775279975 1.016919585 0.881785665 0.960801856 1 17.29639274 4.317118514 6.476858323 0.932180868 0.677771182 0.661826469 0.07295539 0.121827551 7.933751032 0.017835566 0.049643787 20754.79814 -4.317118514 -0.254409686 SLLGLDSGELQSGPESSSS(ph)PGVHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLLGLDSGELQSGPESSSSPGVHVR 25 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 SLLGLDSGELQSGPES(0.012)S(0.056)S(0.202)S(0.731)PGVHVR;SLLGLDSGELQSGPESSS(0.011)S(0.989)PGVHVR 217.84 9.60E-34 269430000 163773 194959 170929 242350 200336 242730 248931 223864 231890 310810 TRUE FALSE 157372.5701 189398.9602 201819.6726 254857.7125 206779.9894 247638.1669 251977.492 219241.1302 205566.8194 289758.5619 0.543116204 0.653644051 0.696509781 0.879551965 0.713628574 0.854636237 0.869611895 0.756633829 0.709441744 1 18.14449177 4.317211506 1.360090889 0.813562899 0.525715058 0.546873048 0.084980112 0.498290605 1.377756884 0.023165657 0.161575413 20759.24266 -4.317211506 -0.287847841 ETAVPGPLGIEDISPNLS(ph)PDDKSFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETAVPGPLGIEDISPNLSPDDKSFSR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ETAVPGPLGIEDISPNLS(1)PDDKSFSR;ETAVPGPLGIEDISPNLS(1)PDDKSFSR 221.55 1.65E-34 557400000 439350 423390 311240 301710 364570 401580 372130 397660 429850 402550 TRUE FALSE 422179.7163 411315.3317 367487.9915 317281.2893 376296.7251 409700.2227 376684.2383 389448.182 381055.2301 375284.9299 1.124957819 1.096008123 0.97922395 0.845441061 1.002696072 1.091704436 1.003728656 1.037739997 1.015375784 1 18.51762683 4.31728914 5.235386551 0.999014652 1.116300977 0.375388196 0.05880759 0.226477496 10.62718126 0.015776397 0.04487855 20762.9539 -4.31728914 0.117286325 S(ph)VDRLDETNLAPVLQSPDGNWVALK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVDRLDETNLAPVLQSPDGNWVALK 25 1 Q8NFW9-5;Q8NFW9-2;Q8NFW9;Q8NFW9-4;Q8NFW9-3;Q8NFW9-6 Q8NFW9-5 MYRIP Rab effector MyRIP 1 S(0.999)VDRLDET(0.001)NLAPVLQSPDGNWVALK;S(0.989)VDRLDET(0.011)NLAPVLQSPDGNWVALK 217.74 9.08E-34 212440000 241910 212010 119327 125306 144842 109601 100755 202050 142906 117713 TRUE FALSE 232455.8898 205963.6824 140892.0433 131773.0577 149500.9745 111817.2073 101988.0698 197877.5969 126683.91 109740.1937 2.118238377 1.876829952 1.283869097 1.200772965 1.362317392 1.018926645 0.929359302 1.803146051 1.154398455 1 16.7437325 4.317578961 3.182542585 1.253589806 2.080036572 0.639873386 0.235577897 0.1635939 3.20648384 0.062861047 0.209018414 20776.81446 -4.317578961 0.826446767 YAHVVLR ddPTM_BT-474_Pertuzumab_2h_R1 5 YAHVVLR 7 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;; 154.29 0.0016884 3252050000 2131100 2259810 2040530 2594220 2449810 2308160 2558080 2378630 2576760 2765790 FALSE TRUE 2047814.256 2195362.431 2409299.162 2728108.005 2528610.364 2354832.577 2589386.548 2329510.459 2284257.007 2578460.58 0.794200335 0.851423694 0.934394414 1.058037508 0.980666675 0.91327073 1.0042374 0.903450096 0.885899527 1 21.29807856 4.317714977 2.913214286 0.959663773 0.804322265 0.562794886 0.049864188 0.197624493 3.244960656 0.013241264 0.046379328 20783.32253 -4.317714977 -0.155341508 EEVSSWR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEVSSWR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 97.075 0.028531 369450000 1349500 1183300 957750 929370 953090 927530 887000 1068900 1131800 992330 FALSE TRUE 1296760.048 1149553.443 1130836.73 977334.8971 983747.0054 946285.2921 897855.3713 1046826.841 1003322.809 925118.6052 1.401723023 1.24260115 1.22236946 1.056442808 1.063373928 1.022879971 0.970530012 1.131559603 1.084534246 1 19.81927881 4.317752965 1.058710347 1.047230586 1.441856223 0.852635107 0.048510191 0.365794036 0.532655564 0.016058792 0.139579811 20785.14053 -4.317752965 0.394625637 DPASDQMQHWK ddPTM_BT-474_Pertuzumab_2h_R1 2 DPASDQMQHWK 11 0 P04040 P04040 CAT Catalase 0 ; 115.29 0.0011435 704020000 284204 326620 316538 420430 355890 342700 453600 386380 433840 462490 FALSE TRUE 273096.9935 317305.1174 373743.4579 442128.4427 367337.5251 349629.6288 459151.2925 378401.118 384592.302 431165.1404 0.633393027 0.735924795 0.866822066 1.025427154 0.851964806 0.810894936 1.064908198 0.877624563 0.891983758 1 18.71788102 4.318113593 2.374929762 0.925187055 0.64306893 0.629915528 0.076232436 0.195468051 2.079718979 0.019315878 0.07873346 20802.40717 -4.318113593 -0.282118126 TPQQLWYTHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPQQLWYTHEK 11 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 105.65 0.0024374 542340000 241700 251890 218000 256700 277620 225240 281590 264000 297340 289130 FALSE TRUE 232254.0968 244706.3438 257397.4494 269948.3178 286549.8994 229794.5071 285036.1827 258548.3077 263587.2098 269546.9676 0.861646113 0.90784306 0.954926155 1.001488981 1.063079663 0.852521211 1.057463882 0.959195758 0.977889724 1 18.04017715 4.318271886 2.030611494 0.9856225 0.863447589 0.362629959 0.055085265 0.389461901 2.90191896 0.013754039 0.064558428 20809.9907 -4.318271886 -0.122174911 DRLPLAVVGSNTIIEVNGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DRLPLAVVGSNTIIEVNGK 19 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 73.688 0.015398 338350000 103070 107290 108750 131190 121750 111930 130350 111430 141640 126440 FALSE TRUE 99041.91045 104230.1942 128403.5441 137960.7316 125666.1993 114193.3013 131945.2623 109128.9316 125561.621 117876.1062 0.840220412 0.884235132 1.089309346 1.170387588 1.066087127 0.968756986 1.119355454 0.925793489 1.065199938 1 16.84691178 4.318475087 5.511685539 1.046929163 0.853498698 0.551144993 0.068196225 0.15265689 7.695597687 0.017568888 0.049663223 20819.7297 -4.318475087 -0.193430466 ILSCGEVIHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILSCGEVIHVK 11 0 Q9H2U2-2;Q9H2U2;H0Y9D8;D6R967;D6RGV9 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ; 149.31 3.44E-05 1161480000 1585000 1737030 1429050 2115980 1570410 1666310 1930590 1898740 1923330 1832310 FALSE TRUE 1523056.448 1687491.605 1687311.124 2225185.981 1620923.664 1700003.93 1954217.138 1859530.355 1705001.642 1708206.012 0.891611689 0.98787359 0.987767935 1.302644977 0.948904086 0.995198424 1.144017247 1.088586706 0.998124131 1 20.70405055 4.318663013 2.341882003 1.071597249 0.910428655 0.219485856 0.097973606 0.447858368 4.618371519 0.024864958 0.102666404 20828.7407 -4.318663013 -0.161168594 SNPETDDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNPETDDYR 9 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 92.538 0.023283 365230000 439230 496760 410600 618780 520840 533620 520790 529920 522190 562720 FALSE TRUE 422064.406 482592.8912 484804.5537 650715.31 537593.2916 544410.162 527163.5838 518976.9668 462913.1804 524606.4732 0.804535261 0.919914099 0.92412995 1.240387497 1.024755353 1.037749608 1.004874341 0.989269087 0.882400817 1 19.00087608 4.318772546 2.241481924 1.022958627 0.825159759 0.367381775 0.087567325 0.35954116 3.361054849 0.023262068 0.099795767 20833.99452 -4.318772546 -0.197798867 QMDTVLSSS(ph)PDVLFDPINGLTPDEEALSNER ddPTM_BT-474_Pertuzumab_2h_R1 5 QMDTVLSSSPDVLFDPINGLTPDEEALSNER 31 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 QMDT(0.001)VLS(0.036)S(0.168)S(0.795)PDVLFDPINGLTPDEEALSNER;QMDTVLS(0.008)S(0.164)S(0.828)PDVLFDPINGLTPDEEALSNER;QMDTVLSS(0.003)S(0.997)PDVLFDPINGLTPDEEALSNER;QMDTVLSS(0.012)S(0.988)PDVLFDPINGLTPDEEALSNER;QMDTVLSS(0.001)S(0.999)PDVLFDPINGLTPDEEALSNER 270.81 9.72E-72 371118000 195416.8 197074.4 176438.8 207363.7 184186.4 219383 195612.1 192252.7 228142 246769 TRUE FALSE 187779.6954 191454.0311 208325.216 218065.7654 190110.9228 223819.0746 198006.0594 188282.6146 202244.2766 230055.1158 0.81623786 0.832209405 0.905544809 0.947884878 0.826371203 0.972893273 0.86068966 0.818423941 0.879112277 1 17.81162001 4.318828141 5.498290299 0.89049861 0.821059226 0.208923488 0.057178668 0.337919469 16.92834639 0.013957373 0.039470986 20836.66173 -4.318828141 -0.069439385 LLPDITLLEPVEGEAAEELSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLPDITLLEPVEGEAAEELSR 21 0 O15160;A0A2R8YEY5;A0A2R8YEZ4;A0A2R8Y5D3;O15160-2 O15160 POLR1C DNA-directed RNA polymerases I and III subunit RPAC1 0 ;;; 167.98 2.65E-11 131909000 44589.3 46385 43913.5 52206.7 51231 53215.9 53368 46487.8 52143.3 55840 FALSE TRUE 42846.70086 45062.14522 51849.6463 54901.09404 52878.89164 54291.96196 54021.13355 45527.81068 46224.21119 52057.90706 0.823058461 0.865615768 0.99599944 1.054615853 1.015770603 1.042914804 1.037712359 0.874560912 0.887938332 1 15.66782969 4.318928466 4.262422326 0.986279954 0.833690183 0.498097987 0.058431622 0.1959757 6.534609158 0.016700172 0.049544253 20841.4757 -4.318928466 -0.152589771 NQGGYGGSSSSSSYGSGR ddPTM_BT-474_Pertuzumab_2h_R1 6 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-2;P09651;P09651-3;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;;;;; 346.46 6.82E-90 1222149000 108595.1 106975.6 84863.8 97955.6 96199.9 92538.4 96410.7 109434.4 113596.6 105573.9 FALSE TRUE 104351.0834 103924.7606 100200.5764 103011.1003 99294.25715 94409.58985 97590.60299 107174.5414 100701.5902 98423.28572 1.060227594 1.05589607 1.018057624 1.046613101 1.008849242 0.959220058 0.991539779 1.088914484 1.023148023 1 16.58671206 4.318948179 1.573030211 1.019938489 1.065970382 0.191519724 0.032582677 1.110190015 4.438661849 0.010265842 0.062235259 20842.42172 -4.318948179 0.046031893 FEGGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FEGGDR 6 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 100.27 0.088053 449540000 470670 529910 589650 754040 596940 575730 708950 694770 777420 787820 FALSE TRUE 452275.696 514797.4856 696212.8717 792956.0948 616141.1172 587371.6551 717626.3422 680422.7567 689170.5408 734460.2497 0.615793293 0.700919465 0.947924509 1.079644671 0.838903286 0.799732396 0.977079893 0.926425572 0.938336065 1 19.48632489 4.319005105 4.126069611 0.934471782 0.636513195 0.696021721 0.074747089 0.117350939 3.701670682 0.019227471 0.057567335 20845.15387 -4.319005105 -0.297958587 TTSSANNPNLMYQDECDRR ddPTM_BT-474_Pertuzumab_2h_R1 5 TTSSANNPNLMYQDECDRR 19 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;; 310.4 2.65E-61 8206920000 1199716 1200076 1034906 1170800 1125505 1282825 1133916 1271081 1360710 1203790 FALSE TRUE 1152829.772 1165851.007 1221936.536 1231225.128 1161707.89 1308764.6 1147793.203 1244832.733 1206247.905 1122256.231 1.027242924 1.038845653 1.088821342 1.097098055 1.035153879 1.16619054 1.022755028 1.109223276 1.074841798 1 20.09797068 4.319009542 5.234750461 1.079560056 1.030606296 0.110336307 0.045126494 0.343275695 15.92775676 0.009966142 0.028371474 20845.36682 -4.319009542 -0.04895376 CIALAQLLVEQNFPAIAIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 CIALAQLLVEQNFPAIAIHR 20 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6UJC5;A0A140T9X9;A0A140TA18;H0Y400;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ; 205.18 8.89E-22 994460000 518890 525900 569390 560700 641440 609130 600510 567330 670670 693820 FALSE TRUE 498611.2051 510901.8469 672291.439 589637.7942 662072.5001 621447.0259 607859.221 555614.4372 594538.3533 646826.9534 0.770857186 0.789858623 1.039368312 0.911585071 1.023569746 0.960762415 0.939755553 0.85898467 0.919161377 1 19.30302027 4.319212799 8.359635074 0.946959218 0.7775987 0.641790908 0.052307741 0.173205 15.85731047 0.013502807 0.037164535 20855.12506 -4.319212799 -0.169360518 LSGEMPPAS(ph)PSFPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSGEMPPASPSFPR 14 0 Q96JM7-2;Q96JM7 Q96JM7-2 L3MBTL3 Lethal(3)malignant brain tumor-like protein 3 1 LSGEMPPAS(0.99)PS(0.01)FPR 79.885 0.018712 147840000 100500 110690 93556 120170 115490 118170 115600 134700 122220 140540 TRUE FALSE 96572.34889 107533.2296 110463.6503 126371.9881 119204.8407 120559.4784 117014.7474 131918.3979 108346.098 131021.1006 0.73707478 0.82073215 0.843098171 0.964516307 0.909814069 0.920153149 0.893098492 1.006848495 0.826936253 1 16.99943965 4.319578787 1.257592131 0.933867123 0.721392125 0.597831921 0.051881327 0.476628129 1.075359205 0.014451458 0.109124257 20872.70748 -4.319578787 -0.212474999 EVLEGLDYLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLEGLDYLHR 11 0 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 0 184.9 4.70E-06 203590000 155800 170350 173890 206750 206350 190880 205590 208570 216760 223780 FALSE TRUE 149711.1638 165491.7848 205315.7912 217420.3923 212987.4352 194739.7244 208106.0719 204262.9566 192154.3135 208623.1813 0.717615189 0.793256932 0.984146584 1.042167946 1.020919314 0.933451993 0.997521324 0.979099999 0.921059263 1 17.67053995 4.319722976 3.541469764 0.986696322 0.732644959 0.875630317 0.035045199 0.071279288 1.71002126 0.009097579 0.028799728 20879.63855 -4.319722976 -0.254051362 TCNVLVALEQQSPDIAQGVHLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;; 260.32 1.01E-43 1164000000 926670 985170 840080 1028860 990330 1078350 1084290 1020330 1207240 1209170 FALSE TRUE 890454.7119 957073.9162 991901.1435 1081959.588 1022184.864 1100154.976 1097559.865 999259.8289 1070199.176 1127271.839 0.789920125 0.849017853 0.879912998 0.959803617 0.90677761 0.975944699 0.973642583 0.886440869 0.949370985 1 20.10440403 4.319733992 1.232352703 0.944458701 0.774168182 0.728841017 0.032783823 0.41667818 0.892272522 0.009817437 0.075538041 20880.16817 -4.319733992 -0.170290519 MDYEDDR ddPTM_BT-474_Pertuzumab_2h_R1 3 MDYEDDR 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 113.7 0.014125 2071490000 2348230 2587310 2738380 3440210 2961150 2804320 3223760 3327760 3230560 3755160 FALSE TRUE 2256458.575 2513522.452 3233266.181 3617759.65 3056398.079 2861025.272 3263213.339 3259040.593 2863840.372 3500819.668 0.644551502 0.717981127 0.923574045 1.033403601 0.873052133 0.817244401 0.932128372 0.930936438 0.818048527 1 21.73926132 4.319746257 4.026853888 0.914827504 0.661974558 0.675060822 0.065854154 0.120125832 3.626905801 0.016488292 0.049763222 20880.75786 -4.319746257 -0.252852945 RQDLLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQDLLSR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 95.605 0.021395 552140000 381900 446570 440570 612150 556320 657890 517680 528380 473920 529650 FALSE TRUE 366974.9258 433834.2608 520190.7994 643743.1349 574214.538 671192.9866 524015.5227 517468.7684 420122.5884 493776.3337 0.743200718 0.878604808 1.053494799 1.303714032 1.16290413 1.359305703 1.061240661 1.047982119 0.850835813 1 18.91349817 4.319809866 2.66479387 1.121857141 0.763156295 0.436176693 0.138139659 0.261748026 3.568936518 0.03713753 0.138713677 20883.81636 -4.319809866 -0.358700846 VEVAAPAHRGT(ph)PDTDLEVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEVAAPAHRGTPDTDLEVQR 20 1 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 1 VEVAAPAHRGT(1)PDTDLEVQR 128.36 2.91E-05 365070000 295250 268580 153810 140300 206580 237340 185760 195090 210380 177910 TRUE FALSE 283711.3036 260920.3614 181606.8885 147540.8998 213224.8333 242139.1774 188033.3864 191061.3233 186498.5444 165859.9972 1.710546897 1.573136173 1.094940863 0.88955084 1.285571186 1.45990101 1.133687384 1.151943365 1.124433543 1 17.33960645 4.319862301 4.654820736 1.154557558 1.673721335 0.653894103 0.146089925 0.126857904 4.872077079 0.038035944 0.110576184 20886.33798 -4.319862301 0.519163777 LTYEIEDEKRR ddPTM_BT-474_Pertuzumab_2h_R1 3 LTYEIEDEKRR 11 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 190.53 1.25E-06 1933070000 888830 853260 525560 599790 639960 778130 682780 734640 783570 674470 FALSE TRUE 854093.5409 828925.8602 620540.383 630745.2338 660544.8946 793864.3217 691136.0659 719469.4273 694622.4186 628787.5461 1.358318157 1.318292427 0.986884023 1.003113433 1.050505689 1.262531878 1.099156734 1.144217044 1.104701298 1 19.26221312 4.319947652 7.095065552 1.092898977 1.344880104 0.62885218 0.078649742 0.146803237 10.5971404 0.020199456 0.055942903 20890.4431 -4.319947652 0.251981127 EDQTEYLEER ddPTM_BT-474_Pertuzumab_2h_R1 13 EDQTEYLEER 10 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;;; 280.25 1.13E-23 1.38235E+11 11002270 11807858 12014648 13412581 13172540 12875235 13771336 15176706 15472411 15547560 FALSE TRUE 10572289.12 11471109.45 14185962.16 14104805.91 13596246.71 13135581.07 13939873.73 14863301.72 13716047.77 14494509.91 0.729399558 0.791410646 0.978712785 0.973113682 0.938027349 0.906245272 0.96173474 1.025443551 0.946292621 1 23.78900322 4.320003278 3.946034537 0.967483515 0.743090839 0.870236981 0.032087211 0.073603954 2.144169125 0.008866885 0.026943137 20893.11899 -4.320003278 -0.224392676 LTPSPDIIVLSDNEAS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLSDNEAS(0.5)S(0.5)PR;LTPSPDIIVLSDNEAS(0.5)S(0.5)PR 257.2 5.77E-31 368590000 504030 564400 465770 660430 607520 604950 625370 566940 599550 638810 TRUE FALSE 484331.9504 548303.8646 549945 694514.8714 627061.4325 617182.5035 633023.4651 555232.4909 531491.5975 595542.8297 0.813261324 0.920679147 0.923434844 1.16618795 1.052924158 1.03633605 1.062935248 0.932313283 0.892448991 1 19.18384574 4.320104297 2.056830292 1.016330389 0.829118329 0.419282293 0.074234398 0.381441651 2.925444644 0.020936219 0.097460027 20897.97939 -4.320104297 -0.187212059 FVPDKEFSGSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 FVPDKEFSGSDR 12 1 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 ;; 119.88 0.00042841 801510000 1162830 1188350 1073080 1196750 1208660 1231830 1285470 1316640 1294680 1368680 FALSE TRUE 1117385.318 1154459.422 1267009.427 1258514.411 1247537.647 1256738.447 1301201.966 1289450.924 1147713.354 1275978.085 0.875708863 0.904764302 0.99297115 0.9863135 0.977710873 0.984921655 1.019768272 1.010558833 0.899477325 1 20.28317212 4.320230344 3.936003131 0.987533808 0.882071518 0.593535262 0.031226243 0.135875904 3.938770414 0.007681193 0.023364871 20904.04562 -4.320230344 -0.10546229 SGGPS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGPSPKR 8 1 Q96E39 Q96E39 RBMXL1 "RNA binding motif protein, X-linked-like-1" 1 SGGPS(1)PKR;S(0.001)GGPS(0.999)PKR 79.659 0.016822 700530000 1035320 968110 552670 612580 731530 822930 728830 745340 803610 679380 TRUE FALSE 994858.5498 940500.4507 652549.7631 644195.3272 755060.3268 839570.2084 737749.6396 729948.4685 712387.5618 633364.9875 1.570750783 1.484926495 1.030290237 1.017099682 1.192140933 1.325570919 1.164809634 1.152492612 1.12476625 1 19.27267759 4.320408641 5.837322671 1.139944799 1.544407645 0.748072327 0.093293538 0.100518598 5.443202601 0.02406372 0.067627234 20912.62939 -4.320408641 0.404462846 MT(ph)PTKK ddPTM_BT-474_Pertuzumab_2h_R1 1 MTPTKK 6 1 Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3;H7C5R6 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 1 MT(0.999)PT(0.001)KK 61.837 0.058907 86571000 193220 183550 126610 135500 149880 139620 158450 170850 159220 189910 TRUE FALSE 185668.7488 178315.3337 149491.2434 142493.1712 154701.0263 142443.2121 160389.1585 167321.8878 141146.0131 177047.2265 1.048696172 1.007162536 0.844358007 0.804831423 0.873783958 0.804549243 0.905911726 0.94506924 0.79722239 1 17.43377472 4.320819022 4.97483846 0.871153173 1.037117056 0.50418279 0.062218203 0.155690132 6.608164843 0.015178725 0.043594609 20932.39986 -4.320819022 0.165963883 AGAAS(ph)PLNS(ph)PLSSAVPSLGK ddPTM_BT-474_Pertuzumab_2h_R1 3 AGAASPLNSPLSSAVPSLGK 20 0 O75962-5;O75962;E7EPJ7;O75962-4 O75962-5 TRIO Triple functional domain protein 2 AGAAS(1)PLNS(1)PLSSAVPSLGK;AGAAS(1)PLNS(1)PLSSAVPSLGK;AGAAS(1)PLNS(1)PLSSAVPSLGK 230.99 1.90E-25 198720000 423974 463059 483291 612577 604580 563643 547301 531938 548864 540461 TRUE FALSE 407404.6274 449853.0107 570632.4345 644192.1724 624026.8648 575040.2476 553999.0334 520953.2944 486559.2597 503855.0951 0.808574988 0.892822193 1.132532825 1.278526661 1.238504623 1.141281002 1.099520554 1.033934755 0.965672997 1 18.94264936 4.320987221 4.131735125 1.119026131 0.829121009 0.560253245 0.09316497 0.161068653 5.065726489 0.025661286 0.076922289 20940.50838 -4.320987221 -0.289905123 QENKRPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 QENKRPSPR 9 2 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 QENKRPS(1)PR;QENKRPS(1)PR;QENKRPS(1)PR;QENKRPS(1)PR;QENKRPS(1)PR 100.73 0.0035157 878842000 862521 835197 561691 586609 654572 794778 694993 750529 867746 765271 TRUE FALSE 828812.7258 811377.9993 663201.0584 616883.9608 675626.9028 810848.9557 703498.5322 735030.3139 769243.112 713438.5135 1.161715705 1.137278103 0.929584044 0.864663106 0.947000884 1.136536562 0.986067501 1.030264417 1.078219212 1 19.44442957 4.321331965 7.180012617 0.997505746 1.153526852 0.418852264 0.072155773 0.224377089 16.22449149 0.018972058 0.052520475 20957.1376 -4.321331965 0.156021105 EVMESAVGNSSGSGQNEES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVMESAVGNSSGSGQNEESPR 21 0 Q9NVF7 Q9NVF7 FBXO28 F-box only protein 28 1 EVMESAVGNSSGSGQNEES(1)PR 211.03 5.11E-32 0 54092 58242 49903 69372 61471 61403 60640 62006 55540 70887 TRUE FALSE 51978.02484 56580.99518 58921.58219 72952.29723 63448.27054 62644.61073 61382.13046 60725.55443 49235.33204 66085.76035 0.786523822 0.856175292 0.89159271 1.103903426 0.960089892 0.94792903 0.928825365 0.918890153 0.745021799 1 16.01205182 4.321416028 2.600289931 0.941105188 0.799866667 0.254646689 0.084425478 0.404933225 5.238070567 0.022029678 0.084034418 20961.19451 -4.321416028 -0.141238521 LAELEEFINGPNNAHIQQVGDR ddPTM_BT-474_Pertuzumab_2h_R1 9 LAELEEFINGPNNAHIQQVGDR 22 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;;; 396.8 3.07E-132 16999009000 7437987 7938955 6974247 8378242 8235703 9152001 8984346 8370222 9269208 9777354 FALSE TRUE 7147302.245 7712543.776 8234648.574 8810644.074 8500611.866 9337060.731 9094299.114 8197373.991 8217006.368 9115125.105 0.784114553 0.846125938 0.903404888 0.966596067 0.932583126 1.024348061 0.997715227 0.899315577 0.901469401 1 23.11983103 4.321417112 1.494287549 0.957227129 0.773640292 0.692373247 0.039343026 0.351385397 1.231127678 0.011935038 0.076640499 20961.24684 -4.321417112 -0.183586837 EVADEVTRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVADEVTRPR 10 1 P33992;B1AHA9 P33992 MCM5 DNA replication licensing factor MCM5 0 ; 171.62 3.62E-06 1005360000 559460 612460 632390 799620 698610 623630 763000 764190 775740 848560 FALSE TRUE 537595.6847 594993.2405 746676.9404 840888.484 721081.4251 636240.2259 772337.8222 748409.2094 687681.2474 791086.2754 0.679566441 0.752121809 0.943862842 1.062954206 0.911507945 0.804261489 0.976300369 0.946052577 0.869287294 1 19.59347552 4.32151097 3.917972895 0.938752215 0.696342141 0.645162242 0.067084696 0.132455187 3.798946321 0.017153755 0.052320502 20965.7774 -4.32151097 -0.242410074 EFEDRDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EFEDRDR 7 1 Q13951-2;A0A494C0A9;Q13951;J3KS23 Q13951-2 CBFB Core-binding factor subunit beta 0 ;;; 116.9 0.0048802 1664520000 1550390 1642300 1363680 1704130 1668810 1721370 1615340 1713320 1828860 1897800 FALSE TRUE 1489799.045 1595463.212 1610127.311 1792080.354 1722488.789 1756177.281 1635109.014 1677939.343 1621255.48 1769260.316 0.842046267 0.901768495 0.91005676 1.012898067 0.973564361 0.992605365 0.924176618 0.94838466 0.91634649 1 20.7547149 4.321584763 1.803802745 0.961870172 0.846656442 0.596808825 0.032123402 0.313996926 1.759240663 0.008845934 0.046978934 20969.34006 -4.321584763 -0.115213731 ASS(ph)VTTFTGEPNTCPR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASSVTTFTGEPNTCPR 16 0 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 AS(0.001)S(0.996)VT(0.003)TFTGEPNTCPR;ASS(0.886)VT(0.114)TFTGEPNTCPR;ASS(0.98)VT(0.02)TFTGEPNTCPR;ASS(0.99)VT(0.01)TFTGEPNTCPR;AS(0.054)S(0.913)VT(0.033)TFTGEPNTCPR 397.61 6.80E-122 7899570000 6837720 5811790 1946480 2332100 4389500 2497450 1523030 4048560 2310060 1559060 TRUE FALSE 6570494.343 5646043.44 2298252.235 2452459.96 4530692.254 2547950.15 1541669.297 3964955.821 2047831.673 1453463.478 4.520577534 3.884544419 1.58122462 1.687321352 3.11716966 1.753019728 1.060686643 2.727936328 1.408932323 1 20.47106339 4.321659065 4.638665369 1.899274632 4.35502982 0.6904042 0.64642334 0.109997648 4.169554107 0.155632917 0.453253445 20972.92794 -4.321659065 2.455755188 AQVIYTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQVIYTR 7 0 P62851 P62851 RPS25 40S ribosomal protein S25 0 98.997 0.048249 0 126590 127760 124280 138480 135180 128580 135910 137780 157140 155250 FALSE TRUE 121642.7228 124116.4099 146740.1606 145626.9694 139528.1875 131179.9757 137573.3072 134934.7949 139302.126 144734.7792 0.840452609 0.857543782 1.01385556 1.006164311 0.964026672 0.906347295 0.950520034 0.932290052 0.96246477 1 17.14305211 4.32168123 7.354251777 0.961213996 0.846197383 0.680208287 0.032195009 0.139380418 10.38187354 0.008528682 0.023583963 20973.99839 -4.32168123 -0.115016613 EKYDTDFYILDKYPLAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKYDTDFYILDKYPLAVR 18 2 P14868;P14868-2 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 152.18 2.38E-08 284590000 160030 173500 193290 210690 183520 192150 211680 254690 246160 232270 FALSE TRUE 153775.8507 168551.9499 228221.8027 221563.7361 189423.0875 196035.4047 214270.6032 249430.5625 218216.9488 216538.146 0.71015594 0.778393798 1.053956575 1.023208798 0.874779298 0.905315799 0.989528206 1.151901257 1.007752919 1 17.72426167 4.321929266 4.985674316 1.006075528 0.728916859 0.668509282 0.072589256 0.128010679 5.419984448 0.020835103 0.059848525 20985.98053 -4.321929266 -0.27715867 DNLTLWTSDQQDEEAGEGN ddPTM_BT-474_Pertuzumab_2h_R1 5 DNLTLWTSDQQDEEAGEGN 19 0 Q04917 Q04917 YWHAH 14-3-3 protein eta 0 ;;;; 338.23 3.26E-75 450052000 1042520 1102010 963410 1195630 1093390 1209370 1140510 1209750 1255950 1308560 FALSE TRUE 1001777.166 1070581.754 1137519.618 1257336.608 1128559.882 1233824.29 1154467.903 1184768.24 1113379.821 1219930.066 0.821175897 0.877576333 0.93244658 1.030662858 0.925102114 1.011389361 0.946339413 0.971177179 0.912658728 1 20.21836701 4.321986998 2.253496663 0.968817142 0.82629137 0.655145207 0.035667212 0.184458687 1.742502113 0.008620511 0.037045908 20988.77048 -4.321986998 -0.142525772 SYETLVDFDNHLDDIR ddPTM_BT-474_Pertuzumab_2h_R1 5 SYETLVDFDNHLDDIR 16 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 ;;;; 211.12 7.92E-12 2516807000 1801248 2106799 1734636 2595422 1922936 2520224 2489117 2055375 2622878 2814357 FALSE TRUE 1730853.237 2046715.155 2048123.312 2729372.04 1984788.983 2571184.656 2519579.558 2012930.788 2325139.885 2623738.094 0.659689792 0.780076015 0.780612713 1.040260858 0.756473745 0.979970014 0.960301474 0.767199589 0.886193592 1 21.32319228 4.322613794 1.73459225 0.894203639 0.667583117 0.416691552 0.093341432 0.472324885 2.402588384 0.024696565 0.136758242 21019.08438 -4.322613794 -0.226620522 GPAFNMAS(ph)PESDFGINLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPAFNMASPESDFGINLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPAFNMAS(0.997)PES(0.003)DFGINLK;GPAFNMAS(0.98)PES(0.02)DFGINLK 295.16 2.83E-49 563070000 789960 813150 852840 856750 841640 1020490 940620 958000 997060 1018550 TRUE FALSE 759087.4899 789959.7582 1006967.159 900966.9702 868712.115 1041125.007 952131.5889 938216.9652 883877.9288 949562.7013 0.799407442 0.831919532 1.060453573 0.948823041 0.914854926 1.096425761 1.002705338 0.98805162 0.930826293 1 19.85690374 4.322697726 6.598041083 0.991805876 0.809806196 0.64538743 0.052610038 0.122564844 7.761257632 0.012729487 0.035420976 21023.14696 -4.322697726 -0.18199968 NVS(ph)ES(ph)PNR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVSESPNR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNR;NVS(1)ES(1)PNR 73.93 0.06183 305230000 785450 809660 687660 839860 791560 825770 804160 847360 892900 937700 TRUE FALSE 754753.7456 786569.2895 811935.4589 883205.2752 817021.2463 842467.6352 814001.5506 829861.7199 791541.7353 874188.7438 0.863376189 0.899770553 0.928787364 1.01031417 0.934605086 0.963713662 0.931150803 0.949293532 0.905458622 1 19.73758528 4.32284985 2.429245309 0.952610808 0.868490886 0.50068224 0.030054667 0.247080971 2.757203604 0.007428842 0.029986167 21030.5122 -4.32284985 -0.084119922 S(ph)PNREWEVLQPAPHQVITNLPEGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPNREWEVLQPAPHQVITNLPEGVR 25 1 O75376;O75376-2;A0A088AWL3 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(1)PNREWEVLQPAPHQVITNLPEGVR;S(1)PNREWEVLQPAPHQVITNLPEGVR 217.4 9.29E-34 1861850000 166862 172324 158393 201748 166401 181301 178474 183969 204280 208472 TRUE FALSE 160340.8486 167409.4882 187018.1385 212160.2385 171753.4393 184967.0304 180658.2182 180169.9759 181090.9908 194352.0058 0.825002284 0.861372578 0.962265029 1.091628757 0.883723523 0.951711456 0.929541311 0.927029156 0.931768057 1 17.56831247 4.322969977 4.3132449 0.955756317 0.834447585 0.44084101 0.052882707 0.195786876 6.57531216 0.0132986 0.039443717 21036.33011 -4.322969977 -0.121308732 DDPIISTHLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DDPIISTHLAK 11 0 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 121.02 0.00042029 398650000 334140 335350 299590 408440 372950 340420 402040 421840 477120 530880 FALSE TRUE 321081.4394 325786.1463 353732.5773 429519.6373 384946.2755 347303.5256 406960.2858 413128.8566 422959.3379 494923.0247 0.648750257 0.658256194 0.714722411 0.867851395 0.777790194 0.701732407 0.822269859 0.834733556 0.854596203 1 18.91684464 4.3231415 0.059730973 1.404249177 7.00E-21 0.762869071 0.05066584 74.30692742 0.802102449 6.302045542 13.35395659 21044.63997 -4.3231415 -1.404249177 RPPPEHFR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPPPEHFR 8 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 0 76.465 0.048482 0 24310 25483 21252 23887 28980 20821 29445 24510 34394 24445 FALSE TRUE 23359.93832 24756.24979 25092.70915 25119.81093 29912.16802 21242.01489 29805.35672 24003.85993 30489.73731 22789.31838 1.025038921 1.086309357 1.101073263 1.102262495 1.312552114 0.932104003 1.307865212 1.053294335 1.337895974 1 14.47607015 4.323328166 1.173115633 1.153025782 1.01611995 0.086238491 0.129837379 2.047549996 3.851564798 0.035780948 0.289954877 21053.68718 -4.323328166 -0.136905832 EYTEEIER ddPTM_BT-474_Pertuzumab_2h_R1 2 EYTEEIER 8 0 P52732 P52732 KIF11 Kinesin-like protein KIF11 0 ; 136.8 0.0018044 394860000 244220 257800 228220 281210 244080 285390 292860 294370 272900 285350 FALSE TRUE 234675.6124 250447.7964 269464.4307 295723.2818 251931.0549 291160.7813 296444.1083 288291.1566 241921.5361 266022.9903 0.882162899 0.9414517 1.012936628 1.111645582 0.947027377 1.094494807 1.114355221 1.083707676 0.90940086 1 18.02119141 4.323424541 2.324059451 1.047205909 0.887101173 0.364058232 0.066255786 0.312935876 3.165650887 0.017011546 0.071362198 21058.35977 -4.323424541 -0.160104736 KPWTSLS(ph)SESVSCPQGS(ph)LSPATSLMQVSERPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPWTSLSSESVSCPQGSLSPATSLMQVSERPR 32 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 2 KPWT(0.003)S(0.002)LS(0.767)S(0.227)ES(0.001)VSCPQGS(0.726)LS(0.269)PAT(0.004)S(0.001)LMQVSERPR 176.22 1.32E-15 117020000 38943 42917 41606 46287 50203 65913 50331 61066 64401 67175 TRUE FALSE 37421.06451 41693.04918 49125.12972 48675.87762 51817.82509 67245.80602 50946.96583 59804.96576 57090.46847 62625.17742 0.597540255 0.665755386 0.784430987 0.777257321 0.827427997 1.073782284 0.8135221 0.954966808 0.911621664 1 15.93445517 4.323454164 0.537866576 0.952700836 0.444604519 0.747193222 0.070325167 1.367696888 0.414254704 0.04098987 0.413806605 21059.79621 -4.323454164 -0.508096317 TETQEKNPLPSKETIEQEK ddPTM_BT-474_Pertuzumab_2h_R1 5 TETQEKNPLPSKETIEQEK 19 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;;; 256.11 3.35E-31 10373083000 5446930 4826220 2520460 2015460 3089580 4052230 2789090 3488190 4211950 2798170 FALSE TRUE 5234057.954 4688580.931 2975963.189 2119478.132 3188959.147 4134168.867 2823223.718 3416157.658 3733827.094 2608647.454 2.006425953 1.797322564 1.140806967 0.812481629 1.222456926 1.584794013 1.082255754 1.309551298 1.431326831 1 21.31487055 4.323803072 4.410040698 1.208807199 1.953222186 0.651683101 0.207510284 0.126026881 4.374851347 0.052993532 0.156365245 21076.72224 -4.323803072 0.744414987 GKFGHEFLEFEFRPDGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKFGHEFLEFEFRPDGK 17 2 P61326;Q96A72;F5H6N1;P61326-2 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ; 153.86 9.58E-08 2133850000 3934900 3751200 2629000 2588780 3198600 3550300 3125500 3313700 3741900 3281300 FALSE TRUE 3781119.758 3644219.449 3104118.782 2722387.246 3301485.874 3622089.499 3163750.804 3245270.937 3317135.199 3059054.628 1.236041921 1.191289431 1.014731399 0.889943978 1.079250381 1.184055187 1.03422501 1.060873809 1.08436612 1 21.54465444 4.324067021 5.121474541 1.046801045 1.223303872 0.483721536 0.070679052 0.177461439 7.735310859 0.018459095 0.052833859 21089.5358 -4.324067021 0.176502827 GPS(ph)PTPEDVSMKEENLCQAFSDALLCK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSPTPEDVSMKEENLCQAFSDALLCK 27 1 H1UBN3;O95067 H1UBN3 CCNB2V;CCNB2 G2/mitotic-specific cyclin-B2 1 GPS(0.848)PT(0.151)PEDVS(0.002)MKEENLCQAFSDALLCK;GPS(0.842)PT(0.158)PEDVSMKEENLCQAFSDALLCK 319.4 1.44E-82 346140000 433320 419340 289920 301480 353670 378410 357510 385130 411720 415760 TRUE FALSE 416385.3753 407380.8338 342314.9932 317039.4189 365046.1167 386061.7095 361885.3143 377176.9309 364983.2717 387600.2049 1.074265106 1.051033587 0.88316515 0.817954725 0.941810949 0.996030716 0.933656148 0.973108183 0.94164881 1 18.56420981 4.324141403 6.732771559 0.935205213 1.066778247 0.497589065 0.05103412 0.179906181 11.55920441 0.013382869 0.03719637 21093.14813 -4.324141403 0.131573035 SEDSGIGLSASS(ph)PELSEHLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SEDSGIGLSASSPELSEHLR 20 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SEDSGIGLSAS(0.008)S(0.992)PELSEHLR;SEDSGIGLSAS(0.002)S(0.998)PELSEHLR;SEDSGIGLSAS(0.042)S(0.958)PELSEHLR 283.55 4.25E-45 1820350000 682500 826550 951670 1211850 1016520 1173350 1213870 1026140 1167940 1430570 TRUE FALSE 655827.1455 802977.6033 1123657.939 1274393.724 1049217.289 1197075.941 1228725.704 1004949.85 1035360.348 1333676.22 0.4917439 0.602078369 0.842526786 0.955549559 0.786710652 0.897576131 0.92130735 0.753518609 0.776320618 1 20.34697703 4.324340716 3.240682517 0.858440555 0.510973782 0.741999482 0.076572098 0.118607393 2.396464514 0.019348742 0.064297524 21102.83078 -4.324340716 -0.347466773 IPVEGPLS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 IPVEGPLSPSR 11 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 IPVEGPLS(0.904)PS(0.096)R;IPVEGPLS(0.986)PS(0.014)R;IPVEGPLS(0.687)PS(0.313)R;IPVEGPLS(0.5)PS(0.5)R 177.16 8.50E-06 2056780000 586975 614950 568494 695100 633200 649380 674250 708410 689200 697660 TRUE FALSE 564035.3681 597412.2281 671233.5119 730974.1943 653567.4531 662510.9085 682501.6732 693781.0859 610964.9054 650406.8668 0.867203895 0.918520788 1.032020949 1.123872197 1.004859399 1.018609954 1.049345737 1.066687825 0.939358018 1 19.31098296 4.324344718 3.536266791 1.036866268 0.877864005 0.591429563 0.045884709 0.141610998 3.369737846 0.011269385 0.035884717 21103.02523 -4.324344718 -0.159002263 SGPKPFSAPKPQTSPS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.19)S(0.149)PS(0.661)PKR 89.829 0.012897 2143900000 169030 159280 76870 73583 101700 134610 113490 127190 143800 118300 TRUE FALSE 162424.1207 154737.4904 90762.11896 77380.62745 104971.2729 137331.9064 114878.9246 124563.4821 127476.4269 110287.4356 1.472734585 1.403038247 0.822959736 0.701626863 0.951797204 1.245218058 1.041632022 1.129443996 1.155856296 1 16.75090892 4.324483201 7.095417504 1.014852428 1.449958997 0.567622432 0.150820756 0.173004305 11.90687069 0.041267902 0.114349656 21109.7554 -4.324483201 0.435106569 AILILDNDGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 AILILDNDGDR 11 0 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8VXB1;F8VUC5;F8W156;F8W651;F8VXR1 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 ;;;;; 237.51 3.24E-15 2445093000 1323980 1457020 1413520 1772670 1664780 1570820 1708350 1798660 1752730 1851990 FALSE TRUE 1272237.398 1415467.216 1668974.508 1864157.711 1718329.161 1602583.057 1729257.298 1761517.042 1553767.438 1726553.068 0.736865505 0.819822595 0.966651149 1.079699052 0.995236806 0.928197972 1.00156626 1.020250739 0.899924519 1 20.71946325 4.324522874 2.908662397 0.992652514 0.749349589 0.770548464 0.046522523 0.114436679 1.867137339 0.011927458 0.042264525 21111.68389 -4.324522874 -0.243302925 ETHQQVVSR ddPTM_BT-474_Pertuzumab_2h_R1 6 ETHQQVVSR 9 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;; 142.98 0.00010303 7545120000 4044030 4105270 3801820 4473780 4168470 4445820 4385510 3858970 4856350 5247090 FALSE TRUE 3885984.837 3988191.719 4488893.445 4704672.322 4302552.623 4535717.526 4439181.183 3779280.921 4305077.507 4891699.921 0.794403766 0.815297705 0.917655113 0.961766339 0.879561848 0.927227263 0.907492539 0.772590507 0.880078005 1 22.22190447 4.325032996 5.683875003 0.893228923 0.800640871 0.313983677 0.057518286 0.278552963 14.02807994 0.015274299 0.043105092 21136.49619 -4.325032996 -0.092588053 AEADKIYSFTDNAPS(ph)PSIGGSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEADKIYSFTDNAPSPSIGGSSR 23 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 AEADKIYSFTDNAPS(0.869)PS(0.129)IGGS(0.001)S(0.001)R;AEADKIYSFTDNAPS(0.997)PS(0.003)IGGSSR 186.02 1.73E-17 890260000 631150 613200 405700 453180 465150 584700 536440 554960 593480 524130 TRUE FALSE 606483.9602 595712.1364 479019.0147 476568.6741 480111.9722 596523.0346 543005.1132 543499.8821 526110.6385 488630.2083 1.241192112 1.219147172 0.980330333 0.975315619 0.982567111 1.220806705 1.111280277 1.11229284 1.076705103 1 18.89838353 4.325044339 7.789609885 1.066970849 1.233830703 0.459303367 0.074466694 0.232589043 18.05348521 0.019710099 0.054388169 21137.04825 -4.325044339 0.166859855 S(ph)PTEDFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPTEDFR 7 0 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.98)PT(0.02)EDFR;S(0.99)PT(0.01)EDFR;S(0.986)PT(0.014)EDFR;S(0.984)PT(0.016)EDFR 110.38 0.0071513 4480940000 3323870 3443040 3179630 3694820 3626820 3498130 3659920 3910360 4086820 3964780 TRUE FALSE 3193969.486 3344847.87 3754259.871 3885510.103 3743479.959 3568864.585 3704711.196 3829609.7 3622901.327 3696241.919 0.864112673 0.904932075 1.015696471 1.051205573 1.012780018 0.965538691 1.002291321 1.036081994 0.980158065 1 21.81762775 4.325099302 3.88346129 1.010701265 0.873151353 0.813870333 0.023876208 0.085918792 2.410353749 0.006269591 0.019244545 21139.72347 -4.325099302 -0.137549911 DLADVAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLADVAAR 8 0 Q9BV20;Q9BV20-2 Q9BV20 MRI1 Methylthioribose-1-phosphate isomerase 0 89.55 0.032796 0 213230 257080 217380 333540 257260 259490 312920 303310 311530 348670 FALSE TRUE 204896.7359 249748.3301 256665.4016 350754.0394 265535.0015 264737.0656 316749.6086 297046.5425 276166.4204 325054.2703 0.630346236 0.768328101 0.789607844 1.07906301 0.816894364 0.814439587 0.974451461 0.913836764 0.849600961 1 18.31032108 4.325323112 1.848890365 0.911815008 0.640807431 0.539728375 0.084080307 0.321248107 1.906015811 0.021913822 0.114501852 21150.62047 -4.325323112 -0.271007578 WIYTDELEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 WIYTDELEFR 10 0 Q9P2R3;Q9P2R3-2;Q9P2R3-4 Q9P2R3 ANKFY1 Rabankyrin-5 0 ;;; 149.94 5.23E-05 141665000 144097 168461 188153 224284 217771 191678 232769 228182 232017 280941 FALSE TRUE 138465.5299 163656.6572 222156.4325 235859.3241 224775.802 195553.8605 235617.6967 223469.962 205679.4029 261912.6158 0.528670715 0.624852135 0.848208216 0.900526778 0.858209145 0.746637805 0.899604228 0.853223359 0.785297807 1 17.99872603 4.325324134 3.254033966 0.856821965 0.544812899 0.759988342 0.064943487 0.105341571 2.143791262 0.015470833 0.051365033 21150.67022 -4.325324134 -0.312009066 ELLVSQHTVQLVGGLS(ph)PLSSPSDTKAES(ph)PAEKVPEESVLPLVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLVSQHTVQLVGGLSPLSSPSDTKAESPAEKVPEESVLPLVQK 44 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 ELLVSQHTVQLVGGLS(1)PLS(0.006)S(0.005)PS(0.002)DT(0.279)KAES(0.707)PAEKVPEESVLPLVQK 340.28 1.03E-133 496150000 323090 299060 226940 183230 249370 262490 246780 288430 336700 275740 TRUE FALSE 310463.2856 290531.1016 267953.1063 192686.5223 257391.2125 267797.7276 249800.1675 282473.8197 298479.2276 257063.8842 1.207728136 1.130190274 1.042359984 0.74956668 1.001273335 1.041755548 0.971743535 1.098846773 1.161109148 1 17.97176741 4.325358093 3.154524947 1.005768775 1.190837489 0.303063873 0.101049991 0.319994471 6.13307803 0.027192622 0.091838122 21152.32414 -4.325358093 0.185068715 RPPDEQR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPPDEQR 7 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;;;; 155.38 0.0025898 2294494000 1122923 1191534 1028285 1334214 1183481 1338577 1293867 1250168 1218411 1315866 FALSE TRUE 1079037.928 1157552.617 1214118.974 1403072.944 1221548.741 1365643.944 1309701.731 1224351.594 1080102.091 1226741.224 0.879597022 0.943599672 0.989710748 1.143739949 0.995767255 1.113229031 1.067626738 0.998052051 0.880464494 1 20.22639952 4.32536692 2.456286044 1.0321107 0.889140665 0.317182656 0.069202489 0.349840464 3.995268636 0.018049111 0.072538847 21152.75405 -4.32536692 -0.142970035 SES(ph)LSNCSIGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SESLSNCSIGKK 12 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.002)ES(0.996)LS(0.001)NCSIGKK;SES(0.998)LS(0.002)NCSIGKK 177.58 1.41E-05 1683710000 1082860 934970 469640 414350 528160 675660 455701 690380 702930 581350 TRUE FALSE 1040540.634 908305.571 554514.3951 435734.6532 545148.7461 689322.3081 461278.0052 676123.4117 623136.3333 541974.6467 1.919906476 1.675918932 1.023137149 0.803976082 1.005856546 1.271871871 0.851106243 1.247518525 1.149751814 1 19.04786584 4.32553127 3.852297271 1.049854837 1.866360342 0.814910331 0.145385687 0.08657986 2.393750679 0.037321249 0.114937331 21160.7604 -4.32553127 0.816505505 DVACGANHTLVLDSQKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVACGANHTLVLDSQKR 17 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 173.37 9.64E-10 1437040000 773320 756000 501620 530700 716980 731460 606560 649580 745050 682280 FALSE TRUE 743097.7994 734439.6202 592273.8925 558089.4906 740042.3128 746250.6224 613983.2627 636165.946 660475.0475 636068.5679 1.168266814 1.154654792 0.93114787 0.877404605 1.163463108 1.173223549 0.965278421 1.000153094 1.038370831 1 19.27882277 4.325753908 8.881090061 1.020411685 1.163630065 0.299145898 0.087455921 0.367366427 33.6013843 0.022784088 0.062636467 21171.61112 -4.325753908 0.14321838 RLKS(ph)EDELRPEVDEHTQK ddPTM_BT-474_Pertuzumab_2h_R1 3 RLKSEDELRPEVDEHTQK 18 3 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCR2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 RLKS(1)EDELRPEVDEHTQK;RLKS(1)EDELRPEVDEHTQK;RLKS(1)EDELRPEVDEHTQK 149.71 4.30E-08 3185430000 2564780 2272200 1449720 1228600 1691080 1724730 1576060 1903320 1892200 1603440 TRUE FALSE 2464545.562 2207399.081 1711716.653 1292008.193 1745475.124 1759605.222 1595348.294 1864015.777 1677405.389 1494837.581 1.648704578 1.476681553 1.145085376 0.864313428 1.167668747 1.177121344 1.067238551 1.246968768 1.122132204 1 20.51155731 4.325761459 3.201506751 1.107650401 1.61757245 0.77754564 0.101195874 0.112281819 2.214022143 0.026598473 0.089143342 21171.9792 -4.325761459 0.509922049 GEGTEQEPSTTPEADDDGRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEGTEQEPSTTPEADDDGRR 20 1 Q10570 Q10570 CPSF1 Cleavage and polyadenylation specificity factor subunit 1 0 ; 242.9 1.32E-29 325130000 187451 202539 216632 261789 231520 229366 241569 263245 240052 262177 FALSE TRUE 180125.2077 196762.786 255782.2214 275299.9617 238967.0511 234003.9377 244525.3937 257808.8988 212802.3033 244419.5183 0.736950997 0.805020759 1.046488526 1.12634197 0.977692178 0.957386461 1.000433171 1.054780324 0.870643657 1 17.89899997 4.325853511 4.744167731 1.009888494 0.755041836 0.681015427 0.064242656 0.108298069 4.177732305 0.015972196 0.046401074 21176.46727 -4.325853511 -0.254846658 SKESVPEFPLS(ph)PPKKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKESVPEFPLSPPKKK 16 3 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 SKESVPEFPLS(1)PPKKK 108.18 0.0059141 1100300000 1216700 1064100 516940 398840 677050 988110 644410 636150 793410 489830 TRUE FALSE 1169150.019 1033752.91 610362.5573 419424.1802 698827.9281 1008090.261 652296.4823 623013.2802 703345.423 456653.3778 2.560257026 2.263758378 1.336599239 0.918473837 1.530324667 2.207561162 1.428428025 1.364302358 1.540217279 1 18.80073998 4.326383099 4.404956526 1.439508584 2.485648822 0.593112696 0.332482031 0.145403263 4.997591224 0.085763577 0.253552257 21202.30605 -4.326383099 1.046140237 LTAEDLFEAR ddPTM_BT-474_Pertuzumab_2h_R1 8 LTAEDLFEAR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;;;; 224.86 8.77E-09 1043431000 1051674 1155234 1077968 1363649 1248071 1312636 1359903 1372518 1322903 1373060 FALSE TRUE 1010573.417 1122287.857 1272780.797 1434027.088 1288216.337 1339178.399 1376545.9 1344175.024 1172732.598 1280061.423 0.789472598 0.876745316 0.994312284 1.120279904 1.006370721 1.046182921 1.07537488 1.050086347 0.916153378 1 20.28778161 4.326394479 2.47750422 1.037136547 0.798447265 0.707745942 0.051241791 0.148478902 1.727012253 0.012896937 0.051569422 21202.86162 -4.326394479 -0.238689282 NYPS(ph)QEELIK ddPTM_BT-474_Pertuzumab_2h_R1 2 NYPSQEELIK 10 0 P38398-7;P38398;P38398-4;P38398-8;P38398-6;E7EUM2;B7ZA85;H0Y8B8;P38398-5;P38398-3;A0A2R8Y7V5;K7EPC7 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 NYPS(1)QEELIK;NYPS(1)QEELIK 102.87 0.0042119 0 248646 231215 156547 190012 177834 179759 177292 201572 188444 188319 TRUE FALSE 238928.6394 224620.9746 184838.5253 199818.5421 183554.1921 183393.8501 179461.7525 197409.4678 167052.6271 175563.9864 1.360920564 1.279425121 1.052827115 1.138152227 1.045511644 1.044598348 1.022201399 1.124430311 0.951519902 1 17.42163741 4.326549326 3.052646036 1.055283337 1.351745208 0.813778148 0.052613491 0.096838864 1.739050962 0.012814834 0.044191975 21210.42282 -4.326549326 0.296461871 T(ph)PPSEEPVLFQSSLMV ddPTM_BT-474_Pertuzumab_2h_R1 2 TPPSEEPVLFQSSLMV 16 0 Q9C073;Q9C073-2 Q9C073 FAM117A Protein FAM117A 1 T(0.906)PPS(0.094)EEPVLFQSSLMV;T(0.9)PPS(0.1)EEPVLFQSSLMV 97.214 0.035205 10456900 15697.3 17157.8 18226 22873 22033 18529.9 20688 20754.6 20558 22572 TRUE FALSE 15083.83216 16668.47634 21519.84364 24053.47827 22741.71145 18904.58727 20941.18593 20326.01026 18224.34203 21043.17833 0.716803893 0.792108306 1.022651773 1.143053482 1.080716567 0.89837129 0.995153185 0.965919213 0.866045126 1 14.361065 4.326873811 4.375883112 0.998201392 0.735692348 0.62267285 0.076083771 0.137473094 4.669554637 0.020287223 0.060099827 21226.27618 -4.326873811 -0.262509044 RLS(ph)ESQLSFR ddPTM_BT-474_Pertuzumab_2h_R1 5 RLSESQLSFR 10 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 RLS(1)ESQLSFR;RLS(0.999)ES(0.001)QLSFR;RLS(0.473)ES(0.447)QLS(0.08)FR;RLS(0.905)ES(0.095)QLSFR;RLS(0.729)ES(0.266)QLS(0.005)FR 171.93 2.37E-06 1461660000 1388940 1183629 700117 642918 634896 449245 415574 723100 461624 495823 TRUE FALSE 1334658.689 1149873.06 826643.7159 676099.075 655318.0064 458329.0417 420659.9189 708167.7323 409222.3788 462240.4666 2.887368774 2.487607951 1.788341298 1.462656613 1.417699344 0.991538117 0.910045635 1.532033181 0.885301934 1 18.81828404 4.326936306 0.883869428 1.124460012 3.362240834 0.914226112 0.19011378 0.356485357 0.329172789 0.068902805 0.685116892 21229.33088 -4.326936306 2.237780822 up MDAEHPELR ddPTM_BT-474_Pertuzumab_2h_R1 5 MDAEHPELR 9 0 Q12765;Q12765-2;Q12765-3;C9K052 Q12765 SCRN1 Secernin-1 0 ;;;; 166.34 6.08E-05 6346549000 7279813 7667811 6797083 8257191 8211964 8417258 8600526 7790075 8639416 8605863 FALSE TRUE 6995309.86 7449132.538 8025467.098 8683345.617 8476109.28 8587460.724 8705781.81 7629207.229 7658705.715 8022980.234 0.871909148 0.928474497 1.000309968 1.082309237 1.056478894 1.070357956 1.085105728 0.95091936 0.954596109 1 22.93570681 4.3269687 2.480628845 1.028758391 0.878115948 0.558788918 0.046092303 0.242495941 2.82761692 0.013303774 0.053198992 21230.91443 -4.3269687 -0.150642443 EFGVTTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 EFGVTTGR 8 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 163.9 0.00077526 594590000 452998 483900 458473 544780 507806 531990 548060 570880 542020 659500 FALSE TRUE 435294.3373 470099.6458 541329.2698 572896.1611 524140.0412 542747.2023 554767.3222 559091.1285 480492.1619 614831.4776 0.707989674 0.764599184 0.880451456 0.931793804 0.85249383 0.88275767 0.902307937 0.909340444 0.781502216 1 19.2298315 4.32712787 3.033575884 0.891515958 0.716500524 0.59460013 0.052629459 0.159198024 2.822800426 0.012364747 0.042838588 21238.69704 -4.32712787 -0.175015434 S(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_BT-474_Pertuzumab_2h_R1 13 SPTMEQAVQTASAHLPAPAAVGR 23 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.591)PT(0.409)MEQAVQTASAHLPAPAAVGR;S(0.978)PT(0.022)MEQAVQTASAHLPAPAAVGR;S(0.974)PT(0.026)MEQAVQTASAHLPAPAAVGR;S(0.851)PT(0.149)MEQAVQTASAHLPAPAAVGR;S(0.97)PT(0.03)MEQAVQTASAHLPAPAAVGR;S(0.84)PT(0.16)MEQAVQTASAHLPAPAAVGR;S(0.96)PT(0.04)MEQAVQTASAHLPAPAAVGR;S(0.962)PT(0.038)MEQAVQTASAHLPAPAAVGR;S(0.968)PT(0.032)MEQAVQTASAHLPAPAAVGR;S(0.971)PT(0.029)MEQAVQTASAHLPAPAAVGR;S(0.948)PT(0.052)MEQAVQTASAHLPAPAAVGR;S(0.526)PT(0.473)MEQAVQT(0.001)ASAHLPAPAAVGR;S(0.98)PT(0.02)MEQAVQTASAHLPAPAAVGR 252.81 1.14E-43 32762150000 1155868 1241592 1276768 1583318 1299240 1378851 1417237 1576766 1465966 1680063 TRUE FALSE 1110695.401 1206183.012 1507508.379 1665033.232 1341031.235 1406732.312 1434581.57 1544205.231 1299555.686 1566270.837 0.709133679 0.770098621 0.962482569 1.063055758 0.856193708 0.898141164 0.915921779 0.985912012 0.829713262 1 20.57890227 4.327296151 4.465207229 0.939651728 0.724650417 0.597711122 0.066001062 0.13269719 4.644832814 0.016164794 0.047652157 21246.92821 -4.327296151 -0.215001311 NKKS(ph)PEIHRR ddPTM_BT-474_Pertuzumab_2h_R1 3 NKKSPEIHRR 10 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NKKS(1)PEIHRR;NKKS(1)PEIHRR;NKKS(1)PEIHRR 136.01 9.20E-05 5298900000 6960450 6007150 3563480 2697390 3632880 4997830 3851830 4087090 5667010 3828050 TRUE FALSE 6688427.919 5835831.964 4207480.105 2836602.621 3749734.884 5098889.547 3898969.848 4002690.163 5023714.783 3568772.764 1.874153487 1.635248964 1.178971143 0.794839798 1.050707101 1.42875153 1.092523987 1.121587287 1.407686932 1 21.76699661 4.327313958 3.200225602 1.128285022 1.831056935 0.676760705 0.175218713 0.138959125 2.735248573 0.045306753 0.152196498 21247.79941 -4.327313958 0.702771913 MIDQVFGVLES(ph)PELSR ddPTM_BT-474_Pertuzumab_2h_R1 6 MIDQVFGVLESPELSR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 MIDQVFGVLES(0.963)PELS(0.037)R;MIDQVFGVLES(1)PELSR;MIDQVFGVLES(0.999)PELS(0.001)R;MIDQVFGVLES(0.999)PELS(0.001)R;MIDQVFGVLES(1)PELSR;MIDQVFGVLES(0.999)PELS(0.001)R 257.56 1.18E-26 416584000 221855 246491 225053 284454 286287 266453 286022 299113 272492 287805 TRUE FALSE 213184.6613 239461.318 265725.0834 299134.705 295495.6814 271840.8622 289522.4228 292936.212 241559.8505 268311.711 0.794541023 0.892474343 0.990359617 1.114877558 1.101314886 1.013153176 1.079052501 1.091775722 0.900295591 1 18.0335505 4.327334519 2.10526819 1.052421948 0.799425686 0.635351476 0.061006921 0.207821063 1.675455177 0.015727123 0.072728705 21248.80539 -4.327334519 -0.252996262 LAVVDEWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAVVDEWR 8 0 Q8NFW8 Q8NFW8 CMAS N-acylneuraminate cytidylyltransferase 0 ; 139.28 0.001557 199092000 512760 537210 500210 626150 616820 493790 624340 591100 567790 641250 FALSE TRUE 492720.7723 521889.2968 590609.0741 658465.6765 636660.5755 503774.7721 631980.8597 578893.5784 503336.8596 597817.5663 0.824199221 0.872990903 0.987941987 1.101449194 1.064974687 0.842689811 1.057146687 0.968344878 0.841957293 1 19.18934576 4.327442559 3.834631282 0.987185679 0.835358482 0.308096889 0.081702304 0.256848736 7.023448077 0.020512528 0.063391437 21254.09216 -4.327442559 -0.151827197 AS(ph)WESLDEEWR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASWESLDEEWR 11 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 AS(0.998)WES(0.002)LDEEWR;AS(0.999)WES(0.001)LDEEWR;AS(0.998)WES(0.002)LDEEWR;AS(0.988)WES(0.012)LDEEWR 237.67 1.44E-15 698300000 674762 747120 713417 876850 777490 903110 927510 953260 910590 976330 TRUE FALSE 648391.5551 725812.8691 842347.3218 922104.3336 802498.6719 921371.503 938861.1448 933574.8479 807223.6407 910202.2995 0.71235983 0.797419287 0.925450663 1.013076251 0.881670671 1.012271122 1.031486237 1.025678411 0.88686179 1 19.79582771 4.32748792 1.743612966 0.984596843 0.699551679 0.755388525 0.051199974 0.213924727 1.09811178 0.014059486 0.078324921 21256.31219 -4.32748792 -0.285045164 SNKPIILR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNKPIILR 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 112.84 0.0027025 2742700000 3404100 3494600 3091200 3559400 3297500 3780500 3635000 3894600 4035900 3750100 FALSE TRUE 3271064.009 3394937.43 3649848.603 3743101.061 3403567.082 3856944.3 3679486.217 3814175.149 3577761.552 3496102.387 0.93563164 0.971063503 1.043976463 1.070649725 0.973531867 1.103212628 1.052453793 1.090979247 1.023357201 1 21.73731601 4.327501712 2.877087381 1.051689666 0.940047588 0.489506705 0.037684516 0.195819378 3.120745569 0.009249632 0.033167534 21256.98724 -4.327501712 -0.111642077 SSATSGDIWPGLSAYDNS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 9 SSATSGDIWPGLSAYDNSPR 20 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLS(0.004)AYDNS(0.996)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLS(0.012)AY(0.054)DNS(0.934)PR;SSATSGDIWPGLS(0.003)AY(0.001)DNS(0.996)PR;SSATSGDIWPGLSAYDNS(1)PR 452.52 4.46E-198 35163470000 1952432 2122056 2087520 2716475 2211985 2372323 2459683 2460505 2600438 2845107 TRUE FALSE 1876128.799 2061537.041 2464781.301 2856672.6 2283135.506 2420292.996 2489785.336 2409694.712 2305247.18 2652405.369 0.707331097 0.777233022 0.929262672 1.077012071 0.860779251 0.912489857 0.938689601 0.908494132 0.869115712 1 21.33886985 4.327589235 3.605115172 0.934388342 0.722255185 0.635646076 0.059925971 0.139503622 3.424441207 0.01497735 0.047459025 21261.27156 -4.327589235 -0.212133157 LSQLEGVNVER ddPTM_BT-474_Pertuzumab_2h_R1 2 LSQLEGVNVER 11 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 134.3 0.00033416 260400000 131315 134907 144548 166843 156760 156994 136656 167432 149378 161279 FALSE TRUE 126183.0646 131059.5844 170671.0391 175453.7872 161802.3278 160168.5262 138328.437 163974.4707 132421.2357 150355.4297 0.839231845 0.871665125 1.135117231 1.166926845 1.076132256 1.065265994 0.920009589 1.090578977 0.880721341 1 17.19801744 4.327606757 7.01728063 1.047057981 0.849581987 0.437247952 0.084578001 0.190536494 12.53487404 0.020840715 0.057800757 21262.12941 -4.327606757 -0.197475994 GS(ph)PIDVLHGLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPIDVLHGLIR 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3 M0QXA7 WIZ Protein Wiz 1 GS(1)PIDVLHGLIR 113.76 0.00072868 19628000 21691 21901 25641 27648 25044 24981 30312 24691 22385 28268 TRUE FALSE 20843.29174 21276.40492 30274.89908 29074.91659 25849.563 25486.13294 30682.96732 24181.12222 19843.94865 26353.38318 0.790915216 0.807350038 1.148805027 1.103270741 0.980882144 0.967091502 1.1642895 0.917571837 0.75299435 1 14.68570056 4.327649108 9.472328722 1.006436147 0.796449512 0.343151498 0.113588349 0.342109976 33.20020055 0.028339839 0.077820603 21264.2029 -4.327649108 -0.209986635 KLESTES(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 KLESTESR 8 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 KLES(0.132)T(0.132)ES(0.735)R 93.258 0.01186 397100000 391950 342300 268740 251730 312320 252120 181080 247550 228680 189890 TRUE FALSE 376632.1607 332537.9391 317307.2961 264721.8155 322366.0564 257218.0391 183296.1112 242438.006 202721.2051 177028.5812 2.127521772 1.878442097 1.792407158 1.495362013 1.820983111 1.452974641 1.035404057 1.36948511 1.145132632 1 17.43362278 4.327885011 0.257511772 0.945459101 2.827029086 0.838423621 0.146879574 2.934326893 0.195993269 0.214127909 1.740213896 21275.75647 -4.327885011 1.881569985 up AAPGEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAPGEFR 7 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 84.359 0.082479 0 175080 184800 193290 185240 237990 346810 178230 234330 196220 200030 FALSE TRUE 168237.68 179529.6849 228221.8027 194800.2586 245645.1645 353822.7358 180411.2321 229491.0036 173945.9282 186481.7899 0.902166802 0.962719658 1.223828894 1.044607405 1.317260868 1.897358106 0.967446913 1.230634925 0.93277702 1 17.50867523 4.328134348 1.574328044 1.2304569 0.863835064 0.133901569 0.264709335 1.025938483 4.079252799 0.074403535 0.46059108 21287.97484 -4.328134348 -0.366621837 LFVT(ph)PPEGSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFVTPPEGSSR 11 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LFVT(1)PPEGSSR;LFVT(0.981)PPEGS(0.018)S(0.001)R 137.95 0.0037189 373200000 493210 526080 538180 605610 587530 639950 631660 602320 606030 713430 TRUE FALSE 473934.8079 511076.7135 635441.0977 636865.6047 606428.436 652890.2275 639390.444 589881.8815 537236.0151 665108.7506 0.712567392 0.768410749 0.955394283 0.957536048 0.911773354 0.981629285 0.961332178 0.886895385 0.807741613 1 19.34323073 4.328225592 4.487466671 0.929891679 0.726472138 0.684211315 0.052640979 0.114943496 4.042390726 0.013267246 0.039083701 21292.44784 -4.328225592 -0.203419541 EELLPHLLPLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EELLPHLLPLLK 12 0 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 65.179 0.074772 0 372090 333470 399620 317800 431270 423170 352620 375090 448440 455140 FALSE TRUE 357548.3114 323959.7621 471840.2235 334201.6961 445142.1912 431726.7873 356935.469 367344.2604 397534.9712 424312.9624 0.842652342 0.763492494 1.11200992 0.787630183 1.049089306 1.017472539 0.841208025 0.865738954 0.936890942 1 18.69476923 4.328290323 22.77528737 0.93713475 0.803065024 0.264369754 0.096596992 14.26121164 3613.754396 0.02284483 0.062563126 21295.62166 -4.328290323 -0.134069726 VQDDEVGDGTTSVTVLAAELLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQDDEVGDGTTSVTVLAAELLR 22 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 336.47 1.34E-80 679795000 380446 398331 352014 415832 398498 444846.9 409940 434196 482285 488188 FALSE TRUE 365577.7497 386970.9899 415630.7603 437293.1394 411316.0501 453842.0091 414956.9683 425229.7009 427538.0287 455122.5919 0.80325116 0.850256605 0.913228145 0.960824945 0.90374782 0.99718629 0.911747682 0.934319035 0.939390916 1 18.79589568 4.328358607 1.818950404 0.94458383 0.799014098 0.727810658 0.030177884 0.211567726 1.203847664 0.007537237 0.040311286 21298.97027 -4.328358607 -0.145569733 HGS(ph)DPAFAPGPR ddPTM_BT-474_Pertuzumab_2h_R1 4 HGSDPAFAPGPR 12 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 HGS(1)DPAFAPGPR;HGS(1)DPAFAPGPR;HGS(1)DPAFAPGPR;HGS(1)DPAFAPGPR 181.66 1.87E-05 5443360000 3221670 3000360 2326540 2440410 2416110 2565290 2790350 1542100 3439240 3218170 TRUE FALSE 3095763.575 2914792.67 2746997.532 2566359.853 2493826.372 2617161.921 2824499.138 1510255.096 3048831.894 3000200.479 1.031852236 0.971532633 0.915604657 0.855396121 0.83121991 0.872329012 0.9414368 0.503384726 1.016209388 1 21.51662748 4.328458797 0.75153371 0.811350228 1.097695073 0.098078598 0.138402953 2.73817254 1.721692314 0.056909234 0.600605293 21303.88439 -4.328458797 0.286344845 SVTEQGAELSNEER ddPTM_BT-474_Pertuzumab_2h_R1 7 SVTEQGAELSNEER 14 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;; 364.95 1.38E-96 14951770000 3467617 3694247 3100617 4141303 3599305 3875921 3580847 4042315 4177700 3970424 FALSE TRUE 3332098.694 3588890.693 3660967.465 4355036.144 3715079.914 3954294.778 3624670.477 3958839.783 3703465.01 3701503.646 0.900201381 0.969576431 0.989048726 1.176558653 1.003667771 1.068294174 0.979242714 1.069522054 1.000529883 1 21.81968002 4.328496946 2.301630959 1.043509007 0.911058746 0.385215116 0.055257822 0.308612335 3.047500603 0.013636845 0.058275664 21305.75584 -4.328496946 -0.132450262 EALSVALEEAQAWR ddPTM_BT-474_Pertuzumab_2h_R1 4 EALSVALEEAQAWR 14 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;; 198.57 5.08E-08 552731000 312158 327619 291751 386279 348811 328050 337922 354799 369103 349906 FALSE TRUE 299958.5203 318275.6269 344476.8957 406214.9055 360030.8226 334683.3958 342057.5905 347472.2767 327203.9748 326206.555 0.919535539 0.975687404 1.056008503 1.245268985 1.103689724 1.025986114 1.04859202 1.06519097 1.003057633 1 18.31542625 4.328756641 3.274076951 1.075643755 0.931456109 0.356656475 0.066520191 0.257982303 5.299321041 0.01755496 0.058355914 21318.49986 -4.328756641 -0.144187646 HQYYNQEWTLWDR ddPTM_BT-474_Pertuzumab_2h_R1 6 HQYYNQEWTLWDR 13 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 242.4 6.23E-17 5121950000 2235370 2256890 2553100 2895530 2484630 2242790 3016980 2139770 3120040 3265550 FALSE TRUE 2148009.269 2192525.707 3014501.963 3044968.65 2564550.38 2288140.75 3053902.704 2095583.002 2765866.139 3044371.39 0.705567421 0.720189959 0.990188639 1.000196185 0.842390777 0.751597114 1.003130799 0.688346701 0.908517978 1 21.53771294 4.328797263 9.160095357 0.878994074 0.710426438 0.317125779 0.105811977 0.37062465 34.01859659 0.026199017 0.071984965 21320.49397 -4.328797263 -0.168567636 DEPNSTPEKTEQFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DEPNSTPEKTEQFYR 15 1 O76021;J3QSV6;I3L3U9;I3L3C4;I3L234 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 88.133 0.0062956 385380000 227330 209790 137680 130840 178030 180930 149730 192700 173940 153180 FALSE TRUE 218445.6923 203806.9946 162561.8387 137592.6681 183756.4966 184588.5286 151562.4405 188720.6777 154195.0604 142804.9822 1.52967837 1.427170058 1.13834851 0.963500475 1.286765306 1.292591657 1.0613246 1.321527266 1.07975967 1 17.12368679 4.328969231 4.178066408 1.162195077 1.505032141 0.558396657 0.119536905 0.155666552 4.889099624 0.029362111 0.088257682 21328.93795 -4.328969231 0.342837065 GHEFYNPQKK ddPTM_BT-474_Pertuzumab_2h_R1 2 GHEFYNPQKK 10 1 P78406 P78406 RAE1 mRNA export factor 0 ; 166.66 3.56E-06 2171480000 3322200 3179200 2303800 2596500 2706100 2844000 2853200 2260700 3778000 3365400 FALSE TRUE 3192364.751 3088532.329 2720147.908 2730505.676 2793144.164 2901507.629 2888118.315 2214015.755 3349137.279 3137458.46 1.017500245 0.984405807 0.866990892 0.870292216 0.890256939 0.924795552 0.920527985 0.705671735 1.067468246 1 21.58116493 4.329051384 4.676352997 0.885662743 1.009004671 0.123709683 0.090612293 0.310299821 11.57598595 0.022020805 0.064274652 21332.97301 -4.329051384 0.123341928 SFSSPPS(ph)PSNKR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFSSPPSPSNKR 12 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SFSSPPS(0.986)PS(0.014)NKR;SFSSPPS(0.999)PS(0.001)NKR;SFSSPPS(0.986)PS(0.014)NKR;SFSSPPS(0.999)PS(0.001)NKR 108.14 0.0010648 5041020000 1205110 1286090 1161410 1425090 1249860 1411360 1489350 1386770 1567030 1622730 TRUE FALSE 1158012.969 1249411.972 1371302.622 1498639.066 1290062.882 1439898.666 1507577.111 1358132.715 1389147.324 1512821.052 0.765465927 0.825882196 0.906453953 0.99062547 0.852753127 0.951797084 0.996533667 0.897748424 0.918249599 1 20.52880991 4.329116137 2.308709016 0.938000688 0.76930503 0.641901294 0.044502954 0.19860598 1.974158901 0.011209923 0.047834616 21336.154 -4.329116137 -0.168695658 SSSSTPTS(ph)PKPLLQSPKPSLAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSSTPTSPKPLLQSPKPSLAAR 23 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.007)S(0.005)S(0.026)S(0.026)T(0.029)PT(0.144)S(0.763)PKPLLQSPKPSLAAR 76.162 0.0085141 803180000 541620 536530 576410 595160 560920 512100 632750 668030 594220 594950 TRUE FALSE 520452.8916 521228.6897 680580.1092 625876.2789 578962.5012 522455.0129 640493.7838 654234.9471 526766.6368 554653.5066 0.938338774 0.939737482 1.227036521 1.128409487 1.043827352 0.941948454 1.154763787 1.179538107 0.949721999 1 19.08122727 4.32921934 15.5911238 1.08902686 0.938791052 0.263019526 0.091716149 1.584030509 268.3169588 0.022774751 0.062375052 21341.22477 -4.32921934 -0.150235808 LS(ph)PSWNPK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSPSWNPK 8 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 LS(0.963)PS(0.037)WNPK;LS(1)PSWNPK;LS(1)PSWNPK 207.88 6.27E-05 1037250000 1313500 1368820 1338400 1530240 1591560 1648140 1440960 1509600 1506200 1566820 TRUE FALSE 1262166.968 1329782.594 1580278.653 1609215.87 1642753.973 1681466.52 1458594.9 1478426.232 1335222.491 1460697.886 0.864084887 0.910374833 1.081865503 1.101676045 1.124636373 1.151139148 0.998560287 1.012136902 0.914099009 1 20.47822639 4.329268125 4.854396504 1.051805283 0.87636473 0.48141647 0.067144558 0.17601572 6.927936161 0.017955656 0.052004343 21343.6222 -4.329268125 -0.175440553 SKS(ph)PSGQKR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.001)KS(0.833)PS(0.165)GQKR;S(0.005)KS(0.498)PS(0.498)GQKR;S(0.001)KS(0.973)PS(0.026)GQKR;S(0.124)KS(0.862)PS(0.015)GQKR 97.779 0.0033708 3542150000 4374190 3898510 2899860 2541890 2844170 3166560 3538370 3331620 3303360 3714650 TRUE FALSE 4203241.819 3787328.312 3423929.209 2673077.248 2935655.311 3230590.013 3581673.631 3262820.883 2928376.422 3463053.447 1.213738651 1.093638423 0.988702387 0.771884491 0.847707191 0.932873276 1.034253062 0.942180343 0.845605321 1 21.72361322 4.329721025 2.35273522 0.914796188 1.199964679 0.63771356 0.074163148 0.21147811 2.19206051 0.020617286 0.086645578 21365.89182 -4.329721025 0.285168491 RSS(ph)LLNAK ddPTM_BT-474_Pertuzumab_2h_R1 3 RSSLLNAK 8 1 E9PCH4;Q8TEU7-2;Q8TEU7-5;Q8TEU7-3;Q8TEU7;Q8TEU7-4;D6RE77;B7Z7Y1;A0A5F9ZHG7 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 1 RS(0.345)S(0.655)LLNAK;RS(0.168)S(0.832)LLNAK;RS(0.198)S(0.802)LLNAK 121.68 0.00087154 1278390000 1146980 1101740 868050 954410 958230 905010 988220 1100390 1139300 1128000 TRUE FALSE 1102154.754 1070319.454 1024925.945 1003667.214 989052.3382 923309.9223 1000314.132 1077666.562 1009971.44 1051599.555 1.048074572 1.017801357 0.974635202 0.954419588 0.94052183 0.878005242 0.951231034 1.024787959 0.96041448 1 20.00415401 4.330141953 2.114564943 0.959085059 1.047836064 0.409713727 0.036096902 0.404561421 3.289722334 0.010759081 0.049845237 21386.61018 -4.330141953 0.088751006 AFCGFEDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFCGFEDPR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 91.626 0.024719 558350000 823530 888930 806590 1040200 984950 924730 963780 1034000 981730 1018800 FALSE TRUE 791345.5371 863578.5868 952358.7555 1093884.847 1016631.811 943428.6742 975575.0279 1012647.539 870288.1261 949795.7685 0.833174418 0.909225557 1.002698461 1.151705327 1.070368857 0.993296354 1.027141897 1.066173984 0.916289749 1 19.8572578 4.330431614 2.700031891 1.038372167 0.844389885 0.555068623 0.058197445 0.194216711 2.710892846 0.01495178 0.056335106 21400.8791 -4.330431614 -0.193982282 KGPQVR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGPQVR 6 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 126.04 0.028323 8179400000 4796450 4911110 4415620 5138480 4839580 5116990 4935280 5599040 5574040 5287460 FALSE TRUE 4608999.431 4771049.951 5213620.759 5403677.569 4995249.486 5220459.044 4995679.433 5483417.867 4941298.347 4929335.625 0.935014327 0.967889045 1.057672099 1.096228372 1.013371754 1.059059362 1.013458976 1.112405055 1.002426843 1 22.23296178 4.330459075 4.025652187 1.051213034 0.942531458 0.498361059 0.037274519 0.150230962 4.431370682 0.008811518 0.02683394 21402.23235 -4.330459075 -0.108681576 KNTFTAWS(ph)DEESDYEIDDR ddPTM_BT-474_Pertuzumab_2h_R1 3 KNTFTAWSDEESDYEIDDR 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 KNTFTAWS(1)DEESDYEIDDR;KNTFTAWS(1)DEESDYEIDDR;KNTFTAWS(1)DEESDYEIDDR 254.11 4.17E-31 1037190000 443820 438270 558520 638890 545410 629940 881690 848440 943080 1042340 TRUE FALSE 426475.0237 425770.9687 659456.9882 671863.1895 562953.608 642677.8184 892480.386 830919.4175 836025.5121 971741.3834 0.438877083 0.438152554 0.678634253 0.691401232 0.579324517 0.661367139 0.918434062 0.855082877 0.860337459 1 19.89021288 4.33050512 0.220513673 1.04953223 1.54E-16 0.835412025 0.074732403 4.011521804 0.205414992 0.151228673 1.160249828 21404.50161 -4.33050512 -1.04953223 down SIDQFANLVLHQTVER ddPTM_BT-474_Pertuzumab_2h_R1 2 SIDQFANLVLHQTVER 16 0 O15116 O15116 LSM1 U6 snRNA-associated Sm-like protein LSm1 0 ; 184.01 1.89E-09 708120000 292010 306050 281300 349050 323890 353340 347600 305170 329650 353090 FALSE TRUE 280597.9264 297321.7537 332137.1675 367064.5123 334308.216 360484.7769 351854.0328 298868.1329 292229.514 329174.8998 0.852428076 0.903233369 1.008999069 1.115104805 1.015594495 1.095116235 1.068896909 0.907931112 0.887763661 1 18.32849481 4.330540345 3.539947036 1.013598392 0.862999363 0.388214755 0.068849166 0.25528825 6.046845404 0.019190769 0.061504359 21406.23777 -4.330540345 -0.150599029 SAFS(ph)PYQTPVAHFPPPPEEPTATAAFGAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SAFSPYQTPVAHFPPPPEEPTATAAFGAR 29 0 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 1 S(0.059)AFS(0.864)PYQT(0.076)PVAHFPPPPEEPTATAAFGAR;S(0.042)AFS(0.958)PYQTPVAHFPPPPEEPTATAAFGAR;S(0.045)AFS(0.954)PYQT(0.001)PVAHFPPPPEEPTATAAFGAR 182.83 6.00E-18 399585000 72457 75661 71513 76174 88467 99842 65427 87948 93914 77833 TRUE FALSE 69625.30033 73503.22236 84436.9899 80105.34927 91312.6214 101860.8736 66227.7152 86131.84307 83253.27644 72561.30158 0.959537644 1.012981035 1.163664213 1.103967921 1.258420389 1.403790608 0.912713992 1.187021748 1.147350924 1 16.14691271 4.330589643 3.524988057 1.155013672 0.96878734 0.208014652 0.126300034 0.336384621 7.907108872 0.031177405 0.100120772 21408.66779 -4.330589643 -0.186226333 RGEEGHDPKEPEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 3 RGEEGHDPKEPEQLRK 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 160.43 5.27E-09 2076240000 2296150 2172970 1220490 1257320 1703370 1955230 1541630 1767930 2053380 1628850 FALSE TRUE 2206413.919 2110999.023 1441059.693 1322210.436 1758160.443 1994766.09 1560496.929 1731421.628 1820288.911 1518526.539 1.452996614 1.390162746 0.948985517 0.870719347 1.15780686 1.313619512 1.027638892 1.140198464 1.198720513 1 20.53424069 4.330990742 6.637680353 1.0907135 1.433667289 0.551509297 0.122512698 0.161393396 9.589862389 0.031632168 0.088076913 21428.4492 -4.330990742 0.342953789 SAPAS(ph)PT(ph)HPGLMSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.503)APAS(0.526)PT(0.844)HPGLMS(0.127)PR 149.6 1.77E-05 540220000 448150 411710 263840 335150 287900 303720 310920 359710 310690 310700 TRUE FALSE 430635.8025 399968.4339 311521.7571 352447.1317 297160.565 309861.4265 314725.132 352281.8628 275421.7737 289656.0123 1.486714531 1.380839399 1.075488662 1.216778236 1.0259085 1.069756585 1.0865479 1.216207667 0.950858128 1 18.14398109 4.331064094 3.550950418 1.095833436 1.468423543 0.750275342 0.081971788 0.107433214 2.557547311 0.020017743 0.064100913 21432.06875 -4.331064094 0.372590106 SKPGAAMVEMADGYAVDR ddPTM_BT-474_Pertuzumab_2h_R1 7 SKPGAAMVEMADGYAVDR 18 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;; 239.56 5.83E-24 9400060000 7999990 8230930 7184590 8283160 8238640 8477190 8785050 9032770 9181050 9085410 FALSE TRUE 7687341.546 7996191.935 8483005.233 8710654.88 8503643.338 8648604.59 8892564.07 8846240.143 8138855.694 8470047.088 0.907591359 0.944055193 1.001529879 1.028406901 1.003966477 1.021081052 1.049883664 1.044414518 0.960898518 1 23.01393856 4.331118773 1.998090178 1.02094975 0.905732222 0.690206931 0.024122186 0.202426262 1.440609957 0.00647614 0.031746947 21434.76728 -4.331118773 -0.115217528 S(ph)PENSTLEEILGQYQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPENSTLEEILGQYQR 16 0 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 S(1)PENSTLEEILGQYQR;S(0.998)PENS(0.002)TLEEILGQYQR;S(1)PENSTLEEILGQYQR;S(1)PENSTLEEILGQYQR 330.13 1.68E-71 378672000 62659.4 63159 73171 72522 71459.5 71356.7 72438 78993 78711 84451 TRUE FALSE 60210.60137 61357.76716 86394.62738 76264.86911 73758.05972 72799.58136 73324.51791 77361.76695 69776.05726 78731.05855 0.764763011 0.7793337 1.097338572 0.968675774 0.936835616 0.924661534 0.931328999 0.982607987 0.88625834 1 16.26464526 4.331314065 9.587481464 0.962130674 0.769501796 0.674567152 0.053841961 0.168862356 15.93700594 0.01285338 0.035290253 21444.40815 -4.331314065 -0.192628879 MQNT(ph)DDEERPQLS(ph)DDER ddPTM_BT-474_Pertuzumab_2h_R1 2 MQNTDDEERPQLSDDER 17 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 2 MQNT(1)DDEERPQLS(1)DDER;MQNT(1)DDEERPQLS(1)DDER 168.92 4.67E-09 1655180000 1219580 1306390 1464910 1640580 1410130 1403830 1663110 1675120 1754600 1919510 TRUE FALSE 1171917.465 1269133.036 1729651.824 1725250.53 1455488.112 1432216.404 1683463.638 1640528.187 1555425.164 1789499.878 0.654885468 0.709211021 0.966555989 0.964096478 0.813349098 0.800344511 0.940745321 0.916752332 0.869195457 1 20.77112501 4.331408049 5.565302373 0.902816912 0.670375409 0.678285689 0.062658475 0.114725831 5.398858793 0.015781726 0.044727373 21449.0494 -4.331408049 -0.232441502 SGIT(ph)SPVEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGITSPVEKR 10 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 S(0.114)GIT(0.564)S(0.323)PVEKR;S(0.014)GIT(0.493)S(0.493)PVEKR 80.69 0.013625 732380000 461900 443470 309080 351150 362170 403720 362730 389950 456420 420080 TRUE FALSE 443848.4373 430822.6698 364937.6314 369272.8936 373819.527 411883.495 367169.1982 381897.3962 404609.1151 391627.6074 1.133343076 1.10008248 0.931848584 0.942918442 0.954528026 1.051722318 0.93754677 0.97515443 1.03314758 1 18.57912294 4.331499916 5.740562433 0.976005193 1.123726359 0.675231982 0.038523355 0.107541135 5.270125799 0.009393025 0.026517662 21453.58703 -4.331499916 0.147721166 S(ph)SPLKITLFLEEDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPLKITLFLEEDK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.672)S(0.328)PLKITLFLEEDK 194.19 1.05E-07 278740000 1127300 982240 514480 391940 677750 788040 616320 697230 703650 578600 TRUE FALSE 1083243.87 954227.4769 607457.9805 412168.0704 699550.4443 803974.7087 623862.7085 682831.9568 623774.6019 539410.9066 2.008197937 1.769017766 1.126150719 0.76410778 1.296878568 1.490468025 1.156563022 1.265884595 1.156399684 1 19.04102517 4.331989783 4.055236017 1.173545733 1.952875479 0.72412784 0.1825115 0.113233745 3.37022076 0.047777691 0.145316842 21477.79944 -4.331989783 0.779329746 VTVLQASSISAEYADIFCQFNFIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTVLQASSISAEYADIFCQFNFIHR 25 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 0 ; 206.49 3.73E-25 312460000 188390 202364 185190 215689 225494 234995 241381 215943 228943 267173 FALSE TRUE 181027.5105 196592.7769 218657.9525 226820.7351 232747.2193 239746.7599 244335.0929 211483.7016 202954.3504 249077.1347 0.72679297 0.789284721 0.877872442 0.910644549 0.93443832 0.962540219 0.980961553 0.849069112 0.814825298 1 17.92623306 4.332332849 1.72269916 0.91767867 0.718145466 0.605076042 0.053325447 0.341146177 1.693364412 0.015291611 0.08722241 21494.77232 -4.332332849 -0.199533204 SLPDCTPHPNS(ph)ISIDAGPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLPDCTPHPNSISIDAGPR 19 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 SLPDCTPHPNS(0.891)IS(0.109)IDAGPR;SLPDCTPHPNS(0.634)IS(0.366)IDAGPR;SLPDCTPHPNS(0.5)IS(0.5)IDAGPR 120.42 2.61E-05 839713000 667220 569820 345034 294926 498390 366878 313936 451104 351714 298837 TRUE FALSE 641144.3047 553569.2915 407389.319 310147.1662 514421.167 374296.5245 317778.0427 441788.5448 311788.9012 278596.5038 2.301336506 1.986992959 1.46229157 1.113248594 1.846473879 1.343507616 1.140639019 1.585764856 1.119141471 1 18.08781763 4.332835792 2.599512224 1.352313019 2.271189193 0.657627683 0.241634466 0.169263655 2.178100187 0.059215741 0.230610661 21519.67917 -4.332835792 0.918876173 IHNAENIQPGEQKYEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHNAENIQPGEQKYEYK 17 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 225.69 1.39E-15 328790000 1012590 928530 578260 564660 736650 910070 728870 484120 1011370 825490 FALSE TRUE 973016.8633 902049.2335 682764.4453 593802.1703 760345.0163 928472.2389 737790.1291 474122.7528 896563.5176 769578.827 1.264349835 1.172133642 0.887192346 0.771593694 0.988001475 1.206468014 0.958693383 0.616080817 1.165005437 1 19.55370958 4.332903927 4.425299971 0.924200523 1.241561444 0.296362045 0.164252224 0.242109884 8.228433848 0.043287629 0.128332016 21523.05556 -4.332903927 0.317360921 IEEELGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEEELGSK 8 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 127.56 0.002724 950470000 1234830 1128340 803260 850330 771170 847460 867470 982700 1199440 1075780 FALSE TRUE 1186571.478 1096160.848 948426.9504 894215.6332 795975.3834 864596.2218 878086.3573 962406.9016 1063284.6 1002916.462 1.183120951 1.092973233 0.945668943 0.891615271 0.793660702 0.862081992 0.875532899 0.95960824 1.060192588 1 19.93577001 4.332934719 2.408796208 0.911210527 1.177622928 0.604611822 0.071129743 0.209867856 2.288526946 0.019569303 0.081109053 21524.58161 -4.332934719 0.266412401 RPPS(ph)PDVIVLSDNEQPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLSDNEQPS(0.063)S(0.937)PR;RPPS(1)PDVIVLSDNEQPS(0.342)S(0.658)PR 214.95 4.30E-24 1437120000 436220 491230 474650 588800 556900 592650 617810 571090 594780 655300 TRUE FALSE 419172.0401 477220.6014 560429.8135 619188.0386 574813.1943 604633.7891 625370.9436 559296.7919 527263.0679 610915.9473 0.686137008 0.781155908 0.917359935 1.013540474 0.940903895 0.989716821 1.023661187 0.915505307 0.86306974 1 19.22061438 4.333093719 2.296158128 0.962021316 0.690866369 0.800301387 0.046431151 0.139043949 1.362616827 0.012471203 0.053903907 21532.46347 -4.333093719 -0.271154947 IPPMLS(ph)PVHVQDSTDLAPPS(ph)PEPPMLAPVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IPPMLSPVHVQDSTDLAPPSPEPPMLAPVAK 31 0 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 2 IPPMLS(0.971)PVHVQDS(0.014)T(0.015)DLAPPS(1)PEPPMLAPVAK;IPPMLS(0.813)PVHVQDS(0.095)T(0.1)DLAPPS(0.993)PEPPMLAPVAK 79.667 0.0009787 87085000 43146 44738 44338 48085 46772 52410 48312 47325 62371 53952 TRUE FALSE 41459.80662 43462.11604 52350.86289 50566.67261 48276.46386 53469.76611 48903.25671 46347.72221 55290.90556 50297.78298 0.82428696 0.864096059 1.040818497 1.005345954 0.959812958 1.063064074 0.972274598 0.921466503 1.099271226 1 15.61820719 4.333185152 5.364763396 0.99900837 0.835293774 0.634138201 0.049582179 0.126725807 5.629339321 0.012257122 0.034935831 21536.99723 -4.333185152 -0.163714596 TGSVQT(ph)SPSSTPVAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSVQTSPSSTPVAGR 16 0 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 TGSVQT(0.508)S(0.443)PS(0.047)S(0.002)TPVAGR 221.46 1.18E-13 667760000 794140 853230 771760 949780 919130 987880 988950 999720 1106000 1177100 TRUE FALSE 763104.1308 828896.7158 911234.1997 998798.2596 948694.6512 1007855.61 1001053.066 979075.4326 980451.5167 1097373.969 0.695391136 0.755345707 0.830377087 0.910171271 0.864513537 0.91842493 0.912226 0.892198522 0.893452501 1 20.06562383 4.333251865 1.073904848 0.910911247 0.653297816 0.842841972 0.032892033 0.336122253 0.500200629 0.009534822 0.084964308 21540.30581 -4.333251865 -0.257613431 GHAVGDIPGVR ddPTM_BT-474_Pertuzumab_2h_R1 6 GHAVGDIPGVR 11 0 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;;;;; 143.96 3.69E-05 5080190000 1126190 1158720 1296247 1410070 1398760 1301903 1458450 1261469 1350520 1538820 FALSE TRUE 1082177.25 1125674.44 1530507.668 1482843.882 1443752.386 1328228.371 1476298.947 1235419.224 1197214.631 1434594.351 0.754343727 0.784663929 1.066857448 1.033632874 1.00638371 0.925856407 1.029070654 0.861162756 0.834531818 1 20.45221142 4.333631747 7.368061288 0.96425676 0.763751936 0.553111705 0.071957608 0.174546809 11.59157074 0.018931806 0.052393113 21559.15558 -4.333631747 -0.200504825 TKGS(ph)PRT(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKGSPRTSPK 10 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 T(0.313)KGS(0.687)PRT(0.617)S(0.383)PK 60.628 0.030145 0 347280 288280 87304 76349 153620 202380 122160 120690 168390 86834 TRUE FALSE 333707.9137 280058.5367 103081.7749 80289.38104 158561.3268 206472.2623 123655.0306 118197.7093 149275.0731 80952.65584 4.12226023 3.459534882 1.273358777 0.991806633 1.958692092 2.55053105 1.527498133 1.460084393 1.843979936 1 16.30479079 4.33397076 4.549399062 1.609754767 3.957270636 0.79619824 0.451874261 0.087332453 3.082229196 0.116681491 0.343661895 21575.99136 -4.33397076 2.347515869 S(ph)PAQSDSTTQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPAQSDSTTQR 11 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(1)PAQSDSTTQR;S(1)PAQSDSTTQR 116.9 0.000972 46767000 27494 30611 34147 49277 33169 31664 36840 38069 44024 41542 TRUE FALSE 26419.50408 29738.00425 40318.1225 51820.19188 34235.91101 32304.26777 37290.85894 37282.86185 39026.58008 38728.32334 0.682175261 0.767861908 1.041050038 1.338043773 0.88400189 0.834125131 0.962883382 0.962676889 1.007701256 1 15.24110142 4.334064701 4.688032142 0.999675828 0.704686695 0.439820375 0.12694438 0.197015454 7.256252992 0.033411781 0.097708592 21580.6589 -4.334064701 -0.294989133 TRS(ph)EREWDRDK ddPTM_BT-474_Pertuzumab_2h_R1 1 TRSEREWDRDK 11 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 T(0.204)RS(0.796)EREWDRDK 91.657 0.058454 845970000 433740 355030 160360 152120 226640 215350 145330 207690 167810 130460 TRUE FALSE 416788.9613 344904.892 189340.6192 159970.9314 233930.0814 219704.5245 147108.592 203401.1289 148760.9123 121623.828 3.426869291 2.835833222 1.556772405 1.315292686 1.923390221 1.806426653 1.209537592 1.672378943 1.22312309 1 16.89206638 4.334313072 3.050283471 1.495875393 3.34433549 0.857100317 0.276928233 0.083046178 1.483535404 0.068096461 0.237639041 21593.00435 -4.334313072 1.848460097 REGTGTEMPMIGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 REGTGTEMPMIGDR 14 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 135.81 4.93E-05 857730000 367520 369470 336530 353750 399670 413960 373610 420370 435350 404970 FALSE TRUE 353156.9121 358933.0773 397348.4571 372007.0799 412525.7485 422330.5548 378182.3509 411689.2126 385930.8931 377541.0212 0.935413352 0.950712789 1.052464328 0.985342146 1.092664705 1.11863488 1.001698702 1.090448957 1.022222412 1 18.52627388 4.334361221 1.273236581 1.055569426 0.9117058 0.447631387 0.043765593 0.604280902 1.38843691 0.012278814 0.094969828 21595.39842 -4.334361221 -0.143863626 VPGGGEQPAQPNGWQYHS(ph)PSRPGSTAFPSQDGETGGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPGGGEQPAQPNGWQYHSPSRPGSTAFPSQDGETGGHR 38 1 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 VPGGGEQPAQPNGWQYHS(0.963)PS(0.037)RPGSTAFPSQDGETGGHR;VPGGGEQPAQPNGWQY(0.066)HS(0.493)PS(0.147)RPGS(0.147)T(0.147)AFPS(0.001)QDGETGGHR 215.98 2.12E-39 1308570000 136590 137867 158249 187474 158330 163332 187100 98147 174119 224515 TRUE FALSE 131251.9118 133935.1681 186848.1145 197149.5556 163422.8282 166634.6849 189389.7858 96120.23015 154353.7411 209308.3991 0.627074271 0.639893902 0.892692865 0.941909434 0.780775301 0.796120393 0.904836053 0.459227774 0.737446475 1 17.67527068 4.334432958 9.330486049 0.785350777 0.631122914 0.181882118 0.143253971 0.586756534 51.76763861 0.038006354 0.104400884 21598.96588 -4.334432958 -0.154227863 VINAAHSFYNGTTTLPISDEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VINAAHSFYNGTTTLPISDEDR 22 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;; 288.82 2.94E-47 3609610000 1177670 1192690 1207920 1389020 1241640 1324600 1335860 1264540 1359890 1416230 FALSE TRUE 1131645.354 1158675.649 1426218.014 1460707.489 1281578.478 1351384.32 1352208.654 1238426.807 1205520.988 1320307.481 0.857107432 0.877580159 1.080216567 1.106338872 0.97066668 1.023537577 1.024161928 0.937983633 0.913060788 1 20.33244252 4.334462309 7.536932126 1.004825955 0.863457947 0.502859682 0.05559322 0.196838154 13.35202011 0.014829082 0.040996445 21600.42564 -4.334462309 -0.141368008 AVPMIEGYMFEEHEMIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVPMIEGYMFEEHEMIR 17 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ; 238.02 3.10E-20 148263000 83539 90693 85088 101527 103818 113322 107104 94447 104519 109410 FALSE TRUE 80274.20352 88106.52444 100465.2944 106766.8206 107157.4003 115613.4485 108414.7708 92496.63644 92654.4413 101999.5632 0.787005365 0.863793154 0.984958084 1.046738018 1.050567246 1.133470035 1.062894461 0.906833652 0.908380765 1 16.63820345 4.3344943 2.434908792 1.014813916 0.792315449 0.58362272 0.064916503 0.246166915 2.74695537 0.019373429 0.079809858 21602.01685 -4.3344943 -0.222498467 RLS(ph)ESLHVVDENKNESK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSESLHVVDENKNESK 17 2 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 RLS(0.935)ES(0.065)LHVVDENKNESK 169.19 1.05E-09 785420000 753450 807640 549510 563320 679950 635880 510960 623280 611130 610250 TRUE FALSE 724004.341 784606.898 648818.6808 592393.0127 701821.2093 648737.9293 517213.2813 610409.0502 541757.0845 568917.2239 1.272600495 1.379123122 1.140444784 1.04126398 1.233608651 1.140302845 0.90911869 1.072931218 0.952259945 1 19.11785923 4.334758132 0.368915332 0.972146262 1.526531147 0.611140835 0.088023026 3.0619153 0.416127359 0.083004919 0.738759712 21615.14396 -4.334758132 0.554384885 DNLSYIEHIFEISR ddPTM_BT-474_Pertuzumab_2h_R1 6 DNLSYIEHIFEISR 14 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;;;;; 252.17 3.39E-24 1046122000 996268 1080568 1059448 1350046 1206606 1117763 1253990 1206729 1336955 1512124 FALSE TRUE 957332.7451 1049751.259 1250913.821 1419722.036 1245417.578 1140364.934 1269336.705 1181809.624 1185189.473 1409706.495 0.679100755 0.744659447 0.887357635 1.0071047 0.883458779 0.808937845 0.90042623 0.838337362 0.840734917 1 20.42696339 4.33478022 3.609394254 0.888535619 0.692667696 0.592315285 0.061786007 0.159064049 3.883396854 0.015725077 0.050185227 21616.24329 -4.33478022 -0.195867923 GIEEEEILPGFILCDPNNLCHSGR ddPTM_BT-474_Pertuzumab_2h_R1 7 GIEEEEILPGFILCDPNNLCHSGR 24 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;;;;;; 308.39 2.15E-73 2944950000 1664332 1798413 1648468 2111507 1924717 1949714 2055348 1834522 2203565 2345425 FALSE TRUE 1599288.065 1747124.022 1946382.838 2220482.129 1986627.27 1989138.553 2080501.964 1796638.48 1953425.539 2186567.276 0.731414982 0.799025963 0.890154563 1.015510547 0.908559866 0.90970837 0.951492317 0.821670799 0.893375457 1 21.06023631 4.335277473 2.759650477 0.917465015 0.741164691 0.603860989 0.052820194 0.198991734 2.901744422 0.014167452 0.052972905 21641.00739 -4.335277473 -0.176300324 RPQS(ph)PGASPS(ph)QAER ddPTM_BT-474_Pertuzumab_2h_R1 1 RPQSPGASPSQAER 14 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 2 RPQS(0.868)PGAS(0.311)PS(0.821)QAER 129.25 4.61E-05 278940000 168560 180240 167150 204720 194470 193190 211240 200110 196310 221900 TRUE FALSE 161972.4888 175099.7317 197357.7232 215285.6237 200725.3042 197096.4342 213825.2183 195977.6586 174025.7118 206870.5154 0.78296556 0.846421886 0.954015718 1.040678143 0.970294408 0.952752662 1.033618628 0.947344566 0.841230136 1 17.65836851 4.335361253 2.917842869 0.971120052 0.792254865 0.587824091 0.052515162 0.176111588 2.878547294 0.013417596 0.048261969 21645.18253 -4.335361253 -0.178865187 MEEEGTEDNGLEDDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEEEGTEDNGLEDDSR 16 0 Q14151;K7ERX3 Q14151 SAFB2 Scaffold attachment factor B2 0 ; 349.17 8.54E-87 570300000 315970 360760 353440 446670 412200 391800 446400 468100 454860 483390 FALSE TRUE 303621.5431 350471.478 417314.4702 469722.6922 425458.7874 399722.4644 451863.1767 458433.5714 403226.1997 450649.5647 0.673742009 0.77770291 0.926028788 1.042323635 0.944101183 0.886991791 1.002693028 1.01727286 0.894766646 1 18.78164647 4.33539919 2.390408498 0.971974645 0.68100045 0.806888121 0.048294977 0.127290721 1.363186438 0.012812503 0.05371201 21647.07339 -4.33539919 -0.290974196 KGAVAEDGDELRTEPEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGAVAEDGDELRTEPEAK 18 2 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 136.2 3.81E-06 2836350000 1783210 1685220 1055430 1049340 1474370 1497320 1270180 1413910 1600410 1402550 FALSE TRUE 1713520.182 1637159.176 1246169.679 1103496.563 1521794.45 1527596.836 1285724.843 1384712.264 1418738.166 1307554.039 1.310477525 1.25207764 0.953054055 0.843939547 1.163848227 1.168285815 0.98330532 1.059009588 1.085032147 1 20.31843914 4.335509501 5.842472028 1.036004777 1.293659175 0.539581779 0.092434875 0.156446576 7.67033664 0.023813838 0.067143838 21652.57246 -4.335509501 0.257654399 QYDPPAESQQSES(ph)PPRR ddPTM_BT-474_Pertuzumab_2h_R1 2 QYDPPAESQQSESPPRR 17 1 Q6P597;Q6P597-3;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 QYDPPAESQQS(0.366)ES(0.634)PPRR;QYDPPAESQQS(0.023)ES(0.977)PPRR 172.24 9.96E-10 1236650000 753020 812070 773780 950780 872460 997260 924640 905560 911670 950920 TRUE FALSE 723591.1459 788910.5587 913619.2586 999849.8697 900523.4682 1017425.28 935956.0209 886859.8695 808181.0436 886513.3414 0.816221383 0.889902635 1.030575871 1.12784526 1.015803628 1.14767058 1.055772065 1.000390889 0.911640024 1 19.75778282 4.336016374 3.160808374 1.042387362 0.828545691 0.581403408 0.063440725 0.169270184 3.237874253 0.016531092 0.05659974 21677.85833 -4.336016374 -0.213841671 S(ph)SSMSSIDLVSASDDVHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSMSSIDLVSASDDVHR 18 0 Q9Y5P4-3;Q9Y5P4;A0A2U3TZL3;A0A2R8YFA1;A0A0A0MRE4 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 1 S(0.453)S(0.094)S(0.453)MS(0.001)SIDLVSASDDVHR 179.84 5.26E-14 495530000 84648 95965 78062 92336 109060 97489 102150 107650 103540 124160 TRUE FALSE 81339.86258 93228.17216 92169.53988 97101.47203 112568.0139 99460.29437 103400.1423 105426.9899 91786.57328 115750.5326 0.702716962 0.805423267 0.796277458 0.838885747 0.972505365 0.859264248 0.893301654 0.910812136 0.792968907 1 16.82065931 4.336212766 0.896882145 0.89855884 0.676371369 0.539518605 0.057814508 0.999082752 0.947822512 0.019170469 0.193077962 21687.66351 -4.336212766 -0.222187471 GHAYSVTGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHAYSVTGAK 10 0 P07384;E9PL37 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 144.77 3.16E-05 1491570000 2656110 2762940 2459430 2913350 2754310 2809590 3128550 2830970 3226660 3393710 FALSE TRUE 2552306.285 2684143.656 2903903.711 3063708.343 2842904.883 2866401.835 3166838.131 2772509.48 2860383.084 3163850.999 0.80670875 0.848378655 0.917838328 0.96834786 0.898558397 0.905985091 1.000944144 0.876308486 0.904082741 1 21.59325023 4.336367467 2.774815299 0.930195365 0.811901877 0.533157004 0.040736488 0.209620874 3.090423243 0.010058435 0.037529613 21695.39025 -4.336367467 -0.118293487 DALDGPAAEAEPEHSFDGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DALDGPAAEAEPEHSFDGLR 20 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 299.23 9.34E-55 5847190000 1764000 1893200 1850330 2049570 2073560 2098470 2308420 2132080 2445600 2461230 FALSE TRUE 1695060.93 1839207.79 2184725.791 2155348.553 2140257.941 2140902.501 2336671.134 2088051.803 2167985.741 2294528.7 0.738740348 0.801562338 0.952145768 0.939342599 0.932765818 0.93304673 1.018366488 0.910013374 0.94485013 1 21.12976642 4.336694907 3.213582601 0.950808246 0.74804631 0.849257015 0.031381915 0.081514835 1.608775418 0.007648332 0.025960455 21711.75389 -4.336694907 -0.202761937 GLEYLYLSVHDEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLEYLYLSVHDEDR 14 0 O43237;O43237-2;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ; 198.23 2.23E-08 561130000 258390 327030 380370 564340 408400 406960 434820 438440 491600 542010 FALSE TRUE 248291.8331 317703.4246 449111.3203 593465.655 421536.5569 415189.01 440141.4572 429386.0608 435795.629 505299.1799 0.491375888 0.628743202 0.888802789 1.174483709 0.834231627 0.821669669 0.8710512 0.849765996 0.862450695 1 18.94677831 4.337143528 3.388387314 0.906653262 0.518048653 0.672971643 0.100347239 0.14061941 3.061896196 0.026345917 0.086927014 21734.19343 -4.337143528 -0.388604609 S(ph)LEDLRAPK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLEDLRAPK 9 1 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 S(1)LEDLRAPK;S(1)LEDLRAPK;S(1)LEDLRAPK;S(1)LEDLRAPK;S(1)LEDLRAPK 153.74 4.69E-05 4609350000 8495060 8050490 5397000 5592890 6209030 6984630 6448110 7738860 8113810 6483380 TRUE FALSE 8163063.663 7820897.907 6372357.956 5881539.723 6408749.089 7125864.004 6527023.899 7579049.837 7192764.305 6044254.898 1.350549208 1.293939127 1.054283458 0.973079366 1.060304239 1.178948295 1.079872376 1.253926243 1.190016706 1 22.52713307 4.337158866 5.340462606 1.111603038 1.335008582 0.530896962 0.083794788 0.17273927 7.498324816 0.022788676 0.065070791 21734.96105 -4.337158866 0.223405544 CGYAGSNFPEHIFPALVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 CGYAGSNFPEHIFPALVGR 19 0 P61160;P61160-2;A0A1B0GWD0;A0A1B0GWH0 P61160 ACTR2 Actin-related protein 2 0 ; 148.26 9.73E-08 596070000 413750 430470 454230 510010 474660 434230 503090 512060 558260 536230 FALSE TRUE 397580.1926 418193.4171 536319.4653 536331.6772 489927.87 443010.4281 509246.9659 501485.7821 494888.6652 499910.6645 0.795302483 0.836536299 1.072830614 1.072855043 0.980030843 0.886179191 1.01867594 1.003150798 0.989954207 1 18.93131078 4.337291842 6.122844936 1.001227735 0.807235395 0.694585615 0.049793182 0.114546403 5.897290895 0.013053159 0.036627623 21741.61704 -4.337291842 -0.19399234 DENGELR ddPTM_BT-474_Pertuzumab_2h_R1 2 DENGELR 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 173.11 0.0020367 572690000 1006840 1016400 884460 957500 1034450 1041960 1052400 1039870 1130060 1140440 FALSE TRUE 967491.5797 987413.2672 1044301.597 1006916.69 1067724.024 1063029.145 1065279.586 1018396.321 1001780.326 1063196.983 0.909983376 0.928720908 0.982227765 0.947065037 1.004257951 0.999842138 1.001958812 0.957862313 0.942233981 1 20.01997749 4.337335528 3.179740922 0.978805468 0.912213662 0.543869854 0.022214038 0.191641378 3.705624912 0.005852223 0.020003652 21743.80419 -4.337335528 -0.066591806 DGMAFNALIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGMAFNALIHK 11 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 65.179 0.066152 204660000 550040 577500 465600 561680 591430 542420 662660 530760 615320 610960 FALSE TRUE 528543.8287 561030.2654 549744.2772 590668.3721 610453.8831 553388.104 670769.8313 519799.6205 545471.4532 569579.135 0.927955039 0.984990901 0.965176291 1.037026 1.071763071 0.971573694 1.177658713 0.912602988 0.95767457 1 19.11953677 4.337490943 1.469956073 1.016865993 0.931588858 0.129900081 0.069143404 1.303579931 4.319047596 0.01945649 0.1320157 21751.5867 -4.337490943 -0.085277135 DVSELTGFPEMLGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVSELTGFPEMLGGR 15 0 P31939-2;P31939;F8WEF0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 211.46 3.18E-09 104539000 86694 92087 85409 101255 88615 100614 102427 112285 107758 107456 FALSE TRUE 83305.90263 89460.76892 100844.3062 106480.7827 91465.38195 102648.484 103680.5323 109966.2755 95525.7636 100177.9094 0.831579568 0.893018925 1.006652133 1.062916798 0.913029454 1.02466187 1.034964024 1.097709826 0.953561161 1 16.61220488 4.337594168 2.82182948 1.020436958 0.838913814 0.60065789 0.049598872 0.175283918 2.674111417 0.013106297 0.048417061 21756.75736 -4.337594168 -0.181523144 VQVAALQAS(ph)PPLDQDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQVAALQASPPLDQDDR 17 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR 243.87 1.85E-20 782120000 264645 297754 284290 367309 314591 350905 352134 344769 359912 431354 TRUE FALSE 254302.3808 289262.3475 335667.527 386265.8615 324710.1052 358000.5395 356443.5212 337649.3997 319056.2986 402138.0094 0.632375888 0.719311134 0.834707287 0.960530595 0.807459374 0.890242979 0.886371129 0.839635627 0.793400005 1 18.61733118 4.337840323 2.497844492 0.873011101 0.640850063 0.653472481 0.060493856 0.174486119 2.05590738 0.014691166 0.059628892 21769.0924 -4.337840323 -0.232161038 S(ph)IEALLEAGQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SIEALLEAGQAR 12 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 S(1)IEALLEAGQAR;S(1)IEALLEAGQAR;S(1)IEALLEAGQAR;S(1)IEALLEAGQAR 190.27 7.19E-06 233415000 105493 112582 114686 144921 118414 96140 129909 158320 134807 124407 TRUE FALSE 101370.2169 109371.2716 135412.3114 152400.3902 122222.8939 98084.01667 131498.8652 155050.6367 119504.2745 115980.8031 0.874025824 0.943011849 1.167540729 1.314013924 1.053820034 0.845691822 1.13379854 1.336864658 1.030379781 1 16.82352651 4.337927424 4.681743024 1.129856943 0.891659776 0.248304923 0.138699289 0.270500805 9.837322709 0.037002307 0.108439646 21773.45879 -4.337927424 -0.238197167 DLPTIPGVTS(ph)PSSDEPPMEASQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVT(0.033)S(0.934)PS(0.027)S(0.006)DEPPMEASQSHLR;DLPTIPGVT(0.162)S(0.776)PS(0.05)S(0.012)DEPPMEASQSHLR;DLPTIPGVT(0.124)S(0.653)PS(0.19)S(0.032)DEPPMEASQSHLR;DLPTIPGVT(0.156)S(0.723)PS(0.109)S(0.012)DEPPMEASQSHLR 187.43 7.41E-18 862840000 218554 236840 280211 333996 261531 279800 324667 281583 295516 365427 TRUE FALSE 210012.6681 230085.5551 330851.361 351233.5736 269943.3821 285457.7477 328640.3719 275768.2126 261970.2626 340676.3038 0.616458103 0.675378805 0.971160475 1.030989152 0.792374988 0.83791489 0.964670475 0.809472833 0.76897119 1 18.37804208 4.338234989 5.793755492 0.888209436 0.63312732 0.562871948 0.08862683 0.146995524 7.036526595 0.022181487 0.062635737 21788.88411 -4.338234989 -0.255082116 NPEDKSPQLSLSPRPAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 NPEDKSPQLSLSPRPASPK 19 2 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 NPEDKS(0.003)PQLS(0.11)LS(0.097)PRPAS(0.79)PK 50.029 0.076661 567990000 308110 269310 115930 98598 141080 193040 157470 180890 247480 163080 TRUE FALSE 296068.7206 261629.5425 136881.1298 103686.6546 145617.9663 196943.4011 159397.165 177154.5583 219387.1079 152034.4463 1.947379214 1.720857008 0.900329716 0.681994489 0.95779588 1.295386709 1.048427964 1.165226451 1.443009221 1 17.21403871 4.338236819 4.906720542 1.064204635 1.888418735 0.704962245 0.201518562 0.111371284 4.3124188 0.053418597 0.154950616 21788.9759 -4.338236819 0.824214101 GLPLGSAVSS(ph)PVLFS(ph)PVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLPLGSAVSSPVLFSPVGR 19 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 2 GLPLGSAVS(0.208)S(0.792)PVLFS(1)PVGR;GLPLGSAVS(0.089)S(0.911)PVLFS(1)PVGR 266.83 2.13E-31 86170000 89762 97045 111475 130152 107095 112883 124897 124720 109389 148749 TRUE FALSE 86254.0018 94277.37162 131621.0122 136869.1603 110539.8079 115165.5716 126425.5268 122144.4884 96971.61932 138674.0977 0.621990719 0.679848459 0.949139128 0.986984322 0.797119359 0.830476444 0.911673693 0.880802474 0.699277088 1 17.08133881 4.338307906 5.58472969 0.87797471 0.638085423 0.536450571 0.086294049 0.146247006 6.686340546 0.020771922 0.058937528 21792.54273 -4.338307906 -0.239889287 YKYEDKDGKQPVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 YKYEDKDGKQPVGR 14 3 A0A499FJT0;Q8NHP1;O43488;H3BLU7 A0A499FJT0;O43488 AKR7L;AKR7A2 Aflatoxin B1 aldehyde reductase member 4;Aflatoxin B1 aldehyde reductase member 2 0 53.169 0.066041 423860000 420400 384710 246030 176630 311320 377830 257760 336290 381280 301110 FALSE TRUE 403970.3032 373738.4475 290493.0939 185745.8955 321333.8905 385469.9815 260914.544 329345.494 337998.6929 280715.5515 1.439073472 1.331377779 1.034830783 0.661687229 1.144695721 1.373169315 0.929462378 1.173235655 1.204061161 1 18.09874947 4.338599205 4.383556632 1.069254576 1.412274203 0.343594562 0.179024785 0.239010199 7.908952997 0.045949153 0.13703963 21807.16479 -4.338599205 0.343019627 IMPDSNDS(ph)PPAEREPGEVVDSLVGK ddPTM_BT-474_Pertuzumab_2h_R1 5 IMPDSNDSPPAEREPGEVVDSLVGK 25 1 Q9Y657 Q9Y657 SPIN1 Spindlin-1 1 IMPDSNDS(1)PPAEREPGEVVDSLVGK;IMPDSNDS(1)PPAEREPGEVVDSLVGK;IMPDS(0.266)NDS(0.734)PPAEREPGEVVDSLVGK;IMPDS(0.156)NDS(0.844)PPAEREPGEVVDSLVGK;IMPDS(0.181)NDS(0.819)PPAEREPGEVVDSLVGK 227.99 2.94E-34 823436000 685896 647668 503016 531561 558379 610070 544677 596277 654065 600877 TRUE FALSE 659090.426 629197.1428 593922.1807 558994.9269 576339.7676 622406.0334 551342.9201 583963.6716 579818.2833 560179.0656 1.176570969 1.12320717 1.060236302 0.997886143 1.028849172 1.111084065 0.984226213 1.042458934 1.035058821 1 19.09552854 4.338615745 2.162100631 1.03131331 1.174737189 0.685195676 0.033255237 0.194239753 1.654707672 0.008489307 0.039218291 21807.99532 -4.338615745 0.14342388 LSAKPAPPKPEPKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSAKPAPPKPEPKPK 15 3 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ; 92.307 0.0023187 6735000000 13619900 11697200 6578900 5313200 7545500 8375200 7137300 9783100 8525100 6477400 FALSE TRUE 13087619.25 11363607.31 7767853.577 5587414.889 7788207.86 8544552.282 7224648.412 9581075.566 7557366.388 6038679.929 2.167298053 1.881803216 1.286349611 0.925270913 1.289720262 1.414970223 1.196395321 1.586617552 1.251493121 1 22.52580178 4.338705409 3.394934299 1.272505843 2.114680335 0.7545271 0.180679526 0.117759596 2.57070868 0.047845157 0.158005314 21812.49825 -4.338705409 0.842174492 ELTDEEAER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELTDEEAER 9 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 146.79 0.00021858 2505900000 1222500 1306720 1164270 1383080 1404190 1448650 1399800 1445550 1537030 1633630 FALSE TRUE 1174723.348 1269453.625 1374679.488 1454460.925 1449357.047 1477942.696 1416931.171 1415698.887 1362552.798 1522982.785 0.771330681 0.833531172 0.90262313 0.955008119 0.951656881 0.970426396 0.930365849 0.929556723 0.89466067 1 20.5384682 4.339163389 1.755002634 0.943889401 0.765736967 0.829423055 0.026613539 0.175563897 0.90754184 0.007135902 0.040584801 21835.51248 -4.339163389 -0.178152434 LVILEGELER ddPTM_BT-474_Pertuzumab_2h_R1 7 LVILEGELER 10 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;;;;; 220.71 1.33E-08 740165800 399403.4 418117 387006.1 469684.7 442963.8 429765 450996 473038 453009 498163 FALSE TRUE 383794.2736 406192.7125 456946.7112 493925.1837 457212.1329 438455.1428 456515.424 463269.6 401585.3175 464421.9763 0.826391285 0.874619922 0.983904153 1.063526725 0.984475663 0.944087845 0.982975499 0.997518687 0.864699213 1 18.82507672 4.339230732 3.71007101 0.980979586 0.836463682 0.541502628 0.047541149 0.159973436 4.077181648 0.011858759 0.037559561 21838.89863 -4.339230732 -0.144515903 FDPFGPIGTS(ph)PPGPNPDHLPPPGYDDMYL ddPTM_BT-474_Pertuzumab_2h_R1 5 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.196)S(0.804)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.29)S(0.71)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.062)S(0.938)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.173)S(0.827)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.224)S(0.776)PPGPNPDHLPPPGYDDMYL 136.48 2.96E-06 888814000 131526 143388 122073 156702 155102 154283 155775 148987 156618 169818 TRUE FALSE 126385.8185 139298.7146 144134.3066 164789.409 160090.9967 157402.708 157681.421 145910.3664 138839.3812 158316.0756 0.798313235 0.879877259 0.910421169 1.040888668 1.01121125 0.994230733 0.995991219 0.921639611 0.87697589 1 17.27244823 4.33929404 1.905676683 0.973357538 0.802987048 0.597113267 0.046518729 0.307475076 1.943318857 0.01345409 0.070402935 21842.08236 -4.33929404 -0.17037049 KIYEDGDDDMKR ddPTM_BT-474_Pertuzumab_2h_R1 5 KIYEDGDDDMKR 12 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;; 192.86 1.99E-06 5791580000 10171520 9494940 6506320 5807390 7644870 8640760 7413230 8619630 10029700 8029380 FALSE TRUE 9774005.753 9224153.608 7682156.756 6107110.094 7890774.186 8815482.087 7503955.326 8441631.628 8891170.504 7485542.941 1.305717679 1.232262467 1.026265806 0.815853992 1.054135184 1.177667693 1.002459726 1.127724695 1.187778973 1 22.83567553 4.339357173 4.379915725 1.051701794 1.287644877 0.436193108 0.101192391 0.200857817 6.628855577 0.02654831 0.079232558 21845.25774 -4.339357173 0.235943083 QTNPSAMEVEEDDPVPEIR ddPTM_BT-474_Pertuzumab_2h_R1 3 QTNPSAMEVEEDDPVPEIR 19 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 331.73 6.32E-75 3009910000 1007930 1081810 990740 1207140 1140840 1185370 1269010 1127520 1300830 1364680 FALSE TRUE 968538.9813 1050957.838 1169788.757 1269440.64 1177536.155 1209338.994 1284540.524 1104236.318 1153165.232 1272249.008 0.761280988 0.826063004 0.919465254 0.997792596 0.925554783 0.950552121 1.00966125 0.867940404 0.906399003 1 20.27894964 4.339883698 2.529999585 0.944615841 0.767339364 0.68907929 0.042554227 0.173594465 2.101232353 0.011295008 0.045541641 21871.75831 -4.339883698 -0.177276476 TASEDSCKR ddPTM_BT-474_Pertuzumab_2h_R1 3 TASEDSCKR 9 1 P15924 P15924 DSP Desmoplakin 0 ;; 109.29 0.0039655 615890000 860070 821520 628903 652692 696540 758220 730770 777370 851440 800290 FALSE TRUE 826457.5135 798091.054 742559.762 686377.5123 718944.8417 773551.7279 739713.3819 761317.0378 754788.1007 746085.6455 1.107724721 1.069704341 0.995274157 0.919971476 0.963622402 1.036813578 0.991459072 1.020415072 1.01166415 1 19.50898173 4.34002684 3.463300306 0.992312945 1.100249315 0.622792578 0.030606395 0.160043273 3.618475143 0.008451741 0.02767097 21878.96836 -4.34002684 0.107936369 FAEMEER ddPTM_BT-474_Pertuzumab_2h_R1 2 FAEMEER 7 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 97.798 0.041823 292730000 2434500 2186290 1773840 1657540 1947230 1782350 1880790 1934370 2098890 2097070 FALSE TRUE 2339357.049 2123939.15 2094412.347 1743085.838 2009864.421 1818390.338 1903807.671 1894424.584 1860632.806 1955033.581 1.196581517 1.086395226 1.071292262 0.891588694 1.028045984 0.930106959 0.973797938 0.968998488 0.951713988 1 20.89876196 4.340068313 1.428290527 0.964502627 1.205589439 0.762642915 0.041231671 0.263936931 0.810546129 0.010601136 0.074482763 21881.05778 -4.340068313 0.241086812 DHPQQQPGMLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DHPQQQPGMLSR 12 0 Q8WUH6 Q8WUH6 TMEM263 Transmembrane protein 263 0 94.688 0.0064691 282970000 165300 175930 171410 226470 192190 173610 201770 186880 220080 217620 FALSE TRUE 158839.8933 170912.6487 202387.6 238158.1438 198371.9659 177120.5131 204239.3216 183020.8627 195097.4411 202880.4036 0.782923784 0.842430544 0.997570965 1.173884415 0.977777855 0.873029184 1.006698124 0.902112079 0.961637682 1 17.63026999 4.340180817 4.230668947 0.982188296 0.797222253 0.463941153 0.07562183 0.198257482 6.210809721 0.020226713 0.061034942 21886.72682 -4.340180817 -0.184966043 DSQQTLINIPSLNDSDS(ph)EIEDISEIESNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSQQTLINIPSLNDSDSEIEDISEIESNR 29 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 DSQQTLINIPS(0.045)LNDS(0.413)DS(0.541)EIEDIS(0.001)EIESNR;DSQQTLINIPS(0.017)LNDS(0.435)DS(0.547)EIEDIS(0.001)EIESNR 110.09 0.00023136 200067000 152994 178436 188172 263170 229980 265510 326640 263200 308060 322230 TRUE FALSE 147014.8253 173347.18 222178.8663 276752.2352 237377.5156 270878.7941 330637.518 257764.828 273090.3203 300405.0751 0.489388621 0.577044778 0.739597579 0.921263514 0.790191429 0.901711777 1.100638922 0.858057501 0.909073591 1 18.19654966 4.340286361 0.812337486 0.943920257 0.340190645 0.816425836 0.075728799 0.620039119 0.462456074 0.028697113 0.304013929 21892.04647 -4.340286361 -0.603729611 down RYPSS(ph)ISSS(ph)PQKDLTQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RY(0.255)PS(0.332)S(0.412)IS(0.001)S(0.02)S(0.98)PQKDLTQAK 158.77 2.40E-11 537060000 1886700 1563100 976130 757200 1019200 1135400 835490 1104900 1258200 1034100 TRUE FALSE 1812965.678 1518521.918 1152538.405 796279.1827 1051983.494 1158358.566 845714.9765 1082083.429 1115374.411 964059.4859 1.880553747 1.575133009 1.195505487 0.825964782 1.091201849 1.201542626 0.877243561 1.122423922 1.156956004 1 19.87876264 4.340320781 2.281939901 1.045211369 1.863300577 0.856256163 0.114191152 0.110710639 1.065920988 0.029462459 0.129965137 21893.78158 -4.340320781 0.818089208 VFGWEEDEDF ddPTM_BT-474_Pertuzumab_2h_R1 2 VFGWEEDEDF 10 0 Q9BWD3;Q17RB0;A6ZKI3 Q9BWD3 FAM127B;FAM127C;FAM127A Protein FAM127B;Protein FAM127C;Protein FAM127A 0 ; 141.39 8.75E-05 24222000 53135 59243 53672 68108 64746 63447 65287 75864 71063 66631 FALSE TRUE 51058.42546 57553.44764 63371.72433 71623.06204 66828.61389 64729.94181 66086.00184 74297.38189 62996.22616 62118.02302 0.821958314 0.926517697 1.020182569 1.153015801 1.075832917 1.042047681 1.06387806 1.196068038 1.014137654 1 15.92272429 4.340362812 1.910017455 1.090084964 0.820953133 0.667135997 0.058075143 0.224901243 1.428163155 0.015568551 0.081480847 21895.90054 -4.340362812 -0.26913183 AGAPGALS(ph)PSYDGGLHGLQSK ddPTM_BT-474_Pertuzumab_2h_R1 6 AGAPGALSPSYDGGLHGLQSK 21 0 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3 K7ENH8 TCF3 Transcription factor E2-alpha 1 AGAPGALS(0.932)PS(0.068)YDGGLHGLQSK;AGAPGALS(0.998)PS(0.002)YDGGLHGLQSK;AGAPGALS(0.996)PS(0.004)YDGGLHGLQSK;AGAPGALS(0.735)PS(0.265)YDGGLHGLQSK;AGAPGALS(0.974)PS(0.026)YDGGLHGLQSK;AGAPGALS(0.84)PS(0.16)YDGGLHGLQSK 339.53 1.80E-80 6358360000 2788310 2922646 2435426 2880815 2875968 3151218 3091199 2908660 3350991 3574398 TRUE FALSE 2679339.763 2839294.998 2875561.654 3029494.207 2968476.123 3214937.787 3129030.018 2848595.155 2970600.55 3332300.84 0.804050982 0.852052421 0.862935789 0.909129863 0.890818766 0.964780175 0.938999859 0.854843332 0.891456292 1 21.66808722 4.340638304 0.986149747 0.915904715 0.786634024 0.504162603 0.039066759 1.058348316 1.262768908 0.013209266 0.127158433 21909.79447 -4.340638304 -0.129270691 RPNT(ph)SPDRGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 RPNT(0.994)S(0.006)PDRGS(1)R 73.208 0.048766 421380000 263000 278320 256020 328920 287280 307560 285820 295370 326850 345010 TRUE FALSE 252721.6692 270382.5861 302288.5091 345895.6006 296520.6221 313779.0739 289317.9507 289270.5063 289747.3583 321642.1654 0.785723069 0.840631656 0.93982861 1.075405024 0.921895989 0.975553294 0.899502558 0.899355052 0.900837606 1 18.29509702 4.340743843 3.419370385 0.947247163 0.796607702 0.535641525 0.052531274 0.19191251 4.239142228 0.014007703 0.046201141 21915.1195 -4.340743843 -0.150639461 IQLVEEELDR ddPTM_BT-474_Pertuzumab_2h_R1 8 IQLVEEELDR 10 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;;;;; 277.36 1.50E-23 25327723000 2362436 2543326 2364284 2940070 2658804 2620574 2888255 3029896 2912698 3037088 FALSE TRUE 2270109.389 2470792.833 2791562.712 3091807.365 2744326.845 2673563.802 2923602.329 2967327.589 2582060.734 2831383.325 0.801766885 0.872645117 0.985935987 1.09197767 0.969253023 0.94426063 1.0325703 1.048013373 0.911943187 1 21.43307565 4.3412983 2.890034516 1.005288572 0.81187235 0.643342915 0.049128938 0.155267129 2.483672974 0.012617645 0.04611892 21943.11607 -4.3412983 -0.193416222 AKYPDYEVTWANDGY ddPTM_BT-474_Pertuzumab_2h_R1 1 AKYPDYEVTWANDGY 15 1 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 158.01 1.51E-05 386480000 294690 303510 272030 311850 320210 284480 303020 332310 390480 349590 FALSE TRUE 283173.189 294854.192 321191.8723 327944.6159 330509.8455 290232.3805 306728.4494 325447.6824 346154.3474 325911.9579 0.868864066 0.904705043 0.985517298 1.006236831 1.01410776 0.890523878 0.941138985 0.998575457 1.062109993 1 18.31412276 4.341349564 3.446708457 0.984054829 0.875309259 0.470573193 0.043207155 0.21634485 4.845890613 0.011463377 0.037681437 21945.70635 -4.341349564 -0.10874557 LAVPTEVSTEVPEMDT(ph)ST ddPTM_BT-474_Pertuzumab_2h_R1 1 LAVPTEVSTEVPEMDTST 18 0 O00488 O00488 ZNF593 Zinc finger protein 593 1 LAVPTEVSTEVPEMDT(0.333)S(0.333)T(0.333) 84.566 0.042423 22753000 16289 17727 19799 18694 20903 25053 21507 19807 24464 27993 TRUE FALSE 15652.40787 17221.44332 23377.11973 19658.79958 21575.36398 25559.58883 21770.2091 19397.97853 21686.94928 26097.00918 0.599777843 0.659901033 0.895777733 0.753297033 0.826737035 0.979406822 0.83420322 0.743302744 0.831012824 1 14.67159686 4.341647024 5.017072005 0.841742216 0.615115027 0.556295941 0.08098003 0.151318116 5.974233579 0.020060652 0.058000105 21960.74272 -4.341647024 -0.226627189 KRT(ph)EEPDRDER ddPTM_BT-474_Pertuzumab_2h_R1 6 KRTEEPDRDER 11 3 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 1 KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER 228.25 3.50E-12 20883461000 6497886 5845366 4616031 4576349 4688482 4483318 4443750 6143152 5628380 4933980 TRUE FALSE 6243941.431 5678661.885 5450250.485 4812534.92 4839291.282 4573973.762 4498133.942 6016293.764 4989469.898 4599797.14 1.357438435 1.234546158 1.184889316 1.046249383 1.05206624 0.994385975 0.97789833 1.307947629 1.084715205 1 22.13313881 4.341714827 1.576798207 1.084499794 1.363629916 0.515910296 0.090861389 0.520823356 2.055097844 0.02810999 0.179504823 21964.17154 -4.341714827 0.279130122 ASSDIVSLAGPSAGPGS(ph)SEGGCSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSDIVSLAGPSAGPGSSEGGCSR 24 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 ASSDIVSLAGPSAGPGS(0.987)S(0.013)EGGCSR;ASSDIVSLAGPSAGPGS(0.967)S(0.033)EGGCSR 368.16 1.23E-118 187054000 165685 230682 272054 357420 296090 375960 416230 283330 359900 432860 TRUE FALSE 159209.847 224103.1752 321220.2096 375866.489 305614.0038 383562.1688 421323.9472 277479.1365 319045.6608 403542.0066 0.394531039 0.55534039 0.796001914 0.931418496 0.75732885 0.950488828 1.044064658 0.687609052 0.790613259 1 18.62235933 4.341914244 2.208793917 0.865917459 0.396554483 0.704817473 0.105553772 0.193902184 1.731831313 0.028369112 0.129371045 21974.25927 -4.341914244 -0.469362976 GFTECEMTKSS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 5 GFTECEMTKSSPLK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 GFTECEMTKS(0.119)S(0.88)PLK;GFTECEMTKS(0.01)S(0.99)PLK;GFTECEMTKS(0.004)S(0.996)PLK;GFTECEMTKS(0.068)S(0.932)PLK;GFTECEMTKS(0.075)S(0.925)PLK 281.67 1.49E-33 3107160000 5130680 4507130 2763630 2401150 3339750 3702200 3180410 3485170 3388550 3275320 TRUE FALSE 4930167.353 4378591.065 3263079.418 2525073.639 3447176.092 3777061.021 3219332.809 3413200.022 3003896.01 3053479.659 1.614606254 1.433967655 1.06864292 0.826949553 1.128933701 1.236969439 1.054316114 1.1178067 0.983761592 1 21.5420228 4.342100717 3.369302471 1.059338585 1.58187362 0.7783559 0.102681622 0.108061745 2.322445998 0.02703966 0.090031649 21983.69637 -4.342100717 0.522535035 FEKEAAEMGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FEKEAAEMGK 10 1 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 71.555 0.046177 197740000 190930 173760 118370 121410 119250 166070 129720 147700 148120 148260 FALSE TRUE 183468.2445 168804.5349 139762.0921 127675.9846 123085.7846 169428.0492 131307.5522 144649.9434 131306.0386 138218.2181 1.327381057 1.221290053 1.01116983 0.923727612 0.890517807 1.225801139 0.950001772 1.046533122 0.949990821 1 17.07658826 4.342291957 3.152046885 1.001281076 1.310750634 0.621074764 0.08756926 0.155551609 2.951590357 0.021846328 0.075587223 21993.37895 -4.342291957 0.309469557 GGTLGGGTLGPPS(ph)PPGAPS(ph)PPEPGGEIELVFRPHPLLVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 2 GGTLGGGTLGPPS(1)PPGAPS(1)PPEPGGEIELVFRPHPLLVEK 102.21 1.83E-05 548200000 153340 155840 141130 153750 161720 183770 159890 175240 185370 175510 TRUE FALSE 147347.3033 151395.5958 166635.3304 161685.0559 166921.8707 187485.9553 161846.7816 171621.2328 164327.5747 163622.5514 0.900531755 0.925273408 1.018412982 0.988158751 1.020164209 1.145844223 0.989147158 1.048884957 1.00430884 1 17.32001208 4.342385242 1.182927543 1.036613208 0.872852429 0.518414557 0.043887152 0.635096909 1.198890845 0.012941188 0.108951481 21998.10357 -4.342385242 -0.163760779 TYDRDNSGMIDKNELK ddPTM_BT-474_Pertuzumab_2h_R1 2 TYDRDNSGMIDKNELK 16 2 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 175.39 1.99E-09 1275890000 1391230 1253360 636270 597990 935760 1088680 794290 845100 1132130 830530 FALSE TRUE 1336859.194 1217615.4 751258.1427 628852.3356 965859.5702 1110693.856 804010.7586 827648.3897 1003615.349 774277.4633 1.726589313 1.572582772 0.970269933 0.812179568 1.247433402 1.434490745 1.038401344 1.068929975 1.296195997 1 19.56249113 4.342550511 5.158351561 1.111789564 1.68597449 0.62045121 0.170541227 0.130496026 5.32385081 0.04407119 0.126783717 22006.47642 -4.342550511 0.574184926 ETEAAPT(ph)SPPIVPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETEAAPTSPPIVPLK 15 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A3B3IT55;Q7Z3B3-4;Q7Z3B3-2 A0A1W2PRB5;Q7Z3B3-4 KANSL1 KAT8 regulatory NSL complex subunit 1 1 ETEAAPT(0.654)S(0.346)PPIVPLK 122.64 0.0012034 82584000 285170 295850 262000 301200 301950 301310 316820 328730 339140 359500 TRUE FALSE 274025.2411 287412.6477 309349.2282 316744.9681 311662.496 307402.6946 320697.3379 321941.6106 300642.249 335150.7448 0.817617879 0.857562312 0.923015189 0.945082095 0.929917361 0.917207255 0.956874908 0.960587484 0.897035897 1 18.35445061 4.342625039 1.903189803 0.942890864 0.813394777 0.730999289 0.025962171 0.199177876 1.251892572 0.006576607 0.034724129 22010.2532 -4.342625039 -0.129496087 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR ddPTM_BT-474_Pertuzumab_2h_R1 8 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 0 ;;;;;;; 365.53 3.16E-148 10637310000 882682 915706 938170 1048078 963892 1030353 1139599 889931 1218019 1140574 FALSE TRUE 848185.8116 889590.9614 1107718.188 1102169.431 994896.4616 1051187.444 1153545.753 871553.6139 1079754.589 1063321.907 0.797675479 0.83661491 1.041752437 1.036534114 0.93564936 0.988588156 1.084850924 0.819651705 1.015454099 1 20.02014699 4.342689088 5.940856369 0.979865182 0.808548175 0.498725533 0.069116166 0.173312442 8.389842364 0.01756208 0.049480955 22013.4995 -4.342689088 -0.171317007 EELEFEVPFR ddPTM_BT-474_Pertuzumab_2h_R1 6 EELEFEVPFR 10 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;; 221.94 1.20E-08 1875560000 1192160 1284280 1252950 1447290 1379130 1368280 1422900 1587770 1587730 1680720 FALSE TRUE 1145569.069 1247653.592 1479385.937 1521984.81 1423490.969 1395947.559 1440313.876 1554981.995 1407497.547 1566883.337 0.731113186 0.796264509 0.944158318 0.971345329 0.908485613 0.890907144 0.919222154 0.992404449 0.898278457 1 20.57946634 4.342841831 3.418198092 0.940668942 0.742474653 0.795165538 0.036521614 0.097282006 2.145123703 0.009330551 0.030858143 22021.24311 -4.342841831 -0.198194289 DYLHLPPEIVPATLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DYLHLPPEIVPATLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;; 107.61 0.0011441 3954140000 961537 996925 938889 1132410 990129 964068 1092620 1098294 1211270 1238891 FALSE TRUE 923959.071 968493.6751 1108567.128 1190853.816 1021977.398 983562.1155 1105991.81 1075613.845 1073771.708 1154979.809 0.799978548 0.838537321 0.959815158 1.031060289 0.884844385 0.851583818 0.957585407 0.931283678 0.929688726 1 20.1394362 4.342926822 4.617907903 0.938850655 0.809562691 0.509758645 0.048955566 0.168892047 5.961290833 0.012479892 0.036784204 22025.55307 -4.342926822 -0.129287963 RS(ph)DSASSEPVGIYQGFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSDSASSEPVGIYQGFEK 18 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 RS(0.771)DS(0.129)AS(0.094)S(0.006)EPVGIYQGFEK;RS(0.849)DS(0.139)AS(0.012)SEPVGIYQGFEK 197.38 1.13E-15 321920000 589140 594350 557030 584990 566740 698160 584780 664490 666920 669590 TRUE FALSE 566115.7575 577399.7199 657697.7121 615181.404 584969.7068 712277.2735 591936.7126 650768.0493 591214.0376 624238.0729 0.906890787 0.924967164 1.053600766 0.985491643 0.937093927 1.141034654 0.948254742 1.042499773 0.94709705 1 19.25173683 4.34312453 6.715136001 1.008438154 0.912082079 0.281697938 0.058248472 0.238606122 13.30268407 0.013223376 0.036829642 22035.58223 -4.34312453 -0.096356075 LLEDS(ph)EES(ph)SEETVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEDSEESSEETVSR 15 0 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 2 LLEDS(1)EES(0.984)S(0.016)EETVSR;LLEDS(1)EES(0.988)S(0.012)EETVSR 200.81 9.83E-09 2063810000 1081440 1112480 980770 1128630 1109350 1193630 1164420 1159990 1241050 1296150 TRUE FALSE 1039176.129 1080753.16 1158016.956 1186878.73 1145033.25 1217766.016 1178670.52 1136035.801 1100171.207 1208360.606 0.859988421 0.894396221 0.95833723 0.982222297 0.947592337 1.007783612 0.975429449 0.94014634 0.910465966 1 20.20461963 4.343254076 2.844126011 0.964501487 0.864040785 0.636258319 0.027238419 0.171227748 2.649324834 0.00710558 0.026350461 22042.15624 -4.343254076 -0.100460702 TVSLTPSPTTQVETPDLVDHDNT(ph)SPLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLTPSPTTQVETPDLVDHDNT(0.863)S(0.137)PLFR 97.387 0.0069275 75455000 50193 52737 48276 54515 64046 51656 53776 59007 64684 60658 TRUE FALSE 48231.40207 51232.99239 57000.54709 57328.52568 66106.09776 52700.51971 54434.12677 57788.48483 57341.3435 56549.57963 0.852904697 0.905983612 1.007974727 1.013774568 1.168993619 0.931934774 0.962591183 1.021908301 1.014001233 1 15.78722868 4.343295244 2.725994361 1.01702545 0.857924347 0.477206668 0.05809526 0.240069544 3.402213099 0.015123775 0.057863225 22044.24577 -4.343295244 -0.159101103 GPAS(ph)DS(ph)ETEDASR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPASDSETEDASR 13 0 Q96ST2;Q96ST2-3 Q96ST2 IWS1 Protein IWS1 homolog 2 GPAS(1)DS(0.985)ET(0.016)EDASR 152.95 6.65E-05 136360000 221430 240920 229390 279650 251570 253590 281940 279560 300890 323210 TRUE FALSE 212776.2708 234049.1975 270845.8758 294082.77 259661.9775 258717.7635 285390.4661 273786.9883 266734.2286 301318.6988 0.706150238 0.776749662 0.898868463 0.975985796 0.861751954 0.858618348 0.947138253 0.908629267 0.885222954 1 18.20093068 4.343353045 2.8685219 0.914376328 0.715286041 0.729477637 0.043814085 0.130257657 2.050774345 0.010800166 0.039816294 22047.17988 -4.343353045 -0.199090286 ETWELEEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETWELEEFR 9 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2;Q9Y4W2-4 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 0 ; 108.98 0.0058716 111733000 127933 143727 155685 198032 152200 147003 187865 190065 185389 205779 FALSE TRUE 122933.2369 139628.0467 183820.7427 208252.4553 157095.6512 149975.5014 190164.1481 186140.0913 164344.4179 191841.405 0.640806592 0.727830609 0.958191182 1.085544881 0.818882927 0.781768156 0.991257065 0.970281109 0.856668131 1 17.5495546 4.34345921 4.124338245 0.932846078 0.66054607 0.571823858 0.087176744 0.151912559 4.561411666 0.0225239 0.068700126 22052.57005 -4.34345921 -0.272300009 WEDIFNQHEEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 WEDIFNQHEEELR 13 0 Q7Z2Y5;Q7Z2Y5-2 Q7Z2Y5 NRK Nik-related protein kinase 0 118.37 0.00043318 18989000 14141 16812 16219 23474 19490 19625 19813 19869 21766 22464 FALSE TRUE 13588.35409 16332.53822 19150.13409 24685.49595 20116.91355 20021.83095 20055.47742 19458.69821 19295.21493 20942.49327 0.648841277 0.779875539 0.914415196 1.178727654 0.960578728 0.956038552 0.957645165 0.929149073 0.921342778 1 14.35414559 4.343475592 2.563634832 0.979571836 0.665496015 0.708548713 0.070547401 0.162923221 2.026206852 0.018982277 0.076232779 22053.40191 -4.343475592 -0.31407582 GELWDTCNIGVPWYDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GELWDTCNIGVPWYDR 16 0 P13807 P13807 GYS1 "Glycogen [starch] synthase, muscle" 0 152.99 1.15E-06 133440000 48489 53385 46947 65030 59025 59137 59685 57123 54126 58045 FALSE TRUE 46593.99627 51862.51207 55431.36723 68386.20609 60923.59273 60332.79066 60415.44288 55943.39009 47981.84339 54113.56045 0.861041038 0.9584014 1.024352616 1.263753586 1.125847056 1.114929237 1.116456622 1.033814623 0.886687976 1 15.72370255 4.343623379 2.503352715 1.08393978 0.875025256 0.346300701 0.093223785 0.330022649 3.897623862 0.024906003 0.10203051 22060.90776 -4.343623379 -0.208914524 SGSGSVGNGSSRYS(ph)PS(ph)QNSPIHHIPSRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSGSVGNGSSRYSPSQNSPIHHIPSRR 28 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 SGSGSVGNGS(0.247)S(0.275)RY(0.186)S(0.376)PS(0.519)QNS(0.378)PIHHIPS(0.019)RR 82.988 0.0075667 171940000 19855 30219 12056 11885 13297 21452 10497 6267.1 13484 9225.5 TRUE FALSE 19079.04465 29357.18371 14234.78738 12498.38627 13724.71008 21885.77414 10625.46543 6137.682195 11953.35285 8600.648668 2.218326243 3.413368554 1.655082998 1.45319112 1.595776157 2.544665523 1.235426052 0.71363015 1.389819921 1 13.07022976 4.34391308 0.314137206 0.877710733 3.86691248 0.453796614 0.560986925 4.963704083 0.481996847 0.648394835 5.59490335 22075.62866 -4.34391308 2.989201748 TGSDHTNPTS(ph)PLLVKPSDLLEENK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSDHTNPTSPLLVKPSDLLEENK 24 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;Q96D71;Q96D71-3;H0YE73 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 TGSDHT(0.013)NPT(0.112)S(0.874)PLLVKPSDLLEENK 121.3 7.76E-05 101890000 64318 70003 70320 86502 77228 74400 82950 77667 90717 99213 TRUE FALSE 61804.38145 68006.58298 83028.38826 90966.37859 79712.10876 75904.41898 83965.16691 76063.14931 80419.18648 92493.21514 0.668204488 0.735260234 0.897670041 0.983492448 0.861815741 0.820648508 0.907798121 0.822364637 0.869460385 1 16.49705992 4.343964615 3.859164862 0.885895558 0.682411845 0.649757993 0.057331502 0.134277314 3.63571909 0.014340491 0.044870069 22078.24838 -4.343964615 -0.203483713 AEQEEMEVEER ddPTM_BT-474_Pertuzumab_2h_R1 2 AEQEEMEVEER 11 0 P78356 P78356 PIP4K2B Phosphatidylinositol 5-phosphate 4-kinase type-2 beta 0 ; 218.15 2.52E-11 1224340000 618770 680200 632380 789490 687330 772470 760870 837500 808890 841720 FALSE TRUE 594587.7843 660801.362 746665.1332 830235.6735 709438.5937 788089.8727 770181.7547 820205.3323 717068.1983 784709.5547 0.757717019 0.842096745 0.951517831 1.058016522 0.904077935 1.004307731 0.981486398 1.045234288 0.913800774 1 19.58179924 4.344278378 2.318607402 0.990114916 0.76240483 0.72512142 0.046611879 0.154187122 1.535799919 0.011586346 0.05079393 22094.20495 -4.344278378 -0.227710086 IETELR ddPTM_BT-474_Pertuzumab_2h_R1 4 IETELR 6 0 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104;REV__P53355-4 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 141.98 0.026948 6367490000 6349550 6716550 6255480 7748460 7007270 7407630 7242000 7417400 7712620 7679070 FALSE TRUE 6101402.566 6525000.57 7385984.388 8148358.949 7232665.203 7557417.354 7330629.762 7264228.098 6837115.712 7158959.749 0.85227502 0.911445349 1.031711959 1.138204325 1.010295554 1.05565859 1.023979743 1.01470442 0.955043184 1 22.77131854 4.344423205 3.525185151 1.032466923 0.863842436 0.642660916 0.04464667 0.137023245 3.18818209 0.011427894 0.037271778 22101.57406 -4.344423205 -0.168624488 S(ph)EPDDELLFDFLNSSQK ddPTM_BT-474_Pertuzumab_2h_R1 5 SEPDDELLFDFLNSSQK 17 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 S(1)EPDDELLFDFLNSSQK;S(1)EPDDELLFDFLNSSQK;S(1)EPDDELLFDFLNSSQK;S(1)EPDDELLFDFLNSSQK;S(1)EPDDELLFDFLNSSQK 197.72 9.56E-12 72468400 93945 105386 108277 134500 114311 108881 113866 147908 152715 131287 TRUE FALSE 90273.52554 102380.4945 127845.0625 141441.5611 117987.9171 111082.6484 115259.5262 144853.6481 135379.4334 122394.8146 0.73756005 0.836477385 1.044530056 1.155617267 0.963994411 0.907576427 0.941702691 1.183494976 1.106087982 1 16.90118291 4.344453525 3.427808887 1.044229189 0.755542878 0.585209769 0.086037929 0.171599309 3.799951654 0.024005769 0.079429375 22103.11713 -4.344453525 -0.288686311 DSALAEAPEGLS(ph)PAPPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DSALAEAPEGLSPAPPAR 18 0 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR 382.37 2.48E-109 1758230000 1203480 1216820 1093230 1182720 1181280 1301260 1244520 1291510 1338300 1427130 TRUE FALSE 1156446.671 1182117.485 1290800.98 1243760.321 1219276.944 1327572.369 1259750.808 1264839.867 1186381.795 1330469.214 0.869202127 0.888496684 0.970184779 0.934828336 0.916426274 0.997822689 0.946847018 0.950672029 0.891701801 1 20.3435037 4.344917029 5.315724154 0.948935511 0.874259017 0.455423332 0.031724403 0.167364761 7.041452176 0.007387449 0.021153785 22126.71943 -4.344917029 -0.074676494 AFVHWYVGEGMEEGEFSEAR ddPTM_BT-474_Pertuzumab_2h_R1 45 AFVHWYVGEGMEEGEFSEAR 20 0 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 324.91 2.84E-67 39855556900 15032485.16 16157335.66 14373918.3 18401739.2 17055227.21 18399557.6 18207150.36 15763978.16 18599599 19267392.9 FALSE TRUE 14444999.02 15696544.27 16971605.08 19351455.17 17603824.08 18771609.26 18429974.91 15438446.5 16488250.5 17962395.22 0.804180002 0.873855857 0.944840868 1.077331555 0.980037677 1.045050453 1.026031033 0.859487074 0.917931618 1 24.09847641 4.345050793 2.522456814 0.979535712 0.812499611 0.500554143 0.059404941 0.284481171 3.413803766 0.017284933 0.070557017 22133.53557 -4.345050793 -0.167036101 GVQKPAGPSTS(ph)PDGNSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GVQKPAGPSTSPDGNSR 17 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GVQKPAGPS(0.003)T(0.31)S(0.687)PDGNSR;GVQKPAGPS(0.032)T(0.194)S(0.774)PDGNSR;GVQKPAGPST(0.035)S(0.965)PDGNSR 192.46 1.12E-10 1029540000 519784 559680 561112 605250 638830 648310 602130 648220 750540 771520 TRUE FALSE 499470.2666 543718.4744 662517.4203 636487.025 659378.5471 661419.2724 609499.0471 634834.0305 665341.8457 719264.2632 0.6944183 0.755937007 0.92110432 0.884914012 0.916740315 0.919577555 0.847392368 0.882615838 0.925031146 1 19.4561624 4.34520513 3.84710313 0.90320925 0.706668638 0.7900243 0.038797544 0.089817433 2.417384782 0.009245054 0.028996275 22141.40265 -4.34520513 -0.196540612 EPS(ph)PALGPNLDGSGLLPR ddPTM_BT-474_Pertuzumab_2h_R1 7 EPSPALGPNLDGSGLLPR 18 0 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR 211.06 3.60E-16 2086816000 224928.5 254640 272851 304767 296528 313335 306737 315241 368613 378623 TRUE FALSE 216138.0455 247377.9165 322161.2452 320496.0614 306066.0924 319670.8484 310490.9392 308731.1632 326769.5976 352978.527 0.612326329 0.70082993 0.912693608 0.907976086 0.8670955 0.90563823 0.879631239 0.874645735 0.925749224 1 18.4292209 4.34552478 3.506662489 0.900804053 0.627921627 0.882837819 0.03724415 0.065070141 1.499314008 0.008745432 0.028634463 22157.70518 -4.34552478 -0.272882426 VSSS(ph)PQKEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSSSPQKEGR 10 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 VS(0.165)S(0.348)S(0.487)PQKEGR 76.24 0.022159 265720000 447670 409960 211760 250290 294680 351820 290250 311090 312580 254230 TRUE FALSE 430174.5615 398268.3422 250029.7426 263207.4969 304158.6498 358934.0415 293802.1663 304665.8828 277097.2288 237010.7757 1.815000015 1.680380738 1.054929852 1.110529663 1.283311482 1.51442077 1.239615226 1.285451608 1.169133463 1 17.85459313 4.345604601 5.624272468 1.232717456 1.778666401 0.707560708 0.139009848 0.107687612 4.838479423 0.034898013 0.099071291 22161.77806 -4.345604601 0.545948945 KGS(ph)ITEYTAAEEKEDGRR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGSITEYTAAEEKEDGRR 18 3 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(1)ITEYTAAEEKEDGRR 184.26 3.27E-13 655540000 584560 497700 325380 194780 331040 453520 330570 378400 460460 400970 TRUE FALSE 561714.7489 483506.0833 384183.404 204832.6191 341688.2022 462690.4851 334615.6145 370585.9078 408190.5112 373811.9448 1.502666667 1.293447387 1.027745125 0.547956324 0.91406443 1.237762708 0.895144254 0.991369893 1.091967544 1 18.51195314 4.346013237 2.900228762 0.95206465 1.469273245 0.539492662 0.166518687 0.202673035 3.259955544 0.044021456 0.161748668 22182.64031 -4.346013237 0.517208595 EYWDYESHVVEWGNQDDYQLVR ddPTM_BT-474_Pertuzumab_2h_R1 4 EYWDYESHVVEWGNQDDYQLVR 22 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1;A0A2R8YDY7;A0A2R8YCK2;V9GY80;A0A2R8Y7T1;A0A2R8YF47;A0A2R8YEL7;A0A2R8Y797;A0A2R8Y3W6 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ;;; 339.55 3.71E-81 1978940000 988110 1023640 879280 1125680 1057690 967540 1087310 975930 1175940 1209370 FALSE TRUE 949493.5688 994446.7894 1038185.455 1183776.48 1091711.559 987104.3217 1100616.825 955776.7045 1042452.221 1127458.293 0.842154051 0.882025345 0.920819388 1.049951459 0.968294407 0.875512937 0.97619294 0.847726883 0.924603799 1 20.10464264 4.346043093 2.942983573 0.93927763 0.849441726 0.272801835 0.055751155 0.391501562 6.485468224 0.014975514 0.05447236 22184.16534 -4.346043093 -0.089835904 RRGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RRGDS(1)ES(1)EEDEQDSEEVR 157.12 3.28E-08 545450000 257360 262810 210650 259430 257210 288480 223140 238550 321190 291650 TRUE FALSE 247302.0867 255314.9161 248719.1409 272819.2134 265483.3932 294313.2633 225870.8541 233623.8591 284729.8577 271896.2857 0.90954566 0.939015829 0.914757405 1.003394411 0.976414196 1.082446796 0.830724309 0.859238877 1.047200248 1 18.05269692 4.34631277 0.003688597 1.881135358 8.72E-08 0.023401118 0.075331815 349806.2797 227.5782172 56664.62208 59417.30116 22197.94495 -4.34631277 -1.881135271 TAS(ph)FSESRADEVAPAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.171)AS(0.808)FS(0.021)ESRADEVAPAKK 131.59 1.38E-05 559000000 872890 755230 319490 341260 471270 602510 372870 468780 594470 388110 TRUE FALSE 838776.4938 733691.5798 377228.95 358872.4695 486428.8275 614693.165 377433.2946 459099.5292 526988.2578 361822.964 2.31819585 2.027763997 1.042578796 0.991845475 1.344383513 1.698878253 1.04314356 1.268851275 1.45648096 1 18.46492445 4.346343512 4.759272258 1.244899348 2.246490283 0.749823807 0.219621095 0.095197505 3.476038396 0.055050858 0.161300732 22199.51631 -4.346343512 1.001590935 QPHVGDYR ddPTM_BT-474_Pertuzumab_2h_R1 5 QPHVGDYR 8 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;; 91.584 0.012384 9264730000 5700850 6468800 5116640 6995560 6549870 6823950 6868770 6705190 7252050 7613630 FALSE TRUE 5478054.479 6284316.158 6041330.667 7356601.69 6760552.517 6961934.944 6952832.062 6566725.483 6428827.687 7097952.059 0.771779583 0.88537033 0.851137147 1.036440036 0.952465227 0.980837133 0.979554667 0.925157768 0.905729939 1 22.7589714 4.346442453 1.408830822 0.96192766 0.772427562 0.640983986 0.044685411 0.409952866 1.208297721 0.012513446 0.09051887 22204.57439 -4.346442453 -0.189500099 GKPDAAK ddPTM_BT-474_Pertuzumab_2h_R1 6 GKPDAAK 7 1 P09429 P09429 HMGB1 High mobility group protein B1 0 ;;;;; 84.743 0.019445 4651700000 7476330 6308360 5380130 4690850 5231090 4035110 6393580 5794880 5189630 6378270 FALSE TRUE 7184146.758 6128451.749 6352439.171 4932945.331 5399352.761 4116702.689 6471826.545 5675213.703 4600524.959 5946264.092 1.208178219 1.030639012 1.068307609 0.829587327 0.908024379 0.6923175 1.08838532 0.954416692 0.773683255 1 22.50355211 4.346454135 1.344113043 0.900569352 1.212775412 0.423483306 0.113204497 0.696894675 1.820058744 0.032592213 0.246756102 22205.17169 -4.346454135 0.31220606 S(ph)SLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHKR 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 S(0.5)S(0.5)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHKR 88.641 9.61E-06 37335000 22845 22298 20697 21145 24059 24428 22601 26515 28692 26222 TRUE FALSE 21952.19214 21662.08287 24437.4083 22236.29598 24832.87958 24921.9509 22877.5978 25967.45598 25435.00445 24445.96058 0.897988527 0.886121157 0.999650156 0.909610236 1.015827523 1.019471123 0.935843683 1.062239133 1.040458376 1 14.57730848 4.346495683 0.445105346 1.028248136 0.81836332 0.515898367 0.041967523 2.786414945 0.557770632 0.030880709 0.299462687 22207.29608 -4.346495683 -0.209884817 LFDSTIADEGTWTLEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFDSTIADEGTWTLEDR 17 0 Q8WVJ2 Q8WVJ2 NUDCD2 NudC domain-containing protein 2 0 ; 198.74 3.24E-11 115765000 71466 75659 69864 79384 82018 88112 81636 94711 82306 88425 FALSE TRUE 68673.02971 73501.2794 82489.97892 83481.01775 84656.18346 89893.68501 82635.08579 92755.18475 72962.96793 82435.89599 0.833047653 0.891617402 1.00065606 1.012677994 1.026933503 1.090467738 1.002416299 1.125179555 0.88508734 1 16.33098506 4.346611176 1.591732682 1.034572285 0.815540666 0.519941191 0.060335317 0.371657594 1.495498353 0.015822262 0.101269191 22213.20251 -4.346611176 -0.219031619 EWSLESSPAQNWT(ph)PPQPR ddPTM_BT-474_Pertuzumab_2h_R1 5 EWSLESSPAQNWTPPQPR 18 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 EWSLESSPAQNWT(1)PPQPR;EWSLES(0.004)S(0.026)PAQNWT(0.97)PPQPR;EWSLESS(0.026)PAQNWT(0.973)PPQPR;EWSLESSPAQNWT(1)PPQPR;EWSLES(0.001)S(0.007)PAQNWT(0.991)PPQPR 192.85 1.72E-13 791304000 343598 364480 339174 389132 366194 411892 402939 449618 378141 436034 TRUE FALSE 330169.8103 354085.3873 400470.2867 409215.1492 377972.9626 420220.7384 407870.288 440333.2312 335216.019 406501.0288 0.8122238 0.871056559 0.985164264 1.006676786 0.929820433 1.033750738 1.003368403 1.083227839 0.824637566 1 18.63289948 4.346661326 2.743648355 0.993941824 0.817645152 0.434459445 0.065408328 0.231649492 3.323530159 0.016226493 0.062147962 22215.76772 -4.346661326 -0.176296672 RKRET(ph)DDEGEDD ddPTM_BT-474_Pertuzumab_2h_R1 4 RKRETDDEGEDD 12 3 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 RKRET(1)DDEGEDD;RKRET(1)DDEGEDD;RKRET(1)DDEGEDD;RKRET(1)DDEGEDD 121.39 0.00088381 448180000 610758 570102 389927 393400 449009 524676 430181 516063 576217 493383 TRUE FALSE 586888.9021 553843.2491 460395.4828 413703.4211 463451.7823 535285.3082 435445.6838 505406.1187 510807.2619 459965.73 1.275940497 1.204096769 1.000934315 0.89942227 1.007578939 1.163750413 0.94669158 1.098790814 1.110533304 1 18.81116685 4.346680858 4.335405763 1.030861317 1.259141889 0.56623737 0.074952967 0.150207014 4.83189101 0.019115864 0.057476351 22216.76688 -4.346680858 0.228280572 KEELAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEELAR 6 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 0 ; 91.906 0.075939 417630000 728510 770430 719750 878400 847330 735720 868040 929800 801010 857700 FALSE TRUE 700039.0238 748458.0907 849824.8358 923734.3293 874585.139 750596.7625 878663.3332 910599.3051 710082.7029 799607.215 0.875478623 0.936032188 1.062802861 1.15523511 1.093768443 0.938706841 1.09886869 1.138808265 0.888039389 1 19.60893196 4.347260646 3.563967741 1.060631324 0.887232384 0.325234761 0.081418951 0.235084382 5.56661478 0.020296826 0.066047544 22246.44634 -4.347260646 -0.17339894 S(ph)DSASSEPVGIYQGFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSASSEPVGIYQGFEK 17 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 S(0.652)DS(0.343)AS(0.005)SEPVGIYQGFEK 378.62 1.09E-91 0 102700 107910 102090 116770 125770 114980 108550 128170 117160 123060 TRUE FALSE 98686.37046 104832.5125 120539.934 122796.5137 129815.5063 117304.9744 109878.4674 125523.2447 103860.488 114725.0366 0.860199076 0.913771881 1.050685513 1.070354975 1.131535976 1.02248801 0.957754912 1.094122508 0.905299236 1 16.80782074 4.347435719 3.908600551 1.036505045 0.871328167 0.457161785 0.062480098 0.174773264 4.815798886 0.015255648 0.047630309 22255.41612 -4.347435719 -0.165176878 VSVT(ph)PPEESQNSDTPPRPDRLPLDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSVTPPEESQNSDTPPRPDRLPLDEK 26 2 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 VS(0.007)VT(0.993)PPEESQNSDTPPRPDRLPLDEK 132.6 0.0025816 184670000 229780 215260 135670 142800 175280 190260 160740 178530 220140 179540 TRUE FALSE 220799.9436 209120.9956 160188.587 150169.9251 180918.0404 194107.1876 162707.1842 174843.2931 195150.6301 167379.5959 1.319156869 1.249381649 0.957037721 0.897181788 1.080884677 1.159682496 0.972084939 1.04459144 1.165916485 1 17.35276414 4.347526801 5.391126701 1.035113521 1.300720411 0.604827311 0.081297054 0.131248371 5.581248862 0.020657296 0.059050944 22260.08412 -4.347526801 0.265606891 S(ph)VASSQPAKPTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVASSQPAKPTK 12 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.998)VAS(0.002)SQPAKPTK;S(0.99)VAS(0.005)S(0.005)QPAKPTK 166.62 3.11E-05 1156900000 1719425 1461161 1091978 926349 1143769 941615 689706 1787154 1136640 835898 TRUE FALSE 1652227.97 1419490.119 1289322.716 974157.9829 1180559.369 960655.1005 698146.8283 1750248.645 1007613.392 779281.8839 2.120192968 1.821536145 1.654501076 1.250071384 1.514932392 1.232744043 0.895884843 2.245976304 1.293002459 1 19.57178575 4.347557996 1.703840012 1.424012417 2.132455365 0.330460069 0.352914182 0.656568186 3.132216754 0.100056419 0.598488776 22261.6831 -4.347557996 0.708442948 GDQENVHPDVMLVQPR ddPTM_BT-474_Pertuzumab_2h_R1 5 GDQENVHPDVMLVQPR 16 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 218.43 1.33E-14 5026390000 2439480 2800800 2862950 3583820 3252670 3398160 3422190 3337410 3667410 3943780 FALSE TRUE 2344142.425 2720923.926 3380348.751 3768781.38 3357295.085 3466873.123 3464071.785 3268491.317 3251100.992 3676664.268 0.637573152 0.740052321 0.919406425 1.025054535 0.913136158 0.942939815 0.942177891 0.888982806 0.884252887 1 21.80996601 4.348344352 2.944174575 0.936864048 0.651423324 0.854594647 0.042376098 0.091822585 1.521240835 0.011144318 0.040675491 22302.02776 -4.348344352 -0.285440724 RTLS(ph)MDKGF ddPTM_BT-474_Pertuzumab_2h_R1 2 RTLSMDKGF 9 2 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 RTLS(1)MDKGF;RTLS(1)MDKGF 156.52 5.57E-05 666250000 879770 819630 464034 497050 709550 434570 763970 720820 681690 599850 TRUE FALSE 845387.6158 796254.9549 547895.2662 522702.8101 732373.3201 443357.3031 773319.6934 705934.8151 604307.4091 559221.6252 1.511721968 1.423862953 0.979746207 0.934697062 1.309629827 0.792811442 1.382850123 1.262352497 1.08062239 1 19.09306063 4.34842313 5.893968354 1.117180193 1.487828938 0.423638706 0.173988716 0.195272298 9.193492753 0.042983573 0.121328677 22306.07357 -4.34842313 0.370648746 GSVFLESDS(ph)SPPSSSDAGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSVFLESDSSPPSSSDAGLR 20 0 Q8TBP0 Q8TBP0 TBC1D16 TBC1 domain family member 16 1 GSVFLES(0.012)DS(0.647)S(0.341)PPSSSDAGLR;GSVFLESDS(0.771)S(0.229)PPSSSDAGLR 316.25 1.97E-66 302380000 345950 384240 383850 471900 427100 403920 496810 471990 441400 487650 TRUE FALSE 332429.8915 373281.8514 453220.2337 496254.8156 440838.0594 412087.5391 502890.1094 462243.2416 391294.1225 454621.0311 0.731224182 0.821083553 0.996918758 1.091579099 0.969682503 0.906441873 1.106174319 1.016766075 0.860703962 1 18.7943049 4.348537451 3.256066163 1.001186358 0.746069121 0.612862866 0.070486317 0.150260523 3.024802264 0.017807652 0.060954507 22311.94605 -4.348537451 -0.255117237 DEEVHAGLGELLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DEEVHAGLGELLR 13 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 ;;;;; 200.05 1.13E-07 4927220000 2876550 3238980 3466700 4010230 3418660 3570070 4082590 4069520 4815860 4817710 FALSE TRUE 2764131.246 3146607.462 4093209.806 4217198.451 3528624.304 3642259.261 4132553.958 3985482.99 4269183.763 4491402.211 0.615427235 0.700584654 0.91134341 0.938949186 0.785639793 0.810940346 0.920103292 0.887358291 0.950523592 1 22.09873449 4.348799818 3.795726325 0.891811511 0.632388441 0.720474495 0.061101942 0.11397433 2.995183213 0.015346232 0.04856832 22325.42929 -4.348799818 -0.25942307 IERDS(ph)REHEEPT(ph)TSEMAEETYSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IERDSREHEEPTTSEMAEETYSPK 24 2 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 2 IERDS(0.929)REHEEPT(0.394)T(0.358)S(0.319)EMAEETYSPK 108.56 0.004359 440920000 299460 230540 93465 85248 99823 102060 40352 99769 85116 73737 TRUE FALSE 287756.7721 223965.2249 110356.2046 89647.6595 103033.8975 104123.7231 40845.83985 97708.73529 75453.98852 68742.72731 4.185995863 3.258020647 1.605350979 1.30410391 1.498833425 1.514687112 0.594184162 1.421368327 1.097628672 1 16.06891947 4.348806339 1.912205622 1.210160641 4.301830819 0.937656383 0.261616302 0.088232755 0.558417402 0.069316005 0.369491094 22325.76449 -4.348806339 3.091670178 up ERETPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERETPPR 7 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 129.47 0.0049893 253140000 298990 308950 270790 311030 317110 314480 335630 326360 354780 342150 FALSE TRUE 287305.1402 300139.0485 319727.7767 327082.2956 327310.1311 320839.0011 339737.5403 319620.552 314506.8618 318975.8757 0.900711189 0.940945919 1.002357235 1.025413896 1.026128168 1.00584096 1.06508851 1.002021081 0.985989492 1 18.28308779 4.348842381 2.183167875 1.018116106 0.900612523 0.781497482 0.020345142 0.148230544 1.283698035 0.005297831 0.024791761 22327.61735 -4.348842381 -0.117503583 SLGYDLPMVEEGEPDPEFEAILDTVDPNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGYDLPMVEEGEPDPEFEAILDTVDPNR 29 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 198.67 3.87E-25 93390000 43777 53591 50705 73466 58436 56216 63237 69057 74374 83748 FALSE TRUE 42066.14644 52062.63715 59868.52143 77257.58906 60315.64701 57352.72604 64010.91332 67630.94882 65931.37532 78075.67337 0.538786854 0.666822775 0.766801218 0.989521905 0.772528041 0.734578692 0.819857333 0.866223062 0.844454777 1 16.25258549 4.348857606 2.151665727 0.846516509 0.546464747 0.622256208 0.081253929 0.233856204 1.958110557 0.020943631 0.099377047 22328.40012 -4.348857606 -0.300051761 RPES(ph)FTTPEGPKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPESFTTPEGPKPR 14 2 F8W8D3;Q14493;H7C4H8 F8W8D3 SLBP Histone RNA hairpin-binding protein 1 RPES(0.621)FT(0.366)T(0.013)PEGPKPR;RPES(0.586)FT(0.365)T(0.049)PEGPKPR 108.18 0.00066187 823440000 397050 360670 218580 283300 282590 228640 261650 317480 270160 271570 TRUE FALSE 381532.847 350384.0447 258082.2683 297921.147 291679.764 233263.2575 264852.151 310923.9271 239492.5694 253176.322 1.506984713 1.383952662 1.019377587 1.176733845 1.152081528 0.92134705 1.046117381 1.22809244 0.945951689 1 17.94978296 4.34893133 4.205653657 1.078692895 1.480344481 0.719783071 0.096429338 0.109749353 3.373028514 0.024229153 0.073685371 22332.1908 -4.34893133 0.401651586 GVTDHTQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVTDHTQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 62.546 0.078954 17789000 21797 26930 27629 34006 37492 42015 43023 29025 29085 29948 FALSE TRUE 20945.14914 26161.98277 32622.1749 35761.05374 38697.96423 42864.57209 43549.52834 28425.62361 25783.39273 27919.59529 0.750195299 0.93704735 1.168432944 1.2808586 1.386050329 1.535286298 1.559819471 1.018124486 0.923487338 1 14.76899041 4.348974 1.945812904 1.26571128 0.742399583 0.381384343 0.205945615 0.434448941 2.867268565 0.059193939 0.310155321 22334.38508 -4.348974 -0.523311697 TLAYIITELDER ddPTM_BT-474_Pertuzumab_2h_R1 2 TLAYIITELDER 12 0 G3V2V6;H0YJH8;G3V2S6;Q9Y5K8 G3V2V6 ATP6V1D V-type proton ATPase subunit D 0 ; 147.72 0.00015312 34051000 38837 40535 39471 48106 42062 42834 41267 48360 43450 50845 FALSE TRUE 37319.2071 39378.98149 46604.28773 50588.75643 43414.96243 43700.13283 41772.03789 47361.3491 38517.73816 47401.22286 0.787304733 0.830758768 0.983187456 1.067245809 0.915903848 0.921919946 0.881243887 0.999158803 0.812589546 1 15.53263666 4.349005306 4.964293889 0.948707893 0.798340127 0.407205097 0.067548772 0.186477274 7.153808777 0.016388412 0.047607804 22335.9951 -4.349005306 -0.150367766 S(ph)RSASLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSASLR 7 1 Q16629;Q16629-4;C9JAB2;H7BZZ6;H7C1N1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 S(0.973)RS(0.027)ASLR 60.398 0.059197 95185000 40904 55618 56922 86028 69915 71150 92560 58496 76247 93386 TRUE FALSE 39305.42646 54031.8291 67209.07162 90467.91539 72163.87947 72588.70175 93692.77697 57288.03716 67591.76021 87060.88304 0.45147057 0.620621193 0.771977831 1.039133905 0.828889818 0.833769418 1.076175358 0.658022698 0.776373474 1 16.40973703 4.349029233 2.210303305 0.868921281 0.462206199 0.574506239 0.122080108 0.257192512 2.291453277 0.032316954 0.149538257 22337.22573 -4.349029233 -0.406715082 GTMTTGHNVADLVVILK ddPTM_BT-474_Pertuzumab_2h_R1 2 GTMTTGHNVADLVVILK 17 0 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 142.01 6.03E-07 770490000 856900 911530 886210 964540 985180 1006140 1081890 1017770 1145560 1093660 FALSE TRUE 823411.4006 885534.0569 1046367.861 1014320.025 1016869.209 1026484.84 1095130.493 996752.6938 1015520.831 1019585.434 0.807594315 0.868523644 1.026267957 0.994835735 0.997335952 1.006766874 1.074093898 0.977605859 0.996013475 1 19.95955124 4.349202226 3.784602659 1.009267584 0.819361736 0.87884258 0.025763471 0.065752494 1.719422788 0.00646845 0.020505778 22346.12513 -4.349202226 -0.189905847 VLMATNRPDTLDPALMRPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLMATNRPDTLDPALMRPGR 20 2 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 153.11 3.19E-08 2338700000 1808380 1869640 1610710 1928660 1913220 1943730 1878510 2015930 1919340 2106100 FALSE TRUE 1737706.51 1816319.698 1901801.127 2028198.374 1974760.459 1983033.552 1901499.767 1974300.341 1701464.57 1963451.971 0.885026237 0.925064491 0.968600788 1.032975802 1.005759493 1.009973038 0.968447304 1.005525152 0.86656796 1 20.90496088 4.349211363 2.481168832 0.987166698 0.88915819 0.357629334 0.043044854 0.309932614 3.581090337 0.010793858 0.045039727 22346.59527 -4.349211363 -0.098008508 VVDDLLDQITGGDHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVDDLLDQITGGDHSR 16 0 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2;H0YBR9;H0YAW8;H0YBF1 Q9H8M2 BRD9 Bromodomain-containing protein 9 0 ; 190.11 9.10E-10 35632000 49404 53369 57794 66294 62290 59225 61327 64256 67575 75216 FALSE TRUE 47473.23706 51846.96837 68238.66142 69715.44128 64293.61442 60422.57008 62077.53817 62929.09115 59904.1693 70121.55332 0.677013483 0.739387049 0.973148172 0.994208456 0.916888052 0.86168328 0.885284698 0.897428653 0.854290392 1 16.09757033 4.349342404 5.086474522 0.916075901 0.692894261 0.747466211 0.050198573 0.098743637 3.901361679 0.012952119 0.03743943 22353.33898 -4.349342404 -0.22318164 ESEKQQDS(ph)QPEEVMDVLEMVENVK ddPTM_BT-474_Pertuzumab_2h_R1 6 ESEKQQDSQPEEVMDVLEMVENVK 24 1 Q9H307 Q9H307 PNN Pinin 1 ES(0.171)EKQQDS(0.829)QPEEVMDVLEMVENVK;ES(0.2)EKQQDS(0.8)QPEEVMDVLEMVENVK;ES(0.003)EKQQDS(0.997)QPEEVMDVLEMVENVK;ES(0.027)EKQQDS(0.973)QPEEVMDVLEMVENVK;ES(0.156)EKQQDS(0.844)QPEEVMDVLEMVENVK;ESEKQQDS(1)QPEEVMDVLEMVENVK 229.65 1.59E-33 344036000 263830 228715 139164 113625 161232 197810 142663 170757 215379 145606 TRUE FALSE 253519.2319 222192.2721 164314.0305 119489.1999 166418.1737 201809.8537 144408.9525 167230.8083 190930.0789 135743.9759 1.867627865 1.636848122 1.210470147 0.880254163 1.225970969 1.486694731 1.063833231 1.231957493 1.406545503 1 17.05052865 4.349543053 3.251902631 1.191123023 1.828554804 0.648013318 0.17009291 0.145845336 2.928047567 0.04311762 0.147902794 22363.66884 -4.349543053 0.637431781 LSVQSNPS(ph)PQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSVQSNPSPQLR 12 0 O75152;E9PBY7;E9PQ61;A0A1W2PPR9 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 LSVQSNPS(1)PQLR;LSVQSNPS(1)PQLR;LSVQSNPS(1)PQLR;LSVQSNPS(1)PQLR 240.46 8.09E-10 894180000 1567980 1649960 1467590 1771410 1608670 1832220 1777700 1831730 1651910 2076930 TRUE FALSE 1506701.608 1602904.756 1732816.159 1862832.682 1660414.332 1869268.744 1799456.024 1793904.135 1464392.102 1936257.681 0.778151391 0.827836487 0.894930554 0.962078912 0.857537893 0.965402881 0.929347391 0.926480061 0.756300216 1 20.88483953 4.350056441 2.521997707 0.91347284 0.782572245 0.330778148 0.063990763 0.328899672 3.93698006 0.015570227 0.064185702 22390.12102 -4.350056441 -0.130900595 S(ph)PGEYINIDFGEPGAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPGEYINIDFGEPGAR 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR 202.18 3.25E-11 179267000 85493 87753 96801 102488 96964 92121 99085 105041 110517 118429 TRUE FALSE 82151.83904 85250.37036 114295.094 107777.418 100082.9351 93983.74974 100297.6319 102871.8666 97971.57349 110407.6983 0.744077091 0.772141541 1.035209462 0.976176658 0.906485115 0.851242723 0.908429696 0.931745414 0.887361796 1 16.75248124 4.350188355 7.561855785 0.930306573 0.751978543 0.652201952 0.052213349 0.134980881 8.341297985 0.013175804 0.03644419 22396.92291 -4.350188355 -0.17832803 TEFS(ph)PAAFEQEQLGSPQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TEFSPAAFEQEQLGSPQVR 19 0 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 TEFS(1)PAAFEQEQLGSPQVR 158.92 3.61E-11 33560000 77014 80163 74553 90517 78306 86222 94186 88711 76434 91550 TRUE FALSE 74004.20774 77876.82973 88026.38552 95188.59322 80824.78361 87965.46792 95338.67644 86879.08685 67757.53276 85349.23696 0.867075212 0.912449045 1.031366989 1.115283471 0.946988942 1.030653244 1.117041931 1.017924588 0.79388563 1 16.38109063 4.350208759 4.209251479 1.01566189 0.877399124 0.226077459 0.086670645 0.280763313 8.631183529 0.021346571 0.064955784 22397.97519 -4.350208759 -0.138262766 S(ph)PSASSLSSMSSVASSVSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSASSLSSMSSVASSVSSR 20 0 J3KP58;P30622-2;P30622-1;P30622;F5H0N7;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 S(0.87)PS(0.129)AS(0.001)SLSSMSSVASSVSSR 192.16 1.26E-17 143640000 12749 16669 22368 22881 20671 24687 30446 23138 27853 31518 TRUE FALSE 12250.75499 16193.61644 26410.39517 24061.89115 21335.90149 25186.18805 30818.60726 22660.19221 24691.24421 29383.25779 0.416929773 0.551117121 0.898824608 0.818898004 0.726124436 0.857161185 1.048849228 0.771194004 0.840316768 1 14.84270674 4.350347421 3.785080176 0.859948099 0.442691019 0.736786794 0.093398767 0.107542649 2.81129648 0.023242002 0.073755755 22405.12759 -4.350347421 -0.41725708 KPQEESER ddPTM_BT-474_Pertuzumab_2h_R1 1 KPQEESER 8 1 P26358;P26358-2;K7EJL0;K7ENQ6;K7ERQ1;K7ELB1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 75.509 0.06126 120660000 162310 178670 139700 197540 198300 227350 227370 244170 273290 293290 FALSE TRUE 155966.7458 173574.5065 164946.8976 207735.0631 204678.4996 231947.1728 230152.6221 239127.8042 242267.2649 273425.2071 0.570418315 0.634815306 0.603261489 0.759750958 0.748572166 0.848302083 0.84173886 0.874563859 0.886045831 1 18.06078673 4.350361036 0.235770609 1.013132856 0.24681812 0.952365954 0.028838745 1.67189534 0.09481977 0.046540779 0.374007967 22405.82998 -4.350361036 -0.766314736 EIQVQHPAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIQVQHPAAK 10 0 P49368;B4DUR8;Q5SZX6;E9PRC8;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 94.767 0.0078793 2726740000 3457200 3318300 2964600 3296500 3271200 3512400 3430800 3691000 4175800 4142700 FALSE TRUE 3322088.802 3223665.333 3500369.167 3466632.76 3376421.119 3583423.135 3472787.157 3614779.56 3701780.69 3862111.239 0.860174292 0.834689923 0.906335667 0.897600443 0.874242328 0.927840477 0.899193975 0.935959463 0.958486294 1 21.88095829 4.350577879 0.081446926 1.119266212 0.614459714 0.828838713 0.019029545 28.61404995 0.422848602 0.749066478 2.078442583 22417.01999 -4.350577879 -0.504806499 VEGDLKGPEVDLK ddPTM_BT-474_Pertuzumab_2h_R1 3 VEGDLKGPEVDLK 13 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 103.85 0.001439 707930000 1648970 1548300 1082610 1026490 1115230 1424240 1230310 1582460 1627770 1291090 FALSE TRUE 1584526.429 1504144 1278261.71 1079467.272 1151102.386 1453039.109 1245366.902 1549781.648 1442992.374 1203643.324 1.316441837 1.249659238 1.061993768 0.896833181 0.956348415 1.207200737 1.034664403 1.287575494 1.1988538 1 20.19897651 4.350653678 4.444698366 1.092308456 1.300540195 0.332319616 0.115247511 0.27066304 8.976911681 0.031768817 0.095013022 22420.93287 -4.350653678 0.20823174 ELEEWYAR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELEEWYAR 8 0 P09496-2;F8WF69;P09496-4;P09496-3;P09496;P09496-5;C9J8P9 P09496-2 CLTA Clathrin light chain A 0 ;;; 208.59 0.00012575 6672000000 5256110 5713900 4563200 5810350 5870600 5649400 5790900 6000200 6045100 6580800 FALSE TRUE 5050695.41 5550945.166 5387871.748 6110222.86 6059433.181 5763634.739 5861770.766 5876293.773 5358885.591 6135076.554 0.823248963 0.904788248 0.878207745 0.995948919 0.987670346 0.939456042 0.955451935 0.957819144 0.873483084 1 22.54864992 4.351071901 1.400199057 0.955492229 0.82425203 0.51606547 0.039332717 0.526348796 1.520455787 0.010920525 0.080387248 22442.5345 -4.351071901 -0.131240199 KLSSWDQAET(ph)PGHT(ph)PSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 KLSSWDQAET(1)PGHT(0.999)PS(0.001)LR;KLSSWDQAET(1)PGHT(1)PSLR 112.85 0.00011663 572800000 921470 729470 332040 326890 380550 367310 214510 485560 300760 245230 TRUE FALSE 885457.9337 708666.2298 392047.0142 343760.8321 392790.7364 374737.2599 217135.2375 475533.0163 266618.9857 228620.3537 3.873049444 3.099751262 1.71483863 1.503631792 1.718091719 1.639124662 0.94976337 2.080011725 1.166208439 1 17.80259432 4.35112323 2.282005276 1.500338666 3.874953642 0.862578076 0.329534122 0.107128813 1.025614139 0.081589196 0.368126165 22445.18711 -4.35112323 2.374614976 ETLIDVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETLIDVAR 8 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 96.492 0.020712 398290000 480210 549630 558000 653500 634110 631450 697810 726020 749010 800750 FALSE TRUE 461442.8623 533955.0905 658843.0126 687227.2133 654506.724 644218.3516 706350.0075 711027.4333 663985.5249 746514.4893 0.618129814 0.715264202 0.882558908 0.920581212 0.876750195 0.862968316 0.946197318 0.952463004 0.889447605 1 19.50981074 4.351264864 2.031786483 0.919641948 0.610881729 0.879648885 0.037994941 0.12003108 0.877023694 0.010208311 0.051496717 22452.50819 -4.351264864 -0.308760219 VLNEAVGALMYHTITLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLNEAVGALMYHTITLTR 18 0 Q13363-2;Q13363;E9PGB1;E7ESU7;D6RAX2;E7EPF8 Q13363-2 CTBP1 C-terminal-binding protein 1 0 ; 248.35 1.73E-24 410540000 243477 254420 240136 276470 285710 299870 273010 263041 280140 278830 FALSE TRUE 233961.6497 247164.1907 283533.917 290738.6498 294900.1216 305933.5769 276351.178 257609.1114 248339.6816 259944.5957 0.900044292 0.950834119 1.090747496 1.118463913 1.134472986 1.176918397 1.063115689 0.991015453 0.955356202 1 17.98784464 4.351291762 4.221262043 1.069655387 0.91135481 0.43038825 0.065623879 0.210033479 6.478617079 0.018309839 0.055700999 22453.89886 -4.351291762 -0.158300577 AVTELNEPLSNEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVTELNEPLSNEDR 14 0 Q04917 Q04917 YWHAH 14-3-3 protein eta 0 ;;; 369.42 1.03E-96 1484880000 512661 561853 494937 622704 604253 609615 564491 684811 641089 651548 FALSE TRUE 492625.6413 545829.5026 584383.1257 654841.8281 623689.3465 621941.833 571399.4097 670669.4135 568315.2644 607418.0736 0.811015778 0.898605962 0.962077276 1.078074322 1.026787601 1.023910647 0.940702021 1.104131475 0.935624554 1 19.21233031 4.351341096 1.896859181 1.02097023 0.810825153 0.625733635 0.0506419 0.245157518 1.518714684 0.012887196 0.069670617 22456.44968 -4.351341096 -0.210145077 KLEAELLQIEER ddPTM_BT-474_Pertuzumab_2h_R1 4 KLEAELLQIEER 12 1 Q969G3;Q969G3-4;Q969G3-2;B4DGM3;Q969G3-5;A0A2R8Y855;A0A2R8Y7I9;A0A2U3TZQ7;J3QKS7;A0A2R8YES3;A0A2R8Y4T4;A0A2R8Y765;A0A2R8Y7U4;Q969G3-6;Q969G3-3;J3QR61 Q969G3 SMARCE1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 0 ;;; 178.67 3.48E-05 1152140000 1509700 1520260 1346370 1439130 1580570 1589980 1522460 1623320 1629450 1549440 FALSE TRUE 1450699.255 1476903.673 1589689.009 1513403.672 1631410.469 1622130.485 1541092.321 1589797.875 1444481.667 1444495.049 1.004295069 1.022435954 1.100515374 1.047704299 1.12939845 1.122974071 1.066872692 1.10059074 0.999990736 1 20.46213383 4.351344078 5.418292417 1.078417499 1.008968303 0.207579161 0.043593282 0.24580787 10.44051072 0.010139622 0.028987274 22456.60386 -4.351344078 -0.069449196 VRYDS(ph)SNQVK ddPTM_BT-474_Pertuzumab_2h_R1 3 VRYDSSNQVK 10 1 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 VRYDS(0.783)S(0.217)NQVK;VRYDS(0.896)S(0.104)NQVK;VRYDS(0.932)S(0.068)NQVK 191.95 4.46E-07 1768150000 1764340 1520630 1091530 1089630 1068630 923340 925480 1379620 1188830 1269520 TRUE FALSE 1695387.642 1477263.121 1288793.752 1145865.935 1103003.454 942010.5674 936806.3011 1351130.365 1053879.002 1183534.28 1.432478697 1.248179412 1.088936564 0.968173001 0.931957336 0.795930108 0.791532884 1.141606448 0.890450763 1 20.17467006 4.351350301 1.294459564 0.931667938 1.48834414 0.757894401 0.094770653 0.387377153 0.913988348 0.030189898 0.239685084 22456.92564 -4.351350301 0.556676202 SS(ph)PLSFPSVPQEETLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPLSFPSVPQEETLR 16 0 Q9ULD5 Q9ULD5 ZNF777 Zinc finger protein 777 1 S(0.184)S(0.816)PLSFPSVPQEETLR 256.98 1.23E-26 299320000 208620 188550 146790 153430 145440 150350 164010 166060 149310 171500 TRUE FALSE 200466.8998 183172.7386 173318.2183 161348.5407 150118.2097 153390.18 166017.2034 162630.803 132360.9548 159884.1522 1.253825954 1.145659129 1.08402375 1.009159059 0.938918633 0.959383265 1.038359344 1.017179005 0.827855375 1 17.28666742 4.351411365 1.068094504 0.971330639 1.29912562 0.749371873 0.05530555 0.513511614 0.740975808 0.017740475 0.165624503 22460.0834 -4.351411365 0.327794981 S(ph)SSPELVTHLK ddPTM_BT-474_Pertuzumab_2h_R1 5 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.333)S(0.333)S(0.333)PELVTHLK;S(0.393)S(0.393)S(0.213)PELVTHLK;S(0.333)S(0.333)S(0.333)PELVTHLK;S(0.405)S(0.405)S(0.191)PELVTHLK;S(0.41)S(0.41)S(0.181)PELVTHLK 229.97 1.38E-12 10513510000 8039040 9072310 7662590 9618790 10049170 10095730 10117330 9850890 10730330 10541980 TRUE FALSE 7724865.429 8813576.602 9047390.466 10115216.9 10372410.68 10299872.58 10241148.91 9647465.679 9512267.924 9827962.305 0.786008858 0.896785756 0.920576431 1.029228297 1.05539789 1.048017102 1.04204194 0.98163438 0.967877941 1 23.22846089 4.351434938 1.336698451 1.018706206 0.772125042 0.841950203 0.031977126 0.279537017 0.716346891 0.010135757 0.078096345 22461.30255 -4.351434938 -0.246581164 GWDLVDAVTPGPQPTLEQLEEGGPRPLER ddPTM_BT-474_Pertuzumab_2h_R1 4 GWDLVDAVTPGPQPTLEQLEEGGPRPLER 29 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;;; 239.13 2.14E-45 628720000 269653 286663 258828 292189 331548 324449 315534 326497 299054 319808 FALSE TRUE 259114.6626 278487.6519 305603.9772 307268.9093 342212.5425 331009.5811 319395.5995 319754.7229 265106.6437 298147.1193 0.869083234 0.934061186 1.025010666 1.030594929 1.147797582 1.110222302 1.07126844 1.072472958 0.889180631 1 18.18566487 4.351571844 1.768273891 1.057945747 0.860851168 0.435256794 0.066120144 0.403730375 2.105192188 0.017961488 0.104406652 22468.38432 -4.351571844 -0.197094579 KKYDVDTLDMVFLDHWK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKYDVDTLDMVFLDHWK 17 2 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 266.23 7.53E-28 344280000 884430 789920 467020 414600 612710 753300 596100 528280 696100 535030 FALSE TRUE 849865.4978 767392.255 551420.9028 435997.5557 632418.3736 768532.2421 603395.2501 517370.8334 617081.6463 498791.9415 1.703847691 1.53850171 1.105512854 0.874107056 1.267900142 1.540787206 1.209713309 1.037247779 1.237152397 1 18.92807863 4.351580493 4.17211463 1.16389621 1.666930672 0.543983707 0.171607383 0.165367818 5.014560429 0.045544481 0.139150745 22468.83179 -4.351580493 0.503034462 KASDVHEVR ddPTM_BT-474_Pertuzumab_2h_R1 11 KASDVHEVR 9 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;; 121.6 0.00039549 66140669000 57270096 58901897 50037010 60272258 56101082 59422666 61673209 62635294 62919437 62906482 FALSE TRUE 55031917.33 57222072.57 59079810.77 63382916.46 57905624.25 60624233.02 62427984.18 61341853.29 55777086.29 58645769.94 0.93837829 0.975723784 1.007401059 1.080775587 0.987379385 1.033735819 1.064492533 1.045972341 0.95108456 1 25.80552372 4.351824188 2.331753724 1.028446796 0.941735058 0.35262479 0.036168686 0.321203287 3.227939963 0.009165432 0.040607017 22481.44321 -4.351824188 -0.086711738 FESIPDMLELDHLTVSGDVTFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FESIPDMLELDHLTVSGDVTFGK 23 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 271.62 1.28E-51 65642000 85917 86632 91782 90050 97687 92431 88473 96702 118820 112050 FALSE TRUE 82559.26865 84161.34018 108369.0491 94697.49129 100829.1911 94300.01815 89555.75904 94705.06991 105332.0517 104460.7537 0.79033767 0.805674258 1.037414007 0.90653655 0.965235148 0.90273155 0.857314885 0.9066091 1.008340913 1 16.67260149 4.351831577 8.928471822 0.935882775 0.794604684 0.541454943 0.054370496 0.196021453 14.4261492 0.01319805 0.036294329 22481.82574 -4.351831577 -0.141278091 MDFELLPDDER ddPTM_BT-474_Pertuzumab_2h_R1 2 MDFELLPDDER 11 0 B3KV94;A0A3B3ISE6;A0A3B3ITA8;A0A3B3ITJ7;A0A3B3ITE7;A0A3B3IT25;A0A3B3IS40;Q9UGL1;Q9UGL1-2;A0A3B3IT51;A0A3B3ITA9 B3KV94 KDM5B Lysine-specific demethylase 5B 0 ; 159.4 6.68E-05 175801000 151924 168675 158749 189185 193554 198843 194585 215088 195166 181743 FALSE TRUE 145986.6421 163864.5542 187438.4757 198948.8605 199779.8402 202863.7417 196966.3894 210646.3576 173011.5739 169433.3847 0.861616749 0.967132625 1.106266489 1.174201063 1.179105526 1.197306788 1.16250047 1.243239979 1.02111856 1 17.37035864 4.351866267 1.913456314 1.16037852 0.854388773 0.600149761 0.073642745 0.238063125 1.505654611 0.018433733 0.09889952 22483.62159 -4.351866267 -0.305989747 VQLPTETLQELLDLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQLPTETLQELLDLHR 16 0 P32456;P32455 P32456 GBP2;GBP1 Interferon-induced guanylate-binding protein 2;Interferon-induced guanylate-binding protein 1 0 ; 221.31 1.07E-14 490710000 232741 250090 212231 278170 252060 257870 260140 271840 271170 286360 FALSE TRUE 223645.2244 242957.6781 250585.8628 292526.387 260167.7388 263084.3081 263323.6711 266226.409 240387.9184 266964.5821 0.83773369 0.910074573 0.938648343 1.095749798 0.974540281 0.98546521 0.98636182 0.99723494 0.900448728 1 18.02628883 4.352001395 2.147929482 0.990797337 0.844622303 0.519735227 0.046148622 0.272535034 2.268402961 0.01180959 0.056519 22490.61831 -4.352001395 -0.146175035 DPAQPMS(ph)PGEATQSGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPAQPMSPGEATQSGAR 17 0 Q9BQG0;Q9BQG0-2 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 DPAQPMS(1)PGEATQSGAR;DPAQPMS(1)PGEATQSGAR 242.9 2.08E-20 941040000 350230 375630 354390 446330 394790 399050 422460 411790 418030 499760 TRUE FALSE 336542.6244 364917.4002 418436.1564 469365.1448 407488.7789 407119.0644 427630.1919 403286.3926 370576.9869 465910.8101 0.722332724 0.783234457 0.898103558 1.007414154 0.874606835 0.873813304 0.917837025 0.865587112 0.795381818 1 18.82969428 4.352061341 3.418031725 0.900102464 0.733524661 0.51711983 0.059644191 0.185201338 4.069092501 0.014868761 0.04973209 22493.72291 -4.352061341 -0.166577803 QGGDVLQNEEGETTSHLMGMFYR ddPTM_BT-474_Pertuzumab_2h_R1 6 QGGDVLQNEEGETTSHLMGMFYR 23 0 P39748;F5H1Y3 P39748 FEN1 Flap endonuclease 1 0 ;;;;; 386.14 6.40E-137 1834477000 1043599 1091303 960434 1225165 1141052 1076107 1132041 1190968 1164136 1187452 FALSE TRUE 1002813.997 1060180.107 1134005.789 1288395.912 1177754.974 1097866.621 1145895.256 1166374.095 1031988.162 1107024.818 0.905864061 0.957684136 1.024372507 1.16383652 1.063892114 0.991727198 1.035112526 1.053611514 0.932217729 1 20.07825614 4.352288553 3.053102047 1.040429521 0.914798132 0.351949628 0.056520038 0.264539994 4.704521561 0.014571075 0.052213411 22505.49417 -4.352288553 -0.125631389 QRDELNR ddPTM_BT-474_Pertuzumab_2h_R1 4 QRDELNR 7 1 P43034;I3L495 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 176.41 0.00068663 959877000 374123 396930 369665 479270 393728 407859 460723 429932 425978 490780 FALSE TRUE 359501.8595 385609.945 436471.6887 504005.1821 406392.6187 416106.1884 466361.4659 421053.754 377622.7633 457539.0335 0.785729377 0.842791362 0.953955087 1.101556688 0.888214095 0.90944413 1.01928236 0.920257559 0.82533453 1 18.8035353 4.35247373 3.644352916 0.95284668 0.797323112 0.377684805 0.072399618 0.231238019 5.675608891 0.018158177 0.058774397 22515.09224 -4.35247373 -0.155523568 VILHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VILHLK 6 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8;Q14568 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AA2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 ; 100.78 0.037275 38335000000 32769000 34413000 33945000 38954000 34260000 32152000 40853000 40628000 41381000 45761000 FALSE TRUE 31488351.25 33431574.93 40079616.6 40964420.61 35362004.01 32802135.47 41352971.23 39789017.6 36683602.36 42661566.71 0.738096457 0.783646207 0.93947831 0.960218383 0.828896047 0.768891956 0.969326127 0.932666582 0.859874711 1 25.34643361 4.352558919 4.868848843 0.903819524 0.749298156 0.437411905 0.067033664 0.188828664 7.040701582 0.016987363 0.049628702 22519.50907 -4.352558919 -0.154521368 DGNLVEDFVFDAGVGDIGNR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGNLVEDFVFDAGVGDIGNR 20 0 Q9H9P8 Q9H9P8 L2HGDH "L-2-hydroxyglutarate dehydrogenase, mitochondrial" 0 98.694 0.0017756 8257900 7886.7 9870.7 7500 14436 8587.1 9489.9 15963 16337 11785 10518 FALSE TRUE 7578.479045 9589.1973 8855.416837 15181.04369 8863.31187 9681.79228 16158.35997 15999.63524 10447.21621 9805.606492 0.772872035 0.977930055 0.903097309 1.548200379 0.903902464 0.987373121 1.64786951 1.63168237 1.065432946 1 13.25939115 4.353084721 0.585627049 1.353163472 0.563585097 0.214595655 0.278498262 3.393092786 1.204026853 0.156756351 1.711018356 22546.79008 -4.353084721 -0.789578375 RDPSEEIEILLR ddPTM_BT-474_Pertuzumab_2h_R1 3 RDPSEEIEILLR 12 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;Q5SVM6;B7Z3B5;F2Z2J1;Q15349;Q15349-3;Q15349-2 E9PGT3 RPS6KA1;RPS6KA2 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-2 0 ;; 199.8 2.68E-07 222391000 96137 103829 92040 117409 102872 107331 114228 120474 118089 121053 FALSE TRUE 92379.85975 100867.8986 108673.6754 123468.4926 106180.9713 109501.3064 115625.9564 117986.1698 104684.0318 112853.9725 0.818578715 0.893791298 0.962958352 1.094055352 0.94087048 0.970291997 1.024562573 1.045476444 0.927606087 1 16.78409768 4.353207362 2.289531652 1.003746085 0.824130052 0.609792126 0.046890573 0.209666083 2.02009028 0.01209421 0.054644075 22553.15799 -4.353207362 -0.179616033 RLSKPPFQTNPS(ph)PEMVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSKPPFQTNPSPEMVSK 18 2 Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 1 RLSKPPFQTNPS(1)PEMVSK 165.46 1.47E-11 330740000 578500 536710 387150 362170 443610 541890 428220 456100 548550 475310 TRUE FALSE 555891.5804 521403.5563 457116.6171 380861.6371 457879.1185 552847.3871 433460.6845 446681.3756 486280.9037 443116.8303 1.254503423 1.176672879 1.031593895 0.859506142 1.033314664 1.247633466 0.978208578 1.008044256 1.097410142 1 18.7573276 4.353234409 3.497703036 1.029595808 1.239563767 0.397781074 0.092474717 0.233728721 5.346765951 0.024056657 0.079579603 22554.56258 -4.353234409 0.209967959 FVSEDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVSEDDR 7 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 143.02 0.020091 0 409340 451150 516270 596750 531850 515010 534820 575530 588920 651550 FALSE TRUE 393342.5403 438283.6437 609571.4734 627548.339 548957.4383 525423.8551 541365.2871 563645.1044 522068.2706 607419.9382 0.647562774 0.72154965 1.003542089 1.033137537 0.903752748 0.865009233 0.891253733 0.927933163 0.859484909 1 19.21233474 4.353387374 5.182727109 0.929898058 0.666321302 0.754269271 0.057724005 0.096435431 3.877172953 0.015019501 0.043307424 22562.50805 -4.353387374 -0.263576756 MALPPQEDATAS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 16 MALPPQEDATASPPR 15 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.003)AS(0.997)PPR;MALPPQEDAT(0.007)AS(0.993)PPR;MALPPQEDAT(0.003)AS(0.997)PPR;MALPPQEDAT(0.141)AS(0.859)PPR;MALPPQEDAT(0.002)AS(0.998)PPR;MALPPQEDAT(0.065)AS(0.935)PPR;MALPPQEDAT(0.163)AS(0.837)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.001)AS(0.999)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.001)AS(0.999)PPR;MALPPQEDAT(0.002)AS(0.998)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.001)AS(0.999)PPR 194.53 5.02E-08 21712250000 8044647 8511216 7450812 9159122 8851859 8909696 8959089 9329487 9473600 9447745 TRUE FALSE 7730253.301 8268484.453 8797339.471 9631825.384 9136587.084 9089856.158 9068733.011 9136829.833 8398196.645 8807840.816 0.877655882 0.938764066 0.998807728 1.093551256 1.037324274 1.032018669 1.029620448 1.037351835 0.953490966 1 23.07035696 4.353448874 2.332646286 1.029782309 0.882450586 0.669988833 0.0336565 0.178164644 1.790514881 0.008623817 0.038324161 22565.7033 -4.353448874 -0.147331723 ELQEVIALTSQELEESR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELQEVIALTSQELEESR 17 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 ;;; 150.45 2.87E-07 41908700 43437.9 46501.1 42275.5 49931.3 49564.9 50988.5 49759.7 55693.9 52356.6 52985.2 FALSE TRUE 41740.29884 45174.93416 49915.62326 52508.26038 51159.20002 52019.5224 50368.67409 54543.8015 46413.29826 49396.46521 0.845005785 0.914537791 1.010510024 1.062996313 1.035685444 1.053102123 1.01968175 1.104204547 0.939607684 1 15.59212019 4.353728175 2.154517457 1.039804949 0.844914111 0.685759255 0.041334693 0.177181451 1.483720239 0.010251835 0.04910638 22580.22033 -4.353728175 -0.194890838 FLPVFDIVIHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLPVFDIVIHR 11 0 Q5JWT2;Q9ULK4-4;Q9ULK4-5;Q9ULK4-3;Q9ULK4 Q5JWT2 MED23 Mediator of RNA polymerase II transcription subunit 23 0 ; 140.3 3.87E-05 149031000 82311 90139 88795 103970 106433 98036 113891 97810 109391 112409 FALSE TRUE 79094.19512 87568.32398 104842.2317 109335.9042 109856.5141 100018.3551 115284.8321 95790.18932 96973.39228 104795.4383 0.754748455 0.835611983 1.000446522 1.043326942 1.04829481 0.954415161 1.100093993 0.914068311 0.925358907 1 16.67721639 4.353848954 3.267152631 0.998586532 0.767506649 0.697735278 0.054561173 0.131490588 2.66007938 0.014114586 0.048565606 22586.50083 -4.353848954 -0.231079883 MESEGGADDS(ph)AEEGDLLDDDDNEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 MESEGGADDSAEEGDLLDDDDNEDR 25 0 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 MESEGGADDS(1)AEEGDLLDDDDNEDR 333.99 3.76E-88 335980000 193150 246110 317050 415560 257020 330240 385680 337650 395370 433100 TRUE FALSE 185601.4845 239091.1838 374347.9877 437007.1014 265287.2817 336917.6791 390400.0672 330677.4095 350489.2551 403765.7512 0.459676146 0.592153205 0.927141509 1.082328306 0.657032651 0.834438478 0.96689743 0.818983305 0.868050978 1 18.62315902 4.353904339 4.068945626 0.884368853 0.488279175 0.645636055 0.110584299 0.127606688 3.725895162 0.02731311 0.08437073 22589.38143 -4.353904339 -0.396089678 GNS(ph)RPGTPS(ph)AEGGSTSSTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.998)RPGT(0.475)PS(0.526)AEGGSTSSTLR 72.474 0.0091731 317250000 97422 103010 130830 129060 121570 122130 124660 149160 132750 138700 TRUE FALSE 93614.64053 100072.2557 154473.8913 135720.8021 125480.4095 124599.5523 126185.6264 146079.7939 117680.7765 129305.7255 0.723979083 0.773919757 1.194640769 1.049611698 0.970416499 0.963604294 0.975870372 1.129724097 0.910097183 1 16.98042663 4.353950946 7.341445577 1.028060452 0.737747107 0.656151679 0.079938884 0.119894943 7.099672696 0.019496529 0.054019813 22591.80579 -4.353950946 -0.290313345 LTGIKHELQANCYEEVKDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LTGIKHELQANCYEEVKDR 19 2 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;; 212.18 5.67E-17 10374560000 9066300 8099750 4867430 4222100 6281470 8001400 5607870 6099960 6829120 5581350 FALSE TRUE 8711978.973 7868753.06 5747082.876 4440003.087 6483519.187 8163193.79 5676500.791 5973993.694 6053906.928 5203320.193 1.674311526 1.512256169 1.104503022 0.853301915 1.246035021 1.568843255 1.090938205 1.148111873 1.163469997 1 22.31100106 4.35421066 4.107936578 1.156973024 1.638786145 0.517709155 0.174696904 0.17369319 5.143015143 0.045457664 0.139942394 22605.32006 -4.35421066 0.481813121 AWLDEDSNLSPS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 4 AWLDEDSNLSPSPLR 15 0 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR 352.05 2.23E-82 738500000 695660 757980 681470 864630 759510 852140 826000 845790 907380 932420 TRUE FALSE 668472.8381 736363.1525 804626.7882 909253.6579 783940.3289 869370.8546 836108.8351 828324.1409 804378.0264 869266.3629 0.769008059 0.847108762 0.925638933 1.046001199 0.901841326 1.000120207 0.961855734 0.952900257 0.925352758 1 19.72943879 4.354212744 2.258660787 0.96598338 0.773580811 0.736939286 0.039177298 0.158042058 1.475436286 0.009587319 0.043960342 22605.42853 -4.354212744 -0.192402569 FTDEEVDELYR ddPTM_BT-474_Pertuzumab_2h_R1 5 FTDEEVDELYR 11 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;; 323.61 5.54E-46 18777330000 6708730 7231810 6007680 7589570 7223620 7410300 7840640 7785250 8136440 8202140 FALSE TRUE 6446545.415 7025565.859 7093401.416 7981268.617 7455974.298 7560141.343 7936596.098 7624481.867 7212825.442 7646601.752 0.843060175 0.91878276 0.927654093 1.043766744 0.975070304 0.988692963 1.037924604 0.997107227 0.943272015 1 22.86638731 4.354289413 1.42207656 0.998605322 0.836203721 0.713286838 0.030875367 0.325910775 0.976750722 0.008515858 0.062234149 22609.41957 -4.354289413 -0.162401601 GRDSPYQS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GRDS(0.022)PYQS(0.978)R;GRDS(0.006)PYQS(0.994)R 136.67 0.0004902 6936192000 1037259 1103306 956574 1216453 1167757 1079359 1206764 1192479 1176225 1248674 TRUE FALSE 996721.7715 1071840.793 1129448.201 1279234.285 1205318.964 1101184.379 1221532.739 1167853.892 1042704.869 1164100.198 0.856216478 0.920746165 0.970232805 1.098903932 1.035408264 0.945953261 1.049336424 1.003224546 0.895717457 1 20.15078381 4.354434128 2.387268194 1.006680348 0.86308345 0.441566305 0.052887339 0.283320121 2.997949943 0.013729609 0.0598784 22616.9547 -4.354434128 -0.143596898 SENEEFVEVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SENEEFVEVGR 11 0 P10644;P10644-2;K7EM13 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ; 270.6 1.19E-26 328900000 281010 301110 266250 331540 316860 323820 295790 349900 333650 360570 FALSE TRUE 270027.8185 292522.6376 314367.2977 348650.8191 327052.0897 330367.8623 299409.9665 342674.4427 295775.4508 336148.2727 0.803299735 0.870219071 0.935204263 1.037193546 0.972939968 0.982803986 0.890708032 1.019414558 0.879895792 1 18.35873821 4.35452162 2.302665279 0.969475216 0.808124676 0.557669685 0.047906531 0.226187457 2.206236666 0.011783439 0.05310821 22621.51151 -4.35452162 -0.16135054 AS(ph)PAPAPSRS(ph)PSAQCPFPGGTVLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPAPAPSRSPSAQCPFPGGTVLSR 25 1 P78411-3;P78411-2;P78411;H0YML8 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 2 AS(1)PAPAPS(0.144)RS(0.555)PS(0.301)AQCPFPGGTVLSR 100.67 0.0034064 414350000 140190 140340 133680 145240 129140 149230 150350 146460 168600 164120 TRUE FALSE 134711.2198 136337.6406 157838.9497 152735.8538 133293.9054 152247.5328 152190.0283 143435.5498 149461.2348 153004.0062 0.880442435 0.891072358 1.03160011 0.998247416 0.871179185 0.995055859 0.994680022 0.937462707 0.976845238 1 17.2232099 4.354895873 8.641169198 0.970440257 0.883359453 0.42031315 0.041929042 0.236040915 16.61604338 0.010206113 0.028091355 22641.01399 -4.354895873 -0.087080804 FLEQVHQLYDDSFPMEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLEQVHQLYDDSFPMEIR 18 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75;D2KFR9;A0A669KB17;E7ENM1;E9PH66;Q67C41 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ; 214.19 1.02E-18 545130000 281486 289618 278683 292562 313784 311778 300341 310299 359797 356172 FALSE TRUE 270485.2159 281358.3782 329047.2174 307661.1599 323877.1473 318082.3648 304016.663 303891.2172 318954.353 332048.1532 0.814596357 0.847342096 0.990962347 0.926555853 0.975392106 0.957940473 0.915580045 0.915202251 0.960566562 1 18.34103295 4.355183069 5.551309898 0.948033797 0.823036699 0.747328064 0.028866805 0.095642919 4.158963801 0.007131898 0.020325852 22655.99128 -4.355183069 -0.124997098 VGS(ph)PLTLTDAQTR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGSPLTLTDAQTR 13 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VGS(0.927)PLT(0.073)LTDAQTR;VGS(0.997)PLT(0.003)LTDAQTR;VGS(0.972)PLT(0.028)LTDAQTR;VGS(0.991)PLT(0.008)LTDAQTR 198.81 1.29E-07 701190000 732780 700880 524033 638030 532670 577310 591020 760300 695900 570440 TRUE FALSE 704142.1475 680891.5886 618737.4202 670958.8048 549803.8143 588983.6037 598253.0796 744599.5393 616904.3495 531803.5907 1.324064297 1.280344098 1.163469805 1.261666556 1.033847503 1.107520923 1.124951185 1.400140112 1.160022911 1 19.02053399 4.355458563 3.478958588 1.177886658 1.317435904 0.208647512 0.108352562 0.424245535 9.610178417 0.028882376 0.096072575 22670.36764 -4.355458563 0.139549247 SLTTECHLLDS(ph)PGLNCSNPFTQLER ddPTM_BT-474_Pertuzumab_2h_R1 2 SLTTECHLLDSPGLNCSNPFTQLER 25 0 Q15398-1;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 SLTTECHLLDS(1)PGLNCSNPFTQLER;SLTTECHLLDS(1)PGLNCSNPFTQLER 268.27 6.43E-46 700400000 171735 191834 199002 271090 237090 219527 234220 205984 201017 257710 TRUE FALSE 165023.4063 186363.0821 234966.0882 285080.9874 244716.2152 223965.9863 237086.4544 201730.3584 178198.3929 240255.0722 0.686867523 0.77568844 0.977985963 1.186576353 1.018568361 0.932200866 0.986811443 0.839650779 0.741705019 1 17.87420736 4.355658183 3.970882045 0.95877715 0.706011211 0.417763472 0.110123001 0.223893789 6.298709667 0.030164399 0.094221705 22680.79027 -4.355658183 -0.252765939 WHPDKNPENKEEAER ddPTM_BT-474_Pertuzumab_2h_R1 2 WHPDKNPENKEEAER 15 2 E9PH18;A0A0J9YX62;O75190-3;O75190;C9JDX6;F8WCZ4;C9J2P2;C9J2C4;O75190-2;C9JDR7;C9JN01;C9JB42;Q8WWF6;Q7Z6W7 E9PH18;Q7Z6W7 DNAJB6;DNAJB3;DNAJB7 DnaJ homolog subfamily B member 6;DnaJ homolog subfamily B member 3;DnaJ homolog subfamily B member 7 0 ; 151.56 1.79E-06 879520000 1196140 1110180 919570 934050 919410 1052870 1084980 875070 1382840 1192230 FALSE TRUE 1149393.526 1078518.753 1085756.755 982256.4324 948983.6576 1074159.753 1098258.31 856999.4987 1225865.801 1111479.2 1.034111593 0.970345422 0.976857466 0.883738024 0.853802444 0.966423621 0.988105139 0.771044117 1.102913847 1 20.08404952 4.355672128 1.644272584 0.921740923 1.031373815 0.064310798 0.087197593 1.055916164 4.575332995 0.023244217 0.147117794 22681.51859 -4.355672128 0.109632892 S(ph)PQQSAALPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQQSAALPR 10 0 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 S(1)PQQSAALPR;S(1)PQQSAALPR 115.42 0.0012854 1679540000 182418 189998 191257 198122 206458 214790 205807 220600 222100 238410 TRUE FALSE 175288.9029 184579.4431 225821.3944 208347.1002 213098.9091 219133.201 208325.7276 216044.5329 196888.1391 222262.2783 0.788657905 0.830457802 1.016013136 0.937392983 0.95877227 0.985921689 0.937296824 0.972025188 0.885836952 1 17.76190359 4.35597442 5.597761288 0.959633294 0.799439363 0.751646254 0.03522064 0.083461449 3.661705856 0.007984262 0.02272915 22697.31158 -4.35597442 -0.160193931 TVANLLSGKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVANLLSGKSPR 12 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 TVANLLSGKS(1)PR;TVANLLSGKS(1)PR 197.79 1.16E-07 13037700000 23184000 20981000 13720500 14965400 16134000 17037300 16150100 17495300 17351800 17358600 TRUE FALSE 22277943.65 20382642.42 16200099.56 15737766.09 16652964.76 17381805.88 16347749.75 17134015.94 15382096.41 16182886.56 1.376635965 1.25951834 1.001063655 0.972494371 1.029047859 1.074085628 1.010187502 1.058773778 0.950516235 1 23.94796563 4.356152074 3.476093063 1.017004618 1.356539602 0.919365536 0.036879187 0.05727403 1.295391061 0.009478834 0.031570291 22706.59814 -4.356152074 0.339534984 TGTGDIATCYS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 TGTGDIATCYSPR 13 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 TGTGDIATCYS(1)PR;TGTGDIATCYS(1)PR;TGTGDIATCYS(1)PR;TGTGDIATCYS(1)PR 186.62 8.60E-07 464130000 1254060 1354140 1195510 1565220 1305750 1381840 1491970 1489550 1618010 1634290 TRUE FALSE 1205049.949 1315521.253 1411565.251 1646001.192 1347750.635 1409781.752 1510229.175 1458790.272 1434340.288 1523598.083 0.790923776 0.86343063 0.926468251 1.080338188 0.884584097 0.925297667 0.991225437 0.957463972 0.941416443 1 20.53905095 4.356472511 2.443523901 0.964472705 0.7985459 0.571070443 0.049719143 0.218789564 2.436123241 0.012563898 0.053901377 22723.35803 -4.356472511 -0.165926805 EAGELPTS(ph)PLHLLSPGTPR ddPTM_BT-474_Pertuzumab_2h_R1 6 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 EAGELPT(0.027)S(0.973)PLHLLSPGTPR;EAGELPT(0.143)S(0.857)PLHLLSPGTPR;EAGELPT(0.046)S(0.954)PLHLLSPGTPR;EAGELPT(0.044)S(0.956)PLHLLSPGTPR;EAGELPT(0.017)S(0.983)PLHLLSPGTPR;EAGELPT(0.046)S(0.954)PLHLLSPGTPR 212.65 4.65E-17 2352192000 721050 836234 806823 1091612 1008909 973960 1010147 947552 989342 1064150 TRUE FALSE 692870.5688 812385.4251 952633.8638 1147950.226 1041361.474 993654.1385 1022509.481 927984.7201 877036.0438 992074.1727 0.698406014 0.818875692 0.960244597 1.15712137 1.049681065 1.001592588 1.030678461 0.935398527 0.884042815 1 19.92008846 4.356601399 2.597581214 1.007059164 0.711694683 0.689447575 0.068146477 0.173915115 2.213661858 0.019062956 0.077652188 22730.10275 -4.356601399 -0.295364481 EVSDS(ph)EAGGGPQGER ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSDSEAGGGPQGER 15 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EVS(0.251)DS(0.749)EAGGGPQGER;EVS(0.262)DS(0.738)EAGGGPQGER 407.23 5.88E-133 1703730000 713360 791020 892360 1036840 885010 766670 1028080 992680 1095070 1231220 TRUE FALSE 685481.1025 768460.8841 1053629.302 1090351.437 913477.1504 782172.5927 1040661.951 972180.8111 970762.2445 1147828.373 0.597198256 0.669491104 0.917932792 0.949925496 0.795830781 0.681436887 0.9066355 0.84697402 0.84573815 1 20.13047551 4.356610701 4.933433359 0.857519137 0.614879125 0.556842618 0.084161047 0.147258618 5.566860641 0.020914934 0.061007945 22730.58962 -4.356610701 -0.242640011 EELDEDDIISDPDSHFPAWR ddPTM_BT-474_Pertuzumab_2h_R1 1 EELDEDDIISDPDSHFPAWR 20 0 Q8IXW5-2;Q8IXW5 Q8IXW5-2 RPAP2 Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 0 179.46 5.82E-17 37914000 32653 37167 32526 46156 38687 30691 47254 43364 41597 49206 FALSE TRUE 31376.88466 36107.03355 38404.17174 48538.11669 39931.40249 31311.59305 47832.30859 42468.51825 36875.08295 45873.23379 0.683991122 0.787104605 0.83718039 1.058092327 0.870472805 0.682567817 1.042706272 0.92577991 0.803847471 1 15.48536499 4.356739634 2.166581352 0.907809282 0.692733902 0.309459272 0.107472793 0.43838969 3.71222139 0.02807476 0.134652207 22737.33883 -4.356739634 -0.21507538 EQMMNSSISSGSGS(ph)LR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQMMNSSISSGSGSLR 16 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UK02;E7EQD7;A0A590UK70;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;A0A590UJ25;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;C9JUA9;Q12959-8;A0A590UJX2;A0A590UJ64;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 1 EQMMNSSISSGSGS(1)LR;EQMMNSSISSGS(0.029)GS(0.971)LR 221.9 1.06E-14 237600000 221940 200060 162684 167276 163694 173278 147617 204170 178336 171443 TRUE FALSE 213266.3394 194354.4847 192084.6177 175909.1344 168959.3662 176781.7999 149423.581 199953.8182 158092.0449 159831.0129 1.334323893 1.215999831 1.201798163 1.100594504 1.057112528 1.10605443 0.934884778 1.251032666 0.989119959 1 17.28618784 4.356979334 0.956022389 1.07205861 1.378276733 0.549196013 0.082046809 0.980745373 1.067186379 0.026967521 0.274660277 22749.89175 -4.356979334 0.306218123 DWEAYWR ddPTM_BT-474_Pertuzumab_2h_R1 2 DWEAYWR 7 0 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ; 121.29 0.010358 308330000 403560 435980 463480 603880 497750 399410 525370 510020 500730 625140 FALSE TRUE 387788.429 423546.2773 547241.1461 635046.3192 513760.5808 407486.3439 531799.6352 499487.9088 443889.2296 582798.711 0.665389991 0.726745391 0.938988257 1.089649492 0.881540352 0.699188821 0.912492813 0.857050469 0.761651015 1 19.15263816 4.357027668 5.029125935 0.886386396 0.680687406 0.36367352 0.104774234 0.221661299 8.576696122 0.026825138 0.077920368 22752.42377 -4.357027668 -0.20569899 STETSDFENIES(ph)PLNER ddPTM_BT-474_Pertuzumab_2h_R1 2 STETSDFENIESPLNER 17 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 STETSDFENIES(1)PLNER;STETSDFENIES(1)PLNER 343.29 7.31E-73 253740000 210707 228900 211440 253110 246740 277690 247770 270990 237660 274040 TRUE FALSE 202472.3375 222371.9961 249651.9115 266173.0374 254676.6162 283305.0821 250802.2834 265393.9618 210681.8332 255479.0267 0.792520388 0.870411943 0.977191414 1.041858664 0.996859192 1.108917181 0.981694218 1.038809194 0.824654125 1 17.96284533 4.357147692 2.28442041 1.006513651 0.794880691 0.496836975 0.068442452 0.253908363 2.428696855 0.017117447 0.078154473 22758.71261 -4.357147692 -0.21163296 IVFLDTQPILSPSILDHLINNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IVFLDTQPILSPSILDHLINNDR 23 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 0 ; 233.28 4.86E-37 388050000 304120 329440 311040 396020 349110 387400 379880 334310 362070 435810 FALSE TRUE 292234.6542 320044.6938 367251.847 416458.6397 360339.4402 395233.4934 384529.0851 327406.3817 320969.3315 406292.2005 0.719272124 0.787720496 0.90391065 1.025022482 0.886897262 0.972781395 0.946434819 0.805839692 0.789996291 1 18.63215814 4.357284552 3.228480611 0.910795683 0.730702359 0.45737515 0.07250434 0.23619898 4.670578658 0.019527688 0.068006612 22765.88575 -4.357284552 -0.180093323 QQHGEANKENIR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQHGEANKENIR 12 1 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 127.02 0.00016655 269030000 258960 244100 178690 187660 192620 226430 229760 211250 244890 224930 FALSE TRUE 248839.5569 237138.507 210983.2579 197345.1551 198815.7972 231008.5697 232571.8716 206887.6137 217091.1139 209695.2908 1.186672128 1.130871877 1.006142089 0.941104373 0.948117607 1.101639283 1.109094395 0.986610681 1.035269381 1 17.67793494 4.357410655 3.766014589 1.016795868 1.175628967 0.54561595 0.05306792 0.176158618 4.559460213 0.014429609 0.046210487 22772.4971 -4.357410655 0.158833099 AVT(ph)PVPTKTEEVSNLK ddPTM_BT-474_Pertuzumab_2h_R1 3 AVTPVPTKTEEVSNLK 16 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(0.999)PVPT(0.001)KTEEVSNLK;AVT(0.991)PVPT(0.009)KTEEVSNLK;AVT(0.999)PVPT(0.001)KTEEVSNLK 193.54 5.78E-10 9424700000 15344700 14306700 10113600 8997800 10540300 13879300 11406700 13328000 15817300 13412900 TRUE FALSE 14745012.16 13898686.92 11941352.5 9462177.536 10879338.32 14159948.96 11546298.61 13052772.14 14021786.42 12504432.34 1.17918285 1.11150083 0.95496958 0.756705885 0.870038561 1.132394384 0.923376471 1.043851635 1.121345299 1 23.57593623 4.357428216 4.084581265 0.972245509 1.164192319 0.29601377 0.106734202 0.271045124 7.953204034 0.028179617 0.087153063 22773.41793 -4.357428216 0.19194681 LQEKLS(ph)PPYSSPQEFAQDVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQEKLSPPYSSPQEFAQDVGR 21 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LQEKLS(0.999)PPYS(0.001)SPQEFAQDVGR;LQEKLS(1)PPYSSPQEFAQDVGR 131.13 8.30E-06 768640000 886260 862840 689280 765900 788960 827320 778380 834150 901970 885460 TRUE FALSE 851623.9794 838232.648 813848.229 805428.1908 814337.6149 844048.9772 787906.0473 816924.511 799582.147 825487.0055 1.03166249 1.015440149 0.985900715 0.975700629 0.98649356 1.022486086 0.954474198 0.989627342 0.968618696 1 19.65488598 4.357440495 2.953782977 0.984485827 1.029645827 0.451998239 0.017200479 0.219313618 3.648428847 0.004194517 0.015502571 22774.06178 -4.357440495 0.04516 FSLCSDNLEGIS(ph)EGPSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSLCSDNLEGISEGPSNR 18 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-5;Q14C86;C9IZ08;H0Y7I9;B4DGD8;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FSLCS(0.438)DNLEGIS(0.562)EGPSNR;FS(0.004)LCS(0.002)DNLEGIS(0.994)EGPSNR 244.27 4.08E-24 259150000 182326 187829 177127 197024 188232 201390 198497 199203 221365 237802 TRUE FALSE 175200.4983 182472.3008 209137.7891 207192.4323 194286.6532 205462.2438 200926.2657 195089.3884 196236.5732 221695.4587 0.79027554 0.823076403 0.943356216 0.93458131 0.876367312 0.926776962 0.906316561 0.879988203 0.885162801 1 17.75821969 4.357624091 5.107442531 0.911624299 0.798391123 0.612594181 0.035675041 0.125639623 4.951682152 0.008402019 0.024329596 22783.69149 -4.357624091 -0.113233176 SVAPAS(ph)PPPPDGPLAHR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVAPASPPPPDGPLAHR 17 0 Q2M2I3 Q2M2I3 FAM83E Protein FAM83E 1 SVAPAS(1)PPPPDGPLAHR;SVAPAS(1)PPPPDGPLAHR;S(0.001)VAPAS(0.999)PPPPDGPLAHR;S(0.001)VAPAS(0.999)PPPPDGPLAHR 167.16 1.45E-09 5462350000 1706630 2043360 1824120 2575060 2378080 2357540 2530900 2253310 2402450 2541890 TRUE FALSE 1639933.013 1985085.373 2153779.061 2707959.155 2454573.103 2405211.074 2561873.911 2206778.361 2129733.948 2369725.526 0.692035003 0.837685779 0.908872795 1.142731141 1.035804812 1.014974539 1.081084659 0.931237958 0.898726002 1 21.17628854 4.357724407 1.947350286 1.011476017 0.697080755 0.689832375 0.068675964 0.237434483 1.560001911 0.019180032 0.102482026 22788.95479 -4.357724407 -0.314395262 NVS(ph)ES(ph)PNRKNEK ddPTM_BT-474_Pertuzumab_2h_R1 3 NVSESPNRKNEK 12 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNRKNEK;NVS(1)ES(1)PNRKNEK;NVS(1)ES(1)PNRKNEK 130.21 0.0010843 733970000 3203530 2688410 1381260 1131460 1786260 2094310 1466060 1737280 2322800 1467910 TRUE FALSE 3078332.506 2611739.179 1630884.408 1189854.786 1843716.675 2136658.383 1484002.081 1701404.561 2059125.482 1368487.148 2.249442028 1.90848645 1.191742582 0.869467271 1.347266343 1.56132879 1.084410681 1.243274051 1.504672868 1 20.38415046 4.357905161 3.537489512 1.229620159 2.187700269 0.744537257 0.203979157 0.109343272 2.549088462 0.051707545 0.170955506 22798.44157 -4.357905161 0.95808011 RY(ph)GCVFQGT(ph)NQQIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RYGCVFQGTNQQIK 14 1 H0YL25;Q13114 H0YL25 TRAF3 TNF receptor-associated factor 3 2 RY(1)GCVFQGT(1)NQQIK 77.746 0.033879 217120000 127300 170520 142500 215060 205330 216660 229350 200200 161220 222070 TRUE FALSE 122324.9753 165656.9366 168252.9199 226159.2724 211934.6259 221041.0136 232156.8539 196065.8 142918.9815 207029.0011 0.590859129 0.800162951 0.812702177 1.092403823 1.023695351 1.0676814 1.121373589 0.947045095 0.690333145 1 17.65947335 4.358481011 1.478603481 0.996383826 0.581228434 0.51765679 0.119615768 0.488450949 1.611462922 0.034372963 0.244177595 22828.69106 -4.358481011 -0.415155393 NYVPPKGDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 NYVPPKGDKK 10 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 100.55 0.0022129 3726700000 6600500 5357700 4101400 3085200 3816100 3310540 3148940 4790000 5398800 4566300 FALSE TRUE 6342545.163 5204903.642 4842614.215 3244427.542 3938848.322 3377481.387 3187477.67 4691084.826 4785950.858 4257020.434 1.489902447 1.222663533 1.137559542 0.762135769 0.925259435 0.793390927 0.748757898 1.101964367 1.124248975 1 22.02141258 4.358843963 1.656225911 0.923910678 1.497961018 0.651472925 0.13107623 0.329623793 1.450511491 0.038186839 0.241772785 22847.7776 -4.358843963 0.57405034 KAS(ph)GSENEGDYNPGRK ddPTM_BT-474_Pertuzumab_2h_R1 6 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.5)GS(0.5)ENEGDYNPGRK;KAS(0.992)GS(0.008)ENEGDYNPGRK;KAS(0.995)GS(0.005)ENEGDYNPGRK;KAS(0.986)GS(0.014)ENEGDYNPGRK;KAS(0.946)GS(0.054)ENEGDYNPGRK;KAS(0.965)GS(0.035)ENEGDYNPGRK 192.6 2.65E-10 3155960000 2724040 2441059 1380244 1646011 1778560 1759299 1810979 1996427 1917554 1647268 TRUE FALSE 2617581.505 2371442.387 1629684.794 1730961.825 1835768.998 1794873.231 1833142.303 1955200.085 1699881.309 1535697.071 1.704490784 1.544212353 1.061201994 1.127150567 1.195397863 1.168767763 1.193687438 1.273167815 1.106911865 1 20.55046223 4.359012793 4.519210027 1.162079621 1.668003744 0.865037065 0.076934506 0.066924435 2.261964761 0.019258639 0.05757001 22856.66132 -4.359012793 0.505924123 S(ph)PVTTLLECMHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPVTTLLECMHK 12 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 S(1)PVTTLLECMHK;S(0.999)PVT(0.001)TLLECMHK 189.1 5.38E-06 370330000 455630 503260 542730 583130 562470 552590 667860 598360 629790 754210 TRUE FALSE 437823.4759 488907.5175 640813.384 613225.4092 580562.3584 563763.7484 676033.4705 586003.6569 558298.8795 703126.6849 0.622680785 0.69533347 0.911376851 0.872140714 0.825686709 0.80179541 0.961467521 0.833425426 0.79402317 1 19.42342512 4.359120341 4.466068556 0.867243967 0.639037893 0.645087699 0.064655806 0.117341379 3.903950929 0.015156715 0.045476865 22862.32222 -4.359120341 -0.228206074 ISNDNPEEHVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISNDNPEEHVLK 12 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 87.498 0.010514 495210000 520530 545280 461940 510410 500290 604930 518770 608890 653300 639280 FALSE TRUE 500187.1121 529729.1483 545422.8338 536752.3213 516382.2822 617162.0991 525118.8624 596316.2087 579140.1229 595980.9962 0.839266882 0.888835637 0.915168164 0.90061986 0.866440852 1.035539896 0.881100011 1.000562455 0.9717426 1 19.1849068 4.359371968 0.240301338 1.011894248 0.747457864 0.501378447 0.044771891 7.074437108 0.412885334 0.068090279 0.555354519 22875.5723 -4.359371968 -0.264436384 EILDHQDGNVEDDGLTGLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EILDHQDGNVEDDGLTGLLR 20 0 Q70CQ2-3;Q70CQ2-2;Q70CQ2;A0A0C4DG73 Q70CQ2-3 USP34 Ubiquitin carboxyl-terminal hydrolase 34;Ubiquitin carboxyl-terminal hydrolase 0 ; 296.04 1.28E-54 139062000 104428 111680 97360 121851 119154 115057 113804 122075 124335 136257 FALSE TRUE 100346.8383 108494.9957 114955.1178 128139.7447 122986.6966 117383.5314 115196.7674 119554.1086 110221.0121 127028.192 0.789957227 0.854101708 0.904957521 1.008750441 0.968184264 0.924074644 0.906859852 0.94116201 0.867689371 1 16.95478919 4.359438945 2.233770583 0.940994503 0.794395021 0.606326444 0.040338915 0.233674915 2.12034633 0.010572074 0.049541458 22879.10043 -4.359438945 -0.146599482 IDDRDS(ph)DEEGASDR ddPTM_BT-474_Pertuzumab_2h_R1 5 IDDRDSDEEGASDR 14 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 IDDRDS(0.971)DEEGAS(0.029)DR;IDDRDS(0.987)DEEGAS(0.013)DR;IDDRDS(0.998)DEEGAS(0.002)DR;IDDRDS(1)DEEGASDR;IDDRDS(1)DEEGASDR 273.52 1.36E-32 2485442000 1583348 1575612 1402250 1570666 1516840 1514948 1601307 1682913 1656299 1727184 TRUE FALSE 1521469.01 1530677.088 1655667.768 1651728.26 1565630.536 1545581.287 1620904.274 1648160.258 1468282.881 1610200.289 0.944894259 0.950612851 1.028237157 1.025790563 0.972320367 0.959868966 1.006647611 1.023574688 0.911863506 1 20.61880872 4.359618282 8.894717588 0.993691025 0.946428076 0.202570332 0.034096042 0.360496221 26.03739428 0.008289874 0.022801234 22888.55006 -4.359618282 -0.04726295 ESSANNSVS(ph)PSESLR ddPTM_BT-474_Pertuzumab_2h_R1 7 ESSANNSVSPSESLR 15 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 ESSANNSVS(1)PSESLR;ESSANNS(0.024)VS(0.976)PSESLR;ESSANNS(0.032)VS(0.967)PS(0.001)ESLR;ESSANNS(0.057)VS(0.942)PSESLR;ESSANNS(0.01)VS(0.98)PS(0.01)ESLR;ESSANNS(0.001)VS(0.999)PSESLR;ESSANNSVS(0.999)PS(0.001)ESLR 380.15 3.09E-98 10918040000 4789909 5092497 4507216 5604387 5377175 5322516 5394617 5697218 5522264 5563059 TRUE FALSE 4602714.061 4947263.972 5321770.194 5893630.085 5550136.717 5430140.92 5460637.937 5579568.457 4895399.742 5186268.059 0.887480942 0.953915979 1.026127098 1.136391335 1.070160018 1.047022803 1.052903142 1.075834954 0.94391568 1 22.30626534 4.359813976 2.526388121 1.053862276 0.894204446 0.531885948 0.047963632 0.211032506 2.525337652 0.012073937 0.050663448 22898.86601 -4.359813976 -0.15965783 FDLGQDVIDFTGHALALYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDLGQDVIDFTGHALALYR 19 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 292.75 1.37E-49 4605500000 1300570 1432420 1423710 1830570 1683470 1327830 1687910 1664410 1729650 1923160 FALSE TRUE 1249742.287 1391568.784 1681006.067 1925045.937 1737620.341 1354679.632 1708567.147 1630039.352 1533307.383 1792902.66 0.697049714 0.776154119 0.937589142 1.073703542 0.969166023 0.755579019 0.952961466 0.909162214 0.855209498 1 20.77386573 4.360047025 3.653895021 0.928767569 0.712322269 0.494436678 0.08047832 0.190405506 4.689436371 0.020812388 0.067825517 22911.15721 -4.360047025 -0.216445299 TVSSPIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVSSPIPYT(0.001)PSPS(0.004)S(0.017)S(0.013)RPIS(0.965)PGLSYASHTVGFTPPTSLTR;TVSSPIPYTPSPSSSRPIS(0.999)PGLSYASHTVGFTPPTSLTR 277.49 6.03E-77 12779400000 1620490 2000960 1614580 2437780 2350080 2373900 2280150 1918510 2398290 2291220 TRUE FALSE 1557159.459 1943894.58 1906370.522 2563594.118 2425672.457 2421901.884 2308055.158 1878892.098 2126046.174 2136033.629 0.72899576 0.910048678 0.892481512 1.200165617 1.135596568 1.133831346 1.080533156 0.879617284 0.995324299 1 21.02650293 4.360220631 1.711737619 1.04903902 0.738365959 0.534236628 0.094138456 0.439840819 2.099977248 0.028919649 0.177547696 22920.31758 -4.360220631 -0.310673061 GSVHS(ph)LDAGLLLPSGDPFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSVHSLDAGLLLPSGDPFSK 20 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 GS(0.36)VHS(0.64)LDAGLLLPSGDPFSK 98.21 0.00053588 187690000 355350 393020 334720 435480 379920 472970 436430 418630 449890 536140 TRUE FALSE 341462.5291 381811.4544 395211.3498 457955.175 392140.4718 482533.7775 441771.1609 409985.1442 398820.3733 499826.7603 0.68316176 0.76388758 0.79069666 0.916227804 0.784552775 0.965402047 0.883848557 0.82025449 0.797917209 1 18.93106862 4.360794672 1.276123858 0.871671044 0.66400821 0.482501322 0.067142246 0.678422106 1.528934347 0.018929534 0.15587291 22950.63322 -4.360794672 -0.207662834 KDDEVQVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDDEVQVVR 9 1 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ; 143.4 0.00016361 2331300000 4453400 4196200 3458400 2645640 3483250 4124600 3074290 2457330 3597100 3157760 FALSE TRUE 4279356.205 4076528.485 4083409.812 2782181.797 3595291.9 4208002.238 3111914.081 2406585.277 3188772.288 2943882.103 1.453643881 1.384745836 1.387083337 0.945072425 1.221275776 1.429405829 1.057078365 0.817486976 1.083186139 1 21.48928846 4.360797416 0.307536988 0.927157827 1.785992284 0.467738616 0.157666097 5.387082985 0.497369725 0.196058619 1.713125547 22950.7782 -4.360797416 0.858834457 DQHDTFFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DQHDTFFLR 9 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 162.36 6.38E-05 545610000 29608 40037 41769 67848 51291 36637 53662 71280 37283 47666 FALSE TRUE 28450.88663 38895.18396 49317.58745 71349.64341 52940.8216 37377.82524 54318.73161 69808.04309 33050.79014 44437.53936 0.64024442 0.875277626 1.109818144 1.605616432 1.19135358 0.84113175 1.222361373 1.570925035 0.743758332 1 15.43949131 4.361232564 2.6171112 1.211927723 0.668740064 0.280623876 0.263155115 0.337831823 4.362484901 0.068323704 0.279075273 22973.7856 -4.361232564 -0.543187659 ACS(ph)PCSSQSSSSGICTDFWDLLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ACSPCSSQSSSSGICTDFWDLLVK 24 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 ACS(0.932)PCS(0.067)S(0.001)QSSSSGICTDFWDLLVK;ACS(0.962)PCS(0.037)SQSSSSGICTDFWDLLVK 173.68 2.49E-12 308790000 167622 179722 159453 158180 207380 242500 182489 226590 285230 275170 TRUE FALSE 161071.1469 174596.5045 188269.7041 166343.6888 214050.566 247403.5161 184722.355 221910.8373 252851.8862 256532.4908 0.627878155 0.680601915 0.733901985 0.64843127 0.834399438 0.964413963 0.720073915 0.865039889 0.985652482 1 17.96878203 4.361378004 0.186228868 1.048582998 0.314147535 0.687013013 0.075920723 8.616116374 0.337660616 0.21764252 1.518030574 22981.48053 -4.361378004 -0.734435463 S(ph)SDSWEVWGSASTNR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSDSWEVWGSASTNR 15 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 S(0.996)S(0.004)DSWEVWGSASTNR;S(0.5)S(0.5)DSWEVWGSASTNR;S(0.929)S(0.071)DSWEVWGSASTNR;S(0.73)S(0.27)DSWEVWGSASTNR 391.76 1.57E-114 1268170000 543891 614397 610472 754220 734480 678847 731267 717020 767320 806160 TRUE FALSE 522635.1384 596874.9991 720797.8703 793145.3846 758105.2162 692573.7515 740216.4643 702213.2864 680217.0505 751558.0651 0.695402209 0.794183479 0.959071433 1.055334806 1.008711437 0.92151729 0.984909215 0.934343358 0.905075844 1 19.51952505 4.361688194 2.950519249 0.97122363 0.708130301 0.826535122 0.042613974 0.104673769 1.735917236 0.011611792 0.043254111 22997.90068 -4.361688194 -0.263093329 MQQENMKPQEQLTLEPYER ddPTM_BT-474_Pertuzumab_2h_R1 4 MQQENMKPQEQLTLEPYER 19 1 P22087;M0QXL5;M0R299 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;; 232.54 7.32E-21 2862330000 910478 943653 871634 945028 942636 1010812 972609 1054749 1132440 1120949 FALSE TRUE 874895.5132 916740.9404 1029157.653 993801.0083 972956.743 1031251.311 984512.0799 1032968.065 1003890.159 1045026.126 0.837199656 0.877242126 0.984815238 0.950981974 0.931035808 0.986818689 0.94209327 0.988461474 0.960636422 1 19.99510758 4.361716052 4.107507224 0.966197665 0.845431282 0.810681958 0.021727093 0.078359594 2.319177349 0.005144491 0.015928178 22999.37593 -4.361716052 -0.120766383 NTGVSPASRPSPGTPT(ph)SPSNLTSGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTGVSPASRPSPGTPTSPSNLTSGLK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 NTGVS(0.006)PAS(0.004)RPS(0.173)PGT(0.097)PT(0.404)S(0.311)PS(0.005)NLTSGLK 106.78 0.0047488 651920000 248970 226330 174090 152820 170520 174330 193660 235040 251470 200620 TRUE FALSE 239239.9771 219875.29 205551.9356 160707.0585 176004.9307 177855.072 196030.069 230186.3419 222924.1798 187031.8287 1.279140448 1.175603594 1.099021151 0.859249785 0.941042666 0.950934786 1.048110743 1.230733525 1.191905043 1 17.51292428 4.361832224 2.53228212 1.043829012 1.266039373 0.353424518 0.106814462 0.406523516 4.885471197 0.032382012 0.136154333 23005.52899 -4.361832224 0.222210362 FDPFGPIGT(ph)SPPGPNPDHLPPPGYDDMYL ddPTM_BT-474_Pertuzumab_2h_R1 4 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.567)S(0.433)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.527)S(0.473)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.548)S(0.452)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.526)S(0.474)PPGPNPDHLPPPGYDDMYL 246.21 2.87E-45 785685000 176172 192523 174235 223063 208356 195124 216897 216318 222064 233485 TRUE FALSE 169287.0035 187032.4325 205723.1403 234575.3082 215057.96 199069.541 219551.4504 211850.9577 196856.2257 217670.853 0.777720127 0.859244267 0.945111105 1.077660628 0.987996128 0.914543855 1.008639638 0.973262864 0.90437568 1 17.73178871 4.361879065 2.46810083 0.980279122 0.785146418 0.670458337 0.046365779 0.178141437 2.023025258 0.012093125 0.051997927 23008.0104 -4.361879065 -0.195132704 SPSDSSTAST(ph)PVAEQIER ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSDSSTASTPVAEQIER 18 0 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 SPSDSSTAS(0.255)T(0.745)PVAEQIER;SPSDSSTAS(0.37)T(0.63)PVAEQIER;SPSDSSTAS(0.135)T(0.865)PVAEQIER;SPSDSSTAS(0.296)T(0.704)PVAEQIER 437.24 1.12E-168 981980000 743110 834680 793930 971620 908750 1016030 976380 957030 1024600 1107980 TRUE FALSE 714068.4396 810875.7436 937410.8119 1021765.425 937980.7691 1036574.823 988329.2305 937266.9961 908291.7035 1032935.528 0.691300106 0.785020673 0.907521125 0.98918606 0.908072909 1.003523255 0.956815991 0.907381895 0.87933049 1 19.97831878 4.362067383 2.197095896 0.944921554 0.692134067 0.820603908 0.040002523 0.138325249 1.206079806 0.010522091 0.050383967 23017.98927 -4.362067383 -0.252787487 DRFTDILVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRFTDILVR 9 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 169.93 5.30E-05 363700000 69944 74753 64358 83176 74003 78395 79936 77386 87379 85028 FALSE TRUE 67210.51115 72621.11763 75988.92224 87468.72333 76383.3737 79980.20061 80914.28068 75787.95206 77460.10224 79268.97782 0.84787912 0.916135412 0.958621195 1.103442049 0.963597309 1.008972271 1.020755949 0.956085901 0.977180536 1 16.27446875 4.362087369 2.276948598 1.000322102 0.853993912 0.607573885 0.039991614 0.226267702 2.142231043 0.010432283 0.048289762 23019.04854 -4.362087369 -0.146328189 YVWLVYEQDRPLKCDEPILSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 YVWLVYEQDRPLKCDEPILSNR 22 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 194.25 2.42E-18 1855200000 582740 536960 338320 449320 411010 468530 353740 423700 516750 473110 FALSE TRUE 559965.8765 521646.4265 399461.9499 472509.459 424230.5099 478003.9976 358069.1759 414950.4469 458090.7064 441065.8383 1.269574354 1.182695147 0.905674199 1.071290084 0.961830351 1.083747496 0.811827045 0.940790265 1.03859938 1 18.7506345 4.362297808 4.658416672 0.971305599 1.249775636 0.629617812 0.077419222 0.118683871 4.177044006 0.019050125 0.056533934 23030.20523 -4.362297808 0.278470038 RWDDDVVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 RWDDDVVFK 9 1 Q9P013 Q9P013 CWC15 Spliceosome-associated protein CWC15 homolog 0 ; 207.88 1.76E-05 592960000 779860 786760 686910 769930 816300 846300 796060 947660 961220 941360 FALSE TRUE 749382.209 764322.3751 811049.9172 809666.1796 842557.0308 863412.7658 805802.4204 928090.4898 852106.3354 877600.8487 0.853898683 0.870922557 0.924167198 0.92259047 0.960068614 0.983833103 0.918187832 1.057531441 0.970949762 1 19.7432054 4.362330914 0.390032004 1.011132373 0.762344828 0.699837863 0.031721671 2.252249728 0.338683718 0.027324419 0.256614896 23031.96089 -4.362330914 -0.248787545 TIYENR ddPTM_BT-474_Pertuzumab_2h_R1 3 TIYENR 6 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;G3V2F7;Q13404-6 I3L0A0 TMEM189-UBE2V1;UBE2V1 Ubiquitin-conjugating enzyme E2 variant 1 0 ;; 130.05 0.037058 1726480000 2010350 2077460 1845750 2223700 2132330 2150580 2164750 2178940 2213920 2326460 FALSE TRUE 1931783.299 2018212.875 2179318.083 2338465.423 2200918.331 2194066.201 2191242.858 2133944.128 1962605.083 2168886.792 0.890679636 0.930529377 1.004809514 1.078186945 1.014768654 1.01160937 1.010307622 0.983889125 0.904890514 1 21.04852332 4.362375432 3.486914832 1.003586593 0.897947982 0.460391024 0.04008466 0.204182262 4.642395821 0.010517087 0.035234293 23034.3219 -4.362375432 -0.105638611 FLDGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLDGDR 6 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 132.72 0.034376 210790000 280670 311460 282920 358220 315120 328230 360100 380400 364430 404810 FALSE TRUE 269701.1061 302577.4658 334049.9375 376707.7771 325256.121 334867.0355 364507.0115 372544.6071 323061.4342 377391.8581 0.714644739 0.801759389 0.885154066 0.998187346 0.861852512 0.887319184 0.965858175 0.98715592 0.856037106 1 18.52570377 4.362452004 1.91934258 0.936616411 0.71126698 0.665109006 0.051492552 0.244339206 1.544480497 0.01374792 0.075387834 23038.38352 -4.362452004 -0.225349431 EELTLEGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EELTLEGIR 9 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 196.95 6.70E-05 393090000 362770 375400 397770 425850 380780 361620 449810 449780 458060 505100 FALSE TRUE 348592.5473 364693.9596 469655.8873 447828.1695 393028.1345 368932.2042 455314.9093 440491.8858 406062.9491 470889.1271 0.740285828 0.774479466 0.99738104 0.951026778 0.834651114 0.783479981 0.966925935 0.935447137 0.862332396 1 18.84502789 4.362495742 6.809112041 0.911464493 0.749321086 0.473004711 0.067314011 0.178812036 9.731457168 0.016959093 0.047251606 23040.70387 -4.362495742 -0.162143407 DFEEYPEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFEEYPEHR 9 0 O14980 O14980 XPO1 Exportin-1 0 ; 121.73 0.0006056 404150000 405210 472770 463470 601390 536450 511580 580690 557570 653100 679210 FALSE TRUE 389373.9452 459287.0625 547229.3388 632427.81 553705.4014 521924.4981 587796.6579 546055.9847 578962.826 633206.5017 0.614924111 0.725335355 0.864219393 0.99877024 0.874446804 0.824256379 0.928285885 0.862366358 0.914334936 1 19.27231654 4.362759274 2.449642073 0.903850894 0.622712986 0.773642358 0.053441996 0.139546285 1.557891405 0.013512884 0.0585945 23054.68934 -4.362759274 -0.281137908 GLCNFLMSDEEYDDR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLCNFLMSDEEYDDR 15 0 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 0 ;;;; 347.75 6.74E-82 737039000 624863 666066 558951 663554 720024 729351 665539 700393 723870 714989 FALSE TRUE 600442.6631 647070.4498 659965.8795 697800.1015 743184.2259 744098.9769 673684.0654 685929.6398 641699.3123 666562.1582 0.900805207 0.970757853 0.990104031 1.046864261 1.114951122 1.116323463 1.010684536 1.029055777 0.962699884 1 19.34637989 4.362827265 1.539297963 1.043542471 0.897227271 0.470794361 0.046043495 0.525651756 1.914236785 0.013758299 0.094861569 23058.29891 -4.362827265 -0.1463152 TEKPERPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEKPERPSR 9 2 Q02241;H7BYN4;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 0 ; 79.974 0.0143 252120000 163986 162079 151837 165922 159548 159585 167966 163327 196776 178853 FALSE TRUE 157577.2458 157456.6656 179277.3235 174485.2543 164680.0063 162811.918 170021.6182 159954.2404 174438.8134 166739.127 0.945052602 0.944329435 1.075196486 1.046456566 0.987650645 0.976446986 1.019686388 0.959308371 1.046178042 1 17.34723316 4.362860401 23.97244397 1.009086957 0.944652499 0.397221736 0.033676062 5.505073659 1122.219702 0.008579372 0.02349558 23060.0583 -4.362860401 -0.064434458 GTQEVAPPTPLT(ph)PTS(ph)HTANTSPRPVSGMER ddPTM_BT-474_Pertuzumab_2h_R1 1 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 2 GTQEVAPPT(0.003)PLT(0.991)PT(0.092)S(0.312)HT(0.252)ANT(0.183)S(0.165)PRPVS(0.003)GMER 86.413 0.019744 503180000 67387 83507 89242 114640 117570 107620 116940 90487 107320 128640 TRUE FALSE 64753.44154 81125.46212 105370.0146 120556.5841 121351.7458 109796.1501 118371.1467 88618.41183 95137.48352 119927.0982 0.539940034 0.676456475 0.878617228 1.005248905 1.01187928 0.915524112 0.987025855 0.73893568 0.793294301 1 16.87179816 4.362897639 2.665405718 0.910597929 0.552903815 0.676649757 0.08777707 0.18625289 2.499967898 0.025264659 0.101981607 23062.03567 -4.362897639 -0.357694114 RGFEGSCSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGFEGSCSQK 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ; 150.09 3.56E-05 211812000 292990 266380 214120 201867 226600 193024 251800 254030 267160 287140 FALSE TRUE 281539.6269 258783.1032 252816.2471 212285.3801 233888.7948 196927.0775 254881.6037 248784.1917 236833.1168 267691.752 1.051730674 0.966720496 0.94443047 0.793021744 0.873724323 0.735648656 0.952145898 0.929368163 0.88472325 1 18.03021316 4.362930233 1.919022625 0.880150927 1.04746086 0.344072527 0.072746061 0.468032053 2.956166223 0.019531085 0.107240611 23063.76651 -4.362930233 0.167309933 KLEQCNTELKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEQCNTELKK 11 2 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 49.448 0.09184 385570000 78645 89761 98125 112080 112630 106620 119030 96255 121290 133450 FALSE TRUE 75571.46645 87201.10417 115858.3703 117864.4622 116252.8462 108775.9295 120486.7247 94267.30061 107521.6677 124411.3126 0.607432434 0.700909767 0.931252696 0.947377371 0.934423436 0.874325069 0.968454734 0.757706824 0.864243495 1 16.92475815 4.363001242 3.967923152 0.897779894 0.626232104 0.713505375 0.065419297 0.119264062 3.352753657 0.017260066 0.054268792 23067.53785 -4.363001242 -0.27154779 SWGHES(ph)PEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SWGHESPEER 10 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 S(0.006)WGHES(0.994)PEER 99.531 0.0026434 0 270470 278470 291320 289010 283470 332870 327760 315570 317660 342970 TRUE FALSE 259899.7334 270528.3083 343968.0044 303925.8407 292588.07 339600.8595 331771.2249 309053.3692 281600.5685 319740.3364 0.81284625 0.84608752 1.075772948 0.950539566 0.915080259 1.062114537 1.037627059 0.966576106 0.880716433 1 18.28654123 4.363038423 6.984647642 0.985277046 0.821625988 0.53351376 0.05885141 0.152031401 8.509181341 0.014425689 0.040117037 23069.51283 -4.363038423 -0.163651059 GVDLDAPGSINGVPLLEVDLDSFEDKPWR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVDLDAPGSINGVPLLEVDLDSFEDKPWR 29 1 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 0 ; 265.23 1.92E-58 700070000 496900 502110 460940 478650 532380 533090 490760 507860 611440 590040 FALSE TRUE 477480.5986 487790.3144 544242.1116 503353.1839 549504.4862 543869.445 496766.0677 497372.5135 542031.8946 550076.0652 0.868026495 0.88676884 0.989394278 0.915061054 0.998960909 0.988716796 0.903086135 0.904188611 0.985376258 1 19.0692716 4.363061872 6.307649244 0.952262729 0.872899256 0.424372103 0.037990148 0.20502374 10.2768879 0.009711724 0.02725234 23070.75844 -4.363061872 -0.079363473 ELAENNHILER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELAENNHILER 11 0 A0A494C0X2;A0A494C167;A0A494C045;Q9UHD2 A0A494C0X2 TBK1 Serine/threonine-protein kinase TBK1 0 137.95 0.0014784 0 166180 173470 212150 190350 211990 247580 193640 196030 229610 260870 FALSE TRUE 159685.5019 168522.8054 250490.2243 200173.9863 218808.8509 252586.2372 196009.8242 191981.912 203545.6354 243201.0425 0.656598756 0.692936197 1.029971836 0.823080297 0.899703589 1.038590273 0.805957993 0.789395925 0.836943926 1 17.89178989 4.363202437 7.862937189 0.88690544 0.666240356 0.507708459 0.089019706 0.186049604 11.82549991 0.022324016 0.06166241 23078.22678 -4.363202437 -0.220665084 GQPEGPLPSSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQPEGPLPSSSPR 13 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4 P49815 TSC2 Tuberin 1 GQPEGPLPSS(0.001)S(0.999)PR;GQPEGPLPSS(0.008)S(0.992)PR 211.09 2.59E-08 1209820000 603400 693070 666210 832870 734390 844740 907100 826250 836710 1046180 TRUE FALSE 579818.4609 673304.3222 786608.9668 875854.5205 758012.3213 861821.2216 918201.3611 809187.6488 741730.1886 975321.2968 0.594489696 0.690341044 0.806512653 0.898016401 0.777192422 0.883628015 0.94143475 0.829662647 0.7604983 1 19.89551803 4.363499805 1.72986449 0.863492465 0.580269554 0.64784271 0.06780756 0.29189458 1.426758954 0.017669379 0.108166865 23094.0342 -4.363499805 -0.28322291 RPPGPTTS(ph)PASTSLSSPGQR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPPGPTTSPASTSLSSPGQR 20 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 RPPGPT(0.004)T(0.247)S(0.748)PAS(0.001)TSLSSPGQR;RPPGPT(0.009)T(0.048)S(0.943)PASTSLSSPGQR;RPPGPT(0.035)T(0.154)S(0.811)PASTSLSSPGQR 179.79 3.49E-17 1804170000 332573 353668 312649 391818 352270 409881 415181 365662 335602 387513 TRUE FALSE 319575.6795 343581.7349 369151.6291 412039.7739 363601.0845 418169.0747 420262.1093 358110.9519 297505.8679 361266.3993 0.884598402 0.951048134 1.021826635 1.140542754 1.006462503 1.157508906 1.16330251 0.991265594 0.823508271 1 18.46270355 4.363828397 2.535999598 1.049153226 0.891266272 0.211465373 0.095938305 0.448988452 5.408685412 0.025395552 0.107071588 23111.51403 -4.363828397 -0.157886954 EPLPVEQDDDIEVIVDETSDHTEETS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPLPVEQDDDIEVIVDETSDHTEETSPVR 29 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5;C9J1B2;C9JAY7;C9JK97 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 EPLPVEQDDDIEVIVDETSDHTEET(0.014)S(0.986)PVR;EPLPVEQDDDIEVIVDETSDHTEET(0.136)S(0.864)PVR 227.66 5.42E-35 236890000 89271 105754 105980 133188 113126 129875 146552 128137 135853 162006 TRUE FALSE 85782.19063 102737.9995 125132.9435 140061.8486 116764.8005 132501.1615 148345.5472 125490.9262 120431.537 151033.1893 0.56796914 0.680234589 0.828512886 0.927358081 0.773106898 0.877298308 0.982204957 0.830883111 0.797384585 1 17.20450609 4.363973287 2.067443886 0.876763669 0.564284626 0.694977973 0.069652401 0.20620533 1.5565999 0.017817798 0.090951497 23119.22583 -4.363973287 -0.312479043 EIIQDVTLHDLDVANAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIIQDVTLHDLDVANAR 17 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;H7C4I3 Q9Y265 RUVBL1 RuvB-like 1 0 138.05 4.94E-06 385200000 100260 111620 121630 146900 144210 127360 134200 121090 138250 153960 FALSE TRUE 96341.72836 108436.7069 143611.2466 154481.5266 148848.6456 129935.3065 135842.3797 118589.4492 122556.4396 143532.1521 0.671220538 0.755487222 1.000551058 1.076285169 1.037040436 0.905269688 0.94642474 0.826222191 0.853860531 1 17.13101442 4.364028889 4.567633147 0.947613219 0.690496229 0.629686143 0.075129322 0.1467811 5.040052587 0.021607234 0.064553688 23122.18594 -4.364028889 -0.25711699 GSPT(ph)SAYPER ddPTM_BT-474_Pertuzumab_2h_R1 3 GSPTSAYPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.265)PT(0.692)S(0.044)AYPER;GS(0.157)PT(0.842)S(0.001)AYPER;GS(0.383)PT(0.568)S(0.049)AYPER 198.93 3.22E-06 8576700000 962530 1036110 979820 1213790 1038510 1041030 1225820 1157530 1185440 1379510 TRUE FALSE 924913.2635 1006561.157 1156895.27 1276433.847 1071914.617 1062080.34 1240821.952 1133626.601 1050873.821 1286074.559 0.719175461 0.782661589 0.899555366 0.992503769 0.833477818 0.825831078 0.964813388 0.881462582 0.817117339 1 20.29454285 4.36403467 3.368804662 0.89845268 0.729940938 0.486057413 0.063449105 0.194728921 4.163787778 0.015558142 0.053287046 23122.49372 -4.36403467 -0.168511743 LCAGIMITAS(ph)HNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LCAGIMITASHNPK 14 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 1 LCAGIMIT(0.001)AS(0.999)HNPK;LCAGIMIT(0.001)AS(0.999)HNPK 128.82 4.61E-05 1720660000 3591100 2737000 2393100 1713280 2044040 1701470 1490060 2320300 1908980 1564160 TRUE FALSE 3450755.842 2658943.44 2825586.404 1801702.586 2109788.403 1735874.889 1508295.8 2272384.994 1692280.593 1458218.05 2.366419646 1.823419646 1.937698141 1.235550874 1.446826421 1.190408313 1.034341743 1.558330041 1.160512719 1 20.47577503 4.364094798 0.80843203 1.229999319 2.611679693 0.795302819 0.191678951 0.701703173 0.506577952 0.070737465 0.789222322 23125.69522 -4.364094798 1.381680374 up TPASPVVHIR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPASPVVHIR 10 0 A0A3B3ITJ4;M0R1W6;M0QYL7;P14866;M0QXS5 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;; 134.25 0.00045709 262720000 351820 380480 346721 491060 397380 365159 420710 388860 438880 491470 FALSE TRUE 338070.4854 369629.0829 409381.1975 516403.6654 410162.0886 372542.7652 425858.7748 380829.9051 389060.1823 458182.2991 0.737851475 0.806729294 0.893489771 1.127070309 0.895194095 0.813088515 0.9294527 0.831175508 0.849138395 1 18.8055622 4.364105661 3.203498144 0.91099604 0.750239299 0.32081247 0.086826644 0.314100209 6.117132162 0.022937873 0.081074231 23126.27368 -4.364105661 -0.160756741 DIVEAHYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIVEAHYR 8 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 109.71 0.0063351 0 71358 78415 69853 96037 84322 102090 68486 74485 98684 102310 FALSE TRUE 68569.25047 76178.68098 82476.99097 100993.4811 87034.29371 104154.3297 69324.15215 72946.85872 87481.80604 95380.45257 0.718902549 0.798682318 0.864715869 1.058848835 0.912496129 1.091988211 0.726817186 0.764798832 0.917187995 1 16.54140601 4.364178182 2.61162974 0.903606009 0.729260797 0.259542224 0.10986223 0.479272742 6.154269531 0.030938425 0.12731863 23130.13577 -4.364178182 -0.174345212 KTENWLSEWWLK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTENWLSEWWLK 12 1 P43155-2;P43155;P43155-3 P43155-2 CRAT Carnitine O-acetyltransferase 0 ; 175.74 4.31E-05 1521330000 2593900 3093600 2254300 3553600 2994200 2887700 3728000 3649600 3567400 3256900 FALSE TRUE 2492527.52 3005373.557 2661702.157 3737001.722 3090511.162 2946091.273 3773624.379 3574234.485 3162443.708 3036307.262 0.820907538 0.989812064 0.87662477 1.230771921 1.017851915 0.970287596 1.242833499 1.177164949 1.041542714 1 21.53388636 4.364324544 0.86125045 1.113905273 0.77179939 0.376780716 0.106035488 1.421222585 1.191759996 0.037953213 0.414171239 23137.93217 -4.364324544 -0.342105883 ITLPVDFVTADKFDENAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITLPVDFVTADKFDENAK 18 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 285.19 1.17E-39 8144900000 8379500 7415100 4810010 5263590 5019980 4866690 5272670 6127500 7900300 5791230 FALSE TRUE 8052019.876 7203628.608 5679285.805 5535244.511 5181452.216 4965097.806 5337198.513 6000964.984 7003491.065 5398984.834 1.491395165 1.33425613 1.051917347 1.025238018 0.959708607 0.919635442 0.988555937 1.111498767 1.297186653 1 22.36425673 4.365454733 2.7342259 1.03846651 1.478257862 0.699895659 0.098971269 0.157704088 2.232884026 0.026966519 0.107149548 23198.22374 -4.365454733 0.439791352 EMVHADVELMR ddPTM_BT-474_Pertuzumab_2h_R1 4 EMVHADVELMR 11 0 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 ;;; 172.17 1.37E-05 824860000 709509 771300 646788 860320 835590 819060 828910 740660 847790 882060 FALSE TRUE 681780.6039 749303.2792 763676.9793 904721.2183 862467.5112 835621.9544 839054.4485 725365.1122 751552.4334 822317.2905 0.829096763 0.911209442 0.928688948 1.100209407 1.048825704 1.016179477 1.02035365 0.882098821 0.913944583 1 19.64933564 4.365524556 2.082900526 0.989900761 0.836465482 0.421030649 0.061051303 0.429055696 3.2930799 0.018346172 0.093289738 23201.95369 -4.365524556 -0.153435279 YHPDKNKEPGAEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YHPDKNKEPGAEEK 14 2 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 70.98 0.025643 88166000 113590 100250 57835 53495 85271 83638 70052 65413 95643 74450 FALSE TRUE 109150.7772 97390.96816 68287.07103 56255.88336 88013.81916 85329.21766 70909.31733 64062.19869 84786.00761 69407.43519 1.572609288 1.403177742 0.983858154 0.810516672 1.268074795 1.22939592 1.021638635 0.922987552 1.221569525 1 16.0828026 4.365602496 4.124102115 1.051213715 1.536943608 0.613010548 0.13924011 0.136453332 4.069075128 0.036141742 0.112058487 23206.11797 -4.365602496 0.485729893 EFVISDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EFVISDR 7 0 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 ;; 139.68 0.0062246 999600000 1175730 1248010 1151220 1408190 1337090 1290000 1355600 1408430 1347190 1424920 FALSE TRUE 1129781.172 1212417.977 1359271.063 1480866.855 1380098.714 1316084.684 1372190.238 1379345.428 1194262.639 1328408.899 0.850476967 0.912684323 1.023232428 1.11476734 1.038911072 0.990722574 1.032957728 1.038344014 0.899017343 1 20.34126786 4.365630255 3.31246167 1.023690983 0.860745825 0.539557883 0.051260942 0.169890843 3.522563562 0.012933445 0.044852642 23207.60132 -4.365630255 -0.162945159 TIQEVLEEQS(ph)EDEDREAKR ddPTM_BT-474_Pertuzumab_2h_R1 3 TIQEVLEEQSEDEDREAKR 19 2 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 TIQEVLEEQS(1)EDEDREAKR;TIQEVLEEQS(1)EDEDREAKR;TIQEVLEEQS(1)EDEDREAKR 266.38 8.60E-32 3821460000 1768380 1573680 939151 846243 1293452 1347280 1050864 1245846 1417990 1218144 TRUE FALSE 1699269.755 1528800.187 1108876.477 889917.7026 1335057.058 1374522.925 1063724.788 1220118.845 1257025.72 1135638.022 1.496312841 1.346203771 0.976434793 0.783627957 1.17560088 1.210353033 0.936675919 1.074390626 1.106889428 1 20.11507163 4.365652414 4.140020981 1.035540553 1.46447833 0.644538549 0.117314342 0.128850678 3.864249138 0.030202821 0.093503839 23208.78544 -4.365652414 0.428937778 EEMAAEAGEAVASPMDDGFVSLDS(ph)PSYVLYR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEMAAEAGEAVASPMDDGFVSLDSPSYVLYR 31 0 P49354;P49354-2;E9PN85 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 EEMAAEAGEAVAS(0.001)PMDDGFVS(0.205)LDS(0.546)PS(0.128)Y(0.114)VLY(0.006)R 76.237 0.0018718 16225000 8977.6 9660.3 10227 10386 10726 11958 12032 10302 11531 13855 TRUE FALSE 8626.745467 9384.797702 12075.2464 10922.0227 11071.01153 12199.79895 12179.25122 10089.2601 10222.04922 12916.58851 0.66788111 0.72656938 0.934863442 0.845581068 0.857115756 0.944506279 0.942915477 0.781108734 0.791389245 1 13.65693746 4.365678138 5.087081777 0.876533433 0.681933227 0.558384882 0.067742092 0.147019419 5.788603768 0.016976842 0.049332623 23210.16019 -4.365678138 -0.194600207 SNS(ph)VGIQDAFNDGSDSTFQKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSVGIQDAFNDGSDSTFQKR 21 1 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;A0A087WUV6 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 S(0.24)NS(0.76)VGIQDAFNDGSDSTFQKR 99.836 0.00047659 243920000 171060 152980 73010 92129 98263 132130 88425 121790 119900 104150 TRUE FALSE 164374.7861 148617.1602 86204.5311 96883.78873 101423.7186 134801.7591 89507.1716 119274.9939 106289.4547 97095.82773 1.69291297 1.530623546 0.887829406 0.997816188 1.044573397 1.388337298 0.921843643 1.228425533 1.094686117 1 16.56712168 4.366502692 5.456836506 1.086985993 1.652763338 0.705011014 0.141105616 0.100330016 4.296012561 0.034126481 0.097794831 23254.26903 -4.366502692 0.565777345 FACNGTVIEHPEYGEVIQLQGDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FACNGTVIEHPEYGEVIQLQGDQR 24 0 K7EM18;P41567;O60739;K7EQP2 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 ; 341.27 2.17E-87 6326500000 690680 744780 667050 817390 736910 868020 831130 797450 854510 914440 FALSE TRUE 663687.462 723539.6036 787600.7734 859575.5959 760613.3794 885571.9591 841301.6176 780982.3788 757509.6072 852504.1643 0.778515214 0.848722662 0.923867362 1.008294894 0.89221075 1.038789013 0.986859247 0.916103887 0.888569979 1 19.70134736 4.366559109 2.096138272 0.95809317 0.778489115 0.61153485 0.047871945 0.249981404 1.946286633 0.012600449 0.063822638 23257.29006 -4.366559109 -0.179604055 KRPQSPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 KRPQS(0.189)PS(0.811)PR 83.397 0.0084513 338270000 96106 90761 58520 65792 79392 74849 71317 83288 89185 74402 TRUE FALSE 92350.07127 88172.58514 69095.86577 69187.533 81945.71578 76362.49806 72189.79878 81568.07369 79061.09269 69362.68627 1.331408517 1.271181811 0.996153256 0.99747482 1.181409201 1.1009161 1.040758406 1.175964745 1.139821667 1 16.08187215 4.366749023 5.885451818 1.089737181 1.316127419 0.629419355 0.068363918 0.126587819 5.910161054 0.017290617 0.048958196 23267.46253 -4.366749023 0.226390238 SLPTTVPES(ph)PNYR ddPTM_BT-474_Pertuzumab_2h_R1 12 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPT(0.001)T(0.004)VPES(0.949)PNY(0.046)R;SLPTTVPES(1)PNYR;SLPT(0.001)T(0.001)VPES(0.998)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR 320.06 5.96E-51 50721068000 4239648.34 4659358.6 4439382 5414369.1 4924751 5376690.2 5277076.2 5320642.3 5457775.1 5973151.9 TRUE FALSE 4073958.196 4526478.255 5241677.081 5693805.338 5083160.088 5485410.56 5341658.637 5210769.177 4838231.352 5568585.001 0.731596661 0.812859686 0.941294257 1.022486922 0.91282796 0.985063631 0.959248828 0.935743852 0.868843943 1 22.40887935 4.366807716 2.839773384 0.953440749 0.740776328 0.761869586 0.041674031 0.120995385 1.853828288 0.010396963 0.040203245 23270.60722 -4.366807716 -0.212664421 MGIDHK ddPTM_BT-474_Pertuzumab_2h_R1 2 MGIDHK 6 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 81.672 0.06126 306480000 661120 679170 598120 685300 651460 701500 714780 721770 747020 789960 FALSE TRUE 635282.6995 659800.7366 706213.5891 720668.4151 672414.8025 715684.8106 723527.6915 706865.1973 662221.4214 736455.3056 0.862622205 0.89591416 0.958936114 0.978563682 0.913042241 0.971796666 0.982446166 0.959820904 0.899201101 1 19.49023845 4.366932499 3.177873981 0.957815992 0.867356983 0.54865141 0.029225183 0.174490055 3.346468104 0.007107711 0.025362144 23277.2944 -4.366932499 -0.090459009 SKIGS(ph)TENLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKIGSTENLK 10 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 S(0.013)KIGS(0.961)T(0.026)ENLK 90.444 0.0065567 121740000 286590 237690 167720 142340 154840 165310 143030 178210 240640 203380 TRUE FALSE 275389.746 230911.3139 198030.7349 149686.1845 159820.5692 168652.6815 144780.4439 174529.9012 213323.556 189604.8914 1.452440092 1.217855258 1.044438956 0.789463728 0.842913746 0.889495414 0.763590237 0.920492609 1.125095215 1 17.53263666 4.366986281 1.777958746 0.891916098 1.465913309 0.749885087 0.10163546 0.216790374 1.131196552 0.027539635 0.165258219 23280.17716 -4.366986281 0.573997211 LQTATMETSRS(ph)PS(ph)PQFAPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQTATMETSRSPSPQFAPQK 20 1 Q13796 Q13796 SHROOM2 Protein Shroom2 2 LQT(0.001)AT(0.009)MET(0.051)S(0.399)RS(0.541)PS(1)PQFAPQK;LQT(0.28)AT(0.146)MET(0.091)S(0.078)RS(0.404)PS(1)PQFAPQK 132.24 7.34E-06 369780000 925280 948540 866140 928480 889960 1060710 983730 1006850 1149290 1071170 TRUE FALSE 889119.0346 921488.5679 1022670.765 976398.9641 918586.3716 1082158.283 995769.182 986058.1957 1018827.417 998618.7018 0.890348872 0.922763179 1.024085332 0.977749528 0.919856968 1.083655134 0.997146539 0.98742212 1.020236668 1 19.9295744 4.366992706 4.698344616 0.999041529 0.89771035 0.490470261 0.039056422 0.161605703 5.771656645 0.009494725 0.028172334 23280.52159 -4.366992706 -0.101331179 DSDIIDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDIIDFR 8 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ; 100.15 0.014677 175254000 419630 430120 411130 432820 449200 507630 435890 447510 494430 512940 FALSE TRUE 403230.3957 417853.3987 485430.3365 455157.8921 463648.926 517894.6264 441224.5522 438268.7621 438304.3792 478198.1169 0.84322874 0.873808123 1.015123898 0.951818663 0.969574972 1.083012685 0.922681492 0.916500393 0.916574875 1 18.86724892 4.367009082 5.904024633 0.966623421 0.850963877 0.459434894 0.049323644 0.184093484 8.629721547 0.012848612 0.036366408 23281.39943 -4.367009082 -0.115659544 VPCNVEGIS(ph)PELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VPCNVEGISPELEK 14 0 Q86VQ1;H7C2L5;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 VPCNVEGIS(1)PELEK 75.564 0.031364 274570000 189240 205870 196080 234790 223880 220070 231880 234030 243440 267680 TRUE FALSE 181844.2916 199998.7892 231516.0178 246907.54 231081.3035 224519.9662 234717.8168 229197.1987 215805.7118 249549.7952 0.728689404 0.801438402 0.927734754 0.989411912 0.92599276 0.899700062 0.940565055 0.918442744 0.86478016 1 17.92896819 4.36742082 3.047488382 0.931310604 0.738384917 0.771738394 0.037536269 0.111781247 1.975805846 0.009339425 0.034320606 23303.48208 -4.36742082 -0.192925687 DLVLPTQALPAS(ph)PALK ddPTM_BT-474_Pertuzumab_2h_R1 5 DLVLPTQALPASPALK 16 0 Q15554;J3KSZ6;U3KQ35;H3BR06 Q15554 TERF2 Telomeric repeat-binding factor 2 1 DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK 276.3 2.85E-35 5085030000 4882260 4606220 3560840 3711700 3844100 3673940 4306630 4668740 4392710 4664940 TRUE FALSE 4691455.882 4474855.116 4204362.998 3903261.282 3967748.968 3748229.584 4359335.826 4572328.887 3894067.977 4348979.459 1.078748687 1.028943723 0.966747035 0.897512007 0.912340241 0.861864173 1.002381333 1.051356745 0.895398107 1 22.05224546 4.367537455 2.641022251 0.951491903 1.073645048 0.382784828 0.055393593 0.351455548 4.617809224 0.016036542 0.06581065 23309.7414 -4.367537455 0.122153145 EEPFFPPPEEFVFIHAVPVEER ddPTM_BT-474_Pertuzumab_2h_R1 7 EEPFFPPPEEFVFIHAVPVEER 22 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;;; 213.72 5.55E-24 2462231000 964671 1022315 945695 1136436 1099140 1077113 1110990 1104355 1158708 1199065 FALSE TRUE 926970.5908 993159.5772 1116603.123 1195087.598 1134494.836 1098892.963 1124586.628 1081549.683 1027176.326 1117851.26 0.829243232 0.888454138 0.998883451 1.069093574 1.014888901 0.983040412 1.006025281 0.967525576 0.918884616 1 20.09229681 4.367611574 3.373259224 0.9958483 0.839059442 0.704479085 0.036084289 0.131631191 2.822466618 0.009781651 0.033637699 23313.71986 -4.367611574 -0.156788858 EQDRVHS(ph)PCPTSGSEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQDRVHSPCPTSGSEKK 17 2 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 EQDRVHS(0.992)PCPT(0.005)S(0.002)GS(0.002)EKK 54.668 0.065302 77406000 62968 55005 33867 26151 43676 47611 33950 48413 50567 34334 TRUE FALSE 60507.14095 53436.31126 39987.52027 27500.65624 45080.87821 48573.72704 34365.49026 47413.25463 44826.84615 32008.5276 1.890344401 1.669439842 1.249277092 0.859166551 1.408402122 1.517524569 1.07363546 1.481269468 1.400465736 1 14.96616869 4.367775485 3.550242599 1.268759694 1.850147784 0.523421315 0.206523596 0.181584373 4.264347594 0.052115388 0.173995951 23322.52056 -4.367775485 0.581388091 ARIPS(ph)GK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARIPSGK 7 1 Q9NTM9;A0A0B4J226 Q9NTM9 CUTC Copper homeostasis protein cutC homolog 1 ARIPS(1)GK;ARIPS(1)GK 60.434 0.059067 728200000 502120 466360 354970 389630 370570 383720 350340 508940 407170 362130 TRUE FALSE 482496.5953 453059.8694 419120.9753 409738.851 382489.7206 391479.0813 354627.5657 498430.2111 360949.7686 337602.6125 1.429185016 1.341991598 1.241462476 1.213672039 1.132958414 1.159585462 1.050428973 1.47638138 1.069155733 1 18.36496654 4.368299871 1.500128877 1.186394184 1.45045167 0.340312647 0.124584161 0.793651328 2.691914314 0.035623195 0.255636597 23350.6982 -4.368299871 0.264057486 SPEYPEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPEYPEGR 8 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 84.498 0.045089 0 152850 166580 173390 184130 172610 204760 196630 193050 219170 214430 FALSE TRUE 146876.453 161829.3015 204725.43 193632.9714 178162.1574 208900.3875 199036.4168 189063.45 194290.7404 199906.4651 0.734725878 0.809525102 1.024106098 0.968617855 0.891227591 1.044990653 0.995647723 0.945759558 0.971908239 1 17.6089656 4.368490071 4.473202156 0.976003879 0.751112756 0.80726704 0.041226521 0.079659659 2.670484736 0.010189397 0.030723348 23360.92693 -4.368490071 -0.224891123 SVPVTVDDDDDDNDPENR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVPVTVDDDDDDNDPENR 18 0 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 0 ;; 350.43 5.27E-90 1278460000 934080 947020 861870 978985 926372 1039206 976485 936179 1061070 1073258 FALSE TRUE 897575.1209 920011.9168 1017629.081 1029510.533 956169.5967 1060219.457 988435.5155 916846.5765 940621.782 1000565.28 0.897068027 0.919492147 1.017054161 1.028928901 0.955629399 1.059620475 0.987877089 0.916328595 0.940090368 1 19.93238387 4.36857607 5.787500413 0.984276751 0.902704124 0.384167372 0.04058089 0.223049999 10.25661405 0.011000934 0.031235115 23365.55332 -4.36857607 -0.081572627 GHTDTEGRPPS(ph)PPPTSTPEK ddPTM_BT-474_Pertuzumab_2h_R1 5 GHTDTEGRPPSPPPTSTPEK 20 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 GHT(0.002)DT(0.013)EGRPPS(0.984)PPPT(0.001)STPEK;GHT(0.173)DT(0.158)EGRPPS(0.612)PPPT(0.056)STPEK;GHT(0.001)DT(0.005)EGRPPS(0.994)PPPTSTPEK;GHTDTEGRPPS(0.997)PPPT(0.003)STPEK;GHT(0.002)DT(0.007)EGRPPS(0.991)PPPTSTPEK 190.33 1.13E-17 6335840000 1376294 1377335 1221614 1336932 1364659 1423690 1385424 1225291 1772470 1604170 TRUE FALSE 1322506.909 1338054.754 1442386.824 1405931.221 1408554.496 1452477.987 1402379.233 1199988.313 1571266.636 1495518.137 0.884313521 0.894709814 0.964472973 0.940096403 0.941850494 0.971220577 0.937721315 0.802389675 1.050650338 1 20.51221398 4.368881774 7.069884883 0.936288144 0.887011721 0.104955309 0.060945249 0.536443797 30.84375015 0.015347262 0.042658881 23382.00633 -4.368881774 -0.049276423 DFQEYVEPGEDFPAS(ph)PQRR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFQEYVEPGEDFPASPQRR 19 1 Q9Y6G9;E9PHI6;C9JGM7 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR 235.76 2.20E-24 1058200000 554520 569120 539180 590570 586760 743370 650990 601050 733290 742910 TRUE FALSE 532848.7453 552889.2548 636621.82 621049.3885 605633.6683 758401.4507 658957.0104 588638.1075 650049.9934 692592.044 0.769354413 0.798289931 0.919187313 0.896703036 0.874445027 1.095019005 0.951436009 0.849905962 0.9385756 1 19.40164629 4.369058196 1.14498104 0.941230547 0.728304448 0.486470692 0.06499357 0.880277253 1.489869041 0.021051034 0.194276492 23391.50668 -4.369058196 -0.2129261 VTAAMVLTSLST(ph)SPLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTAAMVLTSLSTSPLVR 17 0 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 VTAAMVLTSLS(0.002)T(0.922)S(0.076)PLVR 182.09 8.58E-09 220570000 242790 273470 288300 368030 306610 274830 320670 353760 335300 360570 TRUE FALSE 233301.4984 265670.9034 340402.2232 387024.0724 316472.3891 280387.2509 324594.4554 346454.7324 297238.1497 336148.2727 0.694043425 0.790338446 1.012654982 1.151349282 0.941466653 0.83411778 0.965628806 1.030660457 0.884247143 1 18.35873821 4.369417567 4.018260253 0.980149506 0.713754367 0.580231861 0.081626131 0.149839128 4.308846015 0.021456849 0.067471717 23410.87072 -4.369417567 -0.266395139 EDSGSSS(ph)PPGVFLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDSGSSSPPGVFLEK 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 EDSGS(0.001)S(0.004)S(0.995)PPGVFLEK;EDS(0.003)GS(0.016)S(0.081)S(0.899)PPGVFLEK 150.23 3.37E-06 314500000 648310 698740 652430 765400 698760 761460 760310 839360 839570 844170 TRUE FALSE 622973.3285 678812.6193 770338.6142 804902.3857 721236.25 776857.2429 769614.9012 822026.9227 744265.5334 786993.614 0.791586256 0.862538917 0.978837186 1.02275593 0.916444857 0.987120136 0.977917594 1.044515366 0.945707208 1 19.5859924 4.369642757 2.693640132 0.988531808 0.797441209 0.779890886 0.034325235 0.122531418 1.678456517 0.00891907 0.036157072 23423.01285 -4.369642757 -0.191090598 KLITSEEERS(ph)PAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLITSEEERSPAKR 14 3 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KLITSEEERS(1)PAKR 89.468 0.033914 343870000 189340 174130 109930 101540 136160 152730 135520 152450 169120 163120 TRUE FALSE 181940.3835 169163.9829 129796.7964 106780.4916 140539.7101 155818.3052 137178.5343 149301.8542 149922.2066 152071.7371 1.196411555 1.11239594 0.853523468 0.702171841 0.924167191 1.024636847 0.902064624 0.981785683 0.985865023 1 17.21439252 4.370413202 4.858114929 0.919908382 1.176747261 0.531078889 0.08870463 0.156135428 5.847595404 0.023580614 0.0694309 23464.60251 -4.370413202 0.256838879 S(ph)PIRQDR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPIRQDR 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR 118.03 0.003087 15540760000 1909780 1996330 1934921 2266290 2038170 2134340 2218790 2174620 2217260 2391930 TRUE FALSE 1835143.686 1939396.623 2284604.267 2383253.498 2103729.589 2177497.817 2245944.216 2129713.337 1965565.94 2229922.451 0.822963007 0.869714829 1.024521847 1.068760709 0.943409305 0.976490378 1.007184898 0.955061615 0.881450357 1 21.08856211 4.370440072 5.032532154 0.981617085 0.834054464 0.56875281 0.047914419 0.139102607 5.444869325 0.012196188 0.035590877 23466.05433 -4.370440072 -0.147562621 VGDQVWLFIDEPR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGDQVWLFIDEPR 13 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 193.73 3.76E-06 1132440000 648350 684190 647380 704530 719130 692350 766580 753470 845030 865780 FALSE TRUE 623011.7652 664677.5711 764375.9669 740890.8777 742261.4695 706349.7914 775961.6353 737910.5812 749105.7371 807139.9494 0.771875764 0.823497302 0.947017884 0.917921208 0.919619293 0.875126788 0.961371861 0.914228792 0.928098947 1 19.62245932 4.370873017 3.849358731 0.927654999 0.781501268 0.746884908 0.031905452 0.096264298 2.591217243 0.007359387 0.023637456 23489.45915 -4.370873017 -0.146153731 FQELIFEDFAR ddPTM_BT-474_Pertuzumab_2h_R1 6 FQELIFEDFAR 11 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;;;; 189.57 6.17E-06 784535000 797431 838441 679114 846878 839538 800911 893222 838016 862702 928096 FALSE TRUE 766266.5149 814529.4836 801845.0066 890585.4751 866542.5022 817105.9692 904153.518 820710.6768 764771.6857 865235.2313 0.885616405 0.941396575 0.926736427 1.029298673 1.001510885 0.944374362 1.044980007 0.948540521 0.883888748 1 19.72273289 4.371050604 1.653967178 0.977367381 0.888367276 0.268121508 0.045668674 0.711132955 3.084522245 0.012451282 0.081383872 23499.06615 -4.371050604 -0.089000105 HIAFT(ph)PESQR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIAFTPESQR 10 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 HIAFT(1)PESQR 102.73 0.016932 0 105700 116710 139280 145640 138530 158570 169640 92524 181680 178600 TRUE FALSE 101569.1271 113381.5451 164450.9943 153156.4979 142985.9433 161776.394 171716.1051 90613.34707 161056.4481 166503.2629 0.610012833 0.680956896 0.987674304 0.91984082 0.858757605 0.971610953 1.031307748 0.544213642 0.967287038 1 17.34519092 4.371079056 5.797229602 0.882805676 0.627667919 0.375907948 0.133830788 0.226246586 10.48977028 0.034997541 0.099392516 23500.60569 -4.371079056 -0.255137757 AALDGPLDAALDHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 AALDGPLDAALDHLR 15 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 0 ;;; 145.1 4.12E-06 332128000 164352 175372 153858 184648 182487 174597 202870 190019 199246 216197 FALSE TRUE 157928.9421 170370.5623 181663.5632 194177.7054 188356.8601 178127.471 205352.7837 186095.0412 176628.4294 201553.7846 0.783557314 0.845285851 0.901315564 0.963403916 0.934524055 0.883771403 1.018848563 0.923302143 0.876333976 1 17.62080535 4.371193006 1.693671905 0.940847664 0.775945286 0.600616582 0.042656068 0.332999268 1.533191467 0.011200911 0.071449286 23506.77257 -4.371193006 -0.164902378 RDS(ph)QDGSSYR ddPTM_BT-474_Pertuzumab_2h_R1 6 RDSQDGSSYR 10 1 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 RDS(0.947)QDGS(0.027)S(0.027)YR;RDS(0.999)QDGS(0.001)SYR;RDS(0.904)QDGS(0.048)S(0.048)YR;RDS(0.931)QDGS(0.01)S(0.059)YR;RDS(0.916)QDGS(0.069)S(0.015)YR;RDS(0.99)QDGS(0.005)S(0.005)YR 159.77 8.03E-06 52422293000 613735 655384 588610 730180 708453 661354 701446 737831 717283 738423 TRUE FALSE 589749.5577 636693.09 694984.9206 767864.6773 731241.0341 674727.031 710030.506 722594.532 635860.0409 688408.9525 0.856684904 0.924876249 1.009552415 1.115419366 1.062218949 0.9801253 1.031408007 1.049658825 0.923666142 1 19.39290633 4.371397408 2.703406579 1.029001764 0.864134621 0.554174863 0.048575444 0.198322481 2.736288904 0.012481382 0.050619078 23517.83873 -4.371397408 -0.164867144 GYDYGPHFQGILEASLEGDSGR ddPTM_BT-474_Pertuzumab_2h_R1 8 GYDYGPHFQGILEASLEGDSGR 22 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 314.48 2.63E-67 12189982000 2115623 2474609 2393064 3084524 2802768 2897316 3154658 2774810 3143068 3457813 FALSE TRUE 2032942.114 2404035.574 2825543.898 3243716.653 2892921.578 2955901.715 3193265.648 2717509.204 2786280.097 3223612.246 0.63064102 0.745758296 0.876514817 1.006236609 0.897416115 0.916953247 0.990586151 0.843001266 0.864334754 1 21.62024679 4.371453954 2.267020342 0.92283803 0.634461353 0.771715372 0.053627584 0.158461217 1.47721897 0.014129035 0.067040396 23520.90098 -4.371453954 -0.288376678 DPDQTDGLGLSYLSSHIANVER ddPTM_BT-474_Pertuzumab_2h_R1 8 DPDQTDGLGLSYLSSHIANVER 22 0 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;;;;;;; 321.58 1.07E-67 7900202000 1967970 2156028 2217358 2856523 2398329 2358627 2421486 2369608 2538611 2949785 FALSE TRUE 1891059.557 2094540.192 2618083.915 3003948.494 2475473.43 2406320.054 2451120.87 2320674.767 2250438.522 2749993.435 0.687659662 0.761652797 0.952032788 1.092347515 0.900174306 0.875027563 0.891318808 0.843883748 0.818343234 1 21.39099674 4.37152065 4.381449172 0.914089607 0.703893695 0.524958877 0.075908377 0.172141766 5.629127554 0.020413698 0.062115494 23524.51343 -4.37152065 -0.210195912 GISS(ph)LPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GISSLPR 7 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GIS(0.133)S(0.867)LPR 104.06 0.0086403 85203000 432040 399720 279660 331680 357300 304130 268510 423410 330650 314380 TRUE FALSE 415155.3992 388320.377 330200.783 348798.0445 368792.879 310279.717 271796.1057 414666.4355 293115.9982 293086.7626 1.416493176 1.324933182 1.126631514 1.190084607 1.258306161 1.058661654 0.927357153 1.414824852 1.000099751 1 18.16096828 4.371639317 3.258039587 1.144887079 1.404170977 0.345376166 0.136300088 0.285613622 5.745433154 0.034007123 0.120220953 23530.94221 -4.371639317 0.259283897 AHQITDESLESTRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHQITDESLESTRR 14 1 H3BM38;O00161;H3BNG6;H3BU94;H3BNE1;H3BR18;H3BPJ0;O00161-2 H3BM38 SNAP23 Synaptosomal-associated protein;Synaptosomal-associated protein 23 0 92.039 0.0033217 146640000 83511 93186 85380 120280 90944 109800 108300 95201 104380 119740 FALSE TRUE 80247.29779 90528.42652 100810.0653 126487.6652 93869.29635 112020.2312 109625.4078 93235.06608 92531.22 111629.9031 0.718869188 0.810969319 0.903074019 1.133098405 0.840897409 1.003496627 0.982043384 0.835215865 0.82891069 1 16.76836402 4.37165339 2.752681269 0.938165874 0.73098237 0.400304432 0.089959013 0.289205659 4.146280154 0.023320473 0.093243815 23531.70472 -4.37165339 -0.207183504 TQVLS(ph)PDSLFTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQVLSPDSLFTAK 13 0 P55196-5;P55196;J3KN01;A8MQ02;H0Y8L4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TQVLS(0.999)PDS(0.001)LFTAK;TQVLS(1)PDSLFTAK 209.13 4.23E-08 144676000 333960 336600 317710 317750 357120 357020 346420 381760 347170 368310 TRUE FALSE 320908.474 327000.4976 375127.2644 334149.1156 368607.0891 364239.189 350659.5916 373876.5226 307760.7171 343364.0356 0.9346013 0.952343471 1.092505986 0.973162827 1.073516883 1.060795981 1.021247292 1.088863375 0.896310286 1 18.38937941 4.371710803 7.675225417 1.032575211 0.939180788 0.245574777 0.057058895 0.249023854 15.86978132 0.012953097 0.03583053 23534.81578 -4.371710803 -0.093394423 S(ph)RTSPAPWK ddPTM_BT-474_Pertuzumab_2h_R1 6 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.333)RT(0.333)S(0.333)PAPWK;S(0.966)RT(0.034)SPAPWK;S(0.652)RT(0.204)S(0.144)PAPWK;S(0.478)RT(0.261)S(0.261)PAPWK;S(0.974)RT(0.023)S(0.003)PAPWK;S(0.891)RT(0.1)S(0.009)PAPWK 100.38 0.0047544 10752270000 5483000 6354710 6130120 7541130 7252490 7528300 8705320 6463500 9370810 9774860 TRUE FALSE 5268718.298 6173479.893 7237969.048 7930328.623 7485772.927 7680527.384 8811858.31 6330026.466 8307074.934 9112800.026 0.578166786 0.677451483 0.794264005 0.870240607 0.821456951 0.842828479 0.966975933 0.69463024 0.911583148 1 23.11946298 4.371894494 1.63595623 0.853997775 0.558946854 0.597407401 0.080369192 0.37483597 1.580204158 0.021357799 0.141497284 23544.77223 -4.371894494 -0.295050922 RRS(ph)PGLCSDSLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 RRSPGLCSDSLEK 13 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RRS(0.998)PGLCS(0.002)DSLEK;RRS(0.993)PGLCS(0.007)DSLEK;RRS(0.986)PGLCS(0.014)DSLEK 169.72 2.21E-05 2113400000 1363070 1269640 821787 822881 1092190 1223970 980340 1098680 1181920 1072830 TRUE FALSE 1309799.717 1233431.11 970302.1915 865349.987 1127321.283 1248719.512 992337.6942 1075991.874 1047753.397 1000166.269 1.309581975 1.233226064 0.970140888 0.86520613 1.127133876 1.248511924 0.992172727 1.075813 1.047579217 1 19.93180842 4.371929833 5.184111096 1.047142061 1.2912711 0.483342487 0.096358077 0.17115092 6.969298954 0.025039141 0.072609621 23546.68822 -4.371929833 0.24412904 S(ph)RS(ph)RDKEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSRDKEER 9 3 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 2 S(1)RS(1)RDKEER 68.972 0.081193 110830000 143260 116110 48022 44742 71925 84787 66297 59255 80045 53017 TRUE FALSE 137661.2408 112798.6565 56700.64364 47051.13998 74238.53295 86501.45123 67108.36252 58031.36354 70958.62718 49426.11137 2.785192624 2.282167327 1.147179943 0.951949054 1.502010393 1.750116464 1.35775121 1.174103362 1.435650615 1 15.59298579 4.37193198 3.823667994 1.304920221 2.690354953 0.8249277 0.233586758 0.085260546 2.272117937 0.06151136 0.198430943 23546.80459 -4.37193198 1.385434732 QELVDAFVEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 QELVDAFVEHR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;; 196.15 6.15E-08 1469210000 1042660 1066590 1027630 1054890 1122430 1178390 1155540 1122500 1168340 1322850 FALSE TRUE 1001911.694 1036171.898 1213345.601 1109332.999 1158533.98 1202217.853 1169681.844 1099319.983 1035714.941 1233252.191 0.812414283 0.840194654 0.983858459 0.899518369 0.939413681 0.974835368 0.948453084 0.891399172 0.839824124 1 20.23403642 4.372331572 6.360444493 0.929691428 0.819444326 0.474308969 0.045734974 0.168174358 8.702374933 0.011163576 0.031332855 23568.47985 -4.372331572 -0.110247102 GNSRPGT(ph)PSAEGGSTSSTLR ddPTM_BT-474_Pertuzumab_2h_R1 3 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 GNS(0.001)RPGT(0.956)PS(0.041)AEGGS(0.002)TSSTLR;GNSRPGT(1)PSAEGGSTSSTLR;GNSRPGT(0.968)PS(0.032)AEGGSTSSTLR 204.38 1.57E-21 3056760000 599070 775920 850890 1092360 926600 1074300 1160000 843710 1232000 1345360 TRUE FALSE 575657.6821 753791.5213 1004664.751 1148736.831 956404.9305 1096023.082 1174196.427 826287.0937 1092148.525 1254237.569 0.458970211 0.600995808 0.801016311 0.915884565 0.762538896 0.873856046 0.936183428 0.658796319 0.870766872 1 20.25837921 4.372734846 2.436258282 0.838252526 0.465591271 0.679653642 0.09095058 0.185799743 2.039315268 0.023393884 0.104090954 23590.3751 -4.372734846 -0.372661256 LVEDEER ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEDEER 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 152.39 0.004227 584360000 678730 756690 763160 855170 810680 880440 869930 916570 1006940 1007300 FALSE TRUE 652204.4812 735109.9421 901079.9884 899305.4262 836756.2584 898243.1 880576.4636 897642.5092 892636.3926 939074.6738 0.694518231 0.782802436 0.959540294 0.957650601 0.891043366 0.956519354 0.93770654 0.955879798 0.950548894 1 19.84088036 4.372870017 3.238550831 0.948073623 0.706802923 0.913230106 0.026748534 0.059322775 1.180071361 0.006533466 0.023230915 23597.71855 -4.372870017 -0.241270699 SPQLSLSPRPAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPQLSLSPRPASPK 14 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 SPQLSLS(0.001)PRPAS(0.999)PK;SPQLSLS(0.001)PRPAS(0.999)PK;SPQLSLS(0.001)PRPAS(0.999)PK 145.91 5.12E-06 1196020000 1244000 1103610 769420 717430 826750 974530 790320 956950 1032810 937100 TRUE FALSE 1195383.105 1072136.123 908471.3097 754456.6483 853343.1646 994235.6643 799992.1726 937188.6481 915569.7387 873629.3823 1.368295445 1.22722077 1.039881817 0.863588913 0.976779378 1.138051998 0.915711157 1.072753123 1.048007035 1 19.73666185 4.372984371 2.665825119 1.004730167 1.354773715 0.730210283 0.073360801 0.144611938 1.935190557 0.018993725 0.078169989 23603.93289 -4.372984371 0.350043549 YGGDEIPFS(ph)PYR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGGDEIPFSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 YGGDEIPFS(1)PYR 95.273 0.0064401 49171000 63490 64103 66534 71738 66813 69864 72392 69477 71403 74060 TRUE FALSE 61008.74061 62274.8452 78558.17384 75440.40678 68962.10082 71276.69795 73277.95495 68042.27567 63297.63079 69043.85023 0.883623095 0.901960783 1.137801174 1.092644841 0.998815978 1.03233956 1.061324864 0.985493646 0.916774348 1 16.0752253 4.373070526 9.417781496 1.028421125 0.888324234 0.469998769 0.057628387 0.228100878 18.46116714 0.014639333 0.040220751 23608.61589 -4.373070526 -0.140096891 KSDGACDSPSSDKENSSQIAQDHQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSDGACDSPSSDKENSSQIAQDHQK 25 2 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 0 81.949 0.012624 84133000 57951 53548 29174 35955 41205 36420 42974 50360 43394 37801 FALSE TRUE 55686.21085 52020.86347 34446.39077 37810.64186 42530.39625 37156.43735 43499.92867 49320.0484 38468.09504 35240.7046 1.580167351 1.476158438 0.977460331 1.072925252 1.20685431 1.054361364 1.234366031 1.399519362 1.091581326 1 15.10495515 4.373348984 6.166019953 1.160626847 1.554041323 0.626690005 0.122135794 0.137961184 6.917391118 0.032877549 0.092623367 23623.75793 -4.373348984 0.393414476 IQSSLSSAS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 IQSSLSSASPSK 12 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 IQSSLSSAS(0.999)PS(0.001)K;IQSSLSSAS(0.998)PS(0.001)K;IQSSLS(0.047)S(0.019)AS(0.809)PS(0.124)K;IQSSLSSAS(0.999)PS(0.001)K 194.67 1.29E-06 1080607000 1580170 1436820 1173320 1144310 1127230 1133480 1329900 1445680 1472360 1512660 TRUE FALSE 1518415.209 1395843.3 1385365.024 1203367.976 1163488.377 1156399.742 1346175.714 1415826.203 1305223.865 1410206.191 1.076732764 0.989815042 0.982384727 0.853327679 0.825048411 0.820021746 0.954594954 1.003985241 0.925555336 1 20.42747469 4.373603949 1.791322561 0.914535887 1.073591102 0.386759136 0.063672745 0.554684407 2.931955746 0.019506589 0.118058354 23637.63101 -4.373603949 0.159055215 WQRPS(ph)SPPPFLPAASEEAEPAEGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR 179.8 1.62E-17 5720500000 1863660 2023550 1882590 2324670 2112550 2250140 2100990 2422750 2224290 2456220 TRUE FALSE 1790826.107 1965840.335 2222815.891 2444646.497 2180502.089 2295639.372 2126702.544 2372719.366 1971797.924 2289858.032 0.782068618 0.858498784 0.970722141 1.067597407 0.952243353 1.00252476 0.928748645 1.036186232 0.861100512 1 21.12682673 4.373704449 2.860048372 0.982826725 0.790978829 0.586676085 0.054444479 0.167011009 2.593333248 0.012960359 0.050466373 23643.10161 -4.373704449 -0.191847895 VFLALVEEVEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFLALVEEVEDR 12 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ; 170.47 9.55E-05 231800000 115438 126407 112554 130738 150637 144943 127840 144144 146083 145361 FALSE TRUE 110926.5553 122801.9961 132895.0116 137485.4038 155482.3759 147873.8468 129404.5442 141167.376 129500.2703 135515.57 0.818552107 0.906183667 0.980662307 1.014535849 1.147339571 1.091194516 0.95490536 1.041705953 0.955611745 1 17.04809909 4.373819895 1.62356839 1.033573481 0.807286611 0.607087271 0.055104196 0.368233548 1.520030105 0.015843374 0.106311873 23649.38739 -4.373819895 -0.22628687 ISQRDPS(ph)PESNKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISQRDPSPESNKK 13 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 ISQRDPS(0.999)PES(0.001)NKK;ISQRDPS(0.992)PES(0.008)NKK 133.86 5.34E-05 474930000 1441310 1322540 813290 746770 1004710 1203290 958270 1190670 1387720 1068750 TRUE FALSE 1384982.012 1284822.454 960269.5945 785310.8892 1037027.41 1227621.348 969997.5949 1166082.248 1230191.843 996362.6106 1.390038122 1.289512915 0.96377522 0.788177799 1.040813253 1.232102987 0.973538734 1.170339228 1.234682866 1 19.92631136 4.374082074 5.049425687 1.055935579 1.366333206 0.450298076 0.129519901 0.183959587 7.288956336 0.034074046 0.099494712 23663.66857 -4.374082074 0.310397626 T(ph)SPENVQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 T(0.851)S(0.149)PENVQDR 174.23 0.00061294 325020000 242830 272410 285400 309000 318230 308540 314320 321420 412490 338680 TRUE FALSE 233339.9351 264641.1335 336978.1287 324947.527 328466.157 314778.8902 318166.7422 314782.5647 365665.8645 315740.9019 0.739023464 0.838159174 1.067261564 1.029158798 1.04030284 0.996953161 1.007683009 0.996964799 1.158120035 1 18.26838164 4.374275322 3.802686088 1.031931644 0.75711614 0.819835302 0.047414524 0.080872556 2.139872586 0.011530694 0.037392067 23674.20051 -4.374275322 -0.274815504 LVEPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVEPLR 6 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 106.29 0.075031 111790000 128350 148600 122110 178140 173550 165290 155800 148890 166660 155050 FALSE TRUE 123333.9401 144362.0735 144177.9933 187333.8267 179132.3934 168632.277 157706.727 145815.3695 147741.4555 144548.3254 0.853236727 0.99871149 0.997438005 1.295994445 1.239256096 1.166615224 1.091031159 1.00876554 1.022090398 1 17.14119237 4.374667792 1.952681164 1.114935962 0.864833578 0.400833278 0.097206591 0.454089512 2.964655621 0.028465113 0.157913809 23695.60446 -4.374667792 -0.250102384 YFQINQDEEEEEDED ddPTM_BT-474_Pertuzumab_2h_R1 12 YFQINQDEEEEEDED 15 0 P35268;K7ERI7 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;; 336.92 9.73E-69 4764983000 3799027 3946857 3461943 4011306 4193443 4470631 3875490 4300388 4045568 4077777 FALSE TRUE 3650556.825 3834296.503 4087593.111 4218329.983 4328328.902 4561030.222 3922919.406 4211583.485 3586332.081 3801585.532 0.96027218 1.00860456 1.075233761 1.109623853 1.138558864 1.199770513 1.03191665 1.107849199 0.94337798 1 21.85816982 4.374847074 2.504453519 1.087013768 0.963270268 0.221758901 0.069016944 0.404990326 4.72335709 0.017457686 0.076113673 23705.38833 -4.374847074 -0.123743499 VPPGYHPLDVEKEWGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VPPGYHPLDVEKEWGK 16 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 169.09 3.45E-09 410610000 848900 764970 518790 486830 600380 722800 601910 615630 767700 597610 FALSE TRUE 815724.0495 743153.8046 612546.8934 511955.3546 619691.768 737415.5112 609276.3546 602917.0254 680553.9145 557133.3424 1.464145093 1.333888583 1.099461918 0.918909919 1.112286271 1.323588906 1.09359162 1.082177245 1.221527887 1 19.08766313 4.374918696 3.395281441 1.108289124 1.442713301 0.569240971 0.104430567 0.169993252 3.695586989 0.027014545 0.093465811 23709.29804 -4.374918696 0.334424177 FLHKHDLDLICR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLHKHDLDLICR 12 1 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62136 PPP1CC;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 138.42 4.49E-05 329040000 483490 471140 287810 247540 306630 258560 287190 45297 364540 238060 FALSE TRUE 464594.6763 457703.5485 339823.6693 260315.5691 316493.0324 263788.2604 290704.7171 44361.60112 323158.9475 221935.9842 2.093372456 2.062322386 1.531178779 1.172930879 1.426055507 1.188578145 1.309858418 0.199884671 1.456090812 1 17.75978408 4.374934719 0.477841835 0.850428609 2.828417272 0.570277814 0.335143035 2.309559871 0.526062012 0.238050027 2.48779495 23710.17281 -4.374934719 1.977988663 ERDHSPT(ph)PSVFNSDEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.3)PT(0.7)PSVFNSDEER 226.75 2.89E-15 884020000 353960 365130 327960 373060 389080 391660 382220 363510 398340 419340 TRUE FALSE 340126.8519 354716.8499 387229.6674 392313.6713 401595.1116 399579.6335 386897.7227 356003.3915 353122.1132 390937.7283 0.87002821 0.907348726 0.990514958 1.003519596 1.027261076 1.02210558 0.989665859 0.910639638 0.903269466 1 18.5765793 4.3750834 3.824310054 0.978448178 0.877000717 0.46730271 0.040075231 0.220013336 5.87990185 0.011626311 0.037626735 23718.29135 -4.3750834 -0.101447461 ISDYFEYQGGNGSS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 4 ISDYFEYQGGNGSSPVR 17 0 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 ISDYFEYQGGNGSS(1)PVR;ISDYFEYQGGNGS(0.334)S(0.666)PVR;ISDYFEYQGGNGS(0.007)S(0.993)PVR;ISDYFEYQGGNGS(0.002)S(0.998)PVR 453.07 6.01E-183 1934670000 1238030 1322770 1123930 1385830 1309490 1400950 1480290 1449090 1373000 1568250 TRUE FALSE 1189646.419 1285045.895 1327049.153 1457352.852 1351610.935 1429278.169 1498406.232 1419165.785 1217142.796 1462031.031 0.81369437 0.878945705 0.907675094 0.99680022 0.924474862 0.977597697 1.02487991 0.970681029 0.832501343 1 20.4795425 4.37514557 1.419330632 0.963704296 0.801808594 0.4595577 0.051133297 0.576419041 1.684660309 0.014346669 0.110715702 23721.68692 -4.37514557 -0.161895702 RPAEATSS(ph)PT(ph)SPERPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.145)S(0.165)S(0.69)PT(0.856)S(0.143)PERPR;RPAEAT(0.109)S(0.147)S(0.75)PT(0.65)S(0.344)PERPR;RPAEAT(0.135)S(0.233)S(0.63)PT(0.503)S(0.499)PERPR 73.21 0.039402 1224530000 514490 556330 455190 593020 558580 604700 568500 583560 579550 586360 TRUE FALSE 494383.162 540464.0131 537452.9586 623625.8333 576547.233 616927.4483 575457.4731 571509.2821 513761.9137 546645.3149 0.904394767 0.988692299 0.983184057 1.140823522 1.054700767 1.1285699 1.052707226 1.045484643 0.939845087 1 19.06024553 4.375154341 1.739783171 1.054986496 0.907409754 0.369630704 0.057080341 0.491616929 2.412754527 0.015302601 0.095858001 23722.16603 -4.375154341 -0.147576742 FVDESHNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVDESHNLR 9 0 O43422;O43422-2 O43422 PRKRIR 52 kDa repressor of the inhibitor of the protein kinase 0 132.01 0.0013159 0 113460 119420 111710 123240 131830 129290 126630 132820 127970 143260 FALSE TRUE 109025.8578 116014.2585 131898.482 129600.4312 136070.4317 131904.3324 128179.7358 130077.2206 113443.3821 133556.8726 0.816325328 0.868650608 0.987582888 0.970376355 1.01882014 0.987626693 0.959738974 0.97394629 0.849401307 1 17.02709469 4.375158656 3.76655638 0.969770319 0.82574471 0.583111875 0.043456246 0.143532227 3.741240632 0.010653081 0.034749185 23722.4017 -4.375158656 -0.144025609 APQTSS(ph)SPPPVRR ddPTM_BT-474_Pertuzumab_2h_R1 1 APQTSSSPPPVRR 13 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.013)S(0.074)S(0.457)S(0.457)PPPVRR 63.682 0.041163 4297400000 210990 195050 109230 134580 141920 184740 142820 145730 183870 166180 TRUE FALSE 202744.2775 189487.365 128970.2908 141525.6899 146484.9857 188475.5694 144567.8739 142720.6246 162997.8484 154924.4806 1.308665208 1.223095048 0.832471991 0.913514051 0.945525104 1.216564152 0.933150612 0.921227065 1.052111634 1 17.24120561 4.375302657 6.060627713 0.97469272 1.287375078 0.588185175 0.097714369 0.129382006 6.409045663 0.024607809 0.069500496 23730.26875 -4.375302657 0.312682358 S(ph)FEERVETTVTSLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SFEERVETTVTSLK 14 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 S(1)FEERVETTVTSLK;S(1)FEERVETTVTSLK;S(1)FEERVETTVTSLK;S(1)FEERVETTVTSLK 180.31 1.07E-06 318168000 455060 414130 135409 167117 353193 322320 243629 266310 348239 236568 TRUE FALSE 437275.7521 402319.4179 159880.4185 175741.9284 364553.7736 328837.5312 246610.6046 260810.6054 308708.3687 220545.0386 1.982705006 1.824205252 0.72493319 0.796852786 1.652967466 1.491022121 1.118187043 1.182572988 1.399752044 1 17.75071378 4.375679621 7.410891175 1.190143171 1.942240918 0.531193788 0.276400092 0.164982071 10.33249719 0.070808678 0.196290226 23750.87537 -4.375679621 0.752097747 SPS(ph)VPKSPTPKS(ph)PPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSVPKSPTPKSPPSR 16 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 2 S(0.369)PS(0.466)VPKS(0.165)PT(0.192)PKS(0.474)PPS(0.334)R 52.541 0.085204 158720000 447680 393830 202290 201820 320460 341410 292900 251510 346460 224620 TRUE FALSE 430184.1707 382598.354 238848.3029 212235.9544 330767.8869 348313.5441 296484.5978 246316.2306 307131.3133 209406.2873 2.054303986 1.8270624 1.140597572 1.013512808 1.579550887 1.66333852 1.415834269 1.176259957 1.466676656 1 17.67594523 4.375824443 4.828484031 1.324321292 2.002461405 0.582288442 0.21746386 0.13944382 5.240272407 0.055748708 0.164838102 23758.79679 -4.375824443 0.678140113 ILVDVEKVDWDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILVDVEKVDWDK 12 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 161.63 5.91E-05 1131830000 1505060 1377840 881570 804820 1050890 1292380 1061370 1268560 1308010 1115640 FALSE TRUE 1446240.591 1338545.352 1040889.309 846356.8566 1084692.831 1318512.809 1074359.364 1242363.793 1159530.188 1040076.709 1.390513391 1.286967914 1.000781289 0.813744649 1.042896953 1.267707273 1.03296166 1.194492466 1.114850644 1 19.98825851 4.375827808 4.627053256 1.069357386 1.367295829 0.487647573 0.116317513 0.180486449 6.408894317 0.031187454 0.0934064 23758.98089 -4.375827808 0.297938444 LLGSLDEVVLLSPVPELRDS(ph)SK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLGSLDEVVLLSPVPELRDSSK 22 1 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 LLGSLDEVVLLS(0.001)PVPELRDS(0.796)S(0.203)K 78.991 0.0048988 93942000 86275 75833 52317 43941 55589 59926 53544 77444 63325 63390 TRUE FALSE 82903.27762 73670.31709 61771.84569 46208.80028 57377.07067 61137.74478 54199.28749 75844.75434 56136.61148 59096.53884 1.402844892 1.246609675 1.045270111 0.781920586 0.97090408 1.034540194 0.917131334 1.283404339 0.949913693 1 15.85078602 4.375839851 2.825411942 1.009312036 1.384015753 0.56133531 0.119296498 0.222545422 3.367582716 0.033235307 0.131174032 23759.63974 -4.375839851 0.374703717 FLSHS(ph)TDSLNK ddPTM_BT-474_Pertuzumab_2h_R1 3 FLSHSTDSLNK 11 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36 Q12802-2 AKAP13 A-kinase anchor protein 13 1 FLS(0.002)HS(0.997)T(0.001)DSLNK;FLS(0.002)HS(0.998)T(0.001)DSLNK;FLS(0.228)HS(0.764)T(0.008)DSLNK 176.91 5.29E-06 754124000 1685930 1569000 1259160 1331360 1275300 1375510 1332500 1677700 1533080 1373880 TRUE FALSE 1620041.992 1524253.656 1486718.222 1400071.649 1316321.183 1403323.755 1348807.534 1643054.909 1359051.186 1280825.884 1.264841703 1.190055319 1.16074967 1.093100684 1.027712821 1.095639753 1.053076418 1.282808951 1.061074111 1 20.28864294 4.375852697 1.618911926 1.106867747 1.26946217 0.361233824 0.074184015 0.713084402 2.916599701 0.021858977 0.147876582 23760.34253 -4.375852697 0.162594423 SDGAHFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDGAHFQK 8 0 Q9BW83-2;Q9BW83;B1AH58;F5GZ09 Q9BW83-2 IFT27 Intraflagellar transport protein 27 homolog 0 ; 87.323 0.015406 412810000 489160 521380 452330 549860 575950 520980 555540 530080 597910 638600 FALSE TRUE 470043.0864 506510.7529 534076.093 578238.3405 594475.9548 531514.5726 562338.8647 519133.6628 530037.7634 595347.0532 0.789527863 0.85078233 0.897083626 0.971262623 0.998536823 0.892781059 0.944556392 0.871984937 0.890300474 1 19.1833714 4.376068252 2.070553615 0.930447441 0.790778881 0.556760148 0.042732514 0.310964762 2.335721952 0.011802735 0.061880864 23772.1385 -4.376068252 -0.13966856 EDAMAMVDHCLKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDAMAMVDHCLKK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 218.95 1.51E-11 1913920000 3881200 3636500 2625500 2573800 3064300 3544700 2999500 3180000 4067000 3264400 FALSE TRUE 3729518.413 3532790.581 3099986.254 2706634.126 3162865.992 3616376.263 3036208.778 3114331.889 3605331.21 3043299.28 1.225485261 1.160842315 1.018626815 0.889374944 1.039288516 1.188307797 0.997670127 1.023340658 1.184678495 1 21.53720479 4.376083797 4.019710545 1.040088936 1.212401983 0.350168952 0.083780811 0.229051256 6.63481748 0.021254486 0.067228778 23772.98939 -4.376083797 0.172313047 DFIEDYVDILR ddPTM_BT-474_Pertuzumab_2h_R1 6 DFIEDYVDILR 11 0 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 ;;;;; 190.24 5.49E-06 302744500 465788 519391 426672 563204 548094 532367 537493 576462 564374 607379 FALSE TRUE 447584.49 504578.4772 503781.1217 592271.0259 565723.9413 543131.8255 544071.0001 564557.8583 500308.6296 566240.6793 0.790449196 0.891102486 0.88969433 1.045970464 0.999087423 0.95918899 0.960847604 0.997028082 0.883561792 1 19.11105587 4.376196634 1.568784009 0.976517314 0.788164123 0.62487392 0.044513007 0.353932703 1.335825759 0.011959405 0.083653217 23779.16685 -4.376196634 -0.18835319 TSPADGKPRLS(ph)LHEEEGSSGSEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPADGKPRLSLHEEEGSSGSEQK 24 2 Q12955;A0A087WY90;H0Y951;A0A087WX55;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 TSPADGKPRLS(0.999)LHEEEGSSGSEQK 218.16 6.22E-33 207590000 188710 165280 98352 85655 127780 167410 106370 115690 159810 113790 TRUE FALSE 181335.0046 160566.3762 116126.3942 90075.66481 131890.1597 170795.1449 107671.7879 113300.9611 141669.0388 106082.9019 1.709370702 1.513593362 1.094675882 0.849106342 1.243274433 1.610015768 1.014977776 1.068041682 1.335455914 1 16.69483262 4.376621943 3.854859449 1.151823327 1.671923782 0.4689136 0.199946431 0.189460476 5.13712653 0.051619446 0.16666423 23802.46543 -4.376621943 0.520100455 SGAQASSTPLS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 8 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SGAQASSTPLS(0.972)PT(0.028)R;SGAQASSTPLS(1)PTR;SGAQASSTPLS(0.713)PT(0.287)R;SGAQASSTPLS(0.878)PT(0.122)R;SGAQASSTPLS(0.868)PT(0.131)R;SGAQASSTPLS(0.99)PT(0.01)R;SGAQAS(0.003)S(0.002)T(0.003)PLS(0.824)PT(0.169)R;SGAQAS(0.007)S(0.004)T(0.015)PLS(0.79)PT(0.184)R 248.41 6.38E-18 29866930000 5611533 5812827 5111918 5963273 6056656 5348555 6631119 6219784 5955329 6619136 TRUE FALSE 5392228.086 5647050.865 6035755.297 6271038.234 6251473.841 5456706.447 6712272.618 6091343.287 5279305.019 6170816.023 0.873827394 0.915122221 0.978112988 1.016241322 1.013070851 0.884276314 1.087744731 0.987121195 0.855527859 1 22.55702985 4.376646758 2.847388513 0.983038201 0.878322834 0.228901793 0.062733809 0.369557181 5.682773464 0.015538428 0.061044878 23803.8255 -4.376646758 -0.104715367 AQPFGFIDS(ph)DTDAEEERIPATPVVIPMK ddPTM_BT-474_Pertuzumab_2h_R1 8 AQPFGFIDSDTDAEEERIPATPVVIPMK 28 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.999)DT(0.001)DAEEERIPATPVVIPMK;AQPFGFIDS(0.984)DT(0.016)DAEEERIPATPVVIPMK;AQPFGFIDS(0.992)DT(0.008)DAEEERIPATPVVIPMK;AQPFGFIDS(0.957)DT(0.043)DAEEERIPATPVVIPMK;AQPFGFIDS(1)DTDAEEERIPATPVVIPMK;AQPFGFIDS(0.995)DT(0.005)DAEEERIPATPVVIPMK;AQPFGFIDS(0.994)DT(0.006)DAEEERIPATPVVIPMK;AQPFGFIDS(0.839)DT(0.161)DAEEERIPATPVVIPMK 296.41 1.51E-71 4102739000 1050049 1163530 1051888 1348272 1257351 1412621 1553460 1582719 1710596 1532523 TRUE FALSE 1009011.924 1130347.264 1241987.561 1417856.479 1297794.837 1441185.164 1572471.708 1550035.3 1516416.313 1428723.852 0.706232994 0.791158671 0.869298541 0.992393651 0.908359467 1.008721988 1.100612764 1.084908954 1.061378174 1 20.44629566 4.376859194 0.533489792 1.073771046 0.541663657 0.877895505 0.043347013 0.936058933 0.267858804 0.026935734 0.296597581 23815.47206 -4.376859194 -0.532107389 GHTDTEGRPPS(ph)PPPTS(ph)TPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GHTDTEGRPPSPPPTSTPEK 20 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 2 GHT(0.002)DT(0.039)EGRPPS(0.956)PPPT(0.154)S(0.52)T(0.329)PEK;GHTDTEGRPPS(1)PPPT(0.136)S(0.612)T(0.252)PEK;GHTDT(0.003)EGRPPS(0.993)PPPT(0.123)S(0.539)T(0.342)PEK 127.38 3.61E-06 1527600000 1148580 1084380 867950 928570 930110 1006890 1054690 880620 1120100 1154600 TRUE FALSE 1103692.224 1053454.544 1024807.872 976493.609 960027.8329 1027250.006 1067597.612 862434.8893 992950.9438 1076397.914 1.025357082 0.978685048 0.952071589 0.907186456 0.891889348 0.954340391 0.991824304 0.801223115 0.922475723 1 20.03778007 4.377424148 1.355006615 0.91294691 1.036625035 0.246228027 0.053740284 0.904100624 2.339400192 0.01591743 0.129232295 23846.47266 -4.377424148 0.123678125 EKLDQLKQEFEFWYPVDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKLDQLKQEFEFWYPVDLR 19 2 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 133.09 6.96E-06 140190000 400480 372020 230100 219320 319460 329680 273240 330620 387280 316660 FALSE TRUE 384828.7988 361410.3538 271684.1885 230639.1315 329735.721 336346.3555 276583.9929 323792.5815 343317.598 295212.3361 1.303566117 1.224238657 0.920300934 0.781265222 1.116944249 1.139337061 0.936898493 1.096812503 1.162951395 1 18.17139348 4.377498863 5.605647955 1.022199927 1.284283503 0.439317364 0.111836681 0.180485891 8.221618224 0.028858942 0.082533022 23850.57553 -4.377498863 0.262083575 T(ph)SSEEEDSRREEPSLLLVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSEEEDSRREEPSLLLVLK 20 2 A0A087WZV0;O43314-2;O43314;D6RBU4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 T(0.333)S(0.333)S(0.333)EEEDSRREEPSLLLVLK 163.64 9.20E-10 49537000 105020 96521 62210 62641 87911 90570 73658 78425 88681 78938 TRUE FALSE 100915.7023 93768.31558 73452.73085 65873.90952 90738.73715 92401.38745 74559.44864 76805.49634 78614.30466 73591.45895 1.371296394 1.274173891 0.998114889 0.895129822 1.233006363 1.255599342 1.01315356 1.043674055 1.068253107 1 16.16725072 4.377598327 4.693982821 1.068355824 1.34955046 0.509973831 0.103259912 0.164688843 5.986970874 0.027056322 0.080748925 23856.0385 -4.377598327 0.281194636 AGFDSDYDQALADIR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGFDSDYDQALADIR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 ;;; 329.49 1.85E-68 642712000 583150 634370 589090 700980 699790 683990 694800 712450 731620 822180 FALSE TRUE 560359.8533 616278.3887 695551.6672 737157.6618 722299.3809 697820.7464 703303.1702 697737.6585 648569.5648 766493.0163 0.731069744 0.804023488 0.907446842 0.961727825 0.942343068 0.910407181 0.917559789 0.910298781 0.846151956 1 19.54791312 4.377625835 2.534268935 0.923024071 0.735576643 0.747429486 0.037727213 0.14314191 1.711832666 0.009446577 0.040993181 23857.54955 -4.377625835 -0.187447428 LEYDDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEYDDLR 7 0 P15924 P15924 DSP Desmoplakin 0 ; 94.539 0.032864 974170000 1811300 1921910 1904360 2303700 2017210 1825520 2157200 2228600 2298600 2250800 FALSE TRUE 1740512.394 1867099.009 2248520.214 2422594.233 2082095.392 1862433.265 2183600.459 2182578.631 2037672.565 2098351.311 0.829466631 0.889793334 1.071565187 1.154522706 0.992253004 0.887569806 1.040626728 1.040139761 0.971082656 1 21.00082481 4.377638046 4.882761036 1.021907877 0.843299745 0.494977099 0.065715719 0.163005983 6.245617908 0.017259347 0.05091783 23858.22038 -4.377638046 -0.178608132 LALLHEGTGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LALLHEGTGPR 11 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 157.38 0.00040201 151660000 252872 268607 230907 291459 288401 287892 273605 266902 295661 312671 FALSE TRUE 242989.4827 260946.5914 272637.0314 306501.2339 297677.6801 293713.3735 276953.4598 261390.3804 262098.8028 291493.5147 0.833601677 0.895205479 0.935310797 1.051485603 1.021215448 1.007615466 0.950118771 0.896727945 0.899158265 1 18.15310426 4.377720279 2.310955045 0.968909639 0.838541683 0.466770046 0.048090222 0.355381643 3.450120981 0.014552191 0.068750627 23862.73834 -4.377720279 -0.130367956 S(ph)VS(ph)PCSNVESR ddPTM_BT-474_Pertuzumab_2h_R1 7 SVSPCSNVESR 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)VS(1)PCSNVESR;S(1)VS(1)PCSNVESR;S(1)VS(0.999)PCS(0.001)NVESR;S(1)VS(0.999)PCS(0.001)NVESR;S(1)VS(0.924)PCS(0.076)NVESR;S(1)VS(0.954)PCS(0.046)NVESR;S(1)VS(1)PCSNVESR 192.91 1.73E-06 12329150000 4129513 4181868 3454804 4109747 3912589 4161392 4109155 4206296 4693787 4256263 TRUE FALSE 3968127.067 4062605.219 4079163.934 4321851.535 4038440.979 4245538.197 4159444.068 4119434.518 4160967.978 3967982.516 1.000036429 1.023846552 1.028019634 1.089181093 1.017756747 1.069948817 1.048251612 1.038168515 1.048635663 1 21.91997424 4.377859817 2.103070697 1.046023797 1.001966385 0.238721269 0.023778696 0.466372539 3.630905236 0.005689252 0.029488071 23870.40661 -4.377859817 -0.044057413 QRMREEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QRMREEKR 8 3 Q9BZI7-2;Q9BZI7 Q9BZI7-2 UPF3B Regulator of nonsense transcripts 3B 0 48.561 0.087532 2369900000 1764200 1676600 1212400 1403200 1426200 1454200 1434600 1515500 1773400 1656600 FALSE TRUE 1695253.114 1628785.01 1431507.65 1475619.32 1472075.018 1483604.92 1452157.064 1484204.395 1572091.067 1544397.006 1.097679616 1.054641393 0.926903927 0.955466317 0.953171375 0.960637009 0.940274462 0.96102517 1.017931957 1 20.55861223 4.377886566 4.75322771 0.961190263 1.088070877 0.755108112 0.025834572 0.082752377 3.061752661 0.00616617 0.018335266 23871.8769 -4.377886566 0.126880614 SRT(ph)SPAPWK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.165)RT(0.417)S(0.417)PAPWK 71.085 0.081771 4291200000 1931600 2289800 2356700 2762300 2783000 2928800 3307300 2456800 3474100 3615100 TRUE FALSE 1856110.937 2224497.146 2782608.115 2904862.634 2872517.722 2988022.343 3347775.727 2406066.221 3079734.733 3370246.057 0.550734547 0.660039982 0.825639454 0.861914111 0.852316915 0.886588781 0.993332733 0.713914112 0.913801153 1 21.68442249 4.378220124 1.722473056 0.873751161 0.528270739 0.689250906 0.076334981 0.287880464 1.374073387 0.020538715 0.13101963 23890.21863 -4.378220124 -0.345480422 KLS(ph)PTKEAFGEQPLQLTTKPDLLAWDPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSPTKEAFGEQPLQLTTKPDLLAWDPAR 29 3 O00257 O00257 CBX4 E3 SUMO-protein ligase CBX4 1 KLS(0.937)PT(0.063)KEAFGEQPLQLTTKPDLLAWDPAR 133.36 5.28E-05 509980000 308920 276690 177620 142380 222630 259720 184350 250930 278720 212940 TRUE FALSE 296847.0649 268799.0721 209719.8851 149728.2489 229791.0961 264971.7163 186606.1304 245748.2078 247080.8741 198517.3841 1.495320252 1.354032914 1.056430831 0.754232429 1.15753639 1.334753213 0.939998939 1.237917822 1.244630918 1 17.59890582 4.378454576 3.947532739 1.098085532 1.467333754 0.419619699 0.160378217 0.209309616 5.909651546 0.041157441 0.131594737 23903.11915 -4.378454576 0.369248222 AMKPPGGESSNLFGS(ph)PEEATPSSRPNR ddPTM_BT-474_Pertuzumab_2h_R1 4 AMKPPGGESSNLFGSPEEATPSSRPNR 27 2 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BMM8;B4E1P3 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR 274.96 3.85E-61 2084980000 994720 1054400 1144800 1084080 1149440 1188500 1291010 1228900 1319300 1395440 TRUE FALSE 955845.2427 1024329.544 1351690.826 1140029.499 1186412.781 1212532.284 1306809.767 1203522.786 1169538.595 1300925.606 0.734742431 0.787385182 1.039022385 0.876321823 0.911975886 0.932053515 1.004523057 0.925128063 0.899004977 1 20.31110703 4.378599112 6.283174526 0.943102353 0.747808001 0.70072316 0.049355456 0.097209827 5.104192996 0.011543102 0.03247124 23911.07557 -4.378599112 -0.195294352 ESIESEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESIESEIR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 150.35 0.0011413 1726100000 1717800 1944900 1820900 2373100 2208900 1992700 2157500 2341800 2321200 2462500 FALSE TRUE 1650666.477 1889433.356 2149977.136 2495575.975 2279951.275 2032993.759 2183904.13 2293441.012 2057707.107 2295712.682 0.71902137 0.823026928 0.936518386 1.087059367 0.993134417 0.885561062 0.951296801 0.999010473 0.896326062 1 21.13051066 4.37875607 2.489824469 0.972868807 0.726967455 0.698280956 0.054340227 0.170601802 1.960441239 0.014439873 0.06381086 23919.71882 -4.37875607 -0.245901352 EIVLADVIDNDSWR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIVLADVIDNDSWR 14 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 322.77 5.58E-56 2027980000 1147500 1232790 1092740 1297430 1344460 1307620 1339830 1368210 1385500 1442580 FALSE TRUE 1102654.431 1197632.036 1290222.426 1364390.518 1387705.777 1334060.972 1356227.24 1339955.985 1228223.848 1344872.772 0.819894978 0.890516978 0.959363929 1.014512708 1.031849113 0.991960727 1.008442783 0.996344051 0.913263971 1 20.35903827 4.378851756 1.869209842 0.995923677 0.81512711 0.781635376 0.02992024 0.190870621 1.115975142 0.008053086 0.04722888 23924.98953 -4.378851756 -0.180796567 QSS(ph)PSGSEQLVR ddPTM_BT-474_Pertuzumab_2h_R1 5 QSSPSGSEQLVR 12 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 QSS(0.998)PS(0.002)GSEQLVR;QSS(0.999)PS(0.001)GSEQLVR;QSS(0.999)PS(0.001)GS(0.001)EQLVR;QS(0.003)S(0.997)PSGSEQLVR;QS(0.003)S(0.997)PSGSEQLVR 274.68 8.79E-28 3725360000 2233280 2466310 2203570 2733240 2588340 2718440 2815140 2874060 2816060 2963820 TRUE FALSE 2146000.949 2395973.254 2601804.117 2874302.844 2671596.307 2773408.719 2849592.525 2814709.657 2496392.675 2763077.832 0.776670467 0.867139255 0.941632584 1.040254028 0.966891441 1.003738906 1.031310987 1.018686345 0.903482575 1 21.39784477 4.379315438 1.713378912 0.998661822 0.766637617 0.779286392 0.037596791 0.2101255 0.988701648 0.009965614 0.064103275 23950.54709 -4.379315438 -0.232024204 WDPTANEDPEWILVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 WDPTANEDPEWILVEK 16 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ; 132.08 9.55E-05 295300000 139876 149609 146089 143092 165082 177802 165044 177246 171511 173408 FALSE TRUE 134409.4913 145342.2978 172490.532 150476.9953 170392.0125 181397.2783 167063.8578 173585.8082 152041.7903 161662.9217 0.831418175 0.899045349 1.066976461 0.9308071 1.053995627 1.122071013 1.033408626 1.073751522 0.940486468 1 17.3026293 4.379446732 3.909356484 1.033471535 0.843620795 0.577613443 0.056497022 0.139053899 3.869928898 0.013969198 0.044922148 23957.7888 -4.379446732 -0.18985074 KETQS(ph)PEQVKSEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KETQSPEQVKSEK 13 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 KET(0.001)QS(0.999)PEQVKSEK;KET(0.005)QS(0.995)PEQVKSEK;KET(0.006)QS(0.994)PEQVKSEK 205.18 3.75E-08 1373190000 2371390 2002480 995350 773740 1348820 1714070 1194160 1416550 1789970 1217290 TRUE FALSE 2278713.457 1945371.231 1175231.886 813672.8141 1392206.02 1748729.67 1208774.487 1387297.747 1586780.11 1134841.864 2.007956817 1.714222301 1.035590882 0.716992244 1.226784158 1.540945682 1.065147952 1.222459086 1.398238962 1 20.11405985 4.379764371 4.098826847 1.159681142 1.94897108 0.6430787 0.215928528 0.130491206 3.916551979 0.056212123 0.176845153 23975.31774 -4.379764371 0.789289938 AHMGMFTELAILYSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHMGMFTELAILYSK 15 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;A0A087WV74;A0A087WXH4;P53675;P53675-2 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 114.56 0.00059634 780380000 1153430 1203050 1102940 1267430 1291820 1399730 1519610 688650 1647120 1681790 FALSE TRUE 1108352.68 1168740.192 1302265.793 1332842.214 1333372.564 1428033.5 1538207.442 674429.1368 1460145.843 1567880.865 0.706911287 0.745426657 0.830589761 0.850091511 0.85042977 0.910804852 0.981074185 0.430153306 0.931286219 1 20.58038451 4.379771564 3.892209064 0.816964018 0.714175036 0.066168351 0.153133387 0.743814446 20.56155604 0.040336553 0.130042085 23975.71479 -4.379771564 -0.102788982 ISDEDWDIIHR ddPTM_BT-474_Pertuzumab_2h_R1 6 ISDEDWDIIHR 11 0 P51659-3;P51659;P51659-2;A0A2R8YD50;E7ER27;A0A2R8YDT8;A0A2R8YF45 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ;;;;; 240.1 1.14E-15 9475000000 4743170 5521530 4573110 6457180 5494850 5911210 6483730 6005210 6568020 7157220 FALSE TRUE 4557801.673 5364061.371 5399572.705 6790435.834 5671596.841 6030738.716 6563079.827 5881200.315 5822445.905 6672455.114 0.683077157 0.803911196 0.809233275 1.017681755 0.850001498 0.903826045 0.98360794 0.881414744 0.872609228 1 22.66978626 4.379908173 1.439278968 0.920968544 0.670913584 0.631481996 0.059227177 0.407122775 1.227581372 0.015838481 0.122035612 23983.25767 -4.379908173 -0.250054959 DIQHWESLKPEER ddPTM_BT-474_Pertuzumab_2h_R1 4 DIQHWESLKPEER 13 1 P31350;P31350-2;A0A286YFD6;C9JXC1 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 0 ;;; 158.81 2.57E-05 1717950000 3733210 3423420 2418870 3014300 2648960 1745270 3091470 2829950 2753860 3517970 FALSE TRUE 3587312.026 3325787.413 2856013.616 3169868.384 2734166.204 1780560.555 3129304.335 2771510.544 2441253.358 3279694.758 1.093794481 1.014053947 0.870816898 0.966513233 0.833664839 0.542904351 0.954144994 0.845051368 0.744353831 1 21.64513012 4.379946539 0.970957332 0.820502895 1.157096466 0.337884934 0.122359146 1.359965194 1.50440546 0.040052303 0.426152496 23985.37643 -4.379946539 0.336593571 GT(ph)PS(ph)QSPVVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 GT(0.999)PS(0.634)QS(0.367)PVVGR;GT(1)PS(0.761)QS(0.239)PVVGR 130.1 0.0012267 769660000 504579 537349 537154 563454 531281 556349 604334 708928 594186 643771 TRUE FALSE 484859.4948 522024.3326 634229.6767 592533.9285 548370.1359 567598.758 611730.0203 694288.3891 526736.4963 600167.8168 0.8078732 0.869797277 1.056753893 0.98728041 0.913694671 0.945733413 1.019264951 1.156823758 0.877648687 1 19.19500643 4.379960808 4.828371823 1.004288857 0.821727258 0.419503933 0.073965205 0.182487985 6.935665938 0.019718329 0.058425645 23986.16453 -4.379960808 -0.1825616 EGGDGEEQDVGDAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGGDGEEQDVGDAGR 15 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 363.85 1.20E-84 594250000 710120 742710 643190 751160 768110 744850 772440 809750 881850 881860 FALSE TRUE 682367.7253 721528.638 759428.7407 789927.4576 792816.9557 759911.3773 781893.3518 793028.3795 781746.085 822130.8367 0.829998943 0.877632374 0.923732217 0.960829375 0.96434402 0.924319273 0.951057079 0.964601185 0.95087795 1 19.64900848 4.380193208 1.466807287 0.957268075 0.817640701 0.851631387 0.017941597 0.21637228 0.68480395 0.004838964 0.036613953 23999.00346 -4.380193208 -0.139627374 GRSPGQLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GRSPGQLQR 9 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7;Q9C040;Q9C040-2 O75382 TRIM3;TRIM2 Tripartite motif-containing protein 3;Tripartite motif-containing protein 2 0 62.582 0.074488 433450000 116720 120540 121210 120570 146750 137440 120470 132780 126530 149300 FALSE TRUE 112158.4534 117102.3172 143115.3433 126792.6321 151470.347 140219.131 121944.3479 130038.0466 112166.8449 139187.778 0.805806767 0.841326149 1.028217745 0.910946593 1.088244594 1.007409795 0.876113906 0.934263399 0.805867056 1 17.08667301 4.380251409 6.656317853 0.953415503 0.814679015 0.327128448 0.076757586 0.228262536 12.96897071 0.019031376 0.053217384 24002.21984 -4.380251409 -0.138736488 EFHLNESGDPSSK ddPTM_BT-474_Pertuzumab_2h_R1 10 EFHLNESGDPSSK 13 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;;;;;; 191.63 3.40E-06 1.03144E+11 57557700 57849300 49654800 54810900 56303100 58362400 58451500 55122000 67818600 64543100 FALSE TRUE 55308281.45 56199494.6 58628526.93 57639697.12 58114140.34 59542527.72 59166846.94 53983711.44 60120116.85 60171538.35 0.91917679 0.933987997 0.974356457 0.957922943 0.965807788 0.989546376 0.98330288 0.897163558 0.999145418 1 25.84257791 4.380436533 4.471546115 0.964361934 0.922307643 0.261084906 0.028564719 0.304866836 10.43082451 0.007346923 0.022327286 24012.45326 -4.380436533 -0.042054291 SQSFNTDTTTSGISSMSSS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSFNTDTTTSGISSMSSSPSR 22 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 SQSFNTDTTTSGISSMSS(0.023)S(0.756)PS(0.221)R 428.5 1.24E-174 212400000 145200 169610 152530 215010 178610 187050 205530 194730 189560 212360 TRUE FALSE 139525.4235 164772.8889 180095.564 226106.6919 184355.1529 190832.2792 208045.3376 190708.7575 168041.9435 197976.668 0.704756903 0.832284382 0.909680751 1.142087571 0.931196361 0.963912975 1.05085786 0.963289055 0.848796705 1 17.59497089 4.380498931 2.133461197 0.984823701 0.710220899 0.591461034 0.073938929 0.246669656 1.983290864 0.019048636 0.097926986 24015.90354 -4.380498931 -0.274602802 LYIWSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LYIWSGR 7 0 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 0 ; 101.69 0.02763 231000000 927880 677620 775290 475670 671420 611900 622760 434770 703140 561810 FALSE TRUE 891617.4238 658294.9411 915402.1492 500219.3857 693016.8341 624273.0372 630381.5232 425791.8476 623322.495 523758.1083 1.702345815 1.256868258 1.747757476 0.955058027 1.323162015 1.191910974 1.203573774 0.812955143 1.190096125 1 18.99854115 4.380557033 0.373409617 0.968311398 1.97847255 0.481403247 0.204453413 3.796049008 0.516049704 0.178988719 1.692601281 24019.11672 -4.380557033 1.010161151 GHYTIGK ddPTM_BT-474_Pertuzumab_2h_R1 6 GHYTIGK 7 0 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;;;; 123.96 0.0041931 43651900000 58355900 66152500 64385000 80526600 71297500 77791300 83460200 64961000 87029500 94379500 FALSE TRUE 56075286.91 64265895.47 76020801.74 84682587.48 73590848.84 79364293.39 84481610.89 63619532.65 77150276.02 87987092.4 0.637312649 0.7304014 0.863999476 0.962443299 0.836382324 0.901999273 0.960159139 0.72305529 0.876836294 1 26.39078856 4.380703926 2.756048122 0.878413848 0.646287572 0.56349489 0.074377228 0.217226397 3.115304235 0.01946964 0.079133523 24027.24221 -4.380703926 -0.232126276 ESPFS(ph)TSASPLLSGSQHFDVPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESPFSTSASPLLSGSQHFDVPPR 23 0 O14980 O14980 XPO1 Exportin-1 1 ES(0.009)PFS(0.435)T(0.435)S(0.06)AS(0.06)PLLSGSQHFDVPPR 116.35 0.00031216 524450000 214320 241620 238120 309530 284150 302300 305450 237590 260440 280540 TRUE FALSE 205944.1375 234729.2342 281153.581 325504.8804 293289.9428 308412.7131 309188.1885 232683.6835 230875.9431 261538.7759 0.78743252 0.897493052 1.074997694 1.244575988 1.121401375 1.179223662 1.182188711 0.889671838 0.882759898 1 17.99666533 4.380710557 3.227958866 1.075852468 0.803942587 0.405779092 0.114429503 0.261400893 5.176061242 0.032209063 0.116181169 24027.60904 -4.380710557 -0.271909882 TQTGDSSS(ph)ISSFSYR ddPTM_BT-474_Pertuzumab_2h_R1 5 TQTGDSSSISSFSYR 15 0 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 TQTGDSS(0.021)S(0.979)ISSFSYR;TQTGDSS(0.006)S(0.994)ISSFSYR;TQTGDS(0.186)S(0.186)S(0.628)ISSFSYR;TQTGDS(0.001)S(0.015)S(0.983)IS(0.001)SFSYR;TQTGDS(0.019)S(0.218)S(0.761)IS(0.002)SFSYR 379.06 4.47E-98 2460820000 2321670 2241110 1731021 1804010 1922474 1946118 1388612 2202970 1922420 1875098 TRUE FALSE 2230936.57 2177195.737 2043855.001 1897115.172 1984312.122 1985469.839 1405606.249 2157477.9 1704194.941 1748095.942 1.276209455 1.245466959 1.16918926 1.085246597 1.135127698 1.135789971 0.804078435 1.234187351 0.974886389 1 20.73735294 4.380803152 0.552096173 1.035929667 1.398515365 0.411284002 0.105928084 3.006426397 0.921687214 0.059383592 0.667364858 24032.73248 -4.380803152 0.362585698 DTTKLEPAS(ph)PPEDTSAEVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTTKLEPASPPEDTSAEVSR 20 1 E9PFE2;Q9UHL9-2;Q9UHL9;Q9UHL9-3 E9PFE2 GTF2IRD1 General transcription factor II-I repeat domain-containing protein 1 1 DTTKLEPAS(1)PPEDTSAEVSR 89.829 0.0012253 145590000 196270 174700 104490 98631 139550 169920 124050 136140 153390 126330 TRUE FALSE 188599.5514 169717.727 123373.6674 103721.3577 144038.7525 173355.8988 125568.161 133328.6614 135977.8103 117773.5566 1.60137434 1.441051217 1.047549815 0.880684601 1.223014373 1.471942462 1.066182976 1.132076379 1.154569958 1 16.84565612 4.381447769 4.299938986 1.131865357 1.568005162 0.54626863 0.148105833 0.157256966 5.092720727 0.038532412 0.118955919 24068.43038 -4.381447769 0.436139805 LEAAHTLEDCASR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEAAHTLEDCASR 13 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ;; 218.5 2.40E-11 1296290000 610570 686650 580750 769900 737920 735380 737840 729160 783970 858270 FALSE TRUE 586708.2494 667067.4143 685704.4437 809634.6313 761655.867 750249.8874 746869.9066 714102.5912 694977.0123 800138.6084 0.733258267 0.833689822 0.856982073 1.011867972 0.951904906 0.937649902 0.933425657 0.892473609 0.868570776 1 19.60989041 4.38157388 1.729018256 0.93388618 0.73154015 0.682844145 0.044628505 0.296953545 1.426580004 0.012400343 0.079461193 24075.42044 -4.38157388 -0.20234603 DCGVGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCGVGFR 7 0 E9PPJ5;E9PLM6;P21741 E9PPJ5 MDK Midkine 0 ; 114.54 0.013684 1530490000 601550 643590 614400 679220 770300 707840 752520 853820 774220 768190 FALSE TRUE 578040.761 625235.4433 725435.7473 714274.6256 795077.3991 722153.0098 761729.5649 836188.3186 686333.7914 716159.8071 0.80713935 0.873039002 1.012952333 0.997367653 1.110195506 1.008368527 1.063630711 1.167600179 0.958352849 1 19.44992203 4.381649355 1.161752356 1.064650981 0.753380239 0.650043797 0.05903128 0.509968799 0.884651256 0.017739343 0.166895713 24079.60482 -4.381649355 -0.311270742 SLS(ph)YS(ph)PVER ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 SLS(0.959)Y(0.074)S(0.967)PVER;S(0.006)LS(0.985)Y(0.024)S(0.985)PVER;SLS(0.993)Y(0.086)S(0.921)PVER 138.45 0.00019924 2267840000 2061060 2187560 1886610 2302430 2212430 2379880 2258700 2328230 2457810 2481250 TRUE FALSE 1980511.497 2125172.931 2227562.394 2421258.688 2283594.82 2428002.804 2286342.646 2280151.237 2178809.713 2313192.727 0.856180928 0.91871849 0.962981756 1.046717232 0.987204738 1.049632733 0.988392631 0.985716067 0.941905829 1 21.14145404 4.381658984 1.9523457 0.999368938 0.855285254 0.700716321 0.030109164 0.225324551 1.462310629 0.008036358 0.045355846 24080.13869 -4.381658984 -0.144083684 S(ph)PTPPPSSKPSSIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTPPPSSKPSSIPR 15 1 B4E2D5;R4GND2;F6S7C4;Q8NEM7-2;Q8NEM7;Q8NEM7-3;H7C5F9 B4E2D5 SUPT20H Transcription factor SPT20 homolog 1 S(0.617)PT(0.383)PPPSSKPSSIPR;S(0.595)PT(0.405)PPPSSKPSSIPR 103.17 0.00090455 1251460000 1412200 1458740 1308730 1486790 1552810 1533840 1478050 1529190 1635600 1560850 TRUE FALSE 1357009.663 1417138.163 1545246.624 1563523.41 1602757.544 1564855.296 1496138.818 1497611.692 1449933.545 1455132.239 0.932567932 0.973889606 1.061928656 1.07448888 1.10145147 1.075404182 1.028180654 1.029192847 0.996427339 1 20.47271884 4.381965028 3.757796174 1.048868662 0.939951241 0.578883757 0.032295807 0.15489325 4.048622082 0.008680175 0.028570617 24097.11379 -4.381965028 -0.108917421 YLDPEYIDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YLDPEYIDR 9 0 X6RA56;X6RLR1;O75935-2;O75935;X6RCK5;A0A0A0MRV8;O75935-3 X6RA56 DCTN3 Dynactin subunit 3 0 ;; 187.78 9.34E-05 864140000 1514180 1640890 1472640 1853410 1728990 1708170 1844190 1811050 1750780 1973970 FALSE TRUE 1455004.172 1594093.424 1738778.807 1949064.712 1784604.534 1742710.368 1866759.749 1773651.185 1552038.794 1840271.254 0.790646579 0.866227422 0.944849192 1.059118164 0.969750807 0.946985595 1.014393799 0.963798778 0.843375014 1 20.811487 4.381968552 2.462531391 0.972308383 0.796092299 0.5507207 0.052749412 0.226727065 2.537914053 0.013512159 0.060727917 24097.30929 -4.381968552 -0.176216084 VEAVNMAEGIIHDTETK ddPTM_BT-474_Pertuzumab_2h_R1 5 VEAVNMAEGIIHDTETK 17 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;; 253.48 5.17E-27 507919000 586019 793178 595803 1200249 545064 691392 1145283 1035546 958261 824467 FALSE TRUE 563116.7296 770557.34 703477.8557 1262193.995 562596.4786 705372.4199 1159299.316 1014161.613 849483.2286 768625.1157 0.732628583 1.002513871 0.915241828 1.642145135 0.731951724 0.917706702 1.508276652 1.319448965 1.105198375 1 19.55192059 4.382135421 1.629186496 1.186341329 0.737134404 0.187201069 0.265082461 0.870559084 3.59689114 0.0735297 0.502160236 24106.56998 -4.382135421 -0.449206925 S(ph)KEKTDGGESSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKEKTDGGESSK 12 2 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 1 S(0.974)KEKT(0.026)DGGESSK 61.165 0.045284 49528000 149820 119080 46988 33017 66484 83437 60758 73893 86586 59877 TRUE FALSE 143964.8688 115683.955 55479.77684 34721.01133 68622.51824 85124.15331 61501.57458 72367.08373 76757.12028 55821.47746 2.579022902 2.072391493 0.993878689 0.622000938 1.229321067 1.524935512 1.10175469 1.296402156 1.375046376 1 15.76853269 4.38226666 3.828011735 1.157779326 2.48562486 0.802566093 0.239828147 0.092764603 2.502663702 0.064246683 0.209467664 24113.8558 -4.38226666 1.327845534 up DVLEVLDDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVLEVLDDSR 10 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ; 128.27 0.00077717 54516000 88679 97114 88552 108788 100852 93798 110410 120445 112454 114367 FALSE TRUE 85213.32664 94344.4038 104555.3162 114402.5617 104095.9962 95694.65983 111761.2306 117957.7687 99688.69337 106620.8212 0.799218442 0.884859099 0.980627564 1.072985186 0.976319587 0.897523192 1.04821206 1.106329583 0.934983357 1 16.70212967 4.382520332 2.214226341 1.013294836 0.800154386 0.559688131 0.059073973 0.264368877 2.317017384 0.016612594 0.082699977 24127.94488 -4.382520332 -0.21314045 ALEENNNFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEENNNFSK 10 0 E5RGX5;Q93045;Q93045-2 E5RGX5 STMN2 Stathmin;Stathmin-2 0 ; 240.38 6.59E-12 566430000 372710 389280 370750 384220 393840 422300 413320 444770 475050 432000 FALSE TRUE 358144.0811 378178.1155 437752.7723 404049.6402 406508.2213 430839.1953 418378.3338 435585.3441 421124.3156 402740.2552 0.889268149 0.939012454 1.086935727 1.00325119 1.009355822 1.069769386 1.038829192 1.081554025 1.045647437 1 18.61949016 4.38275307 4.804210012 1.044744593 0.900252804 0.748362503 0.030127298 0.086818826 3.306506236 0.007432146 0.022087554 24140.87848 -4.38275307 -0.144491789 AS(ph)SPIKQSHEPVPDTSVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSPIKQSHEPVPDTSVEK 19 1 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 AS(0.498)S(0.498)PIKQS(0.003)HEPVPDTSVEK;AS(0.5)S(0.5)PIKQS(0.001)HEPVPDTSVEK 157.3 4.46E-09 1035490000 1013350 912400 599170 541950 696280 831620 728980 784980 886390 744650 TRUE FALSE 973747.1617 886379.2453 707453.3475 569920.1044 718676.4785 848435.9262 737901.4753 768769.8887 785770.7233 694214.1922 1.402660984 1.276809456 1.019070707 0.82095715 1.035237376 1.222152955 1.062930553 1.107395811 1.131885133 1 19.40502133 4.38276404 3.844203531 1.055033562 1.378969677 0.589810232 0.098850083 0.157641741 4.285908828 0.026717747 0.086967057 24141.4883 -4.38276404 0.323936115 GAEDDRGPWR ddPTM_BT-474_Pertuzumab_2h_R1 3 GAEDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 87.298 0.01183 2007350000 2261470 2626600 2515040 3387880 3011240 3136860 3134870 2898350 2965430 3411840 FALSE TRUE 2173089.252 2551691.94 2969563.675 3562728.893 3108099.269 3200289.458 3173235.477 2838498.06 2628806.818 3180753.038 0.683199615 0.802228878 0.933603973 1.120089756 0.977158312 1.006142074 0.997636547 0.892398129 0.826473098 1 21.60093693 4.382776276 2.576806196 0.971221402 0.693567865 0.628521161 0.072792166 0.20237749 2.505797449 0.02004864 0.086658383 24142.16849 -4.382776276 -0.277653537 VDEDEEALKQLAEWVS ddPTM_BT-474_Pertuzumab_2h_R1 1 VDEDEEALKQLAEWVS 16 1 Q9BY43;Q9BY43-2;H0YIN6 Q9BY43 CHMP4A Charged multivesicular body protein 4a 0 138.02 7.23E-05 36665000 116310 107230 68937 61741 86041 95326 82181 100510 116450 88279 FALSE TRUE 111764.4766 104171.9054 81395.4494 64927.46041 88808.58691 97253.55703 83186.75566 98434.43338 103231.0842 82299.7847 1.358016634 1.265761578 0.989011693 0.788914098 1.079086503 1.181698803 1.010777318 1.196047277 1.254329942 1 16.32860104 4.382928965 4.983939695 1.069148037 1.336880816 0.394332977 0.125423028 0.207722098 8.321068892 0.033377477 0.09816775 24150.65784 -4.382928965 0.267732779 S(ph)PESDRPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPESDRPR 8 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 S(1)PESDRPR;S(1)PESDRPR;S(1)PESDRPR 144.28 0.00035606 1011660000 173606 200013 220293 241111 224414 226327 263462 266833 235541 263418 TRUE FALSE 166821.2856 194308.8251 260104.8455 253554.7676 231632.4801 230903.487 266686.3268 261322.8053 208803.3731 245576.4642 0.67930486 0.791235535 1.059160316 1.032488062 0.943219379 0.940250882 1.085960447 1.064119911 0.850258081 1 17.90581278 4.38295678 4.109583847 1.004012152 0.701221751 0.707750231 0.068596471 0.104942468 3.18035262 0.017392716 0.054816301 24152.20467 -4.38295678 -0.302790402 LGDDEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGDDEVR 7 0 Q14444-2;Q14444;G3V153;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 125.62 0.0093781 1013260000 1756410 1905340 1845210 2095400 2115280 2213200 2065800 2123900 2164800 2400100 FALSE TRUE 1687767.555 1851001.569 2178680.493 2203543.845 2183319.902 2257952.42 2091081.878 2080040.723 1919060.98 2237539.089 0.754296344 0.827248819 0.973694942 0.98480686 0.975768384 1.009123117 0.934545407 0.929610898 0.857665901 1 21.09348146 4.383370752 3.513196155 0.956418346 0.765964942 0.726935763 0.041989349 0.118705322 2.759336694 0.01102614 0.03779658 24175.23766 -4.383370752 -0.190453404 FSS(ph)PTEELDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSSPTEELDYR 11 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 FS(0.099)S(0.897)PT(0.004)EELDYR;FS(0.021)S(0.976)PT(0.002)EELDYR 102.4 0.0022643 287360000 419210 439780 378530 469570 445270 459890 473850 472490 434030 452400 TRUE FALSE 402826.8097 427237.905 446938.7914 493804.564 459592.5139 469189.2909 479649.118 462732.9164 384760.734 421758.545 0.955112385 1.012991699 1.05970299 1.170822903 1.089705281 1.112459478 1.137259988 1.097151254 0.91227727 1 18.68605777 4.383631292 2.421623132 1.086210301 0.959810659 0.209811424 0.069780892 0.421852339 4.542806252 0.017624138 0.080732251 24189.7451 -4.383631292 -0.126399642 TIISYIDEQFER ddPTM_BT-474_Pertuzumab_2h_R1 5 TIISYIDEQFER 12 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310;C9IZU3;C9JQJ4 Q15019-2 2-Sep Septin-2 0 ;;;; 261.41 5.39E-21 1099731600 616871 656028 562413.2 683726 744712 659522 669467 720356 674145 693431 FALSE TRUE 592762.9993 637318.7238 664053.7761 719013.1808 768666.3378 672857.9867 677660.1374 705480.3969 597618.8858 646464.3007 0.916930755 0.985852928 1.027208734 1.112224109 1.189031377 1.040827755 1.048256086 1.091290573 0.924442208 1 19.30221118 4.38379479 2.047696751 1.066690509 0.918684499 0.299037189 0.066407392 0.447459904 3.253990722 0.01749163 0.094475983 24198.8535 -4.38379479 -0.148006011 VVTTNYKPVANHQYNIEYER ddPTM_BT-474_Pertuzumab_2h_R1 1 VVTTNYKPVANHQYNIEYER 20 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 0 142.98 1.04E-07 657490000 199760 228990 185130 204380 231990 227270 171740 228070 238100 248930 FALSE TRUE 191953.1584 222459.4294 218587.1092 214928.0763 239452.169 231865.5551 173841.8055 223360.2748 211071.8862 232069.7494 0.82713563 0.958588657 0.941902638 0.926135685 1.031811211 0.999120117 0.749092917 0.962470444 0.909519172 1 17.82419895 4.383872694 0.00499885 1.839827522 6.59E-08 0.042597035 0.079368273 143380.3568 124.936855 22251.05724 23747.13437 24203.1947 -4.383872694 -1.839827456 ADEGISFR ddPTM_BT-474_Pertuzumab_2h_R1 6 ADEGISFR 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;; 164.72 0.00076407 18723720000 5581250 5789030 5051140 5793950 5868010 5985090 6082320 6343450 6440130 6296680 FALSE TRUE 5363128.58 5623932.532 5963993.36 6092976.454 6056759.871 6106112.621 6156757.252 6212455.541 5709073.442 5870200.255 0.913619357 0.958047816 1.015977837 1.037950358 1.031780792 1.040188129 1.04881554 1.058303852 0.972551735 1 22.48497829 4.384008871 1.916040785 1.033329689 0.909228425 0.703338222 0.024040354 0.20923138 1.294452311 0.006226933 0.036044902 24210.78501 -4.384008871 -0.124101265 LAPGGHVGR ddPTM_BT-474_Pertuzumab_2h_R1 8 LAPGGHVGR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;;;;;; 172.14 5.64E-05 11736660000 10848080 11747340 10645330 12869960 12368690 13297630 12782570 12760760 13477800 14110990 FALSE TRUE 10424125.04 11412317.37 12569177.94 13534180.18 12766540.15 13566517.19 12939006.92 12497245.85 11947856.65 13155240.08 0.792393372 0.867511144 0.955450289 1.028805259 0.970452844 1.031263368 0.983562963 0.949982347 0.908220342 1 23.64913424 4.384048251 2.302341393 0.980404894 0.794384967 0.765201693 0.034353565 0.162432213 1.557572874 0.009358166 0.045007356 24212.98042 -4.384048251 -0.186019927 GYNHGQGSYSYSNSYNS(ph)PGGGGGSDYNYESK ddPTM_BT-474_Pertuzumab_2h_R1 4 GYNHGQGSYSYSNSYNSPGGGGGSDYNYESK 31 0 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK;GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK;GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK;GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK 368.28 3.70E-137 3953210000 1137246 1235783 1160227 1391875 1205316 1315541 1412592 1426738 1462831 1570730 TRUE FALSE 1092801.169 1200539.679 1369905.828 1463709.836 1244086.084 1342142.14 1429879.723 1397275.362 1296776.558 1464343.058 0.746274012 0.81984865 0.935508808 0.999567572 0.849586493 0.916548983 0.976464986 0.954199464 0.885568822 1 20.48182215 4.38406811 2.905554214 0.939491404 0.754197469 0.669185565 0.045412618 0.15093798 2.418782064 0.011392559 0.044663259 24214.08762 -4.38406811 -0.185293935 SSS(ph)VGSSSSYPIS(ph)PAVSR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 S(0.263)S(0.327)S(0.408)VGS(0.011)S(0.002)S(0.004)S(0.003)YPIS(0.982)PAVSR;S(0.013)S(0.02)S(0.967)VGSSSSYPIS(1)PAVSR;S(0.079)S(0.124)S(0.797)VGSSSSYPIS(1)PAVSR;S(0.005)S(0.009)S(0.985)VGSSSSYPIS(1)PAVSR;S(0.257)S(0.327)S(0.416)VGSSSSYPIS(1)PAVSR 253.21 2.46E-30 2381240000 2102075 2324543 2021105 2498092 2586107 2608784 2518067 2566334 2495929 2755921 TRUE FALSE 2019923.585 2258249.31 2386363.633 2627018.827 2669291.48 2661535.4 2548883.857 2513338.306 2212601.604 2569260.016 0.786188853 0.878949307 0.928813595 1.022480719 1.038933959 1.03591516 0.99206925 0.978234313 0.861182438 1 21.29292147 4.384133464 1.676127046 0.991337744 0.778887751 0.638771909 0.048745483 0.332409565 1.473135855 0.013822576 0.092109182 24217.73174 -4.384133464 -0.212449993 GEEDPEEEHELPVDMETINLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEEDPEEEHELPVDMETINLDR 22 0 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C003;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 128.55 1.65E-05 206800000 84495 105710 122510 154040 124910 133910 129710 123010 169510 187430 FALSE TRUE 81192.84199 102695.2543 144650.2822 161990.0229 128927.8436 136617.7519 131297.4298 120469.8005 150267.9354 174735.1992 0.4646622 0.587719331 0.827825664 0.927060052 0.737847006 0.781855932 0.751408019 0.689442088 0.859975186 1 17.41481073 4.384185972 3.58164869 0.800716872 0.485348705 0.639119263 0.089699164 0.143924324 3.46664418 0.022488826 0.076282221 24220.65993 -4.384185972 -0.315368167 ERSLS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSLSR 6 1 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 ERS(0.014)LS(0.986)R 125.49 0.047087 144890000 183630 276210 267980 399460 347350 424600 457680 319550 412330 439070 TRUE FALSE 176453.5366 268332.7612 316409.9472 420076.1785 358522.8282 433185.7029 463281.2247 312951.1808 365524.027 409331.3978 0.431077453 0.655539161 0.772992125 1.026249588 0.875874243 1.058276265 1.131799875 0.76454233 0.89297823 1 18.64290981 4.384283653 1.401229149 0.954866329 0.383528361 0.742912461 0.101941091 0.362238751 1.014950848 0.030595908 0.244774984 24226.10821 -4.384283653 -0.571337968 down KGESGQSWPR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGESGQSWPR 10 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;; 140.24 6.36E-05 12340500000 7897000 8032800 7262100 7710800 7846200 8071200 8129400 8889100 9065100 9055400 FALSE TRUE 7588376.509 7803712.409 8574523.015 8108755.312 8098580.149 8234405.194 8228890.029 8705536.979 8036067.852 8442069.692 0.898876317 0.924383794 1.015689674 0.960517457 0.959312164 0.975401234 0.974747938 1.03120885 0.95190731 1 23.00916531 4.384315677 5.479297085 0.984558558 0.904877451 0.590241426 0.024333438 0.126000341 5.753881515 0.006166492 0.017747441 24227.89469 -4.384315677 -0.079681107 EIAEEYGGVMVSFPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIAEEYGGVMVSFPR 15 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C2D1 Q00341 HDLBP Vigilin 0 ; 204.48 4.27E-11 0 35371 38965 36483 43005 40290 50104 43591 49126 37816 45685 FALSE TRUE 33988.66222 37853.75635 43076.28966 45224.4932 41585.96444 51117.13721 44124.4797 48111.53093 33523.28622 42590.71426 0.798029871 0.888779562 1.011400969 1.061839276 0.976409181 1.200194411 1.036011733 1.129624891 0.78710317 1 15.3782513 4.384319961 1.966792282 1.044246035 0.790054335 0.344456304 0.102398812 0.409331303 2.698825413 0.025911342 0.146075586 24228.13365 -4.384319961 -0.2541917 AIVAIENPADVSVISSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIVAIENPADVSVISSR 17 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 179.02 2.18E-09 82272000 81233 90672 84072 99469 105275 107840 94752 116098 97254 107032 FALSE TRUE 78058.32455 88086.12334 99265.68057 104602.607 108661.266 110020.5987 95911.60332 113700.5357 86214.13364 99782.62731 0.782283717 0.882780156 0.994819271 1.048304798 1.088979805 1.102602744 0.961205431 1.139482281 0.864019479 1 16.60650104 4.384397678 1.816271735 1.042201361 0.771233306 0.53414273 0.074631082 0.313245411 1.697588234 0.018779367 0.115085499 24232.46969 -4.384397678 -0.270968055 SS(ph)LETLEDIEENAPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLETLEDIEENAPLR 16 0 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.206)S(0.794)LETLEDIEENAPLR 104.94 0.0013871 201790000 439190 403780 269140 270230 319030 348900 296150 373850 439960 368000 TRUE FALSE 422025.9692 392264.5897 317779.585 284176.6027 329291.8897 355954.9971 299774.3723 366129.8669 390017.5853 343075.0322 1.230127318 1.143378424 0.926268469 0.828322017 0.959824699 1.037542705 0.873786618 1.067200561 1.136828824 1 18.38816461 4.38459418 4.41214369 0.976915806 1.21185747 0.49237804 0.086231587 0.167569233 5.681891465 0.022476061 0.068857648 24243.43644 -4.38459418 0.234941663 EVYPEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVYPEAR 7 0 O00422;O00422-2;H7BZW6;U3KPY7 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ; 107.32 0.017459 619570000 837900 901540 763720 939400 926220 1017320 934380 963520 945300 1031190 FALSE TRUE 805153.9417 875828.9619 901741.1929 987882.5466 956012.7075 1037890.907 945815.2219 943622.9753 837993.507 961346.5828 0.837527231 0.911043923 0.937998022 1.027602911 0.994451662 1.079621986 0.983844161 0.981563769 0.871687196 1 19.87469712 4.384711566 1.615325533 0.992471001 0.831879289 0.48478314 0.049892757 0.469599823 1.893877241 0.013919739 0.096549199 24249.99015 -4.384711566 -0.160591713 TIPIDGDFFSYTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TIPIDGDFFSYTR 13 0 P05091;P05091-2;F8VP50 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 155 0.00010812 382630000 780140 855090 739060 982230 753450 869440 992350 1033700 958800 919860 FALSE TRUE 749651.2663 830703.6704 872624.5823 1032923.008 777685.4035 887020.6725 1004494.676 1012353.734 849961.0436 857557.0629 0.87417071 0.968686174 1.017570282 1.204494783 0.906861406 1.034357608 1.171344415 1.180508887 0.991142258 1 19.70987315 4.384946809 1.884192914 1.082304079 0.872002958 0.302438384 0.090966767 0.511115169 3.032047278 0.025102042 0.148219053 24263.12912 -4.384946809 -0.21030112 YEDRYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YEDRYDR 7 1 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 188.76 0.00051523 2860400000 2516000 2730900 2596600 3007900 2874000 2906400 2993600 3180300 3300400 3398400 FALSE TRUE 2417671.938 2653017.406 3065863.381 3163138.079 2966444.82 2965169.399 3030236.572 3114625.694 2925752.428 3168223.341 0.763100223 0.837383328 0.967691684 0.998394917 0.936311775 0.935909208 0.956446641 0.983082743 0.92346786 1 21.59524261 4.385268897 3.097614077 0.962596463 0.772249134 0.872736954 0.025492828 0.07777971 1.421197581 0.006430829 0.024066484 24281.13018 -4.385268897 -0.190347329 KS(ph)PVGMLDLSSWSSPEVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPVGMLDLSSWSSPEVLR 19 1 O95613-2;O95613 O95613-2 PCNT Pericentrin 1 KS(1)PVGMLDLSSWSSPEVLR;KS(1)PVGMLDLSSWSSPEVLR 140.57 1.06E-07 353240000 184497 188232 191498 176626 217565 220960 183969 200471 236810 228832 TRUE FALSE 177286.6533 182863.8077 226105.9484 185741.689 224563.1758 225427.9626 186220.4677 196331.2038 209928.3216 213333.0048 0.831032467 0.857175418 1.059873265 0.870665508 1.052641508 1.056695202 0.872909786 0.920303935 0.984040523 1 17.70274766 4.385462697 8.309518272 0.967929606 0.837604224 0.379718664 0.067537212 0.244289376 19.09235247 0.016639077 0.045887967 24291.9678 -4.385462697 -0.130325381 GSLAEAVGS(ph)PPPAATPTPTPPTR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSLAEAVGSPPPAATPTPTPPTR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 GSLAEAVGS(1)PPPAATPTPTPPTR;GSLAEAVGS(1)PPPAATPTPTPPTR;GSLAEAVGS(1)PPPAATPTPTPPTR 258.81 1.22E-43 1004357000 512626 626049 637046 852960 893770 896470 752617 671731 639580 733800 TRUE FALSE 492592.0092 608194.6955 752174.3832 896981.3678 922518.9238 914597.2376 761827.752 657859.5201 566977.5597 684099.0724 0.720059461 0.88904476 1.099510895 1.311186353 1.348516554 1.336936819 1.113621963 0.961643637 0.828794516 1 19.38384575 4.385527428 2.682797231 1.137500572 0.735775901 0.404533869 0.161676765 0.312030339 4.216726934 0.046713211 0.196082158 24295.58875 -4.385527428 -0.401724671 KLGAGEGGEASVS(ph)PEKTSTTSK ddPTM_BT-474_Pertuzumab_2h_R1 3 KLGAGEGGEASVSPEKTSTTSK 22 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KLGAGEGGEAS(0.018)VS(0.981)PEKT(0.001)S(0.001)TTSK;KLGAGEGGEAS(0.006)VS(0.994)PEKTSTTSK;KLGAGEGGEAS(0.165)VS(0.833)PEKT(0.001)S(0.001)TTSK 187.26 1.52E-17 1142170000 1972820 1668770 1003740 737090 1169750 1443100 1119530 1297490 1524450 1121410 TRUE FALSE 1895720.013 1621178.313 1185138.146 775131.3032 1207376.071 1472280.471 1133231.143 1270696.378 1351400.827 1045455.902 1.813295051 1.550690288 1.13360893 0.74142898 1.154879961 1.408266449 1.083958817 1.215447133 1.292642592 1 19.99570078 4.385716224 3.209562941 1.134756661 1.775325434 0.645034532 0.169142024 0.154934664 3.038417752 0.044602167 0.162839039 24306.15282 -4.385716224 0.640568773 VELFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 VELFFK 6 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 101.52 0.084748 84179000 218080 242430 251120 307690 270220 243080 306830 276990 272490 324400 FALSE TRUE 209557.1925 235516.1338 296502.9701 323569.9178 278911.8717 247995.2441 310585.0773 271270.0597 241558.0776 302428.0991 0.692915748 0.778750832 0.98040814 1.069906926 0.922241923 0.820013897 1.026971628 0.896973729 0.798728949 1 18.20623266 4.385843464 4.225828413 0.937628222 0.710302653 0.507831621 0.081868238 0.162416896 5.173020449 0.020588112 0.064262953 24313.2751 -4.385843464 -0.227325569 ALLGPAPEDEDERPEAEDGPGAGDHALGLPAEVVEPEGPVAQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALLGPAPEDEDERPEAEDGPGAGDHALGLPAEVVEPEGPVAQR 43 1 A0A1B0GUA3;Q96EK5;A0A1B0GUH6;A0A1B0GTE6;A0A0D9SFK7;A0A1B0GU96;A0A1B0GVY9 A0A1B0GUA3 KIAA1279;KIF1BP KIF1-binding protein 0 121.85 4.46E-09 94551000 37132 34802 27136 27408 29321 31984 32102 31973 35510 34680 FALSE TRUE 35680.84039 33809.48103 32040.07884 28822.53016 30264.13659 32630.73839 32494.87388 31312.74638 31479.05367 32331.09271 1.103607623 1.045726519 0.990998947 0.891480236 0.936069092 1.009268035 1.005065748 0.96850257 0.973646451 1 14.98063465 4.385870384 2.499746115 0.968915319 1.098829804 0.62355518 0.033603481 0.209256054 2.418258856 0.009316279 0.041651527 24314.78224 -4.385870384 0.129914485 DLFAFQES(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLFAFQESPPR 11 0 E7EX48;P51957-3;P51957-2;P51957 E7EX48 NEK4 Serine/threonine-protein kinase Nek4 1 DLFAFQES(1)PPR;DLFAFQES(1)PPR 155.39 3.31E-05 49347000 67495 78922 63977 81454 74724 82162 95409 88806 97923 117648 TRUE FALSE 64857.22078 76671.22183 75539.06706 85657.8507 77127.56532 83823.37193 96576.64388 86972.12507 86807.19157 109679.5962 0.591333512 0.699047266 0.688724883 0.78098255 0.703207962 0.764256752 0.880534277 0.792965402 0.791461626 1 16.74293564 4.386119867 0.066535041 1.352190108 5.38E-16 0.822836702 0.044995144 47.18409347 0.556888673 3.572816077 8.379807266 24328.75399 -4.386119867 -1.352190108 HIDALEDKIDEEVRR ddPTM_BT-474_Pertuzumab_2h_R1 4 HIDALEDKIDEEVRR 15 2 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ;;; 228.73 3.35E-13 1568350000 815974 751972 532519 579103 668801 691157 661631 502349 856329 679037 FALSE TRUE 784084.834 730526.4948 628757.0291 608990.5752 690313.5916 705132.6681 669728.2381 491975.3176 759122.1219 633045.2192 1.238592142 1.153987855 0.993226092 0.962001697 1.0904649 1.113874091 1.057946917 0.777156675 1.199159395 1 19.27194903 4.386510791 3.396552536 1.0091483 1.225905991 0.30005609 0.106344822 0.271816104 5.947766915 0.027881325 0.09808324 24350.66302 -4.386510791 0.216757692 IPGLLSPHPLLQLSYTATDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IPGLLSPHPLLQLSYTATDR 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 206.7 7.40E-22 11017200000 1077740 1189230 1087180 1466890 1268410 1266330 1315790 1230940 1391910 1485500 FALSE TRUE 1035620.729 1155314.325 1283657.61 1542596.369 1309209.56 1291936.06 1331893.032 1205520.659 1233906.212 1384885.762 0.747802279 0.834230777 0.926905053 1.113879867 0.945355636 0.932882766 0.961734945 0.870483828 0.890980503 1 20.40133554 4.386673399 2.778602424 0.951861946 0.757909833 0.540301426 0.063179298 0.231001486 3.366624433 0.017346348 0.070856805 24359.78207 -4.386673399 -0.193952112 ILPGSMIVS(ph)SDDTVDSTIDR ddPTM_BT-474_Pertuzumab_2h_R1 3 ILPGSMIVSSDDTVDSTIDR 20 0 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 ILPGSMIVS(0.941)S(0.059)DDTVDSTIDR;ILPGSMIVS(0.906)S(0.094)DDTVDSTIDR;ILPGSMIVS(0.881)S(0.119)DDTVDSTIDR 179.46 6.10E-17 128128000 80097 82813 92471 84991 89274 107158 88768 104467 88163 100106 TRUE FALSE 76966.72069 80451.25432 109182.5667 89377.3957 92145.57929 109324.8082 89854.36934 102309.7199 78155.10585 93325.73145 0.824710608 0.862047938 1.169908502 0.957692957 0.987354483 1.171432642 0.962803805 1.09626486 0.837444343 1 16.50998729 4.386763646 8.644058852 1.028179651 0.834088575 0.35709605 0.096664512 0.225111802 18.76936478 0.021834187 0.060133916 24364.84463 -4.386763646 -0.194091076 DLEDSLAR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLEDSLAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 234.63 3.36E-08 8463170000 8728550 9007130 8187340 9090000 9372370 8560380 9314930 10100720 9961740 10285560 FALSE TRUE 8387428.616 8750255.471 9666974.464 9559135.989 9673840.793 8733476.749 9428928.9 9892136.602 8830925.038 9588909.86 0.874700955 0.912539131 1.008141134 0.996894968 1.008857204 0.910789326 0.983316043 1.03162265 0.92095193 1 23.19293538 4.386839129 4.370936411 0.984901448 0.882468532 0.495329753 0.036629148 0.155957945 5.245941481 0.009089208 0.027998947 24369.07973 -4.386839129 -0.102432915 WTS(ph)QDSLLGMEFSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 WTSQDSLLGMEFSGR 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WT(0.183)S(0.817)QDSLLGMEFSGR;WT(0.021)S(0.979)QDSLLGMEFSGR 168.05 1.34E-06 105921000 198121 213679 203822 233894 210961 230086 242262 239033 258660 278140 TRUE FALSE 190378.2123 207585.0841 240657.1694 245965.2974 217746.7522 234738.4966 245226.8748 234096.885 229298.0012 259301.3301 0.734196821 0.800555416 0.928098477 0.948569363 0.839744062 0.905273014 0.945721623 0.902798628 0.884291651 1 17.98427008 4.38688384 3.426980162 0.914485745 0.744268669 0.696930869 0.04094067 0.121124135 2.69597202 0.009832407 0.034409033 24371.58869 -4.38688384 -0.170217076 ASS(ph)HSSQT(ph)QGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.009)S(0.991)HSS(0.017)QT(0.983)QGGGSVTK 360.4 4.60E-87 8054700000 6070300 5045700 2797600 2365400 2749000 2224100 1369900 3045600 2168200 1711500 TRUE FALSE 5833065.965 4901801.576 3303188.552 2487478.577 2837424.082 2269072.826 1386665.246 2982707.296 1922075.026 1595578.581 3.655768532 3.072115429 2.070213647 1.558982182 1.778304194 1.42210033 0.869067348 1.869357819 1.204625738 1 20.60564823 4.386895715 1.027680577 1.372130039 4.236149352 0.887424746 0.28425302 0.33502729 0.423924347 0.089204943 0.931060164 24372.25507 -4.386895715 2.864019312 up PASVPPS(ph)PSLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 PASVPPSPSLSR 12 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 PASVPPS(0.994)PS(0.006)LSR;PASVPPS(1)PSLSR;PASVPPS(0.999)PS(0.001)LSR 202.92 1.38E-07 650840000 380513 537020 647150 769610 697860 783980 934740 587920 1128600 1138420 TRUE FALSE 365642.1313 521704.7154 764104.4008 809329.6643 720307.3007 799832.6127 946179.6277 575779.2465 1000486.059 1061313.799 0.344518399 0.491564998 0.719960865 0.762573392 0.678693993 0.753625001 0.891517314 0.542515557 0.942686376 1 20.01741985 4.386983281 1.918476829 0.764937772 0.324926918 0.584562992 0.126666117 0.303496379 1.878822842 0.031912594 0.185850186 24377.16973 -4.386983281 -0.440010855 DETVSDCSPHIANIGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DETVSDCSPHIANIGR 16 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 254.56 1.39E-26 3439390000 1352000 1475440 1476610 1816520 1510310 1451560 1590510 1743310 1899190 1958400 FALSE TRUE 1299162.345 1433361.896 1743466.274 1910270.815 1558890.493 1480911.538 1609975.137 1707310.039 1683601.913 1825755.824 0.711575079 0.785078638 0.954928502 1.046290413 0.853832957 0.811122451 0.881812955 0.935125068 0.922139692 1 20.8000624 4.387117904 4.207766743 0.919238574 0.726382685 0.552819305 0.064921229 0.158959541 5.044233308 0.017062283 0.053419597 24384.72734 -4.387117904 -0.192855889 SQS(ph)FSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSFSK 6 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75;REV__E7ESW5 COBLL1 Cordon-bleu protein-like 1 1 SQS(0.997)FS(0.003)K 74.376 0.084429 178850000 392850 363540 262970 293210 291970 260360 269580 380180 282440 261010 TRUE FALSE 377496.9877 353172.1951 310494.5287 308342.6032 301361.4802 265624.6576 272879.2007 372329.1501 250378.5953 243331.5602 1.551368788 1.451403159 1.276014211 1.267170617 1.238480861 1.091616136 1.121429544 1.530130945 1.028960629 1 17.89256393 4.38726013 1.322757496 1.213737079 1.605263043 0.433247694 0.143555359 0.812750391 1.956834353 0.042742653 0.36405538 24392.71434 -4.38726013 0.391525964 SSS(ph)VGSS(ph)SSYPISPAVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 SS(0.001)S(0.999)VGS(0.29)S(0.475)S(0.225)S(0.01)YPISPAVSR 318.83 2.68E-61 604280000 739480 671510 351730 488750 541970 463230 426160 696450 471200 405010 TRUE FALSE 710580.3041 652359.1923 415295.4352 513974.4461 559402.9573 472596.828 431375.4736 682068.0641 417711.3514 377578.312 1.881941525 1.727745402 1.099892187 1.361239324 1.481554792 1.251652473 1.14247948 1.806428077 1.106290637 1 18.52641637 4.387307599 6.015613034 1.336768147 1.844762885 0.452485837 0.226341708 0.175668315 9.221710716 0.055218889 0.156493418 24395.38067 -4.387307599 0.507994738 ATGAALT(ph)PTEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ATGAALTPTEER 12 0 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 ATGAALT(0.866)PT(0.134)EER 152.32 0.0007792 241580000 182990 206610 213010 223460 214800 259950 253960 236680 266630 303760 TRUE FALSE 175838.5485 200717.6851 251505.6454 234992.7974 221709.2371 265206.3671 257068.0384 231792.4753 236363.2802 283186.0646 0.620929383 0.708783765 0.888128608 0.82981766 0.782910124 0.936509243 0.907770793 0.818516531 0.834657173 1 18.11139075 4.387442374 3.345673428 0.865307658 0.632989958 0.659907496 0.061266046 0.137347034 2.921890478 0.014890106 0.052982683 24402.95245 -4.387442374 -0.2323177 FSKEEPVSS(ph)GPEEAVGK ddPTM_BT-474_Pertuzumab_2h_R1 3 FSKEEPVSSGPEEAVGK 17 1 O00567 O00567 NOP56 Nucleolar protein 56 1 FSKEEPVS(0.039)S(0.961)GPEEAVGK;FSKEEPVS(0.069)S(0.931)GPEEAVGK;FSKEEPVS(0.139)S(0.861)GPEEAVGK 194.56 4.10E-11 1181870000 1405600 1262470 881040 861200 1011270 1131390 966700 1163550 1148110 930080 TRUE FALSE 1350667.598 1226465.592 1040263.527 905646.6352 1043798.418 1154267.481 978530.7638 1139522.286 1017781.366 867084.8532 1.557710982 1.414470092 1.199725174 1.044472905 1.203801928 1.331204757 1.128529417 1.314199276 1.173796731 1 19.72581366 4.387563198 2.946579508 1.190652269 1.541282995 0.624197166 0.098975526 0.17085886 2.818694543 0.024686463 0.096349376 24409.74252 -4.387563198 0.350630726 SINPLGGFVHYGEVTNDFVMLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SINPLGGFVHYGEVTNDFVMLK 22 0 P39023;G5E9G0 P39023 RPL3 60S ribosomal protein L3 0 212.01 2.60E-23 790480000 658170 684100 646220 701010 711060 708070 751320 676300 847690 854470 FALSE TRUE 632447.9888 664590.1378 763006.3291 737189.2101 733931.8907 722387.6605 760514.8789 662334.1687 751463.785 796595.9858 0.793938207 0.834287581 0.95783351 0.925424209 0.921335161 0.90684321 0.954705889 0.831455569 0.943343675 1 19.60348868 4.387874717 5.052326149 0.919322137 0.803034834 0.542225191 0.042335159 0.146979865 6.124575688 0.010364554 0.030446221 24427.25784 -4.387874717 -0.116287303 LDSLHPDLIYNVSWNHNGSLFCSACK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDSLHPDLIYNVSWNHNGSLFCSACK 26 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ; 303.7 4.29E-71 1767530000 1092540 1245090 1031680 1458440 1367790 1393840 1397730 1071110 1461450 1607960 FALSE TRUE 1049842.329 1209581.252 1218127.526 1533710.263 1411786.208 1422024.4 1414835.838 1048991.204 1295552.323 1499051.437 0.700337762 0.806897764 0.812598885 1.023120505 0.941786368 0.948616148 0.943820741 0.699769987 0.864248078 1 20.51561846 4.388046333 1.906859115 0.895754319 0.705413088 0.357143314 0.0885718 0.587319977 3.578772094 0.02642434 0.15528106 24436.91244 -4.388046333 -0.190341231 CGGIDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 CGGIDKR 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 107.66 0.01191 221767000 497930 473380 373890 385230 402950 445600 425970 443820 554530 445820 FALSE TRUE 478470.3451 459879.6659 441460.2401 405111.7665 415911.2527 454610.3373 431183.1483 434654.9619 491582.0792 415624.2143 1.151209022 1.106479483 1.062161984 0.974706845 1.00069062 1.093801376 1.0374351 1.045788351 1.182756111 1 18.66492018 4.388297738 2.660872207 1.047319872 1.146576281 0.26624946 0.055179812 0.384161934 5.094826396 0.01403118 0.059652768 24451.06261 -4.388297738 0.099256408 DSDYYNMLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSDYYNMLLK 10 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 123.6 0.0069564 0 80289 82870 81923 86448 87032 74890 89324 96768 101660 99839 FALSE TRUE 77151.21712 80506.62874 96728.30847 90909.59164 89831.46332 76404.32711 90417.17383 94769.70698 90119.98299 93076.8156 0.828898331 0.86494825 1.03923096 0.976715749 0.965132539 0.820873884 0.971425303 1.01818811 0.96823234 1 16.50613423 4.388360314 6.667394675 0.967938022 0.837759568 0.447727749 0.055215643 0.181352817 10.98031484 0.014322734 0.040085985 24454.58595 -4.388360314 -0.130178454 YFDEHYEYR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFDEHYEYR 9 0 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 ; 114.51 0.001626 604280000 1441340 1638040 1694310 2220900 1979980 1814350 2055930 1700500 1790740 2171880 FALSE TRUE 1385010.839 1591324.703 2000509.507 2335520.915 2043667.855 1851037.4 2081091.086 1665384.081 1587462.703 2024776.633 0.684031422 0.785926051 0.988014912 1.153470895 1.009330028 0.914193383 1.027812674 0.822502618 0.78401868 1 20.94933133 4.388444093 3.821621656 0.958772557 0.702752246 0.465232533 0.09992887 0.205134188 5.567052744 0.027376493 0.089988048 24459.30387 -4.388444093 -0.256020312 APPQTHLPSGASSGTGSASAT(ph)HGGGSPPGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 APPQTHLPSGASSGTGSASATHGGGSPPGTR 31 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 APPQTHLPS(0.002)GAS(0.043)S(0.179)GT(0.05)GS(0.05)AS(0.118)AT(0.298)HGGGS(0.205)PPGT(0.056)R;APPQTHLPS(0.001)GAS(0.002)S(0.002)GT(0.002)GS(0.006)AS(0.293)AT(0.612)HGGGS(0.082)PPGTR 95.205 0.001451 3935860000 48507 57878 59168 84468 63616 79768 83018 47682 64717 84257 TRUE FALSE 46611.29281 56227.37611 69860.97379 88827.4036 65662.26641 81380.96361 84033.99912 46697.35004 57370.59748 78550.19834 0.593394973 0.715814566 0.889379979 1.130836147 0.835927443 1.036037659 1.069812692 0.594490543 0.730368588 1 16.2613273 4.388470194 3.121777887 0.898756653 0.610581602 0.317790225 0.154207228 0.338370381 6.284026653 0.042582146 0.15933686 24460.77394 -4.388470194 -0.288175051 EESQIPVDEVFFHR ddPTM_BT-474_Pertuzumab_2h_R1 4 EESQIPVDEVFFHR 14 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 ;;; 154.69 6.05E-06 323376000 596623 613900 508787 629676 606997 641360 591320 599415 649910 684490 FALSE TRUE 573306.3136 596392.1731 600736.1288 662173.6538 626521.6098 654328.7386 598556.751 587036.8708 576134.9414 638128.8826 0.898417748 0.934595172 0.941402505 1.037680117 0.981810457 1.025386496 0.937987243 0.919934651 0.902850438 1 19.28348831 4.389338207 2.250483323 0.967002995 0.901960212 0.226902465 0.041693099 0.615928902 5.582668238 0.011944003 0.059451369 24509.71195 -4.389338207 -0.065042782 LISQIVSSITASLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LISQIVSSITASLR 14 0 P68363;P68363-2;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ; 300.27 1.86E-43 1818290000 624610 655910 615690 735320 647110 619680 783990 680750 721170 826920 FALSE TRUE 600199.5507 637204.089 726958.879 773269.9533 667924.8808 632210.3542 793584.7041 666692.2746 639305.805 770911.9719 0.778557828 0.826558819 0.942985588 1.003058691 0.866408754 0.820081121 1.029410274 0.86480986 0.829285091 1 19.55620661 4.389432075 4.395059771 0.915200827 0.788514331 0.310281272 0.070938469 0.238790748 8.161977972 0.017298245 0.053284668 24515.01003 -4.389432075 -0.126686496 EAHEREMAEQFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAHEREMAEQFR 12 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 0 58.274 0.097844 2097200000 1126900 1207100 1265300 1405400 1259900 1301000 1475500 1374300 1364600 1470300 FALSE TRUE 1082859.502 1172674.69 1493967.856 1477932.862 1300425.828 1327307.111 1493557.61 1345920.225 1209696.329 1370715.271 0.789995942 0.855520263 1.089918444 1.078220177 0.948720609 0.968331746 1.089619151 0.98191087 0.882529256 1 20.38649749 4.389451988 5.642889621 1.006309531 0.805448791 0.576211717 0.063461779 0.12722538 6.222806877 0.015866407 0.045480121 24516.13409 -4.389451988 -0.20086074 SFS(ph)LDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SFSLDIK 7 0 Q9BY84;Q13202 Q9BY84 DUSP16;DUSP8 Dual specificity protein phosphatase 16;Dual specificity protein phosphatase 8 1 S(0.002)FS(0.998)LDIK 89.029 0.019063 74886000 394600 364700 219340 232530 337540 244880 269690 379110 335130 277420 TRUE FALSE 379178.5957 354299.1131 258979.6172 244530.9012 348397.2806 249831.6414 272990.5469 371281.246 297087.4474 258630.0963 1.466103911 1.369906744 1.001351432 0.945485095 1.347087155 0.965980545 1.055525056 1.435568603 1.148696349 1 17.98053064 4.389515914 5.891024635 1.138298079 1.44309932 0.376459556 0.156407853 0.213942403 11.09478206 0.040535185 0.115317978 24519.74299 -4.389515914 0.304801241 WTVHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 WTVHGK 6 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 69.39 0.09363 886950000 760180 796190 936030 856940 917830 957180 919430 919990 1044180 1093740 FALSE TRUE 730471.3252 773483.4408 1105191.443 901166.7761 947352.8355 976534.8354 930682.2594 900991.885 925649.064 1019660.016 0.716387143 0.758569944 1.0838823 0.883791423 0.929086971 0.957706314 0.91273782 0.883619904 0.907801669 1 19.95965677 4.389581197 8.567620228 0.933986016 0.726944913 0.670267595 0.058092067 0.131017401 11.16509331 0.013647103 0.037600202 24523.42911 -4.389581197 -0.207041103 SFELPPYTPPPILS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 SFELPPYT(0.003)PPPILS(0.997)PVR;SFELPPYTPPPILS(1)PVR 219.58 4.49E-15 149677000 144411 178722 142270 233329 237120 168831 203459 194376 160057 181582 TRUE FALSE 138767.2585 173625.0235 167981.3538 245371.1377 244747.1801 172244.8785 205948.9921 190362.0677 141888.0004 169283.2894 0.819733944 1.025647742 0.992309131 1.449470521 1.445784643 1.01749487 1.216593751 1.124517773 0.83816897 1 17.36908004 4.389584409 1.957178243 1.165129672 0.83699268 0.213384812 0.185285338 0.625494669 4.057533582 0.050274713 0.288601371 24523.61043 -4.389584409 -0.328136993 SGT(ph)PPRQGSITSPQANEQSVTPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGTPPRQGSITSPQANEQSVTPQR 24 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.069)GT(0.738)PPRQGS(0.159)IT(0.016)S(0.019)PQANEQSVTPQR 70.67 0.049951 260660000 15547 15901 14063 15335 16788 16795 16312 15188 19303 16862 TRUE FALSE 14939.40605 15447.51905 16604.49693 16126.44119 17328.00127 17134.60641 16511.63114 14874.36249 17111.80436 15719.92172 0.950348629 0.982671499 1.056270968 1.025860146 1.102295646 1.089993113 1.050363445 0.946210977 1.088542594 1 13.94030641 4.389687378 3.92823464 1.041187283 0.956181618 0.339265985 0.044428653 0.266584803 7.600111109 0.012057829 0.03911885 24529.42556 -4.389687378 -0.085005664 S(ph)SPSVLIHSLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPSVLIHSLGK 12 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 S(0.5)S(0.5)PSVLIHSLGK;S(0.5)S(0.5)PSVLIHSLGK 245.55 1.15E-16 398270000 597090 665140 619590 750490 687870 753300 764240 748120 865710 914810 TRUE FALSE 573755.0627 646170.8584 731563.6957 789222.8788 709995.9633 768532.2421 773592.9977 732671.0606 767438.2302 852849.1039 0.672750971 0.757661415 0.857787963 0.925395683 0.832498926 0.901135076 0.907069016 0.859086393 0.899852303 1 19.70193098 4.389716066 1.910741578 0.893772754 0.664736069 0.765148781 0.042150957 0.191095409 1.168599248 0.010345056 0.060916577 24531.04593 -4.389716066 -0.229036685 SAS(ph)PPKAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASPPKAK 8 1 P52701;P52701-3;P52701-2;A0A087WWJ1;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 S(0.005)AS(0.995)PPKAK;SAS(1)PPKAK 92.611 0.0070584 1491120000 2493600 2156900 1168570 1072540 1554540 1828460 1495530 1579090 2100800 1542300 TRUE FALSE 2396147.355 2095387.324 1379756.594 1127893.918 1604543.191 1865432.714 1513832.744 1546481.24 1862325.991 1437838.647 1.666492523 1.457317431 0.95960461 0.784437058 1.115941065 1.297386683 1.052853007 1.075559655 1.295225994 1 20.45547036 4.389729482 4.303939176 1.074668402 1.62402751 0.657800197 0.144283784 0.121203669 4.01296229 0.037627062 0.116941656 24531.80378 -4.389729482 0.549359109 RSPT(ph)EDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPTEDFR 8 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RS(0.451)PT(0.549)EDFR 78.136 0.060749 713750000 661520 680060 643440 741300 673080 675630 759400 725550 733980 760440 TRUE FALSE 635667.0671 660665.3546 759723.9212 779558.5818 694730.2295 689291.7015 768693.7644 710567.139 650661.6675 708934.7215 0.896651057 0.931912819 1.071641575 1.099619694 0.979963611 0.972292202 1.08429414 1.002302634 0.917801947 1 19.43529327 4.389760677 6.021293404 1.018694513 0.905131392 0.375652314 0.053135071 0.188207808 10.0692112 0.013275951 0.037641713 24533.56593 -4.389760677 -0.11356312 AAMIWIVGEYAER ddPTM_BT-474_Pertuzumab_2h_R1 2 AAMIWIVGEYAER 13 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 185.08 8.18E-07 183370000 258330 283040 274910 298320 310340 311320 326050 347450 344130 313730 FALSE TRUE 248234.178 274967.9763 324592.3523 313716.331 320322.3679 317615.1037 330040.2974 340275.0361 305065.8051 292480.7877 0.848719603 0.940123208 1.109790338 1.072604917 1.095191142 1.08593493 1.128417015 1.163409873 1.043028527 1 18.15798234 4.389844124 2.928243897 1.099064432 0.856961625 0.758374753 0.044389639 0.112875437 1.837894193 0.011163717 0.043974144 24538.28036 -4.389844124 -0.242102808 SLESINSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLESINSR 8 0 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ; 141.52 0.0014708 585250000 364270 389620 362280 418800 426160 398940 425550 452670 421130 441750 FALSE TRUE 350033.9257 378508.4191 427752.0549 440414.3182 439867.8234 407006.8401 430758.0082 443322.2063 373325.0879 411829.879 0.849947863 0.919089261 1.038662022 1.069408366 1.068081375 0.988288759 1.045961039 1.076469263 0.906503163 1 18.65168898 4.389921144 3.144165213 1.032450188 0.858681515 0.576578218 0.049001009 0.157416602 2.966888931 0.01201753 0.044846689 24542.63248 -4.389921144 -0.173768674 HAIVICNR ddPTM_BT-474_Pertuzumab_2h_R1 2 HAIVICNR 8 0 P53621;A0A3B3IT15;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 104.45 0.0045784 337980000 277050 294890 300640 344690 323930 338620 357650 266830 365780 360010 FALSE TRUE 266222.5797 286480.0259 354972.3357 362479.4922 334349.5026 345467.1284 362027.0277 261319.8673 324258.1879 335626.202 0.793211549 0.853568715 1.057641905 1.080009517 0.996196068 1.029321091 1.078661396 0.778603892 0.966128943 1 18.35649582 4.389930869 5.468313357 0.987258891 0.807282658 0.419797862 0.082640889 0.206593766 9.709616112 0.023023387 0.066423264 24543.18205 -4.389930869 -0.179976234 TPAVEGLTEAEEEELRAELTKVEEEIVTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPAVEGLTEAEEEELRAELTKVEEEIVTLR 30 2 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 203.94 9.32E-26 312450000 156940 141930 77748 86693 118000 102800 87535 127700 150350 114000 FALSE TRUE 150806.6113 137882.2954 91798.79309 91167.23612 121795.5772 104878.6864 88606.27951 125062.9504 133282.8983 106278.6785 1.41897334 1.297365543 0.8637555 0.857813039 1.146001991 0.98682716 0.833716422 1.176745441 1.254088781 1 16.69749267 4.3899982 5.652290795 1.018801599 1.390299388 0.514089833 0.135511076 0.150549987 7.406730479 0.034760277 0.099624983 24546.9874 -4.3899982 0.371497789 LYQEVEIASVDAFQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LYQEVEIASVDAFQGR 16 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 185.87 3.70E-09 28531000 18118 20067 18311 25083 19577 18330 22613 25551 20675 24482 FALSE TRUE 17409.92853 19494.70881 21620.20503 26377.53664 20206.71198 18700.64516 22889.74466 25023.36292 18328.06068 22823.81233 0.762796691 0.854139025 0.947265282 1.155702485 0.885334654 0.819348007 1.002888752 1.096370867 0.803023632 1 14.47825217 4.390436085 2.742688178 0.975146563 0.77295943 0.273358623 0.10548599 0.358766786 5.079729669 0.027565594 0.114696587 24571.7498 -4.390436085 -0.202187133 LKNGFPHPEPDCNPSEAAS(ph)EES(ph)NSEIEQEIPVEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 2 LKNGFPHPEPDCNPS(0.118)EAAS(0.791)EES(0.606)NS(0.486)EIEQEIPVEQK;LKNGFPHPEPDCNPS(0.41)EAAS(0.579)EES(0.548)NS(0.463)EIEQEIPVEQK 139.18 8.24E-10 195550000 123780 109169 89964 78277 88009 105239 90692 101010 111755 100895 TRUE FALSE 118942.5408 106055.607 106222.496 82316.88535 90839.88941 107367.0047 91801.91583 98924.1082 99069.04092 94061.29178 1.264521659 1.127515953 1.129290211 0.875140919 0.965752093 1.141457901 0.975979748 1.05169838 1.053239213 1 16.52131353 4.390601014 1.761501126 1.016974097 1.262172818 0.542687193 0.071449126 0.377792525 1.886020116 0.019329081 0.124284896 24581.08302 -4.390601014 0.245198721 LYGS(ph)VCDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LYGSVCDLR 9 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 LYGS(1)VCDLR 84.882 0.015935 81882000 204790 179020 60847 140820 80980 61950 94566 203070 114040 87042 TRUE FALSE 196786.5804 173914.5249 71843.40643 148087.7371 83584.79524 63202.67145 95723.327 198876.5335 101094.6573 81146.56781 2.425075831 2.143214797 0.885353606 1.824941474 1.030047203 0.778870544 1.179634944 2.450831118 1.245827889 1 16.30824246 4.390625131 6.456246506 1.392249328 2.35651209 0.397011672 0.479620944 0.215906292 12.77522852 0.127962207 0.359525763 24582.44808 -4.390625131 0.964262762 EFADFEYR ddPTM_BT-474_Pertuzumab_2h_R1 5 EFADFEYR 8 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A0G2JQ95;A0A096LP11;A0A140TA66 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;;; 169.06 0.00070539 3284840000 3968980 4133540 3732900 4480230 4388600 3937440 4429520 4452300 4321640 4649350 FALSE TRUE 3813867.874 4015655.486 4407518.068 4711455.207 4529763.305 4017057.735 4483729.791 4360358.449 3831065.545 4334445.383 0.87989755 0.926451975 1.016858601 1.086979946 1.045061802 0.926775488 1.034441409 1.005978404 0.883865225 1 22.04741597 4.390738288 3.771380121 1.004036905 0.888242165 0.342210644 0.055027701 0.232183874 6.178889693 0.013875365 0.04607558 24588.85398 -4.390738288 -0.11579474 VLLQEEGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLLQEEGTR 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 110.76 0.0052003 212750000 197884 212060 177556 235300 215550 204450 222730 218710 229270 251220 FALSE TRUE 190150.4745 206012.2564 209644.3189 247443.8612 222483.3615 208584.1191 225455.8364 214193.5621 203244.2308 234204.6456 0.811898816 0.879624979 0.895133051 1.056528407 0.949952811 0.890606241 0.962644596 0.914557273 0.867806145 1 17.83741017 4.390889754 2.144999689 0.942624745 0.816828484 0.393912662 0.052354996 0.393166539 3.17837295 0.013777724 0.07220666 24597.43116 -4.390889754 -0.12579626 SSSLIQLTSQNSS(ph)PNQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSLIQLTSQNSSPNQQR 18 0 O95639;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 SSSLIQLTSQNSS(1)PNQQR;SSSLIQLTSQNS(0.013)S(0.987)PNQQR 403.16 4.24E-147 998970000 835490 891340 830910 976720 863740 994950 1003450 973640 942750 1122280 TRUE FALSE 802838.1271 865919.8559 981073.9205 1027128.636 891522.9815 1015068.571 1015730.521 953533.9938 835732.9723 1046266.976 0.767335819 0.827628011 0.937689847 0.981707977 0.85209894 0.97018122 0.970813898 0.911367763 0.798776021 1 19.9968196 4.390966592 3.419257295 0.926897957 0.776478632 0.451696528 0.059012329 0.201115777 4.470655334 0.01437568 0.050696863 24601.78347 -4.390966592 -0.150419325 ADEHVIDQGDDGDNFYVIER ddPTM_BT-474_Pertuzumab_2h_R1 3 ADEHVIDQGDDGDNFYVIER 20 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 ;; 277.8 1.35E-44 1845030000 609590 636080 547278 660820 687250 688710 625790 630805 692370 697569 FALSE TRUE 585766.5489 617939.6212 646183.3087 694924.9994 709356.0204 702636.1881 633448.6052 617778.6563 613775.0603 650322.0303 0.900733055 0.950205579 0.993635889 1.068585973 1.09077655 1.080443465 0.974053739 0.949958063 0.943801735 1 19.31079477 4.391082567 2.419902874 1.013378352 0.904160875 0.357517178 0.049343599 0.421864878 4.517946221 0.01505842 0.070176534 24608.35407 -4.391082567 -0.109217478 DFSGGWR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFSGGWR 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ;;; 130.05 0.009748 781120000 1190795 1282533 1121734 1411574 1270600 1278940 1396390 1397380 1507190 1560770 FALSE TRUE 1144257.415 1245956.415 1324456.287 1484425.503 1311470.003 1304801.043 1413479.439 1368523.615 1336100.11 1455057.658 0.78640005 0.8562935 0.910243164 1.020183287 0.901318237 0.896734941 0.971425037 0.940528788 0.918245475 1 20.47264489 4.391843619 2.144191614 0.945033945 0.787615601 0.647921837 0.038636224 0.225174705 1.817433402 0.009853639 0.051779352 24651.51524 -4.391843619 -0.157418344 AYTDELVELHR ddPTM_BT-474_Pertuzumab_2h_R1 4 AYTDELVELHR 11 0 Q03111 Q03111 MLLT1 Protein ENL 0 ;;; 223.78 6.69E-12 656833000 847300 927590 858260 1065310 1065310 1001170 1021730 992360 1011800 1139930 FALSE TRUE 814186.5793 901136.0414 1013366.674 1120290.777 1099576.664 1021414.343 1034234.237 971867.4192 896944.7058 1062721.526 0.766133516 0.847951246 0.953558058 1.05417153 1.034679958 0.961130756 0.973194023 0.914508077 0.844007281 1 20.01933217 4.391873923 2.747960272 0.96740335 0.773849233 0.583973903 0.056097231 0.212668208 3.022670847 0.015651382 0.0652081 24653.23543 -4.391873923 -0.193554118 QAWRKGPDGPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 QAWRKGPDGPQK 12 2 Q9BYZ6-2;E5RI44 Q9BYZ6-2 RHOBTB2 Rho-related BTB domain-containing protein 2 0 ; 68.069 0.030182 6784400000 11841400 10201900 6711100 7076600 6528600 5839800 7453300 5970700 9675600 6550900 FALSE TRUE 11378625 9910951.801 7923945.058 7441824.174 6738598.348 5957884.757 7544515.715 5847402.959 8577266.451 6107201.708 1.863148712 1.622830271 1.297475577 1.218532567 1.103385588 0.975550676 1.235347394 0.957460264 1.404451148 1 22.54208006 4.392034296 1.181489388 1.103996519 2.005243891 0.794078648 0.127059198 0.350814046 0.628716923 0.035431735 0.337440365 24662.34085 -4.392034296 0.901247372 ASFDHS(ph)PDSLPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASFDHSPDSLPLR 13 0 H0Y6H0;Q8NB78;Q8NB78-2 H0Y6H0 KDM1B Lysine-specific histone demethylase 1B 1 ASFDHS(1)PDSLPLR;AS(0.002)FDHS(0.996)PDS(0.002)LPLR 211.77 2.02E-08 136980000 236150 258720 246300 301630 270690 304370 286220 279630 290410 323640 TRUE FALSE 226920.9969 251341.5589 290811.8889 317197.1604 279396.9897 310524.5699 289722.846 273855.5428 257443.8743 301719.5745 0.752092393 0.833030337 0.963848267 1.051297918 0.926015457 1.029182712 0.960238813 0.907649241 0.85325546 1 18.20284877 4.392259662 3.178379482 0.95985865 0.762925708 0.614230943 0.055175203 0.166193894 3.203579131 0.014509364 0.053939638 24675.14208 -4.392259662 -0.196932943 GTVGEPTYDAEFQHFLR ddPTM_BT-474_Pertuzumab_2h_R1 5 GTVGEPTYDAEFQHFLR 17 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 336.91 3.06E-72 4039166000 2240183 2451302 2355688 2640367 2791156 2877116 2731145 2582032 3028434 3042827 FALSE TRUE 2152634.172 2381393.267 2781413.224 2776636.657 2880936.068 2935293.257 2764569.569 2528712.137 2684658.869 2836733.617 0.75884255 0.839484276 0.980498559 0.978814733 1.015582165 1.034744059 0.974560866 0.891416847 0.946390896 1 21.43579925 4.392289136 2.982045958 0.973349612 0.767061929 0.789731652 0.037788414 0.133665725 2.260938063 0.011457055 0.044694138 24676.81672 -4.392289136 -0.206287684 LPSS(ph)PLGCR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPSSPLGCR 9 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 LPS(0.328)S(0.672)PLGCR;LPS(0.021)S(0.979)PLGCR 122.96 0.00059905 1910750000 1452410 1520090 1343290 1606760 1564700 1677930 1569240 1646890 1428660 1731710 TRUE FALSE 1395648.211 1476738.522 1586052.384 1689685.076 1615029.997 1711858.894 1588444.829 1612881.146 1266484.506 1614419.739 0.864489065 0.914717831 0.982428761 1.046620674 1.000378004 1.060355528 0.983910683 0.999046968 0.784482793 1 20.62258429 4.392722924 2.840900687 0.988743244 0.869705983 0.223165465 0.07119614 0.37903775 5.786776375 0.017788488 0.072205685 24701.47709 -4.392722924 -0.11903726 AEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEKPPLSASSPQQRPPEPETGESAGTSR 28 2 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AEKPPLS(0.001)AS(0.184)S(0.815)PQQRPPEPETGESAGTSR;AEKPPLSAS(0.193)S(0.807)PQQRPPEPETGESAGTSR;AEKPPLS(0.001)AS(0.103)S(0.896)PQQRPPEPETGESAGTSR;AEKPPLS(0.01)AS(0.177)S(0.798)PQQRPPEPET(0.011)GES(0.001)AGT(0.001)S(0.001)R 134.6 6.79E-06 1449720000 517189 540131 568160 535796 562021 609570 649392 599853 592770 744840 TRUE FALSE 496976.6821 524726.9927 670839.1507 563448.4958 580098.9159 621895.923 657339.4536 587465.8259 525481.2347 694391.3234 0.715701169 0.755664674 0.966082277 0.811427904 0.835406343 0.895598637 0.946641226 0.846015505 0.756750865 1 19.4053894 4.393537808 7.239214304 0.874837537 0.725549464 0.408606828 0.070756387 0.188746505 13.43675216 0.016524579 0.045945246 24747.86897 -4.393537808 -0.149288073 EVLEGLEYLHK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVLEGLEYLHK 11 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 ;; 209.97 1.44E-08 344940000 701970 727528 644841 742752 694770 757640 756249 751110 872010 843170 FALSE TRUE 674536.2363 706779.6138 761378.1131 781085.5197 717117.908 772959.9999 765504.2015 735599.316 773023.0806 786061.3449 0.858121622 0.899140529 0.968598848 0.993669928 0.912292549 0.983332923 0.973847915 0.935803956 0.983413172 1 19.58428238 4.39354758 3.145355893 0.964871797 0.863247536 0.674561162 0.025635848 0.139544773 2.634799928 0.006216424 0.023340584 24748.42581 -4.39354758 -0.101624262 NSASATTPLSGNSS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 NSASATTPLS(0.03)GNS(0.25)S(0.72)R;NSASATTPLS(0.001)GNS(0.157)S(0.842)R 132.14 5.17E-05 386870000 954770 807400 579060 524400 584110 509950 418680 677270 594070 514010 TRUE FALSE 917456.5328 784373.7425 683709.0231 551464.3468 602898.4286 520261.5384 423803.9311 663284.1378 526633.6641 479195.6449 1.914576108 1.636854907 1.426784718 1.150812518 1.25814672 1.085697552 0.884406892 1.384161448 1.098995097 1 18.87025527 4.393600841 1.033991241 1.126897515 2.084213927 0.81708596 0.127220234 0.465503638 0.594172201 0.041197708 0.435209279 24751.46112 -4.393600841 0.957316412 DLPSHTK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLPSHTK 7 0 Q9P013 Q9P013 CWC15 Spliceosome-associated protein CWC15 homolog 0 ;; 82.452 0.02445 1165160000 830790 818520 700710 770640 779070 840190 838140 800010 935430 917590 FALSE TRUE 798321.8083 795176.611 827343.8842 810412.8228 804129.4941 857179.2175 848397.408 783489.5139 829243.908 855440.812 0.933228573 0.929551875 0.96715503 0.947362823 0.940017688 1.002032175 0.991766346 0.9158898 0.969376135 1 19.70630851 4.393681036 0.826872426 0.964857395 0.918377134 0.208186351 0.02618925 3.102243382 2.29885973 0.010178437 0.120194464 24756.03205 -4.393681036 -0.04648026 YLANIEQQHGNSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 YLANIEQQHGNSGR 14 0 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 ;; 166.79 3.75E-06 1584180000 924440 981260 903820 1067440 1027440 1107440 1066240 995630 1142920 1076280 FALSE TRUE 888311.8628 953275.4256 1067160.379 1122530.706 1060488.541 1129833.196 1079288.964 975069.8926 1013180.513 1003382.597 0.885317192 0.95006175 1.063562775 1.118746438 1.056913429 1.126024309 1.075650472 0.971782743 1.009764885 1 19.93644039 4.393714495 3.368414432 1.053749675 0.894851722 0.58571157 0.0468035 0.17642397 3.817890244 0.013124966 0.046956178 24757.93938 -4.393714495 -0.158897953 SVAS(ph)NQSEMEFSSLQDMPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVASNQSEMEFSSLQDMPK 19 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 S(0.121)VAS(0.697)NQS(0.181)EMEFSSLQDMPK;S(0.012)VAS(0.557)NQS(0.43)EMEFSSLQDMPK 204.53 2.93E-16 428810000 307190 383570 362340 437270 472350 574540 545460 552430 702380 603410 TRUE FALSE 295184.6752 372630.9592 427822.8982 459837.5571 487543.5667 586157.5924 552135.5026 541022.1275 622648.767 562540.5032 0.524734972 0.662407341 0.760519279 0.817430131 0.866681713 1.041982913 0.981503553 0.961747864 1.106851442 1 19.10159745 4.393751414 0.489722312 1.037283856 0.289475125 0.93044877 0.04571164 0.805108808 0.190471634 0.030777319 0.335217874 24760.04408 -4.393751414 -0.747808731 EFFSQYGDVMDVFIPKPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFFSQYGDVMDVFIPKPFR 19 1 Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;A0A087WXQ5;Q13148-4;A0A087WV68;A0A087WXV3;A0A087WX67;A0A087WW61;A0A087WZC9;A0A087WZM1;A0A1W2PNU8;A0A087WYE7 Q13148 TARDBP;TDP43 TAR DNA-binding protein 43 0 ; 237.31 2.96E-24 799360000 566170 623070 627760 683330 683230 642260 643920 768700 820560 850530 FALSE TRUE 544043.4505 605300.6536 741210.1964 718596.7432 705206.7134 655246.9372 651800.4856 752826.0764 727413.4689 792922.8455 0.686124071 0.763379006 0.934782243 0.906263134 0.889376208 0.826369099 0.822022583 0.949431689 0.917382407 1 19.59682097 4.393769843 3.980718522 0.898609878 0.700252802 0.673205941 0.051361326 0.121342331 3.568365241 0.012944979 0.041909626 24761.09481 -4.393769843 -0.198357076 S(ph)PLDNMIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPLDNMIR 8 0 P41212 P41212 ETV6 Transcription factor ETV6 1 S(1)PLDNMIR;S(1)PLDNMIR;S(1)PLDNMIR;S(1)PLDNMIR 96.113 0.00962 266480000 156524 177381 177342 231092 202698 204302 206190 205329 187695 205939 TRUE FALSE 150406.869 172322.2676 209391.6444 243018.6858 209217.9653 208433.1264 208713.4149 201088.8844 166388.6505 191990.5681 0.783407594 0.897555902 1.090635058 1.265784503 1.089730435 1.085642532 1.087102439 1.047389392 0.866650128 1 17.55067591 4.393795933 3.436394343 1.076191514 0.801294923 0.49597612 0.093833568 0.185063401 4.162918423 0.024257368 0.085641717 24762.58236 -4.393795933 -0.274896591 VES(ph)MEALPILSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VESMEALPILSR 12 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 VES(1)MEALPILSR;VES(1)MEALPILSR 180.09 2.09E-05 108575000 104301 101592 77607 99355 78638 85965 91882 98570 99804 118423 TRUE FALSE 100224.8016 98694.69563 91632.31126 104482.7235 81167.46269 87703.2712 93006.4794 96534.49505 88474.66833 110402.1047 0.907816041 0.893956649 0.829986996 0.946383438 0.735198508 0.794398544 0.842433934 0.874389988 0.801385703 1 16.75240815 4.393873637 1.160263204 0.843375169 0.921125957 0.050926405 0.072357335 2.466210633 4.211862312 0.02084166 0.202378113 24767.01329 -4.393873637 0.077750788 DIIHDPGR ddPTM_BT-474_Pertuzumab_2h_R1 7 DIIHDPGR 8 0 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ;;;;;; 130.75 0.0010346 23063050000 16284168 16753238 15311273 16205818 17812254 18113703 16724533 17742761 18617330 18429591 FALSE TRUE 15647764.71 16275452.06 18078360.63 17042202.21 18385201.33 18479974.49 16929212.84 17376366.79 16503968.75 17181338.39 0.910741897 0.947274985 1.052209102 0.991901901 1.070068054 1.075584106 0.985325617 1.011351176 0.960575269 1 24.03433909 4.394029127 4.927801102 1.019294616 0.918724688 0.51034144 0.035719623 0.147234984 6.099481659 0.00897815 0.026655279 24775.88216 -4.394029127 -0.100569928 REDS(ph)MEDRGEEDDSLAIKPPQQMSR ddPTM_BT-474_Pertuzumab_2h_R1 1 REDSMEDRGEEDDSLAIKPPQQMSR 25 3 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;Q9UQ88-9;A0A087X1I0;A0A087WYI9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 REDS(1)MEDRGEEDDSLAIKPPQQMSR 213.52 1.74E-25 410790000 355140 351380 231350 276130 327980 356040 317880 325680 358520 337140 TRUE FALSE 341260.7362 341358.9864 273160.0914 290381.1024 338529.7746 363239.3727 321770.3105 318954.5942 317822.3126 314305.2075 1.085762272 1.086074867 0.869091841 0.923882568 1.077073388 1.15568996 1.023751127 1.014792586 1.011190095 1 18.26180665 4.39403003 24.67424476 1.012838588 1.086130815 0.14787268 0.073075207 44.63581896 13247.95935 0.019439369 0.053236905 24775.93368 -4.39403003 0.073292227 RES(ph)CGSSVLTDFEGKDVATK ddPTM_BT-474_Pertuzumab_2h_R1 3 RESCGSSVLTDFEGKDVATK 20 2 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 RES(0.988)CGS(0.01)S(0.002)VLTDFEGKDVATK;RES(0.612)CGS(0.387)S(0.001)VLTDFEGKDVATK;RES(0.99)CGS(0.01)SVLTDFEGKDVATK 262.79 9.78E-37 2843260000 2082300 1841110 1098920 1027288 1561980 1750290 1253520 1498330 1636240 1306060 TRUE FALSE 2000921.414 1788603.345 1297519.289 1080306.457 1612222.505 1785682.063 1268860.953 1467388.962 1450500.895 1217599.393 1.643333124 1.468958802 1.065637267 0.887242933 1.324099301 1.466559587 1.042100514 1.205149223 1.191279253 1 20.21560811 4.394214891 4.294333444 1.160894472 1.608381952 0.526105519 0.158119054 0.159623382 5.337581401 0.040436438 0.126327011 24786.48203 -4.394214891 0.44748748 EATDLLHDALQIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EATDLLHDALQIR 13 0 Q6P597;Q6P597-3;Q6P597-2;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 0 107.39 0.0012991 52986000 85317 95632 82731 106990 101970 105560 102110 107360 109660 113390 FALSE TRUE 81982.71732 92904.66899 97682.33204 112511.7667 105249.9577 107694.4955 103359.6527 105142.9785 97211.85653 105709.9943 0.775543674 0.878863627 0.924059572 1.064343702 0.995648125 1.018773071 0.977766137 0.994636119 0.919608947 1 16.68975226 4.394307411 1.737453434 0.994778831 0.769513244 0.780365178 0.036901926 0.214864617 1.032636039 0.009815812 0.064652706 24791.76299 -4.394307411 -0.225265586 SSS(ph)MSSLTGAYASGIPSSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSMSSLTGAYASGIPSSSR 20 0 Q96HA1-2;Q96HA1-3;Q96HA1 Q96HA1-2 POM121 Nuclear envelope pore membrane protein POM 121 1 S(0.002)S(0.039)S(0.954)MS(0.005)SLTGAYASGIPSSSR;SSS(0.999)MSSLTGAYASGIPSSSR 444.78 1.15E-197 361100000 628900 548260 307277 458510 379180 273727 294134 714290 298099 225978 TRUE FALSE 604321.8927 532624.1616 362808.7892 482173.756 391376.6691 279261.9475 297733.6999 699539.6619 264260.0513 210672.3088 2.868539754 2.528211537 1.722147497 2.288738178 1.85775089 1.325575008 1.413255029 3.32051073 1.254365383 1 17.68464117 4.394444919 4.100161245 1.9157008 2.805287837 0.236517439 0.635835452 0.33152495 10.2710211 0.162007771 0.517193315 24799.61386 -4.394444919 0.889587037 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR 38 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 168.31 3.09E-18 638370000 617680 644920 584720 649620 649580 685570 736960 659960 692090 759780 FALSE TRUE 593540.3827 626527.513 690391.911 683146.9661 670474.3306 699432.6951 745979.1369 646331.5954 613526.8447 708319.4239 0.837955819 0.8845268 0.974690073 0.964461715 0.946570584 0.987453784 1.053167698 0.912486053 0.866172554 1 19.43404058 4.394714879 3.419740633 0.962516211 0.844653568 0.435679048 0.047585649 0.220395734 4.915301991 0.012326865 0.043724798 24815.03428 -4.394714879 -0.117862643 FGQAATMEGIGAIGGT(ph)PPAFNR ddPTM_BT-474_Pertuzumab_2h_R1 7 FGQAATMEGIGAIGGTPPAFNR 22 0 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 1 FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR 359.95 1.67E-95 3047300000 2050960 2141720 2111050 2212170 2083760 2426650 2320070 2403180 2318870 2729980 TRUE FALSE 1970806.216 2080640.243 2492563.695 2326340.359 2150786.033 2475718.526 2348463.711 2353553.493 2055641.599 2545076.023 0.774360451 0.81751595 0.979367089 0.914055352 0.845077323 0.972748359 0.922747961 0.924747816 0.807693594 1 21.27927732 4.394773334 5.969533288 0.917311288 0.784596996 0.450175337 0.055918786 0.155817599 8.572789986 0.012963808 0.03685658 24818.37455 -4.394773334 -0.132714292 AAEEAEEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAEEAEEAR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 114.89 0.0036388 475490000 713270 761390 660580 802690 797730 826190 775690 813010 847750 884250 FALSE TRUE 685394.6198 739675.9027 779961.5005 844116.9271 823389.7099 842896.1279 785183.1263 796221.0594 751516.9741 824358.9599 0.831427392 0.89727405 0.94614305 1.023967674 0.998824238 1.022486767 0.952477215 0.965866932 0.911638025 1 19.65291316 4.395062318 1.987381471 0.98037484 0.830074162 0.688134843 0.032535197 0.24221029 1.623697921 0.009029901 0.051714826 24834.8944 -4.395062318 -0.150300678 ANGLPAGPEPASEPGS(ph)PYPEGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ANGLPAGPEPASEPGSPYPEGPR 23 0 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 ANGLPAGPEPASEPGS(1)PYPEGPR 262.98 7.80E-44 233320000 36326 40250 36549 46133 45284 49021 42281 44253 43149 44016 TRUE FALSE 34906.33976 39102.10941 43154.21733 48513.92966 46740.60099 50012.23821 42798.44753 43339.16009 38250.90642 41034.75711 0.850653013 0.952902178 1.051650366 1.182264331 1.139049047 1.218777488 1.042980403 1.056157344 0.932158714 1 15.32455879 4.395343112 2.34344832 1.088848931 0.854996989 0.458612518 0.080270061 0.297791703 2.954910202 0.021703856 0.105308267 24850.95666 -4.395343112 -0.233851942 EEDVGQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEDVGQPR 8 0 P53602;H3BP35;H3BQ47 P53602 MVD Diphosphomevalonate decarboxylase 0 118.74 0.0042524 84787000 191670 210530 190330 230040 222800 242130 240010 227810 247820 253310 FALSE TRUE 184179.3245 204525.8905 224726.8649 241912.392 229966.5643 247026.0345 242947.3142 223105.6439 219688.5125 236153.0881 0.779914953 0.866073326 0.951615186 1.02438801 0.97380291 1.04604194 1.028770431 0.944750059 0.930280075 1 17.84936288 4.395590832 1.89038555 0.991433223 0.77283798 0.798355874 0.034844614 0.198842897 1.17826254 0.010000958 0.060447103 24865.13562 -4.395590832 -0.218595243 MS(ph)PMGTASGSNSPTSDSASVQR ddPTM_BT-474_Pertuzumab_2h_R1 4 MSPMGTASGSNSPTSDSASVQR 22 0 Q5QPB1;O76080 Q5QPB1 ZFAND5 AN1-type zinc finger protein 5 1 MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR 372.59 4.13E-113 2263550000 534248 544198 501996 586820 557050 648893 622220 661794 710860 641763 TRUE FALSE 513368.9975 528678.0059 592717.844 617105.8505 574968.0191 662014.0611 629834.9145 648127.7226 630166.153 598295.8204 0.858052121 0.883639811 0.990676892 1.031439347 0.961009587 1.106499558 1.052714883 1.083289738 1.05326852 1 19.19049946 4.395659501 0.76062071 1.060199425 0.774928894 0.752004673 0.038618521 0.792943258 0.483195154 0.01467398 0.177411636 24869.06749 -4.395659501 -0.285270531 EEFLIPIYHQVAVQFADLHDTPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEFLIPIYHQVAVQFADLHDTPGR 24 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 257.2 3.95E-44 888910000 517870 599770 572670 713850 650960 775100 742490 537090 858230 910630 FALSE TRUE 497631.0679 582665.1468 676164.208 750691.884 671898.7196 790773.0531 751576.8147 525998.9038 760807.3284 848952.219 0.586170878 0.686334441 0.796469098 0.884256931 0.791444683 0.931469446 0.885299311 0.619585993 0.896172142 1 19.69532383 4.395885097 2.117888675 0.832526941 0.583695734 0.447613109 0.097357136 0.393184748 3.072062993 0.026550989 0.142672778 24881.98918 -4.395885097 -0.248831206 LAQMCGLHIVVHADELEELINYYQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LAQMCGLHIVVHADELEELINYYQDR 26 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 245.09 1.51E-45 2364080000 467694 511766 498129 557166 614936 626542 733443 310685 703670 636584 FALSE TRUE 449416.0014 497170.9348 588151.9911 585921.404 634715.9749 639211.1085 742419.0948 304269.2462 623792.3316 593467.5987 0.757271336 0.83773897 0.991043138 0.987284572 1.069504007 1.077078361 1.250985052 0.512697318 1.051097538 1 19.17880974 4.395998803 3.447846509 0.970385712 0.769100758 0.157677038 0.178361017 0.498535862 11.30856233 0.047951147 0.169512136 24888.5046 -4.395998803 -0.201284954 FQETEFLS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FQETEFLSPPR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 FQETEFLS(1)PPR;FQETEFLS(1)PPR 167.22 2.05E-05 553960000 571190 585740 541250 585650 585050 636760 629670 583170 628220 708320 TRUE FALSE 548867.2633 569035.2687 639065.915 615875.4667 603868.6646 649635.7235 637376.0898 571127.3357 556907.0993 660344.8555 0.831182766 0.861724391 0.967776018 0.932657325 0.914474701 0.983782516 0.965217014 0.864892534 0.843357974 1 19.33286012 4.396180929 5.727573311 0.928396195 0.838317224 0.353464444 0.047610035 0.215110306 11.27918165 0.01218281 0.034905069 24898.94401 -4.396180929 -0.090078971 NPSDSAVHS(ph)PFTK ddPTM_BT-474_Pertuzumab_2h_R1 6 NPSDSAVHSPFTK 13 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK 207.53 3.42E-08 8466070000 6742080 6783050 8063000 8281810 7752500 7753500 8071660 7435270 8022620 8924410 TRUE FALSE 6478592.06 6589604.055 9520163.46 8709235.207 8001866.203 7910281.082 8170443.39 7281729.076 7111925.811 8319951.762 0.778681445 0.79202431 1.14425705 1.046789147 0.961768341 0.95076045 0.98203014 0.875212896 0.854803731 1 22.98814373 4.396182159 15.41243986 0.968904002 0.782017574 0.492207578 0.077551419 1.151292113 216.8746706 0.020495279 0.056132887 24899.01454 -4.396182159 -0.186886428 EFSGPSTPTGT(ph)LEFEGGEVSLEGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFSGPSTPTGTLEFEGGEVSLEGGK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 EFSGPS(0.062)T(0.248)PT(0.248)GT(0.44)LEFEGGEVSLEGGK;EFS(0.003)GPS(0.073)T(0.267)PT(0.267)GT(0.388)LEFEGGEVSLEGGK 199.89 2.55E-24 868010000 84497 91437 85081 106152 98993 104930 86366 102727 110835 97534 TRUE FALSE 81194.76382 88829.30629 100457.0293 111630.5174 102177.1997 107051.7565 87422.97294 100605.6516 98253.47546 90927.93531 0.892957302 0.976919865 1.104798311 1.227681208 1.123716264 1.177325276 0.961453404 1.106432816 1.080564242 1 16.47243597 4.396235135 3.187165413 1.102861527 0.904368102 0.460774638 0.072833231 0.210933028 4.094771562 0.018560856 0.069346771 24902.05195 -4.396235135 -0.198493424 RIESLIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 RIESLIDR 8 1 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ;;; 144.65 0.0009332 985300000 702910 741840 657020 832890 750630 742420 809370 757390 818690 847220 FALSE TRUE 675439.5001 720683.4495 775758.1293 875875.5527 774774.6957 757432.2411 819275.3122 741749.6318 725755.7434 789837.0348 0.855163116 0.912445755 0.982174924 1.108931987 0.980929814 0.95897281 1.037271331 0.93911731 0.918867705 1 19.59119549 4.396339417 2.981317617 0.991195476 0.86241982 0.44001861 0.050299799 0.249310439 4.215860849 0.013287652 0.052246672 24908.03212 -4.396339417 -0.128775656 NRLENDGATALAEAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 NRLENDGATALAEAFR 16 1 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ; 218.66 1.20E-14 1019190000 493770 466150 352660 393930 382660 426370 419280 431920 486040 425240 FALSE TRUE 474472.9225 452855.8584 416393.5069 414260.7745 394968.6064 434991.4935 424411.2741 423000.7011 430866.7768 396438.116 1.196839818 1.142311599 1.050336711 1.044956975 0.996293218 1.097249422 1.070561222 1.067003106 1.086844981 1 18.59673615 4.396468628 2.982106369 1.054757686 1.191293948 0.701481959 0.031587837 0.140732492 2.381144004 0.00795402 0.031276222 24915.44382 -4.396468628 0.136536262 YYVTIIDAPGHR ddPTM_BT-474_Pertuzumab_2h_R1 10 YYVTIIDAPGHR 12 0 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;;;;; 229.16 8.85E-12 1.3409E+11 33401620 36945850 34937860 42122480 39588900 40487430 43114640 40063920 43675230 48032840 FALSE TRUE 32096247.76 35892190.53 41251908.49 44296426.24 40862312.92 41306113.57 43642289.86 39236586.05 38717400.99 44779532.96 0.716761557 0.80153115 0.921222392 0.989211439 0.912522088 0.92243288 0.974603507 0.876216956 0.864622707 1 25.41633615 4.396641114 2.723666613 0.929381706 0.723399022 0.738448176 0.042690925 0.142629669 1.985949839 0.010997835 0.046626525 24925.34129 -4.396641114 -0.205982684 VFFRPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFFRPGK 7 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 86.086 0.018545 2495700000 3006700 3507900 2735600 3653100 3349600 3471200 4016900 4354900 4177800 4211700 FALSE TRUE 2889194.84 3407858.127 3229983.773 3841636.929 3457342.926 3541390.042 4066060.024 4264969.793 3703553.659 3926437.808 0.735831046 0.86792617 0.822624458 0.978402592 0.880529145 0.901934582 1.035559513 1.086218604 0.943235024 1 21.90478962 4.397047683 0.394014479 1.036067257 0.6146139 0.658670339 0.058147137 2.675640797 0.402817709 0.052946113 0.522491659 24948.68635 -4.397047683 -0.421453357 VQTEKEEKEEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQTEKEEKEEAR 12 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 121.45 0.00021152 1849230000 4122540 3716780 2440570 2051950 2997130 3336230 2910870 3382880 3994800 2931770 FALSE TRUE 3961426.579 3610781.074 2881635.289 2157851.385 3093535.408 3403690.856 2946494.098 3313022.346 3541327.052 2733198.607 1.449373847 1.321082582 1.05430878 0.789496738 1.131837036 1.245314134 1.078038782 1.212141093 1.295671322 1 21.38215887 4.397468731 4.102034403 1.108474035 1.424649538 0.424344925 0.135637109 0.206068375 6.441183246 0.035852268 0.114821922 24972.88577 -4.397468731 0.316175503 IEGYEDQVLITEHGDLGNSR ddPTM_BT-474_Pertuzumab_2h_R1 4 IEGYEDQVLITEHGDLGNSR 20 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;;; 256.11 3.54E-36 4335280000 2056250 2310150 2234800 2768290 2463930 2424970 2698990 2572970 2992870 3018160 FALSE TRUE 1975889.477 2244266.784 2638678.073 2911161.779 2543184.546 2474004.555 2732021.047 2519837.27 2653131.945 2813737.335 0.702229541 0.797610621 0.937784078 1.034624569 0.903845755 0.879259242 0.970958097 0.895548152 0.942920973 1 21.42405623 4.397478031 2.941115856 0.940709429 0.712407148 0.757839023 0.045654054 0.125733427 2.066118013 0.011696597 0.046593827 24973.42055 -4.397478031 -0.228302281 HSVTAAT(ph)PPPSPT(ph)SGESGDLLSNLLQSPSSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8;Q96QU8-2 Q96QU8 XPO6 Exportin-6 2 HSVTAAT(1)PPPS(0.287)PT(0.551)S(0.105)GES(0.057)GDLLSNLLQSPSSAK 266.78 1.51E-59 305190000 404230 418600 370080 416360 463950 443660 430380 348140 584330 476470 TRUE FALSE 388432.2447 406661.9379 436961.6884 437848.3895 478873.3731 452631.1092 435647.1192 340950.7873 517999.3081 444198.2625 0.87445692 0.915496462 0.983708684 0.985704868 1.078062238 1.018984421 0.980749264 0.767564433 1.166144382 1 18.76084422 4.397505315 2.959279798 0.980749159 0.878527443 0.143621314 0.09553532 0.610810924 10.16900521 0.025610165 0.101522625 24974.98956 -4.397505315 -0.102221716 GQS(ph)TDSLPQTICR ddPTM_BT-474_Pertuzumab_2h_R1 3 GQSTDSLPQTICR 13 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 GQS(0.933)T(0.066)DS(0.001)LPQTICR;GQS(0.982)T(0.018)DSLPQTICR;GQS(0.934)T(0.065)DS(0.001)LPQTICR 281.65 5.11E-24 274880000 496240 595120 564430 733390 684730 689680 788360 674210 716640 812130 TRUE FALSE 476846.3922 578147.7603 666435.0567 771240.3458 706754.9623 703625.8021 798008.1855 660287.3279 635290.0316 757123.7117 0.629813047 0.76361069 0.880219502 1.018645082 0.933473554 0.929340597 1.053999727 0.872099655 0.839083523 1 19.53016953 4.397602266 1.936599352 0.945132012 0.622517421 0.735045235 0.062115417 0.217693288 1.366737391 0.016690185 0.09884468 24980.56555 -4.397602266 -0.322614591 GPQGS(ph)PLLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPQGSPLLSR 10 0 Q8TEP8;H0Y966;A0A0A0MR42;K7ENP4;Q8TEP8-1;K7EPA2 Q8TEP8 CEP192 Centrosomal protein of 192 kDa 1 GPQGS(1)PLLSR;GPQGS(0.999)PLLS(0.001)R;GPQGS(1)PLLSR;GPQGS(1)PLLSR 124.45 0.0031158 259480000 333609 335146 349304 372160 337445 355423 362884 369981 378920 419560 TRUE FALSE 320571.1915 325587.9642 412431.003 391367.2222 348299.2249 362609.8966 367325.0829 362340.7631 335906.5902 391142.8275 0.819575789 0.832401725 1.054425581 1.00057369 0.89046558 0.927052399 0.939107296 0.926364329 0.858782436 1 18.57733598 4.397670172 13.42184543 0.944424223 0.822782451 0.453785059 0.054087332 0.677743621 112.123496 0.013436485 0.036807324 24984.4718 -4.397670172 -0.121641772 SEGFDTYR ddPTM_BT-474_Pertuzumab_2h_R1 6 SEGFDTYR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;;;; 214.69 2.03E-05 22243110000 13934690 14760580 12866200 15485100 14496990 14911940 16197810 16657100 15917580 16917900 FALSE TRUE 13390106.91 14339622.71 15191408.55 16284287.87 14963298.85 15213469.64 16396043.64 16313125.06 14110683.05 15772035.56 0.848977727 0.909180217 0.963186298 1.032478516 0.948723377 0.964585046 1.039564207 1.034306891 0.894664674 1 23.91086553 4.398353046 1.912762613 0.992804935 0.84483928 0.520366685 0.0426434 0.332277659 2.022111835 0.011454106 0.068857397 25023.78766 -4.398353046 -0.147965654 SVS(ph)PSPSVLSEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVSPSPSVLSEGR 13 0 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 1 SVS(0.846)PS(0.154)PSVLSEGR;SVS(1)PSPSVLSEGR;SVS(1)PSPSVLSEGR 272.67 4.24E-32 1240550000 565404 660862 554502 809300 738398 782926 893510 923380 806720 989870 TRUE FALSE 543307.3866 642014.8628 654712.8462 851068.07 762149.2423 798757.3001 904445.0427 904311.8803 715144.5276 922825.2232 0.588743538 0.695705803 0.709465704 0.922241881 0.825886878 0.865556424 0.980082707 0.979938408 0.774951215 1 19.81569791 4.398382083 0.628018206 0.936123399 0.449025935 0.716727328 0.070871732 1.242581472 0.493955468 0.034039818 0.410851709 25025.4608 -4.398382083 -0.487097463 AVS(ph)PPHLDGPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVSPPHLDGPPSPR 14 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BRN3;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 2 AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR 126.91 4.36E-05 3409340000 1742290 1871190 1741990 2249220 1974840 1969160 2034810 1935910 2107690 2120150 TRUE FALSE 1674199.381 1817825.493 2056806.343 2365302.514 2038362.522 2008977.764 2059712.613 1895932.782 1868433.867 1976550.352 0.847030979 0.919696021 1.040604071 1.196682144 1.031272753 1.016406064 1.042074446 0.959212994 0.945300415 1 20.91455328 4.398543771 3.548002586 1.029806839 0.858955924 0.464454953 0.064570951 0.21108726 5.073378079 0.017668422 0.061549989 25034.77955 -4.398543771 -0.170850915 FCNVDDDELR ddPTM_BT-474_Pertuzumab_2h_R1 6 FCNVDDDELR 10 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;;;; 285.74 4.23E-24 5326820000 2328360 2564940 2545000 2784820 3013790 2927720 2810090 2901930 3023900 3124060 FALSE TRUE 2237365.117 2491790.423 3004938.113 2928544.894 3110731.292 2986920.504 2844480.722 2842004.131 2680639.549 2912464.634 0.76820336 0.855560749 1.031750937 1.005521186 1.068075216 1.025564558 0.976657601 0.975807259 0.920402438 1 21.4738091 4.398573567 3.670526512 1.000363193 0.782287806 0.804878127 0.038130013 0.093667143 2.401265862 0.010307756 0.035154634 25036.49717 -4.398573567 -0.218075387 KAS(ph)GS(ph)ENEGDYNPGRK ddPTM_BT-474_Pertuzumab_2h_R1 3 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGRK;KAS(1)GS(1)ENEGDYNPGRK;KAS(1)GS(1)ENEGDYNPGRK 104.06 0.00074604 1274200000 2196890 1929380 1259130 1247100 1453260 1466020 1331240 1896690 1780970 1384280 TRUE FALSE 2111033.11 1874355.971 1486682.8 1311462.98 1500005.428 1495663.929 1347532.113 1857522.689 1578801.752 1290521.483 1.635798504 1.452401992 1.15200159 1.016227159 1.162325035 1.158960892 1.044176429 1.439358208 1.223382775 1 20.29952273 4.398772506 3.172437452 1.169370827 1.612604996 0.640192779 0.120987093 0.168856182 3.250368254 0.032965031 0.124151804 25047.96833 -4.398772506 0.443234169 TCNS(ph)PQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_BT-474_Pertuzumab_2h_R1 3 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.115)CNS(0.466)PQNS(0.293)T(0.125)DS(0.001)VSDIVPDSPFPGALGSDTR;T(0.095)CNS(0.9)PQNS(0.004)T(0.001)DSVSDIVPDSPFPGALGSDTR;T(0.16)CNS(0.695)PQNS(0.059)T(0.086)DSVSDIVPDSPFPGALGSDTR 181.05 4.42E-18 1093520000 227616 241757 232117 262941 233902 250878 235311 288136 305550 295180 TRUE FALSE 218720.5151 234862.3271 274065.7053 276511.4165 241425.6703 255950.9251 238190.8064 282185.8909 270865.245 275187.1957 0.794806294 0.853463863 0.995924627 1.004812073 0.87731433 0.930097508 0.865559191 1.025432489 0.984294507 1 18.07005382 4.398773772 4.478713631 0.957174042 0.806751243 0.535982085 0.05181565 0.152024156 5.538027413 0.01332445 0.041073092 25048.04139 -4.398773772 -0.150422799 TMIIS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 5 TMIISPER 8 0 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.001)MIIS(0.999)PER;TMIIS(1)PER;TMIIS(1)PER;TMIIS(1)PER;TMIIS(1)PER 149.23 0.00053348 4878680000 2086140 2202360 2242580 2669440 2261280 2169720 2395330 2527920 2470510 2655970 TRUE FALSE 2004611.342 2139550.849 2647864.092 2807210.118 2334016.125 2213593.225 2424644.765 2475717.569 2190068.062 2476078.786 0.809591098 0.864088357 1.069377964 1.133732147 0.942625953 0.893991434 0.979227631 0.999854117 0.884490459 1 21.23962579 4.398906089 6.163180577 0.987973503 0.822560214 0.429657893 0.07077813 0.176587885 10.56773245 0.018393187 0.052097192 25055.67397 -4.398906089 -0.16541329 LSSRIQSMLGNY(ph)DEMKDFIGDRS(ph)IPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSRIQSMLGNYDEMKDFIGDRSIPK 26 3 Q9UHB7;Q9UHB7-2;Q9UHB7-3;C9JCE0 Q9UHB7 AFF4 AF4/FMR2 family member 4 2 LS(0.084)S(0.087)RIQS(0.246)MLGNY(0.715)DEMKDFIGDRS(0.868)IPK 41.432 0.086675 85474000 211660 178340 97020 86662 131060 137360 104240 145630 166860 118270 TRUE FALSE 203388.0932 173253.9178 114553.6722 91134.63621 135275.6639 140137.5133 105515.7203 142622.6896 147918.7523 110259.4676 1.844631556 1.571329172 1.038946358 0.826547037 1.226884792 1.270979413 0.956976509 1.293518759 1.341551484 1 16.75054301 4.39906476 3.756983229 1.129463369 1.797999869 0.696316688 0.159588533 0.119993033 3.215421328 0.041279229 0.138932086 25064.82983 -4.39906476 0.6685365 SLS(ph)LGDK ddPTM_BT-474_Pertuzumab_2h_R1 3 SLSLGDK 7 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.001)LS(0.999)LGDK;SLS(1)LGDK;SLS(1)LGDK 137.05 0.003064 1327310000 1956030 1767840 1849580 2287110 2404960 2172150 2426120 3031290 2922040 2982760 TRUE FALSE 1879586.185 1717422.934 2183840.25 2405148.021 2482317.723 2216072.361 2455811.582 2968692.802 2590342.269 2780735.008 0.675931428 0.617614742 0.785346408 0.864932478 0.892684026 0.796937628 0.883151963 1.067592846 0.931531506 1 21.40703484 4.399158979 0.335220783 1.021317396 0.389960128 0.761889053 0.063793384 2.586551272 0.278909889 0.070330009 0.655377856 25070.26812 -4.399158979 -0.631357267 LCPGGQLPFLLYGTEVHTDTNKIEEFLEAVLCPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LCPGGQLPFLLYGTEVHTDTNKIEEFLEAVLCPPR 35 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 172.83 2.40E-15 110100000 142930 135780 92618 114210 118770 136890 105380 110460 149540 123610 FALSE TRUE 137344.1376 131907.6873 109356.1329 120104.3918 122590.3449 139658.0096 106669.672 108178.9624 132564.8461 115237.7846 1.191832506 1.144656571 0.948960736 1.042231003 1.063803381 1.211911615 0.925648409 0.938745593 1.150359204 1 16.81425431 4.399206479 6.548587887 1.030188505 1.180472147 0.27718768 0.087021787 0.237381713 15.59308162 0.02214427 0.062220636 25073.01029 -4.399206479 0.150283642 DLADELALVDVIEDKLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLADELALVDVIEDKLK 17 1 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ; 234.48 3.56E-20 873150000 927990 754170 439740 405330 508560 591450 462140 520520 548780 352920 FALSE TRUE 891723.1249 732661.81 519210.8 426249.1299 524918.2943 603409.5242 467795.8076 509771.0801 486484.7951 329016.4141 2.710269417 2.226824495 1.578069597 1.295525426 1.595416739 1.833980004 1.421800821 1.549378871 1.47860342 1 18.32780003 4.39929143 2.404584955 1.491778633 2.700336207 0.801797286 0.205710327 0.130858769 1.374956785 0.050666516 0.242020154 25077.91524 -4.39929143 1.208557574 RKS(ph)VEDRFDQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKSVEDRFDQQK 12 3 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 RKS(1)VEDRFDQQK 173.03 0.00018879 426840000 609890 550720 419640 346450 474860 517520 434530 552370 574460 408570 TRUE FALSE 586054.8245 535014.0048 495478.2828 364330.326 490134.3032 527984.609 439847.9081 540963.3665 509249.7091 380897.19 1.538616823 1.404615258 1.30081895 0.956505681 1.286788971 1.38616042 1.154768057 1.420234595 1.336974182 1 18.53904212 4.399590386 2.628425119 1.247039909 1.524975398 0.318680903 0.146679699 0.377862127 4.858206196 0.037566377 0.165363506 25095.18408 -4.399590386 0.277935489 EDGKVFDEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EDGKVFDEK 9 1 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 0 ;; 116.23 0.0012285 770450000 2477450 2255770 1561660 1310550 1788720 2058910 1838380 2150720 2446630 1911950 FALSE TRUE 2380628.515 2191437.648 1843886.701 1378187.643 1846255.803 2100542.571 1860878.644 2106306.88 2168898.82 1782451.924 1.335591992 1.229451195 1.034466443 0.773197652 1.035795568 1.178456789 1.043999347 1.181690711 1.21680635 1 20.76543173 4.399591808 3.836099153 1.06384383 1.316452862 0.374648862 0.119144669 0.244918161 6.827248847 0.032383026 0.107763825 25095.26628 -4.399591808 0.252609033 MEVQEQEEDISSLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEVQEQEEDISSLIR 15 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 193.11 2.47E-07 162015000 191198 204075 182387 230110 216110 204208 211960 221310 219960 243920 FALSE TRUE 183725.7708 198254.9808 215348.3881 241986.0047 223061.3744 208337.2257 214554.0299 216739.8712 194991.0629 227399.0811 0.807944209 0.871837212 0.947006413 1.064146801 0.980924695 0.916174439 0.943513179 0.953125536 0.857483953 1 17.7948669 4.399633534 2.84397265 0.958508929 0.81484355 0.484221223 0.050807098 0.236383762 3.614165248 0.01330727 0.054723969 25097.67745 -4.399633534 -0.143665379 FFTESR ddPTM_BT-474_Pertuzumab_2h_R1 6 FFTESR 6 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 132.72 0.034376 2238520000 2309650 2424380 2158010 2642480 2457740 2450140 2549400 2600860 2601370 2726980 FALSE TRUE 2219386.325 2355239.056 2548010.412 2778858.709 2536795.439 2499683.51 2580600.32 2547151.332 2306073.383 2542279.216 0.872990784 0.92642816 1.002254353 1.093058029 0.997842968 0.983245072 1.015073523 1.001916436 0.90708895 1 21.27769106 4.399667646 3.117282364 1.003500529 0.879925057 0.489704403 0.042474503 0.20308363 3.771543999 0.01085076 0.041476424 25099.64886 -4.399667646 -0.123575472 SNATNSSYS(ph)PTTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNATNSSYSPTTGR 14 0 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 SNATNSS(0.001)YS(0.999)PTTGR;SNATNSSYS(0.997)PT(0.003)TGR 179.92 1.95E-07 47122000 148976 163410 147837 187480 149266 179553 180041 188480 195119 200167 TRUE FALSE 143153.8532 158749.7068 174554.4345 197155.8653 154067.2764 183183.6847 182244.3956 184587.8221 172969.9091 186609.5108 0.767130532 0.850705337 0.935399454 1.056515632 0.825613206 0.981641739 0.976608292 0.989166208 0.926908325 1 17.50966299 4.399668347 2.334401337 0.963925737 0.769668609 0.563039559 0.05647303 0.234424321 2.299248471 0.014028245 0.069013625 25099.68936 -4.399668347 -0.194257128 YIQDIYSCGEIVEHLEESTAFR ddPTM_BT-474_Pertuzumab_2h_R1 3 YIQDIYSCGEIVEHLEESTAFR 22 0 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 0 ;; 229.66 2.63E-26 93998000 88986 96162 89247 113083 106139 101888 102187 98629 110041 115775 FALSE TRUE 85508.32874 93419.55391 105375.9182 118919.2272 109553.0573 103948.2452 103437.5951 96592.27668 97549.60701 107933.4561 0.792231916 0.865529163 0.976304493 1.101782816 1.015005553 0.963077149 0.958345992 0.894924337 0.903793972 1 16.7197826 4.399825142 3.261663001 0.973128801 0.802603988 0.548824199 0.055310677 0.208624918 4.251582046 0.016096545 0.059515813 25108.75285 -4.399825142 -0.170524813 RNVSSFPDDATS(ph)PLQENR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNVSSFPDDATSPLQENR 18 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 RNVSSFPDDAT(0.216)S(0.784)PLQENR 63.979 0.023918 197140000 49757 62294 67776 96357 73988 99606 84691 77189 50061 46156 TRUE FALSE 47812.44143 60517.43611 80024.63087 101329.9963 76367.89121 101620.1016 85727.47379 75595.02018 44378.28515 43029.81301 1.111146856 1.406407137 1.859748516 2.354878844 1.774766978 2.361620803 1.992280882 1.756805686 1.03133809 1 15.39304895 4.400075141 3.283013321 1.842081893 1.153212197 0.172714147 0.440368687 0.342345774 7.070461621 0.107372117 0.395317539 25123.21072 -4.400075141 -0.688869696 EYSFDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYSFDSR 7 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 82.305 0.088784 0 422590 458040 443370 491310 483040 454580 541920 519110 529200 595780 FALSE TRUE 406074.7156 444977.1477 523496.8217 516666.568 498577.4203 463771.9191 548552.1791 508390.1971 469127.4346 555427.2899 0.731103284 0.801143832 0.942511884 0.930214589 0.897646603 0.834982233 0.987621943 0.915313681 0.844624388 1 19.08323854 4.400083518 3.722749874 0.916231167 0.742616001 0.606383465 0.050547236 0.136984605 3.614985844 0.012144268 0.041156816 25123.69533 -4.400083518 -0.173615167 SLS(ph)PVAAPPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSPVAAPPLR 11 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 S(0.003)LS(0.997)PVAAPPLR;SLS(1)PVAAPPLR 136.96 9.27E-05 403940000 323320 357220 364000 441890 378280 375440 386980 432920 424780 434040 TRUE FALSE 310684.297 347032.4354 429782.8971 464695.9959 390447.7197 383031.654 391715.977 423980.0507 376560.7552 404642.0842 0.767800259 0.857628133 1.062130989 1.148412422 0.964921186 0.946593716 0.968055455 1.0477903 0.930602055 1 18.62628685 4.400084337 4.328920595 1.010762573 0.785626259 0.627586507 0.061906815 0.125274669 4.331743141 0.016116816 0.05047262 25123.7427 -4.400084337 -0.225136314 DQFGFINYEVGDSKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQFGFINYEVGDSKK 15 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 98.573 0.0057479 0 121400 113680 90116 91426 108520 92589 100950 98489 139680 107430 FALSE TRUE 116655.5538 110437.9577 106401.9658 96144.50682 112010.6444 94461.21302 102185.4563 96455.16773 123824.112 100153.6704 1.164765638 1.102685076 1.062387084 0.959969879 1.118387812 0.943162768 1.020286684 0.963071721 1.236341229 1 16.61185577 4.400232421 1.966878466 1.027263899 1.166382418 0.191300855 0.083130539 0.616483389 4.011707908 0.020754862 0.121734788 25132.31076 -4.400232421 0.139118519 VDDDALLVFWDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDDDALLVFWDAR 13 0 G3V4B8;Q96FK6 G3V4B8 WDR89 WD repeat-containing protein 89 0 ; 131.43 0.0003036 42449000 50467 54304 50159 58854 52722 54638 59147 63611 65191 67044 FALSE TRUE 48494.69385 52755.30309 59223.84708 61891.46199 54417.85101 55742.8178 59870.85868 62297.41062 57790.79098 62503.05016 0.775877237 0.844043658 0.947535311 0.990215067 0.870643127 0.891841561 0.957886991 0.996709928 0.924607532 1 15.93163897 4.401154131 2.851760026 0.947741976 0.781859779 0.657041839 0.041077045 0.170700545 2.624946482 0.011111356 0.045731679 25185.7061 -4.401154131 -0.165882197 GLLSNHTGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLSNHTGSPR 11 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 GLLSNHT(0.015)GS(0.985)PR;GLLSNHT(0.067)GS(0.933)PR 87.083 0.0090107 640000000 528840 680460 572330 918150 754180 794450 807060 748590 728610 949280 TRUE FALSE 508172.3481 661053.947 675762.7624 965535.8315 778438.8846 810514.3233 816937.0417 733131.3549 645901.2474 884984.4201 0.574216152 0.746966762 0.763587185 1.091020146 0.879607445 0.915851517 0.923108953 0.828411595 0.729844766 1 19.75529253 4.401230994 1.808701316 0.896691525 0.574561232 0.531792499 0.096760605 0.378241589 1.99777321 0.025932007 0.166642739 25190.16396 -4.401230994 -0.322130293 S(ph)PSAGDVHILTGFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSAGDVHILTGFAK 15 0 A0A3B3ITL0;A0A3B3IRJ9;Q9Y2H2-4;Q9Y2H2 A0A3B3ITL0 INPP5F Phosphatidylinositide phosphatase SAC2 1 S(0.991)PS(0.009)AGDVHILTGFAK;S(0.912)PS(0.088)AGDVHILTGFAK 159.88 4.02E-09 0 274520 289630 276200 321240 281240 294250 313720 310960 344190 361140 TRUE FALSE 263791.4549 281370.036 326115.484 337819.2349 290286.34 300199.9366 317559.3992 304538.5673 305118.9942 336679.6661 0.783508722 0.835720313 0.968622453 1.003384727 0.862203362 0.891648551 0.943209321 0.904535076 0.906259049 1 18.36101707 4.401313143 4.733196647 0.928797231 0.794536792 0.569610808 0.044273136 0.13644777 5.511093905 0.011024531 0.033347668 25194.92922 -4.401313143 -0.134260439 ESSPLFDDGQPWGEETEDGIMHNK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESSPLFDDGQPWGEETEDGIMHNK 24 0 O14777 O14777 NDC80 Kinetochore protein NDC80 homolog 0 ; 129.93 6.69E-05 184588000 169454 177709 177660 182844 207530 226770 200644 204608 244510 239270 FALSE TRUE 162831.5503 172640.9133 209767.114 192280.6008 214205.3909 231355.4448 203099.5413 200382.7733 216754.2499 223064.0298 0.729976727 0.773952275 0.940389691 0.861997342 0.960286565 1.03717056 0.910498844 0.898319525 0.971713145 1 17.76709836 4.401352163 1.308013342 0.947749005 0.68446942 0.71579403 0.049111762 0.432510128 0.997067098 0.014584143 0.130179816 25197.19304 -4.401352163 -0.263279585 TFLDKDAQRLS(ph)PIPEEVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFLDKDAQRLSPIPEEVPK 19 2 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 TFLDKDAQRLS(1)PIPEEVPK 87.511 0.0014114 798030000 524750 468440 252730 256460 372750 447070 329930 367110 452340 351080 TRUE FALSE 504242.1899 455080.5499 298403.9329 269695.9313 384739.8423 456110.0617 333967.782 359529.0502 400992.2596 327301.0389 1.54060675 1.390403622 0.911710925 0.823999619 1.175492273 1.39354908 1.020368842 1.098465961 1.225148142 1 18.32025866 4.40158992 5.596720005 1.088091562 1.506087624 0.510623494 0.153322621 0.150245567 7.954294297 0.039832775 0.11492187 25210.99116 -4.40158992 0.417996062 FLEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 FLEELR 6 0 Q5T508;D6R9F0;Q92535;Q9HBX8-1;O75473-3;O75473-2;O75473;Q9HBX8-2;Q9HBX8 REV__Q8IYE1 LGR6;PIGC;LGR5 Phosphatidylinositol N-acetylglucosaminyltransferase subunit C;Leucine-rich repeat-containing G-protein coupled receptor 6;Leucine-rich repeat-containing G-protein coupled receptor 5 0 ;;; 129.96 0.037149 745620000 878180 962480 876570 1046730 1051660 1093490 1023740 1067950 1125540 1173430 FALSE TRUE 843859.7547 935031.0128 1034985.698 1100751.861 1085487.599 1115601.117 1036268.836 1045896.459 997773.4178 1093952.541 0.771386073 0.854727219 0.94609744 1.00621537 0.992262057 1.019789319 0.947270377 0.956071146 0.912081083 1 20.06111872 4.401599845 2.10362855 0.974416019 0.768643292 0.828632065 0.0303944 0.155025692 1.186547132 0.008490813 0.0465927 25211.56733 -4.401599845 -0.205772727 LS(ph)PTSLVHPVMSTLPELSCK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPTSLVHPVMSTLPELSCK 20 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 LS(0.602)PT(0.199)S(0.199)LVHPVMSTLPELSCK 183.01 2.92E-17 930060000 1046500 1114100 1181400 1371600 1247500 1141100 1242400 1209000 1243500 1435800 TRUE FALSE 1005601.623 1082326.959 1394905.26 1442388.44 1287626.97 1164173.824 1257604.863 1184033.728 1102343.093 1338551.987 0.75126079 0.808580443 1.042100175 1.077573717 0.961955145 0.869726268 0.93952635 0.884563124 0.823534016 1 20.35224174 4.402211378 6.633944031 0.943941804 0.765056493 0.463420862 0.074011636 0.178315757 12.3575434 0.019816374 0.055633551 25247.0929 -4.402211378 -0.178885311 LKNGFPHPEPDCNPSEAASEESNS(ph)EIEQEIPVEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPSEAAS(0.038)EES(0.378)NS(0.584)EIEQEIPVEQK;LKNGFPHPEPDCNPSEAAS(0.001)EES(0.024)NS(0.975)EIEQEIPVEQK 229.74 2.20E-37 531860000 943200 808460 604900 493710 638680 727550 605990 639720 776020 757050 TRUE FALSE 906338.7012 785403.5124 714218.8859 519190.4323 659223.7222 742261.5595 613406.2869 626509.5584 687929.4629 705774.3292 1.284176349 1.112825276 1.011964953 0.735632356 0.934043213 1.051698154 0.869125245 0.887691054 0.974715903 1 19.42884743 4.402565204 2.051929261 0.9172228 1.283546794 0.651333271 0.083300609 0.233474596 1.681348954 0.021927905 0.123766835 25267.67043 -4.402565204 0.366323994 ASS(ph)PIKQSHEPVPDTSVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSPIKQSHEPVPDTSVEK 19 1 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 AS(0.021)S(0.978)PIKQS(0.001)HEPVPDTSVEK 188.49 3.53E-21 0 203570 185110 123560 104490 155630 179560 140000 169180 196990 156050 TRUE FALSE 195614.2593 179830.844 145890.0406 109882.7414 160635.9803 183190.8262 141713.3619 165686.3739 174628.521 145480.5945 1.344607231 1.23611568 1.002814438 0.755308581 1.104174621 1.259211422 0.974104913 1.13888986 1.200356114 1 17.1504672 4.402649529 4.284550091 1.058348346 1.323193382 0.348182593 0.132512072 0.228381996 7.830798507 0.034398323 0.108534356 25272.57702 -4.402649529 0.264845036 TERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTR 34 1 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 182.74 4.18E-20 2100300000 503930 532960 525830 591790 521780 616650 575500 562740 586890 682590 FALSE TRUE 484235.8585 517760.5026 620859.178 622332.3528 538563.5276 629119.0855 582543.1412 551119.2223 520268.7076 636357.5713 0.760949316 0.813631402 0.97564515 0.977960161 0.846322181 0.988625128 0.915433661 0.866052746 0.817572904 1 19.27947812 4.402655558 5.481446374 0.916826605 0.772926458 0.451961186 0.060763965 0.164290692 8.491718649 0.014983082 0.043452934 25272.92789 -4.402655558 -0.143900148 GMYDGPVFDLTTT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 GMYDGPVFDLTTTPK 15 0 Q14195-2;Q14195;H0YBT4 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 1 GMYDGPVFDLTT(0.004)T(0.996)PK 207.52 3.74E-08 62034000 146760 129440 98922 87216 105270 96664 104720 131570 125630 106990 TRUE FALSE 141024.4569 125748.4979 116799.4059 91717.22821 108656.1052 98618.61231 106001.5947 128853.0335 111369.0091 99743.472 1.413871546 1.260719077 1.170997997 0.919531137 1.089355554 0.988722473 1.062742178 1.291844277 1.116554365 1 16.6059348 4.402756708 2.100785903 1.088016534 1.411384717 0.564623198 0.096307564 0.329620523 2.512390943 0.028258936 0.155731147 25278.81477 -4.402756708 0.323368183 AMEVEIEDLHLQIDDIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AMEVEIEDLHLQIDDIAK 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 102.08 0.00057465 43743000 51545 57472 60061 67560 60783 57144 70746 66177 74043 77352 FALSE TRUE 49530.56441 55832.95483 70915.35875 71046.7797 62738.1404 58299.49083 71611.81071 64810.42182 65637.94905 72112.88014 0.68684768 0.774243862 0.983393793 0.985216227 0.869999094 0.808447683 0.993051596 0.898735728 0.910211171 1 16.13796934 4.402983178 4.497628954 0.924454214 0.704504165 0.653372348 0.059665727 0.115310909 4.308178015 0.01487652 0.045966398 25292.00027 -4.402983178 -0.219950048 TEDGGWEWS(ph)DDEFDEESEEGKAAISQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEDGGWEWSDDEFDEESEEGKAAISQLR 28 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;T(0.001)EDGGWEWS(0.999)DDEFDEESEEGKAAISQLR 259.53 6.98E-54 82322000 104540 88982 60848 50058 69786 82653 62975 69701 80385 59620 TRUE FALSE 100454.4612 86444.32048 71844.58716 52641.49938 72030.73007 84324.30029 63745.70689 68261.64999 71260.0318 55581.8843 1.80732378 1.555260704 1.292589988 0.947098143 1.295938973 1.517118417 1.146879198 1.228127669 1.282072976 1 15.76232712 4.402987203 2.454394229 1.219538977 1.79468133 0.625875505 0.151401601 0.20749334 2.280825738 0.039038994 0.184437161 25292.23471 -4.402987203 0.575142353 TDPVPEEGEDVAATISATETLSEEEQEELRR ddPTM_BT-474_Pertuzumab_2h_R1 6 TDPVPEEGEDVAATISATETLSEEEQEELRR 31 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 ;;;;; 298.01 3.15E-81 1400737000 63493.2 54716.7 29994.8 21844 39941.4 43305.5 45155.1 43882 49800.8 45608.5 FALSE TRUE 61011.81555 53156.23329 35415.52759 22971.37146 41226.1514 44181.16688 45707.72162 42975.82137 44147.62197 42519.39567 1.434917279 1.250164365 0.83292641 0.540256302 0.969584604 1.039082663 1.074985213 1.010734529 1.038293731 1 15.37583347 4.402991433 4.39466785 0.941236817 1.39792224 0.553996385 0.148887385 0.154983318 5.562934383 0.040932328 0.127730317 25292.48106 -4.402991433 0.456685423 GAEQDNPNQYSWGENYAGSSGLMSAS(ph)PELGPAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAEQDNPNQYSWGENYAGSSGLMSASPELGPAQR 34 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 GAEQDNPNQYSWGENYAGSSGLMSAS(1)PELGPAQR;GAEQDNPNQYSWGENYAGSSGLMSAS(1)PELGPAQR 279.43 4.02E-74 311970000 237920 252580 228424 267840 256620 282630 273140 259040 275900 312110 TRUE FALSE 228621.8234 245376.6657 269705.2981 281663.2545 264874.4154 288344.9722 276482.769 253690.7335 244580.9887 290970.5117 0.785721625 0.843304238 0.926916259 0.968013057 0.910313605 0.990976613 0.950208897 0.871877813 0.840569676 1 18.15051343 4.403094041 2.81777502 0.928726665 0.790611244 0.51287944 0.047376938 0.234874179 3.517901146 0.012531516 0.052309179 25298.45743 -4.403094041 -0.138115421 ERDLS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 ERDLSR 6 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 ERDLS(1)R;ERDLS(1)R 76.679 0.045069 163282000 61087 66508 72156 83071 69792 70357 77038 75904 78355 88469 TRUE FALSE 58699.6525 64611.25696 85196.1943 87358.30427 72036.92306 71779.66675 77980.81409 74336.55587 69460.46889 82476.91583 0.711710082 0.783385949 1.032970176 1.059184905 0.873419215 0.870300084 0.945486544 0.901301354 0.842180726 1 16.33170276 4.403228174 6.012747263 0.934568743 0.728531295 0.563792627 0.068965269 0.135601193 8.158299698 0.017805288 0.050703953 25306.27214 -4.403228174 -0.206037448 EQQEAIEHIDEVQNEIDRLNEQAS(ph)EEILKVEQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK 33 2 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 EQQEAIEHIDEVQNEIDRLNEQAS(1)EEILKVEQK;EQQEAIEHIDEVQNEIDRLNEQAS(1)EEILKVEQK 330.31 2.03E-117 102475000 114259 95184 65203 46614.5 74933 88350 65773 70208 87161 63832 TRUE FALSE 109793.632 92469.44551 76986.63253 49020.27993 77343.288 90136.49753 66577.94965 68758.18027 77266.84869 59508.60178 1.845004397 1.553883686 1.293705956 0.823751163 1.299699299 1.514680144 1.118795395 1.15543263 1.29841479 1 15.8608106 4.403468744 2.382120289 1.186656474 1.831275468 0.599252924 0.176485935 0.227819168 2.336678586 0.046189366 0.224804648 25320.29402 -4.403468744 0.644618995 VDDQIYSEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 VDDQIYSEFR 10 0 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 ;;; 217.63 1.67E-08 1203780000 970580 1047010 969670 1213830 1021670 1007730 1179870 1204320 1176230 1254080 FALSE TRUE 932648.6606 1017150.3 1144910.939 1276475.912 1054532.943 1028106.991 1194309.602 1179450.371 1042709.302 1169140.045 0.797721937 0.869998684 0.979276131 1.091807536 0.901973162 0.879370265 1.021528266 1.008818727 0.891860053 1 20.15701632 4.403652034 3.231026978 0.975037013 0.80745741 0.454042451 0.062685661 0.216091671 4.328789948 0.016189373 0.060691413 25330.98243 -4.403652034 -0.167579604 EEVFWR ddPTM_BT-474_Pertuzumab_2h_R1 6 EEVFWR 6 0 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ;;;;; 149.11 0.024845 2778060000 2455230 2760650 2611400 3203590 2947740 2772440 3221120 3258530 3337170 3690340 FALSE TRUE 2359276.897 2681918.965 3083338.07 3368927.664 3042556.734 2828500.636 3260541.03 3191240.217 2958348.452 3440389.985 0.685758564 0.779539232 0.896217604 0.979228424 0.884363909 0.822145352 0.947724254 0.927580952 0.859887532 1 21.71414068 4.403767454 2.490513109 0.913764397 0.689640576 0.692528297 0.050493674 0.171471048 1.948227256 0.012792612 0.059717633 25337.71542 -4.403767454 -0.224123821 RPAEATSS(ph)PTS(ph)PERPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.249)S(0.325)S(0.427)PT(0.381)S(0.618)PERPR;RPAEAT(0.066)S(0.423)S(0.51)PT(0.321)S(0.68)PERPR 141.36 7.93E-06 8841730000 1133460 1237410 1068240 1358750 1315380 1370520 1293920 1307300 1339150 1444260 TRUE FALSE 1089163.13 1202120.278 1261294.731 1428875.25 1357690.392 1398232.853 1309755.38 1280303.798 1187135.306 1346438.984 0.808921268 0.892814522 0.936763378 1.061225401 1.008356419 1.038467298 0.972755094 0.950881409 0.881685186 1 20.36071742 4.403774864 1.984840474 0.985367693 0.808444155 0.583581008 0.047581394 0.311238617 2.064739671 0.013418136 0.078656679 25338.14772 -4.403774864 -0.176923537 EDAPIGPHLQSMPSEQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDAPIGPHLQSMPSEQIR 18 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 223.11 5.33E-19 1354290000 536380 594440 512070 656800 625610 638900 602480 643230 722190 751870 FALSE TRUE 515417.6766 577487.1532 604612.4399 690697.5267 645733.3138 651818.9957 609853.3305 629947.0757 640210.0189 700945.1752 0.735318103 0.823869218 0.862567375 0.985380242 0.921232268 0.929914377 0.870044266 0.898710909 0.913352487 1 19.41894208 4.403803404 1.764612576 0.921034206 0.730018928 0.716764611 0.038990458 0.268438505 1.329412284 0.010451573 0.069412288 25339.81291 -4.403803404 -0.191015279 DMEESIR ddPTM_BT-474_Pertuzumab_2h_R1 6 DMEESIR 7 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 206.65 0.0004959 5094540000 4225936 4681864 4262919 5366740 4821693 4600392 5340070 5411270 5490150 6025590 FALSE TRUE 4060781.749 4548341.823 5033323.291 5643718.095 4976787.134 4693415.078 5405423.374 5299525.383 4866931.189 5617471.422 0.722884274 0.809677786 0.896012265 1.004672329 0.885947922 0.835503152 0.962252047 0.943400506 0.866391802 1 22.42148945 4.404282013 2.2988883 0.92513368 0.72468507 0.619888986 0.052026394 0.222930464 2.103308456 0.013390419 0.067609906 25367.75374 -4.404282013 -0.200448611 GFSEEHNTWEPEKNLDCPELISEFMK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFSEEHNTWEPEKNLDCPELISEFMK 26 1 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 183.39 1.04E-17 128940000 121420 113280 57638 69588 90585 99465 86313 86075 125880 90741 FALSE TRUE 116674.7722 110049.3653 68054.46875 73179.44502 93498.74879 101476.2504 87369.32431 84297.52117 111590.6301 84595.03125 1.379215427 1.300896326 0.804473593 0.865056067 1.10525107 1.199553318 1.032794988 0.996483126 1.319115656 1 16.36828531 4.404551261 8.9323375 1.039471615 1.359789467 0.425458271 0.140592822 0.238355712 26.4683384 0.03514205 0.096751852 25383.48576 -4.404551261 0.320317852 MGGAGGEGS(ph)DDDTSLT ddPTM_BT-474_Pertuzumab_2h_R1 6 MGGAGGEGSDDDTSLT 16 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(0.996)DDDT(0.004)SLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT 305.6 7.89E-46 16847580000 4562060 4630380 3810800 4470950 4357540 4615330 4540740 4618810 5095200 5162160 TRUE FALSE 4383769.652 4498326.096 4499496.331 4701696.265 4497704.232 4708655.135 4596310.934 4523429.959 4516814.257 4812522.305 0.910908952 0.934712779 0.934955943 0.976971319 0.934583561 0.978417311 0.95507317 0.939929142 0.938554457 1 22.1983618 4.404908598 1.439198214 0.95626196 0.908065536 0.366628223 0.02031712 0.760533436 2.235072165 0.005407142 0.044475498 25404.37984 -4.404908598 -0.048196423 KAYS(ph)FCGTVEYMAPEVVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAYSFCGTVEYMAPEVVNR 19 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;B4DG22;B1AXG1;B7ZB17;P51812;Q9UK32-2;Q9UK32 E9PGT3;B4DG22;Q9UK32-2 RPS6KA1;RPS6KA3;RPS6KA6 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-3;Ribosomal protein S6 kinase alpha-6 1 KAYS(0.984)FCGT(0.016)VEYMAPEVVNR 129.08 1.24E-05 290090000 166550 130430 66473 68041 79253 87125 57052 90849 64968 57723 TRUE FALSE 160041.0419 126710.2641 78486.14978 71552.60416 81802.24472 88886.72719 57750.21944 88972.9364 57593.10501 53813.3698 2.974001488 2.354624224 1.45848792 1.329643626 1.520110059 1.651759173 1.073157464 1.653361177 1.070237847 1 15.71567703 4.404909117 2.273311796 1.371244513 2.989176521 0.853109815 0.226087449 0.114851507 1.05500813 0.054792231 0.280165609 25404.41023 -4.404909117 1.617932008 up RTNS(ph)SSSSPVVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTNSSSSSPVVLK 13 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 RT(0.07)NS(0.789)S(0.127)S(0.004)S(0.008)S(0.002)PVVLK 108.34 0.0012967 104890000 205430 193100 136610 144260 168140 178220 161800 191070 177090 187010 TRUE FALSE 197401.5685 187592.9771 161298.4659 151705.2759 173548.3758 181823.7305 163780.1568 187124.3377 156987.4856 174343.6461 1.132255593 1.075995491 0.925175476 0.870150873 0.99543849 1.042904256 0.939409955 1.07330747 0.900448563 1 17.41157426 4.404909489 5.028141903 0.975046091 1.120016577 0.458695373 0.059925911 0.16952963 7.737880188 0.015269679 0.04539551 25404.43199 -4.404909489 0.144970487 SPSFGDPQLS(ph)PEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSFGDPQLSPEAR 14 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 SPSFGDPQLS(1)PEAR 99.055 0.0024469 227760000 176380 198060 173540 239320 200810 200870 207970 220510 237390 252670 TRUE FALSE 169486.8746 192411.5227 204902.5384 251671.3339 207269.236 204931.729 210515.1991 215956.3914 210442.4824 235556.4358 0.719517062 0.816838317 0.869866016 1.068412047 0.87991328 0.869989938 0.89369326 0.916792575 0.893384558 1 17.84571322 4.40494941 2.216005399 0.922516578 0.723611339 0.558257625 0.059416352 0.271301582 2.345930992 0.015364081 0.080607233 25406.76733 -4.40494941 -0.198905239 QIAQSKEDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_BT-474_Pertuzumab_2h_R1 2 QIAQSKEDDDVIVNKPHVSDEEEEEPPFYHHPFK 34 2 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;H7C1M2;H7C2G8;J3QSZ5 P18583-7 SON Protein SON 1 QIAQSKEDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;QIAQS(0.488)KEDDDVIVNKPHVS(0.512)DEEEEEPPFYHHPFK 263.76 4.88E-60 854700000 1471318 1158516 701527 558572 765473 952027 731571 384498 1105652 692880 TRUE FALSE 1413817.266 1125476.258 828308.5343 587399.9679 790095.1342 971277.6382 740524.1847 376557.9819 980143.0202 645950.6204 2.188738924 1.742356493 1.282309372 0.909357386 1.22315098 1.503640692 1.146409898 0.582951653 1.517365243 1 19.30106436 4.4050953 1.908293927 1.09522193 2.229824659 0.635153279 0.260495024 0.282456123 1.698810661 0.073455186 0.450386105 25415.30347 -4.4050953 1.134602729 EPS(ph)PEKNSK ddPTM_BT-474_Pertuzumab_2h_R1 5 EPSPEKNSK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK 116.71 0.00076858 7911200000 13705410 11495910 6359990 5312480 7935340 9871210 7562570 8975060 10584380 7417860 TRUE FALSE 13169787.43 11168057.9 7509381.67 5586657.729 8190587.418 10070812.63 7655122.994 8789721.875 9382885.556 6915441.735 1.904402919 1.614944978 1.085886044 0.807852621 1.184391067 1.456279008 1.106960811 1.27102826 1.356802055 1 22.72138998 4.405497094 3.657079397 1.170635883 1.857700828 0.666919647 0.174785418 0.132973216 3.422461113 0.045905209 0.158593384 25438.8277 -4.405497094 0.687064945 QRS(ph)PIALPVKQEPPQIDAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 QRSPIALPVKQEPPQIDAVK 20 2 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 QRS(1)PIALPVKQEPPQIDAVK;QRS(1)PIALPVKQEPPQIDAVK 177.52 3.40E-17 1283310000 1168110 1028080 599850 559460 801480 1100640 757850 770940 919010 743070 TRUE FALSE 1122458.97 998760.165 708256.2386 588333.7976 827260.3321 1122895.695 767124.795 755019.8196 814687.8376 692741.207 1.620315001 1.441750765 1.022396577 0.849283674 1.194183807 1.620945432 1.107375723 1.089901701 1.176034902 1 19.40195697 4.405665291 4.542095554 1.142017826 1.584015601 0.425093852 0.18980861 0.190517692 7.332815365 0.049822234 0.153741164 25448.68175 -4.405665291 0.441997775 NEEDEGHSNSSPR ddPTM_BT-474_Pertuzumab_2h_R1 11 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;;;;;;;;; 216.15 2.80E-11 3604543000 4463768 4585073 4243269 5082605 4611673 4317762 4793034 4715044 5132213 5253371 FALSE TRUE 4289319.012 4454311.207 5010122.099 5344918.853 4760011.65 4405070.106 4851692.584 4617676.694 4549625.696 4897555.503 0.875808147 0.909496831 1.022984241 1.091344212 0.971915815 0.89944261 0.990635549 0.942853367 0.928958476 1 22.22363041 4.405692464 5.9860551 0.978157208 0.883681899 0.336400586 0.050447461 0.221315067 13.56207354 0.013404787 0.038239396 25450.2741 -4.405692464 -0.09447531 SVIEPLPVT(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVIEPLPVTPTR 12 0 E9PM17;B3KNX7;Q13153;Q13153-2;H0YCM0 E9PM17 PAK1 Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 1 1 SVIEPLPVT(0.908)PT(0.092)R;SVIEPLPVT(0.98)PT(0.02)R 139.48 0.00065799 303260000 295460 356280 394500 483360 439160 493730 424430 398630 418780 456010 TRUE FALSE 283913.0966 346119.2432 465794.9256 508306.2675 453285.9802 503713.5589 429624.3013 390398.1512 371241.8501 425124.0365 0.667835907 0.814160606 1.095668289 1.195665791 1.066244064 1.184862571 1.010585769 0.918315874 0.873255375 1 18.69752431 4.405713268 3.788675441 1.042582657 0.692482254 0.617513201 0.09792527 0.152033949 4.192383037 0.027581023 0.093273125 25451.49329 -4.405713268 -0.350100402 WDET(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 2 WDETPGR 7 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDET(1)PGR;WDET(1)PGR 125.82 0.044852 1320360000 4022400 3459700 2061390 2368300 2450600 2201000 1773590 2911600 2226000 2089400 TRUE FALSE 3865200.161 3361032.743 2433929.028 2490528.247 2529425.775 2245505.728 1795295.725 2851474.443 1973313.812 1947883.077 1.984308097 1.725479719 1.249525219 1.278582003 1.298551132 1.152792873 0.921665035 1.46388378 1.013055576 1 20.89347565 4.405722434 1.671918785 1.181433944 2.065594209 0.767070172 0.153802413 0.247159017 1.065809182 0.040780009 0.288226072 25452.03046 -4.405722434 0.884160265 (ac)SQGDSNPAAIPHAAEDIQGDDRWMSQHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQGDSNPAAIPHAAEDIQGDDRWMSQHNR 29 1 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 77.522 0.00031087 860690000 17005.5 23872 28689.8 45918 39855 26291 44265 29078 15846.2 13373 FALSE TRUE 16340.90626 23191.19393 33874.68506 48287.83348 41136.97227 26822.62203 44806.72831 28477.52914 14047.40581 12467.2348 1.31070815 1.860171426 2.717096903 3.873179118 3.299606764 2.151449176 3.593958808 2.284189686 1.126745909 1 13.60585389 4.405958254 3.453738695 2.6506636 1.394914569 0.137649564 0.908855355 0.373167053 8.578643633 0.223323216 0.801737213 25465.85455 -4.405958254 -1.25574903 SIFEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIFEAR 6 0 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 105.42 0.076756 256350000 316310 330200 282450 358070 351310 280020 390900 315410 347780 371260 FALSE TRUE 303948.2555 320783.0193 333494.9981 376550.0356 362610.2052 285682.1963 395683.9511 308896.6733 308301.4724 346114.2295 0.878173243 0.926812572 0.96354027 1.087935726 1.047660496 0.825398588 1.143217809 0.892470309 0.890750643 1 18.40088873 4.406350674 2.657379839 0.982256565 0.883101813 0.118987149 0.09109496 0.636776609 8.369999739 0.02268534 0.100359994 25488.87536 -4.406350674 -0.099154752 EKHLDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKHLDLEK 8 1 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 84.213 0.010582 52708000 111180 92951 68261 57433 71897 40000 84814 74454 89581 93780 FALSE TRUE 106834.9627 90300.12849 80597.28116 60397.12401 74209.6323 40808.82741 85851.9791 72916.49888 79412.14043 87428.19707 1.22197376 1.032849029 0.921868274 0.690819736 0.848806618 0.466769632 0.981971286 0.834015813 0.908312685 1 16.41581103 4.406379827 1.815986544 0.810739847 1.234292893 0.430031156 0.146420842 0.424577794 2.254259244 0.038121313 0.247221389 25490.58643 -4.406379827 0.423553046 ISLSKS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISLSKSPTK 9 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 ISLS(0.093)KS(0.906)PTK;ISLS(0.001)KS(0.995)PT(0.003)K 137.4 0.00035291 1863690000 2291670 1872210 1418760 1079310 1391750 788300 1582630 1631320 1839450 1936860 TRUE FALSE 2202109.003 1818816.404 1675161.492 1135013.318 1436516.903 804239.9661 1601998.699 1597632.672 1630643.348 1805674.747 1.219549095 1.007277976 0.927720507 0.628581266 0.795556844 0.44539581 0.887202251 0.884784303 0.903065932 1 20.78410662 4.406402979 1.783881204 0.786843098 1.229260018 0.43426873 0.151737559 0.45458422 2.307869873 0.041472542 0.274130591 25491.94538 -4.406402979 0.442416919 AEPEDHYFLLTEPPLNTPENR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEPEDHYFLLTEPPLNTPENR 21 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ; 218.76 5.31E-25 2555690000 1884900 2034840 1815370 2262550 2098550 2197230 2234070 2069000 2248470 2582070 FALSE TRUE 1811236.024 1976808.356 2143447.742 2379320.477 2166051.767 2241659.496 2261411.217 2026274.427 1993233.112 2407184.099 0.752429374 0.821211953 0.890437812 0.988424806 0.899828047 0.931237248 0.93944257 0.841761304 0.828035177 1 21.19891505 4.406405489 2.466489554 0.910472253 0.756008028 0.512287418 0.052189919 0.273502813 3.035031393 0.013837884 0.065587269 25492.09272 -4.406405489 -0.154464225 ERLEQQVPVNQVFGQDEMIDVIGVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERLEQQVPVNQVFGQDEMIDVIGVTK 26 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 241.54 3.68E-45 202682000 133659 137442 143740 139941 136494 151192 146349 155585 170097 178347 FALSE TRUE 128435.4585 133522.2887 169717.0155 147163.3718 140884.4535 154249.2058 148140.0628 152372.1154 150788.3017 166267.3988 0.772463269 0.803057543 1.020747402 0.885100584 0.847336606 0.927717682 0.890974803 0.916428094 0.906902392 1 17.34314579 4.406499449 9.780642081 0.915725376 0.780074131 0.546350305 0.049641138 0.221254239 28.6248383 0.011470044 0.031509045 25497.60855 -4.406499449 -0.135651246 LKVSELKEELK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKVSELKEELK 11 2 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 98.942 0.0028936 378130000 1497900 1214600 1008100 623900 952520 759180 993010 1186400 1269700 1162600 FALSE TRUE 1439360.412 1179960.797 1190286.095 656099.5538 983158.6709 774531.1398 1005162.753 1161900.425 1125568.979 1083856.066 1.32799959 1.088669274 1.098195722 0.605338268 0.907093387 0.714607007 0.927395052 1.072006202 1.038485657 1 20.04774175 4.406525989 1.833015279 0.906118916 1.322831172 0.451072067 0.144049705 0.454535269 2.470006199 0.040720656 0.261565336 25499.16678 -4.406525989 0.416712257 VGGS(ph)SVDLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 VGGS(0.937)S(0.063)VDLHR;VGGS(0.917)S(0.083)VDLHR 125.72 0.0032107 0 1779750 1321450 574350 555180 527430 527550 400280 714540 444370 382170 TRUE FALSE 1710195.402 1283763.54 678147.8213 583832.9063 544395.2649 538217.4225 405178.7464 699784.4993 393926.9806 356285.2855 4.800073065 3.603189893 1.903384307 1.638666906 1.527975718 1.510636123 1.13723121 1.964112827 1.105650434 1 18.44267338 4.40660227 1.681724066 1.457594619 5.089980148 0.945003926 0.27303008 0.103980978 0.454704394 0.071004675 0.499923754 25503.64594 -4.40660227 3.632385529 up GQLCELSCSTDYR ddPTM_BT-474_Pertuzumab_2h_R1 4 GQLCELSCSTDYR 13 0 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;;; 300.71 1.51E-40 1448480000 931720 1015010 896700 1091610 1082080 1043670 1145880 1083930 1148810 1304680 FALSE TRUE 895307.3523 986062.9086 1058753.637 1147948.123 1116886.086 1064773.722 1159903.622 1061546.467 1018401.905 1216312.862 0.736083109 0.810698415 0.870461598 0.943793459 0.918255591 0.875411053 0.953622755 0.872757742 0.837286143 1 20.21408294 4.40669475 1.855758517 0.908075353 0.730044262 0.627506757 0.044358045 0.29077875 1.629280903 0.011337827 0.07190874 25509.07733 -4.40669475 -0.178031091 DVDELPSLQPSVGS(ph)PSRPSSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 DVDELPSLQPS(0.025)VGS(0.933)PS(0.042)RPSSSR;DVDELPSLQPS(0.216)VGS(0.717)PS(0.066)RPSSSR;DVDELPSLQPS(0.325)VGS(0.651)PS(0.024)RPSSSR;DVDELPSLQPS(0.007)VGS(0.908)PS(0.085)RPSSSR 174.59 1.48E-12 1939090000 1314500 1369970 1231930 1380610 1366860 1458190 1470690 1484190 1449470 1485590 TRUE FALSE 1263127.887 1330899.797 1454567.155 1451863.448 1410826.293 1487675.601 1488688.744 1453540.958 1284932.242 1384969.666 0.912025669 0.960959528 1.050251995 1.048299817 1.018669454 1.074157534 1.074889061 1.049511042 0.927769231 1 20.40142295 4.406713363 3.416981887 1.036909126 0.918787483 0.463374823 0.041366966 0.183742328 4.136751712 0.010234054 0.037061844 25510.17059 -4.406713363 -0.118121642 NGSFGGQYSECRDPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGSFGGQYSECRDPAR 16 1 O43823 O43823 AKAP8 A-kinase anchor protein 8 0 ; 97.235 0.0028657 546120000 553930 500660 391050 427240 414860 356740 443120 417660 487330 484440 FALSE TRUE 532281.8032 486381.667 461721.4339 449289.9076 428204.3487 363953.5272 448543.0351 409035.175 432010.3415 451628.4473 1.178583427 1.076950909 1.022347987 0.994821983 0.948134138 0.805869359 0.993168251 0.905689572 0.956561404 1 18.78477684 4.406939955 0.916527566 0.928260982 1.235724314 0.682862605 0.052874654 0.737613413 0.690345722 0.01749466 0.204371071 25523.48396 -4.406939955 0.307463332 EGTGTEMPMIGDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EGTGTEMPMIGDR 13 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;; 169.65 1.75E-06 626530000 392451 410435 371627 403672 446873 479550 418628 420850 499510 529050 FALSE TRUE 377113.581 398729.7957 438788.2657 424505.5603 461247.0759 489246.8296 423751.2947 412159.3004 442807.7189 493216.9723 0.764599765 0.808426753 0.889645512 0.860687252 0.935180867 0.991950515 0.859157974 0.835655145 0.897794974 1 18.91186292 4.407189928 1.509693932 0.902688974 0.746852356 0.481378629 0.051638373 0.618174544 2.049915849 0.015250434 0.120299716 25538.17909 -4.407189928 -0.155836618 SEEPAGQILSHLSSELK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEEPAGQILSHLSSELK 17 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 105.39 0.00080404 25646000 40667 45865 43708 53370 45268 56838 54651 53488 47724 58232 FALSE TRUE 39077.68868 44556.97511 51607.00788 56124.4321 46724.08633 57987.3033 55319.83529 52383.45411 42306.5716 54287.89477 0.719823247 0.820753416 0.950617225 1.033829592 0.860672283 1.068144262 1.019008667 0.964919607 0.77930028 1 15.72834292 4.407435613 2.51767443 0.965587553 0.723855439 0.48747729 0.08076416 0.249625526 2.902114886 0.020256682 0.09439343 25552.63038 -4.407435613 -0.241732114 SSESPSSSPSS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPSSSPS(0.035)S(0.965)PAR;SSESPSSSPS(0.001)S(0.999)PAR 202.72 1.68E-08 150539000 154736 195456 198084 271090 245530 243120 278600 197558 241630 263840 TRUE FALSE 148688.7461 189881.7863 233882.1852 285080.9874 253427.6954 248036.053 282009.5901 193478.3583 214201.1754 245969.8818 0.604499807 0.771971694 0.950857005 1.159007702 1.030320028 1.008400098 1.146520818 0.786593695 0.870843104 1 17.90812215 4.407680188 2.487719635 0.993245529 0.612946061 0.59576824 0.105582778 0.236303677 2.672593414 0.029703817 0.140061542 25567.0245 -4.407680188 -0.380299468 TSSAVWNS(ph)PPLQGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSSAVWNSPPLQGAR 15 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 TSSAVWNS(1)PPLQGAR;TSSAVWNS(1)PPLQGAR;TSSAVWNS(1)PPLQGAR;TSSAVWNS(1)PPLQGAR 207.05 3.76E-09 1139310000 971990 1265960 1383980 1681240 1545370 1710860 1911190 1496440 1616090 1915950 TRUE FALSE 934003.5562 1229856.06 1634095.972 1768008.998 1595078.23 1745454.761 1934579.715 1465537.991 1432638.238 1786181 0.522905325 0.688539437 0.914854638 0.989826338 0.893010411 0.977199266 1.083081566 0.820486833 0.802067785 1 20.76844685 4.407728342 2.452824139 0.934855526 0.526412431 0.743894532 0.080201542 0.162611077 1.780261075 0.021558718 0.103039242 25569.85954 -4.407728342 -0.408443094 FDLLWLIQDRPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDLLWLIQDRPDR 13 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 208.68 4.01E-08 3016000000 602700 645190 587080 714740 695920 623220 716030 687730 706580 785040 FALSE TRUE 579145.8177 626789.8129 693178.4155 751627.8171 718304.8988 635821.9354 724792.9893 673528.1352 626372.0006 731868.5416 0.791324924 0.85642404 0.947135143 1.026998394 0.981467105 0.868765221 0.990332209 0.920285676 0.855853155 1 19.48122501 4.407839403 2.995163612 0.948017257 0.798411656 0.493897233 0.052519135 0.217262937 3.71406632 0.013371473 0.053587088 25576.39928 -4.407839403 -0.149605601 FSTIASSYEECR ddPTM_BT-474_Pertuzumab_2h_R1 3 FSTIASSYEECR 12 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;; 221.52 6.28E-11 489780000 364590 380510 348870 389840 405700 329800 390670 454650 412390 430820 FALSE TRUE 350341.4197 369658.2274 411918.5696 409959.6891 418749.7089 336468.782 395451.1363 445261.3186 365577.2161 401640.1777 0.872276827 0.920371636 1.025591045 1.020713843 1.042599153 0.837736862 0.984590582 1.108607513 0.910210772 1 18.61554407 4.40871297 4.240383465 0.997768111 0.881348992 0.233713037 0.07018731 0.273369663 9.411035679 0.018043787 0.057634978 25627.89703 -4.40871297 -0.116419119 EHYPVSSPSS(ph)PSPPAQPGGVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 EHYPVSSPSSPSPPAQPGGVSR 22 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 EHYPVSSPS(0.006)S(0.994)PSPPAQPGGVSR;EHYPVSSPS(0.001)S(0.999)PSPPAQPGGVSR;EHYPVSSPS(0.019)S(0.98)PSPPAQPGGVSR 281.75 6.73E-46 2227760000 217655 246640 221544 281437 283160 323478 280095 207398 282194 353491 TRUE FALSE 209148.802 239606.0687 261581.929 295961.9973 292268.0986 330018.9468 283522.8864 203115.1588 250160.5202 329548.7397 0.634652107 0.727073236 0.793757941 0.898082625 0.886873665 1.001426821 0.860336734 0.616343303 0.759100218 1 18.33013233 4.409079095 2.028028 0.837831158 0.632753757 0.304390276 0.1075625 0.630700898 4.39039844 0.032216918 0.187136671 25649.51133 -4.409079095 -0.205077402 VFGWVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFGWVHR 7 0 O43776;K7EIU7;O43776-2;K7EPK2;K7EMQ6;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 149.94 0.0019825 2325000000 1892850 1876880 2065010 2144500 1947350 1214400 2359300 1910480 2037040 2400500 FALSE TRUE 1818875.329 1823353.22 2438203.243 2255177.902 2009988.281 1238956 2388173.819 1871027.92 1805803.759 2237911.997 0.81275552 0.814756444 1.089499161 1.007715185 0.898153406 0.553621412 1.067143758 0.83605965 0.806914553 1 21.09372187 4.409096102 25 0.900997815 0.813186069 0.059118601 0.147673474 149.3516357 54886.19088 0.036085356 0.09882386 25650.51578 -4.409096102 -0.087811746 LTTPTYGDLNHLVSATMSGVTTCLR ddPTM_BT-474_Pertuzumab_2h_R1 6 LTTPTYGDLNHLVSATMSGVTTCLR 25 0 Q5JP53;P07437;Q5ST81;P68371;M0R2D3;Q13885;Q9BVA1;P04350 Q5JP53;P68371;Q13885;Q9BVA1;P04350 TUBB;TUBB4B;TUBB4A;TUBB2A;TUBB2B Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain 0 ;;;;; 337.4 4.05E-88 13581190000 7193660 7759500 7023600 8703040 8025700 8902760 8308920 7817000 8742230 9206430 FALSE TRUE 6912523.814 7538206.657 8292920.759 9152204.937 8283853.929 9082779.907 8410607.048 7655576.218 7749848.701 8582870.296 0.805386028 0.878285049 0.966217649 1.066333828 0.965161262 1.058245039 0.979929413 0.89195991 0.902943705 1 23.03302877 4.409118191 2.747173956 0.976469995 0.811462805 0.536046448 0.053092975 0.245375617 3.470932583 0.015080307 0.065173915 25651.8204 -4.409118191 -0.16500719 TPLSEAEFEEIMNR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPLSEAEFEEIMNR 14 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 ;; 238.92 5.63E-17 478626000 24436.6 28985 27753.8 38646 32078 32994 30744 38122 34444 29828 FALSE TRUE 23481.59066 28158.37618 32769.52904 40640.52469 33109.818 33661.16129 31120.25427 37334.76738 30534.06152 27807.72299 0.844426948 1.012609921 1.178432662 1.461483369 1.190669873 1.210496857 1.119122708 1.342604261 1.098042495 1 14.763198 4.409486831 2.567644846 1.224735226 0.85593524 0.459343464 0.1227009 0.23637587 2.87132726 0.02990599 0.137475282 25673.60356 -4.409486831 -0.368799987 S(ph)PS(ph)PAPPPRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPAPPPRR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(1)PS(1)PAPPPRR;S(1)PS(1)PAPPPRR 97.551 0.020932 651071000 417966 404495 271346 338149 356021 365610 359884 366404 394995 360348 TRUE FALSE 401631.4266 392959.1986 320384.2583 355600.9104 367472.7388 373002.8847 364288.368 358837.6294 350156.8236 335941.309 1.195540459 1.169725747 0.953691165 1.058520941 1.093859936 1.110321579 1.084380986 1.068155716 1.042315471 1 18.35784968 4.409675841 11.17660961 1.059802511 1.189101942 0.582264529 0.044239731 0.31960811 51.33280172 0.010837034 0.02971654 25684.77943 -4.409675841 0.129299432 EAAIWELEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EAAIWELEER 10 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 123.75 0.0057128 0 72722 80808 69767 91510 83464 84763 86129 91291 90208 94824 FALSE TRUE 69879.94384 78503.43496 82375.44886 96232.84207 86148.69536 86476.96594 87183.07247 89405.80895 79967.96602 88401.48602 0.790483814 0.888032979 0.931833305 1.088588511 0.974516371 0.978229777 0.986217273 1.011360928 0.904599794 1 16.431783 4.409757148 1.913929754 0.991887789 0.788137279 0.666697851 0.044557993 0.246165521 1.485127521 0.011444587 0.07080111 25689.58852 -4.409757148 -0.20375051 YFDDEFTAQSITIT(ph)PPDRYDSLGLLELDQR ddPTM_BT-474_Pertuzumab_2h_R1 9 YFDDEFTAQSITITPPDRYDSLGLLELDQR 30 1 P31751;P31751-2 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFT(0.015)AQS(0.012)IT(0.049)IT(0.912)PPDRY(0.009)DS(0.002)LGLLELDQR;YFDDEFTAQS(0.004)IT(0.058)IT(0.938)PPDRYDSLGLLELDQR;YFDDEFT(0.001)AQS(0.021)IT(0.168)IT(0.81)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.139)IT(0.861)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.003)IT(0.997)PPDRYDSLGLLELDQR;YFDDEFTAQSITIT(0.707)PPDRY(0.107)DS(0.186)LGLLELDQR;YFDDEFT(0.023)AQS(0.02)IT(0.138)IT(0.818)PPDRYDS(0.001)LGLLELDQR;YFDDEFTAQSIT(0.001)IT(0.999)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.011)IT(0.989)PPDRYDSLGLLELDQR 222.52 1.76E-34 5487269000 402500.4 437088.9 370220.1 459413 449474.9 486784.7 449913.6 461387.8 489770.6 512697.4 TRUE FALSE 386770.2394 424623.5525 437127.1076 483123.36 463932.6684 496627.8202 455419.7772 451859.9807 434173.8948 477971.9484 0.809190248 0.888385927 0.914545527 1.010777644 0.970627397 1.039031311 0.952816957 0.945369246 0.908366895 1 18.86656643 4.409793526 1.568351083 0.971813381 0.79989299 0.673989511 0.036479176 0.363615006 1.326202159 0.01045391 0.079857316 25691.74046 -4.409793526 -0.171920391 FTSGAFLS(ph)PSVSVQECR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTSGAFLSPSVSVQECR 17 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;H7C3P6 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 FTSGAFLS(1)PSVSVQECR;FTSGAFLS(1)PSVSVQECR 402.14 3.60E-140 569400000 437030 453060 432620 465030 477490 496840 487330 469030 462160 526160 TRUE FALSE 419950.3844 440139.1724 510804.0576 489030.254 492848.8995 506886.4452 493294.0903 459344.3666 409697.5343 490522.7145 0.856128314 0.897286016 1.041346389 0.996957408 1.004742257 1.033359782 1.005649842 0.936438524 0.835226427 1 18.90396042 4.409807784 6.333403275 0.981341102 0.865835626 0.36797313 0.056153983 0.194395323 13.71154587 0.014411142 0.040801509 25692.58391 -4.409807784 -0.115505476 ESDLSHVQNK ddPTM_BT-474_Pertuzumab_2h_R1 3 ESDLSHVQNK 10 0 O43390;O43390-3;O43390-2 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 145.9 2.96E-05 2225660000 3790950 3878610 3478710 4014070 3858440 3997410 3839230 3976860 4263990 4266690 FALSE TRUE 3642795.483 3767995.84 4107390.28 4221236.634 3982550.227 4078240.369 3886215.645 3894736.451 3779959.731 3977703.286 0.915803724 0.947279264 1.032603486 1.061224614 1.001218527 1.025275159 0.976999883 0.979142025 0.950287002 1 21.92350423 4.409815567 5.206475811 1.002535525 0.922709888 0.493381838 0.029811257 0.159577533 8.022163096 0.00808805 0.023884339 25693.04435 -4.409815567 -0.079825637 LS(ph)PNPPNLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPNPPNLTK 10 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28;A0A2R8YF38 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 LS(1)PNPPNLTK 75.088 0.042005 218640000 248800 261230 231900 259740 300560 212320 265590 294110 332700 308490 TRUE FALSE 239076.6209 253779.9762 273809.4886 273145.2125 310227.7854 216613.2559 268840.3699 288036.5257 294933.2908 287595.6975 0.83129415 0.882419238 0.952063925 0.949754168 1.078694111 0.753186705 0.934785785 1.001532805 1.025513571 1 18.13368257 4.40990368 2.214864105 0.960244074 0.829531259 0.225124511 0.080786524 0.573164925 4.932266624 0.021139042 0.11231914 25698.25774 -4.40990368 -0.130712815 QEFEFWYPVDLR ddPTM_BT-474_Pertuzumab_2h_R1 5 QEFEFWYPVDLR 12 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;;;; 231.54 7.46E-12 424956000 609668 652958 649383 701603 676083 648018 727265 722600 789630 859754 FALSE TRUE 585841.5005 634336.2772 766740.9535 737812.8149 697829.8237 661121.368 736165.4866 707678.0575 699994.5128 801522.0958 0.73091123 0.791414585 0.956606134 0.920514629 0.8706308 0.824832368 0.918459379 0.882917715 0.873331523 1 19.61238277 4.410171974 5.20715496 0.89777797 0.744144087 0.610252368 0.046949439 0.114377969 5.767907784 0.011165924 0.032981334 25714.13824 -4.410171974 -0.153633883 VIENPAEAQSAALEEGHAWR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIENPAEAQSAALEEGHAWR 20 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 0 ; 206.34 7.75E-22 237090000 179965 187024 162349 183039 191850 240860 190186 164303 199811 230950 FALSE TRUE 172931.7688 181690.2586 191689.0757 192485.6647 198021.0295 245730.3542 192513.5532 160910.0856 177129.293 215307.5508 0.803184878 0.843863849 0.890303545 0.894003318 0.919712424 1.141299287 0.894132846 0.747349942 0.822680358 1 17.71603939 4.410277035 1.798341011 0.904794342 0.797458604 0.121522927 0.098477789 1.337825379 6.905433705 0.029751504 0.196967787 25720.3595 -4.410277035 -0.107335739 SLIGS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLIGSPGR 8 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.002)LIGS(0.998)PGR;S(0.041)LIGS(0.959)PGR;S(0.002)LIGS(0.998)PGR 90.149 0.014058 5020300000 3961600 4224000 3613500 4417300 4198200 4467900 4525100 4791400 4660100 4967700 TRUE FALSE 3806776.292 4103535.656 4266539.832 4645277.382 4333238.916 4558243.999 4580479.527 4692455.916 4131104.985 4631233.254 0.82197896 0.886056787 0.921253497 1.003032481 0.935655511 0.98423978 0.989040991 1.013219516 0.8920097 1 22.14296499 4.410539297 1.260533555 0.977636594 0.799021777 0.660481176 0.035247459 0.469143274 0.973860279 0.009940732 0.093953994 25735.89626 -4.410539297 -0.178614816 RSS(ph)AIGIENIQEVQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSAIGIENIQEVQEK 16 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RS(0.191)S(0.809)AIGIENIQEVQEK 260.97 8.72E-27 290240000 385700 364360 274150 301550 334230 285020 268580 421250 366930 329320 TRUE FALSE 370626.4176 353968.8095 323695.0034 317113.0316 344980.8115 290783.2997 271866.9624 412551.0403 325277.6447 307014.8631 1.20719373 1.152937047 1.054330074 1.032891465 1.123661597 0.947131018 0.885517267 1.343749407 1.059485008 1 18.22794897 4.410690311 3.580483164 1.071175077 1.199013576 0.151975276 0.115804457 0.491095733 12.21644576 0.03089467 0.10914632 25744.84678 -4.410690311 0.127838499 KQIT(ph)MEELVR ddPTM_BT-474_Pertuzumab_2h_R1 12 KQITMEELVR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR 184.76 8.86E-07 13988865000 21345770 18616060 9403560 11993970 15430200 10909060 11581860 21104680 12209800 10827680 TRUE FALSE 20511553.71 18085148.2 11102992.47 12612980.23 15926526.4 11129648.67 11723602.27 20668860.98 10823794.69 10094311.59 2.031991338 1.791617787 1.099925673 1.249513661 1.577772417 1.102566388 1.161406814 2.047575092 1.072266751 1 23.26703919 4.410860747 5.470606919 1.358699344 1.978200633 0.39674835 0.303548254 0.194053248 10.74629888 0.077540754 0.226103462 25754.95214 -4.410860747 0.619501289 FSDIQIR ddPTM_BT-474_Pertuzumab_2h_R1 3 FSDIQIR 7 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;; 98.457 0.026169 350821000 648460 688880 647330 762490 708130 663610 764310 734660 763240 874960 FALSE TRUE 623117.4663 669233.8169 764316.9308 801842.2003 730907.6446 677028.6489 773663.8544 719489.0143 676600.195 815698.1799 0.763906898 0.820442945 0.937009484 0.98301335 0.896051582 0.82999897 0.948468286 0.882052985 0.829473709 1 19.63767591 4.410980092 4.138262068 0.908232902 0.774321387 0.451151503 0.054677895 0.179636799 5.953795754 0.01340857 0.043493033 25762.0306 -4.410980092 -0.133911514 GTS(ph)PSSSSRPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GT(0.007)S(0.555)PS(0.019)S(0.112)S(0.112)S(0.195)RPQR;GT(0.016)S(0.939)PS(0.014)S(0.006)S(0.006)S(0.019)RPQR 81.565 0.045519 306704000 224294 242867 211689 265306 253950 262363 264700 253852 264903 276861 TRUE FALSE 215528.3425 235940.671 249945.9113 278998.4745 262118.5324 267668.1596 267939.4778 248609.8675 234832.322 258108.9579 0.835028526 0.914112679 0.968373641 1.080932939 1.015534426 1.037035529 1.038086706 0.963197363 0.909818566 1 17.97762069 4.411038255 2.104029862 1.006243335 0.834920649 0.601629561 0.044197205 0.274093028 2.083164651 0.012295928 0.069069994 25765.48101 -4.411038255 -0.171322686 KREHS(ph)PSKEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KREHSPSKEK 10 3 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.992)PS(0.008)KEK 90.861 0.0075236 422120000 662920 539960 307260 197870 408570 474880 337720 365100 500370 346840 TRUE FALSE 637012.3535 524560.8695 362788.717 208082.0944 421712.0251 484482.399 341853.1184 357560.5574 443570.0953 323348.2179 1.970050609 1.622278524 1.12197531 0.643523245 1.304203957 1.498330197 1.057229017 1.105806489 1.371803124 1 18.30272913 4.411186787 3.123386304 1.136702954 1.928536235 0.604061025 0.22134049 0.169588608 3.174247835 0.057610492 0.224835599 25774.29455 -4.411186787 0.791833281 EMPSVFQNVLGSAVLS(ph)PAHKDTQDFHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EMPSVFQNVLGSAVLSPAHKDTQDFHK 27 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 EMPSVFQNVLGS(0.014)AVLS(0.875)PAHKDT(0.111)QDFHK 80.418 0.0059534 69375000 115090 101190 70846 64794 78841 110490 91377 61908 100730 75171 TRUE FALSE 110592.1556 98304.16028 83649.44816 68138.0261 81376.99237 112724.1835 92495.29906 60629.57817 89295.55269 70079.60121 1.578093392 1.402749995 1.193634763 0.972294718 1.161207983 1.608516338 1.319860522 0.865153013 1.274201781 1 16.09670694 4.411428016 2.689545405 1.167848853 1.565282549 0.310388962 0.196904631 0.374471111 5.048283475 0.053892779 0.238540932 25788.61483 -4.411428016 0.397433696 GVEFPMADLDALS(ph)PIHTPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVEFPMADLDALSPIHTPQR 20 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-5 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 GVEFPMADLDALS(1)PIHTPQR;GVEFPMADLDALS(1)PIHTPQR;GVEFPMADLDALS(1)PIHTPQR;GVEFPMADLDALS(1)PIHTPQR 351.37 2.57E-95 562837000 358825 435006 481727 607326 560779 533996 563481 481522 452341 578380 TRUE FALSE 344801.7223 422600.0548 568785.7849 638670.1676 578816.9658 544793.765 570377.049 471578.4024 400993.146 539205.8074 0.639462182 0.78374537 1.054858418 1.184464557 1.07346204 1.010363311 1.057809544 0.874579606 0.743673641 1 19.04047651 4.411476529 3.818372632 1.000746474 0.663637194 0.523224159 0.113608024 0.176786604 5.012296149 0.03108552 0.105578816 25791.49572 -4.411476529 -0.337109281 WLAPDGLIFPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 WLAPDGLIFPDR 12 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 142 0.00014189 317450000 281350 303200 284680 323840 325800 310960 323370 353420 326390 370010 FALSE TRUE 270354.531 294553.0329 336128.0087 340553.4212 336279.6529 317247.8243 327327.4988 346121.7535 289339.5755 344948.8931 0.783752423 0.853903401 0.974428431 0.987257614 0.974868044 0.919695151 0.948915927 1.003400099 0.838789691 1 18.39602311 4.4116018 3.313111091 0.958515633 0.792716667 0.599787484 0.046269367 0.146921203 3.116671667 0.011106918 0.041490336 25798.93632 -4.4116018 -0.165798965 DAASAALADAAEELLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DAASAALADAAEELLDR 17 0 E5RHA3;Q86X53;H0YB25;H0YBT6 E5RHA3 ERICH1 Glutamate-rich protein 1 0 157.52 5.31E-08 3525600 8706.8 10150 10661 11921 12181 11756 11625 12459 13108 12085 FALSE TRUE 8366.52863 9860.531938 12587.67985 12536.24424 12572.81293 11993.71437 11767.27023 12201.7173 11620.03479 11266.47219 0.742604117 0.87521025 1.117268977 1.112703607 1.115949405 1.064549237 1.044450298 1.083011354 1.031381838 1 13.45974822 4.411691069 3.512376863 1.075647362 0.761618031 0.886005303 0.038826085 0.064403589 1.542575446 0.009768646 0.035021069 25804.23979 -4.411691069 -0.314029331 GESEDDFWWCIDR ddPTM_BT-474_Pertuzumab_2h_R1 5 GESEDDFWWCIDR 13 0 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 ;;;; 244.27 1.16E-16 927880000 561010 621834 529460 705787 678858 672343 646546 633422 673578 756284 FALSE TRUE 539085.109 604099.9032 625145.1998 742212.7517 700694.0841 685938.2361 654458.6234 620341.6143 597116.2493 705060.2111 0.764594428 0.856806119 0.886655054 1.052694139 0.993807441 0.972878948 0.928230828 0.87984204 0.846901073 1 19.42738694 4.411695066 2.013359964 0.945198731 0.766025714 0.50272475 0.058364084 0.385411946 2.629799209 0.016935244 0.099790877 25804.47727 -4.411695066 -0.179173017 TNEGVIEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 TNEGVIEFR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 169.65 0.00013564 2083380000 2245160 2300820 1958490 2274700 2219790 2386160 2241030 2472860 2451570 2501580 FALSE TRUE 2157416.665 2235202.866 2312432.709 2392097.54 2291191.561 2434409.79 2268456.396 2421794.577 2173278.051 2332145.758 0.92507797 0.95843189 0.991547248 1.025706704 0.982439264 1.04384976 0.972690659 1.038440487 0.931879169 1 21.15322653 4.412008367 2.154410236 1.002914922 0.924381962 0.360813996 0.031455929 0.351861095 2.829184246 0.007471922 0.041056099 25823.09943 -4.412008367 -0.078532959 MVQEAEKYKAEDEKQR ddPTM_BT-474_Pertuzumab_2h_R1 1 MVQEAEKYKAEDEKQR 16 3 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 176.81 1.34E-09 422370000 656460 552720 298300 231580 396060 525430 377000 430460 489680 363750 FALSE TRUE 630804.8174 536956.9668 352209.4456 243531.8716 408799.6296 536054.5546 381613.8388 421570.8506 434093.5793 339112.8885 1.86016173 1.58341657 1.038620051 0.718143957 1.205497176 1.580755473 1.125329799 1.243157854 1.280085759 1 18.37140609 4.41232673 4.028858536 1.163808514 1.810646437 0.555320454 0.210828239 0.157794342 4.986190163 0.055719949 0.183713507 25842.03616 -4.41232673 0.646837923 LSMEDSKS(ph)PPPKATEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSMEDSKSPPPKATEEK 17 2 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LS(0.007)MEDS(0.036)KS(0.957)PPPKATEEK 49.973 0.085256 283480000 518410 420380 212920 162280 302260 335180 247260 318990 366380 224020 TRUE FALSE 498149.9641 408391.174 251399.3804 170655.2902 311982.4674 341957.5692 250286.0418 312402.745 324790.0784 208846.9259 2.385239629 1.955456956 1.203749489 0.817130966 1.49383318 1.637359841 1.198418606 1.495845552 1.555158531 1 17.67208638 4.412489416 3.580980601 1.324193768 2.319964494 0.675629618 0.248348389 0.130556456 3.257356078 0.063940588 0.226584956 25851.71836 -4.412489416 0.995770726 RGPEVTSQGVQTSS(ph)PACKQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGPEVTSQGVQTSSPACKQEK 21 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 RGPEVTSQGVQT(0.04)S(0.12)S(0.84)PACKQEK 149.04 4.41E-08 134260000 138550 119310 63528 58128 93296 103480 84347 88339 116140 101810 TRUE FALSE 133135.3128 115907.3956 75008.92277 61127.99305 96296.95057 105572.4365 85379.26382 86514.76878 102956.2741 94914.31802 1.402689453 1.221179249 0.790280374 0.644033422 1.014567165 1.112291999 0.899540402 0.911503876 1.084728587 1 16.53433812 4.412661173 4.72882585 0.926647984 1.365332126 0.582853286 0.132213148 0.128640415 5.537312622 0.034477171 0.105467397 25861.94438 -4.412661173 0.438684143 VQQSSESSTSS(ph)PSQHEATPGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQQSSESSTSSPSQHEATPGAR 22 0 O75152;E9PBY7;E9PQ61;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 VQQSSESS(0.001)T(0.005)S(0.206)S(0.786)PS(0.001)QHEATPGAR;VQQSSESS(0.002)T(0.009)S(0.164)S(0.795)PS(0.03)QHEATPGAR 188.22 1.65E-17 558580000 115119 128081 127281 157964 130460 135727 153967 158777 114780 151153 TRUE FALSE 110620.0222 124428.2553 150283.5081 166116.541 134656.3644 138471.4929 155851.2942 155498.1995 101750.6556 140915.2727 0.78501088 0.883000493 1.066481334 1.178839865 0.95558389 0.982657808 1.105992922 1.103487198 0.722069749 1 17.10446846 4.412892359 3.85977265 1.028924492 0.801640283 0.281655562 0.117767659 0.240165597 6.980818732 0.028740799 0.097207607 25875.715 -4.412892359 -0.227284209 AIIYQYMEEIYHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AIIYQYMEEIYHR 13 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ; 240.6 7.45E-17 506900000 407630 525980 546130 792940 543460 617520 728220 620080 712210 736430 FALSE TRUE 391699.3689 510979.5654 644827.8396 833863.7284 560940.8845 630006.6775 737132.1742 607275.1313 631362.9066 686550.9402 0.570532128 0.744270433 0.939227961 1.214569349 0.8170419 0.917640106 1.073674408 0.884530332 0.91961553 1 19.38900724 4.412977834 2.69903035 0.969967084 0.583966904 0.613108116 0.104195963 0.188336388 2.557887499 0.026382972 0.11681367 25880.8082 -4.412977834 -0.38600018 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEKEK ddPTM_BT-474_Pertuzumab_2h_R1 3 REESPMDVDQPSPSAQDTQSIASDGTPQGEKEK 33 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 REESPMDVDQPS(1)PSAQDTQSIASDGTPQGEKEK;REESPMDVDQPS(0.917)PS(0.083)AQDTQSIASDGTPQGEKEK;REESPMDVDQPS(0.981)PS(0.019)AQDTQSIASDGTPQGEKEK 252.15 1.75E-59 825380000 355178 314270 192572 170506 240732 321330 218514 269819 325330 243869 TRUE FALSE 341297.2511 305307.3273 227374.0441 179305.8351 248475.3634 327827.5128 221188.2397 264247.1434 288399.9023 227351.5354 1.501187359 1.342886586 1.000099004 0.788672198 1.092912625 1.441941055 0.972890899 1.162284402 1.268519704 1 17.79456522 4.413528067 4.413059429 1.096545538 1.470305076 0.395172757 0.168532796 0.197341404 7.481643777 0.043178701 0.136166663 25913.61885 -4.413528067 0.373759538 GIEILTDMSRPVELSDR ddPTM_BT-474_Pertuzumab_2h_R1 14 GIEILTDMSRPVELSDR 17 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;;;;;;;;; 300.03 2.31E-46 11990270000 5614956 6421588 5975110 7367422 6980586 7555589 7469581 7106989 7861852 8602036 FALSE TRUE 5395517.312 6238450.598 7054945.293 7747655.532 7205122.888 7708368.186 7560995.967 6960227.194 6969407.521 8019412.44 0.672807061 0.777918662 0.87973344 0.966112616 0.898460198 0.961213586 0.942836651 0.867922338 0.869067101 1 22.93506511 4.413660873 1.930110086 0.922067702 0.663898287 0.805581248 0.040934097 0.185891432 1.141067135 0.011007615 0.068179572 25921.54438 -4.413660873 -0.258169415 LQEIEELER ddPTM_BT-474_Pertuzumab_2h_R1 2 LQEIEELER 9 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 ; 112.71 0.0044628 98332000 96872 111903 96183 129036 129396 131337 117328 120756 118134 132825 FALSE TRUE 93086.13514 108711.636 113565.4077 135695.5634 133558.1399 133992.7241 118763.8952 118262.3464 104723.9236 123828.6444 0.751733458 0.877919939 0.917117426 1.095833392 1.078572252 1.082081813 0.959098726 0.955048381 0.845716466 1 16.91798556 4.413786116 1.82804452 1.000010618 0.74791994 0.531402768 0.07306183 0.399389516 2.140818726 0.021245475 0.139500617 25929.02078 -4.413786116 -0.252090678 SSS(ph)VGS(ph)SSSYPISPAVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 SSS(1)VGS(0.961)S(0.039)SSYPISPAVSR 361.02 7.02E-91 509180000 375930 334830 179440 246120 297770 220570 213900 353840 247910 215550 TRUE FALSE 361238.24 325280.9762 211868.7996 258822.2827 307348.0425 225030.0765 216517.7722 346533.0803 219768.2961 200950.6065 1.797646926 1.618711095 1.05433272 1.287989557 1.529470589 1.119827805 1.077467622 1.724468945 1.093643358 1 17.61648141 4.414004384 6.039270683 1.284985746 1.756245195 0.414191942 0.22287015 0.177671008 12.14554025 0.054820815 0.156751564 25942.05552 -4.414004384 0.471259449 VWLDPNETNEIANANSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VWLDPNETNEIANANSR 17 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;; 296.49 8.61E-46 1526770000 982620 1041270 981820 1040950 1101740 1142480 1122180 1136500 1112930 1213360 FALSE TRUE 944218.1241 1011573.999 1159256.714 1094673.554 1137178.468 1165581.728 1135913.575 1113030.878 986594.8522 1131178.046 0.834721048 0.89426594 1.024822501 0.967728783 1.005304577 1.030414029 1.004186368 0.983957284 0.872183522 1 20.1093946 4.414146649 4.277619684 0.987599369 0.845818618 0.582204347 0.04243234 0.128338302 4.591716072 0.010419861 0.033381353 25950.55489 -4.414146649 -0.141780751 TFSHELSDFGLESTAGEIPVVAIR ddPTM_BT-474_Pertuzumab_2h_R1 6 TFSHELSDFGLESTAGEIPVVAIR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 309.91 1.97E-73 5828170000 2141681 2318378 2075923 2747240 2420365 2433230 2501301 2362411 2516810 2722110 FALSE TRUE 2057981.739 2252260.129 2451088.465 2889025.386 2498218.238 2482431.578 2531912.67 2313626.387 2231112.28 2537739.065 0.810950884 0.887506584 0.965855197 1.138424917 0.984426757 0.978205999 0.9977041 0.911688053 0.879173242 1 21.27511231 4.414165551 2.829223477 0.981619222 0.818702319 0.43185652 0.063933717 0.280816431 4.236514869 0.017526844 0.07465376 25951.68442 -4.414165551 -0.162916903 LMIEMDGTENK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMIEMDGTENK 11 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 163.38 5.59E-05 142450000 652150 552290 454570 485280 413560 393660 431630 504270 578240 573760 FALSE TRUE 626663.257 536539.2299 536720.9109 510325.359 426862.533 401620.0749 436912.4171 493856.6483 512600.6194 534898.7241 1.171554967 1.003066947 1.003406601 0.95405978 0.79802496 0.750833862 0.816813347 0.923271315 0.958313408 1 19.02890624 4.414329294 1.025924801 0.870161316 1.212039087 0.562802666 0.077421185 0.874644989 1.072347955 0.026192207 0.292474662 25961.47084 -4.414329294 0.341877772 QIGASSRPPPNR ddPTM_BT-474_Pertuzumab_2h_R1 2 QIGASSRPPPNR 12 1 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8 Q06787 FMR1 Fragile X mental retardation protein 1 0 ; 107.09 0.0016888 96403000 41919 43720 40091 45589 41491 41924 47382 48272 47872 52616 FALSE TRUE 40280.75914 42473.14841 47336.33552 47941.85375 42825.5957 42771.732 47961.87509 47275.16633 42437.77126 49052.27145 0.821180303 0.865875262 0.965018217 0.977362563 0.873060399 0.871962312 0.977770726 0.963771196 0.865154049 1 15.58203232 4.41452951 4.451968865 0.935802141 0.829892791 0.396487616 0.047349515 0.189716108 7.352014692 0.011845138 0.03725255 25973.4422 -4.41452951 -0.105909349 NSLSPRSLVY(ph)ESEFSTIEPS(ph)LDMY(ph)DENK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLSPRSLVYESEFSTIEPSLDMYDENK 28 1 E5RI87 E5RI87 RNF130 3 NS(0.127)LS(0.136)PRS(0.16)LVY(0.291)ES(0.197)EFS(0.227)T(0.237)IEPS(0.799)LDMY(0.825)DENK 49.199 0.031028 341900000 105170 145500 145490 232000 168040 182490 188640 182440 169180 216590 TRUE FALSE 101059.8401 141350.4825 171783.2794 243973.5478 173445.1592 186180.0728 190948.6327 178672.5502 149975.3957 201920.1664 0.500494041 0.700031527 0.850748504 1.208267367 0.858978884 0.922047937 0.945664003 0.884867289 0.742745999 1 17.62342548 4.414572234 2.343929669 0.931115035 0.508497401 0.599872667 0.113393036 0.228939086 2.245492822 0.029272466 0.148627844 25975.9975 -4.414572234 -0.422617633 QKIDDRDS(ph)DEEGASDR ddPTM_BT-474_Pertuzumab_2h_R1 3 QKIDDRDSDEEGASDR 16 2 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR 241.44 3.47E-20 1400340000 1805580 1674510 1241190 1223070 1382060 1417970 1483550 1679510 1743990 1525920 TRUE FALSE 1735015.937 1626754.614 1465500.643 1286192.789 1426515.215 1446642.325 1501706.129 1644827.532 1546019.567 1422568.079 1.219636489 1.143533753 1.03017962 0.904134437 1.002774655 1.016923089 1.055630413 1.156238183 1.086780724 1 20.44006627 4.414809657 3.317345556 1.038678888 1.209342614 0.499605824 0.061809627 0.236843806 5.050170904 0.018411356 0.069137876 25990.20214 -4.414809657 0.170663726 DFLLPFLEEPMDTEADLQFRPR ddPTM_BT-474_Pertuzumab_2h_R1 7 DFLLPFLEEPMDTEADLQFRPR 22 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;;;; 255.24 4.08E-37 1582234000 800836 860846 780074 904777 934247 916198 914389 926009 989204 1048144 FALSE TRUE 769538.4437 836295.5149 921050.7245 951472.6494 964297.9032 934724.1513 925579.5661 906886.5906 876913.709 977152.2733 0.787531754 0.855849736 0.942586687 0.973719936 0.98684507 0.956579826 0.947221422 0.928091368 0.897417662 1 19.89822387 4.41489511 2.380762572 0.95283229 0.7880058 0.798291201 0.027688038 0.147823009 1.50361096 0.007523023 0.037643893 25995.31652 -4.41489511 -0.16482649 NSS(ph)VPFGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSVPFGSK 9 0 Q9BXT8-2 Q9BXT8-2 RNF17 RING finger protein 17 1 NS(0.004)S(0.498)VPFGS(0.498)K 63.076 0.082281 716730000 590190 690300 627290 844990 689780 769080 821560 819140 812600 890790 TRUE FALSE 567124.7223 670613.3199 740655.257 888600.0352 711967.4001 784631.3245 831614.497 802224.4727 720357.0547 830455.9999 0.68290761 0.807524204 0.891865743 1.070014589 0.857321038 0.944819864 1.001395013 0.966004789 0.867423506 1 19.66354421 4.41506507 1.947770139 0.956199081 0.676832063 0.67686257 0.060529866 0.237944269 1.49198407 0.015416191 0.094910878 26005.49175 -4.41506507 -0.279367018 LQMEAPHIIVGTPGR ddPTM_BT-474_Pertuzumab_2h_R1 6 LQMEAPHIIVGTPGR 15 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;; 176.04 8.22E-07 11765900000 4977090 5365160 4573400 5581980 5603530 5910970 5592290 5405680 6075690 6520230 FALSE TRUE 4782579.82 5212150.89 5399915.115 5870066.657 5783772.631 6030493.863 5660730.118 5294050.819 5386003.143 6078609.014 0.786788525 0.857457829 0.88834717 0.965692421 0.951496077 0.992084513 0.931254191 0.870931295 0.886058493 1 22.53530979 4.415396261 1.648109935 0.934427381 0.77910459 0.602088074 0.040160218 0.434756903 1.789854903 0.012071439 0.088885649 26025.33096 -4.415396261 -0.155322791 VLSQSTPGT(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSQSTPGTPSK 12 0 Q6MZP7-3;Q6MZP7 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 VLSQSTPGT(0.993)PS(0.007)K;VLSQSTPGT(0.985)PS(0.015)K 241.41 3.37E-15 627230000 1191450 1079840 799310 836250 852150 804350 921020 1035620 1013180 1071440 TRUE FALSE 1144886.817 1049044.02 943763.0976 879408.9627 879560.1787 820614.5081 932291.7183 1014234.085 898168.054 998870.4145 1.146181527 1.050230345 0.944830364 0.880403454 0.880554841 0.821542511 0.933346012 1.015381045 0.899183759 1 19.929938 4.415783123 2.215177703 0.919766153 1.147881519 0.652004923 0.054017489 0.245321932 2.102563263 0.015635153 0.084284088 26048.52422 -4.415783123 0.228115366 TNSS(ph)SSSPVVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TNSSSSSPVVLK 12 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 TNS(0.102)S(0.796)S(0.102)SSPVVLK 224.5 2.09E-11 2145700000 1059800 954650 781730 710940 794160 745440 845690 1041300 941480 897780 TRUE FALSE 1018381.844 927424.3167 923006.0005 747631.6986 819704.8776 760513.3075 856039.8072 1019796.791 834607.1374 836972.5609 1.216744601 1.108070157 1.102791231 0.893257119 0.979368878 0.908647837 1.022781208 1.218435154 0.997173834 1 19.6748208 4.415802737 1.87801529 1.021500601 1.215362623 0.359247261 0.086814747 0.629865774 3.604881608 0.026751105 0.171566984 26049.70066 -4.415802737 0.193862021 AGFNYES(ph)PSKGGNFPSFPHDEVTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGFNYESPSKGGNFPSFPHDEVTDR 25 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.952)PS(0.048)KGGNFPSFPHDEVTDR;AGFNYES(0.98)PS(0.02)KGGNFPSFPHDEVTDR 289.41 5.14E-63 1126030000 888080 803440 555620 553790 666910 707050 682650 686030 757760 812890 TRUE FALSE 853372.8518 780526.6779 656032.8937 582371.1683 688361.7658 721347.0354 691004.4749 671863.2408 671742.2616 757832.2363 1.126070931 1.029946524 0.865670345 0.768469775 0.908330014 0.951855834 0.911817209 0.886559332 0.886399693 1 19.53151898 4.415810943 3.565512489 0.891954254 1.111724555 0.631354669 0.05712035 0.134775619 3.349116908 0.014487468 0.051797425 26050.19284 -4.415810943 0.219770301 DVFLYR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVFLYR 6 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;;;; 155.88 0.022848 3374780000 2194330 2414840 2198010 2615890 2673630 2331180 2839930 2840170 2656780 2887490 FALSE TRUE 2108573.158 2345971.128 2595239.301 2750896.396 2759629.737 2378318.057 2874685.913 2781519.497 2355193.473 2691917.73 0.783297771 0.871486933 0.964085667 1.021909535 1.025153817 0.883503248 1.067895159 1.033285477 0.874912872 1 21.36020289 4.416225325 2.027752597 0.993210274 0.777567764 0.548674197 0.059447166 0.291839527 2.018444591 0.015465791 0.091510834 26075.0605 -4.416225325 -0.21564251 EVFEFRPELVNDDDEEADDTR ddPTM_BT-474_Pertuzumab_2h_R1 5 EVFEFRPELVNDDDEEADDTR 21 1 Q8WU90;Q8WU90-2 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 ;;;; 267.78 3.16E-37 3398363000 2196367 2410923 2231290 2624228 2641048 2572163 2536860 2821357 2817728 2849961 FALSE TRUE 2110530.549 2342165.837 2634533.738 2759664.722 2725999.707 2624173.898 2567906.852 2763094.992 2497871.33 2656930.603 0.794349144 0.881530678 0.991570399 1.038666467 1.025995826 0.987671223 0.966493761 1.039957532 0.940134201 1 21.34132912 4.416605421 2.430315752 1.003544148 0.795766984 0.83438358 0.029875804 0.115415959 1.230570019 0.007588228 0.037367563 26097.89148 -4.416605421 -0.207777164 ESVQVPDDQDFR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESVQVPDDQDFR 12 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5H1Z6;F5GWK5;F5H3G8;F5H5A8 Q9Y365 STARD10 PCTP-like protein 0 ;;; 326.41 1.67E-48 9614340000 3056400 3176030 2697610 3186610 3183660 3225260 3237340 3343750 3446090 3503760 FALSE TRUE 2936952.509 3085452.734 3185128.135 3351071.324 3286065.315 3290476.967 3276959.535 3274700.394 3054904.31 3266447.214 0.899127497 0.944589804 0.975104732 1.02590708 1.006005945 1.007356541 1.003218274 1.002526653 0.935237617 1 21.6392909 4.416700247 1.878716192 0.998601141 0.896079454 0.652113534 0.022691158 0.266039114 1.522734744 0.005968104 0.038351652 26103.59042 -4.416700247 -0.102521688 TDRPLPENPYHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDRPLPENPYHSR 13 1 P51970 P51970 NDUFA8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 0 81.128 0.0095602 346160000 164720 194980 203710 330400 169100 167400 277160 222490 252990 189020 FALSE TRUE 158282.5603 189419.3613 240524.9285 347451.9836 174539.2551 170784.9427 280551.967 217895.5037 224271.6358 176217.507 0.898222674 1.074917949 1.364932081 1.971722273 0.990476247 0.969171256 1.592077721 1.236514506 1.272697813 1 17.42699774 4.416942051 3.817090622 1.319090458 0.928414164 0.165113563 0.290852544 0.354877625 10.18269353 0.072262764 0.247728227 26118.12831 -4.416942051 -0.390676294 VETISLGEHPCDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VETISLGEHPCDR 13 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 0 ; 200.05 1.13E-07 569490000 590720 639800 585400 725170 643070 668850 724050 702120 674190 759490 FALSE TRUE 567634.0093 621553.5304 691194.8022 762596.1106 663754.9306 682374.6053 732911.1405 687620.9766 597658.7776 708049.0658 0.801687392 0.877839631 0.976196192 1.07703851 0.937441997 0.963739151 1.035113491 0.971148766 0.844092319 1 19.43348981 4.417353501 2.899451037 0.979285365 0.808764247 0.488190783 0.058013667 0.217892835 3.470010378 0.01458679 0.061268242 26142.88433 -4.417353501 -0.170521118 SELVAMLEEEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 SELVAMLEEEELR 13 0 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;;; 197.3 3.14E-07 105826000 103133 119253 110577 140318 131778 125963 141472 147538 137497 140235 FALSE TRUE 99102.44834 115852.0212 130560.7237 147559.8288 136016.759 128510.0582 143203.3767 144491.2887 121888.917 130736.7585 0.758030484 0.886147266 0.998653517 1.128678961 1.040386503 0.982968062 1.095356641 1.105207826 0.93232323 1 16.99630531 4.417387835 2.024894404 1.05009659 0.751713728 0.709275786 0.057623254 0.206987783 1.425198423 0.015113178 0.089827722 26144.9512 -4.417387835 -0.298382861 TEDSLMPEEEFLRR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEDSLMPEEEFLRR 14 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 225.86 4.20E-12 610830000 605600 626460 563010 634580 639460 612930 616390 693200 714000 657440 FALSE TRUE 581932.4825 608593.9742 664758.4311 667330.7498 660028.8116 625323.8646 623933.5652 678885.1778 632949.7133 612911.0032 0.949456739 0.992956516 1.084592098 1.088788986 1.076875449 1.020252306 1.017983952 1.107640708 1.032694323 1 19.22531808 4.417545485 4.27798713 1.058747392 0.957552497 0.493873735 0.034237532 0.146167832 5.306504421 0.008489437 0.027328617 26154.44356 -4.417545485 -0.101194895 QVDDLEVWSHTNDTIGSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVDDLEVWSHTNDTIGSVR 19 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 304.77 2.73E-50 566280000 694960 762210 717850 807780 813370 869790 901130 818780 963320 984040 FALSE TRUE 667800.1949 740472.5171 847581.4635 849469.6226 839532.7847 887377.7497 912158.2985 801871.9069 853967.9522 917390.0943 0.727934822 0.807151202 0.923905184 0.925963369 0.915131731 0.967285079 0.994297087 0.874079535 0.930866768 1 19.8071758 4.417730214 1.946279439 0.938573967 0.716652299 0.800706654 0.035797975 0.188548514 1.177152031 0.009642837 0.059831084 26165.57086 -4.417730214 -0.221921668 EMDEAATAEER ddPTM_BT-474_Pertuzumab_2h_R1 4 EMDEAATAEER 11 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 208.75 4.31E-08 951966000 447730 494522 407251 523920 524098 532428 510811 500855 546876 585152 FALSE TRUE 430232.2166 480418.7167 480850.3149 550959.574 540956.0881 543194.059 517062.4578 490512.1692 484796.9292 545519.1338 0.788665676 0.880663366 0.881454536 1.009972959 0.991635407 0.995737867 0.947835604 0.899165838 0.888689139 1 19.05727027 4.417799906 1.565635187 0.95436458 0.782487819 0.60156919 0.043334323 0.467221914 1.682360123 0.01316278 0.102924946 26169.76999 -4.417799906 -0.171876761 QVAPESHWPELR ddPTM_BT-474_Pertuzumab_2h_R1 4 QVAPESHWPELR 12 0 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 0 ;;; 161.76 6.45E-05 2683860000 1120560 1183140 1032240 1266120 1147250 1313460 1254670 1185320 1308670 1332790 FALSE TRUE 1076767.276 1149398.006 1218788.73 1331464.605 1184152.338 1340019.061 1270025.027 1160842.728 1160115.268 1242518.946 0.866600288 0.925054712 0.980901526 1.071584952 0.953025579 1.078469721 1.022137353 0.934265615 0.933680144 1 20.24483642 4.41832162 2.476280703 0.997008011 0.869282276 0.441484686 0.047844984 0.312391061 3.475673652 0.012903908 0.062661408 26201.22643 -4.41832162 -0.127725736 EAAEVLQNNR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAAEVLQNNR 10 0 P61081;M0QX69 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 193.38 1.35E-06 694000000 301100 316470 278370 358560 306430 295740 325300 342870 342340 374720 FALSE TRUE 289332.6791 307444.5855 328677.6513 377065.3246 316286.5992 301720.0654 329281.1187 335789.6147 303478.9984 349339.8806 0.828226879 0.880072968 0.940853506 1.079365241 0.905383601 0.86368629 0.942580956 0.961211798 0.868721309 1 18.41427182 4.418344851 3.104781271 0.94493698 0.834632506 0.290646889 0.059542741 0.326192704 6.04074513 0.015232299 0.060610876 26202.628 -4.418344851 -0.110304474 YDFTSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDFTSSR 7 0 Q9NZ01;M0R2N5 Q9NZ01 TECR Very-long-chain enoyl-CoA reductase 0 ; 137.18 0.019715 215900000 311010 350560 302080 409780 389260 363170 376370 402730 345490 392980 FALSE TRUE 298855.3854 340562.372 356672.5757 430928.7949 401780.9014 370513.5462 380976.1286 394413.4848 306271.4236 366363.1146 0.815735464 0.929576037 0.97354936 1.176234118 1.096673998 1.011328738 1.039886696 1.076564395 0.835977781 1 18.48291473 4.418361158 2.046412305 1.041169903 0.816755153 0.386722783 0.083725697 0.390568688 2.757448575 0.021746326 0.128139295 26203.61186 -4.418361158 -0.22441475 THPVEIFYTPEPER ddPTM_BT-474_Pertuzumab_2h_R1 3 THPVEIFYTPEPER 14 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;; 161.21 4.63E-06 1504150000 759770 820750 892730 958310 851250 882660 1012760 779387 1065200 1155540 FALSE TRUE 730077.3484 797343.0136 1054066.17 1007768.494 878631.2293 900507.99 1025154.46 763292.3861 944282.9617 1077274.247 0.677707975 0.740148589 0.978456668 0.935479983 0.815605898 0.835913411 0.951618832 0.708540456 0.876548348 1 20.03895414 4.418637168 7.42035771 0.86958711 0.692813091 0.416968398 0.083798657 0.198307262 20.89487565 0.020937315 0.058362979 26220.27051 -4.418637168 -0.176774019 EAGELPTS(ph)PLHLLSPGT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 2 EAGELPT(0.183)S(0.817)PLHLLS(0.005)PGT(0.995)PR;EAGELPT(0.145)S(0.855)PLHLLS(0.002)PGT(0.998)PR 134.03 1.87E-05 96142000 99170 107072 97961 127828 103359 114070 111022 120741 108583 129605 TRUE FALSE 95294.32676 104018.4114 115664.7318 134425.2184 106683.6361 116376.5736 112380.7204 118247.6562 96257.11306 120826.7379 0.788685753 0.860889015 0.957277618 1.112545292 0.882947251 0.963169043 0.930098109 0.97865471 0.796654074 1 16.88258022 4.418637171 3.204081108 0.955344247 0.797835169 0.326854246 0.076566883 0.269831292 5.352623206 0.01860896 0.072287113 26220.27069 -4.418637171 -0.157509078 VVPGQFDDADSS(ph)DSENR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVPGQFDDADSSDSENR 17 0 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.116)S(0.884)DSENR;VVPGQFDDADS(0.063)S(0.937)DSENR;VVPGQFDDADS(0.049)S(0.951)DSENR;VVPGQFDDADS(0.118)S(0.882)DSENR 316.84 4.39E-58 882170000 508126 562218 586979 649218 568802 617210 623580 641350 672120 768650 TRUE FALSE 488267.8742 546184.0931 693059.1626 682724.2188 587098.0329 629690.4091 631211.5586 628105.8984 595823.7554 716588.6509 0.681378185 0.762200312 0.967164581 0.95274216 0.819295745 0.878733438 0.880856204 0.876522253 0.831472498 1 19.45078567 4.418715253 5.166597885 0.892409234 0.698726205 0.633501086 0.055627472 0.107452943 5.740628006 0.013429198 0.040066552 26224.9853 -4.418715253 -0.193683029 LYENFISEFEHR ddPTM_BT-474_Pertuzumab_2h_R1 6 LYENFISEFEHR 12 0 Q9UNM6;J3KNQ3;A0A087WUL9;E9PQG3;E9PPD2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;;; 245.15 1.91E-16 1693105000 927273 1027028 969286 1177106 1109933 1013631 1218112 1084237 1218775 1366091 FALSE TRUE 891034.146 997738.167 1144457.542 1237856.582 1145635.003 1034127.313 1233019.619 1061847.127 1080424.772 1273564.44 0.699638054 0.783421817 0.898625547 0.971962268 0.899550087 0.811994494 0.968164296 0.833760031 0.848347157 1 20.28044053 4.419161062 2.900412145 0.897480075 0.70692779 0.561917707 0.059298879 0.19594912 3.122464942 0.014632764 0.061688073 26251.9194 -4.419161062 -0.190552285 LGCEVLGVSVDSQFTHLAWINTPR ddPTM_BT-474_Pertuzumab_2h_R1 3 LGCEVLGVSVDSQFTHLAWINTPR 24 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;; 359.27 2.28E-102 3741700000 1920483 2202413 1819103 2562692 2355023 2198195 2461828 2165962 2685538 2702657 FALSE TRUE 1845428.401 2139602.338 2147855.378 2694952.841 2430774.454 2242644.009 2491956.587 2121234.128 2380686.985 2519603.634 0.73242806 0.849182113 0.852457644 1.069593965 0.96474478 0.890078097 0.989027224 0.841891994 0.944865674 1 21.26476537 4.419206248 1.770009552 0.942562461 0.730422431 0.538602294 0.063534849 0.414410087 2.03720706 0.017447703 0.120314558 26254.65088 -4.419206248 -0.21214003 VCEVCSAYLGLHDNDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VCEVCSAYLGLHDNDR 16 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;; 218.63 1.32E-14 10614110000 2392430 2677010 2686980 3342770 2951790 3095530 2939570 2746900 3087080 3410290 FALSE TRUE 2298931.191 2600664.296 3172577.058 3515290.76 3046737.006 3158123.738 2975545.337 2690175.555 2736647.62 3179308.021 0.723091684 0.81799696 0.997882884 1.105677945 0.958301928 0.993336826 0.935909738 0.846151281 0.860768319 1 21.60028137 4.419287575 3.993831678 0.955242694 0.739536253 0.555176004 0.070591996 0.172263584 5.464131633 0.020163569 0.067552641 26259.56789 -4.419287575 -0.21570644 RKS(ph)PENTEGKDGSK ddPTM_BT-474_Pertuzumab_2h_R1 4 RKSPENTEGKDGSK 14 3 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.907)PENT(0.093)EGKDGSK;RKS(0.999)PENT(0.001)EGKDGSK;RKS(1)PENTEGKDGSK;RKS(0.998)PENT(0.002)EGKDGSK 173.28 1.51E-05 1023710000 2498920 1969090 1077730 779190 1286160 1458090 1118680 1530120 1536940 1030480 TRUE FALSE 2401259.444 1912933.481 1272499.785 819404.0893 1327530.504 1487573.579 1132370.74 1498522.487 1362473.015 960684.6717 2.499529257 1.991218906 1.324575922 0.852937611 1.381858734 1.548451456 1.178712197 1.559848441 1.418231241 1 19.87370344 4.419335966 2.793832602 1.306004434 2.461466717 0.774049168 0.215935035 0.130505601 1.912301768 0.056556126 0.246356173 26262.49402 -4.419335966 1.155462283 GDIFDGTSFSHLPPSSSDGQGVPLS(ph)PVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDIFDGTSFSHLPPSSSDGQGVPLSPVSK 29 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 GDIFDGTSFSHLPPSSSDGQGVPLS(0.999)PVS(0.001)K;GDIFDGTSFSHLPPSSSDGQGVPLS(1)PVSK 210.21 6.38E-26 255520000 388260 418980 352160 461500 429090 444480 436460 433050 432910 465650 TRUE FALSE 373086.37 407031.1006 415803.1458 485318.0703 442892.0695 453467.6901 441801.528 424107.3662 383767.8717 434111.1107 0.859425987 0.937619634 0.957826546 1.117958187 1.020227445 1.044588998 1.01771532 0.976955797 0.884031443 1 18.72770482 4.419598469 2.043257457 1.008488777 0.860986288 0.396229651 0.05638839 0.420658455 2.955509087 0.015323844 0.090732836 26278.37276 -4.419598469 -0.147502489 EGS(ph)PANWKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGSPANWKR 9 1 O96019-2;O96019 O96019-2 ACTL6A Actin-like protein 6A 1 EGS(1)PANWKR 76.655 0.021326 361580000 300530 295830 190060 258470 250750 270320 248990 270070 288890 283470 TRUE FALSE 288784.9553 287393.218 224408.0699 271809.6677 258815.6015 275786.0556 252037.2141 264492.9601 256096.4183 264270.3244 1.092763465 1.087497125 0.849161064 1.028528906 0.979359306 1.043575574 0.95370986 1.000842454 0.969069906 1 18.0116549 4.419968982 24.99999804 0.981047787 1.09145186 0.442990943 0.05020429 58.71109632 25681.61648 0.011353363 0.031092479 26300.80144 -4.419968982 0.110404073 GFGDGYNGYGGGPGGGNFGGS(ph)PGYGGGR ddPTM_BT-474_Pertuzumab_2h_R1 5 GFGDGYNGYGGGPGGGNFGGSPGYGGGR 28 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR 247.42 6.88E-46 2674360000 1324157 1493820 1430980 1703870 1678010 1748000 1651120 1711730 1731970 1735420 TRUE FALSE 1272407.481 1451217.716 1689589.918 1791806.935 1731984.716 1783345.758 1671326.9 1676382.177 1535364.027 1617878.458 0.786466668 0.896988095 1.04432438 1.107504044 1.070528325 1.102274246 1.03303613 1.036160763 0.948998375 1 20.6256718 4.42006785 2.664410318 1.049052743 0.792241658 0.77809396 0.044713127 0.129703173 1.706504404 0.01178614 0.053656877 26306.78954 -4.42006785 -0.256811084 EDVEVAES(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDVEVAESPLR 11 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 EDVEVAES(1)PLR;EDVEVAES(1)PLR 231.32 1.21E-12 1010270000 994300 1044250 1020160 1045960 1037640 1190590 1043240 1154860 1238590 1201980 TRUE FALSE 955441.6567 1014469.012 1204525.605 1099942.121 1071016.633 1214664.546 1056007.483 1131011.737 1097990.456 1120568.824 0.85263987 0.905316113 1.07492336 0.98159265 0.955779431 1.08397139 0.942385207 1.009319297 0.979850976 1 20.09579983 4.42028176 6.525412285 1.001223462 0.865029338 0.578583339 0.043480681 0.111329938 9.561488506 0.009952296 0.028183636 26319.75003 -4.42028176 -0.136194124 SSS(ph)MSSLTGAYTSGIPSSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSMSSLTGAYTSGIPSSSR 20 0 A8CG34-2;A8CG34 A8CG34-2 POM121C Nuclear envelope pore membrane protein POM 121C 1 SS(0.02)S(0.978)MS(0.001)SLTGAYTSGIPSSSR;SSS(0.997)MS(0.003)SLTGAYTSGIPSSSR 357.96 1.99E-95 221710000 367160 324920 199217 306490 222506 168844 201718 456430 189697 156072 TRUE FALSE 352810.9813 315653.5997 235219.9435 322307.9856 229663.1076 172258.1414 204186.6852 447004.561 168163.3918 145501.1044 2.424799335 2.169424081 1.616619643 2.215158345 1.578428621 1.183895765 1.403334264 3.072172976 1.15575337 1 17.15067058 4.420318747 4.195372674 1.782109716 2.379468317 0.139714077 0.585811208 0.445558938 15.71827728 0.150624255 0.491887449 26321.99163 -4.420318747 0.597358601 LQGEGLSVAGIVCHVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQGEGLSVAGIVCHVGK 17 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 191.21 1.13E-17 0 516590 628220 506580 925100 465760 569830 881520 739060 612450 606860 FALSE TRUE 496401.0917 610303.7807 598130.2748 972844.5219 480741.5934 581352.353 892308.3055 723798.1527 542927.2436 565756.8317 0.877410689 1.078738685 1.05722148 1.719545337 0.84973184 1.027565768 1.577194044 1.279344963 0.959647702 1 19.10982257 4.420476431 2.100261846 1.221823885 0.890166659 0.104960534 0.263363419 0.797993923 5.991745725 0.067947273 0.391710441 26331.55037 -4.420476431 -0.331657226 EIAVHIGDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EIAVHIGDR 9 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ;; 121.83 0.00060287 558080000 298058 333484 325047 397610 343110 364160 352560 388468 391030 438360 FALSE TRUE 286409.5638 323973.3628 383790.2235 418130.6997 354146.4448 371523.5647 356874.7347 380446 346641.9137 408669.4867 0.700834227 0.792751535 0.939121309 1.023151259 0.866584015 0.909105223 0.873260046 0.930938111 0.848220689 1 18.640575 4.420691963 3.361980645 0.920065792 0.712829585 0.653751975 0.053307976 0.137552694 3.033038305 0.013105517 0.049304024 26344.62146 -4.420691963 -0.207236207 KLGDVSPT(ph)QIDVSQFGSFK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLGDVSPTQIDVSQFGSFK 19 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 KLGDVS(0.398)PT(0.602)QIDVSQFGSFK 88.474 0.0034437 0 79563 79051 81215 65561 86679 82112 80300 88177 98367 75275 TRUE FALSE 76453.59 76796.54288 95892.35712 68944.61107 89467.10875 83772.3609 81282.73542 86356.11414 87200.79055 70176.5572 1.089446292 1.094333292 1.366444308 0.982445047 1.274885978 1.193737114 1.158260517 1.230555011 1.242591458 1 16.09870155 4.420720916 24.99999661 1.189761977 1.090653459 0.089955919 0.110868069 144.5913787 64090.92294 0.02435297 0.066693376 26346.37788 -4.420720916 -0.099108517 FGINIPSPEHS(ph)NTIDVCNTVDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 FGINIPSPEHSNTIDVCNTVDIK 23 0 C9IZ03;Q9HCI7-2;Q9HCI7 C9IZ03 MSL2 E3 ubiquitin-protein ligase MSL2 1 FGINIPS(0.254)PEHS(0.709)NT(0.036)IDVCNTVDIK 129.24 1.20E-07 0 98497 96800 66838 78618 90385 92812 78463 92907 92814 91470 TRUE FALSE 94647.62835 94039.35878 78917.1134 82675.4844 93292.31561 94688.72223 79423.25366 90988.43798 82278.14383 85274.65543 1.109915108 1.102782044 0.925446289 0.969520006 1.094021608 1.110397008 0.931381701 1.067004464 0.964860467 1 16.3798294 4.420839669 21.65135216 1.014207019 1.108131969 0.28722629 0.061470305 26.81792407 10316.22544 0.015044245 0.041200483 26353.58296 -4.420839669 0.093924951 NYFESTDGLIWVVDSADR ddPTM_BT-474_Pertuzumab_2h_R1 2 NYFESTDGLIWVVDSADR 18 0 V9GYD0;P36404-2;P36404 V9GYD0 ARL2-SNX15;ARL2 ADP-ribosylation factor-like protein 2 0 ; 193.47 2.84E-14 176119000 152855 157077 134482 156152 163125 143766 153800 169186 176565 172088 FALSE TRUE 146881.2576 152597.3178 158785.8889 164211.0234 168372.0638 146673.047 155682.2504 165692.25 156522.0814 160432.3265 0.91553405 0.951163155 0.989737495 1.023553214 1.049489635 0.914236241 0.970392026 1.032785933 0.975626826 1 17.29160534 4.42088169 2.483732729 0.996753827 0.9168367 0.339628161 0.035774199 0.368319285 4.120676237 0.00951902 0.046374759 26356.13297 -4.42088169 -0.079917126 VFDLQFSTDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 VFDLQFSTDSPR 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 VFDLQFS(0.148)T(0.148)DS(0.705)PR;VFDLQFSTDS(1)PR;VFDLQFSTDS(1)PR;VFDLQFST(0.003)DS(0.997)PR 160.81 7.04E-05 213963000 183961 206137 226198 224596 218525 262364 251881 217725 228462 291953 TRUE FALSE 176771.6007 200258.1746 267077.0103 236187.4265 225554.0551 267669.1798 254963.595 213228.9027 202527.9516 272178.7633 0.649468748 0.735759734 0.981255874 0.867765816 0.828698214 0.983431538 0.936750509 0.783414915 0.744099022 1 18.05419498 4.421561474 5.885523889 0.88034391 0.669075139 0.483237408 0.083440033 0.147660603 10.55483117 0.020931871 0.060461295 26397.41946 -4.421561474 -0.211268771 TVS(ph)SSGCEGKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSSSGCEGKR 11 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 T(0.002)VS(0.969)S(0.026)S(0.003)GCEGKR;TVS(0.954)S(0.042)S(0.004)GCEGKR 102.6 0.0017437 776440000 1217650 1029740 581000 709180 930770 768910 623720 872390 715650 636150 TRUE FALSE 1170062.892 1000372.823 685999.6243 745780.8648 960709.0624 784457.887 631353.2719 854374.8416 634412.4122 593062.9939 1.972915026 1.686790162 1.15670617 1.257506998 1.619910654 1.322722704 1.064563594 1.440613983 1.069721798 1 19.17782583 4.421890526 3.67217124 1.273857767 1.930446325 0.636282021 0.182016266 0.133961558 3.579094165 0.044148566 0.156534153 26417.42761 -4.421890526 0.656588559 EIGNLLHPSVPISNDEDVDNKVER ddPTM_BT-474_Pertuzumab_2h_R1 2 EIGNLLHPSVPISNDEDVDNKVER 24 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 126.27 5.58E-05 2096610000 1253590 1473560 1403070 1824870 1603750 1838190 1676680 1648830 1774660 1830460 FALSE TRUE 1204598.317 1431535.512 1656635.96 1919051.759 1655336.075 1875359.461 1697199.711 1614781.084 1573208.037 1706481.314 0.70589599 0.838881446 0.970790566 1.124566524 0.970028832 1.098962787 0.99456097 0.946263561 0.921901707 1 20.70259319 4.421917316 2.354986051 1.006052421 0.708052679 0.727328084 0.059584318 0.179606809 1.772564716 0.016102035 0.082852638 26419.05727 -4.421917316 -0.297999742 ELSEPMEFQYLPDTDDR ddPTM_BT-474_Pertuzumab_2h_R1 5 ELSEPMEFQYLPDTDDR 17 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3 Q04206 RELA Transcription factor p65 0 ;;;; 417.5 1.12E-140 1040560000 450564 484705 428294 513636 486452 510948 502584 558614 557207 573661 FALSE TRUE 432955.4608 470881.688 505696.2531 540144.8155 502099.1704 521279.7186 508734.7733 547078.4257 493955.1974 534806.4295 0.809555452 0.880471255 0.945568761 1.009981903 0.938842809 0.974707277 0.951250294 1.022946613 0.92361492 1 19.02865728 4.421983779 1.852883981 0.975928317 0.801358424 0.76038651 0.029873676 0.205212271 1.128854942 0.007592111 0.050217976 26423.10066 -4.421983779 -0.174569893 WAHDKFS(ph)GEEGEIEDDESGTENREEKDNIQPTTE ddPTM_BT-474_Pertuzumab_2h_R1 3 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE 293.66 5.12E-89 2003680000 1463930 1173500 686900 521580 872290 1017490 778640 662650 1062150 731790 TRUE FALSE 1406717.997 1140032.929 811038.11 548498.8063 900348 1038064.345 788169.2292 648966.0459 941579.1849 682225.2115 2.061955456 1.671050717 1.188812868 0.803984956 1.319722556 1.521586021 1.155291854 0.951248994 1.380158882 1 19.37988854 4.422050653 2.676496002 1.155041326 2.039095356 0.679225473 0.201427116 0.171019558 2.271743592 0.053646543 0.244343483 26427.1697 -4.422050653 0.884054029 IS(ph)DAELEAELEKLSLSEGGLVPSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISDAELEAELEKLSLSEGGLVPSSK 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 IS(1)DAELEAELEKLSLSEGGLVPSSK 95.244 0.0060918 26130000 48860 40897 21797 15742 27846 41305 25148 32660 40492 29748 TRUE FALSE 46950.49718 39730.6576 25736.20277 16554.44651 28741.69188 42140.2154 25455.76875 31985.55959 35895.51792 27733.14146 1.692938294 1.432605738 0.927994501 0.596919268 1.036366252 1.519489433 0.917882627 1.153333445 1.294318495 1 14.75932343 4.422054833 4.134543583 1.059691366 1.646362683 0.450521912 0.231575815 0.183553176 6.321056991 0.060239439 0.198842519 26427.42401 -4.422054833 0.586671317 KSLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_BT-474_Pertuzumab_2h_R1 3 KSLDSDESEDEEDDYQQKR 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.001)LDS(0.999)DES(1)EDEEDDYQQKR;KS(0.018)LDS(0.982)DES(1)EDEEDDYQQKR;KS(0.001)LDS(0.999)DES(1)EDEEDDYQQKR 146.25 6.29E-08 2737920000 4455330 3532270 1911520 1323040 2301330 2521020 2097120 2788890 3113950 2091570 TRUE FALSE 4281210.778 3431533.118 2256974.186 1391322.253 2375354.369 2571996.752 2122785.182 2731298.447 2760467.451 1949906.101 2.195598432 1.759845316 1.157478396 0.71353295 1.218189106 1.319036209 1.088660208 1.40073332 1.415692504 1 20.89497322 4.422190618 2.996164909 1.177033355 2.153406097 0.744333887 0.198156979 0.135256732 2.317025536 0.053516151 0.221012804 26435.688 -4.422190618 0.976372742 IIAPPER ddPTM_BT-474_Pertuzumab_2h_R1 9 IIAPPER 7 0 P60709;P63267-2;Q562R1;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ;;;;;;;; 135.5 0.0071447 19679050000 4048840 4495780 4185980 5440720 4695510 4682170 5061460 5080690 4906670 5117790 FALSE TRUE 3890606.857 4367564.756 4942479.703 5721516.211 4846545.344 4776846.685 5123403.662 4975771.976 4349685.392 4771157.525 0.815442969 0.915409884 1.035907885 1.199188285 1.01580074 1.001192407 1.073828235 1.042885704 0.911662499 1 22.18590789 4.42222018 2.903895545 1.042653867 0.824818238 0.515565563 0.068730635 0.205641378 3.284958864 0.017514482 0.074263205 26437.48753 -4.42222018 -0.217835629 TYADYESVNECMEGVCK ddPTM_BT-474_Pertuzumab_2h_R1 1 TYADYESVNECMEGVCK 17 0 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 318.4 9.39E-51 0 112090 103100 70959 86750 82151 84470 84080 94623 110420 96790 FALSE TRUE 107709.3989 100159.6889 83782.86977 91227.1779 84793.46152 86178.04127 85108.99619 92669.00198 97885.58452 90234.32709 1.193663236 1.109995411 0.928503292 1.011003028 0.93970293 0.955047198 0.943199766 1.026981693 1.084793201 1 16.46138875 4.422346246 4.43589366 0.985541564 1.177813865 0.689757857 0.045902949 0.10277693 4.11430328 0.011702138 0.03727258 26445.16289 -4.422346246 0.192272301 MDEFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDEFSR 6 0 O00422;O00422-2;H7BZW6;U3KQ12;U3KPY7 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ; 175.93 0.0094204 1381900000 1351650 1422250 1300050 1504130 1441290 1466270 1427770 1568750 1591010 1575140 FALSE TRUE 1298826.024 1381688.823 1534997.954 1581758.33 1487650.402 1495918.984 1445243.476 1536354.764 1410405.215 1468454.365 0.884485112 0.940913695 1.045315395 1.077158656 1.013072273 1.01870308 0.98419366 1.046239366 0.960469218 1 20.485867 4.422619678 3.868300562 1.02098213 0.893699919 0.65231506 0.031877225 0.117389804 3.512894832 0.007877466 0.027055974 26461.81797 -4.422619678 -0.127282211 VIENPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIENPR 6 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 142.11 0.026911 298260000 190488 212660 186653 241860 243470 217660 227550 249450 218280 220610 FALSE TRUE 183043.5184 206595.145 220385.3492 254342.4236 251301.4337 222061.2343 230334.825 244298.7703 193501.7695 205667.8882 0.889995614 1.004508515 1.071559353 1.236665703 1.221879778 1.079707855 1.119935771 1.187831374 0.940845803 1 17.64995703 4.422687189 2.096355537 1.127600153 0.889538233 0.364451866 0.089241823 0.374815275 2.796336596 0.022752789 0.132177233 26465.93177 -4.422687189 -0.238061919 GRWES(ph)QQDVSQTTVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GRWESQQDVSQTTVSR 16 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 GRWES(0.51)QQDVS(0.357)QT(0.108)T(0.023)VS(0.001)R;GRWES(1)QQDVSQTTVSR 157.84 7.53E-08 480620000 594572 476222 248636 291374 309375 248643 190261 407955 228085 206312 TRUE FALSE 571335.4689 462640.6148 293570.0561 306411.8471 319326.3278 253670.7318 192589.471 399530.5867 202193.747 192338.3045 2.970471589 2.405348306 1.526321327 1.593088012 1.660232624 1.318877862 1.001305858 2.077228391 1.051240145 1 17.55328658 4.422932575 1.924686186 1.446211282 3.064375689 0.725857806 0.32385114 0.231134369 1.396832409 0.083880523 0.533987295 26480.88983 -4.422932575 1.618164407 LQDLIEEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQDLIEEIR 9 0 O75843;G3V2V9;G3V3Z2;G3V532 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 ; 111.65 0.0048624 22323000 61286 68687 64471 80646 77057 80463 70434 75269 77732 84458 FALSE TRUE 58890.87536 66728.11401 76122.34385 84808.14972 79535.60839 82090.01699 71295.99236 73714.66885 68908.18924 78737.58443 0.747938558 0.847474741 0.966785359 1.077098699 1.010135235 1.042577285 0.905488692 0.936206887 0.875162602 1 16.26476483 4.422951154 2.717955382 0.976096935 0.754578476 0.626165972 0.057812155 0.202115905 2.779734338 0.016167758 0.072771469 26482.02272 -4.422951154 -0.221518459 NVAQYNANHPDFPMQIEQLER ddPTM_BT-474_Pertuzumab_2h_R1 2 NVAQYNANHPDFPMQIEQLER 21 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 174.82 2.50E-12 1157650000 332280 333390 407710 402890 365550 384020 370860 382120 454030 464900 FALSE TRUE 319294.1302 323882.0436 481392.2665 423683.2012 377308.2477 391785.1475 375398.6956 374229.0885 402490.4178 433411.9089 0.736699024 0.747284597 1.110703828 0.977553206 0.870553485 0.903955658 0.866147625 0.863449021 0.92865565 1 18.72537927 4.423032563 24.99887268 0.925967469 0.739344576 0.534610018 0.073024551 64.65900242 29884.07526 0.018731052 0.051297121 26486.98728 -4.423032563 -0.186622893 IRSS(ph)VEKENQK ddPTM_BT-474_Pertuzumab_2h_R1 7 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.399)S(0.601)VEKENQK;IRS(0.012)S(0.988)VEKENQK;IRS(0.375)S(0.625)VEKENQK;IRS(0.033)S(0.967)VEKENQK;IRS(0.191)S(0.809)VEKENQK;IRS(0.052)S(0.948)VEKENQK;IRS(0.142)S(0.858)VEKENQK 172.57 1.04E-05 16631130000 6507110 5795870 3956630 3582100 4717000 5050170 4564500 5199270 6224680 4943730 TRUE FALSE 6252804.947 5630577.462 4671681.056 3766972.61 4868726.589 5152287.898 4620361.716 5091903.258 5518080.422 4608886.764 1.356684438 1.221678412 1.013624612 0.817328089 1.056378002 1.117902904 1.002489745 1.10480112 1.197269689 1 22.13598689 4.423127695 3.41916723 1.039956948 1.338303492 0.546790769 0.094734013 0.179972973 4.126285898 0.025073037 0.093634702 26492.78987 -4.423127695 0.298346543 ETHEALAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETHEALAR 8 0 Q9Y6D9;Q9Y6D9-3 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 0 ; 80.684 0.024813 168942000 311590 305810 201661 253525 261000 288733 263728 263890 309930 292556 FALSE TRUE 299412.7183 297088.5982 238105.6286 266609.4556 269395.302 294571.3791 266955.5822 258440.5793 274748.0457 272740.9215 1.097791694 1.089270347 0.873010281 0.977519083 0.987733342 1.080041005 0.97878815 0.947568036 1.007359087 1 18.05717165 4.423466584 22.88202458 0.981272501 1.095661439 0.458951022 0.048692593 30.75355176 13115.11776 0.012101719 0.033141974 26513.47081 -4.423466584 0.114388939 SLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLDSDESEDEEDDYQQKR 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 SLDS(1)DES(1)EDEEDDYQQKR;S(0.005)LDS(0.995)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;S(0.002)LDS(0.998)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR 259.93 3.57E-30 14031170000 6911890 6315140 4596030 4587030 5117080 5570120 5233050 5846660 6953330 5727600 TRUE FALSE 6641765.697 6135038.39 5426634.859 4823767.168 5281675.525 5682751.643 5297093.631 5725924.428 6164017.129 5339664.55 1.243854485 1.148955769 1.016287598 0.903383934 0.98913995 1.064252555 0.992027417 1.072337855 1.15438284 1 22.34831768 4.423653351 3.103343828 1.023404985 1.233592674 0.570400735 0.062335988 0.188750842 3.497069447 0.016694422 0.067210738 26524.87533 -4.423653351 0.210187689 DSSFFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSSFFDK 7 0 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 108.46 0.029935 208770000 624280 642870 567540 696180 684820 658550 715840 871160 738210 721680 FALSE TRUE 599882.4474 624535.977 670107.1029 732109.9332 706847.8572 671866.3322 724600.6641 853170.2416 654411.4956 672799.9708 0.891620799 0.928263978 0.995997521 1.088153931 1.050606254 0.998612309 1.07699271 1.268088999 0.972668734 1 19.35981812 4.423920852 0.684685967 1.0991976 0.797606573 0.335109665 0.080904083 2.198712426 1.032407787 0.037602205 0.483305856 26541.21817 -4.423920852 -0.301591028 ISIFDNLDVVS(ph)EDEEAPEEAPENGSNK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISIFDNLDVVSEDEEAPEEAPENGSNK 27 0 A0A5F9ZH11;P55201-3;P55201;P55201-2;P55201-4;A0A5F9ZHX4;A0A5F9ZHW9 A0A5F9ZH11 BRPF1 Peregrin 1 IS(0.027)IFDNLDVVS(0.973)EDEEAPEEAPENGSNK;ISIFDNLDVVS(1)EDEEAPEEAPENGSNK 172.74 2.21E-12 51192000 161761 141881 161621 161367 179062 160349 193096 220870 206500 215474 TRUE FALSE 155439.2013 137834.6928 190829.5099 169695.1702 184821.6918 163591.3666 195459.1666 216308.9573 183058.9857 200879.7541 0.773792272 0.686155225 0.949968855 0.844759946 0.920061321 0.814374586 0.97301576 1.076808155 0.911286389 1 17.61597264 4.424059513 0.329261521 1.02263218 0.556899555 0.518790092 0.076436189 4.236598371 0.435138298 0.081930769 0.780435427 26549.69355 -4.424059513 -0.465732625 TITLVKS(ph)PISVPGGSALISNLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TITLVKSPISVPGGSALISNLGK 23 1 P51610-2;P51610;A6NEM2;P51610-4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 TITLVKS(0.999)PIS(0.001)VPGGSALISNLGK;TIT(0.001)LVKS(0.999)PISVPGGSALISNLGK 251.82 1.14E-43 799020000 1139130 1005700 678010 645880 816080 850900 807490 918230 933760 800760 TRUE FALSE 1094611.54 977018.4207 800541.4893 679213.9442 842329.9543 868105.781 817372.3042 899268.2296 827763.4794 746523.812 1.466278132 1.308757209 1.072358947 0.909835605 1.128336352 1.162864154 1.094904531 1.204607563 1.108823947 1 19.50982875 4.424143169 3.247239504 1.096896818 1.447472478 0.710256123 0.079767667 0.139548101 2.858983116 0.021618193 0.084078159 26554.8082 -4.424143169 0.35057566 (ac)S(ph)DQEAKPSTEDLGDKKEGEYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDQEAKPSTEDLGDKKEGEYIK 22 3 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(1)DQEAKPSTEDLGDKKEGEYIK 120.41 4.14E-12 686840000 1079100 771590 278200 161670 447300 547680 274990 393320 465320 204890 TRUE FALSE 1036927.579 749585.0087 328476.9285 170013.8081 461687.8107 558754.4648 278355.4099 385197.8046 412498.8244 191012.6178 5.428581582 3.924269597 1.719660891 0.89006585 2.417053994 2.925222801 1.457261898 2.016609211 2.159537046 1 17.54330842 4.424196101 2.992852255 1.871461834 5.292530963 0.797165421 0.596938657 0.110661998 1.891269544 0.152866537 0.634694523 26558.0449 -4.424196101 3.421069129 YDVYLYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDVYLYDR 8 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8;A0A0C4DH82;H7C4C4 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 83.005 0.043746 317310000 495580 507760 468740 541020 483340 414500 576210 557170 540390 581650 FALSE TRUE 476212.1857 493279.1819 553451.7451 568942.107 498887.0701 422881.474 583261.8303 545664.2448 479047.1927 542254.3274 0.878208179 0.909682334 1.020649752 1.049216352 0.920024138 0.779858182 1.075624114 1.00628841 0.883436366 1 19.04861014 4.424356031 7.460389215 0.969392689 0.88580624 0.115077356 0.082701311 0.412935766 48.60398706 0.020876583 0.058278281 26567.82681 -4.424356031 -0.083586449 ARS(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ARSMDSSDLSDGAVTLQEYLELKK 24 2 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.976)MDS(0.023)S(0.001)DLSDGAVTLQEYLELKK 178.44 2.09E-17 179060000 287010 262810 166780 189870 207640 240770 215950 261580 249080 193510 TRUE FALSE 275793.3319 255314.9161 196920.856 199669.2135 214318.9292 245638.5344 218592.8607 256178.2816 220805.4826 180403.3953 1.528759098 1.415244517 1.09155848 1.106792991 1.187998312 1.361607047 1.211689283 1.420030267 1.22395414 1 17.46086697 4.424429946 6.084536063 1.228202435 1.502721696 0.451034898 0.119528432 0.164413537 13.06285886 0.030580205 0.0879079 26572.3489 -4.424429946 0.274519261 LLETTDRPDGHQNNLR ddPTM_BT-474_Pertuzumab_2h_R1 5 LLETTDRPDGHQNNLR 16 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 240.92 4.20E-20 9386990000 2407980 2679750 2626840 3059480 2784210 3052590 3122590 2753090 3209850 3480260 FALSE TRUE 2313873.479 2603326.154 3101568.422 3217380.129 2873766.643 3114315.461 3160805.19 2696237.729 2845481.285 3244538.89 0.713159422 0.80237169 0.955935042 0.991629393 0.885724209 0.95986381 0.974192419 0.831007986 0.877006373 1 21.62958203 4.424430029 3.564989241 0.926488692 0.725808859 0.655532294 0.052671266 0.142727629 3.590879245 0.013943656 0.050689272 26572.35399 -4.424430029 -0.200679833 RAS(ph)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RASAGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 35 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RAS(0.989)AGPAPGPVVT(0.011)AEGLHPSLPSPTGNSTPLGSSK;RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 213.3 5.19E-29 857290000 368758 406970 339608 437280 419330 469530 428300 396580 451460 490440 TRUE FALSE 354346.5297 395363.6141 400982.7201 459848.0732 432818.1303 479024.2183 433541.6635 388390.4844 400212.1535 457222.062 0.774998757 0.864708086 0.876997751 1.005743404 0.946625647 1.047683955 0.948208102 0.849457007 0.875312429 1 18.80253549 4.424488294 1.628752283 0.943412553 0.767999628 0.473928561 0.058230182 0.58494946 2.314453675 0.01765258 0.134891562 26575.91917 -4.424488294 -0.175412925 RNPSPDHS(ph)YK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNPSPDHSYK 10 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 RNPS(0.013)PDHS(0.987)YK;RNPS(0.148)PDHS(0.852)YK 146.58 1.74E-05 1018410000 965420 930160 876780 989500 968850 955260 1052590 1009310 1298030 1253300 TRUE FALSE 927690.3191 903632.7475 1035233.65 1040568.214 1000013.94 974576.0117 1065471.911 988467.3958 1150683.076 1168412.875 0.793974749 0.773384792 0.886016983 0.890582632 0.855873777 0.834102425 0.911896757 0.84599153 0.984825742 1 20.15611873 4.424509592 0.029836529 1.640367177 4.99E-08 0.650508766 0.041429671 400.4970899 2.060865686 46.22254046 68.46319201 26577.22247 -4.424509592 -1.640367127 ATT(ph)PSQLSIEVEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATTPSQLSIEVEAR 14 0 A0A1W2PQQ1;Q5HYW2;A0A0J9YW69;A0A0J9YY72;Q5HYW2-2 A0A1W2PQQ1 NHSL2 NHS-like protein 2 1 AT(0.114)T(0.88)PS(0.005)QLS(0.001)IEVEAR;AT(0.114)T(0.882)PS(0.004)QLSIEVEAR 140.49 0.00011105 125780000 273590 299510 255270 348110 310390 283760 310660 375770 282700 275590 TRUE FALSE 262897.8003 290968.2681 301402.9675 366075.9988 320373.9762 289497.8216 314461.95 368010.2182 250609.0812 256924.0438 1.023251061 1.132506961 1.173120907 1.42484134 1.246959885 1.126783688 1.223949091 1.43236971 0.975420897 1 17.97098238 4.424654989 2.222563319 1.235554231 1.027559249 0.090998016 0.145796034 0.639144865 5.484330991 0.036742461 0.201858272 26586.12176 -4.424654989 -0.207994982 FLSNGHVTIPGQQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 FLSNGHVTIPGQQDK 15 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 80.361 0.017201 444940000 557400 690810 808790 825250 748920 820870 895620 881010 929800 1057700 FALSE TRUE 535616.1918 671108.7752 954956.3444 867841.2514 773009.692 837468.5538 906580.8655 862816.8356 824253.002 986061.0369 0.543187665 0.680595572 0.968455611 0.880109059 0.78393696 0.849307013 0.919396297 0.875013618 0.835904646 1 19.91131743 4.424728992 4.344289643 0.879971599 0.568570326 0.776678121 0.061175807 0.081332644 3.150154122 0.014780723 0.047744158 26590.65238 -4.424728992 -0.311401273 RLS(ph)NSSLCSIEEEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSNSSLCSIEEEHR 15 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 RLS(0.899)NS(0.096)S(0.004)LCSIEEEHR;RLS(0.594)NS(0.298)S(0.107)LCSIEEEHR 120.32 6.73E-05 215499000 96745 113475 117449 140158 136512 135573 145906 109692 138714 146611 TRUE FALSE 92964.09844 110238.8041 138674.6469 147391.5712 140903.0325 138314.3789 147691.6413 107426.8219 122967.7683 136680.9064 0.680154243 0.80654136 1.014586826 1.078362553 1.030890387 1.011950993 1.080557959 0.785968024 0.899670419 1 17.06045219 4.425224702 3.432304766 0.980150129 0.696788457 0.591984831 0.083814667 0.180936559 4.192540689 0.02399774 0.089755935 26621.02061 -4.425224702 -0.283361672 VGWEQLLTTIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGWEQLLTTIAR 12 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144;P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8;H0YJ11;H0YJW3 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ; 176.78 5.61E-05 565010000 196161 239540 222760 298570 270610 224560 297050 287760 334710 358280 FALSE TRUE 188494.8113 232708.5537 263017.6873 313979.2335 279314.4164 229100.7571 300685.3868 281817.6554 296715.124 334013.3765 0.564333121 0.696704294 0.787446569 0.940019938 0.836237217 0.68590294 0.900219596 0.843731645 0.888333058 1 18.34954635 4.425496439 1.801577812 0.856623632 0.550152637 0.608141476 0.078690113 0.333250762 1.702245489 0.020568582 0.141550653 26637.68256 -4.425496439 -0.306470995 DNFLEWR ddPTM_BT-474_Pertuzumab_2h_R1 3 DNFLEWR 7 0 Q9H089;F8WFC6 Q9H089 LSG1 Large subunit GTPase 1 homolog 0 ;; 89.752 0.046031 144090000 486892 534073 497919 620760 530147 562643 582510 592240 597720 679640 FALSE TRUE 467863.7224 518841.761 587904.0394 652797.498 547199.6597 574020.027 589638.9316 580010.037 529869.3314 633607.3774 0.738412681 0.818869507 0.927868046 1.030287085 0.863625771 0.905955403 0.930606165 0.915409223 0.83627393 1 19.27322961 4.425612369 3.046231289 0.923808977 0.746574835 0.563793759 0.054032998 0.182676275 3.248489584 0.013315332 0.05465484 26644.7941 -4.425612369 -0.177234142 EESDWPASGSSS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESDWPASGSSSPLR 15 0 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L0Y2;A0A087WVQ2;Q9BUL5-2 I3L4Q4 PHF23 PHD finger protein 23 1 EESDWPAS(0.001)GS(0.005)S(0.04)S(0.953)PLR;EESDWPASGSS(0.005)S(0.995)PLR 212.14 1.36E-11 0 563400 682730 652230 925970 957340 725330 737330 804260 721540 731480 TRUE FALSE 541381.7051 663259.2089 770102.4698 973759.4227 988133.7105 739996.6696 746353.6651 787651.7499 639633.8041 681936.2081 0.793889075 0.972611809 1.129288137 1.427933304 1.449011944 1.085140605 1.094462585 1.155022626 0.937967212 1 19.37927726 4.425688344 2.548374642 1.178708647 0.804218219 0.358875413 0.155976192 0.339818964 4.025085542 0.042229789 0.203077738 26649.45574 -4.425688344 -0.374490428 ELHIQGNR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELHIQGNR 8 0 Q15404;Q15404-2 Q15404 RSU1 Ras suppressor protein 1 0 ;;; 143.28 0.0006039 1820430000 1064240 1114150 988330 1189210 1066850 1221430 1156900 1112660 1188850 1341280 FALSE TRUE 1022648.324 1082375.533 1166943.216 1250585.271 1101166.199 1246128.151 1171058.488 1089683.182 1053896.732 1250433.911 0.817834765 0.865599952 0.933230622 1.000121046 0.880627268 0.996556588 0.936521697 0.871444042 0.842824817 1 20.25399738 4.426103637 3.196276771 0.9280807 0.823365986 0.334561535 0.05291921 0.297926355 5.899178692 0.013525462 0.053476956 26674.95142 -4.426103637 -0.104714714 EMSVYEAYR ddPTM_BT-474_Pertuzumab_2h_R1 1 EMSVYEAYR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 74.941 0.092286 90414000 61601 72745 88156 102000 78221 78231 103050 85732 83543 81595 FALSE TRUE 59193.56482 70670.38382 104087.7502 107264.2322 80737.0495 79812.88442 104311.1567 83961.60424 74059.54888 76068.49797 0.778161347 0.929036141 1.368342389 1.410100568 1.061372995 1.049223878 1.371279301 1.103763141 0.973590262 1 16.2150115 4.42612473 6.33285725 1.177909575 0.813175425 0.411229291 0.154310963 0.154677239 13.68266362 0.038251125 0.109261037 26676.24698 -4.42612473 -0.36473415 LQPERGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 7 LQPERGSPK 9 1 S4R3H4;Q9UKV3;E7EQT4;A0A087WYN3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK 83.226 0.0098791 22081190000 7841840 6915280 4755120 4551650 5624000 5691720 5484770 6177920 6903600 5586340 TRUE FALSE 7535372.223 6718062.985 5614475.961 4786561.202 5804901.068 5806810.478 5551894.256 6050343.793 6119932.27 5207972.216 1.446891786 1.289957532 1.078054131 0.919083475 1.114618287 1.114984919 1.06603761 1.161746557 1.175108471 1 22.31229032 4.426573573 2.963842089 1.08453078 1.432709987 0.735981893 0.072163846 0.139050147 2.325147343 0.019277389 0.081123927 26703.83113 -4.426573573 0.348179207 GYNFEDLTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GYNFEDLTDR 10 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ; 145.99 6.85E-05 790760000 686130 813260 710260 1005650 907020 1052460 913340 870080 783970 904470 FALSE TRUE 659315.281 790066.6211 838619.7816 1057551.717 936195.122 1073741.462 924517.7281 852112.5439 694977.0123 843209.4413 0.781911645 0.936975539 0.994556916 1.254198145 1.110275901 1.273398292 1.096427154 1.01055859 0.824204496 1 19.6855315 4.426617903 1.974858953 1.086717786 0.779578275 0.359153217 0.122828677 0.476408618 3.058479192 0.033879415 0.211875442 26706.55704 -4.426617903 -0.307139511 YGYIHLYDLETGTCIYMNR ddPTM_BT-474_Pertuzumab_2h_R1 3 YGYIHLYDLETGTCIYMNR 19 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 332.29 2.60E-75 3582550000 1336980 1460420 1473820 1637200 1681530 1513970 1721290 1408660 1699180 1828140 FALSE TRUE 1284729.343 1418770.252 1740172.059 1721696.088 1735617.94 1544583.511 1742355.662 1379570.679 1506296.21 1704318.449 0.753808271 0.832456078 1.021036919 1.010196239 1.018364813 0.906276354 1.022318137 0.809455932 0.883811479 1 20.7007635 4.426671692 5.17658712 0.949891957 0.770485211 0.491435176 0.068978045 0.157235704 9.06609833 0.018554202 0.055825024 26709.86495 -4.426671692 -0.179406746 NSPTFKS(ph)FEER ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPTFKSFEER 11 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 NSPT(0.059)FKS(0.941)FEER 121.13 0.00025322 844600000 2278800 1907500 552280 726030 1727100 1469000 1099100 1308100 1616200 1088200 TRUE FALSE 2189741.977 1853099.968 652089.2814 763500.4953 1782653.74 1498704.186 1112551.115 1281087.278 1432735.752 1014495.245 2.158454648 1.826622626 0.642772142 0.752591497 1.757182943 1.477290499 1.096654834 1.26278293 1.41226463 1 19.95233067 4.427020946 7.837367618 1.200190848 2.077828976 0.525339548 0.316973621 0.160546061 21.67188965 0.080912857 0.225132183 26731.3533 -4.427020946 0.877638128 MYSIEPADR ddPTM_BT-474_Pertuzumab_2h_R1 2 MYSIEPADR 9 0 A0AVT1;A0AVT1-2;H0Y9U5 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 125.31 0.0011749 304990000 201690 209188 191558 202174 211150 217780 218298 219690 217980 254240 FALSE TRUE 193807.7318 203222.1631 226176.7918 212608.2244 217941.8315 222183.6608 220969.5962 215153.3247 193235.8242 237020.0983 0.8176848 0.857404771 0.954251531 0.897005047 0.91950781 0.937404306 0.932282105 0.907742956 0.815271893 1 17.85464987 4.427113501 5.249645283 0.916924128 0.826159422 0.367844901 0.044591453 0.171818654 10.2628644 0.01033685 0.030973188 26737.05081 -4.427113501 -0.090764706 IQIISTDSAVAS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQIISTDSAVASPQR 15 0 P49116;P49116-2;C9J2Y1;C9JMI6;C9JKS0 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 IQIISTDSAVAS(1)PQR;IQIISTDSAVAS(1)PQR 199.91 7.53E-09 370720000 252510 264630 230570 276800 247273 274850 288470 291620 250170 308650 TRUE FALSE 242641.63 257083.0115 272239.128 291085.6812 255226.7606 280407.6553 292000.3822 285597.9451 221771.7504 287744.8606 0.843252698 0.893440845 0.946112912 1.011610357 0.886989815 0.974501003 1.014789218 0.992538822 0.770723585 1 18.13443064 4.42711966 2.491281235 0.956024551 0.844914028 0.189415996 0.070240149 0.489792954 5.498787536 0.017497656 0.086291063 26737.42995 -4.42711966 -0.111110523 AEQLVLSGADS(ph)DEDTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEQLVLSGADSDEDTSR 17 0 H7C1N2;J3KR05;O75128-2 H7C1N2 COBL Protein cordon-bleu 1 AEQLVLSGADS(1)DEDTSR 209.9 4.05E-12 177820000 95998 100410 86614 109240 91212 109320 101120 104920 101390 119500 TRUE FALSE 92246.29203 97546.40511 102267.0765 114877.8895 94145.91682 111530.5253 102357.5368 102753.3653 89880.63226 111406.1586 0.828017887 0.875592574 0.917966097 1.031162828 0.845069232 1.001116336 0.918778083 0.922331105 0.806783336 1 16.76546946 4.427705244 2.70260991 0.929813259 0.831730265 0.204436933 0.065502069 0.449269815 6.0890396 0.015697289 0.071811928 26773.5059 -4.427705244 -0.098082994 EVYSWGCGEYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVYSWGCGEYGR 12 0 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 0 ; 187.99 2.27E-05 257080000 94452 106126 107532 121867 101650 118150 124864 127519 117743 132515 FALSE TRUE 90760.71142 103099.3904 126965.4244 128156.5705 104919.6646 120539.074 126392.123 124885.6881 104377.3083 123539.641 0.734668732 0.834545005 1.027730236 1.037372049 0.849279338 0.975711706 1.023089609 1.010895669 0.844889198 1 16.91461452 4.427735679 4.090793011 0.973954348 0.751845814 0.574194558 0.066596947 0.13397091 4.601238573 0.016508881 0.055371989 26775.38222 -4.427735679 -0.222108534 DEFSHQVQEWNR ddPTM_BT-474_Pertuzumab_2h_R1 3 DEFSHQVQEWNR 12 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;; 198.57 1.82E-07 1033720000 1036290 1081090 1005160 1139900 1093910 1034650 1125720 1137740 1217660 1281140 FALSE TRUE 995790.6411 1050258.372 1186814.772 1198730.376 1129096.609 1055571.332 1139496.898 1114245.271 1079436.342 1194367.247 0.833739073 0.879342911 0.993676589 1.003653088 0.945351283 0.883791258 0.954059065 0.932916801 0.903772558 1 20.18781508 4.427954524 5.507073251 0.948095041 0.843727275 0.51705917 0.037914728 0.136755197 9.169012509 0.009662851 0.028558934 26788.87798 -4.427954524 -0.104367766 DFFLSDR ddPTM_BT-474_Pertuzumab_2h_R1 5 DFFLSDR 7 0 Q9UPT9-2;Q9UPT9;J3QS30;K7ESK0;K7ERX6;A6NNY8 Q9UPT9-2 USP22;USP27X Ubiquitin carboxyl-terminal hydrolase 22;Ubiquitin carboxyl-terminal hydrolase 27 0 ;;;; 161.6 0.0030313 1328848000 1328898 1439062 1333769 1479820 1534999 1499830 1523750 1692060 1673210 1809920 FALSE TRUE 1276963.197 1398021.361 1574810.728 1556193.688 1584373.637 1530157.59 1542398.108 1657118.37 1483274.215 1687332.506 0.756794048 0.82853934 0.933313809 0.922280393 0.93898128 0.906850063 0.914104424 0.982093549 0.879064565 1 20.68631287 4.428002596 2.296674192 0.935309548 0.753834341 0.754754049 0.033506949 0.156452368 1.448518955 0.0081684 0.043765649 26791.84342 -4.428002596 -0.181475207 LLLHLEELQMEHDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLLHLEELQMEHDIR 15 0 Q5JR04;Q9HCE1;Q9HCE1-2 Q5JR04 MOV10 Putative helicase MOV-10 0 ; 187.37 1.99E-07 35800000 44423 49366 50886 54013 58214 60274 60270 41888 59637 62910 FALSE TRUE 42686.90005 47958.13001 60082.23215 56800.6174 60086.50618 61492.78158 61007.60229 41022.99816 52867.25778 58649.04967 0.727836176 0.817713676 1.024436585 0.968483168 1.02450946 1.048487263 1.040214678 0.699465693 0.901417126 1 15.83982011 4.428037168 4.972897394 0.948690584 0.746349013 0.379697977 0.098884189 0.215414421 11.49171583 0.028128763 0.086022085 26793.97622 -4.428037168 -0.202341571 TSGAPGS(ph)PQT(ph)PPER ddPTM_BT-474_Pertuzumab_2h_R1 1 TSGAPGSPQTPPER 14 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7;K7EIM4 Q96MH2 HEXIM2 Protein HEXIM2 2 T(0.001)S(0.003)GAPGS(0.997)PQT(1)PPER 127.29 0.0004268 40204000 93051 102600 89530 113330 114850 99333 112840 110320 114160 123370 TRUE FALSE 89414.46405 99673.94846 105710.0626 119178.9749 118544.2546 101341.5813 114220.9697 108041.8534 101201.0354 115014.04 0.777422165 0.866624183 0.919105725 1.036212404 1.03069377 0.881123568 0.993104578 0.939379692 0.879901579 1 16.81145046 4.428098251 2.022828381 0.962705497 0.774921242 0.563146234 0.052314809 0.309340566 2.104397986 0.013905314 0.085091915 26797.74503 -4.428098251 -0.187784255 TVNSTRET(ph)PPKSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVNSTRETPPKSK 13 2 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK9;B0QZK8;Q5SSJ5-5;B0QZK7;B0QZK5;B0QZK6 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 TVNSTRET(1)PPKSK 111.34 0.047038 907580000 503130 376130 243620 120910 289760 267030 207980 267480 236530 161680 TRUE FALSE 483467.1234 365403.1407 287647.5533 127150.1796 299080.3936 272429.5296 210525.3215 261956.4445 209680.106 150729.2696 3.207519845 2.4242348 1.908372236 0.843566614 1.984222403 1.807409605 1.396711614 1.737926849 1.391104107 1 17.20160007 4.428208349 1.934020753 1.523088259 3.257686179 0.726485233 0.342787072 0.224520314 1.366440295 0.087070588 0.559239261 26804.53942 -4.428208349 1.734597919 EPEQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPEQLR 6 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646;P51991;P51991-2 F8W6I7;P51991;P51991-2 HNRNPA1;HNRNPA1L2;HNRNPA3 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoprotein A3" 0 ; 144.58 0.026183 2910600000 795550 921210 927050 1149810 947390 873920 1079620 1162510 1151410 1186280 FALSE TRUE 764459.0265 894937.9928 1094588.557 1209151.832 977863.6597 891591.2612 1092832.713 1138503.762 1020706.764 1105932.199 0.691234985 0.809215966 0.989742914 1.093332695 0.884198562 0.806189803 0.988155254 1.029451682 0.92293792 1 20.07683151 4.428657913 3.302911949 0.965824639 0.705429779 0.579960909 0.075792698 0.175157375 3.737305899 0.020437439 0.079224163 26832.30073 -4.428657913 -0.260394861 ATLLNVPDLSDSIHS(ph)ANASER ddPTM_BT-474_Pertuzumab_2h_R1 4 ATLLNVPDLSDSIHSANASER 21 0 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ATLLNVPDLSDSIHS(1)ANASER;ATLLNVPDLSDSIHS(1)ANASER;ATLLNVPDLSDSIHS(1)ANASER;ATLLNVPDLSDSIHS(1)ANASER 239.29 4.12E-30 777216000 250489 310616 338572 458401 289097 311059 334323 447772 409336 468491 TRUE FALSE 240699.6129 301757.5358 399759.4919 482059.1305 298396.0676 317348.8261 338414.5449 438525.3517 362869.8934 436759.6873 0.551103089 0.690900613 0.915284775 1.103717089 0.683204234 0.726598254 0.774830083 1.004042645 0.83082277 1 18.73648018 4.428813738 3.564344434 0.876183166 0.570992283 0.421887558 0.12580415 0.220894605 5.59042202 0.032718691 0.120027709 26841.92994 -4.428813738 -0.305190882 GFTECEMTKS(ph)SPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFTECEMTKSSPLK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 GFTECEMT(0.002)KS(0.581)S(0.417)PLK 78.285 0.033833 323830000 1173500 977650 563950 491300 701510 788720 756130 842850 721070 694630 TRUE FALSE 1127638.323 949768.3792 665868.31 516656.0519 724074.7062 804668.4588 765383.7451 825444.853 639217.1566 647582.0914 1.741305601 1.466637808 1.028237684 0.797823255 1.118120337 1.242573674 1.181909993 1.274656702 0.987082819 1 19.30470356 4.429383809 3.450108934 1.101083416 1.705090819 0.720001114 0.13516569 0.13270238 3.124172224 0.0375931 0.141308778 26877.18675 -4.429383809 0.604007403 KLT(ph)ATPTPLGGMTGFHMQTEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLTATPTPLGGMTGFHMQTEDR 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLT(0.546)AT(0.432)PT(0.022)PLGGMT(0.001)GFHMQTEDR 70.465 0.013305 92234000 115250 120140 109510 118800 117330 134290 113870 131220 136110 132310 TRUE FALSE 110745.9026 116713.7248 129300.893 124931.2822 121104.026 137005.4358 115263.5751 128510.2611 120659.3634 123348.5259 0.897829154 0.946210942 1.048256492 1.012831579 0.981803594 1.110718064 0.93445442 1.041846753 0.978198666 1 16.91238095 4.429613684 4.512929186 1.01433874 0.907001062 0.414382956 0.04508443 0.157237411 6.79919845 0.010192128 0.032576681 26891.41682 -4.429613684 -0.107337678 VTEGGEPYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VTEGGEPYR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 80.438 0.056094 144810000 71431 80705 72230 94579 85679 95725 89647 87445 86730 89079 FALSE TRUE 68639.39755 78403.37242 85283.56775 99460.23352 88434.94285 97660.62509 90744.1268 85639.23019 76884.774 83045.59999 0.826526602 0.944100259 1.026948661 1.197658076 1.064896188 1.175987952 1.092702405 1.031231398 0.925813939 1 16.34161611 4.429711946 2.173526363 1.075201321 0.82580077 0.507205535 0.075312068 0.303014507 2.453767909 0.020048177 0.114195169 26897.50185 -4.429711946 -0.249400551 EYVEPELHINDLWR ddPTM_BT-474_Pertuzumab_2h_R1 4 EYVEPELHINDLWR 14 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 183.06 1.45E-06 849200000 849460 918910 799810 999860 963920 968620 930970 953310 1070170 1118040 FALSE TRUE 816262.1641 892703.5865 944353.4587 1051462.894 994925.3622 988206.1601 942363.4893 933623.8154 948688.7881 1042314.155 0.783124896 0.856463075 0.906016151 1.008777334 0.954535019 0.948088592 0.904106967 0.895722092 0.910175482 1 19.99135874 4.429738139 2.131268202 0.937544737 0.782174957 0.66266542 0.036760892 0.25888409 1.998688276 0.01037016 0.060301204 26899.12415 -4.429738139 -0.15536978 QPEYSPES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 QPEYSPESPR 10 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYSPES(1)PR 166.62 5.76E-06 3662160000 1084356 1262890 967132 1476470 1125900 1302160 1365730 1321580 1402530 1617660 TRUE FALSE 1041978.169 1226873.614 1141914.266 1552670.794 1162115.596 1328490.567 1382444.212 1294288.911 1243320.674 1508094.447 0.690923682 0.813525715 0.757190154 1.02955806 0.770585422 0.880906743 0.916682781 0.85822802 0.824431571 1 20.52429535 4.429824691 1.358985262 0.883316442 0.680212677 0.370651037 0.080216554 0.819095293 2.021313613 0.021224238 0.197254642 26904.48547 -4.429824691 -0.203103765 KPWTSLSSES(ph)VSCPQGSLSPATSLMQVSERPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPWTSLSSESVSCPQGSLSPATSLMQVSERPR 32 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 KPWTSLS(0.009)S(0.042)ES(0.469)VS(0.469)CPQGS(0.009)LS(0.001)PATSLMQVSERPR 145.47 2.47E-10 594600000 41375 47921 41497 58318 49712 58424 62007 41960 54914 51849 TRUE FALSE 39758.01926 46554.34 48996.431 61327.79897 51311.03163 59605.37331 62765.86021 41093.51134 48680.39294 48337.22105 0.82251355 0.963115773 1.01363773 1.268748961 1.061522167 1.233115434 1.298499559 0.850142198 1.007099537 1 15.56084691 4.429888005 1.991334303 1.097360957 0.820496091 0.30438919 0.131380186 0.572792905 3.742286801 0.036945 0.231002104 26908.40804 -4.429888005 -0.276864866 SLEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLEELR 6 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229;J3KSH6;Q9BYE0;Q9BYE0-2;P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P41229-4;P52948-6;REV__O94964-2 KDM5C;HES7;NUP98 Lysine-specific demethylase 5C;Transcription factor HES-7;Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 ; 107.22 0.07317 326810000 638740 670120 614870 729710 692070 652350 710130 721170 679890 741150 FALSE TRUE 613777.3346 651008.8337 725990.6867 767370.4205 714331.0601 665540.964 718820.7834 706277.5875 602711.7375 690951.2504 0.888307727 0.942192135 1.050711879 1.110599945 1.033837134 0.963224198 1.040335021 1.022181503 0.872292708 1 19.3982244 4.430243533 4.445340726 1.016514849 0.898441295 0.312332405 0.059199915 0.210171052 8.80877614 0.014810527 0.047739804 26930.44522 -4.430243533 -0.118073554 GWEEDEDPER ddPTM_BT-474_Pertuzumab_2h_R1 2 GWEEDEDPER 10 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 166.16 1.31E-05 407950000 622170 660660 581730 733440 685720 664610 688730 713720 671640 723480 FALSE TRUE 597854.9086 641818.6237 686861.5515 771292.9263 707776.8066 678048.8696 697158.8838 698981.4326 595398.2429 674478.0552 0.886396383 0.951578215 1.018360117 1.143540432 1.049369659 1.005294189 1.03362723 1.036329392 0.882754062 1 19.36341198 4.430248105 2.787848583 1.028342525 0.891641503 0.334773066 0.060404365 0.306239871 4.453147681 0.015433156 0.069067664 26930.72871 -4.430248105 -0.136701023 LAVLSS(ph)SLTHWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAVLSSSLTHWK 12 0 F5GX19;F5H3Y3;Q6IAA8 F5GX19 LAMTOR1 Ragulator complex protein LAMTOR1 1 LAVLS(0.107)S(0.5)S(0.386)LT(0.007)HWK 74.853 0.022793 153090000 426840 359250 206540 246660 239410 262800 304970 214680 388320 294300 TRUE FALSE 410158.6209 349004.5417 243866.3725 259390.1522 247110.8401 268113.9961 308702.3141 210246.783 344239.5416 274366.7989 1.49492804 1.272036351 0.888833392 0.945413779 0.900658684 0.97721006 1.125144571 0.766298196 1.254669089 1 18.06574639 4.430250011 3.477229242 0.967148724 1.466142147 0.627708918 0.128093774 0.127625018 3.060914081 0.030093044 0.112687996 26930.84692 -4.430250011 0.498993423 ELDDLEQWIQER ddPTM_BT-474_Pertuzumab_2h_R1 5 ELDDLEQWIQER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;;;; 226.4 3.58E-11 217583000 247946 275764 225040 304915 269177 282561 292115 319425 287103 281405 FALSE TRUE 238255.9962 267899.4807 265709.734 320651.6997 277835.3227 288274.577 295689.9908 312828.7621 254512.2711 262345.1887 0.908177495 1.021171694 1.012824879 1.222251116 1.059044856 1.098836912 1.127102777 1.192431863 0.970142705 1 18.00110681 4.430466567 1.567786637 1.107820447 0.899337848 0.327198901 0.077085008 0.607789379 2.166649729 0.02024342 0.16363021 26944.27902 -4.430466567 -0.208482599 DPEKRPTAAELLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPEKRPTAAELLR 13 2 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 68.83 0.027763 63515000 101850 94589 66494 82166 79403 91571 81310 77764 96864 92092 FALSE TRUE 97869.5894 91891.41433 78510.94495 86406.59711 81957.06961 93422.62836 82305.0961 76158.14622 85868.40481 85854.52681 1.139946757 1.070315308 0.914464826 1.006430299 0.954603941 1.088150291 0.958657617 0.887060346 1.000161645 1 16.38960658 4.430545695 4.865148251 0.971368353 1.125917185 0.507436604 0.05258736 0.137772972 7.130011466 0.013610106 0.042140988 26949.18869 -4.430545695 0.154548832 YPDVAS(ph)PTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 YPDVASPTLR 10 0 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 YPDVAS(0.997)PT(0.003)LR;YPDVAS(0.97)PT(0.03)LR;YPDVAS(0.981)PT(0.019)LR;YPDVAS(0.853)PT(0.147)LR 128.33 0.0003488 1168270000 681500 770600 756830 850640 810820 929670 856450 866480 904710 1025220 TRUE FALSE 654866.2266 748623.2425 893606.0166 894541.6323 836900.7617 948468.5644 866931.4913 848586.8852 802011.1137 955780.9362 0.685163516 0.783258186 0.934948567 0.935927469 0.875619852 0.992349322 0.907039949 0.887846632 0.839116039 1 19.86632047 4.430643763 3.029249304 0.916885302 0.693572386 0.726348369 0.047601634 0.129172185 2.269523876 0.01171805 0.04887017 26955.27479 -4.430643763 -0.223312916 LS(ph)NGLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSNGLAR 7 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(1)NGLAR 83.358 0.037532 0 94933 103320 103210 108460 112860 109400 111780 123250 102430 122060 TRUE FALSE 91222.91341 100373.4148 121862.3429 114057.6336 116490.2444 111612.143 113147.9971 120704.8444 90802.57582 113792.7675 0.801658273 0.882072007 1.07091466 1.002327618 1.02370517 0.980836879 0.994333819 1.060742674 0.797964386 1 16.79604934 4.430801807 5.205803045 0.997809164 0.818640778 0.429792611 0.071195252 0.13861286 8.41957821 0.016545476 0.049961109 26965.08583 -4.430801807 -0.179168385 YFQS(ph)PS(ph)RS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 YFQSPSRSR 9 1 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 3 Y(0.002)FQS(0.999)PS(0.999)RS(1)R;Y(0.003)FQS(0.999)PS(0.999)RS(1)R 85.271 0.012171 2819000000 2101800 2258700 2094090 2640700 2145600 2333800 2353800 2586000 2466000 2445500 TRUE FALSE 2019659.332 2194284.087 2472538.646 2776986.843 2214615.173 2380991.035 2382606.509 2532598.196 2186070.018 2279864.107 0.885868296 0.962462667 1.084511414 1.218049284 0.971380341 1.04435656 1.045065143 1.110854892 0.95885979 1 21.1205164 4.430883021 3.635430066 1.062252471 0.89713471 0.362992594 0.071387794 0.213971741 5.679211679 0.017471806 0.06350322 26970.12883 -4.430883021 -0.165117762 RNS(ph)GSSLVSSSSASSNLSHLEEDTWILWGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSGSSLVSSSSASSNLSHLEEDTWILWGR 30 1 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 1 RNS(0.362)GS(0.274)S(0.362)LVS(0.001)SSSASSNLSHLEEDTWILWGR 129.03 4.96E-06 74042000 32792 32043 18090 25405 28145 30354 25812 27948 28569 30761 TRUE FALSE 31510.45239 31129.16501 21359.26541 26716.15509 29050.30949 30967.77868 26127.89498 27370.86403 25325.96689 28677.53007 1.098785436 1.085489752 0.744808404 0.931605861 1.012999007 1.079862129 0.911092933 0.954435893 0.883129294 1 14.80763315 4.430883171 24.99998383 0.942540371 1.095464573 0.343611625 0.084268581 118.02972 63816.03399 0.020848795 0.057096836 26970.13812 -4.430883171 0.152924203 QLGHEEDYALGK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLGHEEDYALGK 12 0 P25098;P35626 P25098 ADRBK1;ADRBK2 Beta-adrenergic receptor kinase 1;Beta-adrenergic receptor kinase 2 0 ; 100.55 0.0031694 317630000 743250 592360 569210 414080 508170 469830 429410 479640 480590 471290 FALSE TRUE 714202.9683 575466.4728 672078.909 435450.7184 524515.7496 479330.2845 434665.248 469735.2664 426035.438 439369.1085 1.625519306 1.309756334 1.529645339 0.991081781 1.193792962 1.090951264 0.989294057 1.069113093 0.96965269 1 18.74507391 4.430910704 0.558411022 1.002924432 1.852643541 0.76122495 0.109983314 1.335364535 0.403504321 0.057268708 0.705819164 26971.84803 -4.430910704 0.849719109 TFVQEDIYDEFVER ddPTM_BT-474_Pertuzumab_2h_R1 5 TFVQEDIYDEFVER 14 0 P05091;P05091-2;S4R3S4 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ;;;; 299.2 2.13E-43 1540380000 460536 652577 494430 1044297 514079 582681 930568 859452 718451 581838 FALSE TRUE 442537.744 633966.1429 583784.4995 1098193.293 530614.8179 594463.209 941956.5695 841704.0159 636895.4545 542429.594 0.815843658 1.168752867 1.076240135 2.024582186 0.978218784 1.095926947 1.736550844 1.551729524 1.17415322 1 19.04907637 4.430933766 1.781078655 1.391858933 0.817530808 0.178614634 0.328952235 0.771976142 3.809717746 0.0867021 0.613062953 26973.2803 -4.430933766 -0.574328125 KGDYQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGDYQK 6 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 81.784 0.097755 403320000 434930 411930 317980 352700 347880 357160 401480 384810 384900 465520 FALSE TRUE 417932.4548 400182.1597 375446.0594 370902.8893 359069.8761 364382.0199 406393.4323 376863.539 341207.7656 433989.9158 0.963000382 0.922100135 0.865103187 0.85463481 0.827369169 0.839609416 0.936412155 0.868369345 0.786211276 1 18.72730199 4.431171586 2.783381158 0.867511137 0.960622838 0.211942473 0.056178132 0.391712957 5.673588322 0.013402577 0.060197142 26988.05498 -4.431171586 0.093111701 RTS(ph)FSFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTSFSFQK 8 1 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 RT(0.162)S(0.838)FSFQK;RT(0.056)S(0.944)FSFQK 172.17 0.00017463 880050000 999230 860990 549720 658730 565880 527260 566540 996370 637310 545890 TRUE FALSE 960178.9869 836435.4082 649066.6325 692727.1342 584082.0441 537921.5585 573473.486 975794.6113 564965.2406 508916.3841 1.886712664 1.643561564 1.275389539 1.36118065 1.147697465 1.056993988 1.12685208 1.917396731 1.110133724 1 18.95706911 4.43150734 2.633350905 1.299372793 1.880618815 0.407278214 0.250468348 0.348208856 4.437652513 0.069410543 0.328207998 27008.92755 -4.43150734 0.581246022 QPPGTQQSHSS(ph)PGEITSSPQGLDNPALLR ddPTM_BT-474_Pertuzumab_2h_R1 4 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 QPPGTQQS(0.003)HS(0.318)S(0.679)PGEITSSPQGLDNPALLR;QPPGTQQSHS(0.209)S(0.791)PGEITSSPQGLDNPALLR;QPPGT(0.01)QQS(0.032)HS(0.176)S(0.782)PGEITSSPQGLDNPALLR;QPPGTQQS(0.093)HS(0.167)S(0.74)PGEITSSPQGLDNPALLR 299.15 3.83E-81 4378160000 222222 250551 239403 277270 265689 306733 268582 272753 308549 340600 TRUE FALSE 213537.3186 243405.5308 282668.4476 291579.9379 274235.128 312935.3514 271868.9869 267120.5552 273523.8111 317530.8586 0.672493122 0.766557089 0.890207802 0.91827276 0.863648746 0.985527368 0.856197058 0.841242821 0.861408596 1 18.27653728 4.431558041 2.469416907 0.894414674 0.673075703 0.681291558 0.051626712 0.188996206 2.072823699 0.013200478 0.066381509 27012.08085 -4.431558041 -0.221338971 SLS(ph)KSDSDLLTCSPTEDATMGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.109)LS(0.478)KS(0.411)DS(0.002)DLLTCSPTEDATMGSR;S(0.001)LS(0.499)KS(0.499)DSDLLTCSPTEDATMGSR 187.04 1.55E-17 901570000 728110 678400 478060 517470 566010 619980 579500 696160 685270 581040 TRUE FALSE 699654.6562 659052.6962 564456.0764 544176.6887 584216.2257 632516.4204 586592.0943 681784.0527 607481.0225 541685.6433 1.291624884 1.216670045 1.04203625 1.004598692 1.078515248 1.167681714 1.082901313 1.258634157 1.121464137 1 19.04709633 4.431811348 5.249975029 1.109912551 1.275715643 0.42685976 0.07447611 0.180643907 11.30446047 0.020092671 0.0605839 27027.84053 -4.431811348 0.165803092 RAPS(ph)WR ddPTM_BT-474_Pertuzumab_2h_R1 1 RAPSWR 6 1 Q13136-2;A0A2R8Y7R9;Q13136;O75335;B1APN9;M0QZB5;O75335-1;O75335-2 Q13136-2 PPFIA1;PPFIA4 Liprin-alpha-1;Liprin-alpha-4 1 RAPS(1)WR 58.23 0.086683 366260000 229910 206040 129770 179070 182580 123070 141910 256390 143830 131060 TRUE FALSE 220924.863 200163.9409 153222.3257 188311.8242 188452.8515 125558.5597 143646.737 251095.4569 127503.0214 122183.1895 1.808144508 1.638228154 1.254037699 1.541225311 1.54237954 1.027625488 1.175666945 2.055073681 1.043539802 1 16.89868628 4.431818879 4.962713887 1.398274529 1.773491635 0.187056193 0.310938426 0.320989073 17.58068692 0.078179267 0.240634112 27028.30921 -4.431818879 0.375217106 ALYETELADAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALYETELADAR 11 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 138.08 0.00015124 1082080000 534480 666380 589360 949390 668960 659610 831810 748620 799880 879960 FALSE TRUE 513591.9307 647375.4949 695870.4622 998388.1317 690477.7059 672947.7661 841989.9396 733160.7354 709080.9758 820359.5254 0.626057131 0.789136317 0.848250603 1.217012908 0.841676953 0.820308347 1.026366993 0.893706616 0.864353925 1 19.64589679 4.43188785 2.153567164 0.941807978 0.629009505 0.447674228 0.111974031 0.353808705 2.796514356 0.028853251 0.16688805 27032.60196 -4.43188785 -0.312798473 VGEGDKEDATRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGEGDKEDATRR 12 2 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ; 172.09 2.06E-05 594000000 1070320 979560 663200 688820 803490 845030 850510 939590 1049830 848260 FALSE TRUE 1028490.711 951623.9079 783054.9928 724370.0827 829334.9856 862117.0856 860918.7958 920187.1382 930657.6996 790806.5946 1.300559098 1.203358589 0.990197854 0.915988925 1.048720371 1.090174376 1.0886591 1.163605797 1.176846154 1 19.59296538 4.43195212 4.910719188 1.067716849 1.280808981 0.525966111 0.075289867 0.153344182 8.200524273 0.021067972 0.065132451 27036.60277 -4.43195212 0.213092132 LDSQPQET(ph)SPELPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LDSQPQET(0.5)S(0.5)PELPR 208.01 9.66E-08 2321500000 749410 767880 663100 789480 715910 760850 771900 826580 801370 822770 TRUE FALSE 720122.2287 745980.8142 782936.9206 830225.1574 738937.8953 776234.9083 781346.7431 809510.8341 710401.8372 767043.0551 0.938828954 0.972540993 1.020720956 1.082370999 0.963359085 1.011983491 1.018647829 1.055365574 0.926156404 1 19.54894803 4.43221071 3.360933004 1.015213288 0.943118515 0.224924866 0.041342708 0.305162178 6.789487576 0.010009855 0.038595306 27052.70585 -4.43221071 -0.072094773 SLETSSALS(ph)PSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLETSSALSPSLK 13 0 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 SLETSS(0.002)ALS(0.998)PSLK 130.24 2.47E-05 0 290100 249740 161560 176610 195540 225210 156060 207880 214300 202490 TRUE FALSE 278762.5713 242617.6597 190757.4859 185724.8633 201829.7217 229763.9005 157969.909 203587.2054 189973.5624 188775.1719 1.476690861 1.285220176 1.010500925 0.983841579 1.069153955 1.21712987 0.836815071 1.078463885 1.006348242 1 17.52630951 4.432662334 2.770122112 1.026776486 1.466704435 0.726790819 0.09064617 0.139514911 1.997746136 0.022375799 0.101288491 27080.85261 -4.432662334 0.439927949 TMPGGNDHEIFTDPR ddPTM_BT-474_Pertuzumab_2h_R1 4 TMPGGNDHEIFTDPR 15 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;;; 70.529 0.046417 2169110000 2954450 3166760 2585450 3214840 3332370 3389280 3226330 3137170 3215030 3487000 FALSE TRUE 2838986.828 3076447.105 3052698.328 3380758.278 3439558.707 3457813.564 3265814.792 3072386.343 2850073.273 3250822.384 0.873313424 0.946359641 0.939054174 1.039970161 1.058058024 1.063673482 1.004611881 0.945110492 0.876723775 1 21.6323733 4.432711704 1.606060957 0.996508056 0.869890051 0.323341751 0.054246062 0.785743791 2.97281337 0.01643725 0.130378356 27083.93131 -4.432711704 -0.126618005 DWQSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 DWQSGR 6 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ;; 202.71 0.00037399 3341463000 812396 838033 755539 818794 796674 903109 872359 849424 929075 929487 FALSE TRUE 780646.6662 814133.1194 892081.7042 861052.0565 822299.7427 921370.4827 883035.1904 831883.0976 823610.301 866532.0176 0.900886119 0.939530338 1.029484989 0.993675985 0.948954829 1.063284984 1.019045081 0.960014265 0.950467247 1 19.72489353 4.432765296 5.240543219 0.994184208 0.909055663 0.449771176 0.034495338 0.153462413 9.653538432 0.008777055 0.026517866 27087.27371 -4.432765296 -0.085128545 KT(ph)SLFEEDEEDDLFAIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSLFEEDEEDDLFAIAK 18 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 KT(0.5)S(0.5)LFEEDEEDDLFAIAK 89.374 0.0017013 71837000 34801 37825 34216 41241 48974 41155 38234 38293 36394 43355 TRUE FALSE 33440.93845 36746.26803 40399.59233 43369.45295 50549.29319 41987.1823 38701.91913 37502.23617 32262.7057 40418.52723 0.827366575 0.909144161 0.999531529 1.073009234 1.250646588 1.038810297 0.957529177 0.927847666 0.798215766 1 15.30272913 4.433005273 2.636378817 1.008914617 0.831518821 0.221577027 0.108307614 0.503319053 6.426965601 0.030595365 0.145041099 27102.24535 -4.433005273 -0.177395796 SPGDGHNAPVEGPEGEYVELLEVTLPVRGSPT(ph)DAEGSPGLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGDGHNAPVEGPEGEYVELLEVTLPVRGSPTDAEGSPGLSR 42 1 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 SPGDGHNAPVEGPEGEY(0.001)VELLEVT(0.32)LPVRGS(0.276)PT(0.372)DAEGS(0.024)PGLS(0.006)R 82.486 0.00058788 24831000 6053.8 6597.9 6349.3 7902.9 5661.5 8452.5 6607.5 7115.7 6626.7 8762 TRUE FALSE 5817.210803 6409.734352 7496.759749 8310.769616 5843.607289 8623.415341 6688.364562 6968.758308 5874.464797 8168.541936 0.712148 0.784685248 0.917759841 1.017411636 0.715379481 1.055685997 0.8187954 0.853121446 0.719157084 1 12.99586287 4.433028571 4.106420937 0.881030763 0.724611543 0.209909148 0.111031881 0.298027499 10.51834866 0.025957404 0.087764335 27103.69935 -4.433028571 -0.15641922 RIS(ph)EMEEELK ddPTM_BT-474_Pertuzumab_2h_R1 3 RISEMEEELK 10 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 RIS(1)EMEEELK;RIS(1)EMEEELK;RIS(1)EMEEELK 229.39 1.01E-09 431119000 1186430 1026940 593230 901210 726240 447221 694370 1351300 647360 623410 TRUE FALSE 1140063.004 997652.6767 700439.8573 947721.5561 749600.1692 456264.115 702867.9078 1323395.183 573874.4068 581185.8854 1.961615092 1.716581049 1.205190757 1.630668569 1.289776968 0.785057116 1.209368509 2.277060087 0.987419724 1 19.14864014 4.433333135 4.468972053 1.379681181 1.916172328 0.216785288 0.398984317 0.328465764 14.16811116 0.105856249 0.342236062 27122.71338 -4.433333135 0.536491147 QFFDER ddPTM_BT-474_Pertuzumab_2h_R1 3 QFFDER 6 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ;; 124.34 0.042799 2494460000 3965600 4319600 3757300 4603500 4594300 4494000 4543100 4865200 4803700 4821400 FALSE TRUE 3810619.968 4196409.237 4436327.691 4841087.187 4742079.832 4584871.759 4598699.817 4764731.92 4258404.115 4494842.284 0.847776124 0.933605447 0.986981836 1.077031602 1.055004722 1.020029507 1.023105935 1.060044295 0.947397894 1 22.09983906 4.433421877 1.816130151 1.030815852 0.839317427 0.716399204 0.035234895 0.238564932 1.233642508 0.00916406 0.063885212 27128.25613 -4.433421877 -0.191498426 ASET(ph)PPPVAQPKPEAPHPGLETTLQER ddPTM_BT-474_Pertuzumab_2h_R1 5 ASETPPPVAQPKPEAPHPGLETTLQER 27 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 AS(0.012)ET(0.988)PPPVAQPKPEAPHPGLETTLQER;AS(0.012)ET(0.988)PPPVAQPKPEAPHPGLETTLQER;AS(0.015)ET(0.985)PPPVAQPKPEAPHPGLETTLQER;ASET(1)PPPVAQPKPEAPHPGLETTLQER;AS(0.048)ET(0.952)PPPVAQPKPEAPHPGLETTLQER 221.72 3.66E-34 6256670000 2885800 2968470 2483317 3008910 2975560 2967100 2981095 2936960 3189820 3170860 TRUE FALSE 2773019.746 2883812.142 2932107.623 3164200.206 3071271.59 3027096.795 3017578.532 2876310.75 2827725.006 2956094.828 0.938068603 0.975547914 0.991885509 1.070398749 1.038962472 1.024018839 1.020798962 0.973010312 0.956574525 1 21.49526112 4.433581368 2.248676333 1.011211917 0.939206928 0.358372355 0.0305916 0.443978506 3.890809318 0.008841085 0.049102339 27138.22057 -4.433581368 -0.072004989 CAGNEDIITLR ddPTM_BT-474_Pertuzumab_2h_R1 2 CAGNEDIITLR 11 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 159.09 0.0028351 266110000 801140 673400 442457 447860 485590 462520 434550 623590 551760 462760 FALSE TRUE 769830.5631 654195.2913 522418.8223 470974.1083 501209.4434 471872.4713 439868.1529 610712.6486 489126.518 431416.853 1.784423946 1.51638789 1.210937446 1.091691493 1.161775299 1.093773848 1.019589638 1.41559757 1.133767757 1 18.71872301 4.433898919 2.107644003 1.154529697 1.802911437 0.790296464 0.109459765 0.185814588 1.391008425 0.030318288 0.180346231 27158.07098 -4.433898919 0.64838174 EPTEEER ddPTM_BT-474_Pertuzumab_2h_R1 6 EPTEEER 7 0 Q15056;Q15056-2 Q15056;Q15056-2;REV__B4E135 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;; 162.31 0.0029707 1518591600 1904891 2099707 1719227 2338887 2086097 2078820 2256715 2229333 2283663 2308093 FALSE TRUE 1830445.754 2039825.412 2029929.563 2459597.238 2153198.205 2120855.165 2284333.353 2183296.494 2024431.15 2151763.805 0.850672248 0.947978308 0.943379361 1.143060977 1.000666616 0.985635672 1.061609712 1.014654345 0.940824056 1 21.03708829 4.434156902 1.75848111 1.020301196 0.847933926 0.469473002 0.054092563 0.432277165 2.058451063 0.014181504 0.102565897 27174.20843 -4.434156902 -0.172367271 AIPELDAYEAEGLALDDEDVEELTASQR ddPTM_BT-474_Pertuzumab_2h_R1 5 AIPELDAYEAEGLALDDEDVEELTASQR 28 0 P49736;F8WDM3;C9J013;C9JZ21;H7C4N9 P49736 MCM2 DNA replication licensing factor MCM2 0 ;;;; 206.46 2.50E-25 482018000 125645 140783 132952 155768 157024 166368 145818 156170 166703 175345 FALSE TRUE 120734.6545 136768.0067 156979.3839 163807.2051 162074.8196 169732.0749 147602.5643 152945.0349 147779.5743 163468.727 0.738579524 0.8366616 0.960302235 1.002070599 0.991472941 1.038315267 0.902940685 0.935622597 0.904023522 1 17.31865514 4.434211291 2.530671404 0.965097732 0.740527918 0.762462189 0.041728821 0.15903311 1.844550664 0.011589122 0.05728488 27177.61178 -4.434211291 -0.224569814 SSLLDDLLTESEDMAQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSLLDDLLTESEDMAQR 17 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ;;; 372.27 1.81E-104 163583000 115715 128383 110100 138782 132074 139215 144628 143708 136037 153046 FALSE TRUE 111192.7299 124721.6425 129997.5192 145944.5557 136322.2802 142030.0227 146398.0007 140740.3796 120594.6501 142680.0581 0.779315143 0.87413507 0.911112043 1.022879845 0.955440319 0.995444105 1.0260579 0.986405399 0.845210267 1 17.12242418 4.434234035 1.46764177 0.978680671 0.759800093 0.604631512 0.050033442 0.440109404 1.31809875 0.013734839 0.119953275 27179.03511 -4.434234035 -0.218880578 EDIYSGGGGGGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDIYSGGGGGGSR 13 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 199.03 8.64E-07 0 253200 270350 245190 291020 294650 263360 281300 299450 280710 318730 FALSE TRUE 243304.6641 262639.8827 289501.2872 306039.5771 304127.6848 268685.3196 284742.6335 293266.2529 248844.9776 297142.1332 0.818815768 0.883886374 0.974285552 1.029943394 1.023509125 0.904231644 0.958270813 0.98695614 0.8374611 1 18.18079366 4.434384667 3.073416745 0.966846289 0.825039844 0.428232927 0.054514166 0.234418737 4.2582386 0.013665617 0.056801672 27188.4636 -4.434384667 -0.141806445 GS(ph)PTSAYPER ddPTM_BT-474_Pertuzumab_2h_R1 5 GSPTSAYPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.993)PT(0.007)SAYPER;GS(0.992)PT(0.008)SAYPER;GS(0.954)PT(0.037)S(0.009)AYPER;GS(1)PTSAYPER;GS(0.763)PT(0.224)S(0.013)AYPER 222.34 5.19E-09 8146200000 1516105 1669480 1626274 1843290 1710260 1705320 1930710 1906620 1771400 2114070 TRUE FALSE 1456853.94 1621868.065 1920177.888 1938422.418 1765272.066 1739802.739 1954338.607 1867247.631 1570318.098 1970882.156 0.739188762 0.822914785 0.974273313 0.983530351 0.895676112 0.882753306 0.991606018 0.947417188 0.796759001 1 20.91041009 4.434494502 3.894889803 0.93414717 0.752370705 0.533190655 0.059482505 0.1507066 4.721538672 0.014489864 0.050727359 27195.3406 -4.434494502 -0.181776465 FCDSPT(ph)SDLEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 FCDSPTSDLEMR 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 FCDS(0.397)PT(0.52)S(0.083)DLEMR 184.96 0.00015254 225360000 118980 131480 117340 137980 148740 139960 142170 154200 153590 163130 TRUE FALSE 114330.1301 127730.3191 138545.9482 145101.1643 153524.3572 142790.0871 143909.919 151015.7161 136155.1071 152081.0598 0.751770998 0.839883147 0.911000676 0.954104111 1.009490316 0.938907759 0.946271148 0.992994896 0.895279841 1 17.21448097 4.434523354 1.389144391 0.964473168 0.72297618 0.82259739 0.0318555 0.273752963 0.711215451 0.008636324 0.079633372 27197.14734 -4.434523354 -0.241496988 QLS(ph)MTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLSMTLR 7 0 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;E5RJQ8;E5RGV7 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 QLS(0.936)MT(0.064)LR 79.16 0.035011 97018000 156620 120080 49698 73882 64921 59531 56172 119810 52477 48999 TRUE FALSE 150499.1172 116655.436 58679.53413 77695.05887 67009.24292 60734.75761 56859.44974 117335.8816 46520.03096 45680.25409 3.294620843 2.553738772 1.284571098 1.700845594 1.466919225 1.329562605 1.24472709 2.56863461 1.018383805 1 15.47928305 4.434647094 3.430379633 1.55537583 3.204756786 0.653435562 0.437813203 0.146588713 3.424393831 0.112178461 0.4283336 27204.89751 -4.434647094 1.649380956 RAPS(ph)PDGFSPYSPEETNR ddPTM_BT-474_Pertuzumab_2h_R1 2 RAPSPDGFSPYSPEETNR 18 1 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 RAPS(1)PDGFSPYSPEETNR;RAPS(1)PDGFSPYSPEETNR 210.31 2.61E-16 567570000 123766 130103 110449 125759 132846 139031 140078 136768 137141 154046 TRUE FALSE 118929.0879 126392.5898 130409.5912 132249.4371 137119.1122 141842.3021 141792.3165 133943.693 121573.3286 143612.3272 0.828125901 0.880095687 0.908066834 0.920878031 0.954786507 0.987674978 0.987326918 0.932675458 0.846538253 1 17.13182007 4.434698363 1.015744937 0.949985318 0.802119409 0.47695561 0.041066711 1.099189147 1.287757207 0.013455108 0.158943933 27208.10925 -4.434698363 -0.147865908 IFYPETTDIYDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IFYPETTDIYDR 12 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 167.12 0.00011648 874340000 410399 453231 393522 519564 480801 389963 507029 518017 501291 535189 FALSE TRUE 394360.1534 440305.2956 464640.1792 546378.7603 496266.4008 397848.319 513234.1726 507319.7679 444386.5473 498940.1723 0.790395673 0.882481147 0.931254297 1.09507871 0.994641098 0.797386823 1.028648726 1.01679479 0.890660989 1 18.92850731 4.434865058 2.154701237 0.97583442 0.790438203 0.354449423 0.077422835 0.426330675 3.365490804 0.020508039 0.119483221 27218.55451 -4.434865058 -0.185396217 NIDDGTSDRPYSHALVAGIDR ddPTM_BT-474_Pertuzumab_2h_R1 8 NIDDGTSDRPYSHALVAGIDR 21 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;;;; 228.29 1.04E-25 32289370000 8702030 8808440 7596220 8754440 9270030 8578790 9375170 10072130 10180490 10079070 FALSE TRUE 8361945.047 8557231.916 8969025.931 9206257.698 9568208.934 8752259.012 9489906.135 9864136.996 9024843.455 9396405.611 0.889908907 0.910692053 0.954516685 0.979763761 1.018283941 0.931447553 1.009950669 1.049777692 0.960456991 1 23.16367756 4.434911466 0.72692475 1.004294951 0.839453535 0.588088704 0.030802549 1.374980036 0.73029669 0.013158323 0.173322115 27221.46321 -4.434911466 -0.164841416 AVEDINEHITDAQLEAMTELHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEDINEHITDAQLEAMTELHDR 23 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 252.84 1.02E-43 235729000 126219 152936 168378 213193 185986 157187 206710 147426 180373 226130 FALSE TRUE 121286.2219 148574.415 198807.6501 224195.9163 191968.4086 160365.4288 209239.7788 144381.6016 159897.8132 210814.0137 0.575323337 0.704765364 0.943047602 1.063477291 0.910605539 0.760696246 0.992532589 0.684876679 0.758478103 1 17.68561125 4.434936029 4.108590729 0.875309829 0.597378775 0.437819791 0.116095637 0.197612149 7.029424915 0.030592557 0.103806287 27223.00289 -4.434936029 -0.277931054 GPVSGS(ph)PDSMNASR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPVSGSPDSMNASR 14 0 A0A499FJS7;O14920-4;O14920-2;O14920 A0A499FJS7 IKBKB Inhibitor of nuclear factor kappa-B kinase subunit beta 1 GPVSGS(1)PDSMNASR 261.84 1.66E-24 441610000 192030 222740 207400 253280 254860 256500 267110 265090 285830 312640 TRUE FALSE 184525.2553 216387.6733 244881.7936 266351.8112 263057.8034 261686.6057 270378.9721 259615.7989 253383.7767 291464.6143 0.633096596 0.742414903 0.840176754 0.913839273 0.902537702 0.897833194 0.927656253 0.890728363 0.869346618 1 18.15296122 4.435068856 1.350943498 0.910378311 0.590875121 0.886952479 0.03311807 0.219167892 0.52956677 0.008746884 0.082917439 27231.33015 -4.435068856 -0.31950319 ELILGSETPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELILGSETPSSPR 13 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 ELILGSETPS(0.021)S(0.979)PR;ELILGSET(0.001)PS(0.024)S(0.976)PR;ELILGSETPSS(1)PR;ELILGSETPSS(1)PR 299.66 7.83E-41 673940000 912970 994720 945580 1055390 1025190 1142520 1059590 1103340 1134860 1107100 TRUE FALSE 877290.1231 966351.5595 1116467.34 1109858.804 1058166.167 1165622.537 1072557.579 1080555.643 1006035.451 1032115.131 0.849992503 0.936282718 1.081727519 1.075324614 1.025240437 1.129353211 1.039184048 1.046933245 0.974731811 1 19.97717248 4.435191947 3.514380311 1.050570499 0.861201361 0.69999643 0.041764036 0.112792099 2.787281836 0.010163151 0.038178464 27239.04937 -4.435191947 -0.189369137 ASSVGVLS(ph)PQKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSVGVLSPQKK 12 1 Q9UGU5 Q9UGU5 HMGXB4 HMG domain-containing protein 4 1 ASSVGVLS(1)PQKK;ASSVGVLS(1)PQKK 117.48 0.00044628 2294550000 2520100 2281600 1786490 1737190 1944850 1676760 2035110 2209400 2377100 2268700 TRUE FALSE 2421611.706 2216531.002 2109348.483 1826846.584 2007407.867 1710665.236 2060016.285 2163775.118 2107261.574 2115038.928 1.144949 1.047985913 0.997309532 0.863741352 0.949111546 0.808810284 0.973985045 1.023042692 0.996322831 1 21.01225279 4.435422048 1.943422574 0.947015209 1.149817049 0.501862186 0.06251651 0.396566291 2.425944759 0.017853009 0.116308923 27253.48522 -4.435422048 0.20280184 QPASAQSTPSTTPHSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 QPASAQSTPSTTPHSSPK 18 0 A0A087WT18;Q96A73-2;Q96A73 A0A087WT18 KIAA1191 Putative monooxygenase p33MONOX 1 QPASAQSTPSTTPHS(0.106)S(0.894)PK;QPASAQSTPSTTPHS(0.078)S(0.922)PK;QPASAQSTPSTTPHS(0.158)S(0.842)PK;QPASAQSTPSTTPHS(0.14)S(0.86)PK;QPASAQSTPSTTPHS(0.004)S(0.996)PK 196.11 1.28E-15 1671717000 472383 486590 544263 754966 519226 731033 1030932 691451 1092866 1117518 TRUE FALSE 453921.7501 472712.9296 642623.4312 793929.8857 535927.3758 745814.9881 1043548.854 677172.2952 968808.4333 1041827.51 0.435697604 0.453734351 0.61682325 0.762055021 0.514410851 0.715871851 1.001652235 0.649985039 0.929912508 1 19.99068501 4.43543592 0.205023151 1.028854054 4.74E-16 0.668510415 0.116819364 7.594953565 0.332810521 0.255394726 2.026079364 27254.35571 -4.43543592 -1.028854054 QQQQQQGEDGS(ph)PQAHR ddPTM_BT-474_Pertuzumab_2h_R1 9 QQQQQQGEDGSPQAHR 16 0 A0A087WUX9;E9PEG3;A0A087WZ66;F5GZG9;P10275-3;P10275-4;P10275 A0A087WUX9 AR Androgen receptor 1 QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR 301.34 3.89E-46 780062000 380978.1 402613.4 361522 427415.3 408068.1 435558.6 431089.2 410182.1 433872.3 441802 TRUE FALSE 366089.0547 391131.26 426857.0674 449474.2549 421193.981 444365.8933 436364.9986 401711.6963 384620.9354 411878.357 0.888828093 0.949628096 1.03636683 1.091279129 1.022617416 1.078876532 1.059451149 0.975316351 0.933821671 1 18.65185879 4.435477129 3.162349847 1.027029328 0.895121749 0.488790562 0.045036572 0.217918747 4.226520403 0.012188246 0.049628465 27256.94191 -4.435477129 -0.131907579 IVLEDGTLHVTEGSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IVLEDGTLHVTEGSGR 16 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 188.59 1.15E-09 183710000 147150 161800 160440 176770 166660 172070 176570 187290 168090 209200 FALSE TRUE 141399.2153 157185.6224 189435.077 185893.1209 172020.7703 175549.3733 178730.9165 183422.3961 149009.1279 195030.6977 0.725010047 0.805953239 0.971309026 0.953148008 0.882018945 0.900111497 0.916424535 0.940479618 0.764029097 1 17.5733417 4.435604323 4.552615995 0.914477595 0.740300557 0.512735805 0.060891238 0.134083828 6.124321539 0.014273374 0.045926239 27264.926 -4.435604323 -0.174177038 IYITLTGVHQVPTENVQVHFTER ddPTM_BT-474_Pertuzumab_2h_R1 2 IYITLTGVHQVPTENVQVHFTER 23 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 348.6 8.52E-102 11757700000 1281640 1530230 1419050 2037960 1692480 2005500 1695430 1352790 1879230 2159660 FALSE TRUE 1231552.092 1486589.339 1675503.902 2143139.36 1746920.156 2046052.584 1716179.18 1324854.414 1665907.689 2013384.305 0.611682573 0.738353495 0.832182856 1.064446244 0.867653608 1.016225556 0.852385298 0.658023613 0.827416646 1 20.94119114 4.435608252 2.414858347 0.875177402 0.615985564 0.397131141 0.110702279 0.406389649 4.216755016 0.032042607 0.166404938 27265.17262 -4.435608252 -0.259191838 LSGQNAMGS(ph)QDSLLEITFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSGQNAMGSQDSLLEITFR 19 0 O75052-3;O75052;E9PIP8;H7C2G1;O75052-2 O75052-3 NOS1AP Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein 1 LSGQNAMGS(0.939)QDS(0.061)LLEITFR;LSGQNAMGS(1)QDSLLEITFR 160.77 3.23E-11 118305000 65856 75506 77045 99296 67455 88751 87483 83594 82517 104057 TRUE FALSE 63282.27471 73352.64281 90968.74536 104420.6785 69624.75134 90545.60603 88553.64312 81867.75469 73150.0161 97009.12671 0.652333207 0.756141667 0.937733886 1.076400562 0.717713412 0.933372035 0.912838267 0.843918067 0.754052929 1 16.56583286 4.435963365 3.957101005 0.890666152 0.669183383 0.383522707 0.101241292 0.206842009 6.752414688 0.024598804 0.08554261 27287.47591 -4.435963365 -0.221482769 TAS(ph)QEGCQELTQEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASQEGCQELTQEQR 15 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 T(0.003)AS(0.997)QEGCQELTQEQR 169.67 3.04E-11 0 94795 106130 91697 114740 121500 111980 122640 100010 128100 130500 TRUE FALSE 91090.3066 103103.2763 108268.6877 120661.7452 125408.1578 114244.3123 124140.905 97944.75855 113558.625 121661.1188 0.748721593 0.847462833 0.889920204 0.991785596 1.030798986 0.939037167 1.020382734 0.805062123 0.933401124 1 16.89250865 4.435985966 1.730368639 0.94789811 0.738901668 0.53149241 0.062417847 0.47649433 2.173726979 0.018401869 0.136097267 27288.89597 -4.435985966 -0.208996441 ATLDEEDLVDS(ph)LSEGDAYPNGLQVNFHSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATLDEEDLVDSLSEGDAYPNGLQVNFHSPR 30 0 B4DKB2;A0A3B3ISF9;P42892-3;P42892-4;P42892;E9PN99;E9PHZ1 B4DKB2 ECE1 Endothelin-converting enzyme 1 1 ATLDEEDLVDS(0.528)LS(0.472)EGDAYPNGLQVNFHSPR 87.372 0.00079786 100560000 35382 42316 43941 52147 41137 46533 50638 61474 45341 50241 TRUE FALSE 33999.23232 41109.18911 51882.11616 54838.31292 42460.20896 47473.92914 51257.72299 60204.54042 40194.07976 46838.13232 0.725887875 0.877686344 1.107689688 1.170804859 0.906530787 1.013574342 1.094358815 1.285374489 0.858148645 1 15.51539593 4.436096399 3.192595762 1.075019304 0.741461318 0.435319098 0.118837355 0.215859844 4.279840948 0.030834106 0.124781668 27295.83591 -4.436096399 -0.333557985 LDGLVET(ph)PTGYIESLPR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDGLVETPTGYIESLPR 17 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W118;F8VUX1;H0YHC3;F8W020;P55209-3;F8VXI6;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 1 LDGLVET(0.999)PT(0.001)GYIESLPR;LDGLVET(0.865)PT(0.135)GYIESLPR;LDGLVET(0.98)PT(0.02)GYIESLPR 191.96 2.38E-09 450181000 573400 499250 333544 341104 446390 409217 327398 472480 401714 410563 TRUE FALSE 550990.8941 485011.8788 393822.8204 358708.4183 460748.5398 417491.6481 331404.7947 462723.1229 356113.1108 382755.2023 1.439538616 1.267159469 1.028915657 0.937174508 1.203768197 1.090753687 0.865840079 1.208927064 0.930393914 1 18.54606246 4.436523738 2.892838694 1.04470618 1.427459448 0.605294851 0.107178577 0.179048213 2.830102249 0.026180425 0.11510998 27322.70785 -4.436523738 0.382753268 FES(ph)PEVAER ddPTM_BT-474_Pertuzumab_2h_R1 2 FESPEVAER 9 0 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 FES(1)PEVAER;FES(1)PEVAER 152.7 8.38E-05 176472000 390000 402400 360270 397610 401480 427570 380790 415880 463710 440420 TRUE FALSE 374758.3688 390923.946 425378.8032 418130.6997 414393.9688 436215.7584 385450.2219 407291.9327 411071.5848 410589.9611 0.912731446 0.95210303 1.036018518 1.018365619 1.009264736 1.062412138 0.938771666 0.991967586 1.001173004 1 18.64733883 4.436597502 4.842473706 1.004931617 0.920558766 0.511370632 0.030264108 0.14209527 7.610250157 0.007708421 0.024161758 27327.34894 -4.436597502 -0.084372852 QDS(ph)DSDVVDIEEAEHDFMGEAHPVVFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QDSDSDVVDIEEAEHDFMGEAHPVVFSR 28 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 QDS(0.707)DS(0.293)DVVDIEEAEHDFMGEAHPVVFSR 53.264 0.050603 23307000 4805.4 4454 2929 3686.6 3402.3 2695.4 2986.9 3171.4 3619 3970.1 TRUE FALSE 4617.599655 4326.976281 3458.335455 3876.865868 3511.738069 2749.902835 3023.454576 3105.909482 3208.186292 3701.201591 1.247594745 1.169073387 0.934381814 1.047461418 0.948810267 0.742975698 0.816884599 0.839162473 0.866795881 1 11.853778 4.436689932 0.706860906 0.845842143 1.411700901 0.711509298 0.080978882 1.057458389 0.52687755 0.03390294 0.448069984 27333.16558 -4.436689932 0.565858758 EGIVALR ddPTM_BT-474_Pertuzumab_2h_R1 3 EGIVALR 7 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;; 99.919 0.02367 859940000 573240 652740 604730 778400 730100 703650 739430 703560 752300 782140 FALSE TRUE 550837.147 634124.4943 714018.1631 818573.3173 753584.3296 717878.2851 748479.3655 689031.2401 666902.0579 729164.9611 0.755435569 0.869658483 0.9792272 1.122617461 1.033489498 0.984521094 1.026488388 0.94495934 0.914610676 1 19.47588571 4.438444752 2.470331774 1.002823484 0.758344647 0.69503359 0.052690324 0.193221015 2.111677792 0.014745149 0.075413328 27443.83198 -4.438444752 -0.244478837 AVEHMFETEDGSKDEWR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVEHMFETEDGSKDEWR 17 1 Q9Y657 Q9Y657 SPIN1 Spindlin-1 0 ;;; 199.68 7.86E-12 824792000 792660 760185 591885 657103 692992 719469 708134 710582 777720 793100 FALSE TRUE 761681.9709 738505.2681 698851.7859 691016.1646 715282.717 734017.1561 716800.3557 695908.2334 689436.4861 739382.6306 1.030159405 0.998813385 0.945182855 0.934585336 0.967405356 0.992743305 0.969457932 0.94120176 0.932448853 1 19.49596163 4.438778699 3.747193251 0.958481432 1.025578174 0.509240221 0.022118479 0.166102022 4.794895859 0.00565398 0.020484865 27464.94283 -4.438778699 0.067096742 ALSSDSILS(ph)PAPDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALSSDS(0.001)ILS(0.999)PAPDAR;ALSSDSILS(1)PAPDAR 206.43 4.09E-09 282680000 124107 219720 311830 382190 344030 485530 321540 171145 306350 385420 TRUE FALSE 119256.7612 213453.8007 368184.6176 401914.8717 355096.0374 495347.7493 325475.1027 167610.7959 271574.4323 359315.1601 0.331900166 0.594057319 1.02468434 1.118558069 0.988257877 1.378588505 0.90582068 0.466472931 0.755811228 1 18.45489028 4.439081743 3.576077874 0.929984777 0.367008249 0.44918927 0.224652403 0.243058839 6.284664724 0.066084248 0.247368975 27484.11409 -4.439081743 -0.562976528 EEMAAEAGEAVASPMDDGFVS(ph)LDSPSYVLYR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEMAAEAGEAVASPMDDGFVSLDSPSYVLYR 31 0 P49354;P49354-2;E9PN85 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 EEMAAEAGEAVAS(0.001)PMDDGFVS(0.595)LDS(0.325)PS(0.068)Y(0.011)VLYR 101.59 0.00012432 19998000 10070 13334 16069 18915 14956 13403 19559 17850 17002 17337 TRUE FALSE 9676.453267 12953.72738 18973.02575 19891.20542 15437.07332 13674.01784 19798.36889 17481.39126 15072.00424 16162.74955 0.598688561 0.801455677 1.173873647 1.23068203 0.955101932 0.846020524 1.224938172 1.081585235 0.932514867 1 13.98038502 4.439308682 4.100407178 1.062760332 0.632516457 0.594685032 0.12230239 0.130943023 4.704162062 0.031292623 0.10729925 27498.47961 -4.439308682 -0.430243874 LS(ph)PPPEELPAS(ph)PLPEALHLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPPPEELPASPLPEALHLSR 21 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 2 LS(1)PPPEELPAS(1)PLPEALHLSR 116.72 6.51E-05 22801000 3602.4 6659.2 7530.8 11441 9253.2 8021.1 10215 10734 9172.4 12885 TRUE FALSE 3461.614225 6469.286136 8891.783082 12031.47138 9550.837582 8183.292138 10340.01423 10512.33915 8131.187606 12012.28747 0.288172776 0.538555721 0.740223967 1.001597024 0.795088996 0.681243448 0.860786445 0.875132165 0.676905845 1 13.55222329 4.439457384 2.019008004 0.833493098 0.271574148 0.737670269 0.10543297 0.20620081 1.381561307 0.027045047 0.170954494 27507.89664 -4.439457384 -0.56191895 down VDTEDIEKKPESFFTQFDAVCLTCCSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDTEDIEKKPESFFTQFDAVCLTCCSR 27 2 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054;M0R286;M0QYP2 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 204.79 1.88E-25 291450000 399180 347647 233595 212643 276401 325565 282333 294396 335087 258157 FALSE TRUE 383579.6043 337732.4479 275810.8128 223617.5307 285291.6892 332148.1474 285788.2757 288316.6197 297049.3286 240671.7964 1.593787099 1.40329051 1.146003881 0.92913891 1.185397265 1.380087539 1.1874606 1.19796596 1.234250681 1 17.87670756 4.439770657 3.113267733 1.168689306 1.57521994 0.591970676 0.117789108 0.183073665 3.42793875 0.030837368 0.128442915 27527.74627 -4.439770657 0.406530634 VSYLVFDEADR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSYLVFDEADR 11 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;; 195.36 2.54E-07 662830000 439381 439563 414967 440100 459813 436223 452015 463828 476220 483960 FALSE TRUE 422209.5048 427027.0936 489960.7678 462813.6137 474603.3027 445043.7279 457546.8948 454249.7897 422161.5021 451180.9581 0.935787509 0.94646524 1.085951787 1.025782683 1.051913416 0.986397409 1.014109498 1.006801775 0.935681115 1 18.78334666 4.43980445 24.84917533 1.014206053 0.938456854 0.376152626 0.037291514 130.7346938 87055.77844 0.009035948 0.024746112 27529.88831 -4.43980445 -0.075749199 DNLTLWTSDQQDDDGGEGNN ddPTM_BT-474_Pertuzumab_2h_R1 6 DNLTLWTSDQQDDDGGEGNN 20 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;; 491.01 2.24E-249 8507780000 10013450 10642600 9404790 11141700 10899060 11459720 11051900 11097000 11963000 11980200 FALSE TRUE 9622113.304 10339083.47 11104444.76 11716724.47 11249638.16 11691443.39 11187156.46 10867843.07 10605010.39 11168770.38 0.861519485 0.925713674 0.994240582 1.049061273 1.007240527 1.046797722 1.001646204 0.973056362 0.94952354 1 23.41296703 4.439869333 2.427552744 1.003984588 0.862029863 0.726793956 0.028147157 0.183972523 1.927152589 0.007943254 0.041483804 27534.00159 -4.439869333 -0.141954725 GDHWTTR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDHWTTR 7 0 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;; 101.28 0.0091723 816207000 756417 887145 1162637 1184641 996837 1003601 1181624 989316 1148397 1313240 FALSE TRUE 726855.3874 861844.4932 1372751.369 1245780.464 1028901.167 1023894.5 1196085.068 968886.2789 1018035.787 1224293.085 0.593693942 0.703952757 1.121260412 1.017550846 0.840404295 0.83631486 0.976959751 0.791384261 0.831529476 1 20.22351754 4.440102754 10.82561172 0.912916796 0.621117746 0.562132687 0.099656659 0.340225759 98.10601438 0.025581519 0.070377217 27548.8043 -4.440102754 -0.29179905 HCAYEHDIQALSPQVQQVQDDGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HCAYEHDIQALSPQVQQVQDDGHR 24 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 58.92 0.026877 167900000 21062 26328 21974 31997 30190 33541 29277 27489 25593 36314 FALSE TRUE 20238.87375 25577.15122 25945.19061 33648.369 31161.08877 34219.222 29635.30068 26921.34254 22687.78993 33854.42043 0.597820713 0.755504034 0.76637527 0.993913603 0.920443722 1.010775596 0.875374628 0.79520908 0.670157387 1 15.0470566 4.440286632 1.615995202 0.883286616 0.583987678 0.44316677 0.102375136 0.598992734 2.283453345 0.029412558 0.236727072 27560.47077 -4.440286632 -0.299298937 TVSQQS(ph)FDGVSLDSSGPEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSQQSFDGVSLDSSGPEDR 20 0 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 1 T(0.001)VS(0.026)QQS(0.973)FDGVSLDSSGPEDR 130.11 3.00E-06 0 32024 33640 32248 30531 35640 36033 31928 39778 36660 37818 TRUE FALSE 30772.46668 32680.62014 38075.93095 32106.70857 36786.39297 36761.61195 32318.74441 38956.5704 32498.51049 35256.55318 0.872815517 0.926937468 1.079967482 0.910659315 1.043391644 1.042688767 0.916673398 1.104945518 0.921772197 1 15.10560382 4.440379181 7.583624453 1.006501122 0.885832545 0.298110522 0.06512525 0.186670098 31.75449238 0.014680379 0.041313881 27566.34461 -4.440379181 -0.120668576 S(ph)KEDSRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKEDSRR 7 2 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 S(0.593)KEDS(0.407)RR;S(0.783)KEDS(0.217)RR 68.847 0.048309 3113960000 5373900 4548500 3219640 2712750 3313120 3438560 4077100 4099500 3515530 3795950 TRUE FALSE 5163882.047 4418781.233 3801500.569 2852755.353 3419689.514 3508090.039 4126996.769 4014843.892 3116461.773 3538846.925 1.459199043 1.248650006 1.07422012 0.806125671 0.966328747 0.991308783 1.166198159 1.134506232 0.880643283 1 21.75484793 4.440598576 2.28920881 1.011263502 1.459733922 0.681808267 0.101547255 0.232901151 2.118928994 0.02925254 0.162436079 27580.27398 -4.440598576 0.44847042 GEDLTEEEDGGIIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEDLTEEEDGGIIRR 15 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 186.56 6.04E-07 1271840000 629920 714410 709890 814630 761670 863120 757300 818520 818550 846530 FALSE TRUE 605302.03 694035.7263 838182.9144 856673.1519 786169.8073 880572.8778 766568.0639 801617.276 725631.6356 789193.7691 0.766987847 0.879423728 1.062074927 1.085504201 0.99616829 1.115787925 0.971330608 1.015742024 0.919459408 1 19.59002004 4.440732172 3.5063593 1.022747273 0.781265437 0.696077233 0.054424326 0.118269802 2.924770826 0.013483733 0.05138032 27588.75944 -4.440732172 -0.241481836 LYPWGVVEVENPEHNDFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYPWGVVEVENPEHNDFLK 19 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0 Q15019-2 2-Sep Septin-2 0 ; 234.49 3.88E-24 224950000 178177 189108 187822 183311 208140 206827 203620 193960 216670 216430 FALSE TRUE 171213.6459 183714.825 221765.6135 192771.7027 214835.0121 211009.1836 206111.9625 189954.6582 192074.53 201771.0033 0.848554267 0.91051153 1.099095558 0.955398444 1.064746711 1.045785471 1.021514286 0.941436852 0.951943177 1 17.62235933 4.441251011 8.563393046 1.006442544 0.863721817 0.547273426 0.048822689 0.161770579 35.20462406 0.012277271 0.034174009 27621.7386 -4.441251011 -0.142720727 DNLEWLAR ddPTM_BT-474_Pertuzumab_2h_R1 6 DNLEWLAR 8 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;; 171.53 0.00067197 3023798000 2890420 3065080 2726720 3171530 3175780 2983740 3104790 3450240 3406980 3611980 FALSE TRUE 2777459.191 2977666.919 3219498.96 3335213.043 3277931.848 3044073.267 3142787.349 3378991.338 3020233.914 3367337.377 0.824823556 0.884279354 0.956096345 0.990460019 0.973449192 0.904000083 0.933315257 1.003460883 0.896920497 1 21.68317684 4.441267968 2.570838945 0.95867916 0.826263464 0.596956857 0.035351991 0.206564592 2.475893552 0.008957168 0.044385022 27622.8171 -4.441267968 -0.132415696 VVNTDHGS(ph)PEQLQIPVTDSGR ddPTM_BT-474_Pertuzumab_2h_R1 6 VVNTDHGSPEQLQIPVTDSGR 21 0 Q6IQ49-3;Q6IQ49-2;Q6IQ49 Q6IQ49-3 SDE2 Protein SDE2 homolog 1 VVNT(0.005)DHGS(0.995)PEQLQIPVTDSGR;VVNTDHGS(1)PEQLQIPVTDSGR;VVNT(0.061)DHGS(0.939)PEQLQIPVTDSGR;VVNTDHGS(1)PEQLQIPVTDSGR;VVNT(0.099)DHGS(0.901)PEQLQIPVTDSGR;VVNTDHGS(1)PEQLQIPVTDSGR 244.14 2.50E-30 4306020000 1487530 1630560 1506610 1776080 1657770 1793040 1805850 1732120 1858000 2076450 TRUE FALSE 1429395.683 1584058.025 1778887.941 1867743.702 1711093.678 1829296.497 1827950.532 1696351.117 1647087.629 1935810.192 0.73839661 0.818292016 0.918937171 0.964838242 0.883916039 0.944977201 0.944281903 0.876300333 0.850851822 1 20.88450607 4.44128262 2.664205015 0.918793802 0.741363383 0.669254118 0.042348845 0.17516181 2.282862966 0.010654907 0.051046209 27623.74906 -4.44128262 -0.177430419 VFEVSLADLQNDEVAFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFEVSLADLQNDEVAFR 17 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RI02;D6RED7;D6RGE0 P61247 RPS3A 40S ribosomal protein S3a 0 ; 249.75 9.80E-21 175931000 82044 89503 88883 86545 102772 97443 90360 101208 100051 107897 FALSE TRUE 78837.62978 86950.46207 104946.1353 91011.59782 106077.7547 99413.36422 91465.85271 99118.01943 88693.62993 100589.0401 0.783759639 0.864412882 1.043315805 0.904786423 1.054565732 0.988312088 0.909302372 0.985375935 0.881742483 1 16.6181136 4.441838254 5.341972448 0.969084253 0.800771354 0.553043174 0.054914227 0.108026802 7.831988057 0.012650316 0.038545299 27659.11337 -4.441838254 -0.168312899 SDIVQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDIVQLR 7 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 ; 102.72 0.044546 0 156819 168953 151441 183275 174010 164009 176587 194124 187795 192937 FALSE TRUE 150690.3401 164134.6259 178809.7575 192733.8447 179607.1897 167325.3744 178748.1245 190115.2716 166477.2989 179869.2051 0.837777317 0.912522106 0.9941099 1.071522191 0.9985433 0.930261376 0.993767245 1.056963983 0.92554642 1 17.45658868 4.442014312 2.584072427 1.001883079 0.840269137 0.576516361 0.043667655 0.215030215 2.607564311 0.011442623 0.056528985 27670.32834 -4.442014312 -0.161613942 ATVTPS(ph)PVKGK ddPTM_BT-474_Pertuzumab_2h_R1 9 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVTPS(1)PVKGK;AT(0.1)VT(0.079)PS(0.822)PVKGK;ATVTPS(1)PVKGK;ATVT(0.002)PS(0.998)PVKGK;ATVT(0.002)PS(0.998)PVKGK;ATVT(0.001)PS(0.999)PVKGK;ATVT(0.002)PS(0.998)PVKGK;ATVTPS(1)PVKGK;ATVT(0.001)PS(0.999)PVKGK 182.33 3.53E-06 1.16447E+11 61331434 54447339 40182570 39806762 42175651 40657666 48817339 51836495 50195454 49326442 TRUE FALSE 58934533.75 52894554.2 47444454.26 41861193.76 43532269.12 41479791.86 49414780.2 50766053.26 44497476.5 45985518.15 1.28158899 1.150243736 1.03172599 0.910312538 0.946651704 0.902018582 1.074572652 1.103957405 0.967641081 1 25.45467626 4.442099037 2.213552271 0.996244522 1.28513391 0.701964133 0.06156705 0.244972961 2.052152792 0.018837961 0.108749596 27675.72693 -4.442099037 0.288889387 LALADAGDTVEDANFVEAMADAGILR ddPTM_BT-474_Pertuzumab_2h_R1 2 LALADAGDTVEDANFVEAMADAGILR 26 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 145.63 2.23E-07 22589000 15008.8 17159.5 16954.9 19590.4 16214.3 21241.4 18743.3 19420.8 21795 22418 FALSE TRUE 14422.2395 16670.12786 20019.02759 20601.46289 16735.84768 21670.91566 18972.68611 19019.75369 19320.92297 20899.60889 0.69007222 0.7976287 0.957866135 0.985734374 0.800773248 1.036905321 0.907801012 0.910053092 0.924463375 1 14.35118832 4.44210596 3.133633576 0.934288141 0.699933532 0.636426334 0.061663906 0.149544273 2.843748273 0.01458514 0.060765984 27676.16808 -4.44210596 -0.234354609 DVNFEFPEFQL ddPTM_BT-474_Pertuzumab_2h_R1 5 DVNFEFPEFQL 11 0 P62081 P62081 RPS7 40S ribosomal protein S7 0 ;;;; 185.96 9.86E-06 247872600 467005 490284 426810 491843 499797 509415 503455 537448 546165 577452 FALSE TRUE 448753.9283 476301.5804 503944.0613 517227.0762 515873.4244 519715.7203 509616.4329 526349.511 484166.6389 538340.6617 0.833587281 0.884758693 0.936106256 0.960780251 0.958265762 0.965403057 0.946643026 0.97772572 0.89936851 1 19.03815987 4.442231089 1.585857183 0.958566879 0.82002281 0.739823634 0.024130311 0.276315745 1.001456267 0.006066913 0.050070665 27684.14331 -4.442231089 -0.138544069 LVREDENDAS(ph)DDEDDDEKRR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVREDENDASDDEDDDEKRR 20 3 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 LVREDENDAS(1)DDEDDDEKRR 137.24 2.82E-06 219790000 127170 113160 62056 72728 96416 96596 85640 102620 115430 92223 TRUE FALSE 122200.0558 109932.7876 73270.89963 76481.5008 99517.3082 98549.2373 86688.08794 100500.8611 102326.8703 85976.65407 1.421316718 1.278635332 0.852218552 0.889561261 1.15749222 1.146232525 1.008274733 1.168931988 1.190170418 1 16.39165735 4.442292246 8.563037082 1.062076135 1.386399696 0.544681057 0.112162788 0.168039186 37.62488359 0.02926004 0.081507446 27688.04208 -4.442292246 0.324323561 VNYEEFAR ddPTM_BT-474_Pertuzumab_2h_R1 6 VNYEEFAR 8 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ;;;;; 217.81 1.68E-05 9916700000 3845660 4234460 3845480 4911180 4695780 3573090 4911650 4869580 4555560 4722190 FALSE TRUE 3695367.356 4113697.347 4540443.778 5164646.588 4846824.028 3645340.328 4971760.242 4769021.471 4038431.927 4402351.865 0.839407541 0.934431748 1.031367759 1.173156246 1.100962435 0.828043836 1.12934186 1.083289482 0.917335109 1 22.06984303 4.442355932 2.689173652 1.043382735 0.844620825 0.28691703 0.096716872 0.358564922 4.773794202 0.024681875 0.11753837 27692.10259 -4.442355932 -0.19876191 S(ph)PGDFTSAAQLASTPFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGDFTSAAQLASTPFHK 18 0 A0A590UJ99;O43683-2;O43683-3;O43683 A0A590UJ99 BUB1 Mitotic checkpoint serine/threonine-protein kinase BUB1 1 S(1)PGDFTSAAQLASTPFHK;S(1)PGDFTSAAQLASTPFHK 186.62 3.03E-14 1377090000 615680 689020 665430 742130 848730 819150 810110 690840 668630 829170 TRUE FALSE 591618.5449 669369.8242 785688.0034 780431.4182 876030.1712 835713.7742 820024.3685 676573.9126 592729.9255 773009.5774 0.765344392 0.865926948 1.016401383 1.009601228 1.13327208 1.081116973 1.060820451 0.875246481 0.766782124 1 19.56012676 4.442737696 3.074623862 0.994438197 0.773768941 0.356433742 0.099324039 0.306875114 5.582823856 0.027549715 0.116756307 27716.45591 -4.442737696 -0.220669256 TSGNVEDDLIIFPDDCEFKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSGNVEDDLIIFPDDCEFKR 20 1 Q16186 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ; 162.76 3.31E-11 126193000 174707 163858 125360 138358 136771 145387 134735 155576 169865 192486 FALSE TRUE 167879.2573 159184.9303 148015.3406 145498.673 141170.3634 148326.8248 136383.9272 152363.3012 150582.6373 179448.7518 0.935527585 0.88707739 0.824833492 0.810809056 0.786689024 0.826569276 0.760016026 0.849063032 0.839140066 1 17.45321236 4.442829749 2.627561119 0.825681013 0.934159341 0.191462039 0.061047663 0.384996356 4.853306525 0.014032483 0.068372056 27722.3313 -4.442829749 0.108478328 EALLSSAVDHGSDEVK ddPTM_BT-474_Pertuzumab_2h_R1 7 EALLSSAVDHGSDEVK 16 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;;; 252.17 1.60E-26 3249260000 3425780 3707900 3429890 3783230 3982920 4276860 4109630 3820330 4050410 4446490 FALSE TRUE 3291896.73 3602154.322 4049747.42 3978482.954 4111034.239 4363341.04 4159924.881 3741438.85 3590624.438 4145325.272 0.79412266 0.868967834 0.97694322 0.959751694 0.991727782 1.052593163 1.003521945 0.90256822 0.866186415 1 21.98305388 4.442952327 2.694841847 0.967899208 0.796377 0.565344202 0.050162596 0.236427614 3.162354666 0.014068349 0.066964011 27730.15689 -4.442952327 -0.171522208 (ac)MEGHDPKEPEQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEGHDPKEPEQLR 13 1 P51991-2 P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 85.554 0.00025327 2152900000 1240780 1148790 768140 968970 1003890 1099710 971490 975260 1155270 1110790 FALSE TRUE 1192288.946 1116027.634 906959.9852 1018978.658 1036181.034 1121946.89 983379.3852 955120.5402 1024128.593 1035555.204 1.151352377 1.077709455 0.875820026 0.9839926 1.000604342 1.083425476 0.949615609 0.922327015 0.988965715 1 19.98197303 4.443159186 7.696479636 0.973689353 1.133609792 0.5525121 0.051886399 0.126862681 23.84136934 0.013308914 0.037490368 27743.36823 -4.443159186 0.159920439 MDANSATSEEMNEIIHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDANSATSEEMNEIIHAR 18 0 Q9UBD5-3;Q9UBD5;Q9UBD5-2 Q9UBD5-3 ORC3 Origin recognition complex subunit 3 0 ; 139.11 5.93E-07 96013000 73870 80746 77313 81991 82915 88977 98186 82734 89814 98962 FALSE TRUE 70983.07873 78443.20314 91285.17892 86222.56534 85582.03628 90776.1759 99387.62964 81025.51399 79618.69125 92259.21559 0.769387408 0.850247887 0.989442392 0.934568593 0.927625882 0.983925295 1.077265062 0.878237621 0.862989033 1 16.49340541 4.443242464 3.609095534 0.953794468 0.779976524 0.515185615 0.059209806 0.180424738 4.793452247 0.015232511 0.057205472 27748.68864 -4.443242464 -0.173817944 KTEYISTEFNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTEYISTEFNR 11 1 B4DGJ5;Q8N7H5-3;Q8N7H5-2;Q8N7H5 B4DGJ5 PAF1 RNA polymerase II-associated factor 1 homolog 0 82.543 0.029904 95541000 117860 108360 73774 95540 94263 94348 93220 98642 102060 98868 FALSE TRUE 113253.9009 105269.6789 87106.60289 100470.8308 97295.055 96255.7812 94360.85425 96605.00823 90474.57667 92171.5823 1.228729052 1.142105585 0.945048362 1.090041294 1.055586251 1.044310826 1.023752136 1.048099705 0.981588624 1 16.4920344 4.443247231 5.677225382 1.030481082 1.209842995 0.739350157 0.039753474 0.071216422 6.205411 0.009233034 0.027652537 27748.99322 -4.443247231 0.179361913 DEQDGASAETEPWAAAVPPEWVPIIQQDIQSQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DEQDGASAETEPWAAAVPPEWVPIIQQDIQSQR 33 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 63.033 0.012339 22681000 6696.4 8106.8 8843.2 8373.3 9269.3 8350.1 11135 9385.1 11041 12044 FALSE TRUE 6434.697285 7875.602001 10441.36296 8805.447016 9567.455453 8518.944743 11271.27346 9191.294405 9787.671968 11228.24915 0.573081092 0.701409623 0.929919065 0.784222624 0.852087919 0.758706422 1.003831791 0.81858661 0.87170064 1 13.45484536 4.443340333 3.708671874 0.866509811 0.590723557 0.609872022 0.079296297 0.132786313 3.768284575 0.018307743 0.067499008 27754.94254 -4.443340333 -0.275786254 QFCQEGQPHVLEALS(ph)PPQTSGLS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 2 QFCQEGQPHVLEALS(1)PPQT(0.007)S(0.023)GLS(0.929)PS(0.042)R;QFCQEGQPHVLEALS(1)PPQTS(0.003)GLS(0.965)PS(0.032)R;QFCQEGQPHVLEALS(1)PPQTSGLS(0.97)PS(0.029)R;QFCQEGQPHVLEALS(1)PPQT(0.001)S(0.009)GLS(0.829)PS(0.162)R 152.87 4.89E-08 2595630000 737030 776080 709720 769430 794020 915460 763530 742970 873930 960390 TRUE FALSE 708226.0528 753946.9583 837982.1916 809140.3745 819560.3744 933971.2284 772874.3085 727627.4099 774725.1302 895341.9299 0.791011824 0.842077125 0.935935383 0.903722195 0.915360207 1.043144744 0.863216926 0.812681039 0.865284094 1 19.77207923 4.443393081 4.06150155 0.906723443 0.79925983 0.287331952 0.063943004 0.291419516 10.35379822 0.017201317 0.059866158 27758.31377 -4.443393081 -0.107463613 EDLAAFVEELDKVESQEREDVLAGMSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 EDLAAFVEELDKVESQEREDVLAGMSGK 28 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ;; 285.04 2.54E-62 250199000 469531 415209 269334 238469 360663 393150 320894 400302 388870 328865 FALSE TRUE 451181.2094 403367.6459 318008.6451 250776.4137 372264.0529 401099.7624 324821.1968 392035.6238 344727.1079 306590.6806 1.47160771 1.315655274 1.037241721 0.817951848 1.214205377 1.308258169 1.059462069 1.27869387 1.124388736 1 18.22595432 4.443570316 4.184402204 1.122267705 1.445069438 0.429503228 0.137064122 0.195974711 7.513471825 0.035800647 0.122498584 27769.64424 -4.443570316 0.322801733 S(ph)PGHMVILDQTK ddPTM_BT-474_Pertuzumab_2h_R1 10 SPGHMVILDQTK 12 0 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 1 S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK 238.07 2.58E-16 13622900000 17937550 14217630 11331230 10769090 10391590 6121990 9836960 15053330 10744430 10021250 TRUE FALSE 17236530.71 13812157.11 13379035.32 11324884.03 10725844.93 6245780.832 9957347.659 14742473.48 9524767.351 9342501.811 1.844958777 1.478421668 1.432061304 1.212189653 1.14806988 0.668534078 1.065811692 1.578000601 1.019509286 1 23.15537751 4.443761274 1.051752474 1.126014141 1.972473784 0.551572971 0.216585126 1.064970691 1.3478802 0.076623615 0.906222215 27781.85716 -4.443761274 0.846459643 ELNSNHDGADETS(ph)EK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELNSNHDGADETSEK 15 0 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.012)S(0.988)EK 169.43 7.72E-07 375470000 237780 249550 302000 370820 302100 292100 393080 452030 449220 544030 TRUE FALSE 228487.2947 242433.0783 356578.118 389958.0646 311817.3209 298006.4621 397890.6306 442695.4225 398226.4289 507182.3635 0.450503233 0.47799982 0.703057014 0.7688715 0.614803162 0.587572604 0.784511961 0.872852556 0.785174047 1 18.95214505 4.443789969 0.149436266 1.098695972 3.14E-13 0.747488988 0.082608636 12.3607822 0.350595015 0.471887512 2.748937513 27783.69285 -4.443789969 -1.098695972 down GLDFSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLDFSDR 7 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;; 189.62 0.0012852 2934200000 2967340 3275600 3015920 3765520 3498620 3840180 3444480 3533690 3331410 3720860 FALSE TRUE 2851373.072 3182183.095 3560963.833 3959858.938 3611156.29 3917831.071 3486634.577 3460718.067 2953242.303 3468842.838 0.821995462 0.917361565 1.026556693 1.141550403 1.041026203 1.129434585 1.005129013 0.997657786 0.851362383 1 21.72602305 4.444053884 2.781759039 1.029862364 0.827717221 0.42431019 0.075629707 0.272872409 3.929366419 0.019875124 0.092145728 27800.58177 -4.444053884 -0.202145144 SGS(ph)GGGSAKEPQEER ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSGGGSAKEPQEER 15 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 S(0.051)GS(0.945)GGGS(0.004)AKEPQEER;S(0.001)GS(0.997)GGGS(0.002)AKEPQEER 198.77 4.70E-09 1040920000 1051350 920930 578060 606170 757680 842100 707800 754720 1000460 745770 TRUE FALSE 1010262.08 894665.9781 682528.3009 637454.5063 782051.4653 859127.839 716462.2681 739134.7683 886891.9751 695258.3336 1.453074391 1.286810866 0.981690212 0.916859929 1.124835802 1.235695852 1.030497922 1.063108103 1.275629406 1 19.40718961 4.444160269 4.218229665 1.079506846 1.42471915 0.569358827 0.105734407 0.135796001 5.325829261 0.026737508 0.091195364 27807.39261 -4.444160269 0.345212304 TDLEKDIISDTSGDFR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDLEKDIISDTSGDFR 16 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YN52 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ;;; 205.31 2.09E-11 1337768000 4074290 3900980 1618150 3986580 3031180 2801340 2367200 4066920 4019450 3061540 FALSE TRUE 3915062.242 3789727.87 1910585.701 4192327.872 3128680.658 2857985.014 2396170.502 3982936.681 3563178.887 2854179.169 1.371694631 1.327782051 0.669399357 1.468838368 1.096175283 1.001333429 0.839530513 1.395475352 1.248407572 1 21.44464447 4.444185153 24.99983184 1.108406001 1.360719152 0.169388586 0.228128923 286.9943913 217840.0887 0.054608232 0.149552869 27808.98599 -4.444185153 0.252313151 ASGDGESLDEDSEFTLASDFEIGHFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASGDGESLDEDSEFTLASDFEIGHFFR 27 0 Q99733;Q99733-2;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ; 311.27 5.14E-82 211380000 75214 80697 70739 84774 83726 84263 87929 80781 89377 103343 FALSE TRUE 72274.55373 78395.60057 83523.11088 89149.1963 86419.12283 85966.85559 89005.1014 79112.84412 79231.29766 96343.48656 0.750175817 0.813709399 0.866930541 0.925326657 0.89698978 0.892295459 0.923831019 0.821154049 0.822383541 1 16.55589951 4.444513144 2.063672644 0.887834098 0.74626129 0.474806163 0.049288898 0.380182487 2.676171681 0.012855663 0.08046915 27829.99602 -4.444513144 -0.141572808 KLEELELDEQQR ddPTM_BT-474_Pertuzumab_2h_R1 3 KLEELELDEQQR 12 1 Q02750;Q02750-2 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 0 ;; 163.33 9.66E-05 1754470000 2512530 2754230 2521300 2936600 2782460 3038230 2982020 3119310 3197660 3471650 FALSE TRUE 2414337.55 2675682.057 2976954.996 3088158.278 2871960.353 3099665.092 3018514.853 3054895.158 2834675.042 3236512.053 0.745968966 0.826717779 0.919803463 0.954162452 0.887362786 0.957717766 0.932644403 0.943884994 0.875842572 1 21.62600845 4.444564449 2.096757177 0.933924531 0.739087036 0.774420289 0.033345995 0.167902218 1.229135326 0.008001864 0.049247403 27833.28384 -4.444564449 -0.194837495 REQEEELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 REQEEELRR 9 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 86.624 0.0078809 90682000 82376 94871 91088 112248 115502 110164 118272 86067 110803 114753 FALSE TRUE 79156.65485 92165.37197 107549.6278 118041.1327 119217.2267 112391.5916 119719.4481 84289.68637 98225.10796 106980.6771 0.739915441 0.861514196 1.005318257 1.103387415 1.114380933 1.050578428 1.119075438 0.787896363 0.918157471 1 16.70699071 4.445155274 2.715748472 1.007437281 0.745623062 0.460903556 0.095748807 0.306684639 4.17266954 0.028030531 0.133203346 27871.17476 -4.445155274 -0.261814219 AATMEIPIHGNGEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AATMEIPIHGNGEAR 15 0 A0A087X1E4;P53365;E9PRV8;E9PPY7 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 145.69 4.02E-06 846020000 568770 614520 564710 653000 631920 696720 654000 639630 659010 758230 FALSE TRUE 546541.8396 596994.4913 666765.6589 686701.4083 652246.2807 710808.1558 662003.8476 626421.417 584201.9476 706874.4067 0.77318097 0.84455525 0.943259018 0.971461693 0.922718767 1.00556499 0.936522586 0.886184888 0.826457914 1 19.43109438 4.445208017 2.956142465 0.933249426 0.778273973 0.527695972 0.050277261 0.219301272 3.638982085 0.013158673 0.057989771 27874.55979 -4.445208017 -0.154975453 SNSGLATYS(ph)PPMGPVSER ddPTM_BT-474_Pertuzumab_2h_R1 4 SNSGLATYSPPMGPVSER 18 0 H0Y465;P21359-2;P21359-6;P21359;J3KSB5;P21359-4 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 SNSGLAT(0.003)YS(0.997)PPMGPVSER;SNSGLATYS(1)PPMGPVSER;SNSGLAT(0.01)YS(0.99)PPMGPVSER;SNSGLAT(0.013)YS(0.987)PPMGPVSER 370.33 1.38E-107 985770000 717700 779920 661220 810130 797070 841090 828480 847300 909700 919110 TRUE FALSE 689651.4905 757677.4452 780717.1628 851940.9064 822708.4804 858097.4161 838619.1861 829802.9589 806434.6698 856857.861 0.804861018 0.884251029 0.91113964 0.994261645 0.960145805 1.001446629 0.978714469 0.968425449 0.941153377 1 19.70869638 4.445305005 1.214311762 0.977015906 0.776561565 0.879401199 0.020556794 0.282218372 0.51273829 0.005870434 0.062790592 27880.78546 -4.445305005 -0.200454341 SDAEEDGGTVS(ph)QEEEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDAEEDGGTVSQEEEDR 17 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 SDAEEDGGTVS(1)QEEEDR;SDAEEDGGT(0.005)VS(0.995)QEEEDR 366.82 1.25E-104 511020000 237260 411950 330160 752300 359410 349300 581650 637110 527970 514110 TRUE FALSE 227987.6169 400201.5893 389827.2564 791126.2932 370970.7491 356363.0853 588768.4067 623953.4559 468037.059 479288.8718 0.475678928 0.834990364 0.813345102 1.650625207 0.774002425 0.743524639 1.228420774 1.301831719 0.976523943 1 18.87053592 4.445722056 1.767664974 1.099993769 0.460710081 0.333476079 0.260348218 0.592489862 2.824169232 0.070888012 0.526470533 27907.57214 -4.445722056 -0.639283687 DAAEFELFFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DAAEFELFFR 10 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977;H0YF31 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ;;; 174.41 7.25E-06 892540000 963320 1035700 907110 1074060 1085370 1029130 1107000 1196660 1116290 1223220 FALSE TRUE 925672.3894 1006162.85 1071044.956 1129492.365 1120281.912 1049939.714 1120547.797 1171948.553 989573.4391 1140370.22 0.811729711 0.882312457 0.939208107 0.99046112 0.982384398 0.920700747 0.982617555 1.027691299 0.867765066 1 20.12107084 4.446003639 1.67506467 0.971721774 0.798002079 0.575750352 0.04262128 0.380544779 1.58061965 0.011343221 0.089319054 27925.67243 -4.446003639 -0.173719696 SSGS(ph)PYGGGYGSGGGSGGYGSR ddPTM_BT-474_Pertuzumab_2h_R1 19 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 SSGS(1)PYGGGYGSGGGSGGYGSR;SS(0.001)GS(0.999)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.04)S(0.162)GS(0.791)PY(0.006)GGGYGSGGGSGGYGSR;S(0.032)S(0.032)GS(0.904)PY(0.032)GGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.021)S(0.13)GS(0.849)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.003)S(0.021)GS(0.975)PYGGGYGSGGGSGGYGSR;S(0.027)S(0.027)GS(0.946)PYGGGYGSGGGSGGYGSR;S(0.158)S(0.158)GS(0.682)PY(0.001)GGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SS(0.001)GS(0.518)PYGGGYGS(0.003)GGGS(0.477)GGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR 595.2 0 26810060400 2778263.1 2875940 2433784.4 2858282.3 2821568.9 2887817.2 2854363.4 3078013 3163406.5 3139611.4 TRUE FALSE 2669685.507 2793921.007 2873623.38 3005798.592 2912327.226 2946210.842 2889295.953 3014450.956 2804309.856 2926962.723 0.912100959 0.954546153 0.981776555 1.02693436 0.994999766 1.006576141 0.987131107 1.02989045 0.958095514 1 21.48097294 4.446093929 1.778350992 1.002636822 0.906569359 0.670629946 0.019499555 0.270052524 1.306595207 0.004898284 0.036180184 27931.47875 -4.446093929 -0.096067463 GS(ph)PPRPPPPPPLLGTVSSPSSSPTHLWTGEVSAAPPPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPPRPPPPPPLLGTVSSPSSSPTHLWTGEVSAAPPPAR 39 1 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 GS(1)PPRPPPPPPLLGTVSSPSSSPTHLWTGEVSAAPPPAR 114.85 3.39E-06 193400000 39489 37688 39941 35407 40319 54438 48055 33940 42597 64902 TRUE FALSE 37945.72622 36613.17514 47159.22718 37234.35951 41615.89725 55538.77366 48643.11146 33239.12714 37761.56714 60506.12973 0.627138546 0.60511514 0.77941239 0.61538161 0.687796384 0.917903259 0.803936918 0.549351401 0.624094903 1 15.88479369 4.446221296 0.995687622 0.729810832 0.57741019 0.10140569 0.134144119 3.712743938 4.09201693 0.044539863 0.547632957 27939.67153 -4.446221296 -0.152400643 DLLHNEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLHNEDR 8 0 Q8N684-2;Q8N684;Q8N684-3;F5H669 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ; 130.56 0.0010426 677740000 392290 474820 485430 612000 511640 493560 614520 559270 518940 690900 FALSE TRUE 376958.8731 461278.5985 573157.9993 643585.3933 528097.3653 503540.1214 622040.6796 547720.8791 460032.1068 644104.7276 0.585244692 0.716154654 0.889852185 0.999193711 0.819893633 0.781767467 0.965744626 0.850359973 0.714219423 1 19.29693576 4.446250434 3.006418587 0.874523925 0.595682439 0.533806496 0.088656557 0.199211646 3.438210652 0.021906977 0.095411467 27941.54615 -4.446250434 -0.278841487 VAEAHVPNFIFDEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VAEAHVPNFIFDEFR 15 0 Q12768;E7EQI7 Q12768 KIAA0196 WASH complex subunit strumpellin 0 ; 138.57 9.74E-06 154030000 154382 164710 152449 165403 178644 150697 191821 164999 189781 205180 FALSE TRUE 148348.5808 160012.6321 179999.9255 173939.4687 184390.2465 153744.1966 194168.5628 161591.713 168237.8565 191282.9758 0.775545132 0.836523122 0.941013829 0.909330629 0.963965798 0.803752639 1.015085435 0.844778331 0.879523417 1 17.54534895 4.446473079 3.706700737 0.912623956 0.783905402 0.356795628 0.062773193 0.224044759 6.379738126 0.01436462 0.053380235 27955.87427 -4.446473079 -0.128718554 GCWDSIHVVEVQEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GCWDSIHVVEVQEK 14 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;; 222.74 3.78E-12 2057650000 2799570 3043700 2792320 3259800 3104800 3019930 3418160 3275340 3511490 3894770 FALSE TRUE 2690159.709 2956896.656 3296954.339 3428038.669 3204668.712 3080995.054 3459992.465 3207703.084 3112880.377 3630973.759 0.740892082 0.814353629 0.908008308 0.944110009 0.882592088 0.848531347 0.952910347 0.883427779 0.857312827 1 21.79192507 4.446676083 2.712771838 0.905033755 0.743787265 0.607070372 0.044187222 0.189437019 2.568905985 0.010623184 0.050726692 27968.94486 -4.446676083 -0.161246491 SLTSS(ph)LENIFSR ddPTM_BT-474_Pertuzumab_2h_R1 8 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 SLTS(0.001)S(0.999)LENIFSR;SLTS(0.006)S(0.994)LENIFSR;SLT(0.004)S(0.225)S(0.771)LENIFSR;SLT(0.001)S(0.225)S(0.774)LENIFSR;SLTS(0.016)S(0.984)LENIFSR;SLT(0.008)S(0.32)S(0.672)LENIFSR;SLTS(0.227)S(0.773)LENIFSR;SLT(0.006)S(0.247)S(0.747)LENIFSR 296.49 2.84E-36 11317560000 5223770 5501550 4378710 5551900 5359100 5195140 5222810 6187510 5494610 5516060 TRUE FALSE 5019619.293 5344651.181 5170040.301 5838434.224 5531480.319 5300189.29 5286728.311 6059735.756 4870884.908 5142452.343 0.976113916 1.039319536 1.005364747 1.135340463 1.075650283 1.030673487 1.028055869 1.178374704 0.947191064 1 22.29402509 4.446752717 1.487993265 1.066748035 0.97423139 0.074903227 0.064669096 1.341003449 4.103656777 0.017571355 0.156734751 27973.88059 -4.446752717 -0.092516645 SVAAEGALLPQT(ph)PPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVAAEGALLPQTPPSPR 17 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 2 SVAAEGALLPQT(1)PPS(1)PR;SVAAEGALLPQT(1)PPS(1)PR 126.38 0.00023226 717170000 625870 672710 622660 698150 693160 716540 702020 737090 738280 800600 TRUE FALSE 601410.3085 653524.9695 735188.513 734181.6052 715456.1209 731028.9297 710611.5308 721868.8339 654473.5495 746374.6489 0.805775369 0.875599098 0.985012707 0.983663642 0.958575056 0.979439657 0.952084227 0.967166871 0.876870015 1 19.50954046 4.446879352 3.357784949 0.962390103 0.81343242 0.712832043 0.032349329 0.116953411 2.621284904 0.007788184 0.031095 27982.03866 -4.446879352 -0.148957683 GS(ph)GGLFSPSTAHVPDGALGQR ddPTM_BT-474_Pertuzumab_2h_R1 6 GSGGLFSPSTAHVPDGALGQR 21 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GS(0.994)GGLFS(0.004)PS(0.001)T(0.001)AHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(0.733)GGLFS(0.264)PS(0.002)T(0.001)AHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR 233.93 5.92E-30 7261830000 2351310 2711074 2507006 3274030 2939903 3232239 2904614 2926183 2991830 3500101 TRUE FALSE 2259418.206 2633756.824 2960077.752 3443003.081 3034467.65 3297597.087 2940161.535 2865756.298 2652210.001 3263036.042 0.69242821 0.807149167 0.907154477 1.055153249 0.929952232 1.010591684 0.901050892 0.878248435 0.812804384 1 21.63778349 4.446951016 2.371496119 0.935189045 0.692931514 0.587006196 0.066486069 0.255696713 2.519953721 0.018020828 0.098134758 27986.65638 -4.446951016 -0.242257531 LDELYGTWR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDELYGTWR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;; 160.26 0.00015221 1379520000 752140 846240 901270 987780 844270 623680 1106640 989720 975570 1135380 FALSE TRUE 722745.5373 822106.0638 1064149.538 1038759.444 871426.7113 636291.2369 1120183.391 969281.9361 864827.3835 1058479.701 0.682814735 0.776685715 1.005356585 0.981369263 0.823281458 0.601136929 1.058294637 0.915730302 0.817046735 1 20.01356217 4.447054427 6.874537233 0.896380449 0.704814095 0.244066693 0.124802048 0.215270102 34.01232734 0.03105927 0.089439887 27993.32116 -4.447054427 -0.191566354 MTEEEVEMLVAGHEDSNGCINYEELVR ddPTM_BT-474_Pertuzumab_2h_R1 16 MTEEEVEMLVAGHEDSNGCINYEELVR 27 0 P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;;;;;;;;;; 403.6 3.37E-165 2355397100 1096464.1 1203786.2 1005871.2 1276780.2 1279146.8 1343730.7 1215136.6 1226460.8 1313864.2 1375209.4 FALSE TRUE 1053613.071 1169455.396 1187654.501 1342674.979 1320291.719 1370901.855 1230007.805 1201133.956 1164719.844 1282065.242 0.821809246 0.912165276 0.926360424 1.04727508 1.029816327 1.069291804 0.959395641 0.936874284 0.908471586 1 20.29003825 4.447196523 1.666804333 0.988383454 0.813481166 0.537173073 0.048930427 0.500973239 2.051940307 0.014875626 0.11814785 28002.48174 -4.447196523 -0.174902288 AGMSSNQS(ph)IS(ph)SPVLDAVPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.006)S(0.043)NQS(0.947)IS(0.666)S(0.338)PVLDAVPR;AGMSSNQS(0.998)IS(0.666)S(0.335)PVLDAVPR;AGMS(0.001)S(0.007)NQS(0.992)IS(0.936)S(0.065)PVLDAVPR;AGMSS(0.001)NQS(0.998)IS(0.687)S(0.314)PVLDAVPR 161.08 4.42E-11 759080000 1128820 1180440 1111560 1240390 1221820 1099870 1119330 1347350 1295080 1298720 TRUE FALSE 1084704.466 1146775.007 1312443.619 1304406.677 1261120.95 1122110.125 1133028.695 1319526.752 1148067.948 1210756.538 0.895889828 0.947155742 1.083986398 1.077348448 1.041597473 0.926784279 0.935802253 1.08983657 0.948223621 1 20.20747736 4.447282597 8.159480507 1.016246021 0.908346152 0.29871534 0.058227823 0.219644467 52.0925718 0.014854965 0.041761924 28008.03222 -4.447282597 -0.107899869 EVLAS(ph)PDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLASPDR 8 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EVLAS(1)PDR 72.096 0.049343 103130000 112910 135060 148040 164490 137040 116180 179500 175810 158640 176110 TRUE FALSE 108497.3524 131208.221 174794.1211 172979.3486 141448.0161 118529.2392 181696.7747 172179.4621 140631.8523 164181.9128 0.660836206 0.799163676 1.06463689 1.053583465 0.86153227 0.721938471 1.106679607 1.048711512 0.856561176 1 17.32493568 4.447316054 4.538347105 0.968229968 0.686189669 0.426597127 0.113572295 0.171626453 8.282500819 0.029649157 0.097989553 28010.18998 -4.447316054 -0.282040299 GEGDAPFSEPGTTSTQRPS(ph)SPETATKQPSS(ph)PYEDKDK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEGDAPFSEPGTTSTQRPSSPETATKQPSSPYEDKDK 37 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GEGDAPFS(0.005)EPGT(0.029)T(0.16)S(0.16)T(0.174)QRPS(0.246)S(0.226)PET(0.001)AT(0.002)KQPS(0.188)S(0.809)PYEDKDK 92.101 0.00024889 223670000 207900 168530 87599 73047 125570 130930 114670 130910 186770 107320 TRUE FALSE 199775.0382 163723.6894 103430.0879 76816.96442 129609.0731 133577.4943 116073.3658 128206.6628 165568.6526 100051.1208 1.996729637 1.636400353 1.033772406 0.76777715 1.295428497 1.335092433 1.160140584 1.28141156 1.654840558 1 16.6103778 4.447564346 3.858004848 1.199045639 1.94302997 0.574302068 0.224808003 0.14916248 4.701638033 0.057612734 0.209084164 28026.20831 -4.447564346 0.743984331 VKSGT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VKSGTPPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKS(0.08)GT(0.92)PPR;VKS(0.138)GT(0.862)PPR 92.866 0.01855 3546000000 2003640 1824050 1229340 1292210 1472000 1824800 1544950 1728190 1834260 1612900 TRUE FALSE 1925335.534 1772029.88 1451509.085 1358901.113 1519348.217 1861698.706 1563857.56 1692502.273 1626042.495 1503656.846 1.280435452 1.178480239 0.965319373 0.903730872 1.010435473 1.238114076 1.040036205 1.125590773 1.081392007 1 20.52004393 4.44758731 5.273012756 1.054191517 1.259252647 0.433508291 0.087112183 0.160761108 11.90274051 0.023048838 0.07139648 28027.6903 -4.44758731 0.20506113 RMS(ph)DEFVDSFK ddPTM_BT-474_Pertuzumab_2h_R1 14 RMSDEFVDSFK 11 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK 221.78 5.00E-12 12419060000 10097504 9531682 9115784 10038806 10620678 9960179 10825991 12274825 11991541 11621779 TRUE FALSE 9702882.38 9259847.762 10763208.95 10556909.98 10962301.75 10161580.64 10958482.72 12021345.57 10630311.54 10834625.56 0.895543859 0.854653233 0.993408484 0.974367774 1.011784089 0.937880187 1.011431605 1.109530321 0.981142494 1 23.36914596 4.447650518 0.528119913 1.033429348 0.787735972 0.493309675 0.047171971 2.508170285 0.666862065 0.029713161 0.367289471 28031.76982 -4.447650518 -0.245693376 NDAPTPGTSTT(ph)PGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NDAPTPGTSTTPGLR 15 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 NDAPTPGT(0.012)S(0.036)T(0.166)T(0.787)PGLR;NDAPTPGTST(0.005)T(0.995)PGLR;NDAPTPGT(0.001)S(0.007)T(0.277)T(0.715)PGLR;NDAPTPGT(0.009)S(0.078)T(0.04)T(0.872)PGLR 185.85 4.54E-06 3760080000 3429430 3098760 2473560 2651450 2292800 2578440 2456120 3490320 2840830 2781600 TRUE FALSE 3295404.084 3010386.399 2920587.316 2788291.652 2366549.994 2630577.823 2486178.731 3418243.672 2518350.888 2593199.754 1.270786826 1.160877173 1.126248493 1.075232113 0.912598418 1.01441388 0.958730128 1.318156716 0.971136483 1 21.30630191 4.447765558 1.435421746 1.056169748 1.291724609 0.325176766 0.106188887 1.035453834 2.884423688 0.032547386 0.301658837 28039.19612 -4.447765558 0.23555486 ANEHQGIGFLNDPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ANEHQGIGFLNDPR 14 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ;; 109.35 0.00077262 1564190000 1438090 1531380 1281420 1603150 1475930 1578290 1571250 1610610 1684610 1782820 FALSE TRUE 1381887.853 1487706.542 1513001.099 1685888.764 1523404.629 1610204.105 1590479.428 1577350.341 1493380.135 1662068.013 0.831426778 0.89509366 0.910312386 1.014331995 0.916571775 0.968795556 0.956928005 0.949028757 0.898507235 1 20.66454799 4.447873438 1.677996517 0.953793039 0.82431276 0.571203032 0.033982228 0.387857766 1.614894382 0.008605072 0.067989825 28046.162 -4.447873438 -0.129480279 DLSDLDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSDLDFR 8 0 P78332;E9PGM9;P78332-3;F8WCA5 P78332 RBM6 RNA-binding protein 6 0 ; 106.04 0.0099378 194069000 338820 370160 311560 379250 387820 398010 369000 428510 416070 432140 FALSE TRUE 325578.5398 359603.3992 367865.8226 398823.1379 400294.5825 406058.0349 373515.9324 419661.1188 368839.4779 402870.7729 0.808146338 0.892602351 0.913111219 0.989953019 0.993605418 1.007911376 0.92713584 1.041676753 0.915528012 1 18.61995762 4.448329841 1.130455361 0.986500034 0.775820562 0.692163471 0.03690108 0.533941014 0.806121085 0.010453391 0.119093059 28075.65136 -4.448329841 -0.210679472 ATSVALPGWS(ph)PSETR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATSVALPGWSPSETR 15 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ATSVALPGWS(0.995)PS(0.005)ETR;ATSVALPGWS(0.976)PS(0.024)ETR;ATSVALPGWS(0.613)PS(0.387)ETR;ATSVALPGWS(0.968)PS(0.032)ETR 207.08 3.75E-09 587330000 821580 871570 827770 896530 818220 901210 958220 954360 887170 1010770 TRUE FALSE 789471.7453 846713.677 977366.4526 942800.0207 844538.7894 919433.0837 969946.983 934652.1325 786462.1809 942309.6476 0.837805012 0.898551425 1.037203063 1.000520395 0.896243386 0.97572288 1.029329356 0.991873674 0.834611195 1 19.84584169 4.448390303 6.227904823 0.973103299 0.851558466 0.348348168 0.058659652 0.152855516 18.75255267 0.014239746 0.041982305 28079.56028 -4.448390303 -0.121544833 TPS(ph)PSQPKK ddPTM_BT-474_Pertuzumab_2h_R1 4 TPSPSQPKK 9 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.076)PS(0.92)PS(0.004)QPKK;T(0.297)PS(0.703)PSQPKK;T(0.007)PS(0.988)PS(0.005)QPKK;T(0.035)PS(0.959)PS(0.006)QPKK 96.604 0.004444 1740130000 3475300 3067480 1907440 1990730 2525210 2743320 2507470 2660690 3226170 2822940 TRUE FALSE 3339481.434 2979998.474 2252156.839 2093471.814 2606435.673 2798791.81 2538157.168 2605745.822 2859948.707 2631739.759 1.268925403 1.132330225 0.855767304 0.795470679 0.990385035 1.0634759 0.964440788 0.990122907 1.086714101 1 21.3275854 4.448433211 5.034328514 0.967315829 1.241508149 0.57896918 0.08291593 0.118557933 7.723306284 0.021917891 0.06927118 28082.33468 -4.448433211 0.27419232 YLGGS(ph)MDLSTFDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLGGSMDLSTFDFR 14 0 O95983-2;O95983 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR 143.46 9.57E-06 36536000 105418 80473 36769 44018 62494 47799 40375 60667 41989 46720 TRUE FALSE 101298.148 78177.98883 43413.97622 46289.77426 64504.17627 48765.52853 40869.12133 59414.20525 37222.58475 43555.61279 2.32571973 1.794900446 0.996748144 1.062774033 1.480961285 1.119615255 0.93832043 1.364099859 0.854599037 1 15.41057102 4.448497932 3.103071219 1.131282983 2.282168385 0.819075671 0.187032369 0.098136724 1.824379483 0.046069638 0.196517891 28086.52 -4.448497932 1.150885402 up ALVVPEPEPDSDS(ph)NQER ddPTM_BT-474_Pertuzumab_2h_R1 5 ALVVPEPEPDSDSNQER 17 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDS(0.004)DS(0.996)NQER;ALVVPEPEPDSDS(1)NQER;ALVVPEPEPDS(0.003)DS(0.997)NQER;ALVVPEPEPDS(0.027)DS(0.973)NQER;ALVVPEPEPDS(0.027)DS(0.973)NQER 313.92 3.46E-58 1685640000 1068847 1177676 999523 1297603 1175389 1294471 1249769 1200295 1225760 1576264 TRUE FALSE 1027075.278 1144089.834 1180159.04 1364572.446 1213196.455 1320646.091 1265064.047 1175508.489 1086616.864 1469502.235 0.698927333 0.778556035 0.803101222 0.928595012 0.825583266 0.898703016 0.860879294 0.799936509 0.739445533 1 20.48689612 4.448538479 1.788291804 0.852574769 0.692214479 0.358370203 0.068838332 0.586336453 2.869820427 0.017815378 0.131699839 28089.14233 -4.448538479 -0.16036029 AHLS(ph)ENELEALEKNDMEQMK ddPTM_BT-474_Pertuzumab_2h_R1 3 AHLSENELEALEKNDMEQMK 20 1 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 1 AHLS(1)ENELEALEKNDMEQMK;AHLS(1)ENELEALEKNDMEQMK;AHLS(1)ENELEALEKNDMEQMK 316.78 1.08E-66 233298000 393646 337852 255772 217979 308589 306547 257966 234704 362080 273861 TRUE FALSE 378261.8791 328216.7918 301995.69 229228.9223 318515.0454 312745.5904 261123.0651 229857.2804 320978.1964 255312.1505 1.481566304 1.285551005 1.182848875 0.897837889 1.247551457 1.224953805 1.022760039 0.900299026 1.257199063 1 17.96190267 4.448550686 1.742432929 1.072475989 1.508065388 0.496576254 0.127050622 0.446587568 2.045900677 0.035357665 0.268827022 28089.9319 -4.448550686 0.435589399 IQVLQQQADDAEER ddPTM_BT-474_Pertuzumab_2h_R1 8 IQVLQQQADDAEER 14 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;Q5VU61;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;;; 387.96 1.36E-113 6084602000 2436301 2675825 2327243 3057757 2628661 2771284 2831066 3017707 2880103 2993666 FALSE TRUE 2341087.663 2599513.091 2747827.579 3215568.205 2713214.268 2827321.261 2865713.433 2955390.296 2553165.782 2790902.335 0.838828229 0.931423883 0.984566011 1.152160778 0.972163817 1.013049158 1.026805344 1.058937197 0.914817315 1 21.41230021 4.448580903 2.195441481 1.024121941 0.837927405 0.480372469 0.058256817 0.301303043 2.46014593 0.014575066 0.08635324 28091.88634 -4.448580903 -0.186194537 EQTPEHGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQTPEHGKK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 109.42 0.0015919 55340000 191050 164268 116134 102093 132865 131772 121399 151781 158287 139959 FALSE TRUE 183583.5548 159583.2375 137121.9972 107362.032 137138.7234 134436.5201 122884.7173 148646.6693 140318.9234 130479.4523 1.406992071 1.223052632 1.050908743 0.82282712 1.051036933 1.030327134 0.941793632 1.139234314 1.075410119 1 16.99346311 4.448637469 2.442895367 1.015463969 1.404825804 0.716348751 0.080130841 0.184754105 1.952394328 0.021734366 0.115379656 28095.5455 -4.448637469 0.389361835 AQVADVVVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AQVADVVVSR 10 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 205.18 4.04E-07 858660000 849430 911690 786070 931640 943120 978510 1037580 924890 1057070 1152350 FALSE TRUE 816233.3365 885689.4938 928130.335 979722.052 973456.3113 998296.1426 1050278.214 905790.6983 937075.8452 1074300.308 0.759781348 0.824433808 0.863939373 0.911962926 0.906130534 0.929252403 0.977639312 0.843144781 0.872266198 1 20.03496591 4.448692083 1.183257131 0.914030837 0.730407268 0.597280965 0.043272066 0.718704648 1.217763873 0.013082572 0.144149021 28099.07887 -4.448692083 -0.183623569 NRDEAIK ddPTM_BT-474_Pertuzumab_2h_R1 3 NRDEAIK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 116.37 0.0049893 4703630000 5649000 6361000 5881900 7632100 6411500 7650600 7105400 6866800 6249000 7607500 FALSE TRUE 5428230.835 6179590.508 6944890.172 8025993.596 6617731.72 7805300.374 7192358.011 6724998.18 5539639.718 7092237.249 0.765376375 0.871317511 0.979224175 1.131658927 0.933095085 1.100541352 1.01411695 0.948219574 0.781084942 1 22.75780937 4.448897722 2.661309101 0.990930659 0.770051812 0.379965963 0.090524496 0.310293961 4.017494894 0.023179077 0.113312236 28112.38695 -4.448897722 -0.220878847 ADGATSDDLDLHDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ADGATSDDLDLHDDR 15 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 ;;; 214.45 2.47E-12 1553000000 1742890 1837190 1704370 1826760 1925610 1928210 1852740 1821070 2104800 2214980 FALSE TRUE 1674775.932 1784795.14 2012387.573 1921039.303 1987548.994 1967199.727 1875414.386 1783464.268 1865871.928 2064957.432 0.811046226 0.864325391 0.974541916 0.930304554 0.962513301 0.952658731 0.908209708 0.863680888 0.903588568 1 20.97768061 4.449264412 5.201955298 0.928371755 0.821971516 0.53281165 0.037946228 0.137752574 9.950553274 0.010170752 0.031789377 28136.13324 -4.449264412 -0.106400239 DISMEIDS(ph)PENMMR ddPTM_BT-474_Pertuzumab_2h_R1 3 DISMEIDSPENMMR 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR 350.92 6.82E-82 432700000 576049 644817 610341 688016 698193 826180 703024 710680 813196 815000 TRUE FALSE 553536.3682 626427.4505 720643.1957 723524.5882 720651.0119 842885.9257 711627.818 696004.2096 720885.3993 759799.3241 0.728529693 0.824464343 0.948465171 0.952257478 0.948475458 1.10935335 0.936599699 0.91603689 0.948783944 1 19.5352589 4.449285928 1.753263298 0.969721927 0.706155285 0.715918881 0.050717806 0.29921273 1.39146307 0.014453479 0.109386152 28137.52721 -4.449285928 -0.263566642 NEHFQK ddPTM_BT-474_Pertuzumab_2h_R1 4 NEHFQK 6 0 P15924 P15924 DSP Desmoplakin 0 ;;; 125.08 0.018076 1788070000 4570110 4266680 3549700 3761230 3748530 4019760 3930620 3406390 4911960 4230320 FALSE TRUE 4391505.049 4144998.464 4191209.753 3955347.531 3869104.872 4101042.301 3978724.103 3336046.856 4354374.893 3943796.658 1.113522179 1.051017287 1.062734749 1.002928871 0.981060944 1.039871641 1.0088563 0.845897277 1.104107354 1 21.91115374 4.449487371 0.570640674 0.972454853 1.166612542 0.231807908 0.06298202 3.656859064 1.139431558 0.035043668 0.450608189 28150.58154 -4.449487371 0.194157689 RQLS(ph)PQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQLSPQSK 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RQLS(1)PQSK;RQLS(0.998)PQS(0.002)K 128.88 0.00068269 1905410000 989260 939870 691370 839780 823320 842610 827880 899680 1044810 924270 TRUE FALSE 950598.6255 913065.8278 816315.9384 883121.1464 849802.8355 859648.1515 838011.8431 881101.2936 926207.549 861668.3696 1.103207056 1.05964877 0.947366722 1.02489679 0.986229581 0.997655457 0.972545671 1.022552672 1.074900254 1 19.7167732 4.449571964 8.165337498 1.003323043 1.092629521 0.502898129 0.032382736 0.13430809 34.23062941 0.007752296 0.021855588 28156.06532 -4.449571964 0.089306479 GDPPRLS(ph)PDPVAGSAVSQELR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDPPRLSPDPVAGSAVSQELR 21 1 Q9BUR4;E9PMG4;E9PMR3 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 GDPPRLS(1)PDPVAGSAVSQELR;GDPPRLS(1)PDPVAGSAVSQELR;GDPPRLS(1)PDPVAGSAVSQELR;GDPPRLS(1)PDPVAGSAVSQELR 174.06 2.12E-12 3739590000 946200 1048010 1065350 1171010 1083590 1146040 1139150 1144010 1153380 1181040 TRUE FALSE 909221.4579 1018121.781 1257882.444 1231445.966 1118444.656 1169213.714 1153091.258 1120385.794 1022453.138 1101047.109 0.825778889 0.924685032 1.142441984 1.118431679 1.015800911 1.061910707 1.047267868 1.017563903 0.928618884 1 20.07044477 4.449637304 5.935634415 1.043560589 0.847682462 0.596167724 0.057327409 0.097712094 10.57739059 0.014521726 0.043473414 28160.30173 -4.449637304 -0.195878127 YRS(ph)PEPDPYLSYR ddPTM_BT-474_Pertuzumab_2h_R1 4 YRSPEPDPYLSYR 13 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BQG1;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR;Y(0.018)RS(0.982)PEPDPYLSYR;YRS(1)PEPDPYLSYR 157.83 2.44E-05 13397600000 2332990 2471910 2227090 2541530 2543260 2407300 2693850 2712580 2699860 2638660 TRUE FALSE 2241814.172 2401413.547 2629574.704 2672698.668 2625066.268 2455977.255 2726818.142 2656564.275 2393383.212 2459941.208 0.911328354 0.976207699 1.068958354 1.086488839 1.067125612 0.998388599 1.108489151 1.079929986 0.972943257 1 21.23019241 4.449731951 3.09181131 1.055325648 0.916706558 0.508494606 0.042518351 0.186110067 3.430026851 0.010460171 0.044890516 28166.43949 -4.449731951 -0.138619089 ERS(ph)HERPDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSHERPDRK 10 3 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 ERS(1)HERPDRK 72.88 0.033299 216890000 115940 96217 56851 61575 66119 73072 62365 92394 83099 59692 TRUE FALSE 111408.9366 93472.98537 67125.24034 64752.89313 68245.77768 74549.56591 63128.24153 90486.03161 73665.9499 55649.00767 2.00199323 1.679688269 1.206225289 1.163594749 1.22636109 1.339638729 1.13440013 1.62601339 1.32376035 1 15.76406834 4.450015049 3.155978432 1.285602445 1.973403044 0.697409219 0.160034262 0.147154625 2.847492108 0.042006609 0.177406716 28184.80594 -4.450015049 0.687800598 EVLAS(ph)PDRLWGSR ddPTM_BT-474_Pertuzumab_2h_R1 9 EVLASPDRLWGSR 13 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(0.983)PDRLWGS(0.017)R;EVLAS(1)PDRLWGSR 218.28 1.48E-11 2191334000 903331 998349 915866 1133662 1083160 1119409 1127991 1100611 945463 1058560 TRUE FALSE 868027.8258 969877.064 1081383.36 1192170.432 1118000.825 1142044.217 1141795.691 1077882.998 838138.0039 986862.7883 0.879583095 0.98278816 1.095778838 1.208040718 1.132883759 1.157247219 1.156995385 1.09223188 0.849295377 1 19.91248998 4.450169333 2.68386551 1.101626605 0.883937918 0.31084626 0.096353786 0.329576331 4.349987315 0.024476071 0.119094982 28194.82044 -4.450169333 -0.217688687 RGAAAADLLS(ph)SSPES(ph)QHGGTQSPGGGQPLLQPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 2 RGAAAADLLS(0.358)S(0.333)S(0.339)PES(0.537)QHGGT(0.152)QS(0.281)PGGGQPLLQPTK 46.846 0.08954 198810000 59898 65781 63725 68773 64924 77269 68189 69708 76664 85528 TRUE FALSE 57557.11994 63904.99029 75241.52505 72322.38277 67012.33942 78831.43212 69023.51738 68268.50544 67961.42412 79735.11238 0.721854127 0.801466109 0.943643557 0.907033058 0.84043701 0.98866647 0.865660251 0.856191249 0.85233998 1 16.28292755 4.45019759 4.071081895 0.897648164 0.734490014 0.548314886 0.054275476 0.145573562 5.300966779 0.01301655 0.045993591 28196.65496 -4.45019759 -0.16315815 DMVTELFDPLVQGEVQHR ddPTM_BT-474_Pertuzumab_2h_R1 5 DMVTELFDPLVQGEVQHR 18 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 ;;;; 238.81 6.79E-24 340058000 363459 386984 314144.3 398521 381532 409912 388050 376453 422874 432952 FALSE TRUE 349254.6205 375947.5952 370917.1631 419088.7166 393804.3233 418200.7015 392799.072 368679.114 374871.1164 403627.7754 0.865288867 0.931421518 0.91895847 1.038304949 0.975662101 1.036104864 0.97317156 0.913413636 0.928754509 1 18.62266593 4.45032362 1.610724564 0.973743851 0.861347195 0.4200338 0.040673402 0.676307724 2.528263111 0.012126768 0.10074365 28204.83866 -4.45032362 -0.112396657 VSHLLGINVTDFTR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSHLLGINVTDFTR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 210.34 5.38E-09 8234600000 2183170 2373470 2150920 2648500 2434310 2233350 2693300 2616800 2619800 2732700 FALSE TRUE 2097849.303 2305780.959 2539639.091 2785189.402 2512611.792 2278509.867 2726261.411 2562762.166 2322411.287 2547611.795 0.823457211 0.905075477 0.996870518 1.093255027 0.986261642 0.894370905 1.070124348 1.005946891 0.911603287 1 21.28071403 4.450464807 2.759393837 0.999066931 0.827687826 0.478666935 0.057399776 0.242371011 3.41499094 0.014669078 0.069620877 28214.00941 -4.450464807 -0.171379104 RTAQEVETYR ddPTM_BT-474_Pertuzumab_2h_R1 4 RTAQEVETYR 10 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 220.5 9.32E-09 3416250000 797427 878040 813940 1024950 917320 956200 908890 926110 983820 1059600 FALSE TRUE 766262.6712 852999.1589 961037.064 1077847.792 946826.4309 975535.0191 920013.2677 906985.5049 872140.8781 987832.3482 0.775701133 0.863505999 0.972874664 1.091124212 0.958488991 0.987551198 0.931345556 0.918157323 0.882883497 1 19.91390669 4.450492701 3.048584686 0.965049408 0.783169835 0.578067976 0.053069031 0.200586158 3.57537644 0.014534728 0.063229053 28215.82161 -4.450492701 -0.181879573 S(ph)RS(ph)KEYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSKEYHR 8 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 S(1)RS(0.999)KEY(0.001)HR 53.08 0.074467 91645000 67222 55551 32522 35016 44790 36093 42206 45668 48762 35767 TRUE FALSE 64594.88992 53966.73987 38399.44885 36823.17996 46230.71103 36822.82519 42722.52965 44724.93984 43226.74219 33344.46923 1.937199524 1.618461505 1.151598743 1.104326469 1.386458147 1.104315829 1.281247854 1.341300098 1.296369179 1 15.02515986 4.450552514 3.1421533 1.22926819 1.909547912 0.798979934 0.118681697 0.10448176 2.000787656 0.029327663 0.124466886 28219.7079 -4.450552514 0.680279723 DGSAFEDGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGSAFEDGLR 10 0 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 124.92 0.00098346 743860000 781330 802800 825700 819230 906260 849730 907040 807640 879770 977720 FALSE TRUE 750794.7598 779904.93 974922.3576 861510.5585 935410.6759 866912.1228 918140.6268 790961.9518 779902.1979 911498.1535 0.823693122 0.855629742 1.069582373 0.945158863 1.026234307 0.951084892 1.007287424 0.867760345 0.855626745 1 19.79788021 4.450711588 24.0860916 0.959257152 0.831677207 0.388209866 0.063296683 128.9191801 117576.4505 0.01600153 0.043825413 28230.04613 -4.450711588 -0.127579946 ETLPLLLQHLWQVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETLPLLLQHLWQVNR 15 0 Q96T76-5;Q96T76;Q96T76-8;Q96T76-9;H0Y746 Q96T76-5 MMS19 MMS19 nucleotide excision repair protein homolog 0 ; 182.57 5.41E-07 197941000 281800 284800 270960 288730 268200 290880 301910 287520 339190 324720 FALSE TRUE 270786.9445 276677.7828 319928.4995 303631.3899 276826.8966 296761.7929 305604.8649 281582.6115 300686.5732 302726.4252 0.894493912 0.913953193 1.056823828 1.002989381 0.914445762 0.980296955 1.009508386 0.930155375 0.993261731 1 18.20765509 4.45078371 24.97660462 0.980331409 0.899358669 0.419706343 0.038277979 179.9432911 170645.0445 0.009499032 0.026015763 28234.73464 -4.45078371 -0.08097274 SIYNLNEDEELTHYGQSLADIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIYNLNEDEELTHYGQSLADIEK 23 0 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 0 198.55 2.77E-24 86802000 29799 30063 29232 26442 30088 33771 32083 31758 28070 33989 FALSE TRUE 28634.42214 29205.63267 34514.87266 27806.67479 31055.80785 34453.87276 32475.64135 31102.1862 24883.61128 31686.89476 0.903667663 0.921694376 1.089247556 0.87754496 0.980083662 1.087322473 1.024891887 0.981547307 0.785296618 1 14.95159867 4.451137164 24.99772597 0.98202821 0.90817408 0.084935932 0.086248211 436.4512837 419883.3753 0.0206804 0.056639326 28257.72301 -4.451137164 -0.07385413 SGTS(ph)QEELR ddPTM_BT-474_Pertuzumab_2h_R1 5 SGTSQEELR 9 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 S(0.001)GT(0.062)S(0.937)QEELR;SGT(0.01)S(0.99)QEELR;S(0.026)GT(0.054)S(0.92)QEELR;SGT(0.012)S(0.988)QEELR;SGT(0.08)S(0.92)QEELR 138 0.0001562 5939000000 4043340 4233300 3506810 4370710 3916090 4161400 4364120 4455090 4629080 4774630 TRUE FALSE 3885321.803 4112570.429 4140568.576 4596282.867 4042054.591 4245546.359 4417529.406 4363090.835 4103606.245 4451240.057 0.872862787 0.923915668 0.930205633 1.03258481 0.908073826 0.953789574 0.992426683 0.980196704 0.921901805 1 22.08577588 4.451158612 1.680360376 0.967934275 0.8676417 0.409948853 0.035692587 0.543808018 2.264136385 0.009297316 0.074034623 28259.1186 -4.451158612 -0.100292576 DSEDSGQHPDVNSSDKGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSEDSGQHPDVNSSDKGK 18 1 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 0 52.814 0.077667 55406000 79507 82679 97181 73378 83897 96482 88637 95827 104360 108590 FALSE TRUE 76399.77854 80321.07587 114743.7685 77165.04737 86595.6232 98432.93215 89721.76612 93848.13896 92513.49031 101235.1026 0.754676753 0.793411315 1.133438556 0.762236076 0.855391272 0.97232017 0.886271302 0.927031598 0.913847944 1 16.6273501 4.451232687 24.99994805 0.922356085 0.764359946 0.318544124 0.092029139 209.2134906 202032.1937 0.021125622 0.057858566 28263.93902 -4.451232687 -0.157996139 KAELEENQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAELEENQR 9 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 0 ; 117.52 0.0018252 477810000 363850 383580 319240 369020 381670 417210 396690 408920 392750 405120 FALSE TRUE 349630.3397 372640.674 376933.7695 388065.1664 393946.7622 425646.2721 401544.8109 400475.6591 348166.6665 377680.8616 0.925729565 0.986654903 0.998021896 1.027494919 1.043067845 1.126999844 1.063185487 1.060354654 0.921854142 1 18.52680815 4.451302721 1.099327673 1.04474515 0.905563613 0.300057327 0.050077282 1.257360263 1.76367808 0.015536542 0.181934157 28268.49717 -4.451302721 -0.139181537 LEDIDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEDIDRK 7 1 Q92783;Q92783-2 Q92783 STAM Signal transducing adapter molecule 1 0 100.45 0.015688 229480000 257770 277480 246250 280140 297540 322390 295790 304530 314660 334200 FALSE TRUE 247696.0634 269566.5421 290752.8528 294598.059 307110.6443 328908.9467 299409.9665 298241.3491 278941.116 311564.3363 0.795007755 0.865203461 0.933203255 0.945544867 0.985705386 1.055669434 0.960989213 0.957238407 0.895292187 1 18.24917058 4.451400585 1.270560664 0.973548647 0.76270947 0.698539837 0.038235339 0.506311944 1.025945227 0.011689192 0.122394129 28274.86791 -4.451400585 -0.210839177 MVIQGPS(ph)SPQGEAMVTDVLEDQKEGR ddPTM_BT-474_Pertuzumab_2h_R1 5 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.622)S(0.378)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.499)S(0.499)PQGEAMVT(0.002)DVLEDQKEGR;MVIQGPS(0.505)S(0.494)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.5)S(0.5)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.5)S(0.5)PQGEAMVTDVLEDQKEGR 174.61 1.45E-12 2050001000 1244512 1112802 840554 798194 925594 1132440 900780 928056 1162135 955400 TRUE FALSE 1195875.095 1081065.977 992460.8058 839388.888 955366.5716 1155338.713 911804.0151 908891.3193 1030214.307 890689.907 1.3426391 1.21374001 1.114260752 0.942403053 1.072614121 1.297127882 1.023705341 1.020435184 1.156647559 1 19.76456372 4.451487813 2.246336086 1.074652695 1.345029188 0.459062976 0.092580652 0.339588916 2.924671038 0.024526448 0.142965508 28280.54748 -4.451487813 0.270376492 YEDYDYR ddPTM_BT-474_Pertuzumab_2h_R1 4 YEDYDYR 7 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ;;; 140.98 0.0060195 6057540000 8451400 9091100 8106000 9775200 9454300 8954800 9586200 9991200 9986300 10659200 FALSE TRUE 8121109.944 8831830.729 9570934.517 10279699.24 9758406.146 9135872.191 9703518.783 9784878.229 8852697.09 9937242.89 0.817239755 0.888760678 0.963137826 1.034461908 0.982003384 0.919356837 0.976479985 0.98466731 0.890860492 1 23.2444142 4.451733788 2.535435906 0.970843062 0.818588684 0.624128621 0.037971847 0.201857897 2.325863555 0.009710128 0.050089923 28296.5695 -4.451733788 -0.152254378 SLTEISTDFDRSS(ph)PPLQPPPVNSLTTENR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLTEISTDFDRSSPPLQPPPVNSLTTENR 29 1 J3KRR7;Q9NQC7-2;Q9NQC7 J3KRR7 CYLD Ubiquitin carboxyl-terminal hydrolase CYLD 1 SLTEISTDFDRS(0.14)S(0.86)PPLQPPPVNSLTTENR;SLTEISTDFDRS(0.167)S(0.833)PPLQPPPVNSLTTENR;SLTEISTDFDRS(0.118)S(0.882)PPLQPPPVNSLTTENR;SLTEISTDFDRS(0.179)S(0.82)PPLQPPPVNSLTTENR 158.97 4.51E-12 2167490000 276592 308586 289390 332392 331398 318656 347787 351256 349070 410614 TRUE FALSE 265782.4789 299785.4294 341689.2104 349546.791 342057.7176 325099.4426 352043.3213 344002.4409 309445.037 382802.748 0.694306611 0.783132908 0.892598635 0.913125083 0.893561291 0.849260995 0.919646798 0.898641513 0.808366812 1 18.54624166 4.451833475 2.430737078 0.894328361 0.692965021 0.666176317 0.046770955 0.184953498 1.92673113 0.011112537 0.059786559 28303.06542 -4.451833475 -0.20136334 DKWLCPLSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DKWLCPLSGK 10 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 60.49 0.089155 540680000 593610 486510 254510 249110 348070 280950 290490 530310 476900 386360 FALSE TRUE 570411.0649 472635.2111 300505.6185 261966.597 359265.9877 286631.0015 294045.1035 519358.9132 422764.3113 360191.4931 1.583632806 1.312177606 0.834294047 0.727298123 0.997430518 0.795773934 0.816357713 1.441896667 1.173720977 1 18.45840458 4.45199228 4.159823883 0.991302402 1.539227052 0.490864057 0.201086757 0.186702804 7.235032582 0.057255545 0.200687285 28313.41665 -4.45199228 0.54792465 DYAFVHMER ddPTM_BT-474_Pertuzumab_2h_R1 7 DYAFVHMER 9 0 Q9BWF3;E9PB51;Q9BQ04;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2;E9PLB0;E9PM61;U3KQD5 Q9BWF3 RBM4;RBM4B RNA-binding protein 4;RNA-binding protein 4B 0 ;;;;;; 148.91 8.89E-05 4020260000 2793454 2960557 2625508 3237739 3163479 2796932 3051287 3060765 3260558 3395358 FALSE TRUE 2684282.729 2876124.813 3099995.7 3404839.098 3265235.175 2853487.881 3088629.563 2997559.133 2890433.125 3165387.378 0.848010815 0.908617009 0.979341651 1.075646893 1.031543626 0.901465616 0.975750894 0.946980188 0.91313725 1 21.59395064 4.452193005 3.002699628 0.976912888 0.852953692 0.42207764 0.049061975 0.275194726 4.730754631 0.013315795 0.058921186 28326.50572 -4.452193005 -0.123959197 VILGSEAAQQHPEEVR ddPTM_BT-474_Pertuzumab_2h_R1 5 VILGSEAAQQHPEEVR 16 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2;E9PKK8;E9PPK9;E9PQ14;E9PNX5 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;;;; 299.31 7.95E-46 8688200000 2443953 2647708 2202262 2777190 2784040 2737250 2929467 2675461 2700160 2866670 FALSE TRUE 2348440.615 2572197.96 2600259.732 2920521.109 2873591.175 2792599.07 2965318.693 2620211.795 2393649.157 2672507.888 0.878740387 0.962465994 0.972966158 1.09280168 1.07524142 1.044935764 1.109564057 0.980431829 0.895656536 1 21.34976278 4.452277378 1.692348926 1.030702796 0.87153534 0.3620767 0.059979484 0.618191157 2.617870019 0.016923646 0.134170407 28332.00944 -4.452277378 -0.159167455 DHPVFCALVNGEGEVTDFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DHPVFCALVNGEGEVTDFLR 20 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 86.539 0.002491 20714000 22539 23660 21158 23875 24619 25420 24254 24995 25186 23986 FALSE TRUE 21658.15096 22985.23997 24981.72126 25107.19161 25410.89249 25934.00982 24550.82771 24478.84452 22326.99087 22361.40686 0.968550463 1.027897758 1.117180212 1.122791235 1.136372709 1.159766467 1.097910693 1.094691612 0.99846092 1 14.44872334 4.45242965 3.293458477 1.099342167 0.974533716 0.359487221 0.051177704 0.232047403 4.974471122 0.012574737 0.051661538 28341.94494 -4.45242965 -0.124808451 LPLQLDDAVRPEAEGEEEGR ddPTM_BT-474_Pertuzumab_2h_R1 8 LPLQLDDAVRPEAEGEEEGR 20 1 P14868;P14868-2;C9J7S3;C9JLC1 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;;;;; 267.55 6.27E-37 15496680000 2975370 3128770 2756940 3398270 3174970 3226950 3160960 3260500 3211900 3461510 FALSE TRUE 2859089.251 3039540.543 3255180.386 3573655.122 3277095.793 3292201.14 3199644.774 3193169.536 2847298.577 3227058.845 0.885973696 0.941891887 1.008714295 1.107403148 1.015505434 1.020186274 0.991504936 0.989498391 0.882320005 1 21.62178845 4.452536046 3.087272731 1.004815463 0.891014625 0.341830245 0.051440248 0.292577322 5.372153857 0.01342121 0.058074662 28348.88915 -4.452536046 -0.113800838 RPERPEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPERPEVK 8 2 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 0 54.416 0.073338 67438000 76844 65599 53790 72421 66835 65059 67518 68408 80514 73035 FALSE TRUE 73840.85152 63728.18075 63511.04955 76158.65649 68984.80847 66374.53756 68344.30548 66995.35089 71374.38826 68088.2744 1.084487045 0.935964104 0.932775138 1.118528222 1.013167232 0.974830661 1.003760282 0.983948433 1.048262552 1 16.05511875 4.452597898 0.005382099 0.954715355 1.058440157 0 0.056922491 1396788.712 1291.747504 12010.37529 12894.45107 28352.92686 -4.452597898 0.103724802 DYASHLS(ph)PGSIIQPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DYASHLSPGSIIQPQR 16 0 C9J0Q5;C9JE98;C9J330;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 DYASHLS(1)PGSIIQPQR;DYASHLS(1)PGSIIQPQR;DYASHLS(1)PGSIIQPQR;DYASHLS(1)PGSIIQPQR 282.49 9.00E-36 1237110000 498290 517770 468360 528840 551940 518880 507660 533910 524180 573750 TRUE FALSE 478816.2759 503003.7065 553003.0706 556133.4958 569693.6514 529372.1091 513872.8949 522884.5719 464677.2839 534889.4015 0.895168748 0.940388247 1.033864326 1.039716798 1.065068124 0.989685172 0.960708688 0.977556427 0.868735261 1 19.02888109 4.452645809 5.481690758 0.992820455 0.904726026 0.271930037 0.050937099 0.205612913 18.0172669 0.013199988 0.040805902 28356.05495 -4.452645809 -0.08809443 DNDFIYHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNDFIYHDR 9 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 122.42 0.00058627 682490000 1059370 1113730 938100 1116450 1088430 1216390 1149930 1109930 1356410 1315350 FALSE TRUE 1017968.649 1081967.511 1107635.538 1174070.118 1123440.339 1240986.239 1164003.187 1087009.558 1202436.023 1226260.173 0.830140839 0.882331119 0.903263078 0.957439656 0.916151698 1.012008925 0.949230198 0.886442846 0.980571701 1 20.22583367 4.452937714 1.087818194 0.950422376 0.804508563 0.576075053 0.035853317 0.899726705 1.226976372 0.011445925 0.135567509 28375.12045 -4.452937714 -0.145913812 FTDEESR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTDEESR 7 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 108.7 0.016738 461840000 933710 981470 863750 1107450 985190 966380 987230 1014280 1036600 1085770 FALSE TRUE 897219.5809 953479.4366 1019848.839 1164605.627 1016879.531 985920.8657 999312.0161 993334.7636 918929.5138 1012229.831 0.886379312 0.941959432 1.007526955 1.150534782 1.004593522 0.974008902 0.987238259 0.981333224 0.907826944 1 19.94910547 4.453068181 3.234951709 1.00315107 0.892303244 0.295261804 0.057050659 0.3219523 6.610622228 0.015169416 0.063299703 28383.64595 -4.453068181 -0.110847826 LREDLER ddPTM_BT-474_Pertuzumab_2h_R1 4 LREDLER 7 1 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ;;; 202.45 0.00028128 15268900000 5418500 5440340 4831290 5356980 5205330 5326620 5704130 5523400 5496760 6123540 FALSE TRUE 5206739.03 5285186.83 5704411.574 5633454.38 5372764.167 5434327.906 5773938.849 5409339.86 4872790.849 5708787.182 0.912056951 0.925798539 0.999233531 0.986804062 0.941139334 0.951923365 1.011412523 0.947546245 0.853559731 1 22.44475285 4.453534437 22.83882162 0.961429396 0.915492312 0.139210113 0.042896958 137.5762272 133213.0786 0.010346407 0.028341123 28414.13484 -4.453534437 -0.045937084 ANGMELDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ANGMELDGR 9 0 P62995;P62995-3;H7BXF3;Q13595;Q13595-3;Q13595-4;Q13595-2 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 0 ; 105.94 0.0070194 784320000 1073370 1139650 1043100 1195920 1138430 1154310 1270480 1168590 1201770 1329800 FALSE TRUE 1031421.514 1107148.298 1231611.374 1257641.575 1175048.635 1177650.939 1286028.514 1144458.208 1065350.108 1239731.462 0.831971718 0.893054933 0.993450124 1.014446768 0.947825131 0.949924218 1.03734442 0.923150088 0.859339414 1 20.24159622 4.453896209 3.804188107 0.964863645 0.84060182 0.443538028 0.048369181 0.193161473 5.935013782 0.0121902 0.045367135 28437.81398 -4.453896209 -0.124261825 (ac)SSS(ph)PVNVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.051)S(0.2)S(0.75)PVNVKK 53.683 0.022271 1231100000 1850400 1695000 1332500 1178500 1406600 1615700 1556200 1625000 1748200 1681500 TRUE FALSE 1778084.322 1646660.26 1573312.391 1239322.526 1451844.566 1648370.561 1575245.241 1591443.182 1549751.665 1567610.507 1.134264101 1.050426909 1.003637309 0.790580645 0.926151337 1.051517933 1.0048703 1.015203186 0.988607602 1 20.58013572 4.453954655 2.499570439 0.971657762 1.130655889 0.366523674 0.067914728 0.385970807 4.29200964 0.01894878 0.099702554 28441.64129 -4.453954655 0.158998127 RAGDLLEDS(ph)PKRPK ddPTM_BT-474_Pertuzumab_2h_R1 8 RAGDLLEDSPKRPK 14 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK 213.99 1.44E-09 22433450000 13959580 11761570 7605280 6134780 9050120 10408990 8790670 10093920 11897700 8566500 TRUE FALSE 13414024.18 11426141.54 8979723.275 6451396.731 9341225.329 10619466.91 8898252.849 9885477.025 10547122.98 7986283.325 1.679632895 1.430720784 1.124393276 0.807809649 1.169658645 1.329713269 1.114191982 1.237806953 1.320654746 1 22.92909282 4.453972 3.019106317 1.146667157 1.659961904 0.589319078 0.146036639 0.191774829 3.338292437 0.038567928 0.170641973 28442.77721 -4.453972 0.513294748 QDPPVTHDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QDPPVTHDLR 10 0 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 68.44 0.059968 490710000 70161 78948 80259 87379 87167 71974 76471 95193 104340 95219 FALSE TRUE 67419.03055 76696.48034 94763.58665 91888.64066 89970.80572 73429.36359 77406.87497 93227.23128 92495.76063 88769.73232 0.759482188 0.863993597 1.067521374 1.035134817 1.013530213 0.827189197 0.871996264 1.050214176 1.041974085 1 16.43778023 4.45419032 4.923301525 0.984236763 0.779850131 0.492741986 0.074990527 0.14847067 9.423275491 0.020137143 0.065186939 28457.07906 -4.45419032 -0.204386632 SDGSGESAQPPEDSS(ph)PPASSESSSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDGSGESAQPPEDSSPPASSESSSTR 26 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 SDGSGESAQPPEDS(0.008)S(0.991)PPAS(0.001)SESSSTR 133.15 3.21E-05 72766000 151680 161220 142740 168550 167710 184820 161000 162710 175830 179790 TRUE FALSE 145752.1779 156622.1635 168536.2932 177248.8857 173104.5445 188557.187 162970.3662 159349.9816 155870.5155 167612.6632 0.869577365 0.93442918 1.005510503 1.057491017 1.032765313 1.124957885 0.972303423 0.950703716 0.929944746 1 17.35477162 4.454206579 2.578591529 1.009311777 0.870920174 0.425435117 0.052484104 0.33608629 4.024550989 0.014963357 0.076423303 28458.14441 -4.454206579 -0.138391603 GAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTK ddPTM_BT-474_Pertuzumab_2h_R1 3 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.01)S(0.492)S(0.492)PES(0.007)QHGGTQSPGGGQPLLQPTK;GAAAADLLS(0.063)S(0.468)S(0.468)PESQHGGTQSPGGGQPLLQPTK;GAAAADLLS(0.063)S(0.553)S(0.384)PESQHGGTQSPGGGQPLLQPTK 323.74 4.22E-105 5000100000 1497400 1830700 1823470 2329950 1905400 2052890 2345750 1990400 2362270 2645320 TRUE FALSE 1438879.953 1778490.228 2153011.592 2450198.999 1966688.921 2094400.842 2374457.99 1949297.544 2094115.013 2466150.12 0.583451892 0.721160571 0.873025358 0.993531975 0.797473319 0.849259267 0.962819729 0.790421284 0.849143366 1 21.23382919 4.454502417 2.573424557 0.880813025 0.586025733 0.657547003 0.071595406 0.189046264 2.252554561 0.017872041 0.091526895 28477.53646 -4.454502417 -0.294787292 SPS(ph)FGAGEGLLR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPSFGAGEGLLR 12 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.043)PS(0.957)FGAGEGLLR;S(0.112)PS(0.888)FGAGEGLLR;S(0.21)PS(0.79)FGAGEGLLR;S(0.03)PS(0.97)FGAGEGLLR;S(0.027)PS(0.973)FGAGEGLLR;S(0.081)PS(0.919)FGAGEGLLR 203.97 1.25E-07 1194242000 1580988 1344965 784799 1128917 1031340 983089 854068 1651840 720474 605503 TRUE FALSE 1519201.241 1306607.915 926629.6371 1187180.542 1064513.988 1002967.733 864520.3397 1617728.927 638688.812 564491.7425 2.691272745 2.314662584 1.641529127 2.103096383 1.885791957 1.776762453 1.53150219 2.865815042 1.131440487 1 19.10659295 4.454561177 4.051473342 1.868792459 2.633128381 0.253450687 0.503103248 0.28995468 10.530144 0.120322425 0.431251652 28481.38975 -4.454561177 0.764335921 TYEQIKVDENENCSSLGS(ph)PSEPPQTLDLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TYEQIKVDENENCSSLGSPSEPPQTLDLVR 30 1 Q96P16;A0A0C4DGQ6;Q96P16-3 Q96P16 RPRD1A Regulation of nuclear pre-mRNA domain-containing protein 1A 1 T(0.007)Y(0.004)EQIKVDENENCS(0.031)S(0.031)LGS(0.781)PS(0.135)EPPQT(0.011)LDLVR 44.107 0.076227 27987000 39325 35721 24599 24640 30715 32492 33365 34086 32095 33948 TRUE FALSE 37788.13552 34702.27205 29044.5865 25911.67335 31702.97587 33149.0105 33773.33085 33382.11219 28451.71015 31648.67172 1.19398804 1.096484312 0.917718973 0.818728621 1.001715843 1.047406058 1.067132648 1.05477135 0.898985916 1 14.94985733 4.454618287 4.555418222 0.984445226 1.176313323 0.468860269 0.074889075 0.175011499 8.828097887 0.020614336 0.06928243 28485.13535 -4.454618287 0.191868097 VLTLSDDLER ddPTM_BT-474_Pertuzumab_2h_R1 4 VLTLSDDLER 10 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;; 226.47 7.02E-09 685624000 496035 573260 544733 687200 624720 691330 671680 625230 598080 643620 FALSE TRUE 476649.4038 556911.1861 643178.3706 722666.4744 644814.6862 705309.1663 679900.2208 612318.782 530188.4658 600027.0441 0.794379867 0.928143475 1.071915636 1.204389838 1.074642706 1.175462295 1.133115961 1.020485306 0.883607616 1 19.194668 4.455146292 2.615472838 1.080283672 0.798037548 0.504350156 0.087437275 0.249971169 3.094317406 0.023087631 0.116602074 28519.78794 -4.455146292 -0.282246124 S(ph)RDREQDRK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRDREQDRK 9 3 O95232;J3KPP4;H0YA81;H0YBV7;H0YAR4;H0YAX1;H0YAY6 O95232 LUC7L3 Luc7-like protein 3 1 S(1)RDREQDRK;S(1)RDREQDRK 110.08 0.012961 579530000 379940 312439 168469 188564 242079 275758 211165 223424 320459 221517 TRUE FALSE 365091.5248 303528.5456 198915.0959 198295.8106 249865.6909 281334.0157 213749.3004 218810.2163 284081.8378 206513.4563 1.767882497 1.469776116 0.963206463 0.960207699 1.209924503 1.362303555 1.035038124 1.059544595 1.375609333 1 17.65587626 4.455310507 3.955607577 1.122038498 1.723262535 0.671294097 0.146049249 0.116067001 3.959171413 0.03689584 0.134449988 28530.57382 -4.455310507 0.601224037 NAS(ph)SPEKAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NASSPEKAK 9 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 NAS(0.5)S(0.5)PEKAK;NAS(0.5)S(0.5)PEKAK 147.96 5.52E-05 1111490000 2721250 2121180 1035130 1074510 1543680 1541400 1528260 1453570 1493920 1344410 TRUE FALSE 2614900.541 2060686.023 1222201.017 1129965.59 1593333.869 1572568.164 1546963.303 1423553.272 1324336.465 1253351.913 2.086325887 1.644140007 0.97514593 0.901554925 1.271258178 1.254690042 1.234260934 1.135796943 1.056635771 1 20.25736012 4.455368076 3.372389665 1.121369544 2.039320253 0.867352164 0.124314241 0.082216515 1.868439889 0.033510932 0.136230978 28534.35603 -4.455368076 0.917950709 AGMSSNQSIS(ph)SPVLDAVPR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQS(0.005)IS(0.497)S(0.497)PVLDAVPR;AGMSSNQS(0.15)IS(0.8)S(0.05)PVLDAVPR;AGMSSNQSIS(0.5)S(0.5)PVLDAVPR 378.75 1.85E-108 3086570000 680580 774230 699520 902460 819060 841280 852420 866100 875620 919590 TRUE FALSE 653982.1812 752149.7185 825938.8247 949036.0688 845405.8088 858291.258 862852.1709 848214.7323 776223.2885 857305.3502 0.762834597 0.877341683 0.963412656 1.106998887 0.986119833 1.001150008 1.006470064 0.989396289 0.905422191 1 19.70944962 4.455478216 2.184293267 0.999847552 0.758838521 0.722504971 0.046315964 0.19742193 1.582126186 0.012105332 0.073472067 28541.59348 -4.455478216 -0.241009031 S(ph)PEPDTLPLAAGSDHPLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPEPDTLPLAAGSDHPLPR 19 0 H3BVB1;H3BME1;H7C112;H3BPZ0;Q6PCT2-2;Q6PCT2-3;Q6PCT2 H3BVB1 FBXL19 F-box/LRR-repeat protein 19 1 S(1)PEPDTLPLAAGSDHPLPR;S(0.999)PEPDT(0.001)LPLAAGSDHPLPR 207.67 1.97E-16 629910000 96068 108663 110373 145043 107172 104045 127823 111807 119837 132492 TRUE FALSE 92313.55635 105564.0376 130319.8563 152528.6866 110619.2847 106148.8612 129387.3361 109498.1464 106233.6062 123518.1988 0.747368058 0.854643596 1.055066035 1.234868125 0.89557074 0.859378312 1.047516377 0.886494034 0.860064405 1 16.91436409 4.455531472 4.783190808 0.976213537 0.76775365 0.316710627 0.110066428 0.212921017 12.47174438 0.028627167 0.0942199 28545.09362 -4.455531472 -0.208459887 IIEEDDAYDFSTDYV ddPTM_BT-474_Pertuzumab_2h_R1 2 IIEEDDAYDFSTDYV 15 0 Q9BVP2-2;Q9BVP2 Q9BVP2-2 GNL3 Guanine nucleotide-binding protein-like 3 0 ; 175.86 1.94E-06 147347000 316370 333910 295000 362190 339160 355620 340550 339460 344930 373840 FALSE TRUE 304005.9106 324387.2137 348313.0622 380882.6693 350069.3894 362810.8801 344717.7528 332450.0324 305774.9925 348519.4838 0.872278093 0.930757759 0.999407719 1.092859042 1.004447113 1.041006018 0.989091769 0.953892244 0.877354084 1 18.41087979 4.455630825 3.024860148 0.995880707 0.877008077 0.359722535 0.052477661 0.304254659 5.318224488 0.014166064 0.062841637 28551.62461 -4.455630825 -0.11887263 QTHTVDSLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QTHTVDSLSR 10 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 60.598 0.097055 188310000 30169 33925 34186 36878 34779 36083 39773 36914 34886 45706 FALSE TRUE 28989.96213 32957.49222 40364.17066 38781.278 35897.69812 36812.62298 40259.75387 36151.713 30925.88753 42610.29191 0.680351174 0.773463188 0.947286884 0.910138754 0.842465435 0.863937357 0.944836378 0.848426786 0.725784456 1 15.37891431 4.455921575 4.598966566 0.879920553 0.697292427 0.461584071 0.07142937 0.150548369 7.8527205 0.017033508 0.057181825 28570.74563 -4.455921575 -0.182628126 SYLEFSEDSVQVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYLEFSEDSVQVPR 14 0 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 151.1 1.64E-05 56985000 62499 69367 70655 69647 66579 77131 73202 76264 84084 88838 FALSE TRUE 60056.46998 67388.72108 83423.93021 73241.49002 68720.574 78690.64167 74097.86797 74689.12175 74539.13683 82820.92313 0.725136448 0.813667833 1.007280854 0.884335591 0.82974895 0.950129976 0.894675707 0.901814649 0.900003695 1 16.33770766 4.456126948 6.718436386 0.912363476 0.745624535 0.597031207 0.051725806 0.087501648 15.76865951 0.012033262 0.035454924 28584.25963 -4.456126948 -0.166738941 ARPSETGSDDDWEYLLNSDYHQNVESHLLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARPSETGSDDDWEYLLNSDYHQNVESHLLNR 31 1 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 0 117.88 2.21E-05 93967000 45269 56709 45949 71328 59023 55813 67506 55301 81280 76736 FALSE TRUE 43499.83743 55091.71484 54253.00643 75009.24663 60921.5284 56941.5771 68332.15862 54159.01502 72053.43515 71538.60237 0.608061047 0.770097724 0.758373866 1.048514287 0.851589581 0.795955962 0.955178832 0.75706001 1.007196573 1 16.12643431 4.456145583 1.536466656 0.890949826 0.588865599 0.483806078 0.097002509 0.582673208 1.916173498 0.025677447 0.227721284 28585.4862 -4.456145583 -0.302084227 AS(ph)SLCLVPHRPPPPPRSPVPCLPLCSEPPLGSLLPTGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSLCLVPHRPPPPPRSPVPCLPLCSEPPLGSLLPTGR 38 2 B0QYD3 B0QYD3 APOBEC3B 1 AS(0.347)S(0.347)LCLVPHRPPPPPRS(0.24)PVPCLPLCS(0.067)EPPLGSLLPTGR 44.641 0.037418 115060000 55034 56067 55670 48184 58315 59746 61456 61726 49444 65045 TRUE FALSE 52883.21044 54468.02406 65730.80737 50670.78201 60190.75494 60954.10506 62208.11691 60451.33653 43831.32441 60639.44421 0.872092598 0.898227627 1.083961244 0.835607626 0.992600703 1.005189046 1.02586885 0.996897932 0.722818703 1 15.88796891 4.456156213 24.95316493 0.963608338 0.878626177 0.079929042 0.098878599 446.6161433 531574.7822 0.023061329 0.063169245 28586.18586 -4.456156213 -0.084982161 LGDAS(ph)DTEAADGER ddPTM_BT-474_Pertuzumab_2h_R1 2 LGDASDTEAADGER 14 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 LGDAS(1)DTEAADGER;LGDAS(0.99)DT(0.01)EAADGER 382.39 6.90E-99 933500000 820680 836020 838030 742560 862970 916970 795950 871370 992360 922450 TRUE FALSE 788606.9183 812177.5281 989480.6629 780883.6106 890728.2138 935511.7617 805691.0742 853375.905 879711.4531 859971.6399 0.917015029 0.944423619 1.150596853 0.908034143 1.035764637 1.087840248 0.936880982 0.992330288 1.022954028 1 19.71392956 4.456192042 24.99877125 1.013000322 0.923866962 0.220739387 0.065273556 285.723655 341280.8883 0.015164849 0.041538864 28588.5443 -4.456192042 -0.08913336 S(ph)PDVISSASTALSQDIPEIASEALSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPDVISSASTALSQDIPEIASEALSR 26 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 S(0.924)PDVIS(0.045)S(0.01)AS(0.01)T(0.011)ALSQDIPEIASEALSR;S(0.799)PDVIS(0.048)S(0.048)AS(0.048)T(0.054)ALS(0.003)QDIPEIASEALSR;S(0.981)PDVIS(0.018)SASTALSQDIPEIASEALSR 215.68 2.67E-34 659530000 177925.7 183933.7 178153.3 192962.8 187474.9 190173.8 179872.7 202471.2 207214.5 202336.8 TRUE FALSE 170972.1669 178688.091 210349.5643 202921.6332 193505.2004 194019.2445 182074.0359 198290.099 183692.3787 188632.3483 0.906377769 0.947282333 1.115129861 1.075752039 1.025832537 1.028557648 0.965232303 1.051198804 0.973811652 1 17.52521758 4.456406087 20.91177064 1.030467207 0.916603776 0.491575057 0.042628246 23.92265635 24149.73756 0.010512556 0.028809924 28602.6378 -4.456406087 -0.113863431 SSS(ph)TGNLLDKDDLAIPPPDYGAASR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSTGNLLDKDDLAIPPPDYGAASR 25 1 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 S(0.113)S(0.113)S(0.769)T(0.006)GNLLDKDDLAIPPPDYGAASR;S(0.116)S(0.116)S(0.766)T(0.003)GNLLDKDDLAIPPPDYGAASR;S(0.133)S(0.133)S(0.703)T(0.031)GNLLDKDDLAIPPPDYGAASR 175.95 6.53E-13 2711900000 1741770 1466630 909120 1014660 926220 769250 817770 2004840 1140780 976140 TRUE FALSE 1673699.703 1424803.148 1073418.207 1067026.724 956012.7075 784804.7621 827778.1139 1963439.353 1011283.437 910025.1683 1.839179575 1.565674443 1.179547824 1.172524411 1.05053436 0.862398964 0.909621121 2.15756599 1.111269745 1 19.79554692 4.456457399 3.02835875 1.23927038 1.820076396 0.266177452 0.348695196 0.433673718 7.599752822 0.09866356 0.438179128 28606.01746 -4.456457399 0.580806016 TYSDDHVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TYSDDHVK 8 0 O43592;F8WDU6;F5GYW6 O43592 XPOT Exportin-T 0 74.127 0.041781 226290000 239050 244810 237810 235750 254460 253990 250240 238280 316730 287020 FALSE TRUE 229707.6617 237828.2585 280787.5571 247917.0858 262644.937 259125.8518 253302.512 233359.4347 280776.1382 267579.8797 0.85846388 0.888812188 1.049359755 0.926516171 0.981557123 0.968405592 0.946642596 0.872111292 1.049317081 1 18.02961011 4.456649091 24.89099095 0.96239445 0.866050909 0.367074209 0.051652697 209.6623515 254917.0777 0.01258453 0.034471885 28618.64653 -4.456649091 -0.09634354 DGFVMGEGAAVLVLEEYEHAVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGFVMGEGAAVLVLEEYEHAVQR 23 0 Q9NWU1 Q9NWU1 OXSM "3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial" 0 ; 111.83 0.00092145 30573000 14288.2 19565.8 17804.7 28358 18405.1 21289.1 30029 23347.3 26489.7 22471.7 FALSE TRUE 13729.80135 19007.80254 21022.40535 29821.55978 18997.11676 21719.58019 30396.50388 22865.1701 23482.70031 20949.67174 0.655370715 0.907307894 1.003471826 1.423485778 0.906797824 1.036750382 1.450929841 1.091433335 1.120910179 1 14.35464002 4.456893749 1.783929876 1.152334959 0.627790337 0.45564675 0.166209103 0.445275601 2.14633939 0.043273402 0.328429927 28634.77326 -4.456893749 -0.524544622 YREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVR ddPTM_BT-474_Pertuzumab_2h_R1 1 YREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVR 33 1 P28072;A0A087X2I4 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 135.45 2.69E-08 99815000 35771 38150 35629 37488 35380 41708 39655 42013 40987 47120 FALSE TRUE 34373.02977 37061.99935 42067.95286 39422.76017 36518.02983 42551.36434 40140.30975 41145.41687 36334.32759 43928.52043 0.782476383 0.84368877 0.957645567 0.897429729 0.831305709 0.968650069 0.91376421 0.936644723 0.827123865 1 15.42287029 4.456905973 4.542033136 0.91346191 0.793421195 0.402908077 0.052645244 0.16635873 8.396600613 0.012205061 0.04134067 28635.57929 -4.456905973 -0.120040715 DKELPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKELPR 6 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ; 99.919 0.034885 901340000 1435810 1516000 1331040 1556370 1577210 1546450 1698720 1658640 1808120 1824700 FALSE TRUE 1379696.958 1472765.164 1571588.537 1636694.442 1627942.392 1577720.279 1719509.444 1624388.504 1602869.798 1701111.444 0.811056185 0.86576642 0.923859834 0.962132404 0.956987503 0.927464385 1.010815282 0.954898346 0.942248554 1 20.69804623 4.457028879 1.156525814 0.96572633 0.775112201 0.830805073 0.023259268 0.375493161 0.594907745 0.006736244 0.07722424 28643.68434 -4.457028879 -0.190614129 S(ph)GSPKLDPSEVYLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSPKLDPSEVYLK 14 1 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 S(0.544)GS(0.456)PKLDPSEVYLK;S(0.564)GS(0.436)PKLDPSEVYLK 117.18 0.00019298 386720000 949970 802710 458860 430050 555710 663840 596220 774970 869580 665130 TRUE FALSE 912844.1222 779817.4967 541786.2093 452244.932 573584.9168 677263.2996 603516.7187 758966.5987 770868.924 620080.1527 1.472138913 1.257607574 0.873735769 0.729333023 0.925017378 1.09221896 0.973288237 1.223981441 1.243176258 1 19.24209519 4.457562305 4.440124667 1.015557721 1.434643882 0.508835046 0.147030076 0.165156833 7.816345172 0.041283407 0.14172845 28678.88782 -4.457562305 0.419086161 QTGIET(ph)PNKSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 QTGIETPNKSGK 12 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 QT(0.009)GIET(0.991)PNKSGK;QTGIET(0.846)PNKS(0.154)GK 112.42 0.0081231 192365000 471619 380263 230960 196477 226217 297186 265019 331667 323222 305559 TRUE FALSE 453187.6081 369418.2716 272699.6097 206617.2015 233493.4753 303195.3045 268262.3818 324817.9605 286531.1936 284863.2168 1.590895494 1.296826862 0.957300183 0.725320748 0.819668745 1.064354001 0.941723487 1.1402594 1.005855361 1 18.11990982 4.457607853 2.719729537 0.960724444 1.579869767 0.770144999 0.111914354 0.153051928 2.075946828 0.032475963 0.159096927 28681.89575 -4.457607853 0.619145324 GPKPEPPGSGS(ph)PAPPRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPKPEPPGSGSPAPPRR 17 2 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.035)GS(0.965)PAPPRR;GPKPEPPGS(0.057)GS(0.943)PAPPRR 123.6 2.77E-05 1010610000 988370 870770 624710 654230 703980 725980 662010 776460 816600 760620 TRUE FALSE 949743.4077 845936.4922 737608.9936 687994.8887 726624.156 740659.813 670111.8764 760425.8297 723902.9915 709102.5299 1.339359779 1.19296781 1.040200764 0.970233302 1.024709581 1.044503131 0.945014082 1.072377826 1.020872104 1 19.43563472 4.457615933 2.11240195 1.014054471 1.35147238 0.904919581 0.034324278 0.109859194 0.809099342 0.008932382 0.056523056 28682.42938 -4.457615933 0.337417909 YFGTDAVPDGS(ph)DEEEVAYTG ddPTM_BT-474_Pertuzumab_2h_R1 3 YFGTDAVPDGSDEEEVAYTG 20 0 Q9NWZ5;Q9NWZ5-4 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 YFGTDAVPDGS(1)DEEEVAYTG;YFGTDAVPDGS(1)DEEEVAYTG;YFGTDAVPDGS(1)DEEEVAYTG 177.88 6.70E-17 108560000 382653 417098 349295 455611 406191 430572 434905 445945 450375 494159 TRUE FALSE 367698.4977 405202.7734 412420.3765 479125.1383 419256.5024 439278.4608 440227.4975 436736.0799 399250.3181 460689.1708 0.798148776 0.879557843 0.895224812 1.040018235 0.910063724 0.953524608 0.955584645 0.948005961 0.866637081 1 18.81343416 4.457656776 1.770092986 0.94922086 0.791177389 0.519723776 0.045867013 0.403318468 1.904294731 0.011642915 0.089308923 28685.12691 -4.457656776 -0.158043471 SSSSSSQPEHSAMLVSTAAS(ph)PSLIK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSSSSQPEHSAMLVSTAASPSLIK 25 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SSSSSSQPEHSAMLVST(0.003)AAS(0.997)PSLIK;SSSSSSQPEHSAMLVSTAAS(1)PSLIK;SSSSSSQPEHSAMLVSTAAS(0.996)PS(0.003)LIK;SSSSSSQPEHSAMLVST(0.001)AAS(0.999)PSLIK 301.4 1.89E-63 3058990000 2010410 2206280 2092250 2465090 2334370 2493700 2315110 2245770 2269930 2863890 TRUE FALSE 1931840.955 2143359.055 2470366.117 2592313.59 2409457.131 2544124.323 2343443.009 2199394.065 2012257.063 2669916.179 0.723558653 0.802781402 0.925259802 0.970934447 0.902446732 0.952885466 0.877721565 0.823768956 0.753677991 1 21.34836302 4.457793363 3.620655181 0.893788342 0.733575455 0.410193633 0.068538928 0.234176632 6.362641902 0.017959954 0.069808461 28694.14989 -4.457793363 -0.160212887 EFSDIFR ddPTM_BT-474_Pertuzumab_2h_R1 5 EFSDIFR 7 0 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ;;;; 134.44 0.0073853 829903000 1621220 1807460 1780630 2081980 1886100 1393280 2179450 2109130 1981460 2313870 FALSE TRUE 1557860.93 1755913.01 2102429.451 2189431.237 1946768.119 1421453.076 2206122.761 2065575.728 1756532.968 2157149.524 0.722184954 0.813996893 0.974633157 1.014964986 0.902472498 0.658949721 1.022702755 0.957548703 0.81428429 1 21.04069475 4.458176187 4.272762312 0.917755455 0.737454999 0.264564141 0.105111461 0.25531218 10.83476376 0.026342009 0.092476872 28719.4545 -4.458176187 -0.180300456 RPPS(ph)PDVIVLS(ph)DNEQPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 3 RPPS(1)PDVIVLS(1)DNEQPS(0.635)S(0.365)PR 182.07 1.98E-17 1502400000 271710 296020 261320 308960 317000 324270 335680 299900 323930 364490 TRUE FALSE 261091.2728 287577.7994 308546.337 324905.4626 327196.5929 330826.9616 339788.1523 293706.9602 287158.8244 339802.7676 0.768361231 0.846307996 0.908015962 0.956158965 0.962901495 0.973585247 0.999956989 0.864345403 0.845075002 1 18.37433808 4.458276285 1.76742775 0.938517785 0.75547575 0.565035564 0.049144188 0.424483385 1.995171467 0.014138106 0.108818447 28726.07467 -4.458276285 -0.183042036 DT(ph)PGHGSGWAETPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 DT(0.996)PGHGS(0.004)GWAETPR 138.73 3.66E-05 0 41126 51167 56377 71672 56506 55135 58719 57494 66482 67176 TRUE FALSE 39518.75045 49707.76726 66565.578 75371.00051 58323.56681 56249.86748 59437.62069 56306.72881 58935.24208 62626.10969 0.63102675 0.793722738 1.062904567 1.203507625 0.931297938 0.898185561 0.949086906 0.899093511 0.941065035 1 15.93447664 4.458318087 4.003530487 0.978047065 0.655738829 0.628662306 0.087837226 0.140835682 4.987875476 0.024219747 0.088326947 28728.83976 -4.458318087 -0.322308236 RGS(ph)GDTSISIDTEASIR ddPTM_BT-474_Pertuzumab_2h_R1 37 RGSGDTSISIDTEASIR 17 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 RGS(0.999)GDT(0.001)SISIDTEASIR;RGS(0.981)GDT(0.018)S(0.001)ISIDTEASIR;RGS(0.964)GDT(0.036)SISIDTEASIR;RGS(0.983)GDT(0.016)S(0.002)ISIDTEASIR;RGS(0.999)GDT(0.001)SISIDTEASIR;RGS(0.999)GDT(0.001)SISIDTEASIR;RGS(0.975)GDT(0.011)S(0.013)IS(0.002)IDTEASIR;RGS(0.895)GDT(0.092)S(0.013)ISIDTEASIR;RGS(0.982)GDT(0.017)S(0.001)ISIDTEASIR;RGS(0.971)GDT(0.027)S(0.002)ISIDTEASIR;RGS(0.819)GDT(0.174)S(0.008)ISIDTEASIR;RGS(0.979)GDT(0.009)S(0.012)ISIDTEASIR;RGS(0.999)GDT(0.001)SISIDTEASIR;RGS(0.997)GDT(0.003)SISIDTEASIR;RGS(0.992)GDT(0.008)SISIDTEASIR;RGS(0.999)GDT(0.001)SISIDTEASIR;RGS(0.94)GDT(0.057)S(0.004)ISIDTEASIR;RGS(0.977)GDT(0.022)S(0.001)ISIDTEASIR;RGS(0.992)GDT(0.007)S(0.001)ISIDTEASIR;RGS(0.978)GDT(0.021)S(0.001)ISIDTEASIR;RGS(0.95)GDT(0.048)S(0.002)ISIDTEASIR;RGS(0.988)GDT(0.009)S(0.002)ISIDTEASIR;RGS(0.914)GDT(0.064)S(0.021)IS(0.001)IDTEASIR;RGS(0.951)GDT(0.044)S(0.005)ISIDTEASIR;RGS(0.985)GDT(0.015)SISIDTEASIR;RGS(0.945)GDT(0.05)S(0.005)ISIDTEASIR;RGS(0.94)GDT(0.048)S(0.011)IS(0.001)IDTEASIR;RGS(0.974)GDT(0.022)S(0.004)ISIDTEASIR;RGS(0.929)GDT(0.051)S(0.02)ISIDTEASIR;RGS(0.911)GDT(0.083)S(0.006)ISIDTEASIR;RGS(0.992)GDT(0.008)SISIDTEASIR;RGS(0.993)GDT(0.004)S(0.002)ISIDTEASIR;RGS(0.967)GDT(0.033)SISIDTEASIR;RGS(0.998)GDT(0.002)SISIDTEASIR;RGS(0.954)GDT(0.044)S(0.002)ISIDTEASIR;RGS(0.752)GDT(0.216)S(0.031)IS(0.001)IDTEASIR;RGS(0.942)GDT(0.048)S(0.009)ISIDTEASIR 205.53 4.78E-12 4180470400 1642740.1 1729146 1425307.5 1743419.1 1658130.6 1800065.7 1709462 1849195.2 1898582.2 1979767.4 TRUE FALSE 1578540.001 1679832.449 1682892.271 1833397.169 1711465.877 1836464.262 1730382.907 1811008.673 1683063.108 1845675.991 0.855263876 0.910144824 0.911802656 0.993347249 0.927284033 0.995009022 0.937533411 0.981217008 0.911895217 1 20.81571788 4.458485729 1.190487496 0.962539475 0.837795042 0.555207078 0.030518672 0.668613264 1.138220603 0.008157082 0.091833186 28739.93151 -4.458485729 -0.124744433 HPKGEEGS(ph)DDDETENGPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 HPKGEEGSDDDETENGPKPK 20 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 HPKGEEGS(1)DDDETENGPKPK 119.33 2.74E-05 258630000 189530 143770 80980 65384 102390 122800 92554 41811 154510 81017 TRUE FALSE 182122.9581 139669.8204 95614.88739 68758.47608 105683.4673 125283.1001 93686.70354 40947.58824 136970.6726 75529.64643 2.411277779 1.849205272 1.265925261 0.910350827 1.399231591 1.658727481 1.240396427 0.542139281 1.813469002 1 16.20475541 4.458521307 2.241285785 1.182730245 2.43932361 0.545872944 0.346294814 0.2820288 2.400694507 0.093086141 0.554370085 28742.28602 -4.458521307 1.256593365 GAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.002)S(0.114)S(0.884)PESQHGGTQSPGGGQPLLQPTK 391.81 1.22E-166 1793400000 835740 1048300 929640 1342000 1057400 1262900 1314400 1225500 1394500 1624900 TRUE FALSE 803078.3568 1018403.51 1097646.628 1411260.781 1091412.231 1288436.703 1330486.02 1200192.997 1236202.206 1514844.076 0.530139286 0.67228273 0.724593802 0.931621151 0.720478265 0.850540807 0.878298989 0.792288141 0.816059043 1 20.53073787 4.458709918 1.285683086 0.841415747 0.479196956 0.656633207 0.075673043 0.511356839 1.059323807 0.02030112 0.214688851 28754.77134 -4.458709918 -0.362218791 AEGSEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEGSEIR 7 0 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 ; 110.61 0.015737 987440000 680740 802150 751170 999030 866240 843680 914210 891970 972720 1040800 FALSE TRUE 654135.9282 779273.4674 886923.1287 1050590.058 894103.3963 860739.7877 925398.3755 873550.5078 862300.9036 970305.689 0.674154481 0.80312161 0.914065679 1.082741315 0.921465685 0.887081048 0.953718386 0.900283815 0.888689939 1 19.88807981 4.458939918 2.39768615 0.941341062 0.673934587 0.703073106 0.056513516 0.193841258 1.943062772 0.014980584 0.083280722 28770.00374 -4.458939918 -0.267406474 TGSSLLKEEEEDGQEGS(ph)IHNLPLVTSQRPFYDGPMPTPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSSLLKEEEEDGQEGSIHNLPLVTSQRPFYDGPMPTPR 39 2 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 TGSSLLKEEEEDGQEGS(1)IHNLPLVTSQRPFYDGPMPTPR 75.659 0.0010706 138670000 56234 42201 18966 21374 26574 28852 20048 29925 29875 27541 TRUE FALSE 54036.31311 40997.4688 22393.5781 22477.1147 27428.77684 29435.40721 20293.35342 29307.03829 26483.71525 25675.62354 2.104576468 1.596746764 0.872172707 0.875426245 1.068280846 1.146433977 0.790374317 1.141434335 1.031473109 1 14.64811169 4.459087616 3.072910511 0.997307026 2.067674092 0.903169212 0.117853752 0.070835368 1.284672032 0.030089712 0.132911597 28779.78967 -4.459087616 1.070367066 up TLSKEEETKK ddPTM_BT-474_Pertuzumab_2h_R1 4 TLSKEEETKK 10 2 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;; 117.86 0.00050716 5222420000 3407630 2877030 1931580 1443300 2161100 2112670 2439380 2468270 3357680 2380450 FALSE TRUE 3274456.052 2794979.921 2280659.474 1517788.886 2230613.744 2155389.635 2469233.862 2417299.362 2976530.243 2219220.001 1.475498621 1.259442471 1.027685165 0.683928986 1.005134121 0.971237477 1.112658439 1.089256298 1.341250638 1 21.08162126 4.459367216 2.868514397 1.025178827 1.462098023 0.467819166 0.152797819 0.255163172 3.924845565 0.040717334 0.190927454 28798.32417 -4.459367216 0.436919196 EREDLYAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EREDLYAK 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 136.57 0.00071634 256780000 406730 398060 305790 339800 400790 357060 385820 394970 407160 407550 FALSE TRUE 390834.5419 386707.7185 361053.0553 357337.1187 413681.7743 364279.9978 390541.7806 386813.7315 360940.9038 379946.2755 1.028657384 1.017795787 0.950273969 0.940493806 1.088790182 0.958767124 1.027886851 1.018074808 0.949978792 1 18.53543591 4.459379173 24.98784721 0.99518546 1.025942035 0.075889067 0.043317268 573.8544462 808213.6446 0.010352421 0.028359676 28799.11704 -4.459379173 0.030756574 S(ph)PPKADEKER ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPKADEKER 10 2 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)PPKADEKER 47.991 0.093414 145080000 216760 192200 128060 131650 165790 171480 159810 171200 197640 161270 TRUE FALSE 208288.7796 186718.6442 151203.2907 138444.4723 171122.7859 174947.4431 161765.8026 167664.6602 175204.7358 150347.0393 1.38538664 1.241917667 1.005695167 0.920832715 1.138185273 1.163624132 1.075949373 1.115184316 1.165335457 1 17.19793693 4.459428234 3.95296013 1.079813353 1.364166655 0.638052307 0.075781606 0.132637915 4.545991315 0.019818969 0.073064972 28802.37056 -4.459428234 0.284353302 TLSS(ph)PSNRPSGETSVPPPPAVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLSSPSNRPSGETSVPPPPAVGR 23 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3 Q8WWM7 ATXN2L Ataxin-2-like protein 1 T(0.001)LS(0.04)S(0.959)PS(0.001)NRPSGETSVPPPPAVGR;TLS(0.025)S(0.971)PS(0.003)NRPSGETSVPPPPAVGR;TLS(0.001)S(0.975)PS(0.024)NRPSGETSVPPPPAVGR;TLS(0.011)S(0.979)PS(0.01)NRPSGETSVPPPPAVGR 211.89 2.45E-25 3076170000 648310 672190 662920 683990 656480 747900 717180 690820 712040 811850 TRUE FALSE 622973.3285 653019.7993 782724.3906 719290.8059 677596.2754 763023.0504 725957.0634 676554.3256 631212.2043 756862.6764 0.82309955 0.862798259 1.034169625 0.950358405 0.895269772 1.008139355 0.959166155 0.893893102 0.833985113 1 19.52967204 4.459838196 24.63531315 0.942161333 0.833024185 0.351334342 0.057314506 187.3020404 266980.8016 0.014152581 0.038777305 28829.57207 -4.459838196 -0.109137147 VVKPKS(ph)PEPEATLTFPFLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVKPKSPEPEATLTFPFLDK 20 2 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 VVKPKS(0.981)PEPEAT(0.019)LTFPFLDK;VVKPKS(1)PEPEATLTFPFLDK 134.81 4.33E-06 327900000 882160 693540 398760 322080 528460 549810 478040 518990 545090 348400 TRUE FALSE 847684.2119 673760.9182 470824.8024 338702.5874 545458.3958 560927.5349 483890.3965 508272.6751 483213.6684 324802.5577 2.609844633 2.074370729 1.449572336 1.042795321 1.679353758 1.726980043 1.489798603 1.564866603 1.487715096 1 18.30920347 4.459887816 2.712545485 1.463097017 2.591982381 0.732974905 0.230212925 0.151185297 2.035013392 0.058069418 0.286879159 28832.86615 -4.459887816 1.128885364 MGQTMER ddPTM_BT-474_Pertuzumab_2h_R1 4 MGQTMER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 108.92 0.016619 1204850000 1023490 1116980 1035270 1248500 1159940 1203950 1173460 1219920 1174130 1258740 FALSE TRUE 983490.8793 1085124.824 1222366.318 1312935.235 1197250.524 1228294.694 1187821.155 1194728.226 1040847.685 1173484.419 0.838094536 0.924703223 1.041655346 1.118834825 1.020252595 1.046707288 1.012217236 1.018103186 0.886971883 1 20.16236726 4.460365643 3.212614904 1.022532219 0.845996085 0.527292022 0.054454136 0.187896772 3.793836131 0.013833345 0.059141228 28864.60658 -4.460365643 -0.176536134 ALPAVQQNNLDEDLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALPAVQQNNLDEDLIR 16 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 301.16 1.44E-45 348300000 45154 55314 63406 68475 51755 79465 48644 64508 72484 67621 FALSE TRUE 43389.33176 53736.49888 74864.87466 72009.00296 53419.74658 81071.83675 49239.31982 63175.88726 64255.9202 63040.96944 0.688271963 0.852405973 1.187559064 1.142257227 0.847381426 1.286018243 0.78106857 1.002140161 1.0192724 1 15.9440021 4.460502862 6.143331997 1.025357281 0.724820011 0.376578709 0.142129383 0.136270667 19.34815097 0.033390193 0.10180085 28873.72805 -4.460502862 -0.30053727 YNYHLDSSGSYVFENTVATVMALR ddPTM_BT-474_Pertuzumab_2h_R1 3 YNYHLDSSGSYVFENTVATVMALR 24 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 309.55 2.01E-73 1074848000 561654 635465 610724 731912 664787 691571 740812 628068 820109 768883 FALSE TRUE 539703.9407 617342.1604 721095.4123 769686.066 686170.4776 705555.0395 749878.2789 615098.1763 727013.6645 716805.8696 0.75292902 0.861240381 1.005984246 1.073771991 0.957261243 0.984304216 1.046138586 0.858109849 1.014240669 1 19.45122293 4.460675374 3.091036647 0.984768007 0.761313204 0.660661856 0.055392317 0.16578423 3.048313628 0.014765906 0.065175979 28885.19965 -4.460675374 -0.223454803 DVVQAYPEVR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVVQAYPEVR 10 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 150.61 4.95E-05 918100000 564580 589300 546160 572720 591510 536000 608090 648860 645220 672740 FALSE TRUE 542515.5894 572493.741 644863.2613 602278.1478 610536.4563 546838.2872 615531.9873 635460.8143 571977.3306 627174.7206 0.865015077 0.912813802 1.028203529 0.960303609 0.973471086 0.871907412 0.98143622 1.013211779 0.91199041 1 19.25850788 4.460800676 11.31236447 0.967935928 0.876908891 0.358799719 0.044129643 0.406619521 279.6907452 0.010814029 0.030204612 28893.5348 -4.460800676 -0.091027038 YFDRVDENNPEYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 YFDRVDENNPEYLR 14 1 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;P35611-5;A0A0A0MSR2;D6RJE2;D6RAH3;D6RF25 P35611 ADD1 Alpha-adducin 0 123.68 9.26E-05 431420000 790780 1009800 1037900 1355700 1206600 1264100 1161700 1181400 1145500 1408300 FALSE TRUE 759875.4433 981001.4927 1225471.618 1425667.839 1245411.385 1289660.968 1175917.232 1157003.677 1015467.642 1312914.587 0.578769899 0.747193689 0.933397824 1.085880113 0.94858523 0.982288552 0.895654024 0.881248246 0.77344532 1 20.32434163 4.460821767 2.677695839 0.935789709 0.583898189 0.687903475 0.077954514 0.17964622 2.343346326 0.021120745 0.105873434 28894.93798 -4.460821767 -0.35189152 GFVLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFVLHK 6 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 105.82 0.032648 2941900000 3646700 3634600 3475000 3526700 3360000 2531000 3916200 3651000 3876500 4196300 FALSE TRUE 3504182.932 3530944.767 4103009.801 3708713.41 3468077.451 2582178.554 3964127.627 3575605.574 3436455.972 3912080.863 0.895733768 0.902574586 1.048804957 0.948015529 0.886504541 0.660052449 1.013304112 0.913990712 0.878421508 1 21.89950476 4.460951446 24.94669766 0.915567676 0.897443729 0.005334601 0.10149099 2318.347106 3576741.067 0.025225428 0.06913181 28903.56724 -4.460951446 -0.018123947 DVDKIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVDKIR 6 1 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 0 76.592 0.068081 2399700000 4562300 4178300 3072800 3069000 3626100 4095600 3538100 3995000 4145400 3619500 FALSE TRUE 4384000.272 4059138.975 3628123.314 3227391.458 3742736.8 4178415.838 3581400.326 3912501.854 3674831.571 3374348.041 1.299214017 1.20294022 1.075207201 0.956448896 1.109173314 1.238288341 1.061360678 1.15948379 1.089049359 1 21.68617735 4.461019363 3.255115322 1.095731426 1.289947261 0.459250693 0.07434347 0.232305735 4.843306911 0.01908096 0.080878175 28908.08765 -4.461019363 0.194215834 DQSSWQNSDASQEVGGHQER ddPTM_BT-474_Pertuzumab_2h_R1 2 DQSSWQNSDASQEVGGHQER 20 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 333.75 6.33E-80 2121100000 826270 897490 808060 970430 955640 970220 966700 935690 981230 995700 FALSE TRUE 793978.4549 871894.4639 954094.4172 1020514.009 986379.0285 989838.5131 978530.7638 916367.6745 869844.8841 928260.3521 0.855340264 0.939277932 1.027830624 1.099383386 1.062610319 1.066337166 1.054155509 0.987188209 0.937069952 1 19.82416997 4.461314756 2.562848423 1.033005298 0.85648609 0.616139466 0.044053544 0.220606687 2.590590891 0.012272743 0.064245934 28927.75671 -4.461314756 -0.176519208 IPVEGPLS(ph)PSRGDFPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IPVEGPLSPSRGDFPK 16 1 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 IPVEGPLS(0.967)PS(0.033)RGDFPK 102.07 0.0009361 183530000 185900 175530 119370 141210 154550 177590 147690 157640 180500 164170 TRUE FALSE 178634.8225 170524.0563 140942.8144 148497.865 159521.2411 181180.9915 149497.4744 154384.6789 160010.3967 153050.6197 1.167161707 1.114167696 0.920890191 0.970253275 1.042277656 1.18379783 0.976784509 1.008716458 1.045473694 1 17.22364936 4.461426392 23.65692878 1.020716689 1.153913251 0.368937683 0.065470508 112.7316298 169921.0429 0.016625639 0.045574226 28935.19359 -4.461426392 0.133196562 SVLNSITEEVLDHMGTFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVLNSITEEVLDHMGTFR 18 0 Q13416 Q13416 ORC2 Origin recognition complex subunit 2 0 ; 241.74 5.24E-24 175872000 127887 133432 131585 131606 136005 159054 127608 146984 145210 138299 FALSE TRUE 122889.0347 129626.65 155365.3366 138398.2014 140379.7243 162270.1809 129169.7049 143948.729 128726.3696 128931.8855 0.953131447 1.005388616 1.205018727 1.073421061 1.088789819 1.258572929 1.001844535 1.116471138 0.998406011 1 16.97624957 4.461622697 24.25274138 1.098522167 0.966195687 0.242811365 0.082007204 169.463853 265183.7996 0.018788177 0.051496466 28948.2755 -4.461622697 -0.13232648 RTAS(ph)PPPPPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RTASPPPPPKR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.474)AS(0.526)PPPPPKR;RT(0.187)AS(0.813)PPPPPKR 56.286 0.072672 1334683000 222201 216424 160077 195175 196479 217789 190736 215933 235251 210570 TRUE FALSE 213517.1393 210251.7994 189006.4748 205248.0051 202798.9255 222192.8428 193070.2842 211473.9081 208546.2927 196307.9063 1.087664492 1.071030726 0.962806228 1.045541206 1.0330655 1.131858859 0.983507429 1.077256194 1.062342809 1 17.58275875 4.461677491 24.99795861 1.040682466 1.083506133 0.119499219 0.046051728 431.513449 698467.4402 0.010807989 0.029624129 28951.92805 -4.461677491 0.042823667 APVPEPGLDLSLSPRPDS(ph)PQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLSLS(0.001)PRPDS(0.999)PQPR;APVPEPGLDLSLSPRPDS(0.999)PQPR 142.21 7.06E-08 1058740000 526610 574730 523130 597890 611890 609280 587600 643140 687550 707320 TRUE FALSE 506029.499 558339.2631 617671.228 628747.1746 631571.9976 621600.0591 594791.2246 629858.9343 609502.2064 659412.5864 0.767394359 0.846722181 0.936699179 0.953495865 0.957779713 0.942657256 0.902001625 0.95518185 0.924310847 1 19.3308219 4.461754908 2.164792986 0.944839011 0.760992386 0.855076523 0.024065086 0.130159971 1.014372591 0.005932608 0.036988472 28957.08948 -4.461754908 -0.183846625 EFLWQHVELVLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFLWQHVELVLSK 13 0 Q8ND04;Q8ND04-2;Q8ND04-3 Q8ND04 SMG8 Protein SMG8 0 112.72 0.00087827 71000000 107320 111740 109840 111010 120890 107530 124210 101900 134660 148880 FALSE TRUE 103125.8158 108553.2846 129690.5314 116739.2394 124778.5366 109704.3303 125730.1191 99795.72939 119373.9613 138796.225 0.743001589 0.782105454 0.934395236 0.841083678 0.899005262 0.790398516 0.90586123 0.71900896 0.860066341 1 17.0826088 4.461800459 24.47454488 0.85164877 0.752777516 0.227290886 0.074605396 236.8091981 378296.3996 0.01767264 0.048438332 28960.12682 -4.461800459 -0.098871254 S(ph)SSPATEQSWMENDFDELREEGFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.332)S(0.332)S(0.332)PAT(0.002)EQS(0.001)WMENDFDELREEGFR 56.903 0.055156 313020000 32976 32346 25597 25331 31564 34621 30496 33054 31521 32051 TRUE FALSE 31687.26146 31423.52375 30222.9473 26638.33595 32579.28473 35321.06034 30869.21917 32371.42335 27942.86823 29880.15722 1.060478405 1.051651888 1.011472165 0.891505883 1.09033177 1.182090846 1.033100962 1.083375268 0.935164699 1 14.86690012 4.461808725 23.58416235 1.036445839 1.058271814 0.01227324 0.077169965 783.5424134 1206807.078 0.019581022 0.053688334 28960.678 -4.461808725 0.021825975 KGVEGLIDIENPNR ddPTM_BT-474_Pertuzumab_2h_R1 5 KGVEGLIDIENPNR 14 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;;; 238.02 4.16E-17 2584710000 2500360 2455980 1921310 2120310 2312140 2486410 2302620 2481000 2602990 2435110 FALSE TRUE 2402643.167 2385937.855 2268533.456 2229739.453 2386512.083 2536686.914 2330800.152 2429766.483 2307509.488 2270177.831 1.058350203 1.050991611 0.999275663 0.982187132 1.051244555 1.117395686 1.026703777 1.070297864 1.016444376 1 21.11437388 4.461850806 24.91829131 1.037735694 1.056510602 0.040356479 0.037624069 840.210137 1371054.944 0.009645053 0.026441705 28963.4843 -4.461850806 0.018774908 MTGS(ph)PTLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 MTGSPTLVK 9 0 B7ZBM3;Q8IVH2-3;Q8IVH2-2;Q8IVH2 B7ZBM3 FOXP4 Forkhead box protein P4 1 MTGS(0.923)PT(0.076)LVK;MTGS(0.861)PT(0.138)LVK 141.91 0.00011075 945290000 1420080 1456190 1371530 1395530 1506220 1339780 1519680 1571230 1610020 1621560 TRUE FALSE 1364581.704 1414660.887 1619395.981 1467553.471 1554668.934 1366871.27 1538278.298 1538783.551 1427257.279 1511730.297 0.902662139 0.935789201 1.071220167 0.97077731 1.028403636 0.904176673 1.017561335 1.017895556 0.944121635 1 20.52776935 4.461982973 24.97312122 0.995122411 0.910943871 0.327483914 0.044133772 203.6450122 335946.563 0.010227178 0.028028857 28972.29999 -4.461982973 -0.08417854 DYIVVGSDSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 DYIVVGSDSGR 11 0 Q15393;Q15393-2;J3QL37;J3QRB2 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;; 283.58 3.50E-27 1147350000 1074480 1132990 1012380 1137590 1175870 1208320 1124790 1207270 1256060 1218970 FALSE TRUE 1032488.134 1100678.235 1195339.586 1196301.156 1213692.926 1232753.058 1138555.516 1182339.453 1113477.335 1136408.076 0.908554027 0.968558969 1.051857701 1.052703849 1.068008009 1.084780269 1.001889674 1.040418031 0.979821737 1 20.11604956 4.462491202 3.018514434 1.03822026 0.912423856 0.623759272 0.03141035 0.163427483 2.836241153 0.007944413 0.035936843 29006.22439 -4.462491202 -0.125796404 KTET(ph)QEKNPLPSKETIEQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTETQEKNPLPSKETIEQEK 20 3 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 KT(0.214)ET(0.777)QEKNPLPS(0.008)KET(0.002)IEQEK 70.449 0.0098558 177850000 459950 359620 138150 131060 326130 256370 225450 366810 292220 229900 TRUE FALSE 441974.6455 349363.9897 163116.7781 137824.0223 336620.2676 261553.9771 228209.1245 359235.2453 259048.4107 214328.6682 2.062134987 1.630038541 0.761059076 0.64304987 1.570579757 1.220340607 1.064762481 1.676095169 1.208650307 1 17.70946531 4.462689885 6.188528326 1.187305718 1.965780534 0.480999827 0.304271601 0.124181104 18.66187836 0.079973243 0.245012936 29019.49733 -4.462689885 0.778474816 VEAPSLDVHMDS(ph)PDINIEGPDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEAPSLDVHMDSPDINIEGPDVK 23 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VEAPSLDVHMDS(1)PDINIEGPDVK;VEAPSLDVHMDS(1)PDINIEGPDVK 257.01 8.69E-44 335440000 422230 436770 416560 401340 419140 489860 430330 455310 525020 505710 TRUE FALSE 405728.7848 424313.7472 491841.6583 422053.2055 432622.0188 499765.3048 435596.5073 445907.6894 465421.9307 471457.8113 0.86058344 0.900003642 1.043235782 0.895208851 0.917626155 1.060042474 0.923935285 0.945806133 0.987197411 1 18.84676915 4.463254733 24.75678291 0.965177871 0.870438459 0.343964056 0.051107668 189.2978132 337965.8391 0.012025806 0.032967822 29057.26493 -4.463254733 -0.094739411 AILLPDLSEPNNEPLFS(ph)PASEVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AILLPDLSEPNNEPLFSPASEVPR 24 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2;H7C4S1 Q8WYP5 AHCTF1 Protein ELYS 1 AILLPDLSEPNNEPLFS(0.966)PAS(0.034)EVPR;AILLPDLSEPNNEPLFS(0.996)PAS(0.004)EVPR 104.06 0.0020091 47715000 32371 35051 39427 36554 37001 38784 37784 38774 37042 43503 TRUE FALSE 31105.90553 34051.3798 46552.33595 38440.55632 38191.17077 39568.23905 38246.41189 37973.30335 32837.14745 40556.50306 0.766977012 0.839603448 1.147839001 0.94782719 0.941678101 0.975632416 0.943040179 0.936306153 0.809664172 1 15.30764564 4.463365164 24.98965391 0.959808371 0.785133512 0.411435068 0.078358156 178.5217444 324307.3618 0.018769504 0.051456985 29064.65446 -4.463365164 -0.174674859 AFLQAILEHEEQDEEEDEVPDDETVNQMIAR ddPTM_BT-474_Pertuzumab_2h_R1 6 AFLQAILEHEEQDEEEDEVPDDETVNQMIAR 31 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532-3;P51532-5;A0A2R8YF58;A0A2R8YF80;A0A2R8Y440;A0A2R8Y4C5 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ;;;;; 243.55 3.73E-46 796875000 228498 252986 227165 282187 263086 275634 284828 258218 291768 291159 FALSE TRUE 219568.0455 245771.087 268218.7688 296750.7049 271548.4001 281207.5083 288313.8103 252885.7081 258647.7198 271438.5416 0.808905192 0.905439167 0.988138115 1.093251913 1.000404727 1.035989608 1.062169759 0.931649966 0.952877651 1 18.05026606 4.464043324 2.299137538 1.008972023 0.806319853 0.670911827 0.044971795 0.230250584 2.075511347 0.012582089 0.074065613 29110.07498 -4.464043324 -0.20265217 WDEAFR ddPTM_BT-474_Pertuzumab_2h_R1 8 WDEAFR 6 0 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;;;;; 170.96 0.012978 5558323000 2665600 2789490 2998120 3025190 2873300 1906800 3230580 3043080 2856320 3373070 FALSE TRUE 2561425.405 2709936.476 3539946.977 3181320.418 2965722.304 1945356.802 3270116.804 2980239.335 2532082.528 3144608.964 0.814544967 0.861772165 1.125719292 1.01167441 0.943113226 0.61863234 1.039912066 0.947729708 0.805213798 1 21.5844492 4.464122554 24.9152006 0.936440254 0.826351604 0.086024439 0.132199327 471.0143122 902815.459 0.032733061 0.0897565 29115.3861 -4.464122554 -0.11008865 GFTGSVADLAFAHLNSPQLACLDEAGNLFVWR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFTGSVADLAFAHLNSPQLACLDEAGNLFVWR 32 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 204.14 5.75E-27 89954000 39132 44847 45448 50340 45195 49452 58051 41229 63498 46737 FALSE TRUE 37602.67818 43568.00747 53661.46459 52938.05343 46648.73822 50451.95332 58761.4455 40377.60674 56289.97325 43571.46136 0.863011637 0.99992073 1.23157367 1.214970804 1.070625973 1.157912811 1.348622325 0.926698474 1.291900053 1 15.41109588 4.46438886 4.105141759 1.149975883 0.884030833 0.369646574 0.122610515 0.20050662 7.685102164 0.028968494 0.105905532 29133.24493 -4.46438886 -0.265945051 FYQNNKDFIDSLGLLHEQNMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYQNNKDFIDSLGLLHEQNMAK 22 1 Q7L2H7;Q7L2H7-2;H0YCQ8 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 168.78 5.43E-12 451400000 163870 168230 170810 141800 176900 173490 163620 159640 221840 172960 FALSE TRUE 157465.7792 163432.2451 201679.1666 149118.315 182590.1492 176998.0867 165622.4305 156343.3782 196657.6532 161245.2651 0.976560639 1.013563065 1.250760241 0.924791899 1.132375261 1.097694785 1.027146009 0.969599809 1.219618158 1 17.29889727 4.464685339 24.97746926 1.070308185 0.98581109 0.102014779 0.098826976 437.672229 879062.6879 0.022986596 0.063033719 29153.14006 -4.464685339 -0.084497095 EREQELFNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EREQELFNR 9 1 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 0 146.11 0.0015969 0 108070 114480 104110 117930 116700 109010 118290 118650 135670 134980 FALSE TRUE 103846.5049 111215.1425 122924.9929 124016.3814 120453.7615 111214.2569 119737.6684 116199.836 120269.3104 125837.6844 0.825241703 0.883798387 0.976853583 0.98552657 0.957215337 0.883791349 0.951524728 0.923410476 0.955749551 1 16.9412045 4.464807838 3.767256148 0.948629555 0.832966758 0.632283722 0.031595028 0.140259381 4.246166542 0.008021885 0.030950157 29161.36429 -4.464807838 -0.115662797 KFSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFSGFSAKPNNSGEAPSSPTPK 22 2 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 KFSGFSAKPNNSGEAPS(0.057)S(0.871)PT(0.072)PK;KFSGFSAKPNNSGEAPS(0.001)S(0.998)PT(0.001)PK 116.38 8.63E-05 7022700000 2104280 1862070 1405120 1226410 1401160 1617970 1629610 1772700 1940590 1803800 TRUE FALSE 2022042.411 1808965.587 1659056.441 1289705.167 1446229.584 1650686.462 1649553.655 1736093.126 1720302.359 1681627.019 1.202432161 1.075723431 0.98657813 0.766938894 0.860018046 0.98160082 0.980927183 1.032388934 1.022998762 1 20.68142632 4.464897438 2.426981443 0.951349397 1.201217455 0.516591047 0.076880248 0.306930075 3.152867102 0.022294083 0.124402854 29167.38125 -4.464897438 0.249868058 GGGGYTCQS(ph)GSGWDEFTK ddPTM_BT-474_Pertuzumab_2h_R1 6 GGGGYTCQSGSGWDEFTK 18 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GGGGYTCQS(0.994)GS(0.006)GWDEFTK;GGGGYTCQS(1)GSGWDEFTK;GGGGYTCQS(0.994)GS(0.006)GWDEFTK;GGGGYTCQS(0.997)GS(0.003)GWDEFTK;GGGGYTCQS(0.996)GS(0.004)GWDEFTK;GGGGYTCQS(0.999)GS(0.001)GWDEFTK 324.29 5.46E-62 4162900000 4965420 4179890 3463490 2896100 3643800 3343880 2699530 3974110 4062190 3314080 TRUE FALSE 4771365.897 4060683.63 4089419.688 3045568.068 3761006.136 3411495.545 2732567.656 3892043.24 3601067.221 3089614.41 1.544324069 1.314301104 1.32360196 0.985743742 1.217305993 1.104181653 0.884436468 1.259718115 1.165539366 1 21.55899537 4.464951934 1.116221433 1.100241004 1.626054703 0.606731772 0.116072779 0.753248439 1.081777136 0.034825644 0.418248831 29171.04145 -4.464951934 0.525813699 AKESWEMNSEEKLEQSTIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKESWEMNSEEKLEQSTIVK 20 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 120.64 1.90E-05 472180000 202720 208370 213800 160590 223830 232200 187910 217820 236590 226590 FALSE TRUE 194797.4783 202427.4916 252438.416 168878.0691 231029.6952 236895.2431 190209.6988 213321.9409 209733.2951 211242.8575 0.922149419 0.958269047 1.195015154 0.799449843 1.093668671 1.121435517 0.900431385 1.009842148 0.992853901 1 17.68854304 4.465253094 24.99874665 1.01191188 0.931179178 0.077451707 0.105054913 482.5261214 1016380.105 0.024262222 0.066549637 29191.27701 -4.465253094 -0.080732703 GLGPS(ph)PAGDGPSGSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLGPSPAGDGPSGSGK 16 0 Q92934;F5GYS3;A8MXU7 Q92934 BAD Bcl2-associated agonist of cell death 1 GLGPS(1)PAGDGPSGSGK;GLGPS(1)PAGDGPSGSGK 205.95 1.90E-12 276270000 830840 856020 795320 800930 854420 951360 845970 916980 864670 904200 TRUE FALSE 798369.8543 831607.1477 939052.0158 842266.0933 881903.1953 970597.151 856323.2339 898044.0426 766516.2866 842957.7286 0.947105444 0.986534816 1.113996567 0.999179514 1.046200972 1.151418533 1.015855487 1.065348845 0.909317586 1 19.68510076 4.465576719 24.5884638 1.043388706 0.956962756 0.175053142 0.063097871 221.612326 472008.4241 0.014679245 0.040276694 29213.03769 -4.465576719 -0.08642595 AFHNEAQVNPER ddPTM_BT-474_Pertuzumab_2h_R1 6 AFHNEAQVNPER 12 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;;; 202.18 1.40E-07 12731520000 3716040 4072070 3823410 4517240 4267790 4403500 4444830 4075680 4519270 4891680 FALSE TRUE 3570813.049 3955938.551 4514385.238 4750375.298 4405067.341 4492541.787 4499227.159 3991515.784 4006261.416 4560362.157 0.78301085 0.86746149 0.989918143 1.041666239 0.965946824 0.985128293 0.986594267 0.875262895 0.87849633 1 22.12071697 4.46581527 3.44984137 0.960701385 0.792111361 0.581715389 0.049727992 0.184964384 4.456397424 0.013970467 0.057418079 29229.08833 -4.46581527 -0.168590024 GLDDDRGPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 103.7 0.0030824 1569360000 1742250 2024430 1832540 2343900 2241890 2427600 2113680 2248300 2302600 2488500 FALSE TRUE 1674160.944 1966695.239 2163720.743 2464868.96 2314002.428 2476687.735 2139547.848 2201871.819 2041218.501 2319951.678 0.721636127 0.847731122 0.932657677 1.062465646 0.997435614 1.067560052 0.922238109 0.949102449 0.879853887 1 21.14566333 4.465841178 1.980293332 0.979510062 0.710282259 0.690050636 0.05522509 0.265618885 1.651577928 0.015333914 0.106525075 29230.83205 -4.465841178 -0.269227803 DLS(ph)PPRYDSLVQSQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSPPRYDSLVQSQAR 16 1 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 DLS(1)PPRYDSLVQSQAR;DLS(1)PPRYDSLVQSQAR 199.81 2.25E-11 1529740000 389830 417260 394610 403130 441210 436690 421560 448890 434800 470110 TRUE FALSE 374595.0126 405360.1533 465924.8051 423935.5876 455401.9203 445520.171 426719.1774 439620.2646 385443.3268 438269.031 0.854714767 0.924911697 1.063102278 0.967295332 1.039092174 1.016544952 0.973646658 1.003083115 0.879467404 1 18.74145721 4.465883749 6.161189784 0.994174345 0.870283872 0.465703882 0.046858368 0.105833778 16.24688656 0.010910321 0.033832738 29233.69752 -4.465883749 -0.123890473 DIS(ph)LDSELHDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DISLDSELHDLR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 DIS(1)LDSELHDLR;DIS(1)LDSELHDLR 194.48 9.52E-07 62930000 78423 86326 90918 91479 92695 99186 93981 91969 89466 107299 TRUE FALSE 75358.14246 83864.067 107348.9051 96200.24215 95676.61886 101191.6089 95131.16759 90069.80801 79310.19475 100031.5432 0.753343796 0.83837622 1.073150545 0.961699071 0.956464489 1.011596999 0.951011697 0.900414061 0.792851857 1 16.61009547 4.465941196 22.39456919 0.951887776 0.774601767 0.472709631 0.07006888 44.29976576 88736.81343 0.017518755 0.048129238 29237.56472 -4.465941196 -0.177286009 YCVEEEEKAAEMHK ddPTM_BT-474_Pertuzumab_2h_R1 1 YCVEEEEKAAEMHK 14 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5;C9J6M0 A0A494C1K3 GTF2I General transcription factor II-I 0 79.771 0.01091 212750000 106900 89184 53381 55517 77689 80045 58111 65107 93281 68319 FALSE TRUE 102722.2298 86640.55964 63028.13415 58382.23902 80187.93724 81663.56474 58822.1798 63762.5177 82692.13195 63691.69328 1.61280419 1.360311764 0.989581701 0.916638199 1.259001498 1.282169786 0.923545548 1.001111988 1.298318944 1 15.95881761 4.466133247 3.41342091 1.079333376 1.586714006 0.593908112 0.140173978 0.160881111 3.773509206 0.03611995 0.149733825 29250.49684 -4.466133247 0.50738063 GYYSPYSVSGSGS(ph)TAGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 GYYSPYSVSGSGS(0.977)T(0.032)AGS(0.991)R;GYYSPYSVSGS(0.001)GS(0.999)TAGS(1)R 294.09 4.28E-49 534240000 3838700 2634500 1036770 958800 1334920 796830 556360 1574120 737680 574250 TRUE FALSE 3688679.36 2559366.639 1224137.402 1008283.783 1377858.914 812942.4486 563168.9001 1541613.872 653941.659 535355.536 6.890148905 4.780685857 2.286587734 1.883390971 2.573726844 1.518509465 1.051953071 2.879607603 1.2215091 1 19.0301378 4.466218061 1.763873326 1.832158934 7.384464958 0.890387136 0.591111245 0.156898484 0.727194449 0.155176763 1.224675833 29256.20972 -4.466218061 5.552306025 LSGINEIPRPFS(ph)PPVTSNTSPPPAAPLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 LSGINEIPRPFS(0.702)PPVT(0.239)S(0.04)NT(0.019)S(0.001)PPPAAPLAR;LSGINEIPRPFS(0.957)PPVT(0.031)S(0.007)NT(0.005)S(0.001)PPPAAPLAR 190.23 2.34E-18 1433780000 371309 406350 385480 449380 429170 413410 441240 438260 434220 454520 TRUE FALSE 356797.8338 394761.2959 455144.811 472572.5557 442974.6428 421769.4334 446640.0271 429209.7778 384929.166 423734.9556 0.842030682 0.931623154 1.074126184 1.115255066 1.045405004 0.995361435 1.054055185 1.012920393 0.908419664 1 18.69280262 4.466226823 3.857544537 1.029233442 0.854368687 0.553614951 0.052575538 0.152493602 4.925228898 0.013497364 0.05150285 29256.80003 -4.466226823 -0.174864755 MLYDMENPPADEYFGR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLYDMENPPADEYFGR 16 0 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 141.58 3.70E-06 37270000 62532 69698 67812 74427 75809 81903 70011 77945 74995 77525 FALSE TRUE 60088.18031 67710.28128 80067.13687 78268.18639 78247.46533 83559.13478 70867.81556 76335.40851 66481.882 72274.1627 0.831392272 0.936853209 1.107825174 1.08293453 1.082647829 1.156141167 0.980541495 1.056192222 0.919856827 1 16.14119237 4.466411341 3.832511255 1.052748826 0.845625112 0.533030952 0.064722744 0.153117264 4.85921415 0.015934187 0.061083311 29269.23295 -4.466411341 -0.207123715 GYSLVSGGTDNHLVLVDLRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GYSLVSGGTDNHLVLVDLRPK 21 1 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 194.18 2.76E-18 501510000 280490 328580 274590 434550 256690 369100 401760 380710 331990 306540 FALSE TRUE 269528.1407 319209.2201 324214.5212 456977.1776 264946.667 376563.4549 406676.8591 372848.2055 294303.887 285777.7728 0.943138923 1.116984071 1.134498733 1.599064802 0.927107327 1.317679298 1.423052798 1.304678813 1.02983477 1 18.12453419 4.466547492 2.013550896 1.25037732 0.938765527 0.145371204 0.196159642 0.714538721 4.629031135 0.048927583 0.334438639 29278.41023 -4.466547492 -0.311611793 SFGTEDRPTDRPAPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFGTEDRPTDRPAPPR 16 2 Q9BX40;Q9BX40-2;Q5TBQ1;Q5TBQ0;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 0 ;;; 268.92 6.90E-28 2174290000 648550 747070 643680 889250 757200 748520 836450 847010 849010 874080 FALSE TRUE 623203.949 725764.2951 760007.2946 935144.2991 781556.0257 763655.5873 846686.7253 829518.9475 752633.9441 814877.7831 0.764782108 0.890641898 0.93266415 1.14758841 0.959108276 0.937141254 1.039035231 1.017967313 0.923615737 1 19.63622417 4.466567058 1.898100142 1.003009307 0.755103121 0.586312393 0.061657108 0.324554856 1.812055843 0.016109396 0.117477408 29279.72935 -4.466567058 -0.247906187 DLDELSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLDELSR 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 221.53 6.01E-05 3157100000 5103270 5661900 6120300 6004270 6189300 5350590 6742400 6419850 6302290 6767700 FALSE TRUE 4903828.566 5500428.156 7226374.355 6314151.094 6388384.455 5458782.596 6824915.508 6287277.854 5586880.461 6309317.651 0.777235961 0.871794457 1.145349585 1.00076608 1.012531752 0.865193813 1.081720066 0.996506786 0.885496779 1 22.58905256 4.466781837 24.58429172 0.999130568 0.800875533 0.466593658 0.0773314 115.3224606 274205.7644 0.018326288 0.050313639 29294.21316 -4.466781837 -0.198255035 AAVAGEDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAVAGEDGR 9 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;B4DSU6;P07910;G3V2Q1;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;P07910-4;A0A0G2JNQ3;O60812;B2RXH8;A0A0G2JPF8;P0DMR1;B7ZW38 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2;HNRNPCL4;HNRNPCL3 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3 0 ;;; 188.58 9.12E-05 2544330000 1881940 2157410 2222160 2552980 1914760 2550690 2463680 2251690 2425870 2682380 FALSE TRUE 1808391.704 2095882.779 2623753.744 2684739.604 1976349.994 2602266.699 2493831.253 2205191.815 2150495.408 2500700.013 0.723154195 0.838118434 1.049207714 1.073595229 0.790318704 1.040615302 0.997253265 0.881829809 0.85995737 1 21.25390057 4.466851497 4.994516062 0.956129272 0.745298461 0.432271435 0.087300161 0.152921337 10.85115006 0.021577377 0.072138375 29298.91225 -4.466851497 -0.210830811 DIDEVSSLLR ddPTM_BT-474_Pertuzumab_2h_R1 8 DIDEVSSLLR 10 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;;;; 302.37 3.06E-32 3297324000 1552968 1621242 1418906 1610070 1588592 1539324 1742798 1711245 1807110 1896882 FALSE TRUE 1492276.294 1575005.766 1675333.878 1693165.906 1639690.504 1570450.186 1764126.883 1675907.193 1601974.449 1768404.493 0.843854616 0.8906366 0.94737029 0.957453972 0.927214623 0.888060505 0.997581091 0.947694489 0.905886892 1 20.75401687 4.467086772 2.526776621 0.945298145 0.84342868 0.497371172 0.033367293 0.265558956 3.001058985 0.008277944 0.044626529 29314.78894 -4.467086772 -0.101869465 IIILYDDDER ddPTM_BT-474_Pertuzumab_2h_R1 4 IIILYDDDER 10 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 0 ;;; 170.18 1.03E-05 264187000 288362 312123 278901 343352 341011 301989 338375 329670 318878 368434 FALSE TRUE 277092.4942 303221.5576 329304.6148 361072.4379 351979.9285 308095.4245 342516.1345 322862.1993 282680.3063 343479.637 0.806721751 0.882793403 0.958731113 1.051219342 1.024747585 0.896983085 0.997194877 0.939974789 0.822989999 1 18.38986505 4.467430079 2.669247113 0.963195377 0.808941961 0.387695541 0.062264848 0.317205701 4.088390106 0.016093287 0.082344686 29337.97125 -4.467430079 -0.154253415 LRLS(ph)PSPTS(ph)QR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 LRLS(0.81)PS(0.238)PT(0.247)S(0.704)QR 122.63 0.0046246 10169000000 685930 754940 732480 779830 719770 894060 834350 802680 781080 886130 TRUE FALSE 659123.0973 733409.8504 864855.4299 820077.1198 742922.0557 912138.5058 844561.0249 786104.3775 692415.073 826111.6258 0.797862028 0.887785412 1.046898994 0.99269529 0.899299843 1.104134692 1.022332816 0.951571619 0.838161637 1 19.65597721 4.467638597 4.503008414 0.982363938 0.813355636 0.407818271 0.070794259 0.173608677 8.808283519 0.017521596 0.061567783 29352.06071 -4.467638597 -0.169008301 SLRQS(ph)FR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLRQSFR 7 1 J3QRV5;Q6P1M3;Q6P1M3-2;A0A087WW77;Q15334 J3QRV5;A0A087WW77 LLGL2;LLGL1 Lethal(2) giant larvae protein homolog 2;Lethal(2) giant larvae protein homolog 1 1 SLRQS(1)FR 79.986 0.018858 511450000 538870 428600 212020 318740 278900 171740 269890 545690 223000 225210 TRUE FALSE 517810.3646 416376.7476 250336.7304 335190.2096 287871.0718 175212.7005 273192.9946 534421.3108 197685.9749 209956.3261 2.466276555 1.983158857 1.192327638 1.596475876 1.371099776 0.834519749 1.301189631 2.545392752 0.941557602 1 17.67972973 4.467705492 3.773282639 1.449966621 2.403962347 0.365137973 0.465925499 0.264716439 8.060035562 0.124459492 0.483670397 29356.58221 -4.467705492 0.953995726 DVFFYQADDEHYIPR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVFFYQADDEHYIPR 15 0 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ;;; 258.23 8.16E-25 1318810000 890490 963560 854179 1019640 986200 978020 1066550 995030 1099750 1182780 FALSE TRUE 855688.6663 936080.2122 1008548.146 1072263.743 1017922.019 997796.2345 1079602.758 974482.2828 974910.9905 1102669.257 0.77601571 0.848922019 0.914642482 0.972425535 0.923143556 0.904891678 0.979081217 0.883748483 0.884137273 1 20.07256869 4.467852738 2.177047541 0.929673109 0.771419014 0.645588838 0.037657747 0.244405847 1.920172799 0.009551383 0.060208486 29366.53713 -4.467852738 -0.158254095 SLS(ph)LGDKEISR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLSLGDKEISR 11 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.034)LS(0.966)LGDKEISR;SLS(1)LGDKEISR;S(0.003)LS(0.997)LGDKEISR;SLS(1)LGDKEISR;SLS(1)LGDKEISR;S(0.002)LS(0.992)LGDKEIS(0.006)R 223.7 4.09E-12 5078000000 6172430 6039140 4556210 5178950 5943740 5807780 5784310 6387300 6150990 5690480 TRUE FALSE 5931204.612 5866909.64 5379618.499 5446236.23 6134925.795 5925217.291 5855100.116 6255400.023 5452755.402 5305058.721 1.118028079 1.10590852 1.014054468 1.026611865 1.156429385 1.116899473 1.103682433 1.179138696 1.027840725 1 22.33893729 4.467982683 24.95656666 1.090538922 1.114998248 0.018442687 0.059273252 886.5587604 2421108.881 0.015074314 0.041382087 29375.32519 -4.467982683 0.024459327 IWDDGDDFCIFSESR ddPTM_BT-474_Pertuzumab_2h_R1 2 IWDDGDDFCIFSESR 15 0 Q6P158-2;Q6P158 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 0 ; 158.31 4.26E-06 71345000 63086 67461 63549 67974 69004 67079 64729 76084 71452 76509 FALSE TRUE 60620.52937 65537.07833 75033.71794 71482.14629 71223.57633 68435.38334 65521.17286 74512.83881 63341.06851 71326.97728 0.849896234 0.918825959 1.051968285 1.00217546 0.998550325 0.959460024 0.918602966 1.04466559 0.888038032 1 16.12216022 4.468362664 6.111056069 0.984942353 0.865086663 0.428930257 0.048445914 0.114519219 17.43187972 0.011369283 0.035660002 29401.03805 -4.468362664 -0.11985569 LDIPTGT(ph)TPQRK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDIPTGTTPQRK 12 1 P52732 P52732 KIF11 Kinesin-like protein KIF11 1 LDIPT(0.088)GT(0.456)T(0.456)PQRK 61.732 0.048505 363630000 132020 135280 128870 113430 151810 121500 131940 144230 152560 136870 TRUE FALSE 126860.5124 131421.9469 152159.6757 119284.1359 156693.1065 123956.8132 133554.7212 141251.6001 135242.0284 127599.673 0.994207191 1.029955201 1.192477004 0.934831047 1.228005549 0.971450869 1.046669776 1.106990299 1.059893221 1 16.96126511 4.469160319 24.99377133 1.072348539 1.003144129 0.065880109 0.086648784 370.9403898 1164590.084 0.019098979 0.052498908 29455.0876 -4.469160319 -0.06920441 LIEECISQIVLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LIEECISQIVLHK 13 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 151.78 4.49E-05 221240000 480480 561860 476870 610980 625150 693970 639300 572880 612820 638170 FALSE TRUE 461702.3104 545836.3029 563051.0169 642512.751 645258.5175 708002.5489 647123.9446 561049.8278 543255.2428 594946.1775 0.776040469 0.917454929 0.946389839 1.079951053 1.084566204 1.190027898 1.08770166 0.943026191 0.91311662 1 19.18239963 4.469196866 1.440691461 1.042773489 0.746825645 0.534069327 0.077107166 0.641951635 1.761148652 0.02424551 0.237955833 29457.56643 -4.469196866 -0.295947844 TSVLGGGEDGIEPVS(ph)PPEGMTEPGHSR ddPTM_BT-474_Pertuzumab_2h_R1 7 TSVLGGGEDGIEPVSPPEGMTEPGHSR 27 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(0.999)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR 203.83 2.37E-25 4557630000 855034 930230 789126 1012821 927481 943470 960622 965326 1096593 1090564 TRUE FALSE 821618.326 903700.7512 931738.6222 1065092.813 957314.2687 962547.6098 972378.3794 945391.6808 972112.3599 1016699.129 0.80812337 0.888857603 0.916434957 1.047598825 0.941590527 0.946737911 0.956407212 0.929863766 0.956145562 1 19.95546138 4.469733108 1.88195922 0.96088563 0.801235329 0.675733888 0.034362313 0.291262188 1.585875507 0.009119583 0.067746822 29493.96145 -4.469733108 -0.159650301 EFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_BT-474_Pertuzumab_2h_R1 7 EFITGDVEPTDAESEWHSENEEEEKLAGDMK 31 1 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFIT(0.001)GDVEPT(0.061)DAES(0.197)EWHS(0.74)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK 399.63 2.25E-156 8529441000 1480255 1274376 797608 844741 1035147 1137444 991242 952080 1524436 1208099 TRUE FALSE 1422404.998 1238032.044 941753.5083 888338.1842 1068443.443 1160443.897 1003373.116 932419.2153 1351388.416 1126273.379 1.262930497 1.09922872 0.836167778 0.788741172 0.948653731 1.030339453 0.890878836 0.827880009 1.199876018 1 20.10312562 4.469930622 3.947957477 0.925190478 1.239812522 0.438688011 0.114646053 0.173151705 5.974759642 0.028082909 0.106801025 29507.37809 -4.469930622 0.314622044 ETLIAEIEELDR ddPTM_BT-474_Pertuzumab_2h_R1 3 ETLIAEIEELDR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;; 185.77 2.94E-05 88025000 135584 146904 131467 154057 155576 148928 158869 157490 165158 171940 FALSE TRUE 130285.2274 142714.4418 155226.0114 162007.9002 160580.2433 151939.4262 160813.2863 154237.7765 146409.9562 160294.3507 0.812787393 0.890327333 0.968381049 1.010690019 1.001783548 0.947877611 1.003237392 0.962215922 0.913381886 1 17.29036406 4.470324827 2.294199241 0.977124086 0.809215509 0.771645207 0.028635322 0.167107303 1.489936801 0.007449912 0.04472444 29534.17387 -4.470324827 -0.167908577 VVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_BT-474_Pertuzumab_2h_R1 6 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDYS(0.008)T(0.027)T(0.963)PGGT(0.002)LFS(0.014)T(0.047)T(0.926)PGGT(0.013)R;VVLGDGVQLPPGDYS(0.003)T(0.012)T(0.979)PGGT(0.016)LFS(0.018)T(0.01)T(0.845)PGGT(0.118)R;VVLGDGVQLPPGDYS(0.002)T(0.004)T(0.984)PGGT(0.01)LFS(0.007)T(0.014)T(0.97)PGGT(0.009)R;VVLGDGVQLPPGDYS(0.023)T(0.085)T(0.884)PGGT(0.008)LFS(0.039)T(0.022)T(0.906)PGGT(0.033)R;VVLGDGVQLPPGDY(0.003)S(0.088)T(0.401)T(0.499)PGGT(0.045)LFS(0.154)T(0.122)T(0.607)PGGT(0.082)R;VVLGDGVQLPPGDYS(0.011)T(0.046)T(0.932)PGGT(0.013)LFS(0.166)T(0.127)T(0.579)PGGT(0.127)R 156.61 3.50E-09 1535051000 1444953 1525360 1336661 1605247 1547003 1655782 1523654 1548867 1671418 1635287 TRUE FALSE 1388482.639 1481858.226 1578225.377 1688093.99 1596763.756 1689263.047 1542300.933 1516882.355 1481685.636 1524527.555 0.910762573 0.972011442 1.035222598 1.107289917 1.04738268 1.108056749 1.011658286 0.994985201 0.971898232 1 20.5399308 4.470345605 2.712157856 1.03657583 0.91266654 0.462102248 0.042660539 0.284962099 3.808255863 0.011793981 0.059913556 29535.58688 -4.470345605 -0.123909289 ILIPS(ph)DIESSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ILIPSDIESSK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ILIPS(1)DIESSK;ILIPS(1)DIESSK;ILIPS(1)DIESSK;ILIPS(1)DIESSK 204.85 3.34E-08 881860000 3696970 3828740 3526260 3281680 3791960 4262890 3464660 4199070 4307170 4141520 TRUE FALSE 3552488.325 3719548.084 4163533.623 3451047.898 3913931.837 4349088.557 3507061.545 4112357.737 3818238.119 3861011.162 0.920092736 0.963361132 1.078353169 0.893819716 1.013706429 1.126411806 0.908327223 1.06509864 0.988921803 1 21.88054729 4.470694651 24.72273707 1.010150194 0.930909804 0.150765829 0.067654833 201.4250317 774873.5424 0.015556055 0.042847753 29559.33441 -4.470694651 -0.07924039 GPS(ph)PEGSSSTESSPEHPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPSPEGSSSTESSPEHPPK 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GPS(0.879)PEGS(0.095)S(0.02)S(0.002)T(0.002)ES(0.001)SPEHPPK 123.39 2.02E-05 550620000 222400 250910 273470 283440 245960 272360 265790 251670 318460 303370 TRUE FALSE 213708.3621 243754.2925 322892.1123 298068.3724 253871.5268 277867.3058 269042.8175 246472.9266 282309.7559 282822.4797 0.755627213 0.861863218 1.141677679 1.053906227 0.897635602 0.982479561 0.951278052 0.871475729 0.998187118 1 18.10953727 4.470867256 24.97903591 0.97603403 0.782186154 0.508536079 0.072804916 114.6036314 457739.2864 0.019270835 0.053075313 29571.08478 -4.470867256 -0.193847876 SCS(ph)ASCVPHGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCSASCVPHGAK 12 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 S(0.171)CS(0.817)AS(0.012)CVPHGAK 108.23 0.0011131 210160000 225250 172050 77602 117700 134630 72962 75117 191150 93367 66586 TRUE FALSE 216446.981 167143.3025 91626.40765 123774.5111 138960.4962 74437.34163 76036.30432 187202.6857 82768.36959 62076.07091 3.486802206 2.692556085 1.476034264 1.993916646 2.238551735 1.19913101 1.224889127 3.015698045 1.333337764 1 15.92174962 4.47087055 3.395862799 1.809999517 3.410755271 0.491229297 0.585085332 0.2118352 4.90126447 0.147953581 0.623716018 29571.30905 -4.47087055 1.600755755 GPSAGGGPGSGT(ph)SPQVEWTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSAGGGPGSGTSPQVEWTAR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3;A0A2R8Y454 Q7Z406 MYH14 Myosin-14 1 GPSAGGGPGS(0.019)GT(0.595)S(0.386)PQVEWTAR;GPSAGGGPGS(0.002)GT(0.722)S(0.276)PQVEWTAR 214.55 7.71E-24 326600000 235640 255330 241760 272240 240750 282530 270680 285450 258920 266450 TRUE FALSE 226430.9283 248048.2384 285451.4099 286290.339 248493.9424 288242.9502 273992.6628 279555.3577 229528.4871 248403.1042 0.911546291 0.998571412 1.149145905 1.152523194 1.000365689 1.160383849 1.103016259 1.125410082 0.924016179 1 17.92232368 4.471374587 4.495593709 1.087443182 0.926375168 0.313338986 0.07577068 0.185992756 9.444720401 0.0177194 0.063078931 29605.64904 -4.471374587 -0.161068014 GPAGEAGAS(ph)PPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPAGEAGASPPVR 13 0 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 GPAGEAGAS(1)PPVR;GPAGEAGAS(1)PPVR;GPAGEAGAS(1)PPVR;GPAGEAGAS(1)PPVR 118.52 0.00044192 2369950000 1201180 1352950 1196440 1623480 1279500 1335800 1501120 1516610 1552520 1632120 TRUE FALSE 1154236.558 1314365.191 1412663.323 1707267.997 1320656.28 1362810.791 1519491.156 1485291.474 1376284.438 1521575.059 0.758580098 0.863818832 0.928421713 1.122039946 0.867953422 0.895657946 0.99863043 0.97615393 0.904513011 1 20.53713407 4.471496272 2.279927213 0.964126513 0.756498283 0.478689803 0.067746988 0.318613254 2.794641189 0.017364554 0.105277069 29613.94545 -4.471496272 -0.207628231 EISDHVLR ddPTM_BT-474_Pertuzumab_2h_R1 5 EISDHVLR 8 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ;;;; 190.26 0.00018736 2762690000 1364339 1728213 1733218 2443050 1817169 1915160 2118743 1969680 1976507 2450270 FALSE TRUE 1311019.124 1678926.057 2046449.048 2569136.103 1875619.891 1953885.847 2144672.811 1929005.42 1752142.212 2284311.03 0.573923212 0.734981373 0.895871456 1.124687518 0.821087788 0.855350178 0.93887075 0.844458304 0.767033118 1 21.12332767 4.471524009 2.725721431 0.902001759 0.579355736 0.553554718 0.095635322 0.22632805 3.058579885 0.024496367 0.124257 29615.83683 -4.471524009 -0.322646022 (ac)MEDLDQSPLVSSSDS(ph)PPRPQPAFK ddPTM_BT-474_Pertuzumab_2h_R1 12 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4 1 MEDLDQSPLVSS(0.001)S(0.014)DS(0.985)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVS(0.003)S(0.008)S(0.043)DS(0.946)PPRPQPAFK;MEDLDQSPLVS(0.016)S(0.014)S(0.115)DS(0.855)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVS(0.011)S(0.058)S(0.058)DS(0.873)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK 169.01 2.76E-62 11524997000 4506003 5535512 4485137 6562427 4607851 6259513 7216522 7363533 7524308 7432373 TRUE FALSE 4329903.421 5377644.618 5295701.027 6901114.644 4756066.712 6386084.642 7304839.955 7211473.47 6670180.1 6928971.757 0.624898408 0.77611005 0.764283824 0.995979618 0.686402958 0.921649686 1.054245884 1.040771087 0.962650785 1 22.72420984 4.471870321 0.349646953 1.046109267 0.416788848 0.616596858 0.091693899 3.573316983 0.404366082 0.091553716 0.942482869 29639.4623 -4.471870321 -0.629320419 GSDALSETS(ph)SVSHIEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALSET(0.014)S(0.6)S(0.386)VSHIEDLEK 274.75 1.32E-39 162170000 342230 284230 169220 177710 217980 175490 186520 306540 257040 227450 TRUE FALSE 328855.2732 276124.0387 199801.8183 186881.6344 224991.5247 179038.528 188802.6876 300209.8419 227861.8968 212044.6089 1.550877784 1.302197873 0.942263137 0.881331694 1.06105751 0.844343692 0.890391359 1.415786251 1.074594152 1 17.69400828 4.472116521 3.415930505 1.033794414 1.526137311 0.551525566 0.155318999 0.204267717 4.795945706 0.04407018 0.18562709 29656.26961 -4.472116521 0.492342896 VISESPPDQWEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VISESPPDQWEAR 13 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 158.94 2.46E-06 0 57314 66162 69165 67928 67458 83425 64914 71022 77923 77322 FALSE TRUE 55074.10552 64275.12454 81664.65407 71433.77222 69627.84783 85111.91066 65708.43695 69555.37088 69077.50772 72084.91207 0.764017101 0.8916585 1.132895244 0.990967044 0.965914306 1.18071741 0.911542167 0.964908868 0.958279697 1 16.1374097 4.472309435 6.143451934 1.008398452 0.792093045 0.499925357 0.078767881 0.106674699 17.07886442 0.019172857 0.061004496 29669.44588 -4.472309435 -0.216305407 DVQEIFR ddPTM_BT-474_Pertuzumab_2h_R1 7 DVQEIFR 7 0 O00148;O00148-2;O00148-3;K7EQN7;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;;;;; 180.7 0.001588 10907500000 7123620 7765110 7296540 8408750 7727480 8298390 8210190 8155550 8529480 9432580 FALSE TRUE 6845221.055 7543656.666 8615187.089 8842726.595 7976041.412 8466189.131 8310668.761 7987135.042 7561249.189 8793702.955 0.778423048 0.857847565 0.97969958 1.005574857 0.90701738 0.962755869 0.945070445 0.908278922 0.859848147 1 23.06803937 4.472422469 3.726258869 0.942026203 0.788313728 0.605864434 0.043301416 0.148017158 4.361526115 0.010962782 0.043540169 29677.16891 -4.472422469 -0.153712476 AKS(ph)PAPGLASGDRPPSVSSVHSEGDCNR ddPTM_BT-474_Pertuzumab_2h_R1 4 AKSPAPGLASGDRPPSVSSVHSEGDCNR 28 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 AKS(1)PAPGLASGDRPPSVSSVHSEGDCNR;AKS(1)PAPGLASGDRPPSVSSVHSEGDCNR;AKS(1)PAPGLASGDRPPSVSSVHSEGDCNR;AKS(0.999)PAPGLAS(0.001)GDRPPSVSSVHSEGDCNR 172.4 1.24E-12 1735950000 117823 154691 165246 196472 186319 212238 173930 188127 191729 202617 TRUE FALSE 113218.3469 150279.3641 195109.6281 206611.9435 192312.1198 216529.5978 176058.6074 184242.1117 169964.7277 188893.5701 0.599376394 0.795576917 1.032907727 1.093800828 1.018097756 1.146304756 0.932051881 0.975375242 0.899790965 1 17.52721407 4.47277931 2.716284217 1.013249018 0.603232385 0.787662452 0.068887991 0.134899264 1.806258107 0.018430235 0.094108344 29701.5634 -4.47277931 -0.410016633 SLLNEIESIYDER ddPTM_BT-474_Pertuzumab_2h_R1 2 SLLNEIESIYDER 13 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 ; 196.38 3.31E-07 177989000 145740 157373 141973 167096 173651 153544 167034 168025 173959 173723 FALSE TRUE 140044.3197 152884.8761 167630.6793 175719.8446 179236.6421 156648.7649 169078.2121 164555.225 154211.9036 161956.5865 0.864702836 0.943986777 1.035034653 1.084981157 1.106695603 0.967226886 1.043972436 1.016045279 0.952180501 1 17.30524762 4.472973312 2.763493844 1.029458284 0.867116595 0.563461399 0.045202368 0.212706839 2.968163233 0.011758483 0.059119627 29714.83425 -4.472973312 -0.162341689 ENFTAGS(ph)DCVTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENFTAGSDCVTLK 13 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 ENFTAGS(1)DCVTLK 148.57 4.55E-05 60860000 195550 161360 86436 101130 132440 116530 110940 163760 142350 135710 TRUE FALSE 187907.6898 156758.1708 102056.908 106349.3314 136700.0529 118886.3164 112297.7169 160378.2988 126191.0248 126518.2408 1.48522212 1.239016365 0.806657659 0.840584968 1.080477028 0.93967728 0.887600999 1.267629851 0.997413685 1 16.94898588 4.473111066 4.693420451 0.994035412 1.441305552 0.622343556 0.125960871 0.123011613 7.191492583 0.033957652 0.119173322 29724.261 -4.473111066 0.44727014 IMDYSLLVGIHDVDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IMDYSLLVGIHDVDR 15 0 P78356 P78356 PIP4K2B Phosphatidylinositol 5-phosphate 4-kinase type-2 beta 0 ;;; 230.97 2.57E-13 2583536000 1165398 1373416 1396917 1661660 1491020 1507663 1575512 1498972 1585919 1694850 FALSE TRUE 1119852.958 1334247.52 1649370.976 1747418.472 1538980.012 1538148.979 1594793.587 1468017.704 1405892.124 1580056.3 0.70874244 0.844430366 1.043868485 1.105921651 0.974003276 0.973477324 1.009327065 0.929092023 0.889773437 1 20.59154453 4.473267623 3.557359739 0.988423517 0.723836558 0.716519761 0.056757689 0.127479957 3.321930472 0.015425033 0.063340494 29734.97811 -4.473267623 -0.264586959 AASDIAMTELPPTHPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AASDIAMTELPPTHPIR 17 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ; 167.71 2.19E-09 1790660000 959650 1022130 930450 1088480 1078190 1066040 1065010 981990 1109350 1214970 FALSE TRUE 922145.8171 992979.8532 1098603.013 1144656.583 1112870.961 1087596.059 1078043.911 961711.5633 983421.2388 1132679 0.814128113 0.876664839 0.969915583 1.010574561 0.982512222 0.960197955 0.95176472 0.849059234 0.868225895 1 20.11130763 4.473304368 3.670944352 0.942455961 0.821659413 0.424503348 0.05017095 0.251400344 7.116917695 0.014371747 0.057786969 29737.49406 -4.473304368 -0.120796548 QGSITSPQANEQS(ph)VTPQRR ddPTM_BT-474_Pertuzumab_2h_R1 2 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITSPQANEQS(0.683)VT(0.317)PQRR;QGSITS(0.002)PQANEQS(0.524)VT(0.474)PQRR 240.3 2.72E-24 1764730000 768990 789690 677510 808650 745780 792360 785880 814420 819880 873580 TRUE FALSE 738937.0206 767168.8144 799951.1281 850384.5234 769768.691 808382.0621 795497.8345 797601.9424 726810.6596 814411.6485 0.907326193 0.941991456 0.982244212 1.044170384 0.945183793 0.99259639 0.976776101 0.979359693 0.892436474 1 19.63539867 4.473642416 3.128005091 0.977649841 0.91001621 0.264030886 0.036795183 0.334486441 6.299611507 0.008944067 0.04047301 29760.65022 -4.473642416 -0.06763363 VELELS(ph)MTK ddPTM_BT-474_Pertuzumab_2h_R1 2 VELELSMTK 9 0 Q5TZA2-2;Q5TZA2;B1AKD8;A0A087WW81 Q5TZA2-2 CROCC Rootletin 1 VELELS(0.5)MT(0.5)K;VELELS(0.5)MT(0.5)K 61.999 0.08968 693810000 367790 503470 400130 827440 407100 478020 705870 609020 542460 424020 TRUE FALSE 353416.3602 489111.5285 472442.3918 870144.2776 420194.7412 487685.8919 714508.6482 596443.5242 480882.215 395300.7477 0.894044249 1.237314959 1.195146719 2.201220925 1.06297482 1.233708498 1.807506442 1.508834799 1.216497104 1 18.59259116 4.47368574 1.977641801 1.459241828 0.88868357 0.159521582 0.347636275 0.73243001 4.501109805 0.087898183 0.625489231 29763.61924 -4.47368574 -0.570558258 YVAEIEKEKEENEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YVAEIEKEKEENEK 14 2 O14818;H0Y586;O14818-2 O14818 PSMA7 Proteasome subunit alpha type-7 0 128.64 4.08E-05 429720000 736120 641690 414120 368370 571560 601410 506600 577380 715030 529660 FALSE TRUE 707351.6166 623389.6295 488960.696 387381.6198 589944.7465 613570.9223 512799.9223 565456.9012 633862.7921 493785.6564 1.43250742 1.262470105 0.990228634 0.784513715 1.194738524 1.242585552 1.038507125 1.14514647 1.283680042 1 18.9135254 4.474446133 4.142085723 1.089810034 1.406817813 0.392317349 0.137999981 0.208465946 8.269688122 0.035531483 0.133296156 29815.77708 -4.474446133 0.317007778 GEVRPELGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GEVRPELGSR 10 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ;; 142.08 3.32E-05 1919450000 361540 421380 373320 463240 481950 521400 496980 447040 430660 490970 FALSE TRUE 347410.6171 409362.655 440787.2285 487147.8719 497452.3594 531943.0652 503062.1899 437808.4678 381773.2823 457716.1646 0.759008844 0.894359183 0.963014336 1.064301219 1.086814052 1.162167969 1.099070185 0.956506459 0.834083023 1 18.80409372 4.47472034 1.594644901 1.033474068 0.730993897 0.494266023 0.085499348 0.567534781 2.010133049 0.025450771 0.229239553 29834.60828 -4.47472034 -0.302480171 SNVSSPATPTASSSSST(ph)TPTRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSSS(0.068)T(0.797)T(0.134)PTRK 203.74 7.34E-23 661840000 98367 90201 59622 81052 76792 83728 74889 98924 81230 84432 TRUE FALSE 94522.70889 87628.5558 70397.02168 85235.10343 79262.08442 85421.03753 75805.51398 96881.18483 72009.11094 78713.34544 1.200847307 1.113261739 0.894346712 1.08285454 1.006971359 1.085216707 0.963057961 1.230810154 0.91482722 1 16.26432064 4.474919108 24.97365365 1.038703665 1.17895097 0.260510303 0.092686895 80.01741375 907461.2435 0.022155836 0.061581119 29848.26611 -4.474919108 0.140247305 S(ph)SPAS(ph)SPELPWRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPASSPELPWRPR 14 1 Q9NYF3 Q9NYF3 FAM53C Protein FAM53C 2 S(0.808)S(0.192)PAS(0.874)S(0.126)PELPWRPR 97.904 0.0015873 114040000 40926 44870 36231 46676 45904 45880 48525 43772 48666 51449 TRUE FALSE 39326.56667 43590.35153 42778.74765 49084.95395 47380.54385 46807.72503 49118.86347 42868.0929 43141.6397 47964.3134 0.819913054 0.908807996 0.891887001 1.023364049 0.987829086 0.975886481 1.024071022 0.893749746 0.899452877 1 15.54967378 4.475004138 1.437308348 0.96530915 0.807489593 0.49249797 0.046509138 0.69499695 1.882202808 0.013752585 0.137565842 29854.11064 -4.475004138 -0.157819557 DQGSTYS(ph)GDLESEAVSTPHSWEEELNHYALK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQGSTYSGDLESEAVSTPHSWEEELNHYALK 31 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5;H7C1I7;Q5VZL5-3 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 DQGS(0.067)T(0.229)Y(0.023)S(0.673)GDLES(0.007)EAVSTPHSWEEELNHYALK 62.938 0.024124 37952000 5178.4 6067 6698.6 5905.4 5778.9 7026.1 6429.2 5881.5 9360.5 6796.4 TRUE FALSE 4976.022403 5893.9751 7909.18603 6210.178402 5964.783567 7168.172556 6507.882473 5760.04497 8297.935282 6336.073774 0.785347927 0.930225138 1.248278715 0.980130381 0.941400586 1.131327193 1.027115956 0.909087421 1.309633628 1 12.62937342 4.475043771 24.98268686 1.052677388 0.821567155 0.337443651 0.123885423 61.11711988 734974.2678 0.029240398 0.081256156 29856.83519 -4.475043771 -0.231110232 KPDIYER ddPTM_BT-474_Pertuzumab_2h_R1 3 KPDIYER 7 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ;; 92.062 0.025567 2636650000 2749980 2871880 2465800 2850940 2867930 3008710 2997260 3029040 2992560 3154660 FALSE TRUE 2642507.741 2789976.794 2911424.911 2998077.355 2960179.573 3069548.178 3033941.364 2966489.265 2652857.135 2940992.068 0.898508966 0.948651587 0.989946536 1.019410214 1.006524161 1.043711818 1.031604742 1.008669591 0.90202798 1 21.48787146 4.47546915 1.815414036 1.006088997 0.889862579 0.445185975 0.036309324 0.456645099 2.254224455 0.009696 0.076190359 29886.09343 -4.47546915 -0.116226418 SVS(ph)SDSLGPPRPAPAR ddPTM_BT-474_Pertuzumab_2h_R1 6 SVSSDSLGPPRPAPAR 16 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 SVS(0.412)S(0.412)DS(0.176)LGPPRPAPAR;S(0.007)VS(0.879)S(0.113)DSLGPPRPAPAR;S(0.004)VS(0.839)S(0.157)DSLGPPRPAPAR;S(0.005)VS(0.96)S(0.035)DSLGPPRPAPAR;S(0.007)VS(0.888)S(0.105)DSLGPPRPAPAR;SVS(0.978)S(0.022)DSLGPPRPAPAR 183.77 1.17E-09 8080670000 3407580 3297270 2538070 2846480 3217940 3138100 3009590 3479000 3358470 3218900 TRUE FALSE 3274408.006 3203235.088 2996755.708 2993387.174 3321447.963 3201554.532 3046422.263 3407157.434 2977230.565 3000881.036 1.091148888 1.067431547 0.998625294 0.997502779 1.10682427 1.066871527 1.015175952 1.135385706 0.992118824 1 21.5169547 4.475584324 24.96524715 1.047999897 1.085219573 0.087238317 0.047937238 116.6625219 1895058.913 0.011837436 0.032931979 29894.02025 -4.475584324 0.037219676 VYTDVNTHRPR ddPTM_BT-474_Pertuzumab_2h_R1 3 VYTDVNTHRPR 11 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1;A0A2R8YDY7;A0A2R8YCK2;V9GY80;A0A2R8Y7T1;A0A2R8YF47;A0A2R8YEL7;A0A2R8Y797;A0A2R8Y3W6;A0A2R8YCC9 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ;; 158.05 1.82E-05 2475660000 1308290 1421160 1341470 1529600 1505500 1526960 1494350 1435860 1476110 1646380 FALSE TRUE 1257160.58 1380629.908 1583903.47 1608542.839 1553925.775 1557836.177 1512638.302 1406208.989 1308548.181 1534869.216 0.819066906 0.899509804 1.031946861 1.047999935 1.012415754 1.014963465 0.985516086 0.916175121 0.852547023 1 20.5496843 4.475631037 4.205375637 0.980818905 0.831400927 0.469992125 0.055390676 0.186286737 7.73125614 0.015167312 0.056650845 29897.23579 -4.475631037 -0.149417978 ALDVDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDVDYR 7 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 81.784 0.090384 0 361060 399290 397840 404040 423350 366750 430160 433690 410760 462600 FALSE TRUE 346949.376 387902.6401 469738.5379 424892.5528 436967.4372 374165.9363 435424.4268 424734.1499 364132.2468 431267.69 0.804487292 0.899447487 1.089204104 0.98521768 1.013216263 0.867595568 1.009638415 0.984850384 0.844329996 1 18.71822411 4.475999043 24.99383778 0.975419441 0.828227298 0.378703381 0.067608918 30.13107027 671100.6117 0.016040403 0.044727882 29922.58041 -4.475999043 -0.147192143 TKGHLDAELDAYMAQTDPETND ddPTM_BT-474_Pertuzumab_2h_R1 1 TKGHLDAELDAYMAQTDPETND 22 1 X6R700;Q9Y3Y2-4;Q9Y3Y2;Q9Y3Y2-3 X6R700 CHTOP Chromatin target of PRMT1 protein 0 185.41 3.25E-17 190670000 357990 378170 289370 258320 334900 346800 290430 294320 341260 322300 FALSE TRUE 343999.355 367384.9619 341665.596 271651.9262 345672.3626 353812.5336 293984.3692 288242.1891 302521.5955 300470.3339 1.144869613 1.222699616 1.137102594 0.904089008 1.150437576 1.177529006 0.97841396 0.959303321 1.006826836 1 18.19686303 4.476158314 0.312188059 0.971110378 1.331122485 0.329713065 0.085272571 7.313902912 0.658917338 0.100626481 0.995571473 29933.55613 -4.476158314 0.360012106 EKAEELAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKAEELAAR 9 1 A0A087WTZ5;Q04323;E9PJ81;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 ; 123.79 0.00049957 1274430000 1349020 1467400 1453620 1295280 1488630 1555190 1568360 1506660 1567530 1716930 FALSE TRUE 1296298.807 1425551.189 1716321.47 1362129.556 1536513.136 1586637.007 1587554.059 1475546.944 1389590.566 1600640.802 0.809862404 0.890612802 1.072271473 0.85099015 0.959936254 0.991251132 0.99182406 0.921847639 0.86814641 1 20.61021816 4.476344789 24.99999363 0.953944326 0.830049961 0.35390483 0.061954494 22.88085357 736739.482 0.014518192 0.040536563 29946.41158 -4.476344789 -0.123894365 KPALPVS(ph)PAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KPALPVSPAAR 11 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR 134.14 9.01E-05 2405000000 3420320 3606210 3220540 3614420 3623360 3569930 3863580 3915810 3509440 4262010 TRUE FALSE 3286650.113 3503364.422 3802563.219 3800960.649 3739908.665 3642116.431 3910863.648 3834947.155 3111063.084 3973340.266 0.827175599 0.881717695 0.957019274 0.956615944 0.941250538 0.916638442 0.984276046 0.96516958 0.782984309 1 21.92192092 4.476810954 3.165201809 0.940411513 0.831036825 0.278850313 0.056702781 0.311126742 6.022418872 0.013561644 0.061319154 29978.57282 -4.476810954 -0.109374688 YISQEEGPLS(ph)PFLGQLDEDYR ddPTM_BT-474_Pertuzumab_2h_R1 3 YISQEEGPLSPFLGQLDEDYR 21 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 YISQEEGPLS(1)PFLGQLDEDYR;YISQEEGPLS(1)PFLGQLDEDYR;YISQEEGPLS(1)PFLGQLDEDYR 147.28 6.50E-08 82754000 90679 97806 83729 101949 103142 108995 94259 101335 106530 115511 TRUE FALSE 87135.16443 95016.66864 98860.69284 107210.6001 106459.6561 111198.9536 95412.56984 99242.39684 94437.16101 107687.3371 0.809149588 0.882338362 0.91803452 0.995572952 0.988599579 1.032609373 0.886014757 0.921579078 0.876956972 1 16.71648909 4.476885216 1.845758522 0.95184944 0.800480297 0.477282165 0.048494098 0.487067749 2.504168957 0.013789378 0.106851221 29983.69947 -4.476885216 -0.151369143 DSNQFHATCLDTFPPISYLNAISWR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSNQFHATCLDTFPPISYLNAISWR 25 0 P53602 P53602 MVD Diphosphomevalonate decarboxylase 0 ; 130.9 8.63E-05 233130000 78330 93069 89127 105693 110928 112469 100378 104692 110324 120149 FALSE TRUE 75268.777 90414.76324 105234.2315 111147.8284 114496.0999 114743.2002 101606.456 102530.0736 97800.48204 112011.2012 0.671975447 0.807193944 0.939497393 0.992292085 1.022184376 1.024390409 0.907109779 0.91535554 0.873131267 1 16.77328348 4.476949752 2.145495754 0.958666581 0.660227379 0.787227766 0.048323962 0.19936473 1.497095885 0.014102358 0.092670893 29988.15532 -4.476949752 -0.298439202 LGADESEEEGRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGADESEEEGRR 12 1 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 0 ; 120.03 0.00035265 194820000 224330 253240 222480 297440 252210 284850 280800 258320 269690 316680 FALSE TRUE 215562.9356 246017.8431 262687.085 312790.914 260322.5637 290609.8622 284236.5144 252985.6017 239075.9218 295230.9815 0.730150117 0.833306321 0.889768017 1.059478624 0.881758962 0.984347444 0.962759779 0.856907363 0.809792795 1 18.1714846 4.477034481 2.151266239 0.929170547 0.725282043 0.45840888 0.069897212 0.38117363 2.881277866 0.018492803 0.121197965 29994.0065 -4.477034481 -0.203888504 LKQNLEEQLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKQNLEEQLDR 11 1 Q8WZA0-2;Q8WZA0 Q8WZA0-2 LZIC Protein LZIC 0 ; 173.19 1.14E-05 536980000 874090 911670 805190 957900 865250 945070 905850 924250 992270 1033340 FALSE TRUE 839929.5964 885670.0642 950705.7444 1007337.334 893081.5521 964179.9629 916936.0633 905163.9145 879631.6695 963350.9614 0.87188328 0.919363866 0.986873717 1.045659759 0.927057311 1.000860539 0.951819327 0.939599327 0.913095751 1 19.87770196 4.477119869 3.617884955 0.967981199 0.877338073 0.408974458 0.037914148 0.229465088 6.243841073 0.009615055 0.039470898 29999.90427 -4.477119869 -0.090643126 S(ph)PS(ph)PYYSR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPSPYYSR 8 0 P62995;P62995-3;H7BXF3;H7C2L4;Q13595;Q13595-3;Q13595-4 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 2 S(1)PS(0.99)PY(0.01)YSR;S(0.993)PS(0.885)PY(0.122)YSR;S(0.998)PS(0.919)PY(0.082)Y(0.001)SR;S(0.994)PS(0.535)PY(0.469)Y(0.001)SR;S(0.999)PS(0.982)PY(0.018)YSR 83 0.027511 4281300000 2730640 2829020 2457060 3016350 2674670 2712180 2713840 3051800 3016790 3163280 TRUE FALSE 2623923.57 2748339.12 2901105.399 3172024.185 2760703.19 2767022.138 2747052.786 2988779.264 2674336.647 2949028.228 0.889758716 0.931947376 0.98374962 1.075616759 0.936139968 0.93828269 0.931511187 1.013479368 0.906853526 1 21.4918082 4.477218084 3.354178022 0.974377956 0.893821726 0.243772482 0.046655248 0.341073288 7.630337948 0.011685605 0.050598755 30006.68944 -4.477218084 -0.080556231 HLSNVS(ph)STGSIDMVDSPQLATLADEVSASLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLSNVSSTGSIDMVDSPQLATLADEVSASLAK 32 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 HLS(0.045)NVS(0.223)S(0.223)T(0.223)GS(0.223)IDMVDS(0.064)PQLAT(0.001)LADEVSASLAK;HLS(0.04)NVS(0.239)S(0.239)T(0.239)GS(0.239)IDMVDS(0.002)PQLATLADEVSASLAK 110.16 1.78E-12 0 26361 36304 31829 47812 41474 48862 52661 34497 41169 48606 TRUE FALSE 25330.78298 35268.64547 37581.20833 50279.58305 42808.04888 49850.02312 53305.48107 33784.62489 36495.66771 45313.87233 0.559007246 0.778318949 0.829353273 1.10958478 0.944700743 1.100105124 1.176361197 0.745569142 0.80539724 1 15.46766516 4.477543016 1.568861745 0.971798004 0.519653213 0.507194 0.129628919 0.59103376 2.00046708 0.038325278 0.353987095 30029.14838 -4.477543016 -0.452144791 ETGLSHLCEFIEDCEFTVLATR ddPTM_BT-474_Pertuzumab_2h_R1 6 ETGLSHLCEFIEDCEFTVLATR 22 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;;;; 271.95 2.45E-45 866740000 548431 591237 511748 608070 629910 631864 599051 601254 680677 722913 FALSE TRUE 526997.7102 574375.4996 604232.2474 639452.5656 650171.6272 644640.723 606382.3653 588837.8948 603409.4006 673949.4586 0.781954349 0.852253077 0.896554244 0.948813828 0.964718673 0.956511968 0.899744569 0.873712245 0.895333312 1 19.36228088 4.477598647 1.775403385 0.925517053 0.770612754 0.637214821 0.036249168 0.390719194 1.817551939 0.010612184 0.085978195 30032.99522 -4.477598647 -0.154904299 S(ph)PSPPTQHTGQPPGQPSAPSQLSAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSPPTQHTGQPPGQPSAPSQLSAPR 26 0 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;I3L460;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 S(0.399)PS(0.35)PPT(0.247)QHT(0.004)GQPPGQPSAPSQLSAPR 91.779 0.0062815 5210200000 46894 51272 45976 59596 46984 55312 55827 57022 50790 57076 TRUE FALSE 45061.33064 49809.77276 54284.88593 62671.7567 48495.28303 56430.44654 56510.22753 55844.47577 45024.53213 53210.19168 0.846855259 0.936094594 1.02019715 1.177814902 0.911390873 1.060519512 1.062018868 1.049507134 0.84616369 1 15.69941498 4.477599875 2.751973147 1.024821744 0.849965896 0.279067943 0.08500974 0.352236819 4.849571414 0.02068706 0.105732717 30033.08011 -4.477599875 -0.174855849 TSPGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSPGSPR 7 0 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 TSPGS(1)PR;TSPGS(1)PR;TSPGS(1)PR;TS(0.001)PGS(0.999)PR 92.491 0.016396 696210000 1897520 1763860 1166110 1837170 1452100 1609430 1768030 1610450 1560850 2081410 TRUE FALSE 1823362.821 1713556.44 1376852.017 1931986.564 1498808.115 1641973.777 1789667.68 1577193.645 1383668.852 1940434.247 0.939667409 0.883078848 0.709558708 0.995646499 0.772408608 0.846188826 0.922302667 0.812804478 0.713071754 1 20.88794812 4.477613035 24.99999815 0.841821607 0.925520311 0.077231388 0.09752388 34.82726823 1770304.457 0.021977933 0.061771807 30033.99023 -4.477613035 0.083698704 QCEGITS(ph)PEGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 QCEGITSPEGSK 12 0 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 1 QCEGIT(0.222)S(0.778)PEGSK;QCEGIT(0.472)S(0.528)PEGSK 194.77 1.15E-06 859750000 1191210 1182430 999970 1071980 1167000 1247630 1028500 1185360 1441220 1193560 TRUE FALSE 1144656.196 1148708.254 1180686.823 1127305.016 1204537.615 1272857.933 1041087.091 1160881.902 1277618.748 1112719.118 1.028701833 1.032343415 1.061082536 1.013108338 1.082517228 1.143916657 0.93562434 1.043283865 1.148195198 1 20.08565803 4.477765229 1.339016272 1.051843081 1.022499176 0.019859315 0.060531871 5.278615931 11.87339788 0.01726835 0.185919534 30044.51715 -4.477765229 -0.029343906 SLDNNYST(ph)PNER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDNNYSTPNER 12 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-27;O60716-29;O60716-25;O60716-26;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 SLDNNYS(0.05)T(0.95)PNER 149.09 0.00090375 0 243420 273430 243110 307550 256790 309340 311180 321300 296150 345110 TRUE FALSE 233906.8773 265632.0441 287045.385 323422.6924 265049.8836 315595.0667 314988.3139 314665.0427 262532.2936 321735.3923 0.727016309 0.825622703 0.892178454 1.005244372 0.823813264 0.980914983 0.979029107 0.978024334 0.815988231 1 18.29551512 4.477869262 1.578268155 0.942110495 0.700808096 0.521822168 0.06496402 0.488923772 1.67991989 0.017071158 0.156859585 30051.71506 -4.477869262 -0.241302399 AEAPAGPALGLPS(ph)PEAESGVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEAPAGPALGLPSPEAESGVDR 22 0 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(1)PEAESGVDR 204.21 1.25E-22 997770000 148620 182840 177370 233920 194870 205440 210490 214240 216200 246130 TRUE FALSE 142811.7661 177625.5822 209424.7046 245992.6392 201138.1705 209594.1376 213066.0396 209815.8691 191657.8824 229459.3959 0.622383605 0.774104636 0.912687422 1.072053024 0.876574131 0.913425823 0.928556614 0.914392145 0.835258376 1 17.80787936 4.478033484 2.434829479 0.93058293 0.61971808 0.722139523 0.061554058 0.1769336 1.811248422 0.015662632 0.090320213 30063.08081 -4.478033484 -0.31086485 TLHSDDEGTVLDDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLHSDDEGTVLDDSR 15 0 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 ;;; 280.87 9.92E-34 4622560000 1779010 1930860 1775070 2067670 2076760 2138260 2061390 1783700 2272870 2254130 FALSE TRUE 1709484.322 1875793.763 2095864.635 2174382.696 2143560.871 2181497.082 2086617.907 1746865.972 2014863.326 2101455.767 0.813476233 0.892616344 0.997339401 1.034703052 1.02003616 1.038088508 0.992939247 0.831264687 0.958794069 1 21.00295766 4.478036341 3.188814246 0.975771767 0.819385739 0.480250682 0.056722125 0.272670274 5.372149171 0.017101291 0.077131109 30063.27859 -4.478036341 -0.156386027 TSFSQEQS(ph)CDSAGEGSER ddPTM_BT-474_Pertuzumab_2h_R1 1 TSFSQEQSCDSAGEGSER 18 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 TSFS(0.001)QEQS(0.62)CDS(0.378)AGEGS(0.001)ER 76.073 0.016614 198620000 106960 112760 96884 118710 101520 118820 114190 114940 136470 126970 TRUE FALSE 102779.8849 109544.1952 114393.094 124836.6373 104785.483 121222.6218 115587.4914 112566.4488 120978.4977 118370.2088 0.868291828 0.925437205 0.966401049 1.054628851 0.885235264 1.024097389 0.976491404 0.95096942 1.022035012 1 16.85294651 4.478097584 2.24976219 0.981921835 0.86588417 0.419259767 0.044146522 0.362643134 3.059060748 0.010686804 0.066949164 30067.51832 -4.478097584 -0.116037665 LFIGGLS(ph)FETTDESLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LFIGGLSFETTDESLR 16 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 1 LFIGGLS(1)FETTDESLR;LFIGGLS(1)FETTDESLR;LFIGGLS(1)FETTDESLR 259.68 9.83E-27 132602000 97894 94068 54535.9 109409 92845 69844 89171 131092 63632.3 56592.7 TRUE FALSE 94068.19425 91385.27274 64391.75027 115055.6116 95831.44374 71256.29353 90262.30137 128384.9044 56409.02807 52759.62602 1.782957942 1.732106151 1.220473971 2.180751083 1.816378374 1.350583749 1.710821478 2.433392995 1.069170355 1 15.68714672 4.4784182 24.9837322 1.696710198 1.770245193 0 0.449165243 534.7288264 10300360 0.108348795 0.305619754 30089.7237 -4.4784182 0.073534995 AGFADPDDFTLGAGPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGFADPDDFTLGAGPR 16 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ;;; 252.21 3.71E-26 524760000 460239 510448 434468 530756 540750 558040 540860 576980 547027 611510 FALSE TRUE 442252.3511 495890.5228 512986.0323 558148.3808 558143.7148 569323.9511 547479.2065 565065.1614 484930.7883 570091.883 0.775756267 0.869843156 0.899830444 0.979049864 0.97904168 0.998652968 0.960335032 0.991182611 0.850618651 1 19.12083493 4.478622479 1.255831393 0.968278173 0.742730871 0.666664311 0.042311475 0.519526661 0.990558085 0.01182783 0.134858296 30103.88033 -4.478622479 -0.225547303 TLHCEGTEINS(ph)DDEQESKEVEETATAK ddPTM_BT-474_Pertuzumab_2h_R1 3 TLHCEGTEINSDDEQESKEVEETATAK 27 1 Q9BPX3;H0Y9Z8 Q9BPX3 NCAPG Condensin complex subunit 3 1 TLHCEGTEINS(1)DDEQESKEVEETATAK;T(0.001)LHCEGT(0.006)EINS(0.986)DDEQES(0.008)KEVEETATAK;TLHCEGTEINS(0.999)DDEQESKEVEETATAK 161.32 7.96E-12 968120000 578430 479730 302982 265959 393670 458600 359366 321752 517080 395780 TRUE FALSE 555824.3161 466048.5701 357737.5872 279685.1759 406332.7531 467873.2062 363764.0286 315107.7088 458383.2462 368973.4681 1.506407274 1.263095074 0.969548269 0.758008909 1.101251955 1.268040243 0.985881263 0.854011836 1.242320345 1 18.49315755 4.478641301 3.003471854 1.009878322 1.492738507 0.515143008 0.14893779 0.216022456 3.672571863 0.038957677 0.184804214 30105.18503 -4.478641301 0.482860185 SILPYPVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 SILPYPVSPK 10 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 SILPYPVS(1)PK;SILPYPVS(1)PK 120.87 0.00055597 1390790000 1669380 1485910 1011450 1166510 1391240 1077620 1254970 1494470 1356660 1255840 TRUE FALSE 1604138.784 1443533.302 1194241.515 1226713.721 1435990.498 1099410.215 1270328.698 1463608.672 1202657.644 1170780.838 1.370144379 1.232966286 1.020038487 1.047773999 1.226523745 0.939040151 1.085026896 1.250113279 1.027226963 1 20.15903961 4.478849772 3.770308995 1.092114703 1.353281953 0.502369228 0.093531427 0.187560397 5.698320643 0.023584715 0.094763781 30119.63966 -4.478849772 0.261167249 AGDLLEDS(ph)PKRPK ddPTM_BT-474_Pertuzumab_2h_R1 9 AGDLLEDSPKRPK 13 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK 193.77 8.28E-07 1.07175E+11 33787162 27738037 17247044 14596580 21322462 22239091 19797192 24224387 28398694 20861537 TRUE FALSE 32466722.36 26946975.34 20363968.51 15349911.24 22008318.35 22688780.66 20039475.96 23724144.94 25174993.31 19448566.52 1.669363258 1.38555072 1.047067839 0.78925669 1.131616479 1.166604266 1.030383187 1.219840286 1.294439531 1 24.21316049 4.478999409 2.993496805 1.091385556 1.653709148 0.667709264 0.131908585 0.168913707 2.847805465 0.035311145 0.168142673 30130.01921 -4.478999409 0.562323592 VEVNGEHATVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEVNGEHATVR 11 0 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8YFL4;A0A2R8YER9;A0A2R8Y897;A0A2R8Y6L2;A0A2R8Y809;A0A2R8Y4V6;A0A2R8Y784;A0A2R8YFM3;A0A2R8YH53;A0A2R8Y4P2;A0A2R8Y6G3;A0A2R8Y787;A0A2R8Y5H6;A0A2R8YF12;A0A2R8Y597;A0A2R8Y3S1 Q15813-2 TBCE Tubulin-specific chaperone E 0 75.479 0.037977 174380000 34513 44893 44383 63825 42930 49615 49092 71019 37924 57909 FALSE TRUE 33164.1938 43612.69559 52403.99539 67119.0159 44310.88244 50618.24929 49692.80258 69552.43283 33619.02651 53986.77185 0.61430222 0.807840404 0.970682143 1.243249292 0.820772958 0.937604668 0.920462567 1.288323611 0.622727112 1 15.72031833 4.479007761 2.45381544 1.001033752 0.612329578 0.276269617 0.181188491 0.403737068 4.20814577 0.045092939 0.25868448 30130.5987 -4.479007761 -0.388704174 ECFGACLFTCYDLLRPDVVLETAWR ddPTM_BT-474_Pertuzumab_2h_R1 2 ECFGACLFTCYDLLRPDVVLETAWR 25 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 267.81 1.11E-45 2200700000 266540 290910 279560 286640 312550 295540 286230 314100 323770 346840 FALSE TRUE 256123.3221 282613.5316 330082.7108 301433.5248 322603.4546 301516.0213 289732.9684 307613.7252 287016.987 323348.2179 0.792097522 0.874022234 1.02082737 0.932225719 0.997696714 0.932480851 0.896040097 0.951338861 0.887640541 1 18.30272913 4.479205157 5.246957128 0.948283864 0.808165516 0.591953077 0.042020573 0.103840967 9.002132544 0.009921469 0.034089413 30144.29678 -4.479205157 -0.140118347 LIFPYVELDLHSYDLGIENR ddPTM_BT-474_Pertuzumab_2h_R1 3 LIFPYVELDLHSYDLGIENR 20 0 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;; 328.83 9.06E-80 6173190000 1826007 2103924 1771666 2414294 2376549 2125865 2351038 2161121 2198391 2594187 FALSE TRUE 1754644.628 2043922.147 2091845.457 2538896.003 2452992.857 2168851.447 2379810.706 2116493.096 1948838.87 2418480.404 0.725515338 0.845126611 0.864942074 1.049789777 1.014270305 0.896782725 0.984010746 0.875133449 0.805811313 1 21.20566942 4.480014775 1.794282446 0.939154075 0.714070264 0.472779157 0.071276577 0.495646494 2.362290187 0.019787763 0.15961746 30200.54465 -4.480014775 -0.225083811 GTQEVAPPTPLT(ph)PTSHTANT(ph)SPRPVSGMER ddPTM_BT-474_Pertuzumab_2h_R1 1 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 2 GTQEVAPPTPLT(1)PT(0.002)S(0.006)HT(0.147)ANT(0.456)S(0.389)PRPVSGMER 157.08 3.33E-09 502510000 187970 256310 263670 338810 304640 348620 368020 272490 299230 363810 TRUE FALSE 180623.9246 249000.2898 311321.0343 356296.0247 314439.0223 355669.3353 372523.9388 266862.9863 265262.6649 339168.8247 0.532548723 0.734148517 0.917894015 1.050497566 0.927087042 1.048649845 1.098343691 0.786814609 0.782096247 1 18.37164404 4.480213044 2.17264771 0.951304357 0.516842908 0.645226936 0.100181307 0.269984556 2.084806414 0.028144252 0.184161082 30214.3353 -4.480213044 -0.434461449 GKGEKEPPS(ph)PGMER ddPTM_BT-474_Pertuzumab_2h_R1 2 GKGEKEPPSPGMER 14 2 P56182 P56182 RRP1 Ribosomal RNA processing protein 1 homolog A 1 GKGEKEPPS(1)PGMER;GKGEKEPPS(1)PGMER 79.467 0.0099177 516010000 859100 713450 467310 465600 527010 561350 571440 615370 592530 517170 TRUE FALSE 825525.4222 693103.1045 551763.3123 489629.6718 543961.7553 572700.8816 578433.4537 602662.3945 525268.4785 482141.6153 1.712205286 1.437550883 1.144400929 1.015530824 1.12821988 1.18782711 1.19971692 1.249969667 1.089448539 1 18.87909743 4.480648273 2.472931592 1.142261724 1.718532998 0.858605461 0.07643628 0.126025441 1.336612063 0.021027833 0.120233563 30244.62978 -4.480648273 0.576271274 GNLELRPGGAHPGTCS(ph)PSRPGS ddPTM_BT-474_Pertuzumab_2h_R1 3 GNLELRPGGAHPGTCSPSRPGS 22 2 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 GNLELRPGGAHPGT(0.126)CS(0.856)PS(0.018)RPGS;GNLELRPGGAHPGT(0.007)CS(0.987)PS(0.007)RPGS;GNLELRPGGAHPGTCS(0.981)PS(0.018)RPGS 146.45 4.45E-08 2917910000 1527630 1719560 1601640 2005870 1815490 1952110 1904640 1780820 1784260 2002530 TRUE FALSE 1467928.531 1670519.832 1891091.976 2109393.191 1873886.885 1991583.002 1927949.554 1744045.445 1581718.285 1866896.859 0.786293321 0.894810993 1.012960072 1.129892731 1.003744195 1.066787912 1.032702768 0.934194857 0.847244601 1 20.83221079 4.480937923 2.839273333 1.005396244 0.790323792 0.486119637 0.071143768 0.258218118 3.823822535 0.019284943 0.096678703 30264.808 -4.480937923 -0.215072453 RLDGESSELQEQMVEQQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLDGESSELQEQMVEQQQR 19 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 221.37 4.30E-19 231400000 189030 169240 122280 109530 139950 149590 136340 176890 187420 139680 FALSE TRUE 181642.4986 164413.4409 144378.7161 115182.8564 144451.6188 152614.8123 138008.5697 173237.1597 166144.8673 130219.3492 1.394896379 1.262588409 1.108734739 0.884529505 1.109294585 1.171982607 1.059816153 1.330348837 1.275884639 1 16.99058431 4.481014811 3.161473084 1.130689285 1.384980334 0.346521148 0.121260249 0.330547008 6.36283159 0.033192901 0.151977235 30270.16657 -4.481014811 0.254291049 EFKEEISR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFKEEISR 8 1 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ; 66.962 0.055019 790800000 914460 1141700 829570 1203670 1208680 1340610 1297450 1451980 1571150 1569420 FALSE TRUE 878721.8922 1109139.834 979491.7527 1265791.553 1247558.29 1367718.053 1313328.581 1421996.106 1392799.639 1463121.786 0.600580144 0.758063918 0.669453331 0.865130685 0.852668795 0.934794401 0.897620823 0.971891827 0.951936915 1 20.48061843 4.481569065 0.3766791 0.995489352 0.390255357 0.892147837 0.041631762 1.378457593 0.180378503 0.034683984 0.374131165 30308.82256 -4.481569065 -0.605233995 AENLQLLTENELHR ddPTM_BT-474_Pertuzumab_2h_R1 4 AENLQLLTENELHR 14 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ;;; 230.36 9.43E-13 1812400000 1096458 1237225 1061799 1317029 1373161 1374636 1308053 1316549 1397425 1454410 FALSE TRUE 1053607.209 1201940.554 1253689.699 1385001.025 1417329.971 1402432.082 1324061.344 1289361.803 1238795.172 1355901.515 0.777052903 0.886451221 0.924617079 1.021461374 1.045304511 1.034317069 0.976517342 0.950925852 0.913632117 1 20.37082096 4.481690655 1.538717302 0.989096364 0.753932393 0.744983096 0.039223104 0.375816145 1.203917449 0.012160666 0.115974135 30317.3093 -4.481690655 -0.235163971 S(ph)TDSPGADAELPESAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 STDSPGADAELPESAAR 17 0 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 S(0.814)T(0.132)DS(0.054)PGADAELPESAAR;S(0.575)T(0.223)DS(0.201)PGADAELPESAAR 236.78 3.54E-20 817680000 162443 213057 206598 283699 242526 306881 265532 227605 218991 280663 TRUE FALSE 156094.548 206980.823 243934.8543 298340.7394 250327.069 313086.3441 268781.66 222904.8772 194132.0598 261653.445 0.596569818 0.791049485 0.932282219 1.140213305 0.956712299 1.196568782 1.027242963 0.851908819 0.74194345 1 17.99729773 4.481694977 2.130210986 0.985569444 0.582328894 0.503282696 0.12244572 0.364794161 2.677944303 0.03413878 0.22920329 30317.61104 -4.481694977 -0.40324055 GVAPADS(ph)PEAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVAPADSPEAPR 12 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPR 207.47 8.20E-08 149910000 91534 100030 91285 110110 100980 113420 91707 117440 104510 110140 TRUE FALSE 87956.75008 97177.24234 107782.2301 115792.7903 104228.1134 115713.4301 92829.3377 115014.823 92646.46294 102680.1197 0.856609345 0.946407568 1.04968937 1.127704084 1.015075885 1.126931196 0.904063396 1.120127473 0.902282382 1 16.64779736 4.481889893 2.898820973 1.038618727 0.860352572 0.326919972 0.078474421 0.286107022 4.45194571 0.018139916 0.089511918 30331.22095 -4.481889893 -0.178266155 YVIS(ph)DEEEEDDD ddPTM_BT-474_Pertuzumab_2h_R1 2 YVISDEEEEDDD 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 YVIS(1)DEEEEDDD;YVIS(1)DEEEEDDD 255.13 4.14E-21 400580000 630610 678850 577050 744480 700120 741030 678910 683230 711700 741180 TRUE FALSE 605965.064 659489.8627 681335.7714 782902.702 722639.9956 756014.1343 687218.7037 669121.0617 630910.7997 690979.2184 0.876965686 0.954427926 0.986043796 1.133033644 1.045820158 1.09411993 0.994557702 0.968366405 0.913067691 1 19.3982828 4.481908213 2.172760675 1.020266427 0.874313812 0.36027851 0.059067934 0.477283916 3.679670712 0.016655619 0.109513591 30332.50048 -4.481908213 -0.145952614 EDTLLLIGHLER ddPTM_BT-474_Pertuzumab_2h_R1 4 EDTLLLIGHLER 12 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ;;; 150.21 6.48E-05 548060000 755419 833014 769578 862331 929118 864205 921262 855052 989488 1002609 FALSE TRUE 725896.3903 809257.2563 908657.8638 906836.0063 959003.9243 881679.8172 932536.6799 837394.8774 877165.4705 934701.3994 0.776607792 0.865792281 0.972137053 0.97018792 1.026000309 0.94327431 0.997684052 0.895895607 0.938444589 1 19.83414603 4.482092675 2.555548308 0.963860097 0.775155368 0.752471481 0.035324162 0.167301591 1.919172893 0.009537277 0.052980462 30345.38661 -4.482092675 -0.188704729 RPAEATSSPTS(ph)PERPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEAT(0.004)S(0.002)S(0.008)PT(0.097)S(0.889)PERPR;RPAEAT(0.018)S(0.004)S(0.018)PT(0.026)S(0.934)PERPR 125.45 6.06E-05 119702000 17800.3 18603.3 15519.8 19527.3 17996.4 19031.6 17932 19349.5 20929.3 18399 TRUE FALSE 17104.6446 18072.7521 18324.5731 20535.10629 18575.27055 19416.43199 18151.45718 18949.92606 18553.49361 17152.81934 0.997191439 1.053631577 1.068312604 1.197185482 1.082928129 1.131967381 1.058220041 1.10477034 1.081658545 1 14.06615811 4.482383284 2.1336135 1.098308675 0.995488403 0.258626596 0.048373672 0.492231298 3.625264167 0.01175725 0.078956995 30365.69907 -4.482383284 -0.102820271 KELNSNHDGADETSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KELNSNHDGADETSEK 16 1 Q01105-2 Q01105-2 SET Protein SET 0 ; 151.62 4.06E-07 692100000 311240 386350 367810 488620 414460 468170 453810 395870 521750 528810 FALSE TRUE 299076.3967 375331.6763 434281.4489 513837.7368 427791.4823 477636.7182 459363.8625 387695.1462 462523.1274 492993.2277 0.606654169 0.761332317 0.880907535 1.042281532 0.867743122 0.968850466 0.931785341 0.786410694 0.938193674 1 18.9112083 4.482484681 2.170850862 0.91784214 0.596027851 0.698163699 0.067819365 0.240859356 1.851784135 0.018485321 0.121863011 30372.78956 -4.482484681 -0.321814289 AVGS(ph)MPQAGRAGGNS(ph)TLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVGSMPQAGRAGGNSTLQR 19 1 Q6NSZ9-4 Q6NSZ9-4 2 AVGS(1)MPQAGRAGGNS(0.555)T(0.445)LQR 79.88 0.0054353 360800000 204700 156690 116250 100030 93120 93908 78056 131280 110610 102520 TRUE FALSE 196700.0977 152221.3546 137258.961 105192.5603 96115.28937 95806.8841 79011.27268 128569.0221 98054.01651 95576.22908 2.058044135 1.592669601 1.436120281 1.100614256 1.005640108 1.002413309 0.826683302 1.345198731 1.025924725 1 16.54436423 4.482790836 1.06822871 1.049586446 2.291001549 0.865429127 0.129601525 0.43224612 0.545460279 0.042684464 0.552963965 30394.20835 -4.482790836 1.241415103 up SVSDNDIR ddPTM_BT-474_Pertuzumab_2h_R1 5 SVSDNDIR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;; 161.02 0.00081417 8804080000 13097040 14261450 12465710 15188820 14858870 14812050 14947200 15451830 15518110 16499910 FALSE TRUE 12585193.2 13854727.41 14718541.1 15972716.82 15336819.05 15111559.8 15130128.3 15132744.31 13756559.21 15382356.4 0.818157691 0.900689534 0.956845669 1.038379063 0.997039637 0.982395636 0.983602766 0.983772832 0.894307663 1 23.87477319 4.483058543 2.014138651 0.983247812 0.809863685 0.694840418 0.034276575 0.244223138 1.555720773 0.008978604 0.064356573 30412.94967 -4.483058543 -0.173384126 EVDDLEQWIAER ddPTM_BT-474_Pertuzumab_2h_R1 4 EVDDLEQWIAER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 284.47 6.19E-28 1247700000 519566 552157 485966 565860 565365 605420 604952 625410 634940 629150 FALSE TRUE 499260.7863 536410.023 573790.8665 595064.1024 583550.4787 617662.0072 612355.5835 612495.0649 562864.2731 586537.1101 0.851200679 0.914537228 0.978268649 1.014537856 0.994908026 1.053065521 1.044018482 1.044256287 0.95963966 1 19.16186286 4.483207136 1.109727509 1.024172616 0.806080455 0.804336018 0.02667889 0.444903863 0.617136635 0.008116846 0.102743074 30423.35719 -4.483207136 -0.21809216 RPLS(ph)SSHEASEGQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.571)S(0.147)S(0.279)HEAS(0.004)EGQAK 159.26 1.09E-06 235960000 390550 312040 177190 208250 181050 179440 145600 429510 192040 170270 TRUE FALSE 375286.8742 303140.9247 209212.1746 218997.8075 186873.6377 183068.3997 147381.8964 420640.4684 170240.4243 158737.4612 2.364198541 1.909699968 1.317976065 1.379622716 1.177249757 1.153277861 0.928463232 2.64991304 1.072465333 1 17.27628311 4.483523505 2.921208632 1.425787841 2.347626757 0.322725684 0.470476406 0.385355814 6.101579977 0.127153309 0.626045244 30445.52767 -4.483523505 0.921838916 RLS(ph)LESEGAGEGAAASPELSALEEAFR ddPTM_BT-474_Pertuzumab_2h_R1 6 RLSLESEGAGEGAAASPELSALEEAFR 27 1 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 RLS(0.75)LES(0.25)EGAGEGAAASPELSALEEAFR;RLS(0.981)LES(0.019)EGAGEGAAASPELSALEEAFR;RLS(0.981)LES(0.019)EGAGEGAAASPELSALEEAFR;RLS(0.863)LES(0.135)EGAGEGAAAS(0.001)PELSALEEAFR;RLS(0.997)LES(0.003)EGAGEGAAASPELSALEEAFR;RLS(0.786)LES(0.214)EGAGEGAAASPELSALEEAFR 197.63 3.60E-25 853905000 112877.5 134364 119701.6 148753 162974 154877 139296 161878 163220 141353 TRUE FALSE 108466.1225 130532.0703 141334.3419 156430.1602 168216.2067 158008.7191 141000.7461 158535.1627 144691.9499 131779.0354 0.823090882 0.990537454 1.072510065 1.187064086 1.276502034 1.199042917 1.069978587 1.203037814 1.097989141 1 17.00776135 4.483805872 1.562840691 1.159583004 0.78489436 0.637310612 0.075900305 0.384555793 1.279117644 0.020227096 0.191066398 30465.32899 -4.483805872 -0.374688643 LYEHIVADDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LYEHIVADDR 10 0 P48449-2;P48449;A0A0G2JQD0;P48449-3 P48449-2 LSS Lanosterol synthase 0 ; 131.82 0.00024004 1662140000 441390 567980 459570 882910 496540 501960 697100 634850 653160 668570 FALSE TRUE 424139.9908 551781.7665 542624.5221 928477.0909 512511.66 512109.9751 705631.3183 621740.1256 579016.0151 623287.1584 0.680488897 0.885276969 0.870585114 1.489645789 0.822272131 0.821627669 1.132112717 0.997517945 0.928971514 1 19.24953746 4.484304712 2.055873547 1.018701104 0.676955317 0.236441524 0.184095392 0.635084165 4.253905525 0.047397124 0.333367153 30500.34221 -4.484304712 -0.341745787 YGVQADR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGVQADR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 130 0.0083885 1113460000 808270 882190 804520 1022550 914050 734810 965870 1016490 909630 1003940 FALSE TRUE 776681.9148 857030.805 949914.6605 1075323.928 943451.2484 749668.3617 977690.606 995499.1263 806372.6159 935942.2496 0.829839571 0.915687699 1.01492871 1.148921238 1.00802293 0.800977156 1.044605697 1.063633068 0.861562363 1 19.83605999 4.485266246 3.139708184 1.000027233 0.835753564 0.229018853 0.093593672 0.376806778 7.108064909 0.02405519 0.11206309 30567.94521 -4.485266246 -0.164273669 LIDLHTNVATAVLEHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LIDLHTNVATAVLEHIK 17 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 ; 279.54 4.09E-36 352700000 625810 644990 590730 653350 626030 460880 759510 510820 786400 807860 FALSE TRUE 601352.6533 626595.5167 697488.0517 687069.4718 646166.8235 470199.3094 768805.1106 500271.3885 697131.1689 753142.9226 0.798457551 0.831974248 0.926103175 0.912269705 0.857960427 0.624316176 1.020795771 0.664244957 0.925629317 1 19.52256414 4.485287892 23.67323207 0.848074624 0.806836668 0.0128555 0.123760752 1058.536393 3068397.068 0.028423043 0.08731691 30569.46878 -4.485287892 -0.041237955 DEDEEKLVASLWGAER ddPTM_BT-474_Pertuzumab_2h_R1 2 DEDEEKLVASLWGAER 16 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3;Q8WVX6;F6QZY1 Q7Z5K2 WAPAL Wings apart-like protein homolog 0 ; 139.88 1.60E-06 54838000 92260 80749 55536 54384 66108 74511 69921 66226 85705 74576 FALSE TRUE 88654.3772 78446.11758 65572.59059 57190.76476 68234.42386 76017.66347 70776.71411 64858.40996 75976.1277 69524.90109 1.275145679 1.128316853 0.943152591 0.822593975 0.981438633 1.093387582 1.018005247 0.932880291 1.092790159 1 16.08524217 4.48552588 3.183051079 0.980811439 1.264891875 0.597477539 0.07536364 0.176843805 3.450436111 0.019822757 0.091418139 30586.22511 -4.48552588 0.284080436 VNIAFNYDMPEDSDTYLHR ddPTM_BT-474_Pertuzumab_2h_R1 9 VNIAFNYDMPEDSDTYLHR 19 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;H0Y400 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;;;;;;; 231.77 2.61E-20 8654670000 4983860 5523047 5239387 5958604 5784838 6232552 5832346 5619795 6352960 6281335 FALSE TRUE 4789085.241 5365535.107 6186260.78 6266128.267 5970912.568 6358578.472 5903723.995 5503744.269 5631798.615 5855894.586 0.817822994 0.916262243 1.056416008 1.070054827 1.019641402 1.085842373 1.008167737 0.939863959 0.961731557 1 22.48145815 4.485845856 3.475614314 1.015132527 0.82718192 0.680007769 0.043689526 0.15392342 3.750198101 0.012575185 0.054408198 30608.76844 -4.485845856 -0.187950607 SCTWPLQRPELQASPAKPSGETAADSMIPEEEDDEDDEDGGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCTWPLQRPELQASPAKPSGETAADSMIPEEEDDEDDEDGGGR 43 2 O43524;A0A2Z4LIS9 O43524 FOXO3 Forkhead box protein O3 0 151.96 3.79E-14 128420000 27725 36814 39205 44067 42754 49628 49743 38643 60591 42429 FALSE TRUE 26641.47635 35764.10076 46290.21561 46341.30315 44129.22124 50631.51216 50351.76971 37845.00855 53712.9637 39555.24604 0.67352574 0.90415569 1.170267417 1.171558966 1.115635109 1.280020155 1.272947959 0.956763321 1.357922629 1 15.27158143 4.486326608 2.326712121 1.163187605 0.658178397 0.646859377 0.117198471 0.220281092 2.00237389 0.029189983 0.180650016 30642.67031 -4.486326608 -0.505009208 SVVLFGVETHVCIQQTALELVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVVLFGVETHVCIQQTALELVGR 23 0 Q96CN7 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ;;; 269.11 1.22E-44 370240000 178713 196515 172151 223694 195043 204973 225558 179127 237920 234674 FALSE TRUE 171728.6984 190910.5846 203262.5152 235238.8741 201316.7352 209117.6945 228318.4463 175427.9649 210912.319 218779.321 0.784940266 0.872617137 0.929075537 1.075233588 0.920181735 0.955838484 1.043601586 0.801848932 0.964041383 1 17.73911686 4.486367336 2.319543249 0.953385955 0.782365439 0.388453689 0.070535412 0.421518623 3.802530634 0.018828778 0.116920989 30645.54405 -4.486367336 -0.171020515 SVYAHFPINVVIQENGSLVEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVYAHFPINVVIQENGSLVEIR 22 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 276.73 1.77E-45 1609440000 802200 893530 819650 999110 943640 910020 940700 973660 1042330 1051990 FALSE TRUE 770849.1371 868047.3993 967778.988 1050674.187 973993.0376 928421.2279 952212.568 953553.5807 924009.0682 980737.7803 0.785989031 0.885096319 0.98678669 1.071309995 0.993122787 0.946655922 0.970914537 0.972281888 0.942157105 1 19.90350793 4.486968506 2.651393841 0.984948372 0.786548147 0.776040328 0.034208889 0.151177147 1.887818663 0.009431156 0.051234367 30687.99435 -4.486968506 -0.198400225 SPSGSAFGS(ph)QENLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSGSAFGSQENLR 14 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SPSGS(0.003)AFGS(0.997)QENLR;SPSGSAFGS(1)QENLR;SPSGSAFGS(1)QENLR 178.03 2.13E-06 1114840000 542001 596450 549950 646310 564368 605300 617490 674940 717330 731620 TRUE FALSE 520819.0017 579439.83 649338.1986 679666.1366 582521.4093 617539.5807 625047.0273 661002.2531 635901.7057 682066.7257 0.763589517 0.849535402 0.952015652 0.996480419 0.854053405 0.905394674 0.916401583 0.969116698 0.932315977 1 19.37955336 4.487096989 2.883535536 0.937565083 0.766405291 0.648111651 0.041722722 0.177458014 2.714776897 0.010629011 0.053456745 30697.07455 -4.487096989 -0.171159792 NLQS(ph)PTQFQTPR ddPTM_BT-474_Pertuzumab_2h_R1 4 NLQSPTQFQTPR 12 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 NLQS(1)PTQFQTPR;NLQS(0.999)PT(0.001)QFQTPR;NLQS(0.981)PT(0.019)QFQTPR;NLQS(0.985)PT(0.015)QFQTPR 257.22 3.57E-21 1629960000 1202610 1310140 1246610 1329030 1307960 1340170 1316090 1470260 1430560 1471750 TRUE FALSE 1155610.672 1272776.09 1471900.158 1397621.398 1350031.721 1367269.156 1332196.703 1439898.617 1268168.826 1372067.062 0.842240663 0.927634024 1.072761091 1.018624699 0.983940041 0.996503155 0.970941392 1.049437493 0.924276124 1 20.38791957 4.487118016 4.673451076 1.004471166 0.856816463 0.621384777 0.039155819 0.10669104 6.112419599 0.009221446 0.034124484 30698.56087 -4.487118016 -0.147654702 EIES(ph)SPQYR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIESSPQYR 9 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 EIES(0.5)S(0.5)PQYR 111.86 0.0021578 282030000 276870 308300 289100 322630 275860 358570 366180 328010 346290 391080 TRUE FALSE 266049.6143 299507.5859 341346.801 339280.973 284733.2874 365820.5311 370661.4204 321236.4789 306980.611 364591.8033 0.729719132 0.821487437 0.936243761 0.930577621 0.780964588 1.003370147 1.016647706 0.881085301 0.841984401 1 18.4759226 4.487193134 2.675471811 0.92065942 0.729418779 0.435046415 0.07101171 0.297600234 3.797700702 0.018102569 0.097555115 30703.87106 -4.487193134 -0.191240642 S(ph)PATSAGPELAGLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPATSAGPELAGLPR 15 0 A1L020 A1L020 MEX3A RNA-binding protein MEX3A 1 S(0.995)PAT(0.002)S(0.003)AGPELAGLPR 66.267 0.061974 211050000 41824 51234 53300 58011 51638 48079 63271 68539 59398 70809 TRUE FALSE 40189.47184 49772.85648 62932.49565 61004.95466 53298.98317 49051.19032 64045.32942 67123.6457 52655.38806 66013.04336 0.608811074 0.753985182 0.953334257 0.924134861 0.807400787 0.743053006 0.970192043 1.016823983 0.797651273 1 16.01046349 4.487237734 3.182548218 0.903360159 0.618131049 0.530226914 0.087711295 0.208666147 4.063999758 0.023402251 0.108458494 30707.02441 -4.487237734 -0.28522911 NNIIQTWR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNIIQTWR 8 0 P41250 P41250 GARS Glycine--tRNA ligase 0 127.02 0.0027782 226970000 329010 296660 246940 235570 257800 207340 326800 291790 285850 288220 FALSE TRUE 316151.9255 288199.5473 291567.5512 247727.7959 266092.3711 211532.5569 330799.4762 285764.4345 253401.5064 268698.6027 1.176604278 1.072575534 1.085110039 0.921954165 0.990300539 0.787248444 1.231117218 1.063512916 0.943069684 1 18.03562929 4.487330947 1.580645053 1.005824794 1.189092073 0.209148443 0.108358637 1.176564066 4.012468001 0.030566667 0.288409351 30713.61578 -4.487330947 0.183267279 AEAGVPAEFSIWTR ddPTM_BT-474_Pertuzumab_2h_R1 3 AEAGVPAEFSIWTR 14 0 Q60FE5;P21333-2;P21333;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ;; 234.92 7.40E-17 312410000 450657 481913 418329 488934 490013 534678 498073 510145 534118 569682 FALSE TRUE 433044.8262 468169.3131 493930.356 514167.9423 505774.7132 545489.5555 504168.5664 499610.3275 473487.1638 531096.9307 0.815378138 0.881513874 0.930019225 0.968124485 0.952320912 1.027099808 0.949296705 0.940714018 0.891526831 1 19.01861567 4.487483967 1.529300695 0.959509655 0.795598418 0.6542476 0.033994215 0.432954081 1.355638096 0.009532687 0.093060194 30724.43936 -4.487483967 -0.163911237 QLHDEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLHDEAR 7 0 P18206;P18206-2 P18206 VCL Vinculin 0 ; 125.49 0.0040439 790400000 129690 142584 134036 141424 164128 189173 155590 155153 170795 171457 FALSE TRUE 124621.5714 138517.6439 158259.2868 148722.9096 169407.3262 192998.2077 157494.157 151949.0363 151407.0676 159844.0647 0.77964466 0.86657984 0.990085476 0.930424973 1.059828693 1.20741554 0.985298749 0.950607936 0.947217327 1 17.28630565 4.487555652 1.276186288 1.016300464 0.727742893 0.519517614 0.074442452 0.810010824 1.592451666 0.023654992 0.272955823 30729.5112 -4.487555652 -0.288557571 ELGTVMR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELGTVMR 7 0 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479;P27482;C9J7T9;P02585 P0DP25 CALM2;CALM3;CALM1;CALML3;TNNC2 "Calmodulin-like protein 3;Troponin C, skeletal muscle" 0 ;; 138.37 0.019389 0 2186000 2394110 1952410 2620280 2583880 2318870 2416420 2476650 2534040 2573690 FALSE TRUE 2100568.703 2325832.327 2305253.918 2755512.965 2666992.847 2365759.14 2445992.871 2425506.312 2246386.403 2399371.684 0.875466155 0.969350577 0.960773995 1.148431059 1.111538018 0.985991106 1.019430581 1.01089228 0.93623944 1 21.19422523 4.488224828 1.825337362 1.029051262 0.869559378 0.364583489 0.06027922 0.589658386 2.908493261 0.016824479 0.136491085 30776.89676 -4.488224828 -0.159491884 EELVAAVEDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EELVAAVEDVR 11 0 P35221-2;P35221;G3XAM7;P26232;P26232-5;P26232-2;P26232-3;E5RIB1;E5RJL0;E5RHV7;E5RG03;E5RIE0;E5RGY6;C9IZ88 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 0 ; 103.7 0.0062791 40215000 45811 57478 59231 76513 54877 58413 67144 72224 67888 84246 FALSE TRUE 44020.65547 55838.78372 69935.35929 80461.8451 56642.16854 59594.15088 67965.72836 70732.54916 60181.63885 78539.94338 0.560487487 0.710960326 0.89044321 1.024470373 0.721189322 0.758775068 0.865365131 0.90059333 0.766255185 1 16.26113894 4.488388522 3.041777468 0.860720685 0.568441608 0.517092541 0.094098937 0.216609499 3.770095439 0.023570596 0.113653492 30788.4994 -4.488388522 -0.292279077 RPTELLSNPQFIVDGATR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPTELLSNPQFIVDGATR 18 1 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;; 201.8 2.19E-15 6701030000 1581974 1805141 1594785 1971211 1926091 2128901 1858242 2039550 2205912 2116336 FALSE TRUE 1520148.707 1753660.146 1882998.125 2072945.436 1988045.466 2171948.837 1880983.721 1997432.58 1955506.118 1972994.678 0.770477855 0.888831666 0.954385811 1.050659416 1.007628398 1.10083867 0.953364823 1.012386198 0.991136033 1 20.91195563 4.488564988 1.523320589 1.015918451 0.73838051 0.808106848 0.037940204 0.277778014 0.859879652 0.010263318 0.100911428 30801.01215 -4.488564988 -0.277537941 AS(ph)GQAFELILSPR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR 224.67 1.44E-11 728825000 220261 236011 209184 249515 245994 253540 242931 259319 234862 233943 TRUE FALSE 211652.9566 229280.1974 246988.2021 262392.4991 253906.6204 258666.7525 245904.0622 253963.972 208201.4504 218097.8322 0.970449612 1.051272243 1.132465186 1.203095402 1.164186814 1.186012487 1.127494298 1.164449777 0.954624116 1 17.7346159 4.488672701 2.641536285 1.1317657 0.970742195 0.244262409 0.07687132 0.370671407 4.580278451 0.018614341 0.101970118 30808.65228 -4.488672701 -0.161023505 EDGSFAGDIWGEIDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDGSFAGDIWGEIDTR 16 0 P53611 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 0 ; 111.94 0.0018099 37882000 40551 45841 43781 49635 50954 52862 52834 53947 57482 64594 FALSE TRUE 38966.22209 44533.65956 51693.2006 52196.6683 52592.98169 53930.90586 53480.5983 52832.9756 50956.88434 60218.99085 0.647075309 0.739528493 0.85842024 0.866780854 0.873362056 0.895579702 0.888101869 0.877347409 0.846192931 1 15.87793091 4.488791529 1.421617554 0.888146034 0.602009055 0.813234968 0.038910653 0.288732962 0.747688267 0.009844582 0.103591503 30817.08305 -4.488791529 -0.286136979 VGWFPSTYVEEDE ddPTM_BT-474_Pertuzumab_2h_R1 1 VGWFPSTYVEEDE 13 0 Q9UKW4-3;Q9UKW4-2;Q9UKW4;Q9UKW4-4 Q9UKW4-3 VAV3 Guanine nucleotide exchange factor VAV3 0 175.51 4.22E-05 18157000 35179 41206 33189 40324 40562 45021 44953 50779 45210 44754 FALSE TRUE 33804.16579 40030.84522 39186.99059 42405.12647 41866.71357 45931.35547 45503.14826 49730.3959 40077.95034 41722.77172 0.810209015 0.959448368 0.93922309 1.016354492 1.003449959 1.100870186 1.090607033 1.19192455 0.96057737 1 15.34854738 4.488896795 0.609178071 1.090638287 0.719381953 0.555539952 0.065958671 1.865031438 0.645422955 0.03282096 0.466048922 30824.55352 -4.488896795 -0.371256334 NTGVSPASRPSPGTPTS(ph)PSNLTSGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTGVSPASRPSPGTPTSPSNLTSGLK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 NTGVSPASRPSPGT(0.016)PT(0.06)S(0.87)PS(0.05)NLT(0.003)S(0.001)GLK 103.85 0.0021365 781990000 271300 253510 191630 224740 205180 230990 217590 249250 239500 225680 TRUE FALSE 260697.2961 246280.143 226261.8038 236338.8583 211779.801 235660.7761 220252.9315 244102.9004 212312.9641 210394.4926 1.239088024 1.17056364 1.075416951 1.123312951 1.006584338 1.120090042 1.046856925 1.160215258 1.009118449 1 17.68273741 4.489157826 1.853274492 1.076436022 1.255717712 0.533520247 0.052494796 0.397994198 2.038567024 0.013055106 0.104451196 30843.08611 -4.489157826 0.179281691 S(ph)RS(ph)PQWR ddPTM_BT-474_Pertuzumab_2h_R1 5 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(1)PQWR;S(1)RS(1)PQWR;S(1)RS(1)PQWR;S(1)RS(1)PQWR;S(1)RS(1)PQWR 99.343 0.0060304 4306850000 838543 986080 829373 1179200 1144070 1111266 1065850 1041207 941160 1042140 TRUE FALSE 805771.8125 957957.9639 979259.1504 1240058.653 1180870.051 1133736.56 1078894.191 1019705.712 834323.4625 971554.9296 0.829363104 0.986004944 1.007929784 1.276364944 1.215443424 1.166929965 1.110481928 1.049560535 0.858750686 1 19.88993604 4.489475023 1.882294411 1.102693585 0.816862027 0.334568821 0.112313347 0.581959864 3.100221672 0.031188005 0.245528103 30865.62127 -4.489475023 -0.285831558 EILEVLDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 EILEVLDGR 9 0 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 0 ;;; 140.14 0.00025547 123031000 263050 290701 247852 322622 303779 288416 303805 318933 307991 333424 FALSE TRUE 252769.7152 282410.4921 292644.3698 339272.5601 313550.3274 294247.9691 307523.0565 312346.9221 273029.1529 310840.8955 0.813180372 0.90853712 0.941460323 1.091466937 1.008716459 0.94661923 0.989326247 1.004845008 0.878356602 1 18.2458168 4.489716012 1.94050011 0.988898051 0.804461013 0.518777052 0.051675096 0.373345934 2.148466571 0.013552958 0.103241167 30882.75331 -4.489716012 -0.184437038 RDS(ph)FIGTPYWMAPEVVMCETSK ddPTM_BT-474_Pertuzumab_2h_R1 10 RDSFIGTPYWMAPEVVMCETSK 22 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(0.986)FIGT(0.014)PYWMAPEVVMCETSK;RDS(0.934)FIGT(0.066)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.997)FIGT(0.003)PYWMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(0.68)FIGT(0.32)PYWMAPEVVMCETSK;RDS(0.989)FIGT(0.011)PYWMAPEVVMCETSK 288.98 4.06E-48 3294611000 3869591 3064776 1537685 2024698 2295991 2190238 1868915 3012876 2625709 2183894 TRUE FALSE 3718363.106 2977371.589 1815578.885 2129192.906 2369843.636 2234526.113 1891787.341 2950659.058 2327649.522 2035976.914 1.826328717 1.462379838 0.891748267 1.045784405 1.16398355 1.097520359 0.929179171 1.449259585 1.14325929 1 20.95728977 4.489868047 3.969487814 1.116618112 1.779090832 0.707048733 0.150231322 0.120335709 4.177795305 0.039385661 0.158906767 30893.5664 -4.489868047 0.66247272 GVGDGTVSWGLEDDEDMTLTR ddPTM_BT-474_Pertuzumab_2h_R1 3 GVGDGTVSWGLEDDEDMTLTR 21 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;E5RIF1;D6RG00;H0YBX6 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 ;; 275.42 2.09E-44 352717000 69753 74158 64556 77566 71371 68931 71649 87384 82175 87561 FALSE TRUE 67026.97564 72043.08645 76222.70524 81569.19056 73666.71303 70324.83205 72525.86189 85579.48986 72846.83851 81630.41548 0.821102958 0.882552 0.933753734 0.999249974 0.902441971 0.861502807 0.888466161 1.048377487 0.892398233 1 16.31681918 4.489939333 2.30203065 0.943516997 0.817922227 0.315630252 0.056065752 0.471104246 4.156513002 0.015169738 0.095942254 30898.63777 -4.489939333 -0.12559477 LEDFFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDFFAR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 91.906 0.037363 32102000 90944 102822 93696 113637 107375 112833 112334 106801 121070 138288 FALSE TRUE 87389.80794 99889.61723 110628.9515 119501.8192 110828.8144 115114.5606 113708.7771 104595.522 107326.6412 128921.6306 0.677852177 0.774808826 0.858110086 0.926933817 0.859660352 0.892903387 0.881999216 0.811310884 0.83249522 1 16.97613482 4.490062606 2.147361959 0.875012949 0.669092199 0.635501581 0.049971258 0.267885031 1.988698837 0.01272813 0.086806642 30907.40945 -4.490062606 -0.20592075 ELNDMQAQLVEECAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELNDMQAQLVEECAHR 16 0 Q13464;A0A0U1RQV4 Q13464 ROCK1 Rho-associated protein kinase 1 0 ; 213.49 1.79E-12 574600000 235454 274570 232331 309820 281660 316700 283340 314280 323300 330020 FALSE TRUE 226252.1974 266739.5324 274318.3799 325809.8473 290719.8497 323103.891 286807.5997 307790.0082 286600.3394 307667.4514 0.735379047 0.866973517 0.891606761 1.05896755 0.944915844 1.050172482 0.932200005 1.000398342 0.931526354 1 18.2310123 4.490271346 1.399175642 0.98574268 0.70044116 0.74120416 0.046409577 0.361904798 0.897941727 0.011955733 0.128245049 30922.26842 -4.490271346 -0.28530152 YLEYLEDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 YLEYLEDGK 9 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;C9JCS7 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 99.802 0.010624 0 36362 47919 54723 58473 47210 63655 50367 64638 52982 61245 FALSE TRUE 34940.93284 46552.39704 64612.66341 61490.79854 48728.55253 64942.14771 50983.40641 63303.20271 46967.70548 57096.8216 0.611959333 0.815323791 1.131633278 1.076956594 0.853437217 1.137403903 0.892928975 1.10869924 0.822597549 1 15.80112282 4.490452579 3.947382908 1.008073117 0.637993983 0.557320323 0.109911488 0.137645079 4.700094544 0.024986525 0.101308233 30935.17514 -4.490452579 -0.370079134 TRAS(ph)LPVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRASLPVVR 9 1 Q5T5P2;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P1;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 T(0.497)RAS(0.503)LPVVR 71.933 0.043428 0 148610 116280 64339 78120 70817 53558 53114 117400 64544 57699 TRUE FALSE 142802.1569 112963.8083 75966.48851 82151.78256 73094.89312 54640.97946 53764.02502 114975.649 57217.23571 53790.99534 2.654759519 2.10005053 1.412252888 1.527240425 1.358868574 1.015801606 0.999498609 2.137451599 1.063695426 1 15.71507706 4.490785692 1.788143206 1.361055517 2.797239532 0.636202955 0.332900336 0.377595297 1.761535546 0.093242986 0.779660212 30958.91214 -4.490785692 1.436184015 GVLEGDDVLFYDES(ph)PPPRPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GVLEGDDVLFYDESPPPRPK 20 1 Q5T670;Q7L590-2;Q7L590 Q5T670 MCM10 Protein MCM10 homolog 1 GVLEGDDVLFYDES(1)PPPRPK;GVLEGDDVLFYDES(1)PPPRPK;GVLEGDDVLFYDES(1)PPPRPK 136.57 3.12E-06 180774000 78812 85202 75094 99092 83001 85556 80598 102483 79331 92492 TRUE FALSE 75731.93991 82772.12238 88665.15626 104206.15 85670.80254 87286.00094 81584.38243 100366.6902 70325.67746 86227.43446 0.878281261 0.959927927 1.028270838 1.208503426 0.993544608 1.012276446 0.946153425 1.163976301 0.815583554 1 16.39585934 4.490850157 2.778357319 1.034651467 0.880834739 0.147305881 0.103108378 0.488769783 6.811413714 0.024934507 0.131036107 30963.50793 -4.490850157 -0.153816728 RIS(ph)SSSVQPCSEEVSTPQDSLAQCK ddPTM_BT-474_Pertuzumab_2h_R1 1 RISSSSVQPCSEEVSTPQDSLAQCK 25 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 RIS(0.904)S(0.017)S(0.033)S(0.046)VQPCSEEVSTPQDSLAQCK 172.52 3.51E-12 544580000 119300 126270 105390 119140 136080 130240 115080 126790 163710 148410 TRUE FALSE 114637.6241 122668.9032 124436.3174 125288.8297 140457.1368 132873.542 116488.3835 124171.7422 145126.3271 138358.0585 0.828557623 0.886604688 0.899378892 0.90554053 1.015171348 0.960359978 0.841934216 0.897466642 1.0489185 1 17.07804715 4.490907631 1.050857635 0.942281778 0.803750659 0.317938135 0.058231363 1.805881398 2.168883291 0.019120936 0.25553115 30967.60588 -4.490907631 -0.138531119 WDETPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 WDETPGR 7 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 132.53 0.0078173 1236120000 1309840 1411350 1213580 1465730 1398340 1564450 1485430 1564410 1591620 1639340 FALSE TRUE 1258650.005 1371099.68 1432900.902 1541376.501 1443318.876 1596084.251 1503609.137 1532104.387 1410945.97 1528306.042 0.823558875 0.897136858 0.937574584 1.008552253 0.944391265 1.044348584 0.983840341 1.00248533 0.923209051 1 20.54350204 4.491272068 1.237550003 0.989235457 0.789412417 0.71996454 0.032617477 0.467922556 0.846885361 0.008959634 0.107116549 30993.60319 -4.491272068 -0.19982304 S(ph)NTPILVDGKDVMPEVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNTPILVDGKDVMPEVNK 18 1 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41 P06744 GPI Glucose-6-phosphate isomerase 1 S(0.581)NT(0.419)PILVDGKDVMPEVNK 79.69 0.0059614 269230000 276490 222230 129440 122020 174770 165110 149730 202840 225520 135600 TRUE FALSE 265684.4651 215892.218 152832.6874 128317.4668 180391.6358 168448.6373 151562.4405 198651.2831 199919.9151 126415.6912 2.101673159 1.707796049 1.208969281 1.015043826 1.426971874 1.332497854 1.198921108 1.571413178 1.581448578 1 16.94781602 4.491409506 3.143711964 1.318068546 2.078095008 0.640843607 0.193053105 0.170894154 3.216697279 0.04994994 0.236495178 31003.41306 -4.491409506 0.760026461 VQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 VQIPVSRPDPEPVS(1)DNEEDS(0.691)Y(0.309)DEEIHDPR 161.99 8.21E-12 3883200000 1364500 1547500 1491200 1770600 1645000 1677100 1680400 1624700 1751900 1773600 TRUE FALSE 1311173.831 1503366.815 1760693.012 1861980.878 1697912.919 1711012.111 1700965.238 1591149.377 1553031.657 1653472.492 0.792981944 0.909217917 1.064845663 1.126103329 1.026877028 1.03479926 1.028723033 0.96230774 0.939254607 1 20.65706761 4.491763559 3.367881853 1.022459592 0.802515366 0.68468868 0.049514357 0.151241105 3.380304504 0.013802262 0.062104456 31028.69848 -4.491763559 -0.219944226 ICDPGLTAFEPEALGNLVEGMDFHR ddPTM_BT-474_Pertuzumab_2h_R1 7 ICDPGLTAFEPEALGNLVEGMDFHR 25 0 E9PF82;E9PBG7;H0Y9C2;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5;H0Y9J2 E9PF82;Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 0 ;;;;;; 234.51 2.18E-38 1389961000 506601 548452 470253 607513 557966 606040 530087 515955 612196 719028 FALSE TRUE 486802.4728 532810.686 555238.1778 638866.8187 575913.4831 618294.544 536574.3633 505300.3489 542702.0766 670327.5931 0.726215775 0.794851191 0.828308701 0.953066568 0.859152285 0.922376686 0.800465875 0.753811053 0.809607246 1 19.3545068 4.491772362 2.225753453 0.853701535 0.723381379 0.27184921 0.071569341 0.617134582 5.000119992 0.019529629 0.128746935 31029.32738 -4.491772362 -0.130320156 VEEEDDAEHVLALTMLCLTEGAKDECNVVEVVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEEEDDAEHVLALTMLCLTEGAKDECNVVEVVAR 34 1 O75607 O75607 NPM3 Nucleoplasmin-3 0 ; 335.9 1.03E-117 293590000 185404 167173 116526 126225 148801 170298 137786 138285 186568 169967 FALSE TRUE 178158.2067 162405.3897 137584.8403 132739.4874 153587.3193 173741.5422 139472.2663 135429.3664 165389.5828 158454.9837 1.124345871 1.024930778 0.868289763 0.837711029 0.969280459 1.096472564 0.880201197 0.854686696 1.043763843 1 17.27371351 4.491870552 4.158294611 0.933775853 1.110314479 0.315061208 0.082089299 0.231473365 9.153564542 0.021002202 0.083258299 31036.34364 -4.491870552 0.176538626 TET(ph)QEKNPLPSKETIEQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TETQEKNPLPSKETIEQEK 19 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 T(0.195)ET(0.804)QEKNPLPS(0.001)KETIEQEK;T(0.025)ET(0.975)QEKNPLPSKETIEQEK 154.69 1.59E-06 1220340000 1663210 1235900 481540 437790 1049450 828120 686460 1236070 993980 790450 TRUE FALSE 1598209.914 1200653.342 568564.9898 460384.3944 1083206.512 844865.1538 694861.1028 1210544.723 881147.5575 736912.1174 2.168793098 1.629303296 0.771550605 0.624748031 1.469926314 1.146493773 0.942936188 1.642726037 1.1957295 1 19.49113305 4.492065286 4.220767086 1.138225042 2.090704638 0.576369733 0.289625943 0.154213652 6.369068123 0.07652801 0.301387109 31050.26324 -4.492065286 0.952479596 S(ph)PTPPPTLHLVPEPAAPPPPPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTPPPTLHLVPEPAAPPPPPPR 23 0 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 S(0.903)PT(0.096)PPPT(0.001)LHLVPEPAAPPPPPPR;S(0.573)PT(0.427)PPPTLHLVPEPAAPPPPPPR 123.14 4.05E-05 537870000 267050 282750 245360 281600 305740 286150 288910 298370 305380 312000 TRUE FALSE 256613.3908 274686.2468 289702.01 296133.4097 315574.4048 291936.1491 292445.767 292208.5552 270714.5427 290867.9621 0.882233261 0.944367488 0.995991473 1.018102536 1.084940406 1.003672412 1.005424471 1.004608941 0.930712825 1 18.15000487 4.492131046 1.976734281 1.009565389 0.873825879 0.559470523 0.034931615 0.344488823 2.071912559 0.009428 0.070874388 31054.96512 -4.492131046 -0.13573951 ET(ph)LS(ph)LT(ph)LAEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETLSLTLAEEK 11 0 H7BZ55 H7BZ55 Putative ciliary rootlet coiled-coil protein-like 3 protein 3 ET(1)LS(1)LT(1)LAEEK;ET(1)LS(1)LT(1)LAEEK 67.897 0.056574 631530000 900790 1440610 1480310 2166100 1608470 1856590 2067600 2158000 1867200 2773100 TRUE FALSE 865586.1309 1399525.213 1747834.946 2277892.681 1660207.898 1894131.522 2092903.907 2113436.546 1655243.284 2585275.467 0.334813888 0.541344716 0.676073002 0.881102501 0.642178336 0.732661392 0.809547738 0.817489886 0.640257994 1 21.30188658 4.492266829 1.534435799 0.778616448 0.273022241 0.66675177 0.102475492 0.389796531 1.223956641 0.026305133 0.259611608 31064.67603 -4.492266829 -0.505594207 LSTTPS(ph)PTSSLHEDGVEDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSTTPSPTSSLHEDGVEDFR 20 0 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 1 LST(0.001)T(0.009)PS(0.954)PT(0.035)S(0.001)SLHEDGVEDFR;LS(0.002)T(0.002)T(0.009)PS(0.416)PT(0.416)S(0.078)S(0.078)LHEDGVEDFR 186.69 2.05E-17 397190000 102123 159656 185383 244810 203334 230376 230755 122334 247284 276644 TRUE FALSE 98131.92026 155102.7672 218885.8319 257444.6734 209874.4228 235034.3606 233579.0487 119807.7601 219213.357 257906.6555 0.380493943 0.6013911 0.848701758 0.998208724 0.813761174 0.911315608 0.905672823 0.464539234 0.849971695 1 17.97648948 4.49233294 2.832782478 0.820299475 0.385799256 0.512874701 0.144856966 0.274779446 4.008076601 0.04046442 0.209793803 31069.40528 -4.49233294 -0.434500218 EALLDESRPLFER ddPTM_BT-474_Pertuzumab_2h_R1 3 EALLDESRPLFER 13 1 A0A5F9ZGM7;Q9BU89 A0A5F9ZGM7 DOHH Deoxyhypusine hydroxylase 0 ;; 134.9 8.22E-05 656020000 655860 737390 664000 796190 772540 839800 763280 815780 868580 951130 FALSE TRUE 630228.2661 716360.3592 783999.5706 837281.4613 797389.4507 856781.3314 772621.249 798933.8579 769982.4398 886709.1179 0.71074973 0.807886538 0.88416771 0.944257191 0.899268356 0.966248473 0.871335631 0.901010085 0.868359673 1 19.75810139 4.492571447 1.774028433 0.914857361 0.690919692 0.744101353 0.039369927 0.262953355 1.199477264 0.009951686 0.084387728 31086.47271 -4.492571447 -0.223937669 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_BT-474_Pertuzumab_2h_R1 8 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER 32 0 P68363;F8VQQ4;Q9BQE3;F5H5D3 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;;;;;; 397.88 9.37E-167 11187299000 687761.1 745507 665062.7 788095.5 797904.9 760543.4 835412.5 721047.4 840130.6 870098.7 FALSE TRUE 660882.6359 724245.8703 785254.3241 828769.2032 823570.2357 775922.1086 845636.5281 706157.5192 744762.4964 811166.14 0.814731537 0.892845293 0.968056093 1.021700934 1.015291683 0.956551402 1.042494856 0.870546099 0.918138048 1 19.62963791 4.492753904 2.484678221 0.970587381 0.812718436 0.522560693 0.048722233 0.300141259 3.18431791 0.013483624 0.079398788 31099.53561 -4.492753904 -0.157868946 (ac)AS(ph)GVAVSDGVIK ddPTM_BT-474_Pertuzumab_2h_R1 12 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(0.994)GVAVS(0.006)DGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.997)GVAVS(0.003)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK 81.338 1.60E-16 48376790000 25567620 20337380 13251060 12027390 16503270 11986050 12686360 18282310 15918470 13070130 TRUE FALSE 24568409.14 19757377.83 15645821.31 12648125.04 17034112.67 12228416.14 12841619.47 17904773.91 14111472.02 12184878.45 2.016303178 1.621466961 1.284035895 1.038018154 1.397971488 1.003573092 1.053898036 1.469425729 1.158113483 1 23.53858852 4.492757422 1.907426714 1.189658805 2.081574925 0.75777045 0.154230764 0.242886678 1.333289442 0.041180519 0.322649129 31099.78752 -4.492757422 0.891916119 ETESAPGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 ETESAPGSPR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR 162.38 7.12E-06 5003628000 3881567 5193658 5273203 6484337 6129796 6933261 6873252 5847715 7335129 8567384 TRUE FALSE 3729871.07 5045539.959 6226188.084 6818994.41 6326966.455 7073456.288 6957368.914 5726957.642 6502475.907 7987107.451 0.466986465 0.63171054 0.779529776 0.853750178 0.792147407 0.885609256 0.871074911 0.717025241 0.814121501 1 22.92924169 4.493084329 1.656899175 0.831085236 0.422005406 0.753942945 0.069890429 0.302648792 1.157369396 0.018686658 0.170784873 31123.20613 -4.493084329 -0.409079831 AVFPSIVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVFPSIVGR 9 0 C9JTX5;F8WCH0;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63267-2;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I" 0 ; 211.39 1.22E-05 3789600000 763010 864260 859510 998230 817740 719470 1046650 961810 958850 1028960 FALSE TRUE 733190.7256 839612.151 1014842.577 1049748.77 844043.3498 734018.1763 1059459.216 941948.2874 850005.3678 959267.6227 0.764323436 0.875263723 1.057934775 1.094323154 0.879883079 0.765186022 1.104445924 0.981945252 0.886098256 1 19.87157384 4.493086356 4.539351633 0.972228763 0.782224957 0.296627513 0.100027252 0.239944874 12.33330742 0.025315174 0.096897107 31123.35137 -4.493086356 -0.190003807 LVIIEGDLER ddPTM_BT-474_Pertuzumab_2h_R1 8 LVIIEGDLER 10 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;;; 251.23 2.17E-13 1809198000 1019946 1145923 1064482 1341956 1176882 1075856 1298849 1269242 1248123 1353044 FALSE TRUE 980085.3827 1113242.398 1256857.577 1411214.51 1214737.478 1097610.545 1314744.703 1243031.709 1106441.31 1261401.125 0.776981535 0.88254432 0.996398015 1.118767442 0.963006497 0.870151868 1.042289147 0.985437293 0.877152626 1 20.26659569 4.493118354 2.912275688 0.984306337 0.78082384 0.470732102 0.068721364 0.247252292 3.854132259 0.017618713 0.089327566 31125.64458 -4.493118354 -0.203482496 IIENELEGFGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 IIENELEGFGIR 12 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 227.36 3.06E-11 34471000 25904 28133 26022 26886 29430 31056 30381 30920 29941 32495 FALSE TRUE 24891.64304 27330.67439 30724.75426 28273.58968 30376.64268 31683.9736 30752.81177 30281.49119 26542.2232 30294.08471 0.82166678 0.902178582 1.014216292 0.933303975 1.002725218 1.045879877 1.015142463 0.999584291 0.87615201 1 14.8867485 4.493131314 2.803459504 0.988932774 0.822126248 0.562077038 0.046113909 0.20776999 2.95306998 0.011575673 0.060719972 31126.57344 -4.493131314 -0.166806526 SSS(ph)PPPRK ddPTM_BT-474_Pertuzumab_2h_R1 5 SSSPPPRK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.214)S(0.152)S(0.634)PPPRK;S(0.294)S(0.294)S(0.411)PPPRK;S(0.294)S(0.294)S(0.412)PPPRK;S(0.304)S(0.304)S(0.391)PPPRK;S(0.296)S(0.296)S(0.408)PPPRK 84.213 0.0091779 10958500000 3005910 2830520 2134910 2502730 2446490 2689950 2684650 2758920 2638360 2969270 TRUE FALSE 2888435.714 2749796.341 2520735.728 2631896.195 2525183.573 2744342.632 2717505.55 2701947.338 2338864.434 2768158.698 1.043450188 0.993366581 0.910618213 0.950775039 0.912225002 0.991396423 0.981701501 0.976081082 0.844917033 1 21.40049522 4.493483398 4.42238726 0.948920781 1.03570085 0.320911313 0.044713362 0.226682018 10.73589536 0.010649985 0.041267484 31151.81806 -4.493483398 0.086780069 TGTLQPWNS(ph)DSTLNSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TGTLQPWNSDSTLNSR 16 0 Q9H0H5;F8VRD2;H0YIK5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 TGTLQPWNS(1)DSTLNSR;TGTLQPWNS(0.999)DS(0.001)TLNSR;TGTLQPWNS(1)DSTLNSR;TGTLQPWNS(1)DSTLNSR 214.39 1.79E-14 580040000 622080 740230 718520 903090 684400 814500 810130 869940 1016810 854990 TRUE FALSE 597768.4259 719119.3652 848372.5474 949698.5831 706414.3476 830969.7481 820044.6133 851975.435 901385.9916 797080.7658 0.749947121 0.902191341 1.064349541 1.191470957 0.886251906 1.042516372 1.028809938 1.068869645 1.130859043 1 19.60436639 4.493535915 2.735930217 1.052349637 0.751574009 0.614717122 0.075999133 0.194780108 2.608806792 0.018952589 0.101794974 31155.58533 -4.493535915 -0.300775628 S(ph)PVIGSEVFLPNSNHVASGAGEAEER ddPTM_BT-474_Pertuzumab_2h_R1 4 SPVIGSEVFLPNSNHVASGAGEAEER 26 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;H3BVD2;P29590-12;P29590-13;P29590-11 P29590-2;P29590-12 PML Protein PML 1 S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER 301.82 7.02E-71 5033570000 261340 317271 297258 421052 364960 349600 380634 328966 325955 364285 TRUE FALSE 251126.5439 308222.7417 350979.1331 442782.5442 376699.2698 356669.1515 385292.3128 322172.7371 288953.9549 339611.6525 0.739452083 0.907574106 1.033471998 1.303790789 1.109205962 1.050226483 1.134508519 0.948650421 0.850836397 1 18.37352643 4.494095747 2.501625737 1.061000492 0.737702351 0.434952068 0.113169863 0.332807552 3.58525124 0.030827649 0.180974598 31195.77269 -4.494095747 -0.323298141 GLLYDS(ph)DEEDEERPAR ddPTM_BT-474_Pertuzumab_2h_R1 10 GLLYDSDEEDEERPAR 16 1 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR 340.9 2.75E-72 85798960000 6490668 7010692 6159635 7361225 7269518 7210678 7479805 7544695 7184289 8122497 TRUE FALSE 6237005.519 6810753.928 7272818.065 7741138.704 7503348.648 7356482.85 7571345.091 7388894.412 6368758.632 7572353.043 0.823654878 0.899423718 0.960443606 1.022289724 0.990887325 0.971492323 0.99986689 0.975772573 0.841054108 1 22.85231024 4.494432182 2.19183475 0.974258843 0.817686408 0.49917732 0.046668224 0.322507717 2.508097973 0.011909858 0.080459945 31219.94847 -4.494432182 -0.156572436 YVSDRPQAFK ddPTM_BT-474_Pertuzumab_2h_R1 1 YVSDRPQAFK 10 1 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 109.66 0.002924 0 477710 405900 290030 293790 306910 248960 352450 351280 401110 365850 FALSE TRUE 459040.5651 394324.1294 342444.8727 308952.5371 316782.0389 253994.1418 356763.3885 344025.9452 355577.6744 341070.6536 1.345881154 1.1561362 1.004029133 0.905831486 0.928787146 0.744696558 1.046010217 1.008664749 1.04253377 1 18.3797111 4.494668685 1.860760308 0.953168797 1.379049878 0.692062659 0.083018724 0.301967108 1.55265024 0.023377352 0.189329066 31236.9545 -4.494668685 0.425881081 QAGIGGEPAAAGAGCS(ph)PRPK ddPTM_BT-474_Pertuzumab_2h_R1 4 QAGIGGEPAAAGAGCSPRPK 20 1 J3QQY0;Q68DK7;J3KSZ8 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 QAGIGGEPAAAGAGCS(1)PRPK;QAGIGGEPAAAGAGCS(1)PRPK;QAGIGGEPAAAGAGCS(1)PRPK;QAGIGGEPAAAGAGCS(1)PRPK 209.52 2.79E-22 1675740000 1625910 1512240 1171960 1249770 1290410 1298530 1400740 1511980 1467650 1538180 TRUE FALSE 1562367.64 1469112.396 1383759.242 1314270.779 1331917.21 1324787.166 1417882.675 1480757.085 1301048.525 1433997.699 1.089518931 1.024487276 0.964966153 0.916508291 0.92881405 0.923841905 0.988762169 1.032607713 0.907287736 1 20.45161128 4.494737709 2.421566902 0.960531002 1.09191756 0.545732954 0.038412909 0.304251516 3.025423085 0.010924018 0.066426041 31241.9195 -4.494737709 0.131386558 GEGPAIPGDT(ph)PPPTPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GEGPAIPGDTPPPTPR 16 0 O75145-2;O75145 O75145-2 PPFIA3 Liprin-alpha-3 1 GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR 187.46 1.49E-08 1363240000 1525920 1733000 1541070 1983030 1775450 1953370 1938820 1815940 1867450 2062070 TRUE FALSE 1466285.359 1683576.537 1819575.63 2085374.416 1832558.962 1992868.48 1962547.859 1778440.204 1655464.905 1922404.162 0.762735219 0.875766173 0.946510451 1.084774189 0.953264146 1.036654268 1.020882028 0.925112544 0.861143009 1 20.87448025 4.494897235 2.091145793 0.981254514 0.752755956 0.577405028 0.058939762 0.317830105 2.196296497 0.015908165 0.113311515 31253.39745 -4.494897235 -0.228498558 SQDIYLR ddPTM_BT-474_Pertuzumab_2h_R1 5 SQDIYLR 7 0 J3QQ67;Q07020;F8VYV2;G3V203;A0A075B7A0;F8VXR6 J3QQ67 RPL18 60S ribosomal protein L18 0 ;;;; 187.63 0.0013526 3832880000 2797010 3021260 2823960 3038670 3076210 2820820 3258700 3250960 3347820 3443930 FALSE TRUE 2687699.757 2935096.623 3334312.391 3195496.123 3175159.088 2877858.913 3298580.945 3183826.54 2967789.509 3210669.554 0.837115035 0.914169638 1.038509985 0.99527406 0.988939857 0.896342294 1.027381015 0.991639434 0.924352214 1 21.61444276 4.495305976 4.254049334 0.983005097 0.84823756 0.554838475 0.041070863 0.142285039 5.96922289 0.009951529 0.039476937 31282.8258 -4.495305976 -0.134767537 SRS(ph)SPATADKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSSPATADKR 11 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.032)RS(0.482)S(0.482)PAT(0.004)ADKR 63.754 0.057203 150170000 65758 58512 40199 41837 44135 39279 40258 52053 36007 39660 TRUE FALSE 63188.10466 56843.29505 47463.85352 43996.21258 45554.64236 40073.24829 40750.68945 50978.08736 31919.63631 36973.79287 1.708997096 1.537394209 1.283716109 1.189929655 1.232079233 1.083828441 1.102150639 1.378762723 0.863304352 1 15.17421543 4.495486471 1.006892537 1.138312447 1.89739525 0.712932732 0.128475973 0.744768338 0.801295327 0.040508791 0.560740288 31295.82978 -4.495486471 0.759082803 EPSAPSIPTPAYQSS(ph)PAGGHAPTPPTPAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPSAPSIPTPAYQSSPAGGHAPTPPTPAPR 30 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 1 EPSAPSIPTPAYQS(0.156)S(0.844)PAGGHAPTPPTPAPR;EPSAPSIPTPAYQS(0.251)S(0.749)PAGGHAPTPPTPAPR 200.84 1.39E-25 1742220000 389100 448050 449720 483940 420430 531020 546100 477440 436930 531930 TRUE FALSE 373893.5418 435272.0527 530994.408 508916.2014 433953.5128 541757.5882 552783.3352 467580.6972 387331.5382 495901.9073 0.753966735 0.87773821 1.070765004 1.026243686 0.875079338 1.092469257 1.114702983 0.942889491 0.781064828 1 18.91969525 4.495509392 4.014335454 0.991027891 0.769960945 0.365447409 0.09692663 0.223249036 7.921797626 0.024248474 0.09902143 31297.48153 -4.495509392 -0.221066946 DNLTLWTSENQGDEGDAGEGEN ddPTM_BT-474_Pertuzumab_2h_R1 24 DNLTLWTSENQGDEGDAGEGEN 22 0 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;;;;;;;;;;;;;;;;;;;; 374.7 7.22E-113 19906697000 20750486.8 22347404.7 19144135.9 23192986.7 22662337.7 23277197.9 22905255.3 24170333.1 24908096.2 24937126.9 FALSE TRUE 19939534.83 21710078.6 22603907.12 24389979.52 23391292.37 23747878.79 23185576.67 23671207.28 22080633.54 23248113.08 0.857684009 0.93384261 0.972289968 1.049116521 1.006158749 1.021497044 0.997310043 1.018199077 0.949781751 1 24.47061029 4.495553789 1.71737008 1.007344156 0.843274057 0.778918702 0.024613605 0.244107535 1.020717768 0.006371859 0.056471929 31300.6812 -4.495553789 -0.164070099 VPS(ph)S(ph)DEEVVEEPQSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR 206.43 5.70E-09 6984330000 789440 823320 680115 819440 820080 808090 848800 863760 872760 806550 TRUE FALSE 758587.812 799839.7197 803026.9096 861731.3966 846458.618 824430.1335 859187.8683 845923.0542 773687.9437 751921.6501 1.008865501 1.063727477 1.067966203 1.146038815 1.125727152 1.096430903 1.142656111 1.125014892 1.028947555 1 19.52022282 4.495683268 1.62503613 1.104671628 1.000498292 0.204194137 0.046480158 0.786600657 2.852072528 0.011905044 0.111925282 31310.01443 -4.495683268 -0.104173336 S(ph)RDESASETSTPSEHSAAPSPQVEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDESASETSTPSEHSAAPSPQVEVR 26 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 S(0.763)RDES(0.189)AS(0.047)ET(0.001)STPSEHSAAPSPQVEVR 129.59 4.73E-05 377960000 33267 43548 36793 54316 52898 49319 53796 63802 53413 64043 TRUE FALSE 31966.88886 42306.05368 43442.31356 57119.25527 54599.51221 50316.26397 54454.37154 62484.4664 47349.78017 59705.31057 0.535411148 0.708581084 0.72761222 0.956686344 0.914483347 0.842743526 0.912052396 1.046547883 0.7930581 1 15.86557164 4.496016618 0.859116338 0.937863023 0.404383929 0.739381838 0.075265919 0.823527909 0.605687233 0.026287024 0.387305316 31334.05622 -4.496016618 -0.533479094 TVFS(ph)PTLPAAR ddPTM_BT-474_Pertuzumab_2h_R1 5 TVFSPTLPAAR 11 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 TVFS(0.982)PT(0.018)LPAAR;TVFS(0.998)PT(0.002)LPAAR;T(0.016)VFS(0.981)PT(0.003)LPAAR;TVFS(0.993)PT(0.007)LPAAR;TVFS(0.951)PT(0.049)LPAAR 207.34 2.44E-08 3776861000 3598480 3945420 3401070 4135640 4042060 4367810 4144380 4293010 4235410 4734550 TRUE FALSE 3457847.423 3832900.485 4015719.005 4349080.876 4172076.531 4456130.111 4195100.162 4204357.843 3754624.013 4413874.711 0.783404072 0.86837546 0.909794516 0.985320418 0.945218613 1.009573312 0.950434808 0.952532212 0.850641275 1 22.07361425 4.496166849 1.516867222 0.955304561 0.760309561 0.626834461 0.041987588 0.445626846 1.351801517 0.011275288 0.113892007 31344.89716 -4.496166849 -0.194995 HIEPELAGRDS(ph)PIR ddPTM_BT-474_Pertuzumab_2h_R1 2 HIEPELAGRDSPIR 14 1 P86791;P86790 P86791 CCZ1;CCZ1B Vacuolar fusion protein CCZ1 homolog;Vacuolar fusion protein CCZ1 homolog B 1 HIEPELAGRDS(1)PIR;HIEPELAGRDS(1)PIR 188.84 4.77E-07 2633500000 953690 1161560 1011660 1470890 1283550 1232010 1451560 955500 1528480 1620690 TRUE FALSE 916418.7404 1128433.446 1194489.466 1546802.809 1324836.551 1256922.086 1469324.625 935768.5911 1354973.358 1510919.223 0.606530598 0.746852267 0.790571361 1.023749507 0.876841416 0.831892313 0.972470668 0.619337273 0.896787424 1 20.5269951 4.496271724 1.952953386 0.860986045 0.593610052 0.375572823 0.110560561 0.575668645 3.341783692 0.030145434 0.232555425 31352.46737 -4.496271724 -0.267375993 SLSS(ph)PTDNLELSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSSPTDNLELSLR 14 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SLS(0.001)S(0.999)PTDNLELSLR;SLS(0.002)S(0.995)PT(0.003)DNLELSLR 287.01 7.08E-34 669410000 968830 1111630 1058970 1244370 1184440 1250700 1219860 1213640 1259790 1288950 TRUE FALSE 930967.0525 1079927.401 1250349.436 1308592.085 1222538.588 1275990.011 1234789.012 1188577.91 1116783.921 1201648.268 0.774741725 0.898705078 1.040528638 1.088997604 1.017384721 1.061866475 1.027579404 0.989122975 0.929376715 1 20.19658324 4.496313884 2.801378333 1.021436051 0.776527457 0.777341378 0.041570772 0.137481503 1.944733608 0.011166725 0.059140622 31355.5111 -4.496313884 -0.244908595 VSPAS(ph)PAGSPSADFAVHGESLGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSPASPAGSPSADFAVHGESLGDR 24 0 A0A0A0MRP9;Q96C92-3;Q96C92;Q96C92-2;Q96C92-4 A0A0A0MRP9;Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 1 VS(0.384)PAS(0.588)PAGS(0.028)PSADFAVHGESLGDR 156.73 1.42E-08 272780000 78211 82218 72154 81340 82010 91418 96537 90599 88292 90074 TRUE FALSE 75154.42765 79873.22314 85193.83286 85537.96715 84647.92613 93266.5346 97718.44868 88728.09899 78269.46231 83973.20775 0.894981026 0.951175086 1.014535888 1.018634031 1.008034924 1.110670142 1.163686029 1.056623909 0.932076604 1 16.35764148 4.496339329 0.895446546 1.05868913 0.840059883 0.387159136 0.059944523 1.575482933 1.276926047 0.021504057 0.313313539 31357.34822 -4.496339329 -0.218629247 IES(ph)S(ph)IQSLQDLS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 2 IESSIQSLQDLSK 13 0 A0A087X043;O43424-2;O43424 A0A087X043 GRID2 "Glutamate receptor ionotropic, delta-2" 3 IES(0.926)S(0.541)IQS(0.541)LQDLS(0.993)K;IES(0.701)S(0.652)IQS(0.652)LQDLS(0.995)K 62.203 0.037003 7367170000 1142330 1313660 1767950 2321920 1610250 1526670 2225830 2172960 2363680 3009330 TRUE FALSE 1097686.481 1276195.703 2087457.893 2441754.569 1662045.154 1557540.313 2253070.373 2128087.617 2095364.956 2805505.399 0.391261582 0.454889769 0.744057699 0.870343921 0.592422725 0.555172809 0.803088946 0.75853984 0.746876109 1 21.41982926 4.49650939 0.124138077 1.103809313 6.28E-18 0.558349835 0.119707304 29.65977366 0.660992824 1.220950374 5.81434686 31369.62952 -4.49650939 -1.103809313 S(ph)PPAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPAIR 6 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PPAIR 79.469 0.070352 655320000 69723 95837 96319 148980 90097 91894 118920 115660 135870 144230 TRUE FALSE 66998.14808 93103.82259 113725.9859 156668.8757 92995.05183 93752.15964 120375.3785 113271.5806 120446.6072 134461.1736 0.498271332 0.692421612 0.84579052 1.165160703 0.691612674 0.697243354 0.895242658 0.842411066 0.895772393 1 17.03683012 4.497285666 2.540548118 0.869996875 0.496349416 0.465411829 0.129846908 0.307114847 3.424636195 0.033376297 0.194681368 31425.75106 -4.497285666 -0.373647459 LTPIHDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LTPIHDR 7 0 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;;;; 157.58 0.0014664 4323270000 4007990 4444330 4074610 5197860 4332160 4318900 4901430 4723600 4949960 5335650 FALSE TRUE 3851353.32 4317582.06 4810982.666 5466122.178 4471507.861 4406231.117 4961415.167 4626056.009 4388061.293 4974261.673 0.774256276 0.867984506 0.967175228 1.098881108 0.898928958 0.885806057 0.997417404 0.929998523 0.882153289 1 22.24605097 4.49742039 2.959071062 0.955844754 0.777953294 0.465511236 0.062317259 0.253065755 4.083597512 0.01593941 0.080674249 31435.50126 -4.49742039 -0.17789146 LLQLVEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLQLVEDR 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 180.54 0.00055502 1290890000 686740 754530 688030 812480 767180 762520 826160 791690 842060 933740 FALSE TRUE 659901.4416 733011.5432 812372.3261 854412.1902 791857.0414 777938.6768 836270.7932 775341.3248 746472.879 870496.9581 0.75807438 0.842061005 0.933228219 0.981522316 0.909660894 0.893671907 0.96068204 0.89068815 0.857524971 1 19.73147973 4.497429288 2.729728935 0.924387887 0.758500297 0.628443971 0.041736788 0.195595372 2.595829933 0.010387156 0.056525524 31436.14535 -4.497429288 -0.165887589 VSDS(ph)PSHIATK ddPTM_BT-474_Pertuzumab_2h_R1 4 VSDSPSHIATK 11 0 Q9P2D3 Q9P2D3 HEATR5B HEAT repeat-containing protein 5B 1 VS(0.005)DS(0.894)PS(0.098)HIAT(0.003)K;VSDS(0.967)PS(0.032)HIATK;VS(0.036)DS(0.962)PS(0.002)HIATK;VSDS(0.792)PS(0.207)HIATK 211.52 9.49E-09 1721450000 3915620 4501290 4242040 5027830 4500270 5368960 5104960 4516950 5315820 5995600 TRUE FALSE 3762593.241 4372917.616 5008670.992 5287316.909 4645025.272 5477524.05 5167436.028 4423673.404 4712390.399 5589512.672 0.673152288 0.782343269 0.896083663 0.945935222 0.83102509 0.979964511 0.924487756 0.791423808 0.843077148 1 22.41429107 4.497486564 2.508187931 0.892185874 0.66971987 0.570910822 0.063222503 0.260676533 2.816890365 0.016562718 0.097921942 31440.29151 -4.497486564 -0.222466004 AELPGSS(ph)SPLLAQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AELPGSSSPLLAQPR 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 AELPGS(0.002)S(0.728)S(0.27)PLLAQPR;AELPGS(0.078)S(0.461)S(0.461)PLLAQPR 240.2 8.23E-18 342150000 373972 438572 422066 519860 406981 455422 500505 525800 478911 604730 TRUE FALSE 359356.7608 426064.356 498342.715 546690.0369 420071.9135 464630.9449 506630.3299 514942.0463 424547.031 563771.0985 0.637416075 0.755739975 0.883945127 0.969702133 0.745110763 0.824148216 0.898645445 0.913388515 0.75304859 1 19.10474999 4.497592609 2.764261873 0.870994961 0.638635286 0.478277178 0.07849526 0.253870307 3.472763242 0.01918652 0.103240611 31447.96945 -4.497592609 -0.232359676 GPGS(ph)PPRT(ph)PPAPGPPSFEEQLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPGSPPRTPPAPGPPSFEEQLR 22 1 A0A6E1YH78;Q6ZTN6-2;Q6ZTN6;Q6ZTN6-3 A0A6E1YH78 ANKRD13D Ankyrin repeat domain-containing protein 13D 2 GPGS(1)PPRT(1)PPAPGPPSFEEQLR;GPGS(1)PPRT(1)PPAPGPPSFEEQLR;GPGS(1)PPRT(0.998)PPAPGPPS(0.002)FEEQLR;GPGS(1)PPRT(1)PPAPGPPSFEEQLR 152.15 9.94E-08 2716800000 889360 988220 856340 1078450 1027280 1096360 1089980 1053120 1015530 1067410 TRUE FALSE 854602.828 960036.9332 1011099.687 1134108.934 1060323.394 1118529.15 1103319.501 1031372.704 900251.2918 995113.3699 0.858799463 0.964751316 1.01606482 1.139678119 1.065530246 1.124021829 1.108737491 1.03643739 0.90467209 1 19.92450137 4.497602404 1.875678271 1.060802236 0.844504226 0.459049043 0.064990357 0.44108034 2.306671605 0.017447245 0.141315833 31448.67876 -4.497602404 -0.21629801 VS(ph)PSDTTPLVSR ddPTM_BT-474_Pertuzumab_2h_R1 6 VSPSDTTPLVSR 12 0 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 VS(0.897)PS(0.103)DTTPLVSR;VS(0.939)PS(0.06)DT(0.001)TPLVSR;VS(0.97)PS(0.03)DTTPLVSR;VS(0.977)PS(0.023)DTTPLVSR;VS(0.908)PS(0.09)DT(0.002)T(0.001)PLVSR;VS(0.927)PS(0.073)DTTPLVSR 211.52 3.24E-08 6659620000 2033810 2257140 2054040 2372970 2443860 2428680 2608840 2485410 2365210 2337840 TRUE FALSE 1954326.457 2192768.577 2425250.72 2495439.266 2522468.976 2477789.574 2640767.764 2434085.415 2096721.277 2179496.014 0.896687328 1.006089739 1.112757584 1.14496161 1.157363427 1.136863549 1.211641474 1.116811134 0.962021157 1 21.05556313 4.497773193 2.212442822 1.120119207 0.88666733 0.454681503 0.070938419 0.323783053 2.568231108 0.017953487 0.121253618 31461.04856 -4.497773193 -0.233451877 RSYS(ph)PDGKESPSDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSYSPDGKESPSDKK 15 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.076)YS(0.923)PDGKES(0.001)PSDKK 100.41 0.011979 128050000 197990 156780 91976 67765 94745 137590 107850 137450 170590 128410 TRUE FALSE 190252.3319 152308.7879 108598.1092 71262.35977 97792.55897 140372.1641 109169.9006 134611.6095 151225.3384 119712.6763 1.589241321 1.272286215 0.907156306 0.595278311 0.816893933 1.172575607 0.91193267 1.124455769 1.263235799 1 16.8692164 4.497972751 3.06234189 0.972406493 1.573873101 0.537073354 0.180906847 0.222233834 3.896502843 0.049232616 0.242503303 31475.50818 -4.497972751 0.601466608 FELAVDAVHR ddPTM_BT-474_Pertuzumab_2h_R1 3 FELAVDAVHR 10 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9;H3BUE3;H3BSQ5 Q8WWM7 ATXN2L Ataxin-2-like protein 0 ;; 157.24 9.51E-06 690730000 654340 693870 635000 704510 676070 686180 722470 699700 771280 768620 FALSE TRUE 628767.6694 674081.507 749758.6255 740869.8455 697816.4055 700055.0297 731311.804 685250.9505 683727.5279 716560.6828 0.877480002 0.940717965 1.046329562 1.033924779 0.973841326 0.97696545 1.020586004 0.95630554 0.954179519 1 19.45072936 4.498066805 4.682303443 0.993345165 0.887942005 0.602520112 0.030001366 0.133250489 7.410626408 0.007825495 0.03014543 31482.3255 -4.498066805 -0.10540316 ADLHDEEDEQDILLAQDLEDMWEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 ADLHDEEDEQDILLAQDLEDMWEQK 25 0 A0A087WT90;Q9H2W6 A0A087WT90;Q9H2W6 MRPL46 "39S ribosomal protein L46, mitochondrial" 0 ;; 236.02 1.99E-38 62480000 37503 49551 40920.9 74316 38189.8 44355.8 71145 59302 58427 52734 FALSE TRUE 36037.3413 48137.854 48316.21691 78151.45767 39418.2096 45252.70467 72015.69379 58077.39298 51794.61191 49162.27921 0.733028287 0.979162373 0.982790418 1.589663029 0.801797847 0.920476133 1.464856694 1.18134053 1.053543748 1 15.58526418 4.498424477 1.859325714 1.151684013 0.711146461 0.219806311 0.228158239 0.75511167 3.857780414 0.059854787 0.490734506 31508.2641 -4.498424477 -0.440537552 RLAVPTEVSTEVPEMDTS(ph)T ddPTM_BT-474_Pertuzumab_2h_R1 2 RLAVPTEVSTEVPEMDTST 19 1 O00488 O00488 ZNF593 Zinc finger protein 593 1 RLAVPTEVSTEVPEMDT(0.057)S(0.471)T(0.471);RLAVPTEVSTEVPEMDT(0.123)S(0.753)T(0.123) 112.3 0.00021117 167032000 138264 152200 145782 156913 175843 190421 177963 174164 180005 216010 TRUE FALSE 132860.49 147859.405 172128.0503 165011.2987 181499.1498 194271.4431 180140.9644 170567.4525 159571.587 201379.4503 0.659751975 0.734232837 0.854744861 0.819404852 0.901279398 0.964703413 0.894534989 0.846995323 0.792392604 1 17.61955695 4.498749911 1.116219046 0.888247951 0.594341656 0.64573155 0.05772264 0.738131943 1.02101264 0.017643023 0.232015381 31531.88336 -4.498749911 -0.293906295 ESDFYLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESDFYLR 7 0 P61326;P61326-2 P61326 MAGOH Protein mago nashi homolog 0 ;;; 208.74 0.00038576 2147230000 1341150 1537350 1291370 1631150 1715840 1644010 1649290 1644500 1767870 1803200 FALSE TRUE 1288736.375 1493506.283 1524749.285 1715333.847 1771031.552 1677253.009 1669474.504 1610540.5 1567188.809 1681067.658 0.766617792 0.88842723 0.907012444 1.020383587 1.053515927 0.997730818 0.993103696 0.958046211 0.932258022 1 20.68094636 4.498752413 1.376684 0.990737532 0.734455166 0.79672408 0.035479095 0.387288017 0.912263655 0.010973467 0.122482108 31532.06502 -4.498752413 -0.256282366 S(ph)PESEILSLHLLVEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPESEILSLHLLVEELR 17 0 A0A0A6YYJ5;O94854-2;O94854 A0A0A6YYJ5 MACF1;KIAA0754 Uncharacterized protein KIAA0754 1 S(0.831)PES(0.169)EILSLHLLVEELR 107.34 0.00076261 0 1850.2 2810.2 2182.8 3709.6 3205.3 2967.7 4537 3371.7 3159.7 2553.7 TRUE FALSE 1777.892138 2730.055847 2577.280516 3901.052901 3308.401385 3027.708927 4592.525163 3302.073217 2801.024103 2380.735624 0.746782684 1.146727851 1.08255637 1.638591392 1.389655093 1.271753527 1.929036184 1.38699702 1.176537232 1 11.21719171 4.498776038 1.207550241 1.434749385 0.632734738 0.361885295 0.253044536 0.986888953 1.663667228 0.071869412 0.894401088 31533.78034 -4.498776038 -0.802014648 RKAS(ph)VHSSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RKASVHSSGR 10 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 RKAS(1)VHSSGR 70.412 0.028207 10577000 25527 17010 3771.2 9910.8 7917.2 6146.2 5738.7 21684 3358.1 4198.5 TRUE FALSE 24529.37662 16524.89145 4452.73973 10422.29758 8171.863928 6270.480375 5808.931927 21236.21782 2976.902566 3914.131855 6.266875395 4.221853546 1.137605961 2.662735432 2.087784528 1.602010511 1.484092039 5.425524384 0.760552448 1 11.93447664 4.498876704 3.740607356 2.32311613 6.048781043 0.513011063 1.298209986 0.196391258 5.707829146 0.332769376 1.427771223 31541.09049 -4.498876704 3.725664913 SLSKS(ph)DSDLLTCSPTEDATMGSR ddPTM_BT-474_Pertuzumab_2h_R1 7 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.003)LS(0.073)KS(0.907)DS(0.017)DLLTCSPTEDATMGSR;S(0.002)LS(0.216)KS(0.775)DS(0.007)DLLTCSPTEDATMGSR;S(0.001)LS(0.046)KS(0.951)DS(0.001)DLLTCSPTEDATMGSR;S(0.005)LS(0.208)KS(0.786)DSDLLTCSPTEDATMGSR;S(0.002)LS(0.052)KS(0.945)DS(0.001)DLLTCSPTEDATMGSR;SLS(0.004)KS(0.995)DS(0.001)DLLTCSPTEDATMGSR;SLS(0.008)KS(0.991)DS(0.001)DLLTCSPTEDATMGSR 285.75 1.45E-52 6866170000 2681630 2365280 1653360 1750620 1989600 2028840 1905980 2353780 2268420 2020790 TRUE FALSE 2576828.935 2297824.53 1952158.931 1840969.708 2053597.291 2069864.535 1929305.953 2305173.62 2010918.472 1883920.093 1.367801609 1.219703818 1.036221726 0.977201589 1.090066027 1.098700811 1.024091181 1.223604774 1.067411765 1 20.84530634 4.498918776 3.103038577 1.077518756 1.36049276 0.678753116 0.066170493 0.168821211 3.054075614 0.017832661 0.087134521 31544.1461 -4.498918776 0.282974004 DVHEDSLTVVFENNWQPER ddPTM_BT-474_Pertuzumab_2h_R1 3 DVHEDSLTVVFENNWQPER 19 0 B4DXZ6;P51114;C9JAJ4;P51114-2 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ;; 274.08 2.14E-39 1420222000 583215 644958 607820 704308 730639 760554 692319 539684 745899 736623 FALSE TRUE 560422.313 626564.4293 717666.5949 740657.4203 754140.667 775932.923 700791.807 528539.3368 661227.6726 686730.8681 0.816072699 0.912387164 1.045047817 1.078526472 1.098160432 1.12989376 1.020475181 0.769645521 0.962862896 1 19.38938529 4.49914272 3.512532423 1.002231584 0.824661999 0.301286732 0.094675063 0.376290206 9.276574209 0.028517446 0.127348497 31560.4161 -4.49914272 -0.177569585 HS(ph)S(ph)PHQS(ph)EDEEDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 3 HS(1)S(1)PHQS(1)EDEEDPR;HS(1)S(1)PHQS(1)EDEEDPR 69.122 0.022592 271910000 230582 317080 324950 485400 364640 404640 478040 144010 568510 436440 TRUE FALSE 221570.6005 308037.1889 383675.6935 510451.5522 376368.9768 412822.098 483890.3965 141036.1432 503975.1282 406879.5301 0.544560697 0.757072219 0.942971236 1.254552059 0.9250133 1.014605227 1.189271912 0.346628751 1.238634758 1 18.63424218 4.499241613 2.659251407 0.952283189 0.545234604 0.242975842 0.245801011 0.519621902 6.46146244 0.065193063 0.365591678 31567.60348 -4.499241613 -0.407048586 AGGLDWPEATEVS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 6 AGGLDWPEATEVSPSR 16 0 Q9Y446;Q9Y446-2;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 AGGLDWPEATEVS(0.987)PS(0.013)R;AGGLDWPEATEVS(0.924)PS(0.076)R;AGGLDWPEATEVS(0.998)PS(0.002)R;AGGLDWPEATEVS(0.996)PS(0.003)R;AGGLDWPEATEVS(0.956)PS(0.044)R;AGGLDWPEATEVS(1)PSR 278.08 2.45E-35 4872840000 2943480 3190500 2922220 3257350 3104380 3383530 3522860 3363980 3356580 3843630 TRUE FALSE 2828445.547 3099510.064 3450330.158 3425462.224 3204235.202 3451947.295 3565973.814 3294512.637 2975555.11 3583297.517 0.789341531 0.864988199 0.962892459 0.955952501 0.894214111 0.963343758 0.99516543 0.919408065 0.830395773 1 21.7728564 4.499261903 3.087557454 0.938808512 0.79274945 0.501478709 0.04777997 0.217708046 3.889095587 0.011793714 0.057915465 31569.07836 -4.499261903 -0.146059062 MEESLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 MEESLKR 7 1 Q14746-2;Q14746;B7Z2Y2 Q14746-2 COG2 Conserved oligomeric Golgi complex subunit 2 0 89.55 0.049912 0 216670 227270 199920 221010 221990 228370 239540 246260 259970 243640 FALSE TRUE 208202.2969 220788.4821 236049.9912 232416.3526 229130.51 232987.7979 242471.5622 241174.6449 230459.2955 227138.0458 0.916633302 0.972045354 1.039235811 1.023238321 1.008772041 1.025754171 1.067507477 1.061797657 1.014622164 1 17.79320985 4.49945564 2.206000975 1.03508962 0.910207176 0.741329925 0.021252628 0.2019814 1.587648131 0.005942527 0.040463723 31583.16436 -4.49945564 -0.124882444 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.135)T(0.135)S(0.729)FRGGMGS(0.001)GGLATGIAGGLAGMGGIQNEK;S(0.158)T(0.158)S(0.673)FRGGMGS(0.012)GGLATGIAGGLAGMGGIQNEK 281.37 3.84E-72 1808050000 3427300 1976950 377990 265040 809430 477560 226060 851710 297630 198961 TRUE FALSE 3293357.327 1920569.322 446301.2013 278718.7462 835466.0511 487216.5904 228826.5899 834121.8909 263844.2902 185485.1943 17.755365 10.35429986 2.406128441 1.502646868 4.504219619 2.626714183 1.233664988 4.496972894 1.422454721 1 17.50094451 4.499535515 2.316466284 2.563813541 18.32154936 0.938039185 1.266104625 0.080723595 0.716232762 0.32256024 2.084087742 31588.97361 -4.499535515 15.75773582 SRKS(ph)PS(ph)PAGGGSS(ph)PYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRKSPSPAGGGSSPYSR 17 2 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 3 S(0.063)RKS(0.942)PS(0.942)PAGGGS(0.463)S(0.467)PY(0.082)S(0.042)R 55.588 0.077695 412210000 385710 328680 204730 211970 267820 287970 243010 334320 350360 249240 TRUE FALSE 370636.0268 319306.3682 241729.2652 222909.7971 276434.6735 293792.9507 245984.0291 327416.1752 310588.6016 232358.7528 1.595102497 1.374195568 1.040327779 0.959334626 1.189689092 1.264393732 1.058638963 1.409097661 1.336677004 1 17.82599447 4.499550411 3.973541312 1.176820808 1.567634264 0.486115446 0.141809128 0.199072229 6.804833078 0.037402132 0.1555263 31590.05714 -4.499550411 0.390813457 NYGYNPS(ph)PVKPEGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NYGYNPSPVKPEGLR 15 1 E9PRF4;Q15047-3;Q15047 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 1 NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR 162.76 9.55E-07 3807290000 3415390 2974200 2401270 2298180 2284420 2295820 2473240 2907930 2942940 3299860 TRUE FALSE 3281912.783 2889378.728 2835232.905 2416789.345 2357900.444 2342243.053 2503508.251 2847880.229 2608869.789 3076357.543 1.066817734 0.939220714 0.921620087 0.785600929 0.766458518 0.761368931 0.813789755 0.925731223 0.84803855 1 21.55279176 4.499637891 1.53057019 0.839340418 1.091828334 0.469369769 0.072050038 0.6169937 1.907391813 0.020332681 0.205687865 31596.42092 -4.499637891 0.252487916 FPLDYYSIPFPTPTT(ph)PLTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FPLDYYSIPFPTPTTPLTGR 20 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;H0Y5H6;H7C2T8 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 FPLDYYSIPFPT(0.006)PT(0.123)T(0.87)PLT(0.001)GR;FPLDYYSIPFPT(0.001)PT(0.143)T(0.855)PLT(0.001)GR 203.99 1.13E-20 259180000 927950 844380 547310 442130 500460 417900 133801 355371 195085 165351 TRUE FALSE 891684.6881 820299.1091 646221.0918 464948.3823 516557.7504 426350.2243 135438.4967 348032.4647 172939.7687 154151.6295 5.784464887 5.321378125 4.192113272 3.016175592 3.350971716 2.765784739 0.878605676 2.257728094 1.121880899 1 17.23399061 4.500030387 0.344026108 0.931885649 9.263986854 0.913701944 0.485472585 1.451806608 0.156727205 0.473822345 5.006657237 31624.98931 -4.500030387 8.332101205 up S(ph)PLAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLAIR 6 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PLAIR 101.28 0.038496 316050000 58346 70744 72407 93080 71604 63326 81469 89346 79481 77991 TRUE FALSE 56065.77382 68726.45039 85492.55559 97883.86995 73907.20769 64606.49511 82466.04199 87500.97388 70458.65009 72708.6001 0.771102369 0.94523138 1.175824531 1.346248859 1.016485087 0.888567446 1.134199281 1.203447374 0.969055242 1 16.1498384 4.500971925 3.495049211 1.104812406 0.786326283 0.38433686 0.126270958 0.243039296 5.899365708 0.03273018 0.14742547 31693.62574 -4.500971925 -0.318486122 SYS(ph)PDGKESPSDKK ddPTM_BT-474_Pertuzumab_2h_R1 6 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.043)YS(0.834)PDGKES(0.119)PS(0.004)DKK;S(0.002)YS(0.998)PDGKESPSDKK;S(0.016)YS(0.984)PDGKESPSDKK;S(0.006)YS(0.994)PDGKESPSDKK;S(0.02)YS(0.979)PDGKESPSDKK;SYS(0.999)PDGKES(0.001)PSDKK 137.44 1.67E-05 17432000000 10554640 8398480 5311470 3982300 5994700 6624370 6045430 7216450 8897010 6194830 TRUE FALSE 10142153 8158963.573 6271370.782 4187826.98 6187524.97 6758319.3 6119415.781 7067427.786 7887058.724 5775248.646 1.756141358 1.412746718 1.085904896 0.725133624 1.071386766 1.170221356 1.059593475 1.22374433 1.365665655 1 22.46145163 4.501226247 2.662765218 1.091079124 1.756959801 0.646845912 0.15683997 0.207939922 2.588946837 0.042585221 0.239860073 31712.19089 -4.501226247 0.665880677 RTDALTSS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 7 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.344)S(0.103)S(0.553)PGR;RTDALT(0.019)S(0.04)S(0.941)PGR;RTDALT(0.001)S(0.011)S(0.989)PGR;RTDALT(0.033)S(0.092)S(0.876)PGR;RTDALT(0.015)S(0.353)S(0.631)PGR;RTDALT(0.084)S(0.396)S(0.52)PGR;RTDALT(0.035)S(0.241)S(0.724)PGR 205.8 3.02E-08 17991227000 4921493 6049973 5647356 7155797 6585597 7096404 7994704 6199068 7913617 8397620 TRUE FALSE 4729155.613 5877433.694 6667958.854 7525108.541 6797428.708 7239898.151 8092545.579 6071055.079 7015296.375 7828841.718 0.604068365 0.750741158 0.851717163 0.961203306 0.868254712 0.92477258 1.033683637 0.775472962 0.896083562 1 22.90036744 4.501236509 1.62993433 0.910560247 0.565502665 0.685419908 0.06864473 0.378134019 1.37230101 0.018789057 0.17909105 31712.94022 -4.501236509 -0.345057582 VTNDIS(ph)PESSPGVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VTNDISPESSPGVGR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 VT(0.009)NDIS(0.457)PES(0.385)S(0.149)PGVGR;VTNDIS(0.999)PES(0.001)SPGVGR;VTNDIS(0.996)PES(0.004)SPGVGR 248.46 2.27E-18 6483600000 2146000 2540860 2350630 2875780 2746980 3070810 2891570 2765300 3081000 3388760 TRUE FALSE 2062131.947 2468397.161 2775441.13 3024199.35 2835339.106 3132903.882 2926957.899 2708195.589 2731257.797 3159236.267 0.652731158 0.781327179 0.878516482 0.957256468 0.89747612 0.991664952 0.926476418 0.857231103 0.864531034 1 21.5911444 4.501616025 1.737557277 0.91990361 0.623755058 0.784977699 0.045774342 0.269451785 1.152529608 0.012750016 0.113670369 31740.66529 -4.501616025 -0.296148552 EVVTEHLINK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVVTEHLINK 10 0 Q13618;Q13618-2;A0A087X1R9;H7C1L6 Q13618 CUL3 Cullin-3 0 ; 152.97 1.71E-05 475830000 1425130 1483710 1285320 1454070 1478980 1518020 1507730 1542580 1730510 1727150 FALSE TRUE 1369434.344 1441396.044 1517605.916 1529114.727 1526552.735 1548715.404 1526182.051 1510725.184 1534069.76 1610168.592 0.850491278 0.895183306 0.942513674 0.949661256 0.948070123 0.961834315 0.947839908 0.938240375 0.952738593 1 20.61878032 4.501924612 1.610417574 0.95326764 0.835567937 0.822518586 0.01602584 0.244050957 0.857852189 0.004048796 0.039161038 31763.22651 -4.501924612 -0.117699702 RGGRIPT(ph)MGCLDLPGEDMR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGGRIPTMGCLDLPGEDMR 19 2 A0A140T901;A0A140T8Y9;Q9H2S5-2;Q9H2S5 A0A140T901 RNF39 RING finger protein 39 1 RGGRIPT(1)MGCLDLPGEDMR 44.616 0.062381 333590000 75964 110450 113630 192370 124710 122140 143230 123510 114120 150260 TRUE FALSE 72995.2429 107300.0741 134165.4687 202298.2388 128721.4104 124609.7545 144982.8916 120959.4753 101165.576 140082.7564 0.521086569 0.765976319 0.957758629 1.444133768 0.918895471 0.889543851 1.034980288 0.863485831 0.722184362 1 17.09591985 4.502116529 2.680035905 0.981141213 0.523151004 0.40126259 0.176652685 0.328639164 4.15262044 0.046607403 0.261551517 31777.26597 -4.502116529 -0.457990209 NELMYQLEQDHDLQAILQER ddPTM_BT-474_Pertuzumab_2h_R1 11 NELMYQLEQDHDLQAILQER 20 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;;;;; 264.64 1.41E-36 6870363000 2614641 2739496 2331437 2656620 2881248 2828090 2707055 2789020 3126607 3132537 FALSE TRUE 2512457.939 2661368.256 2752779.528 2793728.477 2973925.959 2885275.917 2740184.749 2731425.762 2771687.681 2920367.479 0.86032253 0.911312797 0.942614088 0.956635936 1.018339637 0.987983854 0.93830135 0.935302075 0.949088668 1 21.47771849 4.502176921 1.4984504 0.965291893 0.845101395 0.646846926 0.025632218 0.527765802 1.539808573 0.007950415 0.082767659 31781.68516 -4.502176921 -0.120190498 EDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDVSNFDDEFTSEAPILTPPREPR 24 1 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 EDVSNFDDEFTSEAPILT(1)PPREPR;EDVSNFDDEFTSEAPILT(1)PPREPR 98.839 0.0083335 199359000 64292 76925 70236 95490 68426 84293 89518 94417 85981 94578 TRUE FALSE 61779.39756 74731.17432 82929.20759 100418.2503 70626.98443 85997.46221 90613.54806 92467.25596 76220.79734 88172.14782 0.700667944 0.847559872 0.940537456 1.138888559 0.801012408 0.975335912 1.027689019 1.048712754 0.864454357 1 16.42803538 4.502455043 2.08402879 0.983631985 0.685852456 0.48705238 0.089010898 0.355594761 2.41583046 0.022678419 0.165870103 31802.04463 -4.502455043 -0.297779529 EMSPS(ph)PPAAQDPGGTALVSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EMSPSPPAAQDPGGTALVSAR 21 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 EMSPS(1)PPAAQDPGGTALVSAR;EMS(0.001)PS(0.999)PPAAQDPGGTALVSAR 205.06 5.20E-22 346280000 223289 238587 209167 243961 248696 263909 246784 250847 236550 257651 TRUE FALSE 214562.619 231782.7324 246968.1298 256551.8564 256695.5327 269245.4208 249804.2164 245666.9218 209697.8357 240200.0683 0.89326627 0.964956979 1.028176768 1.068075702 1.068673854 1.1209215 1.039983953 1.022759584 0.873013223 1 17.87387704 4.502741598 2.268127755 1.035076255 0.887847477 0.320940352 0.061108545 0.448374486 3.763145263 0.016107395 0.107468828 31823.03509 -4.502741598 -0.147228779 LYGDVPFIEER ddPTM_BT-474_Pertuzumab_2h_R1 4 LYGDVPFIEER 11 0 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 ;;; 180.09 1.59E-05 389908000 477780 519600 474180 581540 525420 492770 552270 553620 559950 594850 FALSE TRUE 459107.8294 504781.5167 559874.8741 611553.3491 542320.6115 502734.147 559028.8455 542187.5535 496386.8235 554560.2797 0.827877232 0.910237417 1.009583439 1.10277164 0.977929057 0.906545538 1.008057854 0.977689123 0.895099851 1 19.08098476 4.503355964 3.250470688 0.98555171 0.833126293 0.45014088 0.054673763 0.2383303 4.807314611 0.014155492 0.0675637 31868.08478 -4.503355964 -0.152425417 LGLHVTPSNVDQVST(ph)PPAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGLHVTPSNVDQVSTPPAAK 20 0 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 LGLHVTPSNVDQVS(0.008)T(0.992)PPAAK;LGLHVT(0.001)PSNVDQVS(0.169)T(0.83)PPAAK 228.31 1.15E-24 749320000 1130850 1282820 1167980 1612760 1296460 1411000 1338170 1389130 1177190 1541500 TRUE FALSE 1086655.132 1246235.23 1379059.968 1695994.737 1338161.813 1439531.387 1354546.925 1360443.98 1043560.326 1437092.832 0.756148182 0.867191876 0.959617874 1.180156702 0.931158923 1.001696867 0.942560491 0.946663952 0.726160693 1 20.45472183 4.503673294 2.757518812 0.964831987 0.757912622 0.27735131 0.103988915 0.397127111 5.367897234 0.026328122 0.144458572 31891.37863 -4.503673294 -0.206919365 LYTDFDEIR ddPTM_BT-474_Pertuzumab_2h_R1 5 LYTDFDEIR 9 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;F8VZ52;B4DDQ3;B4DPZ9;F8VUJ9;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ;;;; 257.22 1.21E-14 662781000 801584 935937 892749 1079788 962493 805457 1140817 1080572 1083975 1293001 FALSE TRUE 770257.2111 909244.9931 1054088.603 1135515.988 993452.4615 821743.8924 1154778.66 1058257.811 960926.7024 1205424.891 0.63899229 0.754294191 0.874453988 0.942004763 0.824151276 0.681704766 0.957984748 0.877912692 0.797168459 1 20.20111033 4.503836584 2.657393545 0.864819566 0.637746507 0.42275089 0.085681951 0.308638035 3.81394318 0.021385449 0.121592659 31903.37171 -4.503836584 -0.227073059 LAEDEAFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAEDEAFQR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 170.3 0.0001345 774160000 457780 486840 406560 506450 489230 459130 527470 508350 495220 548310 FALSE TRUE 439889.4515 472955.7999 480034.4359 532587.9452 504966.5273 468413.9232 533925.3356 497852.3949 439004.7017 511172.4753 0.860549957 0.92523722 0.939085062 1.041894802 0.987859385 0.916352006 1.044511122 0.973942102 0.858819132 1 18.96345063 4.504144884 1.808468162 0.9756665 0.852198186 0.299608636 0.052817572 0.658193499 3.110498488 0.013780701 0.11854361 31926.02751 -4.504144884 -0.123468314 LSPT(ph)SLVHPVMSTLPELSCK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPTSLVHPVMSTLPELSCK 20 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 LS(0.081)PT(0.727)S(0.192)LVHPVMSTLPELSCK 160.2 8.97E-11 802160000 593830 721190 700960 879640 806860 794610 834820 754550 853900 970640 TRUE FALSE 570622.4671 700622.3673 827639.0648 925038.3258 832813.3847 810677.5586 845036.7769 738968.2788 756968.8518 904897.6882 0.630593353 0.774255893 0.914621703 1.022257364 0.92033983 0.895877588 0.933847868 0.816631856 0.836524241 1 19.78739516 4.504326357 2.603913835 0.910020626 0.628185023 0.696449868 0.060254029 0.197785311 2.325330593 0.016534118 0.096030941 31939.37087 -4.504326357 -0.281835602 MQQNIQELEEQLEEEESAR ddPTM_BT-474_Pertuzumab_2h_R1 4 MQQNIQELEEQLEEEESAR 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 383.2 2.06E-126 966808000 395992 442326 353765 470962 443462 475428 450883 461610 472814 482393 FALSE TRUE 380516.1948 429711.2956 417698.205 495268.4053 457726.358 485041.4799 456401.041 452077.5922 419142.1369 449720.0924 0.846117844 0.955508332 0.92879596 1.101281472 1.017802775 1.078540826 1.014855793 1.005242149 0.932006695 1 18.77866782 4.504446158 1.404704894 1.020038758 0.826597743 0.526839624 0.049079017 0.627907079 1.546801655 0.013662275 0.152272657 31948.18259 -4.504446158 -0.193441015 TITVALADGGRPDNTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 TITVALADGGRPDNTGR 17 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 225.37 2.21E-15 10229400000 2504850 2755940 2319090 2931320 2690110 3076110 2886070 2923450 2964240 3384430 FALSE TRUE 2406957.693 2677343.29 2738201.151 3082605.776 2776639.831 3138311.052 2921390.588 2863079.736 2627751.902 3155199.542 0.762854349 0.848549594 0.867837712 0.976992338 0.880020358 0.99464741 0.925897253 0.907416377 0.83283224 1 21.58929982 4.50445867 1.412890589 0.926039317 0.738332361 0.519153211 0.050488233 0.635549476 1.589169589 0.013541079 0.150121734 31949.10307 -4.50445867 -0.187706956 DRKNS(ph)ASAER ddPTM_BT-474_Pertuzumab_2h_R1 2 DRKNSASAER 10 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 DRKNS(0.993)AS(0.007)AER;DRKNS(0.794)AS(0.206)AER 97.273 0.0048601 199222000 399110 344920 236141 264930 297310 325050 271422 302730 286940 259500 TRUE FALSE 383512.34 335083.2193 278816.9316 278603.069 306873.2462 331622.7337 274743.7436 296478.5197 254367.7742 241923.8339 1.585260674 1.385077336 1.152498814 1.151614806 1.268470499 1.370773307 1.13566216 1.22550356 1.05143743 1 17.88419338 4.504516442 2.693806618 1.187472909 1.587597983 0.63080083 0.101190169 0.200652533 2.560860566 0.024910836 0.140067683 31953.35334 -4.504516442 0.400125074 SESIRPDEFSLEIFER ddPTM_BT-474_Pertuzumab_2h_R1 4 SESIRPDEFSLEIFER 16 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ;;; 283.83 1.01E-35 717008000 439668 466058 408368 479303 457844 453668 476883 504348 532732 502283 FALSE TRUE 422485.2885 452766.4822 482169.1817 504039.8853 472570.9681 462841.4778 482719.2368 493933.0376 472258.4968 468262.925 0.90223946 0.966906535 1.029697539 1.076403572 1.009200052 0.988422216 1.030872211 1.05481987 1.008532753 1 18.83695929 4.504702524 2.554018211 1.028411941 0.900574905 0.702696244 0.025088512 0.180473119 2.02352224 0.006659007 0.039470618 31967.0473 -4.504702524 -0.127837037 QDPDVPFWR ddPTM_BT-474_Pertuzumab_2h_R1 1 QDPDVPFWR 9 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 87.308 0.031521 277830000 106680 126680 102310 140710 140520 136660 131300 136170 133940 157580 FALSE TRUE 102510.8277 123067.2104 120799.6929 147972.06 145039.9534 139423.3588 132906.8887 133358.0419 118735.6927 146906.9662 0.697794191 0.837722088 0.822287029 1.007250124 0.987291189 0.949058866 0.904701064 0.907772077 0.80823732 1 17.16454328 4.50470568 1.42355571 0.930010161 0.670286285 0.582106608 0.061405778 0.587562854 1.497419654 0.017516912 0.192991677 31967.27962 -4.50470568 -0.259723876 S(ph)FGNPFEGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFGNPFEGSR 10 0 Q96RR4-6;Q96RR4-5;Q96RR4-2;Q96RR4-3;Q96RR4-4;Q96RR4-7;Q96RR4;F5GZ00 Q96RR4-6 CAMKK2 Calcium/calmodulin-dependent protein kinase kinase 2 1 S(1)FGNPFEGSR;S(1)FGNPFEGSR 93.766 0.0089814 316240000 335950 423900 414620 594110 450040 437400 504500 493630 447790 535710 TRUE FALSE 322820.7026 411810.787 489551.0572 624772.0883 464515.9453 446244.5277 510674.2219 483436.368 396958.7565 499425.8845 0.646383603 0.824568369 0.980227642 1.250980591 0.93009986 0.893515017 1.022522536 0.967984205 0.794830162 1 18.92991107 4.504859081 2.690464766 0.984523983 0.646828816 0.478158135 0.10993531 0.271206889 3.449730118 0.028350928 0.15975635 31978.57306 -4.504859081 -0.337695167 ESILQRPLSLPSLHVFGDTDK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESILQRPLSLPSLHVFGDTDK 21 1 Q8WZ82 Q8WZ82 OVCA2 Ovarian cancer-associated gene 2 protein 0 114.88 0.0001002 169420000 152650 175910 166310 201130 170350 192210 204640 185820 204280 223820 FALSE TRUE 146684.2692 170893.219 196365.9165 211510.3434 175829.4625 196096.6179 207144.4455 181982.7521 181090.9908 208660.472 0.702980626 0.819001401 0.941078656 1.013657936 0.842658222 0.939788049 0.992734482 0.872147706 0.867873963 1 17.6707978 4.505341387 2.707676604 0.92906576 0.70244903 0.631062217 0.056083727 0.198925115 2.568398329 0.014058798 0.078849016 32014.10662 -4.505341387 -0.22661673 RT(ph)SFSFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTSFSFQK 8 1 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 RT(0.479)S(0.479)FS(0.042)FQK;RT(0.508)S(0.49)FS(0.002)FQK 94.616 0.0059965 277770000 1138580 959560 640530 741010 683120 563330 697200 1086270 736040 681600 TRUE FALSE 1094083.035 932194.2883 756288.0195 779253.6149 705093.1752 574720.9186 705732.5422 1063838.145 652487.8249 635434.6249 1.721786934 1.467018403 1.190190131 1.226331686 1.109623473 0.904453261 1.110629661 1.674189764 1.026837065 1 19.27738418 4.505349187 2.144253655 1.191271067 1.754253617 0.453652346 0.198901329 0.456456744 3.320504869 0.057180429 0.408827098 32014.68157 -4.505349187 0.56298255 VGGSS(ph)VDLHR ddPTM_BT-474_Pertuzumab_2h_R1 3 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 VGGS(0.332)S(0.668)VDLHR;VGGS(0.377)S(0.623)VDLHR;VGGS(0.014)S(0.986)VDLHR 127.17 0.00023387 1313580000 1973800 1598023 823797 899770 823150 806460 630962 1066250 621762 585423 TRUE FALSE 1896661.714 1552448.949 972675.4432 946207.2375 849627.3673 822767.1737 638683.9017 1044231.565 551182.1844 545771.7788 3.47519199 2.844502059 1.782201794 1.733704956 1.556744779 1.507529714 1.170239881 1.913311764 1.009913311 1 19.05793827 4.50535034 1.107387516 1.430290487 4.100457519 0.867799826 0.274996508 0.376024462 0.506138075 0.079539834 1.070426704 32014.76658 -4.50535034 2.670167033 up DGMVSFHDNPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DGMVSFHDNPEK 12 0 Q9UNS2-2;Q9UNS2;H7C3P9;K7ELN6 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ;; 198.55 1.82E-07 1295530000 981900 1126670 1008300 1241060 1201520 1217500 1266210 1227890 1311630 1561490 FALSE TRUE 943526.2625 1094538.475 1190522.24 1305111.255 1240167.982 1242118.684 1281706.257 1202533.642 1162739.261 1455728.891 0.648146965 0.751883459 0.817818652 0.896534556 0.851922353 0.85326237 0.880456701 0.826069778 0.798733382 1 20.47331027 4.505423578 1.597434741 0.862169833 0.619744148 0.655323069 0.051566247 0.390150216 1.337197473 0.013041537 0.128570409 32020.16596 -4.505423578 -0.242425685 RADDNATIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RADDNATIR 9 1 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 108.7 0.0041198 440510000 478990 506990 423710 544460 429460 511220 513600 541460 592990 563510 FALSE TRUE 460270.5412 492531.1416 500283.8224 572559.6458 443273.9709 521557.2187 519885.5904 530278.6618 525676.2612 525342.9658 0.876133443 0.937542089 0.95229946 1.089877819 0.843780158 0.992793761 0.989611786 1.009395188 1.000634434 1 19.00290006 4.505940393 1.896722476 0.98643655 0.868950582 0.267154716 0.057278431 0.678905004 3.616938996 0.014559729 0.119494688 32058.2929 -4.505940393 -0.117485968 S(ph)SPGQTPEEGAQALAEFAALHGPALR ddPTM_BT-474_Pertuzumab_2h_R1 7 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 S(0.497)S(0.497)PGQT(0.006)PEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQT(0.001)PEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.492)S(0.492)PGQT(0.015)PEEGAQALAEFAALHGPALR;S(0.495)S(0.495)PGQT(0.01)PEEGAQALAEFAALHGPALR 250.46 2.93E-46 1902628000 538021 589785 565080 578994 599766 633791 577907 605186 698300 676171 TRUE FALSE 516994.5445 572964.9093 667202.5261 608875.9497 619058.0181 646606.6883 584979.5987 592688.6976 619031.9115 630373.3359 0.820140249 0.908929481 1.05842441 0.965897374 0.982049815 1.025751965 0.927989122 0.94021854 0.982008401 1 19.26584699 4.506043867 4.678329636 0.979298656 0.834393089 0.661419841 0.036887459 0.1212472 6.46241455 0.009398038 0.037260088 32065.93201 -4.506043867 -0.144905567 AGLLALEFYTPEAFNWR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGLLALEFYTPEAFNWR 17 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 192.05 4.84E-10 172818000 180405 196231 170595 204534 220617 206404 197948 208677 196344 225709 FALSE TRUE 173354.5732 190634.684 201425.3114 215090.0243 227713.3462 210577.6303 200370.5468 204367.747 174055.8523 210421.5284 0.823844283 0.905965685 0.957246689 1.022186398 1.082177037 1.000741853 0.952234063 0.971230219 0.827177017 1 17.68292279 4.506067703 2.018683565 0.980993621 0.814211777 0.384799275 0.061270112 0.494904053 3.089399533 0.016662697 0.127654002 32067.69197 -4.506067703 -0.166781843 AAS(ph)PS(ph)PQSVR ddPTM_BT-474_Pertuzumab_2h_R1 7 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 AAS(1)PS(1)PQSVR;AAS(1)PS(1)PQSVR;AAS(1)PS(1)PQSVR;AAS(1)PS(1)PQSVR;AAS(1)PS(1)PQSVR;AAS(1)PS(0.999)PQS(0.001)VR;AAS(1)PS(1)PQSVR 150.14 3.23E-05 4474821000 5951975 6987273 6423748 8056033 7612639 7865048 7837108 7510218 8231349 8365795 TRUE FALSE 5719365.237 6788002.815 7584662.159 8471805.829 7857506.447 8024084.659 7933020.872 7355129.374 7296960.77 7799172.253 0.733329775 0.870349134 0.972495787 1.086244226 1.007479537 1.028837984 1.017161901 0.943065384 0.935607079 1 22.89488958 4.506290065 2.115537092 1.000517282 0.718850986 0.813809534 0.040535487 0.190818783 1.340465417 0.011683865 0.08503237 32084.11503 -4.506290065 -0.281666297 AVVVS(ph)PKEENK ddPTM_BT-474_Pertuzumab_2h_R1 6 AVVVSPKEENK 11 1 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 AVVVS(1)PKEENK;AVVVS(1)PKEENK;AVVVS(1)PKEENK;AVVVS(1)PKEENK;AVVVS(1)PKEENK;AVVVS(1)PKEENK 157.38 1.85E-05 7307840000 13814530 10945590 6279160 5436760 9144780 8508830 7764250 9454600 10747290 7289800 TRUE FALSE 13274642.89 10633432.49 7413943.891 5717351.835 9438930.154 8680884.372 7859271.214 9259359.206 9527302.696 6796055.353 1.953286459 1.564647717 1.090918703 0.841275054 1.388883648 1.277341623 1.156446027 1.362460828 1.401887154 1 22.69626617 4.50636705 3.176693198 1.208176743 1.932981454 0.660190767 0.17333086 0.163690358 3.108528162 0.044799126 0.219448597 32089.80296 -4.50636705 0.724804711 EDVQHSIITDLQNGNDQTR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDVQHSIITDLQNGNDQTR 19 0 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6;A0A2R8Y705 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ;; 290.94 1.54E-49 669100000 377323 406445 365408 451473 411937 386026 401087 434333 439731 490688 FALSE TRUE 362576.8 394853.5866 431445.3541 474773.5756 425187.3277 393831.7102 405995.6227 425363.8718 389814.5804 457453.2647 0.792598562 0.863156123 0.9431463 1.037862471 0.929466156 0.860922286 0.887512789 0.929852085 0.852140777 1 18.80326483 4.506488438 3.15572127 0.926587804 0.796309829 0.389239022 0.054459017 0.288062352 5.381784249 0.01406272 0.06926569 32098.77349 -4.506488438 -0.130277975 LYDAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LYDAGR 6 0 Q9BUP0 Q9BUP0;REV__Q8WZ42-3 EFHD1 EF-hand domain-containing protein D1 0 ; 109.88 0.067884 605810000 409160 513230 396850 680070 499130 472190 538590 580870 576120 682010 FALSE TRUE 393169.5748 498593.1829 468569.6229 715168.4942 515184.9697 481738.0053 545181.4255 568874.8315 510721.2729 635816.8552 0.618369223 0.78417736 0.736956907 1.124802667 0.81027259 0.757667875 0.857450414 0.894714927 0.803252177 1 19.27825174 4.506855061 1.663775484 0.875917735 0.601029366 0.357782917 0.108071839 0.704395141 2.676754624 0.028435396 0.269862961 32125.88206 -4.506855061 -0.274888369 MCVGNR ddPTM_BT-474_Pertuzumab_2h_R1 1 MCVGNR 6 0 P56537;B7ZBH1 P56537 EIF6 Eukaryotic translation initiation factor 6 0 96.839 0.097134 209210000 177890 186520 163320 194060 184500 183040 188950 192830 203900 198700 FALSE TRUE 170937.8621 181200.6322 192835.557 204075.4599 190434.6101 186741.1942 191262.4266 188847.9931 180754.1268 185241.872 0.922781984 0.978183983 1.040993351 1.101670252 1.028032205 1.008093862 1.032501046 1.019467095 0.975773592 1 17.49905072 4.507228897 3.099963578 1.028275081 0.925293258 0.517226351 0.031207983 0.215381541 3.849409088 0.008133771 0.04071744 32153.54763 -4.507228897 -0.102981823 SSAQLLEDWGMEDIDHVFSEEDYR ddPTM_BT-474_Pertuzumab_2h_R1 8 SSAQLLEDWGMEDIDHVFSEEDYR 24 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YFD8;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;F5H6N4 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;;;;;;; 294.25 6.67E-62 1708240000 520896 566869 478913 605872 600197 569399 587656 522909 606877 662290 FALSE TRUE 500538.8084 550702.4511 565463.2325 637141.1265 619502.8816 580912.6379 594847.9099 512110.7464 537986.8672 617432.5084 0.810677769 0.891923317 0.91583003 1.031920279 1.003353198 0.940852045 0.963421754 0.829419798 0.871329028 1 19.23592192 4.507537062 0.005538821 1.82464503 4.24E-05 0.065543226 0.069155946 106490.2221 98.61688084 15639.62006 16861.86221 32176.37112 -4.507537062 -1.824602601 AMS(ph)TTSISSPQPGK ddPTM_BT-474_Pertuzumab_2h_R1 10 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMS(0.48)T(0.48)T(0.041)SISSPQPGK;AMS(0.998)T(0.002)TSISSPQPGK;AMS(0.76)T(0.12)T(0.12)SISSPQPGK;AMS(0.385)T(0.385)T(0.229)SISSPQPGK;AMS(0.849)T(0.151)TSISSPQPGK;AMS(0.99)T(0.01)TSISSPQPGK;AMS(0.996)T(0.004)TSISSPQPGK;AMS(0.984)T(0.015)T(0.001)SISSPQPGK;AMS(0.965)T(0.008)T(0.026)SISSPQPGK;AMS(0.972)T(0.027)T(0.001)SISSPQPGK 323.59 1.96E-56 4867690000 7581970 5503110 1933136 2847330 5162190 2843180 2297070 6659940 3442690 2459770 TRUE FALSE 7285658.23 5346166.691 2282496.678 2994281.043 5328236.53 2900671.048 2325182.23 6522409.912 3051890.264 2293167.587 3.177115476 2.33134583 0.995346651 1.305740173 2.32352688 1.264918911 1.013960882 2.844279654 1.330862289 1 21.12891036 4.507692269 4.199456304 1.623763249 3.064587001 0.435734491 0.590633956 0.209843947 8.156765529 0.14844085 0.616715164 32187.87228 -4.507692269 1.440823752 VKS(ph)PQRPSDWSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKSPQRPSDWSK 12 2 Q5UIP0-2;Q5UIP0;H7BZN3 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 VKS(0.999)PQRPS(0.001)DWSK;VKS(1)PQRPSDWSK 123.36 0.0001785 1536410000 1227980 1104360 843320 832060 926700 846220 1035580 1099620 1089150 1074940 TRUE FALSE 1179989.184 1072864.734 995726.6836 875002.7163 956508.1471 863331.1482 1048253.738 1076912.463 965514.2581 1002133.356 1.177477206 1.070580804 0.993606966 0.873139998 0.954471918 0.861493276 1.0460222 1.074619916 0.963458857 1 19.93464307 4.507852652 2.294610505 0.974433148 1.184196004 0.521764018 0.062953629 0.357938186 3.074975431 0.018437101 0.123349069 32199.76125 -4.507852652 0.209762857 DSLIIIDELGR ddPTM_BT-474_Pertuzumab_2h_R1 5 DSLIIIDELGR 11 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y713 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 ;;;; 188.87 6.88E-06 218723000 352863 375700 326266 400488 390131 396429 373282 371326 420146 401073 FALSE TRUE 339072.7238 364985.4038 385229.5239 421157.2337 402679.9179 404445.066 377850.3368 363657.9883 372452.7875 373907.9685 0.906834709 0.976137003 1.03027899 1.126366029 1.076949281 1.08167009 1.010543686 0.97258689 0.996108184 1 18.51232369 4.508530805 2.532558731 1.037138463 0.905318974 0.463479513 0.044224582 0.35124903 3.843012926 0.013104996 0.079219426 32250.08063 -4.508530805 -0.131819489 NKDQEVNFQEYVTFLGALALIYNEALKG ddPTM_BT-474_Pertuzumab_2h_R1 1 NKDQEVNFQEYVTFLGALALIYNEALKG 28 2 P06703 P06703 S100A6 Protein S100-A6 0 108.63 0.0030061 524840000 75150 59824 50633 34735 49002 54555 45944 52435 54714 43697 FALSE TRUE 72213.05492 58117.87809 59783.50943 36527.67751 50578.19383 55658.13948 46506.27642 51352.19893 48503.0961 40737.36327 1.772649212 1.426648006 1.467535074 0.896662783 1.241567686 1.366267598 1.141612335 1.260567568 1.190629246 1 15.31406498 4.508532833 1.413470075 1.188226682 1.848342839 0.62219632 0.145588465 0.529730772 1.319291424 0.039312211 0.441018735 32250.23125 -4.508532833 0.660116156 QLCAEHGISPEGIVEEFATEGTDR ddPTM_BT-474_Pertuzumab_2h_R1 4 QLCAEHGISPEGIVEEFATEGTDR 24 0 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ;;; 220.5 1.00E-32 122759000 84765 94590 87308.2 108940 91753.4 93091 100139.2 101110 109684 119230 FALSE TRUE 81452.29009 91892.38581 103086.7339 114562.4065 94704.73144 94973.3638 101364.7335 99022.04317 97233.13215 111154.4459 0.732784815 0.826709045 0.9274189 1.030659687 0.852010288 0.854427036 0.911926938 0.890850945 0.874757023 1 16.76220613 4.508553302 2.962814155 0.911605563 0.735504242 0.523245472 0.055851615 0.230885712 3.692447593 0.014105897 0.073589595 32251.75126 -4.508553302 -0.176101321 LQTHDVSSLPLPHPS(ph)PYMPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQTHDVSSLPLPHPSPYMPR 20 0 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;Q9UQ26-2;A0A0J9YXG4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 LQTHDVSSLPLPHPS(0.999)PY(0.001)MPR 89.979 0.0012895 118810000 132220 145900 135360 153270 141050 151450 157600 163910 162130 164220 TRUE FALSE 127052.6962 141739.0749 159822.5631 161180.2831 145587.0013 154512.4228 159528.7559 160525.2012 143725.6821 153097.2331 0.82988238 0.925810819 1.043928488 1.052796839 0.950944693 1.009243731 1.042009399 1.048517977 0.938786934 1 17.22408868 4.509119612 3.051745777 1.014974686 0.833138311 0.686185082 0.038413014 0.148268672 2.545145819 0.009673678 0.049308599 32293.83423 -4.509119612 -0.181836375 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_BT-474_Pertuzumab_2h_R1 5 VGDPPQPLPEEPMEVQGAERASPEPQR 27 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR 179.44 1.17E-17 5352020000 315070 338139 306699 337626 351995 329840 367058 350854 381776 368953 TRUE FALSE 302756.7161 328495.6068 362126.3318 355050.9183 363317.2388 336509.5908 371550.1656 343608.7423 338438.389 343963.4847 0.880200165 0.955030465 1.052804579 1.032234333 1.056266886 0.978329403 1.080202353 0.998968663 0.98393697 1 18.39189589 4.509125168 3.19465148 1.024263101 0.883869091 0.662257101 0.032093528 0.144038893 2.763007885 0.007640225 0.037554095 32294.24739 -4.509125168 -0.14039401 LQEEGWLEGELNGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQEEGWLEGELNGR 14 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ;;; 239.03 5.58E-17 120935000 159342 189858 187190 213427 196464 200446 211007 230040 231219 222337 FALSE TRUE 153114.7385 184443.4357 221019.397 224441.993 202783.443 204499.1555 213589.3668 225289.5936 204971.9885 207277.917 0.738692962 0.889836401 1.066294954 1.082807066 0.978316677 0.98659403 1.030449215 1.086896264 0.988875185 1 17.6612069 4.509854553 2.858195152 1.032152696 0.740056344 0.840699735 0.03963888 0.109242334 1.599601691 0.010568425 0.057110673 32348.53022 -4.509854553 -0.292096352 QTLENER ddPTM_BT-474_Pertuzumab_2h_R1 3 QTLENER 7 0 P35579 P35579 MYH9 Myosin-9 0 ;; 102.46 0.019995 743740000 807820 912020 909040 968930 925360 949510 1059720 886080 931970 1055970 FALSE TRUE 776249.5013 886010.0826 1073323.749 1018936.593 955125.0448 968709.7428 1072689.17 867782.1384 826176.6727 984448.2113 0.788512278 0.900006798 1.090279547 1.035033211 0.970213602 0.984012903 1.089634943 0.881490899 0.839228172 1 19.90895579 4.509941713 4.83375153 0.984136176 0.806985299 0.396230265 0.075894037 0.205140984 11.74127069 0.019415843 0.077226372 32355.023 -4.509941713 -0.177150876 YHNTICGR ddPTM_BT-474_Pertuzumab_2h_R1 1 YHNTICGR 8 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 89.698 0.013721 119270000 106590 119580 106620 136150 125830 114720 130950 129820 128680 146220 FALSE TRUE 102424.345 116169.6955 125888.6057 143176.7178 129877.4362 117039.717 132552.6053 127139.1716 114072.7859 136316.3892 0.751372198 0.852206372 0.923503084 1.050326514 0.952764646 0.858588741 0.972389352 0.932677079 0.836823705 1 17.0565995 4.509945719 2.329736264 0.941373211 0.745622283 0.511191225 0.058751857 0.308376124 2.74458027 0.015095921 0.099984474 32355.32148 -4.509945719 -0.195750928 SGDAAIVEMVPGKPMCVESFSQYPPLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGDAAIVEMVPGKPMCVESFSQYPPLGR 28 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 240.86 2.50E-45 1033000000 484760 527640 486270 523860 520690 530500 525260 586460 644650 633450 FALSE TRUE 465815.0433 512592.2238 574149.806 550896.4774 537438.4667 541227.0735 531688.289 574349.3961 571472.0346 590545.8673 0.788787237 0.867997309 0.972235753 0.932859762 0.910070659 0.916486091 0.900333604 0.972573729 0.967701353 1 19.17168959 4.510363778 3.13948512 0.941800321 0.792027994 0.719336708 0.031192903 0.142164575 2.609609311 0.007870665 0.039350811 32386.48221 -4.510363778 -0.149772327 GS(ph)GVFCANCLTTK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSGVFCANCLTTK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(1)GVFCANCLTTK 118.47 0.00023402 0 86496 68141 41017 45987 47144 37026 31478 84086 29823 30281 TRUE FALSE 83115.64069 66197.6854 48429.68432 48360.39458 48660.42958 37774.69109 31863.23718 82349.59472 26437.61807 28230.0409 2.944226719 2.344937637 1.715537165 1.713082696 1.723710913 1.338102599 1.128699646 2.917090875 0.936506545 1 14.7849436 4.510446272 1.88651237 1.661339248 3.073105 0.401984985 0.542344093 0.57389095 2.999184955 0.144996551 1.213974012 32392.63458 -4.510446272 1.411765752 DYDVYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYDVYAR 7 0 P49585;C9JEJ2;C9J050;H7C1T3;H7BZN1;Q9Y5K3-2;Q9Y5K3-4;Q9Y5K3-3;Q9Y5K3 P49585 PCYT1A;PCYT1B Choline-phosphate cytidylyltransferase A;Choline-phosphate cytidylyltransferase B 0 ; 111.28 0.017509 503610000 1179120 1252860 1096110 1260220 1278620 1266620 1321740 1411410 1338530 1491090 FALSE TRUE 1133038.687 1217129.659 1294201.46 1325260.105 1319747.974 1292231.924 1337915.849 1382263.89 1186585.686 1390097.146 0.815078781 0.875571655 0.931015119 0.953357907 0.949392621 0.929598286 0.962462122 0.994364958 0.853599109 1 20.40675428 4.511041941 1.4973081 0.952042667 0.79164521 0.561250491 0.037992931 0.510346917 1.469673198 0.010020318 0.107244896 32437.09411 -4.511041941 -0.160397457 S(ph)RPTSEGSDIES(ph)TEPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.64)RPT(0.349)S(0.011)EGS(0.295)DIES(0.703)T(0.002)EPQK 280.93 7.22E-35 979440000 2272900 2138600 1716200 1738600 1924000 1938900 1971100 2200700 2228700 2008300 TRUE FALSE 2184072.555 2077609.222 2026355.517 1828329.354 1985887.207 1978105.886 1995222.911 2155254.776 1975707.319 1872276.052 1.166533403 1.10967035 1.082295271 0.976527661 1.060680771 1.056524696 1.065667058 1.15114156 1.055243599 1 20.83636173 4.511170987 2.263261133 1.063665858 1.169643739 0.379339997 0.044363854 0.491829449 4.068502393 0.01244374 0.085348726 32446.73387 -4.511170987 0.105977881 TQQYHK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQQYHK 6 0 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 83.614 0.056787 628230000 1122110 1020230 796980 926920 803610 755430 1016210 881410 897350 1039960 FALSE TRUE 1078256.701 991134.0393 941012.0147 974758.4523 829458.8455 770705.3122 1028646.682 863208.5755 795486.59 969522.5829 1.112152228 1.022290823 0.970593188 1.005400462 0.85553329 0.794932811 1.060982694 0.89034396 0.8204931 1 19.88691498 4.511635995 0.889132767 0.908372752 1.174284758 0.395299843 0.078929233 1.692887915 1.328682232 0.027001013 0.409161857 32481.49388 -4.511635995 0.265912006 TGPPPIS(ph)PSKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGPPPISPSKR 11 1 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;E7ERW0;E7EWF5;F8W708;E7EQU6;F8WBN7;E7EUJ2;A0A096LP98 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 TGPPPIS(0.981)PS(0.019)KR;TGPPPIS(0.981)PS(0.019)KR 135.14 0.00058853 400880000 952480 879140 678930 693230 799420 766020 777730 903250 874200 806710 TRUE FALSE 915256.0286 854067.788 801627.7537 729007.6834 825134.0703 781509.4492 787248.0924 884597.5719 774964.4809 752070.8132 1.216981184 1.135621504 1.065893982 0.969333832 1.097149438 1.039143436 1.046773892 1.176215798 1.030440841 1 19.52050898 4.511934814 2.566368716 1.063112751 1.218951107 0.481070605 0.053634312 0.322748662 3.63409798 0.014399598 0.086746347 32503.85065 -4.511934814 0.155838356 RIS(ph)LDQQ ddPTM_BT-474_Pertuzumab_2h_R1 3 RISLDQQ 7 1 Q96PM5-2;Q96PM5;Q96PM5-8;Q96PM5-7;Q96PM5-6 Q96PM5-2 RCHY1 RING finger and CHY zinc finger domain-containing protein 1 1 RIS(1)LDQQ;RIS(1)LDQQ;RIS(1)LDQQ 68.132 0.067031 1034778000 1059110 1199520 976370 1233900 1332190 1367270 1153530 1289970 1207490 1326760 TRUE FALSE 1017718.81 1165310.864 1152821.778 1297581.727 1375041.101 1394917.136 1167647.245 1263331.669 1070420.797 1236897.363 0.822799725 0.942124139 0.932027032 1.049061761 1.111685692 1.12775496 0.944013044 1.021371462 0.865407938 1 20.23829436 4.512170873 1.395922096 1.018857932 0.797908848 0.377490834 0.074392285 0.898795354 2.157950534 0.021693218 0.248862578 32521.52284 -4.512170873 -0.220949084 RTDALTS(ph)SPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.019)S(0.49)S(0.49)PGR;RTDALT(0.153)S(0.703)S(0.144)PGR;RT(0.001)DALT(0.088)S(0.456)S(0.456)PGR 168.76 1.87E-05 670722000 617250 813770 800860 1099670 1002650 1057510 1037590 781750 878412 963360 TRUE FALSE 593127.1876 790562.0764 945593.217 1156424.1 1034901.148 1078893.577 1050288.337 765606.5893 778698.3524 898110.7691 0.660416519 0.88025008 1.052869256 1.287618566 1.152309028 1.201292328 1.169441869 0.852463433 0.867040435 1 19.77653387 4.512288638 2.410717956 1.076164756 0.649731554 0.492634532 0.132402542 0.344150495 3.3239661 0.038406952 0.247031567 32530.34266 -4.512288638 -0.426433202 T(ph)LSDDLDEAAKEFQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLSDDLDEAAKEFQEK 16 1 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 1 T(0.5)LS(0.5)DDLDEAAKEFQEK 76.301 0.0438 13132000 50614 39896 27541 21079 29597 29314 27795 34296 38395 30352 TRUE FALSE 48635.94892 38758.20514 32518.27135 22166.88972 30549.01438 29906.74916 28135.16352 33587.77562 34036.56056 28296.23201 1.718813619 1.369730257 1.149208536 0.783386626 1.079614218 1.056916312 0.994307776 1.187005238 1.202865475 1 14.78832233 4.512406038 2.056325285 1.054620411 1.759847001 0.780717682 0.11185661 0.212746671 1.381427746 0.030736289 0.235222687 32539.13755 -4.512406038 0.70522659 SNEHDHSKS(ph)KEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNEHDHSKSKEK 12 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 SNEHDHS(0.17)KS(0.83)KEK 87.519 0.0049875 43878000 122210 81316 33540 33248 53668 53496 51625 5387.9 51761 31755 TRUE FALSE 117433.8981 78996.9473 39601.42409 34963.93326 55394.27996 54577.72577 52256.80219 5276.637982 45885.30828 29604.20557 3.96679782 2.668436656 1.337695889 1.181046159 1.871162522 1.843580151 1.76518171 0.178239472 1.549959116 1 14.85351452 4.512626411 2.077563421 1.291051426 4.162398776 0.752704832 0.480755049 0.23195823 1.545436342 0.138632984 1.049595293 32555.65301 -4.512626411 2.87134735 KFYPLEIDYGQDEEAVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 KFYPLEIDYGQDEEAVKK 18 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 206.98 4.46E-16 1596190000 993880 874350 658550 588840 731940 750060 769290 775410 1016980 802940 FALSE TRUE 955038.0708 849414.3941 777564.6344 619230.103 755483.5148 765226.7271 778704.8011 759397.5125 901536.6939 748556.1586 1.275840242 1.134737032 1.038752571 0.827232661 1.009254291 1.022270298 1.040275726 1.01448302 1.204367479 1 19.51375103 4.513027775 2.404154048 1.014090395 1.282001687 0.472136421 0.085225195 0.316413885 3.033230177 0.022061616 0.142621462 32585.75406 -4.513027775 0.267911292 AMNGESLDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AMNGESLDGR 10 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 117.53 0.0022008 888310000 665790 852110 704470 1121400 943190 952280 970640 963760 798100 979430 FALSE TRUE 639770.1907 827808.6571 831783.3999 1179275.588 973528.5629 971535.7541 982518.9827 943858.0192 707503.0339 913092.3337 0.700663194 0.906599066 0.910952123 1.291518442 1.066188519 1.064006036 1.076034642 1.033693948 0.774842815 1 19.80040123 4.513067645 1.773119591 1.046000641 0.675220887 0.407210214 0.122766462 0.547251937 2.431349284 0.032579411 0.294404054 32588.74567 -4.513067645 -0.370779754 NTDEMVELR ddPTM_BT-474_Pertuzumab_2h_R1 4 NTDEMVELR 9 0 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;; 135.43 0.00051433 6815620000 3924650 4145450 3494640 4235260 4172220 4052020 4178030 4462660 4318330 4612170 FALSE TRUE 3771270.339 4027225.825 4126199.186 4453842.276 4306423.245 4133954.621 4229161.981 4370504.511 3828131.282 4299783.618 0.87708375 0.936611277 0.959629496 1.035829398 1.001544177 0.961433176 0.983575537 1.016447547 0.89030789 1 22.03583263 4.513120445 1.858347023 0.986325999 0.86835192 0.432219339 0.037455934 0.469082457 2.351076352 0.009598876 0.082398847 32592.70793 -4.513120445 -0.117974078 EAVTHIGR ddPTM_BT-474_Pertuzumab_2h_R1 6 EAVTHIGR 8 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;;;; 171.73 0.00028767 6756320000 4800030 5237430 4509420 5492430 5369930 5723590 5578810 5363470 5690420 6075350 FALSE TRUE 4612439.521 5088063.624 5324372.506 5775894.971 5542658.675 5839324.911 5647085.146 5252712.47 5044467.378 5663861.133 0.814363102 0.898338343 0.940060567 1.01978047 0.978600736 1.030979534 0.997038065 0.927408414 0.890641077 1 22.43335446 4.513366213 1.750132547 0.975062649 0.797851145 0.616092177 0.040229246 0.417644755 1.793548428 0.011621469 0.106615052 32611.15746 -4.513366213 -0.177211503 QVHPDTGISS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 5 QVHPDTGISSK 11 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 1 QVHPDTGIS(0.214)S(0.786)K;QVHPDTGIS(0.183)S(0.817)K;QVHPDTGIS(0.207)S(0.793)K;QVHPDTGIS(0.043)S(0.957)K;QVHPDTGIS(0.027)S(0.973)K 192.65 1.36E-06 1491170000 2957830 2539670 1755820 1957100 2209460 1836410 1902880 2616270 2140210 1639250 TRUE FALSE 2842234.734 2467241.098 2073135.732 2058106.166 2280529.287 1873543.468 1926168.015 2562243.11 1897262.333 1528222.137 1.859830887 1.614451877 1.356567008 1.346732334 1.492276045 1.225962785 1.260397927 1.676616931 1.241483346 1 20.54342283 4.513435444 2.230165856 1.363130655 1.887017483 0.495539904 0.171279023 0.356029711 2.831834264 0.043314305 0.303977048 32616.3564 -4.513435444 0.523886828 VDGAEWGVDLPSVEAQLGSHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VDGAEWGVDLPSVEAQLGSHR 21 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 265.54 6.53E-37 1588630000 1054640 1124930 965600 1154140 1113120 1162630 1170360 1173820 1257480 1274940 FALSE TRUE 1013423.503 1092848.098 1140105.4 1213705.304 1148924.516 1186139.175 1184683.216 1149580.207 1114736.142 1188587.178 0.852628668 0.91945136 0.959210583 1.021132758 0.966630414 0.997940409 0.99671546 0.96718207 0.937866538 1 20.18081629 4.51367544 1.825427684 0.982517811 0.840236304 0.77348803 0.022246167 0.246707887 1.180269652 0.005903882 0.051778364 32634.38557 -4.51367544 -0.142281506 GFGS(ph)LPCILNACSGDAK ddPTM_BT-474_Pertuzumab_2h_R1 3 GFGSLPCILNACSGDAK 17 0 Q8WWL2-4;Q8WWL2-3;Q8WWL2-2;Q8WWL2 Q8WWL2-4 SPIRE2 Protein spire homolog 2 1 GFGS(1)LPCILNACSGDAK;GFGS(1)LPCILNACSGDAK;GFGS(1)LPCILNACSGDAK 157.47 2.59E-08 180402000 305762 254948 160067 185282 190394 176398 191122 275592 222655 203547 TRUE FALSE 293812.483 247677.1327 188994.6676 194844.4262 196518.1959 179964.8884 193461.0082 269900.9289 197380.1378 189760.5804 1.548332548 1.305208554 0.995963794 1.026790843 1.035611271 0.948378678 1.019500509 1.422323479 1.040153532 1 17.5338208 4.514194077 3.175058537 1.085972694 1.537799267 0.590642396 0.127749278 0.21735831 4.078354767 0.036474195 0.182713068 32673.38097 -4.514194077 0.451826573 S(ph)SSLESLQTAVAEVTLNGDIPFHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLESLQTAVAEVTLNGDIPFHR 24 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.332)S(0.332)S(0.332)LES(0.005)LQTAVAEVTLNGDIPFHR 131.97 3.38E-05 27095000 6620.6 7896.4 6859.4 9245.6 8616.4 8229 8170.1 9211.7 10184 8613.8 TRUE FALSE 6361.859633 7671.202403 8099.046167 9722.766524 8893.554331 8395.396018 8270.088128 9021.475176 9027.955015 8030.379654 0.792224018 0.955272694 1.008550843 1.210748052 1.107488651 1.045454434 1.029850204 1.123418265 1.12422518 1 12.97125248 4.514308489 1.707435595 1.09258513 0.761301944 0.708785504 0.058881649 0.317619861 1.278353699 0.015824789 0.149527089 32681.98974 -4.514308489 -0.331283186 TAQVPS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 5 TAQVPSPPR 9 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 TAQVPS(1)PPR;TAQVPS(1)PPR;TAQVPS(1)PPR;TAQVPS(1)PPR;TAQVPS(1)PPR 115.04 0.0016164 28599700000 3098700 3183800 2686370 3177800 3040140 3048960 3032290 3319870 3650570 3474730 TRUE FALSE 2977599.378 3093001.141 3171856.817 3341806.639 3137928.864 3110612.06 3069400.072 3251313.524 3236172.598 3239383.442 0.919187071 0.954811678 0.979154482 1.031618115 0.968680899 0.960248182 0.947526011 1.003682825 0.99900881 1 21.62728782 4.514508319 2.372649715 0.985400813 0.917339288 0.462337408 0.022910716 0.356249023 3.300571741 0.006169062 0.040622278 32697.03103 -4.514508319 -0.068061525 MELQEIQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 MELQEIQLK 9 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 138.66 0.00030332 66790000 142720 151410 134170 148540 151930 138650 152950 174760 174770 164620 FALSE TRUE 137142.3446 147091.935 158417.5036 156206.1672 156816.9664 141453.598 154821.8479 171151.1449 154930.8423 153470.1408 0.893609297 0.958440087 1.032236647 1.017827744 1.021807667 0.921701103 1.008807623 1.115208105 1.009517822 1 17.22759847 4.514730652 2.552244598 1.021582614 0.890627303 0.423111249 0.044552329 0.343027232 3.799546668 0.01268887 0.07749972 32713.77424 -4.514730652 -0.130955311 TVS(ph)DNSLSNSR ddPTM_BT-474_Pertuzumab_2h_R1 6 TVSDNSLSNSR 11 0 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 1 TVS(1)DNSLSNSR;TVS(1)DNSLSNSR;T(0.003)VS(0.924)DNS(0.073)LSNSR;T(0.007)VS(0.965)DNS(0.028)LSNSR;TVS(0.981)DNS(0.019)LSNSR;T(0.002)VS(0.802)DNS(0.196)LSNSR 247.99 3.74E-16 5729280000 2537420 2699960 2210630 2735190 2682820 2738330 2799990 2819430 2779230 2841070 TRUE FALSE 2438254.821 2622959.784 2610140.016 2876353.484 2769115.342 2793700.909 2834257.115 2761207.785 2463743.462 2648641.798 0.920567977 0.990303704 0.985463575 1.085973002 1.045485027 1.054767357 1.070079434 1.042499513 0.930191264 1 21.33682132 4.514887467 1.476675659 1.037154051 0.906489257 0.367784982 0.042888051 0.755946492 2.090298595 0.011710276 0.128528511 32725.58866 -4.514887467 -0.130664794 GTQEVAPPTPLTPTSHT(ph)ANTSPRPVSGMER ddPTM_BT-474_Pertuzumab_2h_R1 6 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.05)S(0.05)HT(0.554)ANT(0.149)S(0.149)PRPVS(0.049)GMER;GTQEVAPPTPLTPT(0.011)S(0.011)HT(0.479)ANT(0.247)S(0.247)PRPVS(0.006)GMER;GTQEVAPPTPLT(0.022)PT(0.251)S(0.251)HT(0.31)ANT(0.081)S(0.081)PRPVS(0.004)GMER;GTQEVAPPTPLTPT(0.034)S(0.034)HT(0.645)ANT(0.14)S(0.14)PRPVS(0.007)GMER;GTQEVAPPTPLTPT(0.072)S(0.072)HT(0.285)ANT(0.285)S(0.285)PRPVS(0.001)GMER;GTQEVAPPTPLTPT(0.054)S(0.054)HT(0.41)ANT(0.284)S(0.197)PRPVS(0.002)GMER 139.73 8.39E-08 7919760000 378111.1 479778 478637.4 566119.8 536251.6 472015 643564.1 567072 590583 640135 TRUE FALSE 363334.1002 466095.2012 565137.8254 595337.3107 553500.6197 481559.4667 651440.23 555361.765 523542.4938 596778.0863 0.608826142 0.781019297 0.94698153 0.997585743 0.927481475 0.806932221 1.091595427 0.930600131 0.8772817 1 19.18683504 4.51499189 2.284430835 0.948620134 0.592996747 0.689944321 0.072204425 0.213058773 1.79614713 0.018191845 0.124955983 32733.4582 -4.51499189 -0.355623386 HWILPQDYDHAQAEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HWILPQDYDHAQAEAR 16 0 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 140.22 2.35E-05 0 62273 55265 41048 40291 50228 48281 56491 36317 61410 58938 FALSE TRUE 59839.30231 53688.89631 48466.28671 42370.42334 51843.62924 49257.2749 57182.35376 35567.04126 54438.99425 54946.07676 1.089055049 0.977119741 0.882070014 0.771127364 0.943536505 0.896465732 1.040699484 0.647308113 0.99077127 1 15.74572885 4.515655161 2.463821124 0.876808166 1.094258465 0.209340623 0.111324382 0.477226266 4.844965463 0.027829366 0.176722079 32783.48818 -4.515655161 0.217450299 DFEPYDFTLDD ddPTM_BT-474_Pertuzumab_2h_R1 2 DFEPYDFTLDD 11 0 Q69YN2;Q69YN2-2;Q69YN2-3 Q69YN2 CWF19L1 CWF19-like protein 1 0 ; 167.33 4.51E-05 86096000 274060 282760 242440 282420 271680 284860 278010 298750 287390 306910 FALSE TRUE 263349.4322 274695.9617 286254.301 296995.73 280418.8339 290620.0644 281412.3695 292580.7081 254766.692 286122.7123 0.920407297 0.960063462 1.000459903 1.038001239 0.980064923 1.015718263 0.983537334 1.02257072 0.890410586 1 18.1262745 4.515663916 2.842835324 0.995141197 0.920716165 0.249093751 0.038015441 0.371958697 5.340905098 0.009003008 0.0497033 32784.14908 -4.515663916 -0.074425031 AVTEQGAELSNEER ddPTM_BT-474_Pertuzumab_2h_R1 6 AVTEQGAELSNEER 14 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 341.16 1.32E-68 6222540000 1416421 1633807 1353200 1873880 1694528 1844740 1722280 1682284 1784620 1795060 FALSE TRUE 1361065.701 1587212.424 1597753.342 1970591.171 1749034.032 1882041.907 1743357.778 1647544.248 1582037.419 1673478.987 0.813315083 0.948450764 0.954749569 1.177541628 1.045148487 1.124628347 1.041756599 0.9845025 0.945358401 1 20.67441901 4.515812434 1.694821509 1.042654352 0.792700244 0.520846305 0.066930458 0.506582375 1.996459786 0.018740129 0.179323266 32795.36238 -4.515812434 -0.249954108 QGQQQAGGDGKTEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 QGQQQAGGDGKTEQK 15 1 Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 229.54 4.09E-13 608500000 1105225 887536 566369 465471 661392 825883 636018 735786 866313 700105 FALSE TRUE 1062031.585 862224.3423 668724.4771 489494.0141 682666.2743 842582.9201 643801.7785 720591.762 767972.7801 652686.2648 1.627170116 1.321039508 1.024572621 0.749968309 1.045933263 1.290946302 0.986387815 1.104040028 1.176633892 1 19.31603015 4.516226852 2.722152055 1.049390806 1.62981818 0.65430027 0.133103824 0.197838717 2.557528586 0.035285961 0.203157859 32826.67174 -4.516226852 0.580427373 RGDPFTDLCFLNS(ph)PIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGDPFTDLCFLNSPIFK 17 1 Q5FBB7-6;Q5FBB7;Q5FBB7-5;Q5FBB7-4;Q5FBB7-3;Q5FBB7-2 Q5FBB7-6 SGOL1 Shugoshin-like 1 1 RGDPFTDLCFLNS(1)PIFK 126.45 2.67E-05 139840000 466430 407980 347370 317900 356980 359360 347460 401830 362950 373000 TRUE FALSE 448201.3999 396344.8099 410147.4862 334306.8571 368462.5859 366626.5054 351712.3194 393532.0701 321749.4376 347736.3778 1.288911453 1.139785295 1.179478227 0.961380167 1.059603221 1.054323128 1.011433781 1.131696582 0.925268273 1 18.40763447 4.516257858 1.081336359 1.03489971 1.342574084 0.627190935 0.063963826 0.822203375 1.030436169 0.018925539 0.266205878 32829.01543 -4.516257858 0.307674373 SSSVGSSSSYPIS(ph)PAVSR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR 437.58 8.10E-170 4976120000 1518630 1737470 1676310 1983170 1678180 1985340 1959950 1701410 1923400 2196300 TRUE FALSE 1459280.261 1687919.057 1979256.506 2085521.641 1732160.184 2025484.935 1983936.454 1666275.289 1705063.696 2047542.645 0.712698348 0.824363322 0.966649711 1.018548574 0.84597026 0.989227228 0.968935353 0.813792715 0.832736598 1 20.96546207 4.516386841 3.351197826 0.92131105 0.719529377 0.480603761 0.070911905 0.233879803 4.983209447 0.018476591 0.089474174 32838.76692 -4.516386841 -0.201781673 SGT(ph)FDLLEMDR ddPTM_BT-474_Pertuzumab_2h_R1 5 SGTFDLLEMDR 11 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 S(0.016)GT(0.984)FDLLEMDR;S(0.294)GT(0.706)FDLLEMDR;S(0.022)GT(0.978)FDLLEMDR;S(0.006)GT(0.994)FDLLEMDR;S(0.099)GT(0.901)FDLLEMDR 250.69 1.01E-15 865415000 1112743 977867 769892 743713 829276 677119 733234 1139555 948973 792605 TRUE FALSE 1069255.773 949979.1906 909028.6106 782096.1171 855950.4157 690810.8101 742207.537 1116022.791 841249.5635 738921.1574 1.447049882 1.285629977 1.23021056 1.058429725 1.158378546 0.934891095 1.004447538 1.510340826 1.138483524 1 19.49506091 4.516396214 1.637836612 1.146956435 1.482181029 0.310981361 0.151765506 0.973532007 3.509961848 0.045589126 0.453086934 32839.47565 -4.516396214 0.335224594 MNWIDAPDDVFYMATEETR ddPTM_BT-474_Pertuzumab_2h_R1 1 MNWIDAPDDVFYMATEETR 19 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 0 96.591 0.0029123 18221000 28364 30142 26131 30443 29814 32609 28926 33211 32914 33860 FALSE TRUE 27255.50352 29282.37967 30853.45298 32014.16688 30772.99439 33268.37632 29280.00504 32525.18124 29177.74071 31566.63204 0.863427669 0.927637121 0.977407186 1.014177466 0.974858336 1.053909593 0.927561895 1.0303659 0.924322261 1 14.94611272 4.516499003 1.899887588 0.991620644 0.851547745 0.512271409 0.038664221 0.368146082 1.94462049 0.009198393 0.077870396 32847.24906 -4.516499003 -0.140072899 VAGPADAPMDS(ph)GAEEEKAGAATVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VAGPADAPMDSGAEEEKAGAATVK 24 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 VAGPADAPMDS(1)GAEEEKAGAATVK 261.26 2.86E-44 278960000 456190 382370 239440 251160 308030 352970 318360 335080 373550 294030 TRUE FALSE 438361.5905 371465.182 282712.1343 264122.3977 317938.0647 360107.2952 322256.1849 328160.4809 331146.17 274115.0862 1.599188124 1.355143152 1.031362915 0.963545646 1.159870728 1.313708414 1.175623675 1.197163153 1.208055254 1 18.0644222 4.516882795 3.468317134 1.145297037 1.581755469 0.670909353 0.103096168 0.154055923 3.565143265 0.027214687 0.128906464 32876.28944 -4.516882795 0.436458432 S(ph)AVLLVDETATTPIFANR ddPTM_BT-474_Pertuzumab_2h_R1 4 SAVLLVDETATTPIFANR 18 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36;A0A087WX73 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(1)AVLLVDETATTPIFANR;S(0.813)AVLLVDET(0.182)AT(0.005)TPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR 283.49 1.94E-39 366583000 89821 78622 57303.2 63226 54885.1 65813 58237.8 95039 60022.4 48884.4 TRUE FALSE 86310.69602 76379.77754 67659.16294 66489.10144 56650.52909 67143.78395 58950.53162 93076.41144 53208.90879 45573.41605 1.89388252 1.675972182 1.484619079 1.458944868 1.243060846 1.473310315 1.29352892 2.04234002 1.167542691 1 15.47590489 4.51700267 1.938699809 1.453701747 1.93347237 0.253766979 0.265544978 0.79958872 4.445045619 0.07064759 0.585696898 32885.36527 -4.51700267 0.479770623 FEEFLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 FEEFLQR 7 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7;Q02218-3 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 120.49 0.010575 52587000 72969 90382 73629 132990 68874 68448 133240 103430 92124 91795 FALSE TRUE 70117.29081 87804.39385 86935.39817 139853.6298 71089.39476 69832.06546 134870.631 101294.1344 81666.46974 85577.64289 0.819341226 1.026020242 1.015865771 1.634230917 0.830700547 0.816008283 1.576003106 1.183651839 0.954296788 1 16.38494632 4.517469549 2.017110156 1.155685784 0.805429064 0.10652164 0.266120341 1.007958922 6.19571413 0.069274109 0.550253774 32920.73695 -4.517469549 -0.35025672 AELPGSSS(ph)PLLAQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AELPGSSSPLLAQPR 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 AELPGSS(0.039)S(0.96)PLLAQPR;AELPGSS(0.002)S(0.998)PLLAQPR 323.16 8.28E-57 411250000 491810 574110 534240 681390 532960 590700 632890 660640 701250 712870 TRUE FALSE 472589.5215 557736.9449 630789.0521 716556.6196 550103.1424 602644.3587 640635.4971 646997.5531 621647.0399 664586.6799 0.711102909 0.839223779 0.949144891 1.078198888 0.827737237 0.906795723 0.963960784 0.973533736 0.935388955 1 19.34209785 4.517865395 2.483252087 0.953256912 0.705239396 0.616495241 0.060720436 0.231751482 2.392775692 0.015516289 0.098375728 32950.75693 -4.517865395 -0.248017516 HPTT(ph)PSSTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HPTTPSSTAK 10 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 HPT(0.032)T(0.968)PSSTAK 95.094 0.028172 54553000 194730 180020 127530 78405 109500 106450 47426 65995 66036 52893 TRUE FALSE 187119.7363 174886.0059 150577.5079 82451.49145 113022.1669 108602.4919 48006.41357 64632.18019 58539.87013 49310.51 3.7947232 3.5466274 3.053659512 1.672087582 2.292050254 2.202420781 0.973553378 1.310718145 1.187168215 1 15.58960755 4.51800539 0.375823809 0.940030784 5.889547386 0.882872044 0.342919437 1.600442536 0.204261643 0.314955868 3.556096669 32961.38029 -4.51800539 4.949516601 up GEVAQMAAYYEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEVAQMAAYYEHR 13 0 P40938 P40938 RFC3 Replication factor C subunit 3 0 100.45 0.0023944 183720000 142480 181610 193890 214430 201130 196900 225280 191540 225480 236890 FALSE TRUE 136911.7241 176430.6606 228930.2361 225496.758 207599.5291 200881.4529 228037.044 187584.6321 199884.4557 220845.2293 0.619944223 0.798888258 1.036609379 1.021062392 0.940022702 0.909602863 1.032564954 0.849394088 0.905088402 1 17.75267614 4.518076512 3.400611652 0.953818619 0.63129606 0.758737096 0.060666143 0.12385839 2.725841343 0.015815622 0.076166792 32966.77862 -4.518076512 -0.322522559 AALSEMVEYITHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALSEMVEYITHNR 14 0 H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;G3V2U3 H0YJ75 PPP2R5C Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 0 ; 257.19 2.45E-24 305100000 254950 294840 252040 336500 297350 330420 332180 284590 347130 391920 FALSE TRUE 244986.2721 286431.4519 297589.2346 353866.8053 306914.5328 337101.3188 336245.3182 278713.117 307725.2577 365374.9093 0.670506556 0.783938482 0.814476383 0.9685033 0.83999893 0.922617591 0.920274791 0.762814057 0.842217815 1 18.47901804 4.518160617 1.664239538 0.877126593 0.6475516 0.509940441 0.067253857 0.562079169 2.107184152 0.018422634 0.181047061 32973.16358 -4.518160617 -0.229574993 S(ph)PPGSGAST(ph)PVGPWDQAVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(0.998)PPGS(0.002)GAS(0.252)T(0.748)PVGPWDQAVQR 186.11 1.80E-16 130460000 97603 114710 99412 134610 111070 123620 123560 136850 131760 142270 TRUE FALSE 93788.56685 111438.5831 117377.9598 141557.2382 114642.6674 126119.6811 125072.1642 134023.9997 116803.1572 132633.9262 0.707123506 0.84019667 0.884976892 1.067277749 0.864354021 0.950885529 0.942987725 1.010480527 0.88064314 1 17.01709032 4.518311296 1.610534494 0.957943516 0.675336846 0.640110011 0.058489056 0.393138591 1.353902932 0.015024614 0.152860149 32984.60561 -4.518311296 -0.28260667 LISS(ph)VEDFTEFV ddPTM_BT-474_Pertuzumab_2h_R1 1 LISSVEDFTEFV 12 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 LIS(0.072)S(0.928)VEDFTEFV 157.91 7.81E-05 169000000 48597 56975 54639 61995 57047 59673 66605 69847 61987 69003 TRUE FALSE 46697.77551 55350.12878 64513.48274 65194.56938 58881.96856 60879.62895 67420.13191 68404.63504 54950.49563 64329.36535 0.725916932 0.860417765 1.002862105 1.013449597 0.915320216 0.946373847 1.048045967 1.063350068 0.854205468 1 15.97318984 4.518671216 2.492465651 0.988136473 0.718235351 0.640113312 0.059966951 0.215527416 2.243545794 0.015759803 0.099776158 33011.95285 -4.518671216 -0.269901122 YEYDPDIS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 3 YEYDPDISPPR 11 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 YEYDPDIS(1)PPR;YEYDPDIS(1)PPR;YEYDPDIS(1)PPR 108.17 0.0022017 1537940000 562150 652960 610180 741600 678250 720680 690980 745300 711960 811390 TRUE FALSE 540180.5565 634338.2201 720453.0994 779874.0649 700066.5272 735252.6434 699436.4199 729909.2946 631141.2856 756433.8326 0.714114749 0.838590492 0.952433734 1.030987816 0.925482834 0.971998623 0.924649837 0.964934755 0.834364168 1 19.52885437 4.518882284 2.464918506 0.951550308 0.707440802 0.693226376 0.04976051 0.187103738 1.894949896 0.012172518 0.078009115 33028.00058 -4.518882284 -0.244109505 IISSIEQKEENKGGEDKLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IISSIEQKEENKGGEDKLK 19 3 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 154.11 1.71E-08 1532130000 3207920 2328200 1567560 722480 1736800 2019040 1354570 1744170 2019300 1241180 FALSE TRUE 3082550.94 2261802.016 1850852.962 759767.2794 1792665.749 2059866.372 1371147.633 1708152.28 1790077.53 1157113.773 2.663999869 1.954692847 1.599542763 0.65660551 1.549256254 1.780176176 1.184972182 1.476218087 1.547019465 1 20.14209929 4.519198109 2.005135406 1.354243079 2.753685253 0.648947741 0.307801509 0.294904952 1.781765913 0.07986722 0.642098984 33052.02779 -4.519198109 1.399442174 YFNEMSAQGLRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFNEMSAQGLRPR 13 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 192.65 2.32E-06 1225980000 536800 629640 593570 699580 672470 649070 746460 677930 764070 807010 FALSE TRUE 515821.2625 611683.2837 700841.3029 735685.4076 694100.6083 662194.6401 755595.4008 663930.5086 677335.9768 752350.4939 0.685612978 0.813029683 0.931535645 0.977849305 0.922576132 0.880167748 1.004313026 0.882475009 0.900293124 1 19.52104539 4.519279249 2.295348609 0.933613176 0.673979615 0.777152965 0.042922163 0.171812805 1.458704137 0.010685464 0.073976646 33058.20349 -4.519279249 -0.259633561 ATSLPSIPNPFPELCS(ph)PPS(ph)QSPILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 ATSLPSIPNPFPELCS(0.982)PPS(0.696)QS(0.322)PILGGPSSAR 116.94 2.27E-05 101920000 49706 67991 75029 87969 82267 92243 82151 60682 90096 90171 TRUE FALSE 47763.43457 66051.96325 88588.40931 92509.09063 84913.19277 94108.21666 83156.38851 59428.89549 79868.67979 84063.63785 0.568181865 0.785737626 1.053825549 1.100464993 1.010106093 1.119487796 0.989207589 0.706951269 0.950097829 1 16.35919427 4.519444988 3.201469119 0.975105745 0.577527027 0.597068835 0.109388969 0.220430595 4.185880653 0.032494972 0.164126553 33070.8219 -4.519444988 -0.397578718 LFGETDYDAFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFGETDYDAFQR 12 0 Q5T9P8;Q5T9P7;Q99633 Q5T9P8 PRPF18 Pre-mRNA-splicing factor 18 0 104.95 0.0048448 62087000 87342 106920 105980 120430 103760 109600 131740 151000 104580 124190 FALSE TRUE 83928.57808 103870.7463 125132.9435 126645.4067 107097.5346 111816.1871 133352.2735 147881.7972 92708.51684 115778.5007 0.724906417 0.897150556 1.080796027 1.093859447 0.925020915 0.965776776 1.151787877 1.27728202 0.800740347 1 16.82100785 4.519631791 2.510267576 1.059994498 0.71543021 0.367805203 0.125044508 0.356148916 3.768435478 0.033517435 0.211249976 33085.04965 -4.519631791 -0.344564288 SET(ph)SPVAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SETSPVAPR 9 0 A0A2R8Y661;A0A2R8YGD3;Q9Y4G8;H0Y8T6;H0Y8H7 A0A2R8Y661 RAPGEF2 Rap guanine nucleotide exchange factor 2 1 S(0.005)ET(0.85)S(0.145)PVAPR 117.53 0.012714 124080000 232280 257960 198810 259330 250000 259440 269810 273830 296080 282780 TRUE FALSE 223202.2408 250603.2334 234739.3895 272714.0524 258041.477 264686.0546 273112.0155 268175.3148 262470.2397 263627.0587 0.846659072 0.950597539 0.890422215 1.034469124 0.978812563 1.004017023 1.035978692 1.017252615 0.995611911 1 18.00813893 4.519642517 0.726173184 1.015640616 0.795615074 0.71850237 0.031462662 1.092262086 0.5365042 0.0118784 0.187182667 33085.8668 -4.519642517 -0.220025542 SPGSTPTT(ph)PTSSQAPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SPGST(0.003)PT(0.194)T(0.793)PT(0.007)S(0.001)S(0.001)QAPQK;SPGSTPT(0.018)T(0.902)PT(0.072)S(0.006)S(0.001)QAPQK 196.22 1.81E-10 624250000 426640 547670 550860 682820 672950 707610 666930 542590 616110 617450 TRUE FALSE 409966.4371 532050.9878 650412.6558 718060.422 694596.0479 721918.359 675092.0888 531385.3269 546171.7757 575629.5615 0.712205322 0.924294066 1.129915312 1.24743493 1.206671954 1.254137048 1.172789123 0.923137661 0.948825099 1 19.13478116 4.519663726 2.615801007 1.113979566 0.705917566 0.5519327 0.113075842 0.277494226 3.245471758 0.032755732 0.198031 33087.48263 -4.519663726 -0.408062 TVMDGGLES(ph)DGPNMTENGLEDESRPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVMDGGLESDGPNMTENGLEDESRPQR 27 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 TVMDGGLES(1)DGPNMTENGLEDESRPQR;TVMDGGLES(1)DGPNMTENGLEDESRPQR;TVMDGGLES(1)DGPNMTENGLEDESRPQR;TVMDGGLES(1)DGPNMTENGLEDESRPQR 220.33 1.70E-34 2668810000 925180 968470 839768 953550 1015230 995900 907430 1063430 1005380 1004770 TRUE FALSE 889022.9428 940850.1838 991532.7581 1002762.83 1047885.795 1016037.78 918535.3998 1041469.799 891253.4773 936716.0329 0.949084794 1.004413452 1.05852011 1.070508878 1.118680324 1.084680677 0.980591094 1.111830867 0.951466022 1 19.83725223 4.520233342 2.486556737 1.055184008 0.946082659 0.240482461 0.052743532 0.43337126 4.477412045 0.012723785 0.081130403 33130.90825 -4.520233342 -0.109101349 GEEDTGQEEGGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEEDTGQEEGGSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 196.57 3.27E-07 99660000 108066 121996 107446 140041 124334 125532 131356 126122 143864 142199 FALSE TRUE 103842.6612 118516.7935 126863.8823 147268.5328 128333.316 128070.343 132963.574 123517.5366 127533.1618 132567.7351 0.78331776 0.894009341 0.95697405 1.110892727 0.968058449 0.966074762 1.002985937 0.931731515 0.962022635 1 17.01637016 4.520806933 2.183759359 0.986341526 0.77336324 0.667073173 0.045668482 0.262692499 1.96569566 0.01236364 0.09083463 33174.69454 -4.520806933 -0.212978286 RLEEWLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLEEWLGR 8 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 207.29 0.0001035 2310010000 1315606 1381788 1214488 1421089 1397164 1424497 1361069 1371835 1477805 1555349 FALSE TRUE 1264190.663 1342380.759 1433972.998 1494431.574 1442105.049 1453301.305 1377726.17 1343506.128 1310050.772 1450003.827 0.871853329 0.925777391 0.988944285 1.030639744 0.994552581 1.002274117 0.950153471 0.926553505 0.903480906 1 20.46762528 4.520906976 3.194690301 0.971768094 0.874162175 0.439562469 0.036488362 0.286939674 5.408860248 0.010330147 0.052472576 33182.33751 -4.520906976 -0.097605919 ENPEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENPEKR 6 1 Q1KMD3;H3BQZ7;Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q1KMD3;Q7Z6E9 HNRNPUL2;HNRNPUL2-BSCL2;RBBP6 Heterogeneous nuclear ribonucleoprotein U-like protein 2;E3 ubiquitin-protein ligase RBBP6 0 ; 128.48 0.026627 610010000 1161050 1046440 736360 909120 908810 947790 1022790 950340 867680 1028600 FALSE TRUE 1115674.882 1016596.556 869436.6322 956039.7921 938042.699 966954.9632 1035307.21 930715.1469 769184.604 958932.0058 1.163455673 1.060134138 0.906671825 0.996983922 0.978216071 1.008366555 1.07964611 0.970574703 0.802126323 1 19.871069 4.521453225 3.797031186 0.975164728 1.153709865 0.436792788 0.069533745 0.220944609 6.309646966 0.01714051 0.07784616 33224.10002 -4.521453225 0.178545137 GLLQDDAHPTLVTYADHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLLQDDAHPTLVTYADHSK 19 0 Q86U44;F5H6D8;B4DTN4;H0YFV6 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 ; 171 6.43E-12 589600000 716760 755240 657040 746550 748280 884570 774190 663520 882180 905130 FALSE TRUE 688748.2268 733701.2947 775781.7438 785079.535 772349.1058 902456.6115 783664.7688 649818.0801 782038.6248 843824.7389 0.816221894 0.869494885 0.919363593 0.930382221 0.915295642 1.069483472 0.92870561 0.770086548 0.926778499 1 19.68658386 4.521505804 2.200029502 0.920822052 0.809982245 0.203567044 0.071671952 0.834587992 6.357411682 0.020648214 0.150786373 33228.12259 -4.521505804 -0.110839807 IPMPDFDLHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IPMPDFDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 154.66 3.19E-05 553560000 1054020 1120870 984030 1185260 1002090 1132270 1193780 1160590 1292610 1225510 FALSE TRUE 1012827.733 1088903.885 1161866.111 1246431.411 1034323.135 1155165.275 1208389.837 1136623.411 1145878.332 1142505.116 0.886497328 0.953084472 1.01694609 1.090963527 0.9053116 1.011081052 1.057666893 0.994851922 1.002952473 1 20.12376919 4.52180497 2.768644939 1.010480825 0.886046606 0.425617525 0.045120599 0.288563967 3.860907747 0.011153963 0.064221824 33251.01984 -4.52180497 -0.12443422 LSST(ph)PPLSALGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSSTPPLSALGR 12 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 LSS(0.056)T(0.943)PPLSALGR;LSS(0.02)T(0.98)PPLSALGR;LSS(0.019)T(0.98)PPLSALGR;LSS(0.018)T(0.861)PPLS(0.122)ALGR 188.15 0.00010704 825320000 1910910 1994570 1601520 2064800 2066850 2017820 2294440 2411660 2533560 2698210 TRUE FALSE 1836229.525 1937686.816 1890950.29 2171364.575 2133332.107 2058621.703 2322520.043 2361858.378 2245960.89 2515457.833 0.729978257 0.770311786 0.751732056 0.863208497 0.848088996 0.818388476 0.923299136 0.938937774 0.892863661 1 21.26238958 4.522364868 0.195419204 1.023988796 0.491438326 0.864947601 0.030542755 4.585617236 0.180878406 0.074746188 0.60812613 33293.91509 -4.522364868 -0.53255047 AMST(ph)TSISSPQPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMS(0.301)T(0.652)T(0.046)SISSPQPGK;AMS(0.408)T(0.586)T(0.006)SISSPQPGK 322.19 3.11E-55 3515000000 2360410 1663000 544730 859890 1545440 809420 683770 1944450 1003160 675520 TRUE FALSE 2268162.568 1615572.868 643174.8285 904269.0259 1595150.481 825787.027 692138.1818 1904296.428 889285.4824 629766.4287 3.601593328 2.565352478 1.021291068 1.43588001 2.532923967 1.311259206 1.099039501 3.023813816 1.412087787 1 19.26445733 4.522941909 3.887719165 1.732051358 3.497475939 0.479708169 0.646185425 0.207768328 6.256486723 0.161807302 0.728663724 33338.18167 -4.522941909 1.76542458 ELFLAGR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELFLAGR 7 0 Q7Z4W1;J3KS22;J3KRZ4 Q7Z4W1 DCXR L-xylulose reductase 0 ;;; 139.92 0.0061873 467516000 359495 435518 371716 549730 455900 406194 517560 465440 482270 567590 FALSE TRUE 345445.538 423097.4531 438893.35 578101.6312 470564.4375 414407.521 523894.0541 455828.5013 427524.7314 529146.6237 0.652835192 0.799584527 0.829436172 1.092516904 0.889289313 0.783161986 0.990073508 0.86144082 0.807951355 1 19.01330802 4.522956858 1.89089893 0.90727075 0.633960168 0.442590987 0.090343944 0.492777766 2.551012564 0.023457111 0.203741303 33339.32922 -4.522956858 -0.273310581 SRESAS(ph)PTIPNLDLLEAHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRESASPTIPNLDLLEAHTK 20 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 S(0.196)RES(0.196)AS(0.592)PT(0.016)IPNLDLLEAHTK 179.2 3.57E-17 124880000 130640 110170 80967 70960 94285 96842 88117 114020 74533 80993 TRUE FALSE 125534.4444 107028.0595 95599.538 74622.2541 97317.76265 98800.21159 89195.4022 111665.4472 66072.32631 75507.27197 1.66254774 1.417453666 1.266097099 0.988279038 1.28885285 1.308486044 1.181282278 1.478870104 0.875045868 1 16.20432797 4.523329056 2.096971684 1.205422656 1.691584012 0.448147066 0.171344781 0.434642978 2.927606532 0.043523626 0.33716987 33367.91386 -4.523329056 0.486161356 YFPSSLS(ph)PVTPSESLPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 YFPSSLSPVTPSESLPRPR 19 1 Q9P0U4;Q9P0U4-2;K7EKZ6;K7EQ21 Q9P0U4 CXXC1 CXXC-type zinc finger protein 1 1 YFPS(0.01)S(0.092)LS(0.895)PVT(0.003)PSESLPRPR 159.74 1.99E-11 287430000 30924 33009 29398 32016 34718 32508 34839 40354 29737 32295 TRUE FALSE 29715.45589 32067.61564 34710.87255 33668.3496 35834.736 33165.33403 35265.3701 39520.6758 26361.38043 30107.63088 0.986974233 1.065099269 1.152892856 1.11826632 1.190221049 1.101559075 1.171310032 1.312646483 0.875571397 1 14.87784157 4.523707188 2.418090676 1.140823716 0.980604315 0.075755603 0.112062623 0.672810635 6.465895918 0.027646848 0.18343521 33396.97932 -4.523707188 -0.160219401 NTDKNGEELHGGKR ddPTM_BT-474_Pertuzumab_2h_R1 2 NTDKNGEELHGGKR 14 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 225.32 1.69E-12 571480000 1116860 948010 650228 541715 761448 851628 800353 835032 1048750 884822 FALSE TRUE 1073211.876 920973.683 767738.6638 569672.9761 785940.6664 868848.5017 810147.9594 817788.2974 929700.2967 824892.2178 1.301032854 1.116477599 0.930713913 0.690602922 0.952779829 1.053287306 0.982125836 0.991388062 1.127056695 1 19.6538461 4.523720715 2.971023326 0.961865721 1.297672495 0.490494801 0.106880186 0.251153144 3.967464529 0.028487434 0.154744631 33398.01959 -4.523720715 0.335806774 TSEEFVHINR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSEEFVHINR 10 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;A0A3B3IS13;A0A3B3ISK3;A0A3B3IU76 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;; 145.89 2.96E-05 2790010000 2665770 2796750 2343070 2825140 2856020 2859430 2795450 2737690 3101980 3043240 FALSE TRUE 2561588.761 2716989.428 2766514.87 2970945.814 2947886.477 2917249.634 2829661.553 2681155.745 2749856.235 2837118.644 0.902883905 0.957658022 0.975114268 1.0471701 1.039042369 1.028243792 0.997371597 0.945027713 0.969242594 1 21.43599505 4.523928135 1.898297837 0.999926805 0.895312447 0.517286142 0.029846606 0.51304639 2.679417076 0.009385429 0.081416888 33413.97437 -4.523928135 -0.104614358 ALIEVLQPLIAEHQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALIEVLQPLIAEHQAR 16 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 221.31 1.07E-14 1007150000 604590 656230 571160 688860 629810 736480 725770 691360 718440 808470 FALSE TRUE 580961.9544 637514.9629 674381.3174 724412.1472 650068.4106 751372.1302 734652.1904 677083.1744 636885.7031 753711.6068 0.77080139 0.845834079 0.894747157 0.961126432 0.862489585 0.996896059 0.974712587 0.898331893 0.844999198 1 19.52365308 4.524097438 1.432262993 0.930919431 0.74093286 0.516536623 0.050402733 0.663098673 1.67531793 0.013896984 0.16147471 33427.0028 -4.524097438 -0.189986572 SGFGEISS(ph)PVIR ddPTM_BT-474_Pertuzumab_2h_R1 6 SGFGEISSPVIR 12 0 P57740;G3V1T4 P57740 NUP107 Nuclear pore complex protein Nup107 1 SGFGEIS(0.034)S(0.966)PVIR;SGFGEIS(0.002)S(0.998)PVIR;SGFGEIS(0.004)S(0.996)PVIR;SGFGEISS(1)PVIR;SGFGEIS(0.029)S(0.971)PVIR;SGFGEIS(0.024)S(0.976)PVIR 273.08 9.77E-28 1434050000 3099610 3395150 3180150 3414730 3303060 3705170 3581230 3661510 3438840 3893200 TRUE FALSE 2978473.814 3298323.646 3754873.847 3590964.625 3409305.925 3780091.076 3625058.164 3585898.539 3048477.3 3629510.096 0.820626954 0.908751748 1.03454013 0.989379979 0.939329506 1.041487963 0.998773407 0.987984175 0.839914264 1 21.7913434 4.524313933 3.671549014 0.981066745 0.827866867 0.452866883 0.054200007 0.201627093 5.263435256 0.012954896 0.060429183 33443.67024 -4.524313933 -0.153199878 RRVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_BT-474_Pertuzumab_2h_R1 7 RRVSEVEEEKEPVPQPLPSDDTR 23 3 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR 200.85 1.31E-23 22445860000 6741250 5949900 4606090 4466200 5058450 5173150 4752340 5863270 5805010 5232380 TRUE FALSE 6477794.497 5780214.678 5438512.925 4696701.117 5221159.638 5277754.637 4810500.559 5742191.426 5146049.601 4877986.242 1.327964897 1.184959201 1.114909443 0.962836073 1.070351448 1.081953572 0.986165258 1.177164334 1.054953693 1 22.21785426 4.524843442 1.82627199 1.060385264 1.354403779 0.688121641 0.058630066 0.329019541 1.55400433 0.015831479 0.143758363 33484.47096 -4.524843442 0.294018515 EATNTTSEPSAPSQDLLDLSPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 EATNTTSEPSAPSQDLLDLSPSPR 24 0 J3KQU4;I3L4I4;O75674;O75674-2;O75674-3;I3NI44 J3KQU4 TOM1L1 TOM1-like protein 1 1 EATNTTSEPSAPSQDLLDLS(0.001)PS(0.999)PR 117.88 0.00040291 477630000 412670 446670 408630 494220 436210 434390 418460 505310 460780 525090 TRUE FALSE 396542.4002 433931.4089 482478.5309 519726.7534 450241.0908 443173.6634 423581.2387 494875.1719 408474.1861 489525.1866 0.810055153 0.886433264 0.985605121 1.061695634 0.919750614 0.905313303 0.865289979 1.010928928 0.834429356 1 18.90102356 4.524982293 3.555745448 0.948516401 0.815679047 0.2978274 0.066067819 0.299794024 7.236263087 0.016208105 0.077232496 33495.17826 -4.524982293 -0.132837353 PY(ph)KCEECGRVFMWFS(ph)DIT(ph)KHK ddPTM_BT-474_Pertuzumab_2h_R1 1 PYKCEECGRVFMWFSDITKHK 21 3 A0A087WT67;O14628-4;O14628-7;O14628-5;O14628-6;O14628 A0A087WT67 ZNF195 Zinc finger protein 195 3 PY(1)KCEECGRVFMWFS(1)DIT(1)KHK 50.425 0.061715 32339000 3930.9 5414.3 5681.3 7521.7 6889.6 8233.2 11817 7819.7 8147.8 10291 TRUE FALSE 3777.276082 5259.889465 6708.03729 7909.895838 7111.210241 8399.680945 11961.61998 7658.220462 7222.895902 9593.981404 0.393713092 0.54824887 0.699192234 0.82446437 0.741215762 0.875515658 1.246783736 0.798231739 0.752856984 1 13.22791393 4.525358881 0.654866308 0.931063286 0.137705952 0.637966538 0.133023405 1.709528145 0.668346553 0.062331082 0.974123922 33524.23536 -4.525358881 -0.793357334 GPANGT(ph)PPPLPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPANGTPPPLPAR 13 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GPANGT(1)PPPLPAR;GPANGT(1)PPPLPAR 94.551 0.0048441 0 409530 487190 474860 554270 500110 513000 531160 582900 554770 579330 TRUE FALSE 393525.1148 473295.8182 560677.7652 582875.9411 516196.4923 523373.2115 537660.495 570862.9113 491794.8354 540091.4631 0.728626801 0.876325309 1.038116326 1.079217097 0.955757548 0.969045518 0.99549897 1.056974513 0.910576947 1 19.04284422 4.52568157 2.861953323 1.004847755 0.728257836 0.759654542 0.047945963 0.136312616 1.965060706 0.012120898 0.068437972 33549.15373 -4.52568157 -0.276589918 KPLFHGDSEIDQLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPLFHGDSEIDQLFR 15 1 P06493;A0A024QZP7;A0A087WZZ9;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 243.69 3.53E-18 7599100000 7198200 8313200 7504200 9302700 8305300 8944300 9437600 8893100 10162200 11072800 FALSE TRUE 6916886.386 8076115.675 8860375.87 9782813.462 8572447.517 9125159.874 9553100.172 8709454.377 9008629.659 10322829.39 0.670057222 0.782354853 0.858328229 0.947687217 0.830435842 0.883978561 0.925434279 0.843708062 0.872689969 1 23.29933512 4.526051729 1.821635279 0.890172605 0.646067733 0.694488539 0.048038153 0.300684006 1.408746412 0.011924618 0.109004579 33577.76063 -4.526051729 -0.244104872 TGQPMIHIYLDKETGKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGQPMIHIYLDKETGKPK 18 2 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 165.33 1.71E-11 1131000000 2035600 1779800 1343400 1088400 1297000 1746500 1572500 1611200 2205400 1593900 FALSE TRUE 1956046.502 1729041.847 1586182.264 1144572.454 1338719.183 1781815.427 1591744.725 1577928.157 1955052.238 1485943.733 1.316366466 1.163598465 1.067457824 0.770266349 0.900921854 1.199113659 1.07120121 1.061903033 1.315697354 1 20.50294806 4.526147801 2.545973696 1.043528413 1.320823088 0.262879102 0.140321671 0.488410286 5.310383959 0.037222845 0.235756893 33585.18931 -4.526147801 0.277294674 EAADAIDAEGASAPLMELLHSR ddPTM_BT-474_Pertuzumab_2h_R1 4 EAADAIDAEGASAPLMELLHSR 22 0 P14923 P14923 JUP Junction plakoglobin 0 ;;; 191.65 1.35E-17 368128000 346913 458919 436869 699751 367462 441684 563490 587688 538682 589234 FALSE TRUE 333355.2564 445831.0794 515820.9464 735865.233 379281.749 450615.1531 570386.1592 575552.0374 477533.0777 549324.6563 0.60684561 0.811598522 0.939009273 1.339581656 0.690450983 0.820307532 1.03834072 1.047744773 0.869309382 1 19.06729952 4.526152197 2.462878972 0.974994834 0.59788471 0.329561412 0.161288693 0.418141163 4.192291215 0.041323249 0.270909971 33585.52929 -4.526152197 -0.377110124 KVPGVTAIELDEDTGTFR ddPTM_BT-474_Pertuzumab_2h_R1 3 KVPGVTAIELDEDTGTFR 18 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ;; 299.57 2.81E-49 1198220000 1408740 1527730 1299180 1525850 1580190 1704140 1601830 1690150 1765820 1832550 FALSE TRUE 1353684.883 1484160.636 1533970.726 1604599.301 1631018.246 1738598.878 1621433.675 1655247.812 1565371.517 1708429.756 0.792356185 0.868727924 0.897883405 0.939224627 0.954688503 1.017658977 0.949078339 0.968870863 0.916263318 1 20.7042395 4.526239422 0.875738535 0.968125701 0.733520888 0.817246894 0.026721646 0.677102854 0.505334305 0.009093034 0.143350393 33592.27543 -4.526239422 -0.234604813 KSHS(ph)PVKRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSHSPVKRPR 10 3 P78549-3;P78549-2;P78549;H3BUV2;H3BRL9;A0A494C106;H3BPD5 P78549-3 NTHL1 Endonuclease III-like protein 1 1 KSHS(1)PVKRPR 74.987 0.028791 444610000 673270 581960 443360 391490 483070 465620 560320 439690 706280 576810 TRUE FALSE 646957.8641 565363.0706 523485.0145 411694.8458 498608.3853 475035.1554 567177.3638 430610.2478 626106.0554 537742.1449 1.203100538 1.051364629 0.97348705 0.765598995 0.92722579 0.883388367 1.054738538 0.800774594 1.164323945 1 19.03655502 4.526302071 2.117937737 0.928092245 1.219267047 0.335588512 0.110873896 0.44543724 3.065879694 0.026951679 0.208422251 33597.12159 -4.526302071 0.291174802 EKETIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKETIR 6 1 Q8TED9-4;Q8TED9-2;Q8TED9 Q8TED9-4 AFAP1L1 Actin filament-associated protein 1-like 1 0 ; 71.995 0.079129 425100000 1453320 1556700 1389860 1562950 1574650 1670110 1590330 1550580 1778820 1762220 FALSE TRUE 1396522.648 1512304.44 1641038.619 1643614.037 1625300.047 1703880.768 1609792.934 1518559.981 1576895.811 1642863.27 0.850054094 0.920529704 0.998889347 1.000456987 0.989309383 1.037140948 0.979870306 0.924337411 0.959846044 1 20.64778098 4.526481255 2.818845447 0.982457633 0.84932 0.695964663 0.028388152 0.198952036 2.763416713 0.008341203 0.047866696 33610.98616 -4.526481255 -0.133137633 LGFSLT(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 3 LGFSLTPSK 9 0 P38432 P38432 COIL Coilin 1 LGFS(0.001)LT(0.999)PSK;LGFS(0.002)LT(0.922)PS(0.076)K;LGFS(0.013)LT(0.982)PS(0.005)K 136.86 0.0020208 1222203000 2100830 1745430 1332920 1270620 1334280 1039200 1388580 1804120 1325110 1379160 TRUE FALSE 2018727.241 1695652.045 1573808.295 1336196.85 1377198.328 1060213.336 1405573.857 1766864.292 1174689.068 1285748.265 1.570079693 1.318805626 1.224040769 1.039236752 1.071125947 0.82458858 1.09319522 1.374191465 0.913622908 1 20.29417678 4.52663039 1.330198976 1.074447657 1.666028529 0.588688842 0.138472559 0.753076201 1.569535848 0.043556562 0.544332113 33622.53002 -4.52663039 0.591580872 S(ph)HSDNDRFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSDNDRFK 9 1 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.988)HS(0.012)DNDRFK;S(0.989)HS(0.011)DNDRFK 111.63 0.0012679 376820000 804110 763090 508780 454040 581610 581400 492600 184815 679630 486070 TRUE FALSE 772684.4922 741327.4203 600727.8637 477473.0588 600318.0139 593156.3063 498628.5862 180998.5057 602481.2516 453148.046 1.705148018 1.635949723 1.325676827 1.053680057 1.324772377 1.308968033 1.100365743 0.399424663 1.329546176 1 18.78962294 4.526720898 0.398463595 0.862324613 2.277157491 0.463842014 0.255140752 4.072234222 0.581370292 0.230799319 2.726829469 33629.53773 -4.526720898 1.414832878 YINTEHGGSQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 YINTEHGGSQAR 12 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 185.57 1.29E-05 3054870000 1500310 1647680 1357790 1886660 1608290 1694620 1770650 1630900 1743430 1734230 FALSE TRUE 1441676.227 1600689.78 1603172.857 1984030.749 1660022.108 1728886.377 1792319.744 1597221.345 1545523.135 1616769.057 0.891702015 0.990054685 0.991590512 1.227157793 1.02675277 1.069346528 1.108581177 0.987909397 0.955933149 1 20.62468219 4.526750273 1.972141964 1.052640439 0.882653765 0.298882738 0.073331838 0.617129066 3.541271526 0.019395537 0.162693614 33631.81252 -4.526750273 -0.169986674 GS(ph)IGLLLGK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSIGLLLGK 9 0 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 GS(1)IGLLLGK;GS(1)IGLLLGK;GS(1)IGLLLGK 141.88 0.00011083 376671000 1055847 919971 631785 545742 661566 501865 428541 723850 498241 462700 TRUE FALSE 1014583.332 893734.3278 745962.6035 573907.81 682845.8712 512013.0542 433785.6129 708902.2445 441682.7705 431360.9169 2.352052057 2.071894539 1.729323576 1.330458527 1.58300357 1.18697136 1.005621038 1.643408609 1.023928579 1 18.71853594 4.527039478 0.711212638 1.232612623 2.899044061 0.792781103 0.202574856 1.044034166 0.486713113 0.083604928 1.335233796 33654.21601 -4.527039478 1.666431438 up AEDQTESSCES(ph)HRK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEDQTESSCESHRK 14 1 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.328)S(0.08)CES(0.592)HRK 95.197 0.0018168 135780000 390000 272580 148480 123220 161800 142750 90626 226420 146650 112540 TRUE FALSE 374758.3688 264806.2853 175313.6389 129579.399 167004.4439 145636.5028 91735.1081 221744.3479 130002.9068 104917.5656 3.57193161 2.523946146 1.670965562 1.235059146 1.591768195 1.388104099 0.874354143 2.113510228 1.239095724 1 16.67889671 4.527190286 1.709857971 1.412979716 3.862962532 0.824924292 0.325717682 0.243393752 0.967149872 0.086971097 0.854620895 33665.90445 -4.527190286 2.449982816 up TQLGEDHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQLGEDHEK 9 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 85.813 0.014561 532770000 1008900 1062700 944170 1131000 1050700 1012500 1078800 1028900 1232100 1167200 FALSE TRUE 969471.0726 1032392.836 1114802.522 1189371.046 1084496.72 1032973.444 1092002.677 1007652.855 1092237.173 1088144.504 0.89093964 0.948764463 1.024498601 1.093026745 0.996647702 0.949298039 1.003545644 0.92602853 1.003761145 1 20.05343873 4.527436046 3.617936707 0.994872049 0.895396131 0.39435553 0.042039595 0.281806926 7.043891759 0.01152514 0.054684114 33684.9608 -4.527436046 -0.099475918 AALCAVHVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALCAVHVIR 10 0 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ; 158.07 8.10E-06 621520000 725940 759290 640530 810580 754400 689830 833080 729300 820730 811710 FALSE TRUE 697569.4622 737635.7926 756288.0195 852414.1309 778665.9611 703778.8352 843275.4822 714239.7001 727564.1712 756732.1587 0.921818181 0.974764696 0.999413083 1.126441002 1.028984895 0.930023691 1.114364538 0.943847426 0.961455335 1 19.52942323 4.527781279 2.449575721 1.014184244 0.919839156 0.176304754 0.061682915 0.642150605 6.341549681 0.015695985 0.104001879 33711.74856 -4.527781279 -0.094345087 ALEEVPIHIEDPPFPSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEEVPIHIEDPPFPSLR 18 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 ; 119.4 7.49E-05 131147000 179187 212011 190354 251944 217652 234956 242619 227551 226702 266000 FALSE TRUE 172184.1739 205964.6539 224755.2022 264946.86 224652.9742 239706.9713 245588.2439 222851.9923 200967.7394 247983.5831 0.694336987 0.830557617 0.906330973 1.068404839 0.905918736 0.966624356 0.990340735 0.898656232 0.810407435 1 17.91988509 4.528272373 2.053286239 0.944834117 0.676693871 0.588969583 0.065904588 0.326235555 2.070774879 0.01720896 0.13864384 33749.89088 -4.528272373 -0.268140246 KS(ph)STSDWPTDNQDGWDGKQENEER ddPTM_BT-474_Pertuzumab_2h_R1 2 KSSTSDWPTDNQDGWDGKQENEER 24 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ISZ3;A5PLL3 A0A3B3IS53 KAT6A;MYST3 Histone acetyltransferase KAT6A;Histone acetyltransferase 1 KS(0.485)S(0.485)T(0.015)S(0.015)DWPTDNQDGWDGKQENEER;KS(0.426)S(0.426)T(0.074)S(0.074)DWPTDNQDGWDGKQENEER 141.49 1.45E-07 757890000 295097 260516 204674 160638 224864 241209 224278 265322 262728 248451 TRUE FALSE 283564.283 253086.3388 241663.1447 168928.5464 232096.9548 246086.4112 227022.7813 259843.008 232904.2189 231623.1925 1.224248228 1.092664064 1.043346058 0.729324834 1.002045401 1.062442878 0.980138383 1.121835017 1.005530648 1 17.82142019 4.528311158 2.3354046 0.996919237 1.231108292 0.360488336 0.096742502 0.468104606 4.106465327 0.026417394 0.184532676 33752.90506 -4.528311158 0.234189055 KQITTS(ph)PITVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQITTSPITVR 11 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 KQIT(0.017)T(0.152)S(0.83)PITVR 103.83 0.0016422 397940000 119450 131860 119230 137410 121830 145880 132750 144530 165000 162620 TRUE FALSE 114781.7619 128099.4819 140777.5133 144501.7466 125748.7726 148829.7936 134374.6342 141545.405 146269.8917 151605.6026 0.757107653 0.844952164 0.928577248 0.953142523 0.829446739 0.981690591 0.886343459 0.93364231 0.964805319 1 17.20996354 4.528625559 2.179058094 0.929288678 0.745406553 0.597161421 0.046477359 0.279899884 2.064151665 0.01112925 0.08398804 33777.34881 -4.528625559 -0.183882126 FNSQSQAEAHYK ddPTM_BT-474_Pertuzumab_2h_R1 1 FNSQSQAEAHYK 12 0 F8VSJ1;F8VRY0;H0YI55;Q96PM9-1;Q96PM9;H0YIX3;F8VWV6;Q96PM9-2;Q96PM9-3 F8VSJ1 ZNF385A Zinc finger protein 385A 0 92.856 0.0030636 0 65075 73750 74178 73290 68368 74854 80060 73348 94521 90129 FALSE TRUE 62531.79706 71646.72221 87583.61468 77072.50568 70567.11881 76367.59917 81039.79823 71833.33817 83791.37234 84024.48255 0.744209249 0.852688645 1.042358275 0.917262485 0.839839969 0.908873186 0.964478397 0.854909617 0.997225687 1 16.35852213 4.528923903 4.641027421 0.928701516 0.759780162 0.486709616 0.062016714 0.18240595 8.202458821 0.014824257 0.063041463 33800.56054 -4.528923903 -0.168921354 EELLDS(ph)RTPAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 EELLDSRTPAGR 12 1 Q9ULH4 Q9ULH4 LRFN2 Leucine-rich repeat and fibronectin type-III domain-containing protein 2 1 EELLDS(0.5)RT(0.5)PAGR 53.569 0.08517 476760000 284790 340560 332960 412010 389970 410880 440010 459840 467440 461190 TRUE FALSE 273660.0919 330847.5622 393133.2787 433273.8855 402513.7392 419188.2751 445394.974 450344.1433 414378.1709 429953.1905 0.636488106 0.769496702 0.914362976 1.007723387 0.936180375 0.974962587 1.035915034 1.047425983 0.963775081 1 18.71382007 4.529344116 1.092130734 1.005749281 0.520744854 0.932699673 0.031908482 0.296600463 0.375326268 0.0105696 0.153218222 33833.28101 -4.529344116 -0.485004427 S(ph)MSVDLSHIPLKDPLLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SMSVDLSHIPLKDPLLFK 18 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.5)MS(0.5)VDLSHIPLKDPLLFK;S(0.555)MS(0.442)VDLS(0.003)HIPLKDPLLFK 146.89 4.86E-08 310750000 1383210 1061850 693170 554490 847490 524200 428720 970240 683960 546900 TRUE FALSE 1329152.624 1031567.078 818441.2385 583107.2954 874750.2855 534799.6832 433966.8036 950204.2049 606319.7282 509857.9759 2.606907584 2.023243975 1.605233766 1.143666125 1.715674417 1.048918931 0.851152329 1.863664491 1.189193377 1 18.95973591 4.529779354 1.328435899 1.303949596 2.895061946 0.677201839 0.299923329 0.557943981 1.154358147 0.085925901 1.085271346 33867.20477 -4.529779354 1.59111235 GTSS(ph)PDYR ddPTM_BT-474_Pertuzumab_2h_R1 5 GTSSPDYR 8 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 GT(0.005)S(0.046)S(0.949)PDYR;GT(0.01)S(0.07)S(0.921)PDYR;GT(0.044)S(0.449)S(0.507)PDYR;GT(0.022)S(0.082)S(0.897)PDYR;GT(0.003)S(0.041)S(0.956)PDYR 119.27 0.0018101 834010000 1585770 1811030 1623340 1963100 1896730 2102060 1981590 1933550 2065870 2201730 TRUE FALSE 1523796.355 1759381.198 1916713.649 2064415.826 1957740.043 2144565.093 2005841.291 1893621.517 1831361.098 2052604.866 0.742371988 0.857145584 0.933795725 1.005754132 0.953783203 1.044801719 0.977217449 0.922545565 0.892213172 1 20.9690245 4.529801166 1.750079589 0.96795697 0.714606921 0.754650908 0.041006194 0.305350837 1.284034334 0.011646935 0.112563396 33868.9058 -4.529801166 -0.253350049 TGPPPIS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 6 TGPPPISPSK 10 0 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;E7ERW0;E7EWF5;F8W708;E7EQU6;F8WBN7;E7EUJ2;A0A096LP98 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 TGPPPIS(1)PSK;TGPPPIS(1)PSK;TGPPPIS(1)PSK;TGPPPIS(1)PSK;TGPPPIS(0.984)PS(0.016)K;TGPPPIS(0.986)PS(0.014)K 228.74 2.04E-09 4454420000 3210670 2905640 2308450 2345920 2533160 2420330 2401640 2929880 3004620 2605380 TRUE FALSE 3085193.467 2822773.992 2725638.266 2466993.212 2614641.392 2469270.731 2431031.989 2869376.954 2663548.134 2428915.292 1.270193933 1.162154152 1.122162751 1.015676924 1.076464626 1.016614593 1.000871458 1.181340891 1.096599846 1 21.21188075 4.52998868 1.545386041 1.066336704 1.300471678 0.60409108 0.054147643 0.555249912 1.693175988 0.015946029 0.175474196 33883.53243 -4.52998868 0.234134974 QEYDESGPSIVHR ddPTM_BT-474_Pertuzumab_2h_R1 23 QEYDESGPSIVHR 13 0 P60709;A0A2R8YFE2;Q9BYX7;P63261;Q6S8J3;A5A3E0;P0CG38;P0CG39 P60709;P63261;Q6S8J3 ACTB;POTEKP;ACTG1;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;;;;;;;;;;;;;;;;;;;;;; 261.27 4.71E-24 2.63576E+11 59126664 69107813.6 60408734.2 81001262.5 71263724.9 71131574.1 76814709.4 74644751.8 80295399.8 83239028.9 FALSE TRUE 56815928.6 67136926.42 71325936.25 85181747.36 73555987.33 72569903.26 77754790.79 73103311.59 71180602.64 77601175.33 0.732152939 0.865153474 0.919134742 1.097686304 0.947872078 0.935165002 1.001979551 0.942038716 0.917261914 1 26.20957517 4.530268983 1.904413492 0.972338586 0.711231187 0.695586347 0.049955214 0.291362477 1.522076257 0.013161778 0.11609843 33905.40867 -4.530268983 -0.261107398 SSKAS(ph)LGS(ph)LEGEAEAEASSPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.137)S(0.167)KAS(0.786)LGS(0.91)LEGEAEAEASSPK;S(0.123)S(0.153)KAS(0.729)LGS(0.996)LEGEAEAEASSPK;S(0.266)S(0.284)KAS(0.764)LGS(0.686)LEGEAEAEASSPK 154.1 2.10E-08 1147970000 1410700 1137720 778360 634260 668720 785900 744560 1307780 1250740 951080 TRUE FALSE 1355568.284 1105273.34 919026.9665 666994.2346 690229.9861 801791.4365 753672.148 1280773.886 1108761.239 886662.5045 1.528843588 1.246554731 1.036501444 0.752252668 0.778458526 0.904280301 0.850010172 1.444488607 1.25048847 1 19.75802554 4.530307451 2.413040929 1.012277761 1.547048609 0.405427331 0.201299537 0.446129683 4.233689194 0.060120401 0.407904457 33908.412 -4.530307451 0.534770848 TVAISDAAQLPHDYCT(ph)TPGGT(ph)LFSTTPGGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.004)CT(0.526)T(0.47)PGGT(0.975)LFS(0.013)T(0.008)T(0.005)PGGTR 114.2 0.00011648 166940000 34436 41909 32072 50158 38186 55438 40024 42098 40755 55194 TRUE FALSE 33090.20305 40713.79635 37868.12384 52746.66039 39414.28737 56558.99434 40513.82568 41228.66159 36128.66326 51455.66122 0.643081874 0.791240369 0.735936978 1.025089546 0.765985441 1.099179235 0.787354097 0.801246367 0.70213194 1 15.65104219 4.530312544 1.429200957 0.865815944 0.616236962 0.240474444 0.125550611 1.256922509 3.133201547 0.033937577 0.402756342 33908.80965 -4.530312544 -0.249578982 ASPSSPGRQDS(ph)DEDDGPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR 211.75 6.95E-17 858770000 809970 872540 764510 906610 815540 918610 940290 952760 1013540 1002230 TRUE FALSE 778315.4769 847656.0135 902673.9634 953400.2507 841772.5848 937184.9236 951797.5503 933085.1731 898487.1883 934348.0694 0.833003784 0.90721653 0.966100314 1.020390882 0.900919703 1.003036186 1.018675568 0.998648366 0.961619355 1 19.83360057 4.530590016 1.669672985 0.98711189 0.810473043 0.684626346 0.032971526 0.361401581 1.344582029 0.008872794 0.090389662 33930.48097 -4.530590016 -0.176638847 WAHDKFS(ph)GEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_BT-474_Pertuzumab_2h_R1 6 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.995)GT(0.005)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.972)GT(0.028)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.858)GT(0.142)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.866)GT(0.134)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.52)GT(0.459)ENREEKDNIQPT(0.01)T(0.01)E;WAHDKFS(1)GEEGEIEDDES(0.86)GT(0.139)ENREEKDNIQPTTE 200.53 5.30E-27 4528890000 2951980 2320670 1767073 1180973 1976290 2175930 1519458 1713998 2317650 1808360 TRUE FALSE 2836613.358 2254486.764 2086422.399 1241923.158 2039859.163 2219928.795 1538053.582 1678603.342 2054560.088 1685878.166 1.682573162 1.337277396 1.237587888 0.73666246 1.209968314 1.316778899 0.912315974 0.995684846 1.218688354 1 20.68506885 4.530667075 1.718698773 1.060048119 1.752998743 0.580340544 0.163112935 0.433675344 1.738493518 0.04380769 0.432900985 33936.502 -4.530667075 0.692950624 TVQTDHNAVQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVQTDHNAVQR 11 0 O43747;O43747-2 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ;;; 187.58 3.53E-06 3300800000 1838470 1958360 1730630 2023420 1947250 1941030 1989140 2047520 2094790 2272550 FALSE TRUE 1766620.56 1902509.49 2043393.339 2127848.949 2009885.065 1980278.957 2013483.69 2005237.996 1856998.221 2118628.164 0.833851164 0.89799122 0.964488896 1.004352243 0.948672872 0.934698684 0.950371436 0.946479439 0.87650974 1 21.01469898 4.530747759 2.87920761 0.951679707 0.833691387 0.552143492 0.033777938 0.222030132 3.225939188 0.008400495 0.047858397 33942.80731 -4.530747759 -0.11798832 GQYISPFHDIPIYADK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQYISPFHDIPIYADK 16 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 196.66 4.53E-11 1102450000 1773090 2544600 2671000 3392300 2718800 2780800 3047000 3279900 3263100 4221600 FALSE TRUE 1703795.683 2472030.499 3153709.116 3567377.01 2806252.671 2837029.681 3084290.097 3212168.919 2892686.568 3935667.272 0.432911515 0.628109626 0.801314974 0.906422409 0.713030975 0.720850998 0.783676537 0.816168821 0.734992663 1 21.90817683 4.530913788 2.393028915 0.799857003 0.417428739 0.667312735 0.084143654 0.214189719 1.989910359 0.02035922 0.139631873 33955.78599 -4.530913788 -0.382428263 EEDACHLIIPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEDACHLIIPLR 12 0 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 0 ;;; 174.24 3.09E-05 720440000 950700 1032770 874200 1048310 1102970 1119450 1034070 1028530 1183450 1199060 FALSE TRUE 913545.5929 1003316.411 1032187.386 1102413.405 1138448.032 1142086.046 1046725.258 1007290.496 1049109.717 1117846.598 0.817236993 0.897543914 0.923371228 0.986193818 1.018429571 1.021684056 0.936376476 0.90109904 0.938509559 1 20.09229079 4.531199635 1.560515233 0.964488681 0.796486927 0.618470239 0.037608707 0.583880306 1.822911346 0.012184753 0.133300906 33978.1426 -4.531199635 -0.168001754 VDHCPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDHCPIK 7 0 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 68.422 0.062495 109490000 108160 119690 111660 130380 118030 108500 147040 114670 135740 142440 FALSE TRUE 103932.9876 116276.5584 131839.4459 137108.9274 121826.5421 110693.9443 148839.5195 112302.0244 120331.3643 132792.4119 0.78267264 0.875626526 0.992823641 1.032505739 0.917420961 0.833586368 1.120843558 0.845696097 0.906161448 1 17.01881318 4.531343662 3.394480338 0.950646359 0.787578779 0.301970955 0.082523053 0.31757583 6.775570587 0.019907523 0.099486487 33989.41284 -4.531343662 -0.16306758 AVQELVHPVVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVQELVHPVVDR 12 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4;H3BNB1 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ; 98.592 0.0042719 600590000 410290 436860 381310 448700 439210 454000 459190 428770 488100 482180 FALSE TRUE 394255.4132 424401.1805 450221.1992 471857.4608 453337.5885 463180.1911 464809.7046 419915.7497 432692.9343 449521.5191 0.877055706 0.944117606 1.0015565 1.049688259 1.008489181 1.030384912 1.034009908 0.934139372 0.962563339 1 18.77803066 4.531405099 2.476999674 1.001249513 0.872984648 0.600906353 0.032277049 0.279421419 2.824135941 0.009363471 0.061996675 33994.22142 -4.531405099 -0.128264865 FAHTNVESLVNEYDDNGEGIILFR ddPTM_BT-474_Pertuzumab_2h_R1 7 FAHTNVESLVNEYDDNGEGIILFR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;; 368.08 1.18E-118 5118763000 1333622 1604256 1446519 1917127 1690792 1850898 1855613 1570954 1909221 2103609 FALSE TRUE 1281502.578 1558504.19 1707937.161 2016070.154 1745177.86 1888324.426 1878322.547 1538513.251 1692494.236 1961129.689 0.653451215 0.794697158 0.870894552 1.028014703 0.889883963 0.962875855 0.957775795 0.784503575 0.863020047 1 20.90325351 4.531442476 1.994890638 0.912987037 0.632667042 0.609814282 0.067685103 0.362905615 2.131913376 0.018943101 0.15924153 33997.14724 -4.531442476 -0.280319994 TVVLHIDGLDDTSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVVLHIDGLDDTSR 14 0 Q9NVT9;E5RJ86 Q9NVT9 ARMC1 Armadillo repeat-containing protein 1 0 ;;; 174.95 2.46E-06 835700000 817010 935200 881340 1080540 971710 915800 1033320 968470 1064970 1149100 FALSE TRUE 785080.3459 908529.0117 1040617.743 1136306.799 1002965.935 934318.1035 1045966.079 948470.7561 944079.0703 1071270.433 0.732849821 0.848085584 0.971386599 1.060709568 0.936239724 0.872158957 0.976379116 0.885370049 0.881270537 1 20.03089129 4.531611062 3.012207188 0.942839147 0.734418212 0.589215909 0.056365124 0.210593478 3.399469232 0.014836971 0.081424815 34010.34689 -4.531611062 -0.208420935 VIQENEHALQK ddPTM_BT-474_Pertuzumab_2h_R1 2 VIQENEHALQK 11 0 Q9NTJ3;E9PD53 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 ; 131.37 0.00020478 570230000 843080 1035290 930080 1302070 1207380 1209110 1231080 1023530 1009790 1200550 FALSE TRUE 810131.5015 1005764.543 1098166.146 1369269.989 1246216.474 1233559.033 1246146.325 1002393.748 895162.8726 1119235.679 0.723825658 0.898617299 0.98117507 1.223397372 1.113453134 1.102144129 1.113390458 0.895605605 0.799798371 1 20.09408243 4.532020043 2.121538212 1.03538348 0.704953711 0.412911688 0.11409811 0.477285594 3.276621458 0.032411851 0.254743569 34042.39001 -4.532020043 -0.330429769 VFS(ph)QENVCDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFSQENVCDR 10 0 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 VFS(1)QENVCDR;VFS(1)QENVCDR 164.92 6.31E-06 1452330000 492430 455070 369570 353510 433840 401170 372210 498310 475930 399570 TRUE FALSE 473185.2912 442091.8492 436359.52 371754.6935 447794.8576 409281.9323 376765.2173 488019.7244 421904.4217 372506.768 1.270273004 1.186802193 1.17141367 0.997981045 1.202112005 1.098723479 1.011431871 1.310096262 1.132608741 1 18.50690711 4.532246844 1.963613258 1.128146649 1.28029812 0.20866 0.093706301 0.896829287 5.05478095 0.024707434 0.211958526 34060.17258 -4.532246844 0.152151472 EENSGLLQELEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 EENSGLLQELEELR 14 0 A0A3B3ISJ8;J3KP58;P30622-2;P30622-1;P30622;F5H0N7;A0A3B3ITA2 A0A3B3ISJ8;J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 0 126.63 0.00073806 0 5479.6 6755.4 5308.3 6279.6 7580.5 7672.3 6300.8 8691.6 6629.8 7628.9 FALSE TRUE 5265.451174 6562.742606 6267.627892 6603.690909 7824.333667 7827.439163 6377.911075 8512.115423 5877.212898 7112.187808 0.740341976 0.922745966 0.881251742 0.928503449 1.100130351 1.100566995 0.896757966 1.196835018 0.826357945 1 12.79607771 4.532477206 0.786566836 1.033539271 0.661196593 0.355198692 0.106460562 2.008749283 1.164667128 0.038302124 0.62225013 34078.24379 -4.532477206 -0.372342679 YVSGS(ph)SPDLVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 YVSGSSPDLVTR 12 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 YVS(0.008)GS(0.807)S(0.185)PDLVTR;YVS(0.003)GS(0.866)S(0.131)PDLVTR 172.33 3.78E-05 217960000 401460 357090 251680 327790 287220 286990 259230 384350 355540 297000 TRUE FALSE 385770.4994 346906.1428 297164.1746 344707.2812 296458.6921 292793.1344 262402.5343 376413.0382 315180.5897 276883.9255 1.393257116 1.252893761 1.073244588 1.244952305 1.070696653 1.057458045 0.947698693 1.359461506 1.138313065 1 18.07892177 4.532929264 2.910213265 1.128968614 1.394639177 0.376616933 0.11354481 0.33952261 5.045016941 0.029183664 0.165681843 34113.73442 -4.532929264 0.265670563 IDVAFVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDVAFVDR 8 0 Q15645 Q15645 TRIP13 Pachytene checkpoint protein 2 homolog 0 75.378 0.08967 116770000 153960 167340 153890 165110 161850 173670 177460 173630 189830 199660 FALSE TRUE 147943.073 162567.627 181701.3463 173631.3469 167056.0522 177181.7264 179631.8086 170044.4798 168281.2942 186136.8504 0.794808082 0.873376909 0.976170736 0.932815542 0.897490486 0.95188957 0.96505237 0.913545488 0.904072965 1 17.50600418 4.533033595 3.328357176 0.937783199 0.798179095 0.682238026 0.031590699 0.143924072 2.923856442 0.007549749 0.038432185 34121.93058 -4.533033595 -0.139604104 EVELVS(ph)E ddPTM_BT-474_Pertuzumab_2h_R1 2 EVELVSE 7 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 EVELVS(1)E;EVELVS(1)E 126.52 0.004137 315220000 538390 575080 532880 566220 595250 573880 562970 591210 613730 629510 TRUE FALSE 517349.1236 558679.2815 629183.2699 595442.6821 614396.7568 585484.2468 569859.7953 579001.3069 544061.9434 586872.727 0.881535467 0.951959864 1.072094921 1.014602749 1.046899487 0.997634103 0.971010867 0.986587518 0.927052695 1 19.16268814 4.533132402 4.466560815 1.001666568 0.890738847 0.493772287 0.037669468 0.184335643 7.370973867 0.009550374 0.041545598 34129.69457 -4.533132402 -0.110927721 DLLEECKK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLLEECKK 8 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;; 76.679 0.050466 788470000 1316920 1062320 717570 673860 790720 627710 644860 668450 1048400 861870 FALSE TRUE 1265453.31 1032023.674 847250.8613 708637.9954 816154.2269 640402.7263 652751.9896 654646.2739 929390.0273 803494.7772 1.574936573 1.284418646 1.05445721 0.881944744 1.015755485 0.797021641 0.81239108 0.814748636 1.15668459 1 19.61592912 4.533167295 1.241611508 0.898125931 1.74447196 0.786661265 0.108170897 0.423114974 0.73437045 0.03109732 0.418527049 34132.4368 -4.533167295 0.846346029 EGDFVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGDFVLR 7 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 100.74 0.022265 1071380000 714290 735310 631070 707990 710390 746510 714000 778680 771220 782110 FALSE TRUE 686374.7571 714339.6787 745118.3871 744529.4487 733240.3395 761604.9437 722738.1456 762599.9859 683674.3388 729136.9931 0.941352261 0.979705714 1.021918232 1.021110513 1.005627676 1.044529287 0.991224081 1.045893972 0.93764868 1 19.47583037 4.533202883 2.818556917 1.012493388 0.940715675 0.328606511 0.029373463 0.304159139 4.188597849 0.006782599 0.039684373 34135.23392 -4.533202883 -0.071777713 SLPLSPELESS(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPLSPELESSP 12 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 SLPLSPELES(0.005)S(0.995)P;SLPLSPELES(0.001)S(0.999)P 252.42 4.89E-21 272780000 173166 203141 192054 227170 228230 266230 246110 234350 256770 303180 TRUE FALSE 166398.4813 197347.6176 226762.43 238894.2709 235571.2252 271613.353 249121.9678 229510.5906 227622.5461 282645.3486 0.588718272 0.698216399 0.802286085 0.84520857 0.833451626 0.96096877 0.881394189 0.812009084 0.805329177 1 18.10863343 4.533545628 1.07941933 0.872294063 0.50154674 0.731301907 0.058115902 0.673253058 0.823739356 0.017883622 0.264018659 34162.18401 -4.533545628 -0.370747323 TIS(ph)EPDEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TISEPDEQR 9 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 T(0.001)IS(0.999)EPDEQR;TIS(1)EPDEQR 149.33 9.22E-05 3337200000 2427300 2678500 2281700 2829400 2746900 2765600 2738600 2955500 3003800 3140100 TRUE FALSE 2332438.432 2602111.803 2694053.946 2975425.673 2835256.533 2821522.327 2772115.806 2894467.892 2662821.217 2927418.23 0.796756134 0.888875999 0.920283244 1.016399243 0.968517755 0.963826179 0.946949014 0.988744233 0.909614209 1 21.48119744 4.533712985 1.542486538 0.968990328 0.770727377 0.768546081 0.029534236 0.319840847 0.965904511 0.007678968 0.085661435 34175.35111 -4.533712985 -0.198262951 S(ph)ITST(ph)PLSGK ddPTM_BT-474_Pertuzumab_2h_R1 4 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 2 S(0.939)IT(0.061)S(0.291)T(0.707)PLS(0.001)GK;S(0.774)IT(0.19)S(0.042)T(0.682)PLS(0.311)GK;S(0.949)IT(0.051)S(0.092)T(0.9)PLS(0.008)GK;S(0.807)IT(0.191)S(0.011)T(0.914)PLS(0.077)GK 215.77 4.26E-08 361110000 2284480 2007430 1582770 1533140 1461950 1711860 1581210 2246260 1953360 1800780 TRUE FALSE 2195199.996 1950180.062 1868811.748 1612265.539 1508974.949 1746474.982 1600561.321 2199873.946 1731622.762 1678811.567 1.307591656 1.161643213 1.113175406 0.960361229 0.898835211 1.040304354 0.953389501 1.310375738 1.031457488 1 20.67900888 4.533721296 1.813208985 1.048657681 1.333178484 0.393166938 0.106263966 0.704246496 3.228381955 0.031672122 0.298261581 34176.00508 -4.533721296 0.284520803 RRS(ph)QS(ph)IEQESQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 RRS(1)QS(0.964)IEQES(0.036)QEK 201.9 4.83E-07 592950000 1074300 992750 779530 810440 860780 926400 864970 951350 1093100 951310 TRUE FALSE 1032315.168 964437.742 920408.4116 852266.9055 888467.7704 945132.4427 875555.7616 931704.29 969015.8706 886876.9264 1.163989205 1.087453866 1.037808499 0.960975396 1.00179376 1.065686134 0.987234796 1.050545191 1.092615945 1 19.75837439 4.533780759 2.192856461 1.02386991 1.172322628 0.58594097 0.036979782 0.303365819 2.259127531 0.009716407 0.074007263 34180.68479 -4.533780759 0.148452718 ELAQPSGGHLPQAS(ph)PISVYLFPGER ddPTM_BT-474_Pertuzumab_2h_R1 4 ELAQPSGGHLPQASPISVYLFPGER 25 0 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 ELAQPSGGHLPQAS(1)PISVYLFPGER;ELAQPSGGHLPQAS(0.999)PIS(0.001)VYLFPGER;ELAQPSGGHLPQAS(1)PISVYLFPGER;ELAQPSGGHLPQAS(1)PISVYLFPGER 243.64 6.55E-39 562030000 288255 345263 331502 418404 363067 427641 379512 345634 360511 417289 TRUE FALSE 276989.6759 335416.4373 391411.7856 439997.8806 374745.3798 436288.194 384156.5814 338496.5371 319587.3027 389025.6443 0.712008784 0.862196213 1.006133635 1.131025389 0.963292228 1.121489548 0.987483954 0.870113685 0.821507033 1 18.56950573 4.534664169 2.786275383 0.985389438 0.709493194 0.4778531 0.090423437 0.295447406 3.951595806 0.024878872 0.147774723 34250.2834 -4.534664169 -0.275896245 SGLEELVLSEMNS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGLEELVLSEMNSPSR 16 0 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 SGLEELVLSEMNS(0.998)PS(0.002)R 176.81 3.20E-09 24323000 76882 84743 77365 90925 82010 93105 87985 93869 83848 93740 TRUE FALSE 73877.36644 82326.21261 91346.57648 95617.65015 84647.92613 94987.64689 89061.78675 91930.57235 74329.92656 87390.90631 0.84536675 0.94204553 1.045264094 1.094137299 0.968612522 1.086928273 1.019119615 1.051946664 0.850545322 1 16.41519554 4.534754766 2.937648171 1.021636609 0.845421729 0.382903888 0.066285637 0.274242153 4.15572265 0.015758798 0.089175614 34257.42895 -4.534754766 -0.17621488 GGSCPSRAKMS(ph)MTGAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSCPSRAKMSMTGAGK 17 2 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7;Q96KQ7-3 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 GGS(0.287)CPS(0.287)RAKMS(0.423)MT(0.002)GAGK 52.693 0.054067 71083000 55316 62199 54873 68809 63844 63664 65283 64599 74792 76061 TRUE FALSE 53154.18956 60425.14542 64789.77174 72360.24074 65897.60024 64951.3297 66081.95288 63265.00808 66301.92571 70909.32072 0.749607936 0.852146725 0.913698948 1.020461626 0.92932212 0.915977322 0.931921956 0.89219594 0.935024127 1 16.11368766 4.535059424 2.082505866 0.937687594 0.735886479 0.731267667 0.037041795 0.24872175 1.622926603 0.009936255 0.080518961 34281.46905 -4.535059424 -0.201801115 VSPATPGPALS(ph)DILR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSPATPGPALSDILR 15 0 Q2M2I3 Q2M2I3 FAM83E Protein FAM83E 1 VSPATPGPALS(1)DILR;VSPATPGPALS(1)DILR;VSPATPGPALS(1)DILR 311.69 3.71E-56 612161000 530860 448501 283360 315642 331862 246556 249061 438282 268561 265008 TRUE FALSE 510113.4043 435710.1906 334569.4553 331932.3214 342536.6426 251541.5312 252109.083 429231.3235 238075.0812 247058.7721 2.064745161 1.763589234 1.354209982 1.343535866 1.386458128 1.018144505 1.020441739 1.737365243 0.963637434 1 17.91449476 4.535071995 1.225755967 1.245212811 2.293989699 0.612680092 0.226244301 0.760784789 1.275361701 0.067696176 0.924936179 34282.46133 -4.535071995 1.048776888 ELSQDSTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSQDSTGR 9 0 P52788;H7C2R7 P52788 SMS Spermine synthase 0 ; 185.81 9.87E-05 451760000 351160 395910 320160 419870 419710 425210 397990 417930 416870 432290 FALSE TRUE 337436.279 384619.0344 378020.0339 441539.541 433210.3533 433808.0375 402860.7207 409299.5995 369548.6653 403010.6133 0.837288815 0.95436453 0.93799027 1.095602762 1.074935347 1.076418395 0.999628068 1.015605014 0.916970058 1 18.62045831 4.535228737 1.446635166 1.025293286 0.811567573 0.524729928 0.053089778 0.654738579 1.673054568 0.01523329 0.181534524 34294.8365 -4.535228737 -0.213725713 ELEIEER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEIEER 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 96.492 0.041043 498930000 870780 1399700 1209850 1960450 1941270 1926710 1740020 1856420 1031030 1410040 FALSE TRUE 836748.9549 1359781.926 1428496.808 2061629.059 2003712.713 1965669.396 1761314.885 1818084.278 913991.7968 1314536.735 0.636535239 1.034419115 1.086692194 1.568331264 1.524272894 1.49533242 1.339874983 1.383060838 0.695295744 1 20.32612303 4.535299014 1.616780132 1.321031263 0.552115556 0.353468366 0.257806898 0.688685882 2.343330794 0.068944028 0.737264188 34300.38651 -4.535299014 -0.768915707 GSPSSYNSSSSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSPSSYNSSSSSPR 14 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 GSPSSYNSSSSS(1)PR;GSPSSYNSSSSS(1)PR;GSPSSYNSSS(0.001)S(0.165)S(0.835)PR;GSPSSYNS(0.003)S(0.024)S(0.024)S(0.137)S(0.812)PR 270.78 6.40E-33 2389430000 1593520 1813990 1632140 2042470 2001870 2078600 1913180 1822510 1927620 2024890 TRUE FALSE 1531243.477 1762256.781 1927104.005 2147882.121 2066261.967 2120630.716 1936594.069 1784874.532 1708804.659 1887742.397 0.811150652 0.933526091 1.020851154 1.137804674 1.09456776 1.123368697 1.025878357 0.945507467 0.905210723 1 20.84823048 4.535407623 2.332737405 1.034099935 0.800827479 0.498368936 0.069501242 0.367418602 3.18774209 0.020287912 0.14505491 34308.96551 -4.535407623 -0.233272456 GSGTAS(ph)DDEFENLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSGTASDDEFENLR 14 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 GSGT(0.001)AS(0.999)DDEFENLR;GSGTAS(1)DDEFENLR;GSGTAS(1)DDEFENLR;GSGTAS(1)DDEFENLR 391.1 4.68E-114 20469200000 6134660 6770830 5829180 7103270 7098830 7465340 6750360 7092050 7726150 7928890 TRUE FALSE 5894910.705 6577732.558 6882642.495 7469870.616 7327170.314 7616294.29 6832972.925 6945596.689 6849109.843 7391859.218 0.797486875 0.88986172 0.931111144 1.010553691 0.991248629 1.030362466 0.924391648 0.939627837 0.926574714 1 22.81750585 4.535444897 1.685341426 0.969736439 0.775319075 0.713131639 0.034927822 0.378077189 1.431840244 0.010243833 0.104959993 34311.91024 -4.535444897 -0.194417364 IMT(ph)IIEPVS(ph)KK ddPTM_BT-474_Pertuzumab_2h_R1 2 IMTIIEPVSKK 11 1 A0A1B0GUF7;A0A1B0GVH7 A0A1B0GUF7 2 IMT(1)IIEPVS(1)KK;IMT(1)IIEPVS(1)KK 61.212 0.079334 271350000 201723 218673 194352 223702 211752 230586 230112 218295 261730 270260 TRUE FALSE 193839.4421 212436.6601 229475.7297 235247.287 218563.1954 235248.6069 232928.1795 213787.132 232019.5077 251955.0495 0.769341367 0.843153017 0.910780436 0.933687527 0.867469002 0.933692765 0.924483077 0.848512988 0.920876593 1 17.94280684 4.535599991 2.323202652 0.908943078 0.761829883 0.585590059 0.03926514 0.279870013 2.403021798 0.009680529 0.069566979 34324.1658 -4.535599991 -0.147113194 TLGT(ph)PTQPGSTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLGTPTQPGSTPR 13 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 TLGT(0.979)PT(0.021)QPGSTPR;TLGT(1)PTQPGSTPR 176.86 0.00017812 866200000 708910 777880 699950 848350 778430 849250 780910 816750 816690 880030 TRUE FALSE 681205.0135 755695.624 826446.5353 892133.4452 803468.9079 866422.4169 790467.0102 799883.8271 723982.775 820424.7843 0.830307697 0.921102871 1.007339797 1.087404308 0.979332808 1.05606563 0.963485045 0.974963022 0.882448689 1 19.64601155 4.53592781 2.790453558 0.99499495 0.828762807 0.492159268 0.0519824 0.263273526 3.528267316 0.013349717 0.079470888 34350.08454 -4.53592781 -0.166232143 FSLS(ph)PSLGPQASR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSLSPSLGPQASR 13 0 Q9NYF3 Q9NYF3 FAM53C Protein FAM53C 1 FSLS(0.705)PS(0.295)LGPQASR;FS(0.005)LS(0.887)PS(0.108)LGPQASR 160.87 5.27E-06 204010000 252392 293043 278718 306902 272447 334153 361727 314036 356529 366252 TRUE FALSE 242528.2416 284685.7006 329088.5426 322741.249 281210.5052 340909.8026 366153.9232 307551.0469 316057.3226 341445.4258 0.710298699 0.833766333 0.963810078 0.945220596 0.823588439 0.998431307 1.072364412 0.900732661 0.925645209 1 18.38129548 4.535941325 2.263792381 0.951226706 0.694621071 0.601120373 0.062955319 0.286475949 2.304864337 0.016590613 0.122808792 34351.15352 -4.535941325 -0.256605635 ERPPLDVDEMLER ddPTM_BT-474_Pertuzumab_2h_R1 4 ERPPLDVDEMLER 13 1 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-5;A0A0G2JMG8;F5H5B1;K7ELX1;K7EPE6;F5GYZ4 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;;; 184 9.01E-06 2166880000 1176650 1314090 1125050 1343140 1405390 1462370 1522150 1437430 1558490 1646490 FALSE TRUE 1130665.217 1276613.44 1328371.562 1412459.616 1450595.646 1491940.123 1540778.527 1407746.568 1381576.749 1534971.766 0.736603267 0.831685291 0.865404557 0.920186057 0.945030833 0.971965841 1.003782976 0.917115611 0.900066555 1 20.54978069 4.536436823 0.853140144 0.955545921 0.659599139 0.835451731 0.031524932 0.717301609 0.498655059 0.011590275 0.188323046 34390.36799 -4.536436823 -0.295946782 EEDEPEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EEDEPEER 8 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 176.29 0.00060758 1101630000 1073930 1190050 1050600 1269980 1145810 1292510 1232720 1362780 1386980 1319260 FALSE TRUE 1031959.628 1156110.939 1240466.79 1335523.82 1182666.019 1318645.438 1247806.396 1334638.117 1229535.845 1229905.345 0.839056137 0.939999931 1.008587202 1.085875287 0.961591088 1.072151969 1.01455482 1.085155148 0.99969957 1 20.23011586 4.536923946 1.776002066 1.036432301 0.814281668 0.703744077 0.038905131 0.286726909 1.240785298 0.00964592 0.093886647 34428.96332 -4.536923946 -0.222150632 SQVEEELFSVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQVEEELFSVR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 202.68 9.12E-08 552080000 558070 627670 544800 701840 647470 663400 661530 676630 656730 723500 FALSE TRUE 536260.0074 609769.4662 643257.479 738062.0465 668296.4606 676814.4025 669626.002 662657.354 582180.7636 674496.7006 0.795052084 0.904036248 0.953685138 1.094241152 0.990807605 1.003436195 0.992778766 0.982447139 0.863133597 1 19.36345186 4.537303845 2.006774151 0.990056097 0.779570052 0.559127617 0.053017228 0.355401622 2.104247312 0.013860921 0.117953794 34459.09325 -4.537303845 -0.210486045 KGAEPSGGAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KGAEPSGGAAR 11 1 O00762;K4DI81;A0A0A0MSE8;A0A087WVK1;O00762-3;O00762-4 O00762 UBE2C Ubiquitin-conjugating enzyme E2 C 0 ;;; 98.105 0.0092504 379651000 505750 519634 442016 500429 499890 497676 575000 514750 550290 582000 FALSE TRUE 485984.7309 504814.5471 521898.1238 526256.2007 515969.4158 507739.3497 582037.022 504120.2326 487823.3862 542580.6216 0.895691279 0.93039546 0.961881245 0.969913373 0.950954375 0.935786 1.072719885 0.929115808 0.899080002 1 19.049478 4.537564143 1.889359132 0.965414655 0.887688535 0.200457754 0.044219667 0.885241959 4.489128439 0.011530714 0.105064504 34479.75276 -4.537564143 -0.07772612 QVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR ddPTM_BT-474_Pertuzumab_2h_R1 3 QVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR 37 1 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 320.84 2.51E-110 1352890000 1950603 1797117 1498296 1596776 1535560 1549408 1611904 1650312 2094423 2107193 FALSE TRUE 1874371.278 1745864.983 1769071.417 1679185.801 1584952.682 1580738.091 1631630.963 1616232.48 1856672.882 1964470.941 0.954135406 0.888720187 0.900533258 0.854777623 0.806808922 0.804663514 0.83057017 0.822731681 0.945126162 1 20.9057094 4.537568789 1.210714829 0.851728535 0.972004297 0.106603648 0.06127052 1.712372503 2.774348182 0.017062894 0.236934965 34480.1216 -4.537568789 0.120275763 GMDDDRGPR ddPTM_BT-474_Pertuzumab_2h_R1 10 GMDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;;;;;; 131.06 0.00036067 4374240000 6562410 7482050 6385670 8241550 7860970 8325730 7799210 7849530 8320080 8867980 FALSE TRUE 6305943.762 7268669.26 7539702.617 8666897.383 8113825.239 8494081.965 7894659.065 7687434.462 7375619.399 8267343.816 0.762753298 0.879202489 0.911986097 1.048329134 0.981430726 1.027425755 0.95492086 0.929855421 0.892138946 1 22.97899246 4.537613708 1.669509635 0.970986298 0.73663133 0.680434297 0.044938586 0.402792752 1.484455118 0.012877658 0.13419977 34483.68811 -4.537613708 -0.234354968 NTHCSSLPHYQK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTHCSSLPHYQK 12 0 P43243;A0A0R4J2E8;P43243-2;B3KM87;A8MXP9;Q68E03 P43243;A8MXP9 MATR3;DKFZp686L22104 Matrin-3 0 80.245 0.012063 340300000 352270 401180 345680 420230 437420 446840 477520 394270 428570 540910 FALSE TRUE 338502.8989 389738.7392 408152.0656 441918.1207 451490.0116 455875.411 483364.0326 386128.1867 379920.5303 504273.6839 0.671268221 0.772871462 0.809386011 0.876345792 0.895327331 0.904023798 0.958535113 0.765711555 0.753401461 1 18.94384741 4.537701565 1.309380559 0.86927503 0.630396305 0.451415507 0.07221349 0.961018678 1.897530312 0.021305185 0.278899688 34490.66473 -4.537701565 -0.238878725 QVELYR ddPTM_BT-474_Pertuzumab_2h_R1 1 QVELYR 6 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 101.69 0.084302 310800000 152640 173380 163560 185960 187500 198160 184930 171030 193070 195390 FALSE TRUE 146674.66 168435.3722 193118.9304 195557.4179 193531.1078 202166.931 187193.2287 167498.1707 171153.503 182156.0613 0.805214271 0.924676187 1.060183938 1.073570742 1.062446709 1.109855635 1.027653032 0.91953114 0.939598177 1 17.47481548 4.537888436 3.033074886 1.021843149 0.806176554 0.595423249 0.056501992 0.228161966 3.708701374 0.016566421 0.091961933 34505.50881 -4.537888436 -0.215666596 ELPPPSEEIKTGEDEDEEDNDALLKENES(ph)PDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELPPPSEEIKTGEDEDEEDNDALLKENESPDVR 33 2 A0A087WWS1;Q96FV9 A0A087WWS1 THOC1 THO complex subunit 1 1 ELPPPSEEIKTGEDEDEEDNDALLKENES(1)PDVR 77.1 0.0010804 76505000 56490 45891 27679 26726 39214 38736 34116 37695 52825 42371 TRUE FALSE 54282.30835 44582.23361 32681.21102 28105.33206 40475.35392 39519.26846 34533.52181 36916.58508 46828.52746 39501.17443 1.374194796 1.128630585 0.827347832 0.711506239 1.024662039 1.000458063 0.874240382 0.934569304 1.185497093 1 15.26960793 4.537989805 3.351033948 0.935915886 1.363637066 0.546100451 0.121334428 0.189974716 3.880969368 0.030447038 0.156229711 34513.56374 -4.537989805 0.42772118 ELELVEDVWR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELELVEDVWR 10 0 A0A1B0GVV3;Q5EBL4-2;Q5EBL4 A0A1B0GVV3 RILPL1 RILP-like protein 1 0 ;; 150.27 5.09E-05 61981800 98222 106071 94674 109808 112140 103351 106537 118274 107942 114463 FALSE TRUE 94383.37565 103045.9589 111783.6978 115475.204 115747.0849 105440.828 107840.8317 115831.6006 95688.87669 106710.3191 0.88448218 0.965660677 1.047543469 1.082137183 1.084685024 0.98810339 1.01059422 1.085477033 0.896716246 1 16.70334017 4.538202678 2.805870971 1.032134337 0.88290073 0.376795446 0.055104192 0.294633976 3.989009782 0.013446888 0.08015579 34530.48497 -4.538202678 -0.149233606 LDDSFVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDDSFVR 7 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7ELJ8;K7EJV7;K7EN19;K7EJL5;K7EJE9 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 134.85 0.019566 0 222680 242900 217550 245880 248520 248640 263290 264810 245930 290150 FALSE TRUE 213977.4194 235972.7298 256866.1244 258569.8963 256513.8715 253667.6712 266512.2218 259341.581 218013.0574 270497.8821 0.791050258 0.872364427 0.949604937 0.955903589 0.948302699 0.937780619 0.985265466 0.95875642 0.805969554 1 18.04525777 4.538268873 2.325410833 0.944991615 0.782409094 0.480989987 0.049569106 0.319608098 2.742093768 0.012160355 0.088030424 34535.74853 -4.538268873 -0.16258252 GGGQEERPFVAR ddPTM_BT-474_Pertuzumab_2h_R1 5 GGGQEERPFVAR 12 1 Q9HA64;I3L2G3 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;;;; 199.82 1.52E-07 5247200000 5188560 5769730 5110565 6290480 5809900 6058420 5904660 6180530 6425730 6952940 FALSE TRUE 4985785.339 5605182.95 6034157.779 6615132.427 5996780.71 6180925.403 5976922.995 6052899.896 5696308.069 6482011.181 0.769172592 0.864728985 0.930908265 1.020537028 0.925141988 0.953550562 0.922078477 0.933799669 0.87878714 1 22.62801008 4.538322718 2.226795449 0.944026151 0.75866316 0.682652619 0.037988913 0.237286349 1.826646053 0.009618546 0.073064723 34540.03062 -4.538322718 -0.185362991 LSSGPEQITLEASSTEGHPGAPS(ph)PQHTDQTEAFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 LSSGPEQITLEASSTEGHPGAPS(1)PQHTDQTEAFQK 343.21 2.81E-118 292660000 46451 55333 52220 61809 61513 82883 58982 39759 70760 74738 TRUE FALSE 44635.64357 53754.95702 61657.31563 64998.9699 63491.62151 84558.95105 59703.83936 38937.96276 62727.62145 69675.92869 0.640617849 0.771499685 0.884915591 0.932875544 0.911241841 1.213603502 0.856878989 0.558843829 0.90027679 1 16.08837271 4.538356656 2.346083728 0.884172452 0.628109638 0.228345867 0.152398319 0.734827378 6.444056098 0.044627561 0.320033361 34542.72983 -4.538356656 -0.256062814 SPIMADLNLSLPSIPEVAS(ph)DDER ddPTM_BT-474_Pertuzumab_2h_R1 1 SPIMADLNLSLPSIPEVASDDER 23 0 Q6WKZ4;Q6WKZ4-1 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 SPIMADLNLSLPS(0.002)IPEVAS(0.998)DDER 95.957 0.0024268 30562000 7257.6 10581 10933 14810 8832.7 10410 15388 14061 13196 16945 TRUE FALSE 6973.964968 10279.24024 12908.8363 15574.34587 9116.811817 10620.49733 15576.32295 13770.63544 11698.0454 15797.30006 0.441465627 0.650696018 0.817154593 0.985886564 0.577112024 0.672298259 0.986011717 0.871708164 0.74050916 1 13.94739039 4.538882252 2.298140332 0.828682351 0.419963244 0.461298393 0.132995629 0.368930454 3.071341503 0.034600308 0.254242436 34584.55974 -4.538882252 -0.408719107 LIETGER ddPTM_BT-474_Pertuzumab_2h_R1 1 LIETGER 7 0 E5RHX8;Q9NPA8-2;Q9NPA8;J3KNT2;E5RI00;E5RHT9;E5RJ84 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 130 0.0083885 247830000 191140 219670 207600 233330 243240 247830 226660 237270 224220 271700 FALSE TRUE 183670.0375 213405.2267 245117.938 245372.1893 251064.0355 252841.2924 229433.9329 232370.2916 198767.4856 253297.517 0.725115823 0.842508167 0.967707623 0.968711388 0.991182379 0.998198859 0.905788322 0.917380851 0.78471944 1 17.95047341 4.538981961 2.798346921 0.940168554 0.722302254 0.551395599 0.061295382 0.237600238 3.193309417 0.015751736 0.0943465 34592.50091 -4.538981961 -0.217866299 VLSTNTDDNIGGAHFTETLAQYLASEFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSTNTDDNIGGAHFTETLAQYLASEFQR 29 0 Q0VDF9 Q0VDF9 HSPA14 Heat shock 70 kDa protein 14 0 ; 259.38 4.53E-58 352720000 160185 181793 156980 201017 201388 194209 209195 179241 186005 203276 FALSE TRUE 153924.7931 176608.4416 185349.778 211391.5115 207865.8279 198136.039 211755.191 175539.6107 164890.4922 189507.9355 0.812234025 0.931931643 0.978058135 1.115475776 1.096871365 1.045528983 1.117394849 0.92629161 0.870098087 1 17.53189874 4.539239952 1.896442283 1.024709314 0.792394431 0.421303345 0.076119776 0.555246624 2.836778018 0.021657517 0.197593956 34613.05653 -4.539239952 -0.232314883 LATQSNEITIPVT(ph)FESR ddPTM_BT-474_Pertuzumab_2h_R1 1 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LATQSNEITIPVT(0.5)FES(0.5)R 87.932 0.049418 29301000 69717 52859 44283 28120 40414 28189 20447 33137 24542 32027 TRUE FALSE 66992.38256 51351.51307 52285.92317 29571.27657 41713.95301 28759.00089 20697.2365 32452.70937 21756.09505 29857.78276 2.243715921 1.719870276 1.751165637 0.990404304 1.397088101 0.963199482 0.693194021 1.086909555 0.728657423 1 14.86581941 4.539244696 0.567639997 0.871922123 2.910074737 0.841451488 0.191005747 1.121736373 0.3222813 0.097019061 1.465296848 34613.43463 -4.539244696 2.038152614 up ALHVNNDR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALHVNNDR 8 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;;; 168.27 0.00030783 2565068000 2157910 2455440 2070490 2894950 2662830 2520530 2656020 2404850 2605820 2722110 FALSE TRUE 2073576.492 2385413.255 2444673.601 3044358.716 2748482.345 2571496.844 2688525.167 2355189.007 2310018.238 2537739.065 0.817096021 0.939975779 0.96332741 1.199634256 1.083043715 1.013302305 1.059417497 0.928065868 0.910266256 1 21.27511231 4.539347563 2.022222619 1.023253992 0.80321418 0.396954252 0.078177832 0.540114033 3.252763786 0.02218569 0.188419707 34621.63418 -4.539347563 -0.220039811 FSEGNILELLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSEGNILELLHR 12 0 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 0 ; 117.63 0.00071289 467060000 331440 370340 348890 388200 406380 344490 402050 375480 434820 432600 FALSE TRUE 318486.9584 359778.2658 411942.184 408235.0485 419451.5818 351455.8238 406970.4082 367726.2068 385461.0565 403299.6167 0.789703102 0.892086803 1.021429644 1.012237631 1.040049542 0.871450925 1.009101897 0.911794089 0.955768467 1 18.62149251 4.539504128 3.350943054 0.97256691 0.79387077 0.576590422 0.05031396 0.188187984 3.832278816 0.012564487 0.064722617 34634.11764 -4.539504128 -0.17869614 FEDYLNAESR ddPTM_BT-474_Pertuzumab_2h_R1 6 FEDYLNAESR 10 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ;;;;; 266.54 2.29E-17 4836960000 2719830 3014530 2659590 3225950 2981200 2891600 3232250 3535550 3336860 3398940 FALSE TRUE 2613536.037 2928558.556 3140237.075 3392441.666 3077093.005 2950070.133 3271807.242 3462539.657 2958073.642 3168726.766 0.824790596 0.924206715 0.991009105 1.07060088 0.971081836 0.930995428 1.032530566 1.092722697 0.933521209 1 21.59547183 4.539627685 1.977273509 1.011690884 0.807198716 0.551503803 0.050096963 0.377661026 2.14658413 0.013882239 0.121029274 34643.97251 -4.539627685 -0.204492168 IIFEDDR ddPTM_BT-474_Pertuzumab_2h_R1 10 IIFEDDR 7 0 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ;;;;;;;;; 175.75 0.0018083 41969760000 42352600 46676080 39555940 49849150 50040850 46008030 46682710 50738170 50382270 53326120 FALSE TRUE 40697413.57 45344923.9 46704578.28 52421870.61 51650459.39 46938343.89 47254026.97 49690409.06 44663085.93 49714294.39 0.818625992 0.912110379 0.939459744 1.05446273 1.038945841 0.944161925 0.950511871 0.999519548 0.89839525 1 25.5671574 4.539769423 1.802929926 0.982702479 0.801507934 0.563059487 0.044324225 0.429887936 1.926753385 0.01200508 0.116019159 34655.28087 -4.539769423 -0.181194545 SSLGQS(ph)AS(ph)ETEEDTVSVSKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 2 SSLGQS(0.997)AS(0.968)ET(0.035)EEDTVSVSKK 100.93 0.0015599 647070000 954420 776290 479120 480340 548310 628540 656890 681280 840250 697240 TRUE FALSE 917120.2112 754150.9693 565707.642 505130.405 565946.8891 641249.5094 664929.2163 667211.3299 744868.3426 650015.3138 1.41092093 1.160204926 0.870298945 0.777105392 0.870667009 0.986514465 1.022943925 1.026454786 1.145924299 1 19.31011418 4.539812198 3.173666598 0.961886608 1.405126007 0.667374896 0.098739779 0.175200146 3.151389456 0.027409428 0.147306478 34658.69435 -4.539812198 0.443239399 SAVENCQDSWR ddPTM_BT-474_Pertuzumab_2h_R1 4 SAVENCQDSWR 11 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 248.88 6.24E-16 4629920000 1099230 1189680 1080860 1122240 1203940 1186490 1283830 1298870 1310720 1373430 FALSE TRUE 1056270.876 1155751.491 1276195.446 1180158.941 1242665.823 1210481.641 1299541.896 1272047.881 1161932.561 1280406.363 0.824949725 0.902644289 0.996711265 0.921706558 0.970524561 0.945388648 1.01494489 0.993472008 0.907471717 1 20.28817032 4.539923997 2.795629036 0.969817143 0.822491499 0.641273002 0.033707083 0.186283773 2.494898358 0.00832497 0.050045328 34667.61756 -4.539923997 -0.147325644 VEGDNDKKNPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEGDNDKKNPR 11 2 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 132.17 0.00010577 192130000 168070 136740 92174 84963 109300 114710 99993 120240 136040 109470 FALSE TRUE 161501.6386 132840.3091 108831.8922 89347.95061 112815.7338 117029.5148 101216.7442 117757.002 120597.3095 102055.4994 1.582488347 1.30164773 1.066399095 0.875483939 1.105435125 1.146724238 0.991781382 1.153852587 1.181683596 1 16.6389944 4.539983551 2.447394293 1.068772148 1.60344675 0.774683367 0.087788865 0.172067637 1.671864819 0.023172868 0.159542789 34672.37178 -4.539983551 0.534674602 SRT(ph)GS(ph)ESSQTGTSTTSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.134)RT(0.866)GS(0.633)ES(0.36)S(0.007)QTGTSTTSSR 159.59 9.78E-11 117520000 40690 51701 46552 58889 61480 64555 64859 55549 63956 65542 TRUE FALSE 39099.78981 50226.5381 54964.98194 61928.26835 63457.56003 65860.34633 65652.76384 54401.89374 56695.98301 61102.78196 0.639901958 0.82200084 0.899549582 1.0135098 1.038537985 1.077861665 1.074464398 0.890334155 0.927878915 1 15.89895045 4.540321832 1.331604618 1.000410843 0.565016124 0.798631549 0.057468101 0.454382212 0.933297184 0.018702196 0.243421217 34699.38934 -4.540321832 -0.435394718 DNQHQGSYSEGAQMNGIQPEEIGR ddPTM_BT-474_Pertuzumab_2h_R1 3 DNQHQGSYSEGAQMNGIQPEEIGR 24 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;; 269.63 3.55E-45 1132390000 284195 327300 308214 392480 339608 326026 326225 369639 347695 386100 FALSE TRUE 273088.3452 317965.7245 363915.126 412735.9398 350531.7997 332618.4691 330217.4391 362005.8255 308226.1213 359949.1031 0.758686 0.883363014 1.011018288 1.146650836 0.973837125 0.924070837 0.917400367 1.005713926 0.856304735 1 18.4574334 4.540546967 3.035739914 0.980812051 0.759877501 0.472586499 0.072648558 0.254236192 4.124515386 0.018834572 0.105238084 34717.38188 -4.540546967 -0.22093455 S(ph)CSASCVPHGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCSASCVPHGAK 12 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 S(0.583)CS(0.416)AS(0.001)CVPHGAK 107.46 0.0011665 197500000 391420 285150 147750 179650 226570 132460 116510 327520 166840 126110 TRUE FALSE 376122.8737 277017.8012 174451.7117 188921.758 233857.8298 135138.432 117935.8842 320756.5975 147901.0227 117568.4574 3.199181839 2.356225533 1.483830915 1.606908539 1.989120509 1.14944463 1.003125216 2.728253859 1.257999177 1 16.84314152 4.540999959 2.521239149 1.623457166 3.260742427 0.520577356 0.50353776 0.303174725 3.164258962 0.1303175 0.872049859 34753.6129 -4.540999959 1.637285261 NPLPNIDHELQELLIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 NPLPNIDHELQELLIDR 17 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 0 ;;; 188.6 4.02E-10 160798000 91297 97140 84764 99209 98260 106585 102822 104771 111789 124085 FALSE TRUE 87729.01231 94369.66231 100082.7404 104329.1884 101420.6221 108740.2217 104080.3664 102607.4422 99099.18138 115680.6124 0.758372647 0.815777686 0.865164337 0.901872718 0.876729644 0.940003856 0.899721779 0.886989099 0.85666197 1 16.81978757 4.541330501 1.071225686 0.905004423 0.711933818 0.645429355 0.03699981 0.791095732 0.941543435 0.010637622 0.161124843 34780.07398 -4.541330501 -0.193070604 RGLDEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGLDEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 115.49 0.0090878 235050000 300610 351160 296540 394520 364380 358670 395400 398550 407000 441090 FALSE TRUE 288861.8289 341145.2606 350131.3745 414881.2245 376100.6136 365922.5531 400239.0235 390319.8032 360799.0663 411214.5814 0.702460083 0.829603998 0.851456612 1.008916617 0.914609137 0.889857923 0.973309415 0.949187653 0.877398523 1 18.6495319 4.541342987 1.306034976 0.941006292 0.653441252 0.736459312 0.044993693 0.468577993 0.9150015 0.012341265 0.163685683 34781.07385 -4.541342987 -0.28756504 YFLNLVLVDEEDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFLNLVLVDEEDRR 14 1 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 238.88 3.89E-17 1555520000 601890 702160 679660 760070 756280 735390 790350 749660 740800 870890 FALSE TRUE 578367.4734 682135.0843 802489.681 799297.3038 780606.433 750260.0897 800022.5397 734179.259 656707.4897 811903.8446 0.71235957 0.840167329 0.988404829 0.984472865 0.961451825 0.924075055 0.985366118 0.904268731 0.808848848 1 19.63094935 4.541425309 3.086832028 0.942339242 0.713730931 0.638919314 0.054583695 0.175989567 2.96291929 0.013728961 0.075810244 34787.66737 -4.541425309 -0.228608312 DPFIGEHTEEILEEFGFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPFIGEHTEEILEEFGFSR 19 0 D6RB81;Q9UHK6;Q9UHK6-5 D6RB81 AMACR Alpha-methylacyl-CoA racemase 0 ; 244.86 1.53E-24 33917000 30365 38271 37341 45421 41250 44452 47084 39351 45840 50703 FALSE TRUE 29178.30223 37179.54855 44089.34935 47765.18325 42576.84371 45350.8499 47660.22808 38538.3881 40636.43538 47268.84065 0.617284068 0.786555118 0.932736 1.010500418 0.900738058 0.959423783 1.00828003 0.815302165 0.859687583 1 15.52860186 4.541593036 2.382723151 0.929619278 0.601829052 0.726325095 0.061663093 0.211773341 1.922523384 0.016733762 0.119190102 34801.10519 -4.541593036 -0.327790226 MDDPTVNWSNER ddPTM_BT-474_Pertuzumab_2h_R1 2 MDDPTVNWSNER 12 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 272.43 2.26E-27 1272350000 493720 544330 501510 579120 563200 496430 558900 592440 624050 636550 FALSE TRUE 474424.8766 528806.2414 592144.013 609008.4526 581315.8395 506468.1547 565739.9854 580205.907 553210.4602 593435.9015 0.799454289 0.891092433 0.997823036 1.026241336 0.97957646 0.85345048 0.953329557 0.97770611 0.93221603 1 19.17873268 4.541938922 3.19107142 0.962897196 0.801548266 0.566033546 0.045273436 0.207384227 3.763239278 0.011833697 0.063676901 34828.83293 -4.541938922 -0.161348929 EEGVIDSSDKEIVAEAERLDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEGVIDSSDKEIVAEAERLDVK 22 2 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;; 136.56 2.43E-06 149530000 250474 211715 145153 117139 175755 197775 168547 200008 239570 179323 FALSE TRUE 240685.1992 205677.0955 171385.376 123184.5578 181408.3192 201774.146 170609.7286 195877.7649 212375.018 167177.2935 1.439700297 1.230293249 1.025171376 0.736849815 1.085125351 1.206947079 1.020531706 1.171676852 1.270358034 1 17.35101938 4.542008647 3.016896693 1.068934075 1.438186618 0.417795499 0.138294596 0.298436852 4.762130081 0.036582583 0.206333766 34834.42508 -4.542008647 0.369252543 SQDQDS(ph)EVNELSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQDQDSEVNELSR 13 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 SQDQDS(1)EVNELSR;SQDQDS(1)EVNELSR 281.09 2.06E-32 1655030000 1667300 1870740 1597220 2134900 1903110 1872630 2011620 1948930 1997800 2176200 TRUE FALSE 1602140.073 1817388.327 1885873.184 2245082.445 1964325.262 1910495.862 2036238.807 1908683.914 1771018.119 2028804.036 0.789696809 0.895792938 0.929549208 1.106603893 0.968218333 0.941685756 1.003664608 0.940792645 0.872937005 1 20.95219809 4.542044782 2.017187623 0.972821129 0.775768869 0.495340894 0.057327594 0.416737666 2.485316315 0.015162793 0.130277721 34837.32356 -4.542044782 -0.19705226 QAHELFR ddPTM_BT-474_Pertuzumab_2h_R1 3 QAHELFR 7 0 E7EPM6;P33121-2;P33121;P33121-3;D6RER0;D6RG07 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ;; 126.52 0.0039439 359934000 244911 304163 269813 370520 334630 307210 365959 304690 388390 422310 FALSE TRUE 235339.6074 295488.569 318574.2111 389642.5816 345393.6779 313421.9967 370437.7157 298398.045 344301.5955 393706.5675 0.597753827 0.750529946 0.809166616 0.989677627 0.877287062 0.796080184 0.940897984 0.757919907 0.874513213 1 18.58676125 4.542051791 1.800088407 0.872533426 0.567022682 0.592358481 0.074748872 0.417824731 1.859491893 0.019504286 0.190234013 34837.88575 -4.542051791 -0.305510745 YQELPNSGPPHDR ddPTM_BT-474_Pertuzumab_2h_R1 4 YQELPNSGPPHDR 13 0 P19525-2;P19525;C9JZT2;F8WBH4 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 ;;; 178.23 1.48E-05 2048730000 1350520 1612560 1415990 1839590 1728300 1767600 1804140 1839420 1765460 2082550 FALSE TRUE 1297740.185 1566571.368 1671890.892 1934531.46 1783892.339 1803342.083 1826219.605 1801435.334 1565052.382 1941497.034 0.66842244 0.806888365 0.861134919 0.996412267 0.918823108 0.928841019 0.940624463 0.927858917 0.806105987 1 20.88873807 4.542365513 1.569987172 0.927722998 0.628123581 0.7118235 0.051889537 0.370748647 1.158554723 0.01352765 0.152442373 34863.06078 -4.542365513 -0.299599417 SAADS(ph)ISESVPVGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAADSISESVPVGPK 15 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 1 SAADS(1)ISESVPVGPK 204.28 5.23E-09 207030000 591700 558940 347730 286580 372880 331990 215320 343970 300930 263640 TRUE FALSE 568575.7098 542999.5785 410572.5462 301370.4281 384874.0238 338703.0653 217955.1506 336866.8993 266769.688 245783.428 2.31331996 2.209260335 1.670464724 1.226162523 1.565907136 1.378054933 0.886777243 1.370584266 1.085385171 1 17.90702812 4.542630885 0.635571278 1.145942672 3.039903348 0.838358941 0.183970537 1.021975757 0.369672047 0.08501218 1.361694519 34884.37006 -4.542630885 1.893960676 up DSQDAGGFGPEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSQDAGGFGPEDR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 300.7 1.51E-40 1331020000 495150 529410 462910 537760 507750 561170 518570 597170 568310 554800 FALSE TRUE 475798.9906 514311.7451 546568.1344 565513.858 524082.2399 572517.2419 524916.4148 584838.2308 503797.8313 517222.9018 0.919910911 0.994371563 1.056736143 1.093365851 1.013261861 1.10690621 1.014874656 1.130727639 0.974043936 1 18.98042663 4.543269547 2.284671876 1.057967523 0.911468728 0.398126109 0.048273502 0.342873282 2.798104994 0.011303703 0.084773918 34935.70785 -4.543269547 -0.146498795 EVYELLDS(ph)PGKVLLQSK ddPTM_BT-474_Pertuzumab_2h_R1 3 EVYELLDSPGKVLLQSK 17 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 EVYELLDS(1)PGKVLLQSK;EVYELLDS(1)PGKVLLQSK;EVYELLDS(1)PGKVLLQSK 239.56 1.66E-20 492256000 947848 792102 609443 427160 606741 756386 674955 687074 898856 738438 TRUE FALSE 910805.0523 769512.0265 719582.9071 449205.7788 626257.3753 771680.6432 683215.3012 672885.6818 796821.6352 688422.9365 1.323031241 1.11778964 1.04526283 0.652514254 0.909698591 1.120939763 0.992435413 0.977430655 1.157459452 1 19.39293564 4.543709741 2.192678359 0.972488436 1.342756041 0.401942065 0.129489103 0.444689869 3.271288926 0.034679768 0.272697395 34971.13606 -4.543709741 0.370267604 SVDTGETDIDPVMDDDDVFPPYVLRPDDGGPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVDTGETDIDPVMDDDDVFPPYVLRPDDGGPR 32 1 Q9UPY3-2;Q9UPY3 Q9UPY3-2 DICER1 Endoribonuclease Dicer 0 ;; 111.2 3.18E-06 57480000 79601 87783 70238 91916 84956 95200 92422 93739 101948 107578 FALSE TRUE 76490.10492 85279.51479 82931.56904 96659.79578 87688.6869 97125.00923 93553.08808 91803.25689 90375.29044 100291.6462 0.762676731 0.850315235 0.826904056 0.963787109 0.874336898 0.968425715 0.932810374 0.915362947 0.901124808 1 16.61384192 4.545196058 0.795086556 0.934996706 0.701362262 0.671968365 0.039427986 1.154614178 0.677581165 0.01358243 0.227091589 35091.02528 -4.545196058 -0.233634445 TDTGIVTVEQS(ph)PSSSK ddPTM_BT-474_Pertuzumab_2h_R1 3 TDTGIVTVEQSPSSSK 16 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 TDTGIVTVEQS(0.921)PS(0.079)SSK;TDTGIVTVEQS(0.781)PS(0.202)S(0.017)SK;TDTGIVTVEQS(0.796)PS(0.158)S(0.031)S(0.015)K 340.75 4.92E-72 367230000 1187280 1067080 860110 881160 882730 861210 917350 1142000 966650 1038350 TRUE FALSE 1140879.785 1036647.923 1015551.01 926636.7732 911123.8121 878624.2563 928576.8037 1118417.301 856919.9445 968021.6296 1.178568484 1.070893347 1.049099502 0.957248004 0.941222576 0.907649405 0.959252123 1.155363957 0.885228096 1 19.88467976 4.545724247 1.432395319 0.98587183 1.211990256 0.444708569 0.07109055 0.919950284 2.260702884 0.021686285 0.269514777 35133.72896 -4.545724247 0.226118426 GESGQSWPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GESGQSWPR 9 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;; 131.5 0.00077069 259380000 425303 492455 451307 561334 518990 565850 541920 522836 505990 527129 FALSE TRUE 408681.6886 478410.6656 532868.2142 590304.515 535683.7847 577291.8747 548552.1791 512039.2539 448552.1365 491426.0833 0.831623926 0.973515004 1.084330344 1.20120713 1.090059732 1.174727786 1.116245551 1.041945618 0.912756062 1 18.90661491 4.545801899 2.436750593 1.086914177 0.820347783 0.4842389 0.078667684 0.312548853 2.983904071 0.020579065 0.144948952 35140.01148 -4.545801899 -0.266566394 DVEDEETWIR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVEDEETWIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 243.29 4.88E-12 2065310000 1588310 1686970 1436740 1695580 1680830 1784010 1751110 1783470 1985500 1879220 FALSE TRUE 1526237.089 1638859.267 1696390.878 1783089.087 1734895.423 1820083.905 1772540.608 1746640.721 1760114.364 1751938.756 0.871170345 0.935454657 0.968293482 1.017780491 0.990271731 1.038896993 1.011759459 0.996975902 1.004666606 1 20.74052091 4.546046182 1.190202924 1.009320078 0.835077989 0.911650809 0.013668924 0.288964174 0.443943651 0.003986899 0.057427864 35159.78265 -4.546046182 -0.174242089 EDFEEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDFEEAR 7 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ; 179.97 0.0016129 817500000 805640 827780 818650 961430 902330 1027080 995540 1075600 1183870 1092330 FALSE TRUE 774154.6981 804172.5249 966598.2658 1011049.518 931354.2639 1047848.261 1007723.716 1053388.484 1049482.041 1018345.516 0.760208285 0.78968534 0.949184977 0.992835439 0.914575897 1.028971253 0.989569552 1.034411668 1.030575599 1 19.95779571 4.546270127 0.790051891 1.013329612 0.623662863 0.86048184 0.03518287 0.664895108 0.384255715 0.01294895 0.217085853 35177.91758 -4.546270127 -0.389666749 LEHGDGGILDLDDILCDVADDKDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEHGDGGILDLDDILCDVADDKDR 24 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 0 ;;; 305.18 7.60E-63 193834000 504454 452471 332410 362075 386869 406571 371902 402194 536279 465680 FALSE TRUE 484739.38 439566.9701 392483.8814 380761.7341 399312.9927 414792.1442 376453.4479 393888.5534 475402.8562 434139.0788 1.116553205 1.012502655 0.90405103 0.877050127 0.919781269 0.95543609 0.86712638 0.907286565 1.095047369 1 18.72779777 4.546297689 2.883143825 0.930225195 1.118383746 0.409738728 0.064213201 0.266762695 3.809107902 0.015640731 0.093006034 35180.15017 -4.546297689 0.18815855 NVES(ph)AWNIRK ddPTM_BT-474_Pertuzumab_2h_R1 2 NVESAWNIRK 10 1 Q6PI26-2;Q6PI26 Q6PI26-2 SHQ1 Protein SHQ1 homolog 1 NVES(1)AWNIRK;NVES(1)AWNIRK 67.456 0.038538 2524600000 2284200 2150500 2206800 2293200 2370400 2249300 2509700 2838400 3047400 2960900 TRUE FALSE 2194930.939 2089169.846 2605617.85 2411552.327 2446646.069 2294782.387 2540414.459 2779786.048 2701471.928 2760355.606 0.795162382 0.756848082 0.943942818 0.873638281 0.886351767 0.831335782 0.920321445 1.007039108 0.978668083 1 21.39642271 4.546831634 0.21402902 1.034673308 0.594180251 0.631068942 0.049741649 7.813605497 0.350016525 0.104360298 0.926906307 35223.42917 -4.546831634 -0.440493057 KVEQNSRPVS(ph)CSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 KVEQNS(0.037)RPVS(0.799)CS(0.163)GR;KVEQNSRPVS(0.963)CS(0.037)GR;KVEQNS(0.001)RPVS(0.987)CS(0.011)GR;KVEQNS(0.001)RPVS(0.994)CS(0.005)GR 158.45 3.99E-06 354115000 461194 370596 226617 204842 229045 236431 148494 283566 182654 149781 TRUE FALSE 443170.0286 360026.9649 267571.733 215413.9202 236412.4404 241211.7968 150311.314 277710.263 161919.8837 139636.1995 3.173747426 2.57832114 1.91620607 1.542679628 1.693059832 1.727430263 1.076449478 1.988812816 1.159583864 1 17.09131347 4.546994843 1.039596542 1.489104074 3.760570291 0.795026531 0.293291262 0.574067514 0.63093431 0.086316596 1.348293004 35236.66872 -4.546994843 2.271466216 IVNGWQVEEADDWLR ddPTM_BT-474_Pertuzumab_2h_R1 6 IVNGWQVEEADDWLR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;;; 361.82 8.61E-83 3096950000 838618 961761 866579 1039342 1065193 1043166 1004632 1036915 1088439 1134607 FALSE TRUE 805843.8814 934332.5179 1023189.102 1092982.565 1099455.9 1064259.531 1016926.987 1015502.343 964883.9678 1057759.057 0.761840682 0.883313181 0.967317741 1.033300124 1.039419982 1.006145515 0.96139757 0.960050718 0.912196366 1 20.01257961 4.54817864 2.031198967 0.986351264 0.741028065 0.797533902 0.035525874 0.229295813 1.381022633 0.010342444 0.089964628 35332.8476 -4.54817864 -0.245323199 RGRS(ph)PS(ph)PKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGRSPSPKPR 10 3 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGRS(1)PS(1)PKPR 73.082 0.066116 280370000 260340 209040 145230 118210 179310 177200 163310 170720 211400 145950 TRUE FALSE 250165.625 203078.3839 171476.2916 124310.8323 185077.669 180783.1054 165308.6366 167194.5723 187402.7583 136064.6765 1.838578766 1.492513627 1.260255755 0.913615756 1.360218344 1.328655681 1.214926907 1.22878749 1.377306462 1 17.05393305 4.548582109 2.251521115 1.217561469 1.878208803 0.661500619 0.141405582 0.24773447 1.936458312 0.035536759 0.27555725 35365.6878 -4.548582109 0.660647334 AGLEDLQVAFR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGLEDLQVAFR 11 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 110.38 0.0041923 104190000 50596 60451 54541 69931 58419 75918 62613 69890 76331 77251 FALSE TRUE 48618.65238 58726.99667 64397.77196 73540.14729 60298.10019 77453.11398 63379.27662 68446.74708 67666.22489 72018.72096 0.67508353 0.815440706 0.894181 1.021125428 0.837255916 1.075458061 0.880038909 0.950402148 0.93956438 1 16.13608436 4.548659448 1.549217362 0.951637886 0.626630941 0.652700602 0.064794599 0.421905031 1.263273601 0.016068983 0.18724581 35371.9863 -4.548659448 -0.325006945 RGMDDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGMDDDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 125.31 0.0065119 33554000 46449 57688 54505 68622 60816 61266 67133 66433 69508 70106 FALSE TRUE 44633.72173 56042.79472 64355.26596 72163.58964 62772.20187 62504.8405 67954.59374 65061.13533 61617.74324 65357.65818 0.682914948 0.857478623 0.984662972 1.104133649 0.960441418 0.956350675 1.03973422 0.995463074 0.942777709 1 15.99606867 4.549602253 2.185379158 1.001366704 0.659194211 0.833287624 0.044281078 0.163469531 1.183805556 0.011549848 0.092922522 35448.85835 -4.549602253 -0.342172493 EVAETSMHNLLETDIEQVSQLSALVDAQLDYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVAETSMHNLLETDIEQVSQLSALVDAQLDYHR 33 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 62.105 0.01177 39808000 4698.9 7562.3 7385.8 11712 10077 14805 9256.2 7219.6 4857.7 6527.8 FALSE TRUE 4515.261793 7346.630608 8720.578356 12316.45772 10401.13586 15104.36724 9369.480144 7070.512737 4306.274261 6085.666292 0.741950277 1.207202343 1.432970186 2.023847042 1.70912031 2.481957853 1.539598081 1.161830504 0.707609332 1 12.57119951 4.549938605 2.138174623 1.554974118 0.683242885 0.193086659 0.478901759 0.75678983 5.183365333 0.131373243 1.084551003 35476.32335 -4.549938605 -0.871731233 HIEPELAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HIEPELAGR 9 0 P86791;P86790 P86791 CCZ1;CCZ1B Vacuolar fusion protein CCZ1 homolog;Vacuolar fusion protein CCZ1 homolog B 0 105.52 0.0030845 180650000 186910 212730 175940 254250 219340 221460 249330 189440 228790 228420 FALSE TRUE 179605.3506 206663.1487 207736.2718 267371.873 226395.2703 225938.0729 252381.3751 185527.9978 202818.7184 212948.9099 0.84341991 0.970482304 0.975521649 1.255568169 1.063143598 1.060996616 1.18517336 0.871232437 0.952429005 1 17.70014782 4.550279327 1.964111787 1.048330539 0.827566616 0.267713045 0.104447902 0.756706696 4.170295556 0.028890973 0.262835667 35504.16692 -4.550279327 -0.220763924 ENISEWR ddPTM_BT-474_Pertuzumab_2h_R1 3 ENISEWR 7 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 ;; 110.12 0.015994 1058180000 1224930 1304950 1080960 1332150 1305330 1335170 1338580 1355680 1329560 1413840 FALSE TRUE 1177058.381 1267734.104 1276313.518 1400902.421 1347317.125 1362168.052 1354961.942 1327684.734 1178633.923 1318079.357 0.893010254 0.96180408 0.968313107 1.062836174 1.022182099 1.033449196 1.027982067 1.007287404 0.894205585 1 20.3300058 4.550355042 1.626606298 1.009099025 0.877509762 0.384876354 0.042839726 0.695727433 2.356876957 0.011563117 0.129038673 35510.35726 -4.550355042 -0.131589264 TDDEVVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDDEVVQR 8 0 P14625;Q96GW1;A0A1W2PRR1;F8VPC7 P14625 HSP90B1 Endoplasmin 0 ; 248.34 6.46E-09 376580000 465170 542970 511840 598170 494820 536650 593630 612050 724950 677760 FALSE TRUE 446990.6421 527485.0272 604340.8738 629041.6254 510736.3347 547501.4307 600895.0215 599410.9536 642656.7152 631854.7115 0.707426302 0.834820122 0.956455436 0.995547891 0.808312932 0.866498929 0.951001885 0.948653136 1.017095708 1 19.26923334 4.551136954 2.634173211 0.936463083 0.699975333 0.597548643 0.060557503 0.244931204 2.808047325 0.015843294 0.104451173 35574.3484 -4.551136954 -0.23648775 IGGAQNR ddPTM_BT-474_Pertuzumab_2h_R1 3 IGGAQNR 7 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ;; 98.513 0.026074 497390000 223788 268741 242530 345046 269721 316489 305245 266248 286338 289020 FALSE TRUE 215042.1175 261076.7698 286360.5661 362853.8654 278396.8209 322888.6244 308980.6796 260749.8858 253834.1107 269444.418 0.798094535 0.968944808 1.062781587 1.346674272 1.033225416 1.198349652 1.146732532 0.96773163 0.942064833 1 18.03962817 4.551997572 2.368571586 1.093408961 0.783593554 0.383558862 0.113951649 0.417841141 3.691444821 0.030188519 0.223677133 35644.91405 -4.551997572 -0.309815407 GCNPSGHTQSVTT(ph)PEPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 GCNPSGHTQSVTTPEPAK 18 0 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 GCNPSGHTQSVT(0.164)T(0.836)PEPAK;GCNPSGHTQSVT(0.203)T(0.797)PEPAK;GCNPSGHTQSVT(0.114)T(0.886)PEPAK 163.95 1.17E-10 1168350000 861410 1014690 927780 1164380 1081000 1067120 1292600 1314210 1069570 1287210 TRUE FALSE 827745.1449 985752.0347 1095450.484 1224473.791 1115771.347 1088697.898 1308419.225 1287071.104 948156.8976 1200026.12 0.689772607 0.821442149 0.912855534 1.020372616 0.929789217 0.9072285 1.090325622 1.072535908 0.79011355 1 20.19463438 4.552098611 1.243943254 0.986486093 0.611225591 0.538810672 0.082765801 0.788479569 1.343115046 0.024551161 0.34910885 35653.20788 -4.552098611 -0.375260502 AKPAMPQDSVPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 13 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 1 AKPAMPQDS(0.005)VPS(0.995)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR 182.09 9.46E-07 50064570000 11011390 11614050 9766830 11728530 11832410 11654860 11893380 12103190 11832150 12198600 TRUE FALSE 10581052.71 11282828.67 11531913.44 12333840.84 12213010.21 11890529.25 12038934.74 11853254.9 10489013.94 11372377.96 0.930416905 0.99212572 1.014028331 1.084543698 1.073918776 1.045562265 1.058611909 1.042284643 0.922323719 1 23.43903062 4.552467115 1.871956494 1.03808924 0.918943775 0.325412389 0.043740528 0.606694399 2.946015011 0.011469756 0.110910297 35683.47288 -4.552467115 -0.119145465 YDEFHDYLER ddPTM_BT-474_Pertuzumab_2h_R1 4 YDEFHDYLER 10 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 0 ;;; 218.11 6.94E-09 1235520000 1584820 1726690 1536080 1757800 1768370 1792580 1847930 1729900 1927440 2038220 FALSE TRUE 1522883.482 1677446.492 1813683.826 1848520.269 1825251.227 1828827.196 1870545.52 1694176.96 1708645.092 1900169.544 0.801446106 0.8827878 0.954485262 0.972818596 0.960572825 0.962454746 0.9844098 0.891592524 0.899206651 1 20.85769672 4.552492465 2.395525563 0.949364925 0.793184023 0.68020171 0.032706802 0.240364833 2.18260297 0.008898213 0.065214549 35685.55579 -4.552492465 -0.156180902 ELPDVLER ddPTM_BT-474_Pertuzumab_2h_R1 4 ELPDVLER 8 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;; 118.06 0.0045586 821980000 1209330 1378150 1269960 1545420 1413690 1517430 1463240 1440600 1470470 1537580 FALSE TRUE 1162068.047 1338846.511 1499470.022 1625179.311 1459162.623 1548113.474 1481147.569 1410851.107 1303548.41 1433438.337 0.810685759 0.934010537 1.046065243 1.133762974 1.017945861 1.080000049 1.033283072 0.984242621 0.909385759 1 20.45104841 4.552884139 2.741011474 1.028171107 0.805723544 0.585658897 0.056205107 0.233065026 2.930970332 0.014928295 0.095008862 35717.75379 -4.552884139 -0.222447563 S(ph)QKFNYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQKFNYR 7 1 F8VUJ3;Q8N4A0 F8VUJ3 POC1B-GALNT4;GALNT4 Polypeptide N-acetylgalactosaminyltransferase;Polypeptide N-acetylgalactosaminyltransferase 4 1 S(1)QKFNYR 83.843 0.013312 205760000 136820 149690 132590 155150 152770 156450 148580 156300 178180 170350 TRUE FALSE 131472.9231 145420.9878 156551.9624 163157.3101 157683.9858 159613.5262 150398.3665 153072.3504 157953.7534 158812.0428 0.827852352 0.915679852 0.985768835 1.027361069 0.992896905 1.005046742 0.94702117 0.963858582 0.994595565 1 17.27696079 4.552907144 2.301516632 0.987018938 0.817570284 0.852473004 0.021163269 0.163071069 1.339692299 0.006147765 0.04716762 35719.64581 -4.552907144 -0.169448655 DRYDSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRYDSDR 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 98.997 0.0098974 28468000 29074 32450 30419 30699 32365 31271 41681 36445 29596 35733 FALSE TRUE 27937.75594 31524.55777 35916.38997 32283.37907 33406.04962 31903.32105 42191.10455 35692.39801 26236.38616 33312.77208 0.838649989 0.946320459 1.078156747 0.969099149 1.002800053 0.957690371 1.26651437 1.07143284 0.787577392 1 15.02378779 4.552926403 3.068400189 1.030175103 0.838114489 0.179454044 0.113993424 0.449879353 7.338785314 0.02867491 0.164138538 35721.22989 -4.552926403 -0.192060614 VVEEIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVEEIRR 7 1 P51659-3;P51659;P51659-2;A0A2R8YD50;E7ER27;A0A2R8YDT8;A0A2R8YF45 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ; 139.68 0.0042901 884880000 585920 680840 593910 797560 663580 618140 780890 752940 771790 896160 FALSE TRUE 563021.5986 661423.1098 701242.7485 838722.1672 684924.6533 630639.2143 790446.7654 737391.5259 684179.6348 835462.285 0.673904267 0.79168518 0.839346983 1.00390189 0.819815168 0.754838639 0.946119028 0.882614978 0.818923424 1 19.67221518 4.553167671 1.93890408 0.881039891 0.653127571 0.42965448 0.076215748 0.509395752 2.705372837 0.019501289 0.181748322 35741.07992 -4.553167671 -0.22791232 AVIVSS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 AVIVSSPK 8 0 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 AVIVS(0.025)S(0.975)PK;AVIVS(0.102)S(0.898)PK;AVIVS(0.044)S(0.956)PK;AVIVS(0.243)S(0.757)PK;AVIVS(0.115)S(0.885)PK;AVIVS(0.003)S(0.997)PK 172.88 0.00029475 6686020000 13471160 11579520 9720980 8426130 9578480 7106190 11465470 12158150 11635080 12098480 TRUE FALSE 12944692.17 11249283.43 11477777.33 8861003.579 9886580.508 7249882.031 11605787.85 11907079.95 10314314.5 11279039.17 1.147676852 0.997361855 1.017620132 0.785616881 0.876544567 0.64277479 1.028969549 1.055682117 0.914467477 1 23.42714084 4.553369785 1.575504993 0.911520394 1.178173561 0.278503913 0.118233763 1.103984913 3.43025705 0.035002824 0.407370028 35757.7172 -4.553369785 0.266653167 ALEESESSQLIS(ph)PPLAQAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEESESSQLISPPLAQAIR 20 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 ALEESES(0.001)S(0.002)QLIS(0.997)PPLAQAIR;ALEESESSQLIS(1)PPLAQAIR 179.69 1.26E-15 44791000 155620 167469 146929 171004 165438 186704 164488 180600 163695 190478 TRUE FALSE 149538.1984 162692.9481 173482.3387 179829.5369 170759.4635 190479.2828 166501.0533 176870.5469 145113.0299 177576.7554 0.842104576 0.916183809 0.976942834 1.012686241 0.961609323 1.072658876 0.937628649 0.99602308 0.817184825 1 17.43808322 4.55346657 2.374265344 0.975655517 0.834455951 0.296107374 0.062176749 0.457774588 4.061174993 0.015077701 0.111943964 35765.68688 -4.55346657 -0.141199566 EAASGT(ph)TPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAASGTTPQK 10 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 EAAS(0.01)GT(0.495)T(0.495)PQK 191.33 8.99E-06 138670000 408920 372760 279900 320950 307970 324660 341000 370400 341340 393310 TRUE FALSE 392938.9543 362129.2498 330484.1563 337514.268 317876.1347 331224.8476 345173.26 362751.1106 302592.5142 366670.7634 1.07163972 0.987614192 0.901310356 0.920483174 0.866925227 0.903330401 0.9413711 0.989310157 0.825243091 1 18.48412571 4.553812294 2.696266906 0.920752317 1.076161917 0.484874529 0.049390464 0.281261723 3.397901583 0.012282741 0.079700709 35794.1698 -4.553812294 0.1554096 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETER ddPTM_BT-474_Pertuzumab_2h_R1 4 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.563)RIS(0.436)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.648)RIS(0.349)EDET(0.003)ER;SLIPDIKPLAGQEAVVDLHADDS(0.444)RIS(0.444)EDET(0.112)ER;SLIPDIKPLAGQEAVVDLHADDS(0.481)RIS(0.481)EDET(0.039)ER 147.72 2.03E-10 1034467000 117076.9 125395.6 114149.2 127369 123203.7 123671.2 129119.6 120483.9 144321.9 149319.8 TRUE FALSE 112501.4053 121819.4403 134778.4997 133942.5294 127166.6589 126171.9164 130699.8043 117995.8654 127939.083 139206.2369 0.808163541 0.875100448 0.968192968 0.962187703 0.913512654 0.906366835 0.938893308 0.847633468 0.919061428 1 17.08686433 4.553977341 3.689325613 0.922675583 0.812064622 0.471872341 0.040119965 0.233423129 5.650156493 0.010253857 0.051181519 35807.77544 -4.553977341 -0.110610961 HYEDGYPGGSDNYGS(ph)LSR ddPTM_BT-474_Pertuzumab_2h_R1 1 HYEDGYPGGSDNYGSLSR 18 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 HYEDGYPGGSDNY(0.002)GS(0.853)LS(0.145)R 78.963 0.0071165 690990000 1003200 691770 395290 317580 339920 283760 255670 529840 327080 270730 TRUE FALSE 963993.8349 672041.3969 466727.6962 333970.3419 350853.8355 289497.8216 258798.9659 518898.6188 289951.2496 252393.216 3.819412623 2.662676151 1.849208563 1.323214416 1.390108027 1.147011105 1.02538004 2.055913495 1.14880762 1 17.94531361 4.554244935 1.354751961 1.35544301 4.38969196 0.886158105 0.289117182 0.303553154 0.639868827 0.086159581 1.154182003 35829.84546 -4.554244935 3.034248949 up DLESAEER ddPTM_BT-474_Pertuzumab_2h_R1 4 DLESAEER 8 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 134.81 0.0020022 2507250000 1494350 1653500 1444130 1728000 1708660 1695650 1801780 1791210 1928180 1932780 FALSE TRUE 1435949.15 1606343.799 1705116.415 1817182.287 1763620.601 1729937.205 1823830.723 1754220.888 1709301.09 1801871.089 0.796921133 0.891486527 0.946303221 1.008497388 0.978771795 0.960078229 1.012187128 0.973555155 0.948625626 1 20.78106437 4.554538415 1.542414667 0.982298576 0.763333929 0.895640715 0.019945092 0.213428369 0.626875248 0.005351853 0.063839299 35854.06614 -4.554538415 -0.218964647 GYIWNYGTLPQTWEDPHEKDK ddPTM_BT-474_Pertuzumab_2h_R1 2 GYIWNYGTLPQTWEDPHEKDK 21 1 Q9H2U2-2;Q9H2U2;H0Y9D8;D6RGV9;D6RGI1 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ; 138.03 1.39E-06 1008390000 569210 529170 391196 481030 445280 455210 514320 521020 601250 480150 FALSE TRUE 546964.6439 514078.5897 461893.8193 505856.0159 459602.8356 464414.6581 520614.402 510260.7549 532998.6206 447629.0128 1.221915086 1.148447878 1.031867475 1.130078707 1.026749434 1.037499011 1.163048835 1.139918862 1.190715091 1 18.77194402 4.55469843 3.987738368 1.097787046 1.216014972 0.298414071 0.062125868 0.309938165 8.756180232 0.015375306 0.073426165 35867.27895 -4.55469843 0.118227926 REFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_BT-474_Pertuzumab_2h_R1 1 REFITGDVEPTDAESEWHSENEEEEKLAGDMK 32 2 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 REFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK 289.26 1.34E-89 128690000 113750 96369 68043 71848 83788 81338 73553 81304 96454 90690 TRUE FALSE 109304.5242 93620.65048 80339.88371 75556.08389 86483.11711 82982.71009 74453.16362 79625.04399 85504.94629 84547.48552 1.292818155 1.107314427 0.950233862 0.893652643 1.022894017 0.981492348 0.880607663 0.941778972 1.011324533 1 16.36747423 4.554811397 2.274059757 0.953440094 1.316837089 0.837899884 0.045730245 0.150447083 1.196567318 0.011879855 0.09295437 35876.60979 -4.554811397 0.363396995 RSSS(ph)LKER ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSSLKER 8 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 RS(0.004)S(0.011)S(0.985)LKER 71.066 0.039145 1229700000 1102400 730900 281200 352840 438120 332560 259000 949120 356460 198650 TRUE FALSE 1059316.989 710055.4476 332019.0953 371050.1147 452212.5277 339284.5911 262169.7195 929520.3403 315996.1552 185195.2586 5.720000595 3.834090857 1.792805593 2.003561633 2.441814824 1.832037136 1.41563948 5.019136816 1.706286423 1 17.49868764 4.55484454 2.936089897 2.39015946 5.757992165 0.520642008 1.059883948 0.264451382 3.892447991 0.279353589 1.672794467 35879.34778 -4.55484454 3.367832705 LTEDLEYHELLDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LTEDLEYHELLDR 13 0 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 ;;;;; 269.7 3.17E-25 8592260000 4360460 4865630 4168540 5224340 5017490 5373160 5221550 4725110 5458370 5845070 FALSE TRUE 4190048.402 4726866.996 4921887.907 5493968.813 5178882.123 5481808.977 5285452.891 4627534.827 4838758.721 5449178.203 0.768932167 0.867445846 0.903234896 1.0082197 0.950396909 1.005988201 0.969954128 0.849217011 0.887979534 1 22.37760724 4.555068922 1.752731499 0.943865113 0.74630869 0.563247581 0.049843626 0.530739066 2.1667744 0.014797523 0.155101111 35897.88996 -4.555068922 -0.197556423 SDVQIHVPTFTFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDVQIHVPTFTFR 13 0 O75569;G5E9Q4;O75569-3;O75569-2;F8WEG8;C9JMM3 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 0 ; 88.561 0.0078519 934540000 1457170 1526680 1252960 1503280 1520020 1410660 1618130 1629210 1616530 1598950 FALSE TRUE 1400222.185 1483140.581 1479397.744 1580864.461 1568912.824 1439184.512 1637933.159 1595566.244 1433028.291 1490651.692 0.939335589 0.99496119 0.992450317 1.060519013 1.052501286 0.965473369 1.098803408 1.070381668 0.961343484 1 20.50751176 4.555256629 1.207482996 1.036739172 0.917319258 0.264891271 0.043499307 1.351466027 2.128283136 0.012737622 0.186701087 35913.40879 -4.555256629 -0.119419914 AQS(ph)LLSTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQSLLSTDR 9 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 1 AQS(0.838)LLS(0.157)T(0.004)DR;AQS(0.993)LLS(0.007)TDR 168.98 6.17E-05 271250000 437740 341120 184291 258550 297840 228000 200631 398690 234670 206570 TRUE FALSE 420632.6369 331391.5916 217596.4832 271893.7965 307420.2941 232610.3162 203086.3822 390456.9122 208031.2454 192578.8299 2.18421016 1.720810079 1.129908637 1.411857142 1.596334832 1.207870649 1.054562344 2.027517315 1.08023943 1 17.55508959 4.555480423 3.359726423 1.379953044 2.172050421 0.4399587 0.301647667 0.2578077 5.10954411 0.074397054 0.397855972 35931.91993 -4.555480423 0.792097377 ASSHSSQTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 193.77 3.21E-10 762420000 290447 506548 417989 804655 546888 722310 677536 537821 533484 699758 FALSE TRUE 279096.0101 492101.747 493528.9104 846183.341 564479.1492 736915.6031 685827.8882 526714.8084 472925.1329 652362.7674 0.427823328 0.754337574 0.756525257 1.297105511 0.865284129 1.129610149 1.051298331 0.80739557 0.724941944 1 19.31531492 4.555551954 1.618000195 0.966336437 0.354627836 0.507971079 0.163760121 0.593461721 1.969191186 0.044815449 0.51150073 35937.83858 -4.555551954 -0.611708601 GTHTGVWVGVSGSETSEALSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GTHTGVWVGVSGSETSEALSR 21 0 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 231.76 4.25E-26 5217740000 1393010 1755420 1678470 2073800 1932770 1956960 2140570 1734110 2235630 2332230 FALSE TRUE 1338569.629 1705357.14 1981806.866 2180829.067 1994939.302 1996531.072 2166766.936 1698300.023 1981850.655 2174265.985 0.615642078 0.784336945 0.911483177 1.003018528 0.917523116 0.918255212 0.996550998 0.781091198 0.911503316 1 21.05209701 4.555811705 2.223848245 0.920688205 0.592803268 0.716114427 0.062281034 0.246671291 1.85240134 0.016915531 0.136177319 35959.33944 -4.555811705 -0.327884937 GDMVTLPAGIYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDMVTLPAGIYHR 13 0 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 167.44 3.19E-05 118130000 111170 139460 128000 168250 156110 201560 127220 154250 149970 157200 FALSE TRUE 106825.3535 135482.7373 151132.4473 176933.4027 161131.4199 205635.6813 128776.9564 151064.6836 132946.0343 146552.704 0.728921068 0.924464262 1.031249805 1.207302205 1.099477632 1.403151738 0.878707475 1.03078742 0.90715511 1 17.16106006 4.556308868 2.013561693 1.077359995 0.695336896 0.361826728 0.141869976 0.555792628 3.239213787 0.037673453 0.340030763 36000.52777 -4.556308868 -0.382023098 GFSVVADTPELQR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFSVVADTPELQR 13 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;; 199.68 2.70E-07 8576200000 8662800 9370400 8016400 9724400 9546800 9758800 9548900 9967900 9936000 10149400 FALSE TRUE 8324248.199 9103165.367 9465141.804 10226277.45 9853881.492 9956129.622 9665762.295 9762059.382 8808106.935 9461972.098 0.879758269 0.962079075 1.000334994 1.080776538 1.04141942 1.052225637 1.021537814 1.031715089 0.930895467 1 23.17370948 4.556837939 1.887512914 1.026329891 0.863224019 0.574884961 0.037516968 0.377462965 1.861535298 0.009790078 0.09518746 36044.41153 -4.556837939 -0.163105873 ASGDGES(ph)LDEDSEFTLASDFEIGHFFR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASGDGESLDEDSEFTLASDFEIGHFFR 27 0 Q99733;Q99733-2;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 AS(0.03)GDGES(0.97)LDEDSEFTLASDFEIGHFFR;AS(0.042)GDGES(0.958)LDEDSEFTLASDFEIGHFFR;AS(0.004)GDGES(0.996)LDEDSEFTLASDFEIGHFFR;AS(0.023)GDGES(0.977)LDEDSEFTLASDFEIGHFFR 188.44 5.46E-18 158142000 33648.7 37007.4 33257.2 40174.8 37168.9 36372.7 38678.4 38002 41889.9 42122.3 TRUE FALSE 32333.6716 35951.98519 39267.51584 42248.22624 38364.47142 37108.18091 39151.75783 37217.24542 37134.73417 39269.3191 0.823382537 0.915523518 0.99995408 1.075858385 0.976957897 0.944966242 0.997006282 0.947743589 0.945642426 1 15.26111496 4.556894322 2.821821058 0.98390238 0.820393785 0.651295567 0.037079406 0.206385472 2.764279072 0.010021354 0.062696117 36049.09135 -4.556894322 -0.163508595 GNSRPGTPSAEGGS(ph)TSSTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 GNSRPGT(0.066)PS(0.15)AEGGS(0.688)T(0.077)S(0.009)S(0.009)TLR 220.1 2.30E-24 308540000 219870 282490 302520 374340 353140 455800 462190 357760 463890 526280 TRUE FALSE 211277.2373 274433.6618 357192.0935 393659.7323 364499.0688 465016.5883 467846.4195 350372.131 411231.152 490634.5868 0.43062035 0.559344305 0.728020615 0.802348108 0.742913522 0.947785991 0.953553687 0.714120326 0.838161766 1 18.90428941 4.556894351 0.845963119 0.858431373 0.243491678 0.76035011 0.083227158 0.950756582 0.635064268 0.030324997 0.518356882 36049.09374 -4.556894351 -0.614939695 down SMIIDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SMIIDRR 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 108.7 0.011536 492520000 425390 456620 399100 469470 446540 447960 489290 482580 495450 490720 FALSE TRUE 408765.2885 443597.6447 471226.2479 493699.403 460903.3646 457018.0581 495278.0774 472614.5544 439208.5931 457483.0973 0.893509052 0.969648162 1.030040783 1.079164249 1.00747627 0.998983483 1.082615031 1.033075445 0.960054253 1 18.80335892 4.557101931 2.418771122 1.028866498 0.886168332 0.565591962 0.035312468 0.262879424 2.43109731 0.008928649 0.065703037 36066.32825 -4.557101931 -0.142698166 WIDNPTVDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 WIDNPTVDDR 10 0 P18206;P18206-2 P18206 VCL Vinculin 0 ; 227.27 6.14E-09 1362860000 567750 685730 652340 847880 634590 648710 790400 780940 759340 916910 FALSE TRUE 545561.7023 666173.6518 770232.3492 891639.1884 655002.1637 661827.3607 800073.1516 764813.3161 673142.9066 854806.869 0.638228028 0.779326507 0.901060084 1.043088469 0.766257487 0.774241978 0.935969493 0.894720602 0.787479524 1 19.70523898 4.5572907 2.74238653 0.883918446 0.632196998 0.438245532 0.088123964 0.306750117 3.840912073 0.022052264 0.142109749 36082.00809 -4.5572907 -0.251721448 DLRPVDNR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLRPVDNR 8 1 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ;;; 76.221 0.033162 1731960000 1063270 1177390 1089110 1217530 1221650 1287450 1213950 1215100 1215930 1300430 FALSE TRUE 1021716.233 1143811.99 1285936.404 1280366.869 1260945.482 1313483.121 1228806.683 1190007.76 1077902.724 1212350.718 0.842756323 0.943466254 1.060696699 1.056102702 1.040083091 1.083418438 1.013573601 0.98157055 0.889101403 1 20.20937568 4.557337473 3.202004495 1.017385173 0.843690383 0.516468308 0.051730955 0.226167143 4.026154505 0.013573449 0.075778233 36085.89433 -4.557337473 -0.17369479 VFEHIGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFEHIGK 7 0 P04040 P04040 CAT Catalase 0 ; 81.297 0.027584 1159230000 1624050 1867120 1675900 2089000 1880180 1954670 2164600 2132100 2325800 2462000 FALSE TRUE 1560580.331 1813871.566 1978772.41 2196813.54 1940657.697 1994194.767 2191091.022 2088071.39 2061784.935 2295246.547 0.679918387 0.790273083 0.862117585 0.957114408 0.845511651 0.868836844 0.954621204 0.909737297 0.898284734 1 21.1302177 4.557471678 1.370005702 0.913850577 0.625599881 0.757807505 0.04311081 0.429852883 0.928356468 0.011688209 0.156698609 36097.04727 -4.557471678 -0.288250695 (ac)AHS(ph)PVQSGLPGMQNLK ddPTM_BT-474_Pertuzumab_2h_R1 12 AHSPVQSGLPGMQNLK 16 0 B4DR80;Q9Y6E0-2 B4DR80 STK24 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit 1 AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.998)PVQS(0.002)GLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK 131.43 1.96E-27 9915850000 4297989 4506550 3805843 4530967 4396359 4639839 4515291 4505984 4935380 5041770 TRUE FALSE 4130018.838 4378027.606 4493643.491 4764810.75 4537771.88 4733659.724 4570550.482 4412933.856 4375136.353 4700286.427 0.878673864 0.931438472 0.956036097 1.013727743 0.965424544 1.007100269 0.97239829 0.938864881 0.930823349 1 22.16431724 4.557483091 1.944175962 0.971966799 0.868891635 0.568767568 0.025960656 0.420539115 2.236292643 0.007230909 0.068166014 36097.99587 -4.557483091 -0.103075164 IFDLQDWTQEDER ddPTM_BT-474_Pertuzumab_2h_R1 3 IFDLQDWTQEDER 13 0 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5;Q5T9Q8 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 ;; 147.24 9.93E-05 63104000 35912.7 52571 42555 81045 44829 49656 68697 69378 59789 57613 FALSE TRUE 34509.19198 51071.72655 50245.63513 85227.74216 46270.9655 50660.07834 69537.73444 67945.32006 53002.00338 53710.82019 0.642499814 0.950864767 0.935484414 1.586789065 0.86148313 0.943200609 1.294669011 1.265021085 0.986803091 1 15.71292513 4.557700126 1.689841997 1.142085009 0.580630543 0.324124209 0.207422158 0.742971582 2.749978074 0.054999524 0.604555727 36116.04007 -4.557700126 -0.561454466 GS(ph)GFSLDVIDGPISQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSGFSLDVIDGPISQR 16 0 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 GS(1)GFSLDVIDGPISQR 125.67 7.95E-05 139320000 251600 285420 255540 331900 283750 250190 283540 342410 307520 350890 TRUE FALSE 241767.1938 277280.1011 301721.7625 349029.3988 292877.0764 255249.0132 287010.0473 335339.1138 272611.6188 327123.9078 0.739069166 0.847630193 0.922347023 1.066963895 0.895309299 0.780282355 0.87737411 1.025113438 0.833358897 1 18.31947768 4.55789137 2.507636816 0.927157596 0.731029295 0.328423492 0.082750023 0.441290694 4.454691484 0.021718807 0.154022773 36131.94748 -4.55789137 -0.1961283 WRVS(ph)LDVNHFAPDELTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 WRVSLDVNHFAPDELTVK 18 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK 190.87 1.54E-14 649630000 1260580 1001690 625960 744540 777370 648840 689250 912390 732200 630310 TRUE FALSE 1211315.14 973122.782 739084.8964 782965.7986 802374.812 661959.9894 697685.2477 893548.8277 649083.7256 587618.5423 2.061397068 1.656045056 1.257763061 1.332438891 1.365468845 1.126513106 1.187309789 1.520627352 1.104600483 1 19.1645204 4.558205244 1.939677726 1.264747742 2.160624246 0.769671311 0.143641031 0.249069321 1.315330464 0.037006405 0.350622006 36158.07024 -4.558205244 0.895876504 VYVPALIFGQLLTSSNYDDDEKKVTGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VYVPALIFGQLLTSSNYDDDEKKVTGGR 28 2 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 92.833 0.0014733 73866000 123860 101070 61593 65129 90025 90302 84344 89930 96158 75639 FALSE TRUE 119019.4143 98187.58256 72724.22523 68490.3155 92920.73588 92127.96831 85376.2271 88072.91407 85242.54697 70515.90316 1.687837905 1.392417571 1.031316653 0.97127474 1.317727374 1.30648498 1.210737199 1.248979452 1.208841455 1 16.10566104 4.558377097 3.380565543 1.181054773 1.679881486 0.648553414 0.11996001 0.169493314 3.383749735 0.030850099 0.16532348 36172.381 -4.558377097 0.498826713 NINMDNDLEVLTSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 4 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 NINMDNDLEVLTS(0.006)S(0.989)PT(0.006)R;NINMDNDLEVLTS(0.001)S(0.999)PTR;NINMDNDLEVLTS(0.184)S(0.815)PT(0.001)R;NINMDNDLEVLTS(0.004)S(0.994)PT(0.002)R 350.9 1.19E-87 2130520000 3105090 3346570 2971320 3420340 3270490 3609680 3266010 3464730 3674820 3831080 TRUE FALSE 2983739.65 3251129.1 3508303.621 3596864.157 3375688.281 3682670.203 3305980.407 3393182.115 3257669.84 3571597.539 0.835407578 0.910273082 0.982278541 1.007074318 0.945148003 1.031098874 0.925630722 0.950046045 0.912104403 1 21.76813809 4.558862776 2.773867333 0.966712346 0.832138771 0.577454218 0.035686551 0.228987439 2.939310054 0.008910076 0.057024891 36212.8559 -4.558862776 -0.134573575 SSS(ph)EITLSECDAEDAGEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSEITLSECDAEDAGEPR 19 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 SS(0.001)S(0.999)EITLSECDAEDAGEPR;SS(0.005)S(0.995)EITLSECDAEDAGEPR 430.75 2.40E-169 1118830000 627950 511940 317710 428470 420380 355140 365280 562310 382830 360920 TRUE FALSE 603409.0198 497339.9724 375127.2644 450583.388 433901.9045 362321.1741 369750.4059 550698.102 339372.7434 336474.5669 1.79332728 1.478090832 1.11487554 1.339130598 1.289553349 1.076815931 1.098895555 1.63667081 1.00861336 1 18.36013793 4.558903742 2.979957493 1.238347286 1.799807495 0.495533467 0.186138656 0.262443755 3.972819612 0.046723995 0.279057616 36216.27189 -4.558903742 0.561460208 DVQLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVQLIR 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 114.94 0.057818 437700000 186380 225920 224700 256220 232210 240820 275580 250230 236070 227460 FALSE TRUE 179096.0635 219476.9828 265308.2884 269443.5449 239679.2455 245689.5454 278952.6305 245062.6631 209272.3233 212053.9316 0.844577897 1.035005487 1.251135909 1.270636875 1.130274943 1.158618204 1.315479644 1.155661964 0.986882543 1 17.69407171 4.558981775 3.167029065 1.173835028 0.84538585 0.465989256 0.102281187 0.220588782 3.823153313 0.024665987 0.139567923 36222.77972 -4.558981775 -0.328449177 YIDENQDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YIDENQDR 8 0 Q96KP4;Q96KP4-2;J3QKT2;A0A087WYZ1;J3KSV5;J3QRA8;J3QRD0;J3QKQ0;J3QLU1;J3QR27;J3QL02;J3QQN6;J3KSS4;J3QRP4 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 215.27 1.97E-05 2230770000 959230 1045040 914000 1079040 1101650 1123110 1190000 1018220 1046480 1107650 FALSE TRUE 921742.2311 1015236.482 1079180.132 1134729.384 1137085.573 1145820.054 1204563.576 997193.4012 927687.9776 1032627.879 0.892617999 0.983158118 1.045081344 1.09887541 1.101157151 1.109615649 1.166503056 0.965685143 0.898375878 1 19.97788902 4.55906034 2.161642755 1.054681325 0.879186467 0.296465282 0.074212913 0.587806671 4.091523903 0.020435513 0.171733731 36229.33313 -4.55906034 -0.175494858 SYS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSPER 6 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 S(0.014)YS(0.986)PER;S(0.075)YS(0.925)PER 111.29 0.029347 1004960000 609800 643100 560710 661390 627810 665360 659590 602940 704170 746460 TRUE FALSE 585968.3418 624759.4177 662042.7699 695524.4172 648004.0788 678814.0351 667662.2597 590489.0783 624235.5737 695901.5993 0.842027583 0.897769768 0.951345378 0.999457995 0.931171992 0.97544543 0.959420499 0.848523813 0.897017013 1 19.4085238 4.559493372 2.94775514 0.938240286 0.840973893 0.34252338 0.044126872 0.400526055 5.910710506 0.01217534 0.073577715 36265.47518 -4.559493372 -0.097266394 EMDEQIR ddPTM_BT-474_Pertuzumab_2h_R1 5 EMDEQIR 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;; 176.65 0.0017308 5221170000 6568780 7297980 6648810 7702320 7274920 6927830 7905530 8195970 7627890 8303370 FALSE TRUE 6312064.815 7089848.756 7850397.869 8099837.658 7508924.409 7067915.469 8002280.241 8026720.355 6762003.906 7740975.354 0.815409496 0.915885716 1.014135495 1.046358797 0.970023035 0.913052315 1.033756068 1.036913307 0.873533837 1 22.88408393 4.559868032 2.823198604 0.99091932 0.811613079 0.494280611 0.05318885 0.252629818 3.374511826 0.01338335 0.084409023 36296.77442 -4.559868032 -0.17930624 VVDYSQFQES(ph)DDADEDYGR ddPTM_BT-474_Pertuzumab_2h_R1 41 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.004)QFQES(0.996)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDY(0.007)S(0.164)QFQES(0.829)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR 413.93 6.55E-148 45155665000 5063843 5533680.9 4879923.6 6090537 5768617.3 5497432.1 5729276.5 5757310 5711337 5861897 TRUE FALSE 4865942.417 5375865.739 5761834.348 6404870.344 5954170.114 5608593.944 5799393.1 5638419.537 5063009.968 5464865.495 0.890404791 0.983714191 1.054341475 1.172008781 1.089536443 1.026300455 1.061214243 1.031758154 0.926465614 1 22.38175456 4.560005462 2.652092195 1.051104346 0.885270726 0.389050765 0.059594222 0.347196196 4.002058732 0.015606899 0.104948326 36308.26211 -4.560005462 -0.16583362 FLSLYGDQIDMHR ddPTM_BT-474_Pertuzumab_2h_R1 4 FLSLYGDQIDMHR 13 0 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ;;; 210.64 2.83E-08 1576847000 1322354 1465714 1301383 1712925 1423210 1355893 1605464 1455507 1625387 1766241 FALSE TRUE 1270674.944 1423913.272 1536571.857 1801329.265 1468988.842 1383310.085 1625112.149 1425450.272 1440879.882 1646611.924 0.7716906 0.864753407 0.933171827 1.093961023 0.892128146 0.840094782 0.986943022 0.865686839 0.875057359 1 20.65106915 4.560007301 2.725170741 0.930595943 0.767726937 0.334898664 0.0719853 0.401912972 4.941521521 0.018432503 0.120511143 36308.4159 -4.560007301 -0.162869005 SAAS(ph)PVVSSMPER ddPTM_BT-474_Pertuzumab_2h_R1 4 SAASPVVSSMPER 13 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER 290.31 1.69E-40 3328860000 1604870 1752570 1518600 1855330 1656640 1726670 1862920 1928860 1938730 2057470 TRUE FALSE 1542149.906 1702588.42 1793044.801 1951083.804 1709927.33 1761584.45 1885718.972 1889028.367 1718653.498 1918115.724 0.803992109 0.887635922 0.934794902 1.017187743 0.891462026 0.918393206 0.983110116 0.984835452 0.89601137 1 20.87125833 4.56025552 1.921176788 0.955513681 0.786536531 0.570560246 0.040803531 0.387550365 1.991261567 0.01062893 0.102501155 36329.17366 -4.56025552 -0.16897715 GEVQFGSWFDHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 GEVQFGSWFDHIK 13 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 151.54 4.48E-05 738700000 561300 661330 642730 672100 694290 588040 779450 730290 809370 851180 FALSE TRUE 539363.7755 642469.5159 758885.6085 706787.1615 716622.4684 599930.5717 788989.1423 715209.2563 717493.7108 793528.8204 0.679702818 0.80963602 0.956342843 0.89068871 0.903083102 0.756028712 0.994279126 0.901302181 0.904181036 1 19.5979231 4.560535411 2.997027614 0.90687287 0.67723122 0.553620589 0.065260363 0.21217306 3.245949387 0.015512878 0.092571327 36352.59442 -4.560535411 -0.22964165 KPPAPPS(ph)PVQSQSPSTNWSPAVPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KPPAPPS(1)PVQSQSPSTNWSPAVPVK;KPPAPPS(1)PVQSQSPSTNWSPAVPVK 220.78 7.34E-34 3077000000 3017500 2844400 2720900 3036000 3216700 2969400 3321200 3583200 3808700 3542600 TRUE FALSE 2899572.764 2763280.497 3212627.156 3192688.324 3320168.077 3029443.302 3361845.839 3509205.668 3376352.343 3302656.547 0.87795165 0.836684184 0.972740311 0.966703101 1.005302256 0.917274703 1.017921722 1.062540297 1.022314096 1 21.65519552 4.56057673 0.46264015 1.030097548 0.740442754 0.638953293 0.040193439 2.55050445 0.479432171 0.029137543 0.399704663 36356.05316 -4.56057673 -0.289654794 TLSDDLDEAAKEFQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLSDDLDEAAKEFQEK 16 1 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 0 152.68 4.78E-07 37747000 110070 88418 61496 49662 65786 84996 64036 82663 85352 66896 FALSE TRUE 105768.3427 85896.40521 72609.69517 52225.06177 67902.06644 86714.67736 64819.69172 80955.98016 75663.19878 62365.07434 1.695954728 1.377315847 1.164268558 0.837408795 1.08878354 1.390436527 1.039358847 1.29809803 1.213230315 1 15.9284507 4.560599032 2.370068513 1.140726135 1.728494054 0.590324204 0.147810818 0.289509052 2.534976684 0.03892474 0.296291628 36357.92019 -4.560599032 0.58776792 KAPAGQEEPGT(ph)PPSS(ph)PLSAEQLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 KAPAGQEEPGT(1)PPS(0.152)S(0.848)PLSAEQLDR 113.65 0.0012023 294550000 478170 446320 330590 374100 360730 391930 399000 422440 433760 506330 TRUE FALSE 459482.5878 433591.3906 390334.9669 393407.3458 372333.2081 399855.0931 403883.0814 413716.4664 384521.3833 472035.8181 0.973406191 0.918556122 0.826918111 0.833426894 0.788781685 0.847086339 0.855619565 0.876451427 0.814602131 1 18.84853681 4.560727351 0.003359643 1.718582091 8.41E-08 0.022043042 0.065194712 446308.3538 246.2232054 61522.78602 64452.2593 36368.66431 -4.560727351 -1.718582007 GEGLYADPYGLLHEGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GEGLYADPYGLLHEGR 16 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 ;;;;; 191.86 6.28E-10 3521187000 3373030 3927800 3300508 4321660 4152910 4230700 4342260 4277990 4219250 4599390 FALSE TRUE 3241208.259 3815782.99 3896983.215 4544701.391 4286492.122 4316247.653 4395401.877 4189648.012 3740298.429 4287869.219 0.755901846 0.889901906 0.908839103 1.059897389 0.999678839 1.006618307 1.025078344 0.977093236 0.872297693 1 22.03182947 4.561016063 1.433716685 0.991151155 0.712088842 0.680587244 0.049152364 0.48921023 1.180870174 0.013679731 0.178349868 36392.84964 -4.561016063 -0.279062312 SKFS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKFSPQK 7 1 Q9NS91;F8WE49 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 S(0.001)KFS(0.999)PQK 76.228 0.025029 411700000 893450 737020 611190 536720 582440 368050 699780 690010 788490 846360 TRUE FALSE 858532.9862 716000.9112 721645.6288 564420.1835 601174.7116 375492.2232 708344.117 675761.0524 698983.9208 789035.2833 1.088079335 0.907438395 0.914592343 0.71532946 0.761911063 0.475887747 0.8977344 0.856439587 0.885871564 1 19.58973029 4.561087192 1.408281545 0.79229806 1.139787708 0.285328928 0.135291434 1.132743634 2.611828987 0.03835559 0.508082535 36398.81053 -4.561087192 0.347489648 GEAIEAILAALEVVSEPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GEAIEAILAALEVVSEPFR 19 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 159.52 7.73E-11 327550000 80146 96369 87524 108200 112080 113880 105830 96262 103950 125920 FALSE TRUE 77013.80571 93620.65048 103341.5338 113784.215 115685.155 116182.7316 107125.1792 94274.15606 92150.03179 117391.3262 0.656043408 0.797509096 0.880316605 0.969272762 0.985465951 0.989704566 0.912547653 0.803075994 0.784981606 1 16.84096629 4.561144463 1.934404365 0.911301704 0.627092684 0.569523263 0.071407228 0.454344323 2.373265752 0.021150505 0.203015452 36403.61081 -4.561144463 -0.28420902 SAAAGALGS(ph)PGLPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAAAGALGSPGLPLR 15 0 O75145-2;O75145;A0A0C4DGR8;A0A0C4DGR7 O75145-2 PPFIA3 Liprin-alpha-3 1 SAAAGALGS(1)PGLPLR;SAAAGALGS(1)PGLPLR 181.69 6.06E-07 429700000 528550 592630 524510 648740 564790 566090 614610 685610 688950 691870 TRUE FALSE 507893.6817 575728.7726 619300.6247 682221.5491 582956.9833 577536.7277 622131.781 671451.9139 610743.2843 645009.0286 0.787421042 0.892590254 0.960142567 1.057693023 0.903796625 0.895393246 0.964531896 1.040996147 0.946875559 1 19.29895983 4.561452359 2.161177545 0.974160327 0.77173617 0.576268347 0.049270568 0.34064665 2.362588008 0.013572249 0.115000048 36429.42858 -4.561452359 -0.202424157 S(ph)PYKFPSS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPYKFPSSPLR 11 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 S(1)PYKFPS(0.123)S(0.877)PLR;S(1)PYKFPS(0.001)S(0.999)PLR 131.56 0.00011431 714100000 1463590 1195390 922380 884330 936770 623360 905780 1162570 901550 932350 TRUE FALSE 1406391.285 1161298.648 1089074.584 929970.3773 966902.0578 635964.7663 916865.2066 1138562.523 799209.8236 869201.104 1.618027495 1.336052891 1.252960424 1.069913939 1.112403163 0.731665852 1.05483668 1.309895395 0.91947631 1 19.72933048 4.562247805 1.042338079 1.044825999 1.790411837 0.644895819 0.14057106 0.998122664 1.085029828 0.047655728 0.775293027 36496.21317 -4.562247805 0.745585838 EADAALFSELHR ddPTM_BT-474_Pertuzumab_2h_R1 2 EADAALFSELHR 12 0 Q96CW5-2;Q96CW5;A0A087WU06;A0A3B3ITE3;Q96CW5-3 Q96CW5-2 TUBGCP3 Gamma-tubulin complex component 3 0 ; 165.7 5.39E-05 219500000 266370 307060 277140 329690 317160 369800 328330 320780 347630 400300 FALSE TRUE 255959.9659 298302.9494 327225.3629 346705.3404 327361.7394 377277.6094 332348.2008 314155.7809 308168.4998 373187.3244 0.685875294 0.799338375 0.876839436 0.929038361 0.877204873 1.010960407 0.890566691 0.84181793 0.825774295 1 18.50954046 4.562515756 1.734918096 0.902558159 0.65270009 0.604927273 0.057015295 0.458406844 1.804255242 0.015570014 0.169171392 36518.73758 -4.562515756 -0.249858069 ALLS(ph)PFSTPVR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALLSPFSTPVR 11 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 ALLS(0.996)PFS(0.004)T(0.001)PVR;ALLS(0.998)PFS(0.002)TPVR;ALLS(1)PFSTPVR 145.09 3.82E-05 141881000 177282 197467 184735 191853 191075 230711 213900 194940 211162 238444 TRUE FALSE 170353.6234 191835.4345 218120.7239 201754.5563 197221.1009 235376.1345 216517.7722 190914.4209 187191.775 222293.9755 0.766343861 0.862980808 0.98122643 0.907602448 0.887208484 1.058850713 0.974015475 0.858837584 0.842091085 1 17.76210932 4.562537481 3.227731274 0.932976185 0.766888662 0.409109869 0.064256869 0.288974823 5.187793815 0.016588268 0.093189484 36520.56447 -4.562537481 -0.166087523 SRS(ph)DIDVNAAAGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSDIDVNAAAGAK 14 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 S(0.02)RS(0.98)DIDVNAAAGAK;S(0.001)RS(0.999)DIDVNAAAGAK 198.67 5.71E-08 706340000 1333600 1151730 839750 835540 946320 842370 901230 1346530 1112100 945840 TRUE FALSE 1281481.438 1118883.788 991511.5051 878662.3195 976759.2422 859403.2986 912259.5223 1318723.685 985859.0703 881777.4143 1.45329356 1.268895948 1.124446475 0.996467255 1.107716331 0.974626118 1.034568937 1.495528989 1.118036201 1 19.750055 4.562549897 2.492528611 1.131053521 1.469379468 0.361680949 0.142604473 0.492334865 4.869572469 0.040989587 0.296934374 36521.60855 -4.562549897 0.338325947 KT(ph)ASFGNILDVPEIVISGNGQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTASFGNILDVPEIVISGNGQPR 23 1 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 KT(0.589)AS(0.411)FGNILDVPEIVISGNGQPR;KT(0.5)AS(0.5)FGNILDVPEIVISGNGQPR 114.92 0.00036509 617320000 778270 565990 288856 381167 328429 228030 280390 771190 388790 349630 TRUE FALSE 747854.348 549848.5194 341058.7048 400839.0745 338993.2171 232640.9228 283821.4967 755264.657 344656.1891 325949.2487 2.29438893 1.686914517 1.046355241 1.229759161 1.040018403 0.713733576 0.870753646 2.317123479 1.057392188 1 18.31428782 4.562654109 2.85158714 1.231286722 2.318281425 0.413870767 0.417942127 0.362053908 4.931553261 0.117191097 0.737732863 36530.37322 -4.562654109 1.086994703 GTSPSSSS(ph)RPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GTS(0.01)PS(0.102)S(0.042)S(0.042)S(0.804)RPQR 136.82 0.00027116 667090000 415180 462810 396420 492230 473940 498350 498220 476710 532970 506810 TRUE FALSE 398954.3066 449611.1119 468061.9123 517634.0493 489184.7105 508426.9784 504317.3654 466865.7719 472469.48 472483.3073 0.844377569 0.951591527 0.99064222 1.095560502 1.035348134 1.076073949 1.067376048 0.988110616 0.999970735 1 18.84990383 4.562988348 1.648539904 1.036838471 0.814402729 0.744812464 0.034727055 0.356288185 1.22813117 0.00988484 0.113465288 36558.49833 -4.562988348 -0.222435741 ELTHIYR ddPTM_BT-474_Pertuzumab_2h_R1 6 ELTHIYR 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;;;;; 177.71 0.00072635 3759220000 2389750 2589570 2309570 2741680 2559430 2503260 2779370 2590630 2828540 2989850 FALSE TRUE 2296355.928 2515717.999 2726960.675 2883178.433 2641756.39 2553877.632 2813384.761 2537132.585 2507455.997 2787344.796 0.823850688 0.902549983 0.978336329 1.034381694 0.947768067 0.9162403 1.009342212 0.910232774 0.899585871 1 21.41046005 4.563794963 2.936185826 0.958904758 0.821881092 0.500892035 0.042841604 0.259406698 3.771889727 0.010967952 0.067325332 36626.46144 -4.563794963 -0.137023667 MCDLVSDFDGFSER ddPTM_BT-474_Pertuzumab_2h_R1 4 MCDLVSDFDGFSER 14 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 312.78 2.08E-55 1327550000 2274500 2547380 2271550 2687050 2534180 2826860 2683010 2671860 2732010 3267760 FALSE TRUE 2185610.025 2474731.217 2682069.615 2825728.973 2615694.201 2884021.046 2715845.479 2616685.157 2421883.678 3046431.705 0.717432799 0.812337665 0.880397093 0.927553691 0.858609171 0.946688233 0.891484117 0.858934455 0.794990308 1 21.53868897 4.564065435 2.038497977 0.890447881 0.699212844 0.530439254 0.052692684 0.386491349 2.301109624 0.013114902 0.119828024 36649.27899 -4.564065435 -0.191235037 FSTELER ddPTM_BT-474_Pertuzumab_2h_R1 1 FSTELER 7 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 114.43 0.013741 131410000 104130 114810 98222 128560 115370 115860 111060 125950 116930 133020 FALSE TRUE 100060.4845 111535.7312 115972.9003 135194.997 119080.9808 118202.7686 112419.1855 123349.0885 103656.5966 124010.4369 0.806871478 0.899406001 0.935186612 1.090190474 0.960249668 0.953167907 0.906530033 0.994666994 0.835869941 1 16.92010202 4.564384844 2.169402142 0.962680424 0.794958131 0.368585854 0.062089318 0.474300651 3.308958678 0.015637846 0.133234013 36676.24323 -4.564384844 -0.167722294 LLAAVEAFYS(ph)PPSHDRPR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 1 LLAAVEAFYS(0.964)PPS(0.035)HDRPR;LLAAVEAFY(0.023)S(0.783)PPS(0.193)HDRPR;LLAAVEAFY(0.172)S(0.731)PPS(0.097)HDRPR;LLAAVEAFY(0.005)S(0.858)PPS(0.137)HDRPR 121.21 2.34E-05 210538000 219675 239951 213830.5 250364 239962 265995 247317 226551 268480 286742 TRUE FALSE 211089.8581 233107.8324 252474.428 263285.316 247680.5957 271373.6011 250343.7394 221872.6427 238003.276 267320.7089 0.789650226 0.872015615 0.944462661 0.984904301 0.926529773 1.015161161 0.936492127 0.829986736 0.890328613 1 18.02821208 4.564414672 2.661493005 0.932800272 0.784373964 0.451803117 0.051747059 0.364991462 4.219993547 0.014623163 0.099288807 36678.76228 -4.564414672 -0.148426308 EALEEFYGR ddPTM_BT-474_Pertuzumab_2h_R1 3 EALEEFYGR 9 0 Q9H2P9-6;Q9H2P9-4;Q9H2P9;Q9H2P9-5;Q9H2P9-3;Q9H2P9-2 Q9H2P9-6 DPH5 Diphthine synthase 0 ;; 134.81 0.00055468 405854000 273030 302454 276743 311827 309826 323263 295893 322530 331147 345644 FALSE TRUE 262359.6857 293828.3081 326756.6162 327920.4288 319791.8347 329799.5993 299514.227 315869.6428 293556.5808 322233.224 0.814191915 0.911849822 1.014037634 1.017649343 0.992423533 1.023481053 0.929495175 0.980251629 0.91100656 1 18.29774573 4.56503804 2.967471747 0.982542642 0.811763548 0.686397382 0.035524175 0.168337643 2.502752458 0.008969867 0.05469301 36731.44725 -4.56503804 -0.170779094 NTSNIPVILEPET(ph)EESENEFYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTSNIPVILEPETEESENEFYIK 23 0 Q6P0N0 Q6P0N0 MIS18BP1 Mis18-binding protein 1 1 NTSNIPVILEPET(0.5)EES(0.5)ENEFY(0.001)IK 89.483 0.021422 26073000 41325 35218 24585 27482 28428 29276 25679 36802 31479 33943 TRUE FALSE 39709.97331 34213.61712 29028.05639 28900.34931 29342.41244 29867.98078 25993.26728 36042.02584 27905.63589 31644.01038 1.254896988 1.081203574 0.917331781 0.913296038 0.927265921 0.943874699 0.82142772 1.138984137 0.881861545 1 14.94964483 4.565161221 2.637297505 0.95009835 1.267418508 0.59883363 0.079635198 0.240746862 2.721003155 0.020320072 0.139627639 36741.86706 -4.565161221 0.317320158 ELTGEDVLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELTGEDVLVR 10 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 131.11 0.0082371 0 55995 68567 59773 82641 73072 75768 79936 69889 77826 82065 FALSE TRUE 53806.65349 66611.53629 70575.31074 86906.11191 75422.42724 77300.08087 80914.28068 68445.76773 68991.51875 76506.66445 0.703293679 0.870663187 0.922472719 1.135928648 0.985828199 1.010370553 1.057610879 0.89463798 0.901771359 1 16.22329781 4.56559522 1.820974563 0.991355309 0.667370056 0.637134079 0.067846283 0.399939877 1.776523966 0.018941017 0.197377447 36778.60227 -4.56559522 -0.323985253 ADRDESSPYAAMLAAQDVAQR ddPTM_BT-474_Pertuzumab_2h_R1 12 ADRDESSPYAAMLAAQDVAQR 21 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;;;;;;;;;; 313.51 1.20E-66 17493170000 8082044 8467226 7275946 8268014 8691260 8258182 8204218 9263090 8760606 9033975 FALSE TRUE 7766188.785 8225749.005 8590871.295 8694727.193 8970822.271 8425168.098 8304623.674 9071803.954 7766138.734 8422095.827 0.922120686 0.976686703 1.020039604 1.032370965 1.065153194 1.000364787 0.98605191 1.077143284 0.922114744 1 23.00574786 4.565686599 2.275572557 1.019444681 0.914646448 0.30771964 0.041195814 0.452261152 3.554442504 0.010037977 0.081343706 36786.34156 -4.565686599 -0.104798233 S(ph)KSMSDVSAEDVQNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSMSDVSAEDVQNLR 16 1 E9PMS6;E9PJ10 E9PMS6 LMO7 1 S(0.472)KS(0.472)MS(0.055)DVS(0.001)AEDVQNLR 79.237 0.011452 507200000 183820 146370 92372 113570 105110 72397 98454 180470 120620 92289 TRUE FALSE 176636.1112 142195.6709 109065.6752 119431.3613 108490.9586 73860.91694 99658.9095 176743.2314 106927.7233 86038.18383 2.052996743 1.652704236 1.267642695 1.388120437 1.26096291 0.858466714 1.158310242 2.054241775 1.242793822 1 16.39268945 4.56577999 2.452977003 1.335304346 2.096648676 0.386132831 0.302562351 0.470375427 4.455806545 0.085366809 0.635939622 36794.25295 -4.56577999 0.76134433 SAAEMYGSVTEHPS(ph)PSPLLSSSFDLDYDFQR ddPTM_BT-474_Pertuzumab_2h_R1 4 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGSVTEHPS(0.862)PS(0.138)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.996)PS(0.004)PLLSSSFDLDYDFQR;SAAEMYGSVT(0.001)EHPS(0.862)PS(0.136)PLLSSSFDLDYDFQR;SAAEMYGSVT(0.002)EHPS(0.789)PS(0.208)PLLSSSFDLDYDFQR 222.34 3.45E-35 848766000 204999 251760.8 246153.2 310123.5 255659 318383 269024.8 248770.6 255778.5 308532 TRUE FALSE 196987.4124 244580.8285 290638.5589 326129.011 263882.5039 324820.9224 272317.206 243633.4002 226743.597 287634.8528 0.684852376 0.850317081 1.010442775 1.133829951 0.917421868 1.12928221 0.946746207 0.847023223 0.788303624 1 18.13387897 4.565894968 2.965784034 0.967309025 0.680988875 0.424728169 0.103572437 0.31124059 4.616021884 0.027742734 0.169648084 36803.99538 -4.565894968 -0.286320151 KQKGS(ph)EENLDEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQKGSEENLDEAR 13 2 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;H0YG19 P35611 ADD1 Alpha-adducin 1 KQKGS(1)EENLDEAR 76.586 0.02226 245470000 225240 190490 142610 124310 141900 172410 148770 183370 209390 182570 TRUE FALSE 216437.3718 185057.4117 168382.7993 130725.654 146464.3424 175896.2483 150590.6918 179583.3454 185620.925 170204.3713 1.271632274 1.087265916 0.989297737 0.768051097 0.860520451 1.033441427 0.88476395 1.055104191 1.09057672 1 17.37690856 4.565912343 2.229348949 0.955586109 1.295291877 0.521613165 0.092857588 0.365719045 2.728561843 0.025436829 0.211162787 36805.46791 -4.565912343 0.339705768 DGVFCLLSDDHGASWR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGVFCLLSDDHGASWR 16 0 Q99519;E9PIF4 Q99519 NEU1 Sialidase-1 0 ;; 241.93 6.32E-20 294604000 219309 278074 236217 338800 284078 344770 324140 266342 322020 402320 FALSE TRUE 210738.1618 270143.6018 278906.6665 356285.5086 293215.6269 351741.4856 328106.9223 260841.9446 285465.6396 375070.5081 0.561862789 0.720247516 0.743611296 0.949916085 0.78176135 0.937800968 0.874787314 0.69544776 0.761098603 1 18.5168023 4.566379609 1.518906627 0.836100603 0.514101551 0.488433925 0.09215572 0.739285714 2.054002763 0.025747259 0.324016913 36845.08891 -4.566379609 -0.321999051 ASS(ph)FADMMGILK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSFADMMGILK 12 0 E9PPF9;E9PLD2;Q9H019-3;Q9H019 E9PPF9 MTFR1L Mitochondrial fission regulator 1-like 1 AS(0.038)S(0.962)FADMMGILK;AS(0.015)S(0.985)FADMMGILK 192.15 4.68E-06 289910000 2532700 1614940 768920 533860 704310 428060 356260 997100 543740 436310 TRUE FALSE 2433719.284 1568883.492 907880.9485 561412.5786 726964.7708 436715.6665 360620.0164 976509.5366 482016.9147 406758.3351 5.983206917 3.857040796 2.231991013 1.380211615 1.787215425 1.073648968 0.886570687 2.400711804 1.185020375 1 18.63381238 4.566402959 1.378980871 1.452067845 7.069023426 0.92328951 0.423691371 0.235628481 0.511346699 0.123104066 1.688548561 36847.06995 -4.566402959 5.616955581 up INS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_BT-474_Pertuzumab_2h_R1 4 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 INS(0.573)S(0.414)PNVNT(0.005)T(0.006)AS(0.002)GVEDLNIIQVTIPDDDNER;INS(0.558)S(0.405)PNVNT(0.015)T(0.021)ASGVEDLNIIQVTIPDDDNER;INS(0.491)S(0.491)PNVNT(0.007)T(0.01)AS(0.001)GVEDLNIIQVTIPDDDNER;INS(0.478)S(0.478)PNVNT(0.017)T(0.024)AS(0.003)GVEDLNIIQVTIPDDDNER 171.79 4.00E-13 659500000 434217 480166 425099 495813 492401 517643 495478 521169 504192 566327 TRUE FALSE 417247.3196 466472.1358 501923.8456 521401.9683 508239.5254 528110.0961 501541.808 510406.678 446958.2379 527969.1679 0.790287284 0.883521547 0.950668857 0.987561396 0.962631071 1.000266925 0.949945259 0.966735766 0.846561248 1 19.01009416 4.566574944 2.017273448 0.960223857 0.771529383 0.619069898 0.041350348 0.317163105 1.832149549 0.010365249 0.09666131 36861.6647 -4.566574944 -0.188694475 NFDEILR ddPTM_BT-474_Pertuzumab_2h_R1 9 NFDEILR 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;;; 211.87 0.00022076 13677960000 11492080 11901140 10247120 11541980 11686070 11356650 11802510 12242950 13141250 12846510 FALSE TRUE 11042956.81 11561731.14 12099002.53 12137662.97 12061963.05 11586289.24 11946952.65 11990128.8 11649510.39 11976404.44 0.922059443 0.965375811 1.010236636 1.013464687 1.007143932 0.967426351 0.997540849 1.001145951 0.97270516 1 23.51369151 4.566875179 2.964864733 0.99643107 0.920901171 0.714250154 0.014523815 0.157595174 2.332557554 0.003697778 0.022679575 36887.15656 -4.566875179 -0.075529898 MEDEGGFPVPQENGQPES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEDEGGFPVPQENGQPESPR 20 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 MEDEGGFPVPQENGQPES(1)PR;MEDEGGFPVPQENGQPES(1)PR;MEDEGGFPVPQENGQPES(1)PR 249.06 2.52E-30 504510000 414770 493870 488960 545740 563560 547770 500730 540230 472680 561110 TRUE FALSE 398560.3298 479785.3111 577325.9489 573905.7068 581687.4192 558846.2847 506858.0835 529074.0617 419023.348 523105.5199 0.761911918 0.917186481 1.103651036 1.097112695 1.111988685 1.068324197 0.968940423 1.011409824 0.801030255 1 18.99674247 4.566908484 3.33593678 1.024731297 0.764113522 0.453546155 0.087185165 0.239058831 4.565914313 0.022150894 0.122357845 36889.98547 -4.566908484 -0.260617776 ANLQIDQINTDLNLER ddPTM_BT-474_Pertuzumab_2h_R1 3 ANLQIDQINTDLNLER 16 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 341.5 9.05E-72 411700000 287627 334187 306944 358400 346502 375767 372916 347732 392986 386950 FALSE TRUE 276386.2189 324656.314 362415.6087 376897.067 357647.5515 383365.2662 377479.8576 340551.2127 348375.8768 360741.5318 0.766161349 0.899969328 1.004640655 1.044784239 0.991423277 1.062714526 1.046399774 0.944031066 0.965721565 1 18.460606 4.567140192 2.166447859 1.007496232 0.744018578 0.823232201 0.035092038 0.194673552 1.348634888 0.009989113 0.086035413 36909.67253 -4.567140192 -0.263477654 KQLLCGAAIGTHEDDKYR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQLLCGAAIGTHEDDKYR 18 2 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 106.57 0.00026737 733410000 560590 477510 338520 344670 448440 437920 376170 393340 505960 425450 FALSE TRUE 538681.523 463891.8823 399698.0943 362458.46 462864.4799 446775.0424 380773.681 385217.3915 448525.542 396633.8925 1.35813286 1.169571968 1.007725517 0.913836328 1.166981664 1.126416705 0.960012969 0.971216527 1.130830094 1 18.59744844 4.567339382 2.593908642 1.030572992 1.372852382 0.617342716 0.079012393 0.234134708 2.536275331 0.020709624 0.145833788 36926.60513 -4.567339382 0.34227939 S(ph)SSTGNLLDKDDLAIPPPDYGAASR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSTGNLLDKDDLAIPPPDYGAASR 25 1 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 S(0.351)S(0.351)S(0.297)T(0.002)GNLLDKDDLAIPPPDYGAASR;S(0.315)S(0.315)S(0.315)T(0.055)GNLLDKDDLAIPPPDYGAASR;S(0.352)S(0.352)S(0.293)T(0.002)GNLLDKDDLAIPPPDYGAASR 143.82 1.92E-07 2839320000 1612660 1288830 836000 943070 838770 682400 777880 1805690 994600 875110 TRUE FALSE 1549635.464 1252073.83 987083.7967 991741.9557 865749.7988 696198.5955 787399.9281 1768401.87 881697.1777 815838.0202 1.899440117 1.534708851 1.209901687 1.215611348 1.06117854 0.853353948 0.965142478 2.167589432 1.080725776 1 19.63792322 4.567925173 2.461882895 1.255162239 1.937838144 0.278359183 0.349129936 0.609416118 5.809326842 0.09923386 0.74137168 36976.44652 -4.567925173 0.682675905 EIS(ph)LPEVS(ph)LLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EISLPEVSLLK 11 0 Q2M3G0-1;Q2M3G0 Q2M3G0-1 ABCB5 ATP-binding cassette sub-family B member 5 2 EIS(1)LPEVS(1)LLK 75.566 0.055171 177250000 227040 367110 356240 614290 446240 470460 461940 421080 276920 438100 TRUE FALSE 218167.0258 356640.3822 420620.4925 645993.5805 460593.7149 479973.0235 467593.3599 412384.5509 245485.2025 408427.0968 0.534163937 0.873204508 1.029854522 1.581661906 1.127725654 1.17517429 1.144863707 1.009689499 0.601050235 1 18.63971906 4.567979176 2.284599942 1.104145777 0.495508787 0.358651868 0.226362741 0.460953887 3.648435258 0.059458834 0.483339891 36981.0447 -4.567979176 -0.60863699 GHAAFTSDPKPTIEVSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHAAFTSDPKPTIEVSGK 18 1 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 105.38 0.00028818 603470000 307960 253220 183750 196450 194690 77253 258790 163090 236820 258870 FALSE TRUE 295924.5827 245998.4135 216957.7125 206588.808 200952.3807 78815.10859 261957.1494 159722.1345 209937.1864 241336.5043 1.226190723 1.01931705 0.898984234 0.856019725 0.83266467 0.326577651 1.085443539 0.661823353 0.869894039 1 17.88068663 4.568110365 1.070875106 0.777414309 1.365458938 0.319759101 0.193945993 1.466080594 1.690280905 0.056257372 0.918437677 36992.21743 -4.568110365 0.588044629 ASGYQSS(ph)QKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASGYQSSQKK 10 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 AS(0.002)GY(0.002)QS(0.244)S(0.752)QKK 54.343 0.084361 129440000 113730 74346 36289 34448 38087 37574 25915 59255 39666 37802 TRUE FALSE 109285.3059 72225.72487 42847.22954 36225.86541 39312.10294 38333.77202 26232.15552 58031.36354 35163.28197 35241.63687 3.10102809 2.049442968 1.215812696 1.027928003 1.115501618 1.087740963 0.744351224 1.646670493 0.997776639 1 15.10499331 4.568415837 1.89266707 1.119780798 3.366808497 0.89527385 0.2165694 0.168820949 0.825397642 0.058719808 0.592063046 37018.246 -4.568415837 2.247027699 up FEEPAPLSYDSRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FEEPAPLSYDSRPR 14 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 ; 202.13 1.54E-08 907160000 339920 374040 337120 375400 351880 376170 391780 429740 412450 423590 FALSE TRUE 326635.5506 363372.7454 398045.0832 394774.439 363198.5398 383776.4151 396574.7208 420865.7188 365630.4051 394899.872 0.827135114 0.920164252 1.007964579 0.999682368 0.919723113 0.971832209 1.004241199 1.065752989 0.925881296 1 18.59112737 4.568582464 2.52292208 0.991568622 0.818094164 0.599891169 0.040305838 0.254650044 2.575328833 0.01092212 0.079584662 37032.45157 -4.568582464 -0.173474458 GLFDDEDEESDLFTEASQDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GLFDDEDEESDLFTEASQDR 20 0 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 0 ;; 249.19 5.31E-30 152528000 185269 207020 179218 233943 213148 227042 199255 217963 215790 229152 FALSE TRUE 178028.4827 201115.9923 211606.6793 246016.8263 220004.099 231632.9448 201693.5423 213461.9879 191294.4239 213631.3309 0.833344444 0.941416184 0.990522684 1.151595251 1.029830681 1.084264858 0.944119673 0.999207312 0.895441802 1 17.70476372 4.569348906 2.223944332 1.015503929 0.819521374 0.41137574 0.066277414 0.443404394 3.273489652 0.017567911 0.147942957 37097.8641 -4.569348906 -0.195982554 HLDVDLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLDVDLDR 8 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 ; 148.27 0.00052397 685790000 192119 230960 205510 258040 271420 241080 302220 179603 302160 312430 FALSE TRUE 184610.7771 224373.2469 242650.2285 271357.4753 280150.4708 245954.8028 305918.6588 175894.1353 267860.0636 291268.8378 0.633815751 0.770330423 0.833079949 0.931639228 0.961827818 0.844425393 1.050296561 0.603889302 0.919631724 1 18.15199183 4.56965915 1.765836836 0.877332841 0.598874566 0.333296624 0.115579694 0.824374396 3.362972782 0.03150963 0.344225377 37124.37492 -4.56965915 -0.278458275 LVLEVAQHLGESTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVLEVAQHLGESTVR 15 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 160.04 1.73E-06 1316500000 529110 771470 558220 1276730 597350 778810 1096040 826160 766130 664710 FALSE TRUE 508431.7962 749468.4309 659102.7715 1342622.188 616564.3052 794558.0718 1109453.665 809099.5073 679162.1343 619688.5996 0.820463369 1.209427495 1.06360319 2.166607856 0.994958283 1.282189268 1.79034061 1.305654982 1.095973259 1 19.2411839 4.570022155 1.742850955 1.386979569 0.760397593 0.158289651 0.355702378 1.074856756 4.23653562 0.090348257 1.00215954 37155.41828 -4.570022155 -0.626581976 ANPELCGSLHLNGS(ph)PSSCIASR ddPTM_BT-474_Pertuzumab_2h_R1 3 ANPELCGSLHLNGSPSSCIASR 22 0 Q9NXR5 Q9NXR5 ANKRD10 Ankyrin repeat domain-containing protein 10 1 ANPELCGSLHLNGS(1)PSSCIASR;ANPELCGSLHLNGS(1)PSSCIASR;ANPELCGSLHLNGS(0.897)PS(0.08)S(0.023)CIASR 304.86 2.43E-56 1476640000 599115 794230 743148 1013930 882596 927600 894110 910008 846230 1032930 TRUE FALSE 575700.9234 771579.338 877451.3748 1066259.049 910985.5019 946356.7075 905052.3856 891216.0168 750169.5181 962968.7311 0.597839686 0.801250667 0.911194047 1.10726238 0.946017739 0.982749156 0.939856463 0.925488012 0.779017526 1 19.87712943 4.57003927 2.068906316 0.952084759 0.562521797 0.671104198 0.076935202 0.289804469 1.778054415 0.020210924 0.185315195 37156.8826 -4.57003927 -0.389562962 MT(ph)KEKY(ph)GK ddPTM_BT-474_Pertuzumab_2h_R1 1 MTKEKYGK 8 2 Q9NW64;E5RJW4;E5RHA8 Q9NW64 RBM22 Pre-mRNA-splicing factor RBM22 2 MT(1)KEKY(1)GK 42.599 0.084986 175920000 129720 156580 136300 184660 150290 181750 157350 184660 194700 199130 TRUE FALSE 124650.399 152114.4917 160932.442 194190.3247 155124.2143 185425.1095 159275.6964 180846.7065 172598.4722 185642.7477 0.671453103 0.819393666 0.866893234 1.046043151 0.83560611 0.99882765 0.857968859 0.974165211 0.929734527 1 17.50216943 4.570214285 1.517972481 0.941765988 0.62018296 0.648837822 0.063054529 0.453990072 1.252751506 0.015608562 0.199048476 37171.85936 -4.570214285 -0.321583028 DIHS(ph)S(ph)S(ph)QLCS(ph)YR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIHSSSQLCSYR 12 0 A0A075B795 A0A075B795 CYP2F1 4 DIHS(1)S(1)S(1)QLCS(1)Y(0.001)R;DIHS(1)S(1)S(1)QLCS(1)Y(0.001)R 48.115 0.080973 2255000000 6397 15453 14048.8 24873 23071.9 16051 24616 21400.8 20818.4 25901.2 TRUE FALSE 6146.998168 15012.29557 16587.73067 26156.69851 23814.02862 16375.56222 24917.25797 20958.866 18455.18251 24146.88865 0.254566883 0.621707243 0.686951057 1.083232663 0.9862152 0.678164481 1.031903461 0.867973771 0.764288218 1 14.55954969 4.570254175 1.425667278 0.904697217 0.124698365 0.719496493 0.126603713 0.45570292 1.070906452 0.03442886 0.464757394 37175.27374 -4.570254175 -0.779998851 down DLIDFDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLIDFDDR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 210.1 9.75E-05 9297900000 9160500 9485900 7956500 9820900 8679300 9139200 9153100 10276500 10056900 9752900 FALSE TRUE 8802497.533 9215371.42 9394416.541 10327757.83 8958477.567 9324000.886 9265118.376 10064286.68 8915282.874 9092327.396 0.968123688 1.013532731 1.033224622 1.135876149 0.985278815 1.025480109 1.019004043 1.106898844 0.98052814 1 23.1162182 4.570270211 2.409786099 1.043186241 0.963986198 0.144314113 0.047726221 0.65016211 5.862214088 0.011815039 0.091098756 37176.64644 -4.570270211 -0.079200043 SGPLFNFDVHDDVR ddPTM_BT-474_Pertuzumab_2h_R1 8 SGPLFNFDVHDDVR 14 0 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ;;;;;;; 225.85 2.62E-12 4063690000 3415829 3707401 3012751 3769610 3783673 3816390 3785480 3709367 4061333 4076288 FALSE TRUE 3282334.626 3601669.553 3557222.124 3964160.024 3905378.278 3893560.021 3831807.837 3632767.275 3600307.504 3800197.383 0.863727406 0.947758548 0.936062463 1.043145822 1.027677745 1.024567839 1.008318108 0.955941734 0.947400133 1 21.85764292 4.570654209 1.389705201 0.997198625 0.839387614 0.615099749 0.032459331 0.681567648 1.499989225 0.010006787 0.138240309 37209.53215 -4.570654209 -0.157811012 YGVIILDEAHER ddPTM_BT-474_Pertuzumab_2h_R1 8 YGVIILDEAHER 12 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;;;;;; 240 3.43E-16 10479300000 5875060 6373400 5524810 6862660 6576190 6649270 6465550 6239080 6895050 6986680 FALSE TRUE 5645456.16 6191636.872 6523266.066 7216842.705 6787719.124 6783722.795 6544677.335 6110240.818 6112352.83 6513465.941 0.866736114 0.950590197 1.001504595 1.107988093 1.042105568 1.041492019 1.004791826 0.938093616 0.938417869 1 22.634994 4.570989894 2.420802581 1.008712478 0.858352554 0.470342887 0.047071948 0.398051871 3.626573762 0.013807829 0.106168441 37238.30406 -4.570989894 -0.150359924 ALRPGDLPPS(ph)PDDVKR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALRPGDLPPSPDDVKR 16 2 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 ALRPGDLPPS(1)PDDVKR;ALRPGDLPPS(1)PDDVKR;ALRPGDLPPS(1)PDDVKR;ALRPGDLPPS(1)PDDVKR 149.84 4.16E-07 1680650000 2295220 2422830 2301340 2545530 2660820 2869810 2790040 2867140 3174100 3102900 TRUE FALSE 2205520.265 2353733.261 2717243.331 2676905.108 2746407.692 2927839.524 2824185.344 2807932.557 2813789.475 2892737.819 0.762433515 0.813669751 0.939332736 0.925388084 0.94941466 1.012134423 0.976301871 0.970683391 0.972708089 1 21.46400414 4.571061926 0.864076136 0.980874378 0.658863202 0.923766765 0.021264805 0.437918111 0.302702438 0.007234954 0.127644504 37244.48096 -4.571061926 -0.322011176 EICELTGIDQSVLER ddPTM_BT-474_Pertuzumab_2h_R1 1 EICELTGIDQSVLER 15 0 E9PDF6;O43795;O43795-2 E9PDF6 MYO1B Unconventional myosin-Ib 0 152.47 3.12E-08 0 21840 27537 26539 31854 31340 26203 29480 38830 29518 24332 FALSE TRUE 20986.46865 26751.67172 31335.18766 33497.98876 32348.07956 26732.84261 29840.78506 38028.14693 26167.24039 22683.97197 0.92516728 1.179320436 1.381380108 1.476725011 1.426032425 1.178490374 1.315500879 1.67643246 1.153556371 1 14.46938566 4.571171275 2.397643768 1.36901285 0.895554182 0.290229828 0.182391104 0.423312498 3.765111723 0.045524342 0.354060436 37253.85976 -4.571171275 -0.473458668 REPGSGTESDT(ph)S(ph)PDFHNQENEPSQEDPEDLDGSVQGVKPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 REPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQK 41 2 Q9HAF1-3;Q9HAF1-2;Q9HAF1;Q9HAF1-4;B1AK63 Q9HAF1-3 MEAF6 Chromatin modification-related protein MEAF6 2 REPGS(0.323)GT(0.415)ES(0.436)DT(0.425)S(0.4)PDFHNQENEPSQEDPEDLDGSVQGVKPQK 96.239 0.0023571 162810000 27547 24429 17930 17472 23424 24060 17655 22199 29376 24347 TRUE FALSE 26470.43279 23732.30884 21170.34985 18373.73201 24177.45423 24546.50968 17871.06717 21740.58289 26041.35963 22697.956 1.16620337 1.045570307 0.932698515 0.809488397 1.065182003 1.081441416 0.787342577 0.957821175 1.147299767 1 14.47027477 4.57121004 2.98104974 0.963002598 1.169310995 0.22951055 0.107541047 0.419054297 6.241809341 0.02683832 0.165696221 37257.18515 -4.57121004 0.206308396 FLQDYFDGNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLQDYFDGNLK 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 150.04 7.93E-05 152220000 914480 981620 901730 968900 997530 990010 1004530 923910 1153500 1079690 FALSE TRUE 878741.1106 953625.1587 1064692.67 1018905.045 1029616.458 1010028.681 1016823.739 904830.9356 1022559.516 1006561.635 0.87301272 0.94740861 1.057752087 1.012262946 1.022904533 1.003444445 1.010195207 0.898932469 1.015893593 1 19.94100408 4.571699506 3.80676214 0.995907776 0.876759895 0.50959723 0.038979338 0.225350558 5.516289489 0.010685252 0.05406395 37299.19907 -4.571699506 -0.11914788 IRS(ph)LTEY(ph)MQSVELK ddPTM_BT-474_Pertuzumab_2h_R1 1 IRSLTEYMQSVELK 14 1 Q12840;J3KNA1 Q12840 KIF5A Kinesin heavy chain isoform 5A;Kinesin-like protein 2 IRS(0.449)LT(0.476)EY(0.645)MQS(0.431)VELK 56.851 0.069456 342590000 257370 311610 293040 344450 305280 392980 341440 326530 384490 430220 TRUE FALSE 247311.6959 302723.1879 345998.8466 362227.1058 315099.6084 400926.3249 345618.6449 319787.0414 340844.3071 401080.8162 0.616613126 0.754768555 0.862666158 0.903127477 0.785626227 0.999614812 0.861718215 0.797313231 0.849814534 1 18.61353344 4.571982172 1.94546262 0.873141235 0.583680303 0.599092726 0.068777433 0.377950953 1.974232227 0.017566129 0.173871515 37323.48358 -4.571982172 -0.289460932 RGPRT(ph)PPITTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGPRTPPITTK 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RGPRT(1)PPITTK 116.96 0.043782 312980000 370570 408430 389450 367850 424200 468200 380160 425660 472310 441430 TRUE FALSE 356087.7147 396781.9763 459832.2783 386834.7826 437844.7782 477667.3248 384812.5118 416869.9723 418695.3489 411531.5529 0.865274393 0.964159306 1.117368219 0.939988149 1.063939752 1.160706443 0.935074137 1.012972078 1.017407647 1 18.65064352 4.572060299 3.840478474 1.028751897 0.870421717 0.366065507 0.06700513 0.252125142 6.26609099 0.015986734 0.080470601 37330.19851 -4.572060299 -0.15833018 ASDVHEVR ddPTM_BT-474_Pertuzumab_2h_R1 9 ASDVHEVR 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;; 141.52 0.00063219 24629254000 26823850 30623700 27317910 36455330 30529970 32493640 33148440 31323130 31301840 33345550 FALSE TRUE 25775544.29 29750342.06 32254864.02 38336793.95 31511994.21 33150683.66 33554120.52 30676296.42 27748586.35 31087026.2 0.829141524 0.957001865 1.037566727 1.23320879 1.013670269 1.066383238 1.079360898 0.986787743 0.892609868 1 24.88980928 4.572324197 2.539725422 1.04376402 0.818759402 0.384527709 0.081726389 0.382158857 3.909919599 0.021294926 0.155879046 37352.88894 -4.572324197 -0.225004618 SSS(ph)PELVTHLK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.117)S(0.031)S(0.851)PELVT(0.001)HLK;S(0.219)S(0.219)S(0.561)PELVTHLK;S(0.043)S(0.272)S(0.686)PELVTHLK 206.32 1.73E-08 6902950000 4514340 5001690 4255260 5138080 5279650 5236380 5574930 5575210 5693730 5733000 TRUE FALSE 4337914.602 4859046.698 5024280.14 5403256.925 5449474.737 5342263.191 5643157.661 5460079.965 5047401.64 5344698.804 0.811629385 0.909133868 0.940049257 1.0109563 1.019603712 0.999544294 1.055842035 1.021587963 0.94437532 1 22.34967722 4.572448844 1.04133113 1.013720261 0.747458202 0.826800816 0.028307168 0.528816645 0.566834069 0.008787813 0.147135297 37363.61114 -4.572448844 -0.266262059 LQLERPVS(ph)PETQADLQR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQLERPVSPETQADLQR 17 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 LQLERPVS(0.999)PET(0.001)QADLQR;LQLERPVS(0.979)PET(0.021)QADLQR;LQLERPVS(0.941)PET(0.059)QADLQR;LQLERPVS(1)PETQADLQR 275.02 6.32E-36 3432370000 2262790 2703440 2288870 3245370 2629050 2737700 3033960 3379320 2630580 2701710 TRUE FALSE 2174357.665 2626340.538 2702519.725 3412863.935 2713615.781 2793058.17 3071090.51 3309535.861 2331967.587 2518720.775 0.863278568 1.042727945 1.072973134 1.354998922 1.077378568 1.108919336 1.219305665 1.313974893 0.925853953 1 21.26425976 4.572457718 1.722684878 1.165118201 0.82038574 0.282632323 0.127319018 0.732893629 2.793526228 0.033014443 0.373847534 37364.37466 -4.572457718 -0.344732461 IGVDHVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGVDHVAR 8 0 Q7L5N1;E7EM64;H7C3T0 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 ; 159.04 0.00036148 179030000 332103 371253 325357 395901 378750 388920 388698 387233 424527 437846 FALSE TRUE 319124.0476 360665.2279 384156.2474 416333.4981 390932.8377 396784.2289 393455.0024 379236.5032 376336.4747 408190.3004 0.781802133 0.883571284 0.94112047 1.019949513 0.957722017 0.972056976 0.963900911 0.929067895 0.921963296 1 18.63888238 4.572492258 1.964119904 0.961977745 0.760525443 0.806242349 0.028005406 0.234081709 1.252331704 0.007683874 0.075375169 37367.3464 -4.572492258 -0.201452302 TPEFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPEFLR 6 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 107.55 0.072514 2263760000 688550 753400 643210 801890 768240 673730 842060 818460 791760 819930 FALSE TRUE 661640.7048 731913.7697 759452.3551 843275.639 792951.1373 687353.2822 852365.3822 801558.515 701882.7241 764395.4108 0.865573884 0.957506755 0.993533379 1.103192964 1.037357271 0.899211681 1.115084379 1.048617644 0.918219438 1 19.54395959 4.57305483 1.927020935 1.023363914 0.846979755 0.325763751 0.065707955 0.614080294 3.125153809 0.017063274 0.171345852 37415.78233 -4.57305483 -0.17638416 GTEDELDKYSEALKDAQEKLELAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTEDELDKYSEALKDAQEKLELAEK 25 3 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;H0YKP3;A0A087WTJ7 J3KN67;P09493-3 TPM3;TPM1 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain 0 75.797 0.013387 74200000 162570 132270 88873 63858 110950 125750 102080 127620 146650 104410 FALSE TRUE 156216.5847 128497.7891 104934.3281 67153.71903 114518.8075 128292.7512 103329.2856 124984.6024 130002.9068 97338.2177 1.604884375 1.320116519 1.078038314 0.689900849 1.176504052 1.31801007 1.061548979 1.284023946 1.335579281 1 16.57071874 4.573318352 2.908457857 1.12861557 1.614804531 0.412695517 0.179857136 0.325454631 4.574000793 0.047409888 0.301633209 37438.49237 -4.573318352 0.486188961 TLPSGS(ph)PRPGQLERPTSLALDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLPSGSPRPGQLERPTSLALDSR 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 T(0.006)LPS(0.187)GS(0.807)PRPGQLERPTSLALDSR 114.91 0.00032547 987140000 501080 580340 506860 637060 648000 645250 608350 590630 644270 679000 TRUE FALSE 481497.2396 563789.2714 598460.877 669938.7429 668843.5085 658297.3971 615795.1693 578433.2841 571135.1706 633010.7252 0.760646258 0.890647265 0.945419806 1.058337112 1.056606913 1.039946672 0.97280369 0.913781175 0.902251965 1 19.27187042 4.573815383 1.840056618 0.987026105 0.73056532 0.655232049 0.05153698 0.426120491 1.922552052 0.015890385 0.168402515 37481.36367 -4.573815383 -0.256460785 SKSDS(ph)YTLDPDTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 SKS(0.08)DS(0.875)YT(0.045)LDPDTLR 245.18 3.22E-17 197630000 494540 424420 291570 324850 338030 304820 299360 565890 379410 331420 TRUE FALSE 475212.8301 412315.9572 344263.1849 341615.5474 348903.0419 310983.6692 303023.6572 554204.1737 336340.9674 308972.6282 1.538041842 1.334474059 1.114219039 1.105649874 1.129236088 1.0065088 0.980745961 1.793699905 1.088578524 1 18.23711951 4.573893389 3.121969896 1.195518045 1.541059555 0.20694478 0.225852061 0.545646288 8.959500548 0.061658772 0.366991112 37488.09651 -4.573893389 0.345541509 ENISNAQALLEYHLSYLQEVEQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENISNAQALLEYHLSYLQEVEQLR 24 0 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 148.02 1.68E-07 98049000 77031 88431 78059 90763 103810 109270 81139 94998 92359 112750 FALSE TRUE 74020.54336 85909.03446 92165.99771 95447.28931 107149.1429 111479.5143 82132.00335 93036.2581 81874.79352 105113.3421 0.704197411 0.817299049 0.87682492 0.908041619 1.019367673 1.060564835 0.781366111 0.885104177 0.778919135 1 16.68158628 4.574022993 1.606588745 0.912875421 0.666855979 0.367804162 0.087798378 0.872908457 2.772557612 0.024896736 0.30442199 37499.2855 -4.574022993 -0.246019443 LFS(ph)QGQDVSNK ddPTM_BT-474_Pertuzumab_2h_R1 3 LFSQGQDVSNK 11 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;H0Y8U8 P55196-5 MLLT4 Afadin 1 LFS(1)QGQDVSNK;LFS(1)QGQDVSNK;LFS(0.996)QGQDVS(0.004)NK 130.27 0.00023884 842300000 2687000 1901140 1332610 903950 1143180 949570 650500 1569720 1074950 786100 TRUE FALSE 2581989.069 1846921.349 1573442.271 950602.9678 1179951.423 968770.956 658461.0136 1537304.733 952926.1826 732856.7468 3.52318387 2.520166945 2.146998411 1.29711976 1.610071038 1.321910401 0.898485299 2.097687904 1.300289841 1 19.48317169 4.574340287 1.076834093 1.409638972 4.189180845 0.816431025 0.329347232 0.56527091 0.655761277 0.10166798 1.684757122 37526.69239 -4.574340287 2.779541874 up RSS(ph)PVPPVPER ddPTM_BT-474_Pertuzumab_2h_R1 3 RSSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.178)S(0.822)PVPPVPER;RS(0.025)S(0.975)PVPPVPER;RS(0.197)S(0.803)PVPPVPER 122.33 0.00024077 8762280000 2527280 2845660 2559650 2972650 2833100 2841220 3063530 3213430 3130070 3452320 TRUE FALSE 2428511.104 2764504.563 3022235.694 3126068.823 2924229.234 2898671.415 3101022.397 3147071.548 2774757.576 3218491.291 0.754549534 0.858944242 0.939022486 0.971283915 0.90857143 0.900630498 0.963501876 0.977809558 0.8621299 1 21.61795313 4.574548236 2.121698163 0.941807907 0.735180949 0.688299417 0.039152308 0.259255763 1.686474663 0.009883233 0.089418253 37544.66523 -4.574548236 -0.206626958 KSS(ph)PSKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.065)S(0.468)PS(0.468)KDR 82.494 0.01585 283640000 974810 867570 721710 593290 722370 792180 862850 876660 834870 892350 TRUE FALSE 936713.3475 842827.753 852139.0514 623909.768 745605.6871 808198.4224 873409.8164 858556.6646 740099.0577 831910.3397 1.12597873 1.013123305 1.024315976 0.749972369 0.896257267 0.971497028 1.049884555 1.032030285 0.889638008 1 19.66606852 4.574731778 1.952492204 0.953383555 1.142138951 0.293462742 0.084182282 0.79228561 4.161485989 0.023976428 0.238624526 37560.53572 -4.574731778 0.188755396 FLSQIESDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FLSQIESDR 9 0 P19367-4;P19367-2;P19367;P19367-3;Q2TB90 P19367-4;Q2TB90 HK1;HKDC1 Hexokinase-1;Putative hexokinase HKDC1 0 ;;; 164.46 0.00014481 787790000 952550 1096040 870640 1362670 1067000 1118470 1124580 1170850 1033970 1143520 FALSE TRUE 915323.2929 1064782.012 1027984.015 1432997.562 1101321.024 1141086.23 1138342.946 1146671.538 916598.0604 1066068.372 0.858597175 0.998793361 0.964275878 1.344189172 1.033067909 1.070368712 1.06779544 1.075607877 0.859792941 1 20.02386854 4.575143335 1.872539887 1.066863492 0.838149544 0.201442016 0.115940065 0.871201444 4.10506259 0.029731076 0.310491874 37596.14668 -4.575143335 -0.228713947 AVEYLLTGIPGSPEPEHGS(ph)VQESQVSEQPATEAGENPLEFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAGENPLEFLR 42 0 P54725-3 P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.001)GIPGS(0.307)PEPEHGS(0.346)VQES(0.346)QVSEQPATEAGENPLEFLR;AVEY(0.001)LLT(0.009)GIPGS(0.412)PEPEHGS(0.504)VQES(0.071)QVS(0.002)EQPATEAGENPLEFLR 125.93 1.33E-08 111346000 8846.1 11824.8 11462.5 15071.1 13563.7 15426.7 14164 11828.7 12208.6 13392.8 TRUE FALSE 8500.384632 11487.56828 13534.02873 15848.92128 13999.98873 15738.63844 14337.34327 11584.43321 10822.73091 12485.69373 0.680809959 0.920058471 1.083962896 1.269366494 1.121282408 1.260533759 1.148301695 0.927816545 0.866810539 1 13.60798836 4.575255045 2.365084549 1.090766181 0.651854517 0.510358518 0.122730893 0.357011355 3.053605495 0.034484537 0.276099199 37605.81842 -4.575255045 -0.438911664 S(ph)PSAMQQQDGLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSAMQQQDGLDR 13 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47;O60343-4;O60343-5 O60343-2 TBC1D4 TBC1 domain family member 4 1 S(0.998)PS(0.002)AMQQQDGLDR 167.18 7.65E-07 0 30877 49045 53332 71774 43825 52390 61114 64241 64721 65570 TRUE FALSE 29670.2927 47646.28462 62970.27876 75478.26474 45234.67093 53449.3617 61861.93141 62914.4009 57374.14341 61128.8855 0.485372708 0.779439773 1.030123128 1.234739749 0.739988478 0.874371605 1.011991809 1.029209029 0.938576631 1 15.89956664 4.575680329 2.72991785 0.982957985 0.466572941 0.621601185 0.120052845 0.21893238 2.65114365 0.030916295 0.211443184 37642.6621 -4.575680329 -0.516385044 ALDSNSLENDDLSAPGREPGHFNPESR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALDSNSLENDDLSAPGREPGHFNPESR 27 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;; 285.36 1.15E-61 2421340000 317607 370896 348519 387530 346546 449059 418124 380011 428799 428312 FALSE TRUE 305194.5673 360318.4092 411504.1361 407530.4697 357692.9668 458139.2807 423241.1266 372163.6401 380123.5352 399302.0467 0.764320067 0.902370554 1.030558544 1.020607014 0.895795475 1.147350194 1.059952309 0.932035393 0.951969914 1 18.60712094 4.576037609 2.594225866 1.003164955 0.751760486 0.554214154 0.067040762 0.271846233 2.91472853 0.017332552 0.125406314 37673.64223 -4.576037609 -0.251404469 DLEHLSK ddPTM_BT-474_Pertuzumab_2h_R1 5 DLEHLSK 7 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;; 124.83 0.0041079 3106100000 5177860 7466000 7668200 9908490 7377530 8210550 8849050 8577530 9743490 11269050 FALSE TRUE 4975503.507 7253076.99 9054014.318 10419868.36 7614834.953 8376572.946 8957347.321 8400401.008 8637449.863 10505787.21 0.473596448 0.690388721 0.861812079 0.99182176 0.724822881 0.797329394 0.85261077 0.799597483 0.822161128 1 23.32468093 4.576057054 2.527110804 0.844345858 0.452706724 0.680744315 0.081502721 0.210060843 2.113652906 0.020049941 0.149351132 37675.32903 -4.576057054 -0.391639134 S(ph)PGSGSQSSGWHEVEPGMPSPTTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGSGSQSSGWHEVEPGMPSPTTLK 25 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.991)PGS(0.003)GS(0.003)QS(0.002)S(0.002)GWHEVEPGMPSPTTLK;S(0.963)PGS(0.037)GSQSSGWHEVEPGMPSPTTLK 190.49 5.48E-18 2992900000 1091880 1286550 1142860 1589180 1256440 1311520 1319720 1372930 1445540 1610360 TRUE FALSE 1049208.122 1249858.854 1349400.225 1671197.77 1296854.534 1338039.833 1335871.128 1344578.516 1281448.359 1501288.883 0.698871573 0.832523885 0.898827827 1.113175345 0.863827441 0.891260735 0.889816173 0.895616114 0.853565476 1 20.51777018 4.576218935 2.330809704 0.921734057 0.68323583 0.480821218 0.073383401 0.368804383 3.037717796 0.01886316 0.154064029 37689.37491 -4.576218935 -0.238498227 NFELVDS(ph)SPCKK ddPTM_BT-474_Pertuzumab_2h_R1 1 NFELVDSSPCKK 12 1 A0A087WUU7;Q96GX5-2;Q96GX5-3;Q96GX5 A0A087WUU7 MASTL Serine/threonine-protein kinase greatwall 1 NFELVDS(0.578)S(0.422)PCKK 55.186 0.079118 869960000 806610 691910 530520 497250 533130 468850 647200 691510 698180 742480 TRUE FALSE 775086.7894 672177.4043 626396.7654 522913.1321 550278.6106 478330.4682 655120.6272 677230.0768 618925.5334 692191.1683 1.119758276 0.971086363 0.904947642 0.75544612 0.794980687 0.691038098 0.946444649 0.978385897 0.894154046 1 19.40081101 4.576528877 2.005481901 0.86594013 1.147801892 0.410539856 0.093080222 0.566088585 3.178104792 0.026633655 0.258771467 37716.28228 -4.576528877 0.281861762 LVIPSELGYGER ddPTM_BT-474_Pertuzumab_2h_R1 1 LVIPSELGYGER 12 0 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 112.36 0.0029836 70382000 117580 128300 114610 128490 124950 133270 131690 137950 140130 144970 FALSE TRUE 112984.8436 124641.0096 135322.5765 135121.3843 128969.1302 135964.8107 133301.6616 135101.2843 124223.0299 135151.0528 0.835989371 0.922234841 1.001269126 0.999780479 0.954259161 1.0060211 0.986316117 0.999631757 0.919142155 1 17.04421322 4.576614525 2.615118817 0.98449165 0.828471118 0.751586807 0.026238003 0.156619313 1.71076872 0.00626407 0.045006433 37723.72103 -4.576614525 -0.156020533 GRDPSSDTYEEDSELLLQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GRDPSSDTYEEDSELLLQIR 20 1 Q9UBE0;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 345.34 5.40E-95 707460000 395390 449510 359360 469980 462600 499720 466280 471250 470180 461790 FALSE TRUE 379937.7217 436690.4149 424304.3459 494235.7241 477479.9491 509824.6808 471986.4741 461518.5228 416807.1376 430512.552 0.882524145 1.014350018 0.9855795 1.14801699 1.109096464 1.184227216 1.096336151 1.072021061 0.96816489 1 18.71569578 4.577211909 1.28979057 1.087539554 0.840885008 0.443950534 0.065117424 0.927996172 1.676614433 0.018729274 0.280178294 37775.6468 -4.577211909 -0.246654546 SGLLHEGDEVLEINGIEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGLLHEGDEVLEINGIEIR 19 0 Q8N3R9-2;Q8N3R9 Q8N3R9-2 MPP5 MAGUK p55 subfamily member 5 0 194.92 2.07E-15 35275000 27765 31406 29443 34105 30863 34508 33222 30178 35145 36573 FALSE TRUE 26679.9131 30510.33163 34764.00506 35865.16314 31855.73642 35205.7754 33628.58077 29554.81375 31155.48694 34095.87813 0.782496729 0.894839297 1.019595533 1.051891463 0.934298753 1.032552242 0.986294608 0.866814858 0.913761095 1 15.05730972 4.577427108 3.239210758 0.969162924 0.781909687 0.542447664 0.054705571 0.237209581 4.1890348 0.015078905 0.087549154 37794.36981 -4.577427108 -0.187253236 (ac)AALGHLAGEAAAAPGPGT(ph)PCASR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALGHLAGEAAAAPGPGTPCASR 23 0 A0A3B3IT54;Q9H7E9;Q9H7E9-2;A0A3B3IRR6;A0A3B3ITA3 A0A3B3IT54 C8orf33 UPF0488 protein C8orf33 1 AALGHLAGEAAAAPGPGT(0.99)PCAS(0.01)R;AALGHLAGEAAAAPGPGT(0.867)PCAS(0.133)R 147.08 1.12E-61 348720000 10634 13395.9 14548.8 13248.7 14457.3 15195 14385.2 14209 15500.6 16807.7 TRUE FALSE 10218.41152 13013.86205 17178.0918 13932.46699 14922.33218 15502.25331 14561.25038 13915.57918 13741.03687 15669.29951 0.652129441 0.830532472 1.096289709 0.889156978 0.952329246 0.989339268 0.929285344 0.888079214 0.876940087 1 13.93565307 4.577461123 3.776473151 0.944690694 0.659594067 0.675637534 0.063949892 0.137231633 3.263453515 0.01539486 0.079093494 37797.33009 -4.577461123 -0.285096627 RLS(ph)DEHEPEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSDEHEPEQR 11 1 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 RLS(1)DEHEPEQR;RLS(1)DEHEPEQR 153.94 1.97E-05 1510810000 745260 901650 789050 972940 1097340 1040150 1013610 919770 978920 1118170 TRUE FALSE 716134.4153 875935.8248 931648.8873 1023153.55 1132636.938 1061182.546 1026014.862 900776.4281 867797.1056 1042435.35 0.68698209 0.84027832 0.893723421 0.981503122 1.086529671 1.017984037 0.984247956 0.864107715 0.832470911 1 19.99152648 4.577561085 1.522350408 0.961153739 0.63452269 0.602665287 0.070123502 0.634827004 1.746919542 0.02181818 0.284366028 37806.03093 -4.577561085 -0.326631049 YRT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YRTPSR 6 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 YRT(1)PSR 89.296 0.081365 172000000 44300 66250 47733 85786 79871 71628 85684 110570 80519 90220 TRUE FALSE 42568.70702 64360.61487 56359.41491 90213.42574 82440.12325 73076.36724 86732.62642 108286.6909 71378.82068 84109.31904 0.506111659 0.765201949 0.670073371 1.072573489 0.980154449 0.868826048 1.03118926 1.28745176 0.848643426 1 16.35997803 4.577846676 0.609063096 1.067635635 0.241809099 0.596216558 0.133780567 2.004117251 0.644466225 0.067158256 1.132018036 37830.90027 -4.577846676 -0.825826536 AAHSEGNTTAGLDMR ddPTM_BT-474_Pertuzumab_2h_R1 7 AAHSEGNTTAGLDMR 15 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;;; 199.58 7.35E-09 3224470000 2259545 2463459 2104345 2500181 2602724 2636929 2551966 2395096 2704857 3067421 FALSE TRUE 2171239.483 2393203.561 2484646.952 2629215.641 2686442.981 2690249.511 2583197.723 2345636.431 2397812.973 2859661.843 0.759264417 0.836883412 0.868860407 0.919414877 0.939426802 0.940757914 0.903322793 0.820249582 0.838495285 1 21.44741313 4.578003589 1.624172523 0.898246228 0.734920165 0.465088191 0.049335333 0.749970443 2.43623878 0.014294004 0.175251133 37844.57119 -4.578003589 -0.163326063 VLPNGEVSLS(ph)VPDLIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLPNGEVSLSVPDLIHK 17 0 A1L170;A1L170-2 A1L170 C1orf226 Uncharacterized protein C1orf226 1 VLPNGEVS(0.087)LS(0.913)VPDLIHK 79.635 0.0084526 17184000 46495 39834 32772 38042 28069 37887 28132 37859 37809 39841 TRUE FALSE 44677.924 38697.97332 38694.62941 40005.35218 28971.86488 38653.1011 28476.28783 37077.19842 33517.08083 37142.53358 1.202877663 1.041877589 1.041787559 1.077076557 0.780018542 1.04066948 0.766675966 0.998240961 0.902390806 1 15.18078461 4.578176795 0.728664464 0.918930626 1.3015694 0.434469132 0.09583873 2.103853917 0.986837645 0.035591848 0.637601641 37859.66745 -4.578176795 0.382638774 KMELSLNIPVNHGPQEESCGSSQLHENSGS(ph)PETSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KMELSLNIPVNHGPQEESCGSSQLHENSGSPETSR 35 1 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 KMELSLNIPVNHGPQEESCGSSQLHENS(0.195)GS(0.798)PET(0.004)S(0.004)R 151.31 2.62E-11 97838000 62613 73793 61866 77462 81007 94215 87008 52527 92872 104810 TRUE FALSE 60166.01474 71688.49589 73046.5624 81459.8231 83612.66372 96120.09185 88072.82993 51442.29909 82329.55991 97711.12534 0.615753984 0.733677927 0.747576718 0.833680124 0.855712831 0.983716967 0.901359284 0.526473305 0.842581227 1 16.57623522 4.578409589 1.329526404 0.818893446 0.571178187 0.238597228 0.125185555 1.860136967 3.621848883 0.039281553 0.576509015 37879.96673 -4.578409589 -0.247715258 TKETDSPS(ph)TPGKDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TKETDSPSTPGKDQR 15 2 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 TKETDS(0.002)PS(0.499)T(0.499)PGKDQR;TKETDS(0.002)PS(0.62)T(0.378)PGKDQR 154.19 1.32E-06 568590000 3312500 2423200 1464120 1379730 1760600 1453880 1617960 2397200 1802010 1472020 TRUE FALSE 3183043.838 2354092.709 1728719.053 1450938.031 1817231.298 1483278.45 1637761.078 2347696.982 1597453.379 1372318.774 2.319463887 1.715412448 1.259706626 1.057289354 1.324204938 1.080855613 1.193426126 1.710751923 1.164054161 1 20.38818421 4.578445235 2.241629056 1.2620147 2.414653397 0.760669681 0.192073841 0.231536127 1.723597262 0.053396731 0.459584476 37883.07595 -4.578445235 1.152638697 up YASICQQNGIVPIVEPEILPDGDHDLKR ddPTM_BT-474_Pertuzumab_2h_R1 7 YASICQQNGIVPIVEPEILPDGDHDLKR 28 1 H3BPS8;P04075;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;;;; 179.47 1.03E-17 36992780000 2843166 2571753 2008828 2087539 2253423 2164206 2254968 2318084 2658685 2160593 FALSE TRUE 2732051.929 2498409.122 2371867.906 2195277.138 2325906.397 2207967.728 2282564.973 2270214.755 2356882.225 2014254.112 1.356359118 1.240364415 1.177541549 1.089870998 1.15472342 1.096171389 1.133206064 1.127074654 1.170101732 1 20.94181427 4.578785093 1.281186982 1.11747348 1.420439255 0.750874107 0.045073273 0.478208219 0.847840172 0.011691982 0.176629929 37912.73303 -4.578785093 0.302965776 RLDQVEQELNELR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLDQVEQELNELR 13 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;;; 260.15 8.49E-24 747350000 336496 374071 317005 408716 384984 386046 392998 391787 380281 415299 FALSE TRUE 323345.3643 363402.8613 374294.8552 429809.8817 397367.36 393852.1146 397807.6271 383696.4615 337113.0951 387170.4288 0.83514995 0.938612131 0.966744429 1.110130965 1.026337061 1.017257738 1.027474201 0.991027292 0.870709822 1 18.56260924 4.579110517 1.900521332 1.007503584 0.814096763 0.456752362 0.056147728 0.511116445 2.488735815 0.01495741 0.155796274 37941.15236 -4.579110517 -0.193406822 EEDEPEERS(ph)GDETPGSEVPGDK ddPTM_BT-474_Pertuzumab_2h_R1 6 EEDEPEERSGDETPGSEVPGDK 22 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK 351.12 2.95E-96 9999910000 6525880 5582760 3836850 3971420 4660400 4954180 4862480 5388200 6002100 4845070 TRUE FALSE 6270841.395 5423545.151 4530254.145 4176385.462 4810305.998 5054356.914 4921988.485 5276931.787 5320766.771 4516909.093 1.388303653 1.200720457 1.002954465 0.924611361 1.064955238 1.118985751 1.089680661 1.168261676 1.177966317 1 22.10690445 4.57942644 3.159157473 1.077317047 1.391172135 0.632337824 0.075249795 0.20100818 3.358750124 0.020749422 0.123863578 37968.76232 -4.57942644 0.313855088 T(ph)QTPPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.812)QT(0.187)PPVS(0.009)PAPQPT(0.853)EERLPS(0.002)S(0.136)PVYEDAASFK 228.04 5.66E-35 193480000 332790 286290 222820 211670 229280 264980 216410 270750 303560 254850 TRUE FALSE 319784.1989 278125.2895 263088.5306 222594.3141 236654.9994 270338.0772 219058.4903 265158.9179 269101.1414 237588.7825 1.345956638 1.17061625 1.107327239 0.936888988 0.996069751 1.137840239 0.922006873 1.116041402 1.132634035 1 17.8581072 4.57964213 1.724066233 1.040296373 1.393777608 0.626159549 0.073768675 0.430031273 1.626005015 0.019489161 0.226037753 37987.62393 -4.57964213 0.353481235 LS(ph)SPVLHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.5)S(0.5)PVLHR;LS(0.671)S(0.329)PVLHR;LS(0.616)S(0.384)PVLHR 132.01 0.00063159 20559078000 1620732 1787112 1510321 1924995 1774172 1751836 1919264 1884827 1915480 2042361 TRUE FALSE 1557392.002 1736145.316 1783269.602 2024344.223 1831239.854 1787259.324 1942752.527 1845904.664 1698042.741 1904030.07 0.817945066 0.911826626 0.936576386 1.063189208 0.961770448 0.938671795 1.020337104 0.969472432 0.891815086 1 20.86062483 4.579961159 1.791593624 0.976528313 0.79559927 0.541796061 0.044569665 0.469510745 1.959957873 0.011605409 0.129352316 38015.53959 -4.579961159 -0.180929043 AGQHS(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGQHSPLR 8 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 AGQHS(1)PLR 76.682 0.036893 152640000 144980 165370 159020 183770 158690 134630 190450 180160 181740 196220 TRUE FALSE 139314.0213 160653.8095 187758.4514 193254.3917 163794.408 137352.3108 192780.7841 176439.633 161109.6371 182929.8446 0.761570763 0.878226349 1.026395948 1.056439927 0.895394671 0.750846922 1.053850915 0.964520762 0.880718165 1 17.48093094 4.579981848 3.53047387 0.952774234 0.763878961 0.306403864 0.088678497 0.319487602 6.670610134 0.022336491 0.121243439 38017.35057 -4.579981848 -0.188895273 VIDFDENTALDDAEEESFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIDFDENTALDDAEEESFR 19 0 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 357.39 1.08E-90 579030000 389777 471258 419352 538890 497540 535080 521200 501500 551150 593910 FALSE TRUE 374544.0839 457818.1832 495138.2348 566702.1775 513543.826 545899.6842 527578.6015 491143.8497 488585.7626 553683.9467 0.676458269 0.82685833 0.894261497 1.023512025 0.92750355 0.985940964 0.95285154 0.8870473 0.882427178 1 19.07870317 4.580344947 1.733072042 0.943801525 0.633792701 0.784332537 0.044470428 0.308594298 1.181489478 0.012348029 0.142779705 38049.14896 -4.580344947 -0.310008824 ETEELMAWMR ddPTM_BT-474_Pertuzumab_2h_R1 4 ETEELMAWMR 10 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;;; 189.7 2.28E-06 127250000 110171 150065 126444 233844 123984 118855 198960 183998 170485 157713 FALSE TRUE 105865.3955 145785.2931 149295.2435 245912.7169 127972.058 121258.3295 201394.932 180198.377 151132.2575 147030.958 0.720021123 0.991527873 1.015400059 1.672523393 0.870374917 0.824712912 1.369745084 1.225581193 1.027894122 1 17.16576043 4.580377683 2.027932823 1.150540889 0.677781561 0.212908788 0.237288912 0.775039537 4.454231136 0.06166582 0.599608146 38052.01705 -4.580377683 -0.472759328 EYVDLER ddPTM_BT-474_Pertuzumab_2h_R1 2 EYVDLER 7 0 Q13951-2;A0A494C0A9;Q13951 Q13951-2 CBFB Core-binding factor subunit beta 0 ; 91.9 0.037373 1338100000 2277220 2579560 2189170 2809040 2691010 2768160 2713800 2681250 2731120 3026220 FALSE TRUE 2188223.725 2505993.474 2584801.717 2954014.891 2777568.781 2824134.092 2747012.296 2625881.251 2421094.707 2821251.424 0.775621664 0.888255989 0.916189778 1.047058361 0.984516572 1.001021769 0.973685746 0.930750527 0.858163398 1 21.42790381 4.580407539 1.705878583 0.96690585 0.745979719 0.597515706 0.0486841 0.489395582 1.798462935 0.013589652 0.159794779 38054.63312 -4.580407539 -0.220926132 LIHEQEQQSSS(ph) ddPTM_BT-474_Pertuzumab_2h_R1 1 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.008)S(0.034)S(0.958) 102.52 0.0029969 445110000 125130 166770 149150 237880 160140 188750 190500 187790 183190 182410 TRUE FALSE 120239.7813 162013.8829 176104.7228 250157.0153 165291.0485 192566.6543 192831.396 183912.0709 162395.0392 170055.2082 0.707063209 0.952713443 1.035573827 1.47103413 0.971984629 1.132377281 1.133934079 1.081484494 0.954954811 1 17.37564367 4.580615042 2.14269763 1.110901496 0.669960832 0.430702581 0.13843785 0.425800747 2.817624524 0.03464849 0.316530854 38072.81965 -4.580615042 -0.440940663 TQS(ph)LSALPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQSLSALPK 9 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 TQS(1)LSALPK;TQS(0.996)LS(0.004)ALPK 178.95 5.28E-05 397440000 1478470 1192830 916880 770260 915270 699010 638570 1112270 780710 660970 TRUE FALSE 1420689.758 1158811.656 1082580.612 810013.2109 944710.4908 713144.4611 646385.0107 1089301.236 692087.0738 616201.9132 2.305558823 1.880571338 1.756860193 1.314525635 1.533118399 1.157322699 1.048982479 1.767766721 1.12314983 1 19.23304364 4.580642188 0.819537612 1.29815839 2.725096759 0.705198915 0.222448716 1.188908406 0.72152958 0.08137964 1.477135742 38075.1995 -4.580642188 1.426938369 up RPLSSS(ph)HEASEGQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.308)S(0.255)S(0.437)HEAS(0.001)EGQAK 174.02 5.74E-07 353000000 366290 281880 163630 213160 187870 165850 139140 422790 182900 152640 TRUE FALSE 351974.9818 273841.0584 193201.5809 224161.2131 193913.0092 169203.6006 140842.8369 414059.2388 162137.9588 142301.5568 2.473444351 1.924371486 1.357691266 1.575254819 1.362690707 1.189049539 0.989749094 2.909730912 1.139396943 1 17.11859192 4.580734051 2.925763502 1.549459326 2.49900846 0.252974144 0.533633687 0.497995711 7.027371148 0.140925824 0.909969949 38083.25416 -4.580734051 0.949549134 NLGSGS(ph)PKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 NLGSGSPKPR 10 1 A0A1C7CYX9 A0A1C7CYX9 1 NLGS(0.002)GS(0.998)PKPR 113.69 0.00088066 381290000 511530 444970 341920 357820 349740 344600 336650 401480 514470 411420 TRUE FALSE 491538.8421 432279.8913 403712.55 376287.1331 360989.7047 351568.0481 340770.0234 393189.2977 456069.5224 383554.1569 1.281536996 1.12703743 1.052556836 0.981053461 0.941170101 0.916606017 0.888453475 1.025120679 1.189061608 1 18.54907077 4.580908877 1.376159186 0.984212565 1.351902118 0.572867937 0.07775579 0.697789042 1.47746498 0.022867689 0.329194376 38098.58775 -4.580908877 0.367689553 SPLVAAMQHFLPVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPLVAAMQHFLPVLK 15 0 O95373;E9PLB2 O95373 IPO7 Importin-7 0 ; 92.063 0.0053871 150306000 153781 179203 149822 195971 187281 192859 195700 183340 218628 222251 FALSE TRUE 147771.0685 174092.3059 176898.1682 206085.0868 193305.0634 196758.7411 198095.0351 179553.9649 193810.266 207197.7418 0.713188605 0.840222989 0.853764943 0.994629985 0.932949663 0.949618173 0.956067539 0.866582634 0.935387926 1 17.66064875 4.581326891 1.319497661 0.936879451 0.661395114 0.762434585 0.040323794 0.507382612 0.965496651 0.011691285 0.174193566 38135.27572 -4.581326891 -0.275484337 AKS(ph)LDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 AKSLDRR 7 2 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AKS(1)LDRR;AKS(1)LDRR;AKS(1)LDRR;AKS(1)LDRR 85.29 0.016475 1338540000 4101900 3284210 2009710 2362740 2565230 2447720 2341980 4048300 2636480 1997770 TRUE FALSE 3941593.213 3190547.546 2372909.303 2484681.295 2647742.953 2497214.575 2370641.852 3964701.19 2337197.843 1862459.258 2.116337952 1.713083136 1.274073133 1.334086254 1.421638052 1.340815679 1.272855683 2.128745191 1.254898776 1 20.82877744 4.58181484 3.143875885 1.447598814 2.124623778 0.384928849 0.281709249 0.332901439 5.488079987 0.073446682 0.443084926 38178.14648 -4.58181484 0.677024964 LGHPEALSAGTGS(ph)PQPPSFTYAQQR ddPTM_BT-474_Pertuzumab_2h_R1 5 LGHPEALSAGTGSPQPPSFTYAQQR 25 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 LGHPEALSAGT(0.046)GS(0.954)PQPPSFTYAQQR;LGHPEALSAGTGS(1)PQPPSFTYAQQR;LGHPEALSAGT(0.001)GS(0.999)PQPPSFTYAQQR;LGHPEALSAGT(0.001)GS(0.999)PQPPSFTYAQQR;LGHPEALSAGT(0.001)GS(0.999)PQPPSFTYAQQR 327.42 5.97E-88 6734280000 501190 571987 540467 548339 543456 644538 650790 563624 640927 737875 TRUE FALSE 481602.9407 555674.4908 638141.4095 576638.8415 560936.7558 657571 658754.5627 551984.9674 568171.6539 687898.069 0.700107999 0.807786089 0.927668558 0.838262044 0.815435863 0.955913426 0.957633976 0.802422615 0.825953262 1 19.39183528 4.581975068 3.037559336 0.880653081 0.696333738 0.439989544 0.066107624 0.28419051 4.350336189 0.016356278 0.10205784 38192.23447 -4.581975068 -0.184319343 GILHLS(ph)PDVYQEMEASR ddPTM_BT-474_Pertuzumab_2h_R1 7 GILHLSPDVYQEMEASR 17 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0;E5RJN7;E5RJ67 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 GILHLS(1)PDVYQEMEASR;GILHLS(1)PDVYQEMEASR;GILHLS(1)PDVYQEMEASR;GILHLS(0.917)PDVY(0.006)QEMEAS(0.076)R;GILHLS(1)PDVYQEMEASR;GILHLS(1)PDVYQEMEASR;GILHLS(1)PDVYQEMEASR 279.15 4.74E-36 914454000 561673 696181 681177 812004 746782 883604 769082 666284 713754 811705 TRUE FALSE 539722.1982 676326.5995 804280.8366 853911.6238 770802.9212 901471.0783 778494.2556 652525.0026 632731.6382 756727.4974 0.71323191 0.893751848 1.062840771 1.128426847 1.018600386 1.191275699 1.028764328 0.862298522 0.836141994 1 19.52941434 4.582633904 2.906727106 1.013535478 0.704562958 0.458954527 0.101531783 0.312473549 4.335159264 0.028426476 0.185776998 38250.21703 -4.582633904 -0.30897252 ELLTTMGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 ELLTTMGDR 9 0 J3QRS3;P19105;O14950;P24844-2;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;;;;; 208.72 2.23E-05 2914780000 1539310 1709980 1470700 1841080 1731850 1695620 1847000 1809450 1865490 1880960 FALSE TRUE 1479152.063 1661213.045 1736488.206 1936098.359 1787556.528 1729906.598 1869604.139 1772084.225 1653727.396 1753560.904 0.843513368 0.947336954 0.990263983 1.104095304 1.019386623 0.986510702 1.066175765 1.010563261 0.943068126 1 20.74185611 4.582814647 1.928859476 1.020612512 0.821028154 0.62144731 0.041587778 0.35380742 1.780730161 0.010842376 0.112537894 38266.13923 -4.582814647 -0.199584359 ARS(ph)VS(ph)PPPKR ddPTM_BT-474_Pertuzumab_2h_R1 3 ARSVSPPPKR 10 2 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 ARS(1)VS(1)PPPKR;ARS(1)VS(1)PPPKR;ARS(1)VS(1)PPPKR 78.814 0.015486 7826700000 161873 166488 142774 155248 158213 166182 160348 173876 187635 172692 TRUE FALSE 155546.8242 161739.9252 168576.4378 163260.3679 163302.0648 169542.3139 162310.3868 170285.3998 166335.4614 160995.417 0.966156845 1.004624406 1.047088426 1.014068418 1.014327413 1.053087827 1.008167747 1.057703399 1.033168922 1 17.29666009 4.5828478 3.007672353 1.030666527 0.96463028 0.502997848 0.018872186 0.218135355 3.264188864 0.004435169 0.028012715 38269.06041 -4.5828478 -0.066036247 QVGFLSLQDDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QVGFLSLQDDPK 12 0 A0A087X1N7;P20929-4;P20929;P20929-3;P20929-2 A0A087X1N7 NEB Nebulin 0 54.7 0.076691 227860000 462700 572600 529110 667130 555950 595430 672640 658600 665210 835140 FALSE TRUE 444617.1725 556270.0086 624731.947 701560.6592 573832.6367 607470.0026 680871.9695 644999.6798 589698.1496 778575.2239 0.571065144 0.714471758 0.802404094 0.901082693 0.737029151 0.780232897 0.874510193 0.828435917 0.757406775 1 19.57047691 4.582857206 1.855835019 0.829702583 0.532997101 0.569143737 0.072610933 0.417489244 1.901417135 0.017812573 0.19301352 38269.88929 -4.582857206 -0.296705482 GPQES(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPQESPQK 8 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 GPQES(1)PQK 92.866 0.010848 0 171170 141840 100650 97325 114270 96063 128770 128520 149930 143570 TRUE FALSE 164480.4872 137794.8621 118839.6939 102347.9549 117945.5983 98005.45968 130345.9258 125866.0171 132910.575 133845.876 1.228879754 1.02950398 0.887884614 0.764670216 0.881204575 0.732226219 0.973850892 0.940380241 0.993012104 1 17.03021316 4.582886671 2.391578935 0.890479932 1.253990421 0.589181595 0.085753959 0.281969112 2.45601172 0.022537703 0.182773076 38272.48581 -4.582886671 0.36351049 KS(ph)PHKDLGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSPHKDLGHR 10 2 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 KS(1)PHKDLGHR 108.59 0.0010117 67668000 51410 44428 32973 25216 37299 34744 26937 9955.4 43098 33952 TRUE FALSE 49400.84036 43160.95694 38931.95458 26517.40078 38498.75621 35446.54748 27266.66306 9749.817511 38205.69572 31652.4008 1.560729648 1.363591887 1.229984254 0.837769019 1.21629814 1.11986916 0.861440598 0.308027741 1.207039427 1 14.95002731 4.584069681 0.466921845 0.776150599 2.033454716 0.405760223 0.253122878 3.900109828 0.734703194 0.187100058 2.681902712 38376.88145 -4.584069681 1.257304117 EFEKDKDDDEVFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFEKDKDDDEVFEK 14 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 135.45 1.85E-05 381890000 450810 358920 268470 171480 302360 302380 248580 354830 399290 305420 FALSE TRUE 433191.8468 348683.953 316988.5011 180330.1034 312085.684 308494.3308 251622.1964 347502.6365 353964.2732 284733.6314 1.521393327 1.224597008 1.113280857 0.633329131 1.096061897 1.083448869 0.883710839 1.22044816 1.243141779 1 18.11925338 4.584252875 2.167414923 1.033639676 1.566720646 0.456028522 0.165427885 0.44218751 2.998478143 0.043914438 0.400956228 38393.07303 -4.584252875 0.53308097 GNEFFCEVDEDYIQDKFNLTGLNEQVPHYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNEFFCEVDEDYIQDKFNLTGLNEQVPHYR 30 1 P67870;Q5SRQ3;Q5SRQ6;N0E472;A0A0G2JM12;N0E644;A0A0G2JM58 P67870 CSNK2B;CSNK2B-LY6G5B-1181;CSNK2B-LY6G5B--991;CSNK2B-LY6G5B-562 Casein kinase II subunit beta 0 330.67 1.52E-105 422790000 358680 316290 220870 288410 269680 239050 326750 266580 325400 332260 FALSE TRUE 344662.3891 307269.7189 260786.1222 303294.8747 278354.5021 243883.7548 330748.8642 261075.0298 288461.9562 309755.7343 1.112690908 0.991974272 0.841908941 0.979142082 0.898625825 0.787342179 1.067773176 0.842841636 0.931256226 1 18.24077146 4.58431646 3.341974267 0.913884524 1.113148198 0.358164129 0.079248357 0.258320849 4.812485563 0.017930833 0.102874978 38398.69457 -4.58431646 0.199263674 SS(ph)KASLGS(ph)LEGEAEAEASSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.349)S(0.401)KAS(0.34)LGS(0.91)LEGEAEAEASSPK 83.834 0.0017841 423580000 433760 329860 226330 166280 178000 243420 238600 362540 342790 256260 TRUE FALSE 416808.1797 320452.7158 267232.8657 174861.7307 183725.5317 248342.1192 241520.0582 355053.4223 303877.9163 238903.2819 1.74467331 1.341349157 1.118581811 0.731935239 0.769037286 1.039509031 1.010953287 1.486180597 1.271970455 1 17.86606715 4.58477125 2.248383537 1.068512443 1.804388331 0.518560841 0.207353913 0.431460008 3.209851856 0.062798986 0.550503248 38438.92646 -4.58477125 0.735875888 S(ph)RGQNRPTNVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRGQNRPTNVK 11 2 Q9BX40;Q9BX40-2;Q5TBQ1;Q5TBQ0;Q5TBP9;Q9BX40-3 Q9BX40 LSM14B Protein LSM14 homolog B 1 S(1)RGQNRPTNVK;S(1)RGQNRPTNVK;S(1)RGQNRPTNVK 111.12 0.0013415 580470000 341453 275677 192713 193063 196692 179063 182440 345781 234413 186599 TRUE FALSE 328108.6393 267814.9619 227540.526 203027.0046 203018.7768 182683.7765 184672.7553 338640.5015 207803.419 173960.4835 1.886110182 1.539516081 1.308001227 1.167086918 1.167039621 1.050145256 1.061578765 1.946651875 1.194543811 1 17.4084001 4.584923136 2.105661825 1.282810127 1.953028529 0.380518221 0.256803766 0.620314949 3.902715812 0.073638226 0.696825477 38452.37209 -4.584923136 0.670218402 SS(ph)SVPHPFQVTLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 S(0.158)S(0.725)S(0.117)VPHPFQVTLLR;S(0.016)S(0.972)S(0.012)VPHPFQVTLLR 213.99 2.75E-10 467710000 573960 425060 245360 303600 341410 300470 215520 426190 300250 258890 TRUE FALSE 551529.0087 412937.705 289702.01 319268.8324 352391.7627 306545.7093 218157.5982 417389.0276 266166.8788 241355.1497 2.285134621 1.710913173 1.200314186 1.322817569 1.460054874 1.270102211 0.903886238 1.729356213 1.102801739 1 17.88079808 4.585428788 2.402594125 1.289424588 2.364196774 0.670830532 0.225831635 0.234899675 2.062978008 0.055575927 0.452181262 38497.16854 -4.585428788 1.074772186 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR 32 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;; 376.96 1.33E-148 4602840000 1207060 1845130 1768250 2570400 1853090 2102410 2476210 2199700 2266320 2975480 FALSE TRUE 1159886.761 1792508.699 2087812.11 2703058.652 1912696.323 2144922.171 2506514.599 2154275.426 2009056.855 2773948.089 0.418135712 0.646194031 0.752650029 0.97444457 0.689521311 0.773238035 0.903591025 0.776609856 0.724258995 1 21.40350936 4.585763353 1.792789316 0.820004284 0.355748556 0.632175191 0.097874408 0.392257239 1.626833518 0.024496953 0.278457157 38526.83682 -4.585763353 -0.464255728 KPPPSPQPTEEDPEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 KPPPSPQPTEEDPEHR 16 1 Q13438-4;Q13438 Q13438-4 OS9 Protein OS-9 0 ;;; 163.51 5.00E-09 593110000 651901 755585 639524 867984 688486 824495 856445 750577 935273 942040 FALSE TRUE 626423.9882 734036.4556 755100.2129 912780.7583 710631.7775 841166.8538 866926.4301 735077.3227 829104.73 878234.7917 0.713276215 0.8358089 0.859793099 1.039335684 0.809159218 0.957792679 0.98712376 0.836994081 0.94405817 1 19.74424716 4.585904312 1.556556713 0.925469658 0.672970907 0.499298952 0.068998667 0.666272193 1.918492786 0.017914589 0.23519721 38539.3435 -4.585904312 -0.252498752 ICRDPQT(ph)PVLQTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ICRDPQTPVLQTK 13 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 ICRDPQT(1)PVLQTK 103.5 0.0025958 763260000 1459600 861700 376990 268480 313530 184150 116890 1163500 147840 71096 TRUE FALSE 1402557.218 837125.1597 445120.4791 282336.285 323614.9772 187873.6392 118320.5348 1139473.318 131057.823 66280.60459 21.16089959 12.63001695 6.715697327 4.259711973 4.882498872 2.834519092 1.785145677 17.19165547 1.977317856 1 16.01629914 4.586199804 1.943003791 5.878279474 23.26354395 0.563512658 4.44164158 0.46256084 2.361248746 1.238252303 12.90108646 38565.57435 -4.586199804 17.38526448 AQES(ph)HESMESYELNPFINRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQESHESMESYELNPFINRR 20 1 P08493-2 P08493-2 1 AQES(0.966)HES(0.017)MES(0.017)YELNPFINRR 48.182 0.059445 807340000 68005 70825 58202 90081 61156 86529 80075 92427 87046 91358 TRUE FALSE 65347.28942 68805.14034 68720.3961 94730.09121 63123.13828 88278.67567 81054.9818 90518.35015 77164.90301 85170.24129 0.767254952 0.807854238 0.806859239 1.112244016 0.741140771 1.036496719 0.951681956 1.062793163 0.906007801 1 16.37806182 4.586465356 0.530210774 0.996143032 0.610276344 0.351830456 0.101585601 3.756766317 0.907567481 0.056059582 0.88413695 38589.16277 -4.586465356 -0.385866688 DIEIIHEELQLKDEEMIGPIIDKLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIEIIHEELQLKDEEMIGPIIDKLEK 26 2 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 122.04 8.34E-05 86856000 113100 100580 76233 75583 102530 97364 79323 83760 119980 91109 FALSE TRUE 108679.927 97711.55688 90009.99889 79483.84769 105827.9706 99332.76679 80293.7786 82030.32673 106360.3734 84938.10628 1.279519072 1.150385394 1.059712805 0.935785493 1.245942195 1.16947235 0.945321036 0.965765901 1.252210322 1 16.37412432 4.586472946 2.496513499 1.063864682 1.293633684 0.245158815 0.111463178 0.538215542 5.190213922 0.028869014 0.225550604 38589.83715 -4.586472946 0.229769002 DQVNLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 DQVNLSPK 8 0 Q5FBB7-6;Q5FBB7 Q5FBB7-6 SGOL1 Shugoshin-like 1 1 DQVNLS(1)PK;DQVNLS(1)PK;DQVNLS(1)PK;DQVNLS(1)PK 174.87 0.00028261 1217780000 3511140 2959960 2118930 2259530 2491180 2062410 2524500 3213300 2397420 2401200 TRUE FALSE 3373920.767 2875544.839 2501867.786 2376144.614 2571311.067 2104113.343 2555395.586 3146944.232 2125274.932 2238564.585 1.507180445 1.284548526 1.117621445 1.061459039 1.148642788 0.939938636 1.141533107 1.40578666 0.949391832 1 21.09414251 4.5870263 2.233812305 1.121847572 1.544880486 0.498087938 0.128037711 0.427438492 3.118611654 0.035170031 0.313088338 38639.03755 -4.5870263 0.423032914 LYDLNHNEIGELIR ddPTM_BT-474_Pertuzumab_2h_R1 5 LYDLNHNEIGELIR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;; 232.17 2.66E-13 2644173000 918494 1017269 913903 1054832 1065061 1082538 998084 1050274 1123828 1112329 FALSE TRUE 882598.239 988257.4841 1079065.602 1109272.006 1099319.654 1104427.66 1010298.851 1028585.475 996255.7569 1036989.966 0.851115505 0.953005831 1.040574776 1.069703702 1.060106356 1.065032157 0.97426097 0.991895301 0.960718801 1 19.9839705 4.587682927 2.724702389 1.020494849 0.843166856 0.666674056 0.036914046 0.22045518 2.619917971 0.010404076 0.073956356 38697.50158 -4.587682927 -0.177327992 FWEVISDEHGIDPSGNYVGDSDLQLER ddPTM_BT-474_Pertuzumab_2h_R1 8 FWEVISDEHGIDPSGNYVGDSDLQLER 27 0 Q13509;G3V5W4;G3V2R8;G3V3R4;G3V2N6;G3V3J6;G3V3W7 Q13509 TUBB3 Tubulin beta-3 chain 0 ;;;;;;; 336.05 2.03E-95 14904901000 2772356 3200213 2673836 3561382 3393260 3490401 3471429 3287313 3332496 3472312 FALSE TRUE 2664009.263 3108946.059 3157057.644 3745185.352 3502407.29 3560979.3 3513913.387 3219428.838 2954205.025 3237129.215 0.822954255 0.960402212 0.975264636 1.156946511 1.081948559 1.100042372 1.085502973 0.994532076 0.912600279 1 21.62628352 4.587780118 1.659550158 1.048093432 0.786228285 0.504665873 0.066413921 0.609282903 2.063525863 0.018757951 0.232776545 38706.16275 -4.587780118 -0.261865147 HLEEEKER ddPTM_BT-474_Pertuzumab_2h_R1 2 HLEEEKER 8 1 Q9H6F5;Q9H6F5-2 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 0 ; 120.99 0.00087272 151693000 364460 313590 220756 259710 263790 299120 289220 214607 350170 340790 FALSE TRUE 350216.5003 304646.7202 260651.5199 273113.6642 272275.0449 305168.4113 292759.5609 210175.2905 310420.1696 317707.9898 1.10232198 0.958889074 0.820412229 0.859637381 0.856997789 0.96053112 0.921473713 0.661536056 0.977061263 1 18.27734185 4.587845244 2.817860134 0.86311656 1.112040935 0.322795349 0.093730515 0.34262527 4.402056548 0.02382361 0.16333299 38711.96749 -4.587845244 0.248924374 NNPHYDPSSKEDNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 NNPHYDPSSKEDNPK 15 1 Q9P016-2;Q9P016 Q9P016-2 THYN1 Thymocyte nuclear protein 1 0 ; 141.85 2.82E-06 215532000 545970 454580 335500 289730 375080 403700 364010 429830 486340 385350 FALSE TRUE 524632.8888 441615.8235 396132.3132 304683 387144.7888 411863.0906 368464.8633 420953.8603 431132.7221 359249.9013 1.46035639 1.229271941 1.102665058 0.848108793 1.077647586 1.146452899 1.025650562 1.171757762 1.200091414 1 18.45462823 4.58786474 2.272641327 1.075376402 1.494229683 0.617549288 0.09510751 0.304842986 2.32098671 0.025501458 0.223162646 38713.70534 -4.58786474 0.418853281 DQYSVIFESGDR ddPTM_BT-474_Pertuzumab_2h_R1 5 DQYSVIFESGDR 12 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;; 298.78 5.02E-36 4105830000 1985500 2198500 1865510 2273890 2242510 2396150 2352880 2373690 2451180 2627820 FALSE TRUE 1907904.465 2135800.933 2202649.155 2391245.735 2314642.371 2444601.795 2381675.249 2324672.472 2172932.323 2449835.411 0.778788835 0.871814051 0.899100872 0.97608424 0.94481546 0.997863687 0.972177657 0.948909654 0.886970738 1 21.2242534 4.588542882 1.161867055 0.960241203 0.725380038 0.763004928 0.031918133 0.577880665 0.793610633 0.009333854 0.154835166 38774.20322 -4.588542882 -0.234861165 ELLLTGPGLEER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLLTGPGLEER 12 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 212.82 3.69E-08 93755000 115419 130748 116141 138288 133149 141534 134543 153598 150234 147789 FALSE TRUE 110908.2979 127019.1951 137130.2622 145425.0603 137431.8585 144395.9145 136189.5775 150426.1476 133180.0662 137779.1194 0.804971743 0.921904535 0.995290599 1.055494192 0.997479583 1.048024658 0.988463115 1.091792053 0.9666201 1 17.07199774 4.58858051 1.582767396 1.027531826 0.759155026 0.782877418 0.035343796 0.307511047 0.920779145 0.008959183 0.116827058 38777.56282 -4.58858051 -0.2683768 IQLTFEATLQQLEAPYNSDTVLVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQLTFEATLQQLEAPYNSDTVLVHR 25 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ; 213.05 5.44E-26 403100000 210035 251222 220956 281174 274790 272100 283000 274140 300110 259350 FALSE TRUE 201826.6 244057.3945 260887.6643 295685.4238 283628.8699 277602.0484 286463.4387 268478.9132 266042.771 241783.9935 0.834739294 1.009402612 1.079011313 1.22293217 1.17306719 1.14814072 1.184790749 1.110408135 1.100332438 1 17.88335921 4.58883227 1.681968209 1.141429378 0.781190452 0.70930293 0.058368386 0.345368256 1.209103658 0.01490984 0.183189582 38800.04868 -4.58883227 -0.360238925 IQRPNTTQEGEEMETDMDVADVAMESS(ph)PGSSISMEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 1 IQRPNTTQEGEEMETDMDVADVAMES(0.046)S(0.954)PGSSISMEHR;IQRPNTTQEGEEMETDMDVADVAMES(0.293)S(0.707)PGSSISMEHR;IQRPNTTQEGEEMETDMDVADVAMES(0.043)S(0.957)PGSSISMEHR;IQRPNTTQEGEEMETDMDVADVAMES(0.196)S(0.804)PGSSISMEHR 295.95 2.21E-92 1962550000 473155 558629 513641 599306 574469 730976 587502 495084 690149 724819 TRUE FALSE 454663.5795 542697.4479 606467.3546 630236.2545 592947.3171 745756.8356 594692.0252 484860.3424 611806.1789 675726.3635 0.672851622 0.803131973 0.897504356 0.932679689 0.877496201 1.103637324 0.880078176 0.717539478 0.905405223 1 19.36607962 4.588944564 2.147309884 0.899496453 0.647840081 0.39235812 0.093330343 0.58277846 3.834419989 0.026556816 0.24918806 38810.08231 -4.588944564 -0.251656372 SCNITECQDPDLLHNWPDAFTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCNITECQDPDLLHNWPDAFTLR 23 0 Q6ZN28 Q6ZN28 MACC1 Metastasis-associated in colon cancer protein 1 0 106.43 0.0014437 62481000 17897 21909 17402 25614 22009 23038 22485 24491 27750 25275 FALSE TRUE 17197.56545 21284.17677 20546.92851 26935.94161 22716.93947 23503.84414 22760.17816 23985.25229 24599.93634 23563.10174 0.729851513 0.903284169 0.871995917 1.143140742 0.964089521 0.997485153 0.965924538 1.017915746 1.044002467 1 14.52424184 4.589659022 1.273263729 1.011122183 0.664295797 0.679820342 0.05956053 0.60395539 1.039379066 0.016272877 0.255509335 38873.98131 -4.589659022 -0.346826386 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 HIKEEPLSEEEPCTSTAIASPEKK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCT(0.002)S(0.002)T(0.002)AIAS(0.994)PEKK 141.69 1.47E-07 542770000 665950 503780 335710 309620 357500 354680 374730 371930 479240 422100 TRUE FALSE 639923.9378 489412.6877 396380.2648 325599.5253 368999.3122 361851.8726 379316.0578 364249.5155 424838.6843 393510.791 1.626191587 1.243708429 1.007291982 0.827422101 0.937710783 0.919547522 0.96392797 0.925640475 1.079611269 1 18.58604367 4.589742295 1.859042177 0.9435188 1.730179359 0.919627071 0.061895876 0.145253998 0.658035608 0.016157155 0.179061572 38881.43588 -4.589742295 0.786660559 RPS(ph)ADSESPGTPSPDGAAWEPPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSADSESPGTPSPDGAAWEPPAR 24 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 RPS(0.993)ADS(0.003)ES(0.004)PGTPSPDGAAWEPPAR;RPS(0.933)ADS(0.048)ES(0.019)PGTPSPDGAAWEPPAR 211.02 2.15E-25 879110000 120212 141650 108282 156876 160225 145338 138534 149630 148880 130093 TRUE FALSE 115513.9821 137610.2807 127850.9661 164972.3892 165378.7826 148276.8339 140229.4205 146540.0882 131979.7666 121281.6852 0.952443742 1.134633646 1.054165482 1.360241564 1.363592387 1.222582236 1.156229156 1.208262302 1.088208548 1 16.88800218 4.590014713 1.470453167 1.206618573 0.912117626 0.26868703 0.112521721 1.092021444 2.702527502 0.030930375 0.433799044 38905.83251 -4.590014713 -0.294500947 HRS(ph)PTPK ddPTM_BT-474_Pertuzumab_2h_R1 5 HRSPTPK 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HRS(0.99)PT(0.01)PK;HRS(0.821)PT(0.179)PK;HRS(0.855)PT(0.145)PK;HRS(0.998)PT(0.002)PK;HRS(0.776)PT(0.224)PK 85.764 0.012458 1693400000 1233960 1663680 1699500 1738560 1810730 2297980 2357170 748302 2794810 2909170 TRUE FALSE 1185735.479 1616233.475 2006637.455 1828287.29 1868973.775 2344446.73 2386017.752 732849.3022 2477554.886 2712129.325 0.437197249 0.595927879 0.739875284 0.674115085 0.689116761 0.864430287 0.879758104 0.270211784 0.913509125 1 21.37099454 4.591021849 2.404147484 0.7107355 0.414223717 0.188401406 0.193537374 0.776519343 6.782797365 0.050039487 0.414629306 38996.16052 -4.591021849 -0.296511783 QKFNDS(ph)EGDDT(ph)EETEDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKFNDSEGDDTEETEDYR 18 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 2 QKFNDS(1)EGDDT(1)EETEDYR;QKFNDS(1)EGDDT(1)EETEDYR 187.51 9.75E-14 446130000 917570 821200 659410 629540 732240 774160 630970 794950 903400 844280 TRUE FALSE 881710.35 797780.18 778580.0555 662030.6348 755793.1646 789814.0456 638691.9996 778534.0047 800849.8194 787096.1636 1.120206642 1.013573966 0.989180346 0.841105148 0.960229766 1.00345305 0.81145358 0.989121839 1.01747392 1 19.58618038 4.591041901 1.78676351 0.943220583 1.146865832 0.382209588 0.066277584 0.637971828 2.603152031 0.017114508 0.198930274 38997.96101 -4.591041901 0.203645249 TTDGVYEGVAIGGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTDGVYEGVAIGGDR 15 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 116.24 0.0010805 111200000 70917 83141 76767 88563 90381 77563 94499 88417 93442 103620 FALSE TRUE 68145.48524 80769.90008 90640.50457 93133.74704 93288.18695 79131.377 95655.50703 86591.15805 82834.8559 96601.7251 0.705427208 0.836112399 0.938290745 0.964100247 0.965698975 0.819150765 0.990204957 0.896372792 0.857488371 1 16.55976133 4.591559581 2.441504144 0.925555414 0.688440483 0.614267626 0.054940187 0.251889814 2.284715466 0.013291561 0.108376803 39044.47439 -4.591559581 -0.237114931 ILDLGITGPEGHVLSRPEEVEAEAVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILDLGITGPEGHVLSRPEEVEAEAVNR 27 1 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 149.04 6.84E-08 397170000 4367.1 6017.8 6108.8 7064.1 9626.9 4613.1 5192.8 7366.3 7975.5 7269.7 FALSE TRUE 4196.428904 5846.178236 7212.79605 7428.679048 9936.557981 4706.380043 5256.35104 7214.183331 7070.154676 6777.316744 0.619187366 0.862609563 1.064255416 1.096109172 1.466149268 0.694431177 0.775579959 1.064460111 1.043208536 1 12.72649848 4.591582666 2.64977911 1.022590737 0.596489916 0.294853914 0.194130888 0.469391064 5.19787688 0.050630242 0.375842964 39046.54985 -4.591582666 -0.426100821 LRLSPS(ph)PT(ph)SQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 LRLS(0.334)PS(0.67)PT(0.737)S(0.259)QR 121.18 0.010456 5299800000 1277100 1446300 1411200 1484900 1403700 1599900 1479400 1449300 1556800 1639400 TRUE FALSE 1227189.52 1405052.94 1666235.232 1561535.867 1448851.285 1632251.074 1497505.34 1419371.449 1380078.591 1528361.978 0.802944288 0.919319481 1.090209817 1.021705518 0.947976531 1.067974144 0.979810648 0.928688013 0.902978882 1 20.54355484 4.591683765 3.772434556 0.989011393 0.80608746 0.518413119 0.055833458 0.201466891 4.650199863 0.014359029 0.075593634 39055.64055 -4.591683765 -0.182923933 RMDEISDHAK ddPTM_BT-474_Pertuzumab_2h_R1 3 RMDEISDHAK 10 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;; 119.03 0.00048474 1186840000 1194170 1281590 1168890 1207300 1245230 1361990 1377250 1215540 1352320 1489760 FALSE TRUE 1147500.516 1245040.308 1380134.425 1269608.898 1285283.954 1389530.371 1394105.197 1190438.674 1198810.303 1388857.228 0.826219206 0.896449457 0.993719438 0.914139245 0.925425542 1.000484674 1.003778624 0.857135384 0.863163095 1 20.40546687 4.591981292 3.624814212 0.939064585 0.827236272 0.317211416 0.053089116 0.323922459 6.965214764 0.013611688 0.074000687 39082.40602 -4.591981292 -0.111828314 NLS(ph)PGAVESDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLSPGAVESDVR 12 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 NLS(1)PGAVESDVR;NLS(1)PGAVESDVR 163.23 6.35E-05 1116670000 437870 515720 488530 505590 581920 578100 512100 538950 610510 640510 TRUE FALSE 420757.5563 501012.1705 576818.2383 531683.5605 600637.9853 589789.5781 518367.233 527820.4942 541207.4643 597127.6872 0.704635818 0.839036912 0.965988097 0.890401788 1.005878639 0.987710988 0.868101152 0.883932374 0.906351315 1 19.18767994 4.592106525 2.64041113 0.930633687 0.691074819 0.686382193 0.048910577 0.214445836 2.353219381 0.012919429 0.096451167 39093.67739 -4.592106525 -0.239558867 DQWEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DQWEDR 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 206.65 0.00025305 5260310000 5198300 5386000 4575900 5640200 4819500 5406800 5228600 5673700 5382100 5744600 FALSE TRUE 4995144.689 5232396.553 5402866.92 5931291.398 4974523.594 5516129.2 5292589.171 5556536.112 4771146.572 5355513.125 0.932710755 0.977011246 1.008842065 1.107511318 0.928860312 1.029990791 0.988250621 1.03753571 0.890885049 1 22.35259338 4.592177977 2.910336365 1.003664877 0.930468354 0.110406523 0.055909529 0.61637196 8.480690937 0.013083627 0.087746039 39100.10984 -4.592177977 -0.073196523 ELDFWQEGWR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELDFWQEGWR 10 0 Q5JRX3-3;Q5JRX3;Q5JRX3-2 Q5JRX3-3 PITRM1 "Presequence protease, mitochondrial" 0 ;;; 142 8.50E-05 288576000 249242 351612 269209 521412 264146 294160 498699 484629 353496 369145 FALSE TRUE 239501.3471 341584.37 317861.0548 548322.1358 272642.496 300108.1167 504802.2275 474621.2418 313368.6161 344142.4803 0.695936598 0.992566712 0.923632138 1.593299773 0.792237261 0.872046126 1.466840789 1.37914169 0.91057813 1 18.39264646 4.592319543 1.420836284 1.165348711 0.60030009 0.190771293 0.260774326 1.446136586 3.269036007 0.074052349 1.077946996 39112.85725 -4.592319543 -0.565048621 DYAVSTVPVADGLHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYAVSTVPVADGLHLK 16 0 O94760;B4DYP1;O94760-2 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ; 203.04 2.88E-11 389380000 266691 289530 255478 296430 282700 276240 281939 305850 350580 331240 FALSE TRUE 256268.4209 281272.8879 301648.5577 311728.7878 291793.3022 281825.7621 285389.4538 299534.0906 310783.6282 308804.8198 0.82987183 0.910843581 0.976825938 1.009468661 0.944911749 0.912633949 0.924174221 0.969978677 1.006407958 1 18.23633574 4.592738448 2.664635937 0.963504178 0.822447712 0.6419655 0.031869665 0.237101931 2.657279189 0.008517493 0.063061023 39150.60236 -4.592738448 -0.141056466 DISSALR ddPTM_BT-474_Pertuzumab_2h_R1 1 DISSALR 7 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9 P13489 RNH1 Ribonuclease inhibitor 0 80.462 0.094441 0 147870 165870 158220 182600 139730 155700 173160 181540 188890 194770 FALSE TRUE 142091.0769 161139.55 186813.8736 192024.0079 144224.5423 158848.3607 175279.1839 177791.1356 167447.9991 181578.0544 0.782534417 0.887439567 1.028835088 1.057528722 0.794283994 0.874821361 0.965310397 0.979144402 0.922181921 1 17.47023032 4.59285501 3.661465285 0.950035541 0.78436828 0.34029449 0.072497315 0.294817357 6.446811252 0.018517316 0.100005202 39161.11151 -4.59285501 -0.165667261 ILHTLLASGEDALDFTQESEPSYISDVGPPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 ILHTLLASGEDALDFTQESEPSYISDVGPPGR 32 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BM93;H3BMX0;H3BP95 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ;; 316.46 3.31E-104 461208000 67271 78982.4 71934.6 85379.3 84359.9 84396.2 92384.5 76508.9 89335.7 96740.1 FALSE TRUE 64641.97495 76729.89928 84934.7824 89785.7359 87073.4128 86102.74899 93515.12915 74928.96448 79194.68586 90187.80686 0.716748496 0.850779079 0.941754605 0.995541848 0.965467682 0.954704987 1.036893261 0.830810362 0.878108567 1 16.46064478 4.59296763 2.189819469 0.945566939 0.692349204 0.622242474 0.05674602 0.333137338 2.292161056 0.015616824 0.14529136 39171.268 -4.59296763 -0.253217736 GMTENEVEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 GMTENEVEDR 10 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 160.75 1.69E-05 177750000 154770 164320 141360 170080 152230 172070 174660 165110 159260 184260 FALSE TRUE 148721.4173 159633.7545 166906.8965 178857.8492 157126.6162 175549.3733 176797.5413 161700.4208 141181.4725 171779.9061 0.865767252 0.929292361 0.971632249 1.041203557 0.9146973 1.021943586 1.029209675 0.941323258 0.821874198 1 17.39020176 4.593193095 2.544423985 0.969804383 0.859025473 0.20490602 0.061688153 0.590904652 5.921189176 0.015501209 0.121158959 39191.6091 -4.593193095 -0.11077891 IILTECAPNPPS(ph)PPEAR ddPTM_BT-474_Pertuzumab_2h_R1 5 IILTECAPNPPSPPEAR 17 0 A0A087WTE6 A0A087WTE6 SRCIN1 1 IILTECAPNPPS(1)PPEAR;IILTECAPNPPS(1)PPEAR;IILTECAPNPPS(1)PPEAR;IILTECAPNPPS(1)PPEAR;IILTECAPNPPS(1)PPEAR 316.9 2.64E-58 1657668000 846701 1004921 875912 1109285 1077318 1166839 1122470 1158612 1174054 1329122 TRUE FALSE 813610.9888 976261.637 1034208.783 1166535.332 1111970.912 1190433.284 1136207.124 1134686.257 1040780.312 1239099.383 0.656614796 0.787880012 0.834645547 0.94143807 0.897402522 0.96072462 0.916962061 0.915734664 0.83994902 1 20.24086047 4.593636502 1.12621294 0.92214902 0.572681113 0.808063221 0.041434857 0.513199006 0.648847658 0.011694165 0.200358924 39231.6435 -4.593636502 -0.349467907 KQPPKEPSEVPTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQPPKEPSEVPTPK 14 2 P17096-2 P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 0 71.08 0.023857 413140000 1124900 1005200 803280 762440 944610 860160 809600 1027100 1039200 959640 FALSE TRUE 1080937.664 976532.6802 948450.5649 801789.6198 974994.2385 877553.0245 819508.127 1005890.026 921234.3727 894642.728 1.208233891 1.091533692 1.060144497 0.89621208 1.089814077 0.980897734 0.9160172 1.124348295 1.0297232 1 19.77095214 4.593637102 1.811980766 1.013658968 1.237595991 0.461261743 0.066548336 0.587209119 2.47531088 0.017603297 0.203427724 39231.69768 -4.593637102 0.223937023 SNDRNS(ph)MDIQCEVDALLER ddPTM_BT-474_Pertuzumab_2h_R1 9 SNDRNSMDIQCEVDALLER 19 1 Q02241;H7BYN4;A0A2U3TZL8;A0A2R8Y531;H0YME6;Q02241-2 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;S(0.008)NDRNS(0.992)MDIQCEVDALLER;S(0.004)NDRNS(0.996)MDIQCEVDALLER;S(0.027)NDRNS(0.973)MDIQCEVDALLER;S(0.017)NDRNS(0.983)MDIQCEVDALLER 283.08 5.15E-40 1918444000 503972 590104 526137 653873 588048 689600 595796 638206 700286 671953 TRUE FALSE 484276.2171 573274.8117 621221.6598 687619.4639 606963.098 703544.1845 603087.5297 625026.8231 620792.4691 626441.0248 0.773059551 0.915129739 0.991668226 1.097660333 0.968907006 1.123081274 0.962720361 0.997742482 0.990983101 1 19.25681917 4.593664776 1.934427476 1.018582975 0.738525442 0.70148537 0.04968558 0.298712524 1.491616014 0.012514102 0.134577829 39234.1977 -4.593664776 -0.280057533 GTEPSPGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 1 GTEPSPGGTPQPS(0.003)RPVS(0.997)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPSRPVS(1)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPS(0.01)RPVS(0.989)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPSRPVS(1)PAGPPEGVPEEAQPPR 341.62 6.16E-118 3696160000 225636 258432 219790 296213 264644 297744 269918 262771 250509 279752 TRUE FALSE 216817.8957 251061.7724 259510.9422 311500.5884 273156.5146 303764.5877 273221.3372 257344.687 222072.2685 260804.1479 0.83134374 0.96264486 0.995041468 1.194385101 1.047362616 1.164722993 1.047611165 0.986735407 0.851490555 1 17.99260729 4.5937832 1.966791006 1.044117626 0.804839768 0.32821945 0.090107618 0.662120318 3.450826661 0.024371855 0.25735488 39244.89756 -4.5937832 -0.239277858 LFDQHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFDQHK 6 0 Q6ZPD8;Q6E213;Q58HT5 Q6ZPD8 DGAT2L6;AWAT2;AWAT1 Diacylglycerol O-acyltransferase 2-like protein 6;Acyl-CoA wax alcohol acyltransferase 2;Acyl-CoA wax alcohol acyltransferase 1 0 74.743 0.079523 102840000 218130 237520 212810 241630 218490 228280 247700 249380 276470 273840 FALSE TRUE 209605.2384 230746.1622 251269.5009 254100.5533 225517.9293 232895.978 250731.4267 244230.2159 245086.2847 255292.5729 0.821039312 0.903849883 0.984241328 0.99533077 0.883370506 0.912270872 0.982133651 0.956667925 0.96002121 1 17.96179204 4.59388082 2.997490448 0.955742425 0.817003083 0.59297031 0.035238049 0.214746023 3.148925467 0.008970399 0.058588253 39253.71994 -4.59388082 -0.138739343 FLMPEAYPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLMPEAYPSSPR 12 0 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 FLMPEAYPS(0.5)S(0.5)PR;FLMPEAYPS(0.5)S(0.5)PR 85.288 0.012334 62065000 101889 112233 103667 119535 108240 108429 117411 118741 107113 135395 TRUE FALSE 97907.06524 109032.2247 122401.933 125704.2157 111721.6379 110621.5087 118847.9109 116288.9569 94953.98129 126224.5761 0.775657707 0.863795531 0.96971554 0.995877503 0.885102104 0.876386454 0.941559201 0.921286175 0.752262232 1 16.94563331 4.593917062 3.460091517 0.916730365 0.775610333 0.288573062 0.068303225 0.323020276 6.356703883 0.016323346 0.092696462 39256.99588 -4.593917062 -0.141120031 SEQFINLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEQFINLR 8 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 133.33 0.0021496 313120000 232740 259580 204920 293670 275780 231380 282160 251210 267270 284060 FALSE TRUE 223644.2635 252177.0326 241953.6024 308826.3439 284650.7142 236058.6621 285613.1585 246022.4257 236930.6301 264820.3632 0.844513091 0.952256955 0.913651803 1.166172949 1.074882274 0.891391656 1.078516603 0.929016269 0.894684333 1 18.01465454 4.594027488 1.730888943 0.998306909 0.824541172 0.223563678 0.085760082 1.078100027 4.034313703 0.023193851 0.281776813 39266.97883 -4.594027488 -0.173765737 SCTPS(ph)PDQISHR ddPTM_BT-474_Pertuzumab_2h_R1 3 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 SCTPS(1)PDQISHR;SCT(0.029)PS(0.971)PDQISHR;S(0.001)CT(0.001)PS(0.999)PDQISHR 150.93 4.41E-05 354970000 708670 724230 613770 687770 694770 700560 704520 754420 763320 774770 TRUE FALSE 680974.3929 703575.6695 724691.8922 723265.8921 717117.908 714725.8032 713142.1265 738840.9634 676671.1137 722294.1378 0.942793742 0.974084701 1.003319637 1.001345372 0.992833626 0.989521811 0.987329246 1.022908708 0.936835949 1 19.46222694 4.594151245 2.861435719 0.994074451 0.940699221 0.333374393 0.020931438 0.32616568 4.309511468 0.004912023 0.033743651 39278.17 -4.594151245 -0.05337523 RDPFIGEHTEEILEEFGFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDPFIGEHTEEILEEFGFSR 20 1 D6RB81;Q9UHK6;Q9UHK6-5 D6RB81 AMACR Alpha-methylacyl-CoA racemase 0 ; 148.44 7.17E-08 55974000 50285 58569 45321 62763 59070 67796 59984 57590 65079 58605 FALSE TRUE 48319.80661 56898.66947 53511.51286 66002.20595 60970.0402 69166.88157 60718.10214 56400.74637 57691.50475 54635.63115 0.884400996 1.041420558 0.97942518 1.20804326 1.115939158 1.265966552 1.111327917 1.032307035 1.055931881 1 15.73755451 4.594229139 1.284175897 1.111043821 0.83796982 0.391562263 0.082277111 1.142491182 1.996490921 0.024229919 0.383695757 39285.21546 -4.594229139 -0.273074001 VVEELTR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVEELTR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 158.36 0.003312 780750000 692780 781090 691490 836890 815500 780540 825900 842900 815010 888350 FALSE TRUE 665705.3917 758814.078 816457.6251 880081.9932 841731.2981 796323.0536 836007.6113 825493.8204 722493.4816 828181.2632 0.80381605 0.916241542 0.985844116 1.062668322 1.016361195 0.961532323 1.009450042 0.996755007 0.872385689 1 19.65958704 4.594257154 2.251859534 0.9921068 0.785373678 0.602569004 0.046199858 0.295450036 2.179204515 0.011811333 0.106843785 39287.74969 -4.594257154 -0.206733122 SVTLGYLFSQGHLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVTLGYLFSQGHLTR 15 0 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 186.77 3.68E-07 733000000 418510 487670 456030 534410 529060 518830 516680 470060 541940 575660 FALSE TRUE 402154.1665 473762.1291 538444.7653 561990.9641 546077.6954 529321.0981 523003.2844 460353.0967 480421.2432 536670.0355 0.749350886 0.882781034 1.003306929 1.047181559 1.017529691 0.986306414 0.974534164 0.857795417 0.895189244 1 19.03367581 4.594409585 2.90656648 0.966373099 0.741395832 0.615755954 0.054326789 0.247251877 3.383699889 0.016038957 0.108408948 39301.54155 -4.594409585 -0.224977267 S(ph)LT(ph)RS(ph)PPAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLTRSPPAIR 10 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)LT(1)RS(1)PPAIR 111.74 0.001434 119550000 200840 186030 137060 173940 166970 158390 164060 201180 187450 173830 TRUE FALSE 192990.9508 180724.6065 161829.7909 182917.0642 172340.7417 161592.7543 166067.8154 197025.5627 166171.4619 162056.3393 1.190888006 1.115196156 0.998602039 1.12872514 1.063461895 0.997139359 1.024753589 1.21578436 1.02539316 1 17.30613593 4.594414358 3.810277482 1.070262224 1.188884553 0.263868735 0.066671851 0.363586784 8.501433336 0.016929118 0.088836162 39301.97348 -4.594414358 0.118622329 IWGDCTVR ddPTM_BT-474_Pertuzumab_2h_R1 2 IWGDCTVR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 101.33 0.012733 377200000 284120 317940 291200 334210 325490 252200 379390 319890 375450 362190 FALSE TRUE 273016.2763 308872.6625 343826.3177 351458.6182 335959.6815 257299.6568 384033.0883 313284.1597 332830.49 337658.5487 0.808557276 0.914748534 1.01826629 1.040869895 0.994968683 0.76201138 1.137341524 0.9278135 0.985701358 1 18.36520556 4.594489216 3.041242799 0.980559623 0.803911906 0.262477837 0.090102246 0.39357683 5.952561276 0.0213213 0.137390442 39308.74839 -4.594489216 -0.176647717 RHPKGEEGS(ph)DDDETENGPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RHPKGEEGSDDDETENGPKPK 21 3 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 RHPKGEEGS(1)DDDETENGPKPK 152.35 3.81E-08 117600000 101060 73896 42936 34309 50493 77921 58475 44518 93559 51231 TRUE FALSE 97110.46347 71788.55843 50695.49031 36079.6916 52117.1532 79496.61601 59190.63454 43598.68774 82938.57455 47761.07874 2.033255237 1.50307657 1.061439391 0.755420366 1.091205529 1.664464416 1.239306902 0.912849728 1.736530597 1 15.5435478 4.594490557 2.800814387 1.169639498 2.071767406 0.440762883 0.293746208 0.300202942 3.774852271 0.074037105 0.521236856 39308.8698 -4.594490557 0.902127908 QS(ph)PSPSTRPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QS(0.862)PS(0.138)PSTRPIR;QS(0.989)PS(0.011)PSTRPIR 114.21 0.0007802 2030650000 1976510 2152600 1801460 1962150 2246700 2371200 2278700 2270200 2340100 2200800 TRUE FALSE 1899265.804 2091209.956 2127023.895 2063416.797 2318967.146 2419147.289 2306587.412 2223319.577 2074461.658 2051737.856 0.925686388 1.019238374 1.036693791 1.005692219 1.130245338 1.179072308 1.124211558 1.083627507 1.011075393 1 20.96841498 4.594667713 0.883134155 1.09171201 0.871587394 0.397429015 0.056120831 1.8131673 1.285874975 0.019841299 0.370201629 39324.90784 -4.594667713 -0.220124616 AGMSSNQSIS(ph)S(ph)PVLDAVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.005)S(0.006)NQS(0.329)IS(0.881)S(0.779)PVLDAVPR 110.74 0.00051328 152710000 100010 107450 97277 104280 107760 105650 102700 120130 112340 111530 TRUE FALSE 96101.49863 104385.6312 114857.1178 109661.9033 111226.1983 107786.3154 103956.8733 117649.2735 99587.63417 103975.9738 0.924266397 1.003939924 1.104650562 1.054685033 1.069729806 1.036646366 0.9998163 1.131504417 0.957794677 1 16.66589067 4.594683889 3.481479396 1.051984009 0.924240085 0.344285427 0.049230893 0.246162604 4.896488852 0.011326572 0.064070087 39326.37257 -4.594683889 -0.127743924 ESYPHIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESYPHIK 7 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 ; 96.964 0.012345 1117910000 1302360 1361910 1163350 1333860 1311750 1393910 1353560 1402450 1565820 1556520 FALSE TRUE 1251462.331 1323069.66 1373593.224 1402700.674 1353943.63 1422095.815 1370125.272 1373488.917 1388074.678 1451095.514 0.862425884 0.911772966 0.946590497 0.966649446 0.933049284 0.980015307 0.944200612 0.946518616 0.956570167 1 20.46871105 4.594754722 1.599920649 0.957210915 0.842365025 0.742000407 0.01826028 0.364203525 1.111323189 0.004538944 0.059841071 39332.78717 -4.594754722 -0.11484589 SAS(ph)TLCLPSVGAARPQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASTLCLPSVGAARPQVK 18 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.979)T(0.021)LCLPSVGAARPQVK 274.69 2.91E-39 1541900000 1153400 791680 441930 437140 450140 317830 326940 781590 480140 344700 TRUE FALSE 1108323.853 769102.0615 521796.5817 459700.8478 464619.1619 324256.7404 330941.1895 765449.8934 425636.5201 321353.162 3.448927797 2.39332346 1.623748086 1.430516025 1.445821037 1.009035475 1.029836419 2.381958493 1.324513247 1 18.29380014 4.594872688 1.659560188 1.449911197 3.846645983 0.743291109 0.382668517 0.403657183 1.353248609 0.111423262 1.417494961 39343.47245 -4.594872688 2.396734787 up VSSAEGAAKEEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSSAEGAAKEEPK 13 1 P05114;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 0 106.14 0.0012745 431470000 788120 630650 388630 357180 509850 626560 503020 617050 622990 506230 FALSE TRUE 757319.3991 612664.4795 458864.086 375614.1026 526249.7883 639229.4725 509176.1092 604307.7019 552270.787 471942.5912 1.604685428 1.298175861 0.972287932 0.795889393 1.115071617 1.354464472 1.078894168 1.28046867 1.170207558 1 18.84825185 4.594937972 3.269161877 1.1133464 1.610541914 0.516663971 0.150847218 0.241950988 4.255234141 0.040373571 0.242232759 39349.38704 -4.594937972 0.497195515 SLS(ph)PS(ph)GLKIQT(ph)GK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSPSGLKIQTGK 13 1 F6VUX8;Q9HC77-2;Q9HC77 F6VUX8 CENPJ Centromere protein J 3 S(0.005)LS(0.995)PS(1)GLKIQT(1)GK 93.228 0.041071 1330800000 219660 279890 279530 344250 272680 310130 321490 291190 292560 343880 TRUE FALSE 211075.4444 271907.8112 330047.2891 362016.7838 281450.9998 316401.0411 325424.4908 285176.8247 259349.8153 320588.7013 0.658399512 0.848151573 1.029503809 1.129225023 0.877919274 0.986937593 1.015084092 0.889541096 0.808979899 1 18.29036406 4.594985155 3.058956876 0.964546433 0.650528175 0.548008554 0.086127639 0.22769163 3.485303233 0.022078988 0.141606013 39353.66236 -4.594985155 -0.314018258 AVTLHDQGTAQWADLSSQFYLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AVTLHDQGTAQWADLSSQFYLR 22 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 337.22 5.25E-81 8078430000 2243703 2518528 2349086 2474239 2613563 2536589 2607162 2656957 2900776 2681307 FALSE TRUE 2156016.606 2446702.047 2773618.095 2601934.771 2697630.627 2587880.568 2639069.228 2602089.909 2571492.07 2499699.689 0.862510251 0.978798397 1.109580526 1.040898946 1.079181887 1.035276589 1.055754513 1.040961009 1.028720402 1 21.25332335 4.595023925 3.22736327 1.050400831 0.859560141 0.795873112 0.028855856 0.104255219 1.786040353 0.006574535 0.039951006 39357.17568 -4.595023925 -0.19084069 YS(ph)ESNFSVDDQDLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YSESNFSVDDQDLSR 15 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 YS(1)ESNFSVDDQDLSR 214.46 1.12E-11 0 70360 94033 89053 116880 92669 99670 103820 116720 122730 115380 TRUE FALSE 67610.25341 91351.27091 105146.8581 122912.1908 95649.78254 101685.3957 105090.5802 114309.6912 108798.2049 107565.2098 0.628551309 0.849264098 0.977517343 1.142676066 0.889226012 0.945337213 0.976994145 1.062701327 1.011462768 1 16.71485201 4.59563247 2.067151716 1.004748676 0.582067543 0.767175238 0.063786581 0.241388712 1.427010138 0.016998484 0.170712645 39412.3626 -4.59563247 -0.422681134 S(ph)SSSSNASGNGGDGKEERPEGSPTLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSSSNASGNGGDGKEERPEGSPTLFK 27 2 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 S(0.284)S(0.284)S(0.284)S(0.062)S(0.062)NAS(0.024)GNGGDGKEERPEGSPTLFK 50.908 0.05534 125750000 102220 83873 57596 66115 66804 53386 64793 96234 60895 56882 TRUE FALSE 98225.12939 81481.02416 68004.87842 69527.20307 68952.81133 54465.5015 65585.95612 94246.73427 53982.45489 53029.33147 1.852279232 1.536527463 1.282401202 1.311108421 1.300276836 1.027082559 1.236786403 1.777256693 1.017973514 1 15.69450294 4.595835839 2.041427474 1.291131738 1.927569903 0.429412439 0.217031037 0.569411476 3.25818134 0.059063299 0.602210388 39430.82274 -4.595835839 0.636438165 APEVNLNAPDVDVHGPDWNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 APEVNLNAPDVDVHGPDWNLK 21 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 257.96 1.69E-36 660980000 919040 969140 854930 1002210 842050 949780 977990 996730 1073820 1076020 FALSE TRUE 883122.9007 941501.0761 1009434.869 1053934.178 869135.303 968985.2023 989958.9342 976147.1772 951924.4554 1003140.207 0.880358393 0.938553823 1.006274957 1.050634967 0.866414582 0.965951913 0.98685999 0.973091469 0.948944573 1 19.93609183 4.595998899 3.444189699 0.97303514 0.880144176 0.292774969 0.044925516 0.331878969 6.458312191 0.010965325 0.062799335 39445.6302 -4.595998899 -0.092890964 AFDTAGNGYCR ddPTM_BT-474_Pertuzumab_2h_R1 7 AFDTAGNGYCR 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 250.62 2.26E-16 5198890000 1669935 1839500 1648451 1869570 1786540 1644010 2213250 1833570 2064130 2086690 FALSE TRUE 1604672.094 1787039.261 1946362.765 1966058.732 1844005.682 1677253.009 2240336.416 1795706.139 1829818.616 1945356.628 0.824872967 0.918617818 1.0005172 1.010641804 0.947901097 0.862182792 1.151632757 0.92307298 0.940608313 1 20.89160323 4.596023307 2.747417468 0.978638885 0.816978025 0.307460298 0.071546815 0.402462459 4.830667689 0.017234648 0.124552645 39447.84714 -4.596023307 -0.161660859 QLT(ph)QPETHFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLTQPETHFGR 11 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 QLT(1)QPETHFGR;QLT(1)QPETHFGR 186.77 1.43E-05 1736080000 4024300 2230500 521030 827100 1496040 740510 442970 2491300 555680 362650 TRUE FALSE 3867025.907 2166888.324 615191.7112 869786.7301 1544161.485 755483.6196 448391.1994 2439853.784 492601.536 338087.3925 11.43794768 6.409255039 1.819623343 2.572668338 4.567344183 2.23458087 1.326258267 7.216636404 1.457024269 1 18.36703669 4.5961679 2.772514191 3.175425131 11.84993427 0.681021337 1.824164222 0.198005994 2.427263318 0.461059266 3.299678543 39460.98307 -4.5961679 8.674509144 IGGELEEQAVMLEDFSHELESTQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGGELEEQAVMLEDFSHELESTQSR 25 0 O43752;O43752-2 O43752 STX6 Syntaxin-6 0 ; 167.72 1.22E-11 74588000 32215 41989 37118 52871 40418 44675 55550 47977 50782 47925 FALSE TRUE 30956.00218 40791.51483 43826.04829 55599.67865 41718.08168 45578.35911 56229.83752 46986.25818 45017.44026 44678.99706 0.69285356 0.912990835 0.980909402 1.244425397 0.933729144 1.020129414 1.258529538 1.051640844 1.007574995 1 15.44730918 4.596344776 1.596991845 1.077874552 0.617063747 0.569831947 0.100611706 0.536381219 1.625284187 0.026618877 0.353518826 39477.05765 -4.596344776 -0.460810805 LNS(ph)KWNILCEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNSKWNILCEK 11 1 Q9Y234 Q9Y234 LIPT1 "Lipoyltransferase 1, mitochondrial" 1 LNS(1)KWNILCEK 79.148 0.073495 138630000 305130 266870 182860 246310 222640 250290 238160 226090 281900 262520 TRUE FALSE 293205.1823 259259.1289 215906.8697 259022.0886 229801.4178 255351.0353 241074.6733 221421.1625 249899.8938 244739.2866 1.198030714 1.059327795 0.882191301 1.058359253 0.938964157 1.0433594 0.985026461 0.904722595 1.021086142 1 17.90088618 4.596463311 3.449006031 0.975654084 1.198828743 0.595398821 0.054918414 0.160835597 3.136539082 0.012781415 0.073178417 39487.83389 -4.596463311 0.223174659 SLSGS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSGSPLK 8 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 SLS(0.003)GS(0.997)PLK;SLSGS(1)PLK 124.67 0.0013583 2287200000 5430800 4805600 3074700 4037100 3463600 2393700 4184900 4207800 3345900 3755800 TRUE FALSE 5218558.332 4668548.993 3630366.686 4245455.215 3575009.84 2442102.254 4236116.058 4120907.46 2966087.459 3501416.321 1.490413551 1.333331591 1.036828059 1.212496552 1.021018214 0.697461264 1.209829301 1.176925873 0.847110765 1 21.73950718 4.596859599 1.141000145 1.028089964 1.663651257 0.515062571 0.153148019 1.133848742 1.474089735 0.047380115 0.813978725 39523.88243 -4.596859599 0.635561293 IGSLGLGTGEDDDYVDDFNSTSHR ddPTM_BT-474_Pertuzumab_2h_R1 3 IGSLGLGTGEDDDYVDDFNSTSHR 24 0 O95684;O95684-2;A0A087WV25;O95684-3 O95684 FGFR1OP FGFR1 oncogene partner 0 ;; 300.41 3.63E-62 407838000 113479 140263 138305 145728 148210 170312 156802 183936 145341 183146 FALSE TRUE 109044.1152 136262.8366 163299.7901 153249.0395 152977.3093 173755.8253 158720.9898 180137.6573 128842.499 170741.3583 0.638650859 0.798065788 0.956416136 0.897550781 0.895959308 1.017655166 0.929598964 1.055032355 0.754606267 1 17.38145304 4.596920916 1.785255189 0.947893407 0.581254923 0.583320523 0.079445501 0.421959938 1.703421595 0.020003791 0.237667025 39529.46311 -4.596920916 -0.366638484 GSDALSETSS(ph)VSHIEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALSETS(0.018)S(0.981)VSHIEDLEK 269.85 1.26E-32 170540000 568000 440630 275150 299450 366990 305850 281660 495570 396700 312780 TRUE FALSE 545801.932 428063.6638 324875.7257 314904.6504 378794.5666 312034.4966 285107.0393 485336.3063 351668.2791 291595.132 1.871779986 1.468006893 1.114132885 1.079937954 1.299042834 1.070095013 0.977749654 1.664418411 1.206015604 1 18.15360711 4.596989806 2.763003455 1.211284271 1.905256401 0.556553499 0.190722125 0.27474667 3.338057917 0.050835936 0.366150349 39535.73396 -4.596989806 0.69397213 IVEYS(ph)PPSAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 IVEYSPPSAPR 11 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 IVEYS(0.995)PPS(0.005)APR;IVEYS(0.998)PPS(0.002)APR;IVEYS(0.857)PPS(0.143)APR;IVEYS(1)PPSAPR 158.34 3.14E-05 1368750000 972530 1086900 970500 1116030 1120170 1264290 1058610 1121310 1164670 1212080 TRUE FALSE 934522.4524 1055902.676 1145890.939 1173628.442 1156201.285 1289854.81 1071565.586 1098154.557 1032461.544 1129984.742 0.827022187 0.934439764 1.01407647 1.038623265 1.023200794 1.141479847 0.948300934 0.971831314 0.91369512 1 20.10787186 4.597350985 2.367865691 1.006960455 0.810931054 0.482337525 0.057500403 0.376899059 3.143806028 0.015411189 0.132861647 39568.6274 -4.597350985 -0.196029402 LPSANQGS(ph)PFK ddPTM_BT-474_Pertuzumab_2h_R1 4 LPSANQGSPFK 11 0 E5RFP7;E5RIE3;E5RFE4;Q56NI9 E5RFP7 ESCO2 N-acetyltransferase ESCO2 1 LPSANQGS(1)PFK;LPSANQGS(1)PFK;LPSANQGS(1)PFK;LPSANQGS(1)PFK 168.18 1.93E-05 917580000 1636920 1408290 989410 1195420 1083980 853820 1207920 1430930 1113610 1321660 TRUE FALSE 1572947.357 1368126.948 1168218.396 1257115.769 1118847.201 871084.8254 1222702.886 1401380.795 987197.6614 1232142.791 1.276595025 1.110363959 0.948119329 1.020267926 0.908049951 0.706967432 0.992338628 1.137352591 0.801203942 1 20.23273803 4.597398517 1.662049862 0.946801599 1.345600434 0.476407852 0.112932005 0.712052015 2.387623213 0.032543758 0.417093298 39572.95827 -4.597398517 0.398798836 HTDVQFYTEVGEITTDLGK ddPTM_BT-474_Pertuzumab_2h_R1 3 HTDVQFYTEVGEITTDLGK 19 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;; 232.84 1.10E-21 661590000 795580 830700 689170 817780 849800 830810 853550 673930 1078660 976160 FALSE TRUE 764487.854 807009.2493 813718.3495 859985.7238 877134.5888 847609.5474 863996.0002 660013.11 956215.0389 910043.8137 0.840056097 0.886780655 0.894152938 0.944993758 0.963837758 0.931394219 0.949400443 0.725254213 1.050735167 1 19.79557648 4.597785564 1.72581444 0.915848567 0.827750761 0.09132556 0.08150262 2.093537176 7.732525101 0.022473659 0.27755525 39608.24171 -4.597785564 -0.088097806 GSLQFEDKWDFMRPIVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSLQFEDKWDFMRPIVLK 18 2 Q93034;E9PP19 Q93034 CUL5 Cullin-5 0 92.307 0.0013268 85466000 173260 153520 113830 117460 124840 155000 140460 136020 170200 152290 FALSE TRUE 166488.8077 149141.7599 134401.6131 123522.1247 128855.592 158134.2062 142178.9915 133211.1395 150879.6095 141975.2627 1.172660677 1.050477084 0.946655147 0.870025682 0.907591855 1.113815204 1.00143496 0.938270069 1.062717594 1 17.11528006 4.597881368 2.885483741 0.975784405 1.18054676 0.42714773 0.068090058 0.304017832 4.077450319 0.017655097 0.121502446 39616.98018 -4.597881368 0.204762355 AAEEAFVNDIDESSPGTEWER ddPTM_BT-474_Pertuzumab_2h_R1 2 AAEEAFVNDIDESSPGTEWER 21 0 P09496-2;P09496-5 P09496-2 CLTA Clathrin light chain A 0 ; 337.03 5.76E-80 1595790000 804940 857190 734670 849670 850930 919870 872440 898340 899200 921080 FALSE TRUE 773482.0549 832743.7805 867441.2116 893521.5705 878300.9362 938470.4017 883117.1817 879788.9651 797126.5858 858694.4312 0.900765193 0.969778946 1.010186139 1.040558245 1.022832924 1.092903794 1.028441725 1.024565821 0.928300635 1 19.71178531 4.598096886 1.748243179 1.024452285 0.87866021 0.472244373 0.038565556 0.564581509 2.155147718 0.010239265 0.124905015 39636.6449 -4.598096886 -0.145792074 LEDVSKPPAYAYPATPSSHPTS(ph)PPPAS(ph)PPPTPGITR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEDVSKPPAYAYPATPSSHPTSPPPASPPPTPGITR 36 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 2 LEDVSKPPAYAYPATPSSHPT(0.466)S(0.534)PPPAS(1)PPPTPGITR;LEDVSKPPAYAY(0.001)PAT(0.002)PS(0.009)S(0.01)HPT(0.484)S(0.527)PPPAS(0.959)PPPT(0.005)PGIT(0.001)R 188.12 4.17E-23 870440000 310592 362563 320170 406751 382331 404528 411424 349707 395105 404346 TRUE FALSE 298453.7213 352223.0582 378031.8411 427743.4679 394629.0238 412707.8333 416459.13 342485.4282 350254.3368 376959.2853 0.791739938 0.934379579 1.002845283 1.134720604 1.046874395 1.094833977 1.10478544 0.908547532 0.929156942 1 18.52404918 4.598301012 2.06375804 1.029458721 0.762534506 0.531936298 0.068796352 0.449223252 2.634535988 0.019770134 0.200855331 39655.27921 -4.598301012 -0.266924214 ERS(ph)AEKTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERSAEKTEK 9 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(0.99)AEKT(0.01)EK;ERS(0.984)AEKT(0.016)EK 74.649 0.031892 457380000 866140 657590 456386 334759 528100 599910 475835 535912 614450 536030 TRUE FALSE 832290.2912 638836.177 538865.1025 352035.9521 545086.8161 612040.5912 481658.4111 524845.2299 544700.212 499724.2107 1.665499236 1.27837748 1.078324986 0.70446047 1.090775281 1.224756732 0.96384846 1.050269766 1.090001646 1 18.93077259 4.598679036 2.145719468 1.022737864 1.738128982 0.713708183 0.125841875 0.263987749 1.710686684 0.033245583 0.323282273 39689.81144 -4.598679036 0.715391118 TPPSTTVGSHS(ph)PPETPVLTR ddPTM_BT-474_Pertuzumab_2h_R1 5 TPPSTTVGSHSPPETPVLTR 20 0 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-4;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 TPPSTTVGSHS(1)PPETPVLTR;TPPSTTVGSHS(1)PPETPVLTR;TPPSTTVGSHS(1)PPETPVLTR;TPPSTTVGSHS(1)PPETPVLTR;TPPSTTVGSHS(1)PPETPVLTR 268.98 2.13E-37 13130260000 2633200 2977221 2726486 2981539 3005312 3185595 3148338 3187749 3152559 3346872 TRUE FALSE 2530291.633 2892313.572 3219222.671 3135416.585 3101980.59 3250009.914 3186868.302 3121920.869 2794693.719 3120185.378 0.810942725 0.926968504 1.031740836 1.004881507 0.994165479 1.041607956 1.021371462 1.000556214 0.895681948 1 21.57320032 4.598687241 2.734740662 1.001287889 0.800457976 0.694558222 0.038213774 0.179655661 2.126751242 0.009439423 0.069147416 39690.56134 -4.598687241 -0.200829913 ADYQAVDDEIEANLEEFDISEDDIDDGFRR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADYQAVDDEIEANLEEFDISEDDIDDGFRR 30 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 123.36 2.62E-05 49550000 17065 15804 16611 17613 16131 21229 19285 20762 20526 22049 FALSE TRUE 16398.08093 15353.28539 19612.97721 18522.00904 16649.86826 21658.26493 19521.0156 20333.25744 18195.97453 20555.60159 0.797742691 0.746914914 0.9541427 0.901068692 0.809991777 1.053642961 0.949668902 0.989183282 0.885207589 1 14.32724397 4.598931053 0.514994094 0.971974539 0.64298209 0.457240972 0.069269306 3.290034197 0.743422485 0.040855234 0.645235055 39712.84974 -4.598931053 -0.328992448 VS(ph)PPQPPPPQPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSPPQPPPPQPPR 13 0 Q15637-5 Q15637-5 SF1 Splicing factor 1 1 VS(1)PPQPPPPQPPR;VS(1)PPQPPPPQPPR;VS(1)PPQPPPPQPPR 159.75 4.39E-05 2860620000 255574 234262 220737 254698 236230 251513 258033 281860 293721 280732 TRUE FALSE 245585.8855 227581.0771 260629.0862 267842.9943 243828.5525 256598.7652 261190.885 276039.4925 260379.0235 261717.7716 0.938361518 0.869566769 0.995840231 1.023403924 0.931646907 0.980440738 0.997986814 1.054722004 0.994884764 1 17.99765237 4.599305359 0.454213886 1.017704829 0.835594745 0.386588509 0.039092464 4.261969339 0.752850338 0.028871172 0.415223498 39747.09191 -4.599305359 -0.182110084 LTDEEAQHVLEVVQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LTDEEAQHVLEVVQR 15 0 Q9BV36-2;Q9BV36-5;C9JKV5;C9JI01;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ;; 186.85 3.65E-07 1381460000 1197680 1277880 1137400 1238940 1270320 1312220 1278430 1290610 1375050 1392270 FALSE TRUE 1150873.341 1241436.114 1342953.481 1302881.842 1311180.996 1338753.987 1294075.809 1263958.452 1218960.089 1297970.313 0.886671544 0.956444151 1.034656547 1.003784007 1.010177955 1.031421115 0.996999543 0.973796118 0.939127865 1 20.30782596 4.59940019 3.267816716 0.998179927 0.884907375 0.630738589 0.026250674 0.181723465 3.178536313 0.006869901 0.041671475 39755.77191 -4.59940019 -0.113272552 MKEEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 MKEEVK 6 1 O95239;O95239-2;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 0 80.18 0.059458 467250000 301010 280050 253880 201200 253770 219980 244890 270270 311460 328310 FALSE TRUE 289246.1964 272063.2482 299761.7635 211583.9561 261932.7425 224428.1463 247887.0371 264688.8301 276104.3665 306073.2713 0.945022724 0.888882741 0.979379095 0.69128531 0.855784438 0.733249739 0.809894428 0.864789104 0.902085848 1 18.22351754 4.599813831 0.004314212 1.696061056 2.10E-07 0.017444243 0.094179215 307298.0642 215.1896965 41034.18179 43590.12644 39793.65509 -4.599813831 -1.696060846 CPPDYPIHPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 CPPDYPIHPPR 11 0 Q9H832-2;Q9H832;I3L4C5;H0Y9X8 Q9H832-2 UBE2Z Ubiquitin-conjugating enzyme E2 Z 0 ;; 120.06 0.00050243 2421390000 2816340 3063740 2613480 3161740 3045720 3202550 3168420 3091220 3477640 3477240 FALSE TRUE 2706274.319 2976365.135 3085793.973 3324917.78 3143688.35 3267307.755 3207196.072 3027385.227 3082872.887 3241723.438 0.834825787 0.918142831 0.951899208 1.025663615 0.969758343 1.007892196 0.989349071 0.933881401 0.950998118 1 21.62832958 4.599823365 1.757101994 0.978062011 0.81022266 0.749200314 0.026204987 0.358917195 1.384620155 0.007519042 0.09180427 39794.52866 -4.599823365 -0.167839351 QLEDLVEELSFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLEDLVEELSFSR 13 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A087WX84;Q99996-4 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ; 108.17 0.0015446 4076600 35100 38208 35572 36640 37250 38597 38520 40608 42114 39810 FALSE TRUE 33728.25319 37118.34525 42000.65169 38530.99479 38448.18008 39377.45778 38991.41928 39769.43061 37333.39528 37113.63324 0.908783384 1.000126962 1.131677177 1.038189782 1.035958399 1.060997115 1.050595587 1.071558539 1.005921329 1 15.17966162 4.599919245 3.718577954 1.053101603 0.91004345 0.589635362 0.035446 0.147121215 3.277005224 0.008067597 0.043555136 39803.31513 -4.599919245 -0.143058153 VAEFHTELER ddPTM_BT-474_Pertuzumab_2h_R1 2 VAEFHTELER 10 0 K7EJR3;R4GMR5;P48556;K7EJC1;K7ERW6 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ; 185.08 1.49E-06 2228400000 1615980 1780450 1586340 1877960 1788140 1705100 1990910 1760360 1873650 2018090 FALSE TRUE 1552825.715 1729673.309 1873026.926 1974881.741 1845657.147 1739578.29 2015275.352 1724007.951 1660961.107 1881402.967 0.825355196 0.919352919 0.995547981 1.049685674 0.981000445 0.924617597 1.071155615 0.916341678 0.88283113 1 20.84337745 4.600253979 2.787501944 0.976900414 0.817814966 0.417740012 0.055279345 0.326748298 4.037922301 0.013952074 0.100503551 39834.00552 -4.600253979 -0.159085448 LLEFDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLEFDR 6 0 Q15650;H0YL91 Q15650 TRIP4 Activating signal cointegrator 1 0 ;; 135.5 0.031577 388804000 255465 305547 279694 369340 297896 259258 351970 358270 318887 343841 FALSE TRUE 245481.1454 296833.0987 330240.9276 388401.6817 307478.0954 264500.3744 356277.5141 350871.5993 282688.2846 320552.3428 0.765806742 0.926005083 1.030224657 1.211663837 0.959213377 0.825139421 1.111448792 1.094584417 0.881878704 1 18.29020043 4.600283539 2.578441948 1.024120808 0.748592894 0.335730594 0.106213823 0.419326234 4.303583785 0.027485809 0.216588119 39836.71687 -4.600283539 -0.275527914 TQIDHYVGIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 TQIDHYVGIAR 11 0 O95197-3;O95197-4;O95197-7;O95197-2;O95197 O95197-3;O95197-7 RTN3 Reticulon-3 0 ;;; 177.04 8.16E-06 3597340000 1788680 2431270 1969000 3453660 1941100 1960740 3093210 3212250 3137020 2992300 FALSE TRUE 1718776.408 2361932.56 2324842.1 3631903.806 2003537.244 2000387.506 3131065.629 3145915.915 2780918.641 2789628.856 0.616130854 0.846683441 0.833387601 1.301930828 0.718209249 0.71708016 1.122395054 1.127718445 0.996877644 1 21.41164176 4.600298789 1.468596986 0.995320126 0.53553297 0.300210565 0.173216086 1.164459306 2.831280916 0.049904202 0.72550569 39838.11576 -4.600298789 -0.459787156 NREEEWDPEYT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NREEEWDPEY(0.048)T(0.952)PK;NREEEWDPEY(0.012)T(0.988)PK 74.147 0.056423 1378260000 1907470 1383060 904370 782260 896510 802810 839490 1442840 977440 920620 TRUE FALSE 1832923.964 1343616.483 1067809.777 822632.5323 925347.0583 819043.3682 849763.9297 1413044.85 866485.109 858265.5874 2.135613953 1.565501988 1.244148422 0.958482484 1.078159339 0.954300604 0.990094374 1.64639579 1.009576898 1 19.71106463 4.600424225 1.820961092 1.134830452 2.302594639 0.728529184 0.197038704 0.375100357 1.585854046 0.057962347 0.68275799 39849.62369 -4.600424225 1.167764187 up LPALGEAHVS(ph)PEVATADK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPALGEAHVSPEVATADK 18 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 LPALGEAHVS(1)PEVATADK;LPALGEAHVS(1)PEVATADK 214.14 3.10E-18 215140000 316290 268960 339060 392440 340980 329210 422350 415400 530280 556550 TRUE FALSE 303929.0371 261289.5241 400335.6843 412693.8754 351947.9314 335866.8518 427518.8456 406821.8448 470084.8375 518854.3728 0.585769443 0.503589327 0.771576198 0.795394425 0.678317366 0.64732393 0.823966932 0.784077125 0.90600535 1 18.98497015 4.6005103 0.098337346 1.222463317 4.77E-17 0.706095281 0.076546981 32.92906452 0.545580417 1.636025505 6.137469481 39857.52248 -4.6005103 -1.222463317 T(ph)ASFGNILDVPEIVISGNGQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TASFGNILDVPEIVISGNGQPR 22 0 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 T(0.5)AS(0.5)FGNILDVPEIVISGNGQPR;T(0.5)AS(0.5)FGNILDVPEIVISGNGQPR 133.84 9.45E-05 77194000 243280 174881 94865 130473 101772 66274 96658 243560 127334 108244 TRUE FALSE 233772.3486 169893.5651 112009.2158 137206.7272 105045.5888 67614.10569 97840.92952 238530.4009 112879.5781 100912.5375 2.316583791 1.683572422 1.109963326 1.359659866 1.040956768 0.670026811 0.969561682 2.36373405 1.118588245 1 16.6227459 4.600853958 2.705250817 1.278476774 2.378426046 0.384666278 0.430210691 0.430591554 4.956473511 0.121325548 0.906024741 39889.07436 -4.600853958 1.099949272 QSSFEPEFVIS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSSFEPEFVISPR 13 0 A0A0A0MSU3;Q9H9A7 A0A0A0MSU3 RMI1 RecQ-mediated genome instability protein 1 1 QSSFEPEFVIS(1)PR 114.63 0.00076373 32005000 37843 47784 49191 55188 53751 49214 46712 51334 53375 57997 TRUE FALSE 36364.05372 46421.24711 58080.90795 58036.25929 55479.94973 50209.1408 47283.67543 50273.93496 47316.09377 54068.81153 0.672551378 0.858558673 1.074203525 1.07337775 1.026098931 0.92861558 0.874509243 0.929813945 0.875108818 1 15.72250902 4.601096776 3.393303783 0.967126032 0.669897357 0.634120031 0.069744602 0.185869577 3.496783204 0.019241298 0.112958592 39911.38288 -4.601096776 -0.297228675 AQYEQTLAELHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQYEQTLAELHR 12 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ; 178.58 2.18E-05 2067340000 1168810 1305910 1146780 1415510 1229620 1268800 1445840 1401850 1407360 1461920 FALSE TRUE 1123131.613 1268666.725 1354028.656 1488564.641 1269171.844 1294456.005 1463534.622 1372901.308 1247602.393 1362902.856 0.824073123 0.930856311 0.993488751 1.092201571 0.931226931 0.949778628 1.073836345 1.007336144 0.915400821 1 20.3782513 4.60114806 2.296341433 0.999648341 0.80693774 0.493172426 0.053392922 0.360415392 2.768455855 0.013626248 0.123443422 39916.09617 -4.60114806 -0.192710601 EVSEDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVSEDRR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 187.55 0.00093429 302180000 344650 387840 327480 433490 399010 431960 395890 389170 397900 411940 FALSE TRUE 331180.697 376779.1829 386662.9208 455862.4708 411844.519 440694.5272 400735.0202 381133.5035 352732.0601 384038.9369 0.86236229 0.981096308 1.006832599 1.187021489 1.072403029 1.147525641 1.043474975 0.992434534 0.918479941 1 18.55089306 4.601461269 1.951203497 1.052419913 0.837089621 0.374859349 0.07308579 0.633335579 3.198065261 0.02023889 0.221737493 39944.89364 -4.601461269 -0.215330292 RRDS(ph)DGVDGFEAEGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRDSDGVDGFEAEGKK 16 3 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK 157.97 8.52E-08 6266900000 452540 397270 310340 264410 339810 406470 335640 377490 424630 400440 TRUE FALSE 434854.2365 385940.2486 366425.3415 278056.2318 350740.2973 414689.1019 339747.6627 369694.6996 376427.7826 373317.8421 1.164836468 1.03381142 0.981537179 0.744824384 0.939521924 1.110820473 0.910076145 0.990294751 1.008330543 1 18.51004494 4.601561004 2.354460653 0.95691392 1.18268873 0.337199718 0.087915767 0.498481042 4.076782075 0.023001096 0.202602131 39954.06795 -4.601561004 0.22577481 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETERNGDDGTHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLIPDIKPLAGQEAVVDLHADDSRISEDETERNGDDGTHDK 41 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.49)RIS(0.49)EDET(0.021)ERNGDDGTHDK;SLIPDIKPLAGQEAVVDLHADDS(0.496)RIS(0.394)EDET(0.109)ERNGDDGTHDK 166.18 4.17E-20 3184390000 1662420 1391930 995830 958230 1211930 1243600 1218350 1091950 1688990 1298840 TRUE FALSE 1597450.788 1352233.519 1175798.633 1007684.365 1250912.829 1268746.444 1233260.532 1069400.851 1497262.936 1210868.41 1.319260438 1.11674688 0.9710375 0.832199731 1.033070827 1.047798781 1.018492614 0.883168511 1.236519942 1 20.20761066 4.601810513 2.592901848 0.991121536 1.341524794 0.470940604 0.102054483 0.29790853 3.09376908 0.024967649 0.19646097 39977.02879 -4.601810513 0.350403258 AGSMKDPLLDDHGDFIR ddPTM_BT-474_Pertuzumab_2h_R1 6 AGSMKDPLLDDHGDFIR 17 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;;;; 192.85 9.81E-11 2444250000 4668070 4853550 4164810 4708140 4817900 4928860 5092240 4930860 5722870 5260730 FALSE TRUE 4485636.664 4715131.506 4917483.813 4951127.67 4972872.129 5028524.926 5154560.356 4829036.018 5073233.79 4904416.071 0.91461177 0.96140528 1.002664485 1.009524395 1.013958044 1.025305531 1.051003887 0.984630168 1.034421574 1 22.22564995 4.601832302 1.281522436 1.017500742 0.883219204 0.78865413 0.017038065 0.470792824 0.810236555 0.004794829 0.077908522 39979.03453 -4.601832302 -0.134281538 IEGEMQVPDVDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IEGEMQVPDVDIR 13 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 153.74 0.0001026 317050000 299690 320250 262420 334350 300290 321840 299600 361360 334230 342060 FALSE TRUE 287977.7835 311116.7836 309845.1315 351605.8436 309949.1006 328347.8253 303266.5944 353897.7897 296289.6116 318891.9715 0.90305749 0.975618113 0.971630393 1.102586064 0.971956425 1.029652217 0.951001033 1.109773282 0.929122205 1 18.28270825 4.602066313 1.58377341 1.018030348 0.881711642 0.238625661 0.0566513 1.008618265 2.966995249 0.014367095 0.19622188 40000.58224 -4.602066313 -0.136318706 GNWEQPQNQNQTQHK ddPTM_BT-474_Pertuzumab_2h_R1 4 GNWEQPQNQNQTQHK 15 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ;;; 238.07 9.32E-18 2588720000 1357720 1439450 1277250 1416340 1326970 1407630 1484130 1453290 1615700 1606530 FALSE TRUE 1304658.801 1398398.295 1508077.487 1489437.477 1369653.195 1436093.243 1502293.227 1423279.054 1432292.51 1497718.292 0.871097594 0.933685796 1.006916651 0.994471046 0.914493201 0.958854045 1.003054603 0.950298238 0.956316363 1 20.51433486 4.602216613 3.39163036 0.970113207 0.870105993 0.551872098 0.028089784 0.199199276 3.740169187 0.006927454 0.040787774 40014.42795 -4.602216613 -0.100007214 QPPPLAPQS(ph)PQGGVMGGSNSNQQQQMR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPPPLAPQSPQGGVMGGSNSNQQQQMR 27 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8;P46937-4;H0YCI3 P46937-6 YAP1 Transcriptional coactivator YAP1 1 QPPPLAPQS(1)PQGGVMGGSNSNQQQQMR;QPPPLAPQS(1)PQGGVMGGSNSNQQQQMR 89.272 0.0045875 639900000 54911 62784 58807 71984 64541 57141 64676 67198 66338 69393 TRUE FALSE 52765.01741 60993.46179 69434.73305 75699.10287 66617.01988 58296.43017 65467.52423 65810.33782 58807.58835 64692.9503 0.815622369 0.942814658 1.073296746 1.170129087 1.029741565 0.901124928 1.011973081 1.017272168 0.909026224 1 15.98132089 4.602442893 3.261742656 1.016457504 0.812168844 0.409487342 0.072615821 0.279684902 4.859732485 0.018960599 0.116064442 40035.28213 -4.602442893 -0.204288661 TAS(ph)FGNILDVPEIVISGNGQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASFGNILDVPEIVISGNGQPR 22 0 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 T(0.117)AS(0.883)FGNILDVPEIVISGNGQPR 139.98 1.40E-07 39949000 102500 73827 37430 61538 39053 31937 40866 105230 51235 48689 TRUE FALSE 98494.18668 71721.52624 44194.43363 64713.98355 40309.17521 32582.78802 41366.13033 103056.9637 45419.01759 45391.25066 2.169893652 1.580073807 0.97363331 1.425692895 0.888038435 0.717820892 0.911323873 2.270414721 1.000611724 1 15.47012662 4.602866744 3.018543065 1.221634394 2.203645076 0.351671706 0.421332202 0.392853161 5.795895426 0.115600606 0.768239443 40074.37368 -4.602866744 0.982010682 RPEEITR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPEEITR 7 1 P98088 P98088 MUC5AC Mucin-5AC 0 ; 94.302 0.022929 152616000 190400 204183 173965 212126 199635 207927 221849 196903 218056 220062 FALSE TRUE 182958.9575 198359.9008 205404.3453 223073.8483 206056.4411 212131.4264 224564.0544 192836.8842 193303.197 205157.0047 0.891799711 0.96686877 1.001205616 1.087332351 1.004384137 1.033995533 1.094596086 0.939947844 0.9422208 1 17.64636889 4.602906786 2.159896077 1.014321289 0.877950541 0.375792812 0.048290961 0.54482586 3.569903861 0.013070849 0.128077621 40078.06874 -4.602906786 -0.136370747 LLEIVER ddPTM_BT-474_Pertuzumab_2h_R1 4 LLEIVER 7 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ;;; 127.12 0.0090405 485622000 461599 532378 441233 575394 572558 560974 565137 572341 555497 585353 FALSE TRUE 443559.2008 517195.1007 520973.6183 605090.1533 590974.8481 572317.2786 572053.3157 560521.9583 492439.3094 545706.5199 0.812816385 0.9477532 0.954677284 1.108819725 1.082953614 1.048763864 1.048280156 1.027149095 0.902388539 1 19.05776576 4.603059562 1.487489119 1.033450108 0.766719874 0.579579362 0.05542867 0.613344485 1.534607843 0.015431181 0.223958534 40092.16987 -4.603059562 -0.266730234 GFCFITFKEEEPVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFCFITFKEEEPVKK 15 2 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 198.59 4.41E-09 4753300000 4354130 3738490 2813310 2182520 3329580 3613490 3089950 3600440 4515490 3297520 FALSE TRUE 4183965.786 3631871.926 3321737.699 2295160.119 3436678.965 3686557.244 3127765.732 3526089.656 4002910.506 3074176.033 1.36100397 1.181413129 1.080529437 0.746593589 1.117918729 1.199201739 1.017432216 1.14700317 1.302108423 1 21.55176835 4.603141613 2.643987824 1.077360939 1.378194295 0.285839654 0.138272204 0.481431703 5.23310226 0.035621019 0.275185561 40099.74523 -4.603141613 0.300833356 VEDVEALDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEDVEALDR 9 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ; 173.48 0.00012889 1614720000 1296360 1408120 1228830 1411820 1412430 1403500 1475050 1535720 1456820 1555910 FALSE TRUE 1245696.818 1367961.796 1450906.916 1484684.199 1457862.094 1431879.732 1493102.103 1504006.845 1291447.901 1450526.83 0.858789229 0.943079279 1.000262033 1.023548251 1.005056965 0.987144603 1.029351593 1.036869374 0.89033024 1 20.46814555 4.603490604 2.098645368 1.002649593 0.840267769 0.538591855 0.03907197 0.359843306 2.187620926 0.009768574 0.099197635 40131.9816 -4.603490604 -0.162381824 GNFTLPEVAECFDEITYVELQKEEAQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNFTLPEVAECFDEITYVELQKEEAQK 27 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 203.78 3.37E-25 250490000 297590 231061 166178 127515 203953 221949 155889 189144 209664 187452 FALSE TRUE 285959.8538 224471.3665 196210.0612 134096.0644 210513.3335 226436.9608 157796.8162 185238.1103 185863.8217 174755.7091 1.636340554 1.2844866 1.122767675 0.767334384 1.204614914 1.295734268 0.902956573 1.059983169 1.063563661 1 17.41498006 4.604056933 1.994260594 1.049227258 1.717566814 0.632833909 0.138505593 0.355276445 1.891297782 0.036304503 0.391760557 40184.34863 -4.604056933 0.668339556 EGNDLYHEMIESGVINLK ddPTM_BT-474_Pertuzumab_2h_R1 7 EGNDLYHEMIESGVINLK 18 0 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;;;; 269.85 4.53E-32 2708900000 2790720 3883262 2704759 5743322 2699025 3530723 5421963 4491003 4320419 3560151 FALSE TRUE 2681655.577 3772515.17 3193569.118 6039735.537 2785841.59 3602116.638 5488318.605 4398262.219 3829983.148 3319018.802 0.807966371 1.136635673 0.96220278 1.819735258 0.839356978 1.085295641 1.65359672 1.325169419 1.153950422 1 21.66232537 4.604471153 1.378838087 1.27731853 0.713425416 0.160563348 0.289790242 1.670848335 3.442446938 0.078859127 1.224711 40222.69378 -4.604471153 -0.563893114 AFDIIER ddPTM_BT-474_Pertuzumab_2h_R1 6 AFDIIER 7 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BV15;H3BRD9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ;;;;; 149.48 0.0046838 785340000 1176874 1325130 1120295 1393880 1378750 1409340 1406400 1384400 1469560 1556860 FALSE TRUE 1130880.463 1287338.59 1322757.227 1465818.314 1423098.746 1437837.82 1423611.944 1355811.656 1302741.71 1451412.485 0.779158561 0.886955709 0.911358584 1.009925385 0.980492286 0.990647273 0.980845871 0.934132557 0.897568212 1 20.46902616 4.604938287 1.440285349 0.966645755 0.73551671 0.753069121 0.033562612 0.472446295 1.086127309 0.009746761 0.146356902 40265.98122 -4.604938287 -0.231129045 EHSELQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EHSELQDR 8 0 A0A669KBH7;A0A669KB27;B7Z2L0;Q9UHQ4 A0A669KBH7 BCAP29 B-cell receptor-associated protein 29 0 76.064 0.036769 20502000 19342 22559 18236 27934 23241 21482 28209 18388 24231 26206 FALSE TRUE 18586.09326 21915.63941 21531.65086 29375.67709 23988.56787 21916.38076 28554.23018 18008.28137 21480.39846 24431.04428 0.760757217 0.897040632 0.881323394 1.202391382 0.981888764 0.897070977 1.168768304 0.737106493 0.879225555 1 14.57642791 4.605305354 1.90213914 0.964433898 0.734241355 0.197014135 0.130058634 1.080834484 5.080377327 0.034949076 0.399551977 40300.02858 -4.605305354 -0.230192543 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER ddPTM_BT-474_Pertuzumab_2h_R1 2 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER 32 0 P23258;K7EIS0;Q9NRH3 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ; 397.12 1.15E-166 163389000 83516 96517 75353 105937 101718 102593 98371 97467 100678 101427 FALSE TRUE 80252.10239 93764.42966 88970.96332 111404.4213 104989.8518 104667.5008 99574.89372 95454.27239 89249.45552 94557.25895 0.848714348 0.991615352 0.940921557 1.178168895 1.110330957 1.1069219 1.053064512 1.009486458 0.94386678 1 16.52890059 4.605360318 1.449184839 1.054532155 0.80983496 0.426516761 0.069613493 0.913368268 2.131586293 0.020113765 0.300902276 40305.12928 -4.605360318 -0.244697194 RSDS(ph)LLSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSDSLLSFR 9 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 RSDS(1)LLSFR;RSDS(1)LLSFR 190.26 2.28E-05 329420000 192425 124323 58438 68809 63020 47052 52240 98013 59865 59338 TRUE FALSE 184904.8183 120777.4298 68999.04655 72360.24074 65047.09553 48003.42368 52879.32875 95988.9973 53069.37617 55318.98441 3.342520118 2.183290801 1.247294166 1.308054396 1.17585484 0.867756778 0.955898401 1.735190881 0.959333884 1 15.75548705 4.605481249 1.741620749 1.177760534 3.766079346 0.894017291 0.238250432 0.215775105 0.806827217 0.067537465 0.849458179 40316.35392 -4.605481249 2.588318812 up TLPS(ph)GSPRPGQLERPTSLALDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLPSGSPRPGQLERPTSLALDSR 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 T(0.03)LPS(0.509)GS(0.461)PRPGQLERPTSLALDSR 65.581 0.015194 1017600000 516120 580140 474730 576540 616810 630070 615610 609700 639450 595330 TRUE FALSE 495949.4598 563594.9752 560524.2713 606295.2985 636650.2538 642810.4471 623144.0193 597109.4819 566862.3168 555007.7688 0.893590122 1.015472227 1.009939505 1.09240867 1.147101517 1.158200809 1.1227663 1.075857881 1.021359247 1 19.08214844 4.605796348 1.132347517 1.09596961 0.836640177 0.567683165 0.050651542 0.938789323 1.184798782 0.015490599 0.274445829 40345.61572 -4.605796348 -0.259329433 DYDVEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYDVEIR 7 0 P50583 P50583 NUDT2 Bis(5-nucleosyl)-tetraphosphatase [asymmetrical] 0 ; 85.064 0.049054 833280000 1051400 1223010 1142890 1174270 1229250 1304090 1315150 1388970 1394520 1411780 FALSE TRUE 1010310.126 1188130.952 1349435.646 1234874.215 1268789.943 1330459.593 1331245.199 1360287.284 1236219.936 1316158.883 0.767620185 0.902726082 1.025283242 0.938240991 0.96400971 1.010865489 1.011462382 1.033528172 0.939263452 1 20.32790223 4.60606389 2.488945502 0.992839221 0.748159178 0.813924449 0.032769216 0.156489991 1.46235766 0.00848341 0.071073445 40370.47786 -4.60606389 -0.244680043 LLLEHLECLVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLLEHLECLVSR 12 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;E9PPF6;O75335;G3V200;O75334-2;O75334-4;O75334-3;B1APN9;O75334;F8VWR9;O75334-5;O75334-6;O75145-2;O75145;R4GN36;R4GNF1 Q13136-2;O75145-2 PPFIA1;PPFIA4;PPFIA2;PPFIA3 Liprin-alpha-1;Liprin-alpha-4;Liprin-alpha-2;Liprin-alpha-3 0 ; 131.06 0.00020543 143721000 292240 334060 277360 368620 342790 323710 376680 343120 358920 398390 FALSE TRUE 280818.9377 324532.9359 327485.1218 387644.5224 353816.1517 330255.638 381289.9225 336034.4521 318176.9063 371406.6905 0.756095528 0.873793995 0.881742656 1.043719815 0.952638067 0.889202178 1.026610269 0.90476144 0.8566806 1 18.50264028 4.606151387 1.576895229 0.94736124 0.718492258 0.504031574 0.058824576 0.667114903 1.929133077 0.015653352 0.217778229 40378.61211 -4.606151387 -0.228868981 SKS(ph)DSYTLDPDTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 SKS(0.907)DS(0.09)YT(0.003)LDPDTLR;S(0.055)KS(0.917)DS(0.028)YTLDPDTLR 252.47 8.76E-24 1465820000 2875880 2514500 1944220 1899320 2158460 1675430 1829990 3467180 2157000 2006700 TRUE FALSE 2763487.43 2442788.922 2295583.803 1997344.133 2227888.826 1709308.343 1852385.965 3395581.521 1912146.403 1870784.422 1.477181122 1.305756502 1.227070194 1.067650612 1.19088485 0.913685363 0.990165379 1.815057621 1.022109432 1 20.83521189 4.606389225 2.06607618 1.195372217 1.513613172 0.134326514 0.243029954 1.335316017 7.764342501 0.068579873 0.716752186 40400.73114 -4.606389225 0.318240955 EFRPEDQPWLLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EFRPEDQPWLLR 12 1 P35269;M0QXD6;M0R0R9;M0R0Z3 P35269 GTF2F1 General transcription factor IIF subunit 1 0 ;;; 226.42 1.40E-11 927890000 649690 711400 618079 728860 730800 749920 694500 770900 740590 777990 FALSE TRUE 624299.3965 691111.5685 729779.6244 766476.5519 754306.8457 765083.8962 702999.4987 754980.6456 656521.328 725296.0443 0.860751139 0.952868245 1.006181724 1.056777516 1.039998566 1.054857395 0.969258697 1.040927565 0.905177042 1 19.46821046 4.606411043 2.106822021 1.014505933 0.841201315 0.52153774 0.043645061 0.374959111 2.293035993 0.010844814 0.110812844 40402.76087 -4.606411043 -0.173304618 SLS(ph)FSEPQQPAPAMK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSFSEPQQPAPAMK 15 0 Q9H8N7 Q9H8N7 ZNF395 Zinc finger protein 395 1 S(0.006)LS(0.992)FS(0.002)EPQQPAPAMK;S(0.1)LS(0.9)FSEPQQPAPAMK 189.1 1.31E-08 252090000 600604 516898 360047 397660 392518 370008 332066 516603 401060 330882 TRUE FALSE 577131.7317 502156.5751 425115.5021 418183.2803 405143.6979 377489.8153 336129.923 505934.9675 355533.3502 308471.0674 1.870942829 1.627888733 1.378137359 1.355664516 1.313392862 1.22374464 1.089664343 1.640137507 1.152566278 1 18.23477565 4.60642562 1.152176277 1.2845838 2.079555482 0.601400348 0.16437211 0.947406885 1.24639557 0.048907556 0.860331114 40404.11703 -4.60642562 0.794971682 DQMDKEWDEFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQMDKEWDEFQK 12 1 Q96NB3;J3QQQ3 Q96NB3 ZNF830 Zinc finger protein 830 0 79.466 0.020938 274940000 106550 116590 106350 99804 118560 135850 118570 126960 121430 131850 FALSE TRUE 102385.9082 113264.9674 125569.8107 104954.8964 122373.5901 138596.9801 120021.0951 124338.2316 107645.7755 122919.6821 0.832949667 0.921455095 1.02155984 0.853849397 0.995557327 1.127540991 0.976418854 1.011540459 0.875740757 1 16.90735641 4.606554795 2.438792119 0.98560413 0.818102242 0.288690011 0.072363516 0.511920726 4.544543704 0.018345434 0.157735516 40416.13644 -4.606554795 -0.167501888 SMSSIPPYPASSLASS(ph)SPPGSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPASSLAS(0.006)S(0.822)S(0.172)PPGSGR 222.39 1.71E-32 376800000 104750 116100 103470 127110 118160 107550 128310 117640 124580 117720 TRUE FALSE 100656.2542 112788.9417 122169.3307 133670.1623 121960.7237 109724.7347 129880.2962 115210.6929 110438.2007 109746.7195 0.917168683 1.027720392 1.113193462 1.217987771 1.111292658 0.999799676 1.183454929 1.049787122 1.0063007 1 16.74381829 4.606590123 2.849271138 1.092024053 0.908682458 0.334049285 0.071722715 0.353413805 4.564282178 0.017751565 0.12717725 40419.42422 -4.606590123 -0.183341595 DYELQLASYTSGLETLLNIPIKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYELQLASYTSGLETLLNIPIKR 23 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 171.58 9.62E-12 259210000 278710 342660 342560 336880 338830 345620 362390 391860 435550 408060 FALSE TRUE 267817.7051 332887.6723 404468.2122 354266.4172 349728.7747 352608.6732 366825.0372 383767.9541 386108.19 380421.7327 0.704002117 0.875049041 1.063210057 0.931246526 0.9193186 0.926888878 0.964258889 1.008796083 1.014947772 1 18.53724014 4.606789511 3.21924316 0.974464031 0.69744331 0.781349807 0.044435134 0.126169968 2.126624784 0.011351429 0.071178699 40437.98538 -4.606789511 -0.277020721 QLLEEELAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLLEEELAR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 128.12 0.00099163 181160000 220010 249410 209160 284480 254570 236320 288560 256740 239490 275080 FALSE TRUE 211411.766 242297.071 246959.8647 299162.0469 262758.4752 241098.5523 292091.4836 251438.2293 212304.0992 256448.5866 0.824382652 0.944817338 0.962999516 1.166557597 1.024604888 0.940143814 1.138986522 0.980462527 0.827862232 1 17.96831009 4.60681436 1.925959267 1.01435159 0.797841597 0.270362096 0.09077599 0.761852945 3.690386224 0.023563134 0.267161318 40440.29922 -4.60681436 -0.216509994 LSEPWEGDFQEDHNANLWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSEPWEGDFQEDHNANLWR 19 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 0 ; 294.45 1.22E-49 336680000 114454 127965 112329 135008 123060 147565 130648 132501 136743 143827 FALSE TRUE 109981.0111 124315.5635 132629.349 141975.7791 127018.3367 150548.8654 132246.9093 129764.808 121220.5079 134085.4692 0.820230647 0.92713673 0.989140358 1.058845376 0.947293823 1.122782851 0.98628815 0.967776813 0.904054024 1 17.03279338 4.606818008 2.10629793 0.998832006 0.797391185 0.48528466 0.056422553 0.432058668 2.639007245 0.014501779 0.148445438 40440.63892 -4.606818008 -0.201440821 SGMS(ph)PEQSR ddPTM_BT-474_Pertuzumab_2h_R1 11 SGMSPEQSR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.118)GMS(0.882)PEQSR;S(0.014)GMS(0.986)PEQSR;S(0.008)GMS(0.992)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;S(0.004)GMS(0.996)PEQSR;S(0.009)GMS(0.991)PEQSR;SGMS(0.999)PEQSR 163.09 6.64E-05 14968197000 6824623 6983543 5852266 6903553 6663948 6865115 6784537 7114222 7394129 7144474 TRUE FALSE 6557909.188 6784379.191 6909900.649 7259846.198 6878299.939 7003932.329 6867568.193 6967310.83 6554778.475 6660572.412 0.984586426 1.018588009 1.037433455 1.089973316 1.032689011 1.051551112 1.031077777 1.046052861 0.98411639 1 22.66721474 4.606877956 2.562193871 1.038323281 0.98073445 0.22237166 0.027213141 0.493146057 4.945133319 0.006584932 0.053450256 40446.22148 -4.606877956 -0.05758883 GFFDPNTHENLTYLQLLER ddPTM_BT-474_Pertuzumab_2h_R1 4 GFFDPNTHENLTYLQLLER 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 ;;; 298.26 8.69E-50 4612443000 2698135 3049109 2734323 3125851 3143452 3394809 3238637 3139793 3193569 3402367 FALSE TRUE 2592688.901 2962151.397 3228475.991 3287176.545 3244563.988 3463454.364 3278272.408 3074955.177 2831048.436 3171921.653 0.817387434 0.933866508 1.017829677 1.036335983 1.02290168 1.091910439 1.033528809 0.969429738 0.892534162 1 21.59692571 4.607041351 2.311518906 1.010681975 0.797263343 0.589942751 0.048995935 0.320089716 2.480771591 0.013338224 0.122457278 40461.44153 -4.607041351 -0.213418632 AGHFDKEIVPVLVSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGHFDKEIVPVLVSTR 16 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 90.223 0.0033188 529400000 1189900 1000200 756420 646810 816970 964220 866200 851580 1116400 969490 FALSE TRUE 1143397.392 971675.2753 893121.9205 680191.9416 843248.582 983717.189 876800.8147 833994.5754 989670.9523 903825.5788 1.265064211 1.075069458 0.988157385 0.752569918 0.932977116 1.08839273 0.97009958 0.922738408 1.094980022 1 19.78568486 4.607101321 2.249949515 0.959780322 1.297128102 0.500514324 0.090682428 0.378313198 2.736794729 0.023794956 0.225627239 40467.02901 -4.607101321 0.33734778 AEELHYPLGER ddPTM_BT-474_Pertuzumab_2h_R1 3 AEELHYPLGER 11 0 Q14257;Q14257-2;A8MXP8;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ;; 119.05 0.00063832 722330000 745810 905010 840070 1034580 904470 968580 985430 917890 1053320 1148540 FALSE TRUE 716662.9207 879200.0009 991889.3363 1087974.798 933563.099 988165.3512 997489.9871 898935.2507 933751.5295 1070748.363 0.669310312 0.821107957 0.926351485 1.01608822 0.871879081 0.922873558 0.93158208 0.839539225 0.872055062 1 20.03018804 4.607125116 2.510835965 0.914586854 0.649612548 0.686840082 0.052701427 0.231066829 2.203751604 0.013726001 0.11422345 40469.24626 -4.607125116 -0.264974306 LEGDSDDLLEDS(ph)DSEEHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEGDSDDLLEDSDSEEHSR 19 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 1 LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR 408.9 7.33E-148 2907200000 1968340 2200230 1928910 2305780 2119190 2445420 2273710 2213430 2729100 2653200 TRUE FALSE 1891415.097 2137481.595 2277506.945 2424781.582 2187355.671 2494868.068 2301536.343 2167721.897 2419304.009 2473496.401 0.76467267 0.864153913 0.920764204 0.98030528 0.884317305 1.008640266 0.930478954 0.876379645 0.978090774 1 21.23812037 4.607157653 1.751402957 0.941202609 0.731624298 0.640632128 0.04314291 0.443878112 1.679811667 0.011298701 0.142147608 40472.27836 -4.607157653 -0.209578311 EEPGPRPR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEPGPRPR 8 1 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;; 133.55 0.00083421 1252160000 1764570 1927150 1652700 1993250 1892220 2049520 2050770 2036110 2216060 2252490 FALSE TRUE 1695608.654 1872189.569 1951379.654 2096121.871 1953084.975 2090962.699 2075867.937 1994063.617 1964502.159 2099926.846 0.80746082 0.8915499 0.929260778 0.998188044 0.930072863 0.99573121 0.988542977 0.949587182 0.935509807 1 21.00190764 4.607573975 1.344856783 0.968688904 0.763217091 0.803224132 0.02533585 0.421032576 0.81120189 0.006919215 0.110656034 40511.09437 -4.607573975 -0.205471812 GT(ph)SPTQIWCNNSQLPVDHILAGSFETAMR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTSPTQIWCNNSQLPVDHILAGSFETAMR 29 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 GT(0.487)S(0.487)PT(0.027)QIWCNNSQLPVDHILAGSFETAMR 123.54 9.25E-05 130380000 12422 15050 14331 14912 20099 16258 14083 15387 16195 19540 TRUE FALSE 11936.53451 14620.78874 16920.93049 15681.61011 20745.50259 16586.7479 14255.35197 15069.25307 14356.61149 18216.5384 0.655258109 0.802610706 0.928877382 0.860844677 1.138827923 0.910532371 0.782549992 0.827229232 0.788108651 1 14.15296122 4.607595659 2.608987452 0.895313896 0.637601398 0.365492464 0.101134071 0.438422339 4.591088304 0.026930645 0.214482163 40513.11707 -4.607595659 -0.257712498 DNALLSAIEESR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNALLSAIEESR 12 0 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ; 207.34 1.85E-07 99914000 81009 94374 78241 104776 96536 93305 108558 100847 110177 122252 FALSE TRUE 77843.07872 91682.54592 92380.88916 110183.5019 99641.16811 95191.69103 109886.5653 98764.47421 97670.16886 113971.7631 0.683003198 0.80443211 0.810559446 0.966761405 0.874261882 0.835221711 0.964156053 0.866569679 0.856968131 1 16.79831691 4.607679959 1.195749808 0.900122862 0.619498564 0.616490477 0.055110012 0.798075261 1.148103508 0.015210973 0.263104471 40520.98178 -4.607679959 -0.280624298 VDIDT(ph)PDIDIHGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 5 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK 265.29 1.63E-26 1638590000 1923060 2445730 2624160 2312770 2500880 2862230 2046970 2786250 3367060 3082010 TRUE FALSE 1847904.689 2375980.175 3098404.086 2432132.337 2581323.076 2920106.252 2072021.431 2728712.964 2984845.465 2873262.718 0.643138088 0.826927576 1.07835739 0.846470572 0.89839438 1.016303255 0.721138871 0.949691425 1.038834857 1 21.45425848 4.608273807 3.627595441 0.929903833 0.642675634 0.45531152 0.099899401 0.219016983 4.639250185 0.023453843 0.131314549 40576.42742 -4.608273807 -0.2872282 VIDPATATSVDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIDPATATSVDLR 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 127.92 0.00039866 228586000 171504 193795 186176 192546 182077 193975 214141 202650 201951 225240 FALSE TRUE 164801.4341 188268.1563 219822.1447 202483.3221 187933.6721 197897.3074 216761.7216 198465.2067 179026.3691 209984.2942 0.784827431 0.896582085 1.046850411 0.964278414 0.894989184 0.942438615 1.032275878 0.9451431 0.852570283 1 17.6799219 4.608581368 3.626956174 0.958886255 0.784537459 0.475647585 0.05591557 0.209044205 4.425831507 0.013584076 0.076111417 40605.17324 -4.608581368 -0.174348796 SIEAVHEDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIEAVHEDIR 10 0 P23919-2;P23919;H7C312;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 ; 143.61 3.37E-05 1666820000 1036910 1161340 1005900 1244190 1168860 1265680 1284500 1132590 1240100 1270580 FALSE TRUE 996386.4108 1128219.72 1187688.506 1308402.795 1206457.443 1291272.917 1300220.095 1109201.621 1099329.047 1184522.485 0.841171378 0.952467965 1.002672825 1.104582489 1.018517976 1.090121068 1.097674474 0.936412466 0.928077821 1 20.17587415 4.608619701 2.009563752 1.024934343 0.815502867 0.48045696 0.058367159 0.512037371 2.762056527 0.01639113 0.178323938 40608.75744 -4.608619701 -0.209431476 VWGSPGGEGTGDLDEFDF ddPTM_BT-474_Pertuzumab_2h_R1 5 VWGSPGGEGTGDLDEFDF 18 0 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 ;;;; 311.33 8.48E-61 343269000 259984 324380 280591 391220 317134 333324 380693 352602 404779 442672 FALSE TRUE 249823.5379 315129 331300.0354 411410.9111 327334.9031 340064.0397 385352.0348 345320.6455 358830.1849 412689.4311 0.605354824 0.763598426 0.802782941 0.99690198 0.793174912 0.82401926 0.933757944 0.836756697 0.869492063 1 18.65469697 4.608867339 1.522935538 0.879505622 0.544318691 0.623304183 0.068496588 0.546748805 1.440598194 0.017634458 0.255740136 40631.91943 -4.608867339 -0.335186931 SLS(ph)PSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSPSVR 7 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.014)LS(0.975)PS(0.011)VR;S(0.037)LS(0.963)PSVR 101.72 0.019978 0 526410 606920 558440 684940 608590 618250 634720 616270 654380 693220 TRUE FALSE 505837.3152 589611.2358 659362.5304 720289.8355 628165.8501 630751.4386 642487.8932 603543.8091 580097.5258 646267.5919 0.78270568 0.912332977 1.020262409 1.114538071 0.97199033 0.975991132 0.994151496 0.933891497 0.897611969 1 19.30177212 4.609097747 2.936585903 0.986683324 0.773719267 0.57645693 0.054043018 0.239569132 3.305901944 0.014549462 0.101480901 40653.48178 -4.609097747 -0.212964057 ALRPEAPPPPPPAFSFQEFLPSLNS(ph)SPLDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALRPEAPPPPPPAFSFQEFLPSLNSSPLDIR 31 1 Q9P107;K7EJC2;Q9P107-2 Q9P107 GMIP GEM-interacting protein 1 ALRPEAPPPPPPAFS(0.004)FQEFLPS(0.049)LNS(0.473)S(0.473)PLDIR 95.172 0.00023945 65220000 46326 54056 54852 50956 53797 52355 61961 60873 53179 58774 TRUE FALSE 44515.5287 52514.37581 64764.97658 53585.84527 55527.42936 53413.65397 62719.29725 59615.95128 47142.34286 54793.18463 0.812428206 0.958410725 1.18198964 0.977965519 1.013400293 0.974822952 1.144655082 1.088017637 0.860368734 1 15.74170884 4.609420239 3.818759989 1.039010029 0.814019032 0.355165671 0.087777592 0.23606232 5.461088272 0.020820848 0.111705118 40683.68083 -4.609420239 -0.224990997 DSS(ph)FER ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSFER 6 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DS(0.429)S(0.571)FER 69.628 0.097556 118450000 105180 115820 108040 103910 121330 125280 101150 127360 132700 126140 TRUE FALSE 101069.4493 112516.927 127565.2313 109272.8076 125232.6896 127813.2474 102387.904 124729.9715 117636.4523 117596.4254 0.859460217 0.956805673 1.084771334 0.929218785 1.064936193 1.086880379 0.870671907 1.060661249 1.000340375 1 16.84348468 4.609431407 3.533539703 1.01150719 0.858303725 0.331528818 0.066038637 0.273045604 5.510575413 0.015153934 0.087126833 40684.72707 -4.609431407 -0.153203466 IFVNDDR ddPTM_BT-474_Pertuzumab_2h_R1 6 IFVNDDR 7 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;K7ERM6;K7ENK6;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 214.59 9.68E-05 12998800000 6166270 6713030 5667960 7303040 6587240 6740660 6878340 7033680 6804470 7081280 FALSE TRUE 5925285.351 6521580.957 6692286.455 7679950.77 6799124.557 6876960.764 6962519.182 6888432.05 6032055.092 6601658.598 0.897544952 0.987870072 1.013728044 1.163336555 1.029911568 1.041701969 1.054662109 1.043439607 0.913718121 1 22.6543971 4.609919356 2.121017838 1.04019356 0.880496461 0.33191787 0.057989963 0.551162022 3.412554221 0.014710014 0.151083022 40730.46386 -4.609919356 -0.159697099 RPQGESYDQAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPQGESYDQAIR 12 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 98.337 0.00708 263170000 88448 115730 106950 137250 142190 130340 133990 122550 115640 136950 FALSE TRUE 84991.35438 112429.4937 126278.2441 144333.4889 146763.6705 132975.5641 135629.8097 120019.2997 102513.032 127674.2545 0.665689059 0.880596438 0.989065842 1.130482332 1.149516565 1.04152215 1.06231135 0.940043082 0.802926419 1 16.96210811 4.610326002 2.041484774 1.021211253 0.616636546 0.575402169 0.092645115 0.411031621 2.30395325 0.025986395 0.279420332 40768.61918 -4.610326002 -0.404574708 ALQSGQCAGAALDVFTEEPPRDR ddPTM_BT-474_Pertuzumab_2h_R1 5 ALQSGQCAGAALDVFTEEPPRDR 23 1 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YF78 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ;;;; 297.48 9.00E-62 5708410000 832332 954449 874250 992965 933976 1031930 1052344 1044014 936715 995193 FALSE TRUE 799803.5452 927229.049 1032246.423 1044212.043 964018.1863 1052796.332 1065222.901 1022454.746 830383.0402 927787.6917 0.86205449 0.999397877 1.112589046 1.125485983 1.039050415 1.134738412 1.148132175 1.102035256 0.895014072 1 19.82343518 4.610476218 2.736200465 1.081284415 0.8482918 0.41631115 0.073674692 0.301389607 3.52719053 0.017938775 0.136355175 40782.72288 -4.610476218 -0.232992616 LQTTDNLLPMS(ph)PEEFDEVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQTTDNLLPMSPEEFDEVSR 20 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta 1 LQTTDNLLPMS(0.998)PEEFDEVS(0.002)R;LQTTDNLLPMS(1)PEEFDEVSR 94.201 0.000903 81024000 110383 130462 110745 146484 151768 146201 129778 130460 140694 146179 TRUE FALSE 106069.1103 126741.3515 130759.085 154044.0568 156649.7556 149157.2844 131366.262 127765.9554 124723.007 136278.1661 0.778327984 0.930019497 0.959501355 1.130364909 1.14948535 1.094506102 0.963956778 0.937537971 0.915209021 1 17.05619491 4.610743575 1.791464649 1.021984546 0.737822567 0.490872823 0.076300386 0.659746893 2.633279334 0.023398581 0.291258323 40807.83697 -4.610743575 -0.284161979 IWDPVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 IWDPVHR 7 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C1S4;A0A494C159 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 81.784 0.026263 237730000 346080 397930 359100 421930 405910 428040 421040 408940 425750 473630 FALSE TRUE 332554.811 386581.426 423997.3581 443705.8579 418966.4638 436695.2621 426192.8135 400495.2461 377420.6449 441550.6182 0.753152181 0.875508741 0.960246324 1.00488107 0.948852626 0.989003852 0.965218473 0.90702001 0.854761899 1 18.75221931 4.611420291 2.424693212 0.951454011 0.734587926 0.67437599 0.042991755 0.252127602 2.192498736 0.011440209 0.100771355 40871.47311 -4.611420291 -0.216866085 AYILVT(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AYILVTPLK 9 0 Q6P0N0 Q6P0N0 MIS18BP1 Mis18-binding protein 1 1 AYILVT(1)PLK 131.82 0.0036043 285660000 785320 653940 431440 545690 517830 420280 460550 690380 454600 483840 TRUE FALSE 754628.8262 635290.2715 509410.8053 573853.1263 534486.4722 428778.3496 466186.3487 676123.4117 402995.7138 451069.0858 1.672978375 1.408410134 1.129340984 1.272206729 1.184932617 0.950582434 1.033514296 1.49893538 0.893423483 1 18.78298889 4.611512996 1.674431371 1.147946233 1.790546198 0.521386081 0.168136074 0.642600658 2.151320107 0.045937492 0.614699132 40880.19855 -4.611512996 0.642599966 WATHGEPSPVNSHPQR ddPTM_BT-474_Pertuzumab_2h_R1 4 WATHGEPSPVNSHPQR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;; 197.17 2.54E-11 2594610000 630170 759430 707080 926030 735390 769360 934770 649640 877200 931060 FALSE TRUE 605542.2597 737771.8 834865.0849 973822.5193 759044.4872 784916.9863 946209.9949 636224.707 777623.9335 867998.4769 0.697630556 0.849969003 0.961827822 1.121917313 0.87447675 0.904283829 1.090105594 0.732979059 0.89588168 1 19.72733299 4.61154169 2.815562286 0.936447412 0.684546972 0.344790546 0.105409983 0.405743684 5.072965009 0.027236691 0.200890469 40882.89959 -4.61154169 -0.25190044 TGQPAQPAPSAQQPPRPPAS(ph)PDEPSVAASSVGSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TGQPAQPAPSAQQPPRPPASPDEPSVAASSVGSSR 35 1 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR;TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR;TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR 321.06 2.37E-105 2882120000 222594 251999 227715 266650 241563 273462 257612 254077 297769 277505 TRUE FALSE 213894.7804 244812.2353 268868.166 280411.8385 249333.0933 278991.589 260764.7327 248830.2212 263967.5115 258709.3392 0.826776417 0.946282945 1.039267337 1.083887576 0.963757606 1.078397826 1.007944798 0.961813833 1.020324633 1 17.98097261 4.611658213 2.714796777 1.016626817 0.814444044 0.694977046 0.039190412 0.198163525 2.273396133 0.010083422 0.077657556 40893.87007 -4.611658213 -0.202182773 QGSITSPQANEQSVT(ph)PQRR ddPTM_BT-474_Pertuzumab_2h_R1 6 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQS(0.001)VT(0.999)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQS(0.011)VT(0.989)PQRR;QGSITSPQANEQS(0.008)VT(0.992)PQRR 331.61 1.61E-75 5389810000 322827 353681 307101 375439 356855 360104 339200 380706 369241 385932 TRUE FALSE 310210.5639 343594.3642 362600.9821 394815.4518 368333.5652 367385.5496 343351.2311 372844.2881 327326.3097 359792.4819 0.862193013 0.954979277 1.007805889 1.097342139 1.023738915 1.02110402 0.954303518 1.036275928 0.909764173 1 18.45680552 4.611688404 2.409508785 1.010271444 0.848462242 0.468580061 0.046879011 0.350819808 3.001880923 0.011743644 0.104327624 40896.71306 -4.611688404 -0.161809203 QLSES(ph)ESSLEMDDER ddPTM_BT-474_Pertuzumab_2h_R1 4 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLSES(0.999)ES(0.001)SLEMDDER;QLS(0.012)ES(0.936)ES(0.026)S(0.026)LEMDDER;QLSES(0.466)ES(0.137)S(0.397)LEMDDER;QLS(0.005)ES(0.993)ES(0.001)S(0.001)LEMDDER 400.14 1.91E-115 1148720000 560440 660360 620410 716180 682150 682470 590260 755650 752830 775570 TRUE FALSE 538537.3852 641527.1794 732531.8879 753142.1356 704091.9743 696270.011 597483.7784 740045.5634 667371.8945 723039.9531 0.744823827 0.887263804 1.013127815 1.041632807 0.973794009 0.962975847 0.826349603 1.0235196 0.923008323 1 19.46371584 4.611900885 2.955501577 0.968657703 0.734649948 0.581988097 0.058546935 0.218260305 3.04799447 0.014631775 0.102154841 40916.72691 -4.611900885 -0.234007756 YNEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 YNEEER 6 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42 K7EP07 TBCB Tubulin-folding cofactor B 0 114.78 0.058137 93490000 166690 176420 152310 174890 164690 183420 166880 189010 182780 201070 FALSE TRUE 160175.5705 171388.6743 179835.8051 183916.0939 169987.4034 187128.8781 168922.3274 185106.8774 162031.5807 187451.3498 0.854491422 0.914310164 0.95937322 0.981140408 0.906834779 0.998279704 0.901152899 0.987492902 0.864392712 1 17.51615669 4.612394419 2.629030713 0.949945071 0.847468251 0.311102396 0.043534432 0.398688496 4.230299995 0.009750215 0.078205978 40963.25118 -4.612394419 -0.10247682 DYSSGFGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYSSGFGGK 9 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 161.02 0.00015087 619180000 357850 386360 345730 358690 377580 380220 391440 419770 416160 432780 FALSE TRUE 343864.8264 375341.3911 408211.1017 377202.0339 389725.2036 387908.3089 396230.5598 411101.6028 368919.2615 403467.4251 0.852274075 0.930289207 1.011757273 0.934900838 0.9659397 0.9614365 0.982063322 1.018921423 0.914371864 1 18.62209267 4.612552916 3.096033357 0.97504075 0.847735408 0.584346902 0.031184008 0.19274199 2.979499262 0.007505641 0.049827761 40978.20356 -4.612552916 -0.127305342 EAPNPIHLTVDTSLQNGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAPNPIHLTVDTSLQNGR 18 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 163.45 3.31E-11 958840000 495460 584760 522240 655040 563430 680010 680480 658860 664960 716730 FALSE TRUE 476096.8754 568083.2173 616620.3852 688846.6929 581553.2376 693760.2681 688807.9178 645254.3108 589476.5285 668185.2387 0.712522289 0.850188218 0.922828505 1.030921746 0.870347329 1.038275358 1.030863715 0.96568178 0.882205254 1 19.34988859 4.613061426 1.42479161 0.975122757 0.643098274 0.679350387 0.056003775 0.533133399 1.178894149 0.015182595 0.236475014 41026.21253 -4.613061426 -0.332024483 IDHLSSSAPGS(ph)PPDLLESVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDHLSSSAPGSPPDLLESVPK 21 0 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 IDHLSSSAPGS(0.999)PPDLLESVPK 146.25 7.12E-08 95728000 109240 140270 122920 171270 151450 158780 164560 123250 161400 220950 TRUE FALSE 104970.78 136269.6369 145134.3783 180109.2652 156321.5268 161990.6404 166573.9345 120704.8444 143078.5486 205984.8597 0.509604348 0.661551714 0.704587602 0.874381086 0.75889814 0.786420131 0.808670767 0.585988915 0.694607113 1 17.65217877 4.613425602 1.78208334 0.759449189 0.465715321 0.383923509 0.105052132 0.776956251 3.046980644 0.028004162 0.354011203 41060.62941 -4.613425602 -0.293733867 CLS(ph)PGGHPTYRPAYLLENEEEER ddPTM_BT-474_Pertuzumab_2h_R1 3 CLSPGGHPTYRPAYLLENEEEER 23 1 Q8NFF5-2;Q8NFF5;Q5T190 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 1 CLS(1)PGGHPTYRPAYLLENEEEER;CLS(1)PGGHPTYRPAYLLENEEEER;CLS(1)PGGHPTYRPAYLLENEEEER 218.6 1.34E-32 710584000 203611 243511 219761 260436 270237 350922 234478 233827 272491 254686 TRUE FALSE 195653.657 236566.3047 259476.7013 273877.1332 278929.4185 358017.8833 237347.6119 228998.3907 241558.9641 237435.8904 0.824027306 0.996337598 1.092828472 1.153478241 1.174756765 1.507850741 0.999628201 0.964464093 1.017364998 1 17.8571785 4.613557824 1.896575019 1.117327746 0.775374132 0.271594726 0.1477685 0.902204234 4.157637212 0.042064606 0.497452196 41073.1323 -4.613557824 -0.341953614 IQPQPPDEDGDHS(ph)DKEDEQPQVVVLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQPQPPDEDGDHSDKEDEQPQVVVLKK 27 2 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 IQPQPPDEDGDHS(1)DKEDEQPQVVVLKK 116.13 0.00032178 148750000 94790 77043 53369 43355 59543 78204 65787 65133 96084 68714 TRUE FALSE 91085.502 74845.80907 63013.96549 45592.55675 61458.25467 79785.33846 66592.12099 63787.98079 85176.94714 64059.93958 1.421879299 1.168371522 0.983671947 0.711717136 0.95938671 1.245479452 1.039528314 0.99575462 1.329644513 1 15.96713482 4.613566058 2.83100991 1.026451656 1.443613057 0.360760854 0.157626721 0.362677079 4.583624221 0.04049661 0.298683131 41073.91103 -4.613566058 0.417161401 DTIEEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTIEEHR 7 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 149.4 0.0020189 351610000 517690 582140 519810 605850 600250 627490 602190 557880 648870 695840 FALSE TRUE 497458.1025 565537.9372 613751.2301 637117.9911 619557.5864 640178.2777 609559.7814 546359.583 575212.9979 648710.137 0.766841882 0.871788346 0.946110127 0.982130469 0.955060744 0.986847964 0.939648923 0.842224519 0.88670265 1 19.30721446 4.61376734 2.515550811 0.934972348 0.752428367 0.58252767 0.045648416 0.326040209 3.099109802 0.013164856 0.11186976 41092.95192 -4.61376734 -0.182543982 EILDESLR ddPTM_BT-474_Pertuzumab_2h_R1 3 EILDESLR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 171.38 0.00067396 570680000 1357000 1507090 1316950 1585840 1464580 1503310 1632150 1621780 1562440 1673720 FALSE TRUE 1303966.94 1464109.269 1554952.16 1667685.392 1511689.546 1533707.958 1652124.74 1588289.676 1385078.361 1560357.454 0.835684757 0.93831658 0.996535862 1.0687842 0.96880977 0.982920904 1.058811708 1.017901169 0.887667347 1 20.57344514 4.613770334 2.191178112 1.003338778 0.815219783 0.520127164 0.047606477 0.365723551 2.449361176 0.01202765 0.12060986 41093.23525 -4.613770334 -0.188118995 DPNNYRPR ddPTM_BT-474_Pertuzumab_2h_R1 3 DPNNYRPR 8 1 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ;; 88.294 0.013422 183390000 170862 206284 199243 239838 201903 204136 223224 217757 219022 245887 FALSE TRUE 164184.5241 200400.9823 235250.6422 252216.0679 208397.3934 208263.7698 225955.8821 213260.2419 194159.5408 229232.8545 0.716234697 0.874224521 1.026251855 1.100261428 0.909107876 0.908524959 0.985704613 0.930321451 0.846997003 1 17.80645431 4.613898363 3.17516738 0.961201736 0.708641518 0.553171146 0.067790974 0.217621448 3.54633595 0.017375239 0.112598969 41105.35122 -4.613898363 -0.252560218 TEESPASDEAGEKEAKS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 1 TEESPASDEAGEKEAKSD 18 2 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEESPASDEAGEKEAKS(1)D 130.09 2.02E-05 0 444230 331090 221560 161340 273110 249810 248390 322060 321630 222810 TRUE FALSE 426869.0005 321647.6374 261600.8206 169666.7767 281894.8312 254861.3294 251429.8711 315409.3485 285119.9108 207718.8802 2.055032263 1.548475695 1.259398377 0.816809606 1.35709778 1.226953126 1.210433403 1.518443331 1.372623954 1 17.66427283 4.614076648 2.356411434 1.244191527 2.137096697 0.654056076 0.187219522 0.283392751 2.285035128 0.050083662 0.460976526 41122.22904 -4.614076648 0.892905171 YLS(ph)FTPPEKDGFPSGTPALNAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.998)FT(0.002)PPEKDGFPSGTPALNAK;YLS(0.996)FT(0.004)PPEKDGFPSGTPALNAK 244.71 4.71E-31 3221800000 4512300 3025900 1668880 1727060 1806280 1897520 1563230 2546100 2535500 1994750 TRUE FALSE 4335954.327 2939604.295 1970483.74 1816193.774 1864380.637 1935889.154 1582361.276 2493522.145 2247680.67 1859643.806 2.331604748 1.580735131 1.059602777 0.976635293 1.002547171 1.040999975 0.850894817 1.340860082 1.208661929 1 20.82659488 4.614151869 2.112235736 1.066926384 2.504895205 0.903116083 0.129304559 0.154120928 0.938389573 0.036320664 0.380820215 41129.35215 -4.614151869 1.437968821 up TVVSGLVNHVPLEQMQNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVVSGLVNHVPLEQMQNR 18 0 Q12904;Q12904-2;A0A5F9ZHC5 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 110.77 0.000324 1531930000 864170 909010 744760 943670 863240 915590 956720 847210 978140 995550 FALSE TRUE 830397.281 883085.9248 879354.6991 992372.9218 891006.8986 934103.8571 968428.6255 829714.8174 867105.6479 928120.5118 0.894708468 0.951477651 0.947457456 1.069228521 0.960012075 1.006446733 1.043429828 0.89397315 0.934259761 1 19.82395262 4.615112157 1.841217968 0.980285065 0.881702837 0.235226857 0.048803604 1.059994874 4.512730966 0.013481609 0.165630063 41220.39574 -4.615112157 -0.098582228 IGEGT(ph)YGVVYK ddPTM_BT-474_Pertuzumab_2h_R1 7 IGEGTYGVVYK 11 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2;G3V317;K7ELV5;G3V5T9;P24941;P24941-2;E7ESI2;Q00526 P06493;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 IGEGT(0.963)Y(0.037)GVVYK;IGEGT(0.766)Y(0.234)GVVYK;IGEGT(0.991)Y(0.009)GVVYK;IGEGT(0.931)Y(0.069)GVVYK;IGEGT(0.994)Y(0.006)GVVYK;IGEGT(0.926)Y(0.073)GVVYK;IGEGT(0.973)Y(0.027)GVVYK 198.4 6.01E-07 60226770000 17879930 16384220 12816330 13968980 14909230 13073080 15819370 16302590 15972730 15888340 TRUE FALSE 17181162.57 15916958.09 15132525.93 14689920.73 15388798.92 13337426.63 16012972.18 15965935.82 14159572.65 14812208.58 1.15993253 1.074583713 1.021625225 0.991744118 1.038926696 0.900434703 1.081065804 1.077890291 0.955939324 1 23.82028343 4.615436194 1.956873528 1.014459549 1.183251823 0.45906499 0.051250222 0.57028348 2.842676561 0.013770778 0.158383211 41251.16271 -4.615436194 0.168792274 SASDNTLVAMDFSGHAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 139.11 5.90E-07 1652680000 609300 680330 611890 693040 673560 729510 694450 696130 732950 769500 FALSE TRUE 585487.8824 660927.6545 722472.1344 728807.8775 695225.6691 744261.192 702948.8868 681754.6722 649748.5888 717381.0796 0.816146256 0.921306225 1.007096723 1.015928491 0.96911626 1.037469782 0.979882111 0.950338239 0.905723063 1 19.45238017 4.615754973 2.770309209 0.981922456 0.805584483 0.677667208 0.035298683 0.203570152 2.440150764 0.00924733 0.070464644 41281.45279 -4.615754973 -0.176337973 VSELYDVTWEEMR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSELYDVTWEEMR 13 0 Q15006 Q15006 EMC2 ER membrane protein complex subunit 2 0 ;;; 240.8 1.70E-16 269312000 95441 120342 118903 149040 115828 126800 143290 116429 130232 133931 FALSE TRUE 91711.0602 116909.964 140391.4171 156731.9723 119553.7128 129363.9829 145043.6259 114024.7005 115448.6093 124859.7341 0.734512698 0.936330394 1.124393049 1.255264345 0.957504144 1.036074471 1.161652529 0.913222356 0.924626423 1 16.92994877 4.615927583 3.157048781 1.046016606 0.724081854 0.458237474 0.103421882 0.265054119 4.261965818 0.02669411 0.175023146 41297.86337 -4.615927583 -0.321934751 GSPSVAASS(ph)PPAIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSPSVAASSPPAIPK 15 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 GSPSVAAS(0.311)S(0.689)PPAIPK;GSPSVAAS(0.078)S(0.922)PPAIPK 222.55 1.45E-12 476980000 838080 866440 722720 855530 867240 857350 811400 900900 910030 899640 TRUE FALSE 805326.9071 841729.9795 853331.5808 899684.0058 895135.5622 874686.2044 821330.1559 882296.1002 806727.2096 838706.5815 0.96020101 1.003604834 1.017437564 1.07270412 1.067280956 1.04289894 0.979281878 1.05197231 0.961870608 1 19.67780665 4.615932097 2.092358266 1.028763371 0.951294346 0.234325624 0.034633153 0.711695509 4.217657807 0.008842245 0.094367999 41298.29257 -4.615932097 -0.077469025 LLDGPSTEKDLDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDGPSTEKDLDEK 14 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 0 ; 131.53 2.20E-05 312150000 562200 468970 330610 310400 379920 454930 376070 443660 552770 415770 FALSE TRUE 540228.6025 455595.4348 390358.5814 326419.7812 392140.4718 464128.9963 380672.4572 434498.266 490021.867 387609.5276 1.393744385 1.175397926 1.007092328 0.842135598 1.011689455 1.197413797 0.982102941 1.120969004 1.264215227 1 18.56424451 4.616379654 2.865543693 1.054243431 1.412379907 0.459799273 0.112835647 0.299923983 3.888422185 0.029133512 0.21371461 41340.87398 -4.616379654 0.358136476 LQVVDQPLPVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LQVVDQPLPVR 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 130.98 0.00049511 191551000 431530 484960 456740 473220 448780 467430 546520 507330 513280 581960 FALSE TRUE 414665.3305 471129.4156 539283.0781 497642.9409 463215.4163 476881.7549 553208.4752 496853.4582 455014.6062 542543.3308 0.76429901 0.86837196 0.993990798 0.917240914 0.853785108 0.878974504 1.019657682 0.915785763 0.838669615 1 19.04937884 4.616693788 3.466586021 0.92444454 0.761735581 0.415594346 0.058816698 0.248205311 4.817930975 0.014246357 0.084746816 41370.7875 -4.616693788 -0.162708959 WFVVLEETPWDATSHIDNMENER ddPTM_BT-474_Pertuzumab_2h_R1 2 WFVVLEETPWDATSHIDNMENER 23 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 ; 185.61 2.98E-17 60156000 25544.6 31365.3 31997.4 37048 29484 33256 32602.9 30928.4 36985 36330 FALSE TRUE 24546.28879 30470.79235 37780.04196 38960.05172 30432.37964 33928.45911 33001.90404 30289.71773 32786.61785 33869.33674 0.724734853 0.899657191 1.115464476 1.150304537 0.898523047 1.001745601 0.974388849 0.894310921 0.968032474 1 15.04769211 4.616938454 3.567107906 0.992526334 0.721993724 0.535712845 0.077991464 0.210464918 4.310361302 0.02076349 0.120128672 41394.10086 -4.616938454 -0.270532611 SFEVNLR ddPTM_BT-474_Pertuzumab_2h_R1 6 SFEVNLR 7 0 Q7Z4W1;J3KS22;J3QS36;J3QL34;J3QS45;J3KRZ4;J3KSZ5 Q7Z4W1 DCXR L-xylulose reductase 0 ;;;;; 186.67 0.0013852 4330470000 3644320 4193650 3461410 4805770 4165470 3955630 4759290 4512690 4347180 4470420 FALSE TRUE 3501895.945 4074051.208 4086963.786 5053796.366 4299456.126 4035615.549 4817535.615 4419501.375 3853706.351 4167634.472 0.840259857 0.977545232 0.980643531 1.212629466 1.03162985 0.968322816 1.155940054 1.06043402 0.924674747 1 21.99079732 4.617028831 1.714172596 1.054808637 0.801610158 0.360056923 0.081949173 0.742755859 2.620124928 0.021388607 0.28522768 41402.71595 -4.617028831 -0.253198479 DEDHIALIIELLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DEDHIALIIELLGK 14 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 ; 122.35 0.00010926 209310000 362040 317530 353880 376670 358600 407010 444640 416180 568000 572880 FALSE TRUE 347891.0765 308474.3553 417833.988 396109.9838 370134.6947 415240.0211 450081.6373 407585.7376 503523.0213 534078.3273 0.651385871 0.577582612 0.782345897 0.741670207 0.693034478 0.777488993 0.842725897 0.763157231 0.942788717 1 19.02669182 4.617105511 0.078959583 1.304766969 2.95E-10 0.773824688 0.057385522 40.69300351 0.530611361 2.433145542 7.203645608 41410.02677 -4.617105511 -1.304766968 VWDYETGDFER ddPTM_BT-474_Pertuzumab_2h_R1 4 VWDYETGDFER 11 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 316.41 1.96E-45 1840620000 1605700 1822720 1630740 2041860 1716030 1525930 1892090 2015150 2146140 2206510 FALSE TRUE 1542947.469 1770737.81 1925450.994 2147240.639 1771227.663 1556785.35 1915245.963 1973536.448 1902519.185 2057061.112 0.750073714 0.86080953 0.936020317 1.043839012 0.861047663 0.756800729 0.931059341 0.959396119 0.924872466 1 20.97215322 4.617392952 2.705051584 0.922753745 0.738179916 0.352499166 0.073343865 0.423558172 4.788695369 0.019317121 0.15227872 41437.44335 -4.617392952 -0.184573829 VCSTLLGLEEHLNALDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VCSTLLGLEEHLNALDR 17 0 H0YCY6;Q3LXA3-2;Q3LXA3;I3L252 H0YCY6 TKFC;DAK Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing);ATP-dependent dihydroxyacetone kinase;FAD-AMP lyase (cyclizing) 0 ;;; 242.42 2.09E-20 1281990000 1228170 1336570 1131540 1364200 1353390 1501150 1345430 1333710 1425300 1462860 FALSE TRUE 1180171.759 1298452.332 1336034.449 1434606.525 1396923.018 1531504.282 1361895.775 1306168.422 1263505.919 1363779.189 0.865368652 0.952098655 0.979655988 1.051934607 1.024302929 1.12298552 0.998618974 0.957756529 0.92647397 1 20.37917864 4.617750527 1.685367817 1.010471919 0.836521634 0.44077093 0.050154122 0.766123842 2.584103781 0.014704938 0.199995131 41471.57477 -4.617750527 -0.173950285 LKFEGKT(ph)FY(ph)LY(ph)VSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKFEGKTFYLYVSQK 15 2 A0A087WVP2;H0Y5N1;B5MC67;Q7Z6J6-2;Q7Z6J6;H0YNI9 A0A087WVP2 FRMD5 FERM domain-containing protein 5 3 LKFEGKT(1)FY(1)LY(0.999)VS(0.002)QK;LKFEGKT(0.999)FY(0.998)LY(0.998)VS(0.006)QK 50.178 0.073187 684480000 343162 597921 581398 947640 664650 727850 635243 729500 721018 714670 TRUE FALSE 329750.8497 580868.8785 686469.5517 996547.814 686029.0709 742567.6257 643017.2939 714435.5701 639171.0594 666264.7643 0.494924642 0.871828903 1.030325463 1.495723423 1.029664343 1.114523333 0.965107759 1.072299795 0.959334928 1 19.34573607 4.618652145 2.20244916 1.091931101 0.422687342 0.60593619 0.145897781 0.325866683 2.196394354 0.03792521 0.384972932 41557.7614 -4.618652145 -0.669243759 SEEELEDYMVEIDILASCDHPNIVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEELEDYMVEIDILASCDHPNIVK 25 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 235.76 2.02E-38 159686000 120417 132686 118557 129242 131826 133096 148237 131567 163511 158747 FALSE TRUE 115710.9705 128901.9252 139982.8872 135912.1951 136066.303 135787.2923 150051.1687 128850.0955 144949.9168 147994.9243 0.781857696 0.870988825 0.945862757 0.918357138 0.919398443 0.917513171 1.01389402 0.870638612 0.979424919 1 17.17518817 4.618755808 1.96603347 0.938966214 0.755323233 0.60309608 0.041463254 0.383810719 1.92699688 0.010062825 0.116581863 41567.68205 -4.618755808 -0.183642981 REEEKEGEDKSQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 REEEKEGEDKSQPK 14 3 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YIS3;H0YIM2;H0YIL7 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ; 104.41 0.00046397 264273000 369510 293860 209360 165350 223270 224530 259360 286490 339900 250990 FALSE TRUE 355069.1407 285479.4005 247196.0092 173883.7333 230451.6823 229070.1504 262534.1253 280573.8814 301315.977 233990.2237 1.517452888 1.22004841 1.056437338 0.743123924 0.984877396 0.978973167 1.121987582 1.199083778 1.287728915 1 17.83608873 4.619002166 2.457914942 1.051130981 1.560957327 0.523283476 0.138119866 0.365202528 3.255147646 0.039077444 0.347964386 41591.26851 -4.619002166 0.509826347 AYT(ph)PVVVTQWYR ddPTM_BT-474_Pertuzumab_2h_R1 2 AYTPVVVTQWYR 12 0 Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 Q5QPR3 CDK11A Cyclin-dependent kinase 11A 1 AYT(1)PVVVTQWYR;AYT(1)PVVVTQWYR 186.56 0.00012966 534530000 583620 521190 431930 459880 468950 352020 437830 599990 497440 482870 TRUE FALSE 560811.4852 506326.1715 509989.3592 483614.4619 484034.2026 359138.0856 443188.2945 587599.9968 440972.6966 450164.7848 1.24579155 1.124757397 1.132894834 1.074305406 1.075237822 0.797792492 0.984502363 1.305299785 0.979580615 1 18.78009368 4.619031292 1.022475249 1.048557072 1.307058619 0.233776835 0.119928383 2.963555995 2.880166289 0.041778105 0.803287619 41594.05791 -4.619031292 0.258501547 GSESATYVPVAPPTPAWQPEIKPEPAWHDQDET(ph)SSVKSDGAGGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSESATYVPVAPPTPAWQPEIKPEPAWHDQDETSSVKSDGAGGAR 45 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 GSESATYVPVAPPT(0.013)PAWQPEIKPEPAWHDQDET(0.247)S(0.247)S(0.247)VKS(0.247)DGAGGAR 58.048 0.010954 197250000 257720 218200 178640 139310 179200 202730 196280 188980 262500 214140 TRUE FALSE 247648.0175 211977.1496 210924.2218 146499.8058 184964.1307 206829.3395 198682.1334 185077.497 232702.1005 199636.1071 1.240497128 1.061817688 1.056543453 0.733834214 0.926506399 1.036031721 0.995221437 0.927074264 1.165631327 1 17.60701315 4.619080207 1.853572611 0.966736426 1.283875601 0.364941236 0.104854931 0.67242148 2.895516281 0.027491572 0.340341785 41598.74295 -4.619080207 0.317139175 LPISDS(ph)PPDTQEIHVIEQEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPISDSPPDTQEIHVIEQEK 20 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 LPISDS(1)PPDTQEIHVIEQEK;LPIS(0.023)DS(0.977)PPDTQEIHVIEQEK 215.07 7.86E-25 183167000 211360 169259 248020 303840 266370 210387 324040 412790 363190 430150 TRUE FALSE 203099.8175 164431.899 292842.7312 319521.2188 274938.033 214641.1693 328005.6985 404265.7422 321962.1938 401015.5574 0.506463687 0.410038703 0.730252794 0.796780107 0.685604406 0.535243996 0.81793759 1.008104885 0.802867091 1 18.61329868 4.619688907 0.203267393 1.05649375 1.34E-17 0.611166229 0.118310695 9.32928066 0.375613722 0.281582858 2.539926061 41657.08795 -4.619688907 -1.05649375 MEDGEFWMSFR ddPTM_BT-474_Pertuzumab_2h_R1 6 MEDGEFWMSFR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;;;; 273.79 9.80E-27 1787901000 1214836 1310886 1146451 1321511 1288562 1138266 1406107 1413261 1356836 1499037 FALSE TRUE 1167358.866 1273500.815 1353640.198 1389714.341 1330009.767 1161282.518 1423315.358 1384076.666 1202813.666 1397505.889 0.835315883 0.911266868 0.968611445 0.994424676 0.951702442 0.830967889 1.018468237 0.990390579 0.860685937 1 20.41442293 4.620032389 2.724059519 0.954009997 0.826933441 0.273901413 0.057812978 0.455542485 5.223496076 0.01438218 0.113422574 41690.04742 -4.620032389 -0.127076556 RDDGTGQLLLPLSDAR ddPTM_BT-474_Pertuzumab_2h_R1 6 RDDGTGQLLLPLSDAR 16 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 193.8 5.07E-10 4926730000 2499790 2710920 2226641 2692230 2761980 2971810 2720620 2769050 2863810 2876110 FALSE TRUE 2402095.443 2633607.216 2629044.56 2831176.313 2850821.595 3031902.034 2753915.761 2711868.15 2538722.295 2681308.508 0.895866864 0.982209697 0.980508044 1.055893533 1.063220285 1.130754639 1.027079037 1.011397287 0.946822153 1 21.35450579 4.620217136 1.301929629 1.035613212 0.859503886 0.437309901 0.04658639 1.084712143 1.894082646 0.014076271 0.24018798 41707.78591 -4.620217136 -0.176109326 ESDTKNEVNGTSEDIKS(ph)EGDTQSN ddPTM_BT-474_Pertuzumab_2h_R1 1 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGT(0.002)S(0.002)EDIKS(0.733)EGDT(0.131)QS(0.131)N 53.089 0.094275 0 81912 70513 58694 45271 61854 63664 57178 70658 84996 66481 TRUE FALSE 78710.78848 68502.03828 69301.31144 47607.44174 63843.59008 64951.3297 57877.76147 69198.88761 75347.61041 61978.18265 1.269975742 1.105260518 1.118156559 0.768132264 1.030097808 1.047970865 0.933840893 1.11650398 1.215711839 1 15.91947283 4.620813189 1.850778405 1.023618841 1.308426334 0.303214351 0.112827877 0.828471137 3.544250903 0.030178881 0.376672121 41765.06764 -4.620813189 0.284807493 IDSLLENDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IDSLLENDR 9 0 E7ERK6;H0YC35;H0YLK8;P10909-4;P10909-6;P10909;P10909-5;P10909-2;E7ETB4 E7ERK6 CLU Clusterin;Clusterin;Clusterin beta chain;Clusterin alpha chain 0 ;;; 131.22 0.00078889 244720000 249232 308457 280155 363421 273800 286011 377120 361311 342936 391178 FALSE TRUE 239491.7379 299660.1084 330785.2405 382177.2014 282607.0257 291794.3384 381735.3074 353849.8016 304007.343 364683.1656 0.656711799 0.821699866 0.907048287 1.047970505 0.774938501 0.800131089 1.046758785 0.970293764 0.833620445 1 18.47628408 4.620949116 2.09281392 0.925694624 0.618591776 0.4439925 0.091864948 0.499982419 2.943155269 0.024267344 0.263894471 41778.14149 -4.620949116 -0.307102848 LTGS(ph)TSS(ph)LNK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LTGS(0.985)T(0.12)S(0.138)S(0.757)LNK 110.74 0.0026987 553180000 3239000 2742200 2102700 1987100 2161200 2347500 2076700 2909400 2856200 2455300 TRUE FALSE 3112416.299 2663995.141 2482704.664 2089654.469 2230716.961 2394968.058 2102115.276 2849319.873 2531976.15 2289000.344 1.359727318 1.163824701 1.08462398 0.912911383 0.974537626 1.04629432 0.918355159 1.244787875 1.10614931 1 21.12628625 4.621563232 1.970166062 1.042042178 1.40954712 0.544606561 0.091991678 0.502917522 2.528195112 0.026256163 0.306724477 41837.25983 -4.621563232 0.367504941 LESSQLQIAGLEHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LESSQLQIAGLEHLR 15 0 Q14789;Q14789-2;Q14789-4;Q14789-3;E7EU81 Q14789 GOLGB1 Golgin subfamily B member 1 0 102.38 0.001556 134160000 37727 44592 42643 44747 45501 46040 47815 49202 42288 55207 FALSE TRUE 36252.58713 43320.27982 50349.53869 47056.39803 46964.58099 46970.96034 48400.17427 48185.96151 37487.64353 51467.78072 0.704374399 0.841697062 0.97827297 0.914288461 0.91250449 0.912628438 0.940397538 0.936235463 0.72837109 1 15.65138195 4.621721933 3.155212217 0.915268648 0.696173981 0.463145278 0.069121027 0.235618435 3.771849174 0.016011731 0.106723068 41852.55088 -4.621721933 -0.219094667 DSSSEKDGRS(ph)PNKR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSSSEKDGRSPNKR 14 3 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 DSS(0.003)S(0.003)EKDGRS(0.994)PNKR;DSSSEKDGRS(1)PNKR;DSS(0.001)S(0.001)EKDGRS(0.999)PNKR 96.143 0.019277 945490000 1345160 1043150 697910 576740 793920 836280 912780 988000 1121480 919360 TRUE FALSE 1292589.66 1013400.383 824037.8619 606505.6205 819457.1578 853190.1546 923950.8747 967597.4547 994174.292 857090.9283 1.508112637 1.18237208 0.961435753 0.707632762 0.956091274 0.995448822 1.078007997 1.128932092 1.159940281 1 19.70908874 4.621801308 2.69427945 1.003225666 1.545287084 0.636003505 0.11802254 0.255275318 2.845458368 0.033632823 0.27042104 41860.20087 -4.621801308 0.542061418 YDECLAVYR ddPTM_BT-474_Pertuzumab_2h_R1 1 YDECLAVYR 9 0 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 105.57 0.0071582 188150000 78732 87283 90672 95193 82485 59793 106240 84390 85404 109900 FALSE TRUE 75655.0664 84793.7743 107058.4474 100105.9221 85138.20494 61002.05543 107540.1969 82647.31701 75709.29596 102456.3751 0.738412484 0.827608572 1.044917383 0.977058988 0.830970302 0.59539541 1.04961938 0.806658609 0.738941778 1 16.64465023 4.621846191 4.460359763 0.874032409 0.741592281 0.087867346 0.137619284 0.561844638 16.5417412 0.033093751 0.160761384 41864.52718 -4.621846191 -0.132440128 GECQACDQLHFCR ddPTM_BT-474_Pertuzumab_2h_R1 1 GECQACDQLHFCR 13 0 Q96H79 Q96H79 ZC3HAV1L Zinc finger CCCH-type antiviral protein 1-like 0 70.373 0.045166 273000000 415590 324720 196810 259960 269530 186350 233080 423650 249830 239540 FALSE TRUE 399348.2833 315459.3035 232377.945 273376.5668 278199.6772 190118.1247 235932.5028 414901.4795 221470.3458 223315.7424 1.788267495 1.412615609 1.040580223 1.224170602 1.24576832 0.851342241 1.056497407 1.857914157 0.991736379 1 17.76872543 4.622254618 3.151044625 1.211893709 1.811078674 0.336928682 0.264582434 0.380553909 6.073194585 0.070541048 0.471580973 41903.91669 -4.622254618 0.599184965 TLLSDPTYR ddPTM_BT-474_Pertuzumab_2h_R1 5 TLLSDPTYR 9 0 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 153.78 0.00017977 1254830000 2591420 2816640 2444770 2828680 2801570 2859120 2848790 2934190 3087830 3222950 FALSE TRUE 2490144.441 2736312.185 2886594.323 2974668.514 2891685.043 2916933.365 2883654.344 2873597.951 2737312.484 3004656.726 0.828761708 0.91069045 0.960706858 0.990019422 0.962401135 0.970804199 0.959728384 0.956381448 0.911023366 1 21.51876875 4.622481654 2.132100953 0.963088634 0.80998793 0.778542275 0.022300567 0.225150119 1.38775148 0.005601398 0.059949686 41925.82852 -4.622481654 -0.153100703 WCNVQSTQDEFEELTMS(ph)QK ddPTM_BT-474_Pertuzumab_2h_R1 1 WCNVQSTQDEFEELTMSQK 19 0 D6RCP9;D6RFG8;P27707 D6RCP9 DCK Deoxycytidine kinase 1 WCNVQSTQDEFEELT(0.001)MS(0.999)QK 71.656 0.012734 42640000 50952 34640 20064 19886 22632 17881 18902 38400 20335 19938 TRUE FALSE 48960.73951 33652.10112 23690.01112 20912.31884 23359.97883 18242.56607 19133.32833 37607.02658 18026.65605 18587.5815 2.63405648 1.810461523 1.274507451 1.125069383 1.256751925 0.98143839 1.02936083 2.023233984 0.969822569 1 14.18205145 4.622779342 2.066718824 1.261565746 2.841190926 0.686944524 0.298602797 0.341680389 1.941622599 0.082998468 0.922246866 41954.57655 -4.622779342 1.57962518 GPWWDDWER ddPTM_BT-474_Pertuzumab_2h_R1 1 GPWWDDWER 9 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 77.318 0.076637 84587000 114100 137770 98593 167780 147080 114440 138690 148650 134250 149240 FALSE TRUE 109640.8459 133840.9345 116410.9483 176439.1459 151810.9618 116754.0552 140387.3297 145580.3256 119010.5028 139131.8419 0.78803561 0.961971988 0.836695229 1.268143536 1.091130253 0.839161285 1.009023728 1.046348008 0.855379338 1 17.08609311 4.623043222 1.505082194 1.008521524 0.75063999 0.20010715 0.124254175 1.454656225 3.643295365 0.033978251 0.523374957 41980.07618 -4.623043222 -0.257881534 S(ph)SLETLEDIEENAPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLETLEDIEENAPLR 16 0 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.5)S(0.5)LETLEDIEENAPLR 118.33 0.00029392 28270000 34129 36162 32857 39103 37514 40205 40585 51686 42006 42157 TRUE FALSE 32795.20095 35130.69517 38794.9908 41121.11052 38720.67188 41017.97265 41081.69137 50618.66604 37237.65498 39301.66884 0.834448051 0.893872861 0.987107976 1.04629426 0.98521699 1.043669998 1.045291271 1.287952078 0.947482794 1 15.26230295 4.623091646 0.543251849 1.101380457 0.66785199 0.395425976 0.088763422 3.273757189 0.807000619 0.05189062 0.888846423 41984.75721 -4.623091646 -0.433528467 ALLEPELRPEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALLEPELRPEDR 12 1 P0DPD7;P0DPD8 P0DPD7 0 122.42 0.00032721 127950000 185010 240680 220440 288200 251770 296190 265470 244030 258800 332960 FALSE TRUE 177779.6047 233816.0421 260278.4117 303074.0365 259868.4107 302179.1647 268718.9013 238990.6952 229422.109 310408.3226 0.572728215 0.753253135 0.838503328 0.976372135 0.837182484 0.973489249 0.865694898 0.769923606 0.739097802 1 18.24380771 4.623165767 1.995926809 0.867754426 0.526441825 0.564339357 0.082491047 0.448038803 2.324128847 0.022108677 0.256066853 41991.92336 -4.623165767 -0.3413126 SS(ph)PGQTPEEGAQALAEFAALHGPALR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 S(0.409)S(0.591)PGQTPEEGAQALAEFAALHGPALR;S(0.003)S(0.997)PGQTPEEGAQALAEFAALHGPALR;S(0.416)S(0.584)PGQTPEEGAQALAEFAALHGPALR;S(0.441)S(0.559)PGQTPEEGAQALAEFAALHGPALR;S(0.024)S(0.976)PGQTPEEGAQALAEFAALHGPALR 326.41 1.49E-84 42471900000 1005220 1089870 954610 1065720 1066280 1176610 1074810 1088980 1248850 1236650 TRUE FALSE 965934.8911 1058787.975 1127129.262 1120721.937 1100577.865 1200401.86 1087963.846 1066492.182 1107085.784 1152890.594 0.837837429 0.9183768 0.977655007 0.97209739 0.954624724 1.041210559 0.943683513 0.925059314 0.960269595 1 20.13682418 4.623273496 2.398112045 0.967326568 0.823810247 0.645045015 0.030580902 0.287924156 2.398406385 0.008218837 0.076606439 42002.34092 -4.623273496 -0.143516321 GLDIYVWR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDIYVWR 8 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 125.25 0.0029544 431190000 882590 990100 888740 1043440 1039760 927270 1019520 1021900 1074510 1122650 FALSE TRUE 848097.407 961863.3174 1049355.088 1097292.063 1073204.825 946020.0347 1031997.191 1000797.408 952536.1295 1046611.916 0.810326535 0.919025766 1.002621002 1.048423056 1.025408567 0.90388808 0.986036157 0.956225888 0.910113974 1 19.99729516 4.623399372 2.834008183 0.977860157 0.799696535 0.580384465 0.043829172 0.244699528 3.072634799 0.011460597 0.087122079 42014.51671 -4.623399372 -0.178163622 VTNDIS(ph)PESS(ph)PGVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTNDISPESSPGVGR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 2 VTNDIS(1)PES(0.337)S(0.663)PGVGR;VTNDIS(1)PESS(1)PGVGR;VTNDIS(1)PES(0.001)S(0.999)PGVGR;VTNDIS(1)PES(0.001)S(0.999)PGVGR 313.08 4.68E-56 1586190000 2397370 2659290 2370280 2808030 2494800 2782100 2874000 2440280 3038560 3151140 TRUE FALSE 2303678.13 2583449.653 2798642.323 2952952.765 2575047.508 2838355.968 2909172.872 2389887.365 2693635.407 2937710.481 0.784174664 0.87940921 0.95266104 1.005188491 0.87654911 0.96617961 0.990285765 0.813520386 0.916916566 1 21.48626079 4.623403479 2.85318206 0.930739494 0.775121092 0.406626726 0.057182098 0.358915722 4.578631947 0.014841008 0.111905485 42014.91402 -4.623403479 -0.155618401 (ac)MEDLDQS(ph)PLVSSSDS(ph)PPRPQPAFK ddPTM_BT-474_Pertuzumab_2h_R1 2 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4 2 MEDLDQS(0.999)PLVS(0.001)S(0.003)S(0.012)DS(0.984)PPRPQPAFK;MEDLDQS(0.999)PLVS(0.001)S(0.001)S(0.006)DS(0.993)PPRPQPAFK 113.65 6.99E-18 139678000 156621 190972 174917 234400 169306 217830 208065 207977 191111 199811 TRUE FALSE 150500.0782 185525.6655 206528.3929 246497.4121 174751.8812 222234.6718 210611.3617 203682.2023 169416.8805 186277.623 0.807934285 0.995963243 1.108712843 1.323279781 0.938125999 1.193029352 1.130631572 1.093433548 0.909485948 1 17.50709485 4.623730939 2.609542038 1.098356952 0.784013146 0.34944033 0.114989701 0.382363978 3.933886298 0.027577169 0.232128581 42046.60538 -4.623730939 -0.314343806 RT(ph)SLGEVSKGDTMENLDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSLGEVSKGDTMENLDGK 19 2 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 RT(0.5)S(0.5)LGEVSKGDTMENLDGK 146.25 5.59E-06 376290000 391920 286200 173030 148150 238840 230880 169980 353590 208070 176460 TRUE FALSE 376603.3331 278037.8562 204300.37 155796.0393 246522.5055 235548.5518 172060.2661 346288.2429 184450.7659 164508.207 2.289267751 1.690115413 1.24188558 0.947041136 1.498542291 1.431834655 1.045906883 2.104990682 1.121225313 1 17.32780003 4.623732954 2.790277517 1.364603202 2.351580954 0.4589571 0.325828903 0.330625018 4.000586408 0.083609503 0.648405716 42046.80051 -4.623732954 0.986977752 FPYSPS(ph)PPMANGAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FPYSPSPPMANGAAR 15 0 Q92908-2;Q92908 Q92908-2 GATA6 Transcription factor GATA-6 1 FPYS(0.04)PS(0.96)PPMANGAAR;FPYS(0.003)PS(0.997)PPMANGAAR 178.22 7.56E-07 567250000 132434 141430 113946 138075 149899 132330 138563 153856 143223 143683 TRUE FALSE 127258.3329 137396.5549 134538.5769 145201.0673 154720.6375 135005.8033 140258.7754 150678.8198 126964.9255 133951.2224 0.950034875 1.025720799 1.004384839 1.083984638 1.155052075 1.007872872 1.047088432 1.124878274 0.94784447 1 17.03134822 4.623797731 1.317865259 1.060789302 0.923773965 0.178011111 0.059337701 1.609952394 2.883407228 0.016368696 0.280291683 42053.07245 -4.623797731 -0.137015336 EIVWLER ddPTM_BT-474_Pertuzumab_2h_R1 4 EIVWLER 7 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;;; 109.01 0.016573 994930000 702430 792670 706690 832540 806360 829080 814760 831280 810550 888920 FALSE TRUE 674978.259 770063.8277 834404.6032 875507.4892 832297.3017 845844.5656 824731.2766 814113.7775 718539.7621 828712.6566 0.814490105 0.929228993 1.00686842 1.056466897 1.004325559 1.020672918 0.995195705 0.982383666 0.867055374 1 19.66051243 4.624000848 2.560704806 0.994023048 0.798481611 0.577423555 0.046267943 0.272301654 2.672723319 0.011825799 0.101979089 42072.74496 -4.624000848 -0.195541437 YFEITEEPPYIHFLNTFTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 YFEITEEPPYIHFLNTFTSK 20 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;; 263.52 1.69E-36 937080000 1494570 1583510 1336580 1552670 1647700 1653000 1692840 1846710 1857950 1874660 FALSE TRUE 1436160.552 1538349.845 1578129.738 1632803.485 1700699.767 1686424.793 1713557.482 1808574.793 1647043.305 1747687.608 0.821749004 0.880220148 0.902981591 0.934265069 0.973114279 0.964946358 0.980471266 1.034838712 0.942412876 1 20.7370159 4.624106887 0.502256788 1.000222076 0.715734656 0.851833925 0.022705489 1.373968867 0.290200015 0.014140821 0.228896677 42083.01884 -4.624106887 -0.284487421 VAVEEVDEEGKFVR ddPTM_BT-474_Pertuzumab_2h_R1 7 VAVEEVDEEGKFVR 14 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;; 237.48 2.46E-17 13992020000 10270350 9035190 6834540 6872380 8047110 8372900 7919320 8928350 9427540 8312910 FALSE TRUE 9868973.368 8777515.228 8069693.412 7227064.355 8305952.601 8542205.775 8016239.007 8743976.452 8357365.183 7749869.201 1.273437411 1.132601725 1.041268337 0.932540172 1.071753908 1.102238703 1.034370878 1.128274068 1.078387901 1 22.88574053 4.624457835 2.625952218 1.055329051 1.291370992 0.633416493 0.052366092 0.255973956 2.672357834 0.013984518 0.117110307 42117.0394 -4.624457835 0.236041941 ADLGPGS(ph)PPWAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADLGPGSPPWAVK 13 0 A0A087WVC5;A0A0C4DH65;A5PL33-3;A5PL33-2;A5PL33 A0A087WVC5 KRBA1 Protein KRBA1 1 ADLGPGS(1)PPWAVK 144.27 4.32E-05 69049000 284980 324300 271000 341240 360210 368160 323150 324860 345220 347490 TRUE FALSE 273842.6665 315051.2815 319975.7284 358851.4373 371796.4818 375604.4474 327104.8064 318151.5275 306032.0729 323954.1928 0.845312926 0.972517993 0.987719053 1.107722775 1.147682265 1.159436907 1.009725491 0.982088007 0.944676994 1 18.3054303 4.624979344 1.59605316 1.048982629 0.801959497 0.444922769 0.068560795 0.858597366 2.49062962 0.020951734 0.308333859 42167.64471 -4.624979344 -0.247023132 S(ph)PSSKPSLAVAVDSAPEVAVKEDLETGVHLDPAVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSSKPSLAVAVDSAPEVAVKEDLETGVHLDPAVK 35 2 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 1 S(0.594)PS(0.1)S(0.1)KPS(0.207)LAVAVDSAPEVAVKEDLETGVHLDPAVK;S(0.857)PS(0.124)S(0.018)KPSLAVAVDSAPEVAVKEDLETGVHLDPAVK;S(0.757)PS(0.104)S(0.104)KPS(0.036)LAVAVDSAPEVAVKEDLETGVHLDPAVK;S(0.622)PS(0.1)S(0.1)KPS(0.177)LAVAVDSAPEVAVKEDLETGVHLDPAVK 199.1 9.91E-28 741570000 762230 642510 489948 393784 549530 570354 558746 607990 729180 649140 TRUE FALSE 732441.2089 624186.2439 578492.5024 414107.2394 567206.1315 581886.9487 565584.1007 595434.794 646406.5434 605173.1696 1.210300201 1.031417576 0.955912343 0.684278914 0.937262523 0.961521392 0.934582247 0.983908117 1.068134835 1 19.2069885 4.625117932 2.386212073 0.934765257 1.239022685 0.433541833 0.09401002 0.415830943 3.412119095 0.024821612 0.234374686 42181.10304 -4.625117932 0.304257428 S(ph)SPQLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPQLAK 7 0 Q13370-2;Q13370 Q13370-2 PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase B" 1 S(0.508)S(0.492)PQLAK 95.741 0.013892 5130300000 3396400 3193800 3384800 3839100 4026100 4997900 4705200 4983800 5687500 5936600 TRUE FALSE 3263664.933 3102715.951 3996508.654 4037236.411 4155603.163 5098960.962 4762783.645 4880882.788 5041878.844 5534508.794 0.589693694 0.560612706 0.722107201 0.729466076 0.750853114 0.921303254 0.860561221 0.881899907 0.9109894 1 22.40002385 4.625356743 0.28144133 0.99238934 0.210078471 0.914022336 0.040616489 2.025211602 0.139952301 0.049877109 0.549421493 42204.30403 -4.625356743 -0.782310869 GDVIHVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDVIHVTR 8 0 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E7EUY6;E7EU80;C9JAD7;C9JDI6;B1ANY6;E7ENL8 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 ; 112.84 0.0029633 496350000 567390 653110 582000 739250 649320 727630 657500 673320 651720 710890 FALSE TRUE 545215.7715 634483.9423 687180.3465 777402.7811 670205.9675 742343.1771 665546.6817 659415.7067 577739.4778 662740.7871 0.822668202 0.957363655 1.036876498 1.173011826 1.011264103 1.120110896 1.004233774 0.994982834 0.871742752 1 19.33808518 4.62544983 2.573081388 1.030645641 0.804474807 0.402945929 0.075549406 0.385205441 3.820098401 0.019436729 0.167488808 42213.35115 -4.62544983 -0.226170834 LTIFDEEVDPDEGLFGPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LTIFDEEVDPDEGLFGPGR 19 0 Q53T59;H7BZZ1;H7C0Y9;F8WDN8 Q53T59 HS1BP3 HCLS1-binding protein 3 0 ;;; 292.79 2.34E-61 287228000 463695 532205 427476 552524 531653 594991 567200 580200 585829 654502 FALSE TRUE 445573.2868 517027.0345 504730.4224 581039.8299 548754.1016 607022.1257 574141.5633 568218.6672 519328.1479 610171.9966 0.730242111 0.847346383 0.827193685 0.952255812 0.899343308 0.994837733 0.940950366 0.931243437 0.851117637 1 19.21885644 4.625581097 0.865864242 0.939076569 0.64983605 0.672057622 0.045667423 1.141080596 0.748880409 0.015044151 0.304318478 42226.11219 -4.625581097 -0.289240519 LMELHGEGSSSGK ddPTM_BT-474_Pertuzumab_2h_R1 7 LMELHGEGSSSGK 13 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;;; 182.1 1.15E-05 9220130000 13018990 13874610 12597970 12890370 13410160 14422170 13442950 14247130 14707040 15372320 FALSE TRUE 12510193.48 13478919.71 14874703.42 13555643.54 13841509.98 14713796.16 13607468.84 13952921.79 13037558.48 14331139.07 0.872937832 0.940533731 1.0379289 0.945887376 0.9658346 1.026701094 0.949503649 0.973608707 0.909736373 1 23.77264995 4.625904449 3.758932368 0.974791511 0.872159761 0.423093701 0.036493131 0.213411698 4.811876413 0.008443289 0.04728565 42257.56311 -4.625904449 -0.10263175 DPNDVRPIQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DPNDVRPIQAR 11 1 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 0 ;;; 136.5 8.93E-05 2975940000 2254100 2439770 2127570 2587030 2401060 2262830 2527690 2520150 2550020 2631400 FALSE TRUE 2166007.28 2370190.148 2512069.227 2720546.928 2478292.275 2308585.973 2558624.626 2468108.022 2260552.42 2453172.934 0.882941129 0.966173283 1.024008211 1.108991091 1.010239531 0.941061244 1.042985837 1.00608807 0.92148107 1 21.22621751 4.626176903 2.830259491 1.009810231 0.874695665 0.370908261 0.048899017 0.352235417 4.398622152 0.012413163 0.09538128 42284.08171 -4.626176903 -0.135114566 GGSGSGPTIEEVD ddPTM_BT-474_Pertuzumab_2h_R1 2 GGSGSGPTIEEVD 13 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 112.11 0.0021562 317320000 730570 805730 675520 889920 779570 881140 785250 827160 824000 867840 FALSE TRUE 702018.5167 782751.3693 797601.4909 935848.8778 804645.577 898957.2545 794860.1244 810078.8569 730462.9745 809060.4238 0.867696029 0.967481966 0.98583674 1.156710735 0.994543242 1.111112629 0.982448407 1.001258785 0.902853425 1 19.62588793 4.626439082 2.016958717 1.021522306 0.845029317 0.319370107 0.066694313 0.666097352 3.533434005 0.017134667 0.198583461 42309.61582 -4.626439082 -0.176492988 LDEDSEHPPMILR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDEDSEHPPMILR 13 0 Q9Y4P8-4;Q9Y4P8;Q9Y4P8-2;Q9Y4P8-6;Q9Y4P8-3;Q9Y4P8-5 Q9Y4P8-4;Q9Y4P8-2 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 0 ; 166.04 3.43E-05 573400000 385320 512180 480750 600930 539080 583060 630090 527860 594140 682780 FALSE TRUE 370261.2684 497573.1279 567632.2192 631944.0693 556419.9978 594849.8727 637801.2299 516959.5065 526695.718 636534.7024 0.581682769 0.781690497 0.891753768 0.992788087 0.874139298 0.934512872 1.001989723 0.812146619 0.827442268 1 19.27987964 4.626445328 1.990109929 0.912237728 0.527574665 0.722025578 0.064601337 0.313484964 1.60592785 0.017171032 0.202067656 42310.22431 -4.626445328 -0.384663063 VSKHS(ph)ESHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSKHSESHSR 10 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 1 VS(0.002)KHS(0.995)ES(0.003)HS(0.001)R 62.14 0.052555 14316000 15043 17072 15153 20029 15737 24182 22084 3688.2 22807 25939 TRUE FALSE 14455.10293 16585.12328 17891.48418 21062.69909 16243.1949 24670.97661 22354.2706 3612.037381 20218.04497 24182.12843 0.597759745 0.685842163 0.739863914 0.871002697 0.671702449 1.020215267 0.924412864 0.149368051 0.83607384 1 14.56165361 4.626624153 2.766409401 0.731580428 0.588404931 0.028554126 0.23783275 1.782108535 21.06959842 0.064064753 0.506979168 42327.64958 -4.626624153 -0.143175497 LTQTSST(ph)EQLNVLETETEVLNK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.181)QT(0.181)S(0.181)S(0.181)T(0.274)EQLNVLETETEVLNK 128.41 6.15E-05 80685000 10872 13427 13107 11653 15300 13438 13197 15063 19158 15754 TRUE FALSE 10447.11022 13044.07511 15475.72646 12254.41273 15792.1384 13709.72557 13358.50883 14751.94379 16983.26416 14686.96755 0.711318398 0.888139438 1.053704682 0.834373242 1.075248403 0.933461964 0.909548468 1.004424074 1.156349267 1 13.84224893 4.626699053 2.806721681 0.987398984 0.691629013 0.503880041 0.086299131 0.270182226 3.306356333 0.020540505 0.159728217 42334.95016 -4.626699053 -0.295769971 LKEENEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKEENEK 7 1 Q5M775-4;Q5M775;J3KSG2;Q5M775-5;Q5M775-3;Q5M775-2;I3L414;I3L3F1;A0A494BZY0;A0A494C199;A0A494C0J4;A0A494C1N2;Q9BXL6-3;Q9BXL6-2;Q9BXL6 Q5M775-4;I3L3F1 SPECC1;CARD14 Cytospin-B;Caspase recruitment domain-containing protein 14 0 ; 107.57 0.0067915 647440000 621660 540570 369585 480050 470990 483260 455010 573930 517200 472790 FALSE TRUE 597364.8399 525153.4729 436377.2309 504825.438 486139.8211 493031.8483 460578.5485 562078.1449 458489.6243 440767.5122 1.355283281 1.191452315 0.990039463 1.145332685 1.102939322 1.118575745 1.04494668 1.275225894 1.040207392 1 18.74965836 4.626748752 3.533991393 1.108350698 1.360128262 0.495131527 0.080505747 0.214934703 4.32731572 0.019422503 0.115846189 42339.79512 -4.626748752 0.251777564 LEQEILDFIGNNES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEQEILDFIGNNESPR 16 0 Q15032-2;Q15032-4;Q15032;Q15032-3;H7C2F9 Q15032-2 R3HDM1 R3H domain-containing protein 1 1 LEQEILDFIGNNES(1)PR 72.446 0.018683 0 11602 13069 11569 13400 13302 13597 13478 14647 13448 16816 TRUE FALSE 11148.58101 12696.28492 13659.77565 14091.57561 13729.87091 13871.94066 13642.9478 14344.53433 11921.43942 15677.03734 0.711140809 0.809865068 0.871323794 0.89886726 0.875794999 0.884857282 0.870250386 0.915002881 0.760439563 1 13.93636532 4.626781818 1.762297838 0.883929557 0.675418624 0.494611983 0.054984327 0.546779611 2.041541604 0.013176925 0.177140947 42343.0189 -4.626781818 -0.208510932 CQVFEETQIGGER ddPTM_BT-474_Pertuzumab_2h_R1 4 CQVFEETQIGGER 13 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 241.92 1.53E-16 773640000 464609 482520 415201 514890 488101 539210 515960 572530 610630 581960 FALSE TRUE 446451.5666 468759.002 490237.0568 541463.5346 503801.2119 550113.1956 522274.4728 560707.0554 541313.8424 542543.3308 0.822886471 0.864002883 0.903590605 0.998009751 0.92859166 1.013952553 0.962641034 1.033478846 0.997733843 1 19.04937884 4.627408329 0.568542009 1.00759509 0.702140209 0.835326187 0.02704148 1.201676976 0.323051609 0.013423847 0.239135837 42404.14679 -4.627408329 -0.30545488 RSDS(ph)QQAVK ddPTM_BT-474_Pertuzumab_2h_R1 3 RSDSQQAVK 9 1 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 RS(0.018)DS(0.982)QQAVK;RSDS(1)QQAVK;RS(0.005)DS(0.995)QQAVK 132.5 0.00057031 343360000 659870 543570 354418 422000 509710 410630 439340 628800 463130 432680 TRUE FALSE 634081.5509 528067.9158 418469.2166 443779.4706 526105.2851 418933.2199 444716.7743 615815.0603 410557.424 403374.1982 1.571943753 1.309126657 1.037421874 1.100168212 1.304261124 1.038572179 1.102491871 1.526659521 1.017807846 1 18.62175928 4.628643166 3.307601541 1.17625989 1.585357433 0.401756591 0.157182097 0.297799947 5.254728089 0.040037968 0.257763685 42524.88675 -4.628643166 0.409097543 LYTLVLTDPDAPSRKDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LYTLVLTDPDAPSRKDPK 18 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 129.05 1.24E-05 1294130000 1040700 902700 697760 603690 805280 851190 737910 899170 974550 931410 FALSE TRUE 1000028.293 876955.8798 823860.7536 634846.5132 831182.5625 868401.645 746940.7633 880601.8253 863923.1696 868324.7711 1.151675418 1.009939955 0.948793333 0.731116438 0.957225442 1.000088531 0.860208977 1.014138781 0.994930927 1 19.72787522 4.629160601 2.426000674 0.935072584 1.174142023 0.3904554 0.081363862 0.439866253 3.744881134 0.020993774 0.197217037 42575.5827 -4.629160601 0.239069439 DVDDFFEHER ddPTM_BT-474_Pertuzumab_2h_R1 3 DVDDFFEHER 10 0 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ;; 199.68 2.74E-07 2114050000 1869820 2019190 1725730 2049590 2059250 2002360 2003360 2028560 2278190 2311000 FALSE TRUE 1796745.367 1961604.678 2037607.8 2155369.586 2125487.646 2042849.091 2027877.719 1986669.527 2019579.422 2154473.912 0.833960141 0.910479662 0.945756543 1.000415727 0.986546012 0.948189291 0.941240322 0.922113522 0.937388664 1 21.0389042 4.629502418 2.048874616 0.956770945 0.81497373 0.697135471 0.025749925 0.351035383 1.930913094 0.007385459 0.085069052 42609.10559 -4.629502418 -0.141797216 LKS(ph)PSMAVPSPGWVASPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKSPSMAVPSPGWVASPK 18 1 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 LKS(0.672)PS(0.328)MAVPSPGWVASPK;LKS(0.946)PS(0.054)MAVPSPGWVASPK 192.57 1.02E-14 1296240000 1791510 1593280 1244490 1289490 1305430 1348420 1324850 1674760 1788250 1456870 TRUE FALSE 1721495.809 1547841.214 1469397.027 1356040.733 1347420.342 1375685.976 1341063.911 1640175.621 1585255.357 1358194.897 1.267488055 1.139631151 1.081874943 0.998413951 0.992067003 1.01287818 0.987386945 1.20761433 1.167178113 1 20.37325909 4.629541061 1.992938566 1.061025706 1.301112668 0.447334081 0.072904053 0.631036926 3.229530701 0.021419366 0.254687803 42612.89707 -4.629541061 0.240086962 LYSLLGIDLTAPSNNSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPR 19 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 LYSLLGIDLTAPS(0.002)NNS(0.051)S(0.948)PR 265.54 2.10E-31 148560000 468860 540980 478010 609220 556810 633670 625360 623520 675530 724470 TRUE FALSE 450536.4328 525551.7801 564397.0403 640661.9172 574720.2993 646483.2416 633013.3427 610644.0941 598846.6665 675401.0016 0.667065094 0.778132959 0.835647325 0.948565246 0.850931962 0.95718431 0.937240752 0.9041208 0.886653507 1 19.36538479 4.629672937 0.968079166 0.924725415 0.557469394 0.817852321 0.039893285 0.650942651 0.549545151 0.011986808 0.241160845 42625.83868 -4.629672937 -0.367256021 TCS(ph)FGGFDLTNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TCSFGGFDLTNR 12 0 O94885;A0A1B0GWB9 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 T(0.002)CS(0.998)FGGFDLTNR;T(0.029)CS(0.971)FGGFDLTNR 216.81 4.00E-11 364220000 1367330 1015790 655320 690640 780280 576670 660920 1068360 742400 705890 TRUE FALSE 1313893.232 986820.6638 773750.9015 726284.0132 805378.4148 588330.6625 669008.5367 1046297.993 658125.8644 658079.4416 1.996557177 1.49954641 1.175771271 1.103641851 1.223831598 0.894011612 1.016607562 1.589926575 1.000070543 1 19.32790223 4.629826761 1.92630529 1.154237775 2.148928081 0.688021 0.182617158 0.385340951 1.804228171 0.051048049 0.631255835 42640.9391 -4.629826761 0.994690306 ESTSSKS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 10 ESTSSKSPPR 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ESTS(0.001)S(0.005)KS(0.994)PPR;ESTSS(0.001)KS(0.999)PPR;ESTSSKS(1)PPR;ESTS(0.002)S(0.002)KS(0.996)PPR;ES(0.001)T(0.002)S(0.01)S(0.053)KS(0.934)PPR;EST(0.001)S(0.001)S(0.018)KS(0.979)PPR;ES(0.009)T(0.008)S(0.011)S(0.041)KS(0.932)PPR;ESTSSKS(1)PPR;ESTSS(0.008)KS(0.992)PPR;ESTS(0.001)S(0.035)KS(0.964)PPR 154.85 8.33E-06 63197820000 7451890 6832990 5422818 5490940 5921700 6396330 6266410 6781270 7529850 6808590 TRUE FALSE 7160661.9 6638119.815 6402841.843 5774328.071 6112176.858 6525668.175 6343100.2 6641234.405 6675092.996 6347438.135 1.128118423 1.045795118 1.008728515 0.90971002 0.962936027 1.028079051 0.999316585 1.046285803 1.051620016 1 22.597743 4.630228804 2.36484136 1.001444564 1.142340289 0.50049643 0.038998808 0.411541138 3.278036552 0.011038165 0.107435974 42680.43178 -4.630228804 0.140895725 S(ph)SDPLGDTASNLGSAVDELMR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSDPLGDTASNLGSAVDELMR 21 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(0.499)S(0.499)DPLGDT(0.001)ASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR 184.35 4.18E-17 131851000 42348.5 47896 42640.3 49989.4 43647.4 53242.6 48985.1 52131.1 56500.6 60302.9 TRUE FALSE 40693.4738 46530.05298 50346.35074 52569.35892 45051.35826 54319.20185 49584.59431 51054.57457 50086.88876 56218.53087 0.72384449 0.827663979 0.89554725 0.935089518 0.801361358 0.96621525 0.881997333 0.908144944 0.890932011 1 15.77875813 4.630478893 1.787506526 0.90558374 0.686092518 0.574654099 0.050196287 0.469432316 1.808122895 0.01205576 0.161957802 42705.01645 -4.630478893 -0.219491222 DASGDGELDLSGIDDLEIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DASGDGELDLSGIDDLEIDR 20 0 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 0 195.2 2.23E-18 20244000 18259 19707 16554 20385 19186 21352 19015 24216 21169 20834 FALSE TRUE 17545.41809 19144.97566 19545.67604 21437.07229 19803.13511 21783.75207 19247.71126 23715.93114 18765.98387 19422.89462 0.903336935 0.985691166 1.006321479 1.10370121 1.019576922 1.121550237 0.990980574 1.221029697 0.966178535 1 14.2454706 4.630650259 0.957299944 1.077460169 0.831800105 0.287825019 0.073300166 1.852225572 1.521811955 0.022506192 0.455144715 42721.87051 -4.630650259 -0.245660064 ELENFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELENFR 6 0 Q96HE7;Q7Z6L1-3;Q7Z6L1;Q7Z6L1-2;Q7Z6L1-4 Q96HE7;Q7Z6L1-3 ERO1L;TECPR1 ERO1-like protein alpha;Tectonin beta-propeller repeat-containing protein 1 0 114.19 0.059325 588000000 658900 728870 651280 777050 729770 679520 744860 775230 732240 805830 FALSE TRUE 633149.4595 708083.3412 768980.7836 817153.6436 753243.7148 693260.36 753975.8195 759221.2296 649119.185 751250.4163 0.842794155 0.942539699 1.023601141 1.087724713 1.002653308 0.92280862 1.003627822 1.010610062 0.864051681 1 19.51893436 4.630946271 3.038752597 0.992756558 0.834833956 0.378087482 0.056794405 0.310146437 4.549946859 0.014166324 0.101379692 42750.99929 -4.630946271 -0.157922602 LPDNYTQDTWR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPDNYTQDTWR 11 0 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 0 184.9 1.09E-05 197980000 25505 38708 37997 51630 41608 34754 48380 44946 48717 49417 FALSE TRUE 24508.2364 37604.08574 44863.90314 54294.63049 42946.35911 35456.74969 48972.08891 44017.84939 43186.8504 46069.94257 0.531978879 0.816239041 0.973821555 1.178526116 0.932199102 0.769628693 1.062994355 0.955457006 0.937419237 1 15.49153818 4.631025029 2.35158875 0.975968037 0.479938139 0.658622365 0.0981258 0.273312822 2.143581804 0.025496641 0.25064034 42758.75274 -4.631025029 -0.496029898 ETLLNGVGYLHEGLSPMER ddPTM_BT-474_Pertuzumab_2h_R1 2 ETLLNGVGYLHEGLSPMER 19 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 198.49 7.39E-16 486036000 115529 140440 129858 152402 151016 157765 142912 149926 139911 170232 FALSE TRUE 111013.999 136434.7887 153326.2293 160267.4855 155873.5668 160955.1164 144660.9998 146829.9757 124028.8898 158702.035 0.699512133 0.859691488 0.966126422 1.009864086 0.982177492 1.014196928 0.911525802 0.925192772 0.781520475 1 17.2759611 4.631243003 2.515327222 0.948307286 0.674519642 0.578531041 0.065120854 0.290216509 2.700736987 0.016794318 0.152036187 42780.21895 -4.631243003 -0.273787644 AFTHTAQYDEAISDYFR ddPTM_BT-474_Pertuzumab_2h_R1 5 AFTHTAQYDEAISDYFR 17 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;;;; 288.16 6.45E-37 2256090000 1079226 1209483 1059094 1281538 1256947 1342835 1271979 1121811 1276043 1345391 FALSE TRUE 1037048.655 1174989.729 1250495.845 1347678.33 1297377.842 1369988.044 1287545.859 1098645.211 1131191.948 1254266.469 0.826816853 0.93679434 0.996993762 1.074475291 1.034371781 1.092262352 1.026532951 0.875926478 0.9018753 1 20.25841245 4.631815395 2.374524459 0.997713393 0.807178567 0.408096012 0.064133826 0.521383106 4.187829634 0.018960342 0.18473568 42836.63964 -4.631815395 -0.190534826 LEEQRPER ddPTM_BT-474_Pertuzumab_2h_R1 5 LEEQRPER 8 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2;Q9HAU6 Q5W0H4 TPT1;TPT1P8 Translationally-controlled tumor protein;Putative translationally-controlled tumor protein-like protein TPT1P8 0 ;;;; 160.59 0.00032147 8607290000 7321250 8005790 6829430 8097580 8303010 8287360 8159370 8359190 8515860 9299630 FALSE TRUE 7035127.456 7777472.708 8063659.921 8515497.074 8570083.857 8454936.097 8259226.811 8186569.805 7549175.274 8669757.777 0.811456056 0.897080738 0.930090566 0.982207034 0.988503264 0.975221721 0.952647931 0.94426742 0.870748119 1 23.04756026 4.632149857 1.622124813 0.956999641 0.777962072 0.635236017 0.034263108 0.526233559 1.574081633 0.0093443 0.139064206 42869.64201 -4.632149857 -0.179037569 SAAEMYGSSFDLDYDFQR ddPTM_BT-474_Pertuzumab_2h_R1 7 SAAEMYGSSFDLDYDFQR 18 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;;;;;; 367.81 3.69E-107 2668720000 1236021 1529898 1616449 1789353 1316302 1554773 1642411 1569056 1694865 1810603 FALSE TRUE 1187715.933 1486266.807 1908577.292 1881701.723 1358642.049 1586211.575 1662511.317 1536654.445 1502471.031 1687969.246 0.703636003 0.880505857 1.130694351 1.114772516 0.804897395 0.939715921 0.984918014 0.910356897 0.89010569 1 20.68685719 4.632171775 3.797432744 0.96634777 0.700951705 0.428679512 0.093614294 0.230013802 5.308511847 0.023791388 0.133561591 42871.80561 -4.632171775 -0.265396065 AASEAPEEEVSLPWVHLAYQR ddPTM_BT-474_Pertuzumab_2h_R1 1 AASEAPEEEVSLPWVHLAYQR 21 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 86.453 0.0027495 138080000 155740 187230 178450 169510 195080 261890 195930 168790 212670 208270 FALSE TRUE 149653.5086 181890.3837 210699.8846 178258.4314 201354.9254 267185.5952 198327.8499 165304.4275 188528.5932 194163.6874 0.77075951 0.936788882 1.085166271 0.918083262 1.037036987 1.376084266 1.02144666 0.851366338 0.97097761 1 17.56691389 4.632571198 2.83585701 1.025740555 0.752147259 0.269445927 0.131475299 0.504483765 6.296016333 0.035632043 0.279039323 42911.2532 -4.632571198 -0.273593296 QEETAVLEEDS(ph)ADWEKELQQELQEYEVVTESEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEETAVLEEDSADWEKELQQELQEYEVVTESEKR 34 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 QEETAVLEEDS(1)ADWEKELQQELQEYEVVTESEKR 211.29 4.07E-28 46335000 42125 33524 24129 20376 27894 26246 24613 35499 36046 28794 TRUE FALSE 40478.70843 32567.92834 28489.64705 21427.6078 28791.23584 26776.7121 24914.22126 34765.93324 31954.2092 26843.75673 1.507937538 1.213240332 1.06131371 0.798234316 1.07254868 0.997502413 0.928119767 1.295121752 1.190377692 1 14.71229897 4.632608334 2.362168412 1.051611551 1.56111381 0.553008159 0.128328627 0.371491585 2.941109741 0.035714128 0.351279265 42914.9226 -4.632608334 0.50950226 VIDTLHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VIDTLHR 7 0 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ;;; 155.51 0.0016062 2890680000 3951940 4385620 3990060 4561900 4214250 4635810 4450280 3970110 4808400 5659200 FALSE TRUE 3797493.816 4260546.412 4711152.6 4797340.206 4349805.179 4729549.254 4504743.858 3888125.841 4262570.59 5275897.343 0.719781597 0.807549149 0.892957594 0.909293698 0.824467365 0.896444519 0.85383463 0.736960101 0.807932815 1 22.33098506 4.632770027 3.281431924 0.850649935 0.714759515 0.289102874 0.06731121 0.387980642 6.731604835 0.017056382 0.112047183 42930.90331 -4.632770027 -0.13589042 QPYAVSELAGHQTSAESWGTGR ddPTM_BT-474_Pertuzumab_2h_R1 6 QPYAVSELAGHQTSAESWGTGR 22 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;;;;; 324.31 4.72E-68 10303620000 1961199 2357942 1954751 2753901 2316290 2710335 2625989 2334843 2577212 2701806 FALSE TRUE 1884553.175 2290695.803 2308017.989 2896030.161 2390795.571 2765139.831 2658126.639 2286627.676 2284657.698 2518810.273 0.748191793 0.909435628 0.916312758 1.149761136 0.949176521 1.097795995 1.055310385 0.90782053 0.907038423 1 21.26431103 4.633222996 1.600863044 1.002433191 0.692231974 0.505513786 0.07718757 0.712002728 2.055646506 0.021375283 0.323312089 42975.70362 -4.633222996 -0.310201217 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(ph)PGKQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDASPGKQK 37 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGKQK 127.77 9.38E-09 55503000 128520 100210 69366 59621 79623 98229 80865 89617 102660 80013 TRUE FALSE 123497.2963 97352.10892 81901.97924 62698.04695 82184.14611 100215.2577 81854.65006 87766.37763 91006.46719 74593.64824 1.655600701 1.305099177 1.097975245 0.84052796 1.101757965 1.343482455 1.097340752 1.176593178 1.220029712 1 16.18676517 4.633255342 2.525164862 1.117941279 1.709256996 0.638179111 0.125796221 0.265082772 2.485248292 0.033175362 0.301124453 42978.90452 -4.633255342 0.591315717 WDET(ph)PKTER ddPTM_BT-474_Pertuzumab_2h_R1 2 WDETPKTER 9 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDET(0.999)PKT(0.001)ER;WDET(1)PKTER 160.52 0.00012298 542600000 2193500 1914490 1468350 1434180 1616460 1661410 1645420 1998080 2075000 1761140 TRUE FALSE 2107775.595 1859890.62 1733713.508 1508198.202 1668454.904 1695004.849 1665557.142 1956818.95 1839454.699 1641856.419 1.283775835 1.132797362 1.05594709 0.918593236 1.01620025 1.032370936 1.01443532 1.191833176 1.120350524 1 20.64689654 4.633441313 2.379971201 1.050975507 1.310541511 0.531032028 0.069163262 0.404553927 3.261541334 0.020028617 0.195811236 42997.31265 -4.633441313 0.259566004 RPS(ph)VGSQSNQAGQGK ddPTM_BT-474_Pertuzumab_2h_R1 5 RPSVGSQSNQAGQGK 15 1 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 RPS(1)VGSQSNQAGQGK;RPS(1)VGSQSNQAGQGK;RPS(1)VGSQSNQAGQGK;RPS(0.999)VGS(0.001)QSNQAGQGK;RPS(1)VGSQSNQAGQGK 226.65 5.13E-13 1875092000 1452208 1270337 920800 1075413 1091983 872045 955906 1547517 962580 813316 TRUE FALSE 1395454.106 1234108.233 1087209.043 1130915.194 1127107.625 889678.3474 967604.6636 1515560.233 853311.9539 758229.3829 1.840411539 1.627618581 1.433878807 1.491521193 1.486499535 1.173363058 1.276137123 1.998814959 1.1254008 1 19.53227484 4.634097897 1.58046679 1.429315542 1.948659565 0.22680702 0.264217312 1.484007958 4.140884902 0.072884645 1.118982239 43062.36689 -4.634097897 0.519344023 GSSCFECTHYQSFLEYR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSSCFECTHYQSFLEYR 17 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 258.92 3.50E-27 6252800000 2196490 2606850 2176660 3060010 2781100 2563180 3039710 2591690 2598250 2915670 FALSE TRUE 2110648.742 2532505.19 2570030.882 3217937.483 2870556.607 2615009.256 3076910.88 2538170.696 2303307.553 2718189.074 0.776490776 0.931688386 0.945493787 1.183853439 1.056054796 0.962040971 1.131970881 0.93377268 0.84736841 1 21.37421438 4.6348326 1.826110536 1.014757532 0.733003351 0.372494981 0.092288028 0.73473402 2.971156217 0.024768659 0.330856404 43135.27791 -4.6348326 -0.281754181 TKKDDSHSAEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 4 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TKKDDS(0.006)HS(0.097)AEDS(0.897)EDEKEDHK;TKKDDSHSAEDS(1)EDEKEDHK;TKKDDSHSAEDS(1)EDEKEDHK;TKKDDS(0.003)HS(0.006)AEDS(0.991)EDEKEDHK 185.18 1.52E-17 504475000 849180 576377 367199 263103 419945 411691 372110 421188 579743 381991 TRUE FALSE 815993.1068 559939.2923 433560.0276 276681.7774 433452.9123 420015.6741 376663.9935 412490.3206 513933.0051 356118.4093 2.29135334 1.572340204 1.217460306 0.776937586 1.21715952 1.179427019 1.057693126 1.158295415 1.443152029 1 18.44199749 4.634855196 1.977875969 1.123795906 2.492830106 0.831651992 0.161395474 0.22152001 1.102546774 0.041612476 0.509508374 43137.52222 -4.634855196 1.3690342 AVFVDLEPTVIDEVR ddPTM_BT-474_Pertuzumab_2h_R1 11 AVFVDLEPTVIDEVR 15 0 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;F8VRK0;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;;;;;;;;; 339.5 6.69E-69 10981416000 2941459 3321056 2897437.7 3564104 3409533 3470949 3489943 3347452 3454535 3683184 FALSE TRUE 2826503.53 3226342.735 3421069.146 3748047.835 3519203.725 3541133.967 3532653.966 3278325.946 3062390.669 3433718.667 0.82316107 0.939606021 0.996316087 1.091541911 1.024895767 1.031282499 1.028812873 0.954745063 0.891858351 1 21.71134041 4.634905699 2.25876243 1.004405283 0.799386261 0.550878603 0.049583759 0.383629594 2.697464574 0.013622197 0.142783973 43142.53884 -4.634905699 -0.205019021 LSLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSLSPK 6 0 Q5FBB7-6;Q5FBB7;Q5FBB7-5;Q5FBB7-4;Q5FBB7-3;Q5FBB7-2 Q5FBB7-6 SGOL1 Shugoshin-like 1 1 LS(0.002)LS(0.998)PK 91.783 0.049826 181490000 483090 405680 294600 318800 327750 259270 341430 406110 324200 348780 TRUE FALSE 464210.3087 394110.4036 347840.7733 335253.3062 338292.3764 264512.617 345608.5225 397723.6866 287398.1752 325156.8199 1.427650537 1.212062548 1.069763117 1.031051129 1.040397604 0.813492447 1.062897966 1.22317498 0.883875587 1 18.31077616 4.635120182 1.499653119 1.024884894 1.537639507 0.618807691 0.10311378 0.682451151 1.663702897 0.030392757 0.490274571 43163.85069 -4.635120182 0.512754613 QLAAEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 QLAAEEER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 121.85 0.0032934 258790000 304320 335220 298330 352220 331550 297160 355130 357760 340940 370940 FALSE TRUE 292426.838 325659.8538 352244.8673 370398.1164 342214.6069 303168.7788 359476.1872 350372.131 302237.9205 345815.9034 0.845614198 0.941714509 1.018590712 1.071084681 0.989586088 0.876676798 1.039501607 1.013175298 0.873985024 1 18.39964469 4.635249839 3.028482885 0.989015627 0.837386228 0.324445415 0.060770466 0.348376761 5.061141625 0.015085139 0.109872438 43176.73907 -4.635249839 -0.151629398 QEPIES(ph)DEEEAEPPREVEPGQR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEPIESDEEEAEPPREVEPGQR 22 1 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 QEPIES(1)DEEEAEPPREVEPGQR 170.11 4.56E-12 744830000 80836 93747 84368 97427 97376 98224 96847 100110 103880 102460 TRUE FALSE 77676.83975 91073.42735 99615.17436 102455.2191 100508.1875 100210.1566 98032.24256 98042.69352 92087.9779 95520.29294 0.813197252 0.953445855 1.04286923 1.072601601 1.052218166 1.049098087 1.026297549 1.02640696 0.964067164 1 16.54351964 4.635380076 2.377883218 1.032561927 0.786877374 0.836693296 0.02913779 0.163184725 1.309270875 0.007592281 0.074864458 43189.68894 -4.635380076 -0.245684553 SSS(ph)MAAGLER ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSMAAGLER 10 0 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6;I3L0Y9 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 S(0.012)S(0.05)S(0.938)MAAGLER 101.79 0.0032457 175940000 735960 437130 186720 235330 255630 171770 137930 368780 187890 156350 TRUE FALSE 707197.8696 424663.4804 220464.4576 247475.4095 263852.5711 175243.3071 139618.0286 361164.5641 166561.5149 145760.2752 4.851787419 2.913437696 1.512514004 1.697824796 1.81018162 1.202270693 0.957860627 2.477798313 1.142708565 1 17.15323806 4.63549827 1.921310301 1.543369554 5.480161628 0.850401581 0.440978003 0.225284132 1.03861919 0.115500878 1.464319149 43201.44471 -4.63549827 3.936792074 up KAQPAQPADEPAEKADEPMEH ddPTM_BT-474_Pertuzumab_2h_R1 2 KAQPAQPADEPAEKADEPMEH 21 2 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ; 159.7 1.25E-11 520460000 405610 346060 251354 236998 329340 341150 290530 311520 391910 325450 FALSE TRUE 389758.3128 336190.7076 296779.2591 249229.4952 339933.5202 348048.2867 294085.593 305087.0031 347422.0198 303406.9816 1.284605617 1.108051983 0.978155669 0.821436257 1.12038793 1.147133414 0.969277607 1.005537188 1.145069299 1 18.21089476 4.635525344 2.955087914 1.021175825 1.301151674 0.419543571 0.093185647 0.307848383 4.225186671 0.023654489 0.177744703 43204.13795 -4.635525344 0.279975848 LDDTVHVVIATPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDDTVHVVIATPGR 14 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ;; 199.31 2.08E-08 3492200000 2239270 2362780 1959060 2424000 2352540 2403230 2332870 2313660 2465110 2563730 FALSE TRUE 2151756.853 2295395.828 2313105.721 2549102.93 2428211.586 2451824.957 2361420.361 2265882.112 2185281.047 2390086.284 0.900284173 0.960381993 0.967791722 1.06653176 1.015951433 1.025831148 0.988006323 0.948033604 0.914310526 1 21.18863127 4.635625602 1.968596663 0.991412416 0.885539709 0.330427469 0.039712642 0.790407083 3.881490496 0.011361225 0.140268404 43214.11292 -4.635625602 -0.105872707 DRESLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DRESLK 6 1 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 0 66.429 0.092506 157610000 179440 218970 196770 262660 217650 257340 238340 208150 231170 241950 FALSE TRUE 172427.2864 212725.19 232330.7161 276215.9141 224650.9099 262543.5911 241256.8762 203851.6298 204928.5507 225562.511 0.764432377 0.943087524 1.030005895 1.224564813 0.995958543 1.163950472 1.069578784 0.90374783 0.908522209 1 17.78316778 4.636120693 2.407912462 1.037334627 0.733382982 0.436096414 0.094817071 0.44041502 3.645621384 0.02586152 0.251796492 43263.4046 -4.636120693 -0.303951645 AGLQMKS(ph)PEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGLQMKSPEKK 11 2 Q9BRQ0 Q9BRQ0 PYGO2 Pygopus homolog 2 1 AGLQMKS(1)PEKK 68.044 0.030427 401050000 827060 635610 432120 312540 508980 526870 526490 633160 712990 550720 TRUE FALSE 794737.5808 617483.0251 510213.6965 328670.2269 525351.8039 537523.6724 532933.3421 620085.0247 632054.3643 513419.2439 1.547931034 1.20268773 0.993756472 0.64015954 1.023241357 1.046948822 1.038008116 1.207755713 1.231068706 1 18.96977785 4.636385332 2.705801767 1.029087573 1.591613344 0.529237398 0.151071268 0.314341128 3.489176359 0.041821332 0.352052633 43289.77537 -4.636385332 0.562525771 IIEGLQDLDDDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 IIEGLQDLDDDVR 13 0 A0A0A0MTH9;O14981 A0A0A0MTH9 BTAF1 TATA-binding protein-associated factor 172 0 ;;; 221.8 4.31E-11 183336000 212147 247998 210307 262824 269979 268598 262705 277447 256707 308304 FALSE TRUE 203856.0607 240925.3399 248314.1532 276388.3781 278663.1197 274029.2356 265920.0624 271717.6225 227566.6976 287422.2955 0.709256254 0.838227735 0.863934904 0.961610781 0.969525065 0.95340285 0.925189404 0.945360283 0.791750331 1 18.13281245 4.636414517 1.300121134 0.934003808 0.642190242 0.620893027 0.054104985 0.725075086 1.233889453 0.014861752 0.267848829 43292.68452 -4.636414517 -0.291813566 FLEMCNDLLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLEMCNDLLAR 11 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 85.958 0.034496 44555000 41112 46543 40716 50019 46404 50369 47571 48994 47420 49601 FALSE TRUE 39505.29759 45215.63921 48074.28692 52600.48658 47896.6268 51387.49569 48153.18813 47982.25678 42037.0804 46241.48009 0.854325976 0.97781557 1.039635557 1.137517365 1.03579355 1.111285703 1.041341844 1.03764535 0.909077312 1 15.49689996 4.637182779 2.285019854 1.045751615 0.829363723 0.481654212 0.058120084 0.386508063 2.791302582 0.014682956 0.153116019 43369.33658 -4.637182779 -0.216387893 FFEDLEQR ddPTM_BT-474_Pertuzumab_2h_R1 3 FFEDLEQR 8 0 Q5VV41;Q5VV41-2;B0QZD3 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ;; 121.99 0.0032795 295223000 535530 620530 534710 672970 635260 668530 681200 651110 668410 710430 FALSE TRUE 514600.8955 602833.092 631343.9916 707702.0623 655693.7148 682048.1346 689536.7294 637664.351 592534.899 662311.9433 0.776976621 0.91019511 0.953242649 1.068532841 0.990007385 1.029798936 1.041105685 0.962785523 0.894646254 1 19.33715135 4.637320959 1.668627803 0.997713112 0.727425662 0.683439861 0.045694275 0.454711378 1.450964516 0.012556266 0.185469877 43383.13762 -4.637320959 -0.270287449 VCGDSDKGFVVINQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VCGDSDKGFVVINQK 15 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 159.22 1.62E-06 309700000 640180 529970 434430 356040 401260 468960 427480 565850 526520 458690 FALSE TRUE 615161.0578 514855.7745 512941.1648 374415.2671 414166.8923 478442.6925 432711.6281 554164.9998 466751.657 427622.5177 1.438560956 1.203995938 1.199518602 0.875574254 0.968533871 1.118843542 1.011900941 1.295920998 1.091503926 1 18.7059783 4.637378182 1.663847159 1.077358751 1.514521104 0.517556022 0.11100075 0.729574678 2.310733791 0.03242677 0.48040261 43388.85423 -4.637378182 0.437162353 FSMPGFK ddPTM_BT-474_Pertuzumab_2h_R1 1 FSMPGFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 97.071 0.050165 0 643550 674110 543890 726440 606370 589940 716340 693830 723550 675930 FALSE TRUE 618399.3545 654885.0428 642183.0218 763931.6555 625874.4417 601868.991 725106.7832 679502.168 641415.6374 630148.659 0.98135471 1.039254838 1.019097657 1.212303866 0.993217129 0.955122228 1.150691623 1.078320422 1.017879874 1 19.26533269 4.637435712 1.921017866 1.061968653 0.969010689 0.072330466 0.073695873 1.583580919 7.275979251 0.01904756 0.24336597 43394.6023 -4.637435712 -0.092957964 IQEEILVHIR ddPTM_BT-474_Pertuzumab_2h_R1 4 IQEEILVHIR 10 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;;; 147.37 2.70E-05 525828000 222127 248097 214621 268158 265123 256799 257565 223142 274841 285594 FALSE TRUE 213446.0313 241021.5165 253407.7889 281997.6665 273650.9221 261991.6517 260717.1575 218534.0397 243642.2019 266250.464 0.801673838 0.905243555 0.951764685 1.05914432 1.027795099 0.984004489 0.979217664 0.820783695 0.915086488 1 18.02242451 4.637531594 2.340684439 0.959888638 0.782318065 0.39970488 0.062027308 0.573053102 4.402053098 0.018622372 0.18880892 43404.18382 -4.637531594 -0.177570573 IQESEVFRVTSTEFIS(ph)LRIDSSDEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 IQESEVFRVTSTEFISLRIDSSDEDR 26 2 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2;C9J1Z6;C9JW66;O43426-5 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 IQES(0.082)EVFRVT(0.082)S(0.127)T(0.127)EFIS(0.372)LRIDS(0.106)S(0.106)DEDR 47.383 0.074213 318140000 175310 138190 89765 123200 116730 89303 100840 185550 84005 66258 TRUE FALSE 168458.6914 134248.9565 105987.5323 129558.3668 120484.7265 91108.76785 102074.1101 181718.3277 74469.10458 61770.28664 2.727180017 2.17335816 1.715833584 2.097422139 1.950528855 1.474961066 1.652479139 2.941840447 1.205581334 1 15.91462541 4.63758782 2.760259877 1.882685474 2.797736776 0.22837376 0.516225646 0.574219501 6.685454084 0.12819545 1.056855159 43409.80355 -4.63758782 0.915051303 LSSPAAFLPACNS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSPAAFLPACNSPSK 16 0 Q86YS7;Q86YS7-5;H0YFE9;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 LSSPAAFLPACNS(0.996)PS(0.004)K;LSSPAAFLPACNS(0.997)PS(0.003)K 291.17 1.64E-45 1424540000 1350840 1276850 1046160 1130950 1130480 1142700 1192830 1286830 1369590 1280530 TRUE FALSE 1298047.679 1240435.488 1235224.384 1189318.465 1166842.916 1165806.177 1207428.21 1260256.511 1214119.885 1193798.563 1.087325551 1.039065992 1.034700847 0.996247191 0.977420272 0.976551835 1.011417042 1.055669315 1.017022405 1 20.18712799 4.637649247 1.427493544 1.009120498 1.107661414 0.558718775 0.022161879 0.93514248 2.005496251 0.007372935 0.124872927 43415.94387 -4.637649247 0.098540916 RGES(ph)LDNLDSPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RGESLDNLDSPR 12 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RGES(1)LDNLDSPR;RGES(1)LDNLDSPR;RGES(1)LDNLDSPR 236.75 2.69E-16 2765610000 2629870 2354870 1732010 2090750 2017540 1495260 1731740 2869970 2021050 2081990 TRUE FALSE 2527091.773 2287711.413 2045022.735 2198653.858 2082436.006 1525495.182 1752933.552 2810704.117 1791628.877 1940974.963 1.301970309 1.178640352 1.053605932 1.132757454 1.072881437 0.785942741 0.903120126 1.448088806 0.92305615 1 20.88835008 4.63775056 1.59261955 1.061433323 1.366238691 0.194566545 0.167131988 1.696155183 4.799667369 0.048932859 0.756184064 43426.07317 -4.63775056 0.304805368 ASAVSELS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 9 ASAVSELSPR 10 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR 174.23 3.33E-06 67090300000 7842680 8376640 7095640 8411950 8481530 8682760 8397550 8604690 8477190 8857680 TRUE FALSE 7536179.395 8137746.429 8377979.99 8846091.748 8754346.115 8858331.356 8500321.729 8427000.145 7514894.93 8257741.444 0.912619927 0.985468785 1.014560706 1.071248332 1.060138075 1.07273053 1.029376106 1.020496973 0.910042411 1 22.97731582 4.637999325 1.994119345 1.028071763 0.893005668 0.358515626 0.044470237 0.632195673 3.198884959 0.011765834 0.144518179 43450.95491 -4.637999325 -0.135066094 AVTEQGHELSNEER ddPTM_BT-474_Pertuzumab_2h_R1 14 AVTEQGHELSNEER 14 0 P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;A0A0J9YWZ2 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;;;;;;;;;; 285.75 1.09E-33 1.86446E+11 43010045.8 47227971.7 38933916.4 51051157.6 46834653.3 50517597.4 49061871.1 45758952.7 48145335.7 51118144.9 FALSE TRUE 41329165.66 45881076.19 45970141.17 53685913.96 48341132.46 51539097.83 49662304.95 44814014.34 42680079.03 47655867.41 0.867241914 0.96275818 0.9646271 1.12653314 1.014379447 1.081484833 1.042102634 0.940367194 0.895589176 1 25.50615051 4.638019918 1.811303233 1.011593663 0.840458107 0.323714542 0.062764163 0.882394992 3.47642931 0.017640443 0.240612774 43453.01529 -4.638019918 -0.171135556 GGFDGEYQDDSLDLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGFDGEYQDDSLDLLR 16 0 Q5F1R6;Q5F1R6-3;Q5F1R6-2 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 0 ; 276.28 6.34E-35 136836000 159747 168318 138438 166131 173003 156362 154707 188464 172870 186529 FALSE TRUE 153503.9106 163517.7354 163456.8261 174705.0408 178567.7986 159523.7468 156600.3505 184572.1525 153246.5223 173895.2247 0.88273793 0.940323322 0.939973058 1.00465692 1.026870053 0.917355534 0.900544284 1.061398626 0.881257795 1 17.40785879 4.638223616 1.502431782 0.972863336 0.861035076 0.179291596 0.054700165 1.525920721 3.720186963 0.014723202 0.239803616 43473.4009 -4.638223616 -0.11182826 ETLVYLTHLDYVDTER ddPTM_BT-474_Pertuzumab_2h_R1 8 ETLVYLTHLDYVDTER 16 0 O14980 O14980 XPO1 Exportin-1 0 ;;;;;;; 245.39 4.06E-20 4385279000 1738079 1888899 1630397 1986041 1926390 1943255 1893553 1808847 1986663 2092536 FALSE TRUE 1670152.951 1835029.45 1925046.006 2088540.814 1988354.084 1982548.948 1916726.868 1771493.677 1761145.345 1950806.673 0.856134529 0.940651616 0.986794864 1.070603686 1.01924712 1.016271358 0.982530404 0.908082642 0.902777999 1 20.89563938 4.639057894 2.580245709 0.983301382 0.843622459 0.41035186 0.047445847 0.456277827 4.486495077 0.013788833 0.124490965 43556.9934 -4.639057894 -0.139678923 S(ph)RS(ph)RT(ph)PLLPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSRTPLLPR 10 2 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)RS(1)RT(1)PLLPR 48.981 0.058657 0 569790 491470 350600 410530 405440 471780 427950 486340 535080 404380 TRUE FALSE 547521.9769 477453.7568 413961.2191 431717.5025 418481.3458 481319.7148 433187.3801 476296.909 474339.9616 376990.9824 1.452347675 1.266485882 1.098066634 1.145166656 1.110056647 1.276740658 1.149065628 1.263417247 1.258226281 1 18.52417049 4.639129204 3.156402431 1.177248857 1.466645528 0.526781562 0.082961854 0.225971448 3.600837695 0.019797051 0.138742904 43564.14595 -4.639129204 0.289396671 LTPRPS(ph)PSPMIESTPMSIAGDATPLLDEMDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LTPRPSPSPMIESTPMSIAGDATPLLDEMDR 31 1 Q7KZ85;Q7KZ85-3;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 LT(0.007)PRPS(0.989)PS(0.004)PMIESTPMSIAGDATPLLDEMDR;LT(0.001)PRPS(0.929)PS(0.07)PMIESTPMSIAGDATPLLDEMDR;LT(0.039)PRPS(0.721)PS(0.195)PMIES(0.022)T(0.022)PMS(0.001)IAGDATPLLDEMDR 353.56 8.26E-121 380075000 51662.9 56966 56028.3 55492.3 63241 76467 77940 56043.8 73408 68831 TRUE FALSE 49643.85675 55341.38546 66153.86015 58356.26425 65275.2042 78013.21513 78893.85303 54886.47595 65075.03159 64169.01506 0.773642181 0.862431586 1.030931519 0.909414991 1.01723868 1.215745871 1.229469596 0.855342347 1.014119221 1 15.96958922 4.639159762 0.953081921 1.044593375 0.645929945 0.398159535 0.109468023 2.007468678 1.616933536 0.038616996 0.800146477 43567.21129 -4.639159762 -0.398663431 LVIIESDLER ddPTM_BT-474_Pertuzumab_2h_R1 4 LVIIESDLER 10 0 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;;; 265.95 2.65E-17 211217000 249048 282704 251950 311756 285468 238943 298125 305301 295884 331409 FALSE TRUE 239314.9288 274641.5587 297482.9696 327845.7645 294650.3375 243774.5912 301773.5429 298996.4277 262296.4888 308962.3732 0.77457629 0.888915876 0.962845302 1.061118741 0.953677091 0.789010612 0.976732344 0.967743821 0.848959328 1 18.23707163 4.639232042 2.782993503 0.94518796 0.76091479 0.339647999 0.072248344 0.402626755 4.775578037 0.018284958 0.150061767 43574.46287 -4.639232042 -0.18427317 KFEEEGNPYYSSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFEEEGNPYYSSAR 14 1 Q9HCC0-2;Q9HCC0 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ; 179.79 2.93E-06 503470000 460500 607750 427920 879100 467880 484580 759270 741060 610620 544490 FALSE TRUE 442503.1509 590417.565 505254.663 924470.4564 482929.7851 494378.5396 768562.1734 725756.852 541304.9775 507611.2073 0.871736369 1.163129491 0.99535758 1.821217584 0.95137731 0.97393149 1.514076447 1.429749465 1.06637712 1 18.9533644 4.639487941 1.525819841 1.265701104 0.790552939 0.11639961 0.274790771 1.76562763 4.468038296 0.073842091 1.192573629 43600.14576 -4.639487941 -0.475148165 SESEVEEAAAIIAQRPDNPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SESEVEEAAAIIAQRPDNPR 20 1 Q16643;Q16643-3;Q16643-2;D6R9W4;D6R9Q9 Q16643 DBN1 Drebrin 0 160.67 2.16E-11 1446700000 1335800 1546300 1348300 1684700 1528800 1739400 1641800 1683600 1931200 1850100 FALSE TRUE 1283595.459 1502201.038 1591967.803 1771647.569 1577975.24 1774571.86 1661892.84 1648833.072 1711978.272 1724791.079 0.744203443 0.870946665 0.922991672 1.027166473 0.91487906 1.028861919 0.963532836 0.955961039 0.992571386 1 20.71799019 4.639489275 1.350553641 0.978522709 0.672556141 0.828820382 0.033776669 0.392095023 0.730157101 0.008808926 0.156376462 43600.27971 -4.639489275 -0.305966569 EQQHVMEELFQSSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQQHVMEELFQSSFR 15 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 254.71 1.05E-24 2276420000 1065340 1188420 969970 1265090 1282170 1228300 1199790 1180720 1233200 1279960 FALSE TRUE 1023705.335 1154527.425 1145265.156 1330381.447 1323412.162 1253137.068 1214473.389 1156337.719 1093212.306 1193267.169 0.857901199 0.967534727 0.959772619 1.114906603 1.109066097 1.050173088 1.017771561 0.969051818 0.916150494 1 20.18648566 4.639624072 1.646770297 1.022516773 0.823287094 0.412773093 0.058682845 0.878868691 2.701451753 0.017383183 0.262278229 43613.81445 -4.639624072 -0.199229679 VPSS(ph)DEEVVEEPQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VPS(0.001)S(0.999)DEEVVEEPQSR;VPS(0.009)S(0.991)DEEVVEEPQSR 335.25 5.28E-69 740040000 294380 327030 277920 347750 308770 329880 368510 345240 361790 362070 TRUE FALSE 282875.3041 317703.4246 328146.3263 365697.4192 318701.8675 336550.3996 373019.9356 338110.6734 320721.1159 337546.6764 0.838033149 0.94121331 0.972150962 1.083398074 0.94417125 0.997048477 1.105091419 1.001670871 0.950153381 1 18.36472749 4.639871519 1.546668062 1.013534193 0.793522712 0.540096813 0.048566022 0.661738259 1.732308769 0.013072401 0.208964093 43638.67131 -4.639871519 -0.220011481 RPS(ph)SMYSTGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.657)S(0.331)MYS(0.011)T(0.001)GGK;RPS(0.677)S(0.28)MYS(0.04)T(0.003)GGK 108.97 0.0021095 535350000 1128540 747640 397070 523890 450700 385800 385750 993790 454950 336290 TRUE FALSE 1084435.409 726318.0392 468829.3818 550928.0257 465197.1748 393601.1403 390470.9239 973267.8892 403305.9833 313512.7788 3.458983118 2.31670952 1.495407567 1.757274545 1.483822052 1.255454855 1.245470521 3.104396232 1.286410031 1 18.25816472 4.640129141 2.535815654 1.701257946 3.647985704 0.507026703 0.561991488 0.369925743 3.476794664 0.150688134 1.396373039 43664.5653 -4.640129141 1.946727758 ILCEQIASDTCHLQR ddPTM_BT-474_Pertuzumab_2h_R1 3 ILCEQIASDTCHLQR 15 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;K7EMK2 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;; 203.04 5.61E-09 925360000 439434 517772 454678 573011 532351 537214 556122 550384 556051 594097 FALSE TRUE 422260.4335 503005.6495 536848.4289 602584.1664 549474.5534 548076.8352 562927.9874 539018.3781 492930.4216 553858.281 0.762397978 0.908184759 0.969288439 1.087975367 0.99208511 0.989561507 1.0163755 0.973206317 0.889993774 1 19.07915735 4.640475384 2.01562532 0.993138921 0.72315202 0.69986463 0.045816516 0.321017418 1.664078338 0.012071882 0.147930778 43699.39092 -4.640475384 -0.269986901 DLGEIHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGEIHSR 8 0 A0A0D9SEU2;A0A0A0MTN6;G5E931;H3BN57;Q8TDH9-2;Q8TDH9 A0A0D9SEU2 BLOC1S5;BLOC1S5-TXNDC5 Biogenesis of lysosome-related organelles complex 1 subunit 5 0 ; 118.18 0.0019367 442150000 436500 487260 414290 511850 487550 513000 528140 500260 528640 534150 FALSE TRUE 419441.0974 473363.8219 489161.4188 538266.6398 503232.4885 523373.2115 534603.5353 489929.4562 468631.0034 497971.5447 0.842299328 0.950584078 0.982307973 1.080918469 1.010564748 1.051010278 1.073562417 0.983850305 0.941079884 1 18.92570378 4.64063044 1.642043652 1.020967642 0.800806823 0.638620251 0.04047258 0.51531649 1.569898819 0.011175608 0.169716562 43714.99569 -4.64063044 -0.220160819 LLSDFLDSEVSELR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLSDFLDSEVSELR 14 0 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 0 ;;; 203.61 3.44E-08 74824000 82492 94803 83798 100539 91597 104121 99403 95602 102702 119501 FALSE TRUE 79268.12144 92099.31126 98942.16268 105727.8298 94543.30069 106226.398 100619.5236 93627.78529 91043.69952 111407.0908 0.71151774 0.826691646 0.888113691 0.949022446 0.848629113 0.953497638 0.903169833 0.840411365 0.81721638 1 16.76548153 4.640835141 2.140038231 0.89371504 0.683270106 0.538721727 0.053697272 0.414895782 2.513278367 0.013495574 0.154495474 43735.6053 -4.640835141 -0.210444934 EDQIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDQIYR 6 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 144.58 0.026183 1942890000 1365350 1558800 1347800 1703650 1570130 1578080 1629490 1602090 1620050 1935380 FALSE TRUE 1311990.613 1514344.55 1591377.442 1791575.581 1620634.657 1609989.859 1649432.186 1569006.282 1436148.716 1804294.989 0.727148621 0.83929987 0.881994048 0.992950483 0.898209366 0.892309666 0.914169909 0.869595211 0.795961151 1 20.7830038 4.641027571 2.058667598 0.902285991 0.698622046 0.497013581 0.055386844 0.478040031 2.61634934 0.014046789 0.168384709 43754.98823 -4.641027571 -0.203663945 MKEEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 MKEEGK 6 1 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ;; 77.058 0.066961 740690000 1036440 934910 781460 773790 800420 799220 926390 900060 917630 999350 FALSE TRUE 995934.779 908247.2822 922687.2055 813725.3946 826166.2362 815380.776 937727.4379 881473.4465 813464.4894 931663.1344 1.068985927 0.974866611 0.990365693 0.873411606 0.886764975 0.875188409 1.006509116 0.946128932 0.873131564 1 19.82944888 4.641091179 1.380525695 0.926122666 1.105883735 0.427670507 0.0498856 1.043181447 2.047135916 0.014141837 0.248547225 43761.39713 -4.641091179 0.179761069 VGGDVPETNYLFMGDFVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGGDVPETNYLFMGDFVDR 19 0 P60510;I3L4X0 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit 0 107.35 0.00068912 98017000 26522 27862 22992 30217 23291 28553 27665 28694 27803 31271 FALSE TRUE 25485.49092 27067.40304 27147.16585 31776.50299 24040.17617 29130.36122 28003.57255 28101.45887 24646.92 29152.98732 0.874198265 0.928460701 0.931196709 1.089991315 0.824621364 0.999223884 0.960573002 0.963930679 0.845433771 1 14.8313561 4.641831145 2.210369835 0.953327111 0.86364357 0.097775502 0.071941863 1.170026762 7.699647439 0.0171211 0.189336414 43836.02292 -4.641831145 -0.089683541 LLIDGDGAGDDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLIDGDGAGDDRR 13 1 Q6I9Y2;H7C5E3 Q6I9Y2 THOC7 THO complex subunit 7 homolog 0 ; 201.09 1.68E-07 992610000 433840 464980 400720 453590 467840 523680 471140 479120 484160 514480 FALSE TRUE 416885.0532 451719.2257 473139.018 476999.8343 482888.4985 534269.1684 476905.9523 469226.0046 429200.1866 479633.8113 0.869173614 0.941800213 0.98645885 0.994508358 1.006785775 1.113910562 0.994312621 0.978300515 0.89484973 1 18.87157384 4.6421944 1.548242886 1.000246362 0.834189817 0.391403826 0.04962369 0.950147459 2.484992738 0.014087538 0.22692185 43872.70375 -4.6421944 -0.166056545 LTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_BT-474_Pertuzumab_2h_R1 7 LTPGCEAEAETEAICFFVQQFTDMEHNR 28 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 283.17 6.64E-62 6917577000 931983.6 1142565 1035731.2 1244975 1226910.3 1386532.1 1304981.6 1084786.4 1490836 1534781.4 FALSE TRUE 895560.6505 1109980.165 1222910.868 1309228.309 1266374.984 1414568.729 1320952.355 1062385.182 1321602.547 1430829.289 0.625903214 0.775760025 0.854686773 0.915013635 0.885063644 0.98863557 0.923207517 0.742496111 0.923661934 1 20.44842012 4.642310318 1.517062992 0.894345543 0.553029363 0.630037918 0.067584862 0.673333671 1.672106648 0.019876076 0.325911093 43884.41545 -4.642310318 -0.34131618 ANS(ph)GGVDLDSSGEFASIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ANSGGVDLDSSGEFASIEK 19 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 ANS(1)GGVDLDSSGEFASIEK;ANS(1)GGVDLDSSGEFASIEK 260.97 4.29E-30 284890000 1953780 1574570 1032830 1392250 1420160 1224740 1258840 1662010 1356350 1194000 TRUE FALSE 1877424.118 1529664.805 1219485.356 1464104.189 1465840.736 1249505.082 1274246.06 1627688.913 1202382.834 1113129.316 1.686618158 1.374202245 1.095546886 1.315304671 1.316864729 1.122515653 1.144742162 1.462263987 1.080182524 1 20.08618978 4.642545842 3.073376883 1.224620359 1.714879285 0.550324869 0.134352362 0.228322328 3.4218556 0.032306264 0.236540895 43908.22109 -4.642545842 0.490258926 AYS(ph)FCGTVEYMAPEVVNR ddPTM_BT-474_Pertuzumab_2h_R1 4 AYSFCGTVEYMAPEVVNR 18 0 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;B4DG22;B1AXG1;B7ZB17;P51812;Q9UK32-2;Q9UK32 E9PGT3;B4DG22;Q9UK32-2 RPS6KA1;RPS6KA3;RPS6KA6 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-3;Ribosomal protein S6 kinase alpha-6 1 AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR 323.91 6.42E-62 2283280000 982350 794870 541070 659650 648200 633970 529613 822010 625020 595640 TRUE FALSE 943958.676 772201.0859 638853.385 693694.6156 669049.9417 646789.3078 536094.5623 805035.2062 554070.3499 555296.7723 1.699917455 1.390609714 1.150471994 1.249232213 1.204851127 1.164763312 0.965419914 1.449738674 0.997791411 1 19.08289948 4.642619116 1.926118439 1.172180631 1.80454189 0.607445813 0.137730185 0.425317132 1.951896049 0.03438185 0.447067703 43915.62985 -4.642619116 0.63236126 APGS(ph)PAAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 APGSPAAPR 9 0 Q5SPY9;Q9NQX5 Q5SPY9 NPDC1 Neural proliferation differentiation and control protein 1 1 APGS(1)PAAPR;APGS(1)PAAPR 87.942 0.013762 480040000 145290 183573 154081 220060 183208 200520 210757 211029 209125 193778 TRUE FALSE 139611.9062 178337.6778 181926.8642 231417.323 189101.0517 204574.6518 213336.3072 206671.1774 185386.0067 180653.2435 0.772817047 0.987182263 1.007050085 1.281002868 1.046762561 1.132416157 1.180916009 1.144021405 1.026198053 1 17.46286363 4.64262153 1.465820815 1.123129495 0.680694348 0.606340127 0.082098466 0.583810843 1.328594957 0.021180691 0.357619854 43915.87397 -4.64262153 -0.442435146 DGDESS(ph)PILTSFELVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGDESSPILTSFELVK 16 0 A8MYT4;A0A1W2PS05;Q8NEB9 A8MYT4 PIK3C3 Phosphatidylinositol 3-kinase;Phosphatidylinositol 3-kinase catalytic subunit type 3 1 DGDES(0.118)S(0.879)PILT(0.003)S(0.001)FELVK;DGDES(0.069)S(0.931)PILTSFELVK 114.73 0.00058846 55959000 148660 166420 147344 169872 165310 150747 168819 174712 198049 198075 TRUE FALSE 142850.2028 161673.8645 173972.3384 178639.1143 170627.3463 153795.2076 170885.0574 171104.1361 175567.3078 184659.2038 0.773588318 0.875525623 0.942126549 0.96739892 0.924012141 0.832859692 0.925407745 0.92659414 0.950763916 1 17.49450565 4.642845809 2.596875269 0.927658762 0.757838461 0.586954909 0.040906034 0.280337384 2.789652783 0.010310804 0.093670264 43938.55896 -4.642845809 -0.169820301 FNPDFAEAHYLSYLNNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FNPDFAEAHYLSYLNNLR 18 0 F5GY68;F5H0F9;Q9UJX4-3;Q9UJX4;H0YFB5;Q9UJX4-2 F5GY68 ANAPC5 Anaphase-promoting complex subunit 5 0 134.37 1.07E-05 92364000 120840 149390 134010 177070 157360 147010 162730 146940 176180 183700 FALSE TRUE 116117.4392 145129.5435 158228.588 186208.6039 162421.6273 149982.6429 164721.5384 143905.6377 156180.785 171257.8354 0.678027017 0.847433013 0.923920285 1.087299764 0.948404065 0.875770984 0.961833589 0.840286445 0.911962858 1 17.38581047 4.642967933 2.29948788 0.936424611 0.643612116 0.615818469 0.064291389 0.342634534 2.494883463 0.017500272 0.185289985 43950.91619 -4.642967933 -0.292812495 LSGINEIPRPFS(ph)PPVTSNT(ph)SPPPAAPLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LSGINEIPRPFS(0.974)PPVT(0.187)S(0.157)NT(0.398)S(0.284)PPPAAPLAR 92.967 0.0031591 222920000 112740 126760 109510 132520 125630 142990 116630 138900 150130 148800 TRUE FALSE 108333.9962 123144.9289 129300.893 139359.3731 129671.003 145881.3558 118057.3528 136031.6665 133087.8718 138721.6435 0.780945161 0.887712442 0.932088821 1.004597189 0.934756825 1.051612078 0.851037732 0.980608815 0.95938794 1 17.08183337 4.643017708 1.594483198 0.963889033 0.73509381 0.571648201 0.049956634 0.589575088 1.659907724 0.012582224 0.198077311 43955.95379 -4.643017708 -0.228795223 LSQEDPDYGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSQEDPDYGIR 11 0 P04040 P04040 CAT Catalase 0 ; 130.01 0.00054242 326740000 408230 503380 416610 601060 505040 512600 587140 524750 534450 631430 FALSE TRUE 392275.9203 489024.0953 491900.6944 632080.7786 521285.0703 522965.1232 594325.595 513913.7291 473781.4766 588662.6837 0.666384894 0.83073738 0.835624048 1.073757172 0.885541219 0.888395235 1.00961996 0.873019037 0.804843741 1 19.16708165 4.643160965 1.571000629 0.924531713 0.605134954 0.513037035 0.077740485 0.705415846 1.911899507 0.02052005 0.32751469 43970.45557 -4.643160965 -0.319396759 S(ph)PQPNKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQPNKR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(1)PQPNKR;S(1)PQPNKR 66.692 0.041151 594130000 727270 683030 531790 653000 614140 610230 711210 654160 588910 762560 TRUE FALSE 698847.4844 663550.6532 627896.2826 686701.4083 633894.3708 622569.2687 719914.0007 640651.3674 522059.4057 710911.132 0.983030723 0.933380592 0.883227529 0.965945499 0.891664714 0.875734309 1.012663846 0.901169413 0.734352554 1 19.4393097 4.643243797 3.209852035 0.909862486 0.986873421 0.085669537 0.074158806 0.736028869 12.17518607 0.017503352 0.121707875 43978.84273 -4.643243797 0.077010934 LQIDVDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQIDVDGR 8 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;; 164.96 0.00076093 957591000 1326106 1482014 1265197 1607820 1481070 1492750 1485440 1508860 1606420 1738780 FALSE TRUE 1274280.311 1439748.412 1493846.242 1690799.783 1528709.962 1522934.428 1503619.259 1477701.514 1424065.936 1621010.882 0.786102256 0.888179363 0.92155226 1.043052704 0.943059654 0.939496733 0.927581225 0.911592593 0.878504859 1 20.62846235 4.643730797 2.085527469 0.943028982 0.760969646 0.559538821 0.043567641 0.435255594 2.454049203 0.011595372 0.138418691 44028.18643 -4.643730797 -0.182059336 LFSASEFEDPLVGEDTER ddPTM_BT-474_Pertuzumab_2h_R1 2 LFSASEFEDPLVGEDTER 18 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ; 255.15 3.47E-30 325980000 360970 536030 461090 750280 481830 606800 642140 682310 729110 708380 FALSE TRUE 346862.8933 520742.9492 544419.2199 789002.0407 497328.4995 619069.9118 649998.7014 668220.0601 646344.4895 660400.7916 0.525230887 0.788525628 0.824376995 1.194732124 0.75307072 0.93741546 0.984248822 1.011840186 0.978715498 1 19.33298232 4.643817681 1.401903542 0.971926681 0.398008449 0.625582313 0.106732465 0.648779797 1.317782762 0.028480205 0.499713004 44036.99547 -4.643817681 -0.573918232 TEMDKS(ph)PFNSPSPQDSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEMDKSPFNSPSPQDSPR 18 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 TEMDKS(1)PFNSPSPQDSPR;TEMDKS(1)PFNSPSPQDSPR 246.39 1.68E-24 1882510000 1414430 1313650 1102360 1096170 1232450 1121940 1170420 1367280 1425970 1367590 TRUE FALSE 1359152.512 1276185.988 1301580.974 1152743.465 1272092.874 1144626.396 1184743.95 1339045.19 1264099.864 1274961.911 1.066033816 1.000960089 1.02087832 0.904139532 0.997749707 0.897773012 0.929238701 1.050262897 0.991480493 1 20.28202272 4.643942484 1.445805832 0.971691507 1.088739095 0.27606881 0.046638444 1.442314361 3.164481997 0.013507189 0.231632718 44049.65224 -4.643942484 0.117047588 EELQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EELQDR 6 0 P54577 P54577;REV__M0R2F5 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 ; 110.63 0.066388 412350000 439320 477970 402400 513830 476460 473730 471840 483030 515800 516860 FALSE TRUE 422150.8887 464338.7636 475122.6313 540348.8279 491785.7686 483309.1452 477614.5191 473055.2617 457248.5464 481852.6118 0.876099617 0.963653101 0.986033114 1.121398566 1.020614513 1.003022778 0.991204587 0.981742653 0.948938607 1 18.8782324 4.644111115 2.150578719 1.007998402 0.856433414 0.470924252 0.042354253 0.495489493 3.025316082 0.011587738 0.133631235 44066.75943 -4.644111115 -0.151564989 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHR ddPTM_BT-474_Pertuzumab_2h_R1 5 VILSNMVSISSEPFGHLVDDDDISDQEDHR 30 0 A8MUM1;Q53HC9;C9JVR6 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHR;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHR;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHR;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHR;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHR 221.47 2.00E-34 763734000 164313 203538 187616 227810 234784 220697 216387 165710 254242 264762 TRUE FALSE 157891.4663 197733.2955 221522.3847 239567.3014 242336.0406 225159.6446 219035.2088 162288.0306 225381.514 246829.4339 0.639678436 0.801092853 0.89747151 0.970578337 0.981795553 0.912207434 0.887395013 0.657490592 0.913106312 1 17.91315492 4.644131198 2.547546207 0.882901466 0.613468704 0.426318689 0.091836389 0.472064457 4.467947509 0.026534363 0.248245949 44068.79728 -4.644131198 -0.269432763 RLSPS(ph)AS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.367)PS(0.718)AS(0.915)PPR;RLS(0.255)PS(0.747)AS(0.998)PPR 142.08 2.43E-05 3857200000 933920 1028270 832310 1036440 1035680 1081200 1044200 1099650 1072050 1112260 TRUE FALSE 897421.3739 998944.7464 982726.9316 1089930.793 1068993.588 1103062.605 1056979.232 1076941.843 950355.3784 1036925.64 0.865463578 0.963371633 0.947731346 1.051117603 1.030925986 1.063781782 1.01933947 1.038591199 0.916512566 1 19.98388101 4.644411337 1.15774749 1.020858792 0.816627615 0.533215052 0.041883123 0.998697142 1.266297518 0.01204237 0.237659392 44097.23274 -4.644411337 -0.204231177 EMQPTHPIR ddPTM_BT-474_Pertuzumab_2h_R1 32 EMQPTHPIR 9 0 B7Z2E6;H0YB80;P63104-2;P27348;P31946-2;P31946;P63104;E7EX29;B0AZS6 B7Z2E6;P27348;P31946-2;P63104 YWHAZ;YWHAQ;YWHAB "14-3-3 protein zeta/delta;14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 176.41 5.32E-05 1.17368E+11 17678010.8 20357922.5 18310049.3 22492135.9 20448981.3 21254169.6 21541867.1 19642149.7 21623493.6 22126882.9 FALSE TRUE 16987134.59 19777334.48 21619082.51 23652957.73 21106741.35 21683943.47 21805502.91 19236532.44 19168885.26 20628209.41 0.823490505 0.958751876 1.048034858 1.146631647 1.023197939 1.051179142 1.057072016 0.932535251 0.929255898 1 24.29811526 4.644680332 2.833679003 1.022934105 0.807425759 0.508245304 0.059728816 0.304254689 3.754845699 0.016455196 0.134573863 44124.5543 -4.644680332 -0.215508347 LGGPEGPGS(ph)PLLAT ddPTM_BT-474_Pertuzumab_2h_R1 3 LGGPEGPGSPLLAT 14 0 Q9C086 Q9C086 INO80B INO80 complex subunit B 1 LGGPEGPGS(1)PLLAT;LGGPEGPGS(1)PLLAT;LGGPEGPGS(1)PLLAT 136.96 2.52E-05 210974000 529050 572080 497430 555810 545050 633700 547350 596140 605750 662940 TRUE FALSE 508374.1411 555764.8385 587326.6663 584495.4207 562582.0283 646513.8482 554048.633 583829.5007 536987.7995 618038.4833 0.822560657 0.899239859 0.950307598 0.945726579 0.910270223 1.046073773 0.896463 0.944649106 0.868858193 1 19.23733715 4.644800233 2.265136096 0.94326586 0.805090203 0.384234791 0.047708661 0.489373097 3.417639761 0.01141752 0.124042374 44136.73798 -4.644800233 -0.138175656 SAFSS(ph)LQNIPESLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAFSSLQNIPESLR 14 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SAFS(0.064)S(0.936)LQNIPESLR;SAFS(0.126)S(0.874)LQNIPESLR 226.79 2.38E-12 166282000 927740 575390 245820 193287 209100 120182 83561 284370 143154 125699 TRUE FALSE 891482.8951 558980.4406 290245.1422 203262.5652 215825.8914 122612.1624 84583.64451 278497.6601 126903.7581 117185.2948 7.607463862 4.770056189 2.476805156 1.734539864 1.841748931 1.046310142 0.721794016 2.376558088 1.082932447 1 16.83843202 4.645469592 1.179487221 1.412441461 9.962461575 0.952255262 0.446714415 0.260974739 0.345647157 0.134424178 2.638114201 44204.81649 -4.645469592 8.550020114 up LDNNLDSVSLLIDHVCSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDNNLDSVSLLIDHVCSR 18 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ; 263.92 6.28E-31 478330000 390000 441350 391880 445230 436590 488440 460350 448580 531920 489190 FALSE TRUE 374758.3688 428763.1301 462701.4333 468208.3737 450633.3139 498316.5915 465983.901 439316.6662 471538.6716 456056.7256 0.821736306 0.940153069 1.014569915 1.026645036 0.988108033 1.092663617 1.021767414 0.96329391 1.033947413 1 18.79885376 4.645673224 1.9690504 1.016362396 0.784809957 0.781520935 0.032058244 0.286288073 1.384960739 0.008716949 0.111972457 44225.54815 -4.645673224 -0.231552439 S(ph)KSDSYTLDPDTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.621)KS(0.379)DSYTLDPDTLR 148.24 4.73E-06 558350000 1365100 1159700 845490 883920 955320 849970 895760 1586000 1036000 880580 TRUE FALSE 1311750.383 1126626.491 998288.8508 929539.2171 986048.7354 867156.9758 906722.5788 1553248.546 918397.6233 820937.5323 1.597868694 1.372365676 1.216035096 1.132289828 1.201125173 1.056300804 1.104496436 1.892042311 1.118718035 1 19.64691292 4.645912235 2.839607826 1.265250024 1.625011464 0.172822637 0.240692902 0.728418516 9.027323963 0.065812663 0.53918331 44249.89405 -4.645912235 0.35976144 QPSS(ph)PSHNTNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QPSSPSHNTNLR 12 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 QPS(0.004)S(0.984)PS(0.012)HNTNLR;QPS(0.266)S(0.726)PS(0.008)HNTNLR 192.68 3.96E-06 668480000 196441 250700 196502 311910 274000 289430 261800 266070 238852 241720 TRUE FALSE 188763.8685 243550.2815 232014.2826 328007.7125 282813.4588 295282.4729 265003.9867 260575.5615 211738.5223 225348.0891 0.837654623 1.080773671 1.029581762 1.455560213 1.255007131 1.310339369 1.175976188 1.1563247 0.939606469 1 17.78179569 4.646000822 1.604785845 1.191281131 0.760421587 0.316990894 0.144973791 0.969750207 2.762814082 0.03900561 0.617360451 44258.921 -4.646000822 -0.430859545 SFLDDPIWR ddPTM_BT-474_Pertuzumab_2h_R1 3 SFLDDPIWR 9 0 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ;; 141.39 0.00024853 281436000 655660 767170 658973 820240 830280 788960 862380 878410 836920 900820 FALSE TRUE 630036.0823 745291.0627 778064.0799 862572.6847 856986.7102 804913.3118 872934.0644 860270.5265 741916.3503 839806.659 0.750215631 0.887455529 0.926480008 1.027108651 1.02045715 0.958450738 1.039446467 1.024367356 0.883437089 1 19.6796977 4.646168919 1.268162606 0.99795751 0.66964356 0.732262212 0.045046954 0.581990955 0.918986494 0.012617989 0.238601343 44276.05512 -4.646168919 -0.328313949 SMEAEMIQLQEELAAAER ddPTM_BT-474_Pertuzumab_2h_R1 6 SMEAEMIQLQEELAAAER 18 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 308.68 9.96E-61 483239000 271899 297066 253838 296352 313471 314981 306851 303967 312016 325106 FALSE TRUE 261272.8865 288593.9685 299712.1732 311646.7622 323554.0794 321350.1316 310606.3343 297689.9752 276597.2518 303086.281 0.862041283 0.952184202 0.988867501 1.02824437 1.06753126 1.060259575 1.024811592 0.98219548 0.912602348 1 18.20936903 4.646188233 1.651316964 1.012751666 0.825824414 0.547349018 0.041218046 0.656146046 2.010610627 0.011979107 0.184811362 44278.0242 -4.646188233 -0.186927252 KMEDEMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KMEDEMDR 8 1 Q9UID3;E9PKX7;Q9UID3-2;E9PJ36;E9PMB6 Q9UID3 VPS51 Vacuolar protein sorting-associated protein 51 homolog 0 74.841 0.064032 172140000 178230 198540 150090 188680 206900 237540 208490 233060 275590 304260 FALSE TRUE 171264.5746 192877.8336 177214.6017 198417.7974 213555.1264 242343.2216 211041.563 228247.2296 244306.1786 283652.1992 0.603783701 0.679980039 0.62476019 0.699510873 0.752876681 0.854367504 0.744015254 0.804672871 0.8612878 1 18.11376352 4.646341304 0.082919295 1.273180829 1.48E-10 0.886700497 0.038636927 26.29894421 0.35755877 1.470848638 4.632601119 44293.63312 -4.646341304 -1.273180829 DREDRS(ph)KDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DREDRSKDR 9 3 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 1 DREDRS(1)KDR 171.05 0.00031631 209980000 296740 233060 162990 145660 201070 190780 216100 197630 255390 209770 TRUE FALSE 285143.0727 226413.357 192445.9187 153177.5301 207537.5992 194637.7023 218744.6964 193548.8714 226399.1979 195562.0911 1.458069257 1.157756883 0.98406556 0.783268011 1.061236347 0.99527317 1.118543452 0.989705471 1.157684481 1 17.57726721 4.646521445 2.583496052 1.009632931 1.505545649 0.672062155 0.094955873 0.228107531 2.231158581 0.024032712 0.222911017 44312.00945 -4.646521445 0.495912718 KPSDSVHITNDDER ddPTM_BT-474_Pertuzumab_2h_R1 4 KPSDSVHITNDDER 14 1 A6NHR9;A6NHR9-2 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 0 ;;; 147.12 5.27E-06 1686020000 1366560 1692320 1524960 1929340 1618560 1788670 1924940 1789290 1950870 2115310 FALSE TRUE 1313153.324 1644056.691 1800554.195 2028913.469 1670622.452 1824838.133 1948497.992 1752340.536 1729415.416 1972038.17 0.665886363 0.833684011 0.913042264 1.028840871 0.847155232 0.925356396 0.988063021 0.88859362 0.876968531 1 20.91125605 4.646544672 2.053114283 0.93066119 0.62018446 0.69666202 0.054445532 0.310931079 1.675487473 0.013617461 0.167419057 44314.3794 -4.646544672 -0.31047673 ELQNTVANLHVR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELQNTVANLHVR 12 0 H3BV04;H3BN93;H3BUB6;H3BPL9;O15127 H3BV04 SCAMP2 Secretory carrier-associated membrane protein 2 0 ;; 168.31 4.69E-05 424431000 221443 284665 253763 378279 247463 220775 362447 330683 311691 309741 FALSE TRUE 212788.7627 276546.6329 299623.619 397802.0245 255422.8721 225239.2218 366882.7348 323854.2805 276309.1444 288761.9662 0.736900242 0.957697569 1.037614555 1.377612259 0.884544719 0.780016928 1.270536905 1.121526788 0.956875132 1 18.13952121 4.646590742 2.331961899 1.067099961 0.693702899 0.249549587 0.165512017 0.647832294 4.867347801 0.042783998 0.451743831 44319.08057 -4.646590742 -0.373397062 AGSSPCLGSSSAASS(ph)PPPPASR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGSSPCLGSSSAASSPPPPASR 22 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGSSPCLGSSSAAS(0.002)S(0.998)PPPPASR;AGSSPCLGSSSAAS(0.045)S(0.955)PPPPASR;AGSSPCLGSSSAAS(0.233)S(0.766)PPPPASR;AGSSPCLGSSSAASS(1)PPPPASR 402.92 1.18E-122 0 383153 428727 325263 431814 403937 452616 451339 417078 438418 468210 TRUE FALSE 368178.9572 416500.1257 384045.2595 454099.9723 416930.0005 461768.2056 456862.6217 408465.1935 388650.6266 436497.7197 0.843484263 0.954186258 0.87983337 1.040326104 0.955171085 1.057893741 1.046655231 0.935778528 0.890384094 1 18.73561459 4.64661977 1.010839452 0.986172288 0.802988523 0.34345734 0.05765821 2.000594134 1.83197052 0.018431335 0.384850373 44322.04291 -4.64661977 -0.183183765 HVQLVLGQLIDENYLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HVQLVLGQLIDENYLDR 17 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 ; 185.33 5.85E-10 498730000 182315 214250 196290 233720 195598 241400 249440 171257 245630 281700 FALSE TRUE 175189.9282 208139.7998 231763.9694 245782.3172 201889.5873 246281.2734 252492.7213 167720.4831 217747.1122 262620.2081 0.667084721 0.792550586 0.882506229 0.935885014 0.768751151 0.93778493 0.961436758 0.638642717 0.829133119 1 18.00261841 4.646783011 2.913079066 0.851143067 0.653062271 0.259822047 0.101352141 0.502977965 6.629052397 0.026087782 0.207455578 44338.70561 -4.646783011 -0.198080796 ELFEER ddPTM_BT-474_Pertuzumab_2h_R1 3 ELFEER 6 0 Q9H307 Q9H307 PNN Pinin 0 ;; 122.78 0.044374 964930000 1250120 1387210 1187520 1437550 1419910 1330300 1396640 1512460 1537130 1604310 FALSE TRUE 1201263.928 1347648.129 1402131.28 1511742.128 1465582.695 1357199.577 1413732.498 1481227.172 1362641.447 1495648.655 0.80317254 0.901045927 0.937473701 1.010760196 0.979897712 0.907432085 0.945230348 0.990357707 0.911070553 1 20.51233988 4.64694617 1.775489127 0.962161141 0.768708398 0.681334779 0.033342499 0.413686809 1.526124652 0.008783816 0.126629858 44355.36631 -4.64694617 -0.193452743 VSGS(ph)PEQAVEENLSSYSLDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSGSPEQAVEENLSSYSLDRR 21 1 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 VS(0.001)GS(0.999)PEQAVEENLSSYSLDRR;VS(0.001)GS(0.999)PEQAVEENLSSYSLDRR;VS(0.007)GS(0.993)PEQAVEENLSSYSLDRR;VSGS(1)PEQAVEENLSSYSLDRR 209.62 1.52E-22 1298410000 225143 256838 241305 234265 249106 319317 249310 240545 293532 291924 TRUE FALSE 216344.1627 249513.2317 284914.1813 246355.4447 257118.7207 325773.8085 252361.1304 235577.6617 260211.4779 272151.7275 0.794939517 0.916816638 1.046894627 0.905213599 0.944762406 1.197030096 0.927281016 0.865611488 0.956126497 1 18.05405167 4.64703507 3.419711393 0.971492907 0.787567398 0.289790277 0.087363565 0.361723896 6.885636771 0.022499946 0.146591597 44364.44674 -4.64703507 -0.18392551 DFNGDFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFNGDFR 7 0 A0A2R8YFH5;Q15437 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 121.31 0.010353 2514530000 4170800 4715340 4172350 4841280 4961340 4933240 5232660 5327540 5064810 5400410 FALSE TRUE 4007800.525 4580863.12 4926386.458 5091139.041 5120926.007 5032993.493 5296698.858 5217524.437 4489874.002 5034635.421 0.796045829 0.909869879 0.978499146 1.011222982 1.017139391 0.999673874 1.052052118 1.036326169 0.891797246 1 22.26345588 4.647222257 1.428442876 1.008543999 0.731863348 0.707834379 0.040769898 0.515517501 1.091977967 0.011099077 0.19436712 44383.57258 -4.647222257 -0.276680651 ATSHVGEIEQELALAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ATSHVGEIEQELALAR 16 0 J3KP58;P30622-2;P30622-1;P30622;F5H0N7 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 0 ;; 228.51 4.04E-15 581530000 181566 208715 183843 220927 209444 235929 222140 206669 222906 229130 FALSE TRUE 174470.2 202762.6526 217067.5197 232329.0689 216180.9565 240699.646 224858.6158 202401.2129 197602.6454 213610.821 0.816766675 0.949215267 1.016182226 1.087627808 1.01203186 1.126813917 1.052655548 0.94752322 0.925059154 1 17.70462521 4.64723268 2.17240538 1.022666673 0.784597068 0.551242607 0.056456522 0.425541232 2.655208653 0.015756199 0.181816489 44384.63783 -4.64723268 -0.238069605 RSPQQTVPYVVPLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSPQQTVPYVVPLSPK 16 1 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 RSPQQTVPYVVPLS(1)PK 133.38 2.08E-05 497490000 551550 472900 355120 345440 386620 361090 354060 380390 420320 404910 TRUE FALSE 529994.8162 459413.355 419298.0836 363268.1998 399055.9834 368391.4872 358393.0922 372534.8136 372607.0357 377485.085 1.40401525 1.217037105 1.110767286 0.962337889 1.05714371 0.975910047 0.949423186 0.98688618 0.987077504 1 18.52606012 4.64731605 1.002744832 0.981528858 1.586357951 0.951207256 0.030322133 0.304076155 0.273035475 0.009156514 0.191969027 44393.159 -4.64731605 0.604829093 IVDQIRPDR ddPTM_BT-474_Pertuzumab_2h_R1 7 IVDQIRPDR 9 1 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 P17844;A0A1X7SBZ2 DDX5;DDX17 Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17 0 ;;;;;; 151.22 7.60E-05 17518640000 5919170 6642320 5826660 6886800 6539270 6785210 6735670 6982760 7085720 7567930 FALSE TRUE 5687842.292 6452887.537 6879667.075 7242228.573 6749611.558 6922411.595 6818103.144 6838563.566 6281378.771 7055347.36 0.806174665 0.914609474 0.975099697 1.026487883 0.956666088 0.981158154 0.966373843 0.969273831 0.890300428 1 22.75028568 4.648048245 2.388826438 0.970932398 0.784836808 0.69809763 0.033021508 0.239485477 1.911597768 0.008193558 0.08445076 44468.0663 -4.648048245 -0.18609559 KPS(ph)PQPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(1)PQPS(0.575)S(0.425)PR;KPS(1)PQPS(0.785)S(0.215)PR 100.11 0.014823 3968200000 3032700 2895900 2383530 2566500 2532500 2712300 2881900 2895800 3113400 2755900 TRUE FALSE 2914178.731 2813311.767 2814286.892 2698957.373 2613960.162 2767144.564 2917169.554 2836000.718 2759979.884 2569240.438 1.134256914 1.094997465 1.095377003 1.050488437 1.017405815 1.077028262 1.135421003 1.103828461 1.074239625 1 21.29291048 4.648714439 1.665979983 1.075170066 1.147241923 0.213644681 0.037879263 1.512269845 4.721619253 0.010711317 0.165476338 44536.33126 -4.648714439 0.072071856 DFMVQGGDFSEGNGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFMVQGGDFSEGNGR 15 0 Q13427;C9JM79;Q13427-2;C9JN15 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G;Peptidyl-prolyl cis-trans isomerase 0 ; 211.38 3.28E-09 482050000 429630 471330 401230 503680 458100 464230 488130 479440 496040 524980 FALSE TRUE 412839.5846 457888.1299 473741.1863 529674.9852 472835.2025 473617.0487 494103.881 469539.3965 439731.6188 489422.637 0.843523682 0.935567943 0.967959286 1.082244557 0.966108158 0.967705645 1.009564829 0.959374089 0.898470127 1 18.90072131 4.648815271 2.203971691 0.982600401 0.822724957 0.480338819 0.04385937 0.4461304 2.883821222 0.011323982 0.129263235 44546.67265 -4.648815271 -0.159875444 LLLQQLEATLETGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLLQQLEATLETGKR 15 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 81.448 0.022403 78170000 51568 56995 51555 52573 53840 61387 57360 60159 66265 54251 FALSE TRUE 49552.66555 55369.5584 60872.13533 55286.29883 55571.8125 62628.2872 58061.98884 58916.69563 58742.87501 50576.53145 0.979756107 1.094767807 1.203564847 1.093121597 1.098766778 1.23828751 1.148002585 1.164901861 1.161465077 1 15.62618048 4.64909552 3.23544758 1.146485247 0.970571552 0.361277894 0.062594754 0.260255486 4.386358572 0.014190348 0.099521287 44575.42785 -4.64909552 -0.175913695 GGNIGDGGGAADR ddPTM_BT-474_Pertuzumab_2h_R1 7 GGNIGDGGGAADR 13 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;; 221.75 4.33E-11 5050750000 2537073 2835562 2365265 2997913 2951175 2983463 2948284 2879076 2966989 3051644 FALSE TRUE 2437921.382 2754694.548 2792721.001 3152635.649 3046102.224 3043790.666 2984365.982 2819622.074 2630188.847 2844953.434 0.856928396 0.968274038 0.981640321 1.108150176 1.07070372 1.069891208 1.049003455 0.991096037 0.924510333 1 21.43997361 4.649356537 1.664249279 1.030836045 0.817095737 0.517481376 0.049864905 0.679429822 2.113543581 0.014218471 0.220414969 44602.22631 -4.649356537 -0.213740307 (ac)MDFQHRPGGK ddPTM_BT-474_Pertuzumab_2h_R1 7 MDFQHRPGGK 10 1 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ;;;;;; 75.294 0.0010091 4315590000 3624420 3739020 3062240 3602310 3679400 3817750 3535620 3793070 4020310 3828870 FALSE TRUE 3482773.659 3632386.81 3615654.887 3788225.651 3797751.243 3894947.521 3578889.975 3714741.779 3563941.263 3569537.224 0.97569333 1.017607208 1.012919788 1.061265204 1.063933783 1.091163161 1.002620158 1.040678818 0.998432301 1 21.76730562 4.649441696 1.473463155 1.038757653 0.959854221 0.261021868 0.029651092 1.280209694 2.921930069 0.008175745 0.14089961 44610.97302 -4.649441696 -0.078903433 GPSLNPVLDYDHGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPSLNPVLDYDHGSR 15 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 149.09 3.42E-06 2962800000 1416640 2104150 2048770 2945570 2216310 2038990 2569000 2186830 2047180 2680140 FALSE TRUE 1361276.143 2044141.702 2419028.314 3097591.221 2287599.624 2080219.775 2600440.19 2141671.196 1814792.709 2498611.731 0.544812996 0.818110984 0.968148946 1.239724917 0.915548261 0.832550232 1.040754015 0.857144457 0.726320415 1 21.2526953 4.649491932 2.663499115 0.94665554 0.504695704 0.469129313 0.130174762 0.341804733 3.6004977 0.033606157 0.303168119 44616.13357 -4.649491932 -0.441959835 TPPAPKT(ph)PPSSGEPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPPAPKTPPSSGEPPK 16 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 T(0.001)PPAPKT(0.999)PPSSGEPPK;TPPAPKT(0.997)PPS(0.001)S(0.001)GEPPK 122.94 0.00014647 619540000 811360 648400 490380 412130 556210 605150 495890 573550 690520 487770 TRUE FALSE 779651.1542 629908.2669 579002.5744 433400.0787 574100.9998 617386.5476 501958.8502 561705.9921 612135.0645 454732.9034 1.71452549 1.385226937 1.273280579 0.953087132 1.26250156 1.35769051 1.103854255 1.235243783 1.34614201 1 18.79465987 4.64974534 1.898972979 1.195586159 1.816756124 0.614608865 0.128148274 0.429168173 1.876852919 0.0324916 0.441453772 44642.17443 -4.64974534 0.621169966 LGSSS(ph)NLQFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.412)S(0.106)S(0.482)NLQFK 140.45 4.12E-05 68733000 150940 115200 80557 72966 87650 79457 78874 136620 110500 87365 TRUE FALSE 145041.0979 111914.6088 95115.44188 76731.784 90469.34185 81063.67498 79839.28361 133798.7493 97956.50325 81447.69073 1.780788339 1.374067304 1.167810174 0.942098951 1.110766199 0.995285124 0.980252269 1.642756818 1.202692211 1 16.31358617 4.649763019 2.26604454 1.158658299 1.871590567 0.51636793 0.192411425 0.467080234 3.241984915 0.055392307 0.613728661 44643.99169 -4.649763019 0.712932268 VLEQLEDLDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLEQLEDLDSR 11 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;;; 294.24 3.58E-35 876710000 611963 655734 536217 652997 659945 658792 669084 683330 640938 755340 FALSE TRUE 588046.8094 637033.1084 633123.34 686698.2534 681172.7303 672113.2256 677272.4501 669218.9967 568181.4053 704180.149 0.835080072 0.904645082 0.899092854 0.975174115 0.967327368 0.954462046 0.961788615 0.950351977 0.806869387 1 19.42558503 4.649763723 1.326043149 0.944332449 0.803670239 0.29875066 0.050189797 1.404952745 2.463871351 0.01372395 0.255493589 44644.06414 -4.649763723 -0.140662209 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 0 155.98 3.80E-14 95568000 18641 21646 24913 26996 22821 34662 33286 29808 26748 35449 FALSE TRUE 17912.48911 21028.67727 29415.33329 28389.2668 23555.05819 35362.88939 33693.36402 29192.45438 23711.67918 33048.00766 0.54201419 0.63630696 0.890078869 0.859031113 0.712752746 1.07004603 1.019527845 0.883334774 0.717491942 1 15.01227568 4.650084854 0.978206027 0.909628356 0.350903451 0.533811279 0.113535485 1.366023891 1.154097816 0.036799861 0.782037309 44677.08751 -4.650084854 -0.558724906 LSRPERPDLVFEEEDLPYEEEIMR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSRPERPDLVFEEEDLPYEEEIMR 24 2 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 ; 130.51 3.53E-05 87078000 48678 54176 49168 51291 60786 60802 59212 53661 63530 61842 FALSE TRUE 46775.60994 52630.95352 58053.75134 53938.13466 62741.23689 62031.4581 59936.65417 52552.8816 56318.34074 57653.38626 0.81132459 0.912885729 1.006944346 0.935558831 1.088248947 1.075937809 1.039603362 0.911531568 0.976843589 1 15.81511773 4.650171174 1.576121709 1.003634798 0.757286103 0.572385824 0.052745211 0.716920532 1.938274717 0.015815229 0.258375978 44685.9684 -4.650171174 -0.246348695 RPQHNSSGAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 7 RPQHNSSGASPR 12 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RPQHNS(0.023)S(0.018)GAS(0.958)PR;RPQHNS(0.034)S(0.026)GAS(0.94)PR;RPQHNS(0.002)S(0.06)GAS(0.939)PR;RPQHNSS(0.002)GAS(0.998)PR;RPQHNSSGAS(1)PR;RPQHNS(0.002)S(0.028)GAS(0.971)PR;RPQHNS(0.009)S(0.045)GAS(0.946)PR 138.01 5.02E-05 2562971000 242828 312125 289580 403128 298428 342206 342157 310884 312426 352068 TRUE FALSE 233338.0133 303223.5006 341913.5477 423933.4844 308027.2076 349125.6398 346344.4197 304464.1368 276960.7103 328222.1208 0.710914952 0.923836272 1.041713907 1.291605463 0.93847181 1.063687112 1.055213521 0.92761614 0.843820976 1 18.32431295 4.65022907 2.733762096 1.021807585 0.681803225 0.413898114 0.111611162 0.364297199 4.094627368 0.0288009 0.25189292 44691.92594 -4.65022907 -0.340004361 SEIIPMFSNLASDEQDSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEIIPMFSNLASDEQDSVR 19 0 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 147.35 2.47E-07 44477000 14170 19539 16360 25728 23423 24053 19490 17080 20075 29583 FALSE TRUE 13616.22073 18981.76685 19316.61593 27055.82516 24176.42207 24539.36814 19728.52445 16727.29203 17796.17016 27579.31706 0.493711309 0.688260946 0.700402257 0.981018678 0.87661424 0.889774322 0.715337672 0.606515817 0.645272329 1 14.75129911 4.650315443 1.802969508 0.787181342 0.434264336 0.353660536 0.128434047 0.944485501 3.606326025 0.037128745 0.533977912 44700.8152 -4.650315443 -0.352917005 EAGEQGDIEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAGEQGDIEPR 11 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 215.84 2.91E-11 1020570000 684790 730180 619860 729710 702440 810790 741270 757150 817440 831960 FALSE TRUE 658027.6497 709355.9813 731882.4907 767370.4205 725034.6205 827184.7293 750341.884 741514.5879 724647.6382 775610.6082 0.848399497 0.914577462 0.943621043 0.98937587 0.934792037 1.066494863 0.967420863 0.956039771 0.934293098 1 19.56497301 4.650331386 1.189587678 0.977124212 0.801797801 0.561329624 0.036128383 0.999478615 1.342712621 0.01052806 0.208974972 44702.45618 -4.650331386 -0.175326411 QEETAVLEEDSADWEKELQQELQEYEVVTESEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEETAVLEEDSADWEKELQQELQEYEVVTESEKR 34 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 234.68 3.86E-47 15679000 17763 12092 7436.5 6556.5 8509.7 12761 7699.3 9464.9 10998 5866.9 FALSE TRUE 17068.80232 11747.148 8780.440974 6894.881751 8783.422229 13019.03616 7793.526337 9269.446507 9749.553147 5469.529637 3.120707529 2.147743733 1.605337489 1.260598663 1.605882555 2.380284417 1.424898822 1.694742898 1.782521312 1 12.41720106 4.650607746 2.296779486 1.629944623 3.335294216 0.649998449 0.342954165 0.291817041 2.095435154 0.084579572 0.924940642 44730.91127 -4.650607746 1.705349592 T(ph)RTPAS(ph)INATPANINLADLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 2 T(0.5)RT(0.5)PAS(1)INATPANINLADLTR;T(0.5)RT(0.5)PAS(1)INATPANINLADLTR 129.35 3.82E-05 214310000 167976 135630 91947 127832 104613 99837 90086 155017 117670 111441 TRUE FALSE 161411.3122 131761.9652 108563.8682 134429.4248 107977.9722 101855.7725 91188.49942 151815.8448 104312.5949 103893.0018 1.553630268 1.268246782 1.044958432 1.293921847 1.039319014 0.980391083 0.877715513 1.461271136 1.004038704 1 16.66473895 4.650628136 2.432461837 1.112517206 1.611505726 0.432701251 0.162319939 0.446437437 3.721824252 0.041978218 0.427350787 44733.01149 -4.650628136 0.498988521 EIIIEERPGQELTDVNGVR ddPTM_BT-474_Pertuzumab_2h_R1 3 EIIIEERPGQELTDVNGVR 19 1 Q9BV20;Q9BV20-2 Q9BV20 MRI1 Methylthioribose-1-phosphate isomerase 0 ;; 257.83 4.78E-31 868130000 583001 666280 585590 691230 681780 706610 729180 720790 720230 726530 FALSE TRUE 560216.6764 647278.3468 691419.1394 726904.4631 703710.0729 720898.1383 738103.923 705905.4346 638472.5099 677321.476 0.827106029 0.95564421 1.020813844 1.073204511 1.038960225 1.06433675 1.089739436 1.042201465 0.942643239 1 19.36948121 4.651026699 1.737388284 1.042508017 0.776730122 0.721822431 0.03951619 0.374807709 1.298919576 0.010407391 0.155796392 44774.08295 -4.651026699 -0.265777895 EPQLAFHQR ddPTM_BT-474_Pertuzumab_2h_R1 3 EPQLAFHQR 9 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 109.42 0.0024522 1024730000 1503240 1606160 1380990 1561100 1613420 1505000 1748930 1626490 1765700 1812460 FALSE TRUE 1444491.719 1560353.889 1630565.613 1641668.558 1665317.12 1535432.131 1770333.929 1592902.413 1565265.138 1689700.47 0.854880344 0.923449994 0.965002758 0.971573712 0.985569424 0.908700778 1.047720564 0.94271289 0.926356574 1 20.68833609 4.651207216 1.877681207 0.968417223 0.830925344 0.476468196 0.036899858 0.555732848 2.354559917 0.009090691 0.125750911 44792.69739 -4.651207216 -0.137491878 AMS(ph)LNTLNVDAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AMSLNTLNVDAPR 13 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 AMS(0.979)LNT(0.021)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.997)LNT(0.003)LNVDAPR;AMS(1)LNTLNVDAPR 190.28 4.77E-06 1470290000 2469410 1596630 848670 1002190 947440 744340 615500 1691430 917550 797180 TRUE FALSE 2372902.727 1551095.676 1002043.548 1053913.146 977915.268 759391.0648 623032.6731 1656501.379 813393.5707 743186.2885 3.19287743 2.087088661 1.348307367 1.418100902 1.315841375 1.021804461 0.838326383 2.228918112 1.094467946 1 19.50336436 4.651231688 1.865789922 1.336904204 3.592218754 0.724964824 0.365477877 0.378950961 1.57918289 0.10057747 1.400842774 44795.22145 -4.651231688 2.255314549 up LKT(ph)PSTPVACSTPAQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKTPSTPVACSTPAQLK 17 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LKT(0.406)PS(0.297)T(0.297)PVACS(0.001)TPAQLK 104.63 0.0019467 0 224570 171400 108330 134460 123430 107820 113960 170360 125900 110900 TRUE FALSE 215793.5561 166511.8398 127907.6408 141399.4967 127400.238 110000.1943 115354.6766 166842.0065 111608.3598 103388.6442 2.087207524 1.610542832 1.237153671 1.367650169 1.232245949 1.063948513 1.115738362 1.613736283 1.079503079 1 16.65771821 4.651414408 1.732776411 1.243733512 2.293837062 0.719174738 0.170843487 0.428268924 1.47314708 0.046720652 0.702294357 44814.07203 -4.651414408 1.05010355 up S(ph)PSPYYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSPYYSR 8 0 P62995;P62995-3;H7BXF3;H7C2L4;Q13595;Q13595-3;Q13595-4 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 1 S(0.991)PS(0.009)PYYSR;S(0.981)PS(0.019)PYYSR;S(0.747)PS(0.253)PYYSR;S(0.771)PS(0.229)PYYSR 178.55 0.00026123 5696810000 509797 617543 696856 919510 806464 898137 1261150 794687 1107119 1257270 TRUE FALSE 489873.5696 599931.2783 822793.3807 966966.0213 832404.647 916297.9455 1276584.331 778276.4357 981443.4925 1172113.983 0.417940215 0.511836977 0.701973863 0.824976099 0.710173805 0.781748157 1.089129854 0.663993815 0.837327689 1 20.16068144 4.651733182 0.721519143 0.850745876 0.148080786 0.63368958 0.116401609 1.721794768 0.738455248 0.04595175 0.968253617 44846.97782 -4.651733182 -0.70266509 IEDFLER ddPTM_BT-474_Pertuzumab_2h_R1 8 IEDFLER 7 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;; 180.7 0.001588 10403940000 5637750 6089250 5348350 5687630 5982890 5542690 6175070 6917630 6264160 6505920 FALSE TRUE 5417420.497 5915590.552 6314915.818 5981169.266 6175335.09 5654766.989 6250642.354 6774778.523 5553078.818 6065268.244 0.893187289 0.975322165 1.041160187 0.986134335 1.01814707 0.932319357 1.030563217 1.116979209 0.915553706 1 22.53214002 4.651848396 2.934307729 1.013222908 0.883583092 0.270056482 0.053860615 0.40641174 5.436472907 0.013811801 0.110812214 44858.8769 -4.651848396 -0.129639816 GDVEEDETIPDSEQDIRPR ddPTM_BT-474_Pertuzumab_2h_R1 5 GDVEEDETIPDSEQDIRPR 19 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 ;;;; 323.72 2.57E-62 4102240000 1310100 1495300 1332640 1520200 1438600 1629880 1667700 1332067 1749310 1818150 FALSE TRUE 1258899.844 1452655.508 1573477.692 1598657.704 1484873.876 1662837.29 1688109.811 1304559.351 1550735.663 1695005.081 0.742711546 0.857021329 0.928302641 0.94315806 0.876029159 0.981022009 0.995932007 0.769649227 0.914885554 1 20.69285817 4.651997705 2.487683007 0.914687956 0.721571976 0.423083503 0.064806109 0.453618678 4.000769422 0.017118175 0.170307379 44874.30181 -4.651997705 -0.19311598 RPET(ph)PSSGPLDEEGAVAPVLANGHAPYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPETPSSGPLDEEGAVAPVLANGHAPYSR 29 1 A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4;H3BMG9;H3BSV5 A0A0A0MTL6 FAM65A Protein FAM65A 1 RPET(0.947)PS(0.051)S(0.002)GPLDEEGAVAPVLANGHAPYSR 154.73 1.23E-08 145920000 42853 49946 45084 49627 53641 55603 52920 52998 52492 53067 TRUE FALSE 41178.25738 48521.58898 53231.68169 52188.25542 55366.41148 56727.33076 53567.65079 51903.57278 46533.32822 49472.72482 0.83234262 0.980774541 1.075980389 1.054889449 1.119130019 1.146638495 1.082771385 1.049135114 0.940585512 1 15.59434574 4.652006564 2.171282647 1.066168994 0.793796428 0.607375918 0.055264445 0.347662304 2.150770704 0.014488002 0.170585111 44875.21723 -4.652006564 -0.272372566 YIASVQGSTPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 YIASVQGSTPSPR 13 0 P49792;F8WBP7 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 YIASVQGST(0.005)PS(0.995)PR 174.39 2.10E-05 209580000 99432 115870 114650 117880 114970 115210 116280 124880 113590 126990 TRUE FALSE 95546.08751 112565.501 135369.8054 123963.8009 118668.1145 117539.6251 117703.0694 122301.1844 100695.7394 118388.8542 0.807053064 0.950811644 1.143433698 1.047090132 1.002358839 0.992826782 0.994207354 1.03304644 0.85055084 1 16.85317374 4.652458942 3.80941913 1.011783394 0.801828437 0.435873201 0.068330403 0.198818408 4.777023173 0.016321323 0.095526001 44921.98533 -4.652458942 -0.209954957 VLDTSSLTQS(ph)APAS(ph)PTNK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 2 VLDTSSLT(0.003)QS(0.997)APAS(0.999)PT(0.001)NK;VLDTSSLT(0.007)QS(0.993)APAS(1)PTNK;VLDTSSLT(0.026)QS(0.974)APAS(1)PTNK 285.96 1.50E-39 245285000 1156240 902800 654340 616780 702400 641580 530820 1031640 762490 675180 TRUE FALSE 1111052.863 877053.0279 772593.7937 648612.0897 724993.3339 654553.1872 537316.3339 1010336.273 675935.3318 629449.4572 1.765118469 1.393365294 1.227411963 1.030443481 1.151789593 1.039882042 0.853629037 1.605111041 1.07385164 1 19.26373101 4.652496625 1.687802492 1.144024083 1.91607341 0.535818331 0.186862044 0.685217417 2.198960986 0.052455867 0.812225039 44925.88334 -4.652496625 0.772049326 TYGFHFTTPALVVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TYGFHFTTPALVVEK 15 0 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 75.669 0.031143 229890000 397700 252970 260740 97480 180490 203870 158300 149570 209910 184850 FALSE TRUE 382157.4443 245755.5433 307861.5181 102510.9545 186295.6248 207992.3911 160237.3228 146481.3272 186081.8968 172329.9449 2.217591636 1.42607568 1.786465599 0.594852825 1.081040355 1.206942829 0.929828666 0.850005072 1.07980013 1 17.39481389 4.652653142 0.896006151 0.961136845 2.699841803 0.693867228 0.25099647 1.048984596 0.722638195 0.080512859 1.743822226 44942.07726 -4.652653142 1.738704959 SYEDMIGEEVPSDQYYWAPLAQHER ddPTM_BT-474_Pertuzumab_2h_R1 3 SYEDMIGEEVPSDQYYWAPLAQHER 25 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;; 178.39 2.92E-17 457700000 259614 313471 275116 363492 267592 345367 393197 289736 379027 373010 FALSE TRUE 249467.9979 304531.114 324835.5811 382251.8657 276199.3397 352350.5574 398009.0625 283752.8504 336001.444 347745.7005 0.71738629 0.875729344 0.934118181 1.099228158 0.794256663 1.013242024 1.144540571 0.815978026 0.966227457 1 18.40767315 4.652915348 1.940507104 0.966078266 0.668897617 0.367444571 0.102789921 0.706091872 3.250654157 0.026269165 0.353110479 44969.21927 -4.652915348 -0.297180649 TLTSIVHLER ddPTM_BT-474_Pertuzumab_2h_R1 1 TLTSIVHLER 10 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 136.02 0.00012868 165060000 32369 38225 34790 42882 38506 40798 35673 37105 43497 47397 FALSE TRUE 31103.98369 37134.86043 41077.3269 45095.14516 39744.58046 41622.96351 36109.57684 36338.76878 38559.40291 44186.75897 0.703920912 0.840406975 0.929629777 1.020557882 0.899468107 0.941978196 0.817203562 0.822390454 0.872646101 1 15.4313265 4.653025864 2.887268164 0.901435783 0.68745202 0.492918552 0.063888742 0.320317132 4.11555285 0.017423253 0.14339322 44980.66418 -4.653025864 -0.213983762 GEGDVWVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEGDVWVR 8 0 K7EIU8;Q13485;A0A087WUF3 K7EIU8 SMAD4 Mothers against decapentaplegic homolog;Mothers against decapentaplegic homolog 4 0 ; 145.34 0.0013282 541860000 700410 759550 646950 766820 765090 817640 748600 802590 753760 804130 FALSE TRUE 673037.2029 737888.3777 763868.2563 806395.6721 789699.8147 834173.241 757761.5907 786016.236 668196.3248 749665.5589 0.897783278 0.984290086 1.018945378 1.075673896 1.053402821 1.112727177 1.010799525 1.048489192 0.891325894 1 19.5158876 4.653203822 1.926949983 1.034167179 0.870814046 0.328520828 0.055422537 0.699348244 3.159796266 0.014115988 0.191430097 44999.09938 -4.653203822 -0.163353133 IDDVVNTR ddPTM_BT-474_Pertuzumab_2h_R1 3 IDDVVNTR 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;; 127.68 0.0027126 1418580000 717500 795600 676410 808450 821990 875140 769990 870840 856690 926370 FALSE TRUE 689459.3068 772910.267 798652.3337 850174.2014 848430.0549 892835.9304 779413.3679 852856.8497 759442.1427 863626.1348 0.798330758 0.89495933 0.924766287 0.984423893 0.982404331 1.033822269 0.902489326 0.987530154 0.879364475 1 19.72004738 4.653307048 1.373647365 0.966622087 0.746774758 0.585215571 0.043601764 0.731605278 1.393105444 0.011613156 0.213759265 45009.79631 -4.653307048 -0.219847329 KGPGRPTGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KGPGRPTGSK 10 2 P26583 P26583 HMGB2 High mobility group protein B2 0 ; 90.827 0.0059425 20500000000 14286500 12671100 10849300 10000300 11734800 11066700 11146700 12908300 12320900 11965300 FALSE TRUE 13728167.79 12309732.63 12810009.85 10516416.68 12112260.5 11290476.26 11283116.65 12641739.09 10922283.09 11154879.57 1.230687225 1.103528958 1.148377243 0.942763802 1.0858262 1.012155818 1.011496052 1.133292297 0.979148454 1 23.4111716 4.654315003 1.156182907 1.038387594 1.291811301 0.520775654 0.059218686 1.167748023 1.456898078 0.016979691 0.345958906 45114.38097 -4.654315003 0.253423706 LFYAVDVDDDIWEDEVED ddPTM_BT-474_Pertuzumab_2h_R1 2 LFYAVDVDDDIWEDEVED 18 0 Q9UBS8;Q9UBS8-2 Q9UBS8 RNF14 E3 ubiquitin-protein ligase RNF14 0 ; 113.22 0.00058892 13293000 26586 30789 23165.1 31261 31519 28518 34785 31489 32585 35485 FALSE TRUE 25546.98973 29910.92787 27351.54887 32874.38396 32532.83726 29094.6535 35210.70924 30838.74115 28886.08741 33081.56934 0.772242376 0.90415686 0.826791153 0.993737135 0.983412755 0.879482264 1.064360305 0.932203089 0.873177663 1 15.01374006 4.654441519 0.869350303 0.959926686 0.705792397 0.437501904 0.063358241 1.921886139 1.234467233 0.020929802 0.455985109 45127.52537 -4.654441519 -0.254134289 EGQRPTQPVYQIQNR ddPTM_BT-474_Pertuzumab_2h_R1 3 EGQRPTQPVYQIQNR 15 1 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0R0U0 Q9H0W8-2 SMG9 Protein SMG9 0 ;; 194.23 5.49E-08 917200000 134307 158863 138638 179841 152986 167878 169906 174835 163585 169209 FALSE TRUE 129058.134 154332.3828 163692.9706 189122.6156 157906.9336 171272.6082 171985.3605 171224.5962 145015.5166 157748.3237 0.818126817 0.978345628 1.037684374 1.198888274 1.001005462 1.085733301 1.090251588 1.085428942 0.919284042 1 17.26726515 4.6545261 2.091354547 1.063032358 0.775873799 0.50461129 0.070109338 0.423085662 2.363142484 0.017245983 0.214443446 45136.31504 -4.6545261 -0.287158559 KAEGEPQEES(ph)PLKSK ddPTM_BT-474_Pertuzumab_2h_R1 7 KAEGEPQEESPLKSK 15 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 KAEGEPQEES(1)PLKSK;KAEGEPQEES(1)PLKSK;KAEGEPQEES(0.999)PLKS(0.001)K;KAEGEPQEES(1)PLKSK;KAEGEPQEES(1)PLKSK;KAEGEPQEES(1)PLKSK;KAEGEPQEES(0.986)PLKS(0.014)K 241.65 5.39E-18 36638390000 13748140 10562530 7432030 5721823 8182580 8762970 8546760 10741620 12190520 9222660 TRUE FALSE 13210847.49 10261296.99 8775163.146 6017126.971 8445780.117 8940163.257 8651357.806 10519801.79 10806703.28 8598001.024 1.5365022 1.193451473 1.020605036 0.699828594 0.982295779 1.039795556 1.006205719 1.22351716 1.256885554 1 23.03556985 4.65487482 2.569104321 1.033857485 1.594002092 0.540137797 0.142518389 0.346562048 3.309741335 0.039864324 0.384963932 45172.57215 -4.65487482 0.560144607 ILDLIDDAWR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILDLIDDAWR 10 0 Q9BS18 Q9BS18 ANAPC13 Anaphase-promoting complex subunit 13 0 ; 135.71 0.00031854 160311000 190582 206018 182365 206247 209689 226590 223820 228944 227700 232310 FALSE TRUE 183133.8447 200142.5684 215322.4122 216891.4324 216433.8371 231171.805 226559.1761 224216.2264 201852.4506 216575.4368 0.845589174 0.924124043 0.994214373 1.001459056 0.999346188 1.067396231 1.046098207 1.035280038 0.932019132 1 17.7245101 4.655056364 1.161329774 1.020057581 0.776001995 0.701283796 0.034472953 0.727808188 0.9168845 0.010225812 0.208424818 45191.45909 -4.655056364 -0.244055586 QETHCQS(ph)TPLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 QETHCQSTPLKK 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 QETHCQS(0.5)T(0.5)PLKK 97.836 0.0022089 365760000 709340 488820 304120 279350 300490 282880 266220 415970 300600 326040 TRUE FALSE 681618.2086 474879.3322 359081.2491 293767.287 310155.5337 288600.0274 269478.08 407380.0741 266477.1482 303957.0204 2.242482203 1.562323948 1.18135534 0.966476401 1.02039273 0.949476433 0.886566396 1.340255519 0.876693514 1 18.21350782 4.655826859 1.516560227 1.027839092 2.593549829 0.904650611 0.124679638 0.275139798 0.668822764 0.035704606 0.615495394 45271.7058 -4.655826859 1.565710737 up GRLS(ph)PVPVPR ddPTM_BT-474_Pertuzumab_2h_R1 9 GRLSPVPVPR 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM0 Q9UKM9 RALY RNA-binding protein Raly 1 GRLS(1)PVPVPR;GRLS(1)PVPVPR;GRLS(1)PVPVPR;GRLS(1)PVPVPR;GRLS(1)PVPVPR;GRLS(1)PVPVPR;GRLS(1)PVPVPR;GRLS(1)PVPVPR;GRLS(1)PVPVPR 109.6 0.0012095 63338370000 3019098 3811283 3716678 4250502 3010472 4165863 4207369 3984527 4295724 4643839 TRUE FALSE 2901108.312 3702588.94 4388364.392 4469870.918 3107306.566 4250099.604 4258860.04 3902245.125 3808091.421 4329307.648 0.670109068 0.855238122 1.013641152 1.03246784 0.717737527 0.981704224 0.983727743 0.901355469 0.879607487 1 22.04570489 4.656128166 3.260347163 0.933140507 0.654688056 0.461292809 0.08761979 0.244131126 4.196899316 0.021097606 0.149968073 45303.12559 -4.656128166 -0.278452451 SGIETFS(ph)PPPPPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGIETFSPPPPPPK 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 SGIET(0.078)FS(0.922)PPPPPPK 158.58 5.30E-06 35050000 132500 144960 123600 147200 151550 147390 138310 149700 149090 179390 TRUE FALSE 127321.7535 140825.8827 145937.2695 154797.0096 156424.7434 150370.3268 140002.6792 146608.6427 132165.9282 167239.7555 0.761312722 0.842059846 0.872623073 0.925599354 0.935332289 0.899130272 0.83713755 0.876637509 0.790278172 1 17.35155831 4.656279616 1.928614765 0.887597193 0.736038819 0.361372927 0.053624301 0.731867982 3.297901661 0.013586024 0.18639176 45318.92671 -4.656279616 -0.151558374 KCTENDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 KCTENDIR 8 1 Q92879-4;G5EA30;Q92879-6;Q92879;Q92879-5;Q92879-3;Q92879-2 Q92879-4 CELF1 CUGBP Elav-like family member 1 0 ; 85.731 0.026513 748650000 2119000 2184500 1869580 2153000 2177400 2312700 2320800 2397900 2551400 2537400 FALSE TRUE 2036187.137 2122200.199 2207454.695 2264116.588 2247438.048 2359464.379 2349202.645 2348382.527 2261775.768 2365539.638 0.860770669 0.897131532 0.933171721 0.957124773 0.950074145 0.997431766 0.993093756 0.992747063 0.956135223 1 21.1737379 4.656567747 0.590361157 0.989837082 0.780451969 0.897528083 0.014107014 0.963743568 0.272751996 0.007067764 0.136489889 45349.00337 -4.656567747 -0.209385112 DNTINLIHTFR ddPTM_BT-474_Pertuzumab_2h_R1 6 DNTINLIHTFR 11 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;;; 191.53 1.79E-06 7481990000 5718060 6217530 5315200 6364940 6225650 5954430 6566370 6257800 6631980 6832900 FALSE TRUE 5494591.894 6040212.132 6275774.876 6693435.316 6425903.686 6074832.654 6646731.2 6128574.243 5879145.434 6370101.597 0.862559538 0.948212841 0.985192274 1.050758016 1.00876 0.953647687 1.043426247 0.962084223 0.922928048 1 22.60288495 4.65663434 2.210004971 0.992059617 0.841947016 0.529492016 0.036919174 0.408158175 2.62627965 0.009529385 0.111976757 45355.9575 -4.65663434 -0.150112601 GRLT(ph)PSPDIIVLSDNEASSPR ddPTM_BT-474_Pertuzumab_2h_R1 6 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 GRLT(0.976)PS(0.024)PDIIVLSDNEASSPR;GRLT(0.94)PS(0.06)PDIIVLSDNEASSPR;GRLT(0.996)PS(0.004)PDIIVLSDNEASSPR;GRLT(0.995)PS(0.005)PDIIVLSDNEASSPR;GRLT(1)PSPDIIVLSDNEASSPR;GRLT(0.999)PS(0.001)PDIIVLSDNEASSPR 254.31 3.54E-36 2545200000 1408260 1549790 1295090 1632510 1504450 1660840 1555910 1741590 1787520 1795870 TRUE FALSE 1353223.642 1505591.507 1529141.572 1716764.037 1552842.001 1694423.323 1574951.692 1705625.558 1584608.223 1674234.125 0.808264281 0.899271783 0.913337955 1.025402607 0.927493937 1.012058766 0.940699791 1.018749727 0.946467522 1 20.67506986 4.65666021 1.063711038 0.982134483 0.739358995 0.703782283 0.035005841 0.766344709 0.7815494 0.009633997 0.204132756 45358.65935 -4.65666021 -0.242775487 DQNDHKYPFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DQNDHKYPFDR 11 1 Q2M389;A0A087X256 Q2M389 KIAA1033 WASH complex subunit 7 0 ; 62.528 0.04831 826140000 190762 219720 202820 236856 218292 207312 226454 203211 261980 264990 FALSE TRUE 183306.8101 213453.8007 239474.0857 249080.1665 225313.5604 211503.9907 229225.4118 199014.6218 232241.1287 247041.9913 0.74200669 0.864038537 0.969365914 1.008250319 0.912045597 0.856145911 0.92788036 0.805590259 0.940087665 1 17.91439676 4.65677256 3.307383154 0.914752918 0.732339978 0.462845039 0.059580604 0.26973811 4.795391774 0.015612999 0.109222791 45370.39496 -4.65677256 -0.18241294 YTQVGPDHNR ddPTM_BT-474_Pertuzumab_2h_R1 6 YTQVGPDHNR 10 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 137.78 8.22E-05 9889821000 5373571 5903008 4769577 6165393 6110247 5805351 6081973 5939477 6258776 6266749 FALSE TRUE 5163565.905 5734659.991 5631545.663 6483589.672 6306788.644 5922739.175 6156406.005 5816824.724 5548305.987 5842296.508 0.883824691 0.981576334 0.963926712 1.109767309 1.07950506 1.013769015 1.05376473 0.995640108 0.949678946 1 22.47810415 4.657313698 1.526228005 1.027364961 0.848191542 0.45607245 0.046081289 0.872173211 2.149521956 0.013016993 0.224468718 45426.96245 -4.657313698 -0.17917342 AAGALGSASSGS(ph)MPNLAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAGALGSASSGSMPNLAAR 19 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 AAGALGSAS(0.001)S(0.017)GS(0.982)MPNLAAR;AAGALGSASS(0.001)GS(0.999)MPNLAAR 335.57 2.03E-75 1003930000 904850 626220 368330 429210 416490 321410 304930 708170 367290 336990 TRUE FALSE 869487.4616 608360.8187 434895.4245 451361.5795 429886.7791 327909.1304 308661.8246 693546.042 325596.779 314165.3671 2.767610795 1.936435019 1.384288244 1.436700626 1.36834554 1.043746908 0.98248202 2.20758274 1.036386607 1 18.26116462 4.657327733 1.811550801 1.365997813 3.093025182 0.629123616 0.348299422 0.505153073 1.930913639 0.095712288 1.408714227 45428.43054 -4.657327733 1.727027369 DLGKMAHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGKMAHIR 9 1 A0A1W2PS94;A0A2R8Y358;Q9BXT5 A0A1W2PS94 TEX15 Testis-expressed sequence 15 protein 0 ; 81.594 0.019006 248720000 210177 262780 275610 260610 270060 162797 354980 257750 312600 324660 FALSE TRUE 201963.0505 255285.7717 325418.8579 274060.1133 278746.7252 166088.8669 359324.3514 252427.3724 277114.9585 302670.489 0.667270374 0.843444541 1.07515886 0.905473521 0.920957726 0.548744833 1.187180001 0.83400061 0.915566494 1 18.20738849 4.657418674 3.813382692 0.915359259 0.659998826 0.191912344 0.157741703 0.363354486 8.853015252 0.03629781 0.214952953 45437.94421 -4.657418674 -0.255360433 LSS(ph)GFDDIDLPSAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.025)S(0.975)GFDDIDLPSAVK;LS(0.059)S(0.941)GFDDIDLPSAVK 290.32 7.14E-44 443750000 1125590 814380 445040 611900 681620 550560 495370 1053340 649640 682040 TRUE FALSE 1081600.698 791154.6798 525468.6279 643480.2323 703544.9263 561692.7004 501432.4862 1031588.161 575895.5907 635844.8233 1.701045064 1.244257484 0.826410169 1.01200829 1.106472681 0.883380158 0.78860827 1.622389808 0.905717196 1 19.2783152 4.657780556 3.336838227 1.054973605 1.736745806 0.451404591 0.225681746 0.267956718 4.865444185 0.058711552 0.407526612 45475.82178 -4.657780556 0.681772202 S(ph)RTASGSSVTSLDGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.495)RT(0.495)AS(0.01)GSSVTSLDGTR 106.7 0.00071771 224790000 157980 103100 53453 81109 80093 70149 68296 100650 70865 57571 TRUE FALSE 151805.9669 100159.6889 63113.14616 85295.04521 82669.26408 71567.46084 69131.82688 98571.54233 62820.70229 53671.66489 2.82841919 1.866155804 1.175911839 1.589200659 1.540277617 1.333430982 1.288050725 1.836565766 1.170463082 1 15.71187302 4.658053576 2.783937257 1.42709231 2.966749684 0.776421019 0.237290092 0.156147229 1.824954218 0.056562528 0.497931044 45504.41922 -4.658053576 1.539657374 EDVSLHGYK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDVSLHGYK 9 0 Q12792;Q12792-3;Q12792-4;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 ; 141.48 0.00010661 1345670000 975300 1182540 1143940 1558730 1218870 1066000 1602320 1515060 1633650 1990180 FALSE TRUE 937184.1977 1148815.117 1350675.405 1639176.242 1258076.06 1087555.25 1621929.671 1483773.482 1448204.901 1855383.336 0.505116209 0.619179387 0.727976466 0.883470391 0.678067996 0.586162023 0.87417497 0.799712627 0.780542151 1 20.82328586 4.658148422 0.081265129 1.255896044 2.46E-11 0.557604727 0.096044636 71.22862226 0.944368963 3.950848127 12.23174152 45514.35803 -4.658148422 -1.255896044 EAASGTT(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 4 EAASGTTPQK 10 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 EAASGT(0.066)T(0.933)PQK;EAAS(0.001)GT(0.147)T(0.852)PQK;EAASGT(0.142)T(0.858)PQK;EAASGT(0.106)T(0.894)PQK 205.12 1.95E-06 4022578000 8005810 7180010 5529520 6289370 5914000 6139080 6632230 7195100 6482210 7572380 TRUE FALSE 7692934.094 6975243.145 6528827.268 6613965.139 6104229.181 6263216.404 6713397.215 7046518.671 5746376.696 7059495.958 1.089728522 0.988065322 0.924829096 0.936889146 0.86468343 0.887204475 0.950974015 0.998161726 0.813992491 1 22.75113375 4.658203146 1.921340509 0.924021843 1.124742192 0.479074854 0.054065141 0.578608512 2.573735697 0.014041812 0.194965141 45520.09357 -4.658203146 0.200720349 GLDDDRGPWR ddPTM_BT-474_Pertuzumab_2h_R1 6 GLDDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;; 120.09 0.00055254 6251060000 1895030 2075710 1791890 2125540 2107980 1825220 2279530 2091690 2179560 2372110 FALSE TRUE 1820970.133 2016512.783 2115724.383 2235239.374 2175785.091 1862127.199 2307427.57 2048495.871 1932145.486 2211444.877 0.823430035 0.911853062 0.956715858 1.010759706 0.983874893 0.842040974 1.043402707 0.926315592 0.873702757 1 21.07655785 4.658463421 2.449588571 0.95404944 0.806211914 0.318913284 0.058347328 0.514764387 4.325441952 0.014176038 0.147707593 45547.3822 -4.658463421 -0.147837526 DGVDLMESYVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGVDLMESYVDR 12 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 0 ; 177.57 5.37E-05 97500000 60298 68220 60510 68891 69781 68251 66158 73350 72893 76867 FALSE TRUE 57941.4875 66274.43239 71445.50304 72446.47277 72025.56924 69631.08198 66967.66139 71835.29687 64618.49223 71660.72962 0.808552855 0.924836137 0.99699659 1.010964766 1.005091207 0.971676989 0.934509902 1.002436024 0.901728081 1 16.12889511 4.65861464 2.64446341 0.978633552 0.789504024 0.70162414 0.033480396 0.201750734 2.066920157 0.008167563 0.077115356 45563.24425 -4.65861464 -0.189129528 SDEGHPFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDEGHPFR 8 0 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2;F8W914;A0A0U1RQR6;H7C106;Q9NQC3-3;Q9NQC3-6 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4;Reticulon 0 ;;; 117.4 0.0020865 3426320000 2351410 3160390 2715400 4160560 2657720 3640510 3903220 3742230 3954670 4173100 FALSE TRUE 2259514.298 3070258.772 3206133.184 4375287 2743207.977 3714123.607 3950988.774 3664951.643 3505752.441 3890452.22 0.580784487 0.789177864 0.824102958 1.124621703 0.705112882 0.954676577 1.015560287 0.942037438 0.901116951 1 21.89150643 4.658703979 1.343880439 0.941808458 0.465119437 0.539190141 0.103804987 0.845942497 1.513833695 0.027782877 0.528863306 45572.61806 -4.658703979 -0.476689021 MPSARPPS(ph)PPLSSWER ddPTM_BT-474_Pertuzumab_2h_R1 4 MPSARPPSPPLSSWER 16 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 MPS(0.001)ARPPS(0.997)PPLS(0.002)SWER;MPSARPPS(0.999)PPLS(0.001)SWER;MPSARPPS(0.987)PPLS(0.01)S(0.003)WER;MPSARPPS(1)PPLSSWER 126.91 4.18E-05 4091820000 1070650 1183110 1032170 1192300 1174000 1222400 1283350 1213220 1124180 1248800 TRUE FALSE 1028807.814 1149368.861 1218706.079 1253834.746 1211762.776 1247117.766 1299056.021 1188166.583 996567.7993 1164217.664 0.883690264 0.987245682 1.046802602 1.076976226 1.04083868 1.071206703 1.115818856 1.020570826 0.855997835 1 20.15092938 4.658737407 2.525280093 1.036422761 0.864671103 0.299163178 0.065989985 0.492480044 4.477747362 0.016640704 0.166930116 45576.12599 -4.658737407 -0.171751658 VKVDPSHDASK ddPTM_BT-474_Pertuzumab_2h_R1 2 VKVDPSHDASK 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 105.17 0.0015031 313760000 678400 596940 515000 516390 495510 487330 512680 546560 788210 677520 FALSE TRUE 651887.378 579915.8557 608071.9561 543040.9498 511448.5292 497184.1465 518954.3312 535273.345 698735.7052 631630.9669 1.032070009 0.918124484 0.962701305 0.859744025 0.809726812 0.787143399 0.82161002 0.84744633 1.106240419 1 19.26872238 4.658742722 1.166046654 0.874382176 1.07796595 0.125944313 0.095137742 2.388558384 3.023854446 0.027848973 0.573291518 45576.6838 -4.658742722 0.203583774 ADTSS(ph)AENILYTVGLWEAPR ddPTM_BT-474_Pertuzumab_2h_R1 6 ADTSSAENILYTVGLWEAPR 20 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 ADT(0.005)S(0.033)S(0.962)AENILYTVGLWEAPR;ADTS(0.017)S(0.983)AENILYTVGLWEAPR;ADTS(0.014)S(0.986)AENILYTVGLWEAPR;ADTS(0.006)S(0.994)AENILYTVGLWEAPR;ADTS(0.065)S(0.935)AENILYTVGLWEAPR;ADTS(0.008)S(0.992)AENILYTVGLWEAPR 388.47 7.69E-131 2870607000 1114220 1186900 972440 1221600 1142850 1195060 1089620 1267330 1269230 1313490 TRUE FALSE 1070675.051 1153050.774 1148181.54 1284646.922 1179610.808 1219224.932 1102955.096 1241159.193 1125152.331 1224526.152 0.874358664 0.941630174 0.937653751 1.049097171 0.963320225 0.995670799 0.900719918 1.013583246 0.918847122 1 20.22379216 4.65891941 1.650454627 0.975028454 0.850646052 0.338858475 0.042304349 0.908533693 2.725225261 0.010584421 0.171572768 45595.22994 -4.65891941 -0.124382402 ALQTS(ph)PQPPEGPGLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALQTSPQPPEGPGLPR 16 0 B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;A0A2R8YGT1;F8W9A8;Q6PFW1;H7C398;Q6PFW1-5 B7WPL9 PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 1 ALQT(0.132)S(0.868)PQPPEGPGLPR;ALQT(0.007)S(0.993)PQPPEGPGLPR 216.6 1.58E-14 414860000 399600 446980 382240 464030 458930 480580 469420 473080 449830 459340 TRUE FALSE 383983.1902 434232.568 451319.2709 487978.6439 473691.9002 490297.6569 475164.9024 463310.7327 398767.1842 428228.4927 0.896678285 1.014020728 1.05392163 1.139528668 1.106166237 1.144944032 1.109605994 1.081924114 0.931201896 1 18.70802126 4.659115902 1.792543099 1.082972289 0.854538537 0.415340183 0.062183977 0.663034229 2.459006109 0.0162285 0.243165888 45615.86365 -4.659115902 -0.228433752 GEDVPS(ph)EEEEEEENGFEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEDVPSEEEEEEENGFEDR 19 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 GEDVPS(1)EEEEEEENGFEDR;GEDVPS(1)EEEEEEENGFEDR 295.82 1.15E-49 1816350000 213420 233450 204956 233030 217640 235340 225140 249410 247290 263810 TRUE FALSE 205079.3105 226792.2346 241996.1084 245056.7062 224640.5883 240098.736 227895.3307 244259.5963 219218.6759 245941.9137 0.833852625 0.922137391 0.983956353 0.996400746 0.913388795 0.976241635 0.92662258 0.993159696 0.891343296 1 17.9079581 4.659724851 2.955178207 0.959928216 0.823220187 0.52840186 0.036048993 0.230212711 3.121944989 0.008201439 0.067137469 45679.86914 -4.659724851 -0.136708029 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR ddPTM_BT-474_Pertuzumab_2h_R1 6 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR 29 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;;;;; 288.32 1.97E-72 735477000 165819.3 185669.6 158083.7 193724.9 188297.4 204631.8 191755.5 169172.6 221013.1 225788.7 FALSE TRUE 159338.8984 180374.4848 186652.9411 203723.0653 194354.1569 208769.5952 194102.2612 165679.1267 195924.6195 210495.8302 0.756969382 0.856902888 0.886729875 0.967824707 0.923315947 0.991799196 0.922119269 0.787089827 0.930776725 1 17.68343213 4.659802155 1.720993308 0.916429587 0.71887327 0.454857549 0.057282797 0.852965645 2.844574299 0.016840523 0.263383881 45688.00086 -4.659802155 -0.197556317 GPASQFYITPST(ph)SLSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPASQFYITPSTSLSPR 17 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 GPASQFYIT(0.002)PS(0.082)T(0.338)S(0.338)LS(0.24)PR 67.645 0.089329 0 39349 53151 52024 54574 56329 53610 57717 59505 61559 64547 TRUE FALSE 37811.19758 51635.18552 61425.89407 57390.57068 58140.87344 54694.03093 58423.35791 58276.20096 54571.0804 60175.1742 0.628352108 0.858081197 1.020784649 0.953725044 0.966193687 0.908913546 0.970888056 0.96844258 0.906870335 1 15.87688079 4.65980404 2.851101369 0.959537173 0.597263493 0.895265621 0.034541967 0.091509168 1.134387424 0.008103109 0.069590877 45688.19918 -4.65980404 -0.36227368 LQELPDAVPHGEMPR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQELPDAVPHGEMPR 15 0 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;;; 170.11 1.16E-06 3138660000 1766370 1969920 1701660 2047430 1951310 2184040 2021890 1884140 2115170 2241130 FALSE TRUE 1697338.308 1913739.81 2009187.815 2153098.108 2014075.658 2228202.785 2046634.495 1845231.851 1875064.769 2089336.269 0.812381584 0.915955865 0.961639275 1.030517748 0.963978699 1.066464417 0.979562038 0.883166524 0.897445182 1 20.99461328 4.659974864 2.164579984 0.969552091 0.785727646 0.473291661 0.051862244 0.544721513 3.301980464 0.014838919 0.181277865 45706.17347 -4.659974864 -0.183824445 TGEEINFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGEEINFGK 9 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 74.464 0.065931 0 104280 141950 130110 163060 168060 172290 157630 169220 174570 158000 FALSE TRUE 100204.6223 137901.725 153623.7713 171475.5461 173465.8025 175773.8218 159559.1231 165725.5479 154753.5455 147298.5193 0.680282618 0.936205779 1.042941722 1.164136252 1.177647972 1.193316964 1.083236436 1.12509989 1.050611685 1 17.1683834 4.659985097 1.496608348 1.121793004 0.551644461 0.839733216 0.057817246 0.339814455 0.793847255 0.015535087 0.274880206 45707.25047 -4.659985097 -0.570148542 VRPEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VRPEEK 6 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 120.65 0.018236 427120000 563000 586800 510840 566230 598470 638210 623670 631230 682940 691190 FALSE TRUE 540997.3376 570065.0385 603160.1516 595453.1982 617720.3311 651115.0435 631302.66 618194.8799 605415.5143 644375.0857 0.839568986 0.884678895 0.936038908 0.924078555 0.958634722 1.010459681 0.979713018 0.95937117 0.939538986 1 19.29754119 4.660523477 0.72593088 0.974266622 0.764934031 0.808420051 0.021521889 1.144166113 0.493005836 0.008966069 0.193099035 45763.94728 -4.660523477 -0.209332591 YLLGDMEGR ddPTM_BT-474_Pertuzumab_2h_R1 6 YLLGDMEGR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;;; 147.29 0.00021579 2214620000 1616620 1768820 1565600 1834400 1792710 1413690 1929380 1850180 1791170 1936550 FALSE TRUE 1553440.703 1718374.985 1848538.747 1929073.604 1850374.145 1442275.78 1952992.33 1811973.136 1587843.891 1805385.744 0.860448084 0.951804894 1.023902373 1.068510489 1.024918997 0.798874028 1.081759029 1.003648745 0.879503949 1 20.78387569 4.660560595 3.234387496 0.988877513 0.852244939 0.173688454 0.081279584 0.474945436 8.025848848 0.019725718 0.143849939 45767.85885 -4.660560595 -0.136632574 RGDS(ph)ESEEDEQDS(ph)EEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RGDS(0.997)ES(0.116)EEDEQDS(0.887)EEVR;RGDS(0.989)ES(0.017)EEDEQDS(0.994)EEVR 183.15 4.73E-10 272460000 321430 350850 304570 345570 339100 334110 369090 361900 421380 389310 TRUE FALSE 308868.1602 340844.1015 359612.5741 363404.9091 350007.4595 340865.9331 373607.0338 354426.6385 373546.709 362941.6869 0.851013183 0.939115328 0.990827417 1.001276299 0.964362795 0.93917548 1.029385842 0.976538798 1.029219631 1 18.46937825 4.660935794 2.069081129 0.989692076 0.824780486 0.73175775 0.026122072 0.29312801 1.575900963 0.006589865 0.085206057 45807.41596 -4.660935794 -0.164911589 YEELFPAFSDSR ddPTM_BT-474_Pertuzumab_2h_R1 7 YEELFPAFSDSR 12 0 P54920;M0R0Y2;M0R2M1;M0R213;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;;;;; 243.53 5.54E-16 780940000 730859 787288 687484 789749 757787 737241 792685 835053 796930 854601 FALSE TRUE 702296.2223 764835.3171 811727.6518 830508.0405 782161.9071 752148.5181 802386.1161 817808.8637 706465.8474 796718.1131 0.881486451 0.959982338 1.018839209 1.042411396 0.981729792 0.944058514 1.007114189 1.026472036 0.886719953 1 19.60370985 4.661124638 3.136208546 0.992162097 0.873589849 0.356915043 0.042839705 0.304223873 4.773578826 0.010395098 0.079077113 45827.33874 -4.661124638 -0.118572248 IDFDSVSSIMASS(ph)Q ddPTM_BT-474_Pertuzumab_2h_R1 2 IDFDSVSSIMASSQ 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;K7EK53 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 1 IDFDSVSSIMAS(0.126)S(0.874)Q;IDFDSVSSIMAS(0.031)S(0.969)Q 122.97 0.00011082 79762000 150768 159644 137959 153269 161731 179324 159177 162489 173510 193522 TRUE FALSE 144875.8199 155091.1094 162891.2602 161179.2315 166933.2245 182950.0541 161125.0557 159133.5454 153813.8722 180414.5826 0.80301613 0.859637327 0.902871918 0.893382504 0.925275674 1.014053584 0.893082219 0.882043697 0.85255787 1 17.46095643 4.66123362 1.220080211 0.918538383 0.759455446 0.392854849 0.047580689 1.478882557 2.081629069 0.014153577 0.287420139 45838.84016 -4.66123362 -0.159082937 GVCLIDEFDKMNDQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVCLIDEFDKMNDQDR 16 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ;;; 214.22 1.57E-14 1315120000 2064280 1912660 1427390 1531610 1844580 1996860 1745540 1879490 2048000 1890580 FALSE TRUE 1983605.655 1858112.809 1685351.125 1610656.576 1903912.591 2037237.877 1766902.441 1840677.875 1815519.626 1762529.333 1.125431287 1.054230857 0.956211675 0.913832494 1.080216116 1.15586041 1.002481155 1.04433886 1.030064914 1 20.74921584 4.661318983 3.93431685 1.026176404 1.128103219 0.194762974 0.062471637 0.389157739 10.23938316 0.016152621 0.093475404 45847.85085 -4.661318983 0.101926815 AES(ph)PESSAIESTQST(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 4 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 AES(0.981)PES(0.019)SAIEST(0.013)QS(0.049)T(0.938)PQK;AES(0.968)PES(0.032)SAIEST(0.003)QS(0.004)T(0.992)PQK;AES(1)PESSAIESTQS(0.001)T(0.998)PQK;AES(0.99)PES(0.01)SAIESTQS(0.071)T(0.929)PQK 401.6 2.58E-109 1241870000 2467520 2209450 1713280 1874160 1932760 1806190 1985930 2198080 2075600 2242570 TRUE FALSE 2371086.59 2146438.649 2022907.808 1970885.622 1994928.981 1842712.399 2010234.405 2152688.88 1839986.59 2090678.736 1.13412288 1.026670723 0.967584245 0.942701328 0.954201593 0.881394337 0.961522385 1.029660293 0.880090546 1 20.99553996 4.66136961 1.715690776 0.9535989 1.179568303 0.631480159 0.043355542 0.529141606 1.746292514 0.011828002 0.186692689 45853.19583 -4.66136961 0.225969403 AELAESR ddPTM_BT-474_Pertuzumab_2h_R1 4 AELAESR 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;; 113.14 0.014418 3312510000 3576110 4200370 3706500 4421290 4691800 4626100 4530980 4247420 4143010 4401850 FALSE TRUE 3436351.668 4080579.56 4376347.001 4649473.307 4842716.008 4719642.912 4586431.489 4159709.293 3672712.874 4103708.779 0.837377078 0.994363826 1.06643703 1.132992997 1.180082766 1.150092067 1.11763084 1.013646318 0.894974052 1 21.96849692 4.661431946 2.090050573 1.078291728 0.793386599 0.435536867 0.080065204 0.55881084 3.082412091 0.022057241 0.282490251 45859.77781 -4.661431946 -0.284905129 YLVLDEADR ddPTM_BT-474_Pertuzumab_2h_R1 5 YLVLDEADR 9 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;D6RCM4;Q9NQI0-3;Q9NQI0-2;Q9NQI0-4;Q9NQI0;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX4;DDX3Y ATP-dependent RNA helicase DDX3X;Probable ATP-dependent RNA helicase DDX4;ATP-dependent RNA helicase DDX3Y 0 ;;;; 185.05 0.00010073 3890960000 3779170 4225680 3552430 4477860 4304380 4158330 4438290 4437520 4424580 4799300 FALSE TRUE 3631475.858 4105167.744 4194433.124 4708962.891 4442834.292 4242414.282 4492607.121 4345883.661 3922320.228 4474239.136 0.811640985 0.917511921 0.937462884 1.052461155 0.992980964 0.948186754 1.004105276 0.971312335 0.876645192 1 22.09321094 4.661437421 1.710523474 0.976922823 0.772222384 0.564147015 0.043768359 0.572364899 1.87414186 0.011530476 0.182569855 45860.35589 -4.661437421 -0.204700439 CVSSPHFQVAER ddPTM_BT-474_Pertuzumab_2h_R1 3 CVSSPHFQVAER 12 0 Q16537-2;Q16537;Q16537-3;H0YN84;E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3;H7C5Q9;H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;Q15173-2;Q15173 Q16537-2;E9PFR3;H0YJ75;Q15173-2 PPP2R5E;PPP2R5C;PPP2R5D;PPP2R5B Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform 0 ;; 183.89 1.50E-05 1769430000 693190 800400 708650 824970 809150 813550 833380 855330 874630 939320 FALSE TRUE 666099.3684 777573.3757 836718.8188 867546.8006 835177.0446 830000.5384 843579.1537 837667.1366 775345.6691 875699.0197 0.760648754 0.887945925 0.95548676 0.990690615 0.953726139 0.947814854 0.963320884 0.956569686 0.885402006 1 19.74007557 4.661653861 2.148480726 0.956423909 0.726162815 0.811643086 0.028908043 0.212751965 1.261289165 0.007123009 0.088414461 45883.21713 -4.661653861 -0.230261094 AVVIVDDR ddPTM_BT-474_Pertuzumab_2h_R1 7 AVVIVDDR 8 0 Q15233;Q15233-2;H7C367;C9IZL7;P23246;P23246-2 Q15233;P23246 NONO;SFPQ "Non-POU domain-containing octamer-binding protein;Splicing factor, proline- and glutamine-rich" 0 ;;;;;; 177.71 0.00058966 10385000000 7975710 8701850 7372090 9012320 8858090 9108020 8706090 9050880 8453330 9097900 FALSE TRUE 7664010.436 8453681.758 8704390.654 9477446.915 9143018.51 9292190.405 8812637.734 8863976.165 7493743.418 8481691.129 0.903594616 0.996697667 1.0262565 1.117400619 1.07797117 1.095558688 1.039018941 1.045071794 0.883519961 1 23.01592052 4.662025089 2.061977808 1.043929416 0.877819792 0.295329949 0.060930093 0.700057256 3.723319238 0.015698253 0.20471276 45922.45407 -4.662025089 -0.166109624 RNDS(ph)YTEEEPEWFSAGPTSQSETIELTGFDDKILEEDHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNDSYTEEEPEWFSAGPTSQSETIELTGFDDKILEEDHK 39 2 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RNDS(0.457)Y(0.086)T(0.457)EEEPEWFSAGPTSQSETIELTGFDDKILEEDHK 52.456 0.017747 26919000 22035 12831 6237 5879.4 8269.5 7277.7 5039.5 7508.7 9052 8093.2 TRUE FALSE 21173.84784 12465.07244 7364.164641 6182.836539 8535.495978 7424.86008 5101.174908 7353.642721 8024.454909 7545.040355 2.806326652 1.65208824 0.976027204 0.819457054 1.131272409 0.984071619 0.676096438 0.974632656 1.063540356 1 12.8813129 4.662049411 1.906250094 0.934772859 3.213964248 0.955337664 0.123484984 0.122273117 0.52951165 0.032811753 0.466782238 45925.02603 -4.662049411 2.27919139 up ASPITNDGEDEFVPSDGLDKDEYTFS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 ASPITNDGEDEFVPSDGLDKDEYT(0.037)FS(0.962)PGK;ASPITNDGEDEFVPS(0.002)DGLDKDEY(0.024)T(0.181)FS(0.793)PGK;ASPITNDGEDEFVPS(0.006)DGLDKDEY(0.038)T(0.15)FS(0.806)PGK;ASPITNDGEDEFVPS(0.006)DGLDKDEY(0.013)T(0.233)FS(0.748)PGK 101.78 9.58E-10 0 1086981 900446 602296 690589 813741 701452 810944 999950 906661 803266 TRUE FALSE 1044500.581 874766.1617 711144.2852 726230.3811 839915.7183 715635.84 820868.5753 979300.6831 803740.6443 748860.0783 1.394787372 1.168130318 0.949635727 0.969781141 1.121592328 0.955633583 1.096157479 1.307721845 1.073285474 1 19.51433666 4.662051189 3.482838089 1.078611792 1.410560715 0.487276861 0.102811345 0.251576563 5.063113123 0.02855785 0.190591019 45925.21402 -4.662051189 0.331948923 TVS(ph)SPIPYTPSPSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.892)S(0.108)PIPYTPSPSSSR 214.45 1.79E-14 108870000 161610 116260 71523 94458 81763 63145 61691 154930 74637 58710 TRUE FALSE 155294.1025 112944.3786 84448.79712 99332.9887 84392.98115 64421.83516 62445.99291 151730.6414 66164.52066 54733.51941 2.837276028 2.06353218 1.542908222 1.814847461 1.541888445 1.177008821 1.140909512 2.772170381 1.208848278 1 15.74013701 4.662277731 2.143431465 1.623278267 3.057116369 0.400022505 0.487083027 0.627502107 3.693555391 0.129999443 1.62238231 45949.17631 -4.662277731 1.433838102 SIYEGDESFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIYEGDESFR 10 0 D6R9C7;D6RCM5;D6RDH6;K4DI92;Q6NW29 D6R9C7 RWDD4 RWD domain-containing protein 4 0 ; 144.66 7.40E-05 362730000 651140 1093370 964530 1589300 1372520 1508100 1344660 1104840 805610 1276320 FALSE TRUE 625692.7289 1062188.158 1138842.027 1671323.963 1416668.352 1538594.815 1361116.351 1082024.668 714160.5302 1189873.71 0.525848016 0.892689829 0.957111681 1.404622986 1.190603961 1.293074049 1.143916653 0.909360934 0.600198596 1 20.18237703 4.662323317 1.872298612 1.080552032 0.409480687 0.377006678 0.210641449 0.767014692 3.168316639 0.058715587 0.852296932 45953.99972 -4.662323317 -0.671071345 ELEAIFGRPVVDGEEGEPHSISPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ; 239.51 9.91E-38 902770000 379754 398498 332659 379229 386498 415425 427016 413251 461888 449918 FALSE TRUE 364912.7938 387133.2272 392777.8813 398801.0541 398930.0592 423825.1781 432241.9495 404717.2224 409456.4106 419444.6531 0.869990334 0.922966175 0.936423622 0.950783497 0.951091059 1.010443631 1.030510096 0.964888262 0.976186983 1 18.67812093 4.662405226 0.551911264 0.994860913 0.802208674 0.777450844 0.020873538 1.871072116 0.461506863 0.012367922 0.230364731 45962.66759 -4.662405226 -0.192652239 QGIETPEDQNDLRK ddPTM_BT-474_Pertuzumab_2h_R1 4 QGIETPEDQNDLRK 14 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 ;;; 169.04 5.44E-06 4853410000 1236340 1289150 1104030 1179410 1225110 1262380 1235140 1353200 1418640 1407000 FALSE TRUE 1188022.466 1252384.704 1303552.78 1240279.491 1264516.776 1287906.189 1250256.013 1325255.947 1257601.935 1311702.637 0.905710206 0.954777912 0.993786811 0.945549286 0.964027014 0.981858351 0.953155066 1.010332609 0.958755361 1 20.32300927 4.662456323 2.998256011 0.975674759 0.899811953 0.526517097 0.020107442 0.238762247 3.353057979 0.004811154 0.03904131 45968.07559 -4.662456323 -0.075862806 SLDADEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLDADEFR 8 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;; 133.55 0.002128 1429960000 2639770 2955500 2622110 2934710 2968800 2946200 2963280 3356350 3419650 3450330 FALSE TRUE 2536604.87 2871212.034 3095983.606 3086170.735 3064294.148 3005774.183 2999545.507 3287040.2 3031465.668 3216636.076 0.788589324 0.892613266 0.962491103 0.959440441 0.952639365 0.934446456 0.932510062 1.021887501 0.942433523 1 21.61712129 4.662562431 1.775097547 0.965006363 0.745199403 0.801864996 0.026927544 0.321808525 1.15722312 0.007371276 0.113093118 45979.30801 -4.662562431 -0.219806959 EAS(ph)PAPLAQGEPGREDLPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EASPAPLAQGEPGREDLPTR 20 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 EAS(1)PAPLAQGEPGREDLPTR;EAS(1)PAPLAQGEPGREDLPTR 217.71 6.30E-25 1570150000 797760 834780 704770 807750 820340 812300 834520 879470 873200 875070 TRUE FALSE 766582.6572 810972.8917 832137.6165 849438.0743 846726.9811 828725.2626 844733.1054 861308.6372 774077.9968 815800.7295 0.939669002 0.994082087 1.020025585 1.041232305 1.037909076 1.015842757 1.035465004 1.055783117 0.948856711 1 19.63785727 4.662690827 1.953395093 1.025335286 0.92195592 0.411416343 0.028354486 0.55742022 2.570220451 0.007061065 0.09809567 45992.90352 -4.662690827 -0.103379366 ERPDLQLQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPDLQLQDR 10 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 0 ; 142.1 3.32E-05 466170000 241050 291070 262460 310590 324130 307030 342950 279770 285540 300620 FALSE TRUE 231629.4995 282768.9686 309892.3604 326619.5871 334555.9358 313238.357 347147.1247 273992.6517 253126.6963 280258.7396 0.826484483 1.008956827 1.105736652 1.165421594 1.193739529 1.117675607 1.238666545 0.977641775 0.903189305 1 18.09639984 4.662862129 2.423018617 1.095874494 0.78873432 0.392687891 0.097974428 0.469119093 3.808408483 0.025943623 0.279215933 46011.04843 -4.662862129 -0.307140174 EDAKEDHER ddPTM_BT-474_Pertuzumab_2h_R1 2 EDAKEDHER 9 1 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 ; 82.171 0.011541 135169000 267821 241172 189855 195697 213271 215291 225048 241045 261990 227507 FALSE TRUE 257354.2592 234294.0107 224166.0218 205796.9456 220131.0554 219644.3315 227802.2047 236067.3365 232249.9936 212097.7482 1.213375726 1.104651099 1.056899584 0.97029293 1.037875495 1.035580686 1.074043485 1.113011988 1.095013952 1 17.69436978 4.663108445 2.346603553 1.053098492 1.237124847 0.612791985 0.040076234 0.365140582 2.724080893 0.0114019 0.127910016 46037.15163 -4.663108445 0.184026355 DMGSCEIYPQTIQHNPNGR ddPTM_BT-474_Pertuzumab_2h_R1 6 DMGSCEIYPQTIQHNPNGR 19 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;;;; 305.33 2.21E-50 6419460000 2365121 2592630 2204415 2631348 2624048 2779629 2672120 2632510 2728320 2832110 FALSE TRUE 2272689.457 2518690.731 2602801.827 2767152.186 2708452.887 2835835.003 2704822.204 2578147.749 2418612.552 2640288.667 0.860773098 0.953945211 0.985801992 1.048049109 1.025816957 1.074062483 1.024441849 0.976464347 0.916040955 1 21.33226424 4.66340784 1.720902312 1.010213219 0.824177901 0.552216352 0.04045877 0.626952429 2.078465013 0.011516791 0.182729192 46068.89971 -4.66340784 -0.186035318 ILSEVT(ph)PDQSKPEN ddPTM_BT-474_Pertuzumab_2h_R1 1 ILSEVTPDQSKPEN 14 1 O43482 O43482 OIP5 Protein Mis18-beta 1 ILSEVT(1)PDQSKPEN 117.7 0.0018343 62264000 128520 109010 143260 140640 155510 190780 152990 200060 255770 246850 TRUE FALSE 123497.2963 105901.1415 169150.2688 147898.4473 160512.1204 194637.7023 154862.3374 195928.6911 226736.0619 230130.6296 0.536639979 0.460178385 0.735018494 0.642671719 0.697482646 0.84577052 0.672932315 0.851380329 0.985249387 1 17.81209349 4.663489558 0.175369251 1.08284057 7.02E-11 0.782097817 0.079042949 7.900096889 0.253958396 0.241022977 1.944153685 46077.56903 -4.663489558 -1.082840569 STS(ph)PIIGS(ph)PPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 STSPIIGSPPVR 12 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 S(0.001)T(0.005)S(0.994)PIIGS(1)PPVR;ST(0.004)S(0.996)PIIGS(1)PPVR;STS(1)PIIGS(1)PPVR;STS(1)PIIGS(1)PPVR 186.69 1.67E-05 2569260000 1749760 1960780 1744610 1877030 1818790 1967910 1996320 2051320 2301020 2261110 TRUE FALSE 1681377.445 1904860.474 2059899.836 1973903.743 1877293.032 2007702.489 2020751.561 2008959.525 2039817.856 2107963.006 0.797631382 0.90364986 0.977199235 0.936403408 0.890572096 0.95243725 0.958627621 0.953033578 0.967672512 1 21.00741812 4.663534805 2.793856729 0.950170824 0.781948026 0.749469066 0.027448647 0.171961187 2.019041115 0.006748069 0.060436559 46082.36984 -4.663534805 -0.168222798 NWDEWVPESR ddPTM_BT-474_Pertuzumab_2h_R1 3 NWDEWVPESR 10 0 H0YMJ0;H0YLJ3;Q9UBU8-2;B3KTM8 H0YMJ0 MORF4L1 0 ;; 94.692 0.01845 351790000 168357 181769 159341 181272 175081 172984 179481 208342 174927 168652 FALSE TRUE 161777.4223 176585.1261 188137.4632 190627.4696 180712.6394 176481.855 181677.5422 204039.6649 155070.0203 157229.0498 1.028928321 1.123107506 1.196582078 1.212418887 1.149359101 1.122450687 1.155496026 1.297722432 0.986268253 1 17.26250827 4.663534986 3.207901065 1.160744086 1.019904227 0.083863033 0.089882458 0.501018822 8.308566597 0.021035284 0.156725566 46082.389 -4.663534986 -0.140839858 LVCSVTDEDGPETHFDELEDVFLLETDNPR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVCSVTDEDGPETHFDELEDVFLLETDNPR 30 0 Q99985-2;Q99985 Q99985-2 SEMA3C Semaphorin-3C 0 ;;; 309.99 3.26E-92 135481000 70346 89082 80770.2 99471 95018 94440 102639 91282 100607 99987 FALSE TRUE 67596.80055 86541.46858 95367.17186 104604.7102 98074.34026 96349.64151 103895.1268 89396.9948 89186.51514 93214.79143 0.72517247 0.928409185 1.023090546 1.122190037 1.052132808 1.033630393 1.114577689 0.959043017 0.95678501 1 16.50827128 4.663828661 2.113698927 1.035624492 0.668630687 0.762155226 0.052507816 0.276835497 1.566877216 0.014242926 0.181876636 46113.56098 -4.663828661 -0.366993805 GDEGIFEESFIEER ddPTM_BT-474_Pertuzumab_2h_R1 4 GDEGIFEESFIEER 14 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 ;;; 221.8 9.61E-12 457733000 223541 262732 233094 272840 288377 280721 276207 284677 300200 313325 FALSE TRUE 214804.7706 255239.1406 275219.2709 286921.3051 297652.9081 286397.371 279587.3039 278798.3205 266122.5545 292103.2187 0.73537283 0.873797768 0.942198693 0.982259992 1.01899907 0.980466331 0.957152424 0.954451381 0.911056563 1 18.15611873 4.66403773 1.611330314 0.970321494 0.670956918 0.874185029 0.02762804 0.297810154 0.833472354 0.007905572 0.133557496 46135.76537 -4.66403773 -0.299364576 FRQS(ph)LPLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 FRQSLPLSR 9 1 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 FRQS(1)LPLSR;FRQS(1)LPLSR 166.7 3.67E-05 2123200000 504910 346820 202468 277940 243163 196638 226803 448640 204767 206668 TRUE FALSE 485177.559 336929.0332 239058.4715 292284.5167 250984.5587 200614.1551 229578.683 439375.4272 181522.7086 192670.1923 2.518176544 1.748734608 1.240765209 1.517019905 1.302664184 1.041230886 1.191563055 2.280453567 0.942142147 1 17.55577387 4.664209721 2.634502064 1.397142448 2.652022309 0.487677795 0.370279282 0.370202886 3.733230067 0.097127254 0.94311327 46154.03987 -4.664209721 1.254879861 NMDPLNDNIATLLHQSSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 NMDPLNDNIATLLHQSSDK 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 190.31 1.21E-14 1054400000 236910 336970 330670 437050 277530 338300 389410 363790 342440 466150 FALSE TRUE 227651.2953 327359.9455 390429.4247 459606.2029 286457.0045 345140.6578 394175.7161 356277.6094 303567.6468 434577.2453 0.52384541 0.753283678 0.898412029 1.057593806 0.659162456 0.794198641 0.907032571 0.819825735 0.698535531 1 18.72925311 4.664563756 2.96306607 0.846922327 0.495576418 0.423501648 0.116455114 0.31003506 4.223757415 0.028185116 0.234274816 46191.67985 -4.664563756 -0.351345909 CTYVVLDEADR ddPTM_BT-474_Pertuzumab_2h_R1 1 CTYVVLDEADR 11 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 175.65 2.23E-05 100060000 134890 144090 122810 140460 155480 134570 137520 157230 143570 152540 FALSE TRUE 129618.3497 139980.6943 145004.4989 147709.1574 160481.1554 137291.0976 139203.0109 153983.1456 127272.5355 142208.3299 0.911468053 0.984335407 1.019662484 1.038681472 1.128493355 0.965422333 0.978866786 1.08279976 0.894972436 1 17.11764645 4.66456497 2.212327498 1.021163922 0.892962265 0.197448241 0.060761856 0.770619037 4.912289197 0.014991268 0.181929127 46191.80896 -4.66456497 -0.128201658 S(ph)KSLCHDEIENLLDSDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSLCHDEIENLLDSDHR 18 1 P30305;G8JLH2;B4DIG0;P30305-3;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 S(0.5)KS(0.5)LCHDEIENLLDSDHR;S(0.5)KS(0.5)LCHDEIENLLDSDHR 205.38 5.85E-16 666550000 736180 542610 325210 451770 489910 384870 466230 544380 455630 386650 TRUE FALSE 707409.2717 527135.2941 383982.6813 475085.9038 505668.4001 392652.3351 471935.8622 533138.3628 403908.7926 360461.8511 1.962508014 1.462388579 1.065251926 1.317992188 1.40283472 1.089303442 1.309253284 1.479042404 1.120531316 1 18.45948706 4.664592176 3.149853574 1.260561231 2.014423814 0.67841489 0.152762106 0.169674674 2.691552552 0.036870604 0.282504634 46194.70268 -4.664592176 0.753862583 DSLLDGHFVLATLSDTDSHS(ph)QDLGS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 DSLLDGHFVLATLS(0.003)DT(0.005)DS(0.145)HS(0.847)QDLGS(1)PER 145.01 4.66E-08 20925000 25486 31232 27991 36884 33228 30557 34611 28293 35376 36147 TRUE FALSE 24489.97894 30341.29394 33049.59636 38787.58766 34296.8088 31174.88348 35034.57977 27708.73966 31360.26479 33698.73149 0.726732962 0.900369023 0.980737105 1.151010318 1.017747769 0.925105548 1.039640907 0.822248745 0.930606685 1 15.04040667 4.664825868 2.56926138 0.976346079 0.695795476 0.480681595 0.080923268 0.400729091 3.782918123 0.022402486 0.225400673 46219.56656 -4.664825868 -0.280550603 HNQGDS(ph)DDDVEETHPMDGNDSDYDPKK ddPTM_BT-474_Pertuzumab_2h_R1 1 HNQGDSDDDVEETHPMDGNDSDYDPKK 27 1 Q9P2K3;Q9P2K3-3;B4DV59;Q9P2K3-2;Q9P2K3-4 Q9P2K3 RCOR3 REST corepressor 3 1 HNQGDS(1)DDDVEETHPMDGNDSDYDPKK 138.84 1.31E-06 176230000 148930 126070 99387 77494 89375 98650 91279 49027 139220 81642 TRUE FALSE 143109.6509 122474.607 117348.4418 81493.47463 92249.82804 100644.7706 92396.09971 48014.57532 123416.3293 76112.31462 1.880243055 1.609129976 1.541779965 1.070700254 1.212022371 1.322319142 1.213944158 0.63083846 1.621502774 1 16.21584227 4.665039238 0.632540539 1.074011763 2.373130368 0.490315287 0.24720824 2.509841535 0.810028393 0.114394603 2.343102876 46242.27991 -4.665039238 1.299118605 AGAAAGDS(ph)DEESRADDKGVMDYYLK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGAAAGDSDEESRADDKGVMDYYLK 25 2 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(1)DEESRADDKGVMDYYLK;AGAAAGDS(1)DEESRADDKGVMDYYLK 221.86 5.70E-34 1190240000 1189210 976100 819678 725122 696392 967740 777000 889650 971153 869156 TRUE FALSE 1142734.358 948262.5837 967812.0482 762545.6333 718792.0811 987308.3659 786509.1584 871278.4166 860911.7828 810287.29 1.410282961 1.170279474 1.194406058 0.941080581 0.887083001 1.218467052 0.97065469 1.07527099 1.062477215 1 19.62807399 4.665276737 1.259599276 1.03224051 1.531789777 0.607053756 0.093611488 0.850317739 1.28607259 0.026314385 0.532601634 46267.5749 -4.665276737 0.499549267 ELDALGHELPVLAPQWEGYDELQTDGNR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELDALGHELPVLAPQWEGYDELQTDGNR 28 0 P55957;P55957-2;B2ZP78;P55957-3 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ;;; 275.79 1.50E-61 1061100000 419685 450302 361913 426571 463295 476660 449431 446008 455691 487820 FALSE TRUE 403283.2462 437459.8279 427318.7298 448586.3804 478197.3044 486298.3918 454931.271 436797.7789 403962.8681 454779.5169 0.886766513 0.961916295 0.939617362 0.986382112 1.051492617 1.069305837 1.000333687 0.960460537 0.888260911 1 18.79480775 4.665406275 1.142823143 0.993674474 0.853591434 0.296942762 0.048226672 2.030982291 2.428794977 0.015617872 0.331245192 46281.37734 -4.665406275 -0.14008304 RLS(ph)DPLLPSPEDETGSLVHLEDPER ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSDPLLPSPEDETGSLVHLEDPER 25 1 Q8WYL5-2;Q8WYL5-5;Q8WYL5-4;Q8WYL5 Q8WYL5-2 SSH1 Protein phosphatase Slingshot homolog 1 1 RLS(0.996)DPLLPS(0.003)PEDETGSLVHLEDPER;RLS(0.911)DPLLPS(0.074)PEDET(0.008)GS(0.008)LVHLEDPER;RLS(1)DPLLPSPEDETGSLVHLEDPER;RLS(1)DPLLPSPEDETGSLVHLEDPER 123.45 7.63E-05 179481000 33379.5 39323.5 35358.2 42047.6 41409 40953.7 41539 39668.9 39977.5 40530.6 TRUE FALSE 32074.99224 38202.03228 41748.21328 44217.68167 42740.95809 41781.81187 42047.36671 38849.72335 35439.4218 37785.42636 0.848872047 1.011025572 1.104876067 1.170231116 1.131149287 1.105765262 1.112793232 1.028166865 0.93791245 1 15.20554228 4.665697182 2.740485968 1.080221977 0.823742525 0.516425746 0.065372491 0.298572959 3.329777227 0.017138113 0.158903783 46312.38871 -4.665697182 -0.256479453 LLVGNDDVHIIAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLVGNDDVHIIAR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ;;; 178.67 1.44E-05 1626970000 949720 1034390 879350 1042860 1068460 1172510 1012220 959500 1148990 1122140 FALSE TRUE 912603.8924 1004890.21 1038268.106 1096682.13 1102827.986 1196218.956 1024607.851 939685.9897 1018561.472 1046136.458 0.872356455 0.960572784 0.992478656 1.048316518 1.054191332 1.143463595 0.979420842 0.898244184 0.973641119 1 19.99663962 4.665976047 1.948024408 1.00797709 0.844206095 0.334479732 0.060298027 0.934591269 4.255592294 0.018457012 0.260734569 46342.13595 -4.665976047 -0.163770994 DLDLEPLS(ph)DLEEGLEETR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLDLEPLSDLEEGLEETR 18 0 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 DLDLEPLS(1)DLEEGLEETR;DLDLEPLS(1)DLEEGLEETR;DLDLEPLS(1)DLEEGLEETR;DLDLEPLS(1)DLEEGLEETR 331.38 6.84E-75 382307000 278209 304644 250795 321493 303804 282779 310496 347220 315772 286908 TRUE FALSE 267336.2847 295955.8514 296119.2354 338085.2923 313576.1316 288496.9851 314295.9429 340049.7857 279926.8864 267475.4656 0.99947965 1.106478498 1.107089335 1.263986181 1.172354746 1.078592328 1.175045876 1.271330755 1.046551637 1 18.02904704 4.666268882 1.649281968 1.161148015 0.959377302 0.170917042 0.084314372 1.18946052 3.519971712 0.021918933 0.365889026 46373.39392 -4.666268882 -0.201770713 NQEIPHK ddPTM_BT-474_Pertuzumab_2h_R1 2 NQEIPHK 7 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 73.931 0.047556 977730000 1602060 1539930 1293570 1481280 1539040 1646000 1560160 1635690 1907300 1867490 FALSE TRUE 1539449.724 1496012.704 1527346.874 1557729.038 1588544.619 1679283.248 1579253.705 1601912.43 1690791.3 1741003.239 0.884231396 0.859281976 0.877279743 0.894730695 0.912430594 0.964549181 0.907094065 0.920108817 0.971159193 1 20.73148746 4.666317023 0.087920368 1.088267421 0.655951962 0.775047655 0.02048096 35.24006606 0.506411554 0.639978642 2.16627998 46378.53471 -4.666317023 -0.43231546 GAEILEVLHSLPAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAEILEVLHSLPAVR 15 0 Q15008;Q15008-4;Q15008-3;Q15008-2;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 188.4 3.01E-07 796610000 522750 603250 555020 581870 685790 671200 568920 588140 604620 648100 FALSE TRUE 502320.3521 586045.9006 655324.4604 611900.3804 707849.0582 684772.1239 575882.6131 575994.7035 535986.0724 604203.6097 0.831375953 0.969947698 1.084608648 1.012738704 1.171540598 1.133346628 0.953126734 0.953312251 0.887095118 1 19.20467528 4.666428609 3.260991105 1.024110861 0.818335368 0.334213772 0.081998273 0.353014031 6.099620748 0.022145766 0.163225658 46390.45251 -4.666428609 -0.205775493 LIEDFLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LIEDFLAR 8 0 A6NKE1;A0A087WWM0;O43617;O43617-2 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 ;;; 112.17 0.0071941 134875000 275246 301893 257167 312059 307694 280556 320245 316999 309090 323615 FALSE TRUE 264489.082 293283.3072 303642.7975 328164.4024 317591.257 286229.0345 324164.2541 310452.8599 274003.399 301696.2678 0.876673364 0.972114469 1.006451952 1.087731064 1.052685402 0.948732434 1.074472205 1.029024529 0.908209442 1 18.20273732 4.666459768 2.106289692 1.019852733 0.850418268 0.387525234 0.051765115 0.559066692 3.12207647 0.013078269 0.169576848 46393.78095 -4.666459768 -0.169434465 FAS(ph)ENDLPEWK ddPTM_BT-474_Pertuzumab_2h_R1 2 FASENDLPEWK 11 0 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 1 FAS(1)ENDLPEWK;FAS(1)ENDLPEWK 185.95 4.45E-06 245690000 1699390 1087930 600980 722820 782250 521990 526410 1355210 540950 442430 TRUE FALSE 1632975.96 1056903.302 709590.4547 760124.8268 807411.7817 532544.9954 532852.363 1327224.44 479543.6238 412463.822 3.959076828 2.562414557 1.720370168 1.842888482 1.957533579 1.291131408 1.291876607 3.217796008 1.162631965 1 18.65390806 4.666509806 2.183378869 1.814968514 4.341183043 0.566598921 0.605061048 0.426147147 2.61587434 0.158472272 1.970125223 46399.12668 -4.666509806 2.526214528 IKEEEPDPEEWQLS(ph)GDSTLNTNDLTHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKEEEPDPEEWQLSGDSTLNTNDLTHLR 28 1 A0A494C1G8;A0A494C0Z6;H0Y6K5;A0A494C070;H0Y7L6;Q02447-4;Q02447-3;Q02447-5;Q02447-6;Q02447-2;Q02447 A0A494C1G8 SP3 Transcription factor Sp3 1 IKEEEPDPEEWQLS(1)GDSTLNTNDLTHLR;IKEEEPDPEEWQLS(0.998)GDS(0.001)T(0.001)LNTNDLTHLR 244.49 1.10E-45 208234000 272170 245720 183965 234000 225210 209149 228590 238320 246040 269190 TRUE FALSE 261533.2955 238712.3062 217211.5678 246076.768 232454.0842 213378.1361 231387.5528 233398.6087 218110.5707 250957.5215 1.04214169 0.951206024 0.865531212 0.980551476 0.926268648 0.850255991 0.9220188 0.930032331 0.869113503 1 17.93708366 4.666932037 3.413484135 0.916195471 1.049512313 0.39938859 0.045614827 0.237700408 4.588943854 0.010421335 0.072534033 46444.25887 -4.666932037 0.133316842 CLAFHDISPQAPTHFLVIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 CLAFHDISPQAPTHFLVIPK 20 0 P49773;D6REP8;D6RE99;D6RD60 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 234.65 9.28E-30 5628600000 3788000 3943700 3299400 3974500 3839500 3923800 4069800 3025000 4961600 4903800 FALSE TRUE 3639960.772 3831229.537 3895674.975 4179624.421 3963001.004 4003141.924 4119607.43 2962532.693 4398379.969 4571661.258 0.796200892 0.838038805 0.852135527 0.914246307 0.866862346 0.875642726 0.901118258 0.648021042 0.962096647 1 22.12428708 4.667078527 2.448371524 0.856096597 0.787942551 0.036106795 0.090090292 1.883519057 15.62456662 0.023237603 0.251275805 46459.92746 -4.667078527 -0.068154046 EAEAMALLAEAER ddPTM_BT-474_Pertuzumab_2h_R1 4 EAEAMALLAEAER 13 0 P54920;M0R0Y2;M0R2M1;M0QZM9;M0QZN5;M0R031 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;; 183.4 2.54E-06 215164000 352578 388435 327265 401242 385796 392288 398952 427027 400026 443252 FALSE TRUE 338798.862 377357.2141 386409.0655 421950.1477 398205.4787 400220.3321 403834.4939 418208.7432 354616.7255 413230.1472 0.819879344 0.913188974 0.935094083 1.021102043 0.963640919 0.968516781 0.977262905 1.012047998 0.858157925 1 18.65658598 4.667100805 1.494926167 0.973769211 0.774821589 0.527085457 0.0432339 0.718629828 1.655888655 0.011190301 0.203502481 46462.31075 -4.667100805 -0.198947622 RS(ph)PQEGGSHVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RSPQEGGSHVGR 12 1 Q8TC76 Q8TC76 FAM110B Protein FAM110B 1 RS(1)PQEGGSHVGR;RS(1)PQEGGSHVGR 112.12 0.00080118 139210000 96042 106038 91855 108703 97854 108380 106550 111485 113863 117637 TRUE FALSE 92288.57246 103013.9001 108455.2418 114313.1749 101001.5628 110571.5179 107853.9908 109182.7958 100937.7496 109669.3412 0.841516612 0.939313567 0.988929455 1.042343955 0.920964434 1.008226334 0.983447056 0.995563524 0.920382565 1 16.74280074 4.667872483 2.477686947 0.98361977 0.821825282 0.59345886 0.035357963 0.280374785 2.397263857 0.008371974 0.089459461 46544.94084 -4.667872483 -0.161794488 ATAPQTQHVS(ph)PMR ddPTM_BT-474_Pertuzumab_2h_R1 34 ATAPQTQHVSPMR 13 0 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PK06;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 1 ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.001)QHVS(0.999)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.002)QHVS(0.998)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.001)QHVS(0.999)PMR;ATAPQT(0.001)QHVS(0.999)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR 213.55 5.24E-09 2.07356E+11 26687313.1 29351797.3 25313225.1 30699967.5 29341110.8 32956297.4 33582668.4 30302956.2 34375014.3 38341815.4 TRUE FALSE 25644343.4 28514712.78 29887887.97 32284396.5 30284894.28 33622696.31 33993663.14 29677189.56 30472906.79 35744890.09 0.717426836 0.797728366 0.836144352 0.903189139 0.847251011 0.94062945 0.951007628 0.830249848 0.852510854 1 25.09123368 4.668042302 0.925637308 0.89819318 0.631780917 0.600875163 0.049562929 1.393261155 1.01586934 0.01626191 0.366249926 46563.1446 -4.668042302 -0.266412263 IYDALDVSLIER ddPTM_BT-474_Pertuzumab_2h_R1 3 IYDALDVSLIER 12 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 208.33 1.58E-07 125158000 191207 206314 173148 208168 206560 214571 212420 224907 224635 245606 FALSE TRUE 183734.419 200430.1267 204439.6953 218911.5754 213204.19 218909.7726 215019.6595 220262.5919 199135.3765 228970.8869 0.802435723 0.875352013 0.892863272 0.956067291 0.931141041 0.956059417 0.939069864 0.961967676 0.869697363 1 17.80480465 4.668475709 1.018698322 0.944995967 0.741981096 0.664361248 0.031894528 0.941673902 0.855388275 0.009171553 0.203691219 46609.63578 -4.668475709 -0.203014871 VVNGAAASQPPS(ph)KR ddPTM_BT-474_Pertuzumab_2h_R1 3 VVNGAAASQPPSKR 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 VVNGAAASQPPS(1)KR;VVNGAAASQPPS(1)KR;VVNGAAASQPPS(1)KR 161.91 2.77E-06 1103270000 1317380 882210 548756 472906 577225 478520 345065 896760 591234 448876 TRUE FALSE 1265895.333 857050.2346 647928.4162 497312.7353 595791.9663 488196.0023 349288.0087 878241.5926 524119.595 418473.2287 3.025033016 2.048040772 1.548315093 1.18839797 1.423727793 1.166612268 0.834672291 2.098680471 1.25245669 1 18.67477581 4.668620422 1.568318477 1.343307397 3.51388909 0.737833919 0.320596413 0.495308577 1.284856345 0.090050951 1.584736829 46625.16927 -4.668620422 2.170581693 up EGERPSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EGERPSLR 8 1 Q7L2H7;J3KNJ2;E9PN86;E7ESM3 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ;;; 143.04 0.00055437 2982230000 2643220 2842520 2358760 2990080 2631970 3058800 2885720 3044110 3313980 3329850 FALSE TRUE 2539920.04 2761454.113 2785040.402 3144398.387 2716629.705 3120651.032 2921036.305 2981248.065 2937790.884 3104316.294 0.818189836 0.889553078 0.897150979 1.01291173 0.875113696 1.005261944 0.940959628 0.96035577 0.946356816 1 21.56584413 4.668752481 0.99742439 0.959768551 0.756273477 0.568111023 0.039848588 1.192156862 1.0308204 0.01138539 0.254212298 46639.34908 -4.668752481 -0.203495074 SYGPAPGAGHVQEESNLSLQALESR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYGPAPGAGHVQEESNLSLQALESR 25 0 Q13155 Q13155 AIMP2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 0 ; 378.75 2.93E-120 1221550000 529150 582910 498730 594170 576710 627700 579040 572800 657090 697470 FALSE TRUE 508470.233 566285.9775 588861.6052 624835.1849 595260.4009 640392.5241 586126.4647 560971.4798 582499.8979 650229.7357 0.781985512 0.870901385 0.905620849 0.960945264 0.915461672 0.984871175 0.901414427 0.862728124 0.895837065 1 19.31059001 4.668815704 1.829825867 0.922279086 0.749283471 0.555624717 0.040402861 0.599246217 2.307441855 0.011126783 0.169863635 46646.13917 -4.668815704 -0.172995615 GLFLPEDENLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLFLPEDENLR 11 0 Q12797;Q12797-10 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 0 ; 105.2 0.0058121 124003000 575500 407750 264200 264220 264310 191610 196484 530600 228060 215609 FALSE TRUE 553008.8238 396121.3692 311946.8171 277856.4259 272811.7712 195484.4855 198888.63 519642.9246 202171.5849 201005.6104 2.751210888 1.970698074 1.551930896 1.382331694 1.35723461 0.972532484 0.989468053 2.585216022 1.005800706 1 17.61687624 4.66888514 1.636845846 1.428278735 3.11702144 0.472606936 0.459456823 0.872215198 2.521187513 0.131774913 2.23750843 46653.59766 -4.66888514 1.688742705 IDEPLEGSEDR ddPTM_BT-474_Pertuzumab_2h_R1 6 IDEPLEGSEDR 11 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;; 236.03 3.58E-15 29089940000 3379930 3501810 2922300 3435670 3288420 3504200 3280490 3702390 3769340 3653460 FALSE TRUE 3247838.599 3401941.807 3450424.616 3612985.34 3394195.016 3575057.325 3320637.618 3625934.353 3341460.326 3406007.9 0.953561675 0.9988062 1.013040697 1.060768338 0.996531751 1.049632717 0.974935383 1.064570153 0.981048906 1 21.69965035 4.668923371 2.015951741 1.021795673 0.93996735 0.28494543 0.030241547 0.680545275 3.373492964 0.007055675 0.09718421 46657.7048 -4.668923371 -0.081828323 RDSIVAELDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ; 205.12 2.80E-07 1143820000 415160 483860 432130 506040 484130 400180 572820 533050 479660 520800 FALSE TRUE 398935.0882 470060.7865 510225.5037 532156.785 499702.4811 408271.9138 579830.3425 522042.3312 425211.0077 485525.7521 0.821655878 0.968148001 1.050872176 1.096042347 1.029198717 0.840886219 1.194231902 1.075210386 0.875774366 1 18.88918829 4.668950565 2.672922326 1.030734379 0.796833766 0.268631872 0.09727789 0.48769398 5.081044765 0.024142474 0.23462078 46660.62648 -4.668950565 -0.233900613 RPTPQDS(ph)PIFLPVDDTSFR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPTPQDSPIFLPVDDTSFR 19 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 RPTPQDS(1)PIFLPVDDTSFR;RPT(0.001)PQDS(0.999)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR 179.64 2.17E-14 4862270000 834716 930902 800626 955345 928562 1022471 980230 923295 1002359 1032570 TRUE FALSE 802094.3759 904353.5864 945316.928 1004650.47 958430.04 1043146.064 992226.348 904228.6356 888575.4086 962633.1142 0.83322957 0.939458214 0.982011645 1.043648359 0.995633774 1.083638251 1.030741965 0.939328413 0.923067569 1 19.87662653 4.669091741 1.828788837 1.001097685 0.793963761 0.573574271 0.044294477 0.57518476 2.210534364 0.012763331 0.195181799 46675.79688 -4.669091741 -0.207133924 ISSPTETER ddPTM_BT-474_Pertuzumab_2h_R1 4 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;; 220.88 1.02E-06 4007980000 1133830 1248930 1069100 1282310 1226760 1232230 1265480 1329370 1322270 1408960 FALSE TRUE 1089518.67 1213311.739 1262310.152 1348490.173 1266219.85 1257146.535 1280967.323 1301918.045 1172171.453 1313529.884 0.829458609 0.923703186 0.96100604 1.026615526 0.963982521 0.95707494 0.975209882 0.991159821 0.892382783 1 20.32501759 4.669462885 2.01853376 0.973212541 0.800460953 0.632275454 0.032972595 0.374203543 1.85954158 0.008193452 0.112954005 46715.70257 -4.669462885 -0.172751587 ALQS(ph)PALGLR ddPTM_BT-474_Pertuzumab_2h_R1 5 ALQSPALGLR 10 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR 141.73 3.88E-05 1354080000 1075390 1165630 1006600 1215710 1136650 989100 1238220 1242210 1212140 1170480 TRUE FALSE 1033362.57 1132387.374 1188515.012 1278452.939 1173211.38 1009100.28 1253373.707 1216557.929 1074542.949 1091202.347 0.946994453 1.037742795 1.089179303 1.171600247 1.075154743 0.924759997 1.148617129 1.114878402 0.984732989 1 20.05748722 4.670204288 2.922215499 1.073325406 0.934885236 0.177703794 0.072595513 0.523680564 6.86820612 0.018023198 0.156167666 46795.52109 -4.670204288 -0.13844017 KVYENYPTYDLTER ddPTM_BT-474_Pertuzumab_2h_R1 2 KVYENYPTYDLTER 14 1 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 ; 232.93 5.71E-17 567770000 546365 550465 397973 418517 436652 447098 391022 439582 414675 441115 FALSE TRUE 525012.4518 534766.2772 469895.574 440116.7125 450697.3081 456138.6279 395807.4442 430504.4781 367602.8325 411237.8881 1.276663622 1.300381829 1.142636872 1.070224134 1.095952783 1.109184346 0.962478059 1.046850231 0.893893396 1 18.64961366 4.670322875 0.389116651 0.966694241 1.561262718 0.805277215 0.053565338 2.242747005 0.280855048 0.044289642 0.626560873 46808.30066 -4.670322875 0.594568477 HMNLILCDCDEFRK ddPTM_BT-474_Pertuzumab_2h_R1 2 HMNLILCDCDEFRK 14 1 P14678-2;P14678;P14678-3;J3QLE5;P63162;P63162-2;J3KRY3;S4R3P3 P14678-2;S4R3P3 SNRPB;SNRPN Small nuclear ribonucleoprotein-associated proteins B and B;Small nuclear ribonucleoprotein-associated protein N 0 ; 105.78 0.00063596 1366210000 3096200 2542430 1995840 1981350 2098320 1443230 2155260 1657230 2468220 2467830 FALSE TRUE 2975197.081 2469922.386 2356532.685 2083607.711 2165814.368 1472413.099 2181636.717 1623007.621 2188038.013 2300681.676 1.293180674 1.073561115 1.024275853 0.905647979 0.941379414 0.639989928 0.948256658 0.705446407 0.951039006 1 21.13362995 4.670613354 0.774870275 0.832739367 1.517540275 0.591600027 0.110501491 1.472064643 0.722058505 0.038364239 0.860499745 46839.619 -4.670613354 0.684800908 DQST(ph)PIIEVEGPLLSDTHVTFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQSTPIIEVEGPLLSDTHVTFK 22 0 P49116;P49116-2 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 DQS(0.113)T(0.887)PIIEVEGPLLSDTHVTFK 158.77 7.50E-11 184890000 145460 151800 109860 136280 125830 141860 125050 134990 152980 140270 TRUE FALSE 139775.2624 147470.8126 129714.1458 143313.4271 129877.4362 144728.5064 126580.3993 132202.4093 135614.3517 130769.388 1.068868369 1.127716623 0.991930511 1.09592489 0.993179201 1.106746071 0.967966596 1.010958386 1.037049679 1 16.99666533 4.671052916 0.299799043 0.99953408 1.161160103 0.22055378 0.04692811 10.01223532 0.761928349 0.050104793 0.597240796 46887.05072 -4.671052916 0.161626022 QAVEQQIQSHR ddPTM_BT-474_Pertuzumab_2h_R1 4 QAVEQQIQSHR 11 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 227.93 3.64E-12 5388450000 3044780 3335470 2851840 3407530 3140730 3524320 3584280 3304290 3513080 3933840 FALSE TRUE 2925786.631 3240345.661 3367230.927 3583393.032 3241754.433 3595584.165 3628145.491 3236055.257 3114289.886 3667397.513 0.797782793 0.883554523 0.9181527 0.977094253 0.883938657 0.980418445 0.989297036 0.882384646 0.849182527 1 21.80632522 4.671306293 1.844045621 0.93293884 0.766104711 0.428893321 0.048955887 0.713881361 2.793136369 0.012840418 0.196502587 46914.41371 -4.671306293 -0.166834129 GPAST(ph)PTYSPAPTQPAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GPAST(0.93)PT(0.067)YS(0.003)PAPTQPAPR 334.61 1.95E-52 0 95267 103680 81646 109550 100260 106590 104690 104680 104660 105240 TRUE FALSE 91543.86032 100723.1479 96401.24841 115203.8886 103484.954 108745.3228 105971.2275 102518.3214 92779.43557 98112.00106 0.933054665 1.026613939 0.982563268 1.174207919 1.054763463 1.10837942 1.080104639 1.044911125 0.945648183 1 16.582142 4.671340302 1.473638849 1.059653506 0.900542238 0.241092424 0.061419789 1.371264896 3.02832363 0.016495182 0.308117523 46918.08759 -4.671340302 -0.159111268 SLAPDRS(ph)DDEHDPLDNTSRPR ddPTM_BT-474_Pertuzumab_2h_R1 7 SLAPDRSDDEHDPLDNTSRPR 21 2 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 SLAPDRS(1)DDEHDPLDNTSRPR;S(0.001)LAPDRS(0.928)DDEHDPLDNT(0.057)S(0.014)RPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(0.994)DDEHDPLDNT(0.005)S(0.001)RPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR 262.78 5.38E-37 26544430000 4227900 4701360 4071500 4824950 4683550 5086840 4654230 4554790 5017370 5335490 TRUE FALSE 4062668.994 4567281.816 4807310.62 5073966.248 4834200.639 5189699.39 4711189.859 4460731.995 4447819.192 4974112.51 0.816762585 0.918210396 0.966466 1.020074684 0.971871993 1.043341778 0.947141797 0.896789525 0.894193524 1 22.24600771 4.671789267 2.425590949 0.96370875 0.794934931 0.504736181 0.045350163 0.433976852 3.48950321 0.012828592 0.143294595 46966.6157 -4.671789267 -0.168773819 EEGFGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEGFGLR 7 0 Q86TU7;Q6NXR6;Q86TU7-3;Q86TU7-2 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 0 100.74 0.046513 0 34424 42456 38149 43717 52523 47997 50674 42499 44006 49214 FALSE TRUE 33078.67202 41245.19645 45043.37292 45973.23961 54212.45 48967.53223 51294.16357 41621.3808 39010.62337 45880.69194 0.720971516 0.898966312 0.981750079 1.002017138 1.181596173 1.067279724 1.117990191 0.907165499 0.850262315 1 15.48559953 4.672493712 1.566853787 1.020563975 0.633638519 0.507586825 0.089718447 0.823600387 2.118419514 0.026319736 0.470514334 47042.85948 -4.672493712 -0.386925456 LDSDAGFHS(ph)LPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDSDAGFHSLPR 12 0 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 LDSDAGFHS(1)LPR 129.38 0.00015155 90473000 136430 87802 48580 51827 48054 42516 32742 94233 44935 36320 TRUE FALSE 131098.1648 85297.97293 57359.48666 54501.79768 49599.70055 43375.70265 33142.70639 92287.05562 39834.16718 33860.01405 3.871769355 2.519135781 1.694018395 1.609621236 1.464845835 1.281030261 0.978815494 2.725546879 1.176436818 1 15.04729495 4.672512096 1.655722288 1.561869228 4.518558679 0.710468829 0.474854963 0.495420157 1.465964164 0.131850999 2.248064747 47044.85084 -4.672512096 2.956689451 GGGGGQDNGLEGLGNDS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 GGGGGQDNGLEGLGNDSR 18 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 GGGGGQDNGLEGLGNDS(1)R 273.6 5.41E-39 341130000 249810 289430 271120 307750 269560 287820 283340 292750 291260 367870 TRUE FALSE 240047.149 281175.7398 320117.415 323633.0144 278230.6422 293639.9176 286807.5997 286704.6102 258197.3859 342953.8372 0.699940117 0.819864685 0.933412548 0.943663488 0.811277239 0.856208287 0.836286312 0.835986011 0.752863382 1 18.38765487 4.672627969 3.582812067 0.862718621 0.691292183 0.357939592 0.068463638 0.268978165 5.883246399 0.016270829 0.108743455 47057.40441 -4.672627969 -0.171426438 LSTDHIPILYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSTDHIPILYR 11 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 72.2 0.046945 1372640000 1197950 1348270 1134690 1463420 1267360 1297370 1499740 1382510 1454500 1614310 FALSE TRUE 1151132.79 1309818.66 1339753.724 1538947.282 1308125.785 1323603.71 1518094.267 1353960.685 1289391.258 1504971.346 0.764886848 0.870327972 0.890218759 1.022575802 0.869203117 0.879487649 1.008719715 0.89965878 0.856754689 1 20.52130459 4.672644462 1.730784861 0.92792607 0.724205328 0.435073527 0.057700223 0.7485887 2.481002653 0.014735165 0.241323261 47059.19154 -4.672644462 -0.203720743 ANNIDYTVHSVR ddPTM_BT-474_Pertuzumab_2h_R1 3 ANNIDYTVHSVR 12 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;; 214.81 4.29E-11 1457110000 585620 654650 566780 660880 671260 732390 676840 622750 744420 782360 FALSE TRUE 562733.323 635980.023 669209.754 694988.096 692851.6875 747199.4276 685123.3704 609889.9949 659916.5625 729370.0603 0.771533346 0.87195795 0.917517445 0.952860741 0.949931626 1.024444885 0.939335747 0.836187318 0.90477605 1 19.47629145 4.672860891 1.73061471 0.93443007 0.729365348 0.538055595 0.048619695 0.737908369 2.444120804 0.01460768 0.239467982 47082.6492 -4.672860891 -0.205064722 YIHPDDELVLEDELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIHPDDELVLEDELQR 16 0 C9IZD2;C9J8Z7;C9JLE1;F8W8R3;A0A087WWF6;P49005 C9IZD2 POLD2 DNA polymerase delta subunit 2 0 ; 199.68 3.75E-11 498640000 508460 570200 483420 596090 586650 639520 570390 553460 606740 653720 FALSE TRUE 488588.8211 553938.4543 570784.7476 626854.2763 605520.13 652451.5326 577370.6034 542030.8576 537865.4189 609442.9621 0.801697372 0.908925837 0.936567953 1.028569227 0.99356325 1.070570296 0.947374306 0.889387344 0.882552515 1 19.21713168 4.673174214 1.794883306 0.966811042 0.7621307 0.466382991 0.055166725 0.782642466 2.846337039 0.016401966 0.259908356 47116.62934 -4.673174214 -0.204680342 RPLEQQQPHHIPTSAPVYQQPQQQPVAQS(ph)YGGYKEPAAPVSIQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPLEQQQPHHIPTSAPVYQQPQQQPVAQSYGGYKEPAAPVSIQR 44 2 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 RPLEQQQPHHIPTSAPVYQQPQQQPVAQS(0.317)Y(0.296)GGY(0.296)KEPAAPVS(0.091)IQR 56.933 0.0086579 297430000 33128 30616 18625 22157 24907 23692 22700 8657.2 27404 20312 TRUE FALSE 31833.32114 29742.86166 21990.95181 23300.52543 25708.15627 24171.06847 22977.80939 8478.425795 24293.21281 18936.25015 1.681078402 1.570683817 1.161315025 1.230471991 1.357616005 1.276444295 1.213429756 0.447735203 1.282894587 1 14.20886305 4.673803543 0.325331833 0.864158882 2.252743887 0.432504524 0.239409188 6.082510423 0.539335594 0.268428322 3.366030197 47184.95478 -4.673803543 1.388585005 SHSS(ph)SPQSVLWNRPQPSEDRLPSQQGLAEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHSSSPQSVLWNRPQPSEDRLPSQQGLAEAR 31 2 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 S(0.003)HS(0.152)S(0.66)S(0.166)PQS(0.018)VLWNRPQPSEDRLPSQQGLAEAR 66.173 0.0031285 165810000 22458 29773 27168 36756 29658 37804 34111 23204 26514 44790 TRUE FALSE 21580.31653 28923.90319 32077.86195 38652.98156 30611.9765 38568.42278 34528.46062 22724.82929 23504.24188 41756.33341 0.516815409 0.692683022 0.768215486 0.925679494 0.733109783 0.923654441 0.826903557 0.54422473 0.562890464 1 15.34970741 4.674041468 2.497903176 0.767332876 0.481370195 0.245057247 0.141458713 0.71623088 6.205498317 0.037593445 0.408365314 47210.81176 -4.674041468 -0.285962681 FNEEHIPDSPFVVPVASPSGDAR ddPTM_BT-474_Pertuzumab_2h_R1 6 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ;;;;; 168.55 9.52E-12 8860630000 1411743 1523977 1317878 1509653 1474540 1564684 1482294 1507623 1641477 1677731 FALSE TRUE 1356570.523 1480514.668 1556047.871 1587566.372 1521969.918 1596322.983 1500434.757 1476490.058 1455143.413 1564096.785 0.867318785 0.946562056 0.994853954 1.015005201 0.97306633 1.020603711 0.959297898 0.943988935 0.930341029 1 20.57689836 4.674147684 2.929807061 0.977156491 0.85637273 0.593313082 0.02803816 0.253079619 3.334541386 0.007551845 0.066295832 47222.35964 -4.674147684 -0.120783762 SSATIQNET(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSATIQNETPK 11 0 F5GX09;Q5HYJ3-3;Q5HYJ3-2;Q5HYJ3 F5GX09 FAM76B Protein FAM76B 1 SSATIQNET(1)PK 211.83 0.0017909 0 509110 412760 329720 311470 297650 285410 317570 441810 373180 402480 TRUE FALSE 489213.4183 400988.4889 389307.7386 327545.004 307224.1826 291181.1857 321456.5167 432686.4691 330818.1709 375219.6711 1.30380536 1.068676617 1.037546186 0.872941984 0.818784851 0.776028573 0.856715523 1.153155078 0.881665319 1 18.51737594 4.674157285 1.359069131 0.920491405 1.427618676 0.575131327 0.103110847 0.968648472 1.742427471 0.032808617 0.654822517 47223.4036 -4.674157285 0.507127271 AAELWGEQAEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAELWGEQAEAR 12 0 Q08379;Q08379-2 Q08379 GOLGA2 Golgin subfamily A member 2 0 ; 158.08 0.00016286 456650000 334080 374940 311090 388380 413790 358040 392750 390380 396120 403220 FALSE TRUE 321023.7843 364247.0783 367310.8832 408424.3383 427099.9311 365279.8141 397556.592 382318.5166 351154.1183 375909.5502 0.853992095 0.968975324 0.977125702 1.086496308 1.136177389 0.971722623 1.057585772 1.017049225 0.934145243 1 18.52002604 4.674215648 1.5692381 1.030559965 0.805442421 0.465829944 0.055455676 0.817111493 2.104074 0.015142436 0.272168502 47229.75018 -4.674215648 -0.225117545 EDAANNYAR ddPTM_BT-474_Pertuzumab_2h_R1 10 EDAANNYAR 9 0 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ;;;;;;;;; 232.37 4.46E-08 34009803000 8882132 9659944 8280406 9806975 9132704 9689443 10506865 9764871 11045046 11291931 FALSE TRUE 8535008.462 9384451.855 9776859.561 10313114.16 9426465.718 9885370.176 10635451.16 9563223.001 9791258.683 10527118.46 0.81076398 0.89145495 0.92873084 0.979671142 0.895445963 0.939038562 1.010290822 0.908436914 0.930098652 1 23.32760725 4.674447159 1.596355207 0.947072396 0.771110973 0.599953566 0.035360429 0.618451933 1.662503211 0.009191 0.163000385 47254.93374 -4.674447159 -0.175961423 FEIWDTAGQER ddPTM_BT-474_Pertuzumab_2h_R1 6 FEIWDTAGQER 11 0 P20339-2;P20339;P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;K7ENY4;F8VWU4;F8VVZ0;F8VUA5;P61020;P61020-2 P20339-2;P51148;P61020 RAB5A;RAB5C;RAB5B Ras-related protein Rab-5A;Ras-related protein Rab-5C;Ras-related protein Rab-5B 0 ;;;;; 197.79 1.30E-07 1221128000 1161438 1600180 1208371 2250630 1376242 1108007 1955340 2095390 1868320 1909680 FALSE TRUE 1116047.719 1554544.433 1426750.52 2366785.284 1420510.074 1130411.661 1979270.036 2052119.464 1656236.146 1780335.673 0.626874884 0.873174906 0.801394109 1.329403955 0.797888901 0.634942993 1.111739806 1.152658735 0.93029431 1 20.76371785 4.674937135 1.400378309 0.991393913 0.518333338 0.241899396 0.18735454 1.648094549 3.188413858 0.054157258 1.062968261 47308.27741 -4.674937135 -0.473060575 ASS(ph)LNFLNK ddPTM_BT-474_Pertuzumab_2h_R1 6 ASSLNFLNK 9 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;AS(0.001)S(0.999)LNFLNK;AS(0.001)S(0.999)LNFLNK 197.07 3.00E-05 6695200000 33880500 21301800 13337710 9564770 12336630 8888080 7741960 28527420 9912870 10394250 TRUE FALSE 32556412.6 20694293.52 15748130.89 10058408.93 12733448.91 9067803.067 7836708.422 27938318.81 8787602.556 9690238.189 3.359712317 2.135581512 1.625154159 1.037993982 1.314049114 0.935766788 0.80872196 2.883140565 0.906851038 1 23.2081007 4.675010128 1.745061363 1.396721385 3.865371563 0.547031563 0.576449238 0.683988024 2.306329941 0.164022284 2.691223206 47316.22936 -4.675010128 2.468650178 WGTIEVENTTHCEFAYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 WGTIEVENTTHCEFAYLR 18 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 150.91 5.15E-08 91556000 76427 88454 77131 91067 94074 103700 102910 91776 93013 103980 FALSE TRUE 73440.14835 85931.37853 91070.28747 95766.97878 97099.97565 105796.8851 104169.4434 89880.79353 82454.55418 96937.34198 0.757604313 0.886463119 0.939475806 0.987926601 1.001677719 1.091394533 1.074605939 0.927205055 0.850596401 1 16.5647649 4.675020481 1.24858723 0.993192604 0.670623391 0.556171468 0.064475325 1.047172648 1.529427405 0.020113173 0.422705951 47317.3573 -4.675020481 -0.322569213 SIIECVDDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIIECVDDFR 10 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 137.95 0.00018038 125663000 165792 181615 147221 184067 190538 189785 175280 186809 181845 204092 FALSE TRUE 159312.6653 176435.518 173827.1096 193566.7199 196666.8278 193622.5827 177425.1291 182951.3289 161202.718 190268.6671 0.837303734 0.927296758 0.913587677 1.017333663 1.033626981 1.017627262 0.932497882 0.961542075 0.847237333 1 17.53767848 4.675578761 1.433606747 0.970066427 0.798867049 0.359189551 0.053176717 1.236032652 2.532020507 0.015166676 0.293609093 47378.22227 -4.675578761 -0.171199378 DHASIQMNVAEVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHASIQMNVAEVDK 14 0 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 ; 125.89 8.86E-05 1133780000 1091500 1529130 1448330 1996280 1522570 1604650 1717550 1191990 1789710 2294000 FALSE TRUE 1048842.973 1485520.71 1710075.449 2099308.25 1571544.847 1637097.122 1738569.891 1167374.99 1586549.624 2138625.337 0.490428574 0.694614753 0.799614322 0.98161572 0.734838786 0.76549038 0.812938041 0.545852969 0.741854871 1 21.02825233 4.675711579 2.832239105 0.773067937 0.45958271 0.353409643 0.123208043 0.442448342 5.330524417 0.03202496 0.296400823 47392.71388 -4.675711579 -0.313485227 QRLT(ph)PRPS(ph)PSPMIESTPMSIAGDATPLLDEMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QRLTPRPSPSPMIESTPMSIAGDATPLLDEMDR 33 2 Q7KZ85;Q7KZ85-3;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 2 QRLT(0.831)PRPS(0.457)PS(0.457)PMIES(0.114)T(0.114)PMS(0.025)IAGDATPLLDEMDR 84.962 0.00080303 33581000 9782 14237 13559 16814 16513 15615 18606 14679 12385 13714 TRUE FALSE 9399.708625 13830.9747 16009.41292 17681.77255 17044.15564 15930.746 18833.70579 14375.87352 10979.10672 12785.13856 0.735205847 1.081800923 1.252189238 1.382994206 1.333122481 1.246036241 1.4730936 1.124420627 0.858739752 1 13.64218018 4.675724163 2.470694207 1.232484794 0.661758271 0.400633583 0.172515676 0.426714146 3.583082093 0.043548995 0.483414513 47394.08712 -4.675724163 -0.570726523 DVDETGITVASLER ddPTM_BT-474_Pertuzumab_2h_R1 1 DVDETGITVASLER 14 0 Q8WU90;H7C466 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 147.62 1.86E-05 73551000 40166 44226 42626 38006 44949 46871 39771 45634 49179 46107 FALSE TRUE 38596.26831 42964.71778 50329.46641 39967.49421 46394.82541 47818.76373 40257.72939 44691.64195 43596.4061 42984.13182 0.897918992 0.999548344 1.170884796 0.929819739 1.079347737 1.112474807 0.936571886 1.039724197 1.014244193 1 15.39151655 4.676036982 4.241665071 1.03500404 0.894193641 0.254449161 0.070167975 0.253252002 8.386100154 0.016015144 0.089461299 47428.23702 -4.676036982 -0.140810399 VYQWDDPDPR ddPTM_BT-474_Pertuzumab_2h_R1 5 VYQWDDPDPR 10 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 205.59 3.86E-07 61388300000 8536620 9887730 8348220 10761670 9832780 10508810 11167880 10803890 11192340 11530100 FALSE TRUE 8202999.453 9605741.622 9856929.059 11317081.08 10149060.3 10721305.34 11304555.86 10580785.9 9921832.485 10749156.06 0.763129627 0.893627516 0.916995623 1.052834382 0.944172756 0.997409032 1.051669154 0.98433643 0.923033625 1 23.35772006 4.67608483 1.213326579 0.993825451 0.677185036 0.744090535 0.041318846 0.643690976 0.875994396 0.011672216 0.249676312 47433.46275 -4.67608483 -0.316640415 AGAESPT(ph)MSVDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGAESPTMSVDGR 13 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 AGAES(0.324)PT(0.676)MSVDGR 232.83 9.61E-13 1396900000 478580 538310 471790 538990 529550 470980 608390 605990 485410 600000 TRUE FALSE 459876.5645 522957.9259 557052.9479 566807.3385 546583.4567 480503.5383 615835.6588 593476.0947 430308.2918 559361.4656 0.822145594 0.934919472 0.995872941 1.01331138 0.977156079 0.859021523 1.100961894 1.060988522 0.769284833 1 19.09342134 4.676445525 2.575290542 0.982584552 0.800152442 0.189922912 0.090834776 0.641409853 6.006653477 0.022552687 0.237923675 47472.87403 -4.676445525 -0.182432111 ELFDYNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELFDYNLR 8 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ; 114.28 0.0062496 244580000 751890 905370 810350 963960 924510 897560 988780 914430 967210 1093160 FALSE TRUE 722505.3075 879549.734 956798.2711 1013710.091 954247.7038 915709.2782 1000880.985 895546.7009 857416.3757 1019119.3 0.708950667 0.863048845 0.938848152 0.994692272 0.936345435 0.898530014 0.982103848 0.878745699 0.841330722 1 19.95889151 4.676962978 2.45494879 0.930107943 0.675547932 0.663695194 0.048560163 0.2747554 2.264347116 0.01230636 0.138501704 47529.47071 -4.676962978 -0.254560012 YDS(ph)SNQVK ddPTM_BT-474_Pertuzumab_2h_R1 3 YDSSNQVK 8 0 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YDS(0.888)S(0.112)NQVK;YDS(0.827)S(0.173)NQVK;YDS(0.905)S(0.095)NQVK 78.342 0.032386 971570000 1371640 1090290 778460 795680 808960 726790 613799 1039190 986030 965990 TRUE FALSE 1318034.792 1059195.997 919145.0387 836745.1402 834980.9331 741486.1918 621310.8558 1017730.363 874100.0082 900562.6369 1.46356815 1.176149169 1.020634214 0.929135971 0.927176966 0.823358822 0.689914094 1.130105027 0.970615449 1 19.7804671 4.677022005 1.282676683 0.922398994 1.664883729 0.709803302 0.107755118 0.715534401 1.112535981 0.032557964 0.679196353 47535.93112 -4.677022005 0.742484735 ESDTKNEVNGTSEDIKSEGDTQS(ph)N ddPTM_BT-474_Pertuzumab_2h_R1 2 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGTSEDIKSEGDT(0.176)QS(0.824)N;ESDTKNEVNGTSEDIKSEGDT(0.127)QS(0.873)N 168.26 8.42E-12 1511040000 1264440 1008710 728520 613040 900470 939990 816840 997910 1225150 878270 TRUE FALSE 1215024.287 979942.5784 860179.7698 644679.0679 929434.4353 958997.2418 826836.7323 977302.8098 1086076.108 818783.9906 1.483937523 1.196826745 1.050557631 0.787361594 1.135139971 1.171245717 1.009835001 1.193602734 1.326450102 1 19.64312337 4.677200114 2.84613998 1.088132598 1.527207023 0.441763619 0.135490837 0.341814542 4.166726009 0.034812827 0.322157602 47555.43006 -4.677200114 0.439074425 ERPIS(ph)LGIFPLPAGDGLLTPDAQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPISLGIFPLPAGDGLLTPDAQK 24 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 ERPIS(1)LGIFPLPAGDGLLTPDAQK 159.75 1.30E-11 107970000 329640 230200 144160 154990 186310 173830 139960 275050 203880 158170 TRUE FALSE 316757.3044 223634.9214 170212.9188 162989.0525 192302.8304 177344.9617 141672.8723 269370.1214 180736.3971 147457.005 2.148133311 1.516611038 1.154322365 1.10533272 1.304128145 1.202689297 0.960774107 1.826770599 1.225688784 1 17.16993483 4.677317436 2.762856637 1.266400728 2.252518172 0.594416108 0.229902267 0.277800248 3.130927383 0.060075976 0.57913571 47568.27861 -4.677317436 0.986117444 ELEEDFIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEEDFIK 8 0 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 ; 103.56 0.011047 65275000 167935 189270 173501 199304 168355 160429 189570 209777 207600 211214 FALSE TRUE 161371.9145 183872.2049 204856.4902 209590.1033 173770.2915 163672.9843 191890.0144 205445.0316 184034.1183 196908.2877 0.819528302 0.93379617 1.040364998 1.064404682 0.882493538 0.831214299 0.974514667 1.043353909 0.934618449 1 17.58716431 4.677425414 3.62846586 0.972631512 0.811151915 0.297812787 0.069707689 0.319765183 7.283096515 0.018474133 0.123726254 47580.10694 -4.677425414 -0.161479597 LEATLQEEAAIQQEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEATLQEEAAIQQEHR 16 0 O95202 O95202 LETM1 "LETM1 and EF-hand domain-containing protein 1, mitochondrial" 0 68.41 0.049075 228210000 69655 101980 84362 148810 91491 115040 132390 109570 100310 97688 FALSE TRUE 66932.80559 99071.63025 99608.09002 156490.1019 94433.89111 117366.1876 134010.2284 107307.3412 88923.22933 91071.50475 0.734947839 1.087844442 1.093734976 1.718321251 1.03692029 1.288725688 1.47148363 1.178275702 0.976411113 1 16.4747121 4.677529249 1.827452143 1.250661619 0.615792147 0.308599028 0.218474186 0.832752822 3.150017434 0.054943235 0.870867478 47591.48424 -4.677529249 -0.634869472 LLSAEFLEQHYDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLSAEFLEQHYDR 13 0 Q9Y376 Q9Y376 CAB39 Calcium-binding protein 39 0 ;;; 236.42 1.03E-16 1792100000 1403790 1597390 1391040 1740730 1611960 1544400 1646330 1564540 1704930 1773740 FALSE TRUE 1348928.335 1551834.001 1642431.872 1830569.284 1663810.157 1575628.826 1666478.279 1532231.702 1511393.494 1653603.01 0.815751016 0.938456203 0.993244365 1.107018597 1.006172671 0.952845887 1.007786191 0.926601907 0.914000207 1 20.65718149 4.678133034 2.656742029 0.986789884 0.79377936 0.514934353 0.050658888 0.351659535 3.569741094 0.013791012 0.140654925 47657.69501 -4.678133034 -0.193010525 S(ph)MGNLLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SMGNLLEK 8 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 S(1)MGNLLEK 80.014 0.027844 288850000 272200 180900 103300 146460 109330 92983 116440 250830 126930 130760 TRUE FALSE 261562.1231 175740.9091 121968.6079 154018.8182 112846.6987 94863.17997 117865.0276 245650.2728 112521.4385 121903.5087 2.145648848 1.441639465 1.000534022 1.263448606 0.925705092 0.778182523 0.966871494 2.01512061 0.923036914 1 16.89538013 4.678549027 2.8563824 1.169672879 2.254159309 0.466062351 0.331964807 0.361850272 4.448471554 0.091260525 0.845419805 47703.36632 -4.678549027 1.08448643 S(ph)LDFFR ddPTM_BT-474_Pertuzumab_2h_R1 8 SLDFFR 6 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR 175.24 0.0044722 498992000 686401 510585 323535.5 376815 326198.3 241635.4 293311.3 584254 320142.2 292887.5 TRUE FALSE 659575.6901 496023.6157 382005.5619 396262.4673 336690.7646 246521.4333 296900.9314 572188.9507 283800.9996 273049.9687 2.41558603 1.816603818 1.3990317 1.45124524 1.233073807 0.902843661 1.087350175 2.095546663 1.039373859 1 18.05880547 4.678832047 1.466065493 1.321359204 2.781206827 0.556370517 0.321836183 0.894646773 1.92810729 0.095692281 1.845325806 47734.46362 -4.678832047 1.459847623 EMFSQLADLDDELDGMGAIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EMFSQLADLDDELDGMGAIGR 21 0 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5;A0A669KB06 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 ; 188.39 5.90E-17 45053000 40704 53726 46755 63318 59135 60495 55864 57278 64829 70460 FALSE TRUE 39113.24268 52193.78708 55204.66856 66585.84957 61037.13098 61718.25035 56547.68034 56095.18928 57469.88371 65687.68144 0.595442583 0.794574964 0.840411282 1.013673311 0.929202091 0.939571149 0.860856695 0.853968173 0.874895908 1 16.00333522 4.678978041 1.61056497 0.910850988 0.506486913 0.76947302 0.054362585 0.451349145 1.231879015 0.015394368 0.275853561 47750.5129 -4.678978041 -0.404364075 LLSGPSQES(ph)PQTLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLSGPSQESPQTLGK 15 0 Q9BWE0;Q9BWE0-4;C9JZE3;C9JYJ8;E7EVL6 Q9BWE0 REPIN1 Replication initiator 1 1 LLSGPS(0.001)QES(0.981)PQT(0.019)LGK 111.77 0.00085629 334350000 106050 119520 109300 115830 102660 134660 125840 118880 118510 133170 TRUE FALSE 101905.4488 116111.4066 129052.9414 121808.0002 105962.1521 137382.9175 127380.0676 116425.0865 105057.2416 124150.2773 0.820823368 0.935248871 1.039489755 0.981133533 0.853499118 1.106585668 1.026015168 0.937775485 0.846210286 1 16.92172796 4.679066531 3.578912642 0.973803597 0.811798286 0.26668366 0.075965807 0.327317946 7.224103099 0.018498154 0.126859216 47760.24337 -4.679066531 -0.162005311 RSIS(ph)SPNVNR ddPTM_BT-474_Pertuzumab_2h_R1 3 RSISSPNVNR 10 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RSIS(0.568)S(0.431)PNVNR;RS(0.002)IS(0.585)S(0.413)PNVNR;RS(0.235)IS(0.684)S(0.081)PNVNR 153.52 9.87E-06 993650000 616420 452240 299006 350844 386340 327766 286429 555210 299378 250977 TRUE FALSE 592329.6249 439342.558 353043.0356 368951.1009 398766.977 334393.6531 289934.4038 543744.7195 265393.8645 233978.1042 2.531560066 1.877707999 1.508872109 1.576861656 1.704291854 1.429166435 1.239151863 2.323912835 1.13426795 1 17.836014 4.679099264 2.321195877 1.57066161 2.697042421 0.440023042 0.35213658 0.493177937 3.490752192 0.087460114 1.066732161 47763.84319 -4.679099264 1.126380811 LNSEQSQALQHQQETGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNSEQSQALQHQQETGR 17 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ; 203.59 9.54E-12 309570000 54816 71887 67678 71752 76453 74522 87723 82987 72549 72909 FALSE TRUE 52673.73012 69836.85314 79908.92009 75455.12932 78912.18018 76028.8859 88796.58031 81273.28945 64313.54167 67970.80849 0.774946353 1.027453619 1.175635863 1.110110811 1.160971628 1.118552031 1.306392881 1.195708735 0.946193566 1 16.05262766 4.679110688 2.335776887 1.146148329 0.711591062 0.539359787 0.096661317 0.346293102 2.492217881 0.023966051 0.290058016 47765.09962 -4.679110688 -0.434557268 EDS(ph)CHRLSPVKGEFHQEFQPEPSLLGDSTNSGEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EDSCHRLSPVKGEFHQEFQPEPSLLGDSTNSGEER 35 2 Q9Y2L9-2;Q9Y2L9;Q9Y2L9-3 Q9Y2L9-2 LRCH1 Leucine-rich repeat and calponin homology domain-containing protein 1 1 EDS(0.5)CHRLS(0.5)PVKGEFHQEFQPEPSLLGDSTNSGEER 118.22 1.62E-06 114170000 42778 47811 42186 49622 43473 51128 54355 32496 62482 61821 TRUE FALSE 41106.18847 46447.47709 49809.94862 52182.99737 44871.34853 52161.84319 55020.21275 31824.94624 55389.30531 57633.80861 0.713230471 0.80590678 0.864248777 0.905423373 0.778559488 0.905056328 0.954651689 0.552192316 0.961055787 1 15.81462774 4.679462936 3.11986781 0.838728399 0.70204719 0.098926057 0.122367939 0.817720406 12.67192648 0.030556885 0.251873344 47803.85673 -4.679462936 -0.136681209 LVTSIGDVVNHDPVVGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LVTSIGDVVNHDPVVGDR 18 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;;;; 289.61 3.89E-49 10692650000 3400980 4024420 3534260 4247410 4306840 4350450 4211540 4165240 4279610 4517090 FALSE TRUE 3268065.942 3909647.482 4172979.401 4466619.339 4445373.42 4438419.08 4263082.086 4079226.338 3793806.614 4211143.471 0.776051912 0.928405197 0.990937362 1.060666627 1.05562146 1.053970046 1.012333613 0.968674273 0.900897023 1 22.0057806 4.679753685 1.958345665 1.008521783 0.723891494 0.706465762 0.045209196 0.389564515 1.757934911 0.012858282 0.191522315 47835.87088 -4.679753685 -0.284630289 LFDFPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 LFDFPGR 7 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 117.62 0.012074 1228854000 3041820 3493070 3046220 3665630 3573010 3569490 3456070 3709650 3617570 3834620 FALSE TRUE 2922942.311 3393451.064 3596739.717 3854813.604 3687939.112 3641667.533 3498366.418 3633044.431 3206918.62 3574897.772 0.817629621 0.949244225 1.00610981 1.078300374 1.031620859 1.01867739 0.978592016 1.016265265 0.897065825 1 21.76947056 4.680458091 2.344609942 1.007016988 0.785826337 0.624391619 0.043512147 0.313279079 2.27271005 0.011059457 0.134037015 47913.52141 -4.680458091 -0.221190651 AGASCVCCSQPQQSSTS(ph)PPPSDALQWVVVEVSGTPNQLETHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGASCVCCSQPQQSSTSPPPSDALQWVVVEVSGTPNQLETHR 42 0 Q13952-3;Q13952 Q13952-3 NFYC Nuclear transcription factor Y subunit gamma 1 AGASCVCCSQPQQSST(0.012)S(0.985)PPPS(0.003)DALQWVVVEVSGTPNQLETHR;AGASCVCCSQPQQSS(0.009)T(0.178)S(0.811)PPPS(0.001)DALQWVVVEVSGTPNQLETHR 161.5 1.93E-19 75490000 49541 52112 44049 50150 53135 52802 52887 49691 54892 56123 TRUE FALSE 47604.88295 50625.81678 52009.63416 52738.24751 54844.13553 53869.69262 53534.24693 48664.86349 48660.89029 52321.73922 0.909849016 0.967586658 0.994034888 1.007960521 1.048209336 1.029585282 1.023174071 0.930107909 0.930031972 1 15.67512288 4.68064263 2.228866183 0.994502368 0.894235835 0.335005073 0.036697076 0.734941424 4.6586708 0.010713163 0.138263601 47933.88508 -4.68064263 -0.100266533 AGTGVDNVDLEAATR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGTGVDNVDLEAATR 15 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YFM8;A0A286YER3;A0A286YFC8;A0A286YFB2 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ; 240.75 1.74E-17 475580000 311010 353850 294100 375100 353160 381560 365630 392470 370110 393440 FALSE TRUE 298855.3854 343758.5445 347250.4122 394458.956 364519.7121 389275.4046 370104.6893 384365.3573 328096.6644 366791.9584 0.814781727 0.937203056 0.946723079 1.075429673 0.993805082 1.061297544 1.009031635 1.04791108 0.894503429 1 18.48460248 4.680907166 1.315539474 1.015556335 0.745954606 0.582748691 0.049729677 0.782080818 1.286126978 0.01320374 0.275280068 47963.09124 -4.680907166 -0.269601729 KQIS(ph)VR ddPTM_BT-474_Pertuzumab_2h_R1 1 KQISVR 6 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 1 KQIS(1)VR 106.04 0.019882 1282200000 4444100 2585900 1034000 1742500 2026000 1269800 1226000 3789000 1645200 1372500 TRUE FALSE 4270419.659 2512152.664 1220866.801 1832430.634 2091168.13 1295476.226 1241004.155 3710755.826 1458443.793 1279539.353 3.337466449 1.963325832 0.954145567 1.432101819 1.63431326 1.012455165 0.969883538 2.900071669 1.139819413 1 20.28719309 4.681353915 3.297847768 1.495197552 3.481885701 0.514794739 0.565451508 0.246543256 4.419015334 0.147454238 1.136489515 48012.45518 -4.681353915 1.986688149 TTS(ph)FAESCKPVQQPSAFGSMK ddPTM_BT-474_Pertuzumab_2h_R1 5 TTSFAESCKPVQQPSAFGSMK 21 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 1 T(0.001)T(0.031)S(0.968)FAESCKPVQQPSAFGSMK;TT(0.003)S(0.997)FAESCKPVQQPSAFGSMK;T(0.001)T(0.005)S(0.994)FAESCKPVQQPSAFGSMK;T(0.026)T(0.026)S(0.948)FAESCKPVQQPSAFGSMK;T(0.092)T(0.092)S(0.817)FAESCKPVQQPSAFGSMK 253.98 1.35E-36 5333310000 7362100 4938950 3218060 2730280 3077240 2567810 2253709 5493860 3659160 2597641 TRUE FALSE 7074380.993 4798095.982 3799635.027 2871190.078 3176222.219 2619732.878 2281290.565 5380409.871 3243787.497 2421700.461 2.92124526 1.981292096 1.568994633 1.185609089 1.311566922 1.081774117 0.942020122 2.221748708 1.339466854 1 21.207589 4.681356026 1.618375668 1.370009869 3.374761154 0.676029176 0.343542967 0.593125679 1.63252951 0.10025103 1.806037563 48012.68864 -4.681356026 2.004751285 AIEVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AIEVGR 6 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 142.63 0.026758 3650600000 1746810 1948550 1701370 1964240 1896840 2043730 1989940 1991860 1942700 2047450 FALSE TRUE 1678542.734 1892979.262 2008845.406 2065614.662 1957853.581 2085055.621 2014293.481 1950727.395 1722172.84 1908774.388 0.879382469 0.991724991 1.052426844 1.082168052 1.025712412 1.092353101 1.055281071 1.021979029 0.902240124 1 20.86421516 4.681517257 2.793073478 1.034254298 0.860888821 0.439898823 0.050391821 0.32699866 3.778792366 0.012519029 0.121178331 48030.51651 -4.681517257 -0.173365476 QEAGISEGQGTAGEEEEKKK ddPTM_BT-474_Pertuzumab_2h_R1 3 QEAGISEGQGTAGEEEEKKK 20 2 O43583;F8VVL1 O43583 DENR Density-regulated protein 0 ;; 196.89 9.61E-22 806300000 1188312 902048 651287 475220 744586 781316 737914 928754 1047938 765935 FALSE TRUE 1141871.453 876322.4742 768989.0487 499746.1612 768536.2849 797114.7448 746944.8123 909574.9053 928980.4716 714057.5402 1.599130867 1.227243499 1.076928686 0.699868194 1.076294614 1.116317243 1.046056893 1.273811779 1.300988253 1 19.44568081 4.681949715 2.585674539 1.081968163 1.671440549 0.511696567 0.155147462 0.375961017 3.534205517 0.042235138 0.454383121 48078.36772 -4.681949715 0.589472386 FAGVDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 FAGVDIR 7 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ; 120.9 0.010447 496030000 1689320 1837620 1588170 1850960 1857520 1683430 1883150 1917870 1825710 1930630 FALSE TRUE 1623299.507 1785212.877 1875187.648 1946488.267 1917268.818 1717470.108 1906196.553 1878265.314 1618463.055 1799866.71 0.901899845 0.991858378 1.041848064 1.081462453 1.065228223 0.95422072 1.059076509 1.043558005 0.899212728 1 20.77945864 4.682046488 2.945926055 1.024220276 0.888968289 0.29558286 0.052966139 0.389255284 5.181299365 0.012836098 0.115784653 48089.08212 -4.682046488 -0.135251987 EALNIIGDISTSTVSTPVPPPVDDTWLQS(ph)ASSHSPTPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EALNIIGDISTSTVSTPVPPPVDDTWLQSASSHSPTPQR 39 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7ENE7 P50570-2 DNM2 Dynamin-2 1 EALNIIGDISTSTVSTPVPPPVDDT(0.146)WLQS(0.201)AS(0.201)S(0.201)HS(0.201)PT(0.051)PQR 130.88 1.49E-08 500520000 123980 145610 134610 144640 130690 159290 156030 148440 135540 170190 TRUE FALSE 119134.7245 141457.3454 158937.0214 152104.8877 134893.7625 162510.9529 157939.5418 145374.6621 120154.0674 158662.8797 0.750867025 0.89155917 1.001727825 0.958667131 0.850191064 1.024253141 0.995441039 0.916248731 0.757291609 1 17.27560511 4.682602087 3.427527864 0.937982062 0.737580949 0.342840931 0.077595222 0.289635993 5.74797487 0.018666092 0.137379258 48150.6425 -4.682602087 -0.200401113 S(ph)PSSDSWTCADTSTER ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSSDSWTCADTSTER 16 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 S(0.673)PS(0.327)SDSWTCADTSTER;S(0.997)PS(0.003)SDSWTCADTSTER 264.31 5.54E-27 934220000 228300 281070 265220 287740 295460 294180 277510 299110 277840 288990 TRUE FALSE 219377.7836 273054.1588 313151.1538 302590.2959 304963.7392 300128.5212 280906.2504 292933.274 246300.768 269416.4499 0.814270189 1.013502178 1.162331231 1.123132222 1.131941793 1.113994789 1.042646989 1.087288004 0.914200926 1 18.03947842 4.682704727 3.369493438 1.079624263 0.794432792 0.548639713 0.069536547 0.188008731 3.568334937 0.016723113 0.12595989 48162.02368 -4.682704727 -0.285191471 S(ph)DSELEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDSELEVR 8 0 Q9BQK8-2;Q9BQK8 Q9BQK8-2 LPIN3 Phosphatidate phosphatase LPIN3 1 S(0.997)DS(0.003)ELEVR;S(0.997)DS(0.003)ELEVR 123.6 0.0014065 188420000 171460 206219 185516 209797 206784 168855 258940 230470 219960 221700 TRUE FALSE 164759.1536 200337.836 219042.868 220624.6483 213435.3952 172269.3638 262108.9852 225710.714 194991.0629 206684.0615 0.797154616 0.969295042 1.059795643 1.067448775 1.032664994 0.833491284 1.268162544 1.092056699 0.943425736 1 17.65706761 4.682734794 2.298019141 1.048607094 0.752172015 0.316827609 0.105263066 0.592717105 4.061671559 0.026804794 0.336506193 48165.35811 -4.682734794 -0.296435078 TGSS(ph)PTQGIVNK ddPTM_BT-474_Pertuzumab_2h_R1 5 TGSSPTQGIVNK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 TGS(0.025)S(0.975)PTQGIVNK;TGS(0.003)S(0.996)PT(0.001)QGIVNK;TGS(0.037)S(0.956)PT(0.007)QGIVNK;TGS(0.058)S(0.941)PTQGIVNK;TGS(0.019)S(0.981)PTQGIVNK 289.31 4.66E-36 2290170000 4766370 4406350 3455500 3917190 3952650 3908890 4167380 4700530 4605990 4191700 TRUE FALSE 4580094.991 4280685.212 4079985.717 4119356.645 4079790.577 3987930.434 4218381.643 4603462.413 4083137.325 3907792.425 1.172041524 1.095422875 1.044064084 1.054139063 1.044014147 1.020507233 1.079479456 1.178021223 1.044870577 1 21.89792241 4.682756537 3.195115819 1.069259301 1.180969203 0.341085834 0.046127532 0.401687699 6.629068996 0.012704837 0.102841797 48167.76961 -4.682756537 0.111709902 QADLYISEGLHPR ddPTM_BT-474_Pertuzumab_2h_R1 6 QADLYISEGLHPR 13 0 P40227;Q92526-3;Q92526 P40227 CCT6A;CCT6B T-complex protein 1 subunit zeta;T-complex protein 1 subunit zeta-2 0 ;;;;; 220.4 2.09E-11 6885460000 4826790 5495370 4709710 5856240 5396800 5930870 5551270 5497630 5802360 6589690 FALSE TRUE 4638153.711 5338647.428 5560859.364 6158481.248 5570392.973 6050796.255 5619208.103 5384102.019 5143700.418 6143364.427 0.754985931 0.869010376 0.905181425 1.002460675 0.906733279 0.984932007 0.914679272 0.876409349 0.837277436 1 22.55059754 4.682902757 1.994087909 0.924860713 0.717651158 0.520746739 0.050972021 0.547357846 2.576177606 0.013418175 0.198708146 48183.98971 -4.682902757 -0.207209555 GVVDSEDLPLNISR ddPTM_BT-474_Pertuzumab_2h_R1 8 GVVDSEDLPLNISR 14 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 ;;;;;;; 375.57 5.51E-97 11575268000 7617909 8412335 6975703 8743340 8302277 9123690 8592837 8664223 8837629 8807750 FALSE TRUE 7320192.694 8172423.442 8236367.706 9194584.825 8569327.28 9308177.263 8697998.71 8485303.767 7834418.406 8211193.247 0.891489516 0.99527842 1.003065871 1.119762323 1.043615346 1.133596176 1.059285593 1.033382544 0.954114484 1 22.96916046 4.682965472 1.535972362 1.051982826 0.844161218 0.458241065 0.050555842 0.852163408 2.050306586 0.013713843 0.259415945 48190.94829 -4.682965472 -0.207821608 ATSLPSIPNPFPELCS(ph)PPSQS(ph)PILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 ATSLPSIPNPFPELCS(0.847)PPS(0.424)QS(0.729)PILGGPSSAR;ATSLPSIPNPFPELCS(0.964)PPS(0.25)QS(0.785)PILGGPSSAR 153.01 3.84E-09 140083000 48578 79229 77446 95588 90931 116021 107293 77686 88250 103068 TRUE FALSE 46679.51805 76969.46649 91442.21498 100521.3081 93855.8782 118367.0241 108606.0838 76081.75695 78232.22997 96087.11256 0.48580415 0.801038396 0.951659515 1.046147662 0.976779047 1.231872006 1.130287725 0.791799805 0.814180257 1 16.55205533 4.683750465 1.727137326 0.995103152 0.34601081 0.618327965 0.123288342 0.604412689 1.956139482 0.036365871 0.624527679 48278.13278 -4.683750465 -0.649092342 EQMQPTHPIR ddPTM_BT-474_Pertuzumab_2h_R1 6 EQMQPTHPIR 10 0 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 ;;;;; 124.1 0.00044442 2753273000 979408 1197280 966850 1392928 1245918 1293909 1304714 1165485 1341705 1334733 FALSE TRUE 941131.6526 1163134.747 1141581.302 1464817.181 1285994.084 1320072.727 1320681.48 1141417.327 1189400.273 1244330.345 0.756335853 0.934747554 0.917426234 1.177193168 1.03348286 1.060869995 1.061359217 0.917294456 0.955855716 1 20.24693811 4.683844699 1.542818303 1.020147862 0.681065794 0.558260624 0.071517749 0.779401232 1.893661052 0.020542295 0.388565951 48288.60941 -4.683844699 -0.339082068 VDIAEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDIAEGR 7 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 97.798 0.027295 1129120000 1767430 2077860 1822760 2301600 1901910 2070110 2109480 2197390 2262290 2412200 FALSE TRUE 1698356.882 2018601.467 2152173.279 2420385.852 1963086.662 2111969.043 2135296.447 2152013.129 2005484.323 2248819.545 0.755221505 0.897627145 0.957023556 1.076291718 0.872940946 0.939145627 0.949518805 0.956952341 0.891794243 1 21.10073647 4.684027129 2.533148096 0.954091031 0.725700399 0.568057248 0.052796087 0.310542734 2.755694444 0.012909173 0.144056625 48308.89786 -4.684027129 -0.228390632 LEGYWGEAQSLCQAVDEHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEGYWGEAQSLCQAVDEHLR 20 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 ;;; 245.03 6.22E-30 373011000 368013 464296 354638 552447 458345 445230 538868 502404 567846 507408 FALSE TRUE 353630.6451 451054.7327 418728.9755 580958.8559 473088.0832 454232.8557 545462.8278 492029.1818 503386.5027 473040.8042 0.747569009 0.953521829 0.885185742 1.228136877 1.000099947 0.960240325 1.153098893 1.040141099 1.064150277 1 18.85160511 4.684098613 1.165965176 1.05919205 0.636439651 0.53316976 0.086897372 1.077350161 1.318404068 0.024303182 0.543062602 48316.85001 -4.684098613 -0.422752399 SAS(ph)VNKEPVSLPGIMR ddPTM_BT-474_Pertuzumab_2h_R1 8 SASVNKEPVSLPGIMR 16 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.008)AS(0.992)VNKEPVSLPGIMR;SAS(1)VNKEPVSLPGIMR;S(0.196)AS(0.804)VNKEPVSLPGIMR;S(0.008)AS(0.992)VNKEPVSLPGIMR;S(0.007)AS(0.993)VNKEPVSLPGIMR;S(0.003)AS(0.997)VNKEPVSLPGIMR;S(0.026)AS(0.974)VNKEPVSLPGIMR;S(0.049)AS(0.951)VNKEPVSLPGIMR 223.44 5.28E-15 4521770000 4216776 3294830 2295416 2613079 2672671 1992356 2372599 4452681 3194753 2771632 TRUE FALSE 4051979.732 3200864.674 2710248.732 2747940.32 2758639.89 2032642.803 2401635.576 4360731.581 2832098.033 2583906.896 1.568160114 1.238769353 1.048895661 1.063482715 1.067623564 0.786654816 0.929459022 1.687650429 1.096052663 1 21.30112266 4.68417716 2.898479318 1.119432738 1.618660657 0.293155382 0.222812079 0.533011172 6.785317864 0.062492743 0.582041656 48325.5895 -4.68417716 0.499227919 S(ph)RNHIMGRY(ph)FS(ph)NQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRNHIMGRYFSNQSK 15 2 A4D0V7 A4D0V7 CPED1 Cadherin-like and PC-esterase domain-containing protein 1 3 S(1)RNHIMGRY(1)FS(1)NQSK 56.851 0.038754 154260000 172470 212300 193460 216670 208000 262890 221000 207110 233440 286920 TRUE FALSE 165729.6817 206245.4119 228422.5255 227852.3647 214690.5089 268205.8159 223704.6641 202833.1061 206940.8699 267486.6528 0.619581127 0.771049358 0.853958592 0.851827044 0.802621389 1.002688594 0.836320847 0.758292438 0.77364933 1 18.02910738 4.684621569 2.094959014 0.848581129 0.571060227 0.459762692 0.079346839 0.576871843 3.08287798 0.020525388 0.289943503 48375.0658 -4.684621569 -0.277520902 DDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_BT-474_Pertuzumab_2h_R1 8 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.002)HS(0.998)AEDS(1)EDEKEDHKNVR;DDS(0.001)HS(0.999)AEDS(1)EDEKEDHKNVR;DDS(0.005)HS(0.995)AEDS(1)EDEKEDHKNVR;DDSHS(1)AEDS(1)EDEKEDHKNVR;DDS(0.143)HS(0.86)AEDS(0.997)EDEKEDHKNVR;DDS(0.106)HS(0.894)AEDS(1)EDEKEDHKNVR;DDS(0.013)HS(0.987)AEDS(1)EDEKEDHKNVR;DDS(0.025)HS(0.975)AEDS(1)EDEKEDHKNVR 230.03 1.05E-25 14363680000 11391580 8091970 5724951 4423943 6543905 6304898 6263133 5411848 9147220 6058489 TRUE FALSE 10946384.46 7861194.938 6759576.997 4652263.228 6754395.647 6432387.357 6339783.095 5300091.448 8108865.934 5648142.144 1.938050456 1.3918196 1.196778839 0.823680267 1.195861484 1.13885012 1.122454594 0.938377844 1.435669593 1 22.42934497 4.684646881 1.793525492 1.087727168 2.158084706 0.728428642 0.155780704 0.371104646 1.321484218 0.039031104 0.649293753 48377.88533 -4.684646881 1.070357538 SAS(ph)QS(ph)SLDKLDQELKEQQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 S(0.394)AS(0.605)QS(0.539)S(0.462)LDKLDQELKEQQK 76.152 0.007178 427480000 1024000 743550 498490 391740 560560 654680 611390 755040 905020 653090 TRUE FALSE 983980.9479 722344.682 588578.2319 411957.7483 578590.9215 667918.0782 618872.3737 739448.1601 802285.9238 608855.6326 1.616115373 1.186397306 0.966695881 0.676609899 0.950292468 1.097005665 1.016451751 1.214488494 1.317694837 1 19.21574066 4.684792675 2.908065513 1.034548368 1.680998717 0.54534944 0.161065576 0.290092559 3.724170253 0.044230606 0.41125236 48394.12865 -4.684792675 0.646450349 RPRDS(ph)PTLSNSGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPRDSPTLSNSGIR 14 2 Q9HD20;Q9HD20-2;Q9HD20-3 Q9HD20 ATP13A1 Manganese-transporting ATPase 13A1 1 RPRDS(0.979)PT(0.02)LS(0.001)NSGIR 74.618 0.025628 133030000 104480 93444 71557 88760 79144 79546 71977 110740 91309 92976 TRUE FALSE 100396.8061 90779.06861 84488.94168 93340.91424 81689.73864 81154.47462 72857.87606 108453.1803 80943.98512 86678.65271 1.158264497 1.047305949 0.974737597 1.076861618 0.942443567 0.936268298 0.840551552 1.251209807 0.933839909 1 16.40338911 4.684856083 2.937611691 1.007020038 1.174976781 0.178782052 0.103920502 0.657251565 8.668987687 0.026535203 0.243385701 48401.19489 -4.684856083 0.167956743 VLTLSERPLDFLDLERPPT(ph)TPQNEEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLTLSERPLDFLDLERPPTTPQNEEIR 27 2 Q9GZY8-5;Q9GZY8-2;Q9GZY8;C9JHF5;A0A0A0MS29;Q9GZY8-4;Q9GZY8-3 Q9GZY8-5 MFF Mitochondrial fission factor 1 VLTLSERPLDFLDLERPPT(0.5)T(0.5)PQNEEIR;VLTLSERPLDFLDLERPPT(0.588)T(0.412)PQNEEIR 164.7 4.91E-10 488850000 60758 96192 74460 152379 84469 107525 110877 112008 100295 94241 TRUE FALSE 58383.51019 93448.69834 87916.57835 160243.2985 87186.0221 109699.2292 112233.9459 109694.9957 88909.93207 87857.97313 0.664521478 1.063633669 1.000667045 1.823890226 0.992351849 1.248597313 1.277447475 1.248549127 1.011973403 1 16.4228856 4.685097936 1.724973578 1.232371736 0.521782506 0.319861376 0.235990018 0.90109807 2.900461204 0.05895738 1.019337387 48428.15634 -4.685097936 -0.71058923 KAS(ph)GSENEGDYNPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.872)GS(0.128)ENEGDYNPGR;KAS(0.982)GS(0.018)ENEGDYNPGR;KAS(0.935)GS(0.065)ENEGDYNPGR 189.61 1.54E-07 4549280000 1663540 1392300 996676 1323390 1350120 1007651 1297570 1465190 1227550 1220310 TRUE FALSE 1598527.018 1352592.967 1176797.524 1391690.316 1393547.836 1028026.394 1313450.05 1434933.314 1088203.67 1137657.317 1.405104151 1.188928289 1.034404215 1.223294832 1.224927591 0.903634494 1.154521692 1.261305398 0.956530279 1 20.11763463 4.685363726 3.236547221 1.116736579 1.430099084 0.380150318 0.117254813 0.315326113 5.388525086 0.028446331 0.228904075 48457.80367 -4.685363726 0.313362505 NSLLAGGDDDTMSVISGIS(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVIS(0.001)GIS(0.5)S(0.5)R 199.89 8.15E-22 54563000 112400 66185 33034 43867 38102 27555 25768 81191 27350 21379 TRUE FALSE 108007.2837 64297.4686 39003.97864 46130.98113 39327.58543 28112.18098 26083.35649 79514.37748 24245.34266 19930.98129 5.419065031 3.22600617 1.956952248 2.314536372 1.973188619 1.410476513 1.308684009 3.989486334 1.216465076 1 14.28272512 4.685472018 2.047968991 2.063353234 6.161643769 0.633174823 0.817905233 0.431433606 2.168586228 0.217118903 3.15818072 48469.88818 -4.685472018 4.098290534 NEEDEGHSNSS(ph)PRHS(ph)EAATAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NEEDEGHSNSSPRHSEAATAQR 22 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.042)NS(0.447)S(0.512)PRHS(0.951)EAAT(0.048)AQR;NEEDEGHS(0.003)NS(0.451)S(0.546)PRHS(0.993)EAAT(0.007)AQR 136.66 5.54E-06 86268000 81032 49695 22429 46696 35630 28508 35576 44362 53796 41205 TRUE FALSE 77865.17985 48277.74726 26482.41923 49105.98616 36776.07131 29084.45129 36011.38973 43445.9092 47689.30361 38414.14865 2.026992205 1.256769939 0.689392325 1.278330716 0.957357448 0.757128618 0.9374512 1.130987168 1.24145153 1 15.22935016 4.685572212 3.327600575 1.005117868 2.109138746 0.746523289 0.179559857 0.130041095 2.393055836 0.043466931 0.337165412 48481.07174 -4.685572212 1.104020878 up REFEER ddPTM_BT-474_Pertuzumab_2h_R1 2 REFEER 6 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ; 116.88 0.037191 580810000 262710 298610 243735 333590 304820 284410 328780 303530 301790 307500 FALSE TRUE 252443.0028 290093.9352 287783.3364 350806.6199 314624.8121 290160.9651 332803.708 297261.9994 267532.0644 286672.7511 0.880596435 1.01193411 1.003874052 1.22371805 1.09750512 1.01216793 1.160918527 1.036938454 0.93323158 1 18.12904525 4.685673584 1.755528865 1.069708663 0.83328579 0.308977959 0.08008494 0.93778969 3.154728361 0.020960641 0.357397511 48492.3894 -4.685673584 -0.236422874 DSIVAELDR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSIVAELDR 9 0 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ;; 143.04 0.00023938 1373930000 1508460 1658380 1436840 1600250 1670260 1604540 1780190 1728870 1648200 1772000 FALSE TRUE 1449507.716 1611084.626 1696508.95 1682839.094 1723985.43 1636984.898 1801976.498 1693168.23 1461103.246 1651980.862 0.877436143 0.975244123 1.026954361 1.018679534 1.043586805 0.990922435 1.090797442 1.02493211 0.88445531 1 20.65576554 4.68571254 2.464998602 1.016362525 0.855145609 0.385091755 0.04987904 0.4415602 3.633460133 0.012235524 0.14257082 48496.73929 -4.68571254 -0.161216916 HQEGEIFDTEKEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HQEGEIFDTEKEK 13 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 206.06 3.90E-08 1451750000 2618000 2032300 1511010 1331170 1725270 1751260 1713740 1474900 2484300 1899830 FALSE TRUE 2515685.666 1974340.794 1784083.119 1399871.843 1780764.876 1786671.677 1734713.263 1444442.8 2202292.679 1771152.822 1.420366235 1.114720745 1.007300498 0.790373268 1.005427005 1.008762008 0.979426078 0.815538209 1.243423296 1 20.75625727 4.686360875 1.959440525 0.961298558 1.526419535 0.56081033 0.117213714 0.456131179 2.038415389 0.02921781 0.447653955 48569.19157 -4.686360875 0.565120977 EKEKEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKEKEER 7 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 63.486 0.044513 45169000 135040 101190 63487 77632 90108 82484 95637 96852 95625 96938 FALSE TRUE 129762.4875 98304.16028 74960.51316 81638.59682 93006.40565 84151.88299 96807.43421 94851.97235 84770.05089 90372.30292 1.435865673 1.087768676 0.82946335 0.903358598 1.029147235 0.931168956 1.071206897 1.049569053 0.938009193 1 16.46359307 4.686540594 3.423828593 0.97752727 1.470125596 0.796705274 0.070641736 0.11782033 2.341411933 0.018458109 0.138404128 48589.29454 -4.686540594 0.492598326 EAEAAEAEEPWGEEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAEAAEAEEPWGEEAR 16 0 E7EN32;A0A5F9ZHS3;O00255-3;O00255-2;O00255 E7EN32 MEN1 Menin 0 191.06 2.48E-12 0 53507 62302 54455 69955 60302 62106 65984 62424 62001 67466 FALSE TRUE 51415.88728 60525.20796 64296.22984 73565.38593 62241.66859 63361.82587 66791.53193 61134.92259 54962.90641 62896.46773 0.817468598 0.962298999 1.02225502 1.169626667 0.989589254 1.007398796 1.061928187 0.97199294 0.873863166 1 15.94069138 4.6866273 2.690177359 1.015439947 0.790962783 0.410837483 0.070001948 0.393948108 4.095430377 0.017871791 0.186370425 48598.99635 -4.6866273 -0.224477164 EVPAHSTEVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVPAHSTEVGR 11 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;; 240.85 1.06E-15 2303280000 899520 1095320 965260 1193790 1114520 1261360 1158120 1093470 1152500 1347050 FALSE TRUE 864365.7639 1064082.546 1139703.954 1255401.645 1150369.548 1286865.563 1172293.419 1070889.462 1021673.032 1255813.104 0.688291722 0.847325564 0.907542652 0.999672357 0.91603563 1.024726975 0.933493539 0.85274589 0.813555002 1 20.26019034 4.686818311 1.966366361 0.927651499 0.632969802 0.587208042 0.062357951 0.510168451 2.299273506 0.017115872 0.261781726 48620.37571 -4.686818311 -0.294681697 EWTAWMMEADPDLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EWTAWMMEADPDLSR 15 0 Q08AF3;B4E128 Q08AF3 SLFN5 Schlafen family member 5 0 ; 184.03 1.12E-06 185065000 273440 308540 257110 323800 317180 329810 314980 326620 319880 327470 FALSE TRUE 262753.6625 299740.7413 303575.4964 340511.3568 327382.3828 336478.9842 318834.8195 319875.1829 283568.5634 305290.1652 0.860668611 0.981822461 0.994383478 1.115369559 1.072364655 1.102161231 1.044366494 1.047774279 0.928849324 1 18.21982159 4.686905343 1.540370871 1.048303429 0.804335912 0.527128315 0.051408387 0.742121968 1.787161192 0.013898533 0.26638267 48630.12024 -4.686905343 -0.243967517 VDSSTNSSPSPQQSESLS(ph)PAHTSDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDSSTNSSPSPQQSESLSPAHTSDFR 26 0 F2Z3H6;Q9BQE9-2;Q9BQE9-3;Q9BQE9 F2Z3H6 BCL7B B-cell CLL/lymphoma 7 protein family member B 1 VDSSTNSSPSPQQSES(0.001)LS(0.999)PAHTSDFR 306.94 9.48E-72 468210000 70691 90200 71958 111060 87807 90522 104180 97655 98474 103970 TRUE FALSE 67928.31757 87627.58432 84962.4113 116791.8199 90631.3919 92352.41686 105454.986 95638.39012 87295.64436 96928.01929 0.700811985 0.904048024 0.876551609 1.204933524 0.935038109 0.952793811 1.087972155 0.986694981 0.900623421 1 16.56462615 4.686979285 1.459452326 1.00456527 0.60776926 0.513395822 0.08820881 0.828572139 1.743574422 0.023315293 0.46514155 48638.40053 -4.686979285 -0.39679601 WIVEER ddPTM_BT-474_Pertuzumab_2h_R1 6 WIVEER 6 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;;;; 129.16 0.037954 4290570000 4192550 4769610 4138280 4915540 4777380 5082370 4820900 4874280 4992960 5334060 FALSE TRUE 4028700.511 4633585.393 4886159.252 5169231.608 4931048.766 5185139.004 4879899.616 4773624.415 4426180.113 4972779.365 0.810150665 0.931789861 0.982581147 1.039505522 0.991608194 1.042704416 0.981322367 0.959950978 0.890081741 1 22.24562099 4.687040929 2.203891887 0.986937489 0.775667014 0.636816912 0.040325938 0.366008211 2.22828835 0.010759881 0.144895381 48645.30479 -4.687040929 -0.211270475 EVSSRPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 EVS(0.059)S(0.048)RPS(0.446)T(0.446)PGLS(0.001)VVSGISATSEDIPNK 180.16 1.12E-17 447550000 121860 140790 161890 217240 195370 211200 255010 239410 316120 312460 TRUE FALSE 117097.5765 136774.807 191147.1242 228451.7824 201654.2535 215470.6087 258130.8887 234466.0998 280235.3829 291296.8059 0.401987163 0.469537613 0.656193684 0.784257767 0.692263868 0.739694375 0.886143904 0.804904465 0.962026968 1 18.15213036 4.687238202 0.305613167 0.968054658 5.81E-19 0.893320209 0.060325459 2.380834531 0.186391021 0.070735185 0.867141649 48667.40641 -4.687238202 -0.968054658 down GLVVDMDGFEEER ddPTM_BT-474_Pertuzumab_2h_R1 9 GLVVDMDGFEEER 13 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;;;;;; 351.07 1.36E-75 4606986000 3099777 3503466 2992012 3677613 3515011 3618805 3663622 3611053 3725591 3828896 FALSE TRUE 2978634.288 3403550.58 3532735.125 3867415.048 3628074.521 3691979.717 3708458.502 3536483.494 3302677.529 3569561.463 0.834453845 0.953492639 0.989683232 1.083442627 1.016392226 1.03429504 1.038911513 0.990733324 0.925233411 1 21.76731541 4.687269749 1.88614175 1.013977486 0.790791817 0.65879779 0.038522999 0.436510907 1.763213961 0.010314279 0.165070293 48670.94166 -4.687269749 -0.223185669 LVEDMENK ddPTM_BT-474_Pertuzumab_2h_R1 1 LVEDMENK 8 0 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 157.86 0.00086109 160220000 164990 177480 154160 157730 175160 166240 174430 193370 194440 186450 FALSE TRUE 158542.0084 172418.4442 182020.1413 165870.4642 180794.1805 169601.4867 176564.7265 189376.8419 172367.9864 173821.5754 0.912096257 0.99192775 1.04716656 0.954257052 1.040113576 0.975721721 1.015781419 1.089489849 0.991637465 1 17.40724764 4.687438248 3.138535278 1.018787862 0.901830225 0.404649791 0.036682718 0.293524135 4.620300462 0.009276402 0.07860311 48689.82888 -4.687438248 -0.116957637 VNNGNTAPEDSS(ph)PAKK ddPTM_BT-474_Pertuzumab_2h_R1 3 VNNGNTAPEDSSPAKK 16 1 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 VNNGNTAPEDS(0.032)S(0.968)PAKK;VNNGNTAPEDS(0.129)S(0.871)PAKK;VNNGNTAPEDS(0.352)S(0.648)PAKK 188.84 6.82E-10 1234460000 937210 797630 622900 623880 618380 612620 740630 785050 879410 829330 TRUE FALSE 900582.7971 774882.3734 735471.8863 656078.5216 638270.7543 625007.5961 749694.0515 768838.4432 779583.0636 773158.7404 1.164809696 1.002229339 0.951255994 0.848568977 0.825536492 0.808381984 0.969650878 0.994412147 1.00830919 1 19.56040512 4.687879825 1.906913408 0.920772735 1.223439151 0.519510411 0.070154905 0.632239832 2.624995774 0.020592722 0.326761189 48739.36031 -4.687879825 0.302666416 SQS(ph)PINCIRPSVLGPLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSPINCIRPSVLGPLKR 18 2 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.025)QS(0.974)PINCIRPSVLGPLKR 61.985 0.043438 286370000 133640 117570 87498 99247 90076 94693 105690 98627 106320 112970 TRUE FALSE 128417.2011 114217.0187 103310.835 104369.1496 92973.37634 96607.75734 106983.4658 96590.31798 94250.99933 105318.4413 1.219323031 1.084492111 0.980937752 0.990986463 0.882783444 0.91729194 1.01580943 0.917126353 0.894914492 1 16.68439855 4.688022007 1.162407465 0.939213708 1.339771927 0.810590962 0.042082805 0.576508226 0.696708752 0.012143514 0.275180695 48755.31955 -4.688022007 0.400558218 ELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.163)S(0.837)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNSNHDGADET(0.163)S(0.837)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 268.5 2.58E-68 2738640000 1482350 1275080 1001560 951990 1134700 1321160 1176080 1051800 1417890 1209810 TRUE FALSE 1424418.123 1238715.967 1182564.172 1001122.318 1171198.656 1347874.76 1190473.219 1030079.962 1256937.071 1127868.491 1.262929264 1.098280497 1.048494732 0.88762327 1.038417746 1.195063761 1.055507116 0.913297934 1.114435842 1 20.10516743 4.688167357 2.134539836 1.025020671 1.31147055 0.409718956 0.083911667 0.601533414 3.357821629 0.022543312 0.316742533 48771.63976 -4.688167357 0.286449879 VMDDLDR ddPTM_BT-474_Pertuzumab_2h_R1 5 VMDDLDR 7 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;; 130.04 0.0083798 2909310000 4182670 4612010 3933220 4674510 4681620 4391940 4911650 4863050 4965380 5247280 FALSE TRUE 4019206.632 4480479.99 4644040.348 4915762.021 4832208.559 4480748.036 4971760.242 4762626.318 4401730.879 4891877.052 0.821608268 0.915902003 0.949337095 1.004882578 0.987802536 0.915956797 1.016329762 0.973578499 0.89980407 1 22.22195671 4.688284312 1.682314772 0.971331608 0.778952863 0.618622566 0.035583826 0.544799595 1.636126655 0.009170611 0.164311243 48784.77566 -4.688284312 -0.192378744 EPVGILTSNHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EPVGILTSNHR 11 0 P43155-2;P43155;P43155-3 P43155-2 CRAT Carnitine O-acetyltransferase 0 134.98 0.0013662 0 96786 180240 150880 309160 180710 152790 245130 209460 172380 212390 FALSE TRUE 93003.49612 175099.7317 178147.3723 325115.7846 186522.7013 155879.5185 248129.9743 205134.5778 152812.1451 198004.6361 0.469703629 0.884321373 0.899713137 1.641960466 0.942011788 0.787251862 1.253152346 1.036008963 0.77176044 1 17.59517468 4.688338823 1.946411102 1.061057062 0.33612662 0.343979801 0.239312696 0.763022638 3.33957743 0.061539336 0.95782778 48790.89929 -4.688338823 -0.724930443 SAST(ph)LCLPSVGAARPQVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASTLCLPSVGAARPQVK 18 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.279)T(0.721)LCLPSVGAARPQVK 272.06 9.18E-39 2216800000 1012100 662910 388290 413310 357340 327410 281920 701770 456770 316310 TRUE FALSE 972546.0131 644004.4559 458462.6405 434640.9786 368834.1656 334030.4545 285370.2213 687278.2043 404919.3845 294886.042 3.298040174 2.183909593 1.554711228 1.473928626 1.250768477 1.132744203 0.967730515 2.330656954 1.373138524 1 18.16979801 4.688624295 1.630442833 1.430399882 3.865903906 0.726594226 0.36585403 0.522768941 1.44895404 0.105951311 1.952938093 48822.98126 -4.688624295 2.435504024 up VEEEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 VEEEEER 7 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ; 200.12 0.0008406 4964500000 3026000 3282500 2823900 3290100 3168600 3279700 3199200 3337100 3541900 3376100 FALSE TRUE 2907740.575 3188886.314 3334241.547 3459902.455 3270520.897 3346017.781 3238352.767 3268187.719 3139838.361 3147433.74 0.923844889 1.013170277 1.059352419 1.099277297 1.039107148 1.063093955 1.028886717 1.038365853 0.997586803 1 21.58574458 4.688680069 2.928729717 1.043739308 0.910188086 0.601183884 0.028435052 0.222731773 2.906976691 0.007020559 0.065830449 48829.25167 -4.688680069 -0.133551222 FKGPGDTSNFDDYEEEEIRVS(ph)INEK ddPTM_BT-474_Pertuzumab_2h_R1 5 FKGPGDTSNFDDYEEEEIRVSINEK 25 2 P17612-2;P17612;K7ERP6 P17612-2 PRKACA cAMP-dependent protein kinase catalytic subunit alpha 1 FKGPGDTSNFDDYEEEEIRVS(1)INEK;FKGPGDTSNFDDYEEEEIRVS(1)INEK;FKGPGDTSNFDDYEEEEIRVS(1)INEK;FKGPGDTSNFDDYEEEEIRVS(1)INEK;FKGPGDTSNFDDYEEEEIRVS(1)INEK 282.44 1.21E-53 2619020000 1838570 1448640 1058746 987928 1316380 1078886 1090960 1624930 1621240 1237970 TRUE FALSE 1766716.652 1407326.206 1250084.954 1038915.082 1358722.558 1100701.814 1104311.495 1591374.628 1437203.632 1154121.189 1.530789546 1.219392052 1.083148776 0.900178501 1.17727893 0.953714241 0.956841886 1.378862673 1.245279651 1 20.13836329 4.688742602 2.584820458 1.100801854 1.59451712 0.47547187 0.14061088 0.416770915 3.880170855 0.038252632 0.424976658 48836.28307 -4.688742602 0.493715266 NRT(ph)PSDVK ddPTM_BT-474_Pertuzumab_2h_R1 4 NRTPSDVK 8 1 P39687;H0YN26;H7BZ09;O95626 P39687 ANP32A;ANP32D Acidic leucine-rich nuclear phosphoprotein 32 family member A;Acidic leucine-rich nuclear phosphoprotein 32 family member D 1 NRT(1)PSDVK;NRT(0.998)PS(0.002)DVK;NRT(0.997)PS(0.003)DVK;NRT(0.998)PS(0.002)DVK 101.93 0.0081854 980410000 2052510 1783050 1419520 1304740 1514050 1608700 1476860 1917820 2112980 1574130 TRUE FALSE 1972295.64 1732199.16 1676058.841 1372077.788 1562750.793 1641229.016 1494934.254 1878216.347 1873123.369 1467512.773 1.343971703 1.180363941 1.14210852 0.934968208 1.064897575 1.118374604 1.018685685 1.279863713 1.27639323 1 20.48494163 4.688826949 2.195152045 1.11214659 1.388983 0.323260067 0.105254262 0.75770134 4.550969305 0.02878717 0.392685793 48845.76871 -4.688826949 0.27683641 NVTELNEPLSNEER ddPTM_BT-474_Pertuzumab_2h_R1 4 NVTELNEPLSNEER 14 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;; 324.67 2.70E-56 1815550000 744720 867260 762040 922330 826240 870890 889080 930280 867720 956830 FALSE TRUE 715615.5191 842526.5939 899757.5795 969931.5618 852816.76 888499.9925 899960.827 911069.3929 769220.0634 892023.0518 0.802238818 0.944512131 1.008670771 1.087339122 0.956047894 0.996050484 1.008898621 1.021351849 0.862332046 1 19.76672147 4.689404408 2.653046021 0.997237101 0.774637172 0.52878662 0.053857826 0.299520214 2.989330577 0.01299279 0.139871216 48910.75966 -4.689404408 -0.222599928 LQSVEYVVFDEADR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQSVEYVVFDEADR 14 0 Q8TDD1-2;Q8TDD1;F8VRX4 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ;;; 190.1 1.49E-06 64683000 49551.7 61230 52980.9 71449 56402.9 58005 70434.1 68291 67388 73706 FALSE TRUE 47615.16478 59483.78035 62555.72718 75136.49145 58217.1505 59177.90084 71296.09359 66880.76699 59738.39675 68713.82697 0.692948812 0.8656741 0.910380486 1.093469754 0.847240695 0.861222602 1.037580015 0.973323273 0.869379561 1 16.06831281 4.689468932 1.854671701 0.95299093 0.6277491 0.517694927 0.075704717 0.592900329 2.28388333 0.019690692 0.323574596 48918.02697 -4.689468932 -0.32524183 EIENGNSFDSS(ph)GDELDVHQLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIENGNSFDSSGDELDVHQLLR 22 0 Q6ZN28 Q6ZN28 MACC1 Metastasis-associated in colon cancer protein 1 1 EIENGNSFDS(0.058)S(0.942)GDELDVHQLLR 155.39 1.26E-08 111890000 26742 31158 26768 34627 27989 30114 34075 33440 35927 32913 TRUE FALSE 25696.89308 30269.40435 31605.57305 36414.10362 28889.2916 30722.92571 34492.02004 32749.45231 31848.71758 30683.77319 0.837475004 0.986495505 1.030041933 1.186754425 0.941516919 1.001276001 1.12411273 1.067321548 1.037966139 1 14.90518828 4.689528137 2.055495476 1.055045759 0.790072659 0.493996068 0.064665717 0.509574309 2.568477345 0.01644021 0.242538383 48924.69615 -4.689528137 -0.2649731 AFGSGYR ddPTM_BT-474_Pertuzumab_2h_R1 3 AFGSGYR 7 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 117.62 0.012074 402058000 462740 502000 452940 479960 515880 418380 524800 510597 523210 534860 FALSE TRUE 444655.6092 487683.4515 534796.3336 504730.7931 532473.7487 426839.9303 531222.6594 500052.9935 463817.3943 498633.4558 0.891748446 0.978039973 1.07252397 1.012228095 1.06786607 0.856019437 1.065357034 1.002846856 0.930177045 1 18.92762016 4.690021445 3.976143841 1.003117761 0.886334138 0.207734653 0.063305155 0.307630191 9.219580634 0.01464328 0.092382939 48980.30051 -4.690021445 -0.116783623 ASYPCMSLHGGIDQYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASYPCMSLHGGIDQYDR 17 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 223.07 3.16E-15 2353000000 256040 376210 348280 489590 406710 344990 411020 401400 375800 491910 FALSE TRUE 246033.6737 365480.8591 411221.9434 514857.7986 419792.1965 351965.9342 416050.1857 393110.9497 333140.7595 458592.4976 0.536497381 0.796962142 0.896704472 1.122691281 0.915392639 0.767491697 0.907232866 0.857211908 0.7264418 1 18.80685323 4.690195353 2.537451858 0.895445861 0.481038471 0.522180589 0.104774547 0.365183774 3.227971365 0.027020746 0.309713944 48999.918 -4.690195353 -0.41440739 TKS(ph)PKPAES(ph)PQSATK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKSPKPAESPQSATK 15 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 2 T(0.403)KS(0.597)PKPAES(0.997)PQS(0.003)ATK 91.166 0.0030749 78399000 244670 296960 239730 325090 302290 350120 328350 292890 324600 370140 TRUE FALSE 235108.0259 288490.9916 283054.5438 341867.9339 312013.4324 357199.6663 332368.4455 286841.7191 287752.7688 345070.0881 0.681334123 0.836035929 0.82028131 0.990720279 0.904203068 1.035151057 0.963191123 0.8312564 0.833896587 1 18.3965299 4.690265247 1.192893886 0.926225968 0.590946668 0.556338246 0.06882995 1.173250368 1.503435634 0.021188743 0.478770089 49007.80447 -4.690265247 -0.335279301 LLAAGQLADALSQFHAAVDGDPDNYIAYYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLAAGQLADALSQFHAAVDGDPDNYIAYYR 30 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ; 277.04 2.16E-71 169749000 128438 168794 148307 199532 173062 193332 187584 173314 185253 214897 FALSE TRUE 123418.501 163980.1604 175109.374 209829.8704 178628.6964 197241.3055 189879.7091 169735.0053 164223.8561 200341.8348 0.616039586 0.81850184 0.874052961 1.047359233 0.891619549 0.984523805 0.947778627 0.847226968 0.819718239 1 17.61210419 4.690424305 1.792339233 0.924561099 0.534767681 0.672760232 0.066722695 0.480919032 1.692981763 0.018027538 0.307522935 49025.75668 -4.690424305 -0.389793418 LVEIVHPSQEEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVEIVHPSQEEDR 13 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PK08 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 218.31 2.44E-11 1980050000 1483410 1993670 1845590 2399420 1985370 2105340 2064470 2050130 1993180 2260020 FALSE TRUE 1425436.697 1936812.484 2179129.168 2523254.354 2049231.229 2147911.417 2089735.601 2007794.099 1766922.562 2106946.832 0.67654137 0.919250763 1.034259211 1.197588053 0.972606996 1.019442629 0.991831198 0.952940088 0.838617537 1 21.00672248 4.690435748 2.868937847 1.002070934 0.637175843 0.575259765 0.083730293 0.263924995 3.252933035 0.021718375 0.211280014 49027.04841 -4.690435748 -0.364895091 GFGDSFGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFGDSFGR 8 0 A0A0A0MQW0;A0A0A0MR39;A0A087WUT0;H0YN19;A0A0C4DGV1 A0A0A0MQW0 MYEF2 0 ;;; 214.25 2.08E-05 966020000 1793620 2079760 1788810 2209540 2174440 2156070 2165380 2212880 2118800 2257580 FALSE TRUE 1723523.347 2020447.281 2112087.759 2323574.624 2244382.837 2199667.213 2191880.568 2167183.255 1878282.707 2104672.096 0.818903501 0.959981978 1.003523429 1.104007902 1.066381239 1.045135352 1.041435658 1.029701139 0.892434841 1 21.00516405 4.690536215 1.898061308 1.030513961 0.766980798 0.581983406 0.052402724 0.492200481 2.009776257 0.01371642 0.22124182 49038.39134 -4.690536215 -0.263533163 VNPSQTHNNLYAWGQETGAPILTDDVSLQVFMDHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNPSQTHNNLYAWGQETGAPILTDDVSLQVFMDHLK 36 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 149.55 1.63E-13 168510000 18935 21315 18937 18720 21871 23481 21930 18688 24799 25424 FALSE TRUE 18194.99927 20707.11707 22359.33715 19686.14144 22574.50058 23955.80191 22198.3859 18302.08627 21983.92149 23702.00983 0.767656388 0.873643932 0.943351948 0.830568445 0.952429804 1.010707618 0.936561332 0.772174444 0.927512968 1 14.53272178 4.69062046 3.113915074 0.908426648 0.753407941 0.298781974 0.069218279 0.444107993 6.840736344 0.018147283 0.15780082 49047.90476 -4.69062046 -0.155018707 ASSNKDFT(ph)PNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSNKDFTPNR 11 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 AS(0.015)S(0.154)NKDFT(0.831)PNR 89.747 0.035772 0 115140 103820 82351 81583 93870 105150 91780 101170 115120 106830 TRUE FALSE 110640.2015 100859.1553 97233.65759 85793.50841 96889.4138 107276.205 92903.23109 99080.80415 102052.0602 99594.30895 1.110908873 1.012699986 0.976297327 0.861429828 0.972840866 1.077131878 0.932816665 0.994844035 1.024677628 1 16.60377569 4.690724441 2.66276997 0.977663915 1.129676436 0.351576217 0.053371301 0.456798804 4.596996165 0.013561253 0.146199166 49059.64944 -4.690724441 0.152012521 ERNHKPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 7 ERNHKPSR 8 2 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R 90.685 0.0067941 3130491000 780781.9 879463.8 1149766 1272865 945313.8 1318313 1567480 1263524 1775289 1948348 TRUE FALSE 750268.0801 854382.3535 1357554.293 1338557.715 975720.6769 1344970.192 1586663.289 1237431.788 1573765.635 1816384.655 0.413055725 0.470375232 0.747393615 0.73693516 0.53717734 0.740465511 0.873528239 0.681260869 0.866427511 1 20.79263832 4.690848676 0.163364822 1.041717961 9.97E-15 0.694051597 0.098098597 13.17365513 0.38194527 0.388995892 2.941953459 49073.68556 -4.690848676 -1.041717961 LKNEITR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKNEITR 7 1 Q86VP6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 109.21 0.0064555 3097550000 3868960 4233550 3654080 4106250 4057270 3903440 4539370 4339080 4673310 4980200 FALSE TRUE 3717756.766 4112813.299 4314453.541 4318174.055 4187775.774 3982370.231 4594924.168 4249476.482 4142815.441 4642886.618 0.800742528 0.885831087 0.929261017 0.930062353 0.901976748 0.857735835 0.989669692 0.915266047 0.892293046 1 22.14659062 4.691014522 2.280804237 0.923749744 0.777249457 0.475824657 0.040231485 0.452304395 2.997848481 0.009669731 0.127291831 49092.4291 -4.691014522 -0.146500287 SVSTTNIAGHFNDES(ph)PLGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 SVSTTNIAGHFNDES(1)PLGLR;SVSTTNIAGHFNDES(1)PLGLR;SVSTTNIAGHFNDES(1)PLGLR;SVSTTNIAGHFNDES(1)PLGLR 307.49 1.77E-56 1843200000 676570 932430 862330 1072500 842390 977700 1112610 971710 1133060 1335240 TRUE FALSE 650128.8964 905838.0093 1018172.213 1127851.854 869486.2394 997469.7639 1126226.454 951643.8489 1004439.779 1244803.005 0.522274523 0.727695873 0.817938428 0.906048466 0.698493043 0.801307323 0.904742718 0.764493534 0.806906615 1 20.24748602 4.69122404 2.091318344 0.826086285 0.455996386 0.590089748 0.080033164 0.416316889 2.190032335 0.019218156 0.280254435 49116.11862 -4.69122404 -0.370089899 SYS(ph)EPEKMNEVGLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSEPEKMNEVGLTR 15 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.055)YS(0.945)EPEKMNEVGLTR;SYS(1)EPEKMNEVGLTR 220.34 6.81E-12 0 364400 267960 177356 200021 217564 201483 203633 335150 230010 210891 TRUE FALSE 350158.8451 260318.0432 209408.1745 210344.1078 224562.1436 205557.1243 206125.1216 328229.0354 203900.2291 196607.1647 1.781007552 1.324051662 1.065109579 1.069870002 1.14218698 1.045522042 1.048411038 1.669466298 1.037094601 1 17.58495637 4.691234295 3.050675366 1.174919249 1.845461489 0.510946059 0.187891946 0.298909586 4.352886299 0.050706156 0.454939515 49117.2785 -4.691234295 0.670542241 S(ph)SSLKER ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLKER 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.333)S(0.333)S(0.333)LKER 90.629 0.010294 1200600000 2303100 1384900 714660 904950 1047400 643610 728330 2228500 811530 593830 TRUE FALSE 2213092.306 1345404.008 843814.9595 951654.5779 1081090.572 656624.2352 737243.5204 2182480.696 719408.5166 553609.3652 3.997570209 2.430240694 1.52420644 1.719000143 1.952803981 1.186078626 1.331703484 3.942275607 1.29948762 1 19.07850882 4.691334895 3.064573467 1.920068468 4.216479436 0.407077799 0.801721654 0.360747032 5.318813939 0.211335149 1.885151694 49128.6573 -4.691334895 2.296410967 WISLNTVALVTDNAVYHWSMEGESQPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 WISLNTVALVTDNAVYHWSMEGESQPVK 28 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 299.36 1.84E-71 1197980000 301587 418660 393590 464590 418360 507150 471780 339140 483190 560650 FALSE TRUE 289800.6466 406720.2267 464720.4684 488567.5456 431816.9293 517404.9205 477553.7848 332136.6405 428340.2969 522676.6761 0.554454905 0.778148797 0.889116522 0.934741434 0.826164528 0.989913926 0.913669591 0.635453342 0.819512935 1 18.99555926 4.691436057 2.767456341 0.857444693 0.514358305 0.479590997 0.100051828 0.378291739 4.223671532 0.027218026 0.279496546 49140.10236 -4.691436057 -0.343086388 MCDHLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 MCDHLIR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;; 160.91 0.0013286 1319320000 806170 946820 820460 1024340 988720 984560 1009000 901280 1034520 1060160 FALSE TRUE 774663.9851 919817.6206 968735.373 1077206.31 1020523.077 1004468.478 1021348.444 882668.253 917085.6267 988354.4189 0.783791695 0.930655646 0.980149787 1.089898815 1.032547695 1.016303928 1.033382787 0.893068555 0.927891462 1 19.91466895 4.691502863 2.179173063 0.994577733 0.741144316 0.604197434 0.052391828 0.449742152 2.637457776 0.015283883 0.212893921 49147.662 -4.691502863 -0.253433417 VPKPEPIPEPKEPS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 5 VPKPEPIPEPKEPSPEK 17 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK 162.01 1.51E-09 8454470000 8106540 5605472 3757722 2619076 4614544 4655446 4573101 5485170 6533080 4329132 TRUE FALSE 7789727.455 5445609.427 4436825.955 2754246.826 4762974.999 4749582.308 4629067.978 5371899.323 5791472.147 4035916.034 1.930101466 1.349287097 1.099335546 0.682434125 1.180147198 1.176828821 1.146968356 1.331023559 1.43498331 1 21.94446473 4.691548726 2.711730179 1.143169023 2.038221263 0.61674723 0.189653732 0.280610633 2.964154343 0.050637079 0.53480833 49152.85243 -4.691548726 0.89505224 DSLLQDGEFSMDLR ddPTM_BT-474_Pertuzumab_2h_R1 36 DSLLQDGEFSMDLR 14 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 347.01 1.97E-81 27972312900 5102103.3 5592670.7 4763219.8 5603421.2 5745711.5 5445896.9 5698508.9 6072546.6 5882002.1 5714097.1 FALSE TRUE 4902707.462 5433173.207 5624039.575 5892614.44 5930527.529 5556016.667 5768248.957 5947146.391 5214301.881 5327076.214 0.920337398 1.019916553 1.055746032 1.106162969 1.113280023 1.042976756 1.082817051 1.116399719 0.978829976 1 22.34491249 4.691867599 1.830667095 1.072794799 0.880571887 0.470277615 0.044632532 0.585669723 2.172216209 0.011152527 0.18756587 49188.9553 -4.691867599 -0.192222912 AGVSVWVQAVEMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGVSVWVQAVEMDR 14 0 Q9Y365;F5H0V7;F5H8G1;F5H1Z6;F5H3G8;F5H5A8 Q9Y365 STARD10 PCTP-like protein 0 ; 174.73 5.81E-06 290300000 193671 229140 207013 209940 238200 252680 227318 249180 233320 223292 FALSE TRUE 186102.1232 222605.1516 244424.8541 220775.0286 245861.9193 257789.3627 230099.9857 244034.3459 206834.4918 208168.234 0.893998665 1.069352164 1.174169802 1.060560607 1.181073186 1.238370321 1.1053559 1.172293876 0.99359296 1 17.66739041 4.691966567 2.977007026 1.1281896 0.867328006 0.419170389 0.076778598 0.283858814 3.865386497 0.017832253 0.166080052 49200.16585 -4.691966567 -0.260861594 ISEGLPT(ph)PTKMT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISEGLPTPTKMTPR 14 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 IS(0.006)EGLPT(0.989)PT(0.176)KMT(0.828)PR;IS(0.001)EGLPT(0.998)PT(0.119)KMT(0.883)PR 158.17 1.95E-07 0 738120 419260 213966 262070 255150 174356 191814 545470 188437 150112 TRUE FALSE 709273.4544 407303.1153 252634.4158 275595.4641 263357.1315 177881.5978 194161.4771 534205.8539 167046.4218 139944.7805 5.068237998 2.910455922 1.805243575 1.969315776 1.881864622 1.271084188 1.387414924 3.817261722 1.193659536 1 17.09449815 4.692570941 2.28136314 1.956094709 5.668260559 0.62743962 0.762946069 0.377764321 2.499075772 0.203532068 2.698146505 49268.68159 -4.692570941 3.712165849 ELFGPELFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELFGPELFR 9 0 P35249;C9J8M3;C9JZI1;P35249-2;C9JXZ7;C9JTT7 P35249 RFC4 Replication factor C subunit 4 0 ; 91.318 0.025205 90972000 99283 109522 93216 114523 111774 100819 106290 121359 107690 113707 FALSE TRUE 95402.9106 106398.5398 110062.2048 120433.5458 115369.3122 102857.6293 107590.8088 118852.8942 95465.48267 106005.5236 0.899980561 1.003707507 1.038268583 1.136106324 1.088333025 0.970304431 1.014954742 1.121195294 0.900570833 1 16.69377992 4.692635396 2.404499752 1.043990418 0.875096427 0.252102258 0.067256603 0.617732296 4.705606711 0.016683662 0.207317785 49275.99425 -4.692635396 -0.16889399 IVGAPMHDLLLWNNATVTTCHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IVGAPMHDLLLWNNATVTTCHSK 23 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 264.59 3.36E-44 935750000 927290 1105180 957110 1176130 1173990 1272570 1232820 993580 1375270 1479100 FALSE TRUE 891050.4816 1073661.348 1130081.068 1236830.21 1211752.455 1298302.237 1247907.62 973062.2258 1219155.115 1378919.24 0.646194829 0.778625258 0.819541156 0.896956236 0.878769706 0.941536096 0.904989635 0.705670207 0.884138157 1 20.39510653 4.69268849 1.421200044 0.867651529 0.569796785 0.503504767 0.072648269 1.074983823 2.099508534 0.021472425 0.445639708 49282.01883 -4.69268849 -0.297854744 RAAEDDEDDDVDTKK ddPTM_BT-474_Pertuzumab_2h_R1 5 RAAEDDEDDDVDTKK 15 2 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;; 227.89 3.77E-13 3335900000 3763930 3144280 2585790 2100158 2597120 2539780 2731620 3249930 3682920 2927560 FALSE TRUE 3616831.454 3054608.213 3053099.774 2208547.406 2680658.723 2591136.092 2765050.383 3182817.81 3264850.362 2729273.754 1.325199222 1.119201842 1.118649153 0.809206993 0.982187558 0.949386659 1.01310848 1.166177561 1.196234111 1 21.38008568 4.693251768 1.794024627 1.028567904 1.401159495 0.426267386 0.105355195 0.85529879 3.003714407 0.030385138 0.52415823 49345.97881 -4.693251768 0.372591591 GYYSPYS(ph)VSGSGSTAGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYS(0.06)PYS(0.937)VS(0.004)GSGSTAGSR;GYYS(0.323)PYS(0.677)VSGSGSTAGSR 382.4 2.10E-109 3168400000 569616 720920 735470 804910 673410 833150 992760 843910 1014580 1221260 TRUE FALSE 547354.777 700360.0675 868385.7894 846451.5016 695070.8442 849996.8638 1004909.694 826482.9636 899409.1319 1138542.972 0.480750213 0.61513714 0.762716745 0.743451518 0.610491533 0.746565465 0.882627813 0.725912841 0.789965029 1 20.11875731 4.693348403 0.090318809 1.212076591 7.93E-15 0.693659309 0.076412937 43.6146699 0.639225902 2.153771631 7.59899974 49356.95999 -4.693348403 -1.212076591 LLPDPGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLPDPGSPR 9 0 A6ND36 A6ND36 FAM83G Protein FAM83G 1 LLPDPGS(1)PR;LLPDPGS(1)PR 87.568 0.014028 168204000 477000 572780 514850 600290 586820 645850 634810 620850 593540 743430 TRUE FALSE 458358.3126 556444.8752 607894.8478 631271.0388 605695.5982 658909.5295 642578.9947 608029.2305 526163.8275 693076.8239 0.661338393 0.802861755 0.87709591 0.910824049 0.873922742 0.95070201 0.927139637 0.877289803 0.759171003 1 19.40265575 4.693367118 1.617587046 0.896912148 0.587829938 0.608679707 0.058828093 0.608859655 1.641225562 0.015221682 0.287901112 49359.08701 -4.693367118 -0.309082209 SSLGQSAS(ph)ETEEDTVSVSKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 1 SSLGQSAS(0.798)ET(0.202)EEDTVSVSKK 237.2 8.35E-30 638130000 582990 390620 189640 338900 271970 297490 361160 408950 372150 333100 TRUE FALSE 560206.1063 379479.9001 223912.1665 356390.6696 280718.162 303505.4516 365579.9841 400505.0396 329905.0922 310538.8403 1.803980802 1.222004628 0.721043997 1.147652478 0.90397118 0.977351018 1.177243992 1.289709974 1.062363381 1 18.2444142 4.693498376 3.736701172 1.058011241 1.850983559 0.697839507 0.150927394 0.135722795 3.463192289 0.039317863 0.271713136 49374.0072 -4.693498376 0.792972318 STPTDLILCVPHLYSCLEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 STPTDLILCVPHLYSCLEDR 20 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 130 1.69E-05 360100000 359750 387790 343600 354820 357630 393380 352140 395030 474510 412350 FALSE TRUE 345690.5723 376730.6089 405696.1633 373132.3027 369133.4937 401334.4131 356449.5947 386872.4925 420645.6141 384421.1672 0.899249578 0.979994446 1.055342936 0.970634124 0.960231967 1.043996656 0.927237169 1.006376666 1.094231145 1 18.55232825 4.693634285 3.830522868 1.002557599 0.89321232 0.32390129 0.046378722 0.261643933 7.158060593 0.010903524 0.073110257 49389.46086 -4.693634285 -0.109345279 SSS(ph)LKER ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSLKER 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.293)S(0.293)S(0.413)LKER;SS(0.01)S(0.99)LKER 97.965 0.0089946 1552970000 2495920 1462850 725920 919850 1091020 724310 684690 2485490 786060 568830 TRUE FALSE 2398376.687 1421130.95 857109.892 967323.5687 1126113.649 738956.0445 693069.441 2434163.763 696829.7642 530302.6374 4.522656532 2.67984892 1.616265565 1.824097224 2.123530169 1.393461002 1.306931914 4.590140782 1.314022815 1 19.0164564 4.694295516 3.146082281 2.109695535 4.768160207 0.38452987 0.976243353 0.361064765 5.717581746 0.254937741 2.225052637 49464.71559 -4.694295516 2.658464672 KGWS(ph)MSEQSEESVGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 KGWSMSEQSEESVGGR 16 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KGWS(0.999)MS(0.001)EQSEESVGGR;KGWS(0.999)MS(0.001)EQSEESVGGR;KGWS(0.99)MS(0.01)EQSEESVGGR 184.6 1.10E-09 1399280000 480948 344239 180265 231676 401906 231851 252948 444818 280092 270067 TRUE FALSE 462152.0204 334421.6408 212842.8955 243632.8261 414833.6715 236539.1861 256043.6533 435632.3529 248297.1304 251775.1215 1.83557461 1.328255305 0.845369051 0.967660445 1.647635672 0.939485937 1.016953747 1.730243839 0.986186121 1 17.94177621 4.694313402 3.898273572 1.188854297 1.871589582 0.331017753 0.290322697 0.269328785 7.756190169 0.072088791 0.47468269 49466.75278 -4.694313402 0.682735285 EAQQKVPDEEENEES(ph)DNEKETEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAQQKVPDEEENEESDNEKETEK 23 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 EAQQKVPDEEENEES(1)DNEKETEK 206.95 6.68E-25 570430000 679110 456840 296930 224820 375860 414310 335830 450260 487000 357480 TRUE FALSE 652569.6304 443811.3705 350591.8562 236422.9871 387949.8782 422687.6321 339939.988 440961.9737 431717.8017 333267.5612 1.958095256 1.331696877 1.051983142 0.709408939 1.164079327 1.268313155 1.020021231 1.323147 1.29540901 1 18.34632137 4.694497837 2.770125929 1.117486926 2.071496206 0.690824088 0.171901111 0.229462954 2.560429886 0.045481717 0.473465449 49487.76465 -4.694497837 0.95400928 GRVEDVVVSDECR ddPTM_BT-474_Pertuzumab_2h_R1 1 GRVEDVVVSDECR 13 1 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 106.52 0.00083515 0 73001 88675 72453 96368 92877 109370 83650 95071 95091 110430 FALSE TRUE 70148.04021 86146.07582 85546.86881 101341.564 95864.47305 111581.5363 84673.73372 93107.75063 84296.66833 102950.4777 0.681376539 0.836771987 0.830951645 0.984371965 0.931170745 1.083836994 0.822470527 0.904393575 0.818807937 1 16.651591 4.694733052 1.267058577 0.926169336 0.5929764 0.485278576 0.078575287 1.172886373 1.726056737 0.022365789 0.499344789 49514.5746 -4.694733052 -0.333192936 VGEEFEEQTVDGRPCK ddPTM_BT-474_Pertuzumab_2h_R1 8 VGEEFEEQTVDGRPCK 16 1 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;;;;; 284.44 8.93E-36 13299940000 4907586 4162009 3221766 3225571 3548863 3694473 3528881 4133381 4376812 4001969 FALSE TRUE 4715792.113 4043312.578 3804010.784 3392043.106 3663015.401 3769177.775 3572068.501 4048025.238 3879974.651 3730912.075 1.263978357 1.083733011 1.019592718 0.90917262 0.981801588 1.010256393 0.957425002 1.08499615 1.039953387 1 21.83109693 4.694760318 2.090219595 1.001875335 1.3217732 0.766541061 0.044306247 0.317572991 1.658178759 0.012492857 0.185266631 49517.6833 -4.694760318 0.319897864 APGFGDNR ddPTM_BT-474_Pertuzumab_2h_R1 2 APGFGDNR 8 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 100.39 0.014279 719710000 461050 734590 571270 1137110 627140 632020 1063570 921080 708460 684510 FALSE TRUE 443031.6563 713640.2124 674511.1968 1195796.383 647312.5277 644799.8774 1076586.288 902059.3761 628038.5909 638147.528 0.694246451 1.118299737 1.05698317 1.873855701 1.014361882 1.010424469 1.687049218 1.413559305 0.984158934 1 19.28353046 4.69492301 1.620432361 1.30649283 0.519612766 0.234971846 0.299772852 1.2397283 3.34805675 0.078697297 1.495752386 49536.23669 -4.69492301 -0.786880064 ICKGDHWTTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ICKGDHWTTR 10 1 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 116.23 0.00067139 230960000 454550 531910 503110 464620 507520 520080 531710 570700 587200 601200 FALSE TRUE 436785.6835 516740.4476 594033.1686 488599.0939 523844.8417 530596.3739 538217.226 558914.8456 520543.5177 560480.1885 0.779306196 0.921960237 1.059864703 0.871750873 0.934635786 0.946681765 0.96027877 0.99720714 0.928745616 1 19.09630385 4.695087241 3.896540505 0.960878273 0.769041745 0.566625733 0.047770649 0.148864117 4.292160374 0.011171192 0.073868201 49554.97262 -4.695087241 -0.191836527 ELGLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELGLGR 6 0 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0;E9PIA9 P07384 CAPN1 Calpain-1 catalytic subunit 0 141.59 0.027066 475640000 280860 338750 301010 360620 320580 398140 356610 364500 378890 376400 FALSE TRUE 269883.6807 329089.1817 355409.2029 379231.6414 330891.7468 406190.6636 360974.2999 356972.9476 335879.9956 350906.0927 0.769105143 0.937826924 1.012832807 1.080721165 0.942963812 1.157548051 1.028692027 1.017289112 0.95717915 1 18.42072547 4.695146839 1.855459917 1.029597694 0.700361751 0.649667511 0.057376673 0.434822594 1.660536943 0.014330642 0.241279297 49561.77349 -4.695146839 -0.329235943 TGS(ph)NAAQYK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSNAAQYK 9 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 T(0.003)GS(0.997)NAAQYK 95.656 0.0055107 0 193000 136350 89056 98361 112980 84252 98139 170600 137690 96409 TRUE FALSE 185457.3466 132461.4315 105150.4002 103437.423 116614.1043 85955.63317 99340.05444 167077.0504 122060.0084 89879.13256 2.063408283 1.473772918 1.169908935 1.150850259 1.297454715 0.956346937 1.105262719 1.858908132 1.358046133 1 16.45569858 4.695267786 2.919180377 1.280731696 2.158860096 0.508592736 0.242338845 0.332516365 4.281215282 0.066927466 0.650932111 49575.57801 -4.695267786 0.8781284 ELAVEGMHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELAVEGMHR 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 129.38 0.00039083 587100000 511450 565640 504080 539930 558870 526620 611860 532920 583600 662990 FALSE TRUE 491461.9686 549508.501 595178.4692 567795.852 576846.5611 537268.6172 619348.1257 521915.0158 517352.1747 618085.0968 0.795136416 0.889049912 0.962939363 0.918637021 0.933280165 0.869247002 1.002043455 0.844406407 0.837024185 1 19.23744595 4.695289245 3.664772326 0.915082853 0.786931928 0.312801192 0.055411112 0.289002046 7.009787441 0.01302036 0.093027754 49578.02767 -4.695289245 -0.128150926 VTAPDVDLHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VTAPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 133.05 0.00016976 963710000 2310393 2500377 2139379 2548966 2237822 2376732 2502885 2578450 2790249 2650988 FALSE TRUE 2220100.287 2429068.696 2526012.376 2680518.441 2309803.577 2424791.149 2533516.055 2525204.106 2473511.631 2471434.222 0.898304421 0.982857919 1.022083596 1.084600358 0.934600467 0.981127124 1.02511976 1.021756551 1.000840568 1 21.23691708 4.695309289 2.946114528 1.00988615 0.885026972 0.460639484 0.035814773 0.307958167 4.066485492 0.008969718 0.086158739 49580.31579 -4.695309289 -0.124859178 SIYGEKFEDENFILK ddPTM_BT-474_Pertuzumab_2h_R1 9 SIYGEKFEDENFILK 15 1 P62937;F8WE65;C9J5S7;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;;;;;;; 265.46 2.99E-25 57868892000 38854274 33250689 25387160 24684999 30235948 29722132 30631736 33838100 36970308 32895734 FALSE TRUE 37335806.02 32302411.91 29975184.55 25958994.76 31208514.73 30323133.87 31006616.35 33139331.41 32773593.63 30667676.64 1.217431841 1.053304829 0.97741948 0.846461082 1.017635444 0.98876528 1.011052018 1.080594784 1.068668945 1 24.87021554 4.695825767 2.986180519 1.001828506 1.242423242 0.543917138 0.060079705 0.286069218 3.919577442 0.016448981 0.15548181 49639.31353 -4.695825767 0.240594736 EQDLQLEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQDLQLEELR 10 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;; 228.84 4.43E-09 1987489000 1197990 1314380 1128950 1287620 1362600 1319170 1265430 1390560 1426140 1434540 FALSE TRUE 1151171.226 1276895.169 1332976.378 1354074.223 1406429.266 1345844.521 1280916.711 1361844.45 1264250.566 1337377.328 0.860767715 0.954775547 0.996709269 1.012484804 1.051632353 1.006331192 0.957782582 1.018294853 0.94532077 1 20.35097513 4.695972909 2.013426371 1.000894327 0.827594458 0.686512476 0.028313804 0.367477504 1.734685768 0.007301549 0.113441574 49656.13451 -4.695972909 -0.17329987 DIPGLTDTTVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIPGLTDTTVPR 12 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ; 127.51 0.00062437 185110000 99684 114244 102099 107264 132691 118881 113465 122324 125902 125126 FALSE TRUE 95788.23907 110985.873 120550.5605 112799.9079 136959.1265 121284.8553 114853.6186 119797.9667 111610.1328 116651.1046 0.821151582 0.951434394 1.033428367 0.966985339 1.174091982 1.039723162 0.984590922 1.026976702 0.956785906 1 16.83184044 4.696055775 1.870963906 1.026761192 0.766279569 0.534293906 0.05753079 0.567157139 2.209707683 0.014945283 0.25056791 49665.6101 -4.696055775 -0.260481623 AILVDLEPGTMDSVR ddPTM_BT-474_Pertuzumab_2h_R1 10 AILVDLEPGTMDSVR 15 0 Q13509;A0A0B4J269;G3V5W4;G3V2R8;G3V3R4;G3V2N6;Q5JP53;P07437;Q13885;Q9BVA1 Q13509;Q5JP53;Q13885;Q9BVA1 TUBB3;TUBB;TUBB2A;TUBB2B Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;;;;;;;;; 300.78 6.32E-44 3371640000 3086138 3397001 2855222 3564318 3280648 3370514 3518264 3470252 3533687 3760269 FALSE TRUE 2965528.315 3300121.857 3371224.129 3748272.879 3386173.022 3438668.102 3561321.567 3398590.084 3132557.666 3505582.631 0.845944491 0.941390406 0.96167299 1.069229647 0.9659373 0.980912009 1.015900049 0.969479382 0.893591165 1 21.74122281 4.696141091 1.9635015 0.984561555 0.812834249 0.493256872 0.04198891 0.571752687 2.526106548 0.010774023 0.172036643 49675.36772 -4.696141091 -0.171727306 ENIVEAIIHSPELIR ddPTM_BT-474_Pertuzumab_2h_R1 6 ENIVEAIIHSPELIR 15 0 O95373;E9PLB2 O95373 IPO7 Importin-7 0 ;;;;; 168.32 1.26E-06 1318475000 866726 951302 830083 948317 1000905 1002787 1021317 1009366 1059622 1193791 FALSE TRUE 832853.3897 924171.7984 980097.4632 997259.754 1033100.018 1023064.04 1033816.183 988522.2394 939338.1529 1112934.472 0.748340006 0.830391925 0.88064256 0.896063316 0.928266708 0.919249125 0.9289102 0.888212437 0.844019281 1 20.08593722 4.696474982 1.160722048 0.911562425 0.677463709 0.670632793 0.037045734 0.865546395 1.030615805 0.010386223 0.24210963 49713.57345 -4.696474982 -0.234098716 IDISPS(ph)TFR ddPTM_BT-474_Pertuzumab_2h_R1 4 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.039)PS(0.953)T(0.008)FR;IDIS(0.019)PS(0.972)T(0.009)FR;IDIS(0.026)PS(0.964)T(0.011)FR;IDIS(0.463)PS(0.535)T(0.002)FR 202.57 2.06E-05 58753624000 3398244 3743408 3059240 4032560 3858433 3686936 3618034 3784792 3661178 4420115 TRUE FALSE 3265436.868 3636649.669 3612112.72 4240680.905 3982543.002 3761488.372 3662312.582 3706634.723 3245576.422 4120736.674 0.792440072 0.882524159 0.876569654 1.029107473 0.966463843 0.912819398 0.888751908 0.899507786 0.787620438 1 21.97447084 4.697289726 1.8287974 0.919279042 0.760379029 0.271795791 0.064030608 1.10446229 4.04765627 0.017018685 0.293328865 49806.92452 -4.697289726 -0.158900014 LKATVT(ph)PS(ph)PVKGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 LKAT(0.006)VT(0.995)PS(0.999)PVKGK;LKAT(0.125)VT(0.879)PS(0.997)PVKGK 96.163 0.0082477 8509000000 12513400 10016900 7834800 5803100 7845000 8707600 9257100 10882900 10169500 9304700 TRUE FALSE 12024362.49 9731227.82 9250722.644 6102598.686 8097341.55 8883673.638 9370391.159 10658164.31 9015100.994 8674484.381 1.38617605 1.121822046 1.066429108 0.703511404 0.933466612 1.024115469 1.08022457 1.228679867 1.039266497 1 23.04834657 4.697671411 2.265907833 1.020275463 1.4575056 0.452450768 0.12546769 0.597386942 3.847968689 0.036716286 0.502763416 49850.71718 -4.697671411 0.437230136 EFSDFIQAVER ddPTM_BT-474_Pertuzumab_2h_R1 3 EFSDFIQAVER 11 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 0 ;; 126.19 0.00072714 104000000 143678 166317 143924 175764 168752 147858 182885 167022 186109 197659 FALSE TRUE 138062.9049 161573.802 169934.2684 184835.2011 174180.0613 150847.7901 185123.2013 163572.9373 164982.6866 184271.3799 0.749236832 0.876825268 0.922195669 1.003059733 0.945236647 0.818617575 1.004622647 0.887674133 0.89532453 1 17.49147249 4.697700229 2.206531657 0.930673583 0.711734658 0.501633141 0.05608338 0.469498691 2.816678049 0.013768012 0.194571987 49854.02521 -4.697700229 -0.218938925 WKGYT(ph)SDDDTWEPEIHLEDCK ddPTM_BT-474_Pertuzumab_2h_R1 1 WKGYTSDDDTWEPEIHLEDCK 21 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 WKGYT(0.5)S(0.5)DDDTWEPEIHLEDCK 210.2 3.17E-22 70763000 169760 116090 67081 89706 96458 110780 93883 105200 125030 95908 TRUE FALSE 163125.5915 112779.2269 79204.02891 94335.73741 99560.65917 113020.0475 95031.96824 103027.5832 110837.1186 89412.06573 1.824424815 1.26134237 0.885831551 1.055067195 1.113503623 1.264035749 1.062853961 1.152278301 1.239621495 1 16.44818191 4.69789957 3.485776529 1.106102788 1.882839458 0.80823967 0.105971596 0.104689175 2.212039734 0.025906692 0.200239576 49876.91342 -4.69789957 0.77673667 LWGIDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LWGIDR 6 0 P10644;P10644-2;K7EPB2;K7EM13;P31321;H7BYW5;C9JSK5 P10644;P31321 PRKAR1A;PRKAR1B "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed;cAMP-dependent protein kinase type I-beta regulatory subunit" 0 ;; 112.56 0.06256 752957000 1206178 1281084 1044563 1312016 1258049 1217150 1249115 1325012 1327918 1426682 FALSE TRUE 1159039.23 1244548.739 1233338.77 1379729.303 1298515.289 1241761.607 1264402.043 1297650.039 1177178.316 1330051.557 0.871424287 0.935714658 0.927286437 1.037350241 0.976289439 0.933619152 0.950641376 0.975638901 0.885062169 1 20.34305074 4.698190545 1.683490083 0.962754987 0.846138185 0.328468171 0.039175037 1.032410767 3.054954447 0.010188105 0.190077466 49910.34187 -4.698190545 -0.116616802 QKETS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 QKETSPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QKET(0.005)S(0.995)PR 99.864 0.026873 647910000 993650 908300 698680 842090 792040 865640 923240 905190 842840 947890 TRUE FALSE 954817.0595 882396.1733 824947.0181 885550.3658 817516.6859 883143.8339 934538.8873 886497.5102 747164.3367 883688.566 1.080490454 0.998537502 0.933526867 1.002106851 0.925118551 0.99938357 1.05754326 1.003178658 0.845506398 1 19.75317849 4.698317655 3.722840656 0.976838697 1.087537815 0.255249273 0.055467347 0.33756657 8.615281974 0.013406218 0.09530755 49924.95192 -4.698317655 0.110699118 SFSSQRPVDR ddPTM_BT-474_Pertuzumab_2h_R1 3 SFSSQRPVDR 10 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 0 ;; 155 1.23E-05 772510000 477319 633180 569190 729460 655330 626160 698390 617910 749700 833410 FALSE TRUE 458664.8458 615122.3263 672055.2946 767107.518 676409.2846 638821.3842 706937.1057 605149.9426 664597.199 776962.3984 0.590330815 0.791701539 0.864977888 0.987316142 0.87058175 0.822203733 0.909872997 0.778866447 0.855378845 1 19.56748525 4.698371132 2.243735783 0.875117055 0.532699582 0.656195449 0.064815784 0.351782705 2.204434065 0.016587006 0.230575558 49931.09975 -4.698371132 -0.342417473 KS(ph)SPFKDLMTVPESR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSSPFKDLMTVPESR 15 2 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 KS(0.643)S(0.357)PFKDLMTVPESR 165.3 7.47E-07 328530000 412450 346520 277990 230120 316980 325980 301950 339700 340210 345820 TRUE FALSE 396330.998 336637.5889 328228.9769 241996.5208 327175.9496 332571.5389 305645.3544 332685.0763 301590.7871 322397.3034 1.229324792 1.044169989 1.018088469 0.750615834 1.014822228 1.031558067 0.948039426 1.031910233 0.935463119 1 18.29848015 4.698589834 2.020962143 0.966513853 1.289964366 0.508807935 0.078719539 0.551422152 2.616744197 0.020379882 0.319161021 49956.25048 -4.698589834 0.323450513 ETEDGHESPLFDFIESCLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETEDGHESPLFDFIESCLR 19 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ; 243.29 1.89E-24 93376000 50890 72322 68998 81994 72798 77772 76246 72166 73086 85405 FALSE TRUE 48901.16254 70259.44737 81467.47345 86225.72017 75139.61378 79344.60313 77179.12136 70675.74688 64789.58368 79620.44328 0.614178476 0.882429744 1.023197939 1.082959559 0.943722626 0.996535561 0.969338001 0.887658294 0.813730507 1 16.28085128 4.698693328 3.145458154 0.961401706 0.57736626 0.69021116 0.070341413 0.185002662 2.925713934 0.018578133 0.16583427 49968.15661 -4.698693328 -0.384035446 KLNTETFGVSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLNTETFGVSGR 12 1 Q9BX40;Q9BX40-2 Q9BX40 LSM14B Protein LSM14 homolog B 0 ; 190.03 1.15E-05 675320000 687940 742070 650460 680050 688770 743530 747470 758550 785330 787310 FALSE TRUE 661054.5442 720906.8902 768012.5914 715147.462 710924.9126 758564.686 756617.7615 742885.6774 696182.6308 733984.7924 0.90063793 0.982182325 1.04636036 0.97433553 0.968582619 1.033488287 1.030835747 1.012126798 0.94849735 1 19.48539065 4.698762765 3.716074034 1.003674407 0.893551971 0.508623418 0.029572201 0.182597909 4.640100383 0.007182072 0.051293282 49976.14633 -4.698762765 -0.110122436 GGGEYGETWHK ddPTM_BT-474_Pertuzumab_2h_R1 4 GGGEYGETWHK 11 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;; 160.77 2.71E-05 2990570000 2476910 2827790 2482570 2809360 2745190 2932680 2940000 2662270 3095820 3182490 FALSE TRUE 2380109.619 2747144.198 2931225.623 2954351.406 2833491.529 2991980.799 2975980.599 2607293.194 2744395.492 2966937.118 0.802211009 0.925919252 0.987963515 0.995758012 0.955022441 1.008440921 1.003048087 0.878782762 0.924992807 1 21.50054292 4.699218102 2.995620283 0.96395899 0.782931942 0.619695118 0.039185946 0.249791734 3.445292348 0.010738978 0.102824788 50028.57144 -4.699218102 -0.181027049 IFDLGR ddPTM_BT-474_Pertuzumab_2h_R1 6 IFDLGR 6 0 P27635;X1WI28;Q96L21;A6QRI9;B8A6G2 P27635 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ;;;;; 177.91 0.0083285 5828550000 5013390 5684600 4976870 5616540 5456260 4923700 6042410 6143480 5893240 6470160 FALSE TRUE 4817461.176 5522480.774 5876301.119 5906410.302 5631765.558 5023260.587 6116358.821 6016614.991 5224264.102 6031930.3 0.798659954 0.915541211 0.974199108 0.979190741 0.933658925 0.832778288 1.013996932 0.997460961 0.866101537 1 22.52418833 4.699237329 2.985147315 0.951623665 0.780279552 0.393528999 0.056089313 0.34578931 4.722930146 0.01397472 0.134468538 50030.78631 -4.699237329 -0.171344113 SLNDLIEER ddPTM_BT-474_Pertuzumab_2h_R1 3 SLNDLIEER 9 0 Q96KB5;Q96KB5-2;E5RFX4 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 0 ;; 216.12 1.43E-06 705911000 590910 696680 612210 718790 715050 687660 719400 702120 757430 809340 FALSE TRUE 567816.5839 676811.3685 722849.9655 755886.838 738050.2326 701564.9564 728204.2324 687620.9766 671449.7218 754522.6809 0.752550716 0.897005995 0.958022845 1.001807974 0.978168386 0.929812945 0.965119076 0.911332415 0.889899984 1 19.52520474 4.6994088 2.481167621 0.951047467 0.7182045 0.758056113 0.034397035 0.236637851 1.941993941 0.009103843 0.112347526 50050.54372 -4.6994088 -0.232842967 AAKPGPAEAPS(ph)PTASPSGDASPPATAPYDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPS(0.857)PT(0.138)AS(0.005)PSGDASPPATAPYDPR 138.69 1.95E-07 4566200000 293540 339720 314660 301680 322080 347450 352780 354980 377040 324640 TRUE FALSE 282068.1323 330031.5182 371526.0616 317249.741 332439.9957 354475.6771 357097.4272 347649.539 334239.9999 302651.8436 0.931988812 1.09046591 1.227569134 1.0482333 1.098423825 1.171232505 1.1798951 1.148678081 1.104371267 1 18.20729961 4.699535436 3.855688323 1.131130132 0.919587191 0.441066102 0.063049007 0.17902027 5.073212235 0.014409234 0.098657966 50065.14016 -4.699535436 -0.211542941 GFAVLEYETAEMAEEAQQQADGLSLGGSHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFAVLEYETAEMAEEAQQQADGLSLGGSHLR 31 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 ;;; 243.28 5.08E-46 356397000 125872.2 139701.8 120143.6 139873.1 132555.3 151556.9 152321.1 130276.8 138973.3 166387.2 FALSE TRUE 120952.9753 135717.6414 141856.2211 147091.9675 136819.0616 154621.4844 154185.2512 127586.5386 123197.6336 155117.6467 0.779749937 0.874933602 0.914507305 0.948260695 0.882034149 0.99680138 0.993989107 0.822514661 0.79422062 1 17.2430033 4.699565746 2.276304161 0.914332453 0.752783787 0.280540514 0.067507853 0.785873033 5.108321854 0.017863895 0.245501018 50068.63433 -4.699565746 -0.161548667 VSDGIYQHVDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSDGIYQHVDVR 12 0 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 0 ; 110.92 0.0014375 931200000 645810 751160 660880 803000 729870 761650 794370 685980 789210 870200 FALSE TRUE 620571.0312 729737.6523 780315.7172 844442.9262 753346.9314 777051.0848 804091.7377 671814.2733 699622.1894 811260.5789 0.764946612 0.8995108 0.96185583 1.040902206 0.928612768 0.957831682 0.991163331 0.828111572 0.862388988 1 19.62980586 4.700091067 3.031983949 0.939645293 0.744580376 0.449591414 0.060014689 0.341060108 4.862937298 0.016120997 0.152493593 50129.23387 -4.700091067 -0.195064917 SRT(ph)PSNDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTPSNDGK 9 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SRT(0.865)PS(0.134)NDGK 90.005 0.074664 28773000 132540 110080 87341 79815 88389 90229 95032 116540 102240 108590 TRUE FALSE 127360.1903 106940.6262 103125.4616 83934.26172 91232.11246 92053.4922 96195.03004 114133.4083 90634.14383 101235.1026 1.258063528 1.056359143 1.01867296 0.829102353 0.901190498 0.909304084 0.950214181 1.12740942 0.895283765 1 16.6273501 4.700116404 1.776911955 0.958071812 1.340752022 0.596881222 0.076900463 0.646348748 2.188660016 0.022651994 0.406092037 50132.15848 -4.700116404 0.38268021 SGS(ph)PISSEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSPISSEER 10 0 H8Y6P7;P0CAP2-3;P0CAP2;P0CAP1-11;P0CAP2-2 H8Y6P7 GCOM1;POLR2M DNA-directed RNA polymerase II subunit GRINL1A 1 S(0.006)GS(0.988)PIS(0.006)SEER 106.29 0.0025556 283560000 179250 200760 189510 183770 194210 202510 196830 201030 206920 217420 TRUE FALSE 172244.7118 195034.5214 223758.6726 193254.3917 200456.941 206604.891 199238.8644 196878.6602 183431.3091 202693.9497 0.849777273 0.962211855 1.103923787 0.953429503 0.988963614 1.01929481 0.982954176 0.97131 0.904966869 1 17.6289435 4.700146456 4.320655175 0.990154246 0.84370698 0.431612608 0.048083623 0.170015695 6.771772249 0.01141491 0.068800956 50135.62758 -4.700146456 -0.146447266 LDSHPCLEVTAAALR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDSHPCLEVTAAALR 15 0 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 237.46 9.73E-18 3735170000 3778150 4273680 3706630 4339150 4372690 4218930 4691130 4342670 4774250 5124000 FALSE TRUE 3630495.721 4151798.831 4376500.495 4563094.052 4513341.545 4304239.655 4748541.452 4252992.347 4232297.155 4776946.916 0.760003363 0.869132294 0.916171055 0.955232313 0.944817186 0.901044062 0.994053636 0.890316016 0.885983711 1 22.18765741 4.700306073 1.685550681 0.933843028 0.707283923 0.680314653 0.037354055 0.499298915 1.47677043 0.009519474 0.178995841 50154.0574 -4.700306073 -0.226559105 DYDEEEQGYDS(ph)EKEKKEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYDEEEQGYDSEKEKKEEK 19 3 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEKKEEK;DYDEEEQGYDS(1)EKEKKEEK 275.42 1.39E-39 1868410000 2141890 1109660 582271 245621 794060 705840 652200 917820 1051950 505200 TRUE FALSE 2058182.571 1078013.583 687500.3222 258297.5292 819601.661 720112.5684 660181.8187 898866.6963 932537.0461 470982.354 4.369978096 2.288861937 1.45971567 0.548422944 1.740196112 1.528958701 1.401712427 1.908493362 1.979982983 1 18.84531348 4.700368454 2.383664452 1.482802929 4.907962179 0.827637659 0.403388878 0.202011793 1.484777857 0.105657666 1.378008913 50161.262 -4.700368454 3.425159251 ELNHMLSDTGNR ddPTM_BT-474_Pertuzumab_2h_R1 8 ELNHMLSDTGNR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;; 198.74 1.80E-07 11682290000 5886453 7057820 5866409 8639330 6540073 7380380 7501680 7452560 6703760 7300190 FALSE TRUE 5656403.909 6856537.884 6926599.604 9085206.857 6750440.388 7529616.34 7593487.804 7298662.032 5942777.269 6805741.629 0.83112234 1.007463735 1.017758237 1.334932672 0.991874325 1.106362356 1.115747294 1.07242714 0.873200541 1 22.69832095 4.700497939 2.041098512 1.077087151 0.77509646 0.276279829 0.112493847 0.802976576 3.898264292 0.027985183 0.43744239 50176.2198 -4.700497939 -0.301990691 AALTGLLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALTGLLHR 9 0 P55084-2;P55084;B5MD38;C9JEY0;C9JE81 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 144.12 0.00010031 355670000 864050 1127810 1002050 1329320 982330 1024770 1376290 1308980 1309640 1286390 FALSE TRUE 830281.9707 1095645.963 1183142.725 1397926.365 1013927.537 1045491.552 1393133.449 1281949.106 1160975.158 1199261.66 0.69232762 0.913600426 0.986559285 1.165655846 0.845459811 0.871779351 1.161659291 1.068948628 0.968074939 1 20.19371504 4.700810184 1.987120097 1.017119333 0.61277544 0.479762662 0.099775118 0.602780312 2.725642028 0.026823355 0.432038371 50212.30803 -4.700810184 -0.404343893 EATDAIGHLDR ddPTM_BT-474_Pertuzumab_2h_R1 6 EATDAIGHLDR 11 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 232.56 2.45E-13 23161440000 13241680 14370300 12032110 14695800 14004300 15062200 14845500 14312930 14978100 14990200 FALSE TRUE 12724180.51 13960473.11 14206579.93 15454252 14454761.03 15366768 15027183.67 14017362.99 13277848.88 13974900.4 0.910502411 0.998967629 1.01657826 1.105857756 1.03433732 1.099597676 1.075298087 1.00303849 0.950121181 1 23.73633467 4.700856 1.840105074 1.040838065 0.875846559 0.410000758 0.045430597 0.77057736 2.851714725 0.012293155 0.213949418 50217.60542 -4.700856 -0.164991506 FVESVDEYQFVER ddPTM_BT-474_Pertuzumab_2h_R1 1 FVESVDEYQFVER 13 0 E9PI78;E9PNF1;Q13405 E9PI78 MRPL49 "39S ribosomal protein L49, mitochondrial" 0 96.604 0.00968 50626000 84320 103900 94243 103110 100890 98394 105300 121370 103360 112830 FALSE TRUE 81024.68118 100936.8737 111274.8065 108431.5195 104135.2185 100383.5941 106588.6929 118863.6671 91627.00612 105187.9236 0.770285014 0.959586141 1.057866747 1.0308362 0.989992148 0.954326225 1.013316826 1.130012486 0.871079141 1 16.68260956 4.701193693 3.079495473 1.015337634 0.74230541 0.544014661 0.063929487 0.231675925 3.448847669 0.015731566 0.146490233 50256.66814 -4.701193693 -0.273032224 ELLS(ph)PLSEPDDRYPLIVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLS(0.97)PLS(0.03)EPDDRYPLIVK;ELLS(0.5)PLS(0.5)EPDDRYPLIVK 214.14 2.91E-18 117977000 186019 211730 185118 212652 201620 219066 216947 221980 251410 238300 TRUE FALSE 178749.1718 205691.6677 218572.9405 223626.9952 208105.2904 223495.6646 219602.0623 217396.0354 222870.9908 222159.7287 0.804597543 0.925872879 0.983854913 1.006604556 0.936737237 1.006013403 0.988487263 0.97855735 1.00320158 1 17.7612378 4.701290465 1.977626471 0.986740936 0.758858117 0.890785541 0.019612911 0.193886925 0.865038591 0.004814021 0.078099253 50267.86788 -4.701290465 -0.227882819 TTNTWVLHMDGENFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTNTWVLHMDGENFR 15 0 Q9NVQ4;Q9NVQ4-3;Q9NVQ4-2;C9JDZ2 Q9NVQ4 FAIM Fas apoptotic inhibitory molecule 1 0 123.97 9.95E-05 112600000 76917 91178 80619 91704 94255 99293 95711 84852 98546 101370 FALSE TRUE 73910.9986 88577.69271 95188.64666 96436.85443 97286.79768 101300.7725 96882.33985 83099.77655 87359.47122 94504.11961 0.782092875 0.937289222 1.007243357 1.020451329 1.029445045 1.071919117 1.025165255 0.879324382 0.924398551 1 16.5280896 4.701349265 2.649023555 0.990834465 0.749538082 0.598505153 0.052414422 0.342573594 3.353081354 0.015350328 0.175635843 50274.67416 -4.701349265 -0.241296382 LVPDSDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVPDSDVR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 113.7 0.0065116 375560000 569390 649190 522690 804980 583700 624000 674760 656480 642960 687800 FALSE TRUE 547137.6093 630675.7368 617151.7102 846525.1143 602475.2406 636617.7075 683017.9147 642923.4586 569973.8763 641214.6934 0.853283019 0.983564075 0.962472814 1.320189826 0.939584272 0.992830816 1.065193798 1.002664888 0.888897092 1 19.29044796 4.701588978 2.062372745 1.028372641 0.814827336 0.174965433 0.109759884 1.108174458 5.518609742 0.027692511 0.430202728 50302.43147 -4.701588978 -0.213545305 FLSDPQVHTVLVER ddPTM_BT-474_Pertuzumab_2h_R1 3 FLSDPQVHTVLVER 14 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 186.68 1.04E-06 1393820000 1606970 2014160 1821990 2106860 1970750 2063140 2217010 1917660 2212000 2320720 FALSE TRUE 1544167.836 1956718.129 2151264.123 2215595.297 2034140.964 2104858.104 2244142.432 1878059.651 1960903.033 2163535.567 0.713724266 0.904407655 0.99432806 1.024062341 0.940192985 0.972878901 1.037257009 0.868051203 0.906341945 1 21.04495941 4.701622202 2.935857367 0.962819096 0.682073735 0.701845477 0.049681654 0.205138499 2.669721584 0.013032901 0.129914881 50306.27977 -4.701622202 -0.280745361 KDDSHSAEDS(ph)EDEKEDHKNVR ddPTM_BT-474_Pertuzumab_2h_R1 12 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR 269.94 2.06E-38 21215611000 6028630 4319350 3070167 2363421.7 3448178 3460504 3470717 4121872 5388574 3836245 TRUE FALSE 5793024.475 4196166.367 3625014.472 2485398.177 3559091.777 3530477.762 3513192.673 4036753.903 4776885.67 3576412.709 1.619786346 1.173289189 1.013589529 0.694941658 0.995156898 0.987156139 0.982323059 1.128715904 1.33566399 1 21.7700818 4.701695327 2.505329043 1.014044703 1.72386963 0.598023689 0.14876327 0.333516301 2.800436865 0.039478091 0.486693218 50314.75086 -4.701695327 0.709824927 RSDS(ph)VSASER ddPTM_BT-474_Pertuzumab_2h_R1 1 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RS(0.001)DS(0.995)VS(0.003)ASER 122.45 0.00029909 48665000 35505 20403 10860 14465 18346 13984 11719 25351 8723.1 6765.4 TRUE FALSE 34117.42535 19821.12642 12822.64358 15211.54038 18936.11575 14266.76606 11862.42063 24827.49299 7732.890258 6307.173432 5.40930509 3.142632216 2.033025367 2.411784066 3.002314104 2.261990449 1.880782375 3.936389772 1.226046872 1 12.62277789 4.701998912 2.850514088 2.421785485 5.815350854 0.57669866 0.811611687 0.265378801 3.179501312 0.192168997 1.998550524 50349.93478 -4.701998912 3.393565368 SDS(ph)LLSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.016)DS(0.984)LLSFR;S(0.011)DS(0.969)LLS(0.02)FR;S(0.011)DS(0.988)LLSFR;SDS(0.991)LLS(0.009)FR 197.86 0.00014749 277662000 1268080 743530 352409 456739 355872 294585 276277 641713 399905 351869 TRUE FALSE 1218522.032 722325.2524 416097.1456 480311.3545 367318.9461 300541.7105 279658.1606 628461.4023 354509.4609 328036.5992 3.714591709 2.201965433 1.268447321 1.464200506 1.119749891 0.916183472 0.852521216 1.915827087 1.080700939 1 18.32349726 4.702084468 1.69505511 1.229826646 4.485633252 0.874644681 0.294673743 0.303074638 0.906580759 0.083245742 1.569462302 50359.85468 -4.702084468 3.255806606 up TEVHIRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TEVHIRPK 8 1 P28838-2;P28838;H0Y9Q1 P28838-2 LAP3 Cytosol aminopeptidase 0 117.04 0.0012956 281520000 315700 351570 320700 313440 326150 367750 357520 355400 355070 386700 FALSE TRUE 303362.095 341543.5678 378657.6239 329616.676 336640.911 375186.157 361895.4367 348060.8658 314763.9422 360508.4646 0.841483973 0.947394032 1.050343227 0.914310504 0.933794748 1.040713863 1.003847267 0.965472104 0.8731111 1 18.45967361 4.702103405 4.065885943 0.973030399 0.834278303 0.357726986 0.052351055 0.217676769 7.282483224 0.012512896 0.081495488 50362.05055 -4.702103405 -0.138752095 AGGIETIANEFSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGGIETIANEFSDR 14 0 Q92598-2;Q92598;Q92598-3;R4GN69 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;; 237.08 6.45E-17 829000000 371868 444730 398928 433171 442128 446210 473736 487720 489900 525870 FALSE TRUE 357334.9874 432046.7358 471023.1637 455527.0072 456349.4487 455232.6719 479533.7229 477648.4116 434288.6058 490252.3565 0.728879694 0.881274164 0.96077695 0.929168419 0.930846007 0.928568044 0.978136497 0.974290904 0.885847054 1 18.90316504 4.702501757 2.207924885 0.948747949 0.681308294 0.82227718 0.030938266 0.217179419 1.29440816 0.007644086 0.110453534 50408.26583 -4.702501757 -0.267439655 AAS(ph)LNYLNQPSAAPLQVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 AASLNYLNQPSAAPLQVSR 19 0 Q9NSK0-3;Q9NSK0;Q9NSK0-5 Q9NSK0-3 KLC4 Kinesin light chain 4 1 AAS(1)LNYLNQPSAAPLQVSR;AAS(1)LNYLNQPSAAPLQVSR;AAS(1)LNYLNQPSAAPLQVSR;AAS(1)LNYLNQPSAAPLQVSR 411.11 9.57E-148 2129640000 2621140 1555380 866340 1040310 1036100 807060 661930 2008980 834200 735220 TRUE FALSE 2518702.951 1511022.085 1022906.91 1094000.524 1069427.097 823379.3062 670030.8973 1967493.861 739505.1133 685422.8945 3.674670005 2.204510671 1.492373421 1.596095684 1.560244203 1.201271963 0.977543795 2.870481679 1.078903432 1 19.38663486 4.702506456 2.242970536 1.57626446 4.116036012 0.614331586 0.526980468 0.403300508 2.507214383 0.138694947 1.967549731 50408.81129 -4.702506456 2.539771553 LTPLEACAHSFFDELRDPNVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTPLEACAHSFFDELRDPNVK 21 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 0 147.06 6.19E-08 324460000 86831 97457 97810 86594 85912 111290 82566 89633 119320 114530 FALSE TRUE 83437.54852 94677.62178 115486.4428 91063.12672 88675.4375 113540.3601 83576.46741 87782.04723 105775.2938 106772.7811 0.781449614 0.886720574 1.081609391 0.85286836 0.83050602 1.063382998 0.782750684 0.82213881 0.990657851 1 16.70418439 4.70253343 4.781455308 0.912221317 0.77739501 0.147387707 0.10036229 0.338956699 18.74368466 0.024182155 0.13363189 50411.94227 -4.70253343 -0.134826307 S(ph)VRPTDSNVSPAISIHEIGAVGATK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVRPTDSNVSPAISIHEIGAVGATK 25 1 A6NIT2;A6NMN0;P46020-3;P46020-2;P46020 A6NIT2 PHKA1 "Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform" 1 S(0.29)VRPT(0.29)DS(0.21)NVS(0.21)PAISIHEIGAVGATK 132.51 4.21E-05 298850000 91662 121030 106640 150490 110550 111590 138770 122190 140890 145890 TRUE FALSE 88079.7477 117578.3429 125912.2202 158256.8069 114105.9411 113846.4263 140468.3088 119666.7338 124896.7579 136008.7404 0.647603584 0.86449108 0.925765652 1.163578212 0.838960355 0.83705228 1.032788837 0.879845909 0.918299497 1 17.05333984 4.702966432 2.346153397 0.945258533 0.59030923 0.490117444 0.093099272 0.448573446 3.145113344 0.023366865 0.314774546 50462.22924 -4.702966432 -0.354949303 SASS(ph)GLGEFNAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASSGLGEFNAR 12 0 Q86YS3-2;Q86YS3 Q86YS3-2 RAB11FIP4 Rab11 family-interacting protein 4 1 SAS(0.108)S(0.892)GLGEFNAR 112.08 0.00024384 0 46505 59044 53066 64703 52973 56520 64154 71082 71406 66060 TRUE FALSE 44687.53319 57360.12293 62656.20665 68042.32958 54676.92465 57662.87312 64939.13584 69614.13186 63300.29024 61585.69736 0.725615445 0.931387082 1.017382433 1.1048398 0.887818552 0.936302999 1.054451579 1.130361997 1.027840764 1 15.91030772 4.703167379 2.042254995 1.027525322 0.652797058 0.632556009 0.067847606 0.45428247 2.198370026 0.01946481 0.3078687 50485.5834 -4.703167379 -0.374728263 SSGGGYGGGPAGGHGGNR ddPTM_BT-474_Pertuzumab_2h_R1 5 SSGGGYGGGPAGGHGGNR 18 0 Q9H2U1-2;Q9H2U1;Q9H2U1-3 Q9H2U1-2 DHX36 ATP-dependent RNA helicase DHX36 0 ;;;; 171.46 1.32E-11 127056000 73699.9 83400.8 73024.4 81794.7 78001.2 86794.4 80853.3 82569.4 92980.6 94947.4 FALSE TRUE 70819.62643 81022.29084 86221.5335 86016.13427 80510.17944 88549.44224 81842.80687 80864.31304 82425.83209 88516.52803 0.800072348 0.915335166 0.974072701 0.971752239 0.909549677 1.000371843 0.924604802 0.913550439 0.931191428 1 16.43365924 4.703508107 3.159267704 0.947558722 0.783853447 0.669398178 0.032111171 0.184294304 2.947187078 0.007815847 0.071129153 50525.2076 -4.703508107 -0.163705275 LTQLQELDLSNNHLETLPDNLGLSHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTQLQELDLSNNHLETLPDNLGLSHLR 27 0 Q9UFC0;H7C5S6 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 0 74.206 0.010149 192170000 31188 43630 44219 44131 41227 48109 49056 41363 43236 47305 FALSE TRUE 29969.13848 42385.71512 52210.35695 46408.6062 42553.1039 49081.79694 49656.362 40508.8396 38328.03054 44100.99022 0.679557042 0.961105746 1.183881738 1.052325718 0.964901325 1.112940927 1.125969321 0.918547166 0.869096824 1 15.42852343 4.703628955 3.86987684 1.028663127 0.656847702 0.561384658 0.091920886 0.165454848 4.791852774 0.023307695 0.162352556 50539.26891 -4.703628955 -0.371815425 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAKK ddPTM_BT-474_Pertuzumab_2h_R1 4 HAPSPEPAVQGTGVAGVPEESGDAAAIPAKK 31 1 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK 237.65 4.01E-46 1866440000 1099270 1013720 737814 776766 776105 872480 830064 570493 1018140 999010 TRUE FALSE 1056309.313 984809.6981 871153.4024 816854.9863 801069.1222 890122.1434 840222.5715 558712.1202 902565.0156 931346.1629 1.134174763 1.05740458 0.935370152 0.877069149 0.860119636 0.955737167 0.902159267 0.599897377 0.969097261 1 19.82895796 4.703677056 0.71340463 0.836984798 1.33004273 0.358088487 0.108223116 2.716660492 1.083683517 0.045564326 1.076245996 50544.86677 -4.703677056 0.493057932 HHDAEHHRGERPGKPD ddPTM_BT-474_Pertuzumab_2h_R1 1 HHDAEHHRGERPGKPD 16 3 Q5T3G2 Q5T3G2 TLE1 0 90.367 0.0032823 13241000 19415 27395 10582 6200.4 9650.5 17109 3608 906.46 5012.8 1605.8 FALSE TRUE 18656.24034 26613.72142 12494.4028 6520.403387 9960.917097 17454.9557 3652.155783 887.7412842 4443.767959 1497.037736 12.46210425 17.77758889 8.346084068 4.355537093 6.653751512 11.65966314 2.439588326 0.592998602 2.968374045 1 10.54789487 4.703764704 0.29580287 0.10465136 27.37942983 0.635354557 3.254262484 4.900234728 0.35829637 3.98920182 48.82151968 50555.06856 -4.703764704 27.27477847 YAALSVDGEDENEGEDYAE ddPTM_BT-474_Pertuzumab_2h_R1 2 YAALSVDGEDENEGEDYAE 19 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 317.77 2.08E-61 860310000 559670 624590 552260 601300 578880 676820 600140 609110 663960 692380 FALSE TRUE 537797.4777 606777.3047 652065.667 632333.1651 597500.2009 690505.7641 607484.6928 596531.6656 588590.0443 645484.4859 0.833168712 0.940033909 1.010195723 0.979625659 0.925661598 1.069748041 0.941129812 0.92416112 0.911857771 1 19.3000229 4.703924169 3.623812349 0.966532252 0.822695096 0.442571569 0.045876561 0.235378096 5.606468327 0.011373127 0.086229555 50573.63493 -4.703924169 -0.143837156 FSLDVCEAMEYLEGNNFVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSLDVCEAMEYLEGNNFVHR 20 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 ; 241.74 9.34E-30 282770000 236470 272000 222080 280370 306390 303700 258480 259980 307030 308660 FALSE TRUE 227228.491 264242.8263 262214.7961 294839.9293 316245.3126 309841.0221 261643.3556 254611.3221 272177.2416 287754.1833 0.789661816 0.918293605 0.911245818 1.024624302 1.099012042 1.076755926 0.909259954 0.884822313 0.945867193 1 18.13447738 4.704123078 1.448892774 0.980303329 0.72667125 0.447001429 0.066565587 1.286948928 2.589498238 0.02167045 0.463844393 50596.80322 -4.704123078 -0.253632079 SS(ph)TDSLPGPISR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 S(0.227)S(0.772)TDSLPGPISR;S(0.036)S(0.963)T(0.001)DSLPGPISR 175.74 2.82E-05 632780000 598210 695280 571650 715910 732170 768910 736770 778980 712590 761080 TRUE FALSE 574831.2918 675451.2952 674959.8713 752858.2009 755720.913 784457.887 745786.8117 762893.7908 631699.7706 709531.3737 0.810156271 0.951968187 0.951275583 1.061064005 1.065098657 1.1056 1.051097724 1.075207974 0.890305621 1 19.43650695 4.704294848 1.107397641 1.044185552 0.713496462 0.562205787 0.059178365 1.102191795 1.162824554 0.017351654 0.421119757 50616.81892 -4.704294848 -0.33068909 (ac)S(ph)QERPTFYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQERPTFYR 9 1 Q16539-2;Q16539;Q16539-5;Q16539-3;Q16539-4;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 1 S(0.998)QERPT(0.002)FYR 64.207 0.0031512 0 22336 29953 27098 33423 33042 27500 31827 38487 25268 31993 TRUE FALSE 21463.08443 29098.76977 31995.21139 35147.96504 34104.82594 28056.06884 32216.50835 37692.23 22399.68257 29826.08561 0.719607819 0.975614774 1.072725795 1.178430368 1.143456315 0.940655412 1.080145372 1.263733716 0.751009799 1 14.86428703 4.704299612 2.278391959 1.077550204 0.64609606 0.347079552 0.134446237 0.555079101 3.588045393 0.033129414 0.46539224 50617.37416 -4.704299612 -0.431454145 S(ph)TSDLDKDDASYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 STSDLDKDDASYLR 14 1 Q8TEP8;H0Y966 Q8TEP8 CEP192 Centrosomal protein of 192 kDa 1 S(0.99)T(0.01)SDLDKDDASYLR 172.93 1.68E-06 158270000 178050 155780 124530 128080 132180 124080 107460 177010 164560 139510 TRUE FALSE 171091.6092 151337.3069 147035.3412 134690.2241 136431.6897 126588.9826 108775.1276 173354.6816 145879.8387 130060.8634 1.315473422 1.163588361 1.130511802 1.035593803 1.048983423 0.973305722 0.836340193 1.332873526 1.121627481 1 16.98882738 4.704612137 1.345809792 1.065031772 1.40878062 0.31402959 0.119520106 1.749982378 2.937003695 0.036086367 0.808917582 50653.81239 -4.704612137 0.343748848 KATKS(ph)PAKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KATKSPAKPK 10 3 P16401 P16401 HIST1H1B Histone H1.5 1 KAT(0.015)KS(0.985)PAKPK;KAT(0.03)KS(0.97)PAKPK 115.8 0.0064889 2223900000 10189900 5557300 2968500 2012100 3537200 2774800 3138900 4531400 2833600 1580070 TRUE FALSE 9791667.442 5398811.245 3504973.984 2115944.722 3650977.25 2830908.357 3177314.797 4437825.006 2511941.607 1473050.452 6.6472044 3.665055219 2.379398465 1.436437374 2.478514736 1.9218 2.156962644 3.012676858 1.705265156 1 20.49037541 4.704786786 1.865445727 2.113296455 7.891502574 0.875146826 0.537066049 0.247182756 0.941244832 0.139207992 2.433146381 50674.18651 -4.704786786 5.778206119 EAELGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAELGAR 7 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YBN4;Q4VXU2;Q4VXU2-2 P11940-2 PABPC1;PABPC3;PABPC1L Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3;Polyadenylate-binding protein 1-like 0 ; 162.21 0.0029787 945760000 1153180 1302560 1137820 1291390 1244660 1203840 1367980 1326590 1376450 1439730 FALSE TRUE 1108112.451 1265412.264 1343449.385 1358038.793 1284695.619 1228182.47 1384721.748 1299195.453 1220201.167 1342215.805 0.825584416 0.942778546 1.000919062 1.011788706 0.957145352 0.915040983 1.031668487 0.96794826 0.90909462 1 20.35618522 4.705362576 3.202537288 0.974370687 0.809455864 0.580907644 0.037745976 0.210280667 3.494745615 0.009158106 0.082631213 50741.41526 -4.705362576 -0.164914823 LSMPQSAAVSTT(ph)PPHNR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSMPQSAAVSTTPPHNR 17 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVST(0.006)T(0.994)PPHNR;LSMPQSAAVS(0.004)T(0.068)T(0.929)PPHNR;LSMPQSAAVST(0.047)T(0.953)PPHNR;LSMPQSAAVST(0.007)T(0.993)PPHNR 192.25 7.26E-10 3382690000 1062730 1215200 1063810 1251130 1133590 1123630 1236500 1247620 1313220 1376620 TRUE FALSE 1021197.337 1180543.686 1256064.131 1315700.969 1170052.952 1146350.568 1251632.657 1221856.211 1164148.771 1283380.301 0.795709063 0.919870505 0.978715452 1.025184014 0.911696206 0.893227493 0.975262481 0.952060905 0.907095714 1 20.29151731 4.705556886 3.183898839 0.953327728 0.778381828 0.587342123 0.040050541 0.218130078 3.564634633 0.009956742 0.090656441 50764.12284 -4.705556886 -0.1749459 LNT(ph)SDFQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LNTSDFQK 8 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 LNT(0.92)S(0.08)DFQK;LNT(0.985)S(0.015)DFQK;LNT(0.887)S(0.113)DFQK;LNT(0.96)S(0.04)DFQK 205.52 0.00088071 7199600000 17374700 10947700 6689000 4363010 6401000 4918000 3068870 8898400 5701200 3520830 TRUE FALSE 16695677.52 10635482.31 7897851.096 4588185.469 6606893.978 5017445.33 3106427.749 8714644.93 5054023.677 3282361.048 5.086484171 3.240192702 2.406149409 1.39783083 2.012848033 1.528608601 0.946400382 2.654992794 1.539752515 1 21.64630251 4.70575266 1.237966343 1.674199316 6.515907708 0.839055586 0.478674156 0.527427283 0.722631086 0.137431537 3.222526684 50787.01172 -4.70575266 4.841708393 DLVEAVAHILGIR ddPTM_BT-474_Pertuzumab_2h_R1 3 DLVEAVAHILGIR 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 225.67 2.80E-11 4660000000 2139286 2350407 2001740 2472491 2176904 2272972 2436377 2032622 2784878 2883910 FALSE TRUE 2055680.338 2283375.694 2363498.946 2600096.557 2246926.094 2318933.051 2466194.111 1990647.645 2468750.325 2688580.207 0.764596992 0.849286805 0.87908813 0.967089079 0.835729612 0.862512134 0.917284931 0.740408503 0.918235699 1 21.35841308 4.705822976 2.813080694 0.874824895 0.748878289 0.211145345 0.069036712 0.66090907 7.599662706 0.017048323 0.184194106 50795.23524 -4.705822976 -0.125946606 YGGPPPGWEGPHPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGGPPPGWEGPHPQR 15 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7;D6RBP6;D6RFL5;D6RA49 B7Z8Z7 RBM47 RNA-binding protein 47 0 ; 192.18 1.45E-07 662170000 411560 445380 377190 447910 415180 410960 466290 460470 489170 479940 FALSE TRUE 395475.7802 432678.1985 445356.6235 471026.6888 428534.6418 419269.8928 471996.5965 450961.1336 433641.4724 447433.2363 0.883876628 0.967022928 0.995358832 1.052730666 0.957762202 0.937055763 1.054898381 1.007884746 0.969175817 1 18.7713129 4.706201872 2.299395624 0.9990125 0.860362508 0.479878563 0.035412468 0.472268191 3.118959623 0.009141089 0.128210623 50839.57039 -4.706201872 -0.138649992 MLAEDELR ddPTM_BT-474_Pertuzumab_2h_R1 11 MLAEDELR 8 0 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ;;;;;;;;;; 175.24 0.00062186 10816199000 13084340 14608070 12372590 15539920 14731990 12462160 15369220 15478290 14983640 15845410 FALSE TRUE 12572989.53 14191462.15 14608592.24 16341937.13 15205857.84 12714153.41 15557313.11 15158657.9 13282760 14772186.27 0.851125846 0.960688004 0.988925537 1.10626395 1.029357305 0.860681905 1.053148994 1.026162115 0.899173607 1 23.81638002 4.706589719 2.322959369 1.000760427 0.821235725 0.291015198 0.067377528 0.669482373 4.541778022 0.01706824 0.236938958 50884.99301 -4.706589719 -0.179524702 GLFS(ph)DEEDSEDLFSSQSASK ddPTM_BT-474_Pertuzumab_2h_R1 4 GLFSDEEDSEDLFSSQSASK 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 GLFS(0.997)DEEDS(0.003)EDLFSSQSASK;GLFS(0.98)DEEDS(0.02)EDLFSSQSASK;GLFS(0.996)DEEDS(0.004)EDLFSSQSASK;GLFS(0.996)DEEDS(0.004)EDLFSSQSASK 242.86 5.33E-30 273964000 330478 324182 268748 326975 329188 339331 351064 375331 401550 426578 TRUE FALSE 317562.5544 314936.6468 317316.7419 343850.2189 339776.631 346192.5053 355360.4262 367580.2837 355967.7274 397685.4921 0.798526878 0.791923902 0.79790877 0.864628521 0.854385281 0.870518317 0.893571511 0.924298952 0.895098601 1 18.60126841 4.706737385 0.112325163 1.084667278 0.502871582 0.931773301 0.016037902 9.877008329 0.182644996 0.201681133 0.938462773 50902.29752 -4.706737385 -0.581795696 ELS(ph)APAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSAPAR 7 0 F5H672;F5H5N2;B4DNC9;B3KQ30;Q9H1K1 F5H672 ISCU "Iron-sulfur cluster assembly enzyme ISCU, mitochondrial" 1 ELS(1)APAR 96.936 0.012972 385280000 601670 643780 539350 649620 603440 656110 656820 673350 633860 689730 TRUE FALSE 578156.0712 625420.0247 636822.5428 683146.9661 622850.1956 669376.9937 664858.3596 659445.0872 561906.8702 643013.9728 0.899134538 0.972638311 0.990371236 1.062413874 0.968641775 1.040999142 1.03397187 1.025553277 0.873864168 1 19.29449056 4.706931236 1.925270784 1.005963227 0.871255119 0.265694896 0.049626459 0.901545288 3.712515872 0.012375447 0.211738315 50925.02325 -4.706931236 -0.134708108 WQVVDTPGILDHPLEDR ddPTM_BT-474_Pertuzumab_2h_R1 5 WQVVDTPGILDHPLEDR 17 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ;;;; 258.82 3.53E-27 1138569000 674805 744743 637915 751722 681240 746899 746706 773711 781037 789011 FALSE TRUE 648432.8746 723503.6588 753200.4308 790518.4625 703152.7033 762001.8095 755844.4114 757733.5975 692376.9541 735570.5822 0.881537259 0.983595152 1.023967583 1.07470103 0.955928255 1.035932959 1.027562045 1.030130372 0.941278745 1 19.48850426 4.707137393 2.788197384 1.014830819 0.861913764 0.522540538 0.036953523 0.285517377 3.197449259 0.008741921 0.096264271 50949.20284 -4.707137393 -0.152917056 LCALRPDDSSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LCALRPDDSSSAR 13 1 K7EIX2;Q6AI08;K7ELR8;K7EKW7;K7EK31;K7ESP5 K7EIX2 HEATR6 HEAT repeat-containing protein 6 0 145 3.79E-05 147030000 131330 161690 146890 168550 163210 142630 168340 154250 181070 201870 FALSE TRUE 126197.4784 157078.7595 173436.2906 177248.8857 168459.7979 145514.0763 170400.1953 151064.6836 160515.6927 188197.1651 0.670559933 0.834649977 0.921566967 0.941825482 0.895123993 0.77320015 0.905434443 0.802693726 0.852912384 1 17.52188537 4.707204736 3.416172874 0.875267077 0.651180741 0.507485732 0.063076408 0.229027952 4.595050206 0.015242084 0.127271168 50957.10375 -4.707204736 -0.224086336 MAPTPIPTRS(ph)PSDSSTASTPVAEQIER ddPTM_BT-474_Pertuzumab_2h_R1 7 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.16)RS(0.817)PS(0.021)DS(0.001)STASTPVAEQIER;MAPTPIPT(0.403)RS(0.563)PS(0.031)DS(0.003)STASTPVAEQIER;MAPTPIPT(0.308)RS(0.676)PS(0.016)DSSTASTPVAEQIER;MAPT(0.017)PIPT(0.212)RS(0.635)PS(0.136)DSSTASTPVAEQIER;MAPTPIPT(0.054)RS(0.893)PS(0.054)DSSTASTPVAEQIER;MAPTPIPT(0.113)RS(0.685)PS(0.172)DS(0.03)STASTPVAEQIER;MAPTPIPT(0.096)RS(0.867)PS(0.036)DS(0.001)STASTPVAEQIER 251.52 1.64E-47 21134780000 2206750 2447440 2009660 2439110 2408280 2867220 2528810 2457080 2559360 2757760 TRUE FALSE 2120507.77 2377641.407 2372850.267 2564992.759 2485744.513 2925197.153 2559758.333 2406340.439 2268832.183 2570974.459 0.824787568 0.924801644 0.922938094 0.997673373 0.966849167 1.137777601 0.995637403 0.93596435 0.882479472 1 21.29388385 4.707796517 1.10920576 0.987143114 0.757821391 0.386948696 0.0623491 1.832818205 1.932120802 0.019850458 0.486992809 51026.5866 -4.707796517 -0.229321723 TGGQVPDTNYIFMGDFVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGGQVPDTNYIFMGDFVDR 19 0 O00743;O00743-3;Q5T1S7 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed;Serine/threonine-protein phosphatase" 0 ; 80.534 0.016659 52428000 18905.8 22825 21888.3 21270 24010 23532 19052.9 24081 24827 24194.5 FALSE TRUE 18166.94043 22174.05335 25844.00271 22367.74725 24782.30346 24007.83316 19286.07509 23583.71893 22008.74304 22555.78496 0.805422665 0.98307611 1.14578157 0.991663437 1.098711638 1.064375866 0.855038968 1.045572964 0.975747157 1 14.46120987 4.707836719 4.162511037 1.021535654 0.793449439 0.429407881 0.074363551 0.183103514 6.733227379 0.017759609 0.116255605 51031.31028 -4.707836719 -0.228086215 QLLDS(ph)DEEQEEDEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLLDSDEEQEEDEGR 15 0 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 QLLDS(1)DEEQEEDEGR;QLLDS(1)DEEQEEDEGR 388.85 2.05E-114 3253000000 855840 973400 836890 993660 1024260 949110 1037780 1031670 986740 1112460 TRUE FALSE 822392.8266 945639.5851 988134.6395 1044942.912 1057206.253 968301.6545 1050480.662 1010365.654 874729.412 1037112.093 0.792964263 0.911800751 0.952775159 1.0075506 1.019375109 0.933651879 1.012890187 0.974210657 0.843428032 1 19.9841404 4.707958978 1.811108297 0.972280562 0.741716187 0.540988455 0.049162022 0.594269513 2.084831756 0.012574189 0.229225417 51045.67818 -4.707958978 -0.230564375 KASVHS(ph)SGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.321)VHS(0.597)S(0.082)GR 128.31 0.00025778 112840000 237270 121040 51885 108470 71163 47847 51824 214410 35289 23169 TRUE FALSE 227997.2261 117588.0577 61261.77368 114068.1497 73452.02252 48814.49912 52458.23761 209982.3586 31283.14066 21599.74299 10.55555273 5.443956335 2.836226972 5.280995692 3.40059706 2.259957405 2.428651009 9.721521161 1.448310782 1 14.39872653 4.707970199 3.204855489 4.097829756 11.27336124 0.421018525 2.409136634 0.324006858 5.392444079 0.608497023 5.565120925 51046.99702 -4.707970199 7.175531479 VTDALPEPEPPGAMAAS(ph)EDEEEEEEALEAMQSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTDALPEPEPPGAMAASEDEEEEEEALEAMQSR 33 0 Q9Y3E7-2;Q9Y3E7-4;Q9Y3E7;Q9Y3E7-3 Q9Y3E7-2 CHMP3 Charged multivesicular body protein 3 1 VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR 280.37 5.61E-74 1037690000 1110473 1206900 1012025 1231647 1195914 1224224 1174726 1267381 1223116 1305043 TRUE FALSE 1067074.487 1172480.394 1194920.43 1295212.449 1234381.66 1248978.648 1189102.648 1241209.139 1084272.999 1216651.275 0.877058619 0.963694707 0.982138805 1.064571645 1.014573103 1.02657078 0.977357006 1.020184801 0.891194561 1 20.21448428 4.708082196 1.933195623 1.001887561 0.844601976 0.41890799 0.042621702 0.66605487 2.766652648 0.010702037 0.183320678 51060.16291 -4.708082196 -0.157285585 IDDIVSGHK ddPTM_BT-474_Pertuzumab_2h_R1 5 IDDIVSGHK 9 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;; 179.8 4.94E-05 3049230000 5187190 5186810 4887790 5272400 5211970 5196610 5787240 6002340 6808580 7050500 FALSE TRUE 4984468.88 5038887.257 5771122.381 5544509.196 5379617.748 5301689.015 5858065.974 5878389.581 6035698.542 6572963.355 0.758329023 0.766608147 0.878009213 0.84353265 0.818446332 0.806590381 0.89123667 0.894328671 0.918261401 1 22.64811251 4.708214168 0.036389304 1.571714897 3.62E-09 0.801294657 0.031305696 202.3227222 1.159235216 19.04922508 32.22252701 51075.68122 -4.708214168 -1.571714893 LSS(ph)PISK ddPTM_BT-474_Pertuzumab_2h_R1 5 LSSPISK 7 0 A0A494C142;Q99728-3;Q99728-2;Q99728 A0A494C142 BARD1 BRCA1-associated RING domain protein 1 1 LS(0.023)S(0.976)PISK;LS(0.014)S(0.985)PISK;LSS(1)PISK;LS(0.002)S(0.998)PISK;LS(0.011)S(0.988)PIS(0.001)K 192.32 0.00053808 1553880000 7031750 6518600 5169410 6171500 6001400 5176120 6406280 7023140 6124480 6536300 TRUE FALSE 6756941.436 6332695.91 6103637.38 6490011.855 6194440.481 5280784.693 6484681.971 6878109.705 5429254.706 6093590.579 1.108860424 1.039238825 1.001648749 1.06505545 1.016550161 0.86661298 1.064180779 1.128744968 0.890977928 1 22.53886114 4.708391227 2.641467126 1.015512285 1.124411049 0.141059487 0.074699415 0.986372685 9.484875626 0.01927696 0.229645597 51096.50867 -4.708391227 0.108898764 IAELLENVTLIHKPVSLQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 IAELLENVTLIHKPVSLQPR 20 1 Q14694;Q14694-3;Q14694-2;J3KT19 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 0 ; 235.84 8.97E-30 937530000 433780 438730 374600 387510 396480 467880 427640 426530 460010 463470 FALSE TRUE 416827.398 426217.85 442298.5529 407509.4375 409233.1393 477340.8542 432873.5862 417722.0064 407791.5933 432078.7641 0.964702348 0.986435542 1.023652606 0.943136926 0.947126249 1.104754257 1.001839531 0.966772823 0.943789946 1 18.7209348 4.708550461 4.86043611 0.991044548 0.963829226 0.028687436 0.046091196 0.770375859 47.29535783 0.011342566 0.063817436 51115.24671 -4.708550461 -0.027215323 LKVEELEGER ddPTM_BT-474_Pertuzumab_2h_R1 1 LKVEELEGER 10 1 Q9Y6D9;Q9Y6D9-3 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 0 74.46 0.03096 0 199350 236410 187790 255110 245960 253130 233060 268090 245320 254000 FALSE TRUE 191559.1816 229667.8183 221727.8304 268276.2577 253871.5268 258248.462 235912.258 262553.8478 217472.3021 236796.3538 0.808961703 0.969895924 0.936365053 1.13294083 1.072109104 1.090593068 0.99626643 1.108774876 0.918393795 1 17.85328734 4.708822181 1.235159672 1.049956671 0.718543152 0.518342987 0.066175432 1.018272272 1.381553455 0.017947326 0.425753025 51147.23734 -4.708822181 -0.331413519 SEAHTADGISIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEAHTADGISIR 12 0 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 0 ; 154.28 7.14E-05 561000000 240440 258340 220493 253390 234910 261950 246990 267180 254390 297050 FALSE TRUE 231043.339 250972.3961 260340.9899 266467.4883 242466.0935 267246.8085 250012.7375 261662.6396 225512.7137 276930.5389 0.834300687 0.906264788 0.94009491 0.96221778 0.875548412 0.965031916 0.902799447 0.944867405 0.814329523 1 18.07916463 4.708829172 3.269379426 0.924438513 0.824677381 0.233474978 0.049453741 0.407382404 7.184558456 0.011018193 0.098544534 51148.06069 -4.708829172 -0.099761132 EAEEVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAEEVYR 7 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 163.34 0.0028812 2038900000 1736580 1815880 1482750 1800050 1773890 1760820 1805350 1907820 1847770 1811150 FALSE TRUE 1668712.534 1764092.88 1750715.909 1892950.796 1830948.783 1796424.987 1827444.413 1868422.85 1638018.896 1688479.197 0.988293215 1.044782123 1.036859626 1.121098086 1.08437746 1.063930778 1.082302001 1.106571436 0.970114941 1 20.68729297 4.708914133 1.567031928 1.069151155 0.96301614 0.154215421 0.044642657 1.475064657 3.577947151 0.011444583 0.23637779 51158.06784 -4.708914133 -0.106135015 FGDILHVINASDDEWWQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FGDILHVINASDDEWWQAR 19 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UK02;E7EQD7;A0A590UK70;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;A0A590UJ25;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;C9JUA9;Q12959-8;A0A590UJX2;A0A590UJ64;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 0 ; 174.02 5.30E-12 469640000 342730 390250 328090 444310 357090 374500 397790 410030 389030 438580 FALSE TRUE 329335.7327 379120.4521 387383.1613 467240.8923 368576.1242 382072.6466 402658.273 401562.7372 344868.9453 408874.586 0.805468826 0.927229192 0.947437612 1.142748677 0.901440532 0.934449486 0.984796529 0.982117136 0.84345899 1 18.64129887 4.709009615 2.296865715 0.970173647 0.771743081 0.306419334 0.073157153 0.662033835 4.338161298 0.018094803 0.257707696 51169.31635 -4.709009615 -0.198430566 FGDFLQHS(ph)PSILQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 FGDFLQHSPSILQSK 15 0 Q96Q89-3;Q96Q89;Q96Q89-2;Q96Q89-5 Q96Q89-3 KIF20B Kinesin-like protein KIF20B 1 FGDFLQHS(1)PSILQSK;FGDFLQHS(0.997)PS(0.003)ILQSK 267.56 1.20E-25 1467900000 1427950 1427070 1283450 1289550 1276350 1347000 1414030 1376140 1425020 1682180 TRUE FALSE 1372144.135 1386371.361 1515397.965 1356103.83 1317404.957 1374237.263 1431335.322 1347722.228 1263257.704 1568244.45 0.874955518 0.884027589 0.966302138 0.864727326 0.840050769 0.876290213 0.912699115 0.85938275 0.805523465 1 20.58071903 4.709081624 0.003787053 1.752757658 3.78E-07 0.062203933 0.053102197 252746.8367 149.9836361 33763.15854 35671.86326 51177.80127 -4.709081624 -1.75275728 MDS(ph)DEDEKEGEEEKVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 MDSDEDEKEGEEEKVAK 17 2 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 1 MDS(1)DEDEKEGEEEKVAK 139.26 4.83E-07 432240000 749080 463210 305360 179450 346490 350020 323370 422030 525620 340950 TRUE FALSE 719805.1254 449999.7043 360545.3447 188711.436 357635.1655 357097.6442 327327.4988 413314.933 465953.8212 317857.1528 2.26455538 1.415729363 1.134299925 0.593698881 1.125144306 1.123453228 1.029794346 1.300316602 1.465922088 1 18.27801903 4.709086782 2.326122992 1.099940544 2.502221966 0.735025077 0.211766891 0.286192084 1.940361906 0.056556597 0.79369917 51178.40916 -4.709086782 1.402281422 ALDLLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALDLLDR 7 0 P27361;E9PBK7;E9PQW4;P27361-3;B3KR49;E9PRH7;H0YEX6 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;;; 162.31 0.0029707 455659000 689860 799620 665260 869570 846030 765630 857740 808450 851670 922590 FALSE TRUE 662899.5085 776815.6205 785487.2806 914448.6119 873243.3233 781111.5632 868237.2787 791755.225 754991.9921 860102.1575 0.77072183 0.903166692 0.91324882 1.063186046 1.01527861 0.908161381 1.00945832 0.920536262 0.877793394 1 19.7141485 4.709149407 1.692166637 0.965160392 0.712445736 0.538532463 0.054861371 0.717115236 2.110193438 0.014867687 0.289260585 51185.78964 -4.709149407 -0.252714656 ARPATDSFDDYPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 159.41 4.48E-06 2203700000 753520 859890 766400 834500 844200 905990 813660 856810 883270 917410 FALSE TRUE 724071.6053 835366.7791 904905.5285 877568.645 871354.4597 924309.7385 823617.8145 839116.5741 783004.8926 855273.0036 0.846597054 0.976725298 1.058031207 1.02606845 1.018802717 1.080718946 0.962988205 0.981109623 0.915502874 1 19.70602548 4.709637531 3.735358216 1.005631311 0.834284369 0.532691489 0.044342331 0.188027732 4.9489329 0.011223043 0.08456829 51243.35209 -4.709637531 -0.171346942 DRDVSEEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DRDVSEEHK 9 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 90.05 0.0070254 57854000 120970 106950 81964 103240 97769 81745 93607 112140 129230 104680 FALSE TRUE 116242.3587 103899.8907 96776.71808 108568.2288 100913.8287 83397.93991 94752.59047 109824.2698 114560.3522 97589.93036 1.191130665 1.064657904 0.991667047 1.112494172 1.034059849 0.854575258 0.970925895 1.125364773 1.173895214 1 16.57444467 4.709691858 3.518022528 1.034971703 1.205280371 0.23329275 0.085628676 0.422438021 9.263507461 0.022382467 0.182327569 51249.76257 -4.709691858 0.170308668 QDPVTYISET(ph)DEEDDFMCKK ddPTM_BT-474_Pertuzumab_2h_R1 2 QDPVTYISETDEEDDFMCKK 20 1 P35251-2;P35251;D6RAD2 P35251-2 RFC1 Replication factor C subunit 1 1 QDPVT(0.308)Y(0.032)IS(0.308)ET(0.352)DEEDDFMCKK;QDPVTYIS(0.108)ET(0.892)DEEDDFMCKK 198.24 9.23E-22 373250000 213684 153487 101037 126751 143016 114836 132602 177298 131351 115821 TRUE FALSE 205332.993 149109.701 119296.6335 133292.6343 147616.2395 117158.0626 134224.8229 173636.7343 116440.5851 107976.3405 1.90164801 1.380947903 1.104840495 1.234461491 1.367116526 1.085034574 1.243094759 1.608099826 1.078389808 1 16.7203557 4.70970262 3.44784626 1.257029464 1.962946197 0.587437589 0.169806176 0.201306435 4.15535278 0.042537306 0.355923111 51251.03255 -4.70970262 0.705916733 RLAEDEAFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLAEDEAFQR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 143 0.0085502 0 70480 83668 66512 87041 87060 91022 93085 92212 84726 85416 FALSE TRUE 67725.56368 81281.87056 78532.19795 91533.19644 89860.36397 92862.5272 94224.20207 90307.78998 75108.25968 79630.69824 0.850495665 1.020735374 0.986205065 1.149471227 1.128463846 1.166164925 1.183264798 1.134082609 0.943207348 1 16.28103709 4.709857957 1.063374593 1.113978272 0.742080722 0.46195998 0.077842922 1.392803738 1.327673294 0.02328574 0.580765906 51269.36721 -4.709857957 -0.371897551 SVDETLR ddPTM_BT-474_Pertuzumab_2h_R1 7 SVDETLR 7 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;;; 196.86 0.0010129 10057020000 8690440 9546420 8136870 9937580 9143260 9221180 9684820 9465280 9686630 10213620 FALSE TRUE 8350807.997 9274165.449 9607383.413 10450459.69 9437361.262 9407638.578 9803345.724 9269818.66 8587044.372 9521842.42 0.877015984 0.973988545 1.00898366 1.097524957 0.991127646 0.988006119 1.029563953 0.973532038 0.901825928 1 23.18280932 4.710240132 2.954469614 1.000617674 0.860431673 0.385876959 0.045908531 0.375429201 4.935782575 0.011642437 0.120544211 51314.5036 -4.710240132 -0.140186002 LVHGDIFRPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVHGDIFRPPR 11 1 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 120.77 0.00025567 291640000 90618 127920 119410 149870 95784 110810 136900 142880 155780 159430 FALSE TRUE 87076.54838 124271.8468 140990.0433 157604.8087 98864.97935 113050.6541 138575.4232 139929.4781 138096.5075 148631.6641 0.585854629 0.836106139 0.948586858 1.060371689 0.665167681 0.760609489 0.932341194 0.941451332 0.929119029 1 17.18138197 4.710267779 3.261685337 0.898230203 0.551874006 0.437327475 0.108040221 0.296070436 5.184189644 0.02751049 0.248892047 51317.77036 -4.710267779 -0.346356197 MIMATNRPDTLDPALLRPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MIMATNRPDTLDPALLRPGR 20 2 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 155.28 1.78E-08 2727100000 1874550 2055890 1786900 2072910 1998800 2165610 2131100 2249500 2231820 2429630 FALSE TRUE 1801290.514 1997258.03 2109832.579 2179893.134 2063093.217 2209400.118 2157181.039 2203047.039 1978473.15 2265068.996 0.795247525 0.881764765 0.931465038 0.962395908 0.910830187 0.975422878 0.952368799 0.972618072 0.873471472 1 21.11112357 4.710406255 1.391537 0.950377895 0.73447508 0.670397852 0.033565595 0.650426946 1.173719715 0.008644195 0.194288118 51334.13582 -4.710406255 -0.215902815 FICEQDHQNFLR ddPTM_BT-474_Pertuzumab_2h_R1 7 FICEQDHQNFLR 12 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;;; 339.13 1.56E-58 11240910000 4275663 4977360 4446250 5083200 4770990 4786221 4909866 4854941 5276730 5864150 FALSE TRUE 4108565.363 4835410.566 5249786.281 5345544.561 4924453.226 4883001.668 4969954.409 4754684.772 4677737.732 5466965.897 0.751525698 0.884477909 0.960274196 0.977789996 0.900765309 0.893183122 0.909088241 0.869711804 0.855636896 1 22.38230895 4.710557562 3.656305144 0.914017138 0.738081997 0.56184828 0.0443959 0.189646529 4.67946578 0.011128325 0.086652862 51352.02353 -4.710557562 -0.175935142 ALEQSQSLPLPAPTSTS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEQSQSLPLPAPTSTSPSR 20 0 O15068-4;O15068-10;O15068;H7BYP9;O15068-5;O15068-3;O15068-6;O15068-8;O15068-2;O15068-9;H3BLT1;H7C2S1;H0Y4M6;H0Y7A3 O15068-4 MCF2L Guanine nucleotide exchange factor DBS 1 ALEQSQSLPLPAPTST(0.019)S(0.976)PS(0.004)R;ALEQSQSLPLPAPTS(0.006)T(0.078)S(0.915)PSR 361.84 6.81E-96 626150000 510670 583480 469410 641730 551720 591600 616870 629820 619310 628860 TRUE FALSE 490712.4518 566839.7217 554242.829 674849.7622 569466.5749 603562.5573 624419.4396 616813.9969 549008.5252 586266.7521 0.837012248 0.966863155 0.945376532 1.151096766 0.9713438 1.029501597 1.065077352 1.052104686 0.936448337 1 19.16119772 4.710851831 1.371057442 1.030672001 0.767975373 0.473278645 0.058939777 0.981973185 1.707969263 0.015547145 0.352998599 51386.8304 -4.710851831 -0.262696628 GVSMSLPS(ph)SPLLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVSMSLPSSPLLPR 14 0 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GVSMS(0.008)LPS(0.71)S(0.282)PLLPR;GVSMSLPS(0.777)S(0.222)PLLPR;GVSMSLPS(0.5)S(0.5)PLLPR;GVSMSLPS(0.5)S(0.5)PLLPR 182.33 1.61E-06 1191965000 1124010 1504800 1390320 1480390 1401270 1589760 1466040 1642890 1719460 1729790 TRUE FALSE 1080082.447 1461884.577 1641581.752 1556793.105 1446343.122 1621906.036 1483981.836 1608963.747 1524274.109 1612629.783 0.669764665 0.906522125 1.017953264 0.96537539 0.896884789 1.005752253 0.920224748 0.997726673 0.945210194 1 20.62098384 4.711098632 3.204970569 0.9663596 0.635859807 0.850671379 0.037434951 0.099974419 1.662244376 0.008536727 0.079481118 51416.04084 -4.711098632 -0.330499793 VVSQSQPGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 4 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 1 VVSQSQPGS(1)R;VVSQSQPGS(1)R;VVSQSQPGS(1)R;VVSQSQPGS(1)R 165.58 6.09E-06 1292990000 848440 1172650 1112820 1220980 1270750 1258480 1145310 1020670 1368310 1354800 TRUE FALSE 815282.0268 1139207.17 1313931.329 1283994.924 1311624.828 1283927.328 1159326.646 999592.8078 1212985.185 1263038.189 0.645492776 0.901957819 1.04029422 1.016592321 1.038468068 1.016538802 0.917887247 0.791419306 0.96037095 1 20.26846683 4.711268942 3.567623637 0.959615658 0.61759488 0.648426008 0.071580398 0.194775684 4.461245665 0.021150789 0.170754009 51436.20781 -4.711268942 -0.342020778 ANS(ph)DIISLNFR ddPTM_BT-474_Pertuzumab_2h_R1 4 ANSDIISLNFR 11 0 Q8TC76 Q8TC76 FAM110B Protein FAM110B 1 ANS(1)DIISLNFR;ANS(1)DIISLNFR;ANS(1)DIISLNFR;ANS(1)DIISLNFR 220.99 9.17E-12 313826000 626970 459580 309146 396269 393589 337139 381207 550780 428767 383673 TRUE FALSE 602467.3192 446473.2284 365015.5591 416720.4906 406249.1476 343956.1816 385872.3253 539406.2005 380095.1677 357686.486 1.684344651 1.24822504 1.020490215 1.165043989 1.135768791 0.961613578 1.078800403 1.508041879 1.062648947 1 18.44833609 4.71135209 3.473079204 1.147531248 1.735365706 0.566559972 0.146909994 0.221094863 4.668055356 0.039187393 0.327919477 51446.05642 -4.71135209 0.587834458 QLPALDGSLMGPES(ph)PPAQEEEAPVS(ph)PHKKPAPQKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLPALDGSLMGPESPPAQEEEAPVSPHKKPAPQKR 35 3 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 2 QLPALDGSLMGPES(1)PPAQEEEAPVS(1)PHKKPAPQKR 69.873 0.002275 461320000 236750 189620 142300 144300 150200 171340 162660 153630 207170 199250 TRUE FALSE 227497.5483 184212.2233 168016.7754 151747.3403 155031.3194 174804.6122 164650.6817 150457.4868 183652.9301 185754.62 1.224720808 0.99169659 0.904509268 0.81692364 0.834602765 0.941051222 0.886388084 0.809979783 0.988685666 1 17.50303857 4.711653649 1.945291188 0.882349305 1.316387745 0.702993509 0.063789819 0.359114303 1.506510426 0.015871118 0.274668401 51481.79118 -4.711653649 0.43403844 RWDQTADQTPGAT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 RWDQTADQTPGATPK 15 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 RWDQTADQT(0.001)PGAT(0.999)PK;RWDQTADQTPGAT(1)PK;RWDQTADQTPGAT(1)PK;RWDQTADQTPGAT(1)PK 193.85 4.46E-08 4731890000 4316260 3603640 2795000 2771350 3062870 2818620 2896400 4078810 3421080 3272090 TRUE FALSE 4147575.787 3500867.716 3300118.674 2914379.706 3161389.995 2875614.428 2931847.01 3994581.148 3032733.341 3050468.43 1.359652094 1.14764922 1.08183997 0.955387598 1.036362142 0.942679622 0.961113703 1.30949762 0.99418611 1 21.54059937 4.711859677 1.908175983 1.049063769 1.444330119 0.489715321 0.100929262 0.745709637 2.974001176 0.029038779 0.51269351 51506.21976 -4.711859677 0.395266349 MPSGEFAR ddPTM_BT-474_Pertuzumab_2h_R1 3 MPSGEFAR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;; 130.64 0.0024179 965570000 902580 948400 870360 980250 937930 615373 1036440 889990 1011740 1121200 FALSE TRUE 867306.1757 921352.5606 1027653.413 1030840.82 968099.3703 627816.2637 1049124.263 871611.3955 896891.5168 1045260.125 0.829751518 0.881457676 0.983155664 0.986205056 0.926180332 0.600631602 1.003696819 0.83387032 0.858055804 1 19.99543059 4.711890064 5.141599161 0.891622024 0.827976261 0.028479257 0.114894171 0.731334958 56.23277935 0.027150736 0.14875544 51509.82372 -4.711890064 -0.063645763 DAIFIMTSNVASDEIAQHALQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAIFIMTSNVASDEIAQHALQLR 23 0 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2R8Y602;A0A2U3TZY2 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 ; 222.57 1.60E-32 239900000 403970 459360 413320 479070 411950 454640 460950 417350 525090 507730 FALSE TRUE 388182.4058 446259.5026 488016.1183 503794.8601 425200.7459 463833.1323 466591.244 408731.5767 465483.9846 473340.9949 0.8200904 0.942786506 1.03100328 1.064338111 0.898296895 0.979913292 0.985740194 0.863503439 0.983400951 1 18.85252035 4.711961513 4.035668297 0.967550613 0.810610798 0.405912493 0.055596468 0.231002795 7.796365121 0.014419236 0.100289619 51518.29878 -4.711961513 -0.156939815 GSRPIDTSR ddPTM_BT-474_Pertuzumab_2h_R1 6 GSRPIDTSR 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;;; 94.804 0.0077286 2601700000 956929 1119860 976921 1138519 1072333 1120452 1151340 1156069 1227660 1316130 FALSE TRUE 919531.1567 1087922.689 1153472.356 1197278.102 1106825.565 1143108.307 1165430.443 1132195.771 1088301.184 1226987.343 0.749421876 0.886661705 0.940084967 0.97578684 0.90206763 0.931638223 0.94983086 0.922744458 0.886970179 1 20.22668894 4.712111348 2.421647209 0.935476731 0.712905364 0.769656147 0.031203243 0.222120169 1.671458452 0.007411367 0.10057899 51536.07599 -4.712111348 -0.222571367 S(ph)PS(ph)PSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 S(1)PS(0.994)PS(0.006)FR;S(1)PS(0.998)PS(0.002)FR 114.89 0.0084828 502090000 544870 558110 468900 527870 549070 554660 524690 613560 571170 613780 TRUE FALSE 523575.878 542193.2492 553640.6606 555113.434 566731.3352 565875.6052 531111.3132 600889.7716 506333.1761 572208.1339 0.915009499 0.947545512 0.96755119 0.970125032 0.99042866 0.988933173 0.928178545 1.050124484 0.88487588 1 19.12618048 4.712202256 1.171359754 0.978577471 0.886335179 0.152753821 0.041469287 2.478665886 2.95174488 0.011320285 0.277161074 51546.86485 -4.712202256 -0.092242292 S(ph)RSDIDVNAAASAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSDIDVNAAASAK 14 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.5)RS(0.5)DIDVNAAASAK;S(0.5)RS(0.5)DIDVNAAASAK;S(0.5)RS(0.5)DIDVNAAASAK 237.16 1.67E-17 6721800000 8802310 7948800 6306000 6868550 6885800 6588650 6807290 9112090 8148690 6935810 TRUE FALSE 8458305.994 7722108.007 7445634.476 7223036.689 7107288.011 6721877.017 6890599.651 8923922.157 7223684.873 6466041.411 1.308111943 1.194255885 1.151498112 1.117072445 1.099171434 1.039566033 1.065659685 1.380121405 1.117172689 1 22.62445132 4.712211596 1.915981094 1.140058619 1.354072051 0.243091545 0.097810956 1.313177641 5.289738948 0.027838433 0.490336263 51547.97339 -4.712211596 0.214013432 LAS(ph)PMKPVPGTPPSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LASPMKPVPGTPPSSK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 LAS(1)PMKPVPGTPPSSK;LAS(1)PMKPVPGTPPSSK 200.74 2.10E-11 3527100000 4102900 3533700 2854900 2765000 3041400 2735300 3013500 3535100 3719900 3667200 TRUE FALSE 3942554.132 3432922.336 3370843.937 2907701.981 3139229.393 2790609.64 3050380.114 3462098.95 3297632.547 3418817.278 1.153192409 1.004125713 0.985967855 0.850499382 0.918220875 0.816250011 0.892232567 1.012659838 0.96455361 1 21.70506589 4.712498781 1.500102938 0.923398108 1.232463555 0.571725212 0.059739674 0.83250924 1.800937799 0.017444442 0.377032652 51582.07175 -4.712498781 0.309065447 VLELVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLELVLR 7 0 K7EIG1;A0A494C0R8;O75153;Q9Y5I4-2;Q9Y5I4 K7EIG1 CLUH;PCDHAC2 Clustered mitochondria protein homolog;Protocadherin alpha-C2 0 107.43 0.0174 12808000 53067 58317 50106 56277 57712 57472 59339 57997 67610 64387 FALSE TRUE 50993.08297 56653.85626 59161.2688 59181.46271 59568.35889 58634.12322 60065.20843 56799.34168 59935.19624 60026.01114 0.849516435 0.943821773 0.985593873 0.985930292 0.992375768 0.97681192 1.000653005 0.946245479 0.998487074 1 15.87330018 4.712696481 2.194210443 0.982778976 0.818831085 0.876928124 0.015459295 0.19256476 1.108614206 0.00394416 0.060333761 51605.55834 -4.712696481 -0.163947891 TMIIS(ph)PERLDPFADGGKT(ph)PDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 T(0.025)MIIS(0.975)PERLDPFADGGKT(1)PDPK 123.24 4.64E-05 84024000 626860 335590 162880 98794 160690 121710 78010 236040 135700 77348 TRUE FALSE 602361.6182 326019.3018 192316.0392 103892.7702 165858.7398 124171.0596 78964.70972 231165.6915 120295.9049 72109.15107 8.353469834 4.52119179 2.667012944 1.440770951 2.300106676 1.721987539 1.095071964 3.205774692 1.668247416 1 16.13789474 4.712716776 1.500498189 1.910066482 10.69523608 0.915750962 0.613486183 0.281549903 0.609248891 0.167635189 3.625654444 51607.96996 -4.712716776 8.785169595 GNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_BT-474_Pertuzumab_2h_R1 5 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK 131.2 6.69E-06 3770800000 1571130 1179646 851233 691422 1035965 1059671 989450 1252857 1484520 1040003 TRUE FALSE 1509728.503 1146003.651 1005069.739 727106.3723 1069287.755 1081098.274 1001559.185 1226985.065 1316003.513 969562.6705 1.557123174 1.181979965 1.036621736 0.749932309 1.102855739 1.115037023 1.033000976 1.265503616 1.357316606 1 19.88697463 4.713030905 3.162461027 1.089358236 1.6129438 0.463094834 0.152758449 0.308718222 4.931166375 0.040349616 0.386909905 51645.31196 -4.713030905 0.523585564 RLS(ph)QSDEDVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSQSDEDVIR 11 1 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 RLS(0.992)QS(0.008)DEDVIR;RLS(0.971)QS(0.029)DEDVIR 140.84 0.00063994 404340000 341490 410600 363220 400190 422730 432520 418060 415170 440070 460810 TRUE FALSE 328144.1933 398890.09 428861.9338 420843.8539 436327.4944 441265.8507 423176.3433 406596.5944 390115.0985 429598.9283 0.763838482 0.928517424 0.998284459 0.979620353 1.015662437 1.027157709 0.985049812 0.946456259 0.908091415 1 18.71263087 4.713052019 2.621159387 0.981447507 0.726143575 0.80212429 0.032631138 0.200144469 1.870722269 0.008858482 0.10929137 51647.82282 -4.713052019 -0.255303932 VDS(ph)TTCLFPVEEK ddPTM_BT-474_Pertuzumab_2h_R1 7 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.967)T(0.032)T(0.001)CLFPVEEK;VDS(0.894)T(0.103)T(0.003)CLFPVEEK;VDS(0.994)T(0.006)TCLFPVEEK;VDS(0.881)T(0.059)T(0.059)CLFPVEEK;VDS(0.993)T(0.007)TCLFPVEEK;VDS(0.942)T(0.058)TCLFPVEEK;VDS(0.983)T(0.017)T(0.001)CLFPVEEK 306.14 1.55E-41 5621000000 11009240 6915960 4297370 4371540 5909030 4186600 4421790 9201500 6832420 5170650 TRUE FALSE 10578986.73 6718723.592 5074000.353 4597155.703 6099099.316 4271255.92 4475905.189 9011485.809 6056832.325 4820437.27 2.19461143 1.393799611 1.052601677 0.953680226 1.265258518 0.886072296 0.928526799 1.86943327 1.256490228 1 22.20073259 4.7131883 3.158317687 1.194126293 2.314820281 0.562934742 0.273620358 0.268591828 4.273361585 0.074895747 0.72011839 51664.03234 -4.7131883 1.120693988 TKKDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_BT-474_Pertuzumab_2h_R1 3 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 TKKDDS(0.108)HS(0.891)AEDS(1)EDEKEDHK;TKKDDS(0.02)HS(0.98)AEDS(1)EDEKEDHK;TKKDDS(0.076)HS(0.924)AEDS(1)EDEKEDHK 100.88 0.000217 449444000 499940 251669 133332 69322 207682 161931 160955 183648 262420 128159 TRUE FALSE 480401.7921 244491.6465 157428.0584 72899.71673 214362.2801 165205.3558 162924.8154 179855.6046 232631.1818 119478.6768 4.020816141 2.04632034 1.317624723 0.610148344 1.794146754 1.382718324 1.363630899 1.505336429 1.947051876 1 16.86639364 4.713199554 2.497138418 1.38166881 4.516084091 0.834801837 0.3555344 0.177807854 1.452903465 0.088082261 1.157083694 51665.37114 -4.713199554 3.13441528 YLAEVACGDDR ddPTM_BT-474_Pertuzumab_2h_R1 6 YLAEVACGDDR 11 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 222.88 1.71E-11 15984610000 3765960 4309580 3739870 4555120 4185910 4186220 4176770 4309980 4530080 4644150 FALSE TRUE 3618782.12 4186674.998 4415747.702 4790210.289 4320553.597 4270868.237 4227886.561 4220977.407 4015844.31 4329597.584 0.835824127 0.966989406 1.01989795 1.106386955 0.997911125 0.98643538 0.976507973 0.974912177 0.927532925 1 22.04580151 4.713326352 3.227706695 0.998560902 0.817190585 0.562885505 0.042882252 0.241354298 4.093623833 0.011356666 0.106106129 51680.45782 -4.713326352 -0.181370318 RGNDPLT(ph)SSPGR ddPTM_BT-474_Pertuzumab_2h_R1 3 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.333)S(0.333)S(0.333)PGR;RGNDPLT(0.375)S(0.375)S(0.25)PGR;RGNDPLT(0.333)S(0.333)S(0.333)PGR 67.136 0.032919 12260850000 2512690 2697290 2289060 2641600 2618710 2662670 2817120 2528840 2763720 2936990 TRUE FALSE 2414491.297 2620365.93 2702744.062 2777933.293 2702943.185 2716511.012 2851596.757 2476618.57 2449994.092 2738065.051 0.881823935 0.95701376 0.987100018 1.014560736 0.987172742 0.992128003 1.041464211 0.904514146 0.894790316 1 21.38472529 4.71365518 3.102880982 0.975988778 0.870037317 0.306628492 0.043109525 0.446830177 6.747907203 0.011355499 0.112150424 51719.60267 -4.71365518 -0.105951462 DPTSLLGVLQAEADSTS(ph)EGLEDAVHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.001)T(0.016)S(0.983)EGLEDAVHSR 170.95 3.19E-12 49562000 32778 36565 32124 33185 36089 32812 36500 37307 41225 41177 TRUE FALSE 31496.99952 35522.202 37929.52139 34897.68183 37249.83546 33475.48112 36946.69792 36536.59741 36545.31083 38388.04511 0.820489802 0.925345427 0.98805556 0.909076816 0.970349893 0.872028805 0.962453228 0.951770201 0.951997184 1 15.22836947 4.713730572 3.784105262 0.946872096 0.810562618 0.54644309 0.035288778 0.165037882 4.5507695 0.007900763 0.060068296 51728.58185 -4.713730572 -0.136309478 IDESIHLQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 IDESIHLQLR 10 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ;; 242.59 2.27E-12 1120010000 567338 702240 641520 675650 711640 660638 717830 702180 733210 839610 FALSE TRUE 545165.8037 682212.8028 757456.9345 710520.3775 734530.5469 673996.553 726615.0183 687679.7376 649979.0747 782742.4669 0.6964817 0.871567382 0.96769623 0.90773199 0.938406408 0.861070635 0.92829385 0.878551716 0.83038688 1 19.57817819 4.713811713 3.680280245 0.908299529 0.678592722 0.65002714 0.047523194 0.142698364 3.605626079 0.010923081 0.086053921 51738.24735 -4.713811713 -0.229706807 DLLYFDGLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DLLYFDGLR 9 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;; 147.29 0.00021579 166300000 316476 338501 305413 361178 313232 263426 333729 347763 330921 396306 FALSE TRUE 304107.768 328847.2829 360607.923 379818.4399 323307.3918 268752.6542 337813.2753 340581.5725 293356.2354 369463.8416 0.82310563 0.890066214 0.976030351 1.028026012 0.875071808 0.727412602 0.914333792 0.921826534 0.794005265 1 18.49507365 4.714136732 4.775113835 0.902249398 0.820002354 0.072734773 0.086266238 0.495595773 29.85795011 0.021350536 0.126379015 51776.98198 -4.714136732 -0.082247043 SGAHSSAS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 5 SGAHSSASPPR 11 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 1 SGAHS(0.029)S(0.173)AS(0.798)PPR;SGAHSSAS(1)PPR;SGAHSSAS(1)PPR;SGAHS(0.004)S(0.218)AS(0.778)PPR;SGAHSS(0.017)AS(0.983)PPR 164.13 2.43E-05 1565509000 109903.4 139011 114167 165883 155394 147953 179358 245397 119376 201619 TRUE FALSE 105608.2536 135046.5424 134799.5165 174444.2415 160392.3891 150944.711 181553.0369 240329.4662 105824.9369 187963.1655 0.561856113 0.718473441 0.717159216 0.928076738 0.853318195 0.80305474 0.965896889 1.278598738 0.56300891 1 17.52009044 4.714164621 0.473832044 0.991766827 0.278909505 0.301328008 0.172734138 5.21232344 0.923275487 0.116821313 2.094559121 51780.30699 -4.714164621 -0.712857322 LKEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKEELR 6 1 Q1MSJ5-1;Q1MSJ5;E5RI67;F2Z2M5 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 0 64.523 0.097088 243460000 1113500 1243100 1071000 1199700 1202300 1285800 1201500 1271100 1308800 1326000 FALSE TRUE 1069983.189 1207648.005 1264553.524 1261616.661 1240973.071 1311799.757 1216204.316 1244851.341 1160230.511 1236188.839 0.865549951 0.976912238 1.022945269 1.020569529 1.003870147 1.061164537 0.983833762 1.007007426 0.93855443 1 20.23746771 4.714257523 2.995186555 1.006323435 0.846460803 0.66564808 0.029467869 0.198499063 2.703808007 0.007084666 0.073667423 51791.38476 -4.714257523 -0.159862632 EQIS(ph)DIDDAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 EQIS(1)DIDDAVR;EQIS(1)DIDDAVR 186.62 4.14E-06 490980000 618150 657120 579160 579310 655390 644030 625960 689310 661470 657140 TRUE FALSE 593992.0146 638379.581 683827.0953 609208.2585 676471.2146 657052.7279 633620.6857 675075.5076 586382.6987 612631.3225 0.969575 1.042028962 1.11621308 0.994412522 1.104206053 1.072509197 1.034261002 1.101927836 0.95715429 1 19.22465961 4.714390518 4.511531228 1.055251855 0.965501979 0.161522697 0.050450096 0.258946425 12.80305178 0.011110905 0.06954875 51807.24741 -4.714390518 -0.089749877 KIGTTPDIILDDLLETDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIGTTPDIILDDLLETDR 18 1 Q10570;A0A087X101 Q10570 CPSF1 Cleavage and polyadenylation specificity factor subunit 1 0 ; 128.14 5.73E-05 18004000 68246 77548 67994 68682 74400 82955 78361 78587 83255 79231 FALSE TRUE 65578.87087 75336.40697 80282.02832 72226.68625 76793.14357 84632.40694 79320.00536 76964.15099 73804.24143 73864.6138 0.887825272 1.019925552 1.08688077 0.977825274 1.039647263 1.145777424 1.073856631 1.04196241 0.999182662 1 16.17259576 4.714431925 3.450749765 1.049402005 0.871710549 0.504533986 0.046485187 0.219941074 4.55788064 0.011486256 0.098777843 51812.18703 -4.714431925 -0.177691456 EYGEQIDPSTHR ddPTM_BT-474_Pertuzumab_2h_R1 3 EYGEQIDPSTHR 12 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;; 110.98 0.0014316 2175760000 1506260 1763930 1582040 1902880 1567990 1729480 1883700 1567340 1858840 2064610 FALSE TRUE 1447393.694 1713624.443 1867949.82 2001087.865 1618425.822 1764451.271 1906753.284 1534973.881 1647832.276 1924772.126 0.751981845 0.890299906 0.970478425 1.039649233 0.840840222 0.916706579 0.990638455 0.797483432 0.856118111 1 20.87625622 4.71449209 3.860284857 0.917679986 0.73954579 0.330021601 0.073488718 0.286198225 8.418657141 0.01852178 0.138069773 51819.36533 -4.71449209 -0.178134196 QDKDDIINIFSVASGHLYER ddPTM_BT-474_Pertuzumab_2h_R1 2 QDKDDIINIFSVASGHLYER 20 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 198.9 9.07E-22 223790000 353680 481810 442760 497600 453300 461140 526240 481570 586110 542240 FALSE TRUE 339857.7946 468069.2505 522776.5811 523281.1956 467880.8062 470464.5668 532680.2825 471625.4112 519577.25 505513.6018 0.672301978 0.925928103 1.034149386 1.035147608 0.925555325 0.930666485 1.053740751 0.932962851 1.027820514 1 18.94739039 4.714649219 3.190291296 0.987389365 0.634753473 0.813902605 0.045747726 0.124233848 2.034406493 0.011044988 0.105668367 51838.11717 -4.714649219 -0.352635892 LCCTLSSLSSAAETGRDPLDS(ph)EEEATSGAQDER ddPTM_BT-474_Pertuzumab_2h_R1 1 LCCTLSSLSSAAETGRDPLDSEEEATSGAQDER 33 1 O43822-2;O43822 O43822-2 C21orf2 Protein C21orf2 1 LCCTLSSLSSAAETGRDPLDS(0.995)EEEAT(0.004)S(0.001)GAQDER 92.283 0.00014958 70562000 84699 99364 80766 112700 95903 103580 100860 103420 107520 115010 TRUE FALSE 81388.86944 96530.23601 95362.21283 118516.4605 98987.80709 105674.4586 102094.3549 101284.3409 95314.78036 107220.2703 0.759080995 0.900298384 0.889404705 1.105354988 0.923219153 0.985582841 0.952192665 0.944637993 0.888962321 1 16.71021815 4.715128281 1.579400763 0.96388715 0.692749481 0.535202356 0.058122508 0.76799761 1.880307938 0.015070437 0.317447434 51895.33039 -4.715128281 -0.271137669 SGSIVELIAGGGSSCS(ph)PVLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 1 SGSIVELIAGGGSS(0.001)CS(0.998)PVLSR;SGSIVELIAGGGSS(0.007)CS(0.993)PVLSR;SGSIVELIAGGGSSCS(1)PVLSR;SGSIVELIAGGGSSCS(1)PVLSR 424.12 8.16E-174 1934620000 1246790 1584480 1360080 1859780 1620130 2100930 2063790 1709020 2106980 2297160 TRUE FALSE 1198064.068 1539292.182 1605876.711 1955763.469 1672242.953 2143412.244 2089047.279 1673728.14 1867804.464 2141571.307 0.559432256 0.718767653 0.74985909 0.913237613 0.780848598 1.00085962 0.97547407 0.781542101 0.872165432 1 21.03023828 4.715157794 0.807197152 0.899980041 0.373284378 0.684150087 0.076328493 1.496261386 0.76612031 0.027923562 0.705398379 51898.85706 -4.715157794 -0.526695663 DEVCVNPYHYQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEVCVNPYHYQR 12 0 Q15796-2;Q15796;B7Z5N5;K7EJX0;P84022-3;P84022-2;P84022;H0YMP2;H0YL71;H3BP09;H3BVD1 Q15796-2 SMAD2;SMAD3 Mothers against decapentaplegic homolog 2;Mothers against decapentaplegic homolog;Mothers against decapentaplegic homolog 3 0 ; 136.38 0.00011104 958440000 911200 1004810 868730 956490 898690 1060200 970050 1003750 1071510 1128510 FALSE TRUE 875589.2966 976153.8026 1025728.836 1005854.564 927597.18 1081637.97 981921.7621 983022.2117 949876.6769 1052075.013 0.832249874 0.927836695 0.974957891 0.956067345 0.881683501 1.028099667 0.933319155 0.934365136 0.90286022 1 20.00480614 4.715372052 3.559182121 0.948039928 0.821440133 0.428552175 0.040970919 0.239938033 5.469574735 0.009434767 0.078369282 51924.46761 -4.715372052 -0.126599795 MMYGVSPWGDSPIDFEDSAHVPCPR ddPTM_BT-474_Pertuzumab_2h_R1 3 MMYGVSPWGDSPIDFEDSAHVPCPR 25 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 172.02 6.40E-12 426462000 219508 284867 256334 291928 267675 289618 305385 282896 334835 362932 FALSE TRUE 210929.3847 276742.8721 302659.2559 306994.4391 276285.0095 295474.2744 309122.393 277054.0987 296825.9345 338350.2924 0.623405357 0.817918229 0.894514539 0.907327246 0.816565009 0.873279205 0.91361645 0.818838065 0.87727406 1 18.36815811 4.715833395 2.671693389 0.877076454 0.580138782 0.715137727 0.049891572 0.219491971 2.154890409 0.011577789 0.141475988 51979.65526 -4.715833395 -0.296937672 GEHVPGFCLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEHVPGFCLPK 11 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 69.721 0.053728 456140000 304650 364830 320500 365540 354770 390710 358110 366740 416650 410290 FALSE TRUE 292743.9412 354425.4056 378421.4795 384405.5632 366181.4992 398610.4239 362492.6573 359166.6908 369353.6387 382500.6929 0.765342251 0.926600689 0.989335409 1.004980044 0.957335519 1.042116868 0.947691505 0.938996184 0.965628679 1 18.54510284 4.715916912 2.620928599 0.976868458 0.728017746 0.828873334 0.029391712 0.18153889 1.688899952 0.007733316 0.096922201 51989.65215 -4.715916912 -0.248850712 QKIPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKIPAR 6 1 A0A3B3ISL2;A0A3B3IRU6;Q9GZU2-2;Q9GZU2-4;Q9GZU2 A0A3B3ISL2 PEG3 Paternally-expressed gene 3 protein 0 ; 84.609 0.050758 2423000000 5658800 2988900 1352650 2241300 2548700 1602610 1594830 4567600 2119090 1691760 FALSE TRUE 5437647.84 2903659.498 1597103.945 2356973.762 2630681.25 1635015.872 1614348.007 4473277.464 1878539.787 1577175.588 3.447712404 1.841050242 1.012635471 1.494426986 1.6679698 1.036673332 1.023568979 2.83625837 1.191078407 1 20.58891185 4.716031029 3.671443095 1.515967122 3.615932137 0.558165958 0.536219141 0.20063715 5.041702371 0.13842721 1.10952169 52003.31505 -4.716031029 2.099965015 VS(ph)PATPGPALSDILR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSPATPGPALSDILR 15 0 Q2M2I3 Q2M2I3 FAM83E Protein FAM83E 1 VS(0.999)PAT(0.001)PGPALSDILR 75.316 0.033767 95310000 29519 39899 37181 40982 48355 54325 50565 40090 30660 43668 TRUE FALSE 28365.36485 38761.11959 43900.43379 43097.08593 49910.38249 55423.48872 51183.8296 39262.12749 27179.60534 40710.32746 0.696760911 0.952120064 1.078361107 1.058627838 1.225988234 1.361411027 1.257268924 0.964426718 0.667634161 1 15.31310721 4.716145084 1.739426758 1.09519351 0.570918542 0.288957266 0.18017134 1.15880479 3.613363129 0.05071663 0.9936329 52016.97392 -4.716145084 -0.524274968 HTKEDSAS(ph)VK ddPTM_BT-474_Pertuzumab_2h_R1 4 HTKEDSASVK 10 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 HTKEDS(0.012)AS(0.988)VK;HTKEDS(0.001)AS(0.999)VK;HTKEDSAS(1)VK;HTKEDS(0.06)AS(0.94)VK 117.2 0.00059712 1244500000 3342220 2501370 1857180 1609850 2090910 2151580 2031810 1846640 3024480 2478010 TRUE FALSE 3211602.347 2430033.377 2192813.739 1692934.551 2158166.019 2195086.422 2056675.899 1808506.239 2681153.71 2310172.176 1.390200428 1.051884099 0.949199268 0.73281748 0.934201373 0.95018304 0.890269531 0.782844784 1.160586098 1 21.13956895 4.71660632 1.967016624 0.902960203 1.521312347 0.610721999 0.111299838 0.440666038 1.886104953 0.027726108 0.48568345 52072.2472 -4.71660632 0.618352144 APSEEELHGDQTDFGQGSQS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 3 APSEEELHGDQTDFGQGSQSPQK 23 0 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.082)QS(0.918)PQK;APSEEELHGDQTDFGQGSQS(1)PQK;APSEEELHGDQTDFGQGS(0.002)QS(0.998)PQK 316.1 1.54E-73 1821300000 538600 550150 674900 751110 705600 618660 840800 889650 1046880 1131660 TRUE FALSE 517550.9165 534460.2607 796869.4431 789874.8771 728296.2648 631169.7291 851089.9619 871278.4166 928042.5713 1055011.66 0.490564167 0.506591804 0.755318138 0.748688291 0.690320583 0.598258534 0.806711427 0.825847192 0.879651483 1 20.00882751 4.71708805 0.135282624 1.119382753 2.58E-17 0.764839065 0.074737712 15.90490375 0.362395193 0.549062862 3.299525015 52130.03903 -4.71708805 -1.119382753 down VPAPFS(ph)PPPSKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPAPFSPPPSKPR 13 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 VPAPFS(0.994)PPPS(0.006)KPR 76.391 0.01744 500430000 343410 439110 347700 541160 420450 420270 470670 553240 440100 460250 TRUE FALSE 329989.1575 426587.0127 410537.1245 569089.3325 433974.1561 428768.1473 476430.2003 541815.4007 390141.693 429076.8576 0.769067713 0.994197206 0.95679158 1.326310945 1.01141357 0.999280525 1.11036098 1.262746734 0.909258298 1 18.71087657 4.717475517 1.416600509 1.100460568 0.650896864 0.342641141 0.125544347 1.230770874 2.294455025 0.034090763 0.779004167 52176.56895 -4.717475517 -0.449563703 ASDSSS(ph)PSCSSGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASDSSSPSCSSGPR 14 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 ASDSS(0.033)S(0.849)PS(0.024)CS(0.067)S(0.027)GPR 118.16 0.00087696 0 121060 133610 112190 140890 134220 135720 129800 128820 136580 154620 TRUE FALSE 116328.8414 129799.5736 132465.2287 148161.3498 138537.3082 138464.3514 131388.5312 126159.822 121076.011 144147.4497 0.80701283 0.900463892 0.91895645 1.027845793 0.961080536 0.96057441 0.911487033 0.875213694 0.839945564 1 17.13718579 4.717607443 2.279697462 0.932720252 0.779437762 0.356411897 0.052606228 0.717947519 4.540490714 0.014427853 0.216551227 52192.42108 -4.717607443 -0.15328249 TDHGAEIVYKS(ph)PVVS(ph)GDT(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDHGAEIVYKSPVVSGDTSPR 21 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 3 T(0.001)DHGAEIVY(0.004)KS(0.995)PVVS(0.996)GDT(0.539)S(0.465)PR 73.212 0.012402 663230000 377480 325080 264270 283720 275380 285150 283840 189610 377780 298700 TRUE FALSE 362727.6643 315809.0367 312029.4677 298362.8232 284237.8478 290915.9284 287313.7188 185694.4872 334895.9982 278468.7829 1.302579271 1.134091345 1.12051866 1.071440827 1.020717097 1.044698531 1.031762756 0.666841307 1.202633899 1 18.08715608 4.717653996 0.457176889 0.928836622 1.517585539 0.332754377 0.128953389 4.985047011 0.823346506 0.091902735 1.603262592 52198.01597 -4.717653996 0.588748917 LDWES(ph)FKEEEGIGEELAIHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDWESFKEEEGIGEELAIHNR 21 1 Q9UEE9 Q9UEE9 CFDP1 Craniofacial development protein 1 1 LDWES(1)FKEEEGIGEELAIHNR;LDWES(1)FKEEEGIGEELAIHNR 64.705 0.014917 45365000 51553 31308 17294.6 20113.2 30095 20815.9 19212.2 45501 28447 23074.2 TRUE FALSE 49538.25177 30415.12649 20420.11894 21151.24466 31063.03301 21236.81176 19447.32465 44561.38845 25217.81582 21511.36388 2.302887536 1.413909721 0.949271234 0.983259117 1.444028988 0.98723688 0.904048891 2.071527807 1.172302043 1 14.39281138 4.717711527 3.810445571 1.246325957 2.388149298 0.489038616 0.336326539 0.220847827 6.258751823 0.088181684 0.682249949 52204.93112 -4.717711527 1.141823341 LPDAYER ddPTM_BT-474_Pertuzumab_2h_R1 4 LPDAYER 7 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 143.85 0.0056153 1432210000 1212600 1448490 1231570 1599050 1442450 1433050 1631350 1533140 1612220 1800760 FALSE TRUE 1165210.251 1407180.483 1454142.095 1681577.162 1488847.714 1462027.253 1651314.949 1501480.123 1429207.545 1678792.921 0.694076224 0.838209684 0.866183123 1.001658478 0.886856083 0.870880044 0.983632304 0.894380781 0.851330457 1 20.67899285 4.718067314 1.509028034 0.920096033 0.613500013 0.639965194 0.052598916 0.66374374 1.443926305 0.013652406 0.300519553 52247.71645 -4.718067314 -0.30659602 S(ph)RECDITK ddPTM_BT-474_Pertuzumab_2h_R1 4 SRECDITK 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)RECDITK;S(1)RECDITK;S(1)RECDITK;S(1)RECDITK 136.53 0.00047661 1296010000 2028990 1730150 1349400 1396240 1455660 1491770 1473600 1832180 1959290 1634120 TRUE FALSE 1949694.828 1680807.816 1593266.597 1468300.114 1502482.626 1521934.611 1491634.358 1794344.843 1736879.613 1523439.597 1.27979792 1.103297971 1.045835096 0.963805928 0.986243648 0.999012114 0.979122743 1.177824737 1.140104023 1 20.53890087 4.718120206 2.345751374 1.041504877 1.330636412 0.545209328 0.066990444 0.484296299 3.306436509 0.019294281 0.280794402 52254.07998 -4.718120206 0.289131534 S(ph)NFSNSADDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNFSNSADDIK 11 0 P45973 P45973 CBX5 Chromobox protein homolog 5 1 S(0.998)NFS(0.002)NS(0.001)ADDIK;S(1)NFSNSADDIK 229.48 2.63E-12 305050000 619810 428640 349280 247140 259080 245720 210810 558600 289590 254370 TRUE FALSE 595587.14 416415.6069 412402.6657 259894.925 267413.5435 250688.6268 213389.9558 547064.7148 256716.9573 237141.2933 2.511528598 1.755981006 1.739058853 1.095949682 1.127654909 1.057127686 0.899843097 2.306914612 1.082548525 1 17.85538738 4.718338953 1.279032012 1.319757694 2.982023705 0.489538618 0.395322263 1.357363764 1.974317043 0.12160847 2.938809308 52280.40621 -4.718338953 1.662266011 QITVNDLPVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 QITVNDLPVGR 11 0 P32119;Q06830;A0A0A0MSI0;A0A0A0MRQ5 P32119;Q06830 PRDX2;PRDX1 Peroxiredoxin-2;Peroxiredoxin-1 0 ;;; 239.54 2.77E-15 3886150000 2617990 2807260 2303880 2924400 2744210 2757820 2732620 2890250 2824040 3030310 FALSE TRUE 2515676.056 2727199.693 2720242.366 3075328.634 2832480.007 2813585.01 2766062.621 2830565.327 2503466.819 2825064.405 0.890484497 0.965358414 0.962895699 1.088587088 1.002624932 0.99593659 0.979114889 1.001947185 0.886162742 1 21.42985233 4.718968786 1.888108631 0.993758374 0.862062367 0.290921321 0.046651312 0.96514333 3.697189947 0.011971994 0.220661492 52356.28049 -4.718968786 -0.131696007 YQEQGGEAS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 5 YQEQGGEASPQR 12 0 Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6 DBNL Drebrin-like protein 1 YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR 247.3 1.33E-16 1163940000 671131.3 752434.7 643368.1 763698 706626 741461.2 771422 810025.8 774141 811841 TRUE FALSE 644902.7468 730975.9991 759639.0273 803112.5453 729355.267 756454.0535 780862.8932 793298.4842 686263.7591 756854.286 0.852083101 0.965808099 1.003679363 1.061119109 0.963666693 0.99947119 1.031721571 1.048152199 0.906731681 1 19.52965605 4.719033694 2.257333869 1.007782462 0.816683163 0.534869871 0.041671518 0.420310566 2.581646785 0.010282685 0.157248406 52364.10603 -4.719033694 -0.191099299 YLQDLLAWVEENQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLQDLLAWVEENQHR 15 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 249.13 1.70E-18 8074200000 831740 962200 794770 993680 1017150 1042790 1042520 979140 1040570 1148180 FALSE TRUE 799234.6813 934758.9981 938402.6186 1044963.944 1049867.554 1063875.928 1055278.672 958920.4168 922448.856 1070412.746 0.746660281 0.873269682 0.876673622 0.976225244 0.980806289 0.99389318 0.985861459 0.89584174 0.861769312 1 20.02973577 4.719060058 1.193622565 0.951329801 0.661616609 0.660912889 0.045528637 0.988439078 1.218853973 0.014196477 0.353474713 52367.28495 -4.719060058 -0.289713192 (ac)S(ph)LPLNPKPFLNGLTGKPVMVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPLNPKPFLNGLTGKPVMVK 21 2 P62306;A0A0B4J254;F8W0W6 P62306 SNRPF Small nuclear ribonucleoprotein F 1 S(1)LPLNPKPFLNGLTGKPVMVK;S(1)LPLNPKPFLNGLTGKPVMVK 110.74 2.48E-08 747110000 1582500 1266300 979970 940900 985340 813420 969870 1223960 1264290 1201400 TRUE FALSE 1520654.15 1230186.364 1157072.378 989459.9618 1017034.356 829867.9097 981739.5592 1198684.798 1120773.1 1120028.108 1.357692847 1.098353117 1.033074411 0.883424224 0.908043601 0.740934896 0.87653118 1.070227425 1.000665154 1 20.09510351 4.719172635 1.333700517 0.927920921 1.528867947 0.697185354 0.086650821 0.800677297 1.286118224 0.027249984 0.647590943 52380.86129 -4.719172635 0.600947026 S(ph)MPVLGSVSSVTK ddPTM_BT-474_Pertuzumab_2h_R1 3 SMPVLGSVSSVTK 13 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK 196.33 1.50E-07 356827000 1394520 611970 250660 272478 343587 233076 226573 694860 218137 148896 TRUE FALSE 1340020.617 594517.2148 295959.8379 286540.6222 354638.7879 237788.9564 229345.8681 680510.8982 193375.0023 138811.1413 9.653552331 4.282921452 2.132104348 2.06424801 2.554829422 1.713039416 1.652215132 4.902422758 1.393079838 1 17.08276384 4.719396149 2.393591756 2.410959494 11.17379223 0.826206617 1.031612834 0.216988504 1.561783844 0.270396416 3.867294906 52407.82658 -4.719396149 8.762832738 SREDMTEAEQIIFDHFSDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SREDMTEAEQIIFDHFSDPK 20 1 Q14997;Q14997-3;Q14997-2 Q14997 PSME4 Proteasome activator complex subunit 4 0 207.82 3.78E-22 57465000 44146 53090 48590 56709 56871 64227 60591 56575 66319 71838 FALSE TRUE 42420.72551 51575.92518 57371.29388 59635.75829 58700.30736 65525.71395 61332.53078 55406.70648 58790.74515 66972.34827 0.633406572 0.770107761 0.856641515 0.890453446 0.876485727 0.978399528 0.915788865 0.827307208 0.877836102 1 16.03127793 4.719525186 1.179606608 0.901814958 0.509365446 0.772486876 0.04738335 0.744867257 0.892730817 0.014280744 0.357557923 52423.40024 -4.719525186 -0.392449512 HPNQAT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 HPNQATPK 8 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 HPNQAT(1)PK;HPNQAT(1)PK;HPNQAT(1)PK 123.01 0.0050262 414080000 553370 446237 337501 333310 351034 346076 384479 388725 390220 433719 TRUE FALSE 531743.6886 433510.7577 398494.9384 350512.169 362325.3274 353073.8938 389184.369 380697.6929 345923.8615 404342.8258 1.315081299 1.072136638 0.985537304 0.866868772 0.896084472 0.873204299 0.96251088 0.941522066 0.855521205 1 18.62521949 4.719632031 1.444504498 0.914210775 1.467371648 0.882494129 0.044645466 0.34624826 0.67472049 0.012029903 0.273994473 52436.29897 -4.719632031 0.553160873 DFSAPTLEDHFNK ddPTM_BT-474_Pertuzumab_2h_R1 4 DFSAPTLEDHFNK 13 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 ;;; 225.63 1.21E-11 1280580000 693690 660130 539810 580350 621710 601100 623160 638330 717190 702350 FALSE TRUE 666579.8279 641303.7387 637365.675 610301.933 641707.8668 613254.6538 630786.4185 625148.2624 635777.5979 654779.2089 1.018022287 0.979419826 0.973405487 0.932072865 0.980037023 0.936582356 0.963357434 0.95474666 0.970980125 1 19.32064899 4.719664935 1.645847687 0.960123531 1.03703147 0.422250337 0.01897619 0.778757062 2.098040469 0.004534506 0.094364722 52440.27187 -4.719664935 0.076907939 LLEQGLR ddPTM_BT-474_Pertuzumab_2h_R1 8 LLEQGLR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 177.71 0.0016898 5311284000 2427600 2896900 2551370 3103150 2689680 2283600 3299140 2840420 3064290 3345580 FALSE TRUE 2332726.708 2814283.248 3012459.314 3263303.943 2776196 2329775.957 3339515.862 2781764.334 2716444.646 3118980.887 0.747913114 0.902308591 0.965847315 1.046272504 0.890097151 0.746967052 1.070707383 0.891882456 0.870939818 1 21.57264328 4.719825986 3.564393117 0.932350662 0.729967751 0.282067001 0.089136223 0.346564112 7.948355518 0.021396111 0.182615011 52459.72209 -4.719825986 -0.202382911 KQPPVSPGTALVGSQKEPSEVPT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVSPGTALVGSQKEPS(0.208)EVPT(0.792)PK 190.25 4.24E-16 1198100000 2130400 1206800 712610 485460 841820 654920 576560 1159800 722990 627320 TRUE FALSE 2047141.613 1172383.246 841394.4789 510514.6488 868897.9048 668162.9311 583616.1137 1135849.725 640919.2062 584831.0576 3.500398253 2.004652848 1.438696642 0.872926706 1.485724627 1.142488796 0.997922573 1.942184345 1.095904873 1 19.1576604 4.719931145 1.873961186 1.285821234 4.148319916 0.844340444 0.295746049 0.298798118 1.120571474 0.079279854 1.478184979 52472.42614 -4.719931145 2.862498683 up APS(ph)PLGPTRDPVATFLETCR ddPTM_BT-474_Pertuzumab_2h_R1 2 APSPLGPTRDPVATFLETCR 20 1 I3L2L9;E7EVV8;Q0VG06-3;Q0VG06 I3L2L9 C17orf70;FAAP100 Fanconi anemia-associated protein of 100 kDa 1 APS(0.998)PLGPT(0.002)RDPVATFLETCR;APS(0.999)PLGPT(0.001)RDPVATFLETCR 180.37 3.32E-17 279930000 58304 72032 63910 74834 75040 83964 73222 70691 83354 84367 TRUE FALSE 56025.41522 69977.71789 75459.95867 78696.19171 77453.72975 85661.80961 74118.11274 69231.20615 73892.00337 78652.74794 0.712313513 0.889704679 0.959406513 1.000552349 0.984755546 1.089114009 0.942346131 0.880213444 0.939471351 1 16.26320955 4.719966705 1.973675382 0.969761197 0.641493924 0.709390016 0.051094039 0.456681005 1.959933722 0.015137611 0.268532577 52476.72278 -4.719966705 -0.328267272 LADELHMPSLPEMMFGDNVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LADELHMPSLPEMMFGDNVLR 21 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 205.02 4.98E-22 299970000 339380 378630 332090 360070 404000 417410 382490 373320 432960 423580 FALSE TRUE 326116.6544 367831.8431 392106.0503 378653.2559 416995.0269 425850.3162 387171.027 365610.8115 383812.1959 394890.5493 0.825840616 0.93147796 0.992948682 0.958881534 1.055976213 1.078400881 0.980451489 0.925853536 0.971945762 1 18.59109332 4.720174652 1.719027624 0.993516199 0.770714514 0.608121249 0.041981047 0.710672253 2.13532074 0.012785612 0.257511467 52501.85547 -4.720174652 -0.222801685 VLAELYVSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLAELYVSDR 10 0 O43776;K7EIU7;O43776-2;K7EJ19;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 84.615 0.034433 126700000 143780 79808 42898 51464 75463 48470 43985 110880 74920 59794 FALSE TRUE 138160.9186 77531.95398 50650.62286 54120.06321 77890.33593 49450.09661 44523.30159 108590.2893 66415.39569 55744.09912 2.478485092 1.39085491 0.908627526 0.970866227 1.397283966 0.887091143 0.798708783 1.948014067 1.191433654 1 15.76653147 4.720217686 3.646395063 1.185685578 2.598203812 0.607129317 0.320307104 0.186981172 4.609495665 0.083984577 0.698182649 52507.05808 -4.720217686 1.412518235 GGRS(ph)PDEVTLTSIVPTR ddPTM_BT-474_Pertuzumab_2h_R1 4 GGRSPDEVTLTSIVPTR 17 1 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR 167.35 1.35E-09 2464110000 717740 753990 617470 782280 753810 717130 710180 738210 816190 802320 TRUE FALSE 689689.9273 732486.9434 729060.5645 822653.5645 778056.9832 731630.8599 718871.3953 722965.7055 723539.5329 747978.1518 0.92207229 0.979289223 0.974708369 1.099836356 1.040213516 0.978144693 0.961086087 0.966559924 0.967327095 1 19.5126366 4.720385819 2.124105648 0.997700423 0.903996975 0.246641146 0.040410741 1.077666814 5.609887109 0.011542189 0.190148907 52527.38962 -4.720385819 -0.093703448 SYVS(ph)EPELATLSGDMAQPSLGLVGPESR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYVSEPELATLSGDMAQPSLGLVGPESR 28 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 S(0.14)Y(0.018)VS(0.831)EPELAT(0.011)LSGDMAQPSLGLVGPESR;S(0.192)Y(0.004)VS(0.804)EPELATLSGDMAQPSLGLVGPESR 147.35 5.20E-08 113721000 112954 76094 46865 52497 47348 32076 33254 98146 44664 37703 TRUE FALSE 108539.6328 73923.87362 55334.54801 55206.37646 48870.99142 32724.5987 33660.9724 96119.2508 39593.92997 35149.34223 3.087956301 2.103136757 1.574269801 1.570623316 1.390381393 0.931015963 0.957655827 2.734596004 1.126448675 1 15.10121007 4.720475683 1.614726524 1.48745857 3.648529732 0.51528535 0.50309217 0.91317488 2.341760549 0.144794611 3.067982681 52538.25973 -4.720475683 2.161071162 ADHGEPIGR ddPTM_BT-474_Pertuzumab_2h_R1 10 ADHGEPIGR 9 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;; 164.46 6.22E-05 66654657000 9048937 10263110 8814375 10606100 9737529 10761529 11074433 8950206 10871223 10837538 FALSE TRUE 8695294.538 9970416.151 10407328.64 11153482.09 10050745.46 10979134.49 11209965.22 8765381.118 9637167.341 10103501.9 0.860621854 0.986827761 1.030071429 1.103922403 0.994778401 1.086666247 1.109512854 0.867558714 0.953844265 1 23.26835209 4.720566815 3.174571835 1.015070104 0.841058781 0.314162549 0.069536508 0.443184757 7.122601043 0.018730368 0.187073214 52549.28545 -4.720566815 -0.174011323 SLSEINKPNFYNNDFDDDFSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSEINKPNFYNNDFDDDFSHR 22 1 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 88.555 0.001601 150480000 215860 185720 140190 159810 166910 184440 186290 172300 183010 219210 FALSE TRUE 207423.9526 180423.4474 165525.4515 168057.8133 172278.8117 188169.5032 188569.8727 168741.9448 162235.472 204362.7114 1.01497945 0.882858943 0.809959167 0.822350673 0.843005118 0.920762412 0.922721525 0.825698307 0.79386044 1 17.64077246 4.720681233 4.057116707 0.860921807 1.025889942 0.3395846 0.060786599 0.222960152 7.811445343 0.014242791 0.104440142 52563.13177 -4.720681233 0.164968134 ILIEELR ddPTM_BT-474_Pertuzumab_2h_R1 3 ILIEELR 7 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 ;; 181.2 0.0030935 35186000 403451 437659 365433 445724 441385 415874 429919 458317 444956 492285 FALSE TRUE 387683.6889 425177.3938 431474.8721 468727.8691 455582.5494 424283.2572 435180.4773 448852.5938 394446.4603 458942.0985 0.844733334 0.926429271 0.940150998 1.021322451 0.992679798 0.924481015 0.948225231 0.978015735 0.859468899 1 18.80795262 4.720916124 1.932581757 0.960071334 0.812783762 0.3890316 0.043069474 0.762845974 3.093495865 0.010913052 0.198519902 52591.56859 -4.720916124 -0.147287572 SKS(ph)MSDVSAEDVQNLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKSMSDVSAEDVQNLR 16 1 E9PMS6;E9PJ10 E9PMS6 LMO7 1 S(0.022)KS(0.977)MS(0.001)DVSAEDVQNLR;SKS(0.789)MS(0.211)DVSAEDVQNLR;S(0.003)KS(0.926)MS(0.07)DVSAEDVQNLR 214.86 1.01E-14 2004170000 3474600 2184290 1427530 1452410 1640530 1467070 1454550 2800050 1763980 1509200 TRUE FALSE 3338808.791 2121996.188 1685516.426 1527369.054 1693299.137 1496735.161 1472351.218 2742227.989 1563740.386 1406980.54 2.373031251 1.508191569 1.197967121 1.08556516 1.20349862 1.063792368 1.046461679 1.949016288 1.111415788 1 20.42417094 4.720942626 2.688518794 1.26007127 2.567541193 0.637317082 0.262386556 0.311722444 3.090540475 0.071603343 0.893202804 52594.77798 -4.720942626 1.307469923 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 274.46 1.21E-71 234090000 84786 145486 138955 170579 120433 172233 161135 132134 148783 190973 FALSE TRUE 81472.46938 141336.8817 164067.2595 179382.6026 124306.8368 175715.6693 163107.0183 129405.3867 131893.7776 178038.2286 0.457612222 0.793856931 0.921528263 1.007551041 0.698203065 0.986954716 0.916134808 0.726840453 0.740817175 1 17.44182753 4.721015811 3.385607349 0.862564215 0.412724885 0.557776079 0.110587111 0.21960861 4.29008934 0.027130796 0.249533755 52603.64173 -4.721015811 -0.44983933 S(ph)FDAVLEALSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFDAVLEALSR 11 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 S(1)FDAVLEALSR 110.92 0.001814 9916400 16690 11536 7625.6 9752.8 9757.6 6470 8879.8 18124 7955.9 8857.1 TRUE FALSE 16037.73635 11207.00457 9003.715551 10256.14318 10071.46207 6600.827833 8988.473649 17749.73307 7052.779586 8257.200728 1.942272796 1.357240177 1.090407736 1.242084759 1.219718691 0.799402612 1.088561844 2.149606586 0.85413687 1 13.01143706 4.721117931 3.73679387 1.251852449 2.003086929 0.272314119 0.35877268 0.37867803 10.10494864 0.094335424 0.7653277 52616.01235 -4.721117931 0.75123448 YTGEDFDEDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 YTGEDFDEDLR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 142.98 8.70E-05 602110000 478330 557520 507641 589281 575450 624400 599500 630930 676300 736150 FALSE TRUE 459636.3348 541620.0755 599383.0211 619693.863 593959.8719 637025.7958 606836.8603 617901.075 599529.2593 686289.9048 0.669740778 0.78920012 0.873367096 0.90296223 0.86546497 0.928216766 0.884228161 0.900349941 0.873580181 1 19.38845861 4.721139416 1.242037318 0.903392152 0.563937728 0.817152659 0.035560758 0.520795383 0.703463994 0.009120101 0.225372507 52618.61536 -4.721139416 -0.339454424 RPKS(ph)ESQGNATK ddPTM_BT-474_Pertuzumab_2h_R1 3 RPKSESQGNATK 12 2 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 RPKS(0.97)ES(0.029)QGNATK;RPKS(0.968)ES(0.032)QGNATK;RPKS(0.959)ES(0.041)QGNATK 168.68 3.61E-05 480490000 795330 398235 198233 169873 235503 180368 138310 467643 161457 100869 TRUE FALSE 764247.6243 386877.7277 234058.1128 178640.1659 243078.1679 184015.1645 140002.6792 457986.0086 143129.0782 94037.05279 8.127090351 4.114098818 2.488998813 1.899678484 2.584919036 1.95683679 1.488803349 4.870271824 1.522049809 1 16.5209417 4.721300781 2.090883525 2.435389588 9.593807528 0.75599943 1.015048511 0.337459358 1.681794837 0.267648652 4.504482821 52638.16989 -4.721300781 7.15841794 DDSHSAEDS(ph)EDEKEDHKNVR ddPTM_BT-474_Pertuzumab_2h_R1 9 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 DDSHS(0.001)AEDS(0.999)EDEKEDHKNVR;DDS(0.007)HS(0.013)AEDS(0.98)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR 321.38 4.45E-67 17806490200 15616496.8 11482008 8695374.9 6177248.8 9923764.9 9643415.5 9879670.2 10329366.3 14057955.6 10291060.2 TRUE FALSE 15006186.84 11154552.37 10266822.57 6496057.351 10242971.81 9838411.969 10000580.56 10116061.28 12462155.42 9594037.526 1.564115921 1.162654653 1.07012533 0.677093177 1.067639331 1.025471491 1.042374551 1.054411268 1.298947954 1 23.19370665 4.721343738 2.2672965 1.023505665 1.686854906 0.562637136 0.141919715 0.427551536 2.646325227 0.036238085 0.558012832 52643.37665 -4.721343738 0.663349242 EQVNDLFSR ddPTM_BT-474_Pertuzumab_2h_R1 3 EQVNDLFSR 9 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A087WW90;A0A0D9SF80;A0A494C0I1;A0A494C1N8;Q86UP8-3;Q86UP8;Q6EKJ0 A0A494C1K3;A0A087WW90 GTF2I;GTF2IRD2B;GTF2IRD2 General transcription factor II-I;General transcription factor II-I repeat domain-containing protein 2A;General transcription factor II-I repeat domain-containing protein 2B 0 ;; 207.83 2.57E-05 671030000 1039420 1092720 913670 1067550 1075930 1057050 1110800 1073700 1077680 1217860 FALSE TRUE 998798.3173 1061556.695 1078790.493 1122646.383 1110538.266 1078424.275 1124394.303 1051527.72 955346.2844 1135373.257 0.879709215 0.934984763 0.950163734 0.988790581 0.978126143 0.949841181 0.990330092 0.926151565 0.841438072 1 20.11473524 4.721852923 2.402327201 0.952948249 0.864336119 0.206850123 0.043244021 0.86831681 6.284801885 0.010897436 0.157232121 52705.13409 -4.721852923 -0.08861213 SSRPEFDWQDPLVLEEQLTTDEILIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSRPEFDWQDPLVLEEQLTTDEILIR 26 1 Q92947-2;Q92947;K7EKH1;K7ES74;K7ERX1 Q92947-2 GCDH "Glutaryl-CoA dehydrogenase, mitochondrial" 0 ; 166.89 1.01E-11 91900000 21531.5 32769.6 27708.9 50067 24622.9 30873.8 45144 36171.6 32421.2 24810.1 FALSE TRUE 20690.02518 31835.04309 32716.51461 52650.96387 25414.91794 31498.08939 45696.48578 35424.64382 28740.8813 23129.68983 0.894522379 1.376371379 1.414481338 2.276336789 1.098800638 1.361803363 1.975663579 1.531565883 1.242596918 1 14.4974583 4.721930105 2.188761159 1.539201121 0.742324948 0.179478228 0.367606299 0.939762066 5.284611288 0.089638391 1.440420553 52714.50167 -4.721930105 -0.796876173 DINAVLIDMER ddPTM_BT-474_Pertuzumab_2h_R1 6 DINAVLIDMER 11 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;;;;; 199.7 1.15E-07 377849000 455784 516759 438121 537203 528291 500829 541547 549559 542889 543736 FALSE TRUE 437971.4574 502021.5393 517299.2106 564928.1112 545283.9598 510956.1055 548174.6142 538210.4146 481262.5167 506908.2764 0.864005339 0.990359721 1.020498648 1.114458251 1.075705379 1.007985329 1.081407899 1.061751089 0.949407495 1 18.95136519 4.722330972 1.842740735 1.047442656 0.809495455 0.573695492 0.045311818 0.5446896 1.94751319 0.011582845 0.22177292 52763.18119 -4.722330972 -0.237947201 EAIAELER ddPTM_BT-474_Pertuzumab_2h_R1 2 EAIAELER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 93.267 0.026033 996860000 1092690 1220010 961270 1310870 1163120 1155090 1296900 1250010 1349370 1340930 FALSE TRUE 1049986.467 1185216.509 1134992.872 1378524.158 1200532.811 1178446.711 1312771.85 1224196.857 1196195.175 1250107.617 0.839916862 0.948091583 0.907916132 1.102724389 0.96034357 0.942676211 1.050127071 0.979273176 0.956873759 1 20.25362087 4.722354799 1.279058757 0.993946473 0.781739011 0.448645324 0.051054561 1.231724471 1.781098627 0.013914586 0.341155045 52766.07607 -4.722354799 -0.212207462 ALYDYEGQEHDELSFK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALYDYEGQEHDELSFK 16 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;H0Y923 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 133.45 3.98E-05 0 90829 87843 69076 76058 90430 82371 85923 89669 89239 90805 FALSE TRUE 87279.30226 85337.80365 81559.56979 79983.36249 93338.76308 84036.59806 86974.55138 87817.30381 79108.96284 84654.69647 1.031003664 1.008069336 0.963438217 0.944818963 1.102582219 0.992698593 1.027403735 1.037358912 0.934489947 1 16.36930249 4.722367592 5.661732204 1.004946755 1.031650397 0.03049551 0.046442428 0.623524611 77.54133942 0.011006983 0.06081361 52767.63041 -4.722367592 0.026703642 KGLVGPELHDR ddPTM_BT-474_Pertuzumab_2h_R1 3 KGLVGPELHDR 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 162.49 1.63E-05 900080000 925600 1031770 853922 991060 1040360 1179650 1084360 1082220 1146770 1169080 FALSE TRUE 889426.5287 1002344.93 1008244.701 1042208.725 1073824.124 1203503.331 1097630.722 1059871.779 1016593.477 1089897.17 0.816064628 0.919669265 0.92508241 0.956245005 0.985252695 1.104235669 1.007095671 0.97245117 0.93274256 1 20.0557606 4.72252274 0.830271124 0.999772952 0.725474678 0.626860299 0.043063711 1.677503778 0.90569137 0.016323489 0.422744264 52786.4845 -4.72252274 -0.274298273 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR ddPTM_BT-474_Pertuzumab_2h_R1 11 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR 30 2 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;;;;;;; 306.47 3.15E-82 18317640000 2060866 2348773 2010205 2424129 2331999 2515617 2391800 2426096 2478068 2739162 FALSE TRUE 1980325.078 2281788.294 2373493.76 2549238.588 2407009.866 2566484.499 2421071.564 2375996.27 2196768.11 2553636.118 0.775492273 0.893544808 0.929456528 0.998277934 0.942581384 1.005031407 0.948087923 0.930436507 0.860251033 1 21.28412153 4.722785512 1.761332739 0.951991424 0.719824729 0.638683967 0.040642122 0.553762107 1.761925604 0.010676487 0.213140368 52818.43298 -4.722785512 -0.232166695 KRS(ph)PSVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRSPSVSR 8 2 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;Q9UQ26-2;D6RDY0;Q9UQ26-5;Q9UQ26-4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 KRS(0.999)PS(0.001)VSR 62.466 0.041461 46705000 45942 60043 57144 51494 58874 61305 72256 49324 65816 67638 TRUE FALSE 44146.53585 58330.63243 67471.19196 54151.61151 60767.73568 62544.6291 73140.29054 48305.44216 58344.8436 63056.81801 0.700107256 0.925048778 1.070006291 0.858774883 0.963698099 0.991877343 1.1599109 0.766062159 0.925274149 1 15.94436475 4.722797281 4.378632937 0.957968616 0.684941354 0.375312782 0.102077989 0.206865241 9.503237179 0.024813095 0.170202081 52819.86431 -4.722797281 -0.273027262 MFLYADNEDR ddPTM_BT-474_Pertuzumab_2h_R1 5 MFLYADNEDR 10 0 A0A087WY55;Q9NP79;Q5TGM0;Q9NP79-2 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 ;;;; 140.11 9.28E-05 1436104000 1549020 1689590 1435570 1618900 1715710 1586570 1684290 1638190 1819180 1877360 FALSE TRUE 1488482.586 1641404.547 1695009.433 1702451.623 1770897.37 1618651.532 1704902.845 1604360.804 1612674.313 1750204.735 0.850461981 0.937835737 0.968463517 0.972715699 1.01182298 0.924835535 0.974116234 0.91667036 0.921420381 1 20.73909226 4.722918998 3.094722529 0.957665036 0.835842318 0.536128083 0.030709424 0.27707242 4.117852158 0.007711253 0.080869032 52834.66991 -4.722918998 -0.121822718 EAEDGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAEDGFR 7 0 F6U236;Q9BY11;Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 F6U236;Q9UNF0-2 PACSIN1;PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 1;Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 148.33 0.0048655 501410000 841980 970150 839660 986760 947030 935970 1031510 1053950 1055210 1035020 FALSE TRUE 809074.4907 942482.2719 991405.2401 1037686.802 977492.08 954895.9547 1044133.928 1032185.564 935426.9846 964917.1735 0.83849113 0.976749402 1.02745113 1.075415414 1.01303211 0.989614426 1.082096947 1.06971416 0.969437596 1 19.88004558 4.722920027 2.033347253 1.035466999 0.785574213 0.710651808 0.036364557 0.36081601 1.665363261 0.009460601 0.165211435 52834.79505 -4.722920027 -0.249892786 SISSS(ph)NPDLAVAPGSVDDEVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SISSSNPDLAVAPGSVDDEVSR 22 0 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 SISS(0.072)S(0.928)NPDLAVAPGSVDDEVSR;SISS(0.001)S(0.999)NPDLAVAPGSVDDEVSR;SIS(0.012)S(0.083)S(0.905)NPDLAVAPGSVDDEVSR 440.09 1.88E-198 1869140000 608300 772540 743230 744100 648550 833110 765440 737830 797230 920880 TRUE FALSE 584526.9635 750507.9156 877548.1941 782503.0902 669411.1997 849956.055 774807.6837 722593.5527 706731.7927 858507.9774 0.680863753 0.874200282 1.022178264 0.91146863 0.779737891 0.990038622 0.902504932 0.84168531 0.823209348 1 19.71147201 4.723133104 4.635049143 0.900963495 0.669887135 0.444830936 0.075467464 0.161474723 9.14749933 0.01805761 0.117453232 52860.72365 -4.723133104 -0.231076359 SIS(ph)SPNVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.039)IS(0.951)S(0.01)PNVNR;SIS(0.914)S(0.086)PNVNR 164.54 6.52E-05 1529250000 1896890 1324690 873220 1213200 1126350 946490 1002450 1947160 1001430 895360 TRUE FALSE 1822757.442 1286911.138 1031030.279 1275813.397 1162580.071 965628.6763 1014718.283 1906950.466 887751.8647 834716.4697 2.18368453 1.541734451 1.235186217 1.528439229 1.392784392 1.15683434 1.215644257 2.284548748 1.063537018 1 19.67092671 4.723182094 3.965970385 1.438865231 2.241425582 0.312574768 0.350825219 0.300883913 9.795753719 0.088550428 0.678919706 52866.68689 -4.723182094 0.802560352 NPVDYMDLPFS(ph)SSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NPVDYMDLPFSSSPSR 16 0 Q9BX66-6;Q9BX66-5;A0A0U1RQI5;Q9BX66-4;Q9BX66-9;Q9BX66-8;Q9BX66-10;Q9BX66-2;Q9BX66;Q9BX66-12;A0A3B3IT56;Q9BX66-3;Q9BX66-11 Q9BX66-6 SORBS1 Sorbin and SH3 domain-containing protein 1 1 NPVDYMDLPFS(0.33)S(0.33)S(0.33)PS(0.009)R 107.34 0.0011912 45150000 104570 122550 108380 119200 102920 139090 116850 121350 136520 123700 TRUE FALSE 100483.2888 119054.994 127966.6769 125351.9263 106230.5153 141902.4951 118280.0453 118844.0801 121022.8219 115321.6888 0.871330361 1.032372967 1.109649696 1.086976158 0.921166836 1.23049269 1.025653079 1.030544049 1.049436781 1 16.81530434 4.723226997 4.00293007 1.057845422 0.857213335 0.34733778 0.075690166 0.231157905 7.766701034 0.017296105 0.13124141 52872.15314 -4.723226997 -0.200632087 T(ph)TSFAESCKPVQQPSAFGSMK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSFAESCKPVQQPSAFGSMK 21 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 1 T(0.333)T(0.333)S(0.333)FAESCKPVQQPSAFGSMK 101.47 0.001484 182750000 266670 168080 108440 108810 134580 110030 90887 191920 138610 116320 TRUE FALSE 256248.2416 163286.523 128037.5202 114425.6971 138908.8879 112254.882 91999.30229 187956.7849 122875.5739 108441.5428 2.363008078 1.505756178 1.180705447 1.055183228 1.280956397 1.035164929 0.848376922 1.733254435 1.133104258 1 16.72655802 4.723311801 2.268883467 1.192367937 2.635199598 0.723081208 0.224786111 0.326359647 2.016495518 0.059732337 0.928540713 52882.47843 -4.723311801 1.442831661 up KGPSS(ph)TGASGQAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KGPSSTGASGQAK 13 1 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 KGPS(0.001)S(0.991)T(0.008)GASGQAK;KGPS(0.024)S(0.961)T(0.015)GASGQAK;KGPS(0.005)S(0.802)T(0.193)GASGQAK;KGPS(0.004)S(0.957)T(0.035)GAS(0.004)GQAK 180.78 7.72E-06 1470107000 1269024 1038415 792952 864857 906830 843726 888120 1176728 1126169 983467 TRUE FALSE 1219429.139 1008800.421 936256.0655 909492.3734 935999.0105 860786.7178 898989.0782 1152428.156 998331.0164 916855.9041 1.330011765 1.100282407 1.021159444 0.991968715 1.020879079 0.93884624 0.98051294 1.256934869 1.088863596 1 19.80633549 4.7233573 3.113663332 1.048966653 1.368005017 0.523310764 0.083061888 0.320533101 4.848993044 0.023589704 0.246077216 52888.01896 -4.7233573 0.319038364 SNS(ph)TTQVSQPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSTTQVSQPR 11 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 SNS(0.492)T(0.492)T(0.016)QVSQPR;SNS(0.995)T(0.005)T(0.001)QVSQPR 184.32 5.20E-06 216380000 375020 283010 205289 259980 269010 210200 222600 355550 241950 206920 TRUE FALSE 360363.8038 274938.8319 242389.2889 273397.599 277662.951 214450.388 225324.2454 348207.7683 214484.8503 192905.1241 1.868088292 1.425254167 1.256520738 1.417264576 1.439375715 1.111688396 1.168057336 1.805072674 1.111867045 1 17.55753194 4.723722785 3.396960907 1.338515122 1.927945337 0.366975614 0.220843655 0.337820428 6.660620533 0.054286454 0.506192115 52932.54612 -4.723722785 0.589430215 DLIDYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLIDYVR 7 0 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2 D6RIC3 NOP16 Nucleolar protein 16 0 ; 114.43 0.013741 473610000 392580 446660 383060 447270 442670 462440 465590 408640 464030 489040 FALSE TRUE 377237.5396 433921.6941 452287.4631 470353.6583 456908.8826 471790.8536 471288.0297 400201.4412 411355.2598 455916.8852 0.82742612 0.951756138 0.99203929 1.031665362 1.002175829 1.03481768 1.033714795 0.877794734 0.902259322 1 18.79841132 4.723811823 2.988984696 0.981042616 0.804855731 0.457354306 0.05104713 0.381901228 5.115960676 0.014304146 0.157969818 52943.39944 -4.723811823 -0.176186885 YENGCAYFHEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 YENGCAYFHEEER 13 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;H3BNL6;Q6P474;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 0 ; 96.993 0.0039827 806320000 427470 600267 535280 699870 667450 747370 641310 630750 710500 853650 FALSE TRUE 410763.9998 583147.9729 632017.0032 735990.3746 688919.1354 762482.3335 649158.5436 617724.7921 629847.0187 795831.5251 0.516144419 0.732753044 0.794159295 0.92480676 0.865659519 0.958095161 0.815698453 0.776200455 0.791432607 1 19.60210352 4.723861832 1.506020572 0.859929829 0.389440752 0.707131689 0.070110171 0.639285416 1.370789773 0.019725875 0.445069572 52949.49622 -4.723861832 -0.470489077 NSLLAGGDDDTMSVIS(ph)GISSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVIS(0.992)GIS(0.004)S(0.004)R;NSLLAGGDDDT(0.005)MS(0.004)VIS(0.85)GIS(0.071)S(0.071)R 306.41 8.40E-56 208595000 217049 115697 63730 72157 78006 68125 50132 138841 69388 56413 TRUE FALSE 208566.4851 112397.4348 75247.42867 75881.03142 80515.13383 69502.53418 50745.53041 135973.8848 61511.36514 52592.09726 3.965738124 2.137154453 1.430774443 1.442821933 1.530935978 1.321539505 0.964888891 2.585443287 1.16959331 1 15.68255841 4.724447257 2.386044078 1.518178685 4.498381519 0.753205127 0.435946831 0.27340378 1.93324758 0.112663636 1.661907115 53020.91967 -4.724447257 2.980202834 VLTEDEMGHPEIGDAIAR ddPTM_BT-474_Pertuzumab_2h_R1 6 VLTEDEMGHPEIGDAIAR 18 0 P14324-2;P14324;A0A087WVN4;A0A087X1D8;A0A087WTP2 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;;;;; 286.02 1.00E-39 8596499000 3645125 4175900 3484801 4434729 4463019 4559154 4381859 3734777 4563400 4549315 FALSE TRUE 3502669.485 4056807.421 4114582.06 4663605.895 4606576.059 4651343.218 4435485.501 3657652.55 4045381.963 4241185.843 0.825870314 0.956526682 0.970148966 1.099599515 1.086152843 1.096708183 1.045812578 0.862412704 0.953832752 1 22.01603627 4.724665756 1.79103071 1.012261869 0.769059173 0.405929095 0.069751821 1.051460093 3.47976144 0.021645206 0.429586668 53047.60191 -4.724665756 -0.243202696 RKS(ph)QVNGEAGSYEMTNQHVK ddPTM_BT-474_Pertuzumab_2h_R1 5 RKSQVNGEAGSYEMTNQHVK 20 2 Q05D32-2;Q05D32;H0YMH7 Q05D32-2 CTDSPL2 CTD small phosphatase-like protein 2 1 RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK 264.07 8.12E-37 1739100000 1551490 865625 508155 590667 598232 442486 470509 1275570 420770 304633 TRUE FALSE 1490856.056 840938.2225 599989.9123 621151.3947 617474.6756 451433.3701 476267.2299 1249229.034 373005.9536 283999.9356 5.249494344 2.961050751 2.112641016 2.187153294 2.174207097 1.589554481 1.676997669 4.398694779 1.313401543 1 18.11553108 4.724866806 2.539457359 2.261975968 5.840631384 0.531726968 0.889183058 0.417420104 3.503344252 0.231359059 3.171993278 53072.16523 -4.724866806 3.578655416 FYEEFDAHGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FYEEFDAHGR 10 0 P18074;A8MX75;K7EIT8;P18074-2 P18074 ERCC2 TFIIH basal transcription factor complex helicase XPD subunit 0 ; 160.36 7.40E-06 254300000 347550 401360 341390 426110 410580 402810 384560 413920 434380 454500 FALSE TRUE 333967.3618 389913.6058 403086.7672 448101.5882 423786.6786 410955.0942 389266.3603 405372.4074 385071.0035 423716.3102 0.788186232 0.920223264 0.951312842 1.057550954 1.000166074 0.969882642 0.918695719 0.956707112 0.908794385 1 18.69273914 4.724959486 2.121618163 0.969471537 0.742141117 0.650990524 0.040368661 0.434243602 2.234351113 0.011047429 0.186461577 53083.49223 -4.724959486 -0.22733042 VDIDVPDVDVQGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 VDIDVPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 274.6 4.83E-39 2960080000 4884310 5139850 4307160 4988830 4323150 5358130 4798970 5203250 6003640 5438780 FALSE TRUE 4693425.765 4993266.51 5085559.624 5246304.114 4462208.046 5466475.06 4857701.23 5095801.069 5322131.957 5070406.586 0.925650771 0.984786215 1.002988525 1.03469101 0.880049355 1.07811375 0.958049645 1.005008372 1.049645993 1 22.27367001 4.725030443 2.943345763 0.998827385 0.914476329 0.163085315 0.050980648 0.671687838 8.587223742 0.011620346 0.131958643 53092.16595 -4.725030443 -0.084351056 RET(ph)PS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 RETPSPR 7 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RET(1)PS(1)PR;RET(1)PS(1)PR 66.595 0.03369 45134000 71388 78667 84598 106279 83239 81814 98968 99468 106232 128215 TRUE FALSE 68598.07804 76423.49418 99886.74047 111764.0719 85916.45803 83468.33514 100179.2 97413.95104 94172.98872 119530.8838 0.573894176 0.63936191 0.835656336 0.935022551 0.718780413 0.698299322 0.838103064 0.814968884 0.787854868 1 16.8670239 4.725271826 0.053230876 1.387331895 4.37E-17 0.473747738 0.089641769 217.5054122 1.822611518 15.82244074 34.12513452 53121.68304 -4.725271826 -1.387331895 RVNNGNTAPEDS(ph)SPAKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVNNGNTAPEDSSPAKK 17 2 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 RVNNGNTAPEDS(0.5)S(0.5)PAKK;RVNNGNTAPEDS(0.579)S(0.421)PAKK 82.36 0.003831 667440000 989630 831540 662920 644780 678410 634330 736890 795670 874500 823640 TRUE FALSE 950954.1655 807825.2934 782724.3906 678057.1731 700231.6738 647156.5872 745908.2802 779239.1364 775230.4262 767854.1292 1.238456797 1.052055674 1.019365998 0.883054668 0.911933201 0.842811887 0.971419247 1.014827044 1.009606378 1 19.55047274 4.72547816 1.492878721 0.949921623 1.344590236 0.711845449 0.055500234 0.658530837 1.378235256 0.01674521 0.382442797 53146.92718 -4.72547816 0.394668613 LSYAS(ph)AESLETMSEAELPLGFSR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSYASAESLETMSEAELPLGFSR 23 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LS(0.09)Y(0.061)AS(0.424)AES(0.424)LET(0.001)MSEAELPLGFSR;LS(0.156)Y(0.131)AS(0.623)AES(0.09)LETMSEAELPLGFSR;LS(0.159)Y(0.029)AS(0.771)AES(0.042)LETMSEAELPLGFSR 168.55 6.13E-12 95605000 69719 77674 65086 82028 72269 78731 71728 90672 83199 89612 TRUE FALSE 66994.3044 75458.81357 76848.48803 86261.47491 74593.59802 80322.99476 72605.82872 88799.59151 73754.59832 83542.49942 0.801918842 0.90323864 0.919872982 1.032546016 0.892882048 0.961462673 0.869088538 1.062927158 0.882839259 1 16.35022269 4.725504743 1.530639043 0.958457498 0.745218267 0.366779984 0.060883608 1.094976959 2.437206349 0.015577242 0.350063399 53150.1804 -4.725504743 -0.213239231 INPSSMFDVHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 INPSSMFDVHVK 12 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 147.73 6.58E-05 2187300000 1480580 1589550 1366980 1498340 1757280 1552790 1640650 1598640 1871960 1905130 FALSE TRUE 1422717.297 1544217.59 1614023.694 1575669.507 1813804.507 1584188.478 1660728.765 1565627.525 1659462.949 1776093.848 0.80103723 0.869445943 0.908749105 0.88715442 1.021232357 0.891950884 0.935045616 0.881500449 0.934332918 1 20.76027638 4.725648927 1.166371501 0.929695811 0.741529655 0.490222103 0.04329984 1.37517439 1.591561023 0.012263332 0.314591683 53167.82893 -4.725648927 -0.188166155 FLLESFNNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLLESFNNDR 10 0 Q13618;Q13618-2;Q13618-3 Q13618 CUL3 Cullin-3 0 ; 128.28 0.00077647 1062290000 334870 424260 372120 460020 396020 378960 455730 469900 432140 429450 FALSE TRUE 321782.9102 412160.5202 439370.3618 483761.6873 408758.343 386622.8308 461307.3601 460196.4008 383085.2789 400362.969 0.803727955 1.029467139 1.097430072 1.208307773 1.020969407 0.965680797 1.152222847 1.149447967 0.956844935 1 18.61094901 4.725675328 2.991048955 1.081240066 0.762420525 0.484165592 0.08078222 0.299163727 4.006227165 0.020115141 0.224551719 53171.06119 -4.725675328 -0.318819541 S(ph)RTPSNDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTPSNDGK 9 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.5)RT(0.5)PSNDGK 77.192 0.020166 561600000 969840 792300 622480 592650 607620 643530 669260 802860 787520 779310 TRUE FALSE 931937.5806 769704.3797 734975.983 623236.7375 627164.6491 656542.6175 677450.6041 786280.6604 698124.0312 726526.6396 1.282730088 1.059430361 1.011629778 0.857830537 0.863236962 0.903673151 0.932451155 1.082246153 0.960906308 1 19.47065617 4.725704504 1.686710473 0.950309232 1.392545098 0.71706295 0.063928499 0.578187985 1.639739336 0.019649706 0.411751665 53174.6334 -4.725704504 0.442235866 IPRPSVSQGCS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 IPRPSVSQGCSR 12 1 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4M5;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 IPRPSVSQGCS(1)R;IPRPSVSQGCS(1)R 109.04 0.00099367 2486300000 632110 968640 887560 1064640 965840 1109690 1014210 790590 1200460 1164000 TRUE FALSE 607406.4424 941015.3356 1047961.836 1119586.198 996907.1208 1132128.692 1026622.205 774264.0402 1064188.814 1085161.243 0.559738422 0.867166369 0.965719926 1.031723354 0.918671881 1.043281539 0.946054987 0.713501376 0.980673444 1 20.049478 4.725810717 3.133449666 0.932838895 0.508911182 0.630869766 0.088617497 0.250549933 3.852905017 0.024496294 0.25745084 53187.63961 -4.725810717 -0.423927713 SSS(ph)DPPAVHPPLPPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSDPPAVHPPLPPLR 16 0 O43150 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 S(0.154)S(0.154)S(0.693)DPPAVHPPLPPLR;S(0.117)S(0.117)S(0.766)DPPAVHPPLPPLR;S(0.181)S(0.153)S(0.666)DPPAVHPPLPPLR;S(0.104)S(0.104)S(0.793)DPPAVHPPLPPLR 173.37 2.73E-09 3142150000 1937750 2256450 1925210 2406860 2218500 2300750 2308570 2428940 2546880 2535950 TRUE FALSE 1862020.588 2192098.255 2273138.273 2531078.333 2289860.067 2347272.741 2336822.97 2378781.54 2257768.86 2364187.848 0.787594179 0.927209848 0.961488012 1.070591043 0.968560967 0.992845278 0.988425252 1.006172814 0.954987084 1 21.17291324 4.725811583 1.707925832 0.996348931 0.719033395 0.81605719 0.029841856 0.348792842 1.020742004 0.007572756 0.157184653 53187.74562 -4.725811583 -0.277315535 VLAMSGDPNYLHR ddPTM_BT-474_Pertuzumab_2h_R1 7 VLAMSGDPNYLHR 13 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;;;;; 202.29 9.50E-08 4494810000 2887570 3406720 2949030 3390270 3258960 3378070 3520930 3318890 3671820 3857660 FALSE TRUE 2774720.572 3309563.681 3481985.322 3565242.241 3363787.408 3446376.89 3564020.195 3250353.762 3255010.387 3596377.252 0.771532122 0.920249309 0.968192455 0.991342674 0.935326628 0.95829126 0.991002874 0.903785541 0.905080351 1 21.77811293 4.726049017 3.080753069 0.952834888 0.745932845 0.74458128 0.032355323 0.177098947 2.587733702 0.008167359 0.08790917 53216.83191 -4.726049017 -0.206902043 AQIHALEGGEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQIHALEGGEVK 12 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ; 87.18 0.0080377 0 498540 568040 468520 610930 560750 625270 591080 573620 575120 596610 FALSE TRUE 479056.5056 551840.0554 553191.9862 642460.1705 578787.033 637913.3878 598313.8139 561774.5465 509834.7887 556201.0733 0.861300937 0.992159278 0.994589929 1.155086175 1.040607544 1.146911465 1.075714957 1.010020609 0.916637549 1 19.085247 4.726133506 1.627759826 1.051157317 0.797781887 0.399694947 0.067397383 0.995011596 2.578417819 0.01834176 0.395709921 53227.1859 -4.726133506 -0.25337543 VS(ph)LDVNHFAPDELTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 VS(1)LDVNHFAPDELTVK 206.34 1.31E-11 76909000 157060 110730 72866 91798 95202 88349 96016 139470 110860 96120 TRUE FALSE 150921.9216 107572.0888 86034.5071 96535.70578 98264.25879 90135.47731 97191.07253 136589.8958 98275.63756 89609.70679 1.684213987 1.200451298 0.96010254 1.077290723 1.096580519 1.005867339 1.084604291 1.524275669 1.096707501 1 16.4513674 4.726203628 4.288517175 1.135529987 1.71998594 0.56195648 0.150533831 0.170140581 7.307094244 0.041329114 0.297678297 53235.78079 -4.726203628 0.584455953 SLTAEIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLTAEIDR 8 0 P54136;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 175.38 0.00061997 623120000 452850 504800 430460 489950 470390 450330 533520 513430 544820 559110 FALSE TRUE 435152.1213 490403.5983 508253.6975 515236.3782 485520.5215 459435.9811 540049.3774 502827.4911 482974.3177 521240.9817 0.834838657 0.940838529 0.975083916 0.988480178 0.931470354 0.881427204 1.036083877 0.964673747 0.926585466 1 18.99159099 4.726438932 3.202879371 0.96253478 0.818100999 0.469834668 0.040627433 0.286211688 4.699749894 0.009914792 0.10167043 53264.63215 -4.726438932 -0.144433781 S(ph)ASDNTLVAMDFSGHAGR ddPTM_BT-474_Pertuzumab_2h_R1 37 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.582)AS(0.418)DNTLVAMDFSGHAGR;S(0.58)AS(0.42)DNT(0.001)LVAMDFSGHAGR;S(0.499)AS(0.499)DNT(0.003)LVAMDFSGHAGR;S(0.585)AS(0.415)DNTLVAMDFSGHAGR;S(0.581)AS(0.419)DNTLVAMDFSGHAGR;S(0.495)AS(0.495)DNT(0.009)LVAMDFSGHAGR;S(0.494)AS(0.494)DNT(0.011)LVAMDFSGHAGR;S(0.414)AS(0.414)DNT(0.173)LVAMDFSGHAGR;S(0.487)AS(0.487)DNT(0.026)LVAMDFSGHAGR;S(0.333)AS(0.333)DNT(0.333)LVAMDFSGHAGR;S(0.465)AS(0.465)DNT(0.07)LVAMDFSGHAGR;S(0.451)AS(0.451)DNT(0.099)LVAMDFSGHAGR;S(0.488)AS(0.488)DNT(0.024)LVAMDFSGHAGR;S(0.386)AS(0.386)DNT(0.228)LVAMDFSGHAGR;S(0.453)AS(0.453)DNT(0.094)LVAMDFSGHAGR;S(0.451)AS(0.451)DNT(0.098)LVAMDFSGHAGR;S(0.468)AS(0.468)DNT(0.064)LVAMDFSGHAGR;S(0.333)AS(0.333)DNT(0.333)LVAMDFSGHAGR;S(0.333)AS(0.333)DNT(0.333)LVAMDFSGHAGR;S(0.333)AS(0.333)DNT(0.333)LVAMDFSGHAGR;S(0.565)AS(0.435)DNTLVAMDFSGHAGR;S(0.5)AS(0.5)DNTLVAMDFSGHAGR;S(0.49)AS(0.49)DNT(0.019)LVAMDFSGHAGR;S(0.481)AS(0.481)DNT(0.037)LVAMDFSGHAGR;S(0.497)AS(0.497)DNT(0.007)LVAMDFSGHAGR;S(0.61)AS(0.39)DNTLVAMDFSGHAGR;S(0.569)AS(0.43)DNT(0.001)LVAMDFSGHAGR;S(0.567)AS(0.432)DNT(0.001)LVAMDFSGHAGR;S(0.561)AS(0.434)DNT(0.005)LVAMDFSGHAGR;S(0.5)AS(0.5)DNTLVAMDFSGHAGR;S(0.389)AS(0.389)DNT(0.223)LVAMDFSGHAGR;S(0.472)AS(0.472)DNT(0.056)LVAMDFSGHAGR;S(0.44)AS(0.44)DNT(0.121)LVAMDFSGHAGR;S(0.485)AS(0.485)DNT(0.03)LVAMDFSGHAGR;S(0.333)AS(0.333)DNT(0.333)LVAMDFSGHAGR;S(0.482)AS(0.482)DNT(0.037)LVAMDFSGHAGR;S(0.405)AS(0.405)DNT(0.19)LVAMDFSGHAGR 336.54 2.63E-75 10775920300 1540800.5 1718587.6 1379039.2 1757185.4 1739550.4 1752368.3 1719267.2 1865979.5 1792387.17 1839604.6 TRUE FALSE 1480584.313 1669575.164 1628262.26 1847873.949 1795504.618 1787802.388 1740308.106 1827446.371 1588922.893 1715006.542 0.863311175 0.973509502 0.949420437 1.077473411 1.046937475 1.042446395 1.014753042 1.065562333 0.926482118 1 20.70978265 4.726472471 1.181929209 1.028420285 0.795575923 0.526015523 0.04446385 1.106560809 1.319545133 0.012360491 0.316689327 53268.74571 -4.726472471 -0.232844362 SVEHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVEHDK 6 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 74.335 0.080597 298620000 459300 510270 436820 453620 490030 521410 574920 490400 452260 585720 FALSE TRUE 441350.0482 495717.5992 515763.091 477031.3826 505792.26 531953.2674 581956.0429 480273.0686 400921.3408 546048.6627 0.808261385 0.90782678 0.944536863 0.87360599 0.926276895 0.974186558 1.065758572 0.879542615 0.734222732 1 19.05867 4.726518106 3.495384891 0.925635897 0.795468235 0.148041712 0.083288287 0.555626418 11.96854854 0.020520911 0.188077232 53274.34344 -4.726518106 -0.130167662 VREEYPDR ddPTM_BT-474_Pertuzumab_2h_R1 8 VREEYPDR 8 1 Q13509;A0A0B4J269;Q13509-2;G3V2A3 Q13509 TUBB3 Tubulin beta-3 chain 0 ;;;;;;; 145.9 0.00051245 19538000000 7095140 8369240 7191390 8952110 8317150 7384020 8650960 8746870 8612870 8663200 FALSE TRUE 6817854.085 8130557.47 8491034.145 9414129.47 8584678.683 7533329.944 8756833.036 8566244.078 7635173.106 8076433.748 0.84416641 1.006701438 1.051334588 1.165629505 1.062929376 0.932754503 1.084245016 1.060646858 0.94536442 1 22.94528696 4.726644843 2.929847167 1.044545754 0.812959923 0.444764889 0.064218522 0.342257264 4.307502508 0.015982839 0.184445301 53289.89237 -4.726644843 -0.23158583 RAVVVS(ph)PKEENK ddPTM_BT-474_Pertuzumab_2h_R1 1 RAVVVSPKEENK 12 2 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 RAVVVS(1)PKEENK 81.651 0.0089079 279200000 273290 216100 154660 188970 205020 214320 193050 208570 252740 197740 TRUE FALSE 262609.5247 209937.0396 182610.5024 198722.7643 211614.6545 218653.6972 195412.6036 204262.9566 224050.0148 184346.8937 1.424540004 1.138815173 0.990580849 1.077982712 1.147915488 1.186099168 1.060026561 1.108035794 1.215371793 1 17.49206358 4.726742792 4.405294716 1.102323341 1.444160436 0.665477849 0.068865095 0.109909693 5.20959974 0.016324536 0.11492316 53301.91244 -4.726742792 0.341837094 GTS(ph)SPDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTSSPDYR 8 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 GT(0.054)S(0.473)S(0.473)PDYR 91.853 0.012789 231580000 274970 337860 298800 354040 376210 391450 366100 355050 372420 420580 TRUE FALSE 264223.8684 328224.5636 352799.8068 372312.0468 388311.1363 399365.3872 370580.4413 347718.0934 330144.4429 392093.742 0.673879331 0.837107376 0.899784335 0.949548557 0.990352803 1.01854568 0.945132252 0.88682388 0.842003857 1 18.58083909 4.726811382 1.434572574 0.943173787 0.568109252 0.736435042 0.050076961 0.662989434 1.255844333 0.015106766 0.355350673 53310.33131 -4.726811382 -0.375064535 GFEDDRIEALLHK ddPTM_BT-474_Pertuzumab_2h_R1 4 GFEDDRIEALLHK 13 1 Q5JRX3-3;Q5JRX3;Q5JRX3-2;H0Y4F7 Q5JRX3-3 PITRM1 "Presequence protease, mitochondrial" 0 ;;; 114.56 0.00044051 474509000 1198370 1533910 1162690 2113710 1164900 1329750 1953790 1703110 1623630 1372290 FALSE TRUE 1151536.376 1490164.389 1372813.947 2222798.826 1202370.066 1356638.456 1977701.066 1667940.183 1439322.329 1279343.576 0.900099392 1.164788268 1.073061195 1.737452603 0.93983359 1.060417609 1.54587173 1.30374687 1.125047529 1 20.28697233 4.727191782 1.642781855 1.25690247 0.786456496 0.134766811 0.238439383 1.785932154 4.727131962 0.061724264 1.328559227 53357.04646 -4.727191782 -0.470445974 LAMDLPGHADEVYAVDWSPDGQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAMDLPGHADEVYAVDWSPDGQR 23 0 A0A0A0MRH0;Q9NVX2;K7EN33;Q9NVX2-2 A0A0A0MRH0 NLE1 Notchless protein homolog 1 0 ; 175.61 1.32E-12 390060000 245590 266450 227690 245240 272390 249060 247730 272990 279540 285390 FALSE TRUE 235992.0713 258851.1069 268838.6479 257896.8658 281151.6717 254096.1638 250761.7938 267352.6611 247807.7911 266060.2811 0.886987228 0.972903982 1.010442622 0.969317422 1.056721697 0.955032306 0.942499921 1.004857471 0.931397163 1 18.02139363 4.727451805 4.190173282 0.984317971 0.880122064 0.404514005 0.034982465 0.196563589 7.783415064 0.008104648 0.06043564 53389.00233 -4.727451805 -0.104195907 SFEAPATINSASLHPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFEAPATINSASLHPEK 17 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 239.58 2.74E-20 645710000 346940 433900 381130 425010 417390 463920 443000 400857 486620 497840 FALSE TRUE 333381.2012 421525.5968 450008.6692 446944.817 430815.7284 473300.7803 448421.5665 392579.1629 431380.9377 464120.8534 0.718306878 0.908223782 0.96959373 0.962992319 0.928240404 1.019779174 0.96617414 0.845855471 0.92945821 1 18.82414099 4.727499055 3.303108645 0.944632648 0.690202558 0.703675039 0.045228515 0.189087409 3.4091375 0.012177208 0.120828835 53394.81113 -4.727499055 -0.25443009 NSPEDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPEDKR 7 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 0 75.738 0.068396 304920000 681840 579950 456040 456910 503910 410690 524170 541240 556300 607720 FALSE TRUE 655192.939 563410.3938 538456.5726 480491.1799 520118.7228 418994.4332 530584.9493 530063.2049 493151.1562 566558.5831 1.156443409 0.994443312 0.950398756 0.848087372 0.918031671 0.739542998 0.936505006 0.935584105 0.870432769 1 19.11186562 4.72765605 1.379372841 0.890907807 1.263221071 0.59582904 0.065838536 0.832844932 1.432289404 0.017840864 0.430252339 53414.11656 -4.72765605 0.372313264 SAEHYTETALDEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAEHYTETALDEIR 14 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBM8 H3BLV9 SRPK1 SRSF protein kinase 1 0 ; 197.19 2.38E-08 584580000 600950 820340 726480 941450 793260 881730 835770 795620 771340 988990 FALSE TRUE 577464.2096 796944.7064 857771.0965 990038.3473 818775.9283 899559.1847 845998.4033 779190.169 683780.7169 922004.8264 0.626313652 0.864360667 0.930332545 1.073788682 0.888038658 0.975655614 0.917563964 0.845104219 0.741623793 1 19.81441478 4.727891338 2.981461046 0.91760218 0.581941186 0.519648856 0.084794946 0.310463067 4.10611955 0.0215958 0.245533795 53443.06263 -4.727891338 -0.335660994 EGDVLTLLESER ddPTM_BT-474_Pertuzumab_2h_R1 6 EGDVLTLLESER 12 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;; 310.88 6.42E-46 4266756000 901225 942273 788788 906960 936674 932042 953622 982084 1004773 1044734 FALSE TRUE 866004.1306 915400.2966 931339.5381 953768.3143 966802.9699 950888.5278 965292.7113 961803.6222 890715.3814 973973.2356 0.889145717 0.93986186 0.956227034 0.979255158 0.992638129 0.976298417 0.991087512 0.987505187 0.914517308 1 19.8935226 4.72798586 1.195985712 0.978709057 0.848894807 0.588415099 0.022648566 1.008776101 1.234166437 0.006337049 0.162592074 53454.69556 -4.72798586 -0.12981425 RPTPQDSPIFLPVDDTSFR ddPTM_BT-474_Pertuzumab_2h_R1 8 RPTPQDSPIFLPVDDTSFR 19 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 247.66 1.43E-24 31393280000 7162850 8650700 7574420 8720510 8024580 8413040 9220050 7971580 8992920 10050630 FALSE TRUE 6882917.903 8403990.506 8943286.186 9170576.566 8282697.903 8583157.433 9332887.73 7806964.087 7972081.423 9369891.878 0.734578157 0.896914352 0.954470585 0.97872811 0.883969422 0.91603591 0.996050739 0.833196817 0.850818934 1 23.15960097 4.728218417 3.913324716 0.920164574 0.718828365 0.515938534 0.055205539 0.194355769 6.06919048 0.013602964 0.110102591 53483.32726 -4.728218417 -0.201336209 FQAQSLGTTYIYDIPEMFR ddPTM_BT-474_Pertuzumab_2h_R1 1 FQAQSLGTTYIYDIPEMFR 19 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 267.07 3.17E-31 46658000 38061 43635 42372 47015 50968 55377 57520 51725 56694 64499 FALSE TRUE 36573.53404 42390.57252 50029.56296 49441.44978 52607.43201 56496.76088 58223.94697 50656.86067 50258.3348 60130.42528 0.608236743 0.704977095 0.832017448 0.822236822 0.87488874 0.939570286 0.968294282 0.842449732 0.835822041 1 15.87580754 4.728469937 0.765232225 0.905871257 0.419267993 0.791323266 0.051166517 1.207475642 0.544492073 0.019621686 0.504651553 53514.31079 -4.728469937 -0.486603264 S(ph)PMSTNSSVHTGSDVEQDAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPMSTNSSVHTGSDVEQDAEK 21 0 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 S(0.89)PMS(0.025)T(0.025)NS(0.025)S(0.035)VHTGSDVEQDAEK 111.49 5.06E-05 0 66527 71322 61452 68283 62292 71420 69776 66827 83526 75448 TRUE FALSE 63927.05129 69287.96639 72557.74339 71807.09381 64295.67875 72864.16133 70629.93956 65446.9991 74044.47865 70337.83976 0.908857189 0.985073847 1.031560589 1.02088853 0.914098001 1.035916963 1.004152812 0.930466436 1.05269765 1 16.10201341 4.728575111 4.819087901 0.993265399 0.904812908 0.278652561 0.042388133 0.226166688 15.14796998 0.010027771 0.066050455 53527.27208 -4.728575111 -0.088452491 DREEDEEDAYER ddPTM_BT-474_Pertuzumab_2h_R1 2 DREEDEEDAYER 12 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 242.4 2.48E-16 648870000 560290 607570 514700 552220 575080 570930 578990 662700 637490 667200 FALSE TRUE 538393.2474 590242.6985 607717.7394 580720.1404 593577.9705 582474.5958 586075.8528 649015.0134 565124.8078 622009.9497 0.865570153 0.948928066 0.977022538 0.933618732 0.954290154 0.936439354 0.942229064 1.043415807 0.908546251 1 19.24657813 4.728597057 3.335314673 0.964454993 0.853406654 0.384436628 0.036231559 0.316765813 5.880007222 0.00901675 0.089035469 53529.977 -4.728597057 -0.111048339 SVEETLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVEETLR 7 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 126.67 0.023124 0 186470 215390 165800 253530 193440 203770 241550 237560 196260 204430 FALSE TRUE 179182.5462 209247.2881 195763.7482 266614.7137 199662.1733 207890.369 244506.1612 232654.303 173981.3876 190583.774 0.940177343 1.097928138 1.027179513 1.398937108 1.047634691 1.090808334 1.282932728 1.220745597 0.912886674 1 17.54006577 4.728842812 1.525128841 1.150091852 0.869921808 0.11851635 0.138004426 1.960402606 4.30080127 0.036034909 0.822938151 53560.27665 -4.728842812 -0.280170044 EYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_BT-474_Pertuzumab_2h_R1 4 EYSPPYAPSHQQYPPSHATPLPK 23 0 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK 231.4 3.85E-33 7644230000 2959520 3241060 2884670 3044630 3091710 3132250 3267850 2664880 3803260 3886080 TRUE FALSE 2843858.686 3148628.142 3405994.038 3201763.719 3191157.66 3195586.241 3307842.926 2609849.297 3371529.869 3622872.34 0.784973474 0.869097182 0.940136366 0.883763881 0.880836353 0.882058748 0.913044296 0.720381248 0.930623426 1 21.78870254 4.728996742 5.275452791 0.877257222 0.78164544 0.150254 0.069176054 0.306990511 29.77201314 0.017014187 0.104897696 53579.26376 -4.728996742 -0.095611782 RLDEYTQEEIDAFPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLDEYTQEEIDAFPR 15 1 H0YAX3;Q9BYD1;E5RJI7 H0YAX3 MRPL13 "39S ribosomal protein L13, mitochondrial" 0 151.59 4.78E-06 178220000 35665 57989 48450 90379 41223 61543 78105 66627 55255 50034 FALSE TRUE 34271.17237 56335.2105 57205.99276 95043.47102 42548.97523 62787.44163 79060.87235 65251.12917 48982.68405 46645.15261 0.734720983 1.207739869 1.226408095 2.037585166 0.912184286 1.346065735 1.694942945 1.398883389 1.050113062 1 15.50943954 4.729145578 2.010792206 1.376894838 0.559357723 0.232641208 0.319815409 0.957905819 4.243738847 0.07859932 1.431231489 53597.62903 -4.729145578 -0.817537115 AEFFQHLIEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEFFQHLIEDR 11 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 ;;; 184.1 5.06E-06 665210000 874310 968920 819970 981560 977740 942070 977860 904260 1011010 1025400 FALSE TRUE 840140.9986 941287.3503 968156.8191 1032218.429 1009189.895 961119.3009 989827.3432 885586.715 896244.3833 955948.7447 0.878855695 0.984662991 1.012770637 1.079784282 1.055694566 1.005408822 1.035439765 0.926395604 0.937544391 1 19.86657374 4.729384439 3.179872677 1.00545014 0.861618217 0.422106846 0.044618163 0.372296617 5.961710458 0.012466427 0.131629679 53627.11569 -4.729384439 -0.143831923 QMGFPLIYVEAEQVEDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 QMGFPLIYVEAEQVEDDR 18 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 186.56 1.10E-13 316144000 115539 134676 114470 142523 143512 126997 123224 149922 148922 156527 FALSE TRUE 111023.6081 130835.1723 135157.2754 149878.6291 148128.1938 129564.9664 124732.0522 146826.0583 132016.9989 145925.2869 0.760825012 0.896590133 0.926208735 1.02709155 1.015096129 0.887885637 0.854766537 1.006172826 0.90468898 1 17.15487038 4.729441811 1.902320803 0.953453132 0.703735437 0.522903011 0.055753205 0.652080378 2.498489915 0.014897247 0.286439633 53634.20043 -4.729441811 -0.249717695 EQAEAEVASLNR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQAEAEVASLNR 12 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;;; 168.83 0.0001058 2033490000 759330 946350 735350 1124950 908650 987360 980170 1022120 983070 1219620 FALSE TRUE 729654.5441 919361.0246 868244.1028 1183008.804 937877.5525 1007325.096 992165.6137 1001012.865 871476.015 1137014.051 0.641728696 0.808574902 0.763617742 1.040452229 0.824860125 0.885939004 0.872606291 0.880387418 0.766460198 1 20.11681865 4.729470844 1.328752719 0.882773251 0.548991675 0.455038515 0.081418211 1.167559138 1.829902272 0.021259777 0.525899715 53637.78604 -4.729470844 -0.333781576 KDTDFEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDTDFEHR 8 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 99.815 0.0042492 302550000 517900 533660 444270 504360 493660 546700 530310 492390 600820 572250 FALSE TRUE 497659.8954 518440.5393 524559.4717 530390.08 509539.0222 557754.6486 536800.0924 482221.9744 532617.4324 533490.9978 0.932836538 0.97178873 0.983258338 0.994187498 0.955103318 1.0454809 1.006202719 0.903898991 0.998362549 1 19.0251044 4.729602482 2.916728179 0.980718805 0.925127353 0.160342201 0.035035102 0.84410404 10.43960608 0.009240075 0.109280993 53654.04664 -4.729602482 -0.055591452 LYTLVLTDPDAPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LYTLVLTDPDAPSR 14 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ;;; 237.37 6.32E-17 702861000 637351 684312 569654 710945 671908 603032 668548 709837 689422 777371 FALSE TRUE 612442.6183 664796.0918 672603.1497 747636.9566 693520.531 615225.7202 676729.8904 695178.6179 611161.7049 724718.9698 0.845076014 0.917315704 0.928088235 1.031623274 0.956950984 0.848916264 0.933782499 0.959238887 0.843308552 1 19.46706213 4.729636555 2.4699258 0.937755582 0.825618336 0.202733858 0.055159127 0.851706189 6.5609829 0.013741447 0.200200865 53658.25623 -4.729636555 -0.112137246 S(ph)TPPPNNLVNPVQELETER ddPTM_BT-474_Pertuzumab_2h_R1 1 STPPPNNLVNPVQELETER 19 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 S(0.5)T(0.5)PPPNNLVNPVQELETER 63.691 0.03807 27897000 15381 19244 16847 20642 18309 18248 17525 22908 22324 22414 TRUE FALSE 14779.89352 18695.17996 19891.62766 21707.33609 18897.92561 18616.98706 17739.47619 22434.94179 19789.87311 20895.87982 0.707311376 0.894682594 0.951940183 1.038833315 0.904385256 0.890940569 0.848946125 1.073653849 0.947070584 1 14.35093088 4.729881389 2.279198661 0.958508273 0.647273496 0.578435049 0.064132509 0.439351574 2.714550047 0.016989623 0.272071384 53688.51467 -4.729881389 -0.311234777 EAS(ph)IDILHSIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EASIDILHSIVK 12 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 1 EAS(1)IDILHSIVK 107.11 0.0011916 16672000 101970 72193 51188 58182 64093 48063 57685 79995 63941 60242 TRUE FALSE 97984.89967 70134.12632 60438.81027 61184.77999 66154.60955 49034.86679 58390.96629 78343.0753 56682.68574 56161.75568 1.744690822 1.248787996 1.076155999 1.08943852 1.17792987 0.873100675 1.03969268 1.39495417 1.00927553 1 15.77730042 4.72994288 2.564901013 1.10589959 1.873304291 0.698000393 0.130288673 0.294314336 2.517145479 0.034798264 0.485179156 53696.11681 -4.72994288 0.7674047 KQISVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQISVR 6 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ; 128.75 0.02644 2185700000 2595100 3178700 2825200 3160800 3071400 2853400 3341700 2895300 3521300 3598900 FALSE TRUE 2493680.623 3088046.588 3335776.486 3323929.267 3170194.37 2911097.703 3382596.724 2835511.043 3121576.786 3355143.297 0.743241168 0.920391862 0.994227725 0.990696662 0.944875998 0.867652271 1.00818249 0.845123678 0.930385533 1 21.67794295 4.730115953 4.457804745 0.940004444 0.731136915 0.565590277 0.053056618 0.142408332 7.092440884 0.012911329 0.092538455 53717.5198 -4.730115953 -0.20886753 ISYT(ph)PPESPVPSYASSTPLHVPVPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 IS(0.038)Y(0.001)T(0.96)PPESPVPSYASSTPLHVPVPR;IS(0.026)Y(0.004)T(0.97)PPESPVPSYASSTPLHVPVPR;IS(0.005)YT(0.995)PPESPVPSYASSTPLHVPVPR;IS(0.01)YT(0.99)PPESPVPSYASSTPLHVPVPR 186.71 5.50E-17 1332600000 454353 585160 435515 646460 626180 597400 665680 622050 639080 645920 TRUE FALSE 436596.3824 568471.8097 514222.2485 679823.8781 646321.6484 609479.8373 673826.791 609204.4501 566534.3176 602171.2631 0.725036894 0.944036763 0.853946842 1.128954369 1.073318652 1.012137036 1.118995263 1.011679712 0.940819253 1 19.19981434 4.730228989 1.046814874 1.039940733 0.591450646 0.621663459 0.071828254 1.141799184 1.022964039 0.021455043 0.57178802 53731.50305 -4.730228989 -0.448490087 VYEIGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VYEIGR 6 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ;; 109.88 0.067884 791450000 791530 957310 829910 953590 925470 957030 994510 934950 1045260 1056000 FALSE TRUE 760596.1325 930008.4561 979893.1982 1002804.894 955238.583 976381.8023 1006681.111 915642.9558 926606.4669 984476.1794 0.772589676 0.944673396 0.995344752 1.018617733 0.970301367 0.991777986 1.022555072 0.930081372 0.941217763 1 19.90899677 4.730268171 3.025879148 0.981443018 0.74099952 0.829960978 0.028540208 0.148170939 2.040838693 0.007502137 0.084974887 53736.35087 -4.730268171 -0.240443498 VDST(ph)TCLFPVEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.066)T(0.934)TCLFPVEEK;VDS(0.395)T(0.594)T(0.011)CLFPVEEK 284.91 1.14E-31 8622900000 2656500 1691070 1172600 1163090 1453790 1117080 1164450 2315400 1789540 1330070 TRUE FALSE 2552681.043 1642842.339 1384514.904 1223117.214 1500552.476 1139668.123 1178700.887 2267586.181 1586398.922 1239983.174 2.058641679 1.324890832 1.116559429 0.986398235 1.210139385 0.919099667 0.95057813 1.828723347 1.279371329 1 20.24188911 4.730495433 3.42540285 1.199916916 2.1600431 0.526364474 0.252188219 0.269535169 5.431278668 0.069057395 0.668219285 53764.47795 -4.730495433 0.960126185 AIVDCGFEHPSEVQHECIPQAILGMDVLCQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIVDCGFEHPSEVQHECIPQAILGMDVLCQAK 32 0 O00148;O00148-2;O00148-3;K7EPJ3;A0A0G2JJL7;F6QYI9;K7EIL8;K7ENP6;K7EN69;K7EL56;F6SXL5;Q13838-2;Q13838;Q5STU3;F6WLT2;F6S4E6;A0A0A0MT12;F6TRA5;F6R6M7;F6U6E2;F6S2B7;A0A0G2JHN7 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ; 129.03 5.79E-08 93422000 48311 63660 56273 74446 60326 80865 72884 30081 69954 77732 FALSE TRUE 46422.95271 61844.47913 66442.78289 78288.16698 62266.44058 82500.1457 73775.97619 29459.81684 62013.11519 72467.1424 0.640606917 0.853414073 0.91686771 1.080326399 0.859236869 1.138448999 1.018061065 0.406526542 0.855741142 1 16.14503939 4.730508418 3.928872995 0.881778392 0.619833988 0.138132375 0.191357515 0.579538179 18.35418264 0.052401877 0.430103263 53766.08548 -4.730508418 -0.261944404 S(ph)LSPILPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSPILPGR 9 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 S(0.887)LS(0.113)PILPGR 100.48 0.0048606 196310000 110610 126860 108650 119780 117160 131350 122290 133080 131070 133960 TRUE FALSE 106287.2389 123242.077 128285.4719 125961.8602 120928.5578 134005.987 123786.6216 130331.8515 116191.4831 124886.7699 0.851068844 0.986830528 1.027214268 1.00860852 0.968305593 1.073019881 0.991190834 1.043600148 0.930374636 1 16.93026112 4.730567783 3.501324449 1.009095296 0.833251751 0.601916524 0.037271579 0.171570597 3.70723615 0.008390387 0.079034434 53773.43537 -4.730567783 -0.175843545 LIHEQEQQSSS ddPTM_BT-474_Pertuzumab_2h_R1 2 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ; 99.568 0.0061284 230350000 201059 242380 215006 253360 207604 227420 254200 252460 232870 233303 FALSE TRUE 193201.392 235467.5597 253862.367 266435.94 214281.7712 232018.5882 257310.9756 247246.6128 206435.5739 217501.18 0.888277443 1.082603596 1.167176964 1.224986181 0.985198201 1.066746342 1.18303255 1.136759868 0.949123926 1 17.7306637 4.730763064 4.640544921 1.102330986 0.876440743 0.313338747 0.087133001 0.197907581 11.49361288 0.020703823 0.1438427 53797.62012 -4.730763064 -0.225890243 (ac)SGEDEQQEQTIAEDLVVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 76.262 6.58E-14 49772000 53945 70884 66495 69018 66544 66186 69822 74629 69706 69987 FALSE TRUE 51836.76976 68862.45772 78512.12567 72580.02725 68684.44819 67524.32627 70676.50252 73087.88507 61793.26711 65246.71815 0.794473212 1.055416421 1.203311491 1.112393532 1.052688168 1.034907627 1.083219272 1.120177185 0.947070885 1 15.99361772 4.730933705 5.021094408 1.079105138 0.782047482 0.598088508 0.066837529 0.100686085 8.00192482 0.015785304 0.102912989 53818.76221 -4.730933705 -0.297057656 SRTS(ph)PVTR ddPTM_BT-474_Pertuzumab_2h_R1 7 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.098)RT(0.035)S(0.866)PVTR;S(0.26)RT(0.186)S(0.554)PVTR;S(0.383)RT(0.186)S(0.431)PVTR;S(0.07)RT(0.039)S(0.891)PVTR;S(0.176)RT(0.118)S(0.706)PVTR;S(0.033)RT(0.165)S(0.802)PVTR;S(0.033)RT(0.16)S(0.807)PVTR 101.39 0.0032862 28465544000 1367218 1717694 1535290 1604383 1508341 1864166 1715797 1694696 1727534 1900547 TRUE FALSE 1313785.609 1668707.049 1812751.055 1687185.399 1556858.158 1901860.714 1736795.437 1659699.935 1531431.583 1771821.259 0.741488794 0.941803266 1.023100409 0.952232281 0.878676757 1.0733931 0.980231741 0.936719732 0.864326227 1 20.75680164 4.731075182 4.541400923 0.962522643 0.72842483 0.554676963 0.05930151 0.135691874 7.257653146 0.014143531 0.100499321 53836.29715 -4.731075182 -0.234097813 RPLPALPVPEAPSPS(ph)PVPS(ph)PAPGRK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPLPALPVPEAPSPSPVPSPAPGRK 25 2 O43281-3;O43281-2;O43281 O43281-3 EFS Embryonal Fyn-associated substrate 2 RPLPALPVPEAPS(0.05)PS(0.95)PVPS(1)PAPGRK 98.37 0.0041371 68407000 41576 46748 40830 42109 46229 51001 40044 47487 45927 50917 TRUE FALSE 39951.16396 45414.79281 48208.88926 44282.25054 47715.99777 52032.27516 40534.07045 46506.37686 40713.5595 47468.34624 0.841637999 0.956738467 1.015600776 0.932879572 1.005217193 1.096146786 0.853917898 0.979734508 0.857699135 1 15.53467817 4.731205145 4.904502059 0.967342563 0.835709749 0.228369783 0.069039324 0.240090923 17.35525617 0.016012085 0.106620495 53852.41013 -4.731205145 -0.131632814 SPS(ph)PPTQHTGQPPGQPSAPSQLSAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPPTQHTGQPPGQPSAPSQLSAPR 26 0 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;I3L460;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 S(0.002)PS(0.996)PPT(0.002)QHTGQPPGQPSAPSQLSAPR;S(0.002)PS(0.988)PPT(0.01)QHT(0.001)GQPPGQPSAPSQLSAPR 197.7 4.13E-25 5414790000 134915 183526 162027 198657 165659 196373 174835 178779 194478 220683 TRUE FALSE 129642.3726 178292.0182 191308.8832 208909.7116 170987.5722 200343.7966 176974.683 175087.1512 172401.6728 205735.9438 0.630139635 0.866606072 0.929875838 1.015426413 0.831102086 0.973790932 0.860203034 0.851028498 0.837975463 1 17.65043434 4.731397621 3.508703694 0.90441134 0.59914064 0.628901728 0.064475451 0.183510205 3.989696154 0.015564387 0.147140672 53876.28248 -4.731397621 -0.3052707 NVSES(ph)PNR ddPTM_BT-474_Pertuzumab_2h_R1 2 NVSESPNR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.01)ES(0.99)PNR;NVS(0.263)ES(0.737)PNR 101.12 0.0058987 560180000 609650 571950 461290 555890 526490 481950 606610 551480 590390 621990 TRUE FALSE 585824.204 555638.546 544655.3643 584579.5495 543425.029 491695.3592 614033.8746 540091.7453 523371.4023 579862.0633 1.010281998 0.95822538 0.939284355 1.008135532 0.937162583 0.847952281 1.058930931 0.931414175 0.90257914 1 19.14535023 4.731737293 4.378420722 0.952663937 1.014086105 0.085521852 0.055638797 0.50337567 23.48473441 0.012857136 0.095155649 53918.43685 -4.731737293 0.061422168 S(ph)IQEIQELDKDDESLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIQEIQELDKDDESLR 16 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 1 S(1)IQEIQELDKDDESLR 123.12 5.43E-05 125000000 129600 97199 69991 87898 103440 59585 87656 140170 72364 61563 TRUE FALSE 124535.0887 94426.97969 82639.93064 92434.42631 106767.2415 60789.84952 88728.76035 137275.4405 64149.54209 57393.28318 2.169854761 1.645261858 1.439888539 1.610544322 1.860274158 1.059180555 1.545978126 2.391838085 1.117718634 1 15.80859429 4.731776685 4.609784511 1.593955002 2.20276701 0.172326622 0.399959338 0.353270994 20.02462535 0.097741731 0.689734146 53923.32762 -4.731776685 0.608812007 DIELTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIELTLR 7 0 I3L1Y8;Q9HBL8;I3L3Z0 I3L1Y8 NMRAL1 NmrA-like family domain-containing protein 1 0 ; 101.28 0.021339 120056000 122610 141740 121941 136992 133158 125062 156068 143044 156625 168199 FALSE TRUE 117818.2656 137697.714 143978.4513 144062.1735 137441.148 127590.8393 157978.0069 140090.0914 138845.5866 156806.7319 0.751359742 0.878136495 0.918190498 0.918724418 0.876500303 0.813682154 1.007469545 0.893393349 0.885456797 1 17.25862797 4.731918648 2.756412528 0.909681749 0.722676824 0.448608537 0.053923886 0.390248085 4.080348707 0.012749061 0.164451831 53940.95709 -4.731918648 -0.187004925 VYNVTQHAVGIVVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 VYNVTQHAVGIVVNK 15 0 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 128.9 6.92E-05 832400000 742960 812270 688060 757490 768210 836910 762360 856660 825180 894840 FALSE TRUE 713924.3018 789104.8549 812407.7478 796584.1497 792920.1723 853832.8936 771689.9897 838969.6716 731509.0258 834231.6898 0.855786601 0.945906113 0.973839471 0.954871602 0.950479563 1.023496115 0.925030779 1.005679456 0.876865546 1 19.67008859 4.732142831 2.984141549 0.965327022 0.838506805 0.391932351 0.040100239 0.346858291 4.571598655 0.008929067 0.10424571 53968.80867 -4.732142831 -0.126820217 VVEVGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVEVGSK 7 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 98.997 0.025247 375640000 414610 457110 393870 423460 463820 470430 451450 462540 513440 486990 FALSE TRUE 398406.5828 444073.6704 465051.0706 445314.8213 478739.1915 479942.4169 456974.9801 452988.3874 455156.4437 454005.7335 0.877536457 0.978123485 1.024328629 0.980857263 1.054478294 1.057128537 1.006540108 0.997759178 1.002534572 1 18.79235099 4.732160783 2.214391409 1.015820345 0.842287783 0.761764948 0.023243233 0.307082959 1.747600368 0.006228733 0.104230137 53971.03958 -4.732160783 -0.173532562 HQRPQPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HQRPQPEK 8 1 O95391;A0A0C4DGD2;E5RGM7;E5RK41 O95391 SLU7 Pre-mRNA-splicing factor SLU7 0 97.431 0.0049491 36361000 134350 116690 93628 95887 97832 86036 104930 76483 116080 107650 FALSE TRUE 129099.4535 113362.1155 110548.6623 100835.7396 100978.8551 87775.70687 106214.1647 74903.59932 102903.085 100358.7696 1.286379396 1.129568606 1.101534652 1.004752648 1.006178688 0.874619201 1.058344628 0.746358286 1.025352198 1 16.61480716 4.732203733 0.572154271 0.912964193 1.51746595 0.603033626 0.086351589 2.317667286 0.580077455 0.042787916 0.935909626 53976.37731 -4.732203733 0.604501758 MLVQCMQDQEHPSIR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLVQCMQDQEHPSIR 15 0 H0Y8C6;O00410-2;O00410;O00410-3;H0Y3V4 H0Y8C6 IPO5 Importin-5 0 204.43 4.91E-09 283240000 87536 141420 142540 145900 109280 157830 146060 123900 127280 183890 FALSE TRUE 84114.99634 137386.8401 168300.1488 153429.9165 112795.0904 161021.4307 147847.526 121341.4217 112831.708 171434.9665 0.490652508 0.801393338 0.981714245 0.894974459 0.657946816 0.939256641 0.86241173 0.707798556 0.658160411 1 17.38730187 4.732207895 5.264719009 0.825920215 0.477839477 0.423844786 0.119973219 0.147497284 14.3295713 0.028957121 0.184854814 53976.89461 -4.732207895 -0.348080738 GLFDDEDEESDLFTEAPQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLFDDEDEESDLFTEAPQDR 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 0 ;;; 343.87 1.67E-80 740460000 414609 475158 408611 486631 485280 527248 484510 497594 520193 539376 FALSE TRUE 398405.6219 461606.9591 482456.0972 511746.0842 500889.4719 537909.3158 490439.5783 487318.51 461142.8715 502843.5831 0.792305272 0.917993139 0.959455611 1.017704315 0.996113879 1.069734872 0.97533228 0.969125443 0.917070212 1 18.93975017 4.732402668 1.522778224 0.991389199 0.716750239 0.72950119 0.036886965 0.589598921 1.280941216 0.010469554 0.242869021 54001.1077 -4.732402668 -0.27463896 S(ph)PTKTDPKNEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTKTDPKNEEEEK 14 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.779)PT(0.111)KT(0.111)DPKNEEEEK;S(0.964)PT(0.018)KT(0.018)DPKNEEEEK 62.765 0.058618 1114540000 596120 381900 272231 183395 307338 309337 317848 391500 495960 319460 TRUE FALSE 572822.9714 371008.5859 321429.1974 192860.0379 317223.8059 315592.0061 321737.9189 383415.3882 439660.7 297822.6897 1.923369143 1.245736469 1.079263631 0.647566638 1.065143177 1.059664079 1.080300226 1.287394821 1.476249847 1 18.18409414 4.732486029 2.853822838 1.091500831 2.065392261 0.613198608 0.198575527 0.29179562 3.37054952 0.052873714 0.65500501 54011.47391 -4.732486029 0.97389143 EGQPSPADEKGNDS(ph)DGEGESDDPEKKK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGQPSPADEKGNDSDGEGESDDPEKKK 27 3 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEKKK;EGQPSPADEKGNDS(1)DGEGESDDPEKKK;EGQPSPADEKGNDS(1)DGEGESDDPEKKK 241.41 2.38E-45 2707310000 908410 540693 373483 218311 451810 464757 431764 607120 704650 409557 TRUE FALSE 872908.3329 525272.965 440979.6862 229578.0569 466342.879 474154.705 437048.057 594582.7598 624661.0861 381817.3396 2.286193534 1.375717943 1.154949345 0.60127719 1.221376901 1.24183649 1.144652198 1.557243996 1.636020739 1 18.5425231 4.732495593 3.262667986 1.213016178 2.428779126 0.592985717 0.269581075 0.244664497 4.224329923 0.071488936 0.746376582 54012.66344 -4.732495593 1.215762949 GTDTQTPAVLS(ph)PSKTQATLKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GTDTQTPAVLSPSKTQATLKPK 22 2 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(0.92)PS(0.062)KT(0.017)QAT(0.001)LKPK;GTDTQTPAVLS(0.995)PS(0.005)KTQATLKPK;GTDTQTPAVLS(0.997)PS(0.002)KTQATLKPK 175 6.36E-18 5014300000 2142980 1537540 1154000 861800 1286170 1165360 1123410 1509130 1110330 1006190 TRUE FALSE 2059229.972 1493690.865 1362553.471 906277.6013 1327540.826 1188924.378 1137158.628 1477965.938 984289.9933 938039.8551 2.195247847 1.592353306 1.452553922 0.966139761 1.415228595 1.267456144 1.212271122 1.575589705 1.049305089 1 19.8392897 4.732586199 1.560282558 1.266428896 2.537490317 0.7144385 0.186633654 0.576466136 1.329565708 0.048990088 1.119296283 54023.9331 -4.732586199 1.271061421 up GSESATYVPVAPPT(ph)PAWQPEIKPEPAWHDQDETSSVKSDGAGGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSESATYVPVAPPTPAWQPEIKPEPAWHDQDETSSVKSDGAGGAR 45 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 GSESATYVPVAPPT(0.2)PAWQPEIKPEPAWHDQDET(0.2)S(0.2)S(0.2)VKS(0.2)DGAGGAR 41.514 0.077992 205650000 166130 127820 97092 87398 117390 106730 101300 112640 153580 121330 TRUE FALSE 159637.4559 124174.6987 114638.6842 91908.62125 121165.956 108888.1537 102539.7397 110313.9446 136146.2423 113112.211 1.411319383 1.097801003 1.013495211 0.81254376 1.071201375 0.962656045 0.906531123 0.975261147 1.203638767 1 16.78739516 4.732965285 2.119308998 0.982668068 1.525792431 0.629675827 0.096353608 0.408161859 2.062511347 0.023931216 0.421273419 54071.11005 -4.732965285 0.543124362 IEDGNDFGVAIQEK ddPTM_BT-474_Pertuzumab_2h_R1 3 IEDGNDFGVAIQEK 14 0 A0A087X1Z3;Q9UL46;H0YM70;H0YKU2 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;; 243.3 3.68E-17 604726000 631050 750170 644940 721914 776920 791840 786430 666460 770860 812040 FALSE TRUE 606387.8683 728775.8861 761495.0046 759172.0681 801910.3374 807851.5473 796054.5656 652697.3681 683355.2045 757039.8075 0.800998656 0.962665211 1.005885024 1.002816577 1.059271031 1.06711898 1.05153594 0.862170472 0.902667466 1 19.53000964 4.733012638 3.329377862 0.990438569 0.776701082 0.458600232 0.06246382 0.330590518 6.075759072 0.017597221 0.179754367 54077.00594 -4.733012638 -0.213737487 YVSHGATGK ddPTM_BT-474_Pertuzumab_2h_R1 3 YVSHGATGK 9 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;; 138.4 0.00013778 254265000 515360 552440 469540 531240 508792 519900 543210 517987 649510 577350 FALSE TRUE 495219.1614 536684.9521 554396.3229 558657.3601 525157.7568 530412.7342 549857.9665 507290.3874 575780.3478 538245.5702 0.92006175 0.997100546 1.03000629 1.03792282 0.975684308 0.985447468 1.021574532 0.942488737 1.069735414 1 19.03790502 4.733203789 5.036308148 1.003143051 0.916347148 0.367801318 0.033861011 0.177540268 14.34711189 0.00802258 0.053426264 54100.81274 -4.733203789 -0.086795902 ASPFLLQYIQEEIPDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPFLLQYIQEEIPDYR 17 0 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7;C9JJS3 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 0 164.33 6.06E-09 44659000 16471 18563 16058 17339 17174 18744 17554 17914 20180 20556 FALSE TRUE 15827.29511 18033.60142 18960.03781 18233.86787 17726.41731 19123.01652 17768.8311 17544.06964 17889.251 19163.72381 0.825898728 0.941028038 0.989371272 0.951478327 0.92499858 0.997875815 0.927211813 0.915483327 0.933495555 1 14.22609031 4.733325452 5.030860236 0.950001408 0.820321224 0.619734556 0.029935691 0.108222546 8.70795236 0.007285865 0.048621999 54115.97055 -4.733325452 -0.129680184 VLEDEEGSKDIELSDDPYDCIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLEDEEGSKDIELSDDPYDCIR 22 1 Q15024 Q15024 EXOSC7 Exosome complex component RRP42 0 ; 140.48 1.18E-07 101088000 254520 205495 155851 176152 189862 199338 185103 198699 244830 228100 FALSE TRUE 244573.077 199634.4838 184016.7426 185243.2258 195969.0837 203368.7509 187368.3459 194595.7962 217037.9248 212650.5838 1.15011712 0.938791139 0.86534793 0.871115529 0.921554412 0.956351717 0.881109012 0.915096459 1.02063169 1 17.69812529 4.733385512 4.744454065 0.920674832 1.162438473 0.635844674 0.04969731 0.101982979 6.478456751 0.011614715 0.081225851 54123.45501 -4.733385512 0.241763641 SSSLIQLT(ph)SQNSSPNQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLIQLTSQNSSPNQQR 18 0 O95639;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 S(0.008)S(0.008)S(0.05)LIQLT(0.467)S(0.467)QNSSPNQQR 107.03 0.0048295 518450000 294420 232260 175310 224080 223160 191860 180130 302500 210090 184310 TRUE FALSE 282913.7409 225636.1722 206992.4167 235644.7957 230338.1441 195739.5407 182334.4848 296253.2693 186241.464 171826.5195 1.646508011 1.313162676 1.204659312 1.371411097 1.340527322 1.13916956 1.061154502 1.72414171 1.083892431 1 17.39059319 4.733415191 4.593498391 1.282898387 1.667956245 0.248483586 0.200374827 0.280850166 15.72768353 0.048228036 0.346877804 54127.1538 -4.733415191 0.385057858 RPPEDFETPSGERPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPPEDFETPSGERPR 15 2 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 0 ; 101.53 0.00097657 470630000 170497 192364 169834 185670 173902 195779 202920 173277 187297 206826 FALSE TRUE 163833.7887 186877.9671 200526.7817 195252.451 179495.7158 199737.7855 205403.3957 169698.7694 166035.8298 192817.4908 0.849683232 0.969196136 1.039982322 1.012628316 0.930909924 1.035890389 1.065273668 0.880100497 0.86110357 1 17.5568764 4.733741316 5.619329714 0.976845553 0.845686241 0.259172736 0.064795996 0.204305391 26.48195545 0.016502524 0.102879672 54167.81476 -4.733741316 -0.131159313 LGIHEDSTNR ddPTM_BT-474_Pertuzumab_2h_R1 13 LGIHEDSTNR 10 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;;;; 222.28 4.98E-09 1.23241E+11 22689517 26248182.5 22611900.1 27068327.2 24236238.5 24727480.3 26725589.2 25029820.3 26454496 27856172 FALSE TRUE 21802785.59 25499610.03 26698373.45 28465326.81 25015819.12 25227486.89 27052664.96 24512945.76 23451492.52 25969448.66 0.839555197 0.981908025 1.028068551 1.096108246 0.963278792 0.971429437 1.041711178 0.943914755 0.903041602 1 24.63031205 4.733765386 4.746999116 0.993829583 0.831242062 0.446226553 0.051130939 0.167918136 10.69288726 0.012831459 0.0900418 54170.81703 -4.733765386 -0.162587521 EKDNIDITLQWLIQHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKDNIDITLQWLIQHSK 17 1 Q96BM9;Q9NVJ2 Q96BM9;Q9NVJ2 ARL8A;ARL8B ADP-ribosylation factor-like protein 8A;ADP-ribosylation factor-like protein 8B 0 151.57 1.47E-07 195090000 184240 235060 203360 264920 192450 229470 249850 245180 274900 223120 FALSE TRUE 177039.6971 228356.3189 240111.6757 278592.5529 198640.329 234110.0406 252907.739 240116.9473 243694.5045 208007.8837 0.851120131 1.097825308 1.154339304 1.33933651 0.954965387 1.125486383 1.215856508 1.154364648 1.17156379 1 17.66627868 4.73380617 2.986014835 1.148669713 0.803794907 0.418839414 0.100831878 0.341839668 4.502399051 0.023743358 0.280058995 54175.90433 -4.73380617 -0.344874806 AAPLDSIHSLAAYYIDCIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAPLDSIHSLAAYYIDCIR 19 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 280.69 1.19E-39 8533500000 1186720 1514400 1315280 1578320 1417140 1486490 1504950 1412520 1539220 1868050 FALSE TRUE 1140341.67 1471210.795 1552980.354 1659777.284 1462723.595 1516547.846 1523368.028 1383350.968 1364494.199 1741525.31 0.654794773 0.844782896 0.891735736 0.953059525 0.839909467 0.870815852 0.874732064 0.794332968 0.783505236 1 20.73192001 4.733856946 4.051408961 0.866355119 0.637268609 0.523833611 0.062355582 0.184566367 6.504997821 0.015085004 0.123168704 54182.23882 -4.733856946 -0.229086509 LGYLVS(ph)PPQQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGYLVSPPQQIR 12 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 LGYLVS(1)PPQQIR;LGYLVS(1)PPQQIR 132.31 0.00019221 181623000 275570 299350 260610 271280 274560 294000 292850 312290 297300 297260 TRUE FALSE 264800.4197 290812.8311 307708.0242 285280.7933 283391.4717 299944.8814 296433.9859 305841.1024 263551.7504 277126.3154 0.955522464 1.049387283 1.110352959 1.02942513 1.022607584 1.082339947 1.069671011 1.10361624 0.951016687 1 18.08018419 4.733978852 5.803834139 1.055012779 0.952720857 0.237119477 0.046839502 0.162895667 24.4690939 0.010753017 0.066038734 54197.44979 -4.733978852 -0.102291922 HPSAVTACNLDLENLVTDSNR ddPTM_BT-474_Pertuzumab_2h_R1 1 HPSAVTACNLDLENLVTDSNR 21 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 255.82 1.98E-36 707070000 153940 206050 181190 195600 216140 234790 182000 190890 215840 223680 FALSE TRUE 147923.8546 200173.6557 213935.0635 205694.9394 223092.3394 239537.6147 184227.3704 186948.0548 191338.7481 208529.9544 0.709365017 0.959927586 1.025920061 0.986404759 1.069833541 1.148696433 0.883457588 0.896504559 0.917560015 1 17.66989511 4.734002003 4.248918059 0.985666152 0.689059453 0.545457347 0.076521103 0.180888792 7.563238418 0.020811185 0.161990184 54200.33901 -4.734002003 -0.296606699 LFDDDETGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFDDDETGK 9 0 P41208;Q12798 P41208 CETN2;CETN1 Centrin-2;Centrin-1 0 102.61 0.0082748 132590000 198980 165630 128630 143750 160470 149390 151450 169510 189410 167410 FALSE TRUE 191203.6416 160906.3946 151876.3024 151168.9547 165631.6633 152410.7682 153303.4904 166009.5593 167908.9709 156071.1716 1.225105442 1.030980885 0.973122075 0.968589863 1.061257256 0.976546576 0.982266544 1.063678561 1.075848724 1 17.25184455 4.734012216 4.616974416 1.014074589 1.237468087 0.729329645 0.038581082 0.097259641 5.55684252 0.009725898 0.070054228 54201.61359 -4.734012216 0.223393498 DDS(ph)HS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 DDS(1)HS(1)AEDS(1)EDEKEDHKNVR;DDS(1)HS(1)AEDS(1)EDEKEDHKNVR 128.4 1.46E-05 621670000 1230200 799080 574330 425890 668900 652360 653710 725390 1180970 691290 TRUE FALSE 1182122.424 776291.0208 678124.2069 447870.2339 690415.776 665551.1662 661710.2985 710410.443 1046911.237 644468.3126 1.834259964 1.204544903 1.052222729 0.694945314 1.071295148 1.032713561 1.026753815 1.102320206 1.624457272 1 19.2977499 4.734110916 2.868958291 1.064985627 1.966016431 0.52754265 0.21416228 0.315307685 3.688931005 0.052937542 0.658260181 54213.93312 -4.734110916 0.901030804 (ac)SAHLQWMVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAHLQWMVVR 10 0 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ; 75.38 0.00017913 95403000 58272 68968 58993 70503 69585 66433 64319 70914 70828 77444 FALSE TRUE 55994.66582 67001.10017 69654.34739 74141.66828 71823.26472 67776.32078 65106.15516 69449.60112 62787.90238 72198.6489 0.775563901 0.928010443 0.964759707 1.026912129 0.994800676 0.938747772 0.901764176 0.961923833 0.869654811 1 16.13968422 4.734118912 3.163633482 0.956215934 0.749693132 0.603844994 0.043924479 0.238815924 3.742393193 0.011071582 0.121596604 54214.93132 -4.734118912 -0.206522802 S(ph)RSPVDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPVDLR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 S(0.5)RS(0.5)PVDLR;S(0.5)RS(0.5)PVDLR 75.695 0.022846 660110000 582010 866900 753250 1122080 922120 1023930 1013490 699330 890430 1131080 TRUE FALSE 559264.4058 842176.8608 889379.031 1179990.683 951780.8272 1044634.566 1025893.394 684888.5911 789352.1194 1054470.944 0.530374411 0.79867242 0.843436261 1.119035749 0.90261456 0.990671741 0.972898684 0.649509211 0.748576453 1 20.00808791 4.734357058 2.111150183 0.892188985 0.433429544 0.440882 0.126797128 0.734519078 3.663988632 0.03592078 0.639434261 54244.66832 -4.734357058 -0.458759441 SLLDS(ph)DDSSDLLDFALSASRPESR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLLDSDDSSDLLDFALSASRPESR 24 1 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 SLLDS(0.999)DDSS(0.001)DLLDFALSASRPESR;SLLDS(1)DDSSDLLDFALSASRPESR 162.91 1.06E-11 32628000 12059.5 14943.5 13129.6 13243.7 14452.2 16595.7 16764.7 12722.5 14546.5 15257.3 TRUE FALSE 11588.20141 14517.32601 15502.41079 13927.20894 14917.06814 16931.27642 16969.87141 12459.77593 12895.2423 14223.90948 0.814698759 1.020628403 1.08988396 0.979140718 1.048731937 1.190339157 1.193052545 0.875974073 0.906589171 1 13.79603043 4.734357141 4.940238517 1.036075693 0.804021305 0.305868164 0.099224962 0.223508124 16.71026946 0.025900037 0.177161679 54244.67874 -4.734357141 -0.232054388 GSEGYLAATYPTVGQT(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSEGYLAATYPTVGQTSPR 19 0 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 GSEGYLAATYPTVGQT(0.5)S(0.5)PR 218.79 3.67E-18 225920000 357740 424610 363790 411360 390370 409250 450910 426820 469340 438520 TRUE FALSE 343759.1253 412500.5385 429534.9455 432590.3389 402926.6056 417525.3154 456428.3715 418006.0178 416062.4908 408818.6498 0.840859695 1.009006166 1.050673558 1.058147272 0.985587633 1.021297134 1.116456824 1.022472967 1.017718959 1 18.64110149 4.734778487 3.328964428 1.036963172 0.815309368 0.736969213 0.034367467 0.153389334 2.812136371 0.008375895 0.08669275 54297.33154 -4.734778487 -0.221653804 VIEEEWQQVDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VIEEEWQQVDR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 ;;; 231.38 2.58E-12 1861790000 534350 626730 538880 588820 581840 665120 620020 591070 638950 675120 FALSE TRUE 513467.0112 608856.274 636267.6033 619209.0708 600555.412 678569.1821 627607.9902 578864.1979 566419.0747 629393.5211 0.815812356 0.967369783 1.010921756 0.983818629 0.954181115 1.07813182 0.997163093 0.91971744 0.899944241 1 19.2636028 4.734953896 4.847954046 0.978702345 0.807428684 0.522313422 0.046942676 0.14616946 10.12893406 0.012056053 0.08421119 54319.26634 -4.734953896 -0.171273661 VALVTFNSAAHNKPSLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VALVTFNSAAHNKPSLIR 18 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 257.02 7.85E-31 1785080000 1789430 2007300 1694020 2085300 1923200 2082750 1958770 1902590 2142590 2361070 FALSE TRUE 1719497.097 1950053.769 2000167.097 2192922.583 1985061.475 2124864.632 1982742.013 1863300.852 1899372.166 2201152.626 0.781180313 0.885923923 0.90869078 0.99626103 0.901828184 0.965341797 0.900774435 0.846511428 0.862898894 1 21.06982775 4.735230012 2.452004988 0.915665193 0.751414493 0.42519841 0.049090186 0.569878193 4.257331029 0.012942016 0.196364617 54353.81257 -4.735230012 -0.1642507 YDSWHK ddPTM_BT-474_Pertuzumab_2h_R1 3 YDSWHK 6 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 119.7 0.020787 1079690000 875220 1135500 1001230 1139550 1039550 1229740 1176330 1089560 1352950 1397570 FALSE TRUE 841015.4348 1103116.652 1182174.533 1198362.312 1072988.07 1254606.185 1190726.278 1067060.205 1199368.788 1302911.339 0.645489382 0.846655193 0.907333061 0.919757374 0.823531147 0.962925218 0.913896627 0.81898144 0.920529857 1 20.31330748 4.735235408 2.685062746 0.897334238 0.596721558 0.687146671 0.052840772 0.258597872 2.493454677 0.012709664 0.172907144 54354.48786 -4.735235408 -0.30061268 LNDDWAYGNDLDARPWDFQAEECALR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNDDWAYGNDLDARPWDFQAEECALR 26 1 Q5VSL9;Q5VSL9-2 Q5VSL9 STRIP1 Striatin-interacting protein 1 0 ; 343.7 5.38E-96 244710000 96460 116680 99936 108897 117469 111219 114328 122330 116982 120945 FALSE TRUE 92690.23656 113352.4006 117996.6583 114517.1872 121247.4971 113467.9244 115727.1803 119803.8428 103702.6938 112753.2874 0.822062387 1.005313488 1.046503042 1.015643888 1.075334474 1.006338059 1.026375221 1.062530818 0.919731 1 16.78280997 4.735287665 4.050958268 1.025135025 0.804962119 0.673867635 0.040711612 0.118513641 4.173614927 0.009210243 0.07617597 54361.02849 -4.735287665 -0.220172906 MLDMGFEPQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLDMGFEPQIR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 P17844;A0A1X7SBZ2;A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX5;DDX17;DDX3X;DDX3Y Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17;ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ; 166.34 4.78E-05 252050000 274870 329070 282300 322880 308980 324220 320530 325420 324810 367710 FALSE TRUE 264127.7765 319685.2458 333317.8897 339543.8755 318918.6223 330775.9505 324452.742 318699.9633 287938.9305 342804.6742 0.770490592 0.932558013 0.972325977 0.990487881 0.930321686 0.964910853 0.946465339 0.929683832 0.839950421 1 18.38702726 4.735313192 4.651443289 0.945480267 0.760283885 0.60921877 0.042096058 0.119962279 7.057919433 0.009958377 0.072218405 54364.22378 -4.735313192 -0.185196382 HS(ph)PS(ph)TS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSPSTSPR 8 0 O95644-6;O95644;K7ER53;O95644-8;O95644-11;O95644-3;O95644-10;O95644-2;O95644-5;O95644-4 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 3 HS(0.626)PS(0.763)T(0.626)S(0.986)PR 52.278 0.096283 749840000 705580 780010 659010 677200 752500 734940 743810 806030 865090 855490 TRUE FALSE 678005.1535 757764.8785 778107.7666 712150.3732 776704.8459 749800.9903 752912.9693 789385.1988 766888.61 797546.9003 0.850113207 0.950119521 0.975626344 0.892926012 0.973867299 0.940134041 0.94403598 0.989766493 0.961559263 1 19.60520983 4.735359053 4.67483719 0.95799562 0.843905244 0.568256335 0.028460649 0.128841752 7.73036993 0.006641642 0.047984893 54369.96498 -4.735359053 -0.114090376 S(ph)IHEVDISNLEAALR ddPTM_BT-474_Pertuzumab_2h_R1 7 SIHEVDISNLEAALR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR 310.99 2.39E-56 1025194000 778319 478668 325331 477513 407804 289330 337152 849469 288838 272292 TRUE FALSE 747901.433 465016.8573 384125.5486 502157.5032 420921.386 295180.4508 341278.167 831927.1683 256050.3211 253849.4203 2.946240461 1.831861017 1.513202387 1.97817077 1.65815382 1.162817116 1.344411843 3.277246674 1.008670104 1 17.95361344 4.735380608 5.009150418 1.756300225 3.002054417 0.257815882 0.639093707 0.253236539 20.04832033 0.159554008 1.092262084 54372.66346 -4.735380608 1.245754192 AWVESR ddPTM_BT-474_Pertuzumab_2h_R1 5 AWVESR 6 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;; 167.23 0.01564 15331390000 12334480 14069990 11922170 13973890 13785030 13621590 13752390 14170220 14563630 14847500 FALSE TRUE 11852434.89 13668727.66 14076771.33 14695084.14 14228438.01 13897027.88 13920695.86 13877600.01 12910427.78 13841865.6 0.85627438 0.987491719 1.016970669 1.061640429 1.027927768 1.003985177 1.005695061 1.002581618 0.93270865 1 23.72253507 4.735437758 3.354916724 1.008608995 0.836637339 0.685671133 0.030278963 0.178205732 3.345241376 0.007630725 0.078608674 54379.81907 -4.735437758 -0.171971656 S(ph)LSSS(ph)PVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(0.586)LS(0.414)S(0.003)S(0.997)PVKK;S(0.998)LS(0.038)S(0.028)S(0.936)PVKK 162.49 4.26E-05 685490000 2752600 2112260 1651200 1376830 1561720 1421220 1546030 2631250 2209780 1907200 TRUE FALSE 2645025.349 2052020.413 1949608.571 1447888.361 1611954.142 1449958.042 1564950.778 2576913.768 1958935.039 1778023.645 1.48762102 1.154101869 1.096503174 0.814324582 0.906598822 0.815488616 0.880163085 1.449313554 1.101748587 1 20.76184308 4.735559453 1.912396141 1.02178612 1.628520632 0.404474111 0.176794185 0.977218541 3.75270613 0.053371704 1.051776362 54395.0591 -4.735559453 0.606734513 ATENDIANFFS(ph)PLNPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATENDIANFFSPLNPIR 17 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 1 ATENDIANFFS(1)PLNPIR;ATENDIANFFS(1)PLNPIR 182.22 7.97E-10 220939000 192759 236300 203402 224650 235140 261610 210540 222230 253170 242630 TRUE FALSE 185225.7652 229560.9554 240161.2661 236244.2134 242703.4916 266899.9334 213116.6515 217640.8728 224431.203 226196.454 0.818871215 1.014874245 1.061737538 1.044420499 1.072976554 1.179947469 0.942175033 0.962176325 0.992195939 1 17.78721679 4.73558788 4.696432551 1.029930052 0.806851466 0.500960699 0.063404237 0.165469256 10.10921025 0.01677184 0.120996908 54398.61972 -4.73558788 -0.223078586 LSSLSLS(ph)PANHENQPSEGER ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSLSLSPANHENQPSEGER 20 0 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 LS(0.002)S(0.001)LS(0.086)LS(0.91)PANHENQPSEGER 134.03 6.25E-06 228700000 74863 93107 81972 101020 76442 92966 91230 94027 83809 99270 TRUE FALSE 71937.27119 90451.67952 96786.16386 106233.6543 78900.82635 94845.83622 92346.50003 92085.30959 74295.35368 92546.35448 0.777310696 0.977366208 1.045812819 1.147896694 0.852554666 1.024846811 0.997840494 0.995018227 0.802790711 1 16.49788854 4.735680981 5.470043917 0.988388673 0.76980879 0.31214469 0.091239254 0.167904223 19.33872798 0.021239048 0.137664875 54410.28253 -4.735680981 -0.218579884 LQQVLQMESHIQSTSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQQVLQMESHIQSTSDR 17 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 188.9 3.85E-10 1530580000 776482 858660 745758 761076 825130 885347 832082 793992 893112 967363 FALSE TRUE 746136.225 834171.8575 880533.0599 800355.2236 851671.0558 903249.3229 842265.2684 777595.7877 791729.67 901842.6424 0.827346357 0.924963867 0.976371064 0.8874666 0.944367693 1.001559785 0.933938172 0.862230007 0.877902233 1 19.7825162 4.735688992 6.098920124 0.929363789 0.824877113 0.318753562 0.04644491 0.164421952 31.23161645 0.011691235 0.071632268 54411.2862 -4.735688992 -0.104486676 ESGVVAVS(ph)PEKSESPQKEDGLSSQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ESGVVAVSPEKSESPQKEDGLSSQLK 26 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 ESGVVAVS(1)PEKSESPQKEDGLSSQLK 173.68 1.79E-12 184160000 257910 199040 156460 118280 165250 142600 160390 229820 244710 188350 TRUE FALSE 247830.5921 193363.5741 184735.8024 124384.445 170565.4163 145483.4697 162352.9008 225074.1367 216931.5467 175592.8867 1.411393119 1.101203914 1.052068827 0.708368359 0.971368599 0.828527125 0.924598392 1.281795299 1.235423318 1 17.42187488 4.735789379 2.261040914 1.004351648 1.512092077 0.37247427 0.160692642 0.75574964 4.517832893 0.045771944 0.763538266 54423.86478 -4.735789379 0.507740429 VYTDVQQVASSLTHPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VYTDVQQVASSLTHPR 16 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 196.52 4.57E-11 826350000 789980 993490 855260 1052100 1004790 1054380 980070 921720 997350 1090890 FALSE TRUE 759106.7082 965156.6379 1009824.507 1106399.007 1037109.983 1075700.286 992064.3898 902686.1599 884135.0092 1017003.049 0.746415371 0.949020398 0.992941475 1.087901367 1.019770771 1.057715891 0.975478285 0.88759435 0.869353352 1 19.95589257 4.736186651 3.233023239 0.983668002 0.713279323 0.558917902 0.063557789 0.285668623 4.771938191 0.017850232 0.193617672 54473.67191 -4.736186651 -0.270388679 SSLFS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSLFSPR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 SSLFS(1)PR;SSLFS(1)PR;SSLFS(0.999)PR;SSLFS(1)PR 93.649 0.015504 318338000 746830 787920 760620 752330 771700 510283 825440 773400 787910 927060 TRUE FALSE 717643.0579 765449.2931 898080.9539 791157.8415 796522.4313 520601.2719 835541.9816 757429.0197 698469.76 864269.4005 0.830346484 0.885660527 1.039121544 0.915406517 0.921613597 0.602359949 0.966761037 0.876380697 0.808162084 1 19.72112156 4.736228711 8.656506035 0.887254963 0.83005375 0.023505422 0.114721342 0.435561634 576.9565871 0.027101707 0.151887869 54478.94775 -4.736228711 -0.057201213 GGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPR 38 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 190.29 7.62E-24 3819600000 154003 236858 209394 243393 268668 249887 277678 161193 262131 267491 FALSE TRUE 147984.3925 230103.0417 247236.1537 255954.5419 277309.9502 254939.8864 281076.3064 157864.3082 232374.9878 249373.5963 0.593424463 0.922724158 0.991428753 1.026389905 1.11202611 1.022321088 1.127129378 0.633043396 0.93183477 1 17.9279492 4.736233765 3.684150836 0.965376058 0.553874364 0.438896289 0.129664597 0.291275532 7.400173704 0.035366153 0.32762897 54479.58178 -4.736233765 -0.411501694 KVTLGDTLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVTLGDTLTR 10 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 138.94 8.26E-05 923220000 3103900 2398700 1820190 1707610 2177930 1998580 2183100 2165100 2454200 2180500 FALSE TRUE 2982596.156 2330291.425 2149138.823 1795739.957 2247985.096 2038992.657 2209817.431 2120389.928 2175609.505 2032812.793 1.467226184 1.14633843 1.057224173 0.883376946 1.105849542 1.003040056 1.087073753 1.043081751 1.070245874 1 20.95504593 4.736341258 2.155046849 1.032675091 1.583116425 0.833741241 0.058752677 0.241248672 1.266306065 0.01453634 0.255969109 54493.06779 -4.736341258 0.550441334 GNGPHDNGIIVSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNGPHDNGIIVSTR 14 0 E2PU09;O15031 E2PU09 PLXNB2 Plexin-B2 0 71.545 0.041119 229940000 81453 104860 83758 123010 106910 113130 130520 113580 93573 113720 FALSE TRUE 78269.72671 101869.4955 98894.93379 129358.5608 110348.8572 115417.5661 132117.3428 111234.5333 82950.98533 106017.6431 0.738270767 0.960873044 0.932815811 1.220160693 1.040853711 1.088663761 1.246182606 1.049207755 0.782426235 1 16.69394485 4.736345532 1.333611189 1.069538366 0.605195079 0.358313532 0.124758751 1.392013715 2.177821715 0.03464816 0.877992364 54493.60407 -4.736345532 -0.464343287 SEESSHYSTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEESSHYSTEK 11 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 171.92 1.40E-05 798200000 956910 1421160 1256750 1681460 1353850 1442540 1426660 1399430 1517760 1767570 FALSE TRUE 919512.8993 1380629.908 1483872.681 1768240.352 1397397.815 1471709.147 1444119.892 1370531.281 1345470.248 1647850.91 0.558007338 0.837836664 0.900489645 1.073058456 0.848012285 0.893108192 0.876365625 0.831708302 0.816499988 1 20.65215429 4.736345912 2.900029331 0.896908388 0.500093589 0.659647731 0.074346264 0.252391066 3.036251064 0.018817799 0.234248281 54493.65175 -4.736345912 -0.396814799 TSHSDSSIYLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSHSDSSIYLR 11 0 Q96JQ2 Q96JQ2 CLMN Calmin 0 ; 97.163 0.0064718 154077000 115493 145996 125500 144486 151927 144181 144929 147281 147117 140173 FALSE TRUE 110979.4059 141832.337 148180.6417 151942.9398 156813.8699 147096.4386 146702.6845 144239.5959 130416.8949 130678.9579 0.849252303 1.085349465 1.13392886 1.162719249 1.19999327 1.125632168 1.122619027 1.103770632 0.997994605 1 16.99566733 4.73635592 3.696771634 1.115593067 0.821115042 0.608489397 0.060978706 0.167321622 4.29930072 0.014617961 0.135022402 54494.90759 -4.73635592 -0.294478025 GHYTEGAELVDAVLDVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHYTEGAELVDAVLDVVR 18 0 P04350;M0R278;M0R1I1;K7ES63;K7ESM5;Q9BUF5;K7EL29 P04350;K7ESM5 TUBB4A;TUBB6 Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 149.57 6.12E-08 61113000 57145 69576 59393 74253 64601 66705 69340 61125 74408 78564 FALSE TRUE 54911.71022 67591.7606 70126.63629 78085.20623 66678.94983 68053.8208 70188.60366 59862.74739 65961.51578 73242.7903 0.749721713 0.922845243 0.957454461 1.066114575 0.910382436 0.929153853 0.958300515 0.817319318 0.90058715 1 16.16039913 4.73659106 4.941220623 0.93385793 0.740567646 0.458500529 0.061875995 0.171677252 12.85197362 0.016222577 0.113692755 54524.42068 -4.73659106 -0.193290284 LALTEWLQEFGVPHQYSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LALTEWLQEFGVPHQYSSR 19 0 O60502;O60502-3 O60502 MGEA5 Protein O-GlcNAcase 0 ; 220.04 2.99E-19 454180000 307820 367440 311850 367720 346820 382030 378120 354460 353000 372020 FALSE TRUE 295790.0541 356960.971 368208.2321 386698.0733 357975.7803 389754.9083 382747.5457 347140.2771 312928.9199 346822.754 0.85285654 1.029231695 1.061661116 1.114973192 1.032157712 1.123787017 1.103582568 1.00091552 0.902273326 1 18.40383903 4.736759491 3.968487848 1.048164199 0.835290691 0.445195672 0.062877651 0.218580503 7.154502984 0.015656194 0.134110115 54545.57086 -4.736759491 -0.212873508 DLEGLSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEGLSQR 8 0 P35579 P35579 MYH9 Myosin-9 0 ; 155 0.00096795 871680000 837440 926810 775670 947200 954460 967520 919530 899080 964080 1039170 FALSE TRUE 804711.919 900378.2862 915850.8237 996085.1055 985161.0727 987083.9173 930783.4832 880513.6838 854641.6802 968786.0903 0.830639423 0.929388123 0.94535918 1.028178579 1.016902578 1.018887376 0.960772964 0.908883491 0.882177902 1 19.88581863 4.73680887 1.882340769 0.968929936 0.787875376 0.46340654 0.045680586 0.851298171 3.130626852 0.01345779 0.270637488 54551.77295 -4.73680887 -0.181054559 GAVEAAHQAFPGWAGQSPGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GAVEAAHQAFPGWAGQSPGAR 21 0 Q8IZ83;F5H4B6;Q8IZ83-3 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 132.48 1.15E-05 251340000 132220 170530 155020 158600 137800 173350 163250 174020 187680 171920 FALSE TRUE 127052.6962 165666.6514 183035.5624 166785.365 142232.4621 176855.2558 165247.9023 170426.4262 166375.3532 160275.7053 0.792713381 1.033635454 1.142004411 1.040615387 0.887423717 1.10344394 1.031022775 1.063332873 1.038057221 1 17.29019623 4.736832723 6.548069028 1.041391371 0.788038764 0.574268583 0.063247202 0.08014587 21.57402591 0.015016338 0.090883393 54554.76921 -4.736832723 -0.253352607 GKYS(ph)PTVQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKYSPTVQTR 10 1 O60437;K7EKI8 O60437 PPL Periplakin 1 GKYS(0.888)PT(0.112)VQTR;GKYS(0.5)PT(0.5)VQTR 128.61 0.00085495 390340000 415970 455030 382360 450360 405360 436320 456920 483570 464530 473650 TRUE FALSE 399713.4325 442052.9899 451460.9576 473603.1336 418398.7725 445142.6893 462511.9236 473584.1105 411798.5019 441569.2636 0.905211176 1.001095471 1.022401228 1.072545516 0.947526939 1.00809256 1.047427803 1.072502435 0.932579633 1 18.75228023 4.736833565 3.040835732 1.019480929 0.887193488 0.336018998 0.044341935 0.401120463 5.552118773 0.010876692 0.127988605 54554.87499 -4.736833565 -0.132287441 EALNIIGDISTSTVSTPVPPPVDDT(ph)WLQSASSHSPTPQR ddPTM_BT-474_Pertuzumab_2h_R1 3 EALNIIGDISTSTVSTPVPPPVDDTWLQSASSHSPTPQR 39 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7ENE7 P50570-2 DNM2 Dynamin-2 1 EALNIIGDISTSTVSTPVPPPVDDT(0.192)WLQS(0.192)AS(0.192)S(0.192)HS(0.192)PT(0.039)PQR;EALNIIGDISTSTVSTPVPPPVDDT(0.336)WLQS(0.191)AS(0.147)S(0.147)HS(0.147)PT(0.032)PQR;EALNIIGDISTSTVSTPVPPPVDDT(0.179)WLQS(0.179)AS(0.179)S(0.142)HS(0.142)PT(0.179)PQR 150.8 3.48E-13 1007710000 279167 369171 317473 424431 332924 364236 400431 332994 382037 385208 TRUE FALSE 268256.845 358642.6045 374847.4332 446335.9348 343632.8028 371601.1015 405331.5944 326117.5575 338669.7614 359117.5191 0.746989024 0.998677551 1.043801578 1.24286873 0.956881201 1.034761831 1.128687889 0.908108183 0.943061097 1 18.45409651 4.736928032 3.607703317 1.032053885 0.715050927 0.462930913 0.091601252 0.256490674 6.074785532 0.02297023 0.219311101 54566.74295 -4.736928032 -0.317002958 LEPQIASASEYAHR ddPTM_BT-474_Pertuzumab_2h_R1 5 LEPQIASASEYAHR 14 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 ;;;; 268.59 3.22E-25 3393860000 3011930 3576120 3030440 3930330 3546120 3790700 3670070 3519690 3707230 3927130 FALSE TRUE 2894220.446 3474132.559 3578107.92 4133174.802 3660184.17 3867350.551 3714985.415 3447007.172 3286400.792 3661141.987 0.790523956 0.948920466 0.977320173 1.128930486 0.999738383 1.056323564 1.01470673 0.941511469 0.897643632 1 21.80386229 4.737063455 2.120912116 1.003471641 0.732845227 0.542948723 0.058525104 0.553708855 2.781501064 0.015911153 0.285905361 54583.76081 -4.737063455 -0.270626414 VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 39 3 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 222.52 5.47E-40 413350000 98321 58502 42818 32513 50193 62888 45663 66984 73155 46963 FALSE TRUE 94478.50662 56833.58024 50556.16508 34190.99983 51807.50343 64159.63845 46221.83745 65600.75699 64850.75109 43782.15418 2.157922752 1.298099221 1.154720822 0.780934617 1.183301836 1.465429001 1.055723235 1.498344662 1.48121426 1 15.41805532 4.737103365 4.241351332 1.220629628 2.229639214 0.627558653 0.219092346 0.145680547 6.04692326 0.055454325 0.44527763 54588.77709 -4.737103365 1.009009585 EENWSFLDWDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EENWSFLDWDSR 12 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 0 ; 165.35 0.00012757 66722000 91521 104343 84843 111850 105352 104606 101639 118464 104460 110436 FALSE TRUE 87944.25814 101367.2398 100176.0174 117622.5919 108740.7428 106721.205 102882.8885 116017.677 92602.13873 102956.0714 0.854192055 0.984567869 0.972997669 1.142454159 1.056185821 1.036570292 0.999289184 1.126865813 0.899433492 1 16.65166938 4.73716162 1.470096171 1.043757664 0.782703527 0.377879169 0.067250642 1.101743432 2.178397182 0.017431345 0.421284049 54596.09995 -4.73716162 -0.261054137 SELVNWYLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SELVNWYLK 9 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 147.51 0.0035881 0 105220 128970 115470 134020 110700 109970 128280 121330 152760 131250 FALSE TRUE 101107.8861 125291.9019 136337.9976 140936.7883 114260.766 112193.6687 129849.929 118824.4931 135419.3252 122360.3206 0.826312693 1.023958594 1.11423374 1.151817743 0.93380571 0.916912184 1.061209454 0.971103153 1.106725812 1 16.90077627 4.737290216 6.993504711 1.028882174 0.82338066 0.405667816 0.074334263 0.112355981 42.49832032 0.018503181 0.110458978 54612.26836 -4.737290216 -0.205501514 LLEVSDDPQVLAVAAHDVGEYVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLEVSDDPQVLAVAAHDVGEYVR 23 0 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 ;; 250.05 4.11E-38 627641000 489244 585643 512692 613574 572375 645794 626396 588071 653735 752432 FALSE TRUE 470123.8036 568941.035 605346.8492 645240.6277 590785.9617 658852.3971 634062.0216 575927.1283 579525.7435 701469.1104 0.670198868 0.811070689 0.862970073 0.919841826 0.84221237 0.939246486 0.903905834 0.821029921 0.826160033 1 19.42002005 4.737381634 1.715296883 0.882992327 0.595936805 0.621495057 0.052491285 0.624633749 1.810282704 0.013525996 0.294640669 54623.76534 -4.737381634 -0.287055522 FYGAEIVSALDYLHSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FYGAEIVSALDYLHSEK 17 0 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 0 238.02 3.10E-20 299720000 261760 310820 267360 264500 290700 320650 321890 278790 348180 339670 FALSE TRUE 251530.1298 301955.7179 315677.8994 278150.8767 300050.6295 327133.7627 325829.3861 273032.8891 308656.0661 316663.8484 0.794312742 0.953552859 0.996886449 0.878379007 0.947536737 1.033063182 1.028944061 0.862216797 0.974712041 1 18.27259265 4.737391509 6.304173146 0.958486052 0.7906976 0.462602315 0.054583736 0.116080587 25.80856956 0.013533514 0.08374309 54625.00742 -4.737391509 -0.167788451 S(ph)LPVSVPVWGFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLPVSVPVWGFK 12 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 S(1)LPVSVPVWGFK;S(1)LPVSVPVWGFK 240.6 3.41E-16 1812080000 9165200 1819530 593160 775610 851400 462660 424920 4822600 395030 151711 TRUE FALSE 8807013.851 1767638.786 700357.2068 815639.325 878786.0542 472015.3022 430120.2981 4723011.625 350187.8505 141435.4788 62.26877389 12.49784566 4.951778808 5.766865087 6.213335306 3.337318939 3.041106104 33.39340075 2.475954784 1 17.10978454 4.737507583 4.837101319 9.383524672 65.10436319 0.764105757 9.02332287 0.090918421 6.242059903 2.371329573 17.0598923 54639.60906 -4.737507583 55.72083852 GEGPDVHMTLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GEGPDVHMTLPK 12 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 125.97 0.00029579 1052910000 2067550 2464700 2080650 2527800 2172610 2479400 2426900 2390500 2486700 2575900 FALSE TRUE 1986747.86 2394409.169 2456669.739 2658260.061 2242493.974 2529535.167 2456601.128 2341135.34 2204420.241 2401431.999 0.827317976 0.997075566 1.023002001 1.10694788 0.933815313 1.053344491 1.02297343 0.974891374 0.917960718 1 21.19546353 4.737530361 5.201173468 1.005755889 0.81964005 0.508524086 0.051931821 0.126178452 11.68141446 0.012315362 0.084210909 54642.47486 -4.737530361 -0.186115839 DNSNLYMVMEYVPGGEMFSHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNSNLYMVMEYVPGGEMFSHLR 22 0 P22694-2;P22694-4;A0A0A0MS54;P22694-9;P22694-6;P22694-7;P22694-5;P22694;P22694-3;P22694-10;A0A087WVC4;P22694-8;B1APG3;B1APF9;B1APF8;B1APG2;B1APG1;B1APF7;B1APG0;P17612-2;P17612;Q15136;K7ERP6 P22694-2;P17612-2 PRKACB;PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit beta;cAMP-dependent protein kinase catalytic subunit alpha 0 ; 104.41 0.00055203 228470000 209730 256330 219270 223260 260560 251740 273550 246620 245180 249580 FALSE TRUE 201533.5197 249019.7194 258896.9666 234782.4754 268941.149 256830.3553 276897.7867 241527.2108 217348.1943 232675.7243 0.866156194 1.070243663 1.112694362 1.009054451 1.15586252 1.103812424 1.190058772 1.038042157 0.934124928 1 17.82796117 4.737585952 6.08859672 1.076903734 0.860850574 0.403122152 0.07311583 0.12144784 22.80729188 0.017315253 0.108965661 54649.46965 -4.737585952 -0.21605316 VSFPSYLAS(ph)PAGSR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSFPSYLASPAGSR 14 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 VSFPSYLAS(1)PAGSR;VSFPSYLAS(0.999)PAGS(0.001)R;VSFPSYLAS(0.999)PAGS(0.001)R 140.19 1.05E-05 406430000 350300 404153 353010 376125 349645 395719 380457 426403 407606 421767 TRUE FALSE 336609.8887 392626.9521 416806.7597 395536.8563 360891.649 403720.7093 385113.1466 417597.629 361336.2757 393200.3454 0.856077297 0.998541727 1.060036606 1.005942291 0.917831465 1.026755734 0.979432371 1.062047971 0.918962254 1 18.58490506 4.737632822 7.311185003 1.00138847 0.854329526 0.443640958 0.046951478 0.087881554 42.18791931 0.010888454 0.064620238 54655.36786 -4.737632822 -0.147058944 GVSMSLPSS(ph)PLLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GVSMSLPSSPLLPR 14 0 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GVSMSLPS(0.046)S(0.954)PLLPR;GVSMSLPS(0.022)S(0.978)PLLPR;GVSMSLPS(0.159)S(0.841)PLLPR;GVSMS(0.031)LPS(0.309)S(0.66)PLLPR 237.21 2.88E-17 886010000 1126433 1402120 1208920 1316010 1238270 1377410 1279660 1411030 1589150 1516890 TRUE FALSE 1082410.753 1362132.91 1427398.736 1383929.434 1278100.079 1405262.174 1295320.862 1381891.737 1408756.354 1414149.689 0.765414554 0.963216922 1.009368914 0.978630087 0.903794053 0.993715294 0.915971535 0.977189153 0.996186164 1 20.43150341 4.737720505 6.518350781 0.968384606 0.761464776 0.772263892 0.03346172 0.05186199 13.59062176 0.007756666 0.04764668 54666.40383 -4.737720505 -0.20691983 DLSSHQLNEFLAQTLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLSSHQLNEFLAQTLQR 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 239.75 2.70E-20 833630000 480310 613720 520350 618970 557140 621590 579830 637220 604730 622490 FALSE TRUE 461538.9542 596217.3065 614388.8201 650915.1159 575060.9141 634158.9757 586926.133 624061.1843 536083.5856 580328.1978 0.795306787 1.027379522 1.058691999 1.121632756 0.990923612 1.092759197 1.011369317 1.075359058 0.923759327 1 19.1465095 4.737776643 4.875299737 1.041282206 0.782373518 0.632157082 0.054332207 0.098674489 6.991106757 0.012076092 0.086625384 54673.47053 -4.737776643 -0.258908687 GFFDPNTHENLTYR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFFDPNTHENLTYR 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 173.25 2.73E-06 3139080000 5647200 6661500 5605400 6932500 6241100 6340700 6761000 6120500 6678700 7082400 FALSE TRUE 5426501.181 6471520.542 6618420.471 7290287.156 6441850.65 6468913.298 6843743.14 5994109.536 5920561.975 6602702.74 0.821860592 0.980132046 1.0023805 1.104136812 0.975638447 0.97973717 1.036506323 0.907826654 0.896687646 1 22.65462527 4.737797382 5.531139775 0.986704523 0.816027358 0.440811483 0.0558477 0.146267964 17.66484666 0.014312234 0.094640767 54676.08146 -4.737797382 -0.170677165 EDALDDSVSSSSVHASPLASS(ph)PVRK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 1 EDALDDSVSSSSVHAS(0.002)PLAS(0.175)S(0.822)PVRK 288.18 1.83E-54 707650000 150360 286000 258740 385220 272160 298490 318330 296810 234890 353140 TRUE FALSE 144483.765 277843.56 305500.0736 405101.2504 280914.2736 304525.6723 322225.8178 290680.7698 208226.2719 329221.5133 0.438864895 0.843941082 0.927946873 1.230482317 0.853268278 0.924987159 0.978750795 0.882933703 0.632480757 1 18.32869909 4.737821989 2.830545335 0.931545738 0.350191306 0.524183786 0.139409496 0.332787075 3.719131799 0.034447887 0.44631758 54679.17954 -4.737821989 -0.581354432 AAVT(ph)PGKK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAVTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK 99.568 0.0039384 2874060000 19894700 5837600 3039710 2994790 3322100 2071120 2804820 17278800 1870530 835470 TRUE FALSE 19117193.13 5671117.364 3589053.215 3149351.471 3428958.364 2112999.465 2839146.226 16921986.74 1658195.276 778882.8727 24.54437477 7.281091371 4.607949848 4.043421137 4.402405655 2.71285907 3.645151698 21.72597105 2.128940479 1 19.57104687 4.7378514 5.952375399 6.710178146 25.03408843 0.491282363 5.668384016 0.127942567 21.57533335 1.492437498 9.520446398 54682.88256 -4.7378514 18.32391028 EATSDPSRT(ph)PEEEPLNLEGLVAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EAT(0.03)S(0.025)DPS(0.152)RT(0.794)PEEEPLNLEGLVAHR 142.59 3.80E-07 228550000 55263 71202 61312 71651 65422 72965 69735 60931 69360 90188 TRUE FALSE 53103.26086 69171.38867 72392.44228 75348.9167 67526.35804 74440.40229 70588.43779 59672.75356 61486.54358 84079.48643 0.63158403 0.822690428 0.861000053 0.896162904 0.803125244 0.885357481 0.839544112 0.70971834 0.731290665 1 16.35946624 4.737864196 6.526250904 0.827470193 0.62778016 0.373852558 0.079256459 0.134161698 35.34433729 0.019340835 0.11901337 54684.49371 -4.737864196 -0.199690033 GEENLAGWRPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GEENLAGWRPR 11 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8;A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A3B3ITW6;A0A087WWA3 KIF1A;KIF1B;KIF1Bbeta Kinesin-like protein KIF1A;Kinesin-like protein;Kinesin-like protein KIF1B 0 ;;; 176.78 7.55E-06 2030650000 1255230 1463300 1233500 1581070 1447630 1531380 1541390 1449160 1522840 1648890 FALSE TRUE 1206174.224 1421568.117 1456420.889 1662669.212 1494194.334 1562345.553 1560253.992 1419234.34 1349973.587 1537209.212 0.784651962 0.924772052 0.94744481 1.081615436 0.972017551 1.016351932 1.01499131 0.923253861 0.878197696 1 20.5518821 4.73787087 1.89883029 0.980334767 0.724310915 0.557689834 0.052620085 0.633372288 2.377501075 0.014295342 0.286725796 54685.3341 -4.73787087 -0.256023852 DLAEVGEGGGHSQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLAEVGEGGGHSQAR 15 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 164.7 1.47E-06 1737730000 721080 950790 829480 936280 890810 943230 881010 914230 982550 998460 FALSE TRUE 692899.3964 923674.4001 979385.4877 984601.523 919463.7127 962302.7569 891792.0639 895350.831 871015.0432 930833.4149 0.744386037 0.992309027 1.052159787 1.057763406 0.98778546 1.033807706 0.958057639 0.961880844 0.935736759 1 19.82816348 4.737874142 6.856244752 0.99765638 0.740355898 0.797460777 0.038310631 0.0511573 17.35121816 0.01013976 0.061443385 54685.74611 -4.737874142 -0.257300482 VDIIPGFEFDR ddPTM_BT-474_Pertuzumab_2h_R1 4 VDIIPGFEFDR 11 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 147.75 8.18E-05 422109000 344734 376371 313475 356453 352908 354878 367834 377015 392950 400368 FALSE TRUE 331261.4142 365637.2676 370126.9057 374849.582 364259.6063 362053.8763 372335.6625 369229.5085 348343.9634 373250.7187 0.887503754 0.979602313 0.991630792 1.004283617 0.975911333 0.970001819 0.997548414 0.989226517 0.93327071 1 18.50978551 4.73788668 5.412080587 0.983633759 0.883843322 0.682781626 0.019404324 0.081264139 8.918996071 0.00449656 0.030136827 54687.32494 -4.73788668 -0.099790437 SCT(ph)PS(ph)PDQISHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 2 S(0.088)CT(0.913)PS(0.999)PDQISHR 78.69 0.044452 220350000 115860 147440 124810 136850 149890 140500 140780 137090 164200 176170 TRUE FALSE 111332.0631 143235.1556 147365.9434 143912.8449 154711.348 143341.0063 142502.9078 134259.0436 145560.7044 164237.849 0.677870928 0.87212026 0.897271514 0.876246528 0.941995703 0.872764756 0.8676618 0.817467133 0.8862799 1 17.32542711 4.73795094 4.827380498 0.883924301 0.666692219 0.65141015 0.04679302 0.109894973 7.482003551 0.011087768 0.080286355 54695.41731 -4.73795094 -0.217232082 GGHGAAS(ph)PSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGHGAASPSEK 11 0 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 1 GGHGAAS(0.999)PS(0.001)EK;GGHGAAS(0.997)PS(0.003)EK 132.06 0.00012264 529190000 560800 619090 503120 674380 565920 603750 638610 621450 715330 625280 TRUE FALSE 538883.316 601434.1594 594044.9758 709184.8326 584123.3308 615958.2387 646425.5002 608616.8403 634128.7373 582929.2287 0.924440377 1.03174473 1.019068777 1.21658822 1.002048451 1.056660412 1.10892621 1.044066433 1.087831432 1 19.15296122 4.737967061 1.730897364 1.072143295 0.875860549 0.341407323 0.059955987 0.992214672 2.939007972 0.014859914 0.322275948 54697.44767 -4.737967061 -0.196282746 ADQELLMYSHDNIICGITSVAFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADQELLMYSHDNIICGITSVAFSR 24 0 P62879;E7EP32;P62879-2 P62879 GNB2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 0 ; 272.35 6.29E-52 780860000 436600 549600 467750 656230 425460 573420 614330 495080 581050 560210 FALSE TRUE 419537.1893 533925.9461 552282.83 690098.1089 439145.3073 585014.9453 621848.3543 484856.425 515091.64 522266.4777 0.803301011 1.02232475 1.057473251 1.321352486 0.840845289 1.120146458 1.190672541 0.928369799 0.986262113 1 18.99442658 4.738036952 3.287796482 1.056917756 0.768536695 0.257419133 0.127777663 0.448751494 7.877970268 0.030520282 0.328718634 54706.25073 -4.738036952 -0.28838106 TSS(ph)VPEYVYNLHLVENDFVGGR ddPTM_BT-474_Pertuzumab_2h_R1 6 TSSVPEYVYNLHLVENDFVGGR 22 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 T(0.116)S(0.116)S(0.767)VPEYVYNLHLVENDFVGGR;T(0.049)S(0.16)S(0.791)VPEYVYNLHLVENDFVGGR;T(0.015)S(0.015)S(0.969)VPEYVYNLHLVENDFVGGR;T(0.108)S(0.108)S(0.784)VPEYVYNLHLVENDFVGGR;T(0.041)S(0.041)S(0.919)VPEYVYNLHLVENDFVGGR;T(0.017)S(0.108)S(0.875)VPEYVYNLHLVENDFVGGR 320.8 8.01E-68 1585748000 420204 201489 125224 198299 144428 131399 156245 379195 157887 121330 TRUE FALSE 403781.9631 195742.731 147854.7624 208533.2352 149073.6578 134055.9778 158157.173 371364.4907 139964.3297 113112.211 3.569746886 1.730518122 1.3071512 1.843596136 1.317927184 1.185159202 1.39823253 3.283151194 1.237393632 1 16.78739516 4.738083068 7.317201265 1.700627006 3.592357751 0.467883496 0.623600141 0.102902187 49.36049638 0.16210792 0.969252658 54712.06016 -4.738083068 1.891730744 STLINSLFLTDLYSPEYPGPSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ; 247.85 9.95E-38 2584200000 748230 906450 767290 919250 871290 862530 846360 885170 900330 953290 FALSE TRUE 718988.3444 880598.9335 905956.3713 966692.6027 899315.8341 879970.9476 856718.0069 866890.9302 798128.3129 888722.8192 0.809013034 0.990858921 1.019391369 1.087732397 1.011919369 0.990152305 0.963987858 0.975434535 0.898062136 1 19.76137401 4.738135048 6.816089428 0.994491955 0.805973921 0.600718346 0.045010478 0.080472097 26.41590581 0.011527197 0.070261489 54718.60892 -4.738135048 -0.188518035 LISGVSRPDEVLECIER ddPTM_BT-474_Pertuzumab_2h_R1 1 LISGVSRPDEVLECIER 17 1 Q9H974-2;Q9H974-3;Q9H974;Q9H974-4 Q9H974-2 QTRTD1 Queuine tRNA-ribosyltransferase subunit QTRTD1 0 166.52 2.13E-09 81114000 26194 34342 29271 32128 29484 38867 33390 34398 30835 35380 FALSE TRUE 25170.30952 33362.59978 34560.92083 33786.12993 30432.37964 39652.91737 33798.63681 33687.66928 27334.74007 32983.68109 0.763114022 1.011488066 1.047818791 1.024328662 0.922649584 1.202198059 1.024707846 1.02134353 0.828735277 1 15.0094648 4.738200963 6.94061709 1.016036153 0.759264793 0.403875003 0.089386183 0.103847171 37.44742392 0.020704022 0.12568687 54726.9144 -4.738200963 -0.25677136 EFAGEDTSDLFLEER ddPTM_BT-474_Pertuzumab_2h_R1 4 EFAGEDTSDLFLEER 15 0 O14980 O14980 XPO1 Exportin-1 0 ;;; 200.21 4.93E-11 513840000 743360 809320 692823 779150 823450 923810 881860 809510 941810 897400 FALSE TRUE 714308.6694 786238.986 818031.5279 819362.0249 849937.0171 942490.0712 892652.4665 792793.3356 834899.6772 836618.2987 0.85380474 0.939782201 0.977783452 0.979373779 1.015919707 1.126547283 1.066976981 0.947616538 0.997945752 1 19.67421003 4.738237243 0.951961823 1.021957638 0.765896817 0.570798133 0.045639814 1.708631845 1.223634826 0.016512786 0.453217699 54731.48643 -4.738237243 -0.256060821 MTDQEAIQDLWQWR ddPTM_BT-474_Pertuzumab_2h_R1 20 MTDQEAIQDLWQWR 14 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;;;;;;;;;; 350.4 1.57E-81 31389940000 6781294 7477116 6225079 7069447 7309396 7127771 7255168 7398480 7499918 7741100 FALSE TRUE 6516273.533 7263875.973 7350089.251 7434302.007 7544509.361 7271899.413 7343958.916 7245698.803 6648558.751 7216788.402 0.902932602 1.006524727 1.018470938 1.030139945 1.045410914 1.007636501 1.017621483 1.004005993 0.921262808 1 22.78292552 4.738250777 6.648187156 1.008686051 0.901010931 0.492099795 0.031186408 0.09450224 27.26860609 0.007466442 0.045939019 54733.19206 -4.738250777 -0.10767512 AGMSSNQS(ph)ISS(ph)PVLDAVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMSS(0.001)NQS(0.998)IS(0.17)S(0.831)PVLDAVPR;AGMSS(0.001)NQS(0.993)IS(0.266)S(0.74)PVLDAVPR 167.97 2.48E-11 452480000 390400 427130 355490 408000 392010 402630 400720 448200 440250 440430 TRUE FALSE 375142.7364 414948.6706 419734.9508 429056.9289 404619.3577 410771.4545 405624.1312 438944.5134 390274.6657 410599.2838 0.913646836 1.010592777 1.022249593 1.04495294 0.985436102 1.000419316 0.987883192 1.069033802 0.950500113 1 18.64737159 4.738255459 6.783483355 1.012473829 0.91199154 0.442807618 0.031347949 0.096022841 30.71714215 0.007265727 0.044434026 54733.78208 -4.738255459 -0.100482288 ATDLRPIYISVQPPSLHVLEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATDLRPIYISVQPPSLHVLEQR 22 1 B1ANH0;B1ANG9;Q16774;Q16774-2;B1ANH2;Q16774-3;B1ANH5;B1ANH3 B1ANH0 GUK1 Guanylate kinase 0 190.8 9.92E-18 810050000 361120 493800 431570 547200 474960 521840 552290 499940 440970 505530 FALSE TRUE 347007.0312 479717.3075 509564.2992 575441.0576 490237.5197 532391.9623 559049.0902 489616.0643 390912.9343 471290.0028 0.736291941 1.017881357 1.081211772 1.220991437 1.04020352 1.129648325 1.186210373 1.038884893 0.829453059 1 18.84625555 4.738294398 2.859924841 1.077685677 0.675633691 0.474647573 0.102787517 0.348387115 4.009457452 0.025363039 0.325442213 54738.68979 -4.738294398 -0.402051986 DFPFELIPEPPEGGLPGPWALHR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFPFELIPEPPEGGLPGPWALHR 23 0 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PK59;Q96KG9-4;Q96KG9-5;Q96KG9-6 E9PS17 SCYL1 N-terminal kinase-like protein 0 87.326 0.0065067 121930000 218430 241990 201870 202530 234650 278880 233430 220980 259080 261200 FALSE TRUE 209893.5141 235088.6821 238352.3996 212982.5976 242197.7304 284519.1447 236286.7862 216416.6858 229670.3246 243508.6913 0.861954918 0.965422141 0.97882502 0.87464064 0.994616369 1.168414742 0.97034231 0.888743168 0.943170953 1 17.89361374 4.738321116 4.615096219 0.972394643 0.855111353 0.16924503 0.075586577 0.390268926 22.24849282 0.019693658 0.14838379 54742.05741 -4.738321116 -0.11728329 ALVAT(ph)PGKK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALVATPGKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK 117.09 0.00070779 10563200000 47311800 12236500 6285190 6776540 6397640 3682370 5930490 40103500 3585230 1792180 TRUE FALSE 45462802.55 11887527 7421063.646 7126278.042 6603425.901 3756830.044 6003069.111 39275348.71 3178249.721 1670794.052 27.2102971 7.114896647 4.441638774 4.265204339 3.95226802 2.248529697 3.592943788 23.50699576 1.902239068 1 20.67210248 4.738353933 7.630158657 6.874065074 27.4151804 0.508400734 6.239395571 0.092257591 55.6671792 1.647219806 9.808887409 54746.19406 -4.738353933 20.54111532 DELSEEINNLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DELSEEINNLR 11 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;A0A087WYS2;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 85.622 0.035079 58259000 13619 23057 19580 23575 23377 26823 21376 21556 13852 30257 FALSE TRUE 13086.75442 22399.43694 23118.54155 24791.70858 24128.94244 27365.37944 21637.60588 21110.86107 12279.57903 28207.66644 0.463943178 0.794090393 0.819583626 0.878899665 0.855403707 0.970139784 0.76708245 0.748408633 0.435327717 1 14.7837997 4.738402649 5.742794409 0.805148514 0.453215172 0.331241636 0.146560205 0.164565412 23.48819923 0.034754932 0.22717361 54752.33543 -4.738402649 -0.351933343 HVTLPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HVTLPS(0.278)S(0.722)PR 135.15 0.00014741 3664100000 1261700 1784900 1538000 1780200 1666600 1691300 1877500 1416700 1933500 2159900 TRUE FALSE 1212391.369 1733996.4 1815950.813 1872076.335 1720207.703 1725499.245 1900477.407 1387444.65 1714017.186 2013608.049 0.602098988 0.861138989 0.90183927 0.929712382 0.854291233 0.856919124 0.94381695 0.68903412 0.851216892 1 20.94135146 4.738409825 8.380519879 0.863188047 0.60042333 0.517323654 0.078568079 0.076226559 79.74097076 0.019404685 0.113944637 54753.24016 -4.738409825 -0.262764717 EHASIDAQSGAGVPNPSTSAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHASIDAQSGAGVPNPSTSASPK 23 0 Q8IXJ6-5;Q8IXJ6-2;Q8IXJ6-3;Q8IXJ6 Q8IXJ6-5 SIRT2 NAD-dependent protein deacetylase sirtuin-2 1 EHASIDAQSGAGVPNPSTSAS(1)PK 218.98 1.39E-32 406690000 299540 393250 329060 432060 332070 402180 405520 289850 446990 509370 TRUE FALSE 287833.6456 382034.895 388528.4619 454358.6684 342751.3331 410312.3552 410482.8751 283864.4962 396249.5691 474869.9162 0.606131565 0.804504312 0.818178724 0.956806597 0.721779421 0.864052114 0.864411202 0.597773172 0.834438139 1 18.85717284 4.738432671 5.968506011 0.810276943 0.600526232 0.262365494 0.10813144 0.197457424 33.6568644 0.026217525 0.168402633 54756.12058 -4.738432671 -0.209750711 S(ph)APASPT(ph)HPGLMSPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(1)APAS(0.229)PT(0.772)HPGLMSPR;S(0.999)APAS(0.148)PT(0.853)HPGLMSPR 117.84 0.00060053 1339250000 1082850 678730 426300 502720 479060 433180 412750 708960 513700 464670 TRUE FALSE 1040531.025 659373.2849 503341.893 528665.4394 494469.4 441939.1964 417801.358 694319.7282 455386.9296 433197.487 2.401978442 1.522107825 1.161922467 1.220379747 1.141441063 1.020179502 0.96445933 1.602778753 1.051222464 1 18.72466535 4.738434743 2.075169288 1.175087889 2.752435096 0.826325177 0.174233447 0.293250222 1.386720665 0.047056462 0.870482018 54756.38175 -4.738434743 1.577347206 up GDFLFSSDHLIEMATK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDFLFSSDHLIEMATK 16 0 E9PDF6;O43795;O43795-2;H7C2Y7 E9PDF6 MYO1B Unconventional myosin-Ib 0 175.45 3.52E-09 189020000 272370 364730 306910 365020 348300 329250 344620 373850 356980 385710 FALSE TRUE 261725.4793 354328.2575 362375.4642 383858.7259 359503.3858 335907.6606 348837.5626 366129.8669 316457.127 359585.5181 0.727853226 0.985379665 1.007758783 1.067503296 0.999771592 0.934152361 0.970110155 1.0181997 0.880060823 1 18.45597539 4.738435306 7.585264472 0.98835831 0.725152 0.722318373 0.047745501 0.05027455 29.29735937 0.011387474 0.067986924 54756.45283 -4.738435306 -0.263206311 KYTGEDFDEDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KYTGEDFDEDLR 12 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 164.33 9.23E-05 2556670000 5615600 6250700 5191300 5177400 6005800 6638000 5886300 6071500 7009700 6495900 FALSE TRUE 5396136.144 6072436.156 6129483.39 5444606.234 6198982.011 6772224.908 5958338.3 5946121.403 6213988.243 6055926.907 0.891050408 1.002726131 1.012146197 0.899054153 1.02362233 1.11828049 0.983885438 0.981868093 1.026100271 1 22.52991636 4.73846136 7.919322326 1.003782326 0.890093969 0.3114298 0.050921438 0.122060687 90.97376698 0.012555027 0.074415584 54759.73775 -4.73846136 -0.113688357 TTDEELSELEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTDEELSELEDR 12 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 0 ; 241.63 6.85E-16 807420000 419950 460720 386420 436840 427030 432730 400380 507640 484040 452420 FALSE TRUE 403537.8897 447580.7167 456254.6899 459385.3648 440765.8078 441480.0971 405279.9702 497157.0566 429093.8085 421777.1904 0.956756076 1.061178098 1.081743395 1.089165975 1.045020494 1.046714017 0.96088641 1.178719637 1.017347116 1 18.68612155 4.738479143 9.683686374 1.061579975 0.956448658 0.199839491 0.055921647 0.109386171 291.3019761 0.013059092 0.075724097 54761.98014 -4.738479143 -0.105131317 DPTSLLGVLQAEADST(ph)SEGLEDAVHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.079)T(0.46)S(0.46)EGLEDAVHS(0.001)R;DPTSLLGVLQAEADS(0.081)T(0.459)S(0.459)EGLEDAVHSR 83.362 0.034145 36741000 18454.3 23941 20018.1 21731.1 22089 22617.9 22887.4 25775 23850 27366 TRUE FALSE 17733.08555 23258.22612 23635.81597 22852.64468 22799.51275 23075.24943 23167.50285 25242.73724 21142.64799 25512.47644 0.695075039 0.911641258 0.926441462 0.895743881 0.893661295 0.904469211 0.908085222 0.989427165 0.828717982 1 14.63891532 4.738494452 5.69324067 0.918994873 0.687810747 0.677354546 0.046087462 0.076420963 10.48525176 0.010458053 0.06873743 54763.91044 -4.738494452 -0.231184126 LEAAEER ddPTM_BT-474_Pertuzumab_2h_R1 2 LEAAEER 7 0 P16949;P16949-2;A2A2D0;E5RIR6;E7EVN3;Q9H169-3;Q9H169;Q9H169-4;Q9H169-2;E5RGX5;Q93045;Q93045-2;A0A0J9YW36;Q9NZ72-2;Q9NZ72;A0A0J9YXY4;H7BZ55 P16949;E5RGX5;A0A0J9YW36;H7BZ55 STMN1;STMN4;STMN2;STMN3 Stathmin;Stathmin-4;Stathmin-2;Stathmin-3;Putative ciliary rootlet coiled-coil protein-like 3 protein 0 ; 139.31 0.0062827 1213810000 1528590 1681010 1428140 1641260 1566030 1551810 1673620 1642910 1670700 1754630 FALSE TRUE 1468851.013 1633069.241 1686236.667 1725965.625 1616402.777 1583188.661 1694102.262 1608983.334 1481049.14 1635787.347 0.897947411 0.99833835 1.030841001 1.055128363 0.9881497 0.967845034 1.035649447 0.983613999 0.905404448 1 20.64155378 4.73851307 11.18775953 0.998518333 0.897828572 0.35632067 0.039460187 0.071460592 546.8925609 0.009536777 0.054962466 54766.2583 -4.73851307 -0.100689761 TLTEPSVDFNHS(ph)DDFTPISTVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 T(0.004)LT(0.026)EPS(0.172)VDFNHS(0.798)DDFTPISTVQK;TLT(0.002)EPS(0.012)VDFNHS(0.986)DDFTPISTVQK 201.21 1.48E-24 413060000 609560 311390 244870 267320 251890 239850 247700 431850 310640 318600 TRUE FALSE 585737.7213 302509.4621 289123.4561 281116.4172 259992.2706 244699.9313 250731.4267 422932.1466 275377.4495 297020.9382 1.972041853 1.018478576 0.973411026 0.946453199 0.87533314 0.823847412 0.844154046 1.423913577 0.927131438 1 18.18020511 4.7385314 6.355423171 0.997038949 1.993284999 0.773295942 0.160753651 0.063139536 14.52718581 0.043260339 0.27140088 54768.56977 -4.7385314 0.99624605 AEAQQVEALPGPSLDQWHR ddPTM_BT-474_Pertuzumab_2h_R1 3 AEAQQVEALPGPSLDQWHR 19 0 H7BZV4;A0A0C4DG62;Q66PJ3-4;Q66PJ3-3;F5H7X4;Q66PJ3-7;F5GYV5;F8WCT1;Q66PJ3-2;Q66PJ3 H7BZV4;F5GYV5;Q66PJ3 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 0 ;; 122.19 3.37E-05 796400000 328113 420640 349160 401350 421210 475430 369010 375780 442070 441750 FALSE TRUE 315289.9812 408643.759 412260.979 422063.7216 434758.6022 485043.5203 373526.0548 368020.0117 391888.0669 411829.879 0.765583065 0.992263505 1.001046791 1.024849685 1.05567523 1.177776419 0.906991148 0.893621445 0.951577549 1 18.65168898 4.738539871 6.743625278 0.996278362 0.761603672 0.461169404 0.076046879 0.118223249 36.60012692 0.020596532 0.126751752 54769.63807 -4.738539871 -0.23467469 SGSTGS(ph)SLSVSVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 SGSTGS(0.921)S(0.079)LSVSVR;SGSTGS(0.931)S(0.069)LSVSVR;SGST(0.002)GS(0.915)S(0.083)LSVSVR 246.47 3.64E-17 620670000 441400 583570 481460 547830 576130 566440 587900 516870 638460 639780 TRUE FALSE 424149.6 566927.155 568470.532 576103.572 594661.7447 577893.8049 595094.8961 506196.4539 565984.6974 596447.1307 0.711126902 0.95050697 0.953094587 0.965892101 0.997006631 0.968893595 0.997732851 0.848686208 0.948926851 1 19.18603474 4.738577589 7.606859887 0.952954716 0.708644162 0.758831573 0.041795336 0.051978498 30.69497951 0.010908839 0.065260288 54774.39501 -4.738577589 -0.244310554 YEGHPAEGTK ddPTM_BT-474_Pertuzumab_2h_R1 1 YEGHPAEGTK 10 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 118.4 0.0008296 121230000 275580 256530 207890 235300 252870 223710 269210 241820 291200 265010 FALSE TRUE 264810.0289 249214.0156 245460.3475 247443.8612 261003.7932 228233.5695 272504.6725 236826.3325 258144.1968 247060.6367 1.071842251 1.008715994 0.993522687 1.001551136 1.056436172 0.923795764 1.102987008 0.95857574 1.0448617 1 17.91450564 4.73858301 22.24480677 1.008751884 1.071842336 0.131717461 0.04749056 0.750150908 719470.9097 0.010051728 0.058095175 54775.07873 -4.73858301 0.063090453 S(ph)NENLDKIDMSLDDIIK ddPTM_BT-474_Pertuzumab_2h_R1 4 SNENLDKIDMSLDDIIK 17 1 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 S(1)NENLDKIDMSLDDIIK;S(1)NENLDKIDMSLDDIIK;S(1)NENLDKIDMSLDDIIK;S(1)NENLDKIDMSLDDIIK 202.17 6.56E-12 321784000 605067 413436 399492 278105 398714 346805 347279 507357 466794 419247 TRUE FALSE 581420.3127 401645.2101 471689.0911 292458.0324 411538.9979 353817.6347 351529.1043 496879.9007 413805.5021 390851.0273 1.487575245 1.027617128 1.206825768 0.748259598 1.052930578 0.905249341 0.899394091 1.271276947 1.058729473 1 18.5762593 4.738591572 22.18086337 1.027982283 1.487575209 0.49196028 0.142608315 0.469776572 327904.5108 0.034937387 0.200883926 54776.1586 -4.738591572 0.459592926 EGDELEDNGKNFYES(ph)DDDQKEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGDELEDNGKNFYESDDDQKEK 22 2 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 EGDELEDNGKNFYES(1)DDDQKEK;EGDELEDNGKNFYES(1)DDDQKEK;EGDELEDNGKNFYES(1)DDDQKEK 206.17 5.01E-23 2599630000 1689480 1109570 989960 701990 983310 968840 997150 1314550 1592135 1038290 TRUE FALSE 1623453.254 1077926.15 1168867.794 738219.788 1014939.059 988430.6086 1009353.42 1287404.083 1411402.51 967965.6935 1.67718057 1.113599539 1.207550848 0.762650777 1.048527924 1.021142191 1.042757431 1.330010032 1.45811212 1 19.88459639 4.738602476 21.2894491 1.114178953 1.677181152 0.469016231 0.181181552 0.419827495 206430.4336 0.046004381 0.264840601 54777.5338 -4.738602476 0.563002199 DGGS(ph)GNS(ph)TIIVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 2 DGGS(1)GNS(0.986)T(0.014)IIVSR;DGGS(1)GNS(0.929)T(0.071)IIVSR 211.9 2.66E-08 215800000 832760 628870 554450 519450 569160 634430 479740 722880 720240 648400 TRUE FALSE 800214.8185 610935.2433 654651.4487 546258.8768 587467.5483 647258.6093 485611.2016 707952.2754 638481.3747 604483.2905 1.323799733 1.010673501 1.082993457 0.903679035 0.971850765 1.070763443 0.803349256 1.171169305 1.056243216 1 19.20534293 4.73860531 20.96991923 1.011011729 1.32380024 0.491782801 0.096305211 0.331506551 149632.565 0.022457829 0.129340482 54777.89138 -4.73860531 0.312788511 EHQFDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHQFDSK 7 0 Q12955;H0Y9E9;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 0 113.26 0.0061705 287330000 870870 1087400 865730 1147800 1078600 1198900 1152200 765220 1091100 1191900 FALSE TRUE 836835.4376 1056388.417 1022186.669 1207038.096 1113294.149 1223142.579 1166300.968 749417.9396 967242.9023 1111171.551 0.753110927 0.950697861 0.919917962 1.086275197 1.001910234 1.100768444 1.049613776 0.674439459 0.870471262 1 20.08365014 4.738605451 10.46767756 0.95095285 0.752749308 0.214631625 0.118064907 0.134386044 611.8990198 0.03226787 0.186869592 54777.9091 -4.738605451 -0.198203542 VSYDEWNR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSYDEWNR 8 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 ; 153.71 0.0010159 304890000 440740 524740 435890 518850 495310 480280 474640 562360 547030 540620 FALSE TRUE 423515.3935 509774.929 514665.0193 545627.9107 511242.096 489991.5907 480448.7863 550747.0695 484933.4477 504003.3259 0.840302775 1.011451518 1.021154014 1.082587917 1.014362544 0.972199122 0.953265111 1.092744911 0.96216319 1 18.94307373 4.738614254 5.598627194 1.01748908 0.834206431 0.575426246 0.044121797 0.100841382 12.83066013 0.01066322 0.070802436 54779.0194 -4.738614254 -0.183282649 GVS(ph)CFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVSCFR 6 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 GVS(1)CFR 73.616 0.08653 233790000 951400 279170 118810 265580 279020 253920 152100 624260 122250 131980 TRUE FALSE 914218.2362 271208.3449 140281.6099 279286.6156 287994.9317 259054.4364 153961.4453 611368.8128 108372.6925 123040.877 7.430199281 2.204213359 1.140121993 2.269868537 2.340644334 2.105433922 1.251303217 4.968826845 0.880786086 1 16.90877817 4.738696467 24.99646654 2.224667222 7.430199379 0.666656052 1.1397387 6.828776973 1255260.687 0.277172049 1.601709518 54789.39022 -4.738696467 5.205532157 NLLDEELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLLDEELQR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 184.36 0.00010261 425990000 701890 810890 669150 787880 723780 786830 819070 795870 818120 885790 FALSE TRUE 674459.3628 787764.2111 790080.2902 828542.5812 747061.041 802740.2417 829094.0237 779435.0064 725250.4474 825794.6543 0.816739802 0.953946852 0.956751519 1.003327615 0.904657153 0.972082148 1.003995387 0.943860562 0.87824551 1 19.65542355 4.738773518 5.952904781 0.957681612 0.812811254 0.534273719 0.039421234 0.100449748 16.89169533 0.00912647 0.058971632 54799.11168 -4.738773518 -0.144870358 SRTS(ph)PVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.116)RT(0.116)S(0.767)PVS(0.001)R 56.043 0.072735 2012800000 1224000 688650 630020 534590 721260 478200 682500 538620 1093200 845370 TRUE FALSE 1176164.727 669010.3763 743878.6287 562180.254 744459.9829 487869.5316 690852.6392 527497.3088 969104.5191 788112.3369 1.492382078 0.848876924 0.943873854 0.713325027 0.944611508 0.619035522 0.876591581 0.669317411 1.229652771 1 19.58804176 4.738774659 8.087777323 0.845143601 1.497379165 0.538365417 0.170843645 0.063266649 52.86358213 0.037692391 0.22401212 54799.2556 -4.738774659 0.652235564 KRQS(ph)VSGLHR ddPTM_BT-474_Pertuzumab_2h_R1 3 KRQSVSGLHR 10 2 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KRQS(1)VSGLHR;KRQS(0.999)VS(0.001)GLHR;KRQS(1)VSGLHR 125.03 0.00021905 407830000 337395 227789 160396 176893 177169 166271 155978 290133 178948 164032 TRUE FALSE 324209.2304 221292.6807 189383.1252 186022.4689 182867.8018 169633.1135 157886.9054 284141.6522 158634.5733 152921.9665 2.120095875 1.447095442 1.238429831 1.216453549 1.195824288 1.109278918 1.03246714 1.858082646 1.037356351 1 17.22243613 4.738775193 2.500009701 1.259587242 2.310746674 0.567878282 0.235890221 0.420057431 3.289215087 0.062159821 0.941358263 54799.32297 -4.738775193 1.051159432 DQITAGNAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DQITAGNAAR 10 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 200.78 5.91E-07 618940000 260170 315920 256860 300960 311050 305360 294410 323470 323160 312560 FALSE TRUE 250002.2688 306910.2709 303280.3158 316492.5817 321055.2057 311534.5884 298013.0776 316790.2315 286476.2316 291390.0328 0.85796438 1.053262763 1.040805387 1.086147589 1.101805723 1.069132617 1.02272914 1.087169072 0.983136687 1 18.152592 4.738787477 7.189662184 1.055522319 0.855346062 0.701548319 0.037257605 0.053035479 22.9006687 0.008471188 0.051472047 54800.87302 -4.738787477 -0.200176258 VTFEDATDFFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTFEDATDFFGR 12 0 Q86WQ0;Q86WQ0-2 Q86WQ0 NR2C2AP Nuclear receptor 2C2-associated protein 0 ; 157.78 0.00016765 121493000 72682 82475 62279 82234 80129 87199 79569 79167 79656 82773 FALSE TRUE 69841.50709 80122.89375 73534.20069 86478.10659 82706.42206 88962.22352 80542.78922 77532.17378 70613.78483 77166.71098 0.905073006 1.038309042 0.95292646 1.120665965 1.071788871 1.152857526 1.043750449 1.004736016 0.915080919 1 16.235691 4.738788228 22.29193597 1.03753089 0.905073005 0.24132131 0.067867922 6.015937135 587305.076 0.016743536 0.097121372 54800.96779 -4.738788228 -0.132457885 SEGEIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEGEIAR 7 0 P50395;P50395-2;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 139.92 0.0061873 725640000 725580 874900 745410 912670 859790 709260 947180 919770 855570 983990 FALSE TRUE 697223.5314 849948.7086 880122.1686 959773.0081 887445.9262 723601.7232 958771.8722 900776.4281 758449.2804 917343.4809 0.760046314 0.926532674 0.95942489 1.046252607 0.967408549 0.788801292 1.045161264 0.981940186 0.826788762 1 19.8071025 4.738799277 3.141539745 0.955434662 0.73058827 0.339636585 0.079672788 0.39801055 6.062340422 0.01928337 0.220935419 54802.36201 -4.738799277 -0.224846392 S(ph)PTPTLPLSTSSFDEQN ddPTM_BT-474_Pertuzumab_2h_R1 1 SPTPTLPLSTSSFDEQN 17 0 Q96HE9 Q96HE9 PRR11 Proline-rich protein 11 1 S(0.851)PT(0.149)PTLPLSTSSFDEQN 160.81 3.19E-09 62988000 29263 37495 29447 40321 33124 36607 38405 36830 36993 34236 TRUE FALSE 28119.36961 36425.67931 34768.72794 42401.97164 34189.46354 37347.21862 38875.01188 36069.44763 32793.70973 31917.16523 0.881010873 1.14125672 1.089342606 1.328500553 1.071193613 1.170129564 1.217997012 1.130095589 1.027463106 1 14.9620449 4.738799625 8.309498608 1.14243713 0.879243421 0.398898494 0.090912271 0.082417614 80.75437805 0.020375569 0.120707229 54802.40592 -4.738799625 -0.263193709 DRDYFDYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRDYFDYSR 9 1 Q9HCG8;B7WP74 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 0 ;;; 196.48 2.70E-05 1685240000 904840 1007330 846850 1013370 957810 973800 972790 1008700 1058190 1112960 FALSE TRUE 869477.8524 978601.9347 999894.6331 1065670.147 988618.8285 993490.9032 984695.295 987869.9925 938068.7075 1037578.228 0.837987758 0.943159666 0.963681201 1.027074507 0.952813775 0.957509397 0.949032341 0.95209206 0.904094441 1 19.98478868 4.738801316 3.109910678 0.961789401 0.818970698 0.597315152 0.030685053 0.250523127 3.699787009 0.007564083 0.087759265 54802.61932 -4.738801316 -0.142818703 ELSEYVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSEYVR 7 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ; 153.15 0.0041078 940550000 1026640 1272750 1042600 1292590 1163200 1056860 1373650 1258060 1201970 1376670 FALSE TRUE 986517.7738 1236452.416 1231021.013 1359300.725 1200615.384 1078230.433 1390461.14 1232080.621 1065527.405 1283426.915 0.768659097 0.963399164 0.95916721 1.059118139 0.93547624 0.840118297 1.083397211 0.959992819 0.830220554 1 20.29156971 4.738819602 22.36453188 0.962106677 0.768658897 0.35702246 0.076522935 5.216554786 449252.3219 0.017841506 0.103895913 54804.92683 -4.738819602 -0.19344778 SITHDIEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 SITHDIEEK 9 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9;K7EJZ2;K7ENQ5;K7EN52;K7EKN4;K7EIR4 Q9UHD8 9-Sep Septin-9 0 ;;; 189.38 3.83E-05 4371010000 5874780 6792680 5489090 6528990 6068360 6602950 6860210 6375590 7421460 7297740 FALSE TRUE 5645187.103 6598959.417 6481090.667 6865951.956 6263554.311 6736466.173 6944167.302 6243931.839 6579006.974 6803457.57 0.829752673 0.969942026 0.952617195 1.00918568 0.920642812 0.990153331 1.020682092 0.917758621 0.967009334 1 22.69783669 4.738842812 23.42622199 0.968882122 0.829752581 0.623616882 0.033072984 6.135431934 508672.5005 0.007643066 0.044658331 54807.8558 -4.738842812 -0.139129541 VTPDTDWAR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTPDTDWAR 9 0 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ;;; 172.11 0.00013131 3701220000 1921050 2093780 1865250 2123330 1972620 1404300 2359510 1970870 2059790 2438570 FALSE TRUE 1845973.242 2034067.444 2202342.167 2232915.316 2036071.114 1432695.908 2388386.389 1930170.846 1825971.275 2273403.482 0.811986635 0.894723467 0.968742322 0.982190506 0.895604819 0.630198695 1.050577431 0.849022561 0.803188387 1 21.11642232 4.738843587 24.96755183 0.894055985 0.81198661 0.047558517 0.113568166 86.15959759 7598477.537 0.026368407 0.154938915 54807.95363 -4.738843587 -0.082069376 LAQGHTTVDELAR ddPTM_BT-474_Pertuzumab_2h_R1 6 LAQGHTTVDELAR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 203.85 8.25E-08 6289680000 2029781 2588774 1997493 2617910 2353103 2707514 2588345 2433103 2471091 2756135 FALSE TRUE 1950454.914 2514944.7 2358484.419 2753020.649 2428792.695 2762261.788 2620021.94 2382858.573 2190583.109 2569459.522 0.759091512 0.978783545 0.917891253 1.071439587 0.945254313 1.075036118 1.019678231 0.927377354 0.852546262 1 21.29303349 4.738846981 23.29122708 0.977105947 0.759091391 0.495206664 0.065831194 7.621709059 619053.9797 0.015784164 0.092210629 54808.38191 -4.738846981 -0.218014557 LGGSAVISLEGKPL ddPTM_BT-474_Pertuzumab_2h_R1 1 LGGSAVISLEGKPL 14 1 G3V1A4;P23528;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 98.156 0.021934 240490000 496670 570100 459690 543150 548980 569800 555850 544590 589160 593810 FALSE TRUE 477259.5873 553841.3062 542766.2087 571182.0366 566638.4403 581321.7464 562652.6586 533344.0262 522281.0268 553590.7198 0.862116308 1.000452656 0.980446726 1.031776755 1.023569254 1.050093012 1.016369383 0.963426602 0.943442525 1 19.07846023 4.738851185 7.675097852 1.001485312 0.860734915 0.65253901 0.030416892 0.066379843 40.97929819 0.008024219 0.048163723 54808.9125 -4.738851185 -0.140750397 SFLEEVLASGLHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFLEEVLASGLHSR 14 0 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ; 186.56 1.05E-06 312170000 304240 367400 284860 391530 315630 328340 389750 357360 364400 410540 FALSE TRUE 292349.9644 356922.1117 336340.5387 411736.9102 325782.5256 334979.2598 394519.8771 349980.3911 323034.8397 382733.7601 0.763846817 0.932559782 0.878784611 1.075778918 0.851198822 0.875227886 1.030794558 0.914422577 0.844019716 1 18.54598164 4.738885903 8.50658624 0.933047558 0.76282867 0.317893372 0.074611827 0.104254061 117.2118446 0.016993475 0.100560131 54813.29422 -4.738885903 -0.170218888 YDDYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YDDYDR 6 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 ; 137.59 0.029481 1441400000 3565400 3894900 3123200 3786300 3690700 3777600 3604200 3960800 3997000 4005100 FALSE TRUE 3426060.226 3783821.266 3687631.715 3981711.397 3809414.717 3853985.66 3648309.278 3879008.096 3543277.317 3733831.01 0.917572385 1.013388462 0.987626838 1.066387682 1.020242937 1.032179992 0.977095447 1.038881536 0.948965635 1 21.8322252 4.738908631 24.44317522 1.012458533 0.91757235 0.426172281 0.031797248 18.06517025 1268115.992 0.007115592 0.041491489 54816.16283 -4.738908631 -0.094886183 LKKNS(ph)LEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKKNSLEVK 9 2 REV__Q8IYE1 1 LKKNS(1)LEVK 46.158 0.089894 888100000 1314800 909050 869420 707620 844780 635820 933340 970560 1171500 933680 TRUE FALSE 1263416.162 883124.7841 1026543.534 744140.353 871953.1159 648676.716 944762.4941 950517.5968 1038516.231 870441.022 1.451466705 1.01457165 1.179337265 0.854900371 1.001737158 0.745227649 1.085383697 1.091995406 1.193092013 1 19.73138702 4.738919189 23.44555962 1.018764754 1.451466977 0.500634012 0.129733596 10.54798733 688999.4725 0.031606282 0.185639878 54817.49547 -4.738919189 0.432702223 AVT(ph)PENHESMTSIFPSAAVGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVTPENHESMTSIFPSAAVGLK 22 0 H0YA93;Q86UW6-2;Q86UW6 H0YA93 N4BP2 NEDD4-binding protein 2 1 AVT(0.998)PENHES(0.002)MTSIFPSAAVGLK;AVT(0.999)PENHES(0.001)MTSIFPSAAVGLK 163.46 5.54E-11 131016000 176006 261820 215290 266840 232860 272570 261620 243870 252650 304190 TRUE FALSE 169127.4909 254353.1499 254197.6921 280611.6444 240350.1534 278081.5522 264821.7838 238833.9993 223970.2312 283586.9404 0.59638674 0.896914187 0.896366003 0.989508346 0.847536043 0.980586595 0.933829264 0.842189697 0.789776253 1 18.11343157 4.738946384 5.919240688 0.904953136 0.587585166 0.669235258 0.065812901 0.079073392 12.94239218 0.01557172 0.101115585 54820.92812 -4.738946384 -0.31736797 NIRDDEGFIIR ddPTM_BT-474_Pertuzumab_2h_R1 4 NIRDDEGFIIR 11 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;; 249.2 2.16E-16 1714890000 955880 1072110 858800 1061950 1030170 1021900 1014530 1052290 1132470 1069470 FALSE TRUE 918523.1528 1041534.473 1014004.264 1116757.367 1063306.354 1042563.518 1026946.122 1030559.844 1003916.753 997033.8443 0.921255741 1.044633017 1.017020906 1.120079698 1.066469669 1.045665124 1.030001266 1.033625739 1.006903386 1 19.92728295 4.738952489 24.58005781 1.043279357 0.921255696 0.545572652 0.032555994 18.99565059 1190946.379 0.007868183 0.046054534 54821.69876 -4.738952489 -0.12202366 SSGHSSSELS(ph)PDAVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGHSSSELSPDAVEK 16 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSGHSSSELS(1)PDAVEK;SSGHSSSELS(1)PDAVEK 296.95 1.07E-45 2085130000 703680 967840 801420 939580 808110 940370 982770 987980 981470 1134030 TRUE FALSE 676179.4076 940238.1508 946254.4215 988071.8364 834103.5921 959384.9257 994797.4332 967577.8677 870057.6403 1057221.138 0.639581809 0.889348611 0.895039257 0.934593342 0.788958489 0.907459084 0.940954922 0.915208591 0.822966557 1 20.01184574 4.738970061 5.556190273 0.897885262 0.630414844 0.658679126 0.056131784 0.084030381 10.32716253 0.012760965 0.085471934 54823.91694 -4.738970061 -0.267470418 DWGSGSDTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DWGSGSDTLR 10 0 Q93084-4;Q93084-2;Q93084-3;Q93084-7;Q93084;Q93084-6;Q93084-5 Q93084-4 ATP2A3 Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 0 ;;; 146.23 6.75E-05 723910000 524142 802320 600020 980610 616750 610340 818270 922660 781030 692290 FALSE TRUE 503657.9512 779438.6192 708456.9614 1031219.4 636588.3239 622681.493 828284.233 903606.7486 692370.7487 645400.5817 0.78038038 1.207681929 1.097701151 1.597797444 0.986346065 0.964798469 1.283364559 1.400071172 1.072776766 1 19.29983535 4.738979794 22.69534832 1.203043564 0.780380015 0.269097431 0.19342574 12.12908673 655807.7483 0.04618952 0.271255434 54825.14558 -4.738979794 -0.422663549 DATLTALDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DATLTALDR 9 0 H0YFD6;P40939;A0A2R8Y4F5;A0A2R8YG21 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 124.92 0.0012006 85515000 36158 49432 37930 65897 37591 31784 54516 54394 45084 47507 FALSE TRUE 34744.90539 48022.24776 44784.79475 69297.95207 38800.14865 32426.69426 55183.18312 53270.74489 39966.25333 44289.30858 0.784498709 1.084285334 1.011187489 1.564665476 0.876061287 0.732156254 1.245970752 1.202790168 0.902390546 1 15.43467085 4.739009477 7.732088416 1.086007956 0.78160104 0.126448583 0.220077222 0.202117275 129.5885026 0.052930769 0.318225993 54828.89291 -4.739009477 -0.304406917 ISNLLSDYGYHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISNLLSDYGYHLR 13 0 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 ; 173.06 2.23E-05 849630000 702080 860310 728600 865650 803540 810810 866550 854140 916310 958360 FALSE TRUE 674641.9374 835774.8011 860274.2276 910326.3002 829386.5939 827205.1337 877155.0981 836501.7105 812294.3303 893449.4236 0.755098072 0.935447244 0.962868412 1.018889571 0.928297195 0.925855579 0.981762453 0.936260843 0.90916655 1 19.76902654 4.739027792 3.781414272 0.95565525 0.734430042 0.770436955 0.032982244 0.117947259 3.261934271 0.007913768 0.0729002 54831.20516 -4.739027792 -0.221225208 LNYSDHDVIK ddPTM_BT-474_Pertuzumab_2h_R1 4 LNYSDHDVIK 10 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ;;; 127.87 0.0003447 1932070000 4051080 4840710 3859410 4735360 4213500 4386960 5144600 4705930 5149210 5403510 FALSE TRUE 3892759.315 4702657.69 4556891.239 4979752.497 4349031.054 4475667.337 5207561.154 4608750.901 4564693.268 5037525.455 0.772752287 0.933525345 0.904589223 0.988531481 0.863326864 0.888465453 1.033753814 0.914883893 0.906138005 1 22.26428379 4.739029949 7.32592044 0.934892882 0.770762568 0.479576347 0.051295753 0.08873103 42.22466893 0.01178591 0.071616744 54831.47756 -4.739029949 -0.164130314 VDATEESDLAQQYGVR ddPTM_BT-474_Pertuzumab_2h_R1 5 VDATEESDLAQQYGVR 16 0 P07237;H7BZ94;I3L3U6;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 ;;;; 359.9 2.31E-87 1031902000 548445 630232 524603 581086 564886 623387 607440 645984 621871 665793 FALSE TRUE 527011.1631 612258.4004 619410.4318 611075.9181 583056.0712 635992.3123 614874.0324 632644.2047 551278.8112 620698.2471 0.849061787 0.986402657 0.997925215 0.984497573 0.939355112 1.024640097 0.990616673 1.019245999 0.888159124 1 19.24353255 4.739056879 24.58535561 0.984499572 0.849061738 0.516848533 0.038209465 24.243103 1200606.771 0.008631639 0.051008692 54834.87763 -4.739056879 -0.135437834 SCVEEPEPEPEAAEGDGDKKGNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCVEEPEPEPEAAEGDGDKKGNAEGSSDEEGKLVIDEPAK 40 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 SCVEEPEPEPEAAEGDGDKKGNAEGS(1)S(1)DEEGKLVIDEPAK 87.753 0.00017838 195900000 172140 98531 65056 46363 83833 72537 72115 86891 106770 59363 TRUE FALSE 165412.5785 95720.99235 76813.06636 48755.79999 86529.56458 74003.74784 72997.56494 85096.67049 94649.91722 55342.29113 2.988900082 1.729617448 1.387963252 0.880986294 1.563534194 1.337200653 1.319019568 1.537642709 1.710263801 1 15.75609475 4.739062653 2.407265581 1.361818091 3.369277426 0.813714618 0.23653868 0.223019775 1.571742806 0.058783767 0.931421372 54835.60672 -4.739062653 2.007459335 SDATADDLIDVVEGNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDATADDLIDVVEGNR 16 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 ; 385.3 6.53E-121 165147000 163064 187552 152083 177970 183908 186841 174814 188533 187856 192936 FALSE TRUE 156691.2786 182203.2006 179567.7812 187155.053 189823.5678 190619.053 176953.426 184639.7277 166531.3744 179868.2729 0.871144622 1.012981321 0.998329379 1.040511759 1.055347699 1.059770297 0.983794547 1.026527495 0.925851857 1 17.45658121 4.739072551 6.697580615 1.01501432 0.868567636 0.559899974 0.03720374 0.082754771 24.61840604 0.00880579 0.054765982 54836.85651 -4.739072551 -0.146446684 DVHEDSVTIFFENNWQSER ddPTM_BT-474_Pertuzumab_2h_R1 1 DVHEDSVTIFFENNWQSER 19 0 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 176.87 4.14E-14 69572000 50812 60551 48080 55454 64660 55929 55357 57696 71265 63291 FALSE TRUE 48826.21086 58824.14477 56769.12553 58315.98759 66739.84762 57059.9227 56034.47553 56504.55744 63175.29597 59004.2442 0.827503369 0.996947687 0.962119358 0.988335473 1.131102492 0.967047769 0.949668558 0.957635475 1.070690708 1 15.84853111 4.739079942 7.346205132 0.998292808 0.825430752 0.483662295 0.054115123 0.094834829 45.76862658 0.013285873 0.080755619 54837.78968 -4.739079942 -0.172862057 IQALGLHLPDPPLES(ph)EDEDEEGATALNNHSSIPMDPEHVELVK ddPTM_BT-474_Pertuzumab_2h_R1 5 IQALGLHLPDPPLESEDEDEEGATALNNHSSIPMDPEHVELVK 43 0 A0A2R8Y7W8;A0A2R8Y6W5;Q16626 A0A2R8Y7W8 MEA1 Male-enhanced antigen 1 1 IQALGLHLPDPPLES(0.95)EDEDEEGAT(0.05)ALNNHSSIPMDPEHVELVK;IQALGLHLPDPPLES(0.963)EDEDEEGAT(0.036)ALNNHSSIPMDPEHVELVK;IQALGLHLPDPPLES(1)EDEDEEGATALNNHSSIPMDPEHVELVK;IQALGLHLPDPPLES(0.995)EDEDEEGAT(0.004)ALNNHS(0.001)S(0.001)IPMDPEHVELVK;IQALGLHLPDPPLES(0.901)EDEDEEGAT(0.064)ALNNHS(0.017)S(0.017)IPMDPEHVELVK 243.96 2.59E-55 2324490000 239415 378042 325827 430575 321623 405321 396996 222406 396194 497956 TRUE FALSE 230058.3971 367260.6123 384711.1869 452797.0274 331968.2959 413516.8683 401854.5558 217813.2384 351219.7181 464228.9966 0.495570933 0.791119501 0.828709946 0.975374289 0.715095994 0.890760533 0.865638637 0.469193523 0.756565662 1 18.82447711 4.739086867 23.13903173 0.787022266 0.495570769 0.289664184 0.143752884 22.6673993 995850.6804 0.036789165 0.21762605 54838.66415 -4.739086867 -0.291451496 DLDSLHR ddPTM_BT-474_Pertuzumab_2h_R1 8 DLDSLHR 7 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;;;;;; 165.11 0.0011727 10063830000 6124136 7847832 6342789 8137707 7147569 7890951 7784702 7051085 7864798 8143350 FALSE TRUE 5884797.995 7624019.515 7489072.067 8557695.033 7377477.048 8050511.436 7879973.512 6905477.631 6972019.103 7591793.651 0.775152522 1.004244829 0.986469392 1.127229668 0.971769965 1.060422847 1.037959391 0.909597646 0.918362567 1 22.85600935 4.739116699 24.28417972 1.000735122 0.775152428 0.554734243 0.060906296 24.7571674 1080734.02 0.01540767 0.091615081 54842.43118 -4.739116699 -0.225582694 IENLSNLHQLQMLELGSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 IENLSNLHQLQMLELGSNR 19 0 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C003;C9J177;Q15435-2;Q15435-5;Q15435-4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 ; 210.61 1.68E-16 1206020000 409950 529810 428380 507540 505370 564660 557440 482040 531610 497190 FALSE TRUE 393928.7008 514700.3375 505797.7953 533734.2002 521625.685 576077.8121 564262.1175 472085.7055 471263.8615 463514.8784 0.849872828 1.110428945 1.091222351 1.151493134 1.125369884 1.24284643 1.217354919 1.018490943 1.016717873 1 18.82225612 4.739119338 6.367180672 1.115196077 0.844072722 0.494208886 0.078132805 0.106150686 24.55089594 0.019603496 0.124005029 54842.76448 -4.739119338 -0.271123354 ARPS(ph)SPSTSWHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ARPSSPSTSWHR 12 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 ARPS(0.464)S(0.464)PS(0.06)T(0.006)S(0.007)WHR 63.31 0.043354 97826000 13116 18033 15652 21987 17656 14918 23357 20454 20012 24253 TRUE FALSE 12603.41222 17518.7165 18480.66458 23121.7517 18223.92127 15219.65218 23642.84995 20031.61775 17740.32166 22610.32271 0.557418502 0.774810547 0.817355188 1.02261927 0.806000052 0.673128481 1.045666188 0.885950104 0.784611608 1 14.46469396 4.739122048 1.642531234 0.881577152 0.44058537 0.445138878 0.110469796 0.934966871 2.422736568 0.028980358 0.657105418 54843.10664 -4.739122048 -0.440991783 ERS(ph)KDKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERSKDKDR 8 3 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 ERS(1)KDKDR 76.927 0.041 46396000 224290 152040 121500 97205 136450 132290 151300 173360 167930 163420 TRUE FALSE 215524.4988 147703.9681 143457.7528 102221.7617 140839.0382 134964.9944 153151.6547 169780.0554 148867.2904 152351.4178 1.414653712 0.969495198 0.941624008 0.670960357 0.924435362 0.885879478 1.005252572 1.114397607 0.977130981 1 17.2170434 4.739147436 4.823481444 0.944975241 1.440595564 0.63476303 0.107429467 0.128940261 8.739802806 0.029269582 0.214958506 54846.3128 -4.739147436 0.495620323 DLYLASVFHATAFELDTDGNPFDQDIYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLYLASVFHATAFELDTDGNPFDQDIYGR 29 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ;;; 248.02 6.74E-46 1222728000 235487 354850 294450 384245 314475 391123 350375 315542 351582 377712 FALSE TRUE 226283.9077 344730.0254 347663.665 404075.9305 324590.374 399031.775 354662.9941 309025.9474 311671.8853 352129.2298 0.642616087 0.978987247 0.987318392 1.147521695 0.921793326 1.133196967 1.007195552 0.877592433 0.885106543 1 18.42574546 4.739166784 5.291309077 0.992385214 0.628021171 0.599963169 0.08594656 0.112362028 11.16348072 0.021593765 0.14905053 54848.7563 -4.739166784 -0.364364043 (ac)VSVINTVDTSHEDMIHDAQMDYYGTR ddPTM_BT-474_Pertuzumab_2h_R1 11 VSVINTVDTSHEDMIHDAQMDYYGTR 26 0 P55735 P55735 SEC13 Protein SEC13 homolog 0 ;;;;;;;;;; 173.47 2.38E-70 3738202100 161382.2 186987.1 147673.3 193794.9 161139 187455.2 175606.97 190236.1 185048.4 191469.9 FALSE TRUE 155075.2052 181654.411 174361.1503 203796.678 166322.1823 191245.6726 177756.1006 186307.6581 164042.4814 178501.4731 0.868761487 1.017663372 0.976805105 1.141708662 0.931769242 1.071395486 0.995824278 1.043731768 0.918997914 1 17.44557645 4.739167493 23.57843349 1.015247999 0.868761395 0.319879613 0.061872788 24.22941242 940849.857 0.013380728 0.079441526 54848.84584 -4.739167493 -0.146486604 S(ph)TPVRDR ddPTM_BT-474_Pertuzumab_2h_R1 2 STPVRDR 7 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.713)T(0.287)PVRDR;S(0.5)T(0.5)PVRDR 104.2 0.0049689 458858000 628980 701670 580010 695380 617260 681240 685370 676260 734730 737420 TRUE FALSE 604398.7662 681659.0586 684830.7093 731268.6451 637114.7285 695015.1396 693757.7631 662294.9947 651326.5306 687473.8866 0.879158871 0.991541747 0.996155232 1.063703887 0.926747533 1.010969512 1.009140531 0.963374766 0.947420031 1 19.39094539 4.739194031 23.9044442 0.989614226 0.879158817 0.461011985 0.035919421 25.15685946 948991.034 0.008373185 0.049734614 54852.19755 -4.739194031 -0.110455409 QESDKNGES(ph)ASPERDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QESDKNGESASPERDR 16 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGES(0.581)AS(0.419)PERDR 79.511 0.0094695 80231000 83273 73707 61960 63672 70658 71832 72179 68733 89207 72666 TRUE FALSE 80018.5991 71604.94853 73157.55029 66958.11955 72930.77874 73284.49226 73062.34819 67313.63953 79080.59535 67744.2671 1.181186284 1.05698905 1.079907621 0.988395364 1.076560156 1.081781461 1.078502305 0.993643336 1.167340038 1 16.04781124 4.739199808 6.980026223 1.055708443 1.183087917 0.341627791 0.051154883 0.117836059 43.27132991 0.011423566 0.070399952 54852.92714 -4.739199808 0.127379473 LSQSSQDSS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 10 LSQSSQDSSPVR 12 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 LSQSSQDS(0.001)S(0.999)PVR;LSQSSQDSS(1)PVR;LSQSSQDS(0.035)S(0.965)PVR;LSQSSQDSS(1)PVR;LSQSSQDS(0.037)S(0.963)PVR;LSQSSQDS(0.034)S(0.966)PVR;LSQSSQDS(0.25)S(0.75)PVR;LSQSSQDS(0.18)S(0.82)PVR;LSQSS(0.001)QDS(0.183)S(0.815)PVR;LSQSSQDS(0.1)S(0.9)PVR 282.32 4.11E-28 18212825000 9336248 10137540 8109600 10288982 9363833 9287801 10031801 10018227 10526104 10179194 TRUE FALSE 8971377.106 9848427.285 9575185.117 10819997.59 9665029.192 9475606.7 10154573.18 9811347.112 9331224.803 9489748.124 0.945375682 1.037796489 1.009003083 1.140177532 1.018470571 0.998509821 1.070057187 1.033889096 0.983295308 1 23.17793837 4.739208224 24.10509746 1.036163731 0.94537564 0.264749941 0.043066145 41.68072875 1550858.842 0.00997383 0.05919392 54853.99017 -4.739208224 -0.090788091 LDLRDPAALFETHGAEEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDLRDPAALFETHGAEEIR 19 1 A0A087WVI0;E9PBL8;Q8WTW3;J3KRP4 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 ;;; 146.89 6.66E-08 322434000 271786 320259 247354 309238 309450 351572 307416 289671 324985 326614 FALSE TRUE 261164.3026 311125.5269 292056.3702 325197.8102 319403.7403 358681.0267 311178.249 283689.1926 288094.0652 304492.1429 0.857704571 1.021785075 0.95915897 1.068000662 1.048972027 1.177964802 1.021958222 0.931679846 0.946146139 1 18.21604548 4.739213607 23.61180764 1.018918552 0.857704488 0.341365679 0.067424748 32.19084901 1163421.243 0.017763173 0.106072425 54854.67002 -4.739213607 -0.161214064 LNDPFQPFPGNDS(ph)PKEKDPEIFCDPFTSATTTTNK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNDPFQPFPGNDSPKEKDPEIFCDPFTSATTTTNK 35 2 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 LNDPFQPFPGNDS(1)PKEKDPEIFCDPFTSATTTTNK 126.83 2.16E-08 217230000 329860 215140 199210 166480 207000 183210 202300 215290 291690 239300 TRUE FALSE 316968.7065 209004.4178 235211.6784 175072.0528 213658.343 186914.6317 204775.8079 210844.1863 258578.5741 223091.9979 1.420798189 0.936853047 1.054325931 0.784752723 0.95771406 0.837836559 0.91789849 0.945099727 1.159067006 1 17.76727924 4.739215757 24.77425729 0.945731432 1.420798351 0.6633208 0.099399619 27.04458296 1022450.352 0.02291274 0.136923377 54854.94154 -4.739215757 0.475066919 SFS(ph)SQRPVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFSSQRPVDR 10 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.032)FS(0.921)S(0.046)QRPVDR;S(0.414)FS(0.571)S(0.015)QRPVDR 107.39 0.0013873 1679760000 3468880 2319660 1674750 1476100 1749510 1452620 1383500 3506260 1945350 1753790 TRUE FALSE 3333312.335 2253505.568 1977414.58 1552281.698 1805784.578 1481992.972 1400431.687 3433854.506 1724522.024 1635004.241 2.038717852 1.378287292 1.20942474 0.949405304 1.104452534 0.906415368 0.85653092 2.100211375 1.054750795 1 20.64086295 4.739227701 2.52824401 1.202279794 2.22090179 0.377417945 0.339112891 0.64264447 5.187984883 0.093847062 1.406472968 54856.45023 -4.739227701 1.018621995 YFDEEFTAQMITIT(ph)PPDQDDSMECVDSER ddPTM_BT-474_Pertuzumab_2h_R1 2 YFDEEFTAQMITITPPDQDDSMECVDSER 29 0 P31749;P31749-2;G3V2I6 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 YFDEEFTAQMITIT(0.404)PPDQDDS(0.23)MECVDS(0.366)ER;YFDEEFTAQMITIT(0.941)PPDQDDS(0.022)MECVDS(0.036)ER 99.614 0.0029832 38198000 19976.5 23979 19262.6 21084.4 23769 25020 25647 21726 23270.1 25920 TRUE FALSE 19195.79629 23295.1424 22743.78031 22172.56841 24533.55147 25525.92154 25960.87566 21277.35051 20628.5758 24164.41531 0.794382816 0.964026735 0.941209627 0.91757107 1.015276023 1.056343438 1.074343216 0.880524119 0.853675768 1 14.56059647 4.739249499 6.606332486 0.966431013 0.791116982 0.366481288 0.068087926 0.141187021 39.13413835 0.017607742 0.110270967 54859.20368 -4.739249499 -0.17531403 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAAGENPLEFLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLR 43 0 P54725-2;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.002)GIPGS(0.983)PEPEHGS(0.015)VQESQVSEQPATEAAGENPLEFLR;AVEY(0.001)LLT(0.035)GIPGS(0.8)PEPEHGS(0.158)VQES(0.005)QVSEQPATEAAGENPLEFLR;AVEY(0.013)LLT(0.076)GIPGS(0.419)PEPEHGS(0.419)VQES(0.069)QVS(0.003)EQPATEAAGENPLEFLR 144.92 2.43E-13 174187000 50547.7 80747.8 62087.3 89762.7 64813.3 91211.6 79820.6 70276.7 76834.8 83524.5 TRUE FALSE 48572.24 78444.9518 73307.85623 94395.3637 66898.07866 93055.96105 80797.46838 68825.46159 68112.83562 77867.31122 0.623782165 1.007418268 0.94144584 1.212259191 0.859129173 1.195058101 1.037630132 0.883881317 0.874729518 1 16.24873019 4.739251002 23.91926147 1.000255757 0.62378197 0.483469733 0.117054171 26.72960254 925717.7545 0.02748233 0.164010691 54859.39352 -4.739251002 -0.376473787 AFMES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 AFMESPK 7 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AFMES(1)PK 72.325 0.054452 106720000 366980 230870 202740 211850 252360 194020 200960 294400 185490 194660 TRUE FALSE 352638.0159 224285.8136 239379.6279 222783.6039 260477.3886 197943.2173 203419.4086 288320.5371 164433.9528 181475.5048 1.943171428 1.235901307 1.319074043 1.227623552 1.435330839 1.090743445 1.12091937 1.588757322 0.906094478 1 17.4694153 4.739280535 24.48448214 1.249981674 1.943171677 0.553074494 0.194257121 33.61984467 1143111.25 0.044085902 0.264714159 54863.12422 -4.739280535 0.693190003 LQDEFENR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQDEFENR 8 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 ; 157.2 0.00088571 1074290000 859100 1007800 802350 952860 954910 971020 983680 995680 1047350 1108720 FALSE TRUE 825525.4222 979058.5307 947352.4932 1002037.219 985625.5474 990654.6897 995718.5701 975118.8601 928459.2188 1033625.407 0.798669824 0.947208267 0.916533675 0.969439424 0.953561649 0.958427186 0.96332633 0.94339676 0.898255028 1 19.97928201 4.739308379 6.911766654 0.948723144 0.796295713 0.746355478 0.026460229 0.052143879 18.17153849 0.005961106 0.036895696 54866.64176 -4.739308379 -0.152427431 S(ph)NIDISSGLEDEEPKRPLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SNIDISSGLEDEEPKRPLPR 20 2 Q9BZ71;Q9BZ71-3 Q9BZ71 PITPNM3 Membrane-associated phosphatidylinositol transfer protein 3 1 S(1)NIDISSGLEDEEPKRPLPR;S(1)NIDISSGLEDEEPKRPLPR;S(1)NIDISSGLEDEEPKRPLPR;S(1)NIDISSGLEDEEPKRPLPR 262.26 1.05E-36 897390000 805410 582642 460592 508724 505604 415039 481646 812510 564127 461971 TRUE FALSE 773933.6868 566025.6206 543831.2202 534979.3066 521867.2118 423431.3729 487540.5278 795731.3846 500089.668 430681.2927 1.796998616 1.314256343 1.262723107 1.242169826 1.21172482 0.983166393 1.132021604 1.847610746 1.161159485 1 18.71626113 4.739326305 4.286310794 1.276306237 1.83677839 0.337387236 0.229842224 0.287924079 12.40149239 0.060813866 0.494168975 54868.90643 -4.739326305 0.560472153 AISPT(ph)SSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AISPTSSSR 9 0 O14795;O14795-2;A0A0U1RRL2;B1AM27 O14795 UNC13B Protein unc-13 homolog B 1 AIS(0.061)PT(0.934)S(0.004)SSR 179.53 0.00055552 608510000 498060 712250 542240 696330 708660 756390 725160 626780 703870 779510 TRUE FALSE 478595.2646 691937.3274 640234.8301 732267.6747 731454.6925 771684.724 734034.725 613836.774 623969.6285 726713.0934 0.65857526 0.952146499 0.881000818 1.007643431 1.00652472 1.061883611 1.010074996 0.844675539 0.858618943 1 19.47102637 4.739342636 7.028257509 0.954711188 0.654203135 0.62263493 0.0699042 0.080812556 30.69912665 0.018552896 0.114418268 54870.96975 -4.739342636 -0.300508053 SGCRPFCEVYVGDER ddPTM_BT-474_Pertuzumab_2h_R1 1 SGCRPFCEVYVGDER 15 1 O14976-2;O14976 O14976-2 GAK Cyclin-G-associated kinase 0 120.63 0.00010946 513400000 371000 418690 346960 412020 396710 406330 396200 421420 427280 439590 FALSE TRUE 356500.9098 406749.3711 409663.3901 433284.4016 409470.5374 414546.271 401048.8141 412717.5297 378776.9657 409816.1778 0.869904433 0.992516629 0.99962718 1.057265245 0.999156597 1.011541988 0.978606595 1.007079642 0.924260647 1 18.64461741 4.739343288 4.775304316 0.999382439 0.862524499 0.599906541 0.031037264 0.118672167 7.726623175 0.007306183 0.054185379 54871.05222 -4.739343288 -0.13685794 EDHLVYADEESSNITDGRIT(ph)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR ddPTM_BT-474_Pertuzumab_2h_R1 6 EDHLVYADEESSNITDGRITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 51 2 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNIT(0.003)DGRIT(0.842)PEPAVS(0.12)NT(0.032)EEPS(0.001)T(0.001)T(0.001)STASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNIT(0.002)DGRIT(0.996)PEPAVS(0.002)NTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESS(0.001)NIT(0.004)DGRIT(0.995)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 367.14 9.15E-183 8994310000 247659.4 316869 267234.3 350518 307995 350618 342927 225491.2 335111 340452 TRUE FALSE 237980.5968 307832.2064 315529.4826 368608.276 317901.9389 357707.7362 347123.8432 220834.7279 297070.6042 317392.8828 0.749798152 0.969877471 0.994129042 1.161362765 1.001603867 1.127018769 1.093672423 0.695777189 0.935971221 1 18.27591025 4.739375727 4.084140829 0.989653241 0.729110047 0.270440942 0.121939136 0.371819876 13.44013949 0.033586455 0.286133118 54875.15078 -4.739375727 -0.260543194 S(ph)ASQLSQTEAGGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SASQLSQTEAGGKK 14 1 A0A590UJL1;F8W6W8;D6RA03 A0A590UJL1;D6RA03 RIMS2 1 S(0.99)AS(0.01)QLSQTEAGGKK;S(0.924)AS(0.076)QLSQTEAGGKK 117.29 0.00019099 459620000 465870 350710 274230 280140 308640 260640 285240 462950 367660 306930 TRUE FALSE 447663.2854 340708.0942 323789.4612 294598.059 318567.6859 265910.3194 288730.8524 453389.9207 325924.7782 286141.3577 1.564482985 1.190698531 1.131571695 1.029554278 1.113322759 0.929297049 1.009049704 1.584496294 1.13903415 1 18.12636851 4.739384199 3.659376067 1.145650645 1.611079691 0.368908828 0.171482917 0.354165641 8.767885189 0.046984657 0.450433838 54876.22128 -4.739384199 0.465429046 LSKPPFQTNPS(ph)PEMVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSKPPFQTNPSPEMVSK 17 1 Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 1 LSKPPFQTNPS(1)PEMVSK 110.44 0.00033802 2155600000 281590 184160 166290 152000 169130 163040 181600 175970 247640 212470 TRUE FALSE 270585.1515 178907.9371 196342.3021 159844.7382 174570.22 166336.7805 183822.4751 172336.158 219528.9454 198079.2177 1.366045134 0.903214074 0.991231208 0.806973796 0.881315173 0.839748776 0.928025046 0.870036544 1.108288633 1 17.595718 4.739385119 24.92276276 0.913908747 1.366045281 0.708468789 0.084504173 32.97438007 996564.1761 0.019159791 0.115694881 54876.33754 -4.739385119 0.452136535 RS(ph)PTEDFR ddPTM_BT-474_Pertuzumab_2h_R1 3 RSPTEDFR 8 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RS(1)PTEDFR;RS(1)PTEDFR;RS(1)PTEDFR 110.39 0.0021043 1327480000 1042992 1258372 1081765 1198800 1209120 1170360 1162239 1253022 1278991 1265067 TRUE FALSE 1002230.72 1222484.463 1277263.999 1260670.212 1248012.443 1194025.481 1176462.829 1227146.658 1133805.304 1179382.885 0.849792491 1.036545873 1.0829935 1.06892361 1.058191075 1.012415473 0.997524081 1.040498953 0.96135472 1 20.16960073 4.739385127 24.99999601 1.032217621 0.849792434 0.699285934 0.035132246 38.02290532 1152705.328 0.0086383 0.051804444 54876.33854 -4.739385127 -0.182425187 DTTALSFFHMLNGAALR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTTALSFFHMLNGAALR 17 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 218.63 4.59E-15 485330000 162894 262540 184788 372690 167794 167310 357410 249070 233790 225297 FALSE TRUE 156527.9224 255052.6163 218183.3022 391924.5756 173191.2464 170693.1228 361784.0905 243926.6175 207251.1393 210037.4335 0.745238217 1.214319809 1.038782938 1.865974884 0.824573237 0.81267953 1.722474344 1.161348305 0.986734297 1 17.68028695 4.739402236 24.99991175 1.203228092 0.745238074 0.129015018 0.33494 141.667111 4207476.429 0.077604274 0.471387587 54878.50043 -4.739402236 -0.457990018 AHVIVMAATNRPNSIDPALR ddPTM_BT-474_Pertuzumab_2h_R1 3 AHVIVMAATNRPNSIDPALR 20 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 204.23 5.91E-22 12433640000 900840 1057860 833327 1139060 941310 1045100 1011340 967340 1176940 1111390 FALSE TRUE 865634.1769 1027690.869 983927.7262 1197847.023 971588.091 1066232.638 1023717.081 947364.091 1043338.705 1036114.565 0.835461836 0.991869918 0.949632173 1.156095149 0.937722645 1.029068284 0.98803464 0.914342991 1.006972337 1 19.9827521 4.739405374 7.053186134 0.993122179 0.833165886 0.37298141 0.062677622 0.121698847 47.05017746 0.014903862 0.0919346 54878.89706 -4.739405374 -0.159956293 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHRSEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 VILSNMVSISSEPFGHLVDDDDISDQEDHRSEEK 34 1 A8MUM1;Q53HC9 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISSEPFGHLVDDDDIS(0.997)DQEDHRS(0.003)EEK;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK 364.73 2.00E-148 963610000 255776 349364 266558 351595 322669 384883 316134 281759 405717 411147 TRUE FALSE 245779.9911 339400.4808 314730.9602 369740.8601 333047.9414 392665.598 320002.9425 275940.5782 359661.7071 383299.6475 0.641221542 0.88547037 0.821109443 0.964626142 0.868897072 1.024435062 0.834863649 0.719908249 0.938330388 1 18.54811315 4.739454709 24.19831852 0.879531033 0.641221434 0.419675288 0.087888873 52.37853222 1417247.186 0.022043673 0.133854736 54885.13154 -4.739454709 -0.238309599 IYQY(ph)IQSR ddPTM_BT-474_Pertuzumab_2h_R1 8 IYQYIQSR 8 0 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5;A0A2R8Y443;A0A2R8YDF3;Q13627-4;Q13627-3;Q9Y463-2;Q9Y463-3;Q9Y463 A0A2R8Y6L5 DYRK1A;DYRK1B Dual specificity tyrosine-phosphorylation-regulated kinase 1A;Dual specificity tyrosine-phosphorylation-regulated kinase 1B 1 IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR 221.7 5.53E-05 19842550000 2863330 3235460 2696700 3177720 3181580 3077790 3112890 3292450 3200690 3346070 TRUE FALSE 2751427.898 3143187.849 3184053.678 3341722.51 3283918.41 3140025.023 3150986.479 3224459.757 2837361.09 3119437.699 0.882026879 1.0076136 1.020713983 1.071257974 1.05272768 1.006599691 1.010113611 1.033666984 0.909574534 1 21.57285457 4.739473174 4.202630811 1.017982872 0.871089669 0.477635622 0.040702585 0.18091469 7.248595389 0.00967159 0.080189018 54887.46506 -4.739473174 -0.146893203 GDS(ph)RSPS(ph)HKR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GDS(1)RS(0.322)PS(0.679)HKR;GDS(0.998)RS(0.381)PS(0.621)HKR 90.498 0.053074 8333460000 13848000 12787500 10608600 11627800 12280800 12211000 12185200 12265900 14739000 13706700 TRUE FALSE 13306804.85 12422813.02 12525810.01 12227912.15 12675823.09 12457914.79 12334326.12 12012604.88 13065890.51 12778333 1.041356869 0.972177906 0.98023819 0.956925457 0.991977833 0.974924882 0.965253145 0.940076055 1.022503523 1 23.60719631 4.739501818 24.28416558 0.973951975 1.0413569 0.410313614 0.022175311 47.08628348 1214606.928 0.005133439 0.03097303 54891.08536 -4.739501818 0.067404925 VETPSHPGGVSEEFWER ddPTM_BT-474_Pertuzumab_2h_R1 1 VETPSHPGGVSEEFWER 17 0 Q92620;H3BQT9 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 135.09 1.48E-05 229830000 126950 161880 135070 164010 134130 171210 158850 154920 154950 157610 FALSE TRUE 121988.6536 157263.3409 159480.1536 172474.5758 138444.4133 174671.9835 160794.0538 151720.8479 137360.7256 146934.9343 0.830222263 1.070292382 1.085379419 1.173815992 0.942215777 1.188770964 1.094321473 1.032571652 0.934840487 1 17.16481792 4.739503724 24.34002326 1.064109356 0.830222161 0.413937093 0.081026294 51.24391324 1322228.321 0.018584223 0.112842989 54891.32621 -4.739503724 -0.233887195 DKYGPPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 DKYGPPVR 8 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 107.15 0.0037006 2308840000 4016260 4773560 3703090 4626660 4665260 5124370 4440890 4584370 4589200 4742610 FALSE TRUE 3859300.119 4637422.743 4372320.738 4865442.477 4815322.325 5227988.272 4495238.94 4489701.157 4068253.255 4421388.8 0.87287056 1.048861105 0.988902115 1.100433076 1.089097237 1.182431247 1.016702928 1.01545043 0.920130176 1 22.07606817 4.739512729 23.56319127 1.044428508 0.872870442 0.351001171 0.068052771 41.33860001 1022694.872 0.016879435 0.102348629 54892.46445 -4.739512729 -0.171558065 SDS(ph)VSASER ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSVSASER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 SDS(0.995)VS(0.005)ASER 160.61 6.84E-05 70175000 207780 105430 79918 75906 96066 83192 75313 157350 79929 68016 TRUE FALSE 199659.7279 102423.2396 94360.96037 79823.51776 99156.05013 84874.19924 76234.70302 154100.6675 70855.79501 63409.21574 3.148749367 1.615273717 1.488126911 1.258863035 1.56374825 1.338515202 1.202265351 2.430256639 1.117436861 1 15.95240491 4.739513164 4.461638577 1.509674047 3.261729343 0.640349276 0.380952421 0.133796667 6.692749183 0.094310278 0.740612317 54892.5194 -4.739513164 1.752055296 AFSLYANIDILRPYFDVEPAQVR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFSLYANIDILRPYFDVEPAQVR 23 1 D6RGY8;D6RFI3;E7EQR8;Q9GZM5;H0Y9A1 D6RGY8 YIPF3 "Protein YIPF3;Protein YIPF3, 36 kDa form III" 0 71.651 0.01986 124390000 46199 50416 41206 46704 50066 47119 50744 47407 56207 51408 FALSE TRUE 44393.492 48978.18504 48652.84082 49114.39904 51676.41836 48071.77846 51365.02025 46428.02888 49826.617 47926.09037 0.926290704 1.021952441 1.015163984 1.024794609 1.078252325 1.003039849 1.071754859 0.968742256 1.039655365 1 15.54852363 4.73952685 5.839196912 1.024316819 0.923329371 0.476254882 0.031002269 0.117430468 18.00954449 0.007153191 0.047116724 54894.24924 -4.73952685 -0.100987448 YGQNGDFTR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGQNGDFTR 9 0 O76094-2;O76094;R4GNC1 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 78.516 0.068746 449430000 246580 301200 237600 291830 277480 241200 304310 318430 302820 341710 FALSE TRUE 236943.381 292610.0709 280539.6054 306891.3813 286405.3962 246077.2293 308034.2368 311854.3092 268445.1431 318565.6773 0.743781888 0.918523531 0.880633494 0.963353566 0.899046622 0.772453678 0.96694107 0.978932545 0.842668128 1 18.28123131 4.739533773 22.94460163 0.91414378 0.74378171 0.374614822 0.065827754 28.15042098 663377.5086 0.015719491 0.095428979 54895.1243 -4.739533773 -0.17036207 AEGNDHIER ddPTM_BT-474_Pertuzumab_2h_R1 2 AEGNDHIER 9 0 A0A0G2JP90;A0A087WW46;J3KN36;A0A0G2JN29;A0A087X117;Q5JPE7-3;Q5JPE7-2;Q15155;P69849;Q5JPE7;A0A087WTD5 A0A0G2JP90 NOMO1;NOMO3;NOMO2 Nodal modulator 2;Nodal modulator 1;Nodal modulator 3 0 ; 175.66 5.37E-05 146585000 118633 198882 149431 209210 158140 252730 198383 152461 243930 201172 FALSE TRUE 113996.6912 193210.0801 176436.5058 220007.3532 163226.7167 257840.3738 200810.8705 149312.6271 216240.089 187546.4413 0.607831801 1.030198594 0.940761683 1.173081993 0.870326921 1.374808138 1.070726105 0.796136819 1.152994893 1 17.51688836 4.739554983 6.608937341 1.035251949 0.599685761 0.412699449 0.156195937 0.121459906 33.63277303 0.037373497 0.235175765 54897.80531 -4.739554983 -0.435566188 MEEIVEGCTGALHILAR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEEIVEGCTGALHILAR 17 0 P14923;A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0;A0A2R8Y7Z0 P14923;A0A2R8Y804 JUP;CTNNB1 Junction plakoglobin;Catenin beta-1 0 ; 222.27 3.42E-15 210045000 148724 202138 150461 261120 142521 171570 211103 203739 193240 197612 FALSE TRUE 142911.7017 196373.2222 177652.6497 274596.4345 147105.3174 175039.263 213686.5417 199531.7185 171304.2053 184227.5632 0.775734636 1.06592748 0.964310913 1.490528506 0.798497873 0.950125268 1.15990538 1.083072017 0.929851116 1 17.4911294 4.739561519 23.82142761 1.058166369 0.775734488 0.178741299 0.174850209 72.90297018 1734585.88 0.040110428 0.244595008 54898.63154 -4.739561519 -0.282431881 IISGHIDLDNR ddPTM_BT-474_Pertuzumab_2h_R1 2 IISGHIDLDNR 11 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 ; 150.06 3.41E-05 550000000 226760 307370 253360 329420 260470 300050 298660 264320 333340 336510 FALSE TRUE 217897.9685 298604.1085 299147.788 346421.4057 268848.2541 306117.2166 302315.0904 258861.6996 295500.6407 313717.878 0.694566628 0.951823691 0.953556711 1.104245024 0.856974604 0.975772304 0.963652733 0.825141689 0.941931147 1 18.25910822 4.739576137 24.52430425 0.94465223 0.694566527 0.533116999 0.072090897 54.92435275 1326151.94 0.017715326 0.108455454 54900.47943 -4.739576137 -0.250085703 NDNGASGQTSESIKKS(ph)EEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDNGASGQTSESIKKSEEK 19 2 Q9NWH9;Q9NWH9-3 Q9NWH9 SLTM SAFB-like transcription modulator 1 NDNGASGQTSES(0.001)IKKS(0.999)EEK 76.237 0.0069207 165140000 130850 88104 79801 55412 90705 73199 81293 111300 114840 71129 TRUE FALSE 125736.2373 85591.36018 94222.81586 58271.81996 93622.6087 74679.13393 82287.88805 109001.6161 101803.8446 66311.36947 1.896149006 1.290749397 1.420914944 0.878760617 1.411863598 1.126188986 1.240931815 1.643784723 1.535239665 1 16.01696863 4.739588144 23.98594201 1.307467309 1.896149299 0.397440881 0.224644714 54.04285657 1261221.719 0.055083946 0.335716274 54901.99724 -4.739588144 0.58868199 S(ph)SSPGKPQAVSSLNSSHSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSPGKPQAVSSLNSSHSR 19 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR;S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR;S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR;S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR 231.49 1.97E-20 9374500000 3750640 4510820 3558530 4368210 3930950 4425230 4525000 4316600 4771800 4871700 TRUE FALSE 3604060.842 4382175.83 4201635.53 4593653.842 4057392.577 4514711.183 4580378.304 4227460.702 4230125.269 4541735.42 0.793542668 0.964868145 0.925116754 1.011431406 0.893357319 0.994049799 1.008508396 0.930802944 0.931389629 1 22.11481223 4.739595736 24.19580298 0.960067604 0.793542583 0.628430536 0.038868821 34.54937749 807407.9466 0.008769162 0.053719049 54902.95702 -4.739595736 -0.166525021 SANPTRPSS(ph)PVTSHISK ddPTM_BT-474_Pertuzumab_2h_R1 2 SANPTRPSSPVTSHISK 17 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.047)ANPT(0.025)RPS(0.217)S(0.707)PVT(0.004)SHISK;S(0.132)ANPT(0.068)RPS(0.134)S(0.658)PVT(0.008)SHISK 126.26 2.67E-05 2175370000 634980 826620 631900 855330 715910 855950 794600 786720 825870 870080 TRUE FALSE 610164.2796 803045.6069 746098.3865 899473.6838 738937.8953 873257.8955 804324.5525 770473.9571 732120.6999 811148.7066 0.752222465 0.99001034 0.919804692 1.10888876 0.910977099 1.076569424 0.991587049 0.949855373 0.902572727 1 19.6296069 4.739606304 24.47038 0.983207516 0.752222365 0.535176439 0.064623673 48.90531441 1144231.166 0.014559633 0.089422549 54904.29311 -4.739606304 -0.230985151 GSGPQRPHSFS(ph)EALR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSGPQRPHSFSEALR 15 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 GSGPQRPHS(0.39)FS(0.61)EALR 77.554 0.015467 267600000 121460 151450 118580 148050 140080 170050 142980 144600 135170 153130 TRUE FALSE 116713.2089 147130.7943 140010.0438 155690.8782 144585.8004 173488.5275 144729.832 141613.9595 119826.0683 142758.3687 0.817557737 1.030628156 0.980748415 1.090590203 1.012800873 1.215259946 1.013809791 0.991983593 0.839362829 1 17.1232158 4.739657078 24.31011193 1.024283078 0.817557644 0.316248491 0.088811193 77.40812888 1715916.848 0.021338065 0.131331308 54910.71236 -4.739657078 -0.206725434 EIEENSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIEENSR 7 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 135.84 0.0070675 399190000 404930 539660 408940 551660 503460 592060 493270 516590 507270 531370 FALSE TRUE 389104.8879 524269.4252 482844.5548 580131.2387 519654.2481 604031.8589 499306.7858 505922.236 449686.8362 495379.8366 0.785467755 1.058318055 0.974695616 1.171083673 1.049001614 1.219330732 1.007927148 1.021281446 0.907761687 1 18.91817562 4.739664858 24.06650008 1.050217826 0.785467613 0.449021392 0.086266926 50.61462352 1102876.342 0.020450287 0.125868146 54911.69612 -4.739664858 -0.264750214 LHKTEDGGWEWS(ph)DDEFDEESEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHKTEDGGWEWSDDEFDEESEEGK 24 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 LHKT(0.003)EDGGWEWS(0.997)DDEFDEESEEGK;LHKT(0.004)EDGGWEWS(0.996)DDEFDEESEEGK 184.4 1.57E-17 485350000 885610 518970 472820 353730 550110 483290 548600 358300 796230 500800 TRUE FALSE 850999.3821 504169.4837 558269.0918 371986.0477 567804.7877 493062.4549 555313.9309 350900.9798 705845.3085 466880.3699 1.822735409 1.079868669 1.195743338 0.7967481 1.216167619 1.056078787 1.189413749 0.751586493 1.511833339 1 18.83269341 4.739690579 6.196938988 1.067163421 1.84120907 0.528728455 0.207069987 0.091638696 18.52799352 0.046124951 0.297195685 54914.94834 -4.739690579 0.774045649 PVFSNQFLLENAAY(ph)LDY(ph)ES(ph)TKEYAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 PVFSNQFLLENAAYLDYESTKEYAIK 26 1 Q9BZA8-3;Q9BZA8-2;Q9BZA8-4;Q9BZA8 Q9BZA8-3 PCDH11Y Protocadherin-11 Y-linked 3 PVFSNQFLLENAAY(0.567)LDY(0.567)ES(0.657)T(0.657)KEY(0.55)AIK 43.256 0.087845 398780000 258780 150210 120460 113860 149050 151550 142690 157060 206840 164100 TRUE FALSE 248666.5915 145926.1579 142229.8016 119736.3282 153844.3286 154614.4448 144436.2829 153816.6561 183360.3903 152985.3608 1.625427362 0.953857004 0.929695501 0.782665267 1.005614706 1.010648627 0.944118327 1.005433822 1.198548602 1 17.22303408 4.739693174 24.94254328 0.975003864 1.625427576 0.798500796 0.097045716 39.89798435 878570.8578 0.02357592 0.145025716 54915.27643 -4.739693174 0.650423712 EVDYSGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVDYSGLR 8 0 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ; 113.5 0.0065976 1543330000 1023490 1130870 966660 1034920 1078250 1020760 1226210 945410 1295750 1222220 FALSE TRUE 983490.8793 1098618.695 1141356.965 1088332.345 1112932.89 1041400.467 1241216.725 925886.9531 1148661.892 1139437.951 0.863136846 0.964175973 1.001684176 0.955148408 0.976738479 0.913959787 1.089323665 0.812582162 1.008095168 1 20.11989093 4.739716391 23.43319343 0.96112045 0.863136771 0.17048281 0.06810022 76.28940692 1546262.322 0.015551558 0.095598719 54918.21224 -4.739716391 -0.09798368 GHESEVFICAWNPVSDLLASGSGDSTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GHESEVFICAWNPVSDLLASGSGDSTAR 28 0 Q9BZK7;A0A0D9SF63;A0A1B0GVH3;O60907;A0A2R8YFW3;Q9BQ87;O60907-2 Q9BZK7;O60907 TBL1XR1;TBL1X;TBL1Y F-box-like/WD repeat-containing protein TBL1XR1;F-box-like/WD repeat-containing protein TBL1X;F-box-like/WD repeat-containing protein TBL1Y 0 116.08 3.46E-10 0 24332 36438 27639 36042 36110 39480 40169 31714 34487 34304 FALSE TRUE 23381.07854 35398.82392 32633.98213 37902.13194 37271.51094 40278.31265 40660.60024 31059.09482 30572.18034 31980.55953 0.73110286 1.106885697 1.020431869 1.185161626 1.165442741 1.259462412 1.271416162 0.971186723 0.955961396 1 14.96490756 4.739732472 6.507033442 1.1114291 0.723373563 0.508677266 0.109729698 0.104559876 26.76356013 0.02801011 0.177601141 54920.24578 -4.739732472 -0.388055537 YLTLDGFDAMFR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLTLDGFDAMFR 12 0 Q7L576;Q7L576-2;Q7L576-3 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ; 190.96 1.39E-05 286300000 283824 350652 286721 317983 326273 316956 343997 361993 354314 371722 FALSE TRUE 272731.8443 340651.7483 338537.8628 334394.1407 336767.8674 323365.0675 348206.9382 354517.718 314093.7601 346544.9378 0.787002823 0.982994443 0.976894555 0.964937312 0.971787005 0.933111502 1.004795916 1.023006483 0.906357952 1 18.40268292 4.739745573 24.88281236 0.976561649 0.787002758 0.748584466 0.032433843 46.22915853 970639.4791 0.0077888 0.048430057 54921.90256 -4.739745573 -0.189558891 QSSGPGASSGTSGDHGELVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSSGPGASSGTSGDHGELVVR 21 0 P29692-3;E9PL71;E9PN91 P29692-3 EEF1D Elongation factor 1-delta 0 330.83 4.36E-80 221890000 81032 114490 94635 117670 97714 112350 115630 98118 126380 115420 FALSE TRUE 77865.17985 111224.8573 111737.6496 123742.9628 100857.0596 114621.794 117045.1145 96091.82901 112033.8722 107602.5006 0.723637271 1.033664243 1.03842986 1.15000081 0.937311484 1.065233553 1.087754596 0.893025984 1.041182794 1 16.71535208 4.739757388 24.90723639 1.023381844 0.723637169 0.635616329 0.068937865 64.80949275 1348650.619 0.016751748 0.104543444 54923.3967 -4.739757388 -0.299744675 LESLSETPGPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 LESLSETPGPSSPR 14 0 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSETPGPS(0.02)S(0.98)PR;LESLSETPGPS(0.02)S(0.98)PR;LESLSETPGPSS(1)PR;LESLSETPGPS(0.02)S(0.98)PR 376.16 2.27E-97 5330900000 2644960 3383610 2702730 3787270 2691700 3240390 3306840 3424120 3104350 3358980 TRUE FALSE 2541592.039 3287112.756 3191173.433 3982731.459 2778280.975 3305912.906 3347310.097 3353410.725 2751957.202 3131473.293 0.811628202 1.049701673 1.019064554 1.27183951 0.887212093 1.055705285 1.068925002 1.070873168 0.878805899 1 21.57841014 4.739800996 24.05365372 1.041787457 0.811628097 0.289170899 0.103673414 74.65906814 1447503.66 0.023377768 0.145002686 54928.91186 -4.739800996 -0.230159361 EENLIPYSPDVQIHAER ddPTM_BT-474_Pertuzumab_2h_R1 2 EENLIPYSPDVQIHAER 17 0 Q8N766-4;Q8N766-3;Q8N766-2;Q8N766 Q8N766-4 EMC1 ER membrane protein complex subunit 1 0 ; 136.49 1.01E-05 296200000 268380 464040 373780 521140 313420 419130 441460 447690 548520 485110 FALSE TRUE 257891.4129 450806.0335 441330.3607 548036.0979 323501.4389 427605.0958 446862.7195 438445.0451 486254.3092 452253.0676 0.570236957 0.996800389 0.975848241 1.211790781 0.715310657 0.945499603 0.988081124 0.969468372 1.075181893 1 18.78677076 4.739827367 24.6413018 0.98200545 0.570236796 0.536169511 0.116067497 68.18396958 1326155.455 0.026808789 0.166775247 54932.24742 -4.739827367 -0.411768654 KEELNAISGPNEFAEFYNR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEELNAISGPNEFAEFYNR 19 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 174.82 6.02E-12 1195510000 725470 795620 665890 695090 767060 823280 675660 795610 923110 783940 FALSE TRUE 697117.8304 772929.6966 786231.1356 730963.6782 791733.1815 839927.2857 683928.9292 779180.3755 818322.4228 730843.0455 0.953854367 1.057586443 1.075786573 1.00016506 1.083314928 1.149258094 0.93580822 1.066139139 1.119696531 1 19.47920208 4.739830123 23.46903134 1.054142644 0.953854301 0.207217239 0.058879165 73.54283573 1359170.915 0.013538677 0.084299668 54932.59601 -4.739830123 -0.100288342 SWASLFHDSKPSSSSPVAYVETKYS(ph)PPAISPLVSEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SWASLFHDSKPSSSSPVAYVETKYSPPAISPLVSEK 36 2 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 S(0.001)WAS(0.001)LFHDS(0.001)KPS(0.001)S(0.001)S(0.001)S(0.001)PVAYVET(0.065)KY(0.349)S(0.571)PPAIS(0.01)PLVSEK 60.802 0.010582 233510000 81695 136560 109250 125430 100640 173810 126890 112750 132060 184190 TRUE FALSE 78502.26908 132665.4425 128993.9053 131903.4573 103877.177 177324.5573 128442.9178 110421.6731 117069.1024 171714.6472 0.457166994 0.772592465 0.751210845 0.768154956 0.604940689 1.032669956 0.748002106 0.643053315 0.681765384 1 17.38965358 4.739851387 24.32452899 0.76158183 0.457166866 0.33923462 0.132568671 89.51404909 1686609.004 0.030546858 0.189898476 54935.28569 -4.739851387 -0.304414964 SAS(ph)PTVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SASPTVPR 8 0 Q92817;K7EKI0;K7EQ87 Q92817 EVPL Envoplakin 1 S(0.018)AS(0.978)PT(0.004)VPR;S(0.011)AS(0.969)PT(0.02)VPR 121.09 0.001519 899230000 762940 880300 698260 891950 825900 844250 845760 874700 844030 886540 TRUE FALSE 733123.4613 855194.7059 824451.1147 937983.6464 852465.8236 861321.3134 856110.6639 856637.1393 748219.2529 826493.8562 0.887028326 1.034726029 0.997528425 1.134894881 1.031424272 1.042138798 1.035834275 1.036471273 0.905293182 1 19.65664457 4.739853222 24.23308182 1.029583808 0.887028259 0.367621347 0.053586654 72.95437316 1367470.519 0.012379898 0.076498669 54935.51777 -4.739853222 -0.142555549 (ac)SAEVPEAASAEEQKEMEDKVT(ph)SPEKAEEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEVPEAASAEEQKEMEDKVTSPEKAEEAK 30 3 P56211 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 SAEVPEAASAEEQKEMEDKVT(0.5)S(0.5)PEKAEEAK 90.867 3.20E-06 192200000 348470 185440 161490 89804 202240 148840 187560 236120 258960 204280 TRUE FALSE 334851.4071 180151.4328 190674.8353 94438.7952 208745.2333 151849.6468 189855.4154 231244.0395 229563.9464 190443.9336 1.758267647 0.945955218 1.001212439 0.495887653 1.096098097 0.797345675 0.996909756 1.214236836 1.205414854 1 17.53900681 4.739926781 24.34265229 0.975902402 1.758268014 0.588277063 0.197175656 60.64015461 1080334.041 0.049383404 0.3087816 54944.82332 -4.739926781 0.782365612 GSTDNLMDDIER ddPTM_BT-474_Pertuzumab_2h_R1 2 GSTDNLMDDIER 12 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 277.96 1.50E-27 3178600000 1212600 1354820 1054870 1208030 1333460 1410550 1314550 1306760 1377820 1392350 FALSE TRUE 1165210.251 1316181.86 1245508.474 1270376.573 1376351.952 1439072.287 1330637.856 1279774.949 1221415.65 1298044.894 0.897665602 1.013972526 0.9595265 0.978684619 1.060326925 1.108646006 1.025109272 0.985925028 0.940965644 1 20.30790885 4.739948762 23.97424207 1.009680299 0.897665539 0.337945251 0.04633749 86.3208392 1490536.757 0.012068841 0.075626458 54947.60428 -4.739948762 -0.11201476 SLQYER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLQYER 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 127.31 0.039818 283580000 144940 183610 174280 161530 167330 150840 189120 172850 201130 184230 FALSE TRUE 139275.5846 178373.6226 205776.2728 169866.5827 172712.3214 153890.0881 191434.5071 169280.5871 178298.5656 171751.938 0.810911284 1.038553769 1.198101606 0.9890228 1.005591689 0.896002048 1.114598818 0.985610929 1.038116761 1 17.38996685 4.739950529 24.27320384 1.030042326 0.81091118 0.423024753 0.076586739 78.11523602 1363973.631 0.018180734 0.113813365 54947.82787 -4.739950529 -0.219131146 NVAEALGHS(ph)PKDPGGGGGPVR ddPTM_BT-474_Pertuzumab_2h_R1 6 NVAEALGHSPKDPGGGGGPVR 21 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 NVAEALGHS(1)PKDPGGGGGPVR;NVAEALGHS(1)PKDPGGGGGPVR;NVAEALGHS(1)PKDPGGGGGPVR;NVAEALGHS(1)PKDPGGGGGPVR;NVAEALGHS(1)PKDPGGGGGPVR;NVAEALGHS(1)PKDPGGGGGPVR 182.4 2.83E-17 4568574000 3091860 2544000 2015080 1864870 2084170 2336510 2227890 2382900 2840860 2648060 TRUE FALSE 2971026.693 2471447.611 2379249.781 1961116.164 2151209.221 2383755.833 2255155.584 2333692.282 2518377.483 2468704.538 1.203476013 1.001111139 0.963764495 0.794390797 0.871391934 0.965589765 0.913497565 0.945310484 1.020121057 1 21.23532275 4.739952698 1.999235624 0.92612322 1.285297088 0.634316913 0.061451923 0.474993652 2.030496909 0.016208573 0.313276655 54948.10225 -4.739952698 0.359173868 TEESPAS(ph)DEAGEKEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEESPASDEAGEKEAK 16 1 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEESPAS(1)DEAGEKEAK;TEESPAS(1)DEAGEKEAK 260.53 5.22E-27 1253930000 1228180 834750 652790 482440 751970 691970 773020 990340 1012260 768940 TRUE FALSE 1180181.368 810943.7473 770763.6742 507338.7862 776157.798 705962.1075 782480.45 969889.1329 897352.4885 716859.0089 1.646322852 1.131245806 1.075195631 0.707724643 1.082720296 0.984799101 1.091540234 1.352970558 1.251783792 1 19.45132987 4.739960625 3.959796327 1.081978145 1.699080715 0.533188749 0.160828667 0.217254655 7.035731298 0.043823721 0.387469222 54949.10525 -4.739960625 0.61710257 HDSPEDVK ddPTM_BT-474_Pertuzumab_2h_R1 9 HDSPEDVK 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;;;;;; 175.44 0.00026609 6312405000 8591825 12757440 10027838 12714210 11101920 13147280 12172840 11396099 13013530 14482130 FALSE TRUE 8256046.98 12393610.3 11840091.39 13370391.9 11459023.34 13413127.01 12321814.86 11160765.57 11536288.63 13501242.44 0.611502758 0.917960726 0.876963098 0.99030826 0.848738432 0.993473532 0.912643034 0.826647298 0.854461261 1 23.68658884 4.739990337 24.39274257 0.90613686 0.61150262 0.688906927 0.060695626 50.44300884 860494.6932 0.014328229 0.089884115 54952.86471 -4.739990337 -0.29463424 DYEPQTICEHLQYLFALLQNSNR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYEPQTICEHLQYLFALLQNSNR 23 0 E9PJ87;E9PRY5;Q86UV5-4;Q86UV5-7;Q86UV5-3;Q86UV5-2;Q86UV5;Q86UV5-8 E9PJ87 USP48 Ubiquitin carboxyl-terminal hydrolase 48 0 155.05 3.30E-08 55128000 34995 40695 29912 38730 42434 40078 41378 38508 40926 37661 FALSE TRUE 33627.35671 39534.41844 35317.76379 40728.85994 43798.92815 40888.40462 41884.39634 37712.79634 36280.25206 35110.18693 0.957766382 1.126009911 1.005912155 1.16002971 1.247470663 1.164573823 1.192941423 1.074126903 1.033325517 1 15.09960206 4.740002906 23.91155216 1.119584888 0.957766287 0.250017726 0.078845523 94.36749893 1564205.556 0.019280716 0.120156812 54954.45511 -4.740002906 -0.161818601 FSFSGNTLVSSSADPEGHFETPIWIER ddPTM_BT-474_Pertuzumab_2h_R1 2 FSFSGNTLVSSSADPEGHFETPIWIER 27 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 183.86 1.40E-17 1937660000 508950 694990 535800 713100 625520 753160 717990 608440 702510 754650 FALSE TRUE 489059.6713 675169.5657 632630.9788 749903.1765 645640.4189 768389.4112 726776.9764 595875.5014 622764.01 703536.8833 0.695144324 0.95967899 0.899215086 1.065904566 0.917706568 1.092180708 1.033033226 0.846971233 0.885190279 1 19.42426653 4.740010293 6.263963425 0.963352661 0.688809895 0.528256237 0.076920751 0.106936034 22.70617163 0.019222442 0.123975258 54955.38989 -4.740010293 -0.274542766 NLVS(ph)PAYCTQESR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLVSPAYCTQESR 13 0 Q9NUQ3 Q9NUQ3 TXLNG Gamma-taxilin 1 NLVS(1)PAYCTQESR;NLVS(1)PAYCTQESR 176.71 1.69E-05 518330000 1133340 709990 610450 576920 794520 656490 625250 832460 808370 632880 TRUE FALSE 1089047.82 689741.7804 720771.8944 606694.9103 820076.4574 669764.6776 632901.9965 815269.4101 716607.2266 590014.4739 1.845798481 1.169025186 1.22161731 1.028271233 1.389926 1.135166521 1.072688933 1.381778662 1.214558724 1 19.17039082 4.740030564 24.92129203 1.19639878 1.845798703 0.713601474 0.126264182 63.92672629 1083697.244 0.028911946 0.182170162 54957.955 -4.740030564 0.649399924 SVS(ph)PLVWCR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVSPLVWCR 9 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 S(0.001)VS(0.999)PLVWCR;SVS(1)PLVWCR;S(0.001)VS(0.999)PLVWCR 164.64 6.51E-05 356616000 317974 389862 325678 350322 345322 378576 365260 401958 386479 429673 TRUE FALSE 305547.2245 378743.5175 384535.2593 368402.1604 356429.5957 386231.0661 369730.1611 393657.4268 342607.5242 400570.865 0.762779451 0.945509398 0.959968118 0.91969285 0.889804094 0.964201593 0.92300812 0.982741036 0.855298161 1 18.61169797 4.740037148 24.8435203 0.938108871 0.762779388 0.621439221 0.040980623 70.98193132 1194187.164 0.009069645 0.056981672 54958.78818 -4.740037148 -0.175329483 VTQVDGHSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTQVDGHSSK 10 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 98.156 0.0055689 474800000 258380 406180 330210 427560 336070 421840 404300 368860 434660 513330 FALSE TRUE 248282.2239 394596.1441 389886.2925 449626.4228 346879.9968 430369.8938 409247.9443 361242.9121 385319.219 478561.7019 0.518809221 0.824546015 0.814704334 0.939536994 0.724838606 0.899298653 0.855162339 0.754851278 0.805161001 1 18.86834542 4.740095148 5.178601422 0.836226306 0.50445165 0.606000818 0.078924955 0.105537117 9.55333603 0.017675669 0.125070798 54966.12834 -4.740095148 -0.331774656 LDYWEDDLRR ddPTM_BT-474_Pertuzumab_2h_R1 6 LDYWEDDLRR 10 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 ;;;;; 155.26 2.09E-05 1680434000 1407398 1609740 1270250 1511927 1560858 1511020 1585743 1584191 1632517 1663732 FALSE TRUE 1352395.33 1563831.791 1499812.432 1589957.734 1611064.415 1541573.86 1605149.797 1551476.902 1447200.514 1551045.95 0.871924736 1.008243367 0.966968407 1.025087448 1.038695479 0.993893095 1.034882169 1.000277846 0.933048124 1 20.56481 4.740136561 24.78308439 1.002380887 0.871924687 0.619194682 0.030113535 79.8378137 1255390.866 0.007096122 0.045602867 54971.37003 -4.740136561 -0.1304562 TGEALKTEENK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGEALKTEENK 11 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7;Q9BZZ5-3 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ; 129.71 0.00021833 381410000 522350 363450 343450 251950 378150 332010 330180 404340 464270 347630 FALSE TRUE 501935.9845 353084.7619 405519.055 264953.1697 390313.5382 338723.4697 334220.8416 395990.2377 411568.016 324084.7105 1.548780206 1.089482936 1.251274873 0.817542948 1.204356533 1.045169546 1.031276178 1.221872631 1.269939626 1 18.30601143 4.740167722 24.25014951 1.109196625 1.548780429 0.504071916 0.13240895 75.32782005 1136486.907 0.030469232 0.193559559 54975.31442 -4.740167722 0.439583804 VDVRPLPAS(ph)PARPCPS(ph)PGPAAAS(ph)SPARPPGLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDVRPLPASPARPCPSPGPAAASSPARPPGLQR 33 3 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 3 VDVRPLPAS(1)PARPCPS(0.977)PGPAAAS(0.624)S(0.399)PARPPGLQR 101.04 6.70E-05 222300000 54393 68145 56256 66391 61072 58089 67494 74791 60960 67145 TRUE FALSE 52267.26143 66201.57132 66422.71061 69817.44747 63036.43634 59263.59938 68320.01176 73246.53971 54040.07637 62597.20934 0.834977501 1.057580234 1.061112968 1.115344409 1.007016719 0.946745071 1.091422645 1.170124683 0.863298491 1 15.93381072 4.740192586 24.05710624 1.047958843 0.834977379 0.329311694 0.083630135 92.7874678 1367579.446 0.020009471 0.126883097 54978.46192 -4.740192586 -0.212981464 FDPFGPIGTS(ph)PPGPRPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.24)S(0.76)PPGPRPDR;FDPFGPIGT(0.123)S(0.877)PPGPRPDR 113.17 0.00015433 205884000 119881 138866 108481 132530 139231 132086 135248 137103 131233 142157 TRUE FALSE 115195.918 134905.6776 128085.9298 139369.8892 143709.4916 134756.8694 136903.2055 134271.7751 116335.98 132528.5798 0.869215668 1.017936492 0.966477797 1.051621389 1.084366042 1.016813654 1.033008923 1.013153354 0.877818054 1 17.01594398 4.740209561 24.49771205 1.011331261 0.869215605 0.380208631 0.052412125 112.2390018 1667292.298 0.012466168 0.079366247 54980.61087 -4.740209561 -0.142115656 STDEVDSKR ddPTM_BT-474_Pertuzumab_2h_R1 2 STDEVDSKR 9 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 117.7 0.0017788 605420000 1056720 1255370 927200 1206050 1230040 1376710 1137600 1242310 1228690 1188640 FALSE TRUE 1015422.214 1219568.077 1094765.665 1268294.385 1269605.354 1404548.019 1151522.289 1216655.864 1089214.262 1108132.354 0.916336582 1.100561745 0.987937642 1.144533305 1.145716348 1.267491211 1.039155914 1.097933708 0.982927949 1 20.07969877 4.740215568 23.75594447 1.092588832 0.916336461 0.26260539 0.084029096 96.25705536 1381461.146 0.020049334 0.127389671 54981.37138 -4.740215568 -0.176252371 TPQAFVHPSEQDGER ddPTM_BT-474_Pertuzumab_2h_R1 1 TPQAFVHPSEQDGER 15 0 Q9BV44 Q9BV44 THUMPD3 THUMP domain-containing protein 3 0 93.226 0.0049386 716560000 135890 190810 151040 213690 149580 190300 190910 172750 183590 196210 FALSE TRUE 130579.2686 185368.2856 178336.2879 224718.5665 154391.3765 194147.9964 193246.4137 169182.6521 162749.6329 182920.5219 0.713857949 1.01338157 0.974938656 1.228503856 0.844035294 1.061378977 1.056450155 0.924897056 0.889728671 1 17.48085742 4.740288832 24.29553329 0.999579928 0.713857804 0.417932206 0.101042729 98.26909987 1381307.295 0.023270302 0.149049851 54990.64729 -4.740288832 -0.285722124 LLHMDS(ph)DDEIPIR ddPTM_BT-474_Pertuzumab_2h_R1 5 LLHMDSDDEIPIR 13 0 Q1MSJ5-1;Q1MSJ5;Q1MSJ5-2 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR 259.96 3.48E-24 502548000 469830 534607 460333 502410 507978 525353 477316 476968 583650 625718 TRUE FALSE 451468.5242 519360.5318 543525.4132 528339.4403 524317.5737 535975.9976 483157.536 467118.4441 517396.4989 583337.5625 0.77394043 0.890325885 0.931751096 0.905718188 0.89882361 0.918809334 0.828264057 0.80076867 0.886958996 1 19.15397145 4.740343496 24.2380915 0.884814105 0.773940372 0.308203009 0.052494112 146.0955927 1985905.675 0.013381708 0.085755502 54997.56937 -4.740343496 -0.110873733 S(ph)PDLEASLDTLENNCHVGSDIDFRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPDLEASLDTLENNCHVGSDIDFRPK 26 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.453)PDLEAS(0.363)LDT(0.184)LENNCHVGSDIDFRPK 141.13 1.84E-07 257630000 62528 75434 65816 65645 76252 66629 68557 72327 85069 79380 TRUE FALSE 60084.33663 73282.69618 77710.41527 69032.94632 78704.71483 67976.28403 69396.02107 70833.42217 75412.32376 74003.5219 0.811911854 0.990259575 1.05009077 0.932833256 1.063526611 0.918554716 0.937739439 0.957162853 1.019036957 1 16.17530631 4.740369682 24.71801662 0.981533361 0.811911787 0.549661977 0.047006951 104.4847353 1427485.463 0.010985747 0.070759743 55000.88555 -4.740369682 -0.169621573 SLPS(ph)SPERR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.077)LPS(0.615)S(0.308)PERR 64.439 0.042575 137040000 13502 42002 38510 46684 38257 52935 41230 29570 64097 59645 TRUE FALSE 12974.32691 40804.14408 45469.61365 49093.36683 39487.57115 54005.38197 41734.58507 28959.36917 56820.97728 55605.19102 0.233329419 0.733818971 0.817722461 0.882891794 0.710141813 0.971229142 0.750551959 0.520803339 1.021864618 1 15.76293195 4.74038268 3.492957013 0.79997577 0.163043858 0.593317172 0.14638391 0.21869297 4.640069349 0.036203349 0.369323332 55002.53164 -4.74038268 -0.636931912 NAINTEMYHEIMR ddPTM_BT-474_Pertuzumab_2h_R1 4 NAINTEMYHEIMR 13 0 A0A0C4DGA2;O75521-2;O75521;F1LLU7 A0A0C4DGA2 ECI2 "Enoyl-CoA delta isomerase 2, mitochondrial" 0 ;;; 274.09 3.69E-32 1899090000 1284480 1583190 1190360 1753220 1292610 1367720 1557290 1605950 1660140 1665840 FALSE TRUE 1234281.102 1538038.971 1405484.531 1843703.894 1334187.975 1395376.235 1576348.581 1572786.571 1471687.867 1553011.173 0.794766402 0.990359244 0.905006066 1.187180058 0.859097473 0.898497229 1.015027199 1.012733584 0.94763508 1 20.56663678 4.740392279 24.09249395 0.980904809 0.794766301 0.294110914 0.085834976 121.6815746 1600298.618 0.019786355 0.127277704 55003.74743 -4.740392279 -0.186138508 QLSES(ph)FK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLSESFK 7 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 1 QLS(0.001)ES(0.999)FK;QLS(0.001)ES(0.999)FK 94.804 0.014614 1621020000 3005400 1606100 1469420 1171620 1518230 1271340 1196580 3110000 1248960 958120 TRUE FALSE 2887945.645 1560295.601 1734976.881 1232087.449 1567065.247 1297047.366 1211224.104 3045777.413 1107183.297 893225.679 3.2331646 1.746810058 1.942372372 1.379368594 1.754388934 1.452093683 1.356011289 3.409863246 1.239533662 1 19.7686652 4.740454963 24.24431458 1.821418333 3.233165317 0.325595606 0.641059808 146.7022402 1877305.103 0.160034576 1.035227255 55011.68699 -4.740454963 1.411746985 ELSSTEAQLHDAQELLQEETR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELSSTEAQLHDAQELLQEETR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;;; 317.99 8.57E-67 956760000 634700 751430 596102 713250 703320 765710 726850 704910 758820 776040 FALSE TRUE 609895.2223 729999.9521 703830.8916 750060.918 725942.9265 781193.1808 735745.4077 690353.3622 672681.9348 723478.1196 0.843004378 1.009014554 0.97284337 1.036743058 1.003406885 1.079774439 1.016955991 0.954214569 0.929788914 1 19.46458986 4.740490852 24.79409241 1.00035187 0.843004319 0.584090392 0.039820797 119.1879527 1530852.54 0.010187923 0.067456685 55016.23314 -4.740490852 -0.157347551 EILNLIHLEELSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EILNLIHLEELSLR 14 0 Q96CX6 Q96CX6 LRRC58 Leucine-rich repeat-containing protein 58 0 107.98 0.00085245 63584000 71509 86027 67496 81395 81968 79673 84414 91221 80691 79290 FALSE TRUE 68714.34922 83573.59419 79694.02864 85595.8057 84604.57516 81284.04265 85447.08378 89337.25447 71531.29596 73919.61768 0.929582043 1.130601007 1.078117435 1.157957906 1.144548333 1.099627476 1.155945965 1.208573005 0.967690286 1 16.17366967 4.740638914 24.32387079 1.119552558 0.92958195 0.335018315 0.071372117 128.5873277 1504796.491 0.016192438 0.106516595 55034.99279 -4.740638914 -0.189970608 TLGEDDPWLDDTAAWIER ddPTM_BT-474_Pertuzumab_2h_R1 5 TLGEDDPWLDDTAAWIER 18 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ;;;; 251.84 4.22E-30 539355000 580540 624717.8 510476.8 605300 614241 587295 593069 633876 633731 629672 FALSE TRUE 557851.855 606901.46 602731.3133 636539.6055 633998.6196 599170.5073 600327.1558 620786.2391 561792.5137 587023.7546 0.950305419 1.033861842 1.026757961 1.084350677 1.080022085 1.020692097 1.022662458 1.057514682 0.957018365 1 19.16305936 4.74064344 5.245373356 1.036640131 0.94652384 0.307198385 0.035810558 0.182836597 17.44251809 0.008412711 0.059479231 55035.56631 -4.74064344 -0.090116291 RSVSDNDIR ddPTM_BT-474_Pertuzumab_2h_R1 6 RSVSDNDIR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 145.99 0.0001537 16927330000 13452540 14726090 11679570 14103380 13535750 13632000 14488640 15061180 14705730 15365640 FALSE TRUE 12926799.86 14306116.33 13790328.11 14831257.13 13971139.69 13907648.38 14665956.31 14750161.37 13036397.18 14324911.52 0.90239998 0.998687937 0.962681556 1.035347207 0.975303734 0.970871503 1.023807812 1.029686037 0.9100508 1 23.77202289 4.740646637 24.5294185 0.993336489 0.902399939 0.344328263 0.035768448 155.3503595 1826590.471 0.008276353 0.054761666 55035.97146 -4.740646637 -0.09093655 ISFEEFER ddPTM_BT-474_Pertuzumab_2h_R1 4 ISFEEFER 8 0 A0A494C1S7;Q9Y5Q9;Q9Y5Q9-2;F8WC64;H0YFI7 A0A494C1S7 GTF3C3 General transcription factor 3C polypeptide 3 0 ;;; 169.57 0.00069853 416330000 580770 667500 538650 587280 650060 614990 627320 691370 668900 730080 FALSE TRUE 558072.8663 648463.5536 635996.0372 617589.5912 670969.7703 627425.5192 634997.3298 677092.9679 592969.2763 680631.0313 0.819934503 0.952738743 0.934421159 0.907377952 0.985805436 0.921829141 0.932953833 0.994801789 0.871205174 1 19.3765134 4.740651573 24.77113142 0.945272607 0.819934454 0.484206655 0.038584936 132.9472356 1574873.292 0.008548057 0.056048203 55036.59706 -4.740651573 -0.125338153 VQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 VQIPVSRPDPEPVS(1)DNEEDS(0.439)Y(0.561)DEEIHDPR;VQIPVS(0.002)RPDPEPVS(0.979)DNEEDS(0.245)Y(0.773)DEEIHDPR 181.38 2.40E-17 4382750000 956460 1230530 978510 1197400 1093860 1198480 1094560 1236500 1319770 1234700 TRUE FALSE 919080.4858 1195436.489 1155348.524 1259197.957 1129045 1222714.087 1107955.553 1210965.843 1169955.243 1151072.669 0.798455658 1.038541285 1.00371467 1.093934372 0.980863355 1.062238831 0.962541795 1.052032487 1.016404328 1 20.13454749 4.740664533 24.96494242 1.024866429 0.798455579 0.764082333 0.037483395 77.01650043 913809.1079 0.008005516 0.052647787 55038.23945 -4.740664533 -0.22641085 ERESLNASIVDAINQAADCWGIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERESLNASIVDAINQAADCWGIR 23 1 A0A087WYB4;Q9UJZ1 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 148.28 9.84E-08 194780000 123420 175770 116780 227850 118730 140150 196150 202660 144520 138320 FALSE TRUE 118596.61 170757.2117 137884.7438 239609.3658 122549.0583 142983.929 198550.5424 198475.0002 128114.6955 128951.4632 0.919699606 1.32419755 1.069276302 1.858136076 0.950350273 1.108819749 1.539730822 1.539145003 0.993510987 1 16.97646862 4.740665775 23.10242769 1.302751229 0.919699241 0.10254781 0.287149414 132.7838242 1456873.587 0.06646978 0.433555423 55038.39683 -4.740665775 -0.383051988 YEKDVADYK ddPTM_BT-474_Pertuzumab_2h_R1 1 YEKDVADYK 9 1 O15347;E7ES08;E7EQU1 O15347 HMGB3 High mobility group protein B3 0 97.214 0.0062404 630610000 1201500 984280 777770 706150 889840 880850 904110 1036500 961940 923070 FALSE TRUE 1154544.052 956209.2981 918330.3404 742594.4861 918462.5117 898661.3905 915174.7686 1015095.913 852744.604 860549.6467 1.341635612 1.111161107 1.06714394 0.862930441 1.067297529 1.044287676 1.063477014 1.17959018 0.990930166 1 19.7148989 4.740697522 2.376050105 1.045397871 1.412485652 0.595316944 0.075847874 0.439702924 2.979958514 0.020542496 0.333445037 55042.42032 -4.740697522 0.367087781 SYSSGGEDGYVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SYSSGGEDGYVR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;; 210.08 1.11E-07 1004630000 608990 676290 566580 701090 664940 673940 691530 655680 705020 781280 FALSE TRUE 585189.9975 657002.8714 668973.6095 737273.3389 686328.399 687567.5286 699993.151 642139.9789 624989.0853 728363.2097 0.803431571 0.902026438 0.91846156 1.012233085 0.942288668 0.943989921 0.961049572 0.881620557 0.858073386 1 19.47429853 4.740705321 2.06509457 0.936522036 0.765499578 0.460511414 0.044576339 0.694180367 3.226433761 0.011861982 0.223093455 55043.40875 -4.740705321 -0.171022458 VEFMDDTSR ddPTM_BT-474_Pertuzumab_2h_R1 6 VEFMDDTSR 9 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;; 257.82 1.16E-14 7837860000 4681820 5127570 4283170 4914240 4718850 4765780 4903360 5022750 5297420 5449310 FALSE TRUE 4498849.298 4981336.724 5057234.098 5167864.515 4870636.096 4862147.337 4963368.786 4919028.457 4696079.09 5080223.38 0.885561315 0.980534979 0.99547475 1.017251433 0.958744475 0.957073533 0.976998139 0.968270111 0.92438437 1 22.2764605 4.740713758 24.86835144 0.975026826 0.885561282 0.545348877 0.024610298 140.8627575 1626817.055 0.005980003 0.039513394 55044.47812 -4.740713758 -0.089465544 TVFAEHISDECKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVFAEHISDECKR 13 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 184.21 6.30E-06 766500000 888120 1162260 891430 1147760 920110 1272850 1139670 1055440 1167180 1319940 FALSE TRUE 853411.2885 1129113.483 1052531.231 1206996.031 949706.1738 1298587.899 1153617.622 1033644.795 1034686.62 1230539.288 0.693526242 0.917576134 0.855341427 0.980867529 0.771780457 1.055299828 0.937489468 0.839993331 0.840839971 1 20.23085929 4.740735619 23.94850131 0.904913864 0.693526107 0.386129914 0.08194501 112.8589292 1242506.393 0.018595521 0.122902564 55047.24892 -4.740735619 -0.211387757 SSQHGGS(ph)STSLASTK ddPTM_BT-474_Pertuzumab_2h_R1 6 SSQHGGSSTSLASTK 15 0 O15075-2;O15075;O15075-3;O15075-4 O15075-2 DCLK1 Serine/threonine-protein kinase DCLK1 1 S(0.057)S(0.057)QHGGS(0.728)S(0.127)T(0.028)S(0.002)LASTK;S(0.021)S(0.021)QHGGS(0.905)S(0.052)T(0.001)SLASTK;SSQHGGS(0.972)S(0.008)T(0.019)S(0.002)LASTK;S(0.004)S(0.004)QHGGS(0.626)S(0.365)T(0.002)SLASTK;S(0.023)S(0.023)QHGGS(0.904)S(0.036)T(0.012)S(0.002)LASTK;SSQHGGS(0.873)S(0.056)T(0.056)S(0.015)LASTK 303.41 1.77E-44 2905851000 1479918 2388900 1715454 2448760 2190730 2167080 2238060 2477710 2240430 2313860 TRUE FALSE 1422081.168 2320770.911 2025474.698 2575140.797 2261196.82 2210899.842 2265450.048 2426544.423 1986105.779 2157140.201 0.659243737 1.075855389 0.938962937 1.193775349 1.048238227 1.024921719 1.050209924 1.124889528 0.920712422 1 21.04068852 4.740793011 24.96396021 1.050768635 0.659243599 0.688793301 0.076968528 103.6762259 1159293.407 0.017306531 0.115241253 55054.52383 -4.740793011 -0.391525036 RDDASMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDDASMDR 8 1 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;H7C0E9;V9GYY9 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 0 69.825 0.055533 116690000 95612 127660 102380 124510 107400 118500 122640 123730 135310 139390 FALSE TRUE 91875.37734 124019.2618 120882.3434 130935.976 110854.6185 120896.1512 124140.905 121174.9323 119950.1761 129948.9911 0.707011086 0.954368793 0.93022918 1.007595172 0.853062556 0.930335435 0.955304877 0.932480746 0.923055847 1 16.98758591 4.740796155 24.79453908 0.939549395 0.707010995 0.74930059 0.040897549 84.05139858 932152.5422 0.009160768 0.061086481 55054.92236 -4.740796155 -0.2325384 ERDPQQEQER ddPTM_BT-474_Pertuzumab_2h_R1 4 ERDPQQEQER 10 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 0 ;;; 146.36 2.63E-05 372278000 197997 225979 191270 219643 228640 216933 225134 226805 232725 242368 FALSE TRUE 190259.0583 219534.3002 225836.7438 230978.8016 235994.4132 221319.5339 227889.2572 222121.3975 206307.0337 225952.1995 0.842032336 0.971596208 0.999489026 1.022246307 1.044443974 0.979497143 1.008572865 0.983045963 0.913056098 1 17.78565808 4.740815835 3.025248102 0.995410513 0.816829725 0.660166642 0.032457922 0.229639514 3.108917279 0.008133562 0.099057932 55057.41728 -4.740815835 -0.178580789 DTFNHLTTWLEDAR ddPTM_BT-474_Pertuzumab_2h_R1 5 DTFNHLTTWLEDAR 14 0 P61019;P61019-2;E9PKL7;H7C125 P61019 RAB2A Ras-related protein Rab-2A 0 ;;;; 203.04 1.56E-08 1864688000 1455429 2217023 1566146 2360402 1852928 1726411 2260214 2303744 2326431 2309539 FALSE TRUE 1398549.226 2153795.675 1849183.421 2482222.63 1912529.112 1761320.213 2287875.175 2256170.881 2062344.306 2153111.866 0.649547869 1.000317591 0.858842241 1.152853537 0.888262771 0.818034697 1.062590017 1.047865147 0.957843546 1 21.03799185 4.740841229 24.48346702 0.97915794 0.649547714 0.510973123 0.095857541 127.2669218 1366150.432 0.022889816 0.152905975 55060.63675 -4.740841229 -0.329610226 EYVESQLQR ddPTM_BT-474_Pertuzumab_2h_R1 4 EYVESQLQR 9 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 185.58 9.93E-05 1664580000 957360 1145740 964440 1123920 1067850 996290 1117080 1170580 1055510 1155830 FALSE TRUE 919945.3128 1113064.617 1138735.762 1181925.646 1102198.365 1016435.666 1130751.159 1146407.114 935692.9299 1077544.605 0.853742211 1.032963844 1.056787586 1.096869346 1.022879573 0.943288716 1.049377589 1.063906876 0.868356563 1 20.03931616 4.740858779 24.02955112 1.022263212 0.853742107 0.365473976 0.06305724 125.0293313 1307153.257 0.014811362 0.098353942 55062.86174 -4.740858779 -0.168521105 ENDPMDSHQSQES(ph)PNLENIANPLEENVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENDPMDSHQSQESPNLENIANPLEENVTK 29 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 ENDPMDSHQSQES(1)PNLENIANPLEENVTK;ENDPMDSHQS(0.035)QES(0.965)PNLENIANPLEENVTK 206.33 6.38E-26 225710000 165779 252600 193055 305790 197177 255233 262153 234045 249230 262610 TRUE FALSE 159300.1734 245396.0953 227944.333 321571.8585 203519.3773 260393.9861 265361.3068 229211.889 220938.4553 244823.1908 0.650674362 1.002340075 0.931056949 1.313486102 0.831291254 1.063600165 1.083889586 0.936234383 0.902440878 1 17.9013807 4.740873373 5.674498586 1.009484622 0.638460561 0.423425534 0.124785486 0.134999957 18.08874014 0.028421276 0.193324831 55064.71213 -4.740873373 -0.371024061 LYDCQEEEIPELEIDVDELLDMESDDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LYDCQEEEIPELEIDVDELLDMESDDAR 28 0 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 ;;; 205.26 2.19E-25 405596000 347105 370272 279281 357641 369866 385499 330979 357607 385706 384433 FALSE TRUE 333539.7529 359712.2051 329753.2893 376098.8949 381763.0758 393294.0539 335029.62 350222.2905 341922.2719 358395.0105 0.930648427 1.003675259 0.920083371 1.049397687 1.065201983 1.097375919 0.934805481 0.977196334 0.954037478 1 18.45119103 4.740882972 22.76022603 0.999487607 0.930648344 0.128625901 0.05427775 140.6391166 1377987.746 0.013772252 0.090947893 55065.92924 -4.740882972 -0.068839263 RQS(ph)FAVLR ddPTM_BT-474_Pertuzumab_2h_R1 4 RQSFAVLR 8 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR 158.05 0.00022495 2232680000 2949970 447982 202921 355027 400696 330767 605016 1692400 284551 269942 TRUE FALSE 2834681.911 435205.992 239593.3387 373349.986 413584.7507 337455.3354 612420.3668 1657451.349 252249.9634 251658.5879 11.26399832 1.729350846 0.952057073 1.483557502 1.643435872 1.340925172 2.43353653 6.586110819 1.002349912 1 17.94110831 4.740884169 24.94600305 2.324986027 11.26400153 0.744899761 1.614141515 120.0510608 1288803.354 0.442690871 2.966482599 55066.08098 -4.740884169 8.939015499 ICYIFHETFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ICYIFHETFGR 11 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ; 193.83 7.79E-07 635500000 729500 933760 715560 1016740 882110 834700 936950 827610 878280 1031790 FALSE TRUE 700990.3335 907130.079 844877.6095 1069214.073 910483.8693 851578.2059 948416.6744 810519.5643 778581.3365 961905.9443 0.728751431 0.943054864 0.878337029 1.111557819 0.946541473 0.885302987 0.985976519 0.842618313 0.809415246 1 19.87553631 4.740888876 24.48653122 0.929872433 0.728751336 0.355413254 0.08263916 187.6754541 1973631.899 0.020065603 0.134924782 55066.6778 -4.740888876 -0.201121097 YIDTEHGGSQAR ddPTM_BT-474_Pertuzumab_2h_R1 4 YIDTEHGGSQAR 12 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;; 169.98 4.24E-05 2095650000 2074730 2695140 2179690 2618650 2514570 2723150 2520740 2400160 2796860 2778870 FALSE TRUE 1993647.258 2618277.246 2573608.47 2753798.84 2595453.428 2778213.959 2551589.57 2350595.857 2479372.178 2590654.66 0.76955346 1.010662396 0.993420123 1.062974113 1.001852338 1.072398418 0.984920765 0.907336626 0.957044648 1 21.30488528 4.74089877 24.9043743 0.995535179 0.769553377 0.701361791 0.044857873 130.0293526 1384891.612 0.012350051 0.082817023 55067.93228 -4.74089877 -0.225981802 QFHDSK ddPTM_BT-474_Pertuzumab_2h_R1 5 QFHDSK 6 0 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;;; 116.54 0.023486 3087774000 5042777 8281226 6386260 9305730 6806220 8568130 8328835 6715763 7071262 9365242 FALSE TRUE 4845699.7 8045053.543 7540399.244 9785999.841 7025148.248 8741383.459 8430765.774 6577080.147 6268561.983 8730925.818 0.555004108 0.921443351 0.863642574 1.120843315 0.8046281 1.00119777 0.965621052 0.753308445 0.717972196 1 23.05770321 4.740900797 24.18316631 0.899058385 0.555003914 0.442174067 0.117876424 131.8650228 1362538.285 0.02855698 0.191203023 55068.18931 -4.740900797 -0.344054471 MDPMNIWDDIITNR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDPMNIWDDIITNR 14 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 162.32 1.04E-05 351230000 88651 106873 92035 97616 119683 113823 106350 105682 105559 104615 FALSE TRUE 85186.42091 103825.0867 108667.7718 102653.9735 123532.7124 116124.579 107651.5431 103499.6298 93576.38486 97529.33287 0.873444106 1.064552413 1.11420604 1.052544608 1.266621115 1.190663113 1.103786317 1.061215398 0.959469137 1 16.57354857 4.740923462 2.950407592 1.102044781 0.834080834 0.37765046 0.083659591 0.421096312 5.288208141 0.021341592 0.268251524 55071.06333 -4.740923462 -0.267963947 RGDLPFVVPR ddPTM_BT-474_Pertuzumab_2h_R1 6 RGDLPFVVPR 10 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 190.57 1.42E-06 9090460000 2031689 2274020 1788662 2141900 2191086 2147160 2204810 2274270 2248650 2355360 FALSE TRUE 1952288.348 2209167.176 2111913.012 2252443.716 2261564.271 2190577.046 2231793.124 2227305.53 1993392.679 2195829.369 0.889089278 1.006074154 0.961783753 1.025782671 1.029936252 0.997608046 1.01637821 1.01433452 0.907808552 1 21.06633452 4.740937556 24.74395201 0.998665672 0.889089233 0.458300841 0.03456227 163.016781 1696886.588 0.007981757 0.053810248 55072.85059 -4.740937556 -0.109576439 (ac)AAAVAAAGAGEPQS(ph)PDELLPK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAAVAAAGAGEPQSPDELLPK 21 0 Q9NS69 Q9NS69 TOMM22 Mitochondrial import receptor subunit TOM22 homolog 1 AAAVAAAGAGEPQS(1)PDELLPK;AAAVAAAGAGEPQS(1)PDELLPK;AAAVAAAGAGEPQS(1)PDELLPK 72.175 1.40E-17 143893000 90379 166344 102021 218578 96578 143743 178975 186152 167037 108401 TRUE FALSE 86846.88876 161600.032 120458.4641 229858.8368 99684.51908 146649.5819 181165.3496 182307.8961 148075.66 101058.9037 0.859368997 1.599067732 1.191962902 2.274503565 0.986400163 1.451129753 1.792670838 1.803976586 1.465241108 1 16.62483691 4.740944643 24.30287991 1.552876543 0.859368631 0.201980752 0.37660201 212.2790919 2163779.036 0.084817423 0.569361742 55073.74922 -4.740944643 -0.693507912 ADEICIAGS(ph)PLTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADEICIAGSPLTPR 14 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 ADEICIAGS(1)PLTPR;ADEICIAGS(0.993)PLT(0.007)PR 213.55 9.19E-10 448540000 400560 523720 402000 509680 492000 546770 478200 491310 540160 503990 TRUE FALSE 384905.6724 508784.0184 474650.3424 535984.6459 507825.6268 557826.064 484052.3546 481164.2768 478843.3013 469854.3084 0.819202177 1.082854854 1.010207492 1.140746475 1.08081509 1.187231987 1.030217976 1.024071224 1.019131447 1 18.84185395 4.740957715 24.4913905 1.066186348 0.81920206 0.616500441 0.057878266 110.8301833 1132268.775 0.01407278 0.094683638 55075.40692 -4.740957715 -0.246984288 MESGIEPSVDLETLDER ddPTM_BT-474_Pertuzumab_2h_R1 2 MESGIEPSVDLETLDER 17 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 ; 262.64 5.49E-27 105999000 62967 79932 61367 71024 77816 82003 73895 77416 75532 91667 FALSE TRUE 60506.18003 77652.41762 72457.382 74689.55715 80319.02231 83661.15684 74799.34911 75817.33255 66957.92402 85458.31244 0.708019832 0.908658449 0.847868159 0.873988206 0.939862022 0.978970383 0.875272949 0.887184996 0.783515636 1 16.38293321 4.740992648 24.47214985 0.895809505 0.708019743 0.478961629 0.059797742 144.2439608 1451322.477 0.013909622 0.093685165 55079.83727 -4.740992648 -0.187789762 YLGEGPR ddPTM_BT-474_Pertuzumab_2h_R1 4 YLGEGPR 7 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 100.07 0.041126 771950000 746918 867798 668740 856810 856377 804387 842256 822230 880762 893172 FALSE TRUE 717727.6188 843049.2507 789596.194 901030.0668 883923.1439 820652.2563 852563.7809 805250.6632 780781.5902 832676.6649 0.861952363 1.012456919 0.948262666 1.082088768 1.061544272 0.98555933 1.023883359 0.967062843 0.9376768 1 19.66739687 4.741046189 24.67392526 1.002545356 0.861952303 0.480872983 0.043669359 174.3889747 1731009.973 0.010798666 0.073633487 55086.628 -4.741046189 -0.140593053 EIYDDLQALHTDDPLTWDYVAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EIYDDLQALHTDDPLTWDYVAR 22 0 Q9NYH9 Q9NYH9 UTP6 U3 small nucleolar RNA-associated protein 6 homolog 0 127.01 1.88E-05 41870000 32244 40438 34429 45648 39494 37622 39388 35834 49125 48449 FALSE TRUE 30983.86883 39284.74783 40651.08617 48003.89875 40764.36038 38382.74262 39870.04213 35094.01538 43548.53595 45167.50608 0.685976967 0.869756851 0.900007322 1.062797195 0.902515191 0.849786627 0.882715155 0.776974831 0.964156309 1 15.46299764 4.741075243 3.028522636 0.902799294 0.65042501 0.444547109 0.076074811 0.398004711 5.403400437 0.019931573 0.242870662 55090.31341 -4.741075243 -0.252374283 GSEVGFHGAAPDISVK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSEVGFHGAAPDISVK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 105.31 0.0012932 248790000 282110 322420 250550 335960 257430 312820 290560 331370 345160 350960 FALSE TRUE 271084.8293 313224.8973 295829.9585 353298.9359 265710.4697 319145.4347 294115.9602 324527.0937 305978.8838 327189.1666 0.828526299 0.957320502 0.904155726 1.079800225 0.812100451 0.975415653 0.898917172 0.991863811 0.935174251 1 18.31976546 4.741108737 23.76831949 0.948933847 0.828526215 0.226121467 0.067651917 168.6472866 1572912.488 0.014685105 0.099380757 55094.56233 -4.741108737 -0.120407632 KVQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVQIPVSRPDPEPVSDNEEDSYDEEIHDPR 30 2 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 KVQIPVSRPDPEPVS(1)DNEEDS(0.159)Y(0.841)DEEIHDPR;KVQIPVSRPDPEPVS(1)DNEEDS(0.219)Y(0.781)DEEIHDPR 167.97 5.60E-12 1247140000 667820 703310 547400 618040 689790 767870 639210 689260 751610 699810 TRUE FALSE 641720.8561 683252.2874 646327.3568 649937.1185 711977.7218 783396.8575 647032.8432 675026.5401 666290.3838 652411.2454 0.983614033 1.047272395 0.990674764 0.996207719 1.091302038 1.200771543 0.991756117 1.034664171 1.021273604 1 19.31542212 4.741150694 21.82594601 1.043382877 0.98361391 0.074405517 0.060990524 119.3019828 1004920.762 0.01515873 0.101241575 55099.88522 -4.741150694 -0.059768967 GNDPLTSS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 8 GNDPLTSSPGR 11 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 GNDPLTSS(1)PGR;GNDPLTSS(1)PGR;GNDPLTSS(1)PGR;GNDPLTS(0.001)S(0.999)PGR;GNDPLT(0.009)S(0.281)S(0.709)PGR;GNDPLT(0.009)S(0.099)S(0.892)PGR;GNDPLTSS(1)PGR;GNDPLTS(0.011)S(0.989)PGR 164.06 2.44E-05 28243370000 5355530 5971680 4951670 6304610 5922930 6232460 6170790 5707040 6134150 6611180 TRUE FALSE 5146229.967 5801373.533 5846546.918 6629991.678 6113446.423 6358484.611 6246309.974 5589187.63 5437827.008 6163398.89 0.834966235 0.94126206 0.948591357 1.075703811 0.991895305 1.031652295 1.013452169 0.906835292 0.882277312 1 22.55529473 4.741154505 1.87253803 0.981412204 0.788833546 0.404413778 0.053970636 0.931774871 3.353251908 0.015266143 0.314950583 55100.36875 -4.741154505 -0.192578658 ADLIPYQDS(ph)PEGPDHSSASSGVPNPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ADLIPYQDSPEGPDHSSASSGVPNPPK 27 0 Q8WUA4;H0Y4Q6;H7C318 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 ADLIPYQDS(1)PEGPDHSSASSGVPNPPK 201.85 2.82E-25 424020000 237170 310230 251550 306170 287350 301950 289420 310790 329270 362090 TRUE FALSE 227901.1342 301382.5441 297010.6807 321971.4704 296592.8737 308055.6359 292962.0085 304372.0779 291892.65 337565.3218 0.675131951 0.892812516 0.879861353 0.953804937 0.878623646 0.912580813 0.867867609 0.901668679 0.864699752 1 18.36480718 4.741211477 4.926258364 0.901785077 0.663035634 0.749072104 0.040018809 0.078230605 5.751250726 0.008630326 0.06396656 55107.59736 -4.741211477 -0.238749442 TYGADLASVDFQHASEDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TYGADLASVDFQHASEDAR 19 0 P30740 P30740 SERPINB1 Leukocyte elastase inhibitor 0 ; 249.14 5.58E-25 593200000 271420 410080 285860 473370 399660 389390 364970 347780 397550 455250 FALSE TRUE 260812.6063 398384.9199 337521.2609 497800.6824 412515.4269 397263.7326 369436.612 340598.2215 352421.7907 424415.512 0.614521852 0.938667199 0.795261369 1.172908785 0.971961239 0.936025478 0.87045973 0.802511246 0.830369722 1 18.69511786 4.74123965 24.46872863 0.915959383 0.614521705 0.429243679 0.106758899 195.0270862 1781128.502 0.026819925 0.184534032 55111.17233 -4.74123965 -0.301437679 DAADKPR ddPTM_BT-474_Pertuzumab_2h_R1 6 DAADKPR 7 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;; 129.4 0.003342 6694580000 10580610 9505690 7402820 8676610 8482680 8843550 9548320 9263660 9118820 11296780 FALSE TRUE 10167108.06 9234597.028 8740674.249 9124410.882 8755533.106 9022372.64 9665175.196 9072362.184 8083689.783 10531639.03 0.965387062 0.876843291 0.829944344 0.866380898 0.831355222 0.856692165 0.917727542 0.861438771 0.767562367 1 23.32822664 4.74125816 0.003974289 1.726222756 2.33E-07 0.031549473 0.063503374 256261.7061 158.1910342 33365.22972 35365.14004 55113.52131 -4.74125816 -1.726222523 T(ph)SSGTSLSAMHSSGSSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSGTSLSAMHSSGSSGK 18 0 Q12888;Q12888-2;A6NNK5;Q12888-3;M0R142 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.354)S(0.354)S(0.278)GT(0.006)S(0.006)LS(0.001)AMHSSGSSGK;T(0.354)S(0.354)S(0.278)GT(0.006)S(0.006)LS(0.001)AMHSSGSSGK 132.14 5.68E-05 370420000 214221 397430 301040 420500 338820 420640 360640 355290 330860 421650 TRUE FALSE 205849.0065 386095.6855 355444.6246 442202.0554 349718.453 429145.629 365053.6202 347953.1373 293302.1599 393091.2699 0.523667205 0.982203664 0.904229251 1.124934816 0.889662223 1.091720071 0.928673945 0.885171368 0.746142645 1 18.5845048 4.741275514 24.8178526 0.949255877 0.523667035 0.606713538 0.103045569 153.7291426 1405207.813 0.024303589 0.167852191 55115.72367 -4.741275514 -0.425588842 DYVAVAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DYVAVAR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 88.734 0.042782 1265800000 1043960 1081220 854990 1053210 1043720 943030 1111480 1060730 1084250 1164790 FALSE TRUE 1003160.889 1050384.664 1009505.712 1107566.294 1077292.202 962098.7127 1125082.625 1038825.555 961170.4855 1085897.736 0.923807884 0.967296118 0.929650812 1.019954511 0.992075189 0.885993847 1.036085248 0.956651368 0.885139046 1 20.05045681 4.741287465 22.1517967 0.96446968 0.923807813 0.056033917 0.048954161 164.9419443 1339504.116 0.011138089 0.075543236 55117.2404 -4.741287465 -0.040661867 RPSASS(ph)PNNNTAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RPS(0.123)AS(0.047)S(0.83)PNNNTAAK;RPS(0.219)AS(0.212)S(0.569)PNNNTAAK 141.84 5.86E-06 525760000 339920 275708 225469 244681 274659 211778 280310 304090 263331 256312 TRUE FALSE 326635.5506 267845.0778 266216.2638 257309.0157 283493.6562 216060.2963 283740.5176 297810.4352 233438.7689 238951.7599 1.366951851 1.120916949 1.114100452 1.076824108 1.186405391 0.904200481 1.187438493 1.246320326 0.976928435 1 17.86635987 4.741303718 4.411840612 1.105257253 1.385929777 0.396579072 0.101043579 0.22347784 10.69070002 0.02434553 0.196768368 55119.3031 -4.741303718 0.280672523 SVFEPEDSSIVDNELWSEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVFEPEDSSIVDNELWSEMR 20 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 0 136.51 3.78E-07 0 26515 33227 27050 31282 30883 31654 33996 32327 30980 30481 FALSE TRUE 25478.76449 32279.39849 31938.53672 32896.46777 31876.37974 32294.06557 34412.05322 31659.43615 27463.28028 28416.49472 0.896618838 1.135938785 1.123943577 1.157653964 1.121756221 1.136454932 1.210988672 1.114121797 0.966455594 1 14.79444098 4.741316066 24.1674696 1.118927558 0.896618708 0.447136687 0.069295958 136.0729046 1193359.724 0.015892987 0.109567307 55120.87027 -4.741316066 -0.22230885 FELDTSER ddPTM_BT-474_Pertuzumab_2h_R1 1 FELDTSER 8 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 121.74 0.0033039 161890000 222540 370930 259260 467140 246850 288950 362260 437630 325570 301030 FALSE TRUE 213842.8908 360351.4396 306114.0492 491249.1514 254790.1544 294792.767 366693.4462 428592.7876 288612.6585 280640.97 0.761980301 1.284030053 1.0907675 1.750454153 0.907886523 1.050426696 1.306628345 1.527192511 1.028405291 1 18.09836611 4.741354513 23.43759264 1.247495069 0.761979862 0.220840669 0.249803453 153.3772851 1286479.867 0.05849062 0.401058657 55125.75029 -4.741354513 -0.485515207 SSGNSSSSGSGSGSTSAGSS(ph)SPGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGSTS(0.001)AGS(0.26)S(0.37)S(0.37)PGAR;SSGNSSSSGSGSGSTSAGS(0.07)S(0.465)S(0.465)PGAR 113.73 0.00208 226760000 152568 224970 143880 286310 157694 177676 216490 275510 213602 164254 TRUE FALSE 146605.4739 218554.0759 169882.3166 301086.4934 162766.3707 181268.7305 219139.4694 269820.6222 189354.7965 153128.9303 0.957398929 1.427255291 1.109407062 1.966228673 1.062936771 1.183765407 1.43107817 1.762048633 1.236571013 1 17.22438735 4.741355045 23.35566324 1.394469124 0.957398517 0.124957691 0.29674007 192.1585596 1605813.876 0.069085743 0.473685324 55125.81779 -4.741355045 -0.437070607 AALS(ph)SSELLELGDSLMR ddPTM_BT-474_Pertuzumab_2h_R1 9 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 AALS(0.495)S(0.495)S(0.011)ELLELGDSLMR;AALS(0.97)S(0.024)S(0.006)ELLELGDSLMR;AALS(0.978)S(0.021)SELLELGDSLMR;AALS(0.969)S(0.027)S(0.004)ELLELGDSLMR;AALS(0.974)S(0.025)S(0.001)ELLELGDSLMR;AALS(0.97)S(0.029)S(0.001)ELLELGDSLMR;AALS(0.945)S(0.022)S(0.033)ELLELGDSLMR;AALS(0.962)S(0.019)S(0.019)ELLELGDSLMR;AALS(0.933)S(0.03)S(0.037)ELLELGDSLMR 283.31 4.47E-36 411472000 346384.7 388686.3 316955 392170 367078.1 359278 343074 434612 363245.1 409282 TRUE FALSE 332847.603 377601.3473 374235.8191 412409.9407 378885.5005 366542.8473 347272.6422 425637.1103 322011.0391 381560.9656 0.872331378 0.98962258 0.98080216 1.0808494 0.992988106 0.960640318 0.910136711 1.11551534 0.843930769 1 18.54155406 4.741358588 4.946942861 0.994279036 0.865890465 0.171930289 0.072956116 0.280148459 20.94051315 0.016694411 0.12360445 55126.26753 -4.741358588 -0.128388571 MS(ph)PPPSGFGER ddPTM_BT-474_Pertuzumab_2h_R1 1 MSPPPSGFGER 11 0 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 MS(0.998)PPPS(0.002)GFGER 62.338 0.0856 188190000 150990 216490 167740 201510 190910 199800 209300 214620 214440 231440 TRUE FALSE 145089.1439 210315.9172 198054.3494 211909.9552 197050.7935 203840.0929 211861.476 210188.022 190097.6702 215764.3627 0.672442576 0.974748168 0.917919655 0.982136033 0.913268489 0.944734758 0.981911347 0.974155414 0.881042948 1 17.71909707 4.741366168 24.96288141 0.952237207 0.672442473 0.845584662 0.035866555 87.3824887 777459.6665 0.008017902 0.055863852 55127.22959 -4.741366168 -0.279794734 LSFQHDPETSVLVLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSFQHDPETSVLVLR 15 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 182.35 5.50E-07 5552990000 2696380 4096770 3291040 4265400 3669870 4088070 3834960 3464870 3869040 4354850 FALSE TRUE 2591002.489 3979934.131 3885804.137 4485537.805 3787914.701 4170733.576 3881893.388 3393319.224 3429842.8 4059892.131 0.638194909 0.980305388 0.957120045 1.104841622 0.933008706 1.027301574 0.95615678 0.835815119 0.844811313 1 21.95300997 4.741389087 24.76388219 0.954827255 0.638194778 0.619002196 0.075628714 169.9811274 1488132.811 0.019767895 0.136935204 55130.1389 -4.741389087 -0.316632478 PLELELCPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 PLELELCPGR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 157.91 0.0098592 0 116370 97526 83188 88393 95794 76390 109180 100420 105820 100720 FALSE TRUE 111822.1317 94744.65397 98221.92211 92954.97332 98875.30101 77934.65814 110516.1775 98346.29191 93807.75723 93898.14469 1.190887553 1.009015186 1.046047528 0.989955378 1.053005907 0.829991459 1.176979352 1.047372046 0.999037388 1 16.51880903 4.741396235 24.11379097 1.022268002 1.190887651 0.292533389 0.080809429 211.516122 1798549.393 0.018665457 0.129347156 55131.0463 -4.741396235 0.168619649 EVS(ph)PGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSPGSR 7 0 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 EVS(1)PGSR 83.168 0.023613 86264000 69547 81769 63930 83820 70785 69997 82555 87915 72477 83875 TRUE FALSE 66829.02635 79437.02818 75483.57312 88145.96025 73061.86381 71412.3873 83565.33278 86099.52453 64249.71481 78194.07154 0.854655923 1.015895791 0.965336267 1.127271653 0.934365769 0.91327112 1.068691413 1.101100414 0.821669898 1 16.25477161 4.741400693 24.2265643 1.00408353 0.854655837 0.178050337 0.087636475 278.0482451 2371622.346 0.020651269 0.142218686 55131.61223 -4.741400693 -0.149427693 DLEELEVILRD ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEELEVILRD 11 1 Q96TC7;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 0 ; 157.24 0.00062904 25420000 56116 68507 52648 78942 52217 63113 69468 65891 67414 68181 FALSE TRUE 53922.92468 66553.24744 62162.66475 83016.20608 53896.60723 64389.1881 70318.17016 64530.32782 59761.44534 63563.04014 0.848337722 1.047043176 0.977968716 1.306045241 0.847923685 1.012997301 1.106274496 1.015217769 0.940191741 1 15.95590051 4.741411781 24.19338978 1.032452282 0.848337615 0.184699574 0.1130379 279.5763964 2372125.057 0.025587152 0.177893585 55133.01988 -4.741411781 -0.184114667 DSQDGSSYR ddPTM_BT-474_Pertuzumab_2h_R1 11 DSQDGSSYR 9 0 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;;;;;; 230.41 2.12E-07 19075366000 18527861 19410508 15908835 18589387 18112744 17800294 18754819 19418270 20263996 19948434 FALSE TRUE 17803771.71 18856939.32 18783915.37 19548787.49 18695356.86 18160228.14 18984346.09 19017275.94 17963712.13 18597308.8 0.957330542 1.01396065 1.010034064 1.051162171 1.005272164 0.976497639 1.020811468 1.022582146 0.965930734 1 24.14859053 4.741451054 24.57770683 1.009687992 0.957330518 0.299373556 0.022711512 256.0594026 2177159.98 0.005383889 0.03695806 55138.0057 -4.741451054 -0.052357475 GASFEELCHNYTQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GASFEELCHNYTQDR 15 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 238.07 9.32E-18 670650000 325390 410200 313330 395840 386920 416070 387860 371300 401400 460550 FALSE TRUE 312673.3991 398501.4976 369955.701 416269.3498 399365.6332 424483.2205 392606.7467 363632.5252 355834.7548 429356.5383 0.72823719 0.928136553 0.86165149 0.969519066 0.930149183 0.988649718 0.914407286 0.846924392 0.828762865 1 18.71181664 4.741452294 24.58184416 0.913043915 0.728237105 0.509866616 0.055772347 188.9134748 1605827.638 0.013777051 0.096113502 55138.16317 -4.741452294 -0.184806809 TTSFFLNS(ph)PEKEHQEMDEGSQSLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TTSFFLNSPEKEHQEMDEGSQSLEK 25 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 T(0.001)T(0.001)SFFLNS(0.998)PEKEHQEMDEGSQSLEK;TTSFFLNS(0.999)PEKEHQEMDEGSQSLEK 380.24 1.08E-120 1499060000 1735700 1180950 915040 900160 1255240 871850 1103060 1220550 1206050 1098310 TRUE FALSE 1667866.925 1147270.462 1080408.083 946617.3655 1295615.935 889479.4044 1116559.578 1195345.216 1069144.26 1023920.485 1.62890278 1.120468316 1.055167953 0.924502809 1.265348192 0.868699686 1.09047489 1.167419964 1.044167272 1 19.96567225 4.741462243 3.6592153 1.062770685 1.69315516 0.721353437 0.106733153 0.140022469 3.456299412 0.024776607 0.241836447 55139.42632 -4.741462243 0.630384474 T(ph)DVNLENGLEPAETHSMVRHKDGGY(ph)SEEEDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDVNLENGLEPAETHSMVRHKDGGYSEEEDVK 32 2 Q8WYP3-2;Q8WYP3;E7EPJ1 Q8WYP3-2 RIN2 Ras and Rab interactor 2 2 T(0.268)DVNLENGLEPAET(0.404)HS(0.407)MVRHKDGGY(0.625)S(0.297)EEEDVK 70.178 0.0026321 153000000 178510 111360 113170 84048 105680 117680 105980 57708 247620 136190 TRUE FALSE 171533.6318 108184.1218 133622.3365 88385.72735 109079.2932 120059.5702 107277.0149 56516.30963 219511.2157 126965.73 1.351023082 0.852073405 1.052428371 0.696138457 0.8591239 0.945606111 0.844928903 0.445130427 1.728901301 1 16.95407962 4.74149182 23.33376982 0.888426719 1.351023531 0.120046642 0.31409725 195.5890679 1556759.05 0.07129539 0.493841152 55143.18155 -4.74149182 0.462596812 EANFTVSSMHGDMPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EANFTVSSMHGDMPQK 16 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 185.99 1.57E-09 631640000 350990 487160 391520 503070 421690 466650 458190 436810 469130 541410 FALSE TRUE 337272.9228 473266.6738 462276.3733 529033.503 435254.0418 476085.9827 463797.4663 427789.7209 415876.3292 504739.8185 0.668211444 0.937644815 0.915870626 1.048131104 0.862333475 0.943230483 0.918884244 0.847545023 0.823941987 1 18.94518038 4.741554182 24.82424653 0.916455881 0.668211344 0.580218635 0.064596314 190.5750414 1580263.035 0.015580588 0.110030719 55151.1004 -4.741554182 -0.248244538 DQEGQDVLLFIDNIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQEGQDVLLFIDNIFR 16 0 P06576;H0YH81;F8W0P7 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 96.591 0.0078187 119050000 8274.4 10785 8198.6 11582 9538.9 8222.7 11411 12092 9178.7 8873.7 FALSE TRUE 7951.0273 10477.42236 9680.269397 12179.74841 9845.727382 8388.968628 11550.65123 11842.29597 8136.772456 8272.676395 0.961119101 1.266509393 1.170149651 1.472286335 1.19015019 1.014057389 1.396241153 1.43149513 0.98357195 1 13.01413843 4.741564413 23.15038102 1.2439155 0.961118794 0.141416558 0.173058761 169.4060683 1305415.518 0.040698265 0.282425061 55152.39959 -4.741564413 -0.282796706 T(ph)YSDTDSCSDIPLEDPDRPVHCSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TYSDTDSCSDIPLEDPDRPVHCSK 24 1 Q9HB20 Q9HB20 PLEKHA3 Pleckstrin homology domain-containing family A member 3 1 T(0.555)Y(0.003)S(0.439)DT(0.003)DSCSDIPLEDPDRPVHCSK;T(0.494)YS(0.494)DT(0.004)DS(0.004)CS(0.004)DIPLEDPDRPVHCSK 185.68 3.38E-17 423070000 533681 723592 529640 724946 657644 689845 663845 699092 703075 826494 TRUE FALSE 512824.1565 702955.8646 625357.7298 762360.5499 678797.7165 703794.1385 671969.3337 684655.5059 623264.8735 770514.8252 0.665560402 0.912319714 0.81161025 0.989417108 0.880966458 0.913407654 0.872104354 0.888568894 0.808894071 1 19.55546319 4.741567195 24.80879228 0.892848407 0.665560309 0.573561534 0.059872009 174.2668269 1437883.047 0.013045473 0.092558479 55152.75295 -4.741567195 -0.227288098 VTENGGS(ph)PQGIKS(ph)PSKPPGPNR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTENGGSPQGIKSPSKPPGPNR 22 2 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6;C9JPJ6;C9JE09 Q92766 RREB1 Ras-responsive element-binding protein 1 2 VT(0.171)ENGGS(0.829)PQGIKS(0.845)PS(0.155)KPPGPNR;VT(0.013)ENGGS(0.987)PQGIKS(0.813)PS(0.187)KPPGPNR 68.461 0.010543 696420000 630550 445110 363260 366510 473930 356160 466640 559430 477440 421740 TRUE FALSE 605907.4089 432415.8986 428909.1627 385425.625 489174.3889 363361.7992 472350.8799 547877.575 423243.0128 393175.1742 1.541062225 1.099804685 1.090885668 0.980289831 1.244163978 0.924172794 1.20137514 1.393469402 1.076474408 1 18.5848127 4.741580576 24.24448083 1.134034 1.541062458 0.478117457 0.132650224 182.8344658 1467693.647 0.033958834 0.237893664 55154.45228 -4.741580576 0.407028458 PAPPKPEPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 PAPPKPEPKPK 11 2 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 69.721 0.030219 689590000 804620 505600 507340 335280 516700 452320 452470 612680 689170 546870 FALSE TRUE 773174.5608 491180.783 599027.6237 352583.841 533320.1248 461466.2203 458007.4632 600027.9439 610938.3108 509830.0078 1.516534039 0.9634207 1.174955602 0.691571378 1.04607441 0.905137425 0.898353287 1.176917668 1.198317677 1 18.95965677 4.741670944 24.53961752 1.007994327 1.516534284 0.517219321 0.147938889 187.504404 1479262.576 0.03552553 0.251303198 55165.92999 -4.741670944 0.508539956 TRPEDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRPEDYR 7 1 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 0 95.741 0.012078 179470000 257140 336560 250360 390920 292960 264790 358140 320430 327980 308600 FALSE TRUE 247090.6845 326961.6383 295605.6212 411095.428 302383.3245 270144.2352 362523.0245 313813.0085 290749.0854 287698.2471 0.858853632 1.136474211 1.027484958 1.428911827 1.051043333 0.938984641 1.260080755 1.090771361 1.010604299 1 18.13419691 4.741672638 23.92413098 1.114604135 0.858853455 0.22256431 0.136901821 235.4163466 1809628.02 0.031607172 0.223431714 55166.14512 -4.741672638 -0.25575068 EGIDPTPYYWYTDQR ddPTM_BT-474_Pertuzumab_2h_R1 6 EGIDPTPYYWYTDQR 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;;; 169.65 2.76E-06 5971060000 950997 1093303 857762 1009622 1074882 1133067 1014911 1047113 1100872 1055105 FALSE TRUE 913830.9859 1062123.069 1012778.674 1061728.712 1109456.556 1155978.391 1027331.784 1025489.751 975905.6258 983641.7986 0.929028217 1.079786433 1.029621429 1.079385518 1.127907087 1.175202592 1.044416561 1.042543894 0.992135173 1 19.90777352 4.741708802 24.34124123 1.067591098 0.929028142 0.362094557 0.053267587 234.796763 1815279.132 0.013315826 0.094595295 55170.73911 -4.741708802 -0.138562955 AFAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 AFASPR 6 0 M0R1U9;M0R364;Q8TBC5-2;Q8TBC5;Q8TBC5-3;M0R3C6 M0R1U9 ZSCAN18 Zinc finger and SCAN domain-containing protein 18 1 AFAS(1)PR 69.998 0.096531 247290000 804300 713280 611820 622780 670970 675660 732370 729680 762600 736090 TRUE FALSE 772867.0668 692937.9528 722389.4839 654921.7504 692552.3594 689322.3081 741332.9631 714611.853 676032.8451 686233.9687 1.126244258 1.00976924 1.052686863 0.954370929 1.009207342 1.004500418 1.080291849 1.041353074 0.985134627 1 19.38834102 4.741716024 24.62034444 1.019309676 1.126244307 0.487727427 0.033895433 223.6758716 1745147.223 0.008353133 0.059456329 55171.6566 -4.741716024 0.10693463 AVTT(ph)PGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.437)T(0.563)PGKK 74.162 0.024431 1997500000 6389300 2747000 1792000 1587800 1794200 1165800 1710500 5247000 1250800 749080 TRUE FALSE 6139599.092 2668658.25 2115854.263 1669746.548 1851912.072 1189373.275 1731433.611 5138647.616 1108814.428 698344.1444 8.791652571 3.8214085 3.029816001 2.391008161 2.651861675 1.703133454 2.479341489 7.358331358 1.587776509 1 19.41357865 4.741725679 3.430800447 3.155561046 9.525752594 0.524818584 1.679140606 0.27890479 5.573182775 0.442654389 4.66267183 55172.88315 -4.741725679 6.370191548 EPRPNSSPSPSPGQASETPHPRPS ddPTM_BT-474_Pertuzumab_2h_R1 2 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 189.62 7.74E-18 738040000 80050 104878 84724 93192 98018 118350 90717 93852 112292 103134 FALSE TRUE 76921.5575 101886.9821 100035.5115 98001.65029 101170.838 120743.1181 91827.22178 91913.9234 99545.08293 96148.64232 0.800027495 1.059681964 1.040425627 1.019272326 1.052233662 1.255796392 0.955054794 0.95595654 1.035324894 1 16.55297887 4.741737292 24.26061136 1.038571773 0.800027359 0.452193175 0.079682757 198.8579703 1518586.296 0.020115448 0.143231934 55174.3584 -4.741737292 -0.238544414 APQQQPPPQQPPPPQPPPQQPPPPPS(ph)YSPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 APQQQPPPQQPPPPQPPPQQPPPPPSYSPAR 31 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 APQQQPPPQQPPPPQPPPQQPPPPPS(0.343)Y(0.313)S(0.343)PAR 47.099 0.061945 161890000 14587 17131 13791 16322 14324 20689 14590 18425 15247 18689 TRUE FALSE 14016.92391 16642.44065 16283.34048 17164.38038 14784.74447 21107.34576 14768.55678 18044.51731 13516.22448 17423.17738 0.804498721 0.955189762 0.934579275 0.985146394 0.848567637 1.211452153 0.847638548 1.035661689 0.77576117 1 14.08872013 4.741761637 5.126755577 0.959902734 0.797080633 0.133464906 0.11437352 0.314688443 27.19527234 0.024930907 0.181296057 55177.45137 -4.741761637 -0.162822101 KVELSSSSQHGPSYDVYNPFYMYQHIS(ph)PDLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVELSSSSQHGPSYDVYNPFYMYQHISPDLSR 32 1 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 KVELSSSSQHGPSYDVYNPFYMYQHIS(1)PDLSR;KVELSSSSQHGPSYDVYNPFYMYQHIS(1)PDLSR 264.54 5.51E-60 727640000 273230 591960 370400 789590 414260 539010 649610 463550 538520 578630 TRUE FALSE 262551.8695 575077.8804 437339.5195 830340.8345 427585.0491 549909.1515 657560.1215 453977.5305 477389.4673 539438.8747 0.486712919 1.06606681 0.810730446 1.539267697 0.792647822 1.01940957 1.218970587 0.841573627 0.884974164 1 19.04109997 4.741772546 24.47776101 1.018099056 0.486712652 0.358228994 0.213848031 247.7827401 1888203.499 0.048467896 0.347445522 55178.83741 -4.741772546 -0.531386404 SSS(ph)TSDILEPFTVER ddPTM_BT-474_Pertuzumab_2h_R1 6 SSSTSDILEPFTVER 15 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 SS(0.007)S(0.99)T(0.003)SDILEPFTVER;SS(0.001)S(0.999)TSDILEPFTVER;SSS(0.999)TSDILEPFTVER;SSS(0.992)T(0.008)SDILEPFTVER;SS(0.002)S(0.984)T(0.014)SDILEPFTVER;SSS(0.957)T(0.043)S(0.001)DILEPFTVER 329.41 8.39E-69 3997810000 5054760 5363610 4213650 5206630 5057160 5144210 5045140 5444850 5430110 5447010 TRUE FALSE 4857214.391 5210645.094 4975150.287 5475344.798 5219828.144 5248229.451 5106883.932 5332411.945 4813706.678 5078079.161 0.956506237 1.026105527 0.979730746 1.078231478 1.027913898 1.033506821 1.005672375 1.050084446 0.947938487 1 22.27585145 4.741772546 23.24890791 1.020607471 0.956506171 0.204837468 0.034697028 162.2790841 1174464.777 0.007755594 0.054628698 55178.83741 -4.741772546 -0.0641013 SPGS(ph)PPGPELPIETALDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGSPPGPELPIETALDDR 19 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.006)PGS(0.994)PPGPELPIETALDDR 102.58 0.00040861 97672000 9616.7 16468 13322 18089 14077 13110 14353 15317 18674 15335 TRUE FALSE 9240.868732 15998.34876 15729.58175 19022.57546 14529.79949 13375.09318 14528.65631 15000.6986 16554.20581 14296.34679 0.646379727 1.119051531 1.100251832 1.330589957 1.016329535 0.935560208 1.016249572 1.049267958 1.157932586 1 13.80335892 4.74177458 24.68692688 1.079587514 0.646379534 0.61295695 0.10350613 182.1982717 1399412.218 0.025904564 0.185562863 55179.0959 -4.74177458 -0.43320798 DLPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLPSPK 6 0 C9JA69;Q8WY36-2;Q8WY36;C9JYU6;C9JZA0;C9J8D0;Q8WY36-3 C9JA69;Q8WY36-3 BBX HMG box transcription factor BBX 1 DLPS(1)PK;DLPS(1)PK 76.679 0.078063 1365550000 4306500 3486500 3058900 3050300 3525600 3080800 3171400 4061700 3753200 3429300 TRUE FALSE 4138197.219 3387068.434 3611711.275 3207726.349 3639004.126 3143095.887 3210212.542 3977824.476 3327152.471 3197030.456 1.2943878 1.059442029 1.129708123 1.003345571 1.138245061 0.983129792 1.004123228 1.244224767 1.040700899 1 21.60830106 4.741778858 24.32343394 1.078821577 1.294387917 0.422247939 0.078710731 220.3385847 1665197.777 0.019063067 0.135980968 55179.6394 -4.741778858 0.21556634 NQALNTDNYGHDLASVQALQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQALNTDNYGHDLASVQALQR 21 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 290.71 1.03E-54 2006650000 830010 918650 731930 836320 819560 908470 835640 928510 1055420 920110 FALSE TRUE 797572.2916 892451.0015 864206.0327 879482.5754 845921.8917 926839.8858 845866.8123 909335.944 935613.1463 857790.1302 0.929798868 1.04040717 1.007479571 1.025288756 0.98616417 1.080497261 0.986099959 1.060091405 1.090725008 1 19.71026519 4.741781014 24.70468725 1.031149063 0.929798823 0.42267936 0.035391842 242.2741341 1858455.846 0.008058188 0.057539516 55179.91332 -4.741781014 -0.10135024 LKS(ph)DERPVHIK ddPTM_BT-474_Pertuzumab_2h_R1 4 LKSDERPVHIK 11 2 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 LKS(1)DERPVHIK;LKS(1)DERPVHIK;LKS(1)DERPVHIK;LKS(1)DERPVHIK 155.28 1.65E-05 5445900000 6475700 5556800 4816750 4690860 5891500 5184480 5059940 5870700 6200500 5672960 TRUE FALSE 6222622.485 5398325.505 5687243.873 4932955.847 6081005.448 5289313.738 5121865.059 5749467.993 5496645.235 5288725.366 1.176582646 1.020723356 1.075352468 0.932730574 1.149805488 1.00011125 0.968449807 1.087117896 1.039313796 1 22.33448863 4.741827712 24.42193284 1.033802443 1.17658272 0.353443125 0.059153426 246.3563733 1841421.766 0.013188098 0.094582775 55185.84699 -4.741827712 0.142780277 SPHS(ph)PSPIATPPSQSSSCSDAPMLSTVHSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPHSPSPIATPPSQSSSCSDAPMLSTVHSAK 31 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.025)PHS(0.487)PS(0.487)PIAT(0.001)PPSQSSSCSDAPMLSTVHSAK 140.9 4.14E-08 588250000 90578 121280 100920 111410 102560 127820 113130 102720 130360 138040 TRUE FALSE 87038.11162 117821.2131 119158.489 117159.8835 105858.9355 130404.608 114514.5188 100598.7961 115562.0793 128690.4278 0.676337107 0.915539836 0.925931252 0.910400916 0.822585932 1.013320184 0.889844884 0.781711568 0.897985042 1 16.97354522 4.741859867 24.67361091 0.895095396 0.676337009 0.509563925 0.066883926 233.1204329 1743305.428 0.016391409 0.117992746 55189.93303 -4.741859867 -0.218758387 AYSDHDDRWETK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYSDHDDRWETK 12 1 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 0 ; 235.31 2.89E-16 891300000 920480 1075810 854180 958010 1036220 1072970 1007630 1008120 1118150 1187620 FALSE TRUE 884506.624 1045128.952 1008549.327 1007453.011 1069550.957 1094666.189 1019961.677 987301.9697 991222.2997 1107181.44 0.798881369 0.943954545 0.910916035 0.909925849 0.966012362 0.988696296 0.921223605 0.891725542 0.895266362 1 20.07846023 4.741865171 24.82829952 0.931466519 0.798881315 0.560002052 0.03633523 231.7010182 1740765.612 0.009008219 0.064890905 55190.60699 -4.741865171 -0.132585204 HPPLYQAGLTPPLS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 1 HPPLYQAGLTPPLSPPK 17 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 HPPLYQAGLTPPLS(1)PPK 112.44 0.00029684 614670000 319350 248960 211270 210290 241920 245240 270470 225000 308860 288290 TRUE FALSE 306869.4489 241859.9046 249451.1887 221143.0921 249701.5765 250198.9208 273780.0928 220353.6714 273799.5076 268763.8615 1.14178092 0.899897416 0.928142598 0.822815578 0.929074226 0.930924714 1.018664084 0.81987835 1.018736322 1 18.03597964 4.741870672 24.35104921 0.92038379 1.14178104 0.463145516 0.067792629 178.7445832 1314877.069 0.015224306 0.10971772 55191.30615 -4.741870672 0.22139725 IYSHDGTDSPPDADEVVIVLNNFK ddPTM_BT-474_Pertuzumab_2h_R1 2 IYSHDGTDSPPDADEVVIVLNNFK 24 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 244.46 9.73E-38 83424000 122197 158897 133581 142068 139746 154924 149743 140699 179225 173059 FALSE TRUE 117421.4061 154365.4131 157722.0582 149400.1465 144241.057 158056.6694 151575.5996 137793.5165 158880.1294 161337.5598 0.727799567 0.956785347 0.977590453 0.926009707 0.894032717 0.979664435 0.939493568 0.85406967 0.984768392 1 17.29972282 4.741882579 24.76415533 0.937028082 0.727799478 0.689450377 0.043538832 167.4911881 1248526.37 0.010615788 0.076736181 55192.81937 -4.741882579 -0.209228605 SRPDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRPDSPR 7 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 S(0.025)RPDS(0.975)PR;S(0.093)RPDS(0.907)PR;S(0.013)RPDS(0.987)PR;S(0.009)RPDS(0.991)PR 80.755 0.052415 570406000 586944 428686 364922 370668 443578 391850 455041 334591 501835 436494 TRUE FALSE 564005.5796 416460.295 430871.523 389798.2199 457846.0892 399773.4755 460609.9279 327681.5789 444868.7947 406929.8726 1.386001907 1.023420307 1.058834831 0.957900233 1.125122828 0.982413685 1.131914757 0.805253192 1.093232089 1 18.63442067 4.741891542 4.928457227 1.009707217 1.406237612 0.591088272 0.091096925 0.118593755 8.720274975 0.02156226 0.16109787 55193.95838 -4.741891542 0.396530395 HSS(ph)EEDKDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSSEEDKDKK 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 HS(0.195)S(0.805)EEDKDKK 107.09 0.0012159 28256000 82875 45526 46737 35242 49710 43272 50960 38210 66077 59874 TRUE FALSE 79636.15338 44227.64305 55183.41556 37060.84384 51308.9673 44146.98949 51583.66372 37420.95015 58576.21598 55818.68065 1.426693581 0.79234483 0.988619131 0.663950552 0.919207812 0.79089991 0.924129039 0.67040191 1.049401657 1 15.7684604 4.741930178 24.71952243 0.847698237 1.426693836 0.626866373 0.128911345 158.5123999 1162805.009 0.027945458 0.202629066 55198.86877 -4.741930178 0.578995599 WDEQTSNTKGDDDEES(ph)DEEAVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 WDEQTSNTKGDDDEESDEEAVKK 23 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 WDEQTSNTKGDDDEES(1)DEEAVKK;WDEQTSNTKGDDDEES(1)DEEAVKK 230.8 1.69E-33 1101020000 693310 422970 421286 278398 404692 327703 394671 559052 621924 461365 TRUE FALSE 666214.6787 410907.3097 497421.7517 292766.1541 417709.2857 334329.3792 399501.1018 547507.3808 551325.7948 430116.3376 1.548917399 0.955339925 1.156481882 0.680667365 0.971154195 0.777299884 0.928821035 1.272928585 1.281806215 1 18.71436741 4.741935089 24.56011697 1.00690157 1.548917661 0.442597351 0.183832422 263.076937 1914616.365 0.047282715 0.34383315 55199.49299 -4.741935089 0.542016091 ACDHCLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ACDHCLR 7 0 C9IYN9;Q6GMV2 C9IYN9 SMYD5 SET and MYND domain-containing protein 5 0 ; 115.46 0.0056756 123403000 151500 164034 134358 154623 160519 151258 166321 138311 165951 210933 FALSE TRUE 145579.2125 159355.9109 158639.4794 162603.1116 165682.2394 154316.5404 168356.4862 135454.8295 147112.9382 196646.32 0.740309875 0.810368131 0.806724882 0.82688103 0.842539232 0.784741562 0.856138504 0.688824634 0.748109287 1 17.58524366 4.741936462 22.62781018 0.804709937 0.740309793 0.060014395 0.077313367 276.749974 1854652.96 0.01769212 0.126248103 55199.66758 -4.741936462 -0.064400144 EQFVEFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EQFVEFR 7 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;; 166.68 0.0025927 5561230000 8158550 10069370 7663880 10149560 9242150 9252280 9942070 9538680 9825060 10642710 FALSE TRUE 7839704.846 9782201.427 9048913.598 10673380.01 9539432.148 9439367.441 10063744.03 9341702.925 8709760.379 9921869.772 0.790143897 0.985923183 0.912016969 1.075742804 0.961455085 0.951369818 1.014299145 0.94152646 0.877834579 1 23.24218059 4.741942974 24.82151315 0.968716286 0.790143823 0.512345623 0.05232058 238.1573544 1747636.314 0.012056685 0.088221188 55200.49526 -4.741942974 -0.178572464 KS(ph)ESDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSESDKDVK 9 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KS(0.839)ES(0.161)DKDVK 89.231 0.0096454 521380000 519130 314440 297750 252200 308240 264030 321450 375270 409830 351520 TRUE FALSE 498841.8257 305472.4791 351560.0484 265216.0722 318154.8195 269368.8675 325384.0013 367520.5434 363307.8165 327711.2373 1.522199329 0.932139165 1.072773858 0.809298071 0.970838907 0.821970189 0.992898516 1.121476781 1.108621784 1 18.32206562 4.741951543 24.79015738 0.984058011 1.522199557 0.720303181 0.101136878 165.4960286 1209835.921 0.025856474 0.18795177 55201.58434 -4.741951543 0.538141546 EEHDKEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EEHDKEER 8 1 Q9Y6I3 Q9Y6I3 EPN1 Epsin-1 0 ; 172.23 0.0001711 164385000 347450 304310 248860 285390 290240 296710 319670 281770 332700 340450 FALSE TRUE 333871.2699 295631.3768 293834.5379 300119.0121 299575.8332 302709.6795 323582.2171 275951.351 294933.2908 317391.0183 1.051924127 0.931442164 0.925780885 0.945581301 0.943869914 0.953743685 1.019506534 0.869436547 0.929242713 1 18.27590178 4.741979099 24.45004579 0.941989357 1.051924184 0.390388478 0.03915239 243.5442687 1741796.802 0.009275147 0.068012323 55205.08702 -4.741979099 0.109934827 AVYDEQGTVDEDSPVLTQDRDWEAYWR ddPTM_BT-474_Pertuzumab_2h_R1 5 AVYDEQGTVDEDSPVLTQDRDWEAYWR 27 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;;; 457.72 3.42E-236 2211504000 588574 658792 469609 631405 657003 695659 646195 639395 601245 647638 FALSE TRUE 565571.8774 640003.8972 554477.7927 663991.8877 678136.0982 709725.7016 654103.3277 626191.2698 532994.1882 603772.9014 0.936729482 1.060007655 0.918354884 1.099737809 1.123164184 1.175484524 1.083359863 1.037130465 0.882772624 1 19.20364648 4.742064796 23.73140678 1.049254218 0.936729404 0.116411165 0.085233749 369.3033442 2500800.056 0.021043488 0.153301609 55215.98147 -4.742064796 -0.112524814 IELPELFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IELPELFDR 9 0 H0YHS6;Q9Y2Z4 H0YHS6 YARS2 "Tyrosine--tRNA ligase;Tyrosine--tRNA ligase, mitochondrial" 0 ; 119.27 0.0019861 33761000 41479 65388 43811 87732 43673 50386 73816 66646 56109 49723 FALSE TRUE 39857.95482 63523.19826 51728.62227 92259.85903 45077.78171 51404.83944 74719.38229 65269.73681 49739.74155 46355.21692 0.859837521 1.370357049 1.115918028 1.990279955 0.972442471 1.108933209 1.611887232 1.40803433 1.07301281 1 15.50044409 4.742080867 23.63870272 1.325826054 0.859837146 0.149399682 0.303006966 276.8633729 1858968.539 0.068987632 0.500472106 55218.02476 -4.742080867 -0.465988908 LKDVLLQVDDERR ddPTM_BT-474_Pertuzumab_2h_R1 5 LKDVLLQVDDERR 13 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 183.89 5.61E-06 4385480000 4104117 4589108 3627037 4104246 4235695 4644400 4411188 4561684 4853547 4397060 FALSE TRUE 3943723.57 4458231.133 4282523.269 4316066.628 4371939.976 4738312.95 4465173.438 4467483.631 4302592.692 4099243.21 0.962061378 1.087574195 1.044710706 1.052893524 1.066523686 1.155899445 1.089267753 1.089831318 1.049606591 1 21.96692616 4.742161642 24.348518 1.076100853 0.962061314 0.408992672 0.038691441 229.8680857 1554163.272 0.009101981 0.067144236 55228.29577 -4.742161642 -0.114039538 GIRPAINVGLSVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIRPAINVGLSVSR 14 1 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 189.23 6.77E-07 1037550000 437540 667630 465690 838930 469590 480780 837950 652210 562190 507260 FALSE TRUE 420440.4531 648589.8461 549850.5422 882227.2778 484694.7888 490501.701 848205.0828 638741.6356 498372.5481 472902.8284 0.889063097 1.371507648 1.162713583 1.865557203 1.024935272 1.037214564 1.793613892 1.350682629 1.053858252 1 18.85118424 4.742249532 23.65017648 1.327582276 0.889062745 0.134921476 0.299063683 312.3425661 2002281.788 0.068791731 0.505624759 55239.47369 -4.742249532 -0.438519531 GLDLHGLLAFIQLQQCAQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDLHGLLAFIQLQQCAQDR 20 0 O95274 O95274 LYPD3 Ly6/PLAUR domain-containing protein 3 0 ; 273.79 1.84E-44 383550000 291870 483720 315050 583120 333870 413190 528480 482950 469300 376090 FALSE TRUE 280463.3977 469924.7792 371986.5432 613214.8931 344609.2318 421544.9849 534947.6963 472976.9137 416027.0315 350617.0893 0.799913656 1.340279164 1.060948124 1.748958941 0.982864904 1.202294462 1.525731953 1.3489842 1.186556629 1 18.41953679 4.742283944 24.23612686 1.289587654 0.799913363 0.268001043 0.228327635 293.187249 1908307.834 0.051062832 0.379271524 55243.8509 -4.742283944 -0.489674291 HKIPVMALVGNDAGWTQISR ddPTM_BT-474_Pertuzumab_2h_R1 1 HKIPVMALVGNDAGWTQISR 20 1 A1L0T0;M0R026 A1L0T0 ILVBL Acetolactate synthase-like protein 0 155.49 1.76E-08 325170000 75365 100920 73511 103700 83851 107250 98009 89958 101990 99992 FALSE TRUE 72419.65248 98041.86041 86796.07294 109051.9694 86548.14357 109418.6685 99208.46346 88100.33586 90412.52278 93219.45278 0.776872748 1.051731774 0.931093998 1.169841339 0.928434366 1.173775057 1.064246362 0.945085315 0.96988901 1 16.50834342 4.742303372 24.64951248 1.025427039 0.776872632 0.431638086 0.0857634 283.1480285 1864697.622 0.019676483 0.146938774 55246.32221 -4.742303372 -0.248554407 LQGQLEQGDDTAAER ddPTM_BT-474_Pertuzumab_2h_R1 1 LQGQLEQGDDTAAER 15 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 277.21 3.91E-21 0 85025 106600 90794 115120 119320 144500 101850 111970 96040 106830 FALSE TRUE 81702.129 103559.8724 107202.4955 121061.357 123158.0362 147421.889 103096.4708 109657.7804 85137.94183 99594.30895 0.820349374 1.039817169 1.07639178 1.215544927 1.236597126 1.480224027 1.035164277 1.101044643 0.854847458 1 16.60377569 4.742314792 1.623258568 1.143454485 0.70219565 0.253275548 0.157288084 1.437061816 3.595577605 0.043299275 1.003930649 55247.77496 -4.742314792 -0.441258835 RSTS(ph)PIIGS(ph)PPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.289)T(0.331)S(0.38)PIIGS(1)PPVR 80.752 0.059262 1014400000 530790 591230 477560 499350 565630 621320 572550 566750 599850 598940 TRUE FALSE 510046.14 574368.6993 563865.7153 525121.5133 583824.0026 633883.5161 579557.0382 555046.4144 531757.5428 558373.2603 0.913450153 1.028646499 1.009836529 0.940448891 1.04558016 1.135232579 1.037938382 0.994041896 0.952333467 1 19.09087033 4.742348073 23.91495723 1.017802522 0.913450077 0.264073767 0.051282742 301.7611959 1905245.71 0.013053615 0.097646742 55252.00883 -4.742348073 -0.104352444 GSRPPLILQSQSLPCSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.074)S(0.925)PR;GSRPPLILQSQSLPCS(0.213)S(0.787)PR 167.1 1.13E-11 1887620000 534980 588700 501290 540590 531520 575820 565120 547790 626930 622120 TRUE FALSE 514072.3901 571910.8524 591884.2541 568489.9147 548616.8235 587463.4749 572036.1076 536477.9451 555763.5347 579983.2583 0.886357292 0.986081657 1.020519551 0.980183318 0.945918379 1.012897298 0.986297621 0.924988674 0.958240651 1 19.14565173 4.742365647 24.7021376 0.976377004 0.886357251 0.492680703 0.028186602 307.2398323 1994493.716 0.007334046 0.055405162 55254.2448 -4.742365647 -0.090019753 WLYDETLEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 WLYDETLEDR 10 0 Q9H5Q4 Q9H5Q4 TFB2M "Dimethyladenosine transferase 2, mitochondrial" 0 ;; 156.92 2.47E-05 96425000 171064 264777 172032 336290 185771 225012 307205 247910 232393 219120 FALSE TRUE 164378.6298 257225.8192 203122.0092 353645.9672 191746.4929 229561.8968 310964.6667 242790.5719 206012.7209 204278.8072 0.804677842 1.259189941 0.994337161 1.731192638 0.938650933 1.12376756 1.522256131 1.188525502 1.008487976 1 17.64018001 4.742377386 24.01248335 1.215937351 0.804677569 0.18668071 0.242094046 337.3078437 2121950.277 0.054456704 0.406114474 55255.73822 -4.742377386 -0.411259782 GSNPLDGRDS(ph)PSAGGPVGQLEPIPIPAPAS(ph)PGTRPTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSNPLDGRDSPSAGGPVGQLEPIPIPAPASPGTRPTLK 38 2 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 2 GSNPLDGRDS(0.971)PS(0.029)AGGPVGQLEPIPIPAPAS(0.999)PGT(0.001)RPTLK 194.77 8.40E-25 259570000 218280 268720 212890 241260 241310 266120 249050 273870 278790 251270 TRUE FALSE 209749.3763 261056.3687 251363.9587 253711.4575 249071.9553 271501.1287 252097.9484 268214.4888 247142.928 234251.2591 0.89540341 1.114428882 1.073052754 1.08307404 1.063268374 1.159016732 1.076186098 1.144986327 1.055033509 1 17.83769728 4.742383585 24.72577848 1.093008738 0.895403321 0.624027206 0.043902988 188.517443 1219213.195 0.009659461 0.072961362 55256.52704 -4.742383585 -0.197605416 VVAEPVELAQEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VVAEPVELAQEFR 13 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 95.618 0.010733 32639000 24782 34075 25007 32714 30326 33841 33287 32649 35984 28266 FALSE TRUE 23813.49204 33103.21436 29526.32118 34402.37346 31301.46333 34525.28821 33694.37626 31974.78674 31899.24718 26351.51864 0.903685756 1.25621657 1.120478921 1.305517679 1.187842862 1.310182107 1.278650264 1.21339446 1.210527849 1 14.68559849 4.742417483 24.86410344 1.221291628 0.903685624 0.508468999 0.089406681 253.7836037 1635998.699 0.01921581 0.145376327 55260.84005 -4.742417483 -0.317606004 ETIEDVEEMLNNLPGVTSVHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETIEDVEEMLNNLPGVTSVHSR 22 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 232.54 2.82E-27 306350000 226170 314890 246580 357370 282990 337540 301490 292880 281460 350030 FALSE TRUE 217331.0264 305909.6455 291142.4911 375813.9085 292092.6304 344365.2901 305179.7248 286831.9257 249509.8408 326322.1563 0.666001441 0.937446752 0.892193452 1.151665314 0.895105112 1.055292396 0.935209942 0.878983912 0.764612013 1 18.31593742 4.742435153 5.057190404 0.945670159 0.651964735 0.412781406 0.10008659 0.172821073 14.08944994 0.023997769 0.177514588 55263.08859 -4.742435153 -0.293705424 EFDSDS(ph)LR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFDSDSLR 8 0 Q12955;D6RFK6;B1AQT1;A0A087WZ26;Q12955-4;Q12955-5;Q12955-6;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 EFDS(0.01)DS(0.99)LR;EFDS(0.027)DS(0.973)LR 121.61 0.0014958 345180000 502640 336330 300950 337120 303440 303680 288320 441370 367590 353860 TRUE FALSE 482996.2731 326738.1977 355338.3596 354518.8036 313200.4232 309820.6177 291848.5464 432255.5553 325862.7243 329892.747 1.464100916 0.990437652 1.077132986 1.074648675 0.949400755 0.939155591 0.884677063 1.310291175 0.987783839 1 18.33163753 4.742468589 24.76719692 1.037754842 1.464101104 0.581554382 0.111494559 269.3954281 1707244.08 0.02847274 0.215989102 55267.34332 -4.742468589 0.426346263 EQFLDGDGWTSR ddPTM_BT-474_Pertuzumab_2h_R1 8 EQFLDGDGWTSR 12 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;; 268.14 1.31E-21 60448960000 21979710 26856990 20723600 26456630 24910170 26073440 25607010 25452980 26432090 26286110 FALSE TRUE 21120718.63 26091054.94 24468815.51 27822059.84 25711428.24 26600662.82 25920396.25 24927367.07 23431629.96 24505728.36 0.861868634 1.064692082 0.998493706 1.135328828 1.049200737 1.085487541 1.057728049 1.01720572 0.956169497 1 24.54661569 4.742569177 24.92066062 1.043853992 0.86186856 0.552885243 0.048099618 278.4650165 1731108.276 0.011377059 0.086072188 55280.14547 -4.742569177 -0.181985431 DLGMMIHEQGDVIDS(ph)IEANVENAEVHVQQANQQLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGMMIHEQGDVIDSIEANVENAEVHVQQANQQLSR 36 0 O15400-2;O15400 O15400-2 STX7 Syntaxin-7 1 DLGMMIHEQGDVIDS(1)IEANVENAEVHVQQANQQLSR;DLGMMIHEQGDVIDS(1)IEANVENAEVHVQQANQQLSR 225.01 5.11E-39 66467000 18789.9 32724.2 21669.7 42936.3 19651.6 25855.4 33154.8 28663 39476.2 31233.3 TRUE FALSE 18055.56993 31790.93786 25585.89683 45152.24759 20283.71156 26378.2139 33560.55836 28071.09903 34995.02727 29117.84077 0.620086155 1.091802723 0.878701722 1.550672934 0.696607682 0.90591243 1.152577165 0.964051533 1.201841426 1 14.82961576 4.742572508 24.49487378 1.044040952 0.620085933 0.259901119 0.217048981 410.646051 2507095.401 0.048818263 0.371459173 55280.56939 -4.742572508 -0.423955019 QDPSVLHTEEMR ddPTM_BT-474_Pertuzumab_2h_R1 5 QDPSVLHTEEMR 12 0 P50502;Q3KNR6;Q8NFI4;F8WAQ7 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 ;;;; 166.38 5.21E-05 6600270000 3428690 3953130 3291770 3901610 3890270 3983340 3998010 3649690 3999490 4257030 FALSE TRUE 3294693.004 3840390.603 3886666.064 4102972.56 4015404.068 4063885.864 4046938.842 3574322.626 3545484.662 3968697.566 0.830169835 0.967670259 0.979330372 1.033833516 1.011768723 1.02398477 1.019714598 0.900628623 0.893362269 1 21.9202342 4.7425818 3.811006876 0.981019279 0.814349146 0.489367924 0.046464315 0.254299161 7.188343111 0.012680303 0.119596034 55281.75218 -4.7425818 -0.166670134 DFQQLLAELEQEVERR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFQQLLAELEQEVERR 16 1 Q6N063 Q6N063 OGFOD2 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 0 ; 159.88 1.44E-08 27451000 27008 24193 17256 21479.1 22989 29210 23678 21942 26680 28691 FALSE TRUE 25952.4975 23503.03933 20374.54306 22587.63893 23728.46206 29800.64621 23967.77845 21488.89003 23651.39825 26747.73301 0.97026905 0.878692759 0.761729715 0.844469283 0.887120492 1.114137269 0.896067657 0.803391077 0.884239357 1 14.707129 4.742587573 22.54570389 0.887340551 0.970269171 0.044039039 0.094314929 337.2388648 1887768.046 0.023692966 0.175964085 55282.48705 -4.742587573 0.08292862 GLVGPELHDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GLVGPELHDR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 182.71 1.75E-06 2332520000 1911810 2162030 1693820 2146040 2013150 2037020 2113610 1994520 2236490 2262740 FALSE TRUE 1837094.352 2100371.021 1999930.953 2256797.382 2077904.798 2078209.94 2139476.991 1953332.465 1982613.031 2109482.604 0.870874378 0.995680655 0.948067051 1.069834554 0.985030544 0.985175197 1.014218836 0.925977043 0.939857493 1 21.00845776 4.742631885 24.61716222 0.982820658 0.870874324 0.432239537 0.039131885 333.862108 2018618.89 0.009630245 0.073574372 55288.12799 -4.742631885 -0.111946334 FSMEPGDEDLDCDNDHVSK ddPTM_BT-474_Pertuzumab_2h_R1 1 FSMEPGDEDLDCDNDHVSK 19 0 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;E7ERW0;E7EWF5;F8W708;E7EQU6;F8WBN7;E7EUJ2 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 0 212.76 6.68E-17 137700000 107190 127650 100370 119780 120520 134380 116840 112960 134370 133180 FALSE TRUE 103000.8963 124009.547 118509.0917 125961.8602 124396.6353 137097.2557 118269.9229 110627.3365 119116.8809 124159.6 0.829584634 0.998791451 0.954489961 1.014515673 1.001909118 1.104201815 0.952563659 0.891009125 0.959385186 1 16.92183629 4.742679902 24.51222402 0.981237732 0.829584556 0.44331267 0.052413197 344.2755081 2048541.92 0.014125527 0.108272458 55294.24112 -4.742679902 -0.151653176 SLQALGEVIEAELR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLQALGEVIEAELR 14 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ;;; 152.99 1.52E-05 39574300 69426 83297.8 63083.2 81719 73731.8 81001 77664.4 81514.6 85383.8 86395 FALSE TRUE 66712.75517 80922.2283 74483.73752 85936.52738 76103.45031 82638.89572 78614.88016 79831.29502 75691.38898 80543.3897 0.828283431 1.004703534 0.924765369 1.066959408 0.944875186 1.026017107 0.976056266 0.991158869 0.939759169 1 16.29747857 4.742685959 24.93175054 0.986102453 0.828283367 0.577185962 0.040504677 260.9000212 1576703.979 0.008662237 0.067089878 55295.01236 -4.742685959 -0.157819087 KYS(ph)ASSGGLCEEATAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYSASSGGLCEEATAAK 17 1 Q9UHV7;J3QRB7 Q9UHV7 MED13 Mediator of RNA polymerase II transcription subunit 13 1 KYS(0.948)AS(0.052)SGGLCEEATAAK;KYS(0.797)AS(0.203)S(0.001)GGLCEEATAAK 311.27 2.45E-58 935440000 1278920 1024510 848390 811740 1015470 868300 917330 1181720 1090240 984860 TRUE FALSE 1228938.392 995291.9779 1001712.945 853633.9987 1048133.515 885857.6209 928556.5589 1157317.069 966480.5259 918154.555 1.338487497 1.084013549 1.09100689 0.929728001 1.141565447 0.964824077 1.011329252 1.26048176 1.052633808 1 19.8083775 4.742700681 4.423020562 1.069495923 1.358180172 0.460875037 0.090070856 0.205445799 9.898768951 0.022791219 0.186614695 55296.88672 -4.742700681 0.288684249 RMS(ph)PKPELTEEQKQEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 RMSPKPELTEEQKQEIR 17 3 P41208 P41208 CETN2 Centrin-2 1 RMS(0.999)PKPELT(0.001)EEQKQEIR;RMS(0.985)PKPELT(0.015)EEQKQEIR;RMS(1)PKPELTEEQKQEIR;RMS(1)PKPELTEEQKQEIR 154.84 8.76E-08 1065230000 1421630 1098330 1022940 902340 1143800 1081840 1024290 1114980 1363450 1123650 TRUE FALSE 1366071.128 1067006.704 1207808.013 948909.8755 1180591.366 1103715.546 1036825.567 1091955.273 1208676.872 1047544.185 1.304070175 1.018579187 1.152990042 0.90584234 1.127008658 1.05362195 0.989767861 1.042395432 1.153819466 1 19.99857967 4.742720852 24.91515952 1.048887591 1.30407028 0.513711839 0.074351307 304.121243 1821275.9 0.016382929 0.12767004 55299.45506 -4.742720852 0.255182689 YLIATSEQPIAALHR ddPTM_BT-474_Pertuzumab_2h_R1 2 YLIATSEQPIAALHR 15 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 200.19 7.04E-09 1600280000 1252770 1333840 1102780 1344880 1337700 1197630 1471460 1478160 1354400 1511650 FALSE TRUE 1203810.363 1295800.189 1302076.877 1414289.418 1380728.335 1221846.899 1489468.168 1447635.479 1200654.19 1409264.599 0.854211739 0.919486795 0.92394067 1.003565561 0.979750954 0.867010283 1.056911646 1.027227591 0.85197215 1 20.42651108 4.742741145 0.976356739 0.976028134 0.790078702 0.235445818 0.062385921 2.806048977 2.114754442 0.019875678 0.552962036 55302.0391 -4.742741145 -0.185949432 EESSIHCK ddPTM_BT-474_Pertuzumab_2h_R1 2 EESSIHCK 8 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 112.17 0.0030923 444330000 579800 707290 549030 669460 631200 706360 660130 669250 718290 755570 FALSE TRUE 557140.775 687118.7817 648251.9341 704010.9108 651503.1212 720643.0832 668208.8684 655429.7536 636752.7305 704394.5709 0.790949843 0.975474273 0.920296608 0.999455334 0.924912184 1.023067345 0.948628647 0.930486663 0.903971661 1 19.42602426 4.74275086 24.91669358 0.95575792 0.790949775 0.636833607 0.037902987 251.2210966 1493792.77 0.008636475 0.067209782 55303.27618 -4.74275086 -0.164808145 LLEPFEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEPFEVR 8 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 107.66 0.0092114 33361000 28626 43583 28545 48734 37401 35216 44193 44493 38486 41680 FALSE TRUE 27507.26427 42340.05551 33703.71648 51249.16758 38604.03713 35928.09165 44733.84715 43574.204 34117.23063 38856.97648 0.707910568 1.089638447 0.86737877 1.318918048 0.993490504 0.924623965 1.151243643 1.121399758 0.878020724 1 15.24588603 4.742769776 24.64458009 1.049085819 0.707910402 0.359203167 0.131678096 362.643943 2123178.855 0.030029834 0.23298267 55305.68499 -4.742769776 -0.341175416 RPPS(ph)PDVIVLS(ph)DNEQPSSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLS(0.999)DNEQPSSPR;RPPS(1)PDVIVLS(1)DNEQPSSPR;RPPS(1)PDVIVLS(1)DNEQPSSPR;RPPS(1)PDVIVLS(1)DNEQPSSPR 171.02 2.95E-11 1109830000 393970 436777 305857 478142 408126 401295 442004 418247 425420 438648 TRUE FALSE 378573.2168 424320.5476 361132.1637 502818.9659 421253.7434 409409.4598 447413.3772 409610.0533 377128.1051 408937.9803 0.925747265 1.037615893 0.883097636 1.229572674 1.030116457 1.001152937 1.094086142 1.00164346 0.922213449 1 18.64152253 4.742821434 23.45782438 1.026108045 0.925747174 0.093978195 0.089059724 437.8999001 2410617.738 0.020461464 0.15758121 55312.26384 -4.742821434 -0.100360871 SPLS(ph)PTETFSWPDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 SPLS(0.999)PT(0.001)ETFSWPDVR;SPLS(0.996)PT(0.004)ETFSWPDVR 241.41 7.36E-18 138836000 638120 372330 374150 232290 415710 345940 391120 397740 585070 420400 TRUE FALSE 613181.5649 361711.5129 441767.2279 244278.5147 429081.6897 352935.1438 395906.6436 389526.53 518655.3064 391925.9335 1.564534297 0.92290783 1.127170187 0.623277242 1.094803005 0.900514902 1.010156792 0.993877916 1.323350312 1 18.58022151 4.742839751 24.68312951 0.992172638 1.564534569 0.498849065 0.169736907 286.2548587 1651116.44 0.038177643 0.298403807 55314.59679 -4.742839751 0.57236193 RQDS(ph)AGPVLDGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQDSAGPVLDGAR 13 1 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 RQDS(1)AGPVLDGAR;RQDS(1)AGPVLDGAR 110.44 0.0011212 621900000 297020 369190 226670 378690 432520 317150 363120 396240 292080 300770 TRUE FALSE 285412.13 358661.0627 267634.3112 398234.2363 446432.3986 323562.9903 367563.9712 388057.5055 258924.3029 280398.58 1.017880084 1.279111551 0.954478126 1.420243413 1.592135019 1.153939475 1.310862456 1.38394961 0.923415172 1 18.09711952 4.742858732 22.54941388 1.252981426 1.017879692 0.066199379 0.208737743 265.1676694 1390933.511 0.048691 0.369487831 55317.01435 -4.742858732 -0.235101734 SGFSLDNGELR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGFSLDNGELR 11 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 143.96 8.59E-05 312870000 331050 384860 306600 353630 356000 335070 378600 391760 381910 407950 FALSE TRUE 318112.2 373884.1696 362009.4403 371880.8867 367451.0633 341845.345 383233.4201 383670.0191 338557.1779 380319.1831 0.8364348 0.983079966 0.951856904 0.977812593 0.966164947 0.898838029 1.007662608 1.008810589 0.89019222 1 18.53685118 4.742933662 24.41033273 0.967101367 0.836434727 0.486435046 0.039554281 269.378352 1503592.022 0.009305294 0.073178963 55326.55918 -4.742933662 -0.13066664 IQQEIAVQNPLVSER ddPTM_BT-474_Pertuzumab_2h_R1 1 IQQEIAVQNPLVSER 15 0 J3KR44;Q96FW1;F5GYN4;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 204.13 1.18E-08 74872000 73952 91759 64557 93393 87872 86492 88578 103090 69161 75704 FALSE TRUE 71061.87408 89142.12316 76223.88596 98213.02392 90698.48268 88240.9275 89662.04406 100961.1555 61310.13323 70576.50065 1.006877267 1.263056716 1.080017928 1.39158251 1.285108809 1.250287655 1.270423487 1.430520847 0.868704635 1 16.10690028 4.743002423 23.64289077 1.23553065 1.006877073 0.085819511 0.167703471 406.8218843 2165259.789 0.03775853 0.291988477 55335.3197 -4.743002423 -0.228653577 EEVSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEVSLR 6 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;; 145.44 0.025929 1700180000 1318560 1593280 1278580 1575300 1444410 1423880 1556730 1494610 1585670 1676400 FALSE TRUE 1267029.217 1547841.214 1509647.848 1656601.422 1490870.759 1452671.829 1575781.727 1463745.781 1405671.389 1562855.935 0.81071402 0.990392767 0.96595458 1.059983448 0.95393998 0.929498233 1.008270623 0.936583948 0.899424802 1 20.57575337 4.743017041 24.45733932 0.970452566 0.810713932 0.552128408 0.043449776 258.063172 1416208.185 0.010391523 0.081982493 55337.18219 -4.743017041 -0.159738634 EIS(ph)TPTHWSK ddPTM_BT-474_Pertuzumab_2h_R1 4 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.498)T(0.498)PT(0.004)HWSK;EIS(0.5)T(0.5)PTHWSK;EIS(0.661)T(0.338)PT(0.001)HWSK;EIS(0.704)T(0.296)PTHWSK 158.04 5.22E-06 2019050000 2118920 2914610 2254880 2973260 2562860 2798810 2671740 2780090 2601620 2949190 TRUE FALSE 2036110.264 2831488.177 2662386.976 3126710.305 2645296.719 2855403.856 2704437.553 2722680.17 2306295.004 2749438.734 0.740554877 1.029842251 0.968338353 1.137217668 0.962122446 1.038540637 0.983632594 0.990267627 0.83882393 1 21.39070571 4.743025635 24.90460295 0.99716746 0.740554769 0.537691913 0.070543755 322.6855953 1799781.114 0.016179296 0.128190134 55338.27726 -4.743025635 -0.256612691 VHPEIINENGNPSYK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHPEIINENGNPSYK 15 0 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 ; 222.45 1.40E-12 1132500000 366850 423870 324760 402450 370820 405060 419500 412290 421170 469200 FALSE TRUE 352513.0964 411781.6426 383451.3562 423220.4927 382747.7621 413250.5907 424633.9665 403776.0674 373360.5473 437420.6661 0.805890356 0.941385889 0.876619204 0.967536574 0.875010697 0.944744094 0.970767957 0.923084113 0.853550315 1 18.73866186 4.743067276 24.7238338 0.926054981 0.8058903 0.400150292 0.044818888 387.2332867 2124300.911 0.009921212 0.078520648 55343.58341 -4.743067276 -0.120164681 QIAGGDVTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 QIAGGDVTAK 10 0 Q68E01-2 Q68E01-2 INTS3 Integrator complex subunit 3 0 64.82 0.07082 347110000 351860 486190 404770 568810 535410 576120 596480 567190 488520 647980 FALSE TRUE 338108.9222 472324.3372 477920.9431 598166.3523 552631.9489 587769.5411 603779.9007 555477.3283 433065.2576 604091.7374 0.559697975 0.781875182 0.791139679 0.990191249 0.914814613 0.9729806 0.999483792 0.91952479 0.716886577 1 19.20440813 4.74306823 1.11068332 0.930735161 0.383718091 0.644473181 0.083606048 1.046704647 1.056107941 0.02452017 0.674646291 55343.70508 -4.74306823 -0.547017069 SGKNS(ph)QEDSEDSEDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 S(0.007)GKNS(0.993)QEDSEDSEDKDVK 200.95 7.60E-16 269830000 337690 191530 175660 111300 177810 162940 158780 207740 283050 178250 TRUE FALSE 324492.7015 186067.7519 207405.6695 117044.2063 183529.4201 166234.7584 160723.1971 203450.0964 250919.3506 166176.9687 1.952693589 1.11969639 1.248101173 0.704334706 1.104421518 1.00034776 0.967180942 1.224297795 1.509952628 1 17.34236092 4.74307031 4.885984391 1.091542124 2.000906059 0.622280255 0.199906936 0.119134574 8.434128878 0.048319403 0.368438844 55343.97012 -4.74307031 0.909363935 AGNS(ph)DS(ph)EEDDANGRVELILEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGNSDSEEDDANGRVELILEPK 22 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 2 AGNS(1)DS(1)EEDDANGRVELILEPK 66.98 0.012111 52846000 71244 61748 50288 47723 63072 67386 56479 69088 65601 60704 TRUE FALSE 68459.70572 59987.0075 59376.16025 50185.98975 65100.76816 68748.59109 57170.2069 67661.30866 58154.2495 56592.46401 1.209696501 1.059982253 1.049188462 0.886796336 1.150343412 1.214801163 1.010208831 1.195588668 1.027597058 1 15.78832233 4.74308924 23.31112618 1.076145082 1.209696639 0.166548645 0.093989942 357.4266291 1839676.768 0.022710343 0.177057828 55346.38254 -4.74308924 0.133551557 AELNPWPEYIYTR ddPTM_BT-474_Pertuzumab_2h_R1 4 AELNPWPEYIYTR 13 0 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 130.56 0.00032707 707525000 630892 709494 582269 695554 694779 700061 695168 658608 740704 771562 FALSE TRUE 606236.0432 689259.9258 687497.9608 731451.6253 717127.1975 714216.7131 703675.6739 645007.5146 656622.3872 719303.4185 0.842809901 0.958232518 0.955782974 1.016888849 0.996974544 0.99292829 0.97827378 0.896711315 0.912858705 1 19.45624093 4.743121007 4.331635563 0.965194259 0.833309176 0.512098571 0.036541763 0.20616768 9.182616039 0.010059235 0.084237335 55350.43107 -4.743121007 -0.131885083 EQPFGEGVPLDGDDPEHIQWIFQK ddPTM_BT-474_Pertuzumab_2h_R1 4 EQPFGEGVPLDGDDPEHIQWIFQK 24 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;;; 219.07 1.12E-32 915930000 620954 685472 558437 612944 644967 694855 680373 617712 709821 726323 FALSE TRUE 596686.4312 665923.0097 659358.9883 644578.1133 665712.9493 708905.4442 688699.6083 604956.0313 629245.0959 677128.4963 0.881201182 0.983451462 0.973757554 0.951928795 0.98314124 1.046928977 1.017088503 0.893413931 0.929284618 1 19.36907011 4.743126284 23.84192346 0.972114983 0.88120111 0.316008219 0.04133509 348.4446022 1819448.021 0.010978078 0.086610341 55351.10361 -4.743126284 -0.090913873 MGPSGGEGMEPERR ddPTM_BT-474_Pertuzumab_2h_R1 16 MGPSGGEGMEPERR 14 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;;;;;;;;;;; 270.85 9.75E-33 97491920000 19388018.6 22052807.1 17132692.3 21631674.2 20100848.2 20605749 22117719.2 21695652.7 21616303.9 20994854.9 FALSE TRUE 18630313.4 21423882.63 20228950.91 22748087.5 20747410.24 21022411.36 22388402.46 21247629.89 19162511.7 19572854.68 0.951844465 1.09457118 1.033520723 1.162226352 1.060009415 1.074059544 1.143849624 1.085566221 0.979035098 1 24.22235085 4.743167129 24.60781284 1.078177075 0.951844401 0.287116149 0.054756302 445.308198 2378713.785 0.012357195 0.099635682 55356.30957 -4.743167129 -0.126332673 LLLNGFDDVHFLGSNVMEEQDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLLNGFDDVHFLGSNVMEEQDLR 23 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 0 153.65 5.66E-14 0 76943 89197 71448 79400 85455 79716 89253 84120 100780 85167 FALSE TRUE 73935.9825 86653.18889 84360.24295 83497.84352 88203.73768 81327.91214 90345.30491 82382.8926 89339.8769 79398.56323 0.931200509 1.091369735 1.0624908 1.051629149 1.11089841 1.024299544 1.137870778 1.037586692 1.125207728 1 16.27682528 4.7431941 24.77202461 1.072769098 0.931200444 0.491801569 0.04268823 323.11378 1727396.36 0.008910542 0.07325504 55359.74743 -4.7431941 -0.141568655 EIILDDDECPLQIFR ddPTM_BT-474_Pertuzumab_2h_R1 4 EIILDDDECPLQIFR 15 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;H0Y7R8;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ;;; 179.6 1.54E-06 133443000 93657 114854 85619 111343 107287 108653 104695 117102 115373 107401 FALSE TRUE 89996.7809 111578.4764 101092.2579 117089.4256 110737.9838 110850.0381 105976.2887 114683.8028 102276.3407 100126.6346 0.89882958 1.114373581 1.00964402 1.169413374 1.105979285 1.107098411 1.058422558 1.145387571 1.021469873 1 16.61146627 4.743206023 24.67756849 1.089370704 0.898829487 0.489281586 0.05538209 305.8664874 1624772.231 0.012155503 0.098704517 55361.26733 -4.743206023 -0.190541217 FTDLFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTDLFEK 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 100.15 0.047103 0 263980 308990 240270 293400 263630 294690 301980 307320 305600 331360 FALSE TRUE 253663.3698 300177.9077 283692.1338 308542.4092 272109.8984 300648.8337 305675.7216 300973.7346 270909.5692 308916.6921 0.821138437 0.971711518 0.918345111 0.998788402 0.88085204 0.973235961 0.989508594 0.974287704 0.876966432 1 18.2368583 4.743217152 24.71436919 0.954185029 0.821138374 0.453938654 0.043629577 356.4069211 1891538.349 0.009784285 0.078895638 55362.68596 -4.743217152 -0.133046655 S(ph)TGDIAGTVVPETNKEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 STGDIAGTVVPETNKEPR 18 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(0.994)T(0.006)GDIAGTVVPETNKEPR 145.77 5.37E-08 331810000 165950 76832 68559 68556 69714 64391 68065 165110 71405 50613 TRUE FALSE 159464.4905 74640.82659 80949.13639 72094.18338 71956.41412 65693.03014 68897.99983 161700.4208 63299.40375 47184.93643 3.379563535 1.581878291 1.715571589 1.527906761 1.524986989 1.392245812 1.46016939 3.426950062 1.341517199 1 15.52603874 4.743242144 24.31639748 1.789177006 3.379564484 0.387914581 0.629106498 401.3513515 2084557.908 0.163444179 1.313666356 55365.87194 -4.743242144 1.590387478 STYNHLSSWLTDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 STYNHLSSWLTDAR 14 0 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 132.44 5.04E-05 1097500000 462030 1042400 630640 1258100 787330 974210 1058100 875230 788010 1059900 FALSE TRUE 443973.3568 1012671.773 744610.6765 1323030.692 812655.1845 993909.1937 1071049.344 857156.1946 698558.4084 988112.0289 0.449314798 1.024855222 0.753569084 1.338948068 0.822432235 1.00586691 1.083935134 0.867468637 0.706962761 1 19.91431509 4.74329309 24.80676517 0.95669132 0.449314567 0.434384404 0.173453339 401.9318279 2106773.951 0.039196015 0.317259276 55372.36715 -4.74329309 -0.507376753 VT(ph)PTKESYTEEIVSEAESHVSGISR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTPTKESYTEEIVSEAESHVSGISR 25 1 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 VT(0.997)PT(0.003)KESYTEEIVSEAESHVSGISR;VT(0.972)PT(0.028)KESYTEEIVSEAESHVSGISR 276.1 6.69E-53 272982000 145702 187825 153519 185469 162820 166823 187551 179363 153097 214786 TRUE FALSE 140007.8048 182468.4149 181263.2983 195041.0773 168057.2532 170196.2754 189846.3052 175659.0914 135718.0704 200238.3529 0.699205735 0.911256072 0.905237661 0.974044555 0.839286035 0.849968415 0.948101612 0.877249981 0.677782595 1 17.6113588 4.743335009 24.46533835 0.88625279 0.699205631 0.304380225 0.085158673 451.0203678 2311050.047 0.019446986 0.156865538 55377.71205 -4.743335009 -0.18704716 LVHDS(ph)LEDLQMTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVHDSLEDLQMTR 13 0 A0A087WYY3;A0A2R8Y635;A0A2R8YDN7;Q9H7F0-2;Q9H7F0 A0A087WYY3 ATP13A3 Probable cation-transporting ATPase 13A3 1 LVHDS(1)LEDLQMTR;LVHDS(1)LEDLQMTR 169.02 1.88E-05 247860000 101822 173831 107650 224746 109398 129113 202104 159582 165059 161983 TRUE FALSE 97842.68367 168873.5101 127104.7497 236345.168 112916.886 131723.7533 204577.4092 156286.5759 146322.1943 151011.7471 0.647914388 1.118280619 0.841687829 1.565078032 0.747735777 0.872274878 1.354711889 1.034929924 0.968945775 1 17.20430125 4.743368089 23.98214444 1.063444221 0.647914079 0.217078067 0.232086624 424.2821792 2116406.248 0.05260928 0.426024513 55381.93031 -4.743368089 -0.415530142 HITDKDDFANNR ddPTM_BT-474_Pertuzumab_2h_R1 3 HITDKDDFANNR 12 1 Q9Y6W3 Q9Y6W3 CAPN7 Calpain-7 0 ;; 243.11 1.51E-16 591140000 413268 501426 392411 467951 472247 495206 521012 356409 581450 595440 FALSE TRUE 397117.0297 487125.8214 463328.3968 492102.0072 487437.2536 505219.4046 527388.3007 349049.0296 515446.2336 555110.3184 0.715383981 0.877529754 0.834660033 0.886494073 0.878090782 0.910124326 0.950060345 0.628792184 0.928547383 1 19.08241498 4.743425165 23.85594525 0.858509908 0.715383872 0.183571797 0.095308738 513.0541599 2515870.418 0.023387324 0.188920278 55389.20928 -4.743425165 -0.143126037 IVLDNSVFSEHR ddPTM_BT-474_Pertuzumab_2h_R1 9 IVLDNSVFSEHR 12 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;;;;; 245.15 1.91E-16 23857600000 9798678 12081830 10247407 12787510 12019589 11997560 12547896 11156127 12281502 13319740 FALSE TRUE 9415734.831 11737268.04 12099341.4 13447474.92 12406210 12240158.88 12701460.9 10925749.08 10887357.38 12417582.15 0.758258308 0.945213641 0.974371762 1.08293827 0.99908419 0.985711932 1.022861033 0.879861228 0.876769507 1 23.56588095 4.743448548 3.140470381 0.97515836 0.72429303 0.557561799 0.058279196 0.300277428 4.533018419 0.015760902 0.186974447 55392.19156 -4.743448548 -0.250865331 MAPTPIPT(ph)RSPSDSSTASTPVAEQIER ddPTM_BT-474_Pertuzumab_2h_R1 3 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPT(0.009)PIPT(0.488)RS(0.488)PS(0.013)DSSTASTPVAEQIER;MAPTPIPT(0.625)RS(0.314)PS(0.061)DSSTASTPVAEQIER;MAPT(0.001)PIPT(0.497)RS(0.497)PS(0.004)DS(0.001)STASTPVAEQIER 161.62 3.57E-11 5441400000 1021920 1130570 846640 999260 1076500 1240750 1130480 996720 1135260 1255400 TRUE FALSE 981982.2366 1098327.251 999646.6814 1050831.928 1111126.6 1265838.815 1144315.152 976137.3837 1006390.044 1170370.64 0.839035262 0.938443954 0.854128297 0.897862517 0.949380104 1.08157089 0.977737405 0.834041243 0.85989003 1 20.15853405 4.743454498 23.50810765 0.926876894 0.839035175 0.127796439 0.071933369 554.2608648 2662214.116 0.018681264 0.15055842 55392.95045 -4.743454498 -0.087841719 LSTIFEECDEELER ddPTM_BT-474_Pertuzumab_2h_R1 2 LSTIFEECDEELER 14 0 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 0 ; 239.02 5.58E-17 90574000 59818 71721 54420 68572 68184 68758 63084 72908 70222 72057 FALSE TRUE 57480.24643 69675.5873 64254.90457 72111.00914 70377.20028 70148.33387 63856.04086 71402.42432 62250.69295 67176.51521 0.855659843 1.037201574 0.956508452 1.07345564 1.047645893 1.044238952 0.950570905 1.062907537 0.926673448 1 16.03566934 4.743531953 24.78183893 1.014781805 0.855659768 0.476681638 0.048692435 380.4032936 1896219.42 0.010852166 0.091189833 55402.8305 -4.743531953 -0.159122037 TSS(ph)GTSLSAMHSSGSSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSSGTSLSAMHSSGSSGK 18 0 Q12888;Q12888-2;A6NNK5;Q12888-3;M0R142 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.137)S(0.137)S(0.681)GT(0.023)S(0.023)LSAMHSSGSSGK;T(0.102)S(0.102)S(0.758)GT(0.017)S(0.017)LS(0.004)AMHSSGSSGK;T(0.003)S(0.123)S(0.874)GTSLSAMHSSGSSGK 238.79 4.38E-24 917500000 637599 1135820 879412 1353520 977425 1205849 1129290 1047260 995402 1370750 TRUE FALSE 612680.9262 1103427.526 1038341.311 1423375.329 1008864.763 1230232.093 1143110.589 1025633.715 882408.138 1277907.882 0.479440604 0.863464058 0.812532207 1.113832499 0.789465952 0.962692312 0.894517207 0.802588144 0.690509974 1 20.28535241 4.74353427 4.722773794 0.878307013 0.454716967 0.526007028 0.114421042 0.149961584 9.271476583 0.026784007 0.210320456 55403.12608 -4.74353427 -0.423590045 DGATILTHAYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGATILTHAYSR 12 0 F5H0D0;Q14232-2;Q14232 F5H0D0 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 139.89 5.92E-05 449940000 208130 240260 196700 229700 219390 231530 227930 214870 234620 286560 FALSE TRUE 199996.0495 233408.02 232248.0656 241554.8445 226446.8786 236211.6952 230719.4755 210432.8594 207986.9212 267151.036 0.748625394 0.873693112 0.86935117 0.904188313 0.847636161 0.884187832 0.86362935 0.78769247 0.778536832 1 18.02729609 4.743538061 23.86448449 0.858728954 0.748625305 0.257874256 0.058849807 412.0678116 1975540.154 0.013796239 0.113638857 55403.60974 -4.743538061 -0.110103649 TVS(ph)LCDITITQMLEEDSNQGHLIGDFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSLCDITITQMLEEDSNQGHLIGDFSK 28 0 P30307-4;P30307-3;P30307-2;P30307;H0Y999 P30307-4 CDC25C M-phase inducer phosphatase 3 1 T(0.026)VS(0.974)LCDITITQMLEEDSNQGHLIGDFSK;T(0.248)VS(0.752)LCDITITQMLEEDSNQGHLIGDFSK 209.18 1.04E-25 227550000 196454 120550 105534 124376 115258 92521 110881 170263 143646 135588 TRUE FALSE 188776.3605 117112.032 124606.3414 130795.0603 118965.3782 94391.83801 112237.9948 166747.0096 127339.9083 126404.504 1.493430649 0.926486227 0.985774537 1.034734176 0.941148254 0.746744262 0.887927181 1.31915402 1.007400087 1 16.94768834 4.743565724 24.67729744 0.996655387 1.493430897 0.55307386 0.13710673 390.9793203 1927618.411 0.037116998 0.308628057 55407.13876 -4.743565724 0.49677551 LVEDEERR ddPTM_BT-474_Pertuzumab_2h_R1 3 LVEDEERR 8 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 147.36 0.00086344 1798910000 820860 991980 774200 831320 910330 1131040 933120 898500 1040310 949670 FALSE TRUE 788779.8837 963689.7017 914115.162 874224.5248 939611.5912 1153910.404 944539.8017 879945.661 922218.3701 885348.005 0.890926369 1.088486896 1.032492485 0.987436036 1.061290686 1.303341056 1.066857096 0.993898056 1.041645054 1 19.75588512 4.743566217 24.02723291 1.06458627 0.890926245 0.266156981 0.08617876 451.2221036 2165770.48 0.021735369 0.178687496 55407.20176 -4.743566217 -0.173660026 AGSST(ph)PGDAPPAVAEVQGR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AGSS(0.026)T(0.974)PGDAPPAVAEVQGR;AGS(0.002)S(0.006)T(0.992)PGDAPPAVAEVQGR;AGS(0.011)S(0.046)T(0.943)PGDAPPAVAEVQGR 345.35 1.49E-89 1248560000 1116250 1263210 1066320 1299170 1201950 1446130 1221450 1177230 1327280 1347380 TRUE FALSE 1072625.716 1227184.488 1259027.744 1366220.319 1240611.813 1475371.739 1236398.47 1152919.789 1176612.739 1256120.752 0.85391927 0.976963787 1.002314261 1.087650464 0.987653306 1.174546107 0.984299056 0.917841527 0.936703527 1 20.26054373 4.743598946 2.464189879 1.009548291 0.817834417 0.315638638 0.069494815 0.734404627 5.471860566 0.018852072 0.298766718 55411.37744 -4.743598946 -0.191713874 RQPQT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQPQTPK 7 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 RQPQT(1)PK 56.432 0.071285 46098000 153480 110730 105750 100300 109910 97251 108550 149420 101060 86084 TRUE FALSE 147481.8319 107572.0888 124861.3774 105476.495 113445.355 99217.48185 109878.4674 146334.4248 89588.09248 80253.454 1.837700741 1.340404474 1.55583805 1.31429228 1.413588441 1.236301703 1.369143157 1.823403448 1.116314476 1 16.29227586 4.743600199 24.14692685 1.401179465 1.837701035 0.282527674 0.219975767 462.45636 2215718.245 0.051727901 0.428328898 55411.53731 -4.743600199 0.43652157 (ac)SETAPAETATPAPVEKS(ph)PAKK ddPTM_BT-474_Pertuzumab_2h_R1 6 SETAPAETATPAPVEKSPAKK 21 2 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETAT(0.001)PAPVEKS(0.999)PAKK;SETAPAETATPAPVEKS(1)PAKK;SETAPAETATPAPVEKS(1)PAKK;SETAPAETATPAPVEKS(1)PAKK;SETAPAETATPAPVEKS(1)PAKK;SETAPAETATPAPVEKS(1)PAKK 164.46 8.66E-27 7883100000 8788120 5210110 4611200 3532840 5254920 3489920 5248430 6367200 5339210 4051850 TRUE FALSE 8444670.555 5061522.764 5444546.416 3715170.296 5423949.274 3560488.574 5312661.856 6235715.095 4733125.265 3777414.59 2.235568893 1.339943669 1.44134203 0.983521985 1.435889322 0.942572886 1.406428055 1.65078917 1.253006561 1 21.8489677 4.743624155 4.646691291 1.302504531 2.296116199 0.625955758 0.222399808 0.134070192 7.780272985 0.054747668 0.435543522 55414.59396 -4.743624155 0.993611669 S(ph)FSLEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SFSLEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER 40 2 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(0.496)FS(0.466)LEGLT(0.038)GGAGVGNKPSSSLEVSSANAEELRHPFSGEER 46.714 0.020738 85192000 33236 28117 25131 24931 25130 33385 24896 24491 38587 29092 TRUE FALSE 31937.10038 27315.13069 29672.73074 26217.6919 25938.32927 34060.06757 25200.6847 23985.25229 34206.76553 27121.57293 1.177553399 1.007136672 1.094063785 0.966672986 0.956372602 1.25582936 0.929174896 0.884360666 1.261238263 1 14.72715323 4.743716867 23.26092199 1.027710305 1.177553563 0.095319863 0.122979877 467.4409454 2108532.43 0.028912086 0.238043281 55426.4249 -4.743716867 0.149843258 FLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAR 34 0 D6RFH4;H3BUX2;O43169 D6RFH4 CYB5B Cytochrome b5 type B 0 ; 339.45 6.12E-118 216674000 71023 198797 116955 299170 100682 156964 195040 175141 166295 162311 FALSE TRUE 68247.34264 193127.5042 138091.3701 314610.1996 103920.528 160137.9196 197426.9579 171524.2771 147417.8888 151317.5314 0.451020724 1.276306205 0.912593332 2.079139123 0.686771235 1.05829059 1.304719658 1.133538695 0.974228745 1 17.20721962 4.743794472 24.52382419 1.170720102 0.451020326 0.266310625 0.351701928 555.8525252 2604401.675 0.079019569 0.667389784 55436.33011 -4.743794472 -0.719699775 KLNLAPAATTSNEPSGNNPPTHLSLDPTNAENTAS(ph)QSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLNLAPAATTSNEPSGNNPPTHLSLDPTNAENTASQSPR 39 1 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 KLNLAPAATTSNEPSGNNPPTHLSLDPTNAENT(0.001)AS(0.912)QS(0.088)PR 314.39 1.72E-110 613900000 59161 112080 77149 106170 100210 119240 111320 94255 77046 115570 TRUE FALSE 56848.92271 108883.5881 91091.54047 111649.4464 103433.3457 121651.1145 112682.3675 92308.60131 68300.06108 107742.341 0.527637716 1.010592374 0.845457224 1.036263417 0.960006482 1.129092921 1.045850373 0.856753255 0.633920337 1 16.71722579 4.743809286 24.78050866 0.948096705 0.527637516 0.47503868 0.132066489 452.4879398 2136252.414 0.032221056 0.274634196 55438.22112 -4.743809286 -0.420459189 ASPDQNASTHT(ph)PQSSVK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPDQNASTHTPQSSVK 17 0 Q14677-2;Q14677;Q14677-3;H0YD52 Q14677-2 CLINT1 Clathrin interactor 1 1 ASPDQNAS(0.002)T(0.063)HT(0.935)PQSSVK;ASPDQNASTHT(0.998)PQS(0.002)SVK;ASPDQNASTHT(1)PQSSVK;ASPDQNASTHT(1)PQSSVK 322.45 9.05E-51 2728600000 1446130 1682512 1346144 1582824 1486465 1659641 1606815 1540167 1641209 1980040 TRUE FALSE 1389613.641 1634528.405 1589422.166 1664513.736 1534278.497 1693200.078 1626479.683 1508362.013 1454905.835 1845930.127 0.752798614 0.885476856 0.861041348 0.901720879 0.831168241 0.917261197 0.881116603 0.817128444 0.788169505 1 20.81591651 4.743877827 24.34039283 0.868380498 0.752798542 0.292365899 0.05637223 516.5808039 2364624.227 0.012729962 0.108071425 55446.97112 -4.743877827 -0.115581956 DLLS(ph)GDDEETQSSADDLTPSVTSHETSDFFPRPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLLSGDDEETQSSADDLTPSVTSHETSDFFPRPLR 35 1 A8MQD4;Q7Z3K6-4;Q7Z3K6-3;Q7Z3K6;Q7Z3K6-2 A8MQD4 MIER3 Mesoderm induction early response protein 3 1 DLLS(1)GDDEETQSSADDLTPSVTSHETSDFFPRPLR 157.86 8.69E-13 60295000 3674.6 4905 4583.7 5695.3 3267.2 3962.4 2815.7 5740.3 5849.4 4204.3 TRUE FALSE 3530.99257 4765.114202 5412.076554 5989.235116 3372.292455 4042.522443 2850.159379 5621.760799 5185.400635 3919.539016 0.900869351 1.215733325 1.380794152 1.528045796 0.860379866 1.031377013 0.727166988 1.434291322 1.322961862 1 11.93646827 4.743911927 23.63151018 1.175862543 0.900869184 0.093623893 0.246719287 695.4731381 3071009.322 0.061213619 0.512963368 55451.32491 -4.743911927 -0.27499336 SYIEGYVPSQADVAVFEAVSS(ph)PPPADLCHALR ddPTM_BT-474_Pertuzumab_2h_R1 3 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 1 SYIEGYVPSQADVAVFEAVS(0.304)S(0.696)PPPADLCHALR;SYIEGYVPSQADVAVFEAVS(0.479)S(0.521)PPPADLCHALR;SYIEGYVPSQADVAVFEAVS(0.229)S(0.771)PPPADLCHALR 114.85 1.42E-06 248872000 186868 219007 166313 196851 191985 252639 206718 183347 250234 224987 TRUE FALSE 179564.992 212761.1348 196369.4587 207010.5037 198160.3719 257747.5337 209247.8767 179560.8204 221828.4854 209748.4301 0.856096953 1.01436342 0.9362142 0.986946618 0.944752587 1.228841301 0.997613554 0.856077065 1.057593067 1 17.67830049 4.743924377 23.89872065 0.994134505 0.856096843 0.180923397 0.091910199 608.7207409 2712046.331 0.022905618 0.193926436 55452.91457 -4.743924377 -0.138037662 LSSWDQAETPGHTPSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 272.16 1.26E-35 3358060000 1588086 1953732 1667533 2102559 1884380 1963960 1996519 1883096 1942718 2385853 FALSE TRUE 1526021.843 1898013.476 1968893.307 2211072.322 1944992.794 2003672.617 2020952.997 1844209.41 1722188.797 2224257.051 0.686081603 0.853324698 0.885191442 0.9940723 0.874446051 0.900827814 0.908596871 0.829135018 0.774275975 1 21.0848921 4.743967354 2.723073961 0.889781793 0.645280565 0.489684508 0.063861914 0.405952748 4.008591244 0.015902861 0.2248631 55458.40234 -4.743967354 -0.244501228 EAPGS(ph)PPLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAPGSPPLSPR 11 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;E9PNR0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 2 EAPGS(1)PPLS(1)PR 124.42 0.00051105 357600000 300800 351880 249290 328800 368530 351880 346330 333320 320400 336740 TRUE FALSE 289044.4034 341844.7269 294342.2484 345769.4074 380384.1021 358995.2547 350568.4901 326436.8255 284029.5352 313932.2999 0.920722091 1.08891225 0.937597847 1.101413928 1.211675582 1.143543544 1.116700927 1.039831918 0.904747729 1 18.26009395 4.743981419 23.27191012 1.067709804 0.92072192 0.177478298 0.089056218 389.8299619 1673422.588 0.022150562 0.185556578 55460.19836 -4.743981419 -0.146987884 QSVEHFTK ddPTM_BT-474_Pertuzumab_2h_R1 2 QSVEHFTK 8 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ; 85.676 0.016574 476880000 730760 942050 772270 905450 814820 938930 980810 932760 1010740 1053610 FALSE TRUE 702201.0913 915183.6564 911836.3681 952180.383 841029.4253 957915.8079 992813.4462 913498.18 896005.0326 982248.0562 0.714891811 0.931723561 0.928315778 0.969388921 0.856229157 0.975228001 1.010756336 0.930007623 0.912198326 1 19.90572788 4.744025612 4.209771375 0.945592811 0.6954583 0.725002801 0.042778848 0.115819919 4.638150844 0.010139107 0.087930746 55465.84221 -4.744025612 -0.250134512 IETWHKPDLGTQENVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 IETWHKPDLGTQENVHK 17 1 F5GWE5;Q00169;I3L4H1;I3L2X8;I3L4C0;I3L459;I3NI10 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 144.33 3.33E-07 679980000 402310 453480 433430 472170 443080 179060 538210 316340 628530 550270 FALSE TRUE 386587.2804 440547.1944 511760.4426 496538.7503 457332.0706 182680.7159 544796.775 309807.4685 557181.9094 512999.7228 0.753581851 0.858766925 0.997584248 0.967912317 0.891485999 0.356102952 1.061982591 0.60391352 1.086125167 1 18.96859852 4.744031638 20.67035324 0.846690129 0.753581425 0.015715328 0.215966789 316.4042152 1194931.888 0.049317421 0.395797413 55466.61182 -4.744031638 -0.093108704 GQGESDPLDHEPAVS(ph)PLLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GQGESDPLDHEPAVSPLLPR 20 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR 232.7 8.39E-27 5688890000 2151200 2937820 2177440 2689860 2761790 2871600 2886530 2650770 2776820 2873530 TRUE FALSE 2067128.726 2854036.25 2570951.845 2828683.997 2850625.484 2929665.719 2921856.218 2596030.673 2461607.035 2678903.254 0.771632467 1.065374887 0.959703133 1.055911218 1.064101691 1.093606391 1.090691205 0.969064736 0.918886127 1 21.35321105 4.744038204 24.74357775 1.026001156 0.771632341 0.638750644 0.056954984 339.1552371 1531991.871 0.014248294 0.122860808 55467.45038 -4.744038204 -0.254368815 LEEDRQS(ph)LDLSSEWWDDKLHAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEDRQSLDLSSEWWDDKLHAR 22 2 E9PJF5;G5E9I4;Q9HCU9;H0YCF7 E9PJF5 BRMS1 Breast cancer metastasis-suppressor 1 1 LEEDRQS(0.997)LDLS(0.003)SEWWDDKLHAR 102.57 0.00029048 78826000 45934 37803 33079 32264 35653 38486 34161 45779 41679 33230 TRUE FALSE 44138.8485 36724.89545 39057.11114 33929.14891 36799.81112 39264.21329 34579.07254 44833.64765 36947.77465 30979.3025 1.424785096 1.185465536 1.260748564 1.09521991 1.187883785 1.267433742 1.116199196 1.447212946 1.192659991 1 14.91901704 4.744076364 23.66421447 1.216532003 1.424785289 0.247541686 0.114797612 431.2511735 1850070.641 0.027118064 0.230613722 55472.32439 -4.744076364 0.208253286 VRPGETLLIHSGSGGVGQAAIAIALSLGCR ddPTM_BT-474_Pertuzumab_2h_R1 2 VRPGETLLIHSGSGGVGQAAIAIALSLGCR 30 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 95.751 0.0004522 420160000 123971 139419 118334 119834 128417 142666 124007 133627 143837 151304 FALSE TRUE 119126.0763 135442.9066 139719.5861 126018.6471 132547.6494 145550.8043 125524.6348 130867.5558 127509.2268 141056.0453 0.844530101 0.960206323 0.990525332 0.89339416 0.939680743 1.031865057 0.889891918 0.927769919 0.903961447 1 17.10590897 4.744105949 24.34245942 0.944753314 0.844530039 0.318170681 0.045387448 528.8289874 2321308.57 0.010627905 0.093029811 55476.10338 -4.744105949 -0.100223275 KNS(ph)ASAER ddPTM_BT-474_Pertuzumab_2h_R1 1 KNSASAER 8 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 KNS(0.66)AS(0.34)AER 58.274 0.064918 118500000 296400 184500 168280 157560 199020 165060 194220 225230 225940 212310 TRUE FALSE 284816.3603 179238.2406 198691.9394 165691.6905 205421.659 168397.6263 196596.9225 220578.9218 200292.2384 197930.0546 1.438974798 0.905563539 1.003849263 0.837122441 1.037849757 0.850793613 0.99326463 1.114428641 1.011934437 1 17.59463117 4.744116438 24.98533165 0.978529485 1.438974996 0.747270983 0.081276696 317.3715991 1427223.967 0.020415922 0.179651293 55477.44326 -4.744116438 0.460445511 DLIHDQDEDEEEEEGQR ddPTM_BT-474_Pertuzumab_2h_R1 3 DLIHDQDEDEEEEEGQR 17 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;R4GNE6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;; 348.25 1.36E-87 8180100000 1558890 1521340 1237270 1377640 1425300 1512120 1599990 1355800 1655460 1718800 FALSE TRUE 1497966.855 1477952.873 1460872.212 1448740.165 1471146.069 1542696.102 1619571.156 1327802.256 1467539.121 1602384.145 0.934836294 0.922346166 0.911686637 0.90411539 0.918098243 0.962750479 1.010725899 0.828641659 0.915847255 1 20.61178862 4.744162269 19.44253414 0.923734675 0.934836391 0 0.049572944 329.8968018 1144066.446 0.011972728 0.094181137 55483.29806 -4.744162269 0.011101716 VVRPDSELGERPPEDNQSFQYDHEAFLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVRPDSELGERPPEDNQSFQYDHEAFLGK 29 2 Q15293 Q15293 RCN1 Reticulocalbin-1 0 98 0.00056972 268430000 42129 59473 46213 52868 56579 45977 67098 49161 65380 56189 FALSE TRUE 40482.5521 57776.88827 54564.7171 55596.52382 58398.91492 46906.68644 67919.1654 48145.80817 57958.3365 52383.26898 0.772814543 1.102964542 1.041643986 1.061341243 1.114839071 0.895451684 1.296581269 0.919106598 1.1064284 1 15.67681847 4.744185825 24.56859602 1.057970142 0.772814387 0.39420886 0.106712618 454.9253591 1986850.622 0.022892768 0.199047099 55486.30756 -4.744185825 -0.285155755 LFEAEAQDLFR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFEAEAQDLFR 11 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 ;;; 152.54 7.65E-05 222446000 303362 355652 284630 345352 306681 294116 353453 354172 367063 378861 FALSE TRUE 291506.2777 345509.1532 336068.9726 363175.6581 316545.6729 300063.227 357778.6635 346858.2244 325395.5471 353200.407 0.825328261 0.978224108 0.951496561 1.028242468 0.896221144 0.849555156 1.012962206 0.982043671 0.921277384 1 18.43012748 4.744231203 24.00894264 0.957651058 0.825328159 0.363279754 0.052605547 402.3037004 1703240.527 0.012800004 0.110389506 55492.10549 -4.744231203 -0.132322898 RVSEVEEEKEPVPQPLPS(ph)DDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RVS(0.04)EVEEEKEPVPQPLPS(0.958)DDT(0.001)R 195.41 1.39E-19 3094100000 1348300 1086400 999540 1003600 1019800 969350 1049800 1204800 1246100 1159500 TRUE FALSE 1295606.945 1055416.936 1180179.113 1055395.916 1052602.793 988950.9212 1062647.766 1179920.459 1104647.952 1080966.032 1.198563976 0.97636457 1.091781867 0.976345125 0.973761212 0.914876963 0.983053801 1.091542587 1.021908107 1 20.04388976 4.744314651 24.65656909 1.007326617 1.198564077 0.561622975 0.05164549 427.5345886 1831959.209 0.013403761 0.118134511 55502.76906 -4.744314651 0.191237459 QADVFPDRDHFGR ddPTM_BT-474_Pertuzumab_2h_R1 4 QADVFPDRDHFGR 13 1 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;A0A0G2JM88 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ;;; 137.46 3.64E-05 3254820000 928630 1475980 913000 1850320 959330 1166700 1705520 1449850 1298700 1143430 FALSE TRUE 892338.1129 1433886.496 1077999.41 1945815.237 990187.7207 1190291.473 1726392.664 1419910.091 1151277.021 1065984.468 0.837102359 1.345128882 1.011271217 1.825369221 0.928895074 1.116612399 1.619528911 1.332017617 1.080012942 1 20.02375499 4.744316713 23.55658412 1.276999831 0.837101918 0.16328882 0.275454025 467.5179417 1913163.95 0.062319596 0.540994237 55503.03258 -4.744316713 -0.439897913 GLQSLPTHDPS(ph)PLQR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLQSLPTHDPSPLQR 15 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GLQSLPTHDPS(1)PLQR;GLQSLPTHDPS(1)PLQR;GLQSLPTHDPS(1)PLQR;GLQSLPTHDPS(1)PLQR;GLQSLPTHDPS(1)PLQR 179.95 4.18E-07 6824280000 2496620 5793450 2931340 7837080 3404550 3685240 6483500 6675580 4405660 3384280 TRUE FALSE 2399049.33 5628226.478 3461098.345 8241552.638 3514060.443 3759758.078 6562847.012 6537726.94 3905547.947 3155059.701 0.760381596 1.78387321 1.09699932 2.612170107 1.113785721 1.191659884 2.080102323 2.072140485 1.23786816 1 21.58923587 4.744333116 24.10800184 1.6435564 0.760380954 0.17181627 0.519085536 614.8138427 2567552.655 0.11975755 1.052505887 55505.12898 -4.744333116 -0.883175446 ELAPEPWVER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELAPEPWVER 10 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 107.08 0.0054243 109170000 177480 221260 169300 211220 193170 206590 224800 208430 208130 226870 FALSE TRUE 170543.8854 214949.8814 199896.2761 222121.0895 199383.4885 210767.3913 227551.1696 204125.8477 184503.955 211503.8928 0.806339227 1.01629279 0.945118661 1.050198588 0.942694178 0.996517788 1.075872253 0.965116268 0.872343069 1 17.69032469 4.744370479 24.58456433 0.986870267 0.806339127 0.485725494 0.055088493 428.3127325 1812348.057 0.012769338 0.114285931 55509.90441 -4.744370479 -0.18053114 DNPGVVTCLDEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNPGVVTCLDEAR 13 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 284.12 2.82E-32 1509220000 362230 449310 366570 386950 467730 418490 379490 431110 448490 463970 FALSE TRUE 348073.6511 436496.1187 432817.3533 406920.5359 482774.9602 426952.1545 384134.3121 422207.4278 397579.2954 432544.8986 0.804711031 1.009134821 1.000629888 0.940759068 1.116126815 0.987070142 0.888079627 0.976100814 0.919163066 1 18.72249037 4.744394395 24.7343785 0.98023971 0.804710942 0.453987322 0.058269038 530.1349138 2247620.519 0.0141351 0.126248993 55512.96131 -4.744394395 -0.175528768 EPRPNSSPS(ph)PSPGQASETPHPRPS ddPTM_BT-474_Pertuzumab_2h_R1 7 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNSS(0.002)PS(0.789)PS(0.208)PGQASETPHPRPS;EPRPNSSPS(0.969)PS(0.031)PGQASETPHPRPS;EPRPNSS(0.001)PS(0.814)PS(0.185)PGQASETPHPRPS;EPRPNS(0.01)S(0.066)PS(0.923)PS(0.001)PGQASETPHPRPS;EPRPNS(0.001)S(0.006)PS(0.992)PSPGQASETPHPRPS;EPRPNS(0.256)S(0.256)PS(0.487)PSPGQASETPHPRPS;EPRPNS(0.123)S(0.123)PS(0.732)PS(0.021)PGQASETPHPRPS 266.95 9.13E-45 16606000000 769964 982842 732049.3 976948 857768 1065268 900780 863372 953300 983120 TRUE FALSE 739872.9556 954812.3085 864346.8929 1027368.403 885358.8867 1086808.449 911804.0151 845543.0665 845085.3806 916532.4067 0.807252368 1.04176601 0.943062009 1.120929708 0.965987542 1.185782893 0.994840999 0.922545739 0.922046372 1 19.80582637 4.74440226 24.37911334 1.008978584 0.807252243 0.359487191 0.081467413 527.9468167 2203205.073 0.019808403 0.175886948 55513.96665 -4.74440226 -0.201726341 ESQSHPGDFVLSVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESQSHPGDFVLSVR 14 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 179.79 1.83E-06 2359500000 1183820 1616120 1263630 1569810 1430150 1520930 1552200 1354920 1613800 1745120 FALSE TRUE 1137555.006 1570029.84 1491996.05 1650828.082 1476152.074 1551684.247 1571196.288 1326940.429 1430608.19 1626921.468 0.699207078 0.965031116 0.917067037 1.014694387 0.907328413 0.953754854 0.965748082 0.815614309 0.879334509 1 20.63371318 4.744407883 24.61646118 0.927535905 0.699206954 0.609813682 0.05636391 387.0562838 1629412.498 0.014272793 0.127950896 55514.68541 -4.744407883 -0.228328951 EEKLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEKLSR 6 1 Q8IY82-2;Q8IY82 Q8IY82-2 DRC7 Dynein regulatory complex subunit 7 0 71.029 0.081451 167060000 346940 417110 350820 467490 396160 420420 419220 461990 451120 501190 FALSE TRUE 333381.2012 405214.4312 414220.9779 491617.2149 408902.8462 428921.1805 424350.5398 452449.7451 399910.7488 467243.9549 0.713505649 0.867243818 0.886519715 1.052163885 0.875137799 0.91798123 0.908199101 0.96833729 0.855892826 1 18.83381647 4.744418589 1.705670317 0.934953314 0.635280797 0.587978532 0.056182872 0.640112562 1.805933097 0.013967073 0.31546333 55516.05396 -4.744418589 -0.299672517 RVS(ph)ISEGDDKIEYR ddPTM_BT-474_Pertuzumab_2h_R1 3 RVSISEGDDKIEYR 14 2 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 1 RVS(0.967)IS(0.033)EGDDKIEYR;RVS(0.999)IS(0.001)EGDDKIEYR;RVS(0.844)IS(0.156)EGDDKIEYR 250.94 6.52E-19 1122900000 850462 741001 647949 684471 705927 720394 718262 760900 806623 793367 TRUE FALSE 817225.0048 719868.377 765047.7978 719796.6303 728633.7831 734960.8603 727052.3052 745187.1491 715058.5387 739631.5464 1.10490826 0.97327971 1.034363396 0.973182707 0.985130754 0.993685118 0.982992557 1.007511311 0.966776691 1 19.49644723 4.744422143 24.90915246 0.992070465 1.104908311 0.766217604 0.018901799 270.6411623 1150082.769 0.004161674 0.037041455 55516.50827 -4.744422143 0.112837847 RPGQSFHVNSEVNSVLS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 RPGQSFHVNSEVNSVLSPR 19 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 RPGQSFHVNSEVNS(0.003)VLS(0.997)PR;RPGQSFHVNSEVNS(0.003)VLS(0.997)PR;RPGQSFHVNSEVNSVLS(1)PR;RPGQSFHVNSEVNSVLS(1)PR 216.87 1.75E-19 3402330000 695927 1104450 866682 1118300 964220 1193130 997290 869805 877351 1125720 TRUE FALSE 668729.4035 1072952.167 1023310.717 1176015.597 995235.012 1217255.906 1009495.133 851843.2228 777757.7926 1049473.982 0.637204366 1.022371384 0.975070116 1.120576229 0.948317947 1.1598724 0.961905822 0.81168589 0.741092972 1 20.00123497 4.744472924 24.57725552 0.967605544 0.637204182 0.416506483 0.118530327 566.7837581 2356013.668 0.030662918 0.275107295 55523.00006 -4.744472924 -0.330401362 DFVTEALQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFVTEALQSR 10 0 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 ; 174.86 6.92E-06 201737000 173743 214380 166087 181648 196364 197439 202071 224700 210689 212850 FALSE TRUE 166952.9315 208266.0923 196102.6155 191022.875 202680.2264 201431.3519 204544.0053 220059.8665 186772.468 198433.4799 0.841354652 1.049551177 0.988253674 0.962654463 1.021401361 1.015107692 1.030793823 1.108985573 0.941234655 1 17.59829593 4.744542782 24.81536016 1.019412328 0.841354565 0.56992915 0.044457449 439.6516606 1823716.538 0.011170082 0.099683745 55531.93179 -4.744542782 -0.178057762 ESEVAHVDQLFDDASR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESEVAHVDQLFDDASR 16 0 E9PRF4;Q15047-3;Q15047;E9PAP1;X6RHV1;B0QZE6;E9PS59;X6R732;E9PQM8;Q15047-2 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 0 ; 163.51 7.71E-09 167438000 232070 264400 218800 256810 263630 257600 242730 261500 287000 281220 FALSE TRUE 223000.4478 256859.5709 258342.0272 270063.9949 272109.8984 262808.8485 245700.6023 256099.9336 254420.9632 262172.7189 0.850586014 0.979734169 0.985388671 1.030099531 1.037903179 1.002426376 0.937170745 0.9768367 0.970432638 1 18.00015804 4.744603677 3.846571124 0.990988179 0.835873643 0.704823847 0.027377254 0.161778621 4.705332993 0.007504005 0.071434412 55539.71891 -4.744603677 -0.155114536 RRS(ph)PQEGPTWSR ddPTM_BT-474_Pertuzumab_2h_R1 6 RRSPQEGPTWSR 12 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 RRS(0.99)PQEGPT(0.005)WS(0.005)R;RRS(1)PQEGPTWSR;RRS(1)PQEGPTWSR;RRS(0.88)PQEGPT(0.101)WS(0.02)R;RRS(1)PQEGPTWSR;RRS(1)PQEGPTWSR 132.63 0.0001398 3297040000 673188 914810 660131 860294 903516 920083 857821 846259 739398 913420 TRUE FALSE 646879.0687 888720.5145 779431.3562 904693.8764 932578.4127 938687.7087 868319.27 828783.4559 655464.6388 851553.2498 0.759646057 1.043646436 0.91530548 1.06240435 1.095149849 1.102324146 1.019688751 0.973260869 0.769728304 1 19.69973722 4.744632401 24.52662023 1.002423345 0.759645916 0.369859985 0.093148465 573.4159757 2316194.557 0.022684537 0.205525178 55543.39231 -4.744632401 -0.242777428 SLHINNIS(ph)PGNTISR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLHINNISPGNTISR 15 0 Q8IZ41 Q8IZ41 RASEF Ras and EF-hand domain-containing protein 1 SLHINNIS(1)PGNTISR 134.52 2.23E-05 389120000 88397 133930 95799 136860 109330 124540 126830 126090 122090 127770 TRUE FALSE 84942.34751 130110.4475 113112.0103 143923.361 112846.6987 127058.2841 128382.1835 123486.1974 108230.855 119116.0241 0.713105967 1.092300121 0.949595247 1.208261962 0.94736791 1.066676672 1.07779104 1.036688375 0.908617089 1 16.86200798 4.744650138 24.84119659 1.036535429 0.713105811 0.57160099 0.082714954 416.923973 1700720.598 0.018134408 0.166984674 55545.6608 -4.744650138 -0.323429618 LDLLEDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LDLLEDR 7 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 198.64 0.00091886 3048310000 2906800 3695230 3053450 3590060 3188720 3130590 3588850 3476380 3661560 3751970 FALSE TRUE 2793199.042 3589845.658 3605276.339 3775343.427 3291288.075 3193892.675 3632771.42 3404591.538 3245915.059 3497845.73 0.79854838 1.026301883 1.030713364 1.079333887 0.94094718 0.913102784 1.03857394 0.973339536 0.927975477 1 21.73803523 4.744696687 24.89384759 0.992534445 0.79854829 0.566752893 0.050807799 501.5956167 2034898.92 0.012555822 0.116192523 55551.61465 -4.744696687 -0.193986156 RPS(ph)HEGYLAAPGLEGPGPDGDGQMQLVTSL ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSHEGYLAAPGLEGPGPDGDGQMQLVTSL 30 1 O94910-2;O94910 O94910-2 LPHN1 Latrophilin-1 1 RPS(0.994)HEGY(0.006)LAAPGLEGPGPDGDGQMQLVTSL 70.249 0.0038769 94073000 59032 87991 60234 87702 72435 82691 89719 97137 67636 57279 TRUE FALSE 56724.96418 85481.58283 71119.6237 92228.31073 74764.93756 84363.06868 90817.00796 95131.087 59958.24483 53399.44231 1.062276341 1.600795423 1.331842068 1.727139961 1.400107086 1.579849246 1.700710795 1.781499635 1.1228253 1 15.70453705 4.744714286 24.10582784 1.522884185 1.062275997 0.166968099 0.251905969 606.9780506 2377609.096 0.056413614 0.514250748 55553.86584 -4.744714286 -0.460608188 TGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPR 39 2 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 156.29 2.52E-14 225860000 19440 28669 23446 22780 26909 26452 28656 24763 25690 31723 FALSE TRUE 18680.26331 27851.38819 27683.21375 23955.67853 27774.55242 26986.87756 29006.7007 24251.6354 22773.7789 29574.37295 0.631636834 0.941740616 0.936054123 0.810014757 0.939142563 0.912508867 0.980805265 0.820021964 0.770051116 1 14.85205996 4.74473939 24.83531261 0.895588264 0.631636706 0.551641178 0.072737355 492.252971 1978530.348 0.017156184 0.159582535 55557.07718 -4.74473939 -0.263951558 (ac)MS(ph)PTPPLFSLPEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSPTPPLFSLPEAR 14 0 A0A087WWS1;Q96FV9;Q96FV9-2;J3KRD7;J3QQZ3;J3KT14 A0A087WWS1 THOC1 THO complex subunit 1 1 MS(0.848)PT(0.152)PPLFS(0.001)LPEAR 45.879 3.88E-05 42416000 1715.1 3238.1 2100.3 3651 2350.5 3190.3 2739.6 2706.8 3531.4 2908.4 TRUE FALSE 1648.071996 3145.752558 2479.870931 3839.428548 2426.105967 3254.810052 2773.128044 2650.903634 3130.530277 2711.411477 0.607828067 1.160190028 0.914605161 1.416025778 0.894776019 1.200411697 1.022761786 0.977684006 1.154575874 1 11.40482835 4.744797801 24.85818855 1.077272426 0.607827842 0.477604857 0.148793196 535.9404408 2135917.934 0.032452472 0.30272584 55564.54997 -4.744797801 -0.469444584 ATS(ph)PTQSTSSWQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSPTQSTSSWQK 13 0 P98088 P98088 MUC5AC Mucin-5AC 1 AT(0.073)S(0.924)PT(0.002)QSTSSWQK;ATS(0.999)PTQSTSSWQK 259.97 5.65E-24 435000000 961490 1042850 823400 987640 1019600 981850 907720 1095870 1057680 995700 TRUE FALSE 923913.9078 1013108.939 972206.6964 1038612.219 1052396.36 1001703.68 918828.9489 1073239.902 937616.6006 928260.3521 0.995317645 1.091406023 1.047342692 1.118880297 1.133729732 1.07911932 0.9898397 1.156184145 1.010079336 1 19.82416997 4.744809667 23.79884113 1.077471638 0.995317573 0.126776562 0.055138806 646.7782114 2463046.685 0.012416696 0.114081157 55566.06809 -4.744809667 -0.082154066 SSSHSSPGS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSHSSPGSPK 11 0 Q6NZY4;Q6NZY4-2;F5GX80 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 SSSHSSPGS(0.999)PK;SSSHSSPGS(1)PK;SSSHSSPGS(1)PK;SSSHSSPGS(1)PK 115.24 0.001206 578313000 637542 1157930 820253 1272290 896179 1137260 1056530 968889 857097 1277620 TRUE FALSE 612626.1538 1124906.97 968490.9635 1337953.039 925005.4114 1160256.176 1069460.13 948881.1036 759802.9418 1191085.659 0.514342649 0.944438346 0.813116131 1.123305472 0.776606959 0.974116485 0.897886833 0.796652278 0.637907892 1 20.18384574 4.744822387 24.73401259 0.879932272 0.51434246 0.423888874 0.129480781 592.4814546 2340228.623 0.029888574 0.278325899 55567.69558 -4.744822387 -0.365589812 GAEFLLR ddPTM_BT-474_Pertuzumab_2h_R1 6 GAEFLLR 7 0 Q9BXT2 Q9BXT2 CACNG6 Voltage-dependent calcium channel gamma-6 subunit 0 ;;;;; 160.69 0.0031102 1031755000 1215554 1481270 1206405 1428950 1357587 1341078 1339875 1391864 1479830 1552060 FALSE TRUE 1168048.806 1439025.63 1424429.22 1502698.281 1401255.019 1368195.516 1356272.791 1363121.522 1311845.902 1446937.594 0.807255828 0.994531925 0.984444129 1.038537037 0.968428096 0.945580184 0.937340212 0.942073471 0.906636131 1 20.46457127 4.744835357 24.93755361 0.966202854 0.807255755 0.644387275 0.035921419 485.5634511 1929710.07 0.009281991 0.087972091 55569.35509 -4.744835357 -0.158947098 KEQTPEHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEQTPEHGK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 81.017 0.025934 313072000 573828 482959 418787 422357 483464 453655 472329 535326 531565 490846 FALSE TRUE 551402.1674 469185.4822 494471.1268 444154.8954 499015.0586 462828.2149 478109.5036 524271.331 471223.9697 457600.5632 1.204985771 1.025316662 1.080573685 0.970617021 1.090503594 1.01142405 1.044818433 1.145696429 1.029771394 1 18.8037293 4.744839124 24.78954806 1.052375025 1.204985847 0.492265405 0.048334787 578.4171147 2283706.561 0.011703478 0.110276648 55569.83715 -4.744839124 0.152610822 MFS(ph)DEILLS(ph)LT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 MFSDEILLSLTR 12 0 Q7Z4H8-3;Q7Z4H8-2;Q7Z4H8 Q7Z4H8-3 KDELC2 KDEL motif-containing protein 2 3 MFS(1)DEILLS(1)LT(1)R 60.474 0.040647 824060000 49731 16657 18429 27484 22473 15492 17861 24505 13477 30755 TRUE FALSE 47787.45754 16181.95867 21759.53025 28902.45253 23195.86445 15805.25885 18079.58826 23998.96319 11947.14746 28671.93646 1.666697944 0.56438318 0.75891387 1.008039781 0.809009342 0.551244904 0.630567394 0.837019265 0.416684359 1 14.80735172 4.744874878 24.96540065 0.732152744 1.666698368 0.701093847 0.183354879 379.4561391 1500257.068 0.042414185 0.398541255 55574.41218 -4.744874878 0.934545624 SYQLRPGTMIEWGNYWAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYQLRPGTMIEWGNYWAR 18 1 O75323;O75323-2;C9K068 O75323 GBAS Protein NipSnap homolog 2 0 ; 223.36 4.73E-19 719930000 309890 488570 350930 592720 320760 313930 606550 501980 366020 344280 FALSE TRUE 297779.1562 474636.462 414350.8574 623310.3502 331077.5367 320277.8797 613973.1403 491613.9376 324470.9441 320961.6089 0.927771883 1.478795123 1.290967037 1.942009053 1.031517563 0.997869748 1.912917692 1.531690781 1.010933816 1 18.29204122 4.744879525 23.6561544 1.398560867 0.927771422 0.109451879 0.346412486 678.7734793 2540974.74 0.081118341 0.738578044 55575.00689 -4.744879525 -0.470789445 RLDEEEEDNEGGEWER ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDEEEEDNEGGEWER 16 1 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 ; 209.12 2.10E-11 1985470000 402110 531870 422810 527060 518400 563020 514000 495100 521970 608720 FALSE TRUE 386395.0966 516701.5884 499221.1724 554261.6298 535074.8068 574404.6502 520290.4858 484876.012 462718.1539 567490.8522 0.680883392 0.910502057 0.879699065 0.976688219 0.942878294 1.0121831 0.916826207 0.854420842 0.815375529 1 19.11423761 4.744897844 4.543806296 0.919987619 0.664152293 0.597793005 0.059611215 0.151535319 8.044525761 0.015173419 0.124631941 55577.35112 -4.744897844 -0.255835326 EEYLLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEYLLLR 7 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 100.74 0.022265 372080000 437540 508880 430690 544100 479550 453530 548090 548090 521540 560030 FALSE TRUE 420440.4531 494367.2406 508525.2636 572181.0662 494975.1613 462700.6873 554797.6894 536771.75 462336.9657 522098.6693 0.805289264 0.946884698 0.974002221 1.095925157 0.948049077 0.886232267 1.062629963 1.028104038 0.885535614 1 18.99396296 4.744908646 2.219863207 0.990994688 0.755497026 0.408150028 0.064628668 0.632388918 3.533236177 0.016499415 0.295101744 55578.73346 -4.744908646 -0.235497662 MLEQLDMR ddPTM_BT-474_Pertuzumab_2h_R1 5 MLEQLDMR 8 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;;; 175.44 0.00061903 2071580000 2925150 3299960 3159770 3312930 2978890 2072484 3527690 3030210 3237910 3675320 FALSE TRUE 2810831.904 3205848.372 3730810.728 3483910.714 3074708.702 2114391.046 3570862.925 2967635.105 2870356.031 3426387.303 0.820348564 0.935635142 1.088846764 1.016788357 0.89736169 0.617090498 1.042165584 0.866111984 0.837720835 1 21.70825681 4.744927318 22.84411756 0.919228772 0.820348409 0.054386105 0.127053296 786.0311354 2820050.296 0.030920642 0.278766758 55581.12313 -4.744927318 -0.098880363 FRIDELEPR ddPTM_BT-474_Pertuzumab_2h_R1 6 FRIDELEPR 9 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 172.88 5.09E-05 6551750000 2638530 3361920 2580790 3212750 3020360 3251720 3124820 3030630 3394570 3423460 FALSE TRUE 2535413.331 3266041.333 3047196.162 3378560.413 3117512.622 3317472.006 3163062.482 2968046.431 3009232.645 3191586.005 0.794405454 1.02332863 0.954759219 1.05858354 0.976791043 1.039443086 0.9910629 0.929959721 0.942864344 1 21.60584209 4.744983703 24.97102336 0.987983765 0.794405366 0.688498682 0.039581842 437.5124134 1700870.395 0.009851105 0.09397468 55588.33974 -4.744983703 -0.193578399 RGPLSQNGSFGPSPVSGGECS(ph)PPLTVEPPVRPLSATLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGPLSQNGSFGPSPVSGGECSPPLTVEPPVRPLSATLNR 39 2 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 RGPLSQNGS(0.001)FGPS(0.003)PVS(0.034)GGECS(0.925)PPLT(0.03)VEPPVRPLS(0.003)AT(0.003)LNR;RGPLSQNGSFGPSPVS(0.001)GGECS(0.982)PPLT(0.014)VEPPVRPLS(0.001)AT(0.001)LNR 109.8 5.49E-06 862370000 43670 100095 60024 122305 65324 79315 82345 101325 105981 71126 TRUE FALSE 41963.32812 97240.3886 70871.67203 128617.1757 67425.20579 80918.80364 83352.76274 99232.60334 93950.48119 66308.57267 0.632849214 1.46648291 1.06881613 1.939676433 1.016839951 1.220336985 1.257043537 1.496527513 1.416867796 1 16.01690778 4.745002614 24.64879915 1.33883316 0.632848827 0.369521533 0.268401132 605.8637855 2318119.787 0.059711033 0.563863351 55590.76038 -4.745002614 -0.705984334 ALDHITTLLRPGGHLLLIGALEESWYLAGEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDHITTLLRPGGHLLLIGALEESWYLAGEAR 32 1 A8MT87;P11086 A8MT87 PNMT Phenylethanolamine N-methyltransferase 0 57.825 0.02464 29078000 15808 23585 17602 20146 22439 21926 24343 17660 27863 21299 FALSE TRUE 15190.20588 22912.37889 20783.07295 21185.73747 23160.77081 22369.35874 24640.91692 17295.31483 24700.10905 19856.39976 0.765003025 1.153903989 1.046668742 1.06694757 1.166413403 1.126556627 1.240955924 0.871019673 1.243936935 1 14.27731645 4.745073189 24.57580154 1.093964061 0.765002836 0.467851096 0.107472155 527.284406 1989688.753 0.024837271 0.235976016 55599.79482 -4.745073189 -0.328961225 EKPTHCSECGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKPTHCSECGK 11 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 ; 125.28 0.00019919 254260000 277440 403420 346630 441640 359260 427600 401290 395750 406470 511810 FALSE TRUE 266597.3381 391914.8566 409273.7517 464433.0933 370815.9242 436246.365 406201.1071 387577.6242 360329.2297 477144.6528 0.558734833 0.821375351 0.857756132 0.973359107 0.777156198 0.914285348 0.851316482 0.812285377 0.755178178 1 18.86406718 4.745131831 3.232209308 0.859383222 0.513472709 0.602429235 0.074631783 0.229585208 3.776969161 0.017329955 0.201239089 55607.30288 -4.745131831 -0.345910513 EDDSSASTSQSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDDSSASTSQSTR 13 0 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 113.38 0.0019229 23301000 6593.4 9488.8 7734.8 7925.7 8291.2 8185.9 8590.5 8324.7 11635 9592.6 FALSE TRUE 6335.722639 9218.188715 9132.65042 8334.746327 8557.893978 8351.424507 8695.633109 8152.792036 10314.24358 8942.884658 0.708465208 1.030784704 1.021219748 0.93199752 0.956950056 0.933862487 0.972352148 0.911651257 1.153346372 1 13.12652455 4.745163053 24.92978058 0.979946444 0.70846508 0.613423072 0.066656785 488.06636 1842812.904 0.015378354 0.147354394 55611.3007 -4.745163053 -0.271481364 SAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_BT-474_Pertuzumab_2h_R1 5 SASPDDDLGSSNWEAADLGNEER 23 0 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 S(0.148)AS(0.852)PDDDLGSSNWEAADLGNEER;S(0.121)AS(0.879)PDDDLGSSNWEAADLGNEER;S(0.147)AS(0.853)PDDDLGSSNWEAADLGNEER;S(0.143)AS(0.857)PDDDLGSSNWEAADLGNEER;S(0.136)AS(0.864)PDDDLGSSNWEAADLGNEER 356.15 4.80E-102 2626880000 805201 986610 732469 891200 949944 965699 920146 927758 989290 986260 TRUE FALSE 773732.8547 958472.8488 864842.442 937194.9388 980499.8115 985226.0954 931407.022 908599.4731 876989.9466 919459.7317 0.841508147 1.042430479 0.940598497 1.019288726 1.066386898 1.071527182 1.012993816 0.988188435 0.953810065 1 19.81042687 4.745185576 24.61271775 1.010983395 0.84150805 0.606938906 0.040816797 438.8395817 1630301.682 0.010275091 0.098134328 55614.18488 -4.745185576 -0.169475345 EESLADDLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 EESLADDLFR 10 0 O60934;A0A0C4DG07;A0A087X1V5 O60934 NBN Nibrin 0 ; 226.46 7.03E-09 96378000 183160 209431 159446 191970 197678 198377 202047 202795 207937 218920 FALSE TRUE 176001.9047 203458.2329 188261.4391 201877.5947 204036.4924 202388.3189 204519.7116 198607.2124 184332.8635 204092.3534 0.862364032 0.996892973 0.922432594 0.989148252 0.999726295 0.991650669 1.002093945 0.973124221 0.903183585 1 17.63886261 4.745192593 24.7876207 0.975696085 0.862363973 0.514302202 0.032941575 558.384788 2086952.834 0.007712891 0.074887693 55615.0834 -4.745192593 -0.113332112 GVAPADS(ph)PEAPRR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVAPADSPEAPRR 13 1 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPRR 156.96 2.91E-05 789110000 289660 342410 242400 327230 324510 337180 341160 325670 306400 356760 TRUE FALSE 278339.767 332644.8021 286207.0722 344118.3795 334948.1589 343998.0106 345335.2181 318944.8007 271618.7565 332596.3274 0.836869634 1.000145746 0.86052385 1.034642752 1.007071129 1.034280845 1.038301357 0.958954668 0.816661924 1 18.34341271 4.745217159 24.25246829 0.97479718 0.836869539 0.241038252 0.071963921 736.4372992 2683028.011 0.017159103 0.163140656 55618.22938 -4.745217159 -0.137927641 ATSS(ph)SNPS(ph)SPAPDWYKDFVTDADAEVLEHSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 2 AT(0.313)S(0.31)S(0.331)S(0.168)NPS(0.456)S(0.421)PAPDWY(0.001)KDFVTDADAEVLEHSGK 68.101 0.005333 20726000 39058 31687 25333 22418 29408 30609 29412 29742 38402 33704 TRUE FALSE 37531.57018 30783.31778 29911.23663 23574.99567 30353.93503 31227.93495 29771.95285 29127.81731 34042.76595 31421.19806 1.194466554 0.979699047 0.951944499 0.750289522 0.966033662 0.993849276 0.947511702 0.927011671 1.083433098 1 14.93945057 4.745219681 3.05207204 0.944230245 1.236254049 0.448123246 0.079629137 0.341042004 4.703849536 0.019547587 0.243178018 55618.55234 -4.745219681 0.292023804 EVS(ph)IEDTGVDVDPEKLEMESK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSIEDTGVDVDPEKLEMESK 21 1 Q8WWK9-6;Q8WWK9-5;Q8WWK9 Q8WWK9-6 CKAP2 Cytoskeleton-associated protein 2 1 EVS(0.996)IEDT(0.004)GVDVDPEKLEMESK 58.92 0.04166 42489000 83659 60079 58122 53999 62884 54794 59434 67347 67070 70424 TRUE FALSE 80389.51379 58365.60574 68625.93832 56785.89486 64906.72097 55901.97222 60161.37107 65956.26092 59456.49478 65654.11975 1.224439747 0.888986189 1.045264769 0.864925081 0.988616118 0.851461758 0.916338096 1.004602014 0.905601888 1 16.00259792 4.745223401 24.8577898 0.942166694 1.224439886 0.649791046 0.062494439 415.9080907 1551643.456 0.013859314 0.134167351 55619.02876 -4.745223401 0.282273192 EEHS(ph)KTPEER ddPTM_BT-474_Pertuzumab_2h_R1 1 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EEHS(0.5)KT(0.5)PEER 86.467 0.01482 0 14568 16415 11929 13196 18391 15869 14185 17468 17566 14249 TRUE FALSE 13998.66645 15946.86027 14084.83566 13877.04714 18982.56322 16189.88205 14358.60027 17107.2797 15571.98132 13283.90254 1.053806772 1.200465016 1.060293511 1.044651382 1.428989949 1.218759473 1.08090226 1.287820326 1.172244472 1 13.69739142 4.745254018 22.82757849 1.178705227 1.053806578 0.061744931 0.122540144 615.7368734 2099745.452 0.028844112 0.266805821 55622.94993 -4.745254018 -0.124898648 LESDYEILER ddPTM_BT-474_Pertuzumab_2h_R1 2 LESDYEILER 10 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 195.48 8.16E-07 690090000 456430 511780 433960 482330 523340 530170 475770 525140 530430 544990 FALSE TRUE 438592.211 497184.5355 512386.2254 507223.1091 540173.7064 540890.4006 481592.6156 514295.6755 470217.8101 508077.3419 0.863239068 0.978560732 1.008480763 0.998318695 1.063172202 1.064582803 0.947872648 1.012238951 0.925484708 1 18.9546886 4.745301616 2.694765623 1.004566677 0.834091 0.50888512 0.040811014 0.383807807 3.668046584 0.010209399 0.147440034 55629.04652 -4.745301616 -0.170475678 ISSLPVSRPIS(ph)PSPSAILER ddPTM_BT-474_Pertuzumab_2h_R1 6 ISSLPVSRPISPSPSAILER 20 1 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P2-8;Q5T5P2-6;Q5T5P1;Q5T5P2-4;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 ISSLPVSRPIS(0.968)PS(0.03)PS(0.003)AILER;ISSLPVSRPIS(0.977)PS(0.016)PS(0.008)AILER;ISSLPVS(0.002)RPIS(0.992)PS(0.005)PS(0.001)AILER;ISSLPVSRPIS(0.995)PS(0.003)PS(0.002)AILER;ISSLPVSRPIS(0.978)PS(0.015)PS(0.007)AILER;ISSLPVSRPIS(0.999)PS(0.001)PSAILER 252.23 2.73E-36 9163010000 1773288 2052392 1602981 2011714 1823195 1959803 1847425 2109406 2002438 1926205 TRUE FALSE 1703985.944 1993859.79 1892675.325 2115538.801 1881839.723 1999431.559 1870034.34 2065846.029 1775129.633 1795741.42 0.948903849 1.110326781 1.053979879 1.178086543 1.047945825 1.113429549 1.041371725 1.150413977 0.988521852 1 20.77614819 4.745313569 24.4306411 1.084816551 0.948903762 0.282612811 0.059275721 624.8745451 2260570.292 0.012716939 0.122192541 55630.57761 -4.745313569 -0.135912789 LHDETLTYLNQGQSYEIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LHDETLTYLNQGQSYEIR 18 0 F8VX55;Q12800-2;Q12800-3;Q12800-4;Q12800;C9JWL3;Q9NZI7-4;Q9NZI7 F8VX55 TFCP2;UBP1 Alpha-globin transcription factor CP2;Upstream-binding protein 1 0 216.93 8.69E-19 350450000 54374 67803 53605 66004 54696 64386 76974 50618 73947 70389 FALSE TRUE 52249.00397 65869.32483 63292.61594 69410.47435 56455.34651 65687.92903 77916.03084 49572.72061 65552.84657 65621.49033 0.796217881 1.003776728 0.964510492 1.057739987 0.860317957 1.001012453 1.187355399 0.755434239 0.998953944 1 16.00188074 4.745330771 23.64494447 0.971779507 0.796217704 0.204517482 0.107961659 627.8224519 2192558.465 0.025477398 0.242977954 55632.78115 -4.745330771 -0.175561803 LLYNNVSNFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLYNNVSNFGR 11 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 286.53 1.60E-27 1890510000 460300 550910 459800 457600 508660 518370 565950 484710 573870 569360 FALSE TRUE 442310.9671 535198.5862 542896.0882 481216.7908 525021.5109 528851.7966 572876.2654 474700.5691 508726.6835 530796.7401 0.833296314 1.008292903 1.022794692 0.906593343 0.989119697 0.996335804 1.079276156 0.894317039 0.958420889 1 19.01779998 4.745407352 24.30533202 0.980441234 0.833296213 0.434733421 0.051384976 535.929343 1902430.489 0.012406773 0.119766737 55642.5919 -4.745407352 -0.147145021 LVPRPGSGSSSGSSNSGSQPGSHPGSQSGS(ph)GER ddPTM_BT-474_Pertuzumab_2h_R1 2 LVPRPGSGSSSGSSNSGSQPGSHPGSQSGSGER 33 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 LVPRPGSGSSSGSSNSGSQPGSHPGS(0.002)QS(0.184)GS(0.814)GER;LVPRPGSGSSSGSSNSGSQPGSHPGS(0.001)QS(0.004)GS(0.995)GER 203.77 2.64E-27 231260000 35314 55020 41281 58894 39180 51481 50891 49583 48966 56807 TRUE FALSE 33933.88984 53450.88347 48741.39499 61933.5264 40440.26028 52521.98109 51513.81928 48559.09372 43407.58496 52959.41129 0.640752777 1.009280167 0.920353792 1.169452698 0.763608569 0.991740275 0.972703775 0.916911509 0.819638737 1 15.69259946 4.745436184 24.70502468 0.94963407 0.640752609 0.440963653 0.104953389 616.89644 2216541.751 0.023538939 0.232086208 55646.28601 -4.745436184 -0.308881461 TPDS(ph)PPTPAPLLLDLGIPVGQR ddPTM_BT-474_Pertuzumab_2h_R1 5 TPDSPPTPAPLLLDLGIPVGQR 22 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 T(0.044)PDS(0.943)PPT(0.013)PAPLLLDLGIPVGQR;T(0.043)PDS(0.957)PPT(0.001)PAPLLLDLGIPVGQR;T(0.04)PDS(0.951)PPT(0.009)PAPLLLDLGIPVGQR;T(0.045)PDS(0.934)PPT(0.021)PAPLLLDLGIPVGQR;T(0.006)PDS(0.994)PPTPAPLLLDLGIPVGQR 162.77 1.66E-11 351857000 28736.4 34318.5 26189 30446.8 30055 34978.4 32863.6 37109.5 26820.9 34151.6 TRUE FALSE 27613.34972 33339.76998 30921.93487 32018.163 31021.74637 35685.68721 33265.79457 36343.17586 23776.30387 31838.48171 0.867294803 1.047153262 0.971212608 1.005643526 0.974347541 1.12083508 1.044829803 1.141485834 0.746778822 1 14.95848392 4.745480743 23.45042241 1.019113456 0.867294629 0.129057246 0.102850011 617.6583546 2092941.387 0.023566398 0.226178075 55651.99574 -4.745480743 -0.151818827 GYNS(ph)DDNLCEPSLEFEVPNHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GYNSDDNLCEPSLEFEVPNHR 21 0 Q9P219;Q9P219-2;A0A0A0MR69 Q9P219 CCDC88C Protein Daple 1 GYNS(1)DDNLCEPSLEFEVPNHR;GYNS(1)DDNLCEPSLEFEVPNHR 229.06 9.27E-26 288650000 163240 190587 140631 202770 165646 174774 169498 185916 199643 196086 TRUE FALSE 156860.4003 185151.6454 166046.15 213234.984 170974.154 178308.05 171572.3672 182076.7696 176980.3636 182804.9206 0.858075373 1.012837317 0.908324292 1.166461949 0.935282013 0.975400714 0.938554426 0.996016787 0.968137855 1 17.47994538 4.745491735 24.45088919 0.98783496 0.85807529 0.255991889 0.06693472 823.9666303 2906605.03 0.015066064 0.148361703 55653.40423 -4.745491735 -0.12975967 RIDFTPVSPAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 3 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RIDFTPVSPAPS(0.956)PT(0.043)R;RIDFTPVSPAPS(0.999)PT(0.001)R;RIDFTPVSPAPS(0.967)PT(0.033)R 167.05 8.17E-07 1167830000 329765 481674 433043 524398 499429 514823 584695 475382 488651 553999 TRUE FALSE 316877.4192 467937.1291 511303.5031 551462.2436 515493.5874 525233.0738 591850.6723 465565.1956 433181.3871 516476.1543 0.613537366 0.906018846 0.989984724 1.06773999 0.998097556 1.016955128 1.145939977 0.901426313 0.838724854 1 18.97834222 4.745528676 2.264401115 0.997745796 0.512028651 0.679173518 0.078686257 0.372451333 2.192672753 0.020678758 0.36352229 55658.13841 -4.745528676 -0.485717146 AAGARPLTSPESLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAGARPLTSPESLSR 15 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 116.96 0.00037163 224810000 164350 139860 108360 131780 135100 148010 145080 136220 161010 152610 FALSE TRUE 157927.0203 135871.3297 127943.0625 138581.1816 139445.6142 151002.8636 146855.5324 133407.0094 142732.8198 142273.5888 1.110023453 0.955000369 0.899274866 0.974047135 0.980122983 1.061355554 1.03220516 0.937679372 1.003227802 1 17.11830834 4.745632828 24.4652377 0.980471953 1.110023535 0.431321107 0.043854339 647.7196412 2240611.786 0.011275566 0.113190893 55671.48788 -4.745632828 0.129551582 KPGINVASDWSIHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPGINVASDWSIHLR 15 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 238.07 6.05E-18 1991170000 1849410 2712600 2318600 2929900 2507700 2682000 2858700 2498700 3015200 3303100 FALSE TRUE 1777133.013 2635239.304 2737622.597 3081112.49 2588362.448 2736231.878 2893685.626 2447100.972 2672927.137 3079378.095 0.577107766 0.855769971 0.889018014 1.000563229 0.840547139 0.88856639 0.939698061 0.794673761 0.868008752 1 21.55420759 4.745647954 3.334426182 0.892432806 0.532172786 0.708851298 0.061953967 0.181633133 3.291968907 0.015060032 0.169328593 55673.42684 -4.745647954 -0.36026002 TSTS(ph)LGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSTSLGK 7 0 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 TST(0.006)S(0.994)LGK 94.909 0.014533 612700000 2310800 1782400 1461400 1533700 1502900 1519100 1508300 2158400 1864600 1755500 TRUE FALSE 2220491.381 1731567.697 1725507.489 1612854.441 1551242.143 1549817.243 1526759.027 2113828.286 1652938.425 1636598.421 1.356772286 1.058028454 1.054325524 0.985491871 0.947845313 0.946974666 0.932885555 1.291598634 1.009984125 1 20.64226893 4.745651103 3.915605272 1.034697589 1.38953367 0.506178915 0.098101494 0.246670703 7.614303465 0.026739203 0.252563963 55673.83052 -4.745651103 0.354836081 DLAMMIHDQGDLIDSIEANVESSEVHVER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLAMMIHDQGDLIDSIEANVESSEVHVER 29 0 Q86Y82 Q86Y82 STX12 Syntaxin-12 0 ; 213.37 1.16E-26 40701000 19244.3 24247 17625.6 24918 22326 23360 24445 17209.7 28339 25368 FALSE TRUE 18492.21148 23555.4993 20810.938 26204.02097 23044.13607 23832.35521 24744.16522 16854.31368 25122.07553 23649.80276 0.781918212 0.996012505 0.879962434 1.10800167 0.974390201 1.007718984 1.04627364 0.712661913 1.062253067 1 14.52954053 4.745653698 24.02419766 0.961263582 0.781918066 0.221463999 0.106022985 832.4633708 2819418.282 0.026223955 0.258596781 55674.16323 -4.745653698 -0.179345516 KQNLER ddPTM_BT-474_Pertuzumab_2h_R1 3 KQNLER 6 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2;CON__Q3MHN2;P02748 F1T0B3 DDX1;C9 ATP-dependent RNA helicase DDX1;Complement component C9;Complement component C9a;Complement component C9b 0 ;; 128.82 0.026397 1083040000 1804590 1816810 1556090 1736480 1719480 1478480 1794260 1858410 1869310 1943050 FALSE TRUE 1734064.628 1764996.358 1837310.078 1826099.941 1774788.636 1508375.879 1816218.691 1820033.184 1657113.766 1811445.493 0.957282256 0.974357972 1.014278423 1.008089919 0.979763754 0.832691839 1.002635021 1.004740795 0.914801893 1 20.78870996 4.745697199 20.56991944 0.971903155 0.957282189 0.004223662 0.0535028 703.84365 2027979.746 0.013008433 0.117156882 55679.74011 -4.745697199 -0.014620966 SETEDSILHQLFIVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SETEDSILHQLFIVR 15 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 ;; 227.42 7.33E-13 173319000 207035 250424 206206 226300 235985 241571 230681 232982 234174 254836 FALSE TRUE 198943.8433 243282.1527 243472.0112 237979.3701 243575.6718 246455.7311 233504.1431 228170.8403 207591.5493 237575.7307 0.837391272 1.024019381 1.02481853 1.001698992 1.025254857 1.037377557 0.982861938 0.960413084 0.873791059 1 17.85802794 4.745711442 24.7376142 0.992799464 0.837391187 0.51304939 0.045257206 641.9093814 2220561.209 0.011366323 0.115867933 55681.56612 -4.745711442 -0.155408276 SEDES(ph)ET(ph)EDEEEKSQEDQEQKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 SEDES(0.987)ET(0.81)EDEEEKS(0.203)QEDQEQKR 151.42 5.38E-08 660060000 1267600 963440 780950 531150 823130 782490 776430 899220 1218100 955120 TRUE FALSE 1218060.791 935963.6345 922085.0371 558562.7152 849606.724 798312.4839 785932.1826 880650.7928 1079826.395 890428.8717 1.367948445 1.051138013 1.035551594 0.627296276 0.95415451 0.896548292 0.882644541 0.989018686 1.212703708 1 19.76414085 4.74575517 1.882984525 0.93531759 1.506428545 0.452882005 0.138396995 0.74906275 2.710786627 0.036027894 0.756501893 55687.1728 -4.74575517 0.571110955 VSAS(ph)SENFHVGENDENQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSASSENFHVGENDENQDR 19 0 Q9UN76 Q9UN76 SLC6A14 Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) 1 VS(0.017)AS(0.84)S(0.143)ENFHVGENDENQDR;VS(0.02)AS(0.931)S(0.049)ENFHVGENDENQDR 171.73 6.25E-12 721560000 350130 575460 393320 681870 390970 537350 537360 435480 605050 611420 TRUE FALSE 336446.5325 559048.4442 464401.6734 717061.3924 403545.9051 548215.5852 543936.3724 426487.1858 536367.2606 570007.9788 0.590248812 0.980773016 0.814728373 1.257984834 0.707965362 0.961768266 0.95426098 0.74821266 0.940982022 1 19.12062259 4.745772562 24.26596974 0.916011663 0.590248578 0.322695656 0.146311997 684.2052585 2302051.886 0.033200128 0.332934814 55689.40293 -4.745772562 -0.325763085 TLVRPSEHALVDNDGLYDPDCDPEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLVRPSEHALVDNDGLYDPDCDPEGR 26 1 P09758 P09758 TACSTD2 Tumor-associated calcium signal transducer 2 0 77.693 0.012969 169770000 38287 66394 46039 72281 49797 52965 62866 71877 52835 45408 FALSE TRUE 36790.70171 64500.50813 54359.27143 76011.43107 51398.76573 54035.98859 63635.37291 70392.71483 46837.3923 42332.47571 0.869089301 1.523664918 1.284103292 1.795581992 1.21416867 1.276466535 1.503228239 1.662853723 1.106417508 1 15.36947724 4.745772797 24.52528197 1.414169172 0.869088962 0.274112932 0.238614155 772.0371497 2625254.239 0.053835204 0.545434794 55689.43314 -4.745772797 -0.54508021 LAQQVCHAIANISDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAQQVCHAIANISDR 15 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 0 129.38 6.62E-05 215920000 169740 191930 143320 167970 185200 207670 179090 182370 176770 207530 FALSE TRUE 163106.3731 186456.3443 169221.1121 176638.9518 191157.1262 211869.2297 181281.757 178603.9958 156703.8107 193473.8083 0.843041105 0.963729127 0.874646102 0.91298638 0.988025862 1.095079647 0.936983453 0.923143021 0.809948448 1 17.56177875 4.745788286 23.71291205 0.944049908 0.843041005 0.150993981 0.072466281 865.50945 2839455.468 0.017899247 0.177468199 55691.4193 -4.745788286 -0.101008902 VGPAT(ph)PSAQVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGPATPSAQVGK 12 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 VGPAT(0.954)PS(0.046)AQVGK 152.95 0.00078515 311390000 922220 549140 457000 387050 420800 369030 383050 903710 482960 451000 TRUE FALSE 886178.6228 533479.0649 539590.0659 407025.6969 434335.4142 376492.0394 387737.8805 885048.0727 428136.4055 420453.3683 2.107673977 1.268818626 1.283352939 0.968063827 1.03301685 0.895443033 0.922189973 2.104985093 1.018273221 1 18.68158628 4.745815049 4.01448035 1.210015339 2.194024177 0.403472281 0.340446194 0.292109447 9.835375321 0.091433167 0.844295915 55694.8513 -4.745815049 0.984008838 YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPR 42 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(1)PR;YSEDPTVPLPSETDGYVAPLTCSPQPEY(0.003)VNQPDVRPQPPS(0.997)PR;YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(1)PR;YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(1)PR;YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(1)PR 219.38 2.44E-44 5152910000 1248960 2775250 1251453 3650310 1645604 1816649 3044140 3330910 1985494 1417995 TRUE FALSE 1200149.262 2696102.587 1477618.396 3838702.937 1698536.347 1853382.887 3081395.096 3262125.544 1760109.045 1321952.936 0.90786081 2.039484549 1.117754162 2.903812105 1.284869001 1.402003685 2.330941604 2.467656341 1.331446073 1 20.33423938 4.745842911 23.81159486 1.853173377 0.90785994 0.133797088 0.617403846 790.8020004 2585629.518 0.142411131 1.42459901 55698.42456 -4.745842911 -0.945313437 S(ph)RT(ph)SVQTEDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.859)RT(0.735)S(0.396)VQT(0.009)EDDQLIAGQSAR;S(0.851)RT(0.723)S(0.425)VQTEDDQLIAGQSAR 182.66 6.59E-14 1920510000 282582 331498 280161 359065 311813 319894 325294 409149 290713 294933 TRUE FALSE 271538.383 322044.0016 330792.3248 377596.3877 321842.7483 326362.4759 329275.0453 400699.9302 257712.479 274956.9252 0.98756699 1.171252557 1.203069625 1.37329288 1.170520612 1.186958559 1.19755138 1.457318923 0.937283099 1 18.0688461 4.745850994 2.29770691 1.224569193 0.926474297 0.114052459 0.146526075 1.013794388 6.205170295 0.035374117 0.613451454 55699.46117 -4.745850994 -0.298094895 ARPSAHS(ph)PGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARPSAHSPGKK 11 2 H9KVB4;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 ARPS(0.017)AHS(0.983)PGKK;ARPS(0.026)AHS(0.974)PGKK 79.875 0.01354 417933000 204384 236867 179190 233998 198610 226591 249187 209749 245102 241009 TRUE FALSE 196396.4473 230111.7851 211573.6191 246074.6648 204998.471 231172.8253 252236.625 205417.6099 217279.0485 224685.2458 0.874095879 1.024151739 0.94164447 1.095197257 0.912380652 1.028874079 1.122622112 0.914246101 0.967037456 1 17.77754587 4.745854175 24.30826684 0.999003132 0.874095791 0.242137715 0.067126531 866.057367 2886324.588 0.015446749 0.156510794 55699.8692 -4.745854175 -0.124907341 EAPCVLIYIPDGHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAPCVLIYIPDGHTK 15 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 118.13 0.00031562 426690000 574230 592730 475720 562760 615990 669280 624190 642640 813660 780430 FALSE TRUE 551788.4568 575825.9207 561693.1863 591804.111 635803.8778 682813.3002 631829.0239 629369.2594 721296.7279 727570.781 0.758398318 0.791436292 0.772011742 0.813397303 0.873872198 0.938483675 0.868409013 0.865028223 0.991376711 1 19.47272808 4.745857941 0.160473181 1.041851717 0.48979767 0.812220255 0.035660444 10.03651435 0.278857935 0.15263184 1.169276585 55700.35214 -4.745857941 -0.552054047 SGS(ph)TESLNPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSTESLNPR 10 0 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.211)GS(0.394)T(0.394)ES(0.002)LNPR 145.41 3.20E-05 229380000 184930 213310 160900 195880 199400 179970 207900 230160 210230 198010 TRUE FALSE 177702.7311 207226.6077 189978.2092 205989.3903 205813.8821 183609.1167 210444.3424 225407.1156 186365.5718 184598.6063 0.962643948 1.122579481 1.029142164 1.115877278 1.114926522 0.994639777 1.140010461 1.221066183 1.009571933 1 17.49403214 4.745912917 23.97303081 1.095903186 0.962643833 0.186685703 0.071025013 758.9692902 2474594.705 0.017419593 0.175813495 55707.40357 -4.745912917 -0.133259353 TPAEGRDS(ph)PTREPGALPCACGQLPDLEDELSLLDPLPR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPAEGRDSPTREPGALPCACGQLPDLEDELSLLDPLPR 38 2 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 T(0.116)PAEGRDS(0.441)PT(0.441)REPGALPCACGQLPDLEDELS(0.001)LLDPLPR;TPAEGRDS(0.954)PT(0.046)REPGALPCACGQLPDLEDELSLLDPLPR;T(0.002)PAEGRDS(0.992)PT(0.005)REPGALPCACGQLPDLEDELSLLDPLPR 317.44 2.45E-110 385414000 45672.6 58741 42772.4 52740.3 55436.5 66594 53708.7 49843.8 56108.3 57417 TRUE FALSE 43887.6643 57065.76419 50502.32415 55462.2332 57219.66537 67940.57631 54366.00314 48814.50811 49739.12101 53528.09545 0.819899605 1.066089942 0.943473212 1.036133132 1.06896509 1.269250769 1.015653605 0.911941807 0.92921522 1 15.7080087 4.745940333 24.0430487 1.024803691 0.819899436 0.29324279 0.096294379 754.813209 2459068.781 0.025160221 0.256601922 55710.92029 -4.745940333 -0.204904255 QPLPPLHPAVSDPRS(ph)PPSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 QPLPPLHPAVSDPRSPPSQK 20 1 O14647 O14647 CHD2 Chromodomain-helicase-DNA-binding protein 2 1 QPLPPLHPAVS(0.01)DPRS(0.981)PPS(0.01)QK 77.023 0.0063615 96668000 179920 164420 123040 146330 184730 148800 154570 185270 180130 147870 TRUE FALSE 172888.5275 159730.9026 145276.065 153882.1088 190672.0082 151808.838 156461.6739 181444.1098 159682.3976 137854.6332 1.254136502 1.158690853 1.053835201 1.116263598 1.383138193 1.101224053 1.134975809 1.316198851 1.158338997 1 17.07278823 4.746000475 22.50950158 1.1739829 1.254136637 0.048092021 0.109225608 819.2666895 2478447.774 0.025929739 0.251998636 55718.63579 -4.746000475 0.080153737 AELELELGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AELELELGR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 209.87 1.79E-05 500950000 729380 799100 645280 823880 791700 757570 819920 837830 850810 886700 FALSE TRUE 700875.0232 776310.4504 761896.4502 866400.5455 817165.7495 772888.5845 829954.4262 820528.5177 754229.6157 826643.0192 0.847856943 0.939112086 0.921675297 1.048095158 0.988535233 0.934972614 1.004005849 0.992603214 0.912400635 1 19.65690492 4.746042242 1.324654938 0.981046784 0.792637849 0.510462319 0.038663435 1.087774934 1.649906976 0.010559793 0.278390229 55723.99469 -4.746042242 -0.188408935 SACMLSSPESSLT(ph)PPLSTNLHLESELDALASLENHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 SACMLSSPESS(0.001)LT(0.998)PPLS(0.001)TNLHLESELDALASLENHVK;SACMLSSPESS(0.001)LT(0.999)PPLSTNLHLESELDALASLENHVK 260.14 5.55E-62 374030000 56207 73491 55794 63065 68460 79398 70537 49768 87026 84780 TRUE FALSE 54010.3683 71395.10864 65877.21693 66319.79221 70662.07807 81003.48196 71400.25291 48740.27341 77147.17332 79037.77509 0.683348794 0.903303624 0.833490275 0.839089817 0.89402919 1.024870473 0.90336871 0.616670615 0.97607977 1 16.27025472 4.746063588 23.5803361 0.866497553 0.683348597 0.214727073 0.110742709 736.8432793 2315619.687 0.028115738 0.285928449 55726.73368 -4.746063588 -0.183148956 ETVS(ph)PPCFDEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETVSPPCFDEYK 12 0 Q13029-5;Q13029-3;Q13029-2;Q13029 Q13029-5 PRDM2 PR domain zinc finger protein 2 1 ETVS(1)PPCFDEYK;ETVS(1)PPCFDEYK 180.84 1.98E-05 343555000 387500 280300 239032 263680 297770 255960 281580 359500 307710 259050 TRUE FALSE 372356.0716 272306.1184 282230.3996 277288.5564 307348.0425 261135.6866 285026.0603 352076.1994 272780.0508 241504.3128 1.541819553 1.127541431 1.168635029 1.148172276 1.272639975 1.081287881 1.180211057 1.457846427 1.129503849 1 17.88168943 4.746104105 24.57292841 1.19950534 1.541819763 0.453101515 0.118281822 735.8892769 2397087.505 0.029470498 0.307870695 55731.93288 -4.746104105 0.342314423 KLENS(ph)PLGEALR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLENSPLGEALR 12 1 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 KLENS(1)PLGEALR;KLENS(1)PLGEALR 239.86 2.12E-16 614720000 829860 1134920 1060470 1709310 934690 1441710 1858830 1818800 1847550 2148320 TRUE FALSE 797428.1537 1102553.193 1252120.519 1797527.694 964755.1527 1470862.364 1881578.918 1781241.144 1637823.87 2002812.373 0.398154198 0.550502487 0.625181138 0.897501792 0.481700216 0.734398481 0.939468391 0.889369952 0.817762009 1 20.93359584 4.746176993 0.247507662 1.002881211 4.77E-16 0.646140221 0.117899477 6.621850984 0.346736553 0.179318533 2.055369861 55741.28716 -4.746176993 -1.002881211 EEEWDPEYT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEWDPEYTPK 11 0 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4;Q9Y2W1;A0A3B3ITZ9 Q9NYF8;Q9NYF8-4;Q9Y2W1 BCLAF1;THRAP3 Bcl-2-associated transcription factor 1;Thyroid hormone receptor-associated protein 3 1 EEEWDPEYT(1)PK 104.41 0.029106 568530000 888100 593140 523120 512780 509960 442590 454940 798510 565380 590330 TRUE FALSE 853392.0702 576224.2279 617659.4207 539244.6373 526363.3265 451539.473 460507.6918 782020.4895 501200.4327 550346.4233 1.550645255 1.047020937 1.12231023 0.97982764 0.956421818 0.820464082 0.83675967 1.420960428 0.9106999 1 19.0699805 4.74619665 4.449387926 1.026424044 1.589986455 0.496268415 0.162642576 0.20162247 9.854432587 0.042437713 0.359718922 55743.81019 -4.74619665 0.563562411 SSSSGHYVSWVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSSGHYVSWVK 12 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 109.6 0.0015805 565730000 465830 748530 559720 738020 658550 646660 650580 647370 644880 856130 FALSE TRUE 447624.8486 727182.6573 660873.8549 776109.3006 679732.8588 659735.9083 658541.9927 634001.5833 571675.926 798143.5525 0.560832506 0.911092566 0.828013774 0.972393122 0.85164236 0.826588032 0.825092166 0.794345304 0.716257024 1 19.60628872 4.746198226 24.71134662 0.849365055 0.560832342 0.552479654 0.079969391 617.3680125 1997426.95 0.018729126 0.200045948 55744.01251 -4.746198226 -0.288532713 GSVILDSGHLSTAS(ph)SSDDLKGEEGSFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSVILDSGHLSTASSSDDLKGEEGSFR 27 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 GSVILDSGHLSTAS(0.547)S(0.409)S(0.044)DDLKGEEGSFR 296.67 6.79E-71 1360300000 399910 610430 529070 665150 541470 727930 620150 579070 616500 706730 TRUE FALSE 384281.0751 593021.1341 624684.7181 699478.4712 558886.8743 742649.2433 627739.5812 567112.0021 546517.5046 658862.5476 0.583249232 0.900068059 0.94812601 1.061645519 0.848260197 1.127168703 0.952762581 0.860744027 0.829486372 1 19.32961799 4.746247965 3.115904067 0.949529756 0.523723571 0.605878988 0.089029624 0.255656523 3.748092693 0.0220503 0.269709606 55750.39706 -4.746247965 -0.425806186 TLAGDVHIVR ddPTM_BT-474_Pertuzumab_2h_R1 5 TLAGDVHIVR 10 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;;;; 200.71 2.55E-07 4916730000 6230190 6884960 5563020 6825800 6674370 6228250 6856260 6733440 7010240 7545240 FALSE TRUE 5986707.287 6688607.682 6568381.463 7178080.356 6889057.173 6354189.482 6940168.961 6594392.111 6214466.945 7034194.174 0.851086441 0.950870493 0.93377881 1.020455247 0.979366933 0.9033287 0.986633122 0.937476553 0.883465368 1 22.74595373 4.746333998 4.478884867 0.954721423 0.843429805 0.371681992 0.040566639 0.22834737 11.43610748 0.009572023 0.080848663 55761.44226 -4.746333998 -0.111291617 QLEVYTSGGDPESVAGEYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLEVYTSGGDPESVAGEYGR 20 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 81.311 0.0084611 0 20997 24820 21223 24333 26959 24978 25959 23977 24349 25880 FALSE TRUE 20176.41403 24112.1579 25058.4682 25588.82905 27826.16072 25483.07227 26276.69401 23481.86657 21585.0036 24127.12455 0.836254398 0.999379675 1.038601519 1.060583452 1.153314423 1.056200138 1.089093479 0.973255911 0.89463639 1 14.55836837 4.7464126 2.618964412 1.037637757 0.792602304 0.445027788 0.065525141 0.481573595 4.233031959 0.017376683 0.261324333 55771.53534 -4.7464126 -0.245035453 S(ph)PQRPGWSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPQRPGWSR 9 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR 114.24 0.0010116 7670770000 285879 331229 282710 321135 328115 305758 300675 364904 386476 361689 TRUE FALSE 274706.5326 321782.6732 333801.9858 337708.8158 338669.117 311940.6363 304354.7506 357368.6049 342604.8647 337191.4819 0.814690013 0.954302497 0.98994786 1.001534244 1.004382184 0.925114224 0.902616961 1.059838768 1.016054329 1 18.36320857 4.746418889 2.602496725 0.987669056 0.776806334 0.599633186 0.042204611 0.36820273 3.179101173 0.011303022 0.171234468 55772.34286 -4.746418889 -0.210862722 DTPSQPSSTSHRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTPSQPSSTSHRPR 14 1 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 0 54.524 0.084103 27054000 4680.8 7631.8 6750.3 9467.5 7212.7 9161.9 9587.8 6184.5 6151.9 10353 FALSE TRUE 4497.869161 7414.148536 7970.22937 9956.11881 7444.703046 9347.159895 9705.138364 6056.787914 5453.562103 9651.782089 0.466014371 0.768163689 0.825778006 1.031531661 0.771329375 0.968438762 1.005528127 0.627530528 0.565031623 1 13.23657963 4.746462741 2.565373553 0.840490586 0.38254144 0.361761483 0.152239195 0.610271661 5.059180901 0.03963646 0.610641886 55777.97464 -4.746462741 -0.457949146 LVHLQTLVLNGNPLLHAQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVHLQTLVLNGNPLLHAQLR 20 0 Q13045-3;Q13045;J3KS54;J3QQQ2;J3KT47;J3QQU5;J3QLR6 Q13045-3 FLII Protein flightless-1 homolog 0 ; 237.31 7.83E-30 256060000 245890 281890 220380 256020 269180 265330 301220 234200 294770 285630 FALSE TRUE 236280.347 273850.7732 260207.5683 269233.2229 277838.4192 270695.1544 304906.4205 229363.6882 261308.9454 266284.0257 0.887324526 1.028416078 0.977180541 1.011075382 1.043391238 1.016565503 1.145042102 0.861349785 0.98131664 1 18.02260636 4.746473227 24.15652679 1.003298885 0.887324434 0.225627433 0.066250815 1015.721321 3100793.392 0.016205812 0.175160388 55779.32148 -4.746473227 -0.115974451 SCTWPLPRPEIANQPS(ph)EPPEVEPDLGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SCTWPLPRPEIANQPSEPPEVEPDLGEK 28 1 P98177-2;P98177 P98177-2 FOXO4 Forkhead box protein O4 1 S(0.148)CT(0.148)WPLPRPEIANQPS(0.704)EPPEVEPDLGEK 88.541 2.07E-06 0 32301 24504 18170 21498 20096 17510 17068 26909 28414 24054 TRUE FALSE 31038.64121 23805.16991 21453.72319 22607.51436 20742.40609 17864.0642 17276.88329 26353.31975 25188.56184 22424.80115 1.384121134 1.061555451 0.956696251 1.008147818 0.924976143 0.796620852 0.77043641 1.175186329 1.123245717 1 14.45280757 4.746490554 2.403013161 0.969455393 1.486263544 0.5241679 0.118440092 0.503385816 3.478241203 0.032832875 0.544465436 55781.54688 -4.746490554 0.516808151 AALEEVEGDVAELELK ddPTM_BT-474_Pertuzumab_2h_R1 2 AALEEVEGDVAELELK 16 0 Q15057;A0A0U1RQT1;A0A087X1H5 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 0 ; 195.88 1.10E-10 18523800 47756 45595 45129 47359 50644 49230 55263 56638 65896 61607 FALSE TRUE 45889.64272 44294.67524 53284.81419 49803.20367 52273.01025 50225.46433 55939.32513 55468.40551 58415.76234 57434.30302 0.798993638 0.771223344 0.92775243 0.867133421 0.910135712 0.874485485 0.973970644 0.96577137 1.017088382 1 15.80962503 4.746503452 0.256417092 1.024518364 0.583433379 0.770479707 0.037650443 4.296277721 0.238881572 0.051732376 0.606391967 55783.20364 -4.746503452 -0.441084984 TCAYTNHTVLPEALER ddPTM_BT-474_Pertuzumab_2h_R1 4 TCAYTNHTVLPEALER 16 0 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;; 173.51 4.20E-09 5433270000 1298320 1444380 1121740 1361250 1257060 1448560 1339930 1439730 1462100 1431310 FALSE TRUE 1247580.219 1403187.697 1324463.371 1431504.276 1297494.477 1477850.876 1356328.464 1409999.072 1296128.538 1334366.099 0.934960968 1.051576249 0.992578702 1.072797246 0.972367687 1.107530292 1.016459025 1.056680827 0.971344025 1 20.34772311 4.74653529 24.4857366 1.030460785 0.934960905 0.290044053 0.042771485 867.4571415 2663389.807 0.009148061 0.102076855 55787.2932 -4.74653529 -0.09549988 EQIVVDLSHPGVSEDDQVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 EQIVVDLSHPGVSEDDQVSR 20 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;; 227.6 3.62E-25 2020490000 725268 821460 635419 771319 774829 796254 777377 782113 807570 816046 FALSE TRUE 696923.7247 798032.7651 750253.3481 811126.866 799752.0785 812354.8014 786890.7723 765962.0932 715898.0392 760774.4776 0.916071379 1.048974155 0.986170502 1.066185696 1.051234107 1.067799756 1.034328563 1.006818861 0.941012166 1 19.53710932 4.746546892 24.42835748 1.024926514 0.916071305 0.413383603 0.037936892 720.7361607 2204510.874 0.009177851 0.10055093 55788.78354 -4.746546892 -0.10885521 HLTYENVER ddPTM_BT-474_Pertuzumab_2h_R1 5 HLTYENVER 9 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;;; 215.06 6.53E-07 7940200000 2201590 3457650 2452600 3709610 2623270 2763600 3600610 2735160 3584790 3434600 FALSE TRUE 2115549.429 3359041.207 2895839.378 3901063.417 2707649.862 2819481.885 3644675.342 2678677.99 3177859.668 3201971.483 0.660702146 1.049054067 0.90439262 1.218331718 0.845619605 0.880545595 1.138259776 0.83657147 0.992469697 1 21.61052903 4.746648169 24.57474814 0.977748281 0.660701946 0.399368735 0.11902059 807.1955066 2452663.914 0.026937973 0.297954873 55801.79494 -4.746648169 -0.317046335 KENNS(ph)PEHLKDEVSIIQSMGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 KENNSPEHLKDEVSIIQSMGYR 22 2 P38398-7;P38398;P38398-4;P38398-8;P38398-6;E7EUM2;B7ZA85;H0Y8B8;P38398-5;P38398-3;Q5YLB2;H0Y8D8;Q3B891;E9PH68;A0A494C182;E7EWN5;H0Y881;A0A0U1RRA9;E7EQW4 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 KENNS(1)PEHLKDEVSIIQSMGYR;KENNS(1)PEHLKDEVSIIQSMGYR 261.86 1.31E-37 352550000 360790 299790 273340 265320 303870 275200 301260 315860 345140 322700 TRUE FALSE 346689.9279 291240.2827 322738.6184 279013.197 313644.2545 280764.7326 304946.91 309337.3806 305961.1541 300843.2416 1.152393938 0.968079858 1.072780019 0.927437145 1.042550442 0.933259232 1.013640554 1.028234435 1.017011891 1 18.19865242 4.746660178 24.82867022 1.002236896 1.15239402 0.520378898 0.043761124 715.3262064 2192729.753 0.009592118 0.107606578 55803.33804 -4.746660178 0.150157123 IEEIKDFLLTAR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEEIKDFLLTAR 12 1 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 122.64 0.00032371 642640000 669250 755670 584780 718340 682880 714360 707040 793010 672010 750330 FALSE TRUE 643094.9701 734119.0315 690462.7544 755413.6135 704845.4554 728804.8486 715692.967 776634.0664 595726.2421 699509.4808 0.919351328 1.049476886 0.987067042 1.079919049 1.007628166 1.041879873 1.023135478 1.11025524 0.851634264 1 19.41598409 4.746672764 24.11951642 1.02587716 0.91935124 0.151324396 0.066128816 1031.182463 3065854.595 0.014693412 0.163409871 55804.95519 -4.746672764 -0.10652592 S(ph)RSPITTNHRPS(ph)PDPEQRPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 2 S(0.5)RS(0.5)PIT(0.159)T(0.114)NHRPS(0.727)PDPEQRPLR;S(0.5)RS(0.5)PIT(0.013)T(0.002)NHRPS(0.985)PDPEQRPLR 130.32 2.16E-05 1312070000 141598 157948 119027 143872 142430 167005 158937 142243 154077 168912 TRUE FALSE 136064.1936 153443.4777 140537.8266 151297.2512 147011.3903 170381.9555 160882.1185 139305.6323 136586.8249 157471.4398 0.864056325 0.974420999 0.892465496 0.960791693 0.933574942 1.081986395 1.021659031 0.884640621 0.867375221 1 17.26473067 4.746676622 23.48700354 0.954813289 0.864056219 0.162891734 0.06325451 889.7720471 2574776.525 0.015947849 0.170057234 55805.4509 -4.746676622 -0.09075707 KKEDCLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KKEDCLK 7 2 Q52LJ0;Q52LJ0-1;H0YNA1 Q52LJ0 FAM98B Protein FAM98B 0 61.962 0.049676 700850000 202110 158460 150400 147140 160280 124550 174130 158260 189160 201360 FALSE TRUE 194211.3178 153940.8759 177580.6256 154733.913 165435.5518 127068.4863 176261.055 154991.8757 167687.3498 187721.7078 1.034570375 0.820048346 0.945978106 0.824272881 0.881280879 0.676898201 0.938948708 0.825647057 0.893276285 1 17.51823597 4.746721987 24.33283802 0.859412416 1.034570503 0.253408522 0.08511484 895.1139428 2668659.905 0.018637302 0.207807989 55811.28046 -4.746721987 0.175158087 TPAPSYPHAASAGTPAS(ph)PPPLHRPEAYPPSSHNGGLGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPAPSYPHAASAGTPASPPPLHRPEAYPPSSHNGGLGAR 39 1 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 TPAPSYPHAAS(0.023)AGT(0.464)PAS(0.496)PPPLHRPEAY(0.006)PPS(0.005)S(0.005)HNGGLGAR;TPAPSYPHAASAGT(0.001)PAS(0.999)PPPLHRPEAYPPSSHNGGLGAR 189.55 3.94E-24 753900000 354275 217330 201679 192693 256490 198796 256510 264756 289828 193047 TRUE FALSE 340429.5413 211131.9612 238126.8816 202637.9088 264740.2338 202815.7913 259649.2461 259288.6961 256927.9405 179971.7547 1.891572051 1.173139427 1.323134744 1.125942841 1.471009905 1.126931232 1.442722201 1.440718831 1.427601464 1 17.45741098 4.746729679 24.56857959 1.306073559 1.891572422 0.563920524 0.159674014 598.1623035 1798929.54 0.036434462 0.406579179 55812.26908 -4.746729679 0.585498863 FVYVWDTTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 FVYVWDTTSR 10 0 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 ; 182.98 4.00E-06 614640000 345200 408150 321650 382890 369740 361240 394150 404390 396320 388940 FALSE TRUE 331709.2024 396509.9616 379779.3101 402650.9988 381633.0229 368544.5203 398973.7256 396039.2052 351331.4151 362596.7474 0.914815714 1.093528733 1.047387526 1.110465005 1.052499852 1.016403272 1.10032351 1.092230441 0.968931513 1 18.46800646 4.746761698 24.54350134 1.060386076 0.91481562 0.453105185 0.0451569 667.2090748 1996706.831 0.01026359 0.114032217 55816.38405 -4.746761698 -0.145570456 ICNAVSPDKDVDGFHVINVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ICNAVSPDKDVDGFHVINVGR 21 1 P13995-2;P13995;B8ZZU9 P13995-2 MTHFD2 "Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial;NAD-dependent methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase" 0 63.184 0.021112 210920000 93873 129500 79550 161460 89479 109470 139650 114050 140250 101070 FALSE TRUE 90204.33938 125806.7868 93926.45458 169792.9699 92357.1733 111683.5584 141359.0785 111694.8276 124329.408 94224.43888 0.957334853 1.335182128 0.996837505 1.802005636 0.980182789 1.1852929 1.500237944 1.1854125 1.319502769 1 16.52381368 4.746777855 23.47905562 1.267416752 0.95733448 0.118655569 0.242485736 876.9058046 2505435.437 0.053099862 0.57122726 55818.4606 -4.746777855 -0.310082271 LEGVLAEVAQHYQDTLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEGVLAEVAQHYQDTLIR 18 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 205.62 9.42E-16 972410000 1565680 807400 809320 695360 1084300 577920 1063370 1243610 825920 820750 FALSE TRUE 1504491.495 784373.7425 955582.1272 731247.6129 1119177.494 589605.9384 1076383.84 1217929.019 732165.0241 765159.8715 1.966244638 1.025110924 1.248865973 0.955679512 1.462671444 0.770565682 1.406743715 1.591731433 0.956878492 1 19.54540169 4.746785873 24.43919193 1.199469655 1.966245164 0.471892752 0.253175615 714.3533054 2122446.691 0.06085351 0.679756416 55819.49108 -4.746785873 0.76677551 SMIEISR ddPTM_BT-474_Pertuzumab_2h_R1 4 SMIEISR 7 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;Q5SZW8;E9PM09;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 166.05 0.0034697 565740000 732931 845134 712101 875742 825121 771097 850303 839277 915729 951375 FALSE TRUE 704287.2462 821031.6058 840793.4913 920939.1496 851661.7663 786689.1097 860709.2625 821945.6367 811779.283 886937.5239 0.794066354 0.925692716 0.947973751 1.038335987 0.960227461 0.886972406 0.970428288 0.926723264 0.915260953 1 19.75847296 4.746803739 2.747384341 0.952885671 0.762083819 0.587579944 0.040439365 0.333989681 3.364597203 0.010214837 0.145642191 55821.78747 -4.746803739 -0.190801853 RLNNLSPAPHLAS(ph)GSPPPGLPSGLPSGLQSGS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 35 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 RLNNLS(0.005)PAPHLAS(0.498)GS(0.498)PPPGLPSGLPS(0.004)GLQS(0.095)GS(0.779)PS(0.123)R 127.66 3.94E-08 662100000 101360 132340 106260 136440 100910 141050 136290 129210 154820 128350 TRUE FALSE 97398.73914 128565.7928 125463.5457 143481.6848 104155.8618 143902.1276 137957.9578 126541.7683 137245.4827 119656.7402 0.813984561 1.074455084 1.048528863 1.199110761 0.870455451 1.202624503 1.152947653 1.057539827 1.146993328 1 16.86854214 4.746823944 4.215814952 1.088109779 0.790270035 0.418829535 0.095273864 0.210676511 8.429675118 0.021402786 0.191036144 55824.38455 -4.746823944 -0.297839744 PSGGFVISGVLS(ph)PDTISSK ddPTM_BT-474_Pertuzumab_2h_R1 2 PSGGFVISGVLSPDTISSK 19 0 Q03188;H0Y8J2;H0Y9W1 Q03188 CENPC Centromere protein C 1 PSGGFVISGVLS(1)PDTISSK;PSGGFVISGVLS(0.978)PDT(0.021)IS(0.001)SK 246.12 1.30E-24 449710000 1397450 1077250 1011860 917690 1209300 940020 1162130 1140650 1181540 1222280 TRUE FALSE 1342836.109 1046527.885 1194725.611 965052.0909 1248198.233 959027.8485 1176352.495 1117095.179 1047416.533 1139493.887 1.178449595 0.918414655 1.048470399 0.846912916 1.095397042 0.841626146 1.032346472 0.980343284 0.919194517 1 20.11996175 4.746877194 24.46976031 0.967055903 1.178449738 0.392856694 0.079654343 737.7026589 2170466.673 0.016776506 0.188477303 55831.22981 -4.746877194 0.211393835 GGDGGERDEDGDALAER ddPTM_BT-474_Pertuzumab_2h_R1 1 GGDGGERDEDGDALAER 17 1 Q8N8J7 Q8N8J7 C4orf32 Uncharacterized protein C4orf32 0 94.856 0.0024733 170500000 110980 163000 106570 180010 130160 119540 161170 164060 144410 159310 FALSE TRUE 106642.7789 158351.3996 125829.5696 189300.3377 134346.7146 121957.1807 163142.4467 160672.1037 128017.1822 148519.7918 0.718037493 1.06619729 0.847224253 1.274579875 0.904571121 0.821151035 1.098455934 1.081822845 0.861953688 1 17.18029567 4.746881794 24.0160565 1.001989277 0.718037243 0.276279977 0.134114292 773.9251569 2233564.522 0.030951984 0.341059374 55831.82113 -4.746881794 -0.283952034 SPGSGSQS(ph)SGWHEVEPGMPSPTTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGSGSQSSGWHEVEPGMPSPTTLK 25 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.198)PGS(0.171)GS(0.171)QS(0.23)S(0.23)GWHEVEPGMPSPTTLK 108.1 0.0022236 1488000000 272350 348940 295380 381350 321530 353550 340800 338030 367330 407410 TRUE FALSE 261706.2609 338988.5728 348761.7367 401031.5192 331872.3045 360699.0232 344970.8123 331049.5624 325632.2384 379815.7578 0.689034764 0.892507922 0.91823925 1.055858034 0.873771816 0.949668401 0.908258294 0.871605655 0.857342624 1 18.53494024 4.746893491 3.115805827 0.923694904 0.650733883 0.601848494 0.058177811 0.260856171 3.819181209 0.014361621 0.176539783 55833.32491 -4.746893491 -0.272961021 FLEEHPGGEEVLR ddPTM_BT-474_Pertuzumab_2h_R1 3 FLEEHPGGEEVLR 13 0 P00167-2;P00167;P00167-3 P00167-2 CYB5A Cytochrome b5 0 ;; 186.13 8.07E-06 1653100000 1339629 2164460 1279682 2654060 1510140 1722790 1951990 2284810 2104350 1507690 FALSE TRUE 1287274.818 2102731.72 1510949.004 2791036.355 1558715.025 1757625.994 1975879.038 2237627.875 1865473.01 1405572.813 0.915836451 1.495996294 1.074970282 1.985693184 1.108953595 1.250469543 1.405746482 1.591968665 1.327197704 1 20.42272676 4.746909978 23.88985468 1.389165155 0.915836001 0.182750777 0.275758175 866.3668803 2478810.58 0.061411217 0.680736539 55835.44449 -4.746909978 -0.473329153 YGREDLDVLGLTFR ddPTM_BT-474_Pertuzumab_2h_R1 3 YGREDLDVLGLTFR 14 1 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 211.7 3.17E-09 657804000 585450 605301 497182 559296 570279 546793 600027 594172 652441 596524 FALSE TRUE 562569.9668 588038.4081 587033.8472 588161.3336 588622.5419 557849.5291 607370.3099 581902.1406 578378.6329 556120.8982 1.011596523 1.057393114 1.055586742 1.057614155 1.058443486 1.003108373 1.092155163 1.046359061 1.040023194 1 19.08503903 4.746997086 24.03288726 1.048850971 1.01159649 0.123687755 0.025933268 1144.38972 3259886.784 0.005695339 0.064719372 55846.64477 -4.746997086 -0.037254481 HMAAASAECQNYAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HMAAASAECQNYAK 14 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 205.96 1.32E-07 0 196370 230930 182150 222060 210320 186820 236380 209360 246900 236220 FALSE TRUE 188695.6433 224344.1025 215068.5569 233520.5432 217085.1338 190597.6284 239272.8891 205036.6428 218872.9471 220220.609 0.856848249 1.018724376 0.976605041 1.060393686 0.985762117 0.865484976 1.086514519 0.931051112 0.993880401 1 17.74858996 4.747009574 24.27193588 0.98826159 0.856848149 0.318768427 0.058688398 852.9059481 2450120.675 0.013253167 0.149615532 55848.25059 -4.747009574 -0.131413441 DDAFAEWTEMAHER ddPTM_BT-474_Pertuzumab_2h_R1 4 DDAFAEWTEMAHER 14 0 E9PKJ0;E9PJW4;E9PQK1;H0YCG9;E9PM62;Q5T9L3-3;Q5T9L3;Q5T9L3-2 E9PKJ0 WLS Protein wntless homolog 0 ;;; 228.25 1.73E-12 163618000 179929 298861 189872 349216 234505 201170 283546 308244 272713 223800 FALSE TRUE 172897.1758 290337.7769 224186.0941 367239.0796 242048.0663 205237.7952 287016.1208 301878.6537 241755.7635 208641.8267 0.828679362 1.391560751 1.074502163 1.760141221 1.16011286 0.983684808 1.375640375 1.446875051 1.158711882 1 17.67066888 4.747097843 24.01059652 1.2856699 0.828678953 0.238799607 0.227968142 849.5956726 2389357.331 0.052591061 0.594886332 55859.60277 -4.747097843 -0.456990948 S(ph)TVPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 STVPSR 6 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3;REV__M0R088 LMO7 LIM domain only protein 7 1 S(0.821)T(0.179)VPSR 105.14 0.034862 84893000 86419 103260 85435 117510 102700 105160 114880 104190 93814 115210 TRUE FALSE 83041.64994 100315.1259 100875.005 123574.7052 106003.4388 107286.4073 116285.9358 102038.4401 83164.62802 107406.7241 0.773151315 0.933974356 0.939187056 1.150530437 0.986934847 0.998879802 1.082669049 0.950019107 0.77429629 1 16.71272479 4.747177672 1.856497618 0.992974955 0.70140082 0.324486859 0.092178628 1.008249994 3.508907891 0.024074724 0.515175397 55869.8714 -4.747177672 -0.291574136 FNHNLLPSETAHKPDLSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 FNHNLLPSETAHKPDLSSK 19 1 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 139.11 3.91E-07 396900000 375690 404520 344400 360760 354380 411570 418490 294530 500850 469710 FALSE TRUE 361007.6195 392983.4857 406640.7411 379378.8668 365778.9545 419892.2274 423611.6058 288447.8526 443995.6077 437896.1233 0.824413828 0.897435407 0.928623752 0.866367265 0.835309872 0.958885464 0.96737921 0.658712962 1.013929067 1 18.74022915 4.747354815 21.94623228 0.884322545 0.824413667 0.024065026 0.099194771 929.4019309 2319045.113 0.023831773 0.257038181 55892.66461 -4.747354815 -0.059908878 ALEATTEHIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEATTEHIR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ; 185.14 1.48E-06 725220000 312850 385020 321300 401200 386750 354080 382120 373490 401860 423240 FALSE TRUE 300623.4761 374039.6066 379366.0573 421905.9801 399190.165 361239.7402 386796.4989 365777.301 356242.5375 394573.5778 0.761894595 0.947959082 0.96145834 1.069270736 1.011700193 0.915519337 0.980289915 0.927019247 0.902854518 1 18.58993483 4.747361068 3.445677398 0.969179363 0.733790427 0.638188152 0.046925403 0.214631426 4.306228792 0.012182934 0.133868196 55893.46947 -4.747361068 -0.235388936 GDSET(ph)DLEALFNAVMNPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDSETDLEALFNAVMNPK 18 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 GDS(0.428)ET(0.572)DLEALFNAVMNPK 199.12 6.10E-15 400790000 409700 352940 305620 352310 336960 347150 266340 389810 420080 420410 TRUE FALSE 393688.4711 342874.4968 360852.3325 370492.7613 347798.6244 354169.6109 269599.5486 381760.2873 372394.2795 391935.2562 1.004473226 0.874824327 0.920693729 0.945290722 0.887387952 0.903643153 0.687867561 0.974039159 0.950142335 1 18.58025583 4.747400631 22.55680661 0.898693577 1.004473449 0.114453483 0.081493492 602.2655498 1536640.973 0.019053577 0.210727384 55898.56138 -4.747400631 0.105779872 LMNESLMLVTALNPHIGYDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LMNESLMLVTALNPHIGYDK 20 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 204.82 9.25E-22 525920000 502930 620860 445130 620180 490410 567850 656710 603970 593960 556110 FALSE TRUE 483274.9396 603153.6807 525574.8929 652187.5641 506184.483 579332.3161 664747.0134 591497.8084 526536.1509 518444.1744 0.932163892 1.16339176 1.013754072 1.257970668 0.976352919 1.117443969 1.282195936 1.140909355 1.015608193 1 18.98382912 4.747417117 23.79625499 1.118940281 0.932163699 0.202027012 0.102304585 858.1476424 2305628.731 0.023373756 0.269997715 55900.68338 -4.747417117 -0.186776581 DQMQQQLNDYEQLLDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DQMQQQLNDYEQLLDVK 17 0 P20700;E9PBF6 P20700 LMNB1 Lamin-B1 0 133.66 4.55E-05 21105000 57695 62899 48820 62684 55109 62873 52666 67868 60302 60875 FALSE TRUE 55440.21561 61105.1821 57642.86 65919.12875 56881.63103 64144.33514 53310.54226 66466.50208 53456.76977 56751.88203 0.976887702 1.07670759 1.015699532 1.16153203 1.00228625 1.130259171 0.939361663 1.171177055 0.941938273 1 15.79238062 4.747420642 23.40753975 1.057754318 0.976887598 0.057059246 0.080536801 1172.025898 3096238.092 0.017104393 0.195977776 55901.13703 -4.747420642 -0.080866719 LYFSMDDGQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LYFSMDDGQTR 11 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 119.22 0.0019862 0 102689 130481 112630 133464 125080 129226 122994 145948 137197 148011 FALSE TRUE 98675.80035 126759.8096 132984.7464 140352.093 129103.3118 131839.0383 124499.2374 142934.1228 121622.9717 137986.0831 0.715114149 0.918641987 0.963754775 1.017146728 0.9356256 0.955451704 0.902259377 1.035858976 0.88141477 1 17.07416324 4.747447878 2.667590522 0.96394566 0.662311981 0.721974149 0.045630622 0.233839822 2.161463278 0.01067795 0.158254131 55904.64288 -4.747447878 -0.301633679 RDPYGFGDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 RDPYGFGDSR 10 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 ;; 110.39 0.0030349 681270000 703163 792099 583651 706176 766862 767404 768612 773501 758721 815634 FALSE TRUE 675682.6126 769509.1121 689129.7189 742621.828 791528.8127 782921.4347 778018.5036 757527.934 672594.1729 760390.3827 0.88859963 1.011992168 0.906284107 0.976632326 1.040950584 1.029630901 1.023182988 0.996235554 0.88453798 1 19.53638076 4.747471934 24.18230861 0.987858856 0.888599548 0.258708527 0.049058233 1049.364731 2847522.194 0.011933561 0.141779244 55907.73967 -4.747471934 -0.099259308 AEVWDLDMLR ddPTM_BT-474_Pertuzumab_2h_R1 5 AEVWDLDMLR 10 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;;;; 193.38 1.35E-06 321021000 517480 590633 531604 593631 532296 351182 618817 561481 571276 699418 FALSE TRUE 497256.3095 573788.7251 627676.6683 624268.3671 549417.7843 358283.1407 626390.2676 549886.2211 506427.1435 652045.7959 0.762609486 0.879982248 0.962626662 0.957399574 0.842606129 0.549475425 0.960653794 0.84332454 0.776674195 1 19.31461377 4.747483423 22.53089237 0.858224338 0.762609291 0.054682558 0.124194752 1038.872168 2623001.858 0.029701544 0.330974149 55909.21866 -4.747483423 -0.095615047 EAVAHENNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAVAHENNR 9 0 Q99747;J3KTJ6 Q99747 NAPG Gamma-soluble NSF attachment protein 0 147.95 9.12E-05 163150000 196220 221870 169250 209120 196580 212460 231140 205160 215550 221860 FALSE TRUE 188551.5055 215542.4848 199837.2399 219912.7083 202903.1742 216756.0868 233968.7605 200923.3743 191081.6677 206833.2246 0.911611303 1.042107646 0.966175721 1.06323686 0.980998941 1.047975185 1.131195246 0.971426978 0.923844165 1 17.65810843 4.747521098 24.02222958 1.016606743 0.911611208 0.22883737 0.056278117 1043.066434 2796259.579 0.01341343 0.160988017 55914.06895 -4.747521098 -0.104995534 IKEEGY(ph)KK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKEEGYKK 8 2 Q4G0S7 Q4G0S7 CCDC152 Coiled-coil domain-containing protein 152 1 IKEEGY(1)KK;IKEEGY(1)KK 78.334 0.024894 3579700000 3872300 5831200 4167700 5751100 4605100 5822100 5240900 4966800 5333800 5860700 TRUE FALSE 3720966.235 5664899.885 4920896.1 6047914.96 4753227.224 5939826.851 5305039.702 4864233.844 4728329.385 5463749.569 0.681027962 1.036815435 0.900644519 1.106916575 0.869957007 1.087133804 0.970952207 0.890273938 0.865400093 1 22.38145993 4.747549562 24.6975224 0.965618994 0.681027787 0.516497051 0.08372807 795.5428152 2185732.785 0.019176337 0.231569722 55917.73378 -4.747549562 -0.284591207 GDSGAAPDVDDKLCLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDSGAAPDVDDKLCLR 16 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 127.3 6.11E-05 287440000 265960 223160 177930 201880 240790 229820 217980 229840 246220 255180 FALSE TRUE 255565.9892 216795.6953 210085.909 212299.051 248535.229 234467.1179 220647.7044 225093.7237 218270.1378 237896.4313 1.074274161 0.911302848 0.883098195 0.892401159 1.044720291 0.985584847 0.927494806 0.946183692 0.917500681 1 17.8599741 4.747592216 24.41534862 0.943746044 1.074274256 0.389174463 0.048411442 943.7238375 2551115.311 0.012043583 0.146791827 55923.22601 -4.747592216 0.130528212 HGEEGVEAEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 HGEEGVEAEKK 11 1 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 166.14 1.35E-05 787600000 1070000 764910 754060 618730 806500 825030 825530 538140 1268300 1091600 FALSE TRUE 1028183.217 743095.5157 890335.416 650662.7294 832441.8049 841712.6719 835633.0831 527027.2209 1124327.901 1017664.96 1.010335678 0.730196622 0.874880684 0.639368314 0.817992009 0.827101949 0.821127892 0.517878911 1.104811451 1 19.95683124 4.747638291 23.67392513 0.784876635 1.010335929 0.093154698 0.160119083 1068.537791 2786539.907 0.036179157 0.426831582 55929.15932 -4.747638291 0.225459294 RKHDNEGS(ph)GSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKHDNEGSGSK 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 RKHDNEGS(0.971)GS(0.029)K 83.499 0.0086938 12821000 16239 10521 10876 8504.8 10505 12337 13496 10621 11728 12427 TRUE FALSE 15604.36193 10220.95138 12841.53514 8943.733747 10842.90287 12586.46259 13661.16809 10401.67264 10396.68661 11585.30822 1.346909519 0.882233876 1.108432757 0.77198928 0.935918377 1.08641586 1.179180374 0.897833052 0.897402677 1 13.50000881 4.747742936 24.54693271 0.976303771 1.346909771 0.480215851 0.116580769 851.8503216 2277173.626 0.028016204 0.345330288 55942.63721 -4.747742936 0.370605999 GT(ph)PTAENPEYLGLDVPV ddPTM_BT-474_Pertuzumab_2h_R1 4 GTPTAENPEYLGLDVPV 17 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GT(0.901)PT(0.099)AENPEYLGLDVPV;GT(0.897)PT(0.103)AENPEYLGLDVPV;GT(0.963)PT(0.037)AENPEYLGLDVPV;GT(0.911)PT(0.089)AENPEYLGLDVPV 131.13 0.00031269 993700000 455814 804540 555739 1458240 615075 679480 1382110 1561020 1126000 913790 TRUE FALSE 438000.285 781595.3069 656173.3996 1533499.941 634859.446 693219.5511 1399024.676 1528784.391 998181.2006 851898.1894 0.51414628 0.917475018 0.770248614 1.800097665 0.745229247 0.813735209 1.642243983 1.79456232 1.171714194 1 19.7003215 4.747745081 0.533258267 1.39691348 1.02E-09 0.260257473 0.3819329 5.487973727 1.185909681 0.227622464 4.825981903 55942.91355 -4.747745081 -1.396913479 FPGLALRPSS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 FPGLALRPSSR 11 1 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 FPGLALRPS(0.012)S(0.988)R;FPGLALRPS(0.135)S(0.865)R 87.573 0.0082507 1434540000 839380 895480 692100 850870 897440 751950 813070 958870 924100 859630 TRUE FALSE 806576.1016 869941.7872 817177.8657 894783.5027 926306.9726 767154.9442 823020.5939 939068.9994 819200.0421 801406.4944 1.006450668 1.085518764 1.019679615 1.116516411 1.155851592 0.957260703 1.026970208 1.171776129 1.022202899 1 19.61217468 4.747838061 22.95155659 1.070192144 1.006450562 0.04535805 0.066663901 1148.143837 2840203.14 0.015973415 0.188929096 55954.89195 -4.747838061 -0.063741582 HTTFEQPVFSVSKQS(ph)PPISTSK ddPTM_BT-474_Pertuzumab_2h_R1 2 HTTFEQPVFSVSKQSPPISTSK 22 1 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 HTTFEQPVFSVSKQS(1)PPISTSK;HTTFEQPVFSVS(0.002)KQS(0.998)PPISTSK 191.92 7.57E-18 1649640000 888740 1262080 972990 1092410 998430 1372600 1235850 830580 1355530 1541920 TRUE FALSE 854007.0582 1226086.714 1148830.937 1148789.411 1030545.408 1400354.912 1250974.702 813428.2327 1201655.917 1437484.385 0.59409832 0.852939153 0.79919542 0.799166532 0.716908941 0.974170521 0.870252724 0.565869265 0.835943632 1 20.45511485 4.747849411 23.65340191 0.801553889 0.594098082 0.234542228 0.118508763 953.3298302 2427489.49 0.029011926 0.349606571 55956.3542 -4.747849411 -0.207455807 THTTALAGR ddPTM_BT-474_Pertuzumab_2h_R1 1 THTTALAGR 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 96.331 0.0074403 42834000 32247 43569 34095 37367 44097 35569 44079 36558 38807 46636 FALSE TRUE 30986.75159 42326.45478 40256.72494 39295.51535 45515.42005 36288.22955 44618.45199 35803.06452 34401.79205 43477.30218 0.712711002 0.973529926 0.92592509 0.903816782 1.046877745 0.834647684 1.026247024 0.823488642 0.791258664 1 15.4079748 4.747942919 24.34114546 0.920198062 0.712710841 0.365470561 0.083728645 961.4712135 2494333.104 0.019304964 0.241513122 55968.40355 -4.747942919 -0.207487221 CEYLMELMTPAACPEPPPEAPTEDDHDEL ddPTM_BT-474_Pertuzumab_2h_R1 5 CEYLMELMTPAACPEPPPEAPTEDDHDEL 29 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;; 228.57 6.94E-35 671713000 437592 520328 389371 515676 472604 533765 493871 427139 534533 527502 FALSE TRUE 420490.4209 505488.7549 459739.0012 542290.1002 487805.7369 544558.094 499915.141 418318.4304 473855.0548 491773.8197 0.855048406 1.027888705 0.934858634 1.10272259 0.991931082 1.107334454 1.016555012 0.850631761 0.963562995 1 18.90763541 4.747951401 23.57520786 0.993373952 0.85504824 0.264023516 0.071698542 892.5053395 2240492.77 0.018735658 0.225799179 55969.49662 -4.747951401 -0.138325712 SQQQPTPVT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 SQQQPTPVTPK 11 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 SQQQPT(0.071)PVT(0.929)PK;SQQQPTPVT(1)PK;SQQQPT(0.001)PVT(0.999)PK;SQQQPTPVT(1)PK;SQQQPTPVT(1)PK 170.89 0.00016973 8864900000 8107150 5328330 3733810 3818960 4167440 3217060 3802200 7040520 3886390 3383500 TRUE FALSE 7790313.615 5176371.245 4408592.525 4016056.983 4301489.492 3282111.157 3848732.461 6895130.802 3445223.3 3154332.531 2.469718566 1.641035368 1.397630872 1.273187574 1.36367661 1.040508927 1.220141638 2.185923879 1.092219437 1 21.58890333 4.748027961 2.292877716 1.38952924 2.754859392 0.528797255 0.322481616 0.556283147 3.370478594 0.087656097 1.542633817 55979.36408 -4.748027961 1.365330151 VLPSDLDLLLHMNNAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLPSDLDLLLHMNNAR 16 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ; 222.16 9.90E-15 810810000 344900 599880 337260 665520 392160 451500 584120 640080 530350 503310 FALSE TRUE 331420.9267 582772.0097 398210.3843 699867.567 404774.1826 460629.6393 591268.6353 626862.1243 470146.8914 469220.3654 0.706322554 1.242000673 0.848663898 1.491554115 0.862652631 0.981691489 1.260108637 1.335965296 1.001974607 1 18.83990611 4.748125435 24.00503616 1.132013892 0.706322151 0.263651857 0.202274108 967.1868936 2427280.649 0.046879853 0.589725537 55991.92961 -4.748125435 -0.425691741 LCDEQLSSQSHYDFGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LCDEQLSSQSHYDFGLR 17 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 286.14 2.15E-36 2488660000 1125950 1460190 1260490 1591510 1463810 1619330 1478120 1325510 1585560 1743010 FALSE TRUE 1081946.629 1418546.811 1488288.582 1673648.022 1510894.778 1652073.962 1496209.675 1298137.755 1405573.876 1624954.38 0.665832003 0.872976391 0.915895609 1.029966159 0.929807505 1.016689442 0.920770265 0.798876431 0.864992823 1 20.63196779 4.74813564 2.470852284 0.925860563 0.603983259 0.591558537 0.066745313 0.446036626 3.317534051 0.018875466 0.306552952 55993.24541 -4.74813564 -0.321877304 ALEAASLSQHPPSLCIS(ph)DS(ph)EEEEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ALEAASLSQHPPSLCISDSEEEEEER 26 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 ALEAASLS(0.004)QHPPS(0.009)LCIS(0.993)DS(0.994)EEEEEER 77.719 0.011384 197430000 39995 47120 35051 44281 43799 48835 37053 45974 47700 49584 TRUE FALSE 38431.95118 45776.18374 41385.49541 46566.34772 45207.83461 49822.47716 37506.4657 45024.62083 42285.29597 46225.63152 0.831399159 0.990277087 0.89529324 1.00737072 0.977981979 1.077810633 0.811378114 0.974018512 0.914758643 1 15.49640541 4.748249389 23.78586228 0.957565788 0.831399023 0.239801057 0.068977329 981.03808 2408340.468 0.015699106 0.198227735 56007.91293 -4.748249389 -0.126166766 LLLIQAFRPDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLLIQAFRPDR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 191.52 1.64E-06 1260420000 787690 961310 865750 888270 821230 715820 993900 846740 958200 1032750 FALSE TRUE 756906.204 933894.38 1022210.284 934113.7212 847645.6088 730294.3708 1006063.646 829254.5231 849429.1531 962800.9226 0.786150269 0.969976615 1.06170472 0.970204431 0.880395509 0.758510252 1.044934235 0.86129386 0.882247963 1 19.876878 4.748389211 23.75994206 0.931742754 0.786150109 0.206695898 0.087955346 1160.394929 2805056.032 0.021382701 0.271585297 56025.94761 -4.748389211 -0.145592645 EQFWPAVCEHFGVEATGEESSIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQFWPAVCEHFGVEATGEESSIR 23 0 P16435;H0Y4R2 P16435 POR NADPH--cytochrome P450 reductase 0 99.957 4.12E-05 0 26222 44884 27110 45779 34911 39561 37298 45406 41723 35112 FALSE TRUE 25197.21525 43603.95227 32009.38006 48141.65968 36033.94402 40360.95053 37754.46408 44468.35023 36986.77996 32733.83297 0.769760611 1.332075969 0.977868375 1.470700352 1.100816518 1.233004108 1.153377428 1.358482836 1.129925114 1 14.99849492 4.748584411 24.37563841 1.211100432 0.769760264 0.416137194 0.150090997 850.676447 2068596.198 0.032196437 0.428756715 56051.13497 -4.748584411 -0.441340168 HSLSFNDCFVK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSLSFNDCFVK 11 0 P55317-2;P55317;P55318 P55317-2 FOXA1;FOXA3 Hepatocyte nuclear factor 3-alpha;Hepatocyte nuclear factor 3-gamma 0 ; 119.39 0.00059311 687380000 943110 751210 681410 712590 791290 640080 768960 725990 1057850 855730 FALSE TRUE 906252.2185 729786.2263 804555.9449 749366.8553 816742.5615 653022.8562 778370.7625 710998.0528 937767.3029 797770.6449 1.135980904 0.914782 1.008505327 0.939326184 1.023781167 0.818559645 0.975682381 0.891231154 1.175484845 1 19.60561451 4.748619256 24.35366394 0.962465644 1.135981041 0.223333127 0.090239899 1330.669731 3221681.112 0.020029475 0.266534916 56055.63235 -4.748619256 0.173515397 DLADVDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLADVDLR 8 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 ; 119.27 0.0040145 250730000 800000 928560 771550 980420 954980 987180 981640 1017340 1049880 1080270 FALSE TRUE 768735.1156 902078.378 910986.248 1031019.594 985697.799 1007141.456 993653.604 996331.5735 930702.0239 1007102.351 0.763313793 0.895716684 0.904561733 1.023748572 0.978746399 1.000038829 0.986646097 0.989305181 0.924138468 1 19.94177888 4.748674804 1.120928485 0.985565963 0.655947411 0.840361883 0.029516429 0.597099156 0.610661796 0.008370444 0.234239685 56062.80251 -4.748674804 -0.329618551 TSS(ph)TDEVLSLEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSTDEVLSLEEK 13 0 K7ENH8;A0A0A0MRB7;P15923-2;K7EMM4 K7ENH8 TCF3 Transcription factor E2-alpha 1 T(0.001)S(0.029)S(0.955)T(0.015)DEVLSLEEK;TS(0.004)S(0.992)T(0.004)DEVLSLEEK 214.48 3.23E-11 243610000 981700 845750 701410 678210 782440 866440 800250 836110 917360 904250 TRUE FALSE 943334.0787 821630.0381 828170.3898 713212.4994 807607.8932 883960.0104 810043.6989 818844.0363 813225.1387 843004.3421 1.119014496 0.974645084 0.982403469 0.846036567 0.958011546 1.048582986 0.960900981 0.971340236 0.964674911 1 19.68518054 4.74878291 3.869292782 0.96451434 1.135656344 0.476038377 0.047742321 0.2381065 7.007550236 0.011863533 0.116964042 56076.75962 -4.74878291 0.171142004 QQGHEPVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 QQGHEPVSPR 10 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 QQGHEPVS(1)PR;QQGHEPVS(1)PR;QQGHEPVS(1)PR;QQGHEPVS(1)PR;QQGHEPVS(1)PR 152.47 1.16E-05 2592990000 1530880 1710750 1320840 1605740 1611090 1639610 1508600 1657000 1778460 1732330 TRUE FALSE 1471051.517 1661961.085 1559545.17 1688612.434 1662912.173 1672764.038 1527062.698 1622782.371 1576576.677 1614997.746 0.910869084 1.029079507 0.965663992 1.045581914 1.029668417 1.035768651 0.945550978 1.004820208 0.976209831 1 20.62310072 4.748802505 24.60132666 1.003061484 0.91086902 0.443610531 0.031148228 1086.25157 2609143.83 0.007380733 0.100629469 56079.28982 -4.748802505 -0.092192464 S(ph)PSYTNDSTATFIIDGMHCK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSYTNDSTATFIIDGMHCK 20 0 Q04656-5;Q04656;Q04656-2;Q04656-3 Q04656-5 ATP7A Copper-transporting ATPase 1 1 S(0.959)PS(0.038)Y(0.003)TNDSTATFIIDGMHCK;S(0.915)PS(0.085)YTNDSTATFIIDGMHCK 259.58 1.72E-36 782470000 640880 943610 569860 1058080 693680 774010 933850 970850 816750 742720 TRUE FALSE 615833.7011 916699.1667 672846.3785 1112687.636 715992.8472 789661.0125 945278.7356 950801.6082 724035.9641 692414.9129 0.889399823 1.323915978 0.971738716 1.606966596 1.034051743 1.140444837 1.365191185 1.373167433 1.045667779 1 19.40127727 4.748944541 23.70383732 1.229921766 0.889399423 0.180545272 0.197397594 1082.302004 2470513.834 0.044195624 0.593794132 56097.63357 -4.748944541 -0.340522343 RLDS(ph)SGER ddPTM_BT-474_Pertuzumab_2h_R1 2 RLDSSGER 8 1 A0A087X2H1;Q9ULT8;G3V4V5;A0A087WVU6 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 RLDS(0.999)S(0.001)GER;RLDS(0.996)S(0.004)GER 143.22 0.00037056 412670000 136962 162854 113046 150733 165803 152007 162688 148466 151808 155577 TRUE FALSE 131609.3736 158209.5634 133475.9269 158512.3482 171136.2041 155080.6857 164679.0244 145400.1252 134575.3923 145039.6312 0.907402842 1.0908023 0.920272106 1.092889901 1.179927187 1.06922973 1.135407082 1.002485486 0.927852554 1 17.14608764 4.749054172 23.69218099 1.050830655 0.907402672 0.210789013 0.080383138 1159.515146 2617823.561 0.019571649 0.268119434 56111.79629 -4.749054172 -0.143427983 DIILPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIILPFR 7 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 103.29 0.019566 14891000 27419 32796 24203 29097 28534 31055 32388 33273 30886 30020 FALSE TRUE 26347.43517 31860.69019 28577.02049 30598.69966 29451.82202 31682.95338 32784.37403 32585.90092 27379.95076 27986.71866 0.941426377 1.138421784 1.021092213 1.093329305 1.052349951 1.132071028 1.171426148 1.164334459 0.978319434 1 14.77245473 4.749065486 24.23443318 1.094730906 0.941426244 0.279990121 0.066163689 1166.37222 2690705.688 0.015829574 0.215495618 56113.25813 -4.749065486 -0.153304662 EAEDSLRR ddPTM_BT-474_Pertuzumab_2h_R1 3 EAEDSLRR 8 1 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776;REV__H7BZ55 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;; 178.94 0.00039597 6397680000 3188440 3641370 2814710 3238680 3308730 3493430 3593190 3423550 3593680 3677230 FALSE TRUE 3063832.24 3537521.693 3323390.71 3405828.663 3415158.305 3564069.548 3637164.534 3352852.496 3185740.512 3428167.937 0.893722914 1.0318986 0.969436379 0.993483612 0.996205078 1.039642635 1.060964515 0.978030411 0.929283679 1 21.70900635 4.749090218 24.51061676 1.000944859 0.893722835 0.442035206 0.03576342 1108.954961 2581338.061 0.008783706 0.123624802 56116.45368 -4.749090218 -0.107222025 DIPRTPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 DIPRTPSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DIPRT(0.003)PS(0.997)R 107.51 0.010492 2382800000 890790 943470 710850 904270 916190 913180 841470 944690 972530 955560 TRUE FALSE 855976.942 916563.1594 839316.4078 950939.4831 945660.0834 931645.1253 851768.1616 925181.8214 862132.4716 890839.0701 0.960865964 1.028876247 0.942163895 1.06746495 1.061538627 1.045806315 0.956141452 1.038551016 0.967775775 1 19.76480531 4.74923926 23.60250367 1.013897597 0.9608659 0.115589509 0.042179745 1517.90007 3354794.565 0.009873054 0.135082504 56135.7152 -4.74923926 -0.053031697 IFPHLYLGSEWNAANLEELQR ddPTM_BT-474_Pertuzumab_2h_R1 1 IFPHLYLGSEWNAANLEELQR 21 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;E9PIT5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 256.13 1.94E-36 240010000 84358 106460 77953 100920 95313 95555 98179 98407 105150 106860 FALSE TRUE 81061.1961 103423.865 92040.84116 106128.4933 98378.82921 97487.18757 99380.54397 96374.86106 93213.81282 99622.27702 0.813685438 1.038160019 0.923898187 1.065308849 0.987518376 0.978568152 0.997573504 0.967402713 0.935672378 1 16.60418077 4.749240047 24.85312572 0.986837269 0.813685332 0.629821129 0.040132355 872.7749492 2031075.658 0.008941643 0.128863127 56135.81685 -4.749240047 -0.173151937 DLQNVNITLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLQNVNITLR 10 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 78.488 0.069448 98090000 58643 82605 63256 81939 57807 75796 77205 79000 67945 83867 FALSE TRUE 56351.16673 80249.18628 74687.76632 86167.88161 59666.41465 77328.64705 78149.85788 77368.62239 60232.16845 78186.61339 0.720726532 1.026380128 0.95525005 1.102079728 0.763128265 0.989026685 0.9995299 0.989537966 0.770364207 1 16.254634 4.749258669 24.12947675 0.957897508 0.720726311 0.321612845 0.10201236 1092.40406 2463839.953 0.023039635 0.326599831 56138.22393 -4.749258669 -0.237171197 WDAENAIQQMGGQWLGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 WDAENAIQQMGGQWLGGR 18 0 C9JTN7;P31483-2;F8W8I6;P31483-3;P31483 C9JTN7 TIA1 Nucleolysin TIA-1 isoform p40 0 162.41 8.30E-11 104330000 42815 58008 41556 45148 55248 53889 48501 58239 58793 55638 FALSE TRUE 41141.74247 56353.66864 49066.09361 47478.09369 57025.10209 54978.6725 49094.56975 57036.3443 52119.06512 51869.5887 0.79317657 1.086449113 0.945951083 0.915335843 1.099393759 1.059940398 0.946500078 1.099610499 1.004809686 1 15.66260131 4.749327056 24.5944834 1.019510847 0.793176408 0.524155503 0.064111902 1007.22006 2300803.194 0.015258099 0.222287018 56147.0646 -4.749327056 -0.226334439 FFDEESYSLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FFDEESYSLLR 11 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 ; 234.71 3.88E-15 186888000 125188 201282 148923 225730 143777 119092 187759 198686 179605 189980 FALSE TRUE 120295.5146 195541.6344 175836.6989 237379.9524 148401.7178 121500.1218 190056.8508 194583.0647 159216.9934 177112.4854 0.679204034 1.104053359 0.992796744 1.340277913 0.837895293 0.686005403 1.073085561 1.09864115 0.898959737 1 17.43430639 4.749327849 23.9046765 1.009069177 0.67920368 0.254160584 0.166428456 1230.406875 2731565.272 0.040850261 0.575960076 56147.16711 -4.749327849 -0.329865497 DLGGFDEDAEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGGFDEDAEPR 12 0 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;G3V1E2;Q9BRK5-4;Q9BRK5-3;H0Y3T6 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 ; 176.95 5.56E-05 297100000 319800 431060 370620 454190 386300 363090 437280 492300 476570 516500 FALSE TRUE 307301.8624 418766.5909 437599.2784 477630.8003 398725.6903 370431.9286 442631.5634 482133.833 422471.7715 481516.9949 0.638195257 0.86968185 0.908793008 0.991929268 0.828061511 0.769301878 0.919243906 1.001281031 0.877376657 1 18.87722719 4.749331486 2.88212151 0.911600317 0.586202159 0.567854822 0.071269981 0.333658095 3.845997421 0.018709414 0.256645501 56147.63728 -4.749331486 -0.325398158 QQPPLGPSS(ph)SLLSLPGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 QQPPLGPSSSLLSLPGLK 18 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 QQPPLGPS(0.01)S(0.495)S(0.495)LLSLPGLK;QQPPLGPS(0.096)S(0.442)S(0.442)LLS(0.02)LPGLK 214.01 1.97E-17 270080000 924680 485750 259490 275540 253860 194690 159653 586940 255570 184187 TRUE FALSE 888542.4833 471896.8856 306385.6153 289760.6524 262025.6374 198626.7652 161606.8812 574819.4839 226558.765 171711.8504 5.174613639 2.748190555 1.784300935 1.687481975 1.525961294 1.156744655 0.941151591 3.347581908 1.319412519 1 17.38963008 4.749332043 1.898140487 1.70323792 6.332010264 0.73445317 0.653275047 0.465321766 1.707292673 0.180968142 3.84127365 56147.70928 -4.749332043 4.628772344 KAQCPIVER ddPTM_BT-474_Pertuzumab_2h_R1 4 KAQCPIVER 9 1 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;; 174.86 8.71E-05 4195900000 4240520 4588780 3742080 4628090 4592810 4707010 5091400 4926390 5225900 5491000 FALSE TRUE 4074795.79 4457912.487 4418357.098 4866946.28 4740541.905 4802188.967 5153710.076 4824658.325 4632677.741 5119089.679 0.796000079 0.870840866 0.86311383 0.950744485 0.92605174 0.938094323 1.006762999 0.94248365 0.904980774 1 22.28745585 4.749336868 0.620028948 0.960282223 0.69275837 0.73656107 0.031219184 1.782577861 0.514269525 0.01424699 0.343117611 56148.33314 -4.749336868 -0.267523853 TSFS(ph)VGSDDELGPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 T(0.002)S(0.005)FS(0.684)VGS(0.31)DDELGPIR 109.79 0.0010196 59829000 62337 70742 58771 67516 65988 69227 66101 75886 72395 76490 TRUE FALSE 59900.80112 68724.50742 69392.22705 71000.50885 68110.56395 70626.81737 66909.96381 74318.92758 64177.0231 71309.26417 0.840014293 0.963752862 0.973116577 0.995670193 0.955143273 0.99042976 0.938306749 1.042205784 0.899981564 1 16.1218019 4.749352516 3.405670604 0.977709993 0.820570121 0.546122974 0.036426787 0.223777259 4.307066423 0.008182697 0.092665794 56150.35626 -4.749352516 -0.157139873 WIVNLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 WIVNLIR 7 0 P60228;E5RGA2;H0YAW4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ; 99.279 0.024765 92885000 153725 180738 174358 166755 159564 118941 189830 162720 170223 200678 FALSE TRUE 147717.257 175583.5292 205868.3692 175361.2455 164696.521 121346.0685 192153.1963 159359.7751 150899.9987 187085.9003 0.789569159 0.938518236 1.100394893 0.937330099 0.880325672 0.648611511 1.027085398 0.851800028 0.806581353 1 17.51334131 4.749372541 22.91189694 0.906139173 0.78956894 0.082895266 0.119601733 1385.313942 2935469.9 0.028901798 0.390870383 56152.94535 -4.749372541 -0.116570233 TLSSS(ph)SMDLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 TLSS(0.015)S(0.873)S(0.113)MDLSR;TLSS(0.007)S(0.985)S(0.007)MDLSR;TLSS(0.08)S(0.884)S(0.036)MDLSR;TLS(0.001)S(0.027)S(0.945)S(0.027)MDLSR 267.37 3.80E-21 1458960000 5083200 2216300 802990 594660 855460 467390 270883 1633740 457515 333912 TRUE FALSE 4884542.924 2153093.294 948108.1554 625350.4739 882976.6478 476840.946 274198.1472 1600002.698 405579.8153 311295.8428 15.69099953 6.916550104 3.045682033 2.008862271 2.836454993 1.531793492 0.880828169 5.139813894 1.302875784 1 18.24792679 4.749383876 1.694669984 2.346163971 20.68789472 0.9240623 1.184613205 0.247926386 0.682027479 0.321738032 7.468663195 56154.41093 -4.749383876 18.34173075 TIS(ph)QSSSLK ddPTM_BT-474_Pertuzumab_2h_R1 6 TISQSSSLK 9 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 TIS(1)QSSSLK;TIS(0.999)QS(0.001)SSLK;TIS(1)QSSSLK;TIS(1)QSSSLK;TIS(1)QSSSLK;T(0.001)IS(0.998)QSSSLK 227.72 1.99E-07 5359280000 6472880 4107620 2842950 2612780 3163860 2378200 2499180 6085120 2485000 1873740 TRUE FALSE 6219912.693 3990474.699 3356734.306 2747625.889 3265628.43 2426288.833 2529765.712 5959460.146 2202913.218 1746829.921 3.560685914 2.284409405 1.921614844 1.572921242 1.869459866 1.388966839 1.44820379 3.411585796 1.261091988 1 20.73630772 4.749398803 2.193017498 1.87112951 4.035544583 0.42185083 0.633007492 0.734268768 3.934761182 0.168889026 3.135650745 56156.34103 -4.749398803 2.164415074 KDDS(ph)HS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 KDDS(1)HS(1)AEDS(1)EDEKEDHKNVR 104.83 0.00026603 813780000 789530 468120 345550 227530 402100 400260 355120 412920 704140 409030 TRUE FALSE 758674.2947 454769.6759 407998.5717 239272.8506 415033.9117 408353.5314 359466.0648 404393.0577 624208.9792 381326.0338 1.989568578 1.192600651 1.069946806 0.62747578 1.088396477 1.070877662 0.942673809 1.060491605 1.636942993 1 18.5406655 4.749445177 2.856696031 1.046383894 2.171527844 0.585464018 0.232461979 0.297774052 3.343135027 0.056775058 0.787542451 56162.33776 -4.749445177 1.12514395 IQIGCHTDDLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQIGCHTDDLTR 12 0 Q9Y4C2-2;Q9Y4C2 Q9Y4C2-2 TCAF1 TRPM8 channel-associated factor 1 0 ; 164.48 5.72E-05 1094610000 1254860 1515080 1085850 1528740 1360890 1240790 1455790 1443470 1477600 1607480 FALSE TRUE 1205818.684 1471871.402 1282087.25 1607638.455 1404664.263 1265879.624 1473606.393 1413661.84 1309869.043 1498603.948 0.804627991 0.982161701 0.855521068 1.072757387 0.937315202 0.844705918 0.983319439 0.943319175 0.874059517 1 20.51518773 4.749548412 23.92340819 0.941854555 0.804627844 0.276886912 0.067357774 1146.47808 2496103.855 0.015198853 0.218790384 56175.68955 -4.749548412 -0.137226711 RLT(ph)VMS(ph)LQESGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLTVMSLQESGLK 13 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 2 RLT(1)VMS(1)LQESGLK 61.641 0.034604 577970000 190790 337720 229580 331480 284930 318230 314990 245740 276560 308060 TRUE FALSE 183333.7159 328088.5563 271070.213 348587.7225 294095.0322 324664.8286 318844.9418 240665.3831 245166.0682 287194.8218 0.638360102 1.142390222 0.943854807 1.213767436 1.024026235 1.13046895 1.110204355 0.837986499 0.85365769 1 18.13167021 4.749594166 24.75284604 1.024748787 0.638359845 0.495465845 0.118049209 1295.268467 2905762.648 0.029724119 0.44447145 56181.60811 -4.749594166 -0.386388942 EVLTPESDISIAHVLAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLTPESDISIAHVLAAR 18 0 Q17RN3 Q17RN3 FAM98C Protein FAM98C 0 191.37 2.29E-14 58232000 16287 23714 18689 17391 19234 24398 25011 22343 15714 21380 FALSE TRUE 15650.48603 23037.69994 22066.51803 18288.55159 19852.67908 24891.34428 25317.0921 21881.60924 13930.2126 19931.91356 0.785197366 1.15581978 1.107094809 0.91755122 0.996024743 1.248818595 1.270178702 1.097817788 0.698889876 1 14.2827926 4.749659427 24.15400563 1.070467306 0.785197098 0.199658015 0.159068839 1628.941083 3544904.777 0.038673785 0.567382746 56190.05115 -4.749659427 -0.285270208 AWDDFFPGSDR ddPTM_BT-474_Pertuzumab_2h_R1 6 AWDDFFPGSDR 11 0 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 ;;;;; 161.27 6.17E-05 1724414000 664916 1119384 622379 1298084 758976 793659 1031319 1223486 1000703 803283 FALSE TRUE 638930.3476 1087460.264 734856.73 1365078.271 783389.1523 809707.3288 1043940.59 1198220.587 887107.3907 748875.9269 0.853185854 1.45212341 0.98127968 1.822836363 1.046086707 1.081230281 1.39401008 1.60002551 1.184585268 1 19.51436719 4.749728192 23.81732156 1.314971875 0.853185324 0.181445621 0.268091837 1324.568202 2824826.979 0.061679938 0.894123136 56198.94881 -4.749728192 -0.461786551 EHGLIFMETSAK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHGLIFMETSAK 12 0 P61019;P61019-2;A0A3B3ITL1;Q8WUD1;H7C125;Q8WUD1-2 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ;;; 186.02 1.23E-05 1666150000 1435630 1981520 1337810 1892300 1574150 1619150 2014440 1641560 2337700 2025780 FALSE TRUE 1379523.992 1925008.99 1579582.026 1989961.83 1624783.964 1651890.322 2039093.319 1607661.212 2072334.096 1888572.116 0.730458732 1.019293345 0.836389573 1.05368591 0.860324025 0.874676857 1.079701062 0.851257518 1.097302072 1 20.84886444 4.749745662 24.02198089 0.952666553 0.730458505 0.341281294 0.0961017 1055.450813 2266702.643 0.02076625 0.306710924 56201.20947 -4.749745662 -0.222208048 GLQEFLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLQEFLDR 8 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;;; 205.36 0.00018638 653568000 833718 949780 801217 971290 968540 956220 937620 965130 963650 961798 FALSE TRUE 801135.3788 922693.2043 946014.7349 1021418.393 999693.9687 975555.4236 949094.874 945199.7282 854260.492 896654.5648 0.893471589 1.029039767 1.05504926 1.139143694 1.114915384 1.08799471 1.058484406 1.054140318 0.952719727 1 19.77419277 4.749905728 2.399488967 1.064856845 0.850630167 0.481192744 0.050573548 0.489907921 3.34780383 0.012986534 0.220150695 56221.92713 -4.749905728 -0.214226679 GS(ph)PSPASVSSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSPSPASVSSGR 12 0 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 GS(0.824)PS(0.134)PAS(0.041)VS(0.001)SGR;GS(0.949)PS(0.051)PASVSSGR;GS(0.809)PS(0.189)PAS(0.001)VSSGR;GS(0.866)PS(0.134)PASVSSGR 293.41 8.80E-22 343950000 807840 952470 701484 1007470 803640 835130 802350 1013550 919680 901260 TRUE FALSE 776268.7197 925306.4882 828257.7632 1059465.647 829489.8104 852016.9008 812169.3993 992619.8383 815281.782 840216.8574 0.923890913 1.101271035 0.985766658 1.260943098 0.987233002 1.014044045 0.966618787 1.181385293 0.970323048 1 19.68040221 4.749930597 23.58125491 1.060415679 0.923890732 0.135372635 0.094951124 1417.771429 2940318.333 0.021592104 0.318810789 56225.14665 -4.749930597 -0.136524947 (ac)ADSRDPASDQMQHWK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADSRDPASDQMQHWK 15 1 P04040 P04040 CAT Catalase 0 ; 88.087 4.88E-06 975070000 746830 919990 636850 869350 770870 923400 864360 816710 928020 1012650 FALSE TRUE 717643.0579 893752.786 751942.9617 914217.2577 795665.7336 942071.7807 874938.2962 799844.6531 822675.0602 944062.3135 0.760164925 0.946709527 0.796497171 0.968386562 0.842810609 0.997891524 0.926780239 0.847237139 0.871420295 1 19.84852256 4.749947741 24.00021037 0.903148478 0.760164776 0.310402964 0.066495423 1206.254551 2542291.635 0.014849784 0.226571529 56227.36623 -4.749947741 -0.142983701 GLEDHESVVEVQAAWPVGGDSR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLEDHESVVEVQAAWPVGGDSR 22 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;;; 264.49 1.73E-37 3384006000 1478833 2014670 1740322 2344505 2106434 2291308 2216006 1936406 1870483 2141357 FALSE TRUE 1421038.571 1957213.584 2054836.899 2465505.184 2174189.363 2337639.818 2243126.144 1896418.539 1658153.612 1996320.983 0.711828701 0.980410265 1.029311877 1.23502443 1.089098086 1.170973925 1.123629999 0.949956723 0.83060471 1 20.92891228 4.749953278 2.224917437 1.061033525 0.615790101 0.47221837 0.108174675 0.606094043 3.372359528 0.029310304 0.537980256 56228.08311 -4.749953278 -0.445243424 RVNNGNTAPEDSS(ph)PAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVNNGNTAPEDSSPAKK 17 2 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 RVNNGNTAPEDS(0.044)S(0.956)PAKK 115.42 0.00016475 482690000 716380 561670 437480 445290 466860 458700 511120 583300 622280 569590 TRUE FALSE 688383.0776 545651.7215 516542.3677 468271.4703 481876.9759 467975.2283 517375.2395 571254.6512 551641.3832 531011.162 1.296362726 1.027571096 0.972752373 0.881848639 0.907470521 0.881290756 0.974320836 1.075786522 1.038850824 1 19.01838266 4.750057866 2.625697604 0.967651617 1.368987145 0.727793348 0.060291976 0.305182744 2.681947362 0.017763312 0.272714588 56241.62574 -4.750057866 0.401335528 ETEAWDFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETEAWDFLR 9 0 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 0 ; 116.05 0.0032026 72340000 94993 113618 97008 109498 102997 80171 109613 109958 106806 119569 FALSE TRUE 91280.56854 110377.7259 114539.5035 115149.2049 106309.992 81792.11255 110954.4767 107687.3289 94681.83065 111470.4851 0.81887657 0.990196874 1.027532117 1.033001738 0.953705296 0.733755778 0.995370896 0.966061364 0.84938924 1 16.76630224 4.750156503 23.64418131 0.950095428 0.818876401 0.168499105 0.087310299 1576.436047 3214243.118 0.021397827 0.32618702 56254.40072 -4.750156503 -0.131219027 WVDLTMDDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 WVDLTMDDIR 10 0 F5GWE5;Q00169 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ; 122.13 0.0011552 167299000 217690 255760 237270 272040 254850 88922 272320 251130 221110 293990 FALSE TRUE 209182.4341 248465.9752 280149.967 286080.017 263047.4817 90720.06377 275652.7336 245944.0777 196010.5198 274077.7954 0.763222843 0.906552736 1.02215492 1.043791295 0.959754807 0.331001144 1.005746318 0.897351343 0.715163808 1 18.06422593 4.750180418 21.59967442 0.87509556 0.763222371 0.026830795 0.203230021 1269.320139 2359178.368 0.048754815 0.667817764 56257.49856 -4.750180418 -0.111873188 S(ph)SEVLYERPQPTPAFSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSEVLYERPQPTPAFSSR 18 1 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 S(0.959)S(0.041)EVLYERPQPTPAFSSR 103.03 0.00033142 300800000 23263 11774 11307 13604 16825 11053 13825 16824 12961 17180 TRUE FALSE 22353.85624 11438.21705 13350.42642 14306.10407 17366.19141 11276.49923 13994.19449 16476.57852 11489.72162 16016.3833 1.395686893 0.7141573 0.833548135 0.89321689 1.084276711 0.704060275 0.873742481 1.02873278 0.717373043 1 13.96726079 4.750272412 24.88355504 0.880731487 1.395687221 0.597653637 0.128699924 1170.380495 2486608.855 0.029903166 0.485748808 56269.41652 -4.750272412 0.514955734 QEQINTEPLEDTVLS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 4 QEQINTEPLEDTVLSPTK 18 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 QEQINTEPLEDTVLS(0.955)PT(0.045)K;QEQINTEPLEDTVLS(0.997)PT(0.003)K;QEQINTEPLEDTVLS(0.992)PT(0.008)K;QEQINTEPLEDTVLS(0.955)PT(0.045)K 191.33 2.42E-14 866030000 2219440 1924150 1524990 1586640 1745930 1649220 1690910 2034080 1799440 1992480 TRUE FALSE 2132701.831 1869275.126 1800589.616 1668526.681 1802089.424 1682568.358 1711603.862 1992075.537 1595175.115 1857527.555 1.148140078 1.006324305 0.969347459 0.898251375 0.970154881 0.905810713 0.921441977 1.072433909 0.858762558 1 20.82495218 4.750278427 2.003656842 0.953967588 1.208865207 0.529064053 0.056668259 0.630009745 2.65459307 0.014644377 0.297823148 56270.1959 -4.750278427 0.254897619 AFHITNDEPIPFWTFLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFHITNDEPIPFWTFLSR 18 0 Q15738 Q15738 NSDHL "Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating" 0 ; 188.1 3.95E-14 316780000 247876 379780 236484 447060 247927 280020 378990 380890 335440 300489 FALSE TRUE 238188.7319 368949.0462 279221.9194 470132.8202 255901.7971 285682.1963 383628.193 373024.4884 297362.2575 280136.6124 0.8502592 1.317032583 0.996734832 1.678226977 0.913489297 1.019795998 1.369432541 1.331580636 1.06149016 1 18.09577102 4.750290039 23.46061409 1.207491073 0.850258683 0.163438054 0.224870721 1249.151294 2498376.988 0.051215197 0.772758354 56271.70047 -4.750290039 -0.357232389 AQLGEDIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQLGEDIRR 9 1 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 98.254 0.0098425 182920000 104040 137170 117030 160970 145160 135840 151190 128250 137330 159860 FALSE TRUE 99974.00178 133258.0459 138179.9243 169277.681 149829.2032 138586.7779 153040.3084 125601.5927 121740.8741 149032.5398 0.670819956 0.894154029 0.927179558 1.135843764 1.005345567 0.929909522 1.026891903 0.842779656 0.816874451 1 17.18526784 4.750363508 2.25117996 0.958657949 0.592787145 0.502453031 0.086664871 0.581677744 3.337582048 0.02353454 0.427826625 56281.22063 -4.750363508 -0.365870804 EQYQQQQQWGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQYQQQQQWGSR 12 0 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 265 3.21E-21 652150000 182593 224730 176261 186373 206174 212470 198813 223450 205416 226950 FALSE TRUE 175457.0637 218320.9204 208115.2836 195991.7329 212805.774 216766.289 201246.133 218835.6794 182098.0369 211578.4744 0.829276533 1.031867354 0.983631649 0.926331157 1.005800683 1.024519577 0.951165441 1.0343003 0.860664287 1 17.69083333 4.750410492 24.43406905 0.982577156 0.829276406 0.43202409 0.051692391 1176.733496 2426325.717 0.011505476 0.184101758 56287.30972 -4.750410492 -0.15330075 FLSNGHVTIPGQQDKDMFQETMEAMR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLSNGHVTIPGQQDKDMFQETMEAMR 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 169.26 5.04E-12 1822140000 1382190 1691460 1414380 1658960 1537870 1737730 1812210 1535060 1927350 1813200 FALSE TRUE 1328172.487 1643221.217 1669989.929 1744579.124 1587336.985 1772868.091 1834388.368 1503360.475 1708565.308 1690390.349 0.785719398 0.972095716 0.987931533 1.03205696 0.93903576 1.048792128 1.085186253 0.889356991 1.01075193 1 20.688925 4.750429052 3.304482561 0.994648288 0.754185726 0.598541759 0.052008262 0.245687322 4.286950189 0.012929419 0.152811161 56289.71533 -4.750429052 -0.240462562 KLPEELGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLPEELGR 8 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 113.62 0.0045108 285980000 298330 370370 262300 320450 341560 391520 307440 362440 356580 349330 FALSE TRUE 286670.9338 359807.4102 309703.4448 336988.4629 352546.5876 399436.8027 311202.5427 354955.4873 316102.5333 325669.5679 0.880250911 1.104823556 0.95097447 1.034755765 1.082528496 1.22650945 0.955577596 1.089925256 0.970623492 1 18.31304939 4.750506687 24.34940507 1.050002998 0.880250763 0.276302502 0.080354346 1684.187236 3432748.524 0.018504063 0.304129118 56299.77864 -4.750506687 -0.169752234 KQVVES(ph)FVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQVVESFVPR 10 1 A2A341;Q9BX26 A2A341 SYCP2 Synaptonemal complex protein 2 1 KQVVES(1)FVPR;KQVVES(1)FVPR 47.261 0.086418 10255900000 9593400 7300900 7029600 6140300 7927300 7422700 8351000 6372200 10048900 8741000 TRUE FALSE 9218479.322 7092685.48 8300005.093 6457201.619 8182288.804 7572792.08 8453202.036 6240611.843 8908191 8148964.284 1.131245518 0.870378766 1.01853497 0.792395376 1.004089418 0.929295039 1.03733453 0.765816566 1.093168492 1 22.95818528 4.750523911 24.15604392 0.933761692 1.131245712 0.220789148 0.102413488 1542.932707 3115365.069 0.022515657 0.35986713 56302.01149 -4.750523911 0.197484021 AALAGGTTMIIDHVVPEPGTSLLAAFDQWR ddPTM_BT-474_Pertuzumab_2h_R1 2 AALAGGTTMIIDHVVPEPGTSLLAAFDQWR 30 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 ; 173.96 7.52E-13 105229000 63191 78335 54549 67674 76023 80479 72380 75505 65994 72588 FALSE TRUE 60721.42586 76100.9625 64407.21774 71166.66325 78468.34884 82106.34052 73265.80809 73945.79536 58502.63779 67671.55011 0.897296216 1.124563607 0.951762116 1.051648191 1.159547088 1.213306632 1.082667797 1.092716145 0.864508611 1 16.04626182 4.750635482 23.99616281 1.069241665 0.89729603 0.198028587 0.096707096 1689.748563 3357897.21 0.023210826 0.37247718 56316.47746 -4.750635482 -0.171945635 GLIAAICAGPTALLAHEIGFGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLIAAICAGPTALLAHEIGFGSK 23 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 170.91 6.78E-12 84953000 186590 206740 164150 177090 198240 207290 192130 196000 203040 210590 FALSE TRUE 179297.8565 200843.9776 193815.5565 186229.6361 204616.5696 211481.5458 194481.3444 191952.5315 179991.7504 196326.5517 0.913263412 1.023009755 0.987210109 0.94857081 1.042225658 1.077192789 0.990601336 0.977720689 0.916797799 1 17.58289577 4.750713451 23.79152933 0.996334997 0.91326331 0.250055611 0.042940804 1479.465303 2896234.142 0.010713487 0.174675913 56326.58886 -4.750713451 -0.083071687 S(ph)RLSAIEIDIPVVSHTT ddPTM_BT-474_Pertuzumab_2h_R1 1 SRLSAIEIDIPVVSHTT 17 1 P56749 P56749 CLDN12 Claudin-12 1 S(0.5)RLS(0.5)AIEIDIPVVSHTT 75.574 0.057186 35250000 22079 38616 23725 44613 20585 30249 33355 47573 31164 16533 TRUE FALSE 21216.12827 37514.70949 28012.63526 46915.48228 21247.13522 30860.65551 33763.20847 46590.60093 27626.39337 15413.20518 1.376490355 2.433933049 1.817443869 3.043849849 1.378502068 2.002221805 2.190537793 3.022771732 1.792384714 1 13.91187928 4.750739542 23.29853498 2.18028494 1.376489054 0.081132663 0.62207122 1496.399996 2862503.566 0.141706262 2.231533369 56329.97285 -4.750739542 -0.803795886 DGYWFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGYWFLK 7 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 0 108.24 0.016978 256560000 252700 281230 233230 260380 262890 272530 271460 305850 278090 297840 FALSE TRUE 242824.2046 273209.5958 275379.8492 273818.243 271346.0956 278040.7433 274782.2087 299534.0906 246522.389 277667.0315 0.874515794 0.983946831 0.99176286 0.986138835 0.977235555 1.001345899 0.989610496 1.07875281 0.887834568 1 18.08299636 4.750830966 3.397486402 0.995935555 0.857065873 0.372582863 0.043700133 0.327393486 6.233491094 0.010417682 0.119815948 56341.83228 -4.750830966 -0.138869682 YEEEEEQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YEEEEEQSR 9 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 268.9 1.31E-15 1522350000 841700 981510 766380 916570 836520 941530 915580 930910 964730 963390 FALSE TRUE 808805.4335 953518.2958 904881.914 963874.2875 863427.4255 960568.3817 926785.1419 911686.3832 855217.8949 898138.7372 0.900535073 1.061660361 1.007507946 1.073190864 0.961351949 1.069510023 1.0318953 1.015084135 0.952211345 1 19.77657879 4.750917519 24.68459748 1.021010289 0.900534984 0.444352996 0.039745726 1435.923065 2868390.564 0.008824044 0.152253648 56353.06202 -4.750917519 -0.120475305 RGS(ph)PVPPVPERR ddPTM_BT-474_Pertuzumab_2h_R1 7 RGSPVPPVPERR 12 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR 130.39 0.00011337 5262360000 668398 604662 469266 548719 619930 644430 596049 631790.8 628110 623728 TRUE FALSE 642276.2672 587417.6318 554072.805 577038.4533 639870.6115 657460.8161 603343.626 618744.0992 556809.5861 581482.347 1.104549898 1.010207162 0.952862641 0.992357646 1.100412789 1.130663415 1.037595774 1.064080625 0.9575692 1 19.14937587 4.750999956 23.38854199 1.033239397 1.10455001 0.142261243 0.055196852 1815.657741 3413659.709 0.014105351 0.226399723 56363.75987 -4.750999956 0.071310613 ASALLFSS(ph)DEEDQWNIPASQTHLASDSR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASALLFSSDEEDQWNIPASQTHLASDSR 28 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 ASALLFS(0.166)S(0.834)DEEDQWNIPASQTHLASDSR;ASALLFS(0.148)S(0.852)DEEDQWNIPASQTHLASDSR;ASALLFS(0.106)S(0.894)DEEDQWNIPASQTHLASDSR;ASALLFS(0.051)S(0.948)DEEDQWNIPASQTHLASDSR;ASALLFS(0.201)S(0.799)DEEDQWNIPASQTHLASDSR 314.37 5.69E-83 3749123000 410389 560442 475066 549877 533475 618950 562620 532009 592178 649948 TRUE FALSE 394350.5442 544458.7429 560920.994 578256.2179 550634.7079 631465.5931 569505.5119 521022.8282 524956.4361 605926.443 0.65082247 0.898555838 0.925724567 0.954334019 0.908748437 1.042148928 0.939892158 0.859878017 0.866369907 1 19.20878314 4.75107553 3.195232915 0.93146528 0.605513224 0.725581629 0.052412314 0.202725373 3.180157712 0.013559514 0.167325979 56373.56884 -4.75107553 -0.325952056 LAALTAGDRVPWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LAALTAGDRVPWAR 14 1 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 113.35 0.00049324 329490000 70909 107930 61882 124890 72528 80229 106160 105410 96432 100220 FALSE TRUE 68137.79789 104851.9421 73065.45396 131335.5879 74860.92899 81851.28535 107459.2178 103233.2467 85485.44364 93432.01013 0.729276806 1.122227189 0.782017361 1.405680855 0.801234276 0.87605185 1.150132783 1.10490234 0.914948137 1 16.51162929 4.751142614 23.83855312 1.02423599 0.729276446 0.188341106 0.178982939 1672.286288 3168295.209 0.040340807 0.676972727 56382.27743 -4.751142614 -0.294959544 GLDEDETNFLDEVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDEDETNFLDEVSR 15 0 H3BQQ6;H3BTI2;H3BTP8;H3BSY6;H3BP64;H3BUL4;H3BMX9;Q9GZU8;H3BU93 H3BQQ6 FAM192A Protein FAM192A 0 ; 277.11 3.37E-33 527650000 306660 366820 289960 318290 351000 347270 307410 347820 361060 379060 FALSE TRUE 294675.3882 356358.6528 342362.2221 334716.985 362290.2338 354292.0373 311172.1755 340637.3955 320073.9825 353385.9286 0.833862823 1.008412118 0.968805474 0.947171231 1.025197113 1.002564077 0.880544895 0.963924616 0.905734939 1 18.43088507 4.75116256 24.37662782 0.96415971 0.833862707 0.453010722 0.043770312 1367.363697 2644898.694 0.01047314 0.182424918 56384.86695 -4.75116256 -0.130297004 FFDHSGTLVMDAYEPEISR ddPTM_BT-474_Pertuzumab_2h_R1 4 FFDHSGTLVMDAYEPEISR 19 0 E9PL01;A0A087WUC6;E9PI68;Q15005;E9PRB9 E9PL01 SPCS2 Signal peptidase complex subunit 2 0 ;;; 231.21 3.91E-20 796061000 335445 542981 282819 654842 378047 389673 487693 591202 474466 367912 FALSE TRUE 322335.4385 527495.7135 333930.6846 688638.4741 390207.2251 397552.455 493661.5328 578993.4721 420606.6088 342992.9925 0.939772665 1.537919797 0.973578737 2.007733362 1.137653636 1.159068738 1.439275856 1.688062102 1.226283388 1 18.38781958 4.751184398 24.11257956 1.387230302 0.939772198 0.128601213 0.310200735 2274.110297 4343629.204 0.070190446 1.203733762 56387.70232 -4.751184398 -0.447458104 SMVEGLGGPLGHAGEESEVDNDVDS(ph)PGSLRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SMVEGLGGPLGHAGEESEVDNDVDSPGSLRR 31 1 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 SMVEGLGGPLGHAGEESEVDNDVDS(0.957)PGS(0.043)LRR;SMVEGLGGPLGHAGEESEVDNDVDS(0.8)PGS(0.2)LRR 138.29 2.40E-07 124651000 53305 72047 56843 57194 59176 83908 55399 60800 72650 75591 TRUE FALSE 51221.78167 69992.2901 67115.79457 60145.78919 61079.44978 85604.67725 56076.98953 59544.45875 64403.07657 70471.15424 0.726847491 0.993204821 0.952386764 0.853480972 0.866729805 1.214747767 0.795743878 0.84494797 0.913892745 1 16.10474522 4.751322081 23.68212637 0.926433387 0.726847223 0.234759839 0.112442296 1563.248824 2900892.527 0.02700861 0.462774018 56405.58147 -4.751322081 -0.199586164 GSGGGGGPQVPHQS(ph)PPKR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSGGGGGPQVPHQSPPKR 18 1 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 GSGGGGGPQVPHQS(1)PPKR;GSGGGGGPQVPHQS(1)PPKR;GSGGGGGPQVPHQS(1)PPKR;GSGGGGGPQVPHQS(1)PPKR 90.308 0.0012836 1315336000 968761 900821 750020 800899 901121 892332 884441 886820 1018950 977451 TRUE FALSE 930900.7491 875130.4671 885565.2981 842233.4934 930106.3753 910375.5644 895265.0535 868506.8571 903283.0678 911247.3731 1.021567553 0.960365421 0.971816572 0.924264385 1.02069581 0.99904328 0.982461053 0.953096692 0.991259996 1 19.79748323 4.751360143 24.08464539 0.9759195 1.021567602 0.194821506 0.026163936 2024.690941 3809709.202 0.006266228 0.111820408 56410.52519 -4.751360143 0.045648102 LQHAVPADDGTTRS(ph)PS(ph)IDSIQKDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQHAVPADDGTTRSPSIDSIQKDPR 25 2 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 2 LQHAVPADDGT(0.162)T(0.174)RS(0.748)PS(0.909)IDS(0.007)IQKDPR 68.934 0.022096 115340000 116500 139430 98275 143070 107010 141750 129010 125340 155380 127010 TRUE FALSE 111947.0512 135453.5929 116035.4786 150453.8598 110452.0738 144616.2821 130588.863 122751.6852 137741.9138 118407.4996 0.945438858 1.143961264 0.979967308 1.270644684 0.93281316 1.221343941 1.102876621 1.036688433 1.163287075 1 16.85340093 4.751379694 23.516468 1.094280956 0.945438637 0.159049056 0.102906895 1537.608072 2820607.519 0.021906515 0.370416514 56413.06478 -4.751379694 -0.148842319 KKEEEQER ddPTM_BT-474_Pertuzumab_2h_R1 4 KKEEEQER 8 2 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 0 ;;; 141.88 0.00035235 445007000 603610 505242 406193 420625 459237 407926 492777 572532 452336 537540 FALSE TRUE 580020.2539 490832.9928 479601.1108 442333.5067 474008.7752 416174.5432 498807.7523 560709.0141 400988.7136 501131.937 1.157420254 0.979448637 0.957035614 0.882668762 0.945876206 0.830469009 0.99536213 1.118885014 0.800165952 1 18.93483096 4.751400623 3.010933205 0.95169454 1.194341219 0.353437635 0.086419463 0.502150308 6.565576249 0.022429958 0.296967974 56415.78336 -4.751400623 0.242646679 EIFDIAFPDEQAEALAVER ddPTM_BT-474_Pertuzumab_2h_R1 2 EIFDIAFPDEQAEALAVER 19 0 K7EKE6;K7EJE8;P36776-2;P36776;P36776-3 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 ; 166.6 4.56E-11 73564000 91050 141933 100420 222541 105098 123380 200616 173793 132101 113720 FALSE TRUE 87491.66534 137885.2098 118568.1278 234026.3677 108478.5726 125874.8281 203071.1986 170204.1138 117105.4483 106017.6431 0.82525571 1.300587391 1.118381095 2.207428507 1.023212453 1.187300759 1.915447209 1.605431972 1.104584528 1 16.69394485 4.751521976 1.51238643 1.464059956 0.583700842 0.152622582 0.386522752 1.925757495 3.983772025 0.101477314 2.559924692 56431.54963 -4.751521976 -0.880359113 YQELLER ddPTM_BT-474_Pertuzumab_2h_R1 5 YQELLER 7 0 Q9H074;Q9H074-3;Q9H074-2;H0YA44 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ;;;; 155.88 0.0036791 2572318000 3174720 3663580 3078960 3908220 3557470 3650960 3779860 3969600 3757440 4061960 FALSE TRUE 3050648.433 3559098.285 3635396.563 4109923.703 3671899.253 3724784.913 3826119.057 3887626.373 3330911.164 3786839.831 0.805592148 0.939859736 0.960008008 1.085317543 0.969647362 0.983613007 1.010372561 1.026614947 0.879601808 1 21.85256297 4.75157935 1.757081888 0.996176961 0.737799163 0.557651875 0.049447205 0.652261642 1.957218481 0.012468791 0.284702518 56439.00515 -4.75157935 -0.258377798 GLESLPPLRPQQNPVLPVAGER ddPTM_BT-474_Pertuzumab_2h_R1 1 GLESLPPLRPQQNPVLPVAGER 22 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 107.39 0.00017682 0 77322 68500 59082 65019 68883 66092 66053 72984 71930 74811 FALSE TRUE 74300.17076 66546.44707 69759.43167 68374.63838 71098.68425 67428.42552 66861.37637 71476.8549 63764.80796 69743.98434 1.065327303 0.954153218 1.000221486 0.980366107 1.019423896 0.966799161 0.958668723 1.024846165 0.914269647 1 16.08978116 4.751597398 24.42072776 0.98303454 1.065327377 0.391364237 0.03175336 1565.824801 2933057.528 0.007030802 0.129229347 56441.3506 -4.751597398 0.082292837 DDTEFQHPCFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDTEFQHPCFLR 12 0 E9PMQ6;Q00613-2;Q00613;E9PI02;A0A087X1F9 E9PMQ6 HSF1 Heat shock factor protein 1 0 140.14 5.94E-05 591880000 365250 407500 341800 412690 442350 393080 408780 382620 430240 449360 FALSE TRUE 350975.6262 395878.499 403570.8633 433988.9804 456578.5895 401028.3469 413782.7719 374718.7633 381400.9589 418924.447 0.83780173 0.944987818 0.963349994 1.035960025 1.089882896 0.957280841 0.987726486 0.894478148 0.910428985 1 18.67633055 4.751678208 2.201974346 0.977154081 0.798660876 0.389368774 0.053507689 0.812751876 4.382621509 0.015356895 0.287607169 56451.85377 -4.751678208 -0.178493205 LESENDEYER ddPTM_BT-474_Pertuzumab_2h_R1 2 LESENDEYER 10 0 O94906 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 255.07 9.25E-17 886860000 397800 440520 370790 439040 448820 434830 429260 431020 499640 463300 FALSE TRUE 382253.5362 427956.8009 437800.0012 461698.907 463256.7029 443622.5605 434513.4123 422119.2864 442922.9619 431920.2783 0.885009469 0.99082359 1.013612982 1.068944734 1.072551409 1.027093616 1.006003733 0.977308331 1.025473876 1 18.72040553 4.75171139 2.211971892 1.023073198 0.846298512 0.697582667 0.02749451 0.433875621 2.368017765 0.008179995 0.152533407 56456.16706 -4.75171139 -0.176774685 ADEQTTCEVLDYFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADEQTTCEVLDYFLR 15 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 0 104.87 0.0031641 12524000 12501 15541 11834 14011 13997 13959 13559 15693 15199 13084 FALSE TRUE 12012.4471 15097.7859 13972.66705 14734.10939 14447.22622 14241.26054 13724.9391 15368.93407 13473.67324 12197.80903 0.98480367 1.237745718 1.145506297 1.207930814 1.184411576 1.167526112 1.12519708 1.25997497 1.104597818 1 13.57433441 4.751711475 24.32766575 1.171817028 0.984803493 0.339376224 0.071066763 1456.055672 2693476.156 0.015232482 0.282861244 56456.1782 -4.751711475 -0.187013535 S(ph)GLSRSSNLRVT(ph)RT(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 SGLSRSSNLRVTRTR 15 3 Q9NSI6-3;Q9NSI6-2;Q9NSI6 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 3 S(0.628)GLS(0.124)RS(0.124)S(0.124)NLRVT(1)RT(1)R;S(0.25)GLS(0.25)RS(0.25)S(0.25)NLRVT(1)RT(1)R 48.44 0.064491 423322000 37097.9 23207.9 21977.5 25160.5 22612.3 28310.3 27696 31486.9 19303.4 26438.9 TRUE FALSE 35648.07305 22546.03341 25949.32314 26459.03642 23339.64517 28882.75366 28034.95193 30836.68451 17112.15896 24648.16975 1.446276677 0.914714303 1.052789047 1.073468606 0.946911896 1.17180115 1.137405017 1.251074008 0.69425678 1 14.5891929 4.751804289 24.11894673 1.053118405 1.446277099 0.405664403 0.149274667 1421.375764 2588487.511 0.035062634 0.648684551 56468.24486 -4.751804289 0.393158694 EAEAGPAETHDLVGPELTSGHNTQGLVLPLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EAEAGPAETHDLVGPELTSGHNTQGLVLPLGK 32 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 68.43 0.0022754 103060000 33163 57625 28729 58602 49712 56233 46146 56538 42521 41458 FALSE TRUE 31866.9533 55981.59142 33920.96937 61626.45624 51311.03163 57370.06979 46710.74855 55370.47054 37694.19434 38650.01273 0.82450046 1.448423622 0.877644455 1.59447441 1.327581235 1.484348018 1.208557132 1.432611961 0.975269907 1 15.23818127 4.751850962 24.02078776 1.2860337 0.824499935 0.236541046 0.231348213 1661.66773 3003182.647 0.050729595 0.93592645 56474.31374 -4.751850962 -0.461533765 AELDELRR ddPTM_BT-474_Pertuzumab_2h_R1 3 AELDELRR 8 1 O00291-3;O00291-4;O00291 O00291-3 HIP1 Huntingtin-interacting protein 1 0 ;; 180.34 0.00038416 557647000 569120 663740 509260 582190 611330 630580 624410 617830 641200 683000 FALSE TRUE 546878.1612 644810.7851 601294.6104 612236.8957 630993.9846 643330.7596 632051.7164 605071.5946 568413.6641 636739.8016 0.858872274 1.012675481 0.944333319 0.961518181 0.990976193 1.010351101 0.992637361 0.950265074 0.892693786 1 19.28034442 4.751971684 24.63649034 0.971710264 0.858872183 0.486225959 0.035124876 1647.697074 3026798.696 0.008446776 0.162757622 56490.01419 -4.751971684 -0.112838081 CSWQDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 CSWQDLK 7 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 95.741 0.051487 0 518490 404280 414750 336100 464190 363950 407290 423650 496540 472960 FALSE TRUE 498226.8376 392750.3302 489704.5511 353446.1613 479121.0929 371309.3184 412274.5369 414901.4795 440174.8609 440925.9979 1.129955684 0.890739789 1.110627528 0.801599731 1.086624729 0.842112554 0.935019796 0.940977582 0.998296455 1 18.75017702 4.752036845 23.88655067 0.953350963 1.129955903 0.23848294 0.093008474 1598.937438 2834014.139 0.019774847 0.368348231 56498.49057 -4.752036845 0.17660494 QTPMAS(ph)SPRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTPMASSPRPK 11 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK4 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 QT(0.001)PMAS(0.499)S(0.499)PRPK 73.156 0.026846 669810000 522310 374300 408950 297410 435140 367640 379710 457790 428540 376440 TRUE FALSE 501897.5478 363625.3305 482856.362 312759.3657 449136.6733 375073.9327 384357.0046 448336.4765 379893.9358 350943.3835 1.430138226 1.036136732 1.375881082 0.891196074 1.279798094 1.068759094 1.095210859 1.277517963 1.082493512 1 18.42087878 4.752172904 24.03420229 1.140388996 1.430138558 0.294471699 0.140319029 1646.328881 2906712.759 0.030337332 0.573803032 56516.19355 -4.752172904 0.289749562 ADELLCWEDSAGHWLYE ddPTM_BT-474_Pertuzumab_2h_R1 2 ADELLCWEDSAGHWLYE 17 0 Q13232;H3BPR2 Q13232 NME3 Nucleoside diphosphate kinase 3;Nucleoside diphosphate kinase 0 ; 100.55 0.0030373 18691000 50147 69441 45969 73382 51722 63266 65232 64039 61873 60275 FALSE TRUE 48187.1998 67460.61067 54276.62087 77169.25381 53385.6851 64545.28187 66030.32873 62716.57227 54849.43643 56192.52056 0.85753761 1.200526511 0.965904721 1.373301163 0.950049661 1.148645429 1.175073267 1.116101781 0.976098525 1 15.77809049 4.752229897 24.21729762 1.109054954 0.85753735 0.247794869 0.126298719 1940.207036 3437290.914 0.027290285 0.531321863 56523.6108 -4.752229897 -0.251517604 VDVRPLPASPARPCPS(ph)PGPAAASSPARPPGLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDVRPLPASPARPCPSPGPAAASSPARPPGLQR 33 3 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 VDVRPLPAS(0.001)PARPCPS(0.996)PGPAAAS(0.001)S(0.001)PARPPGLQR;VDVRPLPAS(0.001)PARPCPS(0.995)PGPAAAS(0.002)S(0.002)PARPPGLQR 98.139 7.48E-05 1165900000 228674 229250 178078 205869 224850 252310 197773 235130 233390 229440 TRUE FALSE 219737.1673 222712.0145 210260.6559 216493.9238 232082.5045 257411.8811 200193.4051 230274.4833 206896.5457 213899.8244 1.027290078 1.041197743 0.982986576 1.012127637 1.085005586 1.203422592 0.935921316 1.076552933 0.967259072 1 17.70657577 4.752336314 19.26446966 1.038006671 1.02728998 0 0.071857781 1531.14856 2140194.499 0.016785084 0.242008715 56537.46265 -4.752336314 -0.010716691 EIDDTYIEDAADVDAR ddPTM_BT-474_Pertuzumab_2h_R1 3 EIDDTYIEDAADVDAR 16 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 ;; 306.08 3.63E-46 914180000 415910 428940 352750 422770 405380 411170 414080 432290 446940 469630 FALSE TRUE 399655.7774 416707.0512 416499.7719 444589.2104 418419.4159 419484.1391 419147.6349 423363.0604 396205.2449 437821.5418 0.912828034 0.951773751 0.951300318 1.015457596 0.955684853 0.958116719 0.957348131 0.966976313 0.904946895 1 18.73998341 4.752380489 2.053049696 0.963636465 0.897525531 0.233855947 0.027800056 1.097709441 4.909076969 0.00681995 0.13714577 56543.21371 -4.752380489 -0.066110934 QEPLGSDSEGVNCLAYDEAIMAQQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEPLGSDSEGVNCLAYDEAIMAQQDR 26 0 J3KR44;Q96FW1;F5H6Q1;F5GYJ8;F5H3F0 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 149.2 1.59E-07 79486000 43289 47032 40016 44712 44045 49175 48941 47681 47255 52127 FALSE TRUE 41597.21802 45690.69341 47247.78135 47019.59168 45461.74743 50169.35219 49539.9546 46696.37069 41890.81051 48596.39186 0.855973385 0.940207527 0.972248752 0.967553143 0.935496354 1.032367842 1.019416313 0.960902011 0.862014831 1 15.56856158 4.752392941 2.088428637 0.970782445 0.820982674 0.362120101 0.044967849 0.802034851 3.75164296 0.011609318 0.229779918 56544.83492 -4.752392941 -0.149799771 YATDTFAGLCHQLTNALVER ddPTM_BT-474_Pertuzumab_2h_R1 2 YATDTFAGLCHQLTNALVER 20 0 Q9UNS2-2;Q9UNS2;H7C3P9;J3QKR0;K7ES36;C9JLV5 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ; 283.88 6.20E-45 685290000 426350 496860 382620 447250 437020 483630 494260 416900 498450 541330 FALSE TRUE 409687.7706 482690.0393 451767.9453 470332.6261 451077.1452 493409.33 500308.9017 408290.8693 441868.0457 504665.2369 0.811801053 0.956455892 0.895183405 0.931969535 0.893814577 0.97769629 0.991367871 0.809033077 0.87556664 1 18.94496719 4.752483837 23.94585609 0.917692945 0.811800923 0.256494571 0.056716563 2105.892135 3621704.321 0.013999427 0.279395222 56556.67079 -4.752483837 -0.105892022 ECPGIEPVCVDLGDWEATER ddPTM_BT-474_Pertuzumab_2h_R1 8 ECPGIEPVCVDLGDWEATER 20 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;;;;;;; 325.24 5.21E-67 1815580000 1175435 1280573 929611 1320252 1123228 1200120 1226030 1241285 1253388 1316780 FALSE TRUE 1129497.701 1244052.312 1097612.387 1388390.364 1159357.649 1224387.249 1241034.522 1215652.031 1111108.649 1227593.318 0.920091112 1.01340753 0.894117271 1.130985599 0.944415086 0.99738833 1.010949232 0.990272604 0.905111353 1 20.22740127 4.752484464 23.38768786 0.988792724 0.920090996 0.093321614 0.062811368 2248.031267 3775822.663 0.013854286 0.26007119 56556.75243 -4.752484464 -0.068701728 (ac)MDLFGDLPEPERS(ph)PRPAAGK ddPTM_BT-474_Pertuzumab_2h_R1 11 MDLFGDLPEPERSPRPAAGK 20 2 Q9H0C8;E9PC05;F8SNU7;F8SNU6 Q9H0C8 ILKAP;ILKAP3;ILKAP2 Integrin-linked kinase-associated serine/threonine phosphatase 2C 1 MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK 134.68 1.17E-24 5814695000 1778530 1876125 1505576 1608982 1800749 1937050 1680565 1850110 1918371 1904874 TRUE FALSE 1709023.081 1822619.752 1777667.075 1692021.754 1858671.727 1976218.478 1701132.257 1811904.582 1700605.567 1775855.187 0.962366241 1.026333546 1.00102029 0.952792641 1.046634737 1.112826368 0.957922847 1.020299738 0.957626263 1 20.76008251 4.752530152 22.96638626 1.009625791 0.962366141 0.08197927 0.046029303 2027.633262 3333311.562 0.010958609 0.20132814 56562.70258 -4.752530152 -0.04725965 LALAGEGEACPLLGS(ph)PGAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LALAGEGEACPLLGSPGAGR 20 0 Q96F46-2;Q96F46 Q96F46-2 IL17RA Interleukin-17 receptor A 1 LALAGEGEACPLLGS(1)PGAGR;LALAGEGEACPLLGS(1)PGAGR 156.39 1.99E-08 53811000 56304 97846 50037 123176 59438 62767 97635 105999 72242 61754 TRUE FALSE 54103.57743 95055.52788 59079.79897 129533.1281 61349.87725 64036.19175 98829.88634 103810.0836 64041.39102 57571.34658 0.939765711 1.651090925 1.026201444 2.249958284 1.06563214 1.112292756 1.716650595 1.803155385 1.112383066 1 15.81306334 4.752549797 23.32392503 1.463207132 0.939764792 0.100071234 0.405449786 1937.753409 3230637.428 0.092639014 1.762139949 56565.26126 -4.752549797 -0.52344234 DNNLLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DNNLLGR 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P17066 A0A0G2JIW1;Q53FA3;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA6 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock 70 kDa protein 6 0 ;;; 147.69 0.0049651 8728300000 2712960 2929960 2454110 2882480 2670360 2884650 2839370 3029570 3214330 3177500 FALSE TRUE 2606934.524 2846400.41 2897622.268 3031245.138 2756254.555 2942979.599 2874119.059 2967008.321 2849452.734 2962285.095 0.880041738 0.960879969 0.978171302 1.023279341 0.930448781 0.993482904 0.970237154 1.001594454 0.961910364 1 21.49827906 4.752567176 2.363944824 0.982712099 0.853394321 0.620389188 0.023989828 0.36557744 2.384597291 0.005623868 0.098429214 56567.52476 -4.752567176 -0.129317778 RNS(ph)TDSRPVSVTYR ddPTM_BT-474_Pertuzumab_2h_R1 4 RNSTDSRPVSVTYR 14 2 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 RNS(0.999)T(0.001)DSRPVSVTYR;RNS(0.837)T(0.163)DSRPVSVTYR;RNS(0.99)T(0.01)DSRPVSVTYR;RNS(0.785)T(0.212)DS(0.002)RPVSVTYR 191.97 2.23E-07 1559350000 321255 386914 283879 373186 354386 322461 365430 374761 364729 368381 TRUE FALSE 308699.9994 375879.5915 335182.2502 392446.1742 365785.1475 328981.3824 369902.2417 367022.0544 323326.493 343430.2268 0.898872538 1.094486048 0.975983545 1.142724617 1.06509305 0.957927861 1.077081203 1.068694674 0.941461956 1 18.3896575 4.752603343 24.3662377 1.041160188 0.8988724 0.301580518 0.062120646 1985.285679 3444682.961 0.014071028 0.282784161 56572.23582 -4.752603343 -0.142287787 AASVPCS(ph)VAPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 AASVPCSVAPEK 12 0 Q9C073;D6RFX7 Q9C073 FAM117A Protein FAM117A 1 AAS(0.442)VPCS(0.558)VAPEK 102.33 0.0024814 133090000 138020 130750 112190 113610 134270 129890 113900 131520 147460 147490 TRUE FALSE 132626.0258 127021.138 132465.2287 119473.4257 138588.9165 132516.4648 115293.9423 128804.066 130720.959 137500.3709 0.964550313 0.923787603 0.963380882 0.868895298 1.007916674 0.963753508 0.838499136 0.936754317 0.950695319 1 17.06907598 4.752643546 22.20719715 0.934253797 0.964550409 0.013452257 0.050293348 2215.47596 3493255.478 0.011589384 0.209598375 56577.47293 -4.752643546 0.030296612 LEVQAEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 LEVQAEEER 9 0 Q9H307 Q9H307 PNN Pinin 0 ; 169.21 0.00013642 1051870000 479740 527070 441320 531090 533200 509230 551320 531120 538320 537840 FALSE TRUE 460991.2304 512038.4797 521076.3411 558499.6185 550350.8622 519526.9795 558067.2191 520152.1864 477212.1704 501411.6177 0.919386815 1.021193888 1.039218723 1.113854563 1.097602933 1.036128724 1.112992199 1.037375617 0.951737362 1 18.9356359 4.752708506 2.032719046 1.055944768 0.877114656 0.386126539 0.04824564 0.746298066 3.249431147 0.012323518 0.250531363 56585.93623 -4.752708506 -0.178830113 LYKSEPELT(ph)TVAEVDESNGEEKSEPVSEIETSVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYKSEPELTTVAEVDESNGEEKSEPVSEIETSVVK 35 2 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-8 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 LY(0.041)KS(0.273)EPELT(0.343)T(0.343)VAEVDES(0.001)NGEEKSEPVSEIETSVVK 128 1.79E-06 59472000 90109 47578 32440 23500 39018 31050 26128 68324 34053 22189 TRUE FALSE 86587.44066 46221.12202 38302.62962 24712.83782 40273.04941 31677.85227 26447.76228 66913.08552 30187.4462 20686.11927 4.18577499 2.234402762 1.851610209 1.194657997 1.946863444 1.531357906 1.278527013 3.234685282 1.459309299 1 14.3363754 4.752766539 2.617194109 1.808065609 4.723129158 0.606536668 0.597131168 0.375205609 3.248402025 0.155357523 2.4368874 56593.49808 -4.752766539 2.915063549 TPGNERPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPGNERPPR 9 1 P82673;H0YG82;P82673-2 P82673 MRPS35 "28S ribosomal protein S35, mitochondrial" 0 ; 118.18 0.00094087 46931000 30897 47044 30416 50535 32245 38097 47727 44055 36531 39437 FALSE TRUE 29689.51108 45702.35118 35912.8478 53143.11741 33282.18971 38867.34744 48311.0973 43145.24885 32384.15403 36765.89686 0.807528542 1.243063683 0.976797817 1.445445969 0.905246235 1.057157604 1.314019279 1.173512753 0.880820456 1 15.16608056 4.752801259 23.57650911 1.125813226 0.807528052 0.209100391 0.174650782 1615.464574 2674425.764 0.039264168 0.777576382 56598.02275 -4.752801259 -0.318285174 RAEATAASTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RAEATAASTSR 11 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ; 163.51 3.83E-05 125972000 37852 42360 31831 41248 38537 36318 40395 43073 38059 44694 FALSE TRUE 36372.70199 41151.93427 37583.56978 43376.81422 39776.5776 37052.37484 40889.36609 42183.5275 33738.70188 41666.83557 0.872941309 0.987642419 0.902002018 1.041039321 0.954633993 0.889253391 0.981340808 1.012400556 0.809725563 1 15.34661192 4.752944829 23.5393658 0.956589867 0.872941177 0.117109264 0.065417764 2300.524942 3764596.052 0.0147923 0.295982801 56616.73614 -4.752944829 -0.08364869 DLFDFSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLFDFSTR 8 0 U3KQC1;A0A0A0MQU0;Q9BV38;K7EIR0 U3KQC1 WDR18 WD repeat-containing protein 18 0 ;;; 175.38 0.00061997 1185740000 1181450 1375090 1154810 1453590 1339320 1357510 1363670 1354470 1411560 1518880 FALSE TRUE 1135277.628 1335873.78 1363509.856 1528609.954 1382400.444 1384959.782 1380359.001 1326499.721 1251325.627 1416004.905 0.80174696 0.943410418 0.962927354 1.079523065 0.976268119 0.978075554 0.974826427 0.936790344 0.883701478 1 20.43339483 4.753101422 2.619868678 0.973460584 0.763028287 0.552267756 0.0463544 0.405329233 3.516867161 0.012114584 0.190229502 56637.15396 -4.753101422 -0.210432296 TREEIQEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TREEIQEVR 9 1 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3;P29803 P08559-3 PDHA1;PDHA2 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial;Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial" 0 101.3 0.0037207 407490000 124630 192120 98071 218390 140000 152740 227240 171790 139660 138390 FALSE TRUE 119759.3218 186640.9257 115794.6113 229661.1341 144503.2271 155828.5075 230021.0311 168242.4765 123806.3823 129016.722 0.928246509 1.446641356 0.897516302 1.780088119 1.120034867 1.207816359 1.782877657 1.304036204 0.959615005 1 16.97719854 4.753319323 22.78528247 1.306933529 0.928245571 0.102202668 0.299523111 1557.245141 2404013.319 0.0674855 1.339675237 56665.57796 -4.753319323 -0.378687958 VEQATKPS(ph)FESGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VEQATKPSFESGR 13 1 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 VEQATKPS(1)FESGR;VEQAT(0.003)KPS(0.997)FESGR;VEQATKPS(0.999)FES(0.001)GR;VEQATKPS(0.999)FES(0.001)GR 178.22 8.95E-06 3938490000 3647750 3146120 2876350 2998810 3066100 2854510 2865760 3694260 3556950 3235450 TRUE FALSE 3505191.897 3056395.738 3396170.429 3153578.943 3164723.891 2912230.148 2900832.028 3617972.24 3153179.948 3016310.09 1.162079426 1.013289631 1.12593544 1.045508867 1.049203761 0.965494283 0.961715454 1.199469594 1.045376587 1 21.52435332 4.753329293 23.53671536 1.054275601 1.162079598 0.195788209 0.068900941 2131.637944 3397040.436 0.017303579 0.351114939 56666.87885 -4.753329293 0.107803996 ETVQTTEDQILKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETVQTTEDQILKR 13 1 P18206;P18206-2 P18206 VCL Vinculin 0 ; 121.75 0.0003897 409710000 181633 223960 161668 188686 201432 208510 201840 212750 221550 233910 FALSE TRUE 174534.5816 217572.8801 190885.0039 198424.1071 207911.2432 212726.2151 204310.1783 208356.6382 196400.5728 218067.0674 0.800371114 0.997733783 0.875349984 0.90992239 0.953427979 0.975508212 0.936914413 0.955470446 0.900642977 1 17.73441238 4.753410651 24.42666746 0.941857847 0.800370975 0.553398724 0.038884988 1474.538133 2425396.09 0.008822833 0.199217857 56677.49551 -4.753410651 -0.141486873 LRDTESGWDDTAVVNDLSSTSSGTES(ph)GPQSPLTPDGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRDTESGWDDTAVVNDLSSTSSGTESGPQSPLTPDGKR 38 2 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30 E9PP16 PPFIBP2 Liprin-beta-2 1 LRDTESGWDDTAVVNDLS(0.001)S(0.001)T(0.001)S(0.001)S(0.002)GT(0.025)ES(0.365)GPQS(0.303)PLT(0.303)PDGKR 79.448 0.00088546 114400000 55292 60885 50065 58349 57783 60384 60467 63626 60732 55620 TRUE FALSE 53131.12751 59148.61941 59112.85919 61360.39888 59641.64267 61605.00585 61207.01323 62312.10087 53837.95797 51852.80786 1.024652853 1.140702343 1.140012694 1.183357303 1.150210473 1.188074637 1.180399206 1.201711218 1.038284332 1 15.66213449 4.753478175 3.500642346 1.151084413 1.007124048 0.180550342 0.064429981 0.425984643 8.877087511 0.014488485 0.165295398 56686.30843 -4.753478175 -0.143960365 IGGVQQDTILAEGLHFR ddPTM_BT-474_Pertuzumab_2h_R1 5 IGGVQQDTILAEGLHFR 17 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2 Q99623-2 PHB2 Prohibitin-2 0 ;;;; 253.02 5.31E-27 1863320000 650247 981476 776079 1412671 669827 878535 1090419 944198 917117 954281 FALSE TRUE 624834.6284 953485.2654 916333.7391 1485579.12 691372.5938 896299.5796 1103763.874 924699.9813 813009.723 889646.6979 0.702340187 1.071757213 1.029997348 1.669852901 0.777131636 1.007478117 1.240676638 1.039401353 0.913856843 1 19.76287299 4.753494195 3.716134213 1.09644603 0.653955123 0.202694411 0.225805052 0.460466861 11.68125111 0.053164643 0.571421804 56688.39939 -4.753494195 -0.442490907 ENLATVEGNFASIDER ddPTM_BT-474_Pertuzumab_2h_R1 2 ENLATVEGNFASIDER 16 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 ; 320.35 1.07E-57 281150000 76891 94482 75770 104351 98828 103256 90501 107309 116380 95036 FALSE TRUE 73886.01471 91787.46587 89463.32449 109736.5676 102006.8924 105343.9071 91608.57831 105093.0317 103169.0303 88599.12707 0.833936148 1.03598612 1.009754017 1.238573914 1.15133067 1.188994864 1.033967053 1.186163285 1.164447481 1 16.43500486 4.753496319 1.214430531 1.140739765 0.69519739 0.583654086 0.07532228 1.000995542 1.223809739 0.020322432 0.567624697 56688.67667 -4.753496319 -0.445542375 MQHNLEQQIQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 MQHNLEQQIQAR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 178.95 2.13E-05 802840000 760460 1165380 685790 1425570 722530 723580 1163190 1077210 1205280 1004790 FALSE TRUE 730740.3825 1132144.503 809727.5083 1499143.839 745770.8336 738211.2834 1177425.467 1054965.237 1068461.667 936734.6783 0.780093232 1.208607442 0.864415001 1.600393231 0.796138812 0.788068703 1.256946598 1.126215631 1.140623585 1 19.83728095 4.753503831 23.13331575 1.091005927 0.780092595 0.134709791 0.232999274 1887.402134 2921709.442 0.053537863 1.105843626 56689.65727 -4.753503831 -0.310913332 LSS(ph)SDRYS(ph)DASDDS(ph)FSEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 3 LS(0.061)S(0.435)S(0.435)DRY(0.316)S(0.719)DAS(0.034)DDS(0.934)FS(0.066)EPR 196.11 6.93E-16 272570000 345080 365740 299710 309570 350190 345560 329020 382700 381000 347050 TRUE FALSE 331593.8921 355309.4533 353874.264 325546.9448 361454.1794 352547.46 333046.6452 374797.1113 337750.4773 323543.9944 1.024880381 1.09817972 1.093743881 1.006190659 1.117171654 1.089643035 1.029370506 1.158411585 1.043908968 1 18.30360237 4.753553837 22.92372858 1.078138057 1.024880258 0.056023517 0.048556076 2010.261347 3073398.027 0.010997755 0.224785459 56696.18498 -4.753553837 -0.053257799 RIQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_BT-474_Pertuzumab_2h_R1 3 RIQPQPPDEDGDHSDKEDEQPQVVVLK 27 2 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 RIQPQPPDEDGDHS(1)DKEDEQPQVVVLK;RIQPQPPDEDGDHS(1)DKEDEQPQVVVLK;RIQPQPPDEDGDHS(1)DKEDEQPQVVVLK 70.091 0.010119 1232400000 605470 468080 368577 314458 422713 434320 404313 437176 575740 440000 TRUE FALSE 581807.563 454730.8167 435187.0629 330687.2151 436309.9475 443102.248 409261.1034 428148.1628 510384.4089 410198.4081 1.418356462 1.108563095 1.060918459 0.806164062 1.063655877 1.08021445 0.997714997 1.043758714 1.244237907 1 18.64596237 4.753627505 2.434935701 1.032205883 1.515049356 0.559165738 0.10120034 0.420365458 2.967842433 0.025277342 0.431487144 56705.80298 -4.753627505 0.482843472 GDVAEGDLIEHFSQFGTVEK ddPTM_BT-474_Pertuzumab_2h_R1 7 GDVAEGDLIEHFSQFGTVEK 20 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;;;;;; 352.39 3.67E-95 2186116000 2668507 4056270 3281500 4494230 3952420 4446960 4111330 3691060 3660761 4418620 FALSE TRUE 2564218.796 3940589.151 3874540.047 4726177.749 4079553.179 4536880.578 4161645.686 3614838.321 3245206.758 4119342.932 0.622482478 0.956606239 0.940572346 1.147313498 0.990340753 1.101360254 1.010269297 0.877527892 0.787797183 1 21.9739828 4.753629173 3.606642803 0.98259405 0.575380589 0.55229192 0.09653113 0.247748811 5.68927718 0.025028118 0.277394058 56706.02077 -4.753629173 -0.407213462 TPQPCS(ph)RPAS(ph)PEPELLPEADSK ddPTM_BT-474_Pertuzumab_2h_R1 5 TPQPCSRPASPEPELLPEADSK 22 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 2 TPQPCS(1)RPAS(1)PEPELLPEADSK;TPQPCS(1)RPAS(1)PEPELLPEADSK;TPQPCS(1)RPAS(1)PEPELLPEADSK;T(0.001)PQPCS(0.999)RPAS(1)PEPELLPEADSK;T(0.003)PQPCS(0.997)RPAS(1)PEPELLPEADSK 204.92 6.32E-23 3886520000 6525510 4951720 3740810 3675950 4100840 3750530 3500480 5903340 4649820 4275070 TRUE FALSE 6270485.855 4810501.794 4416857.581 3865666.22 4232747.243 3826368.286 3543319.921 5781433.966 4121991.927 3985515.701 1.573318568 1.206996071 1.108227369 0.969928739 1.06203251 0.960068552 0.889049294 1.450611263 1.034243053 1 21.92633498 4.753741231 2.056302238 1.078642748 1.726508678 0.533855608 0.144633589 0.664695814 2.976795154 0.040325824 0.815652203 56720.65415 -4.753741231 0.64786593 EVPEYLNHVSK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVPEYLNHVSK 11 0 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 117.23 0.00088222 712590000 315560 424240 341490 451700 373940 432830 425590 405320 420060 504500 FALSE TRUE 303227.5663 412141.0906 403204.8394 475012.2911 385968.1197 441582.1192 430798.4977 396950.0004 372376.5498 470329.7656 0.644712686 0.876281113 0.857281144 1.009955835 0.820632985 0.93887768 0.915949891 0.843982306 0.791735027 1 18.84331311 4.7539029 3.6984415 0.892008691 0.613910232 0.545627319 0.068589291 0.22085474 5.508222365 0.015842709 0.171765013 56741.77279 -4.7539029 -0.278098459 DAMHEMEEMIETK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAMHEMEEMIETK 13 0 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 0 ; 142.57 4.04E-05 60609000 128666 111082 97225 99424 116117 112429 112973 106045 132993 130482 FALSE TRUE 123637.5905 107914.0501 114795.7203 104555.2846 119852.0088 114702.3914 114355.5974 103855.1337 117896.1922 121644.3379 1.016385905 0.887127605 0.943699659 0.859516245 0.985265823 0.942932432 0.940081547 0.853760524 0.969187668 1 16.89230964 4.753912535 24.04931983 0.924136833 1.01638602 0.208403819 0.047968837 2344.661966 3672889.842 0.010950189 0.250443328 56743.03165 -4.753912535 0.092249186 ECISSQS(ph)SDPKDASGDGELDLSGIDDLEIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ECISSQSSDPKDASGDGELDLSGIDDLEIDR 31 1 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 ECIS(0.065)S(0.065)QS(0.433)S(0.433)DPKDAS(0.004)GDGELDLSGIDDLEIDR 65.758 0.0037084 38558000 29151 19624 16697 18247 23161 25413 20380 21735 25183 25261 TRUE FALSE 28011.74669 19064.34273 19714.51932 19188.72986 23905.9946 25926.86827 20629.41654 21286.16465 22324.33142 23550.04997 1.189455934 0.809524513 0.837132802 0.814806333 1.01511439 1.100926253 0.875981858 0.903869193 0.947952613 1 14.5234425 4.753933809 24.37803613 0.919339691 1.189456214 0.439901427 0.09018596 2054.135971 3257268.482 0.022795421 0.53876465 56745.81123 -4.753933809 0.270116523 YYPTEDVPR ddPTM_BT-474_Pertuzumab_2h_R1 5 YYPTEDVPR 9 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;;; 237.81 6.67E-10 5029580000 2559360 2977850 2486810 3084650 2837340 2894760 2975320 2999470 2921180 3263850 FALSE TRUE 2459337.382 2892924.634 2936231.886 3243849.156 2928605.618 2953294.031 3011732.856 2937529.896 2589579.893 3042786.532 0.808251698 0.950748468 0.964981228 1.066078452 0.962474885 0.970588636 0.98979433 0.965407815 0.851055395 1 21.53696169 4.753994891 2.94112686 0.973273491 0.776887211 0.487710643 0.049792325 0.355489882 4.308450069 0.012118572 0.168058722 56753.79286 -4.753994891 -0.19638628 GADS(ph)GEEKEEGINREDKTDK ddPTM_BT-474_Pertuzumab_2h_R1 5 GADSGEEKEEGINREDKTDK 20 3 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(0.956)GEEKEEGINREDKT(0.044)DK;GADS(1)GEEKEEGINREDKTDK;GADS(0.999)GEEKEEGINREDKT(0.001)DK;GADS(1)GEEKEEGINREDKTDK;GADS(1)GEEKEEGINREDKTDK 169.91 5.57E-11 5543570000 5551020 3668210 2838300 1826460 3034360 3255050 3024800 3907980 4726060 3124540 TRUE FALSE 5334080.001 3563596.242 3351243.948 1920723.819 3131962.945 3320869.341 3061818.407 3827278.847 4189577.482 2912912.123 1.831184662 1.223379248 1.150478904 0.659382686 1.075199942 1.140051331 1.051119388 1.313901239 1.438278021 1 21.47403075 4.754103641 2.744009123 1.108915516 1.984312806 0.559470737 0.192751473 0.379508245 3.751663114 0.050934989 0.764535779 56768.00619 -4.754103641 0.87539729 DHPPIPITDLADNIER ddPTM_BT-474_Pertuzumab_2h_R1 1 DHPPIPITDLADNIER 16 0 P10586-2;P10586;H0Y6Z7;H0Y7Z9;H0Y380;H0Y4H1 P10586-2 PTPRF Receptor-type tyrosine-protein phosphatase F 0 135.47 2.27E-05 113770000 26504 60334 28135 71278 30489 41472 61215 54236 46877 36163 FALSE TRUE 25468.19438 58613.33339 33219.62036 74956.66612 31469.70637 42310.59225 61964.16748 53116.00765 41555.71948 33713.6478 0.755426839 1.738563971 0.985346366 2.223333012 0.933441156 1.25499894 1.837954998 1.575504614 1.232608222 1 15.04104511 4.754171672 24.05197474 1.454060797 0.755425962 0.192946328 0.402544574 2615.307191 4029292.429 0.089123132 2.10254698 56776.89936 -4.754171672 -0.698634835 GSLESPATDVFGSTEEGEKR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSLESPATDVFGSTEEGEKR 20 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ;; 286.16 5.53E-45 1262780000 1153320 960970 898090 879720 968970 926790 903550 1098990 1126250 1023320 FALSE TRUE 1108246.979 933564.0765 1060394.841 925122.4546 1000137.8 945530.3288 914607.9152 1076295.472 998402.8216 954009.6249 1.161672745 0.978568824 1.111513776 0.969720253 1.048351897 0.991111939 0.958698834 1.128180937 1.04653328 1 19.8636443 4.754192072 24.1123501 1.031683462 1.161672903 0.345872228 0.055515988 2065.009893 3185298.758 0.013090308 0.299794761 56779.56644 -4.754192072 0.129989441 DLTTAGAVTQCYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLTTAGAVTQCYR 13 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 296.65 2.38E-40 530420000 238219 269950 238267 262429 227757 178681 276723 262915 276890 269346 FALSE TRUE 228909.1381 262251.2903 281327.1471 275972.9921 235083.0107 182294.0522 280109.6189 257485.7134 245458.608 251102.9555 0.911614671 1.044397465 1.120365734 1.099043186 0.936201688 0.725973344 1.115517013 1.025418888 0.97752178 1 17.93791948 4.754213235 22.60315443 1.007403644 0.911614395 0.06102633 0.109435053 2517.605557 3635308.541 0.027401698 0.593941628 56782.33335 -4.754213235 -0.095789249 YVEAAWYPWWEQQGFFKPEYGRPNVSAANPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YVEAAWYPWWEQQGFFKPEYGRPNVSAANPR 31 2 P26640;A0A140T936;P26640-2;A0A140T954 P26640 VARS Valine--tRNA ligase 0 ; 226.89 1.71E-35 549780000 354260 383870 309960 320060 399260 334530 373520 372670 373460 387110 FALSE TRUE 340415.1275 372922.4034 365976.667 336578.335 412102.5605 341294.4258 378091.2495 364974.2343 331066.3865 360890.6949 0.943263798 1.033338927 1.014092833 0.932632345 1.14190409 0.945700265 1.047661397 1.011315169 0.917359165 1 18.46120242 4.754273686 23.09801537 1.00782712 0.943263658 0.080749654 0.061664737 2404.168924 3533924.511 0.013581479 0.294905388 56790.23766 -4.754273686 -0.064563462 EWCISR ddPTM_BT-474_Pertuzumab_2h_R1 2 EWCISR 6 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 109.11 0.069422 401230000 442260 524510 443310 536390 519640 482470 550650 541850 487150 615460 FALSE TRUE 424975.9903 509551.4883 523425.9784 564073.1522 536354.6925 492225.874 557389.0194 530660.6081 431850.7743 573774.346 0.740667465 0.888069486 0.912250577 0.983092319 0.934783328 0.857873618 0.971442908 0.924859419 0.752649151 1 19.13012394 4.754381173 2.660517525 0.918281965 0.701100212 0.380646854 0.067187344 0.507767661 4.590408369 0.015979755 0.248773242 56804.29486 -4.754381173 -0.217181753 SSSHSSPGS(ph)PKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSHSSPGSPKK 12 1 Q6NZY4;Q6NZY4-2;F5GX80 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 SSSHSS(0.003)PGS(0.997)PKK 123.29 0.00016146 124400000 174390 298090 197700 268920 210810 277900 252420 241170 253890 301670 TRUE FALSE 167574.646 289588.7651 233428.7878 282798.9934 217590.8951 283519.3284 255509.1915 236189.7552 225069.4716 281237.6222 0.595847187 1.029694259 0.830005552 1.005551786 0.773690566 1.00811309 0.908517109 0.839822757 0.80028223 1 18.10143008 4.754393352 24.37866005 0.901962515 0.595846862 0.513648745 0.091542412 1674.058913 2577593.184 0.02018476 0.495490312 56805.88783 -4.754393352 -0.306115653 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR ddPTM_BT-474_Pertuzumab_2h_R1 16 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR 34 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;;;;;; 354.89 3.09E-132 22783890000 6520032 7360154 6302511 7383569 7059081 7713856 7498756 7744536 7827466 8212187 FALSE TRUE 6265221.941 7150249.614 7441514.936 7764635.881 7286142.751 7869835.453 7590528.019 7584608.625 6938924.875 7655968.26 0.818344817 0.933944522 0.971988739 1.014193844 0.951694483 1.027934702 0.991452389 0.990679215 0.906341907 1 22.86815342 4.754487081 1.815474704 0.984622045 0.759249752 0.703268159 0.032187666 0.462934954 1.500774994 0.008012066 0.18089728 56818.14895 -4.754487081 -0.225372293 SSGNSSSSGSGSGSTSAGS(ph)SSPGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGS(0.001)T(0.006)S(0.041)AGS(0.317)S(0.317)S(0.317)PGAR 77.847 0.028722 17162000 15407 27109 15020 31109 18771 17476 23522 27832 21504 19411 TRUE FALSE 14804.87741 26335.87786 17734.44812 32714.53922 19374.78626 17829.37669 23809.86927 27257.25947 19062.95607 18096.27568 0.818117367 1.455320328 0.980005413 1.807805086 1.070650481 0.985251165 1.315733121 1.506235866 1.053418748 1 14.14340519 4.754713004 23.87344946 1.267828292 0.81811672 0.180409196 0.265543907 2637.706994 3898445.167 0.060596679 1.490405416 56847.71386 -4.754713004 -0.449711572 LPPEEASPYVVDHGESGPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPPEEASPYVVDHGESGPLR 20 0 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 160.27 2.43E-11 223790000 37378 40809 24880 33404 28172 38203 27465 30884 32521 36398 FALSE TRUE 35917.22644 39645.16728 29376.36945 35127.98444 29078.17797 38975.49083 27801.12489 30246.23461 28829.35242 33932.73104 1.058483221 1.168345903 0.8657237 1.035224203 0.856935975 1.14861049 0.81930113 0.891358688 0.849603069 1 15.05038993 4.754837786 0.514675097 0.906098897 1.255430391 0.210591701 0.109276335 5.990494184 1.204158277 0.061494031 1.277937673 56864.04972 -4.754837786 0.349331493 VHGPGIQSGTTNKPNKFTVETR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHGPGIQSGTTNKPNKFTVETR 22 2 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 215.58 8.49E-26 1775390000 1788040 2098650 1553900 1712060 1849090 2422040 2084500 1647430 2241090 1957330 FALSE TRUE 1718161.42 2038798.557 1834724.296 1800419.622 1908567.659 2471015.308 2110010.735 1613409.995 1986690.859 1824758.296 0.941583016 1.11729787 1.005461546 0.986661974 1.045929022 1.354160337 1.15632341 0.884177372 1.088741925 1 20.79927395 4.755095409 22.82941692 1.06627652 0.941582688 0.094727576 0.119204466 2706.509604 3736640.872 0.030594831 0.730196117 56897.79139 -4.755095409 -0.124693832 MVFETGQFDDAED ddPTM_BT-474_Pertuzumab_2h_R1 2 MVFETGQFDDAED 13 0 Q9NQ92;H9KV77 Q9NQ92 COPRS Coordinator of PRMT5 and differentiation stimulator 0 ; 186.87 1.73E-05 90494000 182905 218300 187650 225130 213480 226460 228300 221070 228210 257310 FALSE TRUE 175756.8704 212074.2977 221562.5293 236748.9863 220346.7781 231039.1764 231094.0037 216504.8272 202304.5575 239882.1645 0.732680025 0.884076972 0.923630691 0.986938678 0.918562572 0.963136117 0.963364676 0.90254658 0.843349725 1 17.87196637 4.755311641 2.07041064 0.935999721 0.669697904 0.676509814 0.042762679 0.434081982 1.972952988 0.010867749 0.220290515 56926.12742 -4.755311641 -0.266301817 AHVQELLQCSER ddPTM_BT-474_Pertuzumab_2h_R1 2 AHVQELLQCSER 12 0 Q9BQS8;Q9BQS8-4 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 0 ; 167.98 0.00017785 272300000 259170 356530 238200 297020 321870 351950 338120 272110 360160 334090 FALSE TRUE 249041.3499 346362.1135 281248.0387 312349.2378 332223.2409 359066.6701 342258.0137 266490.8334 319276.1467 311461.7867 0.799588779 1.112053318 0.902993724 1.00284931 1.06665811 1.152843416 1.098876422 0.855613256 1.025089306 1 18.24869564 4.755366544 24.40626793 1.016577142 0.799588542 0.370206364 0.087356601 3063.232407 4448452.118 0.022247402 0.627533002 56933.32445 -4.755366544 -0.2169886 FLEPTLR ddPTM_BT-474_Pertuzumab_2h_R1 3 FLEPTLR 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;; 184.16 0.0014706 270539000 373054 410900 342230 422520 409350 410790 383409 427870 424840 427740 FALSE TRUE 358474.6372 399181.5343 404078.5739 444326.3078 422517.1145 419096.4553 388101.274 419034.335 376613.9443 398768.7888 0.898953597 1.00103505 1.013315448 1.114245448 1.059554124 1.050976072 0.973248872 1.050820292 0.944441879 1 18.60519297 4.755405722 2.180541044 1.030874312 0.860794678 0.40940266 0.045357905 0.659264818 3.436622923 0.011472159 0.221535389 56938.46074 -4.755405722 -0.170079635 VTLEYRPVIDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTLEYRPVIDK 11 1 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 ; 112.51 0.0013833 570750000 1009680 1351080 885730 1669360 774540 883530 1555540 1307820 1246890 1003570 FALSE TRUE 970220.5893 1312548.521 1045801.114 1755515.87 799453.7825 901395.582 1574577.164 1280813.06 1105348.275 935597.31 1.037006604 1.40289899 1.117789783 1.876358398 0.854484909 0.963443965 1.682964612 1.368978989 1.181435926 1 19.83552819 4.755413776 22.2198354 1.29717758 1.037005637 0.044659258 0.306897394 2166.497756 2856165.347 0.071140659 1.668528256 56939.51665 -4.755413776 -0.260171943 KMLDPGLMTCS(ph)KQAMFLNLVYKSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KMLDPGLMTCSKQAMFLNLVYKSLK 25 3 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 KMLDPGLMT(0.026)CS(0.848)KQAMFLNLVY(0.002)KS(0.124)LK 43.992 0.076712 229100000 238950 155040 107490 93850 131110 97109 89674 159510 161720 104570 TRUE FALSE 229611.5698 150618.411 126915.8341 98693.60975 135327.2722 99072.61051 90771.45724 156216.0628 143362.2236 97487.38076 2.355295301 1.545004182 1.301869361 1.012373181 1.388151689 1.016260871 0.931109817 1.602423427 1.470572114 1 16.57292786 4.755506656 1.940675486 1.230500406 2.730156187 0.721633364 0.214476365 0.456217552 1.751099002 0.057967526 1.245667236 56951.69519 -4.755506656 1.499655782 VARPTSSEVDRFS(ph)PSGSVVPLTER ddPTM_BT-474_Pertuzumab_2h_R1 2 VARPTSSEVDRFSPSGSVVPLTER 24 2 Q5TC79;Q5TC79-2 Q5TC79 ZBTB37 Zinc finger and BTB domain-containing protein 37 1 VARPT(0.031)S(0.01)S(0.01)EVDRFS(0.942)PS(0.003)GS(0.003)VVPLTER;VARPTSSEVDRFS(0.96)PS(0.037)GS(0.003)VVPLTER 101.34 0.001987 564960000 152118 172728 146696 168542 185524 158736 173997 185944 166040 183121 TRUE FALSE 146173.0604 167801.9666 173207.2304 177240.4728 191491.5479 161945.7507 176126.4273 182104.1914 147191.8353 170718.0516 0.856224981 0.982918707 1.014580642 1.038205809 1.121683069 0.948615271 1.031680163 1.066695582 0.862192568 1 17.38125609 4.755549372 2.285722805 1.019132316 0.811247479 0.322832865 0.065795737 0.693014713 4.098878819 0.015940128 0.294015868 56957.29717 -4.755549372 -0.207884837 DDS(ph)HSAEDS(ph)EDEKEDHKNVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.5)HS(0.5)AEDS(1)EDEKEDHKNVR;DDS(0.5)HS(0.5)AEDS(1)EDEKEDHKNVR 142.94 3.06E-07 267978000 311970 202000 142365 116662 173493 170998 136236 150376 232810 161521 TRUE FALSE 299777.8675 196239.1578 168093.5224 122682.9398 179073.5599 174455.6967 137903.2969 147270.6831 206382.3848 150581.0388 1.99080754 1.303212937 1.116299394 0.814730332 1.189217191 1.158550227 0.915807847 0.978016118 1.370573523 1 17.20018059 4.75555528 1.999876865 1.052360997 2.293305082 0.780506908 0.147394716 0.337691052 1.401085233 0.037222758 0.779486168 56958.07198 -4.75555528 1.240944085 EGSLS(ph)PASVGSDTLSDLGISSLQDGLALHIR ddPTM_BT-474_Pertuzumab_2h_R1 5 EGSLSPASVGSDTLSDLGISSLQDGLALHIR 31 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 EGS(0.022)LS(0.862)PAS(0.052)VGS(0.062)DT(0.002)LSDLGISSLQDGLALHIR;EGS(0.105)LS(0.895)PASVGSDTLSDLGISSLQDGLALHIR;EGS(0.004)LS(0.992)PAS(0.003)VGSDTLSDLGISSLQDGLALHIR;EGS(0.037)LS(0.963)PASVGSDTLSDLGISSLQDGLALHIR;EGS(0.019)LS(0.974)PAS(0.007)VGSDTLSDLGISSLQDGLALHIR 285.92 1.66E-72 1472655000 112363 135038 115579 133591 141976 152439 131929 119817 145350 158364 TRUE FALSE 107971.7297 131186.8485 136466.6963 140485.6475 146542.787 155521.421 133543.5866 117342.7371 128850.4774 147637.8652 0.73132817 0.888571833 0.924333985 0.951555668 0.992582674 1.053397926 0.904534798 0.794801096 0.87274682 1 17.17170326 4.755776377 2.453551185 0.927363203 0.681867979 0.442408711 0.068628132 0.656920364 4.715006945 0.020122239 0.345304263 56987.07642 -4.755776377 -0.245495225 LVDLDWR ddPTM_BT-474_Pertuzumab_2h_R1 3 LVDLDWR 7 0 Q9P000;Q9P000-2 Q9P000 COMMD9 COMM domain-containing protein 9 0 ;; 105.12 0.018609 150955000 514400 583420 497297 540540 531160 452698 539260 547490 568500 668380 FALSE TRUE 494296.6793 566781.4328 587169.6302 568437.3342 548245.2438 461851.8637 545859.6252 536184.1402 503966.2633 623110.0273 0.793273511 0.909600886 0.942320946 0.912258364 0.879853027 0.741204352 0.87602446 0.860496729 0.808791772 1 19.24912741 4.755886529 23.20052123 0.874487257 0.793273331 0.126296348 0.067321321 2974.040547 3982254.853 0.015992548 0.426712112 57001.53207 -4.755886529 -0.081213927 KVQVAALQAS(ph)PPLDQDDR ddPTM_BT-474_Pertuzumab_2h_R1 5 KVQVAALQASPPLDQDDR 18 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 KVQVAALQAS(1)PPLDQDDR;KVQVAALQAS(1)PPLDQDDR;KVQVAALQAS(1)PPLDQDDR;KVQVAALQAS(1)PPLDQDDR;KVQVAALQAS(1)PPLDQDDR 239.96 3.79E-24 10410690000 6854580 7448150 6844390 7626240 7726780 8855320 8432100 8298460 8943080 9466770 TRUE FALSE 6586695.435 7235736.055 8081323.526 8019831.16 7975318.896 9034380.638 8535294.562 8127093.901 7927899.051 8825577.236 0.746318939 0.819859808 0.915670818 0.9087033 0.903659747 1.023658895 0.967108931 0.920856923 0.898286745 1 23.07325921 4.75596631 0.87436518 0.95043308 0.616727208 0.754080992 0.038259725 1.172768434 0.682852619 0.013280885 0.379889881 57012.00442 -4.75596631 -0.333705873 FEELNMDLFR ddPTM_BT-474_Pertuzumab_2h_R1 4 FEELNMDLFR 10 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 185.61 3.33E-06 301683000 552380 642890 553180 660880 540779 402195 631300 583150 669650 717310 FALSE TRUE 530792.3789 624555.4067 653151.9314 694988.096 558173.6477 410327.6585 639026.0382 571107.7487 593634.1394 668725.9548 0.793736769 0.933948207 0.976710903 1.039271904 0.834682195 0.613596131 0.955587313 0.854023602 0.887709136 1 19.35105559 4.756024017 22.91253895 0.8917438 0.79373651 0.068955193 0.113411555 3657.527095 4798540.139 0.02802944 0.735950407 57019.58034 -4.756024017 -0.098007289 DLCQAHGLPLDGEER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLCQAHGLPLDGEER 15 0 A6NKF1;F8WC89 A6NKF1 SAC3D1 SAC3 domain-containing protein 1 0 ; 161.91 1.63E-06 395680000 444560 502770 422930 522980 485060 547750 545340 503670 520910 588970 FALSE TRUE 427186.1037 488431.4919 499362.859 549971.0605 500662.3954 558825.8803 552014.034 493269.0385 461778.4806 549078.5373 0.778005467 0.889547594 0.909456162 1.001625493 0.91182292 1.017752184 1.005346224 0.898357894 0.841006248 1 19.06665299 4.756238772 1.450686055 0.949932101 0.704751511 0.483780317 0.054528348 1.11481569 2.068139313 0.015235318 0.400873535 57047.78314 -4.756238772 -0.24518059 (ac)AS(ph)PSSFTYYCPPSSSPVWSEPLYSLRPEHAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASPSSFTYYCPPSSSPVWSEPLYSLRPEHAR 31 1 P49356 P49356 FNTB Protein farnesyltransferase subunit beta 1 AS(0.162)PS(0.162)S(0.162)FT(0.162)Y(0.149)Y(0.149)CPPS(0.026)S(0.023)S(0.006)PVWSEPLYSLRPEHAR;AS(0.974)PS(0.023)S(0.004)FTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.203)PS(0.203)S(0.203)FT(0.203)Y(0.177)Y(0.007)CPPS(0.003)S(0.001)SPVWSEPLYSLRPEHAR 132.12 8.74E-26 1158660000 0 26594.7 8205.2 29252.2 12777.3 24623.8 25459.5 8452.7 13089.3 6646.5 TRUE FALSE 0 25836.24519 9688.062164 30761.90955 13188.29346 25121.71011 25771.08098 8278.148791 11603.45754 6196.326635 0 4.169606723 1.563517021 4.964539696 2.12840514 4.054290806 4.159090134 1.335976826 1.872634905 1 12.59719748 4.756364794 24.32399912 2.85392684 3.45E-06 0.279257267 1.350026531 3360.424287 4590890.4 0.307760453 9.429241583 57064.33937 -4.756364794 -2.85392339 HGVDVEVQGPHEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGVDVEVQGPHEAR 14 0 Q5JR04;Q9HCE1;Q9HCE1-2 Q5JR04 MOV10 Putative helicase MOV-10 0 89.624 0.0035133 764980000 248880 328390 242450 354080 217320 216060 369420 310380 305190 261030 FALSE TRUE 239153.4944 319024.6387 286266.1083 372354.1112 224310.2952 220428.8812 373941.0725 303970.5445 270546.1107 243350.2056 0.982754438 1.310969259 1.176354495 1.53011628 0.921759218 0.905809308 1.536637586 1.249107408 1.111756244 1 17.89267447 4.75647287 22.60771662 1.211449803 0.982753706 0.075975928 0.212564322 2467.659175 3114330.282 0.050322387 1.352773827 57078.54182 -4.75647287 -0.228696097 EESAADWALYTYEDGSDDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EESAADWALYTYEDGSDDLK 20 0 Q16643;Q16643-3;D6R9W4;D6RFI1 Q16643 DBN1 Drebrin 0 ; 154.52 4.05E-08 110723000 152006 129190 125265 108338 130986 131591 127080 129933 160378 148833 FALSE TRUE 146065.4375 125505.6277 147903.172 113929.3372 135199.2836 134251.8602 128635.2431 127249.8381 142172.5618 138752.4083 1.052705601 0.904529364 1.065950305 0.821098088 0.974392339 0.96756418 0.927084759 0.917100032 1.024649327 1 17.08215329 4.756503546 23.51357453 0.950573158 1.052705798 0.161257098 0.065310189 2715.723679 3558727.239 0.014333275 0.415622465 57082.57364 -4.756503546 0.10213264 AYLPVNESFGFTADLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AYLPVNESFGFTADLR 16 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 176.25 7.52E-09 501110000 112520 134774 110898 147061 111567 132841 136100 137796 143433 132745 FALSE TRUE 108122.594 130930.3775 130939.7355 154650.8358 115155.6539 135527.136 137765.6325 134950.4644 127151.0872 123754.0629 0.873689247 1.057988517 1.058064135 1.249662695 0.930520188 1.095132821 1.113221088 1.090473002 1.0274498 1 16.91711636 4.756822508 3.230996509 1.078226405 0.839856875 0.354571804 0.078729298 0.37887418 6.072634832 0.018124974 0.231794355 57124.51264 -4.756822508 -0.23836953 SVADELR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVADELR 7 0 E9PP00;Q9C0D7;Q9C0D7-2;Q5HYM0-2;Q5HYM0;Q5D1E8 E9PP00;Q5D1E8 ZC3H12C;ZC3H12B;ZC3H12A Probable ribonuclease ZC3H12C;Probable ribonuclease ZC3H12B;Ribonuclease ZC3H12A 0 76.833 0.092327 230540000 117840 142580 117950 158690 146120 159690 144270 148240 149050 145910 FALSE TRUE 113234.6825 138513.758 139266.1888 166880.0099 150820.0825 162919.0412 146035.6194 145178.7922 132130.4689 136027.3857 0.832440335 1.018278468 1.023809934 1.226811859 1.108747931 1.197692952 1.073575138 1.067276206 0.971351968 1 17.05353761 4.756903602 1.643749415 1.095353529 0.732384402 0.500866698 0.07577986 0.847042108 2.130349722 0.020226382 0.496181854 57135.18032 -4.756903602 -0.362969127 KTQSNNAENKRPEEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KTQSNNAENKRPEEDR 16 3 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 0 ; 97.579 0.0013254 285540000 194955 216493 150176 199711 187212 233860 192755 227354 206216 187878 FALSE TRUE 187335.9431 210318.8316 177316.1438 210018.1086 193233.844 238588.8094 195113.9933 222659.0604 182807.2242 175152.8557 1.069556887 1.200773066 1.012350858 1.199056149 1.103229766 1.362174818 1.1139641 1.271227121 1.043701077 1 17.41825498 4.757030795 22.6843074 1.160154596 1.069556615 0.024807157 0.110789589 3375.134401 4144957.396 0.024681658 0.704154865 57151.91602 -4.757030795 -0.090597981 YGDFFIR ddPTM_BT-474_Pertuzumab_2h_R1 3 YGDFFIR 7 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90;H0Y7E6 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ;; 83.377 0.051937 347081000 306829 342859 322223 317871 299115 205401 359544 316716 349738 389101 FALSE TRUE 294837.7835 333080.997 380455.8639 334276.3604 308736.3056 209554.349 363944.207 310175.7039 310037.2085 362746.8427 0.812792143 0.918218873 1.048819229 0.921514183 0.851106803 0.577687589 1.003300826 0.855074855 0.854693059 1 18.46860353 4.757100278 21.78791543 0.886265062 0.812791832 0.033691004 0.123994433 2986.816425 3509777.756 0.02989971 0.800876403 57161.0605 -4.757100278 -0.07347323 QS(ph)PECENFLDVGLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSPECENFLDVGLGR 15 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;A0A087X047 Q12802-2 AKAP13 A-kinase anchor protein 13 1 QS(1)PECENFLDVGLGR;QS(1)PECENFLDVGLGR 107.69 0.0011933 82686000 48791 51325 45964 56272 52606 55003 53602 61932 64900 73314 TRUE FALSE 46884.19378 49861.26125 54270.71726 59176.20466 54298.11977 56115.19835 54257.99731 60653.08256 57532.82408 68348.37748 0.685959133 0.729516385 0.794030806 0.865802625 0.79443173 0.821017271 0.793844701 0.887410715 0.841758447 1 16.06061947 4.757300597 0.044673531 1.476704566 2.20E-09 0.793684834 0.037363245 139.151328 0.96607796 11.33743555 21.79766104 57187.43221 -4.757300597 -1.476704563 TEES(ph)PAS(ph)DEAGEKEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEESPASDEAGEKEAK 16 1 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 2 TEES(1)PAS(1)DEAGEKEAK;TEES(1)PAS(1)DEAGEKEAK 175.59 1.97E-09 1091660000 2071600 1483730 1142940 877580 1275530 1130040 1188400 1618450 1682170 1107760 TRUE FALSE 1990639.582 1441415.473 1349494.683 922872.009 1316558.581 1152890.183 1202943.995 1585028.442 1491217.114 1032730.429 1.927550043 1.395732549 1.306725013 0.893623334 1.274832758 1.116351519 1.164818971 1.534793977 1.443955821 1 19.97803229 4.757395802 2.166616596 1.236248317 2.131974137 0.579890085 0.181752308 0.549400523 2.80380196 0.049348829 0.969687258 57199.97015 -4.757395802 0.89572582 LEQGLSEHQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEQGLSEHQR 10 0 Q6UWE0;Q6UWE0-2 Q6UWE0 LRSAM1 E3 ubiquitin-protein ligase LRSAM1 0 61.194 0.093175 235950000 137080 198570 174840 211740 193620 212030 232030 199980 196180 221480 FALSE TRUE 131722.7621 192906.978 206437.4773 222667.9268 199847.9631 216317.3919 234869.6525 195850.3431 173910.4689 206478.9623 0.637947617 0.934269409 0.999799083 1.07840491 0.967885352 1.047648581 1.137499191 0.948524445 0.842267255 1 17.65563527 4.757504954 2.42968536 1.007769933 0.542434577 0.679345343 0.074871824 0.339107451 2.360163128 0.019183037 0.336226277 57214.34807 -4.757504954 -0.465335356 GFCFLEYEDHK ddPTM_BT-474_Pertuzumab_2h_R1 6 GFCFLEYEDHK 11 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5;O43390;O43390-3;B4DT28;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 238.51 1.29E-15 30410600000 20120300 18272800 16337000 16350000 18364300 17358700 18187900 18431300 20592900 20460800 FALSE TRUE 19333976.43 17751677.63 19289459.31 17193825.46 18955004.39 17709704.81 18410488.96 18050687.21 18255280.32 19074971.79 1.013578245 0.930626678 1.011244448 0.901381436 0.993710743 0.928426265 0.965164676 0.946302171 0.957027907 1 24.18517759 4.757555843 23.63257736 0.957350539 1.013578351 0.193290412 0.033033536 2878.919955 3581636.088 0.006890264 0.225876154 57221.05264 -4.757555843 0.056227812 FVQLINTVLNGDQHFMSALDK ddPTM_BT-474_Pertuzumab_2h_R1 1 FVQLINTVLNGDQHFMSALDK 21 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 95.622 0.00088301 0 28608 27966 22667 21341 24950 24810 24478 24232 22601 27154 FALSE TRUE 27489.96773 27168.43706 26763.43112 22442.41157 25752.53941 25311.6752 24777.56909 23731.60073 20035.42923 25314.83539 1.085923227 1.073221952 1.057223194 0.886531997 1.017290415 0.999875164 0.978776623 0.937458228 0.791450109 1 14.62769548 4.757606666 0.422807198 0.923846119 1.234796693 0.410996459 0.06605588 5.477590959 0.761136528 0.050549617 0.871547439 57227.74931 -4.757606666 0.310950574 HKGPPVFTQEER ddPTM_BT-474_Pertuzumab_2h_R1 1 HKGPPVFTQEER 12 1 Q99447-3;Q99447;Q99447-4;I3L1R7;I3L2Q1 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 156.69 4.41E-05 371030000 158700 175100 147220 175760 169780 201050 200710 160300 209700 207720 FALSE TRUE 152497.8285 170106.3194 173825.9289 184830.9947 175241.1279 205115.3688 203166.349 156989.749 185895.7351 193650.9394 0.787488194 0.878417218 0.897625023 0.954454418 0.904933012 1.059201517 1.049136914 0.810684159 0.959952664 1 17.56309897 4.757609771 0.971809966 0.954552447 0.697684186 0.399363549 0.067636711 2.467489566 1.807434191 0.023139369 0.673020986 57228.15846 -4.757609771 -0.256868261 KQEKT(ph)PKT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQEKTPKTPK 10 3 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 2 KQEKT(1)PKT(1)PK 70.622 0.091236 509540000 2197200 1064400 758270 360960 934050 818570 749510 1150800 1135300 650490 TRUE FALSE 2111330.995 1034044.354 895306.2566 379589.1889 964094.5665 835122.0462 758682.7276 1127035.578 1006425.504 606431.7329 3.481564173 1.705129033 1.476351266 0.625938862 1.589782517 1.377108091 1.251060402 1.858470652 1.659585818 1 19.20998572 4.757624598 2.774863679 1.390812938 3.928674772 0.785878212 0.331016113 0.218098797 2.209695275 0.084733372 1.287845895 57230.11225 -4.757624598 2.537861834 NAMS(ph)LPQLNEK ddPTM_BT-474_Pertuzumab_2h_R1 3 NAMSLPQLNEK 11 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK 175.15 1.07E-05 537813000 5150990 2523360 1120000 869830 881050 564809 449027 2011840 925265 708020 TRUE FALSE 4949683.616 2451396.243 1322408.914 914722.0305 909389.7734 576229.825 454522.3267 1970294.801 820232.7962 660065.1748 7.498780129 3.713869989 2.00345203 1.385805623 1.377727243 0.872989285 0.688602193 2.985000385 1.242654252 1 19.33224896 4.757630945 1.52598001 1.469882814 10.05464388 0.907211997 0.599283011 0.346865079 0.725763618 0.17644302 4.544605533 57230.94871 -4.757630945 8.584761064 LLGSENDTGS(ph)PDFYTPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLGSENDTGSPDFYTPR 17 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 LLGSENDT(0.082)GS(0.918)PDFYTPR 282.97 4.73E-36 131550000 55808 68644 52800 71083 74246 71816 73853 74811 68038 87094 TRUE FALSE 53626.96166 66686.34033 62342.13453 74751.60215 76634.19002 73268.16873 74756.83511 73266.12671 60314.61148 81195.0458 0.660470859 0.821310459 0.767807123 0.920642404 0.943828398 0.902372405 0.920706853 0.902347255 0.742836104 1 16.30910408 4.757733799 0.940399865 0.901713871 0.542688299 0.530392411 0.06889805 1.680221981 1.14442466 0.021461176 0.623154445 57244.50425 -4.757733799 -0.359025573 VAS(ph)SPAPPEGPSHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 VASSPAPPEGPSHPR 15 0 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 1 VAS(0.5)S(0.5)PAPPEGPSHPR 80.316 0.011165 269870000 81403 99317 85235 113270 83268 109750 102670 109950 122940 119880 TRUE FALSE 78221.68076 96484.5764 100638.8605 119115.8783 85946.39084 111969.2202 103926.5062 107679.4941 108984.3666 111760.4208 0.699905031 0.863316152 0.900487487 1.065814511 0.769023508 1.001868277 0.929904392 0.963485045 0.975160668 1 16.77004983 4.757762403 1.526453668 0.950605183 0.595368339 0.526998108 0.07347335 0.875407381 1.832631366 0.018425347 0.474760964 57248.27466 -4.757762403 -0.355236844 GPS(ph)PAPAS(ph)SPKR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(0.99)PAPAS(0.505)S(0.505)PKR;GPS(1)PAPAS(0.542)S(0.458)PKR;GPS(0.999)PAPAS(0.923)S(0.078)PKR 83.087 0.0088247 268476000 1009640 917446 755726 790050 850231 891953 833937 938447 1028830 941230 TRUE FALSE 970182.1526 891281.3384 892302.4992 830824.5752 877579.4523 909988.9008 844142.9705 919067.7415 912041.5316 877479.6537 1.105646323 1.01572878 1.016892523 0.946830586 1.000113733 1.037048434 0.962008597 1.047394931 1.039387669 1 19.74300615 4.757763429 3.294508389 1.006765751 1.121567962 0.482439025 0.030698662 0.321639045 5.465619967 0.007605507 0.096072803 57248.40995 -4.757763429 0.114802211 SYS(ph)SPDITQAIQEEEKR ddPTM_BT-474_Pertuzumab_2h_R1 3 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.927)S(0.073)PDITQAIQEEEKR;S(0.001)YS(0.908)S(0.091)PDITQAIQEEEKR;S(0.001)YS(0.959)S(0.04)PDITQAIQEEEKR 328.55 3.78E-72 3654940000 1274480 1063469 858494 840269 959910 880663 899157 1389100 970143 921576 TRUE FALSE 1224671.913 1033139.905 1013642.963 883635.3838 990786.3769 898470.6092 910161.1523 1360414.6 860016.4338 859156.8367 1.425434636 1.202504434 1.179811322 1.02849136 1.153207813 1.045758552 1.059365547 1.583429872 1.001000512 1 19.71256199 4.757780586 2.80991641 1.16478037 1.480133301 0.202110687 0.165364814 0.887648838 9.324616471 0.043763212 0.656769754 57250.67165 -4.757780586 0.31535293 VMEYINR ddPTM_BT-474_Pertuzumab_2h_R1 3 VMEYINR 7 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 164.89 0.0027471 3561970000 1912100 2174640 1816620 2045020 1987200 1479900 2318210 1963070 2068330 2382050 FALSE TRUE 1837373.018 2112621.396 2144923.644 2150563.727 2051120.093 1509824.592 2346580.947 1922531.918 1833541.85 2220711.632 0.827380283 0.951326307 0.965872207 0.968411971 0.923631895 0.679883228 1.056679721 0.865727855 0.825655084 1 21.08259063 4.757790619 23.00788207 0.911726566 0.827380053 0.06403069 0.099966992 4455.848108 5330973.824 0.023019051 0.73061788 57251.99427 -4.757790619 -0.084346512 RLGLPGDEVDNK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLGLPGDEVDNK 12 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 65.329 0.097881 262330000 371350 413790 319890 364870 397860 379360 394280 341120 476210 446700 FALSE TRUE 356837.2315 401989.1143 377701.2389 383700.9844 410657.5282 387030.9191 399105.3166 334075.7528 422152.6372 416444.6111 0.856866008 0.965288309 0.906966326 0.921373393 0.986103595 0.929369498 0.958363504 0.802209331 1.013706567 1 18.6677651 4.757829639 23.13320747 0.930500673 0.85686582 0.135058372 0.058248349 3323.959413 3990359.711 0.013946804 0.446062604 57257.13838 -4.757829639 -0.073634853 YAEIVHLTLPDGTKR ddPTM_BT-474_Pertuzumab_2h_R1 1 YAEIVHLTLPDGTKR 15 1 P21281;H0YC04 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 95.57 0.002619 281780000 420070 457480 351090 430620 416230 433550 444260 384700 530980 472840 FALSE TRUE 403653.2 444433.1183 414539.773 452844.3498 429618.416 442316.678 449696.9868 376755.8106 470705.3764 440814.1256 0.915699331 1.008209793 0.940395847 1.027290923 0.974602198 1.003408585 1.020151036 0.8546818 1.067809195 1 18.74981093 4.757841893 21.85990141 0.979478724 0.915699001 0.116266811 0.055396098 1710.386318 1938947.793 0.013132386 0.382472264 57258.75397 -4.757841893 -0.063779723 LQLLEPFDKWDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LQLLEPFDKWDGK 13 1 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 70.438 0.04103 53726000 98859 128100 99975 123980 91376 92916 134990 116380 132400 102260 FALSE TRUE 94995.48099 124446.7134 118042.7064 130378.6227 94315.19203 94794.82518 136642.048 113976.7123 117370.5071 95333.83912 0.996450808 1.30537818 1.238203638 1.367600674 0.989314947 0.994346038 1.433300592 1.195553577 1.231152633 1 16.54070077 4.758152537 22.9876569 1.205672081 0.996450219 0.133508089 0.149518221 2854.226022 3348765.788 0.035251276 1.172362759 57299.72496 -4.758152537 -0.209221862 S(ph)ASEPSLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASEPSLHR 9 0 Q96II5;P10398;P04049;P04049-2;H7C155 Q96II5;P04049 ARAF;RAF1 Serine/threonine-protein kinase A-Raf;RAF proto-oncogene serine/threonine-protein kinase 1 S(0.5)AS(0.5)EPSLHR 90.05 0.0075314 254980000 115170 159910 130260 159970 152590 158050 166590 163270 157530 167000 TRUE FALSE 110669.0291 155349.5234 153800.8796 168226.0709 157498.1959 161245.8793 168628.7783 159898.4174 139647.8548 155688.9413 0.710834233 0.997819897 0.98787286 1.080526783 1.011620958 1.035692567 1.083113398 1.027037734 0.896967079 1 17.24830695 4.75866499 3.404079714 1.022099965 0.663251735 0.768018028 0.049839717 0.154256948 2.899925619 0.011955509 0.14725537 57367.37661 -4.75866499 -0.35884823 AQPPKPER ddPTM_BT-474_Pertuzumab_2h_R1 1 AQPPKPER 8 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 0 62.546 0.072006 67291000 69970 89142 64369 82339 73931 73469 80813 88074 81208 80059 FALSE TRUE 67235.49504 86599.75744 76001.91018 86588.52566 76309.05776 74954.59352 81802.01367 86255.24112 71989.60829 74636.53262 0.900838942 1.16028645 1.01829369 1.160135963 1.022408934 1.004261464 1.09600501 1.155670529 0.964535808 1 16.18759434 4.758680966 24.10230795 1.073031686 0.900838675 0.319996771 0.07067584 3219.772712 3856886.459 0.01612964 0.614297314 57369.48694 -4.758680966 -0.172193012 EDGSGDRGDGPFR ddPTM_BT-474_Pertuzumab_2h_R1 6 EDGSGDRGDGPFR 13 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;; 166.45 3.06E-05 7235120000 3704820 4101990 3069950 3790820 3675100 3850170 3701230 3938650 4262910 4222750 FALSE TRUE 3560031.539 3985005.261 3624758.256 3986464.674 3793312.929 3928023.075 3746526.76 3857315.501 3779002.328 3936739.381 0.904309682 1.01226037 0.92075139 1.012631086 0.963567197 0.997785907 0.951682699 0.979824959 0.959932056 1 21.90856978 4.759102418 24.15524524 0.975503793 0.904309572 0.38086687 0.027919426 2991.452316 3517578.356 0.005871411 0.230739775 57425.18702 -4.759102418 -0.071194221 RVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_BT-474_Pertuzumab_2h_R1 4 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(1)EVEEEKEPVPQPLPSDDTR 182.91 2.32E-17 6795480000 3565730 3138760 2841270 3040740 3197400 2803320 2912140 3529520 3495270 3423440 TRUE FALSE 3426377.329 3049245.638 3354750.693 3197672.956 3300247.275 2860005.051 2947779.64 3456634.179 3098501.603 3191567.36 1.073571993 0.95540695 1.051129528 1.00191304 1.034052208 0.896113016 0.923615048 1.08305224 0.970840109 1 21.60583367 4.759231378 23.12908121 0.994841985 1.073572207 0.169597338 0.05432797 3425.889761 3833149.186 0.013334296 0.493584381 57442.24141 -4.759231378 0.078730222 ELDKDAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDKDAPR 8 1 Q9H501;A0A087WX71 Q9H501 ESF1 ESF1 homolog 0 61.962 0.075376 220280000 146880 149740 120350 131190 151610 142860 134640 149110 165810 147720 FALSE TRUE 141139.7672 145469.5618 142099.9222 137960.7316 156486.6733 145748.7271 136287.7646 146030.8264 146987.9439 137714.7928 1.024870054 1.056310356 1.031842108 1.001785856 1.136309834 1.058337482 0.9896378 1.060385914 1.067335912 1 17.07132401 4.75949614 21.51310703 1.04616272 1.024869909 0.019701773 0.040655571 3504.581292 3600868.843 0.00953064 0.311442762 57477.27097 -4.75949614 -0.021292811 DFVDDDDDDDLER ddPTM_BT-474_Pertuzumab_2h_R1 2 DFVDDDDDDDLER 13 0 G3V4K3;Q9H9C1;Q9H9C1-2 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 0 ; 304.69 6.55E-41 2378900000 1178630 1352930 1011430 1310320 1303990 1399870 1322080 1436970 1497600 1446920 FALSE TRUE 1132567.837 1314345.761 1194217.9 1377945.772 1345934.023 1428176.331 1338260.011 1407296.067 1327598.726 1348918.82 0.839611562 0.9743698 0.885314878 1.02151868 0.997787267 1.058756324 0.992098258 1.043277065 0.98419468 1 20.3633721 4.759528325 0.676184838 1.021259015 0.753751052 0.630504457 0.039166112 1.918426251 0.651341365 0.015313125 0.399410044 57481.53072 -4.759528325 -0.267507963 SMMQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMMQDR 6 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 101.69 0.084302 170450000 157140 181700 160500 170590 164550 103100 191550 168880 176100 193580 FALSE TRUE 150998.7951 176518.0939 189505.9203 179394.1703 169842.9002 105184.7526 193894.2462 165392.569 156109.8663 180468.6542 0.836703724 0.978109438 1.050076653 0.994046147 0.941121332 0.582842229 1.07439293 0.916461475 0.865024827 1 17.46138875 4.759981808 21.67193608 0.931678066 0.836703127 0.046741785 0.13097676 3009.172602 3044087.537 0.031194716 1.101404981 57541.58329 -4.759981808 -0.09497494 GKLDGNQDLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 GKLDGNQDLIR 11 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;; 142.1 3.45E-05 3917720000 5285400 8024600 4984100 10055500 4182450 3439890 9991600 7735200 6209200 5453600 FALSE TRUE 5078840.725 7795746.265 5884837.741 10574465.56 4316982.303 3509446.933 10113880.19 7575465.417 5504357.647 5084222.814 0.998941413 1.533321129 1.157470464 2.0798588 0.849093846 0.690262221 1.989267693 1.489994773 1.082635016 1 22.27759583 4.760013152 22.07505219 1.355920143 0.998939592 0.040116765 0.437650892 3384.330271 3482255.889 0.103266611 3.792064309 57545.73638 -4.760013152 -0.356980552 SGYHDDS(ph)DEDLLE ddPTM_BT-474_Pertuzumab_2h_R1 4 SGYHDDSDEDLLE 13 0 Q99523;Q99523-2 Q99523 SORT1 Sortilin 1 SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE 185.57 8.96E-06 6620200000 3829300 5485030 3451440 5697200 3974790 3919030 5202260 4899010 5169640 4999450 TRUE FALSE 3679646.722 5328602.315 4075191.985 5991233.175 4102642.73 3998275.472 5265926.814 4797843.732 4582804.14 4660832.798 0.78948267 1.143272575 0.874348461 1.285442631 0.880238126 0.857845721 1.1298253 1.029396234 0.983258645 1 22.15215633 4.760264469 23.48180515 1.021087834 0.789482118 0.223626734 0.129073725 3568.274067 3860440.022 0.029057614 1.267749564 57579.04654 -4.760264469 -0.231605716 HAS(ph)PDKWNDKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 HASPDKWNDKPK 12 2 Q96JM3;A0A2R8Y4S6;S4R3K0;A0A2R8Y735 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 HAS(1)PDKWNDKPK;HAS(1)PDKWNDKPK 130.21 0.00011502 1646130000 3595370 2307250 2829800 2035860 2630020 2560780 2967910 1946850 3872290 3334910 TRUE FALSE 3454858.966 2241449.489 3341207.809 2140930.979 2714616.982 2612560.726 3004232.17 1906646.867 3432723.873 3109033.575 1.11123244 0.720947341 1.0746773 0.68861623 0.873138522 0.840312806 0.966291324 0.613260301 1.104112834 1 21.56803477 4.760284536 23.54129202 0.855982435 1.111233028 0.157674687 0.157481774 3945.128497 4275016.247 0.03455333 1.502440181 57581.70708 -4.760284536 0.255250593 (ac)SETAPAETATPAPVEKS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 6 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETAT(0.001)PAPVEKS(0.999)PAK;SETAPAET(0.001)AT(0.07)PAPVEKS(0.93)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK 195.77 1.65E-45 13908980000 9120580 5637170 4969550 4149540 5572680 3920220 5669360 6697380 5261580 4230720 TRUE FALSE 8764137.65 5476403.431 5867658.232 4363698.257 5751930.313 3999489.534 5738743.324 6559076.763 4664307.497 3944169.566 2.222048901 1.388480728 1.487678999 1.106366799 1.458337482 1.014025758 1.454994068 1.66298042 1.182582903 1 21.91129015 4.760312442 3.564680611 1.337430866 2.347669355 0.622363001 0.213017313 0.224160177 4.864223887 0.051935274 0.621651313 57585.40712 -4.760312442 1.010238489 VFTTVGSAEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFTTVGSAEKR 11 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 166.29 3.30E-05 2500100000 5590900 3394100 2550270 2061740 2377290 2134200 2551320 5115200 2645660 2538610 FALSE TRUE 5372401.447 3297303.591 3011160.519 2168146.648 2453757.692 2177354.986 2582543.817 5009569.332 2345335.768 2366667.684 2.270027805 1.393226271 1.2723208 0.916117909 1.036798579 0.920008754 1.091215229 2.116718527 0.990986519 1 21.17442571 4.760316524 2.68343162 1.229108986 2.50824211 0.479744389 0.338893758 0.524693806 4.797265115 0.095344487 1.531885631 57585.9484 -4.760316524 1.279133123 SVS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 3 SVSPER 6 0 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4;A0A096LNR2;A0A096LNX0;A0A096LNQ0 Q14966 ZNF638 Zinc finger protein 638 1 S(0.061)VS(0.939)PER;S(0.113)VS(0.887)PER;S(0.214)VS(0.786)PER 84.368 0.058668 703970000 602150 684130 560800 726410 695170 761900 731310 615600 700170 741320 TRUE FALSE 578617.3123 664619.2822 662149.0349 763900.1072 717530.7744 777306.14 740259.9905 602887.6449 620689.637 691109.7361 0.837229288 0.961669685 0.958095365 1.105323898 1.038229874 1.124721733 1.071117873 0.872347202 0.898105763 1 19.39855528 4.760539648 1.673412808 1.009391061 0.772103651 0.311577068 0.077741878 1.474455375 3.851112933 0.023275661 0.573696564 57615.54153 -4.760539648 -0.237287409 LVRLSS(ph)DSFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.263)S(0.73)DS(0.007)FAR 178.67 4.51E-06 353290000 74288 110130 56532 110190 83541 93509 102930 100070 96957 90616 TRUE FALSE 71384.74283 106989.2002 66748.58995 115876.9191 86228.17214 95399.81605 104189.6881 98003.51953 85950.84784 84478.49761 0.845004881 1.266466654 0.790125202 1.371673531 1.020711478 1.129279269 1.233327901 1.160100171 1.017428698 1 16.36629656 4.760702877 23.75202321 1.11851089 0.845004309 0.204764065 0.15578034 4325.83779 4640183.531 0.033830928 1.588062682 57637.20026 -4.760702877 -0.273506581 SLNST(ph)PPPPPAPAPAPPPALAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLNSTPPPPPAPAPAPPPALAR 22 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 SLNS(0.011)T(0.989)PPPPPAPAPAPPPALAR;SLNS(0.223)T(0.776)PPPPPAPAPAPPPALAR;SLNS(0.034)T(0.966)PPPPPAPAPAPPPALAR 201.48 1.70E-21 1097730000 527335 542246 493437 610621 577191 583733 670183 690496 703681 680420 TRUE FALSE 506726.1652 526781.675 582612.0423 642135.223 595756.8727 595536.4812 678384.9 676237.0163 623802.083 634334.5473 0.798831102 0.830447714 0.918461788 1.012297416 0.939184024 0.938836587 1.069443408 1.066057365 0.983396042 1 19.27488439 4.760821641 0.526635544 1.031282704 0.604661105 0.754190832 0.042444197 2.119076874 0.442782385 0.026276598 0.564103964 57652.96421 -4.760821641 -0.426621599 GT(ph)RESGQK ddPTM_BT-474_Pertuzumab_2h_R1 4 GTRESGQK 8 1 A0A1W2PQW7;A8K830-4;A8K830-2 A0A1W2PQW7 1 GT(0.978)RES(0.022)GQK;GT(0.651)RES(0.349)GQK;GT(0.5)RES(0.5)GQK;GT(0.972)RES(0.028)GQK 87.616 0.02457 4635370000 714754 1303460 1120180 1743220 1745190 1450260 1912400 2786500 805548 1555620 TRUE FALSE 686820.6235 1266286.597 1322621.444 1833187.793 1801325.621 1479585.251 1935804.523 2728957.801 714105.5682 1450256.472 0.473585629 0.873146662 0.91199141 1.264043863 1.242073838 1.020223167 1.334801506 1.881707032 0.492399505 1 20.46787663 4.76088555 0.793383724 1.275058393 6.88E-06 0.261510874 0.338593502 3.075265358 1.447750808 0.124242906 3.508066353 57661.44871 -4.76088555 -1.275051512 EYLQCLHFDCLLDGGVINLSVPIVLTATHEDKER ddPTM_BT-474_Pertuzumab_2h_R1 1 EYLQCLHFDCLLDGGVINLSVPIVLTATHEDKER 34 1 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 62.393 0.010007 100620000 97980 81212 63211 81317 85240 88535 94418 72726 99102 100510 FALSE TRUE 94150.83328 78895.91327 74634.63382 85513.78012 87981.82201 90325.23836 95573.51573 71224.18269 87852.35643 93702.36817 1.004786059 0.841984198 0.796507445 0.912610661 0.938949823 0.963958971 1.019969053 0.760110807 0.937568155 1 16.51579789 4.7609647 23.16079916 0.898742205 1.00478637 0.1049807 0.08087697 4673.62721 4831270.48 0.019777451 0.900966922 57671.95847 -4.7609647 0.106044166 KNCHLNENIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNCHLNENIEK 11 1 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 68.44 0.037151 167700000 191050 230490 182700 199290 182920 202460 226300 220740 224860 191920 FALSE TRUE 183583.5548 223916.6509 215717.9541 209575.3808 188803.7879 206553.8799 229069.5271 216181.6419 199334.8355 178921.0875 1.026058792 1.251482729 1.205659753 1.171328566 1.055234968 1.154441228 1.280282444 1.20825133 1.114093584 1 17.44896391 4.761081399 23.51759428 1.172060005 1.026058437 0.180850217 0.082086919 4072.770949 4252887.186 0.019272396 0.902647759 57687.45763 -4.761081399 -0.146001568 RLSESS(ph)ALK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSESSALK 9 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RLS(0.204)ES(0.38)S(0.417)ALK 187.76 4.25E-05 1037200000 894960 661330 665420 725800 714330 529680 675750 918050 711370 689710 TRUE FALSE 859983.9738 642469.5159 785676.1962 763258.625 737307.0732 540390.4925 684020.0306 899091.9467 630618.2599 642995.3274 1.337465355 0.999182247 1.22190032 1.187036037 1.146675632 0.84042678 1.063802491 1.398286906 0.980750922 1 19.29444873 4.761113185 23.2274689 1.117695412 1.337465985 0.178903249 0.148886518 4502.548323 4637092.026 0.037154081 1.741534372 57691.67987 -4.761113185 0.219770573 S(ph)PTPPLFSLPEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPTPPLFSLPEAR 13 0 A0A087WWS1;Q96FV9;Q96FV9-2;J3KRD7;J3QQZ3;J3KT14 A0A087WWS1 THOC1 THO complex subunit 1 1 S(0.998)PT(0.002)PPLFSLPEAR 119.39 0.00037008 34051000 10346 13500 11262 12473 12052 13611 14333 14124 15428 13188 TRUE FALSE 9941.666882 13114.99322 13297.29392 13116.73302 12439.66353 13886.22375 14508.41154 13832.33446 13676.67812 12294.76501 0.808609751 1.066713614 1.08154112 1.066855122 1.011785383 1.12944198 1.180047892 1.125058873 1.112398497 1 13.58575654 4.761114922 3.116406718 1.096696196 0.756055835 0.720487848 0.051762669 0.214779479 3.047857839 0.01337241 0.184257317 57691.91061 -4.761114922 -0.340640361 SMDFEEAER ddPTM_BT-474_Pertuzumab_2h_R1 7 SMDFEEAER 9 0 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 ;;;;;; 230.56 1.99E-07 4630480000 3336170 3778170 3097230 3990530 3852580 3704620 3924540 4009900 3839660 3926340 FALSE TRUE 3205788.788 3670420.291 3656968.359 4196481.732 3976501.735 3779529.955 3972569.694 3927094.164 3403797.894 3660405.495 0.875801545 1.00273598 0.999060996 1.146452692 1.086355525 1.032544061 1.085281317 1.072857685 0.929896401 1 21.80357205 4.761208489 1.569298639 1.055661328 0.803997633 0.440823742 0.056732182 0.97373203 2.168028933 0.014878328 0.382960107 57704.34144 -4.761208489 -0.251663696 VESELR ddPTM_BT-474_Pertuzumab_2h_R1 2 VESELR 6 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ; 116.35 0.055015 1660670000 2173800 2475200 2066800 2625900 2356100 2507200 2564900 2530500 2619800 2742700 FALSE TRUE 2088845.493 2404609.719 2440316.736 2761423.014 2431886.096 2557897.302 2596290.013 2478244.291 2322411.287 2556934.486 0.816933521 0.940426801 0.954391577 1.079974097 0.95109441 1.000376551 1.015391684 0.96922479 0.908279543 1 21.28598377 4.761311443 1.811543428 0.987498329 0.755419598 0.584512509 0.042894584 0.634236069 2.018278679 0.010953067 0.256111775 57718.02243 -4.761311443 -0.232078731 QCCGTLPQAPSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 QCCGTLPQAPSGK 13 0 Q9Y6M5 Q9Y6M5 SLC30A1 Zinc transporter 1 0 63.727 0.066864 684550000 352860 574220 493050 728160 672210 660190 721450 606850 573440 826300 FALSE TRUE 339069.8411 557843.8078 582155.1028 765740.4249 693832.2451 673539.4941 730279.3209 594318.3354 508345.4953 770333.965 0.440159537 0.724158395 0.755717818 0.99403695 0.90069019 0.874347393 0.948003534 0.771507375 0.659902741 1 19.55512451 4.76143143 1.475522257 0.865392468 0.259363691 0.62838457 0.100610111 0.81884878 1.568924844 0.027755976 0.739769494 57733.97109 -4.76143143 -0.606028776 DTPGHGSGWAETPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 183 1.46E-06 2374300000 811760 1200860 1026890 1405380 1213410 1421630 1192060 1099600 1090570 1451180 FALSE TRUE 780035.5218 1166612.649 1212471.866 1477911.83 1252440.435 1450376.333 1206648.787 1076892.876 966773.0656 1352890.286 0.576569682 0.86231135 0.896208568 1.092410704 0.925751665 1.072057614 0.891904391 0.795994241 0.714598276 1 20.36761342 4.761500302 2.598528804 0.918918356 0.494063202 0.475931239 0.108738955 0.514529743 4.281816022 0.029174608 0.48904582 57743.12739 -4.761500302 -0.424855154 RGFAFVTFDDHDSVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGFAFVTFDDHDSVDK 16 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 176.21 2.11E-09 686800000 1560440 1954200 1407830 1786690 1597070 1914590 1666610 1693830 1847750 2023410 FALSE TRUE 1499456.28 1898468.129 1662256.198 1878901.285 1648441.207 1953304.322 1687006.472 1658851.819 1638001.166 1886362.638 0.794892906 1.006417372 0.881196523 0.996044582 0.873872909 1.035487176 0.894317157 0.879391791 0.868338427 1 20.84717562 4.7616674 23.87660155 0.930345709 0.794892627 0.311527954 0.062732585 4308.56051 4451971.008 0.014248181 0.742777757 57765.34881 -4.7616674 -0.135453082 RVS(ph)SDLQHATAQLSLEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVSSDLQHATAQLSLEHR 18 1 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 RVS(0.5)S(0.5)DLQHATAQLSLEHR;RVS(0.801)S(0.199)DLQHATAQLSLEHR 204.8 4.86E-16 536940000 2503710 1675710 1423260 1322040 1764400 1609940 1772040 724790 2700210 1804060 TRUE FALSE 2405862.245 1627920.391 1680474.742 1390270.643 1821153.528 1642494.09 1793726.756 709822.8332 2393693.481 1681869.409 1.430469115 0.967923183 0.999170764 0.826622231 1.082815062 0.976588361 1.066507748 0.422043964 1.423233854 1 20.68163426 4.761701095 3.396845914 0.932562492 1.508829928 0.234924281 0.237548666 0.47204173 8.741178587 0.05707009 0.724761566 57769.83068 -4.761701095 0.576267437 LSFDSS(ph)PTSSTDGHSSYGLDSGFCTISR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSFDSSPTSSTDGHSSYGLDSGFCTISR 28 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 LSFDS(0.212)S(0.758)PT(0.012)S(0.012)S(0.004)T(0.002)DGHSSYGLDSGFCTISR 126.74 2.22E-05 402350000 138760 201340 172910 243800 198980 258700 195130 195360 182040 231580 TRUE FALSE 133337.1058 195597.9803 204158.6834 256382.5472 205380.3724 263931.0912 197518.0593 191325.7477 161375.5824 215894.8803 0.617601981 0.905987118 0.945639299 1.187534169 0.951298021 1.222498147 0.9148807 0.886198633 0.747472947 1 17.71996951 4.761836597 2.253299861 0.983425838 0.511774691 0.410874457 0.130817204 0.694465453 3.899476686 0.034291145 0.665765549 57787.85802 -4.761836597 -0.471651147 LSDQFHDILIR ddPTM_BT-474_Pertuzumab_2h_R1 8 LSDQFHDILIR 11 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;;;;;; 250.26 1.32E-16 16413720000 9393690 10967120 9158950 11486590 10546750 11059350 10993780 10644930 11389040 11627260 FALSE TRUE 9026574.21 10654348.48 10814176 12079414.29 10885995.79 11282977.63 11128325.17 10425108.48 10096203.93 10839735.32 0.83273013 0.982897475 0.997642072 1.11436432 1.004267675 1.04089051 1.026623329 0.961749357 0.931406868 1 23.36982619 4.761945882 2.65386039 1.010811341 0.790953734 0.571151353 0.045732657 0.396465569 3.498897161 0.01203044 0.197832711 57802.40152 -4.761945882 -0.219857607 IWYEHR ddPTM_BT-474_Pertuzumab_2h_R1 10 IWYEHR 6 0 O75874;P48735;P48735-2;H0YL11 O75874;P48735 IDH1;IDH2 "Isocitrate dehydrogenase [NADP] cytoplasmic;Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;;;;;; 140.01 0.011834 18864330000 5367230 6528750 5344170 8194680 5612260 4990780 7698210 6436670 6438420 6650950 FALSE TRUE 5157472.718 6342556.442 6309980.399 8617608.417 5792783.44 5091696.991 7792422.997 6303750.515 5707557.554 6200475.232 0.831786682 1.022914568 1.01766077 1.38983031 0.934248299 0.821178507 1.256746089 1.016656027 0.920503242 1 22.56394736 4.761962581 2.7443358 1.053796726 0.782383817 0.13882775 0.156784863 0.970890895 9.432079048 0.038523624 0.611433521 57804.62403 -4.761962581 -0.27141291 HITGSYK ddPTM_BT-474_Pertuzumab_2h_R1 1 HITGSYK 7 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 129.68 0.0036367 494680000 617890 701540 603690 641480 586280 625550 655100 563210 733490 857610 FALSE TRUE 593742.1757 681532.7661 712790.212 674586.8597 605138.2286 638199.0496 663117.3098 551579.5167 650227.2902 799523.3108 0.742620218 0.852423884 0.891518987 0.843736325 0.756873778 0.798224443 0.829390839 0.689885472 0.813268708 1 19.60878057 4.762006192 21.99278985 0.814268253 0.742619797 0.068566285 0.078765778 3491.973176 3275321.482 0.018784621 0.827402516 57810.42903 -4.762006192 -0.071648457 LTPEELER ddPTM_BT-474_Pertuzumab_2h_R1 4 LTPEELER 8 0 Q5H8X8;O95399;O95399-2 Q5H8X8 UTS2 Urotensin-2 0 ;;; 166.68 0.00073762 3515220000 1612110 1855190 1518060 2008630 1697770 1734850 1913860 1823680 1842380 1899450 FALSE TRUE 1549106.959 1802281.798 1792407.211 2112295.635 1752380.314 1769929.856 1937282.391 1786020.371 1633240.746 1770798.56 0.874806991 1.017779119 1.012202772 1.192849194 0.989598904 0.999509428 1.094016245 1.008596015 0.922318768 1 20.75596867 4.762054565 3.148372969 1.03286081 0.846335341 0.305230065 0.068297314 0.480305127 7.014703833 0.016541802 0.227344536 57816.86839 -4.762054565 -0.186525469 APS(ph)PAPSSVPLGSEKPSNVSQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 APSPAPSSVPLGSEKPSNVSQDR 23 1 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 APS(0.998)PAPS(0.002)SVPLGSEKPSNVSQDR;APS(0.991)PAPS(0.004)S(0.005)VPLGSEKPSNVSQDR;APS(1)PAPSSVPLGSEKPSNVSQDR;APS(0.975)PAPS(0.021)S(0.004)VPLGSEKPSNVSQDR 224.56 7.82E-33 8936700000 1880890 2046240 1848400 1833160 1608350 1937000 1800790 1919720 2171330 2230780 TRUE FALSE 1807382.739 1987883.239 2182446.997 1927769.607 1660084.038 1976167.467 1822828.607 1880077.111 1924849.721 2079687.284 0.869064668 0.955856803 1.049411137 0.926951673 0.798237337 0.950223374 0.876491683 0.904019141 0.925547671 1 20.98793518 4.762140342 22.44126152 0.925288977 0.869064412 0.070727595 0.064438108 5006.497363 4764465.107 0.015847 0.743372917 57828.28884 -4.762140342 -0.056224565 ILELEEENDRLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILELEEENDRLR 12 1 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 ; 216.06 3.64E-11 294410000 269540 336850 239010 288220 291930 345580 269280 306070 346110 294690 FALSE TRUE 259006.0788 327243.3678 282204.4237 303095.0687 301320.1936 352567.8644 272575.5292 299749.5475 306821.0438 274730.3838 0.942764594 1.191143707 1.027204999 1.103245533 1.096785108 1.28332316 0.992156475 1.091068062 1.11680783 1 18.06765695 4.762251865 23.75888395 1.100931416 0.942764235 0.243634532 0.083205545 4791.489225 4805017.396 0.018774696 1.030078774 57843.14065 -4.762251865 -0.158167181 TPDGTENGDFLALDLGGTNFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPDGTENGDFLALDLGGTNFR 21 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 257.35 4.13E-36 51630000 42227 47279 40194 49149 43802 50246 51221 51624 50067 49355 FALSE TRUE 40576.72216 45930.64921 47457.94991 51685.58578 45210.93111 51262.00855 51847.85792 50557.94636 44383.60406 46012.14189 0.881869882 0.998228888 1.031422315 1.12330319 0.982586971 1.11409742 1.126829915 1.098795759 0.964606346 1 15.489727 4.762312781 1.412191462 1.068284302 0.79772396 0.454061481 0.057336898 1.076180451 1.852959694 0.015361563 0.419710376 57851.25444 -4.762312781 -0.270560342 DWNEELQTTR ddPTM_BT-474_Pertuzumab_2h_R1 3 DWNEELQTTR 10 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;; 224.31 9.37E-09 799980000 482220 525420 464370 494200 559020 600190 529090 538760 613250 579220 FALSE TRUE 463374.3093 510435.536 548291.9889 519705.7212 577001.386 612326.253 535565.1617 527634.4177 543636.431 539988.9135 0.85811819 0.9452704 1.015376381 0.962437762 1.068543023 1.133960786 0.991807699 0.977120834 1.006754801 1 19.04257026 4.762379828 1.25120801 1.022113891 0.774848118 0.545608497 0.046647532 1.282660525 1.659252209 0.014523016 0.415335199 57860.18629 -4.762379828 -0.247265773 APGFGDNRK ddPTM_BT-474_Pertuzumab_2h_R1 5 APGFGDNRK 9 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;;; 114.97 0.0024887 2460020000 1395070 1957030 1169120 2140630 1204240 1361070 2246700 1884760 1621590 1289850 FALSE TRUE 1340549.122 1901217.421 1380405.991 2251108.171 1242975.473 1388591.768 2274195.787 1845839.047 1437513.901 1202487.311 1.114813529 1.581070672 1.147958884 1.872043182 1.033670345 1.154766255 1.891243065 1.535017485 1.195450371 1 20.19759024 4.762457522 22.59247825 1.41519139 1.114812225 0.049388362 0.313476602 4908.430079 4640221.071 0.072029916 3.61597001 57870.53824 -4.762457522 -0.300379164 STIGVMVTAS(ph)HNPEEDNGVK ddPTM_BT-474_Pertuzumab_2h_R1 18 STIGVMVTASHNPEEDNGVK 20 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77;D6RC77 O95394-4 PGM3 Phosphoacetylglucosamine mutase 1 STIGVMVT(0.028)AS(0.972)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.023)AS(0.977)HNPEEDNGVK;STIGVMVT(0.301)AS(0.699)HNPEEDNGVK;STIGVMVT(0.004)AS(0.996)HNPEEDNGVK;STIGVMVT(0.041)AS(0.959)HNPEEDNGVK;STIGVMVT(0.306)AS(0.694)HNPEEDNGVK;STIGVMVT(0.012)AS(0.988)HNPEEDNGVK;S(0.002)T(0.002)IGVMVT(0.187)AS(0.809)HNPEEDNGVK;STIGVMVT(0.017)AS(0.983)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.002)AS(0.998)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.012)AS(0.988)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK 290.59 1.21E-54 56047260000 34254278 27780168 21039718 20006332 22970667 19776187 19545791 24889322 25862138 21958935 TRUE FALSE 32915582.95 26987904.81 24842063.07 21038861.19 23709539.37 20176075.05 19784998.24 24375348.8 22926376.52 20471636.77 1.607862786 1.318307134 1.213486901 1.02770782 1.158165301 0.98556238 0.966459031 1.190688809 1.119909305 1 24.28712312 4.762591546 1.094683684 1.070619008 1.893934217 0.842229448 0.073458932 0.688615158 0.654741303 0.022642578 0.666005564 57888.40003 -4.762591546 0.823315209 NPGFEIIHGLLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 NPGFEIIHGLLDR 13 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 173.25 2.20E-05 542530000 610270 711450 599670 751290 664040 645810 720560 734680 842820 803530 FALSE TRUE 586419.9737 691160.1426 708043.7086 790064.1669 685399.4497 658868.7207 729378.4288 719508.6013 747146.607 749106.1974 0.782826221 0.922646408 0.94518469 1.054675785 0.91495632 0.879539808 0.973664924 0.960489452 0.997384095 1 19.51481073 4.76279982 2.181306242 0.962842145 0.72839347 0.594368982 0.045399463 0.506029148 2.599559244 0.011719633 0.235990608 57916.16811 -4.76279982 -0.234448675 DKKS(ph)PLIESTANMDNNQSQK ddPTM_BT-474_Pertuzumab_2h_R1 4 DKKSPLIESTANMDNNQSQK 20 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 DKKS(0.94)PLIES(0.03)T(0.03)ANMDNNQSQK;DKKS(1)PLIESTANMDNNQSQK;DKKS(1)PLIESTANMDNNQSQK;DKKS(1)PLIESTANMDNNQSQK 279.44 6.03E-45 2820370000 3887560 2902669 2293247 1811170 2508000 2268888 2494190 3090150 3433470 2735144 TRUE FALSE 3735629.857 2819887.722 2707687.746 1904644.701 2588672.098 2314766.47 2524714.643 3026337.323 3043716.88 2549890.261 1.465015932 1.105885914 1.06188403 0.746951636 1.015209218 0.907790624 0.990126784 1.186850026 1.193665832 1 21.28200373 4.7628207 2.307412253 1.014990209 1.592232558 0.554640706 0.121454745 0.535998023 3.201931766 0.033523661 0.639784614 57918.95265 -4.7628207 0.577242349 REEMEQLFHDDQGGVTR ddPTM_BT-474_Pertuzumab_2h_R1 4 REEMEQLFHDDQGGVTR 17 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;;; 274.43 7.06E-36 673540000 260407 288692 232154 295947 294558 304922 291923 275745 300729 330128 FALSE TRUE 250230.0065 280458.7868 274109.392 311220.8601 304032.7256 311087.7318 295495.641 270050.7694 266591.5047 307768.1365 0.813047151 0.911266481 0.890636033 1.011218587 0.987862906 1.010786026 0.960124217 0.877448759 0.866208919 1 18.23148435 4.762888397 1.399476625 0.950349589 0.755142247 0.407717479 0.051399764 1.544062162 2.599294214 0.015694662 0.431549161 57927.98171 -4.762888397 -0.195207343 KNS(ph)QQDLNTPDTRPAGLEEADQPPLPGEQGINLDNSGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNSQQDLNTPDTRPAGLEEADQPPLPGEQGINLDNSGPK 39 2 Q14686;A0A0D9SFT8;F6M2K2;F6M2K4 Q14686 NCOA6 Nuclear receptor coactivator 6 1 KNS(0.739)QQDLNT(0.216)PDT(0.045)RPAGLEEADQPPLPGEQGINLDNSGPK 82.384 0.00042501 177940000 73459 51569 57132 50056 56035 50023 63075 58368 66001 62689 TRUE FALSE 70588.14107 50098.30261 67457.02329 52639.39616 57837.41666 51034.49933 63846.93072 57162.6804 58508.84318 58443.01819 1.207811356 0.857216211 1.15423579 0.900696059 0.989637744 0.873235177 1.092464638 0.978092545 1.001126311 1 15.83474307 4.762980868 23.79642485 0.986524903 1.207811868 0.371606714 0.087605732 3840.820606 3742588.017 0.018967528 1.145014224 57940.31715 -4.762980868 0.221286965 EEVNDRPVRR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEVNDRPVRR 10 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ; 145.46 1.71E-05 163413000 167775 198065 135732 174685 176552 206726 173918 187003 177411 192880 FALSE TRUE 161218.1675 192416.3801 160261.7917 183700.5138 182230.9554 210906.1414 176046.4605 183141.3227 157272.047 179816.0658 0.896572655 1.070073351 0.891254021 1.021602341 1.013429777 1.17289932 0.979036327 1.018492546 0.874627338 1 17.4561624 4.763058779 23.01351031 1.00700636 0.896572264 0.141061609 0.079773667 4758.959317 4470341.716 0.018585856 1.050210307 57950.71233 -4.763058779 -0.110434096 FLGTEPEPDAVGLDSGHIR ddPTM_BT-474_Pertuzumab_2h_R1 4 FLGTEPEPDAVGLDSGHIR 19 0 Q16762 Q16762 TST Thiosulfate sulfurtransferase 0 ;;; 203.59 4.98E-16 661070000 387132 655720 450086 1124530 465545 584470 924890 765840 602150 482987 FALSE TRUE 372002.4534 637019.5076 531426.5523 1182567.128 480519.6777 596288.3839 936209.0805 750025.1364 533796.4564 450273.8603 0.82616933 1.414737927 1.180229632 2.626328624 1.067172048 1.32427937 2.079199267 1.665708811 1.185492882 1 18.7804432 4.763651801 1.633922662 1.591441201 0.53848282 0.145850124 0.482224133 1.833348233 4.487987681 0.122710563 3.115735114 58029.89715 -4.763651801 -1.052958381 TADGRVS(ph)PAGGTLDDKPK ddPTM_BT-474_Pertuzumab_2h_R1 5 TADGRVSPAGGTLDDKPK 18 2 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 TADGRVS(1)PAGGTLDDKPK;TADGRVS(1)PAGGTLDDKPK;T(0.003)ADGRVS(0.997)PAGGTLDDKPK;TADGRVS(1)PAGGTLDDKPK;T(0.003)ADGRVS(0.996)PAGGTLDDKPK 165.1 1.51E-11 6817920000 5835500 4289790 3720520 2855120 3966000 3797430 3796690 4865380 5453130 3903990 TRUE FALSE 5607442.209 4167449.389 4392900.727 3002473.085 4093569.992 3874216.636 3843155.028 4764908.203 4834113.544 3639569.28 1.54068841 1.145039171 1.206983681 0.82495286 1.124740231 1.064471188 1.05593677 1.309195632 1.328210338 1 21.7953363 4.763707766 3.502224837 1.122354704 1.603916263 0.451194294 0.139965619 0.343832667 6.975636579 0.035810815 0.45071413 58037.3756 -4.763707766 0.481561559 GFEGSFEELCR ddPTM_BT-474_Pertuzumab_2h_R1 6 GFEGSFEELCR 11 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ;;;;; 242.39 2.12E-15 1603796000 1093532 1259827 1016296 1401947 1245837 1244793 1299496 1245070 1325556 1424287 FALSE TRUE 1050795.56 1223897.967 1199963.295 1474301.653 1285910.479 1269963.567 1315399.621 1219358.869 1175084.44 1327818.773 0.791369712 0.921735701 0.903710144 1.110318428 0.968438242 0.956428387 0.990646952 0.918317239 0.88497351 1 20.34062682 4.763933787 1.678510129 0.967753817 0.724479488 0.451519709 0.058913648 0.99108869 2.592017849 0.015895688 0.397195399 58067.58798 -4.763933787 -0.24327433 TVIDSQTHYR ddPTM_BT-474_Pertuzumab_2h_R1 4 TVIDSQTHYR 10 0 Q9Y3Q3 Q9Y3Q3 TMED3 Transmembrane emp24 domain-containing protein 3 0 ;;; 168.22 5.00E-06 1074360000 1082100 1534660 1267610 1460540 1123670 845310 1415590 1344720 1392520 1563130 FALSE TRUE 1039810.336 1490892.999 1496695.325 1535918.644 1159813.866 862402.7474 1432914.414 1316951.062 1234446.968 1457257.813 0.713539036 1.02308115 1.027062824 1.053978665 0.795887904 0.591798335 0.983295064 0.903718649 0.847102659 1 20.47482471 4.763952542 23.16492888 0.908257131 0.713538367 0.166837822 0.133833871 5718.633192 5216850.274 0.033765992 2.08748464 58070.09575 -4.763952542 -0.194718764 KDHPYTWR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDHPYTWR 8 1 Q9Y570;Q9Y570-4;Q9Y570-2;Q9Y570-3 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 123.86 0.00086307 528890000 1686500 1745500 1550500 1679000 1606800 1228200 1965700 1498400 1922600 1883800 FALSE TRUE 1620589.715 1695720.049 1830709.841 1765653.391 1658484.181 1253035.046 1989756.825 1467457.516 1704354.508 1756208.548 0.92277749 0.965557337 1.042421666 1.005377974 0.944354919 0.713488752 1.132984364 0.835582721 0.970473871 1 20.74403274 4.764394998 19.86176556 0.950729447 0.922776904 0.00606325 0.108273093 4004.673986 3078001.339 0.024720296 1.087257778 58129.28727 -4.764394998 -0.027952543 LTEHQVAEPPEDWPALIWQQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTEHQVAEPPEDWPALIWQQQR 22 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ; 161.66 1.71E-11 219540000 123376 145185 123272 136337 147209 144309 148105 136038 160271 176091 FALSE TRUE 118554.3295 141044.466 145549.9926 143373.3689 151944.1112 147227.0269 149917.5533 133228.7678 142077.708 164164.1997 0.722169204 0.859167018 0.886612263 0.873353442 0.925561794 0.896827853 0.913217093 0.811557989 0.865460973 1 17.32478002 4.764458132 2.576402834 0.887082457 0.681018718 0.554296892 0.046242934 0.42609991 3.43801759 0.011350993 0.195896651 58137.73821 -4.764458132 -0.206063739 GIFEALRPLETLPVEGLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIFEALRPLETLPVEGLIR 19 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 188.09 1.55E-14 758540000 389240 438980 383030 419720 488640 471440 454680 453760 480020 483010 FALSE TRUE 374028.0705 426460.7202 452252.0415 441381.7995 504357.5494 480972.8398 460244.5099 444389.6974 425530.142 450295.3025 0.830628409 0.947068996 1.004345457 0.980205205 1.12005954 1.068127598 1.02209485 0.98688504 0.945002401 1 18.7805119 4.764660438 1.434068732 1.020720155 0.744149664 0.609649923 0.045795193 0.915358752 1.628827398 0.013502832 0.369849869 58164.8267 -4.764660438 -0.276570491 KLS(ph)DGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSDGHK 7 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 KLS(1)DGHK;KLS(1)DGHK 82.954 0.014144 327560000 1083050 854750 675180 654440 793750 738230 760310 838740 919610 864090 TRUE FALSE 1040723.209 830373.3669 797200.0453 688215.7268 819281.6896 753157.5164 769614.9012 821419.7259 815219.7281 805564.4146 1.291918051 1.030796981 0.989616759 0.854327369 1.017028154 0.934943876 0.955373509 1.019682239 1.011985775 1 19.61964043 4.76467584 2.437192506 0.971544121 1.377766281 0.801926968 0.047397952 0.250245543 1.728903047 0.011950759 0.218552841 58166.88941 -4.76467584 0.406222159 DAPAPRPLPASEGHLQPPAQTSGPTGS(ph)PPCIQTSPDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DAPAPRPLPASEGHLQPPAQTSGPTGSPPCIQTSPDPR 38 1 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 DAPAPRPLPASEGHLQPPAQT(0.135)S(0.135)GPT(0.164)GS(0.56)PPCIQT(0.004)S(0.001)PDPR 58.044 0.015716 166550000 42624 58525 40587 49611 44403 57098 43703 56077 50180 56486 TRUE FALSE 40958.20696 56855.9243 47921.97375 52171.42966 45831.26282 58252.56068 44237.85039 54918.99035 44483.77677 52660.15291 0.777783669 1.0796764 0.910023445 0.990719297 0.870321491 1.106198092 0.840063083 1.042894624 0.844733149 1 15.68442409 4.764770641 23.78292014 0.964661238 0.77778319 0.275055398 0.091160414 5352.744746 4856915.002 0.019120416 1.392186431 58179.58801 -4.764770641 -0.186878048 FDEDDDK ddPTM_BT-474_Pertuzumab_2h_R1 4 FDEDDDK 7 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 ;;; 144.9 0.005404 12389100000 12417400 9272400 11411200 7067900 8834100 8079300 9785700 12336600 11787000 10680800 FALSE TRUE 11932114.28 9007960.231 13473457.68 7432675.166 9118256.849 8242668.982 9905460.324 12081844.9 10448989.18 9957379.903 1.198318674 0.904651657 1.353112748 0.746448889 0.915728529 0.827794968 0.994785819 1.213355824 1.049371348 1 23.24733474 4.764850536 21.4064547 1.011305985 1.19832041 0.10740554 0.168475966 2677.686649 2180042.328 0.041122178 2.276971267 58190.29196 -4.764850536 0.187014426 S(ph)PGSGSQSSGWHEVEPGMPS(ph)PTTLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGSGSQSSGWHEVEPGMPSPTTLKK 26 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 2 S(0.998)PGS(0.001)GSQSSGWHEVEPGMPS(0.889)PT(0.096)T(0.015)LKK 127.49 9.70E-05 669300000 329760 369920 270960 342780 327590 341250 326380 347980 402360 370480 TRUE FALSE 316872.6146 359370.2438 319928.4995 360470.9169 338127.2299 348150.3088 330374.3361 340794.0914 356685.7796 345387.0596 0.917442058 1.040485547 0.926289768 1.043672329 0.978980597 1.008000442 0.956533625 0.986701968 1.032713212 1 18.39785451 4.764869146 23.82888045 0.993489144 0.917441866 0.306318561 0.035576034 5617.446945 5087830.16 0.007697888 0.581095183 58192.78555 -4.764869146 -0.076047278 ACDLPAWVHFPDTER ddPTM_BT-474_Pertuzumab_2h_R1 2 ACDLPAWVHFPDTER 15 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 0 ; 132.44 4.74E-05 231760000 85212 112043 92349 144410 96711 104644 118506 129297 107405 101340 FALSE TRUE 81881.82083 108847.6433 109038.5186 151863.0174 99821.79715 106759.9734 119956.3119 126626.9718 95212.83468 94476.15154 0.866693017 1.152117667 1.154138021 1.607421714 1.056581958 1.130020345 1.269699389 1.340306201 1.007797557 1 16.52766258 4.764994877 2.231390802 1.223890738 0.76113208 0.231243768 0.173416152 0.901981158 4.900033141 0.04232493 0.845112564 58209.63509 -4.764994877 -0.462758658 VSPAHS(ph)PPENGLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSPAHSPPENGLDK 14 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 VSPAHS(1)PPENGLDK;VS(0.005)PAHS(0.995)PPENGLDK 132.64 3.17E-05 835950000 561240 620940 528890 635420 607750 648510 672810 638070 682000 768710 TRUE FALSE 539306.1203 603231.3992 624472.1881 668214.1023 627298.8307 661623.3165 681044.05 624893.6315 604582.2192 716644.587 0.752543353 0.841744165 0.871383388 0.932420498 0.875327662 0.923223769 0.950323302 0.871971467 0.843629088 1 19.45089828 4.765057511 1.21635706 0.907917182 0.674205021 0.578267571 0.042466697 1.136664725 1.371500281 0.011700862 0.340519763 58218.03078 -4.765057511 -0.233712162 NKKS(ph)PEIHR ddPTM_BT-474_Pertuzumab_2h_R1 22 NKKSPEIHR 9 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR 135.79 0.00011006 37030618300 16370628.7 12257213.7 9713059.7 7979975.4 10632215.9 11340946.8 10878558.9 11566365.6 15109360.9 11172496.3 TRUE FALSE 15730846.43 11907649.97 11468425.65 8391822.887 10974210.78 11570268.51 11011693.96 11327516.11 13394209.59 10415773.17 1.510290803 1.143232458 1.101063307 0.805684105 1.053614609 1.11084106 1.057213303 1.08753483 1.285954424 1 23.3122666 4.765709121 2.407034387 1.060050687 1.633305494 0.590395658 0.111450488 0.43170943 2.875463078 0.028333622 0.528123918 58305.44587 -4.765709121 0.573254808 S(ph)FNDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFNDFR 6 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 S(1)FNDFR;S(1)FNDFR 129.42 0.016995 1376890000 1822350 2261500 1844600 2288000 1979630 2232610 2264900 2334000 2338100 2471600 TRUE FALSE 1751130.547 2197004.234 2177960.253 2406083.954 2043306.597 2277754.904 2292618.524 2285802.084 2072688.69 2304196.331 0.75997454 0.953479617 0.945214704 1.044218291 0.886776257 0.988524664 0.994975338 0.992017066 0.899527815 1 21.13583222 4.765796706 3.197633821 0.970982577 0.721810916 0.654944991 0.045201968 0.227013855 3.442162871 0.010407455 0.14553916 58317.20566 -4.765796706 -0.249171661 GGAEQFMEETER ddPTM_BT-474_Pertuzumab_2h_R1 4 GGAEQFMEETER 12 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 221.55 6.26E-11 2972100000 858080 992690 840921 1011670 1060230 1077110 1033630 963450 1035190 1137830 FALSE TRUE 824545.2849 964379.4531 992894.1309 1063882.41 1094333.261 1098889.902 1046279.873 943554.4208 917679.5711 1060763.761 0.777312834 0.909136878 0.936018148 1.002940004 1.031646538 1.035942161 0.986345793 0.889504766 0.865112106 1 20.01667196 4.766150048 1.644201024 0.968372388 0.700393526 0.545060922 0.05344746 0.951869572 2.355767472 0.016197988 0.414366502 58364.67178 -4.766150048 -0.267978862 ILEVHIDK ddPTM_BT-474_Pertuzumab_2h_R1 4 ILEVHIDK 8 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;;; 118.26 0.00192 1950270000 5865670 5797720 5212340 5749730 6063260 6672070 6586980 6549400 8307250 8505840 FALSE TRUE 5636433.132 5632374.702 6154325.786 6046474.254 6258290.264 6806983.827 6667593.432 6414152.601 7364245.807 7929731.881 0.710797441 0.710285642 0.776107677 0.762506771 0.789218395 0.858412861 0.840834663 0.808873831 0.92868787 1 22.91884066 4.766599985 0.053000785 1.435796392 2.34E-14 0.896941231 0.028054228 64.12554192 0.528090004 4.750098145 10.31391642 58425.16999 -4.766599985 -1.435796392 APGPRDT(ph)DDDEEEPDPYGFIVQTAEIAEIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 APGPRDTDDDEEEPDPYGFIVQTAEIAEIAR 31 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 APGPRDT(1)DDDEEEPDPYGFIVQTAEIAEIAR 80.923 0.0023723 10533000 2237.5 3188.7 1864 2655.5 3059.8 2259.6 3120.5 2730.6 3359.6 2032 TRUE FALSE 2150.056026 3097.761398 2200.866264 2792.550673 3158.221246 2305.29066 3158.689612 2674.212156 2978.232293 1894.37083 1.134971037 1.635245512 1.161792733 1.474130951 1.667161041 1.216916257 1.667408283 1.411662444 1.572148518 1 10.88750306 4.766728065 23.30424384 1.440284305 1.134969914 0.129913726 0.219481738 7109.289161 5881600.573 0.046957111 3.962456498 58442.40298 -4.766728065 -0.30531439 (ac)MDFEDDYTHSACR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDFEDDYTHSACR 13 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-2;E2QRN4 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 ; 116.13 3.10E-23 398090000 35336 39718 38457 36590 27924 36100 31499 36459 44200 43513 FALSE TRUE 33955.03005 38585.28153 45407.03537 38478.41428 28822.20082 36829.96673 31884.49418 35706.10891 39182.6013 40565.82575 0.837035347 0.951177027 1.11934207 0.948542611 0.710504477 0.90790625 0.785993964 0.880201703 0.965901731 1 15.30797724 4.767357173 21.22710376 0.908073523 0.837034527 0.041628308 0.107069349 5137.250911 3786386.193 0.026989881 1.869970066 58527.12256 -4.767357173 -0.071038997 SLFNYHDTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLFNYHDTR 9 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2 D6RGI3 11-Sep Septin-11 0 ;; 117.52 0.0011383 1724590000 1849730 2088210 1891690 1989600 1841870 1356690 2016680 1964620 2057810 2137380 FALSE TRUE 1777440.507 2028656.295 2233560.463 2092283.494 1901115.421 1384123.201 2041360.733 1924049.91 1824216.036 1992613.349 0.892014754 1.018088279 1.120920155 1.050019812 0.954081444 0.694627085 1.024464046 0.965591198 0.915489218 1 20.92623036 4.767361072 21.11186853 0.970593114 0.892013792 0.047258865 0.106967659 4288.667151 3143330.826 0.026902793 1.82588278 58527.64809 -4.767361072 -0.078579322 EDALDDSVSSSSVHASPLAS(ph)SPVRK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 1 EDALDDSVSSSSVHASPLAS(0.5)S(0.5)PVRK;EDALDDSVSSSSVHASPLAS(0.5)S(0.5)PVRK;EDALDDSVSSSSVHAS(0.003)PLAS(0.499)S(0.499)PVRK;EDALDDSVSSSSVHAS(0.001)PLAS(0.499)S(0.499)PVRK 304.86 6.28E-64 4037700000 613015 1186760 1017672 1642972 996397 1276175 1365652 1142078 1107149 1585475 TRUE FALSE 589057.6961 1152914.767 1201587.968 1727765.982 1028447.014 1301980.133 1382365.258 1118493.69 981470.0871 1478089.366 0.398526442 0.780003424 0.812933234 1.168918485 0.695794881 0.88085346 0.935237943 0.756715877 0.664012684 1 20.49530207 4.767504486 2.481531624 0.858573237 0.276319116 0.492856561 0.141182642 0.497017588 3.586015436 0.034512827 0.631515056 58546.97842 -4.767504486 -0.582254121 KVLSPT(ph)AAKPSPFEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVLSPTAAKPSPFEGK 16 2 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 KVLS(0.178)PT(0.822)AAKPSPFEGK 194.08 1.29E-08 1429600000 3065200 2323300 1771400 1577100 2041400 1861600 1677000 2599900 1950400 1457600 TRUE FALSE 2945408.595 2257041.759 2091531.385 1658494.32 2107063.485 1899242.827 1697523.628 2546211.156 1728998.769 1358875.454 2.167533888 1.660962933 1.539163416 1.220490307 1.550593529 1.397657763 1.249212077 1.873763449 1.272374715 1 20.3739818 4.767510589 1.669201893 1.430639948 2.464234658 0.526173899 0.224969975 0.875884444 2.244488961 0.058392015 1.488889868 58547.80109 -4.767510589 1.03359471 LRPSGDDVELIGEEEDVSVYDIADHPDFR ddPTM_BT-474_Pertuzumab_2h_R1 4 LRPSGDDVELIGEEEDVSVYDIADHPDFR 29 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 ;;; 245.8 6.55E-46 217017000 95361 109937 90162.6 114390 111007 118389 125017 112181 120779 129668 FALSE TRUE 91634.18669 106801.7044 106456.9875 120293.6816 114577.641 120782.9067 126546.9954 109864.4231 107068.6743 120885.4709 0.758024815 0.883494961 0.880643362 0.995104546 0.947819785 0.999151559 1.046833789 0.908830667 0.885703414 1 16.88328133 4.767540966 1.029726848 0.966691817 0.649026954 0.643599277 0.047934366 1.288509164 1.060470105 0.015263615 0.458043467 58551.8964 -4.767540966 -0.317664863 CLIDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 CLIDDR 6 0 O95373 O95373 IPO7 Importin-7 0 119.7 0.04836 402980000 766800 813260 759310 864110 836330 934350 955340 932320 944550 1112300 FALSE TRUE 736832.6083 790066.6211 896534.2078 908706.8207 863231.314 953243.1972 967031.7367 913067.2662 837328.6439 1036962.93 0.710567935 0.761904402 0.864576912 0.876315627 0.832461112 0.919264488 0.93256153 0.880520643 0.807481752 1 19.98393289 4.76763684 0.825526869 0.895794491 0.579921817 0.611587259 0.050065926 1.678096368 0.852992652 0.01689603 0.491797241 58564.82367 -4.76763684 -0.315872674 KQAGPASVPLRTEEEFKK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQAGPASVPLRTEEEFKK 18 3 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 45.347 0.08281 734260000 256650 241950 201630 211120 231930 216450 201230 259230 232630 271350 FALSE TRUE 246619.8343 235049.8229 238069.0262 222015.9285 239390.2391 220826.7673 203692.7129 253876.8099 206222.8177 252971.2228 0.974892842 0.929156369 0.941091337 0.87763314 0.946314116 0.872932363 0.805201124 1.003579803 0.815202676 1 17.94861375 4.767735277 1.001316267 0.903891575 1.010977989 0.101474213 0.064063246 4.842583411 3.743639412 0.018882245 0.566936386 58578.09945 -4.767735277 0.107086414 EDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_BT-474_Pertuzumab_2h_R1 7 EDDDVIVNKPHVSDEEEEEPPFYHHPFK 28 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;H7C1M2;H7C2G8;J3QSZ5 P18583-7 SON Protein SON 1 EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK 246.19 6.93E-46 21542660000 8026960 6182250 6074710 6212030 6564510 6276650 7775410 4153915 10087650 8587460 TRUE FALSE 7713257.529 6005938.283 7172545.228 6532633.613 6775663.426 6403568.163 7870567.793 4068135.204 8942542.263 8005823.685 0.963455833 0.750196172 0.895915962 0.815985196 0.846341825 0.799863751 0.983105312 0.508146989 1.117004647 1 22.93261841 4.767829171 21.01769298 0.830965072 0.963457576 0.015119849 0.158088582 3302.776543 2371373.662 0.035566851 2.49934617 58590.76537 -4.767829171 0.132492504 AIEPPPLDAVIEAEHTLR ddPTM_BT-474_Pertuzumab_2h_R1 8 AIEPPPLDAVIEAEHTLR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;; 361.29 4.36E-91 4896534000 1278945 1462678 1224809 1525722 1465912 1529541 1469638 1444918 1566797 1537005 FALSE TRUE 1228962.415 1420963.856 1446159.232 1604464.695 1513064.391 1560469.367 1487623.869 1415079.938 1388940.773 1432902.282 0.85767357 0.991668359 1.009251817 1.119730714 1.055943877 1.089027065 1.038189336 0.987562066 0.969319953 1 20.4505088 4.767853506 1.941855098 1.036755949 0.795130522 0.597962114 0.043448985 0.628553073 2.357327009 0.012198301 0.279383214 58594.04843 -4.767853506 -0.241625427 FKQESTVATER ddPTM_BT-474_Pertuzumab_2h_R1 2 FKQESTVATER 11 1 Q9H307 Q9H307 PNN Pinin 0 ; 170.18 1.46E-05 1515040000 980090 981940 815490 864870 940550 960070 937200 964460 1007350 1064570 FALSE TRUE 941786.9993 953936.0326 962867.1835 909506.0443 970803.6449 979483.2732 948669.7339 944543.564 892999.8512 992465.7257 0.948936548 0.96117781 0.970176761 0.916410533 0.978173472 0.986918992 0.955871532 0.951714039 0.899779033 1 19.92065775 4.768121523 19.93095138 0.956630546 0.948936385 0.006950858 0.028880905 5485.849495 3697778.429 0.006631528 0.409339864 58630.21987 -4.768121523 -0.007694161 KSPENTEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 KSPENTEGK 9 1 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 0 ;; 149.33 0.00014091 1360710000 1870940 1522240 1191340 1196600 1400990 1279620 1377860 1576550 1396180 1356650 FALSE TRUE 1797821.596 1478827.206 1406641.639 1258356.669 1446054.116 1305494.793 1394722.663 1543993.692 1237691.5 1264762.887 1.421469285 1.16925253 1.112178143 0.994934847 1.143340092 1.032205172 1.102754261 1.220777196 0.978595682 1 20.27043551 4.768955514 2.04117094 1.087351158 1.534026637 0.675180273 0.072552138 0.485335036 2.066248675 0.018707128 0.413715537 58742.91769 -4.768955514 0.446675479 SEDES(ph)ETEDEEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDESETEDEEEK 13 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 SEDES(0.915)ET(0.085)EDEEEK 117.48 0.00025165 0 46685 62542 54738 72652 58775 66470 63980 80365 66554 74289 TRUE FALSE 44860.49859 60758.3634 64630.37424 76401.57843 60665.55125 67814.06894 64763.00638 78705.43467 58999.06894 69257.33986 0.64773638 0.877284105 0.933191693 1.103154966 0.875943999 0.979160751 0.935106756 1.136420123 0.851881823 1 16.07967935 4.768976774 1.581778619 0.990595149 0.502538781 0.582766853 0.08453179 0.755379701 1.691325871 0.021970992 0.582615571 58745.79346 -4.768976774 -0.488056368 TSVSQNVIPSS(ph)AQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSVSQNVIPSSAQK 14 0 Q03188;H0Y8J2;Q03188-2 Q03188 CENPC Centromere protein C 1 TSVSQNVIPS(0.037)S(0.963)AQK 259.29 2.16E-24 407920000 1220000 760790 418400 384340 474470 260830 295170 642990 321490 314660 TRUE FALSE 1172321.051 739093.0141 494014.1873 404175.8335 489731.7585 266104.1613 298782.3788 629712.0318 284995.803 293347.7979 3.996351974 2.519511035 1.684056232 1.377804218 1.669457763 0.907128546 1.018526067 2.14663971 0.971528694 1 18.16225264 4.7689837 1.280476529 1.35997308 5.329871256 0.84248034 0.362768362 0.578149669 0.781535267 0.105565149 3.072753996 58746.73027 -4.7689837 3.969898176 up DVQGTDASLDEELDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVQGTDASLDEELDR 15 0 A0A087WYB4;Q9UJZ1;Q9UJZ1-2 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 ;;; 379.37 9.05E-98 1070650000 584730 926790 721010 1455510 700950 745430 1246990 1094690 863990 848590 FALSE TRUE 561878.1051 900358.8566 851312.5458 1530629.046 723496.6933 760503.1053 1262251.037 1072084.269 765913.4773 791114.2435 0.710236366 1.138089554 1.076093058 1.934776245 0.914528716 0.961306299 1.595535723 1.355157334 0.968145225 1 19.59352652 4.769195511 1.880411209 1.266283044 0.51318465 0.190147413 0.311704034 1.383354243 4.765468013 0.07924637 1.874184353 58775.38881 -4.769195511 -0.753098394 IQWIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IQWIDR 6 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 139.27 0.02779 350800000 278340 307930 267060 318850 314340 335760 313950 350370 369400 366580 FALSE TRUE 267462.1651 299148.1379 315323.6827 335305.8867 324451.0316 342549.2972 317792.214 343134.7371 327467.2607 341751.2101 0.782622438 0.875338928 0.922670274 0.981140306 0.949377857 1.002335287 0.929893457 1.004048346 0.958203661 1 18.38258692 4.769341948 0.968365672 0.976978141 0.667973001 0.872538623 0.023424191 0.6141145 0.43998737 0.006700102 0.20183819 58795.21026 -4.769341948 -0.309005141 ATQCQLEADVLWSDVVSHPPEGPWQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATQCQLEADVLWSDVVSHPPEGPWQR 26 0 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ; 153.84 7.54E-08 79815000 26448.4 32687 27090 28993 34410 33008.3 33617.2 30442 36336 34953 FALSE TRUE 25414.76729 31754.79876 31985.76561 30489.3322 35516.8289 33675.75044 34028.61735 29813.36206 32211.28961 32585.60218 0.779938549 0.974503972 0.981591975 0.935668828 1.089954659 1.033454906 1.044283827 0.914924386 0.988512946 1 14.99194704 4.769363746 3.023073362 0.995730536 0.735940347 0.647123545 0.048070149 0.297099291 3.763613008 0.012616531 0.192218112 58798.16138 -4.769363746 -0.259790189 HQNS(ph)LPELEAAEAGAPGSGPVDLFR ddPTM_BT-474_Pertuzumab_2h_R1 4 HQNSLPELEAAEAGAPGSGPVDLFR 25 0 Q96BZ8 Q96BZ8 LENG1 Leukocyte receptor cluster member 1 1 HQNS(1)LPELEAAEAGAPGSGPVDLFR;HQNS(1)LPELEAAEAGAPGSGPVDLFR;HQNS(1)LPELEAAEAGAPGSGPVDLFR;HQNS(1)LPELEAAEAGAPGSGPVDLFR 215.57 1.10E-33 417080000 296406 244194 153757 260307 356033 241773 268562 204998 304807 305258 TRUE FALSE 284822.1258 237229.8262 181544.3102 273741.4755 367485.1248 246661.8157 271848.7421 200764.7197 270206.5872 284582.6038 1.000841661 0.833606212 0.637931862 0.961905162 1.29131268 0.866749451 0.955254251 0.705470809 0.949483853 1 18.11848795 4.769415804 21.29740407 0.89881179 1.000842911 0.020001736 0.168745082 6926.795962 4780531.117 0.042452837 3.607158181 58805.20981 -4.769415804 0.102031121 LNTQEIFDDWAR ddPTM_BT-474_Pertuzumab_2h_R1 5 LNTQEIFDDWAR 12 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 259.35 6.64E-21 1349287000 947993 1106189 919703 1119898 1146358 1297363 1185601 1215418 1312713 1288498 FALSE TRUE 910944.3855 1074641.573 1085913.791 1177696.07 1183231.646 1323596.569 1200110.74 1190319.194 1163699.324 1201226.883 0.758344988 0.894619982 0.904003903 0.980411017 0.985019286 1.101870586 0.999070831 0.990919543 0.968758975 1 20.19607724 4.76942005 0.824496441 1.00993556 0.614356526 0.813669982 0.036975651 1.077115521 0.545020303 0.013516304 0.395130882 58805.7848 -4.76942005 -0.395579034 APS(ph)PPSRR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPPSRR 8 1 Q7Z2K8 Q7Z2K8 GPRIN1 G protein-regulated inducer of neurite outgrowth 1 1 APS(1)PPSRR 99.973 0.0039406 62706000 42813 64063 32085 70287 37861 51304 59369 62684 55327 38974 TRUE FALSE 41139.82063 62235.98596 37883.47323 73914.52049 39078.83345 52341.40203 60095.57558 61389.55349 49046.51091 36334.25627 1.13225988 1.712873535 1.042637916 2.034292926 1.075536903 1.440552454 1.653964654 1.68957782 1.349869681 1 15.14904276 4.769901944 22.62487001 1.47928908 1.132257715 0.068742925 0.322330871 8044.112198 5806571.798 0.070454223 7.553268712 58871.07195 -4.769901944 -0.347031365 LYSNWR ddPTM_BT-474_Pertuzumab_2h_R1 1 LYSNWR 6 0 Q9Y5B9;G3V5A4;G3V401;G3V2X0 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 101.21 0.08557 511400000 379190 511840 411810 492460 355060 327270 444150 472540 465690 518710 FALSE TRUE 364370.8356 497242.8243 486233.2277 517875.9196 366480.8274 333887.6236 449585.6406 462781.8839 412826.8235 483577.3097 0.753490348 1.028259214 1.00549223 1.070926839 0.757853646 0.690453454 0.929707891 0.956996688 0.853693536 1 18.88338703 4.770061436 22.66901365 0.917409703 0.753489342 0.159381319 0.115403735 7475.595658 5379353.866 0.02946997 3.256724281 58892.69597 -4.770061436 -0.163920361 GYEVHGIVR ddPTM_BT-474_Pertuzumab_2h_R1 3 GYEVHGIVR 9 0 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 ;; 124.98 0.00051434 917840000 866190 977050 876030 947100 874200 523320 1059850 877350 933960 1050320 FALSE TRUE 832338.3372 949185.4906 1034348.108 995979.9445 902319.4369 533901.889 1072820.761 859232.4159 827940.7763 979180.8909 0.850035315 0.969366845 1.056340169 1.017156231 0.921504336 0.545253583 1.095630819 0.877501209 0.845544254 1 19.90121588 4.770168682 21.23427396 0.922421928 0.850034362 0.022824347 0.146736853 8256.651295 5546083.526 0.0349296 3.186394105 58907.24099 -4.770168682 -0.072387567 KGGSYVFQSDEGPEPEAEES(ph)DLDSGSVHSASGRPDGPVR ddPTM_BT-474_Pertuzumab_2h_R1 3 KGGSYVFQSDEGPEPEAEESDLDSGSVHSASGRPDGPVR 39 2 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5;I3L1I4;A0A5F9ZHM2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 KGGSYVFQSDEGPEPEAEES(1)DLDSGSVHSASGRPDGPVR;KGGSYVFQSDEGPEPEAEES(1)DLDSGSVHSASGRPDGPVR;KGGSYVFQSDEGPEPEAEES(1)DLDSGSVHSASGRPDGPVR 220.44 7.83E-40 740760000 166382 200947 166966 226668 193995 211135 207428 195560 206876 231228 TRUE FALSE 159879.6075 195216.1883 197140.4703 238366.3626 200235.0254 215404.2944 209966.5659 191521.6177 183392.3038 215566.7216 0.7416711 0.9055952 0.914521819 1.105766052 0.928877258 0.999246511 0.974021242 0.888456327 0.850744968 1 17.71777495 4.770183871 1.972673523 0.956651997 0.667253717 0.489490733 0.066578981 0.749158047 2.911980136 0.01764965 0.404151885 58909.30117 -4.770183871 -0.28939828 DIGISDPQHR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIGISDPQHR 10 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 0 116.23 0.0011174 223190000 169680 236480 208640 239770 236120 255040 241960 237760 283260 286700 FALSE TRUE 163048.718 229735.8219 246345.8892 252144.5584 243715.0142 260197.0835 244921.1789 232850.1729 251105.5123 267281.5536 0.610026078 0.859527412 0.921671869 0.943366854 0.911828785 0.973494355 0.916341497 0.87117936 0.939479395 1 18.02800075 4.770433062 2.242393799 0.927367027 0.512431798 0.892495245 0.033755492 0.209858886 1.141480323 0.008657442 0.177782885 58943.11208 -4.770433062 -0.414935229 FTEQVEAAVEALSSDPAQPMDENEFIDASR ddPTM_BT-474_Pertuzumab_2h_R1 5 FTEQVEAAVEALSSDPAQPMDENEFIDASR 30 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 ;;;; 189.24 2.96E-18 375493000 220258 292738 247704 347980 226867 319587 311478 320983 301607 317496 FALSE TRUE 211650.0739 284389.3989 292469.6229 365939.2895 234164.3831 326049.2681 315289.9609 314354.5889 267369.8378 295991.7131 0.715054052 0.960801895 0.988100714 1.236315996 0.791118037 1.101548637 1.065198608 1.062038479 0.903301768 1 18.17519726 4.770471201 2.176600058 1.027181039 0.616636377 0.396023994 0.111812487 0.684041242 3.436630823 0.026616463 0.561579428 58948.28859 -4.770471201 -0.410544662 MWVFEETVNGR ddPTM_BT-474_Pertuzumab_2h_R1 1 MWVFEETVNGR 11 0 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 74.533 0.053461 0 352160 396760 333130 390330 396620 408500 405740 350640 464090 427580 FALSE TRUE 338397.1979 385444.7933 393334.0014 410474.9781 409377.6425 416760.1499 410705.5675 343399.1615 411408.4488 398619.6258 0.848922572 0.966948861 0.98674018 1.029741015 1.026988176 1.045508357 1.030319485 0.861470784 1.032082773 1 18.60465322 4.770509538 2.358585252 0.994610065 0.806823673 0.448426855 0.050361023 0.703988534 4.387536513 0.014258666 0.279500949 58953.49244 -4.770509538 -0.187786392 AEQEEEFISNTLFK ddPTM_BT-474_Pertuzumab_2h_R1 3 AEQEEEFISNTLFK 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;; 188.4 1.95E-06 98746000 195941 174044 147247 167777 176304 174464 182106 174264 204431 191600 FALSE TRUE 188283.4091 169080.4355 173857.8084 176435.9911 181974.9783 177991.7816 184334.6677 170665.3875 181224.8499 178622.7613 1.05408408 0.946578332 0.973323932 0.987757606 1.01876702 0.996467529 1.031977483 0.955451513 1.014567508 1 17.4465564 4.770796101 23.32043065 0.990811293 1.054084366 0.343930285 0.025843691 6466.974522 4678262.346 0.006133174 0.805108072 58992.40494 -4.770796101 0.063273073 TPEELDDS(ph)DFETEDFDVR ddPTM_BT-474_Pertuzumab_2h_R1 9 TPEELDDSDFETEDFDVR 18 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 1 TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR 360.88 5.28E-91 31488670000 3858991 4489321 3636868 5365795 3653333 4484771 4583088 4675644 4697517 4587672 TRUE FALSE 3708177.365 4361289.961 4294130.949 5642724.323 3770845.774 4575456.142 4639177.202 4579090.317 4164274.564 4276944.889 0.867015466 1.019720869 1.004018303 1.319335289 0.881668077 1.069795441 1.084694174 1.070645154 0.973656353 1 22.02814919 4.770806137 2.09588234 1.058896587 0.80487717 0.207340129 0.106598111 1.135092038 5.15812857 0.025702829 0.561591874 58993.7681 -4.770806137 -0.254019417 VTGVYELSLCHVADAGS(ph)PGMQR ddPTM_BT-474_Pertuzumab_2h_R1 11 VTGVYELSLCHVADAGSPGMQR 22 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR;VTGVYELSLCHVADAGS(1)PGMQR 229.06 1.05E-25 8594417000 2767906 3307872 2647586 3570829 3347961 3726958 3438445 3323596 3561011 4001356 TRUE FALSE 2659733.173 3213534.729 3126063.685 3755119.913 3455651.206 3802319.644 3480525.718 3254962.581 3156779.96 3730340.594 0.713000088 0.861458799 0.838010258 1.006642642 0.926363456 1.019295571 0.933031618 0.872564448 0.846244433 1 21.83087593 4.770976707 1.221425902 0.933427436 0.608390746 0.575684848 0.058734754 1.233922014 1.490231681 0.017418998 0.5173965 59016.9426 -4.770976707 -0.32503669 CPKPVIAAVHGGCIGGGVDLVTACDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 CPKPVIAAVHGGCIGGGVDLVTACDIR 27 1 Q13011;M0R248 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 144.26 1.05E-07 179450000 329200 246910 203070 138540 194560 269030 196390 213870 283130 204070 FALSE TRUE 316334.5001 239868.3686 239769.2663 145690.066 200818.1991 274469.9709 198793.4796 209453.5098 250990.2694 190248.1571 1.662746724 1.260818355 1.260297445 0.765789631 1.055559234 1.442694505 1.044916716 1.100948955 1.319278321 1 17.53752295 4.771027606 1.761817152 1.117174706 1.871322166 0.46357236 0.175947427 0.892726836 2.599499349 0.046200542 1.155905551 59023.85979 -4.771027606 0.75414746 VSTEVDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSTEVDAR 8 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 136.8 0.0018044 1057010000 1885620 2119000 1745590 2093350 2000070 2050360 2063820 2133590 2200720 2313400 FALSE TRUE 1811927.886 2058568.195 2061056.943 2201388.044 2064404.068 2091819.684 2089077.647 2089530.621 1950903.492 2156711.357 0.840134624 0.954494067 0.955648022 1.020715191 0.95719998 0.969911749 0.968640351 0.968850381 0.904573292 1 21.04040168 4.771078374 2.902856685 0.968406414 0.812008425 0.642405761 0.028476277 0.284156168 3.177553756 0.006717749 0.107988508 59030.75995 -4.771078374 -0.156397989 TLTDEVNSPDS(ph)DRR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(0.294)PDS(0.706)DRR;TLTDEVNS(0.079)PDS(0.921)DRR 280.9 2.88E-33 1983690000 703170 835810 780960 918850 897160 1019120 918410 1049280 1056480 1057090 TRUE FALSE 675689.339 811973.5171 922096.8444 966271.9586 926017.9662 1039727.305 929649.7763 1027612.001 936552.8195 985492.3527 0.685636309 0.823926756 0.935671233 0.980496658 0.939650078 1.055033356 0.943335353 1.042739701 0.950340017 1 19.91048515 4.771126572 0.992236652 0.995830585 0.498933088 0.87565817 0.036501424 0.583715973 0.44035487 0.010389084 0.315119118 59037.31154 -4.771126572 -0.496897497 LGGS(ph)AVISLEGKPL ddPTM_BT-474_Pertuzumab_2h_R1 6 LGGSAVISLEGKPL 14 1 G3V1A4;P23528;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 1 LGGS(0.997)AVIS(0.003)LEGKPL;LGGS(1)AVISLEGKPL;LGGS(1)AVISLEGKPL;LGGS(1)AVISLEGKPL;LGGS(1)AVISLEGKPL;LGGS(0.999)AVIS(0.001)LEGKPL 164.93 1.06E-05 733078000 3122270 2365930 1859267 1819585 2484620 1889241 1900438 2650310 2237320 1868440 TRUE FALSE 3000248.237 2298455.993 2195277.906 1913494 2564540.059 1927442.747 1923696.129 2595580.172 1983348.813 1741888.895 1.722410795 1.319519287 1.260285839 1.098516677 1.472275337 1.106524505 1.104373611 1.490095138 1.138619587 1 20.73222117 4.771303024 2.471249514 1.235989343 1.855808707 0.491509832 0.154640327 0.519725295 3.674270613 0.037335356 0.703597951 59061.30295 -4.771303024 0.619819364 DHSSSRPS(ph)SPRPQK ddPTM_BT-474_Pertuzumab_2h_R1 3 DHSSSRPSSPRPQK 14 2 E9PKU9;B7Z503;Q9BSF8;Q9BSF8-2 E9PKU9 BTBD10 BTB/POZ domain-containing protein 10 1 DHS(0.086)S(0.086)S(0.086)RPS(0.427)S(0.314)PRPQK;DHS(0.081)S(0.081)S(0.081)RPS(0.378)S(0.378)PRPQK;DHS(0.185)S(0.185)S(0.185)RPS(0.223)S(0.223)PRPQK 65.943 0.029614 221156000 197038 358946 301149 478262 346927 460949 427332 186263 381701 492213 TRUE FALSE 189337.5371 348709.2115 355573.3233 502945.1591 358086.222 470269.7046 432561.8168 182416.604 338371.9027 458874.9751 0.41261247 0.759922049 0.774880616 1.096039633 0.780356832 1.024831883 0.942657239 0.397530077 0.737394543 1 18.80774161 4.771322326 2.631148029 0.818132449 0.310417472 0.312393245 0.188470237 0.79334298 6.681709325 0.051747945 0.917615687 59063.92794 -4.771322326 -0.507714976 EYWMDPEGEMKPGR ddPTM_BT-474_Pertuzumab_2h_R1 7 EYWMDPEGEMKPGR 14 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;;;;;; 127.02 8.61E-05 11990060000 11694550 12027900 11405120 15176700 14791290 13771140 16667780 19226690 17562080 18696400 FALSE TRUE 11237514.06 11684876.07 13466278.89 15959971.31 15267065.28 14049601.89 16871765.28 18829652.13 15568506.3 17430076.17 0.644719733 0.670385829 0.772588642 0.915657003 0.875903531 0.806055105 0.967968534 1.080296606 0.893197835 1 24.05507554 4.771338168 0.370333257 1.01553352 0.305854716 0.758327154 0.065406902 3.05091252 0.328287814 0.063120642 0.982262372 59066.08254 -4.771338168 -0.709678804 TLVLDFETEGERNS(ph)PNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLVLDFETEGERNSPNPR 18 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 TLVLDFETEGERNS(1)PNPR;TLVLDFETEGERNS(1)PNPR 188.95 2.13E-14 332740000 195636 223520 195718 215230 222130 243680 236830 231060 229980 259500 TRUE FALSE 187990.3288 217145.4284 231088.5963 226338.0461 229275.0132 248607.3766 239728.3964 226288.5303 203873.6346 241923.8339 0.777064111 0.897577659 0.955212195 0.935575642 0.94771569 1.02762664 0.990925088 0.935370966 0.842718269 1 17.88419338 4.771385285 1.730472671 0.955732387 0.704707604 0.56871257 0.046992033 0.752292921 2.093092667 0.012614038 0.319990737 59072.491 -4.771385285 -0.251024783 EEASNFR ddPTM_BT-474_Pertuzumab_2h_R1 6 EEASNFR 7 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;; 181.49 0.0015614 3413440000 1543600 1708390 1421850 1706480 1626660 1641170 1703770 1729400 1842290 1760750 FALSE TRUE 1483274.405 1659668.39 1678809.924 1794551.637 1678982.996 1674355.582 1724621.247 1693687.286 1633160.963 1641492.834 0.903613086 1.011072577 1.022733629 1.093243662 1.022839065 1.020020037 1.050641959 1.031796941 0.994924211 1 20.64657702 4.771511917 2.457832023 1.033178331 0.867867 0.671351255 0.026190408 0.337260938 2.347607154 0.006396678 0.121350095 59089.71792 -4.771511917 -0.165311331 FLSDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLSDFR 6 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 98.03 0.093984 132160000 392110 440760 383700 413020 388270 303340 426320 417550 402840 492090 FALSE TRUE 376785.9077 428189.9563 453043.1254 434336.0117 400759.0572 309473.7426 431537.4317 408927.4466 357111.292 458760.306 0.821313228 0.933363133 0.987537761 0.946760228 0.8735696 0.674587009 0.940659918 0.891374954 0.778426746 1 18.80738104 4.771530911 21.53719165 0.888256459 0.821312436 0.046948387 0.094068833 7775.968454 5078922.271 0.022711932 2.458701125 59092.30237 -4.771530911 -0.066944023 DKGVLQEEEDVLVNVNLVDKER ddPTM_BT-474_Pertuzumab_2h_R1 1 DKGVLQEEEDVLVNVNLVDKER 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 116.24 9.55E-05 35886000 36355 31397 26030 22905 28095 31855 25473 33371 33998 28327 FALSE TRUE 34934.20641 30501.5883 30734.20003 24087.12979 28998.70119 32499.12993 25784.74619 32681.87719 30138.68957 26408.38706 1.322845137 1.154996261 1.163804513 0.912101513 1.098086798 1.230636686 0.976384742 1.237556732 1.141254462 1 14.68870857 4.771738911 1.884111868 1.10266445 1.402254521 0.316775877 0.101027116 1.144075093 3.940836456 0.025858685 0.618727872 59120.6106 -4.771738911 0.299590071 TVEAEAAHGTVTR ddPTM_BT-474_Pertuzumab_2h_R1 7 TVEAEAAHGTVTR 13 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;;;; 295.78 1.11E-40 14299506000 5404170 6523569 5408214 7252902 6401402 6876255 6849790 6811206 7036755 7567494 FALSE TRUE 5192969.062 6337523.199 6385598.575 7627225.141 6607308.909 7015297.587 6933619.779 6670552.216 6237972.073 7054940.891 0.736075488 0.898309893 0.90512432 1.08111822 0.936550569 0.994380775 0.982803384 0.945514969 0.884199056 1 22.75020256 4.771747944 1.546997089 0.969677254 0.636655141 0.656905444 0.051020292 0.701325312 1.480241188 0.0133755 0.363504503 59121.84037 -4.771747944 -0.333022113 SPAPPPPAVFPAARPEPGDGLS(ph)SPAGGSYETGDRDDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 38 2 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SPAPPPPAVFPAARPEPGDGLS(0.497)S(0.497)PAGGS(0.003)YET(0.004)GDRDDGR;SPAPPPPAVFPAARPEPGDGLS(0.5)S(0.5)PAGGSYETGDRDDGR 164.28 3.97E-18 1186390000 190682 235917 201303 250231 261450 261890 241750 274070 228564 233151 TRUE FALSE 183229.9366 229188.8781 237682.9301 263145.4519 269859.7767 267185.5952 244708.6088 268410.3587 202618.3729 217359.4751 0.842981133 1.054423222 1.093501583 1.210646335 1.241536752 1.229233716 1.125824438 1.234868453 0.932181 1 17.72972346 4.7717548 1.51007053 1.158283167 0.704868743 0.425056179 0.100035422 1.022375093 2.03524761 0.025729781 0.708116394 59122.77366 -4.7717548 -0.453414424 DTYYDTPELSLMQADHWLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTYYDTPELSLMQADHWLR 19 0 G3V5B9;G3V5Q5;Q9BU02-2;Q9BU02 G3V5B9 THTPA Thiamine-triphosphatase 0 ;;; 221.24 2.71E-19 423310000 319747 338431 282937 322899 340083 318928 320653 350366 374370 359883 FALSE TRUE 307250.9337 328779.2792 334070.0098 339563.8561 351022.0786 325376.9427 324577.2473 343130.8197 331873.0871 335507.8039 0.915778799 0.979945252 0.995714573 1.012089293 1.046241174 0.969804395 0.967420858 1.02272083 0.989166521 1 18.3559868 4.771789603 1.985690791 1.00167024 0.88559202 0.568873397 0.022152374 0.617450088 2.433015297 0.005850302 0.134418812 59127.51167 -4.771789603 -0.11607822 ELLLPDTER ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLLPDTER 9 0 Q8TEX9;Q8TEX9-2;H0YN14;H0YK93;H0YLV0;H0YL92;H0YKG5 Q8TEX9 IPO4 Importin-4 0 136.39 0.00045139 68587000 90906 111260 97591 117750 109090 122900 119190 118500 124330 136880 FALSE TRUE 87353.29302 108086.9737 115227.8646 123827.0916 112598.9789 125385.1222 120648.6829 116052.9336 110216.5796 127608.9957 0.684538677 0.847016883 0.902976032 0.970363343 0.882374932 0.982572753 0.945455939 0.909441634 0.863705408 1 16.96137051 4.771796101 1.570681276 0.931827894 0.577180555 0.775328988 0.040988593 0.506544864 1.109272995 0.010493493 0.282896695 59128.39639 -4.771796101 -0.354647339 QQPGPSEHIER ddPTM_BT-474_Pertuzumab_2h_R1 3 QQPGPSEHIER 11 0 P50552;K7EQD0 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ;; 200.93 4.52E-08 1365910000 324831 369167 298561 395757 335249 386681 322668 363918 387350 390487 FALSE TRUE 312136.2454 358638.7186 352517.6142 416182.0662 346032.5886 394499.9548 326616.9075 356402.9661 343379.6519 364038.9677 0.857425367 0.985165739 0.968351318 1.143234937 0.950537221 1.083675073 0.897203147 0.979024219 0.943249713 1 18.47373336 4.771884006 3.162482433 0.995010574 0.830907716 0.273601421 0.067136346 0.567269739 8.170622597 0.016022071 0.239254334 59140.36578 -4.771884006 -0.164102858 LVEVDSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVEVDSGR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;;; 201.49 0.00025906 1292350000 1559210 1884650 1471230 2327140 1766130 1746240 1977820 1934150 1979900 2022090 FALSE TRUE 1498274.349 1830901.627 1737113.988 2447243.974 1822939.175 1781550.169 2002025.153 1894209.127 1755150.052 1885132.043 0.794784829 0.971232564 0.921481333 1.298181728 0.967008747 0.945053253 1.062007916 1.004815092 0.931048867 1 20.84623415 4.772167943 1.737593621 1.023599976 0.708282517 0.298712125 0.102446982 1.252579827 3.515646119 0.026450254 0.671693257 59179.04375 -4.772167943 -0.315317459 VLEQLIVAHFPMQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLEQLIVAHFPMQSR 15 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 137.44 1.67E-05 533780000 361500 417780 343700 444600 473010 363870 464860 392750 437870 449190 FALSE TRUE 347372.1803 405865.3234 405814.2356 467545.8593 488224.7962 371227.7007 470549.0957 384639.5753 388164.8333 418765.9612 0.829513887 0.969193681 0.969071685 1.116484869 1.165865523 0.886480123 1.123656503 0.918507259 0.926925465 1 18.67578465 4.772349851 1.819109926 1.01600777 0.759809099 0.277832734 0.08966163 1.282711064 4.037416772 0.023485078 0.578370279 59203.83653 -4.772349851 -0.256198671 VSAGEPGSHPS(ph)PAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 VSAGEPGSHPSPAPR 15 0 A0A1B0GV68;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 VSAGEPGS(0.001)HPS(0.999)PAPR;VSAGEPGSHPS(1)PAPR;VSAGEPGS(0.002)HPS(0.998)PAPR;VSAGEPGSHPS(1)PAPR 216.53 1.41E-12 4003720000 2510660 4733210 2236530 5657970 2020420 2792910 4171110 4590750 3390660 2674840 TRUE FALSE 2412540.632 4598223.485 2640720.722 5949978.51 2085408.644 2849384.554 4222157.292 4495949.408 3005766.492 2493670.704 0.967465603 1.843957776 1.058969301 2.386032165 0.836280685 1.142646681 1.693149494 1.80294431 1.205358224 1 21.24983954 4.772514172 22.40562779 1.481736133 0.967461482 0.081186766 0.459957266 8766.601602 5784577.285 0.103990513 14.33129554 59226.24133 -4.772514172 -0.514274651 NQLKEDQDKVHMWEQTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NQLKEDQDKVHMWEQTVK 18 2 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 101.13 0.00043382 192130000 199060 168100 136830 124740 147570 159180 153700 160190 203520 162950 FALSE TRUE 191280.5151 163305.9526 161558.2248 131177.8463 152316.7231 162398.7287 155581.0266 156882.0205 180417.2628 151913.2514 1.259143053 1.074994782 1.063490007 0.863504962 1.002655935 1.069022796 1.024143879 1.032707938 1.187633476 1 17.2128882 4.772597982 2.155491431 1.026406238 1.333883683 0.452170801 0.075388436 0.68105894 3.319080025 0.019337125 0.416685863 59237.67188 -4.772597982 0.307477445 SILYDER ddPTM_BT-474_Pertuzumab_2h_R1 4 SILYDER 7 0 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ;;; 124.08 0.0097275 6013500000 6837200 7244500 6175190 6915300 6916100 4985950 7400800 6966500 7061300 7823000 FALSE TRUE 6569994.665 7037893.953 7291184.199 7272199.462 7138562.638 5086769.325 7491373.204 6822639.341 6259730.827 7293141.242 0.900845664 0.965001735 0.99973166 0.997128565 0.978804935 0.697473031 1.027180601 0.935487071 0.858303798 1 22.7981089 4.772858862 20.80081017 0.939116488 0.900845028 0.015706699 0.092564753 9163.399902 5556367.32 0.021745465 2.415886589 59273.26654 -4.772858862 -0.03827146 AYHEQLSVAEITNACFEPANQMVK ddPTM_BT-474_Pertuzumab_2h_R1 6 AYHEQLSVAEITNACFEPANQMVK 24 0 P68363;P68363-2;C9JDS9;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ;;;;; 298.66 4.49E-62 2721690000 1520471 1651715 1434288 1668363 1612811 1867060 1799483 1655051 1978910 1984830 FALSE TRUE 1461049.312 1604609.705 1693495.747 1754467.414 1664688.531 1904813.232 1821505.611 1620873.618 1754272.433 1850395.696 0.7895875 0.867171118 0.915207353 0.948157963 0.899639214 1.029408594 0.984387077 0.875960543 0.94805259 1 20.81940238 4.773243876 1.014063718 0.950458908 0.695498013 0.610797772 0.042284514 1.491504943 1.177702772 0.013783992 0.421137742 59325.83721 -4.773243876 -0.254960895 WIDFDNDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 WIDFDNDYK 9 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 203.35 4.27E-05 508690000 1480910 1390690 1384660 1421230 1663010 1671320 1726960 1826050 2105830 2107680 FALSE TRUE 1423034.4 1351028.883 1634898.864 1494579.851 1716502.227 1705115.236 1748095.053 1788341.429 1866785.007 1964924.956 0.724218192 0.687572764 0.832041376 0.760629481 0.873571391 0.867776263 0.889649779 0.910132178 0.950054098 1 20.90604278 4.773252177 0.208837498 1.022426341 0.411316576 0.882879567 0.032300615 3.807296725 0.150521911 0.059539139 0.61594429 59326.97122 -4.773252177 -0.611109766 DYAAYNVLDDPELR ddPTM_BT-474_Pertuzumab_2h_R1 4 DYAAYNVLDDPELR 14 0 Q86SX6 Q86SX6 GLRX5 "Glutaredoxin-related protein 5, mitochondrial" 0 ;;; 207.47 2.19E-08 256128000 299805 428964 308577 653300 293914 398702 546100 490954 431535 361429 FALSE TRUE 288088.2891 416730.3667 364343.7282 687016.8913 303368.0107 406764.0276 552783.3352 480815.6283 382548.9559 336949.0919 0.854990549 1.236775456 1.081302004 2.038933797 0.90033782 1.207197281 1.640554459 1.426968168 1.135331613 1 18.36217111 4.773329713 1.611844283 1.350229774 0.658541046 0.142938878 0.319443396 1.960253555 4.56004432 0.081494577 2.180208635 59337.56394 -4.773329713 -0.691688729 AGMTHIVR ddPTM_BT-474_Pertuzumab_2h_R1 6 AGMTHIVR 8 0 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;; 148.38 0.00052214 3454050000 3709700 4280260 3970740 3789840 3635240 2716270 4340660 3712790 4245860 4711130 FALSE TRUE 3564720.823 4158191.176 4688341.047 3985434.097 3752170.796 2771194.84 4393782.296 3636119.589 3763887.773 4392040.969 0.811631961 0.946756008 1.067462959 0.907421885 0.854311429 0.630958331 1.000396473 0.827888359 0.856979204 1 22.06646008 4.7735352 21.26392223 0.891382169 0.811630747 0.045759664 0.115073793 7831.666968 4760874.564 0.027863991 3.49715489 59365.64628 -4.7735352 -0.079751422 DNWTDAEGYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNWTDAEGYYR 11 0 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 235.32 1.95E-05 0 551300 589430 483030 546750 621050 577290 606200 602080 609940 706500 FALSE TRUE 529754.5865 572620.0335 570324.2659 574967.833 641026.6373 588963.1993 613618.8569 589646.8376 540702.1683 658648.1257 0.80430592 0.869386872 0.865901296 0.872951445 0.973245975 0.894200069 0.931633801 0.89523801 0.82092721 1 19.3291484 4.773717046 0.864803626 0.910771484 0.747123565 0.334523701 0.047666184 2.938905904 1.638436766 0.015530017 0.465371558 59390.50877 -4.773717046 -0.163647918 EQVIAALR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQVIAALR 8 0 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 90.657 0.030103 0 136150 170400 134660 145030 148360 125290 140350 166400 162800 155980 FALSE TRUE 130829.1075 165540.3588 158996.0575 152515.0157 153132.1341 127823.4496 142067.6453 162963.7819 144319.6265 145415.3357 0.899692642 1.138396842 1.093392638 1.048823461 1.053067295 0.879023172 0.976978423 1.120678098 0.992464968 1 17.1498199 4.773882662 23.45302641 1.036763058 0.899691959 0.233387862 0.072635578 12682.92722 8420809.452 0.018265752 3.458708826 59413.16146 -4.773882662 -0.137071099 S(ph)LQTLPTDSSTFDTGETSYLLPEPGSHPCWR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLQTLPTDSSTFDTGETSYLLPEPGSHPCWR 31 0 Q9NQG6-2 Q9NQG6-2 MIEF1 Mitochondrial dynamics protein MID51 1 S(0.84)LQT(0.158)LPTDS(0.001)S(0.001)T(0.001)FDTGETSYLLPEPGSHPCWR 72.035 0.0027029 102070000 15711 18640 15707 20150 16941 16396 20552 20559 19950 20536 TRUE FALSE 15096.99675 18108.40545 18545.6043 21189.94391 17485.92265 16727.53835 20803.52152 20134.44947 17685.35964 19145.07843 0.788557582 0.945851725 0.968687821 1.106808938 0.913337739 0.873725246 1.086625035 1.051677565 0.923754881 1 14.22468595 4.774085439 1.952236442 0.997737762 0.713427421 0.415699035 0.071643786 0.854697247 3.208471709 0.019129159 0.451010599 59440.90859 -4.774085439 -0.284310341 S(ph)LDYLNLDK ddPTM_BT-474_Pertuzumab_2h_R1 4 SLDYLNLDK 9 0 Q96GV9 Q96GV9 C5orf30 UNC119-binding protein C5orf30 1 S(1)LDYLNLDK;S(1)LDYLNLDK;S(1)LDYLNLDK;S(1)LDYLNLDK 159.44 6.93E-05 862010000 2398370 1743310 1310740 1358690 1378410 1061390 1336050 2181460 1625230 1564400 TRUE FALSE 2304639.049 1693592.506 1547619.875 1428812.154 1422747.809 1082852.033 1352400.98 2136412.089 1440740.704 1458441.795 1.580206394 1.16123421 1.061146136 0.979684043 0.975525945 0.742471888 0.927291706 1.464859343 0.987863012 1 20.47599638 4.774159068 2.130668382 1.038335848 1.759794655 0.491840885 0.171343699 0.769500049 3.624958119 0.049952536 1.097167884 59450.98683 -4.774159068 0.721458807 EGHILK ddPTM_BT-474_Pertuzumab_2h_R1 6 EGHILK 6 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 0 ;;;;; 106.84 0.03178 4502380000 12652300 13040800 11117600 12415000 12372000 13735500 13242000 12259500 15447900 15190900 FALSE TRUE 12157834.13 12668889.15 13126797.63 13055739.64 12769956.62 14013241.22 13404059.56 12006337.04 13694319.15 14162006.81 0.858482437 0.89456878 0.926902367 0.921884858 0.901705301 0.989495444 0.946480237 0.847785007 0.966975891 1 23.75552238 4.774725518 1.220917848 0.929945415 0.819473893 0.257609625 0.042100534 2.614756902 3.137453557 0.012393598 0.37322734 59528.57932 -4.774725518 -0.110471522 GTRES(ph)GQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTRESGQK 8 1 A0A1W2PQW7;A8K830-4;A8K830-2 A0A1W2PQW7 1 GT(0.349)RES(0.651)GQK 73.931 0.025611 994630000 354710 598970 569060 811070 743400 655320 964520 1363600 419440 690270 TRUE FALSE 340847.541 581887.9621 671901.8007 852929.4199 767312.1361 668571.0194 976324.0843 1335441.183 371826.9296 643517.3981 0.529663288 0.90423035 1.044108213 1.325417809 1.192372014 1.038932314 1.517168125 2.075221567 0.577804005 1 19.29561963 4.775254815 0.695048239 1.381525316 1.34E-18 0.22402995 0.377180526 3.981618948 1.407921866 0.160258984 4.40374529 59601.17409 -4.775254815 -1.381525316 EREDSGDAEAHAFKS(ph)PSKENK ddPTM_BT-474_Pertuzumab_2h_R1 1 EREDSGDAEAHAFKSPSKENK 21 3 Q9NPI1-2;Q9NPI1 Q9NPI1-2 BRD7 Bromodomain-containing protein 7 1 EREDS(0.001)GDAEAHAFKS(0.981)PS(0.018)KENK 55.358 0.069158 401140000 67855 52746 42076 33622 56671 39763 42355 56776 45280 51514 TRUE FALSE 65203.15158 51241.73572 49680.06918 35357.23545 58493.87418 40567.0351 42873.35316 55603.55576 40140.00423 48024.9109 1.357694379 1.066982422 1.034464578 0.736226987 1.21799027 0.844708181 0.89273155 1.157806537 0.835816319 1 15.55149532 4.775298935 1.946875485 0.972842602 1.496777824 0.417972679 0.139866326 0.839122413 3.120039237 0.034276731 0.815162785 59607.22929 -4.775298935 0.523935223 EKQPVAGSEGAQYR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQPVAGSEGAQYR 14 1 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 114.63 0.00042546 534490000 268380 290630 215470 260900 275910 270340 283180 256270 314950 285670 FALSE TRUE 257891.4129 282341.517 254410.2221 274365.0803 284784.8957 275806.46 286645.6415 250977.9349 279198.1964 266321.3165 0.968346869 1.060153655 0.955275475 1.030203229 1.069328207 1.035615413 1.076315052 0.942387708 1.048350917 1 18.02280838 4.775673013 22.44559907 1.020992736 0.968346383 0.125484113 0.04349228 11027.47272 6668924.632 0.010359744 1.94849717 59658.59386 -4.775673013 -0.052646352 EQELQQTLQQEQSVLDQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EQELQQTLQQEQSVLDQLR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 243.21 4.43E-24 56013000 60690 72360 64858 69683 71914 79390 74948 80715 82045 77342 FALSE TRUE 58318.1677 70296.36365 76579.28336 73279.34798 74227.17912 80995.32019 75865.23604 79048.20704 72731.59556 72103.55745 0.80881124 0.974936135 1.06207358 1.01630697 1.029452384 1.123319335 1.052170499 1.096314937 1.008710224 1 16.13778282 4.775860915 1.723528441 1.056602903 0.705775199 0.786812696 0.037648902 0.421131975 1.150195607 0.009634632 0.250406666 59684.41142 -4.775860915 -0.350827704 VQSYEKEEDLLQAWSTFIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQSYEKEEDLLQAWSTFIR 19 1 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 78.708 0.0088959 2807700000 141330 144590 96306 134890 139290 163930 122500 141300 161740 147220 FALSE TRUE 135806.6674 140466.4348 113710.6365 141851.6891 143770.3893 167244.7769 123999.1916 138382.1056 143379.9533 137248.6583 0.989493588 1.023444867 0.828500897 1.033537893 1.047517631 1.218553092 0.90346378 1.008258349 1.044672896 1 17.06643252 4.776427608 19.23709008 1.009641144 0.989492589 0.004427714 0.095523786 8606.773545 4370609.056 0.023020327 2.652491504 59762.34196 -4.776427608 -0.020148555 KLGCEVLGVSVDSQFTHLAWINTPR ddPTM_BT-474_Pertuzumab_2h_R1 5 KLGCEVLGVSVDSQFTHLAWINTPR 25 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;;; 287.91 2.56E-54 6690624000 3568569.1 3959440 3235513.3 3636602.9 3943446.7 4143481.3 3820045.4 3779632.4 4165429.8 4089087.3 FALSE TRUE 3429105.474 3846520.648 3820242.527 3824288.411 4070291.244 4227265.331 3866796.258 3701581.67 3692587.672 3812129.775 0.899524853 1.009021433 1.002128142 1.00318946 1.06772106 1.10889859 1.014340142 0.97100096 0.968641649 1 21.8621658 4.776452692 3.09263306 1.01767107 0.875056436 0.430648903 0.040259936 0.487807605 6.479212486 0.011148572 0.177057228 59765.79377 -4.776452692 -0.142614634 ADDADEFGYSR ddPTM_BT-474_Pertuzumab_2h_R1 5 ADDADEFGYSR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;; 256.47 3.96E-20 4291220000 1274330 1402180 1176920 1388230 1414020 1391550 1386960 1409100 1529250 1537450 FALSE TRUE 1224527.775 1362191.199 1389615.624 1459876.717 1459503.237 1419688.094 1403934.031 1380001.593 1355655.951 1433317.142 0.854331354 0.950376689 0.969510225 1.018530145 1.018269575 0.990491255 0.979499924 0.962802685 0.945817162 1 20.45092643 4.776482949 1.846495588 0.985622234 0.804039038 0.771074589 0.021655694 0.483595552 1.56774455 0.006299519 0.156760924 59769.95775 -4.776482949 -0.181583195 AGGS(ph)PASYHGSTSPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGGSPASYHGSTSPR 15 0 I3L2B2;O95208-3;O95208-2;F6PQP6 I3L2B2 EPN2 Epsin-2 1 AGGS(0.999)PAS(0.001)YHGSTSPR;AGGS(0.998)PAS(0.002)YHGSTSPR;AGGS(0.672)PAS(0.328)YHGSTSPR;AGGS(0.988)PAS(0.012)YHGSTSPR 270.75 4.67E-21 1463291000 465141 992011 855425 1401000 978037 1316672 1228789 778571 875067 1235246 TRUE FALSE 446962.7755 963719.8176 1010019.326 1473305.778 1009496.448 1343296.01 1243827.287 762493.2368 775733.0627 1151581.688 0.388129457 0.836866223 0.877071368 1.27937583 0.876617316 1.166479134 1.080103392 0.66212692 0.673624 1 20.13518532 4.776646861 2.219995045 0.947531864 0.20970436 0.453455585 0.18551913 0.72198923 3.770557132 0.050472816 1.086101349 59792.52051 -4.776646861 -0.737827504 RLSES(ph)SALK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSESSALK 9 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RLS(0.345)ES(0.634)S(0.021)ALK 191.31 3.82E-05 701480000 930920 766000 719220 817470 796850 596030 790850 1056900 779550 703910 TRUE FALSE 894538.6172 744154.43 849199.053 859659.7247 822481.4039 608082.135 800528.6589 1035074.646 691058.7521 656233.5487 1.363140636 1.133978035 1.294050045 1.309990515 1.253336416 0.926624578 1.219883775 1.577296144 1.053068307 1 19.32384983 4.776932559 21.37182268 1.231227992 1.363142839 0.04254064 0.178319614 10588.17913 5896453.372 0.044332926 8.0051551 59831.86758 -4.776932559 0.131914847 ALQS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 6 ALQSPK 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ALQS(1)PK;ALQS(1)PK;ALQS(1)PK;ALQS(1)PK;ALQS(1)PK;ALQS(1)PK 112.41 0.02834 24758920000 45766000 38498600 30543300 31088500 31242200 27964600 36451700 38364800 34617600 37115700 TRUE FALSE 43977414.12 37400657.62 36063153.74 32692981.21 32247133.74 28530063.37 36897806.81 37572553.47 30687955.18 34601820.58 1.270956654 1.080886988 1.04223284 0.944834135 0.931949048 0.824524921 1.066354492 1.085854815 0.886888454 1 25.04434461 4.777176236 1.363421974 0.974538118 1.412748873 0.605445031 0.075106057 1.08776273 1.681890796 0.022909788 0.674103292 59865.4479 -4.777176236 0.438210755 LQQLPADFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQQLPADFGR 10 0 Q96AG4 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 ; 127.4 0.00083091 169438000 216760 327800 173125 367600 214430 161784 310540 332410 295100 197559 FALSE TRUE 208288.7796 318451.4649 204412.5386 386571.8801 221327.3357 165055.3833 314340.4814 325545.6173 261601.4852 184178.153 1.130909265 1.729040387 1.109863115 2.098901926 1.201702439 0.896172432 1.706719697 1.76755827 1.420371966 1 17.49074241 4.777324277 21.76274265 1.47284131 1.130904411 0.0504321 0.369228315 10525.07345 5908349.065 0.086281052 17.34046379 59885.85816 -4.777324277 -0.341936899 GFGFITFTNPEHASVAMR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFGFITFTNPEHASVAMR 18 0 P98179 P98179 RBM3 RNA-binding protein 3 0 139.49 1.02E-07 269320000 165680 249240 141240 186610 216830 231420 194670 205010 210780 225790 FALSE TRUE 159205.0424 242131.9192 166765.2099 196240.9645 223804.5339 236099.471 197052.4297 200776.4719 186853.1381 210497.0422 0.756329119 1.150286563 0.792244908 0.932274214 1.063219376 1.121628449 0.936129209 0.95382087 0.887675837 1 17.68344044 4.777769177 23.57077783 0.976763263 0.756327845 0.30211235 0.102592016 15033.62824 9037277.077 0.024137047 6.930463768 59947.23788 -4.777769177 -0.220435418 (ac)SNGYEDHMAEDCR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNGYEDHMAEDCR 13 0 Q15717;M0QZR9 Q15717 ELAVL1 ELAV-like protein 1 0 69.346 1.19E-10 193130000 4022.3 11815 10881 15594 14207 16970 11267 13211 11933 12627 FALSE TRUE 3865.104069 11478.04777 12847.43875 16398.80821 14663.98106 17313.14503 11404.88892 12938.18823 10578.41587 11771.76204 0.328336918 0.975049251 1.091377714 1.393063175 1.245691257 1.470735219 0.968834476 1.099086797 0.898626376 1 13.52304266 4.777979859 2.098686011 1.160905128 0.04344459 0.669335318 0.17207459 0.470899414 2.114375925 0.045387053 1.032256978 59976.32609 -4.777979859 -1.117460539 DIS(ph)QNKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DISQNKR 7 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 1 DIS(1)QNKR 87.258 0.020628 64858000 198640 162730 135170 116800 120530 139100 142830 181170 163660 162830 TRUE FALSE 190876.9292 158089.0997 159598.2258 122828.062 124406.9569 141912.6973 144577.9963 177428.7762 145082.0029 151801.3791 1.257412353 1.041420708 1.05136216 0.809136668 0.819537725 0.934857761 0.952415565 1.168821899 0.955735737 1 17.21182537 4.778107047 1.697203064 0.965303903 1.375342878 0.460120408 0.097635203 1.149630593 3.009490976 0.029816898 0.790989837 59993.89338 -4.778107047 0.410038975 GRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_BT-474_Pertuzumab_2h_R1 26 GRSPQPPAEEDEDDFDDTLVAIDTYNCDLHFK 32 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(0.999)PQPPAEEDEDDFDDT(0.001)LVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(0.995)PQPPAEEDEDDFDDT(0.005)LVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK 339.35 1.38E-117 31478413000 852438.2 949711 789353.9 1014645.4 677093.8 813549 855935.8 819206.6 981910.3 1104051.6 TRUE FALSE 819123.9727 922626.1721 932007.7088 1067011.371 698873.137 829999.5182 866410.9984 802289.6974 870447.9592 1029273.202 0.795827552 0.896386082 0.905500801 1.036664871 0.678996729 0.80639379 0.841769704 0.779472055 0.845691851 1 19.97319454 4.778519802 21.14120167 0.853279943 0.795826484 0.029815052 0.098970998 12557.32139 6642668.275 0.023635372 4.776052044 60050.93891 -4.778519802 -0.057453459 DGYDYDGYR ddPTM_BT-474_Pertuzumab_2h_R1 5 DGYDYDGYR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;; 196.95 6.70E-05 22550590000 17029700 17802200 13833200 15742200 17086200 16769500 16985900 17420200 17750800 17939700 FALSE TRUE 16364160.5 17294498.69 16333166.96 16554656.83 17635793.14 17108590.78 17193778.53 17060466.78 15735803.6 16724628.14 0.978446896 1.034073735 0.976593729 0.989837065 1.054480434 1.022957918 1.028051469 1.020080485 0.940876142 1 23.9954708 4.778682384 21.97741272 1.009911776 0.978446467 0.068424532 0.030903183 11573.90296 6339165.008 0.007280478 1.642768495 60073.42365 -4.778682384 -0.031465309 HNTPSLLEAALTQEAS(ph)TPDSQVWPTAPDITR ddPTM_BT-474_Pertuzumab_2h_R1 1 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNT(0.002)PS(0.002)LLEAALT(0.004)QEAS(0.495)T(0.495)PDS(0.002)QVWPTAPDITR 117.32 2.54E-05 141870000 31063 51106 41501 59260 57697 58082 49288 32400 55240 74783 TRUE FALSE 29849.02362 49648.50692 49001.15388 62318.4157 59552.8764 59256.45784 49891.20129 31730.92868 48969.38678 69717.8808 0.428140145 0.712134482 0.702849159 0.893865605 0.85419803 0.849946343 0.715615574 0.455133293 0.702393507 1 16.0892411 4.779237447 2.846216897 0.743725888 0.352840701 0.331918581 0.141155515 0.719961205 7.433656976 0.038884545 0.680710702 60150.25136 -4.779237447 -0.390885187 AMEDLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AMEDLGR 7 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;D6RER0 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 104.45 0.018959 201020000 268880 334600 267700 384550 325550 364830 375220 334990 369910 392700 FALSE TRUE 258371.8723 325057.5356 316079.345 404396.6716 336021.6114 372207.1126 379812.0546 328072.3394 327919.3676 366102.0792 0.705737244 0.887887707 0.863363971 1.10460086 0.917835845 1.016675768 1.037448505 0.896122579 0.89570474 1 18.48188644 4.779339322 1.320898949 0.971755147 0.579827507 0.581177385 0.068903579 1.059808623 1.515995377 0.019115456 0.573398463 60164.36292 -4.779339322 -0.39192764 EKEQMMR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKEQMMR 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 121.62 0.0040315 1199150000 1729070 1832410 1584990 1763500 1461370 1504040 1772830 1776910 1888430 1989560 FALSE TRUE 1661496.033 1780151.461 1871432.951 1854514.446 1508376.293 1534452.719 1794526.424 1740216.188 1674063.343 1854805.329 0.895779199 0.959751103 1.008964618 0.999843173 0.813226202 0.82728505 0.967501223 0.938220394 0.902554741 1 20.82283635 4.779439658 20.74045417 0.932298854 0.895778297 0.029774526 0.065682666 11435.59438 5800855.16 0.016611656 3.397254054 60178.26442 -4.779439658 -0.036520556 FGEEIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 FGEEIAR 7 0 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 146.94 0.0050827 400150000 237250 266190 221450 250630 258600 275170 253900 262940 299390 269120 FALSE TRUE 227978.0077 258598.5218 261470.9411 263565.0443 266918.1039 280734.1259 257007.3042 257510.1971 265404.5023 250892.2627 0.908668945 1.030715412 1.042164227 1.050510851 1.06387539 1.11894294 1.024373177 1.026377595 1.057842516 1 17.93670845 4.779500738 2.641432777 1.049564597 0.871320535 0.66238839 0.029635322 0.343376265 2.864007783 0.007511561 0.140947043 60186.72861 -4.779500738 -0.178244062 RGS(ph)GVFCANCLTTK ddPTM_BT-474_Pertuzumab_2h_R1 3 RGSGVFCANCLTTK 14 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 RGS(1)GVFCANCLTTK;RGS(1)GVFCANCLTTK;RGS(1)GVFCANCLTTK 135.81 1.88E-05 462590000 813840 514690 358340 288690 337071 251092 250816 706530 264413 267335 TRUE FALSE 782034.2331 500011.5451 423100.0092 303589.3255 347913.1948 256169.2523 253885.5612 691939.9086 234397.9447 249228.1623 3.137824497 2.006240147 1.697641251 1.21811806 1.395962605 1.027850344 1.01868729 2.776331142 0.940495418 1 17.92710757 4.779717125 1.592077592 1.465961543 3.873292815 0.516087638 0.518990422 1.066309876 2.37916244 0.148068092 4.106379512 60216.72405 -4.779717125 2.407331272 FLISYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLISYDR 7 0 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ; 134.85 0.0072917 1034090000 1435000 1528920 1277300 1521430 1403090 982220 1575350 1507950 1450420 1663650 FALSE TRUE 1378918.614 1485316.699 1508136.523 1599951.185 1448221.664 1002081.161 1594629.605 1476810.306 1285774.402 1550969.504 0.889068812 0.957669828 0.972383093 1.031581331 0.933752508 0.646099849 1.028150199 0.952185264 0.829013336 1 20.56473889 4.77996894 20.54494006 0.92820621 0.889067633 0.01128035 0.108939547 15380.23706 7629321.407 0.026057625 5.422441312 60251.64933 -4.77996894 -0.039138577 GSEGYLAATYPTVGQTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 GSEGYLAATYPTVGQTSPR 19 0 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 GSEGYLAATYPTVGQT(0.078)S(0.922)PR;GSEGYLAATYPTVGQT(0.001)S(0.999)PR;GSEGYLAATYPTVGQT(0.002)S(0.998)PR;GSEGYLAATYPTVGQT(0.014)S(0.986)PR;GSEGYLAATYPTVGQT(0.288)S(0.712)PR 409.09 1.17E-147 4923360000 2313950 2740770 2330860 2805750 2646440 2848570 2876660 2786760 2920120 2927170 TRUE FALSE 2223518.276 2662605.923 2752098.252 2950555.094 2731565.146 2906170.037 2911865.426 2729212.432 2588640.22 2728910.169 0.814800832 0.975703031 1.008497195 1.081221041 1.000972908 1.064956286 1.067043342 1.000110763 0.948598547 1 21.37989347 4.780260673 2.019630854 1.025667565 0.738882497 0.726931054 0.037960378 0.425686187 1.721413775 0.009824945 0.233417212 60292.13643 -4.780260673 -0.286785068 EKLETAQRPVPEALSPAFSEDSESHGSSSAS(ph)SPLSAEGRPSPLEAPNER ddPTM_BT-474_Pertuzumab_2h_R1 2 EKLETAQRPVPEALSPAFSEDSESHGSSSASSPLSAEGRPSPLEAPNER 49 3 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 EKLETAQRPVPEALSPAFSEDSESHGS(0.001)S(0.025)S(0.021)AS(0.473)S(0.473)PLS(0.007)AEGRPSPLEAPNER;EKLETAQRPVPEALSPAFSEDS(0.001)ES(0.003)HGS(0.136)S(0.155)S(0.136)AS(0.295)S(0.252)PLS(0.019)AEGRPS(0.001)PLEAPNER 138.83 1.17E-12 348270000 135144 162325 135729 176737 157954 183503 168545 155290 157125 186622 TRUE FALSE 129862.4231 157695.6499 160258.2496 185858.4178 163034.7339 187213.5564 170607.7041 152083.2072 139288.8287 173981.9257 0.746413299 0.90639099 0.921120104 1.068262792 0.937078568 1.076051754 0.980605907 0.874132222 0.800593672 1 17.40857791 4.780449705 1.924518567 0.957212517 0.667654167 0.396078377 0.078545266 0.985244271 3.519093994 0.021356661 0.526703398 60318.38495 -4.780449705 -0.28955835 RT(ph)SSEDNLYLAVLR ddPTM_BT-474_Pertuzumab_2h_R1 3 RTSSEDNLYLAVLR 14 1 Q15149-4 Q15149-4 PLEC Plectin 1 RT(0.395)S(0.395)S(0.211)EDNLYLAVLR;RT(0.333)S(0.333)S(0.333)EDNLYLAVLR;RT(0.333)S(0.333)S(0.333)EDNLYLAVLR 203.53 8.74E-09 409255000 151780 175742 97128 116603 123387 149371 113270 109283 108629 102629 TRUE FALSE 145848.2698 170730.0102 114681.1902 122620.8948 127355.8549 152391.384 114656.2321 107026.2679 96297.89133 95677.84642 1.524368234 1.784425723 1.198618013 1.281601744 1.331090317 1.592755164 1.198357158 1.118610753 1.006480548 1 16.5458973 4.780819201 0.172783094 0.872456451 2.262604106 0.541553191 0.166066344 15.15195244 0.457548424 0.550678618 4.722197529 60369.72553 -4.780819201 1.390147655 YEEIDNAPEER ddPTM_BT-474_Pertuzumab_2h_R1 1 YEEIDNAPEER 11 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 192.12 3.57E-06 235970000 107660 162290 129840 242060 111810 138640 198940 194390 154360 131100 FALSE TRUE 103452.5282 157661.6481 153304.9763 254552.7456 115406.4702 141443.3958 201374.6872 190375.7786 136837.6999 122220.4802 0.84644184 1.289977325 1.25433132 2.082733967 0.944248214 1.157280642 1.647634561 1.557642207 1.119597139 1 16.89912653 4.78115967 2.157475731 1.392957195 0.664198342 0.160503735 0.327326625 1.256172254 6.021520617 0.081066753 1.836616181 60417.0714 -4.78115967 -0.728758852 EVIDAFISENGWVEDY ddPTM_BT-474_Pertuzumab_2h_R1 2 EVIDAFISENGWVEDY 16 0 Q9UNE7;Q9UNE7-2;H3BTA3;V9GYH3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 196.15 1.08E-10 31869000 64904 73364 56446 77839 73149 73766 71753 75398 75323 79556 FALSE TRUE 62367.47992 71271.73055 66647.04783 81856.28012 75501.90402 75257.59906 72631.13468 73841.00495 66772.64882 74167.60126 0.840899245 0.960955044 0.898600557 1.103666274 1.017990372 1.014696414 0.979283858 0.99559651 0.900294033 1 16.17850149 4.781549083 1.285590998 0.996937986 0.770690231 0.408234438 0.054666489 1.514235284 2.026497107 0.015191278 0.463272579 60471.26904 -4.781549083 -0.226247755 QSHSGS(ph)IS(ph)PYPK ddPTM_BT-474_Pertuzumab_2h_R1 2 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QS(0.005)HS(0.148)GS(0.847)IS(0.996)PY(0.004)PK;QS(0.001)HS(0.093)GS(0.907)IS(1)PYPK 189.8 1.09E-05 1011410000 1852410 1539680 1263280 1300120 1492320 1416140 1441760 1344700 1892380 1635520 TRUE FALSE 1780015.769 1495769.834 1491582.798 1367219.349 1540321.828 1444775.321 1459404.69 1316931.475 1677564.956 1524744.774 1.167418836 0.980996859 0.978250802 0.896687349 1.010216172 0.947552237 0.957146872 0.863706174 1.10022673 1 20.54013634 4.781862801 2.737326742 0.957284093 1.221297686 0.470670456 0.061688895 0.432832513 3.967695083 0.014593179 0.270119128 60514.96706 -4.781862801 0.264013593 AAESETPGKS(ph)PEKKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 AAESETPGKSPEKKPK 16 3 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AAESET(0.001)PGKS(0.999)PEKKPK;AAESET(0.001)PGKS(0.999)PEKKPK;AAES(0.001)ET(0.018)PGKS(0.981)PEKKPK 168.81 6.00E-09 5020500000 6547300 4086980 3544350 2110310 3778710 3027580 3685930 5038410 4737760 3660430 TRUE FALSE 6291424.278 3970423.332 4184892.889 2219223.352 3900255.639 3088799.742 3731039.514 4934365.073 4199949.347 3412505.816 1.843637672 1.163492034 1.226340148 0.650320753 1.142930108 0.905141239 1.093343049 1.445965323 1.23075229 1 21.70240007 4.781969493 2.93543556 1.103195479 2.015881726 0.554643595 0.20159915 0.415724458 4.656761577 0.053829064 0.938969998 60529.83543 -4.781969493 0.912686247 GSDIDNPTLTVMDISPPSRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSDIDNPTLTVMDISPPSRSPR 22 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 GSDIDNPTLTVMDISPPS(0.06)RS(0.94)PR 154.14 1.74E-08 46007000 30582 34804 28589 32764 29939 36233 35261 39576 31776 31772 TRUE FALSE 29386.82163 33811.424 33755.66826 34454.95397 30902.01512 36965.65609 35692.53467 38758.74177 28168.9217 29620.05414 0.992125858 1.141504463 1.139622099 1.163230621 1.04328017 1.247994211 1.205012472 1.308530416 0.951008447 1 14.85428666 4.782415929 2.869286462 1.156805818 0.952363761 0.103865151 0.106706419 0.925129924 9.688342253 0.025845548 0.461384392 60592.08951 -4.782415929 -0.204442057 RPEDYEAVFVGNIDDHFR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPEDYEAVFVGNIDDHFR 18 1 Q68CQ4;H7C2R4 Q68CQ4 DIEXF Digestive organ expansion factor homolog 0 ; 167.35 1.52E-11 201080000 101300 113742 93993 109671 113360 114469 113912 107580 113433 128885 FALSE TRUE 97341.08401 110498.1895 110979.626 115331.1335 117006.3274 116783.6416 115306.0891 105358.4354 100556.5614 120155.5042 0.810125884 0.919626532 0.92363331 0.959848941 0.973790824 0.971937511 0.959640509 0.876850679 0.83688685 1 16.87454321 4.783081963 2.672383711 0.934716623 0.776887756 0.401729094 0.046344924 0.634564751 5.417278373 0.012223563 0.233278097 60685.08484 -4.783081963 -0.157828867 ELGELSPHWDNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELGELSPHWDNLR 13 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ;;; 216.34 2.76E-11 2657520000 1733470 2093970 1732110 2123230 1984810 2099040 2066830 2010700 2207740 2502860 FALSE TRUE 1665724.076 2034252.026 2045140.808 2232810.155 2048653.216 2141484.027 2092124.484 1969178.342 1957126.611 2333339.063 0.713879994 0.871820156 0.876486765 0.956916288 0.87799208 0.917776615 0.896622577 0.843931503 0.838766488 1 21.15396453 4.783159405 2.647198793 0.89421861 0.665178672 0.584834983 0.046773608 0.410953856 3.415540234 0.011315691 0.217871986 60695.90698 -4.783159405 -0.229039938 DKGLQTSQDAR ddPTM_BT-474_Pertuzumab_2h_R1 7 DKGLQTSQDAR 11 1 P27797 P27797 CALR Calreticulin 0 ;;;;;; 153.75 2.95E-05 5109080000 10548480 12061180 9987930 10440820 9861530 10186780 10956010 11047150 12851750 11930200 FALSE TRUE 10136233.74 11717206.96 11792971.13 10979671.97 10178735.07 10392763.67 11090092.93 10819022.49 11392873.22 11122156.93 0.911355037 1.053501316 1.060313319 0.98718909 0.915176358 0.934419802 0.997117106 0.972744996 1.024340269 1 23.40693326 4.783519046 21.6660132 0.989971857 0.911353442 0.23686272 0.043933618 9030.873271 4351515.034 0.011453508 4.202182687 60746.19026 -4.783519046 -0.078618415 KPSTSGQNFHSDVDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPSTSGQNFHSDVDYR 16 1 Q01804-5;Q01804-3;Q01804;D6RI06 Q01804-5 OTUD4 OTU domain-containing protein 4 0 54.281 0.093776 81823000 123490 154730 127920 146720 152370 167660 150940 145220 162050 181820 FALSE TRUE 118663.8743 150317.2519 151037.9896 154292.2368 157271.1194 171050.2001 152787.2489 142221.1563 143654.7634 169505.1695 0.700060504 0.886800399 0.891052409 0.910250922 0.927824915 1.009114947 0.901372208 0.83903728 0.847494881 1 17.37096975 4.78360496 2.767764554 0.909035322 0.64661242 0.596098639 0.052689365 0.412333166 3.881590418 0.013883063 0.258106353 60758.20848 -4.78360496 -0.262422902 SHPFIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHPFIK 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 106.84 0.03178 677560000 1391200 1566300 1326100 1589400 1582500 1615300 1685600 1500400 1821000 1918100 FALSE TRUE 1336830.366 1521630.658 1565755.769 1671429.124 1633402.55 1647962.473 1706228.877 1469416.216 1614287.714 1788185.379 0.74759048 0.850935633 0.875611549 0.934706851 0.913441397 0.921583686 0.954167782 0.821735953 0.902751881 1 20.77006488 4.783948715 1.37423552 0.90973385 0.667951023 0.587333468 0.043828134 1.073253301 1.672120431 0.012296005 0.370756514 60806.31927 -4.783948715 -0.241782827 LFCDFGDEFEVLDTTGEEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFCDFGDEFEVLDTTGEEPK 20 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 108.56 0.00021032 16985000 7749.3 9450 7765.4 9163 9631.4 7562.7 10860 9134 11685 7976.6 FALSE TRUE 7446.448789 9180.495253 9168.78052 9635.903528 9941.202728 7715.622976 10992.90793 8945.379708 10358.56779 7436.337777 1.001359676 1.234545219 1.232969883 1.295786154 1.336841201 1.03755682 1.478269043 1.202928105 1.392966282 1 12.86037659 4.784627709 2.787898819 1.260612826 0.935288556 0.212766737 0.139206377 0.736689935 7.058998615 0.030860447 0.575008288 60901.46069 -4.784627709 -0.32532427 S(ph)TTPAPK ddPTM_BT-474_Pertuzumab_2h_R1 5 STTPAPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.984)T(0.014)T(0.002)PAPK;S(0.992)T(0.008)TPAPK;S(0.983)T(0.015)T(0.001)PAPK;S(0.852)T(0.137)T(0.011)PAPK;S(0.989)T(0.01)T(0.002)PAPK 125.98 0.0041922 5895360000 4644600 6242550 6135400 7137100 7030500 7998400 8971300 6231630 8781300 9569600 TRUE FALSE 4463083.897 6064518.586 7244203.261 7505446.586 7256642.417 8160133.128 9081093.453 6102944.663 7784483.638 8921442.468 0.50026483 0.679768839 0.811999101 0.841281734 0.813393399 0.914665219 1.017895199 0.684075998 0.872558856 1 23.08884556 4.784763805 1.088414151 0.865956771 0.284783925 0.645778477 0.089037751 1.253175682 1.141532791 0.027147466 0.860136853 60920.54848 -4.784763805 -0.581172846 ISVYYNEASSHK ddPTM_BT-474_Pertuzumab_2h_R1 5 ISVYYNEASSHK 12 0 Q13509;A0A0B4J269;G3V5W4;G3V2R8;G3V3R4;G3V2N6 Q13509 TUBB3 Tubulin beta-3 chain 0 ;;;; 249.75 5.46E-17 8018380000 5266970 6394580 5577210 6518570 6116660 6338610 6868680 6676160 7674750 7557040 FALSE TRUE 5061130.989 6212212.839 6585135.911 6854994.179 6313407.924 6466781.037 6952740.96 6538294.963 6803544.555 7045194.95 0.718380545 0.881765925 0.934698892 0.973002767 0.896129627 0.917899516 0.986877015 0.928050254 0.965699971 1 22.7482082 4.78487497 1.8000831 0.947391241 0.624244644 0.842214751 0.030443116 0.353080074 1.055865876 0.00761045 0.201148736 60936.14417 -4.78487497 -0.323146597 TLQEMEMSLPEDEGHTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLQEMEMSLPEDEGHTR 17 0 Q9NPI1-2;Q9NPI1 Q9NPI1-2 BRD7 Bromodomain-containing protein 7 0 ; 84.581 0.005248 157713000 188460 201540 175518 195808 189646 221930 214200 209121 222050 214210 FALSE TRUE 181094.7748 195792.2765 207238.007 205913.6743 195746.1358 226417.5767 216821.4437 204802.5783 196843.8149 199701.3659 0.906827923 0.980425325 1.037739557 1.031107992 0.980194276 1.133780811 1.085728396 1.025544204 0.985690879 1 17.60748467 4.784917905 1.315613597 1.041286356 0.835072762 0.446120102 0.044131182 1.365657773 1.918342386 0.012663809 0.388719491 60942.16875 -4.784917905 -0.206213594 SLS(ph)PDEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSPDEER 8 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 S(0.001)LS(0.999)PDEER 101.82 0.0053764 293630000 373040 501650 411490 467880 503000 533880 492400 513370 479990 563850 TRUE FALSE 358461.1844 487343.4332 485855.3965 492027.3429 519179.4518 544675.4194 498426.1385 502768.7301 425503.5475 525659.9373 0.681926011 0.92710781 0.924277013 0.936018342 0.987671715 1.036174494 0.948191222 0.956452441 0.809465431 1 19.00377026 4.785076419 2.841251381 0.952043981 0.614599083 0.66447134 0.05670031 0.312508754 3.156929158 0.013922068 0.256293307 60964.41618 -4.785076419 -0.337444898 SGSIVELIAGGGSS(ph)CSPVLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 1 SGSIVELIAGGGS(0.074)S(0.565)CS(0.36)PVLSR 135.04 7.60E-06 133620000 56247 86693 78462 95059 90682 101580 102150 81420 98914 118540 TRUE FALSE 54048.80506 84220.60052 92641.82878 99965.00638 93598.86889 103634.0172 103400.1423 79738.64855 87685.6974 110511.1802 0.489079973 0.762100272 0.838302773 0.904569168 0.846962893 0.937769527 0.935653226 0.721543724 0.793455443 1 16.75383281 4.785092217 1.865129161 0.862212558 0.340627092 0.70200567 0.075449483 0.561410597 1.834482953 0.020514873 0.53020497 60966.63387 -4.785092217 -0.521585466 down IVHSLDYYNTCEYPNEDEMPNR ddPTM_BT-474_Pertuzumab_2h_R1 1 IVHSLDYYNTCEYPNEDEMPNR 22 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 208.44 5.22E-23 216250000 123740 134580 102290 117060 129960 121090 119940 135670 132850 125350 FALSE TRUE 118904.104 130741.9102 120776.0784 123101.4806 134140.2814 123538.5228 121407.8616 132868.3671 117769.425 116859.9328 1.01749249 1.118791591 1.033511448 1.053410503 1.147872313 1.057150383 1.038917776 1.13698822 1.007782754 1 16.83442084 4.785229247 22.15594902 1.07282549 1.017491527 0.064654105 0.049713028 18684.66792 8869608.096 0.011116345 5.14958522 60985.87323 -4.785229247 -0.055333962 FGVQTDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FGVQTDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 129.68 0.0084605 3317920000 2036940 2325180 1930840 2400650 2201010 2299840 2336830 2441730 2209180 2479130 FALSE TRUE 1957334.133 2258868.143 2279785.739 2524547.834 2271807.486 2346344.341 2365428.825 2391307.422 1958403.148 2311216.317 0.846884871 0.977350379 0.98640085 1.092302705 0.982948878 1.015198934 1.023456267 1.034653228 0.847347405 1 21.14022086 4.785317336 2.297489193 1.005139849 0.795820254 0.36434064 0.058855995 0.711218397 3.989289993 0.014197441 0.313402239 60998.24448 -4.785317336 -0.209319595 RKS(ph)PENTEGK ddPTM_BT-474_Pertuzumab_2h_R1 12 RKSPENTEGK 10 2 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.656)PENT(0.344)EGK;RKS(0.998)PENT(0.002)EGK;RKS(1)PENTEGK;RKS(0.99)PENT(0.01)EGK;RKS(0.986)PENT(0.014)EGK;RKS(1)PENTEGK;RKS(0.889)PENT(0.111)EGK;RKS(1)PENTEGK;RKS(1)PENTEGK;RKS(1)PENTEGK;RKS(1)PENTEGK;RKS(1)PENTEGK 220.32 3.08E-09 34846175800 12895786 10139956 8063533 7812944.8 9063316 8146656 9107466 10722104 10879434 9260027 TRUE FALSE 12391804.43 9850774.383 9520792.785 8216171.817 9354845.79 8311386.966 9218925.893 10500688.81 9644446.263 8632837.123 1.435426645 1.141081923 1.102857919 0.951734835 1.083635155 0.962764251 1.067890632 1.216365913 1.117181539 1 23.04140334 4.785652029 2.228032722 1.071629852 1.557221467 0.691566181 0.074414167 0.474528165 2.450995514 0.020932085 0.474875963 61045.27139 -4.785652029 0.485591616 WDQTADQTPGAT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 WDQTADQTPGATPK 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDQTADQT(0.002)PGAT(0.998)PK;WDQTADQTPGAT(1)PK;WDQTADQTPGAT(1)PK;WDQTADQTPGAT(1)PK 289.77 2.15E-42 4897210000 5999200 4822960 3821180 4040020 4048000 3796190 4008840 5553240 5044180 4718150 TRUE FALSE 5764744.632 4685413.903 4511752.228 4248525.916 4178207.596 3872951.563 4057901.383 5438563.653 4471585.833 4398585.498 1.31059056 1.065209237 1.025727982 0.965884582 0.949898007 0.880499325 0.922546893 1.23643468 1.016596321 1 22.06860822 4.785963134 2.263331384 1.008668563 1.41036414 0.514198939 0.090224857 0.704486832 3.790997334 0.026284011 0.589867811 61089.01664 -4.785963134 0.401695577 SRTS(ph)PAPWKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPAPWKR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)RT(0.097)S(0.902)PAPWKR 57.804 0.090742 1658000000 874310 1180800 768330 857210 997850 1268000 1054400 780910 1120500 1225900 TRUE FALSE 840140.9986 1147124.74 907184.3224 901450.7108 1029946.751 1293639.829 1067304.063 764783.9356 993305.5375 1142868.701 0.735115939 1.003723996 0.793778254 0.788761395 0.901194293 1.131923403 0.93388161 0.669179176 0.869133555 1 20.12422824 4.786125479 22.11466313 0.881298647 0.735113636 0.120103861 0.125066853 21670.52648 10074300.9 0.032123699 16.518036 61111.85674 -4.786125479 -0.146185011 EAMEHPYFYTVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAMEHPYFYTVVK 13 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A087WY74 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 132.59 0.00011709 819620000 664370 786220 638090 646910 711790 598830 701990 736160 723850 815900 FALSE TRUE 638405.6859 763797.7754 753407.0572 680297.1026 734685.3718 610938.7529 710581.1636 720958.0387 641681.5826 760638.3663 0.839302505 1.004153628 0.990493105 0.89437653 0.965879982 0.803192134 0.934190537 0.947832861 0.843609278 1 19.53685118 4.786744516 22.25527518 0.928705694 0.839300904 0.157560944 0.063674453 19527.22453 9018311.05 0.014787716 8.709738685 61199.02685 -4.786744516 -0.089404791 FLEEFENNLER ddPTM_BT-474_Pertuzumab_2h_R1 1 FLEEFENNLER 11 0 A0A2R8Y661;A0A2R8YGD3;Q9Y4G8 A0A2R8Y661 RAPGEF2 Rap guanine nucleotide exchange factor 2 0 107.24 0.0035072 0 8778.3 10917 7446.8 7616.2 11372 9562.8 8991.7 10503 9220.2 10638 FALSE TRUE 8435.234331 10605.65785 8792.602413 8009.272995 11737.79071 9756.166368 9101.743114 10286.10938 8173.56155 9917.478785 0.850542211 1.069390525 0.886576377 0.807591644 1.183545835 0.983734534 0.917747677 1.037169789 0.8241572 1 13.27575769 4.786923068 21.96300558 0.969433369 0.850539902 0.094407008 0.108810501 20388.52939 9257969.957 0.025043117 13.85027432 61224.19278 -4.786923068 -0.118893467 IS(ph)PSSLSNNYNNMNNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISPSSLSNNYNNMNNR 16 0 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 IS(0.973)PS(0.016)S(0.011)LSNNYNNMNNR;IS(0.832)PS(0.134)S(0.034)LSNNYNNMNNR 185.02 1.81E-09 267090000 163742 184010 152343 188758 178739 177838 186969 188291 176872 196115 TRUE FALSE 157342.7816 178762.215 179874.769 198499.823 184488.3023 181434.0062 189257.1826 184402.7251 156794.2321 182831.9564 0.860586873 0.977740536 0.983825653 1.085695449 1.009059389 0.992353907 1.035142796 1.008591325 0.857586579 1 17.48015873 4.787185365 2.285080879 1.002431601 0.814109816 0.354483832 0.05430202 0.76236024 4.196039942 0.013438612 0.30161844 61261.18098 -4.787185365 -0.188321784 LSS(ph)PVLHR ddPTM_BT-474_Pertuzumab_2h_R1 9 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.062)S(0.938)PVLHR;LS(0.049)S(0.951)PVLHR;LS(0.023)S(0.977)PVLHR;LS(0.484)S(0.516)PVLHR;LS(0.133)S(0.867)PVLHR;LS(0.133)S(0.867)PVLHR;LS(0.242)S(0.758)PVLHR;LS(0.037)S(0.963)PVLHR;LS(0.034)S(0.966)PVLHR 166.09 0.00033618 86158560000 11038120 12142350 10195670 12269780 11460750 11642550 12686460 12637200 13469770 13343990 TRUE FALSE 10606738.07 11796062.07 12038254.37 12903024.82 11829395.43 11877970.34 12841720.69 12376237.4 11940738.18 12440189.67 0.852618678 0.948222043 0.967690581 1.03720483 0.950901533 0.954806209 1.032276921 0.994859221 0.959851778 1 23.56850515 4.787334704 1.640448786 0.989782964 0.791941001 0.67375864 0.028483972 0.655600574 1.551501207 0.007550497 0.21345111 61282.2503 -4.787334704 -0.197841963 LEEQLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEEQLGR 7 0 Q9BR76;A9Z1Z3-3;A9Z1Z3 Q9BR76 CORO1B;FER1L4 Coronin-1B;Fer-1-like protein 4 0 ;;; 244.84 5.93E-08 2950850000 1942400 2223060 1808320 2307960 2278300 2263270 2397500 2346390 2320390 2371660 FALSE TRUE 1866488.861 2159660.505 2135123.65 2427074.092 2351583.589 2309034.87 2426841.322 2297936.227 2056989.055 2211025.356 0.844173431 0.976768765 0.965671264 1.097714274 1.063571516 1.04432763 1.097608997 1.039307948 0.930332639 1 21.07628414 4.787674341 1.238223236 1.042826079 0.744020628 0.567873478 0.049685037 1.124278138 1.366788632 0.014036635 0.442049895 61330.19434 -4.787674341 -0.298805452 EYIPGQPPLSQSSDS(ph)SPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQS(0.002)S(0.005)DS(0.618)S(0.355)PT(0.02)R 124.84 2.99E-05 3864500000 480240 591460 506420 622250 594740 731990 582130 575130 601990 707580 TRUE FALSE 461471.6899 574592.1399 597941.3593 654364.3971 613870.3522 746791.3393 589254.2811 563253.3645 533654.6189 659654.9764 0.699565237 0.871049504 0.906445613 0.991979778 0.930593074 1.132093846 0.893276489 0.853860555 0.808990515 1 19.33135211 4.787706288 1.760025316 0.93693581 0.599964595 0.428438628 0.084187307 1.089528906 3.063409144 0.023450403 0.637730079 61334.70597 -4.787706288 -0.336971215 FGVEQDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FGVEQDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 143.11 0.0056859 5051040000 3511720 3859080 3183620 3864960 3712060 3701670 3723660 4032860 3889650 3986640 FALSE TRUE 3374478.1 3749022.817 3758970.953 4064431.049 3831461.781 3776520.304 3769231.265 3949580.032 3448113.239 3716621.322 0.907942405 1.008717997 1.011394659 1.093582234 1.030899155 1.016116515 1.014155314 1.062680238 0.927754791 1 21.82556027 4.788048366 2.44354604 1.026105099 0.871780493 0.391209703 0.040890374 0.615898701 4.051897198 0.00980043 0.209385497 61383.03621 -4.788048366 -0.154324606 T(ph)VLSLFDEEEDKMEDQNIIQAPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVLSLFDEEEDKMEDQNIIQAPQK 24 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 T(0.528)VLS(0.472)LFDEEEDKMEDQNIIQAPQK 79.875 0.029359 60097000 68458 46370 38941 27030 44413 43505 23519 56312 64471 44045 TRUE FALSE 65782.58568 45047.573 45978.50494 28425.02154 45841.58448 44384.70091 23806.83256 55149.13752 57152.52236 41061.79292 1.602038805 1.097067853 1.119739341 0.692249888 1.116404843 1.080924571 0.579780639 1.343076705 1.391866217 1 15.325509 4.788052521 2.699875867 1.037423979 1.755247884 0.331651075 0.237530533 0.691175825 5.990005276 0.059437417 1.169381582 61383.62345 -4.788052521 0.717823905 AYS(ph)PEYR ddPTM_BT-474_Pertuzumab_2h_R1 8 AYSPEYR 7 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR 138.26 0.0029403 13196320000 10915730 12194100 10251060 12862080 11773060 12806720 13005460 13579750 13294870 14309020 TRUE FALSE 10489131.2 11846336.21 12103654.58 13525893.49 12151751.17 13065680.65 13164624.71 13299323.42 11785692.09 13339857.33 0.786300104 0.888040697 0.907330137 1.013945888 0.910935617 0.979446806 0.986863981 0.996961443 0.883494613 1 23.6692399 4.788338509 1.0557641 0.969364084 0.68108599 0.653095534 0.040496937 1.126587217 0.954137222 0.01167288 0.374487474 61424.05852 -4.788338509 -0.288278095 DIVNGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DIVNGLR 7 0 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 137.59 0.0066735 1460340000 807433 962930 810350 1030340 914180 773520 1113970 1047750 1024320 1078960 FALSE TRUE 775877.6257 935468.1792 956798.2711 1083515.971 943585.4299 789161.1044 1127603.098 1026113.596 908043.4879 1005881.078 0.771341307 0.929998784 0.951204165 1.077180985 0.938068575 0.784547121 1.121010349 1.020114225 0.902734436 1 19.94002832 4.788383409 1.911896467 0.980822256 0.689247543 0.321510287 0.088296236 1.11202519 3.842040433 0.023181324 0.59955399 61430.40934 -4.788383409 -0.291574714 DDGYSTK ddPTM_BT-474_Pertuzumab_2h_R1 3 DDGYSTK 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;; 151.29 0.0043996 2257140000 2764930 2544040 2060810 2208700 2342250 2358180 2445360 2552250 2397330 2560660 FALSE TRUE 2656873.479 2471486.47 2433244.209 2322691.272 2417590.598 2405864.015 2475287.047 2499545.146 2125195.149 2387224.217 1.112955147 1.035297167 1.019277616 0.972967371 1.012720372 1.007808147 1.036889216 1.04705085 0.890236926 1 21.18690265 4.788786014 1.703241483 1.003753371 1.160197128 0.414098442 0.041308681 1.125907882 2.913246969 0.010713205 0.298658884 61487.38366 -4.788786014 0.156443757 S(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLEPAENVHGAGGGAFPASQTPSKPASADGHR 32 1 P12931;P12931-2 P12931 SRC Proto-oncogene tyrosine-protein kinase Src 1 S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR 180.9 1.02E-19 888820000 146460 203060 176720 241270 190150 180850 256280 224820 254830 246980 TRUE FALSE 140736.1813 197268.9276 208657.2351 253721.9736 196266.3474 184506.9109 259416.4313 220177.3884 225902.7667 230251.8246 0.611227214 0.85675294 0.906213167 1.101932521 0.852398663 0.801326596 1.126663955 0.956246009 0.981111733 1 17.81285306 4.789366315 1.581120768 0.969449202 0.447141448 0.572183445 0.093749619 0.871448257 1.878809042 0.025062072 0.728987496 61569.59751 -4.789366315 -0.522307754 AFEVMDEFDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 AFEVMDEFDGR 11 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ;;; 208.11 4.81E-08 518100000 791590 881260 732340 896590 892970 844560 897750 920550 917140 967420 FALSE TRUE 760653.7877 856127.3276 864690.1288 942863.1173 921693.191 861637.5819 908736.933 901540.3208 813030.1122 901895.7817 0.843394329 0.949253057 0.958747281 1.04542358 1.021950884 0.955362692 1.007585301 0.999605874 0.901467918 1 19.78260121 4.789433752 1.651478839 0.990846533 0.778707616 0.565524365 0.037890448 0.80200957 1.921680559 0.009907173 0.281855227 61579.15884 -4.789433752 -0.212138917 GGDAKS(ph)PVLQEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GGDAKSPVLQEK 12 1 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK 138.01 7.95E-05 1838578000 4206680 3375860 2762730 2576430 3086440 3031340 3036950 3741270 3474870 3058370 TRUE FALSE 4042278.295 3279583.778 3262016.768 2709399.861 3185718.146 3092635.772 3074117.103 3664011.467 3080417.325 2851223.876 1.417734444 1.150237204 1.144075986 0.950258548 1.117316031 1.084669569 1.078174579 1.285066213 1.080384235 1 21.44314989 4.789904496 2.482588459 1.107127402 1.512160714 0.565498049 0.084416797 0.530842888 3.629071248 0.022447351 0.479707411 61645.94239 -4.789904496 0.405033311 VVHIIQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVHIIQSR 8 0 O60885;O60885-2;O60885-3;Q58F21-5;Q58F21-4;Q58F21;Q58F21-3;Q58F21-2;Q15059 O60885;Q15059 BRD4;BRDT;BRD3 Bromodomain-containing protein 4;Bromodomain testis-specific protein;Bromodomain-containing protein 3 0 ; 105.57 0.0043629 626630000 843770 912880 748000 835250 825270 708550 937440 830650 903300 973220 FALSE TRUE 810794.5356 886845.5562 883180.2392 878357.3526 851815.559 722877.3665 948912.6711 813496.7872 800761.1709 907302.9425 0.893631551 0.977452529 0.973412735 0.968097106 0.938843598 0.796732086 1.045860899 0.896609885 0.8825731 1 19.79122481 4.790240729 20.93233957 0.939004323 0.893629907 0.044233587 0.066234871 19956.22424 8081201.931 0.01518039 8.977790936 61693.6875 -4.790240729 -0.045374415 SVDISLGDS(ph)PRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVDISLGDSPRR 12 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SVDIS(0.001)LGDS(0.999)PRR 51.577 0.094787 216630000 174070 196750 155810 199070 199660 208680 198180 201760 200780 227440 TRUE FALSE 167267.152 191138.8826 183968.333 209344.0266 206082.2452 212899.6526 200605.3861 197593.5855 177988.2961 212035.2862 0.788864698 0.901448462 0.867630743 0.987307492 0.971924291 1.004076521 0.946094349 0.931890107 0.839427717 1 17.69394485 4.790460185 1.10949683 0.950037701 0.706792189 0.493049168 0.04940264 1.632983447 1.540907355 0.01481161 0.477954881 61724.87022 -4.790460185 -0.243245512 TTIPHALLTWRPNSGETAPPPPS(ph)PVSEKPLDTISQK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTIPHALLTWRPNSGETAPPPPSPVSEKPLDTISQK 36 2 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 TTIPHALLTWRPNSGETAPPPPS(0.98)PVS(0.017)EKPLDT(0.002)IS(0.001)QK 136.32 2.13E-09 1834700000 1467800 1727300 1521600 1577300 1917300 1989600 1792800 1618200 1941700 1812700 TRUE FALSE 1410436.753 1678039.095 1796586.968 1658704.642 1978971.696 2029831.075 1814740.823 1584783.605 1721286.356 1689924.214 0.834615388 0.99296707 1.063116886 0.981526052 1.171041683 1.20113734 1.073859293 0.937783831 1.018558313 1 20.68852712 4.790559375 1.838725485 1.056105369 0.742273225 0.431640135 0.076722686 1.065251773 3.321034696 0.02240051 0.601489011 61738.96925 -4.790559375 -0.313832144 DKHKEEDKNSER ddPTM_BT-474_Pertuzumab_2h_R1 3 DKHKEEDKNSER 12 3 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;; 157.52 4.44E-05 651880000 584040 477350 380684 352806 419603 454218 467644 286495 621710 498180 FALSE TRUE 561215.0711 463736.4454 449482.0671 371014.3599 433099.9116 463402.5992 473367.1672 280578.7781 551136.0872 464437.8249 1.208375031 0.998489831 0.967798149 0.798846132 0.932525062 0.997771013 1.019226131 0.604125597 1.18667356 1 18.82512595 4.790679676 1.59557807 0.907794735 1.345032314 0.217471002 0.146220968 1.596592624 3.51032758 0.038686143 1.127016693 61756.07357 -4.790679676 0.437237578 S(ph)KPLTR ddPTM_BT-474_Pertuzumab_2h_R1 6 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 S(0.996)KPLT(0.004)R;S(0.932)KPLT(0.068)R;S(0.948)KPLT(0.052)R;S(1)KPLTR;S(1)KPLTR;S(0.999)KPLT(0.001)R 85.862 0.032843 13714630000 7834230 6364290 5503960 5011820 5235870 4852490 4895080 6710500 5802000 5548760 TRUE FALSE 7528059.63 6182786.68 6498648.007 5270480.631 5404286.514 4950610.673 4954987.453 6571925.83 5143381.284 5172937.543 1.455277503 1.195217733 1.256278073 1.018856421 1.044722939 0.957021157 0.957867249 1.270443684 0.994286368 1 22.30255234 4.790851903 0.94783996 1.053059695 1.674842579 0.633771378 0.097199357 1.627507691 1.083947736 0.033250353 1.065972655 61780.56894 -4.790851903 0.621782884 CEYPAACNALETLLIHR ddPTM_BT-474_Pertuzumab_2h_R1 1 CEYPAACNALETLLIHR 17 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 71.781 0.029787 59516000 17391 22786 17315 29838 18649 22870 27809 22746 25619 23292 FALSE TRUE 16711.34049 22136.16559 20444.20567 31377.94276 19248.86202 23332.44707 28149.33486 22276.28715 22710.83852 21714.41209 0.769596728 1.019422745 0.941503992 1.445028427 0.886455592 1.074514335 1.296343403 1.025875674 1.045887792 1 14.40636527 4.790872008 1.491541748 1.104366922 0.617798453 0.27892686 0.1562338 1.620279814 3.028869909 0.040142704 1.20735987 61783.42897 -4.790872008 -0.486568469 IQPAGNTS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 IQPAGNTSPR 10 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 1 IQPAGNT(0.007)S(0.993)PR 103.43 0.0029533 400330000 479680 507440 407170 527480 483530 479140 503230 517730 529490 499250 TRUE FALSE 460933.5753 492968.308 480754.6764 554703.306 499083.1816 488828.5391 509388.6793 507038.6946 469384.515 465435.3528 0.990327814 1.059155273 1.032913967 1.191794527 1.072293238 1.050260871 1.094434869 1.089385865 1.008484878 1 18.82822127 4.791593782 1.741978794 1.076566888 0.955077725 0.152085292 0.051677331 1.732354789 4.711958329 0.013037681 0.363782793 61886.19504 -4.791593782 -0.121489163 S(ph)RENLSAVMLYNPGLEFER ddPTM_BT-474_Pertuzumab_2h_R1 2 SRENLSAVMLYNPGLEFER 19 1 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(0.809)RENLS(0.191)AVMLYNPGLEFER;S(0.5)RENLS(0.5)AVMLYNPGLEFER 217.41 2.18E-19 510862000 466218 405162 320250 342091 359289 335315 367220 438150 378239 343605 TRUE FALSE 447997.6851 393607.1765 378126.2989 359746.3575 370845.857 342095.299 371714.1482 429102.0494 335302.8944 320332.3273 1.39854035 1.228746345 1.180418792 1.123041063 1.157691015 1.067938731 1.16040161 1.339552748 1.046734487 1 18.28920987 4.791871472 1.655243888 1.154092549 1.508553309 0.445829365 0.088551463 1.18719108 2.847302956 0.024334436 0.699565947 61925.77804 -4.791871472 0.35446076 TVEIVHIDIADR ddPTM_BT-474_Pertuzumab_2h_R1 5 TVEIVHIDIADR 12 0 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ;;;; 180.09 1.99E-05 2364140000 2618100 2957560 2472380 2904280 2985510 3046210 2943780 2862540 3099560 3130510 FALSE TRUE 2515781.758 2873213.285 2919194.064 3054170.239 3081541.641 3107806.453 2979806.86 2803427.549 2747710.943 2918477.769 0.862018476 0.984490379 1.000245434 1.046494262 1.055872919 1.064872409 1.021014068 0.960578689 0.941487707 1 21.47678465 4.792174974 2.217123158 1.012441176 0.80957629 0.589383738 0.037251432 0.610602424 3.065882481 0.010781508 0.255913478 61969.06929 -4.792174974 -0.202864887 TIQEVLEEQS(ph)EDEDREAK ddPTM_BT-474_Pertuzumab_2h_R1 5 TIQEVLEEQSEDEDREAK 18 1 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK 261.74 5.10E-31 5573300000 2639926 2268643 1873175 1777321 1999214 1954595 1894821 2136934 2378160 2259966 TRUE FALSE 2536754.773 2203943.523 2211699.391 1869048.75 2063520.534 1994118.25 1918010.386 2092805.566 2108201.247 2106896.49 1.204024396 1.046061605 1.049742786 0.887109907 0.979412393 0.946471865 0.910348655 0.993312 1.000619279 1 21.00668801 4.79342603 1.216881593 0.960453744 1.331863123 0.752294915 0.041732203 0.777231957 0.900201324 0.011636433 0.375591392 62147.83868 -4.79342603 0.371409379 LDADYPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDADYPLR 8 0 O43583;F8VVL1 O43583 DENR Density-regulated protein 0 ;; 98.458 0.017467 625800000 2544780 2673880 2209110 2514700 2638010 2539220 2562150 2886230 2603910 2615070 FALSE TRUE 2445327.184 2597623.56 2608345.318 2644483.968 2722863.987 2590564.768 2593506.358 2826628.342 2308325.053 2437948.98 1.003026398 1.065495456 1.069893316 1.084716699 1.116866682 1.062600075 1.063806659 1.159428834 0.946830747 1 21.2172365 4.793460839 2.463502166 1.075687708 0.980221478 0.059422144 0.05609859 1.37493844 9.119253834 0.013249383 0.292323207 62152.82013 -4.793460839 -0.09546623 S(ph)FGHFPGPEFLDVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFGHFPGPEFLDVEK 15 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 S(1)FGHFPGPEFLDVEK;S(1)FGHFPGPEFLDVEK 237.81 6.12E-18 205850000 559240 371660 268800 272400 281790 181809 244131 545610 265220 206832 TRUE FALSE 537384.2825 361060.6207 317378.1394 286458.5966 290854.0313 185485.3025 247118.7482 534342.9628 235113.3375 192823.0844 2.78692919 1.872496863 1.645955101 1.485603228 1.508398396 0.961945522 1.281582799 2.771156599 1.219321526 1 17.55691825 4.793615662 1.943329827 1.577893715 3.269337277 0.386602801 0.486794527 1.128824815 4.019775355 0.136316526 3.588836627 62174.98115 -4.793615662 1.691443562 TLS(ph)DESIYNSQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLSDESIYNSQR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 TLS(0.999)DES(0.001)IYNSQR;TLS(0.977)DES(0.023)IYNSQR;TLS(0.999)DESIYNSQR;TLS(0.999)DES(0.001)IYNSQR 338.89 1.71E-58 2526640000 1136040 1207000 1014890 1160200 1123110 1149020 1260040 1293340 1272390 1194670 TRUE FALSE 1091642.301 1172577.542 1198303.199 1220078.061 1159235.853 1172253.972 1275460.746 1266632.077 1127953.621 1113753.937 0.980146749 1.05281562 1.075913772 1.095464645 1.040836593 1.052525098 1.145190786 1.137263838 1.012749391 1 20.0869991 4.794193087 1.789168454 1.081395568 0.936559348 0.225990715 0.046066283 1.342155596 3.880148498 0.012345144 0.343579904 62257.70209 -4.794193087 -0.14483622 YQYGGLNSGRPVT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 6 YQYGGLNSGRPVTPPR 16 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 1 YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR 146.15 1.86E-06 20194040000 2760710 3014340 2470250 3148040 2712520 2379340 3142450 3329240 3057540 3321240 TRUE FALSE 2652818.401 2928373.975 2916679.125 3310510.722 2799770.669 2427451.885 3180908.243 3260490.031 2710460.877 3096289.457 0.856773386 0.945768803 0.941991751 1.069186447 0.904234151 0.783987388 1.027329094 1.053031403 0.875390016 1 21.56210892 4.794344895 2.269320729 0.962962928 0.820449682 0.112071306 0.082748862 1.726908201 9.172076124 0.02190132 0.517966904 62279.4681 -4.794344895 -0.142513247 LLEEEDLDELNIRDPEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEEEDLDELNIRDPEHR 18 1 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 0 133.45 7.60E-06 35283000 19397 21542 17159 21990 22114 22943 20397 23379 20710 20644 FALSE TRUE 18638.9438 20927.64325 20260.013 23124.90654 22825.31689 23406.92318 20646.62459 22896.21548 18359.08762 19245.76349 0.96846996 1.08738961 1.052699884 1.201558283 1.185991759 1.216211723 1.072788024 1.189675613 0.953928777 1 14.23225328 4.79434667 1.369758431 1.129036816 0.892281468 0.173148695 0.086514463 2.111193064 3.209071019 0.022758154 0.716644127 62279.72265 -4.79434667 -0.236755348 RRHS(ph)EVETDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRHSEVETDSK 11 2 Q9NX58 Q9NX58 LYAR Cell growth-regulating nucleolar protein 1 RRHS(0.992)EVET(0.008)DSK 106.17 0.001235 186150000 133600 86894 57214 49167 72107 51395 40862 91416 56691 33345 TRUE FALSE 128378.7643 84415.8682 67553.84252 51704.51476 74426.38714 52434.24211 41362.08138 89528.22765 50255.67535 31086.51345 4.129725403 2.715514184 2.173091641 1.663245859 2.394169654 1.68671994 1.330547456 2.879970049 1.616639172 1 14.9240012 4.794695362 1.462087088 1.91678923 5.234967807 0.66064884 0.506552634 0.82709318 1.464805605 0.134522123 4.14704245 62329.74677 -4.794695362 3.318178577 DTCIQS(ph)PSKECQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTCIQSPSKECQK 13 1 Q03188;Q03188-2 Q03188 CENPC Centromere protein C 1 DTCIQS(0.997)PS(0.003)KECQK 235.16 6.75E-17 496460000 359220 285000 229660 216360 266300 220950 266890 309410 279180 275770 TRUE FALSE 345181.2853 276872.079 271164.6708 227526.3655 274865.7813 225417.7604 270156.2797 303020.5754 247488.6568 257091.8523 1.34263798 1.076938365 1.054738485 0.885000297 1.069134548 0.876798539 1.050816186 1.178647136 0.962646831 1 17.97192436 4.794729266 2.232114272 1.01966375 1.455835197 0.578212007 0.084841294 0.60483695 3.072489748 0.022866313 0.548944208 62334.61281 -4.794729266 0.436171447 LPEADDIQYPSMLLLTADHDDR ddPTM_BT-474_Pertuzumab_2h_R1 8 LPEADDIQYPSMLLLTADHDDR 22 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;;;;;; 340.33 3.19E-81 4331170000 1764460 1998290 1678840 1984020 1984210 2036970 2079080 1912160 2198530 2102380 FALSE TRUE 1695502.952 1941300.726 1982243.734 2086415.51 2048033.917 2078158.929 2104524.403 1872673.228 1948962.091 1959983.93 0.865059619 0.990467675 1.011357136 1.064506437 1.044923831 1.060293861 1.073745744 0.955453358 0.994376567 1 20.90241039 4.794802245 2.011379677 1.026313994 0.802545744 0.657325084 0.03479744 0.593598156 2.301416441 0.009900552 0.256345352 62345.08834 -4.794802245 -0.223768251 AVPDSER ddPTM_BT-474_Pertuzumab_2h_R1 2 AVPDSER 7 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 111.73 0.015154 238900000 366940 419760 346590 438140 422180 463390 405950 437310 426180 442560 FALSE TRUE 352599.5791 407788.8558 409226.5229 460752.4579 435759.8031 472760.0633 410918.1375 428279.3957 377801.8331 412585.017 0.854610722 0.988375338 0.991859874 1.116745492 1.056169723 1.14584884 0.995959913 1.038039139 0.915694505 1 18.65433191 4.794848279 1.587645732 1.040762103 0.769430216 0.430512056 0.061723913 1.11724709 2.408469128 0.01642091 0.488899864 62351.69718 -4.794848279 -0.271331887 SNT(ph)PILVDGKDVMPEVNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNTPILVDGKDVMPEVNK 18 1 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41 P06744 GPI Glucose-6-phosphate isomerase 1 S(0.151)NT(0.849)PILVDGKDVMPEVNK 128.98 3.58E-05 260970000 588740 435090 349920 278360 380820 375040 367260 461880 504950 318260 TRUE FALSE 565731.3899 422681.6592 413158.3279 292726.193 393069.4212 382623.5658 371754.6377 452342.0166 447630.1929 296703.9667 1.906720008 1.424590523 1.392493442 0.986593459 1.324786539 1.289580217 1.252947987 1.524556687 1.508676132 1 18.17866469 4.795477162 2.086218927 1.304478996 2.132261608 0.540942782 0.171404102 0.687102354 2.921564133 0.044517572 1.128047505 62442.0513 -4.795477162 0.827782612 SEANDAVNS(ph)STKEEKGEEKPDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEANDAVNSSTKEEKGEEKPDTK 23 3 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 SEANDAVNS(0.977)S(0.019)T(0.003)KEEKGEEKPDTK;SEANDAVNS(0.823)S(0.142)T(0.036)KEEKGEEKPDTK 182.54 2.79E-17 795400000 1559190 970890 779470 416750 813560 772330 738480 978060 1293400 869250 TRUE FALSE 1498255.131 943201.1678 920337.5682 438258.5174 839728.8963 787947.0418 747517.7391 957862.7192 1146578.654 810374.9233 1.848841922 1.163907151 1.135693544 0.540809575 1.036222707 0.972324068 0.922434441 1.181999457 1.414874303 1 19.62823001 4.795585562 2.212125507 1.017420231 2.143527072 0.58097388 0.208942825 0.568162882 2.812996589 0.054475634 1.323853341 62457.63885 -4.795585562 1.126106841 ESGYSDDEIMELWSTR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESGYSDDEIMELWSTR 16 0 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 0 ;;; 311.7 2.59E-57 191126000 245193 265336 218119 266395 267387 258606 252448 281589 279191 267222 FALSE TRUE 235610.5865 257768.8771 257537.9553 280143.6779 275987.7457 263835.1905 255537.5341 275774.0887 247498.4081 249122.8159 0.945760771 1.034706019 1.03377908 1.124520357 1.107838095 1.059056713 1.02574922 1.106980458 0.99347949 1 17.92649763 4.795877925 1.691073501 1.065487655 0.893147836 0.358033286 0.043450415 1.097015652 2.751073558 0.011057951 0.32045384 62499.69895 -4.795877925 -0.172339819 QTPS(ph)PDVVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 QTPSPDVVLR 10 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 QT(0.001)PS(0.999)PDVVLR;QT(0.034)PS(0.966)PDVVLR 160.52 7.71E-06 819000000 642100 704460 577840 706080 634030 640820 692930 735000 761440 760630 TRUE FALSE 617006.0221 684369.4905 682268.542 742520.8734 654424.1508 653777.8195 701410.2846 719821.9931 675004.5234 709111.8526 0.870110999 0.965107956 0.962145167 1.047113894 0.922878596 0.92196713 0.989139135 1.015103598 0.951901341 1 19.43565369 4.795988111 2.538389002 0.977964746 0.836981392 0.418645603 0.037250507 0.654274917 4.676074067 0.009568529 0.210218243 62515.55785 -4.795988111 -0.140983354 RLS(ph)PS(ph)ASPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.895)PS(0.864)AS(0.24)PPR;RLS(0.719)PS(0.858)AS(0.423)PPR 117.63 0.00062303 4275400000 1453730 1695290 1322820 1807690 1639970 1769320 1873930 1781020 1789800 1841810 TRUE FALSE 1396916.624 1646941.989 1561883 1900985.098 1692721.124 1805096.863 1896863.716 1744241.315 1586629.407 1717062.568 0.813550217 0.959162479 0.909624978 1.107114634 0.985823788 1.051270289 1.104714383 1.015828629 0.924037037 1 20.71151118 4.796303595 1.02576522 1.028844986 0.697710035 0.522076114 0.059560853 1.567390118 1.23246021 0.017820645 0.586112519 62560.98751 -4.796303595 -0.331134951 SLLGLDSGELQSGPESSS(ph)SPGVHVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLGLDSGELQSGPESSSSPGVHVR 25 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 SLLGLDSGELQSGPES(0.013)S(0.056)S(0.586)S(0.344)PGVHVR 208.34 1.82E-25 180200000 109790 136600 121310 145640 139130 174980 150130 138880 141750 199390 TRUE FALSE 105499.2854 132704.3017 143233.4155 153156.4979 143605.2428 178518.2155 151967.3358 136012.0795 125659.1343 185885.1377 0.567550944 0.713904852 0.77054797 0.823930841 0.772548277 0.960368417 0.817533546 0.731699592 0.676004202 1 17.5040519 4.796470923 1.267828654 0.813321063 0.433927997 0.427565744 0.091716946 1.636423183 2.072390293 0.025829566 0.836858822 62585.09607 -4.796470923 -0.379393066 DPSVDITQDLVDESEEERFDDMSS(ph)PGLELPSCELSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DPSVDITQDLVDESEEERFDDMSSPGLELPSCELSR 36 1 Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 DPSVDITQDLVDESEEERFDDMS(0.022)S(0.978)PGLELPSCELSR;DPSVDITQDLVDESEEERFDDMS(0.056)S(0.944)PGLELPSCELSR 153.58 8.96E-14 138595000 57280 67232 56771 70837 57369 70192 69079 72270 74196 73007 TRUE FALSE 55041.43427 65314.60919 67030.78256 74492.90606 59214.32599 71611.33033 69924.40947 70777.59924 65773.58114 68062.17086 0.808693487 0.959631589 0.98484638 1.094483251 0.870003487 1.052145846 1.027360846 1.039896294 0.966375011 1 16.05456555 4.796807458 1.876515188 1.009161994 0.725445487 0.517957012 0.056664713 0.732931051 2.373544217 0.013929224 0.381777185 62633.61199 -4.796807458 -0.283716507 SVMEELKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVMEELKR 8 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ; 112.41 0.0048844 2348400000 934850 873220 753960 784540 893140 849290 912770 825620 1022490 943300 FALSE TRUE 898315.0285 848316.6206 890217.3437 825030.2034 921868.6592 866463.2257 923940.7523 808570.6585 906421.2218 879409.4508 1.021498038 0.964643511 1.012289944 0.938163904 1.048281501 0.985278501 1.050637734 0.919447315 1.030715807 1 19.74617551 4.797026517 20.96892454 0.991381282 1.0214997 0.031988019 0.04191224 28160.46309 10097164.12 0.00936041 10.14943009 62665.21249 -4.797026517 0.030118418 FYAFGR ddPTM_BT-474_Pertuzumab_2h_R1 4 FYAFGR 6 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 150.22 0.024519 12040688000 8136270 9436230 7645730 8187540 8264040 7043210 8850910 8333230 9184520 10437920 FALSE TRUE 7818295.573 9167117.959 9027483.489 8610099.921 8529860.352 7185628.532 8959230.084 8161145.888 8141931.794 9730950.381 0.803446248 0.942057826 0.927708306 0.884815931 0.876570121 0.738430292 0.920694252 0.838679221 0.836704687 1 23.21414928 4.797077419 21.57855286 0.876536636 0.803443211 0.103489629 0.068019367 30988.99598 11425187.59 0.015727381 21.01742516 62672.55778 -4.797077419 -0.073093426 TVLSANADHMAQIEGLMDDVDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVLSANADHMAQIEGLMDDVDFK 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 129.78 3.71E-05 306730000 94718 106660 97306 124590 115540 126310 139760 126350 160370 137590 FALSE TRUE 91016.31584 103618.1612 114891.3588 131020.1048 119256.449 128864.0747 141470.4247 123740.8283 142165.4699 128270.9067 0.709563206 0.807807194 0.895693043 1.021432748 0.929723287 1.004624338 1.102903443 0.964683508 1.108322016 1 16.96883446 4.798736732 0.649701602 1.033816493 0.461515495 0.819314429 0.05037339 1.345582464 0.407381929 0.021093408 0.584239101 62912.4694 -4.798736732 -0.572300998 GFVEPDHYVVVGAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFVEPDHYVVVGAQR 15 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 134.21 3.66E-05 1901180000 249120 341380 283350 417070 294160 276090 381090 396810 379030 384640 FALSE TRUE 239384.115 331644.1766 334557.6481 438595.0327 303621.9235 281672.729 385753.8934 388615.7348 336004.1034 358587.9902 0.667574268 0.924861361 0.932986205 1.223116905 0.846715261 0.785505194 1.075757984 1.083738846 0.937019958 1 18.45196764 4.798803934 1.976305344 0.994411572 0.53737829 0.394362113 0.117850157 0.963239777 3.539609353 0.031385412 0.841488724 62922.20514 -4.798803934 -0.457033282 SIFEMYEPSELESSHLTDQDNEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SIFEMYEPSELESSHLTDQDNEIR 24 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 234.04 2.40E-37 377930000 148971 176787 144314 196986 171134 197347 178784 161706 186161 200695 FALSE TRUE 143149.0486 171745.2079 170394.75 207152.4711 176638.6805 201337.4916 180972.0121 158366.7146 165028.7837 187101.7489 0.765086641 0.917924118 0.910706346 1.107164804 0.94407819 1.076085567 0.967238485 0.84642028 0.882026944 1 17.51346352 4.798846682 1.822878203 0.963361351 0.681496402 0.39127073 0.075986352 1.191590745 3.574248367 0.021425984 0.604269344 62928.39894 -4.798846682 -0.281864949 GECEESWIHFI ddPTM_BT-474_Pertuzumab_2h_R1 2 GECEESWIHFI 11 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 ; 119.27 0.0014147 85344000 176158 220290 182558 246070 209800 224100 235680 213370 227230 240690 FALSE TRUE 169273.5506 214007.5449 215550.2916 258769.7022 216548.4075 228631.4555 238564.3223 208963.8349 201435.803 224387.8519 0.7543793 0.953739443 0.9606148 1.153225097 0.965062973 1.018911913 1.063178422 0.9312618 0.897712605 1 17.77563505 4.799005438 2.099493545 1.00086164 0.661056827 0.539932906 0.06753627 0.664138071 2.847386078 0.01750083 0.45106006 62951.4065 -4.799005438 -0.339804812 VIGELVGHTER ddPTM_BT-474_Pertuzumab_2h_R1 1 VIGELVGHTER 11 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 0 113.22 0.0014204 133540000 80994 102590 83668 97119 100910 101680 92975 107240 111350 117550 FALSE TRUE 77828.66494 99664.23365 98788.66878 102131.3232 104155.8618 103736.0393 94112.85586 105025.4565 98710.01482 109588.2338 0.710191799 0.909442832 0.901453243 0.93195519 0.95042924 0.946598332 0.858786136 0.958364351 0.900735521 1 16.74173338 4.799233518 2.713294045 0.928491004 0.646826786 0.764765859 0.036455739 0.265941484 2.261579914 0.008339283 0.179153366 62984.4757 -4.799233518 -0.281664218 SSS(ph)SERPEPQQK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSSERPEPQQK 12 1 P78362;C9J2M4 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 S(0.007)S(0.228)S(0.761)S(0.004)ERPEPQQK;S(0.131)S(0.131)S(0.723)S(0.016)ERPEPQQK;S(0.006)S(0.2)S(0.765)S(0.029)ERPEPQQK 107.74 0.0010791 440470000 728130 631886 529273 454811 591490 609830 596020 574160 757610 672350 TRUE FALSE 699673.8746 613865.23 624924.4047 478283.8502 610515.813 622161.1804 603314.271 562303.3954 671609.289 626811.1356 1.11624353 0.979346401 0.996989953 0.763043001 0.974002819 0.992581569 0.962513645 0.897085842 1.071469939 1 19.25767128 4.79941012 1.988969978 0.946636127 1.182943036 0.266840296 0.07746317 1.143740135 4.26591056 0.019383158 0.519335536 63010.09284 -4.79941012 0.23630691 GPLLVQDVVFTDEMAHFDR ddPTM_BT-474_Pertuzumab_2h_R1 10 GPLLVQDVVFTDEMAHFDR 19 0 P04040 P04040 CAT Catalase 0 ;;;;;;;;; 250.22 3.13E-25 1662495000 1004173 1317649 1090202 1542263 1257238 1377579 1406898 1275748 1376763 1478701 FALSE TRUE 964928.809 1280070.941 1287225.753 1621859.378 1297678.202 1405434.591 1424116.039 1249403.358 1220478.636 1378547.264 0.699960628 0.928565145 0.933755255 1.176498928 0.941337476 1.019504102 1.033055649 0.90631884 0.885336809 1 20.3947173 4.799457555 2.002414096 0.987941814 0.586230037 0.550633543 0.077852505 0.698838448 2.651273415 0.020318686 0.542147898 63016.97547 -4.799457555 -0.401711777 AWEVDTCR ddPTM_BT-474_Pertuzumab_2h_R1 1 AWEVDTCR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 122.18 0.0032608 522350000 268170 347310 266820 281000 296280 255080 276870 312690 324880 345360 FALSE TRUE 257689.6199 337405.0589 315040.3094 295502.4437 305810.1153 260237.8924 280258.4179 306232.8422 288000.9844 321968.4596 0.800356719 1.047944446 0.978481898 0.917799352 0.949813891 0.808271384 0.87045302 0.951126836 0.894500613 1 18.29655984 4.800766907 22.32668994 0.929206973 0.800352138 0.277360228 0.064695823 39798.05535 14281820.43 0.015846115 39.47132045 63207.2516 -4.800766907 -0.128854835 LEEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEELR 6 0 Q07065;F6XZD3;Q8N283;H7C5W5;P41219;P41219-2;Q8IY63-2;Q8IY63;Q9ULE0;Q9ULE0-2;Q66GS9 Q07065;H7C5W5;Q8IY63-2;Q9ULE0;Q66GS9 CKAP4;ANKRD35;PRPH;AMOTL1;WWC3;CEP135 Cytoskeleton-associated protein 4;Ankyrin repeat domain-containing protein 35;Peripherin;Angiomotin-like protein 1;Protein WWC3;Centrosomal protein of 135 kDa 0 110.36 0.066925 119770000 168220 203540 170660 218280 210950 215820 210180 223870 219410 232500 FALSE TRUE 161645.7764 197735.2385 201502.0583 229545.457 217735.3983 220184.0283 212752.2457 219247.0063 194503.4966 216752.5679 0.74576176 0.912262495 0.929640928 1.059020704 1.004534343 1.015831233 0.981544292 1.01150823 0.897352675 1 17.72568956 4.802252732 1.373862063 0.995808987 0.616667728 0.763184086 0.041425688 0.656160059 0.991354362 0.01105327 0.359229854 63423.86906 -4.802252732 -0.379141259 SSPNVANQPPS(ph)PGGK ddPTM_BT-474_Pertuzumab_2h_R1 6 SSPNVANQPPSPGGK 15 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK 284.12 6.26E-34 3352110000 2460180 3187490 2696740 3153830 3036990 3297480 3452610 3092760 3694560 3267790 TRUE FALSE 2364033.446 3096585.906 3184100.907 3316599.544 3134677.541 3364157.305 3494864.074 3028893.425 3275169.038 3046459.673 0.775993678 1.01645393 1.045180718 1.088673378 1.028957504 1.104284207 1.147188688 0.994233882 1.07507382 1 21.53870221 4.802639577 2.291634558 1.062872463 0.673442249 0.78445569 0.044478087 0.328996793 1.7565879 0.011022837 0.273656913 63480.38859 -4.802639577 -0.389430214 GISLNPEQWSQLKEQISDIDDAVRKL ddPTM_BT-474_Pertuzumab_2h_R1 1 GISLNPEQWSQLKEQISDIDDAVRKL 26 3 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 222.36 3.09E-34 254610000 156570 172660 143680 76370 136620 142940 99695 93881 135350 58195 FALSE TRUE 150451.0713 167735.9059 169646.1721 80311.46485 141014.5064 145830.3447 100915.0972 91942.32454 119985.6354 54253.40082 2.773117796 3.091712286 3.126922361 1.480302868 2.599182802 2.687948452 1.86006952 1.694683156 2.211578143 1 15.72742595 4.803073225 0.094733078 4.05E-13 5.863152918 0.582244172 0.442241317 45.9000672 0.682969033 10.03629024 39.21489947 63543.80613 -4.803073225 5.863152918 AGGIETIANEYSDR ddPTM_BT-474_Pertuzumab_2h_R1 3 AGGIETIANEYSDR 14 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;; 339.33 1.92E-68 1428490000 786170 830962 711162 782785 846294 845051 855835 841863 918925 914173 FALSE TRUE 755445.6072 807263.7774 839684.7931 823184.6277 873515.8151 862138.5102 866308.9647 824478.2349 814612.4864 852255.2484 0.886407691 0.947208925 0.985250363 0.965889772 1.024946243 1.011596598 1.016490032 0.967407636 0.955831587 1 19.70092605 4.804026266 1.269285561 0.992838918 0.826186949 0.696313093 0.021627459 0.965781622 1.212027904 0.006538647 0.21805247 63683.40356 -4.804026266 -0.166651969 S(ph)SPEQPIGQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPEQPIGQGR 11 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 S(0.708)S(0.292)PEQPIGQGR 199.95 5.09E-08 408950000 173710 201450 168930 187110 200780 215840 198790 201540 205270 210490 TRUE FALSE 166921.2212 195704.8432 199459.4088 196766.7695 207238.271 220204.4327 201222.8515 197378.1286 181968.6102 196233.3248 0.85062627 0.997306871 1.016440042 1.002718421 1.056080924 1.122156152 1.0254265 1.005833891 0.927307379 1 17.58221054 4.804300408 2.340712182 1.023613548 0.789471661 0.540451262 0.046290146 0.596037808 3.351092835 0.012245856 0.303079864 63723.61538 -4.804300408 -0.234141887 LKSLPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKSLPLR 7 1 Q9BRR8 Q9BRR8 GPATCH1 G patch domain-containing protein 1 0 81.784 0.023952 614200000 494880 600100 635550 666290 834950 754600 920970 1083700 992840 1134600 FALSE TRUE 475539.5425 582985.7356 750408.0227 700677.3067 861806.925 769858.529 932241.1064 1061321.216 880136.9655 1057752.531 0.449575424 0.551155132 0.709436282 0.662420827 0.814752884 0.727824804 0.881341409 1.003373837 0.832082117 1 20.01257071 4.804605191 0.285118001 1.010261832 1.68E-18 0.862804457 0.063373916 2.885910161 0.188568571 0.078135556 1.035869495 63768.35164 -4.804605191 -1.010261832 down GSDALSET(ph)SSVSHIEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GS(0.061)DALS(0.199)ET(0.231)S(0.231)S(0.231)VS(0.048)HIEDLEK 67.11 0.096494 217270000 127290 163940 121880 185910 178970 181280 157770 179010 158730 168690 TRUE FALSE 122315.3661 159264.5917 143906.4272 195504.8374 184726.7326 184945.6058 159700.8365 175313.3809 140711.6359 157264.476 0.777768566 1.012718166 0.915059973 1.243159563 1.174624666 1.176016418 1.015492122 1.114767844 0.894745205 1 17.2628333 4.804809033 1.270775122 1.089198151 0.6222463 0.400565512 0.107094801 1.581191507 1.987260806 0.029953029 1.001694 63798.28915 -4.804809033 -0.466951851 EEIQPGDIVIIDQFIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEIQPGDIVIIDQFIDR 17 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2;J3QSB7;Q13126-7;Q13126-6;Q13126-5;F2Z2F3;A0A2R8Y4K0 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase;Purine nucleoside phosphorylase 0 ; 176.25 2.62E-09 35411000 30589 36358 30959 36472 34792 39233 35056 41925 34410 37066 FALSE TRUE 29393.54806 35321.10544 36553.97998 38354.32429 35911.11628 40026.31814 35485.02581 41059.2341 30503.92106 34555.48681 0.850618839 1.02215621 1.057834323 1.109934422 1.039230513 1.158320193 1.026899896 1.188211711 0.882751883 1 15.07662718 4.804841128 1.936903658 1.074125299 0.756475856 0.351069467 0.081933216 0.90913812 3.13344016 0.019444798 0.546534639 63803.0042 -4.804841128 -0.317649442 QAEVANQETKEDLPAENGETKTEES(ph)PASDEAGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QAEVANQETKEDLPAENGETKTEESPASDEAGEK 34 2 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 QAEVANQETKEDLPAENGET(0.004)KT(0.004)EES(0.55)PAS(0.442)DEAGEK 124.59 4.13E-08 226500000 104900 60930 45881 29261 58233 48507 41956 56289 65207 36525 TRUE FALSE 100800.392 59192.33606 54172.71732 30771.16372 60106.11733 49487.84477 42469.47008 55126.61248 57804.97473 34051.12922 2.960265763 1.738336949 1.590922785 0.90367528 1.765172513 1.453339314 1.247226481 1.618936398 1.697593474 1 15.05541502 4.804862535 2.050941101 1.427648073 3.573341318 0.746032971 0.271267921 0.422066379 1.68133805 0.06592871 1.788473712 63806.14914 -4.804862535 2.145693245 SELLSQLQQHEEESR ddPTM_BT-474_Pertuzumab_2h_R1 2 SELLSQLQQHEEESR 15 0 Q92665 Q92665 MRPS31 "28S ribosomal protein S31, mitochondrial" 0 ; 172.57 1.02E-06 265890000 135171 215400 171143 302190 161919 194983 264810 228400 202644 183322 FALSE TRUE 129888.3679 209257.0029 202072.3472 317786.0621 167127.2717 198925.6899 268050.824 223683.4602 179640.7027 170905.4377 0.760001377 1.224402253 1.182363475 1.85942628 0.977893237 1.163951789 1.568416006 1.30881418 1.051111686 1 17.38283877 4.804979892 2.33827141 1.297352045 0.570802148 0.244700135 0.25909499 0.987951076 5.529472285 0.062634627 1.558722794 63823.39357 -4.804979892 -0.726549898 METEADAPS(ph)PAPSLGER ddPTM_BT-474_Pertuzumab_2h_R1 9 METEADAPSPAPSLGER 17 0 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER 295.16 4.34E-46 8080630000 5079990 6005520 5043170 6322940 5792790 6572680 6071600 6177910 6306960 6603630 TRUE FALSE 4881458.375 5834248.45 5954583.004 6649267.691 5979120.351 6705584.093 6145906.057 6050334 5591020.342 6156360.258 0.792913048 0.947678207 0.967224586 1.080064748 0.971210277 1.089212426 0.998301886 0.982777769 0.90816978 1 22.55364623 4.806936064 1.712554254 1.003678185 0.695399562 0.612013998 0.04972922 0.739056696 1.870391571 0.0129226 0.393158854 64111.51854 -4.806936064 -0.308278623 HDGGSPSIK ddPTM_BT-474_Pertuzumab_2h_R1 1 HDGGSPSIK 9 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 0 76.035 0.085084 238120000 1342900 997300 736780 623420 854040 611130 606580 950720 809100 708470 FALSE TRUE 1290417.983 968857.9805 869932.5356 655594.7809 881510.9722 623487.4673 614003.5075 931087.2998 717254.36 660484.6959 1.953743957 1.466889372 1.317112328 0.992596475 1.33464254 0.94398473 0.929625639 1.409703064 1.085951521 1 19.33316561 4.807043455 1.19212996 1.123908078 2.432460949 0.739462235 0.155742862 0.917008398 0.993389335 0.045420417 1.545716378 64127.37381 -4.807043455 1.308552871 DKVSTTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKVSTTVR 8 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 66.435 0.076054 0 88256 94016 70261 101710 74124 73066 101170 90250 89050 95726 FALSE TRUE 84806.85795 91334.75573 82958.72565 106959.2653 76508.26578 74543.44458 102408.1487 88386.30596 78941.41733 89242.39276 0.950297895 1.023445841 0.929588765 1.198525297 0.857308544 0.835291864 1.147528048 0.990407173 0.88457307 1 16.44544158 4.807835563 18.53500015 0.988765547 0.950288704 0.007734744 0.11212912 23509.7295 6283361.692 0.026150252 39.92153893 64244.4422 -4.807835563 -0.038476843 SGS(ph)FGK ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSFGK 6 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 SGS(1)FGK;SGS(1)FGK;SGS(1)FGK;SGS(1)FGK 107.9 0.032388 4044000000 11646500 8712400 7141200 5527900 7114800 6437700 5976400 10201000 6614700 7796700 TRUE FALSE 11191341.9 8463930.882 8431773.695 5813195.581 7343654.003 6567874.705 6049540.971 9990345.785 5863826.987 7268622.564 1.539678502 1.164447708 1.160023597 0.799765778 1.010322649 0.903592757 0.832281621 1.37444828 0.806731528 1 22.79325056 4.807854397 1.40686779 0.995905402 1.819829227 0.519655659 0.16461356 1.265033448 2.001052084 0.046592068 1.539524033 64247.22842 -4.807854397 0.823923824 KDDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_BT-474_Pertuzumab_2h_R1 10 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.225)HS(0.775)AEDS(1)EDEKEDHKNVR;KDDS(0.016)HS(0.984)AEDS(1)EDEKEDHKNVR;KDDS(0.178)HS(0.822)AEDS(1)EDEKEDHKNVR;KDDS(0.017)HS(0.983)AEDS(1)EDEKEDHKNVR;KDDS(0.459)HS(0.55)AEDS(0.991)EDEKEDHKNVR;KDDS(0.021)HS(0.979)AEDS(1)EDEKEDHKNVR;KDDS(0.154)HS(0.846)AEDS(1)EDEKEDHKNVR;KDDS(0.184)HS(0.817)AEDS(1)EDEKEDHKNVR;KDDS(0.141)HS(0.859)AEDS(1)EDEKEDHKNVR;KDDS(0.159)HS(0.842)AEDS(1)EDEKEDHKNVR 157.75 1.28E-09 26062478000 2338220 1466693 1189729 742180.5 1244315 1187638 1244671.4 1417096 1984500 1129840 TRUE FALSE 2246839.777 1424864.352 1404739.496 780484.5245 1284339.522 1211652.854 1259904.061 1387832.472 1759227.88 1053314.93 2.133113006 1.352742955 1.333636745 0.740979266 1.219330976 1.15032344 1.196132348 1.317585493 1.67018223 1 20.00650542 4.808208095 2.220346259 1.203215751 2.484625259 0.604210683 0.224749025 0.558713902 2.708369305 0.057077543 1.502795938 64299.57392 -4.808208095 1.281409508 RPELEDSTLR ddPTM_BT-474_Pertuzumab_2h_R1 5 RPELEDSTLR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 190.53 1.43E-06 7511040000 2447290 2711110 2196890 2746700 2618850 2657890 2599900 2663290 2806490 2749440 FALSE TRUE 2351647.201 2633791.797 2593916.893 2888457.516 2703087.689 2711634.357 2631718.354 2608292.131 2487909.021 2563217.98 0.917458921 1.027533287 1.011976708 1.126887194 1.054568012 1.057902363 1.026724365 1.017584985 0.97061937 1 21.28952474 4.808227439 2.638242459 1.037139383 0.879572306 0.42867627 0.039687332 0.64213619 4.920218514 0.010160447 0.239671744 64302.43798 -4.808227439 -0.157567076 S(ph)PGSGSQSSGWHEVEPGMPS(ph)PTTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGSGSQSSGWHEVEPGMPSPTTLK 25 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 2 S(0.982)PGS(0.01)GS(0.002)QS(0.003)S(0.003)GWHEVEPGMPS(0.963)PT(0.031)T(0.007)LK;S(0.778)PGS(0.122)GS(0.046)QS(0.026)S(0.028)GWHEVEPGMPS(0.735)PT(0.199)T(0.066)LK 114.61 0.00092703 491830000 232739 305140 246243 325338 294950 318657 314722 275092 304184 344450 TRUE FALSE 223643.3026 296437.706 290744.5877 342128.7332 304437.3346 325100.4629 318573.662 269411.2541 269654.3076 321120.0947 0.696447548 0.92313658 0.905407642 1.065422995 0.948048221 1.012395263 0.992070155 0.838973513 0.839730406 1 18.29275342 4.80967075 2.557075509 0.946955553 0.613540728 0.542314929 0.06939758 0.584534498 4.098848576 0.018604883 0.452588389 64516.49277 -4.80967075 -0.333414825 LDAPVDYFYRPETQHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDAPVDYFYRPETQHR 16 1 Q5T7U0;Q5T7U4;Q9Y5Q8-2;Q9Y5Q8;Q9Y5Q8-3;Q5T7U1 Q5T7U0 GTF3C5 General transcription factor 3C polypeptide 5 0 ;; 172.24 2.79E-09 1003830000 222646 253332 210289 237736 243366 242475 259609 253929 260696 292043 FALSE TRUE 213944.7482 246107.2194 248292.9002 250005.5835 251194.0884 247378.0106 262786.1726 248685.2774 231102.883 272262.6675 0.785802733 0.903933035 0.911960874 0.918251429 0.922616717 0.908600554 0.965193557 0.913402046 0.848823253 1 18.05463965 4.811098436 2.392575385 0.92170635 0.73703935 0.551502879 0.037015336 0.540324614 3.161232949 0.008645967 0.221541146 64728.93114 -4.811098436 -0.184667 GYT(ph)SDSEVYTDHGRPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GYTSDSEVYTDHGRPGK 17 1 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GYT(0.5)S(0.5)DSEVYTDHGRPGK;GYT(0.499)S(0.499)DS(0.001)EVYTDHGRPGK 176.11 1.68E-09 9840300000 5285400 5460300 4665500 5001300 5660900 5425500 5648200 5792300 6010800 6026900 TRUE FALSE 5078840.725 5304577.59 5508659.633 5259417.692 5842987.99 5535207.327 5717324.361 5672686.981 5328479.183 5618692.695 0.90391858 0.944094628 0.980416608 0.936057189 1.039919481 0.985141496 1.017554202 1.00960976 0.94834857 1 22.42180307 4.811412032 0.727231491 0.999557256 0.838548345 0.50615536 0.028278043 2.398519567 0.897270901 0.010575666 0.325044445 64775.68758 -4.811412032 -0.161008911 LKESHWEENR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKESHWEENR 10 1 F8VXG7;Q99590-2;Q99590 F8VXG7 SCAF11 Protein SCAF11 0 ; 58.37 0.067019 196840000 162468 200683 161544 234646 208897 176708 210417 209689 182239 213981 FALSE TRUE 156118.5709 194959.7173 190738.5943 246756.1082 215616.3617 180281.1568 212992.1462 205358.8489 161551.9927 199487.8763 0.782596787 0.977301082 0.956141285 1.236947893 1.080849452 0.903719866 1.06769469 1.029430223 0.809833639 1 17.60594154 4.811690687 1.989726058 1.021356498 0.682712189 0.28423898 0.107298116 1.205183362 4.377390046 0.027536939 0.792712924 64817.26285 -4.811690687 -0.338644309 DHAY(ph)ALAVSSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 DHAYALAVSSTK 12 0 Q9NWU1;Q9NWU1-2 Q9NWU1 OXSM "3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial" 1 DHAY(0.975)ALAVS(0.024)STK 70.488 0.049829 0 46588 71190 51005 99229 78723 80975 70849 78640 51999 72279 TRUE FALSE 44767.28945 69159.7309 60222.7381 104350.2206 81255.19679 82612.36998 71716.07126 77016.05652 46096.29152 67383.47895 0.664365957 1.026360348 0.893731506 1.54860245 1.205862298 1.226003336 1.064297546 1.142951621 0.684088923 1 16.0401073 4.811801977 1.557118039 1.126583847 0.444167292 0.264830949 0.213944928 1.679039156 3.348741528 0.056669287 1.84101518 64833.87468 -4.811801977 -0.682416555 LSSCDSFTSTINELNHCLSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSCDSFTSTINELNHCLSLR 21 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 314.58 1.20E-66 1131130000 608810 661510 618040 634820 717100 763760 741390 712620 811320 776940 FALSE TRUE 585017.0321 642644.3825 729733.5762 667583.1363 740166.1728 779203.7505 750463.3526 697904.148 719222.3549 724317.1618 0.807680755 0.88724169 1.00747796 0.921672399 1.021881314 1.07577701 1.03609771 0.963533911 0.992966055 1 19.46626203 4.81184594 0.982703619 1.008573755 0.669891668 0.725637838 0.039418802 1.209344547 0.848836309 0.013053364 0.448832626 64840.43808 -4.81184594 -0.338682087 IVRPWAEGTEEGAR ddPTM_BT-474_Pertuzumab_2h_R1 3 IVRPWAEGTEEGAR 14 1 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 ;; 243.92 1.34E-17 1047520000 498650 606130 514440 655040 534370 632780 654320 638710 651260 734290 FALSE TRUE 479162.2067 588843.7659 607410.7517 688846.6929 551558.4964 645575.2452 662327.7639 625520.4153 577331.6951 684555.8843 0.699960687 0.860183631 0.887306304 1.006268018 0.805717267 0.943057039 0.967529137 0.913760921 0.843366785 1 19.3848088 4.812058979 1.691696968 0.920659657 0.594279364 0.553191795 0.060242612 0.840530281 2.044002014 0.014987429 0.47068629 64872.25275 -4.812058979 -0.326380293 SAVADKHELLSLASSNHLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SAVADKHELLSLASSNHLGK 20 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 255.6 2.37E-36 1001470000 1280440 1701110 1359630 1822730 1541950 1924140 1742690 1318440 1882490 2128710 FALSE TRUE 1230398.989 1652596.008 1605345.386 1916801.314 1591548.222 1963047.429 1764017.562 1291213.753 1668797.627 1984530.576 0.619994977 0.832739001 0.80892953 0.965871394 0.801977174 0.989174696 0.888884043 0.650639385 0.840902956 1 20.92036636 4.8135326 2.596539416 0.851571348 0.542836169 0.34346248 0.100162803 0.898334409 6.487918606 0.026261486 0.653449951 65092.74697 -4.8135326 -0.308735179 (ac)ADVLDLHEAGGEDFAMDEDGDES(ph)IHKLK ddPTM_BT-474_Pertuzumab_2h_R1 4 ADVLDLHEAGGEDFAMDEDGDESIHKLK 28 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK 186.07 8.13E-83 219401000 300933 200010 152113 83565 167112 155788 110205 164436 122161 110500 TRUE FALSE 289172.2057 194305.9106 179603.2028 87877.79966 172487.3092 158938.1401 111553.7218 161040.3391 108293.7954 103015.7366 2.807068272 1.886176977 1.743454047 0.85305219 1.674378255 1.542853018 1.082880397 1.5632596 1.051235462 1 16.65250521 4.813829222 1.212283878 1.309471294 3.671368887 0.743043426 0.277312938 0.845618582 0.941785671 0.075148294 2.618308978 65137.22035 -4.813829222 2.361897593 up RNS(ph)CNVGGGGGGFK ddPTM_BT-474_Pertuzumab_2h_R1 4 RNSCNVGGGGGGFK 14 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RNS(1)CNVGGGGGGFK;RNS(1)CNVGGGGGGFK;RNS(1)CNVGGGGGGFK;RNS(1)CNVGGGGGGFK 208.37 4.98E-09 6147400000 9436300 7525500 5854600 6152100 5643100 4102380 4905100 9469000 6357000 6135700 TRUE FALSE 9067518.964 7310880.108 6912656.455 6469610.618 5824615.436 4185332.934 4965130.081 9273461.841 5635380.011 5720123.574 1.585196342 1.278098281 1.208480265 1.131026373 1.018267413 0.731685755 0.868010982 1.621199563 0.985185012 1 22.44761488 4.813879581 1.170401076 1.085685517 1.87388316 0.352724722 0.220713125 2.509206356 2.581966371 0.072046828 2.517427285 65144.77385 -4.813879581 0.788197643 KPDHVPISSEDER ddPTM_BT-474_Pertuzumab_2h_R1 3 KPDHVPISSEDER 13 1 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ;; 153.09 2.96E-05 4551500000 3139090 3439970 2926570 3360120 3267800 3467000 3613900 3443060 3843000 3897500 FALSE TRUE 3016410.892 3341865.424 3455466.3 3533536.196 3372911.755 3537105.115 3658127.989 3371959.608 3406758.751 3633518.853 0.830162444 0.919732512 0.950997212 0.972483242 0.928276938 0.973465464 1.006772811 0.928014892 0.937592149 1 21.79293596 4.814078502 1.599164525 0.960798611 0.763988184 0.709548248 0.025785118 0.685092706 1.449687135 0.006820125 0.221632412 65174.61914 -4.814078502 -0.196810427 TSS(ph)KSEAGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSKSEAGAR 10 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 T(0.074)S(0.075)S(0.801)KS(0.05)EAGAR 103.14 0.0075094 158290000 512170 408650 332140 301980 320080 338530 386470 424900 400210 399000 TRUE FALSE 492153.8302 396995.7021 392165.0864 317565.224 330375.6639 345375.3085 391199.7355 416125.6665 354779.8386 371975.3746 1.323081752 1.067263398 1.054277012 0.853726471 0.888165418 0.928489712 1.051681811 1.118691437 0.953772381 1 18.50484759 4.814921985 1.751383021 0.985365829 1.481414992 0.652315337 0.07552219 0.829312727 2.181223592 0.023175771 0.726742085 65301.32369 -4.814921985 0.496049163 GAEDDELEEEADWIYR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAEDDELEEEADWIYR 16 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 264.72 1.15E-26 468660000 257441 289981 242780 294641 291423 298260 297509 292180 331700 331710 FALSE TRUE 247379.9211 281711.0258 286655.7466 309847.4573 300796.8855 304291.0216 301150.0041 286146.3809 294046.8066 309242.9862 0.799953215 0.910969814 0.926959573 1.00195468 0.972687818 0.983986816 0.973829699 0.925312436 0.950860067 1 18.23838135 4.814984314 1.37701582 0.966710295 0.709683167 0.828113132 0.023573281 0.638620279 0.949640985 0.006986974 0.239282529 65310.69626 -4.814984314 -0.257027128 RGAAAADLLS(ph)SSPESQHGGTQSPGGGQPLLQPTK ddPTM_BT-474_Pertuzumab_2h_R1 3 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.191)S(0.191)S(0.191)PES(0.191)QHGGT(0.191)QS(0.047)PGGGQPLLQPTK;RGAAAADLLS(0.406)S(0.294)S(0.294)PES(0.005)QHGGT(0.001)QSPGGGQPLLQPTK;RGAAAADLLS(0.363)S(0.299)S(0.247)PES(0.082)QHGGT(0.007)QS(0.001)PGGGQPLLQPTK 147.03 9.21E-11 1570160000 459026 544340 458599 598247 503840 612900 591752 540762 655023 699726 TRUE FALSE 441086.7564 528815.9562 541478.0408 629122.5994 520046.4712 625293.2579 598994.038 529595.0757 580667.5351 652332.9348 0.676168154 0.810653468 0.830063932 0.964419495 0.797210203 0.958549269 0.918233629 0.811847827 0.890139841 1 19.31524894 4.816538056 1.232737107 0.891800636 0.551845779 0.549495416 0.062810992 1.331978529 1.534243698 0.017155711 0.602846309 65544.7719 -4.816538056 -0.339954857 DMTGLPHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DMTGLPHNR 9 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 0 ; 92.491 0.01004 559480000 732800 808020 639930 809860 803990 790070 871470 801580 861270 896360 FALSE TRUE 704161.3658 784976.0607 755579.5862 851656.9717 829851.0685 806045.7567 882135.3105 785027.0929 763502.2403 835648.7388 0.842652341 0.93936127 0.904183242 1.019156653 0.993062073 0.96457485 1.055629321 0.939422339 0.913664085 1 19.67253711 4.817597 1.041101011 0.980631215 0.765239644 0.48753929 0.042448268 1.832043209 1.447298547 0.012906935 0.455539842 65704.78524 -4.817597 -0.21539157 IS(ph)APNVDFNLEGPK ddPTM_BT-474_Pertuzumab_2h_R1 5 ISAPNVDFNLEGPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK 258.13 2.38E-24 2217670000 4164819 3395875 2760144 2754135 2405830 3027724 2858236 3921932 3863415 3292172 TRUE FALSE 4002053.269 3299027.97 3258963.42 2896276.237 2483215.707 3088946.654 2893215.947 3840942.734 3424856.326 3069190.258 1.303944341 1.074885456 1.061831671 0.943661355 0.809078453 1.006437006 0.942664255 1.251451494 1.115882705 1 21.54942665 4.818171004 2.046215056 1.022948204 1.423821518 0.378652863 0.110195323 1.187851318 4.560815315 0.032225368 0.949841913 65791.68423 -4.818171004 0.400873314 ERKS(ph)ESDKDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 ERKSESDKDVK 11 3 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 ERKS(0.965)ES(0.035)DKDVK;ERKS(0.878)ES(0.122)DKDVK;ERKS(0.792)ES(0.208)DKDVK 114.69 0.0067607 3646590000 4066610 2646310 2202520 1593830 2386910 2093410 2231370 2770080 3229110 2467460 TRUE FALSE 3907682.385 2570839.83 2600564.359 1676087.757 2463687.128 2135740.185 2258678.174 2712876.88 2862554.97 2300336.736 1.698743633 1.117592824 1.130514641 0.728627131 1.071011513 0.928446758 0.981890233 1.179339023 1.244406927 1 21.13341364 4.81880277 2.31777074 1.031686451 1.95541978 0.681093432 0.13581113 0.48422631 2.553169894 0.035421681 0.978277358 65887.46064 -4.81880277 0.923733329 LGEMWNNTAADDKQPYEKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LGEMWNNTAADDKQPYEKK 19 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 277.11 9.59E-40 4226000000 4725800 3710700 3158800 2195440 3227300 3231330 3308200 4028400 4594900 3527000 FALSE TRUE 4541110.511 3604874.469 3729665.427 2308746.922 3331109.035 3296669.707 3348686.741 3945212.132 4073306.215 3288113.148 1.381068809 1.096335286 1.134287434 0.702149475 1.013076158 1.00260227 1.018421992 1.199840746 1.23879746 1 21.64882851 4.818926885 2.050925937 1.03974482 1.525620877 0.354320769 0.138444635 1.151396495 4.438604517 0.037819631 1.1185916 65906.29309 -4.818926885 0.485876057 SWVIGS(ph)PEILR ddPTM_BT-474_Pertuzumab_2h_R1 4 SWVIGSPEILR 11 0 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;E7ERL6 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 SWVIGS(1)PEILR;SWVIGS(1)PEILR;SWVIGS(1)PEILR;SWVIGS(1)PEILR 170 1.70E-05 610310000 525978 599710 499893 606520 576097 562470 603790 646040 624750 642530 TRUE FALSE 505422.1983 582606.858 590234.7852 637822.5699 594627.6832 573843.5288 611179.3626 632699.0482 553830.9992 599010.8708 0.843761312 0.972614833 0.985349038 1.06479298 0.992682624 0.957985166 1.020314309 1.056239676 0.924575874 1 19.19222266 4.818998567 1.944164377 1.006656419 0.771042181 0.578750936 0.03966859 0.68446231 2.307591096 0.010174263 0.309735691 65917.17195 -4.818998567 -0.235614237 ILTEAEIDAHLVALAERD ddPTM_BT-474_Pertuzumab_2h_R1 17 ILTEAEIDAHLVALAERD 18 1 G3V5Z7;P60900;P60900-2;P60900-3;H0YJC4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;;;;;;;;;;;;;;; 266.23 6.43E-31 3315043500 2115792.7 2340613.5 1935015.3 2351799.3 2340466.6 2427676.6 2405949.3 2231966.2 2412200.1 2523009.3 FALSE TRUE 2033105.182 2273861.495 2284715.609 2473175.944 2415749.834 2476765.884 2435394.027 2185875.318 2138377.257 2352123.633 0.864370033 0.96672703 0.971341632 1.051465114 1.027050534 1.052991369 1.035402218 0.929319908 0.909126216 1 21.16553246 4.81976911 1.766729257 0.998300324 0.800613206 0.429382917 0.046150112 1.222904905 3.252824921 0.013470492 0.431605509 66034.22878 -4.81976911 -0.197687118 WLPYEAGQR ddPTM_BT-474_Pertuzumab_2h_R1 2 WLPYEAGQR 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 138.54 0.00031079 441470000 555560 620700 511480 629280 614370 676600 623400 623050 728790 675230 FALSE TRUE 533848.101 602998.2437 603915.8138 661757.2162 634131.769 690281.3156 631029.3557 610183.7998 646060.8145 629496.0707 0.848056288 0.957906287 0.959363913 1.051249161 1.007364142 1.096561754 1.002435734 0.969321062 1.026314293 1 19.26383785 4.82070267 1.184206352 1.017707731 0.749918329 0.689803035 0.035000193 1.105768713 1.156427763 0.010668579 0.381988194 66176.32871 -4.82070267 -0.267789401 DTLENTIGHR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTLENTIGHR 10 0 H3BS70;Q96DC0;P42126-2;P42126 H3BS70 ECI1;DCI "Enoyl-CoA delta isomerase 1, mitochondrial" 0 ;;; 169.58 4.59E-06 1414800000 566660 801620 613430 1163110 578560 698120 1025780 851940 740480 645810 FALSE TRUE 544514.3007 778758.5825 724290.4467 1223138.246 597169.9078 712236.4647 1038333.802 834347.1413 656423.8147 602068.7135 0.904405575 1.293471268 1.203002964 2.031559221 0.991863378 1.182982023 1.72461013 1.385800528 1.090280561 1 19.19956862 4.820831972 2.018350614 1.368119271 0.704705499 0.129377482 0.313339358 1.77449795 6.541407881 0.077180001 2.329663388 66196.03424 -4.820831972 -0.663413772 HFVGMLPEKDCR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFVGMLPEKDCR 12 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 149.23 4.03E-05 5491000000 9185800 9205100 5320800 5801300 6465500 5587900 6874200 4019800 6794900 6344600 FALSE TRUE 8826808.781 8942579.561 6282386.921 6100705.788 6673468.679 5700891.167 6958328.516 3936789.725 6023571.439 5914874.591 1.492307004 1.511879825 1.062133579 1.031417606 1.128251931 0.96382283 1.176411843 0.665574505 1.018376864 1 22.49591615 4.820959061 0.580007165 0.924564456 2.055842343 0.639718027 0.142042072 2.416529103 0.57740698 0.071351861 1.8823478 66215.40832 -4.820959061 1.131277887 SPSHSSSNRPFT(ph)PPTSTGGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSHSSSNRPFTPPTSTGGSK 21 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SPSHSSSNRPFT(0.999)PPTSTGGSK;SPSHSS(0.003)S(0.002)NRPFT(0.994)PPTSTGGSK 176.61 2.67E-13 1041590000 213154 394850 340890 488550 342330 497340 453130 385790 375650 577430 TRUE FALSE 204823.706 383589.2646 402496.4061 513764.124 353341.3553 507396.5556 458675.5405 377823.3017 333007.7869 538320.1518 0.380486789 0.712567165 0.74768965 0.954383971 0.656377723 0.942555381 0.852049731 0.701856136 0.618605463 1 19.03810491 4.82102148 1.93514536 0.80091008 0.190255213 0.521212837 0.123316737 0.806994091 2.677214781 0.030593497 0.944746951 66224.92576 -4.82102148 -0.610654867 TYT(ph)HEVVTLWYR ddPTM_BT-474_Pertuzumab_2h_R1 4 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 T(0.002)YT(0.998)HEVVTLWYR;T(0.039)YT(0.961)HEVVTLWYR;T(0.002)YT(0.998)HEVVT(0.001)LWYR;T(0.214)YT(0.786)HEVVTLWYR 214.47 1.61E-10 1761754000 1762997 1558019 983348 887373 1123490 559665 771456 845653 753900 712362 TRUE FALSE 1694097.128 1513585.824 1161060.858 933170.4269 1159628.076 570981.8098 780897.3093 828189.97 668320.4326 664113.0872 2.550916645 2.279108562 1.748287875 1.405137837 1.746130438 0.859765936 1.175849903 1.247061662 1.006335285 1 19.3410694 4.821583727 0.498809157 1.052169302 3.853063356 0.878718835 0.188034279 1.517982595 0.274008675 0.11254915 2.552573223 66310.7175 -4.821583727 2.800894054 up TANKDHLVTAYNHLFETK ddPTM_BT-474_Pertuzumab_2h_R1 2 TANKDHLVTAYNHLFETK 18 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 231.42 5.16E-20 4262200000 8139900 7210300 5953100 5627900 6658900 7121000 6772400 4953600 9032100 7491500 FALSE TRUE 7821783.709 7004669.304 7028957.596 5918356.593 6873089.566 7264991.499 6855282.657 4851306.429 8006813.874 6984094.032 1.119942497 1.002946019 1.006423677 0.847405056 0.984106104 1.0402196 0.981556466 0.694622152 1.146435577 1 22.73564155 4.822449093 1.177479084 0.935697807 1.228706312 0.122721307 0.115293634 3.277975362 3.376043221 0.034240419 1.234182925 66442.97853 -4.822449093 0.293008505 GVYSST(ph)NELT(ph)T(ph)DSTPKKTQAHTQQNMVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GVYSSTNELTTDSTPKKTQAHTQQNMVEK 29 2 O75113 O75113 N4BP1 NEDD4-binding protein 1 3 GVY(0.012)S(0.013)S(0.138)T(0.453)NELT(0.453)T(0.453)DS(0.453)T(0.453)PKKT(0.453)QAHT(0.118)QQNMVEK 46.66 0.042724 193040000 10802 13134 11163 13641 12158 14971 15208 12498 13348 13808 TRUE FALSE 10379.8459 12759.43118 13180.40242 14345.01364 12549.07311 15273.72388 15394.12005 12239.91193 11832.791 12872.77186 0.806341168 0.991195317 1.023897771 1.114368669 0.974853998 1.186513988 1.195866766 0.950837323 0.919210806 1 13.65203512 4.823547282 1.775943609 1.052313079 0.686524637 0.392625696 0.089301977 1.207326739 3.226731123 0.024340736 0.793995136 66611.20379 -4.823547282 -0.365788443 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHK ddPTM_BT-474_Pertuzumab_2h_R1 4 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHK 32 2 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHK;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHK;MEFDLGAALEPTS(0.002)QKPGVGAGHGGDPKLS(0.998)PHK;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(0.999)PHK 162.23 1.83E-59 7621590000 4659490 3867120 3202310 2834220 3780200 3544320 3809250 2885830 5056480 4501740 TRUE FALSE 4477391.979 3756833.524 3781038.652 2980494.434 3901793.566 3615988.579 3855868.741 2826236.602 4482489.589 4196833.14 1.06685013 0.895159135 0.90092661 0.710177015 0.929699475 0.86159932 0.918756742 0.673421246 1.068064762 1 22.00086967 4.824026296 2.026620245 0.858447829 1.158700448 0.163798762 0.114260205 1.422291797 5.257319859 0.027670005 0.850106525 66684.71443 -4.824026296 0.300252619 GDFIALDLGGSSFR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDFIALDLGGSSFR 14 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;;; 158.02 1.20E-05 303303000 508323 590873 476860 639192 560427 540689 599052 616011 586385 565121 FALSE TRUE 488457.1752 574021.8806 563039.2097 672180.7757 578453.6434 551622.102 606383.3776 603290.1576 519821.0331 526844.8513 0.927136659 1.089546342 1.068700222 1.275860956 1.097958236 1.047029501 1.150971441 1.145100225 0.986668147 1 19.00701864 4.824118395 2.32072432 1.110530671 0.854812598 0.274327912 0.079789567 0.988636625 5.154929217 0.019390646 0.556329506 66698.85746 -4.824118395 -0.255718073 NNS(ph)PPTVGAFGHTR ddPTM_BT-474_Pertuzumab_2h_R1 3 NNSPPTVGAFGHTR 14 0 Q86XL3;F5H1D4;Q86XL3-3 Q86XL3 ANKLE2 Ankyrin repeat and LEM domain-containing protein 2 1 NNS(0.988)PPT(0.012)VGAFGHTR;NNS(0.884)PPT(0.116)VGAFGHTR;NNS(0.966)PPT(0.034)VGAFGHTR 142.88 5.98E-06 814510000 617730 668090 554240 685430 606310 647500 687080 700520 760250 737760 TRUE FALSE 593588.4287 649036.7273 654403.497 720805.1244 625812.5118 660592.8936 695488.6906 686054.0172 673949.6072 687790.8581 0.863036229 0.943654193 0.951457103 1.048000444 0.909887802 0.960456054 1.011192112 0.997474754 0.979875785 1 19.39161041 4.824789723 1.356950652 0.984867951 0.794047179 0.530512606 0.034664695 1.233487029 1.744467086 0.009526708 0.341007601 66802.03969 -4.824789723 -0.190820773 SEPRPPISS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEPRPPISSPR 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 S(0.001)EPRPPIS(0.346)S(0.653)PR 86.288 0.038361 290120000 161990 219870 175070 247930 205810 219400 209850 222650 231110 220530 TRUE FALSE 155659.2517 213599.5229 206709.0434 260725.697 212430.0656 223836.4183 212418.2071 218052.1997 204875.3617 205593.3067 0.757122176 1.038942008 1.005426912 1.26816238 1.033253801 1.088733977 1.033196122 1.060599702 0.996507936 1 17.64943377 4.826205329 2.430065842 1.067916633 0.637974458 0.589252038 0.075360066 0.531004579 3.100566902 0.018252357 0.520339661 67020.13974 -4.826205329 -0.429942175 DVSPFDHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVSPFDHSR 9 0 P18031 P18031 PTPN1 Tyrosine-protein phosphatase non-receptor type 1 0 129.85 0.00037767 163820000 242500 397230 311160 559930 367960 423510 416180 453410 396180 366830 FALSE TRUE 233022.8319 385901.3893 367393.5337 588828.0544 379795.7676 432073.6624 421273.3353 444046.9251 351207.3073 341984.2774 0.681384635 1.128418512 1.074299487 1.721798613 1.110564996 1.263431365 1.23185001 1.298442515 1.026969164 1 18.38357047 4.826656517 1.789764609 1.246152243 0.409155944 0.396481351 0.195517743 1.047516834 2.834166355 0.048083419 1.589816184 67089.80304 -4.826656517 -0.836996299 LVSFHDDSDEDLLHI ddPTM_BT-474_Pertuzumab_2h_R1 3 LVSFHDDSDEDLLHI 15 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 ;; 184.1 4.78E-07 51341000 38365 74766.5 64308 96259.9 79689.6 117404 109751.5 31193.2 100302 98443.1 FALSE TRUE 36865.65339 72634.23262 75929.88612 101227.885 82252.88836 119777.9893 111094.6717 30549.04952 88916.13746 91775.46115 0.401694014 0.791434134 0.827344098 1.102995111 0.896240534 1.305119994 1.210505186 0.332867295 0.968844355 1 16.48582084 4.827043608 1.629988261 0.932218932 0.127624958 0.312061348 0.248944327 1.852015072 4.000248231 0.073029434 2.510060747 67149.6276 -4.827043608 -0.804593974 TVSS(ph)PIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 T(0.002)VS(0.123)S(0.875)PIPYT(0.003)PS(0.041)PS(0.102)S(0.083)S(0.068)RPIS(0.702)PGLSYASHTVGFTPPTSLTR;T(0.003)VS(0.113)S(0.884)PIPYTPS(0.001)PS(0.004)S(0.014)S(0.012)RPIS(0.968)PGLSYASHTVGFTPPTSLTR 246.45 1.92E-50 5945600000 1049710 1414400 1171560 1585630 1553050 1677740 1497500 1526010 1659000 1471850 TRUE FALSE 1008686.173 1374062.697 1383286.953 1667464.554 1603005.264 1711665.052 1515826.853 1494497.36 1470677.275 1372160.289 0.735108122 1.001386433 1.008108867 1.215211203 1.168234701 1.247423546 1.104701007 1.089156546 1.071796996 1 20.38801759 4.827315073 1.292372456 1.130429779 0.509042412 0.714503971 0.073463252 0.877568342 1.10604406 0.020845448 0.75975817 67191.61396 -4.827315073 -0.621387367 TRHS(ph)PT(ph)PQQSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 TRHS(1)PT(0.999)PQQS(0.001)NR;TRHS(1)PT(1)PQQSNR 125.39 0.00070153 3317000000 2652860 2238080 1537730 1235060 1323670 1393490 850300 1213870 1160390 1096220 TRUE FALSE 2549183.298 2174252.15 1815632.018 1298801.595 1366247.048 1421667.323 860706.2258 1188803.16 1028667.392 1021972.043 2.494376745 2.127506486 1.776596562 1.270877813 1.336873212 1.39110197 0.842201342 1.163244306 1.006551401 1 19.9629243 4.82831018 0.533166328 1.017496423 3.740412084 0.933066553 0.130765704 1.014205943 0.205911349 0.0716328 1.763969012 67345.74792 -4.82831018 2.722915662 up IQEQES(ph)S(ph)GEEDSDLSPEER ddPTM_BT-474_Pertuzumab_2h_R1 2 IQEQESSGEEDSDLSPEER 19 0 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 2 IQEQES(0.999)S(0.993)GEEDS(0.008)DLSPEER;IQEQES(1)S(1)GEEDSDLSPEER 282.1 1.45E-39 2408200000 591800 655760 539270 665740 656200 622940 650120 700280 654850 669510 TRUE FALSE 568671.8017 637058.3669 636728.085 700098.9212 677307.2689 635536.2736 658076.363 685818.9733 580514.1734 624163.4914 0.911094304 1.020659452 1.020130292 1.121659518 1.085144002 1.018220839 1.054333315 1.098780981 0.930067493 1 19.25156445 4.828800625 1.789008616 1.051567715 0.842248192 0.341610364 0.052556998 1.16576025 3.136565602 0.013242124 0.443076098 67421.84372 -4.828800625 -0.209319523 YLS(ph)FTPPEK ddPTM_BT-474_Pertuzumab_2h_R1 4 YLSFTPPEK 9 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.875)FT(0.125)PPEK;YLS(0.953)FT(0.047)PPEK;YLS(0.993)FT(0.007)PPEK;YLS(1)FTPPEK 215.72 6.60E-07 1485320000 5149620 3467980 2499070 2765550 2584530 2181820 2224410 3829090 3511200 2997840 TRUE FALSE 4948367.157 3369076.606 2950707.541 2908280.367 2667663.755 2225937.895 2251632.995 3750017.953 3112623.296 2794793.627 1.770566209 1.205483143 1.055787273 1.040606483 0.954511893 0.79645877 0.805652687 1.341787071 1.113722053 1 21.41431032 4.830136438 1.799902335 1.019426261 2.145636627 0.708671452 0.146245625 0.703255022 1.91472559 0.043022562 1.446511798 67629.54072 -4.830136438 1.126210366 SQEEPKDT(ph)FEHDPSESIDEFNK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQEEPKDTFEHDPSESIDEFNK 22 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.005)QEEPKDT(0.995)FEHDPSESIDEFNK 135.26 1.02E-05 332810000 474040 371060 301370 274680 311440 285910 314410 372140 459960 392600 TRUE FALSE 455513.9927 360477.7321 355834.2629 288856.2677 321457.7504 291691.2961 318257.8436 364455.179 407747.2691 366008.8523 1.244543649 0.984888015 0.972201248 0.789205687 0.878278622 0.796951479 0.869535919 0.995755094 1.114036632 1 18.48151902 4.83141628 1.866624834 0.916270135 1.403647709 0.502087516 0.094340967 0.938404852 2.783540242 0.025790183 0.860283205 67829.13521 -4.83141628 0.487377574 KGPST(ph)PYTK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGPSTPYTK 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 KGPS(0.131)T(0.868)PYTK 89.44 0.0070938 1382700000 7806000 4561000 3131900 2966200 3124100 2338900 2428500 6626600 2167100 1764900 TRUE FALSE 7500932.89 4430924.746 3697903.999 3119285.937 3224589.514 2386194.161 2458220.709 6489758.394 1921099.893 1645361.751 4.558835092 2.692979063 2.247471716 1.895805549 1.959805807 1.450255033 1.494030543 3.944274498 1.167585117 1 20.64997338 4.831757291 1.745899888 2.051470118 5.841669488 0.506543739 0.786998489 1.090161341 2.748413552 0.214875254 7.377065414 67882.41602 -4.831757291 3.79019937 S(ph)RDKEER ddPTM_BT-474_Pertuzumab_2h_R1 5 SRDKEER 7 2 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 S(1)RDKEER;S(1)RDKEER;S(1)RDKEER;S(1)RDKEER;S(1)RDKEER 85.958 0.016089 5504840000 13185460 10335700 8321420 8227100 8974450 8880730 10074370 10037950 9695790 11068750 TRUE FALSE 12670157.65 10040935.96 9825285.703 8651701.617 9263121.335 9060304.445 10197663.15 9830662.825 8595164.567 10319053.7 1.227841041 0.973048134 0.952149876 0.838420059 0.897671589 0.878016987 0.988236271 0.952670963 0.832941161 1 23.29880734 4.83229655 2.012584921 0.916133835 1.372396967 0.745258812 0.054267315 0.494252381 1.760618568 0.013858652 0.44984759 67966.75728 -4.83229655 0.456263132 SFEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFEELR 6 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;H3BN59;H3BTB3;H3BMQ5 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ; 140.72 0.027321 1186530000 1484280 1721200 1378400 1838300 1671380 1520160 1843570 1652400 1671400 1816380 FALSE TRUE 1426272.697 1672113.061 1627507.542 1933174.883 1725141.456 1550898.677 1866132.161 1618277.363 1481669.679 1693354.965 0.842276266 0.987455729 0.961114224 1.141624127 1.01877131 0.915873346 1.102032474 0.9556634 0.874990601 1 20.691453 4.832766689 2.417711371 1.000632727 0.779066153 0.268199797 0.075565651 1.114098859 6.29741636 0.018755607 0.564355296 68040.37344 -4.832766689 -0.221566574 AAFFVTLDETEEGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAFFVTLDETEEGYR 15 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 184.03 3.00E-11 0 14900 33734 21047 52483 31446 33333 39569 48100 34332 41180 FALSE TRUE 14317.69153 32771.93935 24850.66109 55191.65392 32457.48915 34007.0161 40053.25726 47106.71819 30434.77529 38390.84192 0.372945495 0.853639506 0.64730701 1.437625516 0.845448746 0.885810636 1.043302393 1.227030089 0.79276134 1 15.22847458 4.833194259 1.113451521 1.031855885 1.09E-11 0.451393744 0.207373274 1.740752865 1.55963536 0.059105165 2.212605751 68107.39329 -4.833194259 -1.031855885 TLHPDLGTDKDKEQWK ddPTM_BT-474_Pertuzumab_2h_R1 3 TLHPDLGTDKDKEQWK 16 2 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 203.53 1.55E-11 8081950000 8277900 6391440 5316690 4223590 5387390 5228890 5644580 6485860 7552000 4884470 FALSE TRUE 7954390.516 6209162.389 6277534.152 4441569.986 5560680.292 5334621.738 5713660.059 6351924.724 6694728.621 4553640.496 1.746820049 1.363560078 1.378574825 0.97538881 1.221150483 1.171507005 1.25474553 1.394911331 1.470192613 1 22.11858897 4.833235198 1.654459183 1.242638167 2.009340808 0.517687406 0.150229372 1.092014368 2.413967667 0.04064514 1.433744488 68113.81381 -4.833235198 0.766702642 ILESITVSSLMAT(ph)PQDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILESITVSSLMATPQDPK 18 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 ILESITVSSLMAT(1)PQDPK;ILESITVSSLMAT(1)PQDPK 248.97 1.56E-23 261770000 221420 187767 145907 161780 146736 153883 161515 198456 164706 182907 TRUE FALSE 212766.6616 182412.069 172275.6406 170129.4852 151455.8967 156994.6197 163491.6689 194357.8142 146009.2654 170518.546 1.247762584 1.069749146 1.010304419 0.997718367 0.888207766 0.920689411 0.958791127 1.139804548 0.856266188 1 17.37956913 4.833249709 1.412680251 0.977182695 1.404144433 0.575296051 0.073226609 1.22808054 1.877556588 0.021439927 0.789477238 68116.08974 -4.833249709 0.426961738 DGAHVVISSR ddPTM_BT-474_Pertuzumab_2h_R1 8 DGAHVVISSR 10 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;;;;; 167.1 5.35E-06 14915250000 3355035 4879717 3406941 7601000 3522541 4479440 6389999 4824143 4379086 4402397 FALSE TRUE 3223916.523 4740552.249 4022651.026 7993288.521 3635846.73 4570017.346 6468201.719 4724522.761 3881990.516 4104218.73 0.785512843 1.155043764 0.980125888 1.947578588 0.885880351 1.113492639 1.575988549 1.151138151 0.945853711 1 21.96867619 4.833400943 1.705026078 1.232442544 0.563304054 0.133403571 0.310767719 2.331420446 5.534717775 0.078336408 2.736868524 68139.81392 -4.833400943 -0.669138491 MGPGIDR ddPTM_BT-474_Pertuzumab_2h_R1 3 MGPGIDR 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 100.67 0.022387 1329380000 1284970 1397720 1141400 1415750 1326070 1399970 1382430 1405730 1351750 1480290 FALSE TRUE 1234751.952 1357858.394 1347676.37 1488817.027 1368724.246 1428278.353 1399348.592 1376701.184 1198305.007 1380028.64 0.894729222 0.983934938 0.976556813 1.078830529 0.99180858 1.034962834 1.013999675 0.99758885 0.868318941 1 20.39626678 4.833668739 2.07462879 1.000140704 0.846916581 0.256565533 0.050569697 1.304249737 4.993291407 0.012640344 0.408458703 68181.84341 -4.833668739 -0.153224122 RCPT(ph)PEIQK ddPTM_BT-474_Pertuzumab_2h_R1 4 RCPTPEIQK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RCPT(1)PEIQK;RCPT(1)PEIQK;RCPT(1)PEIQK;RCPT(1)PEIQK 138.89 7.25E-05 2529590000 2920920 2964040 2747120 3104130 3114770 3037630 3409430 3784360 4010240 4029160 TRUE FALSE 2806767.217 2879508.481 3243585.693 3264334.521 3214959.406 3099052.96 3451155.624 3706211.644 3555014.367 3756261.404 0.747223613 0.766588949 0.863514368 0.869038166 0.855893416 0.825036553 0.918774082 0.986675645 0.94642358 1 21.84086604 4.835081937 0.20198395 1.033225272 0.496814504 0.828705776 0.033658538 6.239387613 0.229401898 0.081875643 0.860864599 68404.06912 -4.835081937 -0.536410768 DFQYIDR ddPTM_BT-474_Pertuzumab_2h_R1 3 DFQYIDR 7 0 Q9H201;I6L9I8;Q9H201-2;D6RFG3;D6REL6;I3L2B2;O95208-3;O95208-2;F6PQP6;O95208;E9PBC1 Q9H201;I3L2B2 EPN3;EPN2 Epsin-3;Epsin-2 0 ;; 166.68 0.0025927 2770680000 1751150 1985294 1675923 2015438 2062756 2085492 2015409 2227622 2181410 2300946 FALSE TRUE 1682713.122 1928675.359 1978799.567 2119454.997 2129106.42 2127662.077 2040074.178 2181620.827 1933785.482 2145100.878 0.78444475 0.899107067 0.922473897 0.98804444 0.992543727 0.991870405 0.951038806 1.017024817 0.901489297 1 21.03261406 4.835859867 1.070749906 0.980120059 0.658987784 0.773248844 0.031887788 0.881244766 0.722163888 0.008965092 0.337489574 68526.70776 -4.835859867 -0.321132275 TTPPEAAQNGQS(ph)PMAALILVADNAGGSHASK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPPEAAQNGQSPMAALILVADNAGGSHASK 31 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 TTPPEAAQNGQS(1)PMAALILVADNAGGSHASK 118.8 1.65E-05 49924000 24033 28274 20560 32271 25051 27275 30251 28877 27860 34221 TRUE FALSE 23093.76379 27467.6532 24275.64935 33936.51018 25856.78817 27826.51919 30621.22079 28280.67986 24697.4496 31903.18119 0.723870251 0.8609691 0.760916261 1.063734365 0.810476799 0.872217696 0.959817161 0.886453288 0.774137521 1 14.96141267 4.835937595 1.100572416 0.897508133 0.626809917 0.25246602 0.09019538 2.876193032 2.502353029 0.025177295 0.950793915 68538.97336 -4.835937595 -0.270698216 DKQPYEQK ddPTM_BT-474_Pertuzumab_2h_R1 6 DKQPYEQK 8 1 P26583 P26583 HMGB2 High mobility group protein B2 0 ;;;;; 161.76 0.00031522 23708139000 9986076 8417616 7080721 6423958 7376836 6927153 7228311 8973025 8754400 7405433 FALSE TRUE 9595809.11 8177553.833 8360364.794 6755499.242 7614118.629 7067224.78 7316773.232 8787728.898 7760637.213 6903856.427 1.389920143 1.184490715 1.210970257 0.978510969 1.102879052 1.023663347 1.059809588 1.272872487 1.124101768 1 22.71897103 4.836242233 1.356503986 1.102957231 1.553484151 0.532410887 0.084892918 1.442008253 1.999115517 0.025225082 0.94748222 68587.06722 -4.836242233 0.45052692 LASLSSHVTELEEDLDTAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 0 ; 307.21 4.88E-51 147526000 117231 168316 136692 201421 161560 176512 178045 160398 165527 202400 FALSE TRUE 112649.4829 163515.7925 161395.2851 211816.3619 166756.7241 180081.1936 180223.968 157085.7252 146737.0689 188691.2677 0.597004219 0.866578483 0.85534051 1.12255519 0.883754326 0.954369515 0.955126171 0.832501298 0.777656914 1 17.52566813 4.836566333 2.013873781 0.92062372 0.444719429 0.533941071 0.091036888 0.825465137 2.915079543 0.023608326 0.787027697 68638.27059 -4.836566333 -0.475904291 S(ph)PGKAEAESDALPDDTVIESEALPSDIAAEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPGKAEAESDALPDDTVIESEALPSDIAAEAR 32 1 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 S(1)PGKAEAESDALPDDTVIESEALPSDIAAEAR;S(0.99)PGKAEAES(0.01)DALPDDTVIESEALPSDIAAEAR;S(0.981)PGKAEAES(0.019)DALPDDTVIESEALPSDIAAEAR;S(0.996)PGKAEAES(0.004)DALPDDTVIESEALPSDIAAEAR 281.79 6.02E-74 1404846000 982816 800788 637803 605802 755725 690324 697672 818926 708691 653502 TRUE FALSE 944406.4642 777950.3103 753068.19 637067.5138 780033.581 704282.8243 706210.3186 802014.8919 628243.3688 609239.7275 1.550139332 1.276919865 1.236078601 1.04567625 1.280339324 1.156002789 1.159166559 1.316419228 1.031192387 1 19.21665049 4.837039225 1.584410361 1.170613237 1.75850038 0.590422976 0.100268862 0.949871773 1.882018037 0.025413114 0.926018394 68713.04974 -4.837039225 0.587887143 LQQELDDLTVDLDHQR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQQELDDLTVDLDHQR 16 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;;; 337.35 8.31E-72 1697210000 524377 601703 494838 622694 598680 667940 621044 591784 616276 645530 FALSE TRUE 503883.7671 584543.0196 584266.2342 654831.312 617937.0859 681446.2044 628644.5222 579563.4536 546318.9321 601807.6781 0.837283713 0.971312 0.970852077 1.088107274 1.026801599 1.132332187 1.044593722 0.963037653 0.907796547 1 19.19894299 4.838119855 1.48784143 1.022243346 0.733826486 0.452465452 0.059960833 1.421159622 2.427327814 0.01735898 0.646144378 68884.23744 -4.838119855 -0.28841686 DPS(ph)KIK ddPTM_BT-474_Pertuzumab_2h_R1 3 DPSKIK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 DPS(1)KIK;DPS(1)KIK;DPS(1)KIK 67.897 0.059085 2340700000 6508300 4779600 3994210 3462670 4270500 3807600 4339100 5293700 5577700 4030400 TRUE FALSE 6253948.441 4643290.488 4716052.598 3641378.814 4407864.511 3884592.281 4392203.204 5184383.245 4944542.88 3757417.418 1.664427383 1.235766478 1.255131404 0.969117457 1.17311015 1.033846349 1.168942046 1.379773038 1.315941864 1 21.84130997 4.838150978 2.227511441 1.175492926 1.880230448 0.580244791 0.127046635 0.731866308 3.308906889 0.034509068 1.116710888 68889.17415 -4.838150978 0.704737522 SQS(ph)SSQFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSSSQFR 8 0 Q16537-2;Q16537 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 1 S(0.007)QS(0.431)S(0.406)S(0.157)QFR 85.154 0.017774 310750000 1750700 1042300 757130 874210 753620 885470 829720 953210 804470 911210 TRUE FALSE 1682280.708 1012574.625 893960.2333 919328.0829 777860.8717 903374.8101 839874.3616 933525.8804 713149.9382 849492.9351 1.980335138 1.191975333 1.052345695 1.082208038 0.915676681 1.063428279 0.988677277 1.0989213 0.839500729 1 19.69624242 4.838338565 2.010800541 1.010874327 2.44554428 0.937605088 0.075230409 0.212607551 0.744796187 0.018122199 0.611342264 68918.93619 -4.838338565 1.434669953 TYQEHK ddPTM_BT-474_Pertuzumab_2h_R1 3 TYQEHK 6 0 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;; 102.8 0.03523 981580000 1514220 1516090 1257420 1248010 1269500 1196710 1470580 1363580 1518000 1697890 FALSE TRUE 1455042.608 1472852.598 1484663.765 1312419.946 1310334.62 1220908.296 1488577.398 1335421.596 1345683.004 1582890.398 0.919231433 0.930482995 0.937944767 0.829128755 0.827811339 0.771315751 0.940417227 0.843660179 0.850142881 1 20.59412993 4.838456203 0.001573756 1.749227428 2.57E-08 0.007524981 0.066516534 4480187.202 1067.123373 586068.1782 600097.1282 68937.6068 -4.838456203 -1.749227403 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK ddPTM_BT-474_Pertuzumab_2h_R1 5 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK 32 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;; 351.66 1.17E-131 9106380000 1123961 1354756 1161827 1381405 1298803 1393086 1403879 1420364 1504860 1625588 FALSE TRUE 1080035.362 1316119.685 1371794.984 1452699.478 1340580.178 1421255.153 1421060.091 1391032.987 1334034.602 1515485.477 0.712666256 0.868447574 0.905185173 0.958570372 0.884587941 0.937821692 0.937692979 0.917879457 0.880268813 1 20.5313486 4.838655655 1.668226355 0.926064587 0.597291543 0.795508717 0.033027734 0.507281244 1.13124977 0.007980753 0.28867429 68969.27415 -4.838655655 -0.328773044 KVLS(ph)PTAAKPSPFEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVLSPTAAKPSPFEGK 16 2 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 KVLS(0.614)PT(0.386)AAKPSPFEGK 148.91 4.62E-07 1626200000 2989000 2249400 1743300 1502300 1873800 1720300 1567500 2368500 1839100 1376300 TRUE FALSE 2872186.575 2185249.314 2058353.089 1579833.883 1934072.479 1755085.645 1586683.534 2319589.647 1630333.078 1283081.975 2.238505903 1.703125254 1.604225708 1.231280552 1.507364702 1.367867119 1.236618988 1.80782654 1.270638283 1 20.29118192 4.83995317 1.281169102 1.405815542 2.747193885 0.623655951 0.208386706 1.178936511 1.427735605 0.057404718 2.203078633 69175.63744 -4.83995317 1.341378343 GILADEDSSRPVWLK ddPTM_BT-474_Pertuzumab_2h_R1 4 GILADEDSSRPVWLK 15 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 213.32 3.96E-10 56243200000 6881020 7564200 6855400 7936600 8150900 8401100 9192700 8813100 9393400 9394900 FALSE TRUE 6612102.131 7348476.422 8094323.278 8346208.877 8413081.101 8570975.998 9305203.012 8631106.405 8327100.612 8758575.055 0.75492898 0.839003648 0.924159835 0.952918577 0.960553634 0.978581098 1.062410604 0.985446417 0.950736913 1 23.06226474 4.840594971 0.707600377 0.998504443 0.564144626 0.887283794 0.027590923 1.024639535 0.352826095 0.011377074 0.368606175 69277.94089 -4.840594971 -0.434359817 LLDIDETEY(ph)HADGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLDIDETEYHADGGK 15 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 LLDIDET(0.019)EY(0.981)HADGGK 110.98 0.0050977 142290000 29182 45703 26026 78174 24409 30112 68188 48357 47919 39204 TRUE FALSE 28041.53518 44399.59519 30729.47715 82208.56951 25194.13765 30720.88527 69022.50514 47358.41105 42479.43601 36548.67816 0.767238012 1.21480714 0.840782176 2.249289814 0.689331022 0.840547095 1.888508932 1.295762622 1.162270105 1 15.15753161 4.841173048 1.379256501 1.295613899 0.484303417 0.085224491 0.461863149 3.926095356 5.605638585 0.123465565 4.724716325 69370.21622 -4.841173048 -0.811310482 MEEADALIESLCR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEEADALIESLCR 13 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;; 229.82 1.19E-11 104912000 178723 218992 178128 210481 224583 228367 209653 206467 224687 248799 FALSE TRUE 171738.3076 212746.5626 210319.692 221343.9496 231806.9162 232984.7372 212218.7961 202203.3843 199181.4737 231947.6221 0.740418488 0.917218123 0.906755112 0.954284194 0.999393372 1.004471333 0.914942754 0.871763127 0.858734709 1 17.82343953 4.841203554 2.369542589 0.934862513 0.657319195 0.584456517 0.049703218 0.710984063 3.723941099 0.013844288 0.448520925 69375.08912 -4.841203554 -0.277543318 RLS(ph)S(ph)LRAST(ph)SK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.209)T(0.771)S(0.02)K 118.48 0.0011441 462110000 1397600 855880 690910 682580 835100 562940 533810 1243400 631030 479220 TRUE FALSE 1342980.247 831471.1404 815772.8062 717808.0356 861961.7499 574323.0325 540342.9265 1217723.355 559398.1199 446762.0026 3.006030592 1.861105321 1.825967297 1.606689986 1.929353313 1.285523454 1.209464823 2.725664556 1.252116601 1 18.76914696 4.841383826 2.22883662 1.696348586 3.595423792 0.430576067 0.472128903 0.961393421 4.31500486 0.119791448 3.967322302 69403.89216 -4.841383826 1.899075207 AGLVGPEFHEK ddPTM_BT-474_Pertuzumab_2h_R1 3 AGLVGPEFHEK 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 186.87 3.84E-06 2931120000 2925760 3170990 2547510 3092670 3116370 3200820 3350340 3238460 3553700 3525370 FALSE TRUE 2811418.065 3080556.47 3007901.726 3252283.069 3216610.871 3265542.773 3391342.463 3171584.669 3150298.874 3286593.55 0.855420064 0.937309839 0.915203441 0.989560473 0.978706622 0.993594956 1.031871575 0.965006662 0.958530109 1 21.64816162 4.841410126 0.756751775 0.990154011 0.768318542 0.746863769 0.023886665 1.563213977 0.614744518 0.009004429 0.305171179 69408.0952 -4.841410126 -0.221835469 IWGEDLR ddPTM_BT-474_Pertuzumab_2h_R1 5 IWGEDLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 139.92 0.0061873 3371710000 4506790 5104500 4192250 5228910 5160400 4945260 5146650 5289830 5151390 5158530 FALSE TRUE 4330659.664 4958924.658 4949882.831 5498774.672 5326388.953 5045256.545 5209636.242 5180593.162 4566625.804 4809138.168 0.900506393 1.031146223 1.029266088 1.143401266 1.107555817 1.049097857 1.083278554 1.07723941 0.949572594 1 22.19734695 4.841543729 1.815185229 1.064841421 0.816057429 0.430721706 0.052242969 1.029499719 2.790942843 0.013303202 0.475275391 69429.45071 -4.841543729 -0.248783991 LENLGIPEEELLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LENLGIPEEELLR 13 0 Q01658 Q01658 DR1 Protein Dr1 0 ;;; 178.32 3.42E-05 124970000 158600 178404 148086 175296 181599 194426 161134 175795 193469 188944 FALSE TRUE 152401.7367 173316.0926 174848.4344 184343.0476 187440.2968 198357.4269 163106.0061 172164.7718 171507.2102 176146.6546 0.865198019 0.983930651 0.99262989 1.046531641 1.064114997 1.126092502 0.925967095 0.977394502 0.973661468 1 17.42641755 4.842107343 1.891353943 1.013276566 0.790373232 0.418396785 0.052364985 1.21994496 3.647493077 0.014759378 0.521450137 69519.61257 -4.842107343 -0.222903333 DVQIILESCHNQNILGTILHPNGNITELLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVQIILESCHNQNILGTILHPNGNITELLLK 31 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 406.49 1.94E-175 228990000 121630 159980 127070 173810 162300 176870 154930 115230 191450 194820 FALSE TRUE 116876.5651 155417.527 150034.3757 182780.3549 167520.5269 180446.4326 156826.0797 112850.4602 169717.3986 181624.6679 0.643506009 0.855707151 0.826068273 1.006363051 0.922344574 0.993512801 0.863462444 0.621338839 0.934440242 1 17.47060063 4.842740609 2.357301111 0.8756082 0.543281746 0.308541405 0.109321761 1.34509022 6.922340475 0.030866744 1.013807251 69621.05637 -4.842740609 -0.332326454 EMLFEFIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EMLFEFIDR 9 0 O60942-2;O60942 O60942-2 RNGTT mRNA-capping enzyme;Polynucleotide 5-triphosphatase;mRNA guanylyltransferase 0 ; 92.062 0.024033 46916000 67090 74748 61075 77034 74423 63349 83991 73993 73690 85786 FALSE TRUE 64468.04863 72616.26023 72112.61111 81009.73397 76816.88338 64629.96018 85018.90698 72465.01869 65325.02013 79975.63781 0.806096086 0.907979758 0.901682226 1.01293014 0.960503542 0.808120597 1.063060068 0.906088662 0.816811493 1 16.28727297 4.84311927 1.756367093 0.935218736 0.738239716 0.199291372 0.07693777 1.975945181 4.933778509 0.019333101 0.70448912 69681.78546 -4.84311927 -0.19697902 GTLDEEDEEADS(ph)DTDDIDHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTLDEEDEEADSDTDDIDHR 20 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 GTLDEEDEEADS(0.789)DT(0.211)DDIDHR;GTLDEEDEEADS(0.5)DT(0.5)DDIDHR 412.43 1.51E-151 1567980000 1031110 1141000 929730 1172750 1094210 1182170 1150640 1077950 1183530 1186920 TRUE FALSE 990813.0812 1108459.797 1097752.893 1233275.768 1129406.258 1206074.287 1164721.877 1055689.956 1049180.636 1106528.851 0.895424534 1.001745048 0.992068929 1.114544611 1.020674931 1.089961898 1.052590608 0.954055518 0.94817287 1 20.07760964 4.844002731 1.941774963 1.023507309 0.831665384 0.357819183 0.050508913 1.314899957 4.172235477 0.013968096 0.494577575 69823.67955 -4.844002731 -0.191841924 VNFEDDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VNFEDDSR 8 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;O94979-5;H0YAB3;H0Y8V7;H0Y9K1 D6REX3 SEC31A Protein transport protein Sec31A 0 ;;; 215.88 1.90E-05 3067590000 3664210 4095880 3318370 4093470 4137020 4303990 4139520 4398850 4261570 4542110 FALSE TRUE 3521008.622 3979069.513 3918073.276 4304734.477 4270091.005 4391019.627 4190180.684 4308012.21 3777814.44 4234468.844 0.831511283 0.939685627 0.925280931 1.01659373 1.008412427 1.036970583 0.989541035 1.01736779 0.892157807 1 22.01374958 4.844296876 1.034845752 0.99709891 0.727442321 0.587494265 0.040434184 1.468445427 1.105024585 0.011945136 0.460234867 69870.98672 -4.844296876 -0.269656589 ADAVQDSEMVELVELEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADAVQDSEMVELVELEIR 18 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 142.97 2.53E-07 25304000 13363.4 17465.9 12489.9 23978.6 13454.3 14478.3 23590 19580.3 12873.5 16272.3 FALSE TRUE 12841.14355 16967.78963 14747.10277 25216.13842 13887.06978 14771.06115 23878.70148 19175.95996 11412.15425 15170.16263 0.846473691 1.118497543 0.972112371 1.662219387 0.915419967 0.973691681 1.574057053 1.26405764 0.752276329 1 13.88894893 4.84453301 1.511812927 1.181696756 0.663776732 0.079400681 0.276260374 3.358691734 5.882571072 0.073016376 2.790607295 69908.9871 -4.84453301 -0.517920024 S(ph)SGPTSLFAVTVAPPGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSGPTSLFAVTVAPPGAR 18 0 Q00839;A0A1X7SBS1;A0A1W2PP22;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.923)S(0.077)GPTSLFAVTVAPPGAR 262.83 7.71E-31 39984000 47628 44349 33985 34861 38830 37188 29066 40056 28915 35189 TRUE FALSE 45766.6451 43084.20994 40126.84549 36660.18039 40079.00221 37939.96684 29421.7184 39228.8296 25632.69042 32805.61769 1.395085608 1.313318053 1.223169942 1.117497032 1.221711556 1.15650823 0.896850005 1.195796097 0.781350641 1 15.00165526 4.844998115 0.285236404 0.942229016 1.777424746 0.61261514 0.111159552 5.939338594 0.381428798 0.127997794 1.768331148 69983.89582 -4.844998115 0.83519573 ELGLPEELVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELGLPEELVSR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;; 180.67 1.53E-05 322044000 307617 351532 269969 367135 349988 375936 350450 351477 345726 384175 FALSE TRUE 295594.9876 341506.6515 318758.4037 386082.8813 361245.6819 383537.6835 354738.9119 344218.8771 306480.6339 358154.4851 0.825328175 0.95351773 0.890002546 1.077978631 1.008630904 1.070872206 0.990463408 0.961090511 0.855721893 1 18.45022248 4.845351671 1.213542767 0.990372365 0.730544131 0.356081714 0.064667787 2.137370473 2.274255321 0.018869938 0.741038426 70040.89246 -4.845351671 -0.259828234 FCFTPHTEEGCLSER ddPTM_BT-474_Pertuzumab_2h_R1 10 FCFTPHTEEGCLSER 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;;; 335.07 5.12E-69 75519330000 12668766 13977992 11315871 14460508 13756798 14713432 13955860 12346182 15171668 15874084 FALSE TRUE 12173656.62 13579353.35 13360900.61 15206816.55 14199297.9 15010947.68 14126655.99 12091229.03 13449443.85 14798918.15 0.822604497 0.917590949 0.90282955 1.027562717 0.959482156 1.014327367 0.95457356 0.817034658 0.908812639 1 23.81898838 4.845670466 1.744606324 0.941160679 0.759815688 0.288983088 0.058770031 1.974134657 4.824833704 0.017440113 0.645812368 70092.32502 -4.845670466 -0.181344991 RDS(ph)SDDWEIPDGQITVGQR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.5)S(0.5)DDWEIPDGQITVGQR;RDS(0.914)S(0.086)DDWEIPDGQITVGQR;RDS(0.751)S(0.249)DDWEIPDGQITVGQR;RDS(0.794)S(0.206)DDWEIPDGQITVGQR 334.98 2.18E-75 4773600000 1948360 2195180 1731200 2272600 2114620 2257020 2249930 2434670 2315110 2338000 TRUE FALSE 1872215.937 2132575.616 2044066.35 2389889.158 2182638.673 2302658.491 2277465.316 2384393.214 2052308.419 2179645.178 0.858954456 0.978404943 0.937797753 1.096457893 1.001373386 1.056437311 1.044878928 1.093936407 0.941579134 1 21.05566187 4.845985778 0.928021758 1.040324663 0.743884451 0.499430561 0.050507451 1.847447356 1.100020295 0.01536877 0.578916024 70143.2328 -4.845985778 -0.296440212 DYIAYAHSTIMPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYIAYAHSTIMPR 13 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 168.61 2.99E-05 681390000 371120 466350 365160 567100 441710 464680 462330 462490 465210 512530 FALSE TRUE 356616.2201 453050.1546 431152.5349 596368.099 455918.0033 474076.148 467988.1328 452939.4199 412401.3111 477815.8866 0.746346512 0.948168881 0.902340309 1.248112747 0.954170876 0.992173264 0.979431923 0.947937129 0.863096692 1 18.8660953 4.846160226 1.854374403 0.98960787 0.621681869 0.356668603 0.096473398 1.302399872 3.678832923 0.02491999 0.90782436 70171.41376 -4.846160226 -0.367926001 S(ph)MDLGIADETK ddPTM_BT-474_Pertuzumab_2h_R1 6 SMDLGIADETK 11 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(1)MDLGIADETK;S(1)MDLGIADETK;S(1)MDLGIADETK;S(1)MDLGIADETK;S(1)MDLGIADETK;S(1)MDLGIADETK 258.65 1.50E-20 2316410000 4787760 4012250 3291530 3152560 3558710 2717220 3507560 4505730 4210240 3807250 TRUE FALSE 4600649.046 3897824.558 3886382.691 3315263.999 3673179.139 2772164.05 3550486.569 4412685.101 3732311.206 3549381.566 1.296183282 1.098170057 1.094946434 0.934039899 1.034878632 0.781027342 1.000311322 1.243226466 1.051538454 1 21.75913624 4.846879915 1.492664184 1.023781553 1.453658648 0.375160762 0.109860352 1.897359625 3.212905106 0.033473163 1.296815177 70287.79439 -4.846879915 0.429877095 EIENMILNDPDFQHEDLNFLTR ddPTM_BT-474_Pertuzumab_2h_R1 12 EIENMILNDPDFQHEDLNFLTR 22 0 Q15067-2;Q15067;I3L0T4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;;;;;;;;;;; 292.49 1.99E-55 2727587000 1035836 1342495 1079149 1586642 1269406 1376672 1473040 1464118 1490856 1597999 FALSE TRUE 995354.3839 1304208.357 1274175.23 1668528.784 1310237.597 1404509.251 1491067.504 1433883.452 1321620.277 1489765.104 0.668128406 0.875445634 0.855285995 1.119994541 0.879492742 0.942772285 1.000874232 0.962489622 0.887133329 1 20.50665344 4.84710839 1.329511257 0.963506453 0.490550782 0.616445812 0.069955121 1.061480629 1.380817844 0.018388168 0.724644968 70324.78127 -4.84710839 -0.472955671 S(ph)PLHVGETR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLHVGETR 9 0 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 S(1)PLHVGETR 108.37 0.0016889 260650000 77411 93165 73929 105630 100960 80986 82051 99650 100540 91273 TRUE FALSE 74385.69254 90508.02542 87289.61484 111081.577 104207.4701 82623.59241 83055.16468 97592.19268 89127.1207 85090.99841 0.874189913 1.063661575 1.025838414 1.305444513 1.224659154 0.971002738 0.976074629 1.14691559 1.047433011 1 16.3767189 4.848532929 1.963026652 1.097171626 0.762143636 0.266809939 0.104595392 1.530262855 4.932253397 0.028048353 1.01782336 70555.8338 -4.848532929 -0.33502799 CPAGQQPPQHR ddPTM_BT-474_Pertuzumab_2h_R1 4 CPAGQQPPQHR 11 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 ;;; 96.89 0.0066753 347161000 239992 268566 222763 264678 253128 268507 275592 263170 287789 294557 FALSE TRUE 230612.8473 260906.7606 263021.2294 278338.0633 261270.092 273936.3955 278964.7773 257735.4475 255120.3992 274606.392 0.839794171 0.950111753 0.957811752 1.013589164 0.951434852 0.997560157 1.015871391 0.938563176 0.92904028 1 18.06700568 4.850359108 1.928945144 0.97509968 0.769571433 0.658928093 0.029226199 0.699298431 2.151080779 0.007639028 0.281902539 70853.14112 -4.850359108 -0.205528246 NYILSAS(ph)ASALWNDEVDKAEQELR ddPTM_BT-474_Pertuzumab_2h_R1 1 NYILSASASALWNDEVDKAEQELR 24 1 B7ZC38;Q9NR46;Q9NR46-2 B7ZC38 SH3GLB2 Endophilin-B2 1 NYILS(0.013)AS(0.839)AS(0.149)ALWNDEVDKAEQELR 180.35 2.16E-17 32673000 37793 25895 15939 14826 20340 11527 10144 21824 19174 14119 TRUE FALSE 36316.00778 25156.49995 18819.53186 15591.17164 20994.25457 11760.08384 10268.14531 21373.32677 16997.4479 13162.70755 2.759007418 1.911194931 1.429761452 1.184495786 1.594979945 0.893439575 0.780093705 1.623778899 1.291333704 1 13.68416866 4.85074502 1.137010416 1.208824643 3.816321139 0.784477181 0.255732011 0.937641214 0.857608656 0.077457293 3.093314959 70916.12883 -4.85074502 2.607496496 up SVSSVLSSLT(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVSSVLSSLTPAK 13 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 SVSSVLSS(0.001)LT(0.999)PAK;SVSSVLSSLT(1)PAK 235.22 1.24E-15 751080000 2838400 1878270 1475560 916660 1413170 1415100 1099500 1787370 1203850 1081780 TRUE FALSE 2727472.19 1824703.579 1742226.516 963968.9325 1458625.896 1443714.292 1112956.01 1750460.185 1067193.995 1008510.077 2.704457052 1.809306243 1.727525144 0.955834705 1.446317622 1.431531845 1.10356459 1.735689335 1.058188727 1 19.94379407 4.850868516 1.215992711 1.314847719 3.591501606 0.750912412 0.252503965 0.910861952 0.965291632 0.069301773 2.780187595 70936.29733 -4.850868516 2.276653887 up ERPGEQSEVAQLIQQTLEQER ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPGEQSEVAQLIQQTLEQER 21 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 ; 210.38 1.89E-22 82264000 39862 48333 39830 46719 47416 51943 44914 47391 54407 50761 FALSE TRUE 38304.14897 46954.59016 47028.16701 49130.17319 48941.1787 52993.32305 45463.67097 46412.35929 48230.94545 47322.91226 0.809420789 0.992216834 0.993771617 1.038189977 1.034196256 1.119823792 0.960711605 0.980758729 1.019188024 1 15.53025124 4.851431675 2.184254854 1.017851736 0.709203527 0.699034724 0.04084049 0.591631991 2.457253993 0.01101139 0.394699644 71028.34167 -4.851431675 -0.30864821 LHLS(ph)PPLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LHLSPPLGR 9 0 Q6P0Q8;A0A669KBJ4 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 LHLS(1)PPLGR;LHLS(1)PPLGR;LHLS(1)PPLGR;LHLS(1)PPLGR 134.38 0.00016133 623900000 305228 378842 272693 342549 385780 481603 380074 319250 401156 405373 TRUE FALSE 293299.3523 368037.7971 321974.6911 360227.9949 398188.9641 491341.3426 384725.4593 312657.3759 355618.4527 377916.7256 0.776095188 0.97385951 0.851972589 0.953194105 1.053642078 1.300131244 1.018016492 0.827318175 0.940996861 1 18.52770884 4.852208676 0.893042789 1.004314649 0.656133562 0.24023113 0.120845676 4.808745347 2.622431642 0.045306123 1.714805993 71155.53297 -4.852208676 -0.348181088 EVVESCR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVVESCR 7 0 O60701-2;O60701;E7ER95;E7ER83;E7ETF4;E7EV97 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 115.46 0.032367 0 110210 127000 100450 120800 124580 126320 110840 165950 141710 142490 FALSE TRUE 105902.8714 123378.0843 118603.5495 127034.5025 128587.2288 128874.2769 112196.4931 162523.0745 125623.6749 132839.0254 0.797227103 0.928778904 0.892836643 0.956304084 0.967992866 0.970153737 0.84460491 1.223458799 0.945683503 1 17.01931952 4.852476639 0.329845074 1.050079296 0.643448807 0.291271032 0.090733869 8.736998621 0.726846763 0.093404462 1.456677672 71199.44995 -4.852476639 -0.406630488 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHR 33 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(0.981)PMVPS(0.019)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.995)PMVPS(0.005)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.965)PMVPS(0.035)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.994)PMVPS(0.006)EQVVEEAVPLPPQALTTSQDGHR 108.04 1.15E-05 619904000 231126 291972 242727 316879 290827 323764 307650 283175 313696 331570 TRUE FALSE 222093.3404 283645.2444 286593.1683 333233.1632 300181.7146 330310.7299 311415.1127 277327.3373 278086.5452 309112.4686 0.718487162 0.917611786 0.927148522 1.078032099 0.971108399 1.068577827 1.007449212 0.897172924 0.899629014 1 18.23777232 4.852563689 1.638653395 0.981863738 0.568487371 0.649865078 0.058330212 0.912355256 1.896810818 0.016645065 0.650137658 71213.72268 -4.852563689 -0.413376367 EGLDWDLIYVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGLDWDLIYVGR 12 0 Q8NBJ5;M0QX72 Q8NBJ5 COLGALT1 Procollagen galactosyltransferase 1 0 ; 150.61 0.0001588 124697000 200960 239570 193361 252920 228870 241170 235240 227760 256330 256770 FALSE TRUE 193106.261 232737.6982 228305.634 265973.2315 236231.8114 246046.6226 238118.9375 223056.6764 227232.493 239378.7392 0.806697628 0.972257181 0.95374232 1.111097971 0.986853771 1.027854953 0.994737203 0.931814902 0.949259294 1 17.8689355 4.852775112 2.170274696 0.993714068 0.716132388 0.582433337 0.047379465 0.769836891 3.135878638 0.01269487 0.460249108 71248.3994 -4.852775112 -0.27758168 DLYANTVLSGGTTMYPGIADR ddPTM_BT-474_Pertuzumab_2h_R1 9 DLYANTVLSGGTTMYPGIADR 21 0 P60709;A0A2R8Y793;P63261 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;;; 367.23 6.48E-112 4145209000 1303870 1395467 1131138 1414141 1341086 1397147 1334585 1415248 1416646 1447064 FALSE TRUE 1252913.319 1355669.647 1335559.799 1487124.986 1384223.249 1425398.27 1350918.05 1386022.634 1255834.285 1349053.066 0.928735385 1.004904611 0.989997971 1.102347286 1.026070274 1.056591698 1.001382439 1.027404087 0.930900582 1 20.36351567 4.852931538 1.777088636 1.02203808 0.878292743 0.275734318 0.042227828 1.558418099 3.917496601 0.010755898 0.412538015 71274.06655 -4.852931538 -0.143745337 GRPS(ph)KTPS(ph)PSQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.801)KT(0.199)PS(0.749)PS(0.251)QPK 72.315 0.021389 566340000 311300 207410 169050 134940 169620 179440 175050 205580 227110 187330 TRUE FALSE 299134.0518 201494.8699 199601.0955 141904.2696 175075.9813 183068.3997 177192.3143 201334.7012 201329.4249 174641.9722 1.712841695 1.153759702 1.142915949 0.812543902 1.002485136 1.048249727 1.014603259 1.152842576 1.152812364 1 17.4140408 4.853787734 1.966617786 1.040509886 2.062544025 0.816878323 0.095137767 0.475123864 1.518800593 0.025870054 0.969974274 71414.71946 -4.853787734 1.022034139 ADATNVNNWHWTER ddPTM_BT-474_Pertuzumab_2h_R1 4 ADATNVNNWHWTER 14 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;; 230.86 7.56E-13 6029140000 1831020 2197630 1804760 2261090 2201450 2295500 2126050 2137610 2263470 2461540 FALSE TRUE 1759461.714 2134955.744 2130920.279 2377785.126 2272261.639 2341916.583 2152069.236 2093467.606 2006530.375 2294817.703 0.766710886 0.930337839 0.928579327 1.036154254 0.990170869 1.020524018 0.937795291 0.912258784 0.874374628 1 21.12994812 4.853955616 1.993747431 0.961348643 0.666349709 0.598709091 0.047901768 0.837182153 2.765056545 0.013337317 0.498722293 71442.33094 -4.853955616 -0.294998934 SVS(ph)PSPVPLLFQPDQNAPPIR ddPTM_BT-474_Pertuzumab_2h_R1 6 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-2;Q02241-3 Q02241-2 KIF23 Kinesin-like protein KIF23 1 S(0.126)VS(0.869)PS(0.005)PVPLLFQPDQNAPPIR;S(0.133)VS(0.863)PS(0.003)PVPLLFQPDQNAPPIR;S(0.005)VS(0.994)PS(0.001)PVPLLFQPDQNAPPIR;S(0.029)VS(0.97)PS(0.001)PVPLLFQPDQNAPPIR;S(0.006)VS(0.992)PS(0.003)PVPLLFQPDQNAPPIR;S(0.003)VS(0.996)PS(0.001)PVPLLFQPDQNAPPIR 419.34 7.38E-153 2801326000 505330 586489 487730 591679 623114 630562 587545 647145 592693 639571 TRUE FALSE 485581.1449 569762.908 575873.6605 622215.6241 643157.0277 643312.3957 594735.5515 633781.2296 525412.9754 596252.2865 0.814388734 0.95557354 0.965822142 1.043544215 1.078665931 1.078926505 0.997456219 1.062941382 0.881192387 1 19.18556337 4.854536585 1.238783832 1.026527705 0.679702045 0.53838279 0.05623834 1.338908569 1.469920073 0.015568967 0.633844835 71537.96552 -4.854536585 -0.346825659 KLGEMWNNTAADDKQPYEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KLGEMWNNTAADDKQPYEK 19 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;; 136.49 2.75E-05 7380350000 2377860 1963430 1671970 1411900 1863020 1724760 1861560 2103110 2241010 1866750 FALSE TRUE 2284930.602 1907434.899 1974132.172 1484768.328 1922945.73 1759635.829 1884342.328 2059680.044 1986619.94 1740313.36 1.312942057 1.096029567 1.134354431 0.853161484 1.104942233 1.011102868 1.082760365 1.183511022 1.141530017 1 20.73091567 4.855178822 2.167108951 1.069876933 1.431962635 0.410090551 0.088828568 1.106947067 4.463743019 0.02342337 0.864340268 71643.83444 -4.855178822 0.362085702 VPDVDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 VPDVDIR 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 79.116 0.077928 324460000 229500 270930 196740 326750 244530 277940 256080 272960 275710 282700 FALSE TRUE 220530.8863 263203.3417 232295.2945 343613.6067 252395.5295 283560.1372 259213.9836 267323.2806 244412.5567 263552.4772 0.836762715 0.998675271 0.881400535 1.303776805 0.957667073 1.07591528 0.983538407 1.0143076 0.927377194 1 18.00773073 4.855457747 1.456730938 1.027016455 0.730095853 0.205147102 0.107820579 2.421885256 3.818282233 0.027840783 1.126832734 71689.86235 -4.855457747 -0.296920602 GIFLGDDEWR ddPTM_BT-474_Pertuzumab_2h_R1 6 GIFLGDDEWR 10 0 Q8TB72-3;Q8TB72;Q8TB72-2;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 0 ;;;;; 164.57 1.42E-05 790948000 1059376 1255225 1011892 1339249 1297921 1339409 1209472 1307221 1274015 1389254 FALSE TRUE 1017974.415 1219427.212 1194763.394 1408367.801 1339669.808 1366492.768 1224273.88 1280226.43 1129394.158 1295158.589 0.785984375 0.941527333 0.922484245 1.087409537 1.034367389 1.055077563 0.945269475 0.988470787 0.872012252 1 20.30469733 4.855564466 1.462681377 0.99442119 0.662085015 0.515788445 0.05949307 1.270899438 2.021953689 0.016410116 0.664152784 71707.48094 -4.855564466 -0.332336175 ALPSLNTGSS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALPSLNTGSSSPR 13 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 ALPSLNTGS(0.019)S(0.634)S(0.347)PR 112.96 0.00090134 7267200000 6302500 7250100 5918800 7595600 6914400 7777500 7530900 7064100 6928300 7674400 TRUE FALSE 6056191.332 7043334.247 6988458.823 7987609.826 7136807.955 7934766.379 7623065.407 6918223.866 6141828.43 7154606.052 0.846474465 0.984447529 0.976777585 1.11642902 0.997512358 1.109043086 1.065476611 0.966960838 0.858443971 1 22.7704409 4.856438516 1.808018293 1.017290297 0.752710502 0.3237934 0.071027144 1.48950255 3.870431742 0.01894348 0.738006474 71851.94286 -4.856438516 -0.264579796 KRDAEDDGEEEDD ddPTM_BT-474_Pertuzumab_2h_R1 2 KRDAEDDGEEEDD 13 2 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ; 93.494 0.022203 599140000 584200 524260 435120 440960 464190 465900 469490 514550 603730 525420 FALSE TRUE 561368.8181 509308.6181 513755.8632 463717.9984 479121.0929 475320.8172 475235.7591 503924.3627 535197.1014 489832.8354 1.146041624 1.03976006 1.048839167 0.946686226 0.978131841 0.970373529 0.970199882 1.028768033 1.092611729 1 18.90192996 4.856998621 1.386812195 0.999365776 1.235555007 0.534302257 0.040304909 1.332801816 1.874683728 0.011562561 0.473744248 71944.66936 -4.856998621 0.236189231 TPVIDADKPVSSQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPVIDADKPVSSQLR 15 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 80.534 0.015219 259330000 154790 154550 140270 143070 158530 157230 169280 162690 199670 175420 FALSE TRUE 148740.6357 150142.3853 165619.9093 150453.8598 163629.2614 160409.2983 171351.6993 159330.3946 177004.2987 163538.6472 0.909513673 0.918085039 1.012726424 0.919989632 1.000554085 0.980864775 1.047774959 0.974267535 1.082339262 1 17.31927209 4.857613315 0.362337505 1.026991705 0.807824213 0.485158665 0.038762417 5.731839833 0.564576391 0.032963525 0.563411495 72046.57086 -4.857613315 -0.219167492 SMDELNHDFQALALEGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SMDELNHDFQALALEGR 17 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 0 ;;; 221.37 3.71E-15 681000000 681950 822540 669040 882330 849070 873390 826780 783070 825790 912540 FALSE TRUE 655298.6401 799081.9646 789950.4107 927867.157 876381.1077 891050.5442 836898.381 766899.3309 732049.7812 850732.853 0.77027546 0.939286595 0.928552845 1.090668068 1.030148424 1.047391718 0.983738171 0.901457288 0.860493137 1 19.69834664 4.857748801 1.763611586 0.981273735 0.65248223 0.484626975 0.065130002 1.231981923 3.009934183 0.018849181 0.74429162 72069.05054 -4.857748801 -0.328791505 GLVYETSVLDPDEGIR ddPTM_BT-474_Pertuzumab_2h_R1 5 GLVYETSVLDPDEGIR 16 0 O75390;B4DJV2;A0A0C4DGI3;F8VPA1;F8VX68;F8VPF9;F8W1S4;H0YH82;F8VRP1;F8VZK9;F8VTT8;F8W4S1;F8VX07;F8W642 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ;;;; 287.13 9.43E-36 532677000 606431 961549 692425 1466890 703089 856170 1250741 1110055 874972 740047 FALSE TRUE 582731.0061 934126.564 817561.6004 1542596.369 725704.4962 873482.344 1266047.942 1087131.976 775648.8467 689922.9575 0.844631998 1.353957792 1.185004197 2.235896562 1.051863093 1.266057803 1.835056985 1.575729528 1.124254293 1 19.39607574 4.860040662 1.671277592 1.469334553 0.48946668 0.161264655 0.36895359 2.184310316 4.68250139 0.093219555 3.770990883 72450.37911 -4.860040662 -0.979867873 VAAASGHCGAFSGSDSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VAAASGHCGAFSGSDSSR 18 0 Q9NZB2;Q9NZB2-6;A0A494C0Y9 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ;;; 198.67 1.71E-15 734170000 265348 345399 266260 377317 333457 358146 345246 314433 316304 366585 FALSE TRUE 254977.9068 335548.5587 314379.1049 396790.3756 344182.9472 365387.9575 349471.2238 307939.8487 280398.496 341755.8714 0.746082008 0.981836998 0.919893793 1.161034553 1.007101782 1.069149027 1.022575625 0.901052109 0.820464312 1 18.3826066 4.860125438 2.461245955 0.990625478 0.633686563 0.395788113 0.088888735 1.030442038 5.593707734 0.023319405 0.877187101 72464.52296 -4.860125438 -0.356938915 EKS(ph)PSLGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKSPSLGKK 9 2 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 EKS(0.802)PS(0.198)LGKK 64.04 0.037631 742890000 2449400 1802300 1588400 987100 1323000 1545700 1692700 1848700 2218000 1790900 TRUE FALSE 2353674.74 1750900.169 1875459.214 1038044.349 1365555.497 1576955.113 1713415.769 1810523.699 1966221.939 1669600.748 1.409723099 1.048693929 1.12329802 0.621732082 0.817893438 0.944510306 1.026242814 1.08440518 1.177659953 1 20.67107172 4.86080571 1.734577968 0.966858318 1.659903638 0.430192028 0.150534947 1.366369425 3.189452768 0.04268619 1.720932155 72578.11932 -4.86080571 0.693045319 WQRPSS(ph)PPPFLPAASEEAEPAEGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.407)S(0.593)PPPFLPAASEEAEPAEGLR;WQRPS(0.173)S(0.827)PPPFLPAASEEAEPAEGLR 217.17 9.42E-34 1345580000 323410 403770 343210 434240 392130 417120 442820 442550 428410 460820 TRUE FALSE 310770.7797 392254.8749 405235.6817 456651.1784 404743.2176 425554.4522 448239.3636 433411.1878 379778.6928 429608.2509 0.723381776 0.913052471 0.943267921 1.062947877 0.942121611 0.990563964 1.043367679 1.008852104 0.884011636 1 18.71266218 4.861630857 1.473335813 0.992517168 0.55600601 0.726427469 0.048576225 0.765246777 1.224028262 0.012756988 0.530627526 72716.14665 -4.861630857 -0.436511158 AAVELEEPEDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAVELEEPEDAR 12 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 225.67 3.99E-11 208773000 201279 222990 182769 219191 217215 227410 211421 221780 231070 238920 FALSE TRUE 193412.7942 216630.5435 215799.424 230503.4738 224201.9177 232008.386 214008.4334 217200.1655 204839.9023 222737.7356 0.868343182 0.972581242 0.96884986 1.034864942 1.00657357 1.041621373 0.960809056 0.975138608 0.919646156 1 17.76498647 4.861883325 2.039469788 0.989619175 0.804294366 0.527255692 0.033913474 0.917131669 3.136226323 0.008980645 0.351954298 72758.43096 -4.861883325 -0.185324809 SEDDESGAGELTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEDDESGAGELTR 13 0 P33993;P33993-3;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 211.84 4.34E-08 1065750000 329980 383850 307060 403290 354930 402580 373000 363650 393170 399460 FALSE TRUE 317084.0168 372902.9738 362552.5725 424103.8452 366346.6458 410720.4434 377564.8856 356140.5004 348538.9899 372404.2184 0.851451195 1.001339285 0.973545826 1.138826641 0.983733878 1.102888805 1.013857703 0.956327783 0.935915794 1 18.50650989 4.862427738 2.247641694 1.014935738 0.770253737 0.393333621 0.059787259 1.089949786 4.707392079 0.015401931 0.595705526 72849.69507 -4.862427738 -0.244682001 S(ph)LSS(ph)SPVKK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(0.995)LS(0.016)S(0.495)S(0.494)PVKK;S(0.993)LS(0.014)S(0.895)S(0.098)PVKK 128.36 0.0014679 1390700000 5803300 4160700 3589000 2935700 3317400 3224800 3170900 5534400 4826400 4036800 TRUE FALSE 5576500.62 4042040.91 4237612.137 3087211.829 3424107.184 3290007.665 3209706.423 5420112.706 4278527.306 3763383.94 1.48177829 1.074044257 1.126011112 0.820328693 0.909847955 0.874215259 0.852877749 1.440223159 1.136883022 1 21.84359905 4.862450111 2.220290757 1.032124479 1.70726418 0.381434468 0.174555533 1.303148163 5.462994093 0.050241823 1.94696346 72853.44801 -4.862450111 0.675139701 TVS(ph)ASS(ph)TGDLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSASSTGDLPK 12 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 2 TVS(1)AS(0.004)S(0.821)T(0.176)GDLPK 195.24 7.29E-07 664550000 1331800 1201200 1012500 999560 1075200 1077700 1045200 1284400 1306900 1171000 TRUE FALSE 1279751.784 1166942.952 1195481.273 1051147.411 1109784.784 1099491.832 1057991.47 1257876.691 1158546.191 1091687.127 1.172269739 1.068935342 1.095076825 0.962865079 1.016577696 1.007149214 0.969134328 1.152231862 1.061243796 1 20.05812801 4.864523891 1.384145817 1.035684288 1.256509097 0.384132523 0.054086761 2.045610966 2.827507144 0.016098414 0.681941648 73202.15907 -4.864523891 0.220824809 EIDGGLETLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIDGGLETLR 10 0 P38117-2;P38117;M0QY67 P38117-2 ETFB Electron transfer flavoprotein subunit beta 0 ; 120.31 0.0013429 483800000 251780 365270 252970 534370 287070 346490 448860 411100 308350 299930 FALSE TRUE 241940.1592 354852.8572 298687.3063 561948.8997 296303.8673 353496.2652 454353.2829 402610.6413 273347.4007 279615.474 0.865260266 1.269074462 1.068207357 2.00972032 1.059683368 1.264222828 1.624921813 1.439872535 0.977583239 1 18.09308468 4.864947515 1.532849004 1.358291413 0.57453327 0.142211559 0.30825513 2.5657164 4.462914469 0.07868552 3.309852062 73273.5975 -4.864947515 -0.783758143 TVLS(ph)LFDEEEDKMEDQNIIQAPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVLSLFDEEEDKMEDQNIIQAPQK 24 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 T(0.03)VLS(0.97)LFDEEEDKMEDQNIIQAPQK;TVLS(1)LFDEEEDKMEDQNIIQAPQK 198.06 1.09E-24 231655000 338980 224930 212133 95801 171872 176515 118594 258560 257260 189312 TRUE FALSE 325732.2868 218515.2166 250470.152 100745.3011 177400.419 180084.2542 120045.3888 253220.6456 228056.9233 176489.7296 1.845616102 1.238118598 1.419176926 0.570828123 1.005160013 1.020366764 0.680183425 1.434761367 1.292182405 1 17.42922471 4.865439646 1.333193376 1.039037279 2.347830463 0.463539729 0.262233509 1.663755365 2.11171006 0.074813687 3.185514703 73356.67639 -4.865439646 1.308793184 S(ph)LTRS(ph)PPAIR ddPTM_BT-474_Pertuzumab_2h_R1 3 SLTRSPPAIR 10 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.942)LT(0.097)RS(0.961)PPAIR;S(0.902)LT(0.126)RS(0.973)PPAIR;S(0.996)LT(0.081)RS(0.923)PPAIR 109.1 0.0011739 1413380000 379179 590890 470400 620780 631030 883370 809880 549930 862470 849330 TRUE FALSE 364360.2655 574038.3957 555411.744 652818.5302 651327.653 901232.3466 819791.5537 538573.7533 764566.0214 791804.1226 0.460164648 0.724975255 0.701450937 0.824469729 0.822586842 1.138201129 1.035346407 0.680185589 0.96559995 1 19.59478405 4.867206756 0.680706576 0.924897107 0.140379008 0.60029578 0.121778574 2.9077393 0.905091341 0.054823002 1.837576551 73655.76686 -4.867206756 -0.784518099 IVDNVRPDR ddPTM_BT-474_Pertuzumab_2h_R1 4 IVDNVRPDR 9 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;;; 117.3 0.0010707 4718160000 3331740 3662730 2916910 3714270 3780390 3765340 3450610 3711560 3660700 3842920 FALSE TRUE 3201531.917 3558272.527 3444060.523 3905963.92 3901989.678 3841477.755 3492839.597 3634914.989 3245152.683 3582635.605 0.89362477 0.993199677 0.961320353 1.09024873 1.089139423 1.072249086 0.974935769 1.014592437 0.905800377 1 21.77258988 4.867902107 1.450818519 1.020208408 0.816297497 0.296153616 0.055574699 2.099057593 3.205383216 0.015713346 0.673975867 73773.79204 -4.867902107 -0.203910911 RVSS(ph)DLQHATAQLSLEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVSSDLQHATAQLSLEHR 18 1 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 RVS(0.435)S(0.554)DLQHAT(0.011)AQLSLEHR 59.429 0.03565 93840000 714890 509840 415240 356830 513730 476020 501030 224250 823560 531420 TRUE FALSE 686951.3084 495299.8624 490283.105 375246.0391 530254.592 485645.4505 507161.755 219619.1591 730072.9214 495426.4501 1.386585856 0.999744487 0.989618348 0.757420277 1.070299319 0.980257414 1.02368728 0.443293165 1.47362524 1 18.91831137 4.868666913 1.919061381 0.921232282 1.649592286 0.187344537 0.246382407 1.772619177 5.155575676 0.061869003 2.563303968 73903.82437 -4.868666913 0.728360004 TIS(ph)DGTISASK ddPTM_BT-474_Pertuzumab_2h_R1 8 TISDGTISASK 11 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 T(0.005)IS(0.989)DGT(0.006)ISASK;TIS(1)DGTISASK;TIS(0.987)DGT(0.012)ISASK;TIS(1)DGTISASK;TIS(1)DGTISASK;T(0.003)IS(0.993)DGT(0.005)ISASK;TIS(1)DGTISASK;T(0.002)IS(0.994)DGT(0.004)ISASK 336.87 1.07E-57 24935640000 30065690 24988890 19943720 19585550 21022120 20034350 19467330 25944230 23003220 20237650 TRUE FALSE 28890689.6 24276231.32 23547993.85 20596362.58 21698315.58 20439458.28 19705577.01 25408472.58 20391990.9 18866935.94 1.531286781 1.286707677 1.248109069 1.091664415 1.150070984 1.083348051 1.044450306 1.346719609 1.080832148 1 24.16935681 4.868783176 1.136716175 1.137499716 1.802192241 0.654828921 0.092048889 1.398137349 1.244808491 0.027807262 1.186365047 73923.61147 -4.868783176 0.664692524 T(ph)MDKALEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TMDKALEK 8 1 A0A0C4DFW2;Q9UK53-3;Q9UK53-4;Q9UK53-5;Q9UK53-2;Q9UK53 A0A0C4DFW2 ING1 Inhibitor of growth protein;Inhibitor of growth protein 1 1 T(1)MDKALEK 104.45 0.02916 13395000 20743 32227 24622 37458 40113 44350 35037 35216 20302 29346 TRUE FALSE 19932.34063 31307.91751 29071.74311 39391.21187 41403.27107 45246.78739 35465.79329 34488.77729 17997.40207 27358.36928 0.728564646 1.144363437 1.062627045 1.439823093 1.513367652 1.653855422 1.296341639 1.260629862 0.657838992 1 14.73969462 4.869303282 1.338841273 1.28596186 0.375857012 0.233987647 0.269324889 2.461782964 3.133466653 0.076169508 3.297311365 74012.19461 -4.869303282 -0.910104848 GQTPLTEGSEDLDGHS(ph)DPEESFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQTPLTEGSEDLDGHSDPEESFAR 24 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 GQTPLTEGSEDLDGHS(1)DPEESFAR;GQTPLTEGSEDLDGHS(1)DPEESFAR 269.59 2.42E-45 308750000 129470 173730 136675 206819 137008 185686 192053 156655 190098 177989 TRUE FALSE 124410.1693 168775.3905 161375.2128 217492.9534 141414.9867 189440.6981 194403.4021 153420.0195 168518.872 165933.6465 0.749758544 1.017125785 0.972528575 1.310722436 0.852238167 1.141665371 1.171573133 0.924586561 1.015579875 1 17.34024693 4.871127757 2.077690694 1.05114345 0.585677872 0.337678263 0.124774039 1.280888352 4.469876136 0.030350072 1.263876142 74323.77444 -4.871127757 -0.465465578 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR 32 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ; 239.69 6.64E-47 1692660000 462370 437410 328020 361550 402120 329290 393560 337410 388250 440340 FALSE TRUE 444300.0692 424935.4951 387300.5108 380209.6388 415054.555 335948.4694 398376.505 330442.3656 344177.4877 410515.3796 1.082298231 1.035126858 0.943449454 0.926176357 1.01105726 0.818357816 0.970430159 0.804945154 0.838403394 1 18.64707675 4.873895932 0.519161746 0.877333635 1.258730994 0.432212543 0.068376424 4.08593182 0.762984338 0.037608416 0.979664035 74799.02408 -4.873895932 0.381397359 GLEGERPAR ddPTM_BT-474_Pertuzumab_2h_R1 6 GLEGERPAR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;; 149.27 8.03E-05 19330950000 3191980 3688990 3050380 3742470 3711240 3864480 3771360 3682250 3747120 3938930 FALSE TRUE 3067233.893 3583783.617 3601651.521 3935619.325 3830615.405 3942622.433 3817515.032 3606210.251 3321762.647 3672142.763 0.835270873 0.975937987 0.980803785 1.071750087 1.04315536 1.073657177 1.039587859 0.982045221 0.904584288 1 21.80819072 4.874213299 1.649936339 1.017153931 0.722766733 0.554620699 0.047492921 1.118921796 2.260920231 0.013276804 0.580522736 74853.70466 -4.874213299 -0.294387198 RVSSDEEHT(ph)VDSCISDMK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVSSDEEHTVDSCISDMK 18 1 Q70CQ2-3;Q70CQ2-2;Q70CQ2;H7C150;H7C183 Q70CQ2-3 USP34 Ubiquitin carboxyl-terminal hydrolase 34 1 RVS(0.024)S(0.006)DEEHT(0.968)VDS(0.003)CISDMK 193.02 8.50E-15 252660000 160240 177060 142040 179200 175640 186030 179340 165680 198770 190770 TRUE FALSE 153977.6436 172010.4222 167709.7877 188448.5335 181289.6201 189791.6541 181534.8166 162258.6501 176206.4629 177848.978 0.865777501 0.967171271 0.942989887 1.05959863 1.019345864 1.067150659 1.020724542 0.912339514 0.990764552 1 17.44029316 4.874520074 1.317784852 1.001719713 0.777928094 0.478829689 0.043676147 1.862605828 2.268966428 0.013717719 0.607067863 74906.59804 -4.874520074 -0.223791619 SSGHS(ph)SSELS(ph)PDAVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSGHSSSELSPDAVEK 16 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.002)S(0.003)GHS(0.868)S(0.122)S(0.018)ELS(0.986)PDAVEK 150.92 2.94E-08 0 435020 511470 417860 534580 500020 538420 521400 459410 575520 579440 TRUE FALSE 418018.9375 496883.3764 493376.5972 562169.7379 516103.5974 549307.2213 527781.0492 449923.023 510189.3824 540194.0127 0.773831119 0.919823924 0.913332221 1.040681171 0.955404142 1.016870251 0.977021286 0.83289154 0.944455826 1 19.04311812 4.874879453 1.772622534 0.953842399 0.665764829 0.506343442 0.055059478 1.285700004 3.060770027 0.015925924 0.693080101 74968.60903 -4.874879453 -0.28807757 RLEELER ddPTM_BT-474_Pertuzumab_2h_R1 2 RLEELER 7 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6;Q9NRD5;Q9NRD5-2;F6V107 O95819-3 MAP4K4;PICK1 Mitogen-activated protein kinase kinase kinase kinase 4;PRKCA-binding protein 0 ; 145.16 0.0036969 739340000 282060 318290 254890 329490 325580 314510 325330 322690 323680 328750 FALSE TRUE 271036.7834 309212.6808 300954.293 346495.0184 336052.5764 320869.6077 329311.4859 316026.3387 286937.2034 306483.4697 0.884343889 1.008904921 0.981959299 1.13055043 1.096478635 1.04693936 1.074483678 1.031136652 0.936224077 1 18.22544974 4.87566311 1.448634799 1.046537543 0.781121231 0.425480631 0.053204849 1.549633823 2.325041131 0.014618588 0.650188993 75104.0073 -4.87566311 -0.265416312 PRPDPSPEIEGDLQPATHGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 PRPDPSPEIEGDLQPATHGSR 21 1 P51970 P51970 NDUFA8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 0 108.25 0.00019462 175200000 43655 73880 55780 104280 54038 70458 90859 74894 79168 57394 FALSE TRUE 41948.91434 71773.01474 65860.68682 109661.9033 55776.18135 71882.70903 91970.95962 73347.41273 70181.18054 53506.65326 0.783994359 1.341384863 1.230887802 2.049500326 1.042415811 1.343434968 1.718869599 1.370809203 1.311634652 1 15.70743067 4.875690264 1.99115104 1.420850312 0.422126806 0.264858189 0.293229293 1.48094895 4.617634974 0.070531333 3.044211922 75108.70332 -4.875690264 -0.998723506 DISLDSELHDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DISLDSELHDLR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;;; 259.23 2.88E-21 1241070000 1445390 1715790 1406970 1798470 1748980 1779980 1730360 1746580 1768340 1909510 FALSE TRUE 1388902.561 1666857.349 1661240.777 1891289.252 1805237.53 1815972.415 1751536.663 1710512.513 1567605.457 1780177.187 0.780204673 0.936343506 0.933188443 1.062416296 1.014077443 1.020107677 0.98391142 0.960866438 0.880589566 1 20.76358941 4.876433687 1.551857639 0.985893411 0.649486796 0.629808012 0.046746473 1.023253777 1.790068254 0.012977041 0.577212788 75237.38409 -4.876433687 -0.336406615 IYEYVESR ddPTM_BT-474_Pertuzumab_2h_R1 2 IYEYVESR 8 0 Q8WWY3-4;Q8WWY3;E7EVX8;Q8WWY3-3;Q8WWY3-2;E7EU94;E7ESX0;E7EN72 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 ; 141.52 0.0014708 585760000 595280 672050 536140 678140 654910 625300 675330 685080 635880 666270 FALSE TRUE 572015.7995 652883.792 633032.4244 713138.8867 675975.7749 637943.9944 683594.8906 670932.8586 563697.5682 621142.9394 0.920908479 1.051100722 1.019141303 1.148107531 1.088277322 1.027048613 1.100543606 1.080158553 0.907516664 1 19.24456578 4.876863424 2.3238881 1.05748609 0.849240383 0.248664075 0.063121405 1.373372959 6.154184483 0.015358277 0.665499093 75311.8688 -4.876863424 -0.208245707 TNSGISSASGGSTEPTT(ph)PDSERPAQALLR ddPTM_BT-474_Pertuzumab_2h_R1 3 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 TNSGISSASGGSTEPT(0.237)T(0.762)PDSERPAQALLR;TNSGISSASGGSTEPT(0.003)T(0.997)PDSERPAQALLR;T(0.009)NS(0.009)GIS(0.029)S(0.025)AS(0.025)GGS(0.018)T(0.016)EPT(0.076)T(0.792)PDS(0.001)ERPAQALLR 186.39 1.08E-17 1588920000 247162 315419 269009 312588 364300 340140 322421 330842 326519 306070 TRUE FALSE 237502.6358 306423.5589 317624.9104 328720.7041 376018.0403 347017.8638 326366.8846 324009.9971 289453.932 285339.6063 0.832350752 1.073890733 1.113146943 1.152033216 1.317791264 1.216157366 1.143784029 1.135524091 1.014419049 1 18.12232049 4.877122402 1.624266169 1.152574652 0.629467785 0.521468796 0.086574109 1.131783687 2.193124378 0.023206257 1.032115606 75356.79196 -4.877122402 -0.523106867 KAPKS(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAPKSPAK 8 2 P10412 P10412 HIST1H1E Histone H1.4 1 KAPKS(1)PAK;KAPKS(1)PAK 96.64 0.0069283 10438100000 32426000 17776000 13291800 5404700 8268900 890110 9862500 9356000 6197300 5746200 TRUE FALSE 31158756.07 17269045.88 15693923.93 5683637.215 8534876.678 908108.6341 9983200.225 9162795.33 5493808.485 5357004.756 5.816451075 3.223638334 2.92960799 1.060972964 1.593218051 0.169517982 1.86357875 1.710432555 1.025537354 1 22.35299515 4.877761457 0.923468779 1.242519633 9.159500435 0.87776288 0.534379423 0.850435727 0.482148157 0.173245166 7.177114604 75467.75959 -4.877761457 7.916980802 QNLHEIGER ddPTM_BT-474_Pertuzumab_2h_R1 1 QNLHEIGER 9 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8-6 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 0 143.61 0.00010153 366630000 64886 73414 62465 69080 75054 75054 68975 74477 84995 83595 FALSE TRUE 62350.18338 71320.3046 73753.81503 72645.22708 77468.18007 76571.6433 69819.13668 72939.02392 75346.72393 77933.03619 0.800048175 0.915148544 0.946374203 0.932149325 0.994035185 0.982531248 0.895886265 0.935919188 0.96681366 1 16.2499474 4.878045734 1.678562314 0.952707267 0.703564006 0.712426842 0.029963388 0.810309105 1.689510046 0.008123253 0.362015846 75517.17482 -4.878045734 -0.249143261 TTNESLLTS(ph)FPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTNESLLTSFPK 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 TTNESLLT(0.048)S(0.952)FPK 102.5 0.0011557 0 328870 259000 216690 192600 195740 204920 192430 324360 282560 205760 TRUE FALSE 316017.3968 251613.5736 255850.7032 202540.1091 202036.1549 209063.6228 194785.0159 317661.8527 250484.9734 191823.6919 1.647436735 1.311691851 1.333780518 1.055865973 1.053238799 1.089873835 1.015437738 1.656009482 1.305808323 1 17.54942139 4.880074419 1.547429049 1.210446573 1.928074626 0.343778017 0.191048475 2.148213904 3.707244943 0.057064518 2.585592363 75870.7573 -4.880074419 0.717628053 YGLFQHICTAYELVLADGSFVR ddPTM_BT-474_Pertuzumab_2h_R1 1 YGLFQHICTAYELVLADGSFVR 22 0 A0A0A0MTI1;Q15392-2;Q15392;A0A3B3IT58;A0A3B3ITT9 A0A0A0MTI1 DHCR24 Delta(24)-sterol reductase 0 225.05 6.40E-26 218890000 52874 84763 67657 116800 68340 79990 117110 92973 107960 93274 FALSE TRUE 50807.62562 82345.64223 79884.12492 122828.062 70538.21816 81607.45261 118543.2272 91053.07506 95704.83341 86956.4689 0.58428805 0.946975461 0.918667995 1.412523571 0.811190002 0.938486275 1.363247941 1.047110999 1.100606253 1 16.40800574 4.880796795 1.358579735 1.091849471 0.243024881 0.41742309 0.176482614 1.688748647 2.176784517 0.047265382 2.1516838 75997.06064 -4.880796795 -0.84882459 LNNEEHNELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNNEEHNELR 10 0 Q13546-2;Q13546 Q13546-2 RIPK1 Receptor-interacting serine/threonine-protein kinase 1 0 ; 179.19 2.13E-06 702790000 363000 451290 362410 486330 416500 448090 458500 443870 463650 500410 FALSE TRUE 348813.5587 438419.6511 427905.5488 511429.5496 429897.1008 457150.6868 464111.2602 434703.9294 411018.3958 466516.785 0.747697768 0.939772512 0.917235055 1.096272559 0.921504037 0.979923342 0.994843648 0.931807693 0.881036672 1 18.83156946 4.882995239 2.011608697 0.966381067 0.61930783 0.569190936 0.056461101 0.877587928 2.75044794 0.014041766 0.636473475 76382.74108 -4.882995239 -0.347073237 LVGSQEELASWGHEYVR ddPTM_BT-474_Pertuzumab_2h_R1 4 LVGSQEELASWGHEYVR 17 0 Q13200;Q13200-3;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 221.24 3.75E-15 2223880000 680530 794790 628650 875530 772380 833990 790890 793650 700080 892990 FALSE TRUE 653934.1352 772123.3674 742261.0392 920716.2082 797224.3042 850853.8492 800569.1484 777260.8502 620609.8534 832506.9919 0.785499872 0.927467727 0.891597364 1.105956127 0.957618749 1.022038082 0.961636546 0.933638826 0.74547104 1 19.66710286 4.884212647 1.692542779 0.957446085 0.677534036 0.243486184 0.088026195 2.083933285 4.370138513 0.022967241 1.058453475 76597.1563 -4.884212647 -0.279912049 ELGDVLFQMAEVHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELGDVLFQMAEVHR 14 0 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;I3L3J7;I3L125;I3L0M4;I3L526;I3L327;I3L1C8;I3L113;I3L2M4;I3L3C5;I3L2J6 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 0 ;;; 173.44 2.70E-06 381333000 615602 730490 588631 793690 701960 680940 775820 751660 740090 792580 FALSE TRUE 591543.5933 709657.1404 695009.7157 834652.436 724539.1809 694709.0733 785314.7172 736137.9583 656078.0859 738897.8506 0.800575604 0.960426586 0.940603245 1.1295911 0.98056745 0.940196365 1.062819058 0.996264853 0.88791446 1 19.49501541 4.884408855 1.68634768 0.998810264 0.674842566 0.449578636 0.063419912 1.283330924 2.667689376 0.016301025 0.752210659 76631.76969 -4.884408855 -0.323967697 DDGSWEVIEGYR ddPTM_BT-474_Pertuzumab_2h_R1 6 DDGSWEVIEGYR 12 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;;;; 265.55 2.89E-21 3310580000 1195460 1729610 1147080 2483880 1316270 1420670 2292970 2055110 1582260 1446780 FALSE TRUE 1148740.102 1680283.216 1354382.873 2612073.344 1358609.02 1449396.921 2321032.053 2012671.26 1402648.478 1348788.302 0.851683025 1.245772382 1.004147849 1.936607354 1.007281141 1.074591853 1.720827538 1.492206937 1.039932268 1 20.3632325 4.884645904 1.280410053 1.344664054 0.529648582 0.129897386 0.318462014 3.452567178 3.882574793 0.087239868 4.021225195 76673.60872 -4.884645904 -0.815015472 DNVYYYDEEGGGEEDQDFDLSQLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNVYYYDEEGGGEEDQDFDLSQLHR 25 0 A0A087WXI5;P12830-2;P12830 A0A087WXI5 CDH1 Cadherin-1;E-Cad/CTF1;E-Cad/CTF2;E-Cad/CTF3 0 259.44 5.31E-45 187270000 34155 67355 29659 112240 40880 51200 101240 101950 80198 71707 FALSE TRUE 32820.18484 65434.10135 35019.04106 118032.7199 42194.94233 52235.29908 102479.0054 99844.69687 71094.25926 66850.22102 0.49095103 0.97881653 0.52384331 1.765629463 0.63118628 0.781378106 1.532964347 1.493558216 1.063485777 1 16.02864471 4.884882147 0.498586274 1.257259225 1.88E-11 0.213528825 0.374274552 7.616186498 1.311272561 0.228970474 5.809423099 76715.32808 -4.884882147 -1.257259225 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR 31 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 299.52 2.25E-81 932980000 521230 601760 535510 588300 650030 645470 619250 669990 698000 694840 FALSE TRUE 500859.7553 584598.394 632288.5694 618662.2335 670938.8053 658521.8456 626828.5667 656154.4724 618765.9663 647777.8679 0.77319677 0.902467378 0.976088565 0.955053058 1.035754444 1.016585898 0.967659745 1.012931292 0.955213194 1 19.30513965 4.88595907 1.18246402 0.996007901 0.608486605 0.880637454 0.024892039 0.613434086 0.579470037 0.006917911 0.317026841 76905.79573 -4.88595907 -0.387521296 S(ph)FSEDVFQSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFSEDVFQSVK 11 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 S(0.998)FS(0.002)EDVFQSVK;S(0.977)FS(0.023)EDVFQSVK 184.11 5.30E-06 112752000 226046 195175 150492 173413 173018 118805 169715 224882 172440 197858 TRUE FALSE 217211.8724 189608.8001 177689.2521 182362.8657 178583.2811 121207.3185 171792.0229 220238.1081 152865.3341 184456.9014 1.177575199 1.027930094 0.963310403 0.988647561 0.968157221 0.657103733 0.931339633 1.193981393 0.828731985 1 17.49292424 4.888438313 1.372275634 0.950190513 1.338697847 0.241969205 0.128292224 3.050707669 3.966690497 0.038270442 1.803334707 77346.08083 -4.888438313 0.388507334 RKS(ph)LSDSESDDSK ddPTM_BT-474_Pertuzumab_2h_R1 8 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 RKS(0.972)LS(0.012)DS(0.016)ESDDSK;RKS(0.993)LS(0.006)DS(0.001)ESDDSK;RKS(0.988)LS(0.009)DS(0.002)ESDDSK;RKS(0.966)LS(0.027)DS(0.005)ES(0.001)DDSK;RKS(0.734)LS(0.181)DS(0.085)ESDDSK;RKS(0.972)LS(0.025)DS(0.003)ESDDSK;RKS(0.995)LS(0.005)DSESDDSK;RKS(0.929)LS(0.07)DS(0.001)ESDDSK 208.52 3.56E-08 16264950000 8625410 7151570 5830950 5704590 6638310 6501720 6369660 6735510 7921400 6799450 TRUE FALSE 8288319.441 6947614.226 6884732.374 5999004.574 6851837.27 6633189.233 6447613.804 6596419.365 7022195.881 6338917.195 1.307529218 1.096025395 1.086105428 0.946376864 1.08091604 1.046423077 1.017147504 1.040622422 1.107791073 1 22.59580499 4.889321213 1.675966739 1.038113553 1.48387722 0.773312598 0.043432573 0.638426897 1.294877765 0.010840954 0.514230542 77503.48176 -4.889321213 0.445763667 VFEEDALSWEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFEEDALSWEDK 12 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 227.94 2.73E-11 213289000 226070 210530 243930 268990 282230 248080 306110 356380 400920 394830 FALSE TRUE 217234.9345 204525.8905 288013.5772 282872.6061 291308.1843 253096.3476 309856.2657 349020.6285 355409.2424 368087.8124 0.590171495 0.555644288 0.782458879 0.768492182 0.79140948 0.687597739 0.841799851 0.948199361 0.965555583 1 18.48969046 4.890306414 0.196688755 1.063756924 0.114814269 0.801238139 0.064358911 7.034521749 0.243884036 0.157307582 1.678090021 77679.49858 -4.890306414 -0.948942655 GEEDTGQEEGGSRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEEDTGQEEGGSRR 14 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 112.42 0.00095313 190643000 223750 263350 215090 258860 247360 286840 259550 252360 272270 281490 FALSE TRUE 215005.6026 255839.5158 253961.5477 272219.7956 255316.559 292640.1013 262726.4505 247148.6778 241363.051 262424.4316 0.819304824 0.974907383 0.967751158 1.037326418 0.972914593 1.11514046 1.00115088 0.941789895 0.919743065 1 18.00154251 4.891162701 2.033768771 0.995349403 0.712131513 0.510941633 0.051049407 1.094550248 3.443770212 0.013726977 0.658745473 77832.80829 -4.891162701 -0.28321789 SES(ph)LSNCSIGK ddPTM_BT-474_Pertuzumab_2h_R1 5 SESLSNCSIGK 11 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SES(0.67)LS(0.33)NCSIGK;SES(0.999)LS(0.001)NCSIGK;SES(1)LSNCSIGK;SES(1)LSNCSIGK;SES(0.965)LS(0.035)NCSIGK 275.17 4.02E-27 4584410000 4755860 3922840 3247460 3014790 3434940 3020140 2893350 4213410 3814530 3380380 TRUE FALSE 4569995.733 3810964.444 3834348.261 3170383.673 3545427.965 3081209.3 2928759.683 4126401.611 3381520.546 3151423.852 1.450136811 1.209283366 1.216703446 1.006016272 1.125024158 0.977719737 0.9293449 1.309376906 1.073013566 1 21.58757237 4.891703974 1.089596137 1.08003625 1.717982056 0.556633736 0.104745502 1.899555803 1.494498568 0.032804044 1.507421054 77929.87395 -4.891703974 0.637945806 LLEEHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLEEHSR 7 0 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ;; 208.67 0.00016742 1386360000 1336570 2081620 1415960 3224740 1452470 1703950 2838500 2359760 1853810 1623800 FALSE TRUE 1284335.367 2022254.236 1671855.47 3391169.218 1499190.017 1738405.036 2873238.412 2311030.131 1643373.261 1513818.58 0.848407718 1.335863004 1.104396189 2.240142421 0.990336647 1.148357577 1.8980071 1.526622914 1.085581379 1 20.52976089 4.892220754 1.558644361 1.435190578 0.463789969 0.125802585 0.395358897 2.969351872 5.084149402 0.101902353 4.911020268 78022.66019 -4.892220754 -0.971400609 VLTLSERPLDFLDLERPPTT(ph)PQNEEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLTLSERPLDFLDLERPPTTPQNEEIR 27 2 Q9GZY8-5;Q9GZY8-2;Q9GZY8;C9JHF5;A0A0A0MS29;Q9GZY8-4;Q9GZY8-3 Q9GZY8-5 MFF Mitochondrial fission factor 1 VLTLSERPLDFLDLERPPT(0.328)T(0.672)PQNEEIR;VLTLSERPLDFLDLERPPT(0.249)T(0.751)PQNEEIR 210.36 6.46E-24 450680000 100218 169115 121258 258705 118388 174631 167170 197796 147246 153255 TRUE FALSE 96301.36976 164292.0058 143172.018 272056.7961 122196.0575 178162.1585 169215.8765 193711.4435 130531.2514 142874.9023 0.674025796 1.149901089 1.002079551 1.904160854 0.855266079 1.246980089 1.184363899 1.355811555 0.913605184 1 17.12439299 4.892223494 1.87898411 1.217760147 0.333705929 0.21583006 0.284312068 1.876163911 4.906212253 0.068573584 3.305996722 78023.1525 -4.892223494 -0.884054218 RTLLEQLDDDQ ddPTM_BT-474_Pertuzumab_2h_R1 3 RTLLEQLDDDQ 11 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;; 158.08 0.00062032 387520000 777330 870590 729040 851740 884900 925620 856750 913440 886160 939500 FALSE TRUE 746951.0842 845761.6256 860793.7454 895698.4035 913363.6121 944336.6706 867235.1628 894577.1448 785566.8319 875866.8282 0.852813533 0.965628105 0.982790668 1.022642227 1.042811056 1.078173805 0.990145003 1.021362056 0.896902139 1 19.74035201 4.892802294 1.425450585 1.0111271 0.74216411 0.51359142 0.04445407 1.370310241 1.922088098 0.012063265 0.581247709 78127.20611 -4.892802294 -0.26896299 ISSIQSIVPALEIANAHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISSIQSIVPALEIANAHR 18 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 212.69 1.64E-16 1364350000 1278780 1849220 1315710 2714100 1318390 1612350 2355400 1960440 1772990 1526890 FALSE TRUE 1228803.864 1796482.056 1553488.065 2854175.026 1360797.212 1644952.822 2384226.09 1919956.229 1571727.608 1423472.38 0.86324391 1.262042089 1.091336991 2.005079316 0.955970225 1.155591668 1.674936671 1.348783619 1.104150407 1 20.44098307 4.89309041 1.679337682 1.333376491 0.558853088 0.137826392 0.309963311 2.689292574 5.435056732 0.078062865 3.781455398 78179.05383 -4.89309041 -0.774523404 CLHMFLQEEAIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 CLHMFLQEEAIDR 13 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 190.85 4.06E-06 197720000 97720 111880 87561 108310 126630 113820 111650 100910 123960 132490 FALSE TRUE 93900.99436 108689.2919 103385.2205 113899.8921 130703.169 116121.5184 113016.4061 98826.17324 109888.5805 123516.3343 0.760231389 0.879958854 0.837016586 0.922144368 1.058185298 0.940130867 0.914991582 0.800106106 0.889668408 1 16.91434232 4.89426782 1.159831434 0.916428679 0.654031465 0.346121146 0.068297678 3.02083266 2.703432356 0.022147221 1.043813945 78391.29158 -4.89426782 -0.262397214 TGSVQTS(ph)PSSTPVAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGSVQTSPSSTPVAGR 16 0 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 TGSVQT(0.031)S(0.934)PS(0.003)S(0.031)TPVAGR;TGSVQT(0.262)S(0.732)PS(0.003)S(0.003)TPVAGR 273.55 1.40E-26 606830000 736370 814010 683500 870380 834880 830730 949980 903700 975890 993970 TRUE FALSE 707591.8463 790795.2318 807023.6544 915300.4161 861734.6734 847527.9298 961606.1394 885038.2792 865111.0585 926647.5266 0.763604095 0.853393776 0.870906824 0.987754664 0.929948712 0.914617377 1.037725901 0.955097007 0.933592368 1 19.82166115 4.8951292 0.698362383 0.971301611 0.591854619 0.759176043 0.037206646 1.697910787 0.540637996 0.014646959 0.535527104 78546.92729 -4.8951292 -0.379446992 GLNNDS(ph)PERR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLNNDSPERR 10 1 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 GLNNDS(1)PERR;GLNNDS(1)PERR 82.069 0.011711 176369000 96022 106251 85991 108519 100685 105679 108988 110044 99206 103250 TRUE FALSE 92269.35408 103220.8255 101531.4866 114119.6786 103923.6245 107815.9018 110321.8277 107771.5529 87944.55079 96256.78553 0.958575061 1.072348562 1.054798225 1.185575416 1.079649854 1.120086248 1.146120007 1.119625514 0.913645207 1 16.55460063 4.89526763 1.836589581 1.092192554 0.872574173 0.166257921 0.074163055 2.103227545 5.182282282 0.018439718 0.905816467 78571.96773 -4.89526763 -0.219618381 FPEAEALS(ph)PEQAAHYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 FPEAEALSPEQAAHYLR 17 0 Q2NKX8 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 FPEAEALS(1)PEQAAHYLR 175.33 8.01E-10 59872000 13794 14981 21122 22771 21369 26177 25610 29060 26183 34864 TRUE FALSE 13254.91523 14553.75655 24939.21526 23946.21404 22056.35329 26706.31688 25923.42284 28459.90084 23210.81561 32502.63023 0.407810541 0.447771656 0.767298372 0.736746961 0.678602105 0.821666329 0.797579232 0.875618393 0.714121148 1 14.98826885 4.895784903 0.556845574 0.842307091 3.49E-20 0.743620354 0.086905496 2.239755592 0.466920443 0.043271793 1.271203468 78665.6078 -4.895784903 -0.842307091 down DLAHTPSQLEGLDPATEAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLAHTPSQLEGLDPATEAR 19 0 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 0 ;;; 265.64 1.96E-31 1373280000 615090 683010 561580 661700 632290 734880 693390 632920 724630 738830 FALSE TRUE 591051.6028 663531.2235 663069.9983 695850.4163 652628.1821 749739.7771 701875.9142 619849.9808 642373.0403 688788.386 0.858103323 0.963331027 0.962661409 1.01025283 0.947501722 1.088490736 1.019000797 0.89991352 0.932613054 1 19.39370129 4.896424872 1.932944149 0.980521352 0.779949417 0.35875914 0.049598836 1.663614266 4.593513764 0.013778736 0.683500987 78781.61362 -4.896424872 -0.200571935 RGY(ph)INK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGYINK 6 1 P14410 P14410 SI "Sucrase-isomaltase, intestinal;Sucrase;Isomaltase" 1 RGY(1)INK 92.76 0.040959 0 99320 194260 171440 235060 207500 166900 243440 383540 99947 172440 TRUE FALSE 95438.4646 188719.895 202423.0217 247191.4748 214174.4259 170274.8324 246419.2915 375619.765 88601.43557 160760.4852 0.593668677 1.173919665 1.259159061 1.537638273 1.332257897 1.059183369 1.532834958 2.336517985 0.551139389 1 17.29455331 4.89710827 1.195996326 1.44695007 2.13E-16 0.16225265 0.445815347 3.220293001 3.063721255 0.131641836 6.315427575 78905.68061 -4.89710827 -1.44695007 GHKHEDGT(ph)QSDSEDPLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GHKHEDGTQSDSEDPLAK 18 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 GHKHEDGT(0.5)QS(0.5)DS(0.001)EDPLAK 101.71 0.00090204 1303900000 458820 394910 330450 319280 349200 347930 414070 323330 520350 427210 TRUE FALSE 440888.8071 383647.5535 390169.6658 335758.0791 360432.3351 354965.383 419137.5125 316653.1225 461282.0495 398274.6862 1.10699681 0.963273757 0.979649672 0.843031432 0.904984293 0.891257706 1.052383009 0.795062135 1.158200773 1 18.60340426 4.897928291 1.791957721 0.935659517 1.219671949 0.1581977 0.100155293 2.201780675 5.098113104 0.024133217 1.204052828 79054.8085 -4.897928291 0.284012432 LVPLLDRPFDETTYEETED ddPTM_BT-474_Pertuzumab_2h_R1 7 LVPLLDRPFDETTYEETED 19 1 O15270 O15270 SPTLC2 Serine palmitoyltransferase 2 0 ;;;;;; 180.17 2.79E-13 697711000 451268 648906 498879 842557 507124 644777 679642 732672 623390 666953 FALSE TRUE 433631.9477 630399.8362 589037.5328 886041.4677 523436.104 657814.8327 687959.6621 717542.0672 552625.3807 621779.6792 0.697404502 1.013863684 0.947341241 1.425008725 0.841835334 1.057954859 1.106436387 1.154013377 0.88878006 1 19.24604394 4.898816407 1.782438038 1.071314518 0.450987369 0.316380898 0.154504674 1.600464402 3.653832879 0.037976595 1.90451284 79216.63804 -4.898816407 -0.620327149 DEILEWESR ddPTM_BT-474_Pertuzumab_2h_R1 4 DEILEWESR 9 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;;; 170.3 0.0001345 1299190000 1170810 1162120 1107680 1234250 1198450 1247170 1455320 1360130 1483190 1396900 FALSE TRUE 1125053.451 1128977.475 1307862.416 1297949.79 1236999.233 1272388.632 1473130.641 1332042.84 1314824.489 1302286.719 0.863906108 0.866919288 1.004281467 0.996669759 0.949867041 0.977041855 1.131187641 1.022849132 1.009627504 1 20.31261568 4.899104944 0.562459776 1.034962961 0.685734595 0.582460834 0.047470982 3.177779939 0.67286956 0.025261142 0.755336659 79269.28558 -4.899104944 -0.349228366 LIEGLSHEVIVSAACGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIEGLSHEVIVSAACGR 17 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 245.19 1.46E-20 2528200000 1523980 1785450 1428370 1815860 1798280 1769510 1713850 1654510 1895180 1964110 FALSE TRUE 1464421.177 1734530.714 1686508.233 1909576.752 1856123.309 1805290.705 1734824.609 1620343.79 1680047.112 1831079.08 0.799758565 0.947272421 0.921046093 1.042869624 1.013677306 0.985916296 0.947432925 0.884911967 0.917517506 1 20.80426267 4.901838313 2.081884904 0.960649931 0.698083376 0.529732691 0.046017109 1.209364589 3.899158948 0.013373014 0.695178705 79769.76505 -4.901838313 -0.262566554 DLSSS(ph)PPGPYGQEMYAFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLSSSPPGPYGQEMYAFR 18 0 O43741;O43741-2 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 DLSS(0.022)S(0.978)PPGPYGQEMYAFR;DLSS(0.004)S(0.996)PPGPYGQEMYAFR;DLSS(0.007)S(0.993)PPGPYGQEMYAFR;DLS(0.006)S(0.044)S(0.95)PPGPYGQEMYAFR 261.17 9.42E-31 575460000 508210 555617 460975 552329 528860 579739 532309 595224 594509 583345 TRUE FALSE 488348.5913 539771.3472 544283.4368 580834.7659 545871.2622 591461.7198 538823.5568 582932.4164 527022.8307 543834.5236 0.897972766 0.992528653 1.000825459 1.068035847 1.003745144 1.087576633 0.990785861 1.071892995 0.96908675 1 19.05280821 4.902260648 1.375466998 1.031442529 0.800998013 0.505604102 0.037410344 1.306185071 1.665615344 0.009229079 0.463017047 79847.37597 -4.902260648 -0.230444516 EENEGVYNGSWGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 EENEGVYNGSWGGR 14 0 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GTY9;P49419-4;A0A1B0GUY0;A0A0J9YWF7;H0YHM6;F8WDY6;A0A0J9YWM6;F8VVF2;F8WD33;A0A1B0GW65;A0A0J9YWK1 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ;; 232.42 4.08E-13 866430000 629280 859170 685290 986180 849290 948900 888120 871430 780990 896210 FALSE TRUE 604687.0419 834667.3128 809137.1472 1037076.868 876608.1842 968087.4081 898989.0782 853434.666 692335.2894 835508.8984 0.723735011 0.998992727 0.968436301 1.241251733 1.049190722 1.158679949 1.075977862 1.021454909 0.828639037 1 19.67229567 4.903047468 1.740531619 1.055691394 0.498548975 0.454679314 0.103983287 1.323963956 2.837136519 0.027097134 1.391774769 79992.16805 -4.903047468 -0.557142419 FLATEGAPDFLCPEELEHVSR ddPTM_BT-474_Pertuzumab_2h_R1 4 FLATEGAPDFLCPEELEHVSR 21 0 A0A494C1T9;Q6ZRV2 A0A494C1T9 FAM83H Protein FAM83H 0 ;;; 232.54 1.30E-26 1010085000 655816 862152 686696 972260 858746 936440 878977 785587 863080 1012603 FALSE TRUE 630185.9857 837564.2691 810797.2427 1022438.455 886368.345 955375.4584 889734.1835 769364.3539 765106.7767 944018.4969 0.66755682 0.8872329 0.858878555 1.083070362 0.93893112 1.012030444 0.942496557 0.814988643 0.810478586 1 19.8484556 4.903188888 1.771315728 0.929420846 0.490901861 0.483093254 0.082127853 1.409171626 3.140064739 0.022994397 1.183584562 80018.22028 -4.903188888 -0.438518985 SAS(ph)ASPLTPCSVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SASASPLTPCSVTR 14 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 S(0.002)AS(0.964)AS(0.033)PLTPCSVTR;S(0.001)AS(0.954)AS(0.045)PLTPCSVTR 156.24 5.90E-06 350420000 445310 290460 217332 215440 210860 188440 175119 408490 192239 151451 TRUE FALSE 427906.7929 282176.3652 256608.7269 226558.8842 217642.5034 192250.3859 177262.1587 400054.5388 170416.8347 141193.0889 3.030649703 1.998514003 1.817431214 1.604603214 1.54145295 1.361613287 1.255459174 2.833386124 1.206977169 1 17.10730995 4.905841935 1.592207924 1.669130487 4.002107346 0.448151693 0.481159958 1.689323109 2.949975873 0.133248158 6.904625262 80508.53707 -4.905841935 2.332976859 SELHLMDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SELHLMDR 8 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ;;; 137.06 0.00076415 1956810000 987350 1822140 1276410 2923460 1166590 1323010 2670380 1955610 1765970 1558240 FALSE TRUE 948763.2704 1770174.351 1507085.681 3074340.121 1204114.427 1349762.169 2703060.909 1915225.97 1565504.489 1452699.017 0.653103815 1.218541715 1.037438357 2.116295313 0.828880871 0.929140967 1.860716417 1.318391455 1.077652336 1 20.47030439 4.90751953 1.734038651 1.315438667 0.198878307 0.174591703 0.394126652 2.506668763 5.273013265 0.100221872 5.283899816 80820.12727 -4.90751953 -1.116560359 RPGFS(ph)PTSHR ddPTM_BT-474_Pertuzumab_2h_R1 3 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 RPGFS(0.587)PT(0.279)S(0.133)HR;RPGFS(0.68)PT(0.241)S(0.079)HR;RPGFS(0.994)PT(0.003)S(0.003)HR 128.96 0.00019338 1977283000 464710 572125 444411 646778 598514 510634 546881 611962 594272 657227 TRUE FALSE 446548.6194 555808.5552 524725.9536 680158.2901 617765.7464 520959.3693 553573.8933 599324.7708 526812.734 612712.4299 0.728806203 0.907127925 0.856398415 1.110077513 1.008247452 0.850251021 0.903480762 0.978150176 0.859804222 1 19.22485059 4.907866805 1.521216375 0.950013382 0.572485487 0.416556265 0.077605483 1.722204807 2.708421016 0.021031595 1.096499346 80884.7794 -4.907866805 -0.377527895 ASSIIDELFQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSIIDELFQDR 12 0 E7ERK6;H0YC35;H0YLK8;P10909-4;P10909-6;P10909;P10909-5;P10909-2;P10909-3 E7ERK6 CLU Clusterin;Clusterin;Clusterin beta chain;Clusterin alpha chain 0 ; 185.18 3.11E-05 60305000 55333 67377 53862 77286 62003 69851 76767 77766 67484 79833 FALSE TRUE 53170.52519 65455.47393 63596.06155 81274.73972 63997.3828 71263.43508 77706.49751 76160.10492 59823.49924 74425.8398 0.714409476 0.879472427 0.854489002 1.092023146 0.859881232 0.957509318 1.044079552 1.023301922 0.803800124 1 16.18351598 4.90822573 1.026271348 0.972029102 0.517568417 0.436262902 0.085178143 2.222754403 1.507609277 0.025145527 1.200169674 80951.65464 -4.90822573 -0.454460685 QGSITS(ph)PQANEQSVT(ph)PQRR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.003)IT(0.437)S(0.561)PQANEQS(0.032)VT(0.968)PQRR 162.83 5.95E-11 173330000 201390 222480 176460 235530 206040 213380 234200 215660 244310 229230 TRUE FALSE 193519.4562 216135.0882 208350.2473 247685.7315 212667.4637 217694.6898 237066.2097 211206.5456 216576.953 213704.0479 0.905548856 1.011375734 0.974947594 1.159012821 0.99514944 1.018673684 1.109320165 0.988313266 1.013443382 1 17.70525471 4.908346126 1.492041553 1.036780547 0.812561135 0.328563769 0.054669915 1.980218362 2.981866532 0.014123157 0.73649382 80974.09935 -4.908346126 -0.224219412 KENS(ph)ESEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 KENSESEKR 9 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KENS(0.986)ES(0.014)EKR;KENS(0.993)ES(0.007)EKR;KENS(0.999)ES(0.001)EKR;KENS(0.997)ES(0.003)EKR 123.84 0.00028517 1055380000 1656270 1245470 1045850 878720 1037570 1107590 1070800 1265000 1273860 1359480 TRUE FALSE 1591541.137 1209950.415 1234858.36 924070.8445 1070944.381 1129986.229 1083904.771 1238877.308 1129256.753 1267401.209 1.255751633 0.954670397 0.974323167 0.729106804 0.844992394 0.891577364 0.85521835 0.977494182 0.891001796 1 20.27344187 4.908529532 1.708529197 0.888276552 1.51262827 0.678151262 0.074287619 0.895096353 1.817556083 0.019689335 1.042620595 81008.30255 -4.908529532 0.624351718 SLS(ph)PVAAPPLREPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLSPVAAPPLREPR 14 1 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 S(0.126)LS(0.874)PVAAPPLREPR;S(0.163)LS(0.837)PVAAPPLREPR;SLS(1)PVAAPPLREPR;S(0.369)LS(0.631)PVAAPPLREPR 115.87 0.00023896 4838150000 4096850 4515530 3729630 4479050 4383020 4775450 4476440 4711720 4718370 4540240 TRUE FALSE 3936740.573 4386751.506 4403657.106 4710214.307 4524003.819 4872012.871 4531224.012 4614421.335 4182760.419 4232725.501 0.93007226 1.03638932 1.040383343 1.112808829 1.068815783 1.151034451 1.070521585 1.090177318 0.98819553 1 22.0131555 4.908822224 1.407739649 1.075724831 0.822930034 0.425485658 0.046421408 1.566524938 2.076048554 0.012036637 0.624405143 81062.91639 -4.908822224 -0.252794796 ALEKEEEEEKQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALEKEEEEEKQK 12 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 82.102 0.0089192 1026700000 505490 363860 331120 215280 332730 309960 341770 403810 490170 333950 FALSE TRUE 485734.892 353483.0691 390960.7497 226390.6266 343432.5626 316227.6036 345952.6835 395471.1824 434527.9566 311331.269 1.560186657 1.135392118 1.255770906 0.727169575 1.103109764 1.015727089 1.111204424 1.270258473 1.395709329 1 18.24809096 4.90913009 2.138845616 1.111115944 1.850418658 0.376680861 0.172422005 1.499295119 5.032319645 0.045217945 2.500102691 81120.40123 -4.90913009 0.739302714 NSSAVEQDHAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NSSAVEQDHAK 11 0 Q9NXV6 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 0 ; 150.14 3.40E-05 403270000 693580 626500 539120 522310 560780 561320 563390 636240 734260 646280 FALSE TRUE 666474.1268 608632.8334 636550.9767 549266.4817 578817.998 572670.275 570284.9353 623101.4217 650909.8831 602506.88 1.106168492 1.010167441 1.05650408 0.911635203 0.960682803 0.950479229 0.946520205 1.034181422 1.080336017 1 19.20061819 4.909772512 1.291069388 0.986666559 1.191014497 0.3262444 0.049614479 2.50475571 2.749714243 0.014571249 0.747997021 81240.48578 -4.909772512 0.204347938 NEQEEQEEKREIK ddPTM_BT-474_Pertuzumab_2h_R1 1 NEQEEQEEKREIK 13 2 Q9C0D0;Q4VY13;Q4VY12 Q9C0D0 PHACTR1 Phosphatase and actin regulator 1;Phosphatase and actin regulator 0 53.252 0.082297 170230000 91411 191320 148840 226310 221830 272310 225690 185630 139760 237550 FALSE TRUE 87838.55706 185863.7409 175738.6989 237989.8862 228965.3634 277816.2948 228452.0617 181796.6756 123895.0307 221460.5269 0.396633018 0.839263518 0.79354412 1.074637948 1.033887919 1.254473195 1.031570117 0.820898777 0.559445209 1 17.75669005 4.910089364 1.415493568 0.961947205 1.00E-17 0.467043632 0.177054042 1.7629716 2.358909456 0.051490657 2.689233046 81299.77873 -4.910089364 -0.961947205 KVS(ph)SAEGAAKEEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVSSAEGAAKEEPK 14 2 P05114;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 KVS(0.986)S(0.014)AEGAAKEEPK 158.65 2.63E-06 383320000 794350 519730 308600 261110 372350 262390 249000 346480 303420 228060 TRUE FALSE 763305.9238 504907.8093 364370.8848 274585.9184 384326.9759 267695.7056 252047.3365 339325.0669 268977.0336 212613.2931 3.59011383 2.374770655 1.713772829 1.291480483 1.807633805 1.25907323 1.185473085 1.595972961 1.265099796 1 17.69787227 4.910284998 1.074124678 1.362006464 5.39480436 0.91723543 0.210522746 0.58782413 0.43705498 0.060076374 2.938029302 81336.40975 -4.910284998 4.032797896 up QPS(ph)PSPSPTER ddPTM_BT-474_Pertuzumab_2h_R1 1 QPSPSPSPTER 11 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;P29590-14;P29590-10;P29590-12;P29590-13;P29590-11;H3BT57 P29590-2;P29590-12 PML Protein PML 1 QPS(0.946)PS(0.052)PS(0.002)PTER 131.32 0.00021582 140270000 119300 130360 111610 126960 126230 146220 144820 125570 143120 145020 TRUE FALSE 114637.6241 126642.2604 131780.4098 133512.4208 130290.3026 149176.6686 146592.3505 122976.9356 126873.6176 135197.6662 0.847926057 0.936719279 0.974723998 0.987534952 0.963702305 1.103396773 1.084281664 0.90960842 0.93843053 1 17.04471072 4.911310103 1.122236331 0.998079412 0.729100427 0.407826029 0.055791227 2.581969881 2.100780422 0.017983211 0.895945957 81528.62211 -4.911310103 -0.268978985 QNRDEVLDNLLAFVCDIRPEIHENYR ddPTM_BT-474_Pertuzumab_2h_R1 2 QNRDEVLDNLLAFVCDIRPEIHENYR 26 2 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 164.46 8.26E-12 279140000 236980 239460 137167 147888 161931 168780 137308 129970 148977 167638 FALSE TRUE 227718.5596 232630.8353 161956.1282 155520.5174 167139.6577 172192.8472 138988.4164 127286.0741 132065.7555 156283.7289 1.457084248 1.488516027 1.03629552 0.9951165 1.069462949 1.101796383 0.889333889 0.814455062 0.845038421 1 17.25380806 4.912365279 0.538437232 0.887498825 2.096726372 0.773500433 0.10493949 2.217433752 0.42929433 0.060154583 1.75690098 81726.94764 -4.912365279 1.209227548 S(ph)AS(ph)PERMD ddPTM_BT-474_Pertuzumab_2h_R1 4 SASPERMD 8 1 Q16629;Q16629-4;C9JAB2;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 2 S(1)AS(1)PERMD;S(1)AS(1)PERMD;S(1)AS(1)PERMD;S(1)AS(1)PERMD 100.93 0.0068034 4914080000 5900850 5570430 5013610 5853410 5614770 5736300 6064380 6274740 7153230 6597300 TRUE FALSE 5670238.258 5411566.79 5919680.854 6155505.192 5795374.176 5852291.916 6138597.697 6145164.426 6341225.319 6150458.995 0.921921155 0.879863892 0.962477899 1.000820459 0.94226694 0.951521166 0.998071478 0.999139159 1.0310166 1 22.55226265 4.912505276 0.313978558 1.015149449 0.795285246 0.605608917 0.027227246 5.576652409 0.411953577 0.030080846 0.48210407 81753.29702 -4.912505276 -0.219864203 SPAAPYFLGSSFS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPAAPYFLGSSFSPVR 16 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 SPAAPYFLGS(0.007)S(0.035)FS(0.958)PVR;SPAAPYFLGSS(0.004)FS(0.996)PVR;SPAAPYFLGS(0.005)S(0.029)FS(0.966)PVR 147.09 1.11E-06 437747000 411256 383050 376978 328238 350029 269072 455200 364901 387170 470720 TRUE FALSE 395183.6609 372125.789 445106.3104 345178.4025 361288.0007 274512.8202 460770.8738 357365.6668 343220.0847 438837.7151 0.900523467 0.847980418 1.014284541 0.786574149 0.823283843 0.625545186 1.049980113 0.814345838 0.782111639 1 18.743328 4.912536163 0.003748502 1.70143754 1.80E-07 0.011473308 0.12215203 649907.0376 359.1431423 79170.73861 83893.7348 81759.11149 -4.912536163 -1.70143736 QGSKDPAEGDGAQPEETPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGSKDPAEGDGAQPEETPR 19 1 Q14697-2;E9PKU7;E9PNH1 Q14697-2 GANAB Neutral alpha-glucosidase AB 0 79.293 0.0048464 0 102160 123950 107470 118660 150060 121410 126390 136270 145180 131980 FALSE TRUE 98167.47426 120415.0674 126892.2197 124784.0568 154886.8162 123864.9934 127936.7986 133455.9769 128699.775 123040.877 0.797844396 0.978659046 1.031301326 1.014167485 1.258824058 1.006697907 1.039791017 1.084647477 1.045992016 1 16.90877817 4.912619082 1.272360761 1.070791401 0.588001173 0.564326537 0.070396982 1.423834312 1.507813872 0.019175056 0.993295377 81774.72313 -4.912619082 -0.482790228 ETIFELEDQVEQHR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETIFELEDQVEQHR 14 0 Q5M775-4;Q5M775;J3KSG2;Q5M775-5;Q5M775-3;Q5M775-2;J3KRN9;J3QQM0 Q5M775-4 SPECC1 Cytospin-B 0 128.21 7.50E-05 31495000 15868 18329 15329 18444 18001 18699 18195 20335 16880 21762 FALSE TRUE 15247.86102 17806.27487 18099.29129 19395.89705 18580.01851 19077.10659 18417.67585 19915.07514 14963.85317 20288.04036 0.751568942 0.877673474 0.89211629 0.956026147 0.915811394 0.940312926 0.907809504 0.981616499 0.73757016 1 14.3083419 4.914461944 1.482518497 0.922051341 0.624223844 0.348827921 0.067782161 1.841605588 2.702355976 0.016915526 0.908653041 82122.45888 -4.914461944 -0.297827497 ADS(ph)LLAVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADSLLAVVK 9 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 ADS(1)LLAVVK;ADS(1)LLAVVK 120.77 0.00066359 73043000 251230 202950 173662 149171 168994 164314 170329 232949 213889 208318 TRUE FALSE 241411.6539 197162.0647 205046.5865 156869.7332 174429.8455 167636.5417 172413.5373 228138.5217 189609.2174 194208.4363 1.243054413 1.015208548 1.055806794 0.807739026 0.898157921 0.863178474 0.887775735 1.174709637 0.97631813 1 17.56724635 4.91551072 1.56002287 0.959611179 1.449543403 0.432257735 0.098688568 1.892935293 3.097957805 0.029546609 1.60791033 82321.01561 -4.91551072 0.489932224 DLWEYIED ddPTM_BT-474_Pertuzumab_2h_R1 2 DLWEYIED 8 0 Q9Y4X5;A0A087WT96 Q9Y4X5 ARIH1 E3 ubiquitin-protein ligase ARIH1 0 ; 90.777 0.030141 24788900 82556 95300 78661 95935 100018 90623 95214 95441 105026 115796 FALSE TRUE 79329.62025 92582.13731 92876.7925 100886.2168 103235.1698 92455.45915 96379.25741 93470.11 93103.88878 107953.0338 0.734853088 0.857614965 0.860344441 0.934538042 0.956297069 0.856441509 0.892788781 0.865840512 0.862448099 1 16.72004426 4.916909778 1.446671904 0.899299748 0.611229376 0.567556831 0.044762031 1.372063989 1.900234157 0.01185393 0.641920798 82586.63629 -4.916909778 -0.288070372 GDMEQNDSDNRR ddPTM_BT-474_Pertuzumab_2h_R1 17 GDMEQNDSDNRR 12 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;;;;;;;;;;;;;;;; 215.51 6.62E-11 5893336500 2912964.3 3306321.7 2682681.6 3318577 3268930.5 3464965.8 3224522.8 3216862.9 3315682.6 3452003 FALSE TRUE 2799122.435 3212028.642 3167501.841 3489849.157 3374078.618 3535029.783 3263985.475 3150433.557 2939300.212 3218195.762 0.869780039 0.998083672 0.98424772 1.084411706 1.048437966 1.098450823 1.01422838 0.978944039 0.913337916 1 21.61782066 4.918140345 1.820864424 1.019200588 0.763094012 0.421378862 0.050754032 1.569575126 3.590234112 0.01408873 0.798683716 82820.97611 -4.918140345 -0.256106576 AATGEEVSAEDLGGADLHCR ddPTM_BT-474_Pertuzumab_2h_R1 1 AATGEEVSAEDLGGADLHCR 20 0 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;D6RD67 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 192.16 1.20E-17 426890000 69264 104280 65099 151090 77789 87668 142740 122530 99142 82132 FALSE TRUE 66557.0863 101306.0365 76863.83742 158887.773 80291.15383 89440.70703 144486.8948 119999.7127 87887.8158 76569.12648 0.869241813 1.323066374 1.003848953 2.075089273 1.048610028 1.168104054 1.887012448 1.567207544 1.147823148 1 16.22447518 4.918589944 1.141034241 1.435696628 0.457398048 0.133346305 0.358561269 4.054795299 3.378878529 0.101272768 5.214688437 82906.76014 -4.918589944 -0.97829858 RVGELER ddPTM_BT-474_Pertuzumab_2h_R1 4 RVGELER 7 1 Q08379;B7ZC06;H0Y7B8 Q08379 GOLGA2 Golgin subfamily A member 2 0 ;;; 151.04 0.0030601 400170000 385510 479517 379053 523796 521187 458182 487153 475155 458755 508512 FALSE TRUE 370443.843 465841.6447 447556.3091 550829.1743 537951.4532 467446.754 493114.9241 465342.8832 406679.0557 474070.0293 0.781411648 0.982643103 0.944072144 1.161915203 1.134751028 0.986028909 1.040173168 0.981591019 0.857845952 1 18.85474066 4.919070115 1.696054035 1.021096596 0.607363866 0.411767521 0.082697474 1.6442413 3.208388667 0.02261606 1.272216756 82998.47538 -4.919070115 -0.413732729 VKDWVER ddPTM_BT-474_Pertuzumab_2h_R1 4 VKDWVER 7 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;; 96.668 0.011457 2972480000 2710670 2913740 3198350 3838750 3764540 4013070 4962370 4616200 5496850 5932320 FALSE TRUE 2604734.02 2830642.988 3776362.992 4036868.348 3885629.848 4094217.025 5023100.968 4520873.857 4872870.633 5530518.682 0.470974635 0.511822335 0.682822572 0.729925813 0.702579644 0.740295307 0.908251334 0.817441205 0.881087455 1 22.39898336 4.919297496 0.24026536 0.992848585 1.89E-14 0.915068463 0.046154462 3.146070567 0.146273005 0.072738655 0.948418338 83041.94175 -4.919297496 -0.992848585 down NSLLAGGDDDTMSVISGISS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVIS(0.005)GIS(0.186)S(0.809)R 129.72 1.68E-05 54854000 147030 83827 59927 55684 59049 46183 35266 118670 46969 46196 TRUE FALSE 141283.905 81436.33604 70757.14197 58557.85791 60948.36471 47116.8519 35697.59586 116219.423 41637.27603 43067.10377 3.280552735 1.890917403 1.642951018 1.359688783 1.415195343 1.094033445 0.828883132 2.698566025 0.966800002 1 15.39429869 4.9193328 1.57337694 1.450266679 4.659015485 0.563852596 0.503732123 1.381749485 2.285829026 0.139665162 7.767095456 83048.69255 -4.9193328 3.208748806 SCTKPS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 6 SCTKPSPSK 9 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 SCT(0.012)KPS(0.986)PS(0.002)K;SCTKPS(0.995)PS(0.005)K;SCTKPS(0.994)PS(0.006)K;SCTKPS(0.988)PS(0.012)K;SCTKPS(0.992)PS(0.008)K;SCT(0.001)KPS(0.993)PS(0.006)K 117.27 0.00071404 9858610000 8061060 6475850 5462500 4873480 5510900 4512250 6222790 6951340 6736000 6641300 TRUE FALSE 7746024.863 6291165.099 6449695.263 5125000.887 5688163.103 4603490.787 6298946.365 6807792.4 5971357.52 6191478.836 1.251078308 1.016100558 1.04170513 0.827750691 0.918708317 0.743520395 1.017357328 1.099542223 0.9644477 1 22.56185261 4.919492767 1.51426814 0.951612211 1.474615697 0.463669652 0.097470178 1.815349573 2.761994455 0.029088113 1.608358915 83079.28813 -4.919492767 0.523003486 GLNVIGASDQS(ph)PLQSPSNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLNVIGASDQSPLQSPSNLR 20 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 GLNVIGASDQS(1)PLQSPSNLR;GLNVIGASDQS(1)PLQSPSNLR 240.94 1.06E-29 245860000 275050 323160 247110 345840 335240 331480 325510 320340 303520 363420 TRUE FALSE 264300.7419 313943.7932 291768.2739 363688.8438 346023.2991 338182.7527 329493.6888 313724.8671 269065.6821 338805.2397 0.780096383 0.926620242 0.861168128 1.073445157 1.02130445 0.9981627 0.972516508 0.925974071 0.794160333 1 18.37009666 4.919601617 1.317941664 0.962436366 0.645869717 0.334371976 0.075514524 2.447817309 2.761321308 0.021561965 1.160438154 83100.11353 -4.919601617 -0.316566648 TLS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 5 TLSPGK 6 0 Q9H307;C9JLG1;Q8NFU7;P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;F5H212;P15822;A0A0D9SFF3;P15822-2;P15822-3 Q9H307;P04626-5;F5H212 PNN;HIVEP1;TET1;ERBB2 Pinin;Methylcytosine dioxygenase TET1;Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase;Zinc finger protein 40 1 T(0.001)LS(0.999)PGK;T(0.031)LS(0.969)PGK;T(0.004)LS(0.996)PGK;T(0.001)LS(0.999)PGK;TLS(1)PGK 118.32 0.023039 11808390000 6663100 9698400 6791690 13731800 7937100 6898500 12042100 13101400 8275000 6223880 TRUE FALSE 6402698.686 9421811.128 8019099.463 14440499.84 8192404.03 7037992.397 12189474.82 12830851.51 7335656.692 5802331.064 1.103470073 1.623797578 1.3820479 2.488741108 1.411915994 1.212959467 2.100789267 2.211327029 1.264260279 1 22.46820118 4.920651924 1.461931268 1.736516468 0.636099877 0.076250963 0.467191873 3.826285026 5.382213882 0.12522655 6.920097503 83301.32773 -4.920651924 -1.100416591 QVSIEEGER ddPTM_BT-474_Pertuzumab_2h_R1 3 QVSIEEGER 9 0 P20340-2;P20340;P20340-4;Q53S08 P20340-2 RAB6A;RAB6C Ras-related protein Rab-6A 0 ;; 152.37 0.003426 300510000 538660 637010 513390 709340 568060 556320 672510 708930 751850 669620 FALSE TRUE 517608.5717 618843.0985 606170.9933 745949.1224 586332.1658 567569.1716 680740.3786 694290.3478 666503.14 624266.041 0.829147411 0.991313091 0.971013884 1.194921834 0.939234441 0.909178354 1.090465177 1.112170617 1.067658813 1 19.25180146 4.920879953 1.401925271 1.045492599 0.664174837 0.370790872 0.08100283 2.091794592 2.6871943 0.023024278 1.263241269 83345.07722 -4.920879953 -0.381317762 EEHETDEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEHETDEKR 9 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ;;; 200.6 1.48E-05 545691000 751676 668016 562839 542563 608206.4 637770.5 662329 527124.8 829978 734250 FALSE TRUE 722299.6709 648964.8377 664556.5276 570564.7415 627769.9112 650666.6565 670434.7804 516239.4887 735762.377 684518.5935 1.055193647 0.948060205 0.970837803 0.833527017 0.917096945 0.950546359 0.979425229 0.754164304 1.074861054 1 19.3847302 4.921288525 1.381993903 0.915298779 1.161106983 0.123423866 0.085519615 3.245762673 4.040411434 0.022768999 1.247874968 83423.52273 -4.921288525 0.245808204 LDNNWGR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDNNWGR 7 0 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;;; 166.05 0.002647 1003960000 807460 949380 706090 1086630 871880 859300 988020 989940 957230 1107900 FALSE TRUE 775903.5705 922304.6119 833696.1699 1142711.105 899924.812 876675.6348 1000111.684 969497.3931 848569.2634 1032860.946 0.751217841 0.892961066 0.807171743 1.106355225 0.87129329 0.848783796 0.968292671 0.938652387 0.821571642 1 19.97821461 4.923506296 1.255242735 0.926054432 0.621484049 0.271243338 0.084998238 2.83049479 2.860130552 0.022912616 1.238664165 83850.62336 -4.923506296 -0.304570384 SDGSLEDGDDVHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDGSLEDGDDVHR 13 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 0 ; 218.85 2.35E-11 363200000 458740 589730 452770 709330 556300 643490 685310 645080 728100 746020 FALSE TRUE 440811.9336 572911.4778 534595.6108 745938.6063 574193.8947 656501.8087 693697.0288 631758.8726 645449.1404 695491.4009 0.633813636 0.823750627 0.768658836 1.072534621 0.825594528 0.943939505 0.997419994 0.908363312 0.928047622 1 19.40767315 4.924104567 0.849921182 0.946416658 0.384435782 0.631237798 0.074508339 1.89399115 0.858843863 0.023525155 1.071075331 83966.21321 -4.924104567 -0.561980876 YTQLQYIGEGAYGMVSSAYDHVR ddPTM_BT-474_Pertuzumab_2h_R1 1 YTQLQYIGEGAYGMVSSAYDHVR 23 0 P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 197.4 2.97E-24 258520000 413190 494780 412590 490210 563070 500690 519610 508660 554760 537730 FALSE TRUE 397042.078 480669.3588 487154.191 515509.7968 581181.6579 510814.2948 525969.1426 498155.9932 491785.9705 501309.0681 0.792010564 0.958828374 0.971764171 1.028327293 1.159328037 1.018960811 1.049191359 0.993710317 0.98100354 1 18.93534081 4.924580726 1.243859669 1.033031306 0.602327061 0.684297249 0.048627236 1.27150441 1.258114557 0.014417502 0.780922652 84058.32397 -4.924580726 -0.430704245 GAGGS(ph)PVGVEEGLVNVGTGQK ddPTM_BT-474_Pertuzumab_2h_R1 4 GAGGSPVGVEEGLVNVGTGQK 21 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 GAGGS(1)PVGVEEGLVNVGTGQK;GAGGS(1)PVGVEEGLVNVGTGQK;GAGGS(1)PVGVEEGLVNVGTGQK;GAGGS(1)PVGVEEGLVNVGTGQK 333.01 3.88E-80 1214620000 663060 659650 604730 690420 673170 730880 724760 830780 805320 816190 TRUE FALSE 637146.8821 640837.4279 714018.1631 726052.6589 694823.1244 745658.8944 733629.8297 813624.1027 713903.4498 760908.7243 0.83734995 0.842200132 0.938375577 0.954191529 0.91314911 0.979958398 0.964149584 1.069279503 0.938224819 1 19.53736388 4.926074176 0.398607507 1.011727903 0.655866773 0.666731532 0.038025705 3.672911085 0.412896706 0.031090977 0.646677051 84347.88092 -4.926074176 -0.35586113 EVLSEPWR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVLSEPWR 8 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ; 114.78 0.006025 743320000 477070 847350 603740 1141100 581320 575200 981640 1022220 818580 736100 FALSE TRUE 458425.577 823184.4076 712849.2481 1199992.308 600018.6857 586830.9381 993653.604 1001110.8 725658.2302 686243.2914 0.668021943 1.199551847 1.038770444 1.748639765 0.874352716 0.85513541 1.447961119 1.458827813 1.057435809 1 19.38836061 4.926491172 2.109327653 1.224493777 0.274251293 0.232146791 0.274507003 2.055181525 6.357214428 0.070448743 4.435626898 84428.90806 -4.926491172 -0.950242484 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR ddPTM_BT-474_Pertuzumab_2h_R1 7 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 0 ;;;;;; 304.26 1.54E-81 3039898000 293656 352138 259339.4 429841 320029 332233 355454 326739 401778 357267 FALSE TRUE 282179.5989 342095.369 306207.7986 452025.1455 330323.0234 338950.9789 359804.1524 319991.7255 356169.8458 333068.9879 0.847210665 1.027100635 0.919352476 1.357151707 0.991755569 1.017659978 1.08026915 0.960737076 1.069357577 1 18.34546151 4.928220814 1.582770031 1.052638964 0.694135236 0.226751122 0.112608885 2.682681718 4.413212573 0.029193325 1.705306773 84765.82899 -4.928220814 -0.358503728 AASIENVLQDSS(ph)PEHCGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AASIENVLQDSSPEHCGR 18 0 K7EPJ5;O60291-4;O60291;O60291-3;O60291-2 K7EPJ5 MGRN1 E3 ubiquitin-protein ligase MGRN1 1 AASIENVLQDS(0.125)S(0.875)PEHCGR 141.11 7.88E-08 170340000 97618 149560 103760 193770 133410 179270 182400 148590 165420 170580 TRUE FALSE 93802.98064 145294.6952 122511.7401 203770.4929 137701.2538 182894.9622 184632.2658 145521.5646 146642.2151 159026.4647 0.589857675 0.913651043 0.770385862 1.281362152 0.865901497 1.150091355 1.161015974 0.915077656 0.9221246 1 17.27890735 4.928822561 1.063437004 1.02926706 0.252666574 0.462027608 0.14084395 2.186263385 1.550734661 0.04041333 2.104329177 84883.35967 -4.928822561 -0.776600486 (ac)ACPLDQAIGLLVAIFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ACPLDQAIGLLVAIFHK 17 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ; 150.94 6.97E-27 7453500000 4776290 5519300 4564780 5373000 6000500 6080700 5274400 5079900 6345200 5960700 FALSE TRUE 4589627.306 5361894.968 5389737.289 5650301.174 6193511.532 6203655.92 5338949.685 4974998.29 5624919.497 5556976.48 0.825921672 0.964894307 0.969904643 1.01679415 1.114547012 1.116372535 0.960765212 0.895270712 1.012226616 1 22.4058687 4.929015756 1.488466544 1.007610354 0.684179277 0.444045636 0.062616281 2.134896555 3.071301304 0.020054506 1.16003137 84921.12831 -4.929015756 -0.323431077 DDYANLHSK ddPTM_BT-474_Pertuzumab_2h_R1 2 DDYANLHSK 9 0 O95749-2;O95749;C9J6G3;C9J7M1 O95749-2 GGPS1 Geranylgeranyl pyrophosphate synthase 0 ; 120.06 0.00072602 869890000 417120 448570 457040 566360 487660 499730 600560 648180 777740 811390 FALSE TRUE 400818.4892 435777.2228 539637.2948 595589.9075 503346.0268 509834.883 607909.8329 634794.8565 689454.2158 756433.8326 0.529879114 0.576094305 0.713396561 0.787365506 0.66541977 0.67399799 0.803652358 0.839194162 0.911453436 1 19.52885437 4.930172469 0.126078031 1.140434625 1.21E-15 0.841948619 0.055339541 15.47537283 0.302481311 0.501930052 3.069513539 85147.61123 -4.930172469 -1.140434625 ELKPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELKPAR 6 1 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 ; 73.039 0.07662 248160000 575050 747450 544000 987970 545200 659800 949490 828290 727530 600910 FALSE TRUE 552576.4102 726133.4578 642312.9012 1038959.25 562736.8531 673141.6081 961110.1426 811185.522 644943.8445 560209.8305 0.986373998 1.296181213 1.146557712 1.854589466 1.00451085 1.201588354 1.715625272 1.448003012 1.151254065 1 19.09560777 4.930264133 1.451863709 1.362305344 0.698727512 0.100034869 0.273216869 3.797518664 5.166565102 0.071619789 4.144161894 85165.58472 -4.930264133 -0.663577832 VLAVNQENEHLMEDYEK ddPTM_BT-474_Pertuzumab_2h_R1 9 VLAVNQENEHLMEDYEK 17 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;;;;;;;; 332.56 4.68E-72 9345705000 6629610 5793470 6092640 8009420 6722690 5880080 8059270 8130720 9855000 10175310 FALSE TRUE 6370517.512 5628245.908 7193715.578 8422787.126 6938931.429 5998979.246 8157901.757 7962817.791 8736301.716 9486127.19 0.671561469 0.593313351 0.75834062 0.887905776 0.731482015 0.632394983 0.859982329 0.839417144 0.920955574 1 23.17738778 4.9315637 0.073720573 1.315982618 2.46E-12 0.598152658 0.080222515 82.8318754 0.90962704 4.45095512 13.65858598 85420.81294 -4.9315637 -1.315982618 ADLSIPDLHEIVTEELEER ddPTM_BT-474_Pertuzumab_2h_R1 4 ADLSIPDLHEIVTEELEER 19 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 0 ;;; 274.23 2.12E-39 211498000 273126 343296 286074 357086 363369 388789 384477 326495 365380 398710 FALSE TRUE 262451.934 333505.5342 337773.9355 375515.2513 375057.0939 396650.58 389182.3445 319752.7642 323903.5942 371705.0166 0.706075846 0.897231728 0.908715031 1.010250695 1.009018112 1.067111183 1.047019349 0.860232577 0.871399577 1 18.50379863 4.932372578 1.313166542 0.974404334 0.490507493 0.605674116 0.06569658 1.6077028 1.760155664 0.020571571 1.170574514 85580.05832 -4.932372578 -0.483896841 RTDEAAFQK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTDEAAFQK 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 125.74 0.0007908 998770000 881960 585650 482530 376080 440900 357090 452810 747100 543050 389640 FALSE TRUE 847492.0281 568947.8354 569733.9048 395489.5339 455081.9489 364310.6045 458351.6242 731672.1239 481405.2407 363249.3357 2.333086243 1.566273574 1.568437568 1.088755009 1.252808757 1.002921599 1.261809945 2.014242152 1.325274937 1 18.47060063 4.932944745 1.547487593 1.354589448 3.103094227 0.536489695 0.28462213 1.662514806 2.579701364 0.085080723 5.07052487 85692.88109 -4.932944745 1.748504779 KEDTAFSDWS(ph)DEDVPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEDTAFSDWSDEDVPDR 17 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KEDTAFS(0.003)DWS(0.997)DEDVPDR 90.912 0.0015058 0 40757 52750 58825 71442 60389 65377 86552 87231 97404 96906 TRUE FALSE 39164.17138 51245.62165 69455.98606 75129.13018 62331.46703 66698.96773 87611.24927 85429.64937 86347.10627 90342.47031 0.433507865 0.56723733 0.768807692 0.831603674 0.689946454 0.73829028 0.969768139 0.945620029 0.955775351 1 16.46311674 4.933981545 0.306952986 1.009437678 3.07E-17 0.826729851 0.074426301 3.720689953 0.261283213 0.089924127 1.447522268 85897.70191 -4.933981545 -1.009437678 down VVSVLTVLHQDWLNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVSVLTVLHQDWLNGK 16 0 A0A0A0MS08;P01857;A0A4W9A917;A0A286YFJ8;A0A286YES1;P01861;P01860 A0A0A0MS08 IGHG1;IGHG4;IGHG3 Ig gamma-1 chain C region;Ig gamma-4 chain C region;Ig gamma-3 chain C region 0 ; 266.28 3.55E-27 1441600000 12756100 4320800 1417340 851250 280890 249260 185368 144356 168345 118038 FALSE TRUE 12257577.51 4197575.015 1673484.867 895183.1145 289925.0819 254300.208 187636.589 141374.9982 149235.1814 110043.1811 111.3887965 38.1447989 15.20752899 8.134834938 2.634648317 2.310912911 1.705117819 1.284722931 1.356151102 1 16.74771023 4.934977874 1.268587079 2.278388586 200 0.99606316 2.064331186 0.1223018 0.123960107 0.620218585 35.32104167 86094.9888 -4.934977874 197.7216114 up FFTEEVDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 FFTEEVDSR 9 0 Q9H845 Q9H845 ACAD9 "Acyl-CoA dehydrogenase family member 9, mitochondrial" 0 ;;; 110.41 0.0053318 231099000 395131 597121 418711 879300 412719 496453 738894 620233 538762 466308 FALSE TRUE 379688.8437 580091.6937 494381.3919 924680.7784 425994.4815 506491.6198 747936.8058 607424.9718 477603.9964 434724.5438 0.873400982 1.334389102 1.137229077 2.127049856 0.979918175 1.165086322 1.720484423 1.397264039 1.098635914 1 18.72974202 4.935117528 1.90116048 1.372833085 0.497021984 0.128745635 0.340198272 2.933446362 7.067426093 0.083809535 5.383071587 86122.67852 -4.935117528 -0.875811101 LES(ph)LNIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LESLNIQR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LES(1)LNIQR;LES(1)LNIQR 131.82 0.0010372 265640000 659100 412090 262770 259090 268180 216894 189855 395650 249580 228160 TRUE FALSE 633341.6433 400337.5967 310258.3843 272461.6659 276806.2533 221279.7453 192178.5023 387479.6892 221248.7247 212706.52 2.977537517 1.882112484 1.458621881 1.280927665 1.301352931 1.040305419 0.903491357 1.821663432 1.040159581 1 17.69850473 4.936832207 1.217401428 1.240510784 4.440498231 0.831744127 0.244113788 0.906348548 0.840284438 0.072167965 4.084924168 86463.37958 -4.936832207 3.199987447 up (ac)MQAHELFR ddPTM_BT-474_Pertuzumab_2h_R1 1 MQAHELFR 8 0 E7EPM6;P33121-2;P33121;P33121-3;D6RER0;D6RG07 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 58.286 0.039321 175640000 88287 128600 104410 163080 102500 109710 173900 173530 113550 108010 FALSE TRUE 84836.64643 124932.4539 123279.2096 171496.5783 105797.0056 111928.4114 176028.2402 169946.5449 100660.28 100694.3865 0.842516146 1.240709222 1.224290786 1.703139413 1.050674315 1.111565553 1.74814353 1.687745969 0.999661287 1 16.61962373 4.940419906 1.387478939 1.380603996 0.400995661 0.172684759 0.286879536 3.097972461 3.754895074 0.080377242 4.824789208 87180.61051 -4.940419906 -0.979608335 KREHS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 7 KREHSPSK 8 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.995)PS(0.005)K;KREHS(1)PSK;KREHS(0.998)PS(0.002)K;KREHS(0.995)PS(0.005)K;KREHS(0.985)PS(0.015)K;KREHS(1)PSK;KREHS(0.996)PS(0.004)K 129.89 0.00055903 849542000 1216381 1013781 848030 805415 872896 806515 1035283 918823 1076760 1155343 TRUE FALSE 1168843.486 984868.9585 1001287.885 846982.5647 900973.4926 822823.2859 1047953.103 899848.984 954530.7189 1077090.59 1.085185867 0.914378946 0.929622722 0.786361494 0.83648813 0.763931366 0.97294797 0.835444105 0.886212105 1 20.03870816 4.940802951 1.438321367 0.863815781 1.264922715 0.427303801 0.071995548 1.696191749 2.216752594 0.018382774 1.117732261 87257.5372 -4.940802951 0.401106934 SLGLSLS(ph)GGDQEDAGR ddPTM_BT-474_Pertuzumab_2h_R1 5 SLGLSLSGGDQEDAGR 16 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 1 SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLS(0.001)LS(0.999)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR 324.45 1.58E-58 2163280000 1268385 1429590 1136488 1450406 1441746 1320365 1384865 1437360 1427081 1437890 TRUE FALSE 1218815.112 1388819.493 1341876.663 1525261.627 1488121.069 1347063.685 1401813.392 1407678.014 1265084.748 1340500.43 0.909223962 1.036045541 1.001026656 1.137830018 1.11012353 1.004896123 1.045738861 1.05011381 0.943740651 1 20.35434025 4.942062498 2.000741138 1.044298574 0.80479525 0.328734179 0.053574117 1.794203339 4.73531009 0.013725001 0.947959662 87510.97005 -4.942062498 -0.239503324 FVVIQNEDLGPAS(ph)PLDSTFYR ddPTM_BT-474_Pertuzumab_2h_R1 5 FVVIQNEDLGPASPLDSTFYR 21 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 FVVIQNEDLGPAS(1)PLDSTFYR;FVVIQNEDLGPAS(1)PLDSTFYR;FVVIQNEDLGPAS(1)PLDSTFYR;FVVIQNEDLGPAS(1)PLDSTFYR;FVVIQNEDLGPAS(1)PLDSTFYR 241.45 3.40E-30 345685000 97591.8 217118 113818.7 354268 172114.2 192550 262883 254007 147648.2 131985 TRUE FALSE 93777.80456 210926.0072 134388.271 372551.8139 177650.4096 196443.4929 266100.2408 248761.6667 130887.7953 123045.5384 0.762139008 1.714210933 1.092183209 3.027755568 1.443777742 1.596510491 2.162615925 2.021704078 1.06373459 1 16.90883282 4.942089204 1.510449232 1.791940587 3.43E-11 0.158997144 0.592656093 3.022646739 4.371252836 0.149848727 9.308649127 87516.35152 -4.942089204 -1.791940587 FQAPS(ph)PSTLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FQAPSPSTLLR 11 0 Q6P9B9 Q6P9B9 INTS5 Integrator complex subunit 5 1 FQAPS(0.991)PS(0.009)TLLR;FQAPS(0.993)PS(0.007)TLLR 157.28 3.22E-05 92146000 148544 155383 128201 152142 150578 149030 157070 166679 162355 173244 TRUE FALSE 142738.7363 150951.629 151369.7725 159994.0669 155421.4781 152043.4887 158992.2696 163237.0204 143925.141 161510.0296 0.883776299 0.934626966 0.93721593 0.990613817 0.962302332 0.941387288 0.984411123 1.010692778 0.891122003 1 17.30126423 4.942512011 0.932513849 0.971563529 0.808735795 0.375626073 0.032926662 2.916318504 1.555876045 0.010287762 0.524610411 87601.59456 -4.942512011 -0.162827734 DLGEGEEGELAPPEDLLGRPQALSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLGEGEEGELAPPEDLLGRPQALSR 25 1 Q8NC44;H7C3D5 Q8NC44 FAM134A Protein FAM134A 0 ; 167.88 1.10E-11 119046000 70589 83841 62672 91850 73711 92700 90218 87784 93085 90785 FALSE TRUE 67830.30384 81449.93677 73998.22453 96590.38951 76081.98126 94574.45751 91322.11487 85971.22972 82518.38104 84636.05109 0.801435121 0.962355116 0.87431093 1.141244048 0.898931133 1.117425214 1.078997823 1.015775531 0.974979102 1 16.3689847 4.943301572 0.82307742 1.03309566 0.620687725 0.431007054 0.07762558 2.907460547 1.210820588 0.025059726 1.179436448 87761.00169 -4.943301572 -0.412407935 GDDSFGDKYR ddPTM_BT-474_Pertuzumab_2h_R1 3 GDDSFGDKYR 10 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 149.96 2.04E-05 1110450000 903870 979400 885450 945370 905550 860720 1071620 1040330 1083370 1163270 FALSE TRUE 868545.7611 951468.4709 1045470.512 994160.659 934677.8381 878124.3481 1084734.806 1018846.822 960390.3795 1084480.687 0.800886334 0.877349392 0.964028705 0.916715873 0.861866744 0.809718752 1.000234324 0.939478992 0.885576287 1 20.04857293 4.945664268 0.01868582 1.727966921 6.84E-08 0.294886261 0.056841694 2576.200308 7.035438566 280.4330437 375.257204 88239.74985 -4.945664268 -1.727966852 RNAEQYKDQADK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNAEQYKDQADK 12 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 74.537 0.020381 229890000 371780 263760 264590 142010 229610 225660 224730 234650 301450 226180 FALSE TRUE 357250.4266 256237.823 312407.2988 149339.1531 236995.6142 230222.9998 227480.313 229804.3955 267230.6598 210860.6271 1.694249094 1.215199948 1.481581948 0.708236313 1.123944367 1.091825453 1.078818346 1.089840235 1.267333136 1 17.68593021 4.947602348 1.06985188 1.076816894 2.184396433 0.517510456 0.176857485 2.005859931 1.402132579 0.04999948 2.794749476 88634.40785 -4.947602348 1.107579539 RQFDEES(ph)LESFSSMPDPVDPTTVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQFDEESLESFSSMPDPVDPTTVTK 25 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 RQFDEES(0.819)LES(0.142)FS(0.033)S(0.006)MPDPVDPTTVTK 88.842 0.0091025 111420000 60876 86168 82642 108730 101190 125770 126380 118140 148210 141440 TRUE FALSE 58496.89862 83710.57301 97577.24776 114341.5683 104444.8682 128313.1556 127926.6762 115700.3677 131385.8221 131860.1428 0.443628358 0.63484364 0.740005628 0.867142761 0.792088238 0.973100384 0.970169405 0.877447614 0.99640285 1 17.00864902 4.948617709 0.545370948 0.958811505 2.96E-12 0.922143556 0.048106881 1.263728426 0.243245914 0.025441029 0.809556688 88841.87354 -4.948617709 -0.958811505 down RLESSGAGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLESSGAGGR 10 1 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 0 ;;; 160.18 1.20E-05 250069000 137366 149438 124511 156263 144802 143531 152455 215553 128566 136443 FALSE TRUE 131997.5849 145176.1746 147012.9074 164327.7522 149459.6878 146433.2952 154320.7899 211101.7552 113971.7267 127201.5941 1.037703857 1.141307824 1.155747367 1.291868654 1.174982821 1.151190724 1.213198553 1.659584196 0.895992912 1 16.95675722 4.949597638 0.711229732 1.255911367 0.845564708 0 0.194900702 9.388661491 2.934284066 0.077989635 3.310358725 89042.56017 -4.949597638 -0.410346659 GKT(ph)PEEIRK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKTPEEIRK 9 2 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 1 GKT(1)PEEIRK;GKT(1)PEEIRK 118.87 0.043844 5026900000 6482800 5361100 4526200 4131400 4743200 4375100 4575700 5708300 5901100 4646800 TRUE FALSE 6229445.009 5208206.677 5344185.025 4344622.049 4895769.336 4463567.52 4631698.785 5590421.61 5231231.867 4332068.097 1.437984092 1.202244877 1.233633661 1.002897912 1.130122894 1.030354884 1.069165738 1.290474084 1.207559934 1 22.04662449 4.950972698 1.340847588 1.126177217 1.700364339 0.522569929 0.092701814 1.90554634 2.108862186 0.027237918 1.697971377 89324.93279 -4.950972698 0.574187122 ELHSEFSEVMNEIWASDQIR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELHSEFSEVMNEIWASDQIR 20 0 H0YFD6;P40939;A0A2R8Y4F5;A0A2R8YG21;A0A2R8Y688 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 ;;; 286.7 2.80E-45 449491000 171740 300083 177360 471250 220111 276082 427661 313545 280078 237279 FALSE TRUE 165028.2109 291524.9267 209412.8974 495571.269 227191.0702 281664.5672 432894.8432 307070.1862 248284.7196 221207.882 0.746032237 1.317877663 0.946679185 2.240296614 1.027047808 1.273302582 1.956959397 1.388152101 1.122404488 1 17.75504327 4.954400118 1.264001503 1.435133347 0.182798061 0.171814704 0.402100714 3.59774755 3.501941347 0.107295157 6.63722453 90032.66751 -4.954400118 -1.252335285 GS(ph)LNEQIALVLMR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSLNEQIALVLMR 13 0 B7Z2R7;Q5T8D3-4;Q5T8D3-2;Q5T8D3-3;Q5T8D3 B7Z2R7 ACBD5 Acyl-CoA-binding domain-containing protein 5 1 GS(1)LNEQIALVLMR;GS(1)LNEQIALVLMR 174.87 2.02E-05 38631000 22381.7 36168 25186 52918 28177 30083 40011 43938 35062 39905 TRUE FALSE 21506.99842 35136.52405 29737.67046 55649.10432 29083.33879 30691.29887 40500.66659 43030.66495 31081.90875 37202.19881 0.578110948 0.944474391 0.799352496 1.495855248 0.781763974 0.824986153 1.088663248 1.156669937 0.835485798 1 15.18310027 4.954491888 1.4719283 1.02109699 0.206892382 0.270573414 0.205768823 2.584014633 3.451855082 0.054286851 3.56441201 90051.69429 -4.954491888 -0.814204608 WLTDEDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 WLTDEDTR 8 0 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 101.33 0.012733 307590000 280010 361580 279780 418410 341320 391690 399270 362760 400160 454370 FALSE TRUE 269066.8996 351268.0924 330342.4697 440004.1902 352298.8678 399610.2402 404156.3857 355268.8792 354735.5144 423595.1152 0.635198306 0.829254351 0.779854294 1.03873764 0.831687749 0.943377829 0.954110119 0.838699188 0.83744005 1 18.69232643 4.958543953 1.125854517 0.906066842 0.403682027 0.553335315 0.075092336 1.875967515 1.431184873 0.020931755 1.250138761 90895.82851 -4.958543953 -0.502384815 SGKPAELLKMFGIDRDAIAQAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGKPAELLKMFGIDRDAIAQAVR 23 3 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 171.84 2.50E-12 298540000 311420 324500 249050 466730 346560 392680 295400 528370 546180 497510 FALSE TRUE 299249.3621 315245.5777 294058.8751 490817.9912 357707.4171 400620.2586 299015.1936 517458.9749 484179.9362 463813.2046 0.64519371 0.679682197 0.63400281 1.058223411 0.771231637 0.863753457 0.644688833 1.115662447 1.043911496 1 18.82318437 4.960323958 0.232408031 1.064286824 0.210831726 0.425128663 0.139805569 12.03935578 0.522271285 0.230494399 3.028272144 91269.14001 -4.960323958 -0.853455098 ALQPIVSEEEWAHTK ddPTM_BT-474_Pertuzumab_2h_R1 5 ALQPIVSEEEWAHTK 15 0 P43155-2;P43155;P43155-3;B7ZBP5;A6PVN3 P43155-2 CRAT Carnitine O-acetyltransferase 0 ;;;; 295.03 4.97E-44 4527160000 2077105 2679862 1997951 3316428 2277655 2379290 3256159 2901088 2877996 2627419 FALSE TRUE 1995929.44 2603434.96 2359025.19 3487589.247 2350917.842 2427400.874 3296008.848 2841179.519 2551297.96 2449461.571 0.814844153 1.062860096 0.963079077 1.423818723 0.959769228 0.990993655 1.345605453 1.159920022 1.04157501 1 21.22403323 4.962083292 1.251437739 1.135539178 0.53933587 0.251276864 0.152234082 3.037419406 2.858899074 0.04169995 2.655522679 91639.62255 -4.962083292 -0.596203308 YPSS(ph)ISSS(ph)PQKDLTQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 YPS(0.084)S(0.916)ISS(0.113)S(0.887)PQKDLTQAK;YPS(0.096)S(0.904)ISS(0.255)S(0.745)PQKDLTQAK 208.92 2.70E-12 702020000 1724060 1379780 1240580 1026430 1138330 1139290 1092620 1420000 1592580 1513580 TRUE FALSE 1656681.829 1340430.025 1464780.403 1079404.175 1174945.418 1162327.224 1105991.81 1390676.504 1411796.995 1411063.878 1.174065791 0.949942838 1.038068102 0.764957697 0.832666356 0.82372403 0.783799959 0.985551771 1.000519549 1 20.42835187 4.96273658 1.188844447 0.88636279 1.417760774 0.438511362 0.092898629 2.297538323 1.945208043 0.027384632 1.707609143 91777.57525 -4.96273658 0.531397985 LADLIER ddPTM_BT-474_Pertuzumab_2h_R1 4 LADLIER 7 0 P05091;F8VP50;Q5SYQ7;Q5SYQ9;Q5SYQ8;P00352 P05091 ALDH2;ALDH1A1 "Aldehyde dehydrogenase, mitochondrial;Retinal dehydrogenase 1" 0 ;;; 153.15 0.0041078 836900000 739030 1193580 830370 1744130 824970 905380 1473150 1354350 1038550 962060 FALSE TRUE 710147.8906 1159540.267 980436.3305 1834144.758 851505.9093 923687.4039 1491178.85 1326382.199 920658.158 896898.8193 0.791781498 1.292832862 1.093140396 2.044985141 0.94938904 1.029868012 1.662594284 1.478853769 1.026490545 1 19.77458572 4.963489539 1.835112252 1.335073159 0.325005165 0.149888579 0.337588803 3.089131457 6.41644754 0.084966477 6.509402464 91936.83287 -4.963489539 -1.010067994 DGAGFLINLIDSPGHVDFSSEVTAALR ddPTM_BT-474_Pertuzumab_2h_R1 9 DGAGFLINLIDSPGHVDFSSEVTAALR 27 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;; 261.6 4.30E-53 5649824700 748423 867947.9 701779.3 903328.6 827155.5 972375.2 902650.2 836941.1 957366.1 970103 FALSE TRUE 719173.8017 843194.8757 828606.4305 949949.4973 853761.7079 992037.2928 913697.1032 819657.9738 848689.9139 904397.0597 0.79519697 0.932328192 0.916197617 1.050367742 0.944012034 1.096904597 1.010283142 0.906303227 0.938404106 1 19.78659678 4.964508302 1.212256926 0.985063506 0.628314471 0.519863917 0.055639824 2.069624557 1.81802635 0.016602782 1.052664459 92152.75043 -4.964508302 -0.356749035 VTHTGQVYDDKDYR ddPTM_BT-474_Pertuzumab_2h_R1 3 VTHTGQVYDDKDYR 14 1 D6RBT3;O75380 D6RBT3 NDUFS6 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial" 0 ;; 189.1 4.55E-07 890970000 614420 822110 590660 1117580 602530 747390 1089540 959800 942190 764510 FALSE TRUE 590407.7871 798664.2277 697405.4012 1175258.438 621910.9247 762502.7379 1102874.116 939979.7946 835236.5412 712729.0567 0.828376199 1.120572004 0.978500027 1.648955415 0.872576919 1.069835347 1.547396035 1.3188459 1.171885071 1 19.44299422 4.965093628 1.010550469 1.2455847 0.467448625 0.185757341 0.234465144 4.347080695 2.643040681 0.070545568 4.069316932 92277.03432 -4.965093628 -0.778136075 GAPPPGEPGLSHS(ph)GSEQPEQTGLLMGGASGGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GAPPPGEPGLSHSGSEQPEQTGLLMGGASGGAR 33 0 P50895 P50895 BCAM Basal cell adhesion molecule 1 GAPPPGEPGLS(0.003)HS(0.976)GS(0.02)EQPEQTGLLMGGASGGAR 274.99 9.10E-74 180840000 36644 84780 42156 119950 50676 57773 105080 94716 79774 49079 TRUE FALSE 35211.91197 82362.15741 49774.52696 126140.6339 52306.03956 58941.20964 106366.0005 92760.0815 70718.38996 45754.83561 0.769577936 1.800075474 1.08785282 2.756880932 1.143180581 1.288196293 2.324694189 2.027328484 1.545593794 1 15.4816366 4.966129797 1.898585722 1.744045588 1.51E-16 0.171128176 0.553817031 2.896035036 6.410272638 0.136682414 10.89520995 92497.45775 -4.966129797 -1.744045588 LMCPQEIVDYIADKK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMCPQEIVDYIADKK 15 1 O14561;H3BNK3 O14561 NDUFAB1 "Acyl carrier protein, mitochondrial;Acyl carrier protein" 0 136.01 4.08E-05 116040000 110190 137230 106020 164350 105210 119440 170830 142080 145920 123920 FALSE TRUE 105883.653 133316.3348 125180.1724 172832.1232 108594.1752 121855.1586 172920.6686 139145.9983 129355.7733 115526.788 0.916529013 1.153986335 1.083559705 1.496035042 0.939991296 1.054778383 1.496801492 1.20444791 1.119703712 1 16.81786789 4.966895752 1.57620917 1.198468017 0.668035089 0.147010053 0.179655297 3.486232133 5.235458984 0.046604022 3.367272935 92660.73744 -4.966895752 -0.530432928 KLPGDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPGDDR 7 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ; 79.116 0.05371 252090000 875890 907320 746900 916100 851490 894040 904000 1029510 1004260 925990 FALSE TRUE 841659.2505 881444.122 881881.4447 963380.0308 878878.9492 912118.1014 915063.4224 1008250.259 890260.615 863271.8725 0.974964293 1.021050436 1.021557024 1.115963651 1.018078982 1.056582672 1.059994483 1.167940588 1.031263317 1 19.71945546 4.967152458 0.685862482 1.078116193 0.87877384 0.211295537 0.048191119 5.113365488 1.467701824 0.019875897 0.850643495 92715.52416 -4.967152458 -0.199342353 SEEWADNHLPLTDAELAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SEEWADNHLPLTDAELAR 18 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ;;; 168.09 2.16E-11 4773840000 2879680 3345710 2681880 3460920 3299520 3521500 3277090 3146680 3532130 3742100 FALSE TRUE 2767138.922 3250293.627 3166555.374 3639538.496 3405652.057 3592707.143 3317196.008 3081699.958 3131177.41 3488644.234 0.793184612 0.931678156 0.907675063 1.043252981 0.976210765 1.02982904 0.950855342 0.883351741 0.897534171 1 21.73423505 4.967273001 1.589358766 0.959031781 0.646372539 0.49436414 0.050991164 1.887383024 2.881301808 0.014899097 1.083108641 92741.26196 -4.967273001 -0.312659241 SEIPS(ph)PQSQLLEDAEANLVGR ddPTM_BT-474_Pertuzumab_2h_R1 6 SEIPSPQSQLLEDAEANLVGR 21 0 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 SEIPS(0.982)PQS(0.018)QLLEDAEANLVGR;SEIPS(0.999)PQS(0.001)QLLEDAEANLVGR;SEIPS(1)PQSQLLEDAEANLVGR;SEIPS(1)PQSQLLEDAEANLVGR;SEIPS(0.993)PQS(0.007)QLLEDAEANLVGR;SEIPS(0.989)PQS(0.011)QLLEDAEANLVGR 265.54 6.85E-37 370913000 59021.9 69985 57286.2 72719.7 72254.4 70767 70774.9 81564.3 71420.7 74687.6 TRUE FALSE 56715.2589 67989.09632 67639.09066 76472.77243 74578.5284 72197.95723 71641.0644 79879.9687 63313.32156 69628.94233 0.814535695 0.976448788 0.971422061 1.09829002 1.071085182 1.036895791 1.028897783 1.147223641 0.90929604 1 16.08739949 4.96749042 1.128371826 1.051854699 0.603005665 0.524567168 0.062547976 1.807616281 1.366475974 0.017504086 1.083660596 92787.70222 -4.96749042 -0.448849034 RGPEEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGPEEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 150.05 0.0031664 152385000 91005 105415 89184 108515 104363 117948 119286 107219 116708 127964 FALSE TRUE 87448.42399 102408.6674 105301.5327 114115.4722 107719.9307 120332.9894 120745.8578 105004.8902 103459.7971 119296.8843 0.733031919 0.85843539 0.882684685 0.956567079 0.902956781 1.008685097 1.012145945 0.880198094 0.867246431 1 16.86419684 4.967742248 0.985889804 0.943896225 0.541861333 0.63504068 0.049790892 1.95232104 1.126014555 0.016109377 0.923709159 92841.52129 -4.967742248 -0.402034892 LLDEEEATDNDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLDEEEATDNDLR 13 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 356.73 7.57E-76 3225670000 1637340 1850420 1496770 1862970 1842610 1956510 1811960 1891720 1842900 1848790 FALSE TRUE 1573350.943 1797647.833 1767269.634 1959118.105 1901879.224 1996071.973 1834135.308 1852655.321 1633701.718 1723569.807 0.91284434 1.042979418 1.025354255 1.136663045 1.103453551 1.158103353 1.064149129 1.074894277 0.947859328 1 20.7169683 4.967948309 1.485861448 1.074829195 0.768753715 0.357544704 0.059530523 2.124602204 2.817251144 0.015876464 1.122318879 92885.58255 -4.967948309 -0.306075479 SYS(ph)PAHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.445)YS(0.555)PAHNR;S(0.035)Y(0.001)S(0.963)PAHNR 92.538 0.0075405 272171000 237020 307770 237200 341870 338210 340020 312940 258080 328030 322000 TRUE FALSE 227756.9964 298992.7009 280067.3165 359513.9517 349088.8318 346895.4374 316769.8533 252750.5578 290793.4096 300190.6532 0.758707821 0.996009362 0.932964813 1.197618739 1.16289041 1.155583739 1.055228902 0.841966781 0.968695749 1 18.19551953 4.970884617 1.564780866 1.03943368 0.508067481 0.393390469 0.104796377 2.47339457 3.62761208 0.0323895 2.384720213 93515.71885 -4.970884617 -0.531366199 VFVLDEADVMIATQGHQDQSIR ddPTM_BT-474_Pertuzumab_2h_R1 3 VFVLDEADVMIATQGHQDQSIR 22 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2;H3BN59 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ;; 347.14 6.38E-96 491848000 322586 379136 291673 404140 386870 410545 392008 336650 362676 447066 FALSE TRUE 309978.9825 368323.4125 344384.7993 424997.7138 399314.0249 418846.5012 396805.5112 329698.0599 321506.5409 416785.8216 0.74373687 0.88372347 0.826287223 1.019702907 0.958079676 1.004944217 0.952060964 0.791049126 0.771395101 1 18.66894667 4.970979633 1.372647001 0.913463264 0.594422023 0.273172912 0.085131106 3.430123984 3.840950936 0.025420337 1.758684001 93536.18073 -4.970979633 -0.319041241 DYIPVDQEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYIPVDQEELR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 195.51 1.48E-07 1169270000 741380 888030 775280 866830 873890 945880 952940 919690 999130 1024690 FALSE TRUE 712406.05 862704.2539 915390.342 911567.2002 901999.4655 965006.3417 964602.3648 900698.0801 885712.9511 955286.8336 0.745750936 0.903083999 0.958236113 0.954234025 0.944218463 1.010174439 1.009751554 0.942856165 0.927169642 1 19.86557446 4.970995742 1.385408329 0.969699745 0.538611112 0.857915485 0.027495749 0.782384388 0.892847392 0.007867335 0.546714642 93539.6504 -4.970995742 -0.431088633 SWDIFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SWDIFFR 7 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;Q02218-3;C9J4G7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 148.07 0.0049062 220530000 480900 795110 528670 1138040 547980 531180 991480 828310 684460 653100 FALSE TRUE 462105.8963 772434.2413 624212.4292 1196774.381 565606.2744 541920.8235 1003614.029 811205.109 606762.9703 608864.9553 0.758962874 1.268646248 1.025206696 1.965582631 0.928951928 0.890050936 1.648336006 1.332323534 0.996547699 1 19.21576275 4.971052307 2.113345337 1.264093416 0.315990272 0.142764302 0.331495362 3.254346106 8.838438568 0.081823795 7.375329549 93551.83422 -4.971052307 -0.948103143 CAAPRPPSSS(ph)PEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 CAAPRPPSSSPEQR 14 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 CAAPRPPS(0.05)S(0.153)S(0.796)PEQR 120.63 7.22E-05 790070000 472260 606350 522410 621510 583550 646400 651650 625390 670410 770540 TRUE FALSE 453803.5571 589057.4917 616821.1079 653586.2056 602320.4157 659470.6509 659625.0876 612475.478 594307.8674 718350.6395 0.631729871 0.820013875 0.85866299 0.909842867 0.838476898 0.918034473 0.918249461 0.852613535 0.827322807 1 19.4543287 4.971386876 1.434700788 0.887091179 0.397139559 0.730150485 0.047631805 1.043384364 1.278360584 0.012096273 0.856247696 93623.93193 -4.971386876 -0.489951621 KLS(ph)LSEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSLSEGK 8 1 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 KLS(0.706)LS(0.294)EGK;KLS(0.828)LS(0.172)EGK 129.82 0.00065807 767740000 1614230 1093180 880880 812530 853630 828400 828580 1381990 860670 762260 TRUE FALSE 1551144.107 1062003.577 1040074.611 854464.7707 881087.7842 845150.8156 838720.4099 1353451.424 762970.3498 710631.4512 2.182768725 1.494450569 1.463592146 1.20240213 1.239866013 1.18929554 1.180246678 1.904575742 1.073651255 1 19.43874202 4.972336121 1.57104784 1.325486397 2.964137921 0.553971518 0.241139508 1.67777881 2.473353992 0.067394837 5.012740998 93828.79107 -4.972336121 1.638651523 FVEVLDER ddPTM_BT-474_Pertuzumab_2h_R1 4 FVEVLDER 8 0 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 ;;; 114.89 0.0059752 211885000 350383 411414 328309 424004 431221 413365 392226 426821 403739 414692 FALSE TRUE 336689.645 399680.8755 387641.7395 445886.8973 445091.6151 421723.5235 397026.1791 418006.9972 357908.2413 386604.5415 0.870889006 1.03382354 1.00268284 1.153341074 1.15128398 1.090839549 1.026956842 1.081226298 0.925773505 1 18.56049906 4.972402432 1.575975906 1.065373914 0.695584791 0.39486812 0.066900695 1.966333172 2.917095204 0.017841795 1.329677099 93843.11862 -4.972402432 -0.369789123 LNNLS(ph)PAPHLAS(ph)GSPPPGLPSGLPSGLQSGSPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 34 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 LNNLS(1)PAPHLAS(0.714)GS(0.286)PPPGLPSGLPSGLQSGSPSR;LNNLS(1)PAPHLAS(0.574)GS(0.426)PPPGLPSGLPSGLQSGSPSR 131.95 2.10E-08 449740000 123070 151219 117951 164875 149209 145665 145371 156475 143443 158188 TRUE FALSE 118260.2883 146906.3822 139267.3695 173384.2185 154008.443 148610.4461 147150.0938 153243.7366 127159.952 147473.7859 0.801907184 0.996152512 0.944353389 1.175695175 1.044310635 1.007707541 0.997805087 1.039125263 0.862254612 1 17.17009901 4.972562562 1.772556987 1.018176001 0.607717556 0.399706117 0.075136378 1.822307219 3.443356475 0.019133226 1.524617789 93877.72609 -4.972562562 -0.410458445 RRVS(ph)HS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 5 RRVSHSPPPK 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRVS(1)HS(1)PPPK;RRVS(1)HS(1)PPPK;RRVS(1)HS(1)PPPK;RRVS(1)HS(1)PPPK;RRVS(1)HS(1)PPPK 83.087 0.0086171 1122591000 1588693 1453700 1199869 1300742 1282726 1458652 1409073 1327475 1657828 1511227 TRUE FALSE 1526605.121 1412241.899 1416712.019 1367873.451 1323986.047 1488146.943 1426317.657 1300062.177 1469638.316 1408870.249 1.083566866 1.002393159 1.005565999 0.970900941 0.939750163 1.056269691 1.012383971 0.922769274 1.043132479 1 20.42610732 4.972808223 1.682918977 0.987711662 1.170568884 0.305910003 0.039524208 2.273773773 3.858637545 0.010442224 0.808114595 93930.84374 -4.972808223 0.182857222 DVEETLFQVAHDPDCGDVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVEETLFQVAHDPDCGDVVR 20 0 Q96BW9-2;Q96BW9-3;Q96BW9 Q96BW9-2 TAMM41 "Phosphatidate cytidylyltransferase, mitochondrial" 0 174.91 2.71E-12 55036000 19693 28717 20416 39724 22210 22965 29204 34658 26315 27966 FALSE TRUE 18923.37579 27898.01928 24105.62535 41774.1604 22924.40482 23429.36803 29561.40729 33942.30019 23327.83152 26071.83791 0.725816717 1.070044213 0.924584812 1.602271407 0.879278434 0.898646582 1.133844395 1.301876005 0.894752092 1 14.67020467 4.973470631 1.71697495 1.107857419 0.382887897 0.184985796 0.216457108 3.048952672 5.383657219 0.055699755 4.378819107 94074.22101 -4.973470631 -0.724969522 EGALCEENMR ddPTM_BT-474_Pertuzumab_2h_R1 7 EGALCEENMR 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;; 220.39 1.36E-08 6208770000 2088120 2295711 1858567 2261240 2241624 2447953 2313974 2358582 2469300 2575730 FALSE TRUE 2006513.962 2230239.57 2194451.4 2377942.867 2313727.872 2497452.287 2342293.106 2309876.457 2188995.416 2401273.513 0.835604087 0.928773652 0.913869823 0.990284053 0.963541995 1.040053236 0.975437864 0.96193809 0.911597702 1 21.19536831 4.97463067 0.935924492 0.976459414 0.711927339 0.614209224 0.033722881 2.062176865 1.06369137 0.010814566 0.613117483 94325.83757 -4.97463067 -0.264532074 S(ph)PPRPPR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPPRPPR 7 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;Q9UQ88-9;Q9UKB5;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2 P21127-2;Q5QPR3 CDK11B;CDK11A;AJAP1 Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A;Adherens junction-associated protein 1 1 S(1)PPRPPR;S(1)PPRPPR;S(1)PPRPPR;S(1)PPRPPR;S(1)PPRPPR 99.442 0.0063743 5679730000 760449 608957 494957 467152 571084 498541 538298 561259 687348 525628 TRUE FALSE 730729.8124 591590.1426 584406.7402 491261.7707 589453.4355 508621.8406 544885.8519 549668.8055 609323.1366 490026.7474 1.491203932 1.207260921 1.192601717 1.002520318 1.202900533 1.037947098 1.111951245 1.121711842 1.24344873 1 18.90250097 4.976032911 1.394693292 1.111740191 1.84260449 0.685579483 0.07746525 1.166246431 1.336403288 0.019524133 1.395118433 94630.88692 -4.976032911 0.7308643 ASS(ph)HSS(ph)QTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 ASS(1)HSS(0.924)QT(0.076)QGGGSVTK;AS(0.001)S(0.999)HSS(0.927)QT(0.073)QGGGSVTK 341.36 5.91E-72 3098700000 5374300 4235500 2541300 2223340 2590900 1987630 1391320 2792600 1975260 1577400 TRUE FALSE 5164266.414 4114707.687 3000569.441 2338086.844 2674238.651 2027821.24 1408347.39 2734931.834 1751036.766 1470561.293 3.5117655 2.79805249 2.040424602 1.589928183 1.8185156 1.378943707 0.957693771 1.85978772 1.190726816 1 20.48793549 4.976788078 0.667983081 1.342147638 5.684139519 0.883159852 0.263177378 1.310108691 0.354870201 0.108904733 4.6419361 94795.57771 -4.976788078 4.341991881 up LQEVECEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQEVECEEQR 10 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ; 190.86 1.99E-06 482610000 170113 195746 153032 209314 194979 172567 189406 199057 208758 194071 FALSE TRUE 163464.7959 190163.5157 180688.2866 220116.7206 201250.6766 176056.423 191724.0073 194946.4034 185060.667 180926.3983 0.903487813 1.051054559 0.99868393 1.2166092 1.11233451 0.973083113 1.059679566 1.077490102 1.022850556 1 17.4650434 4.977281863 1.76682507 1.065641954 0.755430416 0.319163855 0.066538948 2.25154328 4.177077733 0.017382567 1.425575424 94903.41985 -4.977281863 -0.310211539 IVYGHLDDPASQEIER ddPTM_BT-474_Pertuzumab_2h_R1 4 IVYGHLDDPASQEIER 16 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;;; 236.12 1.01E-19 2513290000 854160 1339180 880100 2073740 915580 1126440 1686950 1446820 1180460 946170 FALSE TRUE 820778.4829 1300987.898 1039153.648 2180765.97 945030.4622 1149217.389 1707595.399 1416942.661 1046459.13 882085.0631 0.930498109 1.474900723 1.178065122 2.47228534 1.071359783 1.30284191 1.935862504 1.606356031 1.186347183 1 19.75055826 4.977443783 1.650005499 1.533513736 0.383390876 0.112003944 0.429295937 3.841926283 6.193710578 0.107579455 8.466232776 94938.80991 -4.977443783 -1.150122859 LENS(ph)PLGEALR ddPTM_BT-474_Pertuzumab_2h_R1 3 LENSPLGEALR 11 0 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 LENS(1)PLGEALR;LENS(1)PLGEALR;LENS(1)PLGEALR 160.87 2.83E-05 678909000 305309 446387 414776 714844 380307 550622 720807 710236 653202 814763 TRUE FALSE 293377.1867 433656.4798 489735.2498 751737.1845 392539.92 561755.9541 729628.4517 695569.3784 579053.2474 759578.3763 0.386236886 0.570917358 0.644746171 0.989676915 0.516786591 0.739562857 0.96057033 0.915730885 0.762335087 1 19.53483931 4.977651443 0.384118044 0.915759207 9.82E-32 0.553235797 0.137284387 5.717250253 0.583780982 0.11734672 2.516676083 94984.21611 -4.977651443 -0.915759207 SIRDT(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 SIRDT(1)PAK;SIRDT(1)PAK;S(0.001)IRDT(0.999)PAK 87.878 0.024269 28723900000 22673100 14536600 10331500 10000600 10261800 8255500 8798800 17110800 8646300 7654800 TRUE FALSE 21787010.19 14122030.4 12198631.87 10516732.16 10591880.12 8422431.866 8906482.346 16757456 7664808.272 7136333.578 3.0529697 1.978891576 1.709369628 1.473688421 1.484218752 1.180218354 1.248047369 2.348188438 1.074054091 1 22.76675162 4.977656387 1.289176182 1.494151188 4.517914366 0.648485154 0.363661683 1.589403062 1.547244485 0.105714792 7.315735482 94985.29751 -4.977656387 3.023763178 ATENDIYNFFSPLNPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATENDIYNFFSPLNPVR 17 0 P52597;P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7 P52597;P31943 HNRNPF;HNRNPH1 "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ; 263.59 4.80E-27 329940000 250755 264297 211551 264590 256953 282107 272456 284817 311862 343780 FALSE TRUE 240955.2174 256759.5083 249782.9716 278245.5216 265218.1266 287811.3968 275790.398 278935.4294 276460.7332 320495.4744 0.751820967 0.801133023 0.779365051 0.868173013 0.827525341 0.898020159 0.860512613 0.870325642 0.862604172 1 18.28994446 4.977914449 0.034279248 1.55332739 7.60E-11 0.832393387 0.026940205 212.1455323 1.055210552 18.10247439 30.99612655 95041.75534 -4.977914449 -1.55332739 TLSAS(ph)TQDLSPH ddPTM_BT-474_Pertuzumab_2h_R1 2 TLSASTQDLSPH 12 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 TLSAS(0.963)T(0.037)QDLSPH;T(0.001)LS(0.006)AS(0.836)T(0.156)QDLSPH 201.76 1.52E-07 612490000 621570 549340 342330 387270 392000 343300 220950 464540 367670 314820 TRUE FALSE 597278.3572 533673.3611 404196.6461 407257.0511 404609.036 350241.7612 223654.0522 454947.0867 325933.643 293496.961 2.035041028 1.818326702 1.377174894 1.387602276 1.378579985 1.193340333 0.762031918 1.550091303 1.110517948 1 18.16298604 4.980527306 0.62661217 1.163197965 2.938755811 0.693621616 0.198065966 2.615237618 0.62838296 0.089015475 3.567937434 95615.28114 -4.980527306 1.775557846 LECLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LECLQR 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 112.56 0.06256 329060000 356980 407440 327350 434510 353900 380150 417160 446090 399040 465080 FALSE TRUE 343028.8269 395820.2101 386509.4269 456935.1132 365283.5149 387836.8935 422265.3289 436878.0856 353742.6521 433579.7173 0.791155151 0.912912192 0.891437979 1.05386644 0.84248294 0.894499622 0.97390471 1.007607294 0.815865314 1 18.72593774 4.98075036 1.504003946 0.941050654 0.651371964 0.264046999 0.071695495 2.791085022 3.696184452 0.01871481 1.424846917 95664.40176 -4.98075036 -0.28967869 LCSS(ph)SDTLVSEGEENQKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LCSSSDTLVSEGEENQKPK 19 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 LCS(0.001)S(0.435)S(0.316)DT(0.248)LVSEGEENQKPK 209.67 4.54E-25 0 231860 162610 135800 110910 117510 112170 108080 189750 143890 135820 TRUE FALSE 222798.6549 157972.522 160342.0809 116634.0784 121289.8159 114438.1543 109402.7154 185831.5962 127556.2104 126620.7904 1.759574033 1.247603348 1.266317169 0.921128971 0.95789811 0.903786447 0.864018579 1.467623094 1.00738757 1 16.95015478 4.980820435 1.243148769 1.053304547 2.41521596 0.622132649 0.170459136 1.819657835 1.636887703 0.053054415 3.652820668 95679.83876 -4.980820435 1.361911413 SESGGLGVSMVEYVLSSS(ph)PGDSCLR ddPTM_BT-474_Pertuzumab_2h_R1 5 SESGGLGVSMVEYVLSSSPGDSCLR 25 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLS(0.005)S(0.194)S(0.794)PGDS(0.006)CLR;SESGGLGVSMVEYVLS(0.001)S(0.08)S(0.918)PGDS(0.001)CLR;SESGGLGVSMVEYVLS(0.002)S(0.192)S(0.805)PGDS(0.001)CLR;SESGGLGVSMVEYVLSS(0.006)S(0.994)PGDSCLR;SESGGLGVSMVEYVLS(0.003)S(0.131)S(0.862)PGDS(0.004)CLR 198.1 5.02E-25 228165000 312030.2 365660.3 282200.2 389058 357266.8 402086.6 332389.8 328822.3 346779.3 389378 TRUE FALSE 299835.7148 355232.0263 333200.0536 409137.33 368758.6111 410217.0665 336457.6858 322032.0046 307414.3677 363005.0812 0.825982143 0.978586925 0.917893635 1.127084306 1.015849723 1.130058745 0.926867703 0.887128091 0.846859682 1 18.46963022 4.98086649 2.013815185 0.981181383 0.682662449 0.213008561 0.088946096 3.330641554 7.974363123 0.024662095 2.298581538 95689.98571 -4.98086649 -0.298518935 AES(ph)PDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AESPDLR 7 0 Q6UN15;Q6UN15-5;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 AES(1)PDLR;AES(1)PDLR;AES(1)PDLR 121.09 0.0046906 5122500000 8492900 8989600 7145600 8654700 8542800 9192600 8576100 9208500 9553000 10049700 TRUE FALSE 8160988.079 8733225.41 8436968.873 9101370.104 8817586.92 9378480.67 8681056.877 9018341.257 8468583.489 9369024.868 0.871060563 0.93213814 0.900517289 0.971431951 0.94114244 1.001009262 0.926569947 0.962569892 0.903891665 1 23.15946747 4.981999074 0.803104537 0.955912619 0.800851834 0.401488119 0.031584466 3.514222664 1.336428705 0.010312305 0.531095999 95939.85866 -4.981999074 -0.155060785 IVILPDYLEIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 IVILPDYLEIAR 12 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 110.14 0.003542 144278000 251620 280090 222910 281480 268960 291860 299760 286970 273550 310410 FALSE TRUE 241786.4122 272102.1074 263194.7956 296007.2165 277611.3427 297761.6092 303428.5525 281043.9692 242497.7508 289385.6542 0.835516235 0.940275039 0.909494966 1.022881446 0.959312732 1.028943919 1.048526588 0.971174504 0.837974334 1 18.14263388 4.985763872 1.001242557 0.982850763 0.703355921 0.347136695 0.057920247 3.263570263 1.893574418 0.017820116 1.098441404 96775.15413 -4.985763872 -0.279494842 YQDTHPER ddPTM_BT-474_Pertuzumab_2h_R1 2 YQDTHPER 8 0 C9JAH0;F8WD54;A0A087WUI8;Q96IJ6;Q96IJ6-2 C9JAH0 GMPPA Mannose-1-phosphate guanyltransferase alpha 0 ; 79.974 0.02665 827410000 770740 884350 682260 877290 861590 917200 965370 872780 1004230 942750 FALSE TRUE 740618.6287 859129.2039 805559.5588 922567.042 889303.8248 935746.4124 977184.4868 854756.788 890234.0205 878896.7028 0.842668571 0.977508735 0.916557721 1.049687681 1.011841121 1.064683039 1.111830871 0.972533843 1.012899488 1 19.74533409 4.98718693 0.786070966 1.033026997 0.684004996 0.600810673 0.045684691 2.523714515 0.916208571 0.016431903 0.84263657 97092.77869 -4.98718693 -0.349022001 DADVQFLASVLPPDTDPAFFEHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DADVQFLASVLPPDTDPAFFEHLR 24 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977;H0YF31;H0YDA6 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ;;; 158.94 2.24E-11 1692880000 783930 865760 711850 848030 887860 875760 845460 918340 980800 941240 FALSE TRUE 753293.1489 841069.3725 840497.13 891796.9299 916418.8232 893468.4672 855806.9924 899375.9581 869463.6958 877488.9764 0.858464515 0.958495656 0.95784352 1.016305565 1.044365055 1.018210475 0.975290876 1.024942743 0.990854266 1 19.74302148 4.987429557 1.029008492 1.010543095 0.716643617 0.820350906 0.021194464 1.129517299 0.689984527 0.006502227 0.410622486 97147.03652 -4.987429557 -0.293899479 TLIGHVPDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLIGHVPDQR 10 0 Q16822;Q16822-3;H0YML5;H0YM31;Q16822-2;H0YNG4;H0YMA5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ; 100.48 0.003987 612000000 140402 216605 142383 319420 169458 186144 270060 243490 189662 149035 FALSE TRUE 134914.9346 210427.6375 168114.7754 335905.3045 174908.7705 189907.9592 273365.0751 238461.8464 168132.3649 138940.7267 0.971025111 1.514513724 1.209974781 2.41761586 1.258873295 1.366827162 1.967494208 1.716284721 1.210101378 1 17.08411002 4.991588792 1.488066473 1.592438708 0.381665644 0.125119793 0.404252802 3.887288323 4.926222664 0.103222371 8.279439212 98081.88225 -4.991588792 -1.210773064 LLIDPNCSGHS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLIDPNCSGHSPR 13 0 Q8WYQ5-3;Q8WYQ5;Q8WYQ5-2;C9JSD5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 1 LLIDPNCSGHS(1)PR;LLIDPNCSGHS(1)PR;LLIDPNCSGHS(1)PR;LLIDPNCSGHS(1)PR 174.78 1.25E-05 1022210000 1335570 1539960 1228900 1582910 1423560 1512960 1637640 1479290 1468810 1717670 TRUE FALSE 1283374.448 1496041.849 1450989.567 1664604.175 1469350.1 1543553.088 1657681.928 1448742.145 1302076.847 1601330.681 0.80144249 0.934249163 0.906114886 1.039513072 0.917580683 0.963919012 1.035190263 0.904711414 0.813121776 1 20.61083983 4.993114033 1.749188662 0.94957879 0.656349533 0.312607427 0.064569862 2.498216145 4.366627727 0.016639582 1.502872346 98426.95129 -4.993114033 -0.293229256 IMNVIGEPIDER ddPTM_BT-474_Pertuzumab_2h_R1 3 IMNVIGEPIDER 12 0 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;; 220.94 6.60E-11 473727000 286713 499554 333169 745443 322889 410991 635820 523521 431283 350530 FALSE TRUE 275507.939 485307.209 393380.0496 783915.4026 333275.0179 419301.5196 643601.3554 512710.1084 382325.5619 326788.2909 0.843077756 1.485081389 1.203776453 2.398847892 1.019849937 1.283098359 1.969474958 1.568936595 1.169948779 1 18.31799677 4.994809099 1.877262082 1.51326786 0.184211379 0.147223813 0.420879627 3.432312743 6.873703943 0.10332572 10.02012926 98811.8657 -4.994809099 -1.32905648 NDNDSWDYTKPYLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDNDSWDYTKPYLGR 15 1 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;B7WPG3;Q8WVV9-5;Q8WVV9-3;Q8WVV9-2;H7BXH8 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 0 ; 113.01 0.0006551 1439430000 2102430 1939310 1534670 1715410 1792750 1683590 1521940 1909300 2161800 2050300 FALSE TRUE 2020264.711 1884002.778 1812019.008 1803942.516 1850415.432 1717633.343 1540565.957 1869872.288 1916401.527 1911431.355 1.056938145 0.985650242 0.947990627 0.943765263 0.968078413 0.898611053 0.805975037 0.97825762 1.002600236 1 20.86622196 4.996468199 1.066998932 0.933786185 1.180111515 0.285184954 0.054631639 3.545534353 2.295762451 0.016795976 1.123335603 99190.07048 -4.996468199 0.24632533 VPEEDLKR ddPTM_BT-474_Pertuzumab_2h_R1 6 VPEEDLKR 8 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;;; 126.41 0.0019566 7100960000 4782330 5026600 4029550 4607590 5048800 4969540 4893580 5109290 5314230 5082710 FALSE TRUE 4595431.256 4883246.29 4757779.322 4845388.272 5211199.237 5070027.504 4953469.096 5003781.376 4710980.889 4738453.524 0.969816678 1.030556966 1.004078503 1.022567436 1.099767933 1.069975146 1.04537674 1.055994609 0.994202194 1 22.17598486 4.997476158 0.900324578 1.046227322 0.905680805 0.27384456 0.031773632 3.995434513 1.856824242 0.010361977 0.614180389 99420.54932 -4.997476158 -0.140546516 GSVILDSGHLSTASS(ph)SDDLKGEEGSFR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSVILDSGHLSTASSSDDLKGEEGSFR 27 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 GSVILDSGHLST(0.001)AS(0.213)S(0.7)S(0.086)DDLKGEEGSFR;GSVILDSGHLSTAS(0.05)S(0.854)S(0.095)DDLKGEEGSFR;GSVILDSGHLST(0.001)AS(0.114)S(0.443)S(0.443)DDLKGEEGSFR 279.93 2.88E-61 1509690000 631146 948040 751807 1101270 874860 967450 1055500 994570 891836 1125400 TRUE FALSE 606480.1166 921002.8274 887675.2488 1158106.677 903000.6664 987012.5019 1068417.525 974031.7819 790598.5162 1049175.656 0.578053935 0.877834729 0.846069239 1.103825342 0.860676343 0.94075048 1.018339988 0.928378176 0.753542566 1 20.00082481 4.997767237 1.563745184 0.938750315 0.218977121 0.567131207 0.092392371 1.509352152 2.085503751 0.023485778 2.012623987 99487.20673 -4.997767237 -0.719773194 PVPDS(ph)PVSVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 PVPDSPVSVTR 11 0 G3XAC1;A0A0C4DFT5;Q9BXS9-5;Q9BXS9-7;Q9BXS9-4;Q9BXS9-2;Q9BXS9-3;Q9BXS9 G3XAC1 SLC26A6 Solute carrier family 26 member 6 1 PVPDS(1)PVSVTR;PVPDS(1)PVSVTR 190.68 2.27E-06 486660000 166055 287430 170810 451720 223285 198837 441160 456160 354070 226617 TRUE FALSE 159565.387 279232.7778 201679.1666 475033.3233 230467.1648 202857.6204 446559.048 446740.1366 313877.458 211268.0287 0.755274653 1.321699168 0.95461281 2.248486561 1.090875729 0.960190813 2.113708594 2.114565745 1.485683659 1 17.68871493 4.997803471 0.628244249 1.667630173 6.15E-17 0.168699963 0.483851041 7.172116687 1.70467922 0.221437616 9.254799665 99495.50739 -4.997803471 -1.667630173 GTPTAENPEY(ph)LGLDVPV ddPTM_BT-474_Pertuzumab_2h_R1 4 GTPTAENPEYLGLDVPV 17 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GTPT(0.001)AENPEY(0.999)LGLDVPV;GTPTAENPEY(1)LGLDVPV;GTPTAENPEY(1)LGLDVPV;GTPTAENPEY(1)LGLDVPV 128.54 0.00037714 842441000 480009 1096460 397925 1228460 372814 387158 915917 943145 823948 546081 TRUE FALSE 461249.7176 1065190.034 469838.8993 1291860.968 384805.9009 394986.6 927126.2662 923668.7262 730416.8773 509094.4475 0.906019934 2.092323025 0.922891423 2.537566407 0.75586348 0.775861143 1.821128223 1.814336673 1.434737466 1 18.95757381 4.997835166 21.60712687 1.492282973 0.379755395 0.075683229 0.573581552 5471.877832 86317.64222 0.127789229 143062.4144 99502.76897 -4.997835166 -1.112527578 SENFEELLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SENFEELLK 9 0 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;; 174.02 0.00012793 1365300000 1411490 1268450 1031750 1106000 1150210 1000220 1140700 1298620 1357890 1168920 FALSE TRUE 1356327.41 1232275.048 1218210.176 1163080.793 1187207.549 1020445.134 1154660.228 1271803.043 1203748.02 1089748.007 1.244624814 1.13078899 1.117882454 1.067293342 1.0894331 0.93640468 1.059566267 1.167061591 1.104611352 1 20.05556313 4.997921273 1.064147482 1.069834246 1.414157138 0.471630513 0.058875611 2.916019217 1.874250338 0.019204606 1.289099191 99522.49921 -4.997921273 0.344322892 SSGGGYSGDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSGGGYSGDR 10 0 Q92804-2;Q92804;A0A075B7F4 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 216.12 1.83E-08 787438000 526095 543477 432659 524862 535742 503766 521389 537035 584405 579514 FALSE TRUE 505534.6258 527977.5681 510850.1057 551950.1907 552974.628 513952.4937 527769.9145 525945.0396 518065.7944 540263.0006 0.935719502 0.977260274 0.945558191 1.021632409 1.023528591 0.951300558 0.976875918 0.973498165 0.958914073 1 19.04330236 4.997923275 1.280154266 0.982197875 0.89289574 0.231839741 0.025364448 4.014630055 3.718117996 0.007267604 0.549128742 99522.95785 -4.997923275 -0.089302135 SIIPLPHPVRPEDIE ddPTM_BT-474_Pertuzumab_2h_R1 4 SIIPLPHPVRPEDIE 15 1 P61599;A8MZB2 P61599 NAA20 N-alpha-acetyltransferase 20 0 ;;; 140.84 4.44E-06 560010000 893730 1094020 882700 1094140 1151220 1222350 1099500 987710 1078240 1179850 FALSE TRUE 858802.0435 1062819.621 1042223.526 1150608.697 1188250.037 1247066.754 1112956.01 967313.4433 955842.7156 1099937.709 0.780773345 0.966254373 0.94752959 1.046067143 1.080288481 1.133761253 1.01183549 0.879425658 0.868997133 1 20.06899039 4.998448347 1.643430188 0.997035908 0.564455047 0.405274816 0.077934032 2.508623441 3.822116012 0.023660946 2.108685025 99643.35622 -4.998448347 -0.432580861 KVAGAAT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 KVAGAATPK 9 1 P16402 P16402 HIST1H1D Histone H1.3 1 KVAGAAT(1)PK;KVAGAAT(1)PK;KVAGAAT(1)PK;KVAGAAT(1)PK 81.431 0.012482 2353020000 9750800 4259580 3233340 2453250 2742550 1404340 1958590 6653500 1950080 1282100 TRUE FALSE 9369727.956 4138100.949 3817676.463 2579862.526 2830766.611 1432736.717 1982559.81 6516102.9 1728715.094 1195262.225 7.839056368 3.462086279 3.19400746 2.158407145 2.368322659 1.198679827 1.658681893 5.451609499 1.446306139 1 20.18889573 4.999199146 1.594840484 2.508327453 13.21249968 0.644135516 1.226012862 1.497346996 2.145100497 0.345754014 30.2885546 99815.7665 -4.999199146 10.70417222 LSDETLIDIMTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LSDETLIDIMTR 12 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;;; 214.82 9.98E-11 196380000 277110 324488 239620 370639 299429 313387 321682 331227 319158 343611 FALSE TRUE 266280.2348 315233.9199 282924.6643 389767.7232 309060.4057 319723.8999 325618.8405 324387.0467 282928.5219 320337.9209 0.831247934 0.984066822 0.883206907 1.216739255 0.964794942 0.998083208 1.016485465 1.01264017 0.883218949 1 18.28923507 4.999958034 1.361734406 1.006542777 0.663725471 0.246476957 0.086922977 3.23424717 3.374924932 0.022755123 1.803694218 99990.3375 -4.999958034 -0.342817306 ESGHSNWLGDPEEPLTGFSWR ddPTM_BT-474_Pertuzumab_2h_R1 5 ESGHSNWLGDPEEPLTGFSWR 21 0 Q6DD88;F5H6I7;F5GWF8 Q6DD88 ATL3 Atlastin-3 0 ;;;; 249.2 1.25E-30 1468638000 347025 584341 407268 774745 475463 501537 599365 629225 562569 522359 FALSE TRUE 333462.8793 567676.1668 480870.3872 814729.6823 490756.6992 511678.4218 606700.2082 616231.2839 498708.5256 486979.1597 0.684758008 1.165709365 0.987455783 1.673027821 1.007757087 1.050719341 1.245844296 1.265416131 1.024085971 1 18.89350051 5.002585061 1.89921022 1.184428931 0.175373559 0.326843106 0.199627934 2.251106619 4.514877858 0.048998126 5.084659281 100597.0072 -5.002585061 -1.009055372 WES(ph)QQDVSQTTVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 WESQQDVSQTTVSR 14 0 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 WES(1)QQDVSQTTVSR;WES(0.968)QQDVS(0.032)QTTVSR;WES(1)QQDVSQTTVSR 346.18 9.31E-82 982130000 1907970 1325250 827310 992430 917630 742600 633400 1313960 933150 799890 TRUE FALSE 1833404.423 1287455.168 976823.3204 1043649.431 947146.4023 757615.8808 641151.7387 1286826.267 827222.7241 745712.7378 2.45859341 1.726476031 1.309919049 1.399532794 1.270122333 1.015962102 0.85978381 1.725632675 1.109304806 1 19.50826046 5.003525218 1.115667001 1.220243672 3.72813222 0.74707412 0.22717698 1.453362168 1.016290903 0.069341353 4.910846774 100815.0148 -5.003525218 2.507888549 up SSENGVDYVIMGMPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSENGVDYVIMGMPHR 16 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7;Q02218-3 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 127.75 6.45E-05 138260000 72295 127620 84080 183160 91121 89730 164520 118650 128700 102060 FALSE TRUE 69469.63147 123980.4026 99275.12635 192612.9095 94051.98972 91544.40208 166533.445 116199.836 114090.5156 95147.38529 0.730126543 1.303035309 1.043382601 2.024363664 0.988487381 0.962132609 1.750268223 1.221261474 1.199092494 1 16.53787639 5.003587804 1.976390287 1.306902891 0.139058324 0.186784117 0.334406962 3.280414847 7.085685266 0.081748019 8.91771573 100829.5442 -5.003587804 -1.167844567 SGDGEGTPVEHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGDGEGTPVEHVR 13 0 Q7L576;Q7L576-2;Q7L576-3 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ; 143.42 4.08E-05 1053640000 808760 926450 726270 967760 888920 931520 1017080 926090 991130 1032120 FALSE TRUE 777152.7651 900028.5531 857523.1448 1017706.21 917512.9191 950355.9726 1029527.329 906965.9179 878621.0776 962213.5931 0.80767178 0.935372935 0.891198327 1.057671828 0.953543918 0.987676727 1.069957166 0.942582733 0.913124782 1 19.87599765 5.003980777 1.008502516 0.985455422 0.640134436 0.510135579 0.051865138 2.435287558 1.397332813 0.015569424 1.028598063 100920.8215 -5.003980777 -0.345320986 S(ph)RSAS(ph)PSTQQEKHPTHHER ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSASPSTQQEKHPTHHER 19 2 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 2 S(0.795)RS(0.229)AS(0.913)PS(0.05)T(0.013)QQEKHPTHHER 81.315 0.010659 79244000 77431 82509 39751 35226 48313 68428 36522 3273.5 43158 21056 TRUE FALSE 74404.91092 80155.9241 46934.88996 37044.01808 49867.03152 69811.66104 36968.96716 3205.901081 38258.88477 19629.85837 3.79039469 4.08336742 2.390994835 1.887126101 2.540366344 3.556401669 1.883302797 0.163317586 1.949014815 1 14.26076214 5.004056793 0.234303638 0.618764188 7.216925208 0.547771026 0.788925426 9.751803328 0.42121715 1.395392939 19.15692619 100938.4875 -5.004056793 6.59816102 RMPS(ph)SGDK ddPTM_BT-474_Pertuzumab_2h_R1 1 RMPSSGDK 8 1 Q96GV9 Q96GV9 C5orf30 UNC119-binding protein C5orf30 1 RMPS(0.731)S(0.269)GDK 59.155 0.061503 310630000 282320 539000 374940 574430 618130 805650 602490 533020 253490 498660 TRUE FALSE 271286.6223 523628.2477 442699.9985 604076.4011 638012.7128 821940.795 609863.4528 522012.9507 224714.8779 464885.314 0.583556017 1.126360055 0.952277874 1.299409516 1.372408836 1.768050679 1.311857859 1.122885441 0.48337702 1 18.82651533 5.005722977 1.298124872 1.215105566 2.02E-16 0.223163179 0.315958968 3.797973875 3.566114461 0.09111888 7.199289503 101326.485 -5.005722977 -1.215105566 TPST(ph)PVACSTPAQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSTPVACSTPAQLK 15 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 T(0.003)PS(0.134)T(0.863)PVACSTPAQLK 112.5 0.0045186 0 217250 193130 130900 167800 152690 122580 140150 202530 144590 137150 TRUE FALSE 208759.6298 187622.1215 154556.5419 176460.1781 157601.4125 125058.6516 141865.1976 198347.6847 128176.7494 127860.7083 1.632711351 1.467394667 1.208788406 1.380096985 1.232602373 0.978085083 1.109529264 1.551279414 1.00247176 1 16.96421347 5.006488104 0.82933893 1.19717745 2.094031294 0.439650224 0.170775847 3.834709012 1.507412162 0.06137286 3.488313544 101505.1562 -5.006488104 0.896853845 DDISEIQSLAS(ph)DHS(ph)GR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDISEIQSLASDHSGR 16 0 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 DDISEIQSLAS(1)DHS(1)GR 83.064 0.0018737 0 74256 83706 83670 102560 90402 101220 135000 123910 146760 151660 TRUE FALSE 71353.99343 81318.78684 98791.03023 107853.1339 93309.86243 103266.7378 136652.1704 121351.2152 130100.4201 141387.9331 0.504668198 0.575146585 0.698723208 0.762817105 0.659956337 0.730378721 0.966505185 0.858285516 0.920166362 1 17.10929947 5.006814095 0.212610501 1.042124414 1.36E-09 0.85196154 0.060711817 5.370758064 0.199726407 0.120663753 1.518126726 101581.3769 -5.006814095 -1.042124413 KRS(ph)EGFSMDR ddPTM_BT-474_Pertuzumab_2h_R1 9 KRSEGFSMDR 10 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 KRS(0.992)EGFS(0.008)MDR;KRS(0.951)EGFS(0.049)MDR;KRS(0.88)EGFS(0.12)MDR;KRS(0.885)EGFS(0.115)MDR;KRS(0.999)EGFS(0.001)MDR;KRS(1)EGFSMDR;KRS(0.586)EGFS(0.414)MDR;KRS(0.993)EGFS(0.007)MDR;KRS(0.5)EGFS(0.5)MDR 183 8.96E-07 27970740000 26543130 22152150 17014570 18517260 19191260 17751740 17523450 23610620 19621370 18120300 TRUE FALSE 25505795.13 21520392.37 20089481.29 19472938.01 19808564.31 18110692.35 17737907.22 23123052.45 17394034.34 16892995.94 1.509844389 1.273923965 1.189219565 1.152722588 1.172590367 1.072082916 1.050015479 1.368795241 1.029659535 1 24.00992187 5.007481689 1.179711046 1.143808351 1.886256451 0.582542068 0.099604788 2.047537478 1.587504832 0.028978643 2.165753224 101737.647 -5.007481689 0.742448099 VLQIVTNRDDVQGYAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLQIVTNRDDVQGYAAK 17 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 212.9 1.05E-12 1158430000 574140 588310 543110 581050 606670 614680 669950 636770 717240 690830 FALSE TRUE 551701.9741 571531.9748 641262.0584 611038.0601 626184.0915 627109.2508 678149.0485 623620.477 635821.9221 644039.4688 0.856627584 0.887417623 0.995687515 0.948758717 0.972275958 0.973712453 1.05296194 0.968295434 0.987240616 1 19.29678958 5.007797188 0.75392725 0.993974312 0.70123971 0.715271616 0.028516801 1.979460564 0.649937866 0.010284167 0.536297112 101811.5825 -5.007797188 -0.292734602 ALLDQLHTLLSNTDATGLEEIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALLDQLHTLLSNTDATGLEEIDR 23 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 0 ; 242.9 2.31E-37 227790000 142856 156458 125395 153445 161681 157821 156492 148832 153531 173372 FALSE TRUE 137273.0296 151995.971 148056.6659 161364.3148 166881.6162 161012.2488 158407.1959 145758.5672 136102.8045 161629.36 0.849307512 0.940398273 0.916025813 0.998360167 1.032495681 0.996181936 0.980064488 0.901807488 0.842067336 1 17.30232976 5.008082281 1.425325486 0.959261432 0.738134605 0.272256783 0.053852761 3.575446563 4.020980006 0.015882286 1.351255917 101878.4389 -5.008082281 -0.221126826 RNDDIS(ph)ELEDLSELEDLKDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNDDISELEDLSELEDLKDAK 21 2 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 RNDDIS(1)ELEDLSELEDLKDAK;RNDDIS(1)ELEDLSELEDLKDAK 195.09 6.86E-19 43268000 98909 72203 64501 45161 63338 55304 52987 80798 76471 67932 TRUE FALSE 95043.52693 70143.84113 76157.76552 47491.76462 65375.32429 56422.28477 53635.47076 79129.49306 67790.33267 63330.90513 1.500744806 1.107576798 1.20253714 0.749898719 1.03228154 0.890912338 0.846908325 1.249460953 1.070414713 1 15.95062208 5.009448391 1.313638083 1.001202408 2.004208586 0.532842708 0.141254668 2.080854194 1.986709463 0.040738219 3.30124264 102199.4105 -5.009448391 1.003006177 FAEAFEAIPR ddPTM_BT-474_Pertuzumab_2h_R1 5 FAEAFEAIPR 10 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;; 161.79 1.62E-05 887140000 579497 657472 528330 662419 636360 628762 654354 654715 678432 722030 FALSE TRUE 556849.6166 638721.5423 623810.9836 696606.524 656829.0973 641475.9984 662362.18 641194.9065 601419.2436 673126.265 0.827258786 0.948888159 0.926736953 1.034882399 0.97578884 0.952980194 0.984008817 0.952562602 0.893471663 1 19.36051763 5.009929812 1.647255936 0.966600467 0.681854313 0.558340624 0.036608486 1.619712098 2.413656695 0.009469341 0.907065069 102312.7627 -5.009929812 -0.284746154 RAPEEELPPLDPEEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 RAPEEELPPLDPEEIR 16 1 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 ; 89.049 0.0094959 217190000 129037 151788 111393 164574 150916 164757 137349 157746 137248 158497 FALSE TRUE 123994.0914 147459.1549 131524.193 173067.6839 155770.3502 168088.4994 139029.9181 154488.49 121668.1824 147761.857 0.839148166 0.997951419 0.890109232 1.171260888 1.05419865 1.137563528 0.940905325 1.045523473 0.823407237 1 17.17291438 5.010044258 1.254609447 1.021605451 0.663598531 0.20302049 0.099769482 3.957756512 3.448061567 0.027229552 2.14501528 102339.728 -5.010044258 -0.35800692 DSGRGDSVSDS(ph)GSDALR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 DS(0.001)GRGDS(0.268)VS(0.221)DS(0.385)GS(0.125)DALR 113.14 0.0011224 171020000 158130 167970 104330 129590 138170 137710 109870 125440 124320 100220 TRUE FALSE 151950.1048 163179.6601 123184.7518 136278.1554 142614.3635 140494.5906 111214.6219 122849.6202 110207.7148 93432.01013 1.626317411 1.746507004 1.318442701 1.458581007 1.526397252 1.503709386 1.19032676 1.314855797 1.179549863 1 16.51162929 5.011539735 0.101075532 0.668943834 2.641162304 0.738239571 0.11045439 30.54682816 0.456098794 1.9239951 8.946849656 102692.7384 -5.011539735 1.97221847 KEYEQELSDDLHVER ddPTM_BT-474_Pertuzumab_2h_R1 1 KEYEQELSDDLHVER 15 1 Q7Z7F7;Q7Z7F7-2;X6R631 Q7Z7F7 MRPL55 "39S ribosomal protein L55, mitochondrial" 0 172.24 6.74E-07 185700000 120620 179170 121060 264780 108200 155270 229280 192730 162610 131480 FALSE TRUE 115906.037 174060.247 142938.235 278445.3275 111680.3513 158409.6658 232085.9972 188750.0581 144151.1945 122574.7425 0.945594783 1.420033553 1.166131228 2.271637059 0.911120423 1.29235161 1.89342431 1.539877256 1.176026901 1 16.90330221 5.013054867 1.643431363 1.463446054 0.405032274 0.097272829 0.395230242 4.651623011 6.84986952 0.099393539 9.687188493 103051.6302 -5.013054867 -1.058413779 GLQS(ph)LPTHDPSPLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLQSLPTHDPSPLQR 15 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GLQS(0.999)LPT(0.001)HDPSPLQR;GLQS(0.999)LPT(0.001)HDPSPLQR 123.19 6.72E-05 594310000 340560 608600 246029 666000 294590 286860 439770 672880 356030 221043 TRUE FALSE 327250.5387 591243.3239 290491.9132 700372.3398 304065.7549 292660.5057 445152.0368 658984.7929 315614.967 206071.5607 1.58804319 2.869116543 1.409665226 3.398685085 1.475534779 1.420188718 2.160181809 3.197844431 1.531579447 1 17.65278589 5.013496387 17.46319571 2.160681854 0.602810827 0.013159141 0.802182831 31927368.05 769903779.1 0.184122937 1241316859 103156.4499 -5.013496387 -1.557871027 RFS(ph)DSEGEETVPEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RFSDSEGEETVPEPR 15 1 A0A1B0GWH8;H3BQ48;A0A1B0GWD3;A0A1B0GV71;A0A1B0GW34;A0A0D9SFH9;H3BPL0;Q9UBD8;A0A1B0GV41;H3BR84;O95090;H3BR00;Q9UP10;Q9UBH5;A0A0D9SF04;Q13286-5;Q13286-4;Q13286-6;Q13286-2;Q13286-7;Q13286-3;Q13286 A0A1B0GWH8 CLN3 Battenin 1 RFS(0.999)DS(0.001)EGEETVPEPR;RFS(0.969)DS(0.031)EGEETVPEPR 250.79 3.39E-19 1258940000 163143 273170 190121 395460 222687 275590 414050 358400 318850 364310 TRUE FALSE 156767.1912 265379.4591 224480.0939 415869.738 229849.9296 281162.6186 419117.2678 350998.9148 282655.4847 339634.9592 0.461575544 0.781366735 0.660945194 1.22446093 0.676755803 0.827837686 1.234022754 1.033459322 0.832233188 1 18.37362544 5.01440905 0.66674387 0.995061592 2.93E-18 0.425760171 0.179418576 4.210943567 1.096869426 0.074153756 3.449981224 103373.4594 -5.01440905 -0.995061592 KPGMTR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPGMTR 6 1 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 92.467 0.074917 1492200000 1527700 2202000 1456200 3231600 1440300 1853200 2805900 2408500 2072800 1729700 FALSE TRUE 1467995.795 2139201.116 1719367.733 3398383.263 1486628.558 1890672.974 2840239.444 2358763.633 1837504.434 1612545.878 0.910359088 1.326598607 1.066244227 2.107464543 0.921913961 1.172477012 1.761338689 1.462757535 1.139505213 1 20.62090878 5.015126031 1.460909064 1.380863739 0.42722443 0.102746128 0.35082699 4.863951066 5.661054516 0.090804173 8.160116025 103544.2605 -5.015126031 -0.953639309 DNEGSWFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNEGSWFR 8 0 Q9BPW8;H7C2U6;F8WCR5 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 105.52 0.010171 177400000 83661 127420 91133 159840 88213 110330 130550 150470 116520 116350 FALSE TRUE 80391.43563 123786.1064 107602.7603 168089.3616 91050.45126 112560.9482 132147.71 147362.7419 103293.1381 108469.5109 0.741143156 1.141206459 0.99200927 1.549646165 0.839410545 1.037719699 1.218293591 1.358563717 0.952278085 1 16.72693005 5.015712696 1.924616373 1.15015287 0.298611835 0.229259733 0.201327727 2.992772246 5.934891021 0.050441521 5.857170192 103684.2273 -5.015712696 -0.851541035 EEVGEEAIVELVENGK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEVGEEAIVELVENGK 16 0 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ;; 228.07 1.03E-14 53360000 67294 66620 82936 94298 76213 69587 107913 117410 123373 131616 FALSE TRUE 64664.07608 64720.06283 97924.3801 99164.73108 78664.46036 70994.09682 109233.6716 114985.4425 109368.2143 122701.5311 0.527003009 0.527459293 0.798069749 0.808178433 0.641104146 0.578591776 0.890238863 0.937114977 0.891335367 1 16.90479373 5.017267353 0.162272551 1.095726059 4.49E-20 0.630282508 0.102172956 16.59606418 0.425452269 0.417738086 3.858472715 104056.0541 -5.017267353 -1.095726059 STGLILDSGATHTTAIPVHDGYVLQQGIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 STGLILDSGATHTTAIPVHDGYVLQQGIVK 30 0 O96019-2;O96019 O96019-2 ACTL6A Actin-like protein 6A 0 298.17 2.45E-81 258560000 107570 143550 120610 147230 166800 142250 165660 140880 160360 178480 FALSE TRUE 103366.0455 139456.0946 142406.91 154828.5579 172165.2735 145126.3925 167687.3966 137970.7788 142156.6051 166391.3906 0.621222319 0.838120855 0.855855038 0.930508227 1.034700611 0.872198928 1.007788901 0.829194216 0.854350724 1 17.34422126 5.017771883 1.241773621 0.923594744 0.305359626 0.660215725 0.066365544 1.631525852 1.37449718 0.018764186 1.519173056 104177.0086 -5.017771883 -0.618235117 VSEEIFFGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSEEIFFGR 9 0 Q9Y4W6 Q9Y4W6 AFG3L2 AFG3-like protein 2 0 ;; 170.22 0.00013465 188129000 138870 224151 153567 318994 150622 184847 262666 260629 203332 151414 FALSE TRUE 133442.8069 217758.4329 181319.973 335457.3186 155466.8934 188584.733 265880.5851 255246.9201 180250.6038 141158.5949 0.94533958 1.542650896 1.284512453 2.376456912 1.101363282 1.335977686 1.883559306 1.808227974 1.276936795 1 17.10695745 5.019548459 1.775593726 1.578484579 0.257016608 0.136477721 0.397737241 3.837109027 6.459201752 0.098989865 10.81638896 104604.0401 -5.019548459 -1.321467971 TLS(ph)PGRR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLSPGRR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.001)LS(0.999)PGRR;T(0.002)LS(0.998)PGRR;T(0.001)LS(0.999)PGRR;TLS(1)PGRR 85.533 0.012704 4771000000 3080520 3484030 2891430 3401880 3452730 3778660 3508490 3383110 3907810 3668550 TRUE FALSE 2960129.873 3384668.876 3413975.721 3577451.434 3563790.196 3855067.094 3551427.95 3313247.596 3464211.792 3420075.841 0.865515857 0.989647316 0.998216379 1.046015235 1.042020809 1.127187604 1.038406198 0.968764364 1.012904963 1 21.70559689 5.020158165 1.328429381 1.031721074 0.688926996 0.614537989 0.039309066 1.890082422 1.808559544 0.01213896 1.04334008 104750.997 -5.020158165 -0.342794078 ITPAHDQNDYEVGQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITPAHDQNDYEVGQR 15 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 220.25 1.70E-12 1345950000 335180 390680 309950 402440 375410 402130 382470 340220 439320 461890 FALSE TRUE 322080.795 379538.1889 365964.8598 423209.9766 387485.4036 410261.3441 387150.7823 333194.3381 389450.2354 430605.7789 0.747971372 0.881405238 0.849883763 0.982824656 0.899861132 0.952753921 0.899084038 0.773780461 0.90442408 1 18.71600816 5.020350094 1.674676324 0.897344839 0.585609776 0.363598951 0.061997947 2.856023129 4.287443062 0.017307523 1.795414037 104797.3001 -5.020350094 -0.311735062 VDDHLMGK ddPTM_BT-474_Pertuzumab_2h_R1 3 VDDHLMGK 8 0 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;; 126.52 0.0012156 2369600000 3951600 3685100 3429500 2977870 3446330 3738400 3622570 3418440 4360000 4151900 FALSE TRUE 3797167.103 3580004.556 4049286.939 3131558.228 3557184.334 3813993.009 3666904.095 3347848.019 3865071.079 3870688.115 0.9810057 0.924901322 1.046141363 0.809044318 0.919005673 0.985352706 0.947351992 0.864923218 0.998548827 1 21.88415863 5.020911707 0.001350591 1.871879426 4.21E-08 0 0.067172641 7065857.055 1322.859375 906591.2833 926937.3074 104932.9077 -5.020911707 -1.871879384 RVWGSPGGEGTGDLDEFDF ddPTM_BT-474_Pertuzumab_2h_R1 4 RVWGSPGGEGTGDLDEFDF 19 1 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 ;;; 141.65 3.34E-06 487463000 540895 715682 579876 811690 624519 765683 775322 747872 768731 858216 FALSE TRUE 519756.2254 695271.4501 684672.4925 853581.4182 644607.2208 781165.6349 784810.6226 732428.1819 681467.8797 800088.2659 0.649623607 0.868993434 0.855746199 1.066859064 0.805670135 0.976349321 0.980905053 0.915434225 0.851740875 1 19.60979964 5.024665311 1.355525829 0.934792928 0.342323424 0.573606664 0.07364824 1.724657086 1.701916475 0.018870237 1.683170372 105843.7727 -5.024665311 -0.592469504 SLEAEILQLQEELASSER ddPTM_BT-474_Pertuzumab_2h_R1 4 SLEAEILQLQEELASSER 18 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;;; 277.52 8.96E-39 67076000 98811 111116 89141 111497 112212 109259 108803 111703 119045 115083 FALSE TRUE 94949.35688 107947.0805 105250.7616 117251.3735 115821.4009 111468.2918 110134.5637 109396.294 105531.5107 107288.3259 0.884992436 1.00614004 0.981008518 1.092862365 1.079534049 1.038960119 1.026528867 1.019647693 0.98362529 1 16.71113358 5.025726964 1.408699321 1.033380228 0.725201255 0.607328792 0.034417235 1.70287 1.806981373 0.009720529 0.898143638 106102.8291 -5.025726964 -0.308178973 VDLENR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDLENR 6 0 P20700;E9PBF6;A0A0D9SFE5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ; 114.19 0.059325 1123260000 1414400 1673390 1232420 1990170 1435700 1490050 1743330 1690900 1742750 1738380 FALSE TRUE 1359123.684 1625666.556 1455145.709 2092882.912 1481880.594 1520179.832 1764665.394 1655982.324 1544920.326 1620637.974 0.838634973 1.003102841 0.897884495 1.291394467 0.914381014 0.938013212 1.088870816 1.021808911 0.95327911 1 20.62813042 5.025834258 1.473030799 1.021967918 0.64314805 0.190604378 0.107523638 3.929297258 4.545514793 0.027768381 2.6610479 106129.0455 -5.025834258 -0.378819867 AVSGYQS(ph)HDDSSDNSECSFPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVSGYQSHDDSSDNSECSFPFK 22 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 AVSGYQS(0.58)HDDS(0.407)S(0.013)DNSECSFPFK 188.8 1.52E-17 112120000 103270 117140 90955 118090 120590 122280 113480 104930 138600 128390 TRUE FALSE 99234.09423 113799.2819 107392.5918 124184.6391 124468.8869 124752.5854 114868.8022 102763.1588 122866.7091 119694.0309 0.829064686 0.95075152 0.89722596 1.037517394 1.039892181 1.042262378 0.959686973 0.858548735 1.026506569 1 16.86899168 5.025870994 1.200024483 0.978832778 0.676450516 0.392077118 0.058592698 3.492675021 2.715579204 0.018902296 1.546265822 106138.0231 -5.025870994 -0.302382262 EGNNPAENGDAK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGNNPAENGDAK 12 0 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ;; 206.36 2.12E-07 713360000 1169860 962854 824813 788613 939583 834300 876119 1095810 996056 844448 FALSE TRUE 1124140.578 935394.3467 973875.057 829313.4114 969805.5405 851170.1176 886841.2064 1073181.141 882987.8987 787252.7848 1.42792836 1.188175342 1.23705508 1.053427092 1.231885818 1.081190355 1.1265012 1.363197643 1.121606574 1 19.58646743 5.026994304 1.790244616 1.169395816 1.719801802 0.393161365 0.100186645 2.539259141 4.258467492 0.026085696 3.026847362 106412.9063 -5.026994304 0.550405985 HHGKDS(ph)DKEER ddPTM_BT-474_Pertuzumab_2h_R1 6 HHGKDSDKEER 11 2 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 HHGKDS(1)DKEER;HHGKDS(1)DKEER;HHGKDS(1)DKEER;HHGKDS(1)DKEER;HHGKDS(1)DKEER;HHGKDS(1)DKEER 201.3 2.09E-08 609086000 1045052 729613 505099 552413 446698 371650 333837 7692.91 353122 118050.7 TRUE FALSE 1004210.212 708805.1516 596381.6252 580923.1011 461066.4469 379165.0176 337922.5971 7534.04872 313037.071 110055.0209 9.124619703 6.440461739 5.418940636 5.278478857 4.189417647 3.445231434 3.070487781 0.06845711 2.844368828 1 16.74786544 5.030545827 0.285596124 0.484703564 16.64177371 0.883986668 0.853478655 3.043897589 0.180296307 1.063827908 17.80916333 107286.6851 -5.030545827 16.15707015 IERDS(ph)REHEEPTTSEMAEETYSPK ddPTM_BT-474_Pertuzumab_2h_R1 3 IERDSREHEEPTTSEMAEETYSPK 24 2 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 IERDS(0.981)REHEEPT(0.014)T(0.003)S(0.003)EMAEETYSPK;IERDS(0.995)REHEEPT(0.002)T(0.002)S(0.002)EMAEETYSPK;IERDS(1)REHEEPTTSEMAEETYSPK 186.43 1.11E-17 3749910000 1351430 1320140 1011522 1082630 996300 1390100 960735 895840 1332130 938880 TRUE FALSE 1298614.622 1282490.9 1194326.527 1138504.664 1028346.894 1418208.774 972492.7623 877340.5909 1180912.187 875288.8213 1.483641273 1.465220243 1.364494207 1.300718844 1.174865792 1.620275205 1.111053562 1.002344106 1.349168593 1 19.73939962 5.03218862 0.140884717 0.890621473 2.086884584 0.408118853 0.153576923 30.0856836 0.646488543 0.891166029 6.787359851 107693.2839 -5.03218862 1.196263111 SLTVSDDAESS(ph)EPER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLTVSDDAESSEPER 15 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 SLTVSDDAES(0.016)S(0.984)EPER 250.17 1.03E-18 127880000 142860 153310 127690 146090 157020 159110 141000 159690 176220 180480 TRUE FALSE 137276.8733 148937.7489 150766.4234 153629.7224 162070.6909 162327.3132 142725.6002 156392.3457 156216.2444 168255.9288 0.815881343 0.88518574 0.896054151 0.913071673 0.963239109 0.964764299 0.848264909 0.929490846 0.928444219 1 17.36029782 5.032292365 0.939509781 0.929572324 0.697709666 0.483208246 0.038002788 3.058672809 1.474481717 0.01192634 0.82054615 107719.0129 -5.032292365 -0.231862658 ESAGADTRPTVRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESAGADTRPTVRPR 14 2 O75489;E9PS48;O75489-2;G3V194 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ; 144.27 5.01E-06 1137110000 477990 737020 506560 1042470 499070 633170 913070 820100 601160 568680 FALSE TRUE 459309.6224 716000.9112 598106.6604 1096272.002 515123.0398 645973.1312 924244.4238 803164.6484 532918.8371 530162.7971 0.866355815 1.350530281 1.128156603 2.067802584 0.971631813 1.218442967 1.743321917 1.514939662 1.005198479 1 19.01607591 5.032748257 1.69298063 1.386904641 0.274673196 0.128326248 0.342019415 4.2583603 6.332612701 0.085958257 9.760621944 107832.1482 -5.032748257 -1.112231445 SDPVVSYR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDPVVSYR 8 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 143.85 0.0013837 2209220000 2778300 2330800 1910350 1954940 2008490 1652130 2007010 2509800 2197200 2217200 FALSE TRUE 2669720.964 2264327.866 2255592.741 2055834.688 2073094.905 1685537.201 2031572.389 2457971.753 1947783.067 2067027.069 1.291575231 1.095451482 1.091225545 0.994585276 1.002935538 0.815440313 0.982847501 1.1891338 0.94231135 1 20.97912585 5.0329211 1.072132092 1.003593139 1.595330237 0.512901976 0.088143055 2.884513577 1.785766621 0.02916045 2.24758418 107875.0724 -5.0329211 0.591737098 EFHGLGDCIIK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFHGLGDCIIK 11 0 P12235;V9GYG0 P12235 SLC25A4 ADP/ATP translocase 1 0 145.91 3.60E-05 114060000 142260 269020 155020 401910 160160 188020 367910 318300 285510 186020 FALSE TRUE 136700.3219 261347.813 183035.5624 422652.6233 165311.6919 191821.8932 372412.5926 311726.9938 253100.1018 173420.6997 0.788258392 1.507016253 1.055442417 2.437152105 0.953240831 1.10610725 2.147451794 1.797518948 1.459457275 1 17.40391659 5.032951233 1.294597203 1.579066843 1.15E-14 0.148241567 0.4830925 4.705332138 4.183086629 0.131382003 11.76662497 107882.5573 -5.032951233 -1.579066843 HASS(ph)S(ph)PESPKPAPAPGSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HAS(0.612)S(0.705)S(0.663)PES(0.019)PKPAPAPGSHR 75.797 0.018435 77093000 87468 78020 60005 62657 67303 66007 70843 35349 92986 72557 TRUE FALSE 84049.65386 75794.94599 70849.2383 65890.73528 69467.86212 67341.70676 71709.99783 34619.0308 82430.61911 67642.64976 1.24255413 1.12052006 1.047404833 0.974100446 1.026983159 0.995550987 1.060129934 0.511792943 1.218619013 1 16.04564556 5.032966295 0.456239173 0.889545178 1.576733597 0.175552493 0.172965173 8.850717827 1.173995773 0.118759102 3.478688432 107886.2989 -5.032966295 0.687188419 GADIMYTGTVDCWR ddPTM_BT-474_Pertuzumab_2h_R1 3 GADIMYTGTVDCWR 14 0 P12236;P12235 P12236;P12235 SLC25A6;SLC25A4 "ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed;ADP/ATP translocase 1" 0 ;; 261.22 3.95E-24 968711000 184569 340037 185139 575394 198859 223346 443095 410726 304520 235134 FALSE TRUE 177355.8394 330339.4777 218597.7357 605090.1533 205255.4803 227862.2091 448517.7292 402244.3646 269952.1663 219208.1647 0.809074971 1.506967033 0.9972153 2.760344963 0.936349613 1.039478659 2.046081311 1.834988058 1.231487735 1 17.74194201 5.034054139 1.429454706 1.567031998 6.21E-16 0.102939773 0.561192162 5.268019289 5.654725486 0.147628863 14.41876915 108156.877 -5.034054139 -1.567031998 YYFYDNYFDLPGALLCAR ddPTM_BT-474_Pertuzumab_2h_R1 2 YYFYDNYFDLPGALLCAR 18 0 Q5TFE4;Q5TFE4-2;Q5QPD0 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 222.99 1.25E-18 30931000 101587 94492 79331 90074 93416 48653 96161 98124 96836 109427 FALSE TRUE 97616.86773 91797.18068 93667.87641 94722.72993 96420.81048 49636.79699 97337.84708 96097.70511 85843.58325 102015.4118 0.956883533 0.899836398 0.918173781 0.92851392 0.945159253 0.486561747 0.95414845 0.941992032 0.841476613 1 16.6384276 5.034325166 0.001645946 1.759406021 0.000168336 0.002433424 0.139060752 9289115.773 2167.124427 1142882.774 1173560.943 108224.3949 -5.034325166 -1.759237685 GSGPQRPHS(ph)FSEALR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSGPQRPHSFSEALR 15 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 GSGPQRPHS(0.984)FS(0.016)EALR;GSGPQRPHS(0.999)FS(0.001)EALR;GSGPQRPHS(0.631)FS(0.369)EALR;GSGPQRPHS(0.943)FS(0.057)EALR 212.79 4.24E-10 5850100000 1130260 1260900 968400 1328020 1235500 1214290 1206130 1313590 1247070 1257760 TRUE FALSE 1086088.19 1224940.367 1143411.422 1396559.271 1275240.98 1238843.776 1220890.98 1286463.907 1105507.842 1172570.795 0.926245302 1.044662183 0.9751321 1.191023414 1.087559903 1.056519386 1.041208757 1.097131118 0.942806905 1 20.1612436 5.03434541 1.376177929 1.061340053 0.780489926 0.224663199 0.06629321 3.499219334 3.489730261 0.017456652 1.654026009 108229.4397 -5.03434541 -0.280850127 FNWYVDGVEVHNAK ddPTM_BT-474_Pertuzumab_2h_R1 2 FNWYVDGVEVHNAK 14 0 A0A0A0MS08;P01857 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 ; 170.11 3.22E-06 5105000000 11910500 4210200 1562000 1004200 768990 575796 767410 798048 782142 850179 FALSE TRUE 11445024.49 4090129.218 1844288.147 1056026.882 793725.2617 587438.9896 776801.7931 781568.0299 693356.5192 792595.6191 14.43992903 5.160423701 2.32689672 1.332365278 1.001425245 0.741158512 0.980073286 0.98608674 0.874792268 1 19.59622547 5.034477784 1.254894455 0.942356009 29.50705498 0.997805535 0.189932978 0.118615447 0.099047237 0.059210194 5.20954055 108262.4333 -5.034477784 28.56469897 up EKDHSSSRPS(ph)SPRPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EKDHSSSRPSSPRPQK 16 3 E9PKU9;B7Z503;Q9BSF8;Q9BSF8-2 E9PKU9 BTBD10 BTB/POZ domain-containing protein 10 1 EKDHS(0.001)S(0.001)S(0.001)RPS(0.498)S(0.498)PRPQK;EKDHS(0.014)S(0.014)S(0.014)RPS(0.478)S(0.478)PRPQK 85.808 0.0050119 382110000 422720 697060 595940 809520 616990 864950 826120 669620 812870 997620 TRUE FALSE 406199.6351 677180.5313 703639.6146 851299.4242 636836.0437 882439.8816 836230.3037 655792.113 720596.4054 930050.3088 0.436750175 0.728111721 0.75656081 0.91532621 0.684732898 0.948808761 0.899123731 0.705114666 0.774792932 1 19.82694923 5.035260523 1.331077032 0.827932977 7.93E-10 0.598260904 0.099195695 1.82150601 1.700930382 0.026542094 2.458036779 108457.7331 -5.035260523 -0.827932976 EQSLDALQTHYDELQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 EQSLDALQTHYDELQAR 17 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 ;; 224.19 2.80E-15 1254190000 888440 961900 813220 1036140 1024800 981190 1001680 948400 1013790 1021710 FALSE TRUE 853718.7826 934467.5538 960186.944 1089615.31 1057763.623 1001030.334 1013938.859 928815.2086 898708.8094 952508.6717 0.896284525 0.981059366 1.008061105 1.143942666 1.11050288 1.050940914 1.064493048 0.9751252 0.943517719 1 19.8613727 5.035440599 0.001809848 0.960736636 1.084661632 0 0.072041911 18418670.32 4914.945755 166094.3873 170464.7991 108502.7134 -5.035440599 0.123924996 NEEDAAELVALAQAVNAR ddPTM_BT-474_Pertuzumab_2h_R1 3 NEEDAAELVALAQAVNAR 18 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 290.71 8.50E-49 429185000 298163 310188 253392 301897 301222 300327 306902 341952 366222 329571 FALSE TRUE 286510.4603 301341.7419 299185.5711 317477.9403 310911.0792 306399.8177 310657.9585 334890.5717 324650.0139 307248.8626 0.932502916 0.98077415 0.97375648 1.033292484 1.011919382 0.997236621 1.011095552 1.089965212 1.056635364 1 18.22904814 5.036088285 0.421893956 1.047411215 0.828723 0.556109041 0.027900523 5.03295726 0.583066644 0.022108876 0.583782198 108664.65 -5.036088285 -0.218688215 DASRPHVVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DASRPHVVK 9 1 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;; 83.862 0.0095427 1650340000 3997680 4199030 3403790 4127860 4030440 3971310 4267570 4710030 4771540 4429520 FALSE TRUE 3841446.246 4079277.776 4018930.57 4340899.349 4160082.763 4051612.609 4319797.798 4612766.235 4229894.783 4129504.665 0.930243833 0.987837067 0.9732234 1.051191293 1.007404786 0.981137676 1.046081346 1.117026522 1.02431045 1 21.97753731 5.037045904 0.443003698 1.053736831 0.821278602 0.404222244 0.037630777 6.206963464 0.780928498 0.028359936 0.802541279 108904.5197 -5.037045904 -0.232458229 SYLTPVRDEESESQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SYLTPVRDEESESQR 15 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ; 238.02 8.53E-18 1044160000 365250 419690 332840 418130 424450 390400 410460 441590 416680 377370 FALSE TRUE 350975.6262 407720.8521 392991.592 439709.7394 438102.8197 398294.1555 415483.3323 432471.0122 369380.2333 351810.3938 0.997627223 1.158922133 1.117055093 1.249848632 1.245281059 1.132127312 1.180986519 1.229272983 1.049941218 1 18.42443858 5.037193071 1.773936359 1.17003845 0.795270314 0.223207248 0.079603727 2.9412062 4.720947082 0.019384928 2.388944667 108941.4299 -5.037193071 -0.374768136 FPDSVEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 FPDSVEELR 9 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ;;; 203.93 4.05E-05 1462270000 765920 844560 685160 834200 837400 864520 836090 893420 867080 954200 FALSE TRUE 735986.9996 820473.9757 808983.6533 877253.162 864335.7315 882001.1867 846322.3195 874970.5648 768652.7135 889571.1841 0.827350315 0.922325262 0.909408564 0.986152854 0.971631891 0.991490285 0.951382345 0.983586902 0.864071057 1 19.76275053 5.03750164 1.033471377 0.96391238 0.684221167 0.521243265 0.038592408 2.353734276 1.349560508 0.011019538 0.83820741 109018.8609 -5.03750164 -0.279691213 S(ph)IRDTPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 S(0.876)IRDT(0.124)PAK 127.51 0.0030859 918310000 2452000 1476400 1110500 1014800 1081900 908380 906960 1836200 926260 845820 TRUE FALSE 2356173.129 1434294.518 1311192.053 1067173.95 1116700.296 926748.066 918059.6478 1798281.828 821114.848 788531.858 2.988050648 1.818943018 1.662826986 1.353368211 1.416176512 1.175282972 1.164264498 2.280544293 1.041321083 1 19.58880952 5.037848002 1.371914268 1.440351555 4.744844339 0.653364753 0.352159324 1.734038589 1.707387086 0.100198594 9.638320461 109105.8413 -5.037848002 3.304492784 S(ph)RASPVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.699)RAS(0.3)PVS(0.001)R;S(0.773)RAS(0.226)PVS(0.001)R 56.359 0.071523 344430000 84754 104494 87887 106630 110177 117100 120911 91971 125642 137755 TRUE FALSE 81441.71998 101513.9334 103770.1359 112133.1871 113720.9433 119467.8422 122390.745 90071.76671 111379.6469 128424.7312 0.634159163 0.790454709 0.808022995 0.87314325 0.885506571 0.930255732 0.953015388 0.701358421 0.867275687 1 16.97056353 5.037963516 1.078603309 0.869642555 0.379756387 0.499843387 0.075944265 2.886955987 1.794213935 0.023781492 1.878269806 109134.865 -5.037963516 -0.489886167 LADVAAPPGGPPPPHSPYS(ph)GPPSRGSPVR ddPTM_BT-474_Pertuzumab_2h_R1 3 LADVAAPPGGPPPPHSPYSGPPSRGSPVR 29 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LADVAAPPGGPPPPHS(0.012)PYS(0.411)GPPS(0.323)RGS(0.254)PVR;LADVAAPPGGPPPPHS(0.103)PY(0.003)S(0.407)GPPS(0.268)RGS(0.219)PVR;LADVAAPPGGPPPPHS(0.198)PY(0.005)S(0.411)GPPS(0.213)RGS(0.173)PVR 114.23 0.00013874 2542760000 282191 359257 197085 277260 307858 353530 306527 303977 317271 312532 TRUE FALSE 271162.6637 349011.3421 232702.6436 291569.4218 317760.5322 360678.6188 310278.3691 297699.7687 281255.7262 291363.9293 0.930666553 1.197853636 0.798666617 1.000705278 1.090596674 1.237897291 1.064916889 1.021745449 0.965307294 1 18.15246276 5.038558216 15.97650962 1.0428113 0.467468438 0.076487641 0.115987827 4858544.246 56040035.09 0.027879533 80485288.69 109284.4109 -5.038558216 -0.575342862 ELQDAQEHDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELQDAQEHDAR 11 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 0 131.06 0.00021121 269180000 132650 168680 132980 177170 176510 191560 179630 174100 179980 179110 FALSE TRUE 127465.8913 163869.4116 157012.4441 186313.7649 182187.6045 195433.4744 181828.3657 170504.7742 159549.4249 166978.7202 0.763366082 0.981379013 0.940314095 1.115793466 1.09108277 1.170409464 1.088931365 1.021116787 0.955507533 1 17.34930473 5.040813222 1.073673608 1.064314 0.444777126 0.639005622 0.065638033 1.968892195 1.207821633 0.02030352 1.615134844 109853.3289 -5.040813222 -0.619536873 IAALQAFADQLIAAGHYAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IAALQAFADQLIAAGHYAK 19 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 252.12 7.64E-31 410040000 481580 507520 443650 489440 526630 543130 545860 568130 581280 603830 FALSE TRUE 462759.3212 493046.0265 523827.4239 514700.0571 543569.5322 554112.4607 552540.398 556397.917 515295.5313 562932.0563 0.82205182 0.875853526 0.93053401 0.914320034 0.965604154 0.984332753 0.98154012 0.988392668 0.915377843 1 19.10260128 5.041890902 0.584477115 0.977696749 0.659156802 0.801839659 0.024227842 2.074068403 0.417524787 0.011457831 0.481915748 110126.2631 -5.041890902 -0.318539946 AALLKAS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 AALLKASPK 9 1 P50914 P50914 RPL14 60S ribosomal protein L14 1 AALLKAS(1)PK;AALLKAS(1)PK 74.962 0.023987 10738500000 6898700 4781700 4959100 2345500 4471600 3660400 4097100 5142100 4823600 4031000 TRUE FALSE 6629091.177 4645330.598 5855319.685 2466551.536 4615433.075 3734415.796 4147241.535 5035913.838 4276045.15 3757976.78 1.764005359 1.236125413 1.558104275 0.656350925 1.228169663 0.993730407 1.103583598 1.34005986 1.137858321 1 21.84152472 5.041951612 1.094357667 1.117228721 2.430702497 0.453463291 0.216709398 2.832066747 1.798321151 0.061842941 5.021748457 110141.6586 -5.041951612 1.313473777 ATKS(ph)PAKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATKSPAKPK 9 2 P16401 P16401 HIST1H1B Histone H1.5 1 AT(0.059)KS(0.941)PAKPK 67.456 0.031749 428680000 1812400 953020 761290 668840 828930 515250 723010 1180400 682300 472640 TRUE FALSE 1741569.404 925840.8027 898872.0378 703358.9126 855593.2863 525668.708 731858.4127 1156024.328 604848.1644 440627.6718 3.952473972 2.101186244 2.039980907 1.596265867 1.941760223 1.192999763 1.660945191 2.623585402 1.37269673 1 18.74920057 5.042027669 1.587086087 1.754250299 6.546076399 0.703782342 0.439204293 1.430280946 1.841658241 0.118645368 13.35641666 110160.9491 -5.042027669 4.7918261 VLEGMEVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLEGMEVVR 9 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 103.56 0.0088663 0 73445 97607 72667 88528 73695 53055 83304 78753 86891 111110 FALSE TRUE 70574.6882 94823.34393 85799.54337 93096.94069 76065.4666 54127.80845 84323.49927 77126.72303 77027.49796 103584.4207 0.681325316 0.915420903 0.82830548 0.898754272 0.734333079 0.522547774 0.814055808 0.744578407 0.743620492 1 16.66044751 5.042591406 14.16263966 0.785225245 0.264647265 0.065119575 0.123946618 39049635.24 408587975 0.028752012 513920757.5 110304.0366 -5.042591406 -0.52057798 DFAYGETDPLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFAYGETDPLIR 12 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;;; 154.24 0.00014561 592620000 1264270 1388180 1116350 1384190 1334810 1454220 1385900 1468030 1464690 1568690 FALSE TRUE 1214860.931 1348590.466 1318099.278 1455628.212 1377745.376 1483625.325 1402861.059 1437714.667 1298424.532 1462441.229 0.830707523 0.922150196 0.901300683 0.995341339 0.942085978 1.014485434 0.959259785 0.98309227 0.887847324 1 20.47994722 5.043355239 0.878258843 0.969120591 0.689942629 0.551521802 0.037161445 2.516735817 1.054067012 0.011405277 0.764602216 110498.209 -5.043355239 -0.279177962 VTFSEDDEIINPEDVDPSVGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTFSEDDEIINPEDVDPSVGR 21 0 Q12972;A0A0A0MT09;Q12972-2 Q12972 PPP1R8 Nuclear inhibitor of protein phosphatase 1;Activator of RNA decay 0 ;;; 324.94 3.57E-67 245859000 281656 298700 241441 288121 293712 295845 290432 297008 298128 309342 FALSE TRUE 270648.5721 290181.3685 285074.7595 302990.9593 303159.5132 301827.1886 293986.3937 290874.681 264285.7593 288389.9908 0.938481157 1.00621165 0.988504347 1.050629249 1.051213714 1.046593842 1.019405677 1.00861573 0.916417933 1 18.13766157 5.044996895 1.584569247 1.015094505 0.84811172 0.236881537 0.037757123 3.588285012 4.575245891 0.010214204 1.168736833 110916.6884 -5.044996895 -0.166982785 DIWAELR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIWAELR 7 0 A0A1B0GV75;A0A1B0GTB8;A0A1B0GWC0;A0A1B0GVF3;P23786 A0A1B0GV75 CPT2 "Carnitine O-palmitoyltransferase 2, mitochondrial" 0 ; 98.299 0.026439 104395000 92234 165398 108714 225145 117885 136819 206134 173890 139534 121258 FALSE TRUE 88629.39331 160681.011 128361.0381 236764.7604 121676.8781 139585.5739 208656.7296 170299.1107 123694.6853 113045.0877 0.784018086 1.421388707 1.135485325 2.094427678 1.076357059 1.234777882 1.845783252 1.506470686 1.094206638 1 16.78653878 5.046061538 1.826044608 1.430813531 1.74E-09 0.197894376 0.342509719 3.567347785 5.897833259 0.084415369 11.48641102 111188.9266 -5.046061538 -1.430813529 IDKLEQDMER ddPTM_BT-474_Pertuzumab_2h_R1 1 IDKLEQDMER 10 1 Q8WU90;Q8WU90-2 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 86.772 0.012157 315600000 362850 340130 283820 302350 320320 284510 342620 316630 404060 342510 FALSE TRUE 348669.4208 330429.8254 335112.5875 317954.3197 330623.3837 290262.9871 346813.086 310091.4799 358192.8028 319311.4926 1.091941345 1.034819708 1.049484893 0.99574969 1.035425881 0.909027686 1.086127791 0.971125334 1.121766084 1 18.28460495 5.046130742 1.07074556 1.014900711 1.173964751 0.126585402 0.056083307 5.889941062 3.565830209 0.015314656 1.240639279 111206.6458 -5.046130742 0.15906404 LQVVLEHMPVGPDAILR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQVVLEHMPVGPDAILR 17 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;H0Y710;H0Y4L1 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 85.636 0.0049876 472610000 192120 214270 160800 222500 207070 225580 194290 210570 214030 239560 FALSE TRUE 184611.738 208159.2294 189860.137 233983.2517 213730.5946 230141.3822 196667.7791 206221.6559 189734.2117 223334.3878 0.826615819 0.93205185 0.850116002 1.047681255 0.956998144 1.030478935 0.880597838 0.923376189 0.84955216 1 17.76884588 5.048762002 1.199135605 0.944502876 0.701734918 0.22558608 0.065620159 4.654790958 3.477060951 0.018562299 1.676032456 111882.4587 -5.048762002 -0.242767958 KVPS(ph)PEAFLGKPWSSWIDAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVPSPEAFLGKPWSSWIDAAK 21 2 Q9ULK2;C9IZF2;Q9ULK2-2 Q9ULK2 ATXN7L1 Ataxin-7-like protein 1 1 KVPS(1)PEAFLGKPWSSWIDAAK;KVPS(1)PEAFLGKPWSSWIDAAK 160.57 1.10E-11 449500000 586380 470220 419620 352570 447710 417120 453200 519310 531030 446610 TRUE FALSE 563463.6213 456809.786 495454.6684 370766.18 462110.9987 425554.4522 458746.3972 508586.067 470749.7007 416360.7069 1.353306429 1.097149127 1.189965 0.890492724 1.109881387 1.022081203 1.101800409 1.221503515 1.130629507 1 18.6674744 5.050356635 1.842903051 1.090458246 1.681469485 0.436033689 0.090948334 2.558953356 4.25113596 0.024267802 3.449965061 112294.0215 -5.050356635 0.591011239 RPEDRPAGPQNK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPEDRPAGPQNK 12 2 Q9BTV6 Q9BTV6 DPH7 Diphthine methyltransferase 0 64.65 0.035362 39952000 20851 22297 19810 22130 25631 22147 24120 26817 28778 25604 FALSE TRUE 20036.11987 21661.11139 23390.10767 23272.13195 26455.44439 22594.82751 24415.18778 26263.21958 25511.24209 23869.81827 0.839391387 0.907468634 0.979903048 0.974960583 1.108321986 0.946585653 1.02284766 1.100268937 1.06876566 1 14.54289996 5.050706192 0.596915514 1.051390928 0.607050787 0.65281711 0.04750984 2.979561422 0.61742472 0.022412209 0.988022314 112384.4416 -5.050706192 -0.444340141 FNFLAPELPAVSEFSTSETMGHSADR ddPTM_BT-474_Pertuzumab_2h_R1 3 FNFLAPELPAVSEFSTSETMGHSADR 26 0 P55084-2;P55084;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;; 202.17 4.67E-25 581891000 488126 792705 497052 1223412 551446 713540 961055 836974 677767 588629 FALSE TRUE 469049.4963 770097.8295 586880.3533 1286552.44 569183.7614 727968.2677 972816.6786 819690.1944 600829.7316 548760.6335 0.854743339 1.40334015 1.069465114 2.344469266 1.037216824 1.326567948 1.772752306 1.493711728 1.0948849 1 19.06581746 5.050756214 1.547537461 1.450793792 0.149043653 0.132221635 0.395229732 4.606232129 5.545781182 0.099340025 11.47725617 112397.3867 -5.050756214 -1.301750139 SSTVTGGEEPTPSVAYVHTTPGLPSGWEER ddPTM_BT-474_Pertuzumab_2h_R1 1 SSTVTGGEEPTPSVAYVHTTPGLPSGWEER 30 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-4 Q96PU5-7 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 0 182.23 6.30E-18 70604000 17624 26233 18514 34651 21771 26582 29327 27644 21646 25800 FALSE TRUE 16935.2346 25484.86052 21859.89164 36439.34226 22471.28399 27119.50625 29685.9126 27073.14174 19188.83683 24052.54302 0.704093309 1.059549525 0.908839104 1.514989173 0.934258135 1.127510976 1.234210976 1.125583341 0.797788276 1 14.55390181 5.051047926 1.505574029 1.106999813 0.226896921 0.255628725 0.189058217 3.29187768 3.762256913 0.047967375 5.396409027 112472.9084 -5.051047926 -0.880102891 FGVQMDR ddPTM_BT-474_Pertuzumab_2h_R1 6 FGVQMDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 125.25 0.0094623 2895150000 2705750 3122510 2401790 2739050 2823030 2117590 2968810 2845990 2832490 3214090 FALSE TRUE 2600006.299 3033459.072 2835846.881 2880412.699 2913835.324 2160409.121 3005143.185 2787219.312 2510957.61 2996396.821 0.867710939 1.012368939 0.946418999 0.961292135 0.972446407 0.72100234 1.00291896 0.930190318 0.837992349 1 21.51479727 5.05159388 15.56279005 0.929583202 0.474694852 0.047976358 0.084977362 906233.0486 7135146.536 0.019579893 12429983.88 112614.3877 -5.05159388 -0.45488835 LADVAAPPGGPPPPHSPYSGPPS(ph)RGSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LADVAAPPGGPPPPHSPYSGPPSRGSPVR 29 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LADVAAPPGGPPPPHS(0.087)PY(0.015)S(0.12)GPPS(0.389)RGS(0.389)PVR 68.046 0.0054041 351300000 54849 66065 44809 47214 54698 71485 69161 50130 63653 58218 TRUE FALSE 52705.44044 64180.89088 52906.98307 49650.7202 56457.41085 72930.47568 70007.41301 49094.79798 56427.3783 54274.843 0.971084162 1.18251638 0.974797533 0.914801729 1.04021325 1.343725226 1.289868549 0.904559005 1.039659908 1 15.72799603 5.053647151 11.49300711 1.074833675 0.542100554 0.047018635 0.142402605 230286.5423 1894006.273 0.036378494 2514079.077 113148.0701 -5.053647151 -0.532733121 LHLELK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHLELK 6 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 106.84 0.03178 355810000 430620 600000 398040 543830 424240 316480 580400 365100 646070 553510 FALSE TRUE 413790.8943 582888.5875 469974.6824 571897.1315 437886.0649 322879.4424 587503.1088 357560.5574 572730.8421 516020.2747 0.80188883 1.129584662 0.910767862 1.108284227 0.848583062 0.625710768 1.138527181 0.69291959 1.109899882 1 18.97706823 5.054614026 14.45158386 0.932160419 6.34E-05 0.051743541 0.175318873 1720681.762 12903076.1 0.039919846 44609778.49 113400.2536 -5.054614026 -0.932097065 GTVTDFPGFDER ddPTM_BT-474_Pertuzumab_2h_R1 6 GTVTDFPGFDER 12 0 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 260.98 5.65E-21 4904270000 5214740 5638180 4468010 6095720 4773370 4157910 4661260 5555230 5639070 6309620 FALSE TRUE 5010942.196 5477384.627 5275478.797 6410320.84 4926909.781 4241985.789 4718305.894 5440512.559 4998946.415 5882263.817 0.85187308 0.931169495 0.896844984 1.089771054 0.837587353 0.72114851 0.802124155 0.924901148 0.849833766 1 22.48794006 5.055574449 12.83496458 0.889000304 0.660021598 0.013969026 0.09780464 1286145.458 9891727.997 0.024295622 7049529.992 113651.3109 -5.055574449 -0.228978705 DLSLENGAHAYNR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSLENGAHAYNR 13 0 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 213.18 7.96E-09 322080000 488730 531550 384610 476810 495160 523530 501630 454550 525880 581170 FALSE TRUE 469629.8913 516390.7144 454117.5826 501418.2212 511087.2711 534116.1353 507769.098 445163.3837 466184.3071 541806.8382 0.866784725 0.953090065 0.838154026 0.92545569 0.943301625 0.985805452 0.937177352 0.821627474 0.860425292 1 19.04741908 5.055759825 11.52495119 0.910212256 0.676137208 0.051385784 0.057608559 244231.2199 1919135.147 0.014375682 1188732.609 113699.8324 -5.055759825 -0.234075048 KEWDLKPIADR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEWDLKPIADR 11 2 P30038-2;P30038;P30038-3;Q5TF55 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ; 134.21 8.19E-05 3385100000 2299900 3388500 1983830 3530500 1623170 1645480 3794800 3109700 2748000 2225300 FALSE TRUE 2210017.365 3291863.298 2342352.211 3712709.528 1675380.737 1678752.733 3841241.898 3045483.608 2436058.561 2074578.449 1.06528503 1.586762506 1.129073818 1.789621178 0.807576468 0.809201857 1.851577076 1.468001179 1.174242681 1 20.98438678 5.055941713 11.13904715 1.318994407 5.55E-05 0.029216798 0.357666599 155592.4701 1223426.891 0.085065045 4083226.561 113747.4613 -5.055941713 -1.318938942 S(ph)PAGGESATVAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPAGGESATVAAK 13 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 S(1)PAGGESATVAAK;S(1)PAGGESATVAAK;S(1)PAGGESATVAAK;S(1)PAGGESATVAAK 242.4 1.21E-16 1580450000 754140 754620 824010 1002940 836410 873050 1115850 1169950 1355590 1425940 TRUE FALSE 724667.3751 733098.9765 972926.937 1054701.854 863313.8873 890703.6692 1129506.106 1145790.124 1201709.106 1329359.814 0.54512508 0.551467683 0.731876296 0.793390806 0.64942078 0.670024519 0.84966169 0.861911209 0.903975804 1 20.34230022 5.055950562 0.144342651 1.106105718 7.28E-21 0.804565278 0.063827256 13.6464413 0.29939953 0.362462122 2.901254261 113749.779 -5.055950562 -1.106105718 LTVIDTPGFGDHINNENCWQPIMK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTVIDTPGFGDHINNENCWQPIMK 24 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9;K7EJZ2 Q9UHD8 9-Sep Septin-9 0 236.04 2.12E-37 322830000 108250 124230 102790 119560 132510 133900 132730 129810 141590 147410 FALSE TRUE 104019.4703 120687.082 121366.4396 125730.5059 136772.3045 136607.5497 134354.3894 127129.3781 125517.2968 137425.7894 0.756913755 0.878198208 0.883141658 0.914897462 0.995244816 0.994045953 0.977650483 0.925076572 0.913346013 1 17.06829324 5.058011438 0.780006949 0.961503314 0.545899163 0.793028721 0.032335697 1.918995309 0.635114424 0.012520865 0.776498772 114290.8436 -5.058011438 -0.415604151 NADMSEEMQQDSVECATQALEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NADMSEEMQQDSVECATQALEK 22 0 P63167;F8VXL2;F8VRV5;F8VXI7 P63167 DYNLL1 "Dynein light chain 1, cytoplasmic" 0 56.404 0.024771 0 192230 215830 169790 220600 206290 227150 213230 220820 209700 241050 FALSE TRUE 184717.4391 209674.7397 200474.83 231985.1924 212925.5052 231743.1286 215839.5725 216259.9898 185895.7351 224723.4688 0.821976628 0.933034457 0.892095654 1.032314042 0.947500082 1.031236879 0.96046743 0.962338251 0.827219943 1 17.77779127 5.058682002 1.168083144 0.962937474 0.663348117 0.334002266 0.057939706 3.39167162 2.371502778 0.016040905 1.476937599 114467.4484 -5.058682002 -0.299589356 DVGRPQPGR ddPTM_BT-474_Pertuzumab_2h_R1 7 DVGRPQPGR 9 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;;; 148.94 8.10E-05 3749985000 2169986 2556730 1900978 2477113 1931947 1967417 1835375 2248292 2510821 2842892 FALSE TRUE 2085180.548 2483814.564 2244527.012 2604957.099 1994089.83 2007199.52 1857836.868 2201863.985 2225803.126 2650340.393 0.786759525 0.937168135 0.846882543 0.982876428 0.752390084 0.757336501 0.700980475 0.830785355 0.839817833 1 21.33774623 5.061021439 14.42014432 0.837126899 0.404842532 0.023126394 0.094870509 1758422.907 10976281.9 0.022878286 21710258.98 115085.7199 -5.061021439 -0.432284367 TQEISRPNS(ph)PSEGEGESSDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TQEISRPNSPSEGEGESSDSR 21 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 TQEISRPNS(0.934)PS(0.066)EGEGESSDSR 123.35 1.61E-05 249210000 54526 70628 53833 76603 72881 75316 79202 74840 76658 84271 TRUE FALSE 52395.06364 68613.75859 63561.82061 80556.49001 75225.28355 76838.94112 80171.29777 73294.52785 67956.10522 78563.25011 0.666915683 0.873356926 0.80905284 1.025371149 0.957512367 0.978051965 1.020468192 0.932936554 0.864985921 1 16.26156699 5.061227418 0.894938104 0.964900383 0.353742827 0.700721435 0.05830669 1.964543929 0.833123377 0.018549747 1.341042146 115140.3162 -5.061227418 -0.611157557 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVKLLSISGK ddPTM_BT-474_Pertuzumab_2h_R1 3 CGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK 38 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGS(0.002)GPVHIS(0.002)GQHLVAVEEDAES(0.99)EDEEEEDVKLLS(0.006)IS(0.001)GK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK 232.55 4.25E-41 2069630000 1392640 2230340 804230 844320 1117080 1738220 933060 618180 1054140 921860 TRUE FALSE 1338214.089 2166732.887 949572.251 887895.4564 1153011.893 1773367.999 944479.0674 605414.367 934478.4465 859421.6011 1.557110139 2.521152464 1.104896886 1.033131417 1.341613815 2.063443596 1.098970594 0.704443973 1.087334139 1 19.71300651 5.06125521 0.271721911 0.866155186 3.01763478 0.271660287 0.447971216 13.21860074 0.710043939 0.595797577 9.828406763 115147.6846 -5.06125521 2.151479595 VEAFEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VEAFEHR 7 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ;;; 154.01 0.0017073 1398020000 1768580 2055980 1620310 2135770 1895640 2042660 1927090 2081690 2218780 2128360 FALSE TRUE 1699461.938 1997345.463 1913136.061 2245997.346 1956614.982 2083963.985 1950674.304 2038702.374 1966913.396 1984204.281 0.85649545 1.006622898 0.964183012 1.131938564 0.986095535 1.050276932 0.98310155 1.027465969 0.991285733 1 20.92012913 5.061675036 1.655224985 1.0210021 0.647286759 0.527470934 0.04516241 1.90158664 2.526146799 0.011010916 1.46926243 115259.05 -5.061675036 -0.37371534 HFSTLKDDDLVEFSDLES(ph)EDDERPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HFSTLKDDDLVEFSDLESEDDERPR 25 2 Q9HCK8-2;Q9HCK8;H0YJG4;A0A2R8Y840 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 HFSTLKDDDLVEFSDLES(1)EDDERPR 196.93 4.36E-25 125900000 98798 154060 112650 188950 151550 180520 197820 78889 183460 207780 TRUE FALSE 94936.86493 149666.3596 133008.3609 198701.7321 156424.7434 184170.2381 200240.9803 77259.91458 162634.3899 193706.8755 0.490105809 0.772643507 0.686647598 1.025785644 0.807533253 0.950767687 1.03373192 0.398849625 0.839590177 1 17.56351564 5.062023104 1.448197448 0.820609879 0.086289456 0.247850796 0.182025503 4.516311411 4.689842599 0.052131852 5.991441356 115351.4621 -5.062023104 -0.734320423 S(ph)SSDPPAVHPPLPPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSDPPAVHPPLPPLR 16 0 O43150 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 S(0.333)S(0.333)S(0.333)DPPAVHPPLPPLR;S(0.359)S(0.359)S(0.283)DPPAVHPPLPPLR;S(0.333)S(0.333)S(0.333)DPPAVHPPLPPLR 120.9 6.55E-05 1089640000 843100 972030 805080 975660 938580 977510 968150 1049130 1031820 1054870 TRUE FALSE 810150.7199 944308.6561 950575.8649 1026013.93 968770.2781 997275.9219 979998.5093 1027465.099 914692.1193 983422.7153 0.823807206 0.960226606 0.966599459 1.043309163 0.985100571 1.014086726 0.996518073 1.044784794 0.930110831 1 19.90745215 5.062449369 1.307034447 1.005005149 0.60467373 0.727696516 0.031910845 1.315665181 1.127845069 0.008256424 0.858602867 115464.7366 -5.062449369 -0.400331419 LLDDLFR ddPTM_BT-474_Pertuzumab_2h_R1 6 LLDDLFR 7 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;;;;; 197.62 0.00097263 549720000 1248722 1401612 1183695 1291151 1260218 929687 1377457 1313483 1276446 1475724 FALSE TRUE 1199920.564 1361639.398 1397615.018 1357787.458 1300754.056 948485.9081 1394314.731 1286359.117 1131549.201 1375771.899 0.872179876 0.989727584 1.015876991 0.986927745 0.94547218 0.689420905 1.013478129 0.935009007 0.822483147 1 20.39180986 5.063223689 8.601964743 0.932039144 0.662771469 0.033680022 0.097814192 9531.316703 65823.25991 0.023426748 37526.16574 115670.7867 -5.063223689 -0.269267676 NVADHKK ddPTM_BT-474_Pertuzumab_2h_R1 3 NVADHKK 7 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 ;; 89.296 0.01167 1245027000 3334210 3073690 2515190 2708970 2691310 2757970 2862160 2886080 3013560 3151820 FALSE TRUE 3203905.387 2986031.371 2969740.783 2848780.266 2777878.43 2813738.043 2897187.97 2826481.439 2671473.303 2938344.424 1.090377752 1.016229189 1.010685051 0.969518836 0.945388977 0.957592997 0.985993319 0.961929928 0.909176365 1 21.48657208 5.064005546 0.785699053 0.958797172 1.231228967 0.736228148 0.023982803 1.968376728 0.65571094 0.008288562 0.527005997 115879.2155 -5.064005546 0.272431794 AGGAEDEQENEDDEEER ddPTM_BT-474_Pertuzumab_2h_R1 1 AGGAEDEQENEDDEEER 17 0 A0A087WW42;A0A087WX51;F5H1D6;Q07864 A0A087WW42 POLE DNA polymerase;DNA polymerase epsilon catalytic subunit A 0 194.23 2.00E-10 64447000 25325 25397 32763 39935 33946 37452 47787 43029 42056 54022 FALSE TRUE 24335.271 24672.70243 38684.00291 41996.05014 35037.90392 38209.3051 48371.8316 42140.43611 37281.97919 50363.04182 0.483197006 0.489896987 0.768102988 0.833866435 0.695706666 0.758677469 0.960462868 0.836733338 0.740264643 1 15.6200778 5.064025372 0.536278338 0.863827733 2.03E-16 0.67508697 0.092473032 3.328117672 0.567542499 0.049573327 1.936979356 115884.5054 -5.064025372 -0.863827733 VGDVVEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGDVVEFR 8 0 Q9UHQ9;H7C0R7 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 87.181 0.03856 0 162070 242330 172360 296270 165170 220700 253980 264790 227630 234970 FALSE TRUE 155736.1252 235418.9857 203509.2861 311560.5302 170482.8431 225162.7052 257088.2832 259321.994 201790.3967 219055.2726 0.710944427 1.074701297 0.929031672 1.422291856 0.778264047 1.027880783 1.173622895 1.183819914 0.921184842 1 17.74093541 5.064054368 1.881061027 1.075790761 0.225166339 0.264387418 0.168872115 3.359101529 5.56771073 0.041577256 6.750159003 115892.2429 -5.064054368 -0.850624422 NVNVQNFHISWK ddPTM_BT-474_Pertuzumab_2h_R1 2 NVNVQNFHISWK 12 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 ; 105.65 0.0020072 992620000 1250530 1670500 1317750 1690510 1070480 997420 1255620 1470820 1549400 1854390 FALSE TRUE 1201657.905 1622858.976 1555896.738 1777757.424 1104912.961 1017588.516 1270986.653 1440447.053 1373518.608 1728790.514 0.695085897 0.938725058 0.899991483 1.028324375 0.639124841 0.588612968 0.735188355 0.833210873 0.794496844 1 20.72133163 5.064150425 10.81599409 0.815253349 0.101355239 0.070115622 0.138386163 111961.9432 747678.4199 0.034738489 1590005.486 115917.8788 -5.064150425 -0.71389811 DS(ph)PLAQLADSCEGPGLGALDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSPLAQLADSCEGPGLGALDR 21 0 Q9ULE0;Q9ULE0-2 Q9ULE0 WWC3 Protein WWC3 1 DS(1)PLAQLADSCEGPGLGALDR;DS(1)PLAQLADSCEGPGLGALDR 196.61 1.00E-21 119471000 63165 61968 59796 78363 87344 88478 97058 95807 114282 121520 TRUE FALSE 60696.44197 60200.73331 70602.46735 82407.32382 90153.49908 90267.08578 98245.82484 93828.55197 101309.1865 113289.3422 0.535764802 0.531389204 0.623204849 0.727405793 0.795780939 0.796783564 0.86721154 0.828220468 0.894251697 1 16.78965262 5.064251796 0.245369063 0.989110212 1.59E-18 0.957020089 0.030520177 2.317466399 0.10517733 0.0475228 0.716444042 115944.9389 -5.064251796 -0.989110212 SLETVYLER ddPTM_BT-474_Pertuzumab_2h_R1 3 SLETVYLER 9 0 Q15435;H7C003;C9J177;Q15435-2;H7C3Q5 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 ;; 129.38 0.0009091 740680000 426253 478696 388466 473649 457672 491485 492463 485469 440310 523444 FALSE TRUE 409594.5615 465044.0588 458670.4476 498094.0817 472393.4355 501423.1634 498489.9095 475443.8955 390327.8547 487990.6716 0.839349162 0.952977353 0.939916425 1.020704105 0.96803784 1.027526124 1.021515243 0.974288902 0.799867451 1 18.89649404 5.065843695 1.46859353 0.975589253 0.668635707 0.272302132 0.062824166 3.522441361 3.723344869 0.016677266 1.986875612 116370.713 -5.065843695 -0.306953546 ELPPAAAIGATSLVAAPHSSS(ph)SSPSKDSSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELPPAAAIGATSLVAAPHSSSSSPSKDSSR 30 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 ELPPAAAIGATSLVAAPHS(0.012)S(0.06)S(0.297)S(0.297)S(0.297)PS(0.037)KDSSR;ELPPAAAIGATSLVAAPHS(0.006)S(0.014)S(0.333)S(0.333)S(0.253)PS(0.06)KDSS(0.001)R 259.74 1.75E-58 527250000 279040 454530 362960 525520 446770 575120 502870 513040 493490 632200 TRUE FALSE 268134.8083 441567.2494 428554.946 552642.1502 461140.7628 586749.3204 509024.2735 502445.5447 437471.0841 589380.5309 0.454943444 0.749205694 0.727127761 0.937666111 0.782416009 0.995535634 0.863659803 0.852497696 0.742255743 1 19.16883988 5.065982605 1.004481143 0.873641509 5.35E-18 0.688538608 0.085276719 1.82220921 0.950732179 0.024282965 1.998707226 116407.9403 -5.065982605 -0.873641509 EEGFPIRPHYFWPLLVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEGFPIRPHYFWPLLVGR 18 1 P42704;B8ZZ38;A0A0C4DG06 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 151.62 2.79E-08 758660000 450790 784590 503370 1117380 449880 583130 1045780 798320 703380 631120 FALSE TRUE 433172.6284 762214.2614 594340.1564 1175048.116 464350.7988 594921.2881 1058578.568 781834.413 623535.2512 588373.6803 0.736220268 1.295459479 1.010140624 1.997111963 0.789210691 1.011128315 1.799160302 1.328805892 1.059760612 1 19.16637319 5.065988514 1.832321765 1.293633782 1.03E-07 0.145654103 0.362163398 4.800384442 7.559537863 0.090469319 14.30586336 116409.5242 -5.065988514 -1.293633679 QT(ph)SKGEDVGYVASEITMSDEER ddPTM_BT-474_Pertuzumab_2h_R1 1 QTSKGEDVGYVASEITMSDEER 22 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 QT(0.5)S(0.5)KGEDVGYVASEITMSDEER 69.766 0.029462 51163000 8163.3 13244 11509 12595 14224 13064 14015 16368 12537 15160 TRUE FALSE 7844.269211 12866.29409 13588.93232 13245.02946 14681.52788 13328.16303 14186.51976 16029.99508 11113.85232 14133.1997 0.555024296 0.910359605 0.961490151 0.937157172 1.038797172 0.94303932 1.003772682 1.13420849 0.786364911 1 13.7868005 5.066354966 1.49071622 0.993084255 9.57E-14 0.685379634 0.084440395 1.454796735 1.578920846 0.022201692 2.696426715 116507.7904 -5.066354966 -0.993084255 CVMDDDNEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 CVMDDDNEVR 10 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 169.41 0.0053201 0 79164 110370 93278 117080 115110 115760 120770 118100 123340 130710 FALSE TRUE 76070.18336 107222.3557 110135.4096 123122.5128 118812.6177 118100.7465 122248.0194 115661.1937 109338.9603 121856.8953 0.624258342 0.879903886 0.903809418 1.010386097 0.975017601 0.969175739 1.0032097 0.949155922 0.897273478 1 16.89482836 5.066391303 1.285297797 0.96931301 0.203060075 0.899496434 0.034382505 0.801402441 0.661006465 0.009464082 0.986887687 116517.5388 -5.066391303 -0.766252935 DFQDYMEPEEGCQGS(ph)PQRR ddPTM_BT-474_Pertuzumab_2h_R1 6 DFQDYMEPEEGCQGSPQRR 19 1 O43237;O43237-2;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR 205.07 2.63E-16 6300200000 2477828 2716945 2392543 2639534 2698118 3365370 2944467 2868110 3500100 3303130 TRUE FALSE 2380991.742 2639460.389 2824928.742 2775760.666 2784905.416 3433420.087 2980502.268 2808882.526 3102783.322 3079406.063 0.773198368 0.857132945 0.917361557 0.901394817 0.904364465 1.114961787 0.967882185 0.912150742 1.007591483 1 21.55422069 5.066483998 0.578542212 0.983056852 0.555203062 0.601463472 0.05579129 4.049133145 0.784293351 0.028792995 1.25855378 116542.4109 -5.066483998 -0.42785379 RRS(ph)QSIEQES(ph)QEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 RRS(1)QS(0.06)IEQES(0.94)QEK;RRS(0.994)QS(0.036)IEQES(0.971)QEK 193.71 8.06E-06 3759440000 4927000 4368180 3753510 3775210 4124490 4142980 4064480 4361650 5231250 4623180 TRUE FALSE 4734447.393 4243603.783 4431852.753 3970049.041 4257157.967 4226753.894 4114222.322 4271580.403 4637420.431 4310047.901 1.098467465 0.984583903 1.028260673 0.92111483 0.98772869 0.980674459 0.954565336 0.991074926 1.075955659 1 22.03927247 5.066533737 1.953461516 0.986928449 1.250427136 0.3890195 0.039349062 2.654647684 4.661221502 0.009779718 1.723136148 116555.7591 -5.066533737 0.263498687 ARPEDVISEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 ARPEDVISEGR 11 1 P25325-2;P25325 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 0 ;; 179.98 6.26E-06 2613390000 1256560 1470550 1184740 1469940 1411920 1609480 1547740 1391680 1376300 1556930 FALSE TRUE 1207452.246 1428611.354 1398848.872 1545803.78 1457335.689 1642024.788 1566681.705 1362941.322 1220068.194 1451477.744 0.831877892 0.984246131 0.963741179 1.064986208 1.004035849 1.131277965 1.079370119 0.939002563 0.840569687 1 20.46909102 5.066909848 1.539895296 1.008893849 0.606279519 0.307460995 0.07633994 3.500586294 4.027126614 0.021517208 2.719716334 116656.7434 -5.066909848 -0.40261433 LDYWEDDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDYWEDDLR 9 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 ;;; 170.05 0.00013495 1630960000 1612640 1827720 1504230 1823070 1811820 1738780 1881790 1897670 1956280 2067640 FALSE TRUE 1549616.246 1775595.215 1776077.822 1917158.861 1870098.836 1773939.323 1904819.909 1858482.451 1734211.296 1927596.901 0.803910945 0.921144464 0.921394832 0.994584947 0.970171115 0.92028542 0.988183737 0.96414476 0.899675287 1 20.87837196 5.067501196 1.269747274 0.960317387 0.613821646 0.686073916 0.031498065 1.581075193 1.272324181 0.008401742 0.870348848 116815.6948 -5.067501196 -0.346495741 SSS(ph)PVQVEEEPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVQVEEEPVR 13 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 SS(0.002)S(0.997)PVQVEEEPVR 299.46 8.02E-41 528240000 269120 297570 248070 311450 303670 278290 311000 361200 340610 306030 TRUE FALSE 258602.4929 289083.595 292901.7673 327523.9718 313437.8213 283917.2145 314806.111 353741.0938 301945.3808 285302.3155 0.906415682 1.013253588 1.026636488 1.147989182 1.098616465 0.995145146 1.103412394 1.239881608 1.058334841 1 18.12213193 5.068304109 0.801923089 1.109994332 0.678568961 0.37542206 0.069869233 3.934681998 1.353592916 0.025899208 1.70513341 117031.8606 -5.068304109 -0.431425371 VRGGAPDPSPGATATPGAPAQPSS(ph)PDAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 VRGGAPDPSPGATATPGAPAQPS(0.2)S(0.8)PDAR 208.7 1.07E-25 241200000 138950 154720 99607 104020 83117 154500 91536 97254 92571 104900 TRUE FALSE 133519.6804 150307.5371 117608.2006 109388.4847 85790.53379 157624.0959 92656.24495 95245.67091 82062.72817 97795.02956 1.365301294 1.536964995 1.202598958 1.118548511 0.877248406 1.611780236 0.947453519 0.973931613 0.839129847 1 16.57747352 5.068842567 0.290602702 0.917221338 2.017618957 0.356567681 0.208954474 10.59959875 0.635622201 0.243243839 4.310634572 117177.0518 -5.068842567 1.10039762 (ac)SETAPLAPTIPAPAEKT(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SETAPLAPTIPAPAEKTPVK 20 1 P16402 P16402 HIST1H1D Histone H1.3 1 S(0.002)ET(0.002)APLAPT(0.001)IPAPAEKT(0.995)PVK;S(0.002)ET(0.002)APLAPT(0.006)IPAPAEKT(0.989)PVK;SETAPLAPT(0.001)IPAPAEKT(0.999)PVK;S(0.002)ET(0.002)APLAPT(0.002)IPAPAEKT(0.995)PVK 60.826 3.36E-06 0 2387420 1314230 1101780 815230 1238440 753530 867980 1803040 908990 703840 TRUE FALSE 2294116.987 1276749.447 1300896.155 857304.118 1278275.547 768766.8929 878602.5989 1765806.594 805805.266 656168.2899 3.496232632 1.945765236 1.982564801 1.306530857 1.948091011 1.17160019 1.338989726 2.691087974 1.228046644 1 19.32370635 5.068963411 1.53720195 1.659884102 5.862741627 0.581737992 0.482438698 2.054861062 2.345515364 0.13051034 16.66367781 117209.6614 -5.068963411 4.202857525 RHES(ph)KDK ddPTM_BT-474_Pertuzumab_2h_R1 1 RHESKDK 7 2 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 RHES(1)KDK 58.699 0.056345 23903000 16563 14728 12851 12951 11314 13246 14290 9791.5 13995 10988 TRUE FALSE 15915.69965 14307.97186 15173.46157 13619.40266 11677.92509 13513.8432 14464.88529 9589.302103 12406.34627 10243.77297 1.553695078 1.396748239 1.481237588 1.32952992 1.140002333 1.319225175 1.412066173 0.93611037 1.211111014 1 13.32245956 5.070298849 0.183358539 0.933627577 2.134130069 0.613850604 0.119761697 12.66449404 0.373517037 0.320916999 3.597666149 117570.6311 -5.070298849 1.200502492 ERGDYVLAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERGDYVLAVK 10 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 0 62.408 0.077781 224640000 239050 221720 206330 216340 217920 206360 225760 215750 256010 265960 FALSE TRUE 229707.6617 215396.7627 243618.4208 227505.3333 224929.5947 210532.7406 228522.9184 211294.6871 226948.8181 247946.2923 0.926441205 0.868723467 0.982545125 0.917558925 0.907170632 0.849106226 0.921662979 0.852179257 0.915314425 1 17.91966813 5.070696861 19.54401998 0.905757531 1.424631669 0 0.047660349 1715.549645 434073.8391 0.010573884 73663.72141 117678.4288 -5.070696861 0.518874138 DS(ph)GSFEQYSENIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSGSFEQYSENIK 13 0 Q8IZT6;Q8IZT6-2;Q5VYL4 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 DS(0.998)GS(0.002)FEQYSENIK 199.68 1.22E-07 54168000 36791 42519 42325 43973 46990 45869 54738 63621 63775 72969 TRUE FALSE 35353.16705 41306.39975 49974.06901 46242.4518 48501.47603 46796.50261 55407.90002 62307.20412 56535.52937 68026.74464 0.519695117 0.607208238 0.73462385 0.6797687 0.712976584 0.687913303 0.814501713 0.915922178 0.831077978 1 16.05381443 5.073379644 0.143060405 1.104256299 9.65E-16 0.869640209 0.049053782 10.85535802 0.234320038 0.286494243 2.286320994 118407.6178 -5.073379644 -1.104256299 EDAEGVAAEEEQEGDS(ph)GEQETGATDARPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDAEGVAAEEEQEGDSGEQETGATDARPR 29 1 Q96KC8 Q96KC8 DNAJC1 DnaJ homolog subfamily C member 1 1 EDAEGVAAEEEQEGDS(0.979)GEQET(0.017)GAT(0.004)DARPR 181.38 6.29E-18 271370000 48233 89692 55193 113160 68744 77852 93242 122910 87056 74907 TRUE FALSE 46348.00104 87134.07198 65167.60286 119000.2012 70955.21319 79426.22078 94383.12349 120371.8655 77173.76785 69833.48217 0.663693111 1.247740615 0.933185642 1.704056528 1.01606294 1.137365893 1.351545427 1.723698458 1.105111265 1 16.09163129 5.074745379 1.069218458 1.321361662 2.02E-15 0.27371605 0.269196091 4.061895472 2.348415743 0.079686582 7.20493956 118780.5628 -5.074745379 -1.321361662 SLQSVAEER ddPTM_BT-474_Pertuzumab_2h_R1 4 SLQSVAEER 9 0 P61313;A0A2R8YEM3;E7EQV9;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;; 209.39 1.98E-05 2855210000 1993860 2223320 1795820 2171560 2242230 2296440 2287340 2334650 2427830 2450470 FALSE TRUE 1915937.747 2159913.09 2120364.622 2283634.472 2314353.364 2342875.59 2315333.151 2286438.662 2152232.917 2284497.484 0.83866923 0.945465296 0.928153625 0.999622231 1.013068905 1.025554025 1.01349779 1.000849717 0.94210343 1 21.12344542 5.07474713 0.843429209 1.001953174 0.663463747 0.77332878 0.026049503 1.757817354 0.657724374 0.008884588 0.630015885 118781.0418 -5.07474713 -0.338489427 RRT(ph)AS(ph)PPPPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRTASPPPPPK 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRT(1)AS(1)PPPPPK 82.822 0.019742 911570000 664510 624410 527040 540340 581240 597540 593580 645500 683340 619560 TRUE FALSE 638540.2145 606602.4382 622287.8519 568227.0122 599936.1125 609622.6682 600844.4096 632170.1994 605770.108 577596.6494 1.105512325 1.05021807 1.077374415 0.983778235 1.03867658 1.05544703 1.040249126 1.094483841 1.048777047 1 19.13970285 5.075247698 1.608786255 1.046290606 1.183569651 0.265236677 0.030842664 4.204605319 5.135104331 0.008359679 1.172924088 118918.0277 -5.075247698 0.137279046 S(ph)LGSVQAPSYGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(1)LGSVQAPSYGAR;S(1)LGSVQAPSYGAR 236.05 1.11E-16 676160000 448710 302500 175207 157366 170196 158605 99160 231630 108765 102288 TRUE FALSE 431173.9171 293872.9962 206870.8024 165487.6781 175670.5089 161812.1018 100373.5497 226846.7596 96418.45318 95359.94265 4.52154128 3.081723709 2.16936794 1.735400353 1.842183458 1.696856115 1.052575609 2.378847483 1.011100159 1 16.54109575 5.075850026 0.856601226 1.563887251 8.009829257 0.849767466 0.401662842 1.345297817 0.517059002 0.128939386 9.3292019 119083.071 -5.075850026 6.445942006 up S(ph)SPAPHSGPCPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPAPHSGPCPSR 13 0 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 S(0.5)S(0.5)PAPHSGPCPSR 83.54 0.0065419 51762000 43262 36059 30760 36242 38894 44272 40060 39711 43753 38461 TRUE FALSE 41571.27321 35030.63263 36319.01625 38112.45396 40145.06083 45167.21017 40550.26626 38890.95397 38786.34287 35856.00221 1.159395098 0.976980992 1.012913153 1.062930935 1.119618986 1.259683383 1.130919895 1.084642781 1.081725247 1 15.12992702 5.076219055 20.80949692 1.088548753 3.892053761 0.078662332 0.076664735 1752.329512 509635.4338 0.019055794 14968.11096 119184.3014 -5.076219055 2.803505008 (ac)ATSPQKS(ph)PSVPKS(ph)PTPK ddPTM_BT-474_Pertuzumab_2h_R1 3 ATSPQKSPSVPKSPTPK 17 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 2 AT(0.204)S(0.195)PQKS(0.552)PS(0.245)VPKS(0.616)PT(0.189)PK;AT(0.045)S(0.042)PQKS(0.842)PS(0.157)VPKS(0.788)PT(0.126)PK;AT(0.028)S(0.111)PQKS(0.86)PS(0.314)VPKS(0.659)PT(0.028)PK 69.088 2.83E-07 1053800000 2890720 2459180 2351400 2054370 3035080 2458970 2382750 2865820 3140470 2388780 TRUE FALSE 2777747.467 2389046.594 2776350.287 2160396.282 3132706.105 2508692.058 2411910.807 2806639.816 2783977.012 2226985.803 1.247312607 1.072771363 1.24668522 0.970098812 1.406702324 1.126496655 1.08303825 1.260286353 1.250109905 1 21.08666093 5.077215256 18.67372728 1.16927514 3.406368705 0.035300533 0.128096194 692.7140049 181625.1279 0.027417929 5412.14637 119458.0045 -5.077215256 2.237093565 SVS(ph)TTNIAGHFNDESPLGLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.028)VS(0.937)T(0.028)T(0.007)NIAGHFNDESPLGLR;S(0.008)VS(0.929)T(0.053)T(0.011)NIAGHFNDESPLGLR;S(0.005)VS(0.965)T(0.029)T(0.001)NIAGHFNDESPLGLR 303.15 3.24E-55 672960000 741220 425502 280996 326840 261230 235846 206961 509613 243723 212551 TRUE FALSE 712252.3029 413367.0996 331778.2279 343708.2516 269632.7002 240614.9677 209493.8506 499089.3135 216056.5868 198154.7314 3.594424911 2.086082409 1.674339167 1.734544762 1.360717951 1.214278185 1.05722356 2.518684817 1.090342811 1 17.59626789 5.078356339 1.298994169 1.512807156 6.25769368 0.697668012 0.426794505 1.763022999 1.450283955 0.122672634 13.69639854 119772.286 -5.078356339 4.744886524 SVHELEK ddPTM_BT-474_Pertuzumab_2h_R1 8 SVHELEK 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 150.84 0.0019219 13160500000 13480710 17060440 13930660 17253200 15878270 17395500 17828280 16623620 18647720 19778980 FALSE TRUE 12953868.95 16573892.96 16448240.15 18143639.72 16389008.97 17747248.93 18046467.82 16280336.44 16530909 18439332.07 0.702512917 0.898833694 0.892019304 0.983964042 0.888807084 0.962467017 0.978694226 0.882913566 0.896502593 1 24.13628306 5.078812876 1.535655799 0.933750859 0.394006765 0.737051545 0.041623674 1.38290731 1.540953583 0.010727625 1.450261723 119898.2588 -5.078812876 -0.539744094 VPS(ph)PGMEEAGCSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VPSPGMEEAGCSR 13 0 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 VPS(1)PGMEEAGCSR;VPS(1)PGMEEAGCSR;VPS(1)PGMEEAGCSR;VPS(1)PGMEEAGCSR 217.2 2.75E-11 4906700000 442590 365741 307987 428741 375605 420198 405035 424392 413972 387416 TRUE FALSE 425293.0935 355310.4248 363647.102 450868.3744 387686.6759 428694.6915 409991.9395 415628.1569 366979.6341 361175.9692 1.177523229 0.983759871 1.006841908 1.248334365 1.073401081 1.186941347 1.135158411 1.150763595 1.016068801 1 18.46234238 5.079180315 20.51122622 1.10167378 4.369638839 0.07074945 0.085832864 1548.578721 412585.7898 0.019606266 6655.153715 119999.7428 -5.079180315 3.267965059 LWAHVYAGAPVSSPEYTK ddPTM_BT-474_Pertuzumab_2h_R1 2 LWAHVYAGAPVSSPEYTK 18 0 D6RDM7;P61086;P61086-2 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 179.17 8.50E-14 1001960000 1269350 1442280 1073160 1174400 1244070 1181960 1272760 1261380 1409570 1472280 FALSE TRUE 1219742.399 1401147.587 1267103.884 1235010.925 1284086.641 1205860.041 1288336.418 1235332.062 1249561.523 1372561.164 0.888661599 1.020827066 0.923167519 0.899785712 0.935540561 0.878547399 0.938636799 0.900019682 0.910386769 1 20.38843901 5.079241431 17.01894396 0.928479708 0.000135633 0.079279324 0.042753171 13788770.05 36765619.43 0.009811207 474153218.5 120016.6309 -5.079241431 -0.928344074 DNLLFGDEIITNGFHSCES(ph)DEEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 DNLLFGDEIITNGFHSCESDEEDR 24 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 DNLLFGDEIITNGFHSCES(1)DEEDR;DNLLFGDEIITNGFHS(0.001)CES(0.999)DEEDR;DNLLFGDEIITNGFHSCES(1)DEEDR;DNLLFGDEIITNGFHS(0.114)CES(0.886)DEEDR 269.35 3.23E-45 220274000 107064 115642 134848 179432 136850 175234 200667 170216 208426 230409 TRUE FALSE 102879.8205 112344.0034 159218.0333 188692.507 141251.9045 178777.3515 203122.8228 166700.9801 184766.3543 214803.1932 0.478949214 0.523009001 0.741227497 0.878443678 0.657587545 0.832284422 0.94562292 0.77606379 0.860165771 1 17.71265591 5.079476999 0.530687159 0.872167241 1.74E-20 0.715115844 0.087169717 3.199316054 0.529468107 0.047054502 1.866874376 120081.7475 -5.079476999 -0.872167241 down FDTQYPYGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FDTQYPYGEK 10 0 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 149.96 5.22E-05 442820000 217970 187950 200110 189870 190290 168690 205200 197440 232940 222010 FALSE TRUE 209451.4914 182589.85 236274.3284 199669.2135 196410.8507 172101.0274 207711.299 193362.795 206497.6278 206973.065 1.011974633 0.882191362 1.141570419 0.964711101 0.94896817 0.831514127 1.003566812 0.934241347 0.997702903 1 17.65908351 5.080170717 19.26505733 0.964868933 2.662377039 0.028112336 0.078002048 1063.247119 278682.8091 0.017626811 7063.332332 120273.7125 -5.080170717 1.697508106 ALYEHLTAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALYEHLTAK 9 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 118.5 0.0009801 518910000 552230 957420 604120 1308600 602690 667690 1303000 1042500 909980 741540 FALSE TRUE 530648.2411 930115.319 713297.9226 1376137.003 622076.0712 681191.1493 1318946.504 1020972.011 806682.8853 691314.8353 0.767592729 1.345429422 1.031798952 1.990608233 0.899844817 0.985355896 1.907881093 1.476855347 1.166882069 1 19.39898336 5.080181218 1.575032618 1.362918329 4.89E-10 0.152145636 0.366439565 4.925140319 5.724452768 0.095216062 13.40173983 120276.6208 -5.080181218 -1.362918328 S(ph)RTSVQTEDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 S(0.514)RT(0.243)S(0.243)VQTEDDQLIAGQSAR;S(0.333)RT(0.333)S(0.333)VQT(0.001)EDDQLIAGQSAR;S(0.477)RT(0.261)S(0.261)VQTEDDQLIAGQSAR 258.83 2.92E-31 7108380000 687666 1213065 859545 1465893 949347 1256361 1623502 1285463 1384742 1406168 TRUE FALSE 660791.2525 1178469.574 1014883.902 1541547.913 979883.6084 1281765.48 1643370.903 1258917.74 1227551.893 1310926.989 0.504064115 0.898958969 0.774172712 1.17592202 0.747473823 0.977755047 1.25359453 0.960326357 0.936399894 1 20.32215591 5.083202366 0.927925914 1.007471709 1.69E-14 0.503636381 0.143143992 3.021651695 1.330889845 0.044104851 3.559143658 121116.236 -5.083202366 -1.007471709 ATT(ph)PPNQGRPDS(ph)PVYANLQELK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 2 AT(0.499)T(0.501)PPNQGRPDS(0.98)PVY(0.02)ANLQELK 70.151 0.040791 2179700000 169570 201270 173680 193440 205610 214860 198390 221190 228330 207740 TRUE FALSE 162943.0169 195529.9767 205067.8395 203423.4616 212223.6324 219204.6164 200817.9562 216622.3492 202410.9356 193669.5848 0.841345414 1.00960601 1.058854129 1.050363493 1.095802589 1.131848435 1.03691014 1.11851507 1.045135383 1 17.56323788 5.083307682 1.265910683 1.077830649 0.536344943 0.760697084 0.037951317 1.261315912 0.980667276 0.009821265 1.092837172 121145.6101 -5.083307682 -0.541485706 NYEQWQLQR ddPTM_BT-474_Pertuzumab_2h_R1 4 NYEQWQLQR 9 0 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;A0A590UK95 A0A590UJQ1 ITCH E3 ubiquitin-protein ligase Itchy homolog 0 ;;; 144.5 0.00023128 1171229000 493226 587691 487125 491245 459758 401679 515183 507430 596010 636614 FALSE TRUE 473950.1826 570930.6281 575159.3235 516598.2133 474546.5336 409801.2246 521487.9637 496951.3932 528353.4435 593495.5667 0.798574091 0.9619796 0.969104667 0.870433146 0.799578902 0.690487423 0.878672046 0.837329579 0.890239916 1 19.17887773 5.085039023 12.58391571 0.866528433 6.68E-05 0.057214019 0.086312033 2148938.204 7902736.955 0.021431326 48485226.67 121629.5284 -5.085039023 -0.866461608 SFAGAVSPQEEEEFRR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFAGAVSPQEEEEFRR 16 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;;; 264.16 8.68E-27 6571200000 1524070 1598760 1136150 1513930 1407770 1586970 1554860 1520910 1625050 1633020 FALSE TRUE 1464507.659 1553164.93 1341477.579 1592064.109 1453052.201 1619059.621 1573888.842 1489502.677 1440581.137 1522414.101 0.961964067 1.020198729 0.881151572 1.045749713 0.954439531 1.063481756 1.033811261 0.978382082 0.946247894 1 20.5379294 5.085047343 8.692359729 0.991511697 0.7998594 0.028680388 0.051556435 16949.82935 82336.04992 0.011863746 52379.94698 121631.8585 -5.085047343 -0.191652297 FSCPETDSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSCPETDSHR 10 0 P50416 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ; 112.13 0.0016617 1411320000 471580 807190 544610 1053430 608230 705500 955350 949390 887490 803370 FALSE TRUE 453150.1322 784169.7315 643033.1418 1107797.649 627794.2703 719765.6934 967041.8591 929784.7647 786745.8559 748957.0343 0.60504156 1.047015644 0.85857147 1.479120427 0.83822468 0.961024011 1.291184694 1.241439391 1.05045526 1 19.51452343 5.085259324 1.193413176 1.124680795 8.46E-15 0.365769361 0.18967275 3.292392566 2.290291718 0.052938144 5.586988505 121691.2422 -5.085259324 -1.124680795 S(ph)RSKDSVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSKDSVPK 9 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.575)RS(0.404)KDS(0.021)VPK;S(0.599)RS(0.366)KDS(0.034)VPK 50.909 0.082529 2349210000 3041470 2220180 1964390 1628930 1959680 1718050 1949550 2197260 2958100 2534490 TRUE FALSE 2922605.99 2156862.64 2319398.971 1712999.273 2022714.887 1752790.148 1973409.176 2151885.813 2622308.889 2362826.735 1.236910835 0.912831486 0.981620419 0.724978792 0.85605722 0.741819162 0.835189964 0.910725184 1.109818528 1 21.17208241 5.085330435 1.60026412 0.876064041 1.734106854 0.448227774 0.111830404 2.498529084 2.950921512 0.029444111 4.370163262 121711.1693 -5.085330435 0.858042813 VDENHSEFTLYESR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDENHSEFTLYESR 14 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 0 138.19 1.69E-05 232840000 199690 347380 199830 447820 258460 248570 394440 368400 289380 251420 FALSE TRUE 191885.894 337473.0625 235943.7262 470932.0439 266773.6006 253596.2557 399267.2747 360792.4113 256530.7956 234391.0995 0.818656913 1.439786166 1.006624086 2.009172042 1.138155848 1.081936372 1.703423362 1.53927522 1.094456215 1 17.83855826 5.085848183 1.989035777 1.378846029 4.41E-12 0.167800637 0.324250862 4.774033084 8.142636795 0.079201847 16.88408209 121856.355 -5.085848183 -1.378846029 HALIIYDDLSK ddPTM_BT-474_Pertuzumab_2h_R1 4 HALIIYDDLSK 11 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;; 185.96 4.24E-06 2272210000 3367390 4762460 3184670 6630150 2944530 3479830 6525640 4129960 4984910 3705040 FALSE TRUE 3235788.676 4626639.304 3760210.712 6972332.836 3039243.482 3550194.547 6605502.734 4044674.883 4419043.915 3454094.341 0.936798002 1.33946524 1.088624207 2.01857047 0.87989591 1.027822114 1.91236894 1.170979853 1.279363989 1 21.71987606 5.088549532 1.870927708 1.32764628 0.361417563 0.078602879 0.361098053 7.380843111 11.29834083 0.088600281 17.1830215 122616.6741 -5.088549532 -0.966228716 KPDCDDWESGLNAMECALHLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPDCDDWESGLNAMECALHLEK 22 1 G3V192;P02794;G3V1D1;E9PPQ4 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 0 153.77 2.04E-08 132730000 227300 197650 214520 187850 183390 207220 185280 190820 277780 240910 FALSE TRUE 218416.8647 192013.2155 253288.536 197544.961 189288.9059 211410.1304 187547.5121 186879.5003 246247.5789 224592.9511 0.972500978 0.854938744 1.127767077 0.879568838 0.842808757 0.941303497 0.835055202 0.83208088 1.096417219 1 17.77695312 5.090930144 18.22568342 0.921708113 3.280046082 0 0.103681199 914.7350584 186958.7985 0.023620717 1745.382853 123290.6504 -5.090930144 2.358337969 LEAPLEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEAPLEELR 9 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;; 194.92 7.41E-05 424221000 537109 637340 508295 550258 571634 373899 596914 565438 563545 659520 FALSE TRUE 516118.1865 619163.6872 600155.2135 578656.8813 590021.1268 381459.494 604219.2121 553761.5077 499573.7342 614850.123 0.839421132 1.007015635 0.976100014 0.941134855 0.959617807 0.620410535 0.982709752 0.900644705 0.812513026 1 19.22987525 5.092025555 11.85562867 0.907497231 0.000148985 0.035043447 0.111426981 1967732.095 6518657.257 0.02629941 43924153.62 123602.0162 -5.092025555 -0.907348245 HAS(ph)S(ph)SPESPKPAPAPGSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HAS(0.864)S(0.592)S(0.542)PES(0.002)PKPAPAPGSHR;HAS(0.986)S(0.556)S(0.458)PESPKPAPAPGSHR 135.68 9.69E-06 295577000 239730 227990 162859 175186 188629 211418 203355 86124 298870 232060 TRUE FALSE 230361.0866 221487.9484 192291.2441 184227.3705 194696.4231 215693.0168 205843.7193 84345.5093 264943.5306 216342.3695 1.064798759 1.023784425 0.888828409 0.851554741 0.899945875 0.996998495 0.951472057 0.389870507 1.224649296 1 17.72295671 5.092906764 0.608102161 0.83886835 1.349147442 0.019605565 0.203912848 12.18638491 2.512213872 0.096271958 4.778220033 123853.0665 -5.092906764 0.510279092 TFCQLILDPIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TFCQLILDPIFK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 117.79 0.0004656 0 209550 178350 188490 148970 216420 229870 172030 193830 232020 223370 FALSE TRUE 201360.5543 173263.6326 222554.3359 156658.3596 223381.3458 234518.1289 174135.3546 189827.3428 205682.0623 208240.9509 0.966959445 0.83203439 1.068734727 0.75229372 1.072706136 1.12618641 0.836220512 0.91157547 0.987711886 1 17.66789428 5.095032187 20.14576568 0.947627067 2.555193424 0 0.114792385 7127.997757 1702584.196 0.025769549 66563.31288 124460.6851 -5.095032187 1.607566357 RNS(ph)SSSSSPSERPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSSSSSSPSERPR 14 2 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 RNS(0.804)S(0.066)S(0.066)S(0.043)S(0.016)S(0.005)PSERPR;RNS(0.751)S(0.044)S(0.132)S(0.072)S(0.001)SPSERPR 108.25 0.00065861 521190000 181726 220081 155981 249714 203706 210127 265411 186221 240955 213629 TRUE FALSE 174623.947 213804.5054 184170.2365 262601.7695 210258.3885 214375.9119 268659.1792 182375.4713 213602.7986 199159.7175 0.876803548 1.073532881 0.924736381 1.318548614 1.055727489 1.076401968 1.348963448 0.915724693 1.072520092 1 17.60356635 5.096115459 1.156555335 1.10029172 0.60656451 0.18390744 0.136062884 5.579336816 3.599057167 0.037854388 4.051550445 124771.518 -5.096115459 -0.49372721 RES(ph)ASSSSSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 RESASSSSSVK 11 1 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 RES(0.996)AS(0.002)S(0.001)S(0.001)S(0.001)SVK;RES(0.976)AS(0.01)S(0.01)S(0.004)SSVK 89.231 0.0034719 96681000 307188 254964 258748 264533 273198 239347 238946 352709 273814 258261 TRUE FALSE 295182.7533 247692.6764 305509.5194 278185.5798 281985.6618 244186.7603 241870.2926 345425.4359 242731.7826 240768.7524 1.226001092 1.028757569 1.268891899 1.155405662 1.171188781 1.014196227 1.004575096 1.434677185 1.008153177 1 17.87728864 5.097707777 19.01842217 1.144875897 7.080316517 0.024161983 0.137874974 11629505.6 37381646.1 0.032979342 2932204062 125229.826 -5.097707777 5.93544062 HTVIAAQS(ph)LEALSGLQK ddPTM_BT-474_Pertuzumab_2h_R1 5 HTVIAAQSLEALSGLQK 17 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 HT(0.049)VIAAQS(0.951)LEALSGLQK;HTVIAAQS(1)LEALSGLQK;HT(0.001)VIAAQS(0.999)LEALSGLQK;HTVIAAQS(0.977)LEALS(0.023)GLQK;HT(0.012)VIAAQS(0.988)LEALSGLQK 273.27 7.56E-36 3014539000 3556250 2700620 2103960 1999880 1897994 1698166 1917079 1889008 2248390 2145820 TRUE FALSE 3417267.818 2623600.962 2484192.374 2103094.046 1959044.701 1732504.08 1940540.786 1849999.325 1993162.193 2000481.7 1.708222484 1.31148461 1.2417971 1.051293819 0.979286489 0.866043453 0.97003676 0.92477693 0.996341128 1 20.931916 5.097717379 0.698235601 0.938117753 2.566156206 0.954691532 0.051021203 0.830541547 0.216389349 0.019760487 1.19478104 125232.5949 -5.097717379 1.628038453 YLTESYGTGQDIDDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YLTESYGTGQDIDDR 15 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;; 270.85 5.14E-33 1475130000 419240 461460 370050 459200 448010 457890 488040 448860 483120 498610 FALSE TRUE 402855.6373 448299.6126 436926.2667 482899.367 462420.6485 467148.8495 494012.7795 439590.8841 428278.243 464838.7006 0.866656836 0.964419727 0.939952431 1.03885362 0.994798084 1.004969786 1.062761725 0.94568478 0.921348077 1 18.82637066 5.099523899 1.172427534 0.992742561 0.70566521 0.452734935 0.040855231 3.084420782 2.027597625 0.012001427 1.323273869 125754.6055 -5.099523899 -0.287077351 GLDVDSLVIEHIQVNK ddPTM_BT-474_Pertuzumab_2h_R1 3 GLDVDSLVIEHIQVNK 16 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ;; 262.66 6.74E-27 2152098000 1139495 1197500 1081055 1095354 1247591 1317094 1304384 1243223 1375627 1366249 FALSE TRUE 1094962.276 1163348.472 1276425.686 1151885.351 1287720.898 1343726.543 1320347.442 1217550.011 1219471.59 1273711.738 0.859662546 0.913353028 1.00213074 0.904353251 1.010998689 1.054969113 1.036614017 0.955907035 0.95741568 1 20.28060738 5.09953121 0.788678349 0.996475536 0.690977963 0.52490559 0.040962675 3.546120363 1.142659267 0.015313239 1.082637018 125756.7224 -5.09953121 -0.305497573 AGLTMNDIDAFEFHEAFSGQILANFK ddPTM_BT-474_Pertuzumab_2h_R1 2 AGLTMNDIDAFEFHEAFSGQILANFK 26 0 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 226.18 1.61E-34 36243000 23539.7 39627 24512.4 50007 24795.7 32786.7 50476 39407 35740 28518 FALSE TRUE 22619.7425 38496.87676 28942.33596 52587.86726 25593.27621 33449.66954 51093.74039 38593.23168 31682.94503 26586.45046 0.850799641 1.447988584 1.088612261 1.977995045 0.962643594 1.25814725 1.921796235 1.451612796 1.191695186 1 14.69840356 5.10068261 1.867982132 1.41019813 5.88E-12 0.158178168 0.337446437 5.131317162 7.564187242 0.083039375 17.62513842 126090.5705 -5.10068261 -1.41019813 EAYPGDVFYLHSR ddPTM_BT-474_Pertuzumab_2h_R1 5 EAYPGDVFYLHSR 13 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;;; 225.13 1.30E-11 9821120000 3938880 6491970 4008850 9589180 3953310 4994530 8114160 6521760 5633650 4566960 FALSE TRUE 3784944.215 6306825.372 4733338.371 10084078.73 4080471.806 5095522.819 8213463.517 6387083.377 4994141.67 4257635.731 0.888977934 1.481297549 1.111729295 2.368469114 0.95838913 1.19679633 1.929113723 1.500147918 1.172984723 1 22.02162109 5.103910536 1.832420892 1.462005056 1.28E-10 0.109213939 0.423272215 6.235105635 8.827861242 0.104037113 21.81877851 127031.2396 -5.103910536 -1.462005056 SEASLHPVLMSEAPWNTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEASLHPVLMSEAPWNTR 18 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 ; 237.89 7.28E-24 1125770000 975630 1194090 945920 1250230 1128140 1286400 1147370 1121510 1307400 1404080 FALSE TRUE 937501.301 1160035.722 1116868.786 1314754.52 1164427.648 1312411.889 1161411.857 1098350.427 1158989.433 1308980.411 0.716207281 0.886213203 0.853235676 1.00441115 0.889568429 1.00262149 0.887264506 0.839088513 0.885413887 1 20.32001208 5.104298198 1.456741151 0.914942198 0.433701784 0.519997948 0.058646516 2.606032526 2.499389808 0.016075479 2.353814792 127144.6814 -5.104298198 -0.481240415 VISRPPPSVS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 4 VISRPPPSVSPPK 13 1 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;A0A0C4DGG3 Q8NHM5-4 KDM2B Lysine-specific demethylase 2B 1 VISRPPPS(0.054)VS(0.946)PPK;VISRPPPS(0.049)VS(0.951)PPK;VISRPPPS(0.112)VS(0.888)PPK;VISRPPPS(0.264)VS(0.736)PPK 93.152 0.0034793 1977010000 2088040 1755470 1503590 1436140 1542680 1434330 1716580 1838710 1912570 1730000 TRUE FALSE 2006437.088 1705405.714 1775322.16 1510259.358 1592301.703 1463333.135 1737588.02 1800739.996 1695463.072 1612825.559 1.2440509 1.05740246 1.100752744 0.936405893 0.987274597 0.907310234 1.07735645 1.116512561 1.051237725 1 20.62115898 5.104591528 1.407643208 1.023994881 1.551931755 0.523356443 0.063692936 2.840452787 2.563504297 0.019369533 2.716082738 127230.5861 -5.104591528 0.527936874 LTISSPLEAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTISSPLEAHK 11 0 Q15393;Q15393-2 Q15393 SF3B3 Splicing factor 3B subunit 3 0 66.56 0.062375 210640000 352630 367020 316900 341870 323190 270690 333630 353570 391220 397320 FALSE TRUE 338848.8297 356552.949 374170.8794 359513.9517 333585.6999 276163.5373 337713.0637 346268.6559 346810.3457 370409.1625 0.914796026 0.962592141 1.010155572 0.970586012 0.900587063 0.745563461 0.911729779 0.934827458 0.936289868 1 18.49876026 5.105877769 18.14586253 0.925720484 0.001173049 0.000601829 0.07035467 3231.664022 614512.9693 0.017455286 13509.19135 127607.9608 -5.105877769 -0.924547435 PYHPPPLFPPS(ph)PQPPDSTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 PYHPPPLFPPSPQPPDSTPR 20 0 P54259 P54259 ATN1 Atrophin-1 1 PYHPPPLFPPS(1)PQPPDSTPR;PYHPPPLFPPS(1)PQPPDSTPR 116.65 5.91E-05 1897080000 973370 827500 862100 1006770 959920 925770 1018710 1079830 1241330 1121710 TRUE FALSE 935329.6243 803900.5102 1017900.647 1058729.52 990796.6986 944489.7037 1031177.278 1057531.133 1100419.422 1045735.583 0.894422682 0.768741662 0.973382435 1.012425644 0.947463886 0.903182142 0.986078407 1.011279668 1.052292225 1 19.99608668 5.105949653 0.380525775 1.015015824 0.644285249 0.456242285 0.057291357 7.004819477 0.65268876 0.04942496 1.257339157 127629.0843 -5.105949653 -0.370730575 VVNDDCTHEADVYIENGIIQQVGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VVNDDCTHEADVYIENGIIQQVGR 24 0 Q9BPU6;E9PHT0;E7ESV0;E7EWB4 Q9BPU6 DPYSL5 Dihydropyrimidinase-related protein 5 0 ;; 228.48 3.57E-33 591660000 259552 302947 240147 302119 296425 315966 295226 278841 324117 320273 FALSE TRUE 249408.4209 294307.2482 283546.9049 317711.3978 305959.7793 322355.049 298839.0641 273082.8359 287324.597 298580.6244 0.835313481 0.985687697 0.94964938 1.064072387 1.024714112 1.079624807 1.000865561 0.914603338 0.962301548 1 18.18776102 5.108303381 1.622687335 0.998888197 0.588478573 0.517177274 0.047269165 2.863682595 3.276694636 0.014138682 2.479719012 128322.6681 -5.108303381 -0.410409624 EPSEVPT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 EPSEVPTPK 9 0 P17096;P17096-3;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 EPSEVPT(1)PK;EPSEVPT(1)PK 102.53 0.039901 945460000 2787100 1793960 1440480 1272530 1274010 970030 1062150 2396600 1265480 1332900 TRUE FALSE 2678177.051 1742798.017 1700806.779 1338205.426 1314989.689 989644.6712 1075148.909 2347109.372 1121828.016 1242621.496 2.155263739 1.402517197 1.368724736 1.076921195 1.058238324 0.796416829 0.865226389 1.888836931 0.902791413 1 20.24495549 5.108377302 1.232543255 1.146952154 3.524693089 0.531776518 0.295784607 2.937379639 2.079572926 0.09094632 11.04856879 128344.5118 -5.108377302 2.377740934 FEGNFVHGEK ddPTM_BT-474_Pertuzumab_2h_R1 4 FEGNFVHGEK 10 0 Q8WTS6;D6RJA0;V9GYG1;B5MCZ8 Q8WTS6 SETD7 Histone-lysine N-methyltransferase SETD7 0 ;;; 103.91 0.0027519 1145610000 1756020 1765230 1548910 1838690 1902620 1875240 2001320 2186820 2319630 2324640 FALSE TRUE 1687392.797 1714887.369 1828832.492 1933585.011 1963819.5 1913158.638 2025812.753 2141661.403 2056315.327 2167190.062 0.778608589 0.791295327 0.843872683 0.892208323 0.906159333 0.882783043 0.934764693 0.988220387 0.948839404 1 21.04739425 5.108644051 0.253248216 1.010373027 0.514526086 0.925981113 0.019498494 2.960290629 0.13883493 0.029368587 0.474729189 128423.3666 -5.108644051 -0.495846941 TLLS(ph)PSSIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLLSPSSIK 9 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 TLLS(0.725)PS(0.256)S(0.019)IK 101.48 0.004147 158280000 247550 258200 214290 275390 288100 255470 290620 353790 321450 362640 TRUE FALSE 237875.4723 250836.3888 253016.9699 289602.9109 297366.9981 260635.7784 294176.6945 346484.1129 284960.3436 338078.0698 0.70361107 0.741948122 0.748398055 0.856615488 0.879580856 0.770933704 0.870144268 1.024864207 0.842883254 1 18.36699691 5.110689392 0.199565306 1.023864789 0.362846901 0.661621936 0.059253705 10.01988919 0.327288447 0.133240654 1.698119251 129029.6121 -5.110689392 -0.661017888 FLFVDADQIVR ddPTM_BT-474_Pertuzumab_2h_R1 1 FLFVDADQIVR 11 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 81.594 0.049427 102480000 86316 97081 81088 93025 94900 100550 109850 89189 104960 102320 FALSE TRUE 82942.67529 94312.34493 95742.40539 97826.0314 97952.54469 102583.1899 111194.3772 87347.21598 93045.38083 95389.77526 0.869513269 0.98870497 1.003696729 1.025540013 1.026866291 1.075410751 1.165684444 0.915687407 0.975423001 1 16.54154701 5.111218546 1.307513377 1.026151133 0.64904088 0.364582509 0.061320243 3.740332479 2.924838097 0.017971256 2.376733954 129186.9205 -5.111218546 -0.377110253 (ac)DDDIAALVVDNGSGMCK ddPTM_BT-474_Pertuzumab_2h_R1 24 DDDIAALVVDNGSGMCK 17 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7 C9JTX5;P60709 ACTB "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed" 0 ;;;;;;;;;;;;;;;;;;;;;;; 178.53 9.71E-206 23954137000 7860808 8319840 6716569 7865017 7823200 8129920 8203873 9088158 9316686 9252635 FALSE TRUE 7553598.933 8082566.309 7930402.428 8270931.47 8074840.333 8294312.553 8304274.452 8900484.361 8259094.864 8625945.79 0.875683562 0.937006388 0.919366133 0.958843433 0.936110721 0.961553985 0.962708862 1.031827069 0.957471223 1 23.04025122 5.111695904 0.268934869 1.009387593 0.768388325 0.675237468 0.022996038 6.201395424 0.320428547 0.029887688 0.513232469 129328.9954 -5.111695904 -0.240999267 SSS(ph)VGSSSSYPISPAVSR ddPTM_BT-474_Pertuzumab_2h_R1 9 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 SSS(0.998)VGS(0.002)SSSYPISPAVSR;SSS(0.999)VGS(0.001)SSSYPISPAVSR;SSS(0.989)VGS(0.01)SSSYPISPAVSR;S(0.146)S(0.146)S(0.707)VGSSSSYPISPAVSR;SSS(0.999)VGS(0.001)SSSYPISPAVSR;SSS(0.997)VGS(0.003)SSSYPISPAVSR;SSS(0.999)VGS(0.001)SSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(0.998)VGS(0.002)SSSYPISPAVSR 484.03 1.03E-239 1.00007E+11 7635317 8297528 6666091 8176098 8031312 8330101 8128327 8721862 8400277 8499686 TRUE FALSE 7336920.37 8060890.626 7870801.93 8598067.398 8289646.444 8498541.35 8227803.897 8541752.502 7446712.772 7923994.696 0.925911822 1.017276126 0.993287127 1.085067283 1.046144875 1.072507198 1.038340409 1.077960401 0.939767511 1 22.91779648 5.113460552 1.182184171 1.042287955 0.770981912 0.343943183 0.042690689 3.301595811 2.150892834 0.011501023 1.361363248 129855.5609 -5.113460552 -0.271306043 FFTGDVFGYHGYTFANLGEHEFVEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FFTGDVFGYHGYTFANLGEHEFVEEK 26 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 158.94 1.15E-11 172910000 190160 174320 157640 157630 195620 164540 230840 130940 218460 207110 FALSE TRUE 182728.337 169348.5643 186129.0547 165765.3032 201912.295 167867.1115 233665.089 128236.0432 193661.3367 193082.2552 0.946375609 0.877079896 0.963988402 0.858521685 1.045732011 0.869407245 1.210184171 0.6641524 1.002999144 1 17.55885606 5.113716516 18.05765953 0.930915479 2.696358675 0 0.136132772 4233.155218 705096.5604 0.029749252 15070.90687 129932.1175 -5.113716516 1.765443196 DDFTEER ddPTM_BT-474_Pertuzumab_2h_R1 2 DDFTEER 7 0 P21912 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 ; 113.14 0.014418 376830000 469470 696930 466210 984290 440980 567960 912060 751440 606410 475880 FALSE TRUE 451122.5934 677054.2388 550464.5178 1035089.325 455164.5222 579444.5403 923222.0631 735922.5014 537572.8791 443648.2237 1.016847514 1.526106051 1.240767997 2.333130777 1.025958176 1.306090072 2.080977706 1.658797358 1.211709752 1 18.75905667 5.117682037 1.603806835 1.550243193 0.193871644 0.085319566 0.418812447 6.816740346 7.474160879 0.106221384 19.42274809 131123.954 -5.117682037 -1.356371549 SQDDQHMLPFWTDLCSIFGSNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQDDQHMLPFWTDLCSIFGSNK 22 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;K7EMK2 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ; 216.65 1.33E-25 164556000 299581 329681 286071 309208 333225 348214 323804 328381 402340 379650 FALSE TRUE 287873.0433 320278.8207 337770.3933 325166.2619 343943.4848 355255.1257 327766.8102 321599.8176 356668.0499 353935.9673 0.813347808 0.904906114 0.954326275 0.918714943 0.971767541 1.00372711 0.926062453 0.908638418 1.007719144 1 18.43312885 5.117728609 1.138410578 0.956809717 0.614405281 0.642602429 0.034005911 2.334386466 1.412042019 0.010154595 1.171194643 131138.0161 -5.117728609 -0.342404436 AGCEVTILFADLHAYLDNMK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGCEVTILFADLHAYLDNMK 20 0 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 97.618 0.00069495 94213000 69767 62742 53288 60114 70920 73834 67513 63344 73991 73110 FALSE TRUE 67040.42851 60952.65959 62918.32699 63216.49074 73201.20621 75326.97407 68339.24429 62035.92426 65591.85188 68158.19458 0.983600415 0.894282191 0.923121972 0.927496556 1.073989806 1.105178541 1.002656316 0.91017558 0.962347261 1 16.0565995 5.117913429 18.83895795 0.974578842 2.485917944 0 0.066319602 7101.22514 1127250.919 0.017232891 2980.530059 131193.8356 -5.117913429 1.511339102 VIDGPHSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VIDGPHSGR 9 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ;;; 165.98 6.11E-05 957840000 1886760 2118580 1713560 2046050 2156540 2252770 2081930 2049790 2136450 2226100 FALSE TRUE 1813023.333 2058160.173 2023238.41 2151646.886 2225907.068 2298322.553 2107409.282 2007461.12 1893929.153 2075324.264 0.873609664 0.991729441 0.974902306 1.036776239 1.072558687 1.107452263 1.015460243 0.96729998 0.912594328 1 20.98490534 5.117957119 1.38351739 1.015244021 0.667599084 0.387514483 0.051651008 3.680076374 3.134519993 0.015599107 2.297876501 131207.0344 -5.117957119 -0.347644937 QVEDLQATFSSIHSFQDLSSSILAQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QVEDLQATFSSIHSFQDLSSSILAQSR 27 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 209.89 1.52E-25 230730000 47180 63590 48425 71090 63072 66251 78350 63722 51077 59086 FALSE TRUE 45336.15344 61776.47546 57176.47471 74758.96342 65100.76816 67590.64061 79308.87074 62406.11843 45278.95309 55084.05259 0.823035912 1.121494744 1.037985987 1.357179799 1.181844202 1.227045532 1.439779156 1.132925329 0.821997492 1 15.74934708 5.118237744 1.321857818 1.181791007 0.313858394 0.241191273 0.167957563 4.294869674 3.377161043 0.045953672 6.38351069 131291.8427 -5.118237744 -0.867932613 ALTQPS(ph)PVSTPSSVQFFLQEDDSADR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALTQPSPVSTPSSVQFFLQEDDSADR 26 0 P04920-2;P04920-3;P04920;C9J9M9 P04920-2 SLC4A2 Anion exchange protein 2 1 ALT(0.002)QPS(0.994)PVS(0.004)TPSSVQFFLQEDDSADR;ALTQPS(0.997)PVS(0.003)TPSSVQFFLQEDDSADR 225.72 1.11E-34 118859000 56111 93538 54369 133447 77250 80513 107036 103064 77379 77795 TRUE FALSE 53918.12009 90870.38782 64194.68773 140334.2157 79734.81641 82141.02802 108345.9386 100935.6924 68595.26032 72525.87536 0.743432876 1.252937484 0.885128065 1.934953766 1.099398194 1.132575479 1.493893566 1.39171974 0.945803963 1 16.14620818 5.118731201 1.321206347 1.289012866 1.01E-08 0.185583329 0.298153791 4.918422489 3.860423624 0.077997287 10.85497401 131441.1049 -5.118731201 -1.289012856 TLETVPLER ddPTM_BT-474_Pertuzumab_2h_R1 6 TLETVPLER 9 0 P22626;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 176.09 0.00012428 2407340000 1585540 1781200 1405450 1802440 1749260 1800580 1708360 1825380 1815060 1765640 FALSE TRUE 1523575.344 1730401.92 1659446.079 1895464.144 1805526.537 1836988.961 1729267.421 1787685.265 1609021.998 1646051.63 0.925593898 1.051244012 1.00813732 1.151521684 1.096883295 1.11599717 1.050554788 1.086044467 0.977503967 1 20.65057816 5.120762382 1.373187594 1.071603736 0.713599283 0.365947981 0.052223091 3.177753612 2.656432731 0.013723433 2.031372079 132057.2903 -5.120762382 -0.358004454 GIYAYGFEKPSAIQQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIYAYGFEKPSAIQQR 16 1 P60842;J3KT12;P60842-2;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9;J3QQP0;J3KSN7;J3KT04;J3KS93;Q14240;Q14240-2;E7EQG2;E9PBH4;F8WE11;E7EMV8;P38919;I3L3H2 P60842;Q14240;P38919 EIF4A1;EIF4A2;EIF4A3 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed;Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 237.05 8.68E-20 17231200000 2532500 2876800 2279400 2573800 2467400 2018000 2785800 2674500 2711300 2945500 FALSE TRUE 2433527.1 2794756.481 2691338.285 2706634.126 2546766.162 2058805.343 2819893.454 2619270.64 2403524.591 2745998.661 0.886208407 1.017755952 0.980094536 0.985664765 0.92744625 0.749747395 1.026909988 0.953849933 0.875282506 1 21.38889949 5.122943179 9.580928178 0.945069449 8.48E-05 0.050166437 0.078282814 97646.69233 215797.77 0.018839022 1854795.284 132722.08 -5.122943179 -0.944984625 GAS(ph)PPISAIEEFSIIPEAPMR ddPTM_BT-474_Pertuzumab_2h_R1 10 GASPPISAIEEFSIIPEAPMR 21 0 A0A2R8YF49;C9J591;A0A2R8YFR7;Q12774;A0A5F9ZH52 A0A2R8YF49;A0A2R8YFR7;A0A5F9ZH52 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.5)PPIS(0.5)AIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.973)PPIS(0.027)AIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.988)PPIS(0.012)AIEEFSIIPEAPMR;GAS(0.986)PPIS(0.014)AIEEFSIIPEAPMR;GAS(0.988)PPIS(0.012)AIEEFSIIPEAPMR;GAS(0.999)PPIS(0.001)AIEEFSIIPEAPMR 375.83 1.29E-112 1450598900 265663.2 320026.3 254396.9 333953.7 301279.7 332885.9 314687.5 338701.9 324768.3 321506.4 TRUE FALSE 255280.7884 310899.4633 300372.0789 351189.0905 310970.6352 339617.081 318538.7398 331707.5874 287901.9641 299730.4852 0.851701115 1.037263404 1.002140569 1.171682921 1.037500857 1.133074872 1.062750556 1.106686186 0.960536143 1 18.1933063 5.123212311 1.394999237 1.072535509 0.523591458 0.496173546 0.061737565 2.373718682 2.028699906 0.01546281 2.369922205 132804.3531 -5.123212311 -0.548944051 SLEICHPQER ddPTM_BT-474_Pertuzumab_2h_R1 2 SLEICHPQER 10 0 H7C5Q2;Q9Y305-3;Q9Y305-2;Q9Y305;Q9Y305-4 H7C5Q2 ACOT9 "Acyl-coenzyme A thioesterase 9, mitochondrial" 0 ; 117.14 0.00099771 440570000 230110 374800 217187 533700 223020 288130 444360 383590 303560 280270 FALSE TRUE 221117.0468 364111.071 256437.5222 561244.321 230193.6408 293956.186 449798.2106 375668.7325 269101.1414 261287.0633 0.846260982 1.393528889 0.981439797 2.147998887 0.880998998 1.125031536 1.721471415 1.437762466 1.029906104 1 17.99527617 5.123612437 1.90649034 1.343061612 2.79E-11 0.103767845 0.376539425 7.113022153 10.11481197 0.091967789 24.37159441 132926.7655 -5.123612437 -1.343061612 SYDSLHRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYDSLHRPK 9 1 Q8N8S7 Q8N8S7 ENAH Protein enabled homolog 0 ; 109.29 0.001486 343950000 532490 719910 494660 959570 531510 598470 860330 753240 703270 661030 FALSE TRUE 511679.7021 699378.8717 584056.0657 1009093.523 548606.5019 610571.4734 870858.9759 737685.3308 623437.7379 616257.8493 0.830301314 1.134880266 0.94774625 1.63745342 0.890222335 0.990772733 1.413140582 1.197040057 1.011650787 1 19.23317459 5.12381667 1.426094063 1.164055512 0.335589623 0.140201396 0.220780721 5.916436498 5.244564638 0.05754865 9.129555206 132989.2906 -5.12381667 -0.828465888 AEEDEILNR ddPTM_BT-474_Pertuzumab_2h_R1 3 AEEDEILNR 9 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ;; 209.87 1.79E-05 802890000 819490 1357640 880470 1892070 956970 1078460 1475670 1920410 1523350 1181030 FALSE TRUE 787463.4248 1318921.436 1039590.515 1989719.959 987751.8091 1100267.2 1493729.691 1880752.862 1350425.694 1101037.786 0.71520109 1.197889349 0.944191496 1.807131403 0.897109819 0.999300128 1.356656156 1.708163776 1.226502588 1 20.07043255 5.124770441 1.01199956 1.309579362 7.48E-10 0.206625845 0.298408546 5.608979546 2.72429792 0.092715478 9.566434024 133281.6748 -5.124770441 -1.309579361 S(ph)VAS(ph)NQSEMEFSSLQDMPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVASNQSEMEFSSLQDMPK 19 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 2 S(0.902)VAS(0.578)NQS(0.52)EMEFSSLQDMPK 92.275 0.001026 36833000 58228 53845 49095 53108 49689 52391 47352 60189 60475 58677 TRUE FALSE 55952.38539 52309.39332 57967.55861 55848.91024 51287.29181 53450.38192 47931.50794 58946.07612 53610.13153 54702.75453 1.022844021 0.956247885 1.059682627 1.020952432 0.937563241 0.977105858 0.876217447 1.077570529 0.98002618 1 15.73932586 5.124932587 13.99729358 0.989964798 2.866648451 0.033812021 0.055390992 1058480.821 954474.0727 0.013196532 62394540.32 133331.4453 -5.124932587 1.876683653 GQTTLPFRPVTQEEDDDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQTTLPFRPVTQEEDDDQR 19 1 Q96SB8;Q96SB8-2 Q96SB8 SMC6 Structural maintenance of chromosomes protein 6 0 146.64 1.03E-07 269790000 185640 200720 161130 189680 208110 193050 197560 209760 194230 237660 FALSE TRUE 178384.9836 194995.6621 190249.7753 199469.4075 214804.0472 196953.6033 199977.7984 205428.3827 172181.8247 221563.0765 0.805120539 0.880090966 0.858670941 0.900282713 0.969493882 0.888927913 0.902577277 0.927177876 0.77712328 1 17.75735795 5.125494332 0.938298701 0.907055464 0.680277087 0.22918885 0.05627362 5.778022964 2.452937447 0.016715343 1.579274352 133504.0166 -5.125494332 -0.226778377 HDSPEDVKR ddPTM_BT-474_Pertuzumab_2h_R1 8 HDSPEDVKR 9 1 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;;;;; 157.96 4.37E-05 2162880000 2389146 3491900 2901600 3856060 3526710 4033290 3752520 3813120 3615350 4421450 FALSE TRUE 2295775.533 3392314.431 3425983.666 4055071.719 3640149.83 4114845.887 3798444.462 3734377.739 3204950.625 4121981.253 0.556959237 0.822981528 0.831149745 0.983767628 0.883106838 0.998268947 0.921509398 0.905966697 0.777526735 1 21.97490651 5.125875851 1.190902844 0.919160252 0.046440887 0.731647362 0.065657894 1.674426187 1.081510693 0.017857938 2.254757348 133621.3488 -5.125875851 -0.872719364 TDSVIIADQTPT(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 3 TDSVIIADQTPTPTR 15 0 P17544;K7ELQ4;P17544-2;P17544-1;P17544-3;P17544-4;K7ESA4;P17544-5 P17544 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 TDSVIIADQTPT(1)PTR;TDSVIIADQT(0.026)PT(0.974)PTR;TDSVIIADQT(0.041)PT(0.934)PT(0.025)R 297.56 4.44E-43 967520000 1011870 1041770 983940 1107450 1035940 1218350 1104100 1196020 1391380 1484650 TRUE FALSE 972325.0017 1012059.74 1161759.846 1164605.627 1069261.951 1242985.872 1117612.306 1171321.769 1233436.376 1384093.333 0.702499592 0.731207727 0.839365249 0.841421311 0.772536017 0.898050617 0.807468889 0.846273688 0.891151157 1 20.4005098 5.125996101 0.042589549 1.47589306 1.00E-13 0.753195269 0.040812661 193.0223785 1.145340015 13.81962199 27.70210127 133658.3517 -5.125996101 -1.47589306 ALAPEYAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALAPEYAK 8 0 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 85.212 0.039324 102580000 295160 328190 281600 287250 288040 221400 314310 297130 326500 351330 FALSE TRUE 283624.8209 318830.3425 332491.3842 302075.0069 297305.0682 225876.8597 318156.6198 290994.1617 289437.0888 327534.1062 0.865939808 0.97342639 1.01513515 0.922270387 0.907707205 0.689628516 0.971369435 0.888439268 0.883685343 1 18.32128562 5.126371839 10.13581303 0.911317113 5.66E-05 0.026128768 0.087562814 226686.1419 426245.3874 0.021063966 4473716.746 133774.0386 -5.126371839 -0.911260465 SGVSS(ph)DNEDDDDEEDGNYLHPSLFASK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 S(0.001)GVS(0.025)S(0.974)DNEDDDDEEDGNYLHPSLFASK;SGVS(0.186)S(0.814)DNEDDDDEEDGNYLHPSLFASK;S(0.001)GVS(0.023)S(0.976)DNEDDDDEEDGNYLHPSLFASK 296 7.67E-71 2224950000 1053780 1435690 1130240 1610380 1333860 1510480 1445480 1484210 1475570 1837650 TRUE FALSE 1012597.113 1394745.527 1334499.51 1693491.905 1376764.818 1541022.941 1463170.217 1453560.545 1308069.48 1713184.329 0.591061391 0.814124612 0.778958509 0.988505368 0.803629122 0.89950796 0.854064675 0.848455429 0.763531079 1 20.70824895 5.126532954 1.326419427 0.86596513 0.187119047 0.557417804 0.074278783 2.331769027 1.81475267 0.018795629 2.736049986 133823.6757 -5.126532954 -0.678846083 APVPTGEVYFADSFDR ddPTM_BT-474_Pertuzumab_2h_R1 1 APVPTGEVYFADSFDR 16 0 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8;D6RHJ3;D6RD16 P27824 CANX Calnexin 0 107.53 0.0026075 144200000 21172 34816 22339 36452 32299 26793 35495 39288 31460 30170 FALSE TRUE 20344.57483 33823.08177 26376.15423 38333.29209 33337.92667 27334.77282 35929.39843 38476.68907 27888.79269 28126.55903 0.723322565 1.202531804 0.937766835 1.362885949 1.185282801 0.971849162 1.277418912 1.367984226 0.991546554 1 14.77964545 5.12793899 1.722761207 1.174465517 1.42E-15 0.36568898 0.158596047 3.370602918 4.045299995 0.040807116 9.06893436 134257.6342 -5.12793899 -1.174465517 TDSEKPFR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDSEKPFR 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 106.68 0.0037833 3838490000 3382480 3792490 3019950 3889470 3394860 3659000 3808280 3833990 4014110 4056930 FALSE TRUE 3250288.942 3684331.898 3565722.143 4090206.013 3504058.755 3732987.487 3854886.87 3754816.767 3558445.061 3782150.518 0.859375883 0.974136773 0.942776372 1.081449824 0.926472582 0.987001302 1.01923148 0.992772961 0.940852313 1 21.85077535 5.128328236 1.47656113 0.989913498 0.656984329 0.445335765 0.042284067 2.8298997 2.634927619 0.010664083 1.827360549 134378.0196 -5.128328236 -0.332929169 (ac)VDYSVWDHIEVSDDEDETHPNIDTASLFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDYSVWDHIEVSDDEDETHPNIDTASLFR 29 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 78.45 5.34E-08 74270000 12954.2 17116.9 16192.1 16365.4 18587.5 18554.6 20640 19130.9 20315 19219.4 FALSE TRUE 12447.93554 16628.74277 19118.37266 17210.02026 19185.38382 18929.78672 20892.59849 18735.84023 18008.92637 17917.65292 0.694730253 0.928064789 1.067013227 0.960506397 1.070753179 1.05648808 1.166034334 1.045663755 1.005094052 1 14.12909405 5.130215651 1.164033922 1.058118518 0.167601759 0.800465429 0.053283381 1.414365657 0.871212158 0.015207256 1.902544417 134963.2883 -5.130215651 -0.89051676 LLGWDDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLGWDDR 7 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ;;; 195.98 0.0010592 833190000 1526920 2411860 1655680 2984090 1866720 1905490 2421150 2920340 2342450 2136510 FALSE TRUE 1467246.278 2343076.114 1954898.206 3138099.243 1926764.744 1944020.313 2450780.758 2860033.958 2076544.896 1991802.275 0.736642536 1.176359794 0.981472022 1.57550741 0.967347396 0.97601069 1.230433758 1.435902547 1.0425457 1 20.92564301 5.132178965 1.636733711 1.187740668 1.48E-11 0.262126279 0.201934607 4.268439157 4.667725227 0.052980616 11.02448608 135574.7976 -5.132178965 -1.187740668 INFDDNAEFR ddPTM_BT-474_Pertuzumab_2h_R1 2 INFDDNAEFR 10 0 E9PDQ8;Q96I99;Q96I99-2 E9PDQ8 SUCLG2 "Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial" 0 ; 235.01 9.74E-12 362330000 341390 548790 335000 756680 365780 436910 638110 610420 439850 379210 FALSE TRUE 328048.1014 533139.0465 395541.952 795732.3455 377545.6459 445744.6196 645919.3811 597814.6137 389920.072 353525.7689 0.927932644 1.508062759 1.118848997 2.250846799 1.06794378 1.260854678 1.82707864 1.69100718 1.102946677 1 18.43145585 5.133108202 1.72281983 1.484100253 1.16E-09 0.110264777 0.386215295 6.482667311 7.673586485 0.096081637 22.14823084 135865.1904 -5.133108202 -1.484100252 MVEGFFDR ddPTM_BT-474_Pertuzumab_2h_R1 5 MVEGFFDR 8 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;;; 107.66 0.0092114 1122550000 923940 1363230 927143 1810380 1035430 1040600 1707350 1375230 1184300 1184300 FALSE TRUE 887831.4033 1324352.015 1094698.364 1903813.929 1068735.546 1061641.645 1728245.06 1346831.02 1049863.229 1104086.306 0.804132248 1.199500445 0.991497094 1.724334337 0.967981887 0.961556754 1.565316996 1.21986027 0.950888733 1 20.07442152 5.133157259 1.681718184 1.206692682 0.12780703 0.145833487 0.258761402 5.955663255 6.784813798 0.065430649 14.40539253 135880.5383 -5.133157259 -1.078885652 GATLSHYNIVNNSNILGER ddPTM_BT-474_Pertuzumab_2h_R1 2 GATLSHYNIVNNSNILGER 19 0 E9PF16;Q96CM8-3;Q96CM8;Q96CM8-2;Q96CM8-4 E9PF16 ACSF2 "Acyl-CoA synthetase family member 2, mitochondrial" 0 ; 153.25 4.76E-08 986930000 630580 696210 557790 789510 665060 676300 782920 837660 883290 729710 FALSE TRUE 605936.2365 676354.7725 658595.061 830256.7057 686452.2589 689975.2494 792501.6092 820362.0283 783022.6223 680286.0917 0.890707959 0.994221079 0.96811484 1.220452271 1.009064079 1.014242769 1.16495342 1.205907394 1.151019596 1 19.37578207 5.13421455 0.555464567 1.13265105 0.610687932 0.397788991 0.083586137 5.587671437 0.954789629 0.043557466 2.06753091 136211.7428 -5.13421455 -0.521963118 LALPGHAESYNPPPEYLLSEEER ddPTM_BT-474_Pertuzumab_2h_R1 3 LALPGHAESYNPPPEYLLSEEER 23 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ;; 234.51 4.53E-37 897540000 241424 276322 223990 269372 275957 303019 273742 265828 283609 291655 FALSE TRUE 231988.8832 268441.5671 264469.9756 283274.3212 284833.4075 309146.2518 277092.1365 260338.5589 251414.8953 271900.9471 0.853211016 0.987277058 0.9726703 1.041829108 1.047563131 1.136981151 1.019092208 0.957475734 0.924656196 1 18.05272165 5.139003595 1.342908828 1.016595914 0.602187712 0.433724555 0.054644076 3.583288672 2.778540494 0.016606563 2.623138588 137722.0869 -5.139003595 -0.414408202 EVS(ph)PPGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSPPGAR 8 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 EVS(1)PPGAR 61.161 0.092011 338510000 119780 156490 129210 158660 167220 178320 150440 173060 148180 187200 TRUE FALSE 115098.8652 152027.0584 152561.1213 166848.4616 172598.7832 181925.7526 152281.1297 169486.2505 131359.2276 174520.7773 0.659513824 0.871111514 0.874171681 0.95603781 0.988987018 1.042430337 0.872567336 0.971152279 0.752685323 1 17.41303928 5.139216208 1.208314528 0.940668144 0.24661779 0.532090606 0.077445943 2.638314249 1.706898111 0.02115501 2.892268926 137789.5266 -5.139216208 -0.694050354 IDRPEAISEER ddPTM_BT-474_Pertuzumab_2h_R1 2 IDRPEAISEER 11 1 Q9Y6B6;D6RD69;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ; 174.89 9.55E-06 1873260000 1470500 1600250 1380220 1546230 1676360 1714410 1702370 1783190 1825880 1885240 FALSE TRUE 1413031.234 1554612.437 1629656.457 1626031.116 1730281.642 1749076.545 1723204.113 1746366.503 1618613.757 1757551.016 0.803977365 0.884533321 0.927231382 0.925168659 0.984484448 0.99517825 0.980457522 0.993636309 0.920948378 1 20.74513514 5.139383774 0.660432541 0.981694066 0.590382806 0.839828386 0.023824517 1.82423606 0.414490782 0.009707893 0.603895017 137842.701 -5.139383774 -0.391311259 LSSSDRYS(ph)DASDDS(ph)FSEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 2 LS(0.001)S(0.001)S(0.002)DRYS(0.994)DAS(0.003)DDS(0.998)FS(0.002)EPR;LSSS(0.001)DRY(0.002)S(0.995)DAS(0.03)DDS(0.942)FS(0.029)EPR 191.44 1.15E-13 1203580000 603270 697730 590620 734320 683600 774440 786470 751500 814460 828000 TRUE FALSE 579693.5414 677831.4235 697358.1723 772218.3432 705588.6148 790099.7074 796095.0551 735981.2624 722005.9153 771918.8225 0.750977337 0.878112314 0.90340869 1.000388021 0.914071006 1.023552846 1.031319657 0.953443861 0.935339176 1 19.55808961 5.13984485 0.810122562 0.982391751 0.455932902 0.787099913 0.037008384 1.915875592 0.617634328 0.012774181 1.051696718 137989.1216 -5.13984485 -0.526458849 DKVVHADNAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKVVHADNAR 10 1 O60231;Q5SQH5;A0A140T8Y5 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 0 97.214 0.003732 56621000 87329 94048 72223 79870 81803 68088 84400 86443 96266 97197 FALSE TRUE 83916.08613 91365.84312 85275.30269 83992.10027 84434.26779 69464.78601 85432.91245 84657.92184 85338.28726 90613.76062 0.926085459 1.008299871 0.941085571 0.92692434 0.931804035 0.766603058 0.942824929 0.934272248 0.94178066 1 16.46744253 5.14138512 18.08615654 0.928652858 0.000618784 0 0.061859885 17146.96132 2138706.457 0.014542124 16496.55242 138479.383 -5.14138512 -0.928034074 S(ph)CHDLDLLGQSPGWGQTQAVETNIVCK ddPTM_BT-474_Pertuzumab_2h_R1 2 SCHDLDLLGQSPGWGQTQAVETNIVCK 27 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 S(1)CHDLDLLGQSPGWGQTQAVETNIVCK;S(1)CHDLDLLGQSPGWGQTQAVETNIVCK 329.21 2.29E-95 719330000 646450 452630 271940 392000 287520 271490 291230 406340 352730 279340 TRUE FALSE 621186.0193 439721.4356 321085.6073 412231.167 296768.3419 276979.7138 294794.1599 397948.937 312689.5692 260420.053 2.385323297 1.688508356 1.232952699 1.582947097 1.139575615 1.063588271 1.131994854 1.528104047 1.200712332 1 17.99048102 5.143448059 1.091876593 1.24242588 4.061769022 0.800580012 0.177742038 1.620953356 0.873884114 0.053302754 6.504587021 139138.7376 -5.143448059 2.819343142 up CPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR ddPTM_BT-474_Pertuzumab_2h_R1 5 CPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR 37 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;; 326.8 3.48E-129 2738110000 396493 459123 355030 456348 501015 485962 479434 316018 617048 470838 FALSE TRUE 380997.6152 446029.2616 419191.8186 479900.175 517130.6025 495788.4846 485301.4567 309492.1179 547003.2979 438947.7229 0.867979478 1.016132989 0.954992581 1.093296878 1.17811433 1.129493237 1.105601946 0.705077397 1.246169576 1 18.7436896 5.14510191 1.332497646 1.036918832 0.608612097 0.128069836 0.140634547 8.873563781 6.708244453 0.041473085 6.686409186 139669.6068 -5.14510191 -0.428306735 DDNMFQIGKMR ddPTM_BT-474_Pertuzumab_2h_R1 4 DDNMFQIGKMR 11 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;;; 148.18 3.19E-05 1178180000 4069820 3519120 3035420 2362600 2445820 2897620 1963990 2039880 2683340 1902770 FALSE TRUE 3910766.935 3418758.143 3583987.917 2484534.069 2524492.022 2956211.862 1988025.897 1997755.765 2378738.493 1773893.693 2.204623056 1.927262133 2.020407384 1.400610464 1.423136026 1.66651016 1.120713098 1.126198133 1.340970151 1 20.75848812 5.145369551 0.293056985 1.011919189 3.523669921 0.83050558 0.161925693 3.833175866 0.225122191 0.186101144 3.612483012 139755.7067 -5.145369551 2.511750732 up GDIDHVK ddPTM_BT-474_Pertuzumab_2h_R1 5 GDIDHVK 7 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ;;;; 128.57 0.0037452 1933800000 1945570 3146170 1950220 4436100 2241000 2738760 4496220 3621460 3065740 2784320 FALSE TRUE 1869534.973 3056444.312 2302668.136 4665047.653 2313083.8 2794139.604 4551246.085 3546675.585 2717730.048 2595735.526 0.720233227 1.177486797 0.887096591 1.797196827 0.891109197 1.076434627 1.753355085 1.366347052 1.046998055 1 21.30771197 5.146091987 0.953911798 1.292595171 1.61E-09 0.187731902 0.310267464 6.124005866 2.601241803 0.09448207 9.797740439 139988.3798 -5.146091987 -1.292595169 SLS(ph)LESTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSLESTDR 9 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 SLS(1)LESTDR;SLS(0.984)LES(0.016)TDR 150.15 9.01E-05 307290000 442770 531160 453250 579900 534450 557890 590970 578050 652710 682010 TRUE FALSE 425466.0589 516011.8369 535162.3575 609828.7085 551641.0696 569170.918 598202.4676 566113.0655 578617.0972 635816.8552 0.669164486 0.81157307 0.841692624 0.959126364 0.867610012 0.895180606 0.940840845 0.890371277 0.910037368 1 19.27825174 5.146651137 0.890168281 0.917596422 0.334552701 0.806590083 0.038424366 1.637431015 0.616385862 0.01157316 1.100097491 140168.7294 -5.146651137 -0.583043721 DLPVTEAVFSALVTGHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLPVTEAVFSALVTGHAR 18 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 197.29 1.86E-15 386070000 173425 284590 168686 397470 200748 244002 364030 317890 273600 229088 FALSE TRUE 166647.3593 276473.7718 199171.3126 417983.4743 207205.2417 248935.8876 368485.108 311325.4604 242542.075 213571.6657 0.780287772 1.294524585 0.932573672 1.957111085 0.97019069 1.165584802 1.725346416 1.457709567 1.135647251 1 17.70436073 5.149279503 1.129896284 1.355388762 2.82E-15 0.174757404 0.321539378 5.812175026 3.292470163 0.08915705 11.66175137 141019.608 -5.149279503 -1.355388762 LDELEELLTNNR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDELEELLTNNR 12 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ;;; 198.62 4.21E-07 59850700 66156 103178 66482 139846 76484 88035 123246 104702 90436 82459 FALSE TRUE 63570.55038 100235.4645 78496.77628 147063.4688 78944.17732 89815.12802 124754.3214 102539.8671 80170.08442 76873.97848 0.826944977 1.303893287 1.021109845 1.913046153 1.026929774 1.168342393 1.622842006 1.333869654 1.042876745 1 16.23020771 5.149281732 1.598037174 1.309697932 7.38E-15 0.165158837 0.285448999 5.6534878 5.701515152 0.07144567 15.91834676 141020.3318 -5.149281732 -1.309697932 IACEEEFS(ph)DS(ph)EEEGEGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 IACEEEFSDSEEEGEGGR 18 0 Q13547 Q13547 HDAC1 Histone deacetylase 1 2 IACEEEFS(1)DS(1)EEEGEGGR 158.45 6.65E-11 183410000 396060 456690 349760 485810 437930 443140 442010 450190 484660 464530 TRUE FALSE 380581.5373 443665.6483 412969.4124 510882.7123 452016.4162 452100.5944 447419.4506 440893.4192 429643.4287 433066.9693 0.878805276 1.024473534 0.953592496 1.179685242 1.043756389 1.043950766 1.033141482 1.018072147 0.992094662 1 18.72423061 5.151870059 1.426070863 1.039258669 0.616688056 0.406030218 0.055710736 3.414486982 2.849225714 0.014779864 2.744418711 141863.3002 -5.151870059 -0.422570612 GPGAPGLAHLQESQAGS(ph)DTDVEEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 GPGAPGLAHLQESQAGSDTDVEEGK 25 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 GPGAPGLAHLQESQAGS(0.999)DT(0.001)DVEEGK;GPGAPGLAHLQESQAGS(0.848)DT(0.152)DVEEGK;GPGAPGLAHLQESQAGS(0.999)DT(0.001)DVEEGK 330.25 5.02E-88 1262120000 518480 472860 596580 735990 667440 657360 815150 854330 1023720 963460 TRUE FALSE 498217.2284 459374.4958 704395.2769 773974.5321 688908.8138 670652.2696 825126.0495 836687.7869 907511.5974 898203.996 0.554681599 0.511436709 0.78422639 0.861691259 0.766984802 0.746659192 0.918639923 0.931511985 1.010362458 1 19.77668362 5.152944583 0.281653584 1.016406371 6.85E-15 0.808964793 0.071327763 4.674667518 0.256094337 0.091390574 1.714458889 142214.7305 -5.152944583 -1.016406371 GVDLLLEGVQGES(ph)SPTRR ddPTM_BT-474_Pertuzumab_2h_R1 1 GVDLLLEGVQGESSPTRR 18 1 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 GVDLLLEGVQGES(0.491)S(0.491)PT(0.018)RR 109.05 0.00022889 79800000 37774 48942 39852 48142 54290 56336 52056 45307 50226 54033 TRUE FALSE 36297.75032 47546.22208 47054.1429 50626.61439 56036.28715 57475.15252 52693.0769 44371.39462 44524.55504 50373.29678 0.720575238 0.943877513 0.934108861 1.005028807 1.112420483 1.140984533 1.046051783 0.880851512 0.88389202 1 15.62037153 5.154385902 1.249028736 1.005076457 0.278657811 0.523582546 0.080751529 3.345481826 2.227608159 0.026107564 4.014285377 142687.4913 -5.154385902 -0.726418646 NLGSINT(ph)ELQDVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NLGSINTELQDVQR 14 0 O75396;A0A087X1A9 O75396 SEC22B Vesicle-trafficking protein SEC22b 1 NLGS(0.013)INT(0.987)ELQDVQR 250.08 3.24E-17 185100000 237720 318640 245460 344100 327820 261290 268750 383590 362070 313960 TRUE FALSE 228429.6396 309552.6992 289820.0822 361859.0422 338364.628 266573.4628 272039.0429 375668.7325 320969.3315 292695.2096 0.780435184 1.057594006 0.990177061 1.236299845 1.156030632 0.910754444 0.929427726 1.283480973 1.096599196 1 18.15903961 5.154617958 1.482241931 1.092293214 0.249814421 0.352113581 0.118027156 3.990324101 3.524040961 0.033208793 6.683298443 142763.7534 -5.154617958 -0.842478793 DDLLGFALR ddPTM_BT-474_Pertuzumab_2h_R1 3 DDLLGFALR 9 0 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 ;; 122.18 0.0013797 102477000 260682 233296 190150 219815 207928 159782 227758 225514 243131 257969 FALSE TRUE 250494.2592 226642.6265 224514.3349 231159.6785 214616.193 163012.9015 230545.3705 220857.0571 215531.7882 240496.5299 1.0415712 0.942394581 0.933545008 0.961176773 0.892387899 0.677818102 0.958622441 0.918337812 0.896195002 1 17.87565655 5.155027037 0.847602593 0.892209935 1.229792969 0.209908227 0.081943638 6.866300712 2.349894614 0.027819216 2.54766958 142898.2918 -5.155027037 0.337583033 KPLVIIAEDVDGEALSTLVLNR ddPTM_BT-474_Pertuzumab_2h_R1 3 KPLVIIAEDVDGEALSTLVLNR 22 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 194.62 4.78E-18 1242748700 435826 665217 455823 835768 463107.9 559156.4 822060 723818 558267.9 490783.7 FALSE TRUE 418793.4381 646245.6625 538200.3558 878902.0866 478004.1862 570462.9255 832120.6162 708870.9054 494895.6684 457542.4829 0.915310499 1.412427669 1.176284992 1.920919083 1.044720882 1.246797722 1.818673997 1.549300736 1.081638726 1 18.80354618 5.155161343 1.706762461 1.412129254 6.48E-09 0.138881113 0.307150355 6.235443544 6.856347506 0.077469538 20.47482426 142942.49 -5.155161343 -1.412129247 KLYESLLVGS(ph)LPDMNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLYESLLVGSLPDMNK 16 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 KLYESLLVGS(1)LPDMNK 75.797 0.017453 260100000 253960 219850 186830 200600 247330 231620 220430 259150 229920 227060 TRUE FALSE 244034.9624 213580.0933 220594.337 210952.99 255285.5941 236303.5151 223127.6883 253798.4619 203820.4455 211681.024 1.152842885 1.008971372 1.042107284 0.996560703 1.205991871 1.11631884 1.054075061 1.198966526 0.962865928 1 17.69153242 5.155540245 8.262921427 1.07938365 2.56953145 0.072211087 0.080882729 24371.97601 36653.95933 0.019228522 638324.7666 143067.2551 -5.155540245 1.4901478 FCLEGMEESGSEGLDELIFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 FCLEGMEESGSEGLDELIFAR 21 0 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 103.17 0.00044435 7494400 8624.8 11056 8603.1 11997 11168 10822 9435.2 12424 11701 13767 FALSE TRUE 8287.733281 10740.6937 10157.87154 12616.16661 11527.22886 11040.82825 9550.6708 12167.44006 10372.75153 12834.54883 0.645736238 0.83685791 0.791447497 0.982984815 0.898140559 0.860242803 0.744137634 0.948022421 0.808189807 1 13.64774496 5.15581392 1.269274992 0.88005388 0.279096123 0.452295654 0.077785133 3.233314133 2.20596357 0.020621528 3.268421518 143157.4388 -5.15581392 -0.600957756 HQQQLLAS(ph)PGSSTVDNK ddPTM_BT-474_Pertuzumab_2h_R1 3 HQQQLLASPGSSTVDNK 17 0 F2Z2X4;Q9C0E2 F2Z2X4 XPO4 Exportin-4 1 HQQQLLAS(1)PGSSTVDNK;HQQQLLAS(1)PGSSTVDNK;HQQQLLAS(1)PGSSTVDNK 232.02 1.81E-16 1155400000 980600 951040 779970 873820 952760 993990 998460 774350 1132980 1104880 TRUE FALSE 942277.0679 923917.2704 920927.9293 918917.9549 983406.3907 1014089.159 1010679.452 758359.4019 1004368.86 1030045.493 0.9147917 0.896967441 0.894065296 0.892113951 0.954721318 0.984509097 0.981198849 0.736238745 0.975072331 1 19.97427663 5.156673455 16.07808874 0.910950706 2.188754943 0 0.074607376 25149107.52 4682617.911 0.01867197 1188245500 143441.0499 -5.156673455 1.277804237 MGGEEAEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 MGGEEAEIR 9 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 128.38 0.00097451 1348390000 1974990 2181520 1795430 2088740 2096310 2131040 2223590 2170630 2321700 2369000 FALSE TRUE 1897805.207 2119305.186 2119904.14 2196540.122 2163739.715 2174131.089 2250802.96 2125805.732 2058150.349 2208545.52 0.859300925 0.959593165 0.959864364 0.994564116 0.979712528 0.984417604 1.019133606 0.962536526 0.93190307 1 21.07466514 5.15808116 1.400414077 0.980745582 0.655358299 0.714963852 0.022620882 1.888448057 1.509393215 0.006167403 1.151223832 143906.7484 -5.15808116 -0.325387283 ALESPERPFLAILGGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 138.39 3.48E-06 4535300000 168650 202660 107700 142890 152890 141390 143940 127510 137540 125760 FALSE TRUE 162058.9715 196880.3352 127163.7858 150264.57 157807.8457 144249.0027 145701.5808 124876.8739 121927.0358 117242.1632 1.382258457 1.67926222 1.084625039 1.281659822 1.345999096 1.230350914 1.242740468 1.065119156 1.039958941 1 16.83913197 5.161215522 0.185600669 0.926479168 2.072756315 0.530639896 0.133263777 14.57712144 0.42330292 0.330294684 4.00667332 144949.0998 -5.161215522 1.146277147 RVS(ph)TDLPEGQDVYTAACNSVIHR ddPTM_BT-474_Pertuzumab_2h_R1 4 RVSTDLPEGQDVYTAACNSVIHR 23 1 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RVS(0.961)T(0.039)DLPEGQDVYTAACNSVIHR;RVS(0.981)T(0.019)DLPEGQDVYTAACNSVIHR;RVS(0.919)T(0.081)DLPEGQDVYTAACNSVIHR;RVS(0.5)T(0.5)DLPEGQDVYTAACNSVIHR 298.39 5.51E-62 2963620000 480129 624150 499715 645550 616349 666842 647980 574210 658850 772540 TRUE FALSE 461365.0279 606349.8531 590024.6166 678866.9129 636174.4253 680326.0021 655910.1731 562352.3628 584060.1101 720215.1777 0.640593315 0.841900965 0.8192338 0.942589012 0.883311606 0.94461492 0.910714177 0.780811597 0.810952238 1 19.45806848 5.162582044 1.380935885 0.88088657 0.236072437 0.569519024 0.064096765 2.834377873 2.193290731 0.01809068 3.3833242 145405.905 -5.162582044 -0.644814133 ETHKPLGDWSYAYMQ ddPTM_BT-474_Pertuzumab_2h_R1 3 ETHKPLGDWSYAYMQ 15 1 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ;; 143.38 4.03E-06 1075800000 1202430 1769190 1184450 2315550 1208530 1210450 2373500 1736960 1605060 1389210 FALSE TRUE 1155437.706 1718734.433 1398506.463 2435055.813 1247403.465 1234926.128 2402547.603 1701091.169 1422860.318 1295117.569 0.892148893 1.327087574 1.079829736 1.880181283 0.963158477 0.953524342 1.855080697 1.313464669 1.098634094 1 20.30465164 5.163125125 1.809931246 1.309955763 0.062519509 0.098534636 0.326694077 8.391604384 9.835467841 0.081956156 26.2142565 145587.8475 -5.163125125 -1.247436254 AVLSPGSVFS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVLSPGSVFSPGR 13 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 AVLSPGS(0.002)VFS(0.998)PGR 118.24 0.00046488 46487000 38147 42990 33747 44197 39536 45096 40126 44739 41974 43003 TRUE FALSE 36656.17307 41763.96729 39845.8336 46478.01247 40807.71135 46007.87202 40617.07399 43815.12402 37209.28749 40090.36851 0.914338641 1.041745657 0.993900408 1.159331136 1.017893147 1.147604119 1.013137956 1.092908987 0.928135332 1 15.29096806 5.163273538 1.462142171 1.055207512 0.670474152 0.233730125 0.068386797 4.596658236 3.894590169 0.016859613 3.48689591 145637.6083 -5.163273538 -0.38473336 GITINAAHVEYSTAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 GITINAAHVEYSTAAR 16 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 157.54 5.69E-08 155860000 81313 123770 80670 167200 84472 100170 152240 125030 114630 91437 FALSE TRUE 78135.19806 120240.2008 95248.86349 175829.212 87189.1186 102195.506 154103.1587 122448.0868 101617.683 85243.89055 0.916607602 1.410543325 1.117368798 2.062660572 1.02281956 1.198860181 1.807791241 1.436444137 1.192081712 1 16.37930882 5.163476589 1.686240278 1.403733211 1.46E-11 0.127511665 0.328477015 6.874292044 7.259379801 0.08168377 22.30345618 145705.7159 -5.163476589 -1.403733211 GYSYDDIPDFDD ddPTM_BT-474_Pertuzumab_2h_R1 2 GYSYDDIPDFDD 12 0 Q96A57;Q96A57-2 Q96A57 TMEM230 Transmembrane protein 230 0 ; 98.048 0.010651 123648000 707810 1133190 712200 1297790 855260 1004040 1071610 1307280 1138580 965580 FALSE TRUE 680148.0027 1100872.531 840910.3828 1364769.097 882770.2146 1024342.377 1084724.684 1280284.211 1009333.172 900180.4066 0.755568548 1.222946559 0.934157616 1.516106202 0.980659219 1.137930096 1.205008103 1.422252919 1.121256544 1 19.77985464 5.165176952 1.533299082 1.202386815 2.31E-16 0.302633282 0.180395438 4.193328138 3.812978448 0.046005803 10.49278923 146277.3056 -5.165176952 -1.202386815 DGNGYISAAELR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGNGYISAAELR 12 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;; 212.27 5.16E-08 2165040000 953420 1044050 902900 2137360 1276990 741000 1455550 1599860 1907180 2021120 FALSE TRUE 916159.2923 1014274.716 1066074.115 2247669.406 1318065.543 755983.5277 1473363.456 1566822.332 1690684.922 1884227.742 0.486225349 0.538297305 0.565788355 1.192886271 0.699525601 0.401216642 0.781945528 0.831546154 0.897282682 1 20.84554192 5.165730042 0.121521732 1.108499494 1.23E-13 0.275269512 0.201354181 68.06987241 1.184240138 1.92636654 12.61655998 146463.7138 -5.165730042 -1.108499494 SLDTITLS(ph)GDERDFGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDTITLSGDERDFGR 16 1 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 SLDT(0.001)IT(0.007)LS(0.992)GDERDFGR 116.6 0.00025121 120350000 36981 61409 40042 65289 61997 70900 66688 64015 55798 52815 TRUE FALSE 35535.74164 59657.67545 47278.48013 68658.57311 63991.18981 72333.64658 67504.14769 62693.06788 49464.04496 49237.79301 0.721716784 1.21162367 0.960207134 1.394428323 1.299635623 1.469067604 1.370982401 1.273271283 1.004595087 1 15.58747848 5.165914649 1.037687101 1.273323455 5.08E-11 0.418658968 0.172293898 3.590731302 1.712430891 0.049995129 6.242236696 146525.9847 -5.165914649 -1.273323455 ENTEGEYSGIEHVIVDGVVQSIK ddPTM_BT-474_Pertuzumab_2h_R1 2 ENTEGEYSGIEHVIVDGVVQSIK 23 0 H0YL72;P50213;P50213-2;H0YLI6;H0YMU3 H0YL72 IDH3A "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial" 0 ; 177.41 5.47E-17 134881000 103631 159511 111435 215450 107741 133647 217040 184797 167259 150179 FALSE TRUE 99580.98595 154961.9025 131573.7834 226569.4003 111206.5871 136349.4339 219696.2004 180980.8774 148272.4595 140007.2426 0.711255962 1.106813473 0.939764122 1.618269142 0.794291674 0.973874147 1.569177397 1.29265368 1.05903421 1 17.09514193 5.167061378 1.11279581 1.198855946 3.92E-09 0.207720962 0.255399766 5.79017993 3.10288779 0.073891169 10.21353025 146913.3894 -5.167061378 -1.198855942 FEDLEVSTFER ddPTM_BT-474_Pertuzumab_2h_R1 2 FEDLEVSTFER 11 0 K7ERC8;Q06136 K7ERC8 KDSR 3-ketodihydrosphingosine reductase 0 ; 223.87 1.54E-11 128406000 124238 197476 119622 237680 147094 160060 185795 233870 197537 153936 FALSE TRUE 119382.6416 191844.1778 141240.3564 249946.6933 151825.4121 163296.5229 188068.8148 229040.5028 175113.4279 143509.7776 0.831878103 1.33680214 0.984186295 1.741670132 1.057944724 1.137877332 1.310494782 1.595992319 1.220219492 1 17.13078951 5.170239278 1.575281288 1.304608088 4.99E-16 0.204658292 0.239792568 5.447561725 5.101530455 0.061678558 15.30605679 147992.354 -5.170239278 -1.304608088 ERAS(ph)LDK ddPTM_BT-474_Pertuzumab_2h_R1 4 ERASLDK 7 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 1 ERAS(1)LDK;ERAS(1)LDK;ERAS(1)LDK;ERAS(1)LDK 102.52 0.005197 6155700000 5329510 4497770 3804280 3801380 3914400 3730930 3845900 5084150 4847530 4164930 TRUE FALSE 5121226.857 4369498.003 4491798.022 3997569.677 4040310.231 3806371.961 3892967.275 4979160.526 4297258.717 3882835.581 1.318939922 1.125336861 1.156834465 1.029549048 1.04055661 0.980307273 1.002609354 1.282351627 1.106732085 1 21.88867919 5.170407757 1.289484066 1.082664766 1.709305806 0.42454431 0.085564419 4.290667439 2.921711958 0.02660118 4.644953899 148049.7768 -5.170407757 0.626641039 ELVSSSSSGSDS(ph)DSEVDKK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELVSSSSSGSDSDSEVDKK 19 1 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 ELVSSSSSGS(0.001)DS(0.999)DSEVDKK;ELVSSSSSGSDS(1)DSEVDKK 300.56 4.03E-50 571200000 455640 298640 281370 166351 252460 217741 220968 314950 359080 238270 TRUE FALSE 437833.0851 290123.0796 332219.818 174936.395 260580.6052 222143.8722 223672.2725 308446.1724 318318.7438 222131.7607 1.971051252 1.306085536 1.495598005 0.787534365 1.173090261 1.000054524 1.006935126 1.388573032 1.433017696 1 17.76105616 5.172020765 1.205431243 1.149143577 3.276449346 0.583893545 0.207980204 2.776295395 1.686399176 0.059831343 9.495261745 148600.6691 -5.172020765 2.127305769 GLLGDATEEFIESLDSTTDEEEDEEEVYK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLLGDATEEFIESLDSTTDEEEDEEEVYK 29 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;X6R960 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 114.9 6.91E-11 0 58333 60137 51101 52240 65219 63619 66259 67556 74705 78482 FALSE TRUE 56053.28187 58421.95164 60336.08744 54936.11266 67316.82837 64905.41977 67069.89746 66160.94499 66224.80159 73166.34424 0.766107456 0.798481218 0.824642642 0.750838562 0.920051823 0.887093929 0.916676898 0.904253803 0.905126562 1 16.15889256 5.173409679 0.151182681 1.035997871 0.476096933 0.774051574 0.035690817 12.9733248 0.289419295 0.157447016 1.44860866 149076.6685 -5.173409679 -0.559900939 PLMPY(ph)MRYS(ph)RK ddPTM_BT-474_Pertuzumab_2h_R1 1 PLMPYMRYSRK 11 2 Q969G3;Q969G3-4;Q969G3-2;B4DGM3;Q969G3-5;A0A2R8Y855;A0A2R8Y7I9;A0A2U3TZQ7;J3QKS7;J3QR61;J3QKX6;A0A2R8YEB8 Q969G3 SMARCE1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 2 PLMPY(0.5)MRY(0.5)S(1)RK 66.595 0.018382 99190000 76183 112330 102530 132990 100340 148140 152530 148220 131980 174540 TRUE FALSE 73205.68414 109126.4584 121059.4518 139853.6298 103567.5272 151135.4923 154396.7078 145159.2052 116998.1837 162718.2503 0.449892277 0.670646705 0.743982015 0.859483368 0.636483781 0.928817093 0.948859193 0.89208927 0.719023118 1 17.31201655 5.173987841 0.569009708 0.883492923 1.45E-22 0.629684315 0.09892035 3.984084967 0.685040184 0.048148268 2.581604596 149275.2616 -5.173987841 -0.883492923 LEQDEYALR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEQDEYALR 9 0 P55084-2;P55084;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;; 166.33 0.00014151 947300000 968970 1463890 941780 2014490 941410 1054930 1924850 1551720 1302680 997100 FALSE TRUE 931101.5811 1422141.29 1111980.596 2118458.07 971691.3076 1076261.407 1948406.89 1519676.44 1154805.228 929565.5289 1.001652441 1.529898911 1.19623691 2.27897658 1.045317708 1.157811229 2.096040386 1.634824434 1.242306424 1 19.82619704 5.174013633 1.647414481 1.522632007 7.34E-10 0.083756169 0.416715696 8.536876879 8.469883198 0.105779654 29.5387581 149284.1272 -5.174013633 -1.522632007 DIVENICGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIVENICGR 9 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 111.46 0.0051785 0 291900 436360 321260 482830 356190 402220 479890 479840 425670 402580 FALSE TRUE 280492.2253 423915.44 379318.8284 507748.9142 367647.1748 410353.164 485763.0374 469931.1363 377349.7262 375312.898 0.747355678 1.129498726 1.010673575 1.352868278 0.979575114 1.093362808 1.294288152 1.252104947 1.005427013 1 18.51773435 5.174850354 1.545746304 1.151445594 1.54E-19 0.416969721 0.129964254 3.396425955 3.055437631 0.033631002 8.277419154 149572.0185 -5.174850354 -1.151445594 DTNYTLNTDSLDWALYDHLMDFLADR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTNYTLNTDSLDWALYDHLMDFLADR 26 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ; 258.87 7.78E-53 194395000 80136 106194 79203 128283 84786 100591 122445 111778 113396 101782 FALSE TRUE 77004.19652 103165.4511 93516.74396 134903.701 87513.21869 102625.0189 123943.5185 109469.7452 100523.7615 94888.21448 0.811525403 1.087231451 0.985546461 1.421711872 0.92227701 1.081535989 1.306205615 1.15367062 1.059391433 1 16.53394129 5.17506843 1.294846843 1.137955975 0.265697542 0.28408749 0.143099896 4.482004045 3.04484201 0.037813988 6.805633444 149647.143 -5.17506843 -0.872258433 AILVDLEPGT(ph)MDSVR ddPTM_BT-474_Pertuzumab_2h_R1 1 AILVDLEPGTMDSVR 15 0 Q13509;A0A0B4J269;G3V5W4;G3V2R8;G3V3R4;G3V2N6;Q5JP53;P07437;Q13885;Q9BVA1 Q13509;Q5JP53;Q13885;Q9BVA1 TUBB3;TUBB;TUBB2A;TUBB2B Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-2A chain;Tubulin beta-2B chain 1 AILVDLEPGT(0.532)MDS(0.468)VR 93.494 0.011432 0 21509 22251 17182 13721 17021 20063 12017 16861 15013 14064 TRUE FALSE 20668.4045 21616.42327 20287.16961 14429.14245 17568.49592 20468.68761 12164.06764 16512.81446 13308.78718 13111.43275 1.576365062 1.648669804 1.547288538 1.100500817 1.339937157 1.561132791 0.927745111 1.259421054 1.015052087 1 13.67853772 5.177231075 0.223020227 0.952996749 2.406180532 0.569454123 0.171111083 10.52241106 0.394147198 0.289355931 4.379051424 150394.1955 -5.177231075 1.453183783 LKPGTMIEWGNNWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKPGTMIEWGNNWAR 15 1 Q9BPW8;C9JDV8 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 121.79 0.00010295 758420000 224440 376950 201070 497080 262250 233390 485620 407260 342730 285670 FALSE TRUE 215668.6367 366199.7551 237407.8218 522734.3584 270685.5094 238109.3057 491563.1628 398849.9387 303824.7272 266321.3165 0.809806138 1.375029832 0.891433795 1.962795789 1.016386946 0.894067771 1.845752227 1.497626792 1.140820161 1 18.02280838 5.180104245 1.286664026 1.345513425 3.76E-10 0.115658678 0.366335658 7.778430416 5.178766064 0.099338176 18.15452773 151392.4597 -5.180104245 -1.345513425 KNLTQDEMQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KNLTQDEMQR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 95.018 0.01236 202250000 145240 155210 129680 143340 156940 164390 145140 155280 167280 176860 FALSE TRUE 139563.8602 150783.5628 153116.0607 150737.7946 161988.1176 167714.0784 146916.2667 152073.4137 148291.0757 164881.1147 0.84645146 0.914498686 0.92864523 0.914221103 0.982454042 1.017181857 0.891043629 0.922321601 0.899381812 1 17.33106664 5.180157389 1.12062131 0.942592575 0.693561067 0.358332185 0.040221028 4.800221678 2.546614193 0.012087656 1.785277103 151410.9866 -5.180157389 -0.249031508 HVDLLEVAQETDGFSGSDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVDLLEVAQETDGFSGSDLK 20 0 Q8NBU5 Q8NBU5 ATAD1 ATPase family AAA domain-containing protein 1 0 235.21 1.55E-29 71168000 64213 98855 75042 133790 54914 101860 141400 97394 136730 120840 FALSE TRUE 61703.48497 96035.75219 88603.7587 140694.9179 56680.35868 103919.679 143130.4955 95382.77987 121208.9836 112655.3992 0.547718844 0.852473587 0.78650255 1.24889636 0.503130423 0.922456267 1.270516074 0.846677395 1.075926982 1 16.78155693 5.180500162 0.89860114 0.96968071 4.00E-29 0.268187874 0.209502494 6.165753338 2.256357941 0.065467339 7.060909228 151530.5368 -5.180500162 -0.96968071 ASVITQVFHVPLEER ddPTM_BT-474_Pertuzumab_2h_R1 2 ASVITQVFHVPLEER 15 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62 Q00341 HDLBP Vigilin 0 ; 199.49 7.39E-09 4299300000 1410070 1582620 1234820 1594330 1525150 1489530 1595890 1423390 1630360 1828800 FALSE TRUE 1354962.905 1537485.227 1457979.442 1676613.562 1574207.835 1519649.317 1615420.979 1393996.499 1445288.368 1704933.747 0.794730533 0.901785908 0.855153137 0.983389276 0.923324931 0.891324557 0.947497803 0.817625026 0.847709402 1 20.70128425 5.180671602 1.688773897 0.90235687 0.576157056 0.26153879 0.055893188 5.935643983 5.998838042 0.014730994 4.553029883 151590.366 -5.180671602 -0.326199814 VNPTVFFDIAVDGEPLGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VNPTVFFDIAVDGEPLGR 18 0 P62937;F8WE65;C9J5S7;E5RIZ5 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;; 176.43 2.06E-12 4753670000 270651 314199 244554 323602 315293 305321 298171 324797 334592 334952 FALSE TRUE 260073.6597 305238.3522 288750.3479 340303.138 325434.6857 311494.7998 301820.1059 318089.8284 296610.5189 312265.4027 0.832860949 0.977496545 0.924695292 1.089788158 1.042173366 0.997532218 0.966549939 1.018652165 0.949866736 1 18.25241321 5.181843411 1.241648426 1.005083818 0.547635667 0.568172081 0.043551827 2.764706446 1.731464352 0.012135514 2.112577061 151999.938 -5.181843411 -0.457448151 AQSTDS(ph)LGTSGSLQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQSTDS(1)LGTSGSLQSK;AQSTDS(1)LGTSGSLQSK 313.56 1.02E-57 3360670000 431070 423220 464290 493800 544550 662590 724420 508530 798220 862920 TRUE FALSE 414223.3078 411150.18 548197.5311 519285.0772 562065.9453 675988.0238 733285.6687 498028.6778 707609.412 804473.6598 0.514899777 0.511079729 0.681436271 0.645496681 0.698675387 0.840286087 0.911509855 0.61907394 0.879593015 1 19.61768566 5.184404227 0.168487402 1.007262244 1.03E-21 0.702955001 0.08743524 14.91964663 0.378957294 0.304154281 3.297671419 152898.853 -5.184404227 -1.007262244 TDPSVRPMHER ddPTM_BT-474_Pertuzumab_2h_R1 1 TDPSVRPMHER 11 1 D6RDK6;D6RBN5;Q9NX40 D6RDK6 OCIAD1 OCIA domain-containing protein 1 0 62.088 0.049986 193940000 324350 476450 312660 603910 327860 353100 536760 489610 451530 433910 FALSE TRUE 311674.0434 462862.1125 369164.6171 635077.8675 338405.9147 360239.9239 543329.0294 479499.3824 400274.2074 404520.8892 0.770477006 1.144223017 0.912597166 1.569950735 0.836559801 0.890534787 1.343142082 1.185351351 0.989501947 1 18.62585468 5.185449534 1.872200547 1.115584337 1.25E-11 0.160914546 0.215917938 7.543926394 8.663209698 0.053949929 22.41233279 153267.3096 -5.185449534 -1.115584337 IRIEDPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 IRIEDPPR 8 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 117.76 0.0018394 2687050000 2870360 3231590 2523130 3240430 3035250 3399930 3264700 3543990 3335010 3234460 FALSE TRUE 2758183.158 3139428.217 2979115.718 3407668.981 3132881.573 3468678.914 3304654.375 3470805.368 2956433.646 3015387.143 0.914702831 1.041136036 0.987971221 1.130093357 1.038964957 1.150326227 1.095930379 1.151031428 0.980449112 1 21.52391181 5.185484265 0.811655399 1.090028703 0.688251597 0.346859018 0.06180212 4.427261427 1.35637117 0.01995609 1.891464553 153279.567 -5.185484265 -0.401777106 DLS(ph)PQHMVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSPQHMVVR 10 0 A0A2R8Y3N3;A0A2R8Y5P7;P49590-2;P49590;A0A2R8Y5E8;D6RB22 A0A2R8Y3N3 HARS2 "Probable histidine--tRNA ligase, mitochondrial" 1 DLS(1)PQHMVVR;DLS(1)PQHMVVR 196.15 2.18E-07 321110000 254380 383160 232180 555010 250390 286170 462680 386510 364090 295000 TRUE FALSE 244438.5484 372232.652 274140.0908 583654.1326 258444.0217 291956.5535 468342.4162 378528.4334 322760.0296 275019.3872 0.888804789 1.353477861 0.996802784 2.122229049 0.939730193 1.061585354 1.702943276 1.376369998 1.173590098 1 18.0691738 5.188223355 1.592091399 1.34118504 8.36E-12 0.099789443 0.35322173 8.551893972 7.779908483 0.088990368 25.38051023 154249.3543 -5.188223355 -1.34118504 DSGACFSASEPDAVHVVLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSGACFSASEPDAVHVVLDR 20 0 H0YER3;Q8NB37-3;Q8NB37 H0YER3 PDDC1 Parkinson disease 7 domain-containing protein 1 0 ;; 221.37 7.89E-25 439480000 212016 230407 184905 222365 215314 229164 227781 228028 231592 238760 FALSE TRUE 203730.1803 223836.018 218321.4467 233841.2843 222239.7704 233797.8531 230568.652 223319.1421 205302.6471 222588.5725 0.915276908 1.005604265 0.980829538 1.050553861 0.998432974 1.050358742 1.035851254 1.003282152 0.922341362 1 17.76402 5.191015957 1.617066638 1.010039744 0.720777366 0.354312976 0.035807556 4.286477421 3.960485881 0.009310288 2.799595026 155244.405 -5.191015957 -0.289262378 GQAVTLLPFFTSLTGGSLEELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GQAVTLLPFFTSLTGGSLEELRR 23 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 227.58 1.32E-32 796700000 430350 489810 385240 453410 567300 480610 463360 482020 517680 516370 FALSE TRUE 413531.4462 475841.0984 454861.4376 476810.5444 585547.7197 490328.2635 469030.7383 472066.1186 458915.1367 481395.8 0.859025871 0.988461259 0.944880362 0.990475082 1.216354027 1.018555342 0.974314147 0.980619521 0.953301081 1 18.87686403 5.191233073 1.120096371 1.015708171 0.611892642 0.288192692 0.072063625 5.676655873 2.953775651 0.022238786 3.443319572 155322.0353 -5.191233073 -0.403815528 GLNPDGTPALSTLGGFS(ph)PASKPS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 2 GLNPDGT(0.007)PALS(0.027)T(0.018)LGGFS(0.945)PAS(0.011)KPS(0.517)S(0.476)PR 63.033 0.026696 499360000 91618 112820 125870 137610 123410 150870 145640 155910 178560 183970 TRUE FALSE 88037.46727 109602.4841 148617.509 144712.0686 127379.5947 153920.6948 147422.3859 152690.404 158290.6174 171509.548 0.513309424 0.639045962 0.866526154 0.843755174 0.742696813 0.897446798 0.859557894 0.890273491 0.922925978 1 17.38792937 5.191673489 0.682533592 0.892411659 2.36E-32 0.7988247 0.061978293 2.292367756 0.522607565 0.024423857 1.819139181 155479.6268 -5.191673489 -0.892411659 SAFS(ph)SLQNIPESLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAFSSLQNIPESLRR 15 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.002)AFS(0.563)S(0.436)LQNIPESLRR 95.954 0.0023804 69757000 100380 71961 41494 41882 38472 25429 26471 38304 36667 29826 TRUE FALSE 96457.03862 69908.74274 48992.88883 44043.53504 39709.48682 25943.1918 26794.96002 37513.00901 32504.71588 27805.85845 3.468946617 2.51417315 1.761962822 1.583966023 1.428097855 0.933011719 0.963644408 1.349104509 1.168988037 1 14.76310126 5.193898204 0.662825751 1.107452286 6.671471413 0.96431767 0.144359109 0.953483062 0.206674958 0.06398419 4.579110675 156278.1292 -5.193898204 5.564019127 up NFKPS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 1 NFKPSPSK 8 1 Q9BX63 Q9BX63 BRIP1 Fanconi anemia group J protein 1 NFKPS(0.801)PS(0.199)K 78.692 0.018149 462160000 951140 724280 607290 589230 612040 388210 682880 747820 722100 834270 TRUE FALSE 913968.3973 703624.2435 717040.8121 619640.2309 631726.8224 396059.8722 691237.2897 732377.2557 640130.2353 777764.1498 1.175122815 0.904675593 0.921925769 0.796694256 0.812234432 0.509228758 0.888749231 0.941644399 0.823039009 1 19.56897321 5.194444833 1.173797999 0.824055884 1.764708075 0.402759396 0.124592623 4.183425823 2.336757185 0.036878287 6.231160992 156474.9541 -5.194444833 0.940652191 LAQDGAHVVVSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LAQDGAHVVVSSR 13 0 F5GWZ1;Q9BTZ2-3;Q9BTZ2-2;Q9BTZ2-5;Q9BTZ2-8;Q9BTZ2-4;Q9BTZ2;Q9BTZ2-7 F5GWZ1 DHRS4 Dehydrogenase/reductase SDR family member 4 0 ;;; 127.17 0.00041874 951080000 831702 1001483 780441 1054257 963172 1005343 1051653 981533 1019714 1076250 FALSE TRUE 799198.1663 972921.6854 921484.0495 1108667.33 994153.3021 1025671.724 1064523.444 961264.0005 903960.3417 1003354.629 0.796526117 0.969668806 0.918403148 1.104960597 0.990829437 1.02224248 1.060964303 0.958050098 0.900938029 1 19.93640018 5.195407336 1.296125426 1.001039443 0.432344641 0.518684183 0.057280685 3.141162083 2.053099476 0.015775015 3.15577693 156822.1257 -5.195407336 -0.568694802 NPTDAYQLNYDMHNPFDICAASYRPIYR ddPTM_BT-474_Pertuzumab_2h_R1 3 NPTDAYQLNYDMHNPFDICAASYRPIYR 28 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 248.95 4.06E-46 2449860000 633723 809005 648249 813269 813701 821882 769637 780458 923723 949807 FALSE TRUE 608956.4045 785932.9695 765402.0145 855241.9106 839874.4316 838501.0172 779056.0478 764341.2696 818865.8376 885475.7259 0.687716655 0.887582738 0.864396383 0.965855851 0.948500797 0.94694975 0.87981638 0.863198445 0.924775026 1 19.75609323 5.195807498 1.421691707 0.919169709 0.245510753 0.737220172 0.042165265 2.144655988 1.617372434 0.011928406 2.829951651 156966.689 -5.195807498 -0.673658956 DLDADREVTFLEASR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDADREVTFLEASR 15 1 A0A087WYT5;P20338 A0A087WYT5 RAB4A Ras-related protein Rab-4A 0 ; 151.72 2.70E-06 168326000 166299 238003 148257 235181 180668 208192 226844 246759 246629 213373 FALSE TRUE 159799.8512 231215.3875 175050.3379 247318.7196 186479.3503 212401.7849 229620.1847 241663.3404 218632.7099 198921.0567 0.80333301 1.162347473 0.879999035 1.243300854 0.937454051 1.067769237 1.154328197 1.214870585 1.099092844 1 17.60183647 5.196512054 2.238457293 1.094562142 1.35E-10 0.342201362 0.113343951 6.213061576 8.453178891 0.027856818 22.77202282 157221.543 -5.196512054 -1.094562142 DLEKPFLLPVEAVYSVPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEKPFLLPVEAVYSVPGR 19 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 187.06 1.75E-14 1349730000 894940 1345860 899920 1867740 847660 1162970 1725960 1580900 1364170 1095780 FALSE TRUE 859964.7554 1307477.391 1062555.563 1964134.285 874925.7537 1186486.05 1747082.815 1548253.863 1209315.141 1021561.845 0.841813699 1.2798808 1.040128474 1.922677805 0.85645892 1.161443193 1.710207585 1.515575264 1.183790435 1 19.96234512 5.196584555 1.17340762 1.355313464 7.28E-15 0.145100776 0.317068683 7.018379635 3.903314776 0.088401406 15.07589631 157247.7915 -5.196584555 -1.355313464 SASLSSLLITPFPS(ph)PNSSLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASLSSLLITPFPSPNSSLTR 21 0 A0A087WX11;J3KNG8;Q8TF40-3;Q8TF40;Q8TF40-2 A0A087WX11 FNIP1 Folliculin-interacting protein 1 1 SASLSSLLITPFPS(0.997)PNS(0.001)S(0.001)LT(0.001)R 216.96 6.28E-25 75605000 40343 61630 51983 62213 62095 80644 80943 67627 80937 83652 TRUE FALSE 38766.35096 59872.37274 61377.48446 65423.82039 64092.34207 82274.67693 81933.60465 66230.47882 71749.37108 77986.17553 0.497092603 0.767730592 0.787030317 0.838915615 0.821842354 1.054990534 1.050617037 0.849259223 0.920026794 1 16.25093078 5.197398542 0.593706298 0.955151696 1.52E-15 0.772210285 0.07472027 3.042050992 0.549176708 0.037031617 2.239533942 157542.7935 -5.197398542 -0.955151696 down VGDVT(ph)PQVK ddPTM_BT-474_Pertuzumab_2h_R1 3 VGDVTPQVK 9 0 Q13428-4;Q13428;Q13428-3;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 VGDVT(1)PQVK;VGDVT(1)PQVK;VGDVT(1)PQVK 130.99 0.0038638 704939000 2721690 2096550 1795630 1637660 1714190 1645460 1670930 2353870 1923570 1975700 TRUE FALSE 2615323.346 2036758.447 2120140.285 1722179.829 1769328.478 1678732.329 1691379.341 2305261.762 1705214.398 1841884.079 1.41991745 1.105801646 1.151071508 0.935009889 0.960607944 0.911421271 0.918287617 1.251578092 0.925798978 1 20.81275084 5.198796962 1.120627131 1.008548753 2.097248656 0.603629783 0.102654607 3.136622345 1.612660744 0.032189279 5.154196705 158050.8959 -5.198796962 1.088699903 RDSS(ph)DTTPLLNGSSQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.095)S(0.425)DT(0.425)T(0.045)PLLNGS(0.007)S(0.002)QDR 294.25 4.70E-46 576060000 182230 263420 189250 280720 205120 242830 239160 271690 302220 295800 TRUE FALSE 175108.2501 255907.5195 223451.6848 295207.9928 211717.8711 247740.189 242086.9116 266079.5066 267913.2526 275765.2025 0.634990378 0.927990614 0.810296886 1.070504872 0.76774687 0.898373641 0.877873312 0.964877019 0.971526683 1 18.0730809 5.199764587 1.740724001 0.919858341 7.65E-09 0.496042527 0.085443576 3.482841831 3.482419385 0.020791376 7.94021856 158403.4322 -5.199764587 -0.919858334 SALLDHIWVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SALLDHIWVTR 11 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30 E9PP16 PPFIBP2 Liprin-beta-2 0 144.65 3.66E-05 283470000 257810 288350 224390 293010 285370 278210 265400 305430 277300 284200 FALSE TRUE 247734.5002 280126.5403 264942.2645 308132.2812 294549.1852 283835.5968 268648.0446 299122.7638 245822.0665 264950.8809 0.935020481 1.057277256 0.99996748 1.16297889 1.111712421 1.071276291 1.013954148 1.128974408 0.927802413 1 18.0153654 5.20021942 1.481686307 1.065179914 0.677764898 0.19600543 0.067661456 5.724134389 4.548743522 0.017275292 4.566374299 158569.4134 -5.20021942 -0.387415016 LDLRPGESEDMLELVAEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDLRPGESEDMLELVAEVR 19 1 Q9H7N4;M0R3G4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 0 ; 102.6 0.00035484 43141000 39350 46195 37403 47096 44001 54417 45816 45491 55705 50662 FALSE TRUE 37812.1585 44877.56383 44162.55413 49526.6302 45416.33213 55517.34902 46376.70991 44551.59495 49381.60193 47230.61761 0.80058573 0.950179483 0.935040793 1.0486128 0.961586666 1.175452531 0.981920463 0.94327784 1.045542159 1 15.52743478 5.201238027 0.957354408 1.016001851 0.474413307 0.51817695 0.063701167 3.702046261 1.46380021 0.02010075 2.556731199 158941.7633 -5.201238027 -0.541588545 LGCDLDMFLDLDETR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGCDLDMFLDLDETR 15 0 Q9NVV4-2;Q5T852;Q9NVV4 Q9NVV4-2 MTPAP "Poly(A) RNA polymerase, mitochondrial" 0 87.001 0.017075 10154000 12459 18875 11521 23371 13984 13745 22063 20468 15605 16019 FALSE TRUE 11972.08851 18336.70348 13603.10098 24577.18011 14433.80806 14022.93332 22333.01359 20045.32865 13833.58582 14934.01886 0.801665554 1.227847885 0.910880126 1.645717763 0.966505279 0.938992608 1.495445653 1.342259497 0.92631367 1 13.86631484 5.202413654 1.603057824 1.196253457 3.04E-17 0.138038182 0.251079625 7.610023321 6.743944985 0.064585267 20.54837997 159372.5987 -5.202413654 -1.196253457 EFWPQEVWSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFWPQEVWSR 10 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ; 132.01 0.00054663 301100000 128636 180652 149489 239880 142601 161757 269770 209977 213502 226432 FALSE TRUE 123608.7629 175499.9818 176504.9877 252260.2355 147187.8907 165027.8374 273071.526 205640.9016 189266.148 211095.559 0.58555833 0.831376949 0.836137854 1.195004939 0.697257164 0.7817684 1.293591998 0.974160246 0.896589909 1 17.6875367 5.202948275 0.896068001 0.981377237 2.34E-12 0.325224782 0.168218662 5.449143866 1.926430402 0.054852343 6.359034887 159568.9086 -5.202948275 -0.981377237 LVEPHS(ph)PSPSSK ddPTM_BT-474_Pertuzumab_2h_R1 6 LVEPHSPSPSSK 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 LVEPHS(0.991)PS(0.009)PSSK;LVEPHS(0.999)PS(0.001)PSSK;LVEPHS(0.999)PS(0.001)PSSK;LVEPHS(0.995)PS(0.005)PSSK;LVEPHS(0.997)PS(0.003)PSSK;LVEPHS(0.999)PS(0.001)PSSK 192.65 2.46E-06 4875380000 7247640 7656670 6231030 7400810 7757490 7665910 7647360 8042830 9158670 8566180 TRUE FALSE 6964394.216 7438309.268 7357115.73 7782766.691 8007016.711 7820919.953 7740950.679 7876742.75 8119016.178 7985984.999 0.872077047 0.931420391 0.921253387 0.974553132 1.002633578 0.979330659 0.969316957 0.986320755 1.01665808 1 22.92903893 5.20344679 0.537807756 0.994907557 0.723781148 0.857220925 0.015921568 2.402231082 0.367996068 0.00874214 0.454002276 159752.1789 -5.20344679 -0.271126409 EVPCYVFDEELR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVPCYVFDEELR 12 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 174.4 7.09E-05 54254000 23242 25910 19911 31184 27609 27289 31252 33445 37672 35204 FALSE TRUE 22333.67694 25171.07217 23509.36062 32793.40998 28497.06856 27840.80228 31634.47132 32754.34906 33395.63249 32819.60172 0.68049811 0.766952396 0.716320716 0.999201948 0.868294161 0.848297993 0.963889556 0.998011778 1.017551425 1 15.00227011 5.203800507 0.312590889 1.024575177 0.281518819 0.745850729 0.061466749 4.877485786 0.310279769 0.065310915 1.458989258 159882.3441 -5.203800507 -0.743056358 HGS(ph)ASQVQK ddPTM_BT-474_Pertuzumab_2h_R1 4 HGSASQVQK 9 0 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 HGS(0.996)AS(0.004)QVQK;HGS(0.999)AS(0.001)QVQK;HGS(0.913)AS(0.087)QVQK;HGS(0.794)AS(0.206)QVQK 128.08 0.00044829 443946000 721352 625027 532587 530989 588860 572728 572754 445272 675606 585794 TRUE FALSE 693160.7663 607201.8419 628837.3182 558393.4059 607801.2167 584308.9526 579763.5348 436076.9776 598914.0393 546117.6506 1.269251718 1.111851707 1.151468585 1.022478225 1.112949226 1.069932371 1.061609223 0.798503724 1.096675851 1 19.05885226 5.205755816 0.330432428 0.949842439 1.556176125 0.45319489 0.084823288 8.11511176 0.565420533 0.087174453 2.09502824 160603.7998 -5.205755816 0.606333686 LQPFATEADVEEALR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQPFATEADVEEALR 15 0 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;;; 212.17 2.36E-09 167621000 87595 98486 76587 100189 96603 99754 91673 101899 95059 98486 FALSE TRUE 84171.69056 95677.27571 90427.97457 105359.7663 99710.32323 101771.0942 92794.9216 99794.75004 84268.30084 91815.4555 0.916748603 1.042060677 0.984888373 1.147516676 1.085986261 1.108430968 1.010667769 1.086905788 0.917800825 1 16.48644941 5.205766039 1.393424421 1.054221924 0.652373976 0.243471158 0.064624039 5.242837141 3.751916477 0.016827066 4.064197604 160607.5804 -5.205766039 -0.401847947 T(ph)LSSSDTELLVLNGSDPVAEVAIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLSSSDTELLVLNGSDPVAEVAIR 24 0 Q9Y426-2;Q9Y426-3;Q9Y426 Q9Y426-2 C2CD2 C2 domain-containing protein 2 1 T(0.2)LS(0.2)S(0.2)S(0.2)DT(0.2)ELLVLNGSDPVAEVAIR;T(0.215)LS(0.196)S(0.196)S(0.196)DT(0.196)ELLVLNGSDPVAEVAIR 179.58 1.38E-16 42739000 33109 47905 33449 60461 36990 38885 46114 60910 47442 36981 TRUE FALSE 31815.06368 46538.7963 39493.97837 63581.39946 38179.81694 39671.28134 46678.35693 59652.18721 42056.58305 34476.24393 0.92281119 1.34988012 1.145541795 1.844209003 1.107423913 1.150684553 1.353928143 1.730240317 1.219871374 1 15.07331499 5.207668674 1.50970408 1.371986832 4.93E-13 0.1514248 0.261446731 6.854287124 5.501289683 0.069129406 19.89758295 161312.742 -5.207668674 -1.371986832 NLGLEELGIELDPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLGLEELGIELDPR 14 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 120.53 0.00028872 197480000 244690 359390 231670 499580 241370 290890 429130 394300 335280 275080 FALSE TRUE 235127.2443 349140.5491 273537.9225 525363.3837 249133.8853 296771.9951 434381.8213 386157.5672 297220.42 256448.5866 0.916859194 1.361444622 1.066638448 2.048610954 0.971476929 1.157237788 1.693835896 1.505789415 1.158986384 1 17.96831009 5.209179893 1.455195643 1.377407155 1.29E-11 0.110959623 0.326582721 8.092870122 6.133033602 0.084258272 22.64312125 161875.0416 -5.209179893 -1.377407155 AMDNHS(ph)DS(ph)EEELAAFCPQLDDSTVAR ddPTM_BT-474_Pertuzumab_2h_R1 3 AMDNHSDSEEELAAFCPQLDDSTVAR 26 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 2 AMDNHS(1)DS(1)EEELAAFCPQLDDSTVAR;AMDNHS(1)DS(1)EEELAAFCPQLDDSTVAR;AMDNHS(1)DS(1)EEELAAFCPQLDDSTVAR 143.61 1.37E-07 387014000 95515 137279 96065 137021 115989 139153 127786 124801 149727 155306 TRUE FALSE 91782.1682 133363.9373 113426.0825 144092.6702 119719.8915 141966.769 129349.8833 122223.8157 132730.6187 144786.9863 0.633911725 0.92110445 0.783399706 0.995204569 0.826869145 0.980521611 0.89338059 0.844162993 0.916730309 1 17.14357241 5.210437046 1.796306427 0.900853766 4.13E-13 0.561538511 0.07100625 3.224431224 3.256631491 0.016755356 7.546882 162344.3003 -5.210437046 -0.900853766 ELIIGDR ddPTM_BT-474_Pertuzumab_2h_R1 6 ELIIGDR 7 0 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;;;; 126.67 0.0091423 3953140000 2954080 4375990 2759400 6074380 3022750 3748070 5250270 4692530 3933790 3301130 FALSE TRUE 2838631.288 4251191.05 3258084.963 6387879.48 3119979.499 3823858.543 5314524.375 4595627.616 3487242.651 3077541.525 0.922369776 1.381359444 1.058664826 2.075643636 1.01378957 1.242504289 1.726873328 1.493278833 1.133126108 1 21.55334689 5.210970566 1.406881942 1.397974265 1.73E-08 0.114300684 0.330264623 7.871566361 5.650495378 0.084967821 21.54102803 162543.8589 -5.210970566 -1.397974248 FLSQPFQVAEVFTGHMGK ddPTM_BT-474_Pertuzumab_2h_R1 3 FLSQPFQVAEVFTGHMGK 18 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ;; 324.63 4.39E-62 1037700000 1204430 1763120 1147940 2318300 1135170 1476430 2134550 1905380 1546650 1341280 FALSE TRUE 1157359.544 1712837.544 1355398.294 2437947.741 1171683.774 1506284.426 2160673.261 1866033.237 1371080.776 1250433.911 0.925566345 1.36979454 1.083942367 1.949681402 0.937021752 1.204609386 1.727938792 1.492308567 1.096484 1 20.25399738 5.211961367 1.560674376 1.364180901 8.27E-14 0.105991894 0.313836038 8.464804719 7.05034182 0.079975239 25.47199217 162915.1104 -5.211961367 -1.364180901 KGS(ph)QITQQSTNQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGSQITQQSTNQSR 14 1 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 KGS(0.996)QIT(0.004)QQSTNQSR;KGS(1)QITQQSTNQSR 188.04 5.38E-07 159918000 136068 111645 97452 95255 98619 98166 92223 129824 136386 108583 TRUE FALSE 130750.3121 108460.9939 115063.7442 100171.122 101791.1697 100150.9838 93351.65266 127143.089 120904.0331 101228.5767 1.291634402 1.071446398 1.136672548 0.989553792 1.00555765 0.989354855 0.922186755 1.255999967 1.194366621 1 16.62725709 5.213711244 1.635544369 1.065052975 1.802283798 0.321261657 0.099222886 5.964486576 5.2773502 0.028470373 10.25760933 163572.8587 -5.213711244 0.737230823 DLSLEVDRDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLSLEVDRDR 10 1 E7EMW7;O95071-2;O95071;E5RFK7 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 0 ; 173.64 3.05E-06 387440000 355020 409450 325660 405050 407420 407770 411530 404370 413820 420630 FALSE TRUE 341145.4259 397772.8869 384514.0063 425954.679 420525.0343 416015.3888 416566.4272 396019.6182 366844.8885 392140.3554 0.869957456 1.01436356 0.980551991 1.086230155 1.072383978 1.060883898 1.062289105 1.009892536 0.935493844 1 18.58101059 5.215760359 1.410489999 1.033248901 0.540034853 0.520384518 0.044435733 3.334885601 2.377738867 0.012371953 3.240461501 164346.4619 -5.215760359 -0.493214048 KVNELR ddPTM_BT-474_Pertuzumab_2h_R1 7 KVNELR 6 1 P50502;Q3KNR6;Q8IZP2;F8WAQ7 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;;;;; 125.86 0.028448 5832470000 15196120 15199670 13578260 15359610 15398150 16579540 16809590 17387870 18686270 18542560 FALSE TRUE 14602238.83 14766190.29 16032153.63 16152321.31 15893445.48 16914789.66 17015310.79 17028804.41 16565082.97 17286655.9 0.844711604 0.854195883 0.927429442 0.934380913 0.919405441 0.978488249 0.984303204 0.985083784 0.958258386 1 24.04315547 5.217674337 0.37807653 0.992835686 0.64779646 0.88617064 0.017350667 2.559217558 0.220952777 0.014573114 0.431198302 165072.351 -5.217674337 -0.345039226 (ac)SETAPAAPAAPAPAEKT(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SETAPAAPAAPAPAEKTPVK 20 1 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVK;S(0.005)ET(0.005)APAAPAAPAPAEKT(0.991)PVK;S(0.001)ET(0.001)APAAPAAPAPAEKT(0.997)PVK;SETAPAAPAAPAPAEKT(1)PVK 133.24 3.03E-36 6099000000 10049900 5852400 4550940 3494950 4795240 2868680 3509260 6986010 3657510 2898080 TRUE FALSE 9657138.797 5685495.282 5373396.093 3675324.788 4949483.25 2926686.675 3552207.374 6841746.452 3242324.798 2701790.46 3.574347804 2.104343533 1.988827843 1.360329323 1.831927132 1.083239695 1.314760499 2.532300914 1.200065233 1 21.36548436 5.218518538 1.16539037 1.587624918 7.158599025 0.667564455 0.437446997 2.702523115 1.429766485 0.128692951 23.99456962 165393.5381 -5.218518538 5.570974107 RQEHDISLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RQEHDISLDR 10 1 Q92797;A0A087WUE9;M0R3C7;Q92797-2 Q92797 SYMPK Symplekin 0 85.813 0.0090778 430480000 68833 80349 63447 81306 75995 80720 73136 89550 80553 73724 FALSE TRUE 66142.93026 78057.52519 74913.28427 85502.2124 78439.44819 82352.21371 74031.06025 87700.76121 71408.96115 68730.60781 0.962350434 1.13570253 1.089955213 1.244019442 1.141259341 1.198188352 1.077119243 1.276007357 1.038968859 1 16.0686651 5.219490183 1.457973295 1.15406216 0.560060477 0.242124849 0.084833511 4.903542146 3.639061893 0.020827404 5.97602186 165763.9866 -5.219490183 -0.594001683 DYAPPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 DYAPPPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 120.9 0.010447 737850000 1195190 1320410 1060690 1374540 1173240 1229710 1442820 1396860 1400550 1312610 FALSE TRUE 1148480.653 1282753.2 1252380.278 1445480.174 1210978.33 1254575.579 1460477.663 1368014.353 1241565.436 1223705.756 0.938526805 1.048252976 1.02343253 1.181231818 0.989599276 1.025226508 1.193487614 1.11792753 1.01459475 1 20.22282527 5.220398051 1.119706992 1.082708152 0.686173374 0.221486127 0.070294473 5.906765045 2.923736107 0.020347838 3.575671396 166110.8695 -5.220398051 -0.396534778 HLPNDPMFK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLPNDPMFK 9 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 125.75 0.00049291 660280000 604970 873400 545440 1205050 599970 710920 1097450 747050 900740 662840 FALSE TRUE 581327.1036 848491.4871 644013.1412 1267242.775 619268.5799 725295.2895 1110880.921 731623.1564 798491.7714 617945.2564 0.940742076 1.373085202 1.04218478 2.05073631 1.00214149 1.173720944 1.797701188 1.183961118 1.292172346 1 19.23711951 5.220405703 1.656715862 1.350134886 1.12E-10 0.100463318 0.331047285 9.875031906 8.732061406 0.081466306 31.75793118 166113.7961 -5.220405703 -1.350134886 ATSLPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 ATSLPSIPNPFPELCS(0.001)PPS(0.29)QS(0.708)PILGGPSSAR;ATSLPSIPNPFPELCSPPS(0.037)QS(0.963)PILGGPSSAR 177.6 2.57E-18 557730000 347170 448700 364280 463270 494170 528120 528770 535090 553270 584300 TRUE FALSE 333602.2126 435903.5153 430113.4994 487179.4202 510065.4268 538798.9482 535241.2454 524040.2045 490465.1091 544724.8406 0.612423352 0.800226982 0.789597733 0.894358737 0.936372621 0.989121311 0.982590118 0.962027368 0.900390569 1 19.05516813 5.222581367 0.561234968 0.973282534 0.172390244 0.907016466 0.035172254 1.749532693 0.282364691 0.017639164 1.02536371 166948.0563 -5.222581367 -0.800892291 LNNLSPAPHLAS(ph)GSPPPGLPSGLPSGLQSGS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 34 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 LNNLSPAPHLAS(0.5)GS(0.5)PPPGLPSGLPS(0.007)GLQS(0.272)GS(0.714)PS(0.007)R 160.15 1.92E-14 642270000 61408 99554 65504 106190 99210 102170 121080 85831 106990 134710 TRUE FALSE 59008.10747 96714.81739 77342.02993 111670.4786 102401.1798 104235.9474 122561.8133 84058.55986 94844.94374 125585.9717 0.469862252 0.770108445 0.615849277 0.889195482 0.815387088 0.829996742 0.975919616 0.669330807 0.755219253 1 16.93831579 5.223696567 0.852341269 0.826893239 1.19E-10 0.491648258 0.110119639 4.363054971 1.382802723 0.035656154 4.102996759 167377.3036 -5.223696567 -0.826893239 LDALLADEER ddPTM_BT-474_Pertuzumab_2h_R1 2 LDALLADEER 10 0 Q15628-2;Q15628 Q15628-2 TRADD Tumor necrosis factor receptor type 1-associated DEATH domain protein 0 ; 138.66 0.00013688 48294000 68626 73410 58651 70055 73273 72194 70574 74685 76072 80964 FALSE TRUE 65944.02005 71316.41868 69250.54038 73670.54695 75629.89259 73653.81214 71437.70572 73142.72865 67436.62548 75480.23616 0.873659429 0.944835659 0.917465868 0.97602433 1.001982723 0.975802619 0.946442531 0.969031529 0.893434214 1 16.20381132 5.224371112 1.004609409 0.963618567 0.729516281 0.415715025 0.031546653 4.421393193 1.828116636 0.009402533 1.406164376 167637.4755 -5.224371112 -0.234102286 S(ph)TEDLSPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 STEDLSPQK 9 0 Q96RT1-7;Q96RT1-6;Q96RT1-4;Q96RT1-5;Q96RT1-3;Q96RT1-9;Q96RT1-2;Q96RT1;Q96RT1-8 Q96RT1-7 ERBB2IP Protein LAP2 1 S(0.962)T(0.038)EDLSPQK 98.898 0.004846 0 473610 610100 424520 771980 478260 483040 605710 759610 521270 505640 TRUE FALSE 455100.7976 592700.5454 501240.2074 811821.9803 493643.6672 492807.3998 613122.8602 743923.788 462097.6149 471392.5524 0.965439092 1.257339647 1.063318045 1.722178206 1.047202941 1.045428905 1.300663019 1.578140733 0.980281959 1 18.84656944 5.224674059 1.505507763 1.264270756 0.316503822 0.066798177 0.244030913 10.10131623 7.752237017 0.06435482 20.46381927 167754.4538 -5.224674059 -0.947766934 DS(ph)PTREPGALPCACGQLPDLEDELSLLDPLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSPTREPGALPCACGQLPDLEDELSLLDPLPR 32 1 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 DS(0.995)PT(0.005)REPGALPCACGQLPDLEDELSLLDPLPR;DS(0.887)PT(0.113)REPGALPCACGQLPDLEDELSLLDPLPR 155.86 4.97E-11 62065000 12603 11794.2 15068.7 15569.3 14355.6 15426.8 14947.4 19665.2 22873 22981 TRUE FALSE 12110.46083 11457.84096 17791.94929 16372.83344 14817.36091 15738.74047 15130.33075 19259.10675 20276.55293 21424.4764 0.565262861 0.534801446 0.830449667 0.764211602 0.69160901 0.734614941 0.706217061 0.898930102 0.946419999 1 14.38697233 5.22546681 0.125446907 1.136111165 2.52E-17 0.702461902 0.079601382 24.88816951 0.440340635 0.680721416 4.832586138 168060.9484 -5.22546681 -1.136111165 LVDPLGEMLAPSWEEHATCLANAEEQDMQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LVDPLGEMLAPSWEEHATCLANAEEQDMQR 30 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 346.6 5.02E-120 253947000 90540 111950 91898 109134 113621 127432 109297 108760 118650 125871 FALSE TRUE 87001.5967 108757.2956 108506.0129 114766.4188 117275.7227 130008.7624 110634.6094 106514.068 105181.3494 117345.6451 0.741413085 0.92681152 0.92467013 0.978020265 0.999404133 1.107912972 0.942809674 0.907695108 0.896337903 1 16.84040478 5.225681269 1.288123023 0.970583946 0.291744529 0.593127818 0.05687737 3.312992763 2.019016699 0.017410979 4.026028867 168143.959 -5.225681269 -0.678839418 DFQDYMEPEEGCQGS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 6 DFQDYMEPEEGCQGSPQR 18 0 O43237;O43237-2;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR 343.06 1.05E-75 4176540000 2407270 2564350 2563200 3046000 3044360 3384360 3282250 3349670 3986900 3866970 TRUE FALSE 2313191.227 2491217.249 3026427.258 3203204.425 3142284.604 3452794.078 3322419.157 3280498.144 3534323.826 3605056.678 0.641651833 0.691034142 0.839495056 0.888530947 0.871632511 0.957764159 0.921599701 0.909971309 0.980379545 1 21.78159051 5.2256934 0.505721202 0.955571968 0.190450742 0.92262358 0.031285259 1.722908191 0.235188774 0.017757125 0.866735741 168148.656 -5.2256934 -0.765121226 PAYHSSLMDPDTK ddPTM_BT-474_Pertuzumab_2h_R1 3 PAYHSSLMDPDTK 13 0 O15145;C9JZD1 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ;; 106.54 0.0013657 1243840000 826280 1180460 920470 1274150 1074260 1224270 1255070 1213730 1267930 1405840 FALSE TRUE 793988.0641 1146794.437 1086819.405 1339909.034 1108814.549 1249025.578 1270429.922 1188666.051 1123999.902 1310621.205 0.605810482 0.875000673 0.829239906 1.022346525 0.846022134 0.953002724 0.969334173 0.906948588 0.857608513 1 20.32181935 5.227064192 1.247611131 0.927433818 2.07E-14 0.713037123 0.060537499 2.135105061 1.236052818 0.015608949 3.422754924 168680.233 -5.227064192 -0.927433818 (ac)SETAPLAPTIPAPAEKT(ph)PVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SETAPLAPTIPAPAEKTPVKK 21 2 P16402 P16402 HIST1H1D Histone H1.3 1 SETAPLAPTIPAPAEKT(1)PVKK 83.881 1.99E-07 367840000 1822700 985080 913930 614620 984370 591990 677340 1475700 734380 593630 TRUE FALSE 1751466.869 956986.4829 1079097.481 646340.6119 1016033.155 603960.4434 685629.4895 1445226.279 651016.2612 553422.9113 3.164789229 1.729213705 1.949860512 1.167896375 1.835907286 1.091318106 1.238888878 2.611431962 1.176344976 1 19.07802285 5.227412908 1.496378774 1.578559989 6.66694935 0.51116863 0.478732273 3.843784045 2.905652531 0.130422132 41.60198151 168815.7287 -5.227412908 5.088389362 EFITGDVEPTDAESEWHS(ph)ENEEEEK ddPTM_BT-474_Pertuzumab_2h_R1 5 EFITGDVEPTDAESEWHSENEEEEK 25 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK 421.68 8.66E-181 7692170000 4187030 3540580 4329950 4291820 4385190 4432880 5573240 5274650 6415720 6852890 TRUE FALSE 4023396.239 3439606.125 5112468.284 4513321.345 4526243.619 4522515.871 5641446.978 5165726.634 5687434.362 6388737.656 0.629763884 0.538385877 0.80023137 0.706449629 0.708472293 0.707888806 0.883029995 0.808567656 0.89022819 1 22.60709947 5.228192237 0.108169981 1.168822882 6.57E-17 0.759465965 0.063464985 25.90497381 0.389437801 0.818900238 4.632831766 169118.9357 -5.228192237 -1.168822882 DAWEIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAWEIPR 7 0 J3QRU1;P07947;H0Y3C5;J3KPD6;P07948-2;P08631-3;P08631-2;P07948;P08631-4;P08631;P12931;P12931-2 J3QRU1;P12931 YES1;HCK;LYN;SRC Non-specific protein-tyrosine kinase;Tyrosine-protein kinase Yes;Tyrosine-protein kinase Lyn;Tyrosine-protein kinase HCK;Proto-oncogene tyrosine-protein kinase Src 0 ; 87.323 0.045195 109310000 92555 137472 88706 164248 122147 119965 136102 146250 144067 113468 FALSE TRUE 88937.84828 133551.4332 104737.1475 172724.859 126075.9692 122390.7745 137767.657 143229.8864 127713.1181 105782.7113 0.840759772 1.262507186 0.990115929 1.632826923 1.191839079 1.157001678 1.302364586 1.354000901 1.207315606 1 16.69074433 5.229065605 1.382274613 1.264648457 5.92E-10 0.29160106 0.176577003 4.949692911 3.326953376 0.044902073 12.16785985 169459.3767 -5.229065605 -1.264648456 SQDADS(ph)PGSSGAPENLTFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQDADSPGSSGAPENLTFK 19 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;H0Y8U8 P55196-5 MLLT4 Afadin 1 SQDADS(0.993)PGS(0.007)SGAPENLTFK;SQDADS(1)PGSSGAPENLTFK 268.15 9.52E-32 655830000 995860 1099690 992810 1178120 1037660 1206290 1250660 1427090 1523140 1486650 TRUE FALSE 956940.6902 1068327.918 1172232.852 1238922.914 1071037.276 1230682.01 1265965.951 1397620.093 1350239.533 1385957.871 0.690454385 0.770822793 0.845792557 0.893910948 0.772777657 0.887964949 0.913423111 1.008414557 0.97422841 1 20.40245197 5.229178756 0.224630462 1.039696586 0.356901376 0.80212066 0.044811415 6.6119461 0.245469969 0.082024684 1.305913559 169503.5335 -5.229178756 -0.68279521 LEIS(ph)PDSS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 LEISPDSSPER 11 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 LEIS(1)PDS(0.001)S(0.999)PER;LEIS(1)PDS(0.002)S(0.998)PER 255.93 2.58E-20 606550000 1148860 1431450 1096150 1602850 1185040 1354040 1464680 1616510 1373210 1429340 TRUE FALSE 1103961.281 1390626.448 1294248.689 1685573.281 1223157.888 1381419.617 1482605.192 1583128.504 1217328.958 1332529.529 0.828470407 1.043598973 0.971272051 1.264942535 0.917921788 1.036689684 1.112624644 1.188062605 0.913547454 1 20.34573607 5.231759872 1.387720726 1.070578977 0.320236127 0.262334217 0.108051719 5.371982056 3.610214188 0.028426147 7.885908858 170513.9332 -5.231759872 -0.75034285 (ac)ADGDS(ph)GS(ph)ERGGGGGPCGFQPASR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADGDSGSERGGGGGPCGFQPASR 23 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 2 ADGDS(1)GS(1)ERGGGGGPCGFQPASR;ADGDS(1)GS(1)ERGGGGGPCGFQPASR 88.036 0.00027478 1548960000 18104.4 25730 21246.8 25517 24074 33510 27128 27091 24142 29365 TRUE FALSE 17396.86003 24996.20559 25086.56939 26833.93543 24848.36207 34187.59516 27460.00058 26531.56138 21401.50137 27376.08239 0.63547661 0.913067298 0.916368129 0.980196328 0.907666835 1.248812546 1.003065383 0.969151137 0.781759094 1 14.74062839 5.232585673 1.146229028 0.989514478 3.42E-15 0.463599231 0.10993582 3.938897047 1.980536608 0.031837161 6.149146984 170838.4698 -5.232585673 -0.989514478 EEALCQLQEENRR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEALCQLQEENRR 13 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 0 102.52 0.0026985 270180000 103910 114820 99604 112320 124550 119480 131590 137410 129640 139710 FALSE TRUE 99849.08232 111545.446 117604.6585 118116.8487 128556.2639 121895.9675 133200.4378 134572.4355 114923.8107 130247.3173 0.766611431 0.856412618 0.902933442 0.906865885 0.987016597 0.935880831 1.022673177 1.033206966 0.882350693 1 16.99089413 5.232780185 0.519801151 0.992520948 0.481164699 0.704872622 0.043143915 3.549539618 0.503198691 0.023676178 1.229629146 170915.0023 -5.232780185 -0.511356249 ITHISGTLEDEDEDEDNDDIVMLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITHISGTLEDEDEDEDNDDIVMLEK 25 0 H3BUW8;E7EN44;Q86WA8-2;Q86WA8 H3BUW8 LONP2 "Lon protease homolog 2, peroxisomal" 0 ; 278.52 3.71E-53 282230000 90394 138326 102862 148858 114058 150578 158792 140142 137574 183295 FALSE TRUE 86861.30254 134381.0779 121451.4516 156540.5792 117726.7792 153622.7903 160735.344 137248.0187 121957.1763 170880.2664 0.508316755 0.786404895 0.710740064 0.916083422 0.688943092 0.899008373 0.940631399 0.803182378 0.713699591 1 17.38262628 5.232974554 1.003884442 0.841163834 7.94E-27 0.496597463 0.099323402 3.827641192 1.560296926 0.028418298 4.389504081 170991.5127 -5.232974554 -0.841163834 DSLLDGHFVLATLSDTDS(ph)HSQDLGS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 DSLLDGHFVLAT(0.307)LS(0.07)DT(0.071)DS(0.324)HS(0.322)QDLGS(0.907)PER 52.106 0.040258 59853000 19428 22002 18922 20567 22045 24491 23556 21171 24155 24586 TRUE FALSE 18668.73228 21374.5245 22341.62632 21628.46533 22754.09745 24986.2248 23844.28537 20733.81145 21413.02567 22920.76832 0.814489812 0.932539617 0.974732871 0.943618688 0.992728391 1.090112881 1.040291715 0.904586232 0.934219367 1 14.48436778 5.23631947 1.114614804 0.986101719 0.496426087 0.521228327 0.04995387 4.060045066 1.941840539 0.016297335 3.047111504 172313.5658 -5.23631947 -0.489675631 DTDSEEEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 DTDSEEEIR 9 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;; 164.96 0.00014393 13211000000 6865451 6866688 5948391 14322740 8450000 6791140 9631890 12908650 12561900 12930460 FALSE TRUE 6597141.585 6670856.781 7023397.575 15061938.33 8721801.924 6928461.504 9749767.951 12642081.87 11135925.78 12054668.43 0.547268606 0.553383681 0.582628848 1.249469317 0.723520682 0.574753387 0.808796029 1.048729125 0.923785324 1 23.52308863 5.237260506 0.383713736 0.945880719 2.44E-39 0.326795445 0.192037169 11.11664109 0.971666179 0.167759876 5.226230536 172687.3423 -5.237260506 -0.945880719 YSHVNKK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSHVNKK 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 117.17 0.003435 192100000 823390 745870 634000 645370 656890 774940 711970 644560 928260 807510 FALSE TRUE 791211.0085 724598.5179 748577.9033 678677.623 678019.4634 790609.8178 720683.3018 631249.6108 822887.8164 752816.6284 1.051000972 0.962516622 0.994369512 0.901517843 0.90064358 1.050202384 0.957315865 0.838517093 1.093078693 1 19.52193897 5.237921714 1.376104548 0.952364636 1.260222917 0.085909258 0.071800904 9.133363483 5.982743235 0.019393611 5.472146012 172950.4571 -5.237921714 0.307858281 EVEELEQLTQQLMQDMEHPQR ddPTM_BT-474_Pertuzumab_2h_R1 8 EVEELEQLTQQLMQDMEHPQR 21 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 ;;;;;;; 282.17 4.54E-45 2220024000 866410.9 978751 789883 951469 978051 1021181 930102 967520 1030370 1097585 FALSE TRUE 832550.6042 950837.9798 932632.429 1000574.429 1009510.899 1041829.979 941484.8665 947540.3739 913406.7173 1023244.59 0.813637924 0.929238218 0.911446235 0.977844827 0.98657829 1.018163193 0.920097575 0.926015522 0.892657265 1 19.96471961 5.239142803 1.250916741 0.954206313 0.534404168 0.545258876 0.038728551 3.658990439 2.077504905 0.011463418 2.683667371 173437.4193 -5.239142803 -0.419802145 WIDDVR ddPTM_BT-474_Pertuzumab_2h_R1 6 WIDDVR 6 0 P20340-2;P20340;P20340-4;J3KR73;Q9NRW1-2;Q9NRW1;C9JU14;Q53S08;Q9H0N0 P20340-2 RAB6A;RAB6B;RAB6C Ras-related protein Rab-6A;Ras-related protein Rab-6B;Ras-related protein Rab-6C 0 ;;;;; 132.94 0.034151 5253240000 7074610 10001000 7409630 11677100 8662470 9369000 10372400 11291500 10385200 9832200 FALSE TRUE 6798126.42 9715781.272 8748714.967 12279756.53 8941106.215 9558447.599 10499340.53 11058326.58 9206315.634 9166256.336 0.74164699 1.059950858 0.954447993 1.339669771 0.975437069 1.042786417 1.145433877 1.206416903 1.004370301 1 23.1279012 5.239258296 1.305404276 1.106560469 3.84E-14 0.439240882 0.11403459 3.786856692 2.290381318 0.030158723 7.684712806 173483.5482 -5.239258296 -1.106560469 EEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEPVLTPIDEGHLPMINQDEFR 22 0 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 EEPVLT(1)PIDEGHLPMINQDEFR 181.24 1.85E-16 53983000 43028 42180 48658 71257 58339 51752 69717 70711 79377 85789 TRUE FALSE 41346.41819 40977.0677 57451.58299 74934.58231 60215.52692 52798.4609 70570.2175 69250.79314 70366.45574 79978.43462 0.516969585 0.512351459 0.718338428 0.936934846 0.752897043 0.660158718 0.882365576 0.865868324 0.879817867 1 16.28732342 5.241420853 0.404988976 0.896604105 3.74E-59 0.66285268 0.093628102 5.506056312 0.523331429 0.075808954 2.593381116 174349.5589 -5.241420853 -0.896604105 NGDGFVSLEEFLGDYR ddPTM_BT-474_Pertuzumab_2h_R1 4 NGDGFVSLEEFLGDYR 16 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;;; 209.79 6.21E-11 327188000 183385 204415 231939 282544 229529 245920 298344 310528 361270 390662 FALSE TRUE 176218.1115 198585.2843 273855.5368 297126.1297 236912.0087 250892.6709 301995.2231 304115.4883 320260.1442 364202.1148 0.48384703 0.545261206 0.751932857 0.815827579 0.650495972 0.68888307 0.829196786 0.835018458 0.879347294 1 18.47437977 5.242205305 0.164543234 1.044471061 4.04E-15 0.781579228 0.069856523 12.7363916 0.308024563 0.26258545 2.858718308 174664.7655 -5.242205305 -1.044471061 down HILCEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HILCEK 6 0 Q9Y237;Q9Y237-2;H0Y4T6;J3KMW3;H0Y610;H0Y8P6;A0A494C021;Q9Y237-3 Q9Y237 PIN4 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 0 92.692 0.046466 242090000 507990 390150 348270 314500 369120 327700 391420 380810 472840 419210 FALSE TRUE 488137.1892 379023.304 411210.1362 330731.3827 380993.08 334326.3185 396210.315 372946.1404 419165.1855 390816.5333 1.249018779 0.969824129 1.052182037 0.846257398 0.974864284 0.855455924 1.013801314 0.954274215 1.072536983 1 18.57613198 5.244600615 1.607933395 0.961404238 1.965956564 0.574244596 0.070979973 3.187304754 2.541563349 0.017642481 7.513861495 175630.774 -5.244600615 1.004552326 YLYVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 YLYVDK 6 0 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 116.35 0.055015 769700000 1006200 1018090 1093510 1247680 1137030 995590 1116750 1305090 1446560 1517600 FALSE TRUE 966876.5916 989055.07 1291131.582 1312072.914 1173603.603 1015721.512 1130417.121 1278139.435 1282352.573 1414811.6 0.683396002 0.699071926 0.912581987 0.927383486 0.829512284 0.717919977 0.798987738 0.903399036 0.906376915 1 20.43217852 5.245385598 0.040847415 1.488098611 3.60E-10 0.444546045 0.077439941 460.7542029 2.536395342 32.30209172 64.3789124 175948.5118 -5.245385598 -1.488098611 SGELTALEFSAS(ph)PGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGELTALEFSASPGLR 16 0 A0A2R8YF49;H0Y895;Q12774-2;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 SGELTALEFSAS(1)PGLR;SGELTALEFS(0.006)AS(0.994)PGLR 274.79 3.19E-35 116057000 98549 112798 93949 117141 97769 121832 116921 122594 115708 126054 TRUE FALSE 94697.59613 109581.1115 110927.6742 123186.661 100913.8287 124295.5265 118351.9142 120062.3911 102573.3129 117516.2503 0.805825542 0.932476242 0.943934766 1.048252142 0.858722333 1.057687989 1.007111049 1.021666287 0.872843651 1 16.84250074 5.250035552 1.098914941 0.984901115 0.466726115 0.393973248 0.063876582 4.335837287 1.981986561 0.017646238 3.41561794 177842.4989 -5.250035552 -0.518175 ELEDATETADAMNR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELEDATETADAMNR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 330.93 4.69E-68 3117380000 1620918 1745753 1383458 1714501 1683404 1743784 1717974 1731349 1798831 1742781 FALSE TRUE 1557570.733 1695965.834 1633479.635 1802986.602 1737552.218 1779044.507 1738999.08 1695596.038 1594635.246 1624740.891 0.958657926 1.043837724 1.005378547 1.109707162 1.069433427 1.094971215 1.070323945 1.043610121 0.981470495 1 20.63177823 5.250959686 1.278717679 1.054681939 0.760024894 0.296148403 0.039781429 5.342847551 3.061460761 0.010940214 2.841755001 178221.3323 -5.250959686 -0.294657045 EAEEGEDDRDS(ph)ANGEDDS ddPTM_BT-474_Pertuzumab_2h_R1 23 EAEEGEDDRDSANGEDDS 18 1 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(0.894)ANGEDDS(0.106);EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(0.794)ANGEDDS(0.206);EAEEGEDDRDS(0.823)ANGEDDS(0.177);EAEEGEDDRDS(0.99)ANGEDDS(0.01);EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.976)ANGEDDS(0.024);EAEEGEDDRDS(0.998)ANGEDDS(0.002);EAEEGEDDRDS(0.945)ANGEDDS(0.055);EAEEGEDDRDS(0.995)ANGEDDS(0.005);EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(0.971)ANGEDDS(0.029);EAEEGEDDRDS(0.998)ANGEDDS(0.002);EAEEGEDDRDS(0.977)ANGEDDS(0.023);EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.996)ANGEDDS(0.004) 279.15 8.70E-39 21381730000 2089413.4 2282762.8 3021241 3799050 2364141.1 3254348 3911121 3800082 4375363 4767839 TRUE FALSE 2007756.814 2217660.64 3567246.456 3995119.426 2440185.846 3320153.146 3958986.469 3721608.979 3878690.135 4444909.018 0.451698068 0.498921492 0.802546563 0.898807919 0.54898443 0.746956379 0.890678854 0.837274501 0.872614067 1 22.08372246 5.252577948 0.262442098 0.951340685 9.06E-31 0.61158006 0.111844354 9.316363233 0.435829024 0.156187701 3.002897812 178886.6568 -5.252577948 -0.951340685 SEHQNSS(ph)PTCQEDEEDVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEHQNSSPTCQEDEEDVR 18 0 Q9NP74-3;Q9NP74-2;Q9NP74;S4R313 Q9NP74-3 PALMD Palmdelphin 1 SEHQNS(0.034)S(0.949)PT(0.016)CQEDEEDVR 77.045 0.0091641 50261000 12778 17940 12031 21102 17567 20396 19994 14544 17669 19082 TRUE FALSE 12278.62163 17428.36877 14205.26933 22191.07675 18132.05851 20808.42109 20238.69255 14243.66132 15663.28919 17789.55914 0.69021506 0.979696496 0.798517221 1.247421399 1.01925283 1.169698525 1.137672518 0.80067534 0.880476524 1 14.11874314 5.253508873 1.173029946 1.014574828 0.067248187 0.315700302 0.141523392 6.071516322 3.046462686 0.042491453 9.42786129 179270.5177 -5.253508873 -0.947326641 RDS(ph)SDTTPLLNGSSQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.473)S(0.473)DT(0.049)T(0.005)PLLNGS(0.001)SQDR 245.67 1.43E-20 470150000 289020 395160 305680 427830 322110 368030 343340 469240 439180 437570 TRUE FALSE 277724.7789 383890.4237 360923.1758 449910.3576 332470.9607 375471.8188 347541.8976 459550.03 389326.1276 407932.9942 0.680809797 0.941062452 0.884760931 1.102902594 0.815013655 0.920425227 0.851958294 1.126533123 0.954387444 1 18.63797267 5.255377042 1.475047722 0.965293051 6.78E-17 0.427226882 0.09502058 4.551527687 3.155556435 0.025625182 9.389023865 180043.3322 -5.255377042 -0.965293051 EVMVDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVMVDDR 7 0 P51149;C9J592;C9J8S3;C9IZZ0;C9J4V0;C9J7D1 P51149 RAB7A Ras-related protein Rab-7a 0 ; 103.91 0.019241 693780000 843390 1273040 807790 1534700 942270 1024130 1360350 1461810 1262570 1203370 FALSE TRUE 810429.3864 1236734.146 953775.6222 1613906.051 972578.9703 1044838.61 1376998.37 1431623.113 1119248.347 1121864.678 0.722394957 1.102391554 0.850169937 1.438592446 0.866930735 0.931341035 1.227419311 1.276110337 0.997667873 1 20.09746723 5.255565609 1.217336005 1.107390882 3.49E-12 0.23871993 0.182120573 6.441957184 3.403000214 0.050707363 12.21028032 180121.5224 -5.255565609 -1.107390882 LREETER ddPTM_BT-474_Pertuzumab_2h_R1 2 LREETER 7 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ; 158.07 0.0013079 2173930000 1142680 1287190 1035870 1305290 1196470 1344390 1383530 1346300 1255900 1372640 FALSE TRUE 1098022.802 1250480.601 1223074.752 1372656.173 1234955.544 1371574.487 1400462.054 1318498.435 1113335.497 1279669.87 0.858051618 0.977190001 0.955773657 1.07266429 0.965057921 1.071819005 1.094393239 1.030342642 0.870017747 1 20.28734024 5.256809656 1.005153791 1.020744471 0.569348761 0.33472946 0.063134408 5.148157245 2.027660775 0.018895115 3.21078627 180638.2243 -5.256809656 -0.45139571 RASLS(ph)DLTDLEDIEGLTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 RAS(0.412)LS(0.587)DLTDLEDIEGLTVR 142.41 9.52E-08 20029000 7332.4 13401 8144.1 14731 10777 10946 13967 16764 13563 13072 TRUE FALSE 7045.841702 13018.8166 9615.920035 15491.26868 11123.65199 11167.33562 14137.93232 16417.81754 12023.3851 12186.6218 0.578162006 1.068287571 0.789055424 1.271170053 0.91277568 0.916360236 1.160119068 1.347200054 0.986605255 1 13.57301064 5.257274663 0.72773509 1.111588237 1.29E-29 0.383856176 0.168630934 5.855583771 1.382719876 0.064296513 6.328976552 180831.7406 -5.257274663 -1.111588237 DEEVSSADISSSSEVISQHLVSYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DEEVSSADISSSSEVISQHLVSYR 24 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 199.6 1.63E-24 116600000 67772 93811 69157 97522 91265 73871 95550 106820 88071 92330 FALSE TRUE 65123.39531 91135.60213 81655.20829 102555.1221 94200.62161 75364.72223 96719.36948 104614.1297 78073.5493 86076.40686 0.756576601 1.058775633 0.948636348 1.19144288 1.094383758 0.87555609 1.123645526 1.215363576 0.90702612 1 16.39333024 5.259077744 1.505693687 1.067517575 4.22E-10 0.363805216 0.111029059 5.023047943 3.546427777 0.029831478 11.77410604 181584.0691 -5.259077744 -1.067517574 FNHSVEDLLQEGEEADDDDIYNVLSTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FNHSVEDLLQEGEEADDDDIYNVLSTLK 28 0 Q8WVM7;Q68DW7;Q8WVM7-2 Q8WVM7 STAG1;DKFZp781D1416 Cohesin subunit SA-1 0 ; 162.45 8.57E-12 53190000 30269 27873 19386.9 26433 29994 31416 32593 22698 33287 31774 FALSE TRUE 29086.05402 27078.08933 22890.54409 27797.2103 30958.78425 32051.25304 32991.88288 22229.27837 29508.39931 29621.91868 0.98190986 0.914123411 0.772756969 0.938400061 1.045130958 1.082011378 1.113765899 0.750433441 0.996167724 1 14.85437747 5.261174487 9.616451958 0.947756228 12.0782339 0 0.114419547 584682.5495 65702.51876 0.02905097 143219224.9 182462.864 -5.261174487 11.13047767 SAMDSPVPASMFAPEPS(ph)SPGAAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR 144.72 5.76E-07 657139000 240691 282464 224621 281602 284845 291642 292593 297428 264076 285414 TRUE FALSE 231284.5296 274408.4033 265215.0114 296135.513 294007.2981 297539.2011 296173.8407 291286.0079 234099.1996 266082.6556 0.869220615 1.031290081 0.996739193 1.112945571 1.104947248 1.118220954 1.113089615 1.094720012 0.879798794 1 18.02151495 5.26134831 1.166493263 1.069776869 0.46867741 0.350885427 0.072844441 4.724299768 2.317462872 0.020408734 4.647003124 182535.9078 -5.26134831 -0.601099459 SGVS(ph)SDNEDDDDEEDGNYLHPSLFASK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 S(0.083)GVS(0.459)S(0.459)DNEDDDDEEDGNYLHPSLFASK 129.25 3.47E-05 666320000 115040 157470 131330 179500 148060 177800 171980 177890 184960 208130 TRUE FALSE 110544.1096 152979.1098 155064.2524 188764.0165 152822.4844 181395.2378 174084.7427 174216.5093 163964.1162 194033.1697 0.569717589 0.78841731 0.799163631 0.97284406 0.787610101 0.934867157 0.897190635 0.897869728 0.845031375 1 17.56594377 5.261589858 0.943406981 0.898772999 1.84E-14 0.733001956 0.060735518 2.292827982 0.812214328 0.017170145 2.660824117 182637.4596 -5.261589858 -0.898772999 AIT(ph)SAYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 AITSAYYR 8 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907;P57735 H3BMH2;P57735 RAB11A;RAB11B;RAB25 Ras-related protein Rab-11A;Ras-related protein Rab-11B;Ras-related protein Rab-25 1 AIT(0.756)S(0.244)AYYR 98.033 0.087299 83558000 109870 172760 110310 204360 143620 165980 179310 208730 180010 158600 TRUE FALSE 105576.1589 167833.0539 130245.4708 214907.0441 148239.6677 169336.2293 181504.4494 204419.6526 159576.0195 147857.8807 0.714038091 1.135097116 0.880882846 1.453470339 1.002582121 1.145263468 1.227560198 1.382541475 1.079252717 1 17.17385161 5.261708466 0.890038413 1.19904915 2.56E-10 0.361876997 0.16778769 4.985908942 1.611629215 0.051626027 7.241495124 182687.3457 -5.261708466 -1.19904915 AEDTAVYYCAR ddPTM_BT-474_Pertuzumab_2h_R1 3 AEDTAVYYCAR 11 0 A0A0C4DH42;P0DP02;A0A0J9YVY3;A0A0B4J1X5;A0A0B4J1V1;P01767;P01780;P01772;P01763;P01762 A0A0C4DH42 IGHV3-66;IGHV3-74;IGHV3-21 Ig heavy chain V-III region BUT;Ig heavy chain V-III region JON;Ig heavy chain V-III region KOL;Ig heavy chain V-III region WEA;Ig heavy chain V-III region TRO 0 ;; 197.96 1.29E-07 978840000 4061900 1499640 455096 358619 111788 69943 87043 91635 58325 89763 FALSE TRUE 3903156.457 1456871.736 537341.9708 377127.3696 115383.7625 71357.29538 88108.25827 89742.70523 51704.19052 83683.27206 46.64201532 17.40935434 6.421139584 4.506604012 1.378815141 0.852706803 1.052877787 1.072409133 0.617855746 1 16.35265164 5.261761578 1.023119445 1.042951285 132.1233576 0.99679591 0.778395876 0.246986683 0.099220547 0.25575677 45.73466611 182709.689 -5.261761578 131.0804063 up QVELALWDTAGQEDYDR ddPTM_BT-474_Pertuzumab_2h_R1 6 QVELALWDTAGQEDYDR 17 0 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;U3KQA9;U3KQV3;Q5JR06;E9PN11;P62745;P61586 Q5JR08;P61586 RHOC;RHOA;RHOB Rho-related GTP-binding protein RhoC;Rho-related GTP-binding protein RhoB;Transforming protein RhoA 0 ;;;;; 424.95 3.66E-160 1785514000 1535300 2091070 1498090 2280230 1683210 1782230 2064110 2451770 1967780 1782220 FALSE TRUE 1475298.779 2031434.731 1768828.188 2397912.944 1737351.978 1818267.912 2089371.196 2401140.093 1744405.864 1661508.652 0.887927232 1.22264469 1.06459162 1.443214238 1.045647265 1.094347543 1.257514484 1.445156539 1.049892736 1 20.66406237 5.263394855 1.668914436 1.211087694 1.23E-15 0.211624671 0.156936178 7.302505864 5.792500575 0.040901454 22.05140142 183398.1095 -5.263394855 -1.211087694 FLQPVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLQPVHK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 86.866 0.019762 935820000 1189460 1280100 1037460 1204360 1250460 1256390 1328620 1380580 1412370 1368370 FALSE TRUE 1142974.588 1243592.801 1224952.1 1266517.164 1290682.182 1281795.067 1344880.049 1352070.541 1252043.679 1275689.081 0.895966427 0.974840045 0.960227785 0.992810225 1.011752943 1.004786421 1.054238113 1.059874667 0.981464604 1 20.28284532 5.26510942 0.511100238 1.031217757 0.739188058 0.667036855 0.025618284 4.05433035 0.545780405 0.014780584 0.793754616 184123.5839 -5.26510942 -0.292029699 FMADCPHTIGVEFGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 FMADCPHTIGVEFGTR 16 0 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 ; 150.76 7.08E-07 459610000 333650 452890 369650 490540 444800 429290 528540 481980 504990 497320 FALSE TRUE 320610.5891 439974.0206 436453.9778 515856.8282 459107.396 437970.5379 535008.4306 472026.9446 447665.6523 463636.0734 0.691513468 0.948964168 0.941371914 1.112633071 0.990232258 0.944642928 1.153940475 1.018097969 0.965553972 1 18.82263329 5.265301811 1.163744151 1.028139919 0.005010223 0.698342238 0.06424683 2.465345756 1.196503282 0.01787241 4.126176563 184205.1683 -5.265301811 -1.023129697 AQPFGFIDS(ph)DTDAEEER ddPTM_BT-474_Pertuzumab_2h_R1 4 AQPFGFIDSDTDAEEER 17 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.992)DT(0.008)DAEEER;AQPFGFIDS(0.584)DT(0.416)DAEEER;AQPFGFIDS(0.956)DT(0.044)DAEEER;AQPFGFIDS(0.982)DT(0.018)DAEEER 276.3 9.95E-36 631288000 184840 191216 218805 281942 233880 234954 295589 332835 286205 319629 TRUE FALSE 177616.2484 185762.7069 258347.9308 296493.0604 241402.9626 239704.9309 299206.5066 325961.8409 253716.2083 297980.2431 0.596067198 0.623406119 0.866996845 0.995009123 0.810130766 0.804432295 1.004115251 1.093904205 0.851453122 1 18.18485715 5.265431073 0.510355494 0.982402755 1.23E-14 0.629587116 0.095153414 4.710485188 0.632518415 0.057803164 3.097881933 184260.0026 -5.265431073 -0.982402755 DPYATSVGHLIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DPYATSVGHLIEK 13 0 J3KQU4;I3L4I4;O75674;O75674-2;I3L3M3;I3L4G0;I3L1G1;I3L0N2 J3KQU4 TOM1L1 TOM1-like protein 1 0 176.25 1.69E-05 139330000 155530 170040 166840 228200 187670 195560 224210 230500 250540 303960 FALSE TRUE 149451.7157 165190.6257 196991.6993 239977.4293 193706.576 199514.3572 226953.949 225740.0945 222099.7495 283372.5185 0.527403703 0.582945116 0.695168679 0.846862041 0.683575729 0.704070946 0.800903173 0.796619572 0.783773073 1 18.11234033 5.266265592 0.101084653 1.145891315 1.67E-14 0.757308219 0.063117804 35.16059519 0.48617764 1.126842029 5.865716548 184614.4082 -5.266265592 -1.145891315 HLQDLSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLQDLSGR 8 0 P30533 P30533 LRPAP1 Alpha-2-macroglobulin receptor-associated protein 0 ; 153.08 0.00044675 289610000 83722 114496 87867 121808 111951 109242 141109 96645 119176 128134 FALSE TRUE 80450.05168 111230.6862 103746.5215 128094.5255 115552.0056 111450.9481 142835.9342 94649.24698 105647.6401 119455.3701 0.673473714 0.931148479 0.868496087 1.072321198 0.967323659 0.932992364 1.195726354 0.792339825 0.884410973 1 16.86611219 5.269256442 1.350502517 0.965514122 2.95E-18 0.403813806 0.105799706 4.941316497 2.945026953 0.028792637 9.286080846 185890.1773 -5.269256442 -0.965514122 NKQPT(ph)PVNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 NKQPTPVNIR 10 1 X6R700;Q9Y3Y2-4;Q9Y3Y2;Q9Y3Y2-3;A0A087X1B7 X6R700 CHTOP Chromatin target of PRMT1 protein 1 NKQPT(1)PVNIR 138.42 0.0053343 0 187870 148310 135470 111550 131280 114570 116130 188570 150880 141360 TRUE FALSE 180527.8327 144080.344 159952.4425 117307.1089 135502.7404 116886.6839 117551.2337 184675.9636 133752.7349 131785.5613 1.369860483 1.093293853 1.21373268 0.890136277 1.02820627 0.886946057 0.891988717 1.401336852 1.01492708 1 17.00783279 5.270153834 1.206508265 1.050353174 2.035475639 0.301264712 0.151229738 6.989896648 3.544844412 0.046352417 11.77164799 186274.6834 -5.270153834 0.985122465 ALALLEDEER ddPTM_BT-474_Pertuzumab_2h_R1 2 ALALLEDEER 10 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 0 ; 142.92 8.12E-05 73684000 96117 137978 86718 166292 113918 121377 122590 160274 123948 122997 FALSE TRUE 92360.64138 134043.0025 102389.8716 174874.35 117582.2759 123831.3261 124090.2931 156964.2859 109877.9427 114666.3036 0.80547326 1.168983374 0.892937754 1.525071835 1.025430071 1.079927775 1.082186215 1.36887892 0.958240906 1 16.80708197 5.271748398 1.422259554 1.151832118 3.32E-13 0.189263412 0.185159559 7.330241192 4.659226364 0.04729887 17.49462049 186959.8702 -5.271748398 -1.151832118 ISDYFEFAGGSAPGTS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ISDYFEFAGGSAPGTSPGR 19 0 Q86UE8-2;Q86UE8 Q86UE8-2 TLK2 Serine/threonine-protein kinase tousled-like 2 1 ISDYFEFAGGSAPGT(0.155)S(0.845)PGR 116.13 0.00013042 156590000 75008 86526 71323 90048 79711 93492 98749 96848 76440 100250 TRUE FALSE 72076.60443 84058.3632 84212.65267 94695.38807 82274.97671 95382.4723 99957.5198 94848.05496 67762.85166 93459.97821 0.771202881 0.899404909 0.90105577 1.013218598 0.880323089 1.020570239 1.069522182 1.014852098 0.725046731 1 16.51206108 5.274805913 0.881387026 0.971088781 0.428274217 0.259342783 0.093548554 6.621124641 2.070957928 0.030025894 4.331618792 188280.7473 -5.274805913 -0.542814565 FEWELPLDEAQR ddPTM_BT-474_Pertuzumab_2h_R1 6 FEWELPLDEAQR 12 0 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ;;;;; 218.11 8.16E-11 501248000 492664 724895 510291 866415 573849 641888 775851 899382 769320 706575 FALSE TRUE 473410.1462 704221.7043 602511.9351 911130.782 592307.3742 654867.4152 785346.0966 880809.4474 681990.0189 658718.0459 0.71868404 1.069079113 0.914673492 1.383187826 0.899181946 0.994154357 1.19223407 1.337157002 1.035329187 1 19.32930155 5.27492634 1.009632577 1.133155356 2.14E-15 0.325661407 0.158072712 5.599355911 2.159311289 0.048317345 8.890706971 188332.9635 -5.27492634 -1.133155356 RPADESNLSPSEVVQWSNHR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPADESNLSPSEVVQWSNHR 20 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30 E9PP16 PPFIBP2 Liprin-beta-2 0 109.03 0.00013207 160320000 41321 50667 38511 54109 47376 48833 48048 60141 41858 43929 FALSE TRUE 39706.12964 49222.02677 45470.79437 56901.57197 48899.89207 49820.43672 48636.0258 58899.06733 37106.45532 40953.6497 0.969538244 1.201895976 1.110298953 1.389413945 1.194030139 1.216507859 1.187587093 1.438188483 0.906059792 1 15.32170441 5.278109283 1.444462597 1.218102885 0.341522204 0.112682356 0.153544972 8.36108028 5.343461882 0.038908129 15.53951932 189718.3257 -5.278109283 -0.876580681 SDLESR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDLESR 6 0 P61019;P61019-2;A0A3B3ITL1;Q8WUD1;H7C125;Q8WUD1-2 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 127.66 0.039465 212080000 335930 462560 297660 486500 386280 406090 432950 484650 461300 411380 FALSE TRUE 322801.4842 449368.2417 351453.7834 511608.3233 398705.047 414301.418 438248.5716 474641.8081 408935.1579 383516.8662 0.841687844 1.171703988 0.916397203 1.333991718 1.03960238 1.080269095 1.142710035 1.23760348 1.066276855 1 18.5489305 5.278699306 1.7375933 1.125598041 4.22E-21 0.304724102 0.115953719 6.475169646 5.142520867 0.028281106 19.34879312 189976.2481 -5.278699306 -1.125598041 IPGEETDTIQHMR ddPTM_BT-474_Pertuzumab_2h_R1 3 IPGEETDTIQHMR 13 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ;; 194.7 5.64E-07 735550000 343910 483950 362930 587870 419920 437019 547890 579910 509870 580980 FALSE TRUE 330469.617 470148.2198 428519.5243 618210.0412 433427.1082 445855.8236 554595.2417 567934.6558 451991.6951 541629.7071 0.610139386 0.868025172 0.791166952 1.141388726 0.800227725 0.823174611 1.023938005 1.048566296 0.834503147 1 19.04694734 5.280006485 0.968354838 0.95250212 1.20E-11 0.436192739 0.111974783 4.682549806 1.681291381 0.034390424 5.979979007 190548.9173 -5.280006485 -0.95250212 FRDSILR ddPTM_BT-474_Pertuzumab_2h_R1 4 FRDSILR 7 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 110.03 0.0062893 2116600000 732670 969360 664790 985500 799850 812610 923080 996140 1016640 989910 FALSE TRUE 704036.4464 941714.8019 784932.3412 1036361.773 825577.9017 829041.531 934376.9292 975569.3609 901235.2893 922862.514 0.76288335 1.020428057 0.85054093 1.122986097 0.894583851 0.898336988 1.012476848 1.05711235 0.976565063 1 19.81575621 5.280370845 1.916394558 0.984991414 6.36E-12 0.397178008 0.078870747 6.538616552 5.688337701 0.019770004 19.36458601 190708.849 -5.280370845 -0.984991414 LADDLGFEFFEASAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LADDLGFEFFEASAK 15 0 O95716 O95716 RAB3D Ras-related protein Rab-3D 0 ; 185.59 2.58E-11 0 16407.4 18247.7 14446.7 22285.1 20641 18534.9 19785.1 25147 26497 22924 FALSE TRUE 15766.18067 17727.29346 17057.54006 23435.23668 21304.93651 18909.68838 20027.23597 24627.70566 23489.17164 21371.33706 0.737725516 0.829489208 0.798150345 1.096573257 0.996893009 0.884815411 0.9371073 1.152370841 1.099096962 1 14.38338955 5.281248076 0.408820351 1.064820362 0.297063682 0.576889781 0.086372808 6.3162877 0.594211995 0.069964862 2.588097733 191094.4507 -5.281248076 -0.767756681 LYVPHSLWPQIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYVPHSLWPQIK 12 0 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 125.97 0.00029579 377240000 769050 1055700 802870 1483800 831660 880500 1504800 1334300 1346000 1107800 FALSE TRUE 738994.6758 1025592.47 947966.4687 1560379.096 858411.0992 898304.3133 1523216.193 1306746.239 1193207.723 1032767.719 0.715547806 0.993052407 0.917889329 1.51087129 0.831175378 0.869802857 1.474887493 1.265285712 1.155349553 1 19.97808438 5.283568121 0.746814842 1.177745623 2.66E-14 0.250062092 0.222530472 7.72002386 1.844294123 0.082742727 9.175340956 192118.0283 -5.283568121 -1.177745623 KVTAEADSSS(ph)PTGILATSESK ddPTM_BT-474_Pertuzumab_2h_R1 2 KVTAEADSSSPTGILATSESK 21 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 KVTAEADS(0.045)S(0.205)S(0.743)PT(0.007)GILATSESK;KVT(0.001)AEADS(0.022)S(0.071)S(0.849)PT(0.057)GILATSESK 76.899 0.0064518 1197300000 1054130 1277480 1027030 1240910 1321820 1462530 1293040 1304430 1240530 1180700 TRUE FALSE 1012933.434 1241047.521 1212637.167 1304953.514 1364337.541 1492103.359 1308864.61 1277493.065 1099710.235 1100730.137 0.920237758 1.127476644 1.101666181 1.185534464 1.239484134 1.355557832 1.189087648 1.160586979 0.999073431 1 20.07002938 5.28561176 1.194717539 1.175593801 0.362383992 0.309526824 0.101491238 5.589958907 2.714600067 0.028919644 7.756411242 193024.1994 -5.28561176 -0.813209808 TPAVEGLTEAEEEELRAELTK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPAVEGLTEAEEEELRAELTK 21 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 ; 174.71 2.42E-12 171410000 87480 110113 107264 124220 114656 121833 124746 158042 126323 140708 FALSE TRUE 84061.18489 106972.6851 126648.9909 130631.0091 118344.0144 124296.5467 126272.6789 154778.3775 111983.3426 131177.7218 0.640819064 0.815479058 0.965476371 0.995832274 0.902165495 0.947543112 0.962607652 1.179913596 0.853676532 1 17.0011632 5.287117168 0.835239716 1.001539947 1.05E-10 0.618287875 0.082319216 3.457619731 0.978969318 0.028933119 3.954331399 193694.4459 -5.287117168 -1.001539947 VQQAELHTGSLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 VQQAELHTGSLPR 13 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;; 188.4 6.14E-06 3268370000 1855940 2439710 2186650 2697670 2503330 2863440 2878970 2727540 3139920 3332330 FALSE TRUE 1783407.813 2370131.86 2581826.297 2836897.072 2583851.883 2921340.719 2914203.696 2671215.346 2783489.445 3106628.321 0.574065395 0.762927397 0.831070225 0.913175565 0.831722245 0.940357332 0.938059979 0.859843879 0.895984057 1 21.56691822 5.287538576 0.83015841 0.908725093 3.19E-18 0.855358478 0.043164414 1.822704573 0.510942182 0.013880126 1.879047078 193882.4843 -5.287538576 -0.908725093 GIPNERPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIPNERPTR 9 1 Q96F86;H3BPW9;H3BSQ0;H3BPN4 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 ; 127.76 0.00039786 431700000 188372 251607 187744 276274 214310 212337 282315 266419 235101 253911 FALSE TRUE 181010.214 244431.4147 221673.5171 290532.5342 221203.4758 216630.5996 285770.0554 260917.3545 208413.3201 236713.3818 0.764680951 1.032604971 0.936463817 1.227359991 0.934478119 0.91515992 1.207240813 1.102250124 0.880445873 1 17.85278174 5.287937924 1.517978697 1.043326002 8.47E-09 0.305885452 0.115248701 6.213324393 4.12544642 0.030314566 14.69529843 194060.8475 -5.287937924 -1.043325993 HGEVCPAGWKPGSDTIKPDVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGEVCPAGWKPGSDTIKPDVQK 22 2 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ; 229.66 1.48E-26 22090500000 11516700 9284500 8584500 6876400 7985800 8505300 9322000 7537100 13142200 10838400 FALSE TRUE 11066614.63 9019715.15 10135910.11 7231291.828 8242670.51 8677282.993 9436085.425 7381456.251 11650352.55 10104305.51 1.095237532 0.892660573 1.003127835 0.715664408 0.815758243 0.858770846 0.933867786 0.730525838 1.153008738 1 23.26846683 5.289439469 1.27791595 0.873075742 1.609004681 0.150316472 0.127566186 7.778580386 4.118929728 0.033399026 10.58694734 194732.9616 -5.289439469 0.735928939 GVSFYEVPPHLFAVADTVYR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVSFYEVPPHLFAVADTVYR 20 0 O00159-3;F5H6E2;O00159-2;O00159;I3L3F5;I3L501;I3L3Y6 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 167.14 1.42E-11 339830000 363500 435290 337940 462700 393250 405440 438670 466760 450790 435530 FALSE TRUE 349294.0181 422875.9554 399013.2754 486580.0025 405899.2434 413638.2746 444038.5747 457121.2429 399618.2091 406031.1652 0.860264059 1.041486447 0.982715884 1.198380923 0.999675094 1.018735285 1.093607124 1.125827971 0.984205754 1 18.63123094 5.290883965 1.345845048 1.064175998 0.357546361 0.40569484 0.067559433 4.625741252 2.618328247 0.017821463 6.430743179 195381.7363 -5.290883965 -0.706629637 TQSRPGGPPNPPGPS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 TQSRPGGPPNPPGPSPK 17 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 TQSRPGGPPNPPGPS(1)PK;TQSRPGGPPNPPGPS(1)PK;TQSRPGGPPNPPGPS(1)PK;TQSRPGGPPNPPGPS(1)PK 141.45 3.78E-07 2438900000 1617680 1206620 1088810 921420 964360 1001500 1043180 1277250 1386730 1358950 TRUE FALSE 1554459.277 1172208.379 1285582.187 968974.5966 995379.5152 1021751.016 1055946.749 1250874.341 1229314.224 1266907.106 1.226971788 0.925252036 1.014740687 0.764834763 0.785676795 0.80649245 0.833483958 0.987344956 0.970327041 1 20.27287931 5.291941546 1.297267749 0.882171434 2.049429601 0.551473166 0.089318302 3.945381105 2.121320388 0.026109232 8.682496927 195858.1039 -5.291941546 1.167258167 RFS(ph)DS(ph)EGEETVPEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RFSDSEGEETVPEPR 15 1 A0A1B0GWH8;H3BQ48;A0A1B0GWD3;A0A1B0GV71;A0A1B0GW34;A0A0D9SFH9;H3BPL0;Q9UBD8;A0A1B0GV41;H3BR84;O95090;H3BR00;Q9UP10;Q9UBH5;A0A0D9SF04;Q13286-5;Q13286-4;Q13286-6;Q13286-2;Q13286-7;Q13286-3;Q13286 A0A1B0GWH8 CLN3 Battenin 2 RFS(1)DS(1)EGEETVPEPR 120.92 0.00032953 0 55361 75347 54013 110500 65404 67366 96393 104370 94711 93483 TRUE FALSE 53197.43092 73198.17733 63774.35061 116202.9182 67507.77906 68728.18668 97572.68637 102214.723 83959.80434 87151.31314 0.610403091 0.839897584 0.731765803 1.333346728 0.774604267 0.788607586 1.119577925 1.17284203 0.963379682 1 16.41123478 5.292265749 0.615527201 1.038116923 4.27E-12 0.336152915 0.17421438 7.407697154 1.298971165 0.07886804 6.317653422 196004.3674 -5.292265749 -1.038116923 VGEDEDGS(ph)DEEVVHNEDIHFEPIVSLPEVEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 VGEDEDGSDEEVVHNEDIHFEPIVSLPEVEVK 32 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(0.963)DEEVVHNEDIHFEPIVS(0.037)LPEVEVK 237.23 2.06E-46 2189509000 1000054 849419 723441 638309 770223 753170 867057 358825.4 1219097 899979 TRUE FALSE 960970.7841 825194.4018 854182.8816 671252.204 794997.9223 768399.6134 877668.3029 351415.5301 1080710.219 839022.6207 1.145345501 0.983518658 1.018068954 0.800040651 0.947528592 0.915827052 1.046060358 0.41883916 1.288058501 1 19.67835018 5.293602007 0.69001578 0.868552888 1.565882299 0.055050434 0.211932603 12.55508527 2.623484481 0.082204286 8.136895602 196608.372 -5.293602007 0.697329411 SRPEPSYHSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRPEPSYHSR 10 1 M0QZ22;Q5PRF9;A0A087WZT0;M0R0X3;M0QY61 M0QZ22 SAMD4B Protein Smaug homolog 2 0 ;;; 97.163 0.0037531 134458000 143319 196929 142641 216396 195741 232369 223126 163428 185727 200930 FALSE TRUE 137717.935 191312.7777 168419.4017 227564.2235 202037.187 237067.6604 225856.6827 160053.1547 164644.0496 187320.8321 0.735198181 1.02131074 0.899095951 1.21483671 1.078562297 1.265570186 1.205721116 0.854433289 0.878941481 1 17.51515183 5.294138206 1.227501101 1.060302198 5.49E-10 0.320239515 0.137816937 6.611599546 3.281101335 0.041831085 12.4070069 196851.2633 -5.294138206 -1.060302198 ISIEMNGTLEDQLSHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISIEMNGTLEDQLSHLK 17 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 270.42 1.39E-35 458210000 427270 402030 427230 578690 454740 349380 654070 556320 711100 728950 FALSE TRUE 410571.816 390564.498 504439.9647 608556.2603 469367.1251 356444.703 662074.7043 544831.7976 630378.9092 679577.5672 0.6041574 0.574716584 0.742284603 0.895491979 0.690674836 0.524509225 0.974244496 0.801721281 0.927604058 1 19.3742787 5.295374542 0.105101394 1.180090629 4.55E-09 0.471243335 0.119273562 56.28831148 0.804318195 1.774425378 9.916960813 197412.4517 -5.295374542 -1.180090624 SLGS(ph)PLLHER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLGSPLLHER 10 0 E7EV32;E7EMT6;E7ENY2;E7EVA2;E7EW82;H7C3L4;E7EQA9;Q92844 E7EV32 TANK TRAF family member-associated NF-kappa-B activator 1 S(0.022)LGS(0.978)PLLHER 98.942 0.003242 113530000 60246 77939 56750 82224 78391 71602 73644 69263 74628 93735 TRUE FALSE 57891.51971 75716.25603 67005.9874 86467.59049 80912.51771 73049.8415 74545.2773 67832.69485 66156.54231 87386.24496 0.662478629 0.866455082 0.766779571 0.989487425 0.925918235 0.835942104 0.853055047 0.776239955 0.75705899 1 16.41511859 5.297045425 1.714553572 0.856914955 0.030292451 0.337475064 0.08297692 7.485901309 5.555272796 0.02185996 16.41242585 198173.4294 -5.297045425 -0.826622504 RPISADSAIMNPASK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPISADSAIMNPASK 15 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 142.54 7.33E-06 3561700000 2412000 2441100 2244900 2431800 2444400 2721400 2825600 2903000 3129600 3159300 FALSE TRUE 2317736.373 2371482.218 2650603.368 2557305.489 2523026.346 2776428.573 2860180.538 2843052.036 2774340.928 2945317.797 0.78692234 0.805170233 0.899937986 0.86826131 0.856622789 0.942658404 0.971094033 0.965278531 0.941949603 1 21.48999188 5.298410295 0.249002767 1.007034898 0.526568774 0.854417379 0.026274489 4.789258623 0.202432109 0.039157688 0.741714372 198797.2144 -5.298410295 -0.480466124 SPS(ph)DSSTASTPVAEQIER ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSDSSTASTPVAEQIER 18 0 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 S(0.023)PS(0.66)DS(0.303)S(0.008)T(0.006)ASTPVAEQIER;S(0.47)PS(0.53)DSSTASTPVAEQIER 300.18 1.70E-49 2612010000 135656 154667 183358 208199 196924 213860 215969 221994 242320 313300 TRUE FALSE 130354.4135 150256.0486 216494.8694 218944.1753 203258.2393 218184.3957 218612.0932 217409.7463 214812.8495 292079.9119 0.446297086 0.514434723 0.741217936 0.749603675 0.695899413 0.747002402 0.748466718 0.744350219 0.73545917 1 18.15600361 5.30043169 0.129078083 1.040941483 9.98E-33 0.747441296 0.070938609 23.78016018 0.424441582 0.558258155 4.316787732 199724.6598 -5.30043169 -1.040941483 down SAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEPSANTTLVSETEEEGSVPAFGAAAK 28 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SAEPSANT(0.006)T(0.025)LVS(0.897)ET(0.072)EEEGSVPAFGAAAK 149.74 4.04E-08 148250000 209780 180440 202170 260140 231030 224330 266850 296050 315160 360160 TRUE FALSE 201581.5657 175294.0279 238706.6162 273565.8566 238461.2898 228866.1063 270115.7901 289936.464 279384.3581 335766.0424 0.60036317 0.522071936 0.710931381 0.81475141 0.710200734 0.681623742 0.804476201 0.863507405 0.832080445 1 18.35709681 5.302071064 0.125338389 1.110655606 1.13E-13 0.785433027 0.060617233 20.02936536 0.345801575 0.513194669 3.788993074 200480.0047 -5.302071064 -1.110655606 GEDAEES(ph)LEEEEALDPLGIMR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEDAEESLEEEEALDPLGIMR 21 0 Q53T59;F6TR53;H7BZZ1 Q53T59 HS1BP3 HCLS1-binding protein 3 1 GEDAEES(1)LEEEEALDPLGIMR;GEDAEES(1)LEEEEALDPLGIMR 139.26 1.84E-07 71397000 45059 47430 55053 87875 52141 56389 78967 82888 85547 95798 TRUE FALSE 43298.04446 46077.34284 65002.30175 92410.23928 53818.16262 57529.22422 79933.42177 81176.33383 75836.0632 89309.51613 0.484808857 0.515928703 0.727831754 1.034718844 0.602602779 0.644155592 0.89501573 0.908932635 0.849137544 1 16.44652629 5.303881863 0.313972081 0.929175922 1.77E-47 0.503580632 0.132855351 9.843900085 0.600514897 0.147767925 3.737688298 201317.6551 -5.303881863 -0.929175922 RNSS(ph)EASSGDFLDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSSEASSGDFLDLK 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 RNS(0.076)S(0.922)EAS(0.002)SGDFLDLK 116.6 0.00060447 0 21990 20747 20517 28862 27786 23096 31242 31244 36147 33492 TRUE FALSE 21130.60649 20155.31587 24224.8783 30351.57128 28679.76192 23563.01694 31624.34894 30598.80048 32043.7441 31223.55701 0.676752059 0.645516328 0.775852613 0.972072825 0.918529619 0.754655113 1.012836204 0.97999086 1.026268214 1 14.93034728 5.30517874 0.343827094 1.016781035 0.142369633 0.698633935 0.076877005 5.483678837 0.386808948 0.074460977 2.150440535 201919.7224 -5.30517874 -0.874411402 LDLPPYETFEDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDLPPYETFEDLR 13 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;K7ERN1;K7EKL1;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 0 ; 118.9 0.00090901 31248000 18587.4 26301 18633.7 29050 27642 29774 23049.9 28388 28866 33615 FALSE TRUE 17860.98386 25550.92123 22001.22409 30549.27398 28531.13003 30376.05068 23331.99157 27801.77788 25589.2527 31338.22611 0.569942402 0.815327618 0.702057099 0.974824608 0.910425815 0.969297068 0.74452177 0.887152252 0.816550771 1 14.9356359 5.308602658 0.916842302 0.883576338 1.82E-09 0.5374208 0.088652968 4.187151299 1.327910168 0.027084162 4.728797338 203517.921 -5.308602658 -0.883576336 GVGDDQLGEESEERDDHLLPM ddPTM_BT-474_Pertuzumab_2h_R1 2 GVGDDQLGEESEERDDHLLPM 21 1 P20645;F5GX30;H0YF90 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ; 129.32 1.75E-05 422660000 241219 380770 253396 430580 328250 361960 430760 425730 431240 415950 FALSE TRUE 231791.8948 369910.8124 299190.294 452802.2854 338808.4594 369279.0792 436031.7697 416938.5267 382287.4431 387777.336 0.597744822 0.953925818 0.77155178 1.167686307 0.873719085 0.952296705 1.12443851 1.075200864 0.985842667 1 18.56486896 5.310238597 0.736726069 1.032447167 3.59E-15 0.558733927 0.106914283 4.241370255 0.962888378 0.037632785 4.395308145 204285.9964 -5.310238597 -1.032447167 AQIWDTAGQER ddPTM_BT-474_Pertuzumab_2h_R1 4 AQIWDTAGQER 11 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;; 220.1 2.19E-11 1751120000 922650 1330780 975610 1631560 1145790 1186580 1684020 1614710 1503760 1429750 FALSE TRUE 886591.818 1292827.457 1151924.429 1715765.007 1182645.376 1210573.461 1704629.541 1581365.674 1333059.469 1332911.759 0.665154172 0.969927265 0.864216571 1.287230753 0.887264568 0.908217256 1.278876512 1.186399372 1.000110818 1 20.34614984 5.310536514 0.767747378 1.094436857 1.53E-19 0.399295623 0.144457214 5.730051983 1.385074268 0.05221399 6.58682417 204426.1802 -5.310536514 -1.094436857 SDEDYLYR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDEDYLYR 8 0 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ; 138.83 0.0016017 746030000 997030 1445210 951190 1864060 1156000 1094940 1531410 1850460 1599450 1384470 FALSE TRUE 958064.9653 1403994.026 1123091.192 1960264.36 1193183.79 1117080.437 1550151.854 1812247.354 1417887.141 1290698.614 0.742284028 1.087778363 0.870142092 1.518762273 0.924448029 0.865485114 1.201017679 1.404082514 1.098542391 1 20.29972073 5.311528311 0.942070303 1.153857501 1.67E-13 0.213067558 0.207384609 8.118306764 2.669840175 0.066487889 12.36081888 204893.5612 -5.311528311 -1.153857501 GFSDEDNTWEPEENLDCPDLIAEFLQSQK ddPTM_BT-474_Pertuzumab_2h_R1 5 GFSDEDNTWEPEENLDCPDLIAEFLQSQK 29 0 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;;;; 241.97 1.81E-45 698187000 683393 684932 542702 807637 660791 739172 794692 806348 972914 962349 FALSE TRUE 656685.246 665398.41 640780.3237 849319.2424 682045.9426 754118.5643 804417.6784 789696.632 862472.8815 897168.2451 0.731953287 0.741665138 0.714225372 0.946666634 0.76022078 0.840554231 0.896618536 0.880210191 0.961327918 1 19.77501903 5.312261447 0.141901304 1.064993973 0.336861706 0.681874818 0.056264091 18.93978384 0.375091409 0.287075579 2.601136865 205239.7358 -5.312261447 -0.728132268 IIAEGANGPTTPEADKIFLER ddPTM_BT-474_Pertuzumab_2h_R1 2 IIAEGANGPTTPEADKIFLER 21 1 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ; 222.39 3.60E-25 357290000 231286 327060 205418 423230 210068 275370 396570 365330 283940 263490 FALSE TRUE 222247.0874 317732.569 242541.6021 445072.951 216825.028 280938.1701 401423.3423 357785.8078 251708.3216 245643.5876 0.904754281 1.293469828 0.987372007 1.811864724 0.882681409 1.143682083 1.63416984 1.45652411 1.024689161 1 17.90620705 5.31674608 1.228324617 1.296369302 7.33E-16 0.090993267 0.292695213 11.40047789 5.416695446 0.079756403 26.54435555 207370.0727 -5.31674608 -1.296369302 AS(ph)S(ph)HSSQTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.498)S(0.498)HS(0.498)S(0.498)QT(0.01)QGGGSVTK 61.165 0.046181 98658000 320770 273960 156460 143790 176970 137560 90377 171320 128560 113790 TRUE FALSE 308233.9538 266146.929 184735.8024 151211.0191 182662.4008 140341.5574 91483.06076 167782.1821 113966.4078 106082.9019 2.90559504 2.508857923 1.741428628 1.425404249 1.721883521 1.322942292 0.862373286 1.581613804 1.074314575 1 16.69483262 5.317419701 0.541739571 1.184126515 5.649195562 0.866237692 0.226973873 2.411031854 0.340261919 0.116636453 7.766674792 207691.9679 -5.317419701 4.465069048 up FPEDLENDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 FPEDLENDIR 10 0 O14929;F8W9G7 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 0 108.98 0.0048383 30130000 34136 45948 34189 45164 38976 49762 44450 46199 43528 52530 FALSE TRUE 32801.92738 44637.60803 40367.71283 47494.91945 40229.69844 50768.22173 44993.9924 45244.97451 38586.88392 48972.09631 0.669808521 0.911490653 0.824300283 0.969836356 0.821482057 1.036676507 0.918767947 0.92389295 0.787936128 1 15.57967233 5.318246765 1.409232523 0.915196492 6.92E-17 0.463763049 0.076875758 4.719845694 2.662383845 0.019231722 9.150280044 208087.87 -5.318246765 -0.915196492 IVGCICEEDNTSVVWFWLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 IVGCICEEDNTSVVWFWLHK 20 0 P10606 P10606 COX5B "Cytochrome c oxidase subunit 5B, mitochondrial" 0 147.92 1.16E-07 13129000 21389 32276 16949 44827 21721 21648 42237 30226 36139 26743 FALSE TRUE 20553.09423 31355.52008 20012.06133 47140.52684 22419.67569 22085.73739 42753.90904 29601.82254 32036.65223 24931.67279 0.824376864 1.257658094 0.802676238 1.890788767 0.899244743 0.885850604 1.71484318 1.187317946 1.284978048 1 14.60569206 5.31829499 1.056136112 1.249154876 2.24E-17 0.100251266 0.338660271 12.16535725 4.676797166 0.095425399 22.91542848 208110.9777 -5.31829499 -1.249154876 KLEDQLQGGQLEEVILQAEHELNLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 KLEDQLQGGQLEEVILQAEHELNLAR 26 1 A0A087X1G1;H7BYD0;Q16718-2;Q16718;A0A087WXR5 A0A087X1G1 NDUFA5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 0 ;;; 237.13 3.76E-45 252553000 316252 413618 287882 491983 304579 354184 459369 445449 396344 308714 FALSE TRUE 303892.5222 401822.0196 339908.6813 517374.3016 314376.0601 361345.8432 464990.8952 436250.3225 351352.6907 287804.5258 1.055899039 1.396162963 1.181040084 1.797658672 1.092324936 1.255525229 1.615648308 1.515786874 1.220803216 1 18.13472975 5.318842932 1.610244802 1.380619769 8.01E-10 0.093315859 0.236428111 12.29532764 8.042789174 0.059449249 42.3760829 208373.7135 -5.318842932 -1.380619768 T(ph)PVKPSSVEEEDSFFR ddPTM_BT-474_Pertuzumab_2h_R1 3 TPVKPSSVEEEDSFFR 16 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 T(0.999)PVKPS(0.001)SVEEEDSFFR;T(0.996)PVKPS(0.003)S(0.001)VEEEDSFFR;T(1)PVKPSSVEEEDSFFR 133.94 5.01E-05 733796000 423269 409310 551252 598143 475220 465907 637473 747011 721777 823249 TRUE FALSE 406727.1795 397636.8796 650875.4989 629013.2319 490505.8829 475327.9588 645274.5853 731584.9618 639843.9009 767489.612 0.529944866 0.518100667 0.848057731 0.819572307 0.639104263 0.619328199 0.840760025 0.953218064 0.833684119 1 19.5497877 5.321084444 0.15613083 1.073364057 6.34E-18 0.578264643 0.105523371 22.16192817 0.489851031 0.46088833 4.878133643 209451.9675 -5.321084444 -1.073364057 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR 38 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 85.203 0.00043193 102010000 15457 20676 16592 24673 18863 19819 25360 25948 24040 19258 FALSE TRUE 14852.92335 20086.34072 19590.54349 25946.37649 19469.74553 20219.75376 25670.36327 25412.16473 21311.07998 17953.63851 0.827293217 1.118789415 1.091173997 1.445187641 1.084445669 1.12622039 1.429813977 1.415432572 1.187006187 1 14.13198863 5.323368813 0.871270096 1.270487457 9.96E-10 0.373845855 0.151820935 5.37614704 1.548121779 0.049754191 8.298582389 210556.5775 -5.323368813 -1.270487456 VSGVDGYETEGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSGVDGYETEGIR 13 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ; 191.52 8.14E-06 307780000 170387 217001 167919 200313 201948 209740 204304 220110 218140 242050 FALSE TRUE 163728.0877 210812.3439 198265.6986 210651.1779 208443.8408 213981.0865 206804.3335 215564.6516 193377.6617 225655.7379 0.725565807 0.934221066 0.87862024 0.933506854 0.923724975 0.948263441 0.91645945 0.955281056 0.856958762 1 17.78376394 5.323541649 1.698946139 0.928596245 3.51E-09 0.704200843 0.038734675 3.25762997 2.216664257 0.009154993 8.107705861 210640.3896 -5.323541649 -0.928596242 TLQVVPPSDPDPLLAS(ph)WHGGTGTSPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLAS(0.272)WHGGT(0.243)GT(0.243)S(0.243)PPR;TLQVVPPSDPDPLLAS(0.38)WHGGT(0.207)GT(0.207)S(0.207)PPR 56.709 0.046383 70356000 38942 59255 37282 67806 57188 60758 65606 69662 54315 76100 TRUE FALSE 37420.10359 57565.10542 44019.68673 71305.47579 59027.50396 61986.56839 66408.90585 68223.45536 48149.38891 70945.67922 0.527447253 0.811396917 0.620470298 1.005071437 0.83200985 0.873718725 0.936052859 0.961629462 0.678679652 1 16.1144272 5.324094441 0.660671911 0.902057039 7.49E-18 0.464136854 0.115381256 5.418593335 1.026751497 0.044251837 4.375477067 210908.674 -5.324094441 -0.902057039 GEGGS(ph)EDGS(ph)EDGLPEGIHLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEGGSEDGSEDGLPEGIHLDK 21 0 O75362 O75362 ZNF217 Zinc finger protein 217 2 GEGGS(1)EDGS(1)EDGLPEGIHLDK 92.463 0.00098467 98035000 127240 105490 134220 158170 161400 131530 178570 189730 202230 229230 TRUE FALSE 122267.3201 102481.5285 158476.5397 166333.1727 166591.5776 134189.6267 180755.3931 185812.0092 179273.6982 213704.0479 0.572133852 0.479548841 0.741570135 0.778334216 0.779543388 0.627922718 0.845821101 0.869482871 0.838887705 1 17.70525471 5.324482669 0.171233628 1.034456145 2.00E-18 0.726911439 0.076656819 12.77029853 0.315890815 0.242154187 2.948246645 211097.2954 -5.324482669 -1.034456145 LYGDADYLEER ddPTM_BT-474_Pertuzumab_2h_R1 1 LYGDADYLEER 11 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 121.83 0.00093858 128140000 92100 121470 94531 118540 105060 117840 129150 116000 139240 136300 FALSE TRUE 88500.63018 118005.7945 111614.8545 124657.8636 108439.3503 120222.8055 130730.5763 113604.5595 123434.0589 127068.2796 0.696480903 0.928680194 0.878384872 0.981030545 0.853394338 0.946127593 1.028821487 0.894043422 0.971399466 1 16.95524441 5.324995804 1.4032819 0.943474915 6.26E-14 0.66066496 0.052789273 3.306316113 1.826680146 0.013494865 6.605120563 211346.8619 -5.324995804 -0.943474915 LASTLVHLGEYQAAVDGAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LASTLVHLGEYQAAVDGAR 19 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 286.16 4.09E-40 10885740000 3146900 3765720 3143860 3661730 3939110 4262860 4137110 3782080 4194990 4464300 FALSE TRUE 3023915.669 3658325.353 3712025.437 3850712.324 4065815.051 4349057.95 4187741.19 3703978.726 3718792.322 4161928.985 0.726565898 0.878997543 0.891900234 0.925222977 0.976906397 1.044962076 1.006201981 0.889966825 0.893526136 1 21.98882092 5.325293183 0.858657316 0.961143933 0.29119053 0.694636744 0.047563476 3.565449141 1.002066729 0.01750544 2.857414851 211491.6292 -5.325293183 -0.669953403 AFS(ph)EDEALAQQENR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFSEDEALAQQENR 14 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 AFS(1)EDEALAQQENR;AFS(1)EDEALAQQENR 293.52 1.60E-43 644700000 475870 514300 407260 516670 476520 494650 449380 574820 545850 510970 TRUE FALSE 457272.4743 499632.6676 480860.9414 543335.4006 491847.6986 504652.1619 454879.6469 562949.7661 483887.3964 476361.5468 0.959927344 1.048851804 1.009445336 1.140594585 1.03250924 1.059388956 0.954904211 1.18176996 1.015798609 1 18.86169743 5.325545877 1.245708255 1.060988215 0.704674045 0.132627981 0.064187083 9.517945085 4.526585344 0.017296338 6.226873078 211614.7214 -5.325545877 -0.35631417 VASASAGSCDVPS(ph)PFNHRPGSHLDSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 VASASAGSCDVPSPFNHRPGSHLDSHR 27 1 Q16643;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 VASASAGSCDVPS(0.93)PFNHRPGS(0.024)HLDS(0.046)HR;VASASAGSCDVPS(0.996)PFNHRPGS(0.003)HLDS(0.001)HR 196.3 3.19E-25 2205100000 17684.7 28363 14920.8 29642 26464 22067.1 21464 31698.4 24987 31311 TRUE FALSE 16993.56237 27554.11501 17617.32047 31171.82717 27315.23859 22513.31188 21726.68285 31043.81696 22150.58051 29190.27808 0.582165142 0.943948356 0.603533835 1.067883872 0.935764932 0.771260617 0.744312294 1.0634985 0.758834173 1 14.83320033 5.32727277 1.119586936 0.88856571 1.88E-28 0.240687287 0.148344534 8.08161459 3.320034668 0.041104049 11.6416663 212457.8441 -5.32727277 -0.88856571 (ac)SETAPAAPAAPAPAEKT(ph)PVKK ddPTM_BT-474_Pertuzumab_2h_R1 5 SETAPAAPAAPAPAEKTPVKK 21 2 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVKK;SETAPAAPAAPAPAEKT(1)PVKK;SETAPAAPAAPAPAEKT(1)PVKK;SETAPAAPAAPAPAEKT(1)PVKK;SETAPAAPAAPAPAEKT(1)PVKK 113.13 4.25E-17 7492650000 19368400 10585740 9243320 6148420 9241140 5458040 6865270 14246500 7439730 5811110 TRUE FALSE 18611461.52 10283845.06 10913793.54 6465740.693 9538389.661 5568405.308 6949289.228 13952304.8 6595203.04 5417518.344 3.435421965 1.898257543 2.014537441 1.19348755 1.760656643 1.027851676 1.282744014 2.575405178 1.217384533 1 22.3692007 5.329206474 1.242627085 1.563890735 8.257514565 0.607494805 0.464999742 4.001658371 1.883066748 0.134785762 49.14753922 213405.9254 -5.329206474 6.69362383 AIST(ph)PETPLTK ddPTM_BT-474_Pertuzumab_2h_R1 6 AISTPETPLTK 11 0 A0A3B3ITS5;Q14181;E9PIQ6 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 1 AIS(0.021)T(0.979)PETPLTK;AIS(0.031)T(0.959)PET(0.009)PLTK;AIS(0.004)T(0.996)PETPLTK;AIS(0.012)T(0.987)PET(0.001)PLTK;AIS(0.004)T(0.996)PETPLTK;AIS(0.005)T(0.994)PET(0.002)PLTK 225.55 6.03E-11 3258880000 3685750 4264120 4434940 5192590 4810060 5161040 6678510 5196490 5564460 7244820 TRUE FALSE 3541706.815 4142511.473 5236432.313 5460580.192 4964779.948 5265399.765 6760243.603 5089180.666 4932805.829 6754121.888 0.524377095 0.613330873 0.775294316 0.808481144 0.735074082 0.779583172 1.000906367 0.753492571 0.730340066 1 22.68733678 5.330112579 0.605812163 0.840118371 2.20E-11 0.570036943 0.091733633 5.024090638 0.830215595 0.040536432 3.444946575 213851.637 -5.330112579 -0.840118371 GS(ph)VHS(ph)LDAGLLLPSGDPFSK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSVHSLDAGLLLPSGDPFSK 20 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 2 GS(1)VHS(1)LDAGLLLPSGDPFSK;GS(1)VHS(1)LDAGLLLPSGDPFSK;GS(1)VHS(1)LDAGLLLPSGDPFSK;GS(1)VHS(1)LDAGLLLPSGDPFSK 118.9 3.11E-05 389735000 715892 592314 656484 763527 727261 668495 842021 871346 986485 1034638 TRUE FALSE 687914.1492 575421.7847 775125.2622 802932.72 750654.0105 682012.4269 852325.9049 853352.4006 874503.3585 964561.0467 0.713188814 0.596563366 0.803604152 0.832433284 0.778233802 0.707070257 0.883641225 0.884705435 0.906633501 1 19.87951302 5.332980241 0.117254216 1.119266989 0.177451537 0.694018656 0.061475911 27.68402787 0.440086592 0.624396337 4.210890097 215268.3794 -5.332980241 -0.941815452 FSLYFLAYEDKNDIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 FSLYFLAYEDKNDIPK 16 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 222.5 8.74E-15 983010000 1736100 1281020 1089660 1028120 1069790 1042490 1031840 1253460 1569720 1260840 FALSE TRUE 1668251.293 1244486.564 1286585.801 1081181.396 1104200.767 1063569.862 1044467.967 1227575.613 1391531.966 1175442.184 1.419254231 1.058739069 1.094554729 0.919808232 0.939391815 0.90482533 0.888574513 1.044352185 1.183837015 1 20.16477215 5.335632094 1.233356467 0.982564969 2.5550437 0.680170838 0.086686412 3.255847354 1.497910994 0.02526807 9.347521819 216586.8544 -5.335632094 1.572478731 VLTLS(ph)DDLER ddPTM_BT-474_Pertuzumab_2h_R1 1 VLTLSDDLER 10 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 1 VLT(0.021)LS(0.979)DDLER 89.403 0.012101 30829000 29262 38110 28863 40888 34601 42823 35431 40816 35187 35831 TRUE FALSE 28118.40869 37023.14011 34079.18615 42998.23458 35713.97259 43688.9104 35864.61518 39973.13534 31192.71928 33404.13446 0.841764325 1.108340052 1.020208627 1.287212954 1.069148271 1.307889311 1.07365797 1.19665233 0.93379816 1 15.02773906 5.335644971 1.370859457 1.133236361 7.01E-09 0.31210649 0.116527958 6.026174155 3.15990118 0.029006544 14.15808016 216593.2763 -5.335644971 -1.133236354 RPEFQTLLTESESEHGER ddPTM_BT-474_Pertuzumab_2h_R1 1 RPEFQTLLTESESEHGER 18 1 Q7L775;A0A096LNL1 Q7L775 EPM2AIP1 EPM2A-interacting protein 1 0 205.24 6.39E-16 167160000 45986 58725 48795 54776 53625 68980 57531 57825 60657 66457 FALSE TRUE 44188.81628 57050.2205 57613.34194 57602.99592 55349.89683 70374.82286 58235.08159 56630.89354 53771.47165 61955.8082 0.713231214 0.920821181 0.929910264 0.929743273 0.893377045 1.135887416 0.939945475 0.914053019 0.867900415 1 15.91895192 5.339357307 1.387418068 0.952098693 2.22E-17 0.50485641 0.070228929 4.96752555 2.619348176 0.019334529 9.974806503 218452.6449 -5.339357307 -0.952098693 EVTEEDLNNHFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVTEEDLNNHFK 12 0 H7C126;B9A058;Q6NVY1 H7C126 HIBCH "3-hydroxyisobutyryl-CoA hydrolase, mitochondrial" 0 ; 189.33 8.07E-06 521620000 516640 738370 528940 958880 509270 678690 1010290 865720 821790 714920 FALSE TRUE 496449.1376 717312.4105 624531.2242 1008367.912 525651.1321 692413.5768 1022654.231 847842.5795 728503.8444 666497.8316 0.744862345 1.076241177 0.937034143 1.512935022 0.788676432 1.038883465 1.53436993 1.272086028 1.09303258 1 19.34624066 5.339724945 0.775582273 1.199412863 1.07E-15 0.219436388 0.225725145 8.691709494 2.061240251 0.079726375 11.19429405 218637.6472 -5.339724945 -1.199412863 TLNEWDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLNEWDSR 8 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 163.32 0.00078307 1409230000 949570 1133790 907890 1071720 1115910 1084020 1151110 1132910 1126050 1215560 FALSE TRUE 912459.7546 1101455.419 1071965.919 1127031.598 1151804.259 1105939.627 1165197.629 1109515.013 998225.5248 1133229.038 0.805185645 0.971961873 0.945939331 0.994531167 1.016391409 0.975918892 1.028210175 0.979073934 0.88086829 1 20.11200805 5.339899798 1.500399012 0.982800703 0.225212687 0.625507316 0.039570545 3.854443707 2.214607618 0.010369246 6.783633736 218725.6915 -5.339899798 -0.757588016 S(ph)PEASQTDS(ph)PVESPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPEASQTDSPVESPR 15 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 S(1)PEAS(0.001)QT(0.003)DS(0.996)PVESPR;S(1)PEASQT(0.047)DS(0.953)PVESPR 268.82 1.48E-25 130910000 138143 147844 126123 177249 180471 182061 214465 212270 231260 253840 TRUE FALSE 132744.2188 143627.6339 148916.2317 186396.8421 186276.0136 185742.3982 217089.6868 207886.5503 205008.3343 236647.1907 0.560937227 0.606927272 0.629275299 0.787657109 0.787146524 0.784891625 0.917355859 0.878466166 0.866303689 1 17.85237827 5.341735608 0.236883314 0.998364091 1.43E-17 0.929855532 0.036039657 3.32431917 0.127985638 0.054808544 1.019971786 219652.2254 -5.341735608 -0.998364091 HNS(ph)TTSSTSSGGYRR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNSTTSSTSSGGYRR 15 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12 A0A0A0MRT6 ABI1 Abl interactor 1 1 HNS(0.879)T(0.06)T(0.06)S(0.001)STSSGGYRR;HNS(0.77)T(0.157)T(0.072)S(0.001)STSSGGYRR 82.449 0.0067346 72911000 19964.8 20922.1 9712.8 15184.4 15023.2 13834.2 12381.5 9652.1 11698.3 12050.8 TRUE FALSE 19184.55354 20325.42219 11468.11902 15968.0687 15506.43487 14113.937 12533.0285 9452.780762 10370.35803 11234.58858 1.707632941 1.809182601 1.020786737 1.421330971 1.380240563 1.256293179 1.115575209 0.841399816 0.923074125 1 13.45565967 5.342695201 0.279263229 0.861647362 2.842217459 0.655413884 0.183328425 7.174503229 0.356332868 0.22807405 5.169303632 220138.0933 -5.342695201 1.980570097 LQCSLDAHEICLQDIQLDPER ddPTM_BT-474_Pertuzumab_2h_R1 2 LQCSLDAHEICLQDIQLDPER 21 0 Q06546 Q06546 GABPA GA-binding protein alpha chain 0 ; 177.32 6.51E-17 332880000 314050 360450 261990 360960 381270 372170 324090 345940 371370 354050 FALSE TRUE 301776.5788 350170.3189 309337.4209 379589.1889 393533.8958 379695.5324 328056.3104 338796.2181 329213.6345 330069.8781 0.91428088 1.060897531 0.937187673 1.150026749 1.192274491 1.150348934 0.993899571 1.026437856 0.997405872 1 18.33241196 5.342871302 1.121761212 1.065687433 0.56536264 0.227308028 0.07860029 9.082425531 3.638093142 0.024382833 7.447952566 220227.3751 -5.342871302 -0.500324793 SFS(ph)EDTLMDGPAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 S(0.001)FS(0.952)EDT(0.048)LMDGPAR;SFS(0.955)EDT(0.045)LMDGPAR;SFS(0.996)EDT(0.003)LMDGPAR;SFS(0.999)EDT(0.001)LMDGPAR 185.9 8.67E-06 930690000 1090490 1161910 966100 1152650 1150720 1117560 1132920 1305690 1269710 1283110 TRUE FALSE 1047872.445 1128773.464 1140695.761 1212138.405 1187733.954 1140157.829 1146785.014 1278727.045 1125577.844 1196203.817 0.875998246 0.943629713 0.95359649 1.013320964 0.992919381 0.953146791 0.958686971 1.068987598 0.940958245 1 20.1900318 5.342983951 0.797261007 0.99537912 0.652273299 0.484432476 0.035290755 4.931777545 1.213696933 0.012535213 1.876113272 220284.5058 -5.342983951 -0.343105821 (ac)SDQDHS(ph)MDEMTAVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDQDHSMDEMTAVVK 15 0 P08047;H3BUU5;P08047-3 P08047 SP1 Transcription factor Sp1 1 S(0.303)DQDHS(0.697)MDEMTAVVK 69.01 1.75E-06 143490000 65819 83519 61785 81674 81729 86688 74532 76282 81898 95905 TRUE FALSE 63246.72071 81137.11989 72950.9239 85889.20493 84357.88751 88440.89075 75444.14491 74706.75004 72601.28238 89409.26893 0.707384385 0.907479961 0.815921266 0.960629764 0.94350271 0.989169152 0.843806753 0.835559343 0.812010693 1 16.44813678 5.344062677 1.667313158 0.896284699 7.34E-18 0.409962614 0.068443115 7.490294725 4.718503309 0.018560741 17.86057718 220832.3414 -5.344062677 -0.896284699 GYADS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 3 GYADSPSK 8 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6;Q5T0S3;Q5T0R8 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 1 GYADS(0.999)PS(0.001)K;GYADS(0.898)PS(0.102)K;GYADS(1)PSK 144.77 0.00060851 4822300000 5243800 4828210 5009330 5125580 5227790 5619020 6213180 6601720 6496010 7319410 TRUE FALSE 5038866.499 4690514.178 5914627.363 5390111.798 5395946.613 5732640.434 6289218.755 6465392.175 5758610.178 6823659.841 0.738440458 0.687389801 0.866782269 0.789915078 0.790770164 0.840112281 0.921678235 0.947496259 0.843918119 1 22.7021143 5.344507016 0.159897292 1.038381853 0.352669909 0.705972408 0.049408282 14.22410549 0.321148012 0.183459958 2.044028997 221058.397 -5.344507016 -0.685711944 MREEVITLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 MREEVITLIR 10 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 176.8 2.18E-06 124140000 38979 46144 35457 47095 46176 46080 43095 48671 42647 47038 FALSE TRUE 37455.65759 44828.0183 41864.86864 49525.57859 47661.29298 47011.76917 43622.4095 47665.92684 37805.89135 43852.07436 0.854136506 1.022255365 0.954683883 1.129378241 1.086865186 1.072053486 0.994762737 1.086970857 0.862123215 1 15.42035747 5.348853595 1.344952045 1.036661305 0.317281619 0.308955678 0.074121389 6.590349178 3.279858738 0.019411789 9.688385898 223281.939 -5.348853595 -0.719379687 ESAS(ph)PTIPNLDLLEAHTK ddPTM_BT-474_Pertuzumab_2h_R1 6 ESASPTIPNLDLLEAHTK 18 0 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ES(0.353)AS(0.616)PT(0.031)IPNLDLLEAHTK;ES(0.15)AS(0.732)PT(0.118)IPNLDLLEAHTK;ESAS(0.888)PT(0.112)IPNLDLLEAHTK;ESAS(0.998)PT(0.002)IPNLDLLEAHTK;ESAS(0.991)PT(0.009)IPNLDLLEAHTK;ESAS(0.733)PT(0.267)IPNLDLLEAHTK 323.48 4.61E-62 2158796000 3717340 3116150 2626404 2784350 3434460 2754003 2636987 3138190 2995080 2558725 TRUE FALSE 3572062.243 3027280.453 3101053.627 2928050.637 3544932.525 2809690.828 2669259.236 3073385.28 2655091.075 2385420.277 1.497456141 1.269076348 1.300003046 1.227477885 1.486083002 1.177859874 1.118989078 1.288404106 1.113049596 1 21.18581204 5.350260357 0.034769736 5.27E-07 2.816932909 0.565275143 0.098986809 455.9251709 2.07568891 61.55356999 112.6947869 224006.3642 -5.350260357 2.816932382 MKEEVPTALVEAHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MKEEVPTALVEAHVR 15 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 ; 176.83 4.67E-07 603900000 902710 913700 761610 836290 884010 907690 886380 925600 988540 959150 FALSE TRUE 867431.0952 887642.1706 899249.8689 879451.0271 912444.9845 926044.1137 897227.7836 906486.0365 876325.0835 894185.9162 0.97007913 0.992681896 1.005663199 0.983521448 1.020419767 1.035628158 1.003401829 1.013755663 0.980025594 1 19.7702153 5.351518817 0.840916552 1.008464419 0.895117257 0.327506331 0.015420231 6.610252157 1.740554933 0.005174813 0.885040974 224656.4114 -5.351518817 -0.113347162 NLGS(ph)INTELQDVQR ddPTM_BT-474_Pertuzumab_2h_R1 3 NLGSINTELQDVQR 14 0 O75396;A0A087X1A9 O75396 SEC22B Vesicle-trafficking protein SEC22b 1 NLGS(1)INTELQDVQR;NLGS(1)INTELQDVQR;NLGS(0.853)INT(0.147)ELQDVQR 189.45 1.64E-07 365510000 264260 337684 257609 351737 316964 287814 295160 396325 377705 313680 TRUE FALSE 253932.427 328053.5829 304164.6768 369890.1887 327159.4349 293633.7963 298772.2564 388140.7503 334829.5119 292434.1742 0.868340466 1.121803168 1.04011331 1.264866494 1.118745563 1.004102195 1.021673535 1.327275621 1.144973951 1 18.15775239 5.353220704 1.447641365 1.13534692 1.58E-09 0.315977552 0.105750847 7.376988786 3.9463721 0.029527325 18.79010346 225538.5086 -5.353220704 -1.135346918 LPVPPLQQSLDHYLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPVPPLQQSLDHYLK 15 0 P43155-2;P43155;P43155-3;B7ZBP5;A6PVN3 P43155-2 CRAT Carnitine O-acetyltransferase 0 ; 182.35 5.50E-07 579170000 536320 742340 536670 846000 614830 668310 890930 833700 737630 704700 FALSE TRUE 515360.0215 721169.19 633658.2072 889662.1614 634606.5653 681823.6861 901833.4678 816483.8037 653897.3348 656970.0413 0.784449806 1.097720055 0.964516138 1.35418985 0.965959672 1.037830713 1.372716275 1.242802186 0.995322912 1 19.32546806 5.354945944 1.008494537 1.153268195 4.88E-17 0.293458753 0.149586042 6.749558414 2.291051272 0.044762082 11.33886167 226436.2447 -5.354945944 -1.153268195 ANTIPIIGS(ph)PSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ANTIPIIGSPSSK 13 0 E9PGM7;O94988-6;O94988-5;O94988-1;O94988 E9PGM7 FAM13A Protein FAM13A 1 ANTIPIIGS(0.718)PS(0.237)S(0.045)K;ANTIPIIGS(0.715)PS(0.242)S(0.043)K 159.81 4.71E-05 816040000 1226490 1246090 1120500 1260580 1312610 1270300 1418350 1460640 1676970 1552270 TRUE FALSE 1178557.415 1210552.733 1322999.275 1325638.685 1354831.293 1295986.336 1435708.192 1430477.274 1486607.396 1447133.37 0.814408291 0.836517738 0.914220695 0.916044583 0.936217297 0.895554178 0.992104958 0.988490282 1.027277393 1 20.46476646 5.358168269 0.267206799 1.024732935 0.554178869 0.849220738 0.026154136 4.548023278 0.209311674 0.034173613 0.745018749 228122.577 -5.358168269 -0.470554066 S(ph)LTSS(ph)LENIFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 2 S(0.999)LT(0.002)S(0.345)S(0.653)LENIFSR 123.29 0.00050198 31417000 111500 98098 85185 88757 86739 71047 96498 109950 98003 101210 TRUE FALSE 107142.4567 95300.34109 100579.8244 93337.75941 89529.03871 72483.61902 97678.97139 107679.4941 86878.1103 94354.95655 1.135525474 1.010019448 1.065972876 0.989219463 0.948853584 0.768201499 1.035228831 1.141217144 0.92075831 1 16.52581069 5.358583735 0.979854702 0.986356388 1.453818359 0.2048879 0.092117633 11.46611899 3.718289095 0.03134366 7.564763267 228340.9138 -5.358583735 0.467461971 GTGQS(ph)DDSDIWDDTALIK ddPTM_BT-474_Pertuzumab_2h_R1 5 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 GTGQS(1)DDSDIWDDTALIK;GTGQS(1)DDSDIWDDTALIK;GT(0.001)GQS(0.999)DDSDIWDDTALIK;GTGQS(1)DDSDIWDDTALIK;GTGQS(1)DDSDIWDDTALIK 410.69 2.35E-147 1399210000 1263930 1279120 1242780 1430680 1453030 1479970 1650980 1678580 1861800 1769130 TRUE FALSE 1214534.218 1242640.75 1467377.991 1504517.566 1499768.03 1509896.007 1671185.187 1643916.736 1650456.269 1649305.249 0.73639141 0.753432847 0.889694611 0.912212925 0.909333206 0.91547396 1.013266154 0.996732859 1.000697882 1 20.653427 5.358755099 0.365571803 1.016084571 0.321877639 0.914183748 0.027719889 2.538006455 0.191412394 0.024719626 0.847537084 228431.0303 -5.358755099 -0.694206931 GFVLQDTVEQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GFVLQDTVEQLR 12 0 P56192;P56192-2;H0YHV5;H0YIC2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 143.97 0.00014577 63153000 141037 173466 197135 167544 202928 186872 216670 294470 190424 205820 FALSE TRUE 135525.1181 168518.9195 232761.6797 176190.9659 209455.3634 190650.6799 219321.6723 288389.0916 168807.8658 191879.6281 0.706302798 0.878253315 1.213060928 0.918236958 1.091597714 0.993595213 1.143016976 1.502968786 0.879759188 1 17.54984202 5.3609329 0.635392171 1.154920628 7.78E-18 0.288316747 0.176716658 7.894452472 1.360497613 0.078661729 7.908222372 229579.3912 -5.3609329 -1.154920628 AASPYS(ph)QRPASPTAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AAS(0.001)PYS(0.5)QRPAS(0.25)PT(0.25)AIR 101.53 0.0035126 0 46692 54096 40865 59516 46879 49142 57306 63447 50445 45248 TRUE FALSE 44867.22502 52553.23505 48250.21454 62587.62789 48386.90561 50135.68491 58007.32797 62136.79728 44718.69508 42183.31266 1.063624979 1.245829968 1.14382232 1.483705853 1.147062726 1.188519387 1.375125004 1.473018437 1.060103919 1 15.36438477 5.364785347 1.123179202 1.27533594 0.52968859 0.054426452 0.159423316 12.31836135 4.750750608 0.045038766 15.26120889 231624.9545 -5.364785347 -0.745647351 GS(ph)SGSVDETLFALPAASEPVIR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSSGSVDETLFALPAASEPVIR 22 0 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 GS(0.458)S(0.458)GS(0.084)VDETLFALPAASEPVIR;GS(0.486)S(0.486)GS(0.028)VDETLFALPAASEPVIR;GS(0.979)S(0.019)GS(0.003)VDETLFALPAASEPVIR 208.37 7.31E-23 125176000 74677 95363 81575 121431 86598 101487 126972 120293 115891 124428 TRUE FALSE 71758.54028 92643.34061 96317.41713 127698.0685 89383.50332 103539.1367 128525.9213 117808.9075 102735.5395 116000.3807 0.618606075 0.798646867 0.830319836 1.100841805 0.770544913 0.892575835 1.107978444 1.015590697 0.885648296 1 16.82377001 5.3652555 0.665590943 0.981957813 1.12E-14 0.542220153 0.099953072 5.101600804 0.937551429 0.041049289 4.579358975 231875.8398 -5.3652555 -0.981957813 GSSVDAPPRPCHTTPDSQFGTEHVLR ddPTM_BT-474_Pertuzumab_2h_R1 3 GSSVDAPPRPCHTTPDSQFGTEHVLR 26 1 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ;; 228.71 6.48E-35 870970000 295287 533860 327184 639090 391880 514710 537110 419020 457310 460910 FALSE TRUE 283746.8576 518634.8355 386313.427 672073.5115 404485.1761 525117.7889 543683.3128 410367.0906 405398.086 429692.1552 0.660349169 1.206991632 0.899046963 1.564081409 0.941337121 1.222079069 1.265285638 0.955025791 0.943461688 1 18.71294391 5.365880502 0.002494718 1.017960495 1.145775439 0 0.239613237 40837067.13 12936.495 324124.2905 338806.035 232209.7772 -5.365880502 0.127814944 WESENK ddPTM_BT-474_Pertuzumab_2h_R1 4 WESENK 6 0 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;; 128.38 0.038736 4549320000 5451100 4911100 4242280 4238010 4412690 4441000 4659030 5121700 5524400 4810900 FALSE TRUE 5238064.985 4771040.236 5008954.365 4456734.204 4554628.181 4530800.063 4716048.603 5015935.105 4897293.272 4485053.458 1.167893546 1.063764408 1.116810404 0.99368586 1.015512574 1.01019979 1.05150332 1.118366849 1.091914136 1 22.09669375 5.369827655 1.183732017 1.051418986 1.481778888 0.401449553 0.043592757 6.993291885 2.855777561 0.013491215 5.339186471 234329.8718 -5.369827655 0.430359902 S(ph)LDTITLSGDER ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDTITLSGDER 12 0 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 S(1)LDTITLSGDER;S(1)LDTITLSGDER 175.68 2.83E-05 146109000 74268 107345 90508 132760 94046 104727 133140 151873 147985 125986 TRUE FALSE 71365.52445 104283.6257 106864.8089 139611.7595 97071.075 106844.6517 134769.4071 148736.7695 131186.3632 117452.856 0.607609954 0.887876457 0.909852792 1.188662109 0.826468409 0.909681172 1.147434058 1.26635294 1.116927827 1 16.84172227 5.371227751 0.485356324 1.123082842 1.17E-14 0.531994783 0.12852318 6.813475736 0.782000288 0.083282262 4.968621864 235086.5327 -5.371227751 -1.123082842 LDPDAIPSPIQVIEDDRNNR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDPDAIPSPIQVIEDDRNNR 20 1 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 120.11 3.75E-05 38665000 20470 27355 24723 27818 28425 30509 32923 33000 33718 34690 FALSE TRUE 19670.00977 26574.86218 29190.99606 29253.69031 29339.31594 31125.91288 33325.92152 32318.53847 29890.474 32340.4154 0.608217598 0.82172297 0.902616608 0.904555181 0.907202817 0.962446292 1.030472896 0.999323542 0.924245209 1 14.98105059 5.377299392 0.682068377 0.980517842 1.05E-24 0.905743474 0.035319722 1.962297976 0.369164456 0.014992702 1.814150682 238396.2347 -5.377299392 -0.980517842 FQPVHDLTIGVEFGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 FQPVHDLTIGVEFGAR 16 0 P61019;E9PKL7;A0A3B3ITL1;Q8WUD1;E9PE37;H0YD31 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 150.28 7.55E-07 1213460000 619040 794090 617600 852880 737890 800690 817240 786720 924790 844670 FALSE TRUE 594847.2324 771443.3307 729214.0584 896897.239 761624.902 816880.5004 827241.6276 770473.9571 819811.7162 787459.7485 0.755400176 0.979660652 0.926033438 1.138975345 0.967192169 1.037361595 1.050519254 0.978429638 1.041083964 1 19.58684666 5.378019216 1.196612071 1.022634802 5.33E-14 0.687334237 0.053233725 3.19716679 1.302072179 0.013927448 5.904356968 238791.6938 -5.378019216 -1.022634802 TRSDIVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TRSDIVSR 8 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ; 126.07 0.0011263 219168000 54945 72921 54738 73756 66010 75499 79084 73564 68362 77793 FALSE TRUE 52797.68866 70841.36448 64630.37424 77562.556 68133.2716 77025.64151 80051.85365 72044.87769 60601.83236 72524.01082 0.728002879 0.976798769 0.891158301 1.069474166 0.93945813 1.062070901 1.103797939 0.993393455 0.835610602 1 16.14617109 5.380578374 1.169177981 1.001458887 1.74E-10 0.48873979 0.078501354 5.029814374 1.981393267 0.021931044 8.858689586 240202.9706 -5.380578374 -1.001458887 S(ph)PPPPPPPPSDEALLHCVLEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPPPPPPPPSDEALLHCVLEGK 22 0 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 1 S(1)PPPPPPPPSDEALLHCVLEGK;S(1)PPPPPPPPSDEALLHCVLEGK;S(1)PPPPPPPPSDEALLHCVLEGK 269.89 8.02E-39 416958000 267034 241464 304645 369213 316740 314310 429221 429693 437461 487020 TRUE FALSE 256598.0161 234577.6831 359701.1283 388268.1272 326928.2298 320665.5636 434473.935 420819.6894 387802.2613 454033.7016 0.565151915 0.51665258 0.792234424 0.855152659 0.720052782 0.706259387 0.956920012 0.926846813 0.854126599 1 18.79243986 5.380675584 0.261640656 0.985877739 2.19E-13 0.700132768 0.084164677 7.549306209 0.333053059 0.116930289 2.540253265 240256.7425 -5.380675584 -0.985877739 LEEEEQNEEEEVDN ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEEEQNEEEEVDN 14 0 Q9NRF9 Q9NRF9 POLE3 DNA polymerase epsilon subunit 3 0 196.57 2.13E-07 0 74296 89582 113200 129080 98305 109190 144840 144720 138930 179080 FALSE TRUE 71392.43018 87027.20907 133657.7581 135741.8343 101467.0696 111397.8966 146612.5952 141731.4814 123159.2488 166950.7521 0.427625688 0.521274735 0.800581947 0.813065126 0.607766472 0.667250044 0.878178705 0.848941857 0.737698077 1 17.34906307 5.380742237 0.215679065 0.951778163 5.13E-31 0.611975351 0.10326506 12.7876959 0.422792855 0.198117277 3.409391572 240293.6181 -5.380742237 -0.951778163 VWIPDPDEVWR ddPTM_BT-474_Pertuzumab_2h_R1 3 VWIPDPDEVWR 11 0 Q9ULV0 Q9ULV0 MYO5B Unconventional myosin-Vb 0 ;; 129.38 0.00057264 256859000 429660 536730 441433 496590 530670 564950 508120 556570 562080 588920 FALSE TRUE 412868.4122 521422.9859 521209.7627 522219.0694 547739.4825 576373.6761 514338.5246 545076.635 498275.0348 549031.9238 0.751993453 0.94971342 0.949325058 0.951163396 0.997645963 1.049799932 0.936809869 0.992795886 0.907552026 1 19.06653051 5.381535101 1.364061699 0.977187545 2.93E-16 0.749515911 0.038026406 3.052125051 1.432668855 0.010094004 6.335597811 240732.708 -5.381535101 -0.977187545 ESLQQMAEVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESLQQMAEVTR 11 0 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 197.73 1.30E-07 371970000 227820 293440 225890 286400 260310 272830 311820 304260 310490 298310 FALSE TRUE 218916.5425 285071.3785 266713.3479 301181.1383 268683.1076 278346.8095 315636.1464 297976.9247 275244.4769 278105.198 0.787171704 1.025048725 0.959037623 1.082975581 0.966120409 1.000868777 1.134952344 1.071453992 0.989713529 1 18.08527118 5.383285084 1.322713846 1.038350451 6.20E-18 0.626085092 0.054359786 4.106976059 1.857460225 0.015116526 8.730393103 241704.6935 -5.383285084 -1.038350451 ELPEPLLTFDLYPHVVGFLNIDESQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELPEPLLTFDLYPHVVGFLNIDESQR 26 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 215.84 4.10E-34 955330000 507580 610060 481020 589240 638900 638160 626420 611330 551390 573570 FALSE TRUE 487743.2124 592661.6861 567951.0142 619650.747 659450.7987 651064.0324 634086.3153 598705.8219 488798.5188 534721.593 0.912144224 1.108355626 1.062143406 1.158828735 1.233260088 1.217575727 1.185825154 1.119658958 0.914117786 1 19.02842841 5.386941038 1.323319129 1.130861897 0.199366923 0.266737597 0.095109697 8.12092806 3.644871981 0.026309419 15.53118134 243747.9869 -5.386941038 -0.931494974 YDFGIYDDDPEIITLER ddPTM_BT-474_Pertuzumab_2h_R1 2 YDFGIYDDDPEIITLER 17 0 Q8IXB1-2;Q8IXB1;Q71S60;A0A087WXH7;E7EP04;A0A494C1G5;Q8IXB1-3 Q8IXB1-2 DNAJC10 DnaJ homolog subfamily C member 10 0 ; 180.28 2.02E-09 236160000 330110 437700 329720 419500 409190 437750 433500 430690 472030 498050 FALSE TRUE 317208.9362 425217.2246 389307.7386 441150.4453 422351.968 446601.6049 438805.3027 421796.101 418447.1333 464316.6299 0.683173757 0.915791503 0.838453145 0.950106925 0.909620592 0.961847102 0.945056185 0.90842342 0.901210739 1 18.82474943 5.39079154 1.193707786 0.929981892 7.37E-14 0.758946777 0.040949244 2.844426288 1.126349246 0.010689758 4.798396022 245918.6921 -5.39079154 -0.929981892 RYSPPIQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RYSPPIQR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 114.89 0.0077864 0 61853 73839 56363 68066 84300 82949 58007 85380 70507 63573 FALSE TRUE 59435.71638 71733.18402 66549.04789 71578.89442 87011.58606 84626.28561 58716.90702 83616.87316 62503.34095 59267.14409 1.002844279 1.210336437 1.122865779 1.207733147 1.468125171 1.427878581 0.990715985 1.410847012 1.054603557 1 15.85494492 5.390967413 1.030856016 1.244827263 0.413737581 0.101107727 0.168836284 11.82516769 3.898497662 0.048363059 14.95586975 246018.2999 -5.390967413 -0.831089682 TSSTCS(ph)NESLSVGGTSVTPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSSTCSNESLSVGGTSVTPR 20 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 TSST(0.001)CS(0.999)NESLSVGGTSVTPR 225.3 5.45E-25 175250000 81372 97775 89817 115830 99998 133370 145330 118480 157260 153180 TRUE FALSE 78191.89228 94986.55273 106048.9299 121808.0002 103214.5265 136066.8328 147108.592 116033.3466 139408.5041 142804.9822 0.547543168 0.665148731 0.742613656 0.852967441 0.722765585 0.952815726 1.030136272 0.812530101 0.976215969 1 17.12368679 5.391190897 0.356184236 0.968883208 8.55E-14 0.770213828 0.07306787 4.995698348 0.355316037 0.066307888 2.27626699 246144.9313 -5.391190897 -0.968883208 ENLPENVTASES(ph)DAEVER ddPTM_BT-474_Pertuzumab_2h_R1 1 ENLPENVTASESDAEVER 18 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;K7EMK2 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 1 ENLPENVTAS(0.001)ES(0.999)DAEVER 174.7 2.36E-14 0 41897 49338 37261 43400 46831 49635 43908 46062 52011 56045 TRUE FALSE 40259.61892 47930.92855 43994.89157 45639.8792 48337.36165 50638.65371 44445.35924 45110.8036 46106.92933 52249.02223 0.770533442 0.917355512 0.842023251 0.873506857 0.925134282 0.969178973 0.850644803 0.863380819 0.882445783 1 15.67311642 5.394223692 1.999711682 0.895185105 6.78E-07 0.370089069 0.049887163 12.74443753 7.611705325 0.01250548 40.04250687 247869.8429 -5.394223692 -0.895184427 EACAVPEPQESGS(ph)EEHLPLSQFTTVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EACAVPEPQESGSEEHLPLSQFTTVDR 27 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 EACAVPEPQES(0.027)GS(0.973)EEHLPLSQFTTVDR;EACAVPEPQES(0.15)GS(0.85)EEHLPLSQFTTVDR 206.83 1.68E-25 229400000 169155 215120 163455 214270 220300 233410 211440 199149 213366 227141 TRUE FALSE 162544.2356 208984.9882 192994.9545 225328.5004 227386.1496 238129.7101 214027.666 195036.5036 189145.5862 211756.5378 0.767599609 0.986911622 0.911400217 1.064092296 1.073809347 1.124544785 1.010725186 0.921041237 0.893221943 1 17.69204699 5.394359873 1.302143984 1.00516874 2.58E-08 0.487759617 0.071127818 6.275940823 2.722912471 0.021761914 12.75563764 247947.5794 -5.394359873 -1.005168715 FYHDWNDK ddPTM_BT-474_Pertuzumab_2h_R1 4 FYHDWNDK 8 0 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;; 161.02 0.00034996 1717240000 1924950 1742200 2004240 2320510 2055680 2076390 2409590 2489410 2987540 3194630 FALSE TRUE 1849720.826 1692514.162 2366450.752 2440271.799 2121802.814 2118376.028 2439079.283 2438002.814 2648406.984 2978254.865 0.621075398 0.568290572 0.794576307 0.819362986 0.712431578 0.711280977 0.818962578 0.818601135 0.889247934 1 21.50603579 5.395545532 0.08842341 1.212858265 6.10E-14 0.746820457 0.060434341 47.88656645 0.554597956 1.689676034 7.66382287 248625.421 -5.395545532 -1.212858265 VINAAHSFYNGTTTLPISDEDRT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 VINAAHSFYNGTT(0.001)T(0.005)LPIS(0.009)DEDRT(0.986)PR;VINAAHSFYNGTTTLPIS(0.001)DEDRT(0.999)PR 233.44 3.40E-38 973280000 412650 410610 285060 312910 320580 276430 235100 359530 218690 267970 TRUE FALSE 396523.1818 398899.8048 336576.6831 329059.3226 330891.7468 282019.604 237977.2241 352105.5799 193865.228 249820.1532 1.587234563 1.596747899 1.347275945 1.317184856 1.32451983 1.128890525 0.952594181 1.40943625 0.77601917 1 17.93053034 5.398486327 0.26728318 0.975176344 2.463573358 0.641665678 0.154810535 8.489319324 0.384197673 0.194389914 4.415413003 250314.6839 -5.398486327 1.488397014 GGVILVSHDER ddPTM_BT-474_Pertuzumab_2h_R1 3 GGVILVSHDER 11 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ;; 160.77 2.71E-05 901270000 1099180 1185280 950160 1141400 1133970 1193850 1211250 1117880 1225630 1250030 FALSE TRUE 1056222.83 1151476.975 1121875.048 1200307.791 1170445.175 1217990.465 1226073.64 1094795.387 1086501.621 1165364.355 0.906345579 0.988083229 0.962681794 1.029984988 1.004359856 1.045158503 1.052094682 0.939444718 0.932327831 1 20.15234966 5.404096954 1.282774189 0.997701624 0.605146443 0.321813113 0.038868951 8.780743808 3.669831657 0.011645224 6.882926839 253569.465 -5.404096954 -0.392555182 EWEEAER ddPTM_BT-474_Pertuzumab_2h_R1 2 EWEEAER 7 0 H7C0V9;E9PG40;P05067-7;P05067-11;P05067-8;P05067-9;P05067;A0A0A0MRG2;P05067-10;P05067-3;P05067-4;P05067-5;P05067-6;H7C2L2 H7C0V9 APP Amyloid beta A4 protein;N-APP;Soluble APP-alpha;Soluble APP-beta;C99;Beta-amyloid protein 42;Beta-amyloid protein 40;C83;P3(42);P3(40);C80;Gamma-secretase C-terminal fragment 59;Gamma-secretase C-terminal fragment 57;Gamma-secretase C-terminal fragment 50;C31 0 ; 161.6 0.0030313 755170000 703280 889620 734350 908270 817390 779910 937140 1035880 969170 1005600 FALSE TRUE 675795.0401 864248.9086 867063.3805 955145.9235 843682.0917 795680.3146 948608.9997 1014488.716 859153.8847 937489.8163 0.720855873 0.921875517 0.924877652 1.018833386 0.89993734 0.848734888 1.011860591 1.082133052 0.916440765 1 19.83844349 5.405041666 1.133086127 0.974108152 1.34E-12 0.553875865 0.064742138 5.139519734 1.860938066 0.020557235 8.594391431 254121.6498 -5.405041666 -0.974108152 LPGMEYVDGDFQCHTFDSS(ph)NVE ddPTM_BT-474_Pertuzumab_2h_R1 1 LPGMEYVDGDFQCHTFDSSNVE 22 0 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 LPGMEYVDGDFQCHTFDS(0.419)S(0.581)NVE 142.22 7.51E-08 87295000 80736 66777 38601 51616 40985 29937 29781 45330 41042 34097 TRUE FALSE 77580.74786 64872.58534 45577.05937 54279.90795 42303.31975 30542.34665 30145.46879 44393.91966 36383.08422 31787.57982 2.440599388 2.040815492 1.433800863 1.707582278 1.330812852 0.960826424 0.948341112 1.396580674 1.144569182 1 14.95617556 5.405677164 0.518933503 1.104830696 4.64520144 0.853226559 0.179687996 3.030663908 0.37344868 0.102992459 7.545132111 254493.7753 -5.405677164 3.540370744 up TPGRQS(ph)PGPGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPGRQSPGPGHR 12 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 TPGRQS(1)PGPGHR;T(0.001)PGRQS(0.999)PGPGHR 136.67 6.41E-05 220110000 119402 154154 125527 154280 159404 183346 168314 142444 182713 186863 TRUE FALSE 114735.6378 149757.6789 148212.5212 162242.4093 164531.3744 187053.3817 170373.8771 139502.4816 161972.1862 174206.6026 0.658618193 0.859655585 0.8507859 0.931321815 0.944461186 1.073744502 0.977998965 0.800787568 0.929770651 1 17.41043978 5.407693204 0.928509677 0.939739997 1.63E-16 0.622055083 0.067959294 4.843819403 1.355212346 0.023897106 6.1738436 255677.9081 -5.407693204 -0.939739997 SGGIVIS(ph)PFR ddPTM_BT-474_Pertuzumab_2h_R1 8 SGGIVISPFR 10 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR 142.29 3.78E-05 3840917000 1325237 1348606 1701444 1840024 1617566 1839252 1972252 2058249 2336660 2434590 TRUE FALSE 1273445.273 1310145.077 2008932.779 1934987.859 1669596.479 1876442.936 1996389.01 2015745.439 2071412.153 2269693.051 0.561064974 0.577234475 0.885112099 0.852532839 0.735604525 0.826738635 0.879585462 0.888113676 0.912639774 1 21.11406577 5.40838528 0.47728753 0.90365841 2.72E-57 0.719040343 0.072476021 4.800288467 0.522854417 0.045090619 2.787756536 256085.6717 -5.40838528 -0.90365841 IESS(ph)IQS(ph)LQDLS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 IESSIQSLQDLSK 13 0 A0A087X043;O43424-2;O43424 A0A087X043 GRID2 "Glutamate receptor ionotropic, delta-2" 3 IES(0.283)S(0.859)IQS(0.859)LQDLS(1)K 105.99 0.00094272 1067800000 302660 368850 516600 566530 431570 468790 584950 578040 650300 779350 TRUE FALSE 290831.7126 358330.7591 609961.1117 595768.6812 445451.841 478269.255 592108.7931 566103.272 576480.6703 726563.9303 0.40028372 0.49318545 0.839514716 0.819981087 0.6130938 0.658261765 0.814943831 0.779151357 0.793434199 1 19.47073022 5.409195405 0.176246271 0.975431545 9.67E-35 0.588433558 0.109150562 19.91568569 0.496740801 0.332068816 4.464315559 256563.8151 -5.409195405 -0.975431545 GSS(ph)GSVDETLFALPAASEPVIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSGSVDETLFALPAASEPVIR 22 0 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 GS(0.366)S(0.62)GS(0.015)VDETLFALPAASEPVIR 277.98 1.66E-45 37129000 34494 44083 41424 54592 36545 53672 55970 60027 59252 55550 TRUE FALSE 33145.93634 42825.796 48910.23827 57409.49966 37720.50311 54757.28461 56654.9776 58787.42147 52525.96136 51787.54902 0.640036784 0.82695159 0.944440106 1.108557959 0.728370117 1.057344587 1.093988394 1.135165162 1.014258492 1 15.66031766 5.410353786 0.564681581 1.056947922 2.06E-16 0.555534956 0.107176081 5.820223254 0.8069227 0.053698777 4.750552867 257249.0536 -5.410353786 -1.056947922 FAEHVFR ddPTM_BT-474_Pertuzumab_2h_R1 1 FAEHVFR 7 0 P37235;E9PC71;P61601;P84074;E5RI78;E5RIA5;E5RIZ1;E5RIG4;E5RHC8;E5RK89;E5RHE8;E5RI95;E5RGZ0;E5RJJ6;E5RJT1;E5RFL9;E5RGA9;A0A1B0GXG3 P37235 HPCAL1;NCALD;HPCA Hippocalcin-like protein 1;Neurocalcin-delta;Neuron-specific calcium-binding protein hippocalcin 0 88.942 0.018237 319700000 240980 319350 229250 374370 281220 265500 331880 402780 327180 286470 FALSE TRUE 231562.2352 310242.4507 270680.5746 393691.2806 290265.6967 270868.5919 335941.6467 394462.4522 290039.8981 267067.1317 0.867056285 1.161664667 1.013530092 1.474128538 1.086864171 1.0142341 1.257892143 1.477016096 1.086018696 1 18.02684291 5.412228796 0.992494982 1.220765675 1.29E-14 0.20432009 0.171833779 9.119980208 2.765166005 0.053132508 16.36893184 258362.0944 -5.412228796 -1.220765675 YPRPASVPPS(ph)PSLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YPRPASVPPSPSLSR 15 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 YPRPASVPPS(0.984)PS(0.016)LSR;YPRPAS(0.001)VPPS(0.998)PS(0.001)LSR 126.29 5.16E-05 1912730000 786794 954800 788980 883830 837580 874920 1035680 949930 1100210 1057140 TRUE FALSE 756045.2206 927570.0388 931566.2368 929444.5722 864521.5214 892611.4819 1048354.962 930313.6135 975318.7733 985538.9662 0.767138841 0.941180482 0.945235317 0.94308252 0.877206839 0.90570897 1.063737709 0.943964313 0.989629844 1 19.91055339 5.412963101 1.449955835 0.958267467 1.06E-09 0.572737554 0.049078239 5.608596242 2.589987695 0.013548347 12.58368216 258799.3023 -5.412963101 -0.958267466 IEIDNGDELTADFLYEEVHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 IEIDNGDELTADFLYEEVHPK 21 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ; 189.47 2.15E-17 41985000 41788 44427 41499 56391 49692 52588 55510 57814 76997 76890 FALSE TRUE 40154.87876 43159.98546 48998.79244 59301.34627 51290.38831 53651.36539 56189.34798 56620.1207 68256.62336 71682.17181 0.560179439 0.60210209 0.683556193 0.827281662 0.715525032 0.748461773 0.783867823 0.789877305 0.952211988 1 16.12932673 5.413536097 0.122130952 1.117228082 1.48E-13 0.835779168 0.053293784 19.46066223 0.315746839 0.481545486 3.614211239 259140.9799 -5.413536097 -1.117228082 EEVSEILDEMSHK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEVSEILDEMSHK 13 0 Q5TBH8;O15228;Q5TBH6;O15228-2 Q5TBH8 GNPAT Dihydroxyacetone phosphate acyltransferase 0 ;; 190.85 4.06E-06 175912000 229393 281545 247126 327165 262745 313025 366120 344744 442881 454098 FALSE TRUE 220428.068 273515.6123 291787.1655 344050.0249 271196.4315 319354.58 370600.6861 337624.9159 392607.0056 423341.538 0.520686132 0.64608735 0.689247662 0.812700843 0.640609076 0.754366277 0.875417725 0.797523715 0.927400149 1 18.69146253 5.413631169 0.140522063 1.087598708 1.46E-14 0.81291605 0.059973714 15.02068163 0.285012711 0.322644958 3.052144539 259197.7151 -5.413631169 -1.087598708 VAELALSLSST(ph)SDDEPPSSVSHGAK ddPTM_BT-474_Pertuzumab_2h_R1 5 VAELALSLSSTSDDEPPSSVSHGAK 25 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 1 VAELALSLSS(0.023)T(0.544)S(0.433)DDEPPSSVSHGAK;VAELALSLSS(0.002)T(0.969)S(0.029)DDEPPSSVSHGAK;VAELALSLSS(0.003)T(0.959)S(0.038)DDEPPSSVSHGAK;VAELALSLS(0.003)S(0.09)T(0.527)S(0.38)DDEPPSSVSHGAK;VAELALSLSS(0.004)T(0.589)S(0.408)DDEPPSSVSHGAK 344.07 2.11E-88 3313820000 1472400 1824151 1470849 1819840 1667116 1855135 1836721 1785897 2031540 2147900 TRUE FALSE 1414856.98 1772128 1736664.133 1913762.16 1720740.3 1892647.101 1859199.341 1749017.603 1800928.096 2002420.82 0.706573247 0.884992796 0.867282299 0.955724262 0.859330009 0.945179496 0.928475834 0.873451567 0.899375435 1 20.93331377 5.414459218 1.285712874 0.91301842 1.76E-11 0.695468337 0.041440583 3.620570925 1.483109241 0.010576824 6.661374158 259692.387 -5.414459218 -0.91301842 EVVEAHVDQK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVVEAHVDQK 10 0 P0DPI2-2;A0A0B4J2D5-2;P0DPI2;A0A0B4J2D5;A0A096LNH5;A0A096LPI6;H7C1F6;H7C2G3 P0DPI2-2 C21orf33 0 ; 84.658 0.014771 1209780000 1718060 2122310 1466990 2626500 1509830 1722590 2516100 2126500 2128250 1695720 FALSE TRUE 1650916.316 2061783.797 1732107.726 2762053.98 1558395.053 1757421.95 2546892.784 2082587.032 1886659.982 1580867.374 1.044310448 1.30421048 1.095669222 1.747176281 0.985784816 1.111682092 1.611073026 1.31736986 1.193433436 1 20.59228491 5.415425935 1.51141952 1.291357093 7.83E-13 0.057230525 0.238826476 20.94376361 9.95374114 0.060922014 66.87714985 260271.0926 -5.415425935 -1.291357093 EEDRPPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEDRPPLR 8 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ;;; 173.48 0.00025312 1448380000 1459530 1731160 1388120 1740100 1735270 1799000 1821860 1798500 1854960 1878000 FALSE TRUE 1402489.954 1681789.012 1638984.163 1829906.77 1791086.535 1835377.013 1844156.468 1761360.347 1644392.717 1750801.387 0.801055999 0.960582408 0.93613369 1.045182385 1.023009548 1.048306807 1.053321342 1.006030929 0.939222878 1 20.739584 5.415697547 0.945825826 1.018003076 0.274489523 0.743070121 0.036966485 3.10041853 0.878294757 0.011529284 3.206875501 260433.9196 -5.415697547 -0.743513553 LLIQESVWDEAMR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLIQESVWDEAMR 13 0 Q8IZ83;F5H4B6;Q8IZ83-3 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 ; 171.32 5.88E-05 41822000 48798 60457 47003 62825 58163 65864 62646 60003 61236 65913 FALSE TRUE 46890.92021 58732.82555 55497.48768 66067.40578 60033.86572 67195.81521 63412.68049 58763.91708 54284.746 61448.6538 0.76309109 0.955803291 0.903152213 1.075164413 0.976976093 1.093527865 1.031962078 0.956309267 0.883416359 1 15.90709378 5.417003522 1.096312192 0.998739579 0.094578321 0.548241858 0.062296324 4.941411629 1.682372474 0.01832432 7.417449339 261218.2536 -5.417003522 -0.904161258 S(ph)PPSTGSTYGSSQK ddPTM_BT-474_Pertuzumab_2h_R1 8 SPPSTGSTYGSSQK 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.997)PPST(0.002)GSTYGSSQK;S(0.97)PPS(0.025)T(0.004)GS(0.001)TYGSSQK;S(0.999)PPS(0.001)TGSTYGSSQK;S(0.999)PPS(0.001)TGSTYGSSQK;S(0.996)PPS(0.004)T(0.001)GSTYGSSQK;S(0.984)PPS(0.015)TGSTYGSSQK;S(0.999)PPS(0.001)TGSTYGSSQK;S(0.992)PPS(0.007)T(0.001)GSTYGSSQK 256.96 2.61E-24 12908170000 1256016 1136949 1431299 1640972 1458804 1322575 1778667 1948327 2075376 2282939 TRUE FALSE 1206929.506 1104524.328 1689966.568 1725662.762 1505727.756 1349318.373 1800434.859 1908093.367 1839788.017 2128313.508 0.567082576 0.51896693 0.79404024 0.810812296 0.707474604 0.633984781 0.845944384 0.896528335 0.864434685 1 21.02127925 5.417137113 0.15014598 1.072862895 6.82E-16 0.69031636 0.081040307 19.14972595 0.391883152 0.385338513 4.06908695 261298.6184 -5.417137113 -1.072862895 ALSCHPDKNPDNPR ddPTM_BT-474_Pertuzumab_2h_R1 3 ALSCHPDKNPDNPR 14 1 H0YLQ7;Q9NVM6;S4R343;H0YK99 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 0 ;; 167.55 2.18E-06 529410000 350083 428628 313499 445343 388303 449680 410459 400672 398706 454739 FALSE TRUE 336401.3693 416403.9491 370155.243 468327.2056 400793.1186 458772.8377 415482.32 392397.9832 353446.5664 423939.1225 0.793513388 0.982225813 0.873133012 1.104703909 0.945402529 1.082166786 0.980051847 0.925599838 0.833720097 1 18.69349758 5.42285344 1.535278683 0.972774171 4.67E-12 0.299646498 0.079540197 10.3281205 4.870654342 0.020806425 25.47623157 264760.6506 -5.42285344 -0.972774171 ELNSNHDGADETSEK ddPTM_BT-474_Pertuzumab_2h_R1 8 ELNSNHDGADETSEK 15 0 Q01105-2 Q01105-2 SET Protein SET 0 ;;;;;;; 246.03 3.84E-18 10613900000 6445089 7396723 7460013 9643704 7438716 7682856 9394850 9360488 10793000 12227151 FALSE TRUE 6193207.796 7185775.702 8808203.296 10141416.72 7677989.056 7838208.612 9509826.985 9167190.652 9567823.888 11398995.17 0.543311731 0.630386766 0.772717521 0.889676376 0.673567182 0.687622768 0.834268884 0.804210416 0.83935678 1 23.44240332 5.42453838 0.081389818 1.220652925 1.44E-12 0.634894869 0.07743789 77.98551579 0.822538029 2.904394299 11.9010998 265789.8427 -5.42453838 -1.220652925 ELNNYEIRPGR ddPTM_BT-474_Pertuzumab_2h_R1 6 ELNNYEIRPGR 11 1 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7 B7Z8Z7 RBM47 RNA-binding protein 47 0 ;;;;; 223.31 6.41E-12 5252940000 2325270 2872390 2167654 2974760 2773259 2701753 2940310 2888311 2766969 2874908 FALSE TRUE 2234395.878 2790472.25 2559397.297 3128287.72 2862463.394 2756384.297 2976294.393 2828666.369 2452874.279 2680187.92 0.833671348 1.041147984 0.954932032 1.167189695 1.068008468 1.02842949 1.110479743 1.055398521 0.915187424 1 21.35390273 5.424705416 1.379449759 1.050534204 6.24E-17 0.428419243 0.069373751 6.545387835 2.807372953 0.018149885 15.22994878 265892.089 -5.424705416 -1.050534204 ADIEER ddPTM_BT-474_Pertuzumab_2h_R1 1 ADIEER 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 114.54 0.058621 505790000 600920 671520 520960 685650 613960 703570 648910 671420 691510 727520 FALSE TRUE 577435.382 652368.9071 615109.0607 721036.4787 633708.581 717796.6675 656851.5547 657554.9424 613012.6838 678244.4224 0.851367682 0.961849277 0.906913556 1.063092382 0.93433659 1.058315622 0.968458469 0.96949554 0.903822669 1 19.37144575 5.425508205 1.085222895 0.980264997 0.485472507 0.350801247 0.051251964 7.064900619 2.340256711 0.014063263 5.758190433 266384.0422 -5.425508205 -0.494792491 VASGS(ph)DLHLTDIDSDSNR ddPTM_BT-474_Pertuzumab_2h_R1 1 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VAS(0.286)GS(0.713)DLHLTDIDSDSNR 122.46 3.78E-05 409240000 50063 56142 58164 73440 60011 74338 78776 73065 93175 89469 TRUE FALSE 48106.48261 54540.88513 68675.52865 77230.2472 61941.30832 75841.16529 79740.08425 71556.18222 82598.16462 83409.18494 0.57675282 0.653895433 0.823356908 0.925920176 0.742619753 0.909266352 0.956010832 0.857893316 0.990276607 1 16.34791864 5.427072027 0.470817687 0.938027524 3.15E-16 0.770767362 0.065596026 4.225018964 0.445005784 0.040494642 2.519339973 267344.9758 -5.427072027 -0.938027524 DRIELLQDAEPLDFNAETFTDDPLESESGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRIELLQDAEPLDFNAETFTDDPLESESGR 30 1 Q68DH5 Q68DH5 LMBRD2 LMBR1 domain-containing protein 2 0 ; 164.22 3.08E-12 170148000 35865 47288 36047 48367 38932 44529 48089 53927 51028 47956 FALSE TRUE 34463.35615 45939.39254 42561.49476 50863.22667 40184.28314 45429.40689 48677.52757 52813.3886 45235.51537 44707.89741 0.770856116 1.02754536 0.951990526 1.137678791 0.898818452 1.016138301 1.088790357 1.181298868 1.011801449 1 15.44824208 5.429599319 1.075471944 1.056733986 2.09E-29 0.479268279 0.080742299 5.820657136 1.893629553 0.024670608 10.04320986 268905.2733 -5.429599319 -1.056733986 VEFEELCADLFER ddPTM_BT-474_Pertuzumab_2h_R1 6 VEFEELCADLFER 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;;;; 229.16 1.45E-11 635127000 349503 418135 334883 432678 398775 438744 422037 411565 474248 504233 FALSE TRUE 335844.0364 406210.1992 395403.8075 455008.5634 411601.96 447615.7043 427202.0151 403066.0389 420413.3552 470080.8498 0.714438881 0.864128371 0.841140003 0.967936821 0.87559823 0.952210039 0.908784128 0.857439819 0.894342655 1 18.84254938 5.429678057 1.033825011 0.910241038 0.173469971 0.639460191 0.045533074 4.15621592 1.288924067 0.012989482 4.767547706 268954.0306 -5.429678057 -0.736771067 GAQGEPHDVAPNGPSAGGLAIPQSSSSSSRPPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GAQGEPHDVAPNGPSAGGLAIPQSSSSSSRPPTR 34 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 157.1 1.01E-11 207020000 43950 54078 43967 55967 46660 52877 58982 61149 53287 52057 FALSE TRUE 42232.38541 52535.74839 51912.81494 58855.46358 48160.86128 53946.20917 59703.83936 59886.25178 47238.08316 48531.13302 0.870212228 1.08251642 1.069680671 1.212736236 0.992370429 1.11157943 1.230217298 1.233975967 0.973356281 1 15.56662292 5.431185996 1.223887016 1.126858896 6.26E-07 0.329195768 0.09495445 7.351094362 2.759254266 0.026778194 15.85876663 269889.5048 -5.431185996 -1.126858269 ELEDYIDNLLVR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELEDYIDNLLVR 12 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q7L804;Q7L804-2;Q6WKZ4-1 Q6WKZ4 RAB11FIP1;RAB11FIP2 Rab11 family-interacting protein 1;Rab11 family-interacting protein 2 0 ;; 135.66 0.00028781 75955000 84011 111424 81964 127762 94238 106158 123867 124699 117668 118482 FALSE TRUE 80727.75724 108246.2966 96776.71808 134355.8121 97269.25085 108304.5875 125382.9214 122123.9221 104310.8219 110457.1086 0.730851624 0.979984883 0.876147487 1.216361842 0.880606528 0.980512607 1.13512768 1.105623021 0.944355898 1 16.75312674 5.431415925 0.92310141 1.04100228 7.21E-12 0.41228606 0.102818397 6.178900396 1.6562952 0.031436692 8.757181779 270032.4304 -5.431415925 -1.04100228 HVLTGSADNSCR ddPTM_BT-474_Pertuzumab_2h_R1 7 HVLTGSADNSCR 12 0 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;;;;;; 240.65 3.24E-16 2618552000 1367910 1598540 1209207 1605352.4 1509439 1525129 1552051.9 1398508.6 1747385 1751836 FALSE TRUE 1314450.565 1552951.204 1427737.604 1688204.83 1557991.476 1555968.153 1571046.375 1369628.909 1549029.18 1633182.587 0.804839933 0.950874211 0.874205747 1.033690197 0.953960377 0.952721493 0.96195391 0.838625711 0.94847275 1 20.63925466 5.435031071 1.709385917 0.939655628 0.053226872 0.373714261 0.053457811 11.60847516 5.654349648 0.014413811 30.26025993 272289.6107 -5.435031071 -0.886428756 ASLGS(ph)LEGEAEAEAS(ph)SPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 ASLGS(1)LEGEAEAEAS(0.562)S(0.438)PK;AS(0.062)LGS(0.938)LEGEAEAEAS(0.635)S(0.365)PK 239.8 9.16E-24 404894000 318690 303354 304727 329280 298959 353770 392310 349860 427240 391720 TRUE FALSE 306235.2425 294702.6409 359797.9475 346274.1803 308575.2877 360923.4718 397111.2071 342635.2687 378741.5063 365188.4555 0.838567698 0.806987835 0.985239106 0.94820681 0.844975473 0.988321143 1.08741446 0.938242334 1.037112484 1 18.47828163 5.435517127 0.343500967 1.017115941 0.542307383 0.491937124 0.062000319 9.25386725 0.607523681 0.058376194 2.001163345 272594.5236 -5.435517127 -0.474808558 SVDPTLALSVYLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVDPTLALSVYLR 13 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 187.42 1.62E-05 231930000 141371 176113 130183 174449 163961 152594 177271 175831 195270 175311 FALSE TRUE 135846.065 171090.4297 153709.964 183452.3338 169234.9545 155679.5552 179440.4955 172200.0284 173103.7682 163437.0298 0.831182904 1.04682782 0.940484321 1.122464927 1.035474976 0.952535392 1.097918236 1.053616972 1.059146562 1 17.31837537 5.436085653 1.393257131 1.041671844 1.48E-15 0.534877216 0.055721455 5.672888505 2.388651389 0.014355763 13.35034985 272951.6055 -5.436085653 -1.041671844 HSQAVEELAEQLEQTKR ddPTM_BT-474_Pertuzumab_2h_R1 6 HSQAVEELAEQLEQTKR 17 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 268.23 4.14E-28 5506320000 6738020 6503700 5424570 5959720 6266040 6526490 6610280 5204900 8414660 7603540 FALSE TRUE 6474690.729 6318220.844 6404910.468 6267301.863 6467592.867 6658460.099 6691178.584 5097416.996 7459463.074 7088545.463 0.913401877 0.891328253 0.903557789 0.884144977 0.912400562 0.939326712 0.943942395 0.719106201 1.052326336 1 22.75705819 5.440003416 4.17238676 0.899824371 1.847993368 0 0.083635864 7788.98104 1600.27385 0.019950486 68421.17233 275425.037 -5.440003416 0.948168997 ASS(ph)HS(ph)SQTQGGGSVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.123)S(0.808)HS(0.595)S(0.473)QT(0.001)QGGGSVTK;AS(0.022)S(0.869)HS(0.755)S(0.354)QT(0.001)QGGGSVTK 172.57 2.39E-09 4960030000 2707570 2208750 1331460 1284810 1426500 1161910 675210 1383410 1243890 1000220 TRUE FALSE 2601755.171 2145758.613 1572084.44 1351119.198 1472384.668 1185404.616 683473.422 1354842.1 1102688.822 932474.2085 2.790163146 2.301145268 1.685928067 1.448961468 1.579008464 1.271246545 0.732967642 1.452953967 1.182540827 1 19.8307043 5.441446526 0.526209794 1.124853661 5.735004666 0.881200036 0.198707805 2.615476185 0.319374954 0.106874254 8.681396456 276341.7644 -5.441446526 4.610151005 up SVVDMDLDDTDDGDDNAPLFYQPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVVDMDLDDTDDGDDNAPLFYQPGK 25 0 E7EMW7;O95071-2;O95071;E7ET84 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 0 116.48 0.0012676 51011000 34976 38973 36161 48123 44744 42377 52051 48643 53905 66682 FALSE TRUE 33609.09925 37861.5282 42696.0971 50606.6338 46183.2314 43233.89197 52688.01571 47638.50505 47785.93039 62165.56875 0.540638491 0.609043381 0.686812619 0.814062106 0.742906923 0.695463628 0.847543371 0.766316564 0.768688059 1 15.92382812 5.443260187 0.093695725 1.154507269 1.29E-18 0.764117677 0.05895948 41.97630402 0.509423307 1.317497928 6.617845713 277498.2105 -5.443260187 -1.154507269 ECPSDECGAGVFMASHFDR ddPTM_BT-474_Pertuzumab_2h_R1 11 ECPSDECGAGVFMASHFDR 19 0 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;;;;;;;;; 363.39 3.49E-92 35967100000 5139629 5696806 4551317 5470938 5470304 6144896 5449161 5341043 5737971 6390864 FALSE TRUE 4938766.617 5534338.671 5373841.225 5753293.766 5646261.296 6269150.007 5515849.462 5230748.596 5086620.588 5958005.089 0.828929573 0.928891229 0.901953111 0.965640962 0.947676481 1.052223003 0.925787974 0.877936242 0.853745593 1 22.50639793 5.445600366 1.326607625 0.938481312 0.400355726 0.271163269 0.054623203 11.55161151 4.551429237 0.016001723 13.27595096 278997.535 -5.445600366 -0.538125585 YRDAVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YRDAVSR 7 1 E7EST3;E9PKV8;Q8N5M4;Q8N5M4-2 E7EST3 TTC9C Tetratricopeptide repeat protein 9C 0 66.073 0.062803 24790000 22808 31282 21406 31077 31114 28611 31608 40304 19785 25549 FALSE TRUE 21916.63814 30389.86799 25274.54037 32680.88769 32114.81007 29189.53402 31994.82816 39471.70832 17539.08975 23818.54347 0.920150225 1.275891115 1.061128713 1.372077505 1.348311248 1.225496179 1.343273916 1.657183965 0.736362816 1 14.53979757 5.446797876 0.992554864 1.289112892 9.37E-17 0.074736259 0.243299569 13.1821559 3.780741263 0.071614212 25.40367637 279767.8957 -5.446797876 -1.289112892 SS(ph)SPAPADIAQTVQEDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 S(0.009)S(0.841)S(0.15)PAPADIAQTVQEDLR;S(0.014)S(0.493)S(0.493)PAPADIAQTVQEDLR 377.21 6.05E-108 61318000000 5581870 6808590 5458820 6589300 6492570 7484400 5878530 7220300 6952700 7664400 TRUE FALSE 5363724.349 6614415.68 6445350.205 6929374.563 6701409.41 7635739.696 5950473.209 7071198.282 6163458.644 7145283.361 0.75066643 0.925703761 0.902042631 0.969783032 0.937878748 1.068640572 0.832783377 0.989631611 0.862591213 1 22.76855979 5.447041458 1.293838535 0.948559509 5.06E-11 0.445003048 0.064909269 6.421261417 2.463576009 0.016404569 12.61546121 279924.8522 -5.447041458 -0.948559509 GLFDEYGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLFDEYGSK 9 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 175.91 0.0001246 580330000 680700 805990 635840 745060 716340 746670 820340 751000 969120 868870 FALSE TRUE 654097.4914 783003.9543 750750.4322 783512.6359 739381.7267 761768.179 830379.5663 735491.5876 859109.5605 810020.661 0.80750717 0.966646892 0.926828744 0.967274878 0.912793664 0.940430554 1.02513381 0.907991145 1.060602034 1 19.62759918 5.447413113 1.593600335 0.963268152 1.09E-10 0.495898145 0.047634713 7.55612014 3.411465207 0.01166932 19.69413513 280164.5054 -5.447413113 -0.963268152 KALEIS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 KALEISPR 8 1 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 KALEIS(1)PR 74.698 0.015239 0 369400 432290 322030 404300 406110 394920 395980 434130 474240 419180 TRUE FALSE 354963.4396 419961.5125 380227.9845 425165.9715 419172.897 402905.553 400826.1217 425165.0638 420406.2634 390788.5652 0.908326065 1.074651486 0.972976229 1.087969325 1.072633476 1.031006505 1.025685389 1.087967002 1.075789572 1 18.57602873 5.447597705 1.796438595 1.051574129 5.58E-15 0.52433327 0.038688627 8.450624266 4.034846997 0.009594815 28.14898158 280283.6117 -5.447597705 -1.051574129 IT(ph)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 33 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;IT(0.843)PEPAVS(0.057)NT(0.064)EEPS(0.015)T(0.015)T(0.004)S(0.001)T(0.001)AS(0.001)NYPDVLTRPSLHR 194.25 1.51E-20 1996280000 183715 195194 227970 279257 201790 205702 271389 300463 338483 355967 TRUE FALSE 176535.2147 189627.2582 269169.2502 293669.4872 208280.7586 209861.4354 274710.3398 294258.3341 300059.8289 331857.038 0.531961641 0.571412495 0.81110002 0.884927706 0.627621942 0.632385067 0.827797239 0.886702105 0.904184014 1 18.34020235 5.450738365 0.127058213 1.115588519 3.41E-14 0.593968622 0.098308191 34.52259442 0.578532622 0.808169593 6.604048178 282317.8674 -5.450738365 -1.115588519 NLAS(ph)PEGTLATLGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NLASPEGTLATLGLK 15 0 Q8TDJ6-3;Q8TDJ6;Q8TDJ6-2 Q8TDJ6-3 DMXL2 DmX-like protein 2 1 NLAS(0.98)PEGT(0.02)LATLGLK 125.98 9.14E-05 41836000 109100 123110 135190 120670 129590 150610 143280 152830 150810 185260 TRUE FALSE 104836.2514 119599.0233 159621.8403 126897.7932 133758.38 153655.4374 145033.5035 149674.0071 133690.681 172712.1752 0.606999774 0.692475925 0.924207226 0.734735655 0.774458314 0.889661874 0.839741051 0.866609473 0.774066338 1 17.39801026 5.450767022 0.826400089 0.84889427 4.86E-16 0.497061445 0.078593755 5.565433455 1.25615496 0.024848035 5.693779245 282336.4973 -5.450767022 -0.84889427 VAGDLGAGSSPHPSLTEEEDSQTELLIAEEKLS(ph)PEQEGQLMPR ddPTM_BT-474_Pertuzumab_2h_R1 4 VAGDLGAGSSPHPSLTEEEDSQTELLIAEEKLSPEQEGQLMPR 43 1 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 VAGDLGAGSSPHPSLTEEEDS(0.044)QT(0.044)ELLIAEEKLS(0.911)PEQEGQLMPR;VAGDLGAGSSPHPSLTEEEDSQTELLIAEEKLS(1)PEQEGQLMPR;VAGDLGAGSSPHPSLTEEEDSQTELLIAEEKLS(1)PEQEGQLMPR;VAGDLGAGSSPHPSLTEEEDSQTELLIAEEKLS(1)PEQEGQLMPR 342.05 3.75E-134 1086590000 131862 153242 123464 149130 156067 155201 142021 155877 173720 168360 TRUE FALSE 126708.6873 148871.6882 145776.6912 156826.6172 161087.0368 158339.2706 143759.0955 152658.0855 154000.0339 156956.8272 0.807283694 0.948488134 0.928769355 0.999170408 1.026314303 1.008807793 0.915914892 0.972611948 0.981161741 1 17.26000826 5.452460863 1.133777033 0.980534294 0.243569204 0.73216341 0.03142961 3.871817823 1.283103649 0.009590951 5.029294822 283439.8194 -5.452460863 -0.73696509 RCS(ph)VTSMESTVSSGTQTTVQDDPEQFEVIK ddPTM_BT-474_Pertuzumab_2h_R1 4 RCSVTSMESTVSSGTQTTVQDDPEQFEVIK 30 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 RCS(0.994)VT(0.005)SMESTVSSGTQTTVQDDPEQFEVIK;RCS(0.999)VT(0.001)SMESTVSSGTQTTVQDDPEQFEVIK;RCS(0.995)VT(0.004)SMESTVSSGTQTTVQDDPEQFEVIK;RCS(0.995)VT(0.005)SMESTVSSGTQTTVQDDPEQFEVIK 303.94 1.03E-81 2237890000 869690 1045150 921580 1066200 1201420 1340080 1423440 1307780 1657330 1638900 TRUE FALSE 835701.5533 1015343.345 1088130.006 1121226.71 1240064.765 1367177.336 1440860.485 1280773.886 1469196.846 1527895.843 0.546962384 0.664537017 0.712175513 0.733837136 0.811616034 0.89481056 0.943035804 0.838259945 0.961581807 1 20.54311477 5.453002452 0.270049753 0.991777757 1.84E-24 0.929622357 0.03661392 3.359166688 0.150881591 0.048583297 1.182432886 283793.5053 -5.453002452 -0.991777757 EAYDNGLPLLPHTLCAAILDQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAYDNGLPLLPHTLCAAILDQDR 23 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 0 ; 224.95 1.23E-32 66572000 69362 81644 64646 80285 77252 83142 78355 78726 86351 92172 FALSE TRUE 66651.25636 79315.59306 76328.97024 84428.51847 79736.88074 84823.18821 79313.93193 77100.28059 76548.79649 85929.10834 0.775653997 0.923035216 0.888278393 0.982536885 0.927937951 0.987129854 0.923015884 0.897254517 0.890836621 1 16.3908593 5.455190681 1.374594466 0.935226998 0.097644383 0.607113244 0.038693134 5.517928473 2.193010335 0.010451386 10.38652994 285227.031 -5.455190681 -0.837582614 TELEETTAEAEEEIQALTAHR ddPTM_BT-474_Pertuzumab_2h_R1 3 TELEETTAEAEEEIQALTAHR 21 0 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 0 ;; 230.05 1.07E-25 99928000 41769.4 50575 47078.7 56213 51589.2 52034.9 61207 61407 68776 60631 FALSE TRUE 40137.00567 49132.65052 55586.86835 59114.15967 53248.61347 53087.08133 61956.06958 60138.92399 60968.83681 56524.40837 0.710082721 0.869228921 0.983413537 1.045816513 0.942046366 0.939188624 1.096094083 1.063946103 1.078628482 1 15.78658637 5.456869454 0.736489286 1.037915046 7.90E-16 0.79585925 0.050051195 3.248171273 0.623654308 0.019938569 3.562143896 286331.715 -5.456869454 -1.037915046 SMDSYLNQSYGMDNHSGGGGGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMDSYLNQSYGMDNHSGGGGGSR 23 0 Q5BKZ1;Q5BKZ1-2 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 198.48 2.78E-24 369220000 228310 251210 188560 256630 224760 267020 268190 229000 220550 286260 FALSE TRUE 219387.3928 244045.7368 222636.9865 269874.7051 231989.6095 272419.3273 271472.1894 224271.07 195514.0886 266871.3552 0.822071715 0.914469582 0.834248345 1.011253924 0.869293781 1.020788938 1.017239895 0.840371458 0.73261549 1 18.02578494 5.458004729 1.063573004 0.918585916 0.538983646 0.087358923 0.092348255 19.86371118 6.066605766 0.027500517 12.32383243 287081.1845 -5.458004729 -0.37960227 VNNADDFPNLFR ddPTM_BT-474_Pertuzumab_2h_R1 3 VNNADDFPNLFR 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 222.74 5.60E-11 376469000 517850 573260 592900 701880 686830 700610 766430 780110 861950 910030 FALSE TRUE 497611.8495 556911.1861 700050.219 738104.1109 708922.5107 714776.8142 775809.7996 764000.4559 764105.0496 848392.8575 0.586534699 0.656430781 0.825148648 0.87000274 0.835606411 0.842506874 0.914446406 0.900526742 0.900650026 1 19.69437295 5.458300798 0.501918128 0.918525077 1.41E-20 0.885190732 0.039675328 2.674428838 0.301376707 0.022239576 1.685519481 287276.9612 -5.458300798 -0.918525077 SSESPSSSPSS(ph)PARK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPSSS(0.006)PS(0.138)S(0.856)PARK;SSESPSSSPS(0.193)S(0.807)PARK 193.19 6.32E-08 462010000 140004 192378 139468 178253 207670 190595 209850 181527 209418 206440 TRUE FALSE 134532.4889 186891.5678 164672.97 187452.6587 214349.8942 194448.9615 212418.2071 177778.404 185645.7466 192457.6349 0.699023912 0.971079001 0.855632306 0.9739944 1.113751056 1.010346831 1.103714109 0.923727469 0.964605778 1 17.55418138 5.461597563 0.873017301 1.0093553 2.48E-17 0.616695048 0.070334269 4.840634377 1.156219559 0.023237623 6.309096359 289466.0019 -5.461597563 -1.0093553 EEGLGFPSFLDPDR ddPTM_BT-474_Pertuzumab_2h_R1 6 EEGLGFPSFLDPDR 14 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ;;;;; 226.4 5.62E-12 584335000 319694 340804 372437 444425 413934 401423 443221 499681 510750 575658 FALSE TRUE 307200.005 331084.6036 439744.6507 467361.8275 427248.563 409540.0481 448645.2712 489362.4127 452771.8012 536668.1709 0.572420765 0.616926104 0.819397674 0.870858107 0.796113103 0.763115963 0.835982634 0.911852872 0.843671799 1 19.0336708 5.464144904 0.522972599 0.879797094 3.22E-37 0.724874571 0.063746832 4.623746597 0.549429433 0.034820599 2.924564062 291168.8451 -5.464144904 -0.879797094 GDIYFCTGYDPPMKPYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDIYFCTGYDPPMKPYGR 18 1 Q9NRV9;A0A3B3IRV5 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 112.3 0.00025523 1208810000 1237430 1401590 1020190 1388830 1235270 1310770 1341620 1345680 1421680 1446180 FALSE TRUE 1189069.868 1361618.026 1204561.027 1460507.683 1275003.581 1337274.667 1358039.147 1317891.238 1260296.847 1348228.94 0.88194952 1.009930869 0.893439527 1.083278692 0.945687741 0.991875065 1.007276365 0.977498107 0.934779553 1 20.36263407 5.464952054 2.027759158 0.982895425 7.46E-15 0.265930055 0.048941974 20.24913832 9.232118737 0.011378378 74.9630651 291710.4949 -5.464952054 -0.982895425 GPPDFS(ph)S(ph)DEEREPTPVLGSGAAAAGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 2 GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR 171.93 3.07E-12 7645880000 2745010 3387080 2467580 3631320 3233150 3239550 3347750 3548200 3187960 3148750 TRUE FALSE 2637731.974 3290483.795 2913526.597 3818732.86 3337147.206 3305055.921 3388720.766 3474928.43 2826076.146 2935482.358 0.898568498 1.120934618 0.992520561 1.300887689 1.136830953 1.125898751 1.154399977 1.183767438 0.962729733 1 21.48516616 5.466004543 1.278788047 1.129583964 1.33E-10 0.2731531 0.098041039 8.992586986 3.271985572 0.025531007 20.96256312 292418.2967 -5.466004543 -1.129583964 EWAHATIIPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EWAHATIIPK 10 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 123.75 0.00045382 1116300000 4527700 5450600 5010300 5734300 5286900 5905900 6167400 5980600 6656400 7472400 FALSE TRUE 4350752.478 5295154.225 5915772.664 6030247.91 5456957.94 6025321.344 6242878.486 5857098.52 5900793.378 6966287.692 0.624543899 0.760111333 0.849200166 0.865632913 0.78333801 0.864925712 0.896155709 0.840777582 0.847049912 1 22.73195862 5.466031889 0.868555759 0.867246788 4.27E-15 0.690659528 0.051492789 3.818256016 0.900465975 0.015634558 4.257923561 292436.7095 -5.466031889 -0.867246788 ES(ph)PHFYR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESPHFYR 7 0 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 1 ES(0.999)PHFY(0.001)R;ES(0.996)PHFY(0.004)R 83.948 0.022978 339580000 386630 473860 345090 528740 440360 410110 501050 516770 465100 434230 TRUE FALSE 371520.0722 460345.9768 407455.4395 556028.3348 454524.5793 418402.7052 507181.9998 506098.5189 412303.7979 404819.2153 0.917743175 1.137164342 1.006512102 1.373522584 1.122784102 1.033554459 1.252860488 1.250184032 1.018488704 1 18.62691825 5.46691435 1.166989745 1.159548247 0.081326856 0.201598234 0.121329985 10.32153372 3.429370081 0.033392793 20.48787968 293031.528 -5.46691435 -1.078221391 GHYTEGAELVDSVLDVVR ddPTM_BT-474_Pertuzumab_2h_R1 14 GHYTEGAELVDSVLDVVR 18 0 Q13509;A0A0B4J269;Q13509-2;G3V2A3;Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1 Q13509;Q5JP53;P68371;Q13885;Q9BVA1 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB2B Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;;;;;;;;;;;;; 373.99 9.22E-108 72547389000 15213508.3 18027622 14633318 21062114 18731827 19099923.2 18614477.9 15878406.8 18937121 21199044.8 FALSE TRUE 14618947.58 17513491.87 17277884.08 22149132.23 19334353.23 19486136.73 18842287.45 15550512.15 16787458.41 19763214.61 0.739704945 0.886166153 0.874244621 1.120725179 0.978300019 0.985980121 0.953401955 0.786841233 0.849429546 1 24.23631429 5.467435774 0.006765243 1.790557303 6.29E-05 0.044701291 0.104334701 116586.3431 100.0738709 12455.79347 14069.29621 293383.5599 -5.467435774 -1.790494392 ELQEQMSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELQEQMSR 8 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 126.82 0.0027977 399860000 116330 152100 114150 152210 143130 148190 160360 168110 145230 152840 FALSE TRUE 111783.695 147762.2569 134779.4443 160065.5763 147733.9064 151186.5033 162322.5336 164638.4698 128744.0993 142488.0107 0.784512988 1.037015369 0.945900245 1.123361717 1.036816401 1.06104719 1.139201347 1.155454897 0.903543383 1 17.12048101 5.468173484 0.999026021 1.07169364 5.53E-14 0.479885288 0.079129865 5.624356906 1.569989875 0.023280186 9.174574645 293882.3364 -5.468173484 -1.07169364 FFDS(ph)EDEDFEILSL ddPTM_BT-474_Pertuzumab_2h_R1 6 FFDSEDEDFEILSL 14 0 Q9Y4P1;Q9Y4P1-4 Q9Y4P1 ATG4B Cysteine protease ATG4B 1 FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL 227.93 1.94E-12 2036657000 3211568 3855590 3079295 3746347 3681987 3893419 3750545 3852112 3950694 4385601 TRUE FALSE 3086056.372 3745632.348 3635792.105 3939696.418 3800421.456 3972146.6 3796445.292 3772564.541 3502227.78 4088560.338 0.754802697 0.916125002 0.88925974 0.963590137 0.929525589 0.971526961 0.928553079 0.922712209 0.856591927 1 21.9631615 5.468823895 1.330953043 0.9334533 1.43E-08 0.655923988 0.038439558 4.711969764 1.764582014 0.009976641 9.564920024 294322.7919 -5.468823895 -0.933453285 S(ph)PTQIVK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPTQIVK 7 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.985)PT(0.015)QIVK;S(1)PTQIVK;S(0.993)PT(0.007)QIVK 108.43 0.0076091 621910000 500210 547900 587560 651200 592910 586600 650350 781830 743780 777890 TRUE FALSE 480661.2402 532274.4285 693745.1622 684808.51 611981.4886 598461.4539 658309.1778 765684.9373 659349.2126 725202.8174 0.662795605 0.7339663 0.956622266 0.944299296 0.843876325 0.825233217 0.907758715 1.055821791 0.909192845 1 19.468025 5.469136782 0.712318531 0.943783572 4.11E-16 0.610323617 0.071062828 5.233333721 0.947180157 0.029422515 5.042858863 294534.9135 -5.469136782 -0.943783572 RLS(ph)FEASNPPFDVGRPFDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSFEASNPPFDVGRPFDLR 20 2 Q92545;H7BZ05 Q92545 TMEM131 Transmembrane protein 131 1 RLS(1)FEASNPPFDVGRPFDLR 141.37 1.00E-07 51651000 19912 31365 15397 41130 21421 23177 32069 37862 32767 26053 TRUE FALSE 19133.81703 30470.50091 18179.5804 43252.72423 22110.02592 23645.65482 32461.47001 37080.13647 29047.42753 24288.4071 0.787775705 1.254528581 0.748487965 1.780797071 0.910311896 0.973536664 1.336500573 1.526659871 1.195937939 1 14.56798026 5.469769475 0.701031671 1.258344183 4.79E-12 0.124809523 0.29451432 14.52785977 2.571530974 0.110770792 18.32834431 294964.3129 -5.469769475 -1.258344183 S(ph)SPIMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPIMR 6 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8;K7ENU7;H0Y9S9 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(0.5)S(0.5)PIMR 132.29 0.015696 436200000 208140 249740 198520 245040 234470 250340 264500 245310 249380 258410 TRUE FALSE 200005.6587 242617.6597 234396.9801 257686.5438 242011.9405 255402.0463 267737.0301 240244.2628 221071.4279 240907.6605 0.830217097 1.007098152 0.972974373 1.069648608 1.004583831 1.060165732 1.111367856 0.997246257 0.917660432 1 17.87812074 5.470960471 1.332920699 1.025092104 6.27E-12 0.533117468 0.051679674 6.215370866 2.318909388 0.014244287 13.89901552 295774.3245 -5.470960471 -1.025092104 SIAAELDELADDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SIAAELDELADDR 13 0 H3BU86;O14662;H0YEW0 H3BU86 STX16-NPEPL1;STX16 Syntaxin-16 0 ; 178.81 1.12E-06 0 37292 50189 33593 58519 40589 47722 53288 53639 52477 50459 FALSE TRUE 35834.58741 48757.65886 39664.00237 61539.1726 41894.58205 48686.97154 53940.15448 52531.33591 46520.03096 47041.36699 0.761767561 1.036484736 0.843172827 1.308192694 0.890590234 1.034982073 1.146653636 1.116705131 0.988917498 1 15.52164236 5.471119551 0.923767932 1.066943154 4.30E-15 0.310085894 0.124448379 8.018374216 2.027603457 0.036596821 11.86478382 295882.6851 -5.471119551 -1.066943154 S(ph)PSHTRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSHTRPR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(0.892)PS(0.091)HT(0.017)RPR;S(0.969)PS(0.03)HT(0.001)RPR 57.785 0.066059 735382000 34001 36861 36400 43461 39453 41420 59605 45480 53355 52216 TRUE FALSE 32672.20333 35809.76037 42978.28971 45704.02742 40722.04158 42257.54078 60334.46382 44540.82211 47298.36408 48679.36381 0.671171535 0.735625069 0.882885197 0.938878897 0.836536027 0.86807915 1.23942589 0.914983653 0.971630695 1 15.57102269 5.472591721 0.416571872 1.015457565 0.10942173 0.549429783 0.098754629 7.429931513 0.635582496 0.072523033 3.782241259 296887.3688 -5.472591721 -0.906035835 DNGIRPSSLEQMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DNGIRPSSLEQMAK 14 1 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 149.44 6.83E-06 190560000 105920 148930 89748 206710 103400 123630 196670 186560 166750 128750 FALSE TRUE 101780.5293 144682.6622 105967.46 217378.3279 106725.9549 126129.8833 199076.9063 182707.4708 147821.2391 120029.6478 0.847961576 1.205391042 0.882844047 1.811038621 0.889163276 1.050822739 1.658564446 1.522186178 1.231539388 1 16.87303128 5.47265939 0.600716623 1.345437906 3.98E-17 0.13474894 0.304397676 14.05963808 2.0099059 0.136055597 15.91554927 296933.6318 -5.47265939 -1.345437906 LVRLS(ph)SDSFAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.499)S(0.499)DS(0.002)FAR 136.83 5.52E-05 188760000 51370 67748 46423 78675 58746 66534 72663 74429 68034 65387 TRUE FALSE 49362.40361 65815.89337 54812.66877 82735.42618 60635.61844 67879.36307 73552.27153 72892.01514 60311.06554 60958.28025 0.80977356 1.079687503 0.899183319 1.357246724 0.994706842 1.113538026 1.206600174 1.19576889 0.989382661 1 15.89553458 5.472808317 0.913749566 1.127051356 6.24E-13 0.306424526 0.127027428 7.725524853 1.922665801 0.03759866 11.92762977 297035.4727 -5.472808317 -1.127051356 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK 30 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 202.04 1.96E-25 170318000 146182 190950 128188 241980 130469 168485 242530 205087 190338 158187 FALSE TRUE 140469.0458 185504.293 151354.4231 254468.6168 134665.6539 171891.8821 245498.1547 200851.8818 168731.6282 147472.8536 0.952507817 1.257887729 1.02632057 1.725528534 0.913155544 1.16558321 1.664700646 1.361958333 1.144153816 1 17.17008989 5.473593679 0.979114964 1.297741655 3.22E-11 0.093484285 0.258164845 15.08541089 4.07610294 0.076395238 29.15431368 297573.1069 -5.473593679 -1.297741655 SETEEMGDEEVFSWLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SETEEMGDEEVFSWLK 16 0 Q7LBC6;Q7LBC6-2;Q7LBC6-3 Q7LBC6 KDM3B Lysine-specific demethylase 3B 0 259.85 2.14E-26 32919000 27596 25604 25267 28396 27097 30722 27459 32513 38069 33216 FALSE TRUE 26517.51781 24873.79899 29833.30896 29861.52096 27968.59961 31343.21989 27795.05146 31841.59519 33747.56672 30966.25073 0.856336081 0.803255105 0.96341366 0.964324717 0.903196188 1.012173548 0.897591759 1.028267693 1.089817654 1 14.9184091 5.474364943 0.289277895 1.034412851 0.549630293 0.550199908 0.055156728 9.222430961 0.456025055 0.062320335 1.70857466 298102.0367 -5.474364943 -0.484782558 RS(ph)SDPLGDTASNLGSAVDELMR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSDPLGDTASNLGSAVDELMR 22 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR 256.97 2.43E-37 112250000 63346 78036 62602 71264 81711 87432 76405 74055 79333 86927 TRUE FALSE 60870.36829 75810.48969 73915.57397 74941.94358 84339.30852 89199.93494 77340.06725 72525.73837 70327.45043 81039.35686 0.751121068 0.935477435 0.912094775 0.924759851 1.040720358 1.100698949 0.954351938 0.894944644 0.867818467 1 16.3063351 5.475157943 1.165689433 0.964441553 4.12E-10 0.477858504 0.066104125 7.497393644 2.447898636 0.020965523 13.35244467 298646.8533 -5.475157943 -0.964441553 GAEEEPPPPLQAVLVADSFDRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAEEEPPPPLQAVLVADSFDRR 22 1 Q13144;A0A3B3IUB1;A0A3B3IRP4;A0A3B3ISX3;A0A3B3ISM8;A0A3B3IUF2;A0A3B3ITQ2;A0A3B3IS56;A0A3B3ISS1;C9JRD9;A0A3B3IT53;H7C2X0 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 ; 237.18 2.61E-30 264890000 352140 411620 325550 407020 398690 468680 399050 411080 428980 456670 FALSE TRUE 338377.9795 399881.0006 384384.1268 428026.351 411514.2259 478157.0307 403933.6933 402591.0543 380283.9888 425739.3341 0.794800838 0.939262522 0.902862611 1.005371871 0.966587282 1.123121573 0.94878171 0.945628045 0.893231981 1 18.69961086 5.475260561 0.975551102 0.979189821 0.269572836 0.45736572 0.059590652 6.741685848 1.808933708 0.018658184 7.098541628 298717.4276 -5.475260561 -0.709616985 AERPDVDEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 AERPDVDEKR 10 2 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 101.93 0.0016955 589400000 433470 521540 419060 476270 511360 564690 525690 497270 586630 464330 FALSE TRUE 416529.5132 506666.1898 494793.4639 500850.3518 527808.3588 576108.4187 532123.5515 487001.2007 520038.2218 432880.5155 0.962227447 1.17045275 1.143025491 1.157017546 1.219293407 1.330871679 1.229261961 1.125024535 1.201343565 1 18.72360934 5.479459735 1.314406813 1.189097547 2.14E-09 0.373079353 0.081205042 8.331829332 3.012399308 0.021899964 21.33732766 301619.722 -5.479459735 -1.189097545 LLPVLVHTFWIDTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLPVLVHTFWIDTK 14 0 Q13505-3;Q13505 Q13505-3 MTX1 Metaxin-1 0 148.96 7.62E-06 24309000 52164 66355 47813 71701 54222 63287 66366 67053 75640 68034 FALSE TRUE 50125.37321 64462.62037 56453.87269 75401.4972 55966.09987 64566.7065 67178.20696 65668.33212 67053.66431 63425.99658 0.790296975 1.016343831 0.890074666 1.188810602 0.882384241 1.017984895 1.059158871 1.035353572 1.057195281 1 15.95278666 5.480117492 1.141016164 1.026119735 8.77E-14 0.400318503 0.082596723 7.190706946 2.275091487 0.021790205 13.30193234 302076.8833 -5.480117492 -1.026119735 TELSQSDMFDQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TELSQSDMFDQR 12 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 169.89 9.91E-05 669900000 524830 550470 484040 556680 539210 561910 604550 628500 623560 607800 FALSE TRUE 504319.0634 534771.1346 571516.7954 585410.3215 556554.1793 573272.2052 611948.6637 615521.2554 552776.083 566633.1646 0.890027437 0.943769564 1.008618682 1.033138118 0.982212504 1.011716647 1.079973256 1.086278202 0.975544881 1 19.11205552 5.484536888 0.634646724 1.039940461 0.573766928 0.584272487 0.036076501 5.276990905 0.803864449 0.016175591 2.210652325 305166.5222 -5.484536888 -0.466173533 LKCGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_BT-474_Pertuzumab_2h_R1 3 LKCGSGPVHISGQHLVAVEEDAESEDEEEEDVK 33 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 328.64 2.87E-117 789000000 279534 480746 225054 214804 223374 488063 277488 212472 353287 300770 TRUE FALSE 268609.5022 467035.5948 265726.2641 225890.0602 230559.0276 497931.9683 280883.9812 208084.379 313183.3409 280398.58 0.957956 1.665613267 0.947673359 0.805603438 0.822254619 1.775800606 1.001731111 0.742102114 1.116921993 1 18.09711952 5.486427837 0.288217839 0.972888743 1.56895824 0.012719644 0.33388431 48.4533432 2.369301786 0.398325674 11.00831738 306498.1357 -5.486427837 0.596069497 GGPTSHPSPVPPPASS(ph)PSPLSGSALCGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGPTSHPSPVPPPASSPSPLSGSALCGGK 29 0 J3KR72;P49848-4;P49848-2;P49848;P49848-3 J3KR72 TAF6 Transcription initiation factor TFIID subunit 6 1 GGPTSHPSPVPPPAS(0.189)S(0.795)PS(0.011)PLS(0.003)GS(0.001)ALCGGK 125.79 1.39E-05 201110000 131160 175640 126840 190560 147420 202560 186520 170490 175200 228940 TRUE FALSE 126034.1222 170630.9192 149762.8095 200394.8244 152161.8982 206655.902 188802.6876 166969.3219 155312.0305 213433.6899 0.590507161 0.799456352 0.701683083 0.938909057 0.712923523 0.968244058 0.884596465 0.782300686 0.727682825 1 17.70342839 5.486597462 0.83426998 0.845295163 3.06E-14 0.372867381 0.100266653 7.98350058 1.739307823 0.031532218 8.342483013 306617.8696 -5.486597462 -0.845295163 GQNDLMGTAEDFADQFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GQNDLMGTAEDFADQFLR 18 0 Q5T8U5;O15260-3;O15260-2;O15260 Q5T8U5 SURF4 Surfeit locus protein 4 0 163.64 7.59E-11 22771000 11337 13680 10430 20649 13571 12042 18071 21384 18914 19060 FALSE TRUE 10893.93751 13289.85979 12314.93301 21714.69736 14007.52354 12285.49749 18292.1583 20942.41293 16766.96201 17769.04922 0.613084998 0.747921829 0.693055259 1.222051731 0.788310245 0.691398698 1.02943934 1.178589392 0.943604906 1 14.11707887 5.488029463 0.36516733 1.04426272 2.00E-13 0.360723052 0.162564458 11.90447387 0.832146394 0.147845058 6.082398842 307630.5507 -5.488029463 -1.04426272 LIS(ph)SVEDFTEFV ddPTM_BT-474_Pertuzumab_2h_R1 4 LISSVEDFTEFV 12 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 LIS(0.5)S(0.5)VEDFTEFV;LIS(0.5)S(0.5)VEDFTEFV;LIS(0.5)S(0.5)VEDFTEFV;LIS(0.5)S(0.5)VEDFTEFV 146.81 6.82E-05 197240000 113985.9 142316.3 110204.7 143690.5 132984.4 143261.8 139639.8 154105.7 140527.8 159046.7 TRUE FALSE 109531.205 138257.5785 130121.1408 151106.3839 137261.964 146158.6518 141348.7536 150923.3634 124575.6733 148274.3253 0.73870648 0.932444495 0.877570277 1.019100128 0.925729817 0.985731356 0.953292172 1.017865791 0.840170225 1 17.17790928 5.490590392 1.083564393 0.963205377 3.59E-20 0.569351144 0.055542202 4.977071309 1.463338232 0.014878303 8.149423453 309449.932 -5.490590392 -0.963205377 SS(ph)PQLAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPQLAK 7 0 Q13370-2;Q13370 Q13370-2 PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase B" 1 S(0.036)S(0.964)PQLAK;S(0.065)S(0.935)PQLAK;S(0.41)S(0.59)PQLAK;S(0.037)S(0.963)PQLAK 82.426 0.025723 7626900000 9758400 8874900 9729200 10205700 11049400 13738200 12529500 12938700 15929100 16853900 TRUE FALSE 9377030.94 8621796.541 11487482.86 10732417.4 11404813.99 14015995.82 12682839.77 12671511.32 14120895.35 15712370.34 0.596792892 0.548726663 0.73111075 0.683055272 0.725849362 0.892035734 0.80718819 0.806467201 0.898711973 1 23.9053975 5.491319706 0.165764886 1.040409911 3.16E-14 0.857617476 0.050207798 9.49932698 0.213698796 0.165724481 2.146439095 309970.0304 -5.491319706 -1.040409911 EAQEDELLALASIYDGDEFR ddPTM_BT-474_Pertuzumab_2h_R1 3 EAQEDELLALASIYDGDEFR 20 0 Q9UBS8;E7EP22;D6R988;D6RBK4;D6RAS4;D6R996;D6RDU6;D6RBU3;D6RA38 Q9UBS8 RNF14 E3 ubiquitin-protein ligase RNF14 0 ;; 131.51 3.31E-05 63107000 52153 51944 57579.6 74483 67694 61475.9 79077 79912 76676 97682 FALSE TRUE 50114.8031 50462.60798 67985.51457 78327.07656 69871.43899 62718.98482 80044.76798 78261.78927 67972.06193 91065.91113 0.550313531 0.554132796 0.74655284 0.860114126 0.767262284 0.688720774 0.878976194 0.859397203 0.746405116 1 16.47462349 5.491624776 0.420766714 0.861838614 4.14E-54 0.624067062 0.082997043 6.658604428 0.570651743 0.059502809 3.270096052 310187.8455 -5.491624776 -0.861838614 DSINFLDHINGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSINFLDHINGK 12 0 Q96NC0;R4GNG8;R4GMX9 Q96NC0 ZMAT2 Zinc finger matrin-type protein 2 0 170.66 4.06E-05 254320000 807230 778960 887750 843330 883700 880000 1027800 991220 1176100 1278900 FALSE TRUE 775682.5592 756744.8235 1048186.173 886854.3624 912125.0131 897794.2029 1040378.524 970750.9606 1042594.059 1192278.964 0.650588145 0.6347045 0.87914507 0.743831259 0.765026509 0.75300683 0.872596561 0.814197843 0.874454796 1 20.1852904 5.49452219 0.064766148 1.313490568 7.95E-12 0.69404356 0.058927971 99.91002957 0.81933967 4.517705727 14.34377285 312264.1948 -5.49452219 -1.313490568 DLLLTGHEDGTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLLLTGHEDGTVR 13 0 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 123.28 0.0002253 66670000 75159 93438 78376 88890 94051 99568 103810 100780 98499 96281 FALSE TRUE 72221.70319 90773.23973 92540.28666 93477.62355 97076.23583 101581.3332 105080.4578 98698.85778 87317.80646 89759.80211 0.804610767 1.011290551 1.030976946 1.041419671 1.081511251 1.13170184 1.170685043 1.099588629 0.972794106 1 16.45378187 5.496244967 0.944202161 1.086229258 1.28E-11 0.653647238 0.056720085 4.324773043 1.080375303 0.017871269 6.764264563 313505.3578 -5.496244967 -1.086229258 DLEADIIGDTSGHFQK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLEADIIGDTSGHFQK 16 0 P08133;P08133-2;E5RJF5;E5RK63 P08133 ANXA6 Annexin A6;Annexin 0 ;;; 264.3 5.29E-27 1206850000 1166038 1615640 747523 2312300 1073426 1182735 1335360 1668060 1831200 1653660 FALSE TRUE 1120467.946 1569563.529 882617.0347 2431638.08 1107953.722 1206650.712 1351702.535 1633613.978 1623329.853 1541656.135 0.726794984 1.018102217 0.572512258 1.577289529 0.718677594 0.782697701 0.876786012 1.059648738 1.052977909 1 20.55604958 5.497373426 1.061426757 0.969347067 1.12E-13 0.068215273 0.255596666 23.70086886 6.734887285 0.071953056 38.19902957 314321.0204 -5.497373426 -0.969347067 TLLLSS(ph)DDEF ddPTM_BT-474_Pertuzumab_2h_R1 1 TLLLSSDDEF 10 0 A0A0J9YYJ3;Q9Y519 A0A0J9YYJ3 TMEM184B Transmembrane protein 184B 1 TLLLS(0.082)S(0.918)DDEF 72.485 0.050189 6546800 22136 26504 19128 27385 24287 22824 23888 27801 29192 25741 TRUE FALSE 21270.90065 25748.13187 22584.8551 28798.34313 25068.21341 23285.51692 24180.34849 27226.89963 25878.24654 23997.53914 0.886378412 1.072948844 0.941132129 1.200054012 1.044616003 0.970329365 1.007617837 1.134570485 1.078370844 1 14.55059885 5.498770044 1.450774259 1.057867095 2.44E-09 0.291311885 0.074161799 12.08679221 4.476341097 0.019723753 31.63112884 315333.4514 -5.498770044 -1.057867093 RS(ph)SPVPPVPER ddPTM_BT-474_Pertuzumab_2h_R1 3 RSSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.5)S(0.5)PVPPVPER;RS(0.5)S(0.5)PVPPVPER;RS(0.5)S(0.5)PVPPVPER 84.874 0.0095777 4290470000 1836690 2202910 1816800 2087630 2059320 2269860 2288850 2172650 2367710 2545910 TRUE FALSE 1764910.124 2140085.164 2145136.174 2195372.834 2125559.898 2315758.124 2316861.631 2127784.018 2098937.487 2373473.248 0.743598069 0.901668121 0.90379623 0.924962115 0.895548286 0.975683263 0.976148197 0.89648536 0.884331639 1 21.17856836 5.501927181 1.192014148 0.931960402 3.25E-12 0.694817535 0.03741124 4.585318718 1.449057244 0.010509153 8.233073288 317634.144 -5.501927181 -0.931960402 GWEWEGEWIVDPER ddPTM_BT-474_Pertuzumab_2h_R1 2 GWEWEGEWIVDPER 14 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ; 149.96 1.71E-05 85134000 62834 85182 61905 106404 73385 91280 113447 106005 117824 114515 FALSE TRUE 60378.37781 82752.69276 73092.61057 111895.5232 75745.49517 93125.74414 114835.3983 103815.9597 104449.1135 106758.7971 0.565558806 0.775136991 0.684651875 1.048115249 0.709501205 0.872300426 1.075652794 0.972434709 0.978365403 1 16.70399543 5.502390518 0.340377334 1.019925179 1.57E-15 0.605514899 0.104140808 7.544579323 0.471193142 0.094915051 3.501219244 317973.2003 -5.502390518 -1.019925179 DGSDVIYPAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGSDVIYPAR 10 0 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 200.88 5.87E-07 664630000 954610 1012230 867440 976180 1019740 1047090 1030050 1133450 1148660 1112370 FALSE TRUE 917302.7858 983362.1915 1024205.704 1026560.767 1052540.863 1068262.877 1042656.06 1110043.861 1018268.932 1037028.189 0.884549519 0.948250204 0.987635355 0.989906328 1.014958778 1.030119421 1.005426922 1.07040857 0.981910562 1 19.98402368 5.503756628 0.622346753 1.025798569 0.595233543 0.759294576 0.022987187 3.47477123 0.505859808 0.009651647 1.322160225 318974.987 -5.503756628 -0.430565026 DLLSDLQDIS(ph)DSER ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLSDLQDISDSER 14 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;Q9UQ88-9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 DLLSDLQDIS(1)DSER;DLLSDLQDIS(0.928)DS(0.072)ER 298.1 1.08E-43 6248700000 4213500 4874900 4856000 6160600 5462700 5748500 6809500 6786100 7329600 7786300 TRUE FALSE 4048831.762 4735872.625 5733587.221 6478549.304 5638412.707 5864738.609 6892836.698 6645964.664 6497574.536 7258926.966 0.557772765 0.652420481 0.789867049 0.892494075 0.776755674 0.807934649 0.949566889 0.91555745 0.895115017 1 22.79132487 5.506986345 0.387675874 0.941303247 2.00E-20 0.838650782 0.05219493 4.207439075 0.317423131 0.043559741 2.071472541 321355.9499 -5.506986345 -0.941303247 EFGSVNGDNKPIWMHAEER ddPTM_BT-474_Pertuzumab_2h_R1 2 EFGSVNGDNKPIWMHAEER 19 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ; 278.93 8.68E-40 357400000 218608 248503 266825 245891 272154 284812 293076 312530 317818 358880 FALSE TRUE 210064.5577 241415.9377 315046.213 258581.464 280908.0806 290571.0938 296662.7518 306076.1463 281740.633 334572.7379 0.627859158 0.721564881 0.94163743 0.772870693 0.83960242 0.868484072 0.886691347 0.914826917 0.842090825 1 18.35196037 5.509611741 0.729726305 0.888469484 5.63E-30 0.633639205 0.062913263 4.767422467 0.850514133 0.022086392 4.509972098 323304.4937 -5.509611741 -0.888469484 TIS(ph)PSTSNNIPLMR ddPTM_BT-474_Pertuzumab_2h_R1 3 TISPSTSNNIPLMR 14 0 F8WBA3;Q15139;O94806;O94806-2 F8WBA3;O94806 PRKD1;PRKD3 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1;Serine/threonine-protein kinase D3 1 TIS(0.999)PS(0.001)TSNNIPLMR;TIS(1)PSTSNNIPLMR;TIS(0.972)PS(0.022)T(0.005)S(0.001)NNIPLMR 328.88 2.42E-68 1047696000 440383 552233 530014 562714 572759 661172 664523 723175 685878 721998 TRUE FALSE 423172.3455 536483.8555 625799.3199 591755.737 591182.3134 674541.3508 672655.6313 708241.1835 608020.0049 673096.4324 0.628694976 0.797038626 0.929732041 0.87915447 0.878302551 1.002146674 0.999345114 1.052213545 0.903317824 1 19.36045368 5.514400615 0.543007677 0.995780833 9.07E-14 0.815566249 0.050630635 3.625110343 0.435009396 0.026912692 2.739611117 326889.232 -5.514400615 -0.995780833 QLLAEQELDELADDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLLAEQELDELADDR 15 0 Q96NX8;O14662-4;O14662-3 Q96NX8 STX16 Syntaxin-16 0 ; 184.21 1.10E-06 42148000 27720 37636 25486 42980 31034 28973 40841 42631 38164 41699 FALSE TRUE 26636.67175 36562.65813 30091.88713 45198.20295 32032.23679 29558.85391 41340.82437 41750.65495 33831.78272 38874.68959 0.685193169 0.940526047 0.774074017 1.162664022 0.823986947 0.760362442 1.063438057 1.073980407 0.870277887 1 15.24654354 5.516092211 0.867098038 0.964021346 1.51E-24 0.258118434 0.12873522 10.85113454 2.380095901 0.042302773 13.7048297 328164.9632 -5.516092211 -0.964021346 VAILAQLYHEKPLVFLER ddPTM_BT-474_Pertuzumab_2h_R1 2 VAILAQLYHEKPLVFLER 18 1 Q96F63 Q96F63 CCDC97 Coiled-coil domain-containing protein 97 0 ; 172.97 5.69E-12 144932000 316690 324990 263214 307180 301270 336590 305820 302110 349960 369110 FALSE TRUE 304313.4047 315721.6034 310782.625 323033.5966 310960.6232 343396.0804 309562.7166 295871.3229 310234.008 344109.8509 0.884349587 0.917502369 0.903149457 0.938751378 0.903666728 0.997925748 0.899604344 0.859816486 0.901555149 1 18.39250967 5.519020984 1.373922002 0.918665386 0.706827097 0.059730191 0.042296288 34.66499464 11.78421574 0.011778756 17.12972106 330385.504 -5.519020984 -0.211838289 GPGDLMGPQGLS(ph)PEEMAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPGDLMGPQGLSPEEMAR 18 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 GPGDLMGPQGLS(1)PEEMAR;GPGDLMGPQGLS(1)PEEMAR 258.43 1.22E-30 208743000 189345 225080 196587 221388 217278 240260 261370 227740 237555 274050 TRUE FALSE 181945.1881 218660.9388 232114.644 232813.8612 224266.9442 245118.2218 264568.7242 223037.0894 210588.7523 255488.3494 0.712146712 0.855854834 0.908513615 0.911250402 0.877797147 0.959410566 1.035541248 0.872983406 0.824259708 1 17.96289798 5.519587299 0.993474268 0.926245604 1.61E-10 0.551847751 0.05840616 6.032981436 1.537086838 0.018018391 8.653797265 330816.6036 -5.519587299 -0.926245603 SPGS(ph)TPTTPTSSQAPQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 S(0.038)PGS(0.96)T(0.002)PTTPTSSQAPQK;S(0.226)PGS(0.769)T(0.004)PTTPTSSQAPQK;S(0.007)PGS(0.958)T(0.032)PT(0.003)TPTSSQAPQK;S(0.187)PGS(0.808)T(0.004)PTTPTSSQAPQK 326.09 1.00E-59 3542780000 1413268 1424375 1383911 1485820 1465921 1678440 1826910 1752510 2132260 2115050 TRUE FALSE 1358035.924 1383753.22 1634014.503 1562503.348 1513073.68 1712379.207 1849268.271 1716320.056 1890214.784 1971795.78 0.688730516 0.701773091 0.828693579 0.792426561 0.76735821 0.868436389 0.93785994 0.870434998 0.958626042 1 20.91107871 5.519951726 0.170534248 1.043132143 0.256068582 0.859003714 0.037665713 9.059712854 0.209074574 0.115423066 1.592288295 331094.317 -5.519951726 -0.787063561 ELEEEFYSLVR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELEEEFYSLVR 11 0 Q92613 Q92613 JADE3 Protein Jade-3 0 98.249 0.013172 14812000 19196 17143 14610 16700 19687 16569 16052 18305 18542 20505 FALSE TRUE 18445.7991 16654.09842 17250.352 17561.889 20320.25023 16904.03653 16248.44918 17926.99535 16437.18989 19116.17809 0.964931328 0.871204398 0.902395443 0.918692477 1.062987075 0.884279088 0.849984192 0.937791816 0.859857542 1 14.22250649 5.520569271 0.355239421 0.920149818 0.929793069 0 0.064446727 515.6451313 33.97226682 0.058034401 2.373436403 331565.4512 -5.520569271 0.009643251 VIGHYAGEDATDAFR ddPTM_BT-474_Pertuzumab_2h_R1 5 VIGHYAGEDATDAFR 15 0 O95864-3;O95864 O95864-3 FADS2 Fatty acid desaturase 2 0 ;;;; 204.28 4.98E-09 3181140000 1489210 2301540 1334840 2870190 1721030 1859250 2616230 2927610 2635980 2064570 FALSE TRUE 1431010.027 2235902.333 1576075.281 3018320.85 1776388.493 1896845.309 2648248.205 2867153.83 2336754.601 1924734.835 0.743484246 1.161667723 0.818853201 1.568174896 0.922926348 0.985509939 1.375902881 1.489635756 1.214065729 1 20.87622827 5.521866113 0.510904054 1.26926711 7.75E-14 0.216710527 0.23693497 13.02984901 1.430799448 0.130970657 11.74090533 332557.015 -5.521866113 -1.26926711 (ac)AS(ph)GVQVADEVCR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASGVQVADEVCR 12 0 P60981;F6RFD5 P60981 DSTN Destrin 1 AS(1)GVQVADEVCR;AS(1)GVQVADEVCR 76.943 3.98E-11 5594700000 59769 37673 32056.6 25221 24943.7 32136 25914.8 29936 31888 40461 TRUE FALSE 57433.1614 36598.60293 37849.94072 26522.65883 25746.03676 32785.81194 26231.95307 29317.81114 28268.20793 37720.54043 1.522596462 0.97025659 1.003430499 0.703135706 0.682546869 0.869176623 0.695428877 0.777237304 0.74941153 1 15.20306273 5.522853542 0.967448894 0.771904302 3.914295075 0.808546294 0.105356745 2.840502977 0.699329659 0.029742723 13.39898095 333313.9895 -5.522853542 3.142390773 FSTYSQS(ph)PPDTPSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 FSTYSQSPPDTPSLR 15 0 A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4;H3BMG9;H3BSV5 A0A0A0MTL6 FAM65A Protein FAM65A 1 FSTYS(0.019)QS(0.981)PPDTPSLR;FSTYS(0.002)QS(0.998)PPDTPSLR;FSTYS(0.014)QS(0.986)PPDTPSLR;FSTYSQS(1)PPDTPSLR 352.27 2.19E-82 2939880000 1771540 2082300 1804340 2173680 2121500 2282960 2336790 2274640 2434650 2643190 TRUE FALSE 1702306.258 2022914.843 2130424.375 2285863.885 2189739.974 2329123.015 2365388.335 2227667.889 2158278.739 2464164.387 0.690824958 0.820933398 0.864562602 0.927642611 0.888633886 0.945197905 0.959914991 0.904025681 0.875866379 1 21.23266707 5.526049731 0.747172184 0.929539847 0.099102284 0.829346573 0.033785602 2.919930949 0.526517501 0.01173481 2.669981134 335776.0615 -5.526049731 -0.830437563 VLLGEEEALEDDSESR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLLGEEEALEDDSESR 16 0 P42858 P42858 HTT Huntingtin 0 ; 253.88 3.37E-26 174097000 52311 61997 55902 67696 56860 71230 71148 69384 70904 83076 FALSE TRUE 50266.62829 60228.90626 66004.73493 71189.79867 58688.95354 72670.3194 72018.73051 67951.19615 62855.27517 77449.18852 0.649027178 0.777657034 0.85223275 0.919180692 0.75777364 0.938296718 0.929883603 0.877364856 0.811567899 1 16.2409625 5.529566405 0.798867721 0.89079763 3.66E-15 0.585336912 0.06368432 5.361367811 1.04583594 0.020865258 5.701292795 338506.0268 -5.529566405 -0.89079763 QRPDLGS(ph)AQK ddPTM_BT-474_Pertuzumab_2h_R1 3 QRPDLGSAQK 10 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RFR3 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 QRPDLGS(1)AQK;QRPDLGS(1)AQK;QRPDLGS(1)AQK 153.32 9.97E-06 1830250000 2238870 1836080 1772070 1502550 1499200 1585540 1741580 2099920 1879210 2085720 TRUE FALSE 2151372.485 1783716.796 2092322.468 1580096.786 1547423.13 1617600.705 1762893.977 2056555.918 1665889.959 1944452.327 1.10641565 0.917336348 1.076047193 0.81261791 0.795814383 0.831905562 0.906627513 1.057653042 0.856739935 1 20.89093243 5.52959934 1.027850354 0.910932043 1.757723581 0.276198558 0.093489021 12.03754284 3.12518386 0.029803236 16.54141169 338531.6986 -5.52959934 0.846791539 LNIHQKT(ph)HTGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNIHQKTHTGEK 12 1 Q9GZX5 Q9GZX5 ZNF350 Zinc finger protein 350 1 LNIHQKT(0.948)HT(0.052)GEK;LNIHQKT(0.998)HT(0.002)GEK 121.02 0.00056242 1031980000 1187910 745230 738600 428968 631160 608750 538342 706590 958980 793270 TRUE FALSE 1141485.164 723976.7701 872081.4501 451107.0899 651461.8346 621059.3421 544930.3904 691998.6696 850120.6108 739541.1163 1.543504666 0.978954049 1.179219696 0.609982434 0.880900088 0.839790146 0.736849349 0.935713585 1.149524471 1 19.49627083 5.531342797 1.111218582 0.882668471 4.096349668 0.574664235 0.161543431 5.640862135 1.575917082 0.04528193 32.45886268 339893.4509 -5.531342797 3.213681197 LNNLS(ph)PAPHLAS(ph)GSPPPGLPSGLPSGLQSGS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 34 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 3 LNNLS(1)PAPHLAS(0.571)GS(0.429)PPPGLPSGLPS(0.015)GLQS(0.308)GS(0.64)PS(0.037)R 152.77 4.42E-11 139280000 87800 119980 102770 119670 109190 143970 133070 138800 131580 165250 TRUE FALSE 84368.67893 116558.2879 121342.8251 125846.183 112702.1955 146881.172 134698.5505 135933.7315 116643.59 154057.4703 0.547644193 0.756589652 0.787646486 0.816878161 0.731559432 0.953418044 0.874339623 0.882357287 0.757143356 1 17.23310912 5.531513647 0.581777678 0.874929033 8.39E-29 0.622392154 0.074558426 5.730419486 0.742816082 0.033158957 4.133563213 340027.1904 -5.531513647 -0.874929033 ELEGILLPSDRDR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELEGILLPSDRDR 13 1 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 ;;; 179.93 1.22E-05 1075100000 824960 1038230 770020 1160740 895980 1060100 1067160 1051350 1196790 1185930 FALSE TRUE 792719.6512 1008620.697 909179.743 1220645.931 924800.0104 1081535.948 1080220.223 1029639.255 1060935.417 1105605.905 0.717000197 0.912278681 0.822336186 1.104051566 0.836464428 0.978229172 0.977039123 0.931289577 0.959596373 1 20.0764058 5.53163317 0.9256848 0.957763254 2.63E-19 0.489387674 0.0736573 6.312603322 1.459635837 0.021005572 8.6314658 340120.7829 -5.53163317 -0.957763254 APS(ph)PSSR ddPTM_BT-474_Pertuzumab_2h_R1 8 APSPSSR 7 0 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 APS(0.802)PS(0.185)S(0.013)R;APS(0.847)PS(0.14)S(0.013)R;APS(0.761)PS(0.234)S(0.005)R;APS(0.906)PS(0.093)SR;APS(0.999)PS(0.001)SR;APS(0.998)PS(0.002)SR;APS(0.99)PS(0.009)S(0.001)R;APS(0.999)PS(0.001)SR 113.74 0.0063586 16671320000 1667777 1879576 1395817 2015007 1612977 1824827 1809341 1845625 1803549 1856511 TRUE FALSE 1602598.431 1825972.333 1648072.182 2119001.753 1664859.87 1861726.252 1831484.256 1807512.199 1598817.679 1730767.856 0.925946495 1.055007074 0.952220239 1.224313096 0.9619198 1.075664911 1.058191744 1.044341211 0.923762059 1 20.7229808 5.531846672 1.712928207 1.039422365 2.28E-12 0.126766872 0.08068351 26.63947275 9.514106187 0.019514019 86.94108304 340288.0297 -5.531846672 -1.039422365 GMPTFPWDEDPEEDGS(ph)PDPEPSPEPEPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GMPTFPWDEDPEEDGSPDPEPSPEPEPK 28 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 GMPTFPWDEDPEEDGS(1)PDPEPSPEPEPK;GMPTFPWDEDPEEDGS(1)PDPEPSPEPEPK 221.72 1.49E-34 74466000 127573 115168 131526 150231 146741 140829 168159 185707 210790 216300 TRUE FALSE 122587.3061 111883.5214 155295.674 157984.4399 151461.0575 143676.6589 170216.9801 181872.0856 186862.0029 201649.8083 0.607921759 0.554840703 0.770125572 0.78345941 0.751109355 0.712505804 0.844121706 0.901920448 0.926665909 1 17.62149251 5.536810666 0.160778098 1.071230311 2.55E-09 0.833981374 0.053811201 11.36610038 0.242870608 0.202322222 2.57122281 344199.8415 -5.536810666 -1.071230308 ATCIEMVTSLAYTHHGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATCIEMVTSLAYTHHGR 17 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 61.87 0.038444 338050000 400860 343480 308970 270840 343970 261020 389020 268170 428840 380600 FALSE TRUE 385193.948 333684.2867 364807.752 284818.0849 355034.1074 266298.0032 393780.9431 262632.1958 380159.881 354821.623 1.085598856 0.940428275 1.028144082 0.802707801 1.000598849 0.750512331 1.109799735 0.740180921 1.071411257 1 18.43673441 5.539095594 0.959055058 0.915199747 1.626766246 0.098328734 0.12574106 15.27109137 3.628228844 0.034670352 16.25567978 346015.532 -5.539095594 0.711566499 THT(ph)GEKPYK ddPTM_BT-474_Pertuzumab_2h_R1 2 THTGEKPYK 9 1 O75362;P15621-3;C9J2N8;B9EG95;H9KV89;A0A087X254;E7EX64;B4DI05;F8W7T7;A0A0C4DFQ3;F8WEL6;R4GMT1;E9PJ50;F8W6Y9;Q7Z7L9;Q32M78;Q96RE9-3;Q9H7R0;Q8N184-1;P17025-2;Q6ZMW2;A0A0A0MS50;Q8N7K0-2;Q6ZT77;P17025;Q96RE9-2;Q8N972;Q9Y2A4;Q8N184;P51814-8;P51814;P51814-5;P51814-3;Q9NPC7;P51814-2;Q9HBT7;Q99676;P51814-7;Q8N8J6-2;O95125;Q9P2J8-2;Q8N8J6-3;Q8N8J6;P51814-6;P51814-4;I3L4C4;Q8N7K0;P16415-2;P15621;P16415;Q9NPC7-2;Q96RE9;P15621-2;O75346-2;O95780-2;Q96BR6-2;Q13887-4;Q9UJN7;Q15973;Q9H4T2;Q13360-2;Q8IZC7-2;Q13887-2;O75840;Q15973-1;Q15973-4;O75840-4;O75840-2;Q15973-2;A0A3F2YPB8;C9JN71;Q8IZC7;P0CG31;Q8NDW4;P36508;Q96RE9-4;Q9UC07;Q9H7R0-2;Q14584;P36508-2;O95125-2;Q8N8L2;Q9NPC7-3;O95780;Q13360;O95780-3;Q96BR6;Q13887;Q9UC06;O14978;A6NHJ4;A0A087WXA8;Q2M218;Q2M218-2;Q9P0L1;Q6ZMS4;P57682;Q86YE8;Q86YE8-3;Q86YE8-2;Q86YE8-4;Q86WZ6-2;P17040-3;P17040-2;Q9P2J8;Q86WZ6;Q86XU0;O75346;A6NP11;Q96H40;Q6U7Q0;P17040;P52743;Q8N859;A0A0M3HEQ9;A0A087WT67;O14628-4;O14628-7;O14628-5;O14628-6;O14628;Q9Y4X4;A0A087WUV0;A0A087WVT1;Q96MX3;Q96N95;Q9UEG4 O75362;A6NHJ4;Q9P0L1;P57682;Q86YE8;P52743;Q8N859;A0A087WT67;Q9Y4X4;A0A087WUV0;A0A087WVT1;Q96N95;Q9UEG4 ZNF217;ZNF44;ZNF823;ZNF682;ZNF615;ZNF76;ZNF263;ZSCAN2;ZNF567;MYNN;ZNF48;ZNF699;ZNF300;ZNF442;ZNF182;ZNF782;ZNF433;ZNF826P;ZNF709;ZNF443;ZNF41;ZNF287;ZNF184;ZNF202;ZNF624;ZNF253;ZNF669;KLF5;ZNF391;ZNF124;ZSCAN16;ZNF177;ZNF101;KLF7;ZNF878;ZNF286B;ZNF248;ZNF69;ZNF266;ZNF491;ZNF70;ZNF860;ZNF630;ZKSCAN7;ZNF852;KLF3;ZNF573;ZNF227;ZSCAN20;ZNF677;ZNF716;ZNF486;ZNF322;ZNF137P;ZNF713;ZNF195;KLF12;ZNF396;ZNF629 Zinc finger protein 217;Zinc finger protein 44;Zinc finger and SCAN domain-containing protein 2;Zinc finger protein 699;Zinc finger protein 300;Zinc finger protein 442;Zinc finger protein 567;Zinc finger protein 182;Zinc finger protein 782;Zinc finger protein 433;Putative zinc finger protein 826;Zinc finger protein 709;Zinc finger protein 443;Zinc finger protein 41;Myoneurin;Zinc finger protein 287;Zinc finger protein 184;Zinc finger protein 615;Zinc finger protein 202;Zinc finger protein 624;Zinc finger protein 823;Zinc finger protein 253;Zinc finger protein 682;Zinc finger protein 669;Krueppel-like factor 5;Zinc finger protein 391;Zinc finger protein 124;Zinc finger and SCAN domain-containing protein 16;Zinc finger protein 177;Zinc finger protein 101;Krueppel-like factor 7;Zinc finger protein 878;Putative zinc finger protein 286B;Zinc finger protein 248;Zinc finger protein 76;Zinc finger protein 69;Zinc finger protein 266;Zinc finger protein 491;Zinc finger protein 70;Zinc finger protein 263;Zinc finger protein 860;Zinc finger protein 630;Zinc finger protein with KRAB and SCAN domains 7;Zinc finger protein 852;Krueppel-like factor 3;Zinc finger protein 573;Zinc finger protein 227;Zinc finger and SCAN domain-containing protein 20;Zinc finger protein 677;Zinc finger protein 716;Zinc finger protein 486;Zinc finger protein 322;Putative zinc finger protein 137;Zinc finger protein 713;Zinc finger protein 195;Krueppel-like factor 12;Zinc finger protein 48;Zinc finger protein 396;Zinc finger protein 629 1 T(0.011)HT(0.989)GEKPYK;THT(1)GEKPYK 147.62 0.0001348 344090000 1264440 849870 720960 555730 578290 438700 622390 354710 756670 592870 TRUE FALSE 1215024.287 825632.5397 851253.5097 584411.2919 596891.223 447570.8146 630006.995 347385.1145 670775.9938 552714.3868 2.198285979 1.493777907 1.540132716 1.057347711 1.07992706 0.809768707 1.13984186 0.628507459 1.213603282 1 19.07617464 5.539949056 0.568524268 0.903238835 4.677892726 0.81393699 0.180623376 3.188896034 0.397898013 0.080584722 9.687370885 346696.1794 -5.539949056 3.774653892 up YEEVSVSGFEEFHR ddPTM_BT-474_Pertuzumab_2h_R1 11 YEEVSVSGFEEFHR 14 0 Q9BRA2;I3L2R6;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;;;;;;;;; 237.32 2.73E-17 5394503300 2983627.5 3495932.1 2605343.4 3490018.3 3348591.5 3569819.4 3266308.1 3265291.3 3549740.1 3683666.8 FALSE TRUE 2867024.039 3396231.539 3076186.908 3670138.563 3456301.987 3642003.594 3306282.156 3197861.894 3146788.486 3434168.767 0.834852401 0.98895301 0.895758804 1.068712347 1.006445001 1.06051969 0.962760534 0.931189499 0.916317368 1 21.71152951 5.541580629 1.402104981 0.98239714 1.23E-17 0.38661006 0.054612449 11.75000433 3.819168298 0.015415508 28.00344328 348001.1101 -5.541580629 -0.98239714 VHFEESSKLEDLLR ddPTM_BT-474_Pertuzumab_2h_R1 3 VHFEESSKLEDLLR 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 241.42 1.17E-17 4646750000 6305440 5953500 4484940 4547870 5163120 4885070 5432150 3843100 6258310 5368140 FALSE TRUE 6059016.434 5783712.009 5295468.425 4782586.116 5329196.444 4983849.462 5498630.277 3763738.642 5547892.886 5004551.096 1.210701283 1.15569047 1.058130554 0.955647374 1.064870024 0.995863438 1.098725974 0.752063186 1.108569536 1 22.25480924 5.541639675 0.496225655 0.959285487 1.710800312 0.346502039 0.09740773 9.369853091 0.973730498 0.055791612 4.859826758 348048.4264 -5.541639675 0.751514825 DADSTEFRPNAPVPLVIDMPEHNPGNLGGTMR ddPTM_BT-474_Pertuzumab_2h_R1 3 DADSTEFRPNAPVPLVIDMPEHNPGNLGGTMR 32 1 Q9NRF8;H0Y5S6 Q9NRF8 CTPS2 CTP synthase 2 0 ;; 284.48 3.76E-74 1356740000 707050 821620 672039 813330 797000 847770 835530 834820 887230 933180 FALSE TRUE 679417.7043 798188.2021 793491.3967 855306.0588 822636.2288 864912.4903 845755.4661 817580.6753 786515.37 869974.8874 0.780962433 0.917484187 0.912085404 0.983138791 0.945586178 0.994180985 0.972160781 0.939775029 0.904066751 1 19.73061423 5.543217905 1.03978099 0.959405813 0.125535268 0.768144577 0.02931972 3.773994342 0.967836291 0.00853939 5.214329675 349315.539 -5.543217905 -0.833870546 KQQLEVELR ddPTM_BT-474_Pertuzumab_2h_R1 4 KQQLEVELR 9 1 P15924 P15924 DSP Desmoplakin 0 ;;; 185.08 6.94E-05 1873190000 4016740 4243790 3610740 3783620 3852220 3038220 4205490 4145580 4159730 3903370 FALSE TRUE 3859761.36 4122761.264 4263281.038 3978893.082 3976130.155 3099654.89 4256958.045 4059972.324 3687534.889 3638991.273 1.060667935 1.132940685 1.171555719 1.093405503 1.092646246 0.851789592 1.169818152 1.115686194 1.013339855 1 21.79510716 5.544766648 0.011739853 0.000410956 2.244647584 0.109381894 0.086080794 14056.06025 20.5378692 1760.600042 2183.978784 350563.4613 -5.544766648 2.244236628 TEASPESMLS(ph)PSHGSNPIEDPLEAETQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEASPESMLSPSHGSNPIEDPLEAETQHK 29 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;B5MCW3;Q9H0E9-3;Q9H0E9;H0YAH7 H7C128 BRD8 Bromodomain-containing protein 8 1 TEAS(0.003)PES(0.06)MLS(0.934)PS(0.002)HGSNPIEDPLEAETQHK;TEASPESMLS(0.999)PS(0.001)HGSNPIEDPLEAETQHK 226.5 1.72E-34 79773000 65134 62765 77615 88226 73136 84547 91956 87783 100092 121621 TRUE FALSE 62588.49127 60975.00365 91641.75704 92779.35443 75488.48586 86256.59827 93081.38504 85970.25037 88729.97578 113383.5013 0.552007043 0.537776686 0.808245961 0.818279144 0.665780162 0.760750879 0.820942941 0.758225397 0.782565142 1 16.7908512 5.547732136 0.090896168 1.155836355 6.82E-18 0.646265723 0.077126323 62.72914523 0.716723767 1.920919057 9.629461846 352965.4004 -5.547732136 -1.155836355 DDIPVFLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DDIPVFLR 8 0 A0A1W2PQD2;Q9UBB4-2;Q9UBB4;B1AHE4 A0A1W2PQD2 ATXN10 Ataxin-10 0 ;;;;; 152.39 0.0010652 522570000 475774 512843 531049 615921 583013 567919 618854 684028 709681 781748 FALSE TRUE 457180.2261 498217.2198 627021.3674 647708.7566 601766.1426 579402.7113 626427.7204 669902.5828 629120.9881 728799.5117 0.62730589 0.683613548 0.860348227 0.888733796 0.825695041 0.795009741 0.859533672 0.919186377 0.863229157 1 19.47516247 5.549459303 0.625227342 0.887271464 2.43E-18 0.708539255 0.055820347 4.668511356 0.653648256 0.024011093 3.729576083 354371.9211 -5.549459303 -0.887271464 PPQDQS(ph)VIK ddPTM_BT-474_Pertuzumab_2h_R1 5 PPQDQSVIK 9 0 Q58EX2-2;Q58EX2-3;Q58EX2;Q58EX2-4 Q58EX2-2 SDK2 Protein sidekick-2 1 PPQDQS(1)VIK;PPQDQS(1)VIK;PPQDQS(1)VIK;PPQDQS(1)VIK;PPQDQS(1)VIK 96.143 0.0079382 176311000 531105 631992 515359 631510 583782 678778 602617 678889 623044 771966 TRUE FALSE 510348.8294 613968.2069 608495.8354 664102.3068 602559.8782 692503.3562 609992.0071 664869.7049 552318.6571 719680.0552 0.709132934 0.853112717 0.845508822 0.922774366 0.837260771 0.962237804 0.847587762 0.923840671 0.767450276 1 19.45699615 5.550364807 1.078744458 0.890546502 1.15E-10 0.420633535 0.063614552 7.621843171 1.998508888 0.016638201 11.81798399 355111.5578 -5.550364807 -0.890546502 EDQEAAELLS(ph)EPEEESER ddPTM_BT-474_Pertuzumab_2h_R1 2 EDQEAAELLSEPEEESER 18 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 1 EDQEAAELLS(1)EPEEESER;EDQEAAELLS(1)EPEEESER 303.7 9.10E-50 535800000 312980 362180 341110 400440 398940 404020 459380 438740 456400 503550 TRUE FALSE 300748.3956 351850.981 402756.165 421106.7564 411772.2674 412189.5612 465002.0299 429679.8657 404591.3854 469444.11 0.640647926 0.749505582 0.857942738 0.897032783 0.87714865 0.878037561 0.990537574 0.915295041 0.861852086 1 18.84059388 5.550416408 0.609560463 0.9297177 9.97E-19 0.830691721 0.041466398 3.204231329 0.433742723 0.017821011 2.605174081 355153.7524 -5.550416408 -0.9297177 AMDDSSVTEHQK ddPTM_BT-474_Pertuzumab_2h_R1 2 AMDDSSVTEHQK 12 0 P43155-2;P43155;P43155-3;H0Y4Z7 P43155-2 CRAT Carnitine O-acetyltransferase 0 ; 223.08 2.33E-11 1468510000 1293510 1673180 1223600 1992340 1535650 1578110 2171100 1952480 1849840 1861650 FALSE TRUE 1242958.199 1625462.545 1444731.739 2095164.906 1585045.577 1610020.465 2197670.571 1912160.606 1639853.918 1735558.787 0.716171765 0.936564383 0.83243031 1.207199042 0.913276801 0.927666915 1.266261095 1.10175502 0.944856452 1 20.7269688 5.552025095 0.607017323 1.069951677 1.90E-15 0.388587606 0.123700626 8.483320804 1.140376178 0.054409724 7.90291894 356471.7306 -5.552025095 -1.069951677 LNQVCFDDDGTSSPQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNQVCFDDDGTSSPQDR 17 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BPA9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ; 341.27 3.36E-72 982290000 326840 391710 281810 373720 352110 397700 374980 376030 374960 410300 FALSE TRUE 314066.7315 380538.8143 332739.3358 393007.734 363435.9379 405741.7665 379569.1174 368264.8491 332396.1128 382510.0155 0.821067995 0.994846668 0.869883983 1.027444297 0.950134436 1.060735013 0.992311579 0.96275871 0.868986691 1 18.545138 5.552978656 1.365243955 0.973556337 2.08E-20 0.344213481 0.059561981 11.80149292 3.673649562 0.015590079 27.09257215 357255.2796 -5.552978656 -0.973556337 EAAAALVEEETRR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAAAALVEEETRR 13 1 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 ; 232.37 1.38E-12 1776280000 1044080 1207970 956130 1177530 1147160 1233330 1205370 1243540 1135550 1200750 FALSE TRUE 1003276.199 1173519.878 1128923.96 1238302.464 1184059.443 1258268.778 1220121.679 1217860.464 1006647.125 1119422.133 0.896244741 1.048326493 1.008488154 1.106197946 1.057741676 1.124034214 1.089956722 1.087936739 0.899256049 1 20.09432275 5.554390701 1.326988519 1.060322677 3.39E-13 0.320901767 0.063308874 10.79450189 3.294340717 0.016729085 26.02985038 358418.7338 -5.554390701 -1.060322677 (ac)MEGLDDGPDFLSEEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 MEGLDDGPDFLSEEDR 16 0 G3V5X9;Q9UNH7;G3V2U1;H0YJF8;G3V4Z5 G3V5X9 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ;;; 130.56 4.51E-57 488238000 89793.3 105493 78951.5 108056 100304.4 112562.9 101860.9 108639.4 101469.2 114057.3 FALSE TRUE 86284.07856 102484.4429 93219.79232 113632.7831 103530.7821 114838.999 103107.5042 106395.9584 89950.84181 106332.0975 0.811458446 0.96381474 0.876685352 1.068659284 0.973655035 1.080003138 0.969674319 1.00060058 0.845942514 1 16.69821763 5.558727531 0.965684069 0.988485819 0.219348573 0.349730035 0.068308976 8.824445647 2.045851486 0.019935752 10.32981782 362015.8043 -5.558727531 -0.769137245 RESPSEER ddPTM_BT-474_Pertuzumab_2h_R1 1 RESPSEER 8 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 0 100.25 0.010006 137340000 66096 83392 67095 84513 79890 93960 88098 89427 97059 92487 FALSE TRUE 63512.89525 81013.74181 79220.55902 88874.72606 82459.7344 95859.93558 89176.16968 87580.3012 86041.26922 86222.77311 0.736613924 0.939586363 0.918789273 1.03075699 0.956356789 1.1117705 1.034253092 1.015744426 0.997894943 1 16.39578134 5.560453816 0.771158609 1.026225681 3.14E-20 0.794887083 0.042897857 3.32766228 0.598010998 0.014381877 3.9528797 363457.6519 -5.560453816 -1.026225681 GKFDGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GKFDGAK 7 1 O15347;E7ES08;E7EQU1 O15347 HMGB3 High mobility group protein B3 0 73.665 0.04403 1487900000 2026400 1774300 1513600 1487400 1789900 1249900 1720800 1796200 1939600 1821800 FALSE TRUE 1947206.048 1723698.701 1787141.19 1564164.892 1847473.759 1275173.834 1741859.665 1759107.842 1719424.739 1698407.863 1.146489068 1.01489091 1.052245005 0.920959521 1.08776802 0.750805423 1.025583844 1.035739342 1.012374458 1 20.69575153 5.563557849 0.985433047 0.981136542 1.731628217 0.236561823 0.088384546 12.52841482 2.941369643 0.026137282 14.70657186 366064.6978 -5.563557849 0.750491674 GSS(ph)LSGTDDGAQEVVK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSSLSGTDDGAQEVVK 16 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GSS(1)LSGTDDGAQEVVK;GS(0.001)S(0.999)LSGTDDGAQEVVK;GSS(1)LSGTDDGAQEVVK;GSS(1)LSGTDDGAQEVVK 461.79 1.12E-205 3180800000 2978740 3138720 3392690 4087320 3784990 3640420 4495600 4472050 5149050 5796390 TRUE FALSE 2862327.548 3049206.779 4005824.553 4298267.075 3906737.641 3714031.787 4550618.498 4379700.605 4564551.431 5403795.342 0.52968837 0.564271329 0.741298347 0.795416333 0.722961806 0.687300601 0.842115256 0.810486025 0.844693616 1 22.36554161 5.574235999 0.14198566 1.053371412 8.36E-15 0.817766299 0.056196657 16.45838133 0.30085732 0.309046963 3.266188304 375176.8207 -5.574235999 -1.053371412 S(ph)GTFDLLEMDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGTFDLLEMDR 11 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 S(0.971)GT(0.029)FDLLEMDR 81.239 0.023305 17710000 20125 19428 20082 19510 22057 20558 23202 27487 22578 30200 TRUE FALSE 19338.49275 18873.93246 23711.26412 20516.91344 22766.48344 20973.69685 23485.95302 26919.38384 20015.04009 28154.5271 0.686869741 0.670369365 0.842183001 0.728725202 0.808626029 0.744949356 0.834180341 0.956129853 0.71089953 1 14.7810793 5.574286206 0.057956236 1.343906845 1.82E-16 0.509410183 0.074462918 170.4316755 1.223695472 8.14589554 23.47685391 375220.1963 -5.574286206 -1.343906845 NNTAAETEDDES(ph)DGEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNTAAETEDDESDGEDR 17 0 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 NNTAAETEDDES(1)DGEDR 241.28 2.47E-20 72799000 65429 62943 66207 96287 70453 72799 102790 98943 111130 111040 TRUE FALSE 62871.96234 61147.92727 78172.07767 101256.3836 72719.18473 74271.04566 104047.9748 96899.79247 98514.98829 103519.1619 0.60734613 0.590691869 0.755145968 0.978141455 0.702470764 0.717461814 1.005108357 0.936056578 0.951659446 1 16.65953832 5.575306932 0.249230419 1.018594991 5.16E-15 0.618567735 0.097381558 10.468298 0.396158694 0.142873769 3.516147796 376103.1162 -5.575306932 -1.018594991 MEVDEAEKK ddPTM_BT-474_Pertuzumab_2h_R1 1 MEVDEAEKK 9 1 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 79.148 0.044514 159870000 256210 272120 283170 338070 294420 345390 337190 344720 412940 421900 FALSE TRUE 246197.0299 264359.404 334345.1181 355517.8332 303890.2867 352374.0224 341316.6321 337601.4115 366064.7824 393324.3372 0.625938969 0.672115552 0.850049403 0.903879571 0.772620095 0.895886649 0.867773997 0.858328305 0.930694462 1 18.58535993 5.577380146 0.560546574 0.897550081 5.11E-17 0.732196698 0.056861962 4.736401213 0.56109799 0.02689651 3.399207909 377902.8314 -5.577380146 -0.897550081 GYDFESETDTETIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GYDFESETDTETIAK 15 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 307.95 1.03E-55 200470000 223080 229100 209140 254340 250620 258280 275410 306490 309370 314650 FALSE TRUE 214361.787 222566.2923 246936.2503 267466.5179 258681.4199 263502.5986 278780.55 300160.8744 274251.6146 293338.4752 0.730766009 0.758735424 0.84181337 0.911801691 0.881853019 0.898288567 0.950371579 1.023257771 0.934932297 1 18.16220679 5.577908631 0.304553924 1.008600642 0.28924049 0.887573721 0.030165514 3.925882351 0.199833475 0.034425416 1.152269118 378362.9743 -5.577908631 -0.719360151 S(ph)LS(ph)PGVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSPGVSR 8 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 S(1)LS(1)PGVSR;S(1)LS(1)PGVSR 76.682 0.03912 258790000 797660 817640 901920 1020080 884940 936590 1050290 1120100 1166470 1221270 TRUE FALSE 766486.5653 794321.7078 1064917.007 1072726.451 913404.8988 955528.4915 1063143.763 1096969.544 1034057.216 1138552.295 0.673211559 0.697659397 0.935325511 0.942184611 0.802251159 0.839248663 0.933768056 0.963477522 0.908221098 1 20.11876913 5.578070868 0.631084144 0.926567449 3.10E-13 0.632986269 0.064854544 5.770565715 0.794522855 0.028699431 4.907888126 378504.3438 -5.578070868 -0.926567449 AS(ph)SPGHPAFLEDGSPS(ph)PVLAFAASPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASSPGHPAFLEDGSPSPVLAFAASPR 26 0 Q9C073;D6RJ87;Q9C073-2 Q9C073 FAM117A Protein FAM117A 2 AS(0.5)S(0.5)PGHPAFLEDGS(0.036)PS(0.964)PVLAFAASPR 92.49 0.0049346 49754000 23172 27616 26092 32081 25269 31433 45123 29994 35097 39014 TRUE FALSE 22266.41262 26828.41872 30807.40481 33736.70425 26081.80033 32068.5968 45675.22877 29374.61342 31112.9357 36371.54703 0.612193169 0.73762105 0.847019369 0.927557583 0.71709351 0.881694605 1.255795601 0.807626175 0.855419641 1 15.15052267 5.579095539 0.490837577 0.948567855 5.94E-18 0.38661327 0.131251973 10.88540004 1.082757517 0.077674395 7.097642758 379398.4384 -5.579095539 -0.948567855 KWDEFEDILEER ddPTM_BT-474_Pertuzumab_2h_R1 2 KWDEFEDILEER 12 1 Q5TBH8;O15228;A0A2R8YH69 Q5TBH8 GNPAT Dihydroxyacetone phosphate acyltransferase 0 ; 180.97 3.01E-05 293050000 280740 347140 303340 399240 334780 405060 434460 458110 534740 543000 FALSE TRUE 269768.3704 337239.9071 358160.2858 419844.8242 345548.5027 413250.5907 439777.0514 448649.8684 474038.557 506222.1263 0.532905135 0.666189583 0.707516063 0.829368774 0.682602527 0.81634241 0.868743242 0.88627076 0.936424017 1 18.94941104 5.580237976 0.19269971 1.034205347 1.68E-19 0.8792565 0.046999701 6.966139585 0.183993793 0.105269046 1.819521068 380397.7823 -5.580237976 -1.034205347 SLDTITLS(ph)GDER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDTITLSGDER 12 0 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 SLDT(0.054)IT(0.267)LS(0.679)GDER 77.527 0.014816 0 72487 98978 72784 110730 90138 103980 125220 122770 110020 124920 TRUE FALSE 69654.1279 96155.24435 85937.68787 116444.7886 93037.37063 106082.5468 126752.4798 120234.7566 97530.99084 116459.0571 0.598099707 0.825657074 0.737921893 0.99987748 0.798884801 0.910899929 1.088386622 1.032420831 0.837470208 1 16.82946332 5.580538819 0.427314025 0.997592576 7.60E-11 0.589442929 0.092252113 7.214218485 0.595203329 0.064166629 4.23798529 380661.3809 -5.580538819 -0.997592575 GKYSPT(ph)VQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKYSPTVQTR 10 1 O60437;K7EKI8 O60437 PPL Periplakin 1 GKYS(0.284)PT(0.716)VQTR;GKYS(0.385)PT(0.615)VQTR 143.76 5.40E-05 2318300000 1738470 2000640 1599930 1964760 1883570 1857630 2025130 2123050 2007620 2091750 TRUE FALSE 1670528.67 1943583.706 1889072.941 2066161.499 1944156.74 1895192.551 2049914.147 2079208.276 1779723.394 1950073.909 0.856648901 0.996671817 0.968718638 1.059529841 0.996965669 0.971856781 1.051198181 1.066220242 0.912644072 1 20.89509737 5.584303348 1.259946373 1.013406803 1.95E-12 0.474035407 0.045344537 8.469262969 2.335777333 0.012437365 18.53889651 383975.3529 -5.584303348 -1.013406803 SELVQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SELVQK 6 0 P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 103.29 0.080996 259390000 472650 565790 448300 564540 511280 541980 610220 572740 573400 664620 FALSE TRUE 454178.3155 549654.2232 529317.7824 593675.9771 527725.7855 552939.2069 617688.0549 560912.7189 508310.0359 619604.6954 0.73301303 0.887104677 0.854283039 0.958152805 0.851713664 0.892406418 0.996906672 0.905275126 0.82037796 1 19.24098855 5.586470986 1.059753756 0.91364226 3.21E-14 0.466853214 0.056866511 7.967161437 1.923301695 0.015980065 12.60660368 385896.63 -5.586470986 -0.91364226 DRDNDSDDVESNLLLPAGIALR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRDNDSDDVESNLLLPAGIALR 22 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;Q9NZM1-5;Q9NZM1-8;Q9NZM1-7 Q9NZM1-6 MYOF Myoferlin 0 ;;; 222.51 7.73E-26 863930000 424306 671090 449718 725630 541260 608790 750350 728560 805840 749370 FALSE TRUE 407723.6524 651951.1703 530992.0465 763079.8513 558670.1195 621100.1509 759533.0078 713514.9814 714364.4216 698614.5024 0.583617504 0.933205893 0.760064449 1.092275996 0.799682969 0.889045602 1.087199028 1.021328614 1.022544506 1 19.41413707 5.587255428 0.5017142 1.010910309 1.59E-22 0.534735693 0.105482866 7.852409643 0.79877006 0.057193043 5.603969927 386594.2832 -5.587255428 -1.010910309 LDDLSVLDLSHNQLTECPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDDLSVLDLSHNQLTECPR 19 0 Q13045-3;Q13045;Q13045-2;J3KS54;J3QQQ2;K7EP37;K7EP27 Q13045-3 FLII Protein flightless-1 homolog 0 ; 417.78 2.29E-148 309420000 200456 206850 209300 269030 256050 238470 275100 280890 304790 338700 FALSE TRUE 192621.9579 200950.8405 247125.1659 282914.6705 264286.0808 243292.0268 278466.7561 275089.5233 270191.517 315759.5473 0.610027344 0.636404638 0.782637193 0.895981366 0.836985241 0.770497769 0.881894969 0.871199385 0.855687561 1 18.26846683 5.587282258 0.489913447 0.887891089 2.51E-18 0.742441943 0.057301753 5.006247598 0.49357843 0.033043554 3.054412294 386618.1677 -5.587282258 -0.887891089 EADIDGDGQVNYEEFVQMMTAK ddPTM_BT-474_Pertuzumab_2h_R1 5 EADIDGDGQVNYEEFVQMMTAK 22 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;M0QZ52 P0DP25 CALM2;CALM3 0 ;;;; 293.44 1.87E-55 487405000 488305 481226 355441.4 782429 579452 457460 616686 717564 854900 826705 FALSE TRUE 469221.5008 467501.9056 419677.5677 822810.2545 598090.5998 466710.1546 624233.1877 702746.0526 757855.336 770711.534 0.608815984 0.606584805 0.544532616 1.06759821 0.776023938 0.605557506 0.809944007 0.911814631 0.983319053 1 19.55583146 5.58878406 0.16816732 1.061361311 6.49E-15 0.447094686 0.136033132 26.63699059 0.590979406 0.441566981 6.239807056 387957.4174 -5.58878406 -1.061361311 AVSEDVSNGSSGSPS(ph)PGDTLPWNLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVSEDVSNGSSGSPSPGDTLPWNLGK 26 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 AVSEDVSNGSS(0.001)GS(0.125)PS(0.873)PGDTLPWNLGK 130.83 4.40E-05 82962000 76956 85281 84926 83619 77247 92534 91349 100650 108430 103190 TRUE FALSE 73948.47444 82848.86938 100274.0174 87934.58661 79731.71991 94405.10088 92466.95639 98571.54233 96121.48098 96200.84939 0.768688373 0.861207254 1.04234025 0.914072871 0.828804739 0.98133334 0.961186486 1.02464316 0.999174972 1 16.55376201 5.589929827 0.943905056 0.969938678 5.93E-12 0.503693915 0.061195465 7.56954147 1.630608441 0.02011582 11.01009425 388982.2883 -5.589929827 -0.969938678 DREEILLQELEPVISR ddPTM_BT-474_Pertuzumab_2h_R1 4 DREEILLQELEPVISR 16 1 Q5JU69 Q5JU69 TOR2A Torsin-2A 0 ;;; 139.04 3.03E-06 84082000 64910 78219 61649 75012 76605 78051 74229 79687 89087 86114 FALSE TRUE 62373.24544 75988.2707 72790.34567 78883.37831 79069.0694 79629.2447 75137.43671 78041.4356 78974.21724 80281.42208 0.776932494 0.946523725 0.906689789 0.982585712 0.984898714 0.99187636 0.935925582 0.972098321 0.983717219 1 16.29277855 5.591670744 1.037298676 0.973446929 4.97E-17 0.839948586 0.02535338 3.288794183 0.771857245 0.007207901 5.409167047 390544.6959 -5.591670744 -0.973446929 RKEPEPK ddPTM_BT-474_Pertuzumab_2h_R1 4 RKEPEPK 7 2 P39748;P39748-2 P39748 FEN1 Flap endonuclease 1 0 ;;; 121.62 0.0024862 1775250000 2256310 1875960 1597590 1594740 1637790 1580360 1693710 1842080 2047740 1895320 FALSE TRUE 2168130.911 1822459.458 1886310.051 1677044.723 1690471.003 1612315.962 1714438.13 1804040.404 1815289.14 1766948.288 1.22704831 1.031416409 1.067552494 0.9491193 0.95671787 0.912486219 0.970282006 1.020992191 1.027358385 1 20.75282839 5.59282886 1.004077813 0.979449475 2.193452263 0.768739037 0.039841414 4.400210352 1.000796267 0.012817767 8.666759446 391587.5362 -5.59282886 1.214002788 EVLPLAFLGMHEIADEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVLPLAFLGMHEIADEEK 18 0 J3KN16;Q5VYK3 J3KN16 KIAA0368;ECM29 Proteasome-associated protein ECM29 homolog 0 106.36 0.00045137 11444000 11527 15588 11566 14429 14374 19648 16306 14079 16952 19116 FALSE TRUE 11076.5121 15143.4455 13656.23348 15173.68242 14836.35276 20045.29602 16505.55771 13788.26373 15027.68003 17821.25629 0.621533741 0.849740627 0.766289046 0.851437304 0.832508804 1.124797023 0.926172512 0.773697628 0.843244706 1 14.12131142 5.592994897 0.696863202 0.900663604 4.33E-15 0.419611492 0.098861111 9.939834126 1.521818611 0.040193325 9.28305421 391737.2739 -5.592994897 -0.900663604 IANPVEGSTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IANPVEGSTDR 11 0 F8VZX2;Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 0 ; 208.15 4.78E-08 1059900000 398400 453700 342270 428670 439560 422830 414880 457430 454420 488200 FALSE TRUE 382830.0875 440760.9202 404125.8028 450793.7101 453698.8466 431379.9123 419957.4255 447983.9106 402836.1467 455133.7792 0.841137496 0.968420584 0.887927509 0.99046419 0.996847229 0.947809044 0.922712057 0.984290622 0.885093933 1 18.79593114 5.597965678 1.46656125 0.955535415 7.29E-12 0.389237155 0.041314247 13.1581695 3.745129952 0.01042301 33.36364754 396246.7177 -5.597965678 -0.955535415 WEEIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 WEEIHK 6 0 Q99523;Q99523-2;A0A0J9YX61 Q99523 SORT1 Sortilin 0 88.591 0.05113 164910000 150250 207210 143600 228700 210350 186490 238790 227740 249880 257100 FALSE TRUE 144378.0639 201300.5737 169551.7144 240503.2344 217116.0988 190260.9556 241712.3835 223037.0894 221514.67 239686.388 0.602362383 0.839849836 0.707389835 1.00340798 0.90583408 0.793791242 1.008452693 0.930537154 0.92418544 1 17.87078845 5.598072987 0.530539408 0.946335838 1.87E-13 0.611591043 0.080421459 6.433027427 0.697361517 0.039877553 4.592738895 396344.6383 -5.598072987 -0.946335838 ATMAQNENVVVQPVVAENIPVIPLSDS(ph)PPPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ATMAQNENVVVQPVVAENIPVIPLSDSPPPSR 32 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ATMAQNENVVVQPVVAENIPVIPLS(0.424)DS(0.459)PPPS(0.117)R;ATMAQNENVVVQPVVAENIPVIPLS(0.17)DS(0.661)PPPS(0.17)R 114.35 1.54E-06 197512000 257762 294890 231263 285110 299220 305900 286600 287380 310720 308530 TRUE FALSE 247688.3761 286480.0259 273057.3685 299824.5613 308844.683 312085.5076 290107.4965 281445.5026 275448.3682 287632.9883 0.861126457 0.99599155 0.949325632 1.042385865 1.073745695 1.085012917 1.008603006 0.978488261 0.957638308 1 18.13386962 5.598715937 1.085512486 1.017530531 0.170157607 0.537758863 0.042150523 8.092495512 1.948067008 0.013561522 12.31465346 396931.84 -5.598715937 -0.847372924 SAS(ph)DNTLVAMDFSGHAGR ddPTM_BT-474_Pertuzumab_2h_R1 14 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.149)AS(0.851)DNTLVAMDFSGHAGR;S(0.184)AS(0.816)DNTLVAMDFSGHAGR;S(0.23)AS(0.77)DNTLVAMDFSGHAGR;S(0.156)AS(0.844)DNTLVAMDFSGHAGR;S(0.203)AS(0.796)DNT(0.001)LVAMDFSGHAGR;S(0.197)AS(0.799)DNT(0.004)LVAMDFSGHAGR;S(0.232)AS(0.768)DNTLVAMDFSGHAGR;S(0.321)AS(0.678)DNTLVAMDFSGHAGR;S(0.154)AS(0.845)DNT(0.001)LVAMDFSGHAGR;S(0.033)AS(0.967)DNTLVAMDFSGHAGR;S(0.179)AS(0.748)DNT(0.073)LVAMDFSGHAGR;S(0.432)AS(0.555)DNT(0.013)LVAMDFSGHAGR;SAS(0.91)DNT(0.09)LVAMDFSGHAGR;S(0.263)AS(0.737)DNTLVAMDFSGHAGR 312.03 2.86E-61 18795470000 3198360 3564230 2814517 3544459 3331955 3415707 3437363 3760628 3543163 3722282 TRUE FALSE 3073364.555 3462581.65 3323162.83 3727388.954 3439130.359 3484774.936 3479430.477 3682969.718 3140957.99 3470168.525 0.885652824 0.997813687 0.957637304 1.074123325 0.991055718 1.004209136 1.002669021 1.061323014 0.905131255 1 21.7265743 5.600150252 1.253119358 1.008307561 0.191789341 0.350110317 0.045449766 10.70434884 2.838437636 0.011881454 18.89775991 398244.9266 -5.600150252 -0.81651822 LIPNATGTGTFS(ph)PGAS(ph)PGSEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIPNATGTGTFSPGASPGSEAR 22 0 Q16512;Q16512-2;Q16512-3;K7EN76 Q16512 PKN1 Serine/threonine-protein kinase N1 2 LIPNAT(0.004)GT(0.024)GT(0.17)FS(0.802)PGAS(1)PGSEAR;LIPNAT(0.005)GT(0.036)GT(0.123)FS(0.836)PGAS(0.997)PGS(0.003)EAR 111.57 0.00046892 139180000 163510 158118 170816 174136 171292 195145 183374 231460 210584 201996 TRUE FALSE 157119.8484 153608.6295 201686.251 183123.1798 176801.7627 199090.9656 185618.1859 226680.2701 186679.3872 188314.631 0.834347536 0.815702044 1.071006803 0.972432035 0.938863655 1.057225158 0.98568117 1.20373159 0.991316427 1 17.52278557 5.601144068 0.447988103 1.070261126 0.324265524 0.438865847 0.080094998 8.655895763 0.750317258 0.052626881 4.02343664 399157.2928 -5.601144068 -0.745995602 IWSTVPTDEEDEMEESTNRPR ddPTM_BT-474_Pertuzumab_2h_R1 2 IWSTVPTDEEDEMEESTNRPR 21 1 Q9GZL7 Q9GZL7 WDR12 Ribosome biogenesis protein WDR12 0 ; 226.44 2.21E-25 734530000 152350 170725 145870 155871 174570 183022 173009 175518 176739 190860 FALSE TRUE 146395.9936 165856.0902 172231.9539 163915.521 180185.2026 186722.8302 175126.3359 171893.492 156676.3297 177932.8822 0.822759637 0.932127261 0.967960232 0.921221075 1.012658258 1.049400358 0.984226938 0.966058043 0.88053612 1 17.44097362 5.601237461 1.004732142 0.977399197 0.19579924 0.515375459 0.044075074 7.551900168 1.69382438 0.013695739 9.620324435 399243.1385 -5.601237461 -0.781599958 LKKEDIYAVEIVGGATR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKKEDIYAVEIVGGATR 17 2 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 71.073 0.017598 470270000 436020 388800 259460 264940 329490 398370 337620 371190 395050 335880 FALSE TRUE 418979.8564 377711.8047 306350.1937 278613.5852 340088.3451 406425.3143 341751.8946 363524.7968 350205.5802 313130.5484 1.338035712 1.20624387 0.978346556 0.889768138 1.086091238 1.297942077 1.091403877 1.160936864 1.118401197 1 18.25640474 5.602072515 0.010290779 2.37E-06 2.31769219 0.079441106 0.127882241 32116.98414 40.55703791 4146.318918 5022.164319 400011.5345 -5.602072515 2.317689816 S(ph)PCPQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPCPQEK 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PCPQEK 66.595 0.070748 2418200000 1198500 973280 1047600 1248400 1071700 1025400 1283000 1248100 1294400 1434600 TRUE FALSE 1151661.295 945523.0073 1236924.624 1312830.074 1106172.204 1046134.291 1298701.738 1222326.299 1147465.139 1337433.264 0.861098139 0.706968364 0.924849603 0.981604173 0.827085907 0.782195507 0.971040404 0.913934423 0.857960669 1 20.35103547 5.605053576 0.025254594 1.621770237 1.68E-08 0.233424296 0.077943936 1792.003244 5.550737014 140.2068442 224.2766519 402766.7182 -5.605053576 -1.621770221 Y(ph)SS(ph)GGNFET(ph)PS(ph)K ddPTM_BT-474_Pertuzumab_2h_R1 1 YSSGGNFETPSK 12 0 A0A0G2JMZ8;Q16625-2;Q16625-3;Q16625;Q16625-5;Q16625-4 A0A0G2JMZ8 OCLN Occludin 4 Y(0.646)S(0.646)S(0.709)GGNFET(1)PS(1)K 57.802 0.021803 0 73754 84855 79141 112660 89525 104670 114260 116260 130870 138460 TRUE FALSE 70871.61214 82435.01848 93443.53918 118474.3961 92404.65293 106786.4991 115658.3481 113859.1904 116014.1863 129081.9809 0.549043419 0.638625298 0.723908469 0.917822885 0.715860202 0.827276576 0.89600692 0.882068819 0.898763603 1 16.9779281 5.608656535 0.305661075 0.947875069 6.33E-28 0.800608798 0.060237163 5.777424444 0.291281028 0.06442895 2.250909928 406122.0171 -5.608656535 -0.947875069 RGSGS(ph)ALGGPLDPQFVGPSDTSLGAAPGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSGSALGGPLDPQFVGPSDTSLGAAPGHR 30 1 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 RGS(0.305)GS(0.695)ALGGPLDPQFVGPSDTSLGAAPGHR 253.43 2.18E-58 1505200000 335660 449090 341080 388470 466730 449590 468580 431280 523820 482860 TRUE FALSE 322542.0361 436282.3929 402720.7433 408518.9833 481742.7943 458681.0178 474314.6222 422373.9173 464358.1496 450155.4621 0.716512546 0.969181604 0.894625917 0.907506445 1.07016983 1.018939136 1.053668482 0.938284555 1.031550628 1 18.7800638 5.609451161 0.767724335 1.004442641 1.74E-16 0.689800098 0.05512902 5.263498766 0.884729289 0.019537771 6.195118611 406865.7763 -5.609451161 -1.004442641 VLPSISLS(ph)PGPQPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLPSISLSPGPQPPK 15 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 VLPSIS(0.003)LS(0.997)PGPQPPK;VLPSISLS(1)PGPQPPK 254.1 1.15E-24 966410000 397900 452050 441380 548740 449500 455230 589700 655490 703010 734420 TRUE FALSE 382349.6281 439157.9766 521147.1844 577060.5372 463958.5757 464435.0625 596916.925 641953.9024 623207.2521 684677.0792 0.558437897 0.641408906 0.761157632 0.842821462 0.677631236 0.678327166 0.871822561 0.937600983 0.910220703 1 19.38506419 5.611047562 0.150964652 1.088470349 5.34E-15 0.73791164 0.070828483 18.48460019 0.358387241 0.33426848 4.009603653 408364.1059 -5.611047562 -1.088470349 LISSDGHEFIVK ddPTM_BT-474_Pertuzumab_2h_R1 4 LISSDGHEFIVK 12 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;;; 122.33 0.0003605 1464440000 2865554 3476086 2761549 3602500 3431908 3616549 3633190 3526840 3874370 4398140 FALSE TRUE 2753564.982 3376951.431 3260622.335 3788425.457 3542298.438 3689678.099 3677654.066 3454009.522 3434567.76 4100250.06 0.671560256 0.823596459 0.795225239 0.923949857 0.863922538 0.899866604 0.896934092 0.842389969 0.837648365 1 21.96728047 5.611715503 0.833343781 0.884767003 1.25E-12 0.644244005 0.049292061 5.427484264 0.995303357 0.015350028 6.226039618 408992.6493 -5.611715503 -0.884767003 EEAQAEIEQYR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEAQAEIEQYR 11 0 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 245.58 1.38E-15 873630000 379300 417680 313070 420390 390500 410130 417800 418420 389520 459510 FALSE TRUE 364476.5367 405768.1754 369648.7132 442086.3783 403060.7871 418423.1096 422913.1614 409779.4808 345303.3226 428386.9784 0.850811428 0.947200069 0.862885036 1.03197903 0.940880109 0.976740962 0.987222261 0.956563811 0.806054666 1 18.7085551 5.614220523 0.947402748 0.952940205 0.481561977 0.171827716 0.06282064 15.80892897 3.286555639 0.018585391 11.34359606 411358.5447 -5.614220523 -0.471378228 EDLMGLAIGTHGANIQQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDLMGLAIGTHGANIQQAR 19 0 P51116;A0A087WWR6;Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 P51116;Q06787 FXR2;FMR1 Fragile X mental retardation syndrome-related protein 2;Fragile X mental retardation protein 1 0 ; 132.5 1.35E-05 633580000 1790580 1086300 833130 709970 786090 653550 528510 1154660 762260 624600 FALSE TRUE 1720602.154 1055319.788 983695.1239 746611.6368 811375.2988 666765.2288 534978.0635 1130815.867 675731.4405 582295.2857 2.9548619 1.812344722 1.689340697 1.282187329 1.393408669 1.145063759 0.918740159 1.941997291 1.160461809 1 19.15139141 5.614225128 0.930068855 1.314071624 9.078130695 0.772563066 0.274972071 4.379553347 0.894608103 0.087969313 50.5760322 411362.9063 -5.614225128 7.764059071 up MSCFSRPSMSPT(ph)PLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPS(0.005)MS(0.186)PT(0.809)PLDR 144.27 3.68E-06 1125400000 692970 750220 427420 498770 514870 531060 510750 428590 512400 506010 TRUE FALSE 665887.9663 728824.4601 504664.3019 524511.5795 531431.2611 541798.3971 517000.7113 419739.4667 454234.5002 471737.492 1.411564647 1.544978876 1.06979901 1.111871726 1.126540227 1.14851672 1.095950015 0.889773388 0.962896755 1 18.84762474 5.614513431 0.37656564 0.957539067 2.410900704 0.700790626 0.103656553 6.095550359 0.413436347 0.086646297 4.565723546 411636.0775 -5.614513431 1.453361637 FCDS(ph)PTSDLEMR ddPTM_BT-474_Pertuzumab_2h_R1 3 FCDSPTSDLEMR 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 FCDS(0.901)PT(0.08)S(0.019)DLEMR;FCDS(0.825)PT(0.155)S(0.02)DLEMR;FCDS(0.741)PT(0.175)S(0.084)DLEMR 214.78 4.51E-11 1062520000 1380690 1593340 1181840 1530350 1625710 1634570 1571230 1505850 1622550 1776570 TRUE FALSE 1326731.108 1547899.503 1395424.778 1609331.547 1678002.439 1667622.125 1590459.183 1474753.671 1438364.926 1656241.331 0.80104939 0.934585724 0.84252503 0.971676963 1.01313885 1.006871459 0.960282268 0.890421971 0.868451293 1 20.65948147 5.615619159 0.879730681 0.949215844 0.318039829 0.391971879 0.055147947 10.54698605 2.034827935 0.019061859 9.243103084 412685.4517 -5.615619159 -0.631176015 ALENDFFNS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALENDFFNSPPR 12 0 F5H148;H3BMT1;Q9NYV6-3;Q9NYV6;Q9NYV6-2;A6NIE6 F5H148 RRN3;RRN3P2 RNA polymerase I-specific transcription initiation factor RRN3;Putative RRN3-like protein RRN3P2 1 ALENDFFNS(1)PPR;ALENDFFNS(1)PPR;ALENDFFNS(1)PPR;ALENDFFNS(1)PPR 213.73 5.45E-09 445133000 403664 460885 451726 463759 474446 541100 542950 519964 554305 652760 TRUE FALSE 387888.3646 447741.0111 533362.9368 487693.6576 489706.9865 552041.4127 549594.7845 509226.5617 491382.6202 608547.9838 0.637399802 0.73575301 0.876451736 0.801405428 0.804713843 0.90714525 0.903124814 0.836789498 0.807467338 1 19.2150115 5.61657749 0.699671837 0.870857919 5.98E-16 0.624881023 0.058211704 5.825893832 0.872591958 0.021325574 5.327142895 413597.1044 -5.61657749 -0.870857919 DKDAVDK ddPTM_BT-474_Pertuzumab_2h_R1 3 DKDAVDK 7 1 P25815 P25815 S100P Protein S100-P 0 ;; 85.676 0.01882 1929320000 4669280 3734630 3382610 2936390 3344600 2936400 3933760 4046390 3335090 3568510 FALSE TRUE 4486799.375 3628122.009 3993922.873 3087937.44 3452182.096 2995776.02 3981902.532 3962830.632 2956504.565 3326811.639 1.348678513 1.090570312 1.2005257 0.928197258 1.037684868 0.900494631 1.196912529 1.191179743 0.888690099 1 21.66570875 5.618118532 1.072613273 1.050829073 2.70309864 0.402162372 0.112813761 11.03277576 2.535806478 0.03418182 32.53143354 415067.3117 -5.618118532 1.652269566 ASS(ph)PELPVSVENIK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASSPELPVSVENIK 14 0 Q969R5 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 ASS(1)PELPVSVENIK;AS(0.015)S(0.985)PELPVSVENIK;AS(0.013)S(0.987)PELPVSVENIK 272.72 5.72E-33 220636000 405080 415800 508830 555210 513160 457570 617780 685820 730210 758650 TRUE FALSE 389249.0258 403941.7911 600786.8999 583864.4546 529666.2574 466822.3789 625340.5764 671657.5773 647319.6221 707265.9598 0.550357359 0.571131391 0.84944976 0.825523195 0.74889262 0.660037957 0.884166087 0.949653476 0.915242156 1 19.4318933 5.619067949 0.199941053 1.028910844 5.89E-16 0.681676486 0.084168931 13.21729841 0.361576904 0.190305767 3.573307161 415975.6884 -5.619067949 -1.028910844 SPVSESVS(ph)PVVPDYLPTENGDFLSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPVSESVSPVVPDYLPTENGDFLSSK 26 0 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.035)PVS(0.035)ES(0.035)VS(0.89)PVVPDY(0.003)LPT(0.001)ENGDFLSSK;S(0.018)PVS(0.018)ES(0.14)VS(0.823)PVVPDYLPTENGDFLSSK 112.23 0.0011851 109015000 107491 114881 114681 131444 135748 148274 155062 171080 173998 191892 TRUE FALSE 103290.1329 111604.7064 135406.4078 138227.8406 140114.4577 151272.2019 156959.6951 167547.1382 154246.4765 178894.9839 0.577378586 0.623855985 0.756904441 0.772675888 0.783221836 0.845592194 0.877384551 0.936566999 0.862218007 1 17.44875341 5.619903298 0.246165947 0.991638051 3.10E-15 0.94093867 0.030152078 3.309038216 0.120805043 0.042490535 1.071932862 416776.5717 -5.619903298 -0.991638051 LFEASIETGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFEASIETGDR 11 0 P28838-2;P28838;H0Y9Q1 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 213.98 1.60E-09 376010000 240523 287630 240450 278770 279320 281060 306590 309530 298320 353900 FALSE TRUE 231123.0952 279427.074 283904.6638 293157.3531 288304.5815 286743.2258 310342.1401 303138.0973 264455.9643 329930.0378 0.700521531 0.846928264 0.860499595 0.888543993 0.873835506 0.869103122 0.940630148 0.918795086 0.801551644 1 18.33180061 5.621785299 0.905260365 0.899296623 9.05E-15 0.594487453 0.048772147 6.06543214 1.192803242 0.014491381 7.867958806 418586.5787 -5.621785299 -0.899296623 RPLPALPVPEAPSPS(ph)PVPSPAPGR ddPTM_BT-474_Pertuzumab_2h_R1 5 RPLPALPVPEAPSPSPVPSPAPGR 24 1 O43281-3;O43281-2;O43281 O43281-3 EFS Embryonal Fyn-associated substrate 1 RPLPALPVPEAPS(0.038)PS(0.961)PVPSPAPGR;RPLPALPVPEAPS(0.002)PS(0.998)PVPSPAPGR;RPLPALPVPEAPS(0.002)PS(0.998)PVPSPAPGR;RPLPALPVPEAPS(0.001)PS(0.997)PVPS(0.002)PAPGR;RPLPALPVPEAPS(0.142)PS(0.858)PVPSPAPGR 202.04 8.29E-25 3185600000 1221180 1453010 1275610 1559000 1476090 1597500 1643900 1743810 1691310 1854400 TRUE FALSE 1173454.936 1411571.577 1506141.103 1639460.177 1523569.775 1629802.545 1664018.54 1707799.714 1499319.579 1728799.836 0.678768537 0.816503766 0.871206181 0.948322728 0.881287552 0.942736406 0.962528168 0.987852774 0.867260366 1 20.72133941 5.621895001 0.64593232 0.953014488 8.14E-17 0.82145423 0.038673062 3.440790256 0.466048104 0.015384043 3.134433053 418692.326 -5.621895001 -0.953014488 ESNCYDPER ddPTM_BT-474_Pertuzumab_2h_R1 6 ESNCYDPER 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 188.3 9.20E-05 5539720000 5985170 6813060 5261030 6490070 6308760 6663030 6718990 6534210 6996500 7436380 FALSE TRUE 5751262.939 6618758.199 6211815.152 6825023.29 6511686.995 6797761.032 6801219.009 6399276.28 6202286.652 6932707.359 0.829583977 0.954714783 0.896015774 0.984467242 0.939270426 0.98053483 0.981033622 0.923055878 0.894641347 1 22.72498743 5.622359098 1.355249275 0.950913946 9.01E-11 0.500945852 0.035718241 10.44309723 2.721828287 0.00942217 24.05241839 419139.9896 -5.622359098 -0.950913946 AVDDLNLHSYSNLPIWVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVDDLNLHSYSNLPIWVNK 19 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 246.48 1.16E-24 1557620000 1333070 1515470 1344430 1402720 1438670 1671460 1526470 1476720 1889160 1789820 FALSE TRUE 1280972.151 1472250.279 1587398.408 1475114.547 1484946.127 1705258.066 1545151.396 1446225.216 1674710.477 1668593.897 0.767695575 0.882329896 0.951338975 0.884046472 0.889938606 1.021973093 0.926020045 0.866732893 1.003665709 1 20.67020144 5.624175074 1.043930668 0.935910479 1.49E-09 0.516153542 0.051333616 8.34259431 1.8558361 0.015215716 13.49679856 420896.2666 -5.624175074 -0.935910478 RS(ph)SPPGHYYQK ddPTM_BT-474_Pertuzumab_2h_R1 4 RSSPPGHYYQK 11 1 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 RS(0.971)S(0.029)PPGHYYQK;RS(0.96)S(0.04)PPGHYYQK;RS(0.976)S(0.024)PPGHYYQK;RS(0.914)S(0.086)PPGHYYQK 157.35 1.88E-05 3457070000 834725 1214406 967275 1728340 819920 1104393 1759780 1508750 1502030 1740400 TRUE FALSE 802103.0242 1179772.33 1142083.109 1817539.835 846293.4714 1126724.583 1781316.714 1477593.785 1331525.851 1622521.158 0.494355972 0.727122925 0.703894124 1.120194844 0.52159164 0.694428284 1.097869637 0.910677669 0.820652381 1 20.62980586 5.625236958 0.344836671 0.938492084 2.06E-37 0.310245886 0.174155748 16.42914096 0.978221812 0.162062097 7.231546269 421926.6501 -5.625236958 -0.938492084 DTEGLIQEINDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTEGLIQEINDLR 13 0 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;A0A0A0MTP2;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 0 128.85 0.00037351 10406000 11726 14109 11617 13286 12615 17640 15362 13360 14993 14706 FALSE TRUE 11267.73496 13706.62513 13716.45032 13971.69205 13020.77293 17996.69289 15550.00475 13084.11133 13291.0575 13709.94952 0.821865532 0.99975752 1.000474166 1.019091429 0.949731646 1.312673898 1.134213129 0.954351532 0.969446129 1 13.74293564 5.625258065 0.90708 1.053758387 1.51E-11 0.295718889 0.103058625 12.50738387 2.45129781 0.034466723 19.08578529 421947.1568 -5.625258065 -1.053758387 TT(ph)PPEAAQNGQS(ph)PMAALILVADNAGGSHASK ddPTM_BT-474_Pertuzumab_2h_R1 4 TTPPEAAQNGQSPMAALILVADNAGGSHASK 31 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 2 T(0.469)T(0.531)PPEAAQNGQS(1)PMAALILVADNAGGSHASK;T(0.453)T(0.547)PPEAAQNGQS(1)PMAALILVADNAGGSHASK;T(0.466)T(0.534)PPEAAQNGQS(1)PMAALILVADNAGGSHASK;T(0.454)T(0.546)PPEAAQNGQS(1)PMAALILVADNAGGSHASK 188.49 2.76E-18 280665000 140427 148877 162430 188485 153949 168334 195151 203128 210611 232338 TRUE FALSE 134938.9576 144631.1737 191784.7142 198212.7334 158900.9094 171737.8288 197539.3163 198933.3358 186703.3222 216601.5403 0.622982447 0.667729202 0.885426364 0.915103065 0.733609323 0.792874458 0.911994052 0.918429922 0.861966734 1 17.72468398 5.62582206 0.550100531 0.893677141 1.41E-65 0.588839754 0.074399689 7.296620151 0.808580591 0.038468932 5.165143521 422495.4729 -5.62582206 -0.893677141 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR 42 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 ;; 118.48 5.83E-07 2598930000 225257.9 234561 263658 296029 295001 275083 353643 335251 402169 390430 FALSE TRUE 216454.5722 227871.5499 311306.8656 311307.0922 304489.9751 280645.3667 357970.9888 328327.9497 356516.4612 363985.8283 0.594678571 0.626045115 0.85527194 0.855272563 0.83654349 0.771033774 0.983475072 0.902034981 0.979478962 1 18.47352276 5.626032346 0.332156343 0.972934391 6.84E-17 0.787981365 0.061893145 5.731216921 0.323277669 0.060483891 2.511610198 422700.0953 -5.626032346 -0.972934391 YDDAER ddPTM_BT-474_Pertuzumab_2h_R1 1 YDDAER 6 0 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 115.78 0.056159 190020000 400750 451130 428160 509890 501980 497350 566610 582180 570370 619750 FALSE TRUE 385088.2469 438264.2141 505538.0364 536205.484 518126.6426 507406.7578 573544.3427 570157.7796 505623.9888 577773.7805 0.6665035 0.758539465 0.874975732 0.928054374 0.896763855 0.87821008 0.992679769 0.986818369 0.875124497 1 19.14014521 5.626275784 0.551063593 0.9578048 4.97E-16 0.823693065 0.042229707 3.791252583 0.420881963 0.021349128 2.882530172 422937.1011 -5.626275784 -0.9578048 VLGTPVETIELTEDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLGTPVETIELTEDRR 16 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ;;; 352.27 4.64E-87 2022950000 524448 633200 505092 611750 613510 695530 676160 597470 686750 736293 FALSE TRUE 503951.9924 615141.756 596373.3601 643322.4908 633244.1063 709594.0931 684435.0483 585132.0357 608793.0191 686423.2193 0.734170958 0.896155227 0.868812918 0.937209687 0.922527223 1.033755959 0.997103579 0.852436251 0.886906215 1 19.38873883 5.62996611 0.903215972 0.940347936 3.05E-12 0.569302576 0.054303025 7.581184955 1.469022941 0.018499761 10.28821725 426546.2317 -5.62996611 -0.940347935 AGFAGDDAPR ddPTM_BT-474_Pertuzumab_2h_R1 10 AGFAGDDAPR 10 0 C9JTX5;F8WCH0;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63267-2;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38;P0CG39 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;;;;;;;;; 189.7 2.28E-06 1.08694E+11 103697830 120223270 93281580 119006500 111853340 120887240 120335860 121995930 121599180 121395290 FALSE TRUE 99645204.16 116794620.1 110139636.5 125148439.7 115451204.3 123331662.8 121808566.3 119476671.4 107795750.9 113173078.9 0.880467379 1.032000023 0.973196432 1.105814571 1.02012957 1.089761488 1.076303371 1.055698693 0.952485803 1 26.75395558 5.635301854 1.15688877 1.045463167 5.15E-19 0.471792056 0.047888835 8.613490045 2.017356849 0.01292734 17.85530674 431819.1065 -5.635301854 -1.045463167 AS(ph)DLEDEESAAR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASDLEDEESAAR 12 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 AS(1)DLEDEESAAR;AS(1)DLEDEESAAR;AS(1)DLEDEESAAR;AS(1)DLEDEESAAR;AS(1)DLEDEESAAR 327.32 4.85E-58 9804430000 3838280 3842387 4076805 5362700 4452930 4155695 4973510 5905804 5769700 5814510 TRUE FALSE 3688275.774 3732805.885 4813574.352 5639469.59 4596162.537 4239726 5034377.303 5783847.084 5114747.845 5420688.059 0.680407309 0.688622154 0.888000619 1.040360472 0.84789283 0.782137978 0.928734 1.066995005 0.943560631 1 22.37004456 5.637089364 0.490286019 0.971875252 4.18E-20 0.549372589 0.087057293 8.368492564 0.794425743 0.05534585 5.655171335 433600.0898 -5.637089364 -0.971875252 SGGLQT(ph)PECLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQT(1)PECLSR;SGGLQT(1)PECLSR;SGGLQT(1)PECLSR;SGGLQT(1)PECLSR 211.13 3.96E-07 2067190000 1033700 1264240 1120650 1452640 1307890 1438700 1613730 1557690 1918560 1719020 TRUE FALSE 993301.8612 1228185.113 1323176.384 1527610.924 1349959.47 1467791.5 1633479.31 1525523.157 1700773.112 1602589.244 0.619810638 0.766375487 0.82564911 0.953214262 0.842361494 0.915887527 1.019275099 0.951911516 1.061265772 1 20.61197327 5.639458392 0.391017126 1.00936547 1.94E-16 0.863733276 0.046843129 3.954539374 0.278234637 0.036201006 2.152626143 435971.7931 -5.639458392 -1.00936547 DLPAIQES(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLPAIQESPTR 11 0 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 DLPAIQES(0.942)PT(0.058)R;DLPAIQES(0.993)PT(0.007)R 155.39 3.31E-05 1025950000 266360 309590 294480 340850 347990 338010 362870 406670 436330 406890 TRUE FALSE 255950.3567 300760.7963 347699.0867 358441.3093 359183.4144 344844.7938 367310.9116 398272.1224 386799.6476 379330.9779 0.67474151 0.792871697 0.916611368 0.944930233 0.946886585 0.909086824 0.968312458 1.049933028 1.019689058 1 18.53309767 5.641137846 0.506084286 1.006164981 1.22E-13 0.903324852 0.03309426 3.229583757 0.318154278 0.020991768 2.345491066 437660.9978 -5.641137846 -1.006164981 SS(ph)PIMR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPIMR 6 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8;K7ENU7;H0Y9S9 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(0.314)S(0.686)PIMR;S(0.091)S(0.909)PIMR;S(0.162)S(0.838)PIMR 160.91 0.0090879 771070000 626470 703550 576000 655250 673920 705140 714700 678630 754330 763980 TRUE FALSE 601986.8598 683485.4428 680096.0131 689067.531 695597.2488 719398.4139 723446.7124 664616.0533 668701.6208 712234.9541 0.845208251 0.959634793 0.954875928 0.967472218 0.976640145 1.01005772 1.015741657 0.933141584 0.938877848 1 19.44199371 5.643120946 1.26150313 0.974992932 1.30E-11 0.67910025 0.026519753 7.579542408 1.826421899 0.007929325 16.46149563 439664.0393 -5.643120946 -0.974992932 EAQLFHPGDLQDLSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAQLFHPGDLQDLSNR 16 0 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ; 132.59 3.83E-05 402250000 159727 188251 165769 189239 182577 209555 205616 211904 218376 217356 FALSE TRUE 153484.6923 182882.2658 195727.1458 199005.6475 188449.755 213792.3457 208132.3901 207528.1083 193586.872 202634.2845 0.757446809 0.902523807 0.965913277 0.98209268 0.92999936 1.055065021 1.027133146 1.024151016 0.955351028 1 17.62851876 5.645154685 0.758816289 1.007077647 4.58E-12 0.830678741 0.03318419 3.475047236 0.551240882 0.011929704 4.094163006 441727.7522 -5.645154685 -1.007077647 TPGLHGDCDDDKYR ddPTM_BT-474_Pertuzumab_2h_R1 4 TPGLHGDCDDDKYR 14 1 O95159 O95159 ZFPL1 Zinc finger protein-like 1 0 ;;; 176.75 1.31E-06 1507270000 2030850 2254950 2095890 2696890 2312820 2360780 2631170 3183160 3624600 3608910 FALSE TRUE 1951482.137 2190641.034 2474663.946 2836076.816 2387213.956 2408516.589 2663371.046 3117426.634 3213150.604 3364475.311 0.580025697 0.651109261 0.73552745 0.842947727 0.709535287 0.715866923 0.791615571 0.92657141 0.955022791 1 21.6819501 5.64689731 0.133367163 1.116656866 3.07E-14 0.792792905 0.059542703 20.32409352 0.339008139 0.409127646 4.043278549 443503.7642 -5.64689731 -1.116656866 ESLLGDMEWR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESLLGDMEWR 10 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-5 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 132.84 0.00049541 90577000 110873 134757 119527 144568 140837 143529 161904 169596 148340 186673 FALSE TRUE 106539.9606 130913.8623 141128.1878 152029.1718 145367.15 146431.2547 163885.4296 166093.7833 131501.0651 174029.4714 0.612194933 0.752251106 0.810944184 0.873582908 0.835301911 0.841416419 0.941710782 0.954400321 0.755625263 1 17.40897212 5.650182438 0.53876943 0.906995857 8.74E-16 0.656370891 0.063594286 6.004915583 0.634828275 0.031581218 4.236411587 446871.2738 -5.650182438 -0.906995857 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGK ddPTM_BT-474_Pertuzumab_2h_R1 4 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGK 32 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 476.89 5.83E-283 651863000 144655 147481 168034 191746 177192 165191 220206 153528 279396 258887 FALSE TRUE 139001.7227 143274.9863 198401.4817 201642.034 182891.5416 168531.2752 222900.9469 150357.5931 247680.1374 241352.3529 0.5759286 0.593634098 0.822040802 0.835467447 0.757778159 0.698278982 0.923549923 0.622979604 1.026218035 1 17.88078137 5.6505677 0.080809219 1.21511559 1.23E-11 0.457182166 0.114700026 119.4830481 1.177344326 4.023531608 17.72145592 447267.8692 -5.6505677 -1.21511559 KVFVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVFVGR 6 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YBN4;Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;A0A087WXQ5;Q13148-4;A0A087WV68;A0A087WXV3;K7EJM5;A0A087WX67;A0A087WW61;A0A087WZC9;A0A087WZM1;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 P11940-2;Q13148;B1ANR0 PABPC1;TARDBP;TDP43;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;TAR DNA-binding protein 43;Polyadenylate-binding protein 4 0 ; 138.38 0.019766 4347400000 5104900 6483500 4852600 5858900 6304700 6508400 5856300 6637700 7004800 7284600 FALSE TRUE 4905394.864 6298596.928 5729572.766 6161278.531 6507496.401 6640004.307 5927971.151 6500629.175 6209644.471 6791207.554 0.722315557 0.927463471 0.843675108 0.907243444 0.958223755 0.97773544 0.872889115 0.957212561 0.914365291 1 22.69523669 5.650734215 0.898439525 0.93654895 4.47E-29 0.647455684 0.045429121 5.952021488 1.111494399 0.013620665 8.058463493 447439.3904 -5.650734215 -0.93654895 LNEQASEEILK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNEQASEEILK 11 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ; 202.03 9.63E-08 311210000 312980 295090 337730 418950 350690 342650 413060 500780 517220 542930 FALSE TRUE 300748.3956 286674.3221 398765.3238 440572.0597 361970.2623 349578.6178 418115.1518 490438.718 458507.354 506156.8675 0.594180213 0.566374459 0.787829524 0.870425925 0.715134547 0.690652721 0.826058439 0.968946091 0.905860186 1 18.94922505 5.651872538 0.171382358 1.058426446 1.81E-19 0.694395259 0.078391117 16.33305153 0.363371674 0.256240077 3.894015697 448613.7063 -5.651872538 -1.058426446 LSGLANVVLHELS(ph)GDDDTDQNMR ddPTM_BT-474_Pertuzumab_2h_R1 5 LSGLANVVLHELSGDDDTDQNMR 23 0 Q14789;Q14789-2;E7EU81;F8WF12;C9J8Q0 Q14789 GOLGB1 Golgin subfamily B member 1 1 LSGLANVVLHELS(0.999)GDDDT(0.001)DQNMR;LSGLANVVLHELS(0.991)GDDDT(0.009)DQNMR;LSGLANVVLHELS(1)GDDDTDQNMR;LSGLANVVLHELS(1)GDDDTDQNMR;LSGLANVVLHELS(1)GDDDTDQNMR 294.49 8.21E-62 141046000 134167 160054 124608 158683 148022 163548 153854 167746 172748 172425 TRUE FALSE 128923.6053 155489.4166 147127.4375 166872.6486 152783.2621 166855.0526 155736.9113 164281.9865 153138.3713 160746.5012 0.802030554 0.967295807 0.915276142 1.038110612 0.950460887 1.038001147 0.968835465 1.021994166 0.952670012 1 17.29442781 5.651991242 0.979931867 0.994611795 1.68E-20 0.683582905 0.037549521 5.027236673 1.011189098 0.010098936 8.071278669 448736.3403 -5.651991242 -0.994611795 ERLEQEQLER ddPTM_BT-474_Pertuzumab_2h_R1 1 ERLEQEQLER 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;A0A075B6E5;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 166.29 5.10E-06 1101700000 712310 836820 671180 777720 905040 824100 810320 831540 901570 999800 FALSE TRUE 684472.1377 812954.7129 792477.1563 817858.2224 934151.4335 840763.8666 820236.9386 814368.4084 799227.5533 932082.6555 0.734347039 0.872191654 0.850221975 0.877452464 1.002219522 0.902027156 0.880004508 0.87370836 0.857464248 1 19.83009837 5.657758984 0.978954815 0.904755224 1.45E-16 0.520466122 0.050076133 8.479195549 1.687405741 0.015195211 12.39800119 454735.6303 -5.657758984 -0.904755224 GIPNMLLSEEETES ddPTM_BT-474_Pertuzumab_2h_R1 4 GIPNMLLSEEETES 14 0 F5GYQ2;Q9UI30;Q9UI30-2 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;; 286.08 2.29E-33 302842000 429940 487040 370014 491290 467300 507690 476070 468530 470630 508730 FALSE TRUE 413137.4695 473150.0961 436883.7607 516645.5358 482331.1289 517955.8396 481896.2871 458854.6918 417206.0554 474273.264 0.871095845 0.997631813 0.921164641 1.089341473 1.01698992 1.092104234 1.016073061 0.967490109 0.879674414 1 18.85535902 5.660607687 1.177217594 1.004478573 0.08024878 0.270244408 0.06229689 16.07445619 3.603698818 0.018051957 30.48769079 457728.2189 -5.660607687 -0.924229793 ITLETDEDMVTEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITLETDEDMVTEIR 14 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 259.55 4.67E-24 53803000 40829 46165 36508 42986 45542 45079 47359 42252 48979 50800 FALSE TRUE 39233.35754 44848.4194 43105.80772 45204.51261 47006.89979 45990.52827 47938.59361 41379.48143 43419.10926 47359.27075 0.828419799 0.946982897 0.91018732 0.954501872 0.99255962 0.971098742 1.012232512 0.873735612 0.916802741 1 15.53135925 5.661402487 1.256804973 0.95225209 1.75E-08 0.448776603 0.041384198 12.90232577 2.974536668 0.012155533 27.47174214 458566.6709 -5.661402487 -0.952252073 GVQVETISPGDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GVQVETISPGDGR 13 0 P62942;A0A087WZM5;Q1JUQ3;A0A087WTS4;A0A087WV48 P62942 FKBP1A;FKBP12-Exin Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 ; 157.47 0.00010155 226110000 209359 251830 176275 252610 226250 232290 235400 248850 271690 252670 FALSE TRUE 201177.0188 244648.055 208131.8137 265647.2324 233527.5367 236987.063 238280.8956 243711.1605 240848.8902 235556.4358 0.85405019 1.038596352 0.883575152 1.12774347 0.991386781 1.006073394 1.01156606 1.034618985 1.022467883 1 17.84571322 5.662717718 1.133808872 1.019124357 3.91E-14 0.389780199 0.057680905 11.05907536 2.4178131 0.01510296 22.04781318 459957.5138 -5.662717718 -1.019124357 ADKEEMNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADKEEMNR 8 1 P21283;E7EV59 P21283 ATP6V1C1 V-type proton ATPase subunit C 1 0 ; 114.97 0.0023294 476900000 464510 398570 449320 526810 456460 482560 578090 604200 657810 733450 FALSE TRUE 446356.4357 387203.1738 530522.1191 553998.7272 471142.4504 492317.6938 585164.8383 591723.0589 583138.1666 683772.7782 0.652784741 0.566274625 0.775874875 0.810208807 0.689033646 0.720001892 0.855788439 0.865379667 0.852824484 1 19.38315746 5.667323784 0.102783777 1.161766034 1.39E-15 0.75114148 0.05931777 35.16822328 0.441720023 0.920841461 5.881724968 464861.7186 -5.667323784 -1.161766034 LNNLSPAPHLASGS(ph)PPPGLPSGLPSGLQSGSPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 34 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LNNLSPAPHLAS(0.149)GS(0.642)PPPGLPS(0.1)GLPSGLQS(0.1)GS(0.009)PSR 193.4 7.26E-21 1736300000 225370 247120 254860 304730 291820 344580 339270 355870 349940 456230 TRUE FALSE 216562.2912 240072.3796 300918.8713 320457.1518 301206.6553 351547.6437 343422.0877 348521.1601 310216.2783 425329.1357 0.509164017 0.564439065 0.707496492 0.753433341 0.708173106 0.82653083 0.80742667 0.819415203 0.729355815 1 18.69822016 5.673881141 0.221026474 0.929758241 1.16E-45 0.79833923 0.05895375 8.277512315 0.25424078 0.099318302 2.25244983 471933.8628 -5.673881141 -0.929758241 LLNGNHENGDLDPTS(ph)PLENMDYIK ddPTM_BT-474_Pertuzumab_2h_R1 8 LLNGNHENGDLDPTSPLENMDYIK 24 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73;F8WE35;F5H8I0;F5H2W9;F5H2H9;F5GZ10;F5H502;F5H1K9;F5H6X8;F5H221;F5H592 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 LLNGNHENGDLDPT(0.039)S(0.961)PLENMDYIK;LLNGNHENGDLDPT(0.176)S(0.824)PLENMDYIK;LLNGNHENGDLDPT(0.205)S(0.795)PLENMDYIK;LLNGNHENGDLDPT(0.059)S(0.941)PLENMDYIK;LLNGNHENGDLDPT(0.15)S(0.85)PLENMDYIK;LLNGNHENGDLDPT(0.206)S(0.794)PLENMDYIK;LLNGNHENGDLDPT(0.081)S(0.919)PLENMDYIK;LLNGNHENGDLDPT(0.208)S(0.792)PLENMDYIK 252.44 3.12E-43 2169715000 968351 936443 1079697 1269016 1130674 1144306 1298492 1351294 1505366 1577966 TRUE FALSE 930506.7724 909736.5625 1274822.266 1334510.068 1167043.156 1167444.651 1314383.334 1323389.307 1334483.163 1471088.957 0.632529235 0.618410299 0.866584077 0.907157967 0.793319228 0.793592152 0.893476446 0.899598423 0.907139678 1 20.48845306 5.673909544 0.451954437 0.910187982 3.45E-42 0.688057603 0.065477147 6.652272238 0.553638348 0.043366336 3.865666031 471964.7292 -5.673909544 -0.910187982 DLFSLDSEDPSPAS(ph)PPLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DLFSLDSEDPSPASPPLR 18 0 Q9BTK6;H3BTX0 Q9BTK6 PAGR1 PAXIP1-associated glutamate-rich protein 1 1 DLFSLDSEDPS(0.001)PAS(0.999)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPS(0.002)PAS(0.998)PPLR 278.15 3.82E-39 5184220000 1182865 1326190 1025107 1294352 1269761 1301429 1273520 1317220 1327674 1371509 TRUE FALSE 1136637.328 1288368.36 1210366.638 1361153.662 1310604.016 1327744.786 1289105.719 1290018.947 1176962.014 1278615.474 0.888959465 1.007627693 0.946622861 1.064552784 1.025018109 1.038423837 1.008204378 1.00891861 0.920497239 1 20.28615103 5.673927531 1.303378836 1.007869411 5.38E-11 0.409888478 0.040021677 12.98239191 2.939494553 0.010730715 30.86628785 471984.2761 -5.673927531 -1.007869411 WNDNCPSWNTIDPEER ddPTM_BT-474_Pertuzumab_2h_R1 1 WNDNCPSWNTIDPEER 16 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 121.04 0.00023471 76840000 73231 89308 72487 84924 88003 96516 90027 93723 96955 105840 FALSE TRUE 70369.05156 86761.02328 85587.01336 89306.93782 90833.69642 98467.61965 91128.77736 91787.5873 85949.07487 98671.36253 0.713165905 0.879292847 0.867394664 0.905094807 0.920567975 0.997935137 0.923558518 0.930235328 0.871064032 1 16.59034381 5.675089697 0.793952014 0.935744633 2.19E-13 0.741635854 0.038956362 4.791456294 0.766537027 0.012916948 5.605598086 473248.9918 -5.675089697 -0.935744633 EATDPRPCEVENAVESWR ddPTM_BT-474_Pertuzumab_2h_R1 1 EATDPRPCEVENAVESWR 18 1 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 56.215 0.092827 743030000 871320 1002000 743020 1018400 946370 998310 932350 1022000 974110 1012800 FALSE TRUE 837267.8511 973423.9411 877300.2424 1070959.746 976810.8505 1018496.512 943760.3782 1000895.343 863533.1166 944202.1539 0.88674639 1.030948655 0.929144504 1.134248362 1.034535715 1.078684801 0.999532117 1.060043486 0.914563807 1 19.84873625 5.675713943 1.188531601 1.030139293 1.83E-18 0.276554325 0.062876527 14.69052986 3.202141742 0.016633546 31.66318232 473929.7186 -5.675713943 -1.030139293 DLLLDPAWEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLLLDPAWEK 10 0 O43707;O43707-2;F5GXS2;O43707-3;K7EP19;D6RH00;P12814-3;P12814;P12814-2;P12814-4;P35609-2;P35609;A0A494C1A0;Q08043;A0A494C166;A0A494C033;A0A494C0Q3 O43707;P12814-3 ACTN4;ACTN3;ACTN1;ACTN2 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 112.75 0.0036748 24736000 71209 69598 83815 95568 75889 72883 99117 105480 114830 125960 FALSE TRUE 68426.07355 67613.13318 98962.23495 100500.2759 78330.03861 74356.7442 100330.0235 103301.8011 101794.9798 117428.617 0.582703563 0.575780716 0.842743766 0.855841434 0.667043865 0.633208038 0.854391596 0.879698695 0.866866888 1 16.84142451 5.676809907 0.103513023 1.157499342 5.53E-11 0.575500522 0.091185471 56.136897 0.708456884 1.448496409 9.400124222 475127.2146 -5.676809907 -1.157499342 KSLESINSR ddPTM_BT-474_Pertuzumab_2h_R1 4 KSLESINSR 9 1 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ;;; 145.91 0.00015398 2278330000 1289360 1448660 1154530 1403800 1407190 1323060 1595540 1442840 1419200 1457300 FALSE TRUE 1238970.386 1407345.635 1363179.253 1476250.286 1452453.544 1349813.18 1615066.696 1413044.85 1258098.366 1358595.773 0.911949242 1.035882536 1.00337369 1.086600088 1.069084398 0.993535536 1.188776476 1.040077467 0.926028471 1 20.37368484 5.678134271 1.208403337 1.050134828 1.39E-12 0.232874298 0.066451084 16.84973582 3.679909464 0.018257778 37.87419663 476578.3075 -5.678134271 -1.050134828 LAGLVEELEADEWR ddPTM_BT-474_Pertuzumab_2h_R1 4 LAGLVEELEADEWR 14 0 A0A087WUN5;Q96DE5 A0A087WUN5 ANAPC16 Anaphase-promoting complex subunit 16 0 ;;; 205.07 2.97E-08 131228000 70571 90545 65359.7 88626 88718 91683 85495 92222 96076 108898 FALSE TRUE 67813.0073 87962.74525 77171.65171 93199.99848 91571.69504 93536.89308 86541.31338 90317.58347 85169.85526 101522.2415 0.667962077 0.866438171 0.760145271 0.918025421 0.901986537 0.921343853 0.852436985 0.889633465 0.838928042 1 16.6314363 5.680941594 0.769359704 0.894196313 1.61E-15 0.584509268 0.056464632 6.828342777 1.050036392 0.018344666 7.357039508 479668.936 -5.680941594 -0.894196313 IS(ph)EDETER ddPTM_BT-474_Pertuzumab_2h_R1 2 ISEDETER 8 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 IS(1)EDETER;IS(1)EDETER 188.38 0.00020695 2947500000 1391600 1219960 1650170 1800900 1631090 1469700 1978920 2207500 2299740 2375200 TRUE FALSE 1337214.734 1185167.935 1948392.427 1893844.665 1683555.491 1499418.341 2003138.615 2161914.354 2038683.156 2214325.588 0.603892553 0.535227494 0.879903316 0.855269286 0.760301692 0.677144476 0.904626955 0.976330836 0.92067904 1 21.07843594 5.680963726 0.217995213 1.023155366 1.05E-17 0.614806207 0.094122371 13.31016648 0.400107012 0.175748087 3.930048392 479693.3811 -5.680963726 -1.023155366 DAEGILEDLQSYR ddPTM_BT-474_Pertuzumab_2h_R1 5 DAEGILEDLQSYR 13 0 E5RI16;Q9NUQ9;E5RGI7;E5RJE1;E5RIR8;E5RJL8;E5RK61;E5RFS4;E5RHU5 E5RI16 FAM49B Protein FAM49B 0 ;;;; 264.17 7.44E-24 303628700 394393 446415 349495 418844 440717 418915 482756 485685 490483 475389 FALSE TRUE 378979.6855 433683.6813 412656.521 440460.589 454893.0626 427385.7483 488664.1123 475655.435 434805.4261 443190.4796 0.855116937 0.978549182 0.931104209 0.993840367 1.026405312 0.964338739 1.102605166 1.073252827 0.981080249 1 18.75756736 5.682434787 0.455162217 1.043485735 0.531871512 0.551059912 0.044231328 7.943036174 0.662922855 0.028420552 2.620009841 481320.9741 -5.682434787 -0.511614223 LPS(ph)PTPENK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSPTPENK 9 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 LPS(0.923)PT(0.077)PENK 66.486 0.066707 537340000 177970 205980 188560 205270 202120 200010 223160 240550 254220 243960 TRUE FALSE 171014.7356 200105.6521 222636.9865 215864.0093 208621.3734 204054.3392 225891.0988 235582.5584 225362.0114 227436.3719 0.751923425 0.879831359 0.978897898 0.949118241 0.917273572 0.897193081 0.993205691 1.035817431 0.990879381 1 17.79510346 5.684594854 0.772998669 0.980086389 4.46E-31 0.747211533 0.039311949 5.526604836 0.849916973 0.015961761 6.573125577 483720.9018 -5.684594854 -0.980086389 AFWMAIGGDRDEIEGLS(ph)SDEEH ddPTM_BT-474_Pertuzumab_2h_R1 1 AFWMAIGGDRDEIEGLSSDEEH 22 1 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 1 AFWMAIGGDRDEIEGLS(0.97)S(0.03)DEEH 177.22 3.91E-17 30042000 27970 32224 25869 31323 31462 33487 35941 28803 32119 39951 TRUE FALSE 26876.90148 31305.00307 30544.10375 32939.58378 32474.0038 34164.13008 36380.85671 28208.20798 28472.98577 37245.08319 0.721622807 0.840513711 0.820084187 0.884400865 0.871900424 0.917278931 0.976796226 0.757367297 0.764476364 1 15.18476236 5.687196176 1.004343029 0.870060078 2.59E-12 0.276513894 0.075039834 15.93316076 3.07162616 0.02306822 23.43759924 486626.9709 -5.687196176 -0.870060078 DLEPESDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLEPESDR 8 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 127.56 0.002724 1030650000 483810 533370 424680 520300 482550 543880 501440 521810 592950 557510 FALSE TRUE 464902.1703 518158.8098 501429.123 547152.7454 498071.659 554877.6262 507576.7727 511034.4412 525640.8018 519749.3511 0.894473787 0.996939792 0.964751802 1.052724249 0.958292027 1.067586953 0.976579906 0.983232476 1.011335177 1 18.98745653 5.687407622 1.333176914 1.002433977 8.03E-08 0.475219671 0.033627273 12.07628061 2.657065258 0.008508481 29.60105013 486863.9537 -5.687407622 -1.002433897 RDS(ph)GSFEQYSENIK ddPTM_BT-474_Pertuzumab_2h_R1 3 RDSGSFEQYSENIK 14 1 Q8IZT6;Q8IZT6-2;Q5VYL4 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 RDS(0.706)GS(0.294)FEQYSENIK;RDS(0.77)GS(0.23)FEQYSENIK;RDS(0.975)GS(0.025)FEQYSENIK 256.33 1.60E-24 649638000 487794 508930 556310 517960 557570 609560 649720 700140 754710 857060 TRUE FALSE 468730.4712 494415.8147 656847.592 544691.9777 575504.7454 621885.7208 657671.4677 685681.8643 669038.4848 799010.5628 0.586638642 0.61878508 0.822076231 0.681708106 0.720271761 0.778319774 0.823107351 0.858163704 0.837333717 1 19.60785505 5.689799295 0.105732915 1.14511834 1.40E-17 0.821373962 0.049558089 27.02705049 0.347473477 0.672570838 4.547848095 489552.5254 -5.689799295 -1.14511834 KWSDS(ph)SK ddPTM_BT-474_Pertuzumab_2h_R1 1 KWSDSSK 7 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KWS(0.23)DS(0.759)S(0.011)K 72.096 0.032177 516390000 1114100 994280 1146800 1186600 1305900 1261200 1567700 1477400 1830800 1826700 TRUE FALSE 1070559.74 965924.1079 1354052.27 1247840.568 1347905.459 1286702.328 1586885.982 1446891.174 1622975.259 1702975.982 0.62864054 0.567197728 0.795109435 0.732741143 0.791499982 0.755561054 0.931831099 0.84962512 0.953022988 1 20.69962666 5.691520012 0.179902442 1.046165682 3.51E-13 0.8206187 0.055773388 9.229354958 0.215169282 0.135448612 2.286038749 491496.0276 -5.691520012 -1.046165682 EASFEYLQNEGER ddPTM_BT-474_Pertuzumab_2h_R1 1 EASFEYLQNEGER 13 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4;O00763-3;O00763-2;O00763;F8W8T8;H0YGH5 Q13085 ACACA;ACACB Acetyl-CoA carboxylase 1;Biotin carboxylase;Acetyl-CoA carboxylase 2;Biotin carboxylase 0 196.11 3.36E-07 504170000 140610 184510 153470 181350 179350 233390 192600 217840 229960 241930 FALSE TRUE 135114.8057 179247.9555 181205.4429 190709.4952 185118.9556 238109.3057 194957.0964 213341.5279 203855.9049 225543.8656 0.599062206 0.794736558 0.803415524 0.8455539 0.820766972 1.055711735 0.864386606 0.945898162 0.903841496 1 17.78304852 5.691575876 0.446884835 0.950117839 1.43E-16 0.737182594 0.061606187 5.693184886 0.46115806 0.038245482 3.421265225 491559.2539 -5.691575876 -0.950117839 TDCDIEDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDCDIEDDR 9 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 201.07 5.13E-05 567780000 584350 624190 703670 854570 735790 736040 892290 931150 1085130 1131050 FALSE TRUE 561512.956 606388.7123 830838.8221 898674.4601 759457.3536 750923.2331 903210.1119 911921.4271 961950.5916 1054442.976 0.532520932 0.575079664 0.787940971 0.852274121 0.720245069 0.712151582 0.856575588 0.86483712 0.91228318 1 20.00804965 5.693152512 0.196225402 1.002998436 1.52E-18 0.770138731 0.067059642 11.65344813 0.303186282 0.156482005 3.024331289 493347.0231 -5.693152512 -1.002998436 GS(ph)VHSLDAGLLLPSGDPFSK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSVHSLDAGLLLPSGDPFSK 20 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 GS(0.557)VHS(0.443)LDAGLLLPSGDPFSK;GS(0.562)VHS(0.438)LDAGLLLPSGDPFSK;GS(0.795)VHS(0.205)LDAGLLLPSGDPFSK;GS(0.5)VHS(0.5)LDAGLLLPSGDPFSK 164.27 1.18E-11 1423120000 2412240 2786040 2480940 3064030 2705710 3174750 3185780 3024170 3472860 3893060 TRUE FALSE 2317966.994 2706584.867 2929301.046 3222164.955 2792741.619 3238945.62 3224768.529 2961719.833 3078635.492 3629379.579 0.638667558 0.745743125 0.807107932 0.887800486 0.769481824 0.892424049 0.888517847 0.816040254 0.84825393 1 21.79129152 5.694557128 0.640164643 0.869097881 3.30E-14 0.645223562 0.055868911 6.24775559 0.776175868 0.021800356 5.247165105 494945.2132 -5.694557128 -0.869097881 TLDDSANRR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLDDSANRR 9 1 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 91.265 0.017429 178170000 112920 131360 100880 126180 122990 131310 122300 125040 153840 144150 FALSE TRUE 108506.9616 127613.7414 119111.2601 132692.1649 126946.085 133965.1782 123796.744 122457.8803 136376.7281 134386.5921 0.807424014 0.949601738 0.886332916 0.987391397 0.944633561 0.996864167 0.921198626 0.911235849 1.014809037 1 17.03602968 5.695548322 1.087663504 0.95578378 5.88E-14 0.554703268 0.040254048 9.117455338 1.821718887 0.011350554 16.38840476 496076.1203 -5.695548322 -0.95578378 SSS(ph)DALSASFNGEMLGNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSDALSASFNGEMLGNR 18 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 SS(0.021)S(0.979)DALSASFNGEMLGNR;S(0.002)S(0.257)S(0.742)DALSASFNGEMLGNR 473.57 6.01E-215 422940000 259420 292020 228670 290750 285810 248500 270430 337920 298530 281790 TRUE FALSE 249281.5796 283691.8755 269995.7557 305755.6423 295003.3382 253524.8403 273739.6032 330941.8339 264642.1259 262704.1123 0.948906271 1.079891263 1.027756107 1.163878402 1.122949069 0.965058514 1.042007302 1.25975125 1.007377173 1 18.00307926 5.697790174 1.177923232 1.092708297 5.26E-09 0.136888514 0.085201903 22.42356587 4.639240308 0.024927219 51.17242042 498643.513 -5.697790174 -1.092708291 ATS(ph)SPMLYEVVYEAGALER ddPTM_BT-474_Pertuzumab_2h_R1 2 ATSSPMLYEVVYEAGALER 19 0 Q5T4L2;Q5T4K9;Q5T4L1;Q8TEY5-2;Q8TEY5 Q5T4L2 CREB3L4 Cyclic AMP-responsive element-binding protein 3-like protein 4;Processed cyclic AMP-responsive element-binding protein 3-like protein 4 1 AT(0.068)S(0.466)S(0.466)PMLYEVVYEAGALER;AT(0.053)S(0.473)S(0.473)PMLYEVVYEAGALER 92.211 0.0020484 109988000 44870 63741 44976 67680 59323 63305 63653 83016 70721 73661 TRUE FALSE 43116.43079 61923.16909 53104.16369 71172.97291 61231.17817 64585.07047 64432.00445 81301.69059 62693.04857 68671.87486 0.627861565 0.901725331 0.773302954 1.036420996 0.891648558 0.940487945 0.938258997 1.183915406 0.912936318 1 16.06743173 5.697819359 0.431468981 1.031310508 1.39E-13 0.549448129 0.094547585 8.434698111 0.650467838 0.063937765 5.292483033 498677.0237 -5.697819359 -1.031310508 FVNDYDKDNDGR ddPTM_BT-474_Pertuzumab_2h_R1 8 FVNDYDKDNDGR 12 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;;;;;;; 182.55 1.53E-05 3833220000 4275190 4355550 4480470 5326380 4998620 4871870 6108070 6448420 7253520 7399370 FALSE TRUE 4108110.848 4231333.979 5290190.597 5601275.11 5159405.152 4970382.549 6182822.388 6315257.874 6430130.819 6898204.079 0.595533388 0.613396462 0.766893895 0.811990345 0.747934548 0.720532836 0.896294502 0.915493047 0.932145635 1 22.71778938 5.6988024 0.175374336 1.055859336 4.72E-10 0.847036724 0.050536912 10.18224916 0.229489458 0.152388631 2.481754913 499807.0755 -5.6988024 -1.055859335 SEEKT(ph)PIKKPGDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEKTPIKKPGDGR 14 3 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 S(0.002)EEKT(0.998)PIKKPGDGR;S(0.001)EEKT(0.999)PIKKPGDGR 85.937 0.0077535 1010840000 1688890 1048320 1114860 723860 815770 816470 940670 1743890 997450 910980 TRUE FALSE 1622886.312 1018422.94 1316340.002 761218.5013 842009.9829 832979.5828 952182.2008 1707878.062 884223.6577 849278.5132 1.910900001 1.199162494 1.549950907 0.896311975 0.991441523 0.980808498 1.121166009 2.01097524 1.04114686 1 19.69587822 5.699195071 1.564363936 1.241034066 10.26621286 0.28733937 0.326024598 31.69175473 6.682875684 0.095236279 867.5469401 500259.1844 -5.699195071 9.025178791 S(ph)IEDLQPPSALSAPFTNSLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIEDLQPPSALSAPFTNSLAR 21 0 F8W1F5;Q8IVF7-3;Q8IVF7 F8W1F5 FMNL3 Formin-like protein 3 1 S(1)IEDLQPPSALSAPFTNSLAR 87.49 0.002724 27206000 28637 33845 26008 33219 30685 33098 29759 36727 37555 36591 TRUE FALSE 27517.83438 32879.77374 30708.22414 34933.43657 31672.01089 33767.26424 30123.19954 35968.57462 33291.91384 34112.65898 0.806675152 0.963858424 0.90020025 1.024060792 0.928453303 0.989874881 0.88305047 1.054405482 0.975940159 1 15.05801959 5.70001447 1.004283783 0.976815533 7.59E-11 0.47974258 0.050613021 9.292243221 1.750775515 0.014365203 15.4269771 501203.9322 -5.70001447 -0.976815533 LQGQLQGGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 LQGQLQGGSR 10 0 Q9UP83-3;Q9UP83;Q9UP83-2;U3KQU7 Q9UP83-3 COG5 Conserved oligomeric Golgi complex subunit 5 1 LQGQLQGGS(1)R 130.36 0.00029231 424460000 254890 286850 234350 259460 283150 277810 271810 308180 310310 277430 TRUE FALSE 244928.617 278669.3189 276702.2581 272850.7617 292257.7769 283427.5085 275136.4921 301815.9753 275084.9097 258639.419 0.946988738 1.077443338 1.06983792 1.054946546 1.129981571 1.095840339 1.063784063 1.166937261 1.063584626 1 17.98058265 5.700250198 1.166017272 1.093666564 3.83E-09 0.431292154 0.043948195 10.54380376 2.160501914 0.011970766 23.79111508 501476.0522 -5.700250198 -1.09366656 LPNNSSRPS(ph)TPTINVLESK ddPTM_BT-474_Pertuzumab_2h_R1 1 LPNNSSRPSTPTINVLESK 19 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 LPNNS(0.035)S(0.025)RPS(0.47)T(0.47)PT(0.001)INVLESK 107.17 0.00018147 577170000 360410 425660 363360 434130 426730 550490 527730 501120 673470 660560 TRUE FALSE 346324.7787 413520.5936 429027.2349 456535.5013 440456.158 561621.285 534188.5176 490771.6969 597020.509 615819.6828 0.562380171 0.671496227 0.696676717 0.741346069 0.715235596 0.911989825 0.867443072 0.796940583 0.969472925 1 19.23214845 5.700320323 0.179078621 1.034331574 1.21E-13 0.855217798 0.050999973 9.460922382 0.218684538 0.136842105 2.307007836 501557.0308 -5.700320323 -1.034331574 DQDELKPGPTNR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDELKPGPTNR 12 1 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 79.639 0.020514 332350000 168030 219550 147470 230730 222720 263820 254290 257620 280070 316380 FALSE TRUE 161463.2018 213288.649 174121.1095 242638.003 229883.9911 269154.6212 257402.0771 252300.057 248277.6277 294951.3008 0.547423257 0.723131745 0.590338503 0.822637508 0.779396431 0.91253919 0.87269348 0.855395641 0.841758036 1 18.17011725 5.701696321 0.263124141 0.955821537 3.76E-16 0.787560089 0.061330996 6.800583301 0.264229845 0.075963596 2.296667544 503148.6607 -5.701696321 -0.955821537 KTSS(ph)DDES(ph)EEDEDDLLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSSDDESEEDEDDLLQR 18 1 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 KT(0.101)S(0.394)S(0.505)DDES(1)EEDEDDLLQR 130.69 6.48E-05 453320000 510620 414080 352110 325930 384310 348750 351610 411210 414310 393040 TRUE FALSE 490664.4059 402270.8438 415744.1096 342751.2864 396671.6802 355801.9639 355913.1084 402718.3698 367279.2657 366419.0507 1.339079955 1.097843693 1.134613795 0.935407932 1.082562927 0.971024741 0.971328067 1.099065043 1.002347626 1 18.48313499 5.702819692 0.935152045 1.018512336 2.785819056 0.748602877 0.056065694 5.076085432 0.903130762 0.01672506 13.93041526 504451.8188 -5.702819692 1.767306719 SATDGNTSTT(ph)PPTSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 SATDGNTSTTPPTSAK 16 0 A0A669KAX4;Q13620-1;K4DI93;Q13620;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 SATDGNT(0.343)S(0.08)T(0.04)T(0.533)PPT(0.003)S(0.001)AK;SATDGNTS(0.004)T(0.048)T(0.946)PPT(0.001)SAK 196.15 5.21E-10 763390000 1328270 1413080 1148350 1267130 1370650 1365480 1474030 1529240 1588700 1686650 TRUE FALSE 1276359.74 1372780.342 1355882.39 1332526.731 1414738.202 1393090.941 1492069.62 1497660.66 1408357.436 1572411.693 0.811721094 0.873041296 0.862294777 0.847441377 0.899725058 0.885958141 0.948905192 0.952460902 0.89566711 1 20.58454757 5.703477439 0.11740158 1.051627973 0.558878708 0.785654744 0.02450355 23.94519669 0.342392164 0.23141373 1.883908801 505216.3984 -5.703477439 -0.492749264 DLFDLILTCEER ddPTM_BT-474_Pertuzumab_2h_R1 4 DLFDLILTCEER 12 0 Q9NP77 Q9NP77 SSU72 RNA polymerase II subunit A C-terminal domain phosphatase SSU72 0 ;;; 175.15 6.62E-05 87047000 153712 164915 131426 157186 161851 161102 162135 163962 170453 174777 FALSE TRUE 147704.7651 160211.7857 155177.6018 165298.3883 167057.0844 164359.5928 164119.2566 160576.1274 151103.89 162939.1981 0.906502345 0.983261164 0.952365076 1.01447896 1.025272533 1.00871733 1.007242324 0.985497224 0.927363653 1 17.31397419 5.709579858 1.058402001 0.994417615 0.416941249 0.445469232 0.028032396 10.99632146 2.10463988 0.008407824 11.59628109 512365.4754 -5.709579858 -0.577476366 KQQMAEEMVEAAGEDER ddPTM_BT-474_Pertuzumab_2h_R1 3 KQQMAEEMVEAAGEDER 17 1 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;; 226.57 3.26E-15 1342230000 1602170 1659140 1750690 2086470 1883240 1953670 2157880 2256940 2433480 2589690 FALSE TRUE 1539555.425 1611822.952 2067078.627 2194152.967 1943816.125 1993174.546 2184288.781 2210333.4 2157241.552 2414287.99 0.637685078 0.667618345 0.856185607 0.908819899 0.805130181 0.825574478 0.904734145 0.915521847 0.893531162 1 21.20316635 5.7132946 0.465598334 0.916524314 1.32E-33 0.758502681 0.052792421 5.659873281 0.475012659 0.033351481 3.454539621 516766.7953 -5.7132946 -0.916524314 TEDPDLPAFYFDPLINPISHR ddPTM_BT-474_Pertuzumab_2h_R1 4 TEDPDLPAFYFDPLINPISHR 21 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 315.44 1.12E-66 1236550000 650720 730010 572952 715300 731440 721180 723070 742470 837290 799060 FALSE TRUE 625289.143 709190.8296 676497.1716 752216.7187 754967.4319 735762.7537 731919.147 727137.735 742244.3494 744938.9545 0.839383065 0.952012008 0.908124307 1.009769612 1.013462147 0.987681943 0.982522316 0.976103788 0.996382784 1 19.50676268 5.715837437 0.754668933 0.991913732 0.333238534 0.787646118 0.023796668 4.548204014 0.656019361 0.008453543 3.566935372 519801.391 -5.715837437 -0.658675198 RLS(ph)LPGLLSQVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSLPGLLSQVSPR 14 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 2 RLS(1)LPGLLS(0.195)QVS(0.805)PR;RLS(1)LPGLLS(0.041)QVS(0.959)PR;RLS(1)LPGLLS(0.044)QVS(0.956)PR;RLS(1)LPGLLS(0.003)QVS(0.997)PR 125.62 0.0003155 463040000 313363 346147 266818 342462 340081 331386 338063 332107 357397 354992 TRUE FALSE 301116.4275 336275.2265 315037.9479 360136.5049 351020.0142 338086.852 342200.3161 325248.8744 316826.7909 330948.0756 0.909860034 1.016096636 0.951925607 1.088196401 1.060649812 1.021570684 1.034000018 0.982779168 0.957330815 1 18.33624536 5.718642076 1.299019462 1.016399457 2.31E-11 0.359701934 0.040676517 17.46460013 3.538090169 0.011601728 42.53679999 523169.0891 -5.718642076 -1.016399457 DEEWFR ddPTM_BT-474_Pertuzumab_2h_R1 3 DEEWFR 6 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;; 166.13 0.016431 625940000 823490 847740 828340 1114190 901650 936350 1031630 1149300 1149840 1243950 FALSE TRUE 791307.1004 823563.2852 978039.4643 1171693.479 930652.3911 955283.6385 1044255.397 1125566.553 1019314.984 1159696.159 0.68234002 0.710154362 0.843358372 1.010345228 0.802496744 0.823736141 0.900456028 0.970570218 0.878950039 1 20.14531544 5.722295832 0.546056618 0.922973982 1.42E-08 0.575030676 0.069996365 7.911470199 0.798002692 0.035985552 5.87470309 527589.1212 -5.722295832 -0.922973967 ALFEEVPELLTEAEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALFEEVPELLTEAEK 15 0 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;; 219.42 4.20E-12 20651800 110575 100843 113838 119449 119673 114044 138232 151506 157584 178577 FALSE TRUE 106253.6068 97967.05638 134411.0589 125613.7772 123522.3907 116350.0478 139923.7246 148377.3482 139695.725 166481.8207 0.638229485 0.588454979 0.807361779 0.754519482 0.741957231 0.698875393 0.840474497 0.891252555 0.839104981 1 17.34500512 5.723067271 0.100343418 1.167103434 9.95E-16 0.767251396 0.055876172 35.7924135 0.431906596 0.9357963 5.890806565 528527.1127 -5.723067271 -1.167103434 NLDSLEEDLDFLR ddPTM_BT-474_Pertuzumab_2h_R1 6 NLDSLEEDLDFLR 13 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;;;; 211.46 5.05E-08 1140519000 313093 319632 330118 397803 370014 352183 404964 445505 436149 477284 FALSE TRUE 300856.9794 310516.4083 389777.666 418333.6605 381915.8363 359304.3816 409920.0706 436305.1661 386639.194 444957.1296 0.676148239 0.697856912 0.875989259 0.940166215 0.858320523 0.80750337 0.92125745 0.980555512 0.868935833 1 18.76330682 5.727441254 0.512041068 0.931157287 5.59E-17 0.672365838 0.059326946 6.651034967 0.61934107 0.03353503 4.622886025 533877.0529 -5.727441254 -0.931157287 EIDNEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EIDNEKR 7 1 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8 A0A590UJQ1 ITCH E3 ubiquitin-protein ligase Itchy homolog 0 ; 101.99 0.013952 757950000 606100 724470 564580 721760 716440 725250 745680 737980 794890 845020 FALSE TRUE 582412.9419 703808.8249 666612.165 759010.1201 739484.9433 739915.0519 754805.8549 722740.4551 704657.4197 787786.0427 0.739303453 0.893400983 0.84618428 0.963472414 0.938687541 0.939233512 0.958135603 0.917432419 0.894478172 1 19.58744433 5.733468945 0.804363426 0.939446123 1.18E-11 0.738940218 0.035665671 5.154691187 0.771322334 0.011399943 6.283471348 541338.5376 -5.733468945 -0.939446123 TDTESELDLISR ddPTM_BT-474_Pertuzumab_2h_R1 3 TDTESELDLISR 12 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;; 249.23 1.63E-16 300467000 466609 561468 455100 541348 555057 611801 577242 583653 596758 695643 FALSE TRUE 448373.4044 545455.4824 537346.6936 569287.0352 572910.9125 624172.0354 584306.4603 571600.3616 529016.5337 648526.48 0.691372547 0.841068945 0.828565541 0.877816177 0.88340404 0.962446492 0.900975486 0.881383227 0.815720792 1 19.30680596 5.734518978 0.742514477 0.901256103 4.43E-17 0.629909055 0.048726693 6.794933727 0.942156269 0.016928715 7.190559281 542648.9638 -5.734518978 -0.901256103 VLQASVLDDWFPLQGGQGQVHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLQASVLDDWFPLQGGQGQVHLR 23 0 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ; 200.29 2.46E-24 339290000 100454 127980 90843 166808 100104 125034 154635 166629 152497 144248 FALSE TRUE 96528.14662 124330.1357 107260.3509 175416.9809 103323.9361 127562.2731 156527.4694 163188.0529 135186.1799 134477.9545 0.71779904 0.924539165 0.797605461 1.304429277 0.768333639 0.948573866 1.163963789 1.213492974 1.00526648 1 17.03701016 5.73621757 0.441981552 1.097340047 1.57E-12 0.296557105 0.155862055 14.047211 1.086984926 0.103052966 9.71165702 544775.5027 -5.73621757 -1.097340047 SYDQVHSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SYDQVHSGK 9 0 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;; 125.75 0.00049291 1236510000 2488710 3123170 2492610 3365420 2846400 3020560 3519970 3413580 3785010 3732260 FALSE TRUE 2391448.462 3034100.25 2943080.075 3539109.73 2937957.041 3081637.793 3563048.446 3343088.38 3355351.533 3479470.706 0.68730237 0.872000516 0.845841314 1.017140257 0.844368954 0.885662807 1.024020245 0.960803715 0.964328145 1 21.73043643 5.737692283 0.61446686 0.962916396 1.08E-12 0.662198812 0.057585312 6.537838371 0.742519491 0.024566754 5.861049864 546628.5145 -5.737692283 -0.962916396 DYEEIGPSICR ddPTM_BT-474_Pertuzumab_2h_R1 2 DYEEIGPSICR 11 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 226.09 1.16E-11 841470000 475450 543290 458240 490910 512850 542490 583610 526970 636330 584260 FALSE TRUE 456868.8884 527795.9011 541054.1615 516245.9239 529346.286 553459.5195 590752.3938 516087.8853 564096.4861 544687.5498 0.838772409 0.96898837 0.993329408 0.947783595 0.971834745 1.01610459 1.084571134 0.947493449 1.035633156 1 19.05506937 5.738331534 0.984773296 1.001906499 3.80E-18 0.609640271 0.03858391 8.191059618 1.423091026 0.011770565 13.81291864 547433.7067 -5.738331534 -1.001906499 GSDALSETSSVSHIEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;; 332.52 2.56E-75 1207210000 1364870 1594170 1424830 1635380 1730840 1865350 1868300 1795400 2043460 2177440 FALSE TRUE 1311529.371 1548705.832 1682328.476 1719782.158 1786514.041 1903068.655 1891164.814 1758324.363 1811494.988 2029960.049 0.646086297 0.762924292 0.828749549 0.847200002 0.880073498 0.937490694 0.931626617 0.866186683 0.892379625 1 20.9530199 5.739185143 0.521522447 0.920001468 5.18E-20 0.869119909 0.034041858 3.831189029 0.360973407 0.018123063 2.696125082 548510.7499 -5.739185143 -0.920001468 AATAARPPAPPPAPQPPS(ph)PTPSPPRPTLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.957)PT(0.035)PS(0.008)PPRPTLAR;AATAARPPAPPPAPQPPS(0.494)PT(0.494)PS(0.012)PPRPTLAR;AATAARPPAPPPAPQPPS(0.967)PT(0.032)PS(0.001)PPRPTLAR;AATAARPPAPPPAPQPPS(0.983)PT(0.017)PSPPRPTLAR 261.78 1.22E-58 2686290000 348774 392356 301151 361229 416813 350647 376043 445768 452965 412514 TRUE FALSE 335143.5265 381166.391 355575.6848 379872.072 430220.1687 357737.3226 380645.1267 436562.735 401546.3122 384574.0594 0.871466804 0.99113911 0.924596124 0.987773519 1.118692637 0.930216987 0.989783677 1.135185082 1.044132599 1 18.55290193 5.74462106 0.405041523 1.054680786 0.566872579 0.359372964 0.062877532 13.13369675 0.905320726 0.047818362 3.65876109 555419.4193 -5.74462106 -0.487808206 DTTVISHS(ph)PNTSYDTALEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTTVISHSPNTSYDTALEAR 20 0 Q4VCS5;E7ERM3;Q4VCS5-2;A6NP16 Q4VCS5 AMOT Angiomotin 1 DTTVISHS(1)PNTSYDTALEAR;DTTVISHS(1)PNTSYDTALEAR 219.64 5.85E-25 880060000 324810 365170 317660 359320 343660 382220 356630 429460 383020 409930 TRUE FALSE 312116.0661 354755.7091 375068.2283 377864.5483 354714.136 389948.7503 360994.5446 420591.5009 339541.1754 382165.076 0.816704837 0.928278724 0.98142989 0.988746937 0.928169941 1.020367309 0.9446037 1.100549285 0.888467306 1 18.54383642 5.744747698 0.88796796 0.993413015 2.59E-10 0.450780645 0.054554785 9.297248867 1.486140584 0.016790066 13.64306845 555581.4004 -5.744747698 -0.993413014 WVEENVPSSVTDVALPALLDS(ph)DEER ddPTM_BT-474_Pertuzumab_2h_R1 3 WVEENVPSSVTDVALPALLDSDEER 25 0 Q8NBN3-3;Q8NBN3 Q8NBN3-3 TMEM87A Transmembrane protein 87A 1 WVEENVPSSVTDVALPALLDS(1)DEER;WVEENVPSSVTDVALPALLDS(1)DEER;WVEENVPSSVTDVALPALLDS(1)DEER 162.27 1.26E-11 112885000 73341 100298 66554.6 119378 80285 97167 113489 116954 110727 116022 TRUE FALSE 70474.75264 97437.59924 78582.49672 125539.1129 82867.43994 99131.78331 114877.9123 114538.859 98157.73517 108163.7266 0.651556255 0.90083434 0.726514324 1.160639679 0.766129668 0.916497484 1.062074283 1.058939652 0.907492172 1 16.72285724 5.748106303 0.475018758 1.003225566 1.90E-15 0.384958417 0.120800439 11.79044541 0.987548523 0.06950604 8.122049946 559894.6308 -5.748106303 -1.003225566 VAGGLLGS(ph)GTR ddPTM_BT-474_Pertuzumab_2h_R1 4 VAGGLLGSGTR 11 0 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 1 VAGGLLGS(0.991)GT(0.009)R;VAGGLLGS(0.997)GT(0.003)R;VAGGLLGS(0.987)GT(0.013)R;VAGGLLGS(0.995)GT(0.005)R 113.42 0.00076059 146749000 524457 568743 544161 769110 636834 645031 773810 837970 832270 930230 TRUE FALSE 503960.6406 552523.0065 642502.9975 808803.8593 657318.344 658073.9688 783280.1183 820665.6267 737794.1988 867224.6935 0.581118878 0.637116321 0.740872582 0.93263472 0.757956212 0.758827526 0.9032032 0.946312568 0.850753218 1 19.72604631 5.748234712 0.286744701 0.958503315 1.14E-17 0.727231302 0.068583252 8.118413275 0.349374198 0.082535554 3.031922001 560060.2008 -5.748234712 -0.958503315 QITTS(ph)PITVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.004)T(0.463)S(0.533)PITVR;QIT(0.068)T(0.219)S(0.711)PIT(0.001)VR 161.87 7.28E-06 718600000 2099800 2420500 1747150 2453800 2288400 2261900 2507700 2394300 2311200 2259700 TRUE FALSE 2017737.495 2351469.71 2062898.87 2580440.912 2362008.464 2307637.168 2538389.983 2344856.868 2048842.265 2106648.506 0.957795042 1.116213598 0.979232589 1.224903397 1.121216215 1.095406833 1.204942341 1.113074564 0.972560092 1 21.00651819 5.749116322 1.103342898 1.108256297 3.78E-16 0.162271179 0.08386592 21.17071079 3.825441964 0.023160201 45.98029809 561198.2678 -5.749116322 -1.108256297 AEPDESNAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AEPDESNAR 9 0 P61088;F8VSD4;F8VV71;Q5JXB2;F8VZ29 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ; 163.32 0.00014682 145878000 296040 326980 257480 324010 302900 335710 316950 330090 338330 334960 FALSE TRUE 284470.4295 317654.8505 304012.3636 340732.1949 312643.0536 342498.2862 320828.9289 323273.5261 299924.1968 312272.8608 0.910967507 1.017234894 0.973547182 1.091136111 1.001185478 1.096791714 1.027399333 1.035227734 0.960455532 1 18.25244767 5.749776612 1.10833299 1.030838488 0.103446086 0.384681858 0.042137808 12.65731971 2.288190014 0.01138966 23.14622241 562052.1478 -5.749776612 -0.927392403 RAS(ph)LSDLTDLEDIEGLTVR ddPTM_BT-474_Pertuzumab_2h_R1 7 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 RAS(0.5)LS(0.5)DLTDLEDIEGLTVR;RAS(0.995)LS(0.005)DLTDLEDIEGLTVR;RAS(0.989)LS(0.011)DLTDLEDIEGLTVR;RAS(0.997)LS(0.003)DLTDLEDIEGLTVR;RAS(0.989)LS(0.011)DLTDLEDIEGLTVR;RAS(0.938)LS(0.062)DLTDLEDIEGLTVR;RAS(0.94)LS(0.06)DLTDLEDIEGLTVR 320.78 3.58E-62 1662296000 254185 336903 232413 360806 294488 338809 367787 400094 354909 337756 TRUE FALSE 244251.1692 327294.8563 274415.1991 379427.2409 303960.474 345659.9501 372288.0873 391831.9191 314621.2182 314879.4853 0.775697308 1.039428961 0.871492784 1.204991937 0.965323205 1.09775316 1.182319283 1.24438694 0.999179791 1 18.26444024 5.758741086 0.535693138 1.12967511 3.63E-12 0.401393298 0.109319456 10.10458461 0.96554992 0.054048472 9.0572376 573774.2917 -5.758741086 -1.12967511 IKDAFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKDAFDR 7 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 83.005 0.020932 263710000 381540 345058 391110 418960 497380 419700 496350 574580 570130 625600 FALSE TRUE 366628.995 335217.2837 461792.2772 440582.5758 513378.6794 428186.6216 502424.4798 562714.7222 505411.2326 583227.5548 0.628620839 0.574762425 0.791787482 0.7554214 0.880237354 0.734167338 0.86145532 0.964828766 0.866576396 1 19.15369936 5.760574343 0.21646017 1.009410347 2.46E-11 0.763214604 0.063066164 8.802758009 0.25458365 0.108188794 2.559008494 576201.4446 -5.760574343 -1.009410346 GDVEEDEAVPDSEQDIKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GDVEEDEAVPDSEQDIKPR 19 1 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ;;; 264.23 2.33E-31 2634010000 1470080 1467100 1299250 1351100 1566550 1562650 1600910 1620630 1962540 1946870 FALSE TRUE 1412627.648 1425259.744 1534053.377 1420830.433 1616939.503 1594247.854 1620502.415 1587163.424 1739760.687 1815006.761 0.778304345 0.785264152 0.845205324 0.782823769 0.890872441 0.878370201 0.892835471 0.874466949 0.958542262 1 20.79154349 5.762353475 0.094024388 1.118464384 0.370606267 0.845970581 0.027632454 30.64673062 0.342266026 0.533538007 3.075148513 578566.7545 -5.762353475 -0.747858117 LEEIEADKAPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LEEIEADKAPAR 12 1 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 80.17 0.019209 118450000 151790 142060 126180 155860 142620 156440 164860 166460 195310 203370 FALSE TRUE 145857.879 138008.5879 148983.5329 163903.9533 147207.5018 159603.324 166877.606 163022.5428 173139.2276 189595.5688 0.769310591 0.727910408 0.785796492 0.864492532 0.776429021 0.841809358 0.880176721 0.859843634 0.913202923 1 17.53256572 5.763756426 0.04677837 1.433733009 1.88E-06 0.848629616 0.02964912 123.8835429 0.684231367 6.577205208 16.1592319 580438.787 -5.763756426 -1.433731134 IEVLYEDEGFR ddPTM_BT-474_Pertuzumab_2h_R1 4 IEVLYEDEGFR 11 0 A0A087WW66;Q99460-2;Q99460;C9J9M4 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 163.94 5.43E-05 124391000 152467 153415 183481 229226 193098 175098 230087 248932 245349 289307 FALSE TRUE 146508.4211 149039.7544 216640.0982 241056.3813 199309.1725 178638.6015 232902.8735 243791.4672 217498.0101 269711.9792 0.54320324 0.552588561 0.803227572 0.89375482 0.738970413 0.662330988 0.863524395 0.903895585 0.806408417 1 18.04106007 5.765654491 0.268675815 0.927203633 7.22E-52 0.602410158 0.090964741 12.06068591 0.469684905 0.121623721 4.06649138 582981.1217 -5.765654491 -0.927203633 GDASKEDIDTAMK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDASKEDIDTAMK 13 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0D9SFP2;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 68.83 0.045018 474520000 354260 408620 235320 352070 258220 278470 302690 286260 328900 212340 FALSE TRUE 340415.1275 396966.5577 277847.5587 370240.3749 266525.8808 284100.8542 306394.4108 280348.631 291564.6509 197958.0227 1.719632895 2.005306743 1.403568064 1.870297399 1.346375748 1.435157062 1.547774658 1.416202421 1.472860998 1 17.59483501 5.766923503 0.052874858 9.13E-11 3.784143536 0.593404162 0.172651225 183.1412634 1.142698292 24.10130996 66.45836776 584687.0883 -5.766923503 3.784143536 SDS(ph)DAEAQGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSDAEAQGK 10 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.002)DS(0.998)DAEAQGK 85.522 0.014877 70353000 125310 104870 87579 122540 127810 110960 127140 135630 132760 150340 TRUE FALSE 120412.7467 101879.2103 103406.4735 128864.3041 131921.1247 113203.6872 128695.9774 132829.1931 117689.6414 140157.3379 0.859125526 0.726891733 0.73778851 0.919426025 0.941235947 0.80769005 0.918225041 0.947714869 0.839696609 1 17.09668775 5.768883836 0.142354603 1.026272853 0.454257449 0.389720407 0.067951809 37.490492 0.648444984 0.340568798 4.05263884 587332.2334 -5.768883836 -0.572015405 EEEGTGVVHQAPYFGAEDYR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEGTGVVHQAPYFGAEDYR 20 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 134.06 9.65E-06 651930000 188170 229230 189350 232570 224940 218990 282900 242070 259180 275710 FALSE TRUE 180816.1084 222692.5848 223569.7571 244572.9656 232175.3994 223418.1278 286362.2148 237071.1699 229758.973 257035.9161 0.703466314 0.866387033 0.869799678 0.951512805 0.903279989 0.869209763 1.114094167 0.922327017 0.893878865 1 17.97161044 5.769745795 0.622052232 0.960167061 1.90E-17 0.567032297 0.065724323 8.10697136 0.902864344 0.027612202 7.423195095 588499.0898 -5.769745795 -0.960167061 ADS(ph)PHVSGSEADVASLAPVDSSFSLLSVSHALYDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADSPHVSGSEADVASLAPVDSSFSLLSVSHALYDSR 36 0 A0A499FJD3;A0A3B3ISA1;Q96S15 A0A499FJD3 WDR24 WD repeat-containing protein 24 1 ADS(1)PHVSGSEADVASLAPVDSSFSLLSVSHALYDSR 175.37 2.62E-18 38701000 6356.7 8692.6 6023.8 8032.9 8369.2 8623.6 9799 8969.4 8880.4 9191.1 TRUE FALSE 6108.273136 8444.695559 7112.434659 8447.478932 8638.402919 8797.9751 9918.923093 8784.178756 7872.334222 8568.57861 0.712868892 0.98554217 0.830060035 0.985867005 1.008148879 1.026771825 1.157592588 1.025161716 0.918744471 1 13.06484019 5.772816914 0.559506079 1.036199992 2.13E-15 0.558934769 0.076414993 8.282984381 0.820591978 0.036640538 7.200735343 592675.4173 -5.772816914 -1.036199992 GRLPNNS(ph)SRPSTPTINVLESK ddPTM_BT-474_Pertuzumab_2h_R1 1 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 GRLPNNS(0.271)S(0.271)RPS(0.271)T(0.188)PTINVLESK 123.2 1.40E-05 301680000 149600 194190 164260 176050 194100 242220 204090 197580 249890 257990 TRUE FALSE 143753.4666 188651.8913 193945.4359 185135.9616 200343.4028 247117.8544 206587.7145 193499.904 221523.5348 240516.1075 0.597687482 0.784362816 0.806371922 0.769744544 0.832972913 1.027448253 0.858935049 0.804519522 0.921034093 1 17.87577399 5.775216428 0.488727553 0.900208876 1.97E-13 0.625480939 0.0715903 8.919936888 0.756498316 0.042982312 5.73480071 595959.0617 -5.775216428 -0.900208876 LIALSIDSVEDHLAWSK ddPTM_BT-474_Pertuzumab_2h_R1 3 LIALSIDSVEDHLAWSK 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;; 292.8 4.91E-46 8860751100 8747628 9891396 7861113 9086168 9837957 10535351 8923643 9391567 10939324 11512466 FALSE TRUE 8405761.027 9609303.071 9281790.989 9555106.219 10154403.82 10748383.02 9032853.212 9197627.86 9697537.801 10732716.42 0.783190452 0.895328144 0.864812842 0.890278457 0.946116847 1.001459704 0.841618548 0.856971106 0.903549243 1 23.35551193 5.779426884 1.040773244 0.908170986 2.12E-18 0.353204324 0.052531116 17.21485201 2.857271697 0.016229827 28.73735914 601764.9439 -5.779426884 -0.908170986 DVYIVQDLMETDLYK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVYIVQDLMETDLYK 15 0 P28482;P28482-2;P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49;H0YDH9 P28482;P27361 MAPK1;MAPK3 Mitogen-activated protein kinase 1;Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 123.84 0.00023333 11774000 20983 21155 16317 21193 22686 22666 23913 25820 25845 29763 FALSE TRUE 20162.96116 20551.68011 19265.84487 22286.77327 23415.71579 23124.32205 24205.65445 25286.80798 22911.18395 27747.1255 0.726668467 0.740677809 0.694336603 0.803210166 0.843896994 0.83339523 0.872366201 0.911330724 0.825713783 1 14.7600507 5.780909153 0.120419274 1.077024136 0.241122905 0.827561902 0.0359806 20.00667436 0.287578408 0.307474523 2.723099095 603822.3073 -5.780909153 -0.835901231 VTSSVPLPSGSTSS(ph)PGR ddPTM_BT-474_Pertuzumab_2h_R1 6 VTSSVPLPSGSTSSPGR 17 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 VTSSVPLPSGSTSS(1)PGR;VTSSVPLPSGSTS(0.009)S(0.991)PGR;VTSSVPLPSGSTS(0.006)S(0.994)PGR;VTSSVPLPSGSTS(0.001)S(0.999)PGR;VTSSVPLPSGSTS(0.008)S(0.992)PGR;VTSSVPLPSGSTS(0.002)S(0.998)PGR 303.44 1.48E-46 7014520000 3512220 3886650 3552470 4026220 3733190 4188110 4507520 4244900 4438490 4950200 TRUE FALSE 3374958.559 3775806.547 4194480.353 4234013.697 3853271.447 4272796.454 4562684.378 4157241.332 3934651.223 4614918.545 0.731314871 0.818174039 0.908895859 0.917462281 0.834959796 0.925866061 0.988681454 0.900826589 0.852593862 1 22.13787375 5.781731012 0.732137334 0.921120985 2.02E-10 0.602137262 0.048481224 7.616644731 0.982415326 0.017506218 8.220353413 604966.0629 -5.781731012 -0.921120985 LREVVETPLLHPER ddPTM_BT-474_Pertuzumab_2h_R1 4 LREVVETPLLHPER 14 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;;; 115.8 0.00023938 466902000 295402 331707 208837 232113 269610 245609 250957 232900 253274 246211 FALSE TRUE 283857.3633 322247.0411 246578.4915 244092.3797 278282.2505 250575.3823 254028.2868 228090.5336 224523.3973 229534.9097 1.236663145 1.403912989 1.074252678 1.063421595 1.212374409 1.091665676 1.106708723 0.99370738 0.978166666 1 17.80835406 5.782217711 0.254527079 0.969051579 1.840276854 0.569317231 0.082839361 11.51991512 0.412863348 0.110911968 3.446742853 605644.4074 -5.782217711 0.871225275 VEGIYTY(ph)S(ph)LS(ph)PS(ph)KVS(ph)GDDVIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VEGIYTYSLSPSKVSGDDVIEK 22 1 O95197-7;O95197-2;O95197 O95197-7 RTN3 Reticulon-3 5 VEGIY(0.07)T(0.073)Y(0.901)S(0.974)LS(0.994)PS(0.994)KVS(0.993)GDDVIEK 44.596 0.056371 306240000 119910 118660 140880 148300 155150 132800 169110 184270 222450 200690 TRUE FALSE 115223.7846 115275.933 166340.1499 155953.7808 160140.5407 135485.307 171179.6188 180464.7601 197198.4086 187097.0875 0.615850231 0.616128955 0.889057933 0.833544674 0.855922146 0.724144394 0.914924016 0.964551413 1.053989729 1 17.51342758 5.782747485 0.232324341 1.039544671 1.90E-17 0.702310168 0.078791027 10.63808209 0.335868487 0.128000413 3.440994758 606383.6536 -5.782747485 -1.039544671 S(ph)SPSHSTTSGETDPTTIFPCK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPSHSTTSGETDPTTIFPCK 21 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 S(0.492)S(0.492)PS(0.003)HS(0.003)T(0.003)T(0.003)S(0.003)GET(0.001)DPTTIFPCK;S(0.496)S(0.496)PS(0.001)HS(0.002)T(0.002)T(0.002)S(0.001)GETDPTTIFPCK;S(0.485)S(0.485)PS(0.003)HS(0.006)T(0.006)T(0.007)S(0.007)GETDPTTIFPCK 140.87 1.04E-07 914320000 1082250 1217030 923510 1182300 1165080 1266770 1137770 1161160 1207370 1360520 TRUE FALSE 1039954.474 1182321.496 1090408.8 1243318.645 1202555.856 1292384.957 1151694.37 1137181.64 1070314.419 1268370.769 0.819913624 0.932157635 0.859692471 0.98024858 0.948110668 1.018933099 0.908010811 0.896568786 0.8438498 1 20.2745451 5.783234598 1.119802819 0.93254222 2.21E-11 0.276836103 0.054382425 21.08117274 3.567509469 0.01585655 39.82496833 607064.1663 -5.783234598 -0.93254222 ESVASMGADS(ph)GDDFASDGSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ESVASMGADSGDDFASDGSSSR 22 0 Q92805;Q5T165 Q92805 GOLGA1 Golgin subfamily A member 1 1 ESVASMGADS(1)GDDFASDGSSSR 367.67 6.17E-113 392470000 141620 165160 166890 203680 178600 198170 249130 204350 253620 284450 TRUE FALSE 136085.3338 160449.7985 197050.7354 214191.9492 184344.8312 202177.1332 252178.9275 200130.1011 224830.1209 265183.9481 0.513173345 0.605050945 0.743071882 0.807710839 0.695158333 0.76240336 0.950958492 0.754684069 0.847827036 1 18.01663392 5.785507642 0.219101026 0.950374433 2.05E-30 0.735089077 0.071480014 11.07425731 0.322580497 0.124991679 3.075871464 610249.7945 -5.785507642 -0.950374433 ENAS(ph)PAPGTTAEEAMSR ddPTM_BT-474_Pertuzumab_2h_R1 12 ENASPAPGTTAEEAMSR 17 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 ENAS(1)PAPGTTAEEAMSR;ENAS(0.989)PAPGT(0.005)T(0.005)AEEAMSR;ENAS(0.91)PAPGT(0.045)T(0.045)AEEAMSR;ENAS(0.995)PAPGT(0.002)T(0.003)AEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(0.999)PAPGTT(0.001)AEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(0.997)PAPGT(0.003)TAEEAMSR;ENAS(1)PAPGTTAEEAMSR 332.61 4.89E-72 9769526000 3631094 3757826 3733372 4814003 4239687 4167106 4909366 5044795 5127805 5849597 TRUE FALSE 3489186.832 3650656.482 4408075.369 5062454.272 4376060.383 4251367.738 4969448.29 4940618.22 4545718.074 5453398.585 0.63981878 0.669427775 0.808317107 0.928311803 0.802446459 0.779581333 0.91125712 0.905970496 0.83355691 1 22.37872417 5.788552505 0.452792928 0.900401381 1.16E-27 0.658954641 0.06306842 7.626806958 0.585212345 0.040639071 4.496017236 614543.3233 -5.788552505 -0.900401381 FWQIYIEGQDEPR ddPTM_BT-474_Pertuzumab_2h_R1 3 FWQIYIEGQDEPR 13 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;; 203.51 1.98E-07 118755000 147347 168187 142152 158158 171870 167732 175585 184948 182344 177614 FALSE TRUE 141588.5163 163390.4714 167842.0286 166320.5533 177398.3546 171123.656 177733.8618 181128.7592 161645.0736 165584.0456 0.8550855 0.986752503 1.013636477 1.004447939 1.07134932 1.033454977 1.073375524 1.093878088 0.976211645 1 17.33720415 5.790226342 0.827098738 1.048665661 1.98E-11 0.694338501 0.03548 5.985109649 0.846054841 0.011624095 8.607631136 616916.4373 -5.790226342 -1.048665661 ELEEEAEEEQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEEEAEEEQR 11 0 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 ; 262.63 1.30E-13 206800000 332470 334430 300090 365680 347180 374540 383120 427470 426930 440580 FALSE TRUE 319476.7048 324892.3838 354322.9385 384552.7886 358347.36 382113.4554 387808.7372 418642.5951 378466.6962 410739.1242 0.777809286 0.790994489 0.862647159 0.936245821 0.872445158 0.930306934 0.944172869 1.01924207 0.921428405 1 18.64786285 5.791209008 0.292027908 1.001264224 0.364954036 0.812962011 0.032800869 5.793873687 0.250762382 0.036907414 1.472380618 618313.8975 -5.791209008 -0.636310188 VSGS(ph)PEQAVEENLSSYSLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSGSPEQAVEENLSSYSLDR 20 0 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 VSGS(1)PEQAVEENLSSYSLDR;VSGS(1)PEQAVEENLSSYSLDR;VS(0.147)GS(0.853)PEQAVEENLSSYSLDR 412.49 1.50E-151 766374000 100648 95458 105637 125041 112227 123682 128577 149492 140550 150676 TRUE FALSE 96714.56489 92735.6313 124727.9558 131494.381 115836.8834 126182.9348 130150.5638 146404.938 124595.3532 140470.5803 0.68850406 0.660178317 0.887929384 0.93609908 0.824634476 0.898287275 0.926532542 1.042246267 0.886985395 1 17.09990848 5.792141722 0.380207717 0.982490336 7.81E-15 0.700552096 0.063416847 6.973346677 0.430198865 0.051995456 3.670773009 619643.248 -5.792141722 -0.982490336 RLPEESGGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLPEESGGR 9 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 ; 102.06 0.0058455 394840000 239220 276690 208549 278270 252380 278000 272780 292380 253530 303950 FALSE TRUE 229871.0179 268799.0721 246238.4434 292631.548 260498.0319 283621.3505 276118.3632 286342.2508 224750.3373 283363.1958 0.811223975 0.948602628 0.868985271 1.032708384 0.919307926 1.000911038 0.974432698 1.010513204 0.793152889 1 18.11229286 5.803891908 0.93637434 0.962172944 1.25E-16 0.259214027 0.069707339 16.31962276 2.455692993 0.020155674 25.39056523 636637.0486 -5.803891908 -0.962172944 DVPYPPPLS(ph)PAIEAIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVPYPPPLSPAIEAIQK 17 0 G3V3Y1;Q8N8N7;G3V2R9 G3V3Y1 PTGR2 Prostaglandin reductase 2 1 DVPYPPPLS(1)PAIEAIQK 105.39 0.0015688 0 37404 41013 32923 39243 38667 44124 40538 40041 42030 42741 TRUE FALSE 35942.21033 39843.3494 38872.91847 41268.33593 39910.75917 45016.21751 41034.11617 39214.13936 37258.9306 39846.114 0.902025486 0.999930618 0.975576149 1.035692864 1.001622371 1.129751762 1.029814756 0.984139617 0.935070622 1 15.28215141 5.804196264 1.06978019 1.016846752 0.073012381 0.318778925 0.047885104 18.077896 2.889180797 0.014607761 32.82464541 637083.3628 -5.804196264 -0.943834371 DEQLESLFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEQLESLFQR 10 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 215.06 1.95E-08 139523000 130894 123500 138713 171957 147710 145808 178404 203850 208362 208045 FALSE TRUE 125778.5178 119977.9009 163781.5248 180831.7214 152461.2263 148756.3377 180587.3615 199640.4263 184709.6193 193953.9268 0.648496887 0.618589697 0.844435209 0.932343698 0.786069294 0.766967393 0.931083812 1.029318816 0.952337611 1 17.56535446 5.805685343 0.256591198 1.025579686 6.29E-17 0.689822838 0.075472621 9.984015653 0.35837102 0.110267481 3.555188445 639271.5004 -5.805685343 -1.025579686 DDLDEEEDTHL ddPTM_BT-474_Pertuzumab_2h_R1 2 DDLDEEEDTHL 11 0 O00592-2;O00592 O00592-2 PODXL Podocalyxin 0 ; 223.83 1.55E-11 476960000 367600 505040 426390 667290 416690 442720 685340 598070 829540 714070 FALSE TRUE 353233.7856 490636.7537 503448.158 701728.9169 430093.2123 451672.1017 693727.3959 585719.6455 735374.0969 665705.4029 0.530615771 0.737017833 0.756262689 1.054113297 0.646071386 0.678486459 1.042093684 0.879848117 1.104653941 1 19.34452435 5.806783482 0.216954931 1.047560174 6.96E-14 0.451373872 0.140704709 20.1017381 0.573408133 0.247170361 6.098924096 640889.9807 -5.806783482 -1.047560174 LTVEDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTVEDLEK 8 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 92.062 0.02802 135610000 80387 81781 88385 88260 96461 90745 103120 102940 108710 121860 FALSE TRUE 77245.38717 79448.68595 104358.1356 92815.10918 99563.75567 92579.92607 104382.0134 100814.253 96369.69655 113606.3137 0.67993921 0.699333368 0.918594506 0.816989005 0.876392803 0.814918846 0.918804687 0.887400091 0.848277648 1 16.79368349 5.809691595 0.562018847 0.894390857 1.53E-19 0.608409061 0.058644005 7.437421877 0.71564593 0.026101329 5.664253847 645195.8937 -5.809691595 -0.894390857 SDGTETSTNLHQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SDGTETSTNLHQK 13 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 203.39 8.62E-08 738500000 465920 514000 426310 477000 482010 486050 503450 530510 616210 521620 FALSE TRUE 447711.3313 499341.2233 503353.7002 501618.0272 497514.2894 495878.264 509611.3717 519554.7831 546260.4242 486290.2128 0.920666959 1.026837905 1.035089103 1.031519891 1.023081025 1.019716727 1.047957286 1.06840477 1.123321856 1 18.89145803 5.809848014 1.069410864 1.048171018 2.04E-15 0.566484669 0.031952475 10.87275767 1.717937784 0.009531467 21.96205152 645428.3154 -5.809848014 -1.048171018 RGS(ph)SGSVDETLFALPAASEPVIR ddPTM_BT-474_Pertuzumab_2h_R1 5 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.299)S(0.299)GS(0.299)VDET(0.104)LFALPAASEPVIR;RGS(0.655)S(0.171)GS(0.171)VDET(0.002)LFALPAASEPVIR;RGS(0.444)S(0.133)GS(0.198)VDET(0.225)LFALPAASEPVIR;RGS(0.711)S(0.139)GS(0.139)VDET(0.01)LFALPAASEPVIR;RGS(0.732)S(0.072)GS(0.16)VDET(0.036)LFALPAASEPVIR 181.21 2.64E-17 2484986000 729503 774046 805329 1067661 726718 881390 1105684 1166015 1199360 1152040 TRUE FALSE 700993.2163 751970.966 950869.8647 1122763.112 750093.5445 899212.3097 1119215.692 1141936.383 1063213.681 1074011.305 0.652687 0.700151817 0.885344373 1.045392267 0.69840377 0.837246597 1.042089303 1.063244286 0.989946452 1 20.03457775 5.810003533 0.306018843 1.040186233 7.58E-16 0.532941359 0.103922802 12.0347138 0.550740463 0.118126803 5.275420412 645659.4807 -5.810003533 -1.040186233 SSRPFER ddPTM_BT-474_Pertuzumab_2h_R1 1 SSRPFER 7 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 0 79.906 0.028595 75288000 82931 91187 76969 84314 92738 82695 99264 92831 94525 103490 FALSE TRUE 79689.96483 88586.43604 90879.01047 88665.45564 95721.00199 84367.14956 100478.8225 90914.00741 83794.91828 96480.53012 0.825969392 0.918179408 0.94194145 0.918998429 0.992127654 0.874447409 1.041441443 0.942304186 0.868516354 1 16.55795021 5.812004293 1.00826034 0.950631808 2.69E-09 0.340716781 0.050943935 15.07362628 2.32024781 0.014344715 25.58910769 648640.8454 -5.812004293 -0.950631805 ELPEYYELIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELPEYYELIR 10 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28;A0A0U1RQW7;A0A0U1RRD6;A0A0U1RRF8;A0A0A0MSS5;F6UH26;A0A0U1RR09;A0A0U1RQU0;F6XE55;A0A0U1RRN2;A0A0U1RR83;A0A0U1RQX3;A0A0U1RRF5;F6VDE0;P51531-2;P51531;A0A0U1RRG6;B1ALG1;F6T8Q0;B1ALG2;A0A0U1RR26;A0A1W2PS06;B4DNT1;B1ALF6 A0A2R8Y4P4;F6VDE0 SMARCA4;SMARCA2 Transcription activator BRG1;Probable global transcription activator SNF2L2 0 88.948 0.026068 0 12225 14174 10607 15197 10920 14727 13566 15154 14339 15413 FALSE TRUE 11747.23348 13769.7714 12523.92085 15981.31899 11271.25172 15024.79003 13732.02477 14841.0646 12711.29683 14369.06378 0.817536456 0.958292872 0.871589203 1.112203219 0.784411002 1.045634584 0.955665934 1.032848405 0.884629439 1 13.81067845 5.812816894 0.926015957 0.971429952 2.38E-14 0.182828107 0.090474438 20.63743553 3.039727701 0.025686667 32.05798908 649855.6419 -5.812816894 -0.971429952 LS(ph)PLPVVSR ddPTM_BT-474_Pertuzumab_2h_R1 6 LSPLPVVSR 9 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LS(1)PLPVVSR;LS(1)PLPVVSR;LS(1)PLPVVSR;LS(1)PLPVVSR;LS(1)PLPVVSR;LS(1)PLPVVSR 178.46 5.34E-05 1497021000 868082 923030 1020324 1416423 1027422 926064 1397950 1413410 1462610 1699980 TRUE FALSE 834156.3957 896706.0881 1204719.244 1489524.761 1060469.962 944789.6486 1415058.53 1384222.59 1296580.645 1584838.84 0.526335154 0.565802696 0.760152523 0.939858819 0.669134258 0.596142412 0.892872193 0.873415362 0.818115137 1 20.59590471 5.813798177 0.16061104 1.021027492 4.39E-16 0.52347102 0.109384843 28.3771739 0.555348813 0.405650842 6.15120348 651325.6433 -5.813798177 -1.021027492 EDIDAAIETYNLLSER ddPTM_BT-474_Pertuzumab_2h_R1 2 EDIDAAIETYNLLSER 16 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 126.95 0.00016023 64774000 56791 63532 63616 75541 69755 67079 82699 87925 83809 94629 FALSE TRUE 54571.54493 61720.12956 75112.82633 79439.68006 71998.73292 68435.38334 83711.0951 86109.31802 74295.35368 88219.69354 0.618586879 0.699618499 0.851429237 0.900475584 0.816129937 0.775738167 0.948893515 0.976078181 0.842162908 1 16.42881313 5.815065997 0.396160625 0.937636843 9.35E-31 0.685908373 0.064660407 8.023706688 0.513906513 0.052258531 4.240401195 653229.8126 -5.815065997 -0.937636843 LEQQLVHVERPILR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEQQLVHVERPILR 14 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6;E7EPX3;B9ZVU2;F8WAN0;C9JRG3;C9J1E2 E5RIA4 DNPEP Aspartyl aminopeptidase 0 ;; 230.16 6.10E-13 1184920000 381950 420300 345660 438760 378619 461210 442670 453630 469350 480000 FALSE TRUE 367022.9717 408313.4555 408128.4512 461404.4562 390797.624 470535.9822 448087.5279 444262.382 416071.3557 447489.1725 0.82018291 0.91245438 0.912040953 1.031096358 0.87331191 1.051502497 1.001337139 0.992789121 0.929790889 1 18.77149325 5.817574171 0.62865938 0.987947592 0.280134812 0.508029577 0.049486789 8.865766291 0.949499475 0.019514971 6.145452591 657013.3146 -5.817574171 -0.70781278 IS(ph)MQDVDLS(ph)LGSPK ddPTM_BT-474_Pertuzumab_2h_R1 5 ISMQDVDLSLGSPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 IS(1)MQDVDLS(0.5)LGS(0.5)PK;IS(1)MQDVDLS(0.5)LGS(0.5)PK;IS(1)MQDVDLS(0.5)LGS(0.5)PK;IS(1)MQDVDLS(0.5)LGS(0.5)PK;IS(1)MQDVDLS(0.5)LGS(0.5)PK 87.298 0.010231 586480000 1239774 1203032 847398 904400 1068819 970678 898388 973300 1047136 1067044 TRUE FALSE 1191322.261 1168722.705 1000541.669 951076.1924 1103198.534 990305.7742 909382.7411 953201.0149 928269.5112 994772.1595 1.197583035 1.174864711 1.00579983 0.956074397 1.108996189 0.995510143 0.914161833 0.958210386 0.933147859 1 19.92400661 5.817918824 0.485288854 0.954822668 1.874002508 0.67662989 0.054274167 6.973143929 0.567081928 0.03217316 4.582214572 657534.9229 -5.817918824 0.91917984 DVNQQEFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVNQQEFVR 9 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 204.42 3.86E-05 4277700000 1190680 1290770 1045290 1210890 1226820 1164150 1341170 1340970 1311840 1309220 FALSE TRUE 1144146.909 1253958.503 1234197.155 1273384.178 1266281.779 1187689.911 1357583.64 1313278.501 1162925.423 1220545.363 0.937406297 1.027375582 1.011184994 1.043291152 1.037472115 0.973081334 1.112276266 1.075976805 0.952791644 1 20.21909449 5.817943935 1.200631695 1.035813299 1.20E-10 0.235856385 0.044985583 23.25921757 3.687158161 0.012760584 54.20457855 657572.9433 -5.817943935 -1.035813299 QAHLCVLASNCDEPMYVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QAHLCVLASNCDEPMYVK 18 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 208.13 6.66E-16 471410000 174720 149090 133560 139280 129490 137040 120350 155350 163380 159150 FALSE TRUE 167891.7492 144838.0992 157697.263 146468.2575 133655.1634 139811.0427 121822.8793 152141.9682 144833.7873 148370.6287 1.131569979 0.97619118 1.062860381 0.987178249 0.900819553 0.942309431 0.821071396 1.02541837 0.976162119 1 17.178846 5.819008371 0.662382305 0.946433681 1.708058957 0.412574503 0.061923031 11.71245902 1.317190011 0.024865934 9.326731937 659186.6011 -5.819008371 0.761625276 LLSFS(ph)PEEFPTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLSFSPEEFPTLK 13 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LLSFS(1)PEEFPTLK;LLSFS(1)PEEFPTLK 146.79 4.45E-05 494230000 433710 402580 410540 442620 447320 523600 503500 554550 630910 683270 TRUE FALSE 416760.1337 391098.8126 484733.7104 465463.6712 461708.454 534187.5507 509661.9836 543098.3487 559291.7418 636991.5143 0.654263243 0.613978057 0.760973576 0.730721934 0.724826695 0.838610152 0.800107964 0.852599032 0.87802071 1 19.28091463 5.81941422 0.102199044 1.157271084 6.47E-14 0.904928802 0.033213532 19.23514535 0.230513783 0.467985833 3.169704612 659802.9006 -5.81941422 -1.157271084 MDIDAPDVEVQGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 MDIDAPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 246.21 2.86E-24 4178850000 2665203 2835936 2226164 2789880 2433279 2750214 2747761 2857577 3003352 2903720 FALSE TRUE 2561043.92 2755057.882 2628481.356 2933866.041 2511547.629 2805825.211 2781388.921 2798567.036 2662424.072 2707048.458 0.946065045 1.01773497 0.970976839 1.083787781 0.927780817 1.036488727 1.027461815 1.033807514 0.983515483 1 21.36828928 5.820945138 1.40970574 1.012704722 2.98E-11 0.168667943 0.040495337 38.99297967 5.946978137 0.010109049 109.709867 662132.8554 -5.820945138 -1.012704722 EQLDPDELETITMHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQLDPDELETITMHK 15 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 91.592 0.0041606 0 49215 55664 46197 55227 54114 54999 57472 62216 59943 58658 FALSE TRUE 47291.62339 54076.51722 54545.82555 58077.27209 55854.62596 56111.11746 58175.35953 60931.21786 53138.52194 54685.04141 0.864799992 0.9888722 0.997454224 1.06203215 1.02138765 1.026077992 1.063825829 1.114220933 0.971719515 1 15.73885863 5.821723397 0.825213525 1.048089975 2.93E-13 0.626196229 0.038714467 7.363266611 0.992665239 0.012995381 10.66889623 663320.4662 -5.821723397 -1.048089975 SPHLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPHLEK 6 0 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 81.297 0.06225 154320000 280760 320530 286430 347400 293120 367060 343040 362570 384020 434170 FALSE TRUE 269787.5888 311388.7982 338194.2726 365329.3556 302548.471 374482.2047 347238.2261 355082.8028 340427.6595 404763.2792 0.66653178 0.769310889 0.835535954 0.902575343 0.747470155 0.925188188 0.857879763 0.877260416 0.841053715 1 18.62671889 5.827515665 0.613479376 0.881021912 3.75E-27 0.5661705 0.059680207 8.470988828 0.876481896 0.023810267 7.110403487 672226.5554 -5.827515665 -0.881021912 IVSGS(ph)PISTPSPSPLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 IVSGSPISTPSPSPLPR 17 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 IVSGS(0.993)PIS(0.004)T(0.004)PSPSPLPR;IVS(0.001)GS(0.987)PIS(0.006)T(0.006)PSPSPLPR;IVS(0.002)GS(0.975)PIS(0.011)T(0.011)PSPSPLPR;IVS(0.003)GS(0.775)PIS(0.099)T(0.099)PS(0.02)PS(0.003)PLPR 204.13 9.51E-12 803408000 310584 344040 262896 336236 320320 326891 341499 356059 325261 347054 TRUE FALSE 298446.0339 334228.3161 310407.1553 353589.1803 330623.3837 333500.96 345678.3669 348706.2572 288338.7349 323547.7235 0.922417351 1.033010872 0.959385997 1.092850157 1.021868985 1.030762808 1.068399936 1.07775834 0.891178376 1 18.303619 5.829242279 1.141089701 1.030821017 7.63E-09 0.178565547 0.057619993 25.07176653 3.859218683 0.015751626 54.626153 674904.4301 -5.829242279 -1.03082101 YDDAIQLYDR ddPTM_BT-474_Pertuzumab_2h_R1 4 YDDAIQLYDR 10 0 Q15006;H0YAS9 Q15006 EMC2 ER membrane protein complex subunit 2 0 ;;; 191.45 1.84E-06 812540000 1025240 1144230 886960 1210710 933210 1036250 1189700 1172860 1259670 1246000 FALSE TRUE 985172.4873 1111597.681 1047253.402 1273194.888 963227.5472 1057203.685 1204259.904 1148640.031 1116677.543 1161607.31 0.848111473 0.956947904 0.901555451 1.096063082 0.829219598 0.910121412 1.0367186 0.988836779 0.961321036 1 20.14769101 5.829380827 1.030605942 0.969868232 5.39E-13 0.201402548 0.070287227 24.34587578 3.657153237 0.020527322 43.67466584 675119.7724 -5.829380827 -0.969868232 RKPEEES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 RKPEEESPR 9 2 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 RKPEEES(1)PR;RKPEEES(1)PR;RKPEEES(1)PR;RKPEEES(1)PR;RKPEEES(1)PR;RKPEEES(1)PR 168.83 4.64E-05 7374583000 7127879 6507852 7497590 8437260 7014230 6818841 8897130 9984330 10140810 11298800 TRUE FALSE 6849313.608 6322254.433 8852571.296 8872708 7239849.078 6956722.637 9006015.738 9778150.096 8989667.763 10533522.21 0.650239632 0.600203266 0.840418914 0.842330592 0.68731512 0.660436509 0.854986163 0.928288743 0.853434168 1 23.32848459 5.837770902 0.091001257 1.202029769 2.12E-11 0.580738526 0.081802829 71.98370508 0.762358083 2.000946099 11.293227 688289.1154 -5.837770902 -1.202029769 EMEAELEDER ddPTM_BT-474_Pertuzumab_2h_R1 4 EMEAELEDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 223.08 1.07E-08 3738540000 2385220 2700720 2167420 2629200 2647840 2862690 2569590 2826570 2861040 3042840 FALSE TRUE 2292002.965 2623698.11 2559121.008 2764893.327 2733010.178 2920575.553 2601037.411 2768200.342 2536266.734 2836745.737 0.807969123 0.924897172 0.902132671 0.974670832 0.963431492 1.029551403 0.916908899 0.97583661 0.89407616 1 21.43580541 5.840441364 0.860838811 0.963214476 5.78E-11 0.581725415 0.039008819 8.745556154 1.179510185 0.011956881 12.37696052 692534.421 -5.840441364 -0.963214476 TS(ph)PLNSSGSSQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPLNSSGSSQGR 13 0 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.096)S(0.904)PLNSSGSSQGR 76.262 0.030575 324390000 255800 243050 268230 331550 289070 293310 361640 370960 407480 404730 TRUE FALSE 245803.0532 236118.452 316705.1277 348661.3352 298368.1991 299240.9292 366065.8585 363299.5464 361224.5787 377317.2766 0.65144924 0.625782244 0.839360261 0.924053461 0.790762092 0.79307508 0.970180485 0.962848957 0.957349692 1 18.52541863 5.841388708 0.278041047 1.003083941 3.47E-15 0.745767737 0.06441778 8.236160781 0.325419079 0.081564372 3.143324545 694046.7238 -5.841388708 -1.003083941 LSSSSATLLNS(ph)PDR ddPTM_BT-474_Pertuzumab_2h_R1 6 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR 330.28 2.21E-68 5482720000 2069980 2448690 2440050 2754230 2445160 2565610 3123660 2860920 3027520 3790100 TRUE FALSE 1989082.893 2378855.759 2881021.314 2896376.14 2523810.792 2617488.392 3161888.285 2801841.002 2683848.622 3533393.151 0.562938458 0.673249666 0.815369587 0.819715219 0.714273981 0.74078606 0.894858893 0.792960444 0.75956694 1 21.75262285 5.843080155 0.066753893 1.251902562 2.26E-15 0.609725781 0.071038656 134.0213856 1.036857372 4.922903102 17.96490155 696755.0985 -5.843080155 -1.251902562 QLGEAHGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QLGEAHGR 8 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 98.044 0.0078018 105653000 126337 138098 104943 136161 137010 132440 138063 132556 137321 136829 FALSE TRUE 121399.6104 134159.5803 123908.5345 143188.2855 141417.0511 135118.0275 139752.6563 129818.6723 121732.8958 127561.45 0.951695127 1.051725112 0.971363485 1.122504374 1.108619031 1.059238724 1.095571243 1.017695176 0.954307871 1 16.96083288 5.84466385 1.176937102 1.049933852 2.65E-06 0.188270199 0.054512222 29.68654288 4.423644139 0.015656277 69.00180397 699300.5176 -5.84466385 -1.049931204 AS(ph)PLPFEPWQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPLPFEPWQR 11 0 Q9C073;Q9C073-2 Q9C073 FAM117A Protein FAM117A 1 AS(1)PLPFEPWQR;AS(1)PLPFEPWQR 123.92 0.00037751 41603000 36887 41191 40380 52317 39665 45816 57802 58580 61034 61947 TRUE FALSE 35445.41526 40016.27301 47677.56425 55017.08664 40940.86075 46742.43091 58509.39817 57370.30253 54105.6762 57751.27451 0.613759879 0.692907184 0.825567308 0.9526558 0.708917008 0.809374881 1.013127393 0.993403228 0.93687415 1 15.81756517 5.84556081 0.266854857 1.019197675 5.45E-17 0.664428801 0.079887307 10.45834196 0.389734528 0.107905578 3.878109206 700746.2941 -5.84556081 -1.019197675 MEEIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEEIGR 6 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144;P12814-3;P12814;P12814-2;P12814-4;H9KV75;H0YJ11;H0YJW3 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ; 138.38 0.028678 1254000000 1319130 1355850 1376750 1840180 1508220 1261370 1684700 1741260 1898510 2142380 FALSE TRUE 1267576.941 1317182.486 1625559.351 1935151.91 1556733.266 1286875.766 1705317.863 1705302.373 1682999.104 1997274.694 0.634653283 0.659489899 0.813888723 0.968896224 0.779428724 0.644315862 0.853822395 0.853814639 0.842647788 1 20.92960134 5.848035004 0.055547481 1.335798189 1.25E-13 0.436699435 0.091249018 283.2499893 1.820597916 12.42970958 36.77733738 704749.87 -5.848035004 -1.335798189 YKPESEELTAER ddPTM_BT-474_Pertuzumab_2h_R1 6 YKPESEELTAER 12 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 181.76 1.62E-05 39036000000 16553270 19013770 16653230 20726200 17428350 19768950 21570700 21020400 23508600 24148600 FALSE TRUE 15906349.91 18471515.9 19662839.11 21795881.67 17988948.71 20168691.71 21834688.68 20586321.39 20840002.28 22512993.81 0.706540855 0.820482431 0.87339957 0.968146744 0.799047379 0.895868932 0.969870505 0.914419538 0.925687736 1 24.42425459 5.850134039 0.615362554 0.928928707 4.58E-28 0.646741248 0.050940854 7.73858451 0.784592698 0.021637941 6.917940804 708164.3162 -5.850134039 -0.928928707 ATSS(ph)PMLYEVVYEAGALER ddPTM_BT-474_Pertuzumab_2h_R1 3 ATSSPMLYEVVYEAGALER 19 0 Q5T4L2;Q5T4K9;Q5T4L1;Q8TEY5-2;Q8TEY5 Q5T4L2 CREB3L4 Cyclic AMP-responsive element-binding protein 3-like protein 4;Processed cyclic AMP-responsive element-binding protein 3-like protein 4 1 AT(0.023)S(0.136)S(0.841)PMLYEVVYEAGALER;ATS(0.197)S(0.803)PMLYEVVYEAGALER;AT(0.017)S(0.12)S(0.863)PMLYEVVYEAGALER 216.19 4.08E-19 208303300 101279.6 136106.6 100914.7 138726.2 132276.3 124977.9 152380.5 170666 149422.2 155002.9 TRUE FALSE 97321.48126 132224.973 119152.2311 145885.8758 136531.0873 127505.0388 154245.3781 167141.6875 132460.4183 144504.4155 0.673484481 0.915023756 0.824557718 1.009559987 0.944822944 0.882360849 1.067409446 1.156654534 0.916653085 1 17.14075405 5.851526274 0.415028399 1.045138758 1.62E-15 0.561448202 0.083890458 9.682371617 0.640733003 0.062140286 6.057632374 710438.1481 -5.851526274 -1.045138758 CGESGHLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 CGESGHLAK 9 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;D6RAT4;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ; 103.83 0.0087402 1351100000 2032015 2315455 1981949 2387196 2149856 2561766 2443593 2582363 2704378 2653761 FALSE TRUE 1952601.607 2249420.49 2340131.273 2510399.472 2219008.071 2613566.664 2473498.422 2529036.302 2397388.347 2474019.404 0.789242641 0.909216996 0.945882344 1.014704843 0.896924279 1.056405079 0.999789419 1.02223786 0.969025685 1 21.23842538 5.855231024 0.674700024 1.00275959 2.05E-13 0.722793441 0.03916654 5.895902651 0.647126635 0.014461417 6.394115188 716524.4652 -5.855231024 -1.00275959 AFVGFEYEDSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AFVGFEYEDSR 11 0 Q8ND04;Q8ND04-2 Q8ND04 SMG8 Protein SMG8 0 ;; 154.56 7.43E-05 625480000 448859 540970 404602 517990 511670 533400 537680 555370 535860 618610 FALSE TRUE 431317.094 525542.0653 477722.5817 544723.526 528128.3302 544185.7135 544260.2887 543901.4154 475031.4193 576710.9937 0.747891229 0.911274574 0.828356988 0.944534666 0.915759082 0.943602115 0.943731426 0.943109151 0.823690591 1 19.137489 5.863242061 0.772936677 0.928879629 2.51E-16 0.507938973 0.050643714 10.12597979 1.228151832 0.016391265 12.12232526 729864.198 -5.863242061 -0.928879629 ILPGSMIVSS(ph)DDTVDSTIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILPGSMIVSSDDTVDSTIDR 20 0 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 ILPGSMIVS(0.431)S(0.569)DDTVDSTIDR 145.55 1.51E-07 20351000 13411 15030 12572 15690 13484 16518 14943 16113 18080 16747 TRUE FALSE 12886.88329 14601.35912 14844.04006 16499.76278 13917.72511 16852.00528 15125.8769 15780.26092 16027.6342 15612.71077 0.825409724 0.935222546 0.950766352 1.056816015 0.89143553 1.079377279 0.968818107 1.01073165 1.026576001 1 13.93043343 5.864420401 0.765056245 1.005415137 2.94E-07 0.552832386 0.049010244 8.721392905 1.048202597 0.015618467 11.15784086 731847.175 -5.864420401 -1.005414843 DGNASGTTLLEALDCILPPTRPTDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGNASGTTLLEALDCILPPTRPTDK 25 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 210.22 1.75E-25 500260000 190172 153855 181707 223840 191025 182531 207050 253710 282170 288820 FALSE TRUE 182739.868 149467.206 214545.497 235392.4092 197169.4926 186221.9019 209583.9398 248470.7998 250139.2446 269257.9641 0.678679528 0.555107837 0.79680279 0.874226358 0.732269863 0.69161149 0.77837601 0.922798331 0.928994785 1 18.03862949 5.864630865 0.105435422 1.162321371 1.31E-08 0.61844959 0.080196936 49.37272508 0.603691733 1.146249247 8.359325589 732201.9233 -5.864630865 -1.162321358 KPSETQELVQQVLSLATQDSDNPDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPSETQELVQQVLSLATQDSDNPDLR 26 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 ; 206.94 4.51E-25 1464240000 568200 656060 584840 684360 683280 708110 737070 785850 850160 806420 FALSE TRUE 545994.1158 637349.8111 690533.5977 719679.9016 705258.3217 722428.4694 746090.4831 769621.9229 753653.401 751800.4551 0.726248717 0.847764599 0.918506491 0.957275161 0.938092438 0.960931141 0.992404937 1.023705051 1.002464678 1 19.51999026 5.867761779 0.506636292 1.004076465 2.57E-17 0.960490711 0.016930146 2.493879872 0.204190013 0.010624793 1.906276225 737499.5828 -5.867761779 -1.004076465 DFIIFEAAPQETR ddPTM_BT-474_Pertuzumab_2h_R1 5 DFIIFEAAPQETR 13 0 P60510;H3BTA2 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit;Serine/threonine-protein phosphatase 0 ;;;; 164.13 8.74E-05 274486000 427336 472252 376295 454137 462431 458605 466092 485752 480977 511251 FALSE TRUE 410635.2367 458783.8353 444299.8771 477575.065 477305.5131 467878.3073 471796.1733 475721.0515 426378.5074 476623.5144 0.86155052 0.962570711 0.932182034 1.001996441 1.001430896 0.981651751 0.989871794 0.99810655 0.894581351 1 18.8624906 5.868617997 0.993523211 0.981348859 4.89E-17 0.51331555 0.033156388 11.67055016 1.608104091 0.009562713 20.48211321 738955.009 -5.868617997 -0.981348859 DGVVRPLK ddPTM_BT-474_Pertuzumab_2h_R1 6 DGVVRPLK 8 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 110.41 0.0031297 29729100000 21400900 21541500 20296160 23205900 22479800 24308100 26602100 27022800 31127100 30452600 FALSE TRUE 20564529.17 20927157.51 23964127.6 24403559.28 23202883.18 24799626.44 26927664.46 26464769.74 27593682.1 28390018.28 0.724357729 0.737130822 0.844103986 0.859582373 0.817290181 0.873533303 0.948490564 0.932185724 0.971950135 1 24.75888044 5.869722715 0.200596213 1.0278135 0.262923272 0.907037549 0.027228221 6.377435181 0.160626959 0.056919726 1.30481217 740837.0862 -5.869722715 -0.764890229 VDPSLMEDS(ph)DDGPSLPTK ddPTM_BT-474_Pertuzumab_2h_R1 3 VDPSLMEDSDDGPSLPTK 18 0 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 1 VDPS(0.001)LMEDS(0.999)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK 268.55 1.82E-31 411967000 461687 530165 497039 637713 568796 575995 616596 760266 856685 756637 TRUE FALSE 443643.7616 515045.2133 586865.0039 670625.4444 587091.8399 587642.0135 624142.0863 744566.2414 759437.7103 705389.302 0.628934633 0.730157392 0.831973213 0.950716778 0.832294788 0.833074746 0.884819325 1.055539458 1.076622098 1 19.42806017 5.870182632 0.262536931 1.051265054 5.48E-19 0.754085344 0.066736714 9.044027206 0.32609586 0.095084396 3.405979231 741622.047 -5.870182632 -1.051265054 EGYENFFDK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGYENFFDK 9 0 X6RM59;Q9H0P0-3;Q9H0P0-2;Q9H0P0-1;Q9H0P0;B9A035 X6RM59 NT5C3A 5-nucleotidase;Cytosolic 5-nucleotidase 3A 0 119.68 0.0018329 112280000 93966 110930 90193 118520 109680 100490 117950 137200 116420 131630 FALSE TRUE 90293.70484 107766.385 106492.8814 124636.8314 113207.9568 102521.9767 119393.5074 134366.7721 103204.4897 122714.5829 0.735802565 0.878187274 0.867809505 1.015664386 0.922530592 0.835450639 0.972936587 1.094953582 0.841012431 1 16.90494718 5.871981453 0.606717115 0.970027125 8.08E-17 0.415729015 0.076678206 12.17709159 1.190996388 0.034821503 11.23561496 744700.1692 -5.871981453 -0.970027125 LAILDQELEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAILDQELEHK 11 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 149.38 3.44E-05 75644000 99584 95546 102230 104080 123590 111390 117690 142540 160240 154010 FALSE TRUE 95692.14718 92821.12163 120705.2351 109451.5813 127565.3846 113642.3821 119130.3254 139596.4992 142050.227 143578.7655 0.666478409 0.646482238 0.840690019 0.762310366 0.888469713 0.791498532 0.829721059 0.972264239 0.989354007 1 17.13148287 5.874018837 0.187357317 1.050864181 0.076164048 0.783396362 0.055807442 11.06739491 0.255494049 0.130625983 2.685492289 748201.9527 -5.874018837 -0.974700133 TNS(ph)NASTVSGR ddPTM_BT-474_Pertuzumab_2h_R1 3 TNSNASTVSGR 11 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 T(0.001)NS(0.999)NASTVSGR;TNS(0.999)NAS(0.001)TVSGR;T(0.001)NS(0.995)NAS(0.004)TVSGR 181.91 6.31E-06 296011000 120592 133180 137196 166732 150457 150489 165773 192617 208709 206044 TRUE FALSE 115879.1313 129381.8368 161990.3691 175337.0585 155296.586 153531.9907 167801.7796 188639.3916 185017.2293 192088.4564 0.603259215 0.67355342 0.843311317 0.912793313 0.808463918 0.79927755 0.873565142 0.982044394 0.963187652 1 17.5514113 5.87980389 0.294113569 0.982497375 2.01E-23 0.787915311 0.057045513 7.934867511 0.332596709 0.070681639 3.169968623 758235.1086 -5.87980389 -0.982497375 VDSEGDFS(ph)ENDDAAGDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDSEGDFSENDDAAGDFR 18 0 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 VDSEGDFS(1)ENDDAAGDFR;VDSEGDFS(1)ENDDAAGDFR 434.22 3.18E-169 964520000 279770 295630 294953 360380 355990 344950 372370 405680 428570 470540 TRUE FALSE 268836.2791 287198.9219 348257.5683 378979.255 367440.7417 351925.1253 376927.1754 397302.5662 379920.5303 438669.9067 0.612844134 0.654703953 0.793894368 0.863928091 0.837624683 0.802254999 0.859250133 0.905698249 0.866073839 1 18.74277621 5.880515353 0.346595244 0.920795319 2.62E-36 0.835475728 0.043851415 5.773354444 0.300409582 0.040419955 2.599300141 759478.2709 -5.880515353 -0.920795319 GSSGGSGAKPSDAASEAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSSGGSGAKPSDAASEAAR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 133.09 1.13E-05 363909000 278953 287817 277150 363012 345195 340981 395914 395951 454328 471348 FALSE TRUE 268051.2084 279608.741 327237.1702 381747.0928 356298.5107 347875.8694 400759.314 387774.4735 402754.5901 439423.1801 0.610006983 0.636308583 0.744697105 0.868745915 0.810832307 0.791664812 0.912012229 0.88246249 0.9165529 1 18.74525145 5.881706918 0.252534726 0.974875019 5.90E-17 0.884225734 0.040373388 5.758959446 0.195970242 0.056993088 1.929233561 761564.897 -5.881706918 -0.974875019 LDLMDEGTDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDLMDEGTDAR 11 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4;E5RIK2;A0A1B0GUX5;A0A1B0GU67;A0A0D9SFE4;A0A0D9SFB1;A0A0U1RQP1;Q05193-5;Q05193-3;Q05193-2;Q05193 P50570-2;A0A0D9SFE4 DNM2;DNM3;DNM1 Dynamin-2;Dynamin-3;Dynamin-1 0 ;;; 163.38 5.59E-05 1154591000 871530 1004760 771020 985050 988720 1012100 955880 1078210 1058320 1055090 FALSE TRUE 837469.6441 976105.2286 910360.4652 1035888.549 1020523.077 1032565.355 967578.3454 1055944.587 938183.9504 983627.8145 0.851409071 0.992352203 0.925513138 1.053130598 1.037509373 1.049752091 0.983683392 1.073520463 0.953799737 1 19.90775301 5.899140172 0.792951532 1.02466626 6.77E-13 0.553862756 0.04306382 9.176476256 1.077599901 0.013750346 12.6696789 792757.1588 -5.899140172 -1.02466626 KMMDKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KMMDKR 6 2 Q5T5C7 Q5T5C7 SARS 0 51.572 0.086255 13128000 68470 67652 41738 39159 43418 48817 48086 16857 44547 34623 FALSE TRUE 65794.1167 65722.6312 49280.98506 41180.00068 44814.5794 49804.11319 48674.49085 16508.89706 39490.21132 32277.95337 2.038360857 2.036146172 1.5267692 1.275793425 1.38839594 1.54297618 1.507979465 0.511460466 1.223442232 1 14.97826148 5.901067946 0.269482658 0.866747874 4.258185176 0.624671255 0.263957365 10.80740972 0.398465521 0.349374189 13.55631715 796283.9211 -5.901067946 3.391437302 GEAAAERPGEAAVASS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.215)S(0.712)PS(0.073)K;GEAAAERPGEAAVAS(0.161)S(0.732)PS(0.107)K;GEAAAERPGEAAVAS(0.167)S(0.819)PS(0.014)K;GEAAAERPGEAAVAS(0.013)S(0.962)PS(0.024)K 274.34 1.27E-39 14447200000 4805010 4632020 5754490 5683080 5287140 5326780 6846580 7802730 6874080 7149660 TRUE FALSE 4617224.897 4499919.325 6794454.351 5976384.44 5457205.66 5434491.141 6930370.494 7641600.899 6093763.257 6665407.16 0.692714606 0.675115446 1.019360736 0.896627062 0.818735529 0.815327708 1.03975201 1.14645673 0.914237212 1 22.66826158 5.909590255 0.309484569 1.046482469 3.07E-21 0.465902173 0.106412162 13.67994134 0.604953355 0.1196409 6.184116876 812063.995 -5.909590255 -1.046482469 SKPNLPSES(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 4 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 SKPNLPS(0.027)ES(0.973)R;SKPNLPS(0.002)ES(0.998)R;SKPNLPS(0.008)ES(0.992)R;SKPNLPSES(1)R 130.15 0.00074747 1728950000 2487830 2264130 2686820 3016570 2577780 2577000 3031320 3550950 3684830 4071760 TRUE FALSE 2390602.853 2199559.229 3172388.142 3172255.539 2660696.635 2629108.706 3068418.201 3477621.642 3266543.546 3795976.068 0.629772899 0.579444967 0.835723957 0.835689025 0.700925556 0.692604131 0.808334443 0.916133711 0.860527961 1 21.85603947 5.909727622 0.10142409 1.157784614 7.67E-20 0.644103759 0.074692369 52.34766017 0.607772836 1.228296539 8.54913866 812320.8907 -5.909727622 -1.157784614 SNETQNPHKPS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SNETQNPHKPSPSR 14 1 A0A5S6SZ32;Q96LW4-2;Q96LW4 A0A5S6SZ32 PRIMPOL DNA-directed primase/polymerase protein 1 SNETQNPHKPS(0.999)PS(0.001)R;SNETQNPHKPS(1)PSR;SNETQNPHKPS(1)PSR;SNETQNPHKPS(1)PSR 199.76 1.22E-08 690690000 656266 692250 562334 661040 638940 711930 702370 640491 752350 780650 TRUE FALSE 630618.3992 672507.7078 663960.2629 695156.3536 659492.0854 726325.7124 710965.8142 627264.637 666946.3821 727775.8802 0.866500823 0.924058802 0.91231419 0.95517916 0.906174694 0.998007398 0.976902139 0.861892588 0.916417266 1 19.47313471 5.913857241 1.013422623 0.936633946 0.276518594 0.22529141 0.041376997 30.03541728 3.818033773 0.012847512 36.96808923 820081.9266 -5.913857241 -0.660115352 EQGDGAEDEEWDD ddPTM_BT-474_Pertuzumab_2h_R1 2 EQGDGAEDEEWDD 13 0 Q7Z6K5;H0YMP5 Q7Z6K5 ARPIN Arpin 0 ; 202.65 2.14E-07 516680000 1051250 1140890 909410 1105750 1085110 1100390 1141770 1156170 1192230 1179600 FALSE TRUE 1010165.988 1108352.934 1073760.617 1162817.89 1120013.549 1122640.64 1155743.323 1132294.685 1056893.049 1099704.641 0.918579362 1.007864196 0.976408188 1.057391091 1.018467602 1.020856508 1.050957938 1.02963527 0.961069917 1 20.06868467 5.914875498 1.043251514 1.021489413 1.61E-10 0.498361796 0.02845252 13.6292777 1.736126876 0.008073415 26.97426918 822006.966 -5.914875498 -1.021489412 SLDAFPEDFCR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDAFPEDFCR 11 0 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PK59;Q96KG9-4;E9PPN3;Q96KG9-5;Q96KG9-6 E9PS17 SCYL1 N-terminal kinase-like protein 0 ; 152.28 7.68E-05 348845000 267710 300390 230390 288380 304790 267960 306830 317010 298400 292850 FALSE TRUE 257247.5972 291823.1713 272026.598 303263.3264 314593.8472 273378.3348 310585.0773 310463.6327 264526.883 273015.0087 0.942247089 1.068890581 0.996379647 1.110793607 1.152295065 1.001330792 1.137611734 1.137166906 0.968909674 1 18.05862074 5.91503853 0.927896192 1.081463391 1.48E-14 0.205218264 0.0665332 21.2246412 2.630110307 0.020018188 38.14499471 822315.6021 -5.91503853 -1.081463391 EELVER ddPTM_BT-474_Pertuzumab_2h_R1 1 EELVER 6 0 Q13435;E9PPJ0;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 97.473 0.095458 231070000 320090 360440 274600 362350 344670 350400 345570 372710 390120 372660 FALSE TRUE 307580.5289 350160.6041 324226.3284 381050.9269 355756.6236 357485.3281 349799.189 365013.4083 345835.2131 347419.4063 0.885329154 1.007890169 0.933241847 1.096803806 1.023997558 1.028973401 1.006849884 1.050641967 0.995440113 1 18.40631882 5.915246404 0.885000797 1.027170579 1.12E-09 0.5129338 0.038858672 11.09952048 1.349546865 0.011537168 17.81155327 822709.2952 -5.915246404 -1.027170578 S(ph)PSSVTGNALWK ddPTM_BT-474_Pertuzumab_2h_R1 4 SPSSVTGNALWK 12 0 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 S(0.996)PS(0.004)SVTGNALWK;S(0.874)PS(0.126)SVTGNALWK;S(0.999)PS(0.001)SVTGNALWK;S(0.966)PS(0.034)SVTGNALWK 301.62 1.55E-36 2887530000 1131360 1109540 1310120 1364120 1330020 1471180 1506360 1640670 2004540 1876870 TRUE FALSE 1087145.2 1077897.006 1546887.827 1434522.397 1372801.301 1500928.268 1524795.284 1606789.591 1776993.023 1749747.923 0.621315325 0.616029881 0.884063245 0.819845178 0.784570899 0.857796856 0.871437116 0.918297756 1.015570871 1 20.73871566 5.916746712 0.235675009 1.011791648 2.58E-13 0.793589543 0.05875629 8.726506197 0.266768884 0.09072978 2.821130138 825556.3299 -5.916746712 -1.011791648 SS(ph)MEMEGIFNHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSMEMEGIFNHK 12 0 O75962-5;O75962;E7EPJ7;O75962-4;O75962-2;E7EWP2 O75962-5 TRIO Triple functional domain protein 1 S(0.348)S(0.652)MEMEGIFNHK 207.04 5.35E-08 277740000 299260 356090 253750 370540 295810 370720 348530 340950 389830 388530 TRUE FALSE 287564.5884 345934.6618 299608.2696 389663.6138 305324.9973 378216.2124 352795.4144 333909.2634 345578.1327 362214.517 0.793906856 0.955054658 0.82715699 1.075781327 0.842939703 1.044177399 0.973995789 0.921854999 0.954070355 1 18.46648484 5.918185985 0.786150361 0.962288669 1.72E-09 0.31100466 0.073442161 16.91362723 1.923188266 0.022966547 21.81958319 828296.8025 -5.918185985 -0.962288668 GEEGHDPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GEEGHDPK 8 0 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 101.64 0.0052489 1216363000 3030190 2611610 3082140 3344430 2968980 2791920 3524520 3617670 3968710 4311470 FALSE TRUE 2911766.825 2537129.44 3639151.26 3517036.433 3064479.938 2848374.535 3567654.13 3542963.85 3518198.679 4019450.297 0.724419164 0.63121304 0.905385312 0.875004335 0.762412696 0.708647781 0.887597524 0.881454823 0.87529349 1 21.93856678 5.919166574 0.052882651 1.373872864 1.99E-10 0.487954627 0.076518515 262.9813938 1.582114109 11.89263258 34.02257439 830169.1193 -5.919166574 -1.373872864 SGTSSPQS(ph)PVFR ddPTM_BT-474_Pertuzumab_2h_R1 6 SGTSSPQSPVFR 12 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 SGT(0.003)S(0.049)S(0.226)PQS(0.722)PVFR;SGTSS(0.001)PQS(0.999)PVFR;SGTSSPQS(1)PVFR;SGTSSPQS(1)PVFR;SGTSS(0.004)PQS(0.996)PVFR;SGTSS(0.001)PQS(0.999)PVFR 298.3 2.38E-36 7970380000 2393460 2597190 2108110 2539570 2546340 2454000 2578340 2836400 2758750 2722270 TRUE FALSE 2299920.937 2523120.684 2489092.372 2670637.512 2628245.339 2503621.561 2609894.496 2777827.349 2445588.266 2537888.228 0.906234133 0.994181168 0.980773047 1.052306986 1.035603266 0.986497961 1.028372514 1.094542824 0.963631195 1 21.2751971 5.920254595 0.815430359 1.030051012 0.216860581 0.452885287 0.036439582 11.94318058 1.383312365 0.01230155 13.66116495 832251.5155 -5.920254595 -0.813190431 VFPEHIGEDVLRPAMLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFPEHIGEDVLRPAMLAK 18 1 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 93.768 0.0012546 270890000 270610 254640 238730 279380 284800 249870 344310 310820 354150 392930 FALSE TRUE 260034.262 247377.9165 281873.8215 293798.8353 293960.8506 254922.5426 348523.7688 304401.4584 313948.3767 366316.5011 0.709862267 0.675311966 0.769481639 0.802035492 0.802477775 0.695907888 0.95142798 0.830979378 0.857041317 1 18.48273116 5.922406851 0.064907703 1.30030999 1.73E-11 0.676283371 0.057377424 106.7924302 0.787913905 4.025385075 14.52642914 836386.1856 -5.922406851 -1.30030999 DIIVIGNDITYR ddPTM_BT-474_Pertuzumab_2h_R1 4 DIIVIGNDITYR 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;; 179.19 4.89E-05 439912000 392593 447830 394210 483690 493970 512686 543567 519726 596828 638725 FALSE TRUE 377250.0315 435058.3269 465452.5162 508653.2989 509858.9937 523052.8622 550219.3355 508993.4765 529078.5875 595463.5868 0.633540052 0.730621211 0.781664113 0.854213944 0.856238744 0.878396049 0.924018442 0.854785226 0.888515434 1 19.18365376 5.9226891 0.395998133 0.919459551 1.71E-20 0.884321405 0.033178887 4.488039029 0.268075374 0.024534406 2.368150984 836929.9318 -5.9226891 -0.919459551 KPTETQELVQQVLSLATQDSDNPDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KPTETQELVQQVLSLATQDSDNPDLR 26 1 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 ; 324.02 2.39E-82 1470430000 399530 438120 409480 491670 505400 472350 568450 597850 585020 630610 FALSE TRUE 383915.9259 425625.2466 483482.1448 517045.1476 521656.65 481901.2406 575406.8611 585504.1886 518610.9822 587898.223 0.653031275 0.723977774 0.822390893 0.879480712 0.887324761 0.819701815 0.97875251 0.995927808 0.882144157 1 19.16520689 5.923479222 0.332215098 0.981634713 2.83E-11 0.819428405 0.046157824 6.077260806 0.292557128 0.045308837 2.7968141 838453.9629 -5.923479222 -0.981634713 ETDVVNFDDIASSENLLHLTANRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 ETDVVNFDDIASSENLLHLTANRPK 25 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ; 240.75 8.33E-39 238150000 263100 321750 249409 308480 287970 320550 312370 331760 367040 365020 FALSE TRUE 252817.7611 312574.005 294482.7544 324400.6898 297232.8166 327031.7406 316192.8775 324909.0401 325375.158 340296.8703 0.74293296 0.918533294 0.865370152 0.953287315 0.873451514 0.961018949 0.929167751 0.954781159 0.956150898 1 18.37643436 5.924939502 0.68667723 0.947055499 1.10E-44 0.709902755 0.037351542 7.038386615 0.722248238 0.013059476 7.524586459 841277.9426 -5.924939502 -0.947055499 DRGEWDSLTPEAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRGEWDSLTPEAR 13 1 B7Z7P0;Q14139;Q14139-2 B7Z7P0 UBE4A Ubiquitin conjugation factor E4 A 0 ; 164.88 3.31E-05 392070000 252220 293850 237430 276890 273350 290070 281770 313920 360360 370160 FALSE TRUE 242362.9636 285469.6857 280338.8826 291180.3261 282142.551 295935.4141 285218.3855 307437.4423 319453.4436 345088.7335 0.702320708 0.827235601 0.812367532 0.843783925 0.817594212 0.857563245 0.826507382 0.890893885 0.925713918 1 18.39660785 5.925785547 0.04159517 1.465244889 5.51E-14 0.831134043 0.030570986 183.2838079 0.866197495 9.931819197 22.8120425 842918.4243 -5.925785547 -1.465244889 RPEKPVPPPPPIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPEKPVPPPPPIAK 14 2 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 72.417 0.021758 356390000 1246400 1210600 1290100 1681800 1378100 1556900 1535100 1772900 1919000 1996600 FALSE TRUE 1197689.31 1176074.873 1523249.768 1768597.9 1422427.838 1588381.585 1553887.013 1736288.995 1701163.165 1861368.504 0.643445566 0.631833445 0.818349384 0.950160001 0.764183898 0.853340745 0.834808911 0.932802394 0.913931423 1 20.82793227 5.926672897 0.336003677 0.938287593 1.82E-35 0.692481236 0.065585327 8.987429779 0.438187331 0.062918418 4.00652936 844642.4349 -5.926672897 -0.938287593 TSSVSSISQVS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 TSSVSSISQVSPER 14 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 TSSVSSISQVS(1)PER;TSSVSSISQVS(1)PER 337.49 1.14E-68 500790000 159852 172426 150705 191675 196262 208704 212482 233204 244555 254468 TRUE FALSE 153604.8071 167508.5793 177940.7459 201567.3697 202574.9455 212924.1379 215082.4183 228388.2559 216794.1417 237232.6557 0.647485932 0.706094103 0.750068516 0.849661144 0.853908349 0.897533003 0.90663074 0.962718456 0.913846119 1 17.85594309 5.929081044 0.27395011 0.99562829 8.10E-15 0.968576613 0.019129686 2.407627188 0.089649917 0.021950783 0.905563489 849338.9569 -5.929081044 -0.99562829 EAASS(ph)PAGEPLR ddPTM_BT-474_Pertuzumab_2h_R1 5 EAASSPAGEPLR 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 EAAS(0.005)S(0.995)PAGEPLR;EAAS(0.015)S(0.985)PAGEPLR;EAAS(0.229)S(0.771)PAGEPLR;EAAS(0.015)S(0.985)PAGEPLR;EAASS(1)PAGEPLR 246.63 1.54E-16 3479830000 1958240 2164770 1925173 2201570 2157604 2374110 2294630 2372470 2610580 2727310 TRUE FALSE 1881709.816 2103032.879 2273094.586 2315193.292 2227005.292 2422116.131 2322712.368 2323477.665 2314237.903 2542586.864 0.740076904 0.827123316 0.894008625 0.910566055 0.875881695 0.952618833 0.91352331 0.913824302 0.910190301 1 21.27786563 5.929437622 0.638446695 0.927817076 4.79E-11 0.805242395 0.029431175 5.261208356 0.506684801 0.011236835 5.029051527 850036.5927 -5.929437622 -0.927817076 GFGDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFGDLK 6 0 P24534;C9JZW3;F2Z2G2;F8WF65;F8WFC9 P24534 EEF1B2 Elongation factor 1-beta 0 100.82 0.086601 540170000 949490 928690 825960 934690 940590 1049600 1064400 1039700 1238000 1211900 FALSE TRUE 912382.8811 902204.6705 975229.3454 982929.4629 970844.9316 1070823.631 1077426.446 1018229.832 1097467.43 1129816.934 0.807549306 0.798540581 0.863174658 0.869990026 0.859294017 0.947785079 0.953629224 0.901234352 0.971367482 1 20.1076576 5.929505573 0.180816584 1.015914532 0.46618566 0.85766846 0.024720131 9.668036757 0.209870331 0.063436056 1.278383653 850169.6031 -5.929505573 -0.549728872 KRS(ph)PPLGGAPSPSSLSLPPSTGFPLQASGVPSPYLSSLASSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRSPPLGGAPSPSSLSLPPSTGFPLQASGVPSPYLSSLASSR 42 2 I3NI13;I3L270;Q8NBZ0 I3NI13 INO80E INO80 complex subunit E 1 KRS(0.556)PPLGGAPS(0.117)PS(0.151)S(0.151)LS(0.025)LPPSTGFPLQASGVPSPYLSSLASSR 151.73 5.07E-14 198020000 209990 250450 205260 226630 242030 266700 246900 256380 318750 251700 TRUE FALSE 201783.3586 243307.4112 242355.048 238326.4015 249815.1148 272092.8567 249921.6361 251085.6634 282566.8363 234652.1348 0.859925518 1.036885564 1.032826947 1.015658356 1.064618973 1.159558412 1.065072927 1.070033578 1.204194611 1 17.84016406 5.930910255 0.668182712 1.092880562 5.23E-14 0.564640528 0.0578567 9.704630296 0.968117466 0.021852704 11.58249338 852923.8435 -5.930910255 -1.092880562 ENFSCLTR ddPTM_BT-474_Pertuzumab_2h_R1 3 ENFSCLTR 8 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;C9JF79;C9JRL4 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ;; 144.9 0.0013446 1287940000 1287600 1566590 1165180 1591950 1436830 1562130 1650760 1697870 1588930 1745480 FALSE TRUE 1237279.168 1521912.387 1375753.945 1674110.73 1483046.942 1593717.339 1670962.495 1662808.391 1408561.328 1627257.085 0.760346463 0.935262413 0.845443512 1.02879302 0.91137839 0.979388785 1.026858331 1.021847381 0.865604667 1 20.63401076 5.931136513 0.625412961 0.983850338 4.63E-17 0.506232641 0.060776752 10.29654838 0.972771367 0.024351598 10.17232527 853368.3142 -5.931136513 -0.983850338 AQSNGSGNGS(ph)DSEMDTSSLER ddPTM_BT-474_Pertuzumab_2h_R1 4 AQSNGSGNGSDSEMDTSSLER 21 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AQSNGSGNGS(0.999)DS(0.001)EMDTSSLER;AQSNGSGNGS(0.999)DS(0.001)EMDTSSLER;AQSNGSGNGS(0.67)DS(0.33)EMDTSSLER;AQSNGS(0.007)GNGS(0.987)DS(0.006)EMDTSSLER 413.62 7.01E-152 1042570000 693830 765690 662204 806590 700810 803490 822670 885560 827080 889130 TRUE FALSE 666714.3565 743853.2709 781878.9934 848218.2066 723352.1901 819737.1183 832738.0815 867272.8765 733193.3458 828908.4331 0.804328114 0.897388953 0.943263408 1.023295424 0.872656329 0.988935672 1.00462011 1.04628309 0.884528757 1 19.66085322 5.931895498 0.692163682 0.984992601 8.68E-18 0.48766401 0.053479434 10.91023283 1.116957881 0.020270005 12.28012888 854860.9869 -5.931895498 -0.984992601 AADEDWDSELEDDLLGEDLLSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AADEDWDSELEDDLLGEDLLSGK 23 0 Q96EV2;A8MTF7;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 0 145.75 1.36E-07 7118500 4413.7 4183.1 4649.1 5585.7 4970 5822.3 6123.1 5621.4 7592.5 7728.2 FALSE TRUE 4241.207724 4063.802084 5489.295789 5873.978646 5129.864564 5940.030895 6198.036329 5505.316126 6730.63123 7204.76213 0.58866728 0.564043893 0.761898268 0.815291128 0.712010261 0.824458988 0.860269391 0.764121844 0.934192012 1 12.81473508 5.934410021 0.16804246 1.012058167 8.26E-15 0.784637859 0.06054766 15.03917804 0.298840592 0.190896409 3.394870444 859824.9065 -5.934410021 -1.012058167 TDSTSDGRPAWMR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 199.8 1.05E-07 2937560000 1750450 1928920 1705990 2039800 1944960 2254810 2366620 2301880 2655400 2530800 FALSE TRUE 1682040.479 1873909.09 2014300.343 2145074.322 2007521.405 2300403.803 2395583.403 2254345.374 2353970.124 2359386.662 0.712914295 0.794235689 0.853738972 0.90916608 0.850865794 0.975000766 1.01534159 0.955479409 0.99770426 1 21.16998044 5.934432583 0.32471593 1.011305131 0.129601795 0.896939608 0.030785937 4.478863683 0.208178961 0.03041765 1.806708771 859869.5755 -5.934432583 -0.881703335 SKPDLESS(ph)LESLVFDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKPDLESSLESLVFDLR 17 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 SKPDLES(0.024)S(0.976)LESLVFDLR;SKPDLES(0.041)S(0.959)LESLVFDLR 270 5.79E-29 188596000 145739 153214 152977 188560 173652 188534 208909 211327 232556 263620 TRUE FALSE 140043.3588 148844.4867 180623.3469 198291.6042 179237.6743 192346.2867 211465.6908 206963.0236 206157.2178 245764.7826 0.569826797 0.605637981 0.734943978 0.806834902 0.729305771 0.782643813 0.860439354 0.842118311 0.838839543 1 17.90691867 5.940477508 0.172737517 1.005232955 2.94E-16 0.885240529 0.040369067 9.701743709 0.198734195 0.119359906 2.238195507 871921.744 -5.940477508 -1.005232955 SEIDLFNIR ddPTM_BT-474_Pertuzumab_2h_R1 6 SEIDLFNIR 9 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 241.52 4.88E-10 1091421000 1456125 1555506 1277468 1625084 1218217 911825 1308760 1487169 1581781 1856270 FALSE TRUE 1399218.025 1511144.492 1508334.885 1708954.78 1257402.056 930262.7262 1324776.996 1456458.44 1402223.852 1730543.18 0.808542683 0.873219755 0.871596215 0.987525073 0.726593864 0.537555339 0.765526692 0.841619243 0.81027961 1 20.72279351 5.942637429 12.08054293 0.813584311 0.766203524 0 0.126023461 0 0 0.028892008 0 876268.9616 -5.942637429 -0.047380788 STNS(ph)PTIVSPAIVSPTQDSRPNMSR ddPTM_BT-474_Pertuzumab_2h_R1 3 STNSPTIVSPAIVSPTQDSRPNMSR 25 1 A0A2U3U043 A0A2U3U043 1 S(0.004)T(0.014)NS(0.968)PT(0.014)IVSPAIVSPTQDSRPNMSR;S(0.001)T(0.024)NS(0.759)PT(0.216)IVSPAIVSPTQDSRPNMSR;S(0.001)T(0.019)NS(0.973)PT(0.008)IVSPAIVSPTQDSRPNMSR 152.15 7.94E-08 1050540000 296948 280605 290019 321296 323587 318458 329222 386438 431310 458430 TRUE FALSE 285342.9439 272602.4201 342431.8847 337878.1251 333995.4697 324897.439 333251.1173 378457.9203 382349.497 427380.1278 0.667656087 0.637845334 0.801234925 0.790579868 0.781495086 0.760207174 0.779753422 0.88552999 0.894635647 1 18.7051603 5.945414998 0.079392622 1.234166237 1.44E-10 0.837178839 0.040853636 51.01226056 0.45800079 1.55701949 7.431602756 881891.178 -5.945414998 -1.234166237 DKITTR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKITTR 6 1 P49720 P49720 PSMB3 Proteasome subunit beta type-3 0 ; 102.72 0.032194 426930000 442320 416930 382440 409360 417250 476280 410600 474500 524880 501980 FALSE TRUE 425033.6454 405039.5646 451555.4153 430487.1187 430671.2252 485910.7079 415625.0456 464701.4092 465297.8229 467980.4475 0.908229495 0.865505315 0.964902311 0.919882702 0.920276109 1.038314123 0.888124809 0.992993215 0.994267657 1 18.83608873 5.947916717 0.201854162 1.008578532 0.704660205 0.373945922 0.042482142 23.67384227 0.584992612 0.079043535 1.946975277 886985.9022 -5.947916717 -0.303918327 SAEPSPTVMST(ph)SLGSNLSELDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.006)T(0.767)S(0.228)LGSNLSELDR 359.02 2.07E-95 144570000 186380 168330 154890 142050 166190 161070 145090 182010 187360 175730 TRUE FALSE 179096.0635 163529.3932 182882.0685 149381.2175 171535.6523 164326.9458 146865.6548 178251.4299 166091.6783 163827.6506 1.093198022 0.998179444 1.116307704 0.911819324 1.047049455 1.003047686 0.89646439 1.088042399 1.01381957 1 17.32181935 5.948257301 0.750905179 1.004209932 1.499443582 0.141760442 0.064222168 30.29185994 3.212592206 0.021898667 19.13001718 887681.7696 -5.948257301 0.49523365 QQGDHSLKEHELLEQQKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQGDHSLKEHELLEQQKR 18 2 Q13435;H0YCG1 Q13435 SF3B2 Splicing factor 3B subunit 2 0 203.89 3.64E-16 299540000 411460 405450 223850 212860 289620 345150 265100 9008 356340 186840 FALSE TRUE 395379.6883 393886.963 264304.6745 223845.7301 298935.8903 352129.1695 268344.3731 8821.981652 315889.7771 174185.1604 2.269881587 2.261311825 1.51737768 1.285102184 1.716196085 2.021579615 1.540569659 0.050647148 1.81352864 1 17.41026219 5.95024859 0.240233732 0.825934348 4.770524408 0.332451859 0.514504249 20.64012619 0.638852923 0.803533771 26.64460154 891761.2367 -5.95024859 3.94459006 RLS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSPEK 6 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 RLS(1)PEK;RLS(1)PEK;RLS(1)PEK 88.37 0.031471 2749250000 1317210 1275660 1502450 1609550 1563480 1438530 1930810 1984680 2057440 2163890 TRUE FALSE 1265731.977 1239279.426 1773976.137 1692619.068 1613770.754 1467618.062 1954439.83 1943695.664 1823888.037 2017327.803 0.627429997 0.614317328 0.879369299 0.839040173 0.799954649 0.727505991 0.968826101 0.963500162 0.904110891 1 20.9440141 5.950830887 0.23710816 1.006214926 4.41E-14 0.675947078 0.074854511 11.71548533 0.356288987 0.117265039 3.802735991 892957.7016 -5.950830887 -1.006214926 DLAEWLEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLAEWLEK 8 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;; 140.5 0.0015088 623114000 619808 628968 709803 708817 748048 741044 854698 904787 1030447 1082020 FALSE TRUE 595585.2181 611030.4485 838080.1916 745399.1303 772109.6433 756028.4174 865158.0498 886102.8323 913474.9765 1008733.822 0.590428521 0.605740023 0.830823924 0.738945314 0.765424562 0.74948257 0.857667336 0.878430775 0.905565925 1 19.9441141 5.952542629 0.151815174 1.056493892 3.53E-16 0.832617241 0.050124498 14.43631933 0.254068298 0.20557838 3.074106433 896484.1776 -5.952542629 -1.056493892 SAS(ph)TLCLPSVGAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASTLCLPSVGAAR 14 0 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 S(0.002)AS(0.931)T(0.067)LCLPSVGAAR 282.32 2.35E-33 237900000 231380 153090 115360 135440 112090 87420 103250 194470 108670 100220 TRUE FALSE 222337.4138 148724.0231 136208.1182 142430.0746 115695.4766 89187.6923 104513.6044 190454.1265 96334.23718 93432.01013 2.379670666 1.591788755 1.4578314 1.524424814 1.238285214 0.954573194 1.118605971 2.0384248 1.031062449 1 16.51162929 5.953972296 0.995159527 1.331593257 11.77768816 0.53623722 0.305435257 16.01656285 1.880412976 0.09821171 308.6946203 899440.2046 -5.953972296 10.4460949 KGPGAGSALDDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KGPGAGSALDDGR 13 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 77.24 0.042473 247760000 627500 713910 603090 733030 727780 727660 799220 819220 861890 802550 FALSE TRUE 602976.6063 693549.9858 712081.7787 770861.7661 751189.7047 742373.7838 809001.0934 802302.8207 764051.8605 748192.5737 0.805910975 0.926967214 0.951735962 1.030298607 1.004005828 0.992222871 1.081273888 1.072321283 1.021196798 1 19.51305012 5.960583863 0.557986501 1.046136334 1.07E-11 0.849806309 0.029339298 4.769040244 0.39563926 0.014485744 4.373247428 913237.7656 -5.960583863 -1.046136334 GTLS(ph)DSEIETNSATSTIFGK ddPTM_BT-474_Pertuzumab_2h_R1 5 GTLSDSEIETNSATSTIFGK 20 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6;F8W8U2 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 GT(0.011)LS(0.988)DS(0.001)EIETNSATSTIFGK;GTLS(1)DSEIETNSATSTIFGK;GT(0.001)LS(0.999)DSEIETNSATSTIFGK;GTLS(1)DSEIETNSATSTIFGK;GTLS(1)DSEIETNSATSTIFGK 456.47 8.78E-199 2067862000 1095787 1164853 964747 1191586 1185232 1211525 1222252 1373201 1467657 1399495 TRUE FALSE 1052962.433 1131632.533 1139098.244 1253083.896 1223356.064 1236022.866 1237210.286 1344843.919 1301054.73 1304705.957 0.807049609 0.867346797 0.873068937 0.96043395 0.937648868 0.947357417 0.948267523 1.030763991 0.997201494 1 20.31529327 5.963489284 0.300336467 1.017189485 0.41015253 0.881380525 0.022583143 5.095882728 0.210964166 0.02512378 1.300474293 919367.7887 -5.963489284 -0.607036955 WLEASEEER ddPTM_BT-474_Pertuzumab_2h_R1 3 WLEASEEER 9 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ;; 148.27 0.00021035 385830000 382636 396450 322405 362120 382940 402790 387211 401280 388150 427910 FALSE TRUE 367682.1621 385143.6342 380670.7554 380809.0566 395257.6129 410934.6898 391949.804 392993.4278 344088.8393 398927.2746 0.921677172 0.965448238 0.954235971 0.954582654 0.990801176 1.030099259 0.982509417 0.985125492 0.862535257 1 18.60576624 5.966312131 0.841805116 0.975084506 0.586379578 0.105709454 0.041695135 35.30601859 3.874704686 0.013588982 20.4174855 925363.0002 -5.966312131 -0.388704929 LQQLFNHTMFILEQEEYQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQQLFNHTMFILEQEEYQR 19 0 P35579;P35579-2;A0A494C024;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3 P35579;P35580;P35749 MYH9;MYH10;MYH11 Myosin-9;Myosin-10;Myosin-11 0 ; 272.32 2.39E-39 1565160000 245789 270681 216045 254549 258949 272845 312095 252846 262870 277145 FALSE TRUE 236183.2941 262961.4429 255089.1374 267686.3044 267278.3298 278362.1128 315914.512 247624.6417 233030.0996 258373.7223 0.914114996 1.017756142 0.987287465 1.03604307 1.03446406 1.07736232 1.222703722 0.95839716 0.90191099 1 17.97909982 5.967543641 0.909124 1.038029697 3.19E-11 0.14903155 0.079901278 32.7504249 3.685128031 0.026104316 55.95620458 927990.7372 -5.967543641 -1.038029697 RRES(ph)ASSSSSVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 RRESASSSSSVKK 13 3 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 RRES(1)ASSSSSVKK 134.85 0.00050138 105470000 199450 177290 132890 124920 158450 155750 133740 181450 157860 125320 TRUE FALSE 191655.2735 172233.8628 156906.1791 131367.1362 163546.6882 158899.3717 135376.7501 177702.9941 139940.3946 116831.9648 1.640435251 1.474201543 1.343007279 1.124410913 1.399845397 1.360067615 1.158730407 1.521013487 1.197792016 1 16.83407552 5.969110092 0.032772941 2.55E-23 3.057957851 0.449190518 0.140214873 889.332576 3.27979644 108.8982911 211.4001631 931343.9385 -5.969110092 3.057957851 TS(ph)PAPWK ddPTM_BT-474_Pertuzumab_2h_R1 3 TSPAPWK 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.105)S(0.895)PAPWK;T(0.002)S(0.998)PAPWK;T(0.024)S(0.976)PAPWK 126.62 0.0041269 5034300000 10718600 10296700 11639200 11937200 11772000 10993400 13497700 14086000 16886900 17239300 TRUE FALSE 10299705.26 10003048.2 13742662.35 12553280.32 12150657.07 11215694.08 13662888.89 13795119.18 14969969.91 16071666.86 0.640861048 0.62240266 0.855086313 0.781081417 0.756029675 0.697855063 0.850122704 0.858350245 0.931450984 1 23.93801623 5.96921043 0.088914893 1.202062393 1.44E-12 0.710045731 0.062754115 58.58634292 0.586050326 1.565914065 8.9753663 931559.1382 -5.96921043 -1.202062393 EFQQNNWHAVGCGFR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFQQNNWHAVGCGFR 15 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;E5RJR3;Q9NZL9-5 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 69.331 0.049977 139130000 60545 60384 62084 59251 72450 65704 71775 77976 80969 76831 FALSE TRUE 58178.83446 58661.90744 73303.95985 62308.95121 74780.42005 67032.5799 72653.40392 76365.76835 71777.73857 71627.16794 0.812245355 0.818989625 1.023409999 0.869906671 1.04402313 0.935854116 1.014327468 1.066156468 1.002102144 1 16.12821928 5.972599372 0.421351406 1.028577824 0.198235739 0.583913569 0.057359318 9.040867997 0.560312212 0.037298316 4.677767789 938856.8333 -5.972599372 -0.830342085 EEDFHPELESLDGDLDPGLPSTEDVILK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEDFHPELESLDGDLDPGLPSTEDVILK 28 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 ;; 167.72 5.42E-12 192483000 229273 222962 255993 299307 267239 274245 314151 325692 394580 402643 FALSE TRUE 220312.7577 216603.3421 302256.6296 314754.2701 275834.9851 279790.4218 317995.6739 318966.3464 349788.9326 375371.631 0.586919041 0.577037059 0.805219693 0.83851374 0.73483173 0.745369119 0.847148926 0.849734823 0.931847012 1 18.5179601 5.974734915 0.164473723 1.030835098 7.27E-12 0.780761257 0.060189417 16.10293606 0.308248536 0.206402762 3.627660785 943484.8162 -5.974734915 -1.030835098 TLLEQLDDDQ ddPTM_BT-474_Pertuzumab_2h_R1 4 TLLEQLDDDQ 10 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 312.24 1.45E-41 579810000 926425 1027207 837734 1018698 997039 998795 1104525 1057028 1154407 1097104 FALSE TRUE 890219.2868 997912.0621 989131.1691 1071273.126 1029109.665 1018991.319 1118042.507 1035200.002 1023363.557 1022796.169 0.870378003 0.975670512 0.967085329 1.047396498 1.00617278 0.996279953 1.09312348 1.012127376 1.000554742 1 19.96408723 5.979508954 0.769731577 1.025545594 6.54E-11 0.68379461 0.030540567 8.09731628 0.834874585 0.010302704 11.03895964 953913.4091 -5.979508954 -1.025545594 EELIAELQDCEGLIVR ddPTM_BT-474_Pertuzumab_2h_R1 3 EELIAELQDCEGLIVR 16 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YFM8;A0A286YER3;A0A286YFC8;A0A286YFB2;A0A286YF34 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ;; 222.29 2.27E-14 154535000 168047 191995 148213 181924 188659 204559 189512 187637 215217 199762 FALSE TRUE 161479.5375 186519.4906 174998.3861 191313.1194 194727.3881 208695.3231 191831.3045 183762.2304 190786.4684 186231.9418 0.867088298 1.001544036 0.939679758 1.027284136 1.045617557 1.120620454 1.030066608 0.986738519 1.024456205 1 17.50674101 5.982898744 0.757595616 1.031931503 1.93E-08 0.574808643 0.041329612 11.73219128 1.193594515 0.015560421 15.78096869 961388.1045 -5.982898744 -1.031931484 GLDGPRPNQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GLDGPRPNQK 10 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 108.43 0.0019626 917320000 455240 512500 433670 515620 516490 521210 566990 568830 603500 571850 FALSE TRUE 437448.7175 497884.0018 512043.8159 542231.21 533103.3699 531749.2233 573928.9932 557083.4617 534993.2101 533118.0901 0.820547503 0.933909411 0.960469782 1.017093999 0.999972388 0.997432338 1.076551338 1.044953214 1.003517269 1 19.02409561 5.98302535 0.605973849 1.032584454 5.96E-11 0.86582132 0.024355037 4.565585735 0.397741647 0.010797758 4.611699381 961668.409 -5.98302535 -1.032584454 LITLEEEMTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LITLEEEMTK 10 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 155.42 2.96E-05 35255000 44208 47352 44417 48038 56601 52609 52247 60368 59208 63504 FALSE TRUE 42480.30249 46001.56732 52444.13995 50517.24694 58421.62257 53672.79003 52886.41441 59121.3797 52486.95606 59202.81752 0.717538527 0.777016521 0.885838583 0.853291263 0.986804767 0.906591819 0.893309079 0.998624427 0.886561793 1 15.85337822 5.983624905 0.464694385 0.955901964 9.09E-13 0.744289736 0.044499222 6.54478659 0.446228052 0.025415406 4.396976776 962996.9344 -5.983624905 -0.955901964 ELPTAFDYVEFTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELPTAFDYVEFTR 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 99.539 0.0065474 93813000 41107 46498 38842 45108 50045 48740 45760 52335 53793 55561 FALSE TRUE 39500.49299 45171.92257 45861.61344 47436.02929 51654.74287 49725.55619 46320.02457 51254.26396 47686.64416 51797.80398 0.762590109 0.872081808 0.885396868 0.915792285 0.997238085 0.95999352 0.894246879 0.989506505 0.920630615 1 15.66060331 5.983932528 0.605799386 0.95966843 3.19E-08 0.758523843 0.033956019 6.505649038 0.566086551 0.014279324 6.106537018 963679.2945 -5.983932528 -0.959668398 EQMYNILMWIHDNYRDPESETDNDSQEIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQMYNILMWIHDNYRDPESETDNDSQEIFK 30 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 108.78 0.00015467 153830000 74579 83434 72096 73235 90400 77412 94445 83082 98123 91080 FALSE TRUE 71664.37023 81054.54401 85125.35097 77014.66713 93307.7981 78977.32368 95600.84616 81366.32767 86984.48841 84911.07047 0.843993249 0.954581582 1.002523587 0.907003842 1.098888491 0.930118102 1.125893781 0.958253467 1.0244187 1 16.37366504 5.986002876 0.726234366 1.013871707 1.47E-09 0.382447872 0.063612026 14.47025562 1.430426882 0.02103264 18.11947795 968284.269 -5.986002876 -1.013871706 KWS(ph)DSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KWSDSSK 7 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KWS(0.544)DS(0.445)S(0.012)K 64.439 0.04496 203090000 447450 412580 498480 510520 543990 482660 617960 588640 752250 758430 TRUE FALSE 429963.1593 400813.6224 588566.4246 536867.9984 561487.9324 492419.7159 625522.7793 576484.3783 666857.7337 707060.8606 0.608099222 0.566872874 0.832412678 0.759295314 0.79411542 0.696431868 0.884680251 0.815324975 0.9431405 1 19.43147488 5.986020331 0.139992298 1.066541593 3.67E-17 0.721561586 0.069111994 22.87166518 0.364598503 0.347240297 4.547945023 968323.1862 -5.986020331 -1.066541593 SAS(ph)PHDVDLCLVSPCEFEHRK ddPTM_BT-474_Pertuzumab_2h_R1 3 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.131)AS(0.869)PHDVDLCLVSPCEFEHRK;S(0.077)AS(0.923)PHDVDLCLVSPCEFEHRK;S(0.313)AS(0.687)PHDVDLCLVSPCEFEHRK 190.24 8.80E-18 1869410000 958070 1188430 595900 675250 727780 923540 671370 593940 813030 696260 TRUE FALSE 920627.5652 1154537.14 703592.3857 710099.7334 751189.7047 942214.6116 679586.4269 581674.9314 720738.2429 649101.69 1.418310227 1.778669133 1.083947857 1.093973016 1.157275842 1.451567029 1.046964501 0.896122966 1.110362604 1 19.30808499 5.987131752 0.319875124 0.985545109 2.80328875 0.422708838 0.191612874 14.46040376 0.641457213 0.193725309 11.9049932 970804.4359 -5.987131752 1.81774364 GDS(ph)LILEHQWELEK ddPTM_BT-474_Pertuzumab_2h_R1 3 GDSLILEHQWELEK 14 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK 256.84 1.62E-24 332884000 483680 463170 473950 510740 536570 512790 561500 604780 628940 618550 TRUE FALSE 464777.2509 449960.8451 559603.308 537099.3526 553829.2614 523158.9651 568371.805 592291.0817 557545.3679 576655.0576 0.805988337 0.780294631 0.970429897 0.931404911 0.960416898 0.907230342 0.985635689 1.027115039 0.966861143 1 19.13734906 5.993387303 0.413674963 0.998835822 0.210497703 0.709297483 0.041600267 7.533756451 0.4511162 0.029521557 3.634245949 984889.037 -5.993387303 -0.788338119 LDETDDPDDYGDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDETDDPDDYGDR 13 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 289.96 3.82E-40 8303610000 5640510 5849420 6586280 8460200 6665080 6170460 8556700 9115400 9009600 10332300 FALSE TRUE 5420072.633 5682600.269 7776567.307 8896831.936 6879468.351 6295230.929 8661419.454 8927163.805 7986867.979 9632484.118 0.562686901 0.589941307 0.807327291 0.923627989 0.714194622 0.653541792 0.899188553 0.926776904 0.829159735 1 23.19947647 5.994705177 0.205746972 0.982601843 1.79E-18 0.56285105 0.095921987 19.11810581 0.47611376 0.197081837 5.205504857 987882.2381 -5.994705177 -0.982601843 SGPTDDGEEEMEEDTVTNGS ddPTM_BT-474_Pertuzumab_2h_R1 2 SGPTDDGEEEMEEDTVTNGS 20 0 P09661 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ; 393.37 1.05E-130 402620000 566610 638250 506150 630280 604910 620580 632820 690880 701250 654420 FALSE TRUE 544466.2548 620047.7349 597622.5642 662808.8263 624367.4795 633128.5528 640564.6405 676613.0866 621647.0399 610095.5505 0.892427841 1.016312501 0.979555684 1.086401672 1.023392941 1.037753106 1.049941505 1.109028063 1.018933902 1 19.21867568 5.997016277 0.766857498 1.053714624 5.50E-14 0.594956301 0.035925689 9.726013897 0.976778041 0.012187769 13.62864533 993153.2696 -5.997016277 -1.053714624 IVEPEVVGES(ph)DSEVEGDAWR ddPTM_BT-474_Pertuzumab_2h_R1 6 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 IVEPEVVGES(0.993)DS(0.007)EVEGDAWR;IVEPEVVGES(0.865)DS(0.135)EVEGDAWR;IVEPEVVGES(0.964)DS(0.036)EVEGDAWR;IVEPEVVGES(0.999)DS(0.001)EVEGDAWR;IVEPEVVGES(0.918)DS(0.082)EVEGDAWR;IVEPEVVGES(0.999)DS(0.001)EVEGDAWR 351.48 4.16E-95 1539190000 597589 686196 553556 897320 673508 671316 991610 848116 967425 1034878 TRUE FALSE 574234.5612 666626.3619 653595.883 943630.7927 695171.9965 684890.4695 1003745.62 830602.1082 857606.9698 964784.7913 0.595194458 0.690958614 0.677452515 0.978073868 0.720546181 0.709889372 1.040382922 0.860919571 0.888910125 1 19.87984764 5.997385046 0.227917814 0.988210076 3.97E-14 0.53871378 0.101141246 16.31024127 0.462609614 0.158206786 4.99705152 993996.936 -5.997385046 -0.988210076 SSS(ph)PAPADIAQTVQEDLR ddPTM_BT-474_Pertuzumab_2h_R1 10 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 S(0.163)S(0.163)S(0.674)PAPADIAQTVQEDLR;S(0.056)S(0.118)S(0.826)PAPADIAQTVQEDLR;S(0.025)S(0.12)S(0.855)PAPADIAQTVQEDLR;S(0.144)S(0.144)S(0.712)PAPADIAQTVQEDLR;SS(0.002)S(0.998)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SS(0.002)S(0.998)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR 422.41 1.15E-168 77875289000 8693712 9389584 8459432 8863735 9178822 9968286 10304824 9861364 9802087 11977635 TRUE FALSE 8353952.124 9121802.258 9988239.541 9321193.426 9474067.146 10169851.57 10430937.52 9657723.387 8689395.177 11166379.11 0.748134381 0.81689885 0.894492247 0.834755235 0.848445772 0.91075643 0.934137863 0.864893023 0.778174831 1 23.41265811 5.997810271 0.738175412 0.884090202 1.63E-11 0.36261894 0.056807163 16.81168146 1.652137531 0.019680625 18.81389774 994970.6526 -5.997810271 -0.884090202 EGPDLDRPGSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGPDLDRPGSDR 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 95.401 0.0055338 2240700000 2190330 2317500 1869910 2187720 2225970 2317500 2168300 2370300 2500500 2303700 FALSE TRUE 2104729.482 2251407.169 2207844.333 2300628.491 2297570.347 2364361.438 2194836.304 2321352.477 2216653.723 2147668.347 0.980006752 1.048302999 1.028019217 1.071221492 1.069797555 1.100896906 1.021962403 1.08087102 1.032121056 1 21.03433979 5.998794186 1.089468519 1.057588971 0.031991536 0.3235021 0.029576019 23.04195994 2.45947308 0.007908441 49.78397056 997227.3613 -5.998794186 -1.025597435 GTPKPPGPPAQPPGPPNAS(ph)SNPDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GTPKPPGPPAQPPGPPNASSNPDLR 25 1 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 GTPKPPGPPAQPPGPPNAS(0.555)S(0.445)NPDLR;GTPKPPGPPAQPPGPPNAS(0.568)S(0.432)NPDLR 133.56 1.37E-05 1069900000 315779 331173 311600 386925 345547 337557 388432 445698 397738 427238 TRUE FALSE 303438.0076 321728.2703 367913.0515 406894.2456 356661.8331 344382.6338 393185.747 436494.1805 352588.4497 398300.7897 0.761831298 0.807752027 0.923706558 1.021575292 0.895458513 0.864629553 0.987157839 1.095890824 0.885231611 1 18.60349881 6.007073661 0.492387004 0.989971518 2.09E-11 0.496570674 0.068968879 12.15321849 0.861117108 0.041669683 9.124312025 1016421.074 -6.007073661 -0.989971518 LQQGAGLESPQGQPEPGAAS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LQQGAGLESPQGQPEPGAASPQR 23 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LQQGAGLESPQGQPEPGAAS(1)PQR;LQQGAGLESPQGQPEPGAAS(1)PQR 160.01 1.25E-11 1791700000 650720 772190 578090 870550 678000 811330 823380 821140 912760 933180 TRUE FALSE 625289.143 750167.8973 682563.7225 915479.1898 699808.4857 827735.6485 833456.7707 804183.172 809147.3114 869974.8874 0.718743899 0.862286841 0.78457865 1.052305306 0.804400789 0.951447749 0.958023942 0.924375156 0.930081228 1 19.73061423 6.009574555 0.530567993 0.945941584 6.33E-13 0.493981598 0.07021422 11.84121293 0.89724452 0.032858404 9.327389788 1022291.041 -6.009574555 -0.945941584 CTLPEHES(ph)PSQDISDACEAESTER ddPTM_BT-474_Pertuzumab_2h_R1 3 CTLPEHESPSQDISDACEAESTER 24 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 CTLPEHES(0.901)PS(0.099)QDISDACEAESTER;CTLPEHES(0.985)PS(0.015)QDISDACEAESTER;CTLPEHES(0.984)PS(0.016)QDISDACEAESTER 264.23 2.04E-44 972620000 751826 668263 794416 855617 839288 893346 947606 956504 1285276 1225824 TRUE FALSE 722443.8087 649204.7935 937984.6429 899775.4959 866284.4607 911410.0682 959203.0857 936751.8581 1139376.857 1142797.849 0.632171131 0.568083668 0.820779147 0.787344408 0.758038232 0.797525187 0.839346247 0.819700404 0.997006477 1 20.12413879 6.009605264 0.148814715 1.062212152 2.82E-16 0.768816736 0.06176527 18.57939485 0.31447562 0.261798716 3.905524297 1022363.33 -6.009605264 -1.062212152 EVRPDTQYTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVRPDTQYTGR 11 1 O43709;O43709-3;H7C0G4 O43709 WBSCR22 Probable 18S rRNA (guanine-N(7))-methyltransferase 0 ; 228.93 2.65E-12 1137380000 291580 312360 270530 304100 290160 325970 327840 320930 295510 336180 FALSE TRUE 280184.7312 303451.7986 319420.7889 319794.6374 299493.2599 332561.3367 331852.204 314302.6833 261964.9437 313410.2292 0.893987194 0.968225573 1.019177931 1.020370772 0.955595038 1.06110556 1.058842926 1.002847559 0.835853202 1 18.25769274 6.009605901 11.45938714 0.988627631 0.899862875 0 0.068014673 0 0 0.014917577 0 1022364.831 -6.009605901 -0.088764756 GREEWESAALQNANTK ddPTM_BT-474_Pertuzumab_2h_R1 2 GREEWESAALQNANTK 16 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;X6R960 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ; 247.79 2.27E-20 379530000 326160 327820 298420 314210 322520 384390 360420 378050 438280 444200 FALSE TRUE 313413.3066 318470.8946 352351.1323 330426.4158 332894.1487 392162.6292 364830.9278 370243.1354 388528.2918 414113.9383 0.756828683 0.769041718 0.850855525 0.797911843 0.803870911 0.946992103 0.880991664 0.894061033 0.938215925 1 18.65966824 6.01261798 0.123556523 1.06676859 0.342968892 0.810855696 0.033895605 22.40036774 0.310319117 0.257098361 2.693083813 1029480.157 -6.01261798 -0.723799698 GFGFVTFENIDDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVTFENIDDAK 14 0 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;K7ENX8;K7ELV6;K7EJV5;K7ELT6;K7ER40 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ; 142.07 2.21E-05 303590000 222638 275190 228434 249277 272760 273490 332930 301780 304200 308800 FALSE TRUE 213937.0608 267341.8506 269717.1053 262142.2158 281533.5731 279020.1552 337004.4969 295548.1375 269668.4913 287884.7009 0.743134526 0.928642091 0.936892806 0.910580573 0.977938641 0.969208 1.170623155 1.026619812 0.93672394 1 18.1351316 6.01556437 0.476167333 1.032031608 4.24E-16 0.58467919 0.065194667 10.50178911 0.71548296 0.039629377 7.900981963 1036488.22 -6.01556437 -1.032031608 ENSS(ph)PSVTSANLDHTKPCWYWDK ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSSPSVTSANLDHTKPCWYWDK 23 1 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 1 ENS(0.107)S(0.715)PS(0.175)VT(0.003)SANLDHTKPCWYWDK 186.35 1.67E-17 726080000 176700 140200 183150 194610 193520 179580 226970 238850 256270 273010 TRUE FALSE 169794.3686 136201.6333 216249.2791 204653.8454 199744.7466 183211.2306 229747.7268 233917.664 227179.304 254518.7895 0.66711919 0.535133903 0.849639744 0.804081482 0.784793716 0.719833813 0.902674915 0.919058528 0.892583626 1 17.95741264 6.019281937 0.175172938 1.035704047 8.07E-18 0.666590543 0.075214412 17.10756263 0.347484874 0.203912789 4.140361951 1045398.654 -6.019281937 -1.035704047 DKQS(ph)PSQANGCSDHRPIDILEMLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKQSPSQANGCSDHRPIDILEMLSR 25 2 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 DKQS(1)PSQANGCSDHRPIDILEMLSR;DKQS(0.989)PS(0.011)QANGCS(0.001)DHRPIDILEMLSR;DKQS(0.938)PS(0.062)QANGCSDHRPIDILEMLSR 259.53 2.50E-45 418810000 135247 156165 141045 157980 157116 178212 173712 178910 192733 208010 TRUE FALSE 129961.3977 151711.3271 166534.969 166133.3667 162169.7788 181815.5687 175837.9394 175215.446 170854.7578 193921.2974 0.670175991 0.78233453 0.858776067 0.856705112 0.836265954 0.937574012 0.906748984 0.903538953 0.881052056 1 17.56511173 6.019930634 0.459291737 0.922147017 2.77E-16 0.821026797 0.036064485 5.91571194 0.387632323 0.021303158 3.807861996 1046961.313 -6.019930634 -0.922147017 RNS(ph)SEAS(ph)SGDFLDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 RNSSEASSGDFLDLK 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 2 RNS(0.714)S(0.324)EAS(0.642)S(0.32)GDFLDLK 79.511 0.069035 42530000 53559 48472 55559 60700 60090 53398 70176 78686 74778 86837 TRUE FALSE 51465.85507 47089.62602 65599.7472 63832.73427 62022.84942 54477.74415 71034.83488 77061.1066 66289.51493 80955.45264 0.635730558 0.581673309 0.810319071 0.788492093 0.76613554 0.672934835 0.877455842 0.951895198 0.818839408 1 16.30484063 6.020075154 0.14304624 1.068960069 1.50E-12 0.663679038 0.073511266 25.03008513 0.404484489 0.365974533 5.095529815 1047309.769 -6.020075154 -1.068960069 SLYQSAGVAPESFEYIEAHGTGTK ddPTM_BT-474_Pertuzumab_2h_R1 5 SLYQSAGVAPESFEYIEAHGTGTK 24 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 335.45 5.42E-87 6036530000 3875990 4402380 3869410 4431570 4301100 4940870 4798510 4690400 5312610 5772240 FALSE TRUE 3724512.026 4276828.433 4568698.462 4660283.859 4439448.788 5040777.777 4857235.601 4593541.601 4709544.785 5381281.043 0.692123678 0.794760281 0.848998301 0.866017556 0.824979917 0.936724497 0.902616972 0.853614885 0.875171683 1 22.35951822 6.020625641 0.541468178 0.898803636 1.17E-22 0.701317761 0.042821948 8.314708383 0.635032594 0.020478701 6.400691093 1048638.12 -6.020625641 -0.898803636 ADDPYAHLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADDPYAHLSK 10 0 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ; 107.06 0.0023346 565740000 1117590 1216680 1122680 1346830 1236340 1307130 1409450 1439650 1491330 1674550 FALSE TRUE 1073913.347 1181981.478 1325573.25 1416340.058 1276107.999 1333561.064 1426699.271 1409920.724 1322040.471 1561131.237 0.687907155 0.757131399 0.849110708 0.907252398 0.817425191 0.854227391 0.913888107 0.903140422 0.846847747 1 20.57416039 6.021616454 0.496630397 0.903522277 4.96E-31 0.698520231 0.045455523 8.175509743 0.576989382 0.024451786 5.679912598 1051033.247 -6.021616454 -0.903522277 KDELQSER ddPTM_BT-474_Pertuzumab_2h_R1 1 KDELQSER 8 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 113.93 0.0044169 161180000 232380 259520 221660 282900 278750 267540 309810 326790 371760 399650 FALSE TRUE 223298.3327 252118.7437 261718.8928 297500.5029 287716.2469 272949.8421 313601.5475 320041.6723 329559.3633 372581.3495 0.599327725 0.676681063 0.702447648 0.798484689 0.772223965 0.732591265 0.841699532 0.858984683 0.884529952 1 18.50719593 6.022626518 0.116363121 1.111000832 3.09E-15 0.920165639 0.031068243 16.10747998 0.209068673 0.299844671 2.818933008 1053480.54 -6.022626518 -1.111000832 YLLLTYYDANK ddPTM_BT-474_Pertuzumab_2h_R1 1 YLLLTYYDANK 11 0 A0A087WX87;A0A1W2PS33;A0A087X037;A6QL64-4;A6QL64-5;Q8N2N9-4;Q8N2N9-3;Q8N2N9-2;Q8N2N9;A6QL64 A0A087WX87 ANKRD36B;ANKRD36 Ankyrin repeat domain-containing protein 36A;Ankyrin repeat domain-containing protein 36B 0 84.476 0.027497 0 323660 338200 313290 393050 339850 312980 395960 412920 403820 449840 FALSE TRUE 311011.0094 328554.8671 369908.4721 413335.3576 350781.5839 319308.67 400805.8769 404393.0577 357980.0466 419371.9361 0.741611402 0.783445049 0.882053471 0.985605669 0.836445059 0.761397324 0.955728895 0.964282592 0.853609924 1 18.6778708 6.026180938 0.584778118 0.915254329 9.02E-25 0.373786768 0.072268209 16.50842152 1.337090122 0.034157525 14.2836586 1062137.978 -6.026180938 -0.915254329 ESVPEFPLS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 9 ESVPEFPLSPPK 12 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK 222.79 2.51E-11 14706358000 1865628 1554859 1822803 1784397 1847920 1679633 1933522 2304129 2194057 2279675 TRUE FALSE 1792717.195 1510515.944 2152224.05 1876489.943 1907360.025 1713596.33 1957185.021 2256547.931 1944996.848 2125270.582 0.843524213 0.710740532 1.01268237 0.882941664 0.897466911 0.806295605 0.920910983 1.061769711 0.915176102 1 21.0192151 6.026695121 0.18088131 1.032275164 0.458282408 0.291214136 0.083068814 33.00124122 0.694529087 0.21185103 4.580047142 1063396.242 -6.026695121 -0.573992756 S(ph)DSPEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.544)DS(0.456)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.5)DS(0.5)PEIPFQAAAGPSDGLDASSPGNSFVGLR 148.3 9.06E-09 666170000 222430 241949 210947 258592 250053 230462 287754 278839 279340 291282 TRUE FALSE 213737.1897 235048.8514 249069.8154 271937.9641 258096.1818 235122.0995 291275.6195 273080.8772 247630.4943 271553.2107 0.787091374 0.865571984 0.917204458 1.001416862 0.950444229 0.865841722 1.072628156 1.005625662 0.91190413 1 18.0508754 6.027979875 0.570505805 0.985046354 4.03E-12 0.548242028 0.054212774 10.91885424 0.86539214 0.02569664 9.857945012 1066546.696 -6.027979875 -0.985046354 EACDQHGPDLYPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EACDQHGPDLYPK 13 0 P36551 P36551 CPOX "Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial" 0 ; 120.53 0.00021982 465320000 1043520 1081060 858000 1027830 815390 869870 967200 963040 1012260 904250 FALSE TRUE 1002738.085 1050229.227 1013059.686 1080876.429 841617.7599 887459.3674 979036.8829 943152.8875 897352.4885 843004.3421 1.189481518 1.245817103 1.201725348 1.282171841 0.99835519 1.052734041 1.161366358 1.118799561 1.064469593 1 19.68518054 6.0306965 0.138615413 0.964870904 1.618172136 0.471527642 0.069284422 41.19485606 0.641485898 0.377084649 4.973324811 1073239.134 -6.0306965 0.653301232 DDS(ph)PVSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDSPVSHR 8 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 DDS(1)PVSHR;DDS(1)PVSHR 139.31 0.00043035 185496000 135412 128253 138660 160909 145312 145992 172147 161431 201769 187217 TRUE FALSE 130119.9493 124595.35 163718.9465 169213.5328 149986.0924 148944.0583 174253.7865 158097.3934 178865.029 174536.6258 0.745516585 0.713863634 0.938020577 0.96950157 0.859338788 0.853368498 0.998379484 0.905812134 1.024799398 1 17.41317029 6.034363936 0.44536083 0.962401946 8.41E-18 0.593093368 0.065019828 10.76006396 0.676233589 0.041965089 6.981484002 1082340.565 -6.034363936 -0.962401946 DNFGFIETANHDK ddPTM_BT-474_Pertuzumab_2h_R1 5 DNFGFIETANHDK 13 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;;; 218.28 2.44E-11 4447200000 2365653 2164307 2494883 2672304 2629575 2620586 3109000 3372311 3695583 3671311 FALSE TRUE 2273200.665 2102583.083 2945763.856 2810221.93 2714157.668 2673576.044 3147048.872 3302671.599 3276075.911 3422649.836 0.664163959 0.614314401 0.860667611 0.821066152 0.792998933 0.781142148 0.919477312 0.964945804 0.957175308 1 21.70668227 6.038197407 0.199210139 1.042529848 2.02E-10 0.778295709 0.057573748 11.25147054 0.265136711 0.121731387 3.14749131 1091936.561 -6.038197407 -1.042529848 VEVIGTDES(ph)QEVPYTIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEVIGTDESQEVPYTIR 17 0 P98088 P98088 MUC5AC Mucin-5AC 1 VEVIGTDES(1)QEVPYTIR;VEVIGTDES(1)QEVPYTIR 170.89 1.88E-09 88077000 64960 77865 56606 79893 67094 78531 73194 85146 82562 81139 TRUE FALSE 62421.29138 75644.36644 66835.96339 84016.2873 69252.13944 80118.95063 74089.77007 83387.70535 73189.90789 75643.38326 0.825204911 1.000012998 0.883566553 1.11068918 0.915508224 1.059166674 0.979461347 1.102379372 0.967565235 1 16.20692627 6.038963074 0.651697611 1.024735777 2.38E-10 0.367018329 0.069591067 14.91449823 1.289850932 0.025466994 16.6557141 1093863.355 -6.038963074 -1.024735776 GS(ph)PVPPVPER ddPTM_BT-474_Pertuzumab_2h_R1 3 GSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(1)PVPPVPER;GS(1)PVPPVPER;GS(1)PVPPVPER 103.34 0.0029656 1424710000 653510 743470 639280 791290 821840 792630 836290 874700 915080 1034290 TRUE FALSE 627970.1067 722266.9635 754812.1167 832128.5717 848275.23 808657.5217 846524.7672 856637.1393 811203.9547 964236.6171 0.651261418 0.74905573 0.782807978 0.862992088 0.879737624 0.838650501 0.877922236 0.888409675 0.841291381 1 19.87902769 6.03917039 0.422111985 0.902027933 6.26E-30 0.801185215 0.039525558 6.350122707 0.376426301 0.025551452 3.621522863 1094385.652 -6.03917039 -0.902027933 SVEDEMDS(ph)PGEEPFYTGQGR ddPTM_BT-474_Pertuzumab_2h_R1 8 SVEDEMDSPGEEPFYTGQGR 20 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2;A0A590UK73;B1AKN7 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR 313.56 2.50E-66 2476880000 2497460 2679430 2227450 2666150 2627170 2719360 2800710 2998530 2948910 3029340 TRUE FALSE 2399856.502 2603015.28 2629999.764 2803750.321 2711675.309 2774347.322 2834985.927 2936609.308 2614162.1 2824160.104 0.849759367 0.921695366 0.931250237 0.99277315 0.960170532 0.982361913 1.003833289 1.039816866 0.925642316 1 21.42939045 6.040418605 0.518981253 0.999160905 0.341773789 0.683366878 0.029286531 7.967603009 0.575953839 0.01518322 4.272897919 1097535.571 -6.040418605 -0.657387116 ILDEWFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILDEWFGR 8 0 Q8IYB7;Q8IYB7-3;Q8IYB7-2;H7C440 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 0 ; 101.99 0.011752 120319000 183105 204133 162436 187548 202474 194369 197731 213500 216380 215000 FALSE TRUE 175949.0542 198311.3267 191791.7986 197227.3748 208986.7601 198299.2744 200150.8911 209091.1504 191817.4495 200437.8585 0.877823459 0.989390568 0.956864137 0.983982648 1.042651132 0.989330438 0.998568298 1.043171943 0.956992112 1 17.6127955 6.042733549 0.830524654 1.006336628 4.21E-15 0.613115916 0.027959626 11.13438146 1.080272731 0.008961879 16.76359937 1103401.447 -6.042733549 -1.006336628 VEVGTEVTDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 VEVGTEVTDYR 11 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 201.33 1.02E-07 512220000 331330 382760 343200 353910 402740 455210 415910 429840 461090 496010 FALSE TRUE 318381.2573 371844.0596 405223.8744 372175.3375 415694.4979 464414.6581 421000.031 420963.6538 408748.9962 462414.8009 0.688518743 0.804135289 0.876321159 0.804851698 0.898964516 1.004324812 0.910438053 0.910359385 0.883944449 1 18.81882805 6.043091844 0.458798183 0.937389454 4.52E-15 0.725475862 0.046901167 8.340409036 0.53632247 0.029402088 5.475875232 1104312.134 -6.043091844 -0.937389454 SFLHIGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SFLHIGK 7 0 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 ; 80.18 0.030613 805450000 1604640 1825400 1556970 1905740 1900990 1833180 2013750 2041210 2212400 2368600 FALSE TRUE 1541928.895 1773341.379 1838349.114 2004095.47 1962137.07 1870248.156 2038394.875 1999058.3 1961257.627 2208172.612 0.698282773 0.803080959 0.832520566 0.907580983 0.88857957 0.846966467 0.923113919 0.905299834 0.888181303 1 21.07442152 6.044494729 0.508635018 0.916201245 4.22E-26 0.787458108 0.03539723 6.498212943 0.459756738 0.01791171 4.740279628 1107885.12 -6.044494729 -0.916201245 EFGIADPDEIMWFK ddPTM_BT-474_Pertuzumab_2h_R1 3 EFGIADPDEIMWFK 14 0 Q15067-2;Q15067;Q15067-3;I3L0T4;I3L4S5;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;; 174.84 5.77E-06 245511000 355974 430719 321228 468909 434022 434964 497090 549757 497234 548656 FALSE TRUE 342062.1425 418435.3158 379281.0453 493109.4497 447982.7118 443759.2701 503173.5361 538404.3258 440790.0809 511495.0404 0.668749676 0.81806329 0.74151461 0.964055193 0.875830021 0.867572968 0.983731017 1.052609084 0.861768045 1 18.96436073 6.047776748 0.327138731 1.000142787 5.22E-08 0.652277342 0.06724673 9.621674009 0.425060295 0.064148913 4.508843765 1116289.264 -6.047776748 -1.000142735 KAAGGAT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 KAAGGATPK 9 1 P16403 P16403 HIST1H1C Histone H1.2 1 KAAGGAT(1)PK;KAAGGAT(1)PK 62.303 0.048935 557410000 424220 210660 184499 134231 150449 91827 140964 284300 102449 100980 TRUE FALSE 407641.0134 204652.1831 217842.0735 141158.678 155288.3287 93683.80486 142689.1596 278429.1056 90819.41902 94140.53466 4.330132763 2.173900794 2.314009308 1.499446317 1.649537357 0.995148426 1.515703731 2.957590019 0.964721725 1 16.52252843 6.048084596 1.034478748 1.670496451 36.73214525 0.664773787 0.58270433 15.33279987 1.492289453 0.181273303 1074.090426 1117080.821 -6.048084596 35.0616488 GYELLFQPEVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GYELLFQPEVVR 12 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 94.465 0.015341 38602000 39707 46921 36701 55553 43366 44537 52257 59208 52839 68229 FALSE TRUE 38155.20654 45582.85902 43333.68711 58420.09699 44760.90677 45437.56865 52896.5368 57985.33411 46840.93824 63607.78906 0.599851168 0.716623855 0.681263848 0.918442503 0.70370166 0.714339695 0.831604707 0.911607446 0.736402553 1 15.95691582 6.051603944 0.075474583 1.220049483 2.98E-13 0.530383837 0.082741844 115.5141493 0.960599866 3.472836175 15.9754938 1126169.974 -6.051603944 -1.220049483 SVDISLGDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVDISLGDSPR 11 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SVDISLGDS(1)PR;SVDISLGDS(1)PR 187.97 3.52E-06 425280000 327130 367940 389390 447690 401770 414270 497830 507200 505750 599630 TRUE FALSE 314345.3979 357446.7115 459761.4349 470795.3346 414693.2969 422646.8232 503922.5925 496726.1428 448339.3803 559016.526 0.562318614 0.639420652 0.822446947 0.842185003 0.741826543 0.756054255 0.901444893 0.888571482 0.802014537 1 19.09253141 6.053492173 0.264503951 0.929882339 2.12E-45 0.700555259 0.066532465 11.2426987 0.378516234 0.087402163 3.846786121 1131077.005 -6.053492173 -0.929882339 QGPPS(ph)PCQQLVLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 QGPPSPCQQLVLTK 14 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 QGPPS(1)PCQQLVLTK;QGPPS(1)PCQQLVLTK 208.59 8.21E-09 550045000 339420 398210 312700 384890 365870 407100 379230 441560 409300 448740 TRUE FALSE 326155.0912 386853.4407 369211.846 404754.219 377638.5408 415331.8409 383871.1302 432441.6317 362837.9799 418346.4401 0.779629178 0.924720288 0.882550467 0.967509653 0.902693329 0.992794013 0.917591483 1.033692629 0.867314611 1 18.67433863 6.054206356 0.651151458 0.962004864 6.77E-13 0.496447826 0.050488818 12.03934085 1.022537036 0.018608985 12.65975695 1132938.553 -6.054206356 -0.962004864 TVSS(ph)PPT(ph)SPRPGSAATVSASTSNIIPPR ddPTM_BT-474_Pertuzumab_2h_R1 3 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.073)VS(0.435)S(0.486)PPT(0.529)S(0.475)PRPGSAATVSASTSNIIPPR;T(0.016)VS(0.114)S(0.87)PPT(0.539)S(0.462)PRPGSAATVSASTSNIIPPR;T(0.028)VS(0.159)S(0.813)PPT(0.538)S(0.461)PRPGS(0.001)AATVSASTSNIIPPR 141.01 2.95E-07 6373380000 862483 939956 867994 1096511 967111 1035541 1091972 1344361 1170340 1261930 TRUE FALSE 828776.2108 913149.3752 1024859.824 1153102.064 998219.0036 1056480.349 1105335.88 1316599.476 1037487.91 1176458.357 0.704467103 0.776185039 0.871139907 0.980146945 0.848494974 0.898017632 0.939545266 1.119121189 0.881873892 1 20.16601882 6.057561129 0.355414095 1.007704585 2.56E-17 0.603153059 0.069964135 10.80200499 0.52371154 0.063608165 5.624925682 1141723.997 -6.057561129 -1.007704585 TLHNLVIQYASQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLHNLVIQYASQGR 14 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;G5E9S8;E9PQ02;Q9H0B6;Q9H0B6-2;A8MZ87;A8MX29 Q07866-6;Q9H0B6 KLC1;KLC2 Kinesin light chain 1;Kinesin light chain 2 0 ; 113.69 0.00052117 2424300000 1422150 1717080 1424210 1829940 1729910 1703420 2160690 2129090 2382640 2522440 FALSE TRUE 1366570.806 1668110.56 1681596.428 1924383.423 1785554.126 1737864.32 2187133.171 2085123.547 2112172.696 2351592.892 0.58112559 0.709353462 0.715088243 0.818331876 0.759295596 0.739015807 0.930064544 0.886685597 0.898188076 1 21.16520689 6.058289181 0.163385724 1.046397442 9.22E-16 0.849540616 0.046381582 12.12407373 0.224512836 0.150560057 2.7622361 1143639.59 -6.058289181 -1.046397442 EDGTFYEFGEDIPEAPER ddPTM_BT-474_Pertuzumab_2h_R1 3 EDGTFYEFGEDIPEAPER 18 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;; 319.58 3.86E-61 646610000 467650 508880 430853 528280 456880 556620 502740 582310 555900 570300 FALSE TRUE 449373.721 494367.2406 508717.7214 555544.5941 471575.9601 567875.2378 508892.6825 570285.095 492796.5625 531673.073 0.845206846 0.929833136 0.95682431 1.044898872 0.88696604 1.068091025 0.957153387 1.072623618 0.926878918 1 19.02017988 6.062434558 0.683478242 1.00265097 4.74E-16 0.385212253 0.057044161 14.61637194 1.266147505 0.020150983 17.0948099 1154607.988 -6.062434558 -1.00265097 FEDEDS(ph)DDVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 1 FEDEDS(1)DDVPR;FEDEDS(1)DDVPR 184.31 5.20E-06 274170000 479570 470460 484720 618920 508800 515380 599820 703680 713920 799720 TRUE FALSE 460827.8742 457042.9414 572319.6865 650862.5354 525166.0141 525801.3367 607160.7766 689148.7621 632878.7946 745554.2521 0.618101061 0.613024391 0.767643247 0.872991514 0.704396779 0.705248928 0.814375044 0.924344218 0.84887021 1 19.50795381 6.073182714 0.116446682 1.110599245 8.43E-17 0.697593273 0.067098616 37.07682899 0.475146793 0.671814258 6.486424276 1183539.384 -6.073182714 -1.110599245 VPQALNFS(ph)PEESDSTFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VPQALNFSPEESDSTFSK 18 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 VPQALNFS(0.829)PEES(0.169)DS(0.002)TFSK;VPQALNFS(1)PEESDSTFSK 231.77 6.41E-20 176700000 228101 220463 237548 250760 234844 264920 285900 288680 264870 322740 TRUE FALSE 219186.5607 214175.6111 280478.2078 263701.7537 242397.9705 270276.8639 289398.9297 282718.6571 234803.068 300880.5323 0.728483691 0.711829408 0.932191278 0.876433419 0.805628628 0.898286313 0.961839995 0.939637586 0.780386375 1 18.19883124 6.075305765 0.480292988 0.917908361 1.14E-13 0.445790087 0.071283489 13.71426263 0.89782361 0.040582468 9.393323012 1189339.287 -6.075305765 -0.917908361 TDEGIAYR ddPTM_BT-474_Pertuzumab_2h_R1 6 TDEGIAYR 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ;;;;; 204.1 0.00021008 18212220000 10423350 11255960 9286110 11352030 10622060 11095930 11818300 12409300 12221870 11931170 FALSE TRUE 10015993.96 10934951.04 10964316.65 11937909.63 10963728.21 11320297.31 11962935.89 12153043.62 10834494.56 11123061.23 0.90047099 0.983088272 0.985728337 1.073257567 0.985675434 1.017732176 1.07550751 1.092598824 0.974056902 1 23.40705056 6.075363678 0.663463122 1.041970331 0.17373535 0.481385901 0.039741854 12.69983257 1.064580259 0.015935123 12.41843645 1189497.895 -6.075363678 -0.868234981 EQHLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQHLTK 6 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 72.138 0.086386 929390000 2041130 2223900 1861040 2162900 2165300 2286400 2344300 2210000 2524000 2611600 FALSE TRUE 1961360.383 2160476.549 2197371.327 2274527.528 2234948.841 2332632.575 2372990.245 2164362.728 2237486.101 2434714.006 0.805581427 0.887363585 0.902517224 0.934207271 0.917951281 0.958072517 0.974648455 0.888959739 0.9189934 1 21.21532089 6.075699538 0.72943374 0.938370679 2.04E-08 0.664839843 0.029777063 10.54115224 0.928470462 0.010818719 12.60500077 1190418.145 -6.075699538 -0.938370659 HTANYDTEER ddPTM_BT-474_Pertuzumab_2h_R1 1 HTANYDTEER 10 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 0 95.618 0.0072993 178190000 608990 655660 570700 676770 653620 743700 753120 816050 819360 858780 FALSE TRUE 585189.9975 636961.2188 673838.1852 711698.1808 674644.2809 758738.1235 762336.9078 799198.2823 726349.6878 800614.0657 0.730926451 0.795590842 0.841651695 0.888940391 0.842658542 0.947695221 0.952190251 0.998231628 0.907240728 1 19.61074744 6.078109237 0.270323276 1.002189301 0.21738851 0.86002998 0.031324496 6.073173472 0.208044236 0.038147512 1.802118717 1197041.583 -6.078109237 -0.784800791 S(ph)YDNLTTACDNTVPLASR ddPTM_BT-474_Pertuzumab_2h_R1 4 SYDNLTTACDNTVPLASR 18 0 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(0.643)YDNLT(0.356)T(0.001)ACDNTVPLASR;S(1)YDNLTTACDNTVPLASR;S(1)YDNLTTACDNTVPLASR;S(1)YDNLTTACDNTVPLASR 325.35 2.79E-62 3110950000 902080 913920 907760 948450 977050 1011460 985180 1079140 1182750 1197110 TRUE FALSE 866825.7163 887855.8964 1071812.425 997399.6182 1008477.701 1031912.414 997236.9275 1056855.382 1048489.178 1116028.673 0.776705596 0.79554936 0.960380724 0.893704294 0.903630637 0.924628944 0.893558518 0.9469787 0.939482294 1 20.08994266 6.078489501 0.590895502 0.936845156 7.55E-12 0.67116876 0.038082582 8.790451521 0.680368988 0.016117998 7.993438495 1198090.158 -6.078489501 -0.936845156 AS(ph)PEPQR ddPTM_BT-474_Pertuzumab_2h_R1 3 ASPEPQR 7 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 AS(1)PEPQR;AS(1)PEPQR;AS(1)PEPQR 88.181 0.019717 985880000 1380480 1359270 1463960 1794000 1604120 1622070 1895280 1898310 1941570 2319740 TRUE FALSE 1326529.315 1320504.95 1728530.138 1886588.555 1655717.977 1654869.367 1918475.004 1859109.235 1721171.113 2162621.944 0.613389372 0.610603695 0.799275224 0.8723617 0.765606759 0.76521436 0.887106047 0.859655216 0.795872399 1 21.04435005 6.082735872 0.303198607 0.901710037 4.94E-122 0.66444604 0.065892293 11.0653859 0.43730342 0.070328411 4.302741875 1209862.099 -6.082735872 -0.901710037 SQTDKDYYQLQAILEAER ddPTM_BT-474_Pertuzumab_2h_R1 1 SQTDKDYYQLQAILEAER 18 1 Q13464;A0A0U1RQV4 Q13464 ROCK1 Rho-associated protein kinase 1 0 149.94 5.33E-08 68854000 151460 157110 142810 190850 164520 161830 184570 205320 203380 204200 FALSE TRUE 145540.7758 152629.3766 168618.9438 200699.7914 169811.9352 165102.3135 186828.8229 201080.0702 180293.155 190369.3521 0.764517892 0.801753932 0.885746271 1.054265244 0.892012991 0.867273601 0.98140179 1.056262828 0.947070277 1 17.53844171 6.086164559 0.448102868 0.99352504 1.51E-11 0.579424138 0.06157103 11.51529535 0.700450627 0.041977951 7.851220317 1219451.575 -6.086164559 -0.99352504 IDLGERPVVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDLGERPVVQR 11 1 Q8TC07-2;Q8TC07-3;Q8TC07;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 ; 169.82 1.50E-05 933830000 268700 301120 209242 272540 294780 314360 307730 267430 283510 314000 FALSE TRUE 258198.9069 292532.3524 247056.684 286605.8221 304261.8664 320716.5746 311496.0918 261907.477 251327.1334 292732.5003 0.882030204 0.999316277 0.843967389 0.979070728 1.03938533 1.095596062 1.064098081 0.894699006 0.85855562 1 18.1592234 6.086231072 10.56547538 0.967378593 0.880797678 0 0.085346155 0 0 0.019866936 0 1219638.351 -6.086231072 -0.086580914 EGYSGVGLLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGYSGVGLLSR 11 0 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 125.66 0.00075319 326100000 207240 225590 190140 295010 236820 239690 262630 330610 284320 330500 FALSE TRUE 199140.8317 219156.3941 224502.5276 310235.5015 244437.5304 244536.696 265844.1445 323782.788 252045.1856 308114.9406 0.646319946 0.711281295 0.728632397 1.006882369 0.793332287 0.793654133 0.862808353 1.050850658 0.818023252 1 18.23310912 6.088752724 0.285980428 0.971436864 3.21E-11 0.514217233 0.09079663 14.45154587 0.529283541 0.105044807 5.665939273 1226740.558 -6.088752724 -0.971436863 DLVDDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLVDDFR 7 0 Q6NUQ1 Q6NUQ1 RINT1 RAD50-interacting protein 1 0 ; 115.46 0.013204 231300000 844780 977130 807930 959070 1003640 1034960 1022910 1100720 1127490 1184020 FALSE TRUE 811765.0636 949263.2091 953940.9233 1008567.718 1035922.992 1055887.6 1035428.679 1077989.747 999502.062 1103825.271 0.735410835 0.859975971 0.864213702 0.913702326 0.938484577 0.956571324 0.938036758 0.976594553 0.905489382 1 20.07408039 6.091399743 0.500706171 0.960819533 3.95E-14 0.876586065 0.025186773 4.62117122 0.309765879 0.012653167 3.502373155 1234240.357 -6.091399743 -0.960819533 TPPT(ph)PPSSIVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPPTPPSSIVAK 12 0 Q96QT6;Q96QT6-4 Q96QT6 PHF12 PHD finger protein 12 1 T(0.073)PPT(0.926)PPSSIVAK;T(0.002)PPT(0.998)PPSSIVAK 100.55 0.035429 332120000 1034530 1043240 933070 991120 1073340 1052130 998330 1226810 1202460 1120520 TRUE FALSE 994099.4239 1013487.817 1101696.505 1042271.822 1107864.956 1073404.789 1010547.861 1201475.945 1065961.782 1044626.182 0.951631733 0.970191858 1.054632292 0.997746217 1.060537228 1.027549192 0.967377497 1.150149178 1.020424148 1 19.99455534 6.095174496 0.5380292 1.049719459 0.540568677 0.223518483 0.048790799 20.00697689 1.41882251 0.024306908 8.807140736 1245014.749 -6.095174496 -0.509150781 MVS(ph)PLRR ddPTM_BT-474_Pertuzumab_2h_R1 1 MVSPLRR 7 1 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 MVS(1)PLRR 76.17 0.025411 135060000 70507 78380 67336 78833 77929 80080 83800 94282 83799 89849 TRUE FALSE 67751.50849 76144.67914 79505.11308 82901.58058 80435.65706 81699.27247 84825.56947 92335.04375 74286.48883 83763.4472 0.808843365 0.909044239 0.949162382 0.989710707 0.960271571 0.975357094 1.012680021 1.102330991 0.886860454 1 16.3540332 6.101290785 0.558934062 1.010292629 2.07E-13 0.542011202 0.050940932 11.38321677 0.826623775 0.024650921 10.45312409 1262672.683 -6.101290785 -1.010292629 LEASYSDS(ph)PPGEEDLLVHVAEGSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 LEASYSDS(1)PPGEEDLLVHVAEGSK;LEASYS(0.005)DS(0.995)PPGEEDLLVHVAEGSK 251.19 3.58E-39 205780000 139284 175384 141182 174611 169337 198805 194501 198817 263881 223879 TRUE FALSE 133840.6273 170382.22 166696.728 183622.6946 174783.8784 202824.9733 196881.3614 194711.3595 233926.3352 208715.4759 0.64125876 0.816337261 0.798679289 0.879775176 0.837426538 0.971777356 0.943300254 0.932903315 1.12079056 1 17.67117805 6.104365524 0.259006844 1.04173384 7.30E-21 0.799369427 0.055776378 8.146286059 0.261215462 0.068882126 3.065217851 1271643.936 -6.104365524 -1.04173384 QRS(ph)APDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QRSAPDLK 8 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 QRS(1)APDLK 71.896 0.0288 260050000 189630 224160 185840 205080 216150 209200 267720 255320 226980 222990 TRUE FALSE 182219.05 217767.1763 219425.422 215664.2034 223102.6611 213430.1673 270996.4374 250047.5528 201214.182 207886.6887 0.876530629 1.047528236 1.055504917 1.037412279 1.073193587 1.026665866 1.303577632 1.202806944 0.967903156 1 17.66543786 6.10451894 0.548565503 1.125414454 4.80E-08 0.258001101 0.09723834 19.59417874 1.398464404 0.049197872 19.58477548 1272093.226 -6.10451894 -1.125414406 DYEEVGADSADGEDEGEEY ddPTM_BT-474_Pertuzumab_2h_R1 5 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ;;;; 427.42 7.56E-169 5364900000 2539390 2733150 2458960 2915020 2847150 3068290 3103400 3240390 3507200 3430570 FALSE TRUE 2440147.831 2655203.238 2903348.771 3065464.532 2938731.165 3130332.926 3141380.338 3173474.814 3109077.359 3198214.438 0.762971927 0.830214262 0.907803034 0.958492493 0.918866206 0.978775184 0.982229428 0.992264551 0.972129111 1 21.60883524 6.105627642 0.460529111 0.991773077 6.33E-18 0.95018744 0.01654318 3.004764767 0.184770491 0.009977308 2.123704474 1275344.876 -6.105627642 -0.991773077 IAQLEEELEEEQGNTELINDR ddPTM_BT-474_Pertuzumab_2h_R1 2 IAQLEEELEEEQGNTELINDR 21 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 249.28 1.21E-30 244310000 103383 111519 98240 124352 102363 127680 129390 133003 123042 142203 FALSE TRUE 99342.67806 108338.5873 115994.1533 130769.8216 105655.5989 130261.7771 130973.5135 130256.4416 109074.788 132571.4641 0.749351896 0.817208952 0.874955663 0.986410028 0.796970898 0.982577796 0.987946496 0.98253755 0.822762189 1 17.01641074 6.107228927 0.497930239 0.953672147 1.08E-19 0.456449453 0.068207346 13.69515739 0.901427862 0.036584183 10.26585843 1280055.875 -6.107228927 -0.953672147 IDTGWLDR ddPTM_BT-474_Pertuzumab_2h_R1 5 IDTGWLDR 8 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;;; 146.58 0.0012818 2300480000 1819840 2003020 1786250 2113230 2123160 2341220 2531130 2276860 2524250 2805780 FALSE TRUE 1748718.641 1945895.831 2109065.11 2222294.054 2191453.37 2388561.072 2562106.726 2229842.045 2237707.723 2615742.021 0.668536357 0.743917334 0.806297063 0.849584567 0.837794152 0.913148565 0.979495189 0.85247017 0.855477224 1 21.31878883 6.108898832 0.375798429 0.927378429 8.74E-15 0.774020126 0.044979976 7.992785495 0.399927439 0.036850225 4.125094445 1284987.291 -6.108898832 -0.927378429 LDNVPHT(ph)PSSYIETLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDNVPHTPSSYIETLPK 17 0 Q99733;Q99733-2;E9PNJ7;C9J6D1;A8MXH2;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 LDNVPHT(0.717)PS(0.238)S(0.046)YIETLPK;LDNVPHT(0.994)PS(0.006)SYIETLPK 202.95 3.72E-11 268630000 579360 409040 355990 314490 400260 384480 302670 460620 346160 400980 TRUE FALSE 556717.9707 397374.5797 420325.312 330720.8666 413134.7264 392254.449 306374.166 451108.036 306865.368 373821.2674 1.489262434 1.063006881 1.124401816 0.884703187 1.105166459 1.049310147 0.819573932 1.206747918 0.820887934 1 18.51198912 6.109656868 1.172495749 1.004725504 11.24265208 0.588871997 0.121874497 22.9656133 1.834590815 0.032021966 561.368295 1287232.12 -6.109656868 10.23792658 TVS(ph)PGSVSPIHGQGQVVENLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 T(0.05)VS(0.925)PGS(0.02)VS(0.005)PIHGQGQVVENLK;T(0.001)VS(0.996)PGS(0.003)VSPIHGQGQVVENLK 279.93 3.88E-45 289050000 326280 362890 301200 340460 365400 391240 358360 383400 401230 418750 TRUE FALSE 313528.6169 352540.7325 355633.5402 358031.1814 377153.4228 399151.1409 362745.7169 375482.656 355684.0525 390387.6895 0.803121167 0.903052893 0.910975294 0.917116987 0.966099682 1.022448073 0.929193534 0.961819919 0.911104684 1 18.57454803 6.113633907 0.646048059 0.96170626 3.96E-07 0.686095626 0.032384556 9.595358752 0.757357409 0.013033048 10.14142126 1299074.048 -6.113633907 -0.961705863 LSSERPS(ph)SDGEGVVENGITTCNGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSERPSSDGEGVVENGITTCNGK 24 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 LS(0.026)S(0.026)ERPS(0.474)S(0.474)DGEGVVENGITTCNGK 108.01 0.0014575 628750000 159270 160460 154890 190350 178980 181200 183340 207170 224380 223060 TRUE FALSE 153045.5523 155883.8379 182882.0685 200173.9863 184737.0542 184863.9881 185583.7698 202891.8671 198909.3231 207951.9475 0.735965949 0.749614706 0.879443884 0.962597315 0.888364146 0.888974546 0.892435834 0.975667069 0.956515798 1 17.66589067 6.114328098 0.426558234 0.957702002 1.94E-16 0.777869644 0.040158484 7.725623083 0.438875926 0.028690195 4.804961337 1301152.192 -6.114328098 -0.957702002 DGPGNPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGPGNPLR 8 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 81.89 0.05046 139900000 108870 120020 97624 106120 118750 125240 112590 128540 124520 118490 FALSE TRUE 104615.24 116597.1471 115266.8284 111596.8659 122569.7016 127772.4386 113967.9101 125885.6041 110385.0116 110464.5668 0.947047937 1.055516267 1.043473322 1.010250338 1.109583871 1.156682567 1.031714634 1.139601664 0.999279813 1 16.75322415 6.11644091 0.798541106 1.077327548 1.29E-09 0.25498109 0.055007625 23.14315047 1.985946079 0.01789022 36.18035015 1307497.628 -6.11644091 -1.077327547 T(ph)TPLGGLGPGEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPLGGLGPGEAR 13 0 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 T(0.867)T(0.133)PLGGLGPGEAR 139.48 0.00043471 208830000 186470 160170 179140 199140 184980 171930 201950 232220 251330 234060 TRUE FALSE 179182.5462 155602.1084 211514.5829 209417.6393 190930.0497 175406.5424 204421.5245 227424.5758 222800.0721 218206.9077 0.821158909 0.713094329 0.969330372 0.959720485 0.874995442 0.803854214 0.936824258 1.042242788 1.021049583 1 17.73533725 6.117131028 0.204063131 1.045250167 0.349423612 0.439814872 0.076184528 23.36863436 0.552002542 0.156696232 4.503159062 1309576.968 -6.117131028 -0.695826555 KWENPGLGAESHTDSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KWENPGLGAESHTDSLR 17 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 282.49 3.16E-36 678230000 993460 1084340 853390 998300 1025030 1113600 1041900 1066180 1124620 1156810 FALSE TRUE 954634.4849 1053415.685 1007616.557 1049822.383 1058001.021 1136117.755 1054651.084 1044163.01 996957.8524 1078458.228 0.885184479 0.976779311 0.934312086 0.973447423 0.981031062 1.053464775 0.977924834 0.968199772 0.924428806 1 20.04053887 6.118133917 0.891005844 0.981262955 3.27E-11 0.40386436 0.033291968 23.27171999 2.017128884 0.010829133 38.28078486 1312604.585 -6.118133917 -0.981262955 DEFSYQEMIANLPLCSHPNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEFSYQEMIANLPLCSHPNPR 21 0 P19623;K7ESL0 P19623 SRM Spermidine synthase 0 ; 202.95 6.10E-22 120620000 97774 99205 115007 117948 114781 115072 140246 132941 147045 161177 FALSE TRUE 93952.88399 96375.77053 135791.3232 124035.3104 118473.0351 117398.8347 141962.3725 130195.7219 130353.0681 150260.3382 0.625267353 0.641391945 0.903707025 0.825469395 0.788451806 0.781302878 0.944776074 0.866467648 0.867514805 1 17.19710473 6.118156493 0.319458582 0.921976602 1.87E-64 0.642511926 0.068574154 11.72818276 0.485098722 0.068452191 4.975946961 1312672.82 -6.118156493 -0.921976602 DYSTVSAS(ph)PTALSTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYSTVSASPTALSTLK 16 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 DYSTVSAS(0.998)PT(0.002)ALSTLK;DYSTVS(0.005)AS(0.898)PT(0.097)ALSTLK 251.07 3.64E-21 345100000 317680 349320 342340 442910 330250 369250 447310 499570 468390 493800 TRUE FALSE 305264.7144 339357.7356 404208.4533 465768.6382 340872.7912 376716.488 452784.3136 489253.7049 415220.3309 460354.4862 0.663107939 0.737166131 0.878037394 1.011760833 0.740457194 0.818318273 0.983555775 1.062776012 0.901957825 1 18.81238568 6.119076449 0.305253909 1.002435272 2.32E-13 0.518435649 0.089704062 15.12435996 0.591909281 0.101770864 6.619184843 1315456.373 -6.119076449 -1.002435272 IRDTPEDIVLEAPASGLAFHPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 IRDTPEDIVLEAPASGLAFHPAR 23 1 Q9H6Y2;D6RGJ8 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 171.15 3.91E-12 54982000 26792 30843 22639 27082 27399 34473 32813 26771 30224 28482 FALSE TRUE 25744.93902 29963.38784 26730.3709 28479.70527 28280.31372 35170.06768 33214.57531 26218.16949 26793.09823 26552.88877 0.969572058 1.128441734 1.006684099 1.072565231 1.065056008 1.324528867 1.250883683 0.987394243 1.009046453 1 14.6965812 6.119177142 0.827503684 1.105807028 1.75E-12 0.089318363 0.108463039 55.44096221 4.770168219 0.038376343 93.2952235 1315761.402 -6.119177142 -1.105807028 FLEDTFGNDGRPR ddPTM_BT-474_Pertuzumab_2h_R1 3 FLEDTFGNDGRPR 13 1 O00754;O00754-2;M0R2P5 O00754;M0R2P5 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 ;; 212.1 1.51E-08 999880000 1013610 1101790 925930 1247450 1045520 1136600 1298180 1231350 1187170 1471280 FALSE TRUE 973997.0006 1070368.028 1093266.148 1311831.044 1079150.1 1159582.831 1314067.515 1205922.192 1052407.439 1371628.895 0.710102422 0.7803627 0.797056807 0.956403768 0.786765359 0.84540566 0.95803429 0.879189842 0.76726835 1 20.38745877 6.120823752 0.526716385 0.888221431 1.39E-11 0.388975601 0.071810643 16.69455854 1.137122134 0.035370093 12.55224147 1320759.527 -6.120823752 -0.888221431 NSYVAGQYDDAASYQR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSYVAGQYDDAASYQR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 283.82 3.88E-28 0 68117 67640 71255 74237 73044 74551 69811 85790 98036 99392 FALSE TRUE 65454.91233 65710.97343 84132.36356 78068.38047 75393.5266 76058.4723 70665.3679 84018.40652 86907.36428 92660.09131 0.706398099 0.709161544 0.907967631 0.84252432 0.813656943 0.820833125 0.762630027 0.906737791 0.937915807 1 16.49966048 6.120898822 0.047392287 1.408779341 9.40E-11 0.605588447 0.058334041 285.1946196 1.468087514 13.08698489 35.13947269 1320987.847 -6.120898822 -1.408779341 SPS(ph)MPSLNQTWPELNQSSEDTAIVHPVPIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSMPSLNQTWPELNQSSEDTAIVHPVPIR 30 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2 E9PMG1 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.179)PS(0.777)MPS(0.026)LNQT(0.018)WPELNQSSEDTAIVHPVPIR 108.71 0.00016671 152470000 38277 33885 37252 38842 39148 41766 38048 50106 50625 48638 TRUE FALSE 36781.09252 32918.63298 43984.26507 40846.64027 40407.23097 42610.53714 38513.64281 49071.29359 44878.26224 45343.70494 0.811162047 0.725980222 0.970019215 0.900822735 0.891132099 0.939723324 0.849371326 1.082207412 0.98973523 1 15.46861465 6.12229576 0.242074854 1.031605572 0.300294187 0.500599997 0.069235154 15.87244777 0.463504602 0.098173761 3.890946789 1325243.737 -6.12229576 -0.731311385 ELLVSQHTVQLVGGLS(ph)PLSSPSDTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLVSQHTVQLVGGLSPLSSPSDTK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 ELLVSQHTVQLVGGLS(0.934)PLS(0.054)S(0.009)PS(0.002)DTK;ELLVSQHTVQLVGGLS(1)PLSSPSDTK 251.92 5.78E-45 5861900000 2746500 3181600 2708400 3676000 2956800 3335800 3360600 3825600 3672500 4533000 TRUE FALSE 2639163.744 3090863.883 3197868.128 3865718.801 3051908.157 3403252.162 3401728.028 3746600.023 3255613.196 4225975.872 0.624509894 0.731396481 0.756717081 0.914751744 0.72217832 0.805317461 0.804956803 0.886564461 0.770381397 1 22.0108531 6.124815003 0.055979068 1.314368422 6.49E-14 0.577794977 0.066580715 200.8736896 1.21929151 7.812010273 25.00537673 1332953.51 -6.124815003 -1.314368422 S(ph)PRPSPVPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPRPSPVPK 9 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.997)PRPS(0.003)PVPK;S(1)PRPSPVPK 96.64 0.0053832 709550000 560080 559260 584920 745850 612560 582650 722630 811300 878710 946210 TRUE FALSE 538191.4544 543310.4524 690628.0555 784343.4079 632263.5487 594431.5822 731473.7621 794546.3715 778962.5247 882122.3539 0.610109756 0.615912804 0.782916398 0.889154894 0.716752666 0.673865229 0.829220299 0.900721275 0.883054965 1 19.75061925 6.126199138 0.112846552 1.117352528 9.90E-16 0.662210979 0.073045414 44.54277849 0.54504896 0.816361795 7.623172301 1337208.528 -6.126199138 -1.117352528 GYWGNK ddPTM_BT-474_Pertuzumab_2h_R1 1 GYWGNK 6 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 118.18 0.051381 1753000000 1745200 1858900 1600200 1793000 1908700 1795200 1981500 2015800 2131700 2049400 FALSE TRUE 1676995.655 1805885.992 1889391.736 1885536.945 1970095.069 1831500.174 2005750.19 1974173.026 1889718.353 1910592.313 0.877736 0.945196932 0.988903663 0.986886073 1.031143618 0.958603341 1.049805433 1.033278012 0.989074613 1 20.86558853 6.131343897 0.640454115 1.016121708 0.13368131 0.725913093 0.024940999 8.156204442 0.627693883 0.00996598 7.856576432 1353143.629 -6.131343897 -0.882440398 GT(ph)SPRPPEGGLGYSQLGDDDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTSPRPPEGGLGYSQLGDDDLK 22 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 GT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK 186.13 5.34E-17 1474300000 544030 422480 541780 658770 547360 549750 650230 758430 772820 797960 TRUE FALSE 522768.7061 410431.2841 639691.6978 692769.1986 564966.3315 560866.3217 658187.7092 742768.1555 685092.7135 743913.4585 0.702727851 0.551719127 0.859900692 0.931249718 0.759451688 0.753940281 0.884763815 0.998460435 0.920930662 1 19.50477527 6.133970383 0.203971853 1.027806309 2.05E-11 0.556175538 0.090292748 18.62996178 0.437265274 0.182301964 5.306401883 1361351.84 -6.133970383 -1.027806309 FS(ph)LCSDNLEGISEGPSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 FSLCSDNLEGISEGPSNR 18 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-5;Q14C86;C9IZ08;H0Y7I9;B4DGD8;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FS(0.999)LCS(0.001)DNLEGISEGPSNR;FS(0.5)LCS(0.5)DNLEGISEGPSNR 191.47 2.35E-14 114722000 83559 96127 76921 92485 83164 102263 102853 96126 100453 109000 TRUE FALSE 80293.4219 93385.55208 90822.3358 97258.16193 85839.04559 104330.8279 104111.7458 94140.96451 89049.99657 101617.3329 0.790154786 0.918992355 0.893768152 0.957102092 0.844728386 1.026703073 1.02454712 0.926426248 0.876326843 1 16.63278698 6.139057301 0.64489886 0.954847874 1.01E-14 0.40378594 0.057217453 18.32087617 1.402795448 0.023282052 19.30655979 1377391.19 -6.139057301 -0.954847874 EGNASGVSLLEALDTILPPTRPTDKPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGNASGVSLLEALDTILPPTRPTDKPLR 28 2 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 267.48 1.70E-54 4317200000 2104100 1856000 2109000 2051000 2052300 2117700 2246200 2311900 2714100 2773100 FALSE TRUE 2021869.446 1803068.697 2490143.214 2156852.356 2118314.093 2160521.345 2273689.668 2264158.457 2406006.746 2585275.467 0.782071184 0.697437747 0.963202276 0.83428338 0.81937655 0.835702567 0.879476751 0.875790022 0.930657788 1 21.30188658 6.140912719 0.037155022 1.491526312 3.37E-07 0.511596991 0.058986655 519.4608151 2.08910065 28.07939536 61.27857902 1383288.349 -6.140912719 -1.491525975 DLLHSGPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLHSGPGK 9 0 Q7LBC6;Q7LBC6-2;Q7LBC6-3 Q7LBC6 KDM3B Lysine-specific demethylase 3B 0 ; 138.98 0.00012151 140143000 265040 279790 250910 310680 306080 290850 336620 328330 365900 366230 FALSE TRUE 254681.9438 271810.6631 296255.0185 326714.232 315925.3412 296731.1863 340739.6563 321549.8708 324364.566 341424.9159 0.745938366 0.7961067 0.867701813 0.956913854 0.925314253 0.869096462 0.997992942 0.941787947 0.950031913 1 18.38120882 6.14341343 0.442376237 0.965234553 1.15E-11 0.807514273 0.035098591 6.793412356 0.39111679 0.022458305 4.47878759 1391276.438 -6.14341343 -0.965234552 WDEFEDILEER ddPTM_BT-474_Pertuzumab_2h_R1 1 WDEFEDILEER 11 0 Q5TBH8;O15228;A0A2R8YH69 Q5TBH8 GNPAT Dihydroxyacetone phosphate acyltransferase 0 93.058 0.022178 12703000 14752 18332 12999 19149 16810 17317 18236 20275 20248 20516 FALSE TRUE 14175.47553 17809.18931 15348.20846 20137.28218 17350.70892 17667.1616 18459.17762 19856.31416 17949.53193 19126.43305 0.741145801 0.931129671 0.802460575 1.052850897 0.907158636 0.923703942 0.965113442 1.038160859 0.938467297 1 14.22328023 6.146720263 0.488953881 0.985746209 4.96E-15 0.525489251 0.063691614 12.72509878 0.797858598 0.034042779 9.717954353 1401910.419 -6.146720263 -0.985746209 DVWLEWSDAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVWLEWSDAEK 11 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ; 141.88 8.82E-05 114130000 210327 224739 207174 233590 233906 242068 245324 270027 270482 285669 FALSE TRUE 202107.1883 218329.6638 244614.9504 245645.6079 241429.7989 246962.7808 248326.3485 264450.8481 239778.0173 266320.3842 0.758887416 0.819800799 0.918498789 0.92236878 0.906538941 0.927314601 0.932434629 0.992980124 0.900336706 1 18.02280333 6.153387293 0.500623104 0.956775694 4.56E-16 0.804849216 0.030300549 6.672537226 0.424109366 0.01616868 5.103049037 1423597.752 -6.153387293 -0.956775694 EFSITDVVPYPISLR ddPTM_BT-474_Pertuzumab_2h_R1 2 EFSITDVVPYPISLR 15 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 159.99 4.03E-06 120291000 275380 293040 241480 255010 295250 292740 298270 288480 310070 287320 FALSE TRUE 264617.8452 284682.7861 285120.8077 268171.0967 304746.9844 298659.4034 301920.3175 282522.7872 274872.1535 267859.5605 0.987897705 1.062806142 1.064441408 1.001163058 1.137711806 1.114985042 1.127159012 1.054742219 1.026180111 1 18.03111726 6.153568872 0.929930935 1.074999867 2.58E-08 0.180343847 0.047025752 39.28780473 3.18453844 0.014664907 75.59289385 1424193.084 -6.153568872 -1.074999841 EQMDNAVYTFETLLHQELGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EQMDNAVYTFETLLHQELGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 322.48 7.34E-67 711518000 932639 996768 904174 907726 1047875 1045196 997881 1085148 1192674 1158271 FALSE TRUE 896190.4368 968341.1526 1067578.355 954573.8476 1081580.851 1066330.579 1010093.366 1062739.315 1057286.648 1079820.273 0.829944074 0.896761411 0.988663004 0.884011785 1.001630436 0.987507463 0.935427303 0.984181665 0.979132059 1 20.04235978 6.154385072 0.654901887 0.975290589 1.03E-12 0.633638832 0.034176895 10.81412986 0.819792608 0.012892432 11.92244322 1426872.185 -6.154385072 -0.975290589 KLSEEEILENPDLFLTSEATDYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLSEEEILENPDLFLTSEATDYGR 24 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ; 157.31 1.95E-08 138343000 168172 180377 142661 171490 162878 184592 187800 181532 215564 220619 FALSE TRUE 161599.6523 175232.8246 168443.0162 180340.6195 168117.1188 188324.5767 190098.3526 177783.3008 191094.0784 205676.2786 0.785699029 0.85198364 0.818971528 0.876817787 0.817387012 0.915635862 0.924259977 0.864384079 0.929101206 1 17.65001589 6.154724424 0.030624613 1.555973676 2.35E-11 0.765261937 0.029705435 435.8968014 1.441392754 26.3113057 50.21192204 1427987.558 -6.154724424 -1.555973676 (ac)AAAAKPNNLSLVVHGPGDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAAAKPNNLSLVVHGPGDLR 20 1 Q00796;A0A6I8PIS1;H0YKB3;Q00796-2;A0A6I8PRA7 Q00796 SORD Sorbitol dehydrogenase 0 ; 56.529 1.05E-20 312520000 309270 342510 253450 332240 297540 371520 316230 319900 349460 381640 FALSE TRUE 297183.3865 332741.9502 299254.053 349386.9462 307110.6443 379032.3889 320100.1173 313293.9532 309790.7659 355791.1829 0.835274736 0.935216965 0.841094629 0.982000013 0.863176658 1.065322603 0.899685357 0.880555698 0.870709508 1 18.44067123 6.157933981 0.874937551 0.92575577 8.38E-10 0.139795739 0.067235591 50.88879119 4.122501835 0.020770589 77.94645722 1438579.876 -6.157933981 -0.925755769 LDTGS(ph)PEPETR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDTGSPEPETR 11 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LDTGS(1)PEPETR;LDT(0.003)GS(0.997)PEPETR 179.35 7.49E-06 628140000 523690 555090 487960 603590 575750 574810 621730 633760 652710 728860 TRUE FALSE 503223.6158 539259.3767 576145.2266 634741.3522 594269.5216 586433.052 629338.9177 620672.6345 578617.0972 679493.663 0.740586179 0.793619435 0.847903752 0.934138737 0.874576989 0.863044181 0.92618806 0.913434029 0.851541565 1 19.37410057 6.158076511 0.523500743 0.914032763 2.58E-09 0.661509022 0.040864886 9.763540039 0.639918832 0.020049725 7.558621541 1439052.08 -6.158076511 -0.91403276 ANQIS(ph)PSNSSLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ANQISPSNSSLK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 ANQIS(0.988)PS(0.012)NSSLK;ANQIS(0.783)PS(0.217)NSSLK;ANQIS(0.971)PS(0.028)NS(0.001)SLK 251.02 1.79E-17 394610000 528530 478860 541020 617490 610110 547590 683950 763520 757280 807160 TRUE FALSE 507874.4633 465203.3817 638794.3489 649358.7329 629734.7422 558662.645 692320.3847 747753.0452 671316.7492 752490.3343 0.6749249 0.618218415 0.848907049 0.862946278 0.83686755 0.742418367 0.920038907 0.993704518 0.892126741 1 19.52131353 6.162231625 0.221395423 1.011775448 2.42E-20 0.682166526 0.067866315 13.26953227 0.341088741 0.117755114 4.084458339 1452886.288 -6.162231625 -1.011775448 S(ph)LSTSGESLYHVLGLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.237)LS(0.237)T(0.237)S(0.237)GES(0.029)LY(0.024)HVLGLDK;S(0.509)LS(0.396)T(0.031)S(0.031)GES(0.031)LYHVLGLDK 66.797 0.03947 40187000 49722 66551 42794 82989 56532 49730 74952 79938 80744 75941 TRUE FALSE 47778.80927 64653.03064 50527.82775 87272.07224 58350.40312 50735.57467 75869.285 78287.25237 71578.27963 70797.44843 0.67486626 0.91321131 0.713695604 1.232700813 0.824187939 0.716629989 1.071638692 1.105792004 1.011029087 1 16.11140975 6.168465588 0.331264833 1.038652287 6.80E-15 0.262135159 0.154334599 25.09808026 1.054251671 0.147391841 12.60340199 1473891.75 -6.168465588 -1.038652287 DNYSPGWK ddPTM_BT-474_Pertuzumab_2h_R1 3 DNYSPGWK 8 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 88.948 0.033159 739480000 725932 764786 670521 709828 740907 816470 801357 780147 837110 868253 FALSE TRUE 697561.7749 742975.0521 791699.0604 746462.3081 764738.9465 832979.5828 811164.2467 764036.6918 742084.7823 809445.451 0.861777374 0.917881559 0.978075866 0.922189762 0.944768972 1.029074389 1.002123424 0.943901397 0.916781707 1 19.62657433 6.171011676 0.760130288 0.969684942 0.003230828 0.477080104 0.034670119 18.33806774 1.436630576 0.012723183 24.46195236 1482557.943 -6.171011676 -0.966454114 TPTGS(ph)PATEVSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPTGSPATEVSAK 13 0 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;S4R3G4;F6SRV7;Q8NHM5-5;F8WBN2 Q8NHM5-4;F8WBN2 KDM2B Lysine-specific demethylase 2B 1 TPT(0.001)GS(0.998)PAT(0.001)EVSAK;TPTGS(0.948)PAT(0.052)EVSAK 186.67 7.98E-06 650080000 658050 970350 872180 1002880 1101370 1128290 1206510 803160 1416530 1521120 TRUE FALSE 632332.6785 942676.5681 1029802.328 1054638.757 1136796.566 1151104.797 1221275.63 786574.4653 1255731.453 1418093.188 0.445903474 0.664749381 0.726188051 0.743702012 0.801637421 0.811727189 0.861209715 0.554670506 0.885507006 1 20.43552091 6.172840659 0.097210494 1.077351883 3.54E-38 0.497880189 0.109365617 100.0329905 1.040218347 2.009923273 14.56647794 1488814.737 -6.172840659 -1.077351883 DGDVTVTNDGATILSMMDVDHQIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DGDVTVTNDGATILSMMDVDHQIAK 25 0 P48643;B7ZAR1;E9PCA1 P48643 CCT5 T-complex protein 1 subunit epsilon 0 245.09 8.32E-39 59611000 56433 48901 60428 53219 64875 62267 71576 69096 87732 88355 FALSE TRUE 54227.53597 47506.39136 71348.68381 55965.63897 66961.76329 63526.0814 72451.9685 67669.14345 77773.03116 82370.63715 0.65833576 0.576739394 0.866190748 0.679436762 0.812932443 0.771222411 0.879584898 0.821520214 0.944183921 1 16.32984253 6.175333096 0.126227294 1.091766124 9.39E-13 0.693529801 0.069454261 28.51160868 0.386424823 0.442940012 5.272162225 1497383.682 -6.175333096 -1.091766124 DMLEAGILDTYLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DMLEAGILDTYLGK 14 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 222.49 9.01E-12 98595000 219011 261360 232823 245002 278033 275600 254510 303270 332630 332750 FALSE TRUE 210451.808 253906.2687 274899.2952 257646.5826 286976.1839 281172.8208 257624.7695 297007.3685 294871.2369 310212.5461 0.678411659 0.818491295 0.886164337 0.830548557 0.92509535 0.90638765 0.830478241 0.957431839 0.950545813 1 18.24289751 6.176914761 0.430030701 0.936945903 8.01E-65 0.731688437 0.045580673 9.332779363 0.510724713 0.030126953 5.803559262 1502846.973 -6.176914761 -0.936945903 GHPAGGEENMTETDAFYK ddPTM_BT-474_Pertuzumab_2h_R1 2 GHPAGGEENMTETDAFYK 18 0 P55212;D6RBM3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 ; 264.38 5.83E-31 654230000 279220 282610 273940 326820 337610 322860 347810 380160 390740 419220 FALSE TRUE 268307.7737 274550.2395 323447.0518 343687.2194 348469.5323 329388.4504 352066.6028 372309.5632 346384.8333 390825.856 0.686514901 0.7024874 0.827598908 0.879387108 0.891623537 0.842801072 0.900827306 0.952622651 0.886289451 1 18.57616639 6.177217562 0.324414118 0.954524447 2.03E-19 0.851405019 0.036177006 6.374276267 0.260190375 0.035123679 2.873659763 1503895.16 -6.177217562 -0.954524447 LQEDPNYS(ph)PQRFPNAQR ddPTM_BT-474_Pertuzumab_2h_R1 4 LQEDPNYSPQRFPNAQR 17 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;H0Y710;H0Y4L1 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 LQEDPNYS(1)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR 256.53 2.56E-27 4230400000 2948540 3214410 2738450 3221390 2915560 3606730 3447220 3286310 3536470 3963680 TRUE FALSE 2833307.797 3122738.174 3233348.831 3387646.324 3009341.635 3679660.552 3489408.11 3218446.55 3135024.752 3695216.423 0.766750164 0.845075854 0.875009326 0.916765336 0.814388466 0.995790268 0.944304125 0.870976468 0.848400849 1 21.81722743 6.179079598 0.616944332 0.9130225 1.87E-14 0.413412626 0.055308183 18.38612455 1.313667019 0.023030179 17.6632597 1510356.948 -6.179079598 -0.9130225 YDNGSGYR ddPTM_BT-474_Pertuzumab_2h_R1 3 YDNGSGYR 8 0 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 194.22 0.00038737 1665560000 1448740 1560210 1336440 1532050 1523730 1607180 1677340 1651000 1738740 1807580 FALSE TRUE 1392121.639 1515714.338 1577964.437 1611119.284 1572742.159 1639678.281 1697867.789 1616906.273 1541365.525 1685150.997 0.826110919 0.89945313 0.936393498 0.956068202 0.933294501 0.973015643 1.007546381 0.959502309 0.914675022 1 20.68444644 6.181448461 0.644630481 0.968372445 2.60E-12 0.745203417 0.025340196 8.893080462 0.648061558 0.010300551 9.601285668 1518617.711 -6.181448461 -0.968372445 WNEEILFR ddPTM_BT-474_Pertuzumab_2h_R1 1 WNEEILFR 8 0 P46934-4 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 0 86.136 0.037799 28566000 45539 59379 42257 54955 51720 56729 57540 69165 57185 57882 FALSE TRUE 43759.28553 57685.56906 49893.7799 57791.23414 53383.62077 57876.09925 58244.19173 67736.71858 50693.59854 53961.60058 0.810933795 1.069011453 0.924616382 1.070969606 0.989289054 1.072542301 1.079363679 1.255276305 0.939438378 1 15.71964552 6.185654444 0.488925087 1.093242159 7.62E-15 0.302400066 0.094223785 19.15021291 1.162110831 0.052836515 16.35225397 1533396.418 -6.185654444 -1.093242159 TRS(ph)PS(ph)PDDILER ddPTM_BT-474_Pertuzumab_2h_R1 1 TRSPSPDDILER 12 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 T(0.143)RS(0.862)PS(0.994)PDDILER 91.441 0.068954 0 190170 209740 189640 253230 241470 252340 285300 253820 287500 356560 TRUE FALSE 182737.9462 203758.4206 223912.1665 266299.2306 249237.1018 257442.4877 288791.5867 248578.5283 254864.2053 332409.8736 0.549736818 0.61297343 0.673602634 0.80111709 0.749788504 0.774473047 0.868781615 0.747807295 0.766716712 1 18.34260371 6.186604244 0.141094464 1.001791411 4.59E-31 0.774982707 0.057045787 23.23017381 0.352752866 0.293382714 4.386439226 1536753.616 -6.186604244 -1.001791411 LRDEELAELEDALR ddPTM_BT-474_Pertuzumab_2h_R1 4 LRDEELAELEDALR 14 1 Q15628-2;Q15628 Q15628-2 TRADD Tumor necrosis factor receptor type 1-associated DEATH domain protein 0 ;;; 194 1.77E-07 783660000 631120 684560 579460 805190 615990 736520 789710 819870 841440 825210 FALSE TRUE 606455.1327 665037.0191 684181.312 846745.9524 635803.8778 751412.939 799374.7072 802939.398 745923.2588 769317.7917 0.788302492 0.86445033 0.889335096 1.100645223 0.826451545 0.976726324 1.03906957 1.043703144 0.969590547 1 19.55322015 6.189510962 0.452365252 1.013213645 1.27E-11 0.481123642 0.070362236 14.24160078 0.807751196 0.043483009 10.22594666 1547073.553 -6.189510962 -1.013213645 EAPEEDPRLPDNFRPPGEDFR ddPTM_BT-474_Pertuzumab_2h_R1 3 EAPEEDPRLPDNFRPPGEDFR 21 2 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 0 ;; 84.166 0.001736 565530000 545587 599390 431246 528270 590600 592750 512970 603400 573340 575060 FALSE TRUE 524264.8569 582295.9841 509181.7452 555534.078 609597.1854 604735.8111 519247.8803 590939.5791 508256.8468 536110.674 0.977904157 1.086148835 0.949769833 1.036230213 1.137073397 1.128005542 0.968546059 1.102271616 0.948044632 1 19.03217133 6.192710504 13.0578363 1.040731093 0.656390927 0 0.071028579 0 0 0.0150995 0 1558513.27 -6.192710504 -0.384340166 ALAPTWEQLALGLEHSETVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALAPTWEQLALGLEHSETVK 20 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 334.05 6.16E-80 1088930000 1076430 1191540 968280 1182320 1072870 1228900 1253140 1175460 1360790 1363380 FALSE TRUE 1034361.926 1157558.446 1143269.735 1243339.677 1107379.838 1253749.2 1268476.302 1151186.34 1206318.824 1271037.058 0.81379368 0.910719667 0.899477893 0.978208833 0.871241189 0.98639862 0.997985302 0.905706354 0.949082339 1 20.27757466 6.195497055 0.664330389 0.953042171 3.73E-10 0.53103599 0.040062899 15.20303378 1.104256045 0.015214229 16.86227774 1568545.261 -6.195497055 -0.95304217 VYEGERPLTK ddPTM_BT-474_Pertuzumab_2h_R1 7 VYEGERPLTK 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;;; 147.91 2.38E-05 20116730000 10203540 11503310 9073110 11144620 10717420 11822310 11328760 11865230 13006350 12342680 FALSE TRUE 9804774.376 11175246.86 10712822.81 11719795.17 11062155.55 12061365.21 11467404.75 11620208.85 11529923.68 11506699.29 0.852092692 0.97119483 0.931007454 1.018519289 0.961366528 1.048203738 0.996585073 1.00986465 1.002018336 1 23.45597072 6.199088739 0.64672784 1.007948363 1.11E-19 0.731509475 0.027105389 8.631606676 0.617078933 0.009847213 9.783967037 1581571.168 -6.199088739 -1.007948363 LS(ph)PTFPESIEHPLAR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSPTFPESIEHPLAR 15 0 M9T4I7;Q5U5Q3 M9T4I7 MEX3C RNA-binding E3 ubiquitin-protein ligase MEX3C 1 LS(0.981)PT(0.019)FPESIEHPLAR;LS(0.974)PT(0.026)FPESIEHPLAR;LS(0.998)PT(0.002)FPESIEHPLAR 218.12 1.28E-12 576690000 210346 195494 232001 265696 232815 242840 283486 290212 323078 338843 TRUE FALSE 202125.4458 189918.7025 273928.7415 279408.6024 240303.7059 247750.3912 286955.3865 284219.0208 286403.5399 315892.8618 0.639854426 0.60121239 0.867157111 0.884504325 0.760712681 0.784286134 0.908394653 0.899732331 0.90664771 1 18.26907581 6.201301812 0.237661594 0.971878943 9.35E-23 0.691369188 0.066965372 13.24309871 0.366274879 0.103226599 4.256042813 1589651.091 -6.201301812 -0.971878943 VADMALHYANK ddPTM_BT-474_Pertuzumab_2h_R1 2 VADMALHYANK 11 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 114.89 0.0011962 3359700000 8605700 7587200 7436300 6568300 7062900 5729000 8486500 7232300 9071400 9021300 FALSE TRUE 8269379.73 7370820.485 8780204.83 6907290.75 7290084.593 5844844.305 8590360.326 7082950.478 8041652.702 8410279.316 0.983246741 0.876406146 1.043984926 0.82129148 0.866806478 0.694964351 1.021412013 0.842177794 0.956169516 1 23.00372228 6.210572215 0.002133345 1.787525494 3.96E-05 0.00133449 0.10369044 3792532.66 860.831875 352441.517 368995.8816 1623948.359 -6.210572215 -1.787485853 KLVIIEGDLER ddPTM_BT-474_Pertuzumab_2h_R1 6 KLVIIEGDLER 11 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 160.69 4.36E-05 14409670000 11922100 12501100 10471610 12097820 11626770 12191400 12564110 13286600 13280000 13461300 FALSE TRUE 11456171.15 12144580.87 12364062.87 12722189.94 12000755.62 12437918.46 12717873.34 13012227.07 11772510.07 12549554.16 0.912874753 0.967730065 0.985219292 1.013756328 0.956269479 0.991104409 1.013412363 1.036867677 0.938081937 1 23.58113278 6.212269446 0.844706741 0.998133231 3.86E-07 0.429126218 0.027235371 21.56822084 1.599135646 0.00902302 34.49642018 1630307.198 -6.212269446 -0.998132844 IDDIFER ddPTM_BT-474_Pertuzumab_2h_R1 6 IDDIFER 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 150.17 0.0045767 1071061000 1164509 1322199 1047331 1276511 1275927 1362434 1338472 1332580 1524439 1505003 FALSE TRUE 1118998.701 1284491.179 1236607.009 1342391.886 1316968.351 1389983.349 1354852.621 1305061.757 1351391.076 1403067.806 0.797537151 0.9154876 0.881359407 0.956754819 0.938634858 0.990674394 0.965635883 0.930148744 0.963168758 1 20.4201533 6.215099087 0.592096931 0.963424355 1.56E-10 0.791945011 0.025685265 8.095516435 0.543984777 0.011078875 7.846353199 1640964.125 -6.215099087 -0.963424355 EEEIEVDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEEIEVDSR 9 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 99.442 0.01241 124870000 159520 173340 164460 183160 174470 184880 207860 206550 216740 257610 FALSE TRUE 153285.782 168396.5129 194181.5804 192612.9095 180081.986 188618.4003 210403.8529 202284.6703 192136.5838 240161.8452 0.638260344 0.701179293 0.808544672 0.802012948 0.749835953 0.785380376 0.876091923 0.842284794 0.800029595 1 17.87364744 6.218193489 0.063159728 1.274921473 2.26E-14 0.781483401 0.043428081 103.7902773 0.695273074 3.494360197 13.27308347 1652697.953 -6.218193489 -1.274921473 DECPEVR ddPTM_BT-474_Pertuzumab_2h_R1 3 DECPEVR 7 0 P30153;B3KQV6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;; 164.89 0.0027471 609800000 762380 786860 798530 1052730 861280 938210 1038450 1063530 1197370 1287990 FALSE TRUE 732585.3467 764419.5232 942842.1342 1107061.521 888983.8534 957181.249 1051158.862 1041567.734 1061449.577 1200753.29 0.610104801 0.636616639 0.78520887 0.921972507 0.740355126 0.797150636 0.875416183 0.86742859 0.883986399 1 20.19550833 6.227960759 0.241988592 0.949123016 2.81E-35 0.725686388 0.061371712 12.5016796 0.349864255 0.091520305 4.015030517 1690288.199 -6.227960759 -0.949123016 AATDDDLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AATDDDLHR 9 0 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 0 ; 108.43 0.0026122 237220000 300278 328878 264502 319364 310910 310509 355687 327697 350800 370500 FALSE TRUE 288542.8038 319498.7214 312303.3952 335846.4143 320910.7025 316787.7047 360040.0039 320929.9424 310978.6547 345405.705 0.83537359 0.924995496 0.904163975 0.972324456 0.929083388 0.917146706 1.042368434 0.92913909 0.900328658 1 18.39793239 6.230009692 0.705173109 0.955512695 8.79E-10 0.423015392 0.041403324 19.97496281 1.417280238 0.014951847 24.23130256 1698281.551 -6.230009692 -0.955512695 NENLAANFLLSQNFDDE ddPTM_BT-474_Pertuzumab_2h_R1 4 NENLAANFLLSQNFDDE 17 0 P54725-2;P54725;K7EQ16;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 ;;; 256.57 9.82E-27 486170000 848560 780450 786480 944510 823660 799070 922020 1025390 1148110 1181710 FALSE TRUE 815397.3371 758192.3301 928614.4312 993256.2743 850153.7719 815227.7429 933303.9566 1004215.338 1017781.366 1101671.729 0.740145468 0.68821983 0.842913916 0.901590054 0.77169428 0.739991525 0.847170652 0.911537722 0.92385176 1 20.07126297 6.230901963 0.054284958 1.365793749 1.16E-08 0.622460607 0.058021508 208.9725582 1.20117492 8.291570748 26.32543305 1701774.309 -6.230901963 -1.365793738 DVDVSEDS(ph)PPPLPER ddPTM_BT-474_Pertuzumab_2h_R1 3 DVDVSEDSPPPLPER 15 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 DVDVSEDS(1)PPPLPER;DVDVS(0.047)EDS(0.953)PPPLPER;DVDVSEDS(1)PPPLPER 266.28 2.85E-25 1362380000 1423810 1400870 1363310 1593790 1606400 1583860 1703010 1635690 1982790 1976610 TRUE FALSE 1368165.931 1360918.559 1609690.444 1676045.693 1658071.315 1615886.734 1723851.946 1601912.43 1757711.992 1842732.444 0.742465861 0.738532913 0.873534543 0.909543704 0.899789506 0.876897099 0.935486837 0.86931363 0.953861749 1 20.81341518 6.232047494 0.42742043 0.932361929 1.56E-14 0.754707777 0.039402125 8.782527232 0.4592331 0.026139288 5.449460014 1706268.973 -6.232047494 -0.932361929 TQQS(ph)PIS(ph)NGSPELGIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQQSPISNGSPELGIK 16 0 Q15723-2;Q15723-3;Q15723-1;Q15723 Q15723-2 ELF2 ETS-related transcription factor Elf-2 2 T(0.104)QQS(0.896)PIS(0.621)NGS(0.379)PELGIK 90.714 0.0078316 36919000 71400 68841 77033 75422 79941 83695 91442 102070 96164 102260 TRUE FALSE 68609.60906 66877.72208 90954.57669 79314.53846 82512.37487 85387.37024 92561.09455 99962.21883 85247.86587 95333.83912 0.719677396 0.701510845 0.954063925 0.831966269 0.86550983 0.895666964 0.970915421 1.04854918 0.894203639 1 16.54070077 6.23472631 0.291943054 1.010048322 1.29E-12 0.650753802 0.063762568 11.19579976 0.392465575 0.070753882 4.755212879 1716826.113 -6.23472631 -1.010048322 EATAQKPTGSVGSTVT(ph)TPPPLVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EATAQKPTGSVGSTVTTPPPLVR 23 1 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 EATAQKPTGSVGS(0.075)T(0.263)VT(0.562)T(0.099)PPPLVR;EATAQKPTGSVGS(0.003)T(0.01)VT(0.494)T(0.494)PPPLVR 160.93 2.97E-11 1567850000 1730500 1863020 1441450 1831240 1717400 1783770 1834490 2138050 1833220 2051330 TRUE FALSE 1662870.147 1809888.494 1701952.08 1925750.516 1772641.731 1819839.052 1856941.037 2093898.52 1625120.551 1912391.592 0.869523875 0.946400571 0.889960031 1.006985454 0.926924035 0.951603772 0.971004602 1.094910963 0.849784405 1 20.86694654 6.235145475 0.342268998 0.996056965 0.582487767 0.170923935 0.062988494 27.37964845 1.149012806 0.055864702 5.746049395 1718483.929 -6.235145475 -0.413569198 GQDS(ph)PLLQRPQHLMDQGQMR ddPTM_BT-474_Pertuzumab_2h_R1 5 GQDSPLLQRPQHLMDQGQMR 20 1 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR 276.91 8.81E-45 2434660000 1083119 1310116 994993 1234190 1295090 1266934 1329940 1339940 1481610 1520500 TRUE FALSE 1040789.512 1272752.774 1174810.369 1297886.694 1336747.746 1292552.274 1346216.204 1312269.771 1313423.844 1417515.181 0.734235179 0.897875939 0.828781508 0.91560691 0.94302182 0.91184369 0.949701437 0.925753592 0.926567745 1 20.43493275 6.240904277 0.50235302 0.944746981 2.74E-15 0.757593042 0.034294156 8.526474835 0.503674429 0.017082565 6.589586824 1741423.005 -6.240904277 -0.944746981 DFCIEASER ddPTM_BT-474_Pertuzumab_2h_R1 2 DFCIEASER 9 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 123.35 0.0013029 795740000 441420 394630 358906 354947 381710 349604 420320 418130 438890 381830 FALSE TRUE 424168.8184 383375.5388 423768.298 373265.8572 393988.0488 356673.2324 425464.0019 409495.4694 389069.0472 355968.314 1.191591503 1.076993439 1.190466346 1.04859293 1.106806514 1.001980284 1.195229983 1.150370562 1.092987864 1 18.4413893 6.242557883 2.160413542 1.10585101 42.61515894 0.138657032 0.066117062 1731.0179 19.62996779 0.016185309 354427.8221 1748066.23 -6.242557883 41.50930793 HYIQEDNWR ddPTM_BT-474_Pertuzumab_2h_R1 1 HYIQEDNWR 9 0 G3V1N5;B4E3L3;Q96RU2-2;Q96RU2 G3V1N5 USP28 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 28 0 74.533 0.040821 85601000 215160 231750 209860 227600 263250 281780 252200 261120 335760 303560 FALSE TRUE 206751.3093 225140.7169 247786.3703 239346.4633 271717.6753 287477.7847 255286.499 255727.7808 297645.9324 282999.6108 0.730571002 0.79555133 0.875571417 0.845748383 0.960134449 1.015823958 0.902073675 0.903632977 1.051753858 1 18.11044054 6.243481233 0.368328719 0.981463358 1.04E-08 0.747852702 0.048315399 9.949529185 0.448518601 0.041745086 5.420786603 1751786.733 -6.243481233 -0.981463347 FEAAETLEEAAMR ddPTM_BT-474_Pertuzumab_2h_R1 1 FEAAETLEEAAMR 13 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0 Q07866-6 KLC1 Kinesin light chain 1 0 149.23 3.69E-06 0 22378 24478 21195 24624 24043 28294 25957 27139 28990 30255 FALSE TRUE 21503.44302 23779.91141 25025.40798 25894.84759 24816.36493 28866.12407 26274.66953 26578.57017 25699.17674 28205.8019 0.762376588 0.843085812 0.887243272 0.918068122 0.879831923 1.023410863 0.931534215 0.942308616 0.911130867 1 14.78370433 6.244714855 0.483116331 0.955601057 8.43E-17 0.733395182 0.036595947 9.03183923 0.516830928 0.020097716 6.72154042 1756769.792 -6.244714855 -0.955601057 S(ph)LTEGLVLDTMNDSLSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLTEGLVLDTMNDSLSK 17 0 A0A0D9SFF0;Q08050-2;Q08050;Q08050-3 A0A0D9SFF0 FOXM1 Forkhead box protein M1 1 S(0.999)LT(0.001)EGLVLDTMNDSLSK;S(0.998)LT(0.002)EGLVLDTMNDSLSK 314.42 3.32E-58 76254000 113449 121617 113911 133029 125399 127640 161727 155456 137304 167124 TRUE FALSE 109015.2877 118148.6022 134497.2516 139894.6426 129432.5727 130220.9683 163706.2634 152245.7793 121717.8255 155804.5426 0.699692614 0.758312949 0.863243455 0.897885519 0.830736836 0.835796993 1.050715599 0.977158796 0.781221289 1 17.24937777 6.24883193 0.354996513 0.956233904 1.30E-10 0.49180858 0.076092018 15.43218671 0.66776844 0.067069681 7.840449206 1773503.011 -6.24883193 -0.956233904 SVDFEMPPPS(ph)PPLNLHELSGPAEGASLTPK ddPTM_BT-474_Pertuzumab_2h_R1 11 SVDFEMPPPSPPLNLHELSGPAEGASLTPK 30 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;S(0.001)VDFEMPPPS(0.846)PPLNLHELS(0.152)GPAEGASLTPK 343.06 2.36E-106 8394833000 2568439 2781967 2448982 2864699 2750107 3039197 3056103 3139940 3340761 3410868 TRUE FALSE 2468061.564 2702628.025 2891567.525 3012546.459 2838566.689 3100651.646 3093504.503 3075099.142 2961531.817 3179846.872 0.776157363 0.849923953 0.909341752 0.947387274 0.89267402 0.975094641 0.972847004 0.967058876 0.931344161 1 21.60052586 6.254156238 0.4848697 0.969027085 6.43E-15 0.85720245 0.024412561 6.12749793 0.348809586 0.013459848 4.654669303 1795379.401 -6.254156238 -0.969027085 AGNS(ph)DS(ph)EEDDANGR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGNSDSEEDDANGR 14 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 2 AGNS(1)DS(1)EEDDANGR;AGNS(1)DS(1)EEDDANGR 240.61 3.07E-17 91893000 230060 220260 222740 296590 251200 237050 297130 322020 341700 336270 TRUE FALSE 221069.0009 213978.4005 262994.0728 311897.0454 259280.0761 241843.3134 300766.3658 315370.1745 302911.6485 313494.1334 0.705177473 0.682559505 0.838912263 0.994905525 0.827065162 0.771444463 0.959400301 1.005984294 0.966243436 1 18.25807892 6.258573166 0.260509115 1.011406972 3.97E-18 0.617937672 0.073864907 14.48222324 0.438016404 0.102205681 5.410758094 1813732.212 -6.258573166 -1.011406972 SVSGS(ph)PEPAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 SVSGS(1)PEPAAK;SVSGS(1)PEPAAK;SVS(0.002)GS(0.998)PEPAAK;SVS(0.001)GS(0.999)PEPAAK 236.65 1.55E-15 3156770000 3140700 3394180 3061930 3646340 3511830 4043300 4554840 3969820 5029320 4918370 TRUE FALSE 3017957.972 3297381.31 3615288.863 3834528.044 3624791.201 4125058.296 4610583.494 3887841.83 4458412.678 4585244.419 0.658189116 0.719128798 0.788461537 0.836275604 0.790533911 0.899637603 1.005526221 0.847902854 0.972339154 1 22.12856721 6.259267986 0.232796352 1.001302126 3.63E-11 0.827051763 0.046592606 9.068507743 0.239062197 0.070578871 2.948121831 1816636.291 -6.259267986 -1.001302126 EKFEEMIQQIK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKFEEMIQQIK 11 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 80.469 0.025528 165550000 256170 289350 228150 265980 286940 276600 266850 309400 306260 325700 FALSE TRUE 246158.5932 281098.0213 269381.7802 279707.2597 296169.6857 282193.0415 270115.7901 303010.7819 271494.6487 303640.0489 0.810692114 0.92576069 0.887174736 0.921180393 0.975397306 0.929367001 0.889592105 0.997927589 0.894133201 1 18.21200256 6.259301978 0.660994179 0.946377406 2.83E-12 0.485921998 0.039392731 17.17749975 1.152284472 0.014649464 19.09137671 1816778.485 -6.259301978 -0.946377406 ADKDES(ph)T(ph)MINEIT(ph)LAK ddPTM_BT-474_Pertuzumab_2h_R1 6 ADKDESTMINEITLAK 16 1 Q5THK1-4;Q5THK1-2;Q5THK1;H7BZH1 Q5THK1-4 PRR14L Protein PRR14L 3 ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK 45.33 0.088208 16246040000 10577080 9446070 8930780 4247210 7857450 8155700 6489770 6387400 6730340 6440180 TRUE FALSE 10163716.02 9176677.332 10544770.61 4466409.017 8110192.015 8320613.842 6569193.747 6255497.958 5966340.019 6003980.872 1.692829514 1.52843214 1.756296503 0.743907936 1.350802441 1.385849492 1.094139686 1.04189172 0.993730684 1 22.51748795 6.261414015 0.30346071 0.986774354 3.517597037 0.50202336 0.22423438 15.84576953 0.573531971 0.231240683 17.70452807 1825635.259 -6.261414015 2.530822683 MLSELKDEYDDLAESEQFGVVMGTVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 MLSELKDEYDDLAESEQFGVVMGTVPR 27 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 329.98 3.08E-95 371270000 198010 227770 197740 223320 240300 258760 243590 258740 291990 297120 FALSE TRUE 190271.5503 221274.2226 233476.0167 234845.572 248029.4677 263992.3045 246571.1273 253396.9286 258844.5193 276995.7978 0.686911324 0.798836027 0.842886494 0.847830811 0.895426825 0.953055269 0.890161978 0.914804234 0.934470925 1 18.07950456 6.264480637 0.371133173 0.947936732 2.94E-19 0.895330763 0.027147879 5.638195275 0.25278893 0.02186692 3.004526701 1838571.979 -6.264480637 -0.947936732 RREEGPPPPSPDGASS(ph)DAEPEPPSGR ddPTM_BT-474_Pertuzumab_2h_R1 4 RREEGPPPPSPDGASSDAEPEPPSGR 26 2 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9JWF0;C9IYK2;C9JJ64;F8WCB7 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 1 RREEGPPPPSPDGAS(0.153)S(0.847)DAEPEPPSGR;RREEGPPPPS(0.002)PDGAS(0.33)S(0.668)DAEPEPPSGR;RREEGPPPPSPDGAS(0.096)S(0.904)DAEPEPPSGR;RREEGPPPPS(0.005)PDGAS(0.156)S(0.839)DAEPEPPSGR 221.59 1.42E-34 2763530000 319052 372917 291361 334123 354789 395556 350979 325262 390516 396487 TRUE FALSE 306583.0951 362281.7723 344016.414 351367.1281 366201.1104 403554.4133 355274.386 318545.226 346186.2609 369632.5823 0.829426598 0.980113198 0.930698295 0.950584837 0.990716533 1.091771756 0.961155491 0.861788817 0.936568575 1 18.49573241 6.271016245 11.39515629 0.951014755 0.566803273 0 0.069357376 0 0 0.016002774 0 1866449.505 -6.271016245 -0.384211482 LPGMEYVDGDFQCHTFDS(ph)SNVE ddPTM_BT-474_Pertuzumab_2h_R1 1 LPGMEYVDGDFQCHTFDSSNVE 22 0 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 LPGMEYVDGDFQCHTFDS(0.5)S(0.5)NVE 70.569 0.01117 90302000 51926 44508 22992 32214 24332 23874 18225 25056 18040 24289 TRUE FALSE 49896.67451 43238.67542 27147.16585 33876.5684 25114.66088 24356.74864 18448.043 24538.58484 15992.17483 22643.8844 2.203538653 1.909507868 1.19887407 1.496058177 1.109114516 1.075643569 0.814703108 1.083673826 0.706246974 1 14.46683384 6.273338734 0.416900012 0.881912402 6.857991269 0.870890354 0.16197092 5.528455791 0.27457788 0.104392389 21.47479245 1876457.506 -6.273338734 5.976078867 up VDASGELEDVEWEDWE ddPTM_BT-474_Pertuzumab_2h_R1 2 VDASGELEDVEWEDWE 16 0 Q9NW68-9;Q9NW68-8;Q9NW68;Q9NW68-7 Q9NW68-9 BSDC1 BSD domain-containing protein 1 0 ; 264.61 1.17E-26 52218000 206038 229130 187579 230156 243213 243324 232134 255048 268950 288190 FALSE TRUE 197985.8072 222595.4367 221478.698 242034.3787 251036.167 248244.178 234974.9253 249781.1697 238419.9235 268670.6346 0.736908994 0.828506759 0.824350225 0.900859073 0.934363993 0.923972128 0.87458358 0.929692856 0.887405964 1 18.03547912 6.278440437 0.465718309 0.929163817 1.85E-11 0.76801491 0.033486148 8.581437639 0.464657364 0.019159168 5.966332849 1898630.431 -6.278440437 -0.929163817 LNGTDPEDVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LNGTDPEDVIR 11 0 J3QRS3;P19105;O14950;J3KTJ1;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ; 147.73 8.18E-05 508540000 341260 379030 307200 381830 384120 371390 395390 408600 426620 457970 FALSE TRUE 327923.1819 368220.4355 362717.8736 401536.2921 396475.5686 378899.7603 400228.9011 400162.2672 378191.8861 426951.284 0.768057608 0.862441335 0.849553303 0.940473321 0.928620158 0.887454317 0.937411166 0.937255097 0.885796343 1 18.70371194 6.279076168 0.535093171 0.93422114 2.49E-12 0.706530102 0.032937516 9.935145219 0.590841674 0.015336708 8.305452351 1901411.726 -6.279076168 -0.93422114 SSS(ph)PTSYWK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSPTSYWK 9 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 SS(0.001)S(0.999)PTSYWK;SS(0.003)S(0.939)PT(0.045)S(0.013)YWK;SS(0.033)S(0.967)PTSYWK 175.66 5.64E-05 5390320000 6981800 7289100 7511200 8626200 8052800 7457500 10085300 10112800 10634700 10894500 TRUE FALSE 6708943.537 7081222.005 8868640.926 9071399.216 8311825.625 7608295.76 10208726.92 9903967.146 9427493.44 10156605.81 0.660549761 0.697203587 0.873189439 0.893152632 0.818366468 0.749098262 1.005131745 0.97512568 0.928212989 1 23.27591502 6.28022621 0.241212451 1.009324985 7.33E-15 0.665946745 0.068425517 14.03263679 0.383103344 0.104659651 4.798481394 1906453.471 -6.28022621 -1.009324985 LGGLRPES(ph)PESLTSVSR ddPTM_BT-474_Pertuzumab_2h_R1 6 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.998)PES(0.002)LTSVSR;LGGLRPES(0.999)PES(0.001)LTSVSR;LGGLRPES(0.999)PES(0.001)LTSVSR;LGGLRPES(0.98)PES(0.019)LTSVSR;LGGLRPES(1)PESLTSVSR;LGGLRPES(1)PESLTSVSR 278.64 4.69E-36 37638380000 2104716 2359810 1838700 2698100 2159496 2450120 2730220 2405690 2817640 3067330 TRUE FALSE 2022461.372 2292510.529 2170993.992 2837349.264 2228958.15 2499663.105 2763633.249 2356011.661 2497793.32 2859577.007 0.707258929 0.801695679 0.759201094 0.992226912 0.77947128 0.874137363 0.966448269 0.823902156 0.873483495 1 21.44737033 6.280630462 0.453514198 0.900669556 4.81E-20 0.427246734 0.073150274 18.71454385 0.991132911 0.043114031 12.19870876 1908228.87 -6.280630462 -0.900669556 RQTESDWGK ddPTM_BT-474_Pertuzumab_2h_R1 2 RQTESDWGK 9 1 Q9NYV4-3;J3QSD7;A0A590UJE9;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 ; 93.843 0.014631 216720000 427040 391880 384850 440630 432600 375460 467210 501910 513350 564550 FALSE TRUE 410350.8047 380703.9661 454400.9559 463370.9671 446514.9719 383052.0584 472927.8557 491545.3831 455076.6601 526312.5257 0.779671364 0.723342021 0.86336717 0.880410297 0.848383708 0.727803424 0.898568498 0.93394202 0.864651016 1 19.0055602 6.281496798 0.041172015 1.453392932 4.00E-09 0.536863263 0.056573304 414.3568397 1.789821344 19.97671115 48.65496777 1912039.226 -6.281496798 -1.453392928 DGFNPADVEAGLYGSHLYVWDWQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGFNPADVEAGLYGSHLYVWDWQR 24 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 232.32 4.62E-34 829190000 410900 464860 357530 379400 489680 465540 415980 451200 498480 485020 FALSE TRUE 394841.5737 451602.6479 422143.6242 398980.8795 505431.0019 474953.5378 421070.8877 441882.5623 441894.6402 452169.1634 0.873216499 0.998747116 0.933596668 0.882370829 1.117791842 1.05038905 0.931224245 0.977250547 0.977277258 1 18.78650308 6.283424667 0.736436815 0.990785534 1.93E-17 0.215120683 0.062542291 41.10074317 2.732678854 0.023288253 55.45799488 1920545.792 -6.283424667 -0.990785534 EKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKPELSEPSHLNGPSSDPEAAFLSR 25 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 EKPELSEPSHLNGPS(0.5)S(0.5)DPEAAFLSR;EKPELSEPSHLNGPS(0.789)S(0.211)DPEAAFLSR;EKPELSEPSHLNGPS(0.829)S(0.171)DPEAAFLSR 221.59 6.78E-34 4520370000 773310 859135 773193 933468 888088 948288 1120761 1096280 1173544 1302350 TRUE FALSE 743088.1903 834633.311 912926.1747 981644.3953 916654.1571 967463.0331 1134477.208 1073641.435 1040328.205 1214140.674 0.612028084 0.687427189 0.751911367 0.808509604 0.754981837 0.796829439 0.934386955 0.884280922 0.85684322 1 20.21150416 6.284324569 0.173885526 1.018678179 4.40E-12 0.876691639 0.038476747 10.74128514 0.199068235 0.106634796 2.57005787 1924529.486 -6.284324569 -1.018678179 ALDEEVHK ddPTM_BT-474_Pertuzumab_2h_R1 3 ALDEEVHK 8 0 Q06210-2;Q06210;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;; 143.28 0.0006039 2892100000 3791100 4148940 3847350 4626860 4203820 4808330 5131230 5188560 5733020 5807260 FALSE TRUE 3642939.621 4030616.293 4542651.729 4865652.799 4339039.688 4905557.727 5194027.528 5081414.423 5082231.604 5413929.108 0.672882771 0.744490039 0.839067457 0.898728576 0.801458534 0.906099365 0.959382257 0.938581633 0.938732574 1 22.36824457 6.286059729 0.283442735 0.985247677 1.16E-15 0.875371398 0.034716823 6.722646834 0.222140166 0.040760045 2.707092906 1932234.039 -6.286059729 -0.985247677 SKPDLES(ph)SLESLVFDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKPDLESSLESLVFDLR 17 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 SKPDLES(0.595)S(0.405)LESLVFDLR 108.17 0.00040492 18271000 23598 26977 27656 32330 31259 32978 31010 37861 36927 45676 TRUE FALSE 22675.76407 26207.64237 32654.0544 33998.55517 32264.47412 33644.83776 31389.50966 37079.15712 32735.20177 42582.32384 0.53251589 0.615458247 0.766845288 0.798419441 0.757696415 0.790112768 0.737148817 0.870764058 0.768750947 1 15.37796706 6.287815371 0.150770474 0.994955152 4.17E-29 0.744731048 0.060923313 22.21851043 0.351836693 0.245931964 4.466742132 1940060.938 -6.287815371 -0.994955152 EKPLLIFEILQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKPLLIFEILQR 12 1 Q9H6T3;Q9H6T3-3;Q9H6T3-2 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 0 123.38 0.00021714 0 231450 240310 228450 258840 252110 252160 286790 289850 289110 319840 FALSE TRUE 222404.6781 233456.5941 269735.9968 272198.7634 260219.3471 257258.848 290299.8218 283864.4962 256291.4448 298176.9519 0.74588152 0.782946477 0.904617192 0.912876605 0.872701077 0.862772412 0.973582364 0.952000127 0.859528019 1 18.18580922 6.288750923 0.444471786 0.939260596 2.80E-19 0.650251982 0.044944942 11.5381956 0.597683414 0.028720758 7.657341726 1944244.697 -6.288750923 -0.939260596 QITT(ph)SPITVR ddPTM_BT-474_Pertuzumab_2h_R1 4 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.124)T(0.438)S(0.438)PITVR;QIT(0.01)T(0.831)S(0.159)PITVR;QIT(0.005)T(0.721)S(0.274)PITVR;QIT(0.039)T(0.827)S(0.127)PIT(0.006)VR 132.56 0.0024624 2220490000 2779840 3058010 2404160 3028660 2862730 3091710 3099940 3102090 2907960 3012030 TRUE FALSE 2671200.78 2970798.549 2838645.192 3184969.506 2954812.31 3154226.494 3137877.993 3038030.757 2577860.572 2808022.525 0.951274698 1.057968204 1.010905421 1.134239301 1.052275145 1.123291023 1.117468954 1.081911107 0.91803415 1 21.42112308 6.290637608 12.88642611 1.055309587 0.61904722 0 0.070808024 0 0 0.015270755 0 1952709.359 -6.290637608 -0.436262367 ES(ph)PEGSYTDDANQEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESPEGSYTDDANQEVR 16 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 ES(1)PEGSYTDDANQEVR;ES(1)PEGSYTDDANQEVR 517.16 3.70E-286 2545600000 582410 548890 649910 724280 616650 583430 780860 854990 901230 941840 TRUE FALSE 559648.7733 533236.1946 767363.1942 761660.1776 636485.1073 595227.3543 790416.3983 837334.1577 798926.1487 878048.3379 0.637378091 0.607297083 0.873941856 0.867446751 0.724886182 0.677898162 0.900196907 0.953631049 0.909888572 1 19.74394084 6.295524633 0.147933195 1.068687591 6.67E-14 0.582895248 0.086053324 32.4505316 0.502444025 0.391501767 6.873614412 1974806.886 -6.295524633 -1.068687591 FPAMSDAYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FPAMSDAYDR 10 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ; 100.25 0.0096421 366250000 244470 263420 205936 262310 238360 122710 273230 237380 270040 294540 FALSE TRUE 234915.8421 255907.5195 243153.2162 275847.8505 246027.0659 125191.2803 276573.8705 232478.02 239386.1913 274590.5435 0.855513228 0.931960425 0.885511981 1.004578843 0.895977927 0.455919853 1.007222853 0.846635201 0.871793283 1 18.06692242 6.296538618 15.87195024 0.870176634 0.552011273 0 0.151920489 0 0 0.032735757 0 1979423.028 -6.296538618 -0.318165362 QESDKNGESAS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 2 QESDKNGESASPER 14 1 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGES(0.038)AS(0.962)PER;QESDKNGES(0.213)AS(0.787)PER 74.519 0.019875 427800000 137047 131445 149951 140291 155074 165221 172101 180955 200183 194015 TRUE FALSE 131691.0517 127696.3173 177050.4813 147531.4353 160062.096 168561.8818 174207.2235 177218.216 177459.0651 180874.1912 0.728080943 0.705995236 0.978859837 0.815657747 0.88493607 0.931928876 0.963140304 0.979787192 0.981118776 1 17.46462704 6.297378258 0.300568221 1.004600925 1.28E-19 0.706086835 0.056500213 10.16519248 0.357460064 0.057336976 4.478000961 1983253.631 -6.297378258 -1.004600925 KSLEDQVEMLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSLEDQVEMLR 11 1 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 102.9 0.0044992 238770000 526170 596020 449240 564110 546160 566490 612920 566180 635160 651540 FALSE TRUE 505606.6947 579022.0932 530427.6613 593223.7847 563727.7324 577944.8159 620421.0983 554488.1851 563059.2996 607410.6155 0.832396869 0.953263045 0.87326044 0.976643756 0.928083438 0.951489489 1.021419584 0.912872069 0.926982975 1 19.2123126 6.2999459 0.69019695 0.955390431 2.57E-14 0.430189486 0.04058312 22.09605881 1.423993034 0.014640248 26.50013791 1995013.782 -6.2999459 -0.955390431 EAQSSQATPVQTSQPDSSNIVKVS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 EAQSSQATPVQTSQPDSSNIVKVSPR 26 1 Q8IZH2-2;Q8IZH2;H7C5E4 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 1 EAQSSQATPVQTSQPDSSNIVKVS(1)PR 184.86 9.20E-18 332820000 68353 69191 71046 68752 76153 89899 78752 83297 93588 96199 TRUE FALSE 65681.68919 67217.74043 83885.59261 72300.29896 78602.53041 91716.81937 79715.79053 81576.88784 82964.28259 89683.35604 0.732373231 0.749500726 0.935352961 0.806172986 0.876445016 1.022673809 0.888858246 0.909610115 0.92508004 1 16.45255265 6.300589327 0.390700272 0.947066632 7.83E-14 0.612512419 0.057350356 12.8786241 0.592452508 0.042638225 7.3474971 1997971.676 -6.300589327 -0.947066632 DPDEPVLLEEPVVLALAEK ddPTM_BT-474_Pertuzumab_2h_R1 5 DPDEPVLLEEPVVLALAEK 19 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;;; 202.13 1.32E-15 145222300 98685.4 93254 100148.8 111332.4 109428 109831.6 118405.8 143239 147837.7 150335.6 FALSE TRUE 94828.66547 90594.48723 118247.916 117078.2785 112947.851 112052.4702 119854.8856 140281.0646 131055.7841 140153.2359 0.676607036 0.646395973 0.843704501 0.835359082 0.805888286 0.799499701 0.855170306 1.000912064 0.935089249 1 17.09664553 6.301892638 0.182039826 1.046550972 1.80E-17 0.784753394 0.052445182 14.04696024 0.272655123 0.136054277 3.633229682 2003976.561 -6.301892638 -1.046550972 GAVDGGLSIPHSTK ddPTM_BT-474_Pertuzumab_2h_R1 5 GAVDGGLSIPHSTK 14 0 P46777;A0A2R8Y6J3;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ;;;; 188.48 8.28E-07 3918170000 4380710 4998830 4175800 4729490 4694430 5271510 5214630 5137130 5610300 6044910 FALSE TRUE 4209507.01 4856268.263 4930459.95 4973579.546 4845430.604 5378103.544 5278448.202 5031046.47 4973442.264 5635482.861 0.746964743 0.861730642 0.87489574 0.882547187 0.859807531 0.954328791 0.936645241 0.892744525 0.882522827 1 22.4261078 6.304105386 0.530729304 0.921293696 4.06E-31 0.661576272 0.037215493 12.31538016 0.711839112 0.018216824 10.10000941 2014212.958 -6.304105386 -0.921293696 RPEVDS(ph)PGETPSWAPQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPEVDSPGETPSWAPQPK 18 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 RPEVDS(1)PGETPSWAPQPK 156.74 5.76E-09 187840000 159150 166770 154510 163000 169760 190650 180870 191490 190960 207520 TRUE FALSE 152930.2421 162013.8829 182433.3941 171412.4495 175220.4846 194505.0736 183083.5412 187535.6646 169283.0214 193464.4856 0.790482251 0.837434749 0.94298131 0.886015069 0.905698449 1.005378703 0.94634186 0.969354474 0.875008252 1 17.56170923 6.309598026 0.504663461 0.956756237 2.67E-18 0.616312721 0.041159121 12.15212536 0.677794449 0.021292478 9.706609658 2039849.027 -6.309598026 -0.956756237 ISS(ph)PTETER ddPTM_BT-474_Pertuzumab_2h_R1 2 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 1 IS(0.035)S(0.884)PT(0.081)ETER;IS(0.28)S(0.69)PT(0.03)ETER 142.94 0.00010818 941440000 1197350 1262160 1044450 1199750 1264830 1236840 1225950 1347820 1158230 1317290 TRUE FALSE 1150556.238 1226164.433 1233205.349 1261669.241 1305514.406 1261849.752 1240953.543 1319987.046 1026752.586 1228068.775 0.936882577 0.998449319 1.004182643 1.027360411 1.063062943 1.027507399 1.010491894 1.07484782 0.836070916 1 20.22795993 6.31093093 9.97130665 1.006836794 0.607548468 0 0.065442681 0 0 0.013789203 0 2046119.198 -6.31093093 -0.399288326 S(ph)PHIPYK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPHIPYK 7 0 Q9UPT9-2;Q9UPT9 Q9UPT9-2 USP22 Ubiquitin carboxyl-terminal hydrolase 22 1 S(1)PHIPYK;S(1)PHIPYK 78.334 0.022941 1118840000 1323440 1289200 1324590 1403090 1542880 1694060 1553500 1692960 1780080 1981980 TRUE FALSE 1271718.502 1252433.278 1563972.878 1475503.643 1592508.136 1728315.054 1572512.198 1657999.784 1578012.781 1847738.729 0.688256668 0.677819466 0.846425338 0.798545606 0.861868678 0.935367661 0.851046835 0.897312893 0.854023762 1 20.81732934 6.311474671 0.310947638 0.931888022 3.75E-19 0.756674878 0.046758578 9.212762283 0.334121195 0.045097428 3.9264425 2048682.564 -6.311474671 -0.931888022 DNTFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNTFFR 6 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 0 ; 120.65 0.046517 172513000 268600 290940 250930 298140 297130 268430 311290 317640 358200 350430 FALSE TRUE 258102.815 282642.6761 296278.6329 313527.0411 306687.4563 273857.8385 315099.6601 311080.623 317538.6377 326695.064 0.79004198 0.865157473 0.90689657 0.95969323 0.938757545 0.838267451 0.964506951 0.952204846 0.97197256 1 18.31758513 6.314999854 0.538344342 0.951166877 2.05E-37 0.618210819 0.039457856 13.90762015 0.802025665 0.019913932 12.02433613 2065379.462 -6.314999854 -0.951166877 TDEGHPFK ddPTM_BT-474_Pertuzumab_2h_R1 5 TDEGHPFK 8 0 A8MT72;Q2NKQ5;Q16799-3;Q16799-2;Q16799 A8MT72 RTN1 Reticulon;Reticulon-1 0 ;;;; 95.099 0.0098907 9021810000 6718940 8962630 7224510 10752700 6515800 8327660 10739000 10183200 11128300 11148700 FALSE TRUE 6456356.397 8707024.568 8530139.665 11307648.14 6725386.624 8496050.991 10870427.09 9972913.361 9865062.038 10393588.62 0.621186448 0.837730344 0.820711689 1.087944554 0.647070696 0.817431909 1.045878136 0.959525504 0.949148788 1 23.30919053 6.318258569 0.311534267 0.979918186 5.85E-32 0.357006393 0.120734282 24.28932358 0.879651164 0.123684418 10.91974406 2080935.261 -6.318258569 -0.979918186 TPQMHGTEMANS(ph)PQPPPLS(ph)PHPCDVVDEGVTK ddPTM_BT-474_Pertuzumab_2h_R1 5 TPQMHGTEMANSPQPPPLSPHPCDVVDEGVTK 32 0 Q9UHV7;J3QRB7 Q9UHV7 MED13 Mediator of RNA polymerase II transcription subunit 13 2 TPQMHGTEMANS(1)PQPPPLS(1)PHPCDVVDEGVTK;TPQMHGT(0.002)EMANS(0.998)PQPPPLS(1)PHPCDVVDEGVTK;TPQMHGTEMANS(1)PQPPPLS(1)PHPCDVVDEGVTK;TPQMHGT(0.001)EMANS(0.999)PQPPPLS(1)PHPCDVVDEGVTK;T(0.001)PQMHGT(0.001)EMANS(0.998)PQPPPLS(1)PHPCDVVDEGVTK 157.86 3.09E-12 1236400000 799793 814763 700259 750990 783227 879546 811408 707778 948374 913076 TRUE FALSE 768536.2053 791526.757 826811.3785 789748.6839 808420.2078 897331.0227 821338.2538 693162.137 840718.5594 851232.5492 0.902851055 0.929859599 0.971310812 0.927770777 0.949705469 1.05415497 0.964881165 0.814304079 0.987648511 1 19.69919379 6.319977837 14.45124679 0.942719463 0.563776251 0 0.061272997 0 0 0.014404609 0 2089189.511 -6.319977837 -0.378943212 SEAEEAITSFNGHKPPGSSEPITVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SEAEEAITSFNGHKPPGSSEPITVK 25 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 291.15 4.62E-63 413760000 455300 507750 475370 521170 489150 579830 537650 604010 671760 635820 FALSE TRUE 437506.3726 493269.4671 561279.9335 548067.6462 504883.954 591554.5599 544229.9215 591536.9824 595504.621 592755.3451 0.738089291 0.832163676 0.946899827 0.924610213 0.851757742 0.997974231 0.918135831 0.997944578 1.004638129 1 19.17707724 6.32331542 0.397265664 0.986738032 7.12E-24 0.745242365 0.042803241 9.875371936 0.454191047 0.031747188 6.016200881 2105306.932 -6.32331542 -0.986738032 EPS(ph)PLPELALR ddPTM_BT-474_Pertuzumab_2h_R1 2 EPSPLPELALR 11 0 Q13207 Q13207 TBX2 T-box transcription factor TBX2 1 EPS(1)PLPELALR;EPS(1)PLPELALR 152.38 3.46E-05 114980000 93236 105423 85487 103676 106260 100132 103104 126554 116667 113620 TRUE FALSE 89592.23404 102416.4393 100936.4025 109026.7308 109677.9494 102156.7376 104365.8176 123940.6157 103423.4513 105924.4162 0.845812866 0.966882263 0.952909689 1.029288003 1.035435958 0.9644305 0.985285748 1.170085426 0.976389155 1 16.69267565 6.324767938 0.503716666 1.044954235 1.03E-15 0.446348676 0.057457881 17.32585047 0.952311799 0.032350954 15.12586001 2112360.012 -6.324767938 -1.044954235 SFSSPPS(ph)PSNK ddPTM_BT-474_Pertuzumab_2h_R1 3 SFSSPPSPSNK 11 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SFSS(0.004)PPS(0.992)PS(0.003)NK;SFSS(0.002)PPS(0.996)PS(0.003)NK;SFSSPPS(0.999)PS(0.001)NK 164.13 3.37E-05 699740000 1813400 1860220 1840180 2183520 1997630 2130950 2338480 2306090 2645100 2696340 TRUE FALSE 1742530.323 1807168.347 2172741.461 2296211.729 2061885.583 2174039.269 2367099.018 2258468.436 2344839.337 2513714.49 0.693209324 0.718923471 0.864354909 0.913473562 0.820254484 0.864871201 0.941673777 0.898458614 0.932818483 1 21.26138937 6.326784928 0.328398064 0.948816222 6.33E-31 0.79310494 0.041941921 9.09093187 0.346881309 0.040704128 4.220022547 2122193.246 -6.326784928 -0.948816222 LLEAQIATGGIIDPEESHRLPVEVAYK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEAQIATGGIIDPEESHRLPVEVAYK 27 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 257.53 3.80E-53 1543390000 638180 673430 609410 704430 711940 722980 737240 793830 856140 841620 FALSE TRUE 613239.2201 654224.4358 719543.9433 740785.7167 734840.1967 737599.151 746262.5637 777437.1331 758954.5764 784616.3278 0.781578459 0.833814455 0.917064708 0.944137524 0.936559909 0.940076219 0.95111781 0.990850057 0.967293886 1 19.58162783 6.335940931 0.437575321 0.979997687 4.20E-16 0.937880773 0.016169953 4.408318628 0.217636505 0.01098404 3.019253434 2167409.293 -6.335940931 -0.979997687 RAELGSWS(ph)SQEHLEWEPACQTPQPSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RAELGSWSSQEHLEWEPACQTPQPSAR 27 1 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 RAELGS(0.293)WS(0.352)S(0.352)QEHLEWEPACQT(0.003)PQPSAR 47.099 0.060385 44302000 74600 63686 58656 62824 54636 63983 59496 68516 76036 65668 TRUE FALSE 71684.54953 61869.73764 69256.444 66066.35417 56393.41656 65276.7801 60224.12985 67101.12066 67404.71205 61220.24787 1.17092877 1.010609068 1.131266965 1.079158554 0.921156293 1.066261284 0.983728945 1.096060911 1.101019914 1 15.90172127 6.33665142 2.074048512 1.046128767 75.13806193 0.269393413 0.061488509 1320.371581 11.728943 0.015618105 463807.2048 2170957.991 -6.33665142 74.09193316 DVDYVCISDNYWLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVDYVCISDNYWLGK 15 0 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 136.38 5.41E-05 41183000 49150 52304 47233 57490 57753 62185 63646 62465 76670 74859 FALSE TRUE 47229.16366 50812.34113 55769.05379 60457.06579 59610.67769 63442.42331 64424.91879 61175.07592 67966.74303 69788.73325 0.676744819 0.728088027 0.799112567 0.866286906 0.854159044 0.909063976 0.923142115 0.876575245 0.973892774 1 16.09070652 6.337079303 0.270143889 0.975304294 1.31E-17 0.929984363 0.025654329 5.375447288 0.164047943 0.032519056 2.037296566 2173097.954 -6.337079303 -0.975304294 DYDWINAER ddPTM_BT-474_Pertuzumab_2h_R1 4 DYDWINAER 9 0 O95347-2;O95347;A0A0C4DGE5 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ;;; 201.21 5.08E-05 1475510000 1172290 1236090 1119920 1307360 1262340 1266320 1417840 1410790 1508310 1559460 FALSE TRUE 1126475.611 1200837.923 1322314.456 1374833.006 1302944.313 1291925.858 1435191.95 1381656.693 1337092.972 1453836.385 0.7748297 0.825978725 0.909534573 0.945658686 0.896211105 0.888632222 0.987175699 0.950352259 0.919699758 1 20.47143349 6.340047141 0.468479639 0.954741932 9.58E-19 0.755621577 0.032426703 9.614973424 0.497377839 0.019435214 7.005847541 2187999.11 -6.340047141 -0.954741932 WAHDKFS(ph)GEEGEIEDDESGTENR ddPTM_BT-474_Pertuzumab_2h_R1 8 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR 310.9 2.17E-73 11228020000 3549343 3294207 3565956 4344114 3955616 3698689 4875928 4095871 6046864 5716843 TRUE FALSE 3410630.752 3200259.442 4210403.573 4568314.244 4082851.981 3773479.026 4935601.065 4011289.833 5360449.349 5329636.132 0.639936886 0.600464903 0.789998317 0.857153121 0.766065803 0.708018133 0.926067173 0.752638592 1.005781486 1 22.34560561 6.343879808 0.12099888 1.090082524 7.89E-17 0.615153686 0.08292484 43.28590227 0.537216416 0.643364088 7.686988696 2207393.745 -6.343879808 -1.090082524 SFSS(ph)PENFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SFSSPENFQR 10 0 J3KPD3;Q9Y580;G3V1T9;I3L521;F5GXV8;F5GY08 J3KPD3 RBM7 RNA-binding protein 7 1 S(0.003)FS(0.041)S(0.955)PENFQR 100.09 0.0044616 154580000 99786 114190 93669 120870 102920 124010 128840 134890 122250 141010 TRUE FALSE 95886.2528 110933.413 110597.072 127108.1152 106230.5153 126517.5672 130416.7825 132104.4744 108372.6925 131459.2671 0.729398961 0.84386149 0.841302971 0.96690114 0.808086928 0.962408889 0.992069904 1.004908039 0.824382297 1 17.00425632 6.348537113 0.392311861 0.966740689 4.99E-12 0.505701073 0.065821828 15.51286324 0.693810443 0.048372033 9.154478154 2231192.867 -6.348537113 -0.966740689 SMIGSTAQQFLTFLSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMIGSTAQQFLTFLSHR 17 0 O15357;A0A0A0MTP6;O15357-2 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 0 176.49 1.10E-09 72776000 36812 38609 30803 35972 39357 32722 36872 40599 45558 34984 FALSE TRUE 35373.34634 37507.90912 36369.78731 37828.51923 40622.95365 33383.66126 37323.25057 39760.61646 40386.44683 32614.50252 1.08458948 1.150037751 1.115141563 1.159868044 1.245548775 1.023583335 1.144375897 1.219108476 1.23829719 1 14.993226 6.348609774 0.887195467 1.156540825 2.30E-07 0.031190848 0.078975263 103.2427131 5.970603592 0.024367641 210.5663047 2231566.198 -6.348609774 -1.156540594 VSFQHEVYPAEPATGPAAPSQELEERPLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 VSFQHEVYPAEPATGPAAPSQELEERPLSR 30 1 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 0 105.21 0.00019784 114780000 20585 32403 20517 29484 27479 30759 33119 37272 29048 40631 FALSE TRUE 19780.51544 31478.89817 24224.8783 31005.67277 28362.88699 31380.96805 33524.32023 36502.32018 25750.59282 37879.02618 0.522202322 0.831037683 0.639532764 0.818544612 0.748775506 0.828452345 0.885036486 0.96365519 0.679811374 1 15.20911162 6.349853084 0.204842381 0.964428564 7.24E-12 0.471267406 0.101652364 22.99003988 0.503218661 0.179242743 6.270481803 2237963.939 -6.349853084 -0.964428564 YMADMDELFSQVDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 YMADMDELFSQVDEK 15 0 Q9UNE7;Q9UNE7-2;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 121.08 0.0002728 311915000 56711 63808 53207 69268 62185 67844 64837 72789 82931 78981 FALSE TRUE 54494.67142 61988.25831 62822.68848 72842.92978 64185.237 69215.85216 65630.4946 71285.88171 73517.02056 73631.54652 0.740099509 0.841870927 0.853203436 0.989289689 0.871708392 0.940029857 0.891336631 0.968143209 0.998444607 1 16.16803638 6.349881641 0.410963331 0.966332903 2.71E-17 0.737284275 0.041335332 10.21633765 0.474889023 0.028566175 6.38919062 2238111.098 -6.349881641 -0.966332903 VTLYNTDQDGSDS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTLYNTDQDGSDSPR 15 0 Q9UPW0-2;Q9UPW0;C9JXI1;C9JVP0 Q9UPW0-2 FOXJ3 Forkhead box protein J3 1 VTLYNTDQDGS(0.002)DS(0.998)PR;VTLYNTDQDGSDS(1)PR 252.33 1.27E-24 596080000 450040 488730 407870 464520 467590 475940 487230 562380 504750 506960 TRUE FALSE 432451.9393 474791.8989 481581.182 488493.9329 482630.457 485563.8329 493192.8665 550766.6565 447452.8961 472623.1476 0.915003722 1.004588754 1.018953863 1.033580211 1.021173972 1.027380557 1.043522453 1.165339995 0.946743507 1 18.85033076 6.350570787 0.628341124 1.052924434 7.93E-18 0.273254546 0.05316335 25.32457473 1.500540258 0.022540261 29.92421539 2241665.395 -6.350570787 -1.052924434 EMSGSNETSS(ph)PVSEKPSASR ddPTM_BT-474_Pertuzumab_2h_R1 7 EMSGSNETSSPVSEKPSASR 20 1 A0A087X165;Q9C0H9 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 EMSGSNET(0.001)S(0.006)S(0.991)PVS(0.001)EKPSASR;EMSGSNET(0.005)S(0.092)S(0.902)PVS(0.001)EKPSASR;EMSGSNETS(0.019)S(0.98)PVS(0.001)EKPSASR;EMSGSNET(0.005)S(0.21)S(0.784)PVSEKPSASR;EMSGSNETS(0.187)S(0.813)PVSEKPSASR;EMSGSNET(0.012)S(0.079)S(0.91)PVSEKPSASR;EMSGSNETS(0.017)S(0.983)PVSEKPSASR 181.13 3.15E-17 10478090000 4060380 4059070 3802440 4502900 4718610 4725390 4879600 5441420 5200070 5809660 TRUE FALSE 3901695.861 3943309.298 4489625.493 4735295.209 4870388.376 4820940.623 4939318.004 5329052.775 4609779.854 5416166.553 0.720379594 0.728062784 0.828930471 0.874289068 0.899231648 0.890101989 0.911958293 0.983915971 0.851114863 1 22.36884067 6.352010577 0.310891269 0.965590295 2.55E-10 0.800357603 0.039328654 7.843976478 0.278533791 0.037968094 3.481699829 2249109.382 -6.352010577 -0.965590295 ERDSASFNPELLTHILDGSPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ERDSASFNPELLTHILDGSPEK 22 1 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;; 220.25 6.20E-26 293461000 296749 378583 285306 379012 325939 377605 431204 419475 455557 430463 FALSE TRUE 285151.721 367786.1835 336867.1408 398572.8547 336423.1239 385240.4318 436481.2035 410812.6947 403844.0792 401307.3576 0.710556923 0.916470074 0.839424283 0.993186014 0.838317857 0.95996354 1.087648146 1.023685928 1.006321144 1 18.61434808 6.35555992 0.321550394 1.039652433 1.26E-09 0.643930015 0.063606106 12.45141415 0.457488451 0.061137301 6.199322293 2267565.911 -6.35555992 -1.039652431 EDAMAMVDHCLK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDAMAMVDHCLK 12 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 156.69 6.56E-05 6223590000 5832310 5784370 5713400 6596110 6285710 6257180 6747400 7006080 7874220 7977280 FALSE TRUE 5604376.877 5619405.431 6745938.474 6936536.028 6487895.571 6383704.467 6829976.7 6861402 6980371.557 7436971.72 0.753583191 0.75560398 0.907081367 0.932709749 0.872384058 0.858374175 0.918381427 0.922606977 0.938604021 1 22.82628386 6.361105943 0.424442058 0.935600826 2.15E-35 0.699944626 0.04108806 11.54998055 0.546575653 0.028415227 7.299277359 2296708.847 -6.361105943 -0.935600826 DGWLHTGDIGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGWLHTGDIGK 11 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ; 143.97 3.69E-05 426740000 796560 793640 839600 1000220 905530 852550 1117090 1087100 1275060 1309870 FALSE TRUE 765429.5546 771006.1643 991334.3968 1051841.474 934657.1948 869789.1451 1130761.282 1064651.005 1130320.534 1221151.338 0.626809741 0.631376423 0.811803063 0.861352267 0.765390141 0.712269739 0.925979644 0.871841984 0.925618716 1 20.21981057 6.364640369 0.160116997 1.035661319 4.16E-14 0.724582173 0.063473954 21.29650404 0.351778515 0.220749729 4.759740616 2315476.452 -6.364640369 -1.035661319 THTCPPCPAPELLGGPSVFLFPPKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 THTCPPCPAPELLGGPSVFLFPPKPK 26 1 A0A0A0MS08;P01857;A0A0A0MS07 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 58.284 0.045565 114290000 521980 183860 105770 72209 43953 36582 40866 42353 42828 37279 FALSE TRUE 501580.4445 178616.4928 124884.9918 75935.71514 45366.78816 37321.7131 41366.13033 41478.39575 37966.34499 34754.06013 14.43228339 5.139442476 3.59339287 2.184945151 1.305366567 1.073880662 1.190253173 1.193483455 1.092429053 1 15.08489391 6.365244188 0.839344746 1.149786638 199.9999998 0.990812774 0.379260436 2.490316881 0.143385951 0.124272378 815.6428171 2318698.005 -6.365244188 198.8502131 up GTEASPPQNNSGSSS(ph)PVFTFR ddPTM_BT-474_Pertuzumab_2h_R1 4 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEASPPQNNSGSS(0.039)S(0.961)PVFTFR;GTEASPPQNNSGSS(0.029)S(0.971)PVFTFR;GTEASPPQNNSGSS(0.003)S(0.997)PVFTFR;GTEASPPQNNS(0.001)GS(0.021)S(0.041)S(0.937)PVFTFR 442.05 7.67E-198 1235885000 581302 613021 523508 643194 587581 612018 666466 736044 755150 723871 TRUE FALSE 558584.0752 595538.2413 618117.541 676389.3194 606481.0765 624393.4233 674622.4103 720844.4342 669428.5378 674842.5724 0.82772501 0.882484694 0.915943312 1.002292012 0.898700084 0.925243085 0.999673758 1.068166805 0.991977337 1 19.36419146 6.366463831 0.278150464 1.033002605 0.363004158 0.652771324 0.040537766 13.35822968 0.416089787 0.05192583 3.611315666 2325218.83 -6.366463831 -0.669998447 TSVDTGQVSRPENPSQPAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSVDTGQVSRPENPSQPASPR 21 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 TSVDTGQVSRPENPSQPAS(1)PR;TSVDTGQVSRPENPSQPAS(1)PR;TSVDTGQVSRPENPS(0.007)QPAS(0.993)PR 239.9 3.69E-30 1489910000 891600 924185 861104 993442 927696 994299 1054054 1133943 1057216 1192468 TRUE FALSE 856755.2863 897828.1487 1016724.648 1044713.661 957536.1844 1014404.407 1066953.828 1110526.681 937205.2719 1111701.08 0.770670553 0.807616512 0.914566574 0.939743317 0.861325226 0.912479465 0.959748845 0.998943601 0.843037115 1 20.08433749 6.368098452 0.447417187 0.952074019 6.63E-15 0.561851929 0.049224417 14.31050906 0.700825506 0.030983424 9.855346276 2333987.103 -6.368098452 -0.952074019 FQSPQIQATIS(ph)PPLQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 FQSPQIQATISPPLQPK 17 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 1 FQSPQIQATIS(1)PPLQPK;FQSPQIQATIS(1)PPLQPK 293.83 4.80E-46 1041540000 310040 350450 291530 324280 348380 334480 371270 392350 391480 366570 TRUE FALSE 297923.294 340455.5091 344215.956 341016.1297 359585.9591 341243.4148 375813.7133 384247.8354 347040.8316 341741.8874 0.871778687 0.996235819 1.007239583 0.997876299 1.052215056 0.998541377 1.099700467 1.124380269 1.015505691 1 18.38254756 6.37002003 0.515256557 1.064659538 1.57E-16 0.57916873 0.042151032 14.08051047 0.752844722 0.022924293 13.02019126 2344336.937 -6.37002003 -1.064659538 SIVEEEEDDDYVELK ddPTM_BT-474_Pertuzumab_2h_R1 4 SIVEEEEDDDYVELK 15 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;; 274.05 4.23E-33 260576000 267613 269710 288010 308501 289853 309605 341726 397299 405685 406744 FALSE TRUE 257154.3881 262018.1349 340059.8137 324422.7736 299176.385 315865.4252 345908.145 389094.6368 359633.3396 379194.8666 0.678158938 0.690985448 0.89679435 0.855556871 0.788977941 0.832989719 0.912217373 1.026107342 0.948412996 1 18.53257991 6.374013874 0.207301994 1.040117083 3.26E-16 0.741231644 0.057196458 14.10517203 0.310439128 0.115253267 4.213278782 2365995.279 -6.374013874 -1.040117083 LFDDS(ph)DER ddPTM_BT-474_Pertuzumab_2h_R1 2 LFDDSDER 8 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFDDS(1)DER;LFDDS(1)DER 108.47 0.0039908 300720000 540440 499540 608300 708730 602230 566720 729470 769150 840700 885930 TRUE FALSE 519319.0073 485293.6083 718233.3416 745307.6402 621601.2749 578179.4667 738397.4721 753266.7837 745267.2605 825925.172 0.628772466 0.587575757 0.869610669 0.90239124 0.752612096 0.700038558 0.894024661 0.91202788 0.90234235 1 19.65565156 6.374110513 0.183025948 1.005874821 6.11E-16 0.588197786 0.084073255 24.35856825 0.464837669 0.21495657 6.117703358 2366521.818 -6.374110513 -1.005874821 PRPS(ph)PSSTR ddPTM_BT-474_Pertuzumab_2h_R1 2 PRPSPSSTR 9 1 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 1 PRPS(0.884)PS(0.108)S(0.007)T(0.001)R;PRPS(0.796)PS(0.148)S(0.05)T(0.006)R 88.101 0.0078803 441110000 152305 149205 173680 170615 164759 153091 212520 212411 200622 216070 TRUE FALSE 146352.7522 144949.8195 205067.8395 179420.4606 170058.6229 156186.6049 215120.8833 208024.6386 177848.2316 201435.3864 0.726549366 0.719584687 1.018032845 0.89070974 0.844234103 0.775368259 1.067939884 1.032711493 0.882904612 1 17.61995762 6.374769105 0.323793262 0.992141909 3.59E-13 0.382633058 0.096624639 21.62882915 0.792239775 0.097841048 10.39032922 2370113.289 -6.374769105 -0.992141909 LTPVRPAAAS(ph)PIVSGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTPVRPAAASPIVSGAR 17 1 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR 185.3 3.55E-10 791870000 381000 448450 375170 486610 436250 554150 536540 506240 560410 693450 TRUE FALSE 366110.0988 435660.6451 442971.5646 511724.0004 450282.3774 565355.2927 543106.337 495785.9671 496794.6062 646482.0138 0.566311345 0.673894456 0.685203231 0.791551798 0.696511841 0.874510475 0.840095046 0.766898315 0.768458512 1 19.30225071 6.376929027 0.105431513 1.078441517 1.34E-19 0.737068607 0.059000652 44.81778519 0.480448221 0.753625372 6.954347991 2381930.179 -6.376929027 -1.078441517 SKDAS(ph)PINR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKDASPINR 9 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 S(0.001)KDAS(0.999)PINR;S(0.001)KDAS(0.999)PINR;SKDAS(1)PINR 97.779 0.016995 615790000 563170 556460 568090 616560 629580 572190 722060 730200 869440 885510 TRUE FALSE 541160.6938 540590.3056 670756.5001 648380.7355 649831.0125 583760.0738 730896.7863 715121.1148 770744.8162 825533.619 0.655528353 0.654837421 0.81251264 0.785408033 0.787164808 0.707130589 0.885362836 0.866253171 0.933632257 1 19.65496744 6.379228554 0.103365942 1.143883505 8.23E-13 0.788477469 0.050353041 37.70143938 0.396067528 0.686098281 6.100066596 2394575.604 -6.379228554 -1.143883505 PGDPS(ph)RRPCLISPYHYR ddPTM_BT-474_Pertuzumab_2h_R1 1 PGDPSRRPCLISPYHYR 17 2 H3BVI4;Q96S06-2;Q96S06 H3BVI4 LMF1 Lipase maturation factor;Lipase maturation factor 1 1 PGDPS(0.999)RRPCLIS(0.001)PYHYR 51.348 0.079413 16766000 19804 19618 11148 11269 14572 13258 15810 551.12 18548 9505.9 TRUE FALSE 19030.03779 19058.51385 13162.69159 11850.59444 15040.72161 13526.08584 16003.48751 539.7391794 16442.5088 8862.056926 2.147361267 2.150574523 1.485286282 1.337228427 1.697204356 1.526291916 1.805843456 0.060904504 1.855382891 1 13.11342588 6.380675503 0.244390736 0.888476097 5.028252087 0.303778312 0.490028272 25.06317503 0.667567148 0.692251054 36.03248156 2402566.974 -6.380675503 4.13977599 GPIVESYIGFIESYRDPFGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 GPIVESYIGFIESYRDPFGSR 21 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 171.35 6.40E-12 514230000 486610 572950 442940 507560 557880 533960 575730 538560 547470 551740 FALSE TRUE 467592.7432 556610.027 522989.1111 533755.2324 575824.7169 544757.037 582775.956 527438.5478 485323.5008 514370.1584 0.909058847 1.082119594 1.016756324 1.037687011 1.119475357 1.059075897 1.132989437 1.025406586 0.94352966 1 18.97244742 6.381131273 12.75650358 1.04095873 0.577243446 0 0.067869662 0 0 0.01450313 0 2405089.67 -6.381131273 -0.463715284 MLDAEDIVGTARPDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 MLDAEDIVGTARPDEK 16 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4 P12814-3 ACTN1 Alpha-actinin-1 0 ; 168.41 5.46E-09 3487600000 1714130 1760610 1480560 2110700 1909300 1640000 2241590 2286580 2558980 2629810 FALSE TRUE 1647139.905 1710399.127 1748130.127 2219633.48 1970714.368 1673161.924 2269023.249 2239361.324 2268495.319 2451690.626 0.671838399 0.697640684 0.713030473 0.905348112 0.803818535 0.682452307 0.9254933 0.913394741 0.925277967 1 21.22534551 6.384668587 0.137059852 1.077181922 0.040403968 0.665753309 0.067921045 30.20784081 0.421185155 0.36434396 5.759245086 2424759.037 -6.384668587 -1.036777954 DLDPNPGDLYPESLEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDPNPGDLYPESLEHR 17 0 Q13796 Q13796 SHROOM2 Protein Shroom2 0 ; 137.45 6.93E-06 280060000 490900 532880 437000 567110 501980 592670 534330 566500 651020 655850 FALSE TRUE 471715.0853 517682.7841 515975.621 596378.6151 518126.6426 604654.1935 540869.2904 554801.577 577118.9389 611428.6953 0.771496478 0.846677279 0.84388519 0.975385388 0.847403216 0.988920209 0.884599127 0.907385573 0.943885924 1 19.22182474 6.388438157 0.488121661 0.935410477 1.59E-12 0.564938421 0.047136577 15.15444994 0.772884075 0.024479744 11.51805883 2445896.961 -6.388438157 -0.935410477 GLNPDGTPALSTLGGFS(ph)PASKPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 2 GLNPDGTPALSTLGGFS(0.997)PAS(0.003)KPS(0.249)S(0.75)PR 158.16 1.18E-11 295380000 317300 333160 307880 339240 354730 394950 402800 389420 519610 466370 TRUE FALSE 304899.5652 323658.603 363520.7648 356748.2171 366140.2126 402936.1596 407729.5869 381378.3409 460626.0512 434782.3445 0.701269426 0.744415239 0.836098267 0.820521398 0.842123001 0.92675373 0.93777862 0.877170717 1.059440561 1 18.72993383 6.39218274 0.202452598 1.03159774 0.079840547 0.833597551 0.042600788 10.59729977 0.225501511 0.079836366 2.823543375 2467077.2 -6.39218274 -0.951757193 SGAFGHLFRPDNFIFGQSGAGNNWAK ddPTM_BT-474_Pertuzumab_2h_R1 3 SGAFGHLFRPDNFIFGQSGAGNNWAK 26 1 Q13509;A0A0B4J269;Q13509-2;G3V2A3;G3V542 Q13509 TUBB3 Tubulin beta-3 chain 0 ;; 270.71 1.05E-60 7312480000 1468002 1586195 1362070 1621635 1671473 1756862 1725565 1804997 2016924 1980718 FALSE TRUE 1410630.859 1540958.272 1608226.348 1705327.777 1725237.447 1792386.953 1746682.981 1767723.181 1787971.243 1846562.206 0.76392274 0.834501143 0.87092996 0.923514936 0.934296956 0.970661561 0.945910717 0.957304972 0.968270247 1 20.81641043 6.398172501 0.39371419 0.978054241 4.48E-16 0.97140869 0.01166109 3.011221738 0.130665038 0.008745109 1.821029818 2501338.694 -6.398172501 -0.978054241 IPIFSAAGLPHNEIAAQICR ddPTM_BT-474_Pertuzumab_2h_R1 2 IPIFSAAGLPHNEIAAQICR 20 0 P21281;P15313;C9JL73;C9JNS9 P21281;P15313 ATP6V1B2;ATP6V1B1 "V-type proton ATPase subunit B, brain isoform;V-type proton ATPase subunit B, kidney isoform" 0 ; 214.19 1.28E-24 1177500000 228590 237620 189005 219516 234550 218477 230120 239480 236086 263570 FALSE TRUE 219656.4501 230843.3103 223162.4079 230845.2471 242094.5138 222894.7546 232936.2774 234534.6543 209286.507 245718.1691 0.893936541 0.93946374 0.908204748 0.939471623 0.985252798 0.907115479 0.947981495 0.954486415 0.851733951 1 17.90664501 6.401174121 0.945347957 0.938763064 1.13E-15 0.095463156 0.039676338 102.1792271 5.134143095 0.011400274 185.4540402 2518686.541 -6.401174121 -0.938763064 LAASGEGGLQELSGHFENQK ddPTM_BT-474_Pertuzumab_2h_R1 4 LAASGEGGLQELSGHFENQK 20 0 Q16643;Q16643-3;Q16643-2;D6RFI1 Q16643 DBN1 Drebrin 0 ;;; 388.94 7.06E-131 1505870000 1262850 1378670 1278120 1433040 1432450 1541120 1641390 1674630 1800770 1834570 FALSE TRUE 1213496.426 1339351.681 1509104.716 1506999.366 1478526.055 1572282.502 1661477.822 1640048.305 1596354.139 1710312.94 0.709517187 0.783103285 0.882355901 0.881124928 0.864476916 0.919295215 0.971446677 0.958917089 0.93336962 1 20.70582889 6.401285432 0.318770434 0.981182662 4.29E-14 0.913030677 0.024851033 5.730633978 0.203616948 0.025511021 2.681277591 2519332.168 -6.401285432 -0.981182662 DFAAEVVHPGDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFAAEVVHPGDLK 13 0 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 ; 139.78 3.90E-05 207822000 643990 641190 674600 714310 705020 691410 796320 849240 1011640 1020880 FALSE TRUE 618822.1588 622903.889 796515.2264 751175.6247 727697.6086 705390.7839 806065.6024 831702.8972 896802.8683 951734.8883 0.650204344 0.65449307 0.836908719 0.789269821 0.764601169 0.741163104 0.846943421 0.873880854 0.942282225 1 19.86020023 6.406701699 0.098617388 1.156006819 2.65E-09 0.797494599 0.048616189 42.30480924 0.421366256 0.807436568 6.644249179 2550948.546 -6.406701699 -1.156006816 SSS(ph)PATEQSWMENDFDELR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPATEQSWMENDFDELR 19 0 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.051)S(0.051)S(0.898)PATEQSWMENDFDELR 435.12 1.09E-169 145940000 119330 129630 146740 155380 148300 143900 167550 188770 170230 222430 TRUE FALSE 114666.4517 125933.0793 173259.1822 163399.1804 153070.2042 146809.7566 169600.527 184871.8335 150906.2041 207364.618 0.552970187 0.607302637 0.835529146 0.787980042 0.738169345 0.707978815 0.817885562 0.891530268 0.72773362 1 17.66181023 6.408580238 0.116517313 1.058968419 1.41E-16 0.609556375 0.077716034 48.60787077 0.571159702 0.70815735 8.097561386 2562006.564 -6.408580238 -1.058968419 GDLEEYGQDLLHTVFK ddPTM_BT-474_Pertuzumab_2h_R1 3 GDLEEYGQDLLHTVFK 16 0 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;; 181.58 2.28E-09 236485000 320498 298517 308461 377207 334307 307690 434572 386579 405886 437606 FALSE TRUE 307972.5838 290003.5874 364206.7644 396674.6985 345060.2883 313911.7026 439890.4221 378596.0086 359811.5229 407966.5558 0.754896644 0.710851376 0.892736817 0.97232161 0.845805332 0.769454501 1.078251185 0.928007463 0.881963283 1 18.63809136 6.411569592 0.346170989 0.960249265 1.96E-14 0.404092784 0.085345633 20.63280515 0.791252181 0.07615958 10.46192306 2579702.309 -6.411569592 -0.960249265 AQAEAQQPTFDALRDELR ddPTM_BT-474_Pertuzumab_2h_R1 6 AQAEAQQPTFDALRDELR 18 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 233.85 8.60E-24 9538220000 4111290 4456980 3362610 4448490 4327190 4848570 4393380 4329110 4469240 4628450 FALSE TRUE 3950616.242 4329871.294 3970308.428 4678077.102 4466377.996 4946611.407 4447147.499 4239712.366 3961910.612 4314960.959 0.915562453 1.003455497 0.920126153 1.084152822 1.035091172 1.146386133 1.030634469 0.982561003 0.918179944 1 22.04091608 6.413221681 12.08955783 1.007894897 0.550056039 0 0.071591248 0 0 0.016252249 0 2589534.379 -6.413221681 -0.457838858 DELADEIANSSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DELADEIANSSGK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 178.71 3.34E-05 195210000 432560 379310 467430 479850 459910 453990 519350 615090 641240 626410 FALSE TRUE 415655.077 368492.4502 551904.9989 504615.116 474703.4228 463169.9889 525705.9607 602388.1766 568449.1235 583982.6928 0.711759239 0.630998923 0.945070814 0.864092587 0.812872417 0.793122801 0.900208118 1.031517173 0.973400634 1 19.15556609 6.420998639 0.20193054 1.045144593 7.17E-12 0.595471323 0.07827543 19.64170381 0.412615806 0.159443753 5.742146235 2636323.126 -6.420998639 -1.045144593 LNCS(ph)TSPEIFR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNCSTSPEIFR 11 0 Q9BRS8 Q9BRS8 LARP6 La-related protein 6 1 LNCS(0.333)T(0.333)S(0.333)PEIFR 67.997 0.061305 157330000 142030 162470 141970 163040 172940 164310 179140 214140 192540 207720 TRUE FALSE 136479.3106 157836.5147 167627.1371 171454.5139 178502.7722 167632.4608 181332.3689 209717.9342 170683.6664 193650.9394 0.70476968 0.815056798 0.865614893 0.885379201 0.921775917 0.865642384 0.936387758 1.082968845 0.881398598 1 17.56309897 6.423480915 0.297866204 1.004365895 2.88E-17 0.67914264 0.054731529 12.21779913 0.399572482 0.060680262 5.408350659 2651434.575 -6.423480915 -1.004365895 RVVNGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVVNGK 6 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 84.185 0.090014 427080000 579640 514080 435480 526230 432410 387510 548520 471640 566460 620560 FALSE TRUE 556987.028 499418.9417 514180.9232 553388.7934 446318.8604 395345.7177 555232.9518 461900.4692 502157.8356 578528.9185 0.962764367 0.86325666 0.88877307 0.956544739 0.771471998 0.683363796 0.959732408 0.798405152 0.867990898 1 19.14202955 6.425749817 0.718681291 0.847470764 2.098923958 0.07651046 0.09159246 63.26011477 3.446741333 0.032545005 107.8414282 2665322.817 -6.425749817 1.251453194 DS(ph)QDGSSYR ddPTM_BT-474_Pertuzumab_2h_R1 13 DSQDGSSYR 9 0 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 DS(0.982)QDGS(0.018)SYR;DS(1)QDGSSYR;DS(0.999)QDGS(0.001)SYR;DS(1)QDGSSYR;DS(0.986)QDGS(0.014)SYR;DS(0.999)QDGS(0.001)SYR;DS(0.995)QDGS(0.005)SYR;DS(1)QDGSSYR;DS(1)QDGSSYR;DS(1)QDGSSYR;DS(0.998)QDGS(0.002)SYR;DS(0.999)QDGS(0.001)SYR;DS(0.992)QDGS(0.007)S(0.001)YR 219.93 4.98E-07 11069206000 5414301 5237771 5101614 6408222 6080149 5639801 6692655 7332601 7487841 7603194 TRUE FALSE 5202704.131 5088394.899 6023589.135 6738951.105 6275722.514 5753841.64 6774561.714 7181180.227 6637852.681 7088222.898 0.733992738 0.717866096 0.849802443 0.950725055 0.885373189 0.811746713 0.955748967 1.013114335 0.936462182 1 22.75699254 6.430142341 0.27266034 1.002742462 2.93E-15 0.710153902 0.053554368 12.27645606 0.363165344 0.068732145 4.886670522 2692417.103 -6.430142341 -1.002742462 LDGMGCLEFDEER ddPTM_BT-474_Pertuzumab_2h_R1 4 LDGMGCLEFDEER 13 0 Q13951-2;A0A494C0A9;Q13951;J3KS23;H3BSC0 Q13951-2 CBFB Core-binding factor subunit beta 0 ;;; 176.18 3.95E-05 454868000 305181 343238 261780 322668 337706 357319 323006 339565 387471 389001 FALSE TRUE 293254.1891 333449.1883 309089.4693 339320.9341 348568.6202 364544.235 326959.044 332552.8641 343486.9165 362653.6158 0.8086344 0.919470188 0.852299428 0.935661246 0.961161298 1.005213292 0.901573926 0.916998617 0.947148743 1 18.46823271 6.432274515 0.562088851 0.948389126 1.28E-13 0.549607921 0.038808886 19.31725003 1.010850435 0.0186358 18.06898754 2705668.062 -6.432274515 -0.948389126 FENAAAGNKPEAVEVTFADFDGVLYHISNPNGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FENAAAGNKPEAVEVTFADFDGVLYHISNPNGDK 34 1 O15144;C9JTV5;G5E9J0 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ; 328.6 1.84E-117 513960000 394380 486300 432270 539020 474890 535010 566970 580420 630320 701560 FALSE TRUE 378967.1936 472431.2001 510390.8048 566838.8868 490165.2681 545828.2688 573908.7485 568434.1242 558768.7161 654042.7163 0.579422695 0.722324687 0.780363105 0.86666952 0.749439228 0.834545291 0.877479 0.869108561 0.854330615 1 19.31902534 6.434289268 0.232696982 0.946426454 6.59E-41 0.793279562 0.048802268 11.54702613 0.284358219 0.073262634 3.602980151 2718249.194 -6.434289268 -0.946426454 SIDKPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIDKPFR 7 1 Q9Y450;Q9Y450-4;J3QT46;B7Z524;H0YDX7;H0YES5 Q9Y450 HBS1L HBS1-like protein 0 100.19 0.021428 0 324970 326360 309000 355260 365840 343060 408240 399960 419590 434150 FALSE TRUE 312269.8131 317052.5323 364843.1737 373595.0112 377607.5758 349996.9082 413236.1632 391700.6862 371959.9023 404744.6338 0.771523047 0.783339681 0.901415715 0.923038825 0.932952643 0.864735142 1.020979968 0.967772401 0.918998972 1 18.62665243 6.436234247 0.369066233 0.977694473 4.48E-15 0.726220989 0.041150036 10.36243577 0.415110131 0.032940684 5.813181244 2730450.116 -6.436234247 -0.977694473 WDAEELGR ddPTM_BT-474_Pertuzumab_2h_R1 1 WDAEELGR 8 0 H0Y5G7;A2RRP1-2;A2RRP1;H7BZR3 H0Y5G7 NBAS Neuroblastoma-amplified sequence 0 147.34 0.0021188 0 154650 171160 155250 191580 162490 191210 187350 218930 229530 219230 FALSE TRUE 148606.107 166278.6844 183307.1285 201467.4668 167716.6384 195076.3972 189642.8453 214409.019 203474.7167 204381.3568 0.727102067 0.813570704 0.896887717 0.985742877 0.820606346 0.954472562 0.927887202 1.049063488 0.995563978 1 17.64090408 6.437324528 0.312062915 1.014460983 2.28E-14 0.708370277 0.052135839 11.77847759 0.401709054 0.053881727 5.580026485 2737313.432 -6.437324528 -1.014460983 QEGHAS(ph)PCPPLQPVSVM ddPTM_BT-474_Pertuzumab_2h_R1 1 QEGHASPCPPLQPVSVM 17 0 H0YA27;Q14094-2;Q14094 H0YA27 CCNI Cyclin-I 1 QEGHAS(1)PCPPLQPVSVM 64.327 0.043065 0 64723 63470 51670 71026 71688 81816 74064 71119 103310 99392 TRUE FALSE 62193.5536 61659.89774 61007.91839 74691.66037 73993.90963 83470.37558 74970.41739 69650.3678 91582.68191 92660.09131 0.671201083 0.665441798 0.65840555 0.806082309 0.798552091 0.900823368 0.809090692 0.751676011 0.988372455 1 16.49966048 6.437596637 0.112542086 1.100077547 5.12E-18 0.720385978 0.063145939 42.91385819 0.483515918 0.665471227 7.193522705 2739029.044 -6.437596637 -1.100077547 YSQKEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 YSQKEDR 7 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;; 93.429 0.013627 418012000 972910 956270 1217160 1295790 1091570 1055340 1318840 1519100 1495520 1633410 FALSE TRUE 934887.6016 928998.1159 1437127.888 1362665.877 1126681.34 1076679.698 1334980.358 1487730.054 1325754.839 1522777.686 0.613935711 0.610068117 0.943754233 0.894855428 0.739885639 0.707049826 0.876674495 0.976984407 0.870616146 1 20.5382739 6.438846434 0.205134565 0.989275411 5.69E-20 0.485127289 0.098732932 26.82626783 0.570255774 0.200467078 7.567841767 2746922.673 -6.438846434 -0.989275411 RGS(ph)GSALGGPLDPQFVGPSDTSLGAAPGHR ddPTM_BT-474_Pertuzumab_2h_R1 3 RGSGSALGGPLDPQFVGPSDTSLGAAPGHR 30 1 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 RGS(0.795)GS(0.205)ALGGPLDPQFVGPSDTSLGAAPGHR;RGS(0.818)GS(0.182)ALGGPLDPQFVGPSDTSLGAAPGHR;RGS(0.712)GS(0.288)ALGGPLDPQFVGPSDTSLGAAPGHR 277.44 9.82E-72 2871210000 461472 534400 428184 485770 516410 508480 543113 573910 561350 591810 TRUE FALSE 443437.1641 519159.4352 505566.3737 510840.6479 533020.7966 518761.814 549759.7794 562058.5579 497627.9014 551726.1816 0.803726883 0.940972991 0.916335658 0.925895245 0.966096615 0.940252305 0.996435909 1.018727363 0.90194723 1 19.07359292 6.44071981 0.517654388 0.978603173 8.24E-17 0.619170706 0.03621126 14.56548551 0.731152099 0.018604437 12.63697293 2758797.411 -6.44071981 -0.978603173 ET(ph)HKISEQNDADNASVLSVSSNFEPFATDDLGNTVIHLDQALAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETHKISEQNDADNASVLSVSSNFEPFATDDLGNTVIHLDQALAR 44 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;H0YBA1 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 ET(0.5)HKIS(0.5)EQNDADNAS(0.001)VLSVSSNFEPFATDDLGNTVIHLDQALAR 93.656 3.93E-05 26744000 7746.5 11390 11018 10600 11533 14307 11804 9321.7 18434 16581 TRUE FALSE 7443.758216 11065.16835 13009.19769 11147.06727 11903.96942 14596.29734 11948.46088 9129.203637 16341.4496 15457.9541 0.481548733 0.7158236 0.841585996 0.721121773 0.770086995 0.944258034 0.772965219 0.590582918 1.05715475 1 13.91606177 6.444566283 0.084184935 1.148200911 3.76E-19 0.384051222 0.133135483 175.6797446 1.484025439 3.840557199 24.14173765 2783340.144 -6.444566283 -1.148200911 VIREPK ddPTM_BT-474_Pertuzumab_2h_R1 6 VIREPK 6 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 110.61 0.026042 3125830000 3747010 3855450 3900460 4564130 4342320 4314060 5180230 5073520 5839350 6058600 FALSE TRUE 3600572.707 3745496.341 4605359.887 4799685.296 4481994.666 4401293.249 5243627.204 4968750.039 5176491.469 5648245.626 0.637467445 0.663125613 0.815361121 0.849765682 0.793519787 0.779231914 0.928363876 0.87969794 0.916477755 1 22.4293714 6.447069054 0.192663326 1.000894952 1.21E-12 0.828322195 0.044973752 12.4670284 0.246130942 0.099319974 3.315348605 2799426.402 -6.447069054 -1.000894952 DVSGFSDPYCLLGIEQGVGVPGGS(ph)PGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVSGFSDPYCLLGIEQGVGVPGGSPGSR 28 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 1 DVSGFSDPYCLLGIEQGVGVPGGS(0.815)PGS(0.185)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.838)PGS(0.162)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.757)PGS(0.243)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.861)PGS(0.139)R 138.99 6.81E-07 468290000 269426 287523 252287 307333 281737 344359 315780 325935 366183 374821 TRUE FALSE 258896.5341 279323.1256 297880.873 323194.493 290799.3265 351322.1749 319644.6101 319204.3284 324615.441 349434.0398 0.740902444 0.799358659 0.852466672 0.924908441 0.832200912 1.005403409 0.914749491 0.913489506 0.928974868 1 18.41466063 6.449482063 0.37498685 0.952253889 3.72E-15 0.727242902 0.041943742 10.85549221 0.437165517 0.031829949 6.063315303 2815023.746 -6.449482063 -0.952253889 SVS(ph)PESNDSISEELNHFKPIVCSPCTPPK ddPTM_BT-474_Pertuzumab_2h_R1 3 SVSPESNDSISEELNHFKPIVCSPCTPPK 29 1 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 S(0.038)VS(0.962)PESNDSISEELNHFKPIVCSPCTPPK;S(0.003)VS(0.997)PESNDSISEELNHFKPIVCSPCTPPK;S(0.001)VS(0.999)PESNDSISEELNHFKPIVCSPCTPPK 361.04 7.77E-121 846219000 359690 323370 339497 382194 380430 461507 414440 399971 613597 509424 TRUE FALSE 345632.9171 314147.8042 400851.66 401919.0781 392666.8764 470838.9877 419512.0407 391711.4591 543944.041 474920.2587 0.727770422 0.661474844 0.844039926 0.846287499 0.826805909 0.991406408 0.883331534 0.824794167 1.145337625 1 18.85732577 6.450076611 0.209921799 1.028787677 4.85E-10 0.591287377 0.084867266 19.96661347 0.43407576 0.150541812 6.01982253 2818880.145 -6.450076611 -1.028787676 ELEFYLR ddPTM_BT-474_Pertuzumab_2h_R1 8 ELEFYLR 7 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;;;;; 174.64 0.0019045 7019650000 2834870 3114660 2789760 2864460 2798890 2007149 3321320 2969370 3000830 3523280 FALSE TRUE 2724080.146 3025832.946 3293931.69 3012295.124 2888918.839 2047734.928 3361967.308 2908051.472 2660188.359 3284645.107 0.829337739 0.921205442 1.002827271 0.917083894 0.879522367 0.623426538 1.023540504 0.885347237 0.809886083 1 21.64730607 6.451819469 9.705620324 0.888665147 0.508421001 0 0.112097412 0 0 0.024166846 0 2830215.267 -6.451819469 -0.380244146 EIIEHGIELFNK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIIEHGIELFNK 12 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 92.19 0.0078746 167250000 293460 316680 259220 325640 301860 326500 346850 321970 369480 376370 FALSE TRUE 281991.2588 307648.5965 306066.8203 342446.3194 311569.601 333102.0537 351094.8541 315321.207 327538.1794 350878.1247 0.803672953 0.876796172 0.872288122 0.975969419 0.887971005 0.949338332 1.000617677 0.898663054 0.933481333 1 18.42061048 6.453819786 0.511423284 0.950359693 5.17E-17 0.610385616 0.037571021 15.23786176 0.751460653 0.01911623 12.66975762 2843281.018 -6.453819786 -0.950359693 DVSLGDWEFGK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVSLGDWEFGK 11 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 224.64 1.41E-11 48161000 92928 89697 86588 100480 103680 97420 104630 121960 135090 130560 FALSE TRUE 89296.27102 87138.92938 102236.3777 105665.7848 107014.9614 99389.89915 105910.4932 119441.4834 119755.1495 121717.0549 0.733638117 0.715913883 0.839951129 0.868126368 0.8792109 0.8165651 0.870136838 0.981304415 0.983881426 1 16.89317181 6.456857821 0.175691543 1.043839691 0.136456928 0.815112695 0.040434307 14.52958273 0.258151442 0.11372935 3.161248056 2863240.452 -6.456857821 -0.907382762 VS(ph)PQPMISR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSPQPMISR 9 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 VS(1)PQPMISR;VS(1)PQPMISR;VS(1)PQPMISR 132.69 0.0003126 868530000 858270 892490 982790 974820 1011850 979150 1173080 1248940 1291040 1356430 TRUE FALSE 824727.8595 867037.059 1160402.015 1025130.577 1044397.074 998949.0839 1187436.504 1223148.953 1144486.552 1264557.788 0.65218677 0.685644474 0.917634628 0.81066329 0.825899049 0.78995922 0.939013239 0.967254296 0.905048834 1 20.27020154 6.460205862 0.220430886 1.002137495 6.97E-13 0.705880691 0.060305326 14.85104227 0.340221315 0.103182723 4.618239375 2885398.904 -6.460205862 -1.002137495 TSFSVGS(ph)DDELGPIR ddPTM_BT-474_Pertuzumab_2h_R1 6 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR 432 1.59E-153 7062050000 2489610 2644720 2283560 2681620 2508650 2670250 2714270 2897390 3105790 3076970 TRUE FALSE 2392313.289 2569295.175 2696250.09 2820018.73 2589343.006 2724244.285 2747488.048 2837557.884 2753233.74 2868564.081 0.833975892 0.895672923 0.939930228 0.983076776 0.902661726 0.949689185 0.957792111 0.989191039 0.959795097 1 21.45189732 6.463832429 0.546363393 0.969731855 1.78E-19 0.736799318 0.024744855 12.08013028 0.606172975 0.012219555 11.20256034 2909594.242 -6.463832429 -0.969731855 KIEFSLPDLEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIEFSLPDLEGR 12 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 155.43 0.00011598 1726260000 2252170 2388730 1861890 2218550 2245790 2443600 2359900 2518800 2790700 2820600 FALSE TRUE 2164152.706 2320605.759 2198374.941 2333049.631 2318027.875 2493011.266 2388781.162 2466785.9 2473911.436 2629558.25 0.823009989 0.882507835 0.836024431 0.887240141 0.881527487 0.948072273 0.908434397 0.938098975 0.94080876 1 21.32638902 6.464246541 0.108907357 1.056673069 0.514518855 0.849854895 0.019803607 26.10292705 0.282791383 0.204260822 2.093135828 2912369.945 -6.464246541 -0.542154214 DVNVNFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVNVNFEK 8 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 137.14 0.0017707 1047750000 619230 575810 707370 735770 747970 691670 802260 887510 891900 1029430 FALSE TRUE 595029.807 559388.4626 835207.4944 773743.1779 772029.1343 705656.0413 812078.2979 869182.6084 790655.2511 959705.7892 0.620012731 0.582874949 0.870274519 0.806229562 0.804443552 0.735283718 0.84617422 0.905676113 0.823851705 1 19.87223267 6.468040544 0.181049307 0.983072646 4.91E-22 0.650372205 0.070606881 21.40160521 0.391610553 0.175023327 5.219645157 2937923.914 -6.468040544 -0.983072646 LDEEEEDNEGGEWER ddPTM_BT-474_Pertuzumab_2h_R1 2 LDEEEEDNEGGEWER 15 0 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 ; 230.23 8.28E-13 395600000 236220 260530 224040 270260 261950 306040 268260 305220 300070 352230 FALSE TRUE 226988.2612 253099.9395 264529.0117 284208.151 270375.8596 312228.3385 271543.0461 298917.1003 266007.3116 328373.1484 0.691250982 0.770769293 0.80557443 0.865503627 0.823379929 0.950833952 0.826934381 0.910297026 0.81007632 1 18.32497663 6.473203618 0.365245621 0.906184763 6.68E-33 0.612562796 0.05304476 13.86904079 0.538001109 0.039699805 7.159564762 2973059.619 -6.473203618 -0.906184763 VDFGS(ph)SER ddPTM_BT-474_Pertuzumab_2h_R1 2 VDFGSSER 8 0 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 1 VDFGS(0.649)S(0.351)ER;VDFGS(0.735)S(0.265)ER 96.113 0.00962 635860000 663700 659120 659100 671820 741020 700420 777930 828840 830940 838560 TRUE FALSE 637761.8702 640322.5429 778214.0316 706492.7107 764855.5813 714582.9723 787450.54 811724.1644 736615.1748 781763.5843 0.815798898 0.819074405 0.995459557 0.903716577 0.978371974 0.914065309 1.007274521 1.038324349 0.942248001 1 19.57637286 6.474277984 0.409174235 1.000464496 9.00E-11 0.614450798 0.045782184 13.15541444 0.558148788 0.031626054 8.656695424 2980423.531 -6.474277984 -1.000464496 FVEIHFNEK ddPTM_BT-474_Pertuzumab_2h_R1 3 FVEIHFNEK 9 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;; 170.47 5.77E-05 1633999000 3541060 3858350 3345840 4063180 3931710 4182020 4423650 4248910 4946580 4994530 FALSE TRUE 3402671.46 3748313.636 3950507.716 4272881.207 4058177.023 4266583.31 4477787.952 4161168.524 4385064.976 4656246.034 0.730775701 0.805007641 0.84843191 0.917666544 0.871555539 0.916313974 0.961673399 0.893674538 0.941759723 1 22.15073586 6.475730043 0.368076374 0.950216126 3.80E-17 0.859682482 0.028035344 7.597121993 0.296182977 0.022332727 4.153977907 2990405.226 -6.475730043 -0.950216126 ITSENPDEGFKPSSGTVQELNFR ddPTM_BT-474_Pertuzumab_2h_R1 4 ITSENPDEGFKPSSGTVQELNFR 23 1 Q13085;Q13085-4;Q13085-3;Q13085-2;O00763-3;O00763-2;O00763 Q13085 ACACA;ACACB Acetyl-CoA carboxylase 1;Biotin carboxylase;Acetyl-CoA carboxylase 2;Biotin carboxylase 0 ;;; 216.15 2.37E-32 1399260000 682720 739190 689220 720190 804230 859470 900160 909110 1074230 1109830 FALSE TRUE 656038.5476 718109.0249 813777.3856 757359.0922 830098.7883 876849.0723 911176.4273 890336.5608 952287.9139 1034660.226 0.634061822 0.694052992 0.786516545 0.731988216 0.802291195 0.847475384 0.880652803 0.860511054 0.92038709 1 19.98072564 6.478669228 0.148126786 1.048953273 7.36E-19 0.94286579 0.024839551 9.4612762 0.139276417 0.100612483 1.981379675 3010712.103 -6.478669228 -1.048953273 AS(ph)PTSDIESVER ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPTSDIESVER 12 0 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 AS(0.989)PT(0.006)S(0.005)DIESVER;AS(0.998)PT(0.002)SDIESVER 229.56 8.30E-12 1679850000 244420 270130 246330 309940 304070 261040 310420 381620 371580 403200 TRUE FALSE 234867.7962 262426.1569 290847.3106 325936.0405 313850.6877 266318.4077 314219.0128 373739.4136 329399.7962 375890.9049 0.624829686 0.698144471 0.773754584 0.867102759 0.834951534 0.708499206 0.835931407 0.994276288 0.876317548 1 18.51995448 6.484458624 0.164361157 1.036724253 2.40E-15 0.695272929 0.064407413 22.87968235 0.375111597 0.214793423 5.293731189 3051115.333 -6.484458624 -1.036724253 ENEFSFEDNAIR ddPTM_BT-474_Pertuzumab_2h_R1 4 ENEFSFEDNAIR 12 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;F2Z2R5;K7EMY3 Q14839-2 CHD4;CHD5 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 169.52 0.00010148 789852000 700067 772211 622135 751741 750050 729342 791501 864230 811912 841735 FALSE TRUE 672707.6077 750188.2984 734568.6338 790538.4431 774176.0394 744089.795 801187.626 846383.3485 719747.1536 784723.5387 0.857254274 0.955990564 0.936085892 1.007410131 0.986558962 0.948219033 1.020980749 1.078575201 0.917198374 1 19.58182495 6.486194005 0.532450908 1.008038384 7.86E-17 0.457508996 0.04312058 20.13790896 0.979367203 0.021993334 18.84886386 3063331.557 -6.486194005 -1.008038384 GS(ph)PTTGFIEQK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSPTTGFIEQK 11 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.992)PT(0.008)TGFIEQK;GS(0.802)PT(0.196)T(0.002)GFIEQK;GS(0.986)PT(0.014)TGFIEQK;GS(0.983)PT(0.017)TGFIEQK 225.63 5.59E-12 1058890000 1241520 1222200 1203460 1314780 1337410 1449370 1529690 1635870 1778250 1945270 TRUE FALSE 1193000.026 1187344.053 1420951.993 1382635.953 1380429.007 1478677.254 1548410.804 1602088.713 1576390.515 1813515.13 0.657838474 0.654719684 0.783534678 0.762406627 0.761189683 0.81536527 0.853817417 0.883416237 0.869245858 1 20.79035735 6.489765184 0.119773804 1.090671921 7.65E-16 0.934723281 0.025449476 14.49600357 0.17149427 0.202382945 2.552789318 3088625.014 -6.489765184 -1.090671921 KILDSVGIEADDDR ddPTM_BT-474_Pertuzumab_2h_R1 3 KILDSVGIEADDDR 14 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;; 203.52 2.39E-08 2357270000 1924260 1916670 1860320 2440720 2145660 1892590 2538450 2688330 2848160 3084230 FALSE TRUE 1849057.792 1862008.448 2196521.207 2566685.852 2214677.103 1930859.467 2569516.31 2632815.046 2524848.817 2875332.355 0.643076196 0.647580251 0.763919066 0.892657104 0.77023343 0.671525663 0.893641497 0.915655904 0.878106774 1 21.45529729 6.490484789 0.132879164 1.070016723 2.71E-15 0.662623746 0.069409353 34.6797459 0.455269903 0.421726704 6.630085451 3093746.959 -6.490484789 -1.070016723 ETLAVNYEKEEEFLTNELSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETLAVNYEKEEEFLTNELSR 20 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 178.41 5.65E-17 73495000 44061 36650 35021 42591 51466 41117 50041 51374 55915 62960 FALSE TRUE 42339.04741 35604.77788 41350.07374 44789.12661 53121.45063 41948.41391 50653.41673 50313.10895 49567.76361 58695.66312 0.721331784 0.606599806 0.704482606 0.763073867 0.905031953 0.714676548 0.862983976 0.857186141 0.844487667 1 15.84096629 6.491606431 0.104832396 1.115162781 6.83E-12 0.683539869 0.062025093 45.5590274 0.472148574 0.755087257 7.262544286 3101747.43 -6.491606431 -1.115162781 TSTTGVATTQS(ph)PTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSTTGVATTQSPTPR 15 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 TSTTGVATTQS(0.987)PT(0.013)PR;TSTTGVATTQS(0.991)PT(0.009)PR 259.02 8.00E-25 395560000 432730 449210 425980 488860 467580 474120 520240 576540 515900 603260 TRUE FALSE 415818.4332 436398.9706 502964.0619 514090.1232 482620.1353 483707.0312 526606.8527 564634.2475 457337.1948 562400.6629 0.739363341 0.775957426 0.894316268 0.914099426 0.858142899 0.8600755 0.93635532 1.003971519 0.81318751 1 19.10123877 6.494301243 0.374094007 0.944604689 4.48E-21 0.533636871 0.057239203 16.72308071 0.653081885 0.04585668 9.304263932 3121053.712 -6.494301243 -0.944604689 FEDEDSDDVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 191.45 4.25E-06 1004670000 575690 542630 605320 822580 650150 610790 750000 820590 865980 973720 FALSE TRUE 553191.3983 527154.7237 714714.7893 865033.4524 671062.6652 623140.5923 759178.7244 803644.5297 767677.5809 907769.0771 0.60939661 0.580714564 0.78733106 0.952922361 0.739243803 0.686452764 0.836312608 0.885296217 0.845674963 1 19.79196582 6.496037845 0.158594399 1.002388754 2.81E-22 0.556356229 0.088021168 34.14329825 0.537137902 0.319298565 7.352253278 3133558.773 -6.496037845 -1.002388754 KLEEIIHQITNVEALIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLEEIIHQITNVEALIAR 18 1 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 ; 197.09 1.22E-15 246965000 265250 279210 259830 298450 291720 326610 335400 339780 366600 383460 FALSE TRUE 254883.7368 271247.2042 306787.0609 313853.0403 301103.4387 333214.278 339504.7255 332763.4243 324985.1049 357487.9126 0.712985608 0.758759092 0.85817464 0.877940286 0.842275859 0.932099425 0.949695678 0.930838254 0.909079981 1 18.44753494 6.499691562 0.300071761 0.969044121 5.65E-14 0.889931193 0.027721766 6.7143233 0.213033815 0.029187601 2.921165189 3160032.593 -6.499691562 -0.969044121 DLEEALEAGGCDLETLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLEEALEAGGCDLETLR 17 0 Q9NUY8-2;Q9NUY8;C9IZ32;C9JAM5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 0 81.431 0.021662 24642000 12427 15702 13440 14119 15945 15342 18193 18782 19826 20454 FALSE TRUE 11941.3391 15254.19433 15868.90697 14847.68328 16457.88541 15652.22575 18415.65138 18394.14514 17575.4356 19068.63236 0.626229447 0.799962685 0.832199534 0.778644373 0.863086827 0.820836306 0.965756276 0.964628443 0.921693557 1 14.21891375 6.502796574 0.210595041 1.019860755 3.23E-16 0.812024099 0.046017436 11.54325486 0.247203403 0.082591812 3.477318008 3182706.376 -6.502796574 -1.019860755 FLELGK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLELGK 6 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 ; 116.35 0.055015 1446210000 2162550 2135250 2165920 2396500 2397300 2385500 2867900 2937400 3081700 3205300 FALSE TRUE 2078035.155 2074354.761 2557349.925 2520183.652 2474411.332 2433736.444 2902998.218 2876741.664 2731878.336 2988202.176 0.695413172 0.694181531 0.855815562 0.843377892 0.828060213 0.814448388 0.971486548 0.962699809 0.914221386 1 21.51084633 6.504906375 0.211169487 1.017969329 1.59E-19 0.807935448 0.044574477 11.5467496 0.247854507 0.08210638 3.483463241 3198205.567 -6.504906375 -1.017969329 LKDIALGMQTEIEEQDDILDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LKDIALGMQTEIEEQDDILDR 21 1 O95721;C9JAF7 O95721 SNAP29 Synaptosomal-associated protein 29;Synaptosomal-associated protein 0 ;; 225.84 2.42E-25 186789000 117286 125480 105716 130238 123489 128329 120892 145936 151663 143009 FALSE TRUE 112702.3335 121901.4333 124821.2328 136959.5988 127461.1358 130923.9003 122371.5125 142922.3706 134446.8521 133322.8731 0.845333819 0.914332481 0.936232696 1.027277583 0.956033522 0.982006293 0.917858351 1.07200188 1.008430504 1 17.02456479 6.510004033 0.481391139 1.006472182 1.85E-12 0.592644355 0.039723596 16.02929021 0.730549565 0.023026042 13.18197972 3235966.623 -6.510004033 -1.006472182 DIINEEEVQFLK ddPTM_BT-474_Pertuzumab_2h_R1 4 DIINEEEVQFLK 12 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 253.53 1.02E-20 481422000 577740 526618 534420 595510 607450 621330 681290 709600 826780 861310 FALSE TRUE 555161.2821 511599.3703 631001.5821 626244.3425 626989.1809 633893.7183 689627.8308 694946.512 732927.4005 802972.7065 0.691382506 0.637131706 0.785831918 0.779907383 0.780834985 0.789433704 0.858843427 0.865467165 0.912767513 1 19.61499143 6.510429116 0.106850131 1.125459577 8.43E-09 0.90312898 0.03094306 21.64364908 0.227505277 0.351307928 3.540602805 3239135.502 -6.510429116 -1.125459568 QDQVCIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 QDQVCIAR 8 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 89.355 0.032488 124060000 86573 94622 76203 92993 91204 82923 103010 108770 94711 96724 FALSE TRUE 83189.63145 91923.4732 89974.57723 97792.37987 94137.65949 84599.75988 104270.6672 106523.8615 83959.80434 90172.79733 0.922557954 1.019414679 0.997801775 1.084499791 1.043969604 0.938196023 1.156342825 1.181330342 0.931099032 1 16.46040466 6.510569114 0.546790457 1.070418716 1.92E-08 0.135822715 0.079843418 39.99753306 1.915535009 0.040199848 41.37527186 3240179.825 -6.510569114 -1.070418697 YEDICPSTHNMDVPNIK ddPTM_BT-474_Pertuzumab_2h_R1 2 YEDICPSTHNMDVPNIK 17 0 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ; 186.85 5.00E-10 657370000 925700 971340 1028160 1356160 1049940 1183660 1211870 1186070 1377440 1628230 FALSE TRUE 889522.6206 943638.3342 1213971.383 1426151.58 1083712.274 1207594.416 1226701.228 1161577.24 1221078.786 1517948.532 0.58600315 0.621653709 0.799744759 0.939525649 0.71393216 0.795543716 0.808130975 0.765228343 0.804427002 1 20.53369144 6.511166609 0.066016534 1.212223333 3.11E-28 0.515540308 0.083245622 208.6261757 1.367678725 5.799917812 25.48154598 3244640.679 -6.511166609 -1.212223333 GLEGWEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GLEGWEK 7 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 104.21 0.019083 627030000 1157930 1304050 1101080 1362510 1318150 1321040 1471110 1450050 1554570 1693620 FALSE TRUE 1112676.815 1266859.771 1300069.649 1432829.304 1360549.492 1347752.334 1489113.884 1420105.961 1378101.731 1578909.609 0.704712169 0.80236371 0.823397136 0.907480261 0.861701952 0.853596891 0.943128014 0.899421951 0.872818636 1 20.59049715 6.515431501 0.365611329 0.927194889 1.90E-40 0.758692155 0.037678434 10.71153037 0.405034219 0.029502765 5.702256281 3276660.913 -6.515431501 -0.927194889 AS(ph)PFEEDQNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPFEEDQNR 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 AS(1)PFEEDQNR;AS(1)PFEEDQNR 112.73 0.0016599 368300000 537510 537700 508000 499950 540480 548020 553150 593840 629560 619740 TRUE FALSE 516503.515 522365.3225 599806.9004 525752.4794 557865.0301 559101.3399 559919.6152 581576.9965 558094.9881 577764.4578 0.893969001 0.904114671 1.038151261 0.909977193 0.965557889 0.967697705 0.969113983 1.006598777 0.965955902 1 19.14012193 6.526033327 0.642271095 0.979920361 8.88E-18 0.367222135 0.035600092 28.54837762 1.374153294 0.013809223 33.55440883 3357633.788 -6.526033327 -0.979920361 DGDLFMSYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGDLFMSYR 9 0 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 167.04 0.00014025 327770000 400260 421560 359000 364590 390850 277840 395900 409870 427190 461680 FALSE TRUE 384617.3967 409537.5216 423879.2859 383406.5336 403422.0452 283458.1152 400745.1426 401406.0413 378697.1821 430410.0024 0.893607013 0.951505586 0.984826755 0.890793735 0.937297096 0.65857697 0.931077671 0.932613181 0.879852188 1 18.71535208 6.527010894 11.98814467 0.903463809 0.496726092 0 0.090437183 0 0 0.019842346 0 3365200.104 -6.527010894 -0.406737717 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(ph)PDDDDIVR ddPTM_BT-474_Pertuzumab_2h_R1 2 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLTPDDDDIVR 39 1 P41743 P41743 PRKCI Protein kinase C iota type 1 QVVPPFKPNISGEFGLDNFDS(0.001)QFT(0.004)NEPVQLT(0.995)PDDDDIVR;QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR 276.81 1.55E-76 413650000 193214 192365 188944 212601 179829 230777 198630 234150 264623 234330 TRUE FALSE 185662.9833 186878.9385 223090.3838 223573.3631 185613.3631 235443.4691 201060.8934 229314.7207 234584.1064 218458.6204 0.849877121 0.855443187 1.021202017 1.023412867 0.849649983 1.077748585 0.920361453 1.049694081 1.073814831 1 17.73700051 6.53158715 0.436798484 1.01915068 5.95E-11 0.380321442 0.070219054 23.4675935 0.996744496 0.043825939 17.28438268 3400847.442 -6.53158715 -1.01915068 DLVDEDLSHFQSGS(ph)PPAPNGFK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLVDEDLSHFQSGSPPAPNGFK 22 0 Q70EK8 Q70EK8 USP53 Inactive ubiquitin carboxyl-terminal hydrolase 53 1 DLVDEDLSHFQS(0.01)GS(0.99)PPAPNGFK;DLVDEDLSHFQS(0.091)GS(0.909)PPAPNGFK;DLVDEDLSHFQS(0.004)GS(0.996)PPAPNGFK 135.69 6.09E-09 424000000 259741 256523 279579 293769 282717 293340 330652 352133 381014 421860 TRUE FALSE 249590.0346 249207.2152 330105.1445 308930.4533 291810.8491 299271.5358 334698.6181 344861.3305 337762.8881 393287.0464 0.634625617 0.633652233 0.839349141 0.785508844 0.741979304 0.760949384 0.851028838 0.876869283 0.858820272 1 18.58522314 6.53164603 0.105332353 1.114831741 1.36E-12 0.789141127 0.048945178 39.06685946 0.402820707 0.631882698 6.249168961 3401308.546 -6.53164603 -1.114831741 GRPGS(ph)GTSGVDSLSNFIESVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GRPGSGTSGVDSLSNFIESVK 21 1 Q8IXT5;B9ZVT1;E5RHG1;E5RJ83;E5RJV8 Q8IXT5 RBM12B RNA-binding protein 12B 1 GRPGS(0.68)GT(0.279)S(0.041)GVDS(0.001)LSNFIESVK;GRPGS(0.938)GT(0.031)S(0.031)GVDSLSNFIESVK 217.93 3.41E-25 302170000 366850 350600 365740 410280 375130 346200 449120 464880 478420 449260 TRUE FALSE 352513.0964 340601.2313 431837.3538 431454.6 387196.3971 353200.4012 454616.4649 455280.0655 424111.7673 418831.22 0.841659073 0.813218344 1.031053401 1.030139539 0.924468804 0.84330008 1.085440729 1.08702514 1.012607817 1 18.67600946 6.531711688 0.382565121 1.034936727 7.88E-14 0.369795271 0.077847267 24.10477242 0.935104288 0.064994855 15.20681539 3401822.803 -6.531711688 -1.034936727 GPS(ph)PTPEDVSMK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSPTPEDVSMK 12 0 H1UBN3;O95067 H1UBN3 CCNB2V;CCNB2 G2/mitotic-specific cyclin-B2 1 GPS(0.992)PT(0.008)PEDVSMK;GPS(0.981)PT(0.019)PEDVSMK 201.09 1.60E-07 916190000 1238520 1276630 1360670 1644310 1437420 1389690 1665320 1833040 1837920 2141140 TRUE FALSE 1190117.269 1240221.762 1606573.337 1729173.036 1483655.92 1417790.484 1685700.684 1795187.083 1629287.027 1996118.681 0.596215686 0.621316645 0.804848606 0.866267649 0.743270395 0.710273641 0.844489208 0.899338852 0.816227533 1 20.92876607 6.533823312 0.138310806 1.033987966 1.15E-14 0.676970995 0.067319664 32.91586495 0.444804125 0.360929955 6.33927029 3418403.4 -6.533823312 -1.033987966 EGVQGPLNVS(ph)LSEEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGVQGPLNVSLSEEGK 16 0 P12270 P12270 TPR Nucleoprotein TPR 1 EGVQGPLNVS(1)LSEEGK;EGVQGPLNVS(1)LSEEGK 236.03 1.07E-19 280370000 483600 427260 456070 441470 542170 480540 510500 646460 570580 670820 TRUE FALSE 464700.3774 415074.9631 538491.9942 464254.3196 559609.3904 490256.848 516747.6517 633110.3751 505810.1505 625384.7639 0.743063158 0.663711346 0.861057105 0.742349904 0.894824151 0.783928353 0.826287562 1.012353373 0.808798327 1 19.25438455 6.536685366 0.129355099 1.063524513 0.14846686 0.508626216 0.074404896 41.70614509 0.526404947 0.436359476 6.644094129 3441005.495 -6.536685366 -0.915057653 LKPGGVGAPSSSS(ph)PSPSPSAR ddPTM_BT-474_Pertuzumab_2h_R1 5 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPSS(0.002)S(0.038)S(0.958)PS(0.002)PSPSAR;LKPGGVGAPSS(0.001)S(0.078)S(0.899)PS(0.022)PSPSAR;LKPGGVGAPS(0.001)S(0.013)S(0.247)S(0.738)PS(0.001)PSPSAR;LKPGGVGAPSSS(0.005)S(0.994)PS(0.001)PSPSAR;LKPGGVGAPSSS(0.021)S(0.978)PSPSPSAR 252.66 1.46E-36 6692900000 3366330 3413530 3157990 3732280 3851470 3603830 4096170 4145250 4440440 4613330 TRUE FALSE 3234770.102 3316179.467 3728709.042 3924903.418 3975356.03 3676701.912 4146300.154 4059649.139 3936379.867 4300865.05 0.752120809 0.771049412 0.866967226 0.912584648 0.924315454 0.854874977 0.964061905 0.943914559 0.915253053 1 22.03619543 6.536973602 0.342594087 0.961231139 1.35E-17 0.80699486 0.033382465 9.142612634 0.322772286 0.029277853 4.666544898 3443290.005 -6.536973602 -0.961231139 ERPFYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 ERPFYGR 7 1 Q13232 Q13232 NME3 Nucleoside diphosphate kinase 3 0 ;;; 100.45 0.0089232 1086970000 338062 394762 299758 409198 326341 406216 429751 440020 405420 438304 FALSE TRUE 324850.1633 383503.7743 353930.9387 430316.7578 336838.0546 414429.9658 435010.4213 430933.4332 359398.4213 408617.2797 0.794998595 0.938540276 0.866167331 1.053104651 0.824336296 1.014225258 1.06459135 1.054613827 0.87954778 1 18.64039069 6.542375145 0.412231462 1.008637338 7.95E-11 0.325217198 0.079328794 25.45060169 1.033794934 0.054261089 17.24676264 3486383.397 -6.542375145 -1.008637337 EALEVDWSSEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EALEVDWSSEK 11 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ;; 189.72 6.01E-06 289510000 729870 788940 686160 762330 772390 776330 809400 861440 905730 934530 FALSE TRUE 701345.8735 766440.2037 810164.3755 801673.9427 797234.6258 792027.9245 819305.6793 843650.963 802915.3275 871233.4507 0.805003381 0.879718522 0.929905039 0.920159737 0.915064298 0.909088057 0.940397409 0.968340876 0.921584596 1 19.73269982 6.542970671 0.511417332 0.94863367 6.23E-44 0.749422363 0.024641556 12.32714427 0.559682231 0.01287392 10.41187283 3491167.38 -6.542970671 -0.94863367 RST(ph)SPIIGS(ph)PPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.371)T(0.458)S(0.172)PIIGS(1)PPVR 77.037 0.023406 480640000 419240 511430 378990 438350 477000 487890 471400 543040 511380 526830 TRUE FALSE 402855.6373 496844.5171 447481.9236 460973.296 492343.1382 497755.4701 477169.1342 531826.0342 453330.2863 491147.3348 0.820233785 1.011599742 0.911095087 0.938564181 1.002434714 1.013454487 0.9715397 1.082823822 0.923002639 1 18.90579634 6.545619812 0.502520495 1.007301764 3.44E-14 0.413661496 0.052682566 23.42471105 1.053994256 0.027387599 20.53870418 3512528.136 -6.545619812 -1.007301764 EIPSHVLSK ddPTM_BT-474_Pertuzumab_2h_R1 4 EIPSHVLSK 9 0 E5RHG8;Q15369-2;Q15369 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;;; 167.67 5.98E-05 2004190000 3660860 3785540 3595020 4095210 3918870 4141010 4471760 4513820 4874480 5027770 FALSE TRUE 3517789.544 3677580.106 4244720.085 4306564.279 4044924.013 4224744.059 4526486.737 4420608.04 4321149.466 4687234.66 0.750504252 0.784594835 0.905591547 0.918785722 0.862965972 0.901329753 0.965705168 0.943116434 0.921897404 1 22.16030559 6.546307255 0.359404403 0.95961782 1.35E-20 0.806071755 0.032322699 9.737537459 0.35613377 0.027654352 5.275767365 3518092.506 -6.546307255 -0.95961782 DPILFPSFIHSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DPILFPSFIHSQK 13 0 P04040 P04040 CAT Catalase 0 ; 188.48 6.08E-06 759740000 874470 1031810 970920 1295910 1012760 995840 1397460 1254880 1460060 1579260 FALSE TRUE 840294.7456 1002383.789 1146386.842 1362792.07 1045336.345 1015976.567 1414562.534 1228966.289 1294320.11 1472295.314 0.570737907 0.680830659 0.778639198 0.925624131 0.710004532 0.690063031 0.960787228 0.834728113 0.879117184 1 20.48963565 6.550150744 0.163475634 1.004766277 2.30E-18 0.573619309 0.086728292 31.419155 0.502275483 0.275983034 7.026442031 3549365.663 -6.550150744 -1.004766277 HSPES(ph)PSIAVVESELVAEYITTER ddPTM_BT-474_Pertuzumab_2h_R1 1 HSPESPSIAVVESELVAEYITTER 24 0 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 HS(0.061)PES(0.804)PS(0.135)IAVVESELVAEYITTER 177.87 2.67E-17 76153000 24480 24535 22318 28733 30739 33738 28692 13421 31622 38373 TRUE FALSE 23523.29454 23835.28582 26351.35906 30215.91357 31727.74785 34420.20548 29043.14128 13143.85166 28032.40313 35773.96253 0.657553507 0.666274691 0.736607219 0.844634238 0.886894982 0.962158035 0.811851392 0.367413916 0.783597934 1 15.12662231 6.550790073 9.563346614 0.746939171 0.341674869 0 0.174267347 0 0 0.042150749 0 3554594.568 -6.550790073 -0.405264301 VLDTSSLTQSAPAS(ph)PTNK ddPTM_BT-474_Pertuzumab_2h_R1 6 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQSAPAS(0.999)PT(0.001)NK;VLDTSSLTQSAPAS(0.994)PT(0.006)NK;VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQSAPAS(1)PTNK 493.41 1.39E-240 3007810000 2646320 3045220 2694940 2984610 3142280 3515850 3684910 3415190 4448730 4366120 TRUE FALSE 2542898.889 2958373.307 3181975.607 3138646.08 3243354.29 3586942.896 3730007.031 3344665.133 3943728.821 4070398.803 0.624729667 0.726801832 0.781735589 0.771090557 0.796814869 0.881226403 0.916373852 0.821704529 0.968880203 1 21.95673872 6.552327207 0.171083458 1.02109265 4.40E-13 0.872602438 0.038775025 12.77385564 0.214152148 0.108606634 3.052878203 3567197.928 -6.552327207 -1.02109265 LLEAHEEQNVDSYTESVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEAHEEQNVDSYTESVK 18 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 279.12 3.32E-39 839760000 812240 776620 742050 849450 868700 862840 962490 960910 1118500 1206060 FALSE TRUE 780496.7628 754471.558 876154.9418 893290.2163 896642.5244 880287.216 974269.2405 941066.8727 991532.5691 1124372.482 0.6941621 0.671015673 0.779239047 0.794478903 0.797460396 0.78291423 0.866500431 0.836970744 0.881854176 1 20.10068862 6.566537639 0.075434993 1.216228364 4.46E-20 0.91392459 0.02624022 43.00274383 0.317365433 1.049597706 5.743983323 3685849.849 -6.566537639 -1.216228364 ERVPS(ph)VAEAPQLRPAGTAAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERVPSVAEAPQLRPAGTAAAK 21 2 Q63ZY3-3;Q63ZY3;Q63ZY3-2 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 ERVPS(1)VAEAPQLRPAGTAAAK 62.237 0.022234 777120000 399810 408650 347880 291010 353450 302530 309030 336050 330080 278870 TRUE FALSE 384184.9832 396995.7021 410749.6545 306029.061 364819.0402 308647.3639 312812.0016 329110.4501 292610.7022 259981.8865 1.477737501 1.527012929 1.579916432 1.177116856 1.403247915 1.187187954 1.203206907 1.265897615 1.125504189 1 17.98805159 6.571393721 0.140012487 0.912643484 2.608833581 0.731584747 0.094209953 25.05614317 0.339336757 0.435284319 8.024805508 3727294.606 -6.571393721 1.696190098 WNTTLYEGTWR ddPTM_BT-474_Pertuzumab_2h_R1 2 WNTTLYEGTWR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 276.21 8.24E-27 2849400000 748000 764770 704790 845410 778140 721270 942060 927940 871580 969940 FALSE TRUE 718767.333 742959.5084 832161.231 889041.7114 803169.5798 735854.5736 953589.2121 908777.7147 772641.8924 904245.0999 0.794881093 0.821635095 0.920282821 0.983186651 0.888221103 0.813777784 1.0545694 1.005012595 0.85446069 1 19.78635435 6.571400848 0.412559193 0.966558309 2.06E-15 0.340926031 0.071348268 26.55930663 1.056973097 0.05167407 17.35072104 3727355.775 -6.571400848 -0.966558309 LDLITVEAFKPILSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDLITVEAFKPILSTR 16 1 O95456;O95456-2 O95456 PSMG1 Proteasome assembly chaperone 1 0 176.83 2.78E-09 78817000 116440 106210 114870 128750 120270 123270 133620 123300 159610 163870 FALSE TRUE 111889.3961 103180.9948 135629.5643 135394.8029 124138.5938 125762.6039 135255.2815 120753.8119 141491.7419 152770.9389 0.732399741 0.675396744 0.887796889 0.8862602 0.812579897 0.823210257 0.885346928 0.790423969 0.926169224 1 17.22101061 6.572305512 0.042875296 1.400052069 1.26E-15 0.558991277 0.060000083 437.5331445 1.850508778 18.21533492 48.70365573 3735128.198 -6.572305512 -1.400052069 MKPPGGESSNLFGS(ph)PEEATPSSRPNR ddPTM_BT-474_Pertuzumab_2h_R1 3 MKPPGGESSNLFGSPEEATPSSRPNR 26 2 Q9H910-2;H3BU16;H3BMT0 Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 1 MKPPGGESSNLFGS(1)PEEATPSSRPNR;MKPPGGESSNLFGS(1)PEEATPSSRPNR;MKPPGGESSNLFGS(1)PEEATPSSRPNR 218.63 1.79E-34 410250000 213892 220877 228002 238883 220604 258037 283598 300980 296218 315229 TRUE FALSE 205532.8642 214577.8042 269207.0333 251211.7803 227699.928 263254.6849 287068.7572 294764.6578 262592.5745 293878.2591 0.699380978 0.730158825 0.916049503 0.854815804 0.774810388 0.895795034 0.976828834 1.003016211 0.893542024 1 18.16485911 6.574707591 0.234868675 1.012131917 2.25E-17 0.679543616 0.058585882 15.41143447 0.363130281 0.091742817 5.267338362 3755844.393 -6.574707591 -1.012131917 AVPVES(ph)PVQKV ddPTM_BT-474_Pertuzumab_2h_R1 6 AVPVESPVQKV 11 1 Q8TB61-5;Q8TB61-4;Q8TB61-3;Q8TB61-2;Q8TB61 Q8TB61-5 SLC35B2 Adenosine 3-phospho 5-phosphosulfate transporter 1 1 AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV 177.1 8.61E-06 2864610000 3416740 4379540 3618250 4486800 3497720 4832560 4275220 5151340 5703430 5133830 TRUE FALSE 3283210.023 4254639.807 4272148.263 4718364.286 3610227.34 4930277.674 4327541.421 5044963.029 5056000.537 4786111.121 0.685987003 0.8889555 0.89261368 0.985845119 0.754313314 1.030121857 0.904187411 1.054083974 1.056390127 1 22.19042246 6.576176973 0.277661047 1.035581022 4.12E-14 0.527453993 0.082302713 19.0530801 0.53763196 0.092378906 8.139569327 3768573.351 -6.576176973 -1.035581022 GPENLHYDQGCQTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPENLHYDQGCQTSR 15 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 83.252 0.0087859 1576500000 243980 256030 248760 260240 301190 260790 341000 310520 387360 364480 FALSE TRUE 234444.9919 248728.2751 293716.4656 273671.0176 310878.0499 266063.3525 345173.26 304107.6535 343388.5167 339793.445 0.689963257 0.73199845 0.864397092 0.805404053 0.914903023 0.783014965 1.015832604 0.894977987 1.010580168 1 18.3742985 6.583680632 0.213378024 1.020946388 1.65E-11 0.712193044 0.0596879 14.19192001 0.299639713 0.094174345 4.374253146 3834251.813 -6.583680632 -1.020946388 VVIVDPETGKEMSVYEAYR ddPTM_BT-474_Pertuzumab_2h_R1 3 VVIVDPETGKEMSVYEAYR 19 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 152.01 5.47E-08 930280000 1832710 1956290 1733620 2098110 2081660 2046630 2147470 2367650 2492180 2531780 FALSE TRUE 1761085.667 1900498.525 2046923.698 2206393.709 2148618.484 2088014.261 2173751.38 2318757.2 2209278.174 2360300.286 0.746127803 0.805193532 0.867230204 0.934793646 0.910315733 0.884639244 0.92096391 0.982399237 0.936015721 1 21.17053899 6.589047119 0.338542099 0.970218522 2.47E-15 0.865044413 0.026946225 8.31891884 0.282001775 0.025775284 4.254600525 3881924.806 -6.589047119 -0.970218522 KLPPPPPQAPPEEENES(ph)EPEEPSGVEGAAFQSR ddPTM_BT-474_Pertuzumab_2h_R1 4 KLPPPPPQAPPEEENESEPEEPSGVEGAAFQSR 33 1 R4GMQ1;O60341 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 KLPPPPPQAPPEEENES(0.999)EPEEPS(0.001)GVEGAAFQSR;KLPPPPPQAPPEEENES(1)EPEEPSGVEGAAFQSR;KLPPPPPQAPPEEENES(1)EPEEPSGVEGAAFQSR;KLPPPPPQAPPEEENES(1)EPEEPSGVEGAAFQSR 207.61 1.29E-27 588748000 315499 342244 276159 348185 305041 357271 347734 370982 379091 374693 TRUE FALSE 303168.9503 332483.5362 326067.0744 366154.8696 314852.9208 364495.2644 351989.6727 363321.0921 336058.179 349314.7094 0.867896319 0.951816592 0.933447879 1.048209136 0.901344582 1.043458104 1.007657746 1.040096745 0.962049894 1 18.41416787 6.590970128 0.509158565 1.00992032 5.94E-11 0.453362436 0.043927377 21.092117 0.914284277 0.021579365 19.02930172 3899151.665 -6.590970128 -1.00992032 EKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_BT-474_Pertuzumab_2h_R1 5 EKPELSEPSHLNGPSSDPEAAFLSR 25 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 EKPELSEPSHLNGPS(0.095)S(0.905)DPEAAFLSR;EKPELSEPSHLNGPS(0.007)S(0.993)DPEAAFLSR;EKPELSEPSHLNGPS(0.206)S(0.794)DPEAAFLSR;EKPELSEPSHLNGPS(0.068)S(0.932)DPEAAFLSR;EKPELSEPSHLNGPS(0.018)S(0.982)DPEAAFLSR 273.84 3.24E-53 8985440000 2402329 2567730 2480260 3021284 2763926 2829794 3309990 3301618 3701503 4010420 TRUE FALSE 2308443.327 2494500.854 2928498.155 3177212.829 2852830.19 2887014.374 3350498.648 3233438.435 3281323.897 3738790.681 0.61743048 0.667194574 0.783274167 0.849796926 0.763035546 0.772178659 0.896145019 0.864835373 0.877643114 1 21.83414027 6.591577242 0.158295103 1.016786987 5.19E-16 0.834851136 0.043486416 17.18157266 0.262371585 0.154131203 3.761341155 3904606.221 -6.591577242 -1.016786987 SPWSNKYDPPLEDGAMPSAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPWSNKYDPPLEDGAMPSAR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 78.324 0.0081503 2996370000 3453130 3631840 2979120 3336390 3421260 3712340 3429590 3888650 3751020 3734090 FALSE TRUE 3318177.862 3528263.479 3517513.254 3508581.488 3531307.935 3787406.058 3471562.348 3808348.019 3325219.935 3481176.758 0.95317707 1.013526093 1.010437992 1.00787226 1.014400641 1.087967179 0.997238172 1.09398295 0.95519997 1 21.73114364 6.593018945 0.695011343 1.032312254 1.80E-06 0.179163815 0.040058145 47.09422295 2.049180076 0.014127177 65.54658356 3917589.658 -6.593018945 -1.032310458 AAAGPLDMSLPS(ph)TPDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAGPLDMSLPSTPDIK 17 0 P17544;K7ELQ4;P17544-2;P17544-4 P17544 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 AAAGPLDMSLPS(0.5)T(0.5)PDIK 82.171 0.0081216 84165000 81859 75079 80761 85808 91131 95846 91490 100780 112550 113820 TRUE FALSE 78659.85978 72937.82043 95356.30922 90236.56116 94062.31138 97784.07179 92609.68199 98698.85778 99773.79585 106110.87 0.741298792 0.687373691 0.898647888 0.850398844 0.886453116 0.921527378 0.872763384 0.930148417 0.940278746 1 16.69521293 6.596578968 0.280753451 0.966827656 1.32E-16 0.763820537 0.043312007 10.87229373 0.307374166 0.047336495 4.405356147 3949835.126 -6.596578968 -0.966827656 TGAIVDVPVGEELLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 TGAIVDVPVGEELLGR 16 0 P25705;P25705-2;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 82.85 0.020574 73276000 282560 286650 249800 330070 322020 301750 299120 401960 361270 376850 FALSE TRUE 271517.2428 278475.0227 294944.4168 347104.9523 332378.0658 307851.5917 302780.72 393659.3855 320260.1442 351325.6138 0.772836457 0.79264082 0.839518683 0.987986468 0.946068412 0.87625718 0.861823642 1.120497254 0.911576417 1 18.42244924 6.596914548 0.298859076 1.008268503 6.01E-11 0.487802947 0.071853679 19.29663778 0.58067084 0.078755085 8.799593973 3952888.348 -6.596914548 -1.008268503 ALSAS(ph)HTDLAH ddPTM_BT-474_Pertuzumab_2h_R1 2 ALSASHTDLAH 11 0 Q07866-6;Q07866-4;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 ALS(0.001)AS(0.855)HT(0.144)DLAH;ALSAS(0.994)HT(0.006)DLAH 166.14 1.34E-05 881910000 1691890 1295020 818680 976150 843270 700210 694770 408450 785260 698630 TRUE FALSE 1625769.068 1258087.298 966633.6874 1026529.218 870394.5454 714368.726 703272.8031 400015.3648 696120.5769 651311.1678 2.496147999 1.931622487 1.484134981 1.576096449 1.336372825 1.096816332 1.079780047 0.614169363 1.068798773 1 19.31298744 6.598867708 0.339612386 0.808305361 8.15121453 0.901898897 0.159645309 6.543783174 0.22116512 0.150464163 25.46522976 3970705.782 -6.598867708 7.342909169 up YGQFSGLNPGGRPITPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGQFSGLNPGGRPITPPR 18 1 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 171.71 1.15E-11 1588630000 380030 397680 320700 380060 359430 392070 404760 404240 396010 433580 FALSE TRUE 365178.0075 386338.5558 378657.6239 399674.9421 370991.3924 399997.924 409713.574 395892.3027 351056.605 404213.2404 0.903429109 0.955779072 0.936776894 0.988772515 0.917811084 0.989571553 1.013607505 0.979414485 0.868493582 1 18.62475705 6.599493984 0.732755528 0.967828321 1.09E-08 0.15022152 0.041481485 68.14613139 2.877067812 0.014602882 95.38914086 3976435.885 -6.599493984 -0.96782831 DAEDAVYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DAEDAVYGR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 215.27 1.50E-06 5301450000 4756280 4668600 4728100 5349100 5171300 5011200 5593400 6186300 6342700 6413100 FALSE TRUE 4570399.319 4535456.099 5582572.846 5625167.692 5337639.561 5112529.897 5661853.702 6058550.743 5622703.287 5978735.025 0.764442528 0.758597944 0.933738127 0.940862518 0.892770718 0.855118997 0.946998601 1.013349934 0.940450323 1 22.51140884 6.605179091 0.322975192 0.984051467 1.83E-12 0.675967717 0.047531777 14.37639557 0.463314777 0.04887569 7.048585387 4028831.376 -6.605179091 -0.984051467 IFSIIAEGEMHEAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IFSIIAEGEMHEAIK 15 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 112.72 0.00074127 77523000 110570 108390 92721 139150 130720 108970 136420 133940 166260 157730 FALSE TRUE 106248.8022 105298.8233 109477.7473 146331.5482 134924.7275 111173.4481 138089.5488 131174.0922 147386.8618 147046.8066 0.722550898 0.716090514 0.744509519 0.995135845 0.917563126 0.756041227 0.939085669 0.892056721 1.002312564 1 17.16591593 6.606812533 0.247516879 0.982570676 8.82E-13 0.564692091 0.075725099 20.06986828 0.494431497 0.105589444 7.109771837 4044012.903 -6.606812533 -0.982570676 EIVVLETLEDIDK ddPTM_BT-474_Pertuzumab_2h_R1 4 EIVVLETLEDIDK 13 0 Q15293;Q15293-2;E9PP27 Q15293 RCN1 Reticulocalbin-1 0 ;;; 273.8 8.75E-32 127773000 291666 277215 314922 323595 306441 302225 372535 396873 449893 447877 FALSE TRUE 280267.3703 269309.0996 371835.4108 340295.7767 316297.9531 308336.1966 377094.1948 388677.4339 398823.0327 417541.8919 0.671231739 0.644987018 0.890534382 0.814997928 0.757523878 0.738455716 0.903129008 0.93087051 0.955168908 1 18.67156142 6.609825004 0.134073646 1.087620201 2.05E-15 0.677780854 0.066451877 33.5565427 0.430608311 0.384868342 6.597574138 4072161.593 -6.609825004 -1.087620201 DSGSDLSHRPK ddPTM_BT-474_Pertuzumab_2h_R1 3 DSGSDLSHRPK 11 1 O95251-4;O95251;E7EUP3;D6RFZ5 O95251-4 KAT7 Histone acetyltransferase KAT7;Histone acetyltransferase 0 ;; 189.13 1.71E-06 1077730000 1230520 1314650 1055270 1245410 1249240 1301140 1281860 1339840 1385850 1494960 FALSE TRUE 1182429.918 1277157.469 1245980.763 1309685.759 1289422.939 1327449.942 1297547.786 1312171.836 1228534.118 1393705.028 0.848407586 0.916375735 0.894006076 0.939715172 0.925176356 0.952461185 0.931006031 0.941498961 0.8814879 1 20.41049382 6.61630893 0.62568375 0.93771545 3.88E-10 0.457750192 0.029139672 26.99438836 1.165659679 0.010992025 29.85373815 4133414.228 -6.61630893 -0.93771545 DFEQDILEDMYHAIK ddPTM_BT-474_Pertuzumab_2h_R1 4 DFEQDILEDMYHAIK 15 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 ;;; 202.03 6.11E-09 251497000 462477 457846 468167 503752 525178 509231 591537 575548 735084 727497 FALSE TRUE 444402.8875 444788.6804 552775.1912 529750.7011 542070.8273 519527.9997 598776.4068 563662.7327 651640.346 678222.9802 0.655245989 0.655814818 0.815034594 0.781086334 0.799251637 0.76601356 0.882860688 0.831087635 0.960805465 1 19.37140014 6.620915781 0.115676879 1.099848061 5.37E-12 0.829747971 0.04424938 27.90372853 0.308569938 0.383027374 4.79763715 4177493.485 -6.620915781 -1.099848061 DEELEER ddPTM_BT-474_Pertuzumab_2h_R1 2 DEELEER 7 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 165.11 0.0027282 574710000 737750 752370 775650 888680 810180 857230 924560 1028180 1096510 1213140 FALSE TRUE 708917.9144 730913.1442 915827.2092 934544.8813 836240.1755 874563.7779 935875.0418 1006947.724 972038.7817 1130972.947 0.626821283 0.646269344 0.809769333 0.826319395 0.73939892 0.773284436 0.827495515 0.890337586 0.859471293 1 20.10913299 6.62560429 0.114765731 1.087287489 8.46E-15 0.813063717 0.045603765 32.496768 0.356172713 0.444071828 5.482442066 4222836.731 -6.62560429 -1.087287489 ANQISPS(ph)NSSLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ANQISPSNSSLK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 ANQIS(0.423)PS(0.577)NS(0.001)SLK 252.13 4.96E-21 129180000 272710 252760 264140 306860 293700 259450 358850 373950 362540 406860 TRUE FALSE 262052.1917 245551.5323 311875.9738 322697.0814 303147.1272 264696.2568 363241.7136 366227.8018 321385.9791 379303.0098 0.690878229 0.647375649 0.822234376 0.850763303 0.799221518 0.697849081 0.957655764 0.965528331 0.847306694 1 18.53299129 6.633238234 0.157337686 1.044654761 2.86E-09 0.600532652 0.073551978 28.9251278 0.433685409 0.261711732 6.475161308 4297721.15 -6.633238234 -1.044654758 AELGMGDSTSQS(ph)PPIK ddPTM_BT-474_Pertuzumab_2h_R1 6 AELGMGDSTSQSPPIK 16 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 AELGMGDSTSQS(1)PPIK;AELGMGDSTSQS(1)PPIK;AELGMGDSTS(0.001)QS(0.998)PPIK;AELGMGDSTSQS(1)PPIK;AELGMGDSTSQS(1)PPIK;AELGMGDS(0.117)T(0.117)S(0.117)QS(0.649)PPIK 329.79 1.71E-71 2134710000 1446150 1341000 1553910 1752870 1546460 1630980 1826890 1837670 2264160 2332830 TRUE FALSE 1389632.859 1302755.993 1834736.104 1843335.831 1596203.29 1663959.533 1849248.026 1799721.472 2007142.049 2174825.346 0.638962969 0.599016374 0.843624573 0.847578788 0.733945507 0.765100304 0.850297257 0.827524599 0.92289804 1 21.05246812 6.634281572 0.114558243 1.085734894 1.86E-12 0.703554198 0.063116758 44.44741326 0.485248121 0.605218129 7.475346958 4308058.302 -6.634281572 -1.085734894 AS(ph)PPALLPGPAPR ddPTM_BT-474_Pertuzumab_2h_R1 5 ASPPALLPGPAPR 13 0 A6NEL2 A6NEL2 SOWAHB Ankyrin repeat domain-containing protein SOWAHB 1 AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR 116.71 0.00059116 831480000 277588 309333 255214 311101 269147 330284 312940 337774 369377 336317 TRUE FALSE 266739.5541 300511.1257 301336.847 327156.9599 277804.3577 336962.5688 316769.8533 330798.8489 327446.8715 313537.95 0.850740888 0.958452161 0.961085722 1.04343656 0.886031046 1.074710633 1.010307854 1.055052024 1.044361206 1 18.25828055 6.645023449 0.439290265 1.034031226 8.40E-18 0.51601475 0.049064473 19.39848675 0.756554005 0.029715301 14.89923299 4415942.9 -6.645023449 -1.034031226 DYHFKVDNDENEHQLSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYHFKVDNDENEHQLSLR 18 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 214.74 6.38E-19 174050000 218430 248260 126240 116520 144000 199780 130120 63998 150000 117470 FALSE TRUE 209893.5141 241179.8679 149054.3762 122533.6112 148631.8908 203819.6885 131712.4475 62676.41894 132972.6289 109513.6523 1.916596787 2.202281294 1.361057486 1.118888911 1.357199652 1.861134975 1.202703451 0.572316032 1.214210522 1 16.74075121 6.649706838 0.261395865 0.870230056 5.334633448 0.493425745 0.327733085 20.91098227 0.536035264 0.444804179 36.09933619 4463821.694 -6.649706838 4.464403392 HLDDDEDRKNPAYIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLDDDEDRKNPAYIPR 16 2 O15234;J3KSY7 O15234 CASC3 Protein CASC3 0 ; 149.22 5.15E-07 527860000 372020 466140 358450 428680 470130 492330 545610 450560 605790 599490 FALSE TRUE 357481.0471 452846.1436 423229.8887 450804.2262 485252.1584 502285.2499 552287.3384 441255.7785 537023.2589 558886.0083 0.639631413 0.810265666 0.757274082 0.806612117 0.868248894 0.898725755 0.988193174 0.789527331 0.960881559 1 19.09219453 6.650172701 0.243443494 0.963091691 7.66E-14 0.694614508 0.05965528 16.46347307 0.391390334 0.083412669 5.628710929 4468612.55 -6.650172701 -0.963091691 QLDDEEVSEFALDGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 QLDDEEVSEFALDGLK 16 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 174.62 8.86E-09 34511000 24944 29810 21509 28207 25900 28188 30080 29468 32025 30956 FALSE TRUE 23969.1609 28959.84799 25396.15477 29662.76665 26733.09702 28757.98067 30448.12804 28859.4755 28389.65626 28859.32255 0.830551752 1.003483292 0.879998299 1.02784002 0.926324482 0.996488418 1.055053458 1.0000053 0.983725665 1 14.81674981 6.654080213 0.478425522 1.006620436 2.27E-11 0.465730587 0.048398598 23.13211442 0.927866751 0.025746043 19.38308585 4508999.766 -6.654080213 -1.006620436 EDGWIR ddPTM_BT-474_Pertuzumab_2h_R1 4 EDGWIR 6 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 126.05 0.041086 5948300000 3394250 3625510 2983850 3579330 3634570 3330340 3653050 3932320 3963160 4257600 FALSE TRUE 3261598.957 3522114.005 3523098.07 3764059.65 3751479.245 3397681.757 3697757.119 3851116.218 3513278.692 3969228.96 0.821721042 0.887354708 0.887602632 0.948310034 0.945140551 0.856005484 0.9316059 0.9702429 0.885128756 1 21.92042735 6.655411089 0.529435383 0.937326649 4.97E-29 0.44358676 0.038853282 26.44995651 1.087930589 0.019075927 23.6074242 4522838.595 -6.655411089 -0.937326649 TQSSSCERDS(ph)PSTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQSSSCERDSPSTSR 15 1 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;Q5JS79 A0A2U3TZM1 CASK Peripheral plasma membrane protein CASK 1 TQSSSCERDS(0.97)PS(0.03)TSR;TQSSSCERDS(0.997)PS(0.003)TSR 218.05 1.21E-12 326450000 178681 205404 154213 225550 186374 186259 222480 248310 230130 227682 TRUE FALSE 171697.949 199546.079 182082.7195 237190.6625 192368.889 190025.2846 225202.7768 243182.3117 204006.6072 212260.8953 0.808900522 0.940098169 0.85782508 1.117448705 0.90628511 0.89524396 1.060971577 1.145676463 0.961112535 1 17.69547908 6.656327264 0.347340845 1.049240962 1.68E-17 0.331676612 0.086103857 26.81396791 0.892371742 0.077592871 15.46706109 4532389.906 -6.656327264 -1.049240962 KPITDDDVDR ddPTM_BT-474_Pertuzumab_2h_R1 6 KPITDDDVDR 10 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ;;;;; 138.94 8.26E-05 9773450000 7247100 8021800 6613790 8061760 8005660 8136710 8973260 9230110 9510540 9473170 FALSE TRUE 6963875.32 7793026.118 7809048.976 8477828.4 8263169.324 8301239.851 9083077.44 9039505.003 8430943.371 8831543.758 0.788522993 0.882408142 0.884222418 0.959948638 0.935642686 0.93995343 1.028481281 1.023547553 0.954639823 1 23.07423421 6.661754441 0.345025481 1.011682882 5.64E-10 0.83339934 0.02840005 9.173840648 0.302716225 0.025812562 5.063343671 4589384.468 -6.661754441 -1.011682882 DRPQEADGIDSVIVVDNVPQVGPDR ddPTM_BT-474_Pertuzumab_2h_R1 6 DRPQEADGIDSVIVVDNVPQVGPDR 25 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 326.81 8.74E-88 9638780000 4153350 4281040 3841240 4607740 4637350 4655470 4892600 4821470 5360540 5864350 FALSE TRUE 3991032.49 4158948.931 4535437.516 4845546.014 4786514.574 4749606.793 4952477.102 4721904.96 4752033.972 5467152.351 0.730002062 0.760715755 0.8295795 0.886301625 0.87550415 0.868753327 0.905860452 0.863686368 0.869197284 1 22.38235815 6.666515987 0.3546317 0.912532377 5.82E-38 0.750585249 0.035483579 12.43309698 0.417872852 0.029366641 6.413442751 4639978.704 -6.666515987 -0.912532377 KAGTQIENIDEDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAGTQIENIDEDFR 14 1 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ; 154.82 9.64E-06 1161880000 1077930 1071370 1245270 1423960 1209640 986290 1676380 1556660 1512110 1798680 FALSE TRUE 1035803.304 1040815.577 1470317.99 1497450.746 1248549.169 1006233.46 1696896.04 1524514.427 1340461.612 1676853.802 0.617706387 0.620695481 0.876831354 0.893012107 0.744578429 0.600072265 1.011952287 0.909151666 0.799390866 1 20.67732548 6.668090749 0.165931154 1.003717645 8.34E-14 0.382096861 0.116401177 44.62556772 0.699674187 0.358032255 10.19637833 4656833.908 -6.668090749 -1.003717645 LTPVSLSNS(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTPVSLSNSPIK 12 0 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 LTPVSLS(0.002)NS(0.998)PIK;LTPVSLS(0.015)NS(0.985)PIK 181.72 1.87E-05 394410000 611430 611300 656170 688990 646180 583050 839010 845310 801900 968610 TRUE FALSE 587534.6396 593866.3225 774754.5154 724548.8565 666964.9665 594839.6705 849278.0554 827854.0531 710871.6738 903005.182 0.650643708 0.657655498 0.857973499 0.802375082 0.738605913 0.658733396 0.940501862 0.916776636 0.787228787 1 19.78437474 6.671470808 0.088749413 1.161615632 6.02E-11 0.513106357 0.083497766 101.6963948 0.858741016 1.93956606 14.61687725 4693218.869 -6.671470808 -1.161615632 KLDVVVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDVVVR 7 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 ; 107.66 0.011908 632050000 756580 934500 756820 897340 907980 952550 1069740 1062830 1130330 1202850 FALSE TRUE 727012.0172 907848.975 893594.2094 943651.8249 937186.0013 971811.2136 1082831.798 1040882.189 1002019.677 1121379.898 0.64831911 0.809581995 0.796870187 0.841509489 0.835743536 0.866620862 0.965624406 0.928215488 0.893559514 1 20.09684368 6.674915584 0.230418445 0.98832883 5.60E-15 0.852660756 0.036176908 9.821795262 0.217985638 0.053611771 3.234572108 4730592.996 -6.674915584 -0.98832883 VFNGSGKPIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VFNGSGKPIDR 11 1 P21281;H0YC04 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 63.662 0.066773 515670000 422550 475180 389150 451270 455500 467840 517590 493950 543470 538650 FALSE TRUE 406036.2788 461628.3316 459478.0616 474560.0988 470151.5712 477300.0453 523924.4212 483749.7599 481777.564 502166.7557 0.808568616 0.919272983 0.914990999 0.945024921 0.93624591 0.95048117 1.043327571 0.96332494 0.959397568 1 18.937807 6.678864695 0.428410861 0.986755534 7.94E-14 0.759327635 0.028398929 12.58166217 0.472134105 0.0187468 8.975767455 4773805.215 -6.678864695 -0.986755534 PLTS(ph)PESLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 PLTSPESLSR 10 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 PLT(0.001)S(0.999)PESLSR;PLT(0.003)S(0.997)PESLSR 270.52 1.07E-23 373860000 621740 536370 636300 652810 699940 640760 725680 796010 920240 930320 TRUE FALSE 597441.7134 521073.2528 751293.5644 686501.6023 722454.2058 653716.6062 734561.0889 779572.1153 815778.2132 867308.5978 0.688845602 0.600793367 0.866235578 0.791530955 0.832984024 0.753730112 0.846943165 0.898840525 0.940585871 1 19.72618589 6.679538153 0.134282538 1.067256166 4.45E-18 0.711360037 0.060450368 29.90283215 0.377288004 0.323491839 5.78848595 4781213.677 -6.679538153 -1.067256166 VETQFQNGHYDK ddPTM_BT-474_Pertuzumab_2h_R1 3 VETQFQNGHYDK 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 234.69 5.00E-16 3565780000 2230430 2234450 2384040 2298900 2584420 2702320 2929550 2749590 3541110 3571600 FALSE TRUE 2143262.33 2170725.674 2814889.061 2417546.505 2667550.216 2756962.762 2965402.709 2692810.006 3139138.038 3329692.351 0.643681789 0.651929802 0.845390133 0.72605702 0.801140146 0.827993241 0.890593604 0.808726369 0.942771196 1 21.66695745 6.691848313 0.13112762 1.059016058 1.74E-14 0.791826919 0.0502772 25.83725153 0.317394442 0.283508113 4.844715511 4918677.098 -6.691848313 -1.059016058 AKPS(ph)PHPIKDK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKPSPHPIKDK 11 2 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 AKPS(1)PHPIKDK;AKPS(1)PHPIKDK 85.909 0.0077561 1375860000 3435600 2737900 2562900 2101260 2521400 2607400 2778600 2550800 3290200 3251400 TRUE FALSE 3301332.954 2659817.773 3026073.041 2209706.28 2602503.121 2660123.414 2812605.338 2498125.089 2916710.29 3031179.782 1.08912476 0.877485984 0.998315263 0.728992155 0.858577619 0.877586816 0.927891297 0.824142832 0.962235994 1 21.53144799 6.693671831 1.298796911 0.880153588 34.19338771 0.328424775 0.080178709 249.930079 3.417036723 0.020612511 24322.20678 4939373.082 -6.693671831 33.31323412 EEGWWVVIGDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEGWWVVIGDAK 12 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 169.58 0.00010109 127343000 292500 296160 270290 283540 305120 314920 327930 318680 384480 345330 FALSE TRUE 281068.7766 287713.8068 319137.4156 298173.5334 314934.4619 321287.8982 331943.3054 312099.1466 340835.4423 321940.4915 0.873045746 0.8936863 0.991293186 0.926175928 0.978238122 0.997972938 1.031070382 0.969431168 1.058690818 1 18.29643452 6.698936601 0.351013688 1.017358448 0.281838742 0.698109372 0.030545305 13.27178436 0.433957496 0.024783826 5.472734255 4999615.446 -6.698936601 -0.735519706 VSS(ph)PTVNTTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSSPTVNTTLR 11 0 Q9NSK0-3;Q9NSK0;Q9NSK0-5 Q9NSK0-3 KLC4 Kinesin light chain 4 1 VS(0.004)S(0.994)PT(0.002)VNTTLR;VSS(0.997)PT(0.002)VNTTLR 188.88 3.10E-06 459170000 590610 595650 544450 612470 608950 646030 646650 657740 700620 770740 TRUE FALSE 567528.3082 578662.6452 642844.2262 644079.6501 628537.4298 659093.1692 654563.8961 644157.4391 621088.5548 718537.0933 0.789838567 0.805334409 0.89465698 0.89637634 0.874745974 0.917270904 0.91096744 0.896484601 0.864379251 1 19.45470311 6.701891037 0.448726317 0.915620576 5.09E-22 0.60495266 0.035123385 17.81757836 0.670267646 0.020432448 12.58468138 5033742.977 -6.701891037 -0.915620576 LKDVLLQVDDER ddPTM_BT-474_Pertuzumab_2h_R1 3 LKDVLLQVDDER 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 147.68 6.00E-05 1592060000 3209200 3327640 3058220 3608970 3587100 3622660 3945440 4256050 4326930 4530130 FALSE TRUE 3083780.916 3232738.965 3610908.384 3795229.374 3702482.329 3695912.667 3993725.475 4168161.08 3835755.046 4223300.26 0.730182731 0.765453263 0.854996842 0.89864067 0.876679871 0.875124296 0.945640904 0.986944054 0.908236405 1 22.00993939 6.706056668 0.262404748 0.990655461 5.87E-14 0.870723325 0.02950531 8.668251809 0.217632629 0.03848977 3.356657841 5082257.536 -6.706056668 -0.990655461 T(ph)CNSPQNS(ph)TDSVSDIVPDSPFPGALGSDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 2 T(0.545)CNS(0.449)PQNS(0.458)T(0.458)DS(0.09)VS(0.001)DIVPDSPFPGALGSDTR 89.634 0.0019653 39083000 26489 26161 25020 32477 26789 29647 33273 33270 38815 37356 TRUE FALSE 25453.78059 25414.91389 29541.67057 34153.14186 27650.69251 30246.48265 33680.20493 32582.96287 34408.88393 34825.84485 0.73088767 0.72977164 0.848268598 0.9806838 0.793970473 0.868506788 0.967103744 0.935597198 0.988027256 1 15.08787073 6.712690031 0.242519267 1.001325042 5.29E-18 0.689919423 0.055697406 15.89216511 0.366845185 0.079524656 5.658432052 5160479.192 -6.712690031 -1.001325042 ERPTS(ph)PAPHRPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPTSPAPHRPPK 13 2 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.364)S(0.636)PAPHRPPK 90.725 0.0035788 509830000 167810 157060 159490 184150 157240 179360 207980 182200 218830 209680 TRUE FALSE 161251.7997 152580.8026 188313.3908 193654.0036 162297.7674 182986.7821 210525.3215 178437.5063 193989.3358 195478.1868 0.82490943 0.780551554 0.963347338 0.990668098 0.830260246 0.936098217 1.076976029 0.912825667 0.992383544 1 17.5766481 6.71300355 0.363966497 0.986011917 2.01E-09 0.42803405 0.067151454 24.52831577 0.815987124 0.054965058 14.23141267 5164205.906 -6.71300355 -0.986011915 VWEWDIPVDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VWEWDIPVDFK 11 0 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 0 ; 145.89 0.0030397 0 284990 289370 259341 272520 286950 286190 304780 307030 345800 310410 FALSE TRUE 273852.2757 281117.4509 306209.6877 286584.7899 296180.0074 291976.9579 308509.9888 300689.7232 306546.2337 289385.6542 0.946322915 0.971428427 1.058137068 0.990321343 1.023478542 1.008954499 1.06608598 1.039062299 1.059300035 1 18.14263388 6.718600736 0.57963458 1.037566213 5.72E-09 0.506440899 0.026800155 23.94895527 0.925251971 0.011555075 26.99311449 5231192.909 -6.718600736 -1.037566208 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ; 174.14 1.96E-13 89649000 94067 102694 65311 67920 81217 93838 82420 84123 96206 80638 FALSE TRUE 90390.75764 99765.26767 77114.15054 71425.35934 83829.41856 95735.46865 83428.68061 82385.83065 85285.09821 75176.31644 1.202383436 1.327083747 1.025777189 0.950104537 1.115104098 1.273479111 1.109773458 1.095901403 1.134467639 1 16.19799061 6.719663481 0.01527586 1.23E-07 2.42551889 0.152329529 0.10341751 9604.074969 14.13104125 933.9700069 1342.583827 5244009.633 -6.719663481 2.425518768 ILHGFK ddPTM_BT-474_Pertuzumab_2h_R1 2 ILHGFK 6 0 O14787-2;O14787;K7ESG1;Q92973-2;Q92973;Q92973-3;S4R398 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ; 118.11 0.022145 1397390000 2326700 2414100 2395000 2722200 2729000 2722700 3090800 3015800 3478800 3657800 FALSE TRUE 2235769.992 2345252.232 2827829.776 2862693.068 2816780.763 2777754.859 3128626.135 2953522.676 3083901.208 3410053.948 0.655640651 0.687746372 0.829262475 0.839486152 0.826022346 0.814577981 0.917471155 0.86612198 0.904355548 1 21.70136313 6.721184152 0.204804001 0.976469211 3.86E-26 0.855559495 0.036886848 11.76701673 0.2263647 0.07028789 3.342980632 5262403.582 -6.721184152 -0.976469211 EGTSDPPS(ph)PLLLPSPGGWK ddPTM_BT-474_Pertuzumab_2h_R1 3 EGTSDPPSPLLLPSPGGWK 19 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 EGTSDPPS(1)PLLLPSPGGWK;EGTSDPPS(1)PLLLPSPGGWK;EGTSDPPS(1)PLLLPSPGGWK 191.18 1.07E-14 207014000 636530 638490 610920 706110 698410 668960 758000 765750 869590 850120 TRUE FALSE 611653.7039 620280.8903 721326.8338 742552.4217 720874.9919 682486.8295 767276.6307 749936.9949 770877.7888 792540.6152 0.771763228 0.78264871 0.910144944 0.936926648 0.909574826 0.861137986 0.968122789 0.946244244 0.972666604 1 19.59612535 6.727079479 0.32895145 0.972908367 8.28E-19 0.770886609 0.035496054 12.30607637 0.376371665 0.034140339 6.207012026 5334325.089 -6.727079479 -0.972908367 VPVNLLNS(ph)PDCDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VPVNLLNSPDCDVK 14 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 VPVNLLNS(1)PDCDVK;VPVNLLNS(1)PDCDVK 167.29 3.85E-06 122843000 134932 113462 135415 135142 122413 166655 155262 168451 180263 196373 TRUE FALSE 129658.7083 110226.1749 159887.5028 142116.6948 126350.5253 170024.8783 157162.1428 164972.428 159800.3 183072.4818 0.708237016 0.602090351 0.873356286 0.776286493 0.690166671 0.928729848 0.858469505 0.901131761 0.872879957 1 17.48205543 6.728878719 0.139973178 1.053107222 6.66E-14 0.608478661 0.073146758 33.4509703 0.434027252 0.330670862 6.682028341 5356470.519 -6.728878719 -1.053107222 TVNSTRET(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVNSTRETPPK 11 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK9;B0QZK8;Q5SSJ5-5;B0QZK7;B0QZK5;B0QZK6 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 TVNSTRET(1)PPK;T(0.001)VNS(0.001)T(0.001)RET(0.998)PPK 74.769 0.064536 3409600000 1030950 669270 721380 507800 756040 643780 599560 845960 696800 569990 TRUE FALSE 990659.3342 650183.0749 851749.413 534007.6189 780358.7132 656797.6727 606897.5946 828490.6304 617702.1852 531384.0696 1.864300025 1.223565237 1.602888498 1.0049372 1.468539909 1.236013103 1.142107243 1.559118306 1.162440164 1 19.01939545 6.730933326 1.467918856 1.288867538 199.9466561 0.417905205 0.206083123 485.3822057 3.852446278 0.050631708 322065.1057 5381871.518 -6.730933326 198.6577886 YPIEHGIITNWDDMEKIWHHTFYNELR ddPTM_BT-474_Pertuzumab_2h_R1 2 YPIEHGIITNWDDMEKIWHHTFYNELR 27 1 P68133;P68032;A6NL76 P68133 ACTA1;ACTC1 "Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1" 0 ; 221.6 8.48E-35 538320000 1087750 1266190 428850 374690 598620 532440 489390 71242 378470 263310 FALSE TRUE 1045239.527 1230079.501 506352.7347 394027.7958 617875.156 543206.3016 495379.3012 69770.8278 335507.6723 245475.7792 4.258014909 5.011001513 2.062740106 1.605159569 2.51705141 2.21287128 2.018037392 0.284226933 1.366764874 1 17.90522116 6.734057238 0.315553164 0.838276782 18.81871242 0.708043124 0.733672593 13.29180472 0.391301799 0.740518943 117.6972162 5420723.279 -6.734057238 17.98043564 AVCSTY(ph)LQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AVCSTYLQSR 10 0 Q5SQL3;J3KP92;Q86Z02;Q86Z02-2;H7BXX9;Q9H2X6-2;Q9H2X6-3;Q9H2X6 Q5SQL3 HIPK1;HIPK2 Homeodomain-interacting protein kinase 1;Homeodomain-interacting protein kinase 2 1 AVCS(0.007)T(0.348)Y(0.646)LQSR 145.72 0.00030842 712380000 179080 190830 128160 160980 177270 190160 187270 155770 196500 193710 TRUE FALSE 172081.3556 185387.7152 151321.3629 169288.1971 182972.0505 194005.1655 189561.8663 152553.2951 174194.1438 180589.8492 0.952884984 1.026567751 0.837928397 0.937418121 1.013191225 1.074286104 1.049681735 0.844750111 0.964584358 1 17.46235728 6.742869669 12.35153818 0.965254417 0.972840593 0 0.076119586 0 0 0.017776502 0 5531840.749 -6.742869669 0.007586176 TEDTEHVIIPVCLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEDTEHVIIPVCLR 14 0 Q9Y4E8;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 ; 190.85 5.56E-07 569360000 749230 814420 687540 796490 769270 875250 834720 858130 924360 988740 FALSE TRUE 719949.2633 791193.539 811793.7722 837596.9444 794014.2682 892948.1547 844935.5531 840409.3156 819430.528 921771.7591 0.781049383 0.858339964 0.880688483 0.9086815 0.861400081 0.968730215 0.916642916 0.911732549 0.888973349 1 19.81405004 6.743819203 0.436114883 0.930762099 1.08E-29 0.637593705 0.034596349 17.6729757 0.635547779 0.020998039 12.30880923 5543948.705 -6.743819203 -0.930762099 ADVVPQQADPEFPRAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 ADVVPQQADPEFPRASPR 18 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR 207.88 4.20E-16 2888390000 852985 904261 732734 811921 826496 965949 830397 914773 908932 1018444 TRUE FALSE 819649.4032 878472.3616 865155.3334 853824.3401 853080.9944 985481.1506 840559.6469 895882.6179 805753.8499 949463.8807 0.863276023 0.92522989 0.91120405 0.899269954 0.898487043 1.037934323 0.885299235 0.943566823 0.848640866 1 19.85675359 6.747815801 0.667995342 0.930896864 1.06E-13 0.121206156 0.052495286 92.19411638 3.302552409 0.019304571 112.9369046 5595202.4 -6.747815801 -0.930896864 DKDQPPSPS(ph)PPPQSEALSSTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKDQPPSPSPPPQSEALSSTSR 22 1 H3BU99;H3BPL8;H3BR21;H3BUX9;Q7L1V2 H3BU99 MON1B Vacuolar fusion protein MON1 homolog B 1 DKDQPPSPS(1)PPPQSEALSSTSR;DKDQPPS(0.001)PS(0.999)PPPQSEALSSTSR 204.88 6.75E-23 1214590000 554940 483810 561230 623700 587830 576200 671400 717440 801090 818930 TRUE FALSE 533252.3313 470012.2125 662656.7455 655889.2317 606738.0858 587851.1588 679616.794 702624.6133 710153.6216 763463.1417 0.698465063 0.615631832 0.867961673 0.859097442 0.794718242 0.76997975 0.890176299 0.920312422 0.930174075 1 19.54219898 6.749894285 0.158627704 1.036589474 3.65E-11 0.697717426 0.060449787 24.89692726 0.363963795 0.20639305 5.611215406 5622044.575 -6.749894285 -1.036589474 LKECEDTHLGEEVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKECEDTHLGEEVDR 15 1 O43847;O43847-2;G3V1R5;H0Y5G9 O43847 NRD1 Nardilysin 0 ; 146.78 2.30E-06 658220000 795540 799770 763630 888580 894120 946610 1011270 975130 1232580 1244170 FALSE TRUE 764449.4173 776961.3427 901634.9279 934439.7203 922880.1818 965751.1028 1023646.225 954993.2247 1092662.686 1159901.258 0.65906422 0.66985128 0.777337659 0.80562006 0.795654092 0.832614929 0.882528765 0.823340106 0.942030779 1 20.14557056 6.7570715 0.138464237 1.04658037 1.16E-15 0.905797832 0.031061817 15.87434527 0.202244153 0.155565711 3.11830356 5715727.299 -6.7570715 -1.04658037 MVDPEKPQLGMIDR ddPTM_BT-474_Pertuzumab_2h_R1 3 MVDPEKPQLGMIDR 14 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 112.5 0.00053802 1764110000 3678870 3595230 3482390 3767170 3975370 3699480 4193170 4278170 4526450 4619480 FALSE TRUE 3535095.693 3492697.56 4111735.338 3961594.095 4103241.386 3774286.02 4244487.269 4189824.294 4012626.372 4306598.505 0.820855645 0.811010721 0.954752419 0.919889349 0.952780107 0.876396074 0.985577658 0.972884816 0.931739137 1 22.0381174 6.759999213 0.39138393 0.969424019 2.58E-12 0.626384193 0.038396399 16.41910673 0.553913331 0.027633392 10.3630624 5754388.943 -6.759999213 -0.969424019 GRLPNNSSRPS(ph)TPTINVLESK ddPTM_BT-474_Pertuzumab_2h_R1 3 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 GRLPNNS(0.017)S(0.017)RPS(0.483)T(0.483)PT(0.001)INVLESK;GRLPNNS(0.242)S(0.242)RPS(0.366)T(0.15)PTINVLESK;GRLPNNS(0.011)S(0.011)RPS(0.595)T(0.383)PTINVLESK 160.69 1.09E-11 2556670000 1788800 1938190 1879780 1897910 1984190 2426750 2254540 2103390 2862030 2650110 TRUE FALSE 1718891.718 1882914.719 2219498.061 1995861.363 2048013.273 2475820.548 2282131.735 2059954.261 2537144.353 2470615.689 0.695734155 0.762123679 0.89835828 0.80783967 0.828948542 1.002106705 0.923709723 0.833781745 1.026927969 1 21.23643918 6.760332006 0.254733508 0.976111525 4.90E-15 0.640806557 0.063115122 19.42745386 0.462351181 0.084418685 7.191531748 5758800.139 -6.760332006 -0.976111525 GFRDDFLGGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFRDDFLGGR 10 1 Q15056-2 Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 189.58 9.08E-07 972510000 409999 452480 303664 350042 375200 415937 336709 394534 376446 357754 FALSE TRUE 393975.7858 439575.7134 358542.8398 368107.7096 387268.6487 424347.5311 340829.7455 386386.735 333713.4283 333523.0029 1.181255213 1.3179772 1.075016825 1.103695116 1.161145244 1.272318633 1.021907762 1.158501008 1.000570951 1 18.34742674 6.762641253 0.053441312 0.697271618 1.86431159 0.358149053 0.08366024 373.9869042 1.890214352 10.71732932 38.05237462 5789502.6 -6.762641253 1.167039972 TEEEEIDR ddPTM_BT-474_Pertuzumab_2h_R1 2 TEEEEIDR 8 0 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 204.03 0.00021129 690700000 793650 800320 778400 953320 891380 830100 969660 1094100 1172250 1154690 FALSE TRUE 762633.2806 777495.6572 919074.1954 1002520.959 920052.0472 846885.1907 981526.9891 1071506.453 1039181.094 1076481.818 0.708449755 0.722256191 0.853775865 0.931293908 0.854684243 0.786715741 0.911791516 0.995378124 0.965349416 1 20.03789252 6.765234667 0.209469811 1.01883056 5.16E-15 0.721289432 0.053445563 17.89578928 0.347146355 0.105040527 5.467309038 5824178.372 -6.765234667 -1.01883056 YDLLVSNAIQFLASVCERPHYK ddPTM_BT-474_Pertuzumab_2h_R1 2 YDLLVSNAIQFLASVCERPHYK 22 1 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ; 200.1 1.01E-22 521200000 892590 906880 920560 1149930 1104420 1125780 1208170 1003800 1526820 1539710 FALSE TRUE 857706.596 881016.6703 1086925.67 1209278.025 1139944.672 1148544.043 1222955.946 983071.1792 1353501.795 1435424.07 0.597528364 0.613767519 0.757215719 0.842453495 0.794151844 0.800142666 0.851982331 0.684864633 0.942928172 1 20.45304559 6.76592216 0.116061384 1.045362688 1.90E-22 0.645419281 0.073993644 57.16240069 0.611835285 0.691582281 9.380432592 5833405.414 -6.76592216 -1.045362688 DGAPWCGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGAPWCGR 8 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ;;; 111.04 0.0077025 516833000 834230 850660 779400 931770 872910 915690 914140 1048060 1080030 1077900 FALSE TRUE 801627.3693 826400.0097 920254.9177 979858.7614 900987.9429 934205.8792 925327.5188 1026417.195 957429.5223 1004892.873 0.797724206 0.822376227 0.915774151 0.975087781 0.896600988 0.929657185 0.920822053 1.021419519 0.952767751 1 19.93861028 6.767088249 0.349638702 0.984518078 5.93E-16 0.733587411 0.034942941 13.62890756 0.426306473 0.031354652 7.559821285 5849089.259 -6.767088249 -0.984518078 SKFENEEFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKFENEEFFR 10 1 Q13951-2;A0A494C0A9;Q13951;H3BSC0;J3KRT0 Q13951-2 CBFB Core-binding factor subunit beta 0 ; 153.34 1.50E-05 1006340000 1735960 2062170 1657560 1994790 2167460 1943580 2268590 2413520 2556280 2558050 FALSE TRUE 1668116.764 2003358.931 1957117.964 2097741.351 2237178.319 1982880.519 2296353.683 2363679.969 2266101.811 2384790.995 0.699481325 0.840056397 0.820666452 0.879633207 0.938102469 0.831469308 0.962916116 0.991147641 0.950230782 1 21.1854314 6.767490179 0.24861995 1.005896322 3.96E-16 0.80077987 0.040096861 11.56728624 0.26781289 0.053370599 4.287283162 5854504.971 -6.767490179 -1.005896322 DVAEVDTVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DVAEVDTVR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 106.68 0.0074084 0 252770 243260 243020 279480 254000 283200 288150 329510 334980 328610 FALSE TRUE 242891.4689 236322.463 286939.12 293903.9963 262170.1407 288926.498 291676.4659 322705.5034 296954.4748 306352.952 0.792848469 0.771405862 0.936629199 0.959364009 0.855778079 0.943116416 0.952092885 1.053378142 0.969321408 1 18.22483523 6.768740182 0.278932263 1.020991574 4.06E-19 0.680882249 0.04802349 14.74003007 0.381793404 0.057134531 6.384807156 5871379.906 -6.768740182 -1.020991574 GGS(ph)PAPLPAKVDEATSGLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGSPAPLPAKVDEATSGLIR 20 1 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 GGS(1)PAPLPAKVDEATSGLIR 103.53 0.00017193 95544000 188000 205550 193100 204580 202310 224210 245240 250080 268420 264930 TRUE FALSE 180652.7522 199687.9153 227997.4655 215138.3983 208817.4849 228743.6798 248241.3205 244915.7606 237950.0869 246986.0551 0.731428955 0.808498744 0.923118778 0.871054838 0.845462651 0.92614006 1.005082333 0.991617768 0.963415067 1 17.91407006 6.786864222 0.255058192 1.017004958 1.14E-10 0.807422327 0.037964569 12.15718354 0.28641741 0.053554485 4.709304516 6121589.758 -6.786864222 -1.017004958 HRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 HRDFVAEPMGEKPVGSLAGIGEVLGK 26 2 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 48.867 0.079991 162990000 109570 135780 98473 141690 114740 132070 171010 126130 192610 181300 FALSE TRUE 105287.8833 131907.6873 116269.2616 149002.6379 118430.7163 134740.5459 173102.8715 123525.3714 170745.7203 169020.3895 0.622930071 0.780424703 0.687900803 0.881566054 0.700688933 0.797185158 1.024153784 0.730831184 1.010207826 1 17.36683777 6.78875361 0.115260812 1.097545028 1.34E-10 0.506719975 0.097945204 63.61658201 0.672611684 0.805880662 10.88958242 6148279.616 -6.78875361 -1.097545028 AVYLGELPHDQDVVEYIMNQPNVVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVYLGELPHDQDVVEYIMNQPNVVPR 26 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 239.19 4.97E-45 293730000 202161 229420 215411 228060 230140 266560 261170 294470 283910 326640 FALSE TRUE 194260.3246 222877.1662 254340.5595 239830.2039 237542.6621 271950.0258 264366.2766 288389.0916 251681.727 304516.3819 0.637930621 0.731905341 0.835227839 0.787577346 0.780065298 0.893055487 0.868151247 0.947039663 0.826496511 1 18.21616032 6.789616488 0.188773447 0.992245723 1.67E-14 0.775905455 0.047070453 15.7028984 0.271021051 0.099518024 4.141196005 6160507.466 -6.789616488 -0.992245723 VVVSNR ddPTM_BT-474_Pertuzumab_2h_R1 3 VVVSNR 6 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 127.1 0.040029 2301140000 929402 1092900 913657 970041 1079850 1204800 1093930 1202090 1310650 1304390 FALSE TRUE 893079.9423 1061731.562 1078775.144 1020104.932 1114584.356 1229161.881 1107317.843 1177266.421 1161870.507 1216042.503 0.734415072 0.87310399 0.887119604 0.838872761 0.91656694 1.010788585 0.910591397 0.968112889 0.955452218 1 20.21376222 6.800896053 0.311537026 0.982981491 8.69E-16 0.757746723 0.038603798 13.19371523 0.370728482 0.038117604 6.340546902 6322605.034 -6.800896053 -0.982981491 SRT(ph)SPVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.084)RT(0.458)S(0.458)PVSR 77.062 0.055266 174180000 30294 35329 22324 35734 32612 38113 33983 28515 37633 36465 TRUE FALSE 29110.07699 34321.45151 26358.44339 37578.23602 33660.9946 38883.67097 34398.89412 27926.15529 33361.05961 33995.19307 0.856299799 1.009597193 0.775357955 1.105398518 0.990169243 1.143799092 1.011875239 0.821473649 0.981346379 1 15.05304314 6.804615637 11.19743422 0.965309844 0.382174434 0 0.112403417 0 0 0.025049468 0 6376988.545 -6.804615637 -0.583135411 VANS(ph)PTMVNLLLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VANSPTMVNLLLGK 14 0 Q6UB99;A0A087WTN8;A0A2R8Y438 Q6UB99 ANKRD11 Ankyrin repeat domain-containing protein 11 1 VANS(0.997)PT(0.003)MVNLLLGK;VANS(0.995)PT(0.005)MVNLLLGK 176.04 2.40E-06 400340000 530790 515380 514580 546220 605120 630830 624820 606180 749270 747950 TRUE FALSE 510046.14 500681.867 607576.0528 574410.4797 624584.2344 643585.8148 632466.7341 593662.1712 664216.0108 697290.6803 0.73146846 0.718038949 0.871338267 0.823774784 0.895730076 0.922980664 0.907034544 0.851384061 0.952566884 1 19.41140067 6.810238876 0.26805931 0.953484903 5.98E-23 0.774525708 0.040642683 13.50968321 0.330604492 0.05024216 5.228230719 6460094.577 -6.810238876 -0.953484903 EGAAHAFAQYNMDQFTPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGAAHAFAQYNMDQFTPVK 19 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ; 255.22 6.34E-31 758970000 618210 619340 582910 669720 676830 685360 691260 743710 834180 820970 FALSE TRUE 594049.6697 601677.0296 688254.8038 704284.3295 698600.8516 699218.4488 699719.8467 728352.1286 739487.3836 765364.9707 0.776165219 0.786130869 0.899250462 0.920194099 0.912768259 0.91357519 0.9142303 0.951640272 0.966189219 1 19.54578835 6.811657412 0.32044688 0.969971413 2.31E-20 0.874839205 0.024032621 9.054121704 0.258689925 0.023913542 4.455637766 6481229.678 -6.811657412 -0.969971413 EPGPIAPSTNS(ph)SPVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 EPGPIAPSTNSSPVLK 16 0 Q14674-2;Q14674 Q14674-2 ESPL1 Separin 1 EPGPIAPS(0.01)T(0.01)NS(0.652)S(0.328)PVLK 131.72 4.51E-05 241730000 303640 322700 331180 306000 346610 354680 334880 411060 441550 405360 TRUE FALSE 291773.4131 313496.912 391031.5931 321792.6967 357759.0254 361851.8726 338978.3616 402571.4674 391427.0951 377904.6061 0.772082183 0.829566263 1.034736245 0.851518324 0.94669136 0.957521731 0.896994522 1.065272719 1.035782811 1 18.52766258 6.816083747 0.305294059 1.019537219 7.27E-14 0.530748902 0.064207575 21.4168243 0.587084498 0.065853368 10.42703008 6547624.229 -6.816083747 -1.019537219 DVEDGAFLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVEDGAFLLR 10 0 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P2-8;Q5T5P2-6;Q5T5P1;Q5T5P2-4;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 0 ; 153.08 3.93E-05 117668000 210780 249010 186792 217280 235370 237360 235030 264540 261460 252730 FALSE TRUE 202542.4846 241908.4786 220549.4696 228493.8468 242940.8898 242159.5818 237906.3674 259077.1566 231780.1569 235612.372 0.859642823 1.026722309 0.936069136 0.969787133 1.03110413 1.027788056 1.009736312 1.09959063 0.983735086 1 17.84605577 6.819318563 0.440662668 1.037149195 1.06E-17 0.473819506 0.04419472 24.53997953 0.833972295 0.027484988 19.55241634 6596575.885 -6.819318563 -1.037149195 SDSPES(ph)DAER ddPTM_BT-474_Pertuzumab_2h_R1 2 SDSPESDAER 10 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 SDSPES(1)DAER;SDSPES(1)DAER 189.56 1.05E-06 78508000 161941 145396 163405 188026 164479 162798 204500 213100 222610 231270 TRUE FALSE 155612.1667 141249.4484 192935.9184 197730.0444 169769.6164 166089.8871 207002.7322 208699.4105 197340.2461 215605.8769 0.721743623 0.655128007 0.894854636 0.917090235 0.787407184 0.770340259 0.960097819 0.96796717 0.915282315 1 17.71803698 6.820865158 0.192700668 1.017683141 1.70E-14 0.577405533 0.072152948 25.52622995 0.445443539 0.158454369 7.088945399 6620109.274 -6.820865158 -1.017683141 SDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.188)DS(0.812)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.183)DS(0.817)PEIPFQAAAGPSDGLDASSPGNSFVGLR 172.96 3.06E-13 657150000 467876 476143 417179 543351 494288 499992 544733 600842 616512 614946 TRUE FALSE 449590.8887 462563.8678 492572.5254 571393.4102 510187.2224 510102.1808 551399.6054 588434.4027 546528.1424 573295.1597 0.78422237 0.806851166 0.859195333 0.996682774 0.889920687 0.889772349 0.961807537 1.026407415 0.953310233 1 19.12891857 6.833033239 0.285592661 1.005437283 1.76E-13 0.716561631 0.04229491 14.55369494 0.37350007 0.049610395 6.441300588 6808214.64 -6.833033239 -1.005437283 DEFEER ddPTM_BT-474_Pertuzumab_2h_R1 1 DEFEER 6 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 114.54 0.058621 198010000 328380 321400 321740 383400 346620 373040 418970 420210 452590 485430 FALSE TRUE 315546.5466 312233.9867 379885.5751 403187.3199 357769.3471 380583.1244 424097.4802 411532.5167 401213.8806 452551.3937 0.697261241 0.689941498 0.839430792 0.890920513 0.790560701 0.840972163 0.937125564 0.909360842 0.886559817 1 18.78772211 6.834445415 0.209111917 0.983607221 1.08E-12 0.775418156 0.044774925 15.18175975 0.286852559 0.081704083 4.494357569 6830388.634 -6.834445415 -0.983607221 ISESVLRDS(ph)PPPHEDYEDEVFVR ddPTM_BT-474_Pertuzumab_2h_R1 6 ISESVLRDSPPPHEDYEDEVFVR 23 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 ISESVLRDS(1)PPPHEDYEDEVFVR;ISESVLRDS(1)PPPHEDYEDEVFVR;ISESVLRDS(1)PPPHEDYEDEVFVR;ISES(0.001)VLRDS(0.999)PPPHEDYEDEVFVR;IS(0.001)ES(0.003)VLRDS(0.996)PPPHEDYEDEVFVR;ISES(0.001)VLRDS(0.999)PPPHEDYEDEVFVR 239.97 1.86E-37 3677980000 1085600 1029633 1135483 1317093 1167013 1208341 1431711 1380568 1620383 1725287 TRUE FALSE 1043173.552 1000268.875 1340690.037 1385068.328 1204551.033 1232774.483 1449232.707 1352058.788 1436443.915 1608431.775 0.64856562 0.62189077 0.833538642 0.861129673 0.74889781 0.766444995 0.901022182 0.840606863 0.893071088 1 20.61722331 6.840822989 0.139427647 1.032149069 2.30E-12 0.713488368 0.05922989 31.96145606 0.400924857 0.292454702 6.254868987 6931432.344 -6.840822989 -1.032149069 KRNDS(ph)EEEER ddPTM_BT-474_Pertuzumab_2h_R1 5 KRNDSEEEER 10 2 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 KRNDS(1)EEEER;KRNDS(1)EEEER;KRNDS(1)EEEER;KRNDS(1)EEEER;KRNDS(1)EEEER 162.48 5.32E-06 1414322000 2067877 1858238 2102170 2267320 2092580 2137171 2545470 2696570 2954010 3031780 TRUE FALSE 1987062.081 1805242.872 2482078.882 2384336.657 2159889.736 2180386.062 2576622.223 2640884.887 2618683.169 2826434.84 0.703027734 0.638699625 0.878165966 0.843584513 0.764174608 0.771426261 0.911615646 0.934351944 0.926496918 1 21.43055201 6.842356252 0.142081363 1.06338056 4.67E-08 0.688661854 0.060672485 30.81701751 0.393581497 0.283538796 6.340757015 6955946.8 -6.842356252 -1.063380514 SLCLSPS(ph)EASQMK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLCLSPSEASQMK 13 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 SLCLS(0.051)PS(0.948)EASQMK 150.12 4.62E-05 150750000 142190 162080 140380 156680 175040 176330 166200 198470 231960 224790 TRUE FALSE 136633.0576 157457.6371 165749.7887 164766.2736 180670.3206 179895.5134 168234.0053 194371.5251 205628.8733 209564.7731 0.651984852 0.751355463 0.790923905 0.786230773 0.862121615 0.858424394 0.802778076 0.927500945 0.981218695 1 17.6770367 6.846920707 0.148613722 1.054189812 3.14E-22 0.869079257 0.036882652 17.13619763 0.228421535 0.14747495 3.671149972 7029439.662 -6.846920707 -1.054189812 SHTS(ph)SNYDSYKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SHTSSNYDSYKK 12 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 S(0.005)HT(0.002)S(0.572)S(0.421)NYDSYKK 109.07 0.0010029 93078000 90383 81939 56030 71627 68432 64119 76959 44837 83682 86412 TRUE FALSE 86850.73244 79602.17995 66155.86738 75323.67805 70633.17743 65415.53011 77900.84726 43911.10028 74182.77018 80559.23827 1.078097737 0.988119819 0.821207708 0.93500981 0.876785567 0.812017734 0.967000793 0.545078395 0.920847463 1 16.29776242 6.849687534 0.4922145 0.810420663 3.291901295 0.20194223 0.124997156 40.39590184 1.366902564 0.068032915 89.65302958 7074366.155 -6.849687534 2.481480632 SSSPALKPKPNPPS(ph)PENTASSAPVDWR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPALKPKPNPPSPENTASSAPVDWR 27 2 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SSSPALKPKPNPPS(1)PENTASSAPVDWR 239.93 1.99E-45 944600000 408500 334540 411740 416720 447330 414310 470260 506110 575520 573310 TRUE FALSE 392535.3684 324999.2467 486150.5771 438226.9691 461718.7757 422687.6321 476015.1826 495658.6516 510189.3824 534479.203 0.734425897 0.608067152 0.909578098 0.819913977 0.863866682 0.790840185 0.890614976 0.927367517 0.954554227 1 19.02777429 6.851089877 0.172208958 1.02677318 1.42E-18 0.635259106 0.06646132 24.4119925 0.376296931 0.170922319 6.013404575 7097246.306 -6.851089877 -1.02677318 GEGGTTNPHIFPEGSEPK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEGGTTNPHIFPEGSEPK 18 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;; 177.6 9.30E-14 4126230000 3336920 3159910 3072870 3256960 3485090 3403850 3791860 3805610 4272480 4155600 FALSE TRUE 3206509.477 3069792.461 3628205.965 3425052.096 3597191.085 3472678.179 3838265.917 3727022.824 3787485.982 3874137.511 0.827670538 0.792380872 0.936519665 0.884081189 0.928514043 0.896374527 0.990740754 0.962026467 0.977633337 1 21.88544373 6.853915755 0.224776268 1.009926283 0.278847652 0.754145288 0.032701036 13.30043661 0.268619967 0.047678904 3.197402294 7143577.409 -6.853915755 -0.73107863 TNLSVHEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNLSVHEDK 9 0 P33176;Q12840;J3KNA1 P33176;Q12840 KIF5B;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ; 131.83 0.00032222 1694010000 2393740 2740590 2670940 2972090 2629770 2752430 3228500 3377900 3728200 4030200 FALSE TRUE 2300189.994 2662431.057 3153638.273 3125479.921 2714358.94 2808086.02 3268011.349 3308145.185 3304990.366 3757230.964 0.612203513 0.708615223 0.83935172 0.831857278 0.722436008 0.747381795 0.869792509 0.880474268 0.879634603 1 21.84123837 6.854448347 0.092093815 1.14517808 4.96E-17 0.728998196 0.05504707 67.77859883 0.569137894 1.132944257 9.862071531 7152343.231 -6.854448347 -1.14517808 TSIDAYDNFDNISLAQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSIDAYDNFDNISLAQR 17 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 520.83 2.17E-286 1497880000 693040 729290 619030 728300 731070 758750 787250 797150 866140 858640 FALSE TRUE 665955.2306 708491.3632 730902.4912 765887.6503 754585.5305 774092.4449 796884.601 780688.5739 767819.4184 800483.548 0.831941184 0.885079231 0.913076219 0.956781251 0.942662135 0.967031049 0.995504034 0.975271229 0.959194502 1 19.61051223 6.858894138 0.391385943 0.986970535 8.10E-08 0.935343195 0.012627103 6.293527563 0.198141169 0.009252496 4.107038979 7225936.449 -6.858894138 -0.986970454 AGTQIENIDEDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGTQIENIDEDFR 13 0 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ; 132.79 0.0002669 157354000 185664 188198 204196 280770 191231 153706 313730 263680 244250 318180 FALSE TRUE 178408.0456 182830.7773 241098.7595 295260.5733 197382.1188 156814.0406 317569.5216 258234.9159 216523.764 296629.3852 0.601451018 0.616360976 0.81279459 0.995385448 0.665416606 0.528653089 1.070593601 0.870564175 0.729947115 1 18.178302 6.859169364 0.137515884 1.015752514 2.25E-16 0.24003057 0.15719523 88.02011102 1.084120865 0.798334427 16.71428849 7230517.201 -6.859169364 -1.015752514 VDLVDENFTELR ddPTM_BT-474_Pertuzumab_2h_R1 5 VDLVDENFTELR 12 0 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ;;;; 237.37 9.78E-16 549967000 514592 508769 486872 610811 561016 559236 593178 685903 696220 729806 FALSE TRUE 494481.1757 494259.4063 574860.6008 642335.0289 579061.5891 570544.1351 600437.4898 671738.8634 617188.0244 680375.5896 0.726776773 0.726450822 0.844916557 0.944088881 0.851091071 0.838572318 0.882508866 0.987305943 0.907128406 1 19.37597186 6.860441237 0.239266347 0.98273105 1.02E-13 0.71611009 0.047885268 16.49325018 0.353716004 0.072302573 5.75347296 7251723.507 -6.860441237 -0.98273105 AGSS(ph)TPGDAPPAVAEVQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AGS(0.374)S(0.448)T(0.178)PGDAPPAVAEVQGR 146.67 1.19E-07 397790000 190320 195740 185410 199170 205040 245510 208440 223730 303380 254620 TRUE FALSE 182882.084 190157.6868 218917.7114 209449.1876 211635.2978 250474.3804 210990.9511 219109.8973 268941.5743 237374.3606 0.770437395 0.801087726 0.922246661 0.882358091 0.891567637 1.055187173 0.888853162 0.923056293 1.132984934 1 17.85680459 6.862725304 0.263538895 1.019227652 1.02E-17 0.576495066 0.068035364 21.48845789 0.505415801 0.08345404 8.755666179 7289962.662 -6.862725304 -1.019227652 GLLAQGLRPES(ph)PPPAGPLLNGAPAGES(ph)PQPK ddPTM_BT-474_Pertuzumab_2h_R1 5 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK 247.95 1.27E-46 3161130000 2361020 2221210 2287450 2410830 2411310 2546810 2746080 2976640 2719350 3033260 TRUE FALSE 2268748.728 2157863.266 2700843.099 2535253.225 2488871.976 2598308.243 2779687.348 2915171.344 2410660.788 2827814.598 0.802297551 0.763085128 0.955099072 0.896541529 0.88013973 0.918839674 0.982980762 1.030891963 0.852481909 1 21.4312561 6.867804125 0.304703061 0.986320768 4.40E-16 0.489863238 0.058761868 21.23891147 0.565738063 0.05970751 10.04525213 7375714.972 -6.867804125 -0.986320768 GVNCIDYYSGGDKPYLISGADDR ddPTM_BT-474_Pertuzumab_2h_R1 5 GVNCIDYYSGGDKPYLISGADDR 23 1 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;;; 306.88 7.55E-63 6457090000 2740360 3089690 2408910 2767600 2986670 3103010 3065950 3204850 3295620 3352940 FALSE TRUE 2633263.702 3001575.066 2844253.623 2910436.168 3082738.953 3165754.988 3103472.013 3138668.728 2921515.034 3125842.387 0.842417299 0.960245174 0.909915879 0.931088586 0.986210618 1.01276859 0.992843409 1.004103323 0.934632868 1 21.57581361 6.870143961 0.437306213 0.993581284 2.15E-18 0.640799586 0.030467369 19.3062677 0.628363814 0.019446116 14.70922152 7415560.136 -6.870143961 -0.993581284 ADAEEEAATR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADAEEEAATR 10 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ; 137.05 0.00023632 276620000 257240 293150 269110 278170 285800 296900 315550 346690 343570 358650 FALSE TRUE 247186.7764 284789.649 317744.1633 292526.387 294993.0166 302903.5214 319411.7953 339530.7303 304569.374 334358.316 0.73928706 0.85174986 0.950310335 0.874888923 0.882266127 0.905924892 0.955297894 1.015469674 0.91090713 1 18.35103547 6.882095825 0.313980589 0.980718315 4.14E-22 0.677053247 0.043068556 17.45672161 0.472396034 0.044821213 8.543286158 7622471.775 -6.882095825 -0.980718315 T(ph)MIISPERLDPFADGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TMIISPERLDPFADGGK 17 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.604)MIIS(0.396)PERLDPFADGGK;T(0.5)MIIS(0.5)PERLDPFADGGK 112.58 0.0012541 133316000 210470 252310 212530 235030 247040 255240 274200 273410 313020 306870 TRUE FALSE 202244.5997 245114.3658 250938.8987 247159.9265 254986.266 260401.1277 277555.7416 267763.988 277487.2819 286085.4216 0.706937804 0.856787335 0.877146753 0.863937509 0.891294162 0.910221591 0.970184849 0.935958171 0.969945551 1 18.12608646 6.885389179 0.276126172 0.984961558 8.29E-15 0.871910963 0.028231507 9.582428414 0.232762744 0.032279963 4.008365376 7680494.432 -6.885389179 -0.984961558 AS(ph)LEDAPVDDLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 ASLEDAPVDDLTR 13 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR 253.06 9.43E-24 2104620000 1777420 1744850 1645130 2061190 1944270 1938320 2125220 2344820 2433060 2565800 TRUE FALSE 1707956.461 1695088.586 1942441.587 2167568.263 2006809.21 1977514.158 2151229.078 2296398.648 2156869.229 2392016.081 0.714023821 0.708644311 0.81205206 0.906167931 0.838961421 0.826714408 0.899337214 0.960026425 0.901695121 1 21.18979566 6.887719656 0.199675045 1.001706684 3.61E-16 0.817949534 0.038868309 14.20821875 0.251406101 0.079208401 4.071385352 7721819.678 -6.887719656 -1.001706684 LKDLGHPVEEEDELES(ph)GDQEDEDDESEDPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDLGHPVEEEDELESGDQEDEDDESEDPGK 31 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 LKDLGHPVEEEDELES(0.999)GDQEDEDDES(0.001)EDPGK 95.741 0.00022796 432670000 32980 30291 35369 38056 35671 35768 44384 34838 60042 50147 TRUE FALSE 31691.10514 29427.13034 41760.96508 40020.07472 36818.39011 36491.25347 44927.18467 34118.58313 53226.28388 46750.49902 0.677877366 0.629450614 0.89327314 0.856035241 0.78755074 0.78055324 0.96099904 0.729801475 1.138517984 1 15.51269414 6.889332552 0.138824588 1.061653259 3.61E-13 0.452001719 0.110098698 55.4018192 0.683185956 0.510450822 11.11900656 7750550.524 -6.889332552 -1.061653259 LGDDEDREPSLRPDDDRVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGDDEDREPSLRPDDDRVPR 20 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 138.3 9.00E-07 742260000 561230 573450 542740 629920 634590 640240 714840 739900 791010 880300 FALSE TRUE 539296.5111 557095.7675 640825.1912 662430.2467 655002.1637 653186.0915 723588.4258 724620.8064 701217.861 820676.4969 0.657136537 0.678825054 0.780849937 0.807175847 0.798124677 0.79591178 0.881697512 0.882955475 0.854438824 1 19.64645411 6.889484959 0.135136707 1.042797508 1.27E-14 0.911078197 0.028316431 16.06870926 0.193060175 0.15045909 3.077961234 7753270.913 -6.889484959 -1.042797508 VEELARSLRADIER ddPTM_BT-474_Pertuzumab_2h_R1 4 VEELARSLRADIER 14 2 Q9BX97 Q9BX97 PLVAP Plasmalemma vesicle-associated protein 0 ;;; 90.412 0.0034609 1155140000 3027460 2379460 2228000 1858830 2356980 1882340 2555620 1320900 3010530 2797230 FALSE TRUE 2909143.516 2311600.131 2630649.162 1954764.439 2432794.402 1920402.204 2586896.442 1293622.953 2668787.256 2607771.121 1.115567042 0.886427537 1.008773025 0.749592027 0.932901811 0.736415167 0.991995203 0.496064606 1.023397811 1 21.31438582 6.890652296 0.560664084 0.808545954 4.411700256 0.148123658 0.16131087 55.2421205 1.774064618 0.071206786 213.0665007 7774138.909 -6.890652296 3.603154302 GSS(ph)PSIRPIQGSQGSSS(ph)PVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSSPSIRPIQGSQGSSSPVEK 21 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 2 GS(0.172)S(0.736)PS(0.092)IRPIQGS(0.025)QGS(0.262)S(0.222)S(0.491)PVEK 77.505 0.0055927 343530000 223500 237550 201970 239090 228210 236440 267980 272720 298700 303550 TRUE FALSE 214765.3729 230775.3066 238470.4718 251429.4636 235550.5819 241220.9788 271259.6194 267088.2367 264792.8283 282990.2881 0.758914288 0.815488433 0.842680763 0.888473824 0.832362776 0.852400202 0.958547451 0.943807077 0.935695815 1 18.11039302 6.892725439 0.144559104 1.042161475 0.275654756 0.846497654 0.027974638 19.8761037 0.254673129 0.125400921 3.009462262 7811338.163 -6.892725439 -0.766506719 LPNNSSRPST(ph)PTINVLESK ddPTM_BT-474_Pertuzumab_2h_R1 3 LPNNSSRPSTPTINVLESK 19 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 LPNNSSRPS(0.015)T(0.984)PT(0.001)INVLESK;LPNNSSRPS(0.03)T(0.97)PTINVLESK;LPNNSSRPS(0.088)T(0.911)PTINVLESK 170.18 2.05E-11 1381250000 1209940 1407660 1260150 1428290 1377840 1556630 1683730 1465370 2096890 2027040 TRUE FALSE 1162654.207 1367514.915 1487887.137 1502004.218 1422159.475 1588106.125 1704335.991 1435109.597 1858859.838 1889746.775 0.615243387 0.723649821 0.787347361 0.794817717 0.75256616 0.840380386 0.901885911 0.759418995 0.983655515 1 20.8497615 6.892932614 0.108670705 1.096077011 1.91E-13 0.739550641 0.057571905 46.99954384 0.458073414 0.608091239 7.597709757 7815065.351 -6.892932614 -1.096077011 FIQENVFVAANHNGS(ph)PLSIK ddPTM_BT-474_Pertuzumab_2h_R1 2 FIQENVFVAANHNGSPLSIK 20 0 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 1 FIQENVFVAANHNGS(1)PLSIK;FIQENVFVAANHNGS(1)PLSIK 208.28 3.76E-22 1579690000 1438110 1319100 1390190 1481450 1509640 1857800 1698950 1699820 2014150 2163220 TRUE FALSE 1381907.071 1281480.56 1641428.258 1557907.812 1558198.942 1895365.989 1719742.258 1664718.123 1785512.136 2016703.183 0.685230768 0.6354334 0.81391663 0.772502283 0.772646642 0.939833886 0.852749315 0.825465114 0.885361887 1 20.94356733 6.898724753 0.155191289 1.007058537 7.23E-13 0.750919634 0.052074171 24.21103422 0.331904789 0.183054887 5.210963159 7919992.19 -6.898724753 -1.007058537 EESEES(ph)DEDMGFGLFD ddPTM_BT-474_Pertuzumab_2h_R1 4 EESEESDEDMGFGLFD 16 0 F8VWS0;P05388;P05388-2;Q8NHW5;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 1 EESEES(1)DEDMGFGLFD;EESEES(1)DEDMGFGLFD;EES(0.001)EES(0.999)DEDMGFGLFD;EES(0.009)EES(0.991)DEDMGFGLFD 191.06 2.96E-09 256686000 302394 300974 308437 327228 324502 364143 364032 410210 425221 458850 TRUE FALSE 290576.1082 292390.5162 364178.427 344116.2763 334939.9015 371506.221 368487.1325 401739.0201 376951.6948 427771.6808 0.679278506 0.68352004 0.851338327 0.804439124 0.782987553 0.868468479 0.861410769 0.939143562 0.881198339 1 18.70648145 6.899039089 0.16098875 1.025699659 3.37E-18 0.835030682 0.039195174 16.54554635 0.235125244 0.12176752 3.780167188 7925726.639 -6.899039089 -1.025699659 WDETPASQMGGST(ph)PVLTPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 WDETPASQMGGSTPVLTPGK 20 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDETPASQMGGS(0.033)T(0.967)PVLTPGK 172.66 6.74E-11 105820000 131960 127860 115690 126680 135900 144210 141240 158000 152720 182390 TRUE FALSE 126802.8573 124213.558 136597.7565 133217.97 140271.3469 147126.025 142968.5374 154737.2448 135383.8659 170036.5628 0.74573877 0.730510873 0.803343435 0.783466613 0.824948144 0.865261109 0.840810558 0.910023363 0.796204437 1 17.37548548 6.900178227 0.051034702 1.332318304 5.58E-12 0.774347217 0.036085209 161.1173107 0.757247743 5.203790069 18.04144041 7946542.801 -6.900178227 -1.332318304 FLIIDEADR ddPTM_BT-474_Pertuzumab_2h_R1 3 FLIIDEADR 9 0 Q8N8A6 Q8N8A6 DDX51 ATP-dependent RNA helicase DDX51 0 ;; 136.8 0.00042496 57386000 160120 176235 147440 171025 164244 176385 166516 170989 180849 197948 FALSE TRUE 153862.3334 171208.9504 174085.6878 179851.6207 169527.0574 179951.6256 168553.8726 167458.0174 160319.7797 184540.8056 0.833757785 0.9277566 0.943345225 0.974589984 0.918642665 0.975131895 0.913369117 0.907430835 0.868749755 1 17.49358033 6.907292991 5.178809869 0.925432073 0.883853438 0 0.047860159 0 0 0.010136822 0 8077798.039 -6.907292991 -0.041578635 AQS(ph)TDSLGTSGSLQSK ddPTM_BT-474_Pertuzumab_2h_R1 4 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQS(0.747)T(0.253)DSLGTSGSLQSK;AQS(0.774)T(0.226)DS(0.001)LGTSGSLQSK;AQS(0.933)T(0.067)DSLGTSGSLQSK;AQS(0.481)T(0.481)DS(0.038)LGTSGSLQSK 441.14 6.44E-182 4013780000 3316830 3230600 3230250 3752780 3260520 3586840 3950710 4073450 4615920 4947320 TRUE FALSE 3187204.617 3138466.451 3814028.032 3946461.426 3365397.587 3659368.362 3999059.971 3989331.834 4091940.113 4612233.61 0.691032781 0.68046563 0.826937305 0.85565081 0.729667634 0.793404817 0.867054948 0.864945745 0.887192727 1 22.13703416 6.910638883 0.072299037 1.220198353 1.98E-13 0.765246325 0.045305686 95.59494244 0.628765203 2.135224698 12.22117289 8140271.367 -6.910638883 -1.220198353 CTVDVPEDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 CTVDVPEDLR 10 0 B4DXZ6;P51114;P51114-3;C9JZE0;C9JY20;C9J5B4;C9IZ22;C9JAJ4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 129.38 0.00070858 370070000 356810 374020 319720 381140 383130 375480 381440 427040 448870 442700 FALSE TRUE 342865.4707 363353.3158 377500.5161 400810.6811 395453.7244 383072.4629 386108.1768 418221.4748 397916.1594 412715.5347 0.830754944 0.880396509 0.914674841 0.971154821 0.958175041 0.928175537 0.935531 1.013340763 0.964141463 1 18.65478822 6.912085984 0.387857635 0.983324654 4.41E-17 0.795421145 0.023567383 13.52178634 0.408448223 0.018761177 8.75846471 8167440.596 -6.912085984 -0.983324654 GNAEGS(ph)S(ph)DEEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNAEGSSDEEGK 12 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 GNAEGS(1)S(1)DEEGK 98.943 0.0020793 0 470880 419820 460940 547270 472050 525900 575350 580420 652660 685260 TRUE FALSE 452477.489 407847.1446 544242.1116 575514.6703 487233.917 536534.0583 582391.3054 568434.1242 578572.773 638846.7298 0.708272373 0.638411571 0.851913434 0.900865017 0.762677328 0.839847859 0.911629156 0.889781692 0.905651929 1 19.28511032 6.91815309 0.183777293 0.996141862 1.38E-13 0.690300802 0.057113458 22.10425913 0.356201299 0.132799286 5.722292592 8282340.668 -6.91815309 -0.996141862 S(ph)PVGSGAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPVGSGAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEK 51 0 P16989;P16989-3;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 1 S(0.839)PVGS(0.161)GAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEK;S(0.843)PVGS(0.157)GAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEK;S(0.818)PVGS(0.182)GAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEK 256.94 1.17E-73 591060000 268380 237424 280285 308984 262754 271968 332463 330023 377156 364868 TRUE FALSE 257891.4129 230652.9 330938.7344 324930.7013 271205.721 277467.3793 336531.7816 323207.9097 334342.832 340155.1654 0.758158156 0.678081427 0.972905215 0.95524259 0.797300023 0.815708264 0.98934785 0.950177868 0.9829127 1 18.37583347 6.920301128 0.238831235 0.999019116 1.76E-15 0.471384235 0.08022678 28.03662003 0.585881099 0.118739329 9.979030834 8323406.937 -6.920301128 -0.999019116 YVLGQLVGLNS(ph)PNSILK ddPTM_BT-474_Pertuzumab_2h_R1 2 YVLGQLVGLNSPNSILK 17 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 YVLGQLVGLNS(1)PNSILK;YVLGQLVGLNS(1)PNSILK 281.09 6.21E-36 840900000 696830 715400 755750 687080 700320 820700 795320 906620 887100 1033070 TRUE FALSE 669597.1132 694997.4924 892330.8366 722540.2811 722846.4288 837295.1163 805053.3641 887897.9802 786400.127 963099.2487 0.695252451 0.721626035 0.926520125 0.750224115 0.750541992 0.869375734 0.835898652 0.921917426 0.816530724 1 19.87732495 6.921604818 0.053836342 1.317604513 4.86E-09 0.545914357 0.064280802 264.4402182 1.30394836 8.086726433 30.12663875 8348430.151 -6.921604818 -1.317604508 EFVTHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EFVTHPK 7 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 85.265 0.020938 621320000 1927660 2051720 1724000 2090100 2050740 2167000 2348300 2242100 2353200 2579300 FALSE TRUE 1852324.916 1993206.954 2035565.15 2197970.311 2116703.915 2210818.225 2377039.198 2195799.851 2086074.601 2404601.714 0.770325042 0.828913555 0.846529028 0.914068346 0.880272148 0.919411399 0.988537596 0.913165718 0.867534357 1 21.19736652 6.925406769 0.333555262 0.949385677 6.13E-14 0.694953486 0.036740308 16.28321832 0.448819191 0.033018859 8.383589964 8421835.782 -6.925406769 -0.949385677 HLEAADKGHS(ph)PAQKPK ddPTM_BT-474_Pertuzumab_2h_R1 3 HLEAADKGHSPAQKPK 16 2 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4 Q14966 ZNF638 Zinc finger protein 638 1 HLEAADKGHS(1)PAQKPK;HLEAADKGHS(1)PAQKPK;HLEAADKGHS(1)PAQKPK 194.08 1.29E-10 4955900000 3912690 3048940 2525850 2105870 2524770 2596270 2987450 927470 3890400 3011330 TRUE FALSE 3759777.749 2961987.216 2982327.282 2214554.203 2605981.52 2648768.358 3024011.307 908317.4204 3448778.102 2807369.937 1.339252693 1.055075492 1.062320731 0.788835904 0.928264382 0.94350528 1.0771688 0.323547463 1.228472976 1 21.42078775 6.926333713 0.553548553 0.834374219 7.140240097 0.218843845 0.231194113 49.49463644 1.533937336 0.108922024 330.3794012 8439830.281 -6.926333713 6.305865878 YNPTWHCIVGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YNPTWHCIVGR 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ; 171.05 1.50E-05 1582560000 1014600 1356890 595970 782790 833560 802420 787300 656860 801040 668740 FALSE TRUE 974948.3103 1318192.826 703675.0363 823189.8857 860372.2144 818645.4822 796935.2129 643295.6115 710109.2974 623445.6441 1.563806435 2.114366887 1.128687068 1.320387581 1.38002763 1.313098407 1.278275372 1.031839131 1.139007553 1 19.24990426 6.928305722 0.23855097 0.987522592 4.106318549 0.509587917 0.215863937 22.22681733 0.46245153 0.29230096 24.68144714 8478240.311 -6.928305722 3.118795957 ADVTPPPDGSTTHNLEVS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 ADVTPPPDGSTTHNLEVSPK 20 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 ADVTPPPDGSTT(0.001)HNLEVS(0.999)PK;ADVTPPPDGS(0.003)T(0.002)T(0.014)HNLEVS(0.981)PK;ADVTPPPDGSTTHNLEVS(1)PK;ADVTPPPDGSTTHNLEVS(1)PK 256.12 2.28E-36 823890000 531550 535660 511521 569400 554770 554731 625940 624063 761600 771740 TRUE FALSE 510776.4383 520383.5013 603964.2234 598786.8022 572614.6809 565948.0409 633600.441 611175.881 675146.3609 719469.3624 0.70993494 0.723287924 0.839457877 0.832261711 0.795884732 0.786618681 0.880649648 0.849481455 0.938394873 1 19.45657373 6.933327942 0.05966589 1.292489983 6.14E-15 0.818577769 0.036198251 119.2631755 0.648470302 3.300889061 14.1663915 8576852.519 -6.933327942 -1.292489983 GEKPNPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GEKPNPLR 8 1 P68402;J3KNE3 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ;;; 110.41 0.0031297 2098040000 2677650 2787250 2401220 2647500 2601580 2830110 2826100 3011950 3031590 3085300 FALSE TRUE 2573004.478 2707760.359 2835173.869 2784137.792 2685262.183 2887336.763 2860686.657 2949752.18 2687456.613 2876329.883 0.894544292 0.941394231 0.985691483 0.967948012 0.933572397 1.00382671 0.994561394 1.025526383 0.934335324 1 21.45579772 6.940300788 0.509896617 0.991528531 1.28E-16 0.477528996 0.028048195 30.68162458 0.951801763 0.014820441 28.94276871 8715670.187 -6.940300788 -0.991528531 EHPWEVMPDLYFYR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHPWEVMPDLYFYR 14 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 157.75 5.21E-06 1792220000 1161970 1185520 1354050 1740300 1466980 1251950 1741430 1555390 1745090 2133810 FALSE TRUE 1116558.928 1151710.13 1598756.956 1830117.092 1514166.744 1277265.287 1762742.141 1523270.653 1546994.699 1989285.148 0.561286515 0.578956783 0.803684156 0.91998731 0.761161237 0.642072499 0.886118384 0.76573771 0.777663625 1 20.92381866 6.953805436 0.109908943 1.032310928 2.02E-36 0.460913431 0.100294317 92.1864408 0.89523316 1.076340626 14.19280716 8990946.957 -6.953805436 -1.032310928 LLLFDYDKVELANMNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLLFDYDKVELANMNR 16 1 Q9GZZ9-2;Q9GZZ9;E7EWE1;E7EQ61;C9JRV9;C9J5W5;C9J0F6 Q9GZZ9-2 UBA5 Ubiquitin-like modifier-activating enzyme 5 0 ; 165.86 6.27E-09 641220000 498240 517260 455730 472450 528870 482970 555120 574260 575480 551640 FALSE TRUE 478768.23 502508.2513 538090.5487 496833.2011 545881.5839 492735.9843 561913.7246 562401.3303 510153.923 514276.9315 0.930954124 0.977116064 1.046305046 0.966081056 1.06145454 0.95811411 1.09262868 1.093576818 0.991982902 1 18.97218592 6.954529722 0.474900382 1.044476713 6.21E-16 0.270364622 0.04687944 40.33348136 1.237687322 0.026775955 36.54186103 9005953.955 -6.954529722 -1.044476713 DRGVAASAGSSGENKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DRGVAASAGSSGENKK 16 2 P35249;C9J8M3;C9JZI1;P35249-2;C9JXZ7;C9JTT7;C9JW34;C9JGY5;F8WE44 P35249 RFC4 Replication factor C subunit 4 0 89.484 0.0032478 100650000 60962 61671 56813 74178 63028 69033 72417 79980 87067 94644 FALSE TRUE 58579.53764 59912.20346 67080.3729 78006.33547 65055.35286 70428.89456 73303.26091 78328.38505 77183.51917 88233.67758 0.66391359 0.679017413 0.760258155 0.884087999 0.737307507 0.798208762 0.830785511 0.887737961 0.874762577 1 16.4290418 6.965168837 0.10266921 1.108507787 3.45E-15 0.799987857 0.044414805 43.29799344 0.393190142 0.58760013 6.711109641 9229301.577 -6.965168837 -1.108507787 ELNHPNIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELNHPNIVK 9 0 G3V5T9;P24941;P24941-2 G3V5T9 CDK2 Cyclin-dependent kinase 2 0 82.749 0.019591 0 179770 200310 172040 184520 165210 174200 197490 187290 205620 210630 FALSE TRUE 172744.3897 194597.3549 203131.455 194043.0993 170524.1297 177722.4434 199906.9417 183422.3961 182278.8796 196363.8425 0.879715876 0.991004008 1.034464657 0.988181413 0.868409008 0.905067048 1.018043542 0.934094555 0.928271098 1 17.58316978 6.977763035 8.604800507 0.955029873 0.248152136 0 0.056144509 0 0 0.012543275 0 9500862.539 -6.977763035 -0.706877737 GPS(ph)PEPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPSPEPLK 8 0 Q92674-2;Q92674 Q92674-2 CENPI Centromere protein I 1 GPS(1)PEPLK 82.261 0.022169 0 134680 143460 114560 138950 150180 127370 137150 161720 162970 174570 TRUE FALSE 129416.5567 139368.6613 135263.5404 146121.2262 155010.6761 129945.5087 138828.4827 158380.4255 144470.3288 162746.2184 0.795204693 0.856355758 0.831131695 0.897847136 0.952468682 0.798454858 0.853036612 0.973174228 0.887703138 1 17.3122645 6.978751095 0.028098013 1.55247933 4.58E-10 0.477807801 0.049021256 1165.649341 2.995882882 57.97382385 116.6944846 9522502.499 -6.978751095 -1.552479329 S(ph)PISPELHSAPLTPVAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPISPELHSAPLTPVAR 17 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A0G2JQF5;A0A3B3IT55;A0A0G2JQF4;Q7Z3B3-4;Q7Z3B3-2 A0A1W2PRB5;Q7Z3B3-4 KANSL1 KAT8 regulatory NSL complex subunit 1 1 S(0.868)PIS(0.132)PELHSAPLTPVAR;S(0.999)PIS(0.001)PELHSAPLTPVAR;S(0.999)PIS(0.001)PELHSAPLTPVAR 195.48 1.09E-11 1075110000 262160 247512.7 266688.7 267620.3 237517.1 322693.2 290110 314954.2 330480 334135 TRUE FALSE 251914.4974 240453.8801 314885.2805 281432.2158 245157.0532 329218.2776 293660.453 308450.2857 292965.2959 311503.7388 0.808704571 0.771913304 1.010855541 0.903463364 0.787011591 1.056867821 0.942718871 0.9901977 0.940487254 1 18.24888995 6.986471205 0.3042989 0.990704326 5.21E-13 0.37444462 0.075660932 30.53979724 0.763423375 0.075214123 14.70341322 9693289.98 -6.986471205 -0.990704326 FLEESVSMS(ph)PEER ddPTM_BT-474_Pertuzumab_2h_R1 1 FLEESVSMSPEER 13 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 1 FLEESVSMS(1)PEER 253.15 9.38E-24 214020000 191230 205390 170240 188530 206460 214020 209110 215800 228990 236590 TRUE FALSE 183756.5202 199532.4783 201006.155 198260.0559 213100.9734 218347.631 211669.1507 211343.6546 202996.0152 220565.5486 0.833115241 0.904640274 0.911321629 0.898871366 0.966157112 0.989944406 0.959665515 0.958189781 0.920343256 1 17.75084794 6.992153082 0.410837168 0.968390907 9.35E-10 0.721876347 0.025147394 17.81609121 0.518307654 0.017683645 12.41282495 9820940.558 -6.992153082 -0.968390906 EKEIAETR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKEIAETR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 101.65 0.0047853 739620000 1608820 1698430 1395270 1581760 1609240 1624160 1675010 1808900 1892280 1712750 FALSE TRUE 1545945.536 1649992.439 1647426.327 1663394.823 1661002.666 1657001.628 1695509.273 1771545.583 1677476.307 1596743.917 0.968186269 1.033348192 1.031741101 1.041741763 1.040243616 1.037737868 1.061854224 1.109473826 1.050560638 1 20.60670152 6.995417728 0.532039968 1.061397766 1.05E-15 0.401824876 0.027048137 36.45657143 1.06121613 0.013849702 39.28906271 9895043.961 -6.995417728 -1.061397766 KQELEEILHDLESR ddPTM_BT-474_Pertuzumab_2h_R1 6 KQELEEILHDLESR 14 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;;;;; 171.21 1.98E-06 527709100 616607 654486 548818 625001 621972 700660 667692 667889 745161 767047 FALSE TRUE 592509.3167 635820.7001 648001.621 657257.3765 641978.2942 714827.8253 675863.4144 654096.8588 660573.4472 715094.2235 0.828575169 0.889142548 0.906176556 0.919119963 0.897753433 0.999627464 0.945138965 0.914700241 0.923757213 1 19.44777382 6.997992505 0.434237825 0.948782864 7.52E-14 0.608908256 0.030222162 24.81493184 0.727360911 0.019540599 18.25000761 9953882.4 -6.997992505 -0.948782864 RPDYAPMES(ph)S(ph)DEEDEEFQFIK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPDYAPMESSDEEDEEFQFIK 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 RPDY(0.001)APMES(1)S(1)DEEDEEFQFIK;RPDY(0.076)APMES(0.962)S(0.962)DEEDEEFQFIK;RPDY(0.001)APMES(0.999)S(0.999)DEEDEEFQFIK;RPDY(0.001)APMES(1)S(1)DEEDEEFQFIK 177.12 2.30E-16 364082000 431865 439967 388692 447984 446323 437591 460635 502865 524659 513094 TRUE FALSE 414987.2383 427419.5719 458937.2908 471104.5079 460679.3846 446439.3898 466272.3889 492480.662 465101.9099 478341.6864 0.867553989 0.893544477 0.959434028 0.984870274 0.963075972 0.933306468 0.97476846 1.029558318 0.972321508 1 18.867682 6.998508683 0.40850099 0.995235824 3.74E-17 0.723673752 0.024126494 17.93650445 0.5185068 0.018471278 12.75859232 9965720.04 -6.998508683 -0.995235824 ELVSDANQHVK ddPTM_BT-474_Pertuzumab_2h_R1 5 ELVSDANQHVK 11 0 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;;; 163.78 2.35E-05 4590390000 5302630 5523980 4824570 5642410 5516590 6129950 6120660 5974350 6770930 6981410 FALSE TRUE 5095397.357 5366441.499 5696477.121 5933615.456 5694036.127 6253901.789 6195566.468 5850977.585 6002322.412 6508552.882 0.782877154 0.824521456 0.875229444 0.911664323 0.8748544 0.960874391 0.95191152 0.898967511 0.922220733 1 22.63390538 6.999265415 0.334549556 0.951381061 1.35E-15 0.788758633 0.028216858 14.10895209 0.373056303 0.025820642 7.381346409 9983099.843 -6.999265415 -0.951381061 GS(ph)YGDLGGPIITTQVTIPK ddPTM_BT-474_Pertuzumab_2h_R1 5 GSYGDLGGPIITTQVTIPK 19 0 P61978;P61978-2;S4R359;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK 314.1 1.34E-61 2338685000 896585 867169 822335 934519 918974 933322 964145 1081949 1046502 1105393 TRUE FALSE 861545.467 842438.1892 970949.2272 982749.6376 948533.6333 952194.4103 975944.4949 1059606.375 927707.4803 1030523.748 0.836026796 0.817485469 0.942190056 0.953640942 0.920438404 0.92399075 0.947037365 1.02822121 0.900229114 1 19.97494632 6.999423289 0.348915796 0.980309422 1.18E-13 0.572781256 0.040267961 20.56745876 0.556933949 0.034463474 11.71071162 9986729.548 -6.999423289 -0.980309422 KQVNYNDGSQEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQVNYNDGSQEDR 13 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y7I0;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 149.3 6.24E-05 371990000 241480 237765 219490 282040 250510 243820 306070 298530 322370 364660 FALSE TRUE 232042.6946 230984.175 259156.7255 296596.1182 258567.8817 248750.2075 309815.7762 292365.2512 285775.9091 339961.2534 0.682556298 0.67944265 0.762312537 0.872440948 0.760580446 0.731701642 0.911326727 0.859995803 0.840613176 1 18.3750108 7.00300361 0.083940216 1.160663803 2.05E-11 0.712861008 0.053002595 80.23503401 0.597022931 1.415596882 10.91348384 10069400.4 -7.00300361 -1.160663803 ITVNGDS(ph)SAEAEELANEI ddPTM_BT-474_Pertuzumab_2h_R1 4 ITVNGDSSAEAEELANEI 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 1 IT(0.015)VNGDS(0.493)S(0.493)AEAEELANEI;ITVNGDS(0.685)S(0.315)AEAEELANEI;ITVNGDS(0.63)S(0.37)AEAEELANEI;ITVNGDS(0.5)S(0.5)AEAEELANEI 265.54 4.91E-31 372822000 672355 711017 621083 682866 708225 767234 632110 905324 800131 793698 TRUE FALSE 646078.6233 690739.4913 733326.514 718108.7961 731005.7003 782747.9972 639845.9513 886628.743 709303.4833 739940.1275 0.873149866 0.933507274 0.991061961 0.970495814 0.987925473 1.057853153 0.864726655 1.198243898 0.958595779 1 19.49704901 7.005433036 0.368807519 1.039428904 1.58E-13 0.214354313 0.080050817 41.32639249 1.145578938 0.061651115 26.85088094 10125886.05 -7.005433036 -1.039428904 TMIIS(ph)PERLDPFADGGK ddPTM_BT-474_Pertuzumab_2h_R1 10 TMIISPERLDPFADGGK 17 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;T(0.046)MIIS(0.954)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;T(0.176)MIIS(0.824)PERLDPFADGGK;T(0.361)MIIS(0.639)PERLDPFADGGK;T(0.117)MIIS(0.883)PERLDPFADGGK;T(0.181)MIIS(0.819)PERLDPFADGGK 240.2 1.57E-20 4145259000 4643780 4958360 4456570 5009560 5229090 5592910 5671900 5851860 6944810 6696950 TRUE FALSE 4462295.944 4816952.428 5261971.335 5268103.992 5397288.429 5706002.472 5741314.409 5731017.046 6156464.284 6243359.611 0.714726721 0.771532112 0.842810868 0.843793137 0.864484631 0.913931413 0.919587332 0.917938002 0.98608196 1 22.57389114 7.010048564 0.203349568 1.011126597 3.26E-19 0.958874125 0.017179435 6.417971935 0.110879939 0.032176387 1.916055151 10234074.27 -7.010048564 -1.011126597 RPAEDMEEEQAFK ddPTM_BT-474_Pertuzumab_2h_R1 7 RPAEDMEEEQAFK 13 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;; 254.4 1.33E-23 10152510000 4874550 4611390 4696070 5553870 5347100 4761530 5684070 6327640 6727180 6607220 FALSE TRUE 4684047.197 4479877.672 5544754.313 5840505.896 5519094.328 4857811.399 5753633.349 6196972.023 5963538.729 6159707.104 0.760433429 0.72728745 0.900165254 0.948179158 0.895999474 0.788643245 0.934075801 1.006049787 0.96815297 1 22.55443032 7.01076113 0.227195067 1.009310286 2.67E-15 0.607235272 0.059650854 23.15787014 0.445145832 0.098836959 7.900568417 10250879.54 -7.01076113 -1.009310286 DWTDYDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DWTDYDEK 8 0 Q9NWV4 Q9NWV4 C1orf123 UPF0587 protein C1orf123 0 126.41 0.0028389 219410000 184810 181850 175200 194180 207880 190040 219760 232120 258300 244920 FALSE TRUE 177587.4209 176663.816 206862.5373 204201.6531 214566.649 193882.739 222449.4886 227326.6409 228978.8669 228331.3502 0.777761883 0.773716863 0.905975185 0.894321576 0.939716113 0.849128859 0.974239798 0.995599775 1.002835864 1 17.80076943 7.013475821 0.234007937 1.023567709 1.06E-08 0.785132164 0.038522595 13.77806486 0.272045259 0.056819656 4.944810116 10315156.48 -7.013475821 -1.023567698 EAMFDDDADQFPDDLSLDHSDLVAELLK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAMFDDDADQFPDDLSLDHSDLVAELLK 28 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;H7C5M8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 0 ; 203.78 3.36E-25 117826000 61065 70111 63487 67059 70501 79745 81852 73854 90886 94689 FALSE TRUE 58678.51229 68111.50293 74960.51316 70519.92303 72768.72869 81357.49854 82853.72926 72328.88909 80569.00231 88275.62969 0.664719272 0.77157765 0.849164299 0.798860606 0.824335425 0.921630339 0.938579873 0.819352854 0.912698132 1 16.42972759 7.036884004 0.229672481 0.951199442 2.65E-31 0.738400568 0.046905021 19.09412726 0.367069439 0.073846265 6.236947934 10886392.9 -7.036884004 -0.951199442 ELVGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELVGHK 6 0 K7ER00;Q9Y285;Q9Y285-2 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 91.26 0.048095 1150530000 1075520 1176420 997530 1154810 1105930 1200790 1247010 1235610 1418060 1370190 FALSE TRUE 1033487.489 1142869.653 1177805.861 1214409.882 1141503.243 1225070.797 1262271.281 1210094.222 1257087.774 1277385.811 0.809064482 0.894694182 0.922043952 0.950699368 0.893624489 0.959045252 0.988167608 0.947320858 0.984109705 1 20.2847629 7.036984208 0.3662138 0.977862497 1.57E-17 0.805571455 0.024072267 14.11562778 0.382012692 0.019337718 8.587117477 10888904.97 -7.036984208 -0.977862497 VNEMIIGGGMAFTFLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VNEMIIGGGMAFTFLK 16 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 87.18 0.015255 26650000 23868 27299 19505 25997 22583 16836 22800 26310 27222 26224 FALSE TRUE 22935.21217 26520.45925 23029.98739 27338.70829 23309.4027 17176.43546 23079.03322 25766.68931 24131.87268 24447.82512 0.938128936 1.084777853 0.942005568 1.118247049 0.953434614 0.702575193 0.944011711 1.053946074 0.98707646 1 14.57741851 7.043433427 10.3228856 0.974329826 0.287437426 0 0.108458681 0 0 0.024929007 0 11051810.42 -7.043433427 -0.686892401 DQGGELLSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DQGGELLSLR 10 0 B3KWE1;P12081-4;P12081;P12081-3;P12081-2;A0A2R8Y3N3;A0A2R8Y5P7;P49590-2;P49590;D6RJE6;A0A2R8Y6I1;A0A2R8Y5E8;A0A2R8Y4X6 B3KWE1;A0A2R8Y3N3 HARS;HARS2 "Histidine--tRNA ligase, cytoplasmic;Probable histidine--tRNA ligase, mitochondrial" 0 ; 152.04 4.36E-05 223100000 185283 183422 163582 195529 184848 178017 191773 224477 201694 217115 FALSE TRUE 178041.9355 178190.9841 193144.9063 205620.2751 190793.8038 181616.6257 194119.9753 219841.4715 178798.5427 202409.6077 0.879612078 0.880348449 0.954227956 1.015862229 0.942612389 0.897272752 0.959045263 1.086121721 0.883350078 1 17.62691825 7.047061575 0.420683827 0.986675879 1.61E-09 0.223416975 0.057483001 47.45756472 1.33060156 0.040168131 35.05606536 11144525.32 -7.047061575 -0.986675878 DYFGAHTYELLAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DYFGAHTYELLAK 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 199.8 1.15E-07 7364530000 6050288 5854170 6082911 6695590 6857450 5830600 7791190 7657520 8544980 9270310 FALSE TRUE 5813836.056 5687214.803 7182228.331 7041150.202 7078026.107 5948498.727 7886540.914 7499389.536 7574989.694 8642423.647 0.672708987 0.658057859 0.831043307 0.814719399 0.818986247 0.688290573 0.912538107 0.867741486 0.87648905 1 23.04300452 7.047348851 0.096778495 1.123032746 1.28E-18 0.672744714 0.060405709 66.65331312 0.561941895 0.949333277 9.910635773 11151899.61 -7.047348851 -1.123032746 ETPKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ETPKPR 6 1 A0A0A6YYC7;Q96JP5-2;Q96JP5;H3BTR0 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 0 ;;; 86.113 0.0492 370694000 465760 429029 373389 413458 427713 428220 420557 462241 464936 455310 FALSE TRUE 447557.5843 416793.513 440868.6983 434796.6169 441470.7771 436878.9018 425703.9024 452695.5618 412158.4145 424471.4482 1.05438796 0.981911775 1.038629807 1.024324766 1.040048227 1.029230361 1.002903503 1.066492373 0.97099208 1 18.69530799 7.048076287 10.59430718 1.023986573 1.038597038 0 0.02971457 0 0 0.005982885 0 11170594.49 -7.048076287 0.014610465 AMGISIPS(ph)PVMENNFVDLTEDTEEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 AMGISIPSPVMENNFVDLTEDTEEPK 26 0 Q9NPI1-2;Q9NPI1;I3L4V5 Q9NPI1-2 BRD7 Bromodomain-containing protein 7 1 AMGIS(0.003)IPS(0.997)PVMENNFVDLTEDTEEPK 107.9 0.0017464 27891000 27539 28095 30742 30196 32847 30087 35473 36310 43447 42768 TRUE FALSE 26462.74543 27293.75811 36297.76325 31754.41918 33903.55359 30695.37975 35907.12919 35560.18581 38515.0787 39871.28527 0.663704349 0.684546734 0.910373544 0.796423265 0.850325074 0.769861808 0.900576165 0.89187458 0.965985381 1 15.28306249 7.059389662 0.155475293 1.030544393 1.71E-13 0.701417051 0.0585577 28.42964169 0.373140005 0.199410012 6.325253977 11465411.91 -7.059389662 -1.030544393 EAATLEVERPLPMEVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAATLEVERPLPMEVEK 17 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;; 223.5 2.75E-15 1392320000 1032190 1185910 1042220 1275140 1217670 1244430 1293500 1447900 1615390 1669300 FALSE TRUE 991850.8737 1152089.008 1230572.338 1340950.128 1256837.461 1269593.227 1309330.24 1418000.359 1432017.699 1556236.824 0.637339291 0.740304425 0.790735908 0.861661996 0.807613238 0.815809784 0.841343824 0.911172604 0.920179806 1 20.56963019 7.066366944 0.149375027 1.028756674 2.44E-13 0.879335253 0.033335009 18.426082 0.232380776 0.135438991 3.912327797 11651100.39 -7.066366944 -1.028756674 SGEWTEDEVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGEWTEDEVLR 11 0 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ; 180.27 1.57E-05 553240000 407010 427570 428560 458740 423360 442600 462140 567480 565120 542740 FALSE TRUE 391103.5992 415376.1222 506010.3253 482415.6264 436977.7589 451549.6752 467795.8076 555761.3397 500969.9468 505979.7364 0.772962969 0.820934303 1.000060455 0.953428748 0.863626994 0.892426401 0.924534668 1.098386555 0.990098834 1 18.94872008 7.076168962 0.264179585 1.025171293 4.72E-11 0.502139321 0.064937186 28.10077076 0.601722064 0.088175658 11.82633032 11917055.51 -7.076168962 -1.025171293 PEEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 4 PEEQLRK 7 1 A0A590UK20;Q9BXX2 A0A590UK20 ANKRD30B Ankyrin repeat domain-containing protein 30B 0 ;;; 114.78 0.0093439 6347550000 2569390 2518630 2468600 2710240 2770750 2572400 3007460 3230660 3316400 3284540 FALSE TRUE 2468975.398 2446801.138 2914730.934 2850115.811 2859873.69 2624415.69 3044266.195 3163945.742 2939936.175 3062075.18 0.806307897 0.799066318 0.951880918 0.930779175 0.933965864 0.857070952 0.994184014 1.033268472 0.960112343 1 21.54607827 7.076578138 0.274058571 1.011200195 5.28E-19 0.63362107 0.046389465 19.90538949 0.439061565 0.057130663 8.655837778 11928288.6 -7.076578138 -1.011200195 DFESHITSYK ddPTM_BT-474_Pertuzumab_2h_R1 4 DFESHITSYK 10 0 Q99613-2;Q99613;B5ME19;H3BPE3 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;;; 185.08 1.49E-06 3599300000 6521500 7146600 6099300 6857000 6998700 7651600 7535900 7331000 9180700 9389300 FALSE TRUE 6266632.57 6942785.965 7201579.188 7210890.592 7223819.542 7806320.595 7628126.598 7179612.288 8138545.425 8753354.348 0.715912132 0.793157193 0.822722228 0.82378598 0.825263008 0.891809046 0.871451822 0.820212687 0.929763049 1 23.06140454 7.08109789 0.044178192 1.380485946 1.37E-10 0.819127407 0.031600002 240.2109807 0.946611082 8.339801035 25.44864532 12053075.85 -7.08109789 -1.380485946 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_BT-474_Pertuzumab_2h_R1 2 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 36 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 228.26 1.08E-39 258200000 123676 103389 123412 133994 130354 124889 144133 145182 182475 179285 FALSE TRUE 118842.6052 100440.4469 145715.2937 140909.4464 134546.9548 127414.3411 145896.9428 142183.941 161761.203 167141.8673 0.711028345 0.60092931 0.871806066 0.843052963 0.804986548 0.762312539 0.872892861 0.850678189 0.967807801 1 17.35071363 7.084743437 0.116503277 1.082632101 1.32E-16 0.644306117 0.066383013 51.25039563 0.509608963 0.546786672 8.77884854 12154677.42 -7.084743437 -1.082632101 EGVHGGLINK ddPTM_BT-474_Pertuzumab_2h_R1 6 EGVHGGLINK 10 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;;; 144.65 3.18E-05 26123400000 19073000 18390200 18218900 21448400 20357800 19403900 22030200 23443100 24666900 25665000 FALSE TRUE 18327606.07 17865729.5 21511460.51 22555354.49 21012627.13 19796260.15 22299812.18 22958991.79 21866816.92 23926686.69 0.765990139 0.746686314 0.899057224 0.94268608 0.878208813 0.827371563 0.932005859 0.959555834 0.913909109 1 24.51211729 7.085119705 0.269768605 0.965871442 7.73E-23 0.639892698 0.047247808 21.130682 0.458399871 0.0593318 8.611523659 12165212.65 -7.085119705 -0.965871442 GWEEGVAQMSVGQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GWEEGVAQMSVGQR 14 0 P62942;Q5W0X3;Q1JUQ5 P62942 FKBP1A;FKBP12-Exip2 Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 ; 170.66 7.30E-06 554090000 498590 529630 443680 608880 536510 498060 596450 658760 667040 671230 FALSE TRUE 479104.5516 514525.471 523862.8456 640304.3698 553767.3314 508131.1144 603749.5335 645156.3758 591320.4157 625766.9942 0.765627711 0.822231718 0.837153206 1.023231292 0.884941738 0.812013288 0.964815241 1.030984986 0.944953027 1 19.25526604 7.090838774 0.25276606 1.004863946 1.46E-14 0.524516083 0.063141401 26.48016644 0.542736654 0.087398037 10.34976414 12326471.45 -7.090838774 -1.004863946 SS(ph)DEENGPPSS(ph)PDLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 S(0.075)S(0.925)DEENGPPS(0.013)S(0.987)PDLDR;S(0.354)S(0.646)DEENGPPS(0.002)S(0.998)PDLDR 461.07 1.64E-205 1197960000 829920 977050 811580 985930 901470 1013880 1059480 1095250 1106450 1236060 TRUE FALSE 797485.8089 949185.4906 958250.5595 1036813.965 930466.6012 1034381.348 1072446.233 1072632.705 980850.4346 1152340.555 0.6920574 0.823702235 0.831568893 0.899746139 0.807458001 0.897635116 0.930667786 0.930829606 0.851181042 1 20.13613571 7.092407997 0.258597395 0.952096229 1.86E-32 0.698333591 0.044402183 18.01662921 0.376227405 0.053866562 6.867137579 12371090.88 -7.092407997 -0.952096229 LKLS(ph)PS(ph)PSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 2 LKLS(0.984)PS(0.836)PS(0.154)S(0.027)R 49.298 0.097035 255520000 542990 494520 573310 602200 488860 629660 643450 689440 772070 745130 TRUE FALSE 521769.3505 480416.7738 676919.8702 633279.6142 504584.6259 642392.1566 651324.7336 675202.8231 684427.8504 694661.6814 0.751112901 0.691583812 0.974459781 0.911637465 0.726374636 0.924755422 0.937614311 0.971988007 0.985267892 1 19.40595099 7.094215643 0.196330202 1.027749212 3.35E-20 0.504902588 0.078461402 31.40794162 0.509697678 0.157690818 9.195696953 12422689.87 -7.094215643 -1.027749212 THTGEKPYVCDK ddPTM_BT-474_Pertuzumab_2h_R1 2 THTGEKPYVCDK 12 1 Q49AA0 Q49AA0 ZFP69 Zinc finger protein ZFP69 0 ; 52.344 0.089716 1378410000 5312100 2799400 3389100 1229090 2960700 2402300 2660200 2787700 3468600 2479700 FALSE TRUE 5104497.259 2719563.853 4001585.76 1292523.482 3055933.604 2450876.152 2692756.323 2730133.021 3074859.07 2311747.71 2.208068483 1.176410315 1.730978576 0.55911096 1.32191484 1.060183229 1.164814098 1.180982254 1.330101488 1 21.14055253 7.096919178 1.084559471 1.139148328 200 0.555677963 0.278745361 214.1306563 1.753010652 0.073878991 104188.9301 12500263.78 -7.096919178 198.8608517 YHDGNRNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 YHDGNRNPK 9 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 78.334 0.018064 41858000 64091 82094 29565.2 40309 39827 48784 35777 18307.1 35313 24156.3 FALSE TRUE 61586.25286 79752.7595 34908.28931 42389.35232 41108.07162 49770.4459 36214.84963 17929.05199 31304.41628 22520.17228 2.734714996 3.541392068 1.550089798 1.88228366 1.82538886 2.210038417 1.60810713 0.796132985 1.390061137 1 14.45893024 7.107441871 0.225438154 0.844157837 9.838068754 0.624190432 0.47357729 20.69073062 0.38044545 0.73353102 62.86617833 12806836.69 -7.107441871 8.993910917 KPVTDCVISVPSFFTDAER ddPTM_BT-474_Pertuzumab_2h_R1 2 KPVTDCVISVPSFFTDAER 19 1 Q92598-2;Q92598;Q92598-4 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 151.45 1.05E-07 3484300000 4279300 4517100 4241100 4601000 4593200 5089400 5133100 5245900 5860900 5964000 FALSE TRUE 4112060.225 4388276.731 5007561.113 4838458.161 4740944.449 5192311.155 5195920.413 5137570.332 5195595.203 5560052.968 0.739572132 0.789250886 0.900631908 0.870217998 0.852679727 0.933860016 0.934509157 0.924014638 0.934450667 1 22.4066672 7.107460393 0.257878919 0.972566703 7.25E-16 0.855230295 0.027900403 11.84215537 0.245077059 0.03582628 4.602064068 12807382.89 -7.107460393 -0.972566703 SELEDFELDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SELEDFELDK 10 0 F8W7R3;Q9NVI1-2;Q9NVI1-1;Q9NVI1;H3BP78 F8W7R3 FANCI Fanconi anemia group I protein 0 159.83 0.0090376 0 58026 63442 54362 61571 72006 64739 66518 85211 72806 86535 FALSE TRUE 55758.27977 61632.69628 64186.42268 64748.68669 74322.13838 66048.06694 67332.06718 83451.36307 64541.36811 80673.90737 0.691156305 0.763973115 0.795628038 0.802597628 0.921266129 0.818704202 0.834620132 1.034428179 0.800027793 1 16.29981451 7.113842326 0.181828318 1.002398752 1.94E-13 0.566951242 0.066786138 27.9396239 0.418805911 0.149770011 7.285300907 12996976.28 -7.113842326 -1.002398752 MEDYLQLPDDYDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 MEDYLQLPDDYDTR 14 0 P49750;P49750-1;F8VU51 P49750 YLPM1 YLP motif-containing protein 1 0 95.018 0.0091539 58074000 49326 51044 42846 51364 58946 64317 50022 51415 53902 60784 FALSE TRUE 47398.28539 49588.2751 50589.2253 54014.9022 60842.05162 65617.53381 50634.1842 50353.26228 47783.27094 56667.04554 0.836434738 0.875081357 0.892745066 0.953197783 1.073676085 1.157948737 0.893538453 0.88858104 0.843228555 1 15.79022237 7.118163307 11.97253452 0.94099223 0.245110445 0 0.100233156 0 0 0.02406552 0 13126934.16 -7.118163307 -0.695881785 VGDPQELNGITR ddPTM_BT-474_Pertuzumab_2h_R1 4 VGDPQELNGITR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 131.12 0.0004756 1483300000 713728 762110 634532 790464 744474 778175 859060 853289 927717 919032 FALSE TRUE 685834.7207 740375.369 749206.0475 831259.9418 768420.6823 793910.2317 869573.4333 835668.284 822406.4555 856785.1441 0.800474571 0.864131894 0.874438653 0.970208164 0.896865086 0.92661531 1.0149259 0.975353377 0.959874784 1 19.70857394 7.118759515 0.294628768 0.997652388 1.38E-11 0.799170897 0.029029326 13.35579505 0.304524821 0.030666709 6.315280856 13144967.46 -7.118759515 -0.997652388 QDAPPWGSGVELTHLGS(ph)PSAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QDAPPWGSGVELTHLGSPSAQR 22 0 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 1 QDAPPWGSGVELTHLGS(0.999)PS(0.001)AQR;QDAPPWGSGVELTHLGS(0.998)PS(0.002)AQR 216.43 8.66E-26 293122000 727700 444956 419351 323811 446191 270549 324670 614720 361193 340829 TRUE FALSE 699260.6795 432266.2905 495137.0541 340522.9245 460543.1387 276019.6861 328643.4086 602025.8172 320191.8849 317744.3483 2.200702179 1.36042165 1.558287525 1.071688376 1.449414101 0.868684802 1.034301351 1.894686154 1.007702849 1 18.27750694 7.121718208 1.095933676 1.26318949 199.9983559 0.482045986 0.298642352 322.4882308 2.401156293 0.088424618 158765.774 13234825.13 -7.121718208 198.7351665 EEDGADAS(ph)EEDLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEDGADASEEDLTR 14 0 E5RHA3;Q86X53 E5RHA3 ERICH1 Glutamate-rich protein 1 1 EEDGADAS(1)EEDLTR;EEDGADAS(1)EEDLTR 279.71 3.27E-33 604580000 591350 598100 507060 609530 601110 571800 598260 654570 695660 688290 TRUE FALSE 568239.3882 581042.7736 598697.0215 640987.9163 620445.2491 583362.1878 605581.6848 641052.9008 616691.5932 641671.5052 0.8855612 0.905514377 0.933027284 0.998934675 0.96692037 0.909129022 0.943756548 0.999035948 0.961070561 1 19.29147539 7.127196239 0.460162094 0.972437937 1.88E-13 0.503460582 0.028041335 35.08990241 0.924118389 0.017717353 29.13744675 13402821.67 -7.127196239 -0.972437937 SPQNDDHS(ph)DTDSEENRDNQQFLTTVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPQNDDHSDTDSEENRDNQQFLTTVK 26 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 S(0.013)PQNDDHS(0.987)DTDSEENRDNQQFLTTVK;S(0.027)PQNDDHS(0.96)DT(0.012)DSEENRDNQQFLTTVK 186.01 8.18E-18 665830000 413860 428150 377450 450270 412920 479680 492960 423850 567120 546140 TRUE FALSE 397685.8937 415939.5812 445663.6113 473508.4887 426201.9468 489379.4583 498992.9919 415097.3494 502742.9152 509149.4513 0.781078901 0.816930236 0.87531001 0.929999016 0.837086136 0.96117055 0.980052106 0.815276042 0.987417179 1 18.95772967 7.141197248 0.32417535 0.942923569 1.21E-30 0.490852311 0.055937629 32.26996968 0.771364356 0.053119672 16.36618924 13841949.1 -7.141197248 -0.942923569 GPTSTSIDNIDGT(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GPTSTSIDNIDGTPVR 16 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 GPTSTSIDNIDGT(1)PVR 165.66 1.01E-08 0 172710 177740 206340 230100 181710 190260 214250 258860 249040 274840 TRUE FALSE 165960.3023 172671.0292 243630.228 241975.4886 187554.8672 194107.1876 216872.0556 253514.4505 220770.0233 256224.842 0.647713551 0.673904325 0.950845461 0.944387307 0.731993298 0.75756584 0.846413072 0.989421824 0.861626147 1 17.96705083 7.141451819 0.190546409 0.980500971 2.80E-31 0.409915605 0.095525304 44.91935889 0.697591417 0.216712823 12.14493677 13850065.22 -7.141451819 -0.980500971 T(ph)SPLNSSGSSQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPLNSSGSSQGR 13 0 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.633)S(0.367)PLNSSGSSQGR;T(0.639)S(0.361)PLNSSGSSQGR 158.28 0.00051072 426760000 420940 416380 404910 470390 471610 426620 517860 548830 607640 621290 TRUE FALSE 404489.1994 404505.2501 478086.2442 494666.8843 486779.764 435246.5487 524197.7256 537496.4687 538663.2546 579209.4749 0.698347 0.698374712 0.825411643 0.85403797 0.840420927 0.75144929 0.905022705 0.927982866 0.929997312 1 19.14372568 7.143109666 0.140505018 1.053081924 8.76E-11 0.788111685 0.044616365 27.1506263 0.31671888 0.21237167 5.529208072 13903036.6 -7.143109666 -1.053081923 RQHEAEEGVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RQHEAEEGVR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 150.1 1.44E-05 134011000 73969 80058.7 58928.7 74808.8 80098.4 77986.8 80725 72851.6 76968.4 85641.1 FALSE TRUE 71078.2097 77775.50426 69578.42695 78669.69113 82674.83778 79563.74653 81712.9367 71347.189 68231.26991 79840.55202 0.890251982 0.974135352 0.871467258 0.98533501 1.035499326 0.996533021 1.02345155 0.893620938 0.854594165 1 16.28483408 7.143242395 10.41087808 0.952811749 0.23543151 0 0.064155165 0 0 0.014582499 0 13907286.3 -7.143242395 -0.717380238 FTDDDKTDHLSWEWNLTIK ddPTM_BT-474_Pertuzumab_2h_R1 2 FTDDDKTDHLSWEWNLTIK 19 1 P52565;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 308.84 1.09E-61 1230300000 2446140 2694220 2128570 2775760 2686980 2871660 3030810 2982860 3491110 3435890 FALSE TRUE 2350542.144 2617383.484 2513249.949 2919017.306 2773409.152 2929726.933 3067901.959 2921262.899 3094813.829 3203174.11 0.733816541 0.817121828 0.784612345 0.911288992 0.865831534 0.914632434 0.957769342 0.911990044 0.966170967 1 21.61107079 7.146832106 0.217197827 1.000022542 2.01E-09 0.882315268 0.027721122 10.47790543 0.183459998 0.042389146 3.392611647 14022714.96 -7.146832106 -1.00002254 SNT(ph)PILVDGK ddPTM_BT-474_Pertuzumab_2h_R1 4 SNTPILVDGK 10 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41 P06744 GPI Glucose-6-phosphate isomerase 1 S(0.008)NT(0.992)PILVDGK;S(0.111)NT(0.889)PILVDGK;S(0.002)NT(0.998)PILVDGK;SNT(1)PILVDGK 212.69 4.02E-07 1329100000 3376940 2786400 2501490 2378260 2560190 2075850 2533080 3316160 3216410 2500120 TRUE FALSE 3244965.451 2706934.6 2953564.888 2501002.284 2642540.836 2117825.109 2564080.591 3247680.137 2851296.621 2330784.646 1.392220194 1.161383402 1.267197677 1.073030187 1.133755897 0.908631826 1.100093308 1.393384903 1.223320493 1 21.15238428 7.148642127 1.113843802 1.14810148 61.43636845 0.255984133 0.129166883 671.7561284 4.418009336 0.04096176 102203.6315 14081279.76 -7.148642127 60.28826697 EYQVETIVDTLCTNMLSDKEQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYQVETIVDTLCTNMLSDKEQLR 23 1 Q86VP6;Q86VP6-2 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 197.28 2.73E-24 262640000 127480 126910 114050 142330 138300 140120 145960 153300 173030 172740 FALSE TRUE 122497.9407 123290.6511 134661.372 149675.6684 142748.5451 142953.3224 147746.3021 150134.3014 153388.3598 161040.1659 0.760667005 0.765589444 0.836197425 0.929430664 0.886415785 0.887687376 0.917450012 0.932278606 0.952485108 1 17.29706104 7.153562175 0.237024225 0.983040287 1.41E-14 0.883278874 0.025363977 11.14786506 0.210519728 0.038145798 3.957812315 14241711.22 -7.153562175 -0.983040287 TDCDIEDDRLAAMFR ddPTM_BT-474_Pertuzumab_2h_R1 8 TDCDIEDDRLAAMFR 15 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;;;;;; 329.11 7.43E-69 7577570000 3866169 4113400 3663613 4489604 4184414 4929030 4813885 4691523 5934621 5959210 FALSE TRUE 3715074.841 3996089.859 4325709.366 4721313 4319009.476 5028698.364 4872798.765 4594641.411 5260947.704 5555587.399 0.668709639 0.719292052 0.778623223 0.849831469 0.77741725 0.905160517 0.87709875 0.827030714 0.946965159 1 22.40550803 7.154808755 0.151813713 1.016579672 4.39E-18 0.839211543 0.03893358 21.35617509 0.266892449 0.144175296 4.583407225 14282648.72 -7.154808755 -1.016579672 DFTVSAMHGDMDQK ddPTM_BT-474_Pertuzumab_2h_R1 22 DFTVSAMHGDMDQK 14 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;;;;;;;;;;;;;;;;;; 258 2.30E-24 56028220000 30907256 34006510 30001960 32426674 31164746 35869750 37887490 37678670 44841230 44778620 FALSE TRUE 29699366.27 33036677.63 35423981.56 34100218.53 32167188.36 36595060.92 38351168.44 36900592.3 39751041.56 41745724.18 0.711434928 0.791378717 0.848565506 0.816855359 0.770550493 0.876618184 0.918684948 0.88393705 0.952218277 1 25.3151251 7.159652105 0.102937787 1.102783704 0.150204433 0.824585382 0.034811063 41.89360046 0.364872777 0.446155075 5.594325419 14442823.54 -7.159652105 -0.952579271 LTQDQDVDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTQDQDVDVK 10 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 146.11 6.80E-05 131010000 161550 156450 150560 159390 173800 172720 178320 198560 210600 210440 FALSE TRUE 155236.4474 151988.1992 177769.5412 167616.137 179390.4348 176212.5167 180502.3335 194459.6666 186693.5709 196186.7114 0.791268921 0.774711998 0.906124273 0.854370491 0.914386268 0.898187831 0.920053821 0.991196933 0.951611705 1 17.5818678 7.162499742 0.19693002 1.017917034 0.13568631 0.831673261 0.029366099 13.48645196 0.214498003 0.0550345 3.420388152 14537835.21 -7.162499742 -0.882230723 AIEPNDYTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIEPNDYTGK 10 0 O75223;M0QZK8;O75223-3 O75223 GGCT Gamma-glutamylcyclotransferase 0 ; 143.89 0.011638 0 352040 356930 333550 399520 373240 383600 439880 454960 495820 531260 FALSE TRUE 338281.8876 346750.7059 393829.9048 420139.2751 385245.6036 391356.6548 445263.383 445564.917 439536.5922 495277.287 0.683015144 0.700114289 0.795170534 0.84829102 0.77783822 0.790176867 0.899018378 0.899627196 0.887455581 1 18.91787694 7.170395902 0.123052115 1.067677509 2.08E-21 0.8643618 0.034174666 26.24825863 0.268960835 0.245975696 4.699773276 14804573.57 -7.170395902 -1.067677509 RS(ph)PGGGSEANGLALVSGFK ddPTM_BT-474_Pertuzumab_2h_R1 5 RSPGGGSEANGLALVSGFK 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RS(0.715)PGGGS(0.285)EANGLALVSGFK;RS(0.751)PGGGS(0.249)EANGLALVSGFK;RS(0.989)PGGGS(0.011)EANGLALVSGFK;RS(0.999)PGGGS(0.001)EANGLALVSGFK;RS(1)PGGGSEANGLALVSGFK 205.07 2.63E-16 1612170000 1372000 1445940 1264370 1520480 1444530 1503590 1555610 1699710 1810920 1784500 TRUE FALSE 1318380.723 1404703.207 1492869.785 1598952.155 1490994.619 1533993.62 1574648.021 1664610.395 1605351.954 1663634.226 0.792470306 0.844358204 0.897354576 0.961120017 0.896227426 0.922073853 0.946510956 1.000586769 0.964966895 1 20.66590684 7.173178576 0.284976771 0.994013888 4.91E-15 0.848426402 0.024718828 12.54733752 0.27194804 0.029227899 5.70071312 14899736.07 -7.173178576 -0.994013888 (ac)AGS(ph)PELVVLDPPWDK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGSPELVVLDPPWDK 15 0 Q5SY74;Q96IY1-2;Q96IY1 Q5SY74 NSL1 Kinetochore-associated protein NSL1 homolog 1 AGS(1)PELVVLDPPWDK 48.004 0.00079759 111790000 135390 126050 127290 151910 139170 136590 157270 173540 180520 181510 TRUE FALSE 130098.8091 122455.1774 150294.1346 159750.0933 143646.5294 139351.9434 159194.7173 169956.3384 160028.1264 169216.166 0.768832034 0.723661222 0.888178347 0.944059289 0.848893654 0.823514364 0.940777238 1.004374123 0.945702353 1 17.36850788 7.173290343 0.20313613 1.019180965 4.08E-20 0.652066924 0.053490173 23.74659383 0.387274434 0.106135915 7.232710838 14903571.08 -7.173290343 -1.019180965 WS(ph)GNEPTDEFSDLPLR ddPTM_BT-474_Pertuzumab_2h_R1 3 WSGNEPTDEFSDLPLR 16 0 Q96II8-3;Q96II8;Q96II8-2;E9PD99;Q96II8-4 Q96II8-3 LRCH3 Leucine-rich repeat and calponin homology domain-containing protein 3 1 WS(1)GNEPTDEFSDLPLR;WS(1)GNEPTDEFSDLPLR;WS(1)GNEPTDEFSDLPLR 183.77 2.02E-09 202398000 182379 191561 176791 203799 202798 195293 215480 241376 245767 252051 TRUE FALSE 175251.427 186097.8678 208741.0664 214317.0908 209321.1818 199241.9583 218117.1087 236391.5012 217868.5605 234979.3613 0.745816254 0.791975375 0.888337875 0.912067722 0.890806668 0.847912588 0.928239431 1.006009634 0.927181687 1 17.84217452 7.17398835 0.233758796 0.997390613 2.44E-14 0.773762165 0.037123278 16.89333827 0.312605812 0.059004571 5.992439455 14927543.65 -7.17398835 -0.997390613 DAVSGMGVIVHIIEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAVSGMGVIVHIIEK 15 0 P49720 P49720 PSMB3 Proteasome subunit beta type-3 0 ; 196.8 8.75E-09 1638360000 2389600 2348300 2518400 2806600 2697700 2524700 3086800 2926400 3651200 3765600 FALSE TRUE 2296211.79 2281328.783 2973530.902 2951448.962 2784473.97 2575751.164 3124577.182 2865968.817 3236731.083 3510552.558 0.654088424 0.649848919 0.847026459 0.840736298 0.793172563 0.733716736 0.890052814 0.816386814 0.922000463 1 21.7432667 7.175183783 0.096690797 1.111459213 1.78E-12 0.69090776 0.059163966 70.86866258 0.580333639 0.946281118 10.41244136 14968689.62 -7.175183783 -1.111459213 DGDSYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGDSYR 6 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 106.29 0.075031 77536000 186710 208290 151200 215830 191930 226160 208020 201430 191440 219440 FALSE TRUE 179413.1668 202349.7731 178525.2034 226969.0122 198103.6028 230733.1102 210565.811 197270.4001 169708.5338 204577.1333 0.876995214 0.98911237 0.872654732 1.109454456 0.968356529 1.127853863 1.029273446 0.964283725 0.829557688 1 17.64228537 7.178791499 10.18272377 0.982228355 0.221774311 0 0.09320563 0 0 0.020203331 0 15093553.53 -7.178791499 -0.760454045 ETFLTSPEELYR ddPTM_BT-474_Pertuzumab_2h_R1 4 ETFLTSPEELYR 12 0 O95433;O95433-2;G3V438;H0YJ63;H0YJG7 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;; 245.5 4.19E-16 810889000 919558 977714 808266 923490 961688 952519 983970 1008168 1143925 1085666 FALSE TRUE 883620.6567 949830.554 954337.646 971151.4296 992621.5679 971779.5868 996012.1192 987348.9785 1014071.43 1012132.875 0.873028314 0.938444524 0.942897588 0.959509817 0.980722584 0.960130444 0.984072491 0.975513199 1.001915317 1 19.94896727 7.183107404 0.423531492 0.988097595 1.17E-11 0.901145801 0.011293247 10.78034208 0.271575005 0.007040892 8.208630646 15244297.08 -7.183107404 -0.988097595 ELSDLAR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELSDLAR 7 0 P61077-3;P61077-2;P61077;A0A087WY85;D6RA11;D6RGD0;D6R933;D6RIZ3;D6R980;D6R9F6 P61077-3 UBE2D3 Ubiquitin-conjugating enzyme E2 D3 0 ;; 148.21 0.0048845 1264960000 1704350 1897160 1603300 1789160 1700660 1304380 1955060 1823110 1841200 2003110 FALSE TRUE 1637742.118 1843054.854 1893051.975 1881498.762 1755363.273 1330755.457 1978986.609 1785462.141 1632194.695 1867437.576 0.876999659 0.98694322 1.013716335 1.007529669 0.939984981 0.712610411 1.059733742 0.956102718 0.874029053 1 20.83262859 7.184432502 9.766427687 0.945357696 0.201504642 0 0.095084958 0 0 0.020734899 0 15290880.76 -7.184432502 -0.743853054 KENSETTLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 KENSETTLTR 10 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 ; 194.39 7.51E-07 724500000 454540 474450 427490 491950 508160 528590 496790 594360 600730 629280 FALSE TRUE 436776.0743 460919.1505 504746.9525 517339.5985 524505.4279 539278.452 502869.8646 582086.2583 532537.6489 586658.3051 0.744515283 0.785668841 0.860376386 0.88184143 0.894056086 0.919237736 0.857176759 0.992206627 0.907747567 1 19.16216094 7.185552024 0.235198912 0.983413701 7.15E-15 0.806516987 0.03334815 13.63128244 0.252417516 0.045963941 4.809756786 15330348.36 -7.185552024 -0.983413701 AES(ph)PEEVACR ddPTM_BT-474_Pertuzumab_2h_R1 6 AESPEEVACR 10 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AES(1)PEEVACR;AES(1)PEEVACR;AES(1)PEEVACR;AES(1)PEEVACR;AES(1)PEEVACR;AES(1)PEEVACR 211.46 6.12E-08 4203669000 1295954 1401152 1150590 1323396 1336503 1365127 1327436 1486820 1602129 1547454 TRUE FALSE 1245306.685 1361192.517 1358527.208 1391696.626 1379492.833 1392730.803 1343681.559 1456116.647 1420262.033 1442643.562 0.863211619 0.943540423 0.941692905 0.964685015 0.956225688 0.965401877 0.931402319 1.009339164 0.984485752 1 20.46028346 7.18755761 0.42923644 0.982291426 1.05E-40 0.711309128 0.0210379 22.51274266 0.565193508 0.013739567 17.35966778 15401308.16 -7.18755761 -0.982291426 EELDDVIALD ddPTM_BT-474_Pertuzumab_2h_R1 1 EELDDVIALD 10 0 Q9UBT2;Q9UBT2-2;U3KQ93 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 86.011 0.032219 130310000 270110 262840 242610 296810 279260 282330 300450 333900 344710 345000 FALSE TRUE 259553.8026 255344.0605 286455.0238 312128.3997 288242.6515 288038.906 304126.997 327004.8483 305579.9659 321632.8427 0.80698787 0.793899213 0.890627404 0.970449401 0.89618538 0.895551908 0.945571958 1.016702292 0.950089435 1 18.29505521 7.202144389 0.257903347 1.002787075 1.65E-09 0.733079524 0.036693094 17.29106145 0.3431566 0.049103787 6.999868857 15927381.75 -7.202144389 -1.002787073 SSASAPDVDDPEAFPALA ddPTM_BT-474_Pertuzumab_2h_R1 2 SSASAPDVDDPEAFPALA 18 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 174.1 1.55E-11 169583000 316030 323690 281230 301280 320750 326570 312260 365040 335360 370320 FALSE TRUE 303679.1982 314458.6781 332054.5169 316829.0969 331067.215 333173.4692 316081.5313 357501.7964 297291.3387 345237.8966 0.879623011 0.91084635 0.961813637 0.917712395 0.958953864 0.965054742 0.915547031 1.035523041 0.861120235 1 18.39723131 7.202498805 0.468413877 0.963299313 1.78E-09 0.202605584 0.045528882 61.67289798 1.514007397 0.024673966 52.51027493 15940384.93 -7.202498805 -0.963299311 KFDEGR ddPTM_BT-474_Pertuzumab_2h_R1 4 KFDEGR 6 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6;H0Y4J5;Q13087-2;Q13087 P07237 P4HB;PDIA2 Protein disulfide-isomerase;Protein disulfide-isomerase A2 0 ;;; 124.34 0.029498 20591100000 22308900 23978500 20962300 27227600 23182900 23257000 26789200 27061800 30655900 30662300 FALSE TRUE 21437043.52 23294656.66 24750653.91 28632819.7 23928599.03 23727272.47 27117054.24 26502964.37 27175970.75 28585515.11 0.749926788 0.814911208 0.865846 1.001654845 0.837088257 0.8300453 0.948629197 0.927146643 0.950690259 1 24.76878095 7.203239321 0.285119955 0.957284586 3.85E-112 0.548775772 0.054255242 28.69904217 0.612993308 0.062194638 12.60958637 15967588.11 -7.203239321 -0.957284586 DFQHVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 DFQHVEK 7 0 M0R2W4;Q9UGK3;Q9UGK3-2 M0R2W4 STAP2 Signal-transducing adaptor protein 2 0 ;; 93.551 0.014852 301090000 576130 599920 534230 609930 638960 655510 691220 665210 759980 792870 FALSE TRUE 553614.2027 582810.869 630777.2449 641408.5604 659512.7287 668764.8613 699679.3571 651473.181 673710.2565 739168.2087 0.748969174 0.788468527 0.853360896 0.867743706 0.892236329 0.90475328 0.946576637 0.881359849 0.911443767 1 19.49554318 7.20952242 0.260850049 0.954917701 7.76E-26 0.863549071 0.025321541 12.2249595 0.243970141 0.032052918 4.785056484 16200276.26 -7.20952242 -0.954917701 ELQDAFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELQDAFSR 8 0 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 ; 93.467 0.025702 191725000 325960 341370 332300 448690 328150 355730 431090 462490 446890 523790 FALSE TRUE 313221.1228 331634.4618 392354.002 471846.9447 338705.2428 362923.1043 436365.8084 452939.4199 396160.9207 488313.2368 0.64143484 0.679142888 0.80348836 0.966279243 0.693622899 0.74321783 0.893618636 0.927559169 0.811284419 1 18.89744736 7.212372531 0.137704932 1.023726169 2.15E-14 0.48967329 0.08589259 56.60774319 0.636568008 0.426052241 10.98962134 16306942.17 -7.212372531 -1.023726169 LFEAEEQDLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFEAEEQDLFK 11 0 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8 A0A024R571 EHD1 EH domain-containing protein 1 0 173.71 2.76E-05 50576000 82529 75988 77719 75606 98105 86692 94791 97865 115860 113620 FALSE TRUE 79303.67544 73820.89664 91764.55215 79508.03472 101260.6364 88444.97164 95951.08061 95844.05355 102708.0585 105924.4162 0.748681733 0.696920496 0.866321057 0.750611026 0.955970682 0.834981913 0.905844791 0.904834381 0.969635351 1 16.69267565 7.222989399 0.164325009 1.029447203 7.53E-10 0.693028738 0.054411642 24.22354044 0.319560343 0.142563634 5.793135146 16710498.25 -7.222989399 -1.029447202 VTGTEGSSSTLVDYTSTSSTGGS(ph)PVRK ddPTM_BT-474_Pertuzumab_2h_R1 2 VTGTEGSSSTLVDYTSTSSTGGSPVRK 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 VTGTEGSSSTLVDYTSTS(0.013)S(0.03)T(0.047)GGS(0.91)PVRK;VTGTEGSSSTLVDYTS(0.001)T(0.003)S(0.136)S(0.049)T(0.03)GGS(0.781)PVRK 243.61 1.60E-45 2075010000 565810 564150 520450 565980 657560 542610 620140 661230 741980 699960 TRUE FALSE 543697.5197 548060.9944 614506.8923 595190.2956 678711.0146 553581.946 627729.4588 647575.3694 657753.541 652551.0857 0.833187672 0.839874466 0.941699287 0.912097625 1.040088706 0.848335032 0.961962171 0.992374978 1.007972487 1 19.31573132 7.225272403 0.308523644 0.995063181 7.86E-14 0.515933642 0.05018619 27.12512248 0.601693588 0.048658899 13.75674647 16798573.45 -7.225272403 -0.995063181 LDSSLPPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LDSSLPPVR 9 0 Q9Y4R8;H3BRS3 Q9Y4R8 TELO2 Telomere length regulation protein TEL2 homolog 0 86.472 0.032837 396460000 138220 145740 131540 148210 168230 143950 160020 184790 178270 195210 FALSE TRUE 132818.2096 141583.6379 155312.2041 155859.1359 173641.2707 146860.7676 161978.3726 180974.0219 158033.537 181988.2528 0.729817488 0.777982291 0.853418843 0.856424156 0.954134501 0.806979381 0.890048506 0.994426943 0.868372186 1 17.4734858 7.226139972 0.226344881 0.977731766 1.49E-13 0.632623689 0.051542874 22.5621945 0.397729964 0.078047892 7.573116105 16832164.68 -7.226139972 -0.977731766 TVS(ph)PPIRK ddPTM_BT-474_Pertuzumab_2h_R1 7 TVSPPIRK 8 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 T(0.009)VS(0.991)PPIRK;T(0.042)VS(0.958)PPIRK;T(0.005)VS(0.995)PPIRK;T(0.155)VS(0.845)PPIRK;T(0.003)VS(0.997)PPIRK;T(0.032)VS(0.968)PPIRK;T(0.009)VS(0.991)PPIRK 91.584 0.0075851 10681250000 5592740 5655920 5298620 5804210 5818370 6979450 6707170 6801440 8022190 8177690 TRUE FALSE 5374169.538 5494618.699 6256198.501 6103765.974 6005523.155 7120579.261 6789254.353 6660987.887 7111544.623 7623807.772 0.704919339 0.720718421 0.820613359 0.800619081 0.787732762 0.933992497 0.890533255 0.873708793 0.932807442 1 22.86208031 7.226918969 0.150474603 1.03092295 2.47E-11 0.866094156 0.033426237 18.63369517 0.226436891 0.123813544 4.029076164 16862383.76 -7.226918969 -1.03092295 S(ph)PSQDVK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSQDVK 7 0 Q9UHK0 Q9UHK0 NUFIP1 Nuclear fragile X mental retardation-interacting protein 1 1 S(0.997)PS(0.003)QDVK 66.056 0.072284 167700000 105180 107630 113660 127710 113220 123150 134090 148120 139890 170630 TRUE FALSE 101069.4493 104560.4978 134200.8904 134301.1284 116861.8241 125640.1774 135731.0335 145061.2702 124010.2737 159073.0781 0.635364893 0.657311086 0.843643009 0.844273148 0.734642376 0.789826782 0.85326213 0.911915907 0.779580524 1 17.27933017 7.227943885 0.12497723 1.033531195 7.50E-17 0.639621272 0.06331424 48.45313223 0.496585415 0.417914162 8.550239452 16902225.24 -7.227943885 -1.033531195 IYVASVHQDLSDDDIK ddPTM_BT-474_Pertuzumab_2h_R1 4 IYVASVHQDLSDDDIK 16 0 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5;A0A0J9YVR6;E9PQ56;A0A0J9YWM1;H0YEM1;E9PN18 A0A0J9YVP6;E9PN18 PUF60 Poly(U)-binding-splicing factor PUF60 0 ;;; 261.78 7.52E-27 3272420000 1928480 2024980 2038160 2239250 2008000 2142200 2344370 2516570 2814920 2990030 FALSE TRUE 1853112.87 1967229.553 2406500.851 2354817.961 2072589.144 2185516.752 2373061.101 2464601.95 2495382.083 2787512.605 0.664790848 0.705729384 0.863314787 0.844773924 0.743526375 0.784038339 0.851318519 0.884158136 0.895200287 1 21.4105469 7.228185637 0.074269051 1.199822586 1.61E-16 0.735840395 0.048703517 109.1210678 0.689997432 2.076241347 13.82271358 16911636.58 -7.228185637 -1.199822586 ELLKPNASVALHK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELLKPNASVALHK 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 131.66 7.68E-05 719530000 1250900 1312200 1114000 1312700 1309500 1476300 1495700 1510300 1757600 1867800 FALSE TRUE 1202013.445 1274777.341 1315324.581 1380448.604 1351621.257 1506151.797 1514004.824 1479111.777 1558084.616 1741292.242 0.690299661 0.732086958 0.755372676 0.7927725 0.776217354 0.864962102 0.869471986 0.849433393 0.8947864 1 20.73172692 7.229736199 0.09055091 1.138987894 5.59E-17 0.956439633 0.018032659 24.57117038 0.18707159 0.355900956 3.484781619 16972124.11 -7.229736199 -1.138987894 FDDGAGGDNEVQR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDDGAGGDNEVQR 13 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 218.15 5.73E-11 935420000 566820 618140 494960 590780 590290 618730 636240 640480 656490 724930 FALSE TRUE 544668.0477 600511.2524 584410.2823 621270.2266 609277.2139 631241.1445 644026.4954 627253.8642 581968.0074 675829.8454 0.805924822 0.888553911 0.864729911 0.919270184 0.901524575 0.934023777 0.952941779 0.928123948 0.861116169 1 19.36630054 7.233009482 0.378506707 0.938642838 2.48E-23 0.556669579 0.034305599 28.32276957 0.677995199 0.024848722 17.75853135 17100526.51 -7.233009482 -0.938642838 LDDDSER ddPTM_BT-474_Pertuzumab_2h_R1 1 LDDDSER 7 0 Q86VP6;Q86VP6-2;F5H6I6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 101.41 0.02112 773140000 602980 542320 539980 638750 588250 604790 630170 688900 717960 725660 FALSE TRUE 579414.875 526853.5646 637566.3978 671715.964 607171.5955 617019.2682 637882.209 674673.9743 636460.1907 676510.4018 0.856475929 0.778781173 0.942433991 0.992912987 0.897505188 0.912061761 0.942900815 0.997285441 0.940798824 1 19.36775259 7.239406305 0.314063629 0.980362142 3.71E-13 0.497903562 0.046639255 27.88059052 0.619631536 0.046091901 14.28324118 17354268.21 -7.239406305 -0.980362142 GFPTIYFSPANKK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFPTIYFSPANKK 13 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 186.13 1.29E-05 1710090000 1451540 1600010 1286620 1383960 1389550 1338310 1429210 1515340 1599450 1644150 FALSE TRUE 1394812.212 1554379.281 1519140.855 1455386.341 1434246.138 1365371.545 1446701.1 1484047.699 1417887.141 1532790.256 0.909982437 1.014084788 0.991095063 0.9495013 0.935709326 0.890775199 0.943835005 0.968200113 0.925036636 1 20.54772886 7.239879346 9.115191223 0.952686265 0.097114089 0 0.038107857 0 0 0.008472038 0 17373181.07 -7.239879346 -0.855572176 LQS(ph)PLEPHSK ddPTM_BT-474_Pertuzumab_2h_R1 3 LQSPLEPHSK 10 0 O15211;O15211-2 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 LQS(1)PLEPHSK;LQS(1)PLEPHSK;LQS(1)PLEPHSK 148.72 1.59E-05 1668250000 1178100 1151540 1072030 1141700 1264420 1358820 1225040 1153500 1243560 1367810 TRUE FALSE 1132058.55 1118699.207 1265769.668 1200623.274 1305091.218 1386296.271 1240032.406 1129679.822 1102396.282 1275167.01 0.88777277 0.877296227 0.992630501 0.941541982 1.023466893 1.087148789 0.972447057 0.885907346 0.864511294 1 20.28225478 7.244526089 9.670596098 0.952465551 0.149740814 0 0.070408541 0 0 0.016855652 0 17560063.79 -7.244526089 -0.802724737 KFIEDR ddPTM_BT-474_Pertuzumab_2h_R1 6 KFIEDR 6 1 P40227;P40227-2;Q92526-3;Q92526;Q92526-2;J3KRI6 P40227 CCT6A;CCT6B T-complex protein 1 subunit zeta;T-complex protein 1 subunit zeta-2 0 ;;;;; 108.24 0.049038 7326400000 13296080 14417300 12241910 13994420 14789100 16085000 16403900 17152200 18229600 19682000 FALSE TRUE 12776454.49 14006132.72 14454295.46 14716673.69 15264804.83 16410249.72 16604655.84 16798001.08 16160252.23 18348920.61 0.696305508 0.763321888 0.787746362 0.802045745 0.831918409 0.894344145 0.904939107 0.915476252 0.880719503 1 24.12919186 7.247674261 0.160065629 1.019567477 4.15E-10 0.94521581 0.019624656 10.26959928 0.13130994 0.061150731 2.361914674 17687818 -7.247674261 -1.019567477 ERPQDVDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPQDVDQR 9 1 P31749;G3V4I6 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 0 61.56 0.080597 733440000 426990 445110 359210 443190 434500 470170 451960 425050 453120 486940 FALSE TRUE 410302.7587 432415.8986 424127.2376 466063.089 448476.0871 479677.1595 457491.2217 416272.569 401683.7172 453959.1201 0.903831954 0.952543697 0.93428509 1.026663125 0.987921747 1.056652765 1.00778066 0.9169825 0.884845572 1 18.79220286 7.251446874 3.950277532 0.96780829 0.024870718 0 0.054140316 27611514.36 22950076.75 0.013373633 22664798.21 17842137.17 -7.251446874 -0.942937571 LSEAVWQPEEHYSS(ph)SPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSEAVWQPEEHYSSSPEK 18 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 LSEAVWQPEEHYS(0.002)S(0.499)S(0.499)PEK 243.24 2.86E-24 497360000 448740 546250 443050 558050 537440 586520 582890 567770 701880 724330 TRUE FALSE 431202.7447 530671.4848 523118.9906 586851.0274 554727.2457 598379.8363 590023.5822 556045.3511 622205.5249 675270.4839 0.638562998 0.785865068 0.77468067 0.869060682 0.821488957 0.886133558 0.873758881 0.823440924 0.921416736 1 19.36510597 7.252315687 0.196518531 0.957793993 4.12E-36 0.781771093 0.043000364 20.56132784 0.316645598 0.085500041 5.687114284 17877866.39 -7.252315687 -0.957793993 S(ph)RTS(ph)PITR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.876)RT(0.126)S(0.996)PIT(0.002)R 77.74 0.018453 747610000 91095 95876 82102 95499 124240 128550 87931 89183 125740 107660 TRUE FALSE 87534.90669 93141.71035 96939.65775 100427.7148 128236.2924 131149.3691 89007.12588 87341.33988 111466.5223 100368.0923 0.872138791 0.928001202 0.96584139 1.000594039 1.277659956 1.306683888 0.886806991 0.870210222 1.110577274 1 16.61494117 7.258670099 8.723163067 1.016843626 0.045517679 0 0.152056195 0 0 0.036904233 0 18141370.73 -7.258670099 -0.971325946 ARDS(ph)DEENDPDDEDAVVNAVGCLGPFSGFLAPELQK ddPTM_BT-474_Pertuzumab_2h_R1 2 ARDSDEENDPDDEDAVVNAVGCLGPFSGFLAPELQK 36 1 Q9Y2I9;F8VZ81;Q9Y2I9-2;Q9Y2I9-3 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 ARDS(1)DEENDPDDEDAVVNAVGCLGPFSGFLAPELQK;ARDS(1)DEENDPDDEDAVVNAVGCLGPFSGFLAPELQK 175.75 6.83E-19 42823000 39353 43151 38358.9 39531 42216 42965 45640 49935 49741 49287 TRUE FALSE 37815.04125 41920.37573 45291.20652 41571.19965 43573.91598 43833.78174 46198.55597 48903.8248 44094.61021 45948.74759 0.822983068 0.912329017 0.985689685 0.904729766 0.94831564 0.953971197 1.005436674 1.064312465 0.959647706 1 15.48773792 7.262514776 0.308142944 1.019101183 4.84E-11 0.621912274 0.038546269 23.34699498 0.507082382 0.041132031 12.1628787 18302683.75 -7.262514776 -1.019101183 KDELSDWSLAGEDDRDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDELSDWSLAGEDDRDSR 18 2 B4DXZ6;P51114;P51114-3;H7C4S4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 180.41 4.43E-14 4471020000 2523230 2436080 2394820 2641010 2772920 2735280 2951280 3208910 3439350 3573550 FALSE TRUE 2424619.382 2366605.384 2827617.246 2777312.843 2862113.49 2790589.236 2987398.647 3142644.887 3048929.407 3331510.276 0.727783852 0.710370129 0.84874937 0.83364979 0.859103906 0.837634888 0.896710021 0.943309378 0.91517935 1 21.66774491 7.266095863 0.163456877 1.024430353 6.74E-20 0.882863113 0.029051039 14.86964933 0.192782844 0.085406483 3.525816438 18454227.18 -7.266095863 -1.024430353 ELQELQDSLNAER ddPTM_BT-474_Pertuzumab_2h_R1 4 ELQELQDSLNAER 13 0 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 171.62 5.77E-05 483488000 560831 568957 502102 554887 578291 631744 552565 616128 693976 687507 FALSE TRUE 538913.1045 552730.9034 592843.0006 583524.7846 596892.2552 644518.2965 559327.4558 603404.7415 615198.7539 640941.5385 0.840814758 0.862373353 0.924956435 0.910418111 0.931274101 1.005580475 0.872665325 0.941434913 0.959835986 1 19.28983325 7.268107638 0.37608396 0.955125522 7.85E-18 0.544779804 0.035447121 31.13737582 0.72635525 0.026963105 19.79133482 18539910.69 -7.268107638 -0.955125522 PIGPDDAIDALSSDFTCGS(ph)PTAAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 PIGPDDAIDALSSDFTCGSPTAAGK 25 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0YA91;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;A0A0C4DGB5;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 PIGPDDAIDALSSDFT(0.001)CGS(0.965)PT(0.034)AAGK 234.48 1.41E-38 68091000 73538 53548 79356 69057 74609 74337 77704 84851 97991 94506 TRUE FALSE 70664.05366 52020.86347 93697.39446 72621.04005 77008.86624 75840.14507 78654.9648 83098.7972 86867.47249 88105.02444 0.802043403 0.590441508 1.063473906 0.824255376 0.8740576 0.860792509 0.892740968 0.943178868 0.985953673 1 16.42693667 7.268150003 0.20413298 1.000976036 2.03E-10 0.326855539 0.102717204 43.80421875 0.694221555 0.177475124 13.28666741 18541719.33 -7.268150003 -1.000976036 RES(ph)PSPAPK ddPTM_BT-474_Pertuzumab_2h_R1 6 RESPSPAPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(1)PSPAPK;RES(0.999)PS(0.001)PAPK;RES(0.984)PS(0.016)PAPK;RES(1)PSPAPK;RES(0.999)PS(0.001)PAPK;RES(0.995)PS(0.005)PAPK 136.93 0.00010955 5416150000 5765540 5262150 5677260 6529780 6131020 5370320 7053540 7421110 8026310 8191060 TRUE FALSE 5540216.323 5112078.634 6703267.172 6866782.728 6328229.826 5478911.55 7139863.332 7267861.485 7115196.938 7636272.21 0.725513205 0.669446884 0.877819306 0.899232314 0.828706685 0.717485103 0.934993297 0.951755161 0.931763135 1 22.8644371 7.268408939 0.147982497 1.045668347 1.58E-13 0.573464616 0.070321301 42.3340813 0.500964584 0.285157894 9.127124177 18552777.64 -7.268408939 -1.045668347 WIQDEIEFGYIEAPHK ddPTM_BT-474_Pertuzumab_2h_R1 2 WIQDEIEFGYIEAPHK 16 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 221.49 1.05E-14 258730000 370590 369770 327630 388490 407620 389130 455200 435980 474660 495410 FALSE TRUE 356106.9331 359224.5216 386840.0291 408540.0155 420731.4675 396998.4752 460770.8738 426976.8606 420778.5867 461855.4394 0.771035486 0.777785625 0.83757816 0.884562529 0.910959213 0.859573021 0.99765172 0.924481611 0.911061234 1 18.81708183 7.275457328 0.225615527 0.988668314 2.56E-12 0.796962596 0.03376311 14.7737437 0.254806104 0.04981485 5.017197155 18856336.87 -7.275457328 -0.988668314 DVQIPFVVELEVLDGHDPEPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVQIPFVVELEVLDGHDPEPGR 22 0 Q8N9L9 Q8N9L9 ACOT4 Acyl-coenzyme A thioesterase 4 0 ;;; 194.68 2.78E-18 304485000 92265.5 105552.1 81538.5 115921 102735.8 117800.6 116997 106033.4 132263 147201 FALSE TRUE 88659.66226 102541.8575 96274.32076 121903.6967 106040.3903 120182.6088 118428.8443 103843.7732 117249.0587 137230.9452 0.646061733 0.747221098 0.701549644 0.888310552 0.772714858 0.875769009 0.862989351 0.75670814 0.85439227 1 17.06624632 7.279355239 0.062772646 1.217359623 1.22E-19 0.636726176 0.059709651 198.0472967 1.056477937 4.407217154 22.4574871 19026339.35 -7.279355239 -1.217359623 AADHLKPFLDDSTLR ddPTM_BT-474_Pertuzumab_2h_R1 3 AADHLKPFLDDSTLR 15 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 ;; 132.47 2.84E-05 470380000 643317 544267 443835 438600 497551 417773 438575 546447 494793 467314 FALSE TRUE 618175.4604 528745.0381 524045.8576 461236.1986 513555.1798 426220.6563 443942.412 535162.6785 438626.173 435662.4065 1.4189323 1.213657709 1.20287142 1.058700938 1.178791587 0.978327829 1.019005554 1.228388473 1.006802897 1 18.7328511 7.285218177 0.611868506 1.0745817 9.980658368 0.661765117 0.078099441 44.63211147 0.84652269 0.033183032 503.1887304 19284934.9 -7.285218177 8.906076668 SRSS(ph)PSTDHYK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSSPSTDHYK 11 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.06)RS(0.178)S(0.535)PS(0.034)T(0.194)DHYK;S(0.256)RS(0.256)S(0.489)PSTDHYK;S(0.291)RS(0.291)S(0.322)PS(0.092)T(0.005)DHYK 148.52 2.10E-05 932960000 802680 872870 760900 912040 854170 930080 1032030 1017230 1165180 1241230 TRUE FALSE 771310.3782 847976.6022 898411.5561 959110.4937 881645.1538 948886.8548 1044660.292 996223.845 1032913.651 1157160.387 0.666554427 0.732808185 0.776393287 0.828848364 0.761904023 0.820013255 0.902779169 0.860921145 0.892627905 1 20.14215741 7.288954258 0.107133921 1.091809721 1.42E-17 0.898859968 0.028889762 28.55246617 0.250578072 0.311945663 4.547282775 19451551.98 -7.288954258 -1.091809721 VREMEEEAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VREMEEEAEK 10 1 Q92843-2;Q86U42-2;Q86U42 Q92843-2 PABPN1 Polyadenylate-binding protein 2 0 138.42 5.94E-05 263690000 471670 404570 389980 325430 390840 387740 399960 423440 472730 450880 FALSE TRUE 453236.6149 393032.0597 460458.0611 342225.4813 403411.7236 395580.3685 404854.8301 414695.816 419067.6722 420341.496 1.078258081 0.935030359 1.095438032 0.814160592 0.959723766 0.941092831 0.963156943 0.986568826 0.99696955 1 18.68120236 7.29591045 1.292744918 0.961873892 104.5712867 0.190250726 0.066952081 2356.142886 5.507395999 0.017253941 722990.8611 19765620.36 -7.29591045 103.6094128 KSDTPQS(ph)PSLNSSQPTNSADSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSDTPQSPSLNSSQPTNSADSK 22 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 KSDT(0.042)PQS(0.955)PS(0.003)LNSSQPTNSADSK;KS(0.026)DT(0.134)PQS(0.839)PS(0.001)LNSSQPTNSADSK 185.35 2.19E-17 552460000 266390 271080 249490 247050 265040 288110 260160 310670 309890 300580 TRUE FALSE 255979.1843 263349.0638 294578.3929 259800.2801 273565.2523 293935.7816 263343.9159 304254.5559 274712.5864 280221.4489 0.913488904 0.939789102 1.051234279 0.927124891 0.976246656 1.048941053 0.939770731 1.085764695 0.980341039 1 18.09620786 7.300646123 0.422914716 1.015370596 5.36E-13 0.236355412 0.049037315 56.79261332 1.301536366 0.031235879 45.08327978 19982329.8 -7.300646123 -1.015370596 AGGSAALS(ph)PSKK ddPTM_BT-474_Pertuzumab_2h_R1 6 AGGSAALSPSKK 12 1 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.979)PS(0.021)KK;AGGSAALS(0.976)PS(0.024)KK;AGGSAALS(1)PSKK;AGGSAALS(0.999)PS(0.001)KK;AGGSAALS(0.997)PS(0.003)KK;AGGSAALS(0.997)PS(0.003)KK 178.14 1.37E-05 10620640000 13892900 9844300 10808400 6480230 10467400 8303310 9418100 12089000 11158900 9783900 TRUE FALSE 13349950.11 9563550.203 12761718.31 6814675.447 10804093.43 8471208.617 9533361.525 11839357.93 9892188.454 9121227.738 1.463613287 1.048493742 1.399122868 0.747122607 1.184499909 0.928735567 1.045184025 1.298000474 1.084523788 1 23.1207966 7.30416305 1.186376309 1.085903257 199.8558621 0.293483756 0.17507021 1116.853489 3.809050572 0.047318725 601497.6054 20144804.17 -7.30416305 198.7699589 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSK ddPTM_BT-474_Pertuzumab_2h_R1 4 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.5)PMAQT(0.5)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.598)PMAQT(0.401)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.938)PMAQT(0.062)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.643)PMAQT(0.357)PPCHLPNIPGVTSPGTLIEDSK 222.63 4.61E-35 1171410000 732940 654304 736058 803584 722470 690077 940710 916720 948520 997760 TRUE FALSE 704295.8945 635643.8906 869080.0541 845057.0665 745708.9037 704030.8297 952222.6904 897789.4116 840847.9861 930180.8265 0.757160193 0.683355185 0.934313017 0.908486869 0.801681654 0.756875233 1.023696321 0.965177293 0.903961856 1 19.82715168 7.312707698 0.179332761 1.021859206 9.68E-10 0.444443674 0.082079065 41.36895044 0.575235548 0.201334833 10.96656735 20545073.46 -7.312707698 -1.021859205 YGIICMEDLIHEIYTVGK ddPTM_BT-474_Pertuzumab_2h_R1 3 YGIICMEDLIHEIYTVGK 18 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;; 217.84 8.20E-19 3333610000 2809290 2822100 2630590 2941080 3022320 3164190 3150610 3238880 3616670 3766410 FALSE TRUE 2699499.841 2741616.471 3105996.13 3092869.491 3119535.668 3228172.09 3189168.108 3171995.996 3206120.784 3511307.696 0.768801847 0.780796418 0.884569625 0.880831234 0.888425606 0.919364627 0.90825652 0.903366002 0.913084543 1 21.74357699 7.315644391 0.269826487 0.950864022 3.36E-31 0.836370309 0.025730858 14.01603751 0.27302241 0.030444796 5.771168055 20684469.69 -7.315644391 -0.950864022 LEITSENGEKS(ph)DDGTQDLLHFPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEITSENGEKSDDGTQDLLHFPTK 24 1 E9PRS0;E9PLV1;Q9NQV6-2;Q9NQV6-1;Q9NQV6-5;Q9NQV6;Q9NQV6-4;Q9NQV6-7;Q9NQV6-6 E9PRS0 PRDM10 PR domain zinc finger protein 10 1 LEIT(0.194)S(0.173)ENGEKS(0.633)DDGTQDLLHFPTK 96.748 0.0037927 89137000 133740 99431 85592 91175 92452 84956 88023 111620 93164 89848 TRUE FALSE 128513.2929 96595.32523 101060.3784 95880.55268 95425.80254 86673.86853 89100.2518 109315.008 82588.4133 83762.51493 1.534257813 1.153204692 1.206510794 1.144671369 1.139242328 1.034757237 1.063724649 1.305058809 0.985982971 1 16.35401714 7.318753564 1.157027625 1.120380872 199.9899322 0.648512453 0.092744196 480.6231187 1.764287697 0.026281551 252338.7321 20833083.93 -7.318753564 198.8695513 DLDEDELLGNLSETELK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLDEDELLGNLSETELK 17 0 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 0 165.64 5.69E-09 17802000 56610 63010 51161 62827 64474 66227 64691 73349 81197 79283 FALSE TRUE 54397.61861 61213.01649 60406.93077 66069.509 66547.86476 67566.15532 65482.70781 71834.31752 71979.85697 73913.09179 0.7359673 0.828175564 0.817269706 0.893881008 0.900352876 0.914129739 0.885941938 0.971875425 0.973844487 1 16.1735423 7.324139595 0.205216327 1.010424456 1.38E-11 0.912375738 0.022803934 10.40382455 0.162429361 0.040406397 3.221498872 21093060.35 -7.324139595 -1.010424456 KPNAGGS(ph)PAPVR ddPTM_BT-474_Pertuzumab_2h_R1 4 KPNAGGSPAPVR 12 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 KPNAGGS(1)PAPVR;KPNAGGS(1)PAPVR;KPNAGGS(1)PAPVR;KPNAGGS(1)PAPVR 107.34 0.0011176 1164870000 1384780 1284320 1346870 1507850 1420130 1500840 1514370 1823150 1731410 1891430 TRUE FALSE 1330661.267 1247692.451 1590279.37 1585670.319 1465809.771 1531188.013 1532903.313 1785501.315 1534867.595 1763321.761 0.75463327 0.707580703 0.901865675 0.899251829 0.831277537 0.868354288 0.869327055 1.01257828 0.870441022 1 20.74986432 7.331666549 0.198152246 0.99692152 1.54E-10 0.592620108 0.05718372 27.46078939 0.414717684 0.110625812 8.037632189 21461820.04 -7.331666549 -0.99692152 SVSDYDGK ddPTM_BT-474_Pertuzumab_2h_R1 3 SVSDYDGK 8 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ;; 141.52 0.0014708 1708410000 2508560 2525730 2325730 2776560 2546430 2557740 2882180 3105380 3519560 3619660 FALSE TRUE 2410522.702 2453698.653 2746041.147 2919858.594 2628338.234 2609459.255 2917452.981 3041252.818 3120034.304 3374497.204 0.714335368 0.727130149 0.813763053 0.865272192 0.778882919 0.773288314 0.864559312 0.901246211 0.924592351 1 21.68624113 7.33909562 0.071685193 1.220480016 1.99E-13 0.812530472 0.03750139 94.0698217 0.56269385 1.813004364 11.74963099 21832105.43 -7.33909562 -1.220480016 ENS(ph)FGSPLEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ENS(0.939)FGS(0.061)PLEFR 87.566 0.014296 86274000 89503 85686 67595 98450 98445 73817 89097 102920 115080 107550 TRUE FALSE 86005.12381 83242.31918 79810.92014 103531.0163 101611.5728 75309.63032 90187.39574 100794.666 102016.6009 100265.5427 0.857773483 0.830218607 0.795995493 1.032568253 1.013424653 0.751101807 0.899485439 1.00527722 1.017464207 1 16.61346637 7.34775481 0.147816862 1.039659269 0.370322548 0.254494269 0.086699207 84.48243606 0.977569056 0.348610877 11.68932019 22271773.93 -7.34775481 -0.669336721 LTPPES(ph)QSPLHWLADLAEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LTPPESQSPLHWLADLAEQK 20 0 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 LT(0.012)PPES(0.542)QS(0.446)PLHWLADLAEQK;LT(0.004)PPES(0.498)QS(0.498)PLHWLADLAEQK;LT(0.075)PPES(0.463)QS(0.463)PLHWLADLAEQK 133.95 6.34E-06 117773000 145179 139416 149358 165183 145150 155890 175939 188822 207561 209288 TRUE FALSE 139505.2442 135439.9922 176350.3131 173708.1144 149818.8816 159042.2026 178092.1941 184922.7597 183999.5454 195112.7373 0.714998139 0.694162739 0.903838035 0.890296127 0.767858027 0.81512978 0.912765597 0.947773898 0.943042202 1 17.57394844 7.351254737 0.151323829 1.04091573 3.25E-11 0.66553861 0.057497638 35.63466278 0.420689709 0.220591465 7.880383887 22451984.66 -7.351254737 -1.04091573 LGADESEEEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGADESEEEGR 11 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 0 ; 196.52 1.40E-07 497840000 255890 267060 217610 278250 278110 303750 272300 339460 294690 354070 FALSE TRUE 245889.5359 259443.7103 256936.9677 292610.5158 287055.6607 309892.0331 275632.4889 332450.0324 261238.0266 330088.5235 0.744919979 0.785982219 0.778388067 0.886460737 0.869632357 0.938814927 0.835025968 1.007154168 0.791418083 1 18.33249345 7.35186266 0.217532836 0.969566559 2.59E-12 0.506871484 0.062346879 28.17435421 0.457720998 0.093123965 9.025879738 22483434.84 -7.35186266 -0.969566559 LS(ph)FSDTYQDYEEYWR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSFSDTYQDYEEYWR 15 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 1 LS(1)FSDTYQDYEEYWR;LS(0.926)FS(0.074)DTYQDYEEYWR;LS(1)FSDTYQDYEEYWR 284.86 5.31E-34 140939000 154933 151529 181043 195472 195108 180428 200706 196087 229957 264666 TRUE FALSE 148878.0471 147207.5413 213761.4974 205560.3333 201383.826 184076.3778 203162.3001 192037.7349 203853.2454 246739.9361 0.603380423 0.596610114 0.866343328 0.833105239 0.81617848 0.746033985 0.823386369 0.778300173 0.826186667 1 17.91263172 7.353596026 0.091166538 1.081102554 1.22E-32 0.58099138 0.07357177 114.5460746 0.854810736 1.484131059 15.49637858 22573350.53 -7.353596026 -1.081102554 ALQDEWDAVMLHSFTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALQDEWDAVMLHSFTLR 17 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;;; 213.99 1.69E-13 2749344000 832442 912979 710409 852355 870704 858099 899036 837058 930190 925515 FALSE TRUE 799909.2463 886941.7328 838795.7093 896345.1437 898710.9849 875450.3497 910038.6715 819772.4598 824598.7309 862829.0447 0.927077329 1.027946078 0.97214589 1.038844426 1.041586384 1.014627817 1.054714925 0.950098359 0.955691902 1 19.71871522 7.356724765 0.001740816 0.583156606 1.424811135 0 0.042226798 7803035.627 1149.583452 271416.9944 284528.1581 22736560.39 -7.356724765 0.841654529 VQDTS(ph)NTGLGEDIIHQLSK ddPTM_BT-474_Pertuzumab_2h_R1 5 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.385)S(0.611)NT(0.003)GLGEDIIHQLSK;VQDT(0.167)S(0.665)NT(0.167)GLGEDIIHQLSK;VQDT(0.1)S(0.898)NT(0.002)GLGEDIIHQLSK;VQDT(0.328)S(0.634)NT(0.038)GLGEDIIHQLSK;VQDT(0.026)S(0.706)NT(0.268)GLGEDIIHQLSK 313.66 8.49E-62 2839390000 1594200 1504120 1563440 1634140 1716360 1928100 1835400 1900650 2200000 2306570 TRUE FALSE 1531896.902 1461223.97 1845988.387 1718478.161 1771568.278 1967087.503 1857862.174 1861400.913 1950265.223 2150343.959 0.712396217 0.679530344 0.858461912 0.799164317 0.823853445 0.914778073 0.86398372 0.865629382 0.906955008 1 21.03613601 7.373133425 0.159734447 1.001647973 5.93E-15 0.79724796 0.040562175 23.05221407 0.283870993 0.125268818 5.233688625 23612035.38 -7.373133425 -1.001647973 YSSQDADEQDWEFQKR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSSQDADEQDWEFQKR 16 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 205.18 3.73E-11 973430000 1108000 836020 782910 661960 922140 823610 815060 580880 1258420 843060 FALSE TRUE 1064698.135 812177.5281 924399.2527 696123.8349 951801.4706 840263.9585 825034.9481 568884.625 1115569.437 785958.7953 1.354648795 1.033358915 1.176142131 0.885700165 1.211006832 1.069094161 1.049717814 0.723809732 1.419373947 1 19.58409415 7.380661894 1.175782431 1.033367051 199.9999997 0.172284755 0.179608656 1570.774374 4.549231033 0.049561922 840068.2115 24024916.92 -7.380661894 198.9666327 VTAEADSSS(ph)PTGILATSESK ddPTM_BT-474_Pertuzumab_2h_R1 4 VTAEADSSSPTGILATSESK 20 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 VTAEADSSS(0.999)PT(0.001)GILATSESK;VTAEADSS(0.007)S(0.993)PTGILATSESK;VTAEADSS(0.005)S(0.994)PT(0.001)GILATSESK;VTAEADS(0.001)S(0.009)S(0.988)PT(0.002)GILATSESK 343.59 9.17E-81 1026560000 1889330 1926020 1826230 1947610 2044210 2208550 2176940 2412630 2647040 2664080 TRUE FALSE 1815492.895 1871091.795 2156270.385 2048126.386 2109963.871 2253208.394 2203582.043 2362808.347 2346559.116 2483639.489 0.730980846 0.753366905 0.868189766 0.824647214 0.849545146 0.907220393 0.887239091 0.951349162 0.944806655 1 21.24402434 7.381916632 0.170282514 1.024798896 5.11E-20 0.910900737 0.024281855 12.4231307 0.16150179 0.062515166 3.116743525 24094428.61 -7.381916632 -1.024798896 EFTGS(ph)PPSSATK ddPTM_BT-474_Pertuzumab_2h_R1 6 EFTGSPPSSATK 12 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFTGS(0.975)PPS(0.022)S(0.003)ATK;EFTGS(0.989)PPS(0.01)S(0.002)ATK;EFTGS(0.788)PPS(0.087)S(0.124)AT(0.001)K;EFTGS(1)PPSSATK;EFTGS(0.924)PPS(0.075)S(0.001)ATK;EFTGS(0.999)PPS(0.001)SATK 243.3 2.57E-16 4272310000 6614730 6511580 6360250 7327190 7201030 6888490 7912240 8708600 8852580 9520000 TRUE FALSE 6356219.039 6325876.114 7509688.658 7705347.154 7432657.67 7027779.987 8009072.36 8528764.367 7847672.231 8875201.92 0.7161774 0.712758557 0.846142851 0.868188377 0.837463501 0.791844518 0.902410157 0.960965671 0.884224641 1 23.08134851 7.382557502 0.155222009 1.025949976 1.45E-16 0.765038115 0.043170646 26.54084535 0.317764062 0.153185116 5.969746424 24130009.98 -7.382557502 -1.025949976 FNGEDIDTIS(ph)PTLGFNIK ddPTM_BT-474_Pertuzumab_2h_R1 1 FNGEDIDTISPTLGFNIK 18 0 V9GYD0;P36404-2;P36404 V9GYD0 ARL2-SNX15;ARL2 ADP-ribosylation factor-like protein 2 1 FNGEDIDT(0.096)IS(0.883)PT(0.021)LGFNIK 156.39 1.25E-08 53865000 109840 116450 101190 123560 122570 124160 129060 145410 153950 162570 TRUE FALSE 105547.3314 113128.96 119477.284 129936.9464 126512.5754 126670.6003 130639.4749 142407.2327 136474.2414 151558.9891 0.696410896 0.746435171 0.78832199 0.857335795 0.834741483 0.835784146 0.861971142 0.939615879 0.900469462 1 17.2095199 7.387254869 0.143699055 1.036335959 3.64E-17 0.923560587 0.023407355 15.62081935 0.174404074 0.101688308 3.245518102 24392418.89 -7.387254869 -1.036335959 ILLVDS(ph)PGMGNADDEQQEEGTSSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ILLVDSPGMGNADDEQQEEGTSSK 24 0 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 1 ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK 367.68 7.82E-119 548008000 352482 368579 309586 368653 378212 396666 380783 421515 455441 447796 TRUE FALSE 338706.6138 358067.4878 365535.0769 387679.2255 390377.5325 404686.8583 385443.1363 412810.5679 403741.247 417466.3781 0.811338665 0.857715751 0.875603632 0.928647781 0.935111312 0.969387907 0.923291447 0.988847461 0.967122787 1 18.67130048 7.387756133 0.269460274 0.99561199 5.85E-09 0.921075124 0.016247135 8.524050066 0.160340232 0.018029435 3.697789174 24420588.9 -7.387756133 -0.995611984 IHQPYTLTFAELVEDYEHYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IHQPYTLTFAELVEDYEHYIK 21 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 0 119.87 2.81E-05 85092000 79436 60796 48454 53593 63610 54821 74137 41485 70146 48191 FALSE TRUE 76331.5533 59062.15761 57210.71565 56358.94115 65656.07342 55929.51818 75044.31078 40628.32025 62183.32016 44926.98065 1.699013648 1.314625571 1.273415547 1.254456461 1.46139519 1.244898219 1.670361767 0.904318956 1.384097468 1 15.45529449 7.395074017 0.036258955 2.74E-11 3.262539865 0.276469851 0.204468962 1120.467311 3.434978099 94.17171412 248.4436747 24835563.45 -7.395074017 3.262539865 GS(ph)SPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSSPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 38 1 Q27J81-2;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 GS(0.491)S(0.491)PQNT(0.011)T(0.004)T(0.004)PKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.538)S(0.462)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.361)S(0.361)PQNT(0.088)T(0.088)T(0.088)PKPS(0.015)VEGQQPAAAAACEPVDHAQSESILK 276.65 1.11E-76 7549380000 129835 142032 109551 143056 134104 162397 149766 144243 187807 172441 TRUE FALSE 124760.9047 137981.3864 129349.3026 150439.1373 138417.577 165680.7786 151598.8811 141264.3316 166487.9367 160761.4175 0.776062482 0.85829914 0.804604144 0.935791309 0.861012419 1.030600384 0.943005377 0.878720366 1.035621229 1 17.29456168 7.397381245 0.236387403 0.996482412 7.48E-08 0.605003676 0.054509154 27.47530696 0.468846136 0.076831555 10.09293883 24967855.65 -7.397381245 -0.996482337 IIIDKEYYYTK ddPTM_BT-474_Pertuzumab_2h_R1 1 IIIDKEYYYTK 11 1 Q7L5N1;E7EM64 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 156.8 2.82E-05 420200000 676080 837110 574850 710410 826480 816130 841360 906150 965570 1051100 FALSE TRUE 649658.0462 813236.4424 678738.1825 747074.3452 853064.4798 832632.7078 851656.8154 887437.6858 855962.5416 979908.0608 0.662978571 0.829910963 0.692654964 0.762392285 0.870555631 0.849704928 0.869119104 0.905633622 0.873513114 1 19.90228687 7.400115365 0.11454681 1.078448433 1.41E-09 0.772525315 0.045592541 39.42678039 0.358398103 0.368408595 6.650445485 25125537.75 -7.400115365 -1.078448432 ADLINNLGTIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADLINNLGTIAK 12 0 P08238;P07900;P07900-2;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ; 148.18 0.00015404 708740000 2126790 1229860 1296520 937340 1204810 1066050 1142070 1141040 1378060 1146600 FALSE TRUE 2043672.696 1194785.597 1530830.005 985716.2297 1243563.808 1087606.261 1156046.994 1117477.125 1221628.406 1068939.761 1.91186891 1.117729587 1.432101285 0.922143853 1.163361916 1.017462631 1.081489376 1.045407016 1.142841207 1 20.02774912 7.401899461 0.99354079 1.071400018 199.9999971 0.776206061 0.130221267 171.5248116 0.919982515 0.034920685 76785.32794 25228966.57 -7.401899461 198.9285971 GKEDEGEEAASPMLQIQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKEDEGEEAASPMLQIQR 18 1 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 206.21 8.00E-16 1265380000 869280 935220 909790 875470 991580 1077950 1036600 1134390 1298670 1322170 FALSE TRUE 835307.5766 908548.4413 1074209.291 920653.1116 1023475.071 1099746.888 1049286.221 1110964.45 1151250.426 1232618.248 0.677669325 0.737088261 0.871485793 0.746908553 0.830326074 0.892203964 0.851266175 0.901304562 0.933987816 1 20.23329462 7.403931109 0.134455885 1.047929956 1.90E-11 0.816950347 0.040034482 27.33179564 0.286404426 0.196522016 5.328863442 25347265.24 -7.403931109 -1.047929956 EYDLIVHQLATYPDVNNSIK ddPTM_BT-474_Pertuzumab_2h_R1 2 EYDLIVHQLATYPDVNNSIK 20 0 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 219.34 9.28E-25 386640000 710730 701650 651580 775880 766540 798570 820920 881030 997120 1046770 FALSE TRUE 682953.8858 681639.629 769335.0003 815923.2598 791196.4553 814717.6325 830966.6645 862836.4226 883931.1179 975871.3355 0.699840093 0.69849334 0.788357002 0.836097168 0.810758987 0.834861731 0.851512525 0.88417027 0.905786537 1 19.89633142 7.407539409 0.115526693 1.070942917 6.11E-18 0.942525195 0.020683216 19.81144589 0.181159428 0.180984977 3.348679912 25558738.14 -7.407539409 -1.070942917 DTTINEIEDTFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTTINEIEDTFR 12 0 Q16864;Q16864-2 Q16864 ATP6V1F V-type proton ATPase subunit F 0 ; 316.19 4.23E-46 320410000 197085 199626 174124 197320 197228 204438 214910 238820 230080 247980 FALSE TRUE 189382.7003 193932.8619 205592.0802 207503.7088 203572.0177 208571.8764 217540.1329 233888.2835 203962.283 231184.0937 0.819185686 0.83886767 0.889300284 0.897569143 0.880562388 0.902189563 0.940982268 1.011697128 0.882250503 1 17.81868261 7.423977502 0.163513013 1.016397983 0.331737118 0.665795404 0.034127759 29.17077134 0.361408882 0.101433512 4.669031611 26544680.49 -7.423977502 -0.684660865 ETGYVVERPSTTK ddPTM_BT-474_Pertuzumab_2h_R1 3 ETGYVVERPSTTK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;; 150.22 3.75E-05 1040030000 1056120 1020650 923510 1146900 1145480 1130810 1169360 1239350 1393700 1402670 FALSE TRUE 1014845.663 991542.0613 1090408.8 1206091.646 1182325.404 1153675.753 1183670.977 1213756.989 1235493.019 1307665.912 0.776074113 0.758253352 0.833858856 0.922323994 0.904149442 0.882240443 0.905178431 0.928185845 0.94480785 1 20.31856257 7.426619672 0.217409775 0.983684195 1.87E-15 0.855201681 0.027276935 14.94536827 0.235999917 0.047157566 4.886826593 26706665.84 -7.426619672 -0.983684195 TFEDFVR ddPTM_BT-474_Pertuzumab_2h_R1 5 TFEDFVR 7 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;;; 129.4 0.008525 1688880000 2484190 2731140 2631930 3046730 2946840 2749410 3400610 3237980 3739510 4030860 FALSE TRUE 2387105.108 2653250.561 3107578.298 3203972.1 3041627.785 2805004.954 3442227.682 3171114.581 3315016.502 3757846.262 0.635232243 0.706056176 0.826957273 0.852608616 0.80940719 0.746439518 0.916010779 0.843864906 0.882158628 1 21.84147461 7.434112376 0.130387126 1.026195809 9.85E-19 0.728788404 0.052018992 40.85979158 0.413510639 0.296225827 7.546887633 27171422.55 -7.434112376 -1.026195809 DEASS(ph)VTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DEASSVTR 8 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 DEAS(0.004)S(0.996)VTR 150.66 0.00050931 106570000 213990 224310 223840 265060 234660 217890 269230 284170 311110 315150 TRUE FALSE 205627.0342 217912.8984 264292.8673 278739.7784 242208.052 222295.8851 272524.9173 278301.7902 275794.0971 293804.6098 0.699876814 0.741693259 0.899553167 0.948725 0.824384792 0.756611291 0.927571958 0.947234253 0.938699012 1 18.16449751 7.448175164 0.188392038 0.995416429 2.26E-20 0.562863408 0.065547908 37.82076252 0.525925426 0.151348145 10.4781277 28065653.84 -7.448175164 -0.995416429 EADDIVNWLK ddPTM_BT-474_Pertuzumab_2h_R1 4 EADDIVNWLK 10 0 P07237;I3L312;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ;;; 191.17 1.91E-06 1804570000 2626870 3000990 2364260 2768610 2721470 2894930 2995750 3128460 3346880 3230480 FALSE TRUE 2524209.016 2915404.703 2791534.375 2911498.294 2809008.554 2953467.468 3032412.885 3063856.208 2966956.214 3011676.712 0.838140763 0.968033751 0.926903729 0.966736663 0.932705872 0.980672147 1.006885258 1.017325729 0.985150963 1 21.52213548 7.448260282 0.332567244 1.007382554 2.01E-14 0.713078848 0.026725367 22.05731562 0.444190789 0.023965899 12.8513753 28071154.98 -7.448260282 -1.007382554 SS(ph)PQSTDTAMDLLK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSPQSTDTAMDLLK 14 0 Q9UGU5 Q9UGU5 HMGXB4 HMG domain-containing protein 4 1 S(0.131)S(0.869)PQSTDTAMDLLK;S(0.229)S(0.771)PQSTDTAMDLLK;S(0.274)S(0.726)PQSTDTAMDLLK 183.75 1.44E-06 121643000 227609 209073 207658 239756 226497 203261 233679 263036 270104 265768 TRUE FALSE 218713.7886 203110.4427 245186.4199 252129.8359 233782.4817 207371.0767 236538.8335 257604.2147 239442.9263 247767.2966 0.882738729 0.819762921 0.989583465 1.017607405 0.943556655 0.836959032 0.954681416 1.039702246 0.966402465 1 17.91862625 7.449997615 0.337383427 0.986449558 1.90E-09 0.255284126 0.061652769 58.35630113 1.178512412 0.058978493 33.94359754 28183674.57 -7.449997615 -0.986449556 GFSEEHNTWEPEK ddPTM_BT-474_Pertuzumab_2h_R1 6 GFSEEHNTWEPEK 13 0 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 ;;;;; 213.18 7.96E-09 7707820000 8564590 9093520 7826790 11326400 9247420 8936350 11140900 10728300 12691400 13368100 FALSE TRUE 8229876.354 8834181.713 9241265.059 11910956.86 9544871.663 9117049.12 11277245.67 10506756.86 11250725.48 12462666.68 0.66036239 0.70885164 0.741515865 0.955730998 0.765877152 0.731548821 0.904882234 0.843058482 0.902754263 1 23.57110946 7.451951589 0.104989388 1.082093887 5.73E-15 0.603064241 0.069055644 76.5734895 0.636156957 0.791563189 11.86659105 28310763.96 -7.451951589 -1.082093887 GDDLEEGVTSEEFDKFLEER ddPTM_BT-474_Pertuzumab_2h_R1 3 GDDLEEGVTSEEFDKFLEER 20 1 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6;B7Z2U2 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 ;; 204.29 8.91E-22 136697000 93191 87534 83053 96406 104302 91018 103711 117431 115793 122783 FALSE TRUE 89548.99269 85037.61602 98062.5246 101381.5252 107656.9686 92858.44632 104980.2462 115006.0088 102648.6641 114466.798 0.782314123 0.742902025 0.85668968 0.885684993 0.940508256 0.811226032 0.917123987 1.00471063 0.896754918 1 16.80456967 7.459318551 0.194535685 1.007507446 7.52E-11 0.639705627 0.049778065 26.13280215 0.37204562 0.099675877 7.632696271 28795097.31 -7.459318551 -1.007507446 GRDPVNPEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GRDPVNPEK 9 1 O60568;C9JIX5 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 ; 85.533 0.013453 426490000 283960 338370 284530 312410 311190 362090 345110 366640 421260 408130 FALSE TRUE 272862.5293 328720.0189 335950.9003 328533.5175 321199.709 369411.7079 349333.5594 359068.7559 373440.3309 380486.9916 0.717140232 0.863945486 0.882949766 0.863455321 0.844180527 0.97089182 0.918122215 0.943708363 0.981479891 1 18.5374876 7.460589908 0.214892972 1.001172542 1.29E-14 0.787164335 0.036723209 18.78064453 0.290099778 0.05990015 6.177412635 28879515.8 -7.460589908 -1.001172542 YNPENLATLER ddPTM_BT-474_Pertuzumab_2h_R1 1 YNPENLATLER 11 0 Q9UBQ5;K7ERF1;Q9UBQ5-2;K7ES31 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 93.345 0.02168 64487000 33081 41144 27355 41602 39713 39561 37967 49316 42143 53678 FALSE TRUE 31788.15795 39970.6134 32298.65701 43749.08421 40990.40471 40360.95053 38431.6515 48297.60737 37359.10332 50042.34125 0.635225234 0.798735879 0.645426577 0.874241355 0.819114448 0.806536016 0.767982683 0.965134847 0.746549869 1 15.61086167 7.461629443 0.089843942 1.113988942 6.43E-15 0.488748643 0.080822134 112.5362553 0.810087545 1.463866604 15.4685142 28948725.18 -7.461629443 -1.113988942 ATFVANDLDWLLALPHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATFVANDLDWLLALPHDK 18 0 Q9H1I8;B1AH59 Q9H1I8 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 ; 157.51 3.82E-09 111686000 376940 361540 385900 420020 448020 401310 504220 425770 536230 590910 FALSE TRUE 362208.7681 351229.2332 455640.7143 441697.2825 462430.9702 409424.7632 510390.7952 416977.7007 475359.4185 550887.1394 0.65750086 0.637570217 0.82710356 0.801792692 0.839429598 0.743209877 0.926488855 0.756920376 0.862898014 1 19.07139726 7.463229576 0.090692827 1.096909293 1.41E-18 0.62304308 0.06547864 97.45983675 0.707379858 1.232877394 13.3046826 29055581.78 -7.463229576 -1.096909293 DNPIEDELVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNPIEDELVFR 11 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 ; 174.4 2.57E-05 90766000 111460 112575 102284 119292 122438 116868 119627 137906 145793 144566 FALSE TRUE 107104.02 109364.4712 120768.9941 125448.6744 126376.3295 119231.151 121091.031 135058.1929 129243.1899 134774.4161 0.794691033 0.811463143 0.896082488 0.930804808 0.937687828 0.884671991 0.89847194 1.002105569 0.958959376 1 17.04018713 7.469436006 0.245375131 0.9920635 2.28E-14 0.771779818 0.031735893 19.09410984 0.324975047 0.04598677 7.377457403 29473791.45 -7.469436006 -0.9920635 EDKEAETAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EDKEAETAR 9 1 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8Y6Q1;A0A2R8YFL4 Q15813-2 TBCE Tubulin-specific chaperone E 0 89.171 0.01122 0 457840 395160 370640 350060 348430 411670 377270 435190 412100 418950 FALSE TRUE 439947.1066 383890.4237 437622.8928 368126.6386 359637.5674 419994.2495 381887.1431 426203.1744 365320.1357 390574.1433 1.126411244 0.98288745 1.120460482 0.942526905 0.920792053 1.075325278 0.977758384 1.091222196 0.935341322 1 18.57523692 7.47372252 1.268086679 1.008701895 154.5797729 0.219978926 0.066119965 3033.051416 4.751604828 0.017431915 1355112.921 29766140.01 -7.47372252 153.571071 ETDCGVHINAGPEIGVASTK ddPTM_BT-474_Pertuzumab_2h_R1 1 ETDCGVHINAGPEIGVASTK 20 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9;O94808 Q06210-2 GFPT1;GFPT2 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1;Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2 0 202.53 2.31E-22 0 224710 255360 205030 235180 237460 276350 270310 273270 300310 302380 FALSE TRUE 215928.0848 248077.3828 242083.4819 247317.668 245098.1166 281937.9863 273618.1346 267626.879 266220.0678 281899.5333 0.765975318 0.880020552 0.858758009 0.877325567 0.869452013 1.000136407 0.970622872 0.949369713 0.944379243 1 18.10482156 7.47613136 0.236218702 0.998494128 1.11E-10 0.781733309 0.03289804 18.26081338 0.301566247 0.04770012 6.76724225 29931698.34 -7.47613136 -0.998494128 NVSTGS(ph)AENEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 NVSTGSAENEEK 12 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 NVST(0.008)GS(0.992)AENEEK 109.22 0.0017003 343330000 259490 262670 266730 312660 331220 284730 304560 336610 383550 418030 TRUE FALSE 249348.8439 255178.9088 314934.0444 328796.4201 341873.9921 290487.4357 308287.2964 329658.8859 340011.012 389716.4558 0.639821183 0.654780944 0.808110717 0.843681131 0.877237764 0.745381498 0.791055373 0.845894191 0.872457416 1 18.57206532 7.484912341 0.103470485 1.065060374 1.12E-20 0.695851849 0.056374114 71.6164038 0.582984077 0.732559645 10.76974606 30543045.63 -7.484912341 -1.065060374 INPYMS(ph)SPCHIEMILTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 INPYMSSPCHIEMILTEK 18 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 1 INPYMS(0.948)S(0.052)PCHIEMILTEK;INPY(0.018)MS(0.491)S(0.491)PCHIEMILTEK 226.08 2.39E-19 456147000 782230 789280 678010 699490 790150 795670 756480 772640 971610 826300 TRUE FALSE 751659.5868 766770.5072 800541.4893 735590.7627 815565.8923 811758.9926 765738.0285 756684.714 861316.9061 770333.965 0.975758075 0.995374139 1.039213543 0.95489852 1.058717296 1.053775414 0.994033839 0.982281385 1.118108438 1 19.55512451 7.486906953 0.524130353 1.024759923 8.20E-06 0.122542683 0.043792008 164.2823876 2.862765969 0.021578398 178.828454 30683645.26 -7.486906953 -1.024751721 GHYEVTGS(ph)DDETGK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHYEVTGSDDETGK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVTGS(1)DDETGK;GHYEVTGS(1)DDETGK;GHYEVT(0.094)GS(0.905)DDETGK;GHYEVTGS(1)DDETGK 303.96 2.60E-44 3420360000 1741370 1607590 1989980 2106290 1734860 1718610 2116330 2080020 2596110 2585870 TRUE FALSE 1673315.335 1561743.107 2349613.653 2214995.879 1790663.347 1753361.472 2142230.28 2037066.86 2301410.477 2410726.722 0.69411241 0.647830836 0.974649524 0.918808366 0.742789853 0.727316562 0.888624273 0.845001153 0.954654236 1 21.20103669 7.487108871 0.057349198 1.275678471 3.18E-13 0.377585903 0.095272141 413.3825648 1.945075919 9.742358227 45.7188415 30697914.45 -7.487108871 -1.275678471 TQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 TQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 32 1 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 TQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR;TQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR 441.06 3.90E-231 2605270000 769962 687156 766328 826573 868076 786696 896798 887167 1159082 1098669 TRUE FALSE 739871.0338 667558.9837 904820.5165 869232.5316 895998.4529 802603.5321 907773.2822 868846.6914 1027507.871 1024255.17 0.722350304 0.651750661 0.883393653 0.84864842 0.874780503 0.783597248 0.886276495 0.848271717 1.003175674 1 19.96614374 7.497230315 0.138385823 1.036667128 6.41E-14 0.638389865 0.0627872 44.37518004 0.465749342 0.287588089 8.877157223 31421746.07 -7.497230315 -1.036667128 FKEEGVR ddPTM_BT-474_Pertuzumab_2h_R1 3 FKEEGVR 7 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 89.698 0.016126 944410000 1849250 2169340 1712460 2129770 2053740 1867440 2375520 2216940 2614400 2723630 FALSE TRUE 1776979.266 2107472.547 2021939.615 2239687.685 2119800.412 1905200.916 2404592.324 2171159.414 2317624.272 2539156.114 0.699830647 0.829989356 0.796303781 0.882059859 0.834844459 0.750328389 0.947004523 0.855071259 0.912753753 1 21.27591767 7.50754386 0.047001773 1.349621244 9.40E-09 0.613253984 0.053095426 341.5712019 1.322226786 9.855197678 35.34594379 32176874.77 -7.50754386 -1.349621235 KTVT(ph)PAK ddPTM_BT-474_Pertuzumab_2h_R1 6 KTVTPAK 7 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KTVT(1)PAK;KT(0.011)VT(0.989)PAK;KT(0.001)VT(0.999)PAK;KT(0.001)VT(0.999)PAK;KT(0.01)VT(0.99)PAK;KT(0.059)VT(0.941)PAK 107.95 0.0043142 7455180000 25893400 19782270 18333510 16758110 16813680 16411120 19606540 24720300 16824410 16137030 TRUE FALSE 24881457.3 19218099.03 21646783.08 17622998.07 17354507.29 16742964.09 19846490.7 24209817.17 14914573.51 15044054.58 1.653906343 1.277454753 1.438892884 1.171426092 1.153579123 1.112928964 1.319224853 1.609261455 0.991393206 1 23.84269011 7.512396746 1.071782671 1.254063521 196.2729677 0.322269033 0.182580412 1118.599401 3.432732556 0.055337385 533602.706 32538441.39 -7.512396746 195.0189042 NINDGLSSLFSVVEHSGS(ph)TESVWK ddPTM_BT-474_Pertuzumab_2h_R1 1 NINDGLSSLFSVVEHSGSTESVWK 24 0 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 NINDGLSSLFSVVEHS(0.001)GS(0.811)T(0.181)ES(0.006)VWK 147.41 9.53E-11 0 74976 59717 57954 56557 50558 57320 58258 61558 70832 73529 TRUE FALSE 72045.85503 58013.92963 68427.57698 59475.91355 52184.24399 58479.04967 58970.97883 60286.80579 62791.44831 68548.81534 1.051015319 0.846315569 0.998231357 0.867643201 0.761271274 0.853100807 0.86027714 0.879472614 0.9160107 1 16.06484411 7.513791651 1.223511959 0.875436311 199.9999999 0.306433238 0.069664495 2195.994497 3.626164273 0.019047827 1226881.215 32643119.24 -7.513791651 199.1245636 S(ph)PGLLSSDNPQLSALLMGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPGLLSSDNPQLSALLMGK 19 0 H0Y6I7;F5H5V6;F5H6S1;F8W8R6;A0A087X0R0;O15550 H0Y6I7 KDM6A Lysine-specific demethylase 6A 1 S(1)PGLLSSDNPQLSALLMGK;S(1)PGLLSSDNPQLSALLMGK 239.93 2.78E-24 739170000 222454 224268 228286 241654 241842 224791 257220 285480 294070 300190 TRUE FALSE 213760.2517 217872.0962 269542.3584 254125.7919 249621.0676 229336.428 260367.9353 279584.7382 260688.4064 279857.8639 0.763817206 0.778509823 0.963140198 0.908053068 0.891956596 0.819474661 0.93035776 0.999024056 0.931502881 1 18.09433476 7.519916883 0.231871895 0.986842068 7.68E-20 0.554558346 0.05405886 32.78311069 0.524677824 0.084545601 11.77433913 33106775.47 -7.519916883 -0.986842068 GS(ph)FGAMDDPFK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSFGAMDDPFK 11 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R3I1 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 GS(1)FGAMDDPFK 130.77 0.00022785 126120000 465130 437260 437000 501420 500070 458150 508340 586830 627040 608380 TRUE FALSE 446952.2054 424789.7729 515975.621 527298.3463 516155.2057 467414.1069 514561.217 574711.7554 555861.048 567173.8807 0.78803383 0.74895863 0.909730928 0.929694339 0.910047559 0.824110776 0.907237153 1.013290236 0.980054031 1 19.11343157 7.52815342 0.194561981 1.022169089 1.80E-17 0.639263217 0.050775748 29.46540277 0.409944184 0.108346971 8.780595983 33740648.09 -7.52815342 -1.022169089 EIHDGLDFYYSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIHDGLDFYYSSK 13 0 C9JA08;Q96D46;C9J0B9 C9JA08 NMD3 60S ribosomal export protein NMD3 0 92.468 0.0060592 224240000 196340 191630 191470 209130 207570 198330 231530 249440 272990 284890 FALSE TRUE 188666.8157 186164.9 226072.8882 219923.2244 214246.6776 202340.3685 234363.5334 244288.9768 242001.3197 265594.1465 0.710357582 0.700937511 0.851196802 0.828042437 0.806669425 0.761840466 0.882412269 0.919782985 0.911169628 1 18.01886383 7.546744931 0.096950121 1.122714844 7.04E-13 0.783267481 0.042256251 57.8882348 0.438581829 0.663809657 8.61251782 35216397.82 -7.546744931 -1.122714844 KQDADSLQR ddPTM_BT-474_Pertuzumab_2h_R1 6 KQDADSLQR 9 1 P14324-2;P14324;A0A087WVN4;A0A087X1D8 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;;;;; 192.12 5.63E-05 9216560000 11103010 11631530 10343120 11519080 11933770 11537790 13482630 12741610 14716230 14243400 FALSE TRUE 10669092.09 11299810.15 12212351.87 12113581.1 12317630.55 11771092.02 13647634.46 12478491.3 13045705.27 13278681.83 0.803475242 0.850973786 0.919696098 0.912257802 0.927624497 0.886465401 1.027785335 0.939738707 0.982454842 1 23.6626086 7.55088853 0.255672213 0.995619355 8.06E-18 0.7427109 0.032730936 19.53416682 0.32966507 0.039679885 8.054957016 35554005.07 -7.55088853 -0.995619355 EDYDSVEQDGDEPGPQR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDYDSVEQDGDEPGPQR 17 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ; 383.14 2.58E-121 1118930000 485590 471100 493240 583250 530900 506750 567980 649290 672990 729880 FALSE TRUE 466612.606 457664.6893 582379.4401 613351.6024 547976.8807 516996.8322 574931.1091 635881.9346 596594.9966 680444.5775 0.685746674 0.672596571 0.855880786 0.901398325 0.805321842 0.759792714 0.844934515 0.934509519 0.876772358 1 19.37611813 7.564910979 0.130587171 1.035289935 2.48E-15 0.643898616 0.059371167 51.25257455 0.502855636 0.349371121 9.613555144 36720702.33 -7.564910979 -1.035289935 EVNAVDSEHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVNAVDSEHEK 11 0 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 130.1 0.00023123 494670000 448680 562940 464500 538260 537200 649640 557290 590210 698050 767500 FALSE TRUE 431145.0896 546885.5024 548445.4827 566039.6631 554479.5259 662776.1659 564110.2817 578021.9572 618810.2905 715516.5414 0.602564811 0.764322655 0.76650287 0.791092351 0.774935999 0.926290487 0.788395864 0.807838706 0.864844144 1 19.44862559 7.566456143 0.08556968 1.114099489 5.00E-16 0.708708404 0.054422928 95.36398476 0.642636543 1.263961737 12.53324922 36851582.53 -7.566456143 -1.114099489 DQYLGHLQQYVAAYQQLTSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQYLGHLQQYVAAYQQLTSEK 21 0 Q08379;Q08379-2;A0A1W2PQY5 Q08379 GOLGA2 Golgin subfamily A member 2 0 ; 245.92 2.95E-30 564850000 440220 415540 385110 454360 473760 498490 500050 494140 622870 626030 FALSE TRUE 423015.7157 403689.2061 454707.9437 477809.5741 488998.9207 508569.8093 506169.7615 483935.8363 552164.4089 583628.4305 0.724803134 0.691688727 0.779105198 0.818687968 0.837860007 0.871393138 0.86728085 0.829184822 0.94608895 1 19.15469064 7.56797816 0.11374192 1.068174089 9.01E-12 0.878747564 0.030757329 32.20628467 0.279922102 0.278077707 5.360492181 36980958.22 -7.56797816 -1.068174089 TVENIKDPLFR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVENIKDPLFR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 107.09 0.0020462 1105600000 2686700 2996700 2705600 2765400 3017900 3296600 3262400 3439500 3792300 3893200 FALSE TRUE 2581700.794 2911237.05 3194562.106 2908122.625 3114973.494 3363259.511 3302326.227 3368473.123 3361814.003 3629510.096 0.711308338 0.802101929 0.880163444 0.801243845 0.858235247 0.926642831 0.909854537 0.928079282 0.926244566 1 21.7913434 7.570321437 0.18128622 1.00352115 2.29E-15 0.851958903 0.030491742 17.62663201 0.22820893 0.069469345 4.736758823 37181031.73 -7.570321437 -1.00352115 LLSHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLSHGK 6 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 124.32 0.018405 2515500000 4925300 4911600 4484200 5464900 5000900 4993200 5797000 5849600 6441900 7011600 FALSE TRUE 4732813.831 4771525.977 5294594.69 5746944.144 5161758.49 5094165.925 5867945.42 5728803.716 5710642.519 6536698.087 0.724037391 0.72995967 0.809979996 0.879181518 0.78965839 0.779317915 0.897692588 0.876406351 0.873628007 1 22.64013063 7.571639361 0.059340095 1.260045402 1.83E-09 0.772991606 0.038540615 155.8895243 0.74606745 3.430712775 17.35074711 37294033.88 -7.571639361 -1.260045401 S(ph)LIVEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLIVEGK 7 0 H0Y993;A0A494C028;P35659;B4DFG0;H0Y8X0;A0A494C198;D6R9L5 H0Y993 DEK Protein DEK 1 S(1)LIVEGK;S(1)LIVEGK 93.111 0.015919 563170000 1125140 724710 728070 643170 607560 457690 458440 1175980 540440 596660 TRUE FALSE 1081168.285 704041.9804 859648.4448 676364.0808 627102.7192 466944.8054 464050.5259 1151695.602 479091.5169 556247.6868 1.943681404 1.265698711 1.545441833 1.215940483 1.127380363 0.839454827 0.834251606 2.070472614 0.861291702 1 19.08536791 7.571889088 0.952323461 1.217034378 199.9999175 0.282715363 0.360211677 764.7683502 3.280819966 0.116376583 328536.1389 37315484.76 -7.571889088 198.7828831 SRKS(ph)PHKDLGHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRKSPHKDLGHR 12 3 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(0.24)RKS(0.76)PHKDLGHR 105.46 0.00082511 55518000 113810 103400 63884 53042 73951 87676 64080 11966 80407 54868 TRUE FALSE 109362.1794 100451.1332 75429.25989 55779.50398 76329.70108 89448.86879 64864.23021 11718.89792 71279.53445 51151.74149 2.137995231 1.963787162 1.474617632 1.09047126 1.492220966 1.748696451 1.268074719 0.229100664 1.393491842 1 15.64249574 7.582567786 0.255920808 0.808287911 8.31140894 0.472128434 0.373190474 34.74401125 0.578387289 0.514050605 108.4601845 38244394.23 -7.582567786 7.50312103 KTEEIAQER ddPTM_BT-474_Pertuzumab_2h_R1 3 KTEEIAQER 9 1 Q9NQT8;E7ERX9;A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9 Q9NQT8;A0A1B0GUA8 KIF13B;KIF13A Kinesin-like protein KIF13B;Kinesin-like protein;Kinesin-like protein KIF13A 0 ;; 123.67 0.00088379 738220000 934140 991730 825460 980170 1006510 1067010 1049940 1158850 1210520 1239180 FALSE TRUE 897632.7761 963446.8314 974638.9843 1030756.691 1038885.308 1088585.673 1062789.48 1134919.343 1073106.845 1155249.235 0.777003567 0.83397314 0.843661225 0.892237502 0.899273747 0.942295083 0.919965534 0.982402159 0.928896391 1 20.1397727 7.58702532 0.212657964 1.002606717 1.58E-10 0.925593712 0.017781987 9.248423523 0.135232662 0.027164029 3.039931708 38638950.33 -7.58702532 -1.002606717 LPFGDKTR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPFGDKTR 8 1 O76074-2 O76074-2 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 0 63.48 0.06662 489730000 319770 346060 335790 354140 352870 375560 462570 351720 510560 494800 FALSE TRUE 307273.0349 336190.7076 396474.7226 372417.2078 364220.384 383154.0805 468231.07 344456.8591 452603.3692 461286.7553 0.666121521 0.728810667 0.859497304 0.807344246 0.789574771 0.830620164 1.015054225 0.746730434 0.981175731 1 18.81530434 7.588631634 0.135389953 1.026660924 3.16E-14 0.553526572 0.076619091 57.68526843 0.580437184 0.364373233 11.18989619 38782127.89 -7.588631634 -1.026660924 TS(ph)PQELSEELSR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSPQELSEELSR 12 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-3;K7ERN1;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 T(0.243)S(0.757)PQELSEELSR;T(0.047)S(0.953)PQELSEELSR;T(0.032)S(0.968)PQELSEELSR 165.86 5.61E-05 1263380000 1072560 1095250 933170 1244820 1079870 1052840 1333920 1290100 1431770 1400300 TRUE FALSE 1030643.169 1064014.542 1101814.577 1309065.309 1114604.999 1074129.146 1350244.912 1263458.984 1269241.472 1305456.434 0.789488751 0.815051743 0.84400716 1.002764455 0.853804823 0.822799688 1.034308673 0.967829298 0.972258774 1 20.31612288 7.590362343 0.204003054 1.019855577 2.15E-05 0.535259729 0.060220384 34.35908867 0.485992168 0.110627927 10.89971415 38936987.04 -7.590362343 -1.019834047 TTPDVIFVFGFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPDVIFVFGFR 12 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 96.143 0.013145 277910000 435630 274070 277720 181061 330800 244530 278660 178750 359520 253659 FALSE TRUE 418605.098 266253.7919 327910.1818 190405.5799 341440.4824 249474.5641 282070.3244 175058.75 318708.7968 236478.45 1.770161712 1.125911439 1.386638748 0.805170957 1.443854535 1.054956865 1.192795049 0.740273585 1.347728712 1 17.85134919 7.591771883 0.954100456 1.077607349 199.9985163 0.421817955 0.224701585 477.7047601 1.950167882 0.064962618 205876.8467 39063565.67 -7.591771883 198.920909 YFDPANGK ddPTM_BT-474_Pertuzumab_2h_R1 3 YFDPANGK 8 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 112.94 0.0068495 489400000 1147150 1253710 1118290 1162600 1256720 1303700 1374400 1440370 1468660 1551610 FALSE TRUE 1102318.11 1217955.418 1320389.879 1222601.925 1297143.54 1330061.707 1391220.318 1410625.856 1301943.874 1446518.073 0.762049317 0.841991152 0.912805657 0.845203353 0.896735108 0.919491939 0.961771819 0.975187163 0.900053652 1 20.46415292 7.593768952 0.229234841 0.989390594 1.75E-11 0.767370182 0.032497641 19.50091205 0.300526677 0.04835511 6.968233939 39243610.05 -7.593768952 -0.989390594 GGS(ph)PYNQFDIIPGDTLGGHTGPAGDSWLPAK ddPTM_BT-474_Pertuzumab_2h_R1 3 GGSPYNQFDIIPGDTLGGHTGPAGDSWLPAK 31 0 Q9UPQ9-1;Q9UPQ9;H0Y720;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 GGS(0.997)PY(0.003)NQFDIIPGDTLGGHTGPAGDSWLPAK;GGS(0.997)PY(0.003)NQFDIIPGDTLGGHTGPAGDSWLPAK;GGS(1)PYNQFDIIPGDTLGGHTGPAGDSWLPAK 347.51 1.39E-120 797490000 460589 514094 404534 500107 480651 559750 562738 556820 682580 681710 TRUE FALSE 442588.6727 499432.5425 477642.2926 525917.5822 496111.5759 571068.5285 569624.956 545321.4724 605096.38 635537.1745 0.696400919 0.785843162 0.751556812 0.827516632 0.780617713 0.898560386 0.896288964 0.858048112 0.95210226 1 19.27761699 7.595148454 0.111027025 1.087026372 1.01E-09 0.868951688 0.032364238 31.39798267 0.265525773 0.282182133 5.187689707 39368462.5 -7.595148454 -1.087026371 EILSDDKHDWEQR ddPTM_BT-474_Pertuzumab_2h_R1 4 EILSDDKHDWEQR 13 1 Q7Z460;C9J151;C9JP76;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 0 ;;; 241.42 4.15E-17 1173980000 1016780 1065240 945800 1070760 1057750 1128250 1144170 1186240 1384760 1295270 FALSE TRUE 977043.1135 1034860.398 1116727.099 1126022.052 1091773.489 1151063.988 1158172.695 1161743.729 1227567.85 1207540.209 0.809118492 0.856998707 0.92479496 0.932492387 0.904130133 0.95323036 0.959117291 0.962074572 1.016585486 1 20.2036398 7.595607168 0.252998684 1.002062143 1.14E-17 0.887202947 0.019989019 13.13377339 0.215856822 0.026345251 5.401587983 39410066.49 -7.595607168 -1.002062143 KLWGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLWGDR 6 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 97.071 0.066524 20899000000 31825000 34398000 28469000 32859000 33544000 35026000 36967000 36708000 39407000 40580000 FALSE TRUE 30581243.82 33417002.72 33613981.59 34554856.93 34622973.22 35734249.72 37419413.2 35949966.97 34933682.57 37831480.46 0.808354403 0.883312054 0.888518799 0.913388969 0.915189488 0.944563873 0.989107821 0.95026593 0.923402472 1 25.1730839 7.59739363 0.280149593 0.978052691 3.45E-10 0.833660364 0.021406987 15.95711971 0.277009303 0.023867315 7.321243365 39572512.98 -7.59739363 -0.97805269 GAFGKPQGTVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAFGKPQGTVAR 12 1 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ; 132.99 0.00015614 3126200000 3672900 3734200 3370800 3790500 3744000 3829700 4028700 4209200 4595800 4503200 FALSE TRUE 3529359.007 3627704.272 3979978.543 3986128.159 3864429.16 3907139.158 4078004.436 4122278.549 4074104.051 4198194.253 0.840685017 0.864110628 0.948021531 0.949486355 0.92049794 0.930671361 0.971371068 0.981917058 0.970442006 1 22.00133749 7.598810848 0.29584507 0.987710196 9.49E-12 0.831634051 0.019874387 17.32275692 0.307658376 0.022248643 8.626239525 39701859.48 -7.598810848 -0.987710196 AS(ph)GEMASAQYITAALR ddPTM_BT-474_Pertuzumab_2h_R1 21 ASGEMASAQYITAALR 16 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 1 AS(1)GEMASAQYITAALR;AS(0.998)GEMAS(0.002)AQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR 338.42 7.53E-72 10418716000 3119801.7 3125078.6 3049925.2 3640809.7 3378506.3 3211434.3 3703803.3 4051590.4 4098504 4440867 TRUE FALSE 2997876.4 3035954.418 3601114.529 3828712.325 3487179.023 3276371.702 3749131.553 3967923.642 3633259.008 4140083.123 0.724110196 0.7333076 0.869816963 0.924791172 0.842296862 0.791378242 0.90556915 0.958416419 0.877581174 1 21.9812283 7.60801029 0.182544909 0.988378023 1.74E-17 0.633213835 0.052599371 33.7506448 0.434242668 0.126178898 9.035023454 40551814.35 -7.60801029 -0.988378023 KLDEQYQK ddPTM_BT-474_Pertuzumab_2h_R1 1 KLDEQYQK 8 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 96.665 0.014078 362640000 409060 394840 368790 396880 516970 398630 438410 509850 547750 554820 FALSE TRUE 393073.483 383579.5498 435438.5567 417363.0244 533598.8096 406690.5717 443775.3927 499321.4193 485571.7164 517241.5472 0.75994182 0.741586889 0.841847603 0.806901585 1.03162403 0.786268183 0.857965481 0.965354431 0.93877168 1 18.98047864 7.608584526 0.170469771 1.012915728 8.74E-14 0.526101051 0.067899488 40.35245069 0.490693286 0.172977327 10.17114319 40605468.51 -7.608584526 -1.012915728 SVDFEMPPPS(ph)PPLNLHELSGPAEGAS(ph)LTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVDFEMPPPSPPLNLHELSGPAEGASLTPK 30 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 S(0.001)VDFEMPPPS(0.999)PPLNLHELS(0.206)GPAEGAS(0.459)LT(0.335)PK 71.528 0.00309 92336000 72617 66457 68417 68267 76164 80384 84416 86751 89576 103490 TRUE FALSE 69779.04736 64561.71143 80781.47383 71790.26805 78613.88423 82009.41956 85449.10826 84959.56153 79407.70801 96480.53012 0.723244859 0.669168291 0.837282649 0.74409073 0.814816048 0.850010043 0.885661679 0.880587632 0.823043861 1 16.55795021 7.612433029 0.099239059 1.092181012 7.37E-11 0.760329578 0.043627001 52.82062172 0.40296159 0.555048518 7.824002871 40966893.17 -7.612433029 -1.092181012 KPLPDHVSIVEPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KPLPDHVSIVEPK 13 1 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 138.87 2.86E-05 1632100000 2744200 3450300 2757400 3455100 3011700 3551300 3548500 3770800 3974900 4328300 FALSE TRUE 2636953.63 3351900.822 3255723.518 3633418.125 3108574.066 3623109.719 3591927.604 3692931.662 3523686.016 4035140.386 0.65349737 0.830677623 0.806842689 0.900444044 0.770375692 0.897889385 0.890161744 0.915192858 0.873249919 1 21.94418744 7.620946467 0.178906335 0.981451916 2.91E-23 0.678543804 0.050959289 29.38046433 0.370352512 0.11180339 7.62380108 41777886.6 -7.620946467 -0.981451916 S(ph)SPVPPVPER ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.643)S(0.357)PVPPVPER;S(0.63)S(0.37)PVPPVPER 106 0.0025953 3524300000 1011480 1065100 979670 1201550 1079710 1174460 1189910 1336650 1405380 1514410 TRUE FALSE 971950.2433 1034724.391 1156718.162 1263562.139 1114439.853 1198208.386 1204472.475 1309047.71 1245847.154 1411837.662 0.68842918 0.732891903 0.819299692 0.894976932 0.789354104 0.848687082 0.853123916 0.927194213 0.882429466 1 20.42914278 7.630193685 0.143552516 1.0191843 6.19E-12 0.801813613 0.038702677 29.00523509 0.303539318 0.162310252 5.989311161 42676980.57 -7.630193685 -1.0191843 KPVVDCVVSVPCFYTDAER ddPTM_BT-474_Pertuzumab_2h_R1 2 KPVVDCVVSVPCFYTDAER 19 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 163.91 3.97E-11 3792100000 3726000 3860600 3227000 3622800 3751000 3918600 4030800 4002100 4138200 4446800 FALSE TRUE 3580383.801 3750499.468 3810190.684 3809773.142 3871654.322 3997836.777 4080130.136 3919455.236 3668448.885 4145614.275 0.863655797 0.90469089 0.919089532 0.918988813 0.933915715 0.964353293 0.984203996 0.945446194 0.884898749 1 21.98315446 7.660413871 0.368480858 0.958073883 2.14E-09 0.490077877 0.029051744 44.10594159 0.780476416 0.022798176 28.75797227 45752398.98 -7.660413871 -0.958073881 SLEDLQDEYDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 SLEDLQDEYDFK 12 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75;D2KFR9;A0A669KB17 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ; 179.6 4.77E-05 135320000 235298 250865 200470 268527 241934 272477 266945 300340 325260 333370 FALSE TRUE 226102.294 243710.5758 236699.3884 282385.7107 249716.0268 277986.6716 270211.9528 294137.874 288337.8484 310790.553 0.727506972 0.784163397 0.761604193 0.90860455 0.803486542 0.894450198 0.869434255 0.946418323 0.927756155 1 18.24558313 7.663500627 0.14172916 1.042882772 2.56E-12 0.825270917 0.035326701 23.78370929 0.244098347 0.136405007 4.958601045 46078743.44 -7.663500627 -1.042882772 AQVLVEDISDILEEHAEK ddPTM_BT-474_Pertuzumab_2h_R1 3 AQVLVEDISDILEEHAEK 18 0 Q5VV41;Q5VV41-2;B0QZD3;B0QZD4 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ;; 234.11 9.29E-24 196886000 209964 211200 188378 213013 226093 229401 257612 237714 293741 284970 FALSE TRUE 201758.3748 205176.7828 222422.095 224006.6265 233365.4867 234039.6454 260764.7327 232805.1228 260396.7531 265668.7281 0.759435919 0.772303102 0.837215944 0.843180257 0.878407814 0.880945406 0.981540939 0.876298556 0.980155832 1 18.01926889 7.6740512 0.16562872 1.022431257 3.69E-08 0.850286009 0.030971328 18.65688195 0.217310558 0.081129954 4.601464413 47211869.76 -7.6740512 -1.02243122 ETVQTTQS(ph)PTPVEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ETVQTTQSPTPVEK 14 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 ETVQTT(0.003)QS(0.972)PT(0.024)PVEK;ETVQTT(0.003)QS(0.997)PTPVEK;ETVQTT(0.101)QS(0.864)PT(0.034)PVEK 283.85 3.77E-24 387480000 757520 772638 698620 870500 846110 803012 874600 961790 1034400 1078990 TRUE FALSE 727915.2809 750603.1207 824876.1747 915426.6093 873325.8966 819249.4528 885303.6164 941928.7004 916979.2486 1005909.046 0.723639263 0.746193827 0.820030576 0.910049087 0.868195688 0.814436907 0.880103047 0.936395496 0.911592606 1 19.94006843 7.678988091 0.163709949 1.004918241 4.49E-15 0.803398004 0.036098884 25.80428904 0.297283045 0.112068491 6.168454002 47751617.96 -7.678988091 -1.004918241 TGQPMIHIYLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TGQPMIHIYLDK 12 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 124.45 0.00032283 2312800000 4080300 3720900 3888400 4238700 4232300 3699300 4502200 4784700 5535100 5560300 FALSE TRUE 3920837.365 3614783.575 4591120.377 4457459.815 4368435.773 3774102.381 4557299.27 4685894.273 4906778.653 5183695.928 0.756378734 0.697337117 0.885684739 0.859899939 0.842726085 0.728071714 0.879160223 0.903967813 0.946579182 1 22.30554966 7.694981463 0.060054366 1.268833612 5.15E-11 0.594730812 0.058329409 231.379557 1.095104544 4.877970229 26.00028181 49542904.43 -7.694981463 -1.268833612 GDMS(ph)DEDDENEFFDAPEIITMPENLGHK ddPTM_BT-474_Pertuzumab_2h_R1 38 GDMSDEDDENEFFDAPEIITMPENLGHK 28 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK 319.95 1.59E-82 19802547000 4758206.7 4834960 4293714.6 4950211.1 5079072.3 5244418.2 5597826.9 5598249 6497138 6394819.5 TRUE FALSE 4572250.722 4697071.675 5069684.341 5205692.088 5242445.273 5350463.929 5666334.78 5482643.202 5759610.132 5961692.679 0.766938346 0.787875512 0.850376665 0.873190278 0.879355169 0.897473959 0.950457376 0.919645392 0.966103159 1 22.50729058 7.723939259 0.178672505 1.013991681 2.99E-16 0.959160101 0.014291781 8.817778458 0.107526089 0.032388308 2.377653222 52958936.94 -7.723939259 -1.013991681 VLVTVEEDDTIMEELVDNHGK ddPTM_BT-474_Pertuzumab_2h_R1 10 VLVTVEEDDTIMEELVDNHGK 21 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;;;; 437.13 8.49E-175 1021288000 738398.5 738618.7 677459.3 813787.8 773039 756065.3 862688.3 884522.9 993964 971852.5 FALSE TRUE 709541.0703 717554.0179 799891.2655 855787.4859 797904.5015 771353.4584 873246.1375 866257.193 881133.3738 906028.0645 0.783133656 0.791977695 0.882854844 0.94454854 0.880662016 0.851357136 0.963817978 0.956104151 0.972523267 1 19.78919621 7.725094773 0.20037683 1.006815553 3.26E-15 0.767049875 0.035055218 23.32763607 0.310471358 0.069082344 7.22142142 53100030.74 -7.725094773 -1.006815553 EKEWQR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKEWQR 6 1 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-4;C9JMV9;A0A1B0GV31 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ;; 100.74 0.034032 846610000 1278170 1295450 1136700 1303350 1333810 1464160 1446510 1477890 1634380 1672350 FALSE TRUE 1228217.703 1258505.034 1342126.976 1370616.05 1376713.21 1493766.318 1464212.822 1447371.055 1448852.034 1559080.245 0.787783507 0.807209917 0.860845348 0.879118348 0.88302909 0.958107399 0.939151674 0.928349301 0.929299206 1 20.57226375 7.72749792 0.211511688 0.989384148 2.06E-12 0.91404983 0.018532046 12.28034761 0.169840459 0.032083807 4.004685573 53394671.69 -7.72749792 -0.989384148 VPTTEKPTVTVNFR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPTTEKPTVTVNFR 14 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 109.1 0.00071778 2070460000 841070 772810 755530 885870 860820 899250 960270 1026450 1043020 1170660 FALSE TRUE 808200.0545 750770.2155 892071.0777 931589.8569 888509.0571 917433.4511 972022.0715 1005253.449 924620.7423 1091370.155 0.740537068 0.687915289 0.817386359 0.853596603 0.814122553 0.840625379 0.890643808 0.921093035 0.847210946 1 20.05770907 7.729612708 0.130506754 1.0350295 3.42E-15 0.79666951 0.037501014 31.6318327 0.297885967 0.198060935 5.966176323 53655309.9 -7.729612708 -1.0350295 FS(ph)PGAPGGSGSQPNQK ddPTM_BT-474_Pertuzumab_2h_R1 5 FSPGAPGGSGSQPNQK 16 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK 319.53 5.48E-58 1475730000 1239791 1169054 1400250 1401630 1288740 1313460 1560450 1644690 1644880 1883660 TRUE FALSE 1191338.597 1135713.725 1653306.323 1473968.292 1330193.493 1340019.061 1579547.254 1610726.577 1458160.118 1756078.03 0.678408691 0.646733064 0.941476572 0.83935239 0.757479719 0.763074896 0.899474412 0.917229502 0.830350413 1 20.74392552 7.72976303 0.119286603 1.043413161 2.52E-15 0.499456548 0.077529307 79.00111907 0.689418788 0.574044607 13.57957952 53673884.84 -7.72976303 -1.043413161 LTALDYHNPAGFNCK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTALDYHNPAGFNCK 15 0 Q9Y224;G3V4C6;G3V4E7 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 98.439 0.0037616 0 554660 579270 429320 454220 465840 507360 477800 486140 607050 451760 FALSE TRUE 532983.274 562749.7868 506907.6742 477662.3486 480824.1667 517619.1668 483647.4593 476101.0391 538140.229 421161.8928 1.265506882 1.33618401 1.203593399 1.13415377 1.14166114 1.229026594 1.14836472 1.130446622 1.277751473 1 18.68401538 7.733597919 0.021076624 7.97E-13 2.710455937 0.47844473 0.065875176 2379.101706 4.030066657 191.4331673 348.3155453 54149932.43 -7.733597919 2.710455937 TPS(ph)SEEISPTK ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSSEEISPTK 11 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.235)PS(0.758)S(0.007)EEISPTK;T(0.067)PS(0.924)S(0.01)EEISPTK;T(0.004)PS(0.995)S(0.001)EEISPTK 213.72 1.63E-09 1529030000 1215890 1153760 1164080 1341710 1187580 1189250 1465650 1534240 1615650 1721130 TRUE FALSE 1168371.675 1120855.894 1374455.151 1410955.814 1225779.589 1213297.45 1483587.063 1502557.408 1432248.185 1604556.332 0.728158714 0.69854568 0.856595137 0.879343271 0.763936775 0.75615759 0.924608899 0.936431696 0.892613214 1 20.61374301 7.737055307 0.102628736 1.104947613 3.04E-10 0.641479642 0.057384659 75.95310204 0.581175819 0.729609989 11.78794961 54582736.74 -7.737055307 -1.104947613 PGAGQPGEFHTT(ph)PPGTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 PGAGQPGEFHTTPPGTPR 18 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 PGAGQPGEFHT(0.348)T(0.652)PPGTPR;PGAGQPGEFHT(0.286)T(0.714)PPGTPR 127.58 9.25E-05 790190000 373420 272450 322700 352630 403750 323600 399100 375860 495380 483040 TRUE FALSE 358826.3336 264679.9928 381019.0684 370829.2766 416736.9854 330143.4137 403984.3052 368098.3597 439146.5392 450323.2706 0.796819434 0.58775553 0.84610122 0.823473493 0.925417389 0.733125369 0.897098444 0.817409145 0.975180649 1 18.78060151 7.737204006 0.088964063 1.129727897 1.36E-14 0.456232523 0.084774206 131.792458 0.888740559 1.57600454 18.18219574 54601428.6 -7.737204006 -1.129727897 SKWDEEWDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKWDEEWDK 9 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 88.187 0.011814 791430000 406040 384420 387810 424690 469880 314150 494160 555950 468710 542790 FALSE TRUE 390171.5079 373456.718 457895.8938 446608.3018 484994.1169 320502.3282 500207.6779 544469.4382 415504.0058 506026.3498 0.771049784 0.738018323 0.904885475 0.882579142 0.958436487 0.633370828 0.988501247 1.075970527 0.821111402 1 18.94885299 7.74133645 0.167281383 1.025932747 2.01E-08 0.223025531 0.114117769 77.00976355 0.886565884 0.316643687 19.37811337 55123457.46 -7.74133645 -1.025932726 ATLVDHGIR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATLVDHGIR 9 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;;; 224.86 2.94E-07 3013080000 1724870 1991010 1957190 2219430 2102450 1722500 2599980 2281130 2622850 2849090 FALSE TRUE 1657460.173 1934228.344 2310897.77 2333975.048 2170077.214 1757330.13 2631799.333 2234023.868 2325115.064 2656118.597 0.624015876 0.728216107 0.870028083 0.878716429 0.817010662 0.661615838 0.99084406 0.841085888 0.87538074 1 21.34088813 7.755388816 0.132019613 1.01484173 5.45E-22 0.456886046 0.087888135 76.94755825 0.727052837 0.457614488 14.43505224 56936244.32 -7.755388816 -1.01484173 DSDKPET(ph)PPVVNVPVPVLIGPISGMSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSDKPETPPVVNVPVPVLIGPISGMSR 27 1 A0A286YFF8;Q7Z3U7-2;Q7Z3U7-6;Q7Z3U7-5;Q7Z3U7;Q7Z3U7-3 A0A286YFF8 MON2 Protein MON2 homolog 1 DS(0.032)DKPET(0.968)PPVVNVPVPVLIGPISGMSR;DS(0.013)DKPET(0.987)PPVVNVPVPVLIGPISGMSR 84.478 0.014345 318330000 392900 339170 336560 376330 416960 409970 427350 421830 516130 503080 TRUE FALSE 377545.0336 329497.2037 397383.8787 395752.4364 430371.8971 418259.8743 432580.0371 413119.0631 457541.0862 469005.9435 0.80498987 0.70254377 0.847289644 0.843811133 0.917625678 0.891800797 0.922333806 0.880839718 0.975554985 1 18.83924668 7.762133206 0.163419526 1.01619902 2.69E-14 0.74638462 0.041023646 27.0274522 0.303551049 0.113001048 6.553751313 57827338.78 -7.762133206 -1.01619902 LFDHPESPTPNPTEPLFLAQAEVYK ddPTM_BT-474_Pertuzumab_2h_R1 4 LFDHPESPTPNPTEPLFLAQAEVYK 25 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 301.12 3.06E-63 4748620000 1375354 1632010 1515960 1652970 1501280 1696440 1833420 1725900 2243400 2234000 FALSE TRUE 1321603.645 1585466.673 1789927.694 1738279.98 1549570.035 1730743.179 1855857.942 1690259.562 1988738.637 2082689.19 0.63456595 0.761259376 0.85943102 0.834632449 0.74402366 0.831013666 0.891087327 0.81157552 0.954889787 1 20.99001612 7.763118662 0.079318671 1.156287123 9.20E-14 0.682276684 0.056287529 121.1739519 0.733048076 1.696039238 15.41880852 57958703.52 -7.763118662 -1.156287123 TQT(ph)PPVSPAPQPTEER ddPTM_BT-474_Pertuzumab_2h_R1 7 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 T(0.098)QT(0.901)PPVS(0.001)PAPQPTEER;TQT(1)PPVSPAPQPTEER;T(0.001)QT(0.999)PPVSPAPQPTEER;T(0.037)QT(0.962)PPVSPAPQPTEER;T(0.062)QT(0.938)PPVSPAPQPTEER;TQT(1)PPVSPAPQPTEER;TQT(0.992)PPVS(0.008)PAPQPTEER 206.89 2.11E-10 3858670000 1113409 1198550 1110884 1243394 1106116 1237811 1379682 1441896 1443910 1533697 TRUE FALSE 1069895.745 1164368.528 1311645.45 1307565.713 1141695.226 1262840.387 1396566.961 1412120.344 1280003.39 1429818.336 0.748273902 0.814347178 0.917351119 0.914497793 0.798489708 0.883217367 0.976744336 0.987622209 0.895220993 1 20.44740043 7.766720454 0.196609583 1.002871841 1.77E-14 0.598563922 0.050936849 35.37915221 0.457686181 0.104822067 10.68427635 58441378.86 -7.766720454 -1.002871841 WIGLDLSNGKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 WIGLDLSNGKPR 12 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 200.93 1.41E-07 3964600000 2680560 2853850 2505880 2907130 2920030 2891390 3295550 3485410 3513400 3845200 FALSE TRUE 2575800.752 2772460.992 2958748.259 3057167.328 3013955.417 2949855.887 3335881.927 3413435.066 3114573.561 3584761.179 0.7185418 0.773401868 0.825368305 0.852823152 0.840768817 0.822887701 0.930572989 0.952207105 0.868837115 1 21.77344558 7.772376287 0.146139135 1.02745648 3.25E-11 0.825576829 0.033318979 26.16603725 0.267725937 0.132379009 5.604017014 59207440.54 -7.772376287 -1.02745648 TT(ph)PPEAAQNGQSPMAALILVADNAGGSHASK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPPEAAQNGQSPMAALILVADNAGGSHASK 31 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 T(0.187)T(0.813)PPEAAQNGQSPMAALILVADNAGGSHASK 187.35 6.67E-18 316380000 111880 123220 116410 165150 114420 129220 135380 158190 168190 182730 TRUE FALSE 107507.6059 119705.8862 137447.8765 173673.4113 118100.4232 131832.9169 137036.8209 154923.3212 149097.7763 170353.5343 0.631085268 0.702690946 0.806839007 1.01948816 0.693266645 0.773878379 0.804426051 0.909422407 0.875225612 1 17.37817235 7.773525935 0.1047211 1.067241885 1.17E-12 0.440875249 0.091966617 118.8480411 0.918281833 1.053714392 18.19938864 59364379.79 -7.773525935 -1.067241885 TLEEVVMAEEEDEGTDRPGS(ph)PA ddPTM_BT-474_Pertuzumab_2h_R1 1 TLEEVVMAEEEDEGTDRPGSPA 22 1 A6NKF1;F8WC89 A6NKF1 SAC3D1 SAC3 domain-containing protein 1 1 TLEEVVMAEEEDEGTDRPGS(1)PA 83.606 0.0020699 121080000 178780 183000 188460 202460 189370 218390 231000 208070 243580 271600 TRUE FALSE 171793.0799 177781.0192 222518.9143 212908.9849 195461.258 222805.9954 233827.0471 203773.2818 215929.8196 253204.2901 0.678476182 0.70212483 0.878811786 0.840858521 0.771950815 0.879945578 0.923471901 0.804778156 0.852788946 1 17.94994232 7.778436822 0.170209493 0.955016297 1.32E-52 0.606515582 0.058292987 43.43148584 0.501377007 0.157561957 10.42070812 60039466.1 -7.778436822 -0.955016297 LPEASQS(ph)PLVLK ddPTM_BT-474_Pertuzumab_2h_R1 4 LPEASQSPLVLK 12 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 LPEASQS(1)PLVLK;LPEAS(0.004)QS(0.996)PLVLK;LPEAS(0.006)QS(0.994)PLVLK;LPEAS(0.03)QS(0.97)PLVLK 184 1.56E-05 891840000 1097390 1195140 1029090 1221660 1140990 1195990 1154530 1383970 1453720 1412940 TRUE FALSE 1054502.786 1161055.777 1215069.455 1284710.019 1177690.98 1220173.737 1168659.483 1355390.536 1288699.8 1317240.315 0.800539411 0.881430491 0.922435672 0.975304205 0.894059319 0.926310653 0.887202942 1.028962233 0.978333099 1 20.32908714 7.780652802 0.256167505 0.993609122 9.23E-21 0.602856681 0.040544654 33.47813166 0.509628347 0.053592309 14.14101194 60346599.41 -7.780652802 -0.993609122 GLEDSYEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLEDSYEGR 9 0 Q8NHP8-2;Q8NHP8 Q8NHP8-2 PLBD2 Putative phospholipase B-like 2;Putative phospholipase B-like 2 32 kDa form;Putative phospholipase B-like 2 45 kDa form 0 114.5 0.0044576 0 129840 128970 139690 173480 137650 143010 165410 171730 172530 209560 FALSE TRUE 124765.7093 125291.9019 164935.0904 182433.3236 142077.6373 145901.7602 167434.3371 168183.7155 152945.1177 195366.3145 0.638624471 0.641317835 0.84423505 0.933801326 0.727237127 0.746811243 0.857027669 0.860863429 0.7828633 1 17.57582221 7.78982916 0.085482595 1.099167153 4.33E-20 0.484762207 0.080684058 159.7676297 1.028697151 1.91760314 20.66042064 61635249.78 -7.78982916 -1.099167153 DYDDMS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 17 DYDDMSPR 8 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR 163.84 0.00034991 53212865000 25185750 24773090 21493550 23645650 24449010 26143780 25816080 27517490 29248370 29895860 TRUE FALSE 24201463.05 24066585.73 25377912.61 24866004.83 25235434.61 26672425.14 26132024.91 26949244.22 25928217.66 27870986.77 0.868338938 0.863499593 0.910549483 0.892182434 0.905437429 0.956996082 0.937606735 0.966928241 0.930294211 1 24.73226075 7.792621558 0.128007357 1.024883661 0.486034062 0.836423466 0.016784245 27.74219951 0.253155029 0.090284508 2.671265102 62032824.77 -7.792621558 -0.538849599 TPIHAAATNGHSECLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPIHAAATNGHSECLR 16 0 O15084-2;O15084;O15084-4;O15084-1;B4DIW9 O15084-2 ANKRD28 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit A 0 ; 109.36 0.00056574 199083000 203559 194153 191774 215570 211570 210150 240380 247773 276100 283790 FALSE TRUE 195603.6892 188615.9465 226431.8278 226695.5935 218375.3412 214399.377 243321.8423 242656.401 244758.2855 264568.6505 0.739330563 0.712918731 0.855852828 0.856849793 0.825401425 0.810373325 0.919692646 0.917177453 0.925122024 1 18.0132826 7.7996533 0.127611042 1.054246641 5.85E-11 0.817597778 0.035838414 33.1807081 0.301490185 0.211558948 6.230432819 63045384.81 -7.7996533 -1.054246641 ADQEEQIHPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ADQEEQIHPR 10 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 223.14 4.57E-09 3213420000 2760490 2834830 2337820 2796980 2780740 2970910 2830030 2799120 2759510 3158670 FALSE TRUE 2652606.999 2753983.424 2760316.079 2941332.473 2870185.028 3030983.836 2864664.754 2741317.194 2446261.994 2944730.467 0.900797892 0.935224278 0.937374782 0.998846076 0.97468514 1.029290751 0.972810512 0.930922957 0.830725264 1 21.48970416 7.803786272 17.98161163 0.952473799 0.046359793 0 0.054497677 0 0 0.012231371 0 63648221.39 -7.803786272 -0.906114006 LSAS(ph)SEDISER ddPTM_BT-474_Pertuzumab_2h_R1 2 LSASSEDISER 11 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 LSAS(0.938)S(0.062)EDISER;LSAS(0.5)S(0.5)EDISER 222.72 7.83E-12 589900000 488260 508630 430110 493750 501390 556080 505610 579000 566810 612760 TRUE FALSE 469178.2594 494124.3704 507840.4447 519232.4967 517517.6647 567324.3186 511797.8064 567043.4477 502468.1051 571257.2194 0.821308236 0.864977025 0.888987355 0.908929426 0.90592757 0.993115359 0.895914816 0.992623688 0.879582941 1 19.12378097 7.8069905 0.270108915 0.970065689 2.53E-16 0.559274715 0.038163737 30.91091292 0.476015967 0.040497856 13.70845724 64119555.06 -7.8069905 -0.970065689 NSSNTSVGSPS(ph)NTIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSSNTSVGSPSNTIGR 16 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 NSSNTSVGS(0.26)PS(0.738)NT(0.002)IGR 206.15 2.18E-11 460720000 506260 588890 516060 549760 551450 618350 603260 678660 730010 731620 TRUE FALSE 486474.7995 572095.4338 609323.5217 578133.1795 569187.8901 630853.4607 610642.8763 664645.4338 647142.3253 682066.7257 0.713236376 0.838767546 0.893348845 0.84761968 0.834504703 0.924914582 0.895283193 0.974458083 0.948796211 1 19.37955336 7.809235854 0.171941 1.019679186 2.80E-18 0.794535611 0.035866527 24.80771167 0.285996531 0.092529779 6.449630467 64451919.16 -7.809235854 -1.019679186 KQEELQQLEQQR ddPTM_BT-474_Pertuzumab_2h_R1 4 KQEELQQLEQQR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 203.88 1.92E-07 4073420000 2209070 2242460 2085500 2334590 2259870 2276060 2481070 2737490 2846200 2788290 FALSE TRUE 2122737.102 2178507.236 2462396.242 2455078.47 2332560.771 2322083.493 2511434.077 2680959.875 2523111.308 2599436.635 0.81661429 0.838068991 0.947280733 0.944465596 0.897333191 0.893302595 0.966145527 1.031361888 0.970637743 1 21.30976756 7.812591805 0.223105664 1.017133596 2.13E-15 0.692086068 0.036114893 27.81466639 0.386073246 0.062084457 10.06756873 64951891.8 -7.812591805 -1.017133596 AKGPS(ph)ESSK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKGPSESSK 9 1 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.998)ES(0.002)SK;AKGPS(0.939)ES(0.05)S(0.011)K 138.89 0.00032562 89506000 215572 165304 171073 125462 155267 161582 140344 182517 189587 204665 TRUE FALSE 207147.2079 160589.6918 201989.6966 131937.1089 160261.3041 164849.2987 142061.5719 178747.9602 168065.8786 190802.8573 1.085660932 0.841652447 1.058630355 0.691483926 0.839931364 0.863977097 0.744546355 0.936820144 0.88083523 1 17.54172325 7.815659503 1.038139933 0.85882185 183.154351 0.260153688 0.104284302 1687.274703 2.949657524 0.028486296 731076.8483 65412312.45 -7.815659503 182.2955292 SSS(ph)APNVHINTIEPVNIDDLIR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSSAPNVHINTIEPVNIDDLIR 22 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.03)S(0.03)S(0.941)APNVHINTIEPVNIDDLIR;S(0.031)S(0.031)S(0.937)APNVHINTIEPVNIDDLIR;S(0.004)S(0.019)S(0.977)APNVHINTIEPVNIDDLIR;S(0.131)S(0.131)S(0.738)APNVHINTIEPVNIDDLIR 289.76 1.51E-55 2504175000 327029 339274 292859 364014 360705 345745 387281 401559 429793 453673 TRUE FALSE 314248.3451 329598.2377 345785.1359 382800.8062 372307.4039 352736.2008 392020.6607 393266.6663 381004.7005 422945.3236 0.742999928 0.779292782 0.817564627 0.905083435 0.88027313 0.833999529 0.926882599 0.929828619 0.900836773 1 18.69011165 7.816005463 0.174718446 0.99614883 6.26E-15 0.833764119 0.030065501 21.31184642 0.248239296 0.075155613 5.525339045 65464440.9 -7.816005463 -0.99614883 YGADVHTQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 YGADVHTQSK 10 0 F5H7I4;H9ZYI9;Q06547-4;Q06547-3;Q06547-2;Q06547 F5H7I4 GABPB1 GA-binding protein subunit beta-1 0 ; 106.29 0.0024361 250400000 547580 540210 488360 551400 567440 597670 587000 630020 707890 681600 FALSE TRUE 526179.9682 524803.7397 576617.5155 579857.8201 585692.2229 609755.2969 594183.8816 617009.8668 627533.2949 635434.6249 0.828063105 0.825897298 0.907437985 0.912537336 0.921719088 0.959587773 0.935082632 0.971004479 0.987565471 1 19.27738418 7.822919549 0.224779054 1.005073539 1.10E-06 0.925194021 0.015627346 10.53843308 0.146368254 0.022650082 3.809616228 66514992.88 -7.822919549 -1.005072442 ALDEYYDKHFTEFVPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDEYYDKHFTEFVPLR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 118.48 0.00010016 351920000 309030 364560 272320 319930 348460 370630 345680 372870 440460 404850 FALSE TRUE 296952.7659 354163.1057 321534.2817 336441.6256 359668.5324 378124.3925 349910.5352 365170.1042 390460.8274 377429.1489 0.78677751 0.938356528 0.851906332 0.891403397 0.952943177 1.001842051 0.927089326 0.967519613 1.034527483 1 18.52584632 7.826178762 0.225746107 1.015605895 4.93E-11 0.684932187 0.040017229 27.59951378 0.383855356 0.059187031 10.14131699 67016040.11 -7.826178762 -1.015605895 IHEKDPNSATATAPPS(ph)PLK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHEKDPNSATATAPPSPLK 19 1 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6;C9JPJ6 Q92766 RREB1 Ras-responsive element-binding protein 1 1 IHEKDPNSATATAPPS(1)PLK;IHEKDPNSATATAPPS(1)PLK 97.253 0.0006921 743770000 2002160 1560920 921420 1283250 1482930 1201670 1499910 933350 1352250 1078300 TRUE FALSE 1923913.374 1516404.09 1087941.091 1349478.686 1530629.79 1225968.591 1518266.347 914075.9963 1198748.249 1005265.781 1.913835536 1.508460866 1.082242241 1.342409851 1.522612049 1.219546725 1.510313368 0.909287886 1.192468969 1 19.93914555 7.827124051 0.863715435 1.216168332 199.9885384 0.539835228 0.19423922 410.6606307 1.48663622 0.063799933 159946.5702 67162066.63 -7.827124051 198.7723701 GTFHDDRDDGVDYWAK ddPTM_BT-474_Pertuzumab_2h_R1 8 GTFHDDRDDGVDYWAK 16 1 E9PK91;Q9NYF8-3;H0YF63 E9PK91 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;;;;;; 113.69 0.00038568 4104948000 7016077 6924594 6361181 6999034 7336590 7730093 7576280 7530527 8741470 8938490 FALSE TRUE 6741880.954 6727111.359 7510787.91 7360254.984 7572578.08 7886400.777 7669000.781 7375018.986 7749174.973 8333078.111 0.809050493 0.807278087 0.901322154 0.883257649 0.908737201 0.946397078 0.92030828 0.885029384 0.929929477 1 22.99041807 7.832362035 0.261100675 0.950704319 1.21E-34 0.732154496 0.028771113 26.62301996 0.39924518 0.036693084 11.09220494 67977006.47 -7.832362035 -0.950704319 DSGPLPT(ph)PPGVSLLGEPPKDYR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSGPLPTPPGVSLLGEPPKDYR 22 1 A0A087WZ13;Q8IY67-2;E9PAU2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 DSGPLPT(0.974)PPGVS(0.025)LLGEPPKDYR;DS(0.004)GPLPT(0.993)PPGVS(0.003)LLGEPPKDYR;DSGPLPT(1)PPGVSLLGEPPKDYR 114.74 0.00035309 222105000 323550 319600 326088 306566 370003 378128 320187 347272 357949 360260 TRUE FALSE 310905.3083 310485.3209 385019.3554 322387.908 381904.4825 385774.0072 324105.5443 340100.7118 317316.1302 335859.2693 0.925701139 0.924450653 1.146371086 0.959889863 1.137096747 1.148618015 0.965004018 1.01262863 0.944788961 1 18.35749732 7.844204085 17.17674321 1.02076714 0.005097423 0 0.087780947 0 0 0.019434014 0 69856059.68 -7.844204085 -1.015669716 MFPTPPSLEQHPAFS(ph)PVMNYK ddPTM_BT-474_Pertuzumab_2h_R1 1 MFPTPPSLEQHPAFSPVMNYK 21 0 F8VRB8;H0YHC1;A0A3B3IS46;A0A3B3IRX3;Q71F56 F8VRB8 MED13L Mediator of RNA polymerase II transcription subunit 13-like 1 MFPTPPSLEQHPAFS(1)PVMNYK 120.27 2.52E-05 100650000 112670 109990 106740 105280 129090 134610 114140 98025 146900 127680 TRUE FALSE 108266.7318 106853.1929 126030.2924 110713.5134 133242.2971 137331.9064 115536.8795 96000.74949 130224.5279 119032.1199 0.909558966 0.897683692 1.058792304 0.930114607 1.119381031 1.153738223 0.970636158 0.806511298 1.094028469 1 16.8609914 7.851986262 19.73356726 0.985612542 0.004917552 0 0.106006481 0 0 0.025070993 0 71119101.59 -7.851986262 -0.980694989 DQWLQDAFHIS(ph)L ddPTM_BT-474_Pertuzumab_2h_R1 3 DQWLQDAFHISL 12 0 Q8N5H3-1;Q8N5H3;Q8N5H3-2 Q8N5H3-1 FAM89B Protein FAM89B 1 DQWLQDAFHIS(1)L;DQWLQDAFHIS(1)L;DQWLQDAFHIS(1)L 132.08 0.00019647 47110000 118912 122822 98437 124556 132386 131225 126582 113451 134260 131725 TRUE FALSE 114264.7876 119319.2368 116226.7556 130984.3501 136644.3159 133878.4594 128131.1484 111108.1972 119019.3677 122803.1484 0.930471157 0.971630112 0.946447686 1.066620455 1.112710201 1.090187517 1.043386509 0.904766683 0.969188243 1 16.90598802 7.85426928 17.42264517 1.003178988 0.005007411 0 0.067497922 0 0 0.016828765 0 71493947.97 -7.85426928 -0.998171577 LQAVEVVITHLAPGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQAVEVVITHLAPGTK 16 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ; 158.17 9.58E-09 319270000 513650 543660 406920 494680 511560 514090 492070 539200 542480 542150 FALSE TRUE 493575.9901 528155.3491 480459.4959 520210.4941 528014.792 524485.252 498092.0999 528065.3316 480899.9447 505429.6976 0.976547268 1.044963032 0.950596093 1.029244021 1.044684937 1.037701691 0.985482456 1.044784931 0.951467527 1 18.94715091 7.859332946 3.918118843 1.010362928 0.977974578 0 0.036843745 0 0 0.007578178 0 72332411.74 -7.859332946 -0.03238835 DYEVELLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DYEVELLR 8 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 ;; 165.52 0.00075332 269703000 439377 470630 363523 461810 414894 447027 479089 482502 485230 510314 FALSE TRUE 422205.6611 457208.0932 429219.6926 485644.0694 428239.4423 456066.1922 484952.2345 472538.1651 430148.7247 475749.9782 0.887452823 0.961025989 0.902195927 1.02079683 0.900135495 0.958625776 1.019342631 0.993248947 0.904148701 1 18.85984406 7.865859077 0.372982036 0.979011181 1.52E-11 0.215722323 0.044237713 90.74763513 1.382161846 0.033054441 62.90222771 73427556.68 -7.865859077 -0.979011181 IIAELEVFER ddPTM_BT-474_Pertuzumab_2h_R1 1 IIAELEVFER 10 0 A0A087WTE6 A0A087WTE6 SRCIN1 0 83.783 0.035752 15994000 19995 20359 21068 25059 18601 20063 27440 26085 24816 29099 FALSE TRUE 19213.57329 19778.38125 24875.45626 26352.29799 19199.31806 20468.68761 27775.81893 25546.33563 21998.99172 27128.09881 0.708253587 0.729073622 0.916962756 0.971402315 0.707728108 0.754519797 1.023876355 0.941692811 0.810930094 1 14.72750032 7.868925047 0.171002976 0.985725032 4.06E-16 0.289716149 0.101675905 78.2037738 0.88181861 0.273766173 19.60084027 73947764.17 -7.868925047 -0.985725032 TKPDSEWIVVTSTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TKPDSEWIVVTSTLR 15 1 A0A0A0MTS7;Q8WZ42-5;Q8WZ42-11;Q8WZ42-4;Q8WZ42-7;Q8WZ42-2;Q8WZ42;Q8WZ42-8;Q8WZ42-13;Q8WZ42-12;A0A0A0MRA3;Q8WZ42-3;Q8WZ42-10;Q8WZ42-9 A0A0A0MTS7 TTN Titin 0 43.184 0.078045 89723000 139230 108750 90683 69337 101440 78068 87921 31483 115870 72821 FALSE TRUE 133788.7377 105648.5565 107071.4353 72915.49088 104702.9097 79646.58845 88997.0035 30832.86505 102716.9234 67888.76881 1.970705023 1.556200802 1.577159775 1.0740435 1.542271447 1.173192412 1.310923811 0.454167392 1.513017914 1 16.0508853 7.86894761 0.280212339 0.923353898 8.236391121 0.463035549 0.289991036 38.66751918 0.5849574 0.318838585 136.6200888 73951605.98 -7.86894761 7.313037223 RSGPTDDGEEEMEEDTVTNGS ddPTM_BT-474_Pertuzumab_2h_R1 2 RSGPTDDGEEEMEEDTVTNGS 21 1 P09661 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ; 247.7 4.16E-29 425150000 520910 578655 468035 555588 555161 606163 545789 565862 572529 590508 FALSE TRUE 500552.2613 562152.326 552619.3359 584261.9633 573018.2577 618420.0312 552468.529 554176.752 507537.9082 550512.3672 0.909247986 1.021143864 1.003827287 1.061305791 1.040881717 1.123353567 1.003553348 1.006656317 0.921937341 1 19.07041545 7.871160069 17.77414884 1.014426522 0.014437222 0 0.059096201 0 0 0.013069748 0 74329304.54 -7.871160069 -0.9999893 DRVEEEHEDESR ddPTM_BT-474_Pertuzumab_2h_R1 2 DRVEEEHEDESR 12 1 D4PHA4;Q86WP2-3;Q86WP2;Q86WP2-2;Q86WP2-4 D4PHA4 GPBP1 Vasculin 0 ; 87.498 0.0063175 51559000 24708.4 31335 21394 27662 28202 28486 29180 26659 28236 30941 FALSE TRUE 23742.76841 30441.35648 25260.37171 29089.63914 29109.14294 29062.00644 29537.11357 26108.48233 25030.76765 28845.33851 0.823105903 1.055330187 0.875717638 1.008469328 1.009145479 1.007511367 1.023982213 0.905119637 0.867757806 1 14.81605057 7.8720957 17.85787248 0.960088544 0.020873509 0 0.076923171 0 0 0.016096319 0 74489609.96 -7.8720957 -0.939215035 EDLVGPEVGAS(ph)PQSGRK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDLVGPEVGASPQSGRK 17 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 EDLVGPEVGAS(0.826)PQS(0.174)GRK 117.37 0.00035617 0 113670 108040 104450 115540 122200 133100 129570 122210 160500 163730 TRUE FALSE 109227.6507 104958.805 123326.4385 121503.0332 126130.674 135791.3732 131155.7164 119686.3208 142280.7129 152640.4213 0.71558798 0.687621301 0.807953997 0.796008241 0.82632551 0.88961608 0.859246295 0.784106332 0.93212998 1 17.21977753 7.873289615 0.081820568 1.133053342 4.45E-15 0.772104662 0.042928133 95.6562812 0.582617134 1.212062145 12.24482318 74694670.32 -7.873289615 -1.133053342 ASVDDDDSGWELSMPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASVDDDDSGWELSMPEK 17 0 Q5VZE5;Q5VZE5-2 Q5VZE5 NAA35 "N-alpha-acetyltransferase 35, NatC auxiliary subunit" 0 123.02 0.0001279 56279000 36169 37333 29854 39327 40715 39276 38839 44362 47859 49001 FALSE TRUE 34755.47549 36268.29939 35249.2819 41356.67118 42024.63495 40070.18763 39314.3233 43445.9092 42426.24696 45682.11862 0.760811375 0.7939277 0.771620997 0.905314211 0.919936207 0.877152567 0.860606392 0.951048474 0.928727656 1 15.47934194 7.878069504 0.166413491 1.008950377 2.80E-12 0.799601759 0.034006554 25.72374276 0.283328952 0.09616478 6.382189451 75521308.17 -7.878069504 -1.008950377 DREPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DREPSK 6 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 67.981 0.088777 31165000 79355 85087 68429 80642 87034 89528 82722 78931 84776 94931 FALSE TRUE 76253.71887 82660.40207 80795.64249 84803.94328 89833.52765 91338.3175 83734.37658 77301.04727 75152.58389 88501.23881 0.861611881 0.934002769 0.912932334 0.958223234 1.0150539 1.032056938 0.946137904 0.873445935 0.849169852 1 16.43341003 7.883715363 20.06834773 0.936920924 0.004690305 0 0.061366179 0 0 0.014579016 0 76509499.92 -7.883715363 -0.932230619 TLNPS(ph)PAGWFVQQHPELELMSSFR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLNPSPAGWFVQQHPELELMSSFR 24 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 TLNPS(1)PAGWFVQQHPELELMSSFR;TLNPS(1)PAGWFVQQHPELELMSSFR 203.64 7.57E-25 1317230000 291770 312742 280545 300250 315684 344730 333400 272482 349670 357930 TRUE FALSE 280367.3058 303822.9044 331245.7222 315745.9385 325838.2626 351700.6768 337480.2489 266855.1515 309976.9275 333687.0823 0.840210247 0.910502445 0.992683684 0.946233628 0.976478503 1.053983494 1.011367436 0.799716758 0.928944943 1 18.34813631 7.892192052 17.67101387 0.941488649 0.004707098 0 0.075035673 0 0 0.017854239 0 78017503.97 -7.892192052 -0.93678155 LFDHPES(ph)PTPNPTEPLFLAQAEVYK ddPTM_BT-474_Pertuzumab_2h_R1 5 LFDHPESPTPNPTEPLFLAQAEVYK 25 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LFDHPES(0.499)PT(0.499)PNPT(0.001)EPLFLAQAEVYK;LFDHPES(0.498)PT(0.498)PNPT(0.003)EPLFLAQAEVYK;LFDHPES(0.641)PT(0.359)PNPTEPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK 345.26 5.57E-103 3630888000 1225944 1225478 1188719 1206546 1343491 1336874 1537489 1359571 1781505 1697288 TRUE FALSE 1178032.753 1190528.567 1403546.966 1268815.984 1386705.608 1363906.508 1556305.25 1331495.384 1579276.021 1582329.172 0.744492849 0.75238995 0.887013266 0.801866013 0.876369868 0.861961299 0.983553408 0.841478124 0.99807047 1 20.59361832 7.892460007 0.148123236 1.028622596 3.35E-11 0.690048255 0.050232086 37.33572904 0.374067466 0.172611004 8.189342756 78065654.82 -7.892460007 -1.028622596 RAS(ph)PPMGMPSAWWLQNEAGCLFAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RASPPMGMPSAWWLQNEAGCLFAAR 25 1 E9PN18;E9PMU7;E9PL19 E9PN18 PUF60 1 RAS(1)PPMGMPSAWWLQNEAGCLFAAR 102.45 0.0030159 117080000 46434 39813 34226 33422 36958 35225 41393 38915 38428 37445 TRUE FALSE 44619.30794 38677.57222 40411.39955 35146.91343 38146.78763 35937.27363 41899.57992 38111.39165 34065.81454 34908.8168 1.278167295 1.107959987 1.157627306 1.00682053 1.092755101 1.029461234 1.200257808 1.091741146 0.975851308 1 15.09130384 7.892680669 0.924742513 1.072994831 97.74333794 0.480308676 0.066078647 767.3352782 1.85195088 0.020086855 156489.4884 78105329.61 -7.892680669 96.67034311 SSSPELVTHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 151.15 3.36E-05 558900000 531809 579368 477683 548618 576084 608108 574948 629123 703434 685549 FALSE TRUE 511025.3163 562844.9919 564010.9441 576932.2407 594614.265 620404.3604 581984.3856 616131.3902 623583.1214 639116.1556 0.799581284 0.880661499 0.882485819 0.902703266 0.930369636 0.970722387 0.910608159 0.964036638 0.97569607 1 19.28571863 7.893399649 0.235499812 0.991383372 1.97E-13 0.878171129 0.019724928 15.23436647 0.21128995 0.027126308 5.811686285 78234741.04 -7.893399649 -0.991383372 AEPDHMVLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AEPDHMVLGK 10 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 128.27 0.00033406 430690000 595700 647330 565470 665130 662640 629300 750420 739470 806740 843400 FALSE TRUE 572419.3854 628868.7822 667663.0078 699457.439 683954.4174 642024.8772 759603.8644 724199.6861 715162.2573 786275.7668 0.728013516 0.799806898 0.849146109 0.889582852 0.869865824 0.816539062 0.966078183 0.921050497 0.909556529 1 19.58467587 7.896881111 0.172817797 0.998986341 2.12E-13 0.770570137 0.036735372 26.97818982 0.304061764 0.092195295 6.957791671 78864419.59 -7.896881111 -0.998986341 TEWLDGKHVVFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TEWLDGKHVVFGK 13 1 P62937;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 ; 155.08 2.45E-05 8509400000 24528000 24617000 16002200 14664500 19905600 24136000 18651200 20358200 22735000 17707700 FALSE TRUE 23569418.64 23914947.26 18894153.51 15421336.6 20545881.7 24624046.46 18879458.96 19937796.06 20154218.11 16508341.71 1.427727816 1.448658362 1.144521591 0.934154192 1.244575746 1.491612355 1.143631462 1.207740693 1.220850554 1 23.97669187 7.902347044 0.024315879 6.09E-06 2.882071947 0.224094134 0.155389905 3783.980685 7.186155228 297.3621539 604.2506143 79863261.79 -7.902347044 2.882065862 S(ph)ESEVEEAAAIIAQRPDNPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SESEVEEAAAIIAQRPDNPR 20 1 Q16643;Q16643-3;Q16643-2;D6R9W4;D6R9Q9 Q16643 DBN1 Drebrin 1 S(0.728)ES(0.272)EVEEAAAIIAQRPDNPR;S(0.864)ES(0.136)EVEEAAAIIAQRPDNPR 226.08 1.23E-24 137616000 94768 93075 103281 124928 97225 107418 106523 127749 134330 144892 TRUE FALSE 91064.36179 90420.59213 121946.1742 131375.5491 100352.3304 109590.0656 107826.6603 125110.9385 119081.4216 135078.3358 0.674159637 0.669393738 0.902781142 0.972587856 0.742919505 0.81130749 0.798252804 0.926210245 0.881573058 1 17.04343678 7.906369751 0.145422748 0.993411276 8.48E-32 0.443664731 0.083337885 74.79438244 0.735825422 0.341872989 15.50688499 80606441.85 -7.906369751 -0.993411276 NLDDGIDDER ddPTM_BT-474_Pertuzumab_2h_R1 5 NLDDGIDDER 10 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;; 227.27 6.14E-09 12596060000 2697250 2596010 2608980 2876280 2786460 2661560 2995670 3207970 3423930 3453760 FALSE TRUE 2591838.488 2521974.337 3080480.722 3024725.155 2876089.016 2715378.567 3032331.906 3141724.298 3035259.821 3219833.759 0.804960343 0.783262282 0.956720425 0.939404138 0.893241463 0.843328808 0.941766604 0.975741151 0.942675942 1 21.61855477 7.912464928 0.226286621 0.983495682 2.98E-23 0.552566381 0.046981738 39.20803098 0.527642635 0.075035214 14.10618149 81745702.09 -7.912464928 -0.983495682 RLS(ph)GLSSVGHNWR ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSGLSSVGHNWR 13 1 Q14D93;A0A0G2JR24;Q8WYQ4 Q14D93 C22orf15 Uncharacterized protein C22orf15 1 RLS(0.966)GLS(0.017)S(0.017)VGHNWR;RLS(0.997)GLS(0.001)S(0.001)VGHNWR;RLS(0.988)GLS(0.006)S(0.006)VGHNWR 62.378 0.036251 590050000 698840 456240 397779 255819 441207 336661 366236 324293 468040 343676 TRUE FALSE 671528.5602 443228.4819 469666.5138 269021.8492 455398.8238 343468.5161 370718.1057 317596.2362 414910.0614 320398.5184 2.095916559 1.383366203 1.46588229 0.839647607 1.421351216 1.072004071 1.157053121 0.99125376 1.294981211 1 18.28950795 7.945678336 0.782640094 1.111257597 200 0.732144205 0.17509702 189.5926709 0.775768237 0.054430235 66638.80154 88242608.23 -7.945678336 198.8887424 up VKEEPPS(ph)PPQS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 2 VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR 69.256 0.027429 5757650000 2227090 2311670 1926340 2101780 2227540 2334100 2188760 2442900 2645530 2438040 TRUE FALSE 2140052.861 2245743.435 2274472.489 2210253.118 2299190.847 2381297.101 2215546.7 2392453.261 2345220.525 2272909.379 0.941547815 0.988047942 1.000687713 0.972433454 1.011562919 1.047686777 0.974762443 1.052595094 1.031814355 1 21.11610873 7.94675429 0.369400403 1.026148333 6.69E-15 0.463591422 0.0243992 52.46644565 0.755924566 0.018474791 37.95864755 88461498.14 -7.94675429 -1.026148333 AAYEAELGDARK ddPTM_BT-474_Pertuzumab_2h_R1 2 AAYEAELGDARK 12 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 124.86 0.00050598 2433250000 1623910 1567910 1070350 1152340 1362970 1550320 1289960 1407220 1504360 1320210 FALSE TRUE 1560445.802 1523194.742 1263786.055 1211812.405 1406811.168 1581668.533 1305746.916 1378160.415 1333591.36 1230791.001 1.267839788 1.237573837 1.026808007 0.984580164 1.143013856 1.285082952 1.060900604 1.119735531 1.083523814 1 20.23115437 7.948720775 0.016252816 1.15E-06 2.49304855 0.223057088 0.092320703 8602.983302 10.87570763 655.4314672 1057.081609 88862959.85 -7.948720775 2.4930474 RGEIQHR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGEIQHR 7 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 91.041 0.02677 19329000 27896 24952 22916 27473 24004 29863 28057 24922 29914 29071 FALSE TRUE 26805.79348 24240.39339 27057.43096 28890.88482 24776.11046 30466.85032 28400.36996 24407.35199 26518.28813 27101.99528 0.989070849 0.894413608 0.998355681 1.066005825 0.914180311 1.124155252 1.047906978 0.900573989 0.978462577 1 14.72611145 7.951789562 7.944893507 0.988414999 1.136126608 0 0.070979329 0 0 0.015884677 0 89493102.11 -7.951789562 0.147711609 SSS(ph)PGKPQAVSSLNSSHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSPGKPQAVSSLNSSHSR 19 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.003)S(0.102)S(0.895)PGKPQAVSSLNSSHSR;S(0.295)S(0.295)S(0.41)PGKPQAVSSLNSSHSR;S(0.011)S(0.148)S(0.841)PGKPQAVSSLNSSHSR 238.07 1.86E-24 1702360000 1132330 1412620 1037130 1299670 1241660 1348180 1366450 1421900 1506730 1590680 TRUE FALSE 1088077.292 1372333.461 1224562.462 1366746.124 1281599.122 1375441.123 1383173.024 1392537.268 1335692.327 1482941.827 0.733728911 0.925412876 0.825765677 0.921645138 0.864227509 0.927508482 0.932722376 0.939037016 0.900704467 1 20.50003057 7.956480976 0.233424447 0.965871658 3.46E-34 0.58807085 0.044843277 34.63409711 0.465699613 0.057965279 12.7989079 90465080.88 -7.956480976 -0.965871658 S(ph)PTGPSNSFLANMGGTVAHK ddPTM_BT-474_Pertuzumab_2h_R1 16 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.832)PT(0.165)GPS(0.002)NSFLANMGGTVAHK;S(0.887)PT(0.113)GPSNSFLANMGGTVAHK;S(0.986)PT(0.014)GPSNSFLANMGGTVAHK;S(0.973)PT(0.027)GPSNSFLANMGGTVAHK;S(0.82)PT(0.18)GPSNSFLANMGGTVAHK;S(0.971)PT(0.029)GPSNSFLANMGGTVAHK;S(0.841)PT(0.159)GPSNSFLANMGGTVAHK;S(0.572)PT(0.428)GPSNSFLANMGGTVAHK;S(0.847)PT(0.152)GPSNSFLANMGGTVAHK;S(0.538)PT(0.452)GPS(0.004)NS(0.006)FLANMGGTVAHK;S(0.707)PT(0.293)GPSNSFLANMGGTVAHK;S(0.963)PT(0.037)GPSNSFLANMGGTVAHK;S(0.965)PT(0.035)GPSNSFLANMGGTVAHK;S(0.9)PT(0.1)GPSNSFLANMGGTVAHK;S(0.611)PT(0.389)GPSNSFLANMGGTVAHK;S(0.68)PT(0.32)GPSNSFLANMGGTVAHK 307.53 1.49E-56 44462650000 8176210 7904882 7599948 9019350 8516378 8428692 9141966 9904070 10441882 10897339 TRUE FALSE 7856674.674 7679442.505 8973427.664 9484839.734 8790315.033 8599125.927 9253848.115 9699547.493 9256563.331 10159252.52 0.773351647 0.755906253 0.883276367 0.933615905 0.865252145 0.846432935 0.910878836 0.954750113 0.911146102 1 23.27629092 7.958053963 0.186247794 0.989657558 4.01E-22 0.704811888 0.039476836 31.52932547 0.368053241 0.088900523 8.899872094 90793333.71 -7.958053963 -0.989657558 VKGDVDVSVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VKGDVDVSVPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 66.498 0.057042 308410000 997670 1040400 1003100 1186100 1048100 1083700 1232500 1240900 1488100 1494400 FALSE TRUE 958679.9534 1010728.811 1184382.484 1247314.763 1081813.088 1105613.157 1247583.704 1215274.981 1319177.127 1393182.957 0.688122079 0.725481751 0.850127026 0.895298609 0.776504682 0.793587914 0.895491649 0.872301068 0.946880035 1 20.4099533 7.962929865 0.105380366 1.080754374 2.17E-12 0.727134936 0.048577627 66.90573156 0.499019245 0.547208652 10.47998768 91818430.61 -7.962929865 -1.080754374 ALKEPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 ALKEPPR 7 1 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;; 103.29 0.0076701 4355110000 4694840 4860350 4413110 5163450 4859560 4951340 5435020 5644000 6242300 6186000 FALSE TRUE 4511360.462 4721737.577 5210657.146 5429936.273 5015872.161 5051459.487 5501535.401 5527449.428 5533700.274 5767016.71 0.782269359 0.818748725 0.903527319 0.941550293 0.869751626 0.875922464 0.953965573 0.958459062 0.959542958 1 22.45939377 7.963585762 0.204469755 0.997020757 1.82E-13 0.781895649 0.030682908 25.28864789 0.313744185 0.059105208 8.116449967 91957204.89 -7.963585762 -0.997020757 HFDKS(ph)PTK ddPTM_BT-474_Pertuzumab_2h_R1 1 HFDKSPTK 8 1 H3BPB0;H3BPM0;H3BS25;Q9BY12-2;Q9BY12 H3BPB0 SCAPER S phase cyclin A-associated protein in the endoplasmic reticulum 1 HFDKS(0.801)PT(0.199)K 69.451 0.032634 260620000 350150 269870 253130 248450 265960 224120 307090 213980 344500 303120 TRUE FALSE 336465.7509 262173.5718 298876.2218 261272.5343 274514.8449 228651.86 310848.2593 209561.2382 305393.8043 282589.4124 1.19065236 0.927754404 1.057634181 0.9245659 0.971426504 0.809131022 1.099999666 0.741574981 1.08069797 1 18.10834789 7.969774978 0.981760845 0.93433521 199.9784131 0.258670266 0.11135264 1749.304378 2.728788981 0.031032976 782629.6557 93277087.71 -7.969774978 199.0440779 LEIEPEWAYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEIEPEWAYGK 11 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 214.58 3.13E-11 224660000 541210 547460 501890 568830 605960 520520 623630 692220 681340 776530 FALSE TRUE 520058.9149 531846.9768 592592.6875 598187.3845 625451.2537 531045.271 631262.1705 677925.4151 603997.1396 723934.9314 0.718377982 0.734661299 0.818571755 0.826299932 0.863960594 0.733553871 0.871987444 0.936445232 0.834325177 1 19.46550051 7.970538278 0.070591943 1.18861323 1.79E-11 0.674585458 0.049076992 143.7869716 0.752391887 2.200798867 16.9703039 93441172.25 -7.970538278 -1.18861323 NDVLDSLGISPDLLPEDFVR ddPTM_BT-474_Pertuzumab_2h_R1 1 NDVLDSLGISPDLLPEDFVR 20 0 Q9UBE0;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 203.99 2.34E-21 11712000 16664 14724 12585 17175 18988 15872 16784 18385 20783 20966 FALSE TRUE 16012.75246 14304.08594 14859.38945 18061.40381 19598.76626 16192.94271 16989.40761 18005.34333 18423.80097 19545.95415 0.819236162 0.731818249 0.7602284 0.924048203 1.002701946 0.828454963 0.869203288 0.921180066 0.942588979 1 14.25458239 7.972627255 0.171766235 0.997527783 1.67E-10 0.499017067 0.063219761 51.34601986 0.563046585 0.168523609 13.19085676 93891711.29 -7.972627255 -0.997527782 NPVWYQALTHGLNEEQR ddPTM_BT-474_Pertuzumab_2h_R1 3 NPVWYQALTHGLNEEQR 17 0 O95373 O95373 IPO7 Importin-7 0 ;; 212.55 1.47E-12 1853376000 2798599 2641782 1835615 1770570 2397423 2460125 2226574 2182971 2599475 2008298 FALSE TRUE 2689226.657 2566440.964 2167351.464 1861949.33 2474538.288 2509870.413 2253823.479 2137891.886 2304393.496 1872274.188 1.436342324 1.370761281 1.157603666 0.994485392 1.321675161 1.340546395 1.203789217 1.141869017 1.230799159 1 20.8363603 7.973766247 0.025263969 4.98E-06 2.886168134 0.347098293 0.115418938 2537.521321 4.947951724 193.7695403 408.100484 94138277.47 -7.973766247 2.886163153 ELKIDIIPNPQER ddPTM_BT-474_Pertuzumab_2h_R1 4 ELKIDIIPNPQER 13 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;; 150.34 4.03E-05 2048490000 4042890 4453370 2003250 2146230 2898080 4395810 2913500 2950760 3401620 2500660 FALSE TRUE 3884889.389 4326364.248 2365281.837 2256997.188 2991299.375 4484696.29 2949156.285 2889825.775 3015482.358 2331288.071 1.666413275 1.855782776 1.014581538 0.968133117 1.283110145 1.923698897 1.265032975 1.239583306 1.293483373 1 21.15269585 7.979209927 0.036184424 2.30E-06 3.467659172 0.175095653 0.300264712 1935.158069 5.363390686 149.3599519 433.2534844 95325683.37 -7.979209927 3.467656875 TPVQYSQQQNS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 6 TPVQYSQQQNSPQK 14 0 P46013 P46013 MKI67 Antigen KI-67 1 TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK 343.53 2.43E-69 2283720000 2015180 1148471 867574 926187 1382055 677656 811265 1046505 646246 606460 TRUE FALSE 1936424.538 1115717.732 1024363.921 973987.6221 1426510.054 691358.6686 821193.5037 1024894.306 572886.8634 565383.924 3.424972758 1.973380714 1.811802348 1.722701302 2.523082093 1.222812746 1.452452871 1.812740445 1.013270521 1 19.10887134 7.980300379 0.687781716 1.531908497 199.9999999 0.647508997 0.416122877 168.8280231 0.963329966 0.152742673 51376.35363 95565333.37 -7.980300379 198.4680914 SLEPEPQQSLEDGS(ph)PAKGEPSQAWR ddPTM_BT-474_Pertuzumab_2h_R1 5 SLEPEPQQSLEDGSPAKGEPSQAWR 25 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 SLEPEPQQS(0.001)LEDGS(0.999)PAKGEPSQAWR;SLEPEPQQS(0.012)LEDGS(0.988)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQS(0.004)LEDGS(0.996)PAKGEPSQAWR 159.1 1.45E-11 8385720000 4536220 4329330 4078600 4758590 4686240 4799980 5282760 5270810 5998450 6136580 TRUE FALSE 4358939.507 4205861.747 4815693.748 5004181.4 4836977.166 4897038.884 5347411.997 5161965.932 5317531.104 5720943.971 0.761926621 0.73516919 0.841765585 0.874712534 0.845485848 0.855984416 0.934707983 0.902292691 0.929484912 1 22.44782178 7.981101028 0.144008006 1.026493997 4.22E-21 0.873585854 0.026869209 22.9673238 0.21988487 0.105760942 4.881899034 95741676.6 -7.981101028 -1.026493997 T(ph)TPNSGDVQVTEDAVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTPNSGDVQVTEDAVR 16 0 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 T(0.5)T(0.5)PNSGDVQVTEDAVR 97.836 0.017009 120660000 126510 130850 129630 147340 145920 145250 157830 151050 183980 194040 TRUE FALSE 121565.8493 127118.2861 153057.0246 154944.2351 150613.6493 148187.0545 159761.5708 147930.7647 163095.3617 180897.498 0.672015095 0.702708924 0.846098074 0.856530559 0.832591114 0.819176916 0.883160754 0.817760148 0.901589925 1 17.46481293 7.990009769 0.131400516 1.003910297 8.06E-28 0.755799737 0.043964151 46.70528157 0.415058507 0.244952142 8.707479332 97725920.41 -7.990009769 -1.003910297 ESDLFLLDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESDLFLLDSR 10 0 H0Y4B5;B1AKZ9;B1AL00;P18075 H0Y4B5 BMP7 Bone morphogenetic protein 7 0 ; 143.21 8.00E-05 58723000 124589 147538 127222 150253 142307 141339 173452 160256 182951 197604 FALSE TRUE 119719.9241 143330.3607 150213.8454 158007.5753 146884.4339 144196.9714 175574.7575 156946.6576 162183.1695 184220.1051 0.649874367 0.778038644 0.815404189 0.857710809 0.797331181 0.782742857 0.953070553 0.851951841 0.880377141 1 17.49107099 7.993233029 0.118421921 1.039742713 8.37E-15 0.709508334 0.049996952 55.06129199 0.449534906 0.355076466 9.434031321 98453923.65 -7.993233029 -1.039742713 LIMLVDDFYYGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LIMLVDDFYYGR 12 0 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 0 147.12 0.00070875 0 57303 63156 33352 40597 59449 48665 46615 50133 47721 43435 FALSE TRUE 55063.53541 61354.85272 39379.44831 42692.21604 61361.23108 49649.03964 47185.48831 49097.73603 42303.91214 40493.10876 1.359824847 1.515192451 0.972497531 1.054308186 1.515349968 1.226110841 1.165272061 1.21249609 1.044718804 1 15.30538879 7.994252934 0.028938155 1.75E-06 2.953074486 0.247400587 0.165295471 2290.502136 5.088878768 168.1978587 395.5922665 98685406.4 -7.994252934 2.953072738 ERPGSEEPPAEPVSFYTQPFSHYGQALCVSFPQPCR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPGSEEPPAEPVSFYTQPFSHYGQALCVSFPQPCR 36 1 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 325.06 8.15E-111 385620000 60267 63316 53252 73335 61801 65202 79854 68771 82602 90397 FALSE TRUE 57911.69901 61510.28967 62875.82098 77119.82814 63788.88529 66520.42911 80831.27714 67350.85482 73225.36726 84274.33067 0.687180765 0.729881675 0.746085083 0.915104606 0.756919513 0.789332037 0.959144694 0.799185876 0.868892896 1 16.36280564 7.994687233 0.085093859 1.113875434 2.39E-13 0.601065266 0.063005602 122.969302 0.757589035 1.390565148 16.0328431 98784142.23 -7.994687233 -1.113875434 AEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_BT-474_Pertuzumab_2h_R1 8 AEVPGATGGDSPHLQPAEPPGEPR 24 0 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 1 AEVPGATGGDS(1)PHLQPAEPPGEPR;AEVPGATGGDS(1)PHLQPAEPPGEPR;AEVPGAT(0.001)GGDS(0.999)PHLQPAEPPGEPR;AEVPGAT(0.041)GGDS(0.959)PHLQPAEPPGEPR;AEVPGAT(0.005)GGDS(0.995)PHLQPAEPPGEPR;AEVPGAT(0.1)GGDS(0.9)PHLQPAEPPGEPR;AEVPGAT(0.076)GGDS(0.924)PHLQPAEPPGEPR;AEVPGAT(0.04)GGDS(0.96)PHLQPAEPPGEPR 241.57 8.81E-38 32595090000 4581769 4670756 4349799 5537188 4948301 5105355 4870928 4923842 5188491 5317372 TRUE FALSE 4402708.402 4537550.612 5135904.44 5822962.936 5107467.596 5208588.776 4930539.874 4822162.942 4599515.254 4957221.658 0.888140314 0.915341481 1.036044945 1.174642438 1.030308497 1.050707258 0.994617593 0.972755159 0.927841354 1 22.24110034 7.99481535 24.88374136 1.002685685 0.005762898 0 0.078147633 0 0 0.018545267 0 98813287.93 -7.99481535 -0.996922787 RAADEDWDS(ph)ELEDDLLGEDLLSGK ddPTM_BT-474_Pertuzumab_2h_R1 7 RAADEDWDSELEDDLLGEDLLSGK 24 1 Q96EV2;A8MTF7;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 1 RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK 192.07 4.89E-18 445265000 260454.4 239709.4 179081.3 195633.3 219238.2 233878.8 202767 238068.7 236787.2 213024.6 TRUE FALSE 250275.5541 232873.1226 211445.2746 205729.9581 226290.1958 238607.9896 205248.5232 233152.4982 209908.1097 198596.2541 1.260222934 1.172595745 1.064699209 1.035920637 1.13944846 1.20147276 1.033496448 1.174002497 1.056959058 1 17.59947889 7.99906004 0.014796379 3.25E-06 2.460950781 0.323844981 0.067793178 8221.437074 9.392380207 626.1645261 970.9231324 99783800.17 -7.99906004 2.46094753 LIEIHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LIEIHGK 7 0 A0A0G2JP90;A0A087WW46;J3KN36;A0A0G2JN29;A0A087X117;Q5JPE7-3;Q5JPE7-2;Q15155;P69849;Q5JPE7 A0A0G2JP90 NOMO1;NOMO3;NOMO2 Nodal modulator 2;Nodal modulator 1;Nodal modulator 3 0 ; 94.262 0.01433 349720000 817520 1231490 1111520 1287370 919290 1186190 1149850 1082990 1314290 1365320 FALSE TRUE 785570.4146 1196369.111 1312396.39 1353811.32 948859.7977 1210175.575 1163922.208 1060625.878 1165097.309 1272845.66 0.617176488 0.939916872 1.031072683 1.063609959 0.745463356 0.950763798 0.914425248 0.833271394 0.915348455 1 20.27962606 7.999650015 0.013154204 1.666456685 5.15E-06 0.079060284 0.123967899 30952.41973 31.4483854 1636.812814 2417.676316 99919445.44 -7.999650015 -1.666451535 DEPEEAELILHDALR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEPEEAELILHDALR 15 0 Q6DKK2;K7EJA1 Q6DKK2 TTC19 "Tetratricopeptide repeat protein 19, mitochondrial" 0 ; 145.43 4.06E-06 54083000 78878 80813 81595 103986 72761 81005 86682 91828 96523 102359 FALSE TRUE 75795.36056 78508.29236 96341.03157 109352.7299 75101.42364 82642.9766 87742.84025 89931.71971 85566.1137 95426.13376 0.79428305 0.822712702 1.009587497 1.145941113 0.78701107 0.866041338 0.919484389 0.942422334 0.896673797 1 16.5420968 7.999756034 0.01281986 1.703775556 5.98E-06 0.072944932 0.102062768 27992.00171 27.71990449 1521.146449 2224.701081 99943840.57 -7.999756034 -1.703769579 SVDEALR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVDEALR 7 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ;;; 198.32 0.00093559 10073700000 11833500 12871600 10936800 12975300 12293500 10395600 13527000 12987500 12920700 13695300 FALSE TRUE 11371033.74 12504514.57 12913323.05 13644956.79 12688931.59 10605806.15 13692547.47 12719303.59 11453996.3 12767705.13 0.89060905 0.979386228 1.011405175 1.06870864 0.993830251 0.830674428 1.072436067 0.996209065 0.897106895 1 23.6059959 7.999805612 0.004701521 1.363838512 0.571358782 0.000166001 0.07419548 843812.1347 306.8324419 24112.75482 27723.16193 99955250.53 -7.999805612 -0.79247973 DMFEEALR ddPTM_BT-474_Pertuzumab_2h_R1 2 DMFEEALR 8 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 120.46 0.0034852 888290000 1546560 1702200 1545430 1780950 1624650 1499000 1751410 1757390 1834160 1945870 FALSE TRUE 1486118.725 1653654.923 1824723.579 1872865.043 1676908.343 1529310.807 1772844.279 1721099.282 1625953.846 1814074.492 0.819215932 0.91156947 1.005870259 1.032408014 0.924387808 0.843025363 0.97727204 0.948747855 0.896299382 1 20.79080227 7.99984867 0.008236248 1.784954785 2.46E-06 0.091756128 0.063737431 62557.51345 39.84015077 3818.555887 4875.371511 99965161.06 -7.99984867 -1.784952328 NNSLWDR ddPTM_BT-474_Pertuzumab_2h_R1 4 NNSLWDR 7 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ;;; 157.58 0.0034116 1645920000 1203430 1325820 1168850 1372100 1219300 1176190 1346640 1281740 1531900 1466820 FALSE TRUE 1156398.625 1288008.912 1380087.196 1442914.245 1258519.892 1199973.368 1363120.583 1255271.621 1358005.134 1367470.975 0.845647656 0.941891225 1.009225952 1.055169925 0.920326585 0.877512861 0.996818659 0.917951199 0.993077849 1 20.38307878 7.999868897 0.006692494 1.83331803 1.42E-05 0.089265092 0.059522052 105096.7568 54.39760083 6744.121868 8225.395196 99969816.87 -7.999868897 -1.833303861 ILFIFIDSDHTDNQR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILFIFIDSDHTDNQR 15 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 341.27 1.98E-69 4904600000 738610 926680 760180 1111030 894570 982010 989570 731040 1049670 1097050 FALSE TRUE 709744.3046 900251.9937 897561.4361 1168370.391 923344.6565 1001866.915 1001680.654 715943.7685 930515.8622 1022745.826 0.69395962 0.880230425 0.877599706 1.142385881 0.902809508 0.979585435 0.979403316 0.700021208 0.909821227 1 19.96401622 7.999869739 0.009020509 1.705388073 2.02E-05 0.05049481 0.124938527 99524.93765 69.41034398 5735.850508 7495.5173 99970010.83 -7.999869739 -1.705367871 NLSLCFEGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 NLSLCFEGSPR 11 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 NLSLCFEGS(1)PR;NLSLCFEGS(1)PR 134.37 0.00014914 124808000 147346 169042 158898 184795 135783 161145 169337 199492 176672 206960 TRUE FALSE 141587.5554 164221.0877 187614.4033 194332.2921 140150.5835 164403.4623 171409.3969 195372.4205 156616.9352 192942.4149 0.73383323 0.851140418 0.972385483 1.007203586 0.726385557 0.852085647 0.88839666 1.012594461 0.811728905 1 17.5578108 7.999888247 0.024500099 1.549625308 6.80E-05 0.157120076 0.095274006 4133.127204 7.786414556 170.5205577 352.2078186 99974271.31 -7.999888247 -1.54955729 KQVENER ddPTM_BT-474_Pertuzumab_2h_R1 6 KQVENER 7 1 Q9H307 Q9H307 PNN Pinin 0 ;;;;; 153.78 0.0027629 4027210000 2860320 2997870 2574760 3069570 2887230 2668010 3238940 3247500 3313570 3614260 FALSE TRUE 2748535.532 2912373.683 3040076.407 3227990.876 2980100.375 2721958.99 3278579.117 3180437.99 2937427.425 3369462.951 0.815719173 0.864343584 0.902243607 0.958013465 0.884443728 0.807831702 0.973027205 0.943900567 0.871779114 1 21.68408723 7.999903041 0.020893906 1.600862608 6.22E-07 0.35198195 0.049944451 3328.732835 5.357042455 150.0782179 278.7000524 99977676.94 -7.999903041 -1.600861987 LFQQILSGVDYCHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LFQQILSGVDYCHR 14 0 Q13131-2;Q13131;Q96E92 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 0 ; 115.82 0.00039755 283510000 185641 216960 210760 185603 218575 175083 262369 209648 236830 258095 FALSE TRUE 178385.9445 210772.5132 248849.0203 195181.9931 225605.6634 178623.2982 265579.9503 205318.6955 209946.0513 240613.9958 0.741378089 0.875977777 1.034225044 0.811183042 0.937624857 0.74236454 1.103759361 0.853311524 0.872542973 1 17.87636104 7.999903595 0.020133077 1.598368151 3.60E-06 0.117402351 0.108051977 7449.557083 11.55596826 339.3249946 616.1373573 99977804.49 -7.999903595 -1.598364553 GNDPLTSS(ph)PGRS(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNDPLTSSPGRSSR 14 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 2 GNDPLT(0.047)S(0.455)S(0.499)PGRS(0.568)S(0.432)R 57.745 0.065072 170660000 166390 195060 162770 238710 172980 210570 224420 192910 163820 247270 TRUE FALSE 159887.2948 189497.0798 192186.1598 251029.8517 178544.0588 214827.8697 227166.5191 188926.3411 145223.8404 230522.1827 0.693587459 0.822034034 0.833699202 1.088961803 0.774520078 0.931918426 0.985443208 0.819558183 0.629977726 1 17.81454606 7.999918372 0.014506033 1.581271759 5.99E-07 0.056939731 0.131931841 25661.53244 28.73966278 1261.210128 1938.999864 99981206.16 -7.999918372 -1.58127116 GQPGDIYHQTWAR ddPTM_BT-474_Pertuzumab_2h_R1 3 GQPGDIYHQTWAR 13 0 P04062-4;P04062-5;P04062-2;P04062;A0A0G2JNZ5;A0A0G2JNZ0;A0A0G2JLB3;P04062-3 P04062-4 GBA Glucosylceramidase 0 ;; 145.52 4.18E-05 2051890000 986840 1237490 1051360 1386920 1148430 1200870 1310870 1121330 1221380 1444560 FALSE TRUE 948273.2018 1202197.997 1241364.139 1458499.107 1185370.294 1225152.414 1326912.819 1098174.144 1082734.063 1346718.665 0.70413608 0.892686816 0.921769462 1.083002074 0.88019148 0.909731517 0.985293257 0.815444363 0.803979399 1 20.36101707 7.999939264 0.009281724 1.702490341 1.01E-06 0.066985473 0.099687218 70659.24937 50.70077183 4049.070861 5332.474749 99986016.05 -7.999939264 -1.702489327 ELVEFAQDDDRLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELVEFAQDDDRLR 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 270.79 4.11E-32 4069040000 1765060 2105360 1569850 2053060 1854250 1874410 1888940 2065620 2141270 2244970 FALSE TRUE 1696079.504 2045317.194 1853556.816 2159018.673 1913893.635 1912311.854 1912057.413 2022964.225 1898202.007 2092916.182 0.810390554 0.977257098 0.885633563 1.031583917 0.914462629 0.913706851 0.913585278 0.9665768 0.906965134 1 20.9970831 7.999940466 0.010903276 1.749644072 1.13E-05 0.168795806 0.054953493 21180.00097 17.84629307 1216.951893 1681.589705 99986292.66 -7.999940466 -1.749632808 ALETNTHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALETNTHVK 9 0 Q9NYL9;H0YKU1;H0YNJ8;G5EA42;Q9NZR1 Q9NYL9 TMOD3;TMOD2 Tropomodulin-3;Tropomodulin-2 0 ; 107.24 0.002805 1055030000 595670 658800 566350 605100 654360 613250 682650 663040 680250 763000 FALSE TRUE 572390.5579 640011.669 668702.0434 636329.2835 675408.0837 625650.3352 691004.4749 649347.9923 603030.8718 711321.3304 0.80468634 0.899750425 0.94008434 0.8945736 0.949511922 0.879560767 0.971437866 0.912875749 0.847761548 1 19.4401419 7.999951658 0.0141886 1.675411751 1.44E-06 0.285026374 0.046761366 8889.864098 9.739171019 465.181809 708.4899413 99988869.38 -7.999951658 -1.675410312 VEGFLEEDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 VEGFLEEDRR 10 1 A0A0G2JM25;A0A0G2JNK1;K7ERG0;A0A0G2JMB6;A0A0G2JPH3;A0A0G2JNK3;Q8WX94;Q8WX94-2;Q8WX94-3;Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 A0A0G2JM25;Q9NX02 NLRP7;NLRP2 "NACHT, LRR and PYD domains-containing protein 7;NACHT, LRR and PYD domains-containing protein 2" 0 ;;; 212.82 5.39E-08 2504210000 599990 685430 551960 639930 625450 527460 739770 641110 692140 719330 FALSE TRUE 576541.7275 665882.2075 651711.4503 672956.864 645568.1673 538125.6026 748823.5266 627870.8545 613571.1689 670609.1384 0.859728409 0.992951288 0.971820115 1.003500885 0.962659365 0.802442991 1.116631856 0.936269458 0.91494603 1 19.35511262 7.99995199 0.009232338 1.514530616 0.336064626 0.02993743 0.080364416 77620.76445 55.40222273 3081.351374 4052.040169 99988945.96 -7.99995199 -1.17846599 SDEGQLS(ph)PATR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDEGQLSPATR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 SDEGQLS(0.999)PAT(0.001)R;SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR 187.47 3.75E-06 2695620000 1554060 1768930 1604520 1973160 1771020 1767200 1790180 1688740 1936330 2087910 TRUE FALSE 1493325.617 1718481.848 1894492.456 2074995.024 1827986.467 1802933.995 1812088.758 1653866.929 1716525.936 1946493.996 0.767187374 0.882860082 0.973284511 1.066016658 0.939117444 0.926246882 0.930950089 0.849664542 0.881855243 1 20.89244646 7.999959766 0.006618881 1.768007203 2.16E-06 0.072095237 0.0759636 150767.4208 77.1814576 9340.934569 11367.63223 99990736.21 -7.999959766 -1.768005045 FVDGEWYR ddPTM_BT-474_Pertuzumab_2h_R1 6 FVDGEWYR 8 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 174.21 0.00063579 4272540000 3126330 3399490 2911310 3403920 3368070 2838520 3644900 3372680 3405300 3728470 FALSE TRUE 3004149.567 3302539.874 3437448.479 3579596.719 3476407.03 2895916.819 3689507.377 3303032.979 3018744.62 3475937.406 0.86427033 0.950114886 0.988927037 1.029821973 1.000135107 0.833132615 1.06144241 0.950256749 0.868469212 1 21.72897067 7.999962697 0.003629967 1.874411709 1.73E-05 0.016799086 0.072021906 737530.8665 207.2817477 50707.5784 56469.54125 99991410.92 -7.999962697 -1.874394361 TPALAALAALGAPGPAPTAAS(ph)SP ddPTM_BT-474_Pertuzumab_2h_R1 1 TPALAALAALGAPGPAPTAASSP 23 0 Q86V15 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 TPALAALAALGAPGPAPTAAS(0.5)S(0.5)P 164.81 1.45E-11 113370000 228660 172640 116850 186950 171640 116880 123230 154320 96291 84014 TRUE FALSE 219723.7144 167716.4762 137967.3943 196598.5119 177160.9565 119243.3937 124738.1256 151133.2381 85360.44936 78323.65695 2.805330126 2.141325913 1.76150348 2.510078303 2.261908641 1.522444155 1.592598334 1.929598846 1.089842491 1 16.25716051 7.999966189 0.080792199 0.064115715 6.765931289 0.673304506 0.31770607 119.0607689 0.699841878 8.649432577 89.02408519 99992214.96 -7.999966189 6.701815573 KGQLNADEISLRPAQSFLMNK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGQLNADEISLRPAQSFLMNK 21 2 D3DQV9;P78344 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 125.09 1.33E-05 628000000 83239 69630 68242 55270 57291 80706 75178 57873 74824 77439 FALSE TRUE 79985.92785 67644.22057 80574.84744 58122.49132 59133.81705 82337.93062 76098.05085 56677.90233 66330.29321 72193.98755 1.107930599 0.936978589 1.116088059 0.805087699 0.819096147 1.140509527 1.054077402 0.785077875 0.918778633 1 16.13959107 7.999970586 0.754287128 0.934025546 31.12455779 0.125000955 0.12025091 829.6897759 3.485885589 0.043616862 42588.93474 99993227.35 -7.999970586 30.19053225 YSPTS(ph)PTYS(ph)PTTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.025)S(0.972)PT(0.131)Y(0.079)S(0.777)PT(0.015)T(0.001)PK;YS(0.001)PT(0.053)S(0.943)PT(0.005)Y(0.003)S(0.988)PT(0.006)T(0.001)PK 225.85 3.83E-12 488750000 658140 723420 664000 754380 678000 747690 731220 703360 894810 869000 TRUE FALSE 632419.1612 702788.7699 783999.5706 793313.6422 699808.4857 762808.8041 740168.8891 688835.3702 793234.9201 810141.856 0.780627685 0.867488533 0.967731225 0.979228065 0.863809814 0.941574366 0.913628747 0.85026513 0.979130895 1 19.62781502 7.999975403 0.016292323 1.653169417 8.08E-06 0.290635889 0.057167849 7990.013464 10.04445188 399.4264504 647.4233586 99994336.48 -7.999975403 -1.653161337 TGEPS(ph)PPHDILHEPPDVVS(ph)DDEKDHGK ddPTM_BT-474_Pertuzumab_2h_R1 3 TGEPSPPHDILHEPPDVVSDDEKDHGK 27 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 2 T(0.119)GEPS(0.881)PPHDILHEPPDVVS(1)DDEKDHGK;TGEPS(1)PPHDILHEPPDVVS(1)DDEKDHGK;T(0.141)GEPS(0.859)PPHDILHEPPDVVS(1)DDEKDHGK 257.87 3.09E-53 652820000 522390 383268 363434 273347 386988 402141 427620 65059 675560 478590 TRUE FALSE 501974.4213 372337.5719 429114.6083 287454.4714 399435.8205 410272.5665 432853.3415 63715.50891 598873.261 446174.673 1.125062563 0.834510774 0.961763709 0.64426443 0.895245393 0.919533518 0.970143237 0.142803957 1.34223948 1 18.7672491 7.999975416 0.768542563 0.783590856 66.89377214 0.028790364 0.296584565 1075.608115 4.251942328 0.102165567 123399.1206 99994339.54 -7.999975416 66.11018128 KGQAVDYEGSR ddPTM_BT-474_Pertuzumab_2h_R1 6 KGQAVDYEGSR 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 187.78 5.51E-06 11517580000 5802640 6459640 5367000 6485530 5743070 5851360 6255510 6183240 7023610 6802120 FALSE TRUE 5575866.414 6275417.392 6336936.288 6820248.981 5927801.062 5969678.508 6332066.803 6055553.933 6226319.238 6341406.354 0.879279154 0.989593955 0.999295099 1.075510478 0.93477704 0.941380851 0.998527211 0.954922867 0.981851484 1 22.5963714 7.999975584 0.002926845 1.917579386 4.41E-05 0.038803333 0.048470293 956058.4626 216.5567569 67920.59493 74081.42008 99994378.08 -7.999975584 -1.917535284 KQPPVS(ph)PGTALVGSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 KQPPVSPGTALVGSQK 16 1 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(1)PGTALVGSQK;KQPPVS(0.998)PGT(0.002)ALVGSQK 192.64 3.08E-10 2812900000 3070300 2231760 2375800 1968100 2083240 1693570 1888850 3365200 1918850 1910570 TRUE FALSE 2950309.282 2168112.39 2805159.909 2069673.877 2150249.307 1727815.146 1911966.311 3295707.444 1701030.192 1781165.392 1.65639266 1.217243721 1.574901422 1.161977369 1.207214847 0.970047562 1.073435583 1.850309611 0.955009681 1 20.76439006 7.999977453 0.875921773 1.250051223 160.7259961 0.178565157 0.271601905 1687.705478 4.116735805 0.090077231 537291.145 99994808.53 -7.999977453 159.4759448 LEDVLR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEDVLR 6 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ;; 113.08 0.061517 433842000 609540 695010 622550 705360 689370 657660 764120 708480 777840 873430 FALSE TRUE 585718.5029 675188.9953 735058.6335 741763.7141 711544.2121 670958.3358 773471.5291 693849.6404 689542.8642 814271.8081 0.719315709 0.829193629 0.902719001 0.910953452 0.873841149 0.823997993 0.949893539 0.852110602 0.846821488 1 19.63515093 7.999977883 0.026517689 1.496541213 4.81E-08 0.432414801 0.055044375 1941.566678 3.954664227 74.95579192 164.3021992 99994907.51 -7.999977883 -1.496541165 MLDQTLLDLNEM ddPTM_BT-474_Pertuzumab_2h_R1 9 MLDQTLLDLNEM 12 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;;;; 218.75 1.19E-10 375241700 698232 792966 657486 775832 774481 694477 784653 776322 800993 856457 FALSE TRUE 670944.3215 770351.3861 776308.3459 815872.7825 799392.8847 708519.8008 794255.8181 760290.6794 710067.6327 798448.4045 0.840310179 0.964810477 0.972271147 1.021822798 1.001182894 0.887370802 0.994749083 0.952210155 0.889309351 1 19.60683966 7.999978102 0.004656592 1.856876667 4.13E-05 0.051162185 0.055600243 274696.8959 98.97582583 18413.41792 21140.93064 99994957.99 -7.999978102 -1.856835368 ASIANSDGPTAGS(ph)QTPPFKR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASIANSDGPTAGSQTPPFKR 20 1 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASIANSDGPT(0.01)AGS(0.554)QT(0.436)PPFKR 67.832 0.0077931 0 161800 161150 126180 137860 157190 137430 129900 168670 148780 146300 TRUE FALSE 155476.6771 156554.1598 148983.5329 144974.9711 162246.1591 140208.9288 131489.7551 165186.9056 131891.1181 136390.9707 1.139933797 1.147833753 1.092326949 1.062936721 1.189566716 1.027992748 0.964064955 1.211127868 0.967007695 1 17.05738861 7.999979198 0.044188792 0.78312749 1.615437527 0.22525183 0.075280402 1067.216567 3.576999554 17.31119703 63.61066237 99995210.37 -7.999979198 0.832310036 TAPPALPTGYDS(ph)EEEEESRPMSYDEK ddPTM_BT-474_Pertuzumab_2h_R1 5 TAPPALPTGYDSEEEEESRPMSYDEK 26 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK 322.08 1.62E-82 2442470000 679482 589350 624274 638190 673060 630244 677189 741100 844100 779950 TRUE FALSE 652927.0922 572542.315 737094.1987 671127.0624 694709.5862 642987.9655 685476.6416 725796.026 748281.3068 727123.2918 0.897959259 0.787407475 1.013712815 0.922989361 0.955421995 0.884290151 0.942724087 0.998174634 1.02909825 1 19.47184048 7.999980434 0.170882792 1.027551267 0.324070622 0.366274761 0.0556938 60.41596686 0.654609644 0.138667848 10.89513471 99995494.79 -7.999980434 -0.703480645 VVTDTDETELAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVTDTDETELAR 12 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 144.47 0.00014675 927970000 584640 610790 572300 659260 585760 620070 635940 649100 688920 745250 FALSE TRUE 561791.6224 593370.8672 675727.3407 693284.4876 604601.5024 632608.2402 643722.824 635695.8582 610716.6898 694773.5537 0.808596728 0.8540493 0.972586445 0.997856761 0.870213754 0.910524353 0.926521772 0.914968416 0.879015453 1 19.40618331 7.999980699 0.013450715 1.686334075 2.34E-05 0.240067077 0.052211424 12600.18884 13.08875179 671.1559171 1000.10876 99995555.88 -7.999980699 -1.686310699 GDDDSSKPIVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDDDSSKPIVR 11 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-3;Q8IXQ4-2 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 0 ; 97.779 0.0054833 566010000 1036570 1033750 870570 948680 1028370 997500 964590 1094040 1165260 1094330 FALSE TRUE 996059.6984 1004268.462 1027901.365 997641.4885 1061448.455 1017670.133 976394.941 1071447.692 1032984.57 1020210.054 0.976328055 0.984374206 1.007538948 0.977878511 1.04042148 0.997510394 0.957052851 1.050222635 1.012521456 1 19.96043479 7.99998404 0.363149646 1.0125596 0.51962241 0.130464078 0.025559207 120.4576183 1.68082595 0.020352982 41.15095064 99996325.19 -7.99998404 -0.49293719 DVPPDILLDS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 4 DVPPDILLDSPER 13 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 DVPPDILLDS(1)PER;DVPPDILLDS(1)PER;DVPPDILLDS(1)PER;DVPPDILLDS(1)PER 182.57 1.16E-05 815620000 390215 445460 400382 447947 437918 432516 461427 450190 474043 537549 TRUE FALSE 374964.9664 432755.917 472739.9338 471065.5984 452004.0302 441261.7699 467074.0817 440893.4192 420231.626 501140.3274 0.748223493 0.863542392 0.943328461 0.93998741 0.901951021 0.880515388 0.932022542 0.879780363 0.838550807 1 18.93485511 7.999985566 0.01655337 1.620411147 3.06E-09 0.293207783 0.055074828 7320.143135 9.348847195 357.2460119 583.5465505 99996676.53 -7.999985566 -1.620411144 RKS(ph)VEPPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKSVEPPK 8 2 Q9Y2D9 Q9Y2D9 ZNF652 Zinc finger protein 652 1 RKS(1)VEPPK 55.353 0.098026 173720000 180660 137810 122580 117800 122020 117270 112380 160640 121080 121610 TRUE FALSE 173599.6075 133879.7937 144732.9328 123879.6721 125944.8841 119641.2797 113755.3401 157322.7279 107335.506 113373.2464 1.531221986 1.180876424 1.276605702 1.09267112 1.110887164 1.055286706 1.003370228 1.387653021 0.946744575 1 16.79072071 7.999985615 0.860992736 1.115916194 156.518077 0.52077271 0.123285644 623.6884247 1.619859285 0.039650507 190013.1641 99996687.84 -7.999985615 155.4021608 S(ph)FSELPSCDGNESWAYR ddPTM_BT-474_Pertuzumab_2h_R1 2 SFSELPSCDGNESWAYR 17 0 Q8NEV8-2;Q8NEV8 Q8NEV8-2 EXPH5 Exophilin-5 1 S(0.986)FS(0.014)ELPSCDGNESWAYR;S(0.988)FS(0.012)ELPSCDGNESWAYR 153.24 1.92E-07 276720000 168570 134435 104451 126532 125449 98558 99020 159952 110617 121626 TRUE FALSE 161982.098 130601.0454 123327.6192 133062.3317 129484.181 100550.9103 100231.8364 156648.9353 98060.2219 113388.1627 1.428562684 1.151804936 1.087658679 1.173511666 1.141955015 0.886784898 0.883970901 1.381528121 0.864818863 1 16.79091051 7.999986235 0.875922835 1.064003527 154.2300649 0.365174311 0.150047213 938.3857803 2.292139172 0.048810466 286920.7607 99996830.53 -7.999986235 153.1660614 ADQLDYENFR ddPTM_BT-474_Pertuzumab_2h_R1 1 ADQLDYENFR 10 0 Q8NI27;A0A0C4DG98;H0Y815 Q8NI27 THOC2 THO complex subunit 2 0 100.69 0.0089423 110360000 137420 158100 142460 178180 157010 154750 153770 163090 195180 196420 FALSE TRUE 132049.4745 153591.1428 168205.691 187375.8912 162060.3692 157879.151 155651.8833 159722.1345 173023.9847 183116.2984 0.721123546 0.83876282 0.918573019 1.02326168 0.885013353 0.862179677 0.850016545 0.872244229 0.94488577 1 17.48240068 7.99998751 0.022257457 1.562957026 3.05E-07 0.304487835 0.068527592 4127.27685 7.071166495 177.8594266 343.8607403 99997124.17 -7.99998751 -1.562956721 RGFEVVYMTEPIDEYCVQQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGFEVVYMTEPIDEYCVQQLK 21 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 219.34 8.17E-25 702310000 314460 350250 233195 261510 274960 329310 274610 273660 331710 270720 FALSE TRUE 302170.5555 340261.2129 275338.5239 275006.5624 283804.3381 335968.8738 277970.7593 268008.8254 294055.6714 252383.8933 1.197265608 1.348189096 1.09095125 1.089635947 1.124494652 1.331181913 1.101380741 1.061909387 1.165112669 1 17.94526032 7.99998761 0.020924238 1.13E-06 2.644560222 0.285846353 0.090609688 3623.706281 5.840021446 269.7582838 501.4049681 99997147.2 -7.99998761 2.644559094 CQYVTEK ddPTM_BT-474_Pertuzumab_2h_R1 4 CQYVTEK 7 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;; 173.68 0.001988 3068190000 2153220 1892600 1689730 1797160 1760160 1519300 1833780 1997360 2242090 1900900 FALSE TRUE 2069069.782 1838624.901 1995101.799 1889911.643 1816777.145 1550021.287 1856222.348 1956113.818 1987577.343 1772150.35 1.16754754 1.037510672 1.125808428 1.066451073 1.025182285 0.874655634 1.047440669 1.103808048 1.121562481 1 20.75706958 7.999987735 0.778055166 1.040284745 26.39422008 0.224005709 0.069018269 797.6727364 3.025439382 0.0254759 35568.74699 99997175.94 -7.999987735 25.35393534 IKTEPSS(ph)PLSDPSDIIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 IKTEPS(0.248)S(0.751)PLS(0.001)DPSDIIR;IKTEPS(0.111)S(0.883)PLS(0.004)DPS(0.002)DIIR 185.28 1.55E-09 1095540000 855690 792250 518560 563960 699330 733080 632900 703220 692010 575960 TRUE FALSE 822248.6888 769655.8057 612275.3273 593066.0432 721824.5846 747903.3799 640645.6195 688698.2613 613455.9259 536949.7162 1.531332756 1.433385255 1.140284293 1.104509464 1.344305738 1.392874151 1.193120324 1.282612208 1.142483006 1 19.03442746 7.999988182 0.029427763 2.41E-07 3.082464318 0.453796737 0.117606807 1564.925617 3.531406858 118.8769102 283.8602999 99997278.74 -7.999988182 3.082464077 HYQGEEKS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 4 HYQGEEKSD 9 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 1 HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D 166.04 3.70E-05 1501440000 2628570 2293380 1745460 1842910 2086590 2089080 2124690 1134950 2929710 2390540 TRUE FALSE 2525842.578 2227975.048 2060903.45 1938022.806 2153707.062 2131322.629 2150692.592 1111512.886 2597141.603 2228626.597 1.133362844 0.999707646 0.924741477 0.869604091 0.966383092 0.956339044 0.965030479 0.498743436 1.165355204 1 21.08772348 7.999990337 0.538304328 0.864610729 12.10276156 0.098235565 0.163431684 220.1095416 2.086676826 0.080686401 2846.57943 99997775.09 -7.999990337 11.23815083 S(ph)SDELDAWTDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSDELDAWTDFR 12 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 S(0.991)S(0.009)DELDAWTDFR;S(0.989)S(0.011)DELDAWTDFR 243.3 2.57E-16 348130000 382940 418020 295000 326670 370890 291380 264050 387640 314160 265860 TRUE FALSE 367974.2814 406098.4789 348313.0622 343529.4778 382820.0137 297271.9032 267281.5229 379635.0985 278497.8739 247853.0654 1.484646885 1.638464621 1.405320776 1.386020695 1.544544196 1.19938764 1.078386997 1.531694183 1.123641031 1 17.91912558 7.999991079 0.046029996 0.167375649 3.461179955 0.534442963 0.144030678 467.1807607 1.628436839 29.11745933 112.8524383 99997945.92 -7.999991079 3.293804306 SVGGS(ph)GGGSFGDNLVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.041)VGGS(0.545)GGGS(0.414)FGDNLVTR 202.49 1.11E-11 659500000 631270 672500 545150 504100 552360 580570 532050 601770 559980 537750 TRUE FALSE 606599.2705 653320.9584 643670.7318 530116.6614 570127.161 592309.5232 538561.3871 589343.2392 496413.418 501327.7135 1.209985513 1.303181414 1.283932076 1.057425407 1.137234479 1.181481708 1.074270128 1.175564852 0.990197439 1 18.93539446 7.999991153 0.117576165 0.932152159 2.033308554 0.563994978 0.068747415 72.28604701 0.585808475 0.497883306 13.01445482 99997962.87 -7.999991153 1.101156395 TVTEGGAAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVTEGGAAHR 10 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 142.83 3.51E-05 235170000 153740 161770 128770 159110 155810 145360 157270 156570 181330 173850 FALSE TRUE 147731.6708 157156.478 152041.6035 167321.6862 160821.7702 148299.2788 159194.7173 153336.7748 160746.1786 162074.9847 0.911501989 0.969652894 0.938094203 1.032372062 0.992267687 0.915004121 0.982228798 0.946085388 0.991801288 1 17.30630191 7.999991926 0.005245784 1.872357211 5.44E-06 0.13408845 0.034697517 119920.6712 48.65105973 8030.438846 9383.14971 99998140.97 -7.999991926 -1.872351772 QSPGSTS(ph)PKPPHTLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 QSPGSTSPKPPHTLSR 16 1 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 QS(0.001)PGS(0.152)T(0.056)S(0.79)PKPPHTLSR;QSPGST(0.111)S(0.889)PKPPHTLSR 128.66 3.60E-05 1550400000 1074250 901160 859810 820150 812380 766740 800720 1047330 1064970 970510 TRUE FALSE 1032267.122 875459.7991 1015196.793 862478.0398 838510.9405 782244.0081 810519.4509 1025702.27 944079.0703 904776.4933 1.140908423 0.967597861 1.122041522 0.953249832 0.926760307 0.864571542 0.895822843 1.13365265 1.04343899 1 19.78720192 7.999992271 0.957350254 0.986525257 108.3094725 0.216432653 0.084933256 2419.227227 4.006300834 0.02857231 568762.1149 99998220.25 -7.999992271 107.3229472 (ac)EEEIAALVIDNGSGMCK ddPTM_BT-474_Pertuzumab_2h_R1 10 EEEIAALVIDNGSGMCK 17 0 P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65 P63261 ACTG1 "Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;;;; 186.46 2.06E-160 3761004000 2988442 3184717 2526363 2957780 2985199 3184335 3106064 3326457 3599690 3497331 FALSE TRUE 2871650.383 3093891.989 2982932.993 3110431.38 3081220.637 3248724.435 3144076.94 3257764.501 3191068.282 3260453.656 0.880751787 0.948914573 0.914882807 0.9539873 0.945028196 0.99640258 0.964306588 0.99917522 0.978719104 1 21.63664128 7.999992681 0.228651772 1.005408424 0.362978613 0.776543993 0.017365972 20.76850005 0.271359914 0.023410494 4.987776266 99998314.8 -7.999992681 -0.642429811 ECLPLIIFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ECLPLIIFLR 10 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 147.19 6.36E-05 295020000 356680 406530 368010 387030 386760 371000 405800 392740 429010 444740 FALSE TRUE 342740.5513 394936.1624 434517.5933 407004.6647 399200.4866 378501.8742 410766.3018 384629.7818 380310.5834 414617.3637 0.826643024 0.952531652 1.047996614 0.981639218 0.962816615 0.912894411 0.990711769 0.927674081 0.917256769 1 18.66142101 7.999993113 0.004138327 1.859159503 6.18E-06 0.054704266 0.055899786 401413.2388 128.4937788 27140.44802 30686.65122 99998414.26 -7.999993113 -1.859153319 SYSLS(ph)ELSVLQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 SYS(0.327)LS(0.673)ELSVLQAK 264.58 3.13E-24 692960000 329930 284550 239930 263260 244180 223390 254790 307100 282020 239580 TRUE FALSE 317035.9708 276434.9126 283290.6882 276846.8801 252034.2715 227907.0989 257908.1962 300758.2777 250006.2719 223353.0332 1.419438842 1.237659093 1.268353889 1.239503562 1.128412128 1.02038954 1.154710964 1.346560077 1.119332334 1 17.76896632 7.999993339 0.594537527 1.160100155 16.5723516 0.434760918 0.095926508 191.1275667 1.503537387 0.044770083 3820.468666 99998466.25 -7.999993339 15.41225144 FTISDHPQPIDPLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTISDHPQPIDPLLK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 114.69 0.00058626 897710000 511920 588210 538580 573710 537880 602810 584110 577590 680680 697520 FALSE TRUE 491913.6004 571434.8267 635913.3866 603319.2419 555181.3987 614999.2312 591258.5129 565662.5647 603412.06 650276.3491 0.75646854 0.878756897 0.977912525 0.927788997 0.85376225 0.945750575 0.909241915 0.869880268 0.927931734 1 19.31069343 7.999994244 0.017427329 1.62950372 1.41E-08 0.328119515 0.054169468 6173.82652 8.298610385 298.9414555 501.0939706 99998674.59 -7.999994244 -1.629503706 RT(ph)ASPPPPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RTASPPPPPK 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.587)AS(0.413)PPPPPK;RT(0.718)AS(0.282)PPPPPK 56.956 0.070752 1272160000 1067810 1079760 855370 1020600 1034050 1040620 1027620 1116060 1161520 1185130 TRUE FALSE 1026078.805 1048966.302 1009954.387 1073273.288 1067311.157 1061662.049 1040196.321 1093012.971 1029669.119 1104860.089 0.928695691 0.949410982 0.91410161 0.97141104 0.966014763 0.960901801 0.941473342 0.989277268 0.931945256 1 20.07543226 7.999994723 0.008160517 1.819583538 1.68E-05 0.385085578 0.020350079 18112.66763 11.42875206 1128.28745 1437.333871 99998784.83 -7.999994723 -1.819566787 GRS(ph)IDQDYER ddPTM_BT-474_Pertuzumab_2h_R1 3 GRSIDQDYER 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER 217.57 4.35E-09 1309070000 995840 1131250 674820 909640 980120 855330 878940 952100 901090 841370 TRUE FALSE 956921.4718 1098987.858 796774.9853 956586.6294 1011646.45 872625.3586 889696.7306 932438.8023 798802.0409 784383.2605 1.219966718 1.401085302 1.015798049 1.219539832 1.289734879 1.112498701 1.134262771 1.188754081 1.018382315 1 19.58119922 7.999994929 0.030028458 0.216333743 2.551797429 0.367879237 0.098114944 1446.349693 3.32923464 82.45969548 200.4067698 99998832.45 -7.999994929 2.335463686 KVSS(ph)AEGAAK ddPTM_BT-474_Pertuzumab_2h_R1 4 KVSSAEGAAK 10 1 P05114;A6NL93;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 KVS(0.375)S(0.625)AEGAAK;KVS(0.072)S(0.928)AEGAAK;KVS(0.254)S(0.746)AEGAAK;KVS(0.203)S(0.797)AEGAAK 127.03 0.00022481 726560000 1058230 900318 901793 751098 871913 803191 862380 1043765 1037376 931013 TRUE FALSE 1016873.202 874641.8121 1064767.055 789862.2578 899958.8735 819432.0723 872934.0644 1022210.888 919617.4255 867954.6602 1.171574102 1.007704494 1.226754235 0.910027095 1.036873139 0.944095481 1.00573694 1.177723831 1.059522424 1 19.72726016 7.999995123 0.919942358 1.043273059 67.71604184 0.145786176 0.09218998 2412.947899 4.717240197 0.029172639 338136.0776 99998876.96 -7.999995123 66.67276878 GIHYWEVELQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIHYWEVELQK 11 0 Q14258 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 125.74 0.000322 195210000 326430 321140 295160 295990 330290 318580 341130 331110 386710 381240 FALSE TRUE 313672.7547 311981.4016 348501.9778 311266.0794 340914.0778 325021.9059 345304.851 324272.4628 342812.302 355418.2752 0.882545374 0.877786606 0.9805404 0.875773985 0.959191188 0.914477191 0.971545008 0.912368568 0.964532006 1 18.43915834 7.9999965 0.016286593 1.608902918 0.101852725 0.416820234 0.033761408 4515.286533 5.674222128 205.7871703 333.5023453 99999194.19 -7.9999965 -1.507050193 EVPWS(ph)PSAEKAS(ph)PQENGPAVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVPWSPSAEKASPQENGPAVHK 22 1 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 2 EVPWS(0.933)PS(0.074)AEKAS(0.993)PQENGPAVHK 71.297 0.021957 247220000 160490 152990 141220 164570 181340 177570 145650 175120 199400 208130 TRUE FALSE 154217.8734 148626.875 166741.5954 173063.4774 187172.9658 181160.5871 147432.5083 171503.7108 176764.948 194033.1697 0.794801598 0.765986945 0.859345831 0.891927281 0.964644169 0.933657824 0.759831468 0.883888621 0.911003764 1 17.56594377 7.999996776 0.028002414 1.486974121 7.13E-07 0.391138756 0.06072552 1975.956343 4.246523496 74.04983917 169.5644852 99999257.67 -7.999996776 -1.486973408 ICSWSLDMLSHPQDSMELVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ICSWSLDMLSHPQDSMELVHK 21 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ; 241.52 3.03E-30 572930000 479304 520710 442970 509631 509581 531390 519260 497867 611080 608220 FALSE TRUE 460572.2698 505859.8606 523024.5328 535933.117 525972.1357 542135.0699 525614.8592 487585.8725 541712.7603 567024.7177 0.812261363 0.892130175 0.922401646 0.945167116 0.927600013 0.956104828 0.926969924 0.859902324 0.955360046 1 19.1130521 7.999997137 0.014703098 1.678979632 2.84E-06 0.419718644 0.038613905 7494.344241 8.506756507 389.9066378 602.9563515 99999340.87 -7.999997137 -1.678976787 IGDYYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IGDYYLR 7 0 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 81.635 0.062041 48379000 52388 54910 47377 56947 53207 38728 66095 60327 57192 64302 FALSE TRUE 50340.61904 53344.02056 55939.0778 59886.04149 54918.45148 39511.10669 66903.89038 59081.22637 50699.80393 59946.76827 0.839755345 0.889856486 0.933145846 0.998986988 0.916120302 0.659103198 1.116054999 0.985561492 0.845747075 1 15.87139436 7.99999721 0.071526089 1.077930631 0.556115727 0.058739103 0.113336084 730.9353958 3.850130965 4.790362269 38.26403652 99999357.68 -7.99999721 -0.521814903 RPS(ph)ASSPNNNTAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RPS(0.409)AS(0.409)S(0.183)PNNNTAAK 106.67 0.0005687 214140000 215610 174780 151420 145280 159460 146640 157300 178660 166590 165480 TRUE FALSE 207183.7228 169795.4455 178784.9623 152777.9182 164589.1757 149605.1613 159225.0845 174970.6086 147679.4016 154271.8922 1.342977777 1.100624638 1.158895245 0.990315968 1.066877273 0.96974996 1.0321069 1.134170367 0.957267066 1 17.23511571 7.999997358 0.803962863 1.034588265 79.61019888 0.719002464 0.058705903 280.2028959 0.947392569 0.019497098 40117.88474 99999391.74 -7.999997358 78.57561062 SAEPSPTVMSTS(ph)LGSNLSELDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.003)T(0.043)S(0.953)LGSNLSELDR 237.83 1.63E-30 300410000 261070 271520 215100 224280 238250 239490 214540 263320 239500 232340 TRUE FALSE 250867.0958 263776.5154 253973.3549 235855.1177 245913.5276 244332.6519 217165.6047 257882.35 212312.9641 216603.4049 1.158186299 1.217785637 1.172527066 1.08888001 1.135316999 1.128018519 1.002595526 1.190573852 0.980192182 1 17.7246964 7.999997447 0.081402533 0.888570651 1.726012009 0.476855059 0.058836545 163.7334334 0.968889461 1.472087351 15.40337423 99999412.11 -7.999997447 0.837441358 YELGRPAANTK ddPTM_BT-474_Pertuzumab_2h_R1 2 YELGRPAANTK 11 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 128.28 0.00024538 606260000 559190 500340 441590 467480 465490 418150 488150 517090 542320 565900 FALSE TRUE 537336.2366 486070.7931 521395.1361 491606.6988 480462.9086 426605.2795 494124.1257 506411.9108 480758.1072 527571.0889 1.018509634 0.921337054 0.98829361 0.931830248 0.910707426 0.808621413 0.936601979 0.959893219 0.911266969 1 19.00900598 7.99999755 0.810242545 0.922464876 25.10525564 0.21378148 0.050037592 864.3611905 2.848364598 0.017054347 38406.04121 99999435.97 -7.99999755 24.18279076 KEMTNEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KEMTNEEK 8 1 P11387 P11387 TOP1 DNA topoisomerase 1 0 90.108 0.021534 123090000 115700 103200 72088 86528 93861 82455 85402 110100 90088 83026 FALSE TRUE 111178.3161 100256.837 85115.90519 90993.72045 96880.12431 84122.29659 86447.17522 107826.3965 79861.58792 77402.57507 1.436364565 1.295264879 1.099652113 1.175590352 1.251639551 1.086815219 1.116851412 1.393059552 1.031769135 1 16.24009394 7.999997796 0.022533715 2.66E-07 2.790577741 0.334266285 0.116049997 3670.758883 6.366272578 281.2216343 548.1437459 99999492.41 -7.999997796 2.790577474 IQLVEEELDRAQER ddPTM_BT-474_Pertuzumab_2h_R1 6 IQLVEEELDRAQER 14 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;;; 236.26 2.67E-17 9275850000 4711000 5482150 2614709 3023239 3952110 5169510 3357778 3516720 3528035 2912721 FALSE TRUE 4526888.912 5325804.45 3087245.08 3179268.727 4079233.207 5274041.034 3398871.492 3444098.503 3127547.258 2715439.812 1.66709234 1.961304547 1.136922669 1.170811709 1.50223665 1.94224192 1.251683604 1.268339106 1.151764529 1 21.37275446 7.999997929 0.052673538 0.153638266 3.823432606 0.319991368 0.27015738 569.850693 2.25858968 35.56316971 166.9012814 99999523.08 -7.999997929 3.66979434 GFAFVTFDDHDSVDKIVIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFAFVTFDDHDSVDKIVIQK 20 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 206.98 4.28E-22 178400000 518790 642390 303540 329130 434370 612300 388600 365360 409050 324940 FALSE TRUE 498515.1132 624069.6662 358396.4302 346116.4387 448341.9055 624681.1255 393355.803 357815.1883 362616.3589 302931.5244 1.645636301 2.060101429 1.183093872 1.142556687 1.480010727 2.062119903 1.298497421 1.181175149 1.197024178 1 18.20863219 7.999998281 0.062355466 0.307052907 3.844542647 0.287322686 0.305237916 428.70839 1.990559862 22.06728855 136.4076739 99999604.16 -7.999998281 3.53748974 ERQEQEEARR ddPTM_BT-474_Pertuzumab_2h_R1 3 ERQEQEEARR 10 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;; 124.12 0.00024966 281653000 222818 248848 153963 188736 198934 223473 186085 199379 196188 183344 FALSE TRUE 214110.0262 241751.0987 181787.539 198476.6876 205332.8928 227991.7772 188362.3639 195261.754 173917.5607 170925.9476 1.252647882 1.414361612 1.063545597 1.161185241 1.201297379 1.333862883 1.102011524 1.142376314 1.017502393 1 17.3830119 7.999998293 0.059304035 0.68012498 2.200851832 0.415798859 0.097676696 342.7979895 1.518995627 7.967388746 45.17648214 99999606.97 -7.999998293 1.520726852 QLSILVHPDKNQDDADR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLSILVHPDKNQDDADR 17 1 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 147.06 2.49E-07 412540000 588980 555760 433430 462990 500410 531460 491730 465440 571290 564060 FALSE TRUE 565962.0104 539910.2689 511760.4426 486884.9694 516506.1421 542206.4853 497747.9388 455828.5013 506439.5542 525855.7138 1.076268633 1.026727018 0.973195554 0.925890804 0.982220272 1.031093646 0.946548503 0.866831888 0.963077021 1 19.00430748 7.999998369 0.538658538 0.944197698 6.722469029 0.408530847 0.043264177 122.8908627 1.163745762 0.023051098 817.8179403 99999624.5 -7.999998369 5.778271331 NIDDGTSDRPYSHALVAGIDRYPR ddPTM_BT-474_Pertuzumab_2h_R1 4 NIDDGTSDRPYSHALVAGIDRYPR 24 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;; 280.89 1.84E-52 4166980000 1917170 2009260 1131240 1193470 1596650 2086450 1432970 1423360 1553740 1331220 FALSE TRUE 1842244.877 1951957.872 1335680.232 1255065.13 1648007.697 2128639.449 1450507.116 1393967.119 1377365.949 1241055.284 1.48441806 1.572821048 1.076245555 1.011288656 1.327908369 1.715185034 1.168769139 1.123211139 1.109834483 1 20.24313595 7.999998679 0.047629007 0.378029206 2.848941372 0.239752758 0.208683053 881.870859 3.176030908 40.18700306 163.1216094 99999695.8 -7.999998679 2.470912166 NSLFTGDTLGAGQFSFQRPLLVLVDR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLFTGDTLGAGQFSFQRPLLVLVDR 26 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3;H0YJY1 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 158.91 1.82E-11 115910000 88489 93105 52229 68185 66769 81059 73149 73501 72055 61138 FALSE TRUE 85030.75205 90449.73656 61667.94213 71704.03602 68916.68552 82698.06852 74044.21934 71983.17866 63875.61848 56997.0688 1.491844297 1.58691909 1.08194936 1.258030238 1.209126837 1.45091792 1.299088197 1.262927729 1.120682516 1 15.79860011 7.999998776 0.032634465 1.35E-10 3.211942119 0.437513843 0.133597242 1219.405422 3.045361949 91.75645309 240.7217897 99999718.17 -7.999998776 3.211942119 RGS(ph)FSSENYWR ddPTM_BT-474_Pertuzumab_2h_R1 8 RGSFSSENYWR 11 1 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 RGS(0.999)FS(0.001)SENYWR;RGS(0.979)FS(0.019)S(0.002)ENYWR;RGS(0.999)FS(0.001)SENYWR;RGS(0.999)FS(0.001)SENYWR;RGS(0.827)FS(0.087)S(0.087)ENYWR;RGS(0.979)FS(0.021)SENYWR;RGS(0.995)FS(0.002)S(0.003)ENYWR;RGS(1)FSSENYWR 200.63 2.83E-08 7488690000 1933318 1806542 1202904 1439307 1370202 1103511 1303572 1695800 1312445 1147436 TRUE FALSE 1857761.795 1755021.191 1420295.511 1513589.807 1414275.792 1125824.748 1319525.504 1660781.137 1163461.746 1069719.138 1.736681835 1.640637368 1.327727495 1.414941318 1.322100112 1.052448918 1.233525191 1.552539427 1.087632917 1 20.02880063 7.999998792 0.422431466 1.223536455 11.89887985 0.578418919 0.155316783 64.19533045 0.819859223 0.107095372 580.0021702 99999721.89 -7.999998792 10.67534339 LPIGDVATQYFADRDMFCAGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPIGDVATQYFADRDMFCAGR 21 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 147.1 9.36E-08 587850000 238142 275760 123467 142179 212895 236870 170497 184895 186417 146782 FALSE TRUE 228835.1474 267895.5948 145780.2334 149516.8752 219742.961 241659.6737 172583.5933 181076.8536 165255.7237 136840.3244 1.672278609 1.957724055 1.065330955 1.092637539 1.605834844 1.765997521 1.26120421 1.323271151 1.207653697 1 17.0621339 7.999998792 0.043537174 2.98E-07 3.808310492 0.296170058 0.263955663 911.3349191 3.011180552 68.34882857 246.4495915 99999721.94 -7.999998792 3.808310194 RS(ph)SQPSPTAVPASDSPPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.497)S(0.497)QPS(0.006)PTAVPASDSPPTK 139.47 1.13E-07 1180400000 913170 739010 640700 690900 683490 599210 591520 914440 639790 686280 TRUE FALSE 877482.3068 717934.1584 756488.7423 726557.4318 705475.0766 611326.4368 598759.1987 895556.4944 567163.7214 639797.6443 1.371499746 1.122126917 1.182387508 1.135605044 1.102653445 0.955499668 0.935857148 1.399749596 0.886473601 1 19.28725616 7.999998866 0.814056724 1.085315632 76.69682013 0.291978262 0.139457664 808.7943132 2.616547302 0.047448722 112933.724 99999738.8 -7.999998866 75.6115045 ELMNLDFHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELMNLDFHEK 10 0 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6;H3BR02;H3BP48 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 88.441 0.012192 74506000 190470 148270 143350 113650 148920 124750 127100 129800 169920 168100 FALSE TRUE 183026.2218 144041.4848 169256.5338 119515.4901 153710.147 127272.5305 128655.4878 127119.5846 150631.394 156714.4373 1.167896366 0.919133472 1.080031532 0.76263229 0.980829525 0.81213022 0.820954917 0.811154268 0.9611839 1 17.25777857 7.999998884 0.635424773 0.865977606 24.2292629 0.405029802 0.096208858 176.1329442 1.194708526 0.035917063 5768.986038 99999742.94 -7.999998884 23.3632853 EAWPHIK ddPTM_BT-474_Pertuzumab_2h_R1 6 EAWPHIK 7 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;;; 94.407 0.014223 2440780000 3032790 3135390 2604350 2968030 3041750 3120020 3347840 3153540 3651290 3765030 FALSE TRUE 2914265.214 3045971.747 3075013.978 3121210.384 3139590.651 3183108.942 3388811.867 3088418.297 3236810.867 3510021.165 0.830269983 0.867792986 0.876067076 0.889228366 0.894464878 0.906863176 0.965467645 0.879885947 0.922162778 1 21.7430483 7.999998925 0.023675306 1.544318892 0.036910297 0.751071097 0.023265336 1130.271935 2.05844728 45.9501268 92.630661 99999752.41 -7.999998925 -1.507408595 TICTFDSSGFESMS(ph)PIKETVSSR ddPTM_BT-474_Pertuzumab_2h_R1 4 TICTFDSSGFESMSPIKETVSSR 23 1 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 TICTFDSSGFESMS(1)PIKETVSSR;TICTFDSSGFES(0.001)MS(0.999)PIKETVSSR;TICTFDSSGFESMS(1)PIKETVSSR;TICTFDSSGFES(0.007)MS(0.993)PIKETVSSR 333.99 7.34E-87 1401030000 1122521 962256 815967 849103 891910 783211 775950 1097645 780449 749391 TRUE FALSE 1078651.638 934813.401 963430.388 892925.3076 920599.0952 799048.063 785446.3082 1074978.247 691855.7014 698634.0801 1.543943631 1.338058689 1.379020027 1.27810156 1.317712836 1.143729008 1.124259939 1.538685669 0.99029767 1 19.4141775 7.999998993 0.032664048 4.89E-06 3.210892359 0.44185074 0.140604807 1265.170117 3.162455505 95.12424254 249.7737197 99999768.07 -7.999998993 3.210887466 GSGEQDWVNRPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GSGEQDWVNRPK 12 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ; 143.98 5.71E-05 1807810000 2729800 2702500 2366800 2616100 2677900 2951700 2554100 2892700 3186200 3160900 FALSE TRUE 2623116.398 2625427.346 2794533.409 2751117.235 2764037.086 3011385.396 2585357.84 2832964.734 2824515.934 2946809.428 0.890154746 0.890938967 0.948325122 0.93359184 0.937976192 1.02191386 0.877341377 0.961366795 0.958499694 1 21.49072233 7.999999065 0.351035974 0.962520688 2.37E-09 0.330002582 0.036606241 76.002835 1.072171879 0.029349826 48.452677 99999784.81 -7.999999065 -0.962520686 T(ph)TPPEAAQNGQSPMAALILVADNAGGSHASK ddPTM_BT-474_Pertuzumab_2h_R1 5 TTPPEAAQNGQSPMAALILVADNAGGSHASK 31 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 T(0.473)T(0.473)PPEAAQNGQS(0.055)PMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK 202.62 3.27E-25 735144000 169240 216639 214650 231966 189449 216498 237067 222882 269856 287988 TRUE FALSE 162625.9137 210460.6678 253442.0299 243937.7931 195542.7991 220875.7379 239968.2969 218279.4088 239223.0782 268482.3162 0.605722999 0.783890242 0.943980346 0.908580485 0.72832655 0.822682629 0.89379554 0.813012238 0.891019869 1 18.03446754 7.999999066 0.044650067 1.319008793 7.76E-11 0.391066118 0.084816161 780.2129281 2.64127492 19.90855104 74.139333 99999784.97 -7.999999066 -1.319008793 AKS(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_BT-474_Pertuzumab_2h_R1 47 AKSPQPPVEEEDEHFDDTVVCLDTYNCDLHFK 32 1 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.999)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK 342.91 5.34E-118 2.55062E+11 5967634.7 4957476.4 4297159.8 4106434.8 4621668.3 4859572.4 4456065 4088629.5 5873520.9 5248043.6 TRUE FALSE 5734412.938 4816094.027 5073752.166 4318368.392 4770328.458 4957836.283 4510599.656 4004197.872 5206783.431 4892588.932 1.172061053 0.984365148 1.037028092 0.882634624 0.975011088 1.013335956 0.921924919 0.818421071 1.064218454 1 22.22216664 7.999999271 0.81741115 0.940561884 65.15513507 0.420401697 0.07112152 500.1831081 1.595883241 0.023922952 59575.75944 99999832.18 -7.999999271 64.21457319 VINEEYK ddPTM_BT-474_Pertuzumab_2h_R1 1 VINEEYK 7 0 Q09028-3;Q09028;Q09028-2;E9PNS2;E9PIC4;E9PNS6;Q16576;E9PC52;Q16576-2;C9JAJ9 Q09028-3;Q16576;C9JAJ9 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 84.476 0.050059 157200000 521600 383590 562640 233450 388600 372910 401330 376280 365440 318240 FALSE TRUE 501215.2953 372650.3888 664321.5639 245498.3825 401099.6719 380450.4957 406241.5966 368509.6865 323956.7832 296685.3213 1.68938353 1.256045925 2.239145371 0.827470605 1.351936355 1.282336767 1.369267596 1.242089379 1.091920496 1 18.17857402 7.999999322 0.142797323 0.92261376 3.594548143 0.26214624 0.320375281 100.9939016 0.955867164 1.215505237 55.36533204 99999843.86 -7.999999322 2.671934384 DTIIDVVGAPLT(ph)PNSR ddPTM_BT-474_Pertuzumab_2h_R1 8 DTIIDVVGAPLTPNSR 16 0 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(0.999)PNS(0.001)R;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(0.999)PNS(0.001)R;DTIIDVVGAPLT(0.998)PNS(0.002)R 454.28 1.33E-181 4694865000 4378480 4291960 3362250 3969730 3950720 3700950 3956440 4421470 3903090 4115990 TRUE FALSE 4207364.161 4169557.503 3969883.368 4174608.241 4077798.497 3775785.745 4004860.096 4330165.099 3460027.586 3837210.331 1.096464306 1.086611664 1.034575388 1.087927917 1.062698717 0.983992385 1.043690533 1.128466966 0.901703917 1 21.87162642 7.999999332 0.091520549 0.954097959 1.339582719 0.227144385 0.055487163 271.9455258 1.783781448 0.961311722 13.1603438 99999846.26 -7.999999332 0.38548476 DEPDWESLIFLAR ddPTM_BT-474_Pertuzumab_2h_R1 5 DEPDWESLIFLAR 13 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;; 286.08 1.69E-32 935491000 340939.8 331774 302695.1 360036 367206 353167 356272 382274 388072 445559 FALSE TRUE 327615.4957 322312.1304 357398.838 378617.5011 379017.5145 360308.2787 360632.1633 374379.9083 344019.6935 415380.8921 0.788711041 0.775943565 0.860412322 0.911494747 0.912457751 0.867416594 0.868196323 0.901293043 0.828202982 1 18.66407533 7.999999357 0.027814683 1.486827478 7.84E-07 0.550480143 0.041702071 1334.682149 2.849435598 50.16050766 114.2287177 99999851.99 -7.999999357 -1.486826694 KYEFGESDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KYEFGESDLR 10 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 116.01 0.001839 5532810000 15805800 17817500 14992900 16304400 16969300 18785600 18795200 19083100 22097400 21477800 FALSE TRUE 15188091.86 17309362.35 17702450.55 17145872.04 17515132.95 19165457.7 19025221.28 18689027.32 19588995.79 20023089.48 0.758528891 0.864470109 0.884101855 0.85630502 0.874746775 0.95716786 0.950164124 0.93337381 0.978320344 1 24.25516126 7.999999449 0.188318932 1.00983017 4.79E-10 0.857301642 0.025837328 19.97418459 0.231745069 0.05454694 5.854305593 99999873.11 -7.999999449 -1.00983017 FNDS(ph)EGDDTEETEDYR ddPTM_BT-474_Pertuzumab_2h_R1 7 FNDSEGDDTEETEDYR 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 FNDS(0.999)EGDDT(0.001)EETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR 392.91 1.54E-121 13605513000 2857660 2720845 2437767 2728840 2650407 2886394 2669529 3143793 3099033 3141957 TRUE FALSE 2745979.488 2643249.165 2878325.725 2869675.759 2735659.748 2944758.864 2702199.494 3078872.576 2747243.766 2929149.454 0.9374665 0.902394776 0.982648981 0.979695917 0.933943382 1.005328991 0.922520184 1.05111488 0.93789812 1 21.48205037 7.999999479 0.237240102 0.999366761 0.523442124 0.190721522 0.039186619 67.31035201 0.895986552 0.05112475 12.5727763 99999879.97 -7.999999479 -0.475924638 LDDIHPFYADLMNILYDKDHYK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDDIHPFYADLMNILYDKDHYK 22 1 Q9BZE4-2;Q9BZE4;Q5T3R7 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ; 246.71 3.57E-31 571700000 1187760 1003950 868040 828020 956080 982100 933720 759740 1266950 1074280 FALSE TRUE 1141341.026 975318.329 1024914.137 870754.2114 986833.1815 1001958.735 945147.1447 744051.1035 1123131.147 1001518.059 1.13961103 0.973839983 1.023360616 0.869434359 0.985337381 1.000440008 0.943714531 0.742923302 1.121428753 1 19.933757 7.999999508 0.777392352 0.932220414 44.37164285 0.207108394 0.096722494 607.5367895 2.311241746 0.033516262 46371.34822 99999886.61 -7.999999508 43.43942244 DRIESLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 DRIESLEK 8 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 58.699 0.094209 197910000 153920 167710 143600 175400 169490 167090 197050 186410 194080 221930 FALSE TRUE 147904.6362 162927.075 169551.7144 184452.415 174941.7998 170468.6743 199461.5568 182560.5684 172048.852 206898.4834 0.714865734 0.78747351 0.819492302 0.891511682 0.845544138 0.823924233 0.96405519 0.882367842 0.831561688 1 17.65856354 7.999999509 0.180461748 0.963512409 6.32E-12 0.638936955 0.047333276 37.22822837 0.419382592 0.105499998 9.856460716 99999886.9 -7.999999509 -0.963512409 HFTEDIQTR ddPTM_BT-474_Pertuzumab_2h_R1 3 HFTEDIQTR 9 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;A8MPP7;A8MPY5;E7ETV6;Q9UPE1-2;Q9UPE1-3;Q9UPE1-4;Q9UPE1;H7C2I2;P78362;P78362-2;H7C521 H3BLV9;P78362 SRPK1;SRPK3;SRPK2 SRSF protein kinase 1;SRSF protein kinase 3;SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 ;; 185.29 4.30E-05 1095300000 832050 810840 824500 1013390 888550 831110 1022500 906880 1097710 1177240 FALSE TRUE 799532.5661 787715.6371 973505.4909 1065691.179 917131.0177 847915.6136 1035013.661 888152.6111 973102.5628 1097504.486 0.728500499 0.71773341 0.887017323 0.971013051 0.83565127 0.7725851 0.943060984 0.809247363 0.886650191 1 20.06579541 7.999999539 0.036997633 1.389255253 8.87E-08 0.383888481 0.073787184 1105.611531 3.120726045 33.57689898 100.0836166 99999893.88 -7.999999539 -1.389255164 TRLQQELDDLLVDLDHQR ddPTM_BT-474_Pertuzumab_2h_R1 4 TRLQQELDDLLVDLDHQR 18 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 139.08 3.87E-07 104984000 183123 226506 72635.2 71430 112010 197553 89464 95870 98906 72275.8 FALSE TRUE 175966.3507 220046.2707 85761.9964 75116.51086 115612.9034 201547.657 90558.88719 93890.251 87678.60553 67380.49569 2.611532446 3.265726504 1.272801506 1.114810897 1.715821503 2.991186915 1.343992594 1.393433664 1.301246075 1 16.04004342 7.999999582 0.419947332 1.441796037 30.33170997 0.321928006 0.650597224 95.20080451 1.221625699 0.444351311 2309.853915 99999903.72 -7.999999582 28.88991393 TVS(ph)SPIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 T(0.125)VS(0.868)S(0.007)PIPY(0.006)T(0.075)PS(0.05)PS(0.042)S(0.038)S(0.034)RPIS(0.752)PGLS(0.003)YASHTVGFTPPTSLTR 131.89 1.04E-08 1384300000 37947 36639 21274 20206 24431 26672 15148 31921 18647 16179 TRUE FALSE 36463.98929 35594.09159 25118.68504 21248.83408 25216.8453 27211.32611 15333.38576 31261.8202 16530.27073 15083.18192 2.417526321 2.359852966 1.665343902 1.408776623 1.671851831 1.80408393 1.016588266 2.07262767 1.095940553 1 13.88065319 7.999999586 0.41615066 1.411941193 22.22032389 0.531377165 0.341246419 62.45668484 0.807155608 0.220911199 1078.584228 99999904.63 -7.999999586 20.8083827 QFDTDR ddPTM_BT-474_Pertuzumab_2h_R1 4 QFDTDR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;K7EIV0;A0A075B7C0;U3KPR7 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ;;; 132.96 0.034132 3549140000 5890440 6131740 5263600 5986650 6455650 4781350 6642780 6802000 7007410 7266670 FALSE TRUE 5660235.093 5956868.779 6214849.608 6295621.724 6663301.845 4878032.173 6724076.329 6661536.323 6211958.194 6774491.968 0.835521707 0.87930856 0.917389767 0.929312745 0.983586943 0.720058743 0.992558019 0.98332633 0.916962958 1 22.69168133 7.999999586 0.070897064 1.101503438 0.482240905 0.192879676 0.074308848 407.3263118 2.128364733 3.200063125 25.11976225 99999904.69 -7.999999586 -0.619262532 S(ph)AS(ph)PHDVDLCLVSPCEFEHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(1)AS(1)PHDVDLCLVSPCEFEHR 90.912 0.00098741 31106000 17514 23367 18495 16952 21619 20973 22857 20125 28197 26074 TRUE FALSE 16829.53352 22700.59604 21837.45792 17826.89475 22314.39477 21397.08843 23136.7308 19709.41172 24996.19477 24307.98476 0.692345897 0.933874045 0.898365625 0.733376087 0.917986209 0.880249377 0.951816082 0.810820474 1.028312097 1 14.56914267 7.999999633 0.056865127 1.215426906 0.203538947 0.351171174 0.083520944 474.0133851 2.019412344 7.624452623 40.33611472 99999915.48 -7.999999633 -1.011887959 NFHEVMLALTVLETCVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NFHEVMLALTVLETCVK 17 0 O60784;O60784-4;O60784-2;O60784-3;V9GYF4;B0QY02;V9GZ68;Q6UW50;H7BYN7 O60784 TOM1 Target of Myb protein 1 0 149.57 3.20E-07 52087000 171510 153970 114910 110740 134670 138620 122420 106890 156470 137040 FALSE TRUE 164807.1996 149578.9264 135676.7932 116455.3047 139001.7829 141422.9914 123918.2126 104682.6841 138708.1816 127758.1587 1.289993541 1.170797449 1.061981438 0.911529297 1.088007093 1.106958591 0.969943633 0.819381597 1.085708991 1 16.9630559 7.999999654 0.513724502 0.967041072 12.91785646 0.536099388 0.086035563 86.99422636 0.888101622 0.047344944 1129.421769 99999920.4 -7.999999654 11.95081539 KAQVS(ph)PQS ddPTM_BT-474_Pertuzumab_2h_R1 2 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.978)PQS(0.022);KAQVS(0.97)PQS(0.03) 84.896 0.018142 8932800000 5583200 5446300 4213600 5107200 4960500 4912100 5169900 5280900 5511600 5561300 TRUE FALSE 5365002.371 5290976.856 4975091.251 5370783.204 5120058.988 5011426.028 5233170.783 5171847.57 4885946.275 5184628.198 1.034790185 1.020512302 0.959584962 1.03590518 0.987546029 0.966593136 1.00936279 0.9975349 0.942390869 1 22.3058091 7.999999702 0.667478597 0.98776477 5.985294759 0.25121183 0.025999771 342.2786345 2.053271651 0.009679277 2537.381834 99999931.36 -7.999999702 4.997529989 LDLHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDLHLK 6 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 76.592 0.07465 1171240000 5163500 5093100 4562600 5096400 5428700 4632600 5734800 5615800 6620300 6413200 FALSE TRUE 4961704.711 4947849.775 5387163.314 5359425.815 5603319.066 4726274.346 5804984.198 5499831.768 5868791.299 5978828.252 0.829879117 0.827561784 0.901039984 0.896400697 0.937193515 0.790501775 0.970923391 0.919884555 0.981595565 1 22.51143134 7.999999704 0.085849576 1.092940358 0.365741583 0.518412846 0.046724277 133.4571796 0.827779025 0.971724329 11.454756 99999931.81 -7.999999704 -0.727198774 LEDLLR ddPTM_BT-474_Pertuzumab_2h_R1 5 LEDLLR 6 0 P12956;B1AHC9;P12956-2;A0A494C174;A0A494C0S6;P51449-2;P51449 P12956 XRCC6;RORC X-ray repair cross-complementing protein 6;Nuclear receptor ROR-gamma 0 ;;;; 206.5 0.00025763 1271700000 1775310 1926450 1905780 2353890 1978050 1548920 2223290 2316290 2266290 2576640 FALSE TRUE 1705928.922 1871509.532 2250196.84 2475374.545 2041675.775 1580240.224 2250499.288 2268457.802 2009030.26 2402121.878 0.71017584 0.779106818 0.936753818 1.030494984 0.849946788 0.657851809 0.936879727 0.944355831 0.836356506 1 21.19587792 7.999999732 0.036981571 1.352164629 0.111996768 0.180365808 0.106133059 1799.321102 5.076666022 48.79288322 145.3700408 99999938.24 -7.999999732 -1.240167861 EFFCPEHSECICHICLVEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFFCPEHSECICHICLVEHK 20 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 145.88 4.86E-08 197540000 103260 64985 60768 41273 53097 52547 49549 51152 60612 58400 FALSE TRUE 99224.48504 63131.69143 71750.12938 43403.10448 54804.91323 53609.53634 50155.39548 50095.69332 53731.57987 54444.51598 1.822488147 1.159560156 1.317857788 0.797198831 1.006619533 0.984663659 0.921220339 0.92012377 0.986905272 1 15.73249912 7.999999755 0.752295925 0.943127306 157.9885119 0.845989383 0.109118783 125.1651697 0.530349432 0.035090713 33324.22451 99999943.57 -7.999999755 157.0453846 HKS(ph)DS(ph)PES(ph)DAER ddPTM_BT-474_Pertuzumab_2h_R1 1 HKSDSPESDAER 12 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 3 HKS(1)DS(1)PES(1)DAER 79.462 0.038646 53639000 201660 162140 138150 141600 140380 135840 151060 113890 235050 149710 TRUE FALSE 193778.9043 157515.926 163116.7781 148907.993 144895.4502 138586.7779 152908.7175 111538.1317 208368.1094 139570.0084 1.388399317 1.128580042 1.168709381 1.066905381 1.038156062 0.992955288 1.095570024 0.799155442 1.492928974 1 17.09062943 7.999999773 0.729562893 1.042112639 53.61964578 0.224372993 0.16642009 441.5670049 2.061238823 0.056570188 38051.32893 99999947.79 -7.999999773 52.57753314 DAVIEFLLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAVIEFLLDK 10 0 Q9BY42;A2A2L6;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ; 137.98 0.00017897 170551000 411880 446310 330376 325770 425120 395590 391090 379960 442250 409710 FALSE TRUE 395783.2742 433581.6758 390082.2924 342583.0287 438794.3709 403589.1008 395876.2764 372113.6932 392047.6341 381959.9768 1.036190434 1.135149498 1.021264834 0.896908183 1.148796726 1.056626677 1.036433921 0.974221688 1.026410247 1 18.54306195 7.999999793 0.150574517 0.98785857 1.291750087 0.061089746 0.06690075 188.9822776 1.86326656 0.23570326 12.57029572 99999952.28 -7.999999793 0.303891517 EGPTDHLESACPLNLPLQNNHTAADMY(ph)LSPVRS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 EGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 35 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 EGPTDHLESACPLNLPLQNNHT(0.034)AADMY(0.663)LS(0.316)PVRS(0.986)PK 157.19 2.78E-12 177050000 53919 44446 36323 40017 39050 42163 36299 42004 47083 45343 TRUE FALSE 51811.78587 43178.4436 42887.3741 42082.28217 40306.07871 43015.56475 36743.23802 41136.60272 41738.33523 42271.87822 1.225679767 1.021446063 1.01456041 0.995514842 0.953496282 1.017592938 0.869212336 0.973143481 0.987378299 1 15.3674106 7.999999798 0.868235464 0.963651756 105.2334417 0.781043118 0.039634611 320.1365121 0.807287406 0.012274752 66020.0402 99999953.58 -7.999999798 104.26979 S(ph)PISVPGGSALISNLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPISVPGGSALISNLGK 17 0 P51610-2;P51610;A6NEM2;P51610-4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 S(0.999)PIS(0.001)VPGGSALISNLGK;S(1)PISVPGGSALISNLGK 225.81 2.39E-15 750270000 897430 824450 916540 950740 935050 855440 965370 1100160 1038910 1208250 TRUE FALSE 862357.4434 800937.4932 1082179.166 999807.8053 965126.7324 872737.5829 977184.4868 1077441.312 920977.2923 1126414.151 0.765577601 0.711050631 0.960729377 0.887602312 0.856813394 0.774792808 0.867517942 0.956523238 0.817618716 1 20.10330593 7.999999801 0.037355956 1.395734409 0.01336717 0.344214151 0.072453585 1032.469441 2.941714513 31.02283869 93.44307546 99999954.12 -7.999999801 -1.382367239 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCTSTAIAS(1)PEK;HIKEEPLS(1)EEEPCTSTAIAS(1)PEK 129.9 4.87E-05 2480300000 1287670 983370 761470 739670 870550 841150 896600 589590 1086580 859510 TRUE FALSE 1237346.433 955325.2504 899084.5678 777844.4573 898552.0314 858158.6293 907572.859 577414.7605 963235.9937 801294.6221 1.544184122 1.192227208 1.122039938 0.970734653 1.121375343 1.070965168 1.132633159 0.720602316 1.202099661 1 19.61197327 7.999999804 0.712150891 1.001029379 75.31219798 0.596303667 0.125337576 203.0069761 1.01879198 0.046484987 24070.59214 99999954.98 -7.999999804 74.3111686 DSSEATGWEEPS(ph)PPSIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DSSEATGWEEPSPPSIR 17 0 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 DSSEAT(0.004)GWEEPS(0.973)PPS(0.023)IR;DSSEATGWEEPS(1)PPSIR 235.78 3.78E-20 410530000 278820 300840 260490 317110 305070 321420 324180 322370 355720 402980 TRUE FALSE 267923.4061 292260.3378 307566.3376 333476.0851 314882.8536 327919.3326 328147.4118 315712.9468 315340.1569 375685.8057 0.713158182 0.777938196 0.818679686 0.887646219 0.83815478 0.872855263 0.873462364 0.840364321 0.839372029 1 18.51916708 7.999999843 0.03987393 1.358675151 8.73E-13 0.716048947 0.037712981 475.6086429 1.443628807 13.4933006 43.7392037 99999963.83 -7.999999843 -1.358675151 EDKNGHDGDTHQEDDGEKS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 6 EDKNGHDGDTHQEDDGEKSD 20 2 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D 271.12 1.13E-44 3061170000 2562940 1867710 1342660 1091368 1665470 1649031 1536658 395526 2358560 1361974 TRUE FALSE 2462777.471 1814444.739 1585308.529 1147693.633 1719041.355 1682375.537 1555464.08 387358.2499 2090826.157 1269726.288 1.939612887 1.429004626 1.24854352 0.903890582 1.353867658 1.324990711 1.225038888 0.305072246 1.646674702 1 20.2760861 7.999999843 0.588921282 1.019071576 54.86730298 0.343367689 0.339532145 173.0274427 1.388109266 0.152863439 11948.8875 99999963.86 -7.999999843 53.8482314 RKEEEERR ddPTM_BT-474_Pertuzumab_2h_R1 2 RKEEEERR 8 3 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;Q5JVM0;O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6;Q9H3P7;A0A0J9YYF7;Q86T65-4;Q86T65 Q9UM54-1;O95819-3;Q9H3P7;A0A0J9YYF7 MYO6;MAP4K4;ACBD3;DAAM2 Unconventional myosin-VI;Mitogen-activated protein kinase kinase kinase kinase 4;Golgi resident protein GCP60;Disheveled-associated activator of morphogenesis 2 0 ; 97.431 0.010073 115133000 49367 47105 32389 34898 45439 43981 36531 40290 42967 36361 FALSE TRUE 47437.68306 45761.61152 38242.41279 36699.08996 46900.5867 44870.32595 36978.07731 39457.99742 38089.56629 33898.23708 1.399414458 1.349970248 1.12815344 1.082625326 1.383570083 1.323677271 1.090855469 1.164013259 1.12364446 1 15.04892263 7.999999853 0.048143769 0.539675634 2.414456785 0.442994304 0.102607724 546.6095019 1.988916963 18.74391154 77.22145603 99999966.24 -7.999999853 1.874781152 FGINIPS(ph)PEHSNTIDVCNTVDIK ddPTM_BT-474_Pertuzumab_2h_R1 2 FGINIPSPEHSNTIDVCNTVDIK 23 0 C9IZ03;Q9HCI7-2;Q9HCI7 C9IZ03 MSL2 E3 ubiquitin-protein ligase MSL2 1 FGINIPS(1)PEHSNTIDVCNTVDIK;FGINIPS(0.999)PEHS(0.001)NTIDVCNTVDIK 322.77 5.48E-74 529930000 816140 728000 621920 617300 676250 723830 669690 686540 779900 735500 TRUE FALSE 784244.3465 707238.1528 734314.7785 649158.927 698002.1954 738466.3385 677885.8665 672362.7091 691369.0216 685683.9299 1.143740304 1.031434633 1.070923127 0.946732013 1.017964933 1.076977754 0.988627321 0.98057236 1.008291126 1 19.38718419 7.999999858 0.825334116 1.004181317 42.18814955 0.555176988 0.03610435 437.9289912 1.344765564 0.011954827 33801.29188 99999967.34 -7.999999858 41.18396823 GAKEEHGGLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAKEEHGGLIR 11 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 137.16 5.06E-05 2019430000 3217300 3503600 2356800 2560800 2927300 3383800 2840900 2966700 3136200 2995100 FALSE TRUE 3091564.359 3403680.758 2782726.187 2692963.195 3021459.263 3452222.754 2875667.784 2905436.608 2780191.724 2792239.209 1.107198964 1.218978928 0.996593049 0.964445734 1.08209184 1.23636354 1.029878735 1.040540008 0.995685368 1 21.41299111 7.999999864 0.091441398 0.943562804 1.448540051 0.143396967 0.083170168 326.6495627 2.140992554 1.514458134 20.69010393 99999968.76 -7.999999864 0.504977247 KRTS(ph)ESR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRTSESR 7 2 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 KRT(0.476)S(0.517)ES(0.007)R 63.184 0.063761 129770000 273510 301090 208040 214980 229410 242550 246930 293040 204630 234020 TRUE FALSE 262820.9268 292503.208 245637.4558 226075.1436 236789.181 247454.5272 249952.0032 286988.6216 181401.2603 218169.617 1.204663282 1.340714679 1.125901302 1.03623569 1.085344441 1.134230012 1.145677417 1.315438078 0.831468941 1 17.73509068 7.999999877 0.061571073 0.808204879 1.846661088 0.219417232 0.125197646 609.3656077 2.796294894 9.324817561 56.37832731 99999971.7 -7.999999877 1.03845621 (ac)SLHQFLLEPITCHAWNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLHQFLLEPITCHAWNR 17 0 A0A1W2PNV4;E9PF58;F8WFD3;Q92747 A0A1W2PNV4;Q92747 ARPC1A Actin-related protein 2/3 complex subunit 1A 0 ; 134.14 1.71E-46 3064200000 135602 155368 110398 103242 110453 93068 142041 109902 91316 90534 FALSE TRUE 130302.5239 150937.0568 130349.3744 108570.332 114005.8211 94949.89873 143779.3402 107632.4853 80950.19051 84402.05154 1.54383124 1.788310284 1.544386327 1.286347073 1.350747037 1.124971455 1.703505278 1.275235416 0.959102167 1 16.36499045 7.999999892 0.10089299 0.760138393 3.461642283 0.502309233 0.190272903 110.4445996 0.787740035 2.373666872 41.33957222 99999975.05 -7.999999892 2.70150389 TFS(ph)LTEVR ddPTM_BT-474_Pertuzumab_2h_R1 3 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.375)FS(0.625)LTEVR;T(0.042)FS(0.906)LT(0.053)EVR;T(0.009)FS(0.978)LT(0.013)EVR 163.66 0.00035098 1173768000 1205460 1156920 957340 1047370 1063720 1047570 927430 1250730 1020860 1082340 TRUE FALSE 1158349.29 1123925.774 1130352.634 1101424.891 1097935.52 1068752.583 938780.1658 1224901.988 904976.2526 1009032.148 1.14798056 1.113865179 1.12023451 1.091565708 1.088107571 1.05918586 0.930376864 1.213937525 0.89687554 1 19.94454071 7.999999896 0.133886057 0.972563439 1.574277143 0.261039034 0.079894506 123.5494034 1.111699086 0.374219174 14.12057474 99999976.12 -7.999999896 0.601713704 DLHPDLEGQLK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLHPDLEGQLK 11 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;;; 199.68 4.94E-08 1498850000 2979020 3442420 2791580 3109980 3191500 3370250 3539620 3218780 4226430 4093980 FALSE TRUE 2862596.605 3344245.552 3296080.604 3270486.441 3294157.496 3438398.764 3582938.928 3152311.068 3746663.385 3816691.088 0.750020512 0.876215935 0.863596379 0.856890528 0.863092511 0.900884741 0.938755285 0.825927746 0.981652248 1 21.86389099 7.999999905 0.038127758 1.36121399 0.110078547 0.600059514 0.044366964 628.7214031 1.827290269 16.88903409 52.02998425 99999978.1 -7.999999905 -1.251135442 SIEHLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 SIEHLDK 7 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 76.899 0.039508 378410000 751020 862850 710470 858080 858730 830700 836400 862740 942310 1015600 FALSE TRUE 721669.3081 838242.3628 838867.7333 902365.6116 886351.8303 847497.3232 846636.1134 844924.1175 835342.9193 946812.5074 0.76220931 0.885330893 0.885991394 0.953056286 0.936142925 0.895105754 0.894196165 0.892387998 0.882268572 1 19.85271924 7.999999911 0.018209576 1.614164528 5.96E-06 0.417419583 0.044460858 4502.459811 6.321793166 213.3652463 366.0191893 99999979.55 -7.999999911 -1.614158568 MYFPDVEFDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 MYFPDVEFDIK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 102.06 0.005277 0 154360 151070 116020 133710 141660 132050 139740 126190 170270 132810 FALSE TRUE 148327.4405 146761.6315 136987.3949 140610.7891 146216.6226 134720.1415 141450.1799 123584.1324 150941.6634 123814.6604 1.197979626 1.185333231 1.106390749 1.135655412 1.180931419 1.088079077 1.142434825 0.99813812 1.219093627 1 16.91782262 7.999999915 0.017089185 0.003380498 2.504048321 0.347538202 0.059791225 4283.670027 5.646841938 319.9682327 531.0058259 99999980.39 -7.999999915 2.500667823 MLAEDELRDAVLLVFANK ddPTM_BT-474_Pertuzumab_2h_R1 2 MLAEDELRDAVLLVFANK 18 1 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 225.11 3.87E-19 889620000 809830 933920 457060 579920 686260 831930 622200 554280 596420 503660 FALSE TRUE 778180.9483 907285.516 539660.9092 609849.7407 708334.1761 848752.1946 629814.6697 542833.9243 528716.902 469546.6596 1.657302703 1.932258483 1.149323285 1.298805408 1.508549069 1.80759926 1.341324993 1.156080899 1.126015682 1 18.840909 7.999999915 0.076252611 0.505736918 3.67634163 0.423727005 0.227542758 216.376889 1.207687661 7.990912007 72.69589602 99999980.44 -7.999999915 3.170604712 EQLSAQELMESGLQIQKS(ph)PEPEVLSTQEDLFDQSNK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQLSAQELMESGLQIQKSPEPEVLSTQEDLFDQSNK 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 EQLS(0.237)AQELMES(0.08)GLQIQKS(0.682)PEPEVLSTQEDLFDQSNK 104.4 1.64E-05 74189000 25686 23520 13941 15653 20734 21883 17717 20692 23086 17255 TRUE FALSE 24682.16272 22849.23263 16460.44882 16460.85321 21400.92794 22325.48925 17933.82595 20264.70297 20465.37406 16086.30348 1.534358888 1.420415365 1.023258627 1.023283766 1.330381959 1.387857023 1.114850653 1.259748891 1.272223546 1 13.97354522 7.999999926 0.023421469 9.70E-13 2.892541303 0.228983624 0.156521192 4288.451588 7.727344845 335.8718895 672.0325747 99999983.06 -7.999999926 2.892541303 KFDDRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFDDRPK 7 2 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 86.794 0.011145 448640000 2032600 1952100 1888000 2084700 2133800 2019400 2226100 2396300 2711700 2791800 FALSE TRUE 1953163.745 1896428.019 2229203.598 2192291.617 2202435.615 2060233.652 2253343.678 2346815.568 2403879.184 2602708.899 0.750434958 0.728636237 0.856493632 0.842311492 0.846208969 0.791572831 0.865768614 0.901681924 0.923606626 1 21.31158253 7.999999934 0.065378072 1.215965655 0.027449613 0.810449227 0.033443106 122.7548295 0.595490888 2.022204113 13.60953828 99999984.75 -7.999999934 -1.188516042 DHSVFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DHSVFQR 7 0 Q8WW22-3;Q8WW22;Q8WW22-2 Q8WW22-3 DNAJA4 DnaJ homolog subfamily A member 4 0 85.265 0.020938 157530000 205870 166150 154130 145070 151840 160660 140940 165370 156210 175010 FALSE TRUE 197824.3728 161411.5647 181984.7196 152557.0801 156724.0715 163908.6553 142664.8659 161955.0517 138477.6957 163156.4168 1.212482945 0.989305648 1.11540032 0.935035735 0.960575591 1.004610536 0.874405486 0.992636728 0.848741952 1 17.3158962 7.999999944 0.502406174 0.9378139 9.101416081 0.585494288 0.065225602 71.82297457 0.757336994 0.031128586 619.522479 99999987.15 -7.999999944 8.163602181 AELEQHLEQEQEFQVNK ddPTM_BT-474_Pertuzumab_2h_R1 2 AELEQHLEQEQEFQVNK 17 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 258.61 3.59E-27 416980000 345640 348540 304370 305220 356660 355760 358290 360340 414840 415200 FALSE TRUE 332132.0067 338599.9805 359376.4297 320972.4408 368132.2928 362953.711 362674.8602 352898.8531 367749.1024 387078.1342 0.858049002 0.874758739 0.928433817 0.829218735 0.95105422 0.937675572 0.936955173 0.911699272 0.950064263 1 18.56226529 7.999999944 0.056059739 1.140586124 0.466217687 0.5867287 0.030887682 277.0204973 1.164458074 3.008342867 15.55404492 99999987.18 -7.999999944 -0.674368437 SS(ph)PVPPVPER ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.012)S(0.988)PVPPVPER;S(0.144)S(0.856)PVPPVPER 129.82 0.00030737 3483500000 1578020 1492030 1327050 1516670 1507090 1657430 1695280 1632930 1989120 1989030 TRUE FALSE 1516349.234 1449478.765 1566877.455 1594945.52 1555566.919 1690944.37 1716027.344 1599209.425 1763323.437 1854311.226 0.817742573 0.781680413 0.844991624 0.860128277 0.838892035 0.911898901 0.925425743 0.862427732 0.950931759 1 20.82245197 7.999999947 0.068174827 1.159953211 0.216633067 0.812646314 0.027262538 107.7926845 0.543442183 1.347501624 9.80657489 99999987.83 -7.999999947 -0.943320144 S(ph)RKSPHKDLGHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRKSPHKDLGHR 12 3 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(0.595)RKS(0.405)PHKDLGHR;S(0.5)RKS(0.5)PHKDLGHR 104.45 0.00086932 356664000 387920 357610 207360 180629 251630 285570 232740 53671 274970 170927 TRUE FALSE 372759.6575 347411.3129 244834.5647 189951.2843 259723.9075 291344.4211 235588.3417 52562.67509 243756.5584 159349.962 2.339251624 2.180178197 1.536458256 1.192038466 1.629896262 1.828330659 1.478433623 0.329856841 1.529693231 1 17.28183915 7.999999954 0.252481212 0.901556838 10.60390981 0.505089314 0.385849499 40.71710405 0.557124291 0.531030722 168.3834106 99999989.43 -7.999999954 9.702352973 GDLAFGAPGPRPPS(ph)PFDDPADDPEHK ddPTM_BT-474_Pertuzumab_2h_R1 7 GDLAFGAPGPRPPSPFDDPADDPEHK 26 1 Q7Z3Z5;Q93074-3;Q93074;Q93074-2 Q7Z3Z5 TNRC11;MED12 Mediator of RNA polymerase II transcription subunit 12 1 GDLAFGAPGPRPPS(1)PFDDPADDPEHK;GDLAFGAPGPRPPS(1)PFDDPADDPEHK;GDLAFGAPGPRPPS(1)PFDDPADDPEHK;GDLAFGAPGPRPPS(1)PFDDPADDPEHK;GDLAFGAPGPRPPS(1)PFDDPADDPEHK;GDLAFGAPGPRPPS(1)PFDDPADDPEHK;GDLAFGAPGPRPPS(1)PFDDPADDPEHK 196.06 4.25E-25 5891850000 2575760 2407273 2302747 2394036 2626453 2606281 2734623 2658183 3264482 3262862 TRUE FALSE 2475096.452 2338619.931 2718904.607 2517592.485 2710935.246 2658981.788 2768090.134 2603290.592 2893911.689 3041865.45 0.813677164 0.768811103 0.893828031 0.827647549 0.891208139 0.874128666 0.909997559 0.855820428 0.951360846 1 21.53652491 7.999999958 0.035195956 1.437809926 9.13E-08 0.717600381 0.033949077 510.9456938 1.373776843 16.52593999 46.73256969 99999990.31 -7.999999958 -1.437809835 (ac)AS(ph)PGIEVELLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASPGIEVELLGK 12 0 Q8TCY9 Q8TCY9 URGCP Up-regulator of cell proliferation 1 AS(1)PGIEVELLGK 62.823 8.53E-05 27263000 51965 60732 53647 54480 61741 56932 63109 59927 68684 73275 TRUE FALSE 49934.15035 58999.98282 63342.20627 57291.71933 63726.95534 58083.20405 63881.34682 58689.48651 60887.28027 68312.01898 0.730971666 0.863683781 0.927248341 0.838677003 0.932880572 0.85026332 0.935140664 0.859138514 0.891311385 1 16.05985181 7.999999958 0.024972117 1.528094829 1.50E-07 0.453857375 0.051207895 2008.936768 3.856547329 81.13156427 169.9259741 99999990.35 -7.999999958 -1.528094679 TAS(ph)GSSVTSLDGTR ddPTM_BT-474_Pertuzumab_2h_R1 10 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 TAS(0.843)GS(0.156)SVTSLDGTR;TAS(0.998)GS(0.002)SVTSLDGTR;T(0.011)AS(0.987)GS(0.001)SVTSLDGTR;T(0.007)AS(0.971)GS(0.018)S(0.002)VT(0.002)SLDGTR;TAS(0.925)GS(0.075)SVTSLDGTR;TAS(0.714)GS(0.286)SVTSLDGTR;TAS(0.995)GS(0.004)SVTSLDGTR;TAS(0.966)GS(0.034)SVTSLDGTR;TAS(0.999)GSSVTSLDGTR;TAS(0.985)GS(0.014)S(0.001)VTSLDGTR 350.73 6.92E-82 1.25584E+11 9107010 9589850 6941250 6388140 6671440 6874600 4967581 5988790 6133810 3320050 TRUE FALSE 8751097.981 9316356.867 8195688.282 6717832.671 6886032.926 7013609.122 5028375.742 5865119.394 5437525.604 3095180.056 2.827330825 3.009956351 2.647887403 2.170417407 2.224760047 2.265977744 1.624582625 1.894920259 1.756771983 1 21.56159191 7.999999959 0.099478312 0.305508568 8.322520138 0.91061506 0.171312106 33.0768432 0.233100275 2.154744275 36.20764949 99999990.65 -7.999999959 8.017011571 YQES(ph)PGIQMK ddPTM_BT-474_Pertuzumab_2h_R1 1 YQESPGIQMK 10 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 1 Y(0.003)QES(0.997)PGIQMK 63.727 0.073337 0 131570 128250 130150 145920 130210 142340 150730 158820 163380 178520 TRUE FALSE 126428.0989 124592.4356 153671.0002 153450.9487 134398.3229 145218.2123 152574.6788 155540.3115 144833.7873 166428.6814 0.759653311 0.748623582 0.923344455 0.922022258 0.807543038 0.872555206 0.916757121 0.934576361 0.870245358 1 17.34454456 7.99999996 0.199588043 0.965926974 1.05E-09 0.550824942 0.051618131 42.42008407 0.511522902 0.098296458 12.82114356 99999990.71 -7.99999996 -0.965926973 GEADRDTYRR ddPTM_BT-474_Pertuzumab_2h_R1 7 GEADRDTYRR 10 2 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;;; 175.49 1.57E-06 3499833700 3628112.9 4286769 2361173.6 2807259.3 3051406 3831478 3015022.2 2721342.8 2997678.3 2807555.8 FALSE TRUE 3486322.237 4164514.545 2787890.194 2952142.289 3149557.245 3908953.11 3051920.944 2665146.12 2657394.427 2617397.545 1.331980403 1.591089803 1.065138232 1.127892205 1.203316344 1.493450285 1.166013527 1.018242768 1.015281164 1 21.31970163 7.999999965 0.127062407 0.882938419 2.647095841 0.351552742 0.158654601 97.15042734 0.838447403 0.942702243 30.61800811 99999992.03 -7.999999965 1.764157422 T(ph)PTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_BT-474_Pertuzumab_2h_R1 4 TPTQPPPEPGDLPTIEEALQIIHSAEPR 28 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 T(0.827)PT(0.173)QPPPEPGDLPTIEEALQIIHSAEPR;T(0.97)PT(0.03)QPPPEPGDLPTIEEALQIIHSAEPR;T(0.983)PT(0.017)QPPPEPGDLPTIEEALQIIHSAEPR;T(0.781)PT(0.219)QPPPEPGDLPTIEEALQIIHSAEPR 177.98 6.37E-17 355496000 46678.5 42949.6 55648.7 60184.8 47423.1 56430 54796.2 53516.3 61717.1 70173.7 TRUE FALSE 44854.25261 41724.71946 65705.65799 63290.94474 48948.50708 57571.05326 55466.81229 52411.1697 54711.23355 65420.77279 0.685627068 0.637790073 1.00435466 0.967444162 0.748210469 0.880011819 0.847847097 0.801139569 0.836297574 1 15.99746118 7.999999967 0.035038316 1.378905148 4.87E-08 0.23373089 0.105473088 1869.455237 5.004441221 58.13344634 163.6352608 99999992.46 -7.999999967 -1.378905099 SKTPSS(ph)PCPASK ddPTM_BT-474_Pertuzumab_2h_R1 5 SKTPSSPCPASK 12 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 S(0.003)KT(0.008)PS(0.027)S(0.963)PCPASK;S(0.001)KT(0.004)PS(0.102)S(0.893)PCPASK;S(0.002)KT(0.002)PS(0.044)S(0.952)PCPASK;S(0.017)KT(0.017)PS(0.247)S(0.719)PCPASK;S(0.009)KT(0.009)PS(0.099)S(0.883)PCPASK 120.63 0.00023659 2521970000 3675800 3116490 2429290 2690270 2629510 2632360 2793870 3110900 2506440 2689080 TRUE FALSE 3532145.672 3027610.757 2868316.742 2829115.157 2714090.577 2685588.123 2828062.217 3046658.828 2221919.439 2506946.216 1.408943538 1.207688756 1.144147698 1.128510512 1.082628163 1.071258771 1.128090502 1.215286873 0.886305189 1 21.25749961 7.999999969 0.702065826 1.085914863 42.56556969 0.615095907 0.081656663 204.4129408 1.068073286 0.029974598 13315.50617 99999992.86 -7.999999969 41.47965482 KIPLEDEVPGVPGEMEPEPGYRGDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KIPLEDEVPGVPGEMEPEPGYRGDR 25 2 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 0 135.62 2.15E-05 197350000 124270 139650 85439 90800 104280 138910 99720 99488 103930 100610 FALSE TRUE 119413.391 135667.3187 100879.7279 95486.19888 107634.2609 141718.8554 100940.4032 97433.53803 92132.30211 93795.59509 1.273123657 1.446414606 1.075527351 1.018024341 1.147540679 1.510932952 1.076174239 1.038785861 0.982266833 1 16.51723255 7.99999997 0.117923044 0.894015152 2.238787977 0.255809806 0.155337959 141.1995825 1.147047333 1.181995706 31.14885588 99999993.12 -7.99999997 1.344772825 WQHDLFDSGFGGGAGVETGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 WQHDLFDSGFGGGAGVETGGK 21 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 196.81 9.45E-22 457350000 266000 237200 233110 248910 262490 240040 251040 320340 264780 304770 FALSE TRUE 255604.4259 230435.2882 275238.1625 261756.2749 270933.2292 244893.7733 254112.3026 313724.8671 234723.2844 284127.6564 0.899611214 0.811027308 0.968713028 0.921262922 0.953561623 0.861914593 0.894359619 1.104168707 0.826119102 1 18.11617974 7.99999997 0.150895249 1.010166851 0.466148883 0.10130468 0.078625809 121.3426599 1.198320975 0.269908869 14.48667539 99999993.13 -7.99999997 -0.544017968 STFREES(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 6 STFREESPLR 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 STFREES(1)PLR;ST(0.001)FREES(0.999)PLR;STFREES(1)PLR;ST(0.001)FREES(0.998)PLR;STFREES(1)PLR;STFREES(1)PLR 191.48 4.77E-07 11172460000 6645100 7122060 3798770 3973770 5121360 4746610 4483200 4022620 4352860 4090710 TRUE FALSE 6385402.145 6918945.822 4485292.242 4178856.746 5286093.196 4842589.706 4538066.743 3939551.491 3858741.581 3813642.568 1.674357791 1.814261745 1.176117626 1.095765183 1.386100847 1.269806916 1.18995597 1.033015397 1.011825705 1 21.8627382 7.999999971 0.315317717 1.026791557 8.34272429 0.68680464 0.149567206 31.74206415 0.454736678 0.14687577 133.2114349 99999993.27 -7.999999971 7.315932733 DLGLPTEAYISVEEVHDDGTPTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLGLPTEAYISVEEVHDDGTPTSK 24 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;;; 299.42 4.11E-62 873831000 1060160 1090690 858492 1047450 1043420 1182450 1129120 1116640 1347170 1344650 FALSE TRUE 1018727.775 1059584.589 1013640.601 1101509.02 1076982.552 1206359.949 1142938.508 1093580.994 1194244.909 1253575.658 0.812657592 0.845249812 0.808599461 0.87869369 0.859128482 0.962335174 0.911742743 0.87236936 0.952670788 1 20.25761764 7.999999971 0.083382767 1.092821525 0.316303257 0.739802413 0.031334061 96.83499813 0.585369233 0.782530278 8.636090152 99999993.43 -7.999999971 -0.776518267 EGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSR 39 1 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 68.807 0.002401 32618000 16020 20609 10384 10223 15518 18161 15597 10849 15837 12123 FALSE TRUE 15393.92069 20021.2515 12260.61979 10750.61026 16017.15056 18528.22786 15787.88075 10624.96436 14039.25015 11301.89841 1.362065038 1.771494555 1.084828349 0.951221632 1.41720886 1.639390763 1.396922904 0.940104394 1.242202827 1 13.46427751 7.999999973 0.040333849 0.132308794 3.166046474 0.173714768 0.249189755 1351.477735 4.14796418 84.98668062 279.202785 99999993.79 -7.999999973 3.033737679 GIGTPPNTT(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIGTPPNTTPIK 12 0 O96028;O96028-5;O96028-3;O96028-6;D6RIS1;D6R9V2;O96028-7 O96028 WHSC1 Histone-lysine N-methyltransferase NSD2 1 GIGTPPNT(0.057)T(0.943)PIK 95.417 0.067725 113690000 214820 205970 187470 237080 206120 200840 230560 264020 230380 276530 TRUE FALSE 206424.5969 200095.9373 221349.9992 249315.7272 212750.037 204901.1224 233381.6622 258567.8947 204228.2282 257800.3768 0.800714877 0.776166194 0.858610069 0.967088296 0.825251071 0.794805364 0.905280532 1.002977179 0.792195228 1 17.97589485 7.999999974 0.076038901 1.105629698 0.297857051 0.299617609 0.071330055 260.6849267 1.45131865 2.461073157 22.25858625 99999993.95 -7.999999974 -0.807772648 SQDATFSPGSEQAEKS(ph)PGPIVSR ddPTM_BT-474_Pertuzumab_2h_R1 6 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(0.996)PGPIVS(0.003)R;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR 283.08 2.64E-52 5286890000 3329510 3160170 2579260 2486980 2954170 2887080 2471330 2790830 3018930 2475950 TRUE FALSE 3199389.068 3070045.046 3045389.657 2615333.336 3049193.561 2945458.736 2501574.876 2733198.385 2676233.723 2308251.701 1.386065942 1.330030449 1.319349036 1.13303646 1.320996995 1.276056131 1.083753074 1.184098937 1.159420232 1 21.13836912 7.999999975 0.080375216 0.800988619 2.341612003 0.707639031 0.064517813 103.9290599 0.608083303 1.747076548 17.7803712 99999994.15 -7.999999975 1.540623384 AVAGVMITAS(ph)HNR ddPTM_BT-474_Pertuzumab_2h_R1 4 AVAGVMITASHNR 13 0 Q6PCE3 Q6PCE3 PGM2L1 "Glucose 1,6-bisphosphate synthase" 1 AVAGVMIT(0.002)AS(0.998)HNR;AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR 208.23 4.99E-08 2340630000 3499080 2564540 1533260 1679240 2013680 1201096 1140235 2024040 1544448 1315297 TRUE FALSE 3362332.085 2491401.83 1810354.189 1765905.778 2078451.846 1225382.984 1154189.537 1982242.867 1369128.738 1226210.763 2.742050704 2.031789237 1.476380932 1.440132342 1.695020064 0.99932493 0.941265215 1.616559671 1.116552537 1 20.22577554 7.999999975 0.562267983 1.214270695 77.87968744 0.811461464 0.231430141 60.14253033 0.52802672 0.108622964 5594.363299 99999994.35 -7.999999975 76.66541675 up YFLHDDRDDGVDYWAK ddPTM_BT-474_Pertuzumab_2h_R1 2 YFLHDDRDDGVDYWAK 16 1 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 88.311 0.0037091 1055020000 1342000 1181390 1095540 1227530 1345830 1277580 1352700 1322950 1624480 1589160 FALSE TRUE 1289553.156 1147697.914 1293528.448 1290882.97 1389119.844 1303413.543 1369254.747 1295630.62 1440075.841 1481524.778 0.870422942 0.774673452 0.873106186 0.871320541 0.937628493 0.87977843 0.924219944 0.874525111 0.972022785 1 20.49865132 7.999999977 0.062441098 1.156694825 0.322497943 0.615589296 0.037368198 202.9302041 0.943437702 2.459849464 15.24219713 99999994.74 -7.999999977 -0.834196882 FVEEQHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 FVEEQHTK 8 0 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 105.52 0.004372 515930000 270800 292430 250760 297360 292510 318440 328460 327850 373380 391670 FALSE TRUE 260216.8366 284090.1827 296077.9101 312706.7852 301918.8498 324879.075 332479.7917 321079.7829 330995.4677 365141.842 0.7126459 0.77802692 0.810857251 0.856398115 0.826853609 0.889733899 0.910549692 0.879328924 0.90648463 1 18.47809747 7.999999978 0.143311931 1.01370755 3.59E-15 0.921787025 0.021197209 19.07475584 0.181040173 0.086553909 3.984553813 99999995.05 -7.999999978 -1.01370755 EGLEDKYNLQLNPEWR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGLEDKYNLQLNPEWR 16 1 M0R2P8;M0QYF4;M0R3A4;M0QXD5;M0QYA2;Q9NWS0 M0R2P8 PIH1D1 PIH1 domain-containing protein 1 0 79.311 0.01706 148370000 54562 45099 44312 52341 51372 53268 51681 55758 60766 63810 FALSE TRUE 52429.65672 43812.82068 52320.16412 55042.32528 53024.42703 54345.11546 52313.48754 54606.57782 53868.09843 59488.09186 0.881347091 0.736497328 0.879506511 0.925266277 0.891345232 0.913546119 0.879394277 0.917941324 0.905527421 1 15.86031328 7.999999979 0.071035818 1.107864845 0.369194804 0.490689891 0.044390579 200.3750664 1.048868122 1.87357741 14.7638065 99999995.1 -7.999999979 -0.738670041 AAIPPPVYEEQDRPRS(ph)PTGPSNSFLANMGGTVAHK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAIPPPVYEEQDRPRSPTGPSNSFLANMGGTVAHK 35 2 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 AAIPPPVYEEQDRPRS(0.984)PT(0.016)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.956)PT(0.044)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.997)PT(0.003)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.924)PT(0.071)GPS(0.002)NS(0.003)FLANMGGTVAHK 217.49 8.47E-37 2448720000 703520 801380 377614 411792 581768 781730 474429 466079 515162 426540 TRUE FALSE 676025.6606 778525.427 445857.2498 433044.6345 600481.0961 797537.1162 480235.204 456454.3058 456682.9695 397650.0659 1.700051675 1.957815411 1.121230167 1.089009337 1.510074177 2.00562551 1.207682948 1.147879367 1.148454404 1 18.60113988 7.999999979 0.098482563 0.726156859 3.567257652 0.292421313 0.300605498 182.6748295 1.276346093 4.2807577 70.134848 99999995.24 -7.999999979 2.841100793 IKELVK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKELVK 6 1 C9J384;Q9BQ75-2;Q9BQ75 C9J384 CMSS1 Protein CMSS1 0 92.925 0.09495 0 2170900 2083600 2105400 2316100 2208800 1982800 2418100 2575100 2869700 2775300 FALSE TRUE 2086058.828 2024177.768 2485892.614 2435634.199 2279848.058 2022893.575 2447693.431 2521923.285 2543943.687 2587326.459 0.806260385 0.782343396 0.960795885 0.94137104 0.881159797 0.781847056 0.946031925 0.974721716 0.983232587 1 21.30303067 7.999999979 0.130086732 1.043819745 0.26188768 0.440099906 0.061087571 84.26362202 0.741052579 0.348313024 12.09795357 99999995.25 -7.999999979 -0.781932065 EDSVKPGAHLTVK ddPTM_BT-474_Pertuzumab_2h_R1 6 EDSVKPGAHLTVK 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;; 154.47 2.35E-05 14503450000 24415800 26687800 22080100 24920300 23986000 26699900 25992800 28193200 31477800 31591700 FALSE TRUE 23461603.54 25926690.07 26070465.24 26206439.67 24757531.47 27239790.27 26310907.66 27611000.57 27904572.11 29451966.02 0.796605684 0.880304223 0.885185906 0.889802727 0.840607091 0.92488869 0.89334979 0.937492613 0.94746042 1 24.81186061 7.99999998 0.060743073 1.16570943 0.335257605 0.773862212 0.025718411 151.228043 0.6852748 1.875468602 11.07678555 99999995.29 -7.99999998 -0.830451824 RKDSPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 3 RKDSPSR 7 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKDS(0.155)PS(0.845)R;RKDS(0.29)PS(0.71)R;RKDS(0.42)PS(0.58)R 82.287 0.019609 3559950000 2026240 1820400 1471210 1703400 1644840 1654840 1820960 1738290 1664070 1942130 TRUE FALSE 1947052.301 1768483.974 1737090.374 1791312.678 1697747.772 1688301.999 1843245.453 1702393.704 1475171.75 1810587.805 1.075370272 0.976745767 0.959406867 0.989354216 0.93767768 0.932460715 1.018037042 0.94024366 0.814747424 1 20.78802671 7.99999998 0.766743189 0.945089672 26.03353909 0.349694036 0.05224451 480.1040395 1.911114664 0.017696514 20849.47122 99999995.31 -7.99999998 25.08844942 EES(ph)PLR ddPTM_BT-474_Pertuzumab_2h_R1 6 EESPLR 6 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 EES(1)PLR;EES(1)PLR;EES(1)PLR;EES(1)PLR;EES(1)PLR;EES(1)PLR 142.36 0.012101 18794800000 8863430 8970530 8441330 9794620 9017110 8650830 9776310 10221200 10467140 11440430 TRUE FALSE 8517037.357 8714699.267 9966866.107 10300121.51 9307153.532 8825755.71 9895955.406 10010128.65 9278954.149 10665559.49 0.798555141 0.817087869 0.934490696 0.965736633 0.872636222 0.827500491 0.927842128 0.93854698 0.869992255 1 23.34645631 7.99999998 0.040355112 1.248219905 0.316421202 0.379669446 0.05080924 893.2166739 2.742873164 17.24636557 56.69356391 99999995.46 -7.99999998 -0.931798704 SGAVQGAGSLGPGS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGAVQGAGSLGPGSPVR 17 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR 352.86 1.01E-87 2407050000 876030 933980 875270 917870 857950 901310 1025990 1073630 1001150 1169650 TRUE FALSE 841793.7791 907343.8049 1033450.759 965241.3807 885546.7409 919535.1057 1038546.373 1051459.165 887503.6492 1090428.564 0.771984344 0.832098347 0.94774733 0.885194512 0.8121089 0.84327863 0.952420367 0.96426231 0.813903523 1 20.05646383 7.999999981 0.050463138 1.20403133 0.294467712 0.341849871 0.060490634 571.4404853 2.174609979 9.158962077 40.34032214 99999995.73 -7.999999981 -0.909563618 FDSEYER ddPTM_BT-474_Pertuzumab_2h_R1 4 FDSEYER 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 168.45 0.0024395 4370520000 4503360 4578720 4152420 4792880 4566610 4056410 5136610 5075370 5266920 5611660 FALSE TRUE 4327363.712 4448139.389 4902854.664 5040241.111 4713499.158 4138433.389 5199473.37 4970561.836 4669041.322 5231577.27 0.827162343 0.850248244 0.937165679 0.963426678 0.900970953 0.791048889 0.993863438 0.950107698 0.892472974 1 22.31881454 7.999999982 0.076457798 1.070992652 0.509195768 0.282389036 0.057015807 297.0456402 1.661947526 1.937449258 17.72476888 99999995.85 -7.999999982 -0.561796884 KAGEQQETASR ddPTM_BT-474_Pertuzumab_2h_R1 5 KAGEQQETASR 11 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;; 173.19 2.00E-05 525901000 565552 560257 445630 479423 499255 487397 506719 536482 548232 502545 FALSE TRUE 543449.6026 544279.0189 526165.254 504166.0785 515313.9905 497252.5013 512920.3787 525403.4592 485999.0017 468507.1795 1.159960031 1.16173037 1.123067643 1.076111745 1.099906283 1.061355136 1.094797265 1.121441639 1.037335228 1 18.83771163 7.999999982 0.051685371 0.827851753 1.609213299 0.724817193 0.02570026 283.9259897 1.105316684 3.833199767 17.48667956 99999995.95 -7.999999982 0.781361546 AEFEVHEVYAVDVLVSSGEGK ddPTM_BT-474_Pertuzumab_2h_R1 12 AEFEVHEVYAVDVLVSSGEGK 21 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;;;;;;;;; 189.48 2.15E-17 377750400 530541 489231.6 460516.9 467435.3 523151.3 542342.2 547931 525835.3 639262 630554 FALSE TRUE 509806.8712 475279.1938 543742.548 491559.6919 539978.9367 553308.7309 554636.7435 514976.6173 566695.6578 587846.0159 0.867245601 0.808509679 0.924974455 0.836204854 0.918572078 0.941247735 0.943506851 0.876039989 0.964020581 1 19.16507877 7.999999983 0.070251856 1.107641531 0.420597881 0.56413062 0.037407172 184.7198112 0.957187365 1.626759196 12.54320037 99999996.11 -7.999999983 -0.687043649 S(ph)VPSIAAATGTHSR ddPTM_BT-474_Pertuzumab_2h_R1 4 SVPSIAAATGTHSR 14 0 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 S(1)VPSIAAATGTHSR;S(0.91)VPS(0.09)IAAATGTHSR;S(0.993)VPS(0.007)IAAATGTHSR;S(0.975)VPS(0.025)IAAATGTHSR 216.72 3.88E-12 1313700000 1235500 1115450 731370 801400 800890 731510 520100 1111470 605080 580940 TRUE FALSE 1187215.294 1083638.458 863544.8282 842760.35 826651.3542 746301.6334 526465.1394 1088517.756 536393.8551 541592.4164 2.192082567 2.000837577 1.59445517 1.556078565 1.526334803 1.37797652 0.972068891 2.009846747 0.99040134 1 19.04684801 7.999999983 0.356070145 1.293907715 12.99118341 0.536930517 0.288786005 53.72610401 0.754724992 0.236205935 424.2406317 99999996.17 -7.999999983 11.6972757 ENVFQEHQTLK ddPTM_BT-474_Pertuzumab_2h_R1 6 ENVFQEHQTLK 11 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 162.49 2.51E-05 6458020000 6394320 7071150 6870530 7997580 7179070 7033970 7843370 7780250 8685380 9602410 FALSE TRUE 6144422.905 6869487.725 8112187.605 8410336.062 7409991.306 7176201.693 7939359.508 7619585.119 7699452.074 8952030.218 0.686372002 0.767366459 0.906184118 0.93948924 0.827744224 0.801628404 0.886878095 0.851157216 0.860078875 1 23.09378348 7.999999985 0.035224212 1.401235066 9.26E-09 0.463059837 0.061957659 1080.764254 2.908118808 34.05156068 96.37169958 99999996.51 -7.999999985 -1.401235057 FSHVDSPNSECKGEDATDDQFES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 4 FSHVDSPNSECKGEDATDDQFESPK 25 1 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 FSHVDSPNSECKGEDATDDQFES(1)PK;FSHVDSPNSECKGEDATDDQFES(1)PK;FSHVDSPNSECKGEDATDDQFES(1)PK;FSHVDSPNSECKGEDATDDQFES(1)PK 260.68 2.84E-45 1594890000 923090 774430 774870 707140 787380 704850 813650 711460 878670 715250 TRUE FALSE 887014.6223 752344.0146 914906.2459 743635.5801 812706.7928 719102.5499 823607.6921 696768.1024 778927.0653 666805.4804 1.330244949 1.128281091 1.372073675 1.115221158 1.218806409 1.078429274 1.235154354 1.044934577 1.168147366 1 19.34690644 7.999999985 0.080826313 0.851313251 2.013312967 0.436732984 0.085835306 163.9221372 0.963893733 2.063624093 21.25967007 99999996.66 -7.999999985 1.161999716 VGNHTAEGTGTNK ddPTM_BT-474_Pertuzumab_2h_R1 4 VGNHTAEGTGTNK 13 0 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ;;; 150.22 4.41E-05 206420000 362966 358707 308892 371836 364790 375770 392347 417999 466520 487956 FALSE TRUE 348780.8874 348477.0276 364715.6557 391026.5005 376523.8016 383368.3269 397148.66 409367.1746 413562.6054 454906.3055 0.766709283 0.766041322 0.801737965 0.859575908 0.827695279 0.84274129 0.873033975 0.899893384 0.90911601 1 18.79520991 7.999999986 0.062228753 1.226119791 0.048810873 0.952225542 0.014784938 61.7461393 0.286156017 1.05993121 6.528518949 99999996.87 -7.999999986 -1.177308918 RLS(ph)PS(ph)AS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 RLS(1)PS(1)AS(1)PPR 48.177 0.054449 0 154220 153160 101580 123090 118350 140600 127080 129020 123380 114280 TRUE FALSE 148192.9119 148792.0268 119937.7656 129442.6897 122156.8352 143443.0283 128635.2431 126355.6919 109374.4197 106539.7138 1.390964051 1.396587446 1.125756409 1.214971254 1.146584976 1.34638083 1.207392422 1.185996164 1.026607035 1 16.70103179 7.999999987 0.068400331 0.734855513 2.311302425 0.562644052 0.087554668 213.002746 1.077118588 4.433787468 32.470814 99999997 -7.999999987 1.576446913 VNELREELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 VNELREELQR 10 1 Q9BUJ2-2;Q9BUJ2;Q9BUJ2-3;M0R247;A0A087X1I2 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 163.84 0.0033312 0 322140 341410 211237 234340 270050 266570 222715 223340 263400 233094 FALSE TRUE 309550.4127 331673.3211 249412.2248 246434.3155 278736.4035 271960.228 225440.6528 218727.951 233499.9363 217306.3358 1.424488667 1.526293837 1.147744837 1.134041097 1.282688802 1.251506207 1.037432489 1.006541987 1.074519689 1 17.72937071 7.999999987 0.225494206 0.968631424 3.905587416 0.686362334 0.095652246 28.1142604 0.364624763 0.149966954 30.30735111 99999997.04 -7.999999987 2.936955991 S(ph)GSELPSILPEIWPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SGSELPSILPEIWPK 15 0 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 S(0.874)GS(0.126)ELPSILPEIWPK;S(0.788)GS(0.212)ELPSILPEIWPK 139.77 5.30E-06 60303000 257086 191175 172062 155418 157077 166288 150935 214391 142916 147295 TRUE FALSE 247038.7949 185722.8762 203157.4309 163439.1416 162129.5244 169650.4573 152782.1877 209963.7509 126692.7748 137318.5785 1.79901946 1.35249635 1.479460632 1.190218712 1.18068164 1.235451599 1.112611195 1.52902654 0.92261933 1 17.0671673 7.999999987 0.641823375 1.201937807 49.78960125 0.560151127 0.16652868 167.0311944 1.105650368 0.064899851 11510.09152 99999997.09 -7.999999987 48.58766344 RVS(ph)HS(ph)PPPKQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RVSHSPPPKQR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)HS(1)PPPKQR 52.265 0.077999 32881000 29161 33072 15711 20112 20814 28302 20933 17574 19956 22675 TRUE FALSE 28021.35588 32128.81894 18550.32719 21149.98273 21483.50121 28874.28583 21189.18432 17211.09076 17690.67854 21139.20205 1.325563558 1.51986905 0.877532044 1.000509985 1.016287235 1.365911814 1.002364435 0.814178828 0.836865956 1 14.3676333 7.999999987 0.34963563 0.924100437 6.958771539 0.36226306 0.183663629 65.10603367 0.919456119 0.160513223 258.839887 99999997.1 -7.999999987 6.034671102 GNKHDDGTQS(ph)DSENAGAHRR ddPTM_BT-474_Pertuzumab_2h_R1 2 GNKHDDGTQSDSENAGAHRR 20 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGTQS(1)DSENAGAHRR;GNKHDDGT(0.003)QS(0.997)DSENAGAHRR 222.16 3.49E-25 892740000 310307 299631 225641 194583 242241 290801 230445 160627.9 313798 231039 TRUE FALSE 298179.8594 291085.8172 266419.3481 204625.4519 250032.9018 296681.1955 233265.2548 157310.8777 278176.9666 215390.5227 1.384368521 1.3514328 1.236913048 0.950020685 1.160835206 1.377410629 1.082987552 0.730351901 1.291500494 1 17.71659525 7.999999988 0.273614727 0.985387596 4.184166007 0.272231168 0.174324997 62.88616901 0.884056316 0.211521367 95.42936425 99999997.15 -7.999999988 3.198778412 RAGAES(ph)PTMSVDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RAGAESPTMSVDGR 14 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 RAGAES(0.671)PT(0.3)MS(0.029)VDGR 100.6 0.0012795 0 171510 185160 108730 128200 146940 166310 134230 143370 143300 127420 TRUE FALSE 164807.1996 179879.4181 128379.9297 134816.4174 151666.4585 169672.9021 135872.7469 140409.3594 127033.1848 118789.7299 1.387385927 1.514267422 1.080732567 1.13491644 1.276764066 1.428346561 1.143808871 1.181999147 1.06939535 1 16.85805059 7.999999988 0.07469785 0.755518367 2.401833172 0.416151287 0.124662225 236.6157586 1.29634778 4.650976022 40.54599263 99999997.18 -7.999999988 1.646314804 VEVTEFEDIKS(ph)GYR ddPTM_BT-474_Pertuzumab_2h_R1 1 VEVTEFEDIKSGYR 14 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 1 VEVTEFEDIKS(1)GYR 126.19 5.26E-05 98755000 115860 81090 73158 63876 76840 62635 54103 84847 81955 78813 TRUE FALSE 111332.0631 78777.3926 86379.27799 67172.64801 79311.62838 63901.52261 54765.1287 83094.8798 72651.81198 73474.92531 1.515238874 1.072167032 1.175629341 0.914225468 1.079438027 0.869705173 0.745358072 1.130928401 0.988797357 1 16.16496437 7.999999988 0.797745816 0.964735004 133.996889 0.664286452 0.114442012 300.1594206 1.043740581 0.038504443 72152.62689 99999997.22 -7.999999988 133.032154 SPS(ph)PVQGK ddPTM_BT-474_Pertuzumab_2h_R1 5 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.026)PS(0.974)PVQGK;S(0.012)PS(0.988)PVQGK;S(0.077)PS(0.923)PVQGK;S(0.033)PS(0.967)PVQGK;S(0.131)PS(0.869)PVQGK 128.51 0.0011856 7211790000 9576880 8681080 7342750 8128280 8104690 8224950 8447350 8843360 9502460 8652900 TRUE FALSE 9202604.942 8433504.098 8669748.264 8547781.505 8365384.714 8391264.124 8550731.196 8660741.526 8423780.578 8066831.376 1.140795501 1.045454368 1.074740237 1.059620699 1.037009989 1.040218115 1.059986356 1.073623722 1.044248998 1 22.94357067 7.999999989 0.008168903 7.85E-07 2.230893926 0.47259035 0.025001098 19187.83939 12.11834888 1465.107762 1866.919637 99999997.42 -7.999999989 2.230893141 DGWHYGESEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGWHYGESEK 10 0 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 0 ; 154.05 1.52E-05 679080000 1297930 1357460 1119440 1387850 1261350 1343060 1394880 1483360 1503070 1644260 FALSE TRUE 1247205.461 1318746.57 1321747.71 1459477.105 1301922.468 1370217.593 1411950.959 1452728.098 1332447.795 1532892.806 0.813628622 0.860299275 0.862257103 0.952106435 0.849323882 0.893876981 0.921102215 0.947703644 0.869237425 1 20.54782538 7.99999999 0.060908229 1.13076981 0.406238653 0.561661541 0.035871682 240.5602472 1.09283503 2.595907745 15.40360981 99999997.66 -7.99999999 -0.724531157 QQALTVSTDPEHR ddPTM_BT-474_Pertuzumab_2h_R1 2 QQALTVSTDPEHR 13 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 158.31 4.73E-05 1077250000 816780 900180 889020 1073990 947490 871160 947780 1008200 1036500 1179180 FALSE TRUE 784859.3346 874507.7478 1049685.69 1129418.753 977966.8763 888775.4521 959379.2152 987380.3177 918840.8654 1099313.088 0.713954326 0.795503808 0.954855993 1.027385887 0.889616331 0.808482553 0.872707899 0.898179352 0.835831825 1 20.0681709 7.99999999 0.020204232 1.56555332 4.44E-07 0.200474449 0.081940215 6515.691795 10.14263318 290.3703567 528.3596188 99999997.73 -7.99999999 -1.565552875 SESGVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 SESGVLK 7 0 A0A0G2JML4;A0A140T9Y3;A0A0G2JNW1;A0A087WYQ2;A0A0G2JN18;A0A140T9M2;A0A0G2JP41;A0A0G2JM93;A0A140T8X9;E9PLW3;A0A140T960;A0A0G2JKA5;A0A0G2JN90;A0A0G2JPA5;A0A0G2JM37;F8VVU2;A0A0G2JMH0;A0A0G2JMA0;A0A0G2JQ19;Q5SRN2-2;Q5SRN2;Q5SRN2-3 A0A0G2JML4 C6orf10 Uncharacterized protein C6orf10 0 91.584 0.037913 178320000 212080 209190 210740 226980 236240 207870 247860 267120 265050 307140 FALSE TRUE 203791.6791 203224.106 248825.4059 238694.465 243838.8741 212073.2738 250893.3848 261603.8787 234962.6352 286337.1342 0.71171935 0.709737165 0.868994539 0.833613376 0.851579642 0.740641881 0.876216721 0.913621907 0.820580383 1 18.12735526 7.99999999 0.060200219 1.230952968 5.00E-13 0.603441806 0.055072884 235.2052543 1.056928381 4.361614863 25.36744991 99999997.75 -7.99999999 -1.230952968 GIQLS(ph)PGVGSSAGPPGDLEDDEGLKHLQQEAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIQLSPGVGSSAGPPGDLEDDEGLKHLQQEAEK 33 1 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 GIQLS(0.987)PGVGS(0.007)S(0.007)AGPPGDLEDDEGLKHLQQEAEK 91.176 0.00016541 222340000 445480 421020 348170 282900 395460 400000 325350 333500 380200 308830 TRUE FALSE 428070.1491 409012.9218 411092.064 297500.5029 408180.33 408088.2741 329331.7306 326613.1085 337041.2899 287912.669 1.486805532 1.420614533 1.427835966 1.033301188 1.417722712 1.417402977 1.143859809 1.134417286 1.170637232 1 18.13527175 7.99999999 0.100326893 0.830639017 2.721990492 0.54070882 0.119519311 99.98329233 0.709721313 1.517192081 26.0482487 99999997.76 -7.99999999 1.891351476 RRGEEGHDPKEPEQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRGEEGHDPKEPEQLR 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 127.75 3.87E-05 675810000 114620 124640 66113 68474 92425 114830 83740 67065 85587 63931 FALSE TRUE 110140.5237 121085.3892 78061.08978 72007.95135 95397.93406 117151.9413 84764.83517 65680.08431 75871.52257 59600.89643 1.847967569 2.031603491 1.309730129 1.208168931 1.600612403 1.965607034 1.422207387 1.101998263 1.272992977 1 15.86304641 7.999999991 0.096857457 0.66064873 4.094945051 0.437649077 0.261094272 138.5934245 0.954653907 4.02332792 63.23673477 99999997.93 -7.999999991 3.434296322 LGADES(ph)EEEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGADESEEEGR 11 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 LGADES(1)EEEGR 202.61 4.14E-08 344650000 154100 135860 147200 160960 169250 159370 168780 181150 190530 211750 TRUE FALSE 148077.6016 131985.4058 173802.3144 169267.1649 174694.08 162592.5706 170845.5801 177409.1892 168901.8332 197407.9839 0.750109488 0.668592036 0.880421911 0.857448425 0.884939284 0.823637258 0.865444126 0.898693081 0.855597782 1 17.59082081 7.999999991 0.159511367 0.978336957 9.17E-10 0.617267515 0.052092596 43.02682512 0.443128613 0.155848651 9.895741085 99999997.94 -7.999999991 -0.978336956 HS(ph)YPPALGSPGALAGAGVGAAGPLER ddPTM_BT-474_Pertuzumab_2h_R1 1 HSYPPALGSPGALAGAGVGAAGPLER 26 0 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 HS(0.605)Y(0.294)PPALGS(0.101)PGALAGAGVGAAGPLER 192.22 2.99E-18 393540000 180550 148080 98983 101250 117860 102900 88171 72658 100620 99506 TRUE FALSE 173493.9064 143856.9034 116871.43 106475.5246 121651.0739 104980.7085 89250.06307 71157.58691 89198.03943 92766.36999 1.87022416 1.550744126 1.259846968 1.147781514 1.311370424 1.131667742 0.962095025 0.767062319 0.961534222 1 16.50131427 7.999999991 0.323656251 0.869339257 10.99782121 0.87717875 0.107240385 19.2280868 0.275133638 0.110913144 115.6961818 99999998.04 -7.999999991 10.12848195 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSGSVGNGSSRYSPSQNSPIHHIPSRR 28 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 SGS(0.001)GS(0.001)VGNGS(0.009)S(0.01)RY(0.005)S(0.973)PS(0.002)QNS(0.845)PIHHIPS(0.155)RR 116.94 0.00014319 107510000 46588 59831 21527 21413 29680 53439 25548 8905.3 29640 18832 TRUE FALSE 44767.28945 58124.67846 25417.40777 22518.1275 30634.68415 54519.57319 25860.66407 8721.402443 26275.39146 17556.49187 2.549899479 3.310722831 1.44774981 1.282609742 1.744920591 3.105379686 1.47299724 0.496762252 1.496619693 1 14.09971697 7.999999992 0.189929009 0.787110557 10.29268989 0.346484317 0.69916368 60.31009088 0.703784684 1.523976804 168.2259798 99999998.12 -7.999999992 9.505579333 FHVEEEGKGK ddPTM_BT-474_Pertuzumab_2h_R1 8 FHVEEEGKGK 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;;;; 201.33 1.47E-07 11336640000 35967370 33625100 16200810 15545680 18414610 22196320 16091600 9491050 22268650 12724900 FALSE TRUE 34561725.42 32666145.07 19128656.75 16347994.41 19006932.65 22645144.8 16288533.81 9295056.501 19740806.21 11863031.19 2.913397501 2.753608631 1.612459451 1.378062162 1.602198658 1.908883525 1.373049902 0.783531321 1.664060888 1 23.49996935 7.999999992 0.390900055 1.165245204 31.27685916 0.73234062 0.33468792 35.36945199 0.476701366 0.253393982 813.9730321 99999998.25 -7.999999992 30.11161396 up SEPVINNDNPLES(ph)NDEKEGQEATCSRPQIVPEPMDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEPVINNDNPLESNDEKEGQEATCSRPQIVPEPMDFR 37 2 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5;H7C4B4 P23497 SP100 Nuclear autoantigen Sp-100 1 SEPVINNDNPLES(1)NDEKEGQEATCSRPQIVPEPMDFR;SEPVINNDNPLES(1)NDEKEGQEATCSRPQIVPEPMDFR 129.66 6.78E-09 270639000 125969 107927 88820 85303 110194 96288 89673 100655 111694 97931 TRUE FALSE 121045.9922 104849.0276 104871.7498 89705.49805 113738.4901 98235.00933 90770.445 98576.43908 99014.96538 91298.04614 1.325833326 1.148425756 1.148674635 0.982556603 1.245793255 1.075981508 0.994221112 1.079721234 1.084524473 1 16.47829637 7.999999993 0.664699528 1.065253803 26.15940211 0.537300875 0.072130699 183.9153123 1.11522797 0.027075145 6813.623779 99999998.31 -7.999999993 25.09414831 NQGGYGGSSS(ph)SSSYGSGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-2;P09651;P09651-3;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 NQGGYGGS(0.121)S(0.05)S(0.413)S(0.413)S(0.003)SYGSGR;NQGGYGGS(0.316)S(0.106)S(0.577)S(0.002)SSYGSGR 167.92 2.31E-11 204818000 253150 239280 162902 129191 183259 148599 108001 166768 143023 112951 TRUE FALSE 243256.6181 232455.9687 192342.0151 135858.563 189153.6922 151603.7736 109322.7485 163324.1825 126787.6286 105300.7282 2.310113352 2.207543791 1.826597199 1.290195855 1.796318938 1.439721987 1.038195561 1.551026145 1.204052725 1 16.68415589 7.999999993 0.273683931 1.124789164 10.67482759 0.781114766 0.20438305 23.00974825 0.323493887 0.230874253 104.2812818 99999998.41 -7.999999993 9.550038424 up SDVLVEYQGEGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDVLVEYQGEGR 12 0 H7C3P4;F6S8M0;P15586-2;P15586;H0YFA9 H7C3P4 GNS N-acetylglucosamine-6-sulfatase 0 155.97 0.00016933 222210000 153640 149050 148690 164000 153910 152120 165030 196590 184950 211820 FALSE TRUE 147635.5789 144799.2399 175561.5906 172464.0597 158860.6549 155195.9706 167049.6865 192530.3478 163955.2514 197473.2427 0.747623207 0.73326005 0.889039893 0.873354067 0.804466735 0.785908858 0.845935805 0.974969293 0.830265656 1 17.59129766 7.999999993 0.052576003 1.286502756 0.017395421 0.534901958 0.057408037 352.4631586 1.394528134 7.618871507 35.65627852 99999998.45 -7.999999993 -1.269107335 DKWLAPDGLIFPDR ddPTM_BT-474_Pertuzumab_2h_R1 3 DKWLAPDGLIFPDR 14 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;; 173.03 2.52E-06 5054181000 2302431 2380017 2105033 2278270 2412694 2612060 2558281 2556147 2919536 2946949 FALSE TRUE 2212449.451 2312141.245 2485459.289 2395851.788 2490300.494 2664877.643 2589590.008 2503361.671 2588122.513 2747349.519 0.805303233 0.841589768 0.904675314 0.872059332 0.90643745 0.969981294 0.942577561 0.911191552 0.942043411 1 21.38960903 7.999999994 0.235796243 0.972696634 2.25E-13 0.810343021 0.024211182 22.75536499 0.302004909 0.035895016 8.617248119 99999998.66 -7.999999994 -0.972696634 ELLAKPIGPDDAIDALSSDFTCGS(ph)PTAAGK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELLAKPIGPDDAIDALSSDFTCGSPTAAGK 30 1 P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0 P20810-5 CAST Calpastatin 1 ELLAKPIGPDDAIDALSSDFTCGS(0.998)PT(0.002)AAGK;ELLAKPIGPDDAIDALSSDFTCGS(1)PTAAGK;ELLAKPIGPDDAIDALSSDFTCGS(0.998)PT(0.002)AAGK;ELLAKPIGPDDAIDALSSDFTCGS(0.999)PT(0.001)AAGK 361.83 3.59E-121 3954070000 3388950 3039480 2672230 2701270 2816140 3113050 2728030 2995690 3340150 3224380 TRUE FALSE 3256506.087 2952797.006 3155161.404 2840682.868 2906723.701 3175998.004 2761416.447 2933827.955 2960990.175 3005989.871 1.083339009 0.982304377 1.049624763 0.945007465 0.966977211 1.056556456 0.918637975 0.975993959 0.985029991 1 21.51940872 7.999999994 0.7635293 0.978110657 20.08350617 0.336291935 0.040177322 453.7252674 1.829974016 0.013284162 14936.52855 99999998.72 -7.999999994 19.10539552 QWGWTQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 QWGWTQGR 8 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 141.52 0.0014708 3998500000 3697500 1954060 2290500 1274130 1786390 1201500 1461120 1498190 1761930 1459450 FALSE TRUE 3552997.612 1898332.122 2704444.302 1339888.002 1843850.857 1225795.153 1479001.624 1467251.853 1561923.093 1360600.152 2.611345889 1.39521675 1.987684845 0.984777196 1.355174667 0.900922399 1.087021504 1.078385778 1.147966279 1 20.37581172 7.999999994 0.531141543 1.044645829 58.89173473 0.76348716 0.24991564 53.29789616 0.516546334 0.11084009 3490.18373 99999998.73 -7.999999994 57.84708891 up ATSSSSGS(ph)LSATGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATSSS(0.007)S(0.258)GS(0.734)LSATGR 128.95 0.00017242 0 109410 88705 54256 71849 65678 56153 49865 85853 62610 48869 TRUE FALSE 105134.1362 86175.22025 64061.26612 75557.1355 67790.59252 57288.45213 50475.26279 84080.10555 55502.77528 45559.0591 2.307645029 1.891505706 1.406114775 1.658443721 1.487971742 1.257454681 1.107908367 1.84551892 1.218259911 1 15.47545033 7.999999995 0.603725338 1.368596528 64.61691753 0.629696879 0.235498996 118.3984533 0.901689578 0.100477508 9889.696772 99999998.79 -7.999999995 63.248321 VINQILTEMDGMSTK ddPTM_BT-474_Pertuzumab_2h_R1 3 VINQILTEMDGMSTK 15 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 163.27 2.55E-08 190615000 366430 363080 337620 338958 354734 375075 380853 384570 447800 429022 FALSE TRUE 352109.5105 352725.3139 398635.4443 356451.663 366144.3413 382659.2735 385513.9929 376628.4951 396967.6213 399963.9578 0.880353101 0.881892748 0.996678417 0.89120946 0.91544334 0.956734391 0.963871832 0.941656086 0.992508484 1 18.60951047 7.999999995 0.114506545 1.028156531 0.595142263 0.501387758 0.031813707 88.06142265 0.698304667 0.248970583 6.05328436 99999998.85 -7.999999995 -0.433014267 EGLHNAK ddPTM_BT-474_Pertuzumab_2h_R1 4 EGLHNAK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 117.17 0.0052914 2153400000 4918390 4807870 3922400 5550970 4401040 4592930 5437960 5366680 5495070 5727360 FALSE TRUE 4726173.881 4670754.255 4631264.933 5837456.227 4542603.449 4685802.191 5504511.381 5255856.183 4871292.691 5339440.806 0.885143979 0.874764685 0.867368907 1.093271082 0.850763893 0.877582946 1.03091533 0.98434581 0.912322632 1 22.34825723 7.999999995 0.231277024 0.988037308 0.296249284 0.160296361 0.072405819 88.79876096 1.167135004 0.104721292 23.31269997 99999998.86 -7.999999995 -0.691788024 ALECFCQAASEVGKEEFLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALECFCQAASEVGKEEFLDR 20 1 Q12769;G3V198;E9PR16 Q12769 NUP160 Nuclear pore complex protein Nup160 0 ; 147.9 1.06E-07 132572000 90723 94355 70905 96890 86207 96245 87181 104901 102825 106607 FALSE TRUE 87177.44486 91664.08778 83719.11077 101890.5045 88979.92645 98191.13984 88247.94716 102734.7577 91152.73708 99386.41293 0.877156568 0.922299991 0.842359718 1.025195512 0.895292664 0.987973476 0.887927681 1.033690166 0.917154915 1 16.60076101 7.999999995 0.1888735 0.998741969 0.442438906 0.23984045 0.055795655 69.92182717 0.812872587 0.10457129 11.33255654 99999998.91 -7.999999995 -0.556303063 LWELIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LWELIK 6 0 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3;A0A087WXU8 G3V529 DDX24 ATP-dependent RNA helicase DDX24 0 100.82 0.086601 22174000 95473 88580 68563 72278 81776 72103 72552 82706 71646 75177 FALSE TRUE 91741.80961 86053.78513 80953.85928 76008.27624 84406.39931 73560.97206 73439.91308 80998.0922 63513.04644 70085.19483 1.309004132 1.227845415 1.155077894 1.084512591 1.20433994 1.049593602 1.04786629 1.155709025 0.906226295 1 16.09682209 7.999999996 0.222533386 0.996097595 2.639369198 0.659723509 0.066030786 32.27684187 0.415593033 0.099487378 19.13263972 99999998.97 -7.999999996 1.643271603 QYMEGFNDELEAFK ddPTM_BT-474_Pertuzumab_2h_R1 3 QYMEGFNDELEAFK 14 0 Q16543;K7EKQ2;K7EQA9;K7EL68 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;; 218.5 1.25E-11 200130000 178421 193812 178062 184228 185365 197106 193368 213130 234208 238812 FALSE TRUE 171448.1101 188284.6715 210241.7644 193736.0292 191327.4336 201091.6184 195734.4954 208728.791 207621.6897 222637.0505 0.770078968 0.845702326 0.944325142 0.870187728 0.859369243 0.903226206 0.87916407 0.937529448 0.932556774 1 17.76433418 7.999999996 0.078316764 1.095402049 0.370230566 0.651306865 0.035875261 136.0313004 0.777673651 1.111980493 10.70211183 99999998.98 -7.999999996 -0.725171483 LGHAEQKDEMVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGHAEQKDEMVPR 13 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 212.95 5.88E-09 842710000 999740 1044670 508690 507490 793980 1107410 619430 577610 752200 569630 FALSE TRUE 960669.0555 1014877.034 600621.5987 533681.6197 819519.0878 1129802.589 627010.7696 565682.1517 666813.4095 531048.4527 1.809004528 1.911081803 1.131010919 1.004958431 1.543209633 2.127494362 1.180703505 1.065217587 1.255654557 1 19.01848397 7.999999996 0.117930285 0.839822347 3.666990092 0.250535771 0.3405671 151.5742466 1.231388713 2.667270394 70.3018468 99999998.98 -7.999999996 2.827167746 QEEAEEQGAGS(ph)PGQPAHLAR ddPTM_BT-474_Pertuzumab_2h_R1 2 QEEAEEQGAGSPGQPAHLAR 20 0 Q96S99 Q96S99 PLEKHF1 Pleckstrin homology domain-containing family F member 1 1 QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR 320.76 6.76E-67 1536830000 621680 662330 621430 769250 657130 710290 718920 687650 805630 866850 TRUE FALSE 597384.0583 643440.9969 733736.2246 808951.0847 678267.1832 724652.5505 727718.358 673449.7872 714178.2599 808137.4774 0.739210933 0.796202397 0.907934906 1.001006768 0.839296781 0.896694648 0.900488318 0.833335671 0.883733622 1 19.62424121 7.999999996 0.023066533 1.534957255 9.60E-08 0.333666186 0.063865655 3499.776101 6.211754828 146.2635545 289.6044271 99999999.02 -7.999999996 -1.534957159 DRFGIDDQDYLVSLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 DRFGIDDQDYLVSLTR 16 1 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ;;; 294.05 1.18E-45 2184320000 985062 1019871 883831 1081036 1081791 781270 1134409 1190767 1215499 1282503 FALSE TRUE 946564.688 990785.2776 1043558.922 1136828.398 1116587.79 797067.8147 1148292.237 1166177.245 1077520.649 1195637.929 0.791681716 0.82866665 0.872805133 0.95081326 0.93388455 0.666646478 0.960401312 0.975359862 0.901209825 1 20.18934914 7.999999996 0.062721663 1.16927133 0.288210039 0.250385317 0.083794694 455.2006108 2.125085897 5.801528831 36.23406368 99999999.03 -7.999999996 -0.881061291 AEEAQKTESVDNEGE ddPTM_BT-474_Pertuzumab_2h_R1 2 AEEAQKTESVDNEGE 15 1 Q15651 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 0 ; 123.95 0.0010441 217510000 522680 501100 360190 375150 441030 444780 422900 473120 470700 410280 FALSE TRUE 502253.0877 486809.1186 425284.3454 394511.5365 455216.1305 453773.7563 428075.5767 463349.9067 417268.1093 382491.3702 1.313109594 1.272732293 1.111879584 1.03142598 1.190134382 1.186363384 1.119177085 1.211399636 1.090921631 1 18.54506767 7.999999996 0.018973472 4.78E-13 2.624790362 0.425053759 0.072233424 4140.904305 6.056297612 315.3497016 553.321135 99999999.07 -7.999999996 2.624790362 S(ph)PGEPGGAAPER ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGEPGGAAPER 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 S(1)PGEPGGAAPER 90.614 0.0045168 0 8371.7 7337.9 8105.3 10099 7617.2 8695.5 9511.3 10250 9015.3 11757 TRUE FALSE 8044.524709 7128.630277 9570.108011 10620.2106 7862.214156 8871.328968 9627.702135 10038.33392 7991.920939 10960.68792 0.733943414 0.650381648 0.873130234 0.968936501 0.717310283 0.809377024 0.878384843 0.915848895 0.729144101 1 13.42005073 7.999999996 0.048771881 1.284229536 4.89E-06 0.292086509 0.09388228 672.8026175 2.478560328 15.64511264 65.63308275 99999999.07 -7.999999996 -1.284224646 IACRS(ph)PQPDPVGTPTIFKPQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 IACRSPQPDPVGTPTIFKPQSK 22 2 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 IACRS(1)PQPDPVGTPTIFKPQSK 91.389 0.0011652 372910000 335800 223870 169960 175640 273780 176260 152940 198860 111050 99375 TRUE FALSE 322676.5648 217485.4468 200675.5527 184704.8014 282586.3823 179824.098 154811.7255 194753.4715 98444.06956 92644.24274 3.482964027 2.347533321 2.166087679 1.993699727 3.050231444 1.941017517 1.671034496 2.102164859 1.062603208 1 16.4994137 7.999999996 0.09031356 0.067709335 8.201245474 0.638394045 0.441260621 103.9103347 0.673758396 7.895682339 104.7297295 99999999.1 -7.999999996 8.133536139 LQLPVWEYK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQLPVWEYK 9 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 168.8 0.00013715 223660000 647590 577170 590130 687370 651930 622290 738370 742040 813660 864750 FALSE TRUE 622281.4669 560709.6767 696779.6184 722845.2481 672899.9205 634873.1302 747406.3929 726716.6147 721296.7279 806179.7123 0.771889267 0.695514497 0.864298131 0.896630413 0.834677319 0.787508195 0.927096504 0.901432526 0.8947096 1 19.62074195 7.999999996 0.107672663 1.062028479 0.104077266 0.635173976 0.050183611 72.76936 0.548285842 0.501889875 10.34649381 99999999.1 -7.999999996 -0.957951213 GYSDRDGYGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GYSDRDGYGR 10 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ;;;;; 141.95 3.34E-05 2085090000 1034710 1202600 640408 788735 840368 1020830 800029 767557 825719 742331 FALSE TRUE 994272.3893 1168303.025 756143.9714 829441.7079 867399.1999 1041471.882 809819.9942 751706.6797 731986.8408 692052.2602 1.436701311 1.688171678 1.092611086 1.198524672 1.253372397 1.50490352 1.170171735 1.086199299 1.057704574 1 19.40052146 7.999999996 0.145344243 0.922760575 3.063619056 0.446281977 0.158189827 66.5032357 0.638110735 0.621823917 29.84432311 99999999.11 -7.999999996 2.140858481 GWAPPGPS(ph)PSSGALDLLDTPAGLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GWAPPGPSPSSGALDLLDTPAGLEK 25 0 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3;A6NC58 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 GWAPPGPS(0.333)PS(0.333)S(0.333)GALDLLDTPAGLEK 166.27 9.15E-12 30187000 83113 87123 91846 96326 90032 87477 101180 108940 118820 126840 TRUE FALSE 79864.85207 84638.33734 108444.6153 101297.3964 92927.96104 89245.84488 102418.2711 106690.3509 105332.0517 118249.0138 0.675395502 0.715763579 0.917086847 0.856644746 0.78586669 0.754728027 0.866123681 0.902251507 0.890764737 1 16.85146863 7.999999996 0.069968447 1.188979242 0.004630532 0.59551857 0.060855863 194.9673115 1.006568273 2.973296606 22.74600815 99999999.12 -7.999999996 -1.18434871 EARS(ph)PQPNK ddPTM_BT-474_Pertuzumab_2h_R1 2 EARSPQPNK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EARS(1)PQPNK;EARS(1)PQPNK 100.04 0.0029865 2987200000 5367000 5618500 1821870 1986310 3541800 4494300 2610200 2255180 2492200 1927600 TRUE FALSE 5157251.706 5458265.881 2151122.436 2088823.697 3655725.214 4585177.825 2642144.408 2208609.745 2209295.904 1797041.935 2.869856071 3.037361441 1.197035191 1.162367809 2.034301561 2.551514094 1.470274208 1.229025156 1.229406983 1 20.77719264 7.999999996 0.498282712 1.425780455 55.39392193 0.458517064 0.543785835 100.8969818 1.076226725 0.305732146 5694.389075 99999999.13 -7.999999996 53.96814147 EEEDDVDLELR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEEDDVDLELR 11 0 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 ; 182.16 1.37E-05 353930000 634150 642620 629390 729420 655250 726270 763070 723520 933200 904520 FALSE TRUE 609366.7169 624293.1068 743134.7737 767065.4536 676326.7113 740955.677 772408.6789 708579.0592 827267.0483 843256.0547 0.722635448 0.740336347 0.881268233 0.909647134 0.802041927 0.878684088 0.915983555 0.840289323 0.981038966 1 19.68561125 7.999999996 0.160559932 0.99472947 2.97E-10 0.668272693 0.050562922 42.61407599 0.441031367 0.155090565 10.04689351 99999999.16 -7.999999996 -0.99472947 SAPAS(ph)PTHPGLMS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.004)APAS(0.92)PT(0.151)HPGLMS(0.925)PR 130.4 8.77E-05 379910000 597080 470950 336650 444670 439010 387170 349540 465390 417300 398990 TRUE FALSE 573745.4535 457518.9671 397490.1437 467619.472 453131.1553 394998.8427 353817.7751 455779.5339 369929.8535 371966.0519 1.542467251 1.230001944 1.068619412 1.257156317 1.218205675 1.061921755 0.951209857 1.225325622 0.994525849 1 18.50481143 7.999999996 0.830523518 1.097360119 137.5062045 0.645606709 0.100069588 387.0721723 1.162708244 0.032807902 99618.22753 99999999.17 -7.999999996 136.4088444 HSEKS(ph)PPSTENKHEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSEKSPPSTENKHEAK 16 2 H3BQL3;Q6PH81 H3BQL3 C16orf87 UPF0547 protein C16orf87 1 HS(0.11)EKS(0.89)PPSTENKHEAK;HS(0.098)EKS(0.863)PPS(0.017)T(0.022)ENKHEAK 136.58 7.92E-06 509230000 324270 252062 244775 199094 268190 254819 252711 148133 390070 271820 TRUE FALSE 311597.1699 244873.4386 289011.2875 209369.2652 276816.5749 259971.6148 255803.7528 145074.0018 345790.8889 253409.3893 1.229619671 0.96631557 1.14049163 0.82620958 1.092369054 1.025895747 1.009448598 0.57248866 1.364554367 1 17.95111045 7.999999996 0.641536866 0.949292979 22.21067721 0.07076423 0.198396815 460.0675579 3.049454576 0.078557119 13865.6684 99999999.19 -7.999999996 21.26138423 SNS(ph)PGTASSGSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSPGTASSGSSR 13 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 S(0.004)NS(0.99)PGT(0.006)ASSGSSR 91.616 0.0067658 17102000 38760 36523 32071 31189 33475 29315 29329 38678 30718 29961 TRUE FALSE 37245.21635 35481.3998 37866.94312 32798.66803 34551.75378 29907.76939 29687.93708 37879.28578 27231.02142 27931.71478 1.333438231 1.270290781 1.355697042 1.174244699 1.237007969 1.070745911 1.062875563 1.356138929 0.974914058 1 14.76961653 7.999999997 0.0952335 0.887856329 2.175848838 0.472239838 0.1019296 139.8962161 0.949727378 1.561076122 23.53318673 99999999.21 -7.999999997 1.287992509 GTEVQVDDIKR ddPTM_BT-474_Pertuzumab_2h_R1 3 GTEVQVDDIKR 11 1 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 ;; 176.05 1.46E-05 1315130000 1257430 1229470 1151080 1151970 1190100 1277690 1242830 1344040 1500040 1459530 FALSE TRUE 1208288.245 1194406.719 1359105.762 1211423.31 1228380.647 1303525.767 1258040.125 1316285.104 1329761.748 1360674.733 0.888006675 0.877804732 0.998846917 0.890310726 0.902773174 0.957999539 0.924570799 0.967376752 0.977281135 1 20.3758908 7.999999997 0.068148981 1.089718884 0.586674804 0.449000787 0.033335662 243.3496855 1.226433373 1.622923091 11.80246783 99999999.23 -7.999999997 -0.50304408 SSPS(ph)PALEQPFR ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPSPALEQPFR 12 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 SSPS(1)PALEQPFR;SSPS(1)PALEQPFR;SSPS(1)PALEQPFR;SSPS(1)PALEQPFR 249.19 7.46E-17 1656490000 1017880 1134290 968190 1141830 1094940 1119360 1201490 1375120 1313550 1483240 TRUE FALSE 978100.1243 1101941.16 1143163.47 1200759.983 1130159.739 1141994.226 1216194.194 1346723.291 1164441.311 1382778.834 0.707343865 0.796903404 0.826714614 0.868367344 0.817310558 0.825869039 0.879529079 0.973925301 0.842102354 1 20.39913899 7.999999997 0.116655195 1.051564831 0.074186098 0.712740512 0.042993494 53.13828224 0.427866001 0.329045155 8.41716916 99999999.25 -7.999999997 -0.977378733 SVLLLAYKPMEGNFEEIAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVLLLAYKPMEGNFEEIAR 19 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ;; 207.56 2.84E-16 2403710000 1486180 1380710 1160200 1321920 1264830 1294830 1336770 1337200 1534410 1477230 FALSE TRUE 1428098.443 1341333.503 1369873.949 1390144.45 1305514.406 1321012.35 1353129.791 1309586.353 1360230.21 1377175.896 1.036976066 0.97397399 0.994697883 1.009416773 0.947964896 0.95921832 0.982539554 0.950921633 0.987695336 1 20.39328141 7.999999997 0.713571125 0.971711886 9.071927109 0.391110079 0.020563768 300.9081344 1.499835417 0.007373106 3897.870862 99999999.3 -7.999999997 8.100215223 MPQDGS(ph)DDEDEEWPTLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 MPQDGSDDEDEEWPTLEK 18 0 Q13895;F8WBL2 Q13895 BYSL Bystin 1 MPQDGS(1)DDEDEEWPTLEK 109.54 0.00023147 89089000 118700 101770 85187 90819 91828 98576 92846 91929 101740 107940 TRUE FALSE 114061.0728 98867.61924 100582.1859 95506.17947 94781.73102 100569.2743 93982.27712 90030.63402 90190.90173 100629.1277 1.133479693 0.982495044 0.999533517 0.949090802 0.94189161 0.999405208 0.933947052 0.894677676 0.896270333 1 16.61868844 7.999999997 0.665897531 0.935258248 19.70363357 0.693956852 0.036301997 132.5901669 0.800610331 0.014338307 3681.37393 99999999.33 -7.999999997 18.76837532 (ac)T(ph)T(ph)SQKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_BT-474_Pertuzumab_2h_R1 1 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 31 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.695)T(0.679)S(0.625)QKHRDFVAEPMGEKPVGS(0.001)LAGIGEVLGK 50.706 0.0019726 134790000 131040 96128 69467 55883 97075 105870 65865 88883 92388 60452 TRUE FALSE 125918.8119 93386.52356 82021.23219 58767.12833 100197.5055 108010.7639 66671.07557 87047.53499 81900.50156 56357.53219 2.23428541 1.657037133 1.455373026 1.04275553 1.777890224 1.916527565 1.18300204 1.544559025 1.453230799 1 15.78232082 7.999999997 0.045861085 1.82E-10 4.219412843 0.338978853 0.301291084 788.7641668 2.739690239 63.14583463 243.5463157 99999999.34 -7.999999997 4.219412843 VGYYVNNEYTETELR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGYYVNNEYTETELR 15 0 Q9Y294 Q9Y294 ASF1A Histone chaperone ASF1A 0 182.1 1.30E-06 72732000 59084 50420 40652 30428 34002 40448 28519 27209 33738 25424 FALSE TRUE 56774.93196 48982.07097 47998.7207 31998.39273 35095.70521 41265.88627 28868.02405 26647.12464 29908.20368 23702.00983 2.395363615 2.066578797 2.025090743 1.350028666 1.480705875 1.741028991 1.2179568 1.12425591 1.261842514 1 14.53272178 7.999999997 0.237509779 0.985063258 9.665726027 0.860367029 0.165554459 17.04441857 0.227007148 0.235420219 58.15653336 99999999.36 -7.999999997 8.680662769 up S(ph)PSSGSGGGGPKPYK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSSGSGGGGPKPYK 15 1 Q9ULD5 Q9ULD5 ZNF777 Zinc finger protein 777 1 S(0.922)PS(0.078)SGSGGGGPKPYK;S(0.983)PS(0.017)SGSGGGGPKPYK 168.64 7.52E-07 1555100000 2117780 1606960 1550990 1520180 1469180 1421050 1576590 1771270 1554020 1592770 TRUE FALSE 2035014.816 1561131.074 1831288.395 1598636.672 1516437.509 1449784.605 1595884.78 1734692.656 1377614.165 1484890.269 1.370481616 1.051344403 1.233281969 1.076602565 1.021245502 0.976358075 1.074749302 1.168229526 0.927754861 1 20.50192489 7.999999997 0.752031156 1.052074852 53.06856828 0.550565534 0.084611386 318.4823977 1.351169374 0.029721758 28074.36034 99999999.36 -7.999999997 52.01649342 SKS(ph)PASVDR ddPTM_BT-474_Pertuzumab_2h_R1 4 SKSPASVDR 9 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 1 S(0.24)KS(0.758)PAS(0.001)VDR;S(0.365)KS(0.635)PASVDR;S(0.007)KS(0.992)PAS(0.001)VDR;S(0.056)KS(0.944)PASVDR 151.78 4.97E-05 5065700000 4038760 3787150 3445350 3746190 3889600 3917520 3890330 4035540 4755400 4371080 TRUE FALSE 3880920.794 3679144.19 4068001.386 3939531.315 4014712.516 3996734.939 3937941.022 3952204.689 4215586.928 4075022.858 0.952367859 0.902852405 0.998276949 0.966750728 0.985199999 0.980788348 0.966360474 0.969860741 1.034494057 1 21.95837672 7.999999997 0.238497051 1.000342849 0.585883736 0.38212422 0.02574321 53.02155716 0.707575005 0.03458374 8.685196422 99999999.39 -7.999999997 -0.414459114 SPEDLER ddPTM_BT-474_Pertuzumab_2h_R1 3 SPEDLER 7 0 P06744;A0A2U3TZU2;P06744-2;Q8N196 P06744 GPI;SIX5 Glucose-6-phosphate isomerase;Homeobox protein SIX5 0 ;; 137.18 0.0067653 7208600000 3849500 3674300 2624870 3331800 3025390 2668830 2764540 3460700 2788560 2395280 FALSE TRUE 3699057.284 3569512.562 3099242.399 3503754.597 3122704.417 2722795.571 2798373.267 3389235.336 2472014.359 2233045.552 1.656507759 1.598495184 1.387899318 1.569047525 1.398406053 1.219319314 1.253164435 1.517763636 1.107014748 1 21.09058125 7.999999997 0.06127788 0.446556612 3.388738157 0.695273116 0.115699212 201.7630859 0.921760979 8.788905715 52.69970367 99999999.4 -7.999999997 2.942181545 LLDVVHPAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLDVVHPAAK 10 0 Q99832-3;Q99832;F8WAM2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 111.06 0.0018039 2150900000 5849100 5889300 5268800 5948300 6003600 6060200 6404700 6819100 7456900 7804200 FALSE TRUE 5620510.705 5721342.93 6220989.364 6255292.476 6196711.246 6182741.396 6483082.634 6678283.202 6610423.974 7275614.583 0.77251353 0.786372459 0.85504658 0.859761386 0.851709663 0.849789571 0.891070103 0.917899529 0.908572588 1 22.79463769 7.999999998 0.076963404 1.133068642 0.190107394 0.925472923 0.01698062 53.70752282 0.302275105 0.583268752 5.410277353 99999999.44 -7.999999998 -0.942961248 LPDLS(ph)PVENK ddPTM_BT-474_Pertuzumab_2h_R1 6 LPDLSPVENK 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2;A0A2R8Y7F4 E7EPN9 PRRC2C Protein PRRC2C 1 LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK 194.39 4.91E-07 4147440000 5077690 4584050 5129210 5082460 5321470 5105120 5475760 6175490 6869090 6994980 TRUE FALSE 4879248.261 4453317.382 6056172.346 5344766.37 5492639.915 5208349.024 5542773.989 6047963.973 6089339.701 6521203.774 0.748212819 0.682898056 0.928689327 0.819598122 0.842273928 0.798679079 0.849961783 0.927430607 0.933775406 1 22.63670687 7.999999998 0.091272416 1.117527402 0.046419378 0.619153508 0.056394787 100.1172781 0.655155354 0.987131614 13.42647745 99999999.48 -7.999999998 -1.071108023 METEADAPS(ph)PAPS(ph)LGER ddPTM_BT-474_Pertuzumab_2h_R1 1 METEADAPSPAPSLGER 17 0 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 2 METEADAPS(1)PAPS(1)LGER 185.55 8.38E-10 117930000 347430 292880 200080 193740 210600 187480 161400 241980 180090 168040 TRUE FALSE 333852.0515 284527.3492 236238.9068 203738.9446 217374.1403 191270.9741 163375.2615 236983.0284 159646.9382 156658.5011 2.131081614 1.816226679 1.507986512 1.300529133 1.387566833 1.220942194 1.042875173 1.512736473 1.019076125 1 17.25726353 7.999999998 0.436593668 1.16931195 22.38845264 0.828167408 0.143983273 32.89815884 0.40830881 0.090203133 616.7124544 99999999.48 -7.999999998 21.21914069 up TDVSNFDEEFTGEAPTLS(ph)PPRDAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDVSNFDEEFTGEAPTLSPPRDAR 24 1 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFTGEAPT(0.008)LS(0.992)PPRDAR;TDVSNFDEEFTGEAPT(0.303)LS(0.697)PPRDAR 170.93 4.44E-12 417270000 158237 195106 76251 96344 125395 154046 94306 99208 93995 76869 TRUE FALSE 152052.9231 189541.7679 90031.25189 101316.3254 129428.4441 157160.9157 95460.14504 97159.32013 83325.08166 71662.59416 2.121789266 2.644919154 1.256321418 1.413796508 1.806080921 2.193067632 1.33207772 1.355788487 1.162741632 1 16.12893265 7.999999998 0.137208363 0.807649698 5.833356966 0.461216035 0.373233268 71.83366673 0.658983126 1.742485391 70.59950356 99999999.49 -7.999999998 5.025707268 RGSGDTS(ph)SLIDPDTSLSELR ddPTM_BT-474_Pertuzumab_2h_R1 1 RGSGDTSSLIDPDTSLSELR 20 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.092)GDT(0.258)S(0.442)S(0.208)LIDPDTSLSELR 122.64 3.19E-05 299130000 507080 507390 434290 516130 531250 533150 499310 554180 613840 620640 TRUE FALSE 487262.753 492919.734 512775.8637 542767.5312 548338.1387 543930.6583 505420.7051 542735.9893 544159.4566 578603.5 0.842135855 0.851912811 0.886230145 0.938064722 0.947692399 0.940074953 0.87351823 0.938010208 0.940470385 1 19.14221552 7.999999998 0.287551552 0.952884039 2.34E-13 0.628446278 0.028890312 38.17923123 0.542752105 0.032383756 18.44397383 99999999.51 -7.999999998 -0.952884039 KAEAAAAPTVAPGPAQPGHVS(ph)PTPATTSPGEKGEAGTPVAAGTTAAAIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAEAAAAPTVAPGPAQPGHVSPTPATTSPGEKGEAGTPVAAGTTAAAIPR 50 2 A0A0C4DGH3;Q9Y6R0 A0A0C4DGH3 NUMBL Numb-like protein 1 KAEAAAAPTVAPGPAQPGHVS(0.525)PT(0.099)PAT(0.099)T(0.099)S(0.099)PGEKGEAGT(0.05)PVAAGT(0.013)T(0.015)AAAIPR 47.366 0.0047613 127510000 71445 60582 43092 52182 46347 62590 49363 44222 55604 39927 TRUE FALSE 68652.85041 58854.26068 50879.68298 54875.11927 47837.79335 63855.61268 49967.11916 43308.80025 49292.06703 37222.70873 1.84438083 1.581138576 1.36689899 1.474237667 1.28517765 1.715501501 1.342382671 1.163504799 1.324247179 1 15.18389542 7.999999998 0.088162774 0.702289871 3.456371836 0.614877706 0.14863637 112.0308502 0.711285917 2.980055288 37.35177363 99999999.53 -7.999999998 2.754081966 TPES(ph)FLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPESFLGPNAALVDLDSLVSRPGPTPPGAK 30 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.309)PES(0.691)FLGPNAALVDLDSLVSRPGPTPPGAK 103.37 0.00022184 1091700000 101910 94764 75006 82163 79501 88968 87103 89166 86884 81909 TRUE FALSE 97927.24453 92061.4235 88561.2527 86403.44228 82058.22187 90766.99392 88168.99257 87324.69094 77021.29257 76361.23047 1.282420987 1.205604244 1.159767229 1.131509298 1.074605809 1.188652846 1.154630328 1.143573649 1.008643943 1 16.22055273 7.999999998 0.08056629 0.880900557 1.831798551 0.658379757 0.04838137 134.6826606 0.789690503 1.393203497 14.25239019 99999999.56 -7.999999998 0.950897994 AYSSFGGGRGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 AYSSFGGGRGSR 12 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 1 AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R 86.756 0.0066206 438610000 1033380 936210 662840 692560 740780 677180 773200 980080 662250 616070 TRUE FALSE 992994.3671 909510.2074 782629.9328 728303.1046 764607.8615 690873.0436 782662.6529 959841.0055 587074.1564 574343.0302 1.728922116 1.583566196 1.362652442 1.268062928 1.331273858 1.202892709 1.362709412 1.671198143 1.022166415 1 19.13155313 7.999999998 0.036077607 3.07E-11 3.535821602 0.433294097 0.178175372 1176.260051 3.239779906 92.25805469 267.7022691 99999999.57 -7.999999998 3.535821602 RS(ph)ASPHDVDLCLVSPCEFEHRK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSASPHDVDLCLVSPCEFEHRK 22 2 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHRK 71.556 0.0077198 314790000 290220 325080 125250 131420 174960 259220 128460 102570 148760 136510 TRUE FALSE 278877.8815 315809.0367 147885.4612 138202.6019 180587.7473 264461.606 130032.1319 100451.8937 131873.3885 127264.0561 2.191332652 2.481525785 1.162036365 1.085951573 1.419000406 2.078054198 1.021750649 0.789318655 1.03621865 1 16.95746548 7.999999998 0.320372679 0.965334473 15.22692207 0.506837883 0.398035869 46.74806036 0.669352232 0.39574768 390.6891726 99999999.57 -7.999999998 14.2615876 KTEELEEESFPER ddPTM_BT-474_Pertuzumab_2h_R1 2 KTEELEEESFPER 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 203.27 1.40E-07 1947270000 1054860 1024610 930080 993900 1044160 1118440 1015710 1180240 1252580 1250580 FALSE TRUE 1013634.905 995389.126 1098166.146 1045195.298 1077746.355 1141055.623 1028140.563 1155867.632 1110392.37 1165877.103 0.869418314 0.853768484 0.941922732 0.8964884 0.924408201 0.978710038 0.881860155 0.991414643 0.95240945 1 20.15298429 7.999999998 0.147407522 1.013761708 0.450562694 0.576379842 0.032303089 46.13639406 0.447526 0.11071537 5.541140228 99999999.58 -7.999999998 -0.563199013 KEECPAVR ddPTM_BT-474_Pertuzumab_2h_R1 8 KEECPAVR 8 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 172.23 0.0004566 13532120000 12969373 14460319 11947572 15957260 12978524 12782719 16053756 14875598 17877450 18021300 FALSE TRUE 12462515.56 14047924.86 14106764.03 16780816.1 13395990.01 13041194.34 16250226.67 14568411.7 15848076.82 16800701.3 0.741785438 0.836151099 0.839653285 0.998816407 0.797347073 0.776229165 0.967235021 0.867131166 0.943298529 1 24.00201812 7.999999998 0.042904331 1.323581455 0.111303949 0.388780252 0.070122618 748.5442737 2.438666984 18.05262158 63.90885522 99999999.6 -7.999999998 -1.212277506 LDKDEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDKDEIR 7 1 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ; 109.21 0.0064555 3637300000 4409000 4490100 4207700 4722100 4460300 4457300 5024600 5300500 5893500 5866400 FALSE TRUE 4236691.406 4362046.744 4968124.99 4965808.147 4603769.6 4547429.66 5086092.558 5191042.823 5224494.588 5469063.503 0.774664877 0.797585682 0.908405066 0.907981439 0.841783899 0.831482329 0.929975041 0.949164847 0.95528139 1 22.38286238 7.999999998 0.118631389 1.05384228 0.213068528 0.710373328 0.037944813 56.94864138 0.46489852 0.295148829 7.907693162 99999999.61 -7.999999998 -0.840773752 LDQPMTEIVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDQPMTEIVSR 11 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 149.96 7.94E-05 529230000 384000 348920 288450 273633 344851 274126 276221 306408 302756 278893 FALSE TRUE 368992.8555 338969.1432 340579.3315 287755.2319 355943.4456 279669.0155 279601.4752 300080.5677 268388.4081 260003.3287 1.419185121 1.303710783 1.309903736 1.106736723 1.368995725 1.075636289 1.075376522 1.154141254 1.032249893 1 17.98817057 7.999999998 0.172154101 0.966651256 2.80531086 0.696739853 0.079230843 31.60028016 0.344229432 0.18695158 15.03496575 99999999.63 -7.999999998 1.838659604 QIT(ph)MEELVR ddPTM_BT-474_Pertuzumab_2h_R1 4 QITMEELVR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR 159.36 0.00073903 1140840000 1170600 1088590 627690 862290 949880 710840 718270 1207990 735300 686080 TRUE FALSE 1124851.658 1057544.479 741127.5459 906792.8902 980433.7529 725213.6718 727060.4031 1183044.584 651831.8266 639611.1905 1.758649121 1.653417724 1.158715727 1.41772518 1.532858973 1.133835184 1.136722456 1.849630841 1.019106351 1 19.28683565 7.999999998 0.035866146 9.86E-13 3.573097323 0.28059429 0.255148641 1606.813862 4.400377114 127.7844336 368.5044385 99999999.63 -7.999999998 3.573097323 VELIHGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VELIHGK 7 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 76.774 0.051659 0 454920 492720 420220 504750 486050 462870 542110 553110 597790 640800 FALSE TRUE 437141.2235 478668.108 496163.1017 530800.208 501684.2397 472229.5485 548744.5043 541688.0852 529931.3853 597398.0452 0.731741972 0.801254895 0.830540216 0.888520162 0.839782192 0.790477224 0.918557583 0.906745661 0.887065817 1 19.18833299 7.999999998 0.075112153 1.139870137 0.157236279 0.745675986 0.036633704 113.4785658 0.624827695 1.322598492 11.66194927 99999999.64 -7.999999998 -0.982633858 SS(ph)PQLDPLRKS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_BT-474_Pertuzumab_2h_R1 6 SSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGR 33 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 2 S(0.456)S(0.544)PQLDPLRKS(0.971)PT(0.029)MEQAVQTASAHLPAPAAVGR;S(0.463)S(0.537)PQLDPLRKS(1)PTMEQAVQTASAHLPAPAAVGR;S(0.18)S(0.82)PQLDPLRKS(0.954)PT(0.046)MEQAVQTASAHLPAPAAVGR;S(0.46)S(0.54)PQLDPLRKS(0.88)PT(0.12)MEQAVQTASAHLPAPAAVGR;S(0.467)S(0.534)PQLDPLRKS(0.634)PT(0.186)MEQAVQT(0.135)AS(0.043)AHLPAPAAVGR;S(0.456)S(0.544)PQLDPLRKS(0.994)PT(0.006)MEQAVQTASAHLPAPAAVGR 213.09 2.44E-28 5976710000 2818364 3378120 1855690 1816271 2364950 2980208 2049414 2067982 2484530 1851188 TRUE FALSE 2708219.219 3281779.325 2191054.463 1910008.964 2441020.765 3040469.848 2074495.342 2025277.449 2202496.57 1725805.388 1.569249487 1.901592931 1.269583742 1.106734848 1.414424119 1.761768661 1.202044771 1.173525974 1.276213753 1 20.71883836 7.999999998 0.111354568 0.854673283 3.323236316 0.367758401 0.220581822 119.7650419 0.928026017 2.018617691 45.51168239 99999999.64 -7.999999998 2.468563033 SSESPSS(ph)SPS(ph)SPARK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSESPS(0.006)S(0.981)S(0.083)PS(0.748)S(0.181)PARK;SSES(0.001)PS(0.042)S(0.945)S(0.016)PS(0.557)S(0.44)PARK 106.28 0.0043713 651180000 868970 854750 622940 658210 757290 738020 664430 750470 765080 629640 TRUE FALSE 835009.6917 830373.3669 735519.1152 692180.297 781648.9206 752943.2701 672561.4931 734972.5322 678231.3259 586993.922 1.422518463 1.414620043 1.253026799 1.179194999 1.331613312 1.282710505 1.145772499 1.252095643 1.155431599 1 19.16298604 7.999999999 0.044726715 0.414363898 2.702142931 0.740811003 0.062669581 328.1960457 1.112882604 14.50750468 54.14597265 99999999.68 -7.999999999 2.287779033 KAVAVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KAVAVR 6 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 101.33 0.058763 1308160000 3147500 3203200 3039400 3366300 3355300 3111000 3534500 3639500 3722000 4148500 FALSE TRUE 3024492.22 3111847.872 3588687.191 3540035.146 3463226.272 3173906.552 3577756.268 3564343.053 3299494.164 3867518.4 0.782024003 0.804611006 0.927904361 0.915324707 0.895464718 0.82065713 0.925078021 0.92160985 0.853129532 1 21.88297672 7.999999999 0.036477932 1.315072314 0.210146373 0.456589939 0.047351972 910.3306969 2.534398644 22.17056981 65.08891012 99999999.7 -7.999999999 -1.10492594 FVGHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 FVGHTK 6 0 P63244;J3KPE3;D6RHH4;H0YAF8;D6R9L0;H0Y8W2;D6R9Z1;D6RFX4;E9PD14;D6RFZ9;D6RAU2;H0YAM7 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 71.995 0.086763 1901300000 2622800 2635200 2181800 2617000 2716300 2595500 2675000 2755200 3404800 3240400 FALSE TRUE 2520298.076 2560046.676 2576099.794 2752063.684 2803672.256 2647982.788 2707737.45 2698304.157 3018301.378 3020924.822 0.834280303 0.847438062 0.852752037 0.911000388 0.928084087 0.876547066 0.89632732 0.89320467 0.999131576 1 21.52655885 7.999999999 0.047656478 1.239515355 0.285842402 0.716208001 0.029425525 309.4356796 1.115036701 5.440027774 22.09895723 99999999.71 -7.999999999 -0.953672953 AIGDHFYK ddPTM_BT-474_Pertuzumab_2h_R1 5 AIGDHFYK 8 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;;; 109.86 0.0035366 2620660000 5174160 5301330 4492820 5217800 5240690 4962810 5684910 5584790 6076910 6327860 FALSE TRUE 4971948.107 5150141.259 5304772.516 5487091.283 5409261.553 5063161.418 5754483.629 5469462.135 5387084.653 5899268.406 0.842807576 0.873013551 0.899225489 0.930130807 0.916937691 0.858269377 0.975457164 0.927142445 0.913178429 1 22.49210462 7.999999999 0.063274395 1.106548433 0.493483203 0.590621237 0.029795741 217.7237517 1.02473549 1.913742984 12.14012001 99999999.71 -7.999999999 -0.61306523 SAQGSSS(ph)PVPSMVQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SAQGSSSPVPSMVQK 15 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SAQGSSS(1)PVPSMVQK;SAQGSS(0.003)S(0.997)PVPSMVQK;SAQGS(0.001)S(0.004)S(0.995)PVPSMVQK;SAQGSS(0.005)S(0.995)PVPSMVQK 291.59 6.62E-44 1665060000 2315280 2345360 2378660 2456220 2465180 2713470 2721650 2837710 3086450 3330290 TRUE FALSE 2224796.298 2278472.629 2808536.775 2582985.809 2544474.754 2768338.223 2754958.367 2779110.297 2736089.135 3104726.492 0.716583668 0.733872254 0.904600383 0.831952771 0.819548762 0.891652849 0.887343337 0.895122422 0.881265755 1 21.56603475 7.999999999 0.159698924 0.987853798 1.89E-10 0.736114427 0.041024862 33.88960391 0.349332348 0.123683695 7.881639605 99999999.72 -7.999999999 -0.987853798 ELLS(ph)PGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLSPGVK 8 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 ELLS(1)PGVK;ELLS(1)PGVK 97.597 0.0085165 143421000 414220 394160 420600 382060 438510 491890 445490 484540 577490 577150 TRUE FALSE 398031.8245 382918.9427 496611.7762 401778.1624 452615.0724 501836.3528 450942.0399 474534.0797 511935.7562 538059.1164 0.739754819 0.711667047 0.922968798 0.746717508 0.841199524 0.93267884 0.838090139 0.881936697 0.951448903 1 19.03740516 7.999999999 0.108673579 1.070509249 0.049133279 0.618363251 0.057855149 72.82140407 0.552938644 0.527791092 11.15014458 99999999.73 -7.999999999 -1.02137597 LLEAHEEQNVDSYTESVKEYDSISR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEAHEEQNVDSYTESVKEYDSISR 25 1 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 196.28 5.21E-25 422700000 315820 357170 204078 204324 281110 316530 243544 240501 256334 211425 FALSE TRUE 303477.4052 346983.8613 240959.4343 214869.1861 290152.1584 322930.4535 246524.5643 235534.5703 227236.039 197104.9964 1.539673832 1.760401145 1.222492776 1.090125517 1.472069018 1.638367669 1.250727119 1.194970065 1.152867979 1 17.58860482 7.999999999 0.072484491 0.601572959 3.122725183 0.410821045 0.184590768 251.6954862 1.341913955 7.848643102 64.37615526 99999999.74 -7.999999999 2.521152224 RAS(ph)S(ph)KGGGGYTCQSGSGWDEFTK ddPTM_BT-474_Pertuzumab_2h_R1 5 RASSKGGGGYTCQSGSGWDEFTK 23 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 RAS(0.987)S(0.72)KGGGGY(0.189)T(0.103)CQSGSGWDEFTK;RAS(0.997)S(0.997)KGGGGY(0.004)T(0.002)CQSGSGWDEFTK;RAS(0.961)S(0.726)KGGGGY(0.298)T(0.014)CQSGSGWDEFTK;RAS(0.713)S(0.714)KGGGGY(0.17)T(0.135)CQS(0.117)GS(0.15)GWDEFTK;RAS(0.815)S(0.876)KGGGGY(0.296)T(0.013)CQSGSGWDEFTK 157.08 5.66E-09 3610220000 5990850 5142040 3642970 3421620 4923780 4939390 3086350 3875170 3807830 2626230 TRUE FALSE 5756720.959 4995394.054 4301335.716 3598210.218 5082157.855 5039267.85 3124121.675 3795146.385 3375581.102 2448353.103 2.351262549 2.040307849 1.756828176 1.469645132 2.075745467 2.058227567 1.276009441 1.55008131 1.378714981 1 21.22338021 7.999999999 0.073491536 0.194833067 5.401504781 0.654456618 0.239574769 148.8675841 0.803679215 9.434068947 79.55954306 99999999.74 -7.999999999 5.206671715 WLETCQHESDEQPLDPIPQISST(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 WLETCQHESDEQPLDPIPQISSTPK 25 0 Q96R06;F5GZT2 Q96R06 SPAG5 Sperm-associated antigen 5 1 WLETCQHESDEQPLDPIPQIS(0.326)S(0.237)T(0.437)PK 111.05 0.0098742 58411000 51325 49115 49325 47104 48423 58661 49761 58127 62104 62960 TRUE FALSE 49319.16226 47714.28829 58239.12473 49535.04308 49980.56977 59847.16561 50369.99 56926.65714 55054.21428 58695.66312 0.840252237 0.812909945 0.99222194 0.843930206 0.85152066 1.019618187 0.858155225 0.969861385 0.937960513 1 15.84096629 7.999999999 0.119734167 1.03005108 0.419624127 0.332896719 0.061086119 107.3324116 0.882848229 0.397786154 10.93428299 99999999.74 -7.999999999 -0.610426953 LLS(ph)PLRDTPPPQSLMVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLSPLRDTPPPQSLMVK 17 1 A0A669KBI3;F5GXF9;P51825;P51825-3;P51825-2 A0A669KBI3 AFF1 AF4/FMR2 family member 1 1 LLS(0.996)PLRDT(0.004)PPPQSLMVK 83.871 0.0032843 109870000 149270 135940 116030 125070 127220 142780 114040 137560 152310 132370 TRUE FALSE 143436.3634 132063.1243 136999.2021 131524.8777 131312.1468 145667.1094 115435.6556 134719.3379 135020.4073 123404.462 1.162327205 1.070164905 1.110164089 1.065803258 1.064079408 1.18040391 0.935425298 1.091689358 1.094129055 1 16.91303503 7.999999999 0.066701667 0.9212186 1.428409665 0.213259004 0.06008741 443.7516693 2.192774028 3.053940186 21.3294269 99999999.75 -7.999999999 0.507191066 VTGEADVEFATHEEAVAAMSK ddPTM_BT-474_Pertuzumab_2h_R1 5 VTGEADVEFATHEEAVAAMSK 21 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;; 268.23 2.84E-37 488238500 402339 385090 377143 402890 411855 455450 415994 470949 543764 532505 FALSE TRUE 386615.1471 374107.6102 445301.1296 423683.2012 425102.6901 464659.5111 421085.059 461223.7386 482038.1904 496437.962 0.77877837 0.753583809 0.896992502 0.853446419 0.856305768 0.935987065 0.848212851 0.929066215 0.970993814 1 18.92125392 7.999999999 0.135847923 1.034178744 0.109383669 0.751367387 0.03763254 37.53143923 0.341612487 0.170419977 6.707481856 99999999.75 -7.999999999 -0.924795075 (ac)ADDIDIEAMLEAPYK ddPTM_BT-474_Pertuzumab_2h_R1 6 ADDIDIEAMLEAPYK 15 0 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;F8WF24;F2Z2Z5;A8MYG5;F2Z3E6;F8WF73;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 ;;;;; 57.836 1.94E-05 198782000 282100 276465 244779 272934 294569 282563 297658 336088 334444 360363 FALSE TRUE 271075.2201 268580.4889 289016.0104 287020.1564 304044.0794 288276.6175 301300.8276 329147.6654 296479.3192 335955.293 0.806878849 0.799453066 0.860281164 0.854340332 0.905013511 0.858080297 0.896847985 0.979736507 0.882496348 1 18.35790973 7.999999999 0.111785805 1.054140747 0.243633923 0.755195384 0.030675942 47.27025234 0.367460775 0.259986743 5.922864523 99999999.75 -7.999999999 -0.810506824 VEQATKPSFESGR ddPTM_BT-474_Pertuzumab_2h_R1 6 VEQATKPSFESGR 13 1 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ;;;;; 200.97 9.63E-08 15151110000 9482870 9144900 8616720 9604260 9369390 9337200 9905180 11164300 11354950 11963400 FALSE TRUE 9112268.957 8884096.406 10173952.98 10099937.01 9670764.938 9526004.581 10026402.56 10933753.3 10065983.68 11153108.26 0.817016095 0.796557892 0.912207857 0.905571503 0.867091461 0.854112088 0.898978322 0.980332392 0.90252721 1 23.4109425 7.999999999 0.097930641 1.067029762 0.332308304 0.640770157 0.036450452 85.6985838 0.595904066 0.523674849 8.459888401 99999999.76 -7.999999999 -0.734721458 KGESQTDIEITR ddPTM_BT-474_Pertuzumab_2h_R1 7 KGESQTDIEITR 12 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;;;; 169.04 7.20E-05 10973870000 5653199 6073603 5376318 6056668 5871887 6374242 6709647 6992336 7587106 8099820 FALSE TRUE 5432265.733 5900389.789 6347938.258 6369253.361 6060761.578 6503133.541 6791761.667 6847941.818 6725849.535 7551211.977 0.719389914 0.781383148 0.840651577 0.843474317 0.802621036 0.861203945 0.8994267 0.906866585 0.890698017 1 22.84827679 7.999999999 0.101048752 1.078819384 0.095042792 0.890600658 0.024281093 39.42304217 0.281551339 0.307827221 5.382195301 99999999.77 -7.999999999 -0.983776592 SSWSSSDEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSWSSSDEKR 10 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 0 ; 141.88 5.89E-05 265800000 205580 193593 161180 186232 173750 185003 179847 186521 208820 193077 FALSE TRUE 197545.7063 188071.9172 190308.8114 195843.4558 179338.8265 188743.8874 182048.0214 182669.2762 185115.629 179999.7228 1.097477836 1.044845593 1.057272803 1.088020875 0.996328348 1.048578767 1.011379454 1.014830875 1.028421745 1 17.45763516 7.999999999 0.196211721 0.997072359 1.420558331 0.55384458 0.022236295 38.19173278 0.455448777 0.040217406 4.950020424 99999999.78 -7.999999999 0.423485972 DASVPLIDVTNLPT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 DASVPLIDVTNLPTPR 16 0 Q96A65;Q96A65-2 Q96A65 EXOC4 Exocyst complex component 4 1 DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR 186.94 1.59E-08 129149000 81971 72719 63022 56316 59312 63231 53649 74696 51685 59036 TRUE FALSE 78767.4827 70645.12532 74411.47732 59222.47551 61219.82435 64509.57414 54305.57251 73153.5015 45817.93548 55037.43914 1.431161841 1.283583074 1.352015619 1.076039809 1.112330539 1.172103484 0.986702386 1.32915889 0.832486689 1 15.74812572 7.999999999 0.286982307 1.038959423 4.194001236 0.505408136 0.127094323 47.00757931 0.668016627 0.132928324 74.99089256 99999999.79 -7.999999999 3.155041812 RTSSEELRDAT(ph)SLLAAGEGGLLDEVEPLRPDELER ddPTM_BT-474_Pertuzumab_2h_R1 2 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.059)S(0.059)S(0.059)EELRDAT(0.412)S(0.412)LLAAGEGGLLDEVEPLRPDELER;RT(0.216)S(0.216)S(0.216)EELRDAT(0.283)S(0.071)LLAAGEGGLLDEVEPLRPDELER 140.38 1.51E-10 76039000 23338.2 29456.5 9642.1 13592.2 21251.3 21757.1 13610.7 13443.3 13312.5 12741.9 TRUE FALSE 22426.11734 28616.42946 11384.64196 14293.69507 21934.86736 22197.04347 13777.27182 13165.69116 11801.32081 11878.87976 1.887898336 2.409017519 0.958393568 1.203286451 1.846543428 1.868614205 1.159812381 1.108327672 0.993470853 1 13.53611117 7.999999999 0.176297834 0.879894012 5.767273297 0.372282801 0.384723903 63.43235881 0.702874026 0.953648698 82.68592608 99999999.79 -7.999999999 4.887379284 IS(ph)FVEEDVHPK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISFVEEDVHPK 11 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 IS(1)FVEEDVHPK;IS(1)FVEEDVHPK;IS(1)FVEEDVHPK 188.4 2.04E-06 297948000 827670 685810 616523 627892 732450 599624 604117 741882 694569 621334 TRUE FALSE 795323.7414 666251.3703 727942.4206 660297.5814 756009.9194 611748.8081 611510.3646 726561.8774 615724.439 579250.4948 1.373022118 1.1501956 1.256697106 1.139917164 1.305151962 1.056104075 1.055692434 1.25431378 1.062967481 1 19.14382785 7.999999999 0.080001256 0.86778319 1.975199617 0.451126191 0.088156091 197.0855187 1.148351457 2.395572106 24.13467465 99999999.8 -7.999999999 1.107416427 KPGPPLS(ph)PEIRS(ph)PAGS(ph)PELR ddPTM_BT-474_Pertuzumab_2h_R1 3 KPGPPLSPEIRSPAGSPELR 20 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 3 KPGPPLS(1)PEIRS(1)PAGS(1)PELR;KPGPPLS(1)PEIRS(1)PAGS(1)PELR;KPGPPLS(1)PEIRS(1)PAGS(1)PELR 82.998 0.0021104 866710000 1049130 1066140 731790 823460 971790 899820 876790 899920 886540 890010 TRUE FALSE 1008128.84 1035734.731 864040.7316 865958.8693 1003048.508 918014.9769 887520.4183 881336.3375 785903.6959 829728.83 1.215010017 1.248280997 1.041353151 1.043664916 1.208887135 1.106403615 1.069651175 1.062198041 0.947181377 1 19.66228039 7.999999999 0.16442023 0.966538032 1.979160812 0.513040819 0.065869435 53.30288163 0.561469362 0.189117841 13.17959589 99999999.8 -7.999999999 1.01262278 SPTLYGISHDDLK ddPTM_BT-474_Pertuzumab_2h_R1 3 SPTLYGISHDDLK 13 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 179.83 1.34E-05 905320000 1638030 1580290 1424560 1509420 1651750 1614240 1641570 1670700 1896690 1890200 FALSE TRUE 1574013.977 1535221.676 1682009.681 1587321.347 1704880.039 1646881.039 1661660.025 1636199.461 1681385.703 1762175.07 0.893222247 0.871208373 0.954507704 0.900773921 0.967486187 0.934572885 0.942959671 0.928511298 0.954153609 1 20.74892583 7.999999999 0.066795266 1.070117869 0.620756361 0.587461106 0.023263831 199.6251535 0.987708174 1.215364583 8.510653788 99999999.8 -7.999999999 -0.449361509 SWS(ph)LATFR ddPTM_BT-474_Pertuzumab_2h_R1 3 SWSLATFR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 S(0.002)WS(0.998)LATFR;S(0.006)WS(0.994)LATFR;S(0.037)WS(0.963)LATFR 119.68 0.0017282 123663000 246850 228982 167876 98568 226203 175523 104457 181372 102283 80474 TRUE FALSE 237202.8291 222451.6576 198214.9276 103655.1063 233479.0249 179072.1953 105735.376 177626.6048 90672.26265 75023.4243 3.161716908 2.96509603 2.642040528 1.381636566 3.112081688 2.38688379 1.409364835 2.367615268 1.208586031 1 16.19505349 7.999999999 0.087681879 0.015969935 8.546281626 0.558521804 0.527590252 124.6244573 0.787462055 10.34479272 128.0223769 99999999.84 -7.999999999 8.530311691 KLADQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_BT-474_Pertuzumab_2h_R1 1 KLADQCTGLQGFLVFHSFGGGTGSGFTSLLMER 33 1 P68363;F8VQQ4;Q9BQE3;F5H5D3 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 168.61 1.79E-14 150390000 116290 123600 63059 54339 74932 86819 61613 58902 70063 51532 FALSE TRUE 111745.2582 120075.049 74455.16404 57143.4423 77342.25583 88574.53966 62367.03832 57685.65312 62109.74197 48041.69174 2.326005896 2.499392604 1.549803126 1.189455247 1.609898674 1.843701511 1.298185723 1.200741502 1.292830034 1 15.55199933 7.999999999 0.330700718 1.179604083 15.34637087 0.681808604 0.268624502 34.15488066 0.487653783 0.252024776 295.8689017 99999999.84 -7.999999999 14.16676679 SSS(ph)PVTELASRS(ph)PIRQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.243)S(0.324)S(0.433)PVTELAS(0.034)RS(0.966)PIRQDR 188.23 2.09E-14 952090000 116540 120410 69970 64937 104810 108780 80665 71734 84979 70849 TRUE FALSE 111985.488 116976.0247 82615.13547 68288.40635 108181.3088 110979.6061 81652.2024 70252.66783 75332.54018 66050.33412 1.695456797 1.771013368 1.250790576 1.033884344 1.637861644 1.680227778 1.236211799 1.063623201 1.14053231 1 16.01127824 7.999999999 0.125353299 0.836782333 3.616483781 0.425959759 0.22213698 92.20427534 0.787138895 1.442120129 45.07533164 99999999.84 -7.999999999 2.779701448 TGVIHEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TGVIHEK 7 0 Q96M27;Q96M27-3;Q96M27-2;Q96M27-5 Q96M27 PRRC1 Protein PRRC1 0 ;; 84.568 0.02145 1735440000 2840830 2996700 2775600 3008090 3019720 3020470 3231600 3345870 3926910 3903390 FALSE TRUE 2729807.223 2911237.05 3277212.663 3163337.885 3116852.036 3081545.973 3271149.287 3276776.615 3481143.64 3639009.919 0.750151081 0.800008001 0.900578107 0.869285316 0.856511003 0.846808896 0.898911891 0.900458281 0.956618343 1 21.79511455 7.999999999 0.091583172 1.087219171 0.234462272 0.792199498 0.031069862 72.62159659 0.476631925 0.567344788 7.779672375 99999999.85 -7.999999999 -0.8527569 KVEEDEAGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 KVEEDEAGGR 10 1 Q92890;Q92890-1 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 0 174.24 5.08E-06 1082600000 1916400 2124300 1618100 1886100 1957900 2055700 2065500 2134900 2326700 2385000 FALSE TRUE 1841504.969 2063717.044 1910526.664 1983441.847 2020877.632 2097267.662 2090778.207 2090813.569 2062582.77 2223461.826 0.82821524 0.928154925 0.859257687 0.892051226 0.908887937 0.943244286 0.940325659 0.940341563 0.927644786 1 21.0843762 7.999999999 0.092476091 1.052257091 0.50205522 0.718127176 0.024218907 76.49440303 0.506293407 0.380322663 5.338003473 99999999.85 -7.999999999 -0.550201871 DLSHIGDAVVISCAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLSHIGDAVVISCAK 15 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;; 259.18 1.75E-24 7360480000 10273900 10111400 8175470 10445050 9758560 10368530 10817410 10640060 11883530 12052120 FALSE TRUE 9872384.63 9823032.772 9652959.291 10984120.28 10072452.94 10578188.78 10949796.7 10420339.04 10534561.49 11235819.18 0.878652858 0.874260489 0.859123766 0.977598527 0.896459153 0.941470187 0.974543692 0.92742139 0.937587311 1 23.42160198 7.999999999 0.144854889 1.002549948 0.501135012 0.571435952 0.030091932 51.46054371 0.492486861 0.113362468 5.386689036 99999999.85 -7.999999999 -0.501414937 TMVGFGPEDDHFVAELTYNYGVGDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 TMVGFGPEDDHFVAELTYNYGVGDYK 26 0 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 209.76 1.72E-25 449910000 316810 334440 297800 350500 315920 308560 381290 378930 427940 431630 FALSE TRUE 304428.7149 324902.0987 351619.0845 368589.347 326081.8537 314799.2946 385956.3411 371104.9631 379362.0453 402395.3156 0.756541399 0.807420181 0.873815054 0.915988166 0.810352012 0.782313517 0.959147202 0.922239769 0.942759596 1 18.61825399 7.999999999 0.086422509 1.115494127 0.194966842 0.603806024 0.04977645 122.2292695 0.762584525 1.116550099 13.36407165 99999999.86 -7.999999999 -0.920527285 RS(ph)DSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.374)DS(0.374)MT(0.252)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 96.56 0.00011525 722190000 36797 32431 19824 19583 29094 32787 15535 23185 22789 14552 TRUE FALSE 35358.93256 31506.09963 23406.63778 20593.68098 30029.83493 33449.9756 15725.12198 22706.22165 20202.08826 13566.38008 2.606364583 2.322365985 1.725341443 1.51799381 2.213548106 2.465652253 1.159124386 1.673712628 1.489128872 1 13.7277482 7.999999999 0.079119926 0.211776701 6.045972322 0.528682991 0.362145611 168.1206556 0.969939291 10.91683455 107.3865536 99999999.86 -7.999999999 5.83419562 ELKDEVTR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELKDEVTR 8 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C0K6 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A;Kinesin-like protein 0 85.355 0.015323 305790000 366960 381530 328930 375270 349250 388720 403270 431930 438350 476010 FALSE TRUE 352618.7975 370649.138 388374.968 394637.7297 360483.9434 396580.1847 408205.3389 423010.4946 388590.3457 443769.4187 0.794599138 0.835229113 0.875172898 0.889285546 0.812322635 0.893662718 0.919859102 0.953221373 0.875658234 1 18.75945073 7.999999999 0.07495076 1.118513941 0.306095746 0.699063158 0.0325944 121.5818759 0.668147069 1.174591154 10.31113445 99999999.86 -7.999999999 -0.812418195 ASKS(ph)SPAGNSPAPL ddPTM_BT-474_Pertuzumab_2h_R1 1 ASKSSPAGNSPAPL 14 1 B4DSP0;A0A087WZG9;Q86TG7-2 B4DSP0 PEG10 Retrotransposon-derived protein PEG10 1 AS(0.004)KS(0.498)S(0.498)PAGNSPAPL 94.765 0.010616 130790000 408610 430420 256930 258240 295850 355590 271040 267520 297030 278580 TRUE FALSE 392641.0695 418144.843 303362.9664 271567.7973 305366.2839 362780.2734 274357.0686 261995.6185 263312.3997 259711.5285 1.51183535 1.61003574 1.168076628 1.045651685 1.175790254 1.396858567 1.056391567 1.00879472 1.013864888 1 17.98655053 7.999999999 0.316860457 1.013864136 6.704366933 0.617880866 0.132776724 37.55168781 0.537909344 0.132565475 123.3841934 99999999.87 -7.999999999 5.690502797 GFGFVTYSCVEEVDAAMCARPHK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVTYSCVEEVDAAMCARPHK 23 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 176.46 2.01E-13 687730000 1010600 1155830 499600 709390 806760 1072800 622960 563210 835500 637070 FALSE TRUE 971104.6347 1122866.86 589888.8335 746001.7029 832710.1681 1094492.751 630583.9708 551579.5167 740657.5427 593920.6815 1.635074624 1.890600707 0.993211471 1.256062848 1.40205619 1.842826467 1.061730952 0.928709058 1.247064744 1 19.17991075 7.999999999 0.16591625 0.918402092 4.02865502 0.301478812 0.282563786 75.5720435 0.801374212 0.809973008 58.05081406 99999999.88 -7.999999999 3.110252928 DLPHWNK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPHWNK 7 0 Q7LG56;A0A0C4DGZ6;H0YAV1;Q7LG56-2;Q7LG56-6 Q7LG56 RRM2B Ribonucleoside-diphosphate reductase subunit M2 B 0 108.24 0.0072977 380880000 432640 415020 358220 470100 445090 409060 527530 494750 551860 593650 FALSE TRUE 415731.9505 403184.0359 422958.3226 494361.9173 459406.7241 417331.4735 533986.0699 484533.2396 489215.1664 553441.5567 0.751175884 0.728503364 0.764233039 0.893250446 0.830090763 0.754066023 0.964846357 0.875491249 0.883950908 1 19.07807145 7.999999999 0.096376427 1.098208114 0.024571389 0.650284613 0.05307509 82.152719 0.56346867 0.751014212 11.65933569 99999999.88 -7.999999999 -1.073636726 LLEIDPYLKPYAVDFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEIDPYLKPYAVDFQR 17 1 Q04446 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ; 75.463 0.020041 206518000 533770 557780 325660 376500 414330 431260 403160 349310 442580 392350 FALSE TRUE 512909.6783 541872.6605 384514.0063 395931.2101 427657.3007 439980.3727 408093.9927 342096.6264 392340.1738 365775.785 1.402251596 1.481433935 1.051228709 1.082442377 1.16917882 1.202869054 1.115694394 0.935263187 1.072624788 1 18.48060004 7.999999999 0.354801018 1.017977229 6.615830358 0.619740469 0.100709071 40.1430682 0.564540923 0.08586362 150.9741367 99999999.88 -7.999999999 5.59785313 TVS(ph)SPPT(ph)SPRPGSAATVSASTSNIIPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.049)VS(0.475)S(0.475)PPT(0.524)S(0.476)PRPGS(0.001)AATVSASTSNIIPPR 67.441 0.030751 248270000 76162 76123 75081 77067 75874 83905 71721 90683 94953 96173 TRUE FALSE 73185.50484 73952.04657 88649.80687 81044.43711 78314.55612 85601.61659 72598.74305 88810.36436 84174.33352 89659.11705 0.816263948 0.82481346 0.988742805 0.903917413 0.87347008 0.954745255 0.809719585 0.99053356 0.93882626 1 16.45216267 7.999999999 0.0901147 1.057209469 0.471740099 0.330593773 0.058480653 191.1298078 1.236915654 1.048618622 13.83666127 99999999.88 -7.999999999 -0.58546937 QQTLEAEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQTLEAEEAKR 11 1 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 68.359 0.092123 246040000 303430 327860 296950 331760 334870 358460 344890 347500 450860 423590 FALSE TRUE 291571.6201 318509.7538 350615.4706 348882.1734 345641.3977 365708.3068 349110.867 340324.0036 399680.263 394899.872 0.738343162 0.80655826 0.887859165 0.883469958 0.875263382 0.926078565 0.884049076 0.861798212 1.012105324 1 18.59112737 7.999999999 0.194032247 0.97809678 1.37E-12 0.713471743 0.041223399 34.19164394 0.404750866 0.085106773 10.08832367 99999999.88 -7.999999999 -0.97809678 RPDDVPLSLS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPDDVPLSLSPSK 13 1 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 RPDDVPLS(0.022)LS(0.968)PS(0.01)K 70.907 0.026775 373870000 938830 966870 860670 973840 997230 960610 1045300 1009700 1180400 1222600 TRUE FALSE 902139.4857 939295.8143 1016212.215 1024099.999 1029306.809 980034.1924 1058092.694 988849.3422 1046405.941 1139792.213 0.791494691 0.824093904 0.89157673 0.898497101 0.90306531 0.859835838 0.92832069 0.867569835 0.918067283 1 20.12033941 7.999999999 0.025977929 1.526305882 2.77E-12 0.704142336 0.029807544 1127.194776 2.249830662 44.75849854 96.56358223 99999999.88 -7.999999999 -1.526305882 IACKS(ph)PPPESMDTPTSTR ddPTM_BT-474_Pertuzumab_2h_R1 1 IACKSPPPESMDTPTSTR 18 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 IACKS(1)PPPESMDTPTSTR 83.245 0.0024467 202630000 255770 144450 109130 131540 217560 126530 127080 162350 101200 89825 TRUE FALSE 245774.2256 140330.4274 128852.2186 138328.7952 224558.015 129088.5233 128635.2431 158997.4158 89712.20027 83741.07274 2.934930466 1.67576582 1.538697969 1.651863185 2.681575571 1.541519819 1.536106941 1.898678994 1.071304646 1 16.35364778 7.999999999 0.06443331 1.50E-12 5.679024131 0.402681789 0.455008511 345.1200614 1.651848942 27.58167512 180.7671945 99999999.88 -7.999999999 5.679024131 RNS(ph)VTPLASPEPTK ddPTM_BT-474_Pertuzumab_2h_R1 2 RNSVTPLASPEPTK 14 1 Q5W015;Q5VX20;A0A1W2PR17;Q16875-3;Q16875-2;Q16875;Q16875-4;Q9H178 Q5W015 PFKFB3 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 RNS(0.976)VT(0.024)PLASPEPTK;RNS(0.985)VT(0.015)PLASPEPTK 148.24 4.79E-06 649840000 1128950 994780 693870 683050 900340 741800 755660 1010570 767990 604740 TRUE FALSE 1084829.386 966409.8484 819267.7441 718302.2924 929300.2538 756799.7042 764907.9931 989701.3764 680810.9949 563780.4212 1.924205498 1.714160003 1.453168137 1.274081656 1.648337223 1.342366063 1.356748061 1.755473123 1.207581834 1 19.10477385 7.999999999 0.040784383 8.14E-11 3.962744385 0.498937084 0.192129114 771.4209188 2.393226815 62.91112067 209.406588 99999999.88 -7.999999999 3.962744385 LAHEVGWK ddPTM_BT-474_Pertuzumab_2h_R1 6 LAHEVGWK 8 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;;; 139.68 0.00066172 11520790000 13691980 14025630 12126700 13674480 13730020 14543520 15512450 15448730 17291370 17734710 FALSE TRUE 13156882.28 13625632.76 14318264.45 14380221.55 14171658.56 14837599.94 15702296 15129708.33 15328526.17 16533522.3 0.795770075 0.824121595 0.866014161 0.869761524 0.857146971 0.897425223 0.949724791 0.915092867 0.927118003 1 23.97889077 8 0.113985147 1.047314258 0.270972729 0.914793803 0.016771634 27.39968442 0.216455916 0.139910735 3.359741866 99999999.89 -8 -0.776341528 TDEFPR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDEFPR 6 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ;;; 149.06 0.024861 1613320000 1649680 1666160 1439470 1676930 1673310 1733810 1845830 1855660 2067800 2082800 FALSE TRUE 1585208.682 1618642.748 1699614.25 1763476.558 1727133.536 1768868.826 1868419.82 1817339.973 1833072.013 1941730.101 0.816389817 0.833608516 0.875309215 0.9081986 0.889481775 0.910975642 0.962244865 0.935938507 0.944040581 1 20.88891125 8 0.164823208 1.008624384 0.217444073 0.927986159 0.014409272 14.58248552 0.153883327 0.040243213 2.825835733 99999999.89 -8 -0.791180311 HSPEDPEKYSCFALFVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSPEDPEKYSCFALFVK 17 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 71.697 0.018004 288960000 405360 373470 275880 262950 358330 330190 333260 210380 395830 327950 FALSE TRUE 389518.0831 362819.0013 325737.6529 276520.881 369856.0099 336866.668 337338.5356 206035.5795 350897.0379 305737.6544 1.274027185 1.186700415 1.065415556 0.90443842 1.209716908 1.101816094 1.103359468 0.673896645 1.147706319 1 18.22193472 8 0.322397731 0.94907517 4.177470891 0.23371127 0.144384879 75.39049517 1.07905891 0.140833355 143.8377689 99999999.89 -8 3.228395722 EVDGLLTSEPMGS(ph)PVSSK ddPTM_BT-474_Pertuzumab_2h_R1 9 EVDGLLTSEPMGSPVSSK 18 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(0.944)PVS(0.051)S(0.005)K;EVDGLLTSEPMGS(0.985)PVS(0.012)S(0.002)K;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTS(0.001)EPMGS(0.998)PVS(0.001)SK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(0.987)PVS(0.013)SK 354.36 1.68E-90 7427720000 5609280 5647600 5330230 5566860 5588190 5981820 5939680 6460000 6977470 7296400 TRUE FALSE 5390063.136 5486535.978 6293521.131 5854166.312 5767939.206 6102776.499 6012371.581 6326598.743 6185416.858 6802208.329 0.792399009 0.806581585 0.925217345 0.860627318 0.847950978 0.897175771 0.883885246 0.930080121 0.909324819 1 22.69757176 8 0.060140597 1.172817121 0.280498287 0.732472733 0.030294797 176.9752024 0.794529259 2.381270299 13.82624789 99999999.89 -8 -0.892318833 KDRHDT(ph)PDPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDRHDTPDPSPR 12 2 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 KDRHDT(1)PDPS(1)PR;KDRHDT(1)PDPS(1)PR 100.23 0.0036992 172729000 383580 384950 213553 195522 247856 291612 189473 226969 232270 186605 TRUE FALSE 368589.2695 373971.6029 252146.7776 205612.9139 255828.5133 297508.5944 191791.8273 222282.0108 205903.6834 173966.0771 2.118742203 2.149681185 1.449401985 1.181913838 1.470565512 1.710152918 1.102466817 1.277731926 1.183585253 1 17.40844649 8 0.356900015 1.163607638 14.70444889 0.701873779 0.211369439 35.03222975 0.491755229 0.176380296 321.2225459 99999999.9 -8 13.54084126 up AFMGT(ph)PVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 AFMGTPVQK 9 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AFMGT(1)PVQK;AFMGT(1)PVQK 131.43 0.0037254 254580000 839600 683740 685420 562900 613610 630170 582790 779290 568850 632010 TRUE FALSE 806787.5038 664240.4047 809290.6411 591951.3365 633347.3229 642912.4692 589922.3584 763197.3892 504276.5328 589203.3998 1.369285215 1.127353313 1.373533556 1.004663817 1.074921365 1.091155396 1.001220221 1.295303777 0.855861546 1 19.16840623 8 0.371393349 1.053407725 5.012210496 0.364521602 0.131387299 81.42084464 1.125981638 0.099184619 230.1669291 99999999.9 -8 3.958802771 LLVVDPETDEQLQK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLVVDPETDEQLQK 14 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 113.38 0.0012539 208680000 170256 177356 146566 165825 180488 198375 167261 193488 225950 226780 FALSE TRUE 163602.2073 172297.9805 173053.7365 174383.2481 186293.5604 202386.2784 169307.9902 189492.4052 200301.1033 211419.9886 0.773825637 0.814955964 0.81853063 0.824819116 0.881153961 0.957271258 0.800813543 0.896284247 0.947408542 1 17.68975226 8 0.063648832 1.185133429 0.172892178 0.683419183 0.040984114 183.8244298 0.869925676 2.651809049 17.00044618 99999999.9 -8 -1.012241251 APS(ph)PSINR ddPTM_BT-474_Pertuzumab_2h_R1 2 APSPSINR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 APS(0.905)PS(0.095)INR;APS(0.986)PS(0.014)INR 135.63 0.0008658 294890000 390280 420990 345950 429830 384480 435460 451160 456500 518360 539600 TRUE FALSE 375027.4261 408983.7774 408470.8606 452013.5778 396847.1484 444265.2996 456681.431 447073.1155 459517.9459 503052.4114 0.745503684 0.813004308 0.811984699 0.898541718 0.788878334 0.883139191 0.907820777 0.888720748 0.913459384 1 18.94034919 8 0.081274229 1.119702064 0.173576855 0.797339476 0.031836114 78.65538731 0.464789334 0.80056595 8.347873113 99999999.9 -8 -0.946125209 ANGMELDGRR ddPTM_BT-474_Pertuzumab_2h_R1 2 ANGMELDGRR 10 1 P62995;P62995-3;H7BXF3;Q13595;Q13595-3;Q13595-4;Q13595-2 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 0 ; 117.14 0.0015998 1077870000 793550 966830 515990 646580 733990 762920 711120 700670 715870 630640 FALSE TRUE 762537.1887 939256.955 609240.8711 679950.0713 757599.4549 778346.7651 719822.8993 686200.9196 634607.4388 587926.1911 1.296994759 1.59757631 1.036254007 1.156522845 1.288596199 1.323885169 1.22434229 1.167154874 1.079399844 1 19.16527552 8 0.05265826 0.557740385 2.501921801 0.348555086 0.133279115 506.9776356 2.008841766 16.76602026 78.65005041 99999999.9 -8 1.944181416 RPLEEDFRRS(ph)PTEDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPLEEDFRRSPTEDFR 16 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPLEEDFRRS(0.999)PT(0.001)EDFR;RPLEEDFRRS(0.99)PT(0.01)EDFR 147.53 5.63E-06 1970360000 1913920 2261580 953450 984910 1463990 1894000 1048010 1011760 1103280 757510 TRUE FALSE 1839121.89 2197081.953 1125759.624 1035741.323 1511080.568 1932297.978 1060835.86 990866.8024 978040.2797 706203.173 2.604239064 3.111118778 1.594101623 1.46663363 2.139724977 2.736178555 1.502168074 1.403090273 1.38492762 1 19.42972378 8 0.127110388 0.667706814 7.470894314 0.492429258 0.476907086 76.91856094 0.664039537 2.876475161 93.52521656 99999999.9 -8 6.8031875 TKFAS(ph)DDEHDEHDENGATGPVKR ddPTM_BT-474_Pertuzumab_2h_R1 6 TKFASDDEHDEHDENGATGPVKR 23 2 P05455 P05455 SSB Lupus La protein 1 T(0.015)KFAS(0.985)DDEHDEHDENGATGPVKR;T(0.004)KFAS(0.996)DDEHDEHDENGATGPVKR;T(0.252)KFAS(0.748)DDEHDEHDENGATGPVKR;T(0.001)KFAS(0.999)DDEHDEHDENGATGPVKR;TKFAS(1)DDEHDEHDENGATGPVKR;T(0.287)KFAS(0.713)DDEHDEHDENGATGPVKR 255.9 6.94E-44 7268490000 7494950 7103594 2926547 2031400 3905363 5484138 2929528 706963 4058546 2308478 TRUE FALSE 7202039.068 6901006.454 3455439.144 2136240.797 4030982.548 5595031.028 2965380.44 692363.967 3597836.873 2152122.729 3.346481579 3.206604513 1.605595767 0.992620341 1.873026335 2.599773216 1.377886307 0.321712121 1.671761942 1 21.03732892 8 0.394723193 1.107802029 40.5877044 0.555224237 0.622940284 54.55939356 0.731120558 0.487145922 1667.557829 99999999.91 -8 39.47990237 HPHTGDTKEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPHTGDTKEEK 11 1 P51397;B4DQ75 P51397 DAP Death-associated protein 1 0 ; 101.95 0.0018925 92410000 407300 365710 208940 180480 229770 291110 221970 9483 266390 112037 FALSE TRUE 391382.2657 355280.3089 246700.1058 189794.5944 237160.7607 296996.4437 224686.5353 9287.172736 236150.524 104448.6342 3.747126697 3.401483529 2.361927542 1.817109394 2.27059705 2.843468906 2.151167768 0.088916172 2.260924959 1 16.6724341 8 0.208273617 0.835521841 15.75641674 0.554785905 0.67821203 38.07392525 0.471601603 1.242389174 187.8977892 99999999.91 -8 14.9208949 EGSGGGGGMDDIFSHIFGGGLFGFMGNQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGSGGGGGMDDIFSHIFGGGLFGFMGNQSR 30 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ; 218 1.19E-34 242420000 63655 60144 62009 57649 58288 71449 59429 73983 74085 77444 FALSE TRUE 61167.29223 58428.75201 73215.40568 60624.2718 60162.88646 72893.74773 60156.30988 72455.2252 65675.18139 72198.6489 0.847208267 0.809277637 1.014082767 0.839687068 0.83329657 1.009627588 0.83320548 1.003553755 0.909645574 1 16.13968422 8 0.082545383 1.08066117 0.447249754 0.231720875 0.072504197 254.997119 1.527738918 1.703142783 18.37810627 99999999.91 -8 -0.633411416 FGAVFLWDSGSSVGEITGHNK ddPTM_BT-474_Pertuzumab_2h_R1 2 FGAVFLWDSGSSVGEITGHNK 21 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 275.23 9.13E-45 951430000 916360 997320 843450 999380 954740 1061530 1118900 1094740 1232250 1273010 FALSE TRUE 880547.6381 968877.4101 995880.1774 1050958.122 985450.0792 1082994.864 1132593.433 1072133.236 1092370.146 1186787.899 0.741958727 0.816386324 0.839139141 0.885548397 0.83035063 0.912542894 0.954335171 0.903390772 0.920442606 1 20.17863069 8 0.173276527 0.99834725 8.83E-13 0.85562518 0.026983898 20.98182405 0.229633218 0.066581397 5.465348677 99999999.91 -8 -0.99834725 YESLELCRPVLQQGR ddPTM_BT-474_Pertuzumab_2h_R1 7 YESLELCRPVLQQGR 15 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;; 328.14 7.88E-69 10263600000 3736021 3676714 3375652 4266309 3771817 3421684 4550462 4283851 4764210 5154445 FALSE TRUE 3590013.169 3571857.717 3985707.407 4486493.719 3893140.919 3490872.795 4606151.915 4195387.98 4223396.854 4805329.849 0.747089853 0.743311662 0.829434718 0.933649481 0.810171422 0.726458517 0.958550622 0.873069719 0.878898429 1 22.19620403 8 0.049384086 1.309787284 1.36E-06 0.49417678 0.064360766 440.6597907 1.642779795 10.34857437 44.18611229 99999999.91 -8 -1.309785922 T(ph)SPDTLRR ddPTM_BT-474_Pertuzumab_2h_R1 7 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.743)S(0.257)PDTLRR;T(0.75)S(0.25)PDTLRR;T(0.804)S(0.196)PDTLRR;T(0.649)S(0.351)PDTLRR;T(0.665)S(0.334)PDTLRR;T(0.892)S(0.108)PDTLRR;T(0.841)S(0.159)PDTLRR 147.41 0.00031512 25237220000 9363930 9372910 7000780 7220870 7832800 8270760 7322640 8276370 9215520 7632350 TRUE FALSE 8997977.263 9105603.784 8265976.678 7593539.966 8084749.126 8438000.434 7412256.659 8105460.067 8169412.804 7115404.136 1.264577119 1.279702967 1.161701643 1.067197284 1.136231895 1.185877889 1.0417197 1.139142614 1.148130542 1 22.76251427 8 0.377537102 1.090183382 4.035487508 0.550438036 0.056969667 50.70093414 0.695958264 0.042386642 108.9846458 99999999.91 -8 2.945304126 KSNLDEEVNVIPPHT(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 5 KSNLDEEVNVIPPHTPVR 18 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR 137.38 3.25E-06 4334190000 5961590 5569390 3845750 4534550 4838810 3956620 4249670 4910620 4312290 4586320 TRUE FALSE 5728604.472 5410556.45 4540762.573 4768578.669 4994454.718 4036625.567 4301678.733 4809213.981 3822776.918 4275684.461 1.339809924 1.265424635 1.06199665 1.115278434 1.168106478 0.944088743 1.006079558 1.124782248 0.894073675 1 22.02772396 8 0.385989038 1.003880761 6.30719707 0.681763056 0.074986974 40.89577636 0.555088182 0.055065831 163.0060885 99999999.92 -8 5.303316309 S(ph)PHKVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPHKVGR 7 1 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 1 S(1)PHKVGR 54.066 0.082301 228340000 366660 340960 225910 272650 264740 306490 271030 251050 282320 287650 TRUE FALSE 352330.5218 331236.1546 266736.9623 286721.4992 273255.6025 312687.4378 274346.9462 245865.7298 250272.2172 268167.2093 1.313846397 1.23518515 0.994666585 1.069189257 1.018974703 1.166016675 1.023044342 0.916837411 0.933269276 1 18.03277331 8 0.439291488 0.980563101 8.402345175 0.674849118 0.070629235 50.99140114 0.629246738 0.047159438 337.020525 99999999.93 -8 7.421782074 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_BT-474_Pertuzumab_2h_R1 2 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 37 2 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 224.87 7.65E-40 638670000 389970 462310 222546 229720 323030 397880 249832 175076 298069 216117 FALSE TRUE 374729.5413 449125.3714 262765.0127 241575.8767 333420.5533 405925.4062 252889.5187 171460.6194 264233.4567 201479.2031 1.859891917 2.229140103 1.304179333 1.199011476 1.654863372 2.014726086 1.255164379 0.851009021 1.311467649 1 17.6202714 8 0.157452432 0.828138372 5.376682093 0.410933373 0.32881517 63.74478631 0.650135528 1.098905722 67.06699552 99999999.93 -8 4.548543721 QEYDESGPSIVHRK ddPTM_BT-474_Pertuzumab_2h_R1 3 QEYDESGPSIVHRK 14 1 P60709;A0A2R8YFE2;Q9BYX7;P63261;Q6S8J3;A5A3E0;P0CG38;P0CG39 P60709;P63261;Q6S8J3 ACTB;POTEKP;ACTG1;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;; 145.43 5.57E-06 3381730000 1696250 2344680 1070010 1083830 1182140 1863330 1245040 1148250 1304560 1141660 FALSE TRUE 1629958.675 2277812.022 1263384.609 1139766.596 1220164.607 1901007.809 1260277.172 1124538.236 1156471.818 1064334.351 1.53143481 2.140128259 1.187018541 1.070872696 1.146410999 1.786100211 1.184098935 1.056564824 1.08656816 1 20.02152 8 0.25145021 1.034891135 5.99769305 0.328210614 0.29428991 56.81909799 0.776166652 0.383523879 119.5381317 99999999.93 -8 4.962801916 EDFPWSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EDFPWSGK 8 0 P46063;F5H4P4;F5H3W0;F5H2L2;F8WA66;F8WD97 P46063 RECQL ATP-dependent DNA helicase Q1 0 ; 95.815 0.021828 129136000 286220 287610 262530 297380 301100 311720 313760 351590 375950 383090 FALSE TRUE 275034.206 279407.6444 309975.0109 312727.8174 310785.155 318023.192 317599.8887 344329.5436 333273.7321 357142.9731 0.770095527 0.78234115 0.867929749 0.875637605 0.870198151 0.890464648 0.8892794 0.964122409 0.933166147 1 18.44614221 8 0.153714957 1.023199087 0.047921381 0.907697944 0.020647845 18.1584066 0.181868297 0.070067615 3.976138682 99999999.93 -8 -0.975277706 QFLISPPAS(ph)PPVGWK ddPTM_BT-474_Pertuzumab_2h_R1 2 QFLISPPASPPVGWK 15 0 V9GYW9;E9PD55;E9PDJ2;P53805-4;P53805-3;P53805-2;P53805;H0YF64;Q9UKA8-6;Q9UKA8-5;Q9UKA8-2;Q9UKA8 V9GYW9 RCAN1;RCAN3 Calcipressin-1;Calcipressin-3 1 QFLIS(0.001)PPAS(0.999)PPVGWK;QFLIS(0.006)PPAS(0.994)PPVGWK 163.7 1.60E-06 632530000 686800 698770 623330 653500 718470 756350 701450 818880 834190 885600 TRUE FALSE 659959.0967 678841.7638 735979.5969 687227.2133 741580.24 771643.9152 710034.5549 801969.8418 739496.2484 825617.5232 0.799352095 0.822223057 0.891429235 0.832379636 0.898212816 0.934626378 0.860004221 0.971357583 0.895688654 1 19.65511407 8 0.116436853 1.038450999 0.299507312 0.697548009 0.033830252 50.2832463 0.404255589 0.236125501 6.009254221 99999999.93 -8 -0.738943687 VDNLTYRTS(ph)PDTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.044)S(0.956)PDTLR;VDNLT(0.003)YRT(0.085)S(0.912)PDTLR;VDNLTYRT(0.015)S(0.961)PDT(0.024)LR;VDNLTYRT(0.078)S(0.921)PDTLR 172.37 1.74E-06 3680000000 2095150 2847880 1021720 945240 1698880 2634200 1239270 1158880 1456360 967720 TRUE FALSE 2013269.222 2766661.251 1206367.532 994023.9497 1753526.018 2687465.329 1254436.557 1134948.723 1291040.118 902175.4624 2.23157169 3.066655397 1.337176173 1.101807787 1.943664055 2.978872116 1.39045741 1.258013292 1.431029963 1 19.78304852 8 0.107820972 0.585034751 6.118130699 0.270000061 0.612167054 158.5211694 1.195765863 6.301403508 130.3767761 99999999.94 -8 5.533095948 HQDRLS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 5 HQDRLSPK 8 1 Q8IVM0-2 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 1 HQDRLS(1)PK;HQDRLS(1)PK;HQDRLS(1)PK;HQDRLS(1)PK;HQDRLS(1)PK 91.043 0.0077319 2108650000 2201440 1979790 1695995 1747830 1878340 1857830 1957050 1704910 2346910 2009290 TRUE FALSE 2115405.291 1923328.328 2002499.024 1838035.716 1938758.512 1895396.595 1981000.963 1669703.013 2080498.616 1873198.999 1.129300887 1.026761347 1.069026316 0.981228218 1.034998691 1.011850101 1.05754966 0.891364459 1.110666094 1 20.83707274 8 0.61716145 1.002628422 9.429493062 0.242377523 0.056070458 238.6682223 1.731828897 0.022489649 2725.585777 99999999.94 -8 8.42686464 KHIKEEPLS(ph)EEEPCTSTAIASPEK ddPTM_BT-474_Pertuzumab_2h_R1 3 KHIKEEPLSEEEPCTSTAIASPEK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 KHIKEEPLS(0.999)EEEPCT(0.001)STAIASPEK;KHIKEEPLS(0.997)EEEPCT(0.001)S(0.001)T(0.001)AIASPEK;KHIKEEPLS(0.935)EEEPCT(0.022)S(0.022)T(0.022)AIASPEK 100.24 0.0022966 857940000 990380 871650 586750 519370 714890 784120 628310 244833 959350 569950 TRUE FALSE 951674.8547 846791.3954 692788.7772 546174.7479 737885.0861 799975.4436 635999.4457 239777.113 850448.6099 531346.7788 1.791061681 1.593669952 1.30383547 1.027906387 1.388707179 1.505561858 1.196957375 0.451262946 1.600552866 1 19.01929421 8 0.31602997 0.996421676 8.695592967 0.307205805 0.307053057 63.6832633 0.912289264 0.307355845 282.1110299 99999999.94 -8 7.699171291 LKPNLGNGADLPNYR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKPNLGNGADLPNYR 15 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 240.2 7.16E-18 2700800000 2714400 2838800 2352990 2852500 2610900 3030800 2905000 3230400 3257700 3582600 FALSE TRUE 2608318.247 2757840.203 2778227.635 2999717.867 2694881.97 3092084.853 2940552.259 3163691.111 2887899.553 3339947.311 0.780945926 0.825713685 0.831817803 0.89813329 0.806863618 0.925788512 0.880418757 0.94722785 0.864654225 1 21.67139391 8 0.086382091 1.087910177 0.27478517 0.682811012 0.036439256 87.58998517 0.546246772 0.707216321 8.455628625 99999999.94 -8 -0.813125007 KQLELR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQLELR 6 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 110.9 0.045388 3132100000 5836100 6178900 4979300 5927500 6065700 5805900 6339600 6646300 7181200 7115300 FALSE TRUE 5608018.76 6002683.822 5879170.274 6233418.985 6260808.749 5923299.276 6417185.921 6509051.582 6366020.282 6633374.393 0.845424731 0.904921608 0.88630159 0.939705588 0.943834673 0.892954162 0.967408975 0.981257984 0.95969561 1 22.66131152 8 0.165561832 1.012860497 0.389189625 0.770772498 0.021998668 27.96565362 0.296084653 0.060339527 4.295986307 99999999.94 -8 -0.623670872 S(ph)ESELIDELSEDFDRSECK ddPTM_BT-474_Pertuzumab_2h_R1 1 SESELIDELSEDFDRSECK 19 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 S(0.886)ES(0.114)ELIDELSEDFDRSECK 109.85 0.00014972 27508000 13568 13370 8245.5 7498.7 11281 13082 7147.4 7277.7 10761 9585.1 TRUE FALSE 13037.74756 12988.70069 9735.64527 7885.708806 11643.86361 13346.527 7234.872019 7127.412952 9539.456394 8935.892639 1.459031357 1.453542608 1.089498908 0.882475778 1.30304426 1.49358632 0.80964178 0.797616225 1.067543756 1 13.12539614 8 0.284809611 0.924653551 5.43792492 0.338087129 0.210838999 60.1941014 0.854178187 0.249953751 135.9767575 99999999.94 -8 4.513271369 GFTDADNTWEPEENLDCPELIEAFLNSQK ddPTM_BT-474_Pertuzumab_2h_R1 7 GFTDADNTWEPEENLDCPELIEAFLNSQK 29 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;;; 363.33 2.48E-121 2003894100 1263402.4 1235945.6 1049310 1348399 1267420 1337740 1377576.1 1443202 1687845 1703955 FALSE TRUE 1214027.237 1200697.642 1238943.659 1417990.034 1308187.715 1364790.019 1394435.288 1413399.374 1496247.912 1588544.61 0.764238681 0.755847607 0.779923743 0.892634695 0.823513364 0.859144912 0.877806817 0.889744843 0.941898579 1 20.59927417 8 0.092784432 1.107709235 0.077781784 0.876043108 0.026420454 46.51913008 0.308784917 0.430908344 6.096730729 99999999.94 -8 -1.029927452 ADPSLLGFSVNAS(ph)SER ddPTM_BT-474_Pertuzumab_2h_R1 3 ADPSLLGFSVNASSER 16 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 ADPSLLGFSVNAS(0.941)S(0.059)ER;ADPSLLGFSVNAS(0.961)S(0.039)ER;ADPSLLGFSVNAS(0.948)S(0.052)ER 245.78 3.99E-20 582640000 312868 317965 217737 267185 291695 266495 236170 300261 276698 262085 TRUE FALSE 300640.7727 308896.9495 257086.9194 280974.4499 301077.6346 271883.7115 239060.3191 294060.5054 245288.4031 244333.7495 1.230451271 1.264241842 1.052195695 1.149961683 1.232239243 1.11275545 0.978417102 1.2035198 1.00390717 1 17.89849363 8 0.10708511 0.938251743 1.819523029 0.40552405 0.079371381 122.5790627 0.919357919 0.784426619 15.93945448 99999999.94 -8 0.881271286 DDYVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 DDYVFR 6 0 E7ESC6;Q9UIA9;H0YBE1 E7ESC6 XPO7 Exportin-7 0 ; 111.69 0.064292 807710000 642410 654370 665510 732720 715940 682290 793660 810200 894760 953170 FALSE TRUE 617303.907 635708.0083 785782.4612 770535.767 738968.8603 696086.3713 803373.0485 793469.0869 793190.5959 888610.9469 0.694684112 0.715395202 0.88428177 0.867123874 0.831599996 0.783342107 0.904077371 0.892931929 0.892618529 1 19.76119239 8 0.135592076 1.015966834 9.26E-14 0.703658507 0.047911096 47.32842192 0.430145031 0.236856803 9.271427576 99999999.94 -8 -1.015966834 NGS(ph)EADIDEGLYSR ddPTM_BT-474_Pertuzumab_2h_R1 2 NGSEADIDEGLYSR 14 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 NGS(1)EADIDEGLYSR;NGS(1)EADIDEGLYSR 323.09 2.30E-56 483410000 499420 469360 379290 415760 464150 411040 397250 446280 469300 410200 TRUE FALSE 479902.1143 455974.3124 447836.1403 437217.4234 479079.8063 419351.5104 402111.6643 437064.162 416027.0315 382416.7886 1.254919053 1.192349096 1.1710682 1.143300808 1.25276876 1.096582375 1.051501075 1.142900037 1.087889036 1 18.54478634 8 0.069557863 0.82765528 1.878377241 0.681487524 0.044322321 151.4021532 0.777461604 2.06192457 15.59497487 99999999.95 -8 1.050721961 RRDS(ph)YYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RRDSYYDR 8 2 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RRDS(1)YYDR;RRDS(1)YYDR 127.83 0.00091317 1882790000 1513590 1172430 832790 646780 836000 611340 451480 1029100 531300 396930 TRUE FALSE 1454437.229 1138993.444 983293.6783 680160.3933 862890.6992 623701.7137 457005.3473 1007848.725 470989.0514 370045.5776 3.930427271 3.077981507 2.657223158 1.838044918 2.331849782 1.685472686 1.234997457 2.723579976 1.272786597 1 18.49734345 8 0.402308831 1.634162581 40.97754722 0.725135165 0.465584289 40.48209219 0.535974103 0.32566685 1264.372383 99999999.95 -8 39.34338464 up SSS(ph)LDALGPTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSLDALGPTR 11 0 Q9H425;Q9H425-3;Q9H425-2;E5RI90 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 SSS(1)LDALGPTR;S(0.001)SS(0.999)LDALGPTR 291.93 1.89E-35 1043750000 1114530 1183440 989760 1245700 1207550 1068290 1286090 1427150 1375360 1474450 TRUE FALSE 1070972.935 1149689.45 1168631.649 1309990.726 1246391.942 1089891.556 1301829.554 1397678.854 1219234.899 1374584.188 0.779125022 0.836390713 0.850171026 0.953008726 0.906741073 0.79288818 0.947071533 1.016801201 0.886984522 1 20.39056384 8 0.175144559 1.007459891 0.098171111 0.485298476 0.056216628 50.26983941 0.554420782 0.142374123 12.08993199 99999999.95 -8 -0.909288779 T(ph)SPPCSPANLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.613)S(0.387)PPCSPANLSR 132.14 0.0020814 1624400000 618200 607710 492720 659280 618140 594040 635550 693770 752970 765900 TRUE FALSE 594040.0605 590378.7058 581765.4645 693305.5198 638023.0345 606051.8958 643328.051 679443.4071 667496.0023 714024.9108 0.831959854 0.826832085 0.814769143 0.970982258 0.893558509 0.848782566 0.900988245 0.951568211 0.934835735 1 19.44561488 8 0.093831587 1.071994555 0.350184975 0.605531602 0.039100963 99.7357497 0.668482537 0.63717764 9.263602114 99999999.95 -8 -0.72180958 SSS(ph)PVTELAS(ph)RSPIRQDR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.068)S(0.439)S(0.493)PVT(0.031)ELAS(0.596)RS(0.373)PIRQDR 74.584 0.090045 540810000 507950 522150 253250 297050 393400 470390 277010 270090 315900 274660 TRUE FALSE 488098.7524 507258.7932 299017.9085 312380.7861 406054.0683 479901.6081 280400.1312 264512.5471 280040.3564 256057.0336 1.906211072 1.981038311 1.167778539 1.219965653 1.585795409 1.874198109 1.095069045 1.033021993 1.093663988 1 17.96610566 8 0.184769957 0.91486969 5.344275577 0.486744468 0.270051639 50.47101229 0.577985483 0.627881496 63.31633024 99999999.95 -8 4.429405887 S(ph)RDRHDDYYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRDRHDDYYR 10 2 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 S(1)RDRHDDYYR 122.1 0.00025964 485710000 35375 44009 19284 16500 28296 47502 25582 25391 18080 21720 TRUE FALSE 33992.50589 42753.90641 22769.04777 17351.56698 29206.16654 48462.52299 25895.08017 24866.66698 16027.6342 20248.88505 1.678734696 2.111420273 1.124459332 0.856914686 1.442359244 2.393342787 1.278839803 1.22805117 0.79153169 1 14.30555485 8 0.072010825 0.384529304 3.865418185 0.182369896 0.453630175 451.7558328 2.394236193 19.5974988 158.6526004 99999999.95 -8 3.480888881 KHS(ph)VNEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KHSVNEK 7 1 E9PNQ0;E9PR18;Q96PZ2 E9PNQ0 FAM111A Protein FAM111A 1 KHS(1)VNEK 92.611 0.0095199 98248000 383110 254800 189780 194830 195120 164790 194690 178810 166960 178920 TRUE FALSE 368137.6376 247533.3535 224077.4676 204885.1996 201396.212 168122.1667 197072.6745 175117.511 148007.4008 166801.589 2.207039152 1.483998773 1.343377296 1.228316833 1.207399841 1.007917057 1.181479599 1.049855172 0.887326084 1 17.34777351 8 0.581881613 1.042560503 64.60860495 0.943457532 0.085011216 32.05020492 0.263443221 0.036772976 2575.625644 99999999.95 -8 63.56604444 up EVPWSPS(ph)AEKAS(ph)PQENGPAVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVPWSPSAEKASPQENGPAVHK 22 1 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 2 EVPWS(0.47)PS(0.539)AEKAS(0.992)PQENGPAVHK 73.676 0.018487 174480000 179980 158700 160640 167710 165650 199330 189560 177820 207950 223420 TRUE FALSE 172946.1826 154174.0314 189671.2214 176365.5332 170978.2827 203360.5892 191879.892 174147.9549 184344.3878 208287.5644 0.830324091 0.740197965 0.910621918 0.846740581 0.820876096 0.976345322 0.921225866 0.836093866 0.885047498 1 17.66821718 8 0.0302163 1.470937248 2.42E-08 0.431194908 0.055821013 1367.753955 3.167643475 48.96775316 119.6677923 99999999.95 -8 -1.470937224 SFSKEELMSS(ph)DLEETAGSTSIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 SFSKEELMS(0.214)S(0.785)DLEETAGSTSIPK 194.37 2.01E-18 719040000 260800 266510 152330 160350 227990 237720 157360 181970 192270 146570 TRUE FALSE 250607.6477 258909.3957 179859.4196 168625.6827 235323.5054 242526.8613 159285.8188 178212.2559 170444.3157 136642.6833 1.834036346 1.894791506 1.316275524 1.234063022 1.72218153 1.774898263 1.165710559 1.304220991 1.247372428 1 17.06004869 8 0.096874298 0.704909238 3.860291513 0.509027766 0.214268301 120.3266747 0.828953241 3.208546694 50.45215211 99999999.95 -8 3.155382275 NSLEILLGSIGRS(ph)LPHITDVS(ph)WRLEYQIK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSLEILLGSIGRSLPHITDVSWRLEYQIK 29 2 Q9UBI1;R4GNF2;H0Y4E5 Q9UBI1 COMMD3 COMM domain-containing protein 3 2 NS(0.268)LEILLGS(0.308)IGRS(0.36)LPHIT(0.116)DVS(0.945)WRLEY(0.004)QIK 46.66 0.057987 160900000 44574 41953 38729 43283 46938 39731 46485 40753 63637 50885 TRUE FALSE 42831.9988 40756.54152 45728.19182 45516.84082 48447.8034 40534.38804 47053.89734 39911.43631 56413.19455 47438.51363 0.902895043 0.859144573 0.963946556 0.959491294 1.021275746 0.854461596 0.99189232 0.841329824 1.189185542 1 15.53377119 8 0.113529184 1.044693766 0.573217529 0.148171285 0.091152565 229.8748356 1.809997202 0.71746808 17.04253772 99999999.95 -8 -0.471476237 EEAPAS(ph)PLRPLYPQISPLK ddPTM_BT-474_Pertuzumab_2h_R1 3 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK 153.59 2.68E-08 2356810000 1598730 1540710 1509580 1788430 1609160 1642660 1687110 1954850 2197800 2116370 TRUE FALSE 1536249.864 1496770.459 1782394.686 1880731.087 1660920.093 1675875.711 1707757.357 1914481.664 1948314.958 1973026.375 0.778626117 0.758616549 0.903381074 0.953221463 0.841813426 0.849393466 0.865552219 0.970327457 0.987475374 1 20.91197881 8 0.141284807 1.036306695 0.116045743 0.61326149 0.050696693 54.19906856 0.508738217 0.228863305 10.10263402 99999999.95 -8 -0.920260952 EMGEMHR ddPTM_BT-474_Pertuzumab_2h_R1 1 EMGEMHR 7 0 P16422;B5MCA4 P16422 EPCAM Epithelial cell adhesion molecule 0 109.01 0.0071238 164860000 436860 322240 297480 300750 334560 296750 361840 201990 402870 291800 FALSE TRUE 419787.0282 313050.0307 351241.2534 316271.7435 345321.4262 302750.4883 366268.3062 197818.8359 357137.8866 272036.1261 1.543129709 1.15076639 1.291156651 1.162609349 1.26939547 1.112905454 1.346395831 0.727178551 1.31283257 1 18.05343873 8 0.217584216 0.990504707 3.281554299 0.293285729 0.176197506 59.62547626 0.758032691 0.270333715 47.84281738 99999999.95 -8 2.291049592 RTS(ph)SEDNLYLAVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTSSEDNLYLAVLR 14 1 Q15149-4 Q15149-4 PLEC Plectin 1 RT(0.097)S(0.451)S(0.451)EDNLYLAVLR 158.98 3.05E-06 198520000 56279 65323 36035 34499 44197 50535 43633 40657 32265 30124 TRUE FALSE 54079.55446 63460.052 42547.32609 36279.49752 45618.63664 51556.85232 44166.99371 39817.41874 28602.41247 28083.67465 1.925658061 2.259677652 1.515019905 1.291835843 1.62438275 1.835829996 1.572692828 1.417813703 1.018471152 1 14.7774441 8 0.100269643 0.630336332 4.699013686 0.585546295 0.241115221 97.80404064 0.693914944 3.195381123 54.78125643 99999999.95 -8 4.068677354 GKGFSVVADTPELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKGFSVVADTPELQR 15 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 156.29 1.96E-06 1274760000 1519350 1945020 754880 802730 1174340 1735610 941780 920360 999250 775550 FALSE TRUE 1459972.122 1889549.934 891303.6082 844158.9915 1212113.713 1770705.223 953305.7854 901354.2444 885819.3292 723021.3077 2.019265693 2.613408365 1.232748743 1.167543726 1.676456419 2.449036017 1.318503031 1.246649628 1.225163518 1 19.46367864 8 0.130726616 0.811525933 5.308838775 0.321527253 0.447813954 104.2670713 0.920567182 2.458383157 86.59656685 99999999.95 -8 4.497312842 GESDPAYQQYQDAANNLREDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 GESDPAYQQYQDAANNLREDYK 22 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 217.51 1.15E-25 540380000 436180 499110 283450 282510 371580 481900 302250 310180 390540 294080 FALSE TRUE 419133.6034 484875.8715 334675.7203 297090.375 383532.2082 491644.3482 305949.0259 303774.6746 346207.5365 274161.6997 1.528782481 1.768576253 1.220723831 1.083631942 1.398927015 1.793264153 1.115943716 1.108012808 1.262785929 1 18.06466752 8 0.101109057 0.807289979 3.078663932 0.308022686 0.225114727 160.2206301 1.144843253 2.885872198 50.53469005 99999999.95 -8 2.271373953 VSQPIEGHAASFAQFK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSQPIEGHAASFAQFK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 214.28 1.72E-14 5120400000 2531800 2867500 2689800 2909800 2888100 2684400 3406700 3172700 3603600 3930600 FALSE TRUE 2432854.457 2785721.708 3175906.694 3059975.127 2980998.359 2738680.407 3448392.214 3107182.636 3194534.436 3664376.961 0.663920356 0.760217013 0.866697594 0.835060137 0.81350756 0.747379551 0.941058262 0.847942957 0.871781061 1 21.80513649 8 0.068201036 1.183573732 0.026974192 0.627402734 0.055944061 182.7044679 0.921437614 2.799174513 20.38618345 99999999.96 -8 -1.15659954 DASIVGFFDDSFSEAHSEFLK ddPTM_BT-474_Pertuzumab_2h_R1 8 DASIVGFFDDSFSEAHSEFLK 21 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;;; 422.46 8.66E-174 3381126000 1665635 1700923 1748764 2068449 1836311 1689084 2144018 2051610 2462143 2551169 FALSE TRUE 1600540.143 1652414.341 2064804.556 2175201.901 1895377.611 1723238.436 2170257.134 2009243.537 2182650.849 2378376.051 0.672955037 0.694765801 0.86815731 0.914574421 0.796920912 0.724544142 0.912495369 0.844796404 0.917706368 1 21.18154541 8 0.095995775 1.085783243 0.021107089 0.560993651 0.068592444 116.189748 0.794216997 1.059402522 16.28695615 99999999.96 -8 -1.064676154 AAQEEYVKR ddPTM_BT-474_Pertuzumab_2h_R1 6 AAQEEYVKR 9 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;; 157.75 0.00010873 52566320000 28017410 27820890 18170920 21444680 21699770 23849740 20669100 23128840 22399630 17999800 FALSE TRUE 26922458.64 27027465.46 21454809.45 22551442.5 22397762.81 24331998.08 20922054.63 22651221.37 19856917.91 16780657.51 1.604374478 1.610632088 1.278544028 1.343895046 1.334736901 1.450002663 1.246795879 1.34984111 1.183321803 1 24.00029591 8 0.049198719 0.295512915 3.284726042 0.732957238 0.090689464 277.1036931 1.029348197 14.89602626 63.26395476 99999999.96 -8 2.989213127 TPS(ph)SDVLVFDYTK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPSSDVLVFDYTK 13 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;Q16576;E9PC52;Q16576-2;Q5JP01 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 1 T(0.026)PS(0.953)S(0.021)DVLVFDYTK 84.468 0.010207 73532000 60084 62942 56303 58966 66401 68455 63413 74955 81004 80018 TRUE FALSE 57735.85085 61146.95579 66478.20455 62009.24233 68536.84847 69839.207 64189.06726 73407.15306 71808.76552 74598.30959 0.773956557 0.81968286 0.891148941 0.831241923 0.918745329 0.936203614 0.860462759 0.984032392 0.962605801 1 16.18685532 8 0.164771213 1.022787161 0.052358156 0.77865733 0.033697648 26.5854408 0.280480429 0.090041754 6.316482171 99999999.96 -8 -0.970429005 TVS(ph)SSGCEGK ddPTM_BT-474_Pertuzumab_2h_R1 3 TVSSSGCEGK 10 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 TVS(0.333)S(0.333)S(0.333)GCEGK;T(0.003)VS(0.965)S(0.029)S(0.004)GCEGK;T(0.002)VS(0.492)S(0.492)S(0.014)GCEGK 150.09 2.33E-05 1414820000 1393540 1207310 896170 1063050 1363410 1003030 965960 1198840 1066440 1006310 TRUE FALSE 1339078.916 1172878.701 1058127.854 1117914.138 1407265.321 1023311.954 977781.7074 1174083.535 945382.2021 938151.7274 1.427358579 1.250201504 1.127885632 1.191613366 1.500040217 1.090774471 1.042242613 1.251485768 1.007707149 1 19.83946174 8 0.07437069 0.764732379 2.262101354 0.379921047 0.128121618 260.8505648 1.4234668 4.687831998 40.50154721 99999999.96 -8 1.497368975 KLDEMTDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLDEMTDR 8 1 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 123.75 0.0021395 536660000 708820 666970 663290 742780 688310 699670 835430 796080 885950 937450 FALSE TRUE 681118.5308 647948.6686 783161.2578 781114.9648 710450.1163 713817.8068 845654.2422 779640.6698 785380.6702 873955.6765 0.779351344 0.741397632 0.896110957 0.893769542 0.812913212 0.8167666 0.967616854 0.89208262 0.898650459 1 19.73720059 8 0.097746386 1.071852961 0.207034439 0.592948353 0.049350734 95.5268816 0.663175438 0.689005513 11.07854675 99999999.96 -8 -0.864818523 GAVDDDVAEADIISTVEFNHSGELLATGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 GAVDDDVAEADIISTVEFNHSGELLATGDK 30 0 P63151;P63151-2;E5RIY1 P63151 PPP2R2A Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform 0 ; 268.24 5.69E-59 212772000 166492 160322 155969 155450 172212 174524 178861 184323 205814 209578 FALSE TRUE 159985.3086 155749.7735 184156.0678 163472.7931 177751.3554 178052.9949 181049.9544 180516.6656 182450.8576 195383.0954 0.818828816 0.797150712 0.942538388 0.836678285 0.909758109 0.911301945 0.926640834 0.923911382 0.933810866 1 17.57594612 8 0.132214484 1.018793529 0.323191614 0.685270627 0.033488654 44.16394612 0.393447619 0.157989289 5.749199228 99999999.96 -8 -0.695601916 DSS(ph)TSPGDYVLSVSENSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DSSTSPGDYVLSVSENSR 18 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 DS(0.002)S(0.998)TSPGDYVLSVSENSR;DS(0.003)S(0.994)T(0.003)SPGDYVLSVSENSR;DS(0.006)S(0.981)T(0.013)SPGDYVLSVSENSR;DS(0.01)S(0.951)T(0.039)SPGDYVLSVSENSR 267.46 2.94E-31 1108160000 527110 531620 475841 566110 531690 526640 552520 636920 672500 686180 TRUE FALSE 506509.9584 516458.7181 561836.0537 595327.0049 548792.2917 537289.0216 559281.905 623767.3794 596160.6194 639704.4174 0.791787495 0.807339615 0.878274463 0.930628254 0.857884168 0.839902003 0.874281762 0.975086872 0.931931378 1 19.28704592 8 0.095630611 1.08082178 0.280235132 0.681016001 0.037094188 87.50205375 0.59616514 0.603267651 9.187751839 99999999.96 -8 -0.800586647 NPPGFAFVEFEDPRDAADAVR ddPTM_BT-474_Pertuzumab_2h_R1 5 NPPGFAFVEFEDPRDAADAVR 21 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;; 161.96 1.75E-11 2985253000 585031 672824 235846 353676 449930 563345 283031 301174 356562 261986 FALSE TRUE 562167.3417 653635.7183 278468.6186 371929.2607 464402.4071 574736.2219 286494.818 294954.6517 316086.5766 244241.4549 2.301686837 2.676186639 1.140136586 1.52279334 1.90140698 2.353147717 1.172998327 1.207635501 1.294156132 1 17.89794856 8 0.159668304 0.862354975 6.729936392 0.434568287 0.430873636 62.11933669 0.640231168 1.347068422 85.79054246 99999999.96 -8 5.867581417 SSVVGGFVSHYLLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSVVGGFVSHYLLEK 15 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 181.26 5.95E-07 656090000 1310130 1361880 1244570 1414920 1270090 1292500 1550190 1370120 1755370 1675760 FALSE TRUE 1258928.671 1323040.516 1469491.484 1487944.191 1310943.598 1318635.236 1569161.689 1341826.543 1556107.757 1562259.283 0.805838496 0.846876399 0.940619461 0.952431013 0.839133179 0.844056585 1.004418221 0.858901309 0.996062417 1 20.57520248 8 0.053617969 1.176804952 0.378911776 0.368143455 0.058391882 512.4113623 2.065360068 6.847917709 33.01940998 99999999.96 -8 -0.797893175 EATDEELER ddPTM_BT-474_Pertuzumab_2h_R1 1 EATDEELER 9 0 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 87.308 0.031521 455730000 547100 455230 327460 338280 386040 416590 377640 307820 464590 352440 FALSE TRUE 525718.7271 442247.2861 386639.3063 355738.6713 398457.3272 425013.7352 382261.6713 301463.4094 411851.6909 328568.9249 1.600025709 1.345980258 1.17673729 1.082691163 1.212705454 1.29352992 1.163413952 0.917504324 1.253471219 1 18.32583652 8 0.649836468 1.108630183 45.88989936 0.644604207 0.108022127 140.7505126 0.903969326 0.045245755 9067.737164 99999999.96 -8 44.78126918 MEELHNQEVQK ddPTM_BT-474_Pertuzumab_2h_R1 8 MEELHNQEVQK 11 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;;;; 165.66 2.13E-05 10042720000 12847580 12078150 11628740 12562210 12328910 12232280 13768120 14187190 15567370 16128060 FALSE TRUE 12345482.37 11733692.99 13730312 13210547.16 12725480.59 12479625.08 13936618.37 13894219.57 13800227.42 15035692.13 0.821078422 0.780389282 0.913181241 0.878612507 0.8463515 0.830000041 0.92690235 0.924082473 0.917831205 1 23.84188794 8 0.040763758 1.350355852 0.107176608 0.670795531 0.035348577 437.3689253 1.356214769 11.19348987 37.2363645 99999999.96 -8 -1.243179243 NPDVDTSFLPDRDREEEENRLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NPDVDTSFLPDRDREEEENRLR 22 3 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 ;;; 290.71 9.76E-56 1881200000 604591 694166 390465 426274 525120 632173 444615 510861 488876 455302 FALSE TRUE 580962.9153 674369.0653 461030.7113 448274.0522 542010.9617 644955.9712 450056.3314 500311.5418 433380.846 424463.99 1.368697767 1.588754479 1.086147994 1.056094422 1.276930374 1.519459804 1.060293316 1.178690192 1.021007332 1 18.69528264 8 0.11822472 0.905215509 2.51829602 0.318222066 0.167355736 123.606543 1.006229892 1.235996844 32.80237271 99999999.96 -8 1.613080511 KASGS(ph)ENEGDYNPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.13)GS(0.87)ENEGDYNPGR;KAS(0.058)GS(0.942)ENEGDYNPGR 191.89 9.59E-08 2693500000 1031900 980950 663110 904020 907780 816720 832570 955800 837470 846350 TRUE FALSE 991572.2072 952974.2665 782948.7278 950676.5805 936979.5681 833234.638 842759.2407 936062.396 742403.9166 789025.9606 1.25670416 1.207785693 0.992297804 1.204873639 1.187514245 1.056029433 1.068100776 1.186351835 0.940911901 1 19.58971324 8 0.09537798 0.918530478 1.746440467 0.363106221 0.084131992 174.8603401 1.188642745 1.251485888 18.93646423 99999999.96 -8 0.827909989 GFGFVTFDDHDPVDK ddPTM_BT-474_Pertuzumab_2h_R1 13 GFGFVTFDDHDPVDK 15 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;; 375.57 1.97E-97 83646141000 64395868 59646166 56147555 59585220 64171900 62703578 62449870 67588390 78970960 75194570 FALSE TRUE 61879206.29 57945115.75 66294667.18 62660420.34 66236047.44 63971487.31 63214150.19 66192666.13 70006507.69 70101574.8 0.882707792 0.826587932 0.945694407 0.893851822 0.944858195 0.912554211 0.901750786 0.94423936 0.998643866 1 26.06294352 8 0.08830078 1.069943494 0.490005869 0.597664386 0.031955278 108.5361181 0.690042829 0.606648102 7.631423031 99999999.96 -8 -0.579937625 NNDLCYWVPELVR ddPTM_BT-474_Pertuzumab_2h_R1 1 NNDLCYWVPELVR 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 136.38 1.16E-05 0 115500 98426 84338 89567 94380 87287 91831 99256 98907 99537 FALSE TRUE 110986.1323 95618.98685 99579.75269 94189.5636 97415.81841 89052.00295 92954.85525 97206.32891 87679.49201 92795.27033 1.196032211 1.030429531 1.073112372 1.015025478 1.049792927 0.959661011 1.001719753 1.047535382 0.944870269 1 16.50176365 8 0.7667389 1.005758328 36.7197786 0.706485157 0.036022787 226.8970309 0.903522791 0.011919878 14026.46378 99999999.97 -8 35.71402028 VISHDRDS(ph)PPPPPPPPPPPQPQPSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VISHDRDSPPPPPPPPPPPQPQPSLK 26 1 Q69YN4-3;Q69YN4;Q69YN4-4;Q69YN4-2 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 VIS(0.102)HDRDS(0.898)PPPPPPPPPPPQPQPSLK;VIS(0.001)HDRDS(0.999)PPPPPPPPPPPQPQPSLK 185.96 8.22E-18 2950110000 603596 616825 563145 717183 628188 653644 742710 695972 823625 856713 TRUE FALSE 580006.801 599233.7549 664917.8286 754196.9006 648394.2375 666861.1295 751799.5071 681599.935 730130.5429 798687.0654 0.726200318 0.750273519 0.832513581 0.944295874 0.811825139 0.8349467 0.941294206 0.853400492 0.914163475 1 19.60727082 8 0.170789723 0.976314833 2.13E-12 0.648182039 0.049601066 40.74779272 0.441327397 0.129928017 10.19115837 99999999.97 -8 -0.976314833 LFVGGIKEDTEEHHLR ddPTM_BT-474_Pertuzumab_2h_R1 8 LFVGGIKEDTEEHHLR 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 184 1.22E-09 5134636000 6342740 6741050 3111622 3038641 4725960 5871470 3757325 1097455 4348190 3063334 FALSE TRUE 6094858.709 6548801.854 3673961.313 3195465.626 4877974.795 5990195.146 3803308.267 1074792.171 3854601.7 2855851.66 2.134165018 2.293116952 1.286467839 1.11891863 1.708063085 2.097516209 1.331759741 0.376347338 1.34972056 1 21.44548961 8 0.207424137 0.804688026 8.008748583 0.391832302 0.439533199 52.74921756 0.65173537 0.838627014 125.0190294 99999999.97 -8 7.204060557 EMPSVFQNVLGSAVLS(ph)PAHK ddPTM_BT-474_Pertuzumab_2h_R1 2 EMPSVFQNVLGSAVLSPAHK 20 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 EMPSVFQNVLGSAVLS(1)PAHK;EMPSVFQNVLGSAVLS(1)PAHK 239.47 7.40E-30 1014430000 1287210 1237090 1218780 1267670 1288110 1316980 1572670 1476730 1591910 1720220 TRUE FALSE 1236904.41 1201809.404 1439040.658 1333094.601 1329543.228 1343610.238 1591916.806 1446235.009 1411203.051 1603707.967 0.771277836 0.749394172 0.897320888 0.831257703 0.829043227 0.83781478 0.992647563 0.901806962 0.879962611 1 20.61298002 8 0.122854318 1.03985904 0.131705309 0.629917437 0.048015641 57.41790056 0.482261169 0.3034123 8.960801444 99999999.97 -8 -0.908153732 IRDPNQGGK ddPTM_BT-474_Pertuzumab_2h_R1 6 IRDPNQGGK 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JHW9;F8WCF2;B1AN92;B1AN91;A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4;O43432-2 Q04637-9;A0A0A0MSA7 EIF4G1;EIF4G3 Eukaryotic translation initiation factor 4 gamma 1;Eukaryotic translation initiation factor 4 gamma 3 0 ;;;;; 155.5 6.67E-05 2843990000 2530150 2580610 2134660 2615770 2707630 2793580 2894200 2955850 3383640 3454230 FALSE TRUE 2431268.941 2507013.529 2520440.547 2750770.203 2794723.378 2850068.102 2929620.085 2894810.665 2999543.373 3220271.925 0.754988708 0.778509886 0.782679415 0.854204324 0.867853226 0.885039577 0.909743076 0.898933609 0.931456548 1 21.61875109 8 0.133512058 1.038302995 0.018833008 0.968567405 0.012865969 12.8254742 0.115148339 0.066132912 2.475326918 99999999.97 -8 -1.019469988 LSSAGPRS(ph)PYCK ddPTM_BT-474_Pertuzumab_2h_R1 4 LSSAGPRSPYCK 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LSS(0.001)AGPRS(0.999)PYCK;LSS(0.001)AGPRS(0.998)PY(0.001)CK;LS(0.001)S(0.001)AGPRS(0.933)PY(0.066)CK;LSSAGPRS(0.988)PY(0.011)CK 101.39 0.0016352 3186260000 3083970 3220010 1404520 2041460 2032070 1799040 1899560 1962270 1678530 1551700 TRUE FALSE 2963445.043 3128178.468 1658348.007 2146819.995 2097433.377 1835417.821 1922807.384 1921748.439 1487990.311 1446601.977 2.048555919 2.162432042 1.146374769 1.484043316 1.449903574 1.268778732 1.329188964 1.328456942 1.028610727 1 20.4642366 8 0.37927938 1.165305412 15.90386531 0.692316023 0.207177521 36.81948331 0.50428942 0.15053935 398.4812837 99999999.97 -8 14.7385599 KRS(ph)FVPEEEKHEER ddPTM_BT-474_Pertuzumab_2h_R1 2 KRSFVPEEEKHEER 14 3 A0A0U1RRH6;O94880;O94880-2;B4DG57 A0A0U1RRH6 PHF14 PHD finger protein 14 1 KRS(1)FVPEEEKHEER;KRS(1)FVPEEEKHEER 142.78 6.64E-06 774570000 415590 367670 233932 251030 372260 329478 232550 286490 252179 216393 TRUE FALSE 399348.2833 357184.4116 276208.7162 263985.6884 384234.081 336140.2709 235396.0165 280573.8814 223552.6971 201736.5094 1.979553848 1.770549182 1.369155821 1.30856675 1.904633337 1.666234198 1.166848862 1.390793775 1.108141991 1 17.62211267 8 0.091328494 0.601509254 4.106711314 0.56389533 0.215360396 121.7128027 0.79689899 3.923803881 53.44794618 99999999.97 -8 3.50520206 AYVHEFK ddPTM_BT-474_Pertuzumab_2h_R1 5 AYVHEFK 7 0 Q9H4A4;A6NKB8;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;; 108.09 0.012267 1211470000 4638200 4787760 4307590 4577580 4789300 4759230 5387030 5134780 5933010 6149050 FALSE TRUE 4456934.016 4651217.773 5086067.335 4813829.452 4943352.184 4855464.891 5452958.085 5028744.999 5259519.578 5732569.366 0.777475811 0.811367028 0.88722299 0.839733311 0.862327495 0.846996274 0.951224091 0.877223576 0.91748032 1 22.45075048 8 0.058197733 1.198247069 0.213322284 0.768531453 0.030083295 167.3077003 0.728424244 2.563797418 14.08758642 99999999.97 -8 -0.984924785 LVS(ph)PETEASEESLQFNLEKPATGER ddPTM_BT-474_Pertuzumab_2h_R1 2 LVSPETEASEESLQFNLEKPATGER 25 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LVS(0.916)PET(0.081)EAS(0.004)EESLQFNLEKPATGER;LVS(0.999)PET(0.001)EASEESLQFNLEKPATGER 209.05 1.51E-25 388971000 219755 197252 200906 215464 207804 239720 214727 255045 272387 274146 TRUE FALSE 211166.7316 191626.5661 237214.1833 226584.1229 214488.2044 244567.3026 217354.8933 249778.2316 241466.7697 255577.8472 0.826232531 0.749777683 0.928148452 0.886556191 0.839228465 0.956919018 0.850444965 0.977307831 0.944787556 1 17.96340327 8 0.136047589 1.034145605 0.200931036 0.556555382 0.049916073 53.16766023 0.484494728 0.216964914 8.575949517 99999999.97 -8 -0.83321457 EREVDEDS(ph)EPEREVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EREVDEDSEPEREVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREVDEDS(1)EPEREVR 191.47 1.37E-07 415710000 179670 218540 114990 108460 143570 164870 122080 121540 112780 98506 TRUE FALSE 172648.2978 212307.4532 135771.2509 114057.6336 148188.0594 168203.7844 123574.0516 119030.1565 99977.68721 91834.10088 1.880002048 2.31185857 1.478440466 1.241996519 1.613649592 1.831604848 1.345622708 1.296143321 1.08867715 1 16.48674235 8 0.149592167 0.872675868 5.256819821 0.580172184 0.249034296 50.27611995 0.493220534 0.915157426 47.85880377 99999999.97 -8 4.384143952 LVIIESDLERAEER ddPTM_BT-474_Pertuzumab_2h_R1 3 LVIIESDLERAEER 14 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;; 109.07 0.00071939 61972000 69440 91349 29188.2 38383 58984 77797 45979 36071.6 42934 37927.4 FALSE TRUE 66726.20803 88743.81596 34463.15703 40363.95123 60881.27393 79370.10864 46541.70476 35326.70885 38060.31231 35358.54342 1.887131131 2.509826689 0.974676944 1.141561482 1.721826412 2.244722236 1.316278903 0.999099664 1.076410639 1 15.10977122 8 0.146211694 0.806680648 5.260755083 0.28855638 0.453463885 94.31635893 0.909150733 1.815745927 88.69965116 99999999.97 -8 4.454074435 EITALAPS(ph)TMK ddPTM_BT-474_Pertuzumab_2h_R1 2 EITALAPSTMK 11 0 P60709;P63267-2;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 1 EITALAPS(0.992)T(0.008)MK;EITALAPS(0.987)T(0.013)MK 177.81 8.20E-06 343460000 2160300 1528970 1093500 700430 1119110 812080 594040 1116530 761810 592920 TRUE FALSE 2075873.088 1485365.273 1291119.775 736579.2762 1155107.189 828500.814 601310.0392 1093473.265 675332.5226 552761.0003 3.755462282 2.687174515 2.335764958 1.332545668 2.089704572 1.498840934 1.087830073 1.978202631 1.221744157 1 19.07629631 8 0.490164302 1.399164185 73.86581955 0.834294142 0.33337371 38.34032124 0.418134876 0.174136324 2846.179556 99999999.97 -8 72.46665536 up NSNLVGAAHEELQQSR ddPTM_BT-474_Pertuzumab_2h_R1 6 NSNLVGAAHEELQQSR 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 265.08 4.61E-27 24464230000 7174020 6736910 5239490 6385600 6014030 6193660 5983270 6355320 6693360 6792020 FALSE TRUE 6893651.367 6544779.923 6186382.395 6715161.581 6207476.737 6318900.049 6056495.048 6224080.421 5933557.834 6331990.436 1.088702113 1.033605466 0.977004381 1.060513538 0.980335773 0.997932658 0.956491503 0.982957963 0.937076247 1 22.59422765 8 0.369828155 0.969387174 2.483387246 0.568806625 0.029145697 45.4708998 0.629950108 0.021622845 48.88338209 99999999.97 -8 1.514000072 AELGMGDSTSQS(ph)PPIKR ddPTM_BT-474_Pertuzumab_2h_R1 19 AELGMGDSTSQSPPIKR 17 1 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 AELGMGDS(0.006)T(0.006)S(0.023)QS(0.965)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDS(0.003)T(0.003)S(0.056)QS(0.938)PPIKR;AELGMGDSTS(0.001)QS(0.999)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTS(0.002)QS(0.998)PPIKR;AELGMGDSTS(0.016)QS(0.984)PPIKR;AELGMGDSTS(0.002)QS(0.998)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDS(0.007)T(0.113)S(0.164)QS(0.716)PPIKR;AELGMGDSTS(0.033)QS(0.967)PPIKR 283.55 2.50E-36 63546490000 9819110 9061000 8838000 9398600 9547580 10927040 10306880 10598620 12737020 12391260 TRUE FALSE 9435368.326 8802589.152 10435223.2 9883662.872 9854686.582 11147992.24 10433018.68 10379754.79 11291166.89 11551988.92 0.816774357 0.761997714 0.903326974 0.855581055 0.853072717 0.965027954 0.90313614 0.898525342 0.977421894 1 23.46163793 8 0.134640305 1.030998156 0.193919075 0.69977488 0.038731941 43.07329142 0.389300391 0.179762335 6.89424791 99999999.97 -8 -0.837079081 EANYIAEELDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EANYIAEELDKR 12 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ; 135.14 0.00021331 556120000 276300 280640 254493 285900 284890 277255 316400 343670 337970 364930 FALSE TRUE 265501.8905 272636.422 300485.5463 300655.3333 294053.7456 282861.2861 320272.1978 336573.0944 299605.0625 340212.9661 0.780399094 0.801369875 0.88322779 0.883726851 0.864322571 0.831424179 0.941387395 0.989301197 0.880639753 1 18.3760786 8 0.13653634 1.032856814 0.165851946 0.671888497 0.03990681 45.9689316 0.420080682 0.19399756 7.748521173 99999999.98 -8 -0.867004868 ALRPGDLPPS(ph)PDDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALRPGDLPPSPDDVK 15 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 ALRPGDLPPS(1)PDDVK;ALRPGDLPPS(1)PDDVK 85.498 0.004796 5964200000 1261960 1208150 1047780 1223430 1314320 1278690 1290410 1379380 1532650 1526590 TRUE FALSE 1212641.208 1173694.745 1237137.154 1286571.369 1356596.296 1304545.988 1306202.424 1350895.321 1358669.997 1423192.7 0.852056934 0.824691375 0.869268901 0.904003632 0.953206335 0.916633417 0.917797305 0.94920057 0.954663411 1 20.44069958 8 0.159591815 1.008980113 0.293450691 0.849041925 0.019719975 23.21846717 0.239214682 0.061452667 3.908002702 99999999.98 -8 -0.715529422 TLQTDSIDSFETQRT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 TLQTDSIDSFETQRTPR 17 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFET(0.002)QRT(0.998)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR 248.9 9.95E-21 10399730000 8501130 8527910 5171080 6506810 6551310 5874680 5301830 7070690 4774980 4971850 TRUE FALSE 8168896.441 8284702.356 6105609.186 6842627.244 6762038.836 5993470.055 5366715.381 6924677.781 4232944.289 4635102.171 1.762398355 1.787382899 1.317254499 1.476262441 1.458875897 1.293061045 1.157841873 1.493964432 0.913236458 1 22.14416971 8 0.160235835 0.949027768 4.202783981 0.68360725 0.15525389 37.94652965 0.392133015 0.453391445 29.19002524 99999999.98 -8 3.253756214 RATS(ph)LPSIPNPFPELCS(ph)PPS(ph)QSPILGGPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 3 RAT(0.472)S(0.528)LPSIPNPFPELCS(0.997)PPS(0.663)QS(0.339)PILGGPSSAR 137.18 8.69E-09 107830000 99034 109650 65622 66237 87330 101200 61946 79334 79054 64961 TRUE FALSE 95163.64179 106522.8894 77481.35515 69655.49951 90139.04876 103246.3333 62704.11368 77695.72518 70080.12134 60561.13361 1.571364935 1.758931562 1.279390767 1.150168356 1.488397647 1.704828282 1.035385402 1.282930496 1.157179814 1 15.88610459 8 0.095804443 0.758702648 3.224871686 0.419725693 0.197007159 139.6374918 0.952859257 2.957754072 45.24845777 99999999.98 -8 2.466169038 GLGHPPSS(ph)PLLKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GLGHPPSSPLLKK 13 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 GLGHPPS(0.168)S(0.832)PLLKK 165.86 2.12E-05 974290000 793100 729970 554700 587510 678510 710170 624140 595930 676800 646020 TRUE FALSE 762104.7752 709151.9703 654946.6292 617831.4615 700334.8904 724530.124 631778.412 583623.8372 599972.5014 602264.49 1.26539882 1.17747598 1.087473428 1.025847401 1.162836099 1.203009867 1.049004918 0.969049059 0.996194382 1 19.20003767 8 0.186789215 0.963866336 2.165367692 0.549398178 0.064975418 46.47276494 0.536192467 0.153481076 16.03688526 99999999.98 -8 1.201501356 IKTEPS(ph)SPLSDPSDIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 IKTEPS(0.662)S(0.338)PLSDPSDIIR 173.03 4.02E-09 353970000 323380 335280 215240 220050 274030 309510 238560 265610 261200 229590 TRUE FALSE 310741.9521 325718.1427 254138.656 231406.8069 282844.4238 315768.5043 241479.5686 260125.0607 231549.671 214039.6648 1.451796107 1.521765337 1.187343739 1.08113983 1.321457983 1.475280316 1.128200088 1.215312409 1.081807296 1 17.70751865 8 0.090229748 0.822530206 2.533964726 0.459752656 0.12932372 154.6626693 1.002028092 2.476049845 32.77060356 99999999.98 -8 1.711434519 ATDDYHYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ATDDYHYEK 9 0 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 0 ; 110.14 0.002336 755660000 2013290 2056610 1704550 1945120 1971690 2102880 2097090 2022770 2386900 2363600 FALSE TRUE 1934608.401 1997957.496 2012600.103 2045507.876 2035111.199 2145401.674 2122754.815 1980999.093 2115949.119 2203511.267 0.877966194 0.906715353 0.913360477 0.928294721 0.923576489 0.973628638 0.963351015 0.899019271 0.960262446 1 21.07137284 8 0.065946356 1.068157354 0.625691071 0.61738403 0.02242984 226.8123575 1.109093422 1.378363006 9.425399758 99999999.98 -8 -0.442466283 RAQST(ph)DSLGTSGSLQSK ddPTM_BT-474_Pertuzumab_2h_R1 3 RAQSTDSLGTSGSLQSK 17 1 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 RAQS(0.399)T(0.582)DS(0.019)LGTSGSLQSK;RAQS(0.081)T(0.919)DSLGTSGSLQSK;RAQS(0.154)T(0.423)DS(0.423)LGTSGSLQSK 356.6 1.23E-87 608630000 800280 857270 511276 535370 622690 882970 632810 600536 679130 599470 TRUE FALSE 769004.1728 832821.499 603674.9465 563000.5099 642719.3894 900824.2584 640554.5181 588134.7217 602038.0095 558867.3629 1.376004798 1.490195267 1.080175703 1.007395578 1.150039226 1.611874871 1.146165549 1.052369061 1.077246677 1 19.0921464 8 0.110821625 0.907721341 2.298190669 0.228899233 0.179647924 178.5364763 1.377927688 1.707967572 38.0154115 99999999.98 -8 1.390469328 DRLSASSLTMESFAFLWAGGR ddPTM_BT-474_Pertuzumab_2h_R1 3 DRLSASSLTMESFAFLWAGGR 21 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRI6;A0A1W2PNG3;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;; 216.49 5.62E-25 845350000 386162 398845 316466 282515 304800 388776 322981 324660 355958 310972 FALSE TRUE 371070.3621 387470.3311 373658.4459 297095.633 314604.1688 396637.3171 326933.7381 317955.6575 315551.1401 289909.5895 1.279952011 1.336521265 1.288879221 1.024787188 1.085180278 1.368141419 1.127709293 1.09674074 1.088446714 1 18.14524353 8 0.11868711 0.942622348 2.118110177 0.414150201 0.098079012 100.1652802 0.818010588 0.7252381 19.45595381 99999999.98 -8 1.175487829 AGNALT(ph)PELAPVQIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGNALTPELAPVQIK 15 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 AGNALT(1)PELAPVQIK 152.32 3.19E-05 214020000 242580 238230 214190 245580 243510 248680 265870 285670 295850 319460 TRUE FALSE 233099.7054 231435.9137 252898.8976 258254.4132 251342.7203 253708.48 269123.7966 279770.8147 262266.3483 297822.6897 0.782679472 0.777092954 0.84915927 0.867141498 0.843934089 0.851877606 0.903637654 0.939387174 0.880612383 1 18.18409414 8 0.09246059 1.089409078 0.196871248 0.855252616 0.024260989 51.37690814 0.339998615 0.414474206 5.814999749 99999999.98 -8 -0.89253783 KYELGR ddPTM_BT-474_Pertuzumab_2h_R1 5 KYELGR 6 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;; 135.35 0.021868 3715510000 3148310 3263770 3314550 3757910 3500980 2987510 4012950 4145670 4254690 4710990 FALSE TRUE 3025270.565 3170690.475 3913562.917 3951856.185 3613592.201 3047919.499 4062061.683 4060060.466 3771715.428 4391910.451 0.688827925 0.72193878 0.891084406 0.899803452 0.82278367 0.693984892 0.92489629 0.92444063 0.858786961 1 22.06641721 8 0.103901546 1.066573957 0.068504278 0.475272719 0.074161296 114.7406887 0.839001983 0.871295997 16.3632479 99999999.98 -8 -0.998069679 FFEHEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 FFEHEVK 7 0 J3QL14;R4GN72;F5GYQ1;P61421 J3QL14 ATP6V0D1 V-type proton ATPase subunit d 1 0 105.39 0.02046 0 160570 169360 153050 176220 159310 177470 199710 186250 214300 224480 FALSE TRUE 154294.7469 164530.0186 180709.5396 185314.7353 164434.3508 181058.565 202154.1107 182403.8724 189973.5624 209275.7697 0.737279558 0.786187617 0.863499582 0.885504976 0.785730479 0.865167359 0.965969979 0.871595755 0.907766641 1 17.67504576 8 0.115128662 1.04258333 0.163474366 0.696740596 0.042473777 59.82234711 0.476497963 0.340381621 8.398897247 99999999.98 -8 -0.879108965 ESGPPHMK ddPTM_BT-474_Pertuzumab_2h_R1 5 ESGPPHMK 8 0 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5;Q5JW28;E7EVI1;E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;E5RJN7 O95793-2;E7EPX0 STAU1;STAU2 Double-stranded RNA-binding protein Staufen homolog 1;Double-stranded RNA-binding protein Staufen homolog 2 0 ;;;; 111.01 0.0033162 1883360000 2543860 2714900 2303750 2745280 2539030 2654020 3012570 2956680 3221350 3287070 FALSE TRUE 2444443.139 2637473.71 2720088.872 2886964.23 2620700.206 2707686.103 3049438.733 2895623.525 2855675.853 3064433.821 0.797681817 0.860672432 0.887631788 0.942087315 0.855198826 0.88358446 0.995106735 0.944913055 0.931877149 1 21.54718912 8 0.173994228 1.002698073 0.224894868 0.671776548 0.034998997 35.78639086 0.39282519 0.087786598 7.300654667 99999999.98 -8 -0.777803205 TALATS(ph)PITVGDLGIVR ddPTM_BT-474_Pertuzumab_2h_R1 1 TALATSPITVGDLGIVR 17 0 P13994 P13994 CCDC130 Coiled-coil domain-containing protein 130 1 TALAT(0.034)S(0.579)PIT(0.387)VGDLGIVR 127.61 4.16E-05 54239000 81498 91591 64787 91359 76796 97641 90091 96236 103200 108940 TRUE FALSE 78312.96806 88978.91436 76495.45208 96074.04894 79266.21308 99615.36792 91193.56061 94248.69297 91485.16865 101561.3968 0.771089908 0.876109597 0.753194171 0.945970142 0.780475807 0.980838892 0.897915581 0.927997211 0.90078683 1 16.63199262 8 0.118285207 1.039955082 0.240373531 0.470150568 0.0607794 78.68776631 0.640832792 0.389696457 10.35685088 99999999.98 -8 -0.799581551 SATDGNTS(ph)TTPPTSAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SATDGNTSTTPPTSAK 16 0 A0A669KAX4;Q13620-1;K4DI93;Q13620;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 SATDGNT(0.075)S(0.56)T(0.286)T(0.08)PPTSAK 174.83 3.92E-09 381480000 1052200 1013500 878810 1029500 973370 1066500 1131900 1158200 1212600 1327600 TRUE FALSE 1011078.861 984595.9723 1037630.516 1082632.618 1004679.33 1088065.361 1145752.531 1134282.765 1074950.732 1237680.469 0.816914289 0.795517096 0.838367044 0.874727076 0.811743705 0.879116531 0.925725629 0.916458483 0.868520396 1 20.23920747 8 0.038698639 1.392120152 0.031495742 0.776585068 0.027946718 357.4816062 1.054064177 10.34867314 32.41632806 99999999.98 -8 -1.360624409 MIVDPVEPHGEMK ddPTM_BT-474_Pertuzumab_2h_R1 7 MIVDPVEPHGEMK 13 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;;; 182.33 1.13E-05 6065910000 8366290 7904350 7246180 7794990 8234160 7804960 8651150 8805900 9645470 9763900 FALSE TRUE 8039326.137 7678925.677 8555725.916 8197290.368 8499019.234 7962781.639 8757025.362 8624055.088 8550556.683 9102582.356 0.883191805 0.843598594 0.939922934 0.900545587 0.933693198 0.874782707 0.962037477 0.947429504 0.939355048 1 23.11784446 8 0.072707097 1.088015262 0.516796158 0.603145612 0.027770876 146.9579862 0.785690014 1.034600035 8.538302447 99999999.98 -8 -0.571219104 ITAHSS(ph)PPLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITAHSSPPLTK 11 0 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 ITAHS(0.174)S(0.826)PPLTK;ITAHS(0.006)S(0.994)PPLTK 137.62 4.80E-05 1121170000 1323230 1256660 1184270 1281850 1234680 1458780 1392380 1391090 1679310 1595010 TRUE FALSE 1271516.709 1220821.287 1398293.933 1348006.432 1274394.604 1488277.531 1409420.363 1362363.505 1488681.769 1486978.552 0.855100907 0.821008 0.940359181 0.906540602 0.857036305 1.000873569 0.947841757 0.916195801 1.001145421 1 20.50395241 8 0.163528172 1.012455016 0.311149906 0.573195657 0.040627651 45.41796893 0.476492694 0.112717164 7.724519219 99999999.98 -8 -0.70130511 LMHNAS(ph)DSEVDQDDVVEWK ddPTM_BT-474_Pertuzumab_2h_R1 9 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LMHNAS(0.711)DS(0.289)EVDQDDVVEWK;LMHNAS(0.962)DS(0.038)EVDQDDVVEWK;LMHNAS(0.943)DS(0.057)EVDQDDVVEWK;LMHNAS(0.988)DS(0.012)EVDQDDVVEWK;LMHNAS(0.988)DS(0.012)EVDQDDVVEWK;LMHNAS(0.911)DS(0.089)EVDQDDVVEWK;LMHNAS(0.889)DS(0.111)EVDQDDVVEWK;LMHNAS(0.69)DS(0.31)EVDQDDVVEWK;LMHNAS(0.942)DS(0.058)EVDQDDVVEWK 294.15 8.03E-50 9430540000 4666445 4499780 4053733 4848069 4805430 5226213 5632047 4875190 6401100 6522320 TRUE FALSE 4484075.17 4371450.68 4786332.728 5098278.422 4960001.02 5331890.608 5700973.676 4774515.623 5674473.964 6080557.457 0.737444749 0.718922683 0.787153606 0.83845576 0.815714851 0.876875294 0.937574181 0.785210181 0.933216075 1 22.53577216 8 0.098645401 1.078794586 0.038936368 0.738043788 0.044806735 71.88924382 0.502998599 0.615077427 10.11912682 99999999.98 -8 -1.039858218 EISFAYEVLSNPEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EISFAYEVLSNPEKR 15 1 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ; 197.7 1.33E-08 2316200000 1292890 1472490 1200780 1491580 1494050 1457070 1492280 1574290 1867580 1926820 FALSE TRUE 1242362.429 1430496.027 1417787.657 1568560.623 1542107.475 1486532.954 1510542.969 1541780.361 1655580.148 1796314.765 0.691617334 0.796350425 0.789275735 0.873210338 0.858483995 0.827545919 0.840912182 0.858301892 0.921653699 1 20.77660874 8 0.061584028 1.21554463 0.046727446 0.81418292 0.033492822 146.0125405 0.670162746 2.514320498 15.20726947 99999999.98 -8 -1.168817184 KLDEMTDRDWR ddPTM_BT-474_Pertuzumab_2h_R1 3 KLDEMTDRDWR 11 2 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ;; 127.56 0.00015981 879910000 840630 904830 605580 654010 786900 864720 699110 722810 857670 760450 FALSE TRUE 807777.2502 879025.1343 715021.7771 687763.5345 812211.3531 882205.2309 707665.9173 707883.7209 760310.8972 708944.0442 1.139409036 1.239907637 1.008572937 0.970123863 1.145663554 1.244393317 0.99819714 0.998504363 1.072455441 1 19.43531224 8 0.153852396 0.986511603 1.641017241 0.167454658 0.090036917 121.9073093 1.221808929 0.315182863 17.93405234 99999999.99 -8 0.654505639 KHS(ph)EEAEFT(ph)PPLKCSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 KHSEEAEFTPPLKCSPK 17 2 Q3B726 Q3B726 TWISTNB DNA-directed RNA polymerase I subunit RPA43 2 KHS(1)EEAEFT(0.934)PPLKCS(0.066)PK 92.336 0.0063019 184060000 384220 291090 243130 220740 283980 285270 242330 213370 314200 257400 TRUE FALSE 369204.2576 282788.3982 287068.9994 232132.4179 293114.4746 291038.3549 245295.707 208963.8349 278533.3332 239966.0687 1.538568597 1.178451602 1.196289963 0.967355173 1.221483004 1.212831282 1.022209966 0.87080576 1.160719658 1 17.8724709 8 0.677735722 1.045087958 52.21015414 0.61465266 0.109565302 177.3775238 1.021885906 0.044599476 13697.5013 99999999.99 -8 51.16506619 LDFIESDS(ph)PCSSEALSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDFIESDSPCSSEALSK 17 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 LDFIES(0.009)DS(0.989)PCS(0.002)SEALSK;LDFIESDS(0.998)PCS(0.002)SEALSK 315.47 3.03E-58 156220000 362637 373813 322828 388930 355811 366349 405740 419294 470590 450490 TRUE FALSE 348464.7451 363152.2192 381170.2009 409002.7239 367255.984 373756.8278 410705.5675 410635.4324 417170.5961 419977.911 0.829721602 0.864693618 0.90759583 0.973867228 0.874465 0.889944014 0.97792183 0.977754833 0.993315565 1 18.67995393 8 0.1716287 1.022431922 0.252630884 0.68315134 0.03325835 35.85955991 0.389765074 0.089332679 7.115575378 99999999.99 -8 -0.769801038 DKDGTQVDFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKDGTQVDFR 10 1 P78332;E9PGM9;P78332-3;F8WCA5 P78332 RBM6 RNA-binding protein 6 0 83 0.018649 0 277920 290460 245520 282260 278530 287840 281860 328440 342490 339260 FALSE TRUE 267058.5791 282176.3652 289890.9256 296827.4724 287489.1704 293660.322 285309.487 321657.5992 303611.971 316281.618 0.844369587 0.892168084 0.916559512 0.938491065 0.908965789 0.928477361 0.902074198 1.016997451 0.95994188 1 18.27085018 8 0.144615725 1.025147377 0.426162197 0.681873904 0.027400189 41.79301047 0.399455781 0.110299061 5.215526175 99999999.99 -8 -0.59898518 RGRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 RGRSPQPPAEEDEDDFDDTLVAIDTYNCDLHFK 33 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 RGRS(0.843)PQPPAEEDEDDFDDT(0.157)LVAIDTYNCDLHFK 58.861 0.015417 78816000 40855 47921 16818 16492 23026 33187 19582 16680 17912 15532 TRUE FALSE 39258.34143 46554.34 19857.38671 17343.1541 23766.6522 33858.06388 19821.65037 16335.55217 15878.70485 14480.00381 2.711210712 3.215077884 1.371366125 1.197731322 1.641342953 2.338263465 1.368898147 1.128145572 1.096595351 1 13.82177436 8 0.356200472 1.177662018 24.63668374 0.557030303 0.488149584 47.20765755 0.663078727 0.415533898 747.9574867 99999999.99 -8 23.45902172 GQLHVDGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 GQLHVDGQK 9 0 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 ; 106.18 0.0029779 267050000 414340 422960 367790 420820 420530 418320 452590 443630 528050 524690 FALSE TRUE 398147.1347 410897.5949 434257.8344 442538.5706 434056.7294 426778.717 458128.9318 434468.8855 468107.9778 489152.279 0.813953347 0.840019791 0.88777637 0.904705119 0.88736524 0.872486412 0.936577323 0.888207833 0.956978017 1 18.89992414 8 0.054118621 1.18651887 0.329184207 0.801988838 0.023035869 186.2733692 0.757426325 2.653352598 12.97863555 99999999.99 -8 -0.857334663 VSGRTS(ph)PPLLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.019)GRT(0.26)S(0.722)PPLLDR;VS(0.009)GRT(0.081)S(0.91)PPLLDR 90.89 0.0052117 2625690000 2453940 2732460 837740 936460 1436060 2153930 1111230 1031070 1119710 821940 TRUE FALSE 2358037.312 2654532.916 989138.2534 984790.8128 1482252.174 2197483.94 1124829.565 1009778.044 992605.215 766269.2717 3.077295931 3.464229892 1.290849431 1.285175916 1.934375067 2.867769884 1.467929887 1.317784859 1.2953739 1 19.54749193 8 0.437432351 1.445342826 42.98391487 0.464084236 0.622076946 76.65232442 0.949669069 0.406825753 2819.948188 99999999.99 -8 41.53857204 GS(ph)PRYS(ph)PRHS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPRYSPRHSR 11 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 GS(1)PRY(0.014)S(0.987)PRHS(1)R 63.691 0.048228 155140000 229370 288920 95959 101940 178230 241300 120620 80648 100690 81417 TRUE FALSE 220405.9668 280680.2845 113300.9259 107201.1356 183962.9298 246179.2513 122096.1836 78982.59062 89260.09333 75902.55407 2.903801717 3.697903027 1.492715591 1.412352152 2.423672458 3.243359256 1.608591241 1.040578826 1.175982738 1 16.21186081 8 0.146618692 0.564972407 9.980563755 0.425683871 0.710126929 70.4959266 0.680995033 2.854995146 140.6244432 99999999.99 -8 9.415591349 AAAERPK ddPTM_BT-474_Pertuzumab_2h_R1 4 AAAERPK 7 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ;;; 105.12 0.0072951 657450000 1384080 1281240 966510 1234040 1180240 1114530 1276340 1248400 1197960 1213850 FALSE TRUE 1329988.623 1244700.29 1141179.857 1297728.952 1218203.491 1137066.56 1291960.231 1222620.104 1061972.603 1131634.858 1.175280713 1.099913351 1.008434698 1.146773575 1.076498733 1.004799872 1.141675887 1.080401593 0.938441049 1 20.10997709 8 0.082135954 0.92408941 1.472739736 0.309491578 0.060685048 264.5059227 1.577731174 1.540128837 16.43703311 99999999.99 -8 0.548650326 QGAPTSFLPPEASQLKPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGAPTSFLPPEASQLKPDR 19 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0QYZ0;M0R0K8;M0QYI8;M0QZV6;M0R203 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 148.06 9.05E-08 371530000 211330 220130 200120 196360 213700 243480 234040 234770 280130 274520 FALSE TRUE 203070.99 213852.1079 236286.1356 206494.1631 220573.8546 248403.3324 236904.2515 229921.9175 248330.8168 255926.5159 0.793473819 0.835599653 0.923257736 0.806849429 0.861864015 0.970604127 0.925672944 0.898390371 0.970320781 1 17.9653701 8 0.115935404 1.045926332 0.296414496 0.648200745 0.040549948 65.68556067 0.526214229 0.315063884 7.923947996 99999999.99 -8 -0.749511836 IEDVTPIPSDSTRR ddPTM_BT-474_Pertuzumab_2h_R1 4 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 0 ;;; 229.63 1.94E-12 6066460000 2968880 3233210 1898840 2137000 2459820 2949730 2253160 2402210 2391640 2160670 FALSE TRUE 2852852.887 3141002.016 2242002.627 2247290.826 2538942.344 3009375.562 2280734.846 2352603.524 2120151.054 2014325.896 1.416281691 1.559331597 1.113028746 1.115654041 1.260442686 1.493986433 1.132257124 1.167935898 1.052536264 1 20.94186568 8 0.109482757 0.884922464 2.541607154 0.41314995 0.1409051 117.328023 0.896412078 1.363285729 29.37427671 99999999.99 -8 1.65668469 TRS(ph)LSSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TRSLSSLR 8 1 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 T(0.169)RS(0.831)LSSLR;T(0.001)RS(0.999)LS(0.001)SLR 129.88 0.00064914 227070000 137509 108698 69087 97225 97747 94061 90115 118581 81920 79476 TRUE FALSE 132134.9963 105598.0395 81572.55773 102242.7939 100891.121 95962.97787 91217.85433 116132.2609 72620.78504 74093.01973 1.783366324 1.425209012 1.100947944 1.379924779 1.361681861 1.295168941 1.231126153 1.567384638 0.980129914 1 16.17705001 8 0.034477727 4.38E-11 3.370239047 0.372638585 0.18846271 1380.07061 3.636707754 105.8280969 293.0407279 99999999.99 -8 3.370239047 TDDEVVQREEEAIQLDGLNASQIR ddPTM_BT-474_Pertuzumab_2h_R1 3 TDDEVVQREEEAIQLDGLNASQIR 24 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;; 292.44 6.90E-62 1017800000 452870 527490 279315 307488 400520 465200 324687 316396 356330 308252 FALSE TRUE 435171.3397 512446.5017 329793.4338 323357.4925 413403.0895 474606.6627 328660.6166 309862.312 315880.9123 287373.8175 1.514304064 1.783205256 1.147611278 1.125215565 1.438555165 1.651530633 1.143669314 1.078255197 1.09919865 1 18.1325691 8 0.125936574 0.849632397 3.301757049 0.396808872 0.202504784 91.7778286 0.786432943 1.256486063 39.79226276 99999999.99 -8 2.452124652 SEEVPAFGVAS(ph)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK ddPTM_BT-474_Pertuzumab_2h_R1 4 SEEVPAFGVASPPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 44 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 283.98 2.53E-81 597097000 489128 509964 446731 515852 506472 519685 547435 592482 656616 648200 TRUE FALSE 470012.337 495420.326 527465.2292 542475.1835 522763.1318 530193.3868 554134.6733 580247.0397 582079.7044 604296.8366 0.777783878 0.819829422 0.872857836 0.897696547 0.865076731 0.877372435 0.916990856 0.960202014 0.963234737 1 19.20489786 8 0.140440083 1.03776562 0.149017812 0.905137377 0.019843683 22.78086518 0.212833547 0.093872173 4.07139948 99999999.99 -8 -0.888747808 SQS(ph)GEDESMNQPGPIK ddPTM_BT-474_Pertuzumab_2h_R1 3 SQSGEDESMNQPGPIK 16 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 S(0.003)QS(0.997)GEDESMNQPGPIK;SQS(1)GEDESMNQPGPIK;S(0.036)QS(0.964)GEDESMNQPGPIK 394.86 1.18E-121 1387630000 1073190 1063030 942450 1098420 1132160 1150650 1201460 1285840 1383170 1434900 TRUE FALSE 1031248.548 1032713.425 1112771.68 1155109.588 1168576.955 1173916.931 1216163.827 1259286.955 1226158.34 1337712.945 0.770904215 0.771999276 0.831846387 0.863495859 0.873563315 0.877555185 0.909136621 0.94137308 0.916607965 1 20.35133714 8 0.144805376 1.028290326 0.036479763 0.957715487 0.014002763 12.35911787 0.118247806 0.053885742 2.55791454 99999999.99 -8 -0.991810563 VAALAAS(ph)PASVAVDSGSELNSR ddPTM_BT-474_Pertuzumab_2h_R1 3 VAALAASPASVAVDSGSELNSR 22 0 O15119;O15119-2 O15119 TBX3 T-box transcription factor TBX3 1 VAALAAS(1)PASVAVDSGSELNSR;VAALAAS(1)PASVAVDSGSELNSR;VAALAAS(0.999)PAS(0.001)VAVDSGSELNSR 473.69 1.12E-206 257750000 284566 308246 258337 301779 274922 318675 296969 355958 348331 370742 TRUE FALSE 273444.8461 299455.1259 305024.2426 317353.8504 283765.1158 325118.8268 300603.3955 348607.3429 308789.9252 345631.3141 0.791146042 0.866400449 0.882513332 0.918186048 0.821005228 0.940652116 0.869722688 1.008610414 0.893408417 1 18.39887441 8 0.115447891 1.04335182 0.340770403 0.526260153 0.045788876 74.41614515 0.594093393 0.336882856 8.375635609 99999999.99 -8 -0.702581417 LAEQAERYDEMVESMKK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAEQAERYDEMVESMKK 17 2 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 235.73 2.03E-20 802000000 1547990 1439250 995190 636530 1060950 1294820 771240 885080 1137510 776590 FALSE TRUE 1487492.839 1398203.999 1175042.971 669381.3896 1095076.42 1321002.148 780678.6658 866802.7887 1008384.634 723990.8676 2.054574037 1.931245354 1.623008001 0.924571593 1.512555571 1.824611617 1.078299052 1.197256523 1.392814024 1 19.46561197 8 0.40521859 1.217914828 16.99871569 0.518272025 0.26474968 60.68337621 0.799539947 0.188365248 767.4665914 99999999.99 -8 15.78080087 LLEPVDHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLEPVDHGK 9 0 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 143.03 0.00010291 726970000 1266710 1257950 1143470 1283750 1242370 1224120 1322910 1395760 1590340 1540600 FALSE TRUE 1217205.573 1222074.498 1350120.465 1350004.491 1282331.959 1248872.545 1339100.168 1366937.068 1409811.27 1436253.79 0.847486413 0.85087643 0.940029175 0.939948428 0.892831036 0.869534726 0.93235623 0.951737832 0.981589243 1 20.45387927 8 0.083970263 1.079221555 0.47574186 0.639027507 0.030321208 124.3808367 0.756568311 0.773983395 8.67730063 99999999.99 -8 -0.603479695 SS(ph)PVPPVPERR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPVPPVPERR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.228)S(0.772)PVPPVPERR 107.34 0.0023408 723620000 128270 144110 107960 136920 128410 135280 141670 147750 159590 164460 TRUE FALSE 123257.0666 140000.1239 127470.7736 143986.4576 132540.4243 138015.4543 143403.7998 144698.9109 141474.0123 153320.9777 0.803915214 0.913117865 0.831398126 0.939117789 0.86446373 0.900173325 0.935317541 0.943764598 0.922730955 1 17.22619558 8 0.083670493 1.078929685 0.427163365 0.635508104 0.033227962 106.0273497 0.642893655 0.715923272 7.96218884 99999999.99 -8 -0.651766319 SKNVGWR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKNVGWR 7 1 P27695 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 60.118 0.090684 341450000 439680 449640 296520 315790 386260 428860 378970 360240 369920 352030 FALSE TRUE 422496.8195 436816.7074 350107.7601 332087.9597 398684.4037 437531.843 383607.9482 352800.9181 327928.2324 328186.6945 1.287367302 1.331000661 1.066794498 1.011887335 1.214809772 1.333179712 1.168871117 1.075000675 0.999212454 1 18.32415722 8 0.065761676 0.766662781 2.014927663 0.336101264 0.105165436 378.7809877 1.847426213 6.513274234 44.30867553 99999999.99 -8 1.248264882 AIGGIILTAS(ph)HNPGGPNGDFGIK ddPTM_BT-474_Pertuzumab_2h_R1 5 AIGGIILTASHNPGGPNGDFGIK 23 0 A0A3B3ITK7;P36871;P36871-2 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 1 AIGGIILTAS(1)HNPGGPNGDFGIK;AIGGIILT(0.001)AS(0.999)HNPGGPNGDFGIK;AIGGIILT(0.019)AS(0.981)HNPGGPNGDFGIK;AIGGIILT(0.001)AS(0.999)HNPGGPNGDFGIK;AIGGIILTAS(1)HNPGGPNGDFGIK 325.97 7.21E-75 29657120000 20591390 17525330 12018067 12224663 11540391 10036142 9265132 13658085 11528301 8163815 TRUE FALSE 19786655.71 17025524.75 14189999.05 12855579.32 11911598.16 10239079.67 9378521.457 13376040.77 10219656.6 7610872.538 2.599788081 2.237000378 1.864437878 1.689107163 1.565076553 1.34532271 1.232253123 1.757491103 1.342770694 1 22.85963043 8 0.362828996 1.307959373 18.82178818 0.857696919 0.172679486 23.9445658 0.334217876 0.144341068 290.2894623 99999999.99 -8 17.5138288 up LFIGGLSFETTDDSLREHFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFIGGLSFETTDDSLREHFEK 21 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 230.01 6.49E-26 199800000 807250 892630 388980 409060 625100 759830 465360 392850 482170 355110 FALSE TRUE 775701.7775 867173.0664 459277.3388 430171.6356 645206.9092 775194.2832 471055.2149 384737.5102 427436.083 331058.0834 2.343098738 2.619398558 1.387301389 1.299384178 1.948923592 2.341565792 1.422877853 1.162145042 1.291121119 1 18.33672483 8 0.150084847 0.837282323 6.558255871 0.481167128 0.395220381 63.58950146 0.625399861 1.501698051 79.30915738 99999999.99 -8 5.720973548 EILHNTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 EILHNTEK 8 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 118.5 0.0018756 1632800000 1933510 2066000 1833310 2048970 1917800 2087720 2208900 2166480 2518100 2544000 FALSE TRUE 1857946.292 2007079.703 2164629.899 2154717.587 1979487.779 2129935.129 2235933.179 2121741.431 2232255.845 2371692.614 0.783384103 0.846264685 0.912694118 0.908514693 0.834630832 0.898065422 0.942758419 0.894610633 0.941207908 1 21.17748561 8 0.082296306 1.081202815 0.386246527 0.683519495 0.032999795 117.1609015 0.70005542 0.861928745 9.238709498 99999999.99 -8 -0.694956288 KQNGAIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQNGAIGR 8 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 172.15 0.00045741 304160000 508330 587150 339100 397660 400930 508250 425390 393210 455750 418570 FALSE TRUE 488463.9016 570405.0569 400382.9132 418183.2803 413826.2776 518527.1632 430596.0501 385090.0761 404015.1707 390219.8811 1.2517658 1.461752936 1.026044373 1.071660621 1.060495115 1.32880765 1.103470302 0.986854066 1.035352606 1 18.57392776 8 0.263078438 1.014637493 3.272641848 0.341432397 0.123190139 56.4776108 0.78455799 0.15172691 57.41154659 99999999.99 -8 2.258004355 EGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_BT-474_Pertuzumab_2h_R1 7 EGHSLEMENENLVENGADSDEDDNSFLK 28 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK 376.12 2.88E-127 7120190000 1266540 1224124 1127739 1243970 1332694 1259459 1533477 1336432 1692559 1700579 TRUE FALSE 1217042.217 1189213.182 1331546.524 1308171.441 1375561.313 1284926.124 1552244.15 1308834.212 1500426.798 1585397.27 0.767657571 0.75010422 0.839881933 0.825137942 0.867644558 0.810475802 0.979088447 0.82555599 0.946404303 1 20.59641297 8 0.08651567 1.11238821 0.123991871 0.67491998 0.046723478 93.10307112 0.581417633 0.911867038 10.94123546 99999999.99 -8 -0.988396339 FKDPNCVGTVLASRPHTLDGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FKDPNCVGTVLASRPHTLDGR 21 2 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 195.39 1.49E-19 5278300000 2126200 2174930 1725130 1838680 1897050 2019920 1917410 2020750 2185700 2049500 FALSE TRUE 2043105.753 2112903.126 2036899.366 1933574.495 1958070.336 2060764.166 1940875.837 1979020.806 1937588.499 1910685.539 1.06930508 1.105835095 1.066056828 1.011979447 1.024799893 1.078547005 1.015800767 1.03576479 1.014080266 1 20.86565893 8 0.189305626 1.002341005 1.40369399 0.503057548 0.023592166 45.5427713 0.530277101 0.048914427 5.341079621 99999999.99 -8 0.401352985 FRDQDLASCDRDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FRDQDLASCDRDR 13 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;; 238.47 5.00E-17 2861800000 736730 852900 487325 577744 609213 669543 607856 548872 640298 538085 FALSE TRUE 707937.7771 828576.1271 575395.468 607561.4371 628808.8894 683081.6182 615295.1236 537537.6014 567614.0554 501640.0237 1.411246599 1.651734487 1.147028628 1.211150244 1.253506219 1.361696806 1.226567049 1.071560434 1.131516682 1 18.93629293 8 0.155060645 0.958753142 3.020172937 0.549300695 0.120244065 48.75441586 0.491541591 0.391505035 22.80973515 99999999.99 -8 2.061419795 ESYSIYVYK ddPTM_BT-474_Pertuzumab_2h_R1 3 ESYSIYVYK 9 0 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03 Q16778 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C 0 ;; 201.39 5.02E-05 2990400000 2229920 2382980 1778830 2576510 1951560 2398540 2471300 2484300 2626470 2778950 FALSE TRUE 2142772.261 2315019.744 2100304.151 2709483.99 2014333.7 2447040.122 2501544.509 2432998.337 2328324.137 2590729.241 0.827092321 0.893578421 0.810699983 1.045838348 0.777516102 0.944537192 0.965575433 0.939117179 0.898713806 1 21.30492682 8 0.120434306 1.018449424 0.459212915 0.242344226 0.070909042 132.1520519 1.09217499 0.444413679 12.41550429 99999999.99 -8 -0.559236509 EEPDSENIPQELLSNLGHPES(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EEPDSENIPQELLSNLGHPESPPR 24 0 D6RF40;D6RAG5;D6R9R7;A0A0A0MTL5;Q13309-2;Q13309 D6RF40 SKP2 S-phase kinase-associated protein 2 1 EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLSNLGHPES(1)PPR 179.66 2.40E-17 952235000 161527 166284 171533 221816 171654 194555 205226 191719 211877 254337 TRUE FALSE 155214.3463 161541.7431 202532.8288 233263.9503 177175.4068 198489.0354 207737.6172 187759.9357 187825.6112 237110.5285 0.654607568 0.681292999 0.854170543 0.983777278 0.747227076 0.837116077 0.876121438 0.791866717 0.7921437 1 17.8552002 8 0.045922877 1.283478355 1.57E-12 0.368215882 0.086070482 764.1497856 2.65762668 18.59015772 71.82829275 99999999.99 -8 -1.283478355 AQGAGVTLPPT(ph)PSGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AQGAGVTLPPTPSGSR 16 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 AQGAGVTLPPT(0.997)PS(0.003)GSR 148.46 1.04E-05 75274000 166340 133250 90687 94221 107230 91766 58745 127130 71022 78912 TRUE FALSE 159839.2489 129449.8405 107076.1582 99083.7571 110679.1503 93621.57139 59463.93888 124504.7211 62959.88031 73567.21995 2.172696603 1.759613053 1.455487353 1.34684656 1.504462863 1.272599012 0.808293951 1.692393992 0.85581432 1 16.16677545 8 0.42384177 1.163669869 20.59130516 0.636766455 0.244771766 52.22520915 0.66516768 0.1555919 862.4503177 99999999.99 -8 19.42763529 LPISSS(ph)TSNLHVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPISSSTSNLHVDR 14 0 Q86TV6;Q86TV6-2;G3V3H1 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 LPISS(0.009)S(0.941)T(0.038)S(0.012)NLHVDR;LPISS(0.004)S(0.941)T(0.054)SNLHVDR 148.19 5.04E-06 360250000 392620 356650 270310 283830 310400 284990 216100 329220 247240 219122 TRUE FALSE 377275.9763 346478.6912 319161.03 298478.5003 320384.2979 290752.6931 218744.6964 322421.492 219174.3517 204280.6718 1.846851066 1.696091403 1.562365285 1.461119634 1.568353458 1.423300063 1.070804666 1.578325982 1.072907925 1 17.64019318 8 0.118584282 0.837290713 3.942773697 0.717803899 0.145057678 52.32760289 0.427036365 1.002354727 26.82581322 99999999.99 -8 3.105482984 DNYNHPNKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNYNHPNKR 9 1 O14647;O14647-2 O14647 CHD2 Chromodomain-helicase-DNA-binding protein 2 0 ; 121.73 0.00039313 58618000 93479 98693 69991 80793 79826 73460 83052 77406 81682 71540 FALSE TRUE 89825.73733 95878.37227 82639.93064 84962.73641 82393.67579 74945.41153 84068.41522 75807.53905 72409.8018 66694.53208 1.346823113 1.437574705 1.239081047 1.273908576 1.235388768 1.123711483 1.260499363 1.136637992 1.085693228 1 16.02528087 8 0.111009669 0.889952558 2.466131781 0.802357363 0.054604524 42.3461298 0.327284163 0.457974368 10.23987821 99999999.99 -8 1.576179222 SPSVPKS(ph)PTPKS(ph)PPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSVPKSPTPKSPPSR 16 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 2 S(0.005)PS(0.004)VPKS(0.99)PT(0.004)PKS(0.976)PPS(0.021)R;S(0.295)PS(0.092)VPKS(0.61)PT(0.024)PKS(0.833)PPS(0.146)R 99.407 0.0012897 458680000 845010 775970 445840 404870 684160 702920 556150 600620 712170 478030 TRUE FALSE 811986.075 753840.0954 526413.2057 425765.3892 706166.6277 717133.524 562956.3301 588216.9871 631327.4473 445652.6023 1.822015783 1.691542003 1.181218741 0.955375077 1.584567495 1.609176117 1.263217868 1.319900263 1.416635837 1 18.76556 8 0.036658614 0.001054616 3.56128601 0.285050049 0.234542634 1427.6219 3.993723204 111.709453 329.6942579 99999999.99 -8 3.560231395 ATSS(ph)SSGSLSATGR ddPTM_BT-474_Pertuzumab_2h_R1 3 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATS(0.036)S(0.959)S(0.004)SGSLSATGR;ATS(0.007)S(0.64)S(0.353)S(0.001)GSLSATGR;ATS(0.001)S(0.92)S(0.079)SGSLSATGR 241.15 2.09E-17 1181000000 1082570 1145180 745560 918070 752250 717820 609140 953520 733830 629000 TRUE FALSE 1040261.968 1112520.588 880299.2769 965451.7027 776446.8044 732334.8122 616594.8375 933829.4788 650528.6949 586397.2697 1.773988423 1.89721311 1.501199481 1.646412343 1.324096896 1.248871456 1.051496774 1.592486062 1.10936515 1 19.16151886 8 0.193667879 1.03743184 5.059988729 0.674832402 0.169879933 32.86493781 0.388560636 0.337737844 39.78286794 99999999.99 -8 4.022556889 LMDLDVEQLGIPEQEYSCVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LMDLDVEQLGIPEQEYSCVVK 21 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 128.14 1.87E-05 49202000 39847 42522 33841 46804 42121 45041 40709 48808 52434 53503 FALSE TRUE 38289.73519 41309.31419 39956.82149 49219.56005 43475.86022 45951.75988 41207.20892 47800.09774 46481.91214 49879.19415 0.767649435 0.828187281 0.801071913 0.986775366 0.871623148 0.921261072 0.82614023 0.958317362 0.931889798 1 15.60615054 8 0.206910366 0.972982627 2.03E-11 0.548116666 0.05205894 40.81231015 0.503478434 0.088115776 13.02188795 99999999.99 -8 -0.972982627 DISPVLKDPASFR ddPTM_BT-474_Pertuzumab_2h_R1 4 DISPVLKDPASFR 13 1 H3BQB1;P07741-2;P07741;H3BQZ9;H3BQF1;H3BSW3 H3BQB1 APRT Adenine phosphoribosyltransferase 0 ;;; 168.89 2.69E-05 11190440000 16422390 16882550 13878350 15813480 15803430 16703270 15865280 17516040 19310860 18481240 FALSE TRUE 15780584.84 16401076.2 16386476.57 16629615.6 16311761.68 17041021.56 16059444.04 17154327.65 17118772.13 17229489.15 0.915905556 0.951918891 0.951071528 0.965183323 0.946735073 0.989061336 0.932090551 0.995637625 0.993573981 1 24.03837659 8 0.131636376 1.015062401 0.721539517 0.580506498 0.018023007 57.19924107 0.507804609 0.086989829 3.125868102 99999999.99 -8 -0.293522885 SPAGPAATPAQAQAAST(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 SPAGPAATPAQAQAASTPR 19 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SPAGPAATPAQAQAAS(0.066)T(0.934)PR;SPAGPAATPAQAQAAS(0.161)T(0.839)PR;SPAGPAATPAQAQAAS(0.044)T(0.956)PR;SPAGPAATPAQAQAAS(0.002)T(0.998)PR;SPAGPAATPAQAQAAS(0.001)T(0.999)PR 347.57 1.31E-89 2589680000 1628910 1400764 1056900 1534850 1080559 997245 1229696 1486664 1099806 1350303 TRUE FALSE 1565250.396 1360815.582 1247905.341 1614063.792 1115316.162 1017409.977 1244745.387 1455963.869 974960.6336 1258845.775 1.243401239 1.081002621 0.991309154 1.282177551 0.885983163 0.808208597 0.988798955 1.156586373 0.774487751 1 20.26367011 8 0.44420165 0.968258331 6.696905561 0.275461258 0.138903765 131.3552933 1.603765144 0.0877719 679.8226183 99999999.99 -8 5.72864723 EDLYLKPIQR ddPTM_BT-474_Pertuzumab_2h_R1 6 EDLYLKPIQR 10 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 155.15 1.21E-05 14945490000 18543020 18286910 16482720 18553840 19211490 19179830 20645210 21323260 23774570 24422130 FALSE TRUE 17818338.28 17765385.23 19461514.16 19511405.91 19829445.02 19567659.3 20897872.26 20882927.23 21075780.48 22767997.38 0.782604547 0.78027878 0.854774965 0.856966275 0.870934966 0.859436997 0.917861677 0.917205272 0.925675637 1 24.44050407 8 0.110348636 1.059877276 0.181551277 0.93681837 0.015954638 23.39138957 0.179891662 0.142314388 3.131535099 99999999.99 -8 -0.878325999 SNIHCNTIAPNAGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNIHCNTIAPNAGSR 15 0 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7ER27;A0A2R8Y7W2 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ; 129.36 6.63E-05 870330000 598730 710720 581250 815020 645160 677000 743690 734670 743470 876670 FALSE TRUE 575330.9697 690450.9615 686294.8048 857083.2799 665912.1573 690689.4038 752791.5007 719498.8078 659074.4025 817292.36 0.703947569 0.844802907 0.839717632 1.048686274 0.814778395 0.845094654 0.921079821 0.880344468 0.806412044 1 19.64049272 8 0.024431779 1.515845456 2.99E-08 0.233042118 0.08233136 3559.618124 6.687370594 143.8136138 296.4518448 99999999.99 -8 -1.515845426 WAHDKFSGEEGEIEDDES(ph)GTENR ddPTM_BT-474_Pertuzumab_2h_R1 1 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFSGEEGEIEDDES(0.991)GT(0.009)ENR 185.06 1.90E-17 193780000 160820 155290 110070 106740 136010 156280 122960 114220 140250 121130 TRUE FALSE 154534.9766 150861.2812 129962.0975 112248.8642 140384.8852 159440.0887 124464.8213 111861.3171 124329.408 112925.7572 1.368465268 1.335933316 1.150863193 0.994005858 1.243160893 1.411901878 1.102182747 0.990573983 1.100983611 1 16.78501506 8 0.147513688 0.956216713 2.3457929 0.369610803 0.121086957 82.82519418 0.803855024 0.489776291 24.56520631 99999999.99 -8 1.389576187 TGEEDEEEFFCNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGEEDEEEFFCNR 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 ; 195.8 3.42E-07 227380000 370830 378440 288110 372870 384200 367580 379740 419700 431590 453800 FALSE TRUE 356337.5536 367647.2617 340177.886 392113.8654 396558.1419 375012.7194 384387.3717 411033.0483 382597.7126 423063.7218 0.842278681 0.869011553 0.804081911 0.926843511 0.937348493 0.88642136 0.90858032 0.971562975 0.904350085 1 18.69051545 8 0.110720543 1.040625222 0.39682398 0.616603544 0.034336409 68.32661233 0.526938534 0.30308332 6.729463999 99999999.99 -8 -0.643801242 GKDLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 GKDLLR 6 1 Q9HBL6-2;Q9HBL6 Q9HBL6-2 LRTM1 Leucine-rich repeat and transmembrane domain-containing protein 1 0 ; 86.113 0.0492 952400000 2175590 2153150 1901910 2193240 2257200 2377600 2426420 2546500 2809400 2883600 FALSE TRUE 2090565.538 2091744.27 2245627.445 2306433.379 2329804.888 2425676.701 2456115.254 2493913.885 2490488.69 2688291.204 0.777655908 0.778094377 0.835336381 0.857955186 0.866649002 0.902311735 0.913634375 0.927694843 0.926420727 1 21.35825799 8 0.142453226 1.029195046 0.066314644 0.976174752 0.010233654 9.098561228 0.085952889 0.039628181 1.79223511 99999999.99 -8 -0.962880402 AAAGPLDMSLPST(ph)PDIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAGPLDMSLPSTPDIK 17 0 P17544;K7ELQ4;P17544-2;P17544-4 P17544 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 AAAGPLDMSLPS(0.227)T(0.773)PDIK 211.45 2.75E-11 65907000 144150 137970 121640 143770 144070 158460 147530 161680 186130 188100 TRUE FALSE 138516.4586 134035.2307 143623.0539 151189.9869 148704.1424 161664.1698 149335.5163 158341.2515 165001.3027 175359.8195 0.789898502 0.764344028 0.81901917 0.862170065 0.847994386 0.921899727 0.851594834 0.902950585 0.94092993 1 17.41995869 8 0.095371468 1.089103162 0.161292945 0.870004712 0.024658228 45.10829335 0.306613084 0.361834015 5.474066942 99999999.99 -8 -0.927810216 LASDS(ph)DAESDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LASDSDAESDSR 12 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 LASDS(1)DAESDSR;LAS(0.006)DS(0.994)DAESDSR 325.27 2.19E-47 926800000 644220 726010 606850 702940 616870 723180 787660 748050 817020 877290 TRUE FALSE 619043.1702 705304.9056 716521.2943 739218.8176 636712.1838 737803.1951 797299.6187 732602.5061 724275.3148 817870.3669 0.756896441 0.8623676 0.87608174 0.903833722 0.778500126 0.902102858 0.9748484 0.895744039 0.885562485 1 19.64151267 8 0.083498309 1.082810624 0.334981393 0.522678215 0.049040865 152.5634632 0.923379879 1.185176337 13.12031685 99999999.99 -8 -0.747829231 LAQGLTHLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAQGLTHLGK 10 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 122.51 0.00048662 1639590000 3507200 3593000 3197000 3731900 3668800 3781300 3922900 4005000 4561800 4866800 FALSE TRUE 3370134.747 3490531.158 3774769.017 3924503.806 3786810.284 3857760.477 3970909.624 3922295.35 4043963.589 4537167.301 0.742783883 0.769319473 0.831966019 0.864967841 0.834619936 0.850257489 0.875195769 0.864481094 0.891296997 1 22.11336043 8 0.045245246 1.334862962 4.76E-16 0.896062636 0.02133126 196.1850419 0.672648975 5.018082749 19.01224557 99999999.99 -8 -1.334862962 LPLQFEWRVSEQHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPLQFEWRVSEQHR 14 1 Q6ZU64 Q6ZU64 CCDC108 Coiled-coil domain-containing protein 108 0 62.891 0.047375 599120000 836380 469080 484780 343820 577960 378490 566240 28170 686620 181090 FALSE TRUE 803693.3449 455702.2977 572390.5299 361564.5914 596550.6083 386143.3271 573169.8145 27588.27966 608677.7761 168824.613 4.760522359 2.699264577 3.390444792 2.14165805 3.533552352 2.287245445 3.395060734 0.163413848 3.605385289 1 17.36516572 8 0.139288524 0.740342622 12.20585445 0.347001951 1.038832502 78.68499743 0.730408131 4.242877156 179.6319497 99999999.99 -8 11.46551183 LEITS(ph)ENGEKSDDGTQDLLHFPTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEITSENGEKSDDGTQDLLHFPTK 24 1 E9PRS0;E9PLV1;Q9NQV6-2;Q9NQV6-1;Q9NQV6-5;Q9NQV6;Q9NQV6-4;Q9NQV6-7;Q9NQV6-6 E9PRS0 PRDM10 PR domain zinc finger protein 10 1 LEIT(0.121)S(0.627)ENGEKS(0.252)DDGTQDLLHFPTK 184.19 1.60E-17 94792000 252040 195770 178180 179760 181380 137840 176600 228520 187450 171530 TRUE FALSE 242189.9982 190186.8313 210381.0896 189037.4351 187214.2524 140627.2192 178761.2836 223800.9821 166171.4619 159912.1203 1.514519335 1.189320928 1.315604403 1.182133254 1.1707321 0.879403131 1.117872012 1.399524825 1.039142383 1 17.28691976 8 0.721858705 1.139117035 53.12633896 0.414906755 0.137920704 379.4830279 1.828226506 0.053263777 31956.40184 99999999.99 -8 51.98722193 LEIYVVTAEGLRPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEIYVVTAEGLRPVK 15 1 Q16531;F5GY55;Q16531-2;F5GZY8;F5GYG8;F5H198 Q16531 DDB1 DNA damage-binding protein 1 0 ; 195.84 8.42E-09 940460000 839430 853990 777730 873910 960410 868260 878800 1083990 1088310 1150810 FALSE TRUE 806624.1476 829635.0413 918283.1115 919012.5998 991302.4599 885816.8121 889555.0173 1061605.228 964769.6114 1072864.614 0.751841507 0.773289594 0.855917047 0.856596991 0.923977217 0.825655727 0.829140048 0.989505306 0.899246372 1 20.0330366 8 0.132293774 1.033327005 0.098481128 0.665597809 0.045634665 49.11026265 0.437721803 0.23586754 8.598006111 99999999.99 -8 -0.934845876 RHEHPPNPPVS(ph)PGKTVNDVNSNNNMSYR ddPTM_BT-474_Pertuzumab_2h_R1 1 RHEHPPNPPVSPGKTVNDVNSNNNMSYR 28 2 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 RHEHPPNPPVS(0.945)PGKT(0.055)VNDVNSNNNMSYR 141.9 5.79E-08 193280000 123970 136540 63718 60775 88618 117740 75463 15020 94387 54335 TRUE FALSE 119125.1153 132646.0129 75233.26 63911.60503 91468.47845 120120.7835 76386.53877 14709.83175 83672.58346 50654.84205 2.351702434 2.618624548 1.485213594 1.261707715 1.805720337 2.371358366 1.507980988 0.290393399 1.651818071 1 15.62841256 8 0.192676881 0.794762174 8.762484481 0.378250132 0.525525831 54.91727348 0.647068757 1.129695981 130.8046766 99999999.99 -8 7.967722307 LTLNS(ph)PIFDKPLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTLNSPIFDKPLSR 14 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 LT(0.004)LNS(0.996)PIFDKPLSR;LTLNS(1)PIFDKPLSR 221.51 2.57E-12 3124300000 3050200 3155900 2859800 2857200 3128600 3250900 3186200 3482200 3802100 3642700 TRUE FALSE 2930994.812 3065896.822 3376629.476 3004660.434 3229234.26 3316635.425 3225193.669 3410291.353 3370501.548 3395976.684 0.863078603 0.902802671 0.994302903 0.884770631 0.950900009 0.976636689 0.949710192 1.004215185 0.992498436 1 21.69539512 8 0.218534694 1.008806114 0.297732994 0.594071539 0.031160935 34.7442834 0.442818807 0.048392153 8.702240358 99999999.99 -8 -0.71107312 SPGS(ph)PVGEGTGSPPK ddPTM_BT-474_Pertuzumab_2h_R1 6 SPGSPVGEGTGSPPK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5;A0A0A0MSR2 P35611 ADD1 Alpha-adducin 1 SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK 348.06 2.98E-82 4213010000 2778110 2701240 2590060 2719790 2690720 2959560 2909660 3020110 3587570 3489260 TRUE FALSE 2669538.39 2624203.28 3058141.458 2860158.688 2777269.452 3019404.331 2945269.289 2957743.673 3180324.094 3252929.312 0.820656748 0.806720045 0.940119248 0.87925633 0.853774917 0.928210865 0.905420625 0.90925544 0.97768005 1 21.63330804 8 0.088420089 1.080451613 0.368205126 0.677249308 0.034121568 96.96966518 0.617234249 0.66441929 8.384564049 99999999.99 -8 -0.712246487 TDSTS(ph)DGRPAWMR ddPTM_BT-474_Pertuzumab_2h_R1 1 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 TDS(0.113)T(0.169)S(0.718)DGRPAWMR 121.66 0.00064221 1215900000 2617500 2390700 1906100 2022100 2168700 2198100 1621800 2188000 2346700 1973500 TRUE FALSE 2515205.206 2322519.577 2250574.671 2126460.823 2238458.205 2242547.088 1641648.074 2142817.035 2080312.454 1839833.087 1.367083364 1.262353413 1.223249373 1.155790076 1.21666374 1.218886161 0.892280982 1.164680128 1.130707165 1 20.81114346 8 0.208362576 1.015663439 2.722788548 0.567878468 0.083696427 37.99825446 0.470787833 0.141726606 21.46694233 100000000 -8 1.707125109 GSLS(ph)PVTKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GSLSPVTKPR 10 1 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H4P8;H0YFK8;F5H4Q7 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 GS(0.004)LS(0.995)PVT(0.001)KPR;GS(0.002)LS(0.998)PVTKPR 125.36 0.00024901 1581770000 1908970 1979400 1645370 1952180 1987560 1834450 2007390 2216000 2263200 2333200 TRUE FALSE 1834365.342 1922949.45 1942724.96 2052932.244 2051491.672 1871543.836 2031957.039 2170238.826 2006291.024 2175170.286 0.843320339 0.884045476 0.893136952 0.943803001 0.943140721 0.860412561 0.934159984 0.997732839 0.922360441 1 21.05269692 8 0.134892781 1.017743055 0.463728884 0.562572977 0.033165842 59.6642884 0.540050531 0.164273384 6.334508894 100000000 -8 -0.554014171 QPSGSFST(ph)PGSATYVR ddPTM_BT-474_Pertuzumab_2h_R1 1 QPSGSFSTPGSATYVR 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 QPS(0.001)GS(0.391)FS(0.204)T(0.398)PGS(0.006)ATYVR 146.88 1.21E-05 204640000 111880 105150 77679 93569 86622 74350 86034 115010 76255 77715 TRUE FALSE 107507.6059 102151.225 91717.32326 98398.1073 89408.2753 75853.40794 87086.90983 112635.0033 67598.85209 72451.29383 1.483860401 1.409929617 1.265916982 1.358127676 1.234046634 1.046957258 1.202006275 1.554630668 0.933024775 1 16.14472383 8 0.031185088 4.11E-09 3.145374775 0.358977606 0.158469302 1726.346364 4.123801551 130.157472 327.2558758 100000000 -8 3.145374771 STGVFQDEELLFSHK ddPTM_BT-474_Pertuzumab_2h_R1 2 STGVFQDEELLFSHK 15 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 0 ; 193.54 8.87E-08 213510000 367960 392550 331580 364770 389680 415110 404110 444850 494090 507730 FALSE TRUE 353579.7164 381354.8583 391503.882 383595.8234 402214.4111 423503.8086 409055.6191 435663.692 438002.9746 473340.9949 0.74698731 0.805666237 0.82710749 0.810400594 0.849735002 0.894711874 0.864188024 0.920401353 0.925343419 1 18.85252035 8 0.092803494 1.104371624 0.120955607 0.943803238 0.016409104 29.45812155 0.195571935 0.260472225 3.68713919 100000000 -8 -0.983416018 QLEEQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 QLEEQLR 7 0 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YL42;P09493-3;P09493-4;P09493-10;P09493-8;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;; 92.439 0.038368 521000000 1172050 1233380 1070080 1142500 1218270 1186360 1248140 1386110 1438750 1466470 FALSE TRUE 1126244.99 1198205.21 1263467.26 1201464.562 1257456.761 1210349.012 1263415.111 1357486.344 1275429.132 1367144.681 0.823793565 0.876428974 0.924164997 0.878813032 0.919768609 0.885311576 0.924126852 0.992935395 0.932914526 1 20.3827345 8 0.117934986 1.04024676 0.416865748 0.715673946 0.027084498 52.18757433 0.423985558 0.202480241 5.337401673 100000000 -8 -0.623381013 NAVEEYVYEFR ddPTM_BT-474_Pertuzumab_2h_R1 6 NAVEEYVYEFR 11 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;; 315.5 2.13E-45 3812189000 1194083 1243455 1110464 1231088 1199862 1234827 1237257 1367327 1494810 1501100 FALSE TRUE 1147416.916 1207992.881 1311149.547 1294624.599 1238456.651 1259796.048 1252398.921 1339091.22 1325125.436 1399429.16 0.819917827 0.863204023 0.936917412 0.925109063 0.884972735 0.900221379 0.894935562 0.956883891 0.946904262 1 20.41640703 8 0.076761563 1.084608975 0.473732184 0.683263226 0.027445618 135.4848205 0.760734856 0.956261213 8.821297969 100000000 -8 -0.61087679 SAEPSPTVMS(ph)TSLGSNLSELDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.577)T(0.254)S(0.169)LGSNLSELDR;SAEPSPTVMS(0.522)T(0.195)S(0.283)LGSNLSELDR 257.37 4.04E-37 396840000 655740 627390 489480 516350 569190 582420 459340 603250 558990 573250 TRUE FALSE 630112.9558 609497.4515 577939.9244 542998.8854 587498.5133 594196.9314 464961.5403 590792.6767 495535.7987 534423.2669 1.179052251 1.140477014 1.081427326 1.016046492 1.099313128 1.111847048 0.870024883 1.105477088 0.927234702 1 19.02762329 8 0.272759054 0.985226281 2.452475083 0.424702012 0.070413515 49.25615737 0.691853141 0.076766151 34.14216114 100000000 -8 1.467248802 QTDLELS(ph)PLTK ddPTM_BT-474_Pertuzumab_2h_R1 4 QTDLELSPLTK 11 0 J3KTC5;Q8WVK7 J3KTC5 SKA2 Spindle and kinetochore-associated protein 2 1 QTDLELS(1)PLTK;QTDLELS(1)PLTK;QTDLELS(1)PLTK;QTDLELS(1)PLTK 159 3.06E-05 517301000 1698400 1642210 1659950 1667700 1812190 1797200 1767490 2074080 2190740 2173760 TRUE FALSE 1632024.65 1595375.779 1959939.89 1753770.197 1870480.737 1833540.615 1789121.071 2031249.523 1942056.38 2026529.299 0.805329906 0.787245356 0.967141157 0.865405794 0.922997135 0.904768866 0.882849842 1.002329216 0.958316458 1 20.9505796 8 0.193713134 1.005137257 0.043825483 0.605382533 0.044935959 35.21150857 0.416368544 0.086433934 10.18922727 100000000 -8 -0.961311773 EVEYWDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVEYWDQR 8 0 P0DPD7;P0DPD8 P0DPD7 0 85.064 0.039567 131610000 192250 187730 165780 190140 197620 183250 202520 235320 212590 243830 FALSE TRUE 184736.6575 182376.1242 195740.1338 199953.1482 203976.6268 186955.4406 204998.5003 230460.5598 188457.6744 227315.1769 0.8126895 0.802305093 0.861095754 0.879629556 0.897329556 0.822450322 0.90182496 1.0138371 0.829058917 1 17.79433448 8 0.100811613 1.062762545 0.290558255 0.469757203 0.051428009 103.6035001 0.738439067 0.63723967 11.0753703 100000000 -8 -0.77220429 NSSNTSVGS(ph)PSNTIGR ddPTM_BT-474_Pertuzumab_2h_R1 4 NSSNTSVGSPSNTIGR 16 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 NSSNT(0.008)S(0.269)VGS(0.702)PS(0.016)NT(0.004)IGR;NSSNTSVGS(1)PSNTIGR;NSSNTSVGS(0.999)PS(0.001)NTIGR;NSSNTS(0.071)VGS(0.928)PSNTIGR 372.22 2.35E-104 2465400000 1417965 1445705 1263004 1395772 1466964 1545034 1507596 1637819 1832235 1885489 TRUE FALSE 1362549.36 1404474.909 1491256.918 1467807.96 1514150.229 1576275.646 1526046.411 1603997.465 1624247.364 1757783.151 0.775152134 0.799003511 0.848373656 0.835033582 0.861397624 0.896740673 0.868165342 0.912511572 0.924031706 1 20.74532567 8 0.08018084 1.122419464 0.199278826 0.951978533 0.013527118 36.22429302 0.211489367 0.365998565 3.705301147 100000000 -8 -0.923140639 T(ph)FSLTEVR ddPTM_BT-474_Pertuzumab_2h_R1 3 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.587)FS(0.413)LTEVR;T(0.77)FS(0.23)LTEVR;T(0.575)FS(0.425)LTEVR 222.88 5.37E-05 3898300000 1707990 1487330 1295380 1380750 1414690 1324340 1184400 1723230 1363370 1407040 TRUE FALSE 1641239.863 1444912.805 1529483.982 1452010.673 1460194.789 1351119.062 1198895.041 1687644.698 1208605.953 1311739.928 1.251193036 1.101523842 1.165996361 1.106934875 1.113174005 1.030020535 0.913973126 1.286569588 0.921376203 1 20.32305028 8 0.362158326 1.052025777 3.268607947 0.266567962 0.102218961 106.0094836 1.480676614 0.081590618 162.2556508 100000000 -8 2.21658217 DIVIAETLEDLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIVIAETLEDLDR 13 0 Q96D15 Q96D15 RCN3 Reticulocalbin-3 0 ; 206.11 1.21E-06 12725000 55240 55443 49136 34838 52731 50300 49885 51907 47398 50754 FALSE TRUE 53081.15973 53861.81992 58015.96822 36635.99335 54427.1405 51317.10046 50495.50755 50835.10231 42017.57775 47316.38637 1.121834607 1.138333336 1.226128466 0.774277077 1.150281006 1.084552401 1.067188588 1.074365695 0.888013244 1 15.53005228 8 0.246561353 1.00024228 1.961222444 0.138239575 0.117724992 109.8190263 1.487872841 0.151721409 43.58751719 100000000 -8 0.960980164 LVKPGNQNTQVTEAWNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVKPGNQNTQVTEAWNK 17 1 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 231.21 4.91E-16 2483200000 2542900 2413200 2319900 2359200 2539700 2793900 2823700 2862900 3162700 3320000 FALSE TRUE 2443520.657 2344377.899 2739157.536 2480958.595 2621391.757 2850394.572 2858257.285 2803780.115 2803683.555 3095133.443 0.789471828 0.757440008 0.884988511 0.801567571 0.846939819 0.920927845 0.923468192 0.90586728 0.905836083 1 21.56157018 8 0.116999131 1.04917122 0.155411804 0.779617226 0.032989928 42.15065535 0.340214979 0.237536001 6.125643348 100000000 -8 -0.893759416 RMHS(ph)QPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RMHSQPR 7 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 RMHS(1)QPR;RMHS(1)QPR 89.047 0.011123 440660000 293433 300146 178502 236027 212276 149710 207685 238574 123030 144328 TRUE FALSE 281965.314 291586.13 210761.2822 248208.3818 219104.0503 152737.2388 210226.7112 233647.3635 109064.1502 134552.536 2.095577849 2.16708015 1.566386546 1.844694936 1.628390343 1.135149461 1.562413592 1.736476847 0.810569265 1 17.03781006 8 0.144776177 0.868677899 5.540437892 0.63544612 0.258131861 49.5715298 0.474209411 1.018412296 48.31436395 100000000 -8 4.671759993 ELDDRDHYGNK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELDDRDHYGNK 11 1 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 ; 86.313 0.0087505 1501360000 1453120 1518810 1224650 1420270 1415250 1481730 1424130 1550060 1729930 1684710 FALSE TRUE 1396330.464 1475495.026 1445971.497 1493570.305 1460772.802 1511691.596 1441558.929 1518050.719 1533555.599 1570603.091 0.88904095 0.939444876 0.920647301 0.950953372 0.930071264 0.962491163 0.917837827 0.966540005 0.976411932 1 20.58288721 8 0.048599047 1.125547345 0.614334674 0.683216986 0.0173768 291.5754184 1.070513844 2.706506714 11.29767083 100000000 -8 -0.51121267 TPALAALAALGAPGPAPT(ph)AASSP ddPTM_BT-474_Pertuzumab_2h_R1 1 TPALAALAALGAPGPAPTAASSP 23 0 Q86V15 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 TPALAALAALGAPGPAPT(0.333)AAS(0.333)S(0.333)P 113.76 6.64E-05 97379000 211860 160430 105770 151740 165230 126650 105800 143740 85873 80872 TRUE FALSE 203580.277 155854.6935 124884.9918 159571.3196 170544.773 129210.9498 107094.812 140771.7188 76125.05705 75394.46741 2.700201805 2.067190058 1.656421169 2.116485799 2.262032996 1.713798827 1.420459826 1.867135927 1.009690229 1 16.20217104 8 0.081826559 0.159413508 6.259549868 0.670593559 0.294509962 116.8901856 0.694896672 7.604289225 80.48334852 100000000 -8 6.10013636 RLLEDGEDFNLGDALDSSNSMQTIQK ddPTM_BT-474_Pertuzumab_2h_R1 5 RLLEDGEDFNLGDALDSSNSMQTIQK 26 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;; 313.29 1.29E-81 1039255000 1092510 1183690 644363 598469 808736 1045983 685442 708359 810587 683021 FALSE TRUE 1049813.501 1149932.32 760813.7279 629356.0568 834749.7279 1067133.493 693830.6442 693731.1391 718572.562 636759.3793 1.648681646 1.805913438 1.194821392 0.988373438 1.310934326 1.67588186 1.089627679 1.08947141 1.128483671 1 19.28038878 8 0.373627437 1.120607055 10.04630996 0.421108372 0.21981099 66.743693 0.920582392 0.178016192 428.8070288 100000000 -8 8.925702902 AITTGLQEYVEAVSFQHFIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AITTGLQEYVEAVSFQHFIK 20 0 C4P0D6;C4P0D8;Q99598;Q5VVQ1 C4P0D6 DISC1;TSNAX Translin-associated protein X 0 183.45 4.36E-17 99904000 187310 185880 171080 190270 198510 194680 204590 216790 237420 236150 FALSE TRUE 179989.7181 180578.8844 201997.9617 200089.8575 204895.2544 198616.563 207093.8336 212313.2107 210469.0769 220155.3502 0.817557774 0.820233913 0.917524655 0.908857574 0.930684874 0.902165507 0.940671364 0.964379065 0.956002554 1 17.74816238 8 0.221897559 0.990999928 2.61E-17 0.864412959 0.020477694 17.03273425 0.218963235 0.03188038 6.065958732 100000000 -8 -0.990999928 T(ph)HTDSSEKELEPEAAEEALENGPK ddPTM_BT-474_Pertuzumab_2h_R1 1 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 T(0.272)HT(0.272)DS(0.228)S(0.228)EKELEPEAAEEALENGPK 136.64 2.84E-05 73579000 271290 210840 189400 165510 201030 190650 210620 73240 285380 184850 TRUE FALSE 260687.6869 204827.0496 223628.7932 174051.9909 207496.3125 194505.0736 213197.6306 71727.56841 252984.8588 172329.9449 1.512724252 1.188574915 1.297678087 1.009992727 1.204064173 1.128678326 1.237147907 0.416222314 1.468026111 1 17.39481389 8 0.302274319 0.937233415 5.608523421 0.183973857 0.262959989 75.98885521 1.087187193 0.264002821 192.4075504 100000000 -8 4.671290007 SPS(ph)PEPIYNSEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPSPEPIYNSEGK 13 0 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 1 SPS(1)PEPIYNSEGK;S(0.003)PS(0.997)PEPIYNSEGK 239.98 8.26E-17 1068240000 900420 824750 832890 896880 898040 850150 976880 1019560 1143230 1135230 TRUE FALSE 865230.5909 801228.9375 983411.7505 943168.0843 926926.2722 867340.6155 988835.3497 998505.7297 1013455.323 1058339.861 0.817535673 0.757062043 0.929202222 0.891176945 0.875830446 0.819529385 0.934326851 0.943464162 0.957589675 1 20.01337156 8 0.108826108 1.065069503 0.250252297 0.609302995 0.044661743 74.47339731 0.566145271 0.429657065 9.110789379 100000000 -8 -0.814817205 AVTIHDTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVTIHDTEK 9 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 161.79 6.43E-05 1982430000 1841780 2043400 1662670 1905790 1956890 2170500 2109300 2005040 2452400 2534200 FALSE TRUE 1769801.201 1985124.233 1963151.455 2004148.05 2019835.144 2214388.997 2135114.244 1963635.223 2174013.833 2362556.377 0.749104326 0.840244175 0.83094375 0.848296392 0.854936273 0.937285145 0.903730495 0.831148515 0.920195537 1 21.17191733 8 0.049365407 1.244156078 0.174169879 0.711562104 0.035743368 314.5527798 1.172231569 6.036424971 25.76028946 100000000 -8 -1.069986199 STTS(ph)VSEEDVSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 STTSVSEEDVSSR 13 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 STT(0.018)S(0.981)VS(0.001)EEDVSSR;S(0.045)T(0.101)T(0.086)S(0.733)VS(0.035)EEDVSSR;STT(0.096)S(0.904)VSEEDVSSR 208.87 4.45E-08 1100890000 1804830 1758550 1089060 1150330 1467820 1152310 870590 1386540 1082270 1043580 TRUE FALSE 1734295.248 1708397.876 1285877.368 1209698.669 1515033.763 1175610.498 881244.5408 1357907.464 959415.2468 972897.3971 1.782608581 1.755989769 1.321698847 1.243397991 1.557238993 1.208360205 0.905793914 1.39573553 0.986142269 1 19.89192814 8 0.269177416 1.042494324 6.776856191 0.663848298 0.170981673 31.25209256 0.437306773 0.19855749 83.18218711 100000000 -8 5.734361867 QLS(ph)ESESSLEMDDERYFNEMSAQGLRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.82)ES(0.18)ESSLEMDDERYFNEMSAQGLRPR 329.61 3.91E-96 347670000 20788 19532 11179 8686.4 18801 17223 12415 11355 7877.1 11276 TRUE FALSE 19975.58198 18974.96648 13199.29398 9134.706145 19405.75124 17571.26086 12566.93848 11120.51528 6982.924631 10512.26648 1.900216478 1.805030963 1.25560877 0.868956867 1.846010209 1.671500708 1.195454711 1.057860863 0.664264424 1 13.35978613 8 0.167616686 0.803099433 5.001480894 0.420487744 0.322608491 64.56509283 0.689796352 0.916696939 67.81295223 100000000 -8 4.198381462 QAAPPIELDAVWEDIRER ddPTM_BT-474_Pertuzumab_2h_R1 4 QAAPPIELDAVWEDIRER 18 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 278.82 3.12E-39 371053000 262980 315120 145449 159772 219281 280781 165252 172532 183441 158310 FALSE TRUE 252702.4509 306133.0861 171734.8698 168017.8521 226334.3725 286458.5842 167274.4034 168969.1539 162617.5467 147587.5227 1.712220967 2.074247745 1.163613744 1.138428568 1.533560347 1.940940392 1.133391227 1.144874247 1.10183804 1 17.17121123 8 0.141669708 0.864057348 4.215267487 0.364466012 0.295244452 83.48212658 0.785266009 1.27766592 56.85283344 100000000 -8 3.351210139 GILAADES(ph)TGSIAK ddPTM_BT-474_Pertuzumab_2h_R1 3 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.983)T(0.017)GSIAK;GILAADES(0.986)T(0.014)GSIAK;GILAADES(0.5)T(0.5)GSIAK 294.97 1.43E-43 693630000 1731620 1400530 1049550 982900 1155000 885330 740620 1325910 969190 749210 TRUE FALSE 1663946.376 1360588.256 1239227.032 1033627.587 1192151.624 903231.9792 749683.9291 1298529.495 859171.6144 698465.3394 2.382289116 1.94796818 1.774214069 1.479855232 1.706815724 1.293166501 1.073330181 1.859118015 1.230084824 1 19.413829 8 0.388563738 1.324299805 17.46698202 0.682934445 0.233415946 43.52249836 0.588586901 0.172408084 532.7110139 100000000 -8 16.14268221 DLLHPSPEEEKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLLHPSPEEEKR 12 1 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;; 180.18 1.28E-05 2935520000 3995340 4347880 3708640 4199740 4127680 4428300 4539140 4491740 5471530 5481130 FALSE TRUE 3839197.696 4223882.719 4378873.746 4416489.085 4260450.576 4517843.26 4594691.353 4398983.999 4850424.853 5109888.183 0.751327144 0.826609618 0.856941207 0.864302491 0.833765911 0.884137401 0.899176496 0.860876763 0.949223286 1 22.28486029 8 0.045178003 1.316177454 0.086855897 0.826711151 0.026888929 247.5622044 0.84759217 5.837854973 22.07513408 100000000 -8 -1.229321557 NPPGFAFVEFEDPRDAEDAVR ddPTM_BT-474_Pertuzumab_2h_R1 6 NPPGFAFVEFEDPRDAEDAVR 21 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;;; 170.14 7.84E-12 5022230000 728676 750158 459775 559955 622846 655023 483066 545615 599447 471001 FALSE TRUE 700198.5363 728764.2283 542866.5701 588854.3447 642880.4072 668268.0139 488977.9062 534347.8596 531400.2896 439099.6827 1.594623189 1.65967833 1.236317382 1.341049351 1.464087615 1.521905025 1.113592028 1.216916979 1.210204221 1 18.74418897 8 0.098955137 0.778434331 3.18212301 0.630986838 0.125224543 86.06126156 0.603771952 1.694163621 28.09249642 100000000 -8 2.403688679 NGYGFVEFEDSR ddPTM_BT-474_Pertuzumab_2h_R1 6 NGYGFVEFEDSR 12 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;;;; 188.27 2.19E-05 2039010000 1685380 1573580 1610350 1884180 1769420 1566890 1795720 2002350 2146540 2282960 FALSE TRUE 1619513.486 1528703.039 1901376.067 1981422.756 1826335.001 1598573.589 1817696.559 1961000.773 1902873.778 2128333.086 0.760930466 0.718263062 0.893363957 0.930973995 0.858105817 0.751091829 0.854047034 0.9213787 0.894067658 1 21.02129252 8 0.04246979 1.363343162 1.08E-09 0.485529491 0.061052338 647.6845973 2.089471539 17.68918925 61.8371727 100000000 -8 -1.363343161 FDDDVVSR ddPTM_BT-474_Pertuzumab_2h_R1 3 FDDDVVSR 8 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;; 149.65 0.0011673 900100000 2409570 2536320 2040780 2476120 2371820 2363480 2474470 2713720 2827000 2827810 FALSE TRUE 2315401.34 2463986.637 2409594.343 2603912.85 2448111.744 2411271.185 2504753.304 2657680.734 2506090.812 2636279.91 0.878283574 0.934645304 0.914013089 0.987722449 0.928623601 0.914649152 0.950109013 1.008117812 0.95061636 1 21.33007213 8 0.145535226 1.011779825 0.599790114 0.495065507 0.028040219 61.28377397 0.588626157 0.110019761 5.300986423 100000000 -8 -0.411989711 RKDNPIEDELVFR ddPTM_BT-474_Pertuzumab_2h_R1 1 RKDNPIEDELVFR 13 2 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 147.35 2.40E-05 301550000 83425 77566 55860 65263 73880 66157 70711 71321 76248 67048 FALSE TRUE 80164.65877 75353.89363 65955.1446 68631.23125 76256.4173 67494.73987 71576.38237 69848.19643 67592.6467 62506.77924 1.282495431 1.205531537 1.055167862 1.097980604 1.219970349 1.079798714 1.145097912 1.117449935 1.081365054 1 15.93172505 8 0.065067659 0.855540569 1.741512591 0.488828817 0.058007938 285.1141532 1.377046669 3.518740823 23.47592676 100000000 -8 0.885972021 RTSS(ph)EDNLYLAVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 RTSSEDNLYLAVLR 14 1 Q15149-4 Q15149-4 PLEC Plectin 1 RT(0.303)S(0.138)S(0.559)EDNLYLAVLR;RT(0.097)S(0.367)S(0.537)EDNLYLAVLR 242.24 1.09E-17 477920000 220120 276890 149201 165100 181356 216420 175504 172309 161819 153627 TRUE FALSE 211517.467 268993.3683 176164.9397 173620.8308 187189.4804 220796.1607 177651.8705 168750.7589 143449.9855 143221.7065 1.47685342 1.878160615 1.230015645 1.212252214 1.306990994 1.541638947 1.240397666 1.178248487 1.001593886 1 17.12789064 8 0.136405417 0.876494065 3.516956111 0.49973473 0.178031342 63.93984479 0.583864289 0.82314792 32.78595738 100000000 -8 2.640462045 LSSWDQAET(ph)PGHT(ph)PSLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 LSSWDQAET(1)PGHT(0.973)PS(0.027)LR;LSSWDQAET(1)PGHT(0.998)PS(0.002)LR 181.82 1.33E-09 351560000 683537 543028 385033 467659 424981 323869 279993 569628 364569 328889 TRUE FALSE 656823.6183 527541.3731 454617.0281 491794.937 438650.8998 330417.8531 283419.6381 557864.9827 323184.6555 306613.0551 2.142190645 1.720544394 1.482706038 1.603959547 1.430633473 1.077637914 0.924356068 1.819443019 1.054047276 1 18.2260596 8 0.437717446 1.24018741 20.10292171 0.572954994 0.251589458 68.15361851 0.843861468 0.163628261 1139.527573 100000000 -8 18.8627343 NFRNPLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 NFRNPLAK 8 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 133.55 0.00083421 2057270000 2467300 1855020 1348890 1009640 1634150 1219800 1129650 1072830 1466470 1035480 FALSE TRUE 2370875.188 1802116.646 1592664.429 1061747.641 1686713.919 1244465.192 1143474.995 1050675.686 1300002.474 965346.0173 2.455984845 1.866809013 1.649837882 1.099862249 1.74726356 1.289138992 1.18452345 1.088392832 1.346669951 1 19.88068663 8 0.447769536 1.162111922 30.30843467 0.808953872 0.189098283 34.6641274 0.419887129 0.112317772 922.2409584 100000000 -8 29.14632275 up LCYVALDFEQEMATAASS(ph)SSLEK ddPTM_BT-474_Pertuzumab_2h_R1 5 LCYVALDFEQEMATAASSSSLEK 23 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 1 LCYVALDFEQEMATAAS(0.131)S(0.712)S(0.131)S(0.025)LEK;LCYVALDFEQEMATAAS(0.146)S(0.779)S(0.074)S(0.002)LEK;LCYVALDFEQEMATAAS(0.048)S(0.796)S(0.126)S(0.03)LEK;LCYVALDFEQEMATAAS(0.096)S(0.771)S(0.131)S(0.001)LEK;LCYVALDFEQEMATAAS(0.016)S(0.513)S(0.407)S(0.064)LEK 177.6 3.49E-17 153463000 272889 242824 197578 198161 230293 210512 178368 239707 207599 182508 TRUE FALSE 262224.1962 235898.8973 233284.7397 208388.113 237700.5835 214768.6969 180550.9209 234756.9667 184033.2318 170146.5706 1.541166509 1.386445207 1.371081056 1.224756469 1.397034231 1.262256983 1.061149339 1.379733755 1.081615875 1 17.37641855 8 0.093587211 0.833844664 2.665953543 0.646493256 0.099418321 95.08045014 0.635846368 1.547576856 22.35731358 100000000 -8 1.83210888 ETES(ph)APGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 3 ETESAPGSPR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 2 ET(0.003)ES(0.997)APGS(1)PR;ETES(1)APGS(1)PR;ETES(1)APGS(1)PR 164.06 9.17E-06 1227250000 2738890 2507690 1833100 2081020 2078890 2008220 1700890 2344920 2116500 2013250 TRUE FALSE 2631851.151 2436173.136 2164381.947 2188421.692 2145759.385 2048827.584 1721706.001 2296496.583 1876243.793 1876890.784 1.402239903 1.297983429 1.153174157 1.165982438 1.143252129 1.091607248 0.91731816 1.223564313 0.999655286 1 20.83991327 8 0.385445166 1.048352904 6.547817583 0.688642367 0.077477607 40.13973592 0.545241481 0.05645217 165.6003207 100000000 -8 5.499464679 LRDLEDSLAR ddPTM_BT-474_Pertuzumab_2h_R1 8 LRDLEDSLAR 10 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 246.08 1.27E-12 12860210000 7290498 8331793 4284405 4963248 6052832 6967589 5088307 5312765 5164964 4472157 FALSE TRUE 7005577.278 8094178.421 5058692.29 5219401.824 6247526.838 7108478.423 5150579.223 5203054.546 4578658.94 4169253.823 1.680295222 1.941397373 1.21333277 1.251879124 1.498476011 1.704976172 1.235371949 1.247958212 1.098196256 1 21.99135778 8 0.116375949 0.815026096 3.72153543 0.502294456 0.203349398 86.43598799 0.694609027 1.597875625 40.60676153 100000000 -8 2.906509334 KHEENEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KHEENEAK 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 89.247 0.0091147 69726000 180812 153174 117207 115912 137038 132835 149574 93855 151942 157223 FALSE TRUE 173745.6671 148805.6275 138388.9122 121894.2322 141445.9517 135521.0147 151404.5314 91916.86145 134694.1812 146574.1462 1.18537731 1.015224249 0.944156359 0.831621643 0.965012967 0.92459017 1.032955233 0.627101463 0.91894911 1 17.16127113 8 0.628103092 0.869877992 25.51610835 0.375385079 0.108617881 193.0981606 1.345683071 0.045846547 6582.970496 100000000 -8 24.64623036 CPSQSSSRPAAMISQPPT(ph)PPTGQPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVR 26 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPSQSSSRPAAMIS(0.02)QPPT(0.98)PPTGQPVR 134.14 6.77E-05 145320000 43162 43368 44294 47412 42105 56118 46992 48906 61786 62281 TRUE FALSE 41475.18132 42131.1871 52298.91111 49858.939 43459.34556 57252.74441 47567.10215 47896.07401 54772.31231 58062.6524 0.714317717 0.725615957 0.900732381 0.85870929 0.748490532 0.986051137 0.819237499 0.824903308 0.943331213 1 15.82532286 8 0.086229761 1.09216162 0.144555246 0.485218458 0.071058302 162.4587598 1.01158821 1.532297934 18.2464461 100000000 -8 -0.947606374 EGRGES(ph)ENAGTNQETR ddPTM_BT-474_Pertuzumab_2h_R1 2 EGRGESENAGTNQETR 16 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 EGRGES(0.978)ENAGT(0.021)NQETR;EGRGES(0.976)ENAGT(0.024)NQETR 185.46 4.36E-09 83586000 209891 215034 118894 137784 175013 196742 134522 131424 157218 119590 TRUE FALSE 201688.2277 208901.4409 140380.7906 144895.0488 180642.4521 200720.258 136168.3205 128710.0485 139371.2718 111490.0628 1.809024254 1.873722515 1.259132761 1.29962299 1.62025608 1.800342138 1.221349393 1.154453099 1.250077974 1 16.7665556 8 0.107408984 0.747780735 3.890423492 0.519035642 0.207685986 97.58737344 0.733771143 2.216505795 45.3988342 100000000 -8 3.142642757 AGEVFIHK ddPTM_BT-474_Pertuzumab_2h_R1 6 AGEVFIHK 8 0 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;; 111.04 0.0033105 9168100000 14812900 14752000 12482100 13978500 14481500 14619700 14965500 15534100 16849400 17061300 FALSE TRUE 14233995.49 14331287.4 14737893.13 14699932.06 14947310.6 14915320.35 15148652.27 15213315.41 14936726.75 15905722.95 0.894897738 0.901014524 0.926578011 0.924191381 0.939744182 0.93773294 0.952402623 0.956468024 0.93907877 1 23.92304261 8 0.075013814 1.058659001 0.632144906 0.902376241 0.008802732 59.60152609 0.327785721 0.301989827 2.65560978 100000000 -8 -0.426514095 SSSVS(ph)PSSWK ddPTM_BT-474_Pertuzumab_2h_R1 3 SSSVSPSSWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 SSSVS(0.996)PS(0.004)SWK;SSSVS(0.998)PS(0.001)S(0.001)WK;SSSVS(0.945)PS(0.055)SWK 236.22 4.07E-12 2548100000 2598990 2428120 2512670 2775040 2610990 2504720 2957600 3259490 3016360 3442470 TRUE FALSE 2497418.597 2358872.395 2966765.363 2918260.147 2694974.865 2555367.155 2993795.994 3192180.392 2673955.458 3209308.441 0.778179674 0.735009563 0.924425127 0.909311212 0.839736945 0.796236074 0.932847699 0.99466301 0.833187432 1 21.61383102 8 0.150565622 1.006856259 0.127292043 0.414230341 0.06631429 66.48761368 0.655503171 0.240037474 12.79919513 100000000 -8 -0.879564215 TVFAEHISDECK ddPTM_BT-474_Pertuzumab_2h_R1 4 TVFAEHISDECK 12 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;; 167.84 4.81E-05 7348900000 9449900 11055300 9349000 10857600 9869600 11364400 11020200 11311100 12424600 13572600 FALSE TRUE 9080587.461 10740013.67 11038572.27 11417962.04 10187064.65 11594195.95 11155068.5 11077521.83 11014211.5 12653315.71 0.717644898 0.84879046 0.872385746 0.902369173 0.80509053 0.916297057 0.881592521 0.875463956 0.870460498 1 23.59301215 8 0.030706784 1.461015061 2.95E-10 0.570153317 0.045483065 1033.326326 2.43123646 36.46210299 90.39867669 100000000 -8 -1.461015061 GFAFVTFDDHDTVDK ddPTM_BT-474_Pertuzumab_2h_R1 10 GFAFVTFDDHDTVDK 15 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;;;; 297.5 4.00E-44 19918324000 11147902 10396779 9770764 10674084 11033116 10591141 11075676 11576536 13241472 12866183 FALSE TRUE 10712229.67 10100273.04 11536558.4 11224974.75 11388006.2 10805301.13 11211223.44 11337476.49 11738355.61 11994744.97 0.893076901 0.842058174 0.961801059 0.935824379 0.949416284 0.900836254 0.934677933 0.94520363 0.97862486 1 23.51589915 8 0.097817423 1.037508214 0.588187743 0.536072998 0.029465784 108.5249082 0.753880266 0.406249398 6.543954274 100000000 -8 -0.449320472 RQS(ph)VSGLHR ddPTM_BT-474_Pertuzumab_2h_R1 4 RQSVSGLHR 9 1 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 RQS(1)VSGLHR;RQS(1)VSGLHR;RQS(1)VSGLHR;RQS(0.999)VS(0.001)GLHR 161.93 3.93E-05 1491710000 529210 381233 336921 367981 345475 231712 281714 553410 266727 280546 TRUE FALSE 508527.8881 370360.6081 397810.1195 386972.5435 356587.5171 236397.3754 285161.7002 541981.8901 236449.2692 261544.3695 1.944327416 1.41605269 1.521004334 1.479567479 1.363392061 0.9038519 1.090299519 2.072236887 0.904050313 1 17.99669619 8 0.801958666 1.327628012 151.4694709 0.254465224 0.335466799 857.1943157 2.929157056 0.117755581 233875.486 100000000 -8 150.1418429 FHS(ph)PSTTWS(ph)PNKDTPQEK ddPTM_BT-474_Pertuzumab_2h_R1 5 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 FHS(0.989)PS(0.011)TTWS(1)PNKDTPQEK;FHS(0.884)PS(0.107)T(0.009)T(0.002)WS(0.999)PNKDTPQEK;FHS(0.985)PS(0.015)T(0.005)T(0.015)WS(0.98)PNKDTPQEK;FHS(0.946)PS(0.051)T(0.012)T(0.002)WS(0.989)PNKDTPQEK;FHS(0.994)PS(0.006)T(0.002)T(0.001)WS(0.996)PNKDTPQEK 229.1 2.74E-19 4492240000 4602820 3503410 2993940 2952060 3346730 3301270 3608300 1415869 4521640 3702880 TRUE FALSE 4422936.706 3403496.177 3535011.558 3104416.17 3454380.61 3368023.941 3652459.455 1386630.81 4008362.383 3452080.639 1.281237945 0.985926035 1.024023459 0.899288428 1.000666256 0.975650425 1.05804581 0.401679727 1.161143902 1 21.71903474 8 0.444119435 0.85465646 9.352495531 0.173717115 0.197782674 125.5122474 1.532695662 0.124544236 963.355955 100000000 -8 8.497839071 LRLEIIDKDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRLEIIDKDSK 11 2 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2U3TZY2 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 71.558 0.027393 327420000 325980 320630 286800 253960 251770 298500 283970 281230 310020 268800 FALSE TRUE 313240.3412 311485.9463 338631.1398 267066.906 259868.4107 304535.8745 287445.3098 275422.5022 274827.8293 250593.9366 1.249991702 1.242990755 1.35131418 1.065735706 1.03700997 1.215256357 1.147056125 1.099078876 1.096705822 1 17.93499198 8 0.139951596 0.982238164 2.044529533 0.490100619 0.075312767 67.12177139 0.625389938 0.332594941 14.27848869 100000000 -8 1.062291369 ISHEGS(ph)PVKPVAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 ISHEGSPVKPVAIR 14 1 Q96II8-3;Q96II8;Q96II8-2 Q96II8-3 LRCH3 Leucine-rich repeat and calponin homology domain-containing protein 3 1 ISHEGS(1)PVKPVAIR 94.882 0.002409 97520000 44110 44653 44792 42862 48081 46298 49636 50398 56568 59219 TRUE FALSE 42386.13243 43379.54016 52886.91079 45074.11296 49627.56903 47234.17728 50243.46022 49357.26369 50146.63779 55208.04438 0.767752832 0.785746727 0.957956605 0.816441036 0.898919163 0.855566934 0.910074986 0.89402304 0.908321212 1 15.75259088 8 0.074033426 1.108777314 0.307399775 0.565408071 0.046078432 170.2716637 0.925364639 1.646513646 14.09409426 100000000 -8 -0.801377538 RPLSAS(ph)LGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.319)AS(0.681)LGQLNEVGLPSAAILPDEGAVDLPSR;RPLS(0.256)AS(0.744)LGQLNEVGLPSAAILPDEGAVDLPSR 194.34 7.94E-21 756500000 188795 183201 135522 155301 157662 141289 123316 175692 153180 135655 TRUE FALSE 181416.6827 177976.2869 160013.8401 163316.1032 162733.3414 144145.9604 124825.1781 172063.8988 135791.6486 126466.966 1.434498576 1.407294667 1.26526195 1.291373616 1.2867656 1.139791401 0.987018049 1.360544213 1.07373216 1 16.94840107 8 0.159762978 1.005696903 2.709530407 0.601245939 0.098382947 47.93739222 0.494284425 0.301536545 19.23872695 100000000 -8 1.703833504 ASETPPPVAQPKPEAPHPGLETTLQER ddPTM_BT-474_Pertuzumab_2h_R1 1 ASETPPPVAQPKPEAPHPGLETTLQER 27 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 0 187.48 5.79E-18 132120000 88978 89860 74393 97370 93147 88393 101340 105680 110560 116440 FALSE TRUE 85500.64139 87297.28078 87837.46996 102395.2774 96143.15785 90180.36702 102580.2292 103497.6711 98009.69231 108553.4151 0.787636587 0.804187328 0.80916358 0.943270898 0.885676031 0.830746476 0.944974685 0.953426209 0.902870649 1 16.72804559 8 0.154608766 1.013277702 0.118029055 0.688170856 0.039450492 37.11242926 0.373341975 0.130102059 7.513343563 100000000 -8 -0.895248647 ELDLFLAYYVQEQDSGQSGS(ph)PSHNDPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDLFLAYYVQEQDSGQSGSPSHNDPAK 28 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 ELDLFLAYYVQEQDS(0.009)GQS(0.141)GS(0.758)PS(0.092)HNDPAK 214.98 2.39E-34 90691000 51545 45850 47545 50457 53803 45081 58757 60971 57220 67020 TRUE FALSE 49530.56441 44542.40289 56137.43913 53061.09182 55533.62236 45992.56871 59476.08574 59711.92754 50724.62549 62480.6757 0.792734135 0.712898867 0.898476825 0.849240045 0.888812769 0.736108696 0.951911692 0.955686328 0.811845021 1 15.93112244 8 0.091501225 1.083268477 0.192750187 0.374670156 0.072243067 150.5424366 0.987276089 1.229716953 16.82634367 100000000 -8 -0.890518291 AIGSDT(ph)SDIVHIWCPEGMK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIGSDTSDIVHIWCPEGMK 19 0 Q09GN1;Q71F23-3;Q71F23 Q09GN1 MLF1IP;CENPU Centromere protein U 1 AIGS(0.047)DT(0.476)S(0.476)DIVHIWCPEGMK 87.326 0.010061 59188000 101050 67844 55853 62355 53121 50278 40172 61624 57836 55662 TRUE FALSE 97100.85428 65909.15555 65946.87954 65573.14902 54829.68521 51294.65561 40663.63695 60351.44287 51270.69975 51891.96316 1.871211809 1.270122607 1.270849579 1.26364749 1.056612274 0.988489402 0.783621094 1.163021 0.988027753 1 15.6632235 8 0.550544121 0.99749636 38.43648401 0.833062548 0.113935908 52.75150182 0.48110686 0.054558584 2335.893732 100000000 -8 37.43898765 KYEDICPSTHNMDVPNIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 KYEDICPSTHNMDVPNIKR 19 2 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ; 165.3 1.33E-11 2044960000 2455300 3014700 1793040 1811250 2007960 2842000 2097700 2033920 2238200 2200800 FALSE TRUE 2359344.162 2928723.708 2117082.214 1904728.83 2072547.857 2899467.187 2123372.28 1991918.841 1984128.919 2051737.856 1.14992476 1.427435625 1.031848298 0.928349021 1.010142622 1.413176239 1.034914024 0.970844709 0.967047966 1 20.96841498 8 0.246110701 0.990384373 2.691532566 0.164863853 0.1577888 88.10733709 1.192766033 0.216579913 61.7548352 100000000 -8 1.701148194 HAS(ph)APSHVQPSDSEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HASAPSHVQPSDSEK 15 0 O60343-2;O60343-3;O60343;A0A3B3IRT3 O60343-2 TBC1D4 TBC1 domain family member 4 1 HAS(1)APSHVQPSDSEK;HAS(0.995)APS(0.005)HVQPSDSEK 182.76 3.44E-07 3983500000 6525700 4728800 3335000 3638800 3864500 3258000 3687800 1672000 4385100 3061700 TRUE FALSE 6270668.429 4593939.254 3937708.687 3826598.904 3988805.152 3323878.992 3732932.4 1637472.616 3887321.832 2854328.332 2.196898079 1.609464196 1.37955702 1.34063025 1.397458417 1.164504782 1.307814647 0.573680539 1.361904231 1 21.44471987 8 0.358811358 0.978682252 15.43089707 0.700888114 0.215072314 33.80044062 0.473633567 0.177174271 333.1552565 100000000 -8 14.45221482 up GRDDCGTFEDTGPLLQFDYK ddPTM_BT-474_Pertuzumab_2h_R1 2 GRDDCGTFEDTGPLLQFDYK 20 1 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 0 ; 186.9 2.84E-17 287900000 371500 381250 273780 303300 328950 344160 279260 344320 346900 328060 FALSE TRUE 356981.3693 370377.1233 323258.1362 318953.3493 339530.9755 351119.151 282677.6674 337209.6717 307521.3663 305840.204 1.167215313 1.211015159 1.056951087 1.042875806 1.110158086 1.148047727 0.924265887 1.102568162 1.005496865 1 18.22241854 8 0.251777176 1.010319127 2.19952909 0.417092001 0.063344094 48.86509934 0.667863395 0.078742653 24.67697525 100000000 -8 1.189209964 DAS(ph)PTPSTDAEYPANGSGADR ddPTM_BT-474_Pertuzumab_2h_R1 3 DASPTPSTDAEYPANGSGADR 21 0 O43639;E9PEE2;E7EPF5 O43639 NCK2 Cytoplasmic protein NCK2 1 DAS(0.999)PT(0.001)PSTDAEYPANGSGADR;DAS(0.958)PT(0.041)PSTDAEYPANGSGADR;DAS(1)PTPSTDAEYPANGSGADR 465.02 1.44E-223 1394600000 326899 314025 273495 339242 318837 341201 329773 356993 408040 393312 TRUE FALSE 314123.4257 305069.3145 322921.6304 356750.3203 329092.6817 348100.318 333808.8606 349620.9698 361721.0098 366672.6279 0.856686324 0.831993695 0.880681037 0.972939601 0.897510904 0.949349069 0.910373001 0.953496234 0.986495807 1 18.48413305 8 0.177208432 1.004471541 0.28347228 0.708850755 0.029232018 31.2322308 0.34734508 0.068591087 6.045540317 100000000 -8 -0.720999261 QLLLTADDRVNPCIGGVILFHETLYQK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLLLTADDRVNPCIGGVILFHETLYQK 27 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 190.19 3.83E-18 1768930000 1621490 1823450 959160 912290 1098240 1689140 678550 844610 877790 727370 FALSE TRUE 1558120.378 1771446.991 1132501.548 959373.3962 1133565.887 1723295.568 686854.2979 827168.5083 778146.9592 678104.582 2.297758221 2.612350717 1.670098652 1.414786777 1.671668231 2.541341872 1.012903195 1.21982439 1.147532372 1 19.37114827 8 0.163444675 0.776112547 7.539805884 0.516060262 0.409289039 49.5530974 0.519678872 1.187175622 81.22937423 100000000 -8 6.763693338 SHNVAAGSYEAPLPPGSFHGDFAYGT(ph)YR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 SHNVAAGS(0.059)YEAPLPPGS(0.338)FHGDFAY(0.01)GT(0.579)Y(0.014)R;SHNVAAGSYEAPLPPGS(0.406)FHGDFAY(0.026)GT(0.532)Y(0.036)R 142.64 2.17E-07 976010000 489560 353250 204734 202863 239307 181261 123506 73463 171100 121350 TRUE FALSE 470427.454 343175.6559 241733.9881 213332.7837 247004.527 184926.2216 125017.5034 71945.96338 151677.4453 113130.8564 4.158259461 3.033439919 2.136764414 1.88571704 2.183352401 1.634622308 1.105069893 0.635953494 1.340725688 1 16.78763295 8 0.31713617 0.834353752 32.70220139 0.915495945 0.289860532 15.56197186 0.222912415 0.306596768 286.6839039 100000000 -8 31.86784764 up LCYVALDFEQEMATAAS(ph)SSSLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LCYVALDFEQEMATAASSSSLEK 23 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 1 LCYVALDFEQEMATAAS(0.522)S(0.353)S(0.097)S(0.027)LEK 91.166 0.0034063 17004000 32682 30693 19616 19252 24437 22404 16290 20991 19289 17702 TRUE FALSE 31404.75131 29817.66569 23161.04756 20245.59803 25223.0383 22857.02423 16489.36189 20557.52851 17099.39359 16503.02777 1.902969064 1.806799704 1.403442318 1.226780825 1.528388526 1.385020043 0.999171917 1.245682235 1.036136751 1 14.01044312 8 0.260461546 1.019224571 7.316309588 0.800762561 0.135415939 21.76180657 0.301265865 0.1680639 60.87671078 100000000 -8 6.297085017 VLATEDRS(ph)DHLIQTDTVNLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLATEDRSDHLIQTDTVNLHR 21 1 P51151 P51151 RAB9A Ras-related protein Rab-9A 1 VLAT(0.043)EDRS(0.957)DHLIQTDTVNLHR 87.792 0.0015414 99154000 85386 70511 63409 57971 64678 64040 68846 42129 81913 60835 TRUE FALSE 82049.02072 68500.09532 74868.41683 60962.89026 66758.42661 65334.93268 69688.55794 41259.02143 72614.57965 56714.59126 1.44670038 1.207803738 1.320090918 1.074906632 1.177094379 1.151995125 1.228758885 0.727485123 1.28035093 1 15.79143233 8 0.245643374 0.975755314 3.698569725 0.355724973 0.150072363 49.58051755 0.670647167 0.196102491 55.48192763 100000000 -8 2.72281441 S(ph)FQGDDSDLLLK ddPTM_BT-474_Pertuzumab_2h_R1 4 SFQGDDSDLLLK 12 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK 148.7 6.99E-05 205530000 453771 457613 356502 382722 411177 407395 361320 434937 430493 409153 TRUE FALSE 436037.1276 444562.3253 420929.8417 402474.3283 424402.8816 415632.806 365741.9422 425955.399 381625.2394 381440.7029 1.143132142 1.165482136 1.103526285 1.055142582 1.112631343 1.089639367 0.95884351 1.116701484 1.000483788 1 18.54109927 8 0.172991057 0.992560098 1.709326529 0.519784432 0.044949815 46.87874943 0.512450584 0.107134898 8.7485736 100000000 -8 0.716766431 TS(ph)PSGGTWSSVVSGVPR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSPSGGTWSSVVSGVPR 17 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4 Q99700 ATXN2 Ataxin-2 1 T(0.031)S(0.967)PS(0.002)GGTWSSVVSGVPR;T(0.041)S(0.959)PSGGTWSSVVSGVPR;T(0.127)S(0.872)PS(0.001)GGTWSSVVSGVPR;T(0.149)S(0.85)PSGGTWSSVVSGVPR 263.04 2.34E-27 1551530000 1680050 1629570 1618370 1781110 1729800 1878030 1803810 2029910 2138750 2343490 TRUE FALSE 1614391.789 1583096.259 1910845.459 1873033.301 1785440.588 1916005.053 1825885.566 1987991.649 1895968.066 2184763.335 0.738932114 0.724607665 0.874623548 0.857316337 0.817223797 0.876985174 0.83573609 0.909934553 0.867813935 1 21.05904558 8 0.088931584 1.09010777 0.140119311 0.739579425 0.038572995 81.58835173 0.521953933 0.73973935 9.461868875 100000000 -8 -0.949988458 GTDTQTPAVLS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 4 GTDTQTPAVLSPSK 14 0 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(0.988)PS(0.012)K;GTDTQTPAVLS(0.997)PS(0.003)K;GTDTQTPAVLS(0.998)PS(0.002)K;GTDTQTPAVLS(0.5)PS(0.5)K 343.16 2.98E-69 4840270000 5119650 3987910 3937780 3206720 4055330 2719130 3587120 4268670 3262420 3697300 TRUE FALSE 4919568.418 3874178.711 4649424.441 3372219.203 4185773.372 2774112.672 3631020.248 4180520.473 2892083.759 3446878.578 1.427253182 1.123967272 1.348879671 0.978340005 1.214366354 0.804818797 1.053422732 1.212842396 0.839044281 1 21.71685905 8 0.404343836 1.01105615 7.572235869 0.430072457 0.146702977 75.77356107 0.999832848 0.098935451 397.3061806 100000000 -8 6.561179719 RREDS(ph)YHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 RREDSYHVR 9 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 RREDS(1)YHVR;RREDS(1)YHVR 105.65 0.0015986 194862000 55376 53344 34434.4 46527 38097 38969 36366 47084 27301.9 28363 TRUE FALSE 53211.8447 51822.68135 40657.46207 48928.26405 39322.4246 39756.97988 36811.05799 46111.69895 24202.70277 26441.94875 2.012402535 1.95986619 1.537612165 1.850403104 1.48712279 1.503557104 1.392146182 1.743884287 0.915314639 1 14.69054089 8 0.087156404 0.518573294 4.600315431 0.669897833 0.202741395 101.3287384 0.63689856 4.057710009 49.52223075 100000000 -8 4.081742137 GFAYVQFEDVRDAEDALHNLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 GFAYVQFEDVRDAEDALHNLDR 22 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 ;; 259.2 1.98E-37 207614000 166764 215551 80049.4 79652.6 131161 176644 81842.3 75670.8 90163.2 62690.5 FALSE TRUE 160246.6785 209403.6965 94516.10727 83763.48023 135379.9127 180215.8627 82843.91055 74108.17154 79928.25153 58444.4166 2.741864627 3.58295469 1.617196522 1.433216124 2.316387442 3.083542846 1.417482035 1.268011144 1.367594309 1 15.83477759 8 0.144848973 0.665680529 9.204814976 0.441023348 0.628654526 68.3166936 0.653782969 2.563124804 121.7781492 100000000 -8 8.539134447 SHNVAAGSYEAPLPPGS(ph)FHGDFAYGTYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 SHNVAAGS(0.035)Y(0.003)EAPLPPGS(0.932)FHGDFAY(0.023)GT(0.004)Y(0.003)R 70.178 0.0076091 267490000 71744 70559 45058 44608 60880 65919 44881 44875 61051 52474 TRUE FALSE 68940.16516 68546.7264 53200.98291 46910.22423 62838.26049 67251.92734 45430.2671 43948.31557 54120.74643 48919.88924 1.409246142 1.40120363 1.087512334 0.958919265 1.284513548 1.374735887 0.928666598 0.898373162 1.106313756 1 15.57813352 8 0.292410603 0.986283503 4.675941907 0.395620481 0.150704203 55.87872893 0.796521611 0.173026165 106.8963617 100000000 -8 3.689658403 RGLLYDS(ph)DEEDEERPAR ddPTM_BT-474_Pertuzumab_2h_R1 6 RGLLYDSDEEDEERPAR 17 2 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR 253.18 4.14E-27 6136860000 1330830 1269740 959493 1005901 1116280 1238560 1005048 1057970 1166810 1120360 TRUE FALSE 1278819.692 1233528.258 1132894.729 1057815.671 1152186.16 1263604.532 1017348.078 1036122.55 1034358.62 1044477.019 1.224363647 1.18100086 1.084652614 1.012770651 1.103122557 1.209796394 0.974026292 0.992001289 0.990312473 1 19.99434932 8 0.234346628 0.97873384 2.389212799 0.526373067 0.063934684 41.8320187 0.553497964 0.097234545 22.78480835 100000000 -8 1.410478958 GSNMDFREPTEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GSNMDFREPTEEER 14 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 140.03 9.17E-06 2996500000 2881600 3504900 1552430 1835330 2482660 3083100 1705830 1737940 1931050 1587920 FALSE TRUE 2768983.886 3404943.684 1832988.635 1930051.601 2562517.014 3145442.394 1726706.458 1702050.932 1711845.3 1480368.764 1.870469003 2.300064529 1.238197319 1.303764068 1.73099911 2.124769497 1.166402926 1.149747936 1.156364104 1 20.49752517 8 0.122127519 0.707772192 4.912811781 0.408581501 0.337849956 92.6669519 0.774587872 2.289784785 66.51048174 100000000 -8 4.205039588 ERDQDDHIDWLLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ERDQDDHIDWLLEK 14 1 P49754-2;P49754-3;P49754 P49754-2 VPS41 Vacuolar protein sorting-associated protein 41 homolog 0 ; 78.373 0.013254 102108000 191264 201986 170635 194722 207572 221000 216699 202055 271070 264300 FALSE TRUE 183789.1914 196225.557 201472.5403 204771.6258 214248.7419 225468.7714 219351.0272 197882.4936 240299.27 246398.7256 0.74590155 0.796374074 0.817668759 0.831057974 0.869520495 0.915056565 0.890227929 0.80309869 0.975245588 1 17.91063527 8 0.071785544 1.145654737 0.163597124 0.714456065 0.041272849 149.1241904 0.788087501 1.831705824 14.73657603 100000000 -8 -0.982057612 LCPGGQLPFLLYGTEVHTDTNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LCPGGQLPFLLYGTEVHTDTNK 22 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 276.26 1.83E-45 970380000 712130 676110 698670 808830 787210 730280 786790 861090 1005530 1017180 FALSE TRUE 684299.1723 656828.0048 824935.2108 850573.8132 812531.3246 745046.762 796418.9714 843308.1906 891386.4499 948285.4926 0.721617253 0.692647952 0.869922842 0.896959639 0.856842513 0.785677697 0.839851477 0.889297788 0.939997983 1 19.85496194 8 0.107366537 1.061609601 0.062206939 0.664639532 0.051883857 77.64616702 0.583637793 0.561188878 11.48238483 100000000 -8 -0.999402662 ADFCIIHYAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 ADFCIIHYAGK 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ; 149.31 3.44E-05 6571900000 10286400 10674700 9192100 10529600 10604800 10230300 11741300 11175000 12298700 12743700 FALSE TRUE 9884396.116 10370268.01 10853316.95 11073033.92 10945913.02 10437163.68 11884993.54 10944232.34 10902603.14 11880557.85 0.831980808 0.872877195 0.913535971 0.932029797 0.921329887 0.878507879 1.000373357 0.921188423 0.917684445 1 23.50209924 8 0.289052883 0.957717187 1.39E-11 0.556319789 0.033126635 40.8578895 0.581355368 0.034204819 19.97687601 100000000 -8 -0.957717187 LLEVEHPAAK ddPTM_BT-474_Pertuzumab_2h_R1 5 LLEVEHPAAK 10 0 P17987;E7ERF2;F5H136;F5GZI8;F5H676;F5H726 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;; 143.96 3.31E-05 4495320000 5848870 6080040 5207850 5747390 5861880 6282430 6275990 6486300 7287190 7484150 FALSE TRUE 5620289.694 5906643.212 6149024.343 6044013.487 6050432.694 6409465.039 6352797.443 6352355.638 6459978.742 6977241.854 0.805517397 0.846558473 0.881297291 0.866246808 0.867166829 0.918624461 0.910502685 0.910439364 0.925864242 1 22.73422541 8 0.064235957 1.144695292 0.334468718 0.91609925 0.014519181 79.91774493 0.381427194 0.914122064 5.957917201 100000000 -8 -0.810226574 TRDDGDEEGLLT(ph)HS(ph)EEELEHSQDTDADDGALQ ddPTM_BT-474_Pertuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 2 TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ 177.41 3.19E-18 2425400000 499260 585570 572540 725240 559600 786860 745120 475620 824260 879240 TRUE FALSE 479748.3672 568870.1169 676010.7141 762669.7233 577600.0422 802770.8483 754239.0015 465798.2808 730693.4604 819688.2917 0.585281469 0.69400786 0.824716811 0.930438718 0.704658159 0.979361126 0.92015344 0.568262699 0.891428446 1 19.64471587 8 0.049871958 1.228416935 1.60E-13 0.241290755 0.132602882 991.1329575 3.729701307 21.65953885 93.78956185 100000000 -8 -1.228416935 VNIKPQVDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VNIKPQVDR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 110.38 0.0020941 5294200000 5751700 6103500 5317200 6032000 6026900 5813100 6667100 6709600 7348000 7687400 FALSE TRUE 5526917.205 5929434.156 6278136.32 6343312.243 6220760.712 5930644.865 6748693.964 6571044.415 6513885.845 7166725.551 0.771191413 0.827356108 0.876011824 0.885106064 0.868005991 0.827525042 0.94167049 0.916882385 0.908906836 1 22.77288268 8 0.085132473 1.090695903 0.295048775 0.762378643 0.030008947 85.19894374 0.524563943 0.686386057 7.938004249 100000000 -8 -0.795647129 STFS(ph)TNYR ddPTM_BT-474_Pertuzumab_2h_R1 1 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 ST(0.014)FS(0.957)T(0.028)NYR 121.5 0.0015005 236030000 263850 219360 153020 123850 156390 133360 97832 127270 116180 95691 TRUE FALSE 253538.4503 213104.0676 180674.1179 130241.9133 161420.4264 136056.6306 99029.29728 124641.83 102991.7335 89209.76334 2.842048233 2.388797589 2.02527292 1.459951338 1.809447984 1.525131617 1.110072413 1.397177006 1.154489482 1 16.44491399 8 0.294549745 1.068599339 16.408868 0.927554161 0.152347174 12.43908154 0.17749061 0.156020537 99.9059439 100000000 -8 15.34026866 up S(ph)PHEAGFCVYLK ddPTM_BT-474_Pertuzumab_2h_R1 8 SPHEAGFCVYLK 12 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK 161.04 4.08E-05 8611846400 4632059.6 4228303.3 4557458.3 5327109.4 4601700.7 4411984.9 5553733.9 5455012.9 6027109.6 6379087.4 TRUE FALSE 4451033.59 4107716.23 5381092.395 5602042.155 4749718.582 4501198.258 5621702.157 5342364.977 5342937.386 5947026.128 0.748446954 0.690717703 0.904837524 0.941990506 0.798671215 0.756882206 0.945296361 0.898325459 0.89842171 1 22.50373698 8 0.118104098 1.038633784 0.114357962 0.462530478 0.071087065 93.56958652 0.761075557 0.53700804 14.21167479 100000000 -8 -0.924275822 RPS(ph)T(ph)SSASGQWSPTPEWVLSWK ddPTM_BT-474_Pertuzumab_2h_R1 2 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 2 RPS(0.746)T(0.481)S(0.256)S(0.448)AS(0.069)GQWSPTPEWVLSWK;RPS(0.499)T(0.499)S(0.492)S(0.426)AS(0.077)GQWS(0.005)PT(0.001)PEWVLSWK 116.34 0.00014405 658450000 333445 331238 231146 265956 302773 237768 241791 296709 282687 240883 TRUE FALSE 320413.6008 321791.4166 272919.224 279682.021 312511.9685 242575.8319 244750.1106 290581.8555 250597.5569 224567.7799 1.426801302 1.432936714 1.215308911 1.245423637 1.391615345 1.08018983 1.08987189 1.293960584 1.11591056 1 17.77679142 8 0.136812592 0.977765981 2.542124827 0.606681703 0.092718123 57.14081781 0.523005027 0.433595222 17.42056612 100000000 -8 1.564358846 YGLQDS(ph)DEEEEEHPSK ddPTM_BT-474_Pertuzumab_2h_R1 6 YGLQDSDEEEEEHPSK 16 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK 277.14 1.64E-35 5028350000 2870320 2987850 2670530 2991860 2959850 2963360 3194510 3203290 3771390 3785540 TRUE FALSE 2758144.721 2902639.443 3153154.177 3146270.253 3055056.263 3023281.17 3233605.369 3137140.942 3343277.618 3529142.004 0.781534072 0.822477373 0.893461973 0.891511379 0.865665439 0.856661808 0.91625822 0.888924543 0.947334399 1 21.75088605 8 0.054303256 1.207754808 0.250915635 0.794292705 0.026442019 196.6143781 0.802049307 3.11642586 15.32444613 100000000 -8 -0.956839173 LEYDDLRR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEYDDLRR 8 1 P15924 P15924 DSP Desmoplakin 0 ;;; 183.65 0.00035626 3889660000 4543670 4568680 3453550 3600530 3666220 3955890 3506080 3984050 3679560 3312750 FALSE TRUE 4366098.353 4438385.72 4077683.309 3786353.785 3784147.296 4035880.806 3548988.456 3901777.975 3261871.775 3088374.492 1.413720507 1.43712679 1.320333178 1.226002156 1.225287706 1.30679774 1.149144466 1.263375923 1.05617754 1 21.55841627 8 0.093175949 0.830477629 2.54100589 0.80049756 0.060017962 63.13394192 0.420600659 0.965461581 13.79961607 100000000 -8 1.71052826 SLS(ph)MVDLQDAR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLSMVDLQDAR 11 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 SLS(1)MVDLQDAR;SLS(1)MVDLQDAR;SLS(1)MVDLQDAR;SLS(1)MVDLQDAR 247.69 4.05E-16 1147350000 2531160 2330370 1556970 1792030 1830770 1584940 1351980 2011800 1590770 1457370 TRUE FALSE 2432239.469 2263910.129 1838349.114 1884516.883 1889658.38 1616988.573 1368525.936 1970255.627 1410192.459 1358661.032 1.790173864 1.666280313 1.353059424 1.387039769 1.390824006 1.190133915 1.007260754 1.450145092 1.037928097 1 20.37375414 8 0.285951906 1.099794052 6.768117537 0.742984404 0.130697199 27.68795828 0.39320672 0.142425333 78.97517838 100000000 -8 5.668323485 GYYSPYSVSGSGS(ph)TAGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYSVSGSGS(0.482)T(0.482)AGS(0.035)R 298.93 1.98E-49 517710000 533640 520360 317680 369740 401740 374590 265110 475090 324930 327670 TRUE FALSE 512784.7588 505519.8423 375091.8428 388822.3257 414662.332 382164.4665 268354.4955 465279.2255 288045.3086 305476.619 1.678638321 1.654856086 1.227890514 1.272838252 1.357427397 1.251043264 0.87847802 1.523125491 0.942937334 1 18.22070244 8 0.3542564 1.125313028 8.57186133 0.522616148 0.185570216 51.9670788 0.731165267 0.148912113 259.4552265 100000000 -8 7.446548301 FS(ph)PVTPK ddPTM_BT-474_Pertuzumab_2h_R1 5 FSPVTPK 7 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(0.999)PVT(0.001)PK;FS(1)PVTPK;FS(0.999)PVT(0.001)PK;FS(1)PVTPK;FS(1)PVTPK 152.06 0.0019292 3084150000 7928010 7665360 7915130 8304890 8116700 8313730 8839450 9844220 10127210 10587800 TRUE FALSE 7618174.604 7446751.438 9345570.062 8733506.368 8377781.027 8481839.317 8947629.833 9640933.417 8977611.578 9870678.875 0.771798445 0.754431537 0.946801145 0.884792878 0.848754289 0.85929645 0.906485759 0.976724452 0.909523214 1 23.23471788 8 0.165951031 1.006302334 0.069546236 0.617180495 0.047262808 41.48917905 0.440023704 0.133877582 9.601241985 100000000 -8 -0.936756097 DAS(ph)PINRWS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 DASPINRWSPTR 12 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 DAS(1)PINRWS(0.99)PT(0.01)R;DAS(1)PINRWS(0.655)PT(0.345)R 109.14 0.019489 398810000 676770 673960 613360 669410 670520 735750 696570 764360 848890 826120 TRUE FALSE 650321.0802 654739.3207 724207.7961 703958.3303 692087.8848 750627.3691 705094.832 748575.6989 752527.566 770166.1566 0.844390622 0.850127359 0.940326694 0.91403436 0.898621523 0.974630426 0.915510018 0.971966494 0.977097682 1 19.5548102 8 0.189465973 1.003436081 0.267358208 0.762518966 0.024905018 24.93876499 0.290540857 0.04903976 5.369774 100000000 -8 -0.736077873 T(ph)SPSGGTWSSVVSGVPR ddPTM_BT-474_Pertuzumab_2h_R1 1 TSPSGGTWSSVVSGVPR 17 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4 Q99700 ATXN2 Ataxin-2 1 T(0.846)S(0.151)PS(0.002)GGTWSSVVSGVPR 316.8 2.84E-57 900870000 806170 749580 815230 892430 736040 873470 890600 996830 1013900 1116900 TRUE FALSE 774663.9851 728202.7123 962560.1957 938488.4192 759715.3951 891132.1619 901499.4292 976245.1122 898806.3226 1041251.368 0.743974038 0.699353427 0.924426344 0.901308222 0.729617668 0.855828083 0.865784629 0.937569104 0.863198215 1 19.98988696 8 0.086676687 1.107379323 0.122168982 0.482786284 0.067149959 148.0689518 0.926184503 1.441914526 17.37527238 100000000 -8 -0.985210341 TNNVSEHEDTDKYR ddPTM_BT-474_Pertuzumab_2h_R1 6 TNNVSEHEDTDKYR 14 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;;;; 234.67 1.94E-17 6072005000 2918326 3166695 2695159 2890188 3044381 3206674 3461423 3350894 3913373 3890120 FALSE TRUE 2804274.594 3076383.959 3182234.185 3039350.949 3142306.28 3271515.145 3503784.93 3281696.868 3469143.303 3626638.707 0.773243441 0.848274175 0.877461044 0.838062789 0.866451426 0.902079145 0.966124616 0.904886627 0.956572624 1 21.7902016 8 0.125038027 1.04231747 0.227804501 0.838616565 0.025837804 33.83204148 0.288235031 0.155706295 4.832307752 100000000 -8 -0.81451297 AGYTDKVVIGMDVAASEFFR ddPTM_BT-474_Pertuzumab_2h_R1 4 AGYTDKVVIGMDVAASEFFR 20 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 148.89 9.60E-08 1226636500 2894380 2863637 1740741.8 1950028.6 2224789.2 2501814.1 1895070.9 1864048.2 2536830.7 2117132.3 FALSE TRUE 2781264.43 2781968.877 2055332.566 2050669.81 2296351.565 2552402.495 1918263.345 1825554.953 2248860.314 1973737.044 1.409136257 1.409493167 1.041340625 1.038978225 1.163453649 1.293182647 0.971894078 0.924923084 1.139392059 1 20.91249836 8 0.429430212 1.025973652 9.71359795 0.519118853 0.11668337 64.4559966 0.811895235 0.079669186 484.1867092 100000000 -8 8.687624298 ALPQT(ph)PRPR ddPTM_BT-474_Pertuzumab_2h_R1 7 ALPQTPRPR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR 120.96 0.0010142 65773810000 6073050 5979330 3961444 4883407 4712722 4709708 4156909 5413490 4326659 3886248 TRUE FALSE 5835708.492 5808805.363 4677365.053 5135440.22 4864310.983 4804941.523 4207782.496 5301699.54 3835514.809 3623028.961 1.610726426 1.603300836 1.291009568 1.417443878 1.342608915 1.326222223 1.161399078 1.463333469 1.058648675 1 21.78876491 8 0.093276839 0.799139723 3.024153598 0.675851793 0.112653441 91.18435057 0.608042545 1.811025153 25.95339075 100000000 -8 2.225013874 SLKQPLEQNQTIS(ph)PLSTYEESK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLKQPLEQNQTISPLSTYEESK 22 1 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 SLKQPLEQNQT(0.003)IS(0.973)PLS(0.021)T(0.003)YEESK 135.35 3.74E-06 137250000 168470 150310 91952 116060 128060 118650 104530 115190 98625 84101 TRUE FALSE 161886.0061 146023.306 108569.7719 122049.8705 132179.1662 121049.1843 105809.2694 112811.2862 87429.50347 78404.76436 2.064747053 1.862428988 1.384734368 1.556663954 1.685856303 1.543900875 1.349526018 1.43883203 1.115104473 1 16.2586537 8 0.117208066 0.794831556 4.411798153 0.777460521 0.14369053 48.60718403 0.392902584 1.105318403 28.6444156 100000000 -8 3.616966597 up VTNEFVHINNLK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTNEFVHINNLK 12 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 131.69 0.00019422 600040000 612760 664800 546250 654080 676540 745380 683440 723070 902980 873980 FALSE TRUE 588812.6618 645840.5549 644969.5263 687837.1472 698301.5235 760452.0943 691804.1432 708138.3518 800477.496 814784.5561 0.722660558 0.792651935 0.791582905 0.844195121 0.857038242 0.933316775 0.849063888 0.869111161 0.982440683 1 19.63605911 8 0.129263929 1.03967672 0.024609671 0.831927925 0.033888618 35.21423967 0.308124551 0.191000539 6.514679053 100000000 -8 -1.015067049 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEK ddPTM_BT-474_Pertuzumab_2h_R1 6 REESPMDVDQPSPSAQDTQSIASDGTPQGEK 31 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 REESPMDVDQPS(0.996)PS(0.004)AQDTQSIASDGTPQGEK;REESPMDVDQPS(0.955)PS(0.045)AQDTQSIASDGTPQGEK;REESPMDVDQPS(0.996)PS(0.004)AQDTQSIASDGTPQGEK;REESPMDVDQPS(0.861)PS(0.139)AQDTQSIASDGTPQGEK;REESPMDVDQPS(0.852)PS(0.147)AQDT(0.001)QSIASDGTPQGEK;REESPMDVDQPS(0.969)PS(0.031)AQDTQSIASDGTPQGEK 215.71 5.34E-35 4968920000 3065388 3001829 2848351 2998554 3041071 3228694 3332104 3483707 3929539 3871608 TRUE FALSE 2945589.248 2916219.776 3363111.387 3153309.731 3138889.811 3293980.405 3372883.285 3411767.233 3483474.207 3609380.542 0.816092738 0.807955754 0.93176969 0.873642913 0.86964779 0.912616546 0.934477051 0.945250076 0.965116913 1 21.78331983 8 0.13523484 1.033716214 0.266823316 0.799524059 0.026660016 33.11509527 0.300340855 0.125663223 4.881398173 100000000 -8 -0.766892898 ALTVPELTQQVFDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALTVPELTQQVFDAK 15 0 Q5JP53;P07437;Q5ST81 Q5JP53 TUBB Tubulin beta chain 0 ; 188.96 6.45E-07 392440000 286587 276985 244740 278658 292268 273955 296796 298872 366590 351670 FALSE TRUE 275386.8632 269085.659 288969.9622 293039.5728 301669.0657 279494.5578 300428.2782 292700.1888 324976.2401 327851.0777 0.83997547 0.820755756 0.881406169 0.893819154 0.920140534 0.852504618 0.916355927 0.892783976 0.99123127 1 18.32268111 8 0.044696904 1.274959997 0.238330975 0.713483499 0.030071952 329.4489742 1.116415648 6.601825702 24.61855879 100000000 -8 -1.036629022 KRS(ph)VQEGENPDDGVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KRSVQEGENPDDGVR 15 2 H7C5M1;Q5TCT4;A2A2V2;P42696-2;P42696 H7C5M1 RBM34 RNA-binding protein 34 1 KRS(1)VQEGENPDDGVR 74.698 0.026798 482810000 521760 465800 339290 270390 457470 383590 278760 355750 286510 257880 TRUE FALSE 501369.0424 452515.8401 400607.2505 284344.8603 472184.938 391346.4526 282171.5483 348403.6382 253986.5859 240413.5579 2.085444127 1.882239271 1.666325535 1.182732217 1.964052868 1.627805254 1.173692327 1.449184652 1.056456999 1 17.87515873 8 0.131869971 0.808386145 4.903071801 0.623979528 0.229757235 55.25357343 0.491223279 1.16871321 42.2109686 100000000 -8 4.094685657 RDEELVLPINSSLSVTLHQDQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDEELVLPINSSLSVTLHQDQLK 23 1 P53602;H3BP35;H3BQ47 P53602 MVD Diphosphomevalonate decarboxylase 0 ; 263.08 4.76E-44 159804000 93409 98318 84020 100903 98820 102032 101342 105575 129101 124214 FALSE TRUE 89758.47301 95514.0669 99204.28301 106110.6159 101998.635 104095.1569 102582.2537 103394.8394 114445.9957 115800.8751 0.775110489 0.824812997 0.856679908 0.916319637 0.880810572 0.898915115 0.885850419 0.892867513 0.988299921 1 16.82128663 8 0.120823868 1.033397402 0.275357228 0.805198431 0.028318009 44.60455953 0.369605891 0.202244702 5.701102601 100000000 -8 -0.758040173 KEELER ddPTM_BT-474_Pertuzumab_2h_R1 2 KEELER 6 1 Q5C9Z4 Q5C9Z4 NOM1 Nucleolar MIF4G domain-containing protein 1 0 ; 114.19 0.040888 4109700000 5693400 5509400 4890400 5665100 5131400 5599200 5865200 5995200 6449000 6461500 FALSE TRUE 5470895.634 5352277.306 5774204.066 5957476.49 5296456.141 5712419.66 5936980.072 5871397.025 5716936.556 6023856.85 0.908204788 0.888513363 0.95855599 0.988980422 0.879246681 0.948299371 0.985577881 0.974690663 0.949049205 1 22.52225606 8 0.139516112 1.008969144 0.635583547 0.380920582 0.031931273 79.99850252 0.743550662 0.140084195 5.959209883 100000000 -8 -0.373385597 ISFDDQHFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ISFDDQHFEK 10 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 0 ; 145.28 3.07E-05 810350000 2622400 2586900 2325200 2600600 2622400 2864900 2953400 2886000 3323800 3534100 FALSE TRUE 2519913.709 2513124.145 2745415.364 2734817.278 2706751.878 2922830.241 2989544.593 2826403.091 2946496.159 3294732.259 0.764831103 0.76277037 0.833274193 0.830057517 0.821539253 0.887122234 0.907371027 0.857855167 0.89430519 1 21.6517298 8 0.063664031 1.193735134 0.10698005 0.887324511 0.022566222 97.07970509 0.459518941 1.503173195 9.640794451 100000000 -8 -1.086755084 GS(ph)PGGYLGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPGGYLGAK 10 0 O60551 O60551 NMT2 Glycylpeptide N-tetradecanoyltransferase 2 1 GS(1)PGGYLGAK 91.701 0.0084119 0 451800 500890 413990 453160 487940 498330 561100 510780 599900 625230 TRUE FALSE 434143.1565 486605.1076 488807.2022 476547.6419 503635.0332 508406.574 567966.9096 500232.2145 531801.867 582882.6152 0.744820904 0.83482522 0.838603159 0.817570518 0.864041953 0.872228062 0.974410447 0.858204039 0.912365291 1 19.15284585 8 0.102558726 1.059702912 0.216712592 0.749006824 0.035562864 62.02845037 0.44860212 0.405811835 7.369826914 100000000 -8 -0.84299032 LFDTPHT(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFDTPHTPK 9 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 LFDTPHT(1)PK;LFDTPHT(1)PK 148.28 0.00033258 1358080000 3843000 3182300 2642000 1962640 2319770 2207800 2080650 2467800 2166680 1845610 TRUE FALSE 3692811.311 3091543.92 3119468.171 2063932.086 2394387.509 2252443.229 2106113.617 2416839.068 1920727.57 1720605.191 2.146228159 1.79677705 1.81300637 1.199538451 1.391596121 1.309099403 1.224053971 1.404644761 1.116309296 1 20.71448466 8 0.348126342 1.157525034 13.1894531 0.850693782 0.133223957 22.13162714 0.312905755 0.11093068 174.4183156 100000000 -8 12.03192807 up SNEDQSMGNWQIKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNEDQSMGNWQIKR 14 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 236.12 4.74E-17 949500000 746200 829530 432190 426030 642910 802150 586650 601540 651510 556910 FALSE TRUE 717037.679 805872.6166 510296.347 448017.4594 663589.784 818370.0226 593829.5982 589117.9888 577553.3162 519189.9897 1.381069923 1.552172871 0.982870158 0.862916212 1.278125151 1.576243839 1.143761648 1.134686725 1.112412272 1 18.98590304 8 0.051231153 0.637880925 2.270883623 0.139754658 0.211559599 1107.795738 4.27664379 31.48649975 141.7766911 100000000 -8 1.633002698 DVGSLDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVGSLDEK 8 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 121.85 0.0032934 375260000 558380 592920 487510 524720 608620 536920 609140 630860 670800 683490 FALSE TRUE 536557.8923 576010.5021 575613.9016 551800.8621 628196.815 547776.8903 616594.8375 617832.5205 594653.5962 637196.6135 0.842060176 0.903976088 0.903353674 0.865982101 0.985875947 0.859666983 0.967668102 0.96961049 0.933234081 1 19.28137907 8 0.119602666 1.030261491 0.483707086 0.505322869 0.037689684 72.99279196 0.599854777 0.242651573 6.649655027 100000000 -8 -0.546554404 FDSLTDLVEHYK ddPTM_BT-474_Pertuzumab_2h_R1 2 FDSLTDLVEHYK 12 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4;H0YF12 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 203.51 1.24E-07 827710000 1452560 1393700 1417100 1361560 1452070 1469440 1647680 1623350 1856630 1864120 FALSE TRUE 1395792.349 1353953.041 1673201.493 1431830.275 1498777.15 1499153.084 1667844.801 1589827.255 1645873.146 1737861.492 0.803166625 0.779091456 0.962793353 0.823903563 0.862426124 0.862642443 0.959711006 0.914818162 0.94706808 1 20.72888167 8 0.101863801 1.069257692 0.279192416 0.580344843 0.046635441 86.42752901 0.621470912 0.535434689 9.555794757 100000000 -8 -0.790065276 SEEITTGSAWFSFLESHNK ddPTM_BT-474_Pertuzumab_2h_R1 2 SEEITTGSAWFSFLESHNK 19 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 304.9 2.61E-50 391020000 648110 648070 604850 668520 709000 674070 758980 748010 887180 903370 FALSE TRUE 622781.1447 629587.6781 714159.8498 703022.3973 731805.6289 687700.1572 768268.6243 732563.3321 786471.0458 842183.9453 0.739483516 0.747565519 0.84798559 0.834761101 0.868937995 0.816567641 0.912233757 0.869837684 0.933847113 1 19.68377585 8 0.100782662 1.078651923 0.096701633 0.850277291 0.029394482 45.13230328 0.321604429 0.353151822 6.13336716 100000000 -8 -0.98195029 EEFTAFLHPEEYDYMK ddPTM_BT-474_Pertuzumab_2h_R1 10 EEFTAFLHPEEYDYMK 16 0 O43852;O43852-3;O43852-15;O43852-6;H0Y875;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;;;;;; 217.37 1.43E-14 5606414000 6085890 6612770 5882620 6666460 6321530 6657200 7338290 7078470 8720950 8496450 FALSE TRUE 5848046.69 6424180.274 6945740.292 7010516.8 6524867.754 6791813.145 7428098.188 6932297.121 7730984.317 7920977.874 0.738298577 0.811033736 0.876879143 0.885056986 0.823745232 0.857446297 0.937775399 0.875181983 0.976013876 1 22.91724712 8 0.107513958 1.062989238 0.192504528 0.755876733 0.036805307 58.51166165 0.440316411 0.367554454 7.547718967 100000000 -8 -0.87048471 TTIPEEEEEEEEAAGVVVEEELFHQQGT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 1 TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR 249.81 8.11E-46 667047000 195124 202089 142511 171822 172121 174075 172240 175391 184244 171005 TRUE FALSE 187498.3384 196325.6196 168265.9078 180689.754 177657.4283 177594.9158 174347.9246 171769.1146 163329.3935 159422.679 1.176108315 1.231478613 1.055470331 1.133400562 1.114379895 1.113987777 1.093620592 1.077444662 1.024505387 1 17.28249735 8 0.107847948 0.943009137 1.695911875 0.662307284 0.038011789 66.40798429 0.501037174 0.359063012 7.433972633 100000000 -8 0.752902738 EYIPGQPPLSQS(ph)SDSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLSQS(0.71)S(0.29)DS(0.29)S(0.71)PTR 190.25 1.79E-14 946670000 289820 306630 263820 309170 306170 336980 322170 329440 400740 400520 TRUE FALSE 278493.514 297885.2126 311498.1426 325126.3008 316018.2361 343793.9665 326112.8128 322636.9489 355249.6752 373392.4237 0.745846719 0.797780549 0.834237984 0.870736202 0.846343461 0.920730965 0.873378227 0.86406935 0.951411043 1 18.51033313 8 0.107243898 1.050897422 0.196963676 0.844745583 0.027472981 47.1011931 0.353703675 0.291393177 5.944214312 100000000 -8 -0.853933746 DQDSSDDERALEDWVS(ph)SETSALPRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.001)S(0.004)DDERALEDWVS(0.249)S(0.249)ET(0.249)S(0.249)ALPRPR 91.615 0.0077547 56908000 44875 46905 27715 29680 35966 40149 26975 30665 34497 27795 TRUE FALSE 43121.23539 45567.31532 32723.71702 31211.78836 37122.87905 40960.84029 27305.12812 30031.75703 30581.04518 25912.41989 1.664114566 1.75851254 1.262858396 1.204510751 1.432628801 1.580741608 1.053746745 1.158971534 1.180169406 1 14.66135613 8 0.183739522 0.985287785 4.166132029 0.586180038 0.160928787 40.42650934 0.461168751 0.36515803 36.15916197 100000000 -8 3.180844244 STPLASPSPSPGRS(ph)PQR ddPTM_BT-474_Pertuzumab_2h_R1 4 STPLASPSPSPGRSPQR 17 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 STPLASPSPSPGRS(1)PQR;STPLASPSPSPGRS(1)PQR;STPLASPSPSPGRS(1)PQR;STPLASPSPSPGRS(1)PQR 246.67 6.80E-21 4054650000 2089680 2167350 1200200 1564950 1802190 1518180 1468620 1577850 1431540 1330590 TRUE FALSE 2008012.995 2105539.3 1417102.838 1645717.257 1860159.078 1548878.64 1486593.411 1545266.846 1269037.581 1240467.954 1.618754429 1.697375005 1.14239375 1.326690667 1.49956238 1.248624468 1.198413394 1.24571283 1.02303133 1 20.24245303 8 0.159394279 0.948625291 3.609343461 0.646825163 0.133879998 41.07628562 0.422807971 0.405174006 25.66922296 100000000 -8 2.66071817 GGCVS(ph)PERGPTFNPK ddPTM_BT-474_Pertuzumab_2h_R1 2 GGCVSPERGPTFNPK 15 1 Q9ULD5 Q9ULD5 ZNF777 Zinc finger protein 777 1 GGCVS(1)PERGPTFNPK;GGCVS(1)PERGPTFNPK 128.26 4.43E-05 844420000 510240 426290 371310 378760 392130 383620 393860 421930 367730 362790 TRUE FALSE 490299.2567 414132.6266 438413.9767 398307.849 404743.2176 391377.0592 398680.1765 413216.9981 325986.832 338217.9102 1.449654918 1.224455046 1.296247075 1.177666342 1.196693627 1.157174258 1.178767193 1.221747831 0.963836693 1 18.36759353 8 0.131164407 0.949827264 2.350267524 0.700662097 0.071217994 49.63128258 0.439359749 0.362330944 12.88620225 100000000 -8 1.40044026 S(ph)PYCKR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPYCKR 6 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 S(0.996)PY(0.004)CKR;S(0.958)PY(0.042)CKR;S(0.998)PY(0.002)CKR 82.671 0.03591 347078000 687010 656000 382250 532870 456960 443050 453640 494360 416180 441530 TRUE FALSE 660160.8897 637291.5223 451331.0781 560371.4846 471658.5334 452008.7746 459191.782 484151.2932 368936.9912 411624.7798 1.603792876 1.548234104 1.096462361 1.361364796 1.14584582 1.098108755 1.115559132 1.176195693 0.896294415 1 18.65097031 8 0.332492237 1.028240409 7.559097783 0.747154612 0.109492481 28.08036721 0.400633432 0.093365789 112.9519666 100000000 -8 6.530857373 DLEIERPMPGTHTVTLQCPALLVVGDSSPAVDAVVECNSK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLEIERPMPGTHTVTLQCPALLVVGDSSPAVDAVVECNSK 40 1 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ;;; 373.03 1.82E-162 2077000000 1296812 1198274 774220 807626 913821 903999 681966 797756 863948 472979 FALSE TRUE 1246131.153 1164100.399 914138.7764 849307.6746 943214.8824 922278.4792 690312.1039 781282.0598 765876.245 440943.711 2.826054941 2.640020414 2.073141659 1.926113591 2.139082288 2.091601391 1.565533393 1.771840805 1.736902525 1 18.75023497 8 0.113790306 0.690866449 7.042783383 0.866237529 0.180485867 36.53135367 0.288188252 1.530447404 36.58105515 100000000 -8 6.351916934 MSSCVPRPPS(ph)HGGPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 MSSCVPRPPSHGGPTR 16 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 MSSCVPRPPS(1)HGGPTR 65.184 0.035165 234330000 220580 187390 124300 108720 141590 135210 122740 68406 161050 98325 TRUE FALSE 211959.4897 182045.8207 146763.775 114331.0522 146144.3709 137944.0388 124242.1288 66993.3922 142768.2792 91665.36017 2.312318299 1.985982713 1.601082184 1.247265619 1.594324952 1.504865508 1.355387996 0.730847422 1.557494335 1 16.48408903 8 0.318035414 1.069546853 13.35414752 0.693632168 0.237662444 30.89064815 0.442443191 0.231972532 220.2029513 100000000 -8 12.28460067 GAQPGRHS(ph)VTGYGDCAVGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAQPGRHSVTGYGDCAVGAR 20 1 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 GAQPGRHS(0.981)VT(0.019)GYGDCAVGAR;GAQPGRHS(0.999)VT(0.001)GYGDCAVGAR 202.2 7.15E-22 497350000 391730 359910 210034 241510 262050 258420 167031 300450 216985 200613 TRUE FALSE 376420.7585 349645.7192 247991.816 253974.36 270479.0762 263645.4295 169075.1753 294245.6025 192353.7725 187025.3028 2.0126729 1.869510242 1.325980026 1.357967912 1.446216486 1.409677864 0.904023 1.573293015 1.028490635 1 17.51287394 8 0.40933877 1.189420496 16.6567794 0.653159384 0.202202261 46.2665651 0.605282593 0.133233145 581.1923959 100000000 -8 15.4673589 SNSLSEQLAINTS(ph)PDAVK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 SNSLSEQLAINT(0.191)S(0.809)PDAVK;SNSLSEQLAINT(0.001)S(0.999)PDAVK 250.38 1.06E-22 88755000 265955 244939 231212 240973 248330 280922 239197 298089 287702 302059 TRUE FALSE 255561.1846 237953.5795 272997.1517 253409.6454 256317.76 286602.4353 242124.3644 291933.358 255043.2751 281600.2749 0.90753173 0.845004784 0.969449166 0.899891328 0.91021843 1.017763336 0.859815796 1.036694151 0.905692564 1 18.10328922 8 0.139934255 1.012872332 0.542635066 0.205178064 0.056254469 99.67605116 0.928616334 0.218680425 9.384656022 100000000 -8 -0.470237266 DVHVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVHVVK 6 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 69.432 0.093518 279710000 332450 323990 303300 368010 366880 358600 358520 345720 453650 450400 FALSE TRUE 319457.4865 314750.1224 358113.0569 387003.0402 378681.0284 365851.1377 362907.675 338580.7612 402153.5539 419894.0068 0.760805063 0.749594225 0.852865369 0.921668407 0.901849091 0.871294021 0.864284008 0.806348163 0.957750164 1 18.67966567 8 0.052744263 1.211951174 0.189751615 0.559964277 0.050981657 415.400168 1.648521285 7.212827392 33.91918505 100000000 -8 -1.022199559 SIVEGIIEEEEEDEEGSESISK ddPTM_BT-474_Pertuzumab_2h_R1 2 SIVEGIIEEEEEDEEGSESISK 22 0 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ; 194.18 4.53E-18 50459000 45133 49630 42264 48877 50312 53589 51831 54608 65196 66098 FALSE TRUE 43369.15246 48214.60099 49902.04496 51399.54783 51930.33117 54672.6063 52465.32328 53480.32572 57795.2234 61621.12359 0.703803338 0.782436252 0.809820433 0.834122211 0.84273587 0.887238062 0.851417829 0.867889493 0.937912522 1 15.91113737 8 0.104271583 1.070007862 0.070711272 0.910340663 0.023148361 35.56966259 0.260872245 0.268963526 5.097977744 100000000 -8 -0.99929659 PQYQTWEEFSR ddPTM_BT-474_Pertuzumab_2h_R1 4 PQYQTWEEFSR 11 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 ;;; 210.64 2.81E-08 2930698000 554453 478574 471205 400998 469674 451706 437881 479556 499012 455172 FALSE TRUE 532784.3638 464925.5381 556362.2254 421693.5548 484781.4908 460839.8048 443239.9187 469653.001 442366.2498 424342.795 1.255551809 1.095636696 1.311115051 0.993756839 1.142428943 1.086008317 1.044532684 1.106777366 1.042473809 1 18.69487066 8 0.193426676 1.008299955 2.034113337 0.427040318 0.074890344 51.43150151 0.607568271 0.135130987 15.85107099 100000000 -8 1.025813382 SSS(ph)LIQLTSQNSSPNQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLIQLTSQNSSPNQQR 18 0 O95639;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 SSS(1)LIQLTSQNSSPNQQR 505.22 5.82E-267 518040000 313250 259120 165150 203710 267220 197220 176180 293540 213900 179920 TRUE FALSE 301007.8437 251730.1513 194996.2787 214223.4975 275815.374 201207.9235 178336.1435 287478.2964 189618.9687 167733.8581 1.794556251 1.500771246 1.162533796 1.277163119 1.644363142 1.199566538 1.063208976 1.713895451 1.130475211 1 17.35581441 8 0.033443859 1.22E-11 3.43855799 0.28157438 0.23296402 1838.409822 4.702590114 146.2093805 392.7843596 100000000 -8 3.43855799 SQICDNAALYAQKYDEEFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 SQICDNAALYAQKYDEEFQR 20 1 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ; 144.95 1.37E-07 457230000 405770 452330 241420 248640 312750 429030 256580 256840 307710 273690 FALSE TRUE 389912.0598 439429.9913 285049.9644 261472.3402 322809.8878 437705.2806 259720.1028 251536.1642 272780.0508 255152.7325 1.528151613 1.72222334 1.117173865 1.02476794 1.265163358 1.715463817 1.017900534 0.985825869 1.06908536 1 17.96100157 8 0.223580726 0.984880107 4.389127815 0.345496352 0.229425865 58.82490932 0.759387713 0.371369175 72.68382167 100000000 -8 3.404247708 ASS(ph)KGGGGYTCQSGSGWDEFTK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASSKGGGGYTCQSGSGWDEFTK 22 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 AS(0.157)S(0.838)KGGGGYT(0.005)CQSGSGWDEFTK;AS(0.126)S(0.865)KGGGGYT(0.009)CQSGSGWDEFTK;AS(0.222)S(0.777)KGGGGYT(0.001)CQSGSGWDEFTK;AS(0.004)S(0.994)KGGGGYT(0.002)CQSGSGWDEFTK 273.32 1.37E-45 3275330000 2904230 2452700 2003530 1246840 1717930 1897050 1368130 1070580 1595530 1115630 TRUE FALSE 2790729.481 2382751.397 2365612.439 1311189.562 1773188.779 1935409.651 1384873.584 1048472.149 1414412.123 1040067.386 2.683219873 2.290958671 2.274479971 1.260677509 1.704878743 1.860850245 1.33152294 1.008080979 1.359923541 1 19.98824557 8 0.23826368 0.960813467 11.64770214 0.805218299 0.244933407 20.70885909 0.2762317 0.349199397 87.35558321 100000000 -8 10.68688868 up RSTAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSTAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 38 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 RSTAPSAAASASASAAAS(0.008)S(0.992)PAGGGAEALELLEHCGVCR 110.44 5.74E-06 205700000 66550 71478 33348 41186 40325 67013 37974 30550 32968 33249 TRUE FALSE 63949.15243 69439.51742 39374.72542 43311.6144 41622.09025 68368.04877 38438.73717 29919.13182 29225.61085 30997.01561 2.063074498 2.240200098 1.270274723 1.397283369 1.342777342 2.205633266 1.240078647 0.965226207 0.942852409 1 14.9198417 8 0.180388214 0.828143557 6.5115244 0.488260959 0.34706389 49.34612904 0.555733734 0.825515761 77.02375938 100000000 -8 5.683380843 S(ph)SELEGDTITLKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSELEGDTITLKPR 14 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 S(0.97)S(0.03)ELEGDTITLKPR 140.68 5.98E-06 136600000 166040 157600 149560 175100 159870 157700 163910 173270 201750 192880 TRUE FALSE 159550.9732 153105.4023 176588.8189 184136.932 165012.3637 160888.802 165915.9796 169691.9139 178848.1858 179816.0658 0.88730099 0.851455634 0.982052511 1.024029367 0.917673084 0.894740975 0.922698308 0.943697179 0.994617389 1 17.4561624 8 0.067117606 1.065412221 0.652602757 0.249200468 0.046545933 478.9673179 2.380351544 2.665041542 18.83101866 100000000 -8 -0.412809464 LPEDPLLSGLLDSPALK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPEDPLLSGLLDSPALK 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 216.84 1.20E-14 89235000 165361 164311 156673 166864 164050 183940 196544 193265 222020 226410 FALSE TRUE 158898.5093 159625.0112 184987.2963 175475.871 169326.8172 187659.3928 198949.3643 189274.0102 196817.2204 211075.049 0.752805744 0.756247656 0.876405322 0.831343505 0.802211431 0.889064784 0.942552733 0.896714278 0.932451378 1 17.68739652 8 0.123126768 1.05294534 0.058281188 0.820337183 0.032806585 36.43497067 0.306571786 0.21009846 6.243620409 100000000 -8 -0.994664152 DAGRPGERGS(ph)GGLFSPSTAHVPDGALGQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAGRPGERGSGGLFSPSTAHVPDGALGQR 29 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAGRPGERGS(0.948)GGLFS(0.052)PSTAHVPDGALGQR;DAGRPGERGS(0.913)GGLFS(0.084)PS(0.003)T(0.001)AHVPDGALGQR 152.23 1.48E-08 2135300000 388870 463830 261150 277970 336360 401990 290810 294380 331760 301510 TRUE FALSE 373672.5305 450602.0225 308345.6143 292316.065 347179.3249 410118.5132 294369.0198 288300.9501 294099.9957 281088.4591 1.329376993 1.603061271 1.096970026 1.039943319 1.235124793 1.459037182 1.047246908 1.02565915 1.046289828 1 18.1006647 8 0.182108253 0.958314242 3.053023703 0.36026301 0.159915817 60.76804902 0.688928905 0.367834921 35.3868335 100000000 -8 2.09470946 GLSQNQQIPQNSVT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLSQNQQIPQNSVTPR 16 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 GLSQNQQIPQNSVT(1)PR;GLSQNQQIPQNSVT(1)PR 281.65 1.76E-34 242490000 305030 241887 194546 210008 182191 147899 162192 265630 122925 157730 TRUE FALSE 293109.0904 234988.6196 229704.7899 220846.538 188051.339 150889.6191 164176.9542 260144.6477 108971.0693 147046.8066 1.993304698 1.598053198 1.56212022 1.501879185 1.278853607 1.026133261 1.116494523 1.769128169 0.741063828 1 17.16591593 8 0.346615205 1.159831107 10.54007789 0.532545848 0.253628653 56.0026219 0.792650126 0.223149789 342.0885759 100000000 -8 9.38024678 EEDEENDNDNES(ph)DHDEADS ddPTM_BT-474_Pertuzumab_2h_R1 5 EEDEENDNDNESDHDEADS 19 0 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 EEDEENDNDNES(1)DHDEADS;EEDEENDNDNES(1)DHDEADS;EEDEENDNDNES(0.998)DHDEADS(0.002);EEDEENDNDNES(1)DHDEADS;EEDEENDNDNES(1)DHDEADS 275.96 1.96E-39 369896000 611850 623149 552194 627790 622754 684295 677367 674759 801690 774514 TRUE FALSE 587938.2256 605377.4006 651987.7393 660190.3171 642785.448 698131.9137 685656.82 660824.9909 710685.5122 722055.4769 0.814256306 0.838408433 0.902960728 0.914320767 0.890216152 0.966867417 0.949590221 0.915199748 0.984253336 1 19.46175016 8 0.228726676 0.985368002 1.87E-09 0.836474102 0.023094149 20.22855769 0.264349841 0.03494494 7.454650142 100000000 -8 -0.985368 DVEDEILWVGER ddPTM_BT-474_Pertuzumab_2h_R1 4 DVEDEILWVGER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 256.48 8.37E-21 1253140000 1278300 1376350 1144790 1308490 1318180 1313320 1401160 1525370 1540540 1579620 FALSE TRUE 1228342.623 1337097.846 1351679.019 1376021.326 1360580.457 1339876.23 1418307.815 1493870.576 1365664.358 1472630.93 0.834114371 0.907965341 0.917866786 0.934396594 0.923911368 0.909852022 0.963111521 1.014422925 0.927363625 1 20.48996448 8 0.20343458 1.001367241 0.283015962 0.669278652 0.027765745 31.37586543 0.382986569 0.051901632 7.229744154 100000000 -8 -0.718351279 YLELLER ddPTM_BT-474_Pertuzumab_2h_R1 6 YLELLER 7 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;;;; 182.95 0.0015117 858436000 874604 995768 855849 1024692 996009 1015149 1050233 1027294 1081385 1260994 FALSE TRUE 840423.5088 967369.6716 1010519.953 1077576.477 1028046.534 1035676.008 1063086.066 1006080.02 958630.7083 1175585.753 0.714897664 0.822883119 0.859588465 0.916629411 0.874497272 0.880987206 0.904303291 0.855811681 0.81544941 1 20.16494835 8 0.027699519 1.47688745 1.24E-11 0.483717909 0.050630563 1625.969426 3.457165094 60.80922405 138.0102842 100000000 -8 -1.47688745 DSSSLSSCTSGILEERS(ph)PAFRGPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSSSLSSCTSGILEERSPAFRGPDR 25 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DSSSLSSCTSGILEERS(1)PAFRGPDR 129.88 5.04E-05 166470000 48864 56405 26194 30601 30982 50735 27571 36824 31721 20054 TRUE FALSE 46954.34086 54796.38463 30927.83848 32180.32128 31978.56417 51760.89646 27908.42215 36063.57153 28120.16507 18695.72472 2.51150151 2.930958037 1.654273314 1.72126632 1.710474702 2.768595347 1.492770276 1.928974248 1.504096016 1 14.19042078 8 0.067947436 4.82E-13 6.429266832 0.461969338 0.430709687 254.6735645 1.280021872 21.77759673 157.4866793 100000000 -8 6.429266832 EKLDSVIEFSIPDSLLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EKLDSVIEFSIPDSLLIR 18 1 F8W1A4;P54819-2;P54819;P54819-6;P54819-3;F8VZG5;A0A5F9ZHP2;F8VY04;A0A5K1VW67;P54819-4 F8W1A4 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 0 ; 182.22 6.34E-14 505150000 1574160 1598010 1218490 1431140 1210460 1473040 1256220 1438280 1544780 1323940 FALSE TRUE 1512640.087 1552436.319 1438698.248 1505001.307 1249395.545 1502825.878 1271593.996 1408579.015 1369423.051 1234268.365 1.225535816 1.257778587 1.165628391 1.219346902 1.01225599 1.217584377 1.030241099 1.141225892 1.109501864 1 20.23522468 8 0.130017154 0.981061845 1.886547022 0.494478881 0.064780557 65.80204497 0.578445912 0.315263924 10.93330491 100000000 -8 0.905485177 HRS(ph)EPQHPK ddPTM_BT-474_Pertuzumab_2h_R1 2 HRSEPQHPK 9 1 A0A087WZ32;A0A087X038;A8K727;Q9HB19 A0A087WZ32 PLEKHA2 Pleckstrin homology domain-containing family A member 2 1 HRS(1)EPQHPK;HRS(1)EPQHPK 81.565 0.012635 466190000 1499790 1055900 589530 568840 724990 475360 355280 530380 470410 280280 TRUE FALSE 1441176.549 1025786.766 696071.185 598197.9006 748309.9618 484972.1049 359628.0229 519427.4677 417011.0289 261296.386 5.515485962 3.925759486 2.663914323 2.289346247 2.863835866 1.856023011 1.376322224 1.987886154 1.595931101 1 17.99532765 8 0.417235863 1.52903133 75.05593791 0.921337077 0.358473861 19.51446577 0.25168849 0.240386246 1194.87034 100000000 -8 73.52690658 up LVPVS(ph)PLPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 LVPVSPLPPK 10 0 O95396 O95396 MOCS3 Adenylyltransferase and sulfurtransferase MOCS3;Molybdopterin-synthase adenylyltransferase;Molybdopterin-synthase sulfurtransferase 1 LVPVS(1)PLPPK;LVPVS(1)PLPPK;LVPVS(1)PLPPK;LVPVS(1)PLPPK 119.45 0.0007248 456761000 880840 901240 783270 831700 901430 902820 881730 971380 1044790 1048000 TRUE FALSE 846415.799 875537.5176 924824.3127 874624.1367 930425.3146 921075.639 892520.8755 951320.6635 926189.8193 977018.0265 0.866325673 0.896132409 0.946578556 0.895197543 0.952311308 0.942741704 0.913515259 0.973698169 0.947976183 1 19.89802566 8 0.114353578 1.022032979 0.585837805 0.680586536 0.021619526 57.87740515 0.458447161 0.16519069 4.001745649 100000000 -8 -0.436195174 LGS(ph)VDSFER ddPTM_BT-474_Pertuzumab_2h_R1 4 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 LGS(0.983)VDS(0.017)FER;LGS(1)VDSFER;LGS(1)VDSFER;LGS(1)VDSFER 190.7 3.85E-05 2931740000 5543600 4423980 3911760 3605910 4191800 3982140 3944930 4045230 4953800 4125710 TRUE FALSE 5326949.983 4297812.422 4618702.049 3792011.447 4326633.054 4062661.599 3993209.233 3961694.587 4391465.392 3846271.987 1.384964454 1.117396907 1.200825647 0.985892693 1.124890041 1.056259571 1.038202511 1.030008954 1.141745931 1 21.87502935 8 0.776362023 1.055637475 69.29044924 0.716867657 0.059975175 212.1230882 0.810301704 0.018711007 25396.25993 100000000 -8 68.23481176 SINNAEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SINNAEKR 8 1 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ; 103.83 0.0075308 284750000 186402 221081 131441 157056 170143 145587 159296 197652 149574 143894 FALSE TRUE 179117.2038 214775.9863 155195.3126 165161.679 175615.8041 148530.8689 161245.5121 193570.4171 132594.9866 134147.9312 1.335221514 1.601038379 1.156896802 1.231190653 1.30912048 1.107216992 1.201997755 1.442962373 0.988423641 1 17.03346528 8 0.03201062 0.049303578 3.056523581 0.354413009 0.146461295 1479.686236 3.626235495 105.2785644 271.1910897 100000000 -8 3.007220003 KLSSWDQAET(ph)PGHTPSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLSSWDQAET(1)PGHTPSLR 165.38 2.16E-11 174590000 913260 897060 529040 585670 635860 705820 499050 618340 533110 506820 TRUE FALSE 877568.7895 871476.7271 624649.2964 615896.4989 656313.0144 720092.164 505157.5232 605571.0629 472593.5878 472492.63 1.857317414 1.844423959 1.322029714 1.303504986 1.389043919 1.524028352 1.069133127 1.28165187 1.000213671 1 18.8499323 8 0.246244898 1.03720045 6.439944687 0.750194813 0.146925215 24.94442925 0.337768925 0.194443511 55.56721302 100000000 -8 5.402744238 DLQS(ph)PDFTTGFHSDK ddPTM_BT-474_Pertuzumab_2h_R1 4 DLQSPDFTTGFHSDK 15 0 E9PDR5;Q9P2D0-2;Q9P2D0;E7EPI0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 DLQS(0.996)PDFT(0.004)TGFHSDK;DLQS(0.999)PDFT(0.001)TGFHSDK;DLQS(0.889)PDFT(0.111)TGFHSDK;DLQS(1)PDFTTGFHSDK 174.22 5.96E-07 811127000 775830 717070 803720 875680 831080 788700 906320 962270 1068240 1137620 TRUE FALSE 745509.7059 696619.8657 948970.0827 920873.9497 857812.443 804648.0544 917411.8153 942398.7882 946977.8736 1060567.984 0.702934387 0.656836597 0.894775344 0.868283753 0.808823626 0.758695403 0.865019338 0.88857933 0.892896908 1 20.01640567 8 0.096673675 1.090329739 1.19E-07 0.618613865 0.060098807 97.81030876 0.672636321 0.903972982 14.14143835 100000000 -8 -1.09032962 ILLTQENPFFR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILLTQENPFFR 11 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 117.02 0.0021181 129732000 163826 174852 160587 170122 152720 217902 165735 200793 219128 217472 FALSE TRUE 157423.4988 169865.3922 189608.6431 178902.0168 157632.3775 222308.1277 167763.3145 196646.5544 194253.5081 202742.4277 0.776470424 0.837838404 0.935219358 0.882410351 0.77750069 1.096505207 0.827470187 0.969932917 0.958129535 1 17.62928851 8 0.19115284 0.997397776 0.086320578 0.332195339 0.080669045 63.86590615 0.748513262 0.152679071 17.21665451 100000000 -8 -0.911077199 CIDHYTK ddPTM_BT-474_Pertuzumab_2h_R1 5 CIDHYTK 7 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;; 132.29 0.0033837 965090000 1941930 2108140 1744100 2065100 2127260 2354850 2328240 2220090 2744950 2778190 FALSE TRUE 1866037.229 2048017.911 2059297.667 2171680.058 2195685.25 2402466.68 2356733.698 2174244.366 2433354.784 2590020.717 0.720471932 0.790734181 0.795089265 0.838479802 0.847748142 0.927585893 0.909928512 0.839469874 0.939511707 1 21.30453221 8 0.144938851 1.009115856 0.018441264 0.843190503 0.031303054 30.22078813 0.289348478 0.131399991 6.254503682 100000000 -8 -0.990674592 GKHSYNS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 GKHSYNSR 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 GKHSYNS(1)R 94.465 0.006262 93617000 129970 116100 66929 67260 77823 74440 62157 74173 69474 55562 TRUE FALSE 124890.6287 112788.9417 79024.55913 70731.29666 80326.24747 75945.2278 62917.69596 72641.30163 61587.60278 51798.73625 2.411074821 2.177445819 1.525607859 1.365502361 1.550737591 1.466159858 1.214656969 1.402375944 1.188978868 1 15.66062928 8 0.41829202 1.224677916 25.01589864 0.877162477 0.14619703 24.52994539 0.315753374 0.096400257 487.6046281 100000000 -8 23.79122072 up NNWNDVDDFNWLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 NNWNDVDDFNWLAR 14 0 Q15814 Q15814 TBCC Tubulin-specific chaperone C 0 ;;; 289.75 4.48E-43 516330000 464529 492361 442823 498250 493088 483447 531901 578348 607675 618625 FALSE TRUE 446374.6931 478319.3464 522850.9666 523964.7422 508948.6233 493222.6296 538410.5635 566404.9117 538694.2816 576724.9777 0.773981898 0.82937165 0.906586305 0.908517513 0.882480633 0.855212881 0.933565537 0.982105741 0.934057484 1 19.13752398 8 0.171244534 1.009834392 0.123139875 0.759950468 0.031873822 30.79386306 0.334162588 0.088733425 7.018287239 100000000 -8 -0.886694516 S(ph)AS(ph)PSTQQEKHPTHHER ddPTM_BT-474_Pertuzumab_2h_R1 1 SASPSTQQEKHPTHHER 17 1 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 2 S(0.994)AS(0.823)PS(0.111)T(0.072)QQEKHPTHHER 77.221 0.024217 96371000 125210 112280 68519 66554 82802 97517 78927 34287 80057 62719 TRUE FALSE 120316.6548 109077.8843 80901.9075 69988.85992 85465.40153 99488.86055 79892.93224 33578.96147 70969.26499 58470.98627 2.057715501 1.865504437 1.383624814 1.196984426 1.461671967 1.701508165 1.366368815 0.574284164 1.213751803 1 15.83543331 8 0.231540535 0.888569646 7.576447307 0.573098103 0.26619933 37.66881218 0.495392258 0.428217745 95.74921834 100000000 -8 6.687877662 YKCEGR ddPTM_BT-474_Pertuzumab_2h_R1 3 YKCEGR 6 1 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4;E9PQS6;E9PI38;E9PMD5;E9PNV4;E9PRX2;E9PJR1;E9PM47;E9PN69;E9PNK5;E9PJZ9 Q04206 RELA Transcription factor p65 0 ;; 88.591 0.046631 466076000 508840 530500 395767 420430 429490 446060 471580 451320 478530 452930 FALSE TRUE 488953.9702 515370.6594 467290.9007 442128.4427 443304.9359 455079.6388 477351.3371 442000.0843 424209.2806 422252.6477 1.157965434 1.220526768 1.106661861 1.047070859 1.04985709 1.077742535 1.130487493 1.046766875 1.004633797 1 18.68774694 8 0.241023228 1.018407833 2.101482323 0.608192943 0.041565172 36.12764098 0.484516048 0.059867089 15.68185755 100000000 -8 1.08307449 T(ph)RSEREWDRDK ddPTM_BT-474_Pertuzumab_2h_R1 1 TRSEREWDRDK 11 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 T(0.5)RS(0.5)EREWDRDK 82.925 0.018109 934450000 281830 225210 132240 109420 187600 132620 96048 157130 112040 91050 TRUE FALSE 270815.772 218787.2313 156138.7097 115067.1793 193634.3244 135301.6673 97223.46416 153885.2106 99321.68891 84883.1024 3.190455631 2.577512192 1.839455737 1.355595826 2.281188115 1.593976462 1.145380664 1.812907472 1.170099656 1 16.37318977 8 0.445744517 1.387034836 42.62247242 0.747504756 0.336190611 43.07852275 0.524174016 0.202939766 1612.025583 100000000 -8 41.23543758 up GHYTEGAELVDSVLDVVRK ddPTM_BT-474_Pertuzumab_2h_R1 3 GHYTEGAELVDSVLDVVRK 19 1 Q13509;A0A0B4J269;Q13509-2;G3V2A3;Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1 Q13509;Q5JP53;P68371;Q13885;Q9BVA1 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB2B Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;; 306.26 8.80E-51 2126618000 2881517 3630945 1682373 1764739 1974901 3409690 2068314 1750007 2189185 2078029 FALSE TRUE 2768904.13 3527394.004 1986415.225 1855817.391 2038425.484 3478636.268 2093626.645 1713868.744 1940677.897 1937282.245 1.429272445 1.820795092 1.025361808 0.957948898 1.05220883 1.795626981 1.080702954 0.884676845 1.001752791 1 20.88560273 8 0.293841685 1.004158654 5.977802753 0.232726224 0.290038825 77.24689673 1.101866506 0.316859342 200.5052674 100000000 -8 4.973644099 KYFLHDDRDDGVDYWAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KYFLHDDRDDGVDYWAK 17 2 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 78.285 0.0096008 496470000 683190 678460 449480 460170 604680 653910 454470 494790 625570 504000 FALSE TRUE 656490.1795 659110.9851 530711.0346 483919.4288 624130.0814 667132.5082 460031.9398 484572.4136 554557.9162 469863.6311 1.397193007 1.402770807 1.129500135 1.029914632 1.328321751 1.419842831 0.979075437 1.031304365 1.180252906 1 18.84188258 8 0.178882729 0.992696514 2.685885699 0.348220989 0.138737604 67.41667659 0.754775652 0.341481177 31.0158627 100000000 -8 1.693189185 KS(ph)PEIHRR ddPTM_BT-474_Pertuzumab_2h_R1 4 KSPEIHRR 8 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(1)PEIHRR;KS(1)PEIHRR;KS(1)PEIHRR;KS(1)PEIHRR 79.693 0.014285 370544000 1236625 822451 936292 463841 813642 782340 736908 776858 918836 708845 TRUE FALSE 1188296.328 798995.5027 1105500.792 487779.8896 839813.5339 798159.4508 745926.5005 760815.6108 814533.5894 660834.2968 1.798175933 1.209070877 1.672886528 0.738127382 1.270838299 1.207805731 1.128764812 1.151295589 1.23258371 1 19.33392904 8 0.719019117 1.137921671 91.7604027 0.450156202 0.21384165 281.0595139 1.36966892 0.071457001 41077.6293 100000000 -8 90.62248103 ILLLFGETELS(ph)PTATPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ILLLFGETELSPTATPR 17 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 ILLLFGET(0.005)ELS(0.978)PT(0.016)AT(0.001)PR 118.21 0.00070232 0 129520 135830 94517 113580 112200 107960 105010 121420 120150 106410 TRUE FALSE 124458.2152 131956.2614 111598.3244 119441.8774 115809.0149 110143.0252 106295.1438 118912.6346 106511.0757 99202.75592 1.254584251 1.330167294 1.124951856 1.204017734 1.167397154 1.110281908 1.071493859 1.198682773 1.073670532 1 16.59809258 8 0.126356583 0.975139964 1.988985731 0.647749936 0.054898175 56.555395 0.485916265 0.318346635 10.17740553 100000000 -8 1.013845767 GALQNIIPAS(ph)TGAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 GALQNIIPAS(0.995)T(0.005)GAAK;GALQNIIPAS(0.937)T(0.063)GAAK;GALQNIIPAS(0.5)T(0.5)GAAK 220.64 1.72E-12 678716000 1577640 1403390 1079650 1062680 1283520 1179090 1023730 1361410 1237990 940260 TRUE FALSE 1515984.085 1363366.691 1274766.772 1117525.042 1324805.586 1202932.008 1036258.714 1333296.408 1097458.565 876575.3527 1.729439551 1.555333135 1.45425806 1.274876186 1.511342502 1.372308728 1.182167295 1.521028858 1.251984284 1 19.74151859 8 0.03956295 6.03E-14 3.679176975 0.649058006 0.119404491 542.0152713 1.632765786 41.84749857 134.4276323 100000000 -8 3.679176975 KGPEADSEWR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGPEADSEWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 95.401 0.011941 1686600000 1539940 1649610 1337420 1595870 1622000 1610130 1731330 1871420 2004270 2135590 FALSE TRUE 1479757.442 1602564.738 1579121.545 1678233.042 1674173.103 1642687.932 1752518.534 1832774.523 1776753.672 1990944.587 0.743243911 0.804926841 0.793151931 0.842933074 0.840893872 0.825079684 0.880244757 0.920555266 0.89241744 1 20.92502164 8 0.066887243 1.199888682 0.067804541 0.924666873 0.018899984 66.54498755 0.32966891 1.019172993 7.155196212 100000000 -8 -1.132084141 ESCSS(ph)PSTVGSSLTTR ddPTM_BT-474_Pertuzumab_2h_R1 4 ESCSSPSTVGSSLTTR 16 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;H0YEP9 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 ESCS(0.005)S(0.475)PS(0.26)T(0.26)VGSSLTTR;ESCS(0.001)S(0.981)PS(0.017)T(0.001)VGSSLTTR;ESCS(0.002)S(0.997)PS(0.001)T(0.001)VGSSLTTR;ESCS(0.001)S(0.997)PST(0.002)VGSSLTTR 436.89 6.32E-161 1664200000 1514420 1620380 1351700 1590600 1561050 1653070 1685760 1796780 1926300 2043890 TRUE FALSE 1455234.792 1574168.349 1595982.258 1672691.057 1611262.591 1686496.208 1706390.835 1759675.865 1707634.5 1905455.51 0.763720163 0.826137551 0.837585685 0.877843145 0.845604939 0.885088211 0.895529088 0.923493546 0.896181774 1 20.86170449 8 0.091629203 1.08032089 0.251362947 0.906350327 0.018359068 39.81442938 0.261425238 0.302149642 4.148183543 100000000 -8 -0.828957943 LKTNILQYASTRPPTLS(ph)PIPHIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKTNILQYASTRPPTLSPIPHIPR 24 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 LKTNILQYASTRPPT(0.106)LS(0.893)PIPHIPR;LKTNILQYAST(0.003)RPPT(0.25)LS(0.748)PIPHIPR 173.03 2.45E-12 624410000 365400 359170 211769 199505 268510 314330 207379 211441 218850 199639 TRUE FALSE 351119.764 348926.8233 250040.3691 209801.477 277146.868 320685.968 209916.9662 207074.6695 194007.0655 186117.2727 1.886551199 1.874768624 1.343456013 1.127254198 1.489098051 1.723031739 1.127874717 1.11260318 1.042391513 1 17.50585243 8 0.220241547 0.989975768 5.931302205 0.615696952 0.204583064 36.3503968 0.465341168 0.34539255 63.91767931 100000000 -8 4.941326437 FQEKPDR ddPTM_BT-474_Pertuzumab_2h_R1 5 FQEKPDR 7 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;;; 86.953 0.017964 3718130000 5798740 5979140 5149900 5795030 5961250 6203580 6253210 6716840 7239220 7488800 FALSE TRUE 5572118.83 5808620.781 6080601.489 6094112.193 6152999.02 6329020.638 6329738.655 6578134.907 6417454.095 6981576.906 0.798117518 0.831992666 0.870949582 0.872884776 0.881319379 0.90653168 0.906634524 0.942213342 0.919198368 1 22.7351215 8 0.115344725 1.041055582 0.303635665 0.950808952 0.011877328 18.79008346 0.149898382 0.089410239 2.217508898 100000000 -8 -0.737419917 TGEPSPPHDILHEPPDVVS(ph)DDEKDHGK ddPTM_BT-474_Pertuzumab_2h_R1 3 TGEPSPPHDILHEPPDVVSDDEKDHGK 27 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TGEPSPPHDILHEPPDVVS(1)DDEKDHGK;TGEPSPPHDILHEPPDVVS(1)DDEKDHGK;TGEPSPPHDILHEPPDVVS(1)DDEKDHGK 250.15 2.37E-46 1369220000 1836820 1384240 1186110 1035000 1293900 1242100 1462580 245916 2010630 1377370 TRUE FALSE 1765035.044 1344762.831 1400466.462 1088416.474 1335519.469 1267216.113 1480479.492 240837.7487 1782391.712 1284079.503 1.374552775 1.047258232 1.090638437 0.847623898 1.040059798 0.986867332 1.152950022 0.187556727 1.388069592 1 20.2923031 8 0.449403932 0.8494789 12.16310777 0.117736317 0.298282163 147.2644446 1.777242169 0.181176124 1527.988675 100000000 -8 11.31362887 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_BT-474_Pertuzumab_2h_R1 1 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR 32 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 101.27 4.14E-06 55278000 96687 88358 39099 39208 42416 49852 26311 6197.6 31232 12456 FALSE TRUE 92908.36515 85838.11635 46165.05905 41231.52958 43780.34916 50860.0416 26633.00189 6069.617394 27686.6743 11612.34403 8.000827821 7.391971523 3.975515964 3.550663801 3.770156057 4.379825596 2.293507825 0.522686667 2.384245096 1 13.5033716 8 0.251659549 0.750507277 50.56733179 0.848116127 0.903792016 18.50264609 0.252837007 1.250675086 391.1785165 100000000 -8 49.81682452 up RHS(ph)VTLPSSK ddPTM_BT-474_Pertuzumab_2h_R1 5 RHSVTLPSSK 10 1 Q07352;G3V2D5;G3V515;G3V2P5 Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" 1 RHS(0.963)VT(0.037)LPSSK;RHS(0.986)VT(0.014)LPSSK;RHS(0.999)VT(0.001)LPSSK;RHS(0.942)VT(0.058)LPSSK;RHS(0.917)VT(0.083)LPSSK 157.82 5.20E-06 4296170000 9200180 7884770 4548850 4958350 5268550 3774700 3377690 4525090 4296580 3312990 TRUE FALSE 8840626.794 7659904.08 5370928.384 5214251.038 5438017.696 3851027.02 3419027.181 4431645.31 3808850.251 3088598.236 2.862342758 2.480058426 1.738953393 1.688225738 1.760674999 1.24685269 1.106983466 1.434840329 1.233197056 1 21.55852079 8 0.344022438 1.125791546 22.10995886 0.924073137 0.157810917 14.84153767 0.210435818 0.136789156 200.7809471 100000000 -8 20.98416731 up DSSDSADGRAT(ph)PSENLVPSSAR ddPTM_BT-474_Pertuzumab_2h_R1 3 DSSDSADGRATPSENLVPSSAR 22 1 Q8N684-2;Q8N684;Q8N684-3;F5H669;F5H6M0;F5H047 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 DSSDS(0.003)ADGRAT(0.996)PSENLVPSSAR;DS(0.001)S(0.001)DS(0.038)ADGRAT(0.96)PSENLVPSSAR;DSSDS(0.002)ADGRAT(0.998)PSENLVPSSAR 124.62 7.40E-06 1292220000 1006940 898720 594290 629170 637110 669800 534640 691310 615990 565000 TRUE FALSE 967587.6716 873089.3855 701691.4229 661641.5391 657603.2218 683343.8149 541183.0842 677034.2069 546065.3976 526732.0468 1.836963742 1.657558888 1.332160113 1.256125469 1.248458729 1.297327207 1.027435273 1.285348425 1.036704338 1 19.00670971 8 0.394073878 1.104262611 13.38181067 0.86819128 0.092957893 22.82315581 0.306143768 0.063920453 216.4602137 100000000 -8 12.27754806 DPTVHDDVLELEMDELNRHECMAPLTALVK ddPTM_BT-474_Pertuzumab_2h_R1 1 DPTVHDDVLELEMDELNRHECMAPLTALVK 30 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 57.803 0.028355 81288000 51534 65079 31534 31091 37420 46112 37580 22904 40798 30142 FALSE TRUE 49519.99431 63223.01064 37232.89527 32695.61024 38623.64828 47044.41623 38039.91528 22431.0244 36166.78208 28100.45549 1.762248812 2.249892734 1.324992589 1.163525988 1.374484776 1.674151376 1.353711697 0.798244157 1.287053233 1 14.7783059 8 0.233212546 0.965938 7.101043332 0.480796206 0.281653746 40.72549476 0.537550403 0.416942212 95.86870036 100000000 -8 6.135105332 FDASFFGVHPK ddPTM_BT-474_Pertuzumab_2h_R1 3 FDASFFGVHPK 11 0 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 169.37 1.70E-05 25081785000 13769262 14903174 13612424 14840420 14373355 14352406 17252520 16827270 18281340 18768880 FALSE TRUE 13231144.02 14478150.07 16072491.82 15606335.85 14835687.02 14642621.48 17463661.5 16479780.99 16206118.92 17497647.04 0.756167043 0.827434114 0.918551608 0.891910542 0.847867544 0.836833744 0.998057708 0.941828404 0.926188469 1 24.0606576 8 0.165994439 1.009405235 0.117289219 0.633741233 0.044807838 41.75225216 0.442898799 0.128244332 9.20471429 100000000 -8 -0.892116017 GFSLLATEDKEALKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GFSLLATEDKEALKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 225.67 5.45E-13 2028900000 1140200 931610 828980 712130 791670 879860 925760 969040 1095600 852240 FALSE TRUE 1095639.723 905041.3949 978795.1266 748883.1146 817134.7845 897651.372 937089.7278 949028.9854 971232.0811 794517.0257 1.379000938 1.139108875 1.231937259 0.942563961 1.028467305 1.129807598 1.179445748 1.194472811 1.222418211 1 19.59971861 8 0.012340442 2.14E-11 2.481078146 0.13937916 0.112779871 23807.60105 22.69623228 1897.738181 2736.388683 100000000 -8 2.481078146 FHSS(ph)DS(ph)EEEEHKK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHSSDSEEEEHKK 13 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 FHS(0.095)S(0.905)DS(1)EEEEHKK;FHS(0.448)S(0.552)DS(1)EEEEHKK 126.77 0.00018832 535040000 1057300 854950 686800 610860 740470 730070 731260 379750 1074840 762490 TRUE FALSE 1015979.547 830567.6631 810920.0378 642386.5578 764287.89 744832.5156 740209.3786 371908.0298 952828.6693 710845.8731 1.429254337 1.168421587 1.140781804 0.903693166 1.075180878 1.047811549 1.041307837 0.523190812 1.340415279 1 19.43917726 8 0.490964149 0.925820191 16.1674446 0.296143192 0.196699582 112.9261288 1.228904708 0.106708821 1766.792085 100000000 -8 15.24162441 EQAEAEVASLNRR ddPTM_BT-474_Pertuzumab_2h_R1 3 EQAEAEVASLNRR 13 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;; 214.18 5.01E-11 5493480000 3286360 3480910 1956780 2293750 2427660 3546440 2451970 2467190 2612160 2344920 FALSE TRUE 3157925.418 3381637.855 2310413.674 2412130.712 2505747.889 3618151.447 2481977.942 2416241.664 2315638.548 2186096.48 1.444549885 1.546884086 1.056867204 1.103396275 1.146220175 1.655074001 1.135346937 1.105276774 1.059257251 1 21.05992564 8 0.120608326 0.91919941 2.522045653 0.273487455 0.188002933 137.6300293 1.138785547 1.323395119 37.12032076 100000000 -8 1.602846242 DLDWEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDWEVR 7 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 ; 112.17 0.014922 204219000 315400 337110 286000 311130 331230 362520 360010 340590 401540 420240 FALSE TRUE 303073.8193 327495.9529 337686.562 327187.4566 341884.3138 369850.4028 364415.9101 333556.6975 355958.8626 391776.7705 0.773588028 0.835924888 0.861936152 0.835137459 0.872650804 0.944033518 0.930162117 0.85139478 0.908575723 1 18.57967233 8 0.089184624 1.060647894 0.339965735 0.715016682 0.033034403 99.77669152 0.639898333 0.683602272 8.802309248 100000000 -8 -0.720682158 EREPEAAS(ph)SRGSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EREPEAASSRGSPVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREPEAAS(0.694)S(0.03)RGS(0.277)PVR 104.38 0.0011011 134520000 111840 150850 53740 53786 78737 126100 63045 53852 75356 44196 TRUE FALSE 107469.1692 146547.9057 63452.01344 56561.90191 81269.64711 128649.8284 63816.56357 52739.93738 66801.9028 41202.56555 2.608312558 3.55676652 1.540001517 1.372776213 1.972441425 3.122374218 1.54884927 1.28001586 1.621304448 1 15.33044655 8 0.152917304 0.881581759 8.424646726 0.366104633 0.642398525 74.54244586 0.74364773 2.245354031 125.4342486 100000000 -8 7.543064967 LPAELQELPGLSHQYWSAPSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LPAELQELPGLSHQYWSAPSDK 22 0 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 234.51 1.93E-30 809110000 1048520 957780 981290 1083290 1052140 1025950 1200060 1246190 1378800 1417180 FALSE TRUE 1007542.679 930465.0522 1158630.932 1139198.727 1085983.039 1046695.412 1214746.693 1220455.741 1222284.404 1321193.136 0.762600601 0.704261191 0.876958031 0.862249958 0.82197145 0.792234975 0.91943158 0.923752711 0.925136811 1 20.33340995 8 0.107197852 1.084545362 0.035621154 0.714019692 0.045218523 60.82261003 0.45657971 0.462512682 9.424259465 100000000 -8 -1.048924208 LIDVNHYAK ddPTM_BT-474_Pertuzumab_2h_R1 2 LIDVNHYAK 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 101.38 0.0040217 1425750000 3528300 3823100 3488600 3919600 3614100 3740600 4045500 4131400 4661100 4745600 FALSE TRUE 3390410.135 3714068.931 4119067.623 4121891.026 3730350.809 3816237.495 4095010.039 4046085.146 4131991.469 4424176.285 0.766337035 0.839493884 0.931036052 0.931674228 0.843174089 0.862587123 0.925598298 0.914539766 0.933957239 1 22.07697744 8 0.093304884 1.055364626 0.395750435 0.593002758 0.040285591 118.1305886 0.787932392 0.695244269 9.970645233 100000000 -8 -0.659614192 IYPHGLVLLDLQSYDGDAQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IYPHGLVLLDLQSYDGDAQGK 21 0 P52788;H7C2R7 P52788 SMS Spermine synthase 0 ; 261.31 1.23E-36 1257270000 480300 447530 436490 527550 458920 470950 524260 564570 621430 643670 FALSE TRUE 461529.345 434766.8826 515373.4527 554776.9187 473681.5786 480472.9317 530676.0507 552911.4322 550887.8716 600073.6576 0.769121156 0.724522527 0.85885032 0.924514702 0.789372392 0.800689925 0.884351519 0.921405939 0.918033753 1 19.19478007 8 0.074516687 1.161817573 0.100909974 0.641222783 0.048884184 147.8258785 0.808119757 1.877885895 16.28963526 100000000 -8 -1.0609076 AFGPGLQGGSAGS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 7 AFGPGLQGGSAGSPAR 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR 266.91 3.14E-27 6221640000 1690050 1846150 1870726 1963067 1861474 1954140 2078421 2048708 2344082 2540019 TRUE FALSE 1624000.978 1793499.61 2208807.802 2064381.123 1921350.002 1993654.05 2103857.338 2006401.464 2077991.639 2367981.251 0.685816654 0.757396035 0.932780951 0.871789472 0.811387337 0.841921383 0.888460302 0.847304624 0.877537201 1 21.17522623 8 0.055168218 1.212380002 0.133449866 0.554393311 0.055505826 355.3373351 1.471292918 6.263087865 31.56840438 100000000 -8 -1.078930136 HIKEEPLS(ph)EEEPCTSTAIASPEK ddPTM_BT-474_Pertuzumab_2h_R1 5 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 HIKEEPLS(0.99)EEEPCT(0.009)STAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(0.986)EEEPCT(0.006)S(0.008)T(0.001)AIASPEK;HIKEEPLS(0.996)EEEPCT(0.004)STAIASPEK;HIKEEPLS(0.798)EEEPCT(0.067)S(0.067)T(0.067)AIASPEK 226.57 5.93E-33 4077620000 3003230 2644380 1985950 1939120 2377960 2317810 2051070 1490297 3077960 2063740 TRUE FALSE 2885860.451 2568964.872 2344855.342 2039198.216 2454449.243 2364677.706 2076171.608 1459521.846 2728562.885 1923961.052 1.499957834 1.335247857 1.218764455 1.059895788 1.275727095 1.229067347 1.079113117 0.758602595 1.418200687 1 20.87564816 8 0.340476212 1.029281277 6.248473346 0.349321905 0.16733024 61.8695117 0.87916838 0.148441191 205.3086245 100000000 -8 5.219192069 SHFEQWGTLTDCVVMRDPNTKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHFEQWGTLTDCVVMRDPNTKR 22 2 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 147.35 4.73E-08 1665890000 1733330 2026500 907680 911000 1185060 1836680 1040780 525690 1304800 860420 FALSE TRUE 1665589.547 1968706.204 1071717.967 958016.8192 1223178.531 1873818.928 1053517.377 514834.3178 1156684.574 802142.987 2.076424745 2.454308317 1.336068487 1.194321754 1.524888394 2.336016095 1.31337853 0.641823623 1.441993002 1 19.6134999 8 0.199298058 0.90118276 7.354905215 0.360071018 0.443762257 57.06642561 0.687490029 0.886240624 115.022262 100000000 -8 6.453722455 DSLDPSFTHAMQLLTAEIEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DSLDPSFTHAMQLLTAEIEK 20 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;; 223.46 6.45E-25 1828167000 1234111 1159756 1165659 1167796 1329078 1233309 1307798 1430823 1623977 1505265 FALSE TRUE 1185880.578 1126680.894 1376319.511 1228066.092 1371829.001 1258247.353 1323803.223 1401276.005 1439629.939 1403312.061 0.845058352 0.802872665 0.980765113 0.875119744 0.977565175 0.896626907 0.943342012 0.998549107 1.025880116 1 20.42040443 8 0.205797082 1.023344595 0.014421841 0.582087082 0.046212755 33.92588107 0.41712445 0.076860766 11.1458073 100000000 -8 -1.008922754 DQNGNHVVQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DQNGNHVVQK 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;A0A0C4DG68;H0YC97;Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;H0YDK8 Q8TB72-3;Q5T1Z4 PUM2;PUM1 Pumilio homolog 2;Pumilio homolog 1 0 ; 112.13 0.0016622 354460000 1016590 1076110 910910 967080 1023330 1091000 1079910 1102570 1298830 1274070 FALSE TRUE 976860.5389 1045420.396 1075531.7 1016991.115 1056246.339 1113060.768 1093126.262 1079801.544 1151392.264 1187776.104 0.822428179 0.880149376 0.905500369 0.856214493 0.88926384 0.937096447 0.920313397 0.909095191 0.969368099 1 20.17983148 8 0.060892973 1.14867884 0.394237952 0.794391077 0.022378965 149.6103725 0.679503229 1.681522799 9.973506029 100000000 -8 -0.754440888 TRTDS(ph)TSDGRPAWMR ddPTM_BT-474_Pertuzumab_2h_R1 3 TRTDSTSDGRPAWMR 15 2 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 TRTDS(0.948)T(0.043)S(0.008)DGRPAWMR;TRT(0.001)DS(0.708)T(0.236)S(0.054)DGRPAWMR;T(0.015)RT(0.012)DS(0.714)T(0.211)S(0.048)DGRPAWMR 86.453 0.0059467 1294080000 481310 504100 293628 333997 367610 402920 300902 325298 304066 253717 TRUE FALSE 462499.8731 489723.5616 346693.1113 351234.6252 379434.5095 411067.3185 304584.5287 318580.4826 269549.7024 236532.5216 1.955333118 2.070428025 1.465731262 1.48493164 1.604153657 1.737889216 1.287706767 1.346878139 1.139588335 1 17.85167903 8 0.129328625 0.805219762 4.820272047 0.757809853 0.159400167 41.16085746 0.360301598 0.882328152 30.13765441 100000000 -8 4.015052285 NKEIFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 NKEIFLR 7 1 P14625;Q96GW1;A0A1W2PRR1;F8W026 P14625 HSP90B1 Endoplasmin 0 141.52 0.0023269 705230000 1204600 1491500 832450 864800 1042900 1171000 868060 1022000 1152400 913020 FALSE TRUE 1157522.9 1448963.88 982892.2328 909432.4316 1076445.826 1194678.422 878683.5779 1000895.343 1021584.383 851180.3422 1.359903234 1.702299511 1.154740287 1.068436836 1.264650712 1.403554997 1.032311878 1.175891046 1.200197341 1 19.69910531 8 0.258081844 1.083941309 3.953246738 0.347202614 0.161276893 54.79219648 0.756034855 0.198183626 68.99339174 100000000 -8 2.86930543 GDRS(ph)PEPGQTWTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GDRSPEPGQTWTR 13 1 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GDRS(0.955)PEPGQT(0.006)WT(0.039)R 153.51 0.00012034 351730000 921520 791550 657400 587510 663410 664150 602250 635840 652950 577350 TRUE FALSE 885505.9796 768975.769 776206.8038 617831.4615 684749.1851 677579.568 609620.5157 622709.6818 578829.8534 538245.5702 1.645170956 1.428670874 1.442105326 1.147861674 1.272187312 1.258866966 1.132606656 1.156924861 1.075401054 1 19.03790502 8 0.253883846 1.03895936 4.89033727 0.884207266 0.063757723 15.31390855 0.20999653 0.078020438 25.32468654 100000000 -8 3.851377911 QTPMASS(ph)PRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QTPMASSPRPK 11 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK4 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 QTPMAS(0.024)S(0.976)PRPK 125.22 0.0002016 730090000 426490 321650 356010 264110 397280 286490 310190 386110 365120 314020 TRUE FALSE 409822.2993 312476.8569 420348.9264 277740.7488 410058.872 292283.0241 313986.198 378136.6936 323673.1083 292751.1457 1.399899899 1.067380475 1.435857494 0.948726428 1.400708001 0.998400957 1.072536189 1.291665973 1.10562542 1 18.15931529 8 0.02191932 3.33E-08 2.725422861 0.172844278 0.163454252 4974.606607 8.39476269 375.7929756 719.3136826 100000000 -8 2.725422827 HELS(ph)PPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 HELSPPQK 8 0 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 HELS(1)PPQK;HELS(1)PPQK 89.827 0.0087794 826680000 760740 729720 882740 966860 835070 901310 1046340 763670 1157200 1198810 TRUE FALSE 731009.4398 708909.1001 1042270.754 1016759.76 861930.7849 919535.1057 1059145.422 747899.9476 1025839.507 1117613.531 0.654080699 0.634306118 0.93258602 0.909759709 0.771224364 0.822766619 0.947684859 0.669193712 0.917883937 1 20.09198996 8 0.051177519 1.25055972 7.54E-11 0.314380979 0.10662004 716.1398112 2.761905243 15.60105285 70.14001392 100000000 -8 -1.25055972 DLLIAYYDVDYEK ddPTM_BT-474_Pertuzumab_2h_R1 6 DLLIAYYDVDYEK 13 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 312.78 2.83E-50 1338358000 2275960 2257990 2001680 2061080 2229790 2195200 2301570 2366590 2574150 2489750 FALSE TRUE 2187012.967 2193594.336 2363428.103 2167452.586 2301513.22 2239588.448 2329737.302 2317719.089 2281943.284 2321117.015 0.942224348 0.94505978 1.018228761 0.933797207 0.991554155 0.964875288 1.003713853 0.998536082 0.983122897 1 21.14638782 8 0.259323155 0.99936631 0.622075026 0.31349304 0.023267888 57.6648172 0.797058258 0.027036015 9.608869785 100000000 -8 -0.377291284 LAEDEGDS(ph)EPEAVGQSR ddPTM_BT-474_Pertuzumab_2h_R1 3 LAEDEGDSEPEAVGQSR 17 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR 436.08 3.16E-161 4996610000 1811200 1823360 1075510 1729340 1408030 1356250 1474110 1565560 1248080 1263900 TRUE FALSE 1740416.302 1771359.558 1269878.582 1818591.445 1453320.564 1383674.304 1492150.599 1533230.639 1106403.191 1178294.927 1.477063392 1.503324437 1.077725578 1.543409381 1.233409845 1.174302182 1.266364273 1.301228244 0.938986637 1 20.16826926 8 0.084117742 0.741277177 2.722141938 0.471622344 0.145306549 159.4229091 0.97122292 3.248756767 36.56660906 100000000 -8 1.980864762 TFCPAHK ddPTM_BT-474_Pertuzumab_2h_R1 6 TFCPAHK 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 110.63 0.0067597 14985610000 12016250 12098920 10863640 11850630 11455210 11946630 13907600 12597500 15143500 14763300 FALSE TRUE 11546641.67 11753870.65 12826941.41 12462242.43 11823677.23 12188199.04 14077805.37 12337357.22 13424473.37 13763368.54 0.838940092 0.853996652 0.931962359 0.90546456 0.859068563 0.88555349 1.022845921 0.896390821 0.975377018 1 23.71433027 8 0.102001381 1.053493118 0.441565386 0.520894058 0.041926371 102.1963467 0.735700161 0.489371244 8.763955097 100000000 -8 -0.611927732 EKQPPIDNIIR ddPTM_BT-474_Pertuzumab_2h_R1 3 EKQPPIDNIIR 11 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 0 ;; 150.49 3.09E-05 1264230000 1920900 2000700 1828880 2005750 2111640 2156120 2334580 2348850 2521820 2770400 FALSE TRUE 1845829.104 1943641.995 2159399.299 2109266.998 2179562.818 2199718.224 2363151.288 2300345.427 2235553.566 2582758.34 0.714673563 0.752545046 0.836082596 0.816672224 0.843889567 0.851693397 0.914971893 0.890654534 0.86556823 1 21.30048123 8 0.130201387 1.024119549 0.024128467 0.88224316 0.026078659 25.94599352 0.228341252 0.136955196 4.768889714 100000000 -8 -0.999991082 LDGLVETPTGYIES(ph)LPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LDGLVETPTGYIESLPR 17 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W118;F8VUX1;H0YHC3;F8W020;P55209-3;F8VXI6;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 1 LDGLVETPT(0.002)GYIES(0.998)LPR;LDGLVETPTGYIES(1)LPR 144.97 5.16E-07 62016000 119085 94288 79536 68933 94014 79455 61841 100597 65348 61120 TRUE FALSE 114431.0265 91598.99856 93909.92447 72490.64039 97038.04569 81061.63454 62597.82866 98519.6368 57929.969 56980.28796 2.008256375 1.607555908 1.648112493 1.272205582 1.703010798 1.422625919 1.09858744 1.729012617 1.016666835 1 15.79817529 8 0.11728319 0.876209475 3.887811998 0.535165927 0.222362023 84.24843274 0.681356566 1.593487576 41.36818448 100000000 -8 3.011602524 NSNILEDLETLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NSNILEDLETLR 12 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;; 231.54 7.46E-12 227677000 253423 254818 214732 251267 246145 247565 247519 281875 294027 285052 FALSE TRUE 243518.949 247550.8401 253538.8491 264234.92 254062.4775 252570.9339 250548.2116 276054.1827 260650.2876 265745.1741 0.916362639 0.931534659 0.954067557 0.994316908 0.956037972 0.950425289 0.942813778 1.038792835 0.980827925 1 18.01968397 8 0.20101771 1.009997939 0.560209085 0.469623656 0.025382413 46.53856902 0.563766438 0.04945847 6.610893634 100000000 -8 -0.449788854 GLPSPYNMSS(ph)APGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 12 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 GLPSPYNMS(0.005)S(0.995)APGS(1)R;GLPSPYNMS(0.01)S(0.99)APGS(1)R;GLPSPY(0.001)NMS(0.148)S(0.85)APGS(1)R;GLPSPYNMS(0.006)S(0.994)APGS(1)R;GLPSPYNMS(0.007)S(0.993)APGS(1)R;GLPSPYNMS(0.05)S(0.95)APGS(1)R;GLPSPYNMS(0.049)S(0.951)APGS(1)R;GLPSPYNMS(0.17)S(0.83)APGS(1)R;GLPSPYNMS(0.007)S(0.993)APGS(1)R;GLPSPYNMS(0.001)S(0.999)APGS(1)R;GLPSPYNMS(0.042)S(0.958)APGS(1)R;GLPSPYNMS(0.019)S(0.981)APGS(1)R 206.63 8.48E-09 9097380000 20325610 17667390 10156450 10085390 11340440 10136650 6083080 11533830 7865600 6466830 TRUE FALSE 19531262.69 17163533.34 11991946.44 10605898.19 11705215.55 10341620.01 6157526.553 11295652.38 6972730.063 6028825.844 3.239646192 2.846911452 1.989101486 1.75919797 1.941541497 1.715362207 1.021347558 1.873607344 1.156565183 1 22.52344562 8 0.332377669 1.250173425 23.50396754 0.848844367 0.271301096 20.9320811 0.298660191 0.237500877 286.7720154 100000000 -8 22.25379412 up GFS(ph)VVADTPELQR ddPTM_BT-474_Pertuzumab_2h_R1 4 GFSVVADTPELQR 13 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 GFS(1)VVADTPELQR;GFS(1)VVADTPELQR;GFS(0.999)VVADT(0.001)PELQR;GFS(1)VVADTPELQR 283.21 1.51E-32 444248000 1546530 1376990 992910 807830 1090800 875800 575159 941470 647972 564212 TRUE FALSE 1486089.898 1337719.593 1172350.924 849522.2031 1125886.573 893509.2761 582197.9679 922028.3155 574416.9351 525997.4187 2.82527983 2.543205624 2.228814976 1.615069148 2.140479274 1.698695173 1.106845675 1.752914145 1.092052764 1 19.00469619 8 0.200919368 0.955551421 10.29204411 0.832701286 0.244446207 19.63675842 0.237804365 0.433638158 57.86498436 100000000 -8 9.336492685 up GS(ph)PEEELPLPAFEK ddPTM_BT-474_Pertuzumab_2h_R1 8 GSPEEELPLPAFEK 14 0 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK 320.57 4.02E-56 2910515000 1835866 1925131 1623774 1823756 1839981 1899607 1947495 2112464 2138045 2173632 TRUE FALSE 1764118.327 1870228.149 1917226.082 1917880.266 1899165.66 1938018.355 1971329.026 2068840.88 1895343.095 2026409.969 0.870563388 0.92292684 0.946119547 0.946442376 0.937207026 0.956380192 0.972818461 1.020938957 0.935320653 1 20.95049465 8 0.261422996 0.995790464 0.20725361 0.662178942 0.022909445 29.82364072 0.413403777 0.028522577 10.49855973 100000000 -8 -0.788536854 DVMQNHLLQMLCLVAMEKPASTNSDDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 DVMQNHLLQMLCLVAMEKPASTNSDDVR 28 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 201.79 2.41E-25 1060471000 721440 722958 683805 790376 726947 792481 870274 805527 1014573 1029737 FALSE TRUE 693245.3272 702339.9457 807383.7747 831167.4001 750329.9105 808505.5088 880924.6735 788892.586 899402.9265 959991.9958 0.72213657 0.73161021 0.841031778 0.865806594 0.781600173 0.84220026 0.917637519 0.821769962 0.93688586 1 19.87266285 8 0.075639172 1.154356436 0.05205603 0.745710887 0.042401102 113.7556358 0.630315118 1.47486808 13.19385975 100000000 -8 -1.102300406 EFGSVDDENKPIWMHAEER ddPTM_BT-474_Pertuzumab_2h_R1 3 EFGSVDDENKPIWMHAEER 19 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8 Q07866-6 KLC1 Kinesin light chain 1 0 ;; 225.5 1.03E-19 1762070000 808513 777884 737387 776080 807437 897062 926970 895405 1095630 1094630 FALSE TRUE 776915.4181 755699.5099 870649.234 816133.5818 833408.9444 915201.2083 938314.5361 876914.5738 971258.6757 1020489.735 0.76131625 0.740526322 0.853168047 0.799746978 0.81667548 0.896825492 0.919474742 0.859307589 0.951757418 1 19.96083024 8 0.099429151 1.09421623 0.063749318 0.828514078 0.032732836 49.37534744 0.347812954 0.413736107 6.943629195 100000000 -8 -1.030466912 QKLDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 QKLDPK 6 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ; 96.964 0.037948 2452800000 3410000 2584200 2134100 1950570 2500000 1811880 1978320 1960900 2339200 1953490 FALSE TRUE 3276733.43 2510501.146 2519779.343 2051239.151 2580414.77 1848517.455 2002531.272 1920406.73 2073663.823 1821178.382 1.799238044 1.378503704 1.383598316 1.126325225 1.416892928 1.015011749 1.099579971 1.054485792 1.138638501 1 20.79644081 8 0.394526657 1.054654215 12.14741004 0.805636879 0.105197775 28.02139562 0.375614138 0.07048215 240.4797796 100000000 -8 11.09275582 FFEVILIDPFHK ddPTM_BT-474_Pertuzumab_2h_R1 2 FFEVILIDPFHK 12 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 175.74 2.69E-05 2649200000 1226000 1298990 1161310 1195820 1294440 1306140 1460900 1265460 1520590 1585440 FALSE TRUE 1178086.565 1261944.077 1371184.55 1257536.414 1336076.838 1332551.046 1478778.931 1239327.809 1347978.998 1478056.737 0.797050976 0.853785951 0.927694124 0.850803885 0.90394151 0.901556086 1.000488611 0.838484598 0.911994083 1 20.49527022 8 0.049645391 1.168831767 0.391830537 0.43465188 0.047521526 532.7122481 1.995960796 7.390393501 31.79365142 100000000 -8 -0.77700123 ELLQHPFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELLQHPFLK 9 0 Q13177;A0A087X294;O75914-2;O75914;O75914-4;O75914-3 Q13177 PAK2;PAK3 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34;Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 3 0 ; 90.108 0.011653 1519940000 2231000 2443000 2035870 2348500 2300500 2484100 2572800 2597700 2833100 3034300 FALSE TRUE 2143810.053 2373328.032 2403796.997 2469706.366 2374497.672 2534330.204 2604286.696 2544056.587 2511498.365 2828784.158 0.757855649 0.838992266 0.849763312 0.873062853 0.839405744 0.895907946 0.920638179 0.899346307 0.887836691 1 21.43175067 8 0.086320823 1.080598474 0.291137587 0.833145345 0.024444988 65.43753048 0.407840714 0.513467797 6.129137465 100000000 -8 -0.789460888 KHT(ph)GERPYSCPHCPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KHTGERPYSCPHCPAR 16 2 O15156;O15156-2 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 1 KHT(1)GERPYSCPHCPAR 131.09 4.67E-05 122930000 100570 67574 60088 70812 55223 55055 67956 31591 71917 55807 TRUE FALSE 96639.61321 65646.85568 70947.23825 74466.61581 56999.29795 56168.24982 68787.66586 30938.63481 63753.28366 52027.14218 1.857484558 1.261780927 1.363658184 1.431303214 1.095568497 1.079595139 1.322149612 0.594663353 1.225385078 1 15.66697684 8 0.285172332 0.917035014 7.405883857 0.547612348 0.208225788 37.47760508 0.531954593 0.222771135 121.9265429 100000000 -8 6.488848843 NSMPTVSFLDQDQS(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSMPTVSFLDQDQSPPR 17 0 A7KAX9;A7KAX9-2 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 NSMPTVSFLDQDQS(1)PPR;NSMPTVSFLDQDQS(1)PPR 387.58 8.80E-122 1074520000 562860 591980 535660 599460 525460 610300 593820 654160 713680 701860 TRUE FALSE 540862.8089 575097.31 632465.6777 630398.2024 542361.8981 622640.6841 601087.3468 640651.3674 632666.0384 654322.397 0.826599871 0.878920411 0.966596407 0.963436687 0.828890927 0.951580883 0.918640947 0.979106585 0.966902617 1 19.31964213 8 0.140454603 1.01619609 0.470795621 0.44285639 0.044292209 75.76196482 0.707874426 0.191547802 8.310281286 100000000 -8 -0.545400469 LEESHNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LEESHNR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 113.14 0.0061974 99127000 205351 189279 143429 150850 163162 154715 160954 170545 164532 138227 FALSE TRUE 197325.6559 183880.9482 169349.8109 158635.3866 168410.2539 157843.4433 162923.8032 167023.1862 145855.0171 128864.7622 1.531261553 1.426929637 1.314166945 1.231022228 1.306875915 1.22487669 1.264300655 1.296112167 1.131845624 1 16.97549829 8 0.079965098 0.789361968 2.584036147 0.814225812 0.05978174 93.70940749 0.545793251 1.846972662 18.58948376 100000000 -8 1.794674179 GLS(ph)GPCRPPPPPQAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GLSGPCRPPPPPQAR 15 1 Q9UEE5 Q9UEE5 STK17A Serine/threonine-protein kinase 17A 1 GLS(1)GPCRPPPPPQAR;GLS(1)GPCRPPPPPQAR 105.99 0.00077022 930450000 259530 265040 181816 223667 227130 245400 217273 237380 231770 241380 TRUE FALSE 249387.2807 257481.3187 214674.1957 235210.4807 234435.8427 250362.1561 219932.052 232478.02 205460.4413 225031.1176 1.108234645 1.144203173 0.953975601 1.045235358 1.041792998 1.112566825 0.97734062 1.033092767 0.913031244 1 17.77976499 8 0.249685592 0.985058315 1.830452143 0.313055879 0.058258862 63.18873091 0.860688719 0.074128661 22.43486122 100000000 -8 0.845393828 STTTGHLIYK ddPTM_BT-474_Pertuzumab_2h_R1 6 STTTGHLIYK 10 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;; 114.4 0.0013604 52763145900 29267405 31394523 27019673 31689956 29270076 30967019 35323054 34191759 36495090 38972167 FALSE TRUE 28123602.46 30499181.94 31902728.96 33325478.43 30211574.58 31593193.34 35755348.1 33485687.23 32352320.38 36332547.42 0.774060848 0.839445184 0.878075754 0.917234843 0.831529213 0.869556241 0.984113437 0.921644355 0.890450097 1 25.11475919 8 0.141605075 1.008048234 0.274239739 0.631187718 0.039671817 49.85558891 0.46879471 0.167210167 7.430437751 100000000 -8 -0.733808495 TANKDHLVTAYNHLFETKR ddPTM_BT-474_Pertuzumab_2h_R1 1 TANKDHLVTAYNHLFETKR 19 2 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 127.32 7.61E-06 374120000 388700 418000 175530 182600 263680 403700 219760 136720 295770 214650 FALSE TRUE 373509.1743 406079.0493 207252.1756 192024.0079 272161.5067 411863.0906 222449.4886 133896.6842 262195.4296 200111.5643 1.866504695 2.02926328 1.035683152 0.959584762 1.360048869 2.058167363 1.111627353 0.669110177 1.310246264 1 17.61044502 8 0.403093526 1.086909895 16.43224008 0.292354913 0.387737303 94.48181048 1.249287896 0.293369671 1153.930363 100000000 -8 15.34533019 TFYEDEMASHLDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 TFYEDEMASHLDSK 14 0 Q9ULX6;Q9ULX6-2 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 ; 244.44 1.37E-17 1266220000 944560 968510 802340 907300 924340 979150 920270 969960 1177740 1100810 FALSE TRUE 907645.5509 940889.0431 947340.686 954125.8617 954072.2356 998949.0839 931532.5395 949929.987 1044047.893 1026251.158 0.884428284 0.916821419 0.923108031 0.929719644 0.92966739 0.973396304 0.907704252 0.925631099 1.0173415 1 19.96895242 8 0.031791682 1.26984025 0.443231227 0.55744201 0.02666288 995.54942 2.42343413 19.53764611 50.00554051 100000000 -8 -0.826609023 VTGGLLDRLDDS(ph)PDQCR ddPTM_BT-474_Pertuzumab_2h_R1 5 VTGGLLDRLDDSPDQCR 17 1 Q12955;A0A087WY90;A0A087WVC2;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 VTGGLLDRLDDS(1)PDQCR;VTGGLLDRLDDS(1)PDQCR;VTGGLLDRLDDS(1)PDQCR;VTGGLLDRLDDS(1)PDQCR;VTGGLLDRLDDS(1)PDQCR 271.54 7.89E-36 1225570000 1235100 1311162 1177922 1288062 1264140 1693284 1400212 1403181 1709041 1838389 TRUE FALSE 1186830.927 1273768.944 1390798.708 1354539.034 1304802.211 1727523.363 1417348.213 1374204.822 1515037.831 1713873.276 0.692484645 0.743210692 0.811494483 0.790337917 0.761317788 1.007964467 0.826985422 0.801812387 0.883984745 1 20.70882901 8 0.081430398 1.114355482 0.050114464 0.569502233 0.064729342 154.3097878 0.913403209 1.762319531 18.45412064 100000000 -8 -1.064241018 HTVDDGLDIRK ddPTM_BT-474_Pertuzumab_2h_R1 3 HTVDDGLDIRK 11 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 183.33 3.50E-06 870250000 1350620 1391940 900070 887060 1050780 1287460 1103500 687040 1294510 1066480 FALSE TRUE 1297836.277 1352243.234 1062732.671 932841.2729 1084579.293 1313493.323 1117004.963 672852.3839 1147562.652 994246.3597 1.305346773 1.360068579 1.068882637 0.938239566 1.090855684 1.321094425 1.123469 0.676746138 1.154203524 1 19.92324385 8 0.312799972 0.96112778 4.716641257 0.256332903 0.167747644 71.42135543 1.023236537 0.175070512 152.2175773 100000000 -8 3.755513477 EAVVDLHADDSRIS(ph)EDETERNGDDGTHDK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAVVDLHADDSRISEDETERNGDDGTHDK 29 2 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.213)RIS(0.787)EDETERNGDDGTHDK;EAVVDLHADDS(0.251)RIS(0.748)EDETERNGDDGTHDK 198.14 9.11E-26 548190000 331450 316690 194434 170343 252957 276992 182628 184254 281216 186414 TRUE FALSE 318496.5676 307658.3113 229572.549 179134.4226 261093.5916 282592.968 184863.0561 180449.0905 249293.5386 173788.0137 1.83267281 1.770308001 1.320991845 1.030763968 1.502368236 1.626078588 1.063727308 1.038328747 1.434469117 1 17.40696906 8 0.414018838 1.172998527 14.25800787 0.476937661 0.219260951 67.75377836 0.879029424 0.155056365 730.8400369 100000000 -8 13.08500934 KEDGTFYEFGEDIPEAPER ddPTM_BT-474_Pertuzumab_2h_R1 6 KEDGTFYEFGEDIPEAPER 19 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;;; 226.29 2.46E-19 17884200000 9276270 9630050 8208610 9516500 9494270 10177530 10154230 10816840 11828530 11754730 FALSE TRUE 8913743.113 9355410.403 9692088.427 10007647.71 9799661.817 10383326.63 10278500.5 10593468.47 10485804.86 10958571.67 0.813403734 0.853707097 0.884429898 0.913225556 0.894246268 0.947507298 0.937941624 0.966683323 0.95685872 1 23.38555643 8 0.191792183 1.005376047 0.12471988 0.954598113 0.011404301 9.331795802 0.109614856 0.021417805 2.44213107 100000000 -8 -0.880656166 NDFTEEEEAQVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NDFTEEEEAQVR 12 0 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ; 301.58 3.45E-36 797010000 533540 501760 444470 562620 490340 519630 537530 580370 620170 602090 FALSE TRUE 512688.6669 487450.2961 524795.6162 591656.8856 506112.2314 530137.2746 544108.4529 568385.1567 549770.9016 561309.908 0.913378972 0.868415628 0.934948072 1.054064568 0.901662743 0.944464488 0.969354799 1.012604888 0.979442717 1 19.098438 8 0.261128453 1.0006684 0.210285354 0.336544902 0.043459012 55.89462752 0.774486191 0.053764433 19.69259363 100000000 -8 -0.790383047 TQT(ph)PPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 2 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.048)QT(0.952)PPVSPAPQPT(0.022)EERLPS(0.522)S(0.455)PVYEDAASFK;T(0.116)QT(0.875)PPVS(0.193)PAPQPT(0.136)EERLPS(0.362)S(0.315)PVY(0.004)EDAASFK 137.37 4.69E-06 4282990000 1921920 1873810 1230710 1324440 1446280 1640050 1307250 1514740 1528370 1313730 TRUE FALSE 1846809.242 1820370.773 1453126.674 1392794.507 1492800.91 1673212.935 1323248.517 1483460.09 1354875.845 1224749.897 1.507907244 1.486320414 1.186468092 1.137207287 1.218861837 1.366167034 1.080423456 1.211235121 1.106246956 1 20.22405574 8 0.419414367 1.135743371 8.859275976 0.619961385 0.099983368 52.28947404 0.671660721 0.065715721 338.6154913 100000000 -8 7.723532605 GATELTHEDYMEGILEVQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 GATELTHEDYMEGILEVQAK 20 0 P17980;E9PM69;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 167.99 6.54E-12 0 97339 110180 97310 106580 117650 112800 106820 113780 138150 140500 FALSE TRUE 93534.88427 107037.7743 114896.0816 112080.6066 121434.3191 115080.8933 108127.2951 111430.4032 122467.7912 130983.8099 0.714095004 0.817183241 0.877177735 0.855682902 0.927094114 0.878588685 0.825501222 0.850718905 0.934984189 1 16.99902897 8 0.033812878 1.431859873 2.53E-10 0.600993088 0.04647169 898.3131597 2.322618941 29.57634175 80.31898879 100000000 -8 -1.431859873 TVAISDAAQLPHDYCT(ph)TPGGTLFS(ph)TTPGGTRIIYDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.079)CT(0.433)T(0.434)PGGT(0.109)LFS(0.305)T(0.305)T(0.305)PGGT(0.02)RIIY(0.011)DRK 79.021 0.0039141 113740000 48148 53401 17829 23740 30479 50953 22618 22020 23253 17545 TRUE FALSE 46266.32293 51878.05577 21051.0969 24965.22425 31459.38472 51983.30457 22894.80585 21565.2793 20613.41692 16356.66152 2.828592061 3.171677527 1.287004495 1.526303165 1.923337759 3.178112141 1.399723643 1.318440152 1.26024598 1 13.9975907 8 0.155894126 0.841138697 8.357608023 0.392778831 0.625127222 72.35866104 0.732479996 2.098441878 124.2597718 100000000 -8 7.516469326 S(ph)PSMSISEPISVTLPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSMSISEPISVTLPPR 17 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.963)PS(0.036)MSISEPISVTLPPR 75.376 0.023244 78803000 98999 89697 92319 53337 74167 82690 53844 109180 55854 61355 TRUE FALSE 95130.00963 87138.92938 109003.0969 56089.72896 76552.64891 84362.04846 54502.95898 106925.3948 49513.68808 57199.3712 1.663130339 1.523424603 1.905669497 0.980600447 1.338347735 1.4748772 0.952859408 1.869345634 0.865633433 1 15.80371167 8 0.096624801 0.834470804 3.179764647 0.246250476 0.32170851 225.1282069 1.547523534 4.478801878 69.97701163 100000000 -8 2.345293843 EQDRDVQLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQDRDVQLSK 10 1 Q86TN4;Q86TN4-4;F5H8A0;Q86TN4-3 Q86TN4 TRPT1 tRNA 2-phosphotransferase 1 0 126.19 0.00035481 276780000 284590 277340 203390 226960 237700 230270 251520 223200 253300 223510 FALSE TRUE 273467.9082 269430.5347 240147.0974 238673.4328 245345.8364 234926.2172 254598.177 218590.842 224546.4459 208371.4686 1.312405724 1.293029878 1.152495104 1.145422809 1.177444484 1.127439465 1.221847591 1.049044015 1.077625682 1 17.66879822 8 0.144320871 0.973488916 2.155882217 0.752035052 0.047474402 36.19780062 0.345430735 0.189253916 8.895007311 100000000 -8 1.182393301 SS(ph)REKEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSREKEQR 8 2 H7C1L9 H7C1L9 TRIP12 1 S(0.12)S(0.88)REKEQR 67.334 0.030975 89260000 67531 82563 28611 54201 45653 69512 47224 39716 35188 41020 TRUE FALSE 64891.81386 80208.38408 33781.64415 56998.32011 47121.47021 70917.58027 47801.94144 38895.85072 31193.60576 38241.67886 1.696887161 2.0974075 0.883372413 1.490476407 1.232201922 1.854457816 1.249995891 1.017106254 0.815696556 1 15.22285824 8 0.160701451 0.819184308 4.699913814 0.355169284 0.332154543 68.79940297 0.712502478 0.975285452 63.35049261 100000000 -8 3.880729505 DVLFLK ddPTM_BT-474_Pertuzumab_2h_R1 4 DVLFLK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;; 106.29 0.075031 2462384000 3783810 4175543 2638675 3334145 2753675 2750432 2946542 2970007 3263571 2569659 FALSE TRUE 3635934.522 4056460.602 3115542.27 3506220.623 2842249.457 2806047.62 2982602.662 2908675.318 2893104.102 2395613.707 1.517746585 1.693286605 1.30051947 1.463600168 1.186438969 1.171327252 1.245026547 1.214167088 1.207667202 1 21.19196386 8 0.194772344 1.030269635 3.857509051 0.72758644 0.100017949 25.72065999 0.305242761 0.183608327 22.04457292 100000000 -8 2.827239415 EESFRDPAEVLGTGAEVDYLEQFGTSSFK ddPTM_BT-474_Pertuzumab_2h_R1 1 EESFRDPAEVLGTGAEVDYLEQFGTSSFK 29 1 Q9Y6A5;C9JWI7;A0A494C117 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 0 112.6 0.00025582 88330000 49181 51647 41859 51780 48659 55925 57588 56825 56745 65757 FALSE TRUE 47258.95215 50174.07813 49423.85245 54452.37201 50224.16093 57055.84182 58292.77917 55651.54389 50303.54549 61303.21982 0.770904894 0.818457469 0.80621952 0.888246525 0.819274437 0.930715254 0.950892618 0.907807845 0.820569387 1 15.90367523 8 0.145476748 0.993145434 0.204092979 0.581923992 0.045919623 50.3578544 0.483533088 0.173267386 8.338454814 100000000 -8 -0.789052456 (ac)AS(ph)AVSPANLPAVLLQPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASAVSPANLPAVLLQPR 17 0 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 AS(0.689)AVS(0.311)PANLPAVLLQPR 80.763 5.98E-10 67495000 26315 21029 16095 13349 14595 17968 11239 8579.2 12895 7245.3 TRUE FALSE 25286.58071 20429.27351 19003.72453 14037.94349 15064.46143 18331.32527 11376.54624 8402.036522 11431.21366 6754.569378 3.743625877 3.024511611 2.813462039 2.078288445 2.230262299 2.713914721 1.684274098 1.243904097 1.692367495 1 12.72164808 8 0.174581175 0.782044464 12.87220056 0.856576564 0.307469887 20.98358382 0.230892712 0.795034379 66.82602251 100000000 -8 12.0901561 up GYYSPYSVSGSGSTAGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 4 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYSVSGSGS(0.007)T(0.118)AGS(0.875)R;GYYSPYSVSGSGS(0.001)T(0.018)AGS(0.98)R;GYYSPYSVSGSGSTAGS(1)R;GYYSPYSVSGSGST(0.011)AGS(0.989)R 411.75 2.08E-147 3103430000 1870263 1945555 1122977 1416019 1498364 1293190 1002510 1625634 1307503 1177835 TRUE FALSE 1797171.054 1890069.676 1325923.924 1489099.91 1546560.239 1319339.188 1014779.017 1592064.09 1159080.741 1098059.186 1.636679586 1.721282149 1.207515898 1.356119897 1.408448887 1.201519193 0.92415694 1.44988914 1.055572191 1 20.06652439 8 0.269215634 1.088066672 5.576265203 0.567789587 0.165967892 38.58912743 0.539995795 0.191806655 80.40543213 100000000 -8 4.488198531 KS(ph)RDSESHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSRDSESHSR 10 2 Q15424;Q15424-3;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 KS(0.999)RDS(0.001)ESHSR;KS(0.981)RDS(0.018)ES(0.001)HSR 70.089 0.028712 37317000 47795 39891 25202 28739 28145 30180 25655 21768.7 27798 25027 TRUE FALSE 45927.11856 38753.34774 29756.56202 30222.22323 29050.30949 30790.26028 25968.97356 21319.16874 24642.48758 23331.899 1.968426083 1.660959862 1.275359628 1.295317764 1.245089801 1.319663705 1.113024429 0.913734829 1.056171535 1 14.51001611 8 0.350363274 0.995235422 12.60411372 0.903732367 0.093720685 18.59133961 0.262407306 0.087347343 142.5820511 100000000 -8 11.60887829 VVVAENFDEIVNNENKDVLIEFYAPWCGHCK ddPTM_BT-474_Pertuzumab_2h_R1 2 VVVAENFDEIVNNENKDVLIEFYAPWCGHCK 31 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 178.5 2.27E-18 478850000 441310 422060 224870 215810 258320 264280 163877 188288 217340 123951 FALSE TRUE 424063.1173 410023.262 265509.0112 226947.98 266629.0974 269623.9227 165882.5757 184399.787 192668.4744 115555.6884 3.669772759 3.548274151 2.297671495 1.963970646 2.307364537 2.333281265 1.43552064 1.595765553 1.66732142 1 16.81822875 8 0.252151916 1.195122752 18.30066168 0.862056406 0.304975431 17.35566071 0.237350042 0.400566566 126.3195201 100000000 -8 17.10553893 up GGQSWR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGQSWR 6 0 Q9UBG0 Q9UBG0 MRC2 C-type mannose receptor 2 0 119.22 0.049314 129300000 210540 184710 143740 172590 163050 130120 138610 177080 147080 144110 FALSE TRUE 202311.864 179442.2517 169717.0155 181497.3906 168294.6513 132751.1156 140306.3506 173423.2361 130384.095 134349.3013 1.505864653 1.335639634 1.263251939 1.350936617 1.252664879 0.988104249 1.04434001 1.290838392 0.970485843 1 17.03562929 8 0.217624619 1.00858053 3.541835375 0.666289142 0.101967017 34.20454149 0.434896715 0.171398478 30.35420339 100000000 -8 2.533254845 VGAEDADGIDMAYR ddPTM_BT-474_Pertuzumab_2h_R1 2 VGAEDADGIDMAYR 14 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 254.53 6.85E-24 1060420000 639610 628400 582140 618370 649040 696190 718350 720390 751520 832610 FALSE TRUE 614613.3341 610478.6473 687345.6476 650284.1498 669916.961 710267.4388 727141.3822 705513.6948 666210.6002 776216.5831 0.791806498 0.78647978 0.885507554 0.837761218 0.863054173 0.915037702 0.936776408 0.908913453 0.858279267 1 19.56609973 8 0.127861065 1.012311114 0.265726545 0.713819786 0.033304257 45.54912108 0.395088462 0.185086301 6.119488363 100000000 -8 -0.746584569 LKEINFR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKEINFR 7 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 131.06 0.0031944 1034840000 818300 905110 683080 862910 812590 818790 890550 868280 978400 974870 FALSE TRUE 786319.9313 879297.149 806527.751 907444.8885 838727.6953 835346.4948 901448.8173 850349.7146 867336.1338 908841.1866 0.865189588 0.967492629 0.887424297 0.99846365 0.922853968 0.919133625 0.991866159 0.935641702 0.954331897 1 19.79366869 8 0.089024017 1.02680614 0.700554437 0.310537889 0.03675951 207.2658715 1.327168696 0.644453414 8.263177702 100000000 -8 -0.326251703 NEDVQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 NEDVQLR 7 0 P30153;P30154-4;P30154;P30154-2;P30154-5;E9PPI5;E9PHZ6 P30153 PPP2R1A;PPP2R1B Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform;Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform 0 ; 134.08 0.0074653 1037230000 1614800 1718770 1450140 1682370 1627110 1722180 1723390 1927470 2072700 1957240 FALSE TRUE 1551691.831 1669752.362 1712212.556 1769197.317 1679447.471 1757003.66 1744481.362 1887667.071 1837415.785 1824674.391 0.850393823 0.915096069 0.93836608 0.969596179 0.920409405 0.96291353 0.956050773 1.034522696 1.006982832 1 20.79920761 8 0.236735087 1.019700541 0.089539576 0.764049646 0.024449036 24.46396248 0.325310912 0.036520199 8.905797046 100000000 -8 -0.930160965 VDDFLANEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDDFLANEAK 10 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 117.52 0.0022026 285620000 441870 443440 472980 477590 463210 453920 511610 505100 543730 595230 FALSE TRUE 424601.2319 430793.5254 558458.0074 502238.4771 478109.5703 463098.5734 517871.2362 494669.5085 482008.0499 554914.5419 0.765165084 0.776324087 1.006385606 0.905073555 0.861591352 0.834540345 0.933245026 0.891433673 0.868616721 1 19.08190608 8 0.02400218 1.539874576 2.39E-12 0.315009385 0.064247056 2995.200815 5.529290063 123.7571437 251.8969359 100000000 -8 -1.539874576 VIDFDENTALDDAEEESFRK ddPTM_BT-474_Pertuzumab_2h_R1 4 VIDFDENTALDDAEEESFRK 20 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ;;; 259.49 4.32E-36 681974000 603776 658548 542928 632879 638676 703788 652480 699784 807214 807800 FALSE TRUE 580179.7664 639766.8558 641047.167 665541.961 659219.5936 718019.0756 660465.2454 685333.2159 715582.4508 753086.9865 0.770402061 0.849525841 0.851225925 0.883751775 0.875356506 0.953434448 0.877010568 0.910031946 0.950198933 1 19.52245699 8 0.138586693 1.012222043 0.262117646 0.820390221 0.026115654 32.14789314 0.297240211 0.114403251 4.772457493 100000000 -8 -0.750104397 PMFIVNTNVPR ddPTM_BT-474_Pertuzumab_2h_R1 2 PMFIVNTNVPR 11 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ; 147.75 0.0020174 0 268528 213179 220700 156294 230644 202647 187677 180614 205500 168056 FALSE TRUE 258033.6289 207099.3436 260585.3994 164360.3521 238062.8737 206744.6612 189973.8473 176884.2578 182172.5015 156673.4174 1.646952196 1.321853745 1.663239391 1.049063426 1.519484783 1.319589912 1.212546776 1.128999805 1.162753098 1 17.25740089 8 0.121165263 0.856982681 3.180062604 0.530699714 0.154705471 68.09725861 0.56556925 0.941838832 26.75927028 100000000 -8 2.323079923 TDS(ph)TSDGRPAWMR ddPTM_BT-474_Pertuzumab_2h_R1 6 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 TDS(0.976)T(0.023)S(0.001)DGRPAWMR;TDS(0.979)T(0.021)SDGRPAWMR;TDS(0.977)T(0.022)S(0.001)DGRPAWMR;TDS(0.998)T(0.002)SDGRPAWMR;TDS(0.983)T(0.017)SDGRPAWMR;TDS(0.698)T(0.185)S(0.117)DGRPAWMR 238.64 5.32E-17 16550370000 4533020 4228090 3379970 3426270 3816480 3538000 2919620 3717740 3837690 3274870 TRUE FALSE 4355864.567 4107509.013 3990805.766 3603100.205 3939240.545 3609540.784 2955351.183 3640967.37 3402051.52 3053060.138 1.426720854 1.34537442 1.307149413 1.180160247 1.290259729 1.182269795 0.967996387 1.192563266 1.114308715 1 21.54182458 8 0.185981481 0.994131129 2.963039989 0.751018672 0.069516248 26.85793307 0.308960625 0.146612671 15.1033904 100000000 -8 1.96890886 VQENCIDLVGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQENCIDLVGR 11 0 O75533;H7C341 O75533 SF3B1 Splicing factor 3B subunit 1 0 72.34 0.077895 0 192980 155590 124720 130890 105450 126370 105380 133940 89669 106830 FALSE TRUE 185438.1282 151152.7255 147259.6784 137645.2486 108841.895 128925.288 106669.672 131174.0922 79490.15104 99594.30895 1.861934986 1.517684365 1.478595313 1.382059377 1.092852555 1.294504569 1.071041841 1.317084215 0.798139491 1 16.60377569 8 0.281327056 1.010543285 7.368687233 0.785375701 0.133937295 23.10644032 0.327051209 0.140937665 72.33298389 100000000 -8 6.358143948 LRPLFEACGEVVQIRPIFSNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LRPLFEACGEVVQIRPIFSNR 21 2 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 261.82 6.54E-37 1082230000 342610 304860 207362 234760 263048 240268 227252 243214 219140 253228 FALSE TRUE 329220.4224 296165.6913 244836.9261 246875.9917 271509.1778 245126.3836 230033.178 238191.5459 194264.1459 236076.642 1.394548904 1.254531955 1.037107797 1.045745101 1.150089122 1.038333913 0.974400415 1.008958548 0.822885925 1 17.84889578 8 0.405032039 0.962376535 8.368793225 0.774599928 0.071566699 34.39049989 0.453256044 0.050224784 204.0066497 100000000 -8 7.406416689 (ac)MDLAAAAEPGAGS(ph)QHLEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDLAAAAEPGAGSQHLEVR 19 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 MDLAAAAEPGAGS(1)QHLEVR 118.23 5.77E-25 0 26795 21169 15568 18662 17133 23936 16174 18856 12941 21012 TRUE FALSE 25747.82178 20565.28085 18381.48391 19625.14806 17684.0985 24420.00232 16371.94225 18466.61701 11471.99193 19588.83852 1.314412886 1.049846872 0.938365176 1.001853583 0.902764014 1.246628394 0.835779121 0.942711176 0.585639211 1 14.25774424 8 0.691823165 0.919016026 46.33900657 0.36565838 0.154038694 305.7352456 1.665064486 0.056320237 21450.78472 100000000 -8 45.41999054 DPQFQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DPQFQK 6 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 111.28 0.065105 451350000 753600 733250 556700 646940 600530 549060 610760 653530 657870 545130 FALSE TRUE 724148.4789 712338.4279 657308.0737 680328.6509 619846.5928 560162.3694 618234.6636 640034.3771 583191.3556 508207.8595 1.424906099 1.401667476 1.293384314 1.338681876 1.219671403 1.102230827 1.216499611 1.259394882 1.147544936 1 18.95505916 8 0.111371645 0.929982718 2.456146038 0.800528787 0.056384682 52.58080155 0.407485962 0.547775253 12.35519776 100000000 -8 1.526163319 GGDSIGET(ph)PT(ph)PGASK ddPTM_BT-474_Pertuzumab_2h_R1 1 GGDSIGETPTPGASK 15 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 GGDSIGET(1)PT(1)PGASK 146.33 2.38E-05 0 549020 559000 389540 367440 457480 415710 319520 513300 445310 354640 TRUE FALSE 527563.6914 543057.8673 459938.5433 386403.6224 472195.2597 424115.941 323430.3813 502700.1756 394760.2757 330619.9169 1.59568031 1.642544322 1.391139855 1.168724577 1.428211779 1.282790054 0.978254378 1.520477593 1.194000287 1 18.33481411 8 0.310136726 1.184853336 5.632709919 0.470081752 0.162177312 52.60673627 0.75360795 0.157880076 131.274245 100000000 -8 4.447856583 IQILEGWKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQILEGWKK 9 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 101.95 0.0072145 0 1108000 1169300 765530 762070 925560 913040 930440 697010 1060200 761550 FALSE TRUE 1064698.135 1135952.709 903878.3001 801400.524 955331.478 931502.2944 941827.003 682616.4999 939850.5407 709969.5402 1.499639174 1.600002035 1.273122647 1.128781558 1.34559502 1.31203135 1.326573817 0.961472938 1.323789948 1 19.4373976 8 0.189034531 1.026563091 3.400597593 0.498789829 0.134838012 43.93995242 0.511117492 0.279956842 30.42477276 100000000 -8 2.374034502 TMEEASKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TMEEASKR 8 1 P30419;P30419-2;B7Z8J4;K7EN82 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 ; 76.827 0.055792 296690000 739350 810930 649120 742850 761100 778380 813910 828980 911710 882280 FALSE TRUE 710455.3846 787803.0704 766430.4236 781188.5775 785581.4727 794119.3769 823870.874 811861.2733 808216.503 822522.3897 0.863752031 0.957789211 0.931804937 0.949747493 0.955088254 0.965468402 1.00163945 0.987038509 0.982607298 1 19.64969543 8 0.298142488 0.99737008 0.038438919 0.800208334 0.017193429 22.84864323 0.326489389 0.017144604 11.65929159 100000000 -8 -0.958931161 EATGLS(ph)PQAAQEKDGIVIVK ddPTM_BT-474_Pertuzumab_2h_R1 2 EATGLSPQAAQEKDGIVIVK 20 1 P17029;C9JRM9 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 EAT(0.001)GLS(0.999)PQAAQEKDGIVIVK;EATGLS(1)PQAAQEKDGIVIVK 178.46 3.74E-17 1207540000 1391760 1199180 635430 784750 743610 874250 756800 833810 635930 523280 TRUE FALSE 1337368.481 1164980.561 750266.3361 825251.0415 767528.891 891927.934 766061.9448 816591.5321 563741.8924 487837.7795 2.741420482 2.38804908 1.537942258 1.691650537 1.573328109 1.828328948 1.570321072 1.67389974 1.155592937 1 18.89604196 8 0.499200109 1.456440845 44.79423237 0.752033197 0.244869785 52.47330925 0.558280237 0.126093393 2383.624353 100000000 -8 43.33779153 up AVPKPDLDSYVFLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVPKPDLDSYVFLR 14 1 E5RFF9;Q9BRT9 E5RFF9 GINS4 "DNA replication complex GINS protein SLD5;DNA replication complex GINS protein SLD5;DNA replication complex GINS protein SLD5, N-terminally processed" 0 ; 86.467 0.0066832 871970000 500690 550410 386720 370030 456210 469310 445630 448220 451250 439700 FALSE TRUE 481122.4813 534712.8457 456608.9065 389127.2926 470884.409 478799.7697 451083.7532 438964.1004 400025.9918 409918.7274 1.173702125 1.304436246 1.113901064 0.949279129 1.148726266 1.168035851 1.100422408 1.070856419 0.975866593 1 18.64497838 8 0.194842744 1.002536326 2.055073169 0.373174626 0.080505125 61.33559608 0.728080633 0.162881725 19.57988312 100000000 -8 1.052536843 EAALSTALSEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 EAALSTALSEKR 12 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 227.48 2.06E-11 1537890000 1085650 1143350 744770 744780 872690 1049810 848880 939280 922410 804490 FALSE TRUE 1043221.598 1110742.777 879366.5063 783218.1851 900760.8664 1071037.877 859268.8474 919883.5398 817701.8839 750001.1757 1.39095995 1.480988048 1.172486837 1.044289276 1.201012606 1.428048265 1.14569 1.226509464 1.090267469 1 19.51653333 8 0.088412333 0.873052204 2.253144046 0.397197374 0.121495216 189.7670205 1.207818108 2.519746841 31.79115449 100000000 -8 1.380091842 EAHLPPGAMAAVGLSWEECK ddPTM_BT-474_Pertuzumab_2h_R1 2 EAHLPPGAMAAVGLSWEECK 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 196.31 1.77E-21 3014000000 3220200 3020300 2582200 2923400 3317400 3387900 3382500 3271600 4060800 4026700 FALSE TRUE 3094351.024 2934164.001 3048860.981 3074277.024 3424107.184 3456405.659 3423896.047 3204040.317 3599835.008 3753968.022 0.824288061 0.781616674 0.812170206 0.818940653 0.912130088 0.920733911 0.912073845 0.853507621 0.958941309 1 21.83998493 8 0.087413003 1.097188356 0.227778491 0.746043504 0.034239439 87.65482254 0.552373874 0.744679603 9.15043604 100000000 -8 -0.869409865 MS(ph)GFIYQGKLPTTGMTITK ddPTM_BT-474_Pertuzumab_2h_R1 2 MSGFIYQGKLPTTGMTITK 19 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;E7EUY6;F6SJA5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 MS(1)GFIYQGKLPTTGMTITK;MS(0.985)GFIY(0.008)QGKLPT(0.006)T(0.002)GMTITK 80.061 0.0047438 337640000 697040 603720 410820 235540 528990 529850 347780 491830 353130 233380 TRUE FALSE 669798.9062 586502.4967 485064.3126 247696.2476 546005.4438 540563.93 352036.2357 481673.5386 313044.1628 217572.9647 3.078502456 2.695658891 2.22943284 1.138451406 2.509527985 2.484517921 1.61801461 2.213848302 1.438800833 1 17.73113978 8 0.072056828 6.62E-13 7.071454626 0.506159432 0.467541733 223.1828307 1.183520881 19.65426816 159.3147006 100000000 -8 7.071454626 EVDEDS(ph)EPEREVR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVDEDSEPEREVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EVDEDS(1)EPEREVR;EVDEDS(1)EPEREVR 210.9 1.58E-08 1157700000 1284400 1438040 669240 756470 1066520 1173190 830080 832100 854180 738500 TRUE FALSE 1234204.228 1397028.507 790186.5552 795511.5074 1100825.584 1196912.706 840238.7673 814916.8442 757217.0674 688480.7372 1.792648888 2.029146833 1.147725002 1.155459353 1.598919948 1.738483941 1.220424511 1.18364509 1.099837696 1 19.39305676 8 0.172091194 0.969472659 4.553844017 0.455212628 0.251020616 57.9467084 0.631060706 0.668769153 53.72180379 100000000 -8 3.584371358 HVGNQQYNVTYVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVGNQQYNVTYVVK 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 0 150.16 7.29E-06 270430000 313560 270500 225650 261890 254270 261240 241060 244520 305670 302190 FALSE TRUE 301305.7285 262785.6048 266429.9746 275406.1743 262448.8255 266522.4518 244010.1644 239470.5766 270971.6231 281722.4021 1.069512848 0.932782068 0.945718099 0.977579959 0.931586638 0.946046355 0.866136887 0.850023196 0.961839105 1 18.10391476 8 0.68835735 0.914886654 17.09970109 0.384483787 0.04664386 266.1735169 1.470227428 0.018345228 6617.102406 100000000 -8 16.18481443 IKSEHPGLSIGDTAK ddPTM_BT-474_Pertuzumab_2h_R1 2 IKSEHPGLSIGDTAK 15 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 179.17 4.10E-07 3396900000 5465200 5598100 4053300 3858200 4576600 5030400 4127000 4498800 4797500 4113900 FALSE TRUE 5251613.942 5438447.669 4785821.475 4057322.164 4723810.495 5132118.135 4177507.461 4405898.208 4252907.913 3835261.889 1.36929735 1.418012075 1.247847374 1.057899638 1.231678731 1.338140206 1.089236558 1.148786794 1.108896351 1 21.87089366 8 0.154304675 0.990429523 2.500123385 0.582809161 0.087122877 50.0082272 0.502320976 0.296672433 17.03108695 100000000 -8 1.509693862 S(ph)IPNGLHDPSSTYIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SIPNGLHDPSSTYIR 15 0 A6NKD9 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 1 S(1)IPNGLHDPSSTYIR 81.884 0.0081636 357410000 279070 273240 183160 188640 203380 178510 142200 255320 153430 153390 TRUE FALSE 268163.6359 265447.4627 216261.0864 198375.733 209921.9024 182119.5945 143940.2861 250047.5528 136013.2696 143000.7587 1.875260232 1.856266115 1.512307266 1.387235528 1.467977543 1.273556841 1.006570087 1.748575008 0.951136699 1 17.12566328 8 0.261094915 1.147573589 6.579111028 0.574006952 0.216920451 40.27931184 0.558092307 0.266354305 97.50475097 100000000 -8 5.431537439 EEASLLSHSPGTSNQSQPCS(ph)PKPIR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHSPGTSNQS(0.249)QPCS(0.751)PKPIR;EEASLLSHSPGT(0.013)S(0.01)NQS(0.04)QPCS(0.937)PKPIR;EEASLLSHSPGT(0.011)S(0.041)NQS(0.196)QPCS(0.752)PKPIR 213.37 2.35E-26 4591330000 2272420 2310020 1981170 2255020 2099130 2394290 2375900 2368060 2730210 2610440 TRUE FALSE 2183611.314 2244140.491 2339211.49 2371401.852 2166650.423 2442704.184 2404976.975 2319158.733 2420288.007 2433632.574 0.897264171 0.922136117 0.961201586 0.974428876 0.890294799 1.003727601 0.988225175 0.952961741 0.994516606 1 21.21467994 8 0.225160292 0.994439966 0.491988535 0.47387314 0.028981518 47.34391228 0.613529289 0.04336222 8.714354068 100000000 -8 -0.502451431 LFDHPESPT(ph)PNPTEPLFLAQAEVYK ddPTM_BT-474_Pertuzumab_2h_R1 3 LFDHPESPTPNPTEPLFLAQAEVYK 25 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LFDHPES(0.157)PT(0.843)PNPTEPLFLAQAEVYK;LFDHPES(0.192)PT(0.808)PNPTEPLFLAQAEVYK;LFDHPES(0.422)PT(0.578)PNPTEPLFLAQAEVYK 315.82 4.35E-74 4465920000 937580 959920 842370 974520 1023320 1070120 1122740 1040870 1326470 1343950 TRUE FALSE 900938.3371 932544.0215 994604.9974 1024815.094 1056236.017 1091758.56 1136480.428 1019375.671 1175894.687 1252923.069 0.719069158 0.744294717 0.793827667 0.81793936 0.843017455 0.87136919 0.907063215 0.813597974 0.93852106 1 20.2568664 8 0.102732353 1.073370947 0.032744435 0.858254623 0.030968344 47.00759048 0.340455238 0.378665905 6.906812769 100000000 -8 -1.040626512 NMS(ph)PDEIKIPPEPPGR ddPTM_BT-474_Pertuzumab_2h_R1 1 NMSPDEIKIPPEPPGR 16 1 X6R3T8;J3QLH3;J3QQJ0;Q9UHR5-2;Q9UHR5;J3KS14;F5H478;J3KRU5 X6R3T8 SAP30BP SAP30-binding protein 1 NMS(1)PDEIKIPPEPPGR 103.26 0.00087977 86234000 130170 113000 106090 92036 110990 105520 92525 110700 123380 103260 TRUE FALSE 125082.8125 109777.3506 125262.823 96785.98899 114560.0941 107653.6867 93657.34863 108414.0063 109374.4197 96266.10823 1.299344232 1.140353055 1.301214158 1.005400455 1.190035582 1.118292706 0.972900539 1.126190809 1.13616746 1 16.55474035 8 0.273487343 1.048036068 2.747607527 0.421132817 0.082992888 50.0290331 0.703220956 0.089542585 40.31199668 100000000 -8 1.699571459 VLSSAAS(ph)LPGSELPSSRPEGSQGGELSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 VLSSAAS(0.999)LPGSELPSSRPEGSQGGELSR;VLSSAAS(1)LPGSELPSSRPEGSQGGELSR 274.85 9.74E-62 2079500000 432510 374610 249020 293440 275900 265330 211715 310390 254969 222236 TRUE FALSE 415607.031 363926.4896 294023.4534 308584.4736 284774.5741 270695.1544 214306.0315 303980.338 226025.988 207183.7578 2.005982687 1.75653967 1.419143357 1.48942406 1.374502409 1.306546214 1.034376603 1.467201586 1.090944534 1 17.66055138 8 0.324906154 1.143664894 9.910645161 0.815189517 0.129361382 23.77020454 0.340020834 0.116821829 124.4417829 100000000 -8 8.766980267 up DITEEIMSGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DITEEIMSGAR 11 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JHW9;F8WCF2 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 221.68 1.92E-11 473340000 208246 216274 182058 218947 205129 233830 229803 244624 243280 264560 FALSE TRUE 200107.5161 210106.0773 214959.9305 230246.8809 211727.1606 238558.2028 232615.3979 239572.4289 215663.8743 246641.1156 0.811330729 0.851869636 0.871549457 0.933530001 0.858442276 0.96722804 0.943133092 0.971340194 0.87440358 1 17.91205379 8 0.23540139 0.975558294 0.002942565 0.612963056 0.036951249 30.96041508 0.410562406 0.04904805 11.69752333 100000000 -8 -0.972615728 EVDFKPFGTLLHTYSVLSPTGGENFTFQIYK ddPTM_BT-474_Pertuzumab_2h_R1 2 EVDFKPFGTLLHTYSVLSPTGGENFTFQIYK 31 1 O14929;O14929-2 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 0 ; 267.51 2.35E-59 568150000 237197 253675 221403 245722 271616 219574 282960 286610 336140 309810 FALSE TRUE 227927.079 246440.4374 261415.4472 258403.7419 280352.7753 224013.9367 286422.9491 280691.4033 297982.7964 288826.2927 0.789149342 0.853247933 0.90509574 0.894668347 0.970662237 0.775600914 0.991678931 0.971834665 1.031702459 1 18.13984256 8 0.160001558 1.042317945 0.121857329 0.510896452 0.059562554 51.38698829 0.530444668 0.174150593 11.1620045 100000000 -8 -0.920460617 FAVQDVNDVLDLEWDQHLEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 FAVQDVNDVLDLEWDQHLEQK 21 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 267.57 3.75E-37 63238000 34873 37467 30576 33798 38087 38754 33112 38943 46694 42206 FALSE TRUE 33510.12461 36398.47784 36101.76336 35542.31883 39312.10294 39537.63243 33517.23456 38138.81344 41393.49288 39347.35003 0.85164883 0.92505538 0.917514479 0.90329638 0.999104207 1.004835965 0.851829527 0.969285439 1.05200205 1 15.26397886 8 0.20745092 1.00081758 0.352036813 0.386786755 0.050627797 62.76252834 0.77551543 0.08983591 13.39844113 100000000 -8 -0.648780766 FLKPVELR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLKPVELR 8 1 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 ; 103.56 0.0043308 755660000 2099900 2243500 1885250 2204200 2255100 2224100 2302500 2555800 2653000 2689000 FALSE TRUE 2017833.586 2179517.577 2225956.612 2317959.026 2327637.34 2269072.826 2330678.684 2503021.837 2351842.562 2506871.635 0.804920985 0.869417303 0.887942 0.924642089 0.928502803 0.90514121 0.929716006 0.998464302 0.938158352 1 21.25745669 8 0.219354864 0.995218846 0.037645867 0.836868987 0.022161925 19.34192512 0.247041408 0.035958282 6.556015324 100000000 -8 -0.95757298 AQS(ph)PGAVEEILDR ddPTM_BT-474_Pertuzumab_2h_R1 3 AQSPGAVEEILDR 13 0 H7BXT7;A0A0C4DH16;B8ZZS0;Q9NYM9;E9PHY4 H7BXT7 BET1L BET1-like protein 1 AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR 182.09 1.21E-05 375890000 243827 279840 230265 294087 257021 305000 300820 311698 342031 376411 TRUE FALSE 234297.9713 271859.2372 271879.0077 309264.8653 265288.3139 311167.309 304501.5251 305261.3274 303205.0748 350916.3477 0.667674712 0.774712375 0.774768715 0.88130652 0.755987333 0.88672788 0.867732516 0.86989771 0.864038044 1 18.42076763 8 0.11146687 1.047922799 0.016056731 0.761490335 0.042764317 50.18109643 0.389164846 0.352977184 7.979785876 100000000 -8 -1.031866069 DSSFFDKFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSSFFDKFFK 10 1 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 156.51 9.87E-06 1600400000 2109730 2302400 1228330 1433950 1607510 1607240 1730930 1879190 1684220 1288330 FALSE TRUE 2027279.419 2236737.806 1450316.555 1507956.331 1659217.019 1639739.494 1752113.639 1840384.07 1493034.406 1201070.262 1.687894109 1.862287227 1.207520161 1.255510506 1.381448756 1.365231949 1.458793624 1.532286768 1.243086649 1 20.19588912 8 0.036749257 6.81E-16 3.655017923 0.437249098 0.177782661 1071.855558 3.00569606 85.98032853 254.4309554 100000000 -8 3.655017923 GGDSIGET(ph)PTPGASKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGDSIGETPTPGASKR 16 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GGDS(0.001)IGET(0.805)PT(0.192)PGAS(0.002)KR 66.12 0.032498 299500000 242460 246240 156260 188690 195960 230750 167970 186730 230440 193700 TRUE FALSE 232984.3951 239217.4763 184499.658 198428.3135 202263.2314 235415.9231 170025.6671 182873.9602 204281.4173 180580.5265 1.290196677 1.324713583 1.021702958 1.098835613 1.120072221 1.303661739 0.941550401 1.012700338 1.13124832 1 17.4622828 8 0.346259578 1.039179409 4.306549708 0.365841692 0.104560698 64.7960747 0.917340643 0.09034672 137.6785957 100000000 -8 3.267370299 HLS(ph)ASTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLSASTPK 8 0 I3L2J0 I3L2J0 CIC 1 HLS(0.98)AS(0.008)T(0.012)PK;HLS(0.997)AS(0.002)TPK 79.16 0.025479 0 538950 469270 359740 351690 375870 368990 338790 386380 382680 363060 TRUE FALSE 517887.2382 455886.8791 424753.0204 369840.763 387960.1999 376451.2306 342936.2134 378401.118 339239.7707 338469.6228 1.530084838 1.346906335 1.254922131 1.092685246 1.146218667 1.112215706 1.01319643 1.1179766 1.002275383 1 18.36866683 8 0.40466015 1.033193023 9.735387967 0.936342077 0.040814115 15.80226203 0.2083997 0.02725067 110.007131 100000000 -8 8.702194944 IACKS(ph)PPPESVDTPTSTK ddPTM_BT-474_Pertuzumab_2h_R1 2 IACKSPPPESVDTPTSTK 18 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 IACKS(1)PPPESVDTPTSTK;IACKS(1)PPPESVDTPTSTK 217.26 5.16E-19 882350000 2088400 1328860 1099740 1074040 1742690 980810 1030580 1383020 915960 869830 TRUE FALSE 2006783.019 1290962.214 1298487.482 1129471.333 1798745.207 1000642.65 1043192.546 1354460.154 811984.0608 810915.6393 2.474712438 1.591980906 1.601260869 1.392834567 2.218165638 1.233966398 1.286437819 1.670284908 1.001317549 1 19.62919231 8 0.148551053 0.93895149 5.113359011 0.489972585 0.328662637 66.13385668 0.645324014 1.160424169 59.43149554 100000000 -8 4.174407522 IQFTSLYHKEEAPAS(ph)PLRPLYPQISPLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 IQFTSLYHKEEAPAS(0.995)PLRPLY(0.004)PQISPLK 80.652 0.0026909 1044000000 783020 955370 569170 623480 685180 898890 643490 636830 790760 675010 TRUE FALSE 752418.7127 928123.783 672031.6801 655657.8775 707219.437 917066.1717 651365.2231 623679.238 700996.2399 629290.9715 1.195661064 1.474872237 1.067918833 1.041899387 1.123835347 1.457300698 1.035077973 0.99108245 1.113946126 1 19.26336772 8 0.13457435 0.939285698 2.172307281 0.200040605 0.150576326 120.0710544 1.08479311 0.738750036 28.29234966 100000000 -8 1.233021583 LGGLRPESPESLTS(ph)VSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.121)PES(0.289)LT(0.289)S(0.302)VSR 206.81 1.75E-11 4850300000 339340 356720 279410 415350 319520 373570 404010 414530 447990 489780 TRUE FALSE 326078.2176 346546.6949 329905.6024 436786.2633 329797.651 381123.8414 408954.3952 405969.8106 397136.0533 456606.7643 0.714133568 0.758960931 0.722515802 0.956591749 0.722279381 0.834687243 0.895638057 0.889101613 0.869755081 1 18.80059271 8 0.087317513 1.123425592 0.003578125 0.585489219 0.062934399 111.2848259 0.700611241 1.219576456 14.94798305 100000000 -8 -1.119847467 QKEELQR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKEELQR 7 1 P80303-2;P80303;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 93.551 0.013545 602300000 623570 720440 585110 689860 699320 667900 712090 735760 877330 851240 FALSE TRUE 599200.195 699893.7566 690852.3927 725463.7573 721814.2629 681405.3956 720804.7704 720566.2989 777739.1765 793584.7566 0.755055071 0.881939517 0.87054645 0.914160398 0.909561653 0.858642243 0.908289587 0.907989087 0.980032908 1 19.59802479 8 0.114979318 1.034251861 0.352917243 0.692913593 0.035363497 62.96393051 0.500985663 0.278242465 6.84135043 100000000 -8 -0.681334618 RRS(ph)PPPGPDGHAKK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRSPPPGPDGHAKK 14 3 P57081;P57081-2;P57081-3 P57081 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 1 RRS(1)PPPGPDGHAKK;RRS(1)PPPGPDGHAKK 70.944 0.030541 76227000 150452 148598 84271 84427 90516 127189 97097 61617 123053 78951 TRUE FALSE 144572.1695 144360.1305 99500.6443 88784.28759 93427.52934 129760.8487 98285.30213 60344.58742 109084.5393 73603.57845 1.964200282 1.961319457 1.351845201 1.206249607 1.269334064 1.762969294 1.335333203 0.819859424 1.482054835 1 16.16748829 8 0.355053811 1.138789041 12.45282931 0.504154936 0.256532926 51.36254654 0.722166011 0.221318388 390.7940884 100000000 -8 11.31404027 S(ph)KSDGEAKPEPSPSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSDGEAKPEPSPSPR 16 2 P26358;K7EJL0;K7ENQ6;K7ERQ1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 S(0.5)KS(0.5)DGEAKPEPSPSPR 85.248 0.0037637 303900000 155190 122440 121730 98001 131810 117990 106270 111570 129930 106980 TRUE FALSE 149125.0032 118948.1311 143729.3189 103058.8434 136049.7884 120375.8386 107570.564 109266.0405 115180.8911 99734.14931 1.495225098 1.192651984 1.441124428 1.033335563 1.364124418 1.206967117 1.078573034 1.095572993 1.154879165 1 16.60579995 8 0.162468303 0.976279897 2.700919246 0.504946136 0.115057658 49.13111076 0.512969687 0.303431417 20.3821596 100000000 -8 1.724639348 TGSGSPFAGNS(ph)PAREGEQDAASLK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGSGSPFAGNSPAREGEQDAASLK 24 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGSGSPFAGNS(1)PAREGEQDAASLK 179.67 2.25E-17 112450000 160140 161650 93439 105340 128140 159040 92716 113800 123980 106840 TRUE FALSE 153881.5518 157039.9003 110325.5058 110776.61 132261.7395 162255.8978 93850.68614 111449.9902 109906.3102 99603.63164 1.544939168 1.576648338 1.107645414 1.112174408 1.327880694 1.629015881 0.942241609 1.118935007 1.103436776 1 16.60391072 8 0.191865047 0.995193947 3.478717939 0.374434657 0.190218153 61.17310242 0.718745505 0.395635602 45.16888236 100000000 -8 2.483523992 TWTDFEHMETIEK ddPTM_BT-474_Pertuzumab_2h_R1 3 TWTDFEHMETIEK 13 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-4;H7C5K1;Q7Z2W4-5 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 ;; 232.6 4.74E-13 668420000 830594 825628 703122 827728 869432 821444 928191 878575 1014528 1028078 FALSE TRUE 798133.4682 802081.8978 830191.7863 870447.1413 897398.0699 838054.1605 939550.4791 860432.1192 899363.0347 958445.3613 0.832737577 0.836857196 0.866185825 0.908186503 0.936305924 0.874389083 0.980285906 0.897737267 0.938356083 1 19.87033666 8 0.147744463 1.001528495 0.357951188 0.708984613 0.029107345 37.72920022 0.366618966 0.103047477 5.192584897 100000000 -8 -0.643577307 (ac)ADANKAEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_BT-474_Pertuzumab_2h_R1 2 ADANKAEVPGATGGDSPHLQPAEPPGEPR 29 1 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 1 ADANKAEVPGAT(0.018)GGDS(0.982)PHLQPAEPPGEPR;ADANKAEVPGAT(0.006)GGDS(0.994)PHLQPAEPPGEPR 103.96 6.65E-45 3413500000 2510920 2646550 1258170 1291950 1810280 2187900 1512130 1488440 1637200 1252760 TRUE FALSE 2412790.47 2571072.985 1485549.307 1358627.694 1868509.3 2232140.837 1530635.899 1457703.194 1451351.92 1167909.449 2.065905428 2.201431786 1.271973018 1.163298829 1.599875146 1.911227654 1.310577545 1.248130319 1.242692163 1 20.15549699 8 0.391729075 1.271757034 15.59256683 0.487154027 0.283954173 64.11882851 0.863116178 0.216078115 703.7489924 100000000 -8 14.3208098 (ac)MDDREDLVYQAK ddPTM_BT-474_Pertuzumab_2h_R1 4 MDDREDLVYQAK 12 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 95.502 0.00010907 4726220000 3898050 3958110 3449440 3731180 3844230 3832650 4065670 4335090 4552980 4489020 FALSE TRUE 3745709.896 3845228.578 4072830.54 3923746.647 3967883.149 3910148.809 4115426.886 4245568.877 4036144.798 4184974.677 0.895037649 0.918817645 0.97320315 0.937579543 0.948125964 0.934330339 0.98338155 1.014478988 0.96443709 1 21.99678746 8 0.184968714 1.011370477 0.522489353 0.632789521 0.021367678 36.00657036 0.41264737 0.049334791 4.99244286 100000000 -8 -0.488881124 AAFDDAIAELDTLSEESYKDSTLIMQLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAFDDAIAELDTLSEESYKDSTLIMQLLR 29 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ; 151.66 2.83E-08 5002600000 211663 205508 142033 135528 165992 189296 150990 142266 168527 151904 FALSE TRUE 203390.976 199647.1131 167701.5226 142522.6163 171331.2834 193123.6948 152837.8608 139328.1574 149396.5215 141615.4068 1.436220681 1.409783848 1.18420394 1.00640615 1.209835055 1.363719522 1.079245996 0.983848866 1.054945397 1 17.1116187 8 0.272277324 1.014780667 4.22695394 0.569114421 0.109721145 40.42184191 0.567487815 0.138704144 61.19515388 100000000 -8 3.212173273 AAKLS(ph)EGS(ph)QPAEEEEDQETPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAKLSEGSQPAEEEEDQETPSR 22 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 AAKLS(1)EGS(1)QPAEEEEDQETPSR 74.058 0.0076865 1093500000 438450 370290 304870 276730 358610 337730 292020 332380 353280 303980 TRUE FALSE 421314.8893 359729.6918 359966.7908 291012.0685 370145.0163 344559.132 295593.8281 325516.2368 313177.1355 283391.1638 1.486690282 1.269375117 1.270211766 1.026891822 1.306127585 1.215842891 1.043059438 1.148646388 1.105105506 1 18.11243525 8 0.43505161 1.103983621 8.553982888 0.628876804 0.087869883 54.85305196 0.683006961 0.053912932 359.3738961 100000000 -8 7.449999267 AEPAKIEAFR ddPTM_BT-474_Pertuzumab_2h_R1 4 AEPAKIEAFR 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 118.28 0.00077169 2341290000 7779200 8355100 3669250 3353700 4922470 5533550 3185710 3639410 3714440 2237700 FALSE TRUE 7475180.264 8116820.728 4332365.097 3526784.859 5080805.718 5645442.172 3224697.672 3564254.912 3292792.343 2086138.586 3.583261589 3.890834858 2.076738874 1.69058033 2.435507282 2.70616833 1.545773466 1.70854177 1.578414956 1 20.99240357 8 0.256475786 1.29862668 18.17764234 0.698110849 0.486807757 29.09387593 0.400515358 0.630593243 213.7246757 100000000 -8 16.87901566 AGMSSNQSISSPVLDAVPRT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQSISSPVLDAVPRT(0.997)PS(0.003)R;AGMSSNQSISSPVLDAVPRT(0.998)PS(0.002)R 259.7 1.74E-43 1568200000 595970 641830 319730 361160 469360 530610 397540 359950 388220 355870 TRUE FALSE 572678.8335 623525.6368 377512.3234 379799.5109 484457.3907 541339.2977 402405.2134 352516.9067 344150.8932 331766.6079 1.726149708 1.879410471 1.137885231 1.144779197 1.460235536 1.63168711 1.212916562 1.062544868 1.037328305 1 18.33980916 8 0.204974166 0.983344767 4.876632696 0.512391412 0.211544944 45.60862981 0.559364124 0.402243896 57.51991861 100000000 -8 3.893287929 AIGTEPDSDVLSEIMHSFAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIGTEPDSDVLSEIMHSFAK 20 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 318.55 1.46E-66 667070000 859080 882850 828490 908330 986500 1041400 983730 980010 1200400 1282380 FALSE TRUE 825506.2038 857671.9824 978216.5727 955209.0202 1018231.668 1062457.822 995769.182 959772.451 1064135.624 1195523.26 0.690497819 0.717403007 0.818232991 0.798988235 0.85170377 0.888696905 0.832914938 0.802805335 0.89010031 1 20.18921077 8 0.073024424 1.148366852 0.029995422 0.787210446 0.038706732 124.7669176 0.669688481 1.711046327 14.24502089 100000000 -8 -1.118371431 AKT(ph)QTPPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 3 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.505)QT(0.501)PPVS(0.919)PAPQPT(0.024)EERLPS(0.024)S(0.024)PVY(0.003)EDAASFK;AKT(0.5)QT(0.5)PPVS(0.999)PAPQPTEERLPSSPVYEDAASFK;AKT(0.5)QT(0.5)PPVS(1)PAPQPTEERLPSSPVYEDAASFK 153.89 2.95E-10 4705220000 241881 257349 146308 135547 176679 210423 153243 169924 174564 131745 TRUE FALSE 232428.0231 250009.6585 172749.1102 142542.5969 182362.0405 214677.8972 155118.4337 166415.01 154748.2266 122821.7938 1.892400493 2.035548014 1.406502094 1.160564363 1.484769395 1.747881142 1.262955286 1.354930626 1.259941105 1 16.90620705 8 0.311021749 1.232544571 8.309866943 0.542478527 0.213439846 45.38591563 0.650201085 0.214356212 180.8993688 100000000 -8 7.077322372 ALLPHVLCK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALLPHVLCK 9 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 86.833 0.013871 463390000 682110 656440 504300 547690 571160 492560 512840 555430 571830 509480 FALSE TRUE 655452.3871 637718.9739 595438.2281 575956.3465 589531.8801 502519.9007 519116.2893 543960.1764 506918.2557 474972.4658 1.379979755 1.34264409 1.253626833 1.212609968 1.241191695 1.057997962 1.092939753 1.145245705 1.067258193 1 18.85748436 8 0.191595367 0.991502119 2.891701851 0.892834659 0.039480908 16.32549625 0.191633554 0.081017266 9.206339892 100000000 -8 1.900199733 ALMDEVVK ddPTM_BT-474_Pertuzumab_2h_R1 4 ALMDEVVK 8 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 136.16 0.0018683 569916000 1053460 1155400 780470 976880 843230 871550 868170 940720 966400 853380 FALSE TRUE 1012289.619 1122449.123 921518.2905 1027296.894 870353.2588 889173.3381 878794.9242 921293.8033 856698.3235 795579.8125 1.272392289 1.410856718 1.15829773 1.291255607 1.093986103 1.117641906 1.104596811 1.158015561 1.076822602 1 19.60164714 8 0.169852452 0.992796804 2.469964032 0.655496158 0.067901307 33.6934208 0.363468276 0.164226034 12.66131528 100000000 -8 1.477167228 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEKEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEKEQR 35 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 197.28 1.28E-27 101680000 113570 152750 40088 35384 74316 113460 51790 54098 55307 33249 FALSE TRUE 109131.5588 148393.7196 47332.79335 37210.17248 76706.44163 115754.2389 52423.82151 52980.8574 49028.78123 30997.01561 3.520711807 4.78735506 1.527011308 1.200443712 2.474639578 3.734367217 1.691253834 1.709224464 1.581725861 1 14.9198417 8 0.357626157 1.658166278 32.64398081 0.362694678 0.961028243 70.85105828 0.99389976 0.808631659 1490.666953 100000000 -8 30.98581453 AVETVHNLCCNENK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVETVHNLCCNENK 14 0 X6RLT1;H0UI80;Q8IXH7-4;Q8IXH7 X6RLT1 NELFCD;TH1L Negative elongation factor C/D 0 193.06 3.02E-07 272950000 130100 146470 103170 145180 146140 146600 144230 142280 177380 174700 FALSE TRUE 125015.5482 142292.819 121815.114 152672.7572 150840.7258 149564.3524 145995.1299 139341.8683 157244.566 162867.4134 0.767590923 0.873672738 0.747940373 0.937405181 0.926156575 0.918319689 0.896404792 0.855554008 0.965475922 1 17.31333845 8 0.160618667 0.984913072 0.228442812 0.536484679 0.052205607 56.78767533 0.587880267 0.157067135 10.18634131 100000000 -8 -0.75647026 AWDLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 AWDLHK 6 0 Q658L1-2;Q658L1 Q658L1-2 FAM154B Protein FAM154B 0 79.033 0.068216 78882000 122830 137050 116330 139170 138130 140570 136600 144350 158570 172270 FALSE TRUE 118029.6678 133141.4682 137353.4187 146352.5804 142573.0769 143412.4217 138271.7517 141369.1221 140569.7984 160601.9995 0.734920289 0.82901501 0.855241026 0.911274958 0.887741606 0.892967847 0.860959092 0.880245094 0.875268047 1 17.29313033 8 0.070538447 1.095035215 0.340660577 0.655967574 0.036969939 180.4546384 0.938564896 1.736955023 13.49979264 100000000 -8 -0.754374638 DAVLLVFANK ddPTM_BT-474_Pertuzumab_2h_R1 2 DAVLLVFANK 10 0 P61204;F5H423;P61204-2;P84077;P84085;C9J1Z8 P61204;P84077;P84085 ARF3;ARF1;ARF5 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5 0 ; 169.12 1.10E-05 694550000 1699330 1831490 1543050 1772250 1809850 1678520 1862290 2108920 2117560 2258200 FALSE TRUE 1632918.305 1779257.698 1821913.46 1863716.035 1868065.469 1712460.824 1885081.262 2065370.065 1877183.466 2105250.103 0.775641005 0.845152648 0.86541426 0.885270606 0.8873366 0.813423936 0.895419152 0.981056865 0.891667676 1 21.0055602 8 0.081333216 1.108781658 0.28718269 0.654684746 0.037926457 119.2940375 0.70538595 1.05340464 11.00182948 100000000 -8 -0.821598968 DCLIEDS(ph)DDEAGQS ddPTM_BT-474_Pertuzumab_2h_R1 2 DCLIEDSDDEAGQS 14 0 H3BSW6;Q2VPK5-3;Q2VPK5;H3BPG4 H3BSW6 CTU2 Cytoplasmic tRNA 2-thiolation protein 2 1 DCLIEDS(1)DDEAGQS;DCLIEDS(1)DDEAGQS 214.58 7.15E-12 359350000 423960 450680 356570 438620 418390 452350 431910 455720 499250 510830 TRUE FALSE 407391.1745 437827.0477 421010.1309 461257.2308 431847.8943 461496.8269 437195.8438 446309.2227 442577.233 476231.0291 0.855448615 0.919358506 0.884045988 0.968557701 0.906803354 0.96906081 0.918033091 0.937169557 0.929333046 1 18.8613021 8 0.077121927 1.046207997 0.62506296 0.522010377 0.028009913 173.5801811 0.97874561 0.839804018 7.82364282 100000000 -8 -0.421145037 DELTES(ph)PKYIQK ddPTM_BT-474_Pertuzumab_2h_R1 1 DELTESPKYIQK 12 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 DELT(0.004)ES(0.996)PKYIQK 165.34 3.32E-05 526260000 940270 754140 466850 388700 703590 719560 462930 446250 527940 399830 TRUE FALSE 903523.2089 732632.6656 551220.18 408760.8536 726221.6113 734109.9962 468595.4758 437034.7816 468010.4645 372749.158 2.423944332 1.965484428 1.47879658 1.096611072 1.948285049 1.969447765 1.25713356 1.172463498 1.255564109 1 18.50784557 8 0.380531972 1.269297803 16.84076257 0.540984847 0.310372199 59.68222314 0.816092249 0.253583625 685.4107259 100000000 -8 15.57146477 DGLNQTTIPVS(ph)PPSTTKPSR ddPTM_BT-474_Pertuzumab_2h_R1 6 DGLNQTTIPVSPPSTTKPSR 20 1 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 DGLNQT(0.001)T(0.001)IPVS(0.488)PPS(0.045)T(0.045)T(0.348)KPS(0.073)R;DGLNQTTIPVS(0.521)PPS(0.138)T(0.199)T(0.138)KPS(0.003)R;DGLNQTT(0.001)IPVS(0.619)PPS(0.056)T(0.056)T(0.222)KPS(0.046)R;DGLNQTTIPVS(0.538)PPS(0.039)T(0.055)T(0.291)KPS(0.078)R;DGLNQTTIPVS(0.979)PPS(0.005)T(0.008)T(0.008)KPSR;DGLNQTTIPVS(0.878)PPS(0.032)T(0.045)T(0.045)KPSR 179.79 3.45E-17 16718320000 1647220 1661830 1584030 1654200 1643230 1822230 1839720 1847510 2001240 2169610 TRUE FALSE 1582844.821 1614436.236 1870299.458 1739573.46 1696085.985 1859076.739 1862235.044 1809358.273 1774067.625 2022660.382 0.782555903 0.798174646 0.924673007 0.860042287 0.83854215 0.919124513 0.920685974 0.894543784 0.877096146 1 20.94782267 8 0.08299354 1.072121503 0.354680609 0.634168638 0.037326847 124.1024483 0.747099685 0.932261499 10.18162955 100000000 -8 -0.717440894 DLADALLDTER ddPTM_BT-474_Pertuzumab_2h_R1 4 DLADALLDTER 11 0 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 0 ;;; 120.09 0.0011599 95965000 138146 147335 130219 145313 147477 144677 154534 159094 167543 182326 FALSE TRUE 132747.1016 143133.1501 153752.47 152812.6213 152220.7316 147602.4681 156425.2333 155808.6533 148524.221 169976.8976 0.780971435 0.842074141 0.904549219 0.899019946 0.895537769 0.86836782 0.920273493 0.916646059 0.873790633 1 17.37497915 8 0.069460761 1.09478575 0.412019372 0.657692094 0.031487936 168.7350202 0.86536183 1.495567747 11.28093955 100000000 -8 -0.682766379 DLLVEGLAEILHQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLVEGLAEILHQK 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 ; 192.51 3.65E-07 194057000 255340 266500 239020 267100 293380 262160 297700 296250 347390 347700 FALSE TRUE 245361.0305 258899.6809 282216.231 280885.063 302816.8341 267461.0548 301343.3417 290132.334 307955.7436 324149.9693 0.756936769 0.798703395 0.870634761 0.866528118 0.934187453 0.825115163 0.929641741 0.895055874 0.950040946 1 18.30630191 8 0.156434903 1.000452025 0.134306483 0.7540343 0.035032482 32.47831828 0.329634927 0.107865586 6.454715299 100000000 -8 -0.866145542 DSLHQPQYVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DSLHQPQYVEK 11 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 146.5 3.57E-05 925320000 1177270 1363500 1137150 1318290 1299320 1292340 1402910 1378830 1553850 1641710 FALSE TRUE 1131260.987 1324614.315 1342658.301 1386327.105 1341113.808 1318472 1420079.232 1350356.679 1377463.462 1530515.519 0.73913722 0.865469378 0.877258861 0.905790949 0.876249728 0.861456146 0.927843733 0.882288785 0.89999967 1 20.54558624 8 0.072295283 1.095091172 0.368757417 0.64369597 0.036821469 164.2075722 0.87339697 1.479659855 12.07321374 100000000 -8 -0.726333755 DSMVMHNS(ph)DPNLHLLAEGAPIDWGEEYSNSGGGGS(ph)PSPSTPESATLSEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSMVMHNSDPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR 50 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 DS(0.203)MVMHNS(0.794)DPNLHLLAEGAPIDWGEEY(0.003)S(0.001)NS(0.002)GGGGS(0.247)PS(0.215)PS(0.245)T(0.245)PES(0.015)AT(0.015)LS(0.015)EKR 63.189 0.00039052 80996000 13357 16192 11643 7857.9 10767 14683 11343 9578.9 11732 9609.3 TRUE FALSE 12834.99367 15730.22001 13747.1491 8263.447161 11113.33033 14979.90032 11481.81903 9381.092368 10400.23254 8958.453552 1.432724253 1.755907973 1.534544887 0.922418932 1.240541157 1.67215248 1.281674227 1.047177653 1.160940611 1 13.12903399 8 0.134690495 0.896986809 3.320711243 0.335402468 0.221532359 92.19373766 0.83350106 1.113350428 42.7453611 100000000 -8 2.423724434 DTSLETR ddPTM_BT-474_Pertuzumab_2h_R1 1 DTSLETR 7 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 107.43 0.03986 0 149840 156710 139370 166630 167480 172300 168940 183550 192300 216650 FALSE TRUE 143984.0871 152240.7842 164557.2593 175229.7943 172867.1463 175784.0241 171007.5383 179759.6284 170470.9102 201976.1025 0.712876847 0.753756421 0.814736284 0.867576867 0.855879206 0.870320904 0.846672137 0.890004442 0.844015248 1 17.62382508 8 0.132752256 0.998027523 0.104399614 0.804343054 0.03250993 36.64747628 0.327539019 0.16726231 6.158258734 100000000 -8 -0.893627909 DTVTISGPQAPVFEFVEQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 DTVTISGPQAPVFEFVEQLR 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 224.33 1.36E-24 183185000 48003.2 45481.8 40909.6 49751 48981.6 51172.2 50091.3 52943.6 56310.9 61852.5 FALSE TRUE 46127.18187 44184.7036 48302.87475 52318.65507 50557.13765 52206.93694 50704.33231 51850.29616 49918.72271 57663.17508 0.799941762 0.766255128 0.837672825 0.90731485 0.876766456 0.905377425 0.879319119 0.899192528 0.865695006 1 15.81536266 8 0.113009066 1.018381414 0.304456874 0.718333321 0.032336065 58.97801723 0.462623903 0.280797756 6.5875702 100000000 -8 -0.71392454 DVESCHDMAALNILK ddPTM_BT-474_Pertuzumab_2h_R1 3 DVESCHDMAALNILK 15 0 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ;; 180.85 6.12E-07 636440000 987430 1176400 992110 1247420 1056450 1130980 1294660 1179070 1325900 1482040 FALSE TRUE 948840.1439 1142850.224 1171406.346 1311799.496 1090431.674 1153849.19 1310504.436 1154721.792 1175389.391 1381660.111 0.686739189 0.827157283 0.847825263 0.949437192 0.789218466 0.835117973 0.948499871 0.835749533 0.850708059 1 20.39797132 8 0.034477196 1.414576083 3.09E-14 0.43854735 0.063973704 1093.483023 2.881463928 35.1950855 97.45442213 100000000 -8 -1.414576083 DVMEGVTVDDHMMK ddPTM_BT-474_Pertuzumab_2h_R1 1 DVMEGVTVDDHMMK 14 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 119.87 0.0001625 117570000 93904 77956 87928 80894 94109 91578 92256 97662 99411 108930 FALSE TRUE 90234.12786 75732.77121 103818.5455 85068.94903 97136.10145 93429.76991 93385.05652 95645.24557 88126.28004 101552.0741 0.888550319 0.745753072 1.022318318 0.837687953 0.95651519 0.920018333 0.919578033 0.941834487 0.867793995 1 16.63186018 8 0.265285667 0.94815433 0.172069305 0.154584991 0.070344822 84.92973373 1.1830505 0.076430801 30.00557244 100000000 -8 -0.776085025 DWPELQDDIPHILAQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 DWPELQDDIPHILAQAR 17 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;; 216.93 5.13E-15 479110000 156448 173869 158992 166492 190776 184985 189384 185527 211576 236084 FALSE TRUE 150333.8392 168910.4264 187725.3912 175084.6721 196912.4833 188725.5234 191701.738 181695.8026 187558.7795 220093.8204 0.683044344 0.767447382 0.852933494 0.795500172 0.894675202 0.857477612 0.871000093 0.825537956 0.852176491 1 17.74775911 8 0.075034176 1.109861161 0.155193145 0.692616484 0.043746561 142.7235385 0.785118047 1.618116117 14.23716296 100000000 -8 -0.954668016 DYQGPLKEHEVTIFVR ddPTM_BT-474_Pertuzumab_2h_R1 1 DYQGPLKEHEVTIFVR 16 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 175.39 2.12E-09 497610000 523890 571200 372010 415870 487620 524620 482070 428550 541190 490660 FALSE TRUE 503415.7996 554909.9353 439240.4823 437333.1005 503304.7401 535228.1758 487969.7169 419700.2927 479756.3801 457427.1612 1.100537621 1.213111031 0.960241367 0.956071562 1.100294829 1.170083942 1.066770315 0.917523769 1.048814808 1 18.80318251 8 0.337759297 1.012515581 2.416874149 0.123546676 0.085398292 120.483415 1.714673022 0.080538693 106.4319915 100000000 -8 1.404358568 EIADGLCLEVEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIADGLCLEVEGK 13 0 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ; 221.09 2.70E-07 284260000 295890 300410 267610 318150 278840 300300 313430 329610 359320 358610 FALSE TRUE 284326.2917 291842.6009 315973.08 334569.7596 287809.1418 306372.2718 317265.8501 322803.4383 318531.5 334321.0253 0.850458901 0.872941212 0.945118781 1.000743999 0.860876583 0.916401448 0.948985634 0.965549319 0.952771366 1 18.35087456 8 0.304664168 0.965518305 3.13E-13 0.432912506 0.038986228 58.05206037 0.831010434 0.040475268 30.70424222 100000000 -8 -0.965518305 EKLTHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EKLTHK 6 1 O95149 O95149 SNUPN Snurportin-1 0 72.234 0.051754 92149000 665510 574920 468800 466500 510680 536530 488490 504490 555880 508310 FALSE TRUE 639501.1334 558523.8445 553522.5884 490576.1209 527106.486 547379.0042 494468.2867 494072.1052 492778.8328 473881.7109 1.349495283 1.178614476 1.168060669 1.035229066 1.112316584 1.155096286 1.043442436 1.042606401 1.039877297 1 18.85416746 8 0.480695086 1.048164108 9.232533959 0.816957854 0.042567791 41.02149124 0.458739054 0.023921979 335.5566494 100000000 -8 8.18436985 ELDLYLAYFVHAADSSQSESPS(ph)QPSDADIK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELDLYLAYFVHAADSSQSESPSQPSDADIK 30 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;A0A590UK73;B1AKN7;S4R3K4 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 ELDLYLAYFVHAADSS(0.002)QS(0.007)ES(0.033)PS(0.912)QPS(0.046)DADIK 102.27 0.0002503 32758000 29905 31338 28707 29953 28058 31623 32948 32474 37951 37216 TRUE FALSE 28736.27954 30444.27092 33894.99348 31498.87792 28960.51105 32262.43873 33351.22748 31803.40055 33642.96158 34695.32717 0.828246392 0.877474675 0.976932522 0.9078709 0.834709265 0.929878498 0.961259922 0.916647951 0.969668377 1 15.08245375 8 0.057214748 1.140517673 0.470341637 0.460399988 0.041272047 376.2993756 1.612378178 3.986235048 21.29962431 100000000 -8 -0.670176036 ELEEQLENETLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEEQLENETLHK 13 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ; 188.4 6.14E-06 335940000 411860 396160 396600 454870 430620 450990 454840 489160 555720 573030 FALSE TRUE 395764.0559 384861.9047 468274.4423 478345.8952 444471.2834 460109.3268 460406.468 479058.6751 492636.9954 534218.1677 0.740828522 0.720420847 0.876560309 0.895413006 0.832003309 0.861276075 0.861832292 0.896747254 0.922164436 1 19.02706951 8 0.133900187 1.016497644 0.085291108 0.754950367 0.038602684 42.73146515 0.384530375 0.200267726 7.559096429 100000000 -8 -0.931206535 ELQAHGADELLK ddPTM_BT-474_Pertuzumab_2h_R1 3 ELQAHGADELLK 12 0 O15144;C9JTV5;G5E9J0 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;; 157.56 7.06E-05 2565200000 3454490 3275630 3202220 3491390 3599140 3474460 3978110 4095100 4501460 4511640 FALSE TRUE 3319484.712 3182212.24 3780932.387 3671581.056 3714909.607 3544715.962 4026795.3 4010534.754 3990473.132 4206062.604 0.78921429 0.756577479 0.89892442 0.872925917 0.883227369 0.842763481 0.957378831 0.953512853 0.948743161 1 22.00403889 8 0.159337759 1.027598829 0.011626009 0.773786971 0.035186497 28.02354533 0.288376519 0.105617293 6.683988636 100000000 -8 -1.01597282 ELS(ph)PQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ELSPQHK 7 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHK;ELS(1)PQHK 90.15 0.011175 1546470000 1073000 1029640 971340 1145200 1059120 1082460 1178140 1196810 1360010 1354430 TRUE FALSE 1031065.974 1000275.675 1146882.745 1204303.909 1093187.557 1104348.083 1192558.43 1172095.455 1205627.366 1262693.25 0.81656093 0.792176307 0.908282946 0.953758096 0.865758613 0.874597281 0.944456169 0.928250353 0.954806218 1 20.26807277 8 0.16389892 1.00069262 0.240330445 0.665869454 0.036095425 39.74280869 0.417651868 0.10649665 7.349375667 100000000 -8 -0.760362175 ENREDYR ddPTM_BT-474_Pertuzumab_2h_R1 2 ENREDYR 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 138.54 0.0025311 638170000 1170560 1368090 609110 614420 894080 1092600 672610 695700 760560 560530 FALSE TRUE 1124813.221 1329073.413 719189.7266 646130.2898 922838.8952 1114693.121 680841.6024 681333.5519 674224.4173 522564.8038 2.152485611 2.543365728 1.376268974 1.236459641 1.765979814 2.1331194 1.302884537 1.30382595 1.290221638 1 18.99525043 8 0.185963023 1.031109009 6.555706304 0.481543181 0.346818943 50.58915479 0.581913642 0.775028085 79.81395651 100000000 -8 5.524597296 EPEAASSRGS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EPEAASSRGSPVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EPEAAS(0.006)S(0.021)RGS(0.973)PVR 116.06 0.00037246 308930000 522080 583720 247510 255980 356120 515010 313520 295160 288840 273860 TRUE FALSE 501676.5364 567072.8771 292240.5628 269191.1585 367574.9232 525423.8551 317356.9515 289064.8429 256052.0941 255311.2183 1.964960803 2.221104427 1.144644426 1.054364788 1.439713169 2.057974023 1.243020004 1.132205803 1.002901854 1 17.96189741 8 0.3597552 1.170564039 13.11845774 0.389933861 0.351029356 70.21947272 0.983081705 0.300577345 574.1984124 100000000 -8 11.9478937 EQIEWLIEHK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQIEWLIEHK 10 0 Q93034 Q93034 CUL5 Cullin-5 0 ; 131.37 0.00025196 221292000 385150 385980 371970 405430 435070 431020 445270 427070 519880 549930 FALSE TRUE 370097.9122 374972.2283 439193.2534 426354.2909 449064.4217 439735.5197 450719.3475 418250.8553 460865.4019 512682.7513 0.721884852 0.731392323 0.856656972 0.831614268 0.875910923 0.857714676 0.879138895 0.815808322 0.898929018 1 18.96770683 8 0.076841238 1.113568666 0.148116364 0.748523026 0.038326233 122.1033715 0.686238227 1.360318105 12.5759973 100000000 -8 -0.965452302 ERRPS(ph)PGEMR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERRPSPGEMR 10 2 A0A0G2JHC2;Q6NYC8-2;Q6NYC8;Q6NYC8-3 A0A0G2JHC2 PPP1R18 Phostensin 1 ERRPS(1)PGEMR;ERRPS(1)PGEMR 99.844 0.0034796 747620000 379180 372120 345030 413390 332840 380280 400070 447760 412450 459200 TRUE FALSE 364361.2264 361507.5019 407384.5962 434725.1074 343546.1009 387969.5222 404966.1763 438513.5995 365630.4051 428097.975 0.851116445 0.84445039 0.951615331 1.015480411 0.802494104 0.90626339 0.945966111 1.024330002 0.854081137 1 18.70758149 8 0.165521931 0.991154156 0.464902724 0.171636636 0.06863455 105.5174447 1.116961145 0.192189968 13.67313974 100000000 -8 -0.526251432 ETPEHPLK ddPTM_BT-474_Pertuzumab_2h_R1 4 ETPEHPLK 8 0 Q8N163-2;Q8N163;H0YB24;G3V119;E5RHJ4 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;;; 89.355 0.013965 2686550000 4727100 4696500 3893450 4508230 4454900 4709200 4675900 4827800 5359000 5189400 FALSE TRUE 4542359.706 4562560.418 4597083.024 4740900.291 4598195.904 4804423.251 4733125.063 4728104.243 4750668.787 4837917.316 0.93890809 0.943083588 0.950219428 0.979946531 0.950449461 0.993076759 0.978339387 0.977301581 0.981965684 1 22.20595468 8 0.191418345 0.998718669 0.702015947 0.745198197 0.010415706 25.36647162 0.297574437 0.019692958 2.230922587 100000000 -8 -0.296702722 GAKEEHGGLIRS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 7 GAKEEHGGLIRSPR 14 2 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR 147.06 4.25E-06 34908190000 37000800 41529500 17858100 19202050 27851540 36517900 23960830 21910580 24704280 19686840 TRUE FALSE 35554767.83 40345119.32 21085455.92 20193070.1 28747410.08 37256316.96 24254069.81 21458118.87 21899953.7 18353432.79 1.937227124 2.198232874 1.148856247 1.100233963 1.566323336 2.029937254 1.321500456 1.169161056 1.193234745 1 24.12954659 8 0.336317661 1.230898486 10.1913651 0.353107571 0.33368341 71.9815477 1.025176221 0.312722987 403.3944784 100000000 -8 8.960466613 GDDLSTAILK ddPTM_BT-474_Pertuzumab_2h_R1 4 GDDLSTAILK 10 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 166.07 1.32E-05 395109000 445185 440012 488060 558453 458860 440053 556247 552797 628273 654495 FALSE TRUE 427786.678 427463.2886 576263.2988 587274.8263 473619.6486 448951.1732 563054.5172 541381.5488 556954.083 610165.4707 0.701099453 0.700569451 0.944437741 0.96248453 0.776215095 0.735785938 0.922789873 0.887270052 0.912791873 1 19.21884101 8 0.114246134 1.035841876 0.136425 0.387876631 0.08480928 124.1776187 0.982849308 0.731910821 17.68526638 100000000 -8 -0.899416876 GGGDRYEDRYDR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGGDRYEDRYDR 12 2 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 208.95 3.42E-08 1930970000 1745600 1905120 970350 1035510 1302260 1751120 1208770 1153010 1198520 1160670 FALSE TRUE 1677380.022 1850787.843 1145713.83 1088952.795 1344148.376 1786528.846 1223563.289 1129199.941 1062469.034 1082056.787 1.550177442 1.710435039 1.05882967 1.006373056 1.242216113 1.651049065 1.130775486 1.043568096 0.981897666 1 20.04534478 8 0.366399519 1.089596206 8.371150546 0.353607152 0.219969205 77.21681384 1.073802076 0.184708094 394.320445 100000000 -8 7.281554341 GIITDS(ph)FGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GIITDSFGR 9 0 C9JUH3;A0A0A0MT72;Q9BSQ5-3;Q9BSQ5-4;Q9BSQ5;Q9BSQ5-2 C9JUH3 CCM2 Cerebral cavernous malformations 2 protein 1 GIITDS(1)FGR;GIITDS(1)FGR;GIITDS(1)FGR;GIITDS(1)FGR 183.03 4.79E-05 934750000 1482450 1487380 1056120 1207670 1180520 1084210 935960 1332170 1008930 986930 TRUE FALSE 1424514.215 1444961.379 1246984.377 1269997.993 1218492.498 1106133.469 947414.5585 1304660.224 894400.4962 920084.352 1.548243063 1.570466203 1.355293539 1.380306045 1.324326944 1.202208761 1.029704023 1.417978929 0.972085325 1 19.81140661 8 0.158259694 0.955171907 3.444446888 0.686798465 0.116718929 37.71025889 0.386088516 0.352516736 21.85185079 100000000 -8 2.489274981 GKGDPNKPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GKGDPNKPR 9 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ;;; 65.535 0.03728 17931520000 9714490 8607400 7110560 6953640 7604360 7184890 7351480 8178980 7676810 7011540 FALSE TRUE 9334836.991 8361925.38 8395596.366 7312518.194 7848961.146 7330173.399 7441449.611 8010081.205 6805370.713 6536642.151 1.428078328 1.279238665 1.284389779 1.118696423 1.200763475 1.121397383 1.138420834 1.225412225 1.041111102 1 22.64011829 8 0.327008455 1.096794218 4.34150291 0.744229626 0.060951844 31.29734833 0.447426094 0.055432497 61.16769305 100000000 -8 3.244708692 GKGFSVVADT(ph)PELQR ddPTM_BT-474_Pertuzumab_2h_R1 5 GKGFSVVADTPELQR 15 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 GKGFSVVADT(1)PELQR;GKGFSVVADT(1)PELQR;GKGFSVVADT(1)PELQR;GKGFSVVADT(1)PELQR;GKGFSVVADT(1)PELQR 208.92 4.28E-09 3245930000 5205570 5955190 2852260 2204978 3301660 4540000 2228374 3331680 2746870 2098847 TRUE FALSE 5002130.569 5785353.812 3367726.83 2318777.179 3407860.892 4631801.911 2255645.508 3262879.644 2435056.833 1956690.223 2.556424369 2.956704001 1.721134388 1.185050731 1.741645587 2.367161575 1.152786211 1.667550441 1.244477437 1 20.89998394 8 0.319636952 1.310649295 16.31762317 0.524951107 0.435261544 45.91679189 0.657525292 0.412830077 402.5551531 100000000 -8 15.00697387 GPPASSPAPAPKFS(ph)PVTPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GPPASSPAPAPKFSPVTPK 19 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPASSPAPAPKFS(0.994)PVT(0.006)PK 109.44 0.00029169 0 363570 373000 210860 179360 319630 356960 249310 256720 303730 231610 TRUE FALSE 349361.2825 362362.4052 248967.0926 188616.7911 329911.1892 364177.9758 252361.1304 251418.6423 269251.8437 215922.8484 1.617991264 1.678203154 1.153037274 0.873537898 1.527912362 1.686611577 1.168756027 1.164391097 1.246981715 1 17.72015639 8 0.124397407 0.965545567 2.826185327 0.242378835 0.242482427 150.1164691 1.273641286 1.591824992 48.69117375 100000000 -8 1.86063976 GQLGHGDTK ddPTM_BT-474_Pertuzumab_2h_R1 3 GQLGHGDTK 9 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 93.096 0.0096307 1563400000 559882 554263 488431 542241 539063 539115 582786 581778 645589 634011 FALSE TRUE 538001.1925 538455.9619 576701.3468 570226.123 556402.451 550016.2747 589918.3094 569764.081 572304.4432 591068.8703 0.910217437 0.910986839 0.975692302 0.964737193 0.941349611 0.930545157 0.998053423 0.963955488 0.9682534 1 19.17296671 8 0.199174525 0.991017917 0.618434443 0.529333861 0.02099521 44.47718821 0.53561025 0.039929291 5.17133002 100000000 -8 -0.372583474 GRS(ph)KDRDPNR ddPTM_BT-474_Pertuzumab_2h_R1 2 GRSKDRDPNR 10 3 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 GRS(1)KDRDPNR;GRS(1)KDRDPNR 87.498 0.070925 1310821000 892497 839150 431407 506114 721526 725879 594397 660182 712353 519409 TRUE FALSE 857617.2305 815218.2636 509371.8415 532234.6042 744734.5391 740556.7707 601671.4083 646549.011 631489.6739 484228.9658 1.771098573 1.683538824 1.051923527 1.099138304 1.537980153 1.529352482 1.242534939 1.335213415 1.304113794 1 18.88532986 8 0.073809292 0.752147492 2.8515559 0.328917989 0.207877131 328.4871503 1.780317381 8.351280677 71.04709102 100000000 -8 2.099408408 GS(ph)PRYS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 GSPRYSPR 8 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 GS(1)PRY(0.022)S(0.978)PR;GS(1)PRY(0.024)S(0.976)PR;GS(1)PRY(0.053)S(0.947)PR;GS(1)PRY(0.102)S(0.899)PR;GS(1)PRY(0.022)S(0.978)PR;GS(1)PRY(0.022)S(0.978)PR 100.72 0.0033586 4372680000 4497010 4827650 2818420 3377930 3809300 3493930 3616750 3169630 3380200 3085190 TRUE FALSE 4321261.877 4689970.149 3327771.189 3552265.372 3931829.594 3564579.658 3661012.868 3104176.033 2996493.867 2876227.333 1.502406235 1.630597865 1.156991713 1.235043326 1.367009328 1.239324728 1.272852401 1.079252671 1.041813987 1 21.45574628 8 0.167339849 0.946720271 3.405287075 0.67424023 0.109295584 35.5226314 0.379055546 0.296251641 21.802909 100000000 -8 2.458566804 GSDEPPVFLEIHYK ddPTM_BT-474_Pertuzumab_2h_R1 3 GSDEPPVFLEIHYK 14 0 P28838-2;P28838;H0Y9Q1 P28838-2 LAP3 Cytosol aminopeptidase 0 ;; 194.85 9.63E-08 788690000 1025435 1051910 895907 1186070 985559 1051057 1239795 1126165 1271776 1351839 FALSE TRUE 985359.8665 1021910.557 1057817.324 1247283.215 1017260.4 1072310.093 1254967.982 1102909.299 1127409.32 1260277.74 0.781859296 0.810861387 0.839352541 0.989689157 0.8071716 0.850852204 0.995786835 0.875131936 0.894572112 1 20.26531028 8 0.140573201 0.995693972 0.293168271 0.425283471 0.059734709 76.9277733 0.719241601 0.250162358 10.88016487 100000000 -8 -0.702525701 GSLAADKVVEEIRR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSLAADKVVEEIRR 14 2 P51659-3;P51659;P51659-2;A0A2R8YD50;E7ER27;A0A2R8YDT8;A0A2R8YF45 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 126.16 4.89E-05 342770000 327090 375740 264980 291000 271160 288410 346910 296430 297670 298920 FALSE TRUE 314306.9612 365024.2631 312867.7804 306018.5449 279882.1077 294241.8478 351155.5884 290308.6169 263879.7495 278673.8821 1.12786659 1.309861765 1.1227022 1.098124239 1.004335625 1.055864459 1.260095082 1.041750359 0.946912382 1 18.08821827 8 0.152027886 0.972785759 1.879165161 0.305605426 0.090822719 86.23529131 0.856487698 0.315375839 17.31152042 100000000 -8 0.906379401 GVVEVTHDLQK ddPTM_BT-474_Pertuzumab_2h_R1 4 GVVEVTHDLQK 11 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ;;; 199.68 4.94E-08 6364000000 9999400 11386600 9654800 10875500 10424700 10295100 11911200 11549600 13681900 13058800 FALSE TRUE 9608612.393 11061865.32 11399637.13 11436785.86 10760019.94 10503273.98 12056972.83 11311096.72 12128788.07 12174315.84 0.789252761 0.908623159 0.936367782 0.939419184 0.883829538 0.862740388 0.990361428 0.929095061 0.996260342 1 23.53733736 8 0.147786366 1.014129338 0.408233925 0.524185604 0.04339456 62.6309978 0.608725333 0.160964261 8.117883465 100000000 -8 -0.605895413 GYFEYIEENK ddPTM_BT-474_Pertuzumab_2h_R1 4 GYFEYIEENK 10 0 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 258.47 7.19E-17 2378220000 3120080 2694910 3168620 2999330 3195920 2851800 3337420 3940680 3771920 3892800 FALSE TRUE 2998143.824 2618053.805 3741260.12 3154125.781 3298719.669 2909465.35 3378264.344 3859303.581 3343747.455 3629137.189 0.8261313 0.721398412 1.030895203 0.869111752 0.908954249 0.80169616 0.930872593 1.063421794 0.921361547 1 21.79119516 8 0.171377765 1.030232433 0.051456875 0.295944027 0.085057021 68.73845788 0.746342063 0.218323039 17.31027326 100000000 -8 -0.978775558 IASLEVENQSLR ddPTM_BT-474_Pertuzumab_2h_R1 3 IASLEVENQSLR 12 0 P29692;P29692-2;E9PRY8;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;H0YCK7;E9PIZ1;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;; 225.22 4.24E-11 723268000 419333 478802 370476 459200 426163 443727 502678 487400 528613 532529 FALSE TRUE 402945.0028 465147.0358 437429.2544 482899.367 439870.9199 452699.464 508829.9237 477335.0197 468607.0684 496460.3365 0.811635841 0.936926883 0.881096076 0.972684687 0.886014224 0.911854242 1.02491556 0.961476647 0.943896287 1 18.92131894 8 0.253313558 0.9877532 0.062783411 0.520189792 0.041291987 41.38779883 0.567041079 0.050972577 16.38868442 100000000 -8 -0.924969789 IEYVHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEYVHTK 7 0 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;A0A590UK94;Q8N752 P48729-2 CSNK1A1;CSNK1A1L Casein kinase I isoform alpha;Casein kinase I isoform alpha-like 0 89.55 0.017791 458480000 428110 449050 388760 454270 434630 417350 489350 485460 535260 528070 FALSE TRUE 411378.9879 436243.5337 459017.5799 477714.9291 448610.2687 425789.1029 495338.8117 475435.0814 474499.5288 492303.3485 0.835620942 0.886127496 0.932387686 0.970367012 0.911247648 0.864891747 1.006165839 0.96573603 0.963835672 1 18.90918803 8 0.229944413 0.98967615 0.20821802 0.542181828 0.037090361 41.8577319 0.548522448 0.05658471 12.31926171 100000000 -8 -0.781458131 IGDEYAEDS(ph)S(ph)DEEDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IGDEYAEDSSDEEDIR 16 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 2 IGDEYAEDS(1)S(1)DEEDIR;IGDEYAEDS(1)S(1)DEEDIR 190.46 1.25E-09 1403380000 261369 264210 239296 286360 264259 277150 292310 312020 337300 339560 TRUE FALSE 251154.4105 256674.9895 282542.1103 301139.0739 272759.1307 282754.1629 295887.3772 305576.678 299011.1181 316561.2988 0.793383182 0.810822392 0.892535226 0.951282027 0.861631323 0.893205089 0.934692201 0.965300178 0.94455993 1 18.27212536 8 0.203779791 0.993812046 0.005740822 0.772114738 0.030474275 25.44495864 0.310924193 0.057682293 8.082374573 100000000 -8 -0.988071224 IHEKDPNSATATAPPS(ph)PLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 IHEKDPNSATATAPPSPLKR 20 2 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6 Q92766 RREB1 Ras-responsive element-binding protein 1 1 IHEKDPNSATATAPPS(1)PLKR;IHEKDPNSATATAPPS(1)PLKR 178.53 3.21E-17 802370000 921270 628480 484750 562960 599840 434560 484770 386810 544170 506810 TRUE FALSE 885265.7499 610556.3657 572355.1082 592014.4331 619134.3984 443347.1009 490702.7603 378822.2383 482398.1029 472483.3073 1.8736445 1.292228437 1.211376358 1.252984865 1.310383645 0.938333893 1.038561051 0.801768512 1.020984436 1 18.84990383 8 0.382182606 0.930875098 13.3047278 0.801708654 0.125622102 29.63596592 0.404356866 0.097907951 272.0163437 100000000 -8 12.3738527 ILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVR 36 1 P38606;C9JVW8 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 177.71 4.56E-23 167790000 255116 252589 220330 248896 260941 259515 267550 256855 324917 297679 FALSE TRUE 245145.7847 245385.409 260148.5322 261741.5524 269334.4042 264762.5711 270824.3569 251550.8545 288033.7843 277516.9362 0.883354321 0.884217779 0.937414977 0.943155239 0.970515198 0.954041129 0.975884069 0.906434245 1.037896239 1 18.08221629 8 0.270716884 0.983559294 0.187378823 0.560858151 0.031223357 42.02203192 0.588992671 0.036404027 15.64801173 100000000 -8 -0.79618047 IPPNATLVFEVELFEFKGEDLTEEEDGGIIRR ddPTM_BT-474_Pertuzumab_2h_R1 2 IPPNATLVFEVELFEFKGEDLTEEEDGGIIRR 32 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 212.39 5.77E-28 330910000 226290 185212 106746 83048 143139 216990 126501 133486 138181 98955 FALSE TRUE 217446.3366 179929.9351 126037.3768 87334.11723 147743.1959 221377.6865 128049.1571 130729.4675 122495.2722 92252.68971 2.357073136 1.950403134 1.366218992 0.946683696 1.601505565 2.399688152 1.388026273 1.417080281 1.327823314 1 16.49330335 8 0.109891734 0.883261723 4.165762697 0.287915051 0.406747423 174.9225176 1.340604255 4.0034863 87.12344418 100000000 -8 3.282500974 ISVYYNEATGGK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISVYYNEATGGK 12 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 ;; 255.52 8.96E-21 1271216000 843824 942186 797925 942569 840576 927151 966768 1047602 1073650 1118307 FALSE TRUE 810846.4252 915315.7778 942127.7972 991215.099 867613.8904 945898.6285 978599.596 1025968.653 951773.7531 1042563.071 0.777743283 0.877947631 0.903665038 0.950748331 0.832193193 0.907281924 0.938647861 0.984083056 0.912917194 1 19.99170323 8 0.185136323 0.99422923 0.214701029 0.584563382 0.041107908 41.32033069 0.47384062 0.0901128 9.145957638 100000000 -8 -0.779528201 ITGMLLEIDNSELLHMLESPESLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ITGMLLEIDNSELLHMLESPESLR 24 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YB75;H0YAS6;H0YAS7;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0Y6X6;H0YER0 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ;;; 169.41 7.01E-12 623646000 86907.1 98317.7 88280.3 89604.3 109118.3 108734.3 98244.2 116360.2 101297.5 134153.4 FALSE TRUE 83510.67445 95513.77546 104234.514 94228.78866 112628.1892 110932.982 99446.54191 113957.3212 89798.63247 125067.0707 0.667727116 0.763700428 0.833428922 0.753426047 0.900542314 0.886987929 0.795145687 0.911169667 0.718003803 1 16.93234246 8 0.097053895 1.031580313 0.159911404 0.424103226 0.073413662 133.5510027 0.92152053 0.981100107 15.49824789 100000000 -8 -0.87166891 KAAALEFLNRFEEAKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAAALEFLNRFEEAKR 16 3 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 123.03 3.95E-05 189340000 212430 250790 106360 105480 162390 209140 125020 120050 157330 108470 FALSE TRUE 204128.0007 243637.7147 125581.618 110923.8354 167613.4218 213368.9541 126550.0322 117570.9255 139470.558 101123.2303 2.018606409 2.409314992 1.241867152 1.096917445 1.657516491 2.1099895 1.251443727 1.162650018 1.379213832 1 16.62575493 8 0.292100644 1.210334982 9.2622056 0.366751077 0.369091255 60.26279773 0.858881366 0.408753724 251.2230156 100000000 -8 8.051870618 KDNDFIYHDR ddPTM_BT-474_Pertuzumab_2h_R1 4 KDNDFIYHDR 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 143.17 2.24E-05 7248400000 8755200 9309100 8325400 9257800 9041500 9373300 10314500 10192700 11346000 11546400 FALSE TRUE 8413037.105 9043613.583 9829984.978 9735596.167 9332328.059 9562834.548 10440731.94 9982217.183 10058049.65 10764352.04 0.781564656 0.840144725 0.91319802 0.904429373 0.866966077 0.888379952 0.969935942 0.927340275 0.934385052 1 23.35975814 8 0.184538448 0.990197588 0.171858737 0.766711681 0.028891722 28.16715752 0.322285938 0.064899275 6.517861091 100000000 -8 -0.818338851 KFDLGQDVIDFTGHALALYR ddPTM_BT-474_Pertuzumab_2h_R1 2 KFDLGQDVIDFTGHALALYR 20 1 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 213.5 4.39E-23 3791000000 1921500 2152530 1339680 1550330 1804250 1962600 1641380 1691400 1919810 1766710 FALSE TRUE 1846405.656 2091141.952 1581789.977 1630342.717 1862285.34 2002285.117 1661467.699 1656471.999 1701881.217 1647049.158 1.121038584 1.26962935 0.960378122 0.989856744 1.130679877 1.215680241 1.008754166 1.005721044 1.033291088 1 20.65145218 8 0.185651751 0.995803126 1.723281574 0.168455194 0.091102028 100.1545968 1.150724124 0.202717719 20.76234541 100000000 -8 0.727478448 KHPDSSVNFAEFSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KHPDSSVNFAEFSK 14 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 170.79 2.02E-06 21072000000 6065600 5519400 5100600 4593700 4964800 4994200 5169900 5517200 5377500 5053000 FALSE TRUE 5828549.646 5361992.116 6022391.882 4830781.408 5124497.301 5095186.146 5233170.783 5403267.892 4767068.744 4710755.809 1.237285455 1.138244548 1.278434316 1.025479053 1.08782911 1.081606934 1.110898334 1.147006576 1.011954119 1 22.16752712 8 0.187816502 1.024122919 1.923547674 0.479385887 0.063256583 54.03171214 0.625748054 0.132126799 14.05649598 100000000 -8 0.899424755 KMDLIDLEDETIDAEVMNSLAVTMDDFR ddPTM_BT-474_Pertuzumab_2h_R1 14 KMDLIDLEDETIDAEVMNSLAVTMDDFR 28 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;;;;;;; 277.98 7.60E-62 3444157000 1216181.8 1277035 1080830.3 1243526 1249280 1382881 1353230 1521116 1588930 1704048 FALSE TRUE 1168652.071 1240615.212 1276160.378 1307704.526 1289464.226 1410843.801 1369791.234 1489704.423 1408561.328 1588631.311 0.735634544 0.780933375 0.803308086 0.823164265 0.811682495 0.888087621 0.862246151 0.937728227 0.886650866 1 20.59935291 8 0.100148009 1.094269689 0.046030738 0.918980436 0.021161495 29.62585592 0.209977034 0.249823957 4.269795098 100000000 -8 -1.048238951 KRS(ph)SSEDAESLAPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KRSSSEDAESLAPR 14 2 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 KRS(0.94)S(0.058)S(0.002)EDAESLAPR;KRS(0.604)S(0.069)S(0.326)EDAES(0.001)LAPR 167.99 2.80E-06 1460960000 603750 662590 334830 337070 452220 527310 346030 384030 364540 320110 TRUE FALSE 580154.7825 643693.5819 395341.2293 354466.2231 466766.067 537972.5695 350264.8186 376099.6463 323158.9475 298428.6646 1.944031695 2.156942876 1.324742815 1.187775389 1.5640792 1.802683969 1.173696968 1.260266492 1.082868323 1 18.18702659 8 0.221653206 1.04372155 6.456245884 0.567749053 0.247339985 39.09391754 0.502260495 0.40070567 75.93147339 100000000 -8 5.412524333 KRSGNS(ph)DSIER ddPTM_BT-474_Pertuzumab_2h_R1 1 KRSGNSDSIER 11 2 C9J8U3;A0A0A0MRW7;Q7Z2E3-4;Q7Z2E3-5;Q7Z2E3-10;Q7Z2E3-8;Q7Z2E3-7;Q7Z2E3;A0A5F9ZI51;A0A5F9ZGW5;Q7Z2E3-13;Q7Z2E3-9;Q7Z2E3-11 C9J8U3 APTX Aprataxin 1 KRS(0.329)GNS(0.569)DS(0.102)IER 76.262 0.026279 0 183900 192640 101320 107300 162320 166410 139040 154020 141090 125950 TRUE FALSE 176712.9847 187146.0958 119630.7779 112837.7659 167541.1702 169774.9242 140741.6131 150839.4332 125074.0547 117419.2943 1.504973997 1.593827462 1.018834073 0.960981468 1.42686235 1.445886089 1.198624246 1.284622208 1.065191674 1 16.84130997 8 0.039336051 0.297260457 2.823353014 0.253940581 0.191265407 1341.041861 4.017302247 71.34617126 227.6767616 100000000 -8 2.526092557 KS(ph)PRPAGPQLFLPDPDPQR ddPTM_BT-474_Pertuzumab_2h_R1 5 KSPRPAGPQLFLPDPDPQR 19 2 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR 119.76 2.79E-05 5519170000 11089200 11417000 8046400 7647900 8504100 9256900 6927400 8547200 8773900 7608400 TRUE FALSE 10655821.8 11091398.34 9500563.471 8042609.036 8777642.1 9444080.86 7012179.593 8370697.333 7777923.655 7093076.291 1.502284956 1.563693648 1.339413688 1.13386755 1.237494387 1.331450625 0.988594977 1.180122276 1.096551529 1 22.75798003 8 0.240492446 1.02067525 4.439143683 0.732383625 0.096502005 24.66348447 0.330429376 0.129763887 33.69134472 100000000 -8 3.418468432 KSEAPSGESR ddPTM_BT-474_Pertuzumab_2h_R1 5 KSEAPSGESR 10 1 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;;;; 182.35 2.87E-06 746427000 1553000 1604320 1400470 1623580 1603340 1692110 1736460 1666430 1970090 2022270 FALSE TRUE 1492307.043 1558566.364 1653566.082 1707373.158 1654912.887 1726325.624 1757711.317 1632017.638 1746453.642 1885299.852 0.79154891 0.826694153 0.877083866 0.905624194 0.877798238 0.915676953 0.93232454 0.865654149 0.926353249 1 20.84636257 8 0.116461648 1.012428146 0.390775351 0.757256039 0.027294271 56.97758463 0.458154802 0.22501365 5.729823314 100000000 -8 -0.621652795 KTEFLDLDNSPLSPPS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 KTEFLDLDNSPLSPPSPR 18 1 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 KTEFLDLDNSPLS(0.002)PPS(0.998)PR 201.97 8.23E-16 123660000 215240 215010 189810 229460 221890 218140 217800 247780 253320 272050 TRUE FALSE 206828.1828 208878.1253 224112.8893 241302.4581 229027.2934 222550.9403 220465.5016 242663.2564 224564.1756 253623.8112 0.815491976 0.823574586 0.883642937 0.951418784 0.903019682 0.87748441 0.869261843 0.956784204 0.88542229 1 17.95233067 8 0.084760522 1.058154419 0.445011787 0.561875081 0.036660998 139.5998776 0.856194058 0.871739814 9.982004486 100000000 -8 -0.613142631 LAEQAERYDEMVESMK ddPTM_BT-474_Pertuzumab_2h_R1 5 LAEQAERYDEMVESMK 16 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;; 267.62 2.16E-27 2571576000 2143871 2104163 1258706 1067552 1734850 1777646 1290745 1334199 1686314 1205486 FALSE TRUE 2060086.151 2044154.331 1486182.174 1122648.487 1790653.026 1813591.22 1306541.523 1306647.324 1494890.704 1123837.359 1.833082104 1.818905836 1.322417485 0.998942131 1.593338227 1.613748827 1.162571712 1.162665855 1.330166409 1 20.10000183 8 0.435722588 1.220896518 15.58066121 0.473296851 0.216249353 75.80614118 0.94258081 0.142319735 959.2012508 100000000 -8 14.35976469 LAS(ph)YLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LAS(0.998)Y(0.002)LDR 89.886 0.018403 39598000 77448 64188 48197 42968 60280 48472 42351 52780 46407 42079 TRUE FALSE 74421.24654 62357.42109 56907.27004 45185.58363 62218.96094 49452.13705 42869.30421 51690.07456 41139.07191 39228.95185 1.897100051 1.589576528 1.450644673 1.151842746 1.586046989 1.260603068 1.092797594 1.317651176 1.048691591 1 15.25963117 8 0.299121491 1.103302407 7.550554846 0.739375904 0.13973567 28.11847844 0.40192651 0.140162194 96.89438063 100000000 -8 6.447252439 LGSDEKELILLFWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSDEKELILLFWK 14 1 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 144.12 8.15E-06 62304000 216390 214610 134410 99534 164270 205200 132590 125300 148200 124080 FALSE TRUE 207933.2396 208489.5329 158700.8769 104670.9617 169553.8937 209349.2846 134212.6761 122712.5112 131376.9573 115675.9511 1.797549427 1.802358494 1.371943567 0.904863636 1.465766152 1.809790908 1.160247008 1.060829931 1.135732675 1 16.81972944 8 0.264699724 1.079659732 6.306182393 0.426831366 0.252958877 53.62626075 0.746465662 0.327233596 127.2164974 100000000 -8 5.22652266 LLEELEEGQKGVGDGTVSWGLEDDEDMTLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLEELEEGQKGVGDGTVSWGLEDDEDMTLTR 31 1 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;E5RIF1;D6RG00;H0YBX6 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 ;;; 266.67 4.63E-59 162790000 243956 276716 111730 91270.3 163870 219668 115734 134057 136598 90314.8 FALSE TRUE 234421.9298 268824.3306 131922.0964 95980.77112 169141.0274 224109.8375 117150.3873 131288.6761 121091.9677 84197.69815 2.784184544 3.192775296 1.566813575 1.13994531 2.008855718 2.66170979 1.391372803 1.559290562 1.438186202 1 16.36149317 8 0.3949975 1.481597072 26.97337736 0.444787379 0.533442319 68.84102814 0.922111312 0.39544701 1359.819915 100000000 -8 25.49178029 LLGGQLGLEDFIFAHVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLGGQLGLEDFIFAHVK 17 0 Q8TF65 Q8TF65 GIPC2 PDZ domain-containing protein GIPC2 0 ; 197.14 1.54E-11 300040000 668070 713110 609040 718720 693780 719690 805120 803870 890670 947330 FALSE TRUE 641961.0858 692772.801 719107.076 755813.2253 716096.0638 734242.6249 814973.2994 787269.8036 789564.8756 883166.4953 0.726885688 0.784419251 0.81423727 0.855799251 0.810827933 0.83137509 0.922785572 0.891417199 0.894015885 1 19.75232592 8 0.090845128 1.104354832 0.094162233 0.882465671 0.025193323 48.48209424 0.315969503 0.453813069 6.103904582 100000000 -8 -1.010192599 LPLPS(ph)PALEYTLGSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LPLPSPALEYTLGSR 15 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 LPLPS(1)PALEYTLGSR;LPLPS(1)PALEYTLGSR;LPLPS(1)PALEYTLGSR;LPLPS(1)PALEYTLGSR 142.85 4.74E-06 879432000 467174 408824 291569 333881 342533 317279 262960 367845 314766 268672 TRUE FALSE 448916.3236 397164.7398 344262.0042 351112.6384 353550.885 323694.5988 266178.1831 360248.8722 279035.0833 250474.6061 1.792262819 1.585648725 1.374438749 1.401789362 1.411523869 1.292325014 1.062695286 1.438265051 1.11402544 1 17.93430482 8 0.225155932 1.091731182 4.70199389 0.759677791 0.11285476 26.04596128 0.337525803 0.171416547 34.44649982 100000000 -8 3.610262708 LS(ph)PCLHR ddPTM_BT-474_Pertuzumab_2h_R1 3 LSPCLHR 7 0 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 LS(1)PCLHR;LS(1)PCLHR;LS(1)PCLHR 120.15 0.0029763 1072020000 824830 813600 787230 970290 893770 803930 978130 980770 1091720 1166870 TRUE FALSE 792594.7317 790396.9246 929499.9728 1020366.783 922518.9238 820186.0154 990100.6475 960516.7568 967792.5225 1087836.856 0.728597057 0.726576711 0.854447952 0.937977766 0.848030584 0.753960496 0.910155454 0.8829603 0.889648588 1 20.05303078 8 0.102891398 1.052399333 0.158500983 0.558812663 0.057764826 101.9507462 0.739351315 0.703799044 12.88840228 100000000 -8 -0.893898349 LVEALCAEHQINLIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LVEALCAEHQINLIK 15 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ; 220.21 1.70E-12 2376700000 2578500 2684700 2224700 2616900 2764300 2822000 2629600 2808100 3113000 3270900 FALSE TRUE 2477729.369 2608134.985 2626752.778 2751958.523 2853216.22 2879062.774 2661781.831 2750111.754 2759625.291 3049359.03 0.812541044 0.855305971 0.861411448 0.902471141 0.935677364 0.944153426 0.872898798 0.901865516 0.904985364 1 21.54007459 8 0.07831233 1.05935608 0.474747959 0.663463086 0.029075122 147.7674989 0.844724936 0.973849077 9.371557077 100000000 -8 -0.584608122 LVILEGELERAEER ddPTM_BT-474_Pertuzumab_2h_R1 4 LVILEGELERAEER 14 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 190.27 5.68E-07 137923000 203394 237671 77744 90398 143653 202211 106375 94637 107706 78357 FALSE TRUE 195445.1376 230892.8558 91794.07021 95063.45161 148273.7292 206299.845 107676.8491 92682.71288 95479.66642 73049.8106 2.675505056 3.16075913 1.256595595 1.301351103 2.029761994 2.824098287 1.474019552 1.268760482 1.307048788 1 16.15659291 8 0.191783355 1.041026856 8.92420093 0.397185036 0.577176598 59.89017377 0.703471394 1.23055452 140.2904804 100000000 -8 7.883174074 LYSLLGIDLTAPS(ph)NNSSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPR 19 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 LYSLLGIDLTAPS(0.333)NNS(0.333)S(0.333)PR 152.02 6.28E-08 131250000 117050 113580 138970 154190 127310 128860 143590 147550 181050 185950 TRUE FALSE 112475.5566 110340.8096 164084.9704 162147.7644 131405.0418 131465.6375 145347.2974 144503.0409 160497.963 173355.4409 0.64881469 0.636500412 0.946523337 0.935348574 0.758009331 0.758358877 0.838435163 0.833565074 0.925831703 1 17.40337359 8 0.095454679 1.072931377 0.03373087 0.428439559 0.090530926 162.5094494 1.105449791 1.45821901 22.10824043 100000000 -8 -1.039200507 MALPPQEDATAS(ph)PPRQK ddPTM_BT-474_Pertuzumab_2h_R1 2 MALPPQEDATASPPRQK 17 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.008)AS(0.992)PPRQK;MALPPQEDAT(0.367)AS(0.633)PPRQK 148.75 2.12E-07 1282590000 1383590 1616820 695730 721690 1072910 1390110 869250 906860 945290 780420 TRUE FALSE 1329517.773 1570709.877 821463.8874 758936.5074 1107421.125 1418218.977 879888.1415 888133.0241 837984.6422 727561.4583 1.827361466 2.158868998 1.129064601 1.043123572 1.522099765 1.94927722 1.20936607 1.220698285 1.151771624 1 19.47270959 8 0.379297322 1.227624508 12.19797749 0.327459498 0.324066635 84.02157116 1.150757191 0.255639945 676.8833374 100000000 -8 10.97035298 MIPCDFLIPVQTQHPIRK ddPTM_BT-474_Pertuzumab_2h_R1 4 MIPCDFLIPVQTQHPIRK 18 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;;; 142.01 7.52E-08 6772540000 11059450 11895420 6826960 7771010 8224050 8794240 7081150 8017800 8050040 6363490 FALSE TRUE 10627234.47 11556174.27 8060743.537 8172072.757 8488584.037 8972065.558 7167811.232 7852229.628 7136233.208 5932485.154 1.791363011 1.947948283 1.358746516 1.377512551 1.430864775 1.512362075 1.208230791 1.323598698 1.202907891 1 22.50020515 8 0.193521854 1.044562322 4.883643672 0.743934564 0.134673947 26.87961356 0.317636931 0.264039241 31.02328099 100000000 -8 3.83908135 MTESWFSSLSRDPLELFR ddPTM_BT-474_Pertuzumab_2h_R1 1 MTESWFSSLSRDPLELFR 18 1 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 141.97 1.06E-07 47603000 119000 155470 78022 91444 105900 111750 101230 90861 99878 88464 FALSE TRUE 114349.3484 151036.1478 92122.31099 96163.4358 109306.3697 114009.6616 102468.883 88984.6886 88540.26816 82472.25448 1.386519008 1.831357088 1.117009733 1.166009543 1.325371428 1.382400206 1.242464919 1.078965152 1.073576425 1 16.33162123 8 0.159627959 0.940698816 3.34925234 0.427368392 0.173622484 58.12337348 0.59893351 0.517617494 32.94000388 100000000 -8 2.408553524 NADSELMPPPPERGDPPRLS(ph)PDPVAGSAVSQELR ddPTM_BT-474_Pertuzumab_2h_R1 1 NADSELMPPPPERGDPPRLSPDPVAGSAVSQELR 34 2 Q9BUR4;E9PMG4;E9PMR3 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 NADSELMPPPPERGDPPRLS(0.966)PDPVAGS(0.025)AVS(0.009)QELR 56.69 0.021932 360410000 127680 142570 76325 77828 89717 127470 91425 84682 97377 73109 TRUE FALSE 122690.1244 138504.0432 90118.62534 81844.71241 92602.82878 130047.5307 92543.8865 82933.28711 86323.1712 68157.26231 1.800103471 2.032124509 1.322216038 1.200821595 1.358664149 1.908050974 1.357799351 1.216793109 1.266529322 1 16.05657977 8 0.143478359 0.965791301 4.069047176 0.440459923 0.243185469 74.05854142 0.703529524 1.026666409 47.42543987 100000000 -8 3.103255875 NDIASHPPVEGSYAPR ddPTM_BT-474_Pertuzumab_2h_R1 4 NDIASHPPVEGSYAPR 16 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 147.92 9.82E-07 3650050000 1035220 1041510 922450 971980 1001720 1072590 1065500 1063190 1250770 1178600 FALSE TRUE 994762.4579 1011807.155 1089157.235 1022144.004 1033941.234 1094278.505 1078539.908 1041234.755 1108787.833 1098772.372 0.905339889 0.92085238 0.9912492 0.930260016 0.940996752 0.995910101 0.9815863 0.947634634 1.009115137 1 20.06746111 8 0.237164234 0.992414613 0.508562408 0.519282921 0.024621223 44.85013877 0.596920007 0.034661971 8.513420705 100000000 -8 -0.483852205 NGYGFVEFDDLRDADDAVYELNGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NGYGFVEFDDLRDADDAVYELNGK 24 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ; 118.67 0.000441 187565000 266760 303790 122980 139429 194166 234780 134526 142014 158968 122522 FALSE TRUE 256334.7243 295126.2066 145205.2217 146624.9474 200411.5257 239527.4125 136172.3694 139081.3613 140922.6191 114223.4758 2.244150972 2.58376139 1.271237989 1.283667358 1.754556358 2.097006861 1.192157466 1.217625013 1.233744798 1 16.80149967 8 0.24788841 1.097611764 9.290386337 0.510065268 0.361474903 42.68295566 0.579618642 0.495249014 145.4612981 100000000 -8 8.192774573 NLQEEIDALESR ddPTM_BT-474_Pertuzumab_2h_R1 3 NLQEEIDALESR 12 0 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 ;; 168.98 0.00010482 327873000 271614 276477 248291 275493 283021 282807 292006 295076 323037 342806 FALSE TRUE 260999.0246 268592.1467 293162.7069 289711.2267 292124.6275 288525.5513 295579.6568 288982.5775 286367.194 319587.4443 0.816674839 0.840433977 0.917316097 0.906516298 0.914067911 0.902806279 0.924878815 0.904236329 0.896052705 1 18.2858512 8 0.064240396 1.095537499 0.473414356 0.686325025 0.026053014 195.2407558 0.931895064 1.714632291 11.17673291 100000000 -8 -0.622123143 NTEDLTEEWLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NTEDLTEEWLR 11 0 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;;; 298.78 2.38E-35 1040120000 889710 999780 777110 1015250 910510 927850 969840 1036880 1067140 1146970 FALSE TRUE 854939.1496 971267.2533 917551.0637 1067647.174 939797.3811 946611.7627 981709.192 1015468.066 946002.741 1069284.7 0.799543049 0.90833363 0.858098001 0.998468578 0.87890286 0.885275701 0.918098979 0.949670434 0.884706141 1 20.0282146 8 0.064651903 1.090039637 0.510734935 0.37147299 0.046664523 331.7009881 1.592596889 2.694661294 17.76930431 100000000 -8 -0.579304702 NTHNNNKS(ph)KR ddPTM_BT-474_Pertuzumab_2h_R1 1 NTHNNNKSKR 10 2 E7EPV1;Q5MJ70-1;Q5MJ70 E7EPV1 SPDYA Speedy protein A 1 NTHNNNKS(1)KR 54.784 0.064041 102900000 147210 99229 50934 46098 63971 66993 41292 1334.2 54178 14681 TRUE FALSE 141456.8705 96399.08608 60138.90682 48477.1233 66028.68531 68347.64436 41797.34385 1306.648304 48027.94057 13686.64279 10.3353958 7.043296704 4.393985269 3.541929459 4.824315671 4.993747948 3.053878477 0.095468869 3.5091104 1 13.74048099 8 0.319114955 1.572377507 82.96801598 0.79041935 1.2623444 26.47024874 0.379079142 1.299319153 1255.93774 100000000 -8 81.39563847 QGEAEFNR ddPTM_BT-474_Pertuzumab_2h_R1 1 QGEAEFNR 8 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 94.85 0.023421 794250000 587600 615110 545190 802310 661500 550520 678380 753360 811150 867750 FALSE TRUE 564635.9424 597567.6651 643717.9607 843717.3152 682777.7483 561651.8916 686682.2174 737802.8527 719071.6526 808976.5196 0.697963326 0.738671211 0.795718967 1.042944134 0.844001935 0.694274652 0.848828366 0.912020108 0.888865913 1 19.6257383 8 0.088259164 1.086555317 0.14253279 0.349409372 0.091146012 210.6511582 1.338707866 1.917814338 24.0990102 100000000 -8 -0.944022527 QLEEEDGSRDSPLFDFIESCLR ddPTM_BT-474_Pertuzumab_2h_R1 1 QLEEEDGSRDSPLFDFIESCLR 22 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 64.87 0.021525 19216000 19844 23660 8123.7 9252.7 14118 22633 11111 11463 13405 8837.5 FALSE TRUE 19068.47454 22985.23997 9591.833301 9730.232956 14572.11829 23090.65477 11246.97974 11226.28504 11883.3206 8238.928253 2.31443629 2.789833733 1.164208864 1.181007123 1.768691005 2.802628456 1.36510228 1.362590461 1.442338158 1 13.00824096 8 0.122148308 0.831238097 5.532307599 0.273047404 0.547333285 135.277506 1.130919059 3.73594016 108.5679821 100000000 -8 4.701069502 QQGDHSLK ddPTM_BT-474_Pertuzumab_2h_R1 3 QQGDHSLK 8 0 Q13435;H0YCG1 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;; 110.87 0.0033424 2195600000 822450 801090 860150 924030 865730 855840 997300 1022280 1088350 1174260 FALSE TRUE 790307.7447 778243.6975 1015598.239 971719.299 893576.9917 873145.6712 1009505.256 1001169.561 964805.0707 1094726.324 0.721922664 0.710902515 0.927718843 0.887636734 0.816256056 0.797592651 0.922153084 0.914538674 0.881320792 1 20.06213882 8 0.15989705 0.990480216 0.003465951 0.570392891 0.058369678 50.21551139 0.518098903 0.182700993 11.68667184 100000000 -8 -0.987014264 QSSESDIES(ph)VIYTIEAVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSSESDIESVIYTIEAVAK 19 0 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 QS(0.23)S(0.23)ES(0.23)DIES(0.293)VIY(0.008)T(0.009)IEAVAK 55.33 0.066985 59219000 7212.5 5833.2 5034.2 5381.9 4753.9 5300.2 6194 5215.6 4871.5 5182.2 TRUE FALSE 6930.627526 5666.842847 5943.991925 5659.660504 4906.813511 5407.373675 6269.804025 5107.896037 4318.507743 4831.204978 1.434554642 1.172966759 1.230333209 1.171480103 1.015650036 1.119259833 1.297772306 1.057271646 0.893877979 1 12.23816735 8 0.308129654 1.038809837 4.073581325 0.538435579 0.101862691 49.17902552 0.70437462 0.103245758 83.0065312 100000000 -8 3.034771489 RAASVAAATT(ph)SPTPR ddPTM_BT-474_Pertuzumab_2h_R1 1 RAASVAAATTSPTPR 15 1 Q9Y2D9 Q9Y2D9 ZNF652 Zinc finger protein 652 1 RAASVAAAT(0.006)T(0.575)S(0.416)PT(0.003)PR 78.794 0.012808 321760000 110080 115460 73964 74901 76070 93946 70578 72757 64821 57850 TRUE FALSE 105777.9519 112167.1938 87330.94012 78766.64959 78516.86064 95845.65249 71441.75468 71254.54252 57462.79183 53931.76797 1.961329211 2.079798198 1.61928569 1.460487066 1.455855493 1.777165038 1.324669251 1.321197973 1.065472058 1 15.71884771 8 0.144284823 0.835724703 5.228298759 0.787883574 0.155820098 31.99440975 0.30525907 0.621702541 29.198713 100000000 -8 4.392574056 RES(ph)CGSSVLTDFEGK ddPTM_BT-474_Pertuzumab_2h_R1 5 RESCGSSVLTDFEGK 15 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 RES(0.981)CGS(0.019)SVLTDFEGK;RES(0.942)CGS(0.058)S(0.001)VLTDFEGK;RES(0.975)CGS(0.025)SVLTDFEGK;RES(0.981)CGS(0.019)SVLTDFEGK;RES(0.944)CGS(0.049)S(0.007)VLTDFEGK 236.15 6.52E-18 5199490000 4314700 4222630 3909080 4450030 4681300 4107540 4497650 5277030 5132350 5410590 TRUE FALSE 4146076.754 4102204.727 4615537.713 4679696.582 4831878.266 4190597.273 4552693.586 5168057.486 4549747.145 5044125.92 0.82196139 0.813263743 0.915032215 0.927751737 0.957921817 0.830787601 0.902573341 1.024569483 0.901989208 1 22.26617286 8 0.202534417 0.990326835 0.13230333 0.450965261 0.050994603 47.87573283 0.582751503 0.095504973 13.10082184 100000000 -8 -0.858023505 RGGGSGGGEES(ph)EGEEVDED ddPTM_BT-474_Pertuzumab_2h_R1 8 RGGGSGGGEESEGEEVDED 19 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGS(0.001)GGGEES(0.999)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED 297.5 9.94E-50 5281705000 4748636 4544313 3638546 3892895 4234002 4213591 3949740 4400383 4463784 4377367 TRUE FALSE 4563054.055 4414713.643 4296112.201 4093807.777 4370192.52 4298792.697 3998078.1 4309513.553 3957073.954 4080884.034 1.118153326 1.081803258 1.052740574 1.003166898 1.070893582 1.053397416 0.979708824 1.056024508 0.969660966 1 21.96045028 8 0.333016374 1.008382845 2.1560887 0.561703292 0.030285602 45.12398534 0.643656745 0.026190995 31.96507451 100000000 -8 1.147705855 RIDFIPVS(ph)PAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 5 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 2 RIDFIPVS(1)PAPS(0.987)PT(0.013)R;RIDFIPVS(1)PAPS(0.99)PT(0.01)R;RIDFIPVS(1)PAPS(0.968)PT(0.032)R;RIDFIPVS(1)PAPS(0.972)PT(0.028)R;RIDFIPVS(1)PAPS(0.977)PT(0.023)R 114.72 0.0020436 891809000 775746 767062 572454 607948 681775 616035 505733 716827 566384 561372 TRUE FALSE 745428.9887 745186.1428 675909.172 639324.2691 703704.912 628491.6498 511922.3117 702024.272 502090.4628 523349.7744 1.424341855 1.423877833 1.291505614 1.221600353 1.344616825 1.200901731 0.97816477 1.341405512 0.959378388 1 18.99741595 8 0.134053792 0.921562155 2.736224645 0.595669927 0.109002672 55.86725913 0.503192732 0.50923655 19.28496123 100000000 -8 1.81466249 RKDPELWGSVLLESNPYR ddPTM_BT-474_Pertuzumab_2h_R1 2 RKDPELWGSVLLESNPYR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 192.55 9.51E-15 1969860000 2093250 2264410 1447560 1346690 1782350 1866500 1623090 1614210 1802480 1475950 FALSE TRUE 2011443.476 2199831.244 1709166.293 1416192.832 1839680.906 1904241.909 1642953.861 1580875.999 1597870.027 1375982.592 1.461823346 1.598734793 1.242142381 1.029222928 1.336994318 1.383914244 1.194022272 1.148906977 1.161257444 1 20.39203079 8 0.203580137 1.059783793 3.28128028 0.50183578 0.127083342 46.98559485 0.573784598 0.239986232 33.51236603 100000000 -8 2.221496487 RKHS(ph)PS(ph)PPPPTPTESR ddPTM_BT-474_Pertuzumab_2h_R1 4 RKHSPSPPPPTPTESR 16 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 RKHS(1)PS(1)PPPPTPTESR;RKHS(1)PS(1)PPPPTPTESR;RKHS(1)PS(1)PPPPTPTESR;RKHS(1)PS(1)PPPPTPTESR 181.26 1.25E-09 1295350000 1240280 1232870 957430 1077710 1170740 1222850 1108100 1103060 1382460 1247930 TRUE FALSE 1191808.486 1197709.755 1130458.899 1133330.742 1208397.915 1247576.865 1121661.259 1080281.426 1225528.937 1163406.59 1.024412701 1.029485105 0.971679986 0.974148464 1.038672057 1.072348116 0.964118021 0.928550204 1.053396936 1 20.14992395 8 0.372375213 0.991716748 1.448858372 0.001012524 0.043090256 262.6677766 3.628303101 0.036475563 86.04529394 100000000 -8 0.457141624 RPLFLAPDFDRWLDES(ph)DAEMELR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPLFLAPDFDRWLDESDAEMELR 23 2 H3BS72;Q9P035;H3BPZ1 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 1 RPLFLAPDFDRWLDES(1)DAEMELR;RPLFLAPDFDRWLDES(1)DAEMELR;RPLFLAPDFDRWLDES(1)DAEMELR;RPLFLAPDFDRWLDES(1)DAEMELR;RPLFLAPDFDRWLDES(1)DAEMELR;RPLFLAPDFDRWLDES(1)DAEMELR 275.19 5.30E-52 830518000 1055068 1040754 947473 480632 642630 715157 689747 672091 875506 383917 TRUE FALSE 1013834.776 1011072.715 1118702.448 505437.4751 663300.7776 729617.9645 698188.3301 658212.086 776122.2293 357913.9596 2.832621497 2.824904388 3.125618371 1.41217592 1.853240869 2.038528939 1.95071556 1.83902323 2.168460348 1 18.44925329 8 0.175638279 1.264917588 8.629401231 0.572200033 0.411424616 43.85984842 0.484699733 1.000712713 85.73939609 100000000 -8 7.364483643 RPNTSPDRGS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 3 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.215)S(0.075)PDRGS(0.71)R;RPNT(0.001)S(0.001)PDRGS(0.999)R;RPNT(0.378)S(0.043)PDRGS(0.578)R 109.83 0.001477 1152350000 535680 706200 240672 301875 402840 548270 357290 326910 319060 263109 TRUE FALSE 514745.0334 686059.8674 284166.7841 317454.8049 415797.7144 559356.395 361662.6219 320159.1943 282841.6464 245288.3931 2.098529926 2.796952024 1.158500737 1.294210464 1.695138156 2.280403031 1.474438384 1.305235809 1.153098371 1 17.90411944 8 0.15925949 0.93869509 6.106635699 0.375167072 0.439930376 71.88135149 0.739423633 1.379269161 87.15616913 100000000 -8 5.167940609 RPS(ph)GRSPTSTEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSGRSPTSTEK 12 2 A1L390-3;A1L390;A1L390-2;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RPS(0.586)GRS(0.399)PT(0.012)S(0.002)T(0.001)EK 60.55 0.071785 36773000 44110 53071 19579 21976 33299 36698 25623 22863 30077 19637 TRUE FALSE 42386.13243 51557.46704 23117.36083 23110.18399 34370.09258 37440.0587 25936.58194 22390.87106 26662.78505 18306.9685 2.315300452 2.81627551 1.262762911 1.262370883 1.877432224 2.045126079 1.416760068 1.223079128 1.456428193 1 14.16010529 8 0.316514268 1.270921206 13.68118251 0.464192849 0.401222734 50.937195 0.729671749 0.393870053 364.4672779 100000000 -8 12.4102613 RRGDDWNDREWDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRGDDWNDREWDR 13 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 220.4 9.14E-12 346080000 46139 57571 30047 32244 41751 43064 34372 38413 28299 31173 FALSE TRUE 44335.83687 55929.13145 35477.16129 33908.1167 43093.95883 43934.78359 34792.65482 37619.75813 25086.61616 29061.62494 1.525580106 1.924501178 1.220756285 1.166766028 1.482847532 1.511780008 1.197202665 1.294482267 0.863221386 1 14.82682775 8 0.128777167 0.829480217 3.661274451 0.470397466 0.209794901 75.21282471 0.656129433 1.145360332 38.64747053 100000000 -8 2.831794234 RRHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR 40 2 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 88.987 0.00020467 26662000 12023 11172 8650.8 5976.5 7811.2 11452 6440.1 8678.1 9113.7 6131.2 FALSE TRUE 11553.12787 10853.3855 10214.192 6284.947881 8062.454342 11683.56729 6518.91587 8498.894202 8079.150984 5715.928363 2.021216351 1.898796628 1.786969911 1.099549799 1.410524036 2.044036689 1.14048243 1.486879062 1.413445108 1 12.48077212 8 0.219299827 1.204623826 5.500533473 0.428951872 0.278187949 52.7059762 0.673081843 0.43984619 80.11989346 100000000 -8 4.295909647 RT(ph)HTGEKPYACSHCDK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTHTGEKPYACSHCDK 16 2 A0A2R8Y595;A0A2R8YFL0;P49711-2;P49711 A0A2R8Y595 CTCF Transcriptional repressor CTCF 1 RT(0.741)HT(0.259)GEKPYACSHCDK 94.057 0.0042422 31610000 136400 102110 82948 75301 90676 89936 91090 59540 87346 83940 TRUE FALSE 131069.3372 99197.92278 97938.54877 79187.29363 93592.67589 91754.56754 92204.78667 58310.47819 77430.84826 78254.66903 1.674907566 1.267629446 1.25153617 1.011917814 1.196001172 1.172512371 1.178265627 0.745137369 0.989472567 1 16.25588921 8 0.387670253 0.961706443 10.91235093 0.707069497 0.125108536 40.001892 0.541666983 0.0988398 300.891631 100000000 -8 9.950644492 RT(ph)SSEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_BT-474_Pertuzumab_2h_R1 2 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.333)S(0.333)S(0.333)EELRDATSLLAAGEGGLLDEVEPLRPDELER;RT(0.441)S(0.441)S(0.118)EELRDATSLLAAGEGGLLDEVEPLRPDELER 220.85 1.43E-36 58774000 18034 22399.4 9593.6 9242.6 14459.7 18101.4 8778.1 13054.6 10661.1 9037.5 TRUE FALSE 17329.21134 21760.59104 11327.37693 9719.611694 14924.80938 18467.42271 8885.529014 12785.01795 9450.896623 8425.382075 2.056786409 2.582742343 1.344434808 1.153610793 1.771410394 2.191879555 1.054614371 1.517440733 1.121717275 1 13.0405264 8 0.183591941 1.02277031 6.316077854 0.396338304 0.404279962 59.6722901 0.680337211 0.898373881 88.72820215 100000000 -8 5.293307544 RTPDGTENGDFLALDLGGTNFR ddPTM_BT-474_Pertuzumab_2h_R1 1 RTPDGTENGDFLALDLGGTNFR 22 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 105.51 0.00082855 201590000 83825 87942 45335 55772 55995 74367 61917 51743 58531 44747 FALSE TRUE 80549.02633 85433.98026 53528.04297 58650.3996 57796.13003 75870.75169 62674.75877 50674.48897 51886.80626 41716.24583 1.930879079 2.047978637 1.283146216 1.405936666 1.385458564 1.818733929 1.502406497 1.214742313 1.243803349 1 15.34832171 8 0.138768108 0.930705731 4.34762047 0.55952117 0.215135601 61.70689561 0.571128794 0.998047765 41.79424159 100000000 -8 3.416914739 S(ph)LGDLGPFPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGDLGPFPR 10 0 Q5SZD1 Q5SZD1 C6orf141 Uncharacterized protein C6orf141 1 S(1)LGDLGPFPR;S(1)LGDLGPFPR 96.113 0.0073024 96681000 212394 173333 142944 166460 155798 176351 128677 169047 173894 172256 TRUE FALSE 204093.4077 168389.7126 168777.1606 175051.0205 160809.3842 179916.938 130251.7876 165556.1204 154154.2821 160588.9477 1.270905692 1.048575976 1.050988645 1.090056464 1.001372675 1.120356915 0.81108812 1.030930975 0.959930832 1 17.29301308 8 0.497314228 0.979789284 9.057648406 0.506809618 0.078339324 86.67000317 0.926951261 0.039825165 730.3601287 100000000 -8 8.077859122 S(ph)LPTTVPES(ph)PNYR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR 272.05 6.13E-32 5907010000 3044250 2615310 1981450 2097159 2162270 2325080 1737780 2414090 2133090 1994750 TRUE FALSE 2925277.344 2540723.919 2339542.092 2205393.627 2231821.378 2372094.711 1759047.471 2364238.198 1890950.566 1859643.806 1.573030994 1.36624224 1.25805925 1.185922605 1.200133795 1.27556401 0.94590559 1.27133927 1.016834815 1 20.82659488 8 0.374422353 1.090011514 7.599781038 0.702419778 0.097340115 36.54044229 0.503513427 0.070341256 171.7023595 100000000 -8 6.509769524 S(ph)PLLAGGS(ph)PPQPVVPAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLLAGGSPPQPVVPAHK 18 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4;C9JIY9 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 S(1)PLLAGGS(1)PPQPVVPAHK 98.74 0.00038302 0 122730 114360 121590 129190 111470 130490 133760 145460 137370 157650 TRUE FALSE 117933.5759 111098.5648 143564.0178 135857.5114 115055.5338 133128.5972 135396.9949 142456.2002 121776.3335 146972.2251 0.802420837 0.755915376 0.976810535 0.924375414 0.782838619 0.905807864 0.921242057 0.969272936 0.828566986 1 17.16518401 8 0.170913925 0.975293876 0.265091587 0.285464542 0.070280652 77.51363364 0.839969932 0.179547364 14.11528643 100000000 -8 -0.710202289 S(ph)PSHSGEPFGLPGLEPEPGGPQAGEPPPPLAGDKPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSHSGEPFGLPGLEPEPGGPQAGEPPPPLAGDKPHK 37 1 A0A087WVT1;Q96MX3 A0A087WVT1 ZNF48 Zinc finger protein 48 1 S(0.333)PS(0.333)HS(0.333)GEPFGLPGLEPEPGGPQAGEPPPPLAGDKPHK 81.91 0.00078804 189210000 50268 44988 35912 37568 33857 40696 34158 35924 32305 32982 TRUE FALSE 48303.47099 43704.98629 42402.09726 39506.88898 34946.04115 41518.901 34576.03582 35182.15685 28637.87183 30748.09976 1.570941663 1.421388204 1.37901521 1.284856277 1.136526856 1.350291606 1.124493419 1.14420589 0.93137046 1 14.90820963 8 0.178582617 0.928962054 3.658491713 0.826646094 0.079182353 21.43636232 0.239710119 0.175604468 15.86420676 100000000 -8 2.729529659 S(ph)RTGSESSQTGTSTTSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.332)RT(0.332)GS(0.332)ES(0.005)SQTGTSTTSSR;S(0.333)RT(0.333)GS(0.333)ES(0.002)SQTGTSTTSSR;S(0.332)RT(0.332)GS(0.332)ES(0.002)S(0.002)QTGTSTTSSR 118.36 6.36E-05 97699000 42109.4 59867.2 20986.2 24472.5 34502 44436 27869.5 28348 30281 25717.9 TRUE FALSE 40463.71809 58159.84607 24778.87318 25735.52866 35611.78816 45334.52637 28210.57528 27762.60389 26843.62783 23976.00373 1.687675668 2.425752295 1.033486375 1.073386914 1.485309586 1.890829134 1.176617071 1.157932915 1.119603923 1 14.54930359 8 0.255571332 1.086106039 6.92466124 0.299096957 0.371681399 62.70765244 0.862098941 0.475044828 158.5959015 100000000 -8 5.838555201 S(ph)VELCCASR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVELCCASR 9 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(1)VELCCASR;S(1)VELCCASR 111.86 0.0021578 648130000 151959 145456 106830 125641 127391 91795 84880 162870 105674 89189 TRUE FALSE 146020.2743 141307.7373 126136.5574 132125.3471 131488.6472 93651.15779 85918.78683 159506.6776 93678.33054 83148.14959 1.756145807 1.699469417 1.517009796 1.589035327 1.581377912 1.1263168 1.033321695 1.918343082 1.126643599 1 16.34339654 8 0.044171327 1.17E-07 3.995306386 0.380657509 0.248805833 783.7551316 2.625916321 61.04361575 224.1940308 100000000 -8 3.995306269 SANPPHTIQASEEQSST(ph)PAPVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SANPPHTIQASEEQSSTPAPVKK 23 1 Q9Y450;Q9Y450-4;J3QT46;B7Z524;H0YDX7;E9PHZ9;E9PS53 Q9Y450 HBS1L HBS1-like protein 1 SANPPHTIQASEEQSS(0.069)T(0.931)PAPVKK 223.57 1.10E-32 271950000 189780 168520 124540 126340 137960 133340 108290 178640 108610 114120 TRUE FALSE 182363.1878 163713.9746 147047.1484 132860.4225 142397.6087 136036.2262 109615.2854 174951.0216 96281.04813 106390.5508 1.714091961 1.538801834 1.382144818 1.248799086 1.338442255 1.278649515 1.030310348 1.644422558 0.904977439 1 16.6990105 8 0.404476935 1.20497781 9.965362452 0.452515747 0.19245839 75.39553822 0.994625019 0.131207013 528.0589327 100000000 -8 8.760384642 SAT(ph)FPNAGPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SATFPNAGPR 10 0 Q86X27;Q86X27-3 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(0.001)AT(0.999)FPNAGPR 163.59 7.17E-05 277660000 357900 178130 183690 106550 201950 150020 82727 195550 86388 74497 TRUE FALSE 343912.8723 173049.9068 216886.8692 112049.0583 208445.9052 153053.5072 83739.43777 191511.8242 76581.59641 69451.25183 4.951859948 2.491674408 3.122864793 1.613348288 3.001326825 2.203754477 1.205729711 2.75749996 1.102666898 1 16.08371308 8 0.615641159 1.894543867 199.9999854 0.62855874 0.700980652 119.9802369 0.875193357 0.27123486 32118.69105 100000000 -8 198.1054415 SDQDYILK ddPTM_BT-474_Pertuzumab_2h_R1 5 SDQDYILK 8 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7;F8VZ69 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;; 130.75 0.002407 1461820000 1096660 1065190 1008400 1054570 1064820 1125120 1117620 1199570 1268710 1312530 FALSE TRUE 1053801.315 1034811.824 1190640.312 1108996.484 1099070.902 1147870.697 1131297.768 1174798.46 1124691.36 1223631.174 0.861208293 0.845689327 0.973038557 0.906315978 0.898204398 0.938085529 0.924541473 0.960091967 0.919142454 1 20.22273734 8 0.108790585 1.022130111 0.555877551 0.530879655 0.031192596 87.6832116 0.666383713 0.289614414 6.135909402 100000000 -8 -0.46625256 SGEHDFGAAFDGDGDRNMILGK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGEHDFGAAFDGDGDRNMILGK 22 1 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 145.75 1.22E-07 116630000 46347 61981 26656 37371 43227 38588 32859 37227 34211 30654 FALSE TRUE 44535.708 60213.36257 31473.33216 39299.72179 44617.43571 39368.2758 33261.13827 36458.24944 30327.5107 28577.77728 1.558403495 2.106999505 1.101321907 1.37518469 1.56126333 1.377583547 1.16388122 1.275755252 1.061227065 1 14.80260609 8 0.157062751 0.914641912 4.211838928 0.463710224 0.228046777 54.26366253 0.55240659 0.68113118 41.25796045 100000000 -8 3.297197016 SKS(ph)HESQLGNR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKSHESQLGNR 11 1 A8MY87;A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;J3QLI1 A8MY87 KSR1 Kinase suppressor of Ras 1 1 S(0.168)KS(0.831)HES(0.001)QLGNR;S(0.072)KS(0.901)HES(0.026)QLGNR 78.814 0.017473 129784000 116015 131716 101422 141343 113285 136533 130418 144132 146412 160612 TRUE FALSE 111481.0055 127959.5886 119751.2115 148637.7292 116928.9149 139293.7908 132014.0945 141155.6238 129791.9236 149733.6062 0.744528956 0.854581626 0.799761754 0.992681155 0.780912969 0.930277406 0.881659755 0.942711709 0.866818925 1 17.19203853 8 0.165362309 0.980958287 0.194259359 0.426465086 0.062901117 57.890802 0.612371418 0.157907055 11.20060804 100000000 -8 -0.786698928 SLIPDIKPLAGQEAVVDLHADDSRIS(ph)EDETER ddPTM_BT-474_Pertuzumab_2h_R1 9 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDSRIS(1)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.02)RIS(0.98)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.038)RIS(0.962)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.008)RIS(0.992)EDET(0.001)ER;SLIPDIKPLAGQEAVVDLHADDS(0.023)RIS(0.977)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.001)RIS(0.999)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.421)RIS(0.548)EDET(0.031)ER;SLIPDIKPLAGQEAVVDLHADDS(0.201)RIS(0.795)EDET(0.004)ER;SLIPDIKPLAGQEAVVDLHADDS(0.281)RIS(0.719)EDETER 284.16 3.49E-74 15422764000 2875432 2719734 2570912 2952947 2903788 3085080 3046143 2973088 3743585 3594210 TRUE FALSE 2763056.938 2642169.849 3035532.988 3105348.949 2997190.978 3147462.431 3083422.609 2911692.694 3318628.925 3350770.955 0.824603345 0.78852595 0.905920765 0.926756555 0.894478023 0.939324852 0.920212885 0.868962019 0.990407572 1 21.67606164 8 0.22914203 0.964230986 0.061513721 0.615985255 0.03901292 37.96964873 0.496665396 0.059817943 12.84962829 100000000 -8 -0.902717264 SLKDMEESIR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLKDMEESIR 10 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 224.66 3.52E-09 7538090000 11452580 13781720 7914460 8807730 10257180 11731940 10120770 9808900 11407080 9868060 FALSE TRUE 11005000.51 13388678.84 9344778.978 9262298.001 10587111.51 11969167.86 10244631.01 9606342.787 10112196.1 9199687.507 1.19623634 1.455340611 1.015771348 1.00680572 1.150812079 1.301040699 1.113584674 1.044203162 1.099189086 1 23.13315343 8 0.258100945 1.055863164 2.609712898 0.206873066 0.123703029 80.30399905 1.108082952 0.157262126 54.76472629 100000000 -8 1.553849734 SPT(ph)GPSNSFLANMGGTVAHK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.159)PT(0.839)GPS(0.001)NSFLANMGGTVAHK;S(0.394)PT(0.606)GPSNSFLANMGGTVAHK 315.06 7.73E-66 13816210000 3880860 3724940 3951910 4176500 3984280 3981830 4660040 4009730 5561640 5190040 TRUE FALSE 3729191.701 3618708.358 4666108.047 4392049.666 4112437.985 4062345.331 4717070.963 3926927.674 4930305.943 4838513.968 0.770730792 0.747896644 0.964368002 0.907726979 0.849938227 0.839585327 0.974900764 0.811597879 1.018971109 1 22.2061326 8 0.128534965 1.015089843 0.269251658 0.400197694 0.072020672 98.74923701 0.860155607 0.397325433 13.3349865 100000000 -8 -0.745838185 SQLDIIIHSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SQLDIIIHSLK 11 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 143.42 3.72E-05 2760600000 2824000 3067000 2685600 2892000 3076800 2931100 3178700 3121100 3704500 3661900 FALSE TRUE 2713634.958 2979532.163 3170947.661 3041256.467 3175768.066 2990368.85 3217601.881 3056648.194 3283980.691 3413876.251 0.794883809 0.872770992 0.928840833 0.890851408 0.930252837 0.875945298 0.942506888 0.895359987 0.961950712 1 21.70297933 8 0.099214835 1.036565034 0.479139692 0.639935422 0.032310979 91.85436742 0.645857023 0.417698039 6.972086578 100000000 -8 -0.557425341 SRT(ph)AS(ph)GSSVTSLDGTR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 S(0.147)RT(0.851)AS(0.402)GS(0.336)S(0.255)VT(0.009)SLDGTR;S(0.398)RT(0.603)AS(0.969)GS(0.03)SVTSLDGTR 99.392 0.010652 231290000 330260 316200 213270 246770 268160 260650 212220 286780 280200 225940 TRUE FALSE 317353.0741 307182.2856 251812.6332 259505.8293 276785.6099 265920.5216 214817.2118 280857.8928 248392.8707 210636.8826 1.506635829 1.458349943 1.19548215 1.232005649 1.314041523 1.262459444 1.019846141 1.333374713 1.179246805 1 17.68439855 8 0.372354755 1.162015068 6.113329899 0.550160715 0.104820899 52.77786396 0.729052876 0.079402856 187.2449873 100000000 -8 4.95131483 SSEPVQADESQS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSEPVQADESQSPR 14 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 SSEPVQADESQS(1)PR 265.43 9.56E-25 440710000 172100 189920 153240 173190 191870 193640 197070 194240 208790 233890 TRUE FALSE 165374.1417 184503.6676 180933.8768 182128.3567 198041.6728 197555.5335 199481.8016 190228.8761 185089.0345 218048.422 0.758428519 0.846159151 0.8297876 0.835265649 0.908246301 0.9060168 0.91485093 0.872415743 0.848843724 1 17.73428902 8 0.07049014 1.102664151 0.321963579 0.674046619 0.035159351 160.7192527 0.835397039 1.602218615 12.43592753 100000000 -8 -0.780700571 SSRDPPS(ph)SPSSLSSPIQESTAPELPSETQETPGPALCSPLRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSRDPPSSPSSLSSPIQESTAPELPSETQETPGPALCSPLRK 42 2 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 S(0.036)S(0.036)RDPPS(0.432)S(0.432)PS(0.026)S(0.026)LS(0.007)S(0.002)PIQESTAPELPSETQETPGPALCSPLRK 70.025 0.0011307 292910000 40582 43142 19591 22856 27905 36852 22132 22612 26638 17825 TRUE FALSE 38996.01057 41911.6324 23131.5295 24035.6009 28802.58967 37597.17269 22402.85804 22145.0543 23614.16592 16617.69687 2.346655549 2.522108372 1.391981673 1.446385807 1.733247988 2.262477946 1.348132549 1.332618742 1.421025194 1 14.02043283 8 0.177588576 1.043024336 6.633228141 0.523908443 0.337568373 49.00708843 0.545855546 0.83106598 73.75154697 100000000 -8 5.590203805 SSS(ph)DNNTNTLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSDNNTNTLGR 12 0 A0A087X2H1;Q9ULT8;H0YJP0;H0YJ72 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 S(0.003)S(0.061)S(0.936)DNNTNTLGR 99.669 0.0014258 0 68241 89952 56687 75411 78664 75480 69718 85329 96298 84861 TRUE FALSE 65574.06628 87386.65703 66931.6019 79302.97075 81194.299 77006.25732 70571.22974 83566.92633 85366.65475 79113.28888 0.828862852 1.104576213 0.84602224 1.002397598 1.026304179 0.973366907 0.892027506 1.056294429 1.079043179 1 16.27163243 8 0.318894006 1.015085299 4.08E-06 0.163694365 0.083195689 122.4803107 1.754086227 0.075184629 72.40566882 100000000 -8 -1.015081217 STS(ph)LSALVR ddPTM_BT-474_Pertuzumab_2h_R1 3 STSLSALVR 9 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.001)T(0.002)S(0.994)LS(0.003)ALVR;S(0.001)T(0.003)S(0.996)LSALVR;S(0.004)T(0.004)S(0.992)LSALVR 197.79 2.88E-05 456539000 1082110 972900 731200 745760 868620 718740 611034 931530 731311 669759 TRUE FALSE 1039819.945 945153.8446 863344.1055 784248.763 896559.9512 733273.4152 618512.0169 912293.58 648295.6412 624395.6264 1.665322275 1.513709905 1.382687625 1.256012582 1.435884419 1.174373081 0.990577113 1.461082592 1.038277038 1 19.25210091 8 0.239024267 1.084884611 4.479748569 0.626128192 0.136952175 35.77216502 0.477882085 0.190000148 48.13726333 100000000 -8 3.394863959 SVGGSGGGS(ph)FGDNLVTR ddPTM_BT-474_Pertuzumab_2h_R1 3 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.032)VGGS(0.073)GGGS(0.895)FGDNLVTR;S(0.002)VGGS(0.083)GGGS(0.915)FGDNLVTR;SVGGS(0.003)GGGS(0.997)FGDNLVTR 187.33 4.96E-10 1083060000 1246190 1228960 823670 988690 1009540 904730 858880 1056110 944420 878480 TRUE FALSE 1197487.517 1193911.264 972525.4914 1039716.409 1042012.771 923024.2605 869391.2304 1034300.959 837213.4009 818979.7671 1.462169842 1.457803125 1.187484149 1.269526368 1.272330298 1.127041592 1.061553979 1.262913934 1.022263839 1 19.64346829 8 0.217671643 1.030790782 3.432384047 0.737290579 0.080053515 26.957216 0.342792638 0.127996541 22.68578091 100000000 -8 2.401593265 T(ph)PPKSPGDPSKDR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPPKSPGDPSKDR 13 2 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 T(0.531)PPKS(0.467)PGDPS(0.002)KDR 70.281 0.073024 102840000 203990 177700 125230 116650 161720 130280 126310 168190 151750 104450 TRUE FALSE 196017.8453 172632.17 147861.8467 122670.3205 166921.8707 132914.3509 127855.8196 164716.8177 134523.9762 97375.50847 2.013009723 1.772849998 1.5184706 1.259765648 1.714207949 1.364966951 1.313018248 1.691563108 1.381497035 1 16.57127134 8 0.050845245 0.198895414 3.98800589 0.546787768 0.189866121 429.1906124 1.64503416 28.4814186 126.8310055 100000000 -8 3.789110475 T(ph)PS(ph)PPPPIPEDIALGK ddPTM_BT-474_Pertuzumab_2h_R1 3 TPSPPPPIPEDIALGK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 T(1)PS(1)PPPPIPEDIALGK;T(1)PS(1)PPPPIPEDIALGK;T(1)PS(1)PPPPIPEDIALGK 114.31 0.0031477 646640000 678122 615001 644630 718856 685110 657267 690965 825231 901992 900901 TRUE FALSE 651620.2425 597461.7736 761128.9807 755956.2443 707147.1854 670557.3891 699421.2364 808189.6915 799601.6496 839882.1728 0.775847212 0.7113638 0.906233047 0.900074164 0.841959989 0.798394597 0.832761141 0.962265562 0.952040269 1 19.67982742 8 0.090149214 1.116345752 0.12207892 0.572180376 0.056891734 119.3440635 0.772604716 1.11136637 14.67791895 100000000 -8 -0.994266832 TDMDNQIVVSDYAQMDR ddPTM_BT-474_Pertuzumab_2h_R1 4 TDMDNQIVVSDYAQMDR 17 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 321.85 2.82E-58 575810000 337765 344910 299590 346162 328229 381003 352014 361111 408644 422160 FALSE TRUE 324564.7704 335073.5045 353732.5773 364027.4623 338786.7839 388707.1417 356322.0526 353653.9317 362256.4463 393566.7272 0.824675329 0.851376606 0.898786795 0.92494471 0.860811549 0.987652448 0.905366303 0.898586967 0.920444797 1 18.58624873 8 0.120954171 1.002194166 0.493120114 0.563107625 0.03485148 77.59316752 0.643522945 0.235851105 6.668433098 100000000 -8 -0.509074052 TES(ph)PATAAETASEELDNR ddPTM_BT-474_Pertuzumab_2h_R1 6 TESPATAAETASEELDNR 18 0 Q9NTJ3;Q9NTJ3-2;C9JR83;C9JWF0;C9IYK2;C9JJ64 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4 1 TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(0.999)PAT(0.001)AAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(0.999)PAT(0.001)AAETASEELDNR 418.11 4.78E-148 4257150000 528795 510411 466565 514373 495235 581853 527264 585013 628039 619741 TRUE FALSE 508129.1068 495854.578 550883.6742 540919.8522 511164.6835 593618.4663 533716.8146 572932.2771 556746.6457 577765.3901 0.879473079 0.858228247 0.953472956 0.936227509 0.884727075 1.027438605 0.923760446 0.991634817 0.963620624 1 19.14012426 8 0.214843457 1.001023969 0.273555267 0.506575005 0.037368182 38.0613001 0.480326639 0.056435654 9.537470545 100000000 -8 -0.727468703 TLDRS(ph)GDLGDMEPLK ddPTM_BT-474_Pertuzumab_2h_R1 3 TLDRSGDLGDMEPLK 15 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 T(0.007)LDRS(0.993)GDLGDMEPLK;TLDRS(1)GDLGDMEPLK;T(0.005)LDRS(0.995)GDLGDMEPLK 213.21 2.96E-10 1068974000 1810047 1894875 941478 1243705 1374520 1587867 1289538 1255205 1358404 1098608 TRUE FALSE 1739308.362 1840835.02 1111624.018 1307892.764 1418732.684 1619974.759 1305319.752 1229284.578 1204203.673 1024198.302 1.698214456 1.797342387 1.085360145 1.276991733 1.385212885 1.581700298 1.274479512 1.200240789 1.17575246 1 19.96606364 8 0.17455232 1.03908397 3.69821441 0.487957911 0.179975791 55.10605423 0.606287093 0.45935575 38.59061601 100000000 -8 2.65913044 TLTVHEK ddPTM_BT-474_Pertuzumab_2h_R1 4 TLTVHEK 7 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ;;; 114.78 0.0058274 1150780000 1712230 1820990 1529250 1756920 1753830 1833130 1854420 1912020 2170430 2149390 FALSE TRUE 1645314.159 1769057.148 1805619.493 1847594.852 1810243.535 1870197.145 1877114.947 1872536.119 1924051.886 2003809.901 0.821092938 0.882846795 0.901093209 0.922040984 0.903400834 0.933320643 0.936772967 0.934487906 0.960196815 1 20.93431422 8 0.159997879 0.999483755 0.395567413 0.893778672 0.014750121 20.12057246 0.207691978 0.04474056 2.867401259 100000000 -8 -0.603916343 TQT(ph)PPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.16)QT(0.84)PPVS(0.941)PAPQPT(0.025)EERLPS(0.018)S(0.016)PVYEDAASFK 87.753 0.0027879 446050000 408220 388550 313010 297630 327360 338990 304310 317120 378810 305850 TRUE FALSE 392266.3111 377468.9344 369577.8699 312990.72 337889.8317 345844.6101 308034.2368 310571.3612 335809.0769 285134.5071 1.375723742 1.323827615 1.29615273 1.09769499 1.185019082 1.212917418 1.080312025 1.089210017 1.177721632 1 18.12128312 8 0.228357304 1.040134745 3.029175876 0.760065349 0.056022082 23.38743158 0.305370749 0.081885152 17.36062351 100000000 -8 1.989041131 TQT(ph)PPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_BT-474_Pertuzumab_2h_R1 3 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 TQT(1)PPVS(0.346)PAPQPT(0.65)EERLPS(0.002)S(0.002)PVYEDAASFK;T(0.001)QT(0.999)PPVS(0.343)PAPQPT(0.568)EERLPS(0.072)S(0.017)PVYEDAASFK;T(0.005)QT(0.995)PPVS(0.256)PAPQPT(0.349)EERLPS(0.331)S(0.065)PVYEDAASFK 239.63 7.27E-45 5130140000 1736950 1705410 1236550 1306680 1342010 1507520 1207450 1496720 1415170 1242160 TRUE FALSE 1669068.074 1656773.377 1460022.092 1374117.911 1385176.97 1538003.087 1222227.134 1465812.209 1254525.834 1158027.397 1.441302752 1.430685821 1.260783722 1.186602247 1.196152159 1.328123231 1.055438876 1.265783705 1.083330013 1 20.14323795 8 0.170072832 1.02082228 2.746794941 0.679269317 0.080972316 36.07771594 0.389555862 0.204970194 15.86680878 100000000 -8 1.725972661 TRS(ph)NPEGAEDR ddPTM_BT-474_Pertuzumab_2h_R1 5 TRSNPEGAEDR 11 1 M0R3H9;M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R2I2 M0R3H9 BABAM1 BRISC and BRCA1-A complex member 1 1 T(0.171)RS(0.829)NPEGAEDR;T(0.008)RS(0.992)NPEGAEDR;T(0.181)RS(0.819)NPEGAEDR;T(0.003)RS(0.997)NPEGAEDR;T(0.078)RS(0.922)NPEGAEDR 187.46 2.17E-06 3442120000 1430447 1495878 1196789 1308823 1448170 1394432 1350124 1511975 1682172 1490967 TRUE FALSE 1374543.55 1453217.024 1413075.395 1376371.512 1494751.703 1422628.37 1366647.221 1480752.188 1491218.887 1389982.477 0.988892718 1.045493053 1.016613819 0.990207815 1.075374494 1.02348655 0.983211835 1.065302773 1.072832868 1 20.40663526 8 0.489364787 1.035261666 0.042383918 0.085372833 0.032872857 282.8787033 3.09173732 0.017795141 287.1247425 100000000 -8 -0.992877749 TRTFS(ph)ATVR ddPTM_BT-474_Pertuzumab_2h_R1 4 TRTFSATVR 9 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TRT(0.002)FS(0.997)AT(0.001)VR;TRT(0.001)FS(0.951)AT(0.048)VR;TRTFS(0.998)AT(0.002)VR;T(0.002)RT(0.014)FS(0.965)AT(0.02)VR 106.01 0.0018202 2771720000 879580 995170 536136 661230 635860 888480 623610 739340 669663 607438 TRUE FALSE 845205.0412 966788.726 633027.7015 695356.1595 656313.0144 906445.6743 631241.9257 724072.3706 593645.6637 566295.6832 1.492515423 1.707215426 1.117839532 1.227902985 1.15895818 1.600657927 1.114686099 1.278611849 1.04829629 1 19.11119601 8 0.15282212 0.993788974 3.022109484 0.381541411 0.181609121 74.23712902 0.74025132 0.601965833 33.56515472 100000000 -8 2.02832051 TSEEWMSDLDDLLGSQ ddPTM_BT-474_Pertuzumab_2h_R1 2 TSEEWMSDLDDLLGSQ 16 0 Q92585 Q92585 MAML1 Mastermind-like protein 1 0 ; 141.73 3.67E-06 22272000 55345 58279 47730 57067 58458 59341 56786 61271 69266 70175 FALSE TRUE 53182.05621 56616.93998 56355.87275 60012.23471 60338.35466 60540.91568 57480.96405 60005.73244 61403.21407 65421.98474 0.812908022 0.865411531 0.861421019 0.917309906 0.922294774 0.925390997 0.878618469 0.917210517 0.938571557 1 15.99748791 8 0.089287799 1.052732876 0.455984832 0.783407327 0.022703975 81.78147506 0.525019246 0.463215529 5.980753397 100000000 -8 -0.596748044 TTGVVLDSGDGVTHAVPIYEGFAMPHSIMR ddPTM_BT-474_Pertuzumab_2h_R1 1 TTGVVLDSGDGVTHAVPIYEGFAMPHSIMR 30 0 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 172.06 7.31E-13 189280000 120280 113830 68664 76909 95398 101610 81363 68763 97089 80243 FALSE TRUE 115579.3246 110583.6799 81073.11222 80878.28271 98466.56331 103664.6238 82358.74473 67343.02002 86067.86375 74808.07014 1.545011446 1.478231956 1.083748212 1.08114382 1.316255895 1.385741186 1.100933958 0.900210631 1.150515761 1 16.19090629 8 0.31699529 1.037139073 5.932355853 0.51377967 0.141889543 49.27956568 0.705898321 0.149401947 139.3689177 100000000 -8 4.89521678 TVDGPSGK ddPTM_BT-474_Pertuzumab_2h_R1 7 TVDGPSGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;; 150.4 0.0011395 4226319000 16462840 15867540 12526200 14141270 14158120 14533240 14642650 14820390 16206160 14810460 FALSE TRUE 15819454.01 15415013.3 14789962.98 14871102.64 14613528.79 14827112.07 14821851.13 14514343.77 14366504.66 13807334.35 1.145728322 1.116436591 1.07116715 1.077043712 1.058388854 1.073857683 1.073476658 1.051205352 1.040498064 1 23.71893148 8 0.140026586 0.995673413 1.468531423 0.853507075 0.014433768 30.03637824 0.279973561 0.06618876 2.845988196 100000000 -8 0.472858011 VDNAYWLWTFQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDNAYWLWTFQGR 13 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 174.05 4.80E-05 710460000 331200 339190 329350 340270 348980 315660 417810 397770 389430 436780 FALSE TRUE 318256.3378 329516.6333 388870.8714 357831.3755 360205.2586 322042.8615 422923.2838 389555.9105 345223.539 407196.5016 0.781579254 0.809232476 0.95499561 0.878768295 0.884598117 0.790878262 1.038622096 0.956677941 0.847805759 1 18.63536564 8 0.207847302 0.975257631 0.080840647 0.322895922 0.070166605 62.00684821 0.767079923 0.121840851 18.29436507 100000000 -8 -0.894416984 VDNEFDQR ddPTM_BT-474_Pertuzumab_2h_R1 3 VDNEFDQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 113.66 0.0065285 916380000 1199150 1290230 1102520 1255320 1283560 1354420 1369740 1428510 1563230 1614440 FALSE TRUE 1152285.892 1253433.904 1301769.889 1320107.216 1324846.873 1381807.3 1386503.288 1399010.769 1385778.684 1505092.541 0.765591391 0.83279524 0.864910199 0.87709372 0.8802428 0.918087933 0.921207999 0.929518107 0.920726564 1 20.52142076 8 0.178474028 0.992050963 0.097082076 0.934470286 0.015359153 12.99561666 0.145259686 0.034946932 3.150989587 100000000 -8 -0.894968887 VDNLTYRT(ph)SPDTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.948)S(0.052)PDTLR;VDNLTYRT(0.771)S(0.229)PDTLR 166.91 6.03E-06 982190000 610820 797890 259480 279553 445750 681780 347360 327510 394210 252940 TRUE FALSE 586948.4791 775134.9584 306373.8081 293980.7638 460087.9536 695566.0587 351611.0956 320746.804 349460.9335 235808.1485 2.489093285 3.28714238 1.299250302 1.246694678 1.951111344 2.949711717 1.491089675 1.360202377 1.481971406 1 17.84725405 8 0.15142096 0.936837393 7.297605982 0.323908073 0.614602654 85.8592506 0.850157406 2.219277845 120.3641341 100000000 -8 6.360768589 VDVKS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 7 VDVKSPK 7 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDVKS(1)PK;VDVKS(1)PK;VDVKS(1)PK;VDVKS(1)PK;VDVKS(1)PK;VDVKS(1)PK;VDVKS(1)PK 85.355 0.01264 10747480000 12167350 10926530 9817330 8229660 9855810 9794090 8864450 10136730 10988540 8516020 TRUE FALSE 11691836.51 10614916.06 11591539.92 8654393.739 10172831.08 9992133.21 8972935.791 9927402.983 9741167.007 7939222.38 1.472667719 1.337022136 1.460034669 1.090080782 1.281338473 1.258578326 1.130203358 1.250425106 1.226967396 1 22.92056628 8 0.128824372 0.991181121 2.468431243 0.594577584 0.091226629 60.87908731 0.531242905 0.483328171 16.32583109 100000000 -8 1.477250122 VFGVDDNQDYNRPVINEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VFGVDDNQDYNRPVINEK 18 1 Q5SW79;H0Y2V6 Q5SW79 CEP170 Centrosomal protein of 170 kDa 0 118.72 8.62E-05 331390000 146150 157400 138090 144820 158420 158420 142290 168310 207790 178520 FALSE TRUE 140438.2964 152911.1061 163045.9348 152294.1776 163515.7232 161623.3609 144031.3876 164834.3397 184202.5503 166428.6814 0.8438347 0.918778571 0.979674497 0.915071707 0.982497258 0.971126849 0.865424075 0.990420271 1.106795708 1 17.34454456 8 0.198869286 1.019096135 0.33455426 0.376258708 0.056499718 65.0089809 0.782084837 0.107575545 13.85957731 100000000 -8 -0.684541875 VIKDEALS(ph)DGDDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIKDEALSDGDDLR 14 1 Q01831-2;Q01831;E7EUB5;Q01831-3 Q01831-2 XPC DNA repair protein complementing XP-C cells 1 VIKDEALS(1)DGDDLR;VIKDEALS(1)DGDDLR 90.718 0.0034164 603580000 1607090 1162000 1239850 859370 1178700 870660 706850 1095280 737760 614350 TRUE FALSE 1544283.146 1128860.898 1463918.475 903722.1887 1216613.956 888265.3417 715500.6417 1072662.085 654012.5777 572739.5273 2.696309705 1.970984791 2.555993441 1.577893869 2.124201139 1.550906301 1.249260105 1.87286198 1.14190229 1 19.12751965 8 0.145027844 0.819340712 7.155103995 0.696703792 0.301421829 38.97906531 0.37338155 1.082735124 51.63098999 100000000 -8 6.335763282 VKDEPQRR ddPTM_BT-474_Pertuzumab_2h_R1 10 VKDEPQRR 8 2 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;;;;;;; 136.21 0.0004504 30883960000 20031800 19052730 13261530 13328150 15847520 14585420 14245960 16828830 14502190 12959670 FALSE TRUE 19248935.11 18509364.79 15658183.47 14016017.42 16357269.87 14880347.19 14420306.32 16481308.78 12855962.19 12081900.01 1.593204305 1.531991225 1.296003399 1.160083878 1.353865689 1.231623104 1.193546239 1.364132195 1.064067918 1 23.52634402 8 0.38943668 1.178387253 8.014983844 0.645820905 0.10705632 46.9952261 0.634749243 0.077936675 244.3351525 100000000 -8 6.83659659 VKVDGPRS(ph)PSYGR ddPTM_BT-474_Pertuzumab_2h_R1 4 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VKVDGPRS(0.899)PS(0.101)YGR;VKVDGPRS(0.999)PS(0.001)YGR;VKVDGPRS(0.889)PS(0.111)YGR;VKVDGPRS(0.815)PS(0.185)YGR 102.89 0.0013021 3100660000 2934240 3728440 883550 1047810 1982440 3233320 1536450 991880 1596140 1001490 TRUE FALSE 2819566.657 3622108.542 1043227.139 1101887.6 2046206.983 3298699.946 1555253.535 971397.3314 1414952.879 933658.1903 3.019913161 3.879480285 1.117354456 1.180183081 2.191601814 3.533091639 1.665763286 1.040420725 1.515493457 1 19.83253495 8 0.273831948 1.318104634 15.92683617 0.299287688 0.864921018 68.97258142 0.969825461 1.056786701 478.5110644 100000000 -8 14.60873154 VLAGDKNFITAEELRR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLAGDKNFITAEELRR 16 2 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 211.9 3.32E-12 2259770000 2360500 2680700 1568180 1632060 2004230 2378500 1857430 2008990 1983890 1816980 FALSE TRUE 2268249.05 2604249.061 1851585.01 1716290.812 2068697.878 2426594.9 1880161.784 1967503.654 1758687.124 1693914.326 1.339057717 1.537414862 1.093080672 1.013209928 1.221252956 1.432536972 1.109950931 1.161513085 1.038238533 1 20.69192948 8 0.158594405 1.002372427 2.461884503 0.323664833 0.144681228 84.53505093 0.86686692 0.461571193 28.79673576 100000000 -8 1.459512076 VLRHEEFEEGCK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLRHEEFEEGCK 12 1 Q9HC38-2;F6TLX2;I3L3Q4;Q9HC38-3;I3L1F4 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 103.44 0.0013494 268570000 318390 290200 205762 208750 288290 282910 229230 222122 288950 240580 FALSE TRUE 305946.9668 281923.7801 242947.7706 219523.6125 297563.1097 288630.634 232035.3853 217535.1031 256149.6074 224285.3023 1.364097262 1.256987316 1.08320861 0.978769497 1.326716939 1.286890541 1.034554574 0.969903515 1.142070411 1 17.77497556 8 0.245667831 1.028642151 2.805707687 0.320303642 0.119197574 66.87227404 0.904581761 0.172577185 48.84603741 100000000 -8 1.777065536 VMATTGGTNLRDDIMR ddPTM_BT-474_Pertuzumab_2h_R1 1 VMATTGGTNLRDDIMR 16 1 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 97.579 0.0027592 628750000 200880 227210 152220 163700 179340 187880 150770 179040 192260 165990 FALSE TRUE 193029.3875 220730.1933 179729.5401 172148.5766 185108.634 191679.0623 152615.1684 175342.7614 170435.4508 154747.3495 1.247384128 1.426390785 1.161438569 1.112449274 1.19619906 1.238658129 0.986221534 1.133090564 1.101378805 1 17.23955517 8 0.170685461 0.988226157 2.424277874 0.517454802 0.084599461 44.67940623 0.483695167 0.20978836 16.42370581 100000000 -8 1.436051717 VTEKIPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 VTEKIPVR 8 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 96.331 0.0082232 1359320000 3863820 4148470 2448200 2350820 3028280 3718380 2901730 3075980 3120700 2529820 FALSE TRUE 3712817.643 4030159.697 2890644.2 2472146.102 3125687.376 3793568.191 2937242.24 3012459.938 2766451.219 2358473.038 1.57424638 1.708800411 1.22564225 1.048197737 1.325301297 1.608484867 1.245399965 1.277292506 1.172984034 1 21.16942168 8 0.096629434 0.863640019 2.811245058 0.391965739 0.176651333 163.9758942 1.127210586 2.70884862 42.32824352 100000000 -8 1.947605039 VVDLMAHMASKE ddPTM_BT-474_Pertuzumab_2h_R1 15 VVDLMAHMASKE 12 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;; 191.53 8.42E-06 43208193000 34827900 38332480 25330400 26821060 30551810 24446200 31096670 29184890 31094260 25871260 FALSE TRUE 33466787.16 37239275.2 29908166.75 28205298.12 31534536.72 24940518.91 31477240.35 28582211.82 27564569.96 24118976.52 1.387570784 1.543982398 1.240026364 1.169423508 1.307457499 1.034062075 1.305081927 1.185050775 1.142858195 1 24.52366535 8 0.210476912 1.066790266 3.116008226 0.553673872 0.103433731 38.80069153 0.483696588 0.169835961 26.66219341 100000000 -8 2.04921796 VWAHYEEQPVEEVMPVLEEK ddPTM_BT-474_Pertuzumab_2h_R1 4 VWAHYEEQPVEEVMPVLEEK 20 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 216.04 1.15E-24 926850000 528915 514377 501900 509666 579460 576276 614082 579931 703670 720887 FALSE TRUE 508244.4171 499707.4716 592604.4947 535969.9233 598098.8572 587928.6956 621597.3192 567955.2222 623792.3316 672060.6814 0.756247808 0.743545167 0.881772303 0.797502276 0.889947699 0.874814897 0.924912491 0.84509515 0.928178584 1 19.35823198 8 0.119914462 1.031403329 0.14347136 0.739061161 0.039013592 48.57897947 0.400070293 0.261239424 7.210967798 100000000 -8 -0.887931968 YDDYRDYDS(ph)PERER ddPTM_BT-474_Pertuzumab_2h_R1 1 YDDYRDYDSPERER 14 2 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3 P52756 RBM5 RNA-binding protein 5 1 YDDYRDYDS(1)PERER 150.7 5.62E-06 323330000 262890 260900 151340 196730 214580 246790 172350 225360 205160 190110 TRUE FALSE 252615.9682 253459.3874 178690.5045 206883.2589 221482.1606 251780.2629 174459.2709 220706.2372 181871.0969 177233.6804 1.425327103 1.430085901 1.008219793 1.167290881 1.249661803 1.420611829 0.984346037 1.245283835 1.026165549 1 17.43529327 8 0.133053142 0.969882792 2.318632133 0.338283492 0.143521556 103.857656 0.929902423 0.712673733 26.41116184 100000000 -8 1.34874934 YEKESR ddPTM_BT-474_Pertuzumab_2h_R1 1 YEKESR 6 1 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 0 64.836 0.096335 106050000 148000 164260 82821 90553 103430 144120 100900 99119 93202 89279 FALSE TRUE 142215.9964 159575.4656 97788.59704 95226.45118 106756.9199 147034.2051 102134.8444 97072.15801 82622.09969 83232.05381 1.708668594 1.917235708 1.174891073 1.144107911 1.282641903 1.766557455 1.227109505 1.166283344 0.992671644 1 16.34485162 8 0.228339387 1.04963621 5.171819361 0.447394905 0.234971246 50.31547289 0.656944313 0.365168031 77.39678888 100000000 -8 4.122183151 YELISETGGSHDKR ddPTM_BT-474_Pertuzumab_2h_R1 4 YELISETGGSHDKR 14 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6;Q96SI9;Q96SI9-2 Q12906;Q12906-7;Q96SI9 ILF3;STRBP Interleukin enhancer-binding factor 3;Spermatid perinuclear RNA-binding protein 0 ;;; 178.58 1.28E-06 8089900000 2673360 2737780 2516710 3149220 2703060 2926120 3088660 3084220 3425740 3724980 FALSE TRUE 2568882.136 2659701.195 2971535.481 3311751.622 2790006.38 2985288.151 3126459.945 3020529.779 3036864.357 3472683.787 0.739739721 0.765892134 0.855688471 0.953657697 0.803415039 0.859648714 0.900300787 0.869796954 0.874500687 1 21.72761962 8 0.093387757 1.051952089 0.267130421 0.581830042 0.048731919 117.2134606 0.782415268 0.819752073 11.7815644 100000000 -8 -0.784821668 YGKIETIEVMEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGKIETIEVMEDR 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 142.1 3.66E-05 956430000 1025670 1179300 498920 524870 814420 1118540 741320 694610 702990 530540 FALSE TRUE 985585.6825 1145667.519 589085.9424 551958.6036 840616.5589 1141157.645 750392.4959 680266.0608 623189.5224 494606.0532 1.992668056 2.316323286 1.191020487 1.115956022 1.699567875 2.307205174 1.517151865 1.375369461 1.259971483 1 18.91592037 8 0.053687719 2.35E-14 4.668047974 0.294167286 0.385623858 621.8554982 2.509574345 48.56599014 234.6443974 100000000 -8 4.668047974 AIGGIILT(ph)ASHNPGGPNGDFGIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIGGIILTASHNPGGPNGDFGIK 23 0 A0A3B3ITK7;P36871;P36871-2 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 1 AIGGIILT(0.547)AS(0.453)HNPGGPNGDFGIK 115.55 0.0020674 66276000 73235 65894 44635 44535 48730 41471 37753 51049 43667 33595 TRUE FALSE 70372.89523 64014.76764 52701.5374 46833.45669 50297.44471 42309.57203 38215.03251 49994.82031 38710.10523 31319.58073 2.246929672 2.043921603 1.68270252 1.495341113 1.605942466 1.350898417 1.220164243 1.59628 1.235971374 1 14.93477728 8 0.300159118 1.216783513 10.52051417 0.852295471 0.138838032 20.27178597 0.289861094 0.143972688 101.2737423 100000000 -8 9.303730658 up EMQDVDLAEVKPLVEK ddPTM_BT-474_Pertuzumab_2h_R1 7 EMQDVDLAEVKPLVEK 16 1 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1;E5RJ98 Q92597 NDRG1 Protein NDRG1 0 ;;;;;; 219.79 1.10E-14 3537630000 5940980 5344570 4099550 3720880 4154860 4029290 3453030 4612590 4468100 2833930 FALSE TRUE 5708799.933 5192148.096 4840429.879 3912915.063 4288504.845 4110765.004 3495289.214 4517338.405 3960900.02 2641985.397 2.160799201 1.965244813 1.832118332 1.481050981 1.623212926 1.555937822 1.322978249 1.709827166 1.499213442 1 21.33319106 8 0.151101874 1.091330233 4.795237717 0.762910473 0.152048572 36.77963854 0.363597289 0.555655293 29.94612128 100000000 -8 3.703907484 up ST(ph)FSTNYR ddPTM_BT-474_Pertuzumab_2h_R1 1 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.026)T(0.536)FS(0.428)T(0.01)NYR 98.257 0.024267 0 159380 134420 104810 92541 105960 99912 72002 98614 83944 80595 TRUE FALSE 153151.2534 130586.4732 123751.4985 97317.0521 109368.2996 101932.2891 72883.18201 96577.58644 74415.02904 75136.22886 2.038314349 1.737996106 1.647028342 1.295208098 1.455600065 1.35663302 0.970013842 1.285366432 0.990401437 1 16.19722109 8 0.253469572 0.98200875 7.962900909 0.880818618 0.115507591 14.97773088 0.205254989 0.138969625 44.79777467 100000000 -8 6.98089216 up TAS(ph)GSS(ph)VTSLDGTR ddPTM_BT-474_Pertuzumab_2h_R1 3 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 TAS(0.999)GS(0.333)S(0.662)VT(0.005)S(0.001)LDGTR;TAS(1)GS(0.015)S(0.979)VT(0.005)SLDGTR;T(0.004)AS(0.994)GS(0.051)S(0.841)VT(0.108)S(0.001)LDGTR 184.59 1.86E-06 2504910000 5178630 5476770 3750450 3704800 4368750 3921970 3118480 4262200 4216160 2556950 TRUE FALSE 4976243.414 5320577.882 4428239.743 3896005.172 4509274.811 4001274.921 3156644.891 4174184.081 3737559.192 2383765.499 2.087555767 2.232005574 1.857665842 1.634391123 1.891660406 1.678552241 1.324226268 1.751088386 1.567922346 1 21.18481089 8 0.06005672 2.48E-14 5.319681644 0.774379801 0.161133503 160.2770483 0.718626552 12.87417693 74.57330314 100000000 -8 5.319681644 up YSDESGNMDFDNFISCLVR ddPTM_BT-474_Pertuzumab_2h_R1 4 YSDESGNMDFDNFISCLVR 19 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EMQ1 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ;;; 365.28 1.85E-107 404685000 232112 231589 193759 246636 261796 195693 248935 259055 263094 285508 FALSE TRUE 223040.8064 224984.3085 228775.5614 259364.9135 270216.9061 199650.0465 251981.541 253705.4237 233228.6721 266170.2889 0.837962822 0.845264546 0.859508259 0.97443225 1.015203114 0.750083893 0.946692969 0.953169585 0.876238566 1 18.02199001 8 0.091346159 1.032845382 0.526137194 0.186626359 0.072711203 273.4844476 1.790904516 1.274177633 17.36419763 100000000 -8 -0.506708187 YWDVPPPGFEHITPMQYK ddPTM_BT-474_Pertuzumab_2h_R1 1 YWDVPPPGFEHITPMQYK 18 0 P26368-2;P26368;K7ELP8 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 156.5 1.11E-08 236540000 1093800 1172100 1087200 1213600 1113600 1222400 1215900 1284300 1376600 1474400 FALSE TRUE 1051053.087 1138672.856 1283681.225 1276234.041 1149419.955 1247117.766 1230780.548 1257778.756 1220334.139 1374537.575 0.764659407 0.828404313 0.933900425 0.928482469 0.836223015 0.907299872 0.895414262 0.915055928 0.887814318 1 20.39051491 8 0.111642357 1.010578636 0.428167677 0.529867183 0.042745328 97.26562056 0.755300421 0.385197913 8.745102567 100000000 -8 -0.582410959 (ac)AAADGDDSLYPIAVLIDELR ddPTM_BT-474_Pertuzumab_2h_R1 4 AAADGDDSLYPIAVLIDELR 20 0 P30153;C9J9C1;M0QXG4;M0R0K6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;; 82.55 7.32E-44 4612960000 0 17952 0 0 0 0 20974 12819 0 0 FALSE TRUE 0 17440.02654 0 0 0 0 21230.68609 12554.28317 0 0 0 (ac)ADVLDLHEAGGEDFAMDEDGDESIHK ddPTM_BT-474_Pertuzumab_2h_R1 7 ADVLDLHEAGGEDFAMDEDGDESIHK 26 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;;;;; 128.52 6.77E-53 1504137000 424931 467864 352710 438753 400497 455794 439606 360847 516711 539396 FALSE TRUE 408324.2267 454520.9768 416452.543 461397.0949 413379.3497 465010.467 444986.0297 353395.3833 458056.1335 502862.2285 0.812000193 0.903867801 0.828164295 0.917541762 0.822052893 0.924727372 0.884906451 0.702767803 0.910897871 1 18.93980367 (ac)AEVEETLKR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEVEETLKR 9 1 Q9NP97;Q8TF09;H3BNG9;H3BPA0;Q7Z4M1;Q9NP97-2 Q9NP97 DYNLRB1;DYNLRB2 Dynein light chain roadblock-type 1;Dynein light chain roadblock-type 2 0 65.252 0.0024203 0 197930 184490 181400 170310 182260 194690 167830 223890 205280 192250 FALSE TRUE 190194.6768 179228.5258 214183.0152 179099.7195 188122.5584 198626.7652 169883.9537 219266.5933 181977.475 179228.7363 1.061184053 0.999998826 1.195026086 0.999280156 1.049622747 1.108230574 0.947861137 1.223389719 1.015336485 1 17.45144244 (ac)AS(ph)PTDGTDLEASLLSFEK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASPTDGTDLEASLLSFEK 18 0 G3V5T8 G3V5T8 LIN52 1 AS(0.473)PT(0.473)DGT(0.055)DLEASLLSFEK;AS(0.459)PT(0.459)DGT(0.082)DLEASLLSFEK;AS(0.333)PT(0.333)DGT(0.333)DLEASLLSFEK 89.013 3.73E-14 107541000 85235 85046 68472 77566 84465 85263 83666 86732 86981 85639 TRUE FALSE 81903.92197 82620.57135 80846.41355 81569.19056 87181.89343 86987.07628 84689.92954 84940.95389 77107.28153 79838.59425 1.025868789 1.034845016 1.012623209 1.021676187 1.09197681 1.089536672 1.060764287 1.063908435 0.965789569 1 16.2847987 (ac)ASGRPEELWEAVVGAAER ddPTM_BT-474_Pertuzumab_2h_R1 2 ASGRPEELWEAVVGAAER 18 1 Q96B36;H9KV91;M0R2V8 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 ; 55.314 3.40E-05 69153000 2172.9 0 0 2768.7 3864.9 964.16 624.03 0 1009 0 FALSE TRUE 2087.980666 0 0 2911.592939 3989.218019 983.6559758 631.6670658 0 894.4625501 0 0 (ac)MDIRPNHTIYINNMNDK ddPTM_BT-474_Pertuzumab_2h_R1 1 MDIRPNHTIYINNMNDK 17 1 P08579 P08579 SNRPB2 U2 small nuclear ribonucleoprotein B 0 76.341 8.28E-11 498940000 166840 150030 130280 121570 133510 147210 162080 143540 167980 155620 FALSE TRUE 160319.7083 145751.2913 153824.4941 127844.2423 137804.4704 150186.6871 164063.5835 140575.8488 148911.6146 145079.7188 1.105045624 1.00462899 1.060275656 0.881199959 0.949853443 1.035201118 1.130851265 0.968955896 1.026412347 1 17.14648633 (ac)MDNYADLS(ph)DTELTTLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDNYADLSDTELTTLLR 17 0 P50402;Q5HY57;F8WEQ1 P50402 EMD Emerin 1 MDNY(0.039)ADLS(0.478)DT(0.478)ELT(0.004)T(0.001)LLR 42.556 0.035214 9938900 1689.1 1722.4 0 0 1987.3 0 0 1058.4 922.01 0 TRUE FALSE 1623.088105 1673.278838 0 0 2051.223309 0 0 1036.54367 817.3472902 0 0 (ac)MDNYADLSDTELTTLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 MDNYADLSDTELTTLLR 17 0 P50402;Q5HY57;F8WEQ1 P50402 EMD Emerin 0 43.991 0.020562 9543400 0 752.31 1831.3 0 0 0 0 0 0 1439.4 FALSE TRUE 0 730.8548554 2162.256647 0 0 0 0 0 0 1341.908156 0 0.544638508 1.611329835 0 0 0 0 0 0 1 10.39007022 (ac)MEVAEPSS(ph)PTEEEEEEEEHSAEPRPR ddPTM_BT-474_Pertuzumab_2h_R1 3 MEVAEPSSPTEEEEEEEEHSAEPRPR 26 1 M0R3H9;M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8 M0R3H9 BABAM1 BRISC and BRCA1-A complex member 1 1 MEVAEPS(0.194)S(0.668)PT(0.138)EEEEEEEEHSAEPRPR;MEVAEPS(0.103)S(0.808)PT(0.089)EEEEEEEEHSAEPRPR;MEVAEPS(0.042)S(0.742)PT(0.217)EEEEEEEEHSAEPRPR 108.71 3.90E-08 4658610000 0 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK ddPTM_BT-474_Pertuzumab_2h_R1 1 MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK 32 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 151.99 2.49E-60 51914000 24938 25520 26253 20722 22375 28846 25544 18780 28911 30648 FALSE TRUE 23963.39539 24792.19459 30997.50109 21791.4649 23094.7122 29429.28588 25856.61511 18392.18644 25629.14448 28572.18366 0.838696673 0.867703879 1.084883867 0.762681115 0.808293565 1.029997785 0.904957613 0.643709513 0.896996351 1 14.80232368 (ac)MVDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_BT-474_Pertuzumab_2h_R1 12 MVDYSVWDHIEVSDDEDETHPNIDTASLFR 30 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDY(0.021)S(0.022)VWDHIEVS(0.956)DDEDET(0.002)HPNIDTASLFR;MVDY(0.011)S(0.013)VWDHIEVS(0.973)DDEDET(0.003)HPNIDTASLFR;MVDY(0.003)S(0.003)VWDHIEVS(0.964)DDEDET(0.029)HPNIDTASLFR;MVDY(0.03)S(0.033)VWDHIEVS(0.936)DDEDETHPNIDTASLFR;MVDY(0.163)S(0.179)VWDHIEVS(0.658)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(0.992)DDEDET(0.007)HPNIDTASLFR 139.67 3.26E-81 1402193000 49069.9 42935.2 35467.95 55284.28 44012 54844.1 41802.29 54229 51220.7 44182.4 TRUE FALSE 47152.19406 41710.73013 41877.79755 58137.50832 45427.68595 55953.08528 42313.87893 53109.1522 45406.34087 41189.88669 1.14475173 1.012644935 1.016700965 1.411451038 1.10288446 1.358418043 1.027288063 1.289373593 1.102366248 1 15.33000254 (ac)MVNPTVFFDIAVDGEPLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MVNPTVFFDIAVDGEPLGR 19 0 P62937;F8WE65;C9J5S7;E5RIZ5 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 50.088 0.0063174 374770000 813.98 983.92 1587.17 0 0 1197.8 937.47 992.78 0 0 FALSE TRUE 782.1687617 955.859565 1874.006925 0 0 1222.020337 948.9430383 972.2787461 0 0 0 (ac)S(ph)YGRPPPDVEGMTSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SYGRPPPDVEGMTSLK 16 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(0.534)Y(0.466)GRPPPDVEGMTSLK;S(0.557)Y(0.443)GRPPPDVEGMTSLK 74.46 0.0073345 375659000 452920 452700 349750 389770 432110 424930 376330 494970 435080 430460 TRUE FALSE 435219.3857 439789.4392 412957.6051 409886.0764 446009.2106 433522.3757 380935.6391 484748.6965 385691.5424 401304.5608 1.084511436 1.09589943 1.029037907 1.021384047 1.11139831 1.080282703 0.949243234 1.207932189 0.961094341 1 18.61433803 (ac)SAADEVDGLGVARPHYGSVLDNER ddPTM_BT-474_Pertuzumab_2h_R1 2 SAADEVDGLGVARPHYGSVLDNER 24 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 166.49 7.85E-118 1717070000 9182.6 0 9153.4 0 0 6544.6 9716.9 11184 0 0 FALSE TRUE 8823.73384 0 10807.623 0 0 6676.936296 9835.818329 10953.04649 0 0 0 (ac)SLICSISNEVPEHPCVSPVSNHVYER ddPTM_BT-474_Pertuzumab_2h_R1 3 SLICSISNEVPEHPCVSPVSNHVYER 26 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;; 86.856 1.79E-17 3225860000 6221.8 0 0 16415.3 16900.1 0 7958.4 11640 0 0 FALSE TRUE 5978.645177 0 0 17262.4956 17443.70706 0 8055.79728 11399.62993 0 0 0 (ac)SQPGQKPAAS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQPGQKPAASPR 12 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 1 SQPGQKPAAS(1)PR 41.476 0.065531 359280000 139440 143390 172980 188030 136460 151630 159030 153710 184000 192990 TRUE FALSE 133990.5306 139300.6576 204241.3339 197734.2508 140849.3598 154696.0625 160976.2567 150535.8348 163113.0914 179918.6154 0.744728556 0.774242606 1.135187337 1.099020523 0.782850399 0.859811322 0.894717072 0.836688491 0.906593745 1 17.45698494 AAAAPGAS(ph)PSPGGDAAWSEAGPGPRPLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAAAPGASPSPGGDAAWSEAGPGPRPLAR 29 1 P52701;P52701-3;P52701-2;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 AAAAPGAS(0.971)PS(0.029)PGGDAAWSEAGPGPRPLAR 205.44 1.32E-25 545280000 107360 112860 100590 111400 100710 116850 106110 124040 111240 130280 TRUE FALSE 103164.2525 109641.3433 118768.8506 117149.3674 103949.4286 119212.7871 107408.6059 121478.5307 98612.50156 121456.0196 0.849395961 0.902724655 0.977875375 0.964541468 0.855860656 0.981530496 0.884341561 1.000185344 0.811919425 1 16.89007447 AAAT(ph)PAKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AAATPAKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAAT(1)PAKK 96.113 0.01774 89193000 325400 108020 61029 51585 72675 45243 49878 231710 39452 29118 TRUE FALSE 312683.0083 104939.3754 72058.29788 54247.30803 75012.65738 46157.84446 50488.42188 226925.1075 34973.57436 27145.81192 11.51864638 3.865766685 2.654490427 1.99836749 2.763323403 1.700367062 1.859897285 8.359488681 1.288359857 1 14.72844201 AAGTDGSDFQHR ddPTM_BT-474_Pertuzumab_2h_R1 2 AAGTDGSDFQHR 12 0 A0A3B3ITE9;Q8N5M9 A0A3B3ITE9 JAGN1 Protein jagunal homolog 1 0 ; 176.8 2.41E-05 198990000 184384 291640 151153 293840 197633 186683 216600 264820 206379 178091 FALSE TRUE 177178.0694 283322.7127 178469.7095 309005.1176 203990.0449 190457.8582 219250.8156 259351.3745 182951.7211 166028.7379 1.067153022 1.706467906 1.074932639 1.861154409 1.22864299 1.147137902 1.32055943 1.562087249 1.101928036 1 17.34107345 AAHACATVGNR ddPTM_BT-474_Pertuzumab_2h_R1 1 AAHACATVGNR 11 0 G3V2H2;G3V3U8;Q9Y2U9-2;Q9Y2U9 G3V2H2 KLHDC2 Kelch domain-containing protein 2 0 76.143 0.03616 14968000 7413.6 11247 5219.5 8056.6 9424.4 9780 8059.6 19917 5606.9 6978 FALSE TRUE 7123.868316 10926.24657 6162.779757 8472.402092 9727.544385 9977.758301 8158.235796 19505.70699 4970.428218 6505.373845 1.095074393 1.679572432 0.947336756 1.302369748 1.49530905 1.5337717 1.254076398 2.998399086 0.76404959 1 12.66741625 AAKLS(ph)EGSQPAEEEEDQETPSR ddPTM_BT-474_Pertuzumab_2h_R1 3 AAKLSEGSQPAEEEEDQETPSR 22 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 AAKLS(0.979)EGS(0.021)QPAEEEEDQETPSR;AAKLS(0.957)EGS(0.043)QPAEEEEDQETPSR;AAKLS(0.999)EGS(0.001)QPAEEEEDQETPSR 292.25 1.23E-55 706940000 377610 350786 237195 242381 317731 351323 263656 279487 307761 272166 TRUE FALSE 362852.5837 340781.9267 280061.4129 254890.3125 327951.1062 358426.9918 266882.701 273715.4958 272825.2615 253731.9544 1.430062621 1.343078476 1.103768792 1.004565283 1.29251007 1.412620624 1.051829288 1.078758473 1.075249912 1 17.95294569 AAS(ph)PYSQRPAS(ph)PTAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 2 AAS(0.971)PY(0.009)S(0.07)QRPAS(0.607)PT(0.343)AIR 135.18 0.00057032 0 128440 152110 109860 163420 118070 121670 136110 153680 135170 129940 TRUE FALSE 123420.4228 147771.9717 129714.1458 171854.1258 121867.8288 124130.2508 137775.7549 150506.4543 119826.0683 121139.0481 1.018832695 1.21985416 1.070787231 1.418651777 1.006016068 1.024692308 1.137335625 1.24242725 0.989161383 1 16.88630445 AASPYSQRPAS(ph)PTAIR ddPTM_BT-474_Pertuzumab_2h_R1 1 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AASPYSQRPAS(0.826)PT(0.174)AIR 188.09 7.48E-10 613020000 113490 138710 87381 156170 99396 136770 126480 134620 145050 136560 TRUE FALSE 109054.6853 134754.1266 103172.6905 164229.9524 102593.1626 139535.5831 128027.9001 131840.05 128584.5321 127310.6696 0.856602873 1.058466875 0.810400973 1.289993627 0.805848897 1.096024266 1.005633703 1.035577383 1.010005937 1 16.95799381 AATAARPPAPPPAPQPPSPT(ph)PSPPRPTLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.379)PT(0.595)PS(0.025)PPRPTLAR 200.59 1.05E-23 651090000 64520 112030 97034 83007 83346 87676 93001 99816 101990 90453 TRUE FALSE 61998.48707 108835.0141 114570.2023 87291.00122 86026.89978 89448.86879 94139.17406 97754.76472 90412.52278 84326.53774 0.73521917 1.290637764 1.358649428 1.035154574 1.020164021 1.060743998 1.116364748 1.15924082 1.072171646 1 16.3636991 ADHDFVVQEDFMK ddPTM_BT-474_Pertuzumab_2h_R1 6 ADHDFVVQEDFMK 13 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;;;;; 197.07 3.18E-07 3681454000 6420430 6150570 5347810 5805880 6175840 6257770 6407430 5896260 7338770 7436670 FALSE TRUE 6169512.497 5975161.766 6314278.228 6105522.163 6374491.502 6384306.397 6485846.045 5774500.171 6505703.596 6932977.717 0.889879176 0.861846383 0.91075992 0.880649327 0.919444972 0.920860654 0.935506547 0.832903322 0.938370764 1 22.72504369 ADHPPAEVTSHAASGAK ddPTM_BT-474_Pertuzumab_2h_R1 4 ADHPPAEVTSHAASGAK 17 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 226.7 1.15E-15 1278910000 1290070 1425530 1291420 1483210 1434040 1515360 1593920 1118530 1722170 1747480 FALSE TRUE 1239652.638 1384875.28 1524808.321 1559758.646 1480167.199 1546001.617 1613426.87 1095431.965 1526676.482 1629121.623 0.760933144 0.850074826 0.935969605 0.957423082 0.908567646 0.948978637 0.990366125 0.672406498 0.937116333 1 20.63566288 ADLLLSTQPGREEGSPLELER ddPTM_BT-474_Pertuzumab_2h_R1 3 ADLLLSTQPGREEGSPLELER 21 1 F5GZS6;J3KPF3;P08195-2;P08195-3;P08195;P08195-4;F5GZI0 F5GZS6 SLC3A2 4F2 cell-surface antigen heavy chain 0 ;; 152.81 4.47E-08 716130000 252094 457305 227509 375769 224747 277943 387710 388954 324456 243748 FALSE TRUE 242241.8878 444263.1091 268624.9372 395162.4831 231976.1914 283563.1979 392454.911 380921.964 287625.1151 227238.7309 1.066023767 1.955050125 1.182126551 1.738975049 1.020847945 1.247864732 1.727059949 1.676307391 1.265739841 1 17.79384922 AEDGHAVAK ddPTM_BT-474_Pertuzumab_2h_R1 2 AEDGHAVAK 9 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 90.15 0.011625 784940000 965450 1061260 859750 1093240 853400 1047930 1056160 1105470 1116910 1116510 FALSE TRUE 927719.1466 1030993.904 1015125.95 1149662.247 880850.386 1069119.863 1069085.602 1082641.658 990123.0593 1040887.783 0.891276814 0.990494769 0.975250134 1.104501624 0.846249135 1.027123077 1.027090162 1.040113714 0.951229398 1 19.98938311 AEDREQLVAK ddPTM_BT-474_Pertuzumab_2h_R1 6 AEDREQLVAK 10 1 Q13268;C9JZP6;Q13268-2;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;;; 173.71 3.04E-06 6354310000 5657820 7586510 4539010 8729970 4572090 6043990 8693960 7172150 6845160 5623620 FALSE TRUE 5436706.139 7370150.163 5359310.077 9180524.798 4719155.427 6166203.619 8800359.283 7024042.596 6068126.134 5242727.208 1.036999623 1.405785552 1.022237066 1.751097174 0.900133698 1.17614428 1.678584243 1.339768849 1.157436939 1 22.32188605 AEEQQLPPPLSPPS(ph)PSTPNHR ddPTM_BT-474_Pertuzumab_2h_R1 3 AEEQQLPPPLSPPSPSTPNHR 21 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AEEQQLPPPLS(0.058)PPS(0.741)PS(0.157)T(0.045)PNHR;AEEQQLPPPLS(0.004)PPS(0.701)PS(0.238)T(0.057)PNHR;AEEQQLPPPLS(0.033)PPS(0.889)PS(0.059)T(0.018)PNHR 120.93 1.97E-05 699420000 463530 501450 371890 492420 416990 471670 485330 508020 484550 512310 TRUE FALSE 445414.7351 487149.137 439098.7956 517833.8552 430402.8621 481207.4906 491269.6137 497529.2095 429545.9154 477610.7874 0.932589353 1.019970968 0.919365323 1.084217252 0.901158168 1.007530615 1.028598237 1.041704297 0.899363931 1 18.8654759 AELNEFLTR ddPTM_BT-474_Pertuzumab_2h_R1 6 AELNEFLTR 9 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82;E9PQX2;H0YES8 P23396 RPS3 40S ribosomal protein S3 0 ;;;;; 150.27 0.00019926 3341610000 2211615 2434120 2073273 2411260 2320880 2057392 2439480 2418773 2535250 2530290 FALSE TRUE 2125182.641 2364701.281 2447959.551 2535705.418 2395533.213 2098993.876 2469335.086 2368824.492 2247459.049 2358911.205 0.900916761 1.002454555 1.037749766 1.074947379 1.015524963 0.889814704 1.046811377 1.004202484 0.952752712 1 21.16968968 AELRDDPIISTHLAK ddPTM_BT-474_Pertuzumab_2h_R1 4 AELRDDPIISTHLAK 15 1 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ;;; 162.41 9.59E-07 1913070000 3753540 4665510 3656590 4324430 4192300 4759800 4564050 4606610 5007800 5580700 FALSE TRUE 3606847.507 4532454.223 4317417.153 4547614.351 4327149.137 4856046.417 4619906.209 4511481.894 4439335.538 5202714.218 0.693262662 0.871171091 0.829839382 0.874084979 0.831709941 0.933367895 0.887980007 0.867140055 0.853272994 1 22.31083303 AEMELGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEMELGLR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 157.34 0.00088039 138340000 140590 159130 121810 165250 127490 108810 154570 144940 136570 157680 FALSE TRUE 135095.5874 154591.7682 143823.7766 173778.5723 131590.8316 111010.2128 156461.6739 141946.9383 121067.1461 147000.1932 0.919016394 1.0516433 0.978391753 1.182165605 0.895174549 0.755170523 1.06436373 0.965624162 0.823584946 1 17.16545853 AESDLFLAEHHK ddPTM_BT-474_Pertuzumab_2h_R1 2 AESDLFLAEHHK 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 146.36 3.74E-05 1515460000 996790 995620 875740 926140 982520 948740 1130960 555560 1291880 1152890 FALSE TRUE 957834.3448 967225.8924 1034005.699 973938.1964 1014123.648 967924.1728 1144801.027 544087.4919 1145231.198 1074803.733 0.891171397 0.899909316 0.96204141 0.90615446 0.943543101 0.900558998 1.065125652 0.506220322 1.065525884 1 20.03564181 AET(ph)PPLPIPPPPPDIQPLER ddPTM_BT-474_Pertuzumab_2h_R1 4 AETPPLPIPPPPPDIQPLER 20 0 U3KPW8;A0A669KB72;Q8IX15;Q8IX15-3 U3KPW8 HOMEZ Homeobox and leucine zipper protein Homez 1 AET(1)PPLPIPPPPPDIQPLER;AET(1)PPLPIPPPPPDIQPLER;AET(1)PPLPIPPPPPDIQPLER;AET(1)PPLPIPPPPPDIQPLER 178.51 6.89E-16 887200000 268849 282082 217678 251334 252524 256408 246944 292374 283781 272267 TRUE FALSE 258342.0839 274037.2975 257017.2568 264305.3779 260646.6638 261592.7454 249966.1745 286336.3747 251567.3706 253826.1136 1.017791591 1.079626102 1.012572163 1.04128521 1.026870956 1.030598238 0.984792979 1.128080837 0.991101219 1 17.95348098 AEYLCR ddPTM_BT-474_Pertuzumab_2h_R1 1 AEYLCR 6 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 100.82 0.086601 209290000 274510 301720 227130 350550 265680 234200 325370 337760 316690 337320 FALSE TRUE 263781.8457 293115.241 268177.4435 368641.9275 274225.8385 238935.6845 329351.9754 330785.138 280740.6789 314473.0159 0.838805978 0.932083919 0.852783641 1.172252972 0.872017072 0.759797097 1.047313946 1.051871293 0.892733763 1 18.2625767 AFAIDSSHPWLHECMIR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFAIDSSHPWLHECMIR 17 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 217.37 2.89E-15 755260000 503590 694050 630920 603720 699390 654540 661010 198079 731900 647520 FALSE TRUE 483909.1461 674256.3735 744941.2787 634878.0615 721886.5145 667775.2473 669099.6381 193988.5994 648817.7804 603662.8936 0.801621486 1.11694189 1.234035232 1.051709602 1.195843777 1.106205557 1.108399481 0.321352532 1.074801495 1 19.2033836 AFAMIIDKLEEDISSSMTNSTAASRPPVTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 AFAMIIDKLEEDISSSMTNSTAASRPPVTLR 31 2 F8VZX2;F8W1G6;F8W0G4;F8VXH9;H3BND9;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 0 ; 145.67 8.59E-08 457620000 231202 238127 198185 181476 213250 230211 182378 248392 254451 216007 FALSE TRUE 222166.3702 231335.8511 234001.4381 190841.9981 220109.3799 234866.0241 184609.9965 243262.6184 225566.7892 201376.6535 1.103237969 1.148771951 1.162008773 0.947686809 1.093023328 1.166302151 0.916739817 1.207998118 1.120123834 1 17.61953691 AFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDK ddPTM_BT-474_Pertuzumab_2h_R1 3 AFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDK 41 2 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ;; 88.95 8.51E-05 243713000 60715 53079 40357.9 34483 49995 50836 52973 41863.1 68618 58632 FALSE TRUE 58342.19068 51565.23889 47651.47029 36262.67176 51603.13458 51863.93875 53621.29942 40998.61236 60828.77231 54660.80242 1.067349693 0.943367763 0.871766754 0.663412723 0.944061051 0.948832371 0.980982661 0.750055077 1.112840822 1 15.73821902 AFS(ph)FSK ddPTM_BT-474_Pertuzumab_2h_R1 1 AFSFSK 6 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 AFS(0.998)FS(0.002)K 69.628 0.097556 475320000 2615000 1246800 730840 846640 1182700 570880 1024500 2641900 785010 643120 TRUE FALSE 2512802.909 1211242.485 862919.0454 890335.1919 1220742.62 582423.5847 1037038.137 2587343.842 695898.9558 599560.9096 4.191071948 2.020215904 1.439251678 1.48497872 2.036061058 0.971416874 1.729662693 4.315397819 1.160681 1 19.1935468 AGADGPPAPPGAPQAPSPPQGS(ph)PQDQHHFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 AGADGPPAPPGAPQAPSPPQGSPQDQHHFLR 31 0 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 AGADGPPAPPGAPQAPS(0.233)PPQGS(0.767)PQDQHHFLR 83.998 0.0012495 340170000 165510 175560 179120 180790 176330 201190 193170 85789 211690 218060 TRUE FALSE 159041.6862 170553.2007 211490.9685 190120.5936 182001.8146 205258.1996 195534.0722 84017.42717 187659.8387 203290.602 0.782336639 0.838962544 1.040338149 0.935215852 0.895279038 1.009678744 0.961845114 0.413287316 0.923111235 1 17.633184 AGGPTT(ph)PLS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 2 AGGPT(0.018)T(0.982)PLS(0.994)PT(0.006)R;AGGPT(0.001)T(0.999)PLS(1)PTR 189.23 4.35E-05 879440000 1353710 1467220 1334570 1490960 1244350 1412350 1435890 1534110 1452510 1611010 TRUE FALSE 1300805.517 1425376.322 1575756.486 1567908.624 1284375.648 1440908.685 1453462.851 1502430.092 1287627.154 1501894.858 0.866109575 0.949052002 1.049178961 1.043953654 0.855170148 0.959393847 0.967752732 1.000356373 0.857335084 1 20.51835239 AGGPTTPLS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 5 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 AGGPTT(0.001)PLS(0.998)PT(0.002)R;AGGPT(0.004)T(0.027)PLS(0.485)PT(0.485)R;AGGPTT(0.004)PLS(0.767)PT(0.229)R;AGGPT(0.009)T(0.145)PLS(0.825)PT(0.02)R;AGGPTT(0.009)PLS(0.961)PT(0.029)R 140.53 6.27E-05 5497420000 1558809 1749453 1505359 1847456 1512526 1151913 1934860 1606009 1530902 1924023 TRUE FALSE 1497889.021 1699560.313 1777410.858 1942803.426 1561177.772 1175205.47 1958539.395 1572844.353 1357120.423 1793707.208 0.835080003 0.947512674 0.99091471 1.083121825 0.870363772 0.655182443 1.091894701 0.876867944 0.756600864 1 20.77451298 AGLYGLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGLYGLPR 8 0 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 126.68 0.0028126 729840000 1296230 1349780 1253100 1106690 1173780 899320 1394520 1379230 1457600 1572980 FALSE TRUE 1245571.899 1311285.596 1479563.045 1163806.404 1211535.7 917504.8666 1411586.553 1350748.419 1292139.359 1466440.664 0.849384451 0.89419615 1.008948457 0.793626658 0.826174376 0.625667911 0.962593706 0.921106767 0.881139886 1 20.48388727 AGNLGGGVVTIER ddPTM_BT-474_Pertuzumab_2h_R1 1 AGNLGGGVVTIER 13 0 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4;K7EJT5 P35268 RPL22 60S ribosomal protein L22 0 100.02 0.0060314 280100000 142810 162620 130820 128110 159160 129770 130110 196340 154200 151930 FALSE TRUE 137228.8273 157982.2368 154462.0841 134721.7725 164279.5259 132394.0383 131702.3251 192285.5104 136695.8625 141639.6458 0.968858871 1.115381474 1.090528596 0.951158637 1.159841406 0.934724438 0.929840825 1.357568422 0.965096049 1 17.11186562 AGTFQAFEQFGQQLLAHGHYASPEIK ddPTM_BT-474_Pertuzumab_2h_R1 1 AGTFQAFEQFGQQLLAHGHYASPEIK 26 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 223.12 1.36E-34 196050000 226720 211770 186120 196630 219350 196230 240690 77481 268630 225240 FALSE TRUE 217859.5317 205730.5269 219756.0242 206778.0979 226405.592 200197.905 243635.6362 75880.99027 238136.2486 209984.2942 1.037503936 0.979742451 1.046535528 0.984731257 1.078202505 0.953394661 1.160256471 0.361365075 1.134066953 1 17.6799219 AGYPLEHPFDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 AGYPLEHPFDFR 12 0 O95470 O95470 SGPL1 Sphingosine-1-phosphate lyase 1 0 ; 116.01 0.00088778 143024000 187447 327010 182555 334800 197541 140702 278240 292360 250060 191984 FALSE TRUE 180121.364 317683.995 215546.7494 352079.0681 203895.0857 143547.0908 281645.1844 286322.6638 221674.2371 178980.7527 1.006372816 1.774961778 1.204301279 1.967133688 1.139201186 0.802025294 1.573605989 1.59973997 1.238536735 1 17.44944493 AHDGGIYAISWSPDSTHLLSASGDK ddPTM_BT-474_Pertuzumab_2h_R1 4 AHDGGIYAISWSPDSTHLLSASGDK 25 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ;;; 271.94 3.49E-53 3474660000 1488430 1809330 1521700 1827460 1758560 1768480 1928060 849930 2051970 2134160 FALSE TRUE 1430260.51 1757729.68 1796705.04 1921775.43 1815125.679 1804239.877 1951656.175 832378.6485 1819038.968 1989611.442 0.718864236 0.883453745 0.903043178 0.965904894 0.912301589 0.906830268 0.980923277 0.418362415 0.914268449 1 20.92405528 AHEEQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHEEQLK 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 143.56 0.0024137 1458090000 2673000 2695700 2488700 2524100 2413500 2579500 2905700 1715260 3267100 3199000 FALSE TRUE 2568536.205 2618821.275 2938463.451 2654369.103 2491132.419 2631659.257 2941260.826 1679839.282 2896232.505 2982328.881 0.86125183 0.878112837 0.985291552 0.890032324 0.835297688 0.882417521 0.986229535 0.563264264 0.97113116 1 21.50800793 AHLMEIQVNGGTVAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHLMEIQVNGGTVAEK 16 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 154.88 3.12E-07 693920000 317997 351604 275705 293691 301324 326190 332690 236262 409570 389800 FALSE TRUE 305569.3257 341576.5982 325531.0265 308848.4277 311016.3601 332785.7853 336761.5597 231383.1071 363077.3307 363398.4988 0.84086568 0.939950493 0.895796289 0.849889113 0.855854829 0.915759934 0.92670047 0.636720041 0.999116209 1 18.47119293 AHQLEEDIVSVTHK ddPTM_BT-474_Pertuzumab_2h_R1 3 AHQLEEDIVSVTHK 14 0 B8ZZD4;Q86VP1-2;Q86VP1;Q86VP1-4;Q86VP1-3 B8ZZD4 TAX1BP1 Tax1-binding protein 1 0 ;; 216.39 3.55E-12 678797000 536864 598625 504250 621514 556756 618185 632350 291248 682410 747050 FALSE TRUE 515882.7613 581552.8011 595379.192 653590.412 574664.5624 630685.1243 640088.8885 285233.627 604945.6777 696451.6381 0.7407302 0.835022519 0.854875141 0.938457714 0.825132042 0.905569159 0.919071553 0.409552669 0.868611178 1 19.40966365 AHT(ph)PLNTPDPSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 AHTPLNTPDPSTK 13 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 AHT(1)PLNTPDPSTK 95.651 0.01692 721490000 368410 312360 277400 242380 317400 351390 329800 161230 458550 396400 TRUE FALSE 354012.1299 303451.7986 327532.3507 254889.2608 327609.4593 358495.3466 333836.1911 157900.5442 406497.3264 369551.4749 0.957950797 0.821135401 0.886296965 0.689726001 0.88650562 0.970082305 0.90335505 0.427276184 1.099974845 1 18.49541581 AHTDFFEAFK ddPTM_BT-474_Pertuzumab_2h_R1 2 AHTDFFEAFK 10 0 P61201;P61201-2;B4DIH5;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 ; 129.85 0.00029216 818980000 1091140 1104340 956240 1027000 1050790 885660 1199840 873360 1248190 1310270 FALSE TRUE 1048497.042 1072845.304 1129053.839 1080003.593 1084589.615 903568.652 1214524.001 855324.8108 1106500.704 1221524.246 0.858351397 0.878284085 0.924299164 0.884144213 0.887898557 0.739705868 0.994269254 0.700211079 0.905836055 1 20.22025107 AHTPTPGIYMGRPT(ph)HSGGGGGGGGGGGGGGGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.005)PT(0.02)PGIY(0.06)MGRPT(0.778)HS(0.138)GGGGGGGGGGGGGGGGR 111.72 2.97E-06 145710000 3693.2 5292.7 4763.4 4949.3 4861.3 3185.4 4149.7 8147.9 4449.5 4332.9 TRUE FALSE 3548.865661 5141.757378 5624.252341 5204.733966 5017.668129 3249.81097 4200.48527 7979.643018 3944.411414 4039.428824 0.878556305 1.272892184 1.392338518 1.288482653 1.24217268 0.8045224 1.039871094 1.975438451 0.976477514 1 11.97993559 AHVDEFK ddPTM_BT-474_Pertuzumab_2h_R1 6 AHVDEFK 7 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ;;;;; 146.21 0.0022347 3606370000 6277810 5682710 4875570 5336800 5525410 5608560 6095340 4789770 7068470 6462070 FALSE TRUE 6032466.245 5520644.675 5756693.955 5612232.888 5703139.831 5721968.926 6169936.594 4690859.576 6266086.919 6024388.243 1.001340883 0.916382619 0.955564901 0.931585526 0.946675347 0.949800825 1.024159856 0.778644965 1.040120036 1 22.52238332 AIAELGIYPAVDPLDSTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 AIAELGIYPAVDPLDSTSR 19 0 P06576;H0YH81 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 163.27 6.05E-11 17071000 13830 22392 13380 29533 14217 17429 23680 24648 16740 14445 FALSE TRUE 13289.50831 21753.40208 15798.06364 31057.20167 14674.30272 17781.42632 23969.80292 24139.01019 14839.74538 13466.62728 0.986847563 1.615356364 1.173126968 2.306234591 1.089679131 1.320406806 1.779941066 1.792505999 1.101964513 1 13.71710095 AIGPHDVLATLLNNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 AIGPHDVLATLLNNLK 16 0 O75533;H7C341 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 199.13 3.89E-11 307020000 465260 492340 376180 402000 420170 365660 491920 474270 537720 548770 FALSE TRUE 447077.1248 478298.9453 444164.0941 422747.2682 433685.1496 373053.8957 497940.2641 464476.1588 476680.2799 511601.3191 0.873877975 0.934905614 0.868184028 0.826321693 0.847701391 0.72918869 0.973297459 0.907886945 0.931741694 1 18.96466046 AIGSSPLGS(ph)GEGLLGLSPGPNGHSHLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AIGSSPLGSGEGLLGLSPGPNGHSHLLK 28 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 AIGS(0.102)S(0.437)PLGS(0.452)GEGLLGLS(0.009)PGPNGHSHLLK 121.38 8.19E-05 248930000 189870 224560 190750 203230 200670 224240 220870 35086 253910 254360 TRUE FALSE 182449.6705 218155.7687 225222.7682 213718.7247 207124.7328 228774.2864 223573.0731 34361.46184 225087.2013 237131.9706 0.769401401 0.919976198 0.949778166 0.901264912 0.873457646 0.964755135 0.942821301 0.144904383 0.949206472 1 17.85533066 AINQIAAALFTIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 AINQIAAALFTIHK 14 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 83.499 0.010202 0 83850 81078 76480 69962 76681 58426 87833 83072 98824 89477 FALSE TRUE 80573.0493 78765.73482 90301.63729 73572.7472 79147.514 59607.41375 88907.92653 81356.53417 87605.91382 83416.64309 0.965910954 0.94424484 1.082537416 0.881991225 0.948821615 0.714574593 1.06582959 0.975303383 1.050221042 1 16.34804764 AIPPERHS(ph)PHHLK ddPTM_BT-474_Pertuzumab_2h_R1 4 AIPPERHSPHHLK 13 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 AIPPERHS(1)PHHLK;AIPPERHS(1)PHHLK;AIPPERHS(1)PHHLK;AIPPERHS(1)PHHLK 90.754 0.0034328 1242250000 1744650 1829370 1466010 1605110 1663750 1786580 1794080 345247 2105180 1500370 TRUE FALSE 1676467.149 1777198.159 1730950.618 1687949.919 1717266.03 1822705.872 1816036.488 338117.5288 1866208.792 1398748.604 1.198547863 1.270562955 1.237499443 1.206757179 1.227715992 1.303097545 1.298329438 0.241728591 1.33419886 1 20.41570526 AISS(ph)PTVSR ddPTM_BT-474_Pertuzumab_2h_R1 2 AISSPTVSR 9 0 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 AIS(0.001)S(0.999)PTVSR;AIS(0.001)S(0.999)PTVSR 219.72 5.06E-07 1226100000 1317240 1604080 1215290 1343120 1402990 1372670 1315280 1636500 1544720 1383460 TRUE FALSE 1265760.805 1558333.209 1434919.937 1412438.584 1448118.448 1400426.328 1331376.79 1602705.703 1369369.862 1289757.022 0.981394777 1.208237817 1.112550591 1.095119903 1.122783922 1.085806322 1.032269464 1.24264158 1.061727006 1 20.29866787 AITHLNNNFMFGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 AITHLNNNFMFGQK 14 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 203.74 1.46E-08 2826600000 2819300 2795800 2236300 2595300 2653900 2517600 2781900 2811300 3017000 2884100 FALSE TRUE 2709118.639 2716066.521 2640449.156 2729243.744 2739265.104 2568507.597 2815945.724 2753245.673 2674522.808 2688757.338 1.007572755 1.010156805 0.982033268 1.015057664 1.018784799 0.955276834 1.04730378 1.023984438 0.994705908 1 21.35850813 AKEALELTDTGLLSGSEER ddPTM_BT-474_Pertuzumab_2h_R1 1 AKEALELTDTGLLSGSEER 19 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 175.77 1.76E-12 136140000 292510 308670 217000 225090 277470 303670 252940 277700 338150 289580 FALSE TRUE 281078.3858 299867.0338 256216.7271 236706.9219 286395.0745 309810.4155 256035.5554 271965.398 299764.6296 269966.4887 1.041160283 1.110756506 0.949068636 0.876801128 1.060854167 1.147588417 0.948397546 1.007404287 1.110377185 1 18.04242081 AKEGTSDPPS(ph)PLLLPSPGGWK ddPTM_BT-474_Pertuzumab_2h_R1 2 AKEGTSDPPSPLLLPSPGGWK 21 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 AKEGTSDPPS(1)PLLLPSPGGWK;AKEGT(0.001)S(0.001)DPPS(0.997)PLLLPSPGGWK 136.53 2.90E-06 829890000 2594340 2431530 1839580 1890840 2290980 2510890 2212440 2348420 2656590 2467840 TRUE FALSE 2492950.325 2362185.145 2172033.027 1988426.479 2364671.452 2561661.916 2239516.503 2299924.306 2355025.041 2300690.999 1.083565905 1.026728555 0.944078552 0.864273594 1.027809234 1.113431538 0.973410381 0.999666756 1.023616401 1 21.1336358 AKELATK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKELATK 7 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 68.016 0.082346 0 308140 301580 226900 191790 283570 268670 271670 311510 325520 261640 FALSE TRUE 296097.5481 292979.2337 267905.8774 201688.3049 292691.2866 274102.6915 274994.7787 305077.2096 288568.3343 243918.8898 1.213918071 1.201133844 1.098340016 0.82686628 1.199953341 1.123745241 1.127402552 1.2507322 1.183050376 1 17.89604196 AKT(ph)PVTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 AKTPVTLK 8 1 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 AKT(0.967)PVT(0.033)LK 84.479 0.028167 3157600000 5250600 3682600 1516300 2014600 1594400 1155900 1622000 7227600 1946300 1107200 TRUE FALSE 5045400.747 3577575.854 1790329.14 2118573.747 1645685.324 1179273.09 1641850.521 7078347.534 1725364.184 1032208.358 4.887967346 3.465943505 1.734464875 2.052467151 1.59433443 1.14247582 1.590619286 6.857479385 1.671527042 1 19.97730279 AKVDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_BT-474_Pertuzumab_2h_R1 4 AKVDEFPLCGHMVSDEYEQLSSEALEAAR 29 1 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;; 297.7 4.18E-81 1162500000 363674 381030 327065 302708 334795 415217 343839 359038 400122 385386 FALSE TRUE 349461.218 370163.3975 386172.921 318330.7962 345563.9852 423612.9722 348047.0045 351623.7398 354701.828 359283.463 0.972661572 1.030282314 1.074841903 0.88601572 0.961814336 1.179049458 0.968725367 0.978680558 0.987247855 1 18.45476301 ALDYCHSK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALDYCHSK 8 0 P19784 P19784 CSNK2A2 Casein kinase II subunit alpha 0 107.47 0.0039978 240160000 270530 247750 229880 254040 256700 233150 254960 251070 281810 317110 FALSE TRUE 259957.3885 240684.4126 271424.4297 267151.0348 264956.9886 237864.4527 258080.2767 245885.3168 249820.1102 295631.8572 0.879328063 0.814135577 0.918116309 0.903661186 0.896239638 0.804596822 0.872978573 0.831728079 0.845037854 1 18.17344222 ALEEEEDDRPYDPEEEYDPER ddPTM_BT-474_Pertuzumab_2h_R1 1 ALEEEEDDRPYDPEEEYDPER 21 1 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 107.41 0.000343 0 75479 71882 70227 74503 81093 72963 78767 75400 75303 92631 FALSE TRUE 72529.19723 69831.99574 82918.58109 78348.10876 83701.42999 74438.36185 79730.97411 73842.96365 66754.91914 86357.01986 0.839876102 0.808642955 0.960183448 0.907258135 0.969248709 0.861983912 0.923271487 0.8550893 0.773010917 1 16.39802584 ALEHSALAINHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALEHSALAINHK 12 0 Q9NRF8;P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8;A0A3B3ISY3 Q9NRF8;P17812 CTPS2;CTPS1 CTP synthase 2;CTP synthase 1;CTP synthase 0 ; 174.77 1.71E-05 800730000 790040 806750 651270 763010 809890 738270 821710 455470 924090 916260 FALSE TRUE 759164.3634 783742.2799 768968.9764 802389.0375 835940.8474 753198.3252 831766.3328 446064.3853 819191.1773 854200.8941 0.888742178 0.917515172 0.90022029 0.939344647 0.978623241 0.881757828 0.9737362 0.522200794 0.959014657 1 19.70421588 ALELDSNLYR ddPTM_BT-474_Pertuzumab_2h_R1 6 ALELDSNLYR 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 275.44 1.75E-23 2595891000 2332920 2579170 2072210 2489000 2397600 1995805 2740370 2564530 2573230 2800690 FALSE TRUE 2241746.907 2505614.597 2446704.443 2617457.588 2474720.981 2036161.545 2773907.468 2511571.559 2281127.718 2610996.772 0.858578966 0.959639102 0.937076778 1.002474464 0.947806986 0.779840698 1.062394063 0.961920592 0.873661639 1 21.31616924 ALHHGIDLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALHHGIDLEK 10 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 90.629 0.0061879 472030000 577900 505240 445110 511430 515610 526780 545200 124400 664880 562380 FALSE TRUE 555315.0291 490831.0499 525551.2784 537824.9636 532195.0639 537431.8525 551872.3207 121831.0965 589405.6098 524289.5017 1.059176328 0.93618325 1.002406641 1.025816771 1.01507862 1.025066973 1.052609901 0.23237371 1.124198764 1 19.00000413 ALLDSLQLGPDSLTVHLIHEVTK ddPTM_BT-474_Pertuzumab_2h_R1 2 ALLDSLQLGPDSLTVHLIHEVTK 23 0 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 249.34 3.47E-38 2031200000 1277920 1510670 1261490 1292670 1419200 1603230 1454830 73920 1807440 1521030 FALSE TRUE 1227977.474 1467587.171 1489469.305 1359384.854 1464849.857 1635648.409 1472634.645 72393.52617 1602266.989 1418009.283 0.865986907 1.03496302 1.050394608 0.958657231 1.033032628 1.153482159 1.03852257 0.051052928 1.129941114 1 20.43543555 ALMDEEDMDDVVDADEYLIPQQGFFSSPSTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALMDEEDMDDVVDADEYLIPQQGFFSSPSTSR 32 0 P00533;E9PFD7;Q504U8 P00533 EGFR Epidermal growth factor receptor;Receptor protein-tyrosine kinase 0 97.469 5.65E-05 17087000 13325 25786 10087 28588 11281 12268 20949 24053 14851 10566 FALSE TRUE 12804.24427 25050.60853 11909.94528 30063.43011 11643.86361 12516.06737 21205.38013 23556.29714 13165.17674 9850.355409 1.299876374 2.543117226 1.209087874 3.052014761 1.182075481 1.270620891 2.152752794 2.391415961 1.336517942 1 13.26596006 ALQHCEELIQQYNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ALQHCEELIQQYNR 14 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3;Q8WVX6;F6QZY1 Q7Z5K2 WAPAL Wings apart-like protein homolog 0 164.93 4.04E-06 280770000 196030 194310 196760 173230 182720 209170 170350 246970 189470 223250 FALSE TRUE 188368.9309 188768.469 232318.9089 182170.4211 188597.3547 213399.5607 172434.7943 241869.9832 167962.1599 208129.0786 0.905058208 0.906977873 1.116225135 0.875276162 0.906155718 1.025323141 0.828499292 1.162115283 0.807009578 1 17.66711902 ALTNLPHTDFTLCK ddPTM_BT-474_Pertuzumab_2h_R1 1 ALTNLPHTDFTLCK 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 155.98 3.03E-07 0 282420 301730 228730 227350 283500 261040 283680 275360 315220 295310 FALSE TRUE 271382.7142 293124.9558 270066.5991 239083.5607 292619.035 266318.4077 287151.7607 269673.7198 279437.5471 275308.3907 0.985740803 1.064714937 0.980960291 0.868420901 1.062877286 0.967345772 1.043018558 0.97953324 1.014998295 1 18.07068905 ALVADSHPESER ddPTM_BT-474_Pertuzumab_2h_R1 2 ALVADSHPESER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 145.09 6.36E-05 1822880000 1384960 1416890 1101780 1522820 1296110 1496760 1442750 1456580 1511930 1578670 FALSE TRUE 1330834.232 1376481.684 1300896.155 1601412.923 1337800.555 1527025.513 1460406.806 1426501.114 1340302.045 1471745.275 0.904255821 0.935271686 0.883913934 1.088104681 0.908989197 1.037561009 0.992295903 0.969258158 0.910688873 1 20.48909657 ALVEFESNPEETREPGS(ph)PPSVQR ddPTM_BT-474_Pertuzumab_2h_R1 7 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 ALVEFESNPEETREPGS(0.999)PPS(0.001)VQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(0.998)PPS(0.002)VQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEET(0.046)REPGS(0.953)PPSVQR 246.57 8.08E-38 30772650000 3173050 3687110 2763120 4246430 3479200 3937010 3861220 3629900 3799860 4484240 TRUE FALSE 3049043.698 3581957.233 3262477.249 4465588.761 3591111.628 4016619.04 3908474.765 3554941.297 3368515.823 4180518.431 0.729345833 0.856821299 0.780400159 1.068190186 0.859011074 0.960794482 0.934925854 0.850358958 0.805765093 1 21.99525043 ALYDYAGQEADELS(ph)FR ddPTM_BT-474_Pertuzumab_2h_R1 2 ALYDYAGQEADELSFR 16 0 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 ALYDYAGQEADELS(1)FR;ALYDYAGQEADELS(1)FR 216.17 1.62E-14 69499000 74064 74087 51161 74456 60577 57037 65700 93949 67044 59917 TRUE FALSE 71169.497 71974.1113 60406.93077 78298.68308 62525.51422 58190.32722 66504.05625 92008.92032 59433.44619 55858.76822 1.274097143 1.288501583 1.081422536 1.401725917 1.119350036 1.041740251 1.190575059 1.647170592 1.06399493 1 15.76949614 AMGIMNSFVNDIFER ddPTM_BT-474_Pertuzumab_2h_R1 9 AMGIMNSFVNDIFER 15 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L 0 ;;;;;;;; 346.79 7.14E-82 19692941000 3403796 3524941 2803340 3739359 3501834 3341916 3752796 3744658 3307321 3575807 FALSE TRUE 3270771.889 3424413.134 3309965.898 3932347.766 3614473.671 3409491.831 3798723.84 3667329.504 2931887.786 3333614.407 0.981148834 1.027237321 0.992906045 1.179604863 1.084250675 1.022761308 1.139521065 1.100106088 0.879492175 1 21.66865581 AMLDQLMGTS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 AMLDQLMGTSR 11 0 Q9Y383;V9GZ75;F8WEU3 Q9Y383 LUC7L2;C7orf55-LUC7L2 Putative RNA-binding protein Luc7-like 2 1 AMLDQLMGT(0.158)S(0.842)R;AMLDQLMGT(0.104)S(0.896)R 124.42 0.00036668 136825000 469800 490570 298300 368820 501850 389290 371630 472510 426810 495670 TRUE FALSE 451439.6966 476579.4239 352209.4456 387854.8444 517992.461 397161.7105 376178.1191 462752.5034 378360.3181 462097.8294 0.976935332 1.031338807 0.762196711 0.839334919 1.120958438 0.859475386 0.814065973 1.001416743 0.818788348 1 18.81783879 AMLPGS(ph)PLFTR ddPTM_BT-474_Pertuzumab_2h_R1 8 AMLPGSPLFTR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(0.999)PLFT(0.001)R;AMLPGS(1)PLFTR 187.58 3.70E-06 1774701000 2446610 2727260 1936090 2881690 2069050 1612147 2606020 2783130 2463420 2676180 TRUE FALSE 2350993.776 2649481.215 2285984.531 3030414.366 2135602.872 1644745.717 2637913.252 2725657.393 2183782.889 2494919.945 0.94231231 1.061950393 0.916255664 1.214633909 0.85598052 0.659237873 1.057313786 1.092482907 0.875291768 1 21.25056209 AMS(ph)TTS(ph)ISSPQPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 2 AMS(0.956)T(0.043)T(0.118)S(0.335)IS(0.342)S(0.206)PQPGK 123.02 0.00015401 119420000 481250 400110 216310 288740 414630 297830 286360 586810 372710 326410 TRUE FALSE 462442.218 388699.2545 255402.0288 303641.906 427966.9505 303852.3267 289864.5593 574692.1684 330401.5233 304301.96 1.519682022 1.277347194 0.83930458 0.997830924 1.40638907 0.998522411 0.952555677 1.888558879 1.085768634 1 18.2151441 AMS(ph)TTSIS(ph)SPQPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 2 AMS(0.98)T(0.019)T(0.001)S(0.001)IS(0.807)S(0.193)PQPGK 218.12 8.04E-12 97717000 422240 340070 165860 195920 358960 241360 236150 459110 306810 241440 TRUE FALSE 405738.394 330371.5366 195834.5915 206031.4547 370506.2744 246240.4646 239040.0743 449629.2181 271982.2151 225087.0537 1.802584321 1.46775006 0.870039339 0.915341204 1.646057684 1.093978798 1.061989441 1.997579206 1.20834233 1 17.78012355 ANHGPGMAMNWPQFEEWSADLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 ANHGPGMAMNWPQFEEWSADLNR 23 0 Q9UNF0-2;Q9UNF0 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 82.475 0.0086793 332540000 112560 108450 103880 89915 121030 111130 129770 103480 131680 108360 FALSE TRUE 108161.0308 105357.1122 122653.4268 94555.52393 124923.0399 113377.1247 131358.1641 101343.1018 116732.2384 101020.6807 1.070682063 1.042926176 1.214141758 0.936001651 1.236608574 1.122315985 1.300309632 1.003191635 1.155528132 1 16.62429114 ANVSS(ph)PHR ddPTM_BT-474_Pertuzumab_2h_R1 3 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.187)S(0.813)PHR;ANVS(0.07)S(0.93)PHR;ANVS(0.098)S(0.902)PHR 79.036 0.01873 1089670000 1758310 1965590 1983550 2374220 2087590 1350940 2301110 1671270 2110210 2240530 TRUE FALSE 1689593.301 1909533.298 2342021.609 2496753.779 2154739.228 1378256.932 2329271.673 1636757.69 1870667.808 2088776.907 0.80889122 0.914187289 1.121240665 1.195318547 1.0315794 0.659839223 1.115136645 0.783596221 0.895580471 1 20.99422698 APAPLGTVADSLRAS(ph)DGQLQAK ddPTM_BT-474_Pertuzumab_2h_R1 2 APAPLGTVADSLRASDGQLQAK 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 APAPLGTVADS(0.029)LRAS(0.971)DGQLQAK;APAPLGTVADS(0.02)LRAS(0.98)DGQLQAK 126.68 1.17E-05 248610000 186693 190760 118480 128536 164709 172028 135671 184682 186839 163088 TRUE FALSE 179396.8312 185319.7116 139891.9716 135169.7584 170007.0146 175506.524 137331.3823 180868.2522 165629.82 152041.9045 1.179917022 1.218872601 0.920088261 0.889029632 1.118158939 1.15432995 0.903246922 1.189594755 1.089369543 1 17.21410948 APEPQLS(ph)PGSDASEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 APEPQLSPGSDASEVR 16 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 APEPQLS(0.953)PGS(0.047)DASEVR;APEPQLS(0.537)PGS(0.463)DASEVR 123.42 9.23E-05 415340000 171227 182851 185514 178268 187815 174879 189168 143364 236812 202712 TRUE FALSE 164535.2595 177636.2685 219040.5065 187468.4328 193856.24 178415.1732 191483.0946 140403.4833 209930.0946 188982.1357 0.870639222 0.939963282 1.159054033 0.991990233 1.02579135 0.94408486 1.013233838 0.742945796 1.110846238 1 17.52789034 APS(ph)PAPRPVPGSPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPAPRPVPGSPAR 15 1 Q5TZA2-2;Q5TZA2 Q5TZA2-2 CROCC Rootletin 1 APS(1)PAPRPVPGSPAR 79.311 0.012307 93486000 101820 119220 98753 93542 92235 109320 111430 115920 120810 113120 TRUE FALSE 97840.76183 115819.9623 116599.8638 98369.71383 95201.82254 111530.5253 112793.7137 113526.2115 107096.1553 105458.2816 0.927767457 1.098253836 1.105649192 0.932783204 0.90274392 1.057579581 1.069557667 1.076503521 1.01553101 1 16.68631287 APS(ph)PPEAALQPAPTEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 APSPPEAALQPAPTEPR 17 0 Q9NVR5-2;Q9NVR5 Q9NVR5-2 DNAAF2 Protein kintoun 1 APS(1)PPEAALQPAPTEPR 172.93 1.62E-09 75640000 18371 17224 14468 22249 13468 22076 15144 14543 21716 18032 TRUE FALSE 17653.04101 16732.78838 17082.68944 23397.27356 13901.21045 22522.39185 15329.3368 14242.68197 19250.89072 16810.67658 1.050108895 0.995366742 1.016180959 1.391810344 0.826927482 1.339767126 0.911881014 0.847240258 1.145158592 1 14.03709017 APS(ph)PTKPLR ddPTM_BT-474_Pertuzumab_2h_R1 4 APSPTKPLR 9 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 APS(0.557)PT(0.443)KPLR;APS(0.988)PT(0.012)KPLR;APS(0.976)PT(0.024)KPLR;APS(0.846)PT(0.154)KPLR 122.18 0.00035919 4800670000 2571300 2258510 1964590 2579960 2453610 1896700 2444820 2624220 2145670 2397510 TRUE FALSE 2470810.753 2194099.506 2319635.115 2713112.045 2532532.594 1935052.574 2474740.438 2570028.94 1902102.537 2235124.512 1.105446582 0.981645315 1.037810244 1.213852754 1.13306108 0.865747104 1.107204733 1.149837034 0.85100518 1 21.09192377 APVILGSPDDVLEFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 APVILGSPDDVLEFLK 16 0 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 204.49 5.83E-11 129511000 166501 150638 118852 153444 151723 91159 162711 163951 182602 186611 FALSE TRUE 159993.9568 146341.9517 140331.2002 161363.2632 156603.3081 93002.29744 164702.3059 160565.3546 161873.7865 173971.6708 0.91965523 0.841182654 0.80663248 0.927526088 0.90016557 0.534582999 0.946719113 0.922939659 0.930460608 1 17.40849287 AQAVLEEDHYGMEDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 AQAVLEEDHYGMEDVK 16 0 K7EKE6;K7EJE8;P36776-2;P36776;P36776-3;K7ER27 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 ; 140.02 2.40E-05 123480000 180703 237090 148126 310660 168416 197266 290860 254130 258210 204176 FALSE TRUE 173640.927 230328.4253 174895.6632 326693.1998 173833.2536 201254.8537 294419.6317 248882.1267 228899.0833 190346.9777 0.912233696 1.210045088 0.918825533 1.716303583 0.913244096 1.057305223 1.546752333 1.307518143 1.202535948 1 17.53827214 AQPFGFIDS(ph)DTDAEEERIPATPVVIPMKK ddPTM_BT-474_Pertuzumab_2h_R1 1 AQPFGFIDSDTDAEEERIPATPVVIPMKK 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.995)DT(0.005)DAEEERIPATPVVIPMKK 253.11 3.72E-58 445880000 178620 168220 99976 124360 124480 203930 142120 192380 158910 144750 TRUE FALSE 171639.3329 163422.5303 118043.8872 130778.2345 128484.0122 208053.6043 143859.3071 188407.2858 140871.203 134945.9536 1.271911668 1.211022087 0.874749365 0.969115643 0.952114597 1.541755042 1.066051284 1.396168472 1.043908315 1 17.04202219 AQS(ph)PGS(ph)PLHAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 2 AQS(1)PGS(1)PLHAR;AQS(1)PGS(1)PLHAR 81.703 0.030626 963260000 617900 755680 628590 762160 710960 761470 651460 651920 657310 682680 TRUE FALSE 593751.7849 734128.7463 742190.1959 801495.1689 733828.6741 776867.4451 659432.7624 638457.6242 582694.9245 636441.4755 0.932924405 1.153489794 1.166156237 1.259338368 1.153018309 1.220642392 1.036124746 1.003167846 0.915551464 1 19.27966833 AREESWGPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 AREESWGPPR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 170.02 4.06E-06 1363390000 1053221 940610 856428 915760 980720 854520 1025920 558570 1198010 1056650 FALSE TRUE 1012059.959 913784.7238 1011203.591 963022.4833 1012265.749 871798.9799 1038475.516 547035.3343 1062016.927 985082.1543 1.02738635 0.927622858 1.026517013 0.977606263 1.027595257 0.885001293 1.054201938 0.555319505 1.078099855 1 19.90988452 ARPDAEK ddPTM_BT-474_Pertuzumab_2h_R1 4 ARPDAEK 7 1 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 117.4 0.0047788 2230150000 1993240 1890750 1916380 2045090 1835130 1383010 2318340 2175580 2291370 2434240 FALSE TRUE 1915341.977 1836827.661 2262712.496 2150637.34 1894158.623 1410975.41 2346712.538 2130653.513 2031263.284 2269366.757 0.843998429 0.809400973 0.99706779 0.947681697 0.834663951 0.621748515 1.034082539 0.938875793 0.895079333 1 21.11385835 AS(ph)PNLIGATGANSLGK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASPNLIGATGANSLGK 16 0 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078 Q02078-8 MEF2A Myocyte-specific enhancer factor 2A 1 AS(1)PNLIGATGANSLGK;AS(1)PNLIGATGANSLGK;AS(1)PNLIGATGANSLGK;AS(1)PNLIGATGANSLGK 190.25 9.30E-10 333160000 478233 482692 412819 450663 369452 466911 412472 512104 471792 502242 TRUE FALSE 459543.1256 468926.0968 487424.5764 473921.7714 381335.7591 476352.2603 417519.9557 501528.8734 418236.1501 468224.702 0.981458526 1.001497988 1.041005685 1.012167383 0.814428964 1.017358243 0.891708519 1.071128608 0.893238115 1 18.83684152 ASNGDAWVEAHGK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASNGDAWVEAHGK 13 0 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 140.74 3.95E-05 2768690000 2907080 3997650 2621740 5169930 2368560 2020490 5514820 3674880 3604370 3403060 FALSE TRUE 2793468.1 3883640.936 3095546.738 5436750.707 2444746.883 2061345.692 5582312.017 3598992.444 3195217.028 3172567.715 0.880507006 1.224131771 0.975722827 1.713675229 0.770589347 0.649740487 1.75955646 1.134409969 1.007139111 1 21.59721953 ASPSS(ph)PGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_BT-474_Pertuzumab_2h_R1 2 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.06)PS(0.445)S(0.496)PGRQDS(1)DEDDGPQRVEEVDQGR;AS(0.076)PS(0.428)S(0.495)PGRQDS(1)DEDDGPQRVEEVDQGR 102.05 0.0018618 504500000 167154 178111 142718 155814 191736 209060 163402 179593 172839 181237 TRUE FALSE 160621.4369 173031.4487 168510.3173 163855.5792 197903.3626 213287.3364 165401.7626 175884.3418 153219.0413 168961.6566 0.950638388 1.024087075 0.997328748 0.969779668 1.171291562 1.262341651 0.978930758 1.04097193 0.906827291 1 17.36633636 ASQVSNSDHK ddPTM_BT-474_Pertuzumab_2h_R1 3 ASQVSNSDHK 10 0 E9PS17;Q96KG9-2;Q96KG9;E9PK59;Q96KG9-4;E9PPN3;H0YDH0 E9PS17 SCYL1 N-terminal kinase-like protein 0 ;; 174.4 3.12E-06 571250000 342974 408030 320520 418240 355788 390320 433550 349235 368613 482340 FALSE TRUE 329570.1969 396393.3839 378445.0939 439825.4165 367232.2441 398212.5378 438855.9146 342023.1752 326769.5976 449670.6822 0.732914575 0.881519298 0.841604999 0.978105609 0.816669306 0.885564822 0.975949583 0.760608127 0.726686463 1 18.7785093 ASS(ph)LNENVDHSALLK ddPTM_BT-474_Pertuzumab_2h_R1 4 ASSLNENVDHSALLK 15 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 AS(0.12)S(0.88)LNENVDHSALLK;AS(0.134)S(0.866)LNENVDHSALLK;AS(0.131)S(0.869)LNENVDHSALLK;AS(0.02)S(0.98)LNENVDHSALLK 327.16 5.89E-69 3671690000 8373800 1851300 879606 951230 1377830 723670 1211610 9945230 1125910 1230340 TRUE FALSE 8046542.638 1798502.737 1038570.371 1000323.094 1422149.153 738303.1032 1226438.046 9739857.525 998101.417 1147007.976 7.015245584 1.56799497 0.905460461 0.872115203 1.239877301 0.643677393 1.069249797 8.491534261 0.870178271 1 20.12944399 ASS(ph)LNVLNVGGK ddPTM_BT-474_Pertuzumab_2h_R1 6 ASSLNVLNVGGK 12 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 AS(0.001)S(0.999)LNVLNVGGK;AS(0.002)S(0.998)LNVLNVGGK;AS(0.005)S(0.995)LNVLNVGGK;AS(0.007)S(0.993)LNVLNVGGK;ASS(1)LNVLNVGGK;AS(0.004)S(0.996)LNVLNVGGK 253.71 4.53E-21 1878970000 15255000 5303030 3282060 2890520 3012490 2496660 2510850 10891080 3224100 3290960 TRUE FALSE 14658817.73 5151792.777 3875201.251 3039700.084 3109389.477 2547144.176 2541578.533 10666175.39 2858113.685 3068060.348 4.777877901 1.67916931 1.263078562 0.990756289 1.013470768 0.830213192 0.828399133 3.476520727 0.93157023 1 21.54889543 ASTSKS(ph)ESSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AST(0.006)S(0.032)KS(0.946)ES(0.015)SQK 173.72 3.12E-05 24948000 116450 59089 37988 42515 54439 46288 47666 135510 41271 30582 TRUE FALSE 111899.0053 57403.83957 44853.27664 44709.20425 56190.07988 47223.97507 48249.35077 132711.6711 36586.0891 28510.6539 3.924813708 2.013417152 1.573211081 1.568157798 1.970845007 1.656362398 1.692327049 4.654809799 1.283242721 1 14.79921351 AT(ph)TPPNQGRPDSPVYANLQELK ddPTM_BT-474_Pertuzumab_2h_R1 1 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 AT(0.901)T(0.099)PPNQGRPDSPVYANLQELK 89.727 0.0040193 584470000 363800 355390 323900 339120 325980 352990 335900 425210 389560 354300 TRUE FALSE 349582.2938 345254.6252 382435.9351 356622.0238 336465.4427 360127.6997 340010.8447 416429.2649 345338.782 330302.9454 1.058368684 1.045266565 1.157833863 1.079681634 1.018657107 1.090295151 1.029390895 1.260749475 1.045521352 1 18.33343031 ATQQQHDFTLTQTADGR ddPTM_BT-474_Pertuzumab_2h_R1 6 ATQQQHDFTLTQTADGR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;; 300.54 2.37E-46 5463790000 2899040 3034210 2416460 2940460 3082110 2939860 2983260 2304750 3499080 3141090 FALSE TRUE 2785742.312 2947677.302 2853168.076 3092217.493 3181248.867 2999305.983 3019770.028 2257156.107 3101879.108 2928341.177 0.951303876 1.006603098 0.974329118 1.055962166 1.086365514 1.024233791 1.031222063 0.770796834 1.059261514 1 21.48165222 ATQRPPYCDGTHR ddPTM_BT-474_Pertuzumab_2h_R1 4 ATQRPPYCDGTHR 13 1 P0C7P0 P0C7P0 CISD3 "CDGSH iron-sulfur domain-containing protein 3, mitochondrial" 0 ;;; 148.91 2.61E-05 1475260000 312548 478283 305603 741740 290117 410003 608270 496220 385084 318620 FALSE TRUE 300333.2786 464642.8371 360832.2602 780021.2903 299448.8768 418293.5416 615714.1902 485972.8836 341370.8787 297039.5836 1.011088404 1.564245517 1.214761534 2.625984324 1.008111017 1.40820808 2.072835488 1.636054285 1.149243729 1 18.18029567 ATS(ph)PLVSLYPALECR ddPTM_BT-474_Pertuzumab_2h_R1 6 ATSPLVSLYPALECR 15 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3;Q96G74-4 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AT(0.028)S(0.972)PLVSLYPALECR;AT(0.007)S(0.993)PLVSLYPALECR;AT(0.017)S(0.983)PLVSLYPALECR;ATS(1)PLVSLYPALECR;AT(0.068)S(0.932)PLVSLYPALECR;AT(0.094)S(0.906)PLVSLYPALECR 288.06 1.24E-34 1315446000 1116361 1196798 919091 1082599 1048796 1207759 1029762 1092771 1175691 1324156 TRUE FALSE 1072732.378 1162666.493 1085191.189 1138472.064 1082531.476 1232180.714 1042364.535 1070204.897 1042231.487 1234469.735 0.868982323 0.941834749 0.879074762 0.922235703 0.876920224 0.998145746 0.844382415 0.866934901 0.844274637 1 20.23546004 ATSSSS(ph)GSLSATGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATSS(0.001)S(0.093)S(0.882)GS(0.024)LSATGR 131.29 2.15E-05 0 83238 100660 88657 104050 87208 92573 89485 100290 96025 90177 TRUE FALSE 79984.96694 97789.27536 104679.2921 109420.033 90013.12452 94444.88949 90580.1442 98218.97645 85124.64457 84069.23147 0.951417844 1.163199349 1.245155811 1.301546726 1.07070236 1.123418019 1.077447035 1.168310626 1.012554095 1 16.35929026 AVPEHAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 AVPEHAAR 8 0 X6RA56;X6RLR1;O75935-2;O75935 X6RA56 DCTN3 Dynactin subunit 3 0 ; 144.38 0.00058641 165744000 297160 315770 293750 313910 313800 248330 338610 308040 320410 350820 FALSE TRUE 285546.6587 306764.5488 346837.1594 330110.9327 323893.662 253351.4027 342754.0105 301678.8664 284038.4001 327058.6489 0.873074782 0.937949661 1.060473895 1.009332527 0.990322877 0.774635997 1.04798944 0.922399904 0.868463198 1 18.31918984 AVT(ph)TPGKK ddPTM_BT-474_Pertuzumab_2h_R1 2 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.5)T(0.5)PGKK;AVT(0.591)T(0.409)PGKK 88.496 0.0085404 5125700000 16397600 6774900 4456500 4458600 4812000 3382200 4807800 14535500 3361500 2168180 TRUE FALSE 15756763.66 6581686.485 5261888.684 4688708.88 4966782.35 3450590.401 4866639.295 14235336.85 2979916.613 2021327.237 7.795256192 3.256121208 2.60318497 2.319618909 2.457188652 1.707091429 2.407645434 7.042569151 1.474237599 1 20.94687147 AVTGYRDPYTEQTISLFQAMK ddPTM_BT-474_Pertuzumab_2h_R1 1 AVTGYRDPYTEQTISLFQAMK 21 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 185.87 3.14E-17 216570000 134460 139360 105900 128330 131610 129080 134820 139050 129550 158200 FALSE TRUE 129205.1545 135385.5892 125038.4857 134953.1267 135843.3552 131690.086 136469.9675 136178.5689 114844.0271 147484.9731 0.8760564 0.917961921 0.847804919 0.915029673 0.921065735 0.892905109 0.925314387 0.923338602 0.778682904 1 17.17020844 AYEDTADDGGELADERPAFPMVTAPLAQPERGS(ph)MGS(ph)LDR ddPTM_BT-474_Pertuzumab_2h_R1 1 AYEDTADDGGELADERPAFPMVTAPLAQPERGSMGSLDR 39 2 C9JJX6;E9PDC3;O00192-2;O00192 C9JJX6 ARVCF Armadillo repeat protein deleted in velo-cardio-facial syndrome 2 AYEDTADDGGELADERPAFPMVT(0.001)APLAQPERGS(0.999)MGS(1)LDR 67.501 0.0021459 28309000 6196 8017.6 5387.5 8646.8 6220.8 6897.1 5942.7 9425.1 7751.2 6113.6 TRUE FALSE 5953.85347 7788.945898 6361.141094 9093.062384 6420.897682 7036.564088 6015.42854 9230.468391 6871.316272 5699.520427 1.044623587 1.366596716 1.116083568 1.595408333 1.126568062 1.234588801 1.055427139 1.619516679 1.205595516 1 12.47662482 AYEFAER ddPTM_BT-474_Pertuzumab_2h_R1 7 AYEFAER 7 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;;; 173.59 0.0019951 16725211000 7282560 7908380 7089330 7833500 7899230 6669410 8236990 7674280 7744440 8468310 FALSE TRUE 6997949.504 7682840.746 8370529.632 8237787.874 8153315.907 6804270.04 8337796.748 7515803.436 6865323.639 7894743.821 0.886406154 0.973158968 1.06026615 1.043452208 1.032752435 0.861873443 1.056119988 0.952000927 0.869606892 1 22.91246102 AYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHK ddPTM_BT-474_Pertuzumab_2h_R1 1 AYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHK 39 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9 Q13630 TSTA3 GDP-L-fucose synthase 0 267.53 1.15E-63 1424200000 471270 495490 380700 508120 522330 535010 524750 95199 610670 519260 FALSE TRUE 452852.2474 481359.1103 449500.9586 534344.1341 539131.2188 545828.2688 531172.0475 93233.10738 541349.3017 484090.0577 0.935471076 0.994358596 0.928548214 1.10381142 1.113700251 1.127534557 1.097258741 0.192594551 1.118282215 1 18.88491594 AYSPELIVHPVLDSPNAVHEVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 AYSPELIVHPVLDSPNAVHEVEK 23 0 Q8IW45-2;Q8IW45 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 ; 215.79 1.53E-32 148868000 269990 275760 219422 262630 261600 268830 299440 178382 313560 317050 FALSE TRUE 259438.4923 267895.5948 259076.4364 276184.3658 270014.6016 274265.9268 303104.6363 174698.3494 277965.9834 295575.9211 0.877738929 0.906351214 0.876514012 0.934393995 0.913520291 0.927903483 1.025471341 0.591043914 0.940421609 1 18.17316922 CDELTR ddPTM_BT-474_Pertuzumab_2h_R1 1 CDELTR 6 0 P17844;P17844-2;J3KTA4;J3QSF1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 100.74 0.086812 228940000 249480 303230 228810 287880 261460 263920 267250 262250 315290 321920 FALSE TRUE 239730.0458 294582.1773 270161.0569 302737.5213 269870.0984 269256.6432 270520.6854 256834.4459 279499.601 300116.0717 0.798791096 0.98156082 0.900188568 1.008734786 0.899219082 0.897175022 0.901386867 0.855783712 0.93130501 1 18.19516105 CGAALAGHQLIR ddPTM_BT-474_Pertuzumab_2h_R1 2 CGAALAGHQLIR 12 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 131.82 0.00019196 684650000 686040 795960 634460 692260 725390 618220 704990 722160 801430 815140 FALSE TRUE 659228.7983 773260.0001 749121.0355 727987.6216 748722.8281 630720.832 713617.8785 707247.1436 710455.0263 759929.8417 0.867486394 1.017541301 0.985776573 0.957966883 0.985252568 0.829972449 0.93905758 0.930674261 0.934895549 1 19.53550671 CGESGHLAR ddPTM_BT-474_Pertuzumab_2h_R1 5 CGESGHLAR 9 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ;;;; 197.81 2.74E-05 3548628000 3542300 3623780 2904490 3944930 3303700 3556360 3626260 3793190 4146930 4057840 FALSE TRUE 3403863 3520433.342 3429395.953 4148528.31 3409966.511 3628272.036 3670639.255 3714859.301 3676187.892 3782998.882 0.899779013 0.930593281 0.906528408 1.096624249 0.901392418 0.95909942 0.970298794 0.981987946 0.971765524 1 21.85109892 CHEDNVVVAVDSTTNR ddPTM_BT-474_Pertuzumab_2h_R1 1 CHEDNVVVAVDSTTNR 16 0 Q13144;A0A3B3IUB1;A0A3B3ITG6;A0A3B3IRP4;A0A3B3ISX3;A0A3B3ISM8;A0A3B3IUF2;A0A3B3ITQ2;A0A3B3ISV1;A0A3B3IS56;A0A3B3ISS1;A0A3B3ISI2;A0A3B3IST9;A0A3B3ITK8 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 80.585 0.0069959 0 96605 104750 100380 115310 92650 117530 111630 84360 119830 122030 FALSE TRUE 92829.5698 101762.6326 118520.8989 121261.1629 95630.17139 119906.5371 112996.1613 82617.93652 106227.4008 113764.7994 0.815977968 0.894500171 1.041806425 1.065893524 0.840595438 1.053986275 0.993243621 0.726217046 0.933745775 1 16.79569471 CKDGVVFGVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 CKDGVVFGVEK 11 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 120.84 0.00038678 1241120000 2274940 2197610 1986330 1831410 1912740 1536530 2344770 2348850 2612410 2492150 FALSE TRUE 2186032.83 2134936.314 2345304.017 1925929.29 1974265.019 1567599.689 2373465.997 2300345.427 2315860.169 2323354.461 0.940895101 0.91890254 1.009447356 0.828943376 0.849747661 0.67471396 1.021568614 0.990096632 0.996774366 1 21.14777784 CPEGTKPMLIFAGDDFDVTEDYRR ddPTM_BT-474_Pertuzumab_2h_R1 2 CPEGTKPMLIFAGDDFDVTEDYRR 24 2 Q9H7B2;Q5VXN0 Q9H7B2 RPF2 Ribosome production factor 2 homolog 0 ; 105.16 0.0016418 83895000 52974 59052 46780 45078 55928 55543 45464 58424 54082 56813 FALSE TRUE 50903.71751 57367.89478 55234.18662 47404.48098 57726.97491 56666.11752 46020.40203 57217.52398 47942.83809 52965.00491 0.961082088 1.083128282 1.042843038 0.895015134 1.089907855 1.069878453 0.868883183 1.080289223 0.905179527 1 15.69275184 CQHGEEECK ddPTM_BT-474_Pertuzumab_2h_R1 2 CQHGEEECK 9 0 P13284 P13284 IFI30 Gamma-interferon-inducible lysosomal thiol reductase 0 ; 146.11 9.56E-05 711800000 1217010 999540 885910 1063010 987470 1104940 1089310 803650 1387480 1285220 FALSE TRUE 1169447.904 971034.0979 1046013.644 1117872.073 1019232.869 1127282.644 1102641.302 787054.3467 1229979.087 1198170.905 0.976027626 0.810430377 0.873008717 0.932982156 0.850657336 0.940836269 0.92027047 0.656879869 1.026547283 1 20.19240228 CQQEHWHAEHKR ddPTM_BT-474_Pertuzumab_2h_R1 1 CQQEHWHAEHKR 12 1 A0A0A0MRY2;B0QZE2;B7Z2J6;E7ENI9;J3QKD2;Q15326-5;Q15326-2;Q15326 A0A0A0MRY2 ZMYND11 Zinc finger MYND domain-containing protein 11 0 81.431 0.0071844 8937600 17062 16729 14138 17981 16154 16217 18227 6847.3 22779 13703 FALSE TRUE 16395.19818 16251.9053 16693.0511 18909.00156 16673.60808 16544.91885 18450.06748 6705.900862 20193.22342 12774.8836 1.283393155 1.272176389 1.306708665 1.480170164 1.305186693 1.29511308 1.444245447 0.524928529 1.580697253 1 13.64102253 CSDAAGYPHATHDLEGPPLDAYSIQGQHTIS(ph)PLDLAK ddPTM_BT-474_Pertuzumab_2h_R1 2 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.287)IS(0.713)PLDLAK;CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.044)IS(0.956)PLDLAK 329.37 8.66E-129 2506000000 924770 962580 986350 977960 938600 1122740 1140710 82411 1246320 994710 TRUE FALSE 888628.966 935128.1609 1164605.386 1028432.633 968790.9214 1145442.572 1154670.35 80709.18405 1104842.979 927337.4057 0.958258516 1.008401209 1.255859387 1.10901666 1.044701654 1.235195049 1.24514588 0.087033245 1.191414227 1 19.82273482 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 275.8 9.78E-77 774970000 359420 407320 315880 374910 380710 428980 395440 15544 507610 344800 FALSE TRUE 345373.469 395703.6324 372966.5427 394259.15 392955.8829 437654.2695 400279.513 15223.01097 449988.2409 321446.3889 1.074435679 1.23100973 1.160276039 1.226516034 1.22246165 1.361515589 1.245245014 0.047357853 1.399885817 1 18.29421862 DADPILISLR ddPTM_BT-474_Pertuzumab_2h_R1 6 DADPILISLR 10 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;; 210.6 1.73E-07 1605258000 1725190 1928510 1594150 1775910 1752960 1319914 2052460 2062250 1953940 2102960 FALSE TRUE 1657767.668 1873510.783 1882248.367 1867564.928 1809345.55 1346603.565 2077578.619 2019663.817 1732136.923 1960524.646 0.84557349 0.955617052 0.96007381 0.952584264 0.922888449 0.686858779 1.059705433 1.030164972 0.883506834 1 20.90280835 DAEVIVDWRPLDDALDSSSILYAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DAEVIVDWRPLDDALDSSSILYAR 24 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5;F8WDJ1;F8WF35 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 ; 172.8 4.54E-12 139181000 43048 45937 36436 39771 39187 50780 40889 43186 49179 50859 FALSE TRUE 41365.63657 44626.92174 43020.79571 41823.58608 40447.48544 51806.80639 41389.41181 42294.19401 43596.4061 47414.27463 0.87243002 0.941212791 0.907338477 0.882088493 0.853065575 1.092641547 0.872931457 0.892013942 0.9194785 1 15.53303384 DAHNALLDIQSSGR ddPTM_BT-474_Pertuzumab_2h_R1 5 DAHNALLDIQSSGR 14 0 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;;;; 222.75 3.78E-12 3984000000 2100280 2333070 2185060 2515100 2330520 2492740 2471220 1247580 2561350 2715940 FALSE TRUE 2018198.736 2266533.128 2579948.948 2644904.612 2405483.292 2543144.911 2501463.53 1221817.037 2270596.286 2531986.965 0.797081013 0.895159872 1.018942429 1.044596457 0.950037787 1.004406794 0.987944869 0.482552657 0.896764603 1 21.27183855 DALHLAQTNGMFFSTVGCHPTR ddPTM_BT-474_Pertuzumab_2h_R1 1 DALHLAQTNGMFFSTVGCHPTR 22 0 E5RG17;Q6P1N9;H0YBX2;G5EA19;U3KQS5;Q6P1N9-2;E5RK70 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 143.31 6.27E-08 201880000 67933 61645 51132 59585 73127 52843 57174 66445 65045 63559 FALSE TRUE 65278.10326 59886.94496 60372.68983 62660.18899 75479.19637 53911.52167 57873.71251 65072.88753 57661.36429 59254.09232 1.101664049 1.01068032 1.018877979 1.057482893 1.273822506 0.909836259 0.97670406 1.098200732 0.973120371 1 15.85462718 DAVTYTEHAK ddPTM_BT-474_Pertuzumab_2h_R1 4 DAVTYTEHAK 10 0 P62805 P62805 HIST1H4A Histone H4 0 ;;; 173.71 3.33E-06 20352130000 25066100 26324700 19886600 38389500 18807100 17867000 31167600 23416100 33246700 22155800 FALSE TRUE 24086489.1 25573945.33 23480551 40370786.7 19412047.45 18228282.98 31549038.41 22932549.35 29472674 20655167.93 1.166124099 1.238137856 1.136788191 1.954512635 0.939815523 0.88250471 1.527416215 1.110257221 1.426891037 1 24.29999945 DCEQAENWMAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCEQAENWMAAR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 207.29 1.87E-07 958850000 499090 554270 398330 533670 489250 530220 514090 480990 538990 624300 FALSE TRUE 479585.011 538462.7623 470317.0918 561212.7727 504987.1706 540941.4117 520381.5872 471057.3884 477806.1148 582015.6049 0.824007135 0.925168943 0.808083302 0.96425726 0.867652287 0.929427677 0.894102465 0.809355255 0.820950694 1 19.15069831 DCTSALALVPFSIKPLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DCTSALALVPFSIKPLLR 18 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ; 195.62 1.86E-15 388960000 825960 950830 597230 779380 770350 976090 845860 863670 987220 964950 FALSE TRUE 793680.5701 923713.2594 705162.7463 819603.8952 795129.0074 995827.2086 856211.8877 845834.9127 875154.9244 899593.077 0.882266205 1.026812325 0.783868578 0.911082929 0.883876308 1.10697518 0.951776875 0.940241687 0.972834214 1 19.77891303 DDLLSDYFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DDLLSDYFR 9 0 Q9P219;Q9P219-2;A0A0A0MR69;Q9P219-3 Q9P219 CCDC88C Protein Daple 0 84.743 0.035561 27615000 72340 78687 65507 81924 67016 72385 87405 67934 92332 89231 FALSE TRUE 69512.87282 76442.9238 77345.5721 86152.10746 69171.6305 73848.67429 88474.68854 66531.13916 81850.85845 83187.30489 0.835618763 0.918925356 0.92977615 1.035640084 0.831516667 0.887739715 1.063559983 0.799775149 0.98393449 1 16.34407576 DDSFFGETSHNYHK ddPTM_BT-474_Pertuzumab_2h_R1 5 DDSFFGETSHNYHK 14 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;; 230.36 5.45E-13 3321420000 6354710 6104990 7526960 8695250 7647630 6917300 8965810 813772.3 10328580 9043670 FALSE TRUE 6106360.908 5930881.663 8887249.108 9144012.895 7893622.964 7057172.545 9075536.265 796967.6176 9156122.899 8431134.176 0.724263282 0.703450039 1.054098882 1.084553122 0.936246868 0.837037153 1.076431246 0.094526739 1.085989466 1 23.00729529 DEALQNIS(ph)ADDLPDSASQAAHPQDSAFSYR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEALQNISADDLPDSASQAAHPQDSAFSYR 30 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 DEALQNIS(1)ADDLPDSASQAAHPQDSAFSYR;DEALQNIS(1)ADDLPDSASQAAHPQDSAFSYR 206.73 7.77E-26 636450000 137771 152481 129452 120466 143275 147279 157026 135633 148989 169983 TRUE FALSE 132386.757 148132.3912 152846.856 126683.2647 147883.5705 150257.0823 158947.7312 132832.1312 132076.3933 158469.9 0.835406326 0.934766736 0.964516643 0.799415313 0.933196591 0.948174273 1.00301528 0.838216792 0.833447824 1 17.27384931 DEDSLHQTDLFDSHMLWFLMHHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DEDSLHQTDLFDSHMLWFLMHHLR 24 0 Q5TAQ9;V9GY98 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 0 ; 97.253 0.0018486 94284000 52265 63623 48904 76045 61246 63388 65319 22042.6 71253 60224 FALSE TRUE 50222.42602 61808.53433 57742.04066 79969.69156 63216.03321 64669.74879 66118.39346 21587.41261 63164.65816 56144.97484 0.894513287 1.100873845 1.028445392 1.424342816 1.125942854 1.15183503 1.177636888 0.384494118 1.125027811 1 15.77686928 DEHLDFIQSHLR ddPTM_BT-474_Pertuzumab_2h_R1 5 DEHLDFIQSHLR 12 0 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;;; 246.51 8.70E-17 948417000 379335 400443 438945 500947 424919 368038 515519 194295 551229 523511 FALSE TRUE 364510.1688 389022.7577 518272.1258 526800.9347 438586.9055 375479.9805 521828.0757 190282.7404 488655.7949 488053.1337 0.746865748 0.797090995 1.061917423 1.079392587 0.898645814 0.769342423 1.069203412 0.389881198 1.001234827 1 18.8966787 DEHLLK ddPTM_BT-474_Pertuzumab_2h_R1 4 DEHLLK 6 0 O00505;O00629 O00505;O00629 KPNA3;KPNA4 Importin subunit alpha-4;Importin subunit alpha-3 0 ;;; 132.8 0.014739 1782510000 3821120 3722390 3485330 3719460 3601380 3709760 4011330 2446760 4798120 4483860 FALSE TRUE 3671786.406 3616231.082 4115206.662 3911421.776 3717221.658 3784773.889 4060421.856 2396233.551 4253457.533 4180164.168 0.878383302 0.865093077 0.984460537 0.935710087 0.889252553 0.905412739 0.971354639 0.573239101 1.017533609 1 21.99512817 DEISVQHIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DEISVQHIR 9 0 Q6DKK2 Q6DKK2 TTC19 "Tetratricopeptide repeat protein 19, mitochondrial" 0 154.56 7.54E-05 195050000 161530 173110 167890 225910 138390 146370 183960 176090 172270 177480 FALSE TRUE 155217.229 168173.0723 198231.4577 237569.2422 142841.44 149329.7017 186211.3575 172453.68 152714.6318 165459.1215 0.938100164 1.016402546 1.198069081 1.435818346 0.863303508 0.902517192 1.125422133 1.042273635 0.922974995 1 17.3361153 DEKDEHGR ddPTM_BT-474_Pertuzumab_2h_R1 5 DEKDEHGR 8 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;; 126.07 0.00074205 685948000 2298560 1931220 1811508 1809079 1862190 1908543 2256620 2041700 2162610 2469670 FALSE TRUE 2208729.734 1876143.496 2138887.792 1902445.784 1922089.033 1947135.047 2284237.191 1999538.182 1917119.579 2302397.051 0.959317479 0.814865314 0.928983032 0.826289185 0.834820837 0.845699071 0.992112629 0.868459322 0.832662454 1 21.13470522 DELEVIHLIEEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 DELEVIHLIEEHR 13 0 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;; 311.7 7.57E-51 647380000 601764 596400 513706 569261 601879 566200 605815 92830 682585 602943 FALSE TRUE 578246.3976 579391.2559 606544.1015 598640.6284 621238.9846 577648.9519 613229.1452 90913.02806 605100.8124 562105.1336 1.028715739 1.030752472 1.079058107 1.064997618 1.105200696 1.027652867 1.090950978 0.161736698 1.076490458 1 19.10048047 DELTES(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 3 DELTESPK 8 0 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 DELTES(1)PK;DELTES(1)PK;DELTES(1)PK 208.33 5.89E-05 2340620000 3036060 2251040 3100850 2689450 2960090 2318000 2625270 3059480 3097530 2755180 TRUE FALSE 2917407.419 2186842.543 3661242.573 2828252.837 3055303.983 2364871.548 2657398.84 2996300.669 2745911.38 2568569.205 1.135810323 0.851385487 1.425401569 1.101100501 1.189496463 0.920696061 1.034583314 1.166525186 1.069043176 1 21.29253351 DETAVQDYHGHK ddPTM_BT-474_Pertuzumab_2h_R1 4 DETAVQDYHGHK 12 0 P48147 P48147 PREP Prolyl endopeptidase 0 ;;; 126.1 0.00016971 3022890000 3115070 3114550 3203370 3318400 3144080 3188540 3682200 314125 4469210 3625960 FALSE TRUE 2993329.621 3025726.083 3782290.218 3489663.022 3245212.189 3253014.463 3727263.865 307638.209 3961884.017 3380370.5 0.885503415 0.895087117 1.118898126 1.032331522 0.960016717 0.962324829 1.102619925 0.091007246 1.172026563 1 21.68874995 DFFHGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFFHGLR 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ;;; 134.66 0.0031526 1779790000 2685960 2933080 2367030 2662690 2749200 2388810 2807640 2669090 2916270 3053580 FALSE TRUE 2580989.714 2849431.43 2794804.975 2800111.75 2837630.515 2437113.375 2842000.738 2613972.359 2585227.256 2846758.307 0.906641673 1.000939006 0.981750003 0.983614149 0.996793619 0.856101261 0.998328777 0.918227709 0.908130223 1 21.44088858 DFHKDEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFHKDEVR 8 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 104.2 0.0027798 520980000 1102410 1041940 941830 1078650 1004620 910830 1130960 592970 1225370 1195950 FALSE TRUE 1059326.598 1012224.891 1112039.632 1134319.256 1036934.515 929247.6067 1144801.027 580724.9623 1086271.135 1114947.241 0.950113655 0.907867973 0.997392155 1.017374826 0.930030118 0.833445362 1.026775963 0.520854208 0.974280302 1 20.08854401 DFLFPHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFLFPHLR 8 0 Q9H2M9;F8WDJ2;Q9H2M9-2 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 100.15 0.0063088 273260000 358470 410460 328440 393090 381300 385730 417170 378750 436840 483800 FALSE TRUE 344460.5961 398754.0827 387796.4141 413377.422 393564.8608 393529.7249 422275.4512 370928.6801 387251.7546 451031.7951 0.763716882 0.884093066 0.859798396 0.916515036 0.872587842 0.872509941 0.9362432 0.822400292 0.858590811 1 18.78286961 DFLSNEASLGAIGT(ph)SLPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFLSNEASLGAIGTSLPSR 19 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 DFLSNEASLGAIGT(0.5)S(0.5)LPSR 181.15 3.59E-13 102900000 284380 226980 196450 212760 210240 206470 174790 295930 221790 189500 TRUE FALSE 273266.1152 220506.7526 231952.885 223740.5691 217002.5605 210644.9649 176929.1323 289818.9421 196613.329 176664.9962 1.546803957 1.248163232 1.312953273 1.266468026 1.228327995 1.192341264 1.001495124 1.640500089 1.112916159 1 17.43065669 DFSDITKK ddPTM_BT-474_Pertuzumab_2h_R1 1 DFSDITKK 8 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 81.525 0.036294 468930000 874670 750360 748790 494530 722560 732330 687990 798080 829210 765710 FALSE TRUE 840486.9294 728960.4675 884113.0097 520052.7526 745801.7986 747138.2144 696409.8274 781599.3691 735081.5571 713847.7797 1.177403577 1.021170743 1.238517559 0.728520516 1.044763071 1.046635201 0.97557189 1.094910416 1.029745526 1 19.44525694 DFSETYER ddPTM_BT-474_Pertuzumab_2h_R1 2 DFSETYER 8 0 O94992;Q96MH2 O94992;Q96MH2 HEXIM1;HEXIM2 Protein HEXIM1;Protein HEXIM2 0 ; 129.77 0.0025041 912660000 791070 853240 699060 875670 857560 844900 893420 663680 1014090 948080 FALSE TRUE 760154.1098 828906.4306 825395.6925 920863.4336 885144.1962 861984.4569 904353.9412 649974.7761 898974.7546 883865.6971 0.860033501 0.937819437 0.933847411 1.041859003 1.001446486 0.975243705 1.023180268 0.735377307 1.017094291 1 19.75346764 DFTDLIVINEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DFTDLIVINEDR 12 0 Q9H9Y2 Q9H9Y2 RPF1 Ribosome production factor 1 0 152.85 0.00068626 0 29237 34872 23574 34186 31182 29442 26219 36185 33551 34152 FALSE TRUE 28094.38572 33877.4847 27834.3462 35950.34356 32184.99735 30037.33741 26539.87596 35437.7671 29742.43114 31838.85462 0.882393103 1.06402963 0.874225739 1.129134323 1.010871708 0.94341765 0.833568804 1.113035237 0.934155185 1 14.95850082 DFTPAELR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFTPAELR 8 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 ; 103.91 0.010893 1283810000 1339560 1804860 1186510 1955340 1402720 1294220 1640250 1884930 1644880 1457210 FALSE TRUE 1287208.514 1753387.16 1400938.751 2056255.332 1447839.763 1320390.015 1660323.87 1846005.537 1458160.118 1358511.869 0.947513632 1.290667531 1.03123041 1.513608662 1.065754224 0.97193852 1.222163684 1.358843879 1.073351033 1 20.37359574 DFVEHSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 DFVEHSAR 8 0 Q16822;H0YM31;Q16822-2 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ; 161.92 0.00034476 860940000 619410 1056470 635140 1357660 626140 640920 1252810 954250 836260 694440 FALSE TRUE 595202.7724 1026340.51 749923.9266 1427728.995 646280.3617 653879.8415 1268142.264 934544.404 741331.2707 647404.9603 0.919367025 1.58531456 1.158353693 2.20531056 0.998262913 1.010001285 1.958808383 1.443523701 1.145081234 1 19.30430889 DFWEQEVR ddPTM_BT-474_Pertuzumab_2h_R1 4 DFWEQEVR 8 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ;;; 132.76 0.0022067 750070000 749060 1167990 756650 1568700 707025 683692 1401820 1180400 944100 786131 FALSE TRUE 719785.9071 1134680.069 893393.4866 1649660.795 729767.1012 697516.7207 1418975.892 1156024.328 836929.726 732885.6472 0.982125806 1.548236172 1.219008027 2.250911587 0.99574484 0.951740184 1.936149109 1.577359759 1.141964956 1 19.48322859 DFYFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DFYFGK 6 0 Q15691;Q15555-4;Q15555-5;Q15555-3;Q15555 Q15691;Q15555-4 MAPRE1;MAPRE2 Microtubule-associated protein RP/EB family member 1;Microtubule-associated protein RP/EB family member 2 0 ; 119.7 0.04836 4178700000 3682100 3632900 3077900 3366900 3254500 3447300 3677300 3633600 3729600 3859700 FALSE TRUE 3538199.461 3529293.249 3634144.998 3540666.112 3359183.948 3517006.768 3722303.897 3558564.89 3306231.444 3598279.081 0.983303235 0.980828104 1.009967519 0.983988744 0.933552921 0.97741356 1.034467815 0.988963004 0.918836858 1 21.77887566 DGAAYFYGPIFIHPEETEHEPTK ddPTM_BT-474_Pertuzumab_2h_R1 2 DGAAYFYGPIFIHPEETEHEPTK 23 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9 Q86U86-8 PBRM1 Protein polybromo-1 0 ; 149.85 5.23E-08 261460000 311140 294340 267670 241120 283120 286880 292240 108266 359290 288940 FALSE TRUE 298980.3048 285945.7114 316043.9233 253564.2321 292226.8119 292680.9102 295816.5205 106030.2693 318504.9055 269369.8364 1.10992496 1.06153575 1.173271393 0.941323778 1.084853508 1.086539287 1.098179828 0.393623394 1.182407465 1 18.03922878 DGEERGEEDPEEEHELPVDMETINLDR ddPTM_BT-474_Pertuzumab_2h_R1 1 DGEERGEEDPEEEHELPVDMETINLDR 27 1 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C003;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 95.823 0.0028419 57174000 38810 29804 36218 26563 35625 35173 38847 33750 38283 39655 FALSE TRUE 37293.26229 28954.0191 42763.39827 27933.91961 36770.91048 35884.22216 39322.42121 33053.05071 33937.27434 36969.13153 1.008767606 0.783194463 1.156732563 0.755601186 0.994638201 0.970653642 1.06365553 0.894071603 0.917989494 1 15.17403353 DGHADAAQDTEQFVATVLQAASR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGHADAAQDTEQFVATVLQAASR 23 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 ;;; 203.71 1.85E-24 164662000 109290 124855 113425 131245 129679 135634 139191 54722 148433 141530 FALSE TRUE 105018.826 121294.2576 133923.4206 138018.5702 133850.2428 138376.6124 140894.4611 53591.97158 131583.5081 131944.047 0.795934552 0.919285564 1.015001613 1.04603863 1.014447001 1.048752221 1.067834921 0.406171955 0.997267486 1 17.00956674 DGHGEAIMFK ddPTM_BT-474_Pertuzumab_2h_R1 3 DGHGEAIMFK 10 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;; 98.048 0.0056425 1676990000 2493340 2627970 2532270 2799870 2823260 2492970 3353970 1005640 3460130 3370820 FALSE TRUE 2395897.516 2553022.869 2989907.519 2944371.626 2914072.722 2543379.561 3395016.888 984873.1826 3067350.548 3142511.359 0.76241491 0.812414842 0.95143889 0.936948603 0.927306981 0.809346179 1.080351509 0.313403221 0.976082565 1 21.58348653 DGHNLISLLEVLSGDSLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGHNLISLLEVLSGDSLPR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;E9PIA2;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ; 226.44 1.50E-19 1189520000 578160 570820 479980 624730 640630 538940 603900 190622 633900 621630 FALSE TRUE 555564.868 554540.7725 566723.0631 656972.3902 661236.4458 549837.7361 611290.7088 186685.5891 561942.3295 579526.4464 0.958653175 0.956886051 0.977907163 1.1336366 1.140994427 0.948770741 1.054810721 0.322134719 0.969657784 1 19.14451497 DGLILTSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DGLILTSR 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 161.02 0.00081417 1941180000 1308780 1350230 1097710 1279720 1268800 1140310 1276710 1359580 1294230 1307430 FALSE TRUE 1257631.431 1311722.762 1296090.615 1345766.503 1309612.104 1163367.849 1292334.759 1331504.198 1147314.436 1218876.602 1.031795531 1.076173553 1.063348508 1.104103976 1.07444191 0.954459088 1.060267099 1.092402788 0.941288425 1 20.21712064 DGNPDNETYLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DGNPDNETYLHR 12 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ; 208.82 6.24E-08 1032900000 410270 381560 376720 469250 426290 385190 462840 447880 445020 522970 FALSE TRUE 394236.1948 370678.2824 444801.6841 493468.0487 440002.005 392978.8057 468504.3744 438631.1215 394503.1953 487548.7761 0.808608726 0.760289638 0.91232243 1.012140883 0.902477919 0.806029725 0.960938469 0.899666132 0.809156365 1 18.89518703 DGPEETDWWWAALHGQEGYVPR ddPTM_BT-474_Pertuzumab_2h_R1 3 DGPEETDWWWAALHGQEGYVPR 22 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 ;; 229.15 3.05E-26 622381000 394637 393487 335130 349294 406109 359641 373662 371374 417386 410985 FALSE TRUE 379214.1497 382265.136 395695.4459 367321.1052 419171.8648 366913.1874 378234.9873 363704.9971 370006.0911 383148.6199 0.989731217 0.997694148 1.03274663 0.958690926 1.094018987 0.95762628 0.987175649 0.949253053 0.965698614 1 18.54754458 DGYNYTLSK ddPTM_BT-474_Pertuzumab_2h_R1 6 DGYNYTLSK 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;; 202.97 4.41E-05 4370210000 2976740 3013830 2597400 2730440 2654940 2023290 3330710 3242890 3310330 3410860 FALSE TRUE 2860405.71 2927878.519 3066807.959 2871358.336 2740338.556 2064202.31 3371472.225 3175923.188 2934555.216 3179839.414 0.899544077 0.920763013 0.964453722 0.902988473 0.861785203 0.649153005 1.060264934 0.99876842 0.922862709 1 21.60052248 DHENIVIAK ddPTM_BT-474_Pertuzumab_2h_R1 6 DHENIVIAK 9 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 130.98 0.00034591 12371840000 24138500 25122000 26844000 29591400 25611500 26304600 29461900 6520040 34718700 29177800 FALSE TRUE 23195140.73 24405545.16 31695307.94 31118615.7 26435317.16 26836497.03 29822463.55 6385398.896 30777578.73 27201561.62 0.852713571 0.897211179 1.165201777 1.144001074 0.971830865 0.986579279 1.096351157 0.234743835 1.13146367 1 24.69718614 DHIMEIFSTYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHIMEIFSTYGK 12 0 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 0 ; 172.13 3.66E-05 2804000000 4202600 4354800 3622200 3944800 4133200 4452800 4356300 1783250 4940300 4305500 FALSE TRUE 4038357.746 4230605.368 4276812.115 4148391.601 4266148.132 4542838.667 4409613.703 1746425.264 4379497.855 4013884.65 1.00609711 1.053992762 1.06550449 1.033510418 1.062847716 1.131781071 1.098590041 0.435096027 1.091087123 1 21.93656773 DHLVTAYNHLFETK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHLVTAYNHLFETK 14 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 238.17 1.48E-17 4358200000 5264900 4778300 5373400 5782300 5595800 4799900 5807600 965110 6710100 5800100 FALSE TRUE 5059141.887 4642027.562 6344492.911 6080725.196 5775793.989 4896957.267 5878675.146 945180.1412 5948397.579 5407254.061 0.935621266 0.858481497 1.173329908 1.124549564 1.068156577 0.905627369 1.087183084 0.174798545 1.100077324 1 22.36646471 DHNEEEGEETGLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DHNEEEGEETGLR 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 188.92 5.70E-06 527090000 240820 248070 267670 328960 274920 286470 322020 114874 347290 346510 FALSE TRUE 231408.4882 240995.2865 316043.9233 345937.665 283763.0515 292262.6197 325960.9771 112501.8118 307867.0952 323040.5691 0.716344974 0.746021737 0.978341278 1.070879939 0.87841305 0.904724198 1.009040375 0.348259081 0.9530292 1 18.30135583 DHNEEEGEETGLRDEKPIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DHNEEEGEETGLRDEKPIK 19 2 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 203.56 3.00E-16 617870000 379390 311160 345840 346470 379080 372520 412180 154140 573450 464470 FALSE TRUE 364563.0194 302286.0215 408340.9812 364351.3582 391273.4525 380052.6096 417224.3821 150956.9551 508354.3601 433011.0332 0.841925474 0.698102354 0.943026736 0.841436662 0.903610815 0.877697288 0.963542151 0.348621498 1.173998631 1 18.72404426 DHPLPEVAHVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DHPLPEVAHVK 11 0 H3BN72;H3BNV9;P13073;Q86WV2;H3BPG0 H3BN72 COX4I1 "Cytochrome c oxidase subunit 4 isoform 1, mitochondrial" 0 ;;; 152.85 1.89E-05 2025920000 2044215 3617519 1821834 5058376 1900676 2153168 4948788 2242150 3600382 2326140 FALSE TRUE 1964324.818 3514350.9 2151079.93 5319439.392 1961812.97 2196706.532 5009352.748 2195848.819 3191681.729 2168588.466 0.905808017 1.620570687 0.991926299 2.452950145 0.90464973 1.012966068 2.309960062 1.012570552 1.471778431 1 21.04832487 DHS(ph)PTPSVFNS(ph)DEER ddPTM_BT-474_Pertuzumab_2h_R1 2 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 DHS(0.996)PT(0.004)PSVFNS(1)DEER;DHS(0.989)PT(0.011)PSVFNS(1)DEER 220.63 8.68E-13 811020000 626020 618200 623020 704580 711220 700700 705520 356610 875710 772900 TRUE FALSE 601554.4463 600569.5413 735613.573 740943.4582 734097.0372 714868.6341 714154.3648 349245.8789 776303.0721 720550.7946 0.83485363 0.833486752 1.020904534 1.028301494 1.018799844 0.992114143 0.991122861 0.484692934 1.077374528 1 19.45874061 DHTYAK ddPTM_BT-474_Pertuzumab_2h_R1 3 DHTYAK 6 0 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;; 126.16 0.017613 1961460000 3773700 3660000 3202720 3789170 3616040 3688500 4205600 2091930 4020400 4468000 FALSE TRUE 3626219.632 3555620.384 3781522.748 3984729.518 3732353.211 3763083.997 4257069.391 2048730.914 3564021.047 4165378.38 0.87056188 0.85361282 0.907846155 0.956630864 0.896041817 0.903419486 1.022012649 0.491847493 0.855629602 1 21.99001612 DHVIASK ddPTM_BT-474_Pertuzumab_2h_R1 2 DHVIASK 7 0 Q92805;H0YE54 Q92805 GOLGA1 Golgin subfamily A member 1 0 ; 79.116 0.033497 148387000 624510 622690 538380 650210 604220 623800 669710 367550 785040 708420 FALSE TRUE 600103.4588 604931.4909 635677.2422 683767.416 623655.285 636413.6634 677906.1113 359959.9641 695925.5504 660438.0824 0.908644542 0.91595489 0.962508461 1.035324028 0.944305457 0.96362351 1.026449155 0.545032114 1.053733225 1 19.33306379 DIAAYIK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIAAYIK 7 0 Q96FJ2 Q96FJ2 DYNLL2 "Dynein light chain 2, cytoplasmic" 0 108.24 0.039056 0 623820 550620 438800 593530 507090 519510 544340 509130 673080 595070 FALSE TRUE 599440.4247 534916.8567 518100.9211 624162.1544 523401.0104 530014.8481 551001.7958 498616.2876 596674.7802 554765.3789 1.080529621 0.964221772 0.933909975 1.125092117 0.943463724 0.955385589 0.993215901 0.89878768 1.07554437 1 19.08151823 DIDIS(ph)SPEFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIDISSPEFK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 DIDIS(0.5)S(0.5)PEFK 140.63 0.0047233 0 363840 340780 314250 330870 301800 356520 349450 367620 360700 349660 TRUE FALSE 349620.7306 331061.2881 371041.9655 347946.2404 311507.6711 363729.0787 353726.6736 360028.5185 319754.8482 325977.2168 1.072531185 1.015596401 1.138245087 1.067394353 0.955611788 1.115811351 1.085126983 1.104459146 0.980911646 1 18.31441161 DIKPDNFLMGIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DIKPDNFLMGIGR 13 1 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;A0A590UK94 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 ; 109.99 0.00099749 1455040000 1858660 1857610 1584470 1428870 1707400 1552430 1814450 1881910 1946330 1917040 FALSE TRUE 1786021.512 1804632.782 1870818.975 1502614.152 1762320.072 1583821.198 1836655.782 1843047.901 1725390.778 1787197.173 0.999342176 1.009755839 1.046789354 0.840765739 0.986080382 0.886203952 1.02767384 1.031250457 0.965417137 1 20.76926738 DILQDYTHEFHK ddPTM_BT-474_Pertuzumab_2h_R1 4 DILQDYTHEFHK 12 0 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;O95249-2 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 ;;; 175.28 1.63E-05 687806000 775465 1010680 817230 1158020 897230 923460 1033510 117485.9 1267410 901910 FALSE TRUE 745158.9705 981856.396 964921.6402 1217785.551 926090.2178 942132.9939 1046158.405 115059.7751 1123538.93 840822.8324 0.886225899 1.167732795 1.1475921 1.448325978 1.101409455 1.120489308 1.244207893 0.136841878 1.336237418 1 19.68144232 DILVDLGHLEGADAGEEDLEQQFHYHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DILVDLGHLEGADAGEEDLEQQFHYHLR 28 0 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 0 ;;; 239.51 1.07E-45 238945000 80924 83578 90989 125976 107322 99184 130154 17705.4 138593 115332 FALSE TRUE 77761.40061 81194.43727 107432.7363 132477.6365 110774.1096 101189.5684 131746.8636 17339.7773 122860.5037 107520.4609 0.723224212 0.755153359 0.999184113 1.232115593 1.03026074 0.941119184 1.225318999 0.161269559 1.142670917 1 16.7142517 DIMVHFK ddPTM_BT-474_Pertuzumab_2h_R1 1 DIMVHFK 7 0 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 67.032 0.066262 495180000 423410 443230 421950 416720 426010 421060 500650 423680 456870 553740 FALSE TRUE 406862.6691 430589.5144 498205.7512 438226.9691 439712.9985 429574.1217 506777.1045 414930.8599 405008.033 516234.6966 0.788135071 0.834096424 0.965076068 0.848890964 0.851769556 0.832129503 0.981679666 0.803763991 0.784542449 1 18.97766758 DIQLAR ddPTM_BT-474_Pertuzumab_2h_R1 6 DIQLAR 6 0 K7EK07;Q71DI3;Q16695;P84243;P68431;Q6NXT2 K7EK07 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A;H3F3C Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3C 0 ;;;;; 161.58 0.019678 3803640000 1831060 2096930 1418920 3418420 1490920 1280910 2513730 1663280 2059200 1247390 FALSE TRUE 1759500.151 2037127.61 1675350.408 3594845.066 1538876.796 1306810.878 2544493.78 1628932.687 1825448.249 1162903.164 1.513023788 1.751760312 1.440662008 3.091267765 1.323306053 1.123748665 2.188053019 1.400746629 1.569733667 1 20.14929954 DIRPGAAFEPTYIYR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIRPGAAFEPTYIYR 15 1 Q14694;Q14694-3;Q14694-2;J3KT19 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 0 168.41 1.15E-06 696380000 183920 197110 190880 206140 155650 179580 176760 235190 198230 225020 FALSE TRUE 176732.2031 191488.6158 225376.2621 216778.9101 160656.6236 183211.2306 178923.2418 230333.2443 175727.7614 209779.195 0.842467734 0.912810328 1.074349924 1.033367061 0.765836782 0.873352721 0.852912234 1.097979446 0.837679644 1 17.67851208 DISENKR ddPTM_BT-474_Pertuzumab_2h_R1 13 DISENKR 7 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;;;;; 174.27 0.0013346 81637779000 26858890 26336311 21449888 22899779 20835988 16142240 27783820 25906829 30401241 28734231 FALSE TRUE 25809214.88 25585225.2 25326359.91 24081639.34 21506196.48 16468647.15 28123846.7 25371843.93 26950219.57 26788035.94 0.963460514 0.955098957 0.945435491 0.89896995 0.802828417 0.614776208 1.049865946 0.947133414 1.006054331 1 24.67508547 DITLFHAMDTLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 DITLFHAMDTLHK 13 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;Q13330-2 E7ESY4 MTA1 Metastasis-associated protein MTA1 0 ; 194.3 6.58E-07 320550000 585840 593130 482860 470040 540810 533840 556400 207562 621660 556490 FALSE TRUE 562944.7251 576214.5131 570123.5432 494298.8207 558205.6448 544634.6106 563209.3896 203275.7722 551091.763 518798.4366 1.085093334 1.11067126 1.098930727 0.952776234 1.07595861 1.049800023 1.085603483 0.391820325 1.062246383 1 18.98481461 DIVHSGLAYTMER ddPTM_BT-474_Pertuzumab_2h_R1 2 DIVHSGLAYTMER 13 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 215.51 2.90E-11 854790000 395180 561670 368590 733910 342420 325750 675320 534180 454470 440450 FALSE TRUE 379735.9287 545651.7215 435202.4122 771787.1831 353434.2503 332336.8882 683584.7682 523148.9963 402880.4709 410617.9292 0.924791398 1.328855081 1.059871918 1.879574973 0.860737501 0.809357957 1.664770872 1.27405298 0.98115655 1 18.6474371 DIVQFVPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 DIVQFVPFR 9 0 O75131 O75131 CPNE3 Copine-3 0 99.442 0.01241 109160000 170030 213730 133680 233990 143430 92315 186700 176780 155180 165600 FALSE TRUE 163385.0396 207634.6297 157838.9497 246066.2519 148043.5562 94181.67255 188984.8904 173129.4312 137564.617 154383.7645 1.058304545 1.344925293 1.022380496 1.59386094 0.958932156 0.610049074 1.224124124 1.121422526 0.891056242 1 17.23616152 DKDNFWMTR ddPTM_BT-474_Pertuzumab_2h_R1 4 DKDNFWMTR 9 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 167.12 5.49E-05 8272710000 6472770 6786940 5648630 6272160 6426210 5454500 7207290 7115410 7785420 7612550 FALSE TRUE 6219806.992 6593383.116 6669463.094 6595866.929 6632914.881 5564793.727 7295494.971 6968474.297 6901651.761 7096945.208 0.87640623 0.929045233 0.939765335 0.929395217 0.934615484 0.78411113 1.027976792 0.981897717 0.972482041 1 22.75876674 DKEGAALR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKEGAALR 8 1 Q9BQS8;Q9BQS8-4 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 0 64.711 0.085006 0 236490 254780 206390 215920 227330 176250 250570 264640 270760 274700 FALSE TRUE 227247.7093 247513.9239 243689.2641 227063.6571 234642.2759 179813.8958 253636.5506 259175.0915 240024.4599 256094.3243 0.887359413 0.966495156 0.951560581 0.886640724 0.9162338 0.702139324 0.990402858 1.012029814 0.937250213 1 17.96631575 DKGHDGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DKGHDGVK 8 1 C9K0G7;C9JM78;C9JQ90;A0A0G2JRX6;E9PCG9;Q02338 C9K0G7 BDH1 "D-beta-hydroxybutyrate dehydrogenase, mitochondrial" 0 ; 96.331 0.0054176 83677000 250782 353180 212599 496090 201433 280998 546430 409100 315034 281304 FALSE TRUE 240981.1622 343107.6522 251020.3685 521693.2644 207912.2754 286679.9721 553117.3738 400651.942 279272.6611 262251.0295 0.918895009 1.308317656 0.957175913 1.989289671 0.7927987 1.093150988 2.109114213 1.527742113 1.064905871 1 18.00058891 DKHIEEVR ddPTM_BT-474_Pertuzumab_2h_R1 8 DKHIEEVR 8 1 P16949 P16949 STMN1 Stathmin 0 ;;;;;;; 152.97 0.00026949 16001610000 21876880 21590660 21076650 23137480 22586670 22660610 24035050 10475820 26491970 23664670 FALSE TRUE 21021907.34 20974915.52 24885669.5 24331608.12 23313190.75 23118823.06 24329198.13 10259490.66 23484712.63 22061840.82 0.952862797 0.950732792 1.127996059 1.102882045 1.056720105 1.047909975 1.102772807 0.465033301 1.0644947 1 24.39504984 DKHIEEVRK ddPTM_BT-474_Pertuzumab_2h_R1 5 DKHIEEVRK 9 2 P16949 P16949 STMN1 Stathmin 0 ;;;; 149.96 4.86E-05 10690000000 18230430 17193430 13559560 13998240 15634400 16428560 16084340 6870490 20386690 16740980 FALSE TRUE 17517964.64 16703090.21 16010074.12 14720690.84 16137294.67 16760756.74 16281184.96 6728611.981 18072478.42 15607098.51 1.122435706 1.070223924 1.025820021 0.943204839 1.033971475 1.073918815 1.043191017 0.431125105 1.157965294 1 23.89569902 DKLESEMEDAYHEHQANLLR ddPTM_BT-474_Pertuzumab_2h_R1 17 DKLESEMEDAYHEHQANLLR 20 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;;;;;;;;;;;;; 381.77 1.75E-113 30383030000 10831701.3 9654899.9 8134065.1 8638678.6 9483757 9682301.4 9675029 3418267.3 12229497 8998122 FALSE TRUE 10408386.44 9379551.608 9604071.605 9084521.838 9788810.657 9878084.168 9793434.899 3347678.886 10841255.77 8388671.182 1.240767007 1.118121262 1.14488593 1.082951238 1.166908375 1.177550527 1.167459623 0.399071416 1.292368664 1 23.00001087 DKLFDQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DKLFDQR 7 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 79.906 0.028595 3774080000 12476300 12204400 10794700 11111400 11366100 9974500 12801600 12925500 14083300 14079300 FALSE TRUE 11988712.4 11856342.46 12745542.42 11684860.69 11731700.93 10176191.22 12958269.81 12658583.91 12484622.83 13125696.47 0.913377239 0.903292445 0.971037419 0.89022786 0.893796452 0.775287715 0.98724436 0.96441236 0.951158885 1 23.64589064 DKS(ph)HSHT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 DKS(1)HS(0.267)HT(0.681)PS(0.052)R 82.55 0.040508 93394000 277430 241440 230140 262280 256900 247630 277550 6655.5 331460 197230 TRUE FALSE 266587.7289 234554.3676 271731.4174 275816.3022 265163.4218 252637.2483 280946.7399 6518.061599 293834.0504 183871.4364 1.449859391 1.275643309 1.477833766 1.50004975 1.44211318 1.37398855 1.527952059 0.035449017 1.598040762 1 17.48833786 DKSHS(ph)HTPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.347)HS(0.653)HTPSR 116.51 0.00065259 80570000 104220 104580 99200 118420 122860 105340 128750 4498.8 145330 93883 TRUE FALSE 100146.9672 101597.4808 117127.6467 124531.6704 126811.9035 107470.047 130325.681 4405.898208 128832.7477 87524.22079 1.144220037 1.160792748 1.338231242 1.422825239 1.448877834 1.227889217 1.489024179 0.050339188 1.471966805 1 16.41739469 DKSHSHT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 2 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKSHS(0.002)HT(0.997)PSR;DKSHS(0.011)HT(0.988)PSR 118.37 0.0012232 214990000 91626 124121 116216 129879 127000 157100 131682 13141.3 154907 117599 TRUE FALSE 88045.15462 120581.1906 137218.8164 136582.0708 131085.0703 160276.6696 133293.5637 12869.92756 137322.6068 109633.915 0.803083194 1.099853003 1.251609198 1.245801272 1.195661674 1.461925989 1.215805928 0.117390021 1.252555898 1 16.74233464 DKYAENLKGESAMWR ddPTM_BT-474_Pertuzumab_2h_R1 1 DKYAENLKGESAMWR 15 2 Q08379;Q08379-2;B7ZC06 Q08379 GOLGA2 Golgin subfamily A member 2 0 168.64 6.99E-07 636340000 740890 796180 574960 551570 748210 747160 684380 775710 905430 775930 FALSE TRUE 711935.1997 773473.7259 678868.0619 580036.5938 772276.8542 762268.0871 692755.6472 759691.3174 802649.3823 723375.57 0.984184743 1.069256079 0.938472476 0.801847087 1.067601515 1.053765317 0.957670781 1.050203171 1.109588733 1 19.46438535 DLAVPAALT(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLAVPAALTPR 11 0 Q8TEM1 Q8TEM1 NUP210 Nuclear pore membrane glycoprotein 210 1 DLAVPAALT(1)PR;DLAVPAALT(1)PR 131.08 0.0023557 585990000 482730 733430 467880 764320 518130 537220 516140 799730 528780 426590 TRUE FALSE 463864.3779 712513.2945 552436.3239 803766.6468 534796.122 548082.9565 522456.6757 783215.296 468755.1112 397696.6793 1.166377297 1.791599808 1.389089607 2.021054458 1.344733687 1.378143155 1.313706407 1.969378516 1.178674944 1 18.60130899 DLDDFQSWLSR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLDDFQSWLSR 11 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 256.38 3.98E-20 853860000 1182760 1227390 981350 1162440 1064900 1092610 1134220 1165220 1265520 1322810 FALSE TRUE 1136536.432 1192386.039 1158701.775 1222433.668 1099153.476 1114703.323 1148100.924 1141157.8 1121863.475 1233214.9 0.921604524 0.966892338 0.93957815 0.99125762 0.891291108 0.903900303 0.93098204 0.925351939 0.90970639 1 20.2339928 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDK 32 0 Q15029;Q15029-3;K7EIV5;K7EIT3 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 233.49 1.57E-46 428880000 298247 281955 229735 263016 284120 254225 297732 34737 412300 302425 FALSE TRUE 286591.1775 273913.9195 271253.2249 276590.2873 293258.9778 259365.6037 301375.7333 34019.66881 365497.4325 281941.4854 1.016491692 0.971527546 0.962090501 0.981020182 1.040141281 0.919927067 1.068930076 0.120662161 1.296359179 1 18.10503625 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDKK ddPTM_BT-474_Pertuzumab_2h_R1 3 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDKK 33 1 Q15029;Q15029-3;K7EIV5;K7EIT3 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;; 284.01 1.52E-74 4714060000 2562640 1919190 1687320 1436810 1826230 1893720 2028550 188204 2797190 1676790 FALSE TRUE 2462489.196 1864456.58 1992256.258 1510963.936 1884972.346 1932012.316 2053376.002 184317.5216 2479664.718 1563219.52 1.575267686 1.19270298 1.274457127 0.96657182 1.205827027 1.235918751 1.313555758 0.117908918 1.586254961 1 20.57608896 DLDFLHSVFQDQHLHTLLDLYDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLDFLHSVFQDQHLHTLLDLYDK 23 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 96.131 0.0012905 74101000 112030 101060 104740 158610 123680 105700 155110 3606.5 171990 101250 FALSE TRUE 107651.7437 98177.86775 123668.8479 166795.8811 127658.2795 107837.3264 157008.2826 3532.024515 152466.4162 94392.24732 1.140472304 1.040105205 1.310158953 1.767050641 1.352423352 1.142438383 1.663359937 0.037418587 1.615242995 1 16.52638075 DLDPEREVTFLEASR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLDPEREVTFLEASR 15 1 M0R0X1;P61018;P61018-2 M0R0X1 RAB4B Ras-related protein Rab-4B 0 67.646 0.050145 23906000 50076 72588 41986 50653 52880 74255 59474 64250 68547 54165 FALSE TRUE 48118.97456 70517.86131 49573.80417 53267.2074 54580.93322 75756.48698 60201.8606 62923.21505 60765.83193 50496.3563 0.952919737 1.396494054 0.981730323 1.054872298 1.080888548 1.500236701 1.192202072 1.246094167 1.203370627 1 15.62389167 DLEGAVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLEGAVSR 8 0 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 0 120.46 0.0034852 166230000 212560 207710 192260 201590 208000 215580 212480 188750 230910 238910 FALSE TRUE 204252.9202 201786.3142 227005.6588 211994.0841 214690.5089 219939.1753 215080.3938 184852.2465 204698.0649 222728.4129 0.917049233 0.905974732 1.019203863 0.951805301 0.963911636 0.987476957 0.965662131 0.829944613 0.919047831 1 17.76492609 DLEIIR ddPTM_BT-474_Pertuzumab_2h_R1 1 DLEIIR 6 0 Q8IZ41 Q8IZ41 RASEF Ras and EF-hand domain-containing protein 0 98.133 0.093712 88904000 233340 237820 212490 344690 234120 238950 218560 256660 261420 290010 FALSE TRUE 224220.8148 231037.6065 250891.6698 362479.4922 241650.6824 243781.7327 221234.8027 251359.8813 231744.6976 270367.3644 0.829319083 0.854532155 0.927965808 1.34069248 0.893786434 0.901668488 0.818274806 0.929697569 0.857147452 1 18.04456149 DLESLFHR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLESLFHR 8 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 175.44 0.00026609 223270000 306350 385650 375090 487080 334190 322630 380360 390330 402750 448010 FALSE TRUE 294377.5033 374651.6396 442877.1068 512218.2572 344939.5249 329153.7997 385014.9595 382269.5491 357031.5085 417665.8837 0.704815775 0.89701279 1.06036218 1.226382803 0.825874313 0.78807921 0.921825254 0.915252033 0.854825645 1 18.67198978 DLIDEGHAATQLVNQLHDVVVENNLSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLIDEGHAATQLVNQLHDVVVENNLSDK 28 0 P35249;H7C1P0 P35249 RFC4 Replication factor C subunit 4 0 194.77 3.97E-19 319520000 156940 134290 127810 130330 165320 120040 153220 120500 179390 150270 FALSE TRUE 150806.6113 130460.1807 150908.1101 137056.3469 170637.6679 122467.291 155095.1522 118011.6329 159026.3993 140092.0791 1.07648207 0.931245946 1.077206585 0.978330451 1.218039372 0.874191402 1.107094371 0.842386191 1.135156251 1 17.09601586 DLIQGLLTVDPNKR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLIQGLLTVDPNKR 14 1 O75582-3;O75582 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 ; 87.824 0.010887 354660000 324220 342330 285250 331480 344490 325560 373470 219490 399250 384030 FALSE TRUE 311549.124 332567.0836 336801.0204 348587.7225 355570.8337 332143.0463 378040.6376 214957.4548 353928.8138 358019.306 0.870202022 0.92890824 0.940734242 0.973656215 0.993161061 0.927723842 1.055922491 0.600407439 0.98857466 1 18.44967786 DLLFGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLLFGR 6 0 O43633;M0R1L7;M0QXX8 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;;; 106.29 0.075031 762540000 670396 741996 673495 753728 764015 858167 661452 735686 737521 767890 FALSE TRUE 644196.1832 720835.0006 795210.5283 792627.9924 788590.2363 875519.7247 669547.0474 720493.827 653800.708 715880.1263 0.899865996 1.006921374 1.110815204 1.107207706 1.101567438 1.222997667 0.93527816 1.006444795 0.913282383 1 19.4493585 DLLPYGFAIHHAGMTR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLLPYGFAIHHAGMTR 16 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 123.36 5.11E-05 1144900000 1215440 1294150 1024020 1164730 1295130 1219500 1241250 617410 1338610 1329080 FALSE TRUE 1167939.261 1257242.109 1209083.193 1224841.855 1336789.033 1244159.126 1256440.789 604660.2677 1186656.605 1239060.228 0.94260088 1.014673929 0.975806636 0.988524873 1.078873329 1.004115133 1.014027212 0.487999093 0.957706961 1 20.24081488 DLMPHDLAR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLMPHDLAR 9 0 P55084-2;P55084;B5MD38;C9JEY0;C9JE81;C9K0M0 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;; 178.55 5.08E-05 2333430000 1588470 2497870 1529730 3231770 1465480 1304410 3087030 2241960 1910050 1640320 FALSE TRUE 1526390.836 2426633.193 1806186.24 3398562.037 1512618.495 1330786.064 3124809.997 2195662.743 1693229.132 1529219.665 0.998150149 1.586844093 1.181116278 2.22241586 0.989144025 0.870238654 2.043401656 1.435805981 1.10725043 1 20.54436423 DLMSWINGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 DLMSWINGIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 169.12 1.10E-05 200039000 196495 224935 170308 189455 204370 195436 223630 217468 221080 221100 FALSE TRUE 188815.7582 218520.074 201086.4441 199232.7953 210943.7467 199387.8498 226366.8508 212977.2098 195983.9252 206124.7001 0.916026843 1.060135316 0.975557243 0.966564391 1.023379278 0.967316628 1.098203421 1.033244486 0.950802719 1 17.65315787 DLPAHLQHDCPK ddPTM_BT-474_Pertuzumab_2h_R1 1 DLPAHLQHDCPK 12 0 Q9BUZ4;F6SA91;K7EJG7;K7ER49;J9JIG0;C9JJ10;A0A0C4DFM9;Q9BUZ4-2 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 0 61.167 0.05018 122730000 39822 47901 32467 39232 39058 45418 46338 34896 48975 50667 FALSE TRUE 38265.71221 46534.91038 38334.50912 41256.76822 40314.33604 46336.38308 46905.09831 34175.38541 43415.56332 47235.27896 0.810108738 0.985172765 0.811565211 0.873431239 0.853479368 0.98096982 0.993009872 0.723513995 0.919134263 1 15.52757716 DLVEMCR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLVEMCR 7 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 158.12 0.0033328 1387040000 1395540 1538540 1209810 1423770 1425070 1323640 1524800 1465490 1605770 1642940 FALSE TRUE 1341000.754 1494662.346 1428449.579 1497250.94 1470908.671 1350404.908 1543460.959 1435227.119 1423489.722 1531662.21 0.875519906 0.975843326 0.932613973 0.977533382 0.960334897 0.881659741 1.007703231 0.93703893 0.929375754 1 20.54666673 DLYDAGVKR ddPTM_BT-474_Pertuzumab_2h_R1 4 DLYDAGVKR 9 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2 Annexin A2;Annexin 0 ;;; 111.61 0.003363 3702020000 4840060 5106940 2104350 5094910 3741090 3292410 2896390 4853720 4759880 3928550 FALSE TRUE 4650905.104 4961295.071 2484652.856 5357858.916 3861425.557 3358984.786 2931836.887 4753488.986 4219558.377 3662465.809 1.269883556 1.354632461 0.678409843 1.462910289 1.054323988 0.917137514 0.800509012 1.297893068 1.152108606 1 21.80438386 DLYEDELVPLFEK ddPTM_BT-474_Pertuzumab_2h_R1 7 DLYEDELVPLFEK 13 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;;; 259.55 1.30E-23 854802600 1340434 1197347 1033951 1041035 1160102 1116762 1138910 1362318 1297719 1282792 FALSE TRUE 1288048.357 1163199.836 1220808.946 1094762.941 1197417.734 1139343.693 1152848.321 1334185.657 1150407.38 1195907.355 1.07704694 0.972650457 1.020822341 0.91542454 1.001262957 0.952702304 0.963994674 1.115626266 0.961953595 1 20.1896742 DMASPNWSILPEEER ddPTM_BT-474_Pertuzumab_2h_R1 4 DMASPNWSILPEEER 15 0 Q15814 Q15814 TBCC Tubulin-specific chaperone C 0 ;;; 257.8 1.97E-24 291625000 103216 107844 85396 120155 102768 117530 105191 109303 121998 115552 FALSE TRUE 99182.20461 104768.3947 100828.9568 126356.2139 106073.6261 119906.5371 106478.3589 107045.8549 108149.2985 107725.5601 0.920693329 0.972549083 0.93597988 1.172945528 0.984665347 1.113074158 0.988422421 0.993690399 1.003933499 1 16.71700107 DMDDAYDR ddPTM_BT-474_Pertuzumab_2h_R1 3 DMDDAYDR 8 0 P07686;Q5URX0;H0Y9B6;H0YA83;H0Y9M3 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ;; 99.802 0.015249 1075320000 1227660 1256490 1003670 1408390 1284470 1280230 1290950 1328290 1355040 1364810 FALSE TRUE 1179681.69 1220656.135 1185055.496 1481077.177 1325786.144 1306117.128 1306749.032 1300860.347 1201221.54 1272370.203 0.927152874 0.959356115 0.931376334 1.16403007 1.041981446 1.026522882 1.027019518 1.022391395 0.944081791 1 20.27908706 DMEDLLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DMEDLLR 7 0 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4;M0R2C7 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 0 ;;; 145.04 0.0074714 97631000 548400 622570 526010 597630 530000 562640 620930 617580 637370 684600 FALSE TRUE 526967.9217 604814.9132 621071.708 628473.7559 547047.9313 574016.9663 628529.1271 604826.7572 565018.4297 638231.4322 0.825669021 0.947642004 0.973113634 0.984711382 0.857130977 0.899386864 0.98479814 0.947660561 0.885287689 1 19.28372014 DMFQETMEAMR ddPTM_BT-474_Pertuzumab_2h_R1 3 DMFQETMEAMR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 160.91 6.26E-05 295843000 298478 268180 283375 267677 266171 180870 329574 316325 351552 363510 FALSE TRUE 286813.1498 260531.769 334587.1661 281491.842 274732.6319 184527.3153 333607.4252 309792.7782 311645.2908 338889.1439 0.846333248 0.768781691 0.987305649 0.83063104 0.810685845 0.544506422 0.984414612 0.914141936 0.919608363 1 18.3704539 DMGEDLECLCQIMR ddPTM_BT-474_Pertuzumab_2h_R1 3 DMGEDLECLCQIMR 14 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 ;; 172.13 6.76E-06 159251000 128902 139038 107775 113789 123649 142279 129330 118907 142929 152701 FALSE TRUE 123864.3673 135072.7724 127252.3399 119661.6639 127626.2824 145155.9789 130912.7792 116451.5289 126704.2991 142358.4253 0.870088069 0.948821765 0.89388696 0.840566083 0.896513727 1.019651479 0.919599799 0.818016417 0.890037235 1 17.11916835 DMNETLPGERPDTIHLEGLPCK ddPTM_BT-474_Pertuzumab_2h_R1 1 DMNETLPGERPDTIHLEGLPCK 22 1 Q02040;X6RAJ1;Q02040-2;Q02040-3 Q02040 AKAP17A A-kinase anchor protein 17A 0 97.509 0.00078194 132800000 162410 161310 135350 143570 151500 158600 155920 140600 178040 172320 FALSE TRUE 156062.8376 156709.5967 159810.7558 150979.6649 156373.1351 161807.0007 157828.1956 137696.5609 157829.6456 160648.6129 0.971454623 0.975480547 0.994784536 0.939813063 0.973386152 1.007210693 0.982443563 0.85712885 0.982452589 1 17.293549 DMNQPSSSFFSIS(ph)PTSNSSATIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 DMNQPSSSFFSISPTSNSSATIAR 24 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0;E5RJN7;E5RJ67 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 DMNQPSSSFFSIS(0.781)PT(0.176)S(0.04)NS(0.002)SATIAR 120.63 8.57E-05 70504000 12731 20279 11727 20027 23449 27864 12297 13432 12172 19858 TRUE FALSE 12233.45845 19700.66278 13846.32977 21060.59587 24203.25838 28427.42917 12447.49436 13154.62451 10790.28559 18512.99997 0.660803677 1.064152909 0.74792469 1.137611187 1.307365549 1.535538768 0.672365061 0.710561472 0.582849112 1 14.17625108 DNFHGLAIFLDTYPNDETTER ddPTM_BT-474_Pertuzumab_2h_R1 3 DNFHGLAIFLDTYPNDETTER 21 0 Q12907;D6RBV2;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ;; 253.13 2.35E-36 831379000 575240 840253 560089 802998 577822 417811 698379 733666 816233 715700 FALSE TRUE 552758.9848 816289.8071 661309.5414 844440.823 596408.1694 426259.4247 706925.9711 718515.5407 723577.6518 667225.0015 0.828444653 1.223410102 0.991134235 1.265601291 0.893863641 0.638854095 1.059501622 1.076871429 1.084458241 1 19.34781382 DNHVVAAGGVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DNHVVAAGGVEK 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ; 135.02 0.00013504 802300000 1039520 1025790 895550 1084850 1009360 1124200 1103790 175437 1257230 1160650 FALSE TRUE 998894.4091 996535.4736 1057395.806 1140839.239 1041826.981 1146932.094 1117298.512 171814.1646 1114514.521 1082038.142 0.923160072 0.920979987 0.977226001 1.054342906 0.962837576 1.059973812 1.032586994 0.158787531 1.03001408 1 20.04531992 DNIACVILTFKEPFGTEGR ddPTM_BT-474_Pertuzumab_2h_R1 2 DNIACVILTFKEPFGTEGR 19 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 231.06 3.88E-20 550260000 673590 713740 468300 498820 634090 829100 617350 602770 730270 697300 FALSE TRUE 647265.3581 693384.834 552932.2273 524564.16 654486.0807 845864.9701 624905.314 590322.5889 647372.8111 650071.2499 0.995683717 1.06662898 0.850571729 0.806933332 1.006791303 1.301188093 0.961287419 0.908089058 0.995849011 1 19.31023833 DNIQGITKPAIR ddPTM_BT-474_Pertuzumab_2h_R1 4 DNIQGITKPAIR 12 1 P62805 P62805 HIST1H4A Histone H4 0 ;;; 169.58 3.96E-05 10786950000 6972310 7850920 6114120 12426580 5946570 5586560 9261190 6291950 9666360 4970960 FALSE TRUE 6699824.417 7627019.448 7219077.492 13067917.28 6137846.825 5699524.071 9374531.214 6162019.034 8569075.337 4634272.452 1.445712242 1.645785725 1.557758541 2.819842256 1.324446693 1.229863831 2.022870108 1.32966266 1.849065938 1 22.14391143 DNTVHDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 DNTVHDLR 8 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 110.87 0.0033424 546100000 436510 492590 367890 483010 445730 512900 435840 461650 490070 494680 FALSE TRUE 419450.7066 478541.8155 434375.9067 507938.204 460067.3103 523271.1894 441173.9403 452116.7662 434439.3081 461174.883 0.909526347 1.037658019 0.941889775 1.101400407 0.997598367 1.134648067 0.95663046 0.980358608 0.942027253 1 18.81495442 DPDDHTVCHLLFANQTEK ddPTM_BT-474_Pertuzumab_2h_R1 2 DPDDHTVCHLLFANQTEK 18 0 P00387-2;P00387;P00387-3 P00387-2 CYB5R3 NADH-cytochrome b5 reductase 3;NADH-cytochrome b5 reductase 3 membrane-bound form;NADH-cytochrome b5 reductase 3 soluble form 0 ; 253.1 9.78E-31 1060050000 382410 591540 395660 876830 391650 461570 681330 62674 862730 510550 FALSE TRUE 367464.9944 574669.8584 467164.5634 922083.3014 404247.7779 470903.2616 689668.3203 61379.76 764796.5073 475969.9937 0.77203395 1.207365729 0.981500031 1.937271915 0.849313577 0.989354934 1.448974367 0.128957205 1.606816642 1 18.8605111 DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_BT-474_Pertuzumab_2h_R1 4 DPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 35 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.985)PT(0.015)MGR;DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.998)PT(0.002)MGR;DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(1)PTMGR;DPLGGLADMFGQMPGSGIGT(0.002)GPGVIQDRFS(0.991)PT(0.006)MGR 339.97 2.71E-118 3244070000 955340 968040 842810 825410 884920 1061860 914050 1000130 1076090 1204330 TRUE FALSE 918004.2566 940432.447 995124.5152 868009.509 913384.2555 1083331.537 925236.4173 979476.966 953936.7745 1122759.656 0.81763203 0.837607979 0.886320157 0.773103579 0.813517168 0.96488285 0.824073444 0.872383471 0.849635778 1 20.0986177 DQDS(ph)SDDERALEDWVSSETSALPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPR 24 1 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.5)S(0.5)DDERALEDWVSSETSALPR 122.68 7.17E-05 22601000 11915 11609 8335.2 10905 14284 11622 9136.9 10022 13213 12569 TRUE FALSE 11449.34863 11277.92269 9841.556056 11467.80836 14743.45783 11857.0048 9248.720115 9815.042198 11713.11563 11717.69043 0.977099429 0.962469759 0.839888723 0.978674801 1.258222165 1.011889234 0.789295482 0.837626003 0.999609582 1 13.51640062 DQFLDTLQAHGHDVNSFVR ddPTM_BT-474_Pertuzumab_2h_R1 2 DQFLDTLQAHGHDVNSFVR 19 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 0 ; 238.65 1.70E-24 309600000 159788 177689 150903 177169 177469 193748 192684 33591 196514 193149 FALSE TRUE 153543.3083 172621.4837 178174.5289 186312.7133 183177.4516 197665.7173 195042.1244 32897.33411 174206.5546 180066.8462 0.852701714 0.95865223 0.989491029 1.03468638 1.017274726 1.09773521 1.083165105 0.18269512 0.967454911 1 17.45817305 DQHSFELDEK ddPTM_BT-474_Pertuzumab_2h_R1 4 DQHSFELDEK 10 0 Q6DD88;F5H6I7;F5GWF8 Q6DD88 ATL3 Atlastin-3 0 ;;; 206.36 1.52E-07 2290600000 4055000 5706090 3464200 5852610 4045960 4482960 5499640 2631350 6931860 4701110 FALSE TRUE 3896526.117 5543357.9 4090258.001 6154663.903 4176101.978 4573608.523 5566946.239 2577011.703 6144984.314 4382699.632 0.889069853 1.264827245 0.933273631 1.404308855 0.95286064 1.043559656 1.270209393 0.587996422 1.402100264 1 22.06338838 DQS(ph)PPPS(ph)PPPSYHPPPPPTK ddPTM_BT-474_Pertuzumab_2h_R1 3 DQSPPPSPPPSYHPPPPPTK 20 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 2 DQS(0.995)PPPS(0.991)PPPS(0.009)Y(0.005)HPPPPPTK;DQS(0.998)PPPS(0.885)PPPS(0.065)Y(0.052)HPPPPPTK;DQS(1)PPPS(0.995)PPPS(0.004)Y(0.002)HPPPPPTK 70.983 0.0094821 1539710000 845860 1140560 843880 1163370 827420 919300 1077520 1092580 991920 973200 TRUE FALSE 812802.8561 1108032.346 996387.888 1223411.665 854034.7157 937888.8759 1090707.012 1070017.841 879321.4001 907284.2972 0.895863467 1.221262562 1.098209118 1.348432535 0.941308825 1.033732071 1.202166747 1.179363342 0.969179565 1 19.79119516 DREGFFTNGLTLGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 DREGFFTNGLTLGAK 15 1 C9J0J7;G5E9Q6;P35080-2;C9J712;C9JQ45;C9J2N0;P35080 C9J0J7 PFN2 Profilin;Profilin-2 0 ; 141 4.41E-06 1090570000 1018890 995140 819670 889410 893210 818200 1004190 1076470 1080110 1057280 FALSE TRUE 979070.6524 966759.5815 967802.6025 935312.5567 921940.9108 834744.5646 1016479.578 1054240.518 957500.441 985669.4839 0.993305229 0.980815169 0.981873354 0.94891094 0.935344886 0.846880804 1.031258038 1.06956798 0.971421411 1 19.91074444 DRSPAAET(ph)PPLQR ddPTM_BT-474_Pertuzumab_2h_R1 1 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 DRSPAAET(1)PPLQR 103.28 0.002624 772710000 285140 302870 232650 297460 276300 260400 274920 332410 288180 290460 TRUE FALSE 273996.4136 294232.4441 274695.0303 312811.9462 285187.4404 265665.4664 278284.5532 325545.6173 255467.0145 270786.8855 1.011852598 1.086583066 1.014432548 1.155196071 1.0531804 0.981086901 1.027688445 1.202220768 0.94342462 1 18.04679834 DRVHHEPQLSDK ddPTM_BT-474_Pertuzumab_2h_R1 3 DRVHHEPQLSDK 12 1 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11;O43852-12;O43852-2;O43852-4;O43852-8;O43852-7 O43852;O43852-2 CALU Calumenin 0 ;; 137.59 5.38E-05 801180000 1592780 1659720 1419760 1584090 1504160 1654570 1703530 573450 2034140 1794510 FALSE TRUE 1530532.397 1612386.411 1676342.214 1665845.075 1552542.672 1688026.539 1724378.31 561608.0571 1803232.955 1672966.239 0.914861496 0.963788971 1.002017958 0.99574339 0.928017934 1.009002154 1.030731087 0.335695989 1.077865717 1 20.6739769 DS(ph)HSPDLQLPTPEVIPSSGSK ddPTM_BT-474_Pertuzumab_2h_R1 3 DSHSPDLQLPTPEVIPSSGSK 21 0 H3BQK9;H3BPE1;H0Y4F5;H0Y6T5 H3BQK9 MACF1 1 DS(0.542)HS(0.458)PDLQLPTPEVIPSSGSK;DS(0.531)HS(0.469)PDLQLPTPEVIPSSGSK;DS(0.64)HS(0.36)PDLQLPTPEVIPSSGSK 232.19 1.70E-26 529403000 891272 883220 842022 935890 919310 1036660 1168350 285610 1402000 1360280 TRUE FALSE 856440.1049 858031.4304 994194.1061 984191.3951 948880.441 1057621.975 1182648.617 279712.0537 1242850.838 1268147.024 0.675347644 0.676602487 0.783973851 0.776086192 0.748241665 0.833990031 0.932580051 0.220567528 0.980052639 1 20.27429058 DSAATTDEER ddPTM_BT-474_Pertuzumab_2h_R1 1 DSAATTDEER 10 0 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 136.57 0.0096812 0 53052 48719 39117 40952 52510 41334 41766 46189 48742 49669 FALSE TRUE 50978.66919 47329.58182 46186.31205 43065.53763 54199.03184 42169.8018 42277.1448 45235.18101 43209.0125 46304.87439 1.100935266 1.02212958 0.997439528 0.930043288 1.170482213 0.910698978 0.913017158 0.976898903 0.933141771 1 15.49887645 DSAIPVESDTDDEGAPR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 180.28 2.02E-09 74729000 34718 32496 26883 30233 27241 32649 33541 34065 31122 37046 FALSE TRUE 33361.18218 31569.2459 31741.35611 31793.32875 28117.2315 33309.18515 33951.48479 33361.54585 27589.16103 34536.84142 0.965959271 0.914074495 0.919057876 0.920562722 0.814122842 0.964453719 0.98305124 0.965969801 0.79883278 1 15.07584853 DSDKEGTSNSTSEDGPGDGFTILSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSDKEGTSNSTSEDGPGDGFTILSSK 26 1 Q9P0M6;Q5SQT3 Q9P0M6 H2AFY2 Core histone macro-H2A.2;Histone H2A 0 131.27 5.91E-05 165570000 127440 142870 121480 150040 78125 147490 114070 105440 167380 153460 FALSE TRUE 122459.5039 138795.4875 143434.1383 157783.5824 80637.96158 150472.3489 115466.0228 103262.6272 148379.7241 143066.0175 0.855965002 0.970149934 1.002573083 1.102872542 0.563641618 1.051768627 0.807082107 0.721783055 1.037141641 1 17.1263215 DSEDNPQTLLFSATCPHWVFNVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSEDNPQTLLFSATCPHWVFNVAK 24 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 231.29 1.29E-33 280140000 259870 229620 192300 175120 221870 217090 251130 221530 229850 265650 FALSE TRUE 249713.9931 223071.4624 227052.8877 184157.9642 229006.65 221479.7085 254203.4041 216955.3281 203758.3916 247657.2889 1.008304638 0.900726417 0.916802767 0.743600017 0.924691743 0.894299173 1.026432152 0.876030458 0.822743367 1 17.91798556 DSELASQNKPLWQCYLGR ddPTM_BT-474_Pertuzumab_2h_R1 1 DSELASQNKPLWQCYLGR 18 1 Q9NTI5-2;Q9NTI5;Q9NTI5-3 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 139.67 1.21E-07 323350000 159470 164430 147460 150850 146790 178380 153390 144740 192810 190690 FALSE TRUE 153237.7361 159740.6174 174109.3022 158635.3866 151511.6337 181986.9658 155267.2327 141751.0684 170923.0171 177774.3965 0.86197866 0.898558063 0.979383453 0.892341022 0.852269149 1.023696153 0.873394796 0.797364926 0.961460258 1 17.43968803 DSHS(ph)PDLQLPTPEVIPSSGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 DSHSPDLQLPTPEVIPSSGSK 21 0 H3BQK9;H3BPE1;H0Y4F5;H0Y6T5 H3BQK9 MACF1 1 DS(0.225)HS(0.775)PDLQLPTPEVIPSSGSK 210.62 1.25E-22 455390000 593590 635320 597330 635730 590900 726920 812760 175880 1118800 1022400 TRUE FALSE 570391.8466 617201.2956 705280.8185 668540.1015 609906.8351 741618.8205 822706.8 172248.0165 991798.5144 953151.9373 0.598426992 0.647537157 0.739945848 0.7013993 0.639884169 0.778069887 0.863143396 0.180714123 1.040546082 1 19.86234668 DSLITPHVS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 2 DSLITPHVSR 10 0 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37;H7BZ48;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5;RGPD6;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 DSLITPHVS(1)R;DSLITPHVS(1)R 138.02 4.88E-05 556510000 463840 504280 462670 528130 496350 552920 513650 465400 584590 628620 TRUE FALSE 445712.62 489898.4281 546284.761 555386.8526 512315.5485 564100.4212 519936.2024 455789.3274 518229.794 586043.0075 0.760545923 0.835942792 0.932158142 0.947689582 0.874194457 0.962558061 0.887198031 0.777740407 0.884286285 1 19.16064702 DSPAFPDS(ph)PWR ddPTM_BT-474_Pertuzumab_2h_R1 5 DSPAFPDSPWR 11 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 DSPAFPDS(1)PWR;DSPAFPDS(1)PWR;DSPAFPDS(1)PWR;DSPAFPDS(1)PWR;DSPAFPDS(1)PWR 165.44 2.26E-05 1669260000 1360460 1329330 1178780 1444720 1231980 1212050 1318540 1440910 1099900 1403630 TRUE FALSE 1307291.719 1291418.81 1391811.768 1519282.172 1271607.756 1236558.481 1334676.687 1411154.705 975043.9632 1308560.89 0.999030102 0.986900052 1.063620179 1.161032845 0.971760478 0.944975882 1.019957648 1.078402018 0.745126933 1 20.31954963 DSSGQHVDVSPTSQR ddPTM_BT-474_Pertuzumab_2h_R1 4 DSSGQHVDVSPTSQR 15 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;;; 129.65 6.46E-05 1502490000 791000 1536930 887950 2233030 944200 1180740 1854300 1424970 1167980 1026140 FALSE TRUE 760086.8455 1493098.261 1048422.317 2348276.946 974571.0505 1204615.372 1876993.478 1395543.872 1035395.807 956638.6238 0.794539157 1.560775641 1.095943955 2.454716847 1.018745246 1.259216743 1.962071603 1.458799422 1.082326995 1 19.86761452 DTDSEEEIREAFR ddPTM_BT-474_Pertuzumab_2h_R1 6 DTDSEEEIREAFR 13 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;; 299.2 7.19E-41 21816500000 5367870 5634830 3682330 5278150 5875670 5158490 5478820 5383120 6229170 5563630 FALSE TRUE 5158087.706 5474130.165 4347808.944 5550555.954 6064666.262 5262798.202 5545871.438 5271956.691 5522060.736 5186800.385 0.994464279 1.055396344 0.838244895 1.070131014 1.169249983 1.014652158 1.069227853 1.016417888 1.064637219 1 22.30641342 DTDSINLYK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTDSINLYK 9 0 O14980 O14980 XPO1 Exportin-1 0 76.17 0.084194 274710000 254420 269810 260730 256200 272280 279860 273340 250760 340410 329030 FALSE TRUE 244476.9851 262115.283 307849.7109 269422.5127 281038.1335 285518.9609 276685.2167 245581.7184 301768.0839 306744.505 0.797005264 0.854506857 1.003603018 0.878328734 0.916196147 0.930803833 0.902005455 0.800606741 0.983776658 1 18.22667797 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK ddPTM_BT-474_Pertuzumab_2h_R1 3 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;; 219.21 1.97E-36 1295930000 274216 301897 239140 249785 270823 278747 283955 19731.9 320763 244569 FALSE TRUE 263499.3356 293287.1931 282357.9176 262676.4338 279534.2678 284383.4553 287430.1262 19324.42937 284351.329 228004.1238 1.155677938 1.286324073 1.238389521 1.152068785 1.226005316 1.247273298 1.260635648 0.084754736 1.247132395 1 17.79870039 DTLWHLFNTLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTLWHLFNTLQR 12 0 Q7Z434;Q7Z434-5;Q7Z434-2 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 0 ; 151.66 6.92E-05 193436000 202642 299900 214893 309920 221250 217590 317600 277330 264960 261210 FALSE TRUE 194722.5266 291347.1456 253728.9454 325915.0083 228366.7072 221989.8189 321486.8838 271603.0386 234882.8516 243518.014 0.799622678 1.196409008 1.041930908 1.338360982 0.937781577 0.911595061 1.320177011 1.115330378 0.964539944 1 17.89366897 DTQDFHK ddPTM_BT-474_Pertuzumab_2h_R1 1 DTQDFHK 7 0 O75362 O75362 ZNF217 Zinc finger protein 217 0 71.223 0.054899 219330000 350100 369350 292120 312420 323380 361650 349230 338530 387230 400450 FALSE TRUE 336417.7049 358816.4996 344912.5822 328544.0336 333781.8114 368962.8108 353503.9812 331539.2372 343273.2738 373327.1648 0.901133742 0.961131505 0.923888253 0.880043202 0.894073196 0.988309573 0.946901309 0.888066202 0.919497176 1 18.51008096 DTS(ph)GLER ddPTM_BT-474_Pertuzumab_2h_R1 2 DTSGLER 7 0 Q9H307 Q9H307 PNN Pinin 1 DT(0.009)S(0.991)GLER;DT(0.003)S(0.997)GLER 140.11 0.0027759 745780000 1356070 1228560 1031170 1111240 1092020 1202200 1072420 1407390 1298750 1247340 TRUE FALSE 1303073.285 1193522.672 1217525.357 1168591.23 1127145.815 1226509.308 1085544.597 1378326.905 1151321.345 1162856.551 1.120579563 1.02637137 1.047012511 1.004931544 0.969290506 1.054738271 0.933515485 1.18529401 0.990080285 1 20.14924171 DTSFEQHVLWHTGGK ddPTM_BT-474_Pertuzumab_2h_R1 6 DTSFEQHVLWHTGGK 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 270.75 1.28E-33 25265020000 17010030 18781730 16825260 20216030 19830160 21832120 22401860 3070100 24361700 22800930 FALSE TRUE 16345259.22 18246093.45 19865958.76 21259381.73 20468015.11 22273580.42 22676020.66 3006701.362 21596261.95 21256602.7 0.768949745 0.858372982 0.93457826 1.000130737 0.962901523 1.04784291 1.066775391 0.141447879 1.015979 1 24.3414077 DTVLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 DTVLQR 6 0 P22102;P22102-2;F8WD69 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 98.133 0.093712 2799520000 659170 699240 593370 650900 661910 594060 704750 675230 730000 669620 FALSE TRUE 633408.9076 679298.3598 700605.1584 684493.027 683200.9363 606072.3002 713374.9413 661286.2645 647133.4604 624266.041 1.014645786 1.088155234 1.122286193 1.096476473 1.094406698 0.97085579 1.142741867 1.059301998 1.036630888 1 19.25180146 DVDIIDHHDNTYTVK ddPTM_BT-474_Pertuzumab_2h_R1 7 DVDIIDHHDNTYTVK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;;;;; 184.51 2.67E-07 13854290000 10279390 10263660 8914770 9234680 9289890 10150760 10200340 3887630 12538840 11932140 FALSE TRUE 9877660.074 9970950.466 10525867.25 9711282.941 9588707.749 10356015.32 10325174.81 3807349.082 11115483.45 11123965.53 0.887962125 0.896348558 0.946233357 0.873005487 0.861986467 0.930964348 0.92819191 0.342265451 0.999237495 1 23.40716784 DVFHTTVNFINQNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVFHTTVNFINQNLR 15 0 P55957;P55957-2;P55957-4 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ; 236.3 1.05E-17 984420000 356840 432120 364010 451870 378770 359150 454500 392890 411460 490350 FALSE TRUE 342894.2983 419796.3607 429794.7044 475191.0649 390953.481 366412.2591 460062.307 384776.6842 364752.7858 457138.1577 0.750088988 0.918313979 0.940185581 1.03949114 0.855219531 0.801535056 1.006396642 0.841707649 0.797904921 1 18.80227072 DVLLQVDDERR ddPTM_BT-474_Pertuzumab_2h_R1 6 DVLLQVDDERR 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 250.48 1.77E-16 8403890000 5388050 5363640 3735730 5093440 5007790 4701000 5147060 5647830 5696210 4685760 FALSE TRUE 5177479.049 5210674.239 4410859.512 5356313.049 5168870.113 4796057.441 5210051.26 5531200.337 5049600.121 4368389.302 1.185214662 1.192813616 1.009722167 1.226152863 1.183243927 1.097900647 1.192671005 1.266187593 1.15594096 1 22.05867 DVLSYHIPFLVSSIEDFKDHIPR ddPTM_BT-474_Pertuzumab_2h_R1 2 DVLSYHIPFLVSSIEDFKDHIPR 23 1 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 202.47 1.34E-24 250560000 195637 239627 180451 240460 214591 222275 236179 159441 277110 260180 FALSE TRUE 187991.2898 232793.0726 213062.5098 252870.1694 221493.5144 226769.5528 239069.4293 156148.4876 245653.6345 242557.7769 0.775037157 0.95974277 0.878399005 1.042515201 0.913157753 0.93490943 0.985618488 0.643757911 1.012763382 1 17.88796891 DVQGTDASLDEELDRVK ddPTM_BT-474_Pertuzumab_2h_R1 4 DVQGTDASLDEELDRVK 17 1 A0A087WYB4;Q9UJZ1;Q9UJZ1-2 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 ;;; 307.55 5.53E-48 1893100000 1030920 1538030 761980 1573890 871240 1124920 1645460 1478450 1352330 987030 FALSE TRUE 990630.5067 1494166.89 899686.7362 1655118.652 899264.2258 1147666.653 1665597.632 1447919.491 1198819.168 920177.5789 1.076564491 1.623781023 0.977731643 1.798694827 0.977272481 1.247223014 1.810082825 1.573521811 1.302812843 1 19.81155278 DVQIGDIVTVGECRPLSK ddPTM_BT-474_Pertuzumab_2h_R1 5 DVQIGDIVTVGECRPLSK 18 1 P62280;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;;; 258.87 1.03E-30 4146520000 2804261 2594015 2398749 2158034 2643969 2687484 2547013 2925393 3000638 2762061 FALSE TRUE 2694667.38 2520036.232 2832256.304 2269410.393 2729014.664 2741826.768 2578184.107 2864982.612 2660018.154 2574984.148 1.046479211 0.978660872 1.099912132 0.88132985 1.059818044 1.064793649 1.00124271 1.112621456 1.033023118 1 21.29613212 DVVNVYEPQLQHHVAQK ddPTM_BT-474_Pertuzumab_2h_R1 2 DVVNVYEPQLQHHVAQK 17 0 Q16222;Q16222-3;Q16222-2 Q16222 UAP1 UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 ; 137.73 3.48E-06 509470000 937840 936350 791540 992820 1000570 1006600 1046250 301710 1209010 1139420 FALSE TRUE 901188.176 909646.2148 934588.8857 1044059.559 1032754.243 1026954.142 1059054.32 295479.5831 1071768.253 1062246.069 0.848379865 0.856342275 0.879823342 0.982879194 0.972236352 0.966776129 0.996995284 0.278164911 1.008964199 1 20.01868657 DWHRPCLK ddPTM_BT-474_Pertuzumab_2h_R1 6 DWHRPCLK 8 1 P50238 P50238 CRIP1 Cysteine-rich protein 1 0 ;;;;; 147.19 0.00032526 42451570000 14511530 14648870 12659700 14688900 14715350 14426910 15132830 8253250 16280830 14997900 FALSE TRUE 13944403.36 14231098.57 14947589.4 15446995.89 15188682.6 14718632 15318030.1 8082817.503 14432698.43 13982078.87 0.997305443 1.017809919 1.069053432 1.104771045 1.086296447 1.05267837 1.095547396 0.578084102 1.032228366 1 23.73707554 DYAFIHFDER ddPTM_BT-474_Pertuzumab_2h_R1 8 DYAFIHFDER 10 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;;; 188.61 1.10E-06 19432770000 9387500 9602060 9084210 10512130 9831160 7910430 9987880 9372260 10481460 11171690 FALSE TRUE 9020626.122 9328218.65 10725928.82 11054662.29 10147388.19 8070384.314 10110114.66 9178719.556 9291648.603 10415021.49 0.8661169 0.895650447 1.029851819 1.061415217 0.974303145 0.774879277 0.970724321 0.881296267 0.892139168 1 23.31216248 DYEHQFHLR ddPTM_BT-474_Pertuzumab_2h_R1 4 DYEHQFHLR 9 0 Q15276-2;Q15276;A0A087WZZ3 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;;; 177.06 3.04E-05 948500000 588300 612380 540194 592160 589240 526555 646630 21329.8 684020 584330 FALSE TRUE 565308.5856 594915.522 637819.0724 622721.4486 608193.4397 537202.3029 654543.6514 20889.33218 606372.9172 544752.8086 1.037734137 1.092083441 1.170841274 1.143126641 1.116457648 0.986139574 1.2015425 0.038346442 1.113115724 1 19.0552422 DYS(ph)YER ddPTM_BT-474_Pertuzumab_2h_R1 3 DYSYER 6 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 DYS(1)YER;DYS(1)YER;DYS(1)YER 160.26 0.0092973 1579840000 1706530 1616050 1321110 1327540 1436980 1562980 1484890 1731390 1724580 1561120 TRUE FALSE 1639836.921 1569961.836 1559863.965 1396054.498 1483201.767 1594584.526 1503062.528 1695636.191 1528812.908 1455383.952 1.126738356 1.078726912 1.071788625 0.959234501 1.019113729 1.095645259 1.032760136 1.165078253 1.050453323 1 20.47296838 DYSGQGVVK ddPTM_BT-474_Pertuzumab_2h_R1 2 DYSGQGVVK 9 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 107.15 0.0065596 64501000 161798 176009 167676 194716 160342 165942 178938 175756 186246 205033 FALSE TRUE 155474.7553 170989.3957 197978.7831 204765.3161 165499.546 169297.4609 181127.8968 172126.5772 165104.1349 191145.9323 0.813382495 0.894548964 1.035746776 1.071251235 0.86582824 0.88569743 0.947589596 0.900498248 0.863759605 1 17.54431497 EALAAVLTYAKPDEFSALCDLLGTR ddPTM_BT-474_Pertuzumab_2h_R1 1 EALAAVLTYAKPDEFSALCDLLGTR 25 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 0 155.25 5.66E-08 86844000 62724 51714 43956 47879 63021 68859 48723 51026 62716 56400 FALSE TRUE 60272.67673 50239.16735 51899.827 50350.04093 65048.1277 70251.37616 49319.28665 49972.29527 55596.74261 52579.97776 1.146304721 0.955480955 0.987064453 0.95758962 1.237127334 1.336086076 0.937986069 0.950405409 1.057374784 1 15.68222591 EALAEAALESPRPALVR ddPTM_BT-474_Pertuzumab_2h_R1 5 EALAEAALESPRPALVR 17 1 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;; 285.94 2.10E-36 5569570000 2084021 2103034 1755706 2133850 2046080 2212848 2024028 2190910 2307235 2593090 FALSE TRUE 2002575.155 2043057.529 2073001.13 2243978.254 2111894.021 2257593.303 2048798.66 2145666.943 2045327.356 2417457.705 0.828380638 0.845126484 0.857512885 0.928238889 0.873601229 0.933870859 0.847501347 0.887571658 0.846065415 1 21.20505922 EALEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EALEHK 6 0 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 74.517 0.080118 1018400000 865970 802170 701390 768840 752190 786880 912410 814380 962730 936000 FALSE TRUE 832126.935 779292.897 828146.7753 808519.9245 776384.8745 802791.2527 923576.3465 797562.7684 853444.9265 872603.8863 0.953613602 0.89306604 0.949052357 0.926560078 0.889733459 0.919995046 1.058414203 0.914003228 0.978043921 1 19.73496737 EALPESGELLDVWTELQDIHDAHGLR ddPTM_BT-474_Pertuzumab_2h_R1 4 EALPESGELLDVWTELQDIHDAHGLR 26 0 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 0 ;;; 177.38 1.50E-17 146970000 95447 99783 80003 101931 99474 103686 100503 13724.6 109592 95959 FALSE TRUE 91716.82572 96937.28654 94461.32176 107191.6711 102673.6715 105782.602 101732.9858 13441.18221 97151.57561 89459.61146 1.025231657 1.083587162 1.055910262 1.198213019 1.147709786 1.182462122 1.137194586 0.150248609 1.085982535 1 16.44894887 EALVVLHEDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 EALVVLHEDVR 11 0 E9PF16;Q96CM8-3;Q96CM8;Q96CM8-2;D6RF87 E9PF16 ACSF2 "Acyl-CoA synthetase family member 2, mitochondrial" 0 ;;; 158.31 3.00E-05 860965000 689809 1051450 623547 1448900 616489 667687 1288890 1027750 819620 716906 FALSE TRUE 662850.5017 1021463.675 736235.8136 1523677.903 636318.9286 681188.0886 1304663.821 1006526.603 726580.1737 668349.3181 0.991772541 1.528338023 1.101573374 2.279762785 0.952075376 1.019209671 1.952068755 1.505988824 1.087126379 1 19.35024281 EAPSPLMIHSPQMSQFQSLTHQS(ph)PPQQNVQPK ddPTM_BT-474_Pertuzumab_2h_R1 5 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 EAPSPLMIHSPQMSQFQSLTHQS(1)PPQQNVQPK;EAPSPLMIHSPQMS(0.001)QFQS(0.001)LT(0.004)HQS(0.994)PPQQNVQPK;EAPSPLMIHSPQMSQFQSLT(0.001)HQS(0.999)PPQQNVQPK;EAPSPLMIHS(0.002)PQMS(0.02)QFQS(0.072)LT(0.072)HQS(0.833)PPQQNVQPK;EAPSPLMIHSPQMSQFQSLTHQS(1)PPQQNVQPK 245.41 6.06E-47 1604600000 496729 568859 458478 576664 539988 560605 573580 462615 625806 591968 TRUE FALSE 477316.2815 552635.6983 541335.1734 606425.6981 557357.2044 571940.8172 580599.6436 453061.8386 554767.1265 551873.4801 0.864901646 1.001381147 0.980904488 1.098849138 1.009936561 1.036362206 1.052052082 0.820952365 1.005243315 1 19.07397803 EAYPDHTQFEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EAYPDHTQFEK 11 0 Q9P016-2;Q9P016 Q9P016-2 THYN1 Thymocyte nuclear protein 1 0 ;; 172.11 1.37E-05 1228880000 4220920 2693110 1951190 1924160 2274340 1848030 1935030 4327950 2067300 1824690 FALSE TRUE 4055961.78 2616305.14 2303813.437 2023466.128 2347496.212 1885398.433 1958711.476 4238576.32 1832628.771 1701102.121 2.384314104 1.538005924 1.354306369 1.189503031 1.379985471 1.108339358 1.151436737 2.491664826 1.077318491 1 20.69803832 ECHLNADTVSSK ddPTM_BT-474_Pertuzumab_2h_R1 4 ECHLNADTVSSK 12 0 P63010;P63010-2;P63010-3;A0A087X253 P63010 AP2B1 AP-2 complex subunit beta 0 ;;; 205.96 9.57E-08 5458500000 7853200 8444200 7135600 8328100 8005800 8311900 8708100 7758400 9772100 9814900 FALSE TRUE 7546288.262 8203379.684 8425161.651 8757914.239 8263313.828 8479972.313 8814672.333 7598186.329 8662812.176 9150128.081 0.824719413 0.896531678 0.920769805 0.957135699 0.903081766 0.926759958 0.963338683 0.830391254 0.946742177 1 23.12536051 EDAEHHPDEDVDESES ddPTM_BT-474_Pertuzumab_2h_R1 3 EDAEHHPDEDVDESES 16 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ;; 184.21 1.86E-09 750830000 752110 832590 730591 870740 816770 842700 870640 264775 958790 970950 FALSE TRUE 722716.7097 808845.3484 862625.0456 915678.9957 843042.1488 859739.9714 881295.1528 259307.3037 849952.1788 905186.6917 0.798417295 0.893567433 0.952980257 1.011591315 0.931346159 0.949792987 0.973605954 0.286468312 0.938979977 1 19.78785585 EDENSWFNLFVIHQNR ddPTM_BT-474_Pertuzumab_2h_R1 4 EDENSWFNLFVIHQNR 16 0 F8W7U8;P49959-2;P49959;P49959-3;F5GXT0 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ;;; 224.67 7.59E-15 554424000 551400 555438 444599 576509 581099 594289 534292 525047 572805 608049 FALSE TRUE 529850.6784 539597.4521 524947.9294 606262.6986 599790.5771 606305.9308 540830.8253 514204.596 507782.5778 566865.2996 0.934702969 0.95189713 0.92605409 1.06950046 1.058083071 1.069576725 0.954072909 0.90710191 0.895772908 1 19.11264643 EDFPQKWPDLLTEMVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 EDFPQKWPDLLTEMVNR 17 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 180.14 7.99E-10 4435900000 962660 1028200 787360 890790 903850 1038450 931500 986770 1122440 1047990 FALSE TRUE 925038.1829 998876.7427 929653.4667 936763.7787 932923.1561 1059448.17 942899.9756 966392.8547 995025.3169 977008.7038 0.946806491 1.022382645 0.951530384 0.958808018 0.954877016 1.08437946 0.965088614 0.989134335 1.018440586 1 19.89801189 EDGVTPYMIFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 EDGVTPYMIFFK 12 0 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;P13693-2;H0YCX0 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 156.12 0.00061674 0 62106 73951 44110 58033 61525 71085 60051 65614 73203 61991 FALSE TRUE 59678.82886 71841.98989 52081.65822 61028.09008 63504.0075 72522.3874 60785.9221 64259.04797 64893.30233 57792.29435 1.032643357 1.243106727 0.901186894 1.055990089 1.098831742 1.25487988 1.051799773 1.111896468 1.12287119 1 15.81858953 EDSARPGAHAK ddPTM_BT-474_Pertuzumab_2h_R1 4 EDSARPGAHAK 11 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;;; 115.33 0.00068384 8952000000 16661200 17256900 12664200 14414000 15011700 16390400 15417700 16326300 18398400 17428000 FALSE TRUE 16010061.88 16764750.11 14952902.65 15157908.27 15494564.96 16721825.12 15606386.42 15989156.2 16309890.76 16247586.04 0.985380957 1.03183021 0.920315339 0.932932944 0.953653357 1.029188279 0.9605357 0.984094263 1.003834707 1 23.95372205 EDSQRPGAHLTVK ddPTM_BT-474_Pertuzumab_2h_R1 9 EDSQRPGAHLTVK 13 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;;;;;;; 123.76 0.00020036 70561520000 49344530 55072420 44748850 51989340 48417020 52193290 53094030 53654740 56979600 60418040 FALSE TRUE 47416091.21 53501808.5 52835962.63 54672516.07 49974397.42 53248674.08 53743810.62 52546750.87 50511514.69 56325872.34 0.841817255 0.949862049 0.938040734 0.970646593 0.88723699 0.945367943 0.954158514 0.932906117 0.896772879 1 25.74729442 EDTEEHHLR ddPTM_BT-474_Pertuzumab_2h_R1 12 EDTEEHHLR 9 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;F8VYN5;P22626;P22626-2;A0A087WUI2 F8W6I7;P22626 HNRNPA1;HNRNPA1L2;HNRNPA2B1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoproteins A2/B1" 0 ;;;;;;;;;;; 218.55 5.26E-07 15604904000 9907939 9802624 9180446 10500657 10408632 10216682 10647715 3105794 11365935 11419579 FALSE TRUE 9520725.79 9523062.761 10839556.81 11042597.17 10743435.1 10423270.31 10778024.92 3041658.269 10075721.71 10646120.74 0.894290608 0.894510122 1.018169629 1.037241398 1.009140828 0.979067452 1.012389882 0.285705784 0.946421889 1 23.3438245 EDTHHLVNYIPQGSIDSLFEGTWYLVR ddPTM_BT-474_Pertuzumab_2h_R1 3 EDTHHLVNYIPQGSIDSLFEGTWYLVR 27 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;; 298.25 9.63E-71 4283960000 1076549 922035 992002 1160457 1131067 1082938 1240483 414888 1400240 1255810 FALSE TRUE 1034476.275 895739.4646 1171278.828 1220348.325 1167448.797 1104835.748 1255664.402 406320.4178 1241290.625 1170752.87 0.883599179 0.765096962 1.000449248 1.042362018 0.997177822 0.94369681 1.072527289 0.347059083 1.06024991 1 20.15900514 EEAIEHNYGGHDDDLSVR ddPTM_BT-474_Pertuzumab_2h_R1 3 EEAIEHNYGGHDDDLSVR 18 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;; 245.1 2.00E-24 2472720000 1246522 1290656 1250302 1350696 1349169 1162565 1431034 275597 1560958 1370894 FALSE TRUE 1197806.542 1253847.755 1476259.384 1420405.582 1392566.246 1186072.861 1448547.422 269905.8256 1383764.592 1278042.128 0.937219921 0.981069189 1.155094462 1.111391832 1.089609032 0.928038939 1.133411325 0.211186955 1.082722206 1 20.28550396 EEASLLSHS(ph)PGTSNQSQPCS(ph)PKPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 2 EEAS(0.001)LLS(0.111)HS(0.673)PGT(0.208)S(0.019)NQS(0.253)QPCS(0.735)PKPIR;EEASLLSHS(1)PGTSNQS(0.114)QPCS(0.886)PKPIR 201.25 8.32E-25 485830000 379140 412420 345040 358150 373410 441310 408040 433950 434120 416440 TRUE FALSE 364322.7896 400658.1854 407396.4034 376634.1644 385421.0718 450233.5906 413033.7156 424988.7809 384840.5176 388234.1479 0.938409956 1.032001403 1.04935747 0.970121167 0.992754177 1.159696006 1.063877863 1.094671304 0.991258805 1 18.56656749 EEAT(ph)SPGAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEATSPGAK 9 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 EEAT(0.995)S(0.005)PGAK 162 0.0007166 335670000 848010 777390 605880 708550 712000 750060 792420 759610 814570 820510 TRUE FALSE 814868.8317 755219.5983 715375.9937 745118.3504 734902.1266 765226.7271 802117.873 743923.788 722103.4286 764936.1269 1.06527696 0.987297595 0.935210103 0.974092247 0.960736591 1.000379901 1.048607648 0.972530597 0.944004869 1 19.54497976 EEDGSTCLHHAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 EEDGSTCLHHAAK 13 0 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7;H0Y4K5;A0A0G2JRR0;A0A0G2JRN8 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 0 176.05 9.96E-06 177750000 260260 233320 203350 191520 227330 254970 248320 68836 290820 246010 FALSE TRUE 250088.7515 226665.942 240099.8685 201404.3702 234642.2759 260125.6681 251359.0144 67414.51254 257807.3328 229347.5236 1.090435805 0.988307781 1.046882324 0.878162393 1.023086154 1.134198722 1.0959744 0.293940442 1.124090327 1 17.8071758 EEFTAFLHPEEFEHMK ddPTM_BT-474_Pertuzumab_2h_R1 6 EEFTAFLHPEEFEHMK 16 0 Q15293;Q15293-2;E9PP27 Q15293 RCN1 Reticulocalbin-1 0 ;;;;; 243.69 2.99E-20 2149544000 1738412 1917422 1576398 1628917 1661576 1900891 1799556 552659 2215489 1907138 FALSE TRUE 1670472.937 1862739.002 1861288.185 1712985.602 1715022.101 1939328.318 1821579.505 541246.3985 1963995.977 1777965.845 0.939541635 1.047679857 1.046863859 0.96345248 0.964597889 1.090756791 1.024530089 0.304418895 1.104630881 1 20.76179618 EEGAAPSPT(ph)HVAELATMEVESAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EEGAAPSPTHVAELATMEVESAR 23 0 Q9NRS6 Q9NRS6 SNX15 Sorting nexin-15 1 EEGAAPS(0.476)PT(0.524)HVAELATMEVESAR 64.733 0.085469 23738000 18671 17929 20348 17485 18385 20343 20073 21302 20324 22169 TRUE FALSE 17941.31668 17417.68247 24025.33624 18387.40295 18976.37022 20754.3494 20318.65938 20862.10626 18016.90473 20667.47388 0.86809432 0.84275817 1.162470865 0.889678296 0.918175599 1.00420349 0.983122538 1.009417328 0.871751663 1 14.33507444 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_BT-474_Pertuzumab_2h_R1 11 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 37 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;; 351.12 2.66E-145 10128800000 674346 699354 532594 551484 592577 710622 616919 706105 732322 692770 FALSE TRUE 647991.8128 679409.1087 628845.5833 579946.1553 611637.7774 724991.2637 624469.0393 691523.685 649191.8767 645848.0708 1.003319267 1.051964292 0.973674168 0.897960653 0.947030432 1.122541502 0.966897739 1.070721918 1.005177388 1 19.3008353 EEPVS(ph)S(ph)GPEEAVGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 2 EEPVS(1)S(1)GPEEAVGK;EEPVS(1)S(1)GPEEAVGK 158.65 7.36E-06 694130000 1642470 1554970 1359540 1251050 1465750 1464850 1386410 1762420 1657140 1427990 TRUE FALSE 1578280.457 1510623.778 1605239.121 1315616.84 1512897.18 1494470.271 1403377.3 1726025.411 1469028.414 1331270.965 1.185544114 1.134722996 1.205794434 0.988241218 1.136430689 1.122589097 1.05416353 1.296524491 1.103478144 1 20.34437281 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 40 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 385.71 2.42E-180 1281780000 148566 154640 138246 149700 150288 159052 163107 88747 178122 171918 FALSE TRUE 142759.8765 150229.8186 163230.1275 157426.0349 155122.15 162268.1404 165103.1523 86914.34344 157902.3373 160273.8407 0.890724748 0.937332118 1.018445223 0.982231624 0.967856946 1.012443077 1.030131627 0.542286521 0.985203428 1 17.29017945 EES(ph)KTCK ddPTM_BT-474_Pertuzumab_2h_R1 1 EESKTCK 7 1 Q9BTE3 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 EES(0.5)KT(0.5)CK 58.64 0.065612 185050000 21222 21345 29634 20452 27676 26046 19620 62445 24653 23901 TRUE FALSE 20392.62078 20736.2615 34989.523 21507.53017 28566.22367 26572.66797 19860.11543 61155.48893 21854.49479 22282.16398 0.915199296 0.930621528 1.57029286 0.965235252 1.282021966 1.19255329 0.891301018 2.744593792 0.980806658 1 14.44360173 EETQPPVALKK ddPTM_BT-474_Pertuzumab_2h_R1 1 EETQPPVALKK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 84.718 0.020249 0 416930 395640 348860 321840 384110 373570 408080 356770 478130 430520 FALSE TRUE 400635.9147 384356.7346 411906.7623 338450.201 396465.247 381123.8414 413074.2051 349402.5748 423854.6869 401360.4969 0.998194685 0.957634689 1.026276292 0.84325738 0.987803359 0.949579852 1.029185005 0.870545501 1.056044853 1 18.6145391 EFLEFR ddPTM_BT-474_Pertuzumab_2h_R1 3 EFLEFR 6 0 O75323;C9K068;H7C333;C9J7B1 O75323 GBAS Protein NipSnap homolog 2 0 ;; 121.14 0.046022 1015810000 867720 1458460 944800 2178860 961850 1018140 1805460 1569730 1145970 970110 FALSE TRUE 833808.5431 1416866.149 1115546.377 2291311.226 992788.7788 1038727.488 1827555.76 1537314.527 1015884.29 904403.5856 0.921942987 1.566630397 1.233460807 2.533505243 1.097727601 1.148522081 2.020730334 1.699810296 1.123264332 1 19.78660719 EFLEKEELPR ddPTM_BT-474_Pertuzumab_2h_R1 1 EFLEKEELPR 10 1 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 118.48 0.00074692 225830000 126020 137250 101810 109980 116650 144830 124330 136670 134150 134490 FALSE TRUE 121094.9991 133335.7644 120209.3318 115656.081 120402.1532 147758.5618 125851.5877 133847.7167 118921.8544 125380.8725 0.965817167 1.063445817 0.958753352 0.922437998 0.960291237 1.178477697 1.003754283 1.067528994 0.948484821 1 16.93595775 EFQLWEEQLHSYPHK ddPTM_BT-474_Pertuzumab_2h_R1 1 EFQLWEEQLHSYPHK 15 0 P49750;H0YIQ2;F8VU51 P49750 YLPM1 YLP motif-containing protein 1 0 149.3 1.96E-06 55693000 59767 64701 64310 74685 65451 68956 68973 4655.2 80412 70401 FALSE TRUE 57431.23956 62855.79083 75932.24757 78539.5018 67556.29086 70350.33757 69817.11221 4559.068493 71283.96687 65632.67756 0.875040326 0.957690485 1.156927469 1.19665241 1.029308774 1.071879743 1.063755355 0.069463393 1.086104811 1 16.00212667 EFTMAEIEHFVDPSEKDHPK ddPTM_BT-474_Pertuzumab_2h_R1 4 EFTMAEIEHFVDPSEKDHPK 20 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 307.22 3.65E-56 1551390000 1847200 1531740 1583280 1541280 1699900 1643780 1857370 826260 2415130 2140860 FALSE TRUE 1775009.382 1488056.275 1869413.916 1620825.646 1754578.827 1677018.358 1880101.05 809197.4423 2140974.567 1995857.645 0.889346686 0.74557235 0.93664692 0.812094815 0.879110207 0.840249485 0.942001577 0.405438456 1.072709054 1 20.92857739 EGAGGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGAGGLR 7 0 Q9H1J1;Q9H1J1-2;A0A087WZ33 Q9H1J1 UPF3A Regulator of nonsense transcripts 3A 0 88.734 0.069045 0 102060 89443 91004 104460 99834 96305 96031 97698 115000 116420 FALSE TRUE 98071.38237 86892.17321 107450.4472 109851.1931 103045.2513 98252.35308 97206.2561 95680.50216 101945.6821 108534.7697 0.903594144 0.800592966 0.990009446 1.012129048 0.949421568 0.905261543 0.895623185 0.881565441 0.939290537 1 16.72779777 EGDIVKR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGDIVKR 7 1 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 81.297 0.044229 1126400000 1183200 1766800 993370 2029100 1021600 1333800 2007800 1678400 1560200 1121800 FALSE TRUE 1136959.236 1716412.594 1172894.056 2133822.094 1054460.692 1360770.35 2032372.057 1643740.453 1383092.637 1045819.487 1.087146731 1.641213054 1.121507173 2.040334992 1.008262616 1.301152223 1.943329688 1.571724828 1.322496525 1 19.99620243 EGDYVLFHHEGGVDVGDVDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 EGDYVLFHHEGGVDVGDVDAK 21 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 156.39 8.95E-09 1644850000 2408200 2164400 2024360 2205030 2397200 2489900 2585700 625470 3280000 2894700 FALSE TRUE 2314084.882 2102673.431 2390206.884 2318831.863 2474308.115 2540247.484 2617344.57 612553.8259 2907668.151 2698639.391 0.857500594 0.779160579 0.885708143 0.859259622 0.916872452 0.941306754 0.969875627 0.226986172 1.077457092 1 21.36380078 EGLISQDGSSLEALLR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGLISQDGSSLEALLR 16 0 Q92785;J3KMZ8;Q92785-2 Q92785 DPF2 Zinc finger protein ubi-d4 0 86.313 0.01594 13311000 14355 16588 13186 16710 13567 15889 15022 19167 16118 16920 FALSE TRUE 13793.99073 16114.92648 15569.00352 17572.4051 14003.39488 16210.28647 15205.84373 18771.19475 14288.35221 15773.99333 0.87447677 1.021613623 0.987004571 1.114011191 0.887752048 1.027659016 0.963981879 1.190009046 0.905817057 1 13.94526032 EGS(ph)PYEAPVYIPEDIPIPADFELR ddPTM_BT-474_Pertuzumab_2h_R1 1 EGSPYEAPVYIPEDIPIPADFELR 24 0 D6RFY3;D6RDW0;Q9HAZ2-2;Q9HAZ2-3;Q9HAZ2 D6RFY3 PRDM16 PR domain zinc finger protein 16 1 EGS(0.792)PY(0.202)EAPVY(0.007)IPEDIPIPADFELR 59.282 0.048216 11073000 8030.1 6480.2 6134.6 7085.1 4667.7 6695.7 5790.3 6674.9 7103.7 7496 TRUE FALSE 7716.274814 6295.391041 7243.258683 7450.76286 4817.84081 6831.091642 5861.163423 6537.060982 6297.317757 6988.289243 1.104172215 0.900848666 1.036485244 1.066178374 0.689416342 0.977505567 0.838712197 0.935430798 0.901124372 1 12.77072361 EHDPVGQMVNNPK ddPTM_BT-474_Pertuzumab_2h_R1 6 EHDPVGQMVNNPK 13 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;;;; 194.24 1.18E-06 5003250000 7371250 7479100 6290670 6888580 7121880 7920230 7419480 5329930 9185040 8376080 FALSE TRUE 7083173.401 7265803.391 7427534.004 7244100.439 7350961.738 8080382.477 7510281.816 5219865.083 8142392.766 7808760.641 0.907080358 0.930468191 0.951179623 0.927688883 0.94137368 1.034784244 0.961776415 0.668462682 1.042725362 1 22.89666216 EHDQLIEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHDQLIEK 8 0 O14980 O14980 XPO1 Exportin-1 0 ;;; 122.28 0.0013971 4377580000 8323800 8009300 7100600 7035700 7748900 7390100 8053900 4467060 9656700 8583700 FALSE TRUE 7998496.694 7780882.606 8383836.372 7398813.32 7998150.406 7539532.885 8152466.037 4374813.65 8560511.9 8002318.353 0.999522431 0.972328551 1.047675936 0.924583726 0.999479157 0.942168576 1.018763023 0.546693278 1.069753979 1 22.93198659 EHELLEQQKR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHELLEQQKR 10 1 Q13435;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;; 208.6 7.19E-08 1542320000 2047610 1881430 1646280 1645060 1741430 1758460 1881470 889400 2191430 1907950 FALSE TRUE 1967587.137 1827773.459 1943799.417 1729961.744 1797444.677 1794017.266 1904495.993 871033.5792 1942668.054 1778722.847 1.106179718 1.027576309 1.092806235 0.972586452 1.010525434 1.00859854 1.070709805 0.489696065 1.092170181 1 20.7624103 EHEVFQR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHEVFQR 7 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;; 176.65 0.00074396 3858170000 3208460 3330900 2987400 3520080 3178110 3421370 3492000 1628720 3693780 3730980 FALSE TRUE 3083069.836 3235905.993 3527289.634 3701751.751 3280336.794 3490552.446 3534736.141 1595086.363 3274477.58 3478277.401 0.886378365 0.930318551 1.01409095 1.06424857 0.943092346 1.003529058 1.01623181 0.45858515 0.94140783 1 21.72994157 EHEVTIFVR ddPTM_BT-474_Pertuzumab_2h_R1 4 EHEVTIFVR 9 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;; 196.88 2.89E-05 5659400000 2113070 1992970 1980650 2480200 2256210 2167010 2451370 1188290 2551050 2607170 FALSE TRUE 2030488.888 1936132.447 2338597.514 2608203.419 2328783.044 2210828.427 2481370.599 1163751.396 2261465.499 2430584.054 0.835391348 0.796570867 0.962154553 1.073076825 0.958116647 0.909587317 1.020894791 0.478794961 0.93042061 1 21.2128716 EHEWFK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHEWFK 6 0 Q13131-2;Q13131;A0A087WXX9;P54646 Q13131-2;A0A087WXX9 PRKAA1;PRKAA2 5-AMP-activated protein kinase catalytic subunit alpha-1;5-AMP-activated protein kinase catalytic subunit alpha-2 0 ; 121.87 0.019465 565050000 1424270 1414300 1146360 1353490 1391080 1436870 1424590 773750 1633950 1526240 FALSE TRUE 1368607.954 1373965.549 1353532.753 1423343.781 1435825.352 1465924.496 1442024.559 757771.7921 1448470.846 1422866.405 0.961866798 0.965632152 0.951271846 1.000335503 1.009107634 1.030261513 1.013464478 0.53256707 1.017994972 1 20.44036878 EHFQDDVFNEK ddPTM_BT-474_Pertuzumab_2h_R1 6 EHFQDDVFNEK 11 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;;; 215.77 1.26E-11 4528550000 8110890 8248970 7515940 8325630 8316440 8096720 8822140 6198150 10233300 9286060 FALSE TRUE 7793907.452 8013717.452 8874237.549 8755316.762 8583945.845 8260441.226 8930107.988 6070156.037 9071658.685 8657106.885 0.90029008 0.92568078 1.025081204 1.011344422 0.99154902 0.954180344 1.031534912 0.701176053 1.04788572 1 23.04545354 EHFQSYDLDHMEK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHFQSYDLDHMEK 13 0 Q13564-2;Q13564;Q13564-4;Q13564-3;H3BMR3;J3QRA5 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ;;; 226.19 6.47E-12 1538090000 1346680 1292860 1184840 1346150 1324900 1374720 1485510 324346 1617520 1406410 FALSE TRUE 1294050.257 1255988.899 1398966.945 1415624.963 1367516.612 1402517.78 1503690.116 317648.1418 1433905.911 1311152.598 0.986956254 0.957927323 1.066974925 1.079679791 1.042988142 1.069683104 1.146846003 0.242266341 1.093622446 1 20.32240417 EHGVLGGK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHGVLGGK 8 0 O95865;A0A140T971;Q5SSV3;Q5SRR8 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ;;; 82.452 0.020235 1712840000 3654780 3762990 3183850 3526530 3586770 3683390 3799660 2841730 4371860 4110240 FALSE TRUE 3511947.157 3655673.21 3759242.519 3708534.636 3702141.714 3757870.669 3846161.376 2783047.282 3875584.781 3831849.784 0.916514831 0.9540231 0.981051641 0.967818376 0.966150012 0.980693629 1.003734904 0.726293419 1.011413547 1 21.86960957 EHLIDELDYILLPTEGWNK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHLIDELDYILLPTEGWNK 19 0 Q9Y4E8;F8W0H4;H0YI31;Q9Y4E8-4;F8VZG8;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 91.957 0.0019935 155040000 337930 334610 297660 353260 322940 314290 342300 209620 450550 417070 FALSE TRUE 324723.322 325067.2504 351453.7834 371491.7909 333327.6584 320645.1591 346489.1698 205291.2737 399405.4529 388821.4774 0.835147596 0.836032136 0.903894985 0.955430223 0.857276868 0.824659073 0.891126622 0.527983369 1.027220655 1 18.56874839 EHMGDILYK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHMGDILYK 9 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;;; 121.73 0.0006056 1374470000 4272210 4582860 3914460 4485750 4360440 4767450 4754590 2779790 5624100 5596700 FALSE TRUE 4105247.31 4452161.32 4621889.999 4717260.095 4500697.513 4863851.105 4812778.095 2722386.365 4985675.746 5217630.524 0.786802992 0.853291796 0.885821634 0.904100065 0.86259414 0.932195387 0.922406842 0.521766797 0.955544039 1 22.31496336 EHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQR 34 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 0 109.81 6.95E-06 124710000 54225 69366 53804 44719 58252 69898 59956 54455 75619 60935 FALSE TRUE 52105.82705 67387.7496 63527.57966 47026.95295 60125.72848 71311.38545 60689.75946 53330.48522 67035.04814 56807.81817 0.917229859 1.186240763 1.118289378 0.827825367 1.058405875 1.255309353 1.068334631 0.938787775 1.180032085 1 15.79380187 EHQETKPVKEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EHQETKPVKEEK 12 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 0 88.087 0.006116 164600000 226190 195690 160950 145600 190240 221320 181200 134970 292160 236370 FALSE TRUE 217350.2447 190109.1128 190037.2453 153114.4334 196359.2424 225795.242 183417.5798 132182.8223 258995.2216 220360.4494 0.986339633 0.862718847 0.862392711 0.694836273 0.891082056 1.024663195 0.83235254 0.599848216 1.175325347 1 17.74950578 EHS(ph)PYGPSPLGWPSSETR ddPTM_BT-474_Pertuzumab_2h_R1 1 EHSPYGPSPLGWPSSETR 18 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 EHS(1)PYGPSPLGWPSSETR 160.3 2.64E-11 101260000 39305 71989 44351 66796 46214 46106 57270 42610 58375 45851 TRUE FALSE 37768.91715 69935.9442 52366.21228 70243.34956 47700.51528 47038.29491 57970.88739 41730.08861 51748.51473 42745.47093 0.883577051 1.636101853 1.225070426 1.643293384 1.115919751 1.100427575 1.356187828 0.97624585 1.210619829 1 15.38348395 EHSLQVS(ph)PSLEK ddPTM_BT-474_Pertuzumab_2h_R1 3 EHSLQVSPSLEK 12 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 EHSLQVS(0.986)PS(0.014)LEK;EHSLQVS(0.998)PS(0.002)LEK;EHSLQVS(1)PSLEK 255.21 2.53E-21 1718040000 2819560 2854560 2976070 2870470 2998230 3482090 3316160 2070290 3404380 3549100 TRUE FALSE 2709368.478 2773150.744 3513912.051 3018615.301 3094670.791 3552500.246 3356744.158 2027537.788 3017929.055 3308716.296 0.8188579 0.838134943 1.062016727 0.912322191 0.935308595 1.073679315 1.014515558 0.612786835 0.912114786 1 21.65784016 EHTIEEWK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHTIEEWK 8 0 A0A286YFJ4;A0A286YFC0;P53779-2;A0A286YEW9;A0A1P0B7D2;A0A286YEX7;P53779;D6RDG1;A0A286YF85;A0A286YF97;A0A286YFA6;A0A286YF62;F8W9R5;A0A286YFJ6;A0A286YEQ0;A0A286YEQ7;D6RJF9;A0A286YFI3;A0A286YES9;A0A286YEN5;A0A286YFM6;A0A286YFN2;A0A286YFD7;A0A286YFB6;A0A286YES0;A0A286YEV8;A0A286YF02;P53779-3;P45983;P45983-4;P45983-3;P45983-2;A0A286YES8;P45983-5 A0A286YFJ4 MAPK10;MAPK8 Mitogen-activated protein kinase 10;Mitogen-activated protein kinase 8 0 ; 175.44 0.00026609 368510000 752160 773970 631920 689480 723680 774360 785800 519210 897820 867290 FALSE TRUE 722764.7556 751897.1334 746122.001 725064.1454 746957.8244 790018.0898 795416.8555 508488.1321 795903.2376 808547.6758 0.893904933 0.929935433 0.922792834 0.896748784 0.923826568 0.977082878 0.983759992 0.628890723 0.984361543 1 19.62497332 EHVEEISELFYDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 EHVEEISELFYDAK 14 0 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 ;;; 206.18 1.12E-08 1605750000 1758990 1692770 1548860 1652060 1677750 1742350 1846370 1343590 2187590 2095050 FALSE TRUE 1690246.726 1644493.857 1828773.456 1737323.015 1731716.352 1777581.511 1868966.428 1315844.397 1939263.954 1953150.397 0.865395071 0.841969906 0.936319834 0.889497817 0.886627243 0.910109899 0.956898368 0.673703571 0.992890234 1 20.89737161 EHYPNGVCTVYGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EHYPNGVCTVYGK 13 0 P47755;F8W9N7;A0A0D9SET8 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ; 122.34 0.00023618 584280000 1578980 1680600 1347990 1616900 1583980 1557600 1727440 1225190 1951030 1945720 FALSE TRUE 1517271.716 1632670.933 1591601.779 1700348.403 1634930.155 1589095.739 1748580.927 1199889.398 1729557.254 1813934.651 0.83645335 0.900071528 0.877430605 0.93738129 0.901317009 0.876049056 0.963971291 0.661484358 0.953483772 1 20.79069105 EIAEAYLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 EIAEAYLGK 9 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 152.47 0.00018705 894430000 868230 948270 868480 1018520 816990 596750 1138610 1160490 1199310 1382200 FALSE TRUE 834298.6117 921226.2681 1025433.655 1071085.939 843269.2253 608816.6939 1152544.65 1136525.476 1063169.357 1288582.363 0.647454626 0.714914541 0.795784332 0.831212633 0.65441624 0.472470143 0.894428391 0.881996765 0.825068996 1 20.29735332 EIAQDFK ddPTM_BT-474_Pertuzumab_2h_R1 1 EIAQDFK 7 0 K7EK07;Q71DI3;Q16695;P84243;P68431;K7EMV3;A0A590UJJ6;B4DEB1;K7ES00 K7EK07 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1 0 93.429 0.034761 501270000 1010900 970170 820450 1356400 771560 768120 1235000 988220 1277800 847090 FALSE TRUE 971392.9104 942501.7015 968723.5658 1426403.967 796377.9281 783651.9127 1250114.299 967812.9117 1132749.501 789715.8398 1.230053725 1.193469415 1.226673592 1.806224334 1.008436058 0.992321381 1.582992561 1.22552045 1.434376068 1 19.5909741 EIEQEAAVELSQLRDPQHDLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EIEQEAAVELSQLRDPQHDLDR 22 1 P47985 P47985 UQCRFS1 "Cytochrome b-c1 complex subunit Rieske, mitochondrial;Cytochrome b-c1 complex subunit 11" 0 ;; 236.93 9.96E-31 862990000 108526 214123 99905 294489 92524 136969 222461 187650 154993 86454 FALSE TRUE 104284.6839 208016.4217 117960.0559 309687.6126 95500.11849 139738.607 225183.5443 183774.9619 137398.8444 80598.39357 1.293880428 2.580900344 1.463553436 3.842354653 1.184888609 1.733764171 2.793896184 2.280131821 1.70473428 1 16.29846346 EITALAPSTMK ddPTM_BT-474_Pertuzumab_2h_R1 2 EITALAPSTMK 11 0 P60709;P63267-2;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ; 171.85 3.27E-05 1406320000 2691170 2811700 2287130 2528130 2428850 2193800 2796310 2745570 3029800 2908640 FALSE TRUE 2585996.101 2731513.069 2700465.268 2658607.092 2506976.166 2238160.139 2830532.078 2688873.02 2685869.806 2711635.222 0.953666658 1.007330576 0.995880731 0.980444224 0.924525595 0.825391307 1.043846921 0.991605729 0.9904982 1 21.37073168 EITLENKDNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 EITLENKDNIR 11 1 Q9NT62;Q9NT62-2;C9JNW8 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 131.17 0.00019048 335670000 301330 384680 231740 286240 301120 398270 282100 331650 379950 365500 FALSE TRUE 289553.6905 373709.303 273620.573 301012.8807 310805.7983 406323.2923 285552.4242 324801.3116 336819.6689 340744.3594 0.84976811 1.096743916 0.803008371 0.883397985 0.912137764 1.192457868 0.838025388 0.953211117 0.988482009 1 18.37833025 EIYEELGRPGEEDLD ddPTM_BT-474_Pertuzumab_2h_R1 2 EIYEELGRPGEEDLD 15 1 A6NHN7;A6NHB5;Q14202-2;Q14202 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 0 ; 122.7 0.00087495 447838000 424879 439172 324757 458776 427269 392753 406954 454682 461364 437775 FALSE TRUE 408274.259 426647.2446 383447.8141 482453.4843 441012.4954 400694.7348 411934.4248 445292.6578 408991.8929 408124.1093 1.000367902 1.045386035 0.939537276 1.18212444 1.080584277 0.981796286 1.009336169 1.09107168 1.002126274 1 18.63864841 EKEELMLR ddPTM_BT-474_Pertuzumab_2h_R1 6 EKEELMLR 8 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 145.72 0.00051509 5944770000 8151360 8028620 6831880 7349710 6541760 6068420 8076080 8569050 8484370 8946540 FALSE TRUE 7832795.839 7799651.618 8066552.69 7729029.414 6752181.651 6191127.61 8174917.483 8392096.123 7521259.887 8340582.877 0.939118519 0.93514467 0.96714496 0.926677371 0.809557527 0.742289562 0.980137432 1.006176217 0.901766699 1 22.99171678 EKEPEYTLLTER ddPTM_BT-474_Pertuzumab_2h_R1 4 EKEPEYTLLTER 12 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ;;; 89.992 0.0083094 572230000 1247100 1111860 1426020 1044430 1175450 1139130 1263460 1312250 1318640 1376970 FALSE TRUE 1198361.953 1080150.841 1683733.536 1098333.157 1213259.417 1162163.989 1278922.601 1285151.579 1168953.515 1283706.595 0.933517018 0.841431247 1.311618669 0.855595166 0.945122056 0.905319014 0.996273296 1.001125634 0.910608016 1 20.29188407 EKEQEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 EKEQEDR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;; 112.41 0.0058006 541633000 2010720 1828890 1552680 1696130 1694700 1714120 2071630 1918160 1704700 2161630 FALSE TRUE 1932138.839 1776731.848 1833283.815 1783667.473 1749211.565 1748780.681 2096983.228 1878549.326 1511189.603 2015220.875 0.95877274 0.881656135 0.909718552 0.885097755 0.867999923 0.867786109 1.040572403 0.932180363 0.749887827 1 20.94250654 EKLEMEMEAAR ddPTM_BT-474_Pertuzumab_2h_R1 9 EKLEMEMEAAR 11 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;;;;; 174.9 9.54E-06 14926940000 12940980 12880530 10803430 11388560 12072060 10391360 13372080 13625850 14497020 14174870 FALSE TRUE 12435232.19 12513189.9 12755850.12 11976324.95 12460368.77 10601480.42 13535731.52 13344471.44 12851379.07 13214793.43 0.941008443 0.946907718 0.965270489 0.906281662 0.942910598 0.80224337 1.024286273 1.009813094 0.972499429 1 23.65565054 EKQAFER ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQAFER 7 1 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 78.516 0.032033 264820000 367140 395540 304940 309460 338580 388710 335780 409380 389700 369730 FALSE TRUE 352791.7629 384259.5865 360049.4414 325431.2677 349470.7332 396569.9825 339889.3761 400926.1599 345462.8898 344687.8578 1.023510852 1.114804533 1.044566651 0.944133251 1.013875961 1.150519154 0.986078762 1.16315719 1.002248504 1 18.39493095 EKQPMVPESLADYITAAYVEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 EKQPMVPESLADYITAAYVEMR 22 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 198.39 1.73E-22 255800000 377760 344390 294370 311960 328030 372800 345190 360270 383010 373970 FALSE TRUE 362996.7216 334568.3344 347569.2072 328060.293 338581.3829 380338.2714 349414.5385 352830.2986 339532.3105 348640.6788 1.041177188 0.959636539 0.996926717 0.940969637 0.971147096 1.090917654 1.002219648 1.012017014 0.973874626 1 18.41138138 ELAAEVEVQDGPNEDGEMFMRPGK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELAAEVEVQDGPNEDGEMFMRPGK 24 1 P08574 P08574 CYC1 "Cytochrome c1, heme protein, mitochondrial" 0 219.04 1.02E-32 115970000 54134 87331 54483 173000 42281 57336 138870 115290 93902 62295 FALSE TRUE 52018.38343 84840.40539 64329.29007 181928.5507 43641.00676 58495.3732 140569.5326 112909.2212 83242.63863 58075.70416 0.895699573 1.460858833 1.107679898 3.132610329 0.751450325 1.007226241 2.420453348 1.94417309 1.433347039 1 15.82564712 ELAPYDENWFYTR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELAPYDENWFYTR 13 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;; 287.57 8.39E-33 6861520000 656400 716940 637980 776780 623850 638450 780030 706300 703131 749600 FALSE TRUE 630747.1623 696493.5732 753277.1778 816869.7089 643916.7018 651359.8964 789576.2405 691714.6582 623314.5166 698828.9243 0.902577355 0.996658193 1.077913566 1.168912277 0.92142251 0.932073464 1.129856268 0.989819731 0.891941497 1 19.4145798 ELDRYS(ph)LDSEDLYSR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELDRYSLDSEDLYSR 15 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 ELDRYS(0.942)LDS(0.057)EDLYS(0.001)R;ELDRYS(1)LDSEDLYSR;ELDRYS(1)LDSEDLYSR 286.55 1.82E-34 623090000 806339 768697 467177 589481 862368 518866 581319 939728 719590 667178 TRUE FALSE 774826.3804 746774.5142 551606.2762 619904.1851 890106.8499 529357.826 588433.3558 920322.2884 637905.16 621989.4398 1.245722726 1.200622497 0.886841867 0.996647443 1.431064248 0.851072047 0.946050396 1.479642948 1.025588409 1 19.24653056 ELEAELEDER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEAELEDER 10 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 136.63 0.00026164 348590000 493140 537850 429090 512190 498300 561280 482240 500860 538180 541450 FALSE TRUE 473867.5436 522511.0446 506636.1081 538624.1873 514328.272 572629.4662 488141.7974 490517.066 477088.0626 504777.1092 0.938765913 1.03513221 1.003682811 1.067053512 1.018921545 1.134420432 0.967044243 0.971749822 0.945145994 1 18.94528696 ELEDDEQFVSLYGTEEYLHPDMYER ddPTM_BT-474_Pertuzumab_2h_R1 2 ELEDDEQFVSLYGTEEYLHPDMYER 25 0 A0A494C0X2;A0A494C167;A0A494C045;Q9UHD2;A0A494C1I2;A0A494C079;A0A494C0R4;A0A494C0A8;A0A494C1M6;A0A494C148 A0A494C0X2 TBK1 Serine/threonine-protein kinase TBK1 0 ; 237.32 1.82E-38 110015000 38063 42159 30973 40223 39899 38449 42726 37476 42885 48427 FALSE TRUE 36575.45588 40956.6666 36570.51009 42298.91385 41182.38757 39226.46512 43248.89357 36702.1075 38016.87459 45146.99616 0.810141515 0.907184754 0.810031967 0.936915353 0.912184444 0.86886102 0.957957278 0.812946832 0.842068749 1 15.46234238 ELPQLVASVIESESEILHHEK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELPQLVASVIESESEILHHEK 21 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ;;; 212.18 6.31E-23 161638000 282294 338651 293385 332806 348704 373205 384579 113619.1 444503 420079 FALSE TRUE 271261.6384 328993.0051 346406.1958 349982.1575 359920.3808 380751.4608 389285.5928 111272.8259 394044.8829 391626.6752 0.692653631 0.840067917 0.884531667 0.893662714 0.919039493 0.97223066 0.994022158 0.284129843 1.006174778 1 18.57911951 ELQQAELPNRS(ph)PGFGIK ddPTM_BT-474_Pertuzumab_2h_R1 4 ELQQAELPNRSPGFGIK 17 1 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK 223.07 1.91E-15 1641920000 2178450 2189900 1607640 1839890 2110590 2082700 1944320 2153090 2199860 2163870 TRUE FALSE 2093313.766 2127446.196 1898176.31 1934846.943 2178479.044 2124813.621 1968115.17 2108627.939 1950141.115 2017309.158 1.037676232 1.054596014 0.940944675 0.959122669 1.079893499 1.05329102 0.975614056 1.045267619 0.966704141 1 20.94400077 ELQREPLTPEEVQSVR ddPTM_BT-474_Pertuzumab_2h_R1 3 ELQREPLTPEEVQSVR 16 1 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BUG4 Q6FI81-3 CIAPIN1 Anamorsin 0 ;; 217.88 1.26E-14 734050000 528720 576600 400991 525080 512580 572830 507960 576290 582700 521390 FALSE TRUE 508057.0379 560155.9326 473458.9937 552179.4417 529067.6012 584413.0151 514176.5664 564389.4101 516554.3389 486075.7909 1.045221851 1.152404508 0.97404356 1.135994534 1.088446722 1.202308418 1.05781151 1.161114009 1.062703283 1 18.89082176 ELSLAGNELGDEGAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ELSLAGNELGDEGAR 15 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 133.98 8.84E-05 130100000 120740 117200 94413 119360 120890 109770 113090 116560 109750 136600 FALSE TRUE 116021.3473 113857.5708 111475.5293 125520.1839 124778.5366 111989.6246 114474.0292 114152.9953 97291.64011 127347.9603 0.911057759 0.894066701 0.875361718 0.985647384 0.979823598 0.879398652 0.898907442 0.896386522 0.763982712 1 16.95841633 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(ph)SPQRDDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQRDDLK 42 2 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(0.551)S(0.449)PQRDDLK 136.46 8.03E-10 1128500000 110330 110870 114900 106680 121200 114680 117860 16074 155770 106240 TRUE FALSE 106018.1816 107708.0962 135664.9859 112185.7676 125098.5081 116998.9082 119302.4059 15742.06628 138087.6426 99044.27017 1.070412064 1.087474278 1.369740882 1.132683066 1.263056488 1.181278917 1.204536171 0.158939697 1.394201223 1 16.5957859 ELVEPLT(ph)PSGEAPNQALLR ddPTM_BT-474_Pertuzumab_2h_R1 4 ELVEPLTPSGEAPNQALLR 19 0 P00533;E9PFD7;Q504U8 P00533 EGFR Epidermal growth factor receptor;Receptor protein-tyrosine kinase 1 ELVEPLT(1)PSGEAPNQALLR;ELVEPLT(0.816)PS(0.184)GEAPNQALLR;ELVEPLT(0.994)PS(0.006)GEAPNQALLR;ELVEPLT(1)PSGEAPNQALLR 300.28 7.65E-49 1121320000 645970 1368040 536100 1605930 671800 671670 886920 1001280 590340 285147 TRUE FALSE 620724.7782 1329024.839 632985.1955 1688812.24 693409.0571 685251.6276 897774.3923 980603.2181 523327.0781 265833.7397 2.33501127 4.999458835 2.381131892 6.352888996 2.608431337 2.577745129 3.377202583 3.688783896 1.968625498 1 18.0201647 ELWDSIMTR ddPTM_BT-474_Pertuzumab_2h_R1 2 ELWDSIMTR 9 0 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 88.921 0.028981 149392000 258871 308949 247633 271344 307436 246848 307033 287116 332173 330266 FALSE TRUE 248754.0351 300138.077 292385.7917 285348.0964 317324.9581 251839.4357 310790.5617 281186.9543 294466.1136 307896.7896 0.807913702 0.97480093 0.949622736 0.926765416 1.030621198 0.817934594 1.009398513 0.913250686 0.956379292 1 18.2320873 EMEKGS(ph)PSLRH ddPTM_BT-474_Pertuzumab_2h_R1 3 EMEKGSPSLRH 11 2 F5GXK4;B9A071;Q9P2M4-2;Q9P2M4 F5GXK4 TBC1D14 TBC1 domain family member 14 1 EMEKGS(0.996)PS(0.004)LRH;EMEKGS(0.997)PS(0.003)LRH;EMEKGS(0.989)PS(0.011)LRH 121.18 0.00021754 356900000 326070 371740 278142 307840 333004 372050 309314 346549 350045 352950 TRUE FALSE 313326.8239 361138.3392 328408.4466 323727.6593 343715.3761 379573.1059 313099.4773 339392.642 310309.3591 329044.3821 0.952232711 1.097536864 0.998067326 0.983841928 1.044586672 1.153562032 0.951541781 1.031449435 0.943062322 1 18.32792266 EMGTPLADT(ph)PTRPVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 EMGTPLADTPTRPVTR 16 1 Q9BPU6 Q9BPU6 DPYSL5 Dihydropyrimidinase-related protein 5 1 EMGTPLADT(0.999)PT(0.001)RPVTR;EMGTPLADT(1)PTRPVTR 178.71 4.44E-09 783680000 165865 161037 166522 172259 157755 165169 182902 201355 143246 180264 TRUE FALSE 159382.8124 156444.3824 196616.2297 181149.3076 162829.3328 168508.8303 185140.4094 197196.9489 126985.3146 168054.5587 0.94839922 0.930914244 1.169954753 1.077919629 0.968907562 1.00270312 1.101668475 1.173410292 0.755619577 1 17.35857015 EMTHLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 EMTHLQK 7 0 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 107.43 0.0074794 420410000 391490 411760 329670 373030 366310 415920 399640 402250 423360 448270 FALSE TRUE 376190.138 400017.008 389248.7025 392282.123 378092.6938 424330.1874 404530.9139 393943.3969 375301.9477 417908.2736 0.900173942 0.957188534 0.931421384 0.938679963 0.90472651 1.015366802 0.967989723 0.942655175 0.898048618 1 18.6728268 EMTNHQK ddPTM_BT-474_Pertuzumab_2h_R1 4 EMTNHQK 7 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 124.59 0.0041312 833810000 646460 669330 550620 701560 634440 639710 737850 681330 697920 832850 FALSE TRUE 621195.6285 650241.3637 650129.2825 737767.5957 654847.3388 652645.3745 746880.029 667260.2974 618695.0475 776440.3277 0.800055853 0.837464697 0.837320344 0.950192268 0.843396866 0.840560892 0.961928435 0.859383875 0.796835282 1 19.56651553 ENENGEEEEEEAEFGEEDLFHQQGDPR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENENGEEEEEEAEFGEEDLFHQQGDPR 27 0 Q03252 Q03252 LMNB2 Lamin-B2 0 133.75 2.99E-05 222880000 126940 131140 123500 142160 124490 136190 121290 126130 153160 168890 FALSE TRUE 121979.0445 127400.0156 145819.1972 149496.8946 128494.3339 138943.8551 122774.3833 123525.3714 135773.9189 157450.9299 0.77471149 0.809141081 0.926124713 0.94948245 0.816091299 0.882458143 0.779762834 0.784532499 0.862325291 1 17.26454275 ENNS(ph)PEHLKDEVSIIQSMGYR ddPTM_BT-474_Pertuzumab_2h_R1 1 ENNSPEHLKDEVSIIQSMGYR 21 1 P38398-7;P38398;P38398-4;P38398-8;P38398-6;E7EUM2;B7ZA85;H0Y8B8;P38398-5;P38398-3;Q5YLB2;H0Y8D8;Q3B891;E9PH68;A0A494C182;E7EWN5;H0Y881;A0A0U1RRA9;E7EQW4 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 ENNS(1)PEHLKDEVSIIQSMGYR 191.51 8.56E-18 72867000 68352 66973 58297 61521 62454 57290 72284 70029 62357 71602 TRUE FALSE 65680.72827 65062.99561 68832.56471 64696.10618 64462.88963 58448.44305 73168.63321 68582.87668 55278.49478 66752.33276 0.983946561 0.974692463 1.031163434 0.969196184 0.965702425 0.875601505 1.096120992 1.02742292 0.828113303 1 16.02653063 ENPYYDSR ddPTM_BT-474_Pertuzumab_2h_R1 4 ENPYYDSR 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 200.54 0.00027688 9708970000 9057170 9380080 8526110 8969360 9298300 9176410 9363800 9454680 10472670 10931120 FALSE TRUE 8703205.783 9112569.302 10066967.74 9432269.744 9597388.264 9361963.297 9478396.985 9259437.554 9283856.407 10190745.51 0.854030334 0.894200458 0.987853905 0.925572103 0.941774894 0.918673054 0.930098488 0.908612383 0.911008562 1 23.28075626 EPAAAISRPR ddPTM_BT-474_Pertuzumab_2h_R1 4 EPAAAISRPR 10 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 189.58 9.08E-07 1089220000 678750 685110 613760 717940 630140 629890 672230 730740 667420 697290 FALSE TRUE 652223.6996 665571.3336 724680.085 754992.9694 650409.0254 642626.8074 680456.9518 715649.9636 591657.2797 650061.9272 1.003325487 1.023858352 1.11478623 1.161416994 1.000533946 0.988562444 1.046757122 1.100895059 0.910155256 1 19.31021764 EPFFHGHDNYDQLVR ddPTM_BT-474_Pertuzumab_2h_R1 4 EPFFHGHDNYDQLVR 15 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ;;; 275.23 9.70E-34 2198700000 639079 664705 612879 903499 765349 688967 862510 245349 901720 909750 FALSE TRUE 614103.0861 645748.2642 723639.8687 950128.6917 789967.1457 702898.3848 873065.6554 240282.4574 799360.5259 848131.8222 0.724065611 0.761377238 0.853216269 1.120260633 0.93142024 0.828760773 1.029398535 0.283307914 0.942495618 1 19.69392899 EPTPSIAS(ph)DISLPIATQELR ddPTM_BT-474_Pertuzumab_2h_R1 4 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 EPTPSIAS(1)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR 273.33 1.98E-44 641010000 183238 307016 156927 318821 210026 208855 235524 334961 241772 193861 TRUE FALSE 176076.8564 298260.2043 185287.1997 335275.39 216781.677 213078.1912 238406.4132 328043.9383 214327.0562 180730.6218 0.974250266 1.65030254 1.025211986 1.855111141 1.199473973 1.178982228 1.319125729 1.81509882 1.185892319 1 17.46348144 EQDYLCHVYVR ddPTM_BT-474_Pertuzumab_2h_R1 5 EQDYLCHVYVR 11 0 O15498;O15498-2 O15498 YKT6 Synaptobrevin homolog YKT6 0 ;;;; 201 4.49E-08 2519460000 2506910 3111510 2440770 2967220 2737790 2343690 3099360 3037110 3062570 2955850 FALSE TRUE 2408937.186 3022772.781 2881871.434 3120358.58 2825853.502 2391081.018 3137290.895 2974392.617 2714919.893 2755647.647 0.87418186 1.096937333 1.045805489 1.132350351 1.02547708 0.867702016 1.138494937 1.079380602 0.985220261 1 21.39396 EQHDAQVR ddPTM_BT-474_Pertuzumab_2h_R1 6 EQHDAQVR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;;;;; 174.41 0.00027212 1656959000 795415 970319 706460 1130309 748097 696102 980294 811834 983397 965679 FALSE TRUE 764329.3024 942646.4522 834133.0371 1188644.383 772160.2194 710177.6594 992291.1312 795069.3442 871765.8953 900272.7012 0.848997533 1.047067684 0.926533745 1.320315924 0.857695916 0.788847266 1.10221173 0.883142789 0.968335366 1 19.78000255 EQLEQAHSHRPSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQLEQAHSHRPSGK 14 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 0 57.136 0.076905 112280000 153870 177020 165090 189260 180050 180490 193440 101660 200110 200680 FALSE TRUE 147856.5903 171971.5629 194925.4354 199027.7313 185841.4718 184139.6315 195807.3766 99560.68547 177394.3517 187087.7649 0.790306038 0.919202616 1.041893015 1.063820135 0.993338458 0.984241977 1.046607066 0.532160324 0.948187883 1 17.51335569 EQS(ph)PSQHGKDPASLLASELVQLHMQLEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 EQSPSQHGKDPASLLASELVQLHMQLEEK 29 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 EQS(0.826)PS(0.174)QHGKDPASLLASELVQLHMQLEEK 145.47 3.70E-08 137380000 186830 188870 160610 143620 160950 198560 178470 154690 225180 204770 TRUE FALSE 179528.477 183483.6125 189635.7998 151032.2454 166127.1029 202575.0192 180654.1692 151495.5974 199618.5104 190900.7455 0.940428371 0.961146653 0.993373804 0.79115587 0.870227628 1.061153631 0.946325111 0.793583058 1.045666479 1 17.54246321 EQSIFGDHRDEEEETHMKK ddPTM_BT-474_Pertuzumab_2h_R1 2 EQSIFGDHRDEEEETHMKK 19 2 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 ; 115.15 4.62E-05 720940000 977200 964300 783280 779180 916690 1037730 964860 712490 1224880 1045000 FALSE TRUE 939009.9436 936799.1081 924836.12 819393.5732 946176.1664 1058713.612 976668.2453 697776.8325 1085836.758 974221.2192 0.963857002 0.961587666 0.949308126 0.841075473 0.97121285 1.086728138 1.002511777 0.716240643 1.114568987 1 19.89388988 EQSNDIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 EQSNDIAR 8 0 P45973 P45973 CBX5 Chromobox protein homolog 5 0 89.355 0.032488 187650000 215880 235610 162310 258930 193190 183630 208720 217580 234200 243440 FALSE TRUE 207443.1709 228890.6335 191643.0276 272293.4083 199404.1318 187343.1244 211274.3778 213086.897 207614.5978 226951.592 0.914041488 1.008543855 0.844422486 1.199786289 0.878619665 0.825476141 0.930922652 0.938909021 0.914796834 1 17.79202508 EQWDTIEELIR ddPTM_BT-474_Pertuzumab_2h_R1 6 EQWDTIEELIR 11 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;;;; 183.99 1.19E-05 477247000 717877 716729 574311 842391 612536 605361 814952 578116 858708 644815 FALSE TRUE 689821.5732 696288.5907 678101.7732 885866.9005 632238.7767 617601.8142 824925.6264 566177.7026 761231.0678 601141.1057 1.147520219 1.158278121 1.128024297 1.473642198 1.051731067 1.027382437 1.372266209 0.941838276 1.266310124 1 19.19734415 EQWIQDAEECDR ddPTM_BT-474_Pertuzumab_2h_R1 3 EQWIQDAEECDR 12 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ;; 252.21 1.10E-20 1269230000 898457 1058582 743821 1004213 934992 1053391 879976 915780 983786 1035224 FALSE TRUE 863344.3071 1028392.278 878246.0009 1056040.553 965066.8668 1074691.288 890745.4095 896868.823 872110.7376 965107.3564 0.894557793 1.065572934 0.909998245 1.09422081 0.999958047 1.113545846 0.92294956 0.92929436 0.903641167 1 19.88032991 ERDFTSLENTVEER ddPTM_BT-474_Pertuzumab_2h_R1 3 ERDFTSLENTVEER 14 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 ;; 207.85 8.08E-09 201360000 435504 672634 395801 747016 475508 478134 542922 593557 534546 631402 FALSE TRUE 418484.0222 653451.1369 467331.0452 785569.5853 490803.1467 487802.1971 549566.4418 581299.8405 473866.5791 588636.5801 0.710937846 1.110109631 0.793921175 1.334557878 0.833796545 0.828698408 0.933626044 0.987536045 0.805024008 1 19.16701767 ERDTSPDKGELVS(ph)DEEEDT ddPTM_BT-474_Pertuzumab_2h_R1 2 ERDTSPDKGELVSDEEEDT 19 2 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 ERDTSPDKGELVS(0.929)DEEEDT(0.071);ERDTSPDKGELVS(0.971)DEEEDT(0.029) 122.84 2.55E-05 401790000 562550 555320 463140 504990 488730 710930 540390 597420 681130 603360 TRUE FALSE 540564.9241 539482.8173 546839.7005 531052.5944 504450.4443 725305.4917 547003.4545 585083.0682 603810.9779 562493.8898 0.961014749 0.959090982 0.972170028 0.944103757 0.896810532 1.289445992 0.972461149 1.040158976 1.073453399 1 19.1014779 ERDVIMR ddPTM_BT-474_Pertuzumab_2h_R1 3 ERDVIMR 7 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;; 143.01 0.002235 9134060000 1412970 1610060 1375880 1731090 1511560 1520410 1626120 1451280 1735130 1862170 FALSE TRUE 1357749.57 1564142.665 1624532.122 1820431.762 1560180.7 1551153.732 1646020.943 1421310.561 1538165.317 1736043.567 0.78209418 0.900981228 0.935766909 1.048609492 0.898699047 0.893499311 0.948144951 0.818706735 0.886017693 1 20.72737172 EREELQR ddPTM_BT-474_Pertuzumab_2h_R1 1 EREELQR 7 1 A0A494C108;Q8N9T8;H0YFD2;H0YH26;H0YG91 A0A494C108 KRI1 Protein KRI1 homolog 0 189.53 0.00050501 149070000 96776 106870 88387 102390 103850 88261 107040 111830 106740 115400 FALSE TRUE 92993.88693 103822.1722 104360.4971 107674.3602 107190.4296 90045.69789 108349.9875 109520.6714 94623.32269 107583.8552 0.864385151 0.965034875 0.970038644 1.00084125 0.996343079 0.836981513 1.007121257 1.018002852 0.879530879 1 16.71510207 ERLELCDER ddPTM_BT-474_Pertuzumab_2h_R1 2 ERLELCDER 9 1 P07919 P07919 UQCRH "Cytochrome b-c1 complex subunit 6, mitochondrial" 0 ; 76.221 0.025419 1125900000 483130 624520 479750 884300 388020 559050 706290 623260 573300 571510 FALSE TRUE 464248.7455 606709.3011 566451.497 929938.829 400501.0157 570354.374 714933.7883 610389.4632 508221.3875 532801.1187 0.871335906 1.138716267 1.063157484 1.74537702 0.751689517 1.070482689 1.341839878 1.145623464 0.953866968 1 19.02323759 ERPEISPPS(ph)DFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 ERPEIS(0.264)PPS(0.368)DFEHT(0.368)IHVGFDAVTGEFTGMPEQWAR 190.52 6.30E-21 97361000 21938 25617 24979 31477 32830 31417 31187 5379.6 31328 31261 TRUE FALSE 21080.63871 24886.42824 29493.26095 33101.53174 33886.00677 32052.27327 31568.67584 5268.50938 27771.77678 29143.66463 0.723335208 0.853922407 1.01199562 1.135805403 1.162722918 1.099802433 1.083208863 0.180777176 0.952926721 1 14.83089468 ERPTS(ph)PAPHRPPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.166)S(0.834)PAPHRPPKR;ERPT(0.179)S(0.821)PAPHRPPKR 116.06 0.00027356 303874000 43278 40847 34955 33862 36235 42780 38847 39368 41800 42854 TRUE FALSE 41586.64791 39682.08355 41272.14607 35609.62188 37400.53168 43645.04091 39322.42121 38555.03704 37055.03924 39951.46041 1.040929355 0.993257397 1.033057256 0.891322157 0.9361493 1.092451702 0.984254913 0.965047001 0.927501495 1 15.28596062 ERTAADELEAFLGGGAPGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERTAADELEAFLGGGAPGGR 20 1 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 0 96.718 0.0012563 0 50544 53305 35229 49395 47595 58267 44064 49402 53514 49616 FALSE TRUE 48568.6846 51784.79359 41595.66396 51944.28187 49125.9364 59445.19866 44603.26841 48381.83144 47439.31507 46255.46413 1.05000967 1.119538947 0.899259466 1.122986935 1.062056934 1.285149761 0.964281069 1.045970078 1.025593753 1 15.49733618 ERVDDSTGTVIS(ph)DVEEDAGELSR ddPTM_BT-474_Pertuzumab_2h_R1 1 ERVDDSTGTVISDVEEDAGELSR 23 1 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 ERVDDSTGTVIS(1)DVEEDAGELSR 156.92 7.47E-09 21983000 9865 11588 10489 12324 11527 8740.2 11471 10433 10668 13113 TRUE FALSE 9479.464894 11257.52159 12384.59563 12960.04312 11897.77642 8916.932832 11611.38553 10217.5549 9457.013364 12224.84483 0.775426194 0.92087235 1.013067716 1.060139683 0.973245599 0.729410717 0.949818643 0.835802421 0.773589644 1 13.57752853 ESEEQKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESEEQKR 7 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 109.01 0.011422 831510000 696680 802070 493730 994640 533700 590390 1134490 892830 652060 668510 FALSE TRUE 669452.9754 779195.7489 582957.994 1045973.49 550866.9452 602328.0903 1148374.228 874392.7485 578040.8825 623231.2223 1.074164694 1.250251465 0.935379957 1.678307267 0.883888556 0.966460069 1.842613443 1.402998947 0.927490251 1 19.24940798 ESGS(ph)PYSVLVDTK ddPTM_BT-474_Pertuzumab_2h_R1 6 ESGSPYSVLVDTK 13 0 Q9Y2D9;D6RF85 Q9Y2D9 ZNF652 Zinc finger protein 652 1 ESGS(1)PYSVLVDTK;ESGS(1)PYSVLVDTK;ESGS(1)PYSVLVDTK;ESGS(0.995)PYS(0.005)VLVDTK;ES(0.001)GS(0.997)PYS(0.002)VLVDTK;ESGS(1)PYSVLVDTK 354.59 4.44E-76 2245100000 2694750 2312190 2053380 1969720 2144550 2007390 2248460 2700490 2283500 2149720 TRUE FALSE 2589436.191 2246248.605 2424471.443 2071377.485 2213531.398 2047980.801 2275977.326 2644723.938 2024286.653 2004117.55 1.292058039 1.120816793 1.209745129 1.033560874 1.104491799 1.021886566 1.135650614 1.319645117 1.010063833 1 20.9345357 ESHPHGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESHPHGVK 8 0 E9PM92;O00193;E9PQA1;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 ; 93.374 0.011114 208046000 494440 506390 424720 478750 482500 461150 509300 15712.9 573050 446970 FALSE TRUE 475116.7382 491948.253 501476.3518 503458.3449 498020.0507 470474.769 515532.9657 15388.42312 507999.7664 416696.3238 1.140199016 1.180591776 1.203457586 1.208214031 1.195163053 1.129059082 1.237191058 0.036929587 1.219112667 1 18.66863685 ESHT(ph)PVSIQEEIVGDFK ddPTM_BT-474_Pertuzumab_2h_R1 2 ESHTPVSIQEEIVGDFK 17 0 Q12830-4;Q12830;E7ETD6;E9PE19;A0A2R8Y7Q1;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 ES(0.03)HT(0.965)PVS(0.005)IQEEIVGDFK;ES(0.12)HT(0.88)PVSIQEEIVGDFK 200.74 4.46E-11 225871000 263690 250964 228282 219035 251528 260714 256652 185948 327120 278710 TRUE FALSE 253384.7033 243806.7524 269537.6355 230339.4226 259618.6266 265985.8157 259792.9839 182108.1088 289986.709 259832.7235 0.975183956 0.938321968 1.037350615 0.886491199 0.99917602 1.023680975 0.999847057 0.700866721 1.116051532 1 17.98722361 ESQFLKEELVAAVEDVR ddPTM_BT-474_Pertuzumab_2h_R1 2 ESQFLKEELVAAVEDVR 17 1 P35221-2;P35221;G3XAM7;E5RIB1;E5RJL0;E5RHV7;E5RG03;E5RIE0;E5RGY6 P35221-2 CTNNA1 Catenin alpha-1 0 ; 212.35 1.51E-12 121822000 308260 357500 274820 326850 273920 344570 322700 364550 343330 323020 FALSE TRUE 296212.8584 347304.45 324486.0873 343718.7677 282730.8856 351537.4415 326649.2991 357021.9151 304356.6178 301141.5677 0.983633248 1.15329296 1.077520084 1.141385994 0.938863697 1.167349444 1.084703456 1.185561721 1.010676208 1 18.20008234 ET(ph)TMSPLLFQAQPLSHR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETTMSPLLFQAQPLSHR 17 0 Q5VVP1 Q5VVP1 SPATA31A6 Spermatogenesis-associated protein 31A6 1 ET(0.35)T(0.35)MS(0.299)PLLFQAQPLSHR;ET(0.333)T(0.333)MS(0.333)PLLFQAQPLSHR 71.08 0.058372 1540970000 1290510 1138160 1032170 1016470 1139980 1116350 1156470 811280 1477070 1326540 TRUE FALSE 1240075.442 1105700.791 1218706.079 1068930.139 1176648.492 1138923.362 1170623.226 794526.7845 1309399.206 1236692.264 1.002735667 0.894079168 0.985456216 0.864346102 0.951448089 0.920943225 0.946576007 0.642461191 1.058791458 1 20.23805512 ETAIQTEDSAISES(ph)PEEPLPNLKPKPNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETAIQTEDSAISESPEEPLPNLKPKPNLR 29 2 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 ETAIQTEDSAISES(1)PEEPLPNLKPKPNLR;ETAIQTEDSAISES(1)PEEPLPNLKPKPNLR 324.03 3.91E-93 691310000 446920 427730 294140 347310 354440 427970 373660 402160 441170 420410 TRUE FALSE 429453.8723 415531.5592 347297.6411 365234.7107 365840.8845 436623.8466 378232.9629 393855.2555 391090.2311 391935.2562 1.095726566 1.060204594 0.886109722 0.931875112 0.933421729 1.114020338 0.965039396 1.004898766 0.997843968 1 18.58025583 ETGEHLVHVK ddPTM_BT-474_Pertuzumab_2h_R1 6 ETGEHLVHVK 10 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 ;;;;; 173.32 1.99E-06 9379440000 9500460 9799550 8943100 9772450 9814450 10117520 10434090 860080 12168810 10508520 FALSE TRUE 9129171.52 9520076.429 10559317.11 10276807.32 10130140.7 10322103.19 10561785.51 842319.0474 10787457.7 9796768.58 0.931855381 0.971756794 1.07783674 1.048999701 1.034028784 1.053623254 1.078088701 0.085979274 1.101124071 1 23.22387453 ETLAQLQQEFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 ETLAQLQQEFQR 12 0 O15212 O15212 PFDN6 Prefoldin subunit 6 0 152.14 0.00070149 0 33314 38412 33081 37823 36826 33920 36534 38770 37937 44812 FALSE TRUE 32012.05205 37316.52737 39059.47258 39775.04956 38010.54173 34605.88564 36981.11402 37969.38595 33630.5508 41776.84333 0.766263066 0.89323473 0.934955096 0.952083652 0.909847148 0.828350897 0.885206039 0.908862014 0.805004594 1 15.35041587 ETSMVHELNR ddPTM_BT-474_Pertuzumab_2h_R1 2 ETSMVHELNR 10 0 B4DR61;P61619-3;P61619 B4DR61 SEC61A1 Protein transport protein Sec61 subunit alpha isoform 1 0 ; 143.4 3.40E-05 277440000 340090 581530 317960 693780 393030 308380 492210 503050 467550 352030 FALSE TRUE 326798.9068 564945.3338 375422.445 729586.0689 405672.1669 314615.6549 498233.8132 492661.8417 414475.6841 328186.6945 0.995771347 1.721414497 1.143929511 2.223082413 1.236101809 0.958648416 1.518141416 1.501163362 1.262926532 1 18.32415722 EVLAELEALER ddPTM_BT-474_Pertuzumab_2h_R1 4 EVLAELEALER 11 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ;;; 155.15 7.37E-05 129341000 149060 249575 155999 355320 159616 183523 290152 248970 195911 174259 FALSE TRUE 143234.5704 242457.3654 184191.4895 373658.1078 164750.1936 187233.9608 293702.967 243828.6825 173672.0046 162456.2827 0.881680708 1.492446837 1.133791112 2.300053291 1.014120173 1.152519051 1.807889249 1.500887983 1.0690384 1 17.30969201 EVLAGR ddPTM_BT-474_Pertuzumab_2h_R1 3 EVLAGR 6 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;; 109.8 0.068051 870370000 1055930 1024210 998950 994990 1032070 922390 968390 1067240 1136210 1192440 FALSE TRUE 1014663.088 995000.5336 1179482.487 1046341.553 1065267.469 941041.3578 980241.4465 1045201.121 1007232.204 1111674.977 0.912733586 0.895046263 1.060995805 0.941229743 0.958254428 0.846507637 0.881769822 0.940203875 0.906049183 1 20.08430361 EVPIPEHIDIYHLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 EVPIPEHIDIYHLTR 15 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ;;; 183.01 3.02E-07 1455160000 563469 669390 584945 699933 660573 720285 683526 129989 738392 763517 FALSE TRUE 541448.0085 650299.6526 690657.5735 736056.626 681820.9305 734849.6562 691891.1957 127304.6817 654572.8358 711803.3135 0.760670818 0.913594585 0.97029272 1.034073054 0.957878276 1.032377403 0.972025815 0.178848116 0.919597905 1 19.44111912 EVQLEEDPDLQLPFLLPEDGYSCDVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVQLEEDPDLQLPFLLPEDGYSCDVVR 27 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;H0YA98;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 65.071 0.025897 14597000 9853.2 10737 6945.3 12179 9647.1 11404 9623 11417 8952.4 11677 FALSE TRUE 9468.126051 10430.79127 8200.470207 12807.55965 9957.407733 11634.59669 9740.769153 11181.23496 7936.161084 10886.10639 0.869744031 0.958174659 0.753296901 1.176505097 0.914689548 1.068756475 0.894789083 1.027110572 0.72901741 1 13.41020042 EVSSEDIADMHSNLSNYHQYIVK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVSSEDIADMHSNLSNYHQYIVK 23 0 Q8TBX8;Q8TBX8-3;F8VNT5 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 244.72 1.06E-37 377700000 218240 215490 156120 243430 224410 174410 244690 105510 249330 272850 FALSE TRUE 209710.9395 209344.4362 184334.3569 255993.4515 231628.3515 177936.6897 247684.5894 103331.1816 221027.1037 254369.6265 0.824433886 0.822993056 0.724671257 1.006383722 0.910597522 0.699520191 0.973719201 0.406224529 0.868920974 1 17.95656689 EVVVYLDDNQKPPVGEGLNR ddPTM_BT-474_Pertuzumab_2h_R1 1 EVVVYLDDNQKPPVGEGLNR 20 1 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 148.06 1.05E-07 169800000 143230 153310 107300 114030 141600 145110 129500 160800 167920 140760 FALSE TRUE 137632.4133 148937.7489 126691.4969 119915.102 146154.6926 148044.2236 131084.8597 157479.4238 148858.4256 131226.1998 1.048818098 1.134969611 0.965443616 0.913804577 1.113761526 1.128160564 0.998922928 1.200060842 1.134365133 1 17.00169626 EVWDYVFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 EVWDYVFFK 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 133.23 0.00065763 299200000 542360 587360 578420 558790 579100 495190 607620 549290 644620 683130 FALSE TRUE 521163.9716 570609.0679 682953.3609 587629.2189 597727.2774 505203.0811 615056.2353 537946.9695 571445.4401 636860.9966 0.818332374 0.895971132 1.072374293 0.922696196 0.938552181 0.793270563 0.965762134 0.844685061 0.897284404 1 19.28061899 EVWEMELDR ddPTM_BT-474_Pertuzumab_2h_R1 2 EVWEMELDR 9 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 0 ; 146.69 0.00021909 104860000 206136 219412 178360 203275 213412 171678 219046 213054 209558 229063 FALSE TRUE 198079.9772 213154.5846 210593.6196 213766.0471 220276.5908 175149.4468 221726.7505 208654.3604 185769.8544 213548.359 0.92756497 0.998156041 0.986163605 1.001019386 1.03150683 0.820186339 1.038297609 0.977082481 0.869919372 1 17.70420329 EWLSPLPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 EWLSPLPDR 9 0 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 0 87.639 0.030999 91367000 83128 95362 91753 95276 96190 81590 100700 90586 102840 97249 FALSE TRUE 79879.26586 92642.36913 108334.8081 100193.2058 99284.03871 83239.8057 101932.3967 88715.36744 91166.03434 90662.23861 0.881064345 1.021840742 1.194927566 1.105126096 1.095098028 0.918130933 1.124309286 0.978526108 1.005556842 1 16.46821416 EYHTDTTVK ddPTM_BT-474_Pertuzumab_2h_R1 4 EYHTDTTVK 9 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ;;; 117.7 0.0011094 2000130000 2448080 2451380 2054270 2599100 2407580 1999500 2569650 2190510 2527840 2889060 FALSE TRUE 2352406.327 2381469.043 2425522.286 2733239.862 2485021.997 2039931.26 2601098.145 2145275.203 2240890.201 2693381.393 0.873402606 0.884193025 0.900549136 1.014798673 0.922640219 0.757386706 0.965737029 0.796498858 0.831998842 1 21.3609871 EYSPPYAPS(ph)HQQYPPSHATPLPK ddPTM_BT-474_Pertuzumab_2h_R1 2 EYSPPYAPSHQQYPPSHATPLPK 23 0 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 EYS(0.204)PPYAPS(0.796)HQQYPPSHATPLPK;EYS(0.456)PPYAPS(0.525)HQQY(0.005)PPS(0.013)HATPLPK 179.86 3.04E-17 1866830000 469030 520110 470650 458530 477560 478130 503030 376210 539520 557150 TRUE FALSE 450699.7891 505276.972 555706.9246 482194.7883 492921.1511 487798.1162 509186.2316 368441.132 478275.9515 519413.7342 0.867708648 0.972783234 1.069873374 0.928344317 0.94899522 0.93913211 0.980309526 0.709340373 0.920799586 1 18.98652464 EYVAYSHTGR ddPTM_BT-474_Pertuzumab_2h_R1 4 EYVAYSHTGR 10 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ;;; 184.71 1.53E-06 5728340000 2712030 4432610 2881730 4378820 2879610 1499950 4310100 3993800 3707090 3598940 FALSE TRUE 2606040.869 4306196.303 3402522.715 4604811.425 2972235.271 1530280.017 4362848.293 3911326.634 3286276.685 3355180.588 0.776721491 1.283446953 1.014110158 1.37244816 0.885864469 0.45609468 1.300331883 1.165757411 0.979463429 1 21.67795899 FAELETILGDIDR ddPTM_BT-474_Pertuzumab_2h_R1 3 FAELETILGDIDR 13 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ;; 189.13 1.28E-05 136172000 142388 143439 124369 142129 147420 136040 138332 151408 158671 170690 FALSE TRUE 136823.3195 139348.2602 146845.2449 149464.2947 152161.8982 138790.822 140024.9484 148281.3719 140659.3333 159129.0143 0.85982635 0.875693605 0.922806225 0.939264881 0.956217186 0.872190547 0.879946055 0.931831147 0.883932663 1 17.27983738 FAHIDGDHLTLLNVYHAFK ddPTM_BT-474_Pertuzumab_2h_R1 2 FAHIDGDHLTLLNVYHAFK 19 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 331.02 9.94E-76 4251500000 4101800 4530000 4046300 4607900 4517700 4239700 4785500 765490 5280900 4666900 FALSE TRUE 3941497.121 4400808.835 4777556.419 4845714.271 4663015.923 4325429.639 4844066.381 749682.364 4681434.371 4350806.706 0.905923289 1.011492611 1.098085192 1.113750759 1.071758926 0.994167273 1.113372004 0.172308819 1.075992267 1 22.05285149 FARPDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 FARPDFR 7 1 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 ; 89.142 0.016498 553990000 485840 837590 477870 848400 506390 328460 782520 834630 757990 635150 FALSE TRUE 466852.8357 813702.7533 564231.7392 892186.0257 522678.4942 335101.6862 792096.7138 817394.5988 671946.153 592130.7248 0.788428663 1.374194446 0.952883739 1.506738273 0.882707943 0.565925179 1.337705815 1.380429295 1.134793593 1 19.17555619 FAS(ph)DDEHDEHDENGATGPVK ddPTM_BT-474_Pertuzumab_2h_R1 9 FASDDEHDEHDENGATGPVK 20 0 P05455 P05455 SSB Lupus La protein 1 FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK 282.35 5.18E-45 31549980000 11775590 9994700 11000000 11002900 11244270 10288730 12416830 3033989 16273090 12817380 TRUE FALSE 11315386.92 9709660.942 12987944.69 11570760.99 11605952.16 10496775.17 12568790.88 2971336.067 14425837.05 11949247.44 0.946953939 0.812575101 1.086925747 0.968325499 0.971270552 0.878446549 1.051847905 0.248663029 1.207259045 1 23.51041642 FDDKPDYSYLR ddPTM_BT-474_Pertuzumab_2h_R1 2 FDDKPDYSYLR 11 1 P48730-2;H7BYT1;P48730;H0Y645;B0QY35;B0QY34;A0A669KBC0;P49674 P48730-2;P49674 CSNK1D;CSNK1E Casein kinase I isoform delta;Casein kinase I isoform epsilon 0 ; 103.75 0.0024553 873250000 964420 974010 840080 881020 887460 667840 1001200 1008460 1121280 1165520 FALSE TRUE 926729.4002 946232.1885 991901.1435 926489.5478 916005.9569 681344.1824 1013452.985 987634.9486 993996.9952 1086578.292 0.852887828 0.870836639 0.912866703 0.852667087 0.843018827 0.627054845 0.932701299 0.908940438 0.914795558 1 20.0513607 FEENQKEFER ddPTM_BT-474_Pertuzumab_2h_R1 1 FEENQKEFER 10 1 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 83.182 0.014393 196220000 231200 226270 156740 160090 211760 233950 175190 215930 278880 201880 FALSE TRUE 222164.4484 219817.0011 185066.4047 168352.2641 218571.4527 238680.6293 177334.0276 211470.97 247222.7116 188206.4878 1.180429277 1.167956555 0.983315755 0.894508293 1.161338566 1.268184918 0.942231215 1.123611479 1.313571676 1 17.52195684 FEFIGDAVTDDER ddPTM_BT-474_Pertuzumab_2h_R1 2 FEFIGDAVTDDER 13 0 A1A4S6 A1A4S6 ARHGAP10 Rho GTPase-activating protein 10 0 ; 220.1 4.97E-11 102568000 119413 126098 121706 149713 128716 150804 149867 159010 156231 191696 FALSE TRUE 114746.2079 122501.8085 143700.9815 157439.7059 132856.267 153853.3602 151701.1172 155726.3879 138496.3119 178712.2592 0.642072393 0.685469531 0.804091349 0.880967577 0.743408805 0.860899867 0.848856804 0.871380557 0.774968167 1 17.44727908 FELLDR ddPTM_BT-474_Pertuzumab_2h_R1 4 FELLDR 6 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YGP5;A0A2R8YFV8;F6VDE0;P51531-2;P51531;A0A0U1RQZ9 A0A2R8Y4P4;F6VDE0 SMARCA4;SMARCA2 Transcription activator BRG1;Probable global transcription activator SNF2L2 0 ;;; 110.61 0.066431 596172000 590170 617990 588570 694600 638610 565100 642830 642230 677510 736350 FALSE TRUE 567105.5039 600365.5303 694937.6917 730448.3892 659151.4706 576526.7092 650697.1458 628967.7261 600601.9052 686476.3586 0.826110756 0.874561116 1.012325746 1.06405469 0.960195442 0.839834762 0.947879905 0.916226347 0.874905447 1 19.38885051 FFEHFIEGGR ddPTM_BT-474_Pertuzumab_2h_R1 8 FFEHFIEGGR 10 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;;;;;; 205.18 1.73E-07 9827792000 3987576 4483464 3635133 4179143 4122072 3330795 4274521 3743501 4206601 4541242 FALSE TRUE 3831737.121 4355599.996 4292082.396 4394829.071 4254662.189 3398145.957 4326833.867 3666196.396 3729085.29 4233659.634 0.905064992 1.02880259 1.013799589 1.038068586 1.004960851 0.802649776 1.022007965 0.865963897 0.880818396 1 22.01347386 FFEHHPIPQEEASLAETALTSGSS(ph)PSAPASDSIGPQILTSPSPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSK 45 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 FFEHHPIPQEEASLAET(0.001)ALT(0.064)S(0.342)GS(0.064)S(0.491)PS(0.036)APASDSIGPQILTSPSPSK 265.21 8.97E-68 152570000 42025 41051 43627 44755 43833 53345 52724 7502.2 60341 55834 TRUE FALSE 40382.61654 39880.26567 51511.36938 47064.81091 45242.92825 54423.67245 53369.25208 7347.276948 53491.34265 52052.31345 0.775808295 0.76615741 0.989607684 0.904182884 0.869181891 1.045557226 1.02530029 0.141151785 1.027645826 1 15.66767466 FFVTLLEAQADYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 FFVTLLEAQADYHR 14 0 Q68EM7;Q68EM7-6;Q68EM7-5;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 0 105.19 0.0024868 0 87803 86516 75337 79529 81762 77631 90403 84252 88201 92719 FALSE TRUE 84371.56169 84048.64839 88952.07176 83633.50122 84391.94898 79200.75201 91509.37896 82512.16676 78188.79225 86439.05954 0.97608144 0.972345706 1.029072646 0.967542933 0.976317297 0.916261149 1.058657735 0.95457039 0.904553944 1 16.39939576 FGDVVHFMELWGK ddPTM_BT-474_Pertuzumab_2h_R1 1 FGDVVHFMELWGK 13 0 Q9NV88-3;Q9NV88-2;Q9NV88;G3XAN1 Q9NV88-3 INTS9 Integrator complex subunit 9 0 136.27 7.43E-05 48320000 167110 170840 143180 168150 191580 151280 172520 166470 195980 223530 FALSE TRUE 160579.1565 165967.8105 169055.811 176828.2417 197742.3447 154338.9853 174631.3514 163032.3363 173733.172 208390.114 0.770569934 0.796428426 0.81124679 0.848544292 0.948904633 0.740625274 0.838002091 0.782341989 0.833692005 1 17.66892731 FGHLGLAINLITYDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 FGHLGLAINLITYDDR 16 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 163.23 7.80E-09 376110000 121955 133364 140895 150351 141201 115542 137504 123295 155970 174257 FALSE TRUE 117188.8638 129560.5893 166357.8607 158110.6331 145742.8584 117878.3384 139186.8151 120748.9152 138264.9395 162454.4182 0.721364584 0.797519641 1.024027925 0.973261515 0.897130777 0.725608695 0.856774575 0.743278739 0.851099903 1 17.30967545 FGIDDQDYQNSVTR ddPTM_BT-474_Pertuzumab_2h_R1 2 FGIDDQDYQNSVTR 14 0 P78356;P78356-2;A0A087WT35 P78356 PIP4K2B Phosphatidylinositol 5-phosphate 4-kinase type-2 beta 0 ; 327.18 5.92E-68 703920000 811580 890090 726910 887470 893410 422250 899510 933570 964280 1013360 FALSE TRUE 779862.5564 864705.5047 858278.807 933272.4331 922147.344 430788.1843 910518.4725 914291.4533 854818.977 944724.2246 0.825492282 0.915299388 0.908496665 0.987878165 0.976102147 0.455993583 0.963792871 0.967786608 0.9048344 1 19.84953373 FGSGMNMGR ddPTM_BT-474_Pertuzumab_2h_R1 2 FGSGMNMGR 9 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R019;M0QYL3 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 99.139 0.012888 566370000 464650 487700 434560 517580 479220 392710 563030 496310 506610 553420 FALSE TRUE 446490.9643 473791.2735 513094.6587 544292.3658 494634.5465 400650.8653 569920.5296 486061.0251 449101.7567 515936.3705 0.865399282 0.918313382 0.994492128 1.054960257 0.958712304 0.776550924 1.104633366 0.942094903 0.870459581 1 18.97683363 FGVSSESKPEEVKK ddPTM_BT-474_Pertuzumab_2h_R1 1 FGVSSESKPEEVKK 14 2 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 0 59.248 0.0576 205130000 167520 196360 147200 140230 183440 160010 174080 114500 238010 174340 FALSE TRUE 160973.1332 190760.0051 173802.3144 147467.2871 189340.5142 163245.5118 176210.4431 112135.535 210992.1026 162531.7965 0.990410102 1.173678069 1.069343465 0.907313463 1.164944449 1.004391235 1.084159819 0.689929832 1.298158927 1 17.31036246 FHDIDDVKK ddPTM_BT-474_Pertuzumab_2h_R1 3 FHDIDDVKK 9 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;H0Y9D8;D6R967 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ;; 145.17 6.35E-05 905835000 1737236 1716211 1308637 1616364 1451810 1466478 1850079 808170 2045880 1602659 FALSE TRUE 1669342.897 1667266.343 1545136.816 1699784.74 1498508.787 1496131.19 1872720.82 791481.0071 1813640.279 1494109.478 1.11728285 1.115893023 1.034152342 1.137657424 1.002944435 1.001353121 1.253402677 0.529734279 1.213860367 1 20.51085443 FHMVDGNVSGEFTDLVPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FHMVDGNVSGEFTDLVPEK 19 0 O95433;O95433-2;G3V438;H0YJ63 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 66.827 0.026627 669830000 646730 651110 580880 555460 612700 686980 663130 320640 738020 701870 FALSE TRUE 621455.0766 632540.9803 685857.9376 584127.3572 632408.0519 700871.2063 671245.5833 314018.672 654243.0636 654331.7197 0.949755388 0.966697718 1.048180788 0.8927083 0.966494567 1.071125219 1.025849066 0.479907457 0.999864509 1 19.31966268 FHNLEGFLEEFADIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHNLEGFLEEFADIAK 16 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 173.03 4.36E-09 395560000 483000 413080 429410 467820 470160 428640 503290 155550 564890 500590 FALSE TRUE 464123.826 401299.3628 507013.9392 491964.2463 485283.1234 437307.3945 509449.4136 152337.8381 500766.0554 466684.5934 0.994512852 0.859894174 1.086416707 1.054168604 1.039852462 0.937051278 1.09163538 0.326425685 1.073028899 1 18.83208832 FHSPPDKDEAEAPSQK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHSPPDKDEAEAPSQK 16 1 F5H8D7;P18887;M0QYS5;M0QZ96;M0R0D2;M0R1U8 F5H8D7 XRCC1 DNA repair protein XRCC1 0 ; 213.51 1.05E-12 726730000 775640 641900 623310 562830 652340 685580 682600 321780 899060 732460 FALSE TRUE 745327.1313 623593.6405 735955.9825 591877.7237 673323.1085 699442.8973 690953.863 315135.1306 797002.478 682849.8318 1.091494933 0.913222222 1.077771346 0.866775821 0.986048582 1.024299729 1.011867955 0.461499902 1.167170937 1 19.38120882 FHTEALTALLSDDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 FHTEALTALLSDDSK 15 0 B7Z7P8;P62495-2;P62495;I3L492;D6RJE8 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 151.56 2.98E-06 1187100000 1090300 821640 1016600 1011800 1092300 1103400 1210900 569370 1404200 1245900 FALSE TRUE 1047689.871 798207.6317 1200322.234 1064019.119 1127434.822 1125711.504 1225719.356 557612.3105 1244801.103 1161514.083 0.902003588 0.687213046 1.033411692 0.916062177 0.970659622 0.96917594 1.055277223 0.480073654 1.071705562 1 20.14757522 FHVDISLTDFIQK ddPTM_BT-474_Pertuzumab_2h_R1 2 FHVDISLTDFIQK 13 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ; 231.83 1.76E-12 426630000 646060 661470 596700 619200 658710 679360 719220 358410 843860 783040 FALSE TRUE 620811.2609 642605.5232 704536.9635 651156.9862 679898.0054 693097.1247 728022.0295 351008.7083 748068.5505 730004.0033 0.850421721 0.880276711 0.965113835 0.89199098 0.931362023 0.949442909 0.997284982 0.48083121 1.024745819 1 19.47754485 FIIPNVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 FIIPNVVK 8 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2 P00338 LDHA L-lactate dehydrogenase A chain 0 83.377 0.042351 92195000 782090 693360 769750 605060 661470 632720 700420 711950 643530 770220 FALSE TRUE 751525.0582 673586.0517 908860.948 636287.2191 682746.7833 645514.0319 708991.9495 697247.9837 570479.1723 718052.3134 1.046616025 0.938073785 1.265730826 0.886129335 0.950831535 0.898979113 0.987382028 0.971026721 0.794481351 1 19.45372943 FIKDNWEELYNR ddPTM_BT-474_Pertuzumab_2h_R1 2 FIKDNWEELYNR 12 1 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 164.68 5.17E-05 2115150000 1775430 1868180 1491140 1724370 1700010 1523360 1873200 1849300 1956380 1877880 FALSE TRUE 1706044.233 1814901.336 1760622.168 1813364.942 1754692.366 1554163.383 1896124.782 1811111.309 1734299.944 1750689.515 0.974498458 1.036678017 1.005673566 1.035800424 1.002286442 0.887743583 1.083073135 1.034513141 0.99063822 1 20.73949181 FISDKDASIVGFFDDSFSEAHSEFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FISDKDASIVGFFDDSFSEAHSEFLK 26 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 255.42 8.02E-53 9866200000 1015840 1173450 874280 1000990 1003150 1162860 1049550 1046360 1279600 1153420 FALSE TRUE 976139.8497 1139984.355 1032281.844 1052651.214 1035417.231 1186373.826 1062394.707 1024752.3 1134345.173 1075297.836 0.907785561 1.060156839 0.959996207 0.97893921 0.962912038 1.103297883 0.988000414 0.95299392 1.054912541 1 20.03630488 FITEIWHPNVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FITEIWHPNVDK 12 0 P62253;K7EPR7;I3L2H7 P62253 UBE2G1 "Ubiquitin-conjugating enzyme E2 G1;Ubiquitin-conjugating enzyme E2 G1, N-terminally processed" 0 ; 156.69 7.34E-05 960670000 2136140 2154450 1796430 1965360 1984690 1837790 2164600 2187130 2435200 2261580 FALSE TRUE 2052657.287 2093007.195 2121084.862 2066792.465 2048529.356 1874951.373 2191091.022 2141965.001 2158766.305 2108401.172 0.973561063 0.992698744 1.006015786 0.98026528 0.971603214 0.889276385 1.03921922 1.01591909 1.023887832 1 21.00771797 FITLLLPGGAQTAVRPGS(ph)PSTSTMR ddPTM_BT-474_Pertuzumab_2h_R1 2 FITLLLPGGAQTAVRPGSPSTSTMR 25 1 H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5 H0Y4W2 TRRAP Transformation/transcription domain-associated protein 1 FITLLLPGGAQTAVRPGS(0.934)PS(0.054)T(0.01)S(0.001)TMR;FITLLLPGGAQTAVRPGS(0.986)PS(0.012)T(0.002)STMR 190.25 5.39E-18 1098110000 867770 858440 808990 759270 883600 851350 881020 879050 924400 929410 TRUE FALSE 833856.589 833958.1317 955192.4889 798456.0157 912021.7965 868564.8803 891802.1863 860897.3103 819465.9874 866460.2329 0.962371448 0.962488641 1.102407765 0.921514901 1.05258356 1.002429018 1.029247682 0.993579714 0.945762952 1 19.72477401 FLMPEAYPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLMPEAYPSSPR 12 0 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 FLMPEAYPS(0.13)S(0.87)PR;FLMPEAYPSS(1)PR 226.51 1.59E-11 223330000 460320 513410 477290 527530 474170 471830 514720 523800 513820 564040 TRUE FALSE 442330.1855 498768.0495 563546.9203 554755.8865 489422.1087 481370.7259 521019.2973 512983.347 455493.3077 525837.0684 0.841192476 0.948522041 1.071713947 1.054995777 0.930748588 0.915437033 0.990837901 0.975555695 0.866225177 1 19.00425632 FLQDYFDGNLKR ddPTM_BT-474_Pertuzumab_2h_R1 2 FLQDYFDGNLKR 12 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 136.24 0.00018182 15972100000 4066760 4770000 3382190 3758470 4186830 4387810 4104250 4436600 4508600 4287740 FALSE TRUE 3907826.523 4633964.27 3993426.969 3952445.087 4321503.189 4476534.525 4154479.039 4344982.66 3996802.63 3997327.551 0.977609784 1.159265587 0.999024203 0.988771882 1.081098092 1.119881838 1.039314138 1.086971884 0.999868682 1 21.93060436 FLQEHGSDSFLAEHK ddPTM_BT-474_Pertuzumab_2h_R1 5 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;;; 298.78 2.02E-44 3159690000 1814840 2958860 2313960 2936960 2384890 2546490 2695500 1296350 2697090 2943560 FALSE TRUE 1743914.046 2874476.21 2732144.046 3088536.858 2461602.153 2597981.773 2728488.335 1269579.919 2390927.65 2744190.059 0.635493172 1.047477087 0.995610357 1.125482124 0.897023202 0.946720787 0.994278194 0.462642853 0.871268971 1 21.38794897 FLSAQSHSTS(ph)PQGLDSPLPLEGSGAHQVLHNESK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESK 34 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLSAQSHS(0.001)T(0.03)S(0.969)PQGLDSPLPLEGSGAHQVLHNESK;FLSAQSHS(0.001)T(0.006)S(0.993)PQGLDSPLPLEGSGAHQVLHNESK 256.88 7.27E-60 1562400000 326953 387890 358586 405470 389600 470720 427780 72928 451730 493820 TRUE FALSE 314175.3153 376827.757 423390.4669 426396.3553 402131.8378 480238.2809 433015.2996 71422.01131 400451.5042 460373.1316 0.682436254 0.818526823 0.919668065 0.926197308 0.87349111 1.043150106 0.940574655 0.1551394 0.869841172 1 18.81244411 FLSPVVPNYDNVHPNYHK ddPTM_BT-474_Pertuzumab_2h_R1 2 FLSPVVPNYDNVHPNYHK 18 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 150.59 3.11E-08 1132510000 2177800 2200200 2133700 2321100 2388500 2251400 2504100 196744 2924600 2664500 FALSE TRUE 2092689.168 2137452.45 2519307.054 2440892.249 2465328.272 2296924.851 2534745.925 192681.1676 2592611.669 2484031.042 0.842456931 0.860477351 1.014201116 0.982633553 0.992470799 0.924676388 1.020416364 0.077567939 1.043711461 1 21.24425177 FNADEFEDMVAEKR ddPTM_BT-474_Pertuzumab_2h_R1 6 FNADEFEDMVAEKR 14 1 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;; 195.15 9.91E-08 3482820000 3523571 3559162 2727043 2731836 3092552 3639159 3112413 3537020 3874173 3591015 FALSE TRUE 3385865.95 3457658.185 3219880.333 2872826.383 3192026.744 3712745.288 3150503.641 3463979.301 3434393.123 3347792.356 1.011372747 1.032817396 0.961792128 0.858125618 0.953472141 1.109013013 0.941069011 1.034705541 1.025868022 1 21.67477862 FNAHHGDTK ddPTM_BT-474_Pertuzumab_2h_R1 5 FNAHHGDTK 9 0 P53602 P53602 MVD Diphosphomevalonate decarboxylase 0 ;;;; 160.75 3.76E-05 1882400000 2762320 2683440 2475620 2617700 2723920 2808840 3205580 1231533 3670870 3318750 FALSE TRUE 2654365.48 2606910.919 2923019.604 2752799.811 2811537.361 2865636.669 3244810.847 1206101.413 3254168.227 3093968.106 0.857916239 0.842578472 0.944747814 0.889731153 0.908715689 0.926201102 1.048753812 0.38982348 1.051778207 1 21.56102689 FNFLNPNDPYHAYYR ddPTM_BT-474_Pertuzumab_2h_R1 2 FNFLNPNDPYHAYYR 15 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 236.17 1.06E-17 1639710000 1166430 1252070 995310 1235710 1100480 1095850 1199510 1105220 1259540 1311980 FALSE TRUE 1120844.626 1216362.19 1175184.658 1299485.141 1135877.939 1118008.838 1214189.962 1082396.821 1116562.3 1223118.426 0.916382749 0.99447622 0.960810198 1.062436076 0.92867372 0.914064259 0.992700246 0.884948504 0.912881595 1 20.22213267 FNGGHS(ph)PTHS(ph)PEK ddPTM_BT-474_Pertuzumab_2h_R1 4 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 2 FNGGHS(0.917)PT(0.083)HS(1)PEK;FNGGHS(0.905)PT(0.095)HS(1)PEK;FNGGHS(0.524)PT(0.477)HS(0.999)PEK;FNGGHS(0.801)PT(0.199)HS(1)PEK 153.36 2.41E-05 2965670000 5386600 4663570 4408470 4458600 4407500 4827340 5586700 1397280 6255100 5354200 TRUE FALSE 5176085.717 4530569.55 5205178.595 4688708.88 4549271.24 4924952.122 5655071.706 1368425.68 5545047.272 4991555.265 1.036968528 0.907646877 1.042796948 0.939328252 0.911393543 0.986656836 1.132927796 0.274148158 1.110885681 1 22.25105797 FPEDGPELEEILTQLATADAR ddPTM_BT-474_Pertuzumab_2h_R1 1 FPEDGPELEEILTQLATADAR 21 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 141.85 3.54E-07 239730000 17200 17748 21830 25656 16490 12481 26619 17516 24946 21752 FALSE TRUE 16527.80498 17241.84442 25775.16661 26980.10923 17020.41583 12733.37437 26944.77128 17154.28848 22114.23466 20278.71767 0.815032058 0.850243329 1.271045193 1.330464267 0.839324069 0.627918125 1.328721654 0.845925702 1.090514451 1 14.30767881 FPELGPDGHQR ddPTM_BT-474_Pertuzumab_2h_R1 3 FPELGPDGHQR 11 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ;; 131.83 0.00019525 799730000 993690 1116590 905590 1051320 993110 1008660 1133460 1039650 1170680 1226600 FALSE TRUE 954855.4962 1084745.946 1069250.258 1105578.751 1025054.285 1029055.796 1147331.623 1018180.864 1037789.314 1143521.289 0.835013309 0.948601444 0.935050591 0.966819561 0.896401575 0.899900864 1.003332105 0.890390825 0.907538254 1 20.12505179 FRADNLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 FRADNLNK 8 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 128.12 0.0010461 734100000 825260 977640 707660 760560 810100 537640 978970 982020 1023760 1059620 FALSE TRUE 793007.9268 949758.6644 835549.9038 799812.5927 836157.6022 548511.4492 990950.9277 961740.9438 907547.0568 987850.9936 0.802760671 0.961439195 0.845825847 0.809649024 0.84644102 0.555257273 1.003138058 0.973568838 0.918708452 1 19.91393392 FRDYEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 FRDYEEK 7 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 82.279 0.022728 214900000 145140 128960 117650 95035 127630 112030 121310 125200 138370 133400 FALSE TRUE 139467.7683 125282.1871 138911.9721 99939.76774 131735.3349 114295.3234 122794.6281 122614.5762 122662.8177 124364.6992 1.12144177 1.007377398 1.116972686 0.803602376 1.059266301 0.919033489 0.987375267 0.985927494 0.986315397 1 16.92421751 FRGPFTDVVTTNLK ddPTM_BT-474_Pertuzumab_2h_R1 2 FRGPFTDVVTTNLK 14 1 O95292;E5RK64;O95292-2 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ; 148.72 7.01E-06 1100950000 972950 1405740 802110 1192950 849550 769360 1211650 1385250 1250360 1031720 FALSE TRUE 934926.0383 1365649.672 947069.1198 1254518.292 876876.5473 784916.9863 1226478.535 1356644.103 1108424.375 961840.6854 0.972017562 1.419829388 0.984642399 1.304289069 0.911665061 0.816057169 1.275136885 1.41046654 1.152399136 1 19.87543843 FRPLNESEVNRGDK ddPTM_BT-474_Pertuzumab_2h_R1 3 FRPLNESEVNRGDK 14 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;; 209.39 3.77E-09 1011880000 881460 887530 612240 638190 748620 878400 755900 809830 925470 849140 FALSE TRUE 847011.5687 862218.5134 722885.3872 671127.0624 772700.0422 896161.8498 765150.9303 793106.7275 820414.5255 791626.9915 1.069962972 1.089172707 0.913164148 0.847781935 0.976091076 1.132050649 0.966554878 1.001869234 1.036365023 1 19.59446128 FS(ph)PDSQYIDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 FSPDSQYIDNR 11 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 FS(0.948)PDS(0.052)QYIDNR 83.243 0.013184 0 109930 225890 102760 112320 131180 131980 106370 135160 138030 122320 TRUE FALSE 105633.8141 219447.8384 121331.0179 118116.8487 135399.5238 134648.726 107671.7879 132368.8988 122361.4131 114035.1574 0.926326726 1.92438756 1.063979045 1.03579327 1.187348945 1.180765029 0.944198178 1.16077271 1.073014812 1 16.79911916 FT(ph)DTRK ddPTM_BT-474_Pertuzumab_2h_R1 2 FTDTRK 6 1 P13639 P13639 EEF2 Elongation factor 2 1 FT(1)DTRK;FT(1)DTRK 84.498 0.032689 758490000 787150 511240 157971 276750 568900 280850 324620 784970 485500 300510 TRUE FALSE 756387.3078 496659.9358 186519.8737 291033.1007 587199.1852 286528.9794 328592.7967 768760.0952 430388.0754 280156.19 2.699877192 1.772796581 0.665771025 1.038824452 2.095970769 1.022747273 1.172891438 2.744041083 1.53624332 1 18.09587184 FTIGDHSR ddPTM_BT-474_Pertuzumab_2h_R1 6 FTIGDHSR 8 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;;;;; 199.68 0.00012597 4760140000 3984820 4391350 3886540 4486530 4289830 3319280 4605980 4290550 4437480 4904560 FALSE TRUE 3829088.829 4266112.998 4588924.234 4718080.351 4427816.278 3386398.116 4662349.361 4201948.643 3933755.874 4572369.783 0.837440761 0.933020119 1.003620541 1.031867626 0.96838543 0.740622101 1.019678981 0.918987055 0.860331964 1 22.12451065 FTNEDHLAVHK ddPTM_BT-474_Pertuzumab_2h_R1 1 FTNEDHLAVHK 11 0 P17544;K7ELQ4;P17544-2;P17544-1;P17544-3;P17544-4;K7ESA4;P17544-5;B8ZZU6;E9PBF9;P15336-5;P15336;E9PEK8;H7C2N6;P15336-3;P15336-7 P17544;B8ZZU6 ATF7;ATF2 Cyclic AMP-dependent transcription factor ATF-7;Cyclic AMP-dependent transcription factor ATF-2 0 58.511 0.061215 131260000 73845 83888 79665 81709 88529 94594 97819 36269 105630 90557 FALSE TRUE 70959.05576 81495.59637 94062.23764 85926.01128 91376.61568 96506.75549 99016.13818 35520.03248 93639.32524 84423.49373 0.840513139 0.965318927 1.114171346 1.017797387 1.082360036 1.143126768 1.172850516 0.420736348 1.10916193 1 16.36535691 FTVTIGEDEREFDKENEVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 FTVTIGEDEREFDKENEVFR 20 2 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 0 ; 198.24 8.86E-22 381970000 297620 277680 218616 227030 266650 279330 255030 284220 303930 296220 FALSE TRUE 285988.6814 269760.8383 258124.7743 238747.0455 275227.0394 284978.244 258151.1334 278350.7577 269429.1406 276156.7556 1.035602699 0.976839541 0.93470382 0.864534511 0.996633375 1.031943772 0.93479927 1.007944771 0.97563842 1 18.07512789 FVHSENQHLVSPEALDFLDK ddPTM_BT-474_Pertuzumab_2h_R1 2 FVHSENQHLVSPEALDFLDK 20 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A087WY74 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 145.61 8.27E-08 1263730000 1230770 1169600 1023900 1050170 1083890 1073370 1235320 391150 1518160 1428100 FALSE TRUE 1182670.148 1136244.153 1208941.507 1104369.4 1118754.306 1095074.277 1250438.216 383072.6158 1345824.841 1331373.515 0.888308303 0.853437552 0.908040826 0.829496296 0.840300857 0.822514692 0.939209171 0.287727382 1.010854449 1 20.34448394 FVPDKEFSGSDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 FVPDKEFSGSDRR 13 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 123.02 0.0001284 178590000 182560 174980 132470 142420 160840 165870 157680 175890 181470 150830 FALSE TRUE 175425.3534 169989.7417 156410.2758 149770.3133 166013.5647 169224.005 159609.735 172257.81 160870.2864 140614.1498 1.247565438 1.208909217 1.112336675 1.06511552 1.180631999 1.203463559 1.135090141 1.225038948 1.144054753 1 17.10138225 FWSLEDGLNR ddPTM_BT-474_Pertuzumab_2h_R1 2 FWSLEDGLNR 10 0 K7EIN2;Q9BRJ7;K7ENA3;W4VSQ8;Q9BRJ7-2 K7EIN2 NUDT16L1 Protein syndesmos 0 ; 151.48 4.59E-05 90814000 99381 106156 82609 109268 104755 88408 109585 112142 112305 119918 FALSE TRUE 95497.08065 103128.5348 97538.28393 114907.3346 108124.5397 90195.67033 110926.134 109826.2285 99556.60722 111795.847 0.854209554 0.922471966 0.872467864 1.02783187 0.967160611 0.806789096 0.992220525 0.982382006 0.890521516 1 16.77050707 FYAGGSER ddPTM_BT-474_Pertuzumab_2h_R1 2 FYAGGSER 8 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 100.74 0.013699 651110000 361930 391770 349610 424720 346510 328250 403810 367110 400040 408100 FALSE TRUE 347785.3755 380597.1032 412792.304 446639.8501 357655.8088 334887.4399 408751.9476 359529.0502 354629.1363 380459.0235 0.914120454 1.000362929 1.084984922 1.173949946 0.940063941 0.88021947 1.074365233 0.944987576 0.932108622 1 18.53738155 GAGHPCYLDKPEEWHTGLLDFLQGLQ ddPTM_BT-474_Pertuzumab_2h_R1 2 GAGHPCYLDKPEEWHTGLLDFLQGLQ 26 1 F8W9U3;Q96IU4;Q96IU4-2 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 119.52 0.00022193 405690000 626500 626770 479540 552180 614900 612830 627050 397540 719020 636680 FALSE TRUE 602015.6874 608895.1333 566203.5453 580678.076 634678.8169 625221.8425 634724.0255 389330.6601 637399.864 593557.0965 1.014250678 1.025840878 0.953915889 0.978301969 1.069280143 1.053347431 1.069356308 0.6559279 1.073864448 1 19.17902729 GAGTDDHTLIR ddPTM_BT-474_Pertuzumab_2h_R1 5 GAGTDDHTLIR 11 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 196.88 5.90E-08 13293600000 7920370 8757750 7018280 9521140 7089730 6933020 7289210 8280530 8821000 9656170 FALSE TRUE 7610833.184 8507987.545 8286639.317 10012527.18 7317777.604 7073210.415 7378417.532 8109534.162 7819677.061 9002149.005 0.845446257 0.945106279 0.920517902 1.112237441 0.812892299 0.785724654 0.819628461 0.900844249 0.868645593 1 23.10183801 GAGVHSGERPPHSLSSNAR ddPTM_BT-474_Pertuzumab_2h_R1 2 GAGVHSGERPPHSLSSNAR 19 1 Q147X3;Q147X3-2;J3KNC2 Q147X3 NAA30 N-alpha-acetyltransferase 30 0 ; 128.59 1.37E-05 117749000 51638 62162 50775 73692 68705 70245 66191 47404 73109 68332 FALSE TRUE 49619.92987 60389.20062 59951.17198 77495.25295 70914.95872 71665.40203 67001.06526 46425.09083 64809.97282 63703.81278 0.77891617 0.947968387 0.941092367 1.216493167 1.113198027 1.124978222 1.051759107 0.728764713 1.01736411 1 15.9590921 GALQNIIPASTGAAK ddPTM_BT-474_Pertuzumab_2h_R1 2 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 241.52 1.61E-17 434930000 1052360 1044820 889110 937660 942410 1010200 975040 1075970 1173160 1003990 FALSE TRUE 1011232.608 1015022.757 1049791.955 986052.745 972723.4735 1030626.936 986972.8312 1053750.843 1039987.795 935988.863 1.080389573 1.084438925 1.121585947 1.05348769 1.039246846 1.101110256 1.0544707 1.125815579 1.111111292 1 19.83613184 GALSS(ph)SLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GALSSSLR 8 0 A0A1W2PR28;Q5JU85-3;Q5JU85;A0A1W2PRJ5;A0A1W2PQS2;A0A1W2PPE7;A0A1W2PPU7 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 GALS(0.132)S(0.735)S(0.132)LR 78.264 0.032597 176690000 306750 331740 274540 363730 349690 291620 294180 386540 329810 315440 TRUE FALSE 294761.8709 322279.1 324155.4851 382502.1489 360938.0964 297516.7562 297780.2628 378557.8139 292371.3515 294074.9678 1.002335809 1.095907967 1.102288602 1.300696049 1.22736763 1.011703779 1.012599831 1.287283364 0.994206864 1 18.16582446 GATYGKPVHHGVNQLK ddPTM_BT-474_Pertuzumab_2h_R1 2 GATYGKPVHHGVNQLK 16 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 171.81 3.09E-09 9806000000 8247300 8091100 7011800 7419400 8313100 9049000 9149200 4190700 10453600 9763300 FALSE TRUE 7924986.398 7860349.75 8278988.237 7802316.123 8580498.411 9231976.98 9261170.646 4104160.581 9266951.153 9102022.995 0.870684067 0.863582717 0.909576722 0.857206813 0.942702344 1.014277484 1.017484866 0.450906417 1.018119945 1 23.1177558 GDECQLVGPAQPSHWK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDECQLVGPAQPSHWK 16 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 94.203 0.0038037 0 123550 134680 100860 133510 117390 120050 119390 126740 115860 160520 FALSE TRUE 118721.5294 130839.0583 119087.6456 140400.4671 121165.956 122477.4933 120851.1305 124122.7747 102708.0585 149647.8374 0.793339426 0.874313057 0.795785944 0.938205787 0.809673952 0.81843811 0.807570177 0.829432465 0.686331726 1 17.1912119 GDGGITHSEEINGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDGGITHSEEINGK 14 0 O75363;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 247.14 8.52E-18 1797000000 2241900 2441400 1842770 2489100 2182900 2220900 2573700 2697300 2213400 2249100 FALSE TRUE 2154284.069 2371773.662 2175799.531 2617562.749 2253114.961 2265808.12 2605197.71 2641599.812 1962144.111 2096766.454 1.02743158 1.131157768 1.037692838 1.248380689 1.074566486 1.080620169 1.242483494 1.259844561 0.935795261 1 20.99973475 GDQLLSVNGVSVEGEHHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDQLLSVNGVSVEGEHHEK 19 0 Q9NUP9;G3V1D4;O14910 Q9NUP9 LIN7C;LIN7A Protein lin-7 homolog C;Protein lin-7 homolog A 0 131.11 9.39E-06 117590000 89204 83960 88750 101090 94091 86984 95457 45116 111120 120250 FALSE TRUE 85717.80906 81565.54301 104789.0992 106307.267 97117.52247 88742.87608 96625.23132 44184.33883 98506.12345 112105.3604 0.764618291 0.72757933 0.934737633 0.948279963 0.866305787 0.791602433 0.861914461 0.394132258 0.878692358 1 16.77449574 GDQPAASGDS(ph)DDDEPPPLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 GDQPAASGDSDDDEPPPLPR 20 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 GDQPAASGDS(1)DDDEPPPLPR;GDQPAASGDS(1)DDDEPPPLPR 385.91 9.22E-131 337980000 254974 335260 231293 464610 307520 256630 348270 402200 364670 310210 TRUE FALSE 245009.3342 325698.7131 273092.7902 488588.5778 317411.6601 261819.2344 352532.2324 393894.4294 323274.1904 289199.2004 0.84719921 1.126208899 0.944306865 1.689453419 1.097553726 0.905324891 1.218994492 1.362017699 1.117825326 1 18.14170404 GDTPGHATPGHGGAT(ph)SSARK ddPTM_BT-474_Pertuzumab_2h_R1 1 GDTPGHATPGHGGATSSARK 20 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDTPGHATPGHGGAT(0.333)S(0.333)S(0.333)ARK 98.3 0.00062434 51893000 21007 26119 23161 27062 26534 29098 27301 11444 30233 36299 TRUE FALSE 20186.02322 25374.11169 27346.70791 28458.67306 27387.49021 29686.3815 27635.1178 11207.6774 26801.07659 33840.4364 0.596505996 0.749816326 0.808107425 0.840966491 0.80931256 0.877245824 0.816630066 0.33119187 0.791983776 1 15.04646055 GDYPQAMK ddPTM_BT-474_Pertuzumab_2h_R1 2 GDYPQAMK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 83.005 0.043746 764720000 739940 821000 646510 657980 683890 605960 787530 780390 829020 839310 FALSE TRUE 711022.3268 797585.8838 763348.7385 691938.4267 705887.9429 618212.9264 797168.0277 764274.6738 734913.1251 782462.7861 0.908697946 1.019327562 0.97557194 0.884308416 0.902136121 0.790086043 1.018793535 0.976755301 0.93923077 1 19.57766261 GEDEEENNLEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 GEDEEENNLEVR 12 0 P04843;F8WF32 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 220.82 6.67E-11 725470000 277490 444040 219970 488200 309040 288140 334860 423680 363880 278560 FALSE TRUE 266645.384 431376.414 259723.4722 513396.0605 318980.5523 293966.3882 338958.1168 414930.8599 322573.8679 259692.8831 1.026772012 1.661102179 1.00011779 1.976935426 1.228299168 1.131977067 1.305226823 1.597775245 1.242135957 1 17.98644695 GEDIFLDMFEDEYR ddPTM_BT-474_Pertuzumab_2h_R1 3 GEDIFLDMFEDEYR 14 0 Q2KHT3;Q2KHT3-2 Q2KHT3 CLEC16A Protein CLEC16A 0 ;; 221.28 1.01E-11 70129000 44011 49028 38972.1 41619 50706 34978.8 49789 47838 49511 42124 FALSE TRUE 42291.00146 47629.76944 46015.2254 43766.96158 52337.00454 35686.0953 50398.33268 46850.12858 43890.71885 39270.90396 1.076904201 1.212851364 1.17173838 1.114488264 1.332717082 0.908715912 1.28335046 1.192998476 1.117639637 1 15.26117319 GEDSVPDTVHHVVVPVNPK ddPTM_BT-474_Pertuzumab_2h_R1 3 GEDSVPDTVHHVVVPVNPK 19 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;; 113.88 9.74E-05 2757560000 1759820 1617440 1697650 1973790 1810290 2089380 1986750 558860 2310530 2323020 FALSE TRUE 1691044.289 1571312.195 2004453.119 2075657.538 1868519.622 2131628.695 2011064.441 547319.3457 2048248.321 2165679.786 0.780837638 0.72555149 0.925553783 0.958432337 0.862786657 0.98427695 0.928606553 0.25272404 0.945776164 1 21.04638851 GEEGHDPKEPEQLRK ddPTM_BT-474_Pertuzumab_2h_R1 4 GEEGHDPKEPEQLRK 15 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 174.83 5.35E-07 1760870000 1888390 1773180 1286190 1198120 1496050 1749350 1523770 1624910 1920390 1658120 FALSE TRUE 1814589.631 1722610.643 1518633.144 1259955.117 1544171.807 1784723.056 1542418.353 1591355.041 1702395.378 1545814.055 1.173873161 1.114371186 0.982416442 0.815075469 0.998937616 1.154552224 0.997803292 1.029460843 1.101293763 1 20.55993536 GEGLY(ph)ADPYGLLHEGR ddPTM_BT-474_Pertuzumab_2h_R1 4 GEGLYADPYGLLHEGR 16 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR 220.6 6.58E-14 1521780000 1577240 1694320 1184630 1754640 1408640 1443780 1491010 1447050 1658600 1651140 TRUE FALSE 1515599.717 1645999.653 1398718.993 1845197.181 1453950.185 1472974.221 1509257.426 1417167.912 1470322.681 1539306.817 0.984598847 1.069312261 0.908668095 1.198719554 0.944548656 0.956907489 0.980478622 0.920653307 0.955184935 1 20.55384939 GELFLR ddPTM_BT-474_Pertuzumab_2h_R1 1 GELFLR 6 0 F5H0D0;Q14232-2;Q14232;H0YGG4 F5H0D0;H0YGG4 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 114.67 0.058367 163460000 126080 137430 121470 139510 133730 106590 150580 127610 132370 159760 FALSE TRUE 121152.6542 133510.631 143422.3311 146710.1278 138031.5469 108745.3228 152422.8431 124974.8089 117343.9125 148939.3129 0.813436371 0.896409607 0.962958189 0.98503293 0.926763688 0.730131761 1.023388923 0.839098868 0.787863931 1 17.18436508 GENHPHFEGGVK ddPTM_BT-474_Pertuzumab_2h_R1 2 GENHPHFEGGVK 12 0 F6WE04;Q5SRH9-5;Q5SRH9-6;Q5SRH9-4;Q5SRH9;A0A0A0MRQ0;A0A0A0MSH8;E9PAZ4;A0A0A0MSW9;Q5SRH9-3 F6WE04 TTC39A Tetratricopeptide repeat protein 39A 0 ; 99.011 0.0023343 265140000 360540 382560 328540 349560 413000 429730 398340 9971.3 460280 365880 FALSE TRUE 346449.6982 371649.7634 387914.4863 367600.8335 426284.5201 438419.435 403215.0041 9765.38917 408030.9441 341098.6217 1.015687769 1.089566887 1.137250231 1.077696625 1.249739791 1.285315762 1.182106811 0.028629225 1.196225719 1 18.3798294 GESRPET(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 GESRPETPK 9 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GES(0.004)RPET(0.996)PK 68.548 0.093375 707330000 852720 780420 685460 686010 829150 734820 746040 861900 861860 825360 TRUE FALSE 819394.7597 758163.1857 809337.87 721415.0583 855820.3628 749678.5639 755170.2607 844101.4638 764025.266 769457.632 1.064899126 0.985321549 1.051829024 0.937563068 1.112238448 0.974294792 0.981431893 1.097008371 0.992940006 1 19.55348237 GEYNVYSTFQSHEPEFDYLK ddPTM_BT-474_Pertuzumab_2h_R1 1 GEYNVYSTFQSHEPEFDYLK 20 0 P63151;P63151-2;E5RIY1;Q00005-3;Q00005-5;Q00005-4;Q66LE6;Q00005-2;Q00005;Q00005-6;Q00005-7;H0YB06 P63151 PPP2R2A;PPP2R2B;PPP2R2D Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform;Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform;Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform 0 189.48 2.17E-17 135010000 106950 115220 83219 106510 108890 117820 104340 101460 131600 131850 FALSE TRUE 102770.2758 111934.0384 98258.5245 112006.9939 112392.5457 120202.4011 105616.9441 99364.81554 116661.3197 122919.6821 0.836076648 0.910627465 0.799371776 0.911220986 0.914357602 0.97789385 0.859235416 0.808371889 0.949085759 1 16.90735641 GFGFVTYATVEEVDAAMNARPHK ddPTM_BT-474_Pertuzumab_2h_R1 2 GFGFVTYATVEEVDAAMNARPHK 23 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;A0A2R8Y4L2;F8W646;F8VYN5 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ; 290.01 1.03E-61 5527400000 4015090 4250260 2875210 3188700 3549810 4406700 3160090 3233420 3856200 3384770 FALSE TRUE 3858175.844 4129046.746 3394824.406 3353269.189 3663992.863 4495806.493 3198764.127 3166648.747 3418460.343 3155516.513 1.222676487 1.308516919 1.075837947 1.062668877 1.161138865 1.424745038 1.013705399 1.003527864 1.083328301 1 21.58944474 GFGSDKEAILDIITSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GFGSDKEAILDIITSR 16 1 E5RK69;P08133;P08133-2;E7EMC6;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 125.18 7.16E-05 207600000 547520 712260 316730 823920 469230 498030 464860 663660 653250 522900 FALSE TRUE 526122.3131 691947.0422 373970.1566 866442.6099 484323.2091 508100.5078 470549.0957 649955.1891 579095.7986 487483.5172 1.079261748 1.41942654 0.767144208 1.777378269 0.993517097 1.042292693 0.965261551 1.333286493 1.187928983 1 18.89499391 GGAESHTFK ddPTM_BT-474_Pertuzumab_2h_R1 8 GGAESHTFK 9 0 P50238;K4DIB9;H3BRQ4 P50238 CRIP1 Cysteine-rich protein 1 0 ;;;;;;; 135.79 0.00021091 24119730000 33888190 36226810 29696660 33259290 31544090 25346380 39217590 36722820 36818240 35228450 FALSE TRUE 32563802.07 35193656.85 35063507.06 34975805.94 32558734.3 25858901.17 39697546.6 35964480.93 32638787.75 32842395.7 0.991517256 1.071592254 1.067629395 1.064959032 0.99136295 0.787363425 1.20872871 1.095062652 0.993800454 1 24.96905603 GGFDS(ph)PFYR ddPTM_BT-474_Pertuzumab_2h_R1 3 GGFDSPFYR 9 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6S1;A0A2R8YEH9 A0A2R8YFV7 TSC1 Hamartin 1 GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR 138.65 0.00013697 1200640000 1888960 1901290 1796720 1688180 1795750 1999800 1814590 1989970 2135710 2142990 TRUE FALSE 1815137.355 1847067.071 2121427.272 1775307.172 1853511.93 2040237.326 1836797.495 1948876.424 1893273.154 1997843.379 0.908548375 0.924530467 1.061858649 0.888611786 0.927756374 1.021219855 0.919390136 0.975490093 0.947658447 1 20.93001206 GGLVSDAYGEDDFSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GGLVSDAYGEDDFSR 15 0 X6R3T8;J3QLH3;J3QQJ0;Q9UHR5-2;Q9UHR5;J3KS14;F5H478;J3KRU5 X6R3T8 SAP30BP SAP30-binding protein 0 86.288 0.017715 154480000 177620 177500 160970 189550 197260 169990 177870 195560 209820 217820 FALSE TRUE 170678.414 172437.8738 190060.8598 199332.6982 203605.047 173427.3143 180046.8263 191521.6177 186002.1132 203066.8574 0.840503548 0.849167983 0.93595214 0.981611184 1.002650308 0.85404047 0.886638167 0.943145623 0.915964898 1 17.63159527 GGPPCKPPAPEDEDEAWR ddPTM_BT-474_Pertuzumab_2h_R1 2 GGPPCKPPAPEDEDEAWR 18 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 0 ; 184.8 5.14E-14 1348250000 556240 550480 536430 509270 527880 636210 578070 586120 663870 652840 FALSE TRUE 534501.5258 534780.8494 633374.8338 535553.4857 544859.7396 649074.6021 585144.5936 574016.4172 588510.2608 608622.5653 0.878215098 0.878674042 1.040669324 0.879943525 0.895234207 1.066464898 0.961424415 0.943140215 0.966954389 1 19.2151883 GGQVSLTVHGTQQVHS(ph)PPEQSPVQANSSSSK ddPTM_BT-474_Pertuzumab_2h_R1 4 GGQVSLTVHGTQQVHSPPEQSPVQANSSSSK 31 0 P22670 P22670 RFX1 MHC class II regulatory factor RFX1 1 GGQVSLTVHGTQQVHS(1)PPEQSPVQANSSSSK;GGQVSLTVHGTQQVHS(1)PPEQSPVQANSSSSK;GGQVSLTVHGT(0.001)QQVHS(0.999)PPEQSPVQANSSSSK;GGQVSLTVHGT(0.003)QQVHS(0.997)PPEQSPVQANSSSSK 197.3 2.17E-25 2129780000 518975 641638 448258 696538 574420 604241 625164 290819 628339 643895 TRUE FALSE 498692.8832 623339.1125 529268.192 732486.4097 592896.741 616459.167 632814.944 284813.486 557012.5909 600283.4181 0.830762384 1.038408015 0.881697172 1.220234289 0.987694684 1.026946853 1.054193611 0.474465023 0.927916005 1 19.19528429 GGSDGYGSGR ddPTM_BT-474_Pertuzumab_2h_R1 6 GGSDGYGSGR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 196.32 7.81E-07 7199117000 3244943 3519337 2678855 3429069 3513906 3337330 3370825 3295242 3338962 3626769 FALSE TRUE 3118127.04 3418968.955 3162983.689 3606043.662 3626933.978 3404813.099 3412078.165 3227194.101 2959937.032 3381124.705 0.922215923 1.011192799 0.935482706 1.066521935 1.072700446 1.007006069 1.009154782 0.95447355 0.875429713 1 21.6890718 GHDDLGDHYLDCGDLSNALK ddPTM_BT-474_Pertuzumab_2h_R1 3 GHDDLGDHYLDCGDLSNALK 20 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6;J3KSA5;J3KRJ4;J3QLT0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ;; 158.64 1.54E-11 2901730000 2721790 2788620 2304760 2747290 2845560 3024290 2861820 513273 3616230 3073610 FALSE TRUE 2615419.438 2709091.288 2721281.401 2889077.966 2937090.022 3085443.216 2896843.809 502673.7332 3205730.731 2865431.657 0.912748846 0.945439156 0.949693354 1.008252268 1.025007878 1.076781297 1.01096245 0.175426879 1.118760143 1 21.45032106 GHGDSVDQLCWHPSNPDLFVTASGDK ddPTM_BT-474_Pertuzumab_2h_R1 2 GHGDSVDQLCWHPSNPDLFVTASGDK 26 0 Q96J01;Q96J01-2 Q96J01 THOC3 THO complex subunit 3 0 ; 151.01 7.29E-08 417250000 292961 417694 318955 418217 376009 472200 400854 179462 431200 461969 FALSE TRUE 281511.7602 405781.7761 376597.2636 439801.2295 388103.671 481748.2075 405759.7712 175756.047 382251.9837 430679.4282 0.653645709 0.942189827 0.87442594 1.021180026 0.901142812 1.118577243 0.942138734 0.408090184 0.887555706 1 18.71625489 GHHVTDSENDEPLNLNAS(ph)DS(ph)ESEELHR ddPTM_BT-474_Pertuzumab_2h_R1 2 GHHVTDSENDEPLNLNASDSESEELHR 27 0 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 GHHVTDSENDEPLNLNAS(1)DS(0.971)ES(0.029)EELHR;GHHVTDS(0.005)ENDEPLNLNAS(0.994)DS(0.856)ES(0.145)EELHR 207.78 1.08E-25 346470000 44989 62251 63078 88314 74020 82967 84239 16426.9 85780 84552 TRUE FALSE 43230.78014 60475.66243 74477.59776 92871.89612 76400.92052 84644.64959 85269.94208 16087.67877 76042.61402 78825.21773 0.548438449 0.76721212 0.944844809 1.178200312 0.969244649 1.073827032 1.081759677 0.204093046 0.964699067 1 16.26636963 GHTDSVQDISFDHSGK ddPTM_BT-474_Pertuzumab_2h_R1 4 GHTDSVQDISFDHSGK 16 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 300.89 3.73E-46 2225440000 1424830 1726810 1390660 1730510 1452270 1350330 1750270 696824 1934340 1901830 FALSE TRUE 1369146.068 1677563.07 1641983.197 1819821.828 1498983.583 1377634.598 1771690.328 682434.3409 1714761.833 1773017.36 0.772212444 0.9461628 0.926095386 1.026398201 0.845442136 0.777000061 0.99925154 0.384899977 0.967143284 1 20.75777523 GIFEPFGR ddPTM_BT-474_Pertuzumab_2h_R1 2 GIFEPFGR 8 0 Q14498-2;Q14498;G3XAC6;H0Y4X3;A0A0U1RQH7;A0A0U1RQW2;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 ; 187.63 0.00046808 842630000 1055050 1242040 1046770 1204210 1142240 1095370 1141320 1207320 1194810 1310560 FALSE TRUE 1013817.48 1206618.235 1235944.624 1266359.422 1178981.187 1117519.132 1155287.816 1182388.42 1059180.178 1221794.604 0.829777343 0.987578625 1.011581341 1.036474886 0.964958581 0.914653845 0.94556631 0.967747293 0.866905267 1 20.22057034 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK ddPTM_BT-474_Pertuzumab_2h_R1 8 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK 33 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;; 302.75 3.98E-90 8298530000 4332161 4459074 3637662.4 4052802 4815268 4903960 4409457 4415644 5054123 4465661 FALSE TRUE 4162855.359 4331905.575 4295068.915 4261967.597 4970155.468 5003121.431 4463421.254 4324459.408 4480400.146 4163197.803 0.999917745 1.040523602 1.031675438 1.023724502 1.193831209 1.201749633 1.072113665 1.038735033 1.076191994 1 21.98926068 GIPVVEHK ddPTM_BT-474_Pertuzumab_2h_R1 4 GIPVVEHK 8 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4;J3KTB7 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ;;; 103.83 0.0046967 1300940000 2180640 2129360 1737880 2338610 2233670 2163840 2183640 2211840 2273780 2289520 FALSE TRUE 2095418.178 2068632.738 2051953.575 2459305.942 2305518.024 2207594.327 2210364.04 2166164.731 2015670.027 2134448.771 0.981713971 0.969164857 0.961350585 1.152197221 1.080146807 1.034269062 1.035566686 1.014859087 0.94435156 1 21.02543211 GISQEQMQEFR ddPTM_BT-474_Pertuzumab_2h_R1 1 GISQEQMQEFR 11 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 210.08 3.25E-08 168870000 116900 140840 123360 168640 140830 103270 149650 144840 129700 176980 FALSE TRUE 112331.4188 136823.3811 145653.8961 177343.5306 145359.9248 105358.1902 151481.4615 141849.0034 114976.9997 164992.987 0.680825415 0.829267859 0.882788407 1.074854961 0.881006687 0.638561627 0.918108486 0.859727471 0.69685992 1 17.33204518 GIVDQSQQAYQEAFEISKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GIVDQSQQAYQEAFEISKK 19 1 B7Z2E6;H0YB80;P63104-2;P63104;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 216.04 6.29E-19 1185700000 790510 833990 592500 559070 642150 830740 651210 815020 825200 719180 FALSE TRUE 759615.9952 810205.4218 699577.9301 587923.6697 662805.3379 847538.132 659179.7028 798189.5522 731526.7555 670469.298 1.13296164 1.208415395 1.043415309 0.876883806 0.98856926 1.264096856 0.983161652 1.190493815 1.091066746 1 19.35481174 GIWHNNEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GIWHNNEK 8 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 163.99 0.00033272 1186670000 943340 951640 835930 1072120 846930 848350 994880 970770 932350 925480 FALSE TRUE 906473.2299 924500.159 987001.1462 1127452.242 874172.2726 865504.2183 1007055.639 950723.2603 826513.5367 862796.4153 1.050622388 1.071515994 1.143956012 1.306741917 1.013184869 1.003138403 1.16719961 1.101909145 0.957947347 1 19.71866066 GKPIFPVYPLVGSSS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 GKPIFPVYPLVGSSSPTR 18 1 A6NEL2 A6NEL2 SOWAHB Ankyrin repeat domain-containing protein SOWAHB 1 GKPIFPVYPLVGS(0.002)S(0.212)S(0.784)PT(0.003)R 248.54 9.83E-25 633710000 673040 721350 561180 678240 594110 678400 695300 698290 674880 759280 TRUE FALSE 646736.8527 700777.8043 662597.7094 713244.0477 613220.0877 692117.7128 703809.2894 683870.0675 598270.4517 707853.2893 0.913659458 0.990004306 0.936066441 1.007615644 0.866309583 0.977770003 0.994286952 0.966118372 0.845189901 1 19.43309085 GKTPEEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 GKTPEEIR 8 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;; 85.862 0.014995 1781520000 4773410 4867040 4180810 4898370 4469090 3623690 5073200 5223690 5360610 5542260 FALSE TRUE 4586859.86 4728236.785 4936375.369 5151175.463 4612842.339 3696963.495 5135287.339 5115818.976 4752096.026 5166877.794 0.887743052 0.915105209 0.95538845 0.996960963 0.892771713 0.715512083 0.993885968 0.990118052 0.919722938 1 22.30086133 GKVEEVELPVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 GKVEEVELPVEK 12 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;Q99873-5;H0YDE4;E9PNR9;Q9NR22-2;Q9NR22 E9PKG1 PRMT1;PRMT8 Protein arginine N-methyltransferase 1;Protein arginine N-methyltransferase 8 0 ; 104.17 0.0019766 1036400000 969080 950640 857900 727500 986010 1033080 937770 979320 1224090 1164680 FALSE TRUE 931207.2822 923528.678 1012941.614 765046.3622 1017725.907 1053969.585 949246.7098 959096.6998 1085136.435 1085795.186 0.857627013 0.850555141 0.932903025 0.704595463 0.937309283 0.970689131 0.874241037 0.88331272 0.999393301 1 20.05032056 GKYGQFSGLNPGGRPIT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GKYGQFSGLNPGGRPITPPR 20 2 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 1 GKYGQFSGLNPGGRPIT(1)PPR 139.36 1.02E-05 495960000 913950 763330 517140 589730 656620 634440 645700 957290 636420 690060 TRUE FALSE 878231.8236 741560.5758 610598.7017 620166.036 677740.7786 647268.8115 653602.2698 937521.627 564176.2697 643321.6216 1.365152039 1.152705818 0.949134432 0.964006207 1.053502254 1.00613564 1.015980573 1.457314033 0.876973897 1 19.29518065 GLAPDLPEDLYHLIK ddPTM_BT-474_Pertuzumab_2h_R1 4 GLAPDLPEDLYHLIK 15 0 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ;;; 189.69 2.48E-07 4015308000 2978353 2924081 2835382 2729086 2932385 2903389 3082754 3125655 3383384 3478220 FALSE TRUE 2861955.672 2840689.073 3347798.6 2869934.456 3026707.827 2962097.515 3120481.666 3061109.132 2999316.433 3242637.061 0.882601296 0.876042869 1.032430869 0.885061881 0.933409373 0.913484136 0.962328379 0.944018425 0.924962114 1 21.62873613 GLGGEVPGSHQGPDPYR ddPTM_BT-474_Pertuzumab_2h_R1 4 GLGGEVPGSHQGPDPYR 17 0 K7EM09;K7EPR0;K7ELQ9;Q6UW68 K7EM09 TMEM205 Transmembrane protein 205 0 ;;; 151.44 2.50E-07 6374110000 2292120 3811110 2102380 4631660 2499180 2417770 3466890 4064900 3236310 2617580 FALSE TRUE 2202541.416 3702420.874 2482326.833 4870700.528 2579568.394 2466658.966 3509318.837 3980958.394 2868937.657 2440288.975 0.902574014 1.517205918 1.01722659 1.995952355 1.05707497 1.010806094 1.43807511 1.631347121 1.175654886 1 21.21862057 GLGTDEDTIIDIITHR ddPTM_BT-474_Pertuzumab_2h_R1 6 GLGTDEDTIIDIITHR 16 0 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;;;;; 224.16 8.06E-15 1363193000 944863 1331066 667495 2093716 936542 1052080 1098236 1209304 1282893 1328053 FALSE TRUE 907936.7094 1293105.301 788126.1948 2201772.934 966666.724 1073353.778 1111676.541 1184331.45 1137264.365 1238102.787 0.733329025 1.044424836 0.636559584 1.778344218 0.780764516 0.866934304 0.897887116 0.956569569 0.918554078 1 20.23969966 GLMEEDAEPIFEDVMMSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 GLMEEDAEPIFEDVMMSSR 19 0 Q8WVM7;Q68DW7;Q8WVM7-2 Q8WVM7 STAG1;DKFZp781D1416 Cohesin subunit SA-1 0 70.412 0.050102 8167900 10702 10858 8285.5 9545.7 12080 11860 10369 11414 10467 11945 FALSE TRUE 10283.75401 10548.34047 9782.87416 10038.35472 12468.56417 12099.81733 10495.89892 11178.29691 9278.830041 11135.95451 0.923473062 0.947232719 0.878494443 0.901436398 1.119667305 1.086554127 0.942523509 1.003802314 0.833231676 1 13.4429376 GLPEER ddPTM_BT-474_Pertuzumab_2h_R1 2 GLPEER 6 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31;C9JXD9;F8WC73 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 110.54 0.066582 640760000 2709050 2483400 2180360 2015740 2191400 2287080 2398600 2558920 2745030 2529240 FALSE TRUE 2603177.331 2412575.864 2574399.554 2119772.583 2261888.371 2333326.325 2427954.784 2506077.408 2433425.703 2357932.322 1.104008502 1.023174347 1.091803836 0.898996364 0.959267724 0.989564587 1.029696553 1.062828388 1.032016772 1 21.16909088 GLPVTCEVAPHHLFLSHDDLER ddPTM_BT-474_Pertuzumab_2h_R1 2 GLPVTCEVAPHHLFLSHDDLER 22 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 213.45 3.06E-24 828980000 291800 330204 327511 355330 366009 399967 364010 12120.1 391930 341424 FALSE TRUE 280396.1334 320786.9052 386699.5231 373668.6239 377782.0119 408054.6068 368464.8633 11869.8157 347439.7495 318299.0484 0.880920426 1.007816099 1.214893746 1.173954574 1.186877604 1.281985004 1.157605922 0.037291395 1.09155133 1 18.28002332 GLQVDLQS(ph)DGAAAEDIVASEQSLGQK ddPTM_BT-474_Pertuzumab_2h_R1 3 GLQVDLQSDGAAAEDIVASEQSLGQK 26 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 GLQVDLQS(1)DGAAAEDIVASEQSLGQK;GLQVDLQS(1)DGAAAEDIVASEQSLGQK;GLQVDLQS(1)DGAAAEDIVASEQSLGQK 207.55 1.66E-25 284144000 163213 166264 153227 152247 156623 164185 167696 168262 177222 180190 TRUE FALSE 156834.4555 161522.3135 180918.5274 160104.4859 161660.921 167504.9332 169748.3138 164787.3309 157104.5015 167985.5708 0.933618612 0.961524926 1.076988497 0.953084751 0.962350042 0.997138816 1.010493419 0.980961223 0.935226167 1 17.35797779 GMGS(ph)LDAMDK ddPTM_BT-474_Pertuzumab_2h_R1 3 GMGSLDAMDK 10 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 GMGS(1)LDAMDK;GMGS(1)LDAMDK;GMGS(1)LDAMDK 146.5 2.99E-05 616246000 1105380 988150 845663 849356 944580 924510 887141 975760 1060680 1109450 TRUE FALSE 1062180.528 959968.9295 998493.1158 893191.3649 974963.2735 943204.2256 897998.0969 955610.215 940276.0531 1034305.963 1.026950018 0.928128584 0.965374997 0.863565905 0.942625594 0.911919934 0.868213207 0.92391444 0.909088883 1 19.98023159 GNKHDDGT(ph)QSDSENAGAHR ddPTM_BT-474_Pertuzumab_2h_R1 1 GNKHDDGTQSDSENAGAHR 19 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGT(0.499)QS(0.499)DS(0.002)ENAGAHR 70.453 0.031484 4634300 3345.1 4989.9 3503.7 3807 3537.3 5694.9 4108.2 3528.2 6075.3 4861 TRUE FALSE 3214.369794 4847.592938 4136.896529 4003.479726 3651.080467 5810.05478 4158.477381 3455.341437 5385.657414 4531.76014 0.709298307 1.069693185 0.912867495 0.883427102 0.805664985 1.282074647 0.91762963 0.762472269 1.188425081 1 12.14585579 GNKLER ddPTM_BT-474_Pertuzumab_2h_R1 2 GNKLER 6 1 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2;H3BN59;H3BMQ5 Q9NUU7;REV__Q8IV53-2 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ; 66.138 0.093207 670930000 1763540 1785280 1398180 1589540 1634260 1889760 1782190 1751080 1889530 1877660 FALSE TRUE 1694618.907 1734365.562 1650862.228 1671576.35 1686827.457 1927972.242 1804000.974 1714919.586 1675038.476 1750484.416 0.968085686 0.990791776 0.943088789 0.954922155 0.963634661 1.101393548 1.030572428 0.979682864 0.956899965 1 20.73932279 GNS(ph)IIMLEALERV ddPTM_BT-474_Pertuzumab_2h_R1 1 GNSIIMLEALERV 13 1 P62308;A8MWD9;Q49AN9;F5H013 P62308 SNRPG;SNRPGP15 Small nuclear ribonucleoprotein G;Putative small nuclear ribonucleoprotein G-like protein 15 1 GNS(1)IIMLEALERV 78.326 0.024929 4842700 8404.5 8479 5354.6 5714.2 8879.6 5651.1 8218.3 8675 6675.1 7873.4 TRUE FALSE 8076.042848 8237.187222 6322.295332 6009.110547 9165.220398 5765.369114 8318.878014 8495.858218 5917.370632 7340.127605 1.100259189 1.122213082 0.861333164 0.818665679 1.248645922 0.785458976 1.133342424 1.15745375 0.80616727 1 12.84158943 GNTFVHDPK ddPTM_BT-474_Pertuzumab_2h_R1 1 GNTFVHDPK 9 0 Q92878-2;Q92878;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;E7ESD9;E9PM98 Q92878-2 RAD50 DNA repair protein RAD50 0 61.353 0.089726 443550000 402650 433070 349290 362740 408070 397940 437860 445770 425800 444570 FALSE TRUE 386913.9928 420719.2676 412414.4729 381461.0549 421195.9421 405986.6195 443218.6617 436564.6937 377464.9691 414458.8779 0.933540125 1.015104972 0.995067291 0.920383361 1.016255085 0.979558265 1.069391163 1.053336572 0.910741666 1 18.66086944 GNVCGDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 GNVCGDSK 8 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 84.213 0.040972 61557000 215730 195217 165878 186888 179685 183665 226580 203747 179902 241550 FALSE TRUE 207299.0331 189649.6023 195855.8445 196533.3121 185464.7312 187378.8321 229352.9538 199539.5532 159480.2792 225189.6033 0.920553303 0.842177434 0.869737508 0.87274594 0.823593667 0.83209362 1.0184882 0.886095762 0.70820445 1 17.7807807 GPPDFSSDEEREPT(ph)PVLGSGAAAAGR ddPTM_BT-474_Pertuzumab_2h_R1 5 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(0.999)PVLGS(0.001)GAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR 269.35 1.39E-53 11045010000 4418470 6757770 3309586 7269440 3809707 4283949 4731209 6332110 5322440 4287640 TRUE FALSE 4245791.308 6565045.016 3907701.812 7644616.67 3932249.686 4370573.384 4789110.951 6201349.716 4718258.925 3997234.324 1.06218224 1.642396839 0.977601385 1.91247649 0.9837426 1.093399343 1.198106131 1.551410103 1.180380869 1 21.93057072 GPSLDIDT(ph)PDVNIEGPEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 GPSLDIDTPDVNIEGPEGK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPSLDIDT(1)PDVNIEGPEGK;GPSLDIDT(1)PDVNIEGPEGK 149.52 9.47E-07 129645000 248580 285680 258600 246000 242690 292010 200134 298470 304610 265360 TRUE FALSE 238865.2188 277532.6861 305334.7725 258696.0895 250496.3443 297914.6423 202583.2998 292306.4902 270031.9498 247386.9308 0.965553103 1.121856701 1.234239705 1.045714455 1.012569029 1.204245678 0.81889249 1.181576121 1.091536844 1 17.91640976 GPSPAPASS(ph)PKR ddPTM_BT-474_Pertuzumab_2h_R1 3 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GPSPAPAS(0.036)S(0.964)PKR;GPSPAPAS(0.085)S(0.915)PKR;GPSPAPAS(0.265)S(0.735)PKR 129.29 0.00014504 1150297000 844869 768000 659866 727243 755867 741575 802313 821023 852503 770880 TRUE FALSE 811850.5854 746097.392 779118.4648 764776.0984 780180.1485 756570.1546 812131.9465 804068.5881 755730.4334 718667.611 1.12966074 1.038167549 1.084115178 1.064158293 1.085592472 1.052740019 1.130052244 1.118832372 1.051571578 1 19.45496514 GRDVIAQSQSGTGK ddPTM_BT-474_Pertuzumab_2h_R1 3 GRDVIAQSQSGTGK 14 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;; 239.16 2.16E-17 602640000 630810 709740 477860 590150 630330 675330 605380 624230 694530 681790 FALSE TRUE 606157.2478 689498.9101 564219.9319 620607.7122 650605.1369 688985.6353 612788.8215 611339.4324 615689.8661 635611.756 0.953659592 1.084779983 0.887680139 0.976394326 1.023588898 1.083972455 0.964092964 0.961812658 0.968657141 1 19.27778628 GRPTSTNPIASIFAWTR ddPTM_BT-474_Pertuzumab_2h_R1 2 GRPTSTNPIASIFAWTR 17 1 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 195.97 1.50E-11 843750000 442890 674560 464730 990540 414470 437390 848970 626570 557650 468580 FALSE TRUE 425581.3692 655322.2093 548717.0489 1041661.888 427801.804 446234.3255 859359.9488 613631.1105 494347.9099 436842.6592 0.974221176 1.500133275 1.256097676 2.38452419 0.979304092 1.021498968 1.967207027 1.404695942 1.131638359 1 18.73675422 GS(ph)PTSAYPERK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSPTSAYPERK 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.809)PT(0.152)S(0.039)AYPERK 98.582 0.0033157 249300000 203000 220620 166740 175480 170780 256250 170120 195360 244400 234460 TRUE FALSE 195066.5356 214328.1336 196873.6271 184536.5438 176273.2938 261431.5506 172201.9794 191325.7477 216656.7366 218579.8154 0.892427031 0.980548608 0.900694452 0.844252446 0.806448178 1.196046168 0.787821964 0.875312972 0.991201938 1 17.73780066 GSEEVDSHCKK ddPTM_BT-474_Pertuzumab_2h_R1 1 GSEEVDSHCKK 11 1 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2;Q9Y4W2-4 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 0 134.2 9.47E-05 92613000 168610 157640 155920 163710 165520 168520 156030 160920 203520 201320 FALSE TRUE 162020.5348 153144.2615 184098.2124 172159.0927 170844.1011 171927.5899 157939.5418 157596.9458 180417.2628 187684.4171 0.863260452 0.815966844 0.980892369 0.91727963 0.910273233 0.916046162 0.841516543 0.839691159 0.961279927 1 17.51794935 GSET(ph)PGATPGSK ddPTM_BT-474_Pertuzumab_2h_R1 5 GSETPGATPGSK 12 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GSET(1)PGATPGSK;GSET(1)PGATPGSK;GSET(1)PGATPGSK;GSET(1)PGATPGSK;GSET(1)PGATPGSK 285.58 2.25E-27 7102200000 11136650 11148810 8976220 10605800 9850650 10111280 10326720 12580460 12265220 11103410 TRUE FALSE 10701417.41 10830856.85 10598422.63 11153166.61 10167505.1 10315737.01 10453101.49 12320669.1 10872923.65 10351366.15 1.033816914 1.04632149 1.023867041 1.077458419 0.982237992 0.996558025 1.009828204 1.190245705 1.050385378 1 23.30331785 GSFS(ph)SENYWR ddPTM_BT-474_Pertuzumab_2h_R1 1 GSFSSENYWR 10 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 GS(0.068)FS(0.931)S(0.001)ENYWR 120.55 0.00057114 267000000 258800 252010 247670 254890 241510 193390 237100 315700 255170 252760 TRUE FALSE 248685.8099 244822.9215 292429.4784 268044.9034 249278.3885 197300.4783 240001.7007 309180.6847 226204.1714 235640.3401 1.055361785 1.038968631 1.240999221 1.137517046 1.057876544 0.837294999 1.018508548 1.312087245 0.959955207 1 17.84622701 GSFSEQGINEFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 GSFSEQGINEFLR 13 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 297.52 2.20E-40 1045850000 507210 623560 529600 686530 517860 487420 590550 553090 621010 692710 FALSE TRUE 487387.6724 605776.6793 625310.5009 721961.8956 534517.4372 497275.9664 597777.3276 541668.4982 550515.5483 645792.1347 0.754712927 0.938036633 0.968284479 1.117947799 0.827692702 0.770024811 0.925649749 0.838766019 0.852465552 1 19.30071034 GSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNK ddPTM_BT-474_Pertuzumab_2h_R1 4 GSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNK 40 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;; 255.11 3.13E-63 2716830000 973690 1100660 915610 965250 1121240 1196640 1178910 491326 1285860 1147120 FALSE TRUE 935637.1183 1069270.254 1081081.095 1015066.668 1157305.703 1220836.881 1193337.853 481179.9464 1139894.564 1069424.541 0.874897744 0.99985573 1.010899838 0.949170914 1.082176123 1.141583005 1.11586915 0.449942869 1.065895274 1 20.02840326 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR 34 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 114.52 3.80E-06 9670900 2924.7 9399.4 4561.1 9837.1 5882.3 4760.6 7878.8 6108.7 6058.5 6449.7 FALSE TRUE 2810.399491 9131.338315 5385.392231 10344.79391 6071.509522 4856.862594 7975.223111 5982.55321 5370.764479 6012.856074 0.46739843 1.51863577 0.895646289 1.720445955 1.009754673 0.807746358 1.326361884 0.994960321 0.893213543 1 12.55383471 GTHDRDPSEKPPR ddPTM_BT-474_Pertuzumab_2h_R1 4 GTHDRDPSEKPPR 13 2 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 0 ;;; 147.73 2.58E-05 210812000 158862 166117 144369 147122 152083 175619 150221 163960 169811 177167 FALSE TRUE 152653.4974 161379.5058 170459.6898 154714.9841 156974.8878 179170.1365 152059.4495 160574.1687 150534.7672 165167.3213 0.924235474 0.977066798 1.032042467 0.936716675 0.950399187 1.084779575 0.920638831 0.972190912 0.911407693 1 17.33356875 GTHMQHAYDFYKPDMLSEYPIVDGK ddPTM_BT-474_Pertuzumab_2h_R1 1 GTHMQHAYDFYKPDMLSEYPIVDGK 25 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 75.539 0.019973 919450000 641700 593270 547890 550440 654470 665780 819620 125040 898490 783630 FALSE TRUE 616621.6546 576350.5205 646905.9107 578848.2744 675521.6219 679242.5278 829650.7547 122457.8803 796497.182 730554.0421 0.844046599 0.788922499 0.885500419 0.792341485 0.924670295 0.929763561 1.135645971 0.167623301 1.090264561 1 19.47863147 GTLDPVEK ddPTM_BT-474_Pertuzumab_2h_R1 4 GTLDPVEK 8 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 118.74 0.0042524 1165570000 2861930 3082530 2613470 2815480 2674950 2301210 3207230 3122330 3694540 3630990 FALSE TRUE 2750082.612 2994619.263 3085782.165 2960787.26 2760992.196 2347742.043 3246481.04 3057852.794 3275151.308 3385059.813 0.812417731 0.88465771 0.911588668 0.874663203 0.815640594 0.693559988 0.959061647 0.903337892 0.967531296 1 21.6907499 GTPGPPPAHGAALQPHPR ddPTM_BT-474_Pertuzumab_2h_R1 1 GTPGPPPAHGAALQPHPR 18 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 86.367 0.0020015 99699000 43069 47408 51471 53823 47211 41679 56860 47896 50416 63007 FALSE TRUE 41385.81586 46055.97026 60772.95467 56600.81148 48729.58469 42521.77794 57555.86969 46906.93086 44692.98704 58739.47977 0.704565584 0.784071811 1.034618538 0.963590616 0.829588292 0.723904572 0.979849837 0.798558841 0.760867941 1 15.84204287 GVVHDDMECSHYMK ddPTM_BT-474_Pertuzumab_2h_R1 2 GVVHDDMECSHYMK 14 0 F8VQZ7;P50579-3;P50579;F8VRR3;P50579-2 F8VQZ7 METAP2 Methionine aminopeptidase 2 0 ; 172.57 1.64E-06 658080000 661680 660170 575870 695940 651390 684080 715000 264990 804230 915850 FALSE TRUE 635820.8141 641342.598 679942.5192 731857.5468 672342.5509 697912.5663 723750.3839 259517.8639 712937.182 853818.6637 0.744678983 0.751146145 0.796354716 0.857158057 0.787453565 0.817401394 0.847662876 0.303949626 0.834998358 1 19.70357017 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_BT-474_Pertuzumab_2h_R1 5 GYDSEDDTWEPEQHLVNCEEYIHDFNR 27 0 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(0.999)EDDT(0.001)WEPEQHLVNCEEYIHDFNR;GYDS(0.999)EDDT(0.001)WEPEQHLVNCEEYIHDFNR;GYDS(0.996)EDDT(0.004)WEPEQHLVNCEEYIHDFNR;GY(0.001)DS(0.991)EDDT(0.007)WEPEQHLVNCEEYIHDFNR 296.18 1.96E-70 2809970000 196273 210740 161412 276275 241660 216841 232665 151421 249739 231683 TRUE FALSE 188602.4342 204729.9015 190582.739 290533.5859 249433.2134 221225.6736 235512.4239 148294.1034 221389.6757 215990.904 0.873196189 0.947863534 0.882364652 1.345119542 1.154832026 1.024236065 1.090381213 0.686575687 1.024995366 1 17.72061103 GYEVIYLTEPVDEYCIQALPEFDGKR ddPTM_BT-474_Pertuzumab_2h_R1 1 GYEVIYLTEPVDEYCIQALPEFDGKR 26 1 P14625 P14625 HSP90B1 Endoplasmin 0 187.62 1.80E-17 129010000 153670 184130 131490 161200 151570 183570 163720 161080 193690 177270 FALSE TRUE 147664.4065 178878.7927 155253.168 169519.5513 156445.3867 187281.9112 165723.6543 157753.6417 171703.1232 165263.345 0.893509728 1.082386374 0.939428934 1.025754085 0.946642988 1.133233211 1.002785308 0.954559172 1.038966767 1 17.33440725 HADGEKEDQFNGS(ph)PPRPQPR ddPTM_BT-474_Pertuzumab_2h_R1 7 HADGEKEDQFNGSPPRPQPR 20 2 Q69YN4-3;Q69YN4;Q69YN4-4;Q69YN4-2 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR 239.51 5.98E-30 11797120000 2323870 2180139 1833636 1849612 2080490 2140910 2180288 1184435 2606660 2256033 TRUE FALSE 2233050.591 2117963.57 2165014.814 1945070.697 2147410.85 2184200.667 2206971.017 1159976.003 2310762.885 2103229.875 1.061724454 1.007005271 1.029376218 0.924801763 1.021006251 1.038498308 1.04932468 0.551521266 1.098673479 1 21.00417511 HAEATLGSGNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 HAEATLGSGNLR 12 0 Q9H8S9;Q7L9L4;Q7L9L4-2;D6RCK3;Q9H8S9-2 Q9H8S9 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 0 ;;; 179.35 2.08E-05 2202400000 952650 1053550 854780 1022270 1006210 993610 1017750 726310 1112110 1107790 FALSE TRUE 915419.3848 1023503.786 1009257.76 1075029.477 1038575.658 1013701.475 1030205.529 711311.4447 985867.9351 1032758.397 0.886382902 0.991038939 0.977244788 1.040930271 1.005632742 0.981547551 0.997528108 0.688749128 0.954596872 1 19.97807136 HAPTYTIPLS(ph)PVLSPTLPAEAPTAQVPPSLPR ddPTM_BT-474_Pertuzumab_2h_R1 3 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 HAPTYTIPLS(0.997)PVLS(0.003)PTLPAEAPTAQVPPSLPR;HAPTYTIPLS(0.999)PVLSPTLPAEAPTAQVPPSLPR;HAPT(0.057)Y(0.006)T(0.051)IPLS(0.885)PVLS(0.001)PTLPAEAPTAQVPPSLPR 199.15 5.55E-27 587232000 617760 667826 488576 638691 608379 654279 681274 552516 769855 773401 TRUE FALSE 593617.2562 648780.2564 576872.5515 671653.9191 627948.0631 667508.9697 689611.635 541106.3515 682464.2879 721017.8614 0.823304509 0.899811629 0.800080806 0.931535757 0.870918873 0.925787009 0.956441819 0.750475655 0.946528962 1 19.45967547 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR ddPTM_BT-474_Pertuzumab_2h_R1 2 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR 32 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 340 2.03E-117 552860000 287972 282207 267307 289955 292443 290136 323197 181541 357830 311936 FALSE TRUE 276717.7359 274158.7327 315615.3211 304919.6123 301849.6947 296002.7487 327152.3816 177792.1149 317210.6385 290808.2969 0.951546909 0.942747286 1.085303702 1.048524459 1.03796796 1.017862117 1.124976093 0.611372223 1.090789506 1 18.1497089 HATALEELSEQLEQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 HATALEELSEQLEQAK 16 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 129.01 5.77E-05 43757000 38947 35023 36930 39333 33094 38752 43415 31983 44921 44911 FALSE TRUE 37424.90818 34024.17833 43604.0725 41362.98084 34158.49857 39535.59199 43946.32576 31322.53987 39821.7564 41869.13797 0.89385428 0.812631451 1.041437073 0.987910973 0.815839547 0.944265727 1.04961143 0.748105679 0.951100461 1 15.35359959 HCPYLDTINR ddPTM_BT-474_Pertuzumab_2h_R1 2 HCPYLDTINR 10 0 Q53GS9;B9A018;Q53GS9-3;F8WC91;A0A087X1B2;C9JIU2 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 ; 196.88 3.25E-07 804390000 688070 712940 592980 617050 635440 679580 690270 556720 772960 767370 FALSE TRUE 661179.4637 692607.6492 700144.6768 648896.0244 655879.5047 693321.5732 698717.7307 545223.5375 685216.8213 715395.3464 0.924215494 0.968146708 0.978682179 0.907045353 0.916807061 0.969144651 0.976687554 0.762128997 0.957815598 1 19.44838121 HDELLAEHIK ddPTM_BT-474_Pertuzumab_2h_R1 1 HDELLAEHIK 10 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 0 118.28 0.00048931 178130000 227410 215110 180300 195920 218250 185420 208050 62158 264060 212200 FALSE TRUE 218522.5658 208975.2734 212884.2208 206031.4547 225270.2095 189169.3194 210596.1781 60874.41558 234085.0158 197827.505 1.104611645 1.056350953 1.076110325 1.041470218 1.138720369 0.956233661 1.064544479 0.30771462 1.183278411 1 17.5938835 HDMLAWINESLQLNLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 HDMLAWINESLQLNLTK 17 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 290.2 5.77E-46 821760000 939650 887730 874780 878050 959480 950270 964070 617280 1121620 1071210 FALSE TRUE 902927.4392 862412.8096 1032872.205 923366.2657 990342.5456 969485.1105 975868.577 604532.9523 994298.3998 998655.9926 0.904142614 0.863573459 1.034262262 0.924608947 0.991675365 0.970789859 0.977181917 0.605346543 0.995636543 1 19.92962827 HDNLLHGTK ddPTM_BT-474_Pertuzumab_2h_R1 2 HDNLLHGTK 9 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 190.57 2.13E-05 646840000 621250 629410 568840 575010 534220 525200 631420 96950 717860 608840 FALSE TRUE 596970.8632 611459.8431 671642.0418 604686.335 551403.6715 535819.9038 639147.5068 94947.94862 636371.5423 567602.7245 1.051740658 1.07726728 1.183296015 1.065333743 0.971460579 0.944005165 1.126047285 0.167278881 1.121156603 1 19.11452199 HEDLVPPAGS(ph)PELS(ph)PPQPLFRPR ddPTM_BT-474_Pertuzumab_2h_R1 1 HEDLVPPAGSPELSPPQPLFRPR 23 1 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 2 HEDLVPPAGS(1)PELS(1)PPQPLFRPR 61.101 0.073148 273670000 57637 57793 53740 58206 60924 65272 60532 36650 65765 64928 TRUE FALSE 55384.48232 56144.80023 63452.01344 61210.01864 62883.67579 66591.84456 61272.80872 35893.16469 58299.63291 60530.36873 0.9149867 0.927547633 1.04826742 1.011228247 1.038878122 1.100139417 1.012265579 0.592977797 0.963146832 1 15.88537152 HEEAPGHRPTTNPNASK ddPTM_BT-474_Pertuzumab_2h_R1 5 HEEAPGHRPTTNPNASK 17 1 P21291;E9PS42;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;;; 105.39 0.00051873 2457796000 506381 463730 431946 473789 475021 470430 507985 130538.8 556848 504318 FALSE TRUE 486591.0707 450504.8744 510008.2508 498241.3071 490300.4819 479942.4169 514201.8724 127843.1282 493636.9495 470160.0927 1.034947624 0.958194627 1.084754446 1.05972692 1.042837301 1.020806369 1.093674007 0.271914036 1.049933751 1 18.84279256 HEENHRPLFHK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEENHRPLFHK 11 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 68.536 0.036754 55190000 31068 34642 29528 41008 39622 37316 38424 22721 46607 38271 FALSE TRUE 29853.82821 33654.04408 34864.36645 43124.42779 40896.47761 38070.55509 38894.24441 22251.80341 41316.36875 35678.87108 0.836736906 0.943248569 0.977171233 1.20868252 1.146237994 1.067033623 1.090119817 0.623668932 1.158006616 1 15.12278235 HEHPPNPPVS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 2 HEHPPNPPVSPGK 13 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 HEHPPNPPVS(1)PGK;HEHPPNPPVS(1)PGK 154.39 2.97E-05 963500000 1163370 1040060 1121080 1077170 1137060 1216330 1318570 21552.9 1641320 1061020 TRUE FALSE 1117904.214 1010398.507 1323684.094 1132762.873 1173634.568 1240925.026 1334707.054 21107.82508 1455004.235 989156.1703 1.130159471 1.02147521 1.338195256 1.145181021 1.18650078 1.254528924 1.349339057 0.021339224 1.47095502 1 19.91583879 HEIVDT(ph)PPGPEHLQDK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEIVDTPPGPEHLQDK 16 0 A0A499FJD3;A0A3B3ISA1;Q96S15 A0A499FJD3 WDR24 WD repeat-containing protein 24 1 HEIVDT(1)PPGPEHLQDK 127.32 0.00012483 273170000 99138 89819 85414 87047 84450 91506 98854 45829 129810 116250 TRUE FALSE 95263.57736 87257.45006 100850.2098 91539.5061 87166.41095 93356.31402 100063.8048 44882.61513 115074.513 108376.284 0.879007601 0.805134176 0.930556079 0.844645182 0.804294148 0.86140907 0.923299832 0.414136871 1.061805303 1 16.72568956 HEIVPK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEIVPK 6 0 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 71.359 0.088439 308460000 616390 598740 507410 572180 591630 593400 634140 423790 771150 732010 FALSE TRUE 592300.7973 581664.5214 599110.2743 601710.2784 610660.3163 605398.9546 641900.795 415038.5884 683612.2849 682430.3107 0.867928619 0.852342741 0.877906894 0.881716813 0.89483176 0.887122018 0.94061003 0.608177248 1.001732007 1 19.3803222 HELQANCYEEVKDR ddPTM_BT-474_Pertuzumab_2h_R1 37 HELQANCYEEVKDR 14 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 287.85 2.36E-34 1.50025E+11 39165312.4 35156485.4 31321434.1 32827814 35250189 35029403.7 38491162.7 27529530.77 44155809.3 39790374.6 FALSE TRUE 37634688.69 34153856.86 36981913.98 34522061.41 36384043.34 35737722.24 38962229.06 26961036.34 39143426.94 37095337.09 1.014539607 0.920704852 0.996942389 0.930630751 0.980825252 0.963402008 1.050326864 0.726803918 1.055211518 1 25.14473451 HELTEISNVDVETQSGK ddPTM_BT-474_Pertuzumab_2h_R1 3 HELTEISNVDVETQSGK 17 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 202.03 1.10E-11 1024390000 798910 760540 707330 663070 631550 743720 738580 448340 857440 738110 FALSE TRUE 767687.714 738850.1438 835160.2655 697291.1222 651864.3793 758758.528 747618.963 439081.6223 760107.0059 688117.1523 1.115635196 1.073727259 1.213689068 1.013331988 0.947315987 1.102658937 1.086470466 0.638091379 1.104618601 1 19.39229468 HEMPPHIYAITDTAYR ddPTM_BT-474_Pertuzumab_2h_R1 6 HEMPPHIYAITDTAYR 16 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ;;;;; 195.2 5.25E-11 1444771000 624356 639792 529708 624531 582368 621018 640067 321391 696400 675870 FALSE TRUE 599955.4773 621545.7586 625438.0189 656763.1198 601100.3956 633575.4095 647900.3314 314754.1635 617347.5915 630092.7229 0.952170142 0.986435386 0.992612668 1.042327734 0.953987205 1.00552726 1.028261886 0.499536262 0.97977261 1 19.26520462 HENAIK ddPTM_BT-474_Pertuzumab_2h_R1 2 HENAIK 6 0 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0;E9PIA9 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 80.462 0.064449 1484420000 1910210 1831790 1632330 1943520 1777230 1835420 1976900 1397210 2215520 2232270 FALSE TRUE 1835556.881 1779549.143 1927328.342 2043825.3 1834396.217 1872533.45 2001093.894 1368357.125 1964023.458 2081076.365 0.882022838 0.855109968 0.926120913 0.982100097 0.881465115 0.89979084 0.961566777 0.657523745 0.943753671 1 20.98889847 HEQNIDCGGGYVK ddPTM_BT-474_Pertuzumab_2h_R1 4 HEQNIDCGGGYVK 13 0 P27797 P27797 CALR Calreticulin 0 ;;; 169.04 2.92E-05 25351000000 17245900 18442800 15169200 18800900 16161900 18102300 17840100 12274600 21480200 20941800 FALSE TRUE 16571911.16 17916829.4 17910611.88 19771216.7 16681762.19 18468340.91 18058432.48 12021125.22 19041857.75 19523393.23 0.848823305 0.91771083 0.917392364 1.012693668 0.854449941 0.945959582 0.924963825 0.615729299 0.975335461 1 24.21870048 HEYGSPGILEFFHHQLK ddPTM_BT-474_Pertuzumab_2h_R1 1 HEYGSPGILEFFHHQLK 17 0 Q7L576;Q7L576-2;Q7L576-3;Q96F07;Q96F07-2;E7EVJ5;H7C229;E7EW33 Q7L576 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 238.32 1.05E-20 606020000 429380 469150 417650 431360 402600 460980 481410 55971 566040 449150 FALSE TRUE 412599.3549 455770.3013 493128.6456 453622.5413 415549.9946 470301.3314 487301.6396 54815.17929 501785.5122 418728.6704 0.985362083 1.088462132 1.177680633 1.083332891 0.992408746 1.123164867 1.163764686 0.130908589 1.1983548 1 18.67565618 HFDETVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFDETVNR 8 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 172.21 0.00028488 758140000 157642 308590 158321 308590 179854 155319 293680 172508 217670 207620 FALSE TRUE 151481.1764 299789.3153 186933.1265 324516.3669 185639.1672 158459.6566 297274.1437 168945.6495 192961.0141 193557.7125 0.782615037 1.548836838 0.965774622 1.676587116 0.959089487 0.818668781 1.53584241 0.872843801 0.996917207 1 17.56240427 HFIMQVVCEATQCPDTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFIMQVVCEATQCPDTR 17 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 241.87 2.22E-20 2378200000 883630 833320 604280 826910 866350 887010 829920 520630 942570 946450 FALSE TRUE 849096.7627 809554.5295 713486.8381 869586.9242 894216.9345 904945.9499 840076.8092 509878.8086 835573.4052 882346.0985 0.962317127 0.917502249 0.808624687 0.98553949 1.013453719 1.025613364 0.952094434 0.577867131 0.946990536 1 19.75098514 HFLLEEDKPEEPTAHAFVSTLTR ddPTM_BT-474_Pertuzumab_2h_R1 5 HFLLEEDKPEEPTAHAFVSTLTR 23 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 269.07 8.13E-45 14020530000 7623080 7128880 6125810 6120280 7029580 7179740 7951450 3988050 9908450 8702230 FALSE TRUE 7325161.606 6925571.322 7232880.135 6436148.384 7255692.825 7324919.262 8048762.224 3905695.374 8783684.296 8112820.211 0.902911862 0.853657685 0.891537092 0.793330583 0.894349022 0.902881991 0.992104104 0.481422646 1.082691847 1 22.95177209 HFLVEDK ddPTM_BT-474_Pertuzumab_2h_R1 3 HFLVEDK 7 0 P53992;P53992-2 P53992 SEC24C Protein transport protein Sec24C 0 ;; 139.28 0.0027038 730770000 1243800 1266170 1152300 1180030 1281110 1226870 1348040 1008340 1634470 1586850 FALSE TRUE 1195190.921 1230060.071 1360546.243 1240931.49 1322318.067 1251678.152 1364537.717 987517.4266 1448931.818 1479371.236 0.807904664 0.831474914 0.919678719 0.838823589 0.893837892 0.846087933 0.922376807 0.667525096 0.979424084 1 20.4965527 HFTEFVPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 HFTEFVPLR 9 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 143.7 0.00010131 952560000 450490 553040 460140 584310 450080 430800 533400 463320 537460 618020 FALSE TRUE 432884.3528 537267.8407 543297.5338 614466.3091 464557.232 439511.0712 539927.9088 453752.2801 476449.794 576160.9549 0.751325388 0.932496095 0.942961388 1.066483773 0.806297664 0.762826893 0.937112979 0.787544307 0.826938705 1 19.13611237 HGDEIITSTTSNYETQTFSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGDEIITSTTSNYETQTFSSK 21 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 213.15 5.65E-23 1341870000 417310 419990 336280 359860 402740 388510 415640 349320 470510 448940 FALSE TRUE 401001.0638 408012.2964 397053.2765 378432.4177 415694.4979 396365.9384 420726.7267 342106.4199 417099.6773 418532.8939 0.958111225 0.974863153 0.948678783 0.904187994 0.993218225 0.947036527 1.005241721 0.817394343 0.996575618 1 18.67498149 HGDGTTLDIMLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGDGTTLDIMLK 12 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 147.37 6.55E-05 242040000 1103890 1110020 945590 1038000 1001080 1061240 1121460 805540 1348950 1266340 FALSE TRUE 1060748.758 1078363.316 1116479.148 1091571.304 1033280.647 1082699 1135184.763 788905.3175 1195822.851 1180569.664 0.898505858 0.913426246 0.945712211 0.924614055 0.87523903 0.917098781 0.961556779 0.668241224 1.012920193 1 20.17105174 HGEIDYEAIVK ddPTM_BT-474_Pertuzumab_2h_R1 3 HGEIDYEAIVK 11 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;; 140.07 3.88E-05 2147460000 3841110 3635080 3262380 3371960 3477550 3727680 3694160 2567190 4634530 4322570 FALSE TRUE 3690995.175 3531411.078 3851964.637 3545987.26 3589408.554 3803056.244 3739370.235 2514176.629 4108437.584 4029798.484 0.915925496 0.876324484 0.955870288 0.879941584 0.890716637 0.943733603 0.927929833 0.623896366 1.0195144 1 21.94227627 HGGS(ph)PQPLAT(ph)TPLSQEPVNPPSEAS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 HGGS(0.997)PQPLAT(0.79)T(0.213)PLSQEPVNPPS(0.045)EAS(0.795)PT(0.16)R 126.71 0.00010186 328060000 89669 84344 79765 99804 83017 98097 94081 43692 102450 104040 TRUE FALSE 86164.63635 81938.5917 94180.30986 104954.8964 85687.3172 100080.5886 95232.39142 42789.74493 90820.30551 96993.27813 0.888356781 0.844786291 0.970998317 1.082084227 0.883435624 1.031830148 0.981845271 0.441161963 0.936356697 1 16.56559715 HGGS(ph)PQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 6 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HGGS(1)PQPLATTPLSQEPVNPPS(0.001)EAS(0.854)PT(0.145)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.006)EAS(0.895)PT(0.099)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.005)EAS(0.824)PT(0.17)R;HGGS(0.999)PQPLAT(0.001)TPLSQEPVNPPS(0.353)EAS(0.548)PT(0.099)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.001)EAS(0.842)PT(0.157)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.01)EAS(0.85)PT(0.14)R 257.14 7.44E-54 24644910000 1774390 1786450 1717540 2110880 1853190 1923950 2035630 1166580 2239670 2092890 TRUE FALSE 1705044.877 1735502.195 2027937.684 2219822.77 1912799.539 1962853.587 2060542.649 1142489.715 1985432.051 1951136.696 0.873872589 0.889482628 1.039362177 1.137707457 0.980351373 1.006005162 1.056072931 0.585550832 1.017577115 1 20.89588343 HGGVCAPAAVATS(ph)PPGAIPK ddPTM_BT-474_Pertuzumab_2h_R1 4 HGGVCAPAAVATSPPGAIPK 20 0 Q9Y6A5;A0A494BZT8;E7EMT0 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 HGGVCAPAAVAT(0.035)S(0.965)PPGAIPK;HGGVCAPAAVAT(0.088)S(0.912)PPGAIPK;HGGVCAPAAVAT(0.004)S(0.996)PPGAIPK;HGGVCAPAAVAT(0.003)S(0.997)PPGAIPK 204.31 6.28E-22 5179660000 1430470 1356250 1293510 1381940 1433960 1459540 1454940 1107710 1518840 1668320 TRUE FALSE 1374565.651 1317571.078 1527276.031 1453262.089 1480084.626 1489052.899 1472745.991 1084835.401 1346427.651 1555323.2 0.883781358 0.847136516 0.981966983 0.934379484 0.951625119 0.957391299 0.94690672 0.697498373 0.865689942 1 20.56878298 HGITQANELVNLTEFFVNHILPDLK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGITQANELVNLTEFFVNHILPDLK 25 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 185.35 1.00E-17 924860000 323600 353422 306970 309106 329087 342765 358931 173624 443806 410690 FALSE TRUE 310953.3542 343342.7506 362446.3075 325058.9977 339672.3822 349695.9431 363323.7049 170038.6037 393427.0035 382873.6005 0.812156685 0.896752218 0.946647424 0.8489982 0.887165847 0.913345665 0.948939035 0.444111591 1.027563674 1 18.54650866 HGIVEDWDLMER ddPTM_BT-474_Pertuzumab_2h_R1 10 HGIVEDWDLMER 12 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;;;;;;;; 245.58 1.35E-16 7765780000 3366753 3723332 3181889 3925291 3703049 3828313 3861641 2385024 4107613 4086006 FALSE TRUE 3235176.571 3617146.217 3756927.123 4127875.739 3822160.934 3905724.112 3908900.918 2335772.421 3641333.993 3809257.174 0.849293293 0.949567344 0.9862624 1.083643228 1.003387474 1.025324344 1.026158314 0.613183178 0.955917079 1 21.86107826 HGLYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HGLYEK 6 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 97.596 0.040892 2843600000 7801600 7814100 6790600 6912100 7423300 6869900 7719000 5407300 8701600 8485900 FALSE TRUE 7496704.847 7591249.519 8017812.476 7268834.309 7662077.186 7008814.085 7813467.431 5295637.365 7713830.848 7911142.435 0.947613434 0.959564258 1.013483519 0.918809688 0.968517158 0.885942093 0.987653489 0.669389713 0.975059027 1 22.91545462 HGNEVCK ddPTM_BT-474_Pertuzumab_2h_R1 3 HGNEVCK 7 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 0 ;; 77.282 0.038468 773700000 1051760 1047150 808420 993110 919400 950490 1015230 731820 1068900 1117750 FALSE TRUE 1010656.056 1017286.307 954519.4772 1044364.526 948973.336 969709.559 1027654.688 716707.6613 947562.9532 1042043.797 0.969878674 0.976241412 0.916007062 1.002227094 0.910684694 0.930584263 0.986191455 0.687790344 0.909331216 1 19.99098448 HIDYFNNQIIVDLVEQQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 HIDYFNNQIIVDLVEQQHK 19 0 J3QRN6;O94832;K7EIG7 J3QRN6 MYO1D Unconventional myosin-Id 0 ; 111.57 0.00012353 442940000 248040 261410 225945 243080 248400 251630 252990 207974 295490 277130 FALSE TRUE 238346.3226 253954.8427 266778.2876 255625.3879 256390.0116 256718.131 256086.1673 203679.2642 261947.214 258359.7383 0.922536631 0.982950534 1.032584602 0.9894165 0.992376031 0.993646041 0.99119998 0.788355282 1.013885584 1 17.97902174 HILRPGTALVLLEAQAATGFIIDPVENR ddPTM_BT-474_Pertuzumab_2h_R1 1 HILRPGTALVLLEAQAATGFIIDPVENR 28 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 121.86 2.87E-05 45260000 118000 80941 69759 52017 99954 82715 90271 108590 76766 67211 FALSE TRUE 113388.4295 78632.64193 82366.00308 54701.6036 103169.1112 84387.55397 91375.7635 106347.5786 68051.84551 62658.7391 1.809618757 1.254934955 1.314517404 0.873008369 1.646523895 1.346780276 1.458308367 1.697250536 1.086071097 1 15.93522812 HIYYITGETK ddPTM_BT-474_Pertuzumab_2h_R1 7 HIYYITGETK 10 0 P07900;P07900-2;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ;;;;;; 183.47 2.37E-06 23783350000 26639990 25831880 22542610 23760680 24771560 25841630 25575020 21103650 31372210 29749450 FALSE TRUE 25598869.74 25095180.07 26616561.08 24986971.54 25568359.72 26364165.46 25888014.75 20667852.25 27810968.24 27734493.25 0.922997565 0.904836438 0.959691632 0.900934851 0.92189749 0.950591209 0.933423031 0.74520389 1.002757396 1 24.72517803 HKDAAIYLVTSLASK ddPTM_BT-474_Pertuzumab_2h_R1 2 HKDAAIYLVTSLASK 15 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 169.04 7.33E-07 1911310000 3886000 3846300 3266500 2967700 3661300 3656200 3636500 2648600 4694700 4236900 FALSE TRUE 3734130.824 3736607.29 3856829.213 3120863.353 3779069.04 3730130.869 3681004.575 2593905.484 4161777.338 3949930.989 0.945366092 0.945993057 0.976429518 0.790105792 0.956743054 0.944353428 0.931916174 0.656696406 1.053632924 1 21.91339602 HKDSMDELFSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 HKDSMDELFSHR 12 1 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 166.38 3.36E-05 41289000 24422 30834 27079 32426 29586 34766 35315 12285 38067 32183 FALSE TRUE 23467.56124 29954.64451 31972.77767 34099.50975 30537.66056 35468.99234 35747.19553 12031.31046 33745.79375 30003.21674 0.782168173 0.998381099 1.065644992 1.136528461 1.017812884 1.182172986 1.191445432 0.401000685 1.124739192 1 14.87282956 HKEEDKNSER ddPTM_BT-474_Pertuzumab_2h_R1 6 HKEEDKNSER 10 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;;;; 237.37 2.16E-12 1229254000 691012 544190 491953 459535 521382 510790 561738 419010 699341 642447 FALSE TRUE 664006.4871 528670.234 580859.8505 483251.6564 538152.7255 521118.5238 568612.7177 410357.2971 619954.7416 598933.4925 1.108648114 0.882686042 0.969823625 0.80685362 0.898518337 0.870077447 0.949375389 0.685146685 1.035097802 1 19.19203628 HKMS(ph)PPPSGFGER ddPTM_BT-474_Pertuzumab_2h_R1 8 HKMSPPPSGFGER 13 1 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(0.999)PPPS(0.001)GFGER;HKMS(0.98)PPPS(0.02)GFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER 132.62 7.07E-05 11831370000 2779742 2664427 2313033 2497948 2550658 2870931 2809626 1847026 3350632 2973307 TRUE FALSE 2671106.609 2588440.151 2731049.516 2626867.396 2632702.231 2928983.192 2844011.043 1808884.268 2970282.302 2771922.269 0.963629695 0.933806904 0.985254726 0.947669935 0.949774913 1.056661374 1.026006781 0.652573951 1.07156046 1 21.40245537 HKYENK ddPTM_BT-474_Pertuzumab_2h_R1 2 HKYENK 6 1 Q9UDW1 Q9UDW1 UQCR10 Cytochrome b-c1 complex subunit 9 0 ; 114.19 0.015322 3351400000 457070 703710 441030 971040 348130 494780 911630 590340 653290 553160 FALSE TRUE 439207.1991 683640.8798 520733.9317 1021155.491 359327.9176 504784.7906 922786.8006 578149.2727 579131.258 515693.9805 0.851681842 1.32567163 1.009773143 1.980157864 0.69678517 0.978845613 1.789407741 1.121109213 1.123013415 1 18.97615568 HLAEYTHVEAECPFLTFDDLLNR ddPTM_BT-474_Pertuzumab_2h_R1 6 HLAEYTHVEAECPFLTFDDLLNR 23 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;;; 210.06 4.22E-25 1363788000 519552 576190 558592 681476 641000 670129 651142 121966.8 711718 623404 FALSE TRUE 499247.3334 559757.6253 659542.0002 716647.058 661618.3471 683679.4675 659110.8706 119448.143 630926.7564 581180.2918 0.859023165 0.963139379 1.134832013 1.233089057 1.138404651 1.176363819 1.134090195 0.20552683 1.085595581 1 19.14862626 HLEPEPEEEIIAEDYDDDPVDYEATR ddPTM_BT-474_Pertuzumab_2h_R1 4 HLEPEPEEEIIAEDYDDDPVDYEATR 26 0 O60828-2;O60828;A0A5H1ZRR1;O60828-3;O60828-5;O60828-4;O60828-6;O60828-10;O60828-9;O60828-8;O60828-7 O60828-2 PQBP1 Polyglutamine-binding protein 1 0 ;;; 212.63 5.99E-26 1039920000 454009 504389 414062 518808 475271 515010 515660 265525 536194 574135 FALSE TRUE 436265.8263 490004.3196 488892.2142 545583.7431 490558.5233 525423.8551 521970.8013 260041.816 475327.505 535248.3251 0.81507182 0.915471 0.913393263 1.019309576 0.916506415 0.981645024 0.975193713 0.485833965 0.88805043 1 19.02984885 HLFLTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLFLTSK 7 0 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 125.01 0.0040911 443530000 772910 753110 865090 875950 784800 564960 940890 664930 1035500 1067100 FALSE TRUE 742703.8227 731632.0402 1021431.007 921157.8845 810043.8047 576383.8783 952404.8933 651198.9631 917954.3812 994824.3665 0.746567784 0.7354384 1.026745063 0.925950264 0.814258106 0.57938255 0.957359837 0.654586865 0.922730094 1 19.92408232 HLFSS(ph)TENLAAGSWK ddPTM_BT-474_Pertuzumab_2h_R1 3 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.416)S(0.461)T(0.122)ENLAAGSWK;HLFS(0.119)S(0.762)T(0.119)ENLAAGSWK;HLFS(0.121)S(0.776)T(0.103)ENLAAGSWK 273.43 1.22E-33 2820240000 2328510 2518480 2022220 2869910 1925730 1819550 2431480 2453310 2827760 2668120 TRUE FALSE 2237509.255 2446655.416 2387680.138 3018026.399 1987672.854 1856342.548 2461237.18 2402648.291 2506764.54 2487405.856 0.899535253 0.983617294 0.959907742 1.213322865 0.799094707 0.746296606 0.989479531 0.965925318 1.00778268 1 21.24621049 HLFSST(ph)ENLAAGSWK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.318)S(0.221)T(0.461)ENLAAGSWK 197.38 3.11E-08 1601100000 1116600 1222100 989800 1434300 1006700 841850 1268400 1130400 1390500 1188700 TRUE FALSE 1072962.038 1187246.905 1168678.878 1508324.395 1039081.42 858872.7838 1283923.059 1107056.845 1232656.269 1108188.29 0.968212755 1.071340417 1.054585117 1.361072309 0.937639776 0.775024237 1.158578438 0.998979014 1.112316635 1 20.0797716 HLLDEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLLDEK 6 0 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 0 117.7 0.022498 178640000 446250 421050 404650 428800 445820 444050 469290 285990 570950 536970 FALSE TRUE 428810.0566 409042.0663 477779.2564 450930.4194 460160.2052 453028.9952 475033.3114 280084.2066 506138.1496 500600.5436 0.856591272 0.817102721 0.95441218 0.900778925 0.919216351 0.904971041 0.948926879 0.559496409 1.011061926 1 18.93330033 HLLQAPLDDAQEILQAR ddPTM_BT-474_Pertuzumab_2h_R1 3 HLLQAPLDDAQEILQAR 17 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;; 271.68 1.29E-35 469875000 291006 315235 275310 308344 317939 327082 312678 258488 354189 333407 FALSE TRUE 279633.1638 306244.8064 325064.6412 324257.6708 328165.7967 333695.8221 316504.6469 253150.1325 313982.9496 310825.0469 0.899648103 0.985264249 1.045812249 1.043216028 1.055789422 1.073580863 1.018272659 0.814445731 1.010159743 1 18.24574324 HLLS(ph)PQLVQYQCGDSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLLSPQLVQYQCGDSGK 17 0 Q9P209 Q9P209 CEP72 Centrosomal protein of 72 kDa 1 HLLS(1)PQLVQYQCGDSGK;HLLS(1)PQLVQYQCGDSGK 203.71 1.02E-17 265350000 355500 373050 307760 357290 349380 354270 390670 278090 471860 443630 TRUE FALSE 341606.667 362410.9793 363379.0781 375729.7797 360618.125 361433.5821 395451.1363 272347.3443 418296.431 413582.545 0.82596974 0.876272424 0.878613187 0.908475912 0.871937487 0.873909179 0.956160121 0.65850783 1.011397691 1 18.65781577 HLNDLLEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 HLNDLLEDR 9 0 O95239;O95239-2;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 0 ; 161.17 6.47E-05 254650000 199372 218510 193779 229533 241440 149528 216950 198608 257780 259360 FALSE TRUE 191580.3218 212278.3087 228799.1759 241379.2256 249206.1369 152551.5586 219605.099 194506.6754 228517.8951 241793.3162 0.792330925 0.877932906 0.946259307 0.998287419 1.030657674 0.630917186 0.908234779 0.804433631 0.945095996 1 17.88341484 HLPDYRDPPDGSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 HLPDYRDPPDGSGR 14 1 Q96HQ2;Q96HQ2-2 Q96HQ2 CDKN2AIPNL CDKN2AIP N-terminal-like protein 0 86.497 0.004396 228260000 74129 79049 61382 79599 76431 54787 78462 66498 67969 82586 FALSE TRUE 71231.95673 76794.59992 72475.09284 83707.11393 78889.47253 55894.83068 79422.24143 65124.79306 60253.44407 76992.37666 0.925181944 0.997431217 0.941328168 1.087213015 1.024640048 0.725978767 1.03155981 0.845860277 0.78258974 1 16.23242799 HLQGGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 HLQGGEK 7 0 Q8N163-2;Q8N163;E5RHH8;E5RGU7;E5RFJ3;H0YC58 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 163.67 0.0012263 234190000 919450 837250 667920 841630 818160 862810 840370 656710 902880 956330 FALSE TRUE 883516.8775 813372.4498 788628.0018 885066.6252 844476.8594 880256.6094 850654.6994 643148.709 800388.8476 891556.9173 0.990982023 0.912305691 0.884551492 0.992720272 0.947193436 0.987325197 0.954122707 0.721377061 0.89774285 1 19.76596738 HLTGEFEK ddPTM_BT-474_Pertuzumab_2h_R1 6 HLTGEFEK 8 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;;; 208.37 5.58E-05 21886890000 14183600 14253300 13436100 15006800 13869800 14159100 15537100 10179400 16687500 16667800 FALSE TRUE 13629289.23 13846809.84 15864302.15 15781302.75 14315934.71 14445406.7 15727247.68 9969191.833 14793204.96 15538875.06 0.877109133 0.891107611 1.020942771 1.015601367 0.921298013 0.929630147 1.012122668 0.641564579 0.952012607 1 23.88937873 HLVYESDK ddPTM_BT-474_Pertuzumab_2h_R1 1 HLVYESDK 8 0 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 101.54 0.005321 452010000 792280 772920 820360 769800 672200 613020 907580 576720 1061900 1041600 FALSE TRUE 761316.8217 750877.0784 968617.3008 809529.4703 693821.9235 625415.6844 918687.2355 564810.5305 941357.5638 971051.5042 0.784012813 0.773261846 0.997493229 0.833662753 0.714505791 0.64406026 0.946074674 0.581648376 0.969420839 1 19.88918829 HNDDEQYAWESSAGGSFTVR ddPTM_BT-474_Pertuzumab_2h_R1 33 HNDDEQYAWESSAGGSFTVR 20 0 P08238;P07900;P07900-2;Q14568 P08238;P07900 HSP90AB1;HSP90AA1;HSP90AA2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 325.08 5.87E-67 11227963600 4818643.4 5041477.1 4444985.1 5577606.81 5168658.52 5620839.25 5370727.6 2643014.4 6140692.4 5807253.7 FALSE TRUE 4630325.489 4897699.109 5248292.786 5865467.766 5334913.115 5734496.471 5436456.171 2588435.229 5443626.743 5413923.234 0.855262494 0.904648791 0.969406576 1.08340431 0.985406125 1.059212741 1.004162035 0.478107117 1.005486503 1 22.368243 HNIMDFAMPYFIQVMK ddPTM_BT-474_Pertuzumab_2h_R1 3 HNIMDFAMPYFIQVMK 16 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 147.64 1.01E-06 2426640000 1281630 1227910 990870 1092360 1273040 1294290 1310090 702480 1417340 1439970 FALSE TRUE 1231542.483 1192891.209 1169942.251 1148736.831 1313988.488 1320461.431 1326123.273 687973.5425 1256449.505 1342439.549 0.917391389 0.888599572 0.871504606 0.855708424 0.978806449 0.983628225 0.987845802 0.512480091 0.935944941 1 20.35642569 HNIQFSSFDIFSDEEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNIQFSSFDIFSDEEVR 17 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ; 266.7 1.11E-27 612280000 235367 245520 178576 251660 243006 252603 245910 139469 249730 276150 FALSE TRUE 226168.5974 238518.01 210848.6556 264648.2028 250822.5087 257710.8057 248919.5201 136588.9164 221381.6974 257446.1145 0.87850849 0.926477412 0.819001118 1.027975129 0.974271875 1.001028142 0.966880081 0.53055342 0.859914696 1 17.97391097 HNIVFGDYTWTEFDEPFLTR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNIVFGDYTWTEFDEPFLTR 20 0 Q15645;Q15645-2;H0YAL2 Q15645 TRIP13 Pachytene checkpoint protein 2 homolog 0 ; 137.09 4.23E-06 328720000 260678 281632 217736 245263 280164 288136 277144 193021 307700 278894 FALSE TRUE 250490.4156 273600.1311 257085.7387 257921.0528 289175.7295 293962.3073 280535.7712 189035.0489 272771.186 260004.261 0.963408887 1.052290951 0.988775098 0.991987792 1.112196117 1.13060573 1.078966053 0.727045965 1.049102753 1 17.98817574 HNMSGGEFQGK ddPTM_BT-474_Pertuzumab_2h_R1 2 HNMSGGEFQGK 11 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 0 ; 127.34 0.00028859 421110000 1005310 1038790 836290 925930 966110 999520 1014870 736520 1243070 1198450 FALSE TRUE 966021.3738 1009164.726 987426.2062 973717.3583 997185.8055 1019730.979 1027290.283 721310.6046 1101961.905 1117277.914 0.864620487 0.903235188 0.883778506 0.871508643 0.892513665 0.912692327 0.919458149 0.645596405 0.986291675 1 20.09155666 HNQLPLVIEFTEQTAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 HNQLPLVIEFTEQTAPK 17 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 62.203 0.063774 1542700000 1246800 1100100 1174400 1005100 996180 1126900 1134900 845640 1400200 1328900 FALSE TRUE 1198073.678 1068726.225 1386640.204 1056973.331 1028223.034 1149686.69 1148789.246 828177.2385 1241255.166 1238892.419 0.967052231 0.862646513 1.119257962 0.853159899 0.829953447 0.927995581 0.927271188 0.668481965 1.001907144 1 20.24061948 HNQVESIFLSAIDMYGHQFCIENLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 HNQVESIFLSAIDMYGHQFCIENLQK 26 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 246 1.30E-45 319630000 146000 156990 182010 165710 171000 174190 174980 83042 215910 201050 FALSE TRUE 140294.1586 152512.7989 214903.2558 174262.313 176500.3703 177712.2411 177121.4576 81327.15368 191400.802 187432.7044 0.748504158 0.813693637 1.14656221 0.929732693 0.941673284 0.948138916 0.944986939 0.433900551 1.021170785 1 17.51601318 HNVEVLGILSDDVETDTVAPGENLK ddPTM_BT-474_Pertuzumab_2h_R1 4 HNVEVLGILSDDVETDTVAPGENLK 25 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;;; 203.25 5.30E-25 1133310000 1644480 1516100 1505360 1615510 1591160 1695880 1747790 1031570 2278670 2107030 FALSE TRUE 1580211.904 1472862.312 1777412.039 1698886.665 1642341.106 1730171.856 1769179.977 1010267.719 2020004.935 1964318.981 0.80445789 0.749808115 0.904848986 0.864873109 0.836086767 0.880799846 0.900658189 0.514309401 1.028348732 1 20.90559779 HNVFQNDEFDVFSR ddPTM_BT-474_Pertuzumab_2h_R1 2 HNVFQNDEFDVFSR 14 0 Q9H1I8;H7C3Y4;Q9H1I8-3 Q9H1I8 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 ; 242.26 1.78E-17 302540000 368890 410300 336920 393040 397150 421520 430560 257310 455080 443100 FALSE TRUE 354473.371 398598.6457 397808.9387 413324.8415 409924.6904 430043.4232 435829.3221 251996.4586 403421.2263 413088.4423 0.858105274 0.964923258 0.963011544 1.000572273 0.992341224 1.041044433 1.055050874 0.610030281 0.976597709 1 18.65609117 HPAKPDPSGECNPDLR ddPTM_BT-474_Pertuzumab_2h_R1 5 HPAKPDPSGECNPDLR 16 1 Q16576;E9PC52;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;; 250.41 4.69E-21 15692500000 4009540 4004620 3385250 4177330 3971700 3832920 4192080 3426990 4573930 4484700 FALSE TRUE 3852842.744 3890412.159 3997039.979 4392922.502 4099453.338 3910424.269 4243383.929 3356221.459 4054716.642 4180947.274 0.921523878 0.930509739 0.956013008 1.050700287 0.98050826 0.935296241 1.014933614 0.802741876 0.969808126 1 21.99539842 HPDIEAQER ddPTM_BT-474_Pertuzumab_2h_R1 2 HPDIEAQER 9 0 P48449-2;P48449;A0A0G2JQD0;P48449-3;H7C3A5 P48449-2 LSS Lanosterol synthase 0 ; 104.79 0.0032022 660320000 495120 515210 413320 445160 373020 447780 556030 504460 550100 525470 FALSE TRUE 475770.163 500516.7152 488016.1183 468134.7609 385018.5271 456834.4184 562834.8615 494042.7247 487654.9542 489879.4489 0.971198453 1.021714049 0.996196349 0.955612165 0.785945457 0.932544567 1.148925236 1.008498572 0.995459098 1 18.90206724 HPDSHQLFIGNLPHEVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPDSHQLFIGNLPHEVDK 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 199.41 5.65E-16 627200000 708270 657090 715620 773440 760020 746780 769080 35012 1015060 912700 FALSE TRUE 680590.0254 638350.4366 844948.4529 813357.3311 784466.7335 761880.4033 778492.2311 34288.98996 899834.6443 850882.0161 0.799864156 0.750222034 0.993026574 0.955899074 0.921945368 0.895400759 0.914923828 0.040298172 1.057531629 1 19.69859958 HPDSHQLFIGNLPHEVDKSELK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPDSHQLFIGNLPHEVDKSELK 22 1 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 196.81 7.00E-23 1735040000 2956100 2650200 2411600 2287200 2520100 2946000 3112300 407350 3786800 3028700 FALSE TRUE 2840572.344 2574618.891 2847429.766 2405242.666 2601161.305 3005570.138 3150389.258 398938.0801 3356938.34 2823563.451 1.00602391 0.911833198 1.008452551 0.851846508 0.921233523 1.064459925 1.115749411 0.141288867 1.188901329 1 21.42908562 HPELADK ddPTM_BT-474_Pertuzumab_2h_R1 6 HPELADK 7 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435;Q9NQ39 P46783 RPS10;RPS10-NUDT3;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ;;;;; 122.74 0.0043113 13841060000 23419400 22429000 18763700 21381300 20657200 21332800 24370800 17770200 27732100 26521500 FALSE TRUE 22504143.96 21789346.88 22154717.99 22484791.46 21321657.6 21764163.83 24669057.14 17403239.16 24584068.27 24725175.18 0.910171264 0.881261577 0.896038868 0.90938856 0.862346068 0.880243059 0.997730328 0.703867173 0.994292986 1 24.55947741 HPEPVPEEGS(ph)EDELPPQVHKV ddPTM_BT-474_Pertuzumab_2h_R1 2 HPEPVPEEGSEDELPPQVHKV 21 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV 191.41 6.84E-18 335890000 318040 353830 274890 307670 308150 367360 366220 143422 415410 362030 TRUE FALSE 305610.6452 343739.1148 324568.7379 323548.8856 318061.9246 374788.2709 370701.9099 140460.2856 368254.3983 337509.3856 0.905487842 1.018457944 0.961658406 0.958636706 0.942379496 1.110452885 1.098345485 0.416167051 1.091093801 1 18.3645681 HPESNTAGMDIFAK ddPTM_BT-474_Pertuzumab_2h_R1 3 HPESNTAGMDIFAK 14 0 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 ;; 114.69 0.00046281 1068980000 1619090 1770430 1332230 1557160 1582160 1700170 1627620 1244720 1860490 1792630 FALSE TRUE 1555814.173 1719939.07 1572993.596 1637525.214 1633051.613 1734548.602 1647539.3 1219016.097 1649294.975 1671213.573 0.930948741 1.029155757 0.941228351 0.979841978 0.977165121 1.037897627 0.985834083 0.729419696 0.986884622 1 20.67246468 HPGSFDVVHVK ddPTM_BT-474_Pertuzumab_2h_R1 4 HPGSFDVVHVK 11 0 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;;; 174.4 6.39E-06 2491370000 3034660 3336450 2927900 3579450 3235400 3158600 3657990 1896500 3788650 3878820 FALSE TRUE 2916062.132 3241297.713 3457036.661 3764185.843 3339469.579 3222469.056 3702757.576 1857336.612 3358578.335 3616104.067 0.806409904 0.896350783 0.956011386 1.04095064 0.923499301 0.891143893 1.023963223 0.513629193 0.92878365 1 21.78600477 HPNYS(ph)PPGS(ph)PIEK ddPTM_BT-474_Pertuzumab_2h_R1 4 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 2 HPNYS(1)PPGS(1)PIEK;HPNY(0.001)S(0.999)PPGS(1)PIEK;HPNYS(1)PPGS(1)PIEK;HPNY(0.302)S(0.702)PPGS(0.996)PIEK 139.11 2.18E-05 3157390000 1891700 1872660 1679550 1760370 1951210 1999000 1921250 1245940 2204910 2049830 TRUE FALSE 1817770.273 1819253.57 1983082.046 1851222.907 2013972.442 2039421.15 1944762.832 1220210.904 1954617.861 1910993.188 0.951217557 0.951993749 1.037723242 0.968722923 1.053887818 1.067204824 1.017671253 0.638521849 1.022828272 1 20.86589121 HPPLYSDHSPLCADSLGQEPGAASFQNDS(ph)PPQVR ddPTM_BT-474_Pertuzumab_2h_R1 2 HPPLYSDHSPLCADSLGQEPGAASFQNDSPPQVR 34 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 HPPLYSDHSPLCADSLGQEPGAASFQNDS(1)PPQVR;HPPLYSDHSPLCADSLGQEPGAASFQNDS(1)PPQVR 304.95 3.06E-90 2416500000 308580 429250 369340 509880 432220 533630 461980 97558 455270 514960 TRUE FALSE 296520.3524 417008.2103 436087.9539 536194.9679 446122.7488 544420.3642 467633.8494 95543.39321 403589.6582 480081.3005 0.61764612 0.868619981 0.908362716 1.116883676 0.929264998 1.134017017 0.974072202 0.199015027 0.840669399 1 18.87291922 HPVSLEQYLMEGSYNK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPVSLEQYLMEGSYNK 16 0 K7EJR3;R4GMR5;P48556;K7EJC1 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ; 135.45 2.28E-05 527050000 605510 631900 505720 631690 552600 585470 622410 523920 724690 710910 FALSE TRUE 581845.9998 613878.8307 597114.8537 664291.5966 570374.8809 597308.6045 630027.2398 513100.8689 642426.2293 662759.4325 0.877914325 0.926246841 0.90095263 1.002311795 0.860606206 0.90124497 0.950612257 0.774188708 0.969320387 1 19.33812577 HPVTGQFLYQDSNWASK ddPTM_BT-474_Pertuzumab_2h_R1 2 HPVTGQFLYQDSNWASK 17 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 204.05 9.13E-12 1382380000 223715 271706 185508 306440 199730 195559 340500 231482 285690 246639 FALSE TRUE 214971.9705 263957.2109 219033.4222 322255.4051 206154.4968 199513.337 344667.1409 226701.8158 253259.6689 229933.9208 0.934929347 1.14796986 0.952592908 1.401513113 0.896581488 0.867698582 1.498983445 0.985943331 1.101445441 1 17.81085979 HQILEQAVEDYAETVHQLSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HQILEQAVEDYAETVHQLSK 20 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 254.73 2.25E-36 153730000 285700 275340 272520 289130 292550 312600 339580 184900 381070 340790 FALSE TRUE 274534.5281 267487.5728 321770.4262 304052.0339 301960.1364 318920.9862 343735.8816 181081.7504 337812.5312 317707.9898 0.864109613 0.841929008 1.012786699 0.957017273 0.950432933 1.00381796 1.081923945 0.569962847 1.063279937 1 18.27734185 HQPAPVK ddPTM_BT-474_Pertuzumab_2h_R1 4 HQPAPVK 7 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;Q659C4-4 A0A3B3ISF0 LARP1B La-related protein 1B 0 ;;; 73.039 0.049975 536660000 1205150 1214450 1011770 1158660 1183400 1259700 1251840 983020 1418000 1291370 FALSE TRUE 1158051.406 1179815.075 1194619.346 1218458.581 1221465.136 1285171.997 1267160.392 962720.2935 1257034.585 1203904.36 0.961913126 0.979990699 0.992287582 1.012089184 1.014586521 1.0675034 1.052542407 0.799665094 1.0441316 1 20.19928936 HQQGQGDDSSHKK ddPTM_BT-474_Pertuzumab_2h_R1 1 HQQGQGDDSSHKK 13 1 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5;A0A2R8Y443;A0A2R8YDF3;Q13627-4;Q13627-3;E7EMI5 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 0 162.32 1.65E-05 27838000 37457 31312 30629 28753 32076 32941 36835 10874 39131 33614 FALSE TRUE 35993.13903 30419.01242 36164.34164 30236.94578 33107.75367 33607.08959 37285.79775 10649.4481 34689.01293 31337.29384 1.148572025 0.97069685 1.154035247 0.964886947 1.056496896 1.072431135 1.189821876 0.339833049 1.106956239 1 14.93559298 HRDTHPGSPGS(ph)PGPALRPLPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDTHPGS(0.266)PGS(0.734)PGPALRPLPAR 123.85 1.12E-05 211880000 128750 125380 119600 118430 89087 134590 123550 33098 128530 133210 TRUE FALSE 123718.3077 121804.2852 141214.3805 124542.1865 91952.56426 137311.502 125062.0419 32414.51473 113939.8132 124187.568 0.996221358 0.980809006 1.137105611 1.002855507 0.740432925 1.105678323 1.007041557 0.261012557 0.917481637 1 16.92216123 HRGS(ph)ADYSMEAK ddPTM_BT-474_Pertuzumab_2h_R1 6 HRGSADYSMEAK 12 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 HRGS(1)ADYSMEAK;HRGS(1)ADYSMEAK;HRGS(1)ADYSMEAK;HRGS(1)ADYSMEAK;HRGS(1)ADYSMEAK;HRGS(1)ADYSMEAK 182.04 1.05E-05 4852110000 4518130 4520490 3666060 3857960 4206930 4184400 4340820 2984520 5172140 4319450 TRUE FALSE 4341556.485 4391570.051 4328598.593 4057069.778 4342249.724 4269011.435 4393944.254 2922888.619 4585020.351 4026889.804 1.078141369 1.090561268 1.074923527 1.007494611 1.078313521 1.060126212 1.091150855 0.725842713 1.138600899 1 21.94123456 HRPDLIDFDK ddPTM_BT-474_Pertuzumab_2h_R1 2 HRPDLIDFDK 10 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3 Q01082;Q01082-3 SPTBN1;SPTB "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic" 0 ; 96.015 0.0042232 231907000 448900 421900 406520 417270 421800 424020 459220 347640 543070 544130 FALSE TRUE 431356.4917 409867.8251 479987.207 438805.3547 435367.5801 432593.9749 464840.0717 340461.1125 481422.9703 507275.5904 0.850339539 0.807978607 0.946205999 0.865023595 0.858246658 0.852779008 0.916346224 0.671156111 0.949036341 1 18.95241022 HRPS(ph)PPATPPPK ddPTM_BT-474_Pertuzumab_2h_R1 4 HRPSPPATPPPK 12 1 A9Z1X7;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HRPS(1)PPATPPPK;HRPS(1)PPATPPPK;HRPS(1)PPATPPPK;HRPS(1)PPATPPPK 139.6 3.57E-05 3602020000 2248050 2268880 1946910 2316500 2366470 2482280 2385580 1696570 2882290 2540740 TRUE FALSE 2160193.721 2204173.764 2298759.946 2436054.843 2442589.657 2532473.402 2414775.442 1661535.237 2555104.523 2368653.417 0.911992318 0.930559848 0.970492318 1.028455588 1.031214461 1.069161653 1.019471833 0.701468279 1.078716078 1 21.17563569 HS(ph)PESPSIAVVESELVAEYITTER ddPTM_BT-474_Pertuzumab_2h_R1 4 HSPESPSIAVVESELVAEYITTER 24 0 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 HS(0.332)PES(0.332)PS(0.332)IAVVES(0.005)ELVAEYITTER;HS(0.301)PES(0.301)PS(0.301)IAVVES(0.096)ELVAEYITTER;HS(0.293)PES(0.293)PS(0.293)IAVVES(0.122)ELVAEYITTER;HS(0.271)PES(0.271)PS(0.271)IAVVES(0.187)ELVAEYITTER 96.79 0.0040304 55276000 33564.1 27441.4 26285 31528.3 26026.4 31594.2 33766.1 20127.9 34727.4 34808.1 TRUE FALSE 32252.37786 26658.79814 31035.28421 33155.47934 26863.56279 32233.05637 34179.33963 19712.25183 30785.29114 32450.51638 0.993894134 0.821521538 0.956387992 1.021724245 0.827831597 0.99329872 1.053275678 0.607455721 0.948684168 1 14.98595382 HSAS(ph)PVVFTSAR ddPTM_BT-474_Pertuzumab_2h_R1 4 HSASPVVFTSAR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 HS(0.024)AS(0.976)PVVFTSAR;HS(0.012)AS(0.988)PVVFTSAR;HS(0.001)AS(0.997)PVVFT(0.002)SAR;HS(0.001)AS(0.999)PVVFTSAR 171.81 2.41E-05 1645340000 1114909 1375756 1082029 1315747 1119572 1194152 1247617 872975 1416396 1405560 TRUE FALSE 1071337.124 1336520.786 1277575.71 1383652.86 1155584.05 1218298.572 1262885.71 854947.7612 1255612.664 1310360.169 0.817589811 1.019964447 0.974980574 1.055933241 0.881882766 0.929743288 0.963769916 0.652452495 0.958219498 1 20.32153198 HSDENDGGQPHKR ddPTM_BT-474_Pertuzumab_2h_R1 3 HSDENDGGQPHKR 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ;; 85.672 0.0037329 146798000 99590 101980 81166 90014 87435 100444 101371 39459.7 127767 101003 FALSE TRUE 95697.9127 99071.63025 95834.50173 94659.63333 90247.42618 102475.0465 102611.6086 38644.84341 113263.4258 94161.97685 1.016311636 1.052140509 1.017762211 1.005285111 0.95842748 1.088284783 1.089735072 0.410408157 1.202857349 1 16.52285699 HSLDS(ph)DEEEDDDDGGSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSLDSDEEEDDDDGGSSK 18 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 HSLDS(1)DEEEDDDDGGSSK 262.5 8.05E-31 562790000 548770 459610 463910 509660 484890 464060 587010 245710 743500 511620 TRUE FALSE 527323.4617 446502.3728 547748.8566 535963.6137 500486.9272 473443.6112 594194.004 240636.0026 659100.997 476967.5217 1.105575197 0.936127414 1.148398647 1.123689956 1.049310287 0.992611844 1.245774559 0.504512345 1.381857185 1 18.86353151 HSLSGS(ph)SPGMK ddPTM_BT-474_Pertuzumab_2h_R1 4 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLS(0.072)GS(0.582)S(0.346)PGMK;HSLS(0.046)GS(0.706)S(0.248)PGMK;HSLS(0.007)GS(0.496)S(0.496)PGMK;HSLS(0.001)GS(0.683)S(0.316)PGMK 195.29 1.47E-07 329975000 1793820 1805920 1582320 1849060 1753670 1848000 1909020 1055460 2342310 2095150 TRUE FALSE 1723715.531 1754416.93 1868280.423 1944490.208 1810078.388 1885367.826 1932383.158 1033664.382 2076420.789 1953243.624 0.882488753 0.898206915 0.956501483 0.995518523 0.926703851 0.965249702 0.98932009 0.529204022 1.063062878 1 20.89744047 HSLSGSS(ph)PGMK ddPTM_BT-474_Pertuzumab_2h_R1 7 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLSGS(0.001)S(0.999)PGMK;HSLSGS(0.007)S(0.993)PGMK;HSLS(0.002)GS(0.335)S(0.663)PGMK;HSLS(0.005)GS(0.398)S(0.596)PGMK;HSLS(0.008)GS(0.01)S(0.983)PGMK;HSLS(0.001)GS(0.228)S(0.771)PGMK;HSLS(0.001)GS(0.007)S(0.992)PGMK 238.07 1.40E-15 2768879000 4561170 4836140 4049105 4501700 4518730 4848550 5061810 2834056 6014750 5172180 TRUE FALSE 4382914.434 4698218.022 4780868.345 4734033.276 4664079.054 4946591.003 5123757.945 2775531.753 5331980.796 4821863.642 0.908966897 0.974357297 0.991498039 0.981784975 0.967277261 1.025867044 1.062609465 0.575613904 1.10579253 1 22.20115942 HSNLVQLLGVIVEEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSNLVQLLGVIVEEK 15 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 108.36 0.0010847 47995000 96589 90326 87883 76512 93029 100690 88180 79339 117140 103450 FALSE TRUE 92814.1951 87749.99092 103765.413 80460.79349 96021.36227 102726.0208 89259.17322 77700.62192 103842.7583 96443.23936 0.962371191 0.909861505 1.075922104 0.834281325 0.995625644 1.065144861 0.925509904 0.805661677 1.076724081 1 16.55739249 HSQQLFPDGS(ph)PGDQWVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HSQQLFPDGSPGDQWVK 17 0 H0Y9T5;Q8IU60;Q8IU60-2 H0Y9T5 DCP2 m7GpppN-mRNA hydrolase 1 HSQQLFPDGS(1)PGDQWVK 159.46 2.07E-09 515720000 605290 587420 571130 537330 515630 587380 627650 323270 638920 644370 TRUE FALSE 581634.5976 570667.3567 674345.8957 565061.6657 532215.7072 599257.226 635331.3685 316594.3615 566392.4802 600726.246 0.968219054 0.949962417 1.122551079 0.940630894 0.885953811 0.997554593 1.057605478 0.52701936 0.942846237 1 19.19634817 HSS(ph)IS(ph)PSTLTLK ddPTM_BT-474_Pertuzumab_2h_R1 4 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.018)S(0.982)IS(0.978)PS(0.009)T(0.014)LTLK;HS(0.003)S(0.997)IS(0.73)PS(0.104)T(0.166)LTLK;HS(0.051)S(0.949)IS(0.634)PS(0.146)T(0.208)LT(0.012)LK;HS(0.018)S(0.982)IS(0.676)PS(0.3)T(0.023)LT(0.001)LK 199.3 2.53E-07 856090000 2294070 2367990 2121220 2280710 2284410 2421270 2522030 1407820 3147850 2848720 TRUE FALSE 2204415.208 2300457.244 2504571.64 2398417.716 2357890.122 2470229.738 2552895.358 1378748.025 2790519.265 2655773.657 0.830046342 0.866209828 0.943066678 0.90309568 0.887835496 0.930135643 0.961262399 0.519151179 1.050736857 1 21.34070077 HSS(ph)IS(ph)PVR ddPTM_BT-474_Pertuzumab_2h_R1 1 HSSISPVR 8 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.135)S(0.868)IS(0.997)PVR 68.49 0.082412 78906000 173230 154210 185740 230110 200950 190140 206840 110360 255910 242560 TRUE FALSE 166459.9801 149812.0818 219307.3498 241986.0047 207413.7392 193984.7611 209371.3698 108081.0274 226860.1697 226131.1951 0.736121259 0.66250073 0.969823512 1.070113323 0.917227449 0.857841666 0.925884505 0.477957176 1.00322368 1 17.7868005 HSVTAAT(ph)PPPS(ph)PTSGESGDLLSNLLQSPSSAK ddPTM_BT-474_Pertuzumab_2h_R1 2 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8;Q96QU8-2 Q96QU8 XPO6 Exportin-6 2 HS(0.001)VT(0.009)AAT(0.852)PPPS(0.714)PT(0.217)S(0.194)GES(0.014)GDLLSNLLQSPSSAK;HS(0.01)VT(0.043)AAT(0.882)PPPS(0.844)PT(0.166)S(0.051)GES(0.006)GDLLSNLLQSPSSAK 116.14 3.11E-06 476390000 481290 475180 413540 466870 502220 509060 490770 334770 604710 508200 TRUE FALSE 462480.6547 461628.3316 488275.8771 490965.2166 518374.3624 519353.542 496776.1901 327856.8825 536065.856 473779.1613 0.976152377 0.974353389 1.030598044 1.036274401 1.094126557 1.096193299 1.048539553 0.692003594 1.13146778 1 18.85385522 HTEVLPAEEENDSLGADGTHGAGAMESAAGVLIK ddPTM_BT-474_Pertuzumab_2h_R1 2 HTEVLPAEEENDSLGADGTHGAGAMESAAGVLIK 34 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ; 198.85 2.40E-27 211700000 184711 186841 184868 205336 184892 200204 200733 110665 245161 247600 FALSE TRUE 177492.2899 181512.4776 218277.76 215933.4156 190839.2191 204252.2621 203189.6305 108379.7291 217331.3511 230829.8315 0.768931333 0.786347572 0.94562197 0.935465811 0.826752842 0.884860768 0.880257241 0.469522195 0.941521942 1 17.81647016 HTGYVIELQHVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 HTGYVIELQHVVK 13 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 183.89 5.76E-06 283470000 339270 335500 264430 299120 326180 289870 349880 214710 382820 405020 FALSE TRUE 326010.9533 325931.8685 312218.3832 314557.619 336671.8759 295731.37 354161.9361 210276.1635 339363.8785 377587.6346 0.863404739 0.863195292 0.82687661 0.833071823 0.89163904 0.783212539 0.937959572 0.55689367 0.898768517 1 18.52645199 HTLQQHQETPK ddPTM_BT-474_Pertuzumab_2h_R1 2 HTLQQHQETPK 11 0 Q7Z417;Q7Z417-2 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 ; 96.745 0.0039229 306650000 539000 556720 418490 411670 506040 554450 545220 383270 615130 579900 FALSE TRUE 517935.2841 540842.8907 494120.4523 432916.338 522317.2362 565661.3589 551892.5655 375355.3406 545303.0212 540622.8565 0.958034382 1.000407001 0.913983651 0.80077328 0.966139759 1.046314177 1.020845787 0.694301649 1.008656986 1 19.04426298 HTVDDGLDIR ddPTM_BT-474_Pertuzumab_2h_R1 4 HTVDDGLDIR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;; 183.03 1.71E-06 4935860000 3312640 3563400 3066480 3551810 3596100 3091090 3687990 2107450 4100000 3921180 FALSE TRUE 3183178.366 3461775.321 3620661.149 3735119.34 3711771.822 3153593.958 3733124.725 2063930.421 3634585.189 3655594.986 0.870768884 0.946979995 0.990443734 1.021754148 1.015367358 0.862675972 1.021208514 0.564594937 0.994252701 1 21.80167481 HVCEMLVQR ddPTM_BT-474_Pertuzumab_2h_R1 3 HVCEMLVQR 9 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;; 147.2 9.30E-05 1289370000 181887 213166 202704 202252 204296 156642 219043 200958 201268 227970 FALSE TRUE 174778.655 207086.7144 239337.1219 212690.25 210867.3664 159809.4086 221723.7138 196808.1471 178420.9004 212529.3888 0.822374053 0.974390956 1.126136593 1.000756889 0.992179799 0.751940282 1.043261428 0.926027916 0.839511662 1 17.69730283 HVEAVAYYK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVEAVAYYK 9 0 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 62.262 0.083771 140230000 190390 207180 171750 185750 198950 152280 187940 173130 211830 222180 FALSE TRUE 182949.3483 201271.4293 202789.0456 195336.5798 205349.4074 155359.2059 190240.0659 169554.805 187783.9465 207131.5507 0.883251961 0.971708214 0.979035038 0.943055653 0.99139608 0.7500509 0.91845045 0.818585119 0.906592674 1 17.6601878 HVENDGYK ddPTM_BT-474_Pertuzumab_2h_R1 2 HVENDGYK 8 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ; 100.57 0.0060112 687320000 1160650 1095920 1002150 955590 1097280 1115110 1099460 939680 1287520 1180360 FALSE TRUE 1115290.515 1064665.435 1183260.798 1004908.114 1132575.008 1137658.288 1112915.52 920275.2796 1141366.127 1100413.166 1.013519785 0.967514264 1.07528775 0.913209825 1.02922706 1.033846489 1.011361509 0.836299772 1.037215986 1 20.06961388 HVIDFFK ddPTM_BT-474_Pertuzumab_2h_R1 2 HVIDFFK 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 101.64 0.0089085 1066480000 2269290 2304640 2046950 2098880 2283400 2153990 2261700 1789990 2617700 2595400 FALSE TRUE 2180603.638 2238913.924 2416879.399 2207203.448 2356847.635 2197545.154 2289379.361 1753026.081 2320549.67 2419611.246 0.901220657 0.925319688 0.998870956 0.912214081 0.974060456 0.908222408 0.946176525 0.724507329 0.959058888 1 21.20634384 HVINFDLPSDIEEYVHR ddPTM_BT-474_Pertuzumab_2h_R1 8 HVINFDLPSDIEEYVHR 17 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;;;;;; 343.55 3.46E-73 6615747000 2601393 2958379 2510515 3072475 2965799 3307855 3146579 1232436 3179406 3378083 FALSE TRUE 2499727.686 2874008.927 2964220.907 3231045.803 3061196.618 3374742.094 3185087.775 1206985.766 2818493.16 3149282.43 0.79374516 0.912591675 0.941236924 1.025962541 0.972029879 1.071590805 1.011369366 0.383257391 0.894963606 1 21.58659171 HVQGWPADHAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 HVQGWPADHAEK 12 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 0 159.08 4.15E-05 213240000 444950 431230 367150 446390 465920 438030 501320 146130 591790 527690 FALSE TRUE 427560.8621 418931.7426 433502.1722 469428.2414 480906.7399 446887.2667 507455.3041 143112.3644 524612.4802 491949.0863 0.869116081 0.851575405 0.881193165 0.954221188 0.977553884 0.908401457 1.031519965 0.290908894 1.066395883 1 18.90814949 HVSDDMK ddPTM_BT-474_Pertuzumab_2h_R1 4 HVSDDMK 7 0 Q01518-2;Q01518;Q5T0S3 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;;; 182.13 0.00066183 4120510000 4008480 5360400 4137820 5415200 4810990 5113500 5053400 3746420 5197200 5859400 FALSE TRUE 3851824.17 5207526.64 4885616.119 5694679.121 4965739.863 5216898.474 5115245.021 3669055.118 4607235.644 5462537.619 0.70513458 0.953316389 0.894385807 1.042497007 0.909053669 0.955032045 0.936422846 0.671675945 0.843424058 1 22.38113988 HWVAPGGPYSAETPGVPS(ph)PIAALK ddPTM_BT-474_Pertuzumab_2h_R1 2 HWVAPGGPYSAETPGVPSPIAALK 24 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 HWVAPGGPYSAETPGVPS(1)PIAALK;HWVAPGGPYSAETPGVPS(1)PIAALK 160.52 1.32E-11 3111100000 1773550 1792830 1412150 1518010 1569680 1715200 1743100 1137580 1951580 1895180 TRUE FALSE 1704237.705 1741700.244 1667356.918 1596354.678 1620170.183 1749882.519 1764432.579 1114088.575 1730044.82 1766817.771 0.964580351 0.985783748 0.943706219 0.903519709 0.916999031 0.990414828 0.998650007 0.630562242 0.979186903 1 20.75272182 HYEDFPK ddPTM_BT-474_Pertuzumab_2h_R1 3 HYEDFPK 7 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ;; 102.72 0.0085375 760860000 1230690 1136830 1008990 1036270 1170720 1195170 1204370 815270 1502680 1362650 FALSE TRUE 1182593.274 1104408.721 1191336.938 1089752.019 1208377.272 1219337.156 1219109.44 798434.3896 1332102.066 1270356.502 0.930914489 0.869369126 0.937797332 0.857831654 0.951211152 0.959838561 0.959659307 0.628512066 1.048604911 1 20.27680199 HYEVEILDAK ddPTM_BT-474_Pertuzumab_2h_R1 4 HYEVEILDAK 10 0 Q9NZ01;M0R3C3;Q9NZ01-2 Q9NZ01 TECR Very-long-chain enoyl-CoA reductase 0 ;;; 132.78 0.0002146 1761980000 2306410 3518850 1821780 3966550 2305290 2316360 3233810 3006460 3842430 2646420 FALSE TRUE 2216272.947 3418495.843 2151016.171 4171264.121 2379441.746 2363198.386 3273386.334 2944375.55 3406253.455 2467175.616 0.898303685 1.385590803 0.871853693 1.690704177 0.964439552 0.957855765 1.326774759 1.193419524 1.380628697 1 21.23442898 HYLDQLNHILGILGSPSQEDLNCIINMK ddPTM_BT-474_Pertuzumab_2h_R1 1 HYLDQLNHILGILGSPSQEDLNCIINMK 28 0 P27361;E9PBK7;E9PQW4;P27361-3;E9PJF0;B3KR49;E9PRH7 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 123.14 2.56E-05 51705000 49795 53344 42592 48808 62724 48984 59092 48721 60868 68929 FALSE TRUE 47848.95635 51822.68135 50289.32185 51326.98673 64741.57442 49974.49004 59815.18557 47714.89432 53958.51982 64260.37743 0.744610571 0.806448443 0.78258678 0.798734598 1.007488238 0.777687465 0.930825307 0.74252434 0.839685697 1 15.97164183 IADPEHDHTGFLTEYVATR ddPTM_BT-474_Pertuzumab_2h_R1 5 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;;;; 253.1 4.18E-31 3095942000 2121101 2285806 1876777 2385406 2248646 2379234 2660674 66629.8 2833199 1959542 FALSE TRUE 2038206.028 2220617.051 2215952.353 2508517.09 2320975.741 2427343.742 2693236.124 65253.87135 2511586.127 1826820.475 1.115712275 1.215563916 1.213010464 1.373160157 1.270500179 1.328725934 1.474275202 0.035719915 1.374840145 1 20.80090343 IAPELYHK ddPTM_BT-474_Pertuzumab_2h_R1 2 IAPELYHK 8 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ; 83.005 0.023797 0 1080950 1099070 1004880 990220 892860 704680 1181010 973360 1192080 1319270 FALSE TRUE 1038705.279 1067725.6 1186484.169 1041325.373 921579.6528 718929.1124 1195463.554 953259.7759 1056760.076 1229914.668 0.844534427 0.86812982 0.964688202 0.846664732 0.749303734 0.584535766 0.971989021 0.775061718 0.859214142 1 20.23012679 IATETDQIGSEIIEELGEQR ddPTM_BT-474_Pertuzumab_2h_R1 1 IATETDQIGSEIIEELGEQR 20 0 Q9UEU0;H0YJL5;H0YJJ5;Q9UEU0-2 Q9UEU0 VTI1B Vesicle transport through interaction with t-SNAREs homolog 1B 0 106.52 0.00055857 8647800 2594.9 3330.5 2646.8 3477.1 2835.6 2600.9 2820.9 4895.4 4193.4 2145.1 FALSE TRUE 2493.488439 3235.517401 3125.135638 3656.553548 2926.809649 2653.49198 2855.423018 4794.308279 3717.382812 1999.810466 1.246862381 1.617912025 1.562715913 1.82845005 1.46354352 1.326871733 1.427846822 2.397381332 1.858867565 1 10.96564756 IAWALSR ddPTM_BT-474_Pertuzumab_2h_R1 1 IAWALSR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 97.602 0.049637 0 178660 149900 134820 130510 144920 133520 151530 150750 172530 169860 FALSE TRUE 171677.7697 145624.9988 159184.9731 137245.6367 149581.4834 136219.8659 153384.4695 147636.9598 152945.1177 158355.2309 1.084130715 0.919609652 1.005239752 0.866694684 0.944594521 0.860217027 0.968610058 0.932315017 0.965835589 1 17.272805 ICLVNDPRPQHK ddPTM_BT-474_Pertuzumab_2h_R1 2 ICLVNDPRPQHK 12 1 Q13867;K7ESE8 Q13867 BLMH Bleomycin hydrolase 0 ; 136.7 6.33E-05 1003160000 965380 990600 790200 1011460 1027310 327450 1039000 1060820 1159060 1193370 FALSE TRUE 927651.8823 962349.0579 933006.7179 1063661.572 1060354.359 334071.2634 1051715.593 1038913.696 1027488.368 1112541.987 0.83381292 0.865000215 0.838626073 0.956064206 0.953091543 0.300277443 0.945326653 0.933819765 0.923550194 1 20.08542835 IDFIPVS(ph)PAPS(ph)PTR ddPTM_BT-474_Pertuzumab_2h_R1 1 IDFIPVSPAPSPTR 14 0 Q96E09 Q96E09 FAM122A Protein FAM122A 2 IDFIPVS(1)PAPS(0.991)PT(0.009)R 104.41 0.0015484 63923000 65744 65053 59449 64269 63164 57252 52450 78242 61631 72048 TRUE FALSE 63174.6518 63197.75213 70192.75674 67585.93079 65195.72742 58409.67467 53091.89879 76626.27536 54634.90726 67168.12479 0.940545117 0.940889035 1.045030764 1.006220302 0.97063492 0.86960407 0.790432947 1.140813081 0.813405279 1 16.03548913 IDILDSALLRPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 IDILDSALLRPGR 13 1 P62195-2;P62195 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 232.5 5.93E-13 3385600000 2259700 2308250 1948580 2510520 2275680 2163610 2568900 2393560 2492840 2760200 FALSE TRUE 2171388.426 2242420.97 2300731.752 2640088.238 2348879.314 2207359.677 2600338.967 2344132.15 2209863.254 2573249.195 0.843831382 0.871435605 0.894095976 1.02597457 0.912806781 0.857810305 1.010527457 0.910961967 0.858783229 1 21.29515974 IDIS(ph)PSTLR ddPTM_BT-474_Pertuzumab_2h_R1 6 IDISPSTLR 9 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 IDIS(0.892)PS(0.106)T(0.001)LR;IDIS(0.989)PS(0.011)TLR;IDIS(0.714)PS(0.285)TLR;IDIS(0.5)PS(0.5)TLR;IDIS(0.752)PS(0.248)TLR;IDIS(0.982)PS(0.017)TLR 183.08 4.78E-05 60296136000 4552016 4594200 4083135 5099229 4466609 4339241 4669595 4819032 4959457 5421138 TRUE FALSE 4374118.182 4463177.914 4821048.323 5362400.82 4610281.535 4426983.426 4726742.9 4719517.305 4396480.233 5053959.495 0.865483427 0.883105201 0.953915109 1.061029639 0.912211809 0.875943591 0.935255398 0.933825708 0.869908086 1 22.26898267 IDSDDALNHDFFWSDPMPSDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDSDDALNHDFFWSDPMPSDLK 22 0 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 0 199.04 1.81E-22 125090000 137200 134630 116040 113330 124320 139390 131490 127600 152440 155040 FALSE TRUE 131838.0723 130790.4842 137011.0093 119178.9749 128318.8657 142208.5613 133099.214 124965.0154 135135.6503 144539.0027 0.912128006 0.904880218 0.947917218 0.824545435 0.887780207 0.98387673 0.920853275 0.864576433 0.934942457 1 17.14109932 IDTHPS(ph)PSHSSTVK ddPTM_BT-474_Pertuzumab_2h_R1 3 IDTHPSPSHSSTVK 14 0 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594;B7ZBA0 Q8NI27 THOC2 THO complex subunit 2 1 IDTHPS(0.877)PS(0.121)HS(0.001)S(0.001)TVK;IDTHPS(0.997)PS(0.003)HSSTVK;IDT(0.001)HPS(0.499)PS(0.499)HS(0.001)STVK 151.44 4.47E-06 1482770000 1123080 1414470 1256950 1731960 1334750 1453520 1532260 187131 1555720 1721010 TRUE FALSE 1079188.792 1374130.701 1484108.826 1821346.663 1377683.446 1482911.17 1551012.256 183266.6795 1379121.188 1604444.46 0.672624587 0.856452644 0.924998567 1.135188353 0.858666959 0.924252106 0.96669738 0.114224384 0.859563059 1 20.61364242 IDTHPSPS(ph)HSSTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 IDTHPSPSHSSTVK 14 0 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594;B7ZBA0 Q8NI27 THOC2 THO complex subunit 2 1 IDT(0.001)HPS(0.377)PS(0.619)HS(0.003)STVK 124.29 6.31E-05 303290000 216430 329730 260090 367070 295360 317460 333340 52844 306580 382380 TRUE FALSE 207971.6763 320326.4232 307094.0487 386014.5267 304860.5226 323879.2587 337419.5146 51752.75293 271778.3237 356481.062 0.583401753 0.898579076 0.861459644 1.082847219 0.855194161 0.908545483 0.946528583 0.145176725 0.762392039 1 18.44346591 IEDHLDEAIHVLR ddPTM_BT-474_Pertuzumab_2h_R1 1 IEDHLDEAIHVLR 13 0 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3 K7ENH8 TCF3 Transcription factor E2-alpha 0 160.38 2.54E-05 67744000 67749 70498 64462 71376 69684 72332 74560 19400 79053 80110 FALSE TRUE 65101.29418 68487.46606 76111.71735 75059.72391 71925.44915 73794.6026 75472.48758 18999.38322 70079.23486 74684.07835 0.871689062 0.917029005 1.019115708 1.005029795 0.963062687 0.988090156 1.010556591 0.254396702 0.938342367 1 16.18851309 IEIPIHIVPHVTIGK ddPTM_BT-474_Pertuzumab_2h_R1 1 IEIPIHIVPHVTIGK 15 0 X6RJS7;P46736-2;P46736-3;P46736;A0A087WZR3;H9KVA9;A0A0D9SF50;P46736-4 X6RJS7 BRCC3 Lys-63-specific deubiquitinase BRCC36 0 161.04 9.68E-07 89980000 263930 280250 231950 252600 258940 307470 274200 85368 312980 314670 FALSE TRUE 253615.3238 272257.5444 273868.5247 265636.7163 267269.0403 313687.2541 277555.7416 83605.12097 277451.8225 293357.1206 0.864527588 0.928075459 0.933566992 0.905506284 0.911070574 1.069301653 0.94613603 0.284994347 0.94578179 1 18.16229849 IEYAKPTR ddPTM_BT-474_Pertuzumab_2h_R1 5 IEYAKPTR 8 1 A0A3B3ITJ4;M0R1W6;B4DVF8;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;; 144.77 0.0011027 8018590000 4380920 4770020 3171430 4453710 4541440 4635850 4534040 4737260 5258710 4979460 FALSE TRUE 4209708.803 4633983.7 3744577.949 4683566.507 4687519.542 4729590.063 4589528.938 4639433.926 4661763.287 4642196.739 0.9068355 0.998230786 0.806639218 1.008911679 1.009763223 1.018825855 0.988654552 0.999404848 1.004214933 1 22.14637624 IFCCHGGLSPDLQSMEQIR ddPTM_BT-474_Pertuzumab_2h_R1 2 IFCCHGGLSPDLQSMEQIR 19 0 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;F8W1A0;P62140;E7ETD8;P62136;P62136-2;P62136-3 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 256.96 5.61E-31 2177840000 1012080 1040910 870220 976580 1021180 838660 1004700 1060260 952670 995830 FALSE TRUE 972526.7947 1011224.266 1027488.112 1026981.411 1054027.182 855618.2798 1016995.819 1038365.26 844526.8955 928381.5471 1.047550759 1.089233483 1.106751976 1.106206186 1.135338359 0.921623531 1.095450273 1.118468224 0.909676521 1 19.82435832 IFVGGIKEDTEEYNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 IFVGGIKEDTEEYNLR 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 261.74 6.88E-27 6722170000 3723970 3859960 2868730 3033900 3380910 3705410 3605080 3543850 3922340 3568850 FALSE TRUE 3578433.135 3749877.72 3387173.326 3190479.943 3489660.041 3780335.929 3649200.047 3470668.259 3477092.407 3327128.611 1.075531954 1.127061247 1.018047007 0.958928949 1.04885036 1.13621575 1.096801619 1.0431422 1.045073039 1 21.6658462 IFYPEIEEVQALDDT(ph)ERGSGGFGSTGKN ddPTM_BT-474_Pertuzumab_2h_R1 1 IFYPEIEEVQALDDTERGSGGFGSTGKN 28 2 P33316-2;H0YNW5;P33316;A0A0C4DGL3 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 IFYPEIEEVQALDDT(0.565)ERGS(0.412)GGFGS(0.011)T(0.012)GKN 88.24 0.0054065 58352000 33147 34135 25966 25815 32912 39080 26731 32732 38834 33268 TRUE FALSE 31851.57859 33161.50322 30658.63381 27147.31524 33970.64437 39870.22438 27058.14197 32056.07276 34425.72713 31014.72873 1.026982337 1.069217903 0.988518522 0.875303972 1.095306835 1.285525491 0.872428781 1.03357579 1.109979953 1 14.92066589 IFYPETTDIYDRK ddPTM_BT-474_Pertuzumab_2h_R1 1 IFYPETTDIYDRK 13 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 183.79 1.61E-05 140870000 80685 92694 69101 73869 67651 85015 80775 92382 95178 78206 FALSE TRUE 77531.741 90050.45788 81589.08784 77681.38794 69827.05585 86734.06155 81763.54861 90474.27942 84373.79246 72909.03796 1.063403704 1.235106928 1.11905314 1.065456219 0.957728394 1.189620162 1.121445995 1.240919946 1.15724737 1 16.15381004 IGEEQS(ph)AEDAEDGPPELLFIHGGHTAK ddPTM_BT-474_Pertuzumab_2h_R1 3 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 Q16576;E9PC52;Q16576-2;Q5JNZ6 Q16576 RBBP7 Histone-binding protein RBBP7 1 IGEEQS(1)AEDAEDGPPELLFIHGGHTAK;IGEEQS(1)AEDAEDGPPELLFIHGGHTAK;IGEEQS(1)AEDAEDGPPELLFIHGGHTAK 218.19 5.49E-34 325811000 370440 318370 313851 330724 345285 370813 383040 131418 493860 412004 TRUE FALSE 355962.7953 309290.3993 370570.8573 347792.7053 356391.4056 378311.0929 387727.7581 128704.1724 437799.0832 384098.6021 0.926748479 0.805236982 0.964780541 0.905477665 0.927864365 0.984932231 1.009448501 0.335081075 1.139809103 1 18.55111719 IGEEQSAEDAEDGPPELLFIHGGHTAK ddPTM_BT-474_Pertuzumab_2h_R1 4 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 Q16576;E9PC52;Q16576-2;Q5JNZ6 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;; 275.69 4.04E-61 5617170000 2316760 2088360 1808820 1865010 2088940 2063600 2177390 220869 2757540 2123800 FALSE TRUE 2226218.458 2028802.018 2135714.011 1961263.39 2156132.652 2105327.406 2204037.55 216307.978 2444515.62 1979953.134 1.12437937 1.024671737 1.078668971 0.990560512 1.088981661 1.063321838 1.113176626 0.109249039 1.234633072 1 20.91703485 IGEEQSPEDAEDGPPELLFIHGGHTAK ddPTM_BT-474_Pertuzumab_2h_R1 4 IGEEQSPEDAEDGPPELLFIHGGHTAK 27 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;;; 233.22 3.47E-45 2763640000 2195680 1954460 1736680 1820230 1917160 1964820 2094160 235686 2540030 2005740 FALSE TRUE 2109870.398 1898720.714 2050536.708 1914172.288 1978827.193 2004550.007 2119788.957 230819.0017 2251696.443 1869889.443 1.128339649 1.015418704 1.096608527 1.023682066 1.058258925 1.072015254 1.133644005 0.123439919 1.204186938 1 20.83452154 IGEMPLTDSILCDGLTDAFHNCHMGITAENVAK ddPTM_BT-474_Pertuzumab_2h_R1 1 IGEMPLTDSILCDGLTDAFHNCHMGITAENVAK 33 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 140.55 2.79E-10 386590000 73431 78262 60905 62458 77802 76684 80213 42241 99219 81110 FALSE TRUE 70561.23534 76030.04439 71911.88832 65681.46486 80304.57199 78234.60302 81194.67069 41368.70859 87956.07508 75616.34745 0.933147893 1.005470999 0.951009811 0.868614619 1.062000145 1.034625523 1.073771392 0.54708684 1.163188623 1 16.20641054 IGTSTS(ph)FDSGIAGLSSISQCTSSSQLDETSHR ddPTM_BT-474_Pertuzumab_2h_R1 1 IGTSTSFDSGIAGLSSISQCTSSSQLDETSHR 32 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 IGT(0.008)S(0.037)T(0.17)S(0.785)FDSGIAGLSSISQCTSSSQLDETSHR 212.46 6.33E-28 160310000 21147 17446 10789 14837 25309 19354 17771 21014 23126 22557 TRUE FALSE 20320.55186 16948.45716 12738.8123 15602.73935 26123.08697 19745.35114 17988.48681 20580.05356 20500.83343 21029.1943 0.966301969 0.805948955 0.605767968 0.741956117 1.242229569 0.938949484 0.855405422 0.978642038 0.974874888 1 14.36010596 IHEAIIQSPPIDYFDVFK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHEAIIQSPPIDYFDVFK 18 0 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ; 152.71 3.85E-08 941380000 569340 464320 474480 505580 483660 522600 513590 333940 639760 678940 FALSE TRUE 547089.5634 451078.0482 560229.0908 531673.0444 499217.3631 533167.3301 519875.4681 327044.0223 567137.1269 632954.7891 0.864342245 0.712654452 0.885101275 0.839985815 0.788709355 0.842346625 0.821346922 0.516694127 0.896015224 1 19.27174293 IHEDIFDIIDR ddPTM_BT-474_Pertuzumab_2h_R1 8 IHEDIFDIIDR 11 0 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ;;;;;;; 181.31 6.28E-06 1571933000 929525 1033128 836840 1078980 1027738 986016 1045128 594854 1101335 1153404 FALSE TRUE 893198.1354 1003664.201 988075.6034 1134666.287 1060796.126 1005953.919 1057918.589 582570.057 976316.068 1075282.92 0.830663371 0.933395465 0.918898259 1.055225807 0.986527459 0.935524875 0.983851384 0.541783047 0.907962035 1 20.03628487 IHEGCEEPATHNALAK ddPTM_BT-474_Pertuzumab_2h_R1 6 IHEGCEEPATHNALAK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 320.57 2.57E-58 25766620000 21038910 20415930 17229040 18824040 19901250 21466650 20608260 4980056 24741570 21347020 FALSE TRUE 20216686.14 19833687.67 20342710.79 19795550.96 20541391.78 21900720.37 20860470.05 4877216.103 21933010.7 19901167.32 1.015854287 0.996609261 1.022186812 0.994692956 1.032170196 1.100474159 1.04820334 0.245071861 1.102096693 1 24.24634972 IHLDEK ddPTM_BT-474_Pertuzumab_2h_R1 7 IHLDEK 6 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;; 149.06 0.010686 12020340000 14388950 14054130 11759820 12885130 13303900 13323110 14792530 9126680 16843380 16069810 FALSE TRUE 13826613.93 13653319.97 13885081.07 13550133.1 13731832.03 13592512.41 14973565.41 8938210.869 14931390.12 14981387.46 0.922919454 0.91135217 0.926822106 0.904464499 0.91659281 0.907293297 0.999477882 0.596621034 0.996662703 1 23.8366679 IHLFDIDVPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHLFDIDVPGK 11 0 Q9NQR4;H7C579 Q9NQR4 NIT2 Omega-amidase NIT2 0 ; 115.18 0.0011584 717580000 728780 745330 596890 692650 673100 721280 752210 514770 873280 837010 FALSE TRUE 700298.4719 724073.9182 704761.3007 728397.7495 694750.8728 735864.7758 761415.771 504139.8196 774148.9155 780318.5672 0.897452017 0.927920914 0.903171256 0.933462025 0.890342614 0.943031227 0.97577554 0.646069235 0.992093419 1 19.5737037 IHQIGPGMVQQIQSVCMECQGHGER ddPTM_BT-474_Pertuzumab_2h_R1 2 IHQIGPGMVQQIQSVCMECQGHGER 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 341.69 1.05E-88 1948520000 105129 94074 99288 107481 122459 114578 114618 44469 124506 117064 FALSE TRUE 101020.4425 91391.10163 117231.5502 113028.1073 126398.0049 116894.8457 116020.7294 43550.69961 110372.6009 109135.151 0.925645326 0.837412152 1.074186906 1.035670966 1.158178678 1.071101699 1.063092215 0.39905291 1.011338692 1 16.73575632 IHRAS(ph)DPGLPAEEPK ddPTM_BT-474_Pertuzumab_2h_R1 6 IHRASDPGLPAEEPK 15 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 IHRAS(1)DPGLPAEEPK;IHRAS(1)DPGLPAEEPK;IHRAS(1)DPGLPAEEPK;IHRAS(1)DPGLPAEEPK;IHRAS(1)DPGLPAEEPK;IHRAS(1)DPGLPAEEPK 132.79 2.73E-05 10381290000 9504700 8556650 7660810 7565530 8309620 9293030 9026040 4731380 11875060 11275550 TRUE FALSE 9133245.816 8312622.72 9045288.781 7955987.91 8576906.474 9480941.434 9136503.378 4633675.35 10527052.97 10511846.96 0.868852625 0.790786125 0.860485205 0.756859184 0.81592764 0.901929173 0.869162519 0.440805062 1.00144656 1 23.32551284 IHTDFEK ddPTM_BT-474_Pertuzumab_2h_R1 6 IHTDFEK 7 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;;; 181.81 0.0006665 8222290000 9856680 9470540 8278610 9261640 9197100 9335160 9834460 7234000 11607900 10923350 FALSE TRUE 9471470.048 9200449.472 9774738.984 9739634.35 9492933.074 9523923.331 9954817.063 7084615.372 10290219.86 10183501.77 0.930079874 0.903466182 0.959860292 0.956413085 0.932187501 0.935230684 0.977543608 0.695695403 1.010479507 1 23.27973041 IHTLELK ddPTM_BT-474_Pertuzumab_2h_R1 2 IHTLELK 7 0 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 129.39 0.0036649 822770000 2086760 1973290 1710000 1826560 1891390 1799190 1982050 1335170 2246000 2122300 FALSE TRUE 2005207.112 1917013.701 2019035.039 1920828.98 1952228.277 1835570.855 2006306.921 1307598.273 1991043.496 1978554.731 1.013470631 0.968895968 1.020459534 0.970824284 0.986694099 0.927733171 1.014026496 0.660885571 1.006312065 1 20.91601554 IIAELNETWEEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IIAELNETWEEK 12 0 O43896;A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;O60333-3 O43896;A0A3B3ITW6;A0A087WWA3;O60333-3 KIF1C;KIF1A;KIF1B;KIF1Bbeta Kinesin-like protein KIF1C;Kinesin-like protein KIF1A;Kinesin-like protein;Kinesin-like protein KIF1B 0 ; 130.56 0.00049846 32290000 78095 73467 53918 56564 71234 72064 63759 63575 86757 81258 FALSE TRUE 75042.96106 71371.79309 63662.182 59483.27482 73525.3063 73521.18345 64539.30171 62262.15403 76908.70908 75754.32328 0.990609616 0.942148118 0.840376882 0.785212939 0.970575713 0.970521289 0.851955359 0.821895719 1.015238547 1 16.2090406 IIDSLFNTVTDKK ddPTM_BT-474_Pertuzumab_2h_R1 1 IIDSLFNTVTDKK 13 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 86.498 0.014108 178170000 185320 202830 190110 189160 190890 203070 200740 206810 232490 234230 FALSE TRUE 178077.4895 197045.487 224467.106 198922.5703 197030.1502 207176.2145 203196.7162 202539.3012 206098.7099 218365.3935 0.815502341 0.90236591 1.027942672 0.910961976 0.902295676 0.948759376 0.930535342 0.927524724 0.943824965 1 17.73638471 IILWDHDLNPER ddPTM_BT-474_Pertuzumab_2h_R1 2 IILWDHDLNPER 12 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ; 230.59 5.45E-12 332450000 184770 217083 196348 210239 204065 191670 240310 214530 230387 263450 FALSE TRUE 177548.9841 210892.0054 231832.4513 221089.46 210628.9361 195545.6987 243250.9857 210099.8805 204234.4336 245606.2968 0.722900782 0.858658789 0.943919005 0.900178305 0.857587687 0.796175429 0.990410217 0.855433607 0.831552107 1 17.90598802 IISNASCTTNCLAPLAK ddPTM_BT-474_Pertuzumab_2h_R1 1 IISNASCTTNCLAPLAK 17 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 218.16 1.10E-14 324140000 105470 119040 88129 89224 97012 114540 93179 92783 105600 116200 FALSE TRUE 101348.1158 115645.0958 104055.8707 93828.86133 100132.4791 116856.0773 94319.35247 90866.99863 93612.73071 108329.6705 0.935552701 1.067529286 0.960548207 0.866141851 0.924331059 1.078707955 0.870669615 0.838800656 0.864146732 1 16.72506891 IIVDELKQEVISTSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IIVDELKQEVISTSSK 16 1 P63244;J3KPE3;H0YAF8;H0Y8W2;D6RAC2;D6REE5;H0YAM7;D6RF23;H0Y9P0 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 216.93 1.34E-14 641640000 1098640 1159480 821350 756330 1029950 1137120 984510 1055900 1209420 1045910 FALSE TRUE 1055703.934 1126412.766 969786.2158 795364.2819 1063079.277 1160113.346 996558.7279 1034095.296 1072131.712 975069.5841 1.082695996 1.155212699 0.994581547 0.815700023 1.09025991 1.189774929 1.022038575 1.060534871 1.099543796 1 19.89514565 IKDAFDRNPELQNLLLDDFFK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKDAFDRNPELQNLLLDDFFK 21 2 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 155.01 1.60E-08 743550000 226300 218050 164500 131180 216130 214840 174220 234480 222760 221200 FALSE TRUE 217455.9458 211831.4275 194228.8093 137950.2155 223082.0177 219184.212 176352.1565 229637.9061 197473.2187 206217.927 1.054495838 1.027221205 0.941861904 0.668953556 1.081778005 1.062876614 0.855173743 1.113569074 0.95759482 1 17.65381023 IKEEEPDPEEWQLSGDSTLNTNDLTHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 IKEEEPDPEEWQLSGDSTLNTNDLTHLR 28 1 A0A494C1G8;A0A494C0Z6;H0Y6K5;A0A494C070;H0Y7L6;Q02447-4;Q02447-3;Q02447-5;Q02447-6;Q02447-2;Q02447 A0A494C1G8 SP3 Transcription factor Sp3 0 ; 231.21 2.08E-35 174143000 381665 322010 249137 284753 303071 263635 303660 320715 300287 276534 FALSE TRUE 366749.1098 312826.5901 294161.5979 299449.1365 312819.554 268965.8803 307376.2819 314092.1232 266199.6787 257804.1059 1.42258832 1.213427494 1.141027591 1.161537499 1.213400201 1.043295565 1.192286216 1.218336388 1.032565706 1 17.97591572 IKQHLENDPGSNEDTDIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKQHLENDPGSNEDTDIPK 19 1 O43396;K7ER96;K7EML9 O43396 TXNL1 Thioredoxin-like protein 1 0 166.76 1.16E-11 809150000 1797000 1738800 1153900 1015700 1414900 1608800 1403600 1502300 2003300 1509100 FALSE TRUE 1726771.253 1689211.126 1362435.398 1068120.399 1460411.543 1641331.038 1420777.677 1471276.98 1775893.783 1406887.313 1.22736998 1.200672656 0.968404069 0.75920821 1.038044433 1.166640017 1.009873118 1.045767466 1.262285733 1 20.42407535 IKVDNHLFNK ddPTM_BT-474_Pertuzumab_2h_R1 1 IKVDNHLFNK 10 1 P78356;P78356-2;A0A087WT35;P48426-2;P48426 P78356 PIP4K2B;PIP4K2A Phosphatidylinositol 5-phosphate 4-kinase type-2 beta;Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha 0 88.681 0.0072275 719550000 2476500 2307600 2166500 2032700 2047500 1030300 2509000 2321100 3012600 2914100 FALSE TRUE 2379715.642 2241789.507 2558034.744 2137607.891 2113359.697 1051133.372 2539705.893 2273168.474 2670622.278 2716725.411 0.875950007 0.825180748 0.94158752 0.786832516 0.777906994 0.386911893 0.93484085 0.836731038 0.983029888 1 21.37343732 ILDVASLEVLNEVNRR ddPTM_BT-474_Pertuzumab_2h_R1 2 ILDVASLEVLNEVNRR 16 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 227.41 8.11E-15 563390000 255930 303740 210881 260680 251990 317980 279460 281090 293600 283150 FALSE TRUE 245927.9727 295077.6326 248991.8877 274133.726 260095.4872 324409.7735 282880.1151 275285.3933 260271.7589 263971.9983 0.931644168 1.117836871 0.943251138 1.038495476 0.985314688 1.228955251 1.071629252 1.042858315 0.985982455 1 18.01002537 ILENLR ddPTM_BT-474_Pertuzumab_2h_R1 5 ILENLR 6 0 P12532;P12532-2;P17540;P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1;A0A2R8YCK2;V9GY80;P19784;H3BSA1;H3BNI9 P12532;P68400;P19784 CKMT1A;CKMT2;CSNK2A1;CSNK2A3;CSNK2A2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial;Casein kinase II subunit alpha;Casein kinase II subunit alpha 3;Casein kinase II subunit alpha" 0 ;;;; 180.48 0.0071962 2498220000 1088895 1202692 1023590 1281698 1045787 899699 1224296 1203615 1114083 1216659 FALSE TRUE 1046339.78 1168392.402 1208575.483 1347846.587 1079425.689 917891.5302 1239279.301 1178759.93 987616.9685 1134253.602 0.922491917 1.03009803 1.065524923 1.188311489 0.95166168 0.809247181 1.092594547 1.039238427 0.870719711 1 20.11331181 ILLSQTTGVAIPLHASSLDDVSLAST(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILLSQTTGVAIPLHASSLDDVSLASTPK 28 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 ILLSQTTGVAIPLHASSLDDVSLAS(0.196)T(0.804)PK 233.07 1.74E-44 129320000 129370 158190 127470 172280 120030 146290 149560 167270 156280 182660 TRUE FALSE 124314.0774 153678.5761 150506.6646 181171.3914 123890.874 149248.084 151390.36 163815.816 138539.7496 170288.2755 0.730021354 0.902461286 0.883834569 1.063909955 0.727536136 0.876443687 0.889023978 0.961991162 0.813560118 1 17.37761958 ILNHVLQHAEPGNAQSVLEAIDTYCEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILNHVLQHAEPGNAQSVLEAIDTYCEQK 28 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 278.67 6.79E-62 1622900000 714830 732610 538400 717170 762360 702310 757830 137800 800770 728720 FALSE TRUE 686893.6533 711716.6801 635700.8566 754183.2296 786882.0018 716511.1894 767104.5502 134954.3818 709869.9467 679363.1453 1.011084658 1.047623329 0.93573056 1.110132681 1.158264188 1.054680688 1.129152436 0.198648371 1.044904999 1 19.37382343 ILSISADIETIGEILKK ddPTM_BT-474_Pertuzumab_2h_R1 1 ILSISADIETIGEILKK 17 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 124.43 8.06E-05 1140300000 15103 14442 11321 13495 14617 14315 11998 14370 15202 16840 FALSE TRUE 14512.75806 14030.1283 13366.95653 14191.47857 15087.16908 14604.45911 12144.83511 14073.25448 13476.33269 15699.4118 0.924414128 0.893672227 0.851430404 0.903949699 0.961002187 0.930255177 0.773585359 0.89641922 0.858397299 1 13.93842289 IMDPNIVGSEHYDVAR ddPTM_BT-474_Pertuzumab_2h_R1 9 IMDPNIVGSEHYDVAR 16 0 P06576;H0YH81 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;;;;;; 214.28 1.72E-14 15379420000 5765038 9820760 6352730 14849310 6625180 8299090 12209640 9293100 7886850 6806150 FALSE TRUE 5539733.941 9540681.54 7500809.627 15615684.67 6838284.932 8466903.286 12359065.23 9101194.237 6991567.852 6345163.398 0.873064032 1.503614792 1.182130255 2.461037437 1.077716128 1.334386958 1.947793059 1.434351437 1.101873571 1 22.59722589 IMKDILEK ddPTM_BT-474_Pertuzumab_2h_R1 2 IMKDILEK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 122.26 0.0012751 9001200000 20895000 22242000 13950300 11956400 16584100 22859000 17291800 20255000 20895000 16766100 FALSE TRUE 20078400.3 21607679.94 16471429.53 12573471.24 17117542.64 23321224.64 17503422.22 19836727.17 18523087.2 15630517.11 1.284564046 1.382403396 1.053799399 0.804418123 1.095136041 1.492031548 1.119823618 1.269102425 1.185059142 1 23.89786217 IMQNTDPHSQEYVEHLKDEAQVCAIIER ddPTM_BT-474_Pertuzumab_2h_R1 2 IMQNTDPHSQEYVEHLKDEAQVCAIIER 28 1 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ; 158.12 7.20E-12 311000000 172184 182828 141435 152935 174778 197785 186394 95947 232030 219610 FALSE TRUE 165454.8589 177613.9244 166995.4507 160827.9937 180399.8931 201784.3482 188675.1455 93965.66092 205690.9271 204735.6191 0.8081391 0.867528207 0.815663886 0.78553988 0.881135847 0.985584966 0.921555059 0.458960983 1.004666057 1 17.64340259 INFS(ph)DLDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 INFSDLDQR 9 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 INFS(1)DLDQR 109.15 0.0026189 57248000 115790 106970 90658 97959 96327 105830 100380 132590 107920 122410 TRUE FALSE 111264.7988 103919.3203 107041.9173 103014.6757 99425.44544 107969.9551 101608.4805 129851.9702 95669.37404 114119.0617 0.974988728 0.910621931 0.937984555 0.902694731 0.871243103 0.946116744 0.890372555 1.137863984 0.838329484 1 16.80018026 INLAEDVLAWEHER ddPTM_BT-474_Pertuzumab_2h_R1 3 INLAEDVLAWEHER 14 0 K7EQ66;K7ELZ9;K7ENM2;A0A0C4DGP7;K7EMW4;Q969V3-2;Q969V3 K7EQ66 NCLN Nicalin 0 ;; 136.48 2.69E-05 191532000 65024 106599 64287.7 115464 70823.2 62049 92353 109852 87527 62809 FALSE TRUE 62482.79019 103558.9009 75905.91746 121423.1109 73101.29255 63303.67329 93483.24364 107583.5178 77591.3019 58554.89049 1.067080643 1.768578167 1.296320714 2.073663017 1.24842335 1.081099679 1.596506165 1.837310546 1.325103698 1 15.83750205 IPNPDFFEDLEPFR ddPTM_BT-474_Pertuzumab_2h_R1 1 IPNPDFFEDLEPFR 14 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 72.958 0.086486 17885000 6855.3 10385 7990 14715 8443.3 5416.9 10301 11632 10346 7096.8 FALSE TRUE 6587.387297 10088.82997 9433.970737 15474.44291 8714.886413 5526.433429 10427.06672 11391.79514 9171.565454 6616.127415 0.995656051 1.524884473 1.425905238 2.338897355 1.317218649 0.83529731 1.576007544 1.721822211 1.386243777 1 12.6917713 IPQNPSPHT(ph)HQQQNAPVTVIQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 IPQNPSPHTHQQQNAPVTVIQSK 23 0 F8W108;F8WCU9;Q68CP9-3;Q68CP9 F8W108 ARID2 AT-rich interactive domain-containing protein 2 1 IPQNPS(0.343)PHT(0.657)HQQQNAPVTVIQSK;IPQNPS(0.433)PHT(0.567)HQQQNAPVTVIQSK 119.85 0.00027209 322660000 143879 124775 109960 124492 123280 143684 131798 30830 169074 146547 TRUE FALSE 138256.0496 121216.5392 129832.218 130917.047 127245.4132 146589.3889 133410.9833 30193.34973 149881.4283 136621.2412 1.01196599 0.887245191 0.950307704 0.958248117 0.93137357 1.072961918 0.976502499 0.221000406 1.09705802 1 17.05982228 IQHILCTGNLCTK ddPTM_BT-474_Pertuzumab_2h_R1 1 IQHILCTGNLCTK 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 142.1 4.02E-05 644450000 498310 483010 300100 350060 374100 504520 382430 482610 519210 397020 FALSE TRUE 478835.4943 469235.0277 354334.7457 368126.6386 386133.2662 514721.7401 387110.2927 472643.9348 460271.4575 370129.4818 1.293697254 1.267759124 0.957326458 0.994588804 1.04323834 1.390653178 1.045878029 1.276969164 1.243541734 1 18.49767053 IQHYAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 IQHYAGK 7 0 E9PDF6;O43795;O43795-2;A0A0U1RRI3 E9PDF6 MYO1B Unconventional myosin-Ib 0 ; 81.297 0.027584 531670000 1532900 1709660 1408210 1571760 1384540 1387010 1684060 1614580 1674760 1736010 FALSE TRUE 1472992.573 1660902.171 1662704.872 1652878.722 1429074.987 1415056.293 1704670.03 1581238.359 1484648.266 1618428.496 0.910137567 1.026243776 1.027357635 1.02128622 0.883001621 0.874339704 1.053287207 0.977020834 0.917339425 1 20.6261622 IRDEMVATEQER ddPTM_BT-474_Pertuzumab_2h_R1 3 IRDEMVATEQER 12 1 P16615-5;P16615-2;P16615-3;P16615;H7C5W9;P16615-4 P16615-5 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 0 ;; 211.83 2.49E-08 907130000 320147 454174 298610 534094 350294 320405 449250 518410 444622 348643 FALSE TRUE 307635.3013 441221.4022 352575.4695 561658.6553 361561.5246 326883.8086 454748.0559 507704.6523 394150.3746 325029.0991 0.946485414 1.357482771 1.084750475 1.728025758 1.1123974 1.005706288 1.399099518 1.562028304 1.212661807 1 18.31020936 IRELEEAMAGER ddPTM_BT-474_Pertuzumab_2h_R1 2 IRELEEAMAGER 12 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 164.2 5.28E-05 306830000 188912 213220 162387 185892 195518 194314 185869 199888 219630 205435 FALSE TRUE 181529.1102 207139.1744 191733.9432 195485.9084 201807.014 198243.1622 188143.7204 195760.2429 194698.5232 191520.7045 0.947830213 1.081549773 1.001113398 1.020703787 1.053708603 1.035100423 0.982367525 1.022136189 1.01659256 1 17.54714084 IRPDNELFEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 IRPDNELFEVR 11 1 Q92805 Q92805 GOLGA1 Golgin subfamily A member 1 0 140.91 3.50E-05 280560000 157460 162320 145690 176910 173640 135630 165090 172630 172200 180040 FALSE TRUE 151306.2891 157690.7925 172019.4239 186040.3463 179225.2883 138372.5315 167110.4208 169065.1302 152652.5779 167845.7304 0.901460459 0.939498384 1.024866247 1.108400826 1.06779772 0.824403047 0.995619134 1.007265003 0.909481448 1 17.35677631 IS(ph)ESVLRDSPPPHEDYEDEVFVRDPHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 ISESVLRDSPPPHEDYEDEVFVRDPHPK 28 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 IS(0.39)ES(0.357)VLRDS(0.253)PPPHEDY(0.001)EDEVFVRDPHPK 68.708 0.0078953 351300000 519840 532920 399930 457450 478480 565960 574520 402200 621660 567020 TRUE FALSE 499524.0781 517721.6434 472206.2474 481059.0493 493870.7437 577404.099 581551.1476 393894.4294 551091.763 528615.2304 0.944967245 0.979392219 0.893289145 0.910036302 0.934272634 1.092295617 1.100140734 0.745143929 1.042519646 1 19.01185847 IS(ph)QEHLADHFDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISQEHLADHFDSR 13 0 P19174-2;P19174;V9GY71;V9GYH5 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 IS(1)QEHLADHFDSR;IS(1)QEHLADHFDSR 164.59 2.37E-05 423370000 320250 358970 382910 387730 384960 349340 439150 71719 552510 457910 TRUE FALSE 307734.2759 348732.5271 452110.3548 407740.7918 397342.588 356403.8942 444524.4491 70237.97759 489791.3811 426895.3478 0.720865846 0.816904023 1.059066015 0.955130558 0.930772823 0.834874158 1.041296072 0.164532075 1.147333611 1 18.70352292 IS(ph)WYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 ISWYLR 6 0 M0QYT0;M0R076;Q13011;M0R248;M0QZW4 M0QYT0;Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 1 IS(1)WYLR 92.439 0.049043 12747000 35102 36160 29586 37522 32157 32360 33159 44900 37654 33051 TRUE FALSE 33730.17503 35128.7522 34932.84834 39458.51492 33191.35911 33014.34137 33564.80976 43972.79931 33379.67578 30812.42633 1.094693896 1.140083933 1.133725983 1.280603952 1.077206928 1.071461917 1.089327059 1.427112517 1.08331864 1 14.91122467 ISESVLRDS(ph)PPPHEDYEDEVFVRDPHPK ddPTM_BT-474_Pertuzumab_2h_R1 4 ISESVLRDSPPPHEDYEDEVFVRDPHPK 28 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 IS(0.001)ES(0.005)VLRDS(0.994)PPPHEDYEDEVFVRDPHPK;IS(0.3)ES(0.3)VLRDS(0.359)PPPHEDY(0.04)EDEVFVRDPHPK;IS(0.043)ES(0.036)VLRDS(0.92)PPPHEDYEDEVFVRDPHPK;IS(0.004)ES(0.086)VLRDS(0.91)PPPHEDYEDEVFVRDPHPK 178.33 8.06E-18 2329250000 1542460 1544570 1171530 1197410 1368540 1629210 1474730 1063970 1814840 1659910 TRUE FALSE 1482178.958 1500520.376 1383251.532 1259208.474 1412560.332 1662153.742 1492778.187 1041998.648 1608826.972 1547482.817 0.957799945 0.969652367 0.893871981 0.813714026 0.912811642 1.074101582 0.964649281 0.673350706 1.039641251 1 20.56149196 ISEVFDCWFESGSMPYAQVHYPFENKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISEVFDCWFESGSMPYAQVHYPFENKR 27 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 191.42 3.17E-18 339830000 440690 470060 362598 380610 426940 516300 401220 374770 507960 497720 FALSE TRUE 423467.3476 456654.349 428127.5245 400253.3277 440672.9128 526739.9397 406130.2504 367030.8685 450298.5103 464008.9811 0.912627481 0.984149807 0.922670771 0.862598234 0.949707723 1.135193415 0.875263771 0.790999492 0.970452144 1 18.8237932 ISGLIYEETR ddPTM_BT-474_Pertuzumab_2h_R1 8 ISGLIYEETR 10 0 P62805 P62805 HIST1H4A Histone H4 0 ;;;;;;; 204.34 4.39E-07 2936822000 1841815 2048260 1406982 3160570 1249608 716467 2483760 1391306 1887716 1068348 FALSE TRUE 1769834.834 1989845.63 1661254.946 3323687.396 1289802.776 730954.4536 2514156.998 1362575.045 1673430.394 995987.8384 1.776964302 1.997861373 1.667947019 3.337076286 1.29499852 0.733898975 2.524284837 1.368063939 1.680171513 1 19.9257686 ISHQDHSDK ddPTM_BT-474_Pertuzumab_2h_R1 3 ISHQDHSDK 9 0 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 0 ;; 107.55 0.001593 124746000 110143 111774 117598 138204 123516 113217 144844 18563.1 153318 127513 FALSE TRUE 105838.4898 108586.315 138850.5746 145336.725 127489.0043 115506.3253 146616.6442 18179.7655 135913.9834 118876.4309 0.890323582 0.913438552 1.168024422 1.222586545 1.072449798 0.971650347 1.233353349 0.15292994 1.143321534 1 16.85910318 ISRPGDSDDSR ddPTM_BT-474_Pertuzumab_2h_R1 7 ISRPGDSDDSR 11 1 A0A3B3ITJ4;M0R1W6;B4DVF8;M0QYL7;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;; 140.14 3.53E-05 29923280000 5957250 6304130 5411370 6501700 5870690 6011080 6052190 6278080 6565840 6695770 FALSE TRUE 5724434.084 6124342.385 6389324.934 6837253.516 6059526.075 6132628.156 6126258.512 6148435.454 5820513.369 6242259.534 0.917045191 0.981109861 1.023559642 1.095317085 0.970726392 0.982437229 0.981416822 0.984969532 0.932436939 1 22.57363691 ISTAS(ph)GDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 ISTASGDGR 9 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;P63092-2;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 1 IS(0.059)T(0.293)AS(0.648)GDGR 73.841 0.03202 0 203620 280580 174110 300390 182550 204600 243240 268280 214350 189270 TRUE FALSE 195662.3053 272578.1331 205575.5501 315893.1639 188421.8865 208737.1522 246216.8439 262739.9242 190017.8866 176450.5743 1.108878824 1.544784618 1.165060249 1.7902643 1.06784513 1.182978027 1.395387036 1.489028445 1.076890157 1 17.4289046 ISYFTFIGTPVQATNMNDFKR ddPTM_BT-474_Pertuzumab_2h_R1 2 ISYFTFIGTPVQATNMNDFKR 21 1 O43396;K7ER96;K7EME7 O43396 TXNL1 Thioredoxin-like protein 1 0 ; 288.57 4.78E-46 448110000 580170 576390 465610 459490 566250 593100 518740 610390 637030 560550 FALSE TRUE 557496.315 559951.9215 549756.0844 483204.334 584463.9455 605092.8884 525088.4953 597785.2332 564717.025 522583.4492 1.066808212 1.071507187 1.051996739 0.924645307 1.11841266 1.157887586 1.004793581 1.143903876 1.080625546 1 18.99530191 ITDLYTDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 ITDLYTDLR 9 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 98.033 0.014629 278060000 349140 401230 333810 379450 358520 324030 393980 397120 373500 423380 FALSE TRUE 335495.2228 389787.3132 394136.8926 399033.46 370052.1214 330582.1086 398801.6451 388919.3332 331101.8458 394704.0955 0.849991745 0.987543118 0.998562967 1.010968633 0.937543151 0.837544156 1.01038132 0.985344053 0.838860933 1 18.59041196 ITDSAGHILYSK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITDSAGHILYSK 12 0 P49755;G3V2K7 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 168.02 4.77E-05 1272920000 2660400 3962900 2701900 3655400 2864200 1967020 3709100 3592500 3937800 3821900 FALSE TRUE 2556428.627 3849881.972 3190193.433 3844055.632 2956329.594 2006794.492 3754493.075 3518313.62 3490797.453 3563039.309 0.717485384 1.080505052 0.89535735 1.078869835 0.829721296 0.563225471 1.053733274 0.987447321 0.979724654 1 21.76467697 ITEYLCEPLRK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITEYLCEPLRK 11 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;K7ERB2;K7EN71;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 121.02 0.0006739 1637170000 1477630 1503500 1274970 1328580 1333330 1116980 1591810 1542720 1677940 1691150 FALSE TRUE 1419882.586 1460621.652 1505385.441 1397148.173 1376217.77 1139566.101 1611291.047 1510862.293 1487467.286 1576606.904 0.900593916 0.926433627 0.954826112 0.88617408 0.87289848 0.722796594 1.021999233 0.958299934 0.943461101 1 20.58839157 ITGEAFVQFASQELAEK ddPTM_BT-474_Pertuzumab_2h_R1 2 ITGEAFVQFASQELAEK 17 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 171.91 3.88E-09 268338000 328815 339577 270909 282626 304711 335170 286350 346400 372800 328542 FALSE TRUE 315964.5463 329892.5964 319868.2826 297212.3617 314512.306 341947.367 289854.437 339246.7189 330481.3069 306289.5577 1.031587719 1.077061193 1.044332967 0.970364004 1.026846323 1.116418626 0.946341231 1.107601322 1.078983265 1 18.22453666 ITLDNAYMEK ddPTM_BT-474_Pertuzumab_2h_R1 4 ITLDNAYMEK 10 0 P14618;P14618-3;B4DNK4;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 188.99 2.47E-06 1704350000 2217420 2103030 1856050 1941240 1958720 1745070 2204670 2239110 2273180 2313720 FALSE TRUE 2130760.775 2043053.643 2191479.523 2041427.629 2021724.008 1780356.511 2231651.411 2192871.596 2015138.136 2157009.684 0.98783088 0.947169435 1.015980382 0.946415607 0.937280914 0.825381789 1.034604262 1.016625754 0.934227673 1 21.04060122 IVLDKLER ddPTM_BT-474_Pertuzumab_2h_R1 1 IVLDKLER 8 1 P30047;H0YNX7;P30047-2 P30047 GCHFR GTP cyclohydrolase 1 feedback regulatory protein 0 82.749 0.017753 224360000 312640 339320 315640 350810 293160 166970 416170 371030 382640 417090 FALSE TRUE 300421.6832 329642.9258 372683.1694 368915.3461 302589.7576 170346.2478 421263.213 363368.1008 339204.3114 388840.1228 0.772609784 0.847759546 0.958448338 0.948758434 0.778185532 0.438088144 1.083384117 0.9344923 0.872349049 1 18.56881757 IVNHWAS(ph)PELR ddPTM_BT-474_Pertuzumab_2h_R1 5 IVNHWASPELR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR 190.87 2.18E-06 1492740000 1252740 1372850 1278180 1322950 1334030 1066980 1495800 1269780 1286280 1426810 TRUE FALSE 1203781.536 1333697.662 1509175.559 1391227.608 1376940.286 1088555.067 1514106.048 1243558.599 1140266.887 1330170.888 0.904982621 1.002651369 1.134572687 1.045901411 1.035160444 0.818357308 1.138279346 0.934886345 0.857233381 1 20.34318017 IWNVHSVLNVLHSLVDK ddPTM_BT-474_Pertuzumab_2h_R1 2 IWNVHSVLNVLHSLVDK 17 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 241.32 1.35E-20 120715000 167423 177598 183997 142492 170446 122971 197540 99704 204636 216907 FALSE TRUE 160879.9241 172533.0789 217249.3509 149846.0292 175928.5504 125457.5579 199957.5536 97645.07756 181406.5792 202215.6957 0.795585741 0.853213092 1.07434465 0.741020763 0.870004427 0.62041454 0.988833003 0.482875858 0.897094454 1 17.62553546 IYHTIAYLTPLPQPNR ddPTM_BT-474_Pertuzumab_2h_R1 2 IYHTIAYLTPLPQPNR 16 0 P10620;F5H760 P10620 MGST1 Microsomal glutathione S-transferase 1 0 ; 204.28 2.56E-11 1753110000 737540 1244890 833480 1545510 865830 660440 1241880 1213160 1085680 946090 FALSE TRUE 708716.1214 1209386.956 984108.3767 1625273.956 893680.2083 673794.5493 1257078.499 1188107.822 962438.1579 882010.4816 0.803523468 1.37117073 1.115755875 1.842692338 1.013230825 0.76393032 1.425242132 1.347045015 1.091186758 1 19.75043627 IYLTADNLVLNLQDESFTRGS(ph)DSLIK ddPTM_BT-474_Pertuzumab_2h_R1 1 IYLTADNLVLNLQDESFTRGSDSLIK 26 1 Q99623-2;Q99623 Q99623-2 PHB2 Prohibitin-2 1 IYLTADNLVLNLQDES(0.018)FT(0.018)RGS(0.963)DSLIK 142.79 1.66E-07 171240000 90863 101050 75229 107330 63625 85729 110010 99725 94325 83990 TRUE FALSE 87311.97351 98168.15294 88824.55376 112869.3142 65671.55591 87462.49912 111356.3353 97665.6439 83617.62144 78301.28249 1.115077183 1.253723436 1.134394622 1.441474655 0.838703452 1.116999573 1.422152125 1.247305801 1.067895937 1 16.25674832 IYNISGNGS(ph)PLADSK ddPTM_BT-474_Pertuzumab_2h_R1 4 IYNISGNGSPLADSK 15 0 Q53HL2 Q53HL2 CDCA8 Borealin 1 IYNISGNGS(1)PLADSK;IYNISGNGS(1)PLADSK;IYNISGNGS(1)PLADSK;IYNISGNGS(1)PLADSK 289.81 7.35E-44 3456160000 2582820 2236560 2084090 2207690 2457970 2211360 2524110 2716360 2290170 2455910 TRUE FALSE 2481880.539 2172775.499 2460731.423 2321629.145 2537032.837 2256075.214 2555000.813 2660266.217 2030199.503 2289569.028 1.083994633 0.948988859 1.074757473 1.014002686 1.10808314 0.985371127 1.115930894 1.161906972 0.886716879 1 21.12664463 KAAEAHVDAHYYEQNEQPTGTCAACITGDNR ddPTM_BT-474_Pertuzumab_2h_R1 1 KAAEAHVDAHYYEQNEQPTGTCAACITGDNR 31 1 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 253.76 9.38E-59 163890000 71909 67552 50627 59855 56632 65560 70586 12454 70246 63439 FALSE TRUE 69098.71678 65625.4831 59776.42509 62944.12372 58453.61971 66885.66812 71449.85258 12196.82055 62271.96858 59142.22002 1.168348377 1.109621571 1.01072339 1.064284088 0.988356874 1.130929277 1.208102309 0.206228656 1.052919024 1 15.85190078 KAALEEVER ddPTM_BT-474_Pertuzumab_2h_R1 1 KAALEEVER 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 89.403 0.01945 496450000 339370 350400 324180 377410 326630 339980 345850 323040 424310 439910 FALSE TRUE 326107.0452 340406.9351 382766.5373 396888.1753 337136.3506 346854.6285 350082.6158 316369.1111 376144.1077 410114.5039 0.795160966 0.830029009 0.933316266 0.967749669 0.8220542 0.8457507 0.853621641 0.771416539 0.917168508 1 18.64566724 KAHS(ph)NMLTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KAHSNMLTVK 10 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 KAHS(1)NMLTVK 55.353 0.056164 415900000 340960 403760 375230 409880 356530 370820 401970 377610 422580 423710 TRUE FALSE 327634.9062 392245.1601 443042.4079 431033.9559 367998.1112 378318.2345 406889.4291 369812.2215 374610.49 395011.7443 0.829430798 0.992996198 1.121593002 1.091192761 0.931613089 0.957739206 1.030069194 0.936205637 0.948352791 1 18.59153602 KAS(ph)SPSPLTIGTPESQR ddPTM_BT-474_Pertuzumab_2h_R1 1 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KAS(0.578)S(0.381)PS(0.042)PLTIGTPESQR 102.66 0.00057393 570970000 171280 181290 130920 161680 163610 157190 197860 168960 188630 159690 TRUE FALSE 164586.1882 176119.7867 154580.1563 170024.3242 168872.6642 160368.4895 200281.4699 165470.917 167217.5132 148874.0541 1.105539775 1.183011961 1.038328386 1.142068208 1.134332408 1.077209125 1.345308094 1.111482575 1.123214614 1 17.18373282 KCSTPEEIK ddPTM_BT-474_Pertuzumab_2h_R1 2 KCSTPEEIK 9 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 99.752 0.0082166 1553400000 1293990 1222640 1042800 910670 1048230 823270 1224440 1207660 1375580 1286930 FALSE TRUE 1243419.44 1187771.504 1231257.157 957669.7878 1081947.27 839917.0835 1239425.063 1182721.399 1219429.925 1199765.085 1.036385752 0.990003393 1.026248532 0.798214417 0.901799264 0.70006795 1.033056453 0.985794147 1.016390576 1 20.19432052 KDPEDTGAEKS(ph)PTTSADLK ddPTM_BT-474_Pertuzumab_2h_R1 4 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDT(0.001)GAEKS(0.77)PT(0.199)T(0.026)S(0.003)ADLK;KDPEDT(0.001)GAEKS(0.745)PT(0.174)T(0.056)S(0.024)ADLK;KDPEDT(0.011)GAEKS(0.59)PT(0.291)T(0.047)S(0.06)ADLK;KDPEDTGAEKS(0.856)PT(0.143)TS(0.001)ADLK 169.6 7.21E-12 2936520000 1883980 1486510 1355140 1338930 1873420 1395690 1680200 1929110 1661770 1405990 TRUE FALSE 1810351.979 1444116.19 1600043.943 1408032.338 1933680.256 1423911.808 1700762.79 1889273.204 1473132.836 1310761.045 1.381145698 1.101738716 1.220698425 1.074209783 1.47523476 1.086324478 1.297538401 1.44135593 1.123875967 1 20.32197327 KDPELWGSVLLESNPYRR ddPTM_BT-474_Pertuzumab_2h_R1 2 KDPELWGSVLLESNPYRR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 192.69 9.09E-15 4908800000 537110 611830 440300 414570 442860 544480 518590 549360 627730 562980 FALSE TRUE 516119.1474 594381.2074 519872.0044 435966.0074 457104.9941 555489.7587 524936.6595 538015.524 556472.7221 524848.8631 0.983367182 1.132480699 0.990517539 0.83065057 0.870926901 1.058380417 1.000167279 1.025086576 1.060253267 1 19.00154251 KDPSGASNPSADS(ph)PLHR ddPTM_BT-474_Pertuzumab_2h_R1 8 KDPSGASNPSADSPLHR 17 1 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPS(0.001)ADS(0.999)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR 240.2 1.59E-20 34426970000 13714390 13658060 11274470 12557830 11612720 13054810 13395410 13361380 14784530 14549730 TRUE FALSE 13178416.48 13268545.5 13312017.53 13205941.11 11986253.69 13318787.2 13559347.03 13085462.83 13106252.14 13564263.83 0.971554125 0.978198719 0.981403613 0.973583327 0.883664151 0.981902695 0.999637519 0.964701292 0.966233944 1 23.69330741 KDS(ph)QNSSQHSVSSHR ddPTM_BT-474_Pertuzumab_2h_R1 5 KDSQNSSQHSVSSHR 15 1 A0A087WT53;Q96QZ7-7;Q96QZ7-6;Q96QZ7-2;Q96QZ7;A0A087WXD2;H7C5T8;H7C4U7;H7C535;Q96QZ7-4;Q96QZ7-3;Q96QZ7-5 A0A087WT53 MAGI1 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1" 1 KDS(0.495)QNS(0.252)S(0.252)QHSVSSHR;KDS(0.927)QNS(0.037)S(0.037)QHSVSSHR;KDS(0.999)QNSSQHSVSSHR;KDS(0.817)QNS(0.092)S(0.092)QHSVSSHR;KDS(0.754)QNS(0.123)S(0.123)QHSVSSHR 191.95 7.25E-08 253446700 102492.3 151485.5 93577.7 157876.2 140277.3 142587.9 144747.1 32886.8 149461.3 171020.7 TRUE FALSE 98486.7876 147165.2819 110489.272 166024.2096 144789.4468 145471.125 146518.5583 32207.67609 132495.0798 159437.3157 0.617714788 0.923029099 0.692995059 1.041313377 0.908127725 0.91240325 0.918972812 0.202008394 0.83101675 1 17.2826298 KDSGSSS(ph)VFAESPGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 KDS(0.092)GS(0.17)S(0.234)S(0.504)VFAESPGGK 114.46 0.00035623 178690000 139980 143300 143460 150170 181230 191510 132190 153460 172840 149920 TRUE FALSE 134509.4268 139213.2243 169386.4133 157920.2917 187059.4275 195382.4634 133807.7808 150290.9974 153219.9278 139765.7849 0.962391668 0.996046525 1.211930469 1.129892354 1.338377828 1.397927709 0.957371512 1.075306074 1.096262064 1 17.0926517 KDVFFYQADDEHYIPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KDVFFYQADDEHYIPR 16 1 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 189.87 6.15E-10 37440000 71617 74328 62864 71280 65359 78997 66084 67999 76081 79572 FALSE TRUE 68818.12846 72208.23821 74224.9232 74958.76934 67461.33159 80594.37347 66892.75576 66594.79689 67444.60384 74182.51756 0.927686613 0.973386191 1.000571639 1.01046408 0.909396632 1.086433517 0.901732079 0.897715514 0.909171137 1 16.17879161 KEDIFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KEDIFR 6 1 P49756;P49756-2;P49756-3;H0YE46 P49756 RBM25 RNA-binding protein 25 0 ; 91.626 0.076449 492740000 1317130 1310370 975980 1238620 1251930 939060 1294440 1154480 1331890 1486030 FALSE TRUE 1265655.103 1272999.531 1152361.297 1302545.327 1292199.465 958048.4366 1310281.744 1130639.585 1180699.431 1385379.864 0.913579832 0.918881213 0.831801678 0.940208069 0.932740181 0.691542054 0.945792398 0.816122432 0.852256815 1 20.40185018 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_BT-474_Pertuzumab_2h_R1 2 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 41 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 385.44 2.14E-194 2563300000 389024 411247 334171 353958 403274 384588 395334 213933 465170 428276 FALSE TRUE 373820.512 399518.6382 394563.1333 372225.8148 416245.6745 392364.6329 400172.2157 209515.2088 412365.8518 399268.4851 0.936263507 1.000626529 0.988215068 0.93226946 1.042520735 0.982708748 1.002263466 0.524747674 1.032803407 1 18.60699968 KEKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KEKPELSEPSHLNGPSSDPEAAFLSR 26 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 KEKPELSEPSHLNGPS(0.58)S(0.42)DPEAAFLSR 136.73 1.00E-05 534890000 83779 74840 55588 47074 79779 72412 62731 72274 76361 83839 TRUE FALSE 80504.82406 72705.63648 65633.98815 49503.49478 82345.16399 73876.22025 63498.72074 70781.51664 67692.81941 78160.50985 1.029993589 0.930209342 0.839733368 0.633356856 1.053539238 0.945186008 0.812414362 0.905591798 0.866074435 1 16.25415226 KENALVQMADGNQAQLAMSHLNGHK ddPTM_BT-474_Pertuzumab_2h_R1 1 KENALVQMADGNQAQLAMSHLNGHK 25 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 126.59 5.29E-05 412190000 286000 345510 276860 315420 299300 344690 343020 68064 375780 307620 FALSE TRUE 274822.8038 335656.3931 326894.7607 331698.864 308927.2563 351659.868 347217.9814 66658.45461 333123.0298 286784.6234 0.958289885 1.170412797 1.139861534 1.156613141 1.077209973 1.22621591 1.21072733 0.232433852 1.161579118 1 18.12960815 KEPFFHGHDNYDQLVR ddPTM_BT-474_Pertuzumab_2h_R1 3 KEPFFHGHDNYDQLVR 16 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ;; 196.87 1.82E-11 925400000 974850 1000610 907810 966760 1069300 917920 1111990 207084 1215520 1129700 FALSE TRUE 936751.7842 972073.5825 1071871.461 1016654.599 1103695.006 936480.9713 1125598.866 202807.643 1077539.265 1053184.413 0.889447064 0.922985159 1.017743377 0.965314894 1.047959875 0.889189927 1.06875762 0.192566127 1.023124965 1 20.00632664 KFDHES(ph)SPGTDEDKSG ddPTM_BT-474_Pertuzumab_2h_R1 1 KFDHESSPGTDEDKSG 16 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KFDHES(0.5)S(0.5)PGTDEDKSG 77.847 0.011889 199730000 106630 132670 95147 93561 101140 127090 115950 105030 125680 129690 TRUE FALSE 102462.7817 128886.3815 112342.1794 98389.69442 104393.26 129659.8469 117369.0308 102861.0938 111413.3333 120905.9808 0.84745834 1.066005012 0.929169746 0.813770285 0.863425112 1.072402259 0.970746278 0.850752735 0.921487362 1 16.88352609 KFDLDK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFDLDK 6 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 89.298 0.080693 1819100000 1836600 1695700 1700800 1336200 1553500 858330 1952700 2047500 1967000 2151000 FALSE TRUE 1764823.642 1647340.296 2008172.394 1405161.442 1603469.738 875686.0207 1976597.727 2005218.409 1743714.406 2005310.854 0.880074846 0.821488745 1.001426981 0.70072001 0.799611559 0.436683429 0.985681458 0.9999539 0.869548181 1 20.93539446 KFGNPGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFGNPGEK 8 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5;J3QKN9 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 80.755 0.03949 558080000 1141800 1093800 1044100 1016300 1045100 1119600 1226600 844790 1421900 1288300 FALSE TRUE 1097177.194 1062605.895 1232792.096 1068751.365 1078716.591 1142239.079 1241611.498 827344.7913 1260491.873 1201042.294 0.913520864 0.88473645 1.026435208 0.88985323 0.898150379 0.951039847 1.033778331 0.688855668 1.049498323 1 20.19585552 KFNALFAQGNYSEAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KFNALFAQGNYSEAAK 16 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 203.2 4.55E-11 1681200000 1491600 1486100 1116700 1016700 1346200 934360 1565800 1425700 1634900 1574000 FALSE TRUE 1433306.623 1443717.883 1318512.531 1069172.009 1389501.746 953253.3994 1584962.729 1396258.797 1449313.006 1467391.578 0.976771739 0.983866818 0.898541705 0.728620789 0.946919531 0.649624418 1.080122547 0.951524336 0.98767979 1 20.48482248 KFTDFDEVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KFTDFDEVR 9 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4 P50570-2 DNM2;DNM3 Dynamin-2;Dynamin-3 0 149.31 0.000141 481020000 1035100 1158300 1022600 1121200 1046200 743780 1278000 1217500 1245300 1352700 FALSE TRUE 994647.1476 1125266.418 1207406.568 1179065.266 1079851.973 758819.7412 1293640.546 1192358.2 1103938.765 1261080.424 0.788726182 0.892303454 0.957438197 0.934964372 0.856291123 0.601721926 1.025819227 0.94550528 0.875391247 1 20.26622885 KGDVLHMHYTGK ddPTM_BT-474_Pertuzumab_2h_R1 1 KGDVLHMHYTGK 12 1 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 172.57 1.44E-05 1181400000 2232200 2713400 2353700 2864400 2455000 2610700 2852000 127470 3102800 2643900 FALSE TRUE 2144963.156 2636016.489 2779065.948 3012232.027 2533967.305 2663490.143 2886903.629 124837.7 2750583.152 2464826.298 0.870228932 1.069453247 1.127489572 1.22208694 1.028051067 1.080599531 1.171240193 0.050647666 1.115933871 1 21.23305455 KGQTHTLEDFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KGQTHTLEDFQR 12 1 Q99714;Q99714-2;Q5H928 Q99714 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 0 ; 126.1 0.00019051 362800000 155460 182047 128373 249780 138400 151157 238810 213255 179311 160214 FALSE TRUE 149384.4513 176855.1978 151572.8567 262671.1757 142851.7617 154213.4981 241732.6282 208851.2097 158956.367 149362.5631 1.000146544 1.184066436 1.014798177 1.758614544 0.956409416 1.032477583 1.618428495 1.398283515 1.06423165 1 17.18845906 KGSS(ph)GNASEVSVACLTER ddPTM_BT-474_Pertuzumab_2h_R1 1 KGSSGNASEVSVACLTER 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 KGS(0.342)S(0.651)GNAS(0.007)EVSVACLTER 177 1.02E-13 337000000 172030 164540 138970 154380 181420 167260 155340 185180 192030 182190 TRUE FALSE 165306.8774 159847.4803 164084.9704 162347.5703 187255.5391 170642.1118 157241.0974 181355.9683 170231.5595 169850.109 0.973251524 0.941109083 0.966057492 0.955828473 1.102475236 1.004662951 0.925763888 1.067741253 1.002245806 1 17.37390262 KHDNEGSGSKR ddPTM_BT-474_Pertuzumab_2h_R1 1 KHDNEGSGSKR 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 78.548 0.017765 31706000 67832 62036 56200 58211 53742 60058 63106 35740 67784 73195 FALSE TRUE 65181.05045 60266.79402 66356.59016 61215.27669 55470.66024 61272.41391 63878.31011 35001.95651 60089.44449 68237.43745 0.955209528 0.883192515 0.972436724 0.897092256 0.812906555 0.897929585 0.936118244 0.512943595 0.880593509 1 16.05827585 KHEDFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 KHEDFEK 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 133.12 0.0021441 1218320000 3143670 2781000 2840630 2786860 2860940 2889220 3078190 2470000 3808450 3612200 FALSE TRUE 3020811.901 2701688.603 3353995.03 2930690.179 2952964.733 2947642.008 3115861.81 2418993.637 3376130.722 3367542.477 0.897037505 0.802273059 0.995977053 0.870275638 0.876890122 0.875309526 0.925262809 0.718326095 1.002550301 1 21.68326471 KHEETECPLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KHEETECPLR 10 1 O14545;F8VNX8;F8VVF3;O14545-2;S4R2Z9 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 0 ; 128.17 0.00021864 471390000 142511 137611 116642 133324 135481 128763 144464 78232 145616 153050 FALSE TRUE 136941.5126 133686.469 137721.8041 140204.8676 139838.8694 131366.6761 146231.9936 76616.48186 129086.2822 142683.7872 0.959755241 0.936942253 0.965223918 0.98262648 0.98006138 0.920683973 1.024867622 0.536966977 0.904701821 1 17.12246189 KHFTILDAPGHK ddPTM_BT-474_Pertuzumab_2h_R1 2 KHFTILDAPGHK 12 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1;H3BSV8 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 182.07 7.06E-06 668520000 520310 549540 505330 597950 531280 641980 613170 198309 721290 714560 FALSE TRUE 499975.71 533867.6573 596654.372 628810.2712 548369.1037 654961.2755 620674.1579 194213.8498 639412.1831 666162.2147 0.750531476 0.801407894 0.895659284 0.943929657 0.823176535 0.983185868 0.931716246 0.291541378 0.959844568 1 19.345514 KHKEDKDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KHKEDKDDR 9 3 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 ; 63.283 0.033767 128677000 525830 371200 357920 322870 367800 383710 432680 191037 544590 507040 FALSE TRUE 505279.9823 360613.7394 422604.1059 339533.3594 379630.621 391468.8791 437975.2673 187092.0192 482770.4263 472697.7292 1.068928305 0.762884434 0.894026097 0.718288535 0.803114967 0.828159001 0.926544048 0.395796315 1.02130896 1 18.85055841 KHNGVGGS(ph)PPK ddPTM_BT-474_Pertuzumab_2h_R1 3 KHNGVGGSPPK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 KHNGVGGS(1)PPK;KHNGVGGS(1)PPK;KHNGVGGS(1)PPK 98.694 0.0032647 473880000 1027760 874200 861020 782910 939750 1009270 979150 348002 1377160 1033350 TRUE FALSE 987594.003 849268.6719 1016625.467 823316.0789 969977.9122 1029678.131 991133.1306 340815.6371 1220830.57 963360.2841 1.025155406 0.881569114 1.055291031 0.85462946 1.006869318 1.06884013 1.028829138 0.353777961 1.267262716 1 19.87771592 KHNVGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KHNVGVK 7 1 O75874;C9J4N6;C9JLU6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 83.614 0.014379 607420000 1318600 1168700 1145000 1271100 1204700 1282500 1316900 688460 1661100 1573400 FALSE TRUE 1267067.654 1135369.82 1351926.97 1336701.623 1243450.27 1308433.029 1333016.616 674243.0604 1472538.892 1466832.217 0.863812261 0.774028418 0.921664356 0.911284609 0.847711317 0.892012743 0.908772388 0.459659294 1.003890476 1 20.48427243 KHQLLEADISAHEDR ddPTM_BT-474_Pertuzumab_2h_R1 1 KHQLLEADISAHEDR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 127.75 3.10E-05 232760000 96010 135110 113920 164070 130850 138900 147640 64100 172230 163600 FALSE TRUE 92257.82306 131256.7951 134507.8781 172537.6724 135058.9091 141708.6532 149446.8625 62776.3126 152679.1724 152519.2263 0.60489307 0.860591797 0.881907687 1.131251951 0.88552055 0.929119932 0.979855892 0.41159606 1.001048695 1 17.21863159 KHS(ph)PDLR ddPTM_BT-474_Pertuzumab_2h_R1 4 KHSPDLR 7 1 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 KHS(1)PDLR;KHS(1)PDLR;KHS(1)PDLR;KHS(1)PDLR 117.7 0.0031683 587931000 1585620 1581260 1265480 1360200 1432990 1454690 1501920 1072820 1672950 1626390 TRUE FALSE 1523652.217 1536164.013 1494180.386 1430400.085 1479083.425 1484104.828 1520300.946 1050665.892 1483043.73 1516233.157 1.004893087 1.013144981 0.985455555 0.943390585 0.975498668 0.97881043 1.002682826 0.692944807 0.978110605 1 20.53206019 KHS(ph)PS(ph)PPPPTPTESR ddPTM_BT-474_Pertuzumab_2h_R1 4 KHSPSPPPPTPTESR 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR;KHS(0.998)PS(0.999)PPPPT(0.003)PTESR;KHS(1)PS(1)PPPPTPTESR 137.99 4.67E-05 7618280000 2298710 2039000 1678930 1911240 2057380 2115860 2168490 1634840 2657460 2311080 TRUE FALSE 2208873.872 1980849.716 1982349.999 2009879.325 2123557.496 2158644.139 2195028.629 1601079.983 2355796.282 2154548.493 1.025214275 0.919380428 0.920076761 0.932854068 0.985616013 1.00190093 1.018788222 0.743116244 1.093406015 1 21.03895414 KIDTHPS(ph)PSHSSTVK ddPTM_BT-474_Pertuzumab_2h_R1 6 KIDTHPSPSHSSTVK 15 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594 Q8NI27 THOC2 THO complex subunit 2 1 KIDT(0.021)HPS(0.969)PS(0.01)HSSTVK;KIDT(0.001)HPS(0.961)PS(0.038)HSSTVK;KIDTHPS(0.893)PS(0.107)HSSTVK;KIDTHPS(0.963)PS(0.037)HSSTVK;KIDTHPS(0.965)PS(0.034)HSSTVK;KIDT(0.001)HPS(0.964)PS(0.036)HSSTVK 191.95 7.25E-08 5675020000 5264940 7326360 5676580 7096200 5944240 7308130 6904780 678261 7290440 7787560 TRUE FALSE 5059180.324 7117419.386 6702464.281 7462435.732 6135441.878 7455905.396 6989282.763 664254.6733 6462859.815 7260101.625 0.69684704 0.980347074 0.923191524 1.027869322 0.845090358 1.026969839 0.962697649 0.091493853 0.890188616 1 22.79155831 KIPNPDFFEDLEPFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KIPNPDFFEDLEPFR 15 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 199.58 1.18E-08 1797550000 683680 1087720 614070 976530 695220 529860 818560 1133480 853240 586550 FALSE TRUE 656961.0298 1056699.291 725046.1089 1026928.83 717582.3827 540574.1322 828577.7821 1110073.242 756383.7723 546822.4461 1.201415623 1.932435836 1.325926019 1.877993191 1.312276751 0.988573414 1.515259273 2.030043298 1.383234682 1 19.06071294 KKEPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKEPPR 6 2 R4GMQ1;O60341;O60341-2;O75494-2;O75494 R4GMQ1;O75494-2 KDM1A;SRSF10 Lysine-specific histone demethylase 1A;Serine/arginine-rich splicing factor 10 0 ; 78.616 0.038986 1674370000 1213950 1360540 989340 1395330 1474450 1448290 1546130 1670700 1784000 1687720 FALSE TRUE 1166507.492 1321738.731 1168135.746 1467343.149 1521877.023 1477575.416 1565052.001 1636199.461 1581487.799 1573409.221 0.741388493 0.840047658 0.742423351 0.932588375 0.967248064 0.939091621 0.994688464 1.039907126 1.005134442 1 20.58546251 KKGGSYVFQSDEGPEPEAEES(ph)DLDSGSVHSASGRPDGPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 KKGGSYVFQSDEGPEPEAEESDLDSGSVHSASGRPDGPVR 40 3 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5;I3L1I4;A0A5F9ZHM2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 KKGGSYVFQSDEGPEPEAEES(0.998)DLDS(0.001)GSVHSASGRPDGPVR;KKGGSYVFQSDEGPEPEAEES(1)DLDSGSVHSASGRPDGPVR 193.73 4.90E-25 955860000 702330 791810 574060 608970 641540 763270 660010 748480 768530 772970 TRUE FALSE 674882.1671 769228.3541 677805.4119 640399.0147 662175.7167 778703.8424 668087.3998 733023.6264 681289.6963 720616.0534 0.936535016 1.067459364 0.940591607 0.888682693 0.918902255 1.080608514 0.927105907 1.017218008 0.945426754 1 19.45887127 KLAEPAER ddPTM_BT-474_Pertuzumab_2h_R1 1 KLAEPAER 8 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 0 98.048 0.012505 243080000 303470 335500 250450 305090 304810 263680 314260 357560 317800 298780 FALSE TRUE 291610.0569 325931.8685 295711.8862 320835.7315 314614.4905 269011.7903 318106.0079 350176.261 281724.6763 278543.3645 1.046910801 1.170129718 1.0616368 1.151834049 1.129499139 0.965780645 1.142034055 1.257169639 1.011421244 1 18.08754242 KLDALCNIHENIR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLDALCNIHENIR 13 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 134.37 6.25E-05 667460000 830830 885460 697190 709600 805110 721330 897350 790840 926030 892070 FALSE TRUE 798360.2451 860207.5478 823187.7419 746222.541 831007.0943 735915.7868 908332.0377 774508.8776 820910.9566 831649.3043 0.959972239 1.034339286 0.989825564 0.897280305 0.999227787 0.884887155 1.092205612 0.931292642 0.98708789 1 19.66561577 KLEEAASR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLEEAASR 8 1 Q9UH65;E7EMB1;E9PJM7 Q9UH65 SWAP70 Switch-associated protein 70 0 83.883 0.028614 94878000 186650 214970 180380 191380 201320 160550 189480 201430 216820 223060 FALSE TRUE 179355.5116 208839.2661 212978.6785 201257.1447 207795.6406 163796.431 191798.9129 197270.4001 192207.5026 207951.9475 0.862485366 1.00426694 1.02417256 0.967806011 0.999248351 0.787664809 0.922323235 0.94863454 0.924288062 1 17.66589067 KLESTESR ddPTM_BT-474_Pertuzumab_2h_R1 8 KLESTESR 8 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 171.56 0.00046283 25986710000 32005900 32100200 25960500 29132100 29775600 29578200 30456100 32990900 32072700 31472400 FALSE TRUE 30755074.04 31184733.73 30652139.84 30635611.17 30733359.22 30176291.47 30828830.86 32309626.39 28431941.56 29340746.32 1.048203536 1.062847325 1.044695302 1.044131967 1.047463445 1.028477297 1.050717338 1.101186249 0.969025847 1 24.80640223 KLEVEANNAFDQYR ddPTM_BT-474_Pertuzumab_2h_R1 6 KLEVEANNAFDQYR 14 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;;; 305.23 4.30E-44 8095580000 5143370 5263940 4174319 4835544 4864895 4649371 5309770 5132340 5235200 5398697 FALSE TRUE 4942361.414 5113817.585 4928711.301 5085107.005 5021378.766 4743384.467 5374752.554 5026355.385 4640922.044 5033038.444 0.981983641 1.016049776 0.979271539 1.010345353 0.997683372 0.942449481 1.067894198 0.998672162 0.922091515 1 22.26299819 KLFVGGLK ddPTM_BT-474_Pertuzumab_2h_R1 3 KLFVGGLK 8 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;; 131.06 0.0030715 0 16306200 16393000 13802800 12459300 12943200 10450600 15714400 16206900 16918700 16320500 FALSE TRUE 15668935.68 15925487.69 16297273 13102325.97 13359529.78 10661918.29 15906717.53 15872221.85 14998160.1 15215098 1.029828114 1.046689787 1.071125076 0.861139768 0.878044281 0.700745949 1.045456134 1.043188933 0.985741933 1 23.85900029 KLGPIS(ph)PPQPPSVSAWNKPLTSFGSAPSSEGAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLGPISPPQPPSVSAWNKPLTSFGSAPSSEGAK 33 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2 E7EPN9 PRRC2C Protein PRRC2C 1 KLGPIS(0.958)PPQPPS(0.039)VS(0.003)AWNKPLTSFGSAPSSEGAK;KLGPIS(1)PPQPPSVSAWNKPLTSFGSAPSSEGAK 205.28 1.95E-27 820770000 552110 498290 475660 433690 542590 566160 472850 510910 563010 553710 TRUE FALSE 530532.9308 484079.2571 561622.343 456072.7929 560042.9001 577608.1431 478636.8797 500359.53 499099.4651 516206.7285 1.027752839 0.937762393 1.087979509 0.883508036 1.084919799 1.118947335 0.927219374 0.969300674 0.966859666 1 18.97758942 KLHELTVMQDR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLHELTVMQDR 11 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 200.82 2.96E-08 1265990000 811330 899600 846600 861030 857370 688140 1009810 902580 966300 990030 FALSE TRUE 779622.3266 873944.2888 999599.4525 905467.8615 884948.0847 702054.6623 1022168.357 883941.4076 856609.6751 922974.3863 0.844684683 0.94687816 1.08301971 0.981032491 0.958800263 0.760643711 1.107472073 0.957709575 0.928096909 1 19.81593109 KLNCQVIGASVDSHFCHLAWVNTPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KLNCQVIGASVDSHFCHLAWVNTPK 25 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 147.41 9.63E-08 4320700000 3428200 3810600 3293400 3367100 3598700 3973000 3792700 408190 4189500 3667500 FALSE TRUE 3294222.154 3701925.419 3888590.641 3540876.435 3714455.454 4053336.782 3839116.197 399760.7339 3713925.524 3419096.958 0.963477256 1.082720222 1.137315112 1.035617439 1.086384943 1.185499221 1.12284508 0.116919976 1.086229952 1 21.7051839 KLPEEEAECYFHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLPEEEAECYFHSR 14 1 J3QQZ9;Q9NVS9-3;Q9NVS9;J3QQV6 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 92.977 0.0030802 183950000 178150 206840 144620 154060 190510 195740 181360 186620 207240 192540 FALSE TRUE 171187.701 200941.1257 170756.0511 162011.0551 196637.9272 199697.9969 183579.5379 182766.2318 183714.984 179499.0943 0.95369674 1.119454817 0.951291992 0.902573106 1.095481445 1.112529273 1.022732391 1.018201415 1.023486969 1 17.45361704 KLPFQR ddPTM_BT-474_Pertuzumab_2h_R1 2 KLPFQR 6 1 K7EK07;Q71DI3;Q16695;P84243;P68431;Q6NXT2;K7EMV3;A0A590UJJ6;B4DEB1;K7ES00;K7EP01;P0DPK2;P0DPK5;Q5TEC6;A0A590UJL8 K7EK07;Q5TEC6 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A;H3F3C;HIST2H3PS2 Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3C 0 ; 99.511 0.062077 6346300000 9734700 10689000 7857300 13735500 8188900 7554200 11213500 8501300 11888600 9084500 FALSE TRUE 9354257.162 10384160.19 9277288.895 14444390.8 8452303.405 7706951.1 11350734.17 8325745.184 10539055.97 8469198.723 1.104503208 1.22610893 1.095415186 1.705520354 0.998005087 0.909997669 1.34023708 0.983061734 1.244398238 1 23.01379405 KLPVNGFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLPVNGFR 8 1 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 86.833 0.025259 478660000 260270 373690 236550 249970 343350 212410 348660 317620 317770 343830 FALSE TRUE 250098.3607 363032.7271 279299.847 262870.9817 354394.1646 216705.0757 352927.0054 311061.036 281698.0818 320542.0878 0.780235639 1.13255869 0.871335957 0.820082578 1.105608836 0.676058103 1.101031717 0.970421819 0.878817767 1 18.29015427 KLS(ph)PPPLPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 KLSPPPLPPR 10 1 F5GWN5;O00750 F5GWN5 PIK3C2B Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta 1 KLS(1)PPPLPPR 69.602 0.0346 413290000 353620 378400 352740 344190 366900 285440 372830 371140 365260 375570 TRUE FALSE 339800.1395 367608.4025 416487.9647 361953.6871 378701.6717 291211.7924 377392.8051 363475.8293 323797.2161 350132.3094 0.97049067 1.049912826 1.189515944 1.033762602 1.081595904 0.83171928 1.077857698 1.038109936 0.92478531 1 18.41754067 KLVIIESDLER ddPTM_BT-474_Pertuzumab_2h_R1 4 KLVIIESDLER 11 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;;; 160.69 4.36E-05 2909940000 3774500 4214720 3468740 3676200 3955050 3400880 4046390 4042400 4162100 4206400 FALSE TRUE 3626988.367 4094520.312 4095618.48 3865929.123 4082267.775 3469648.124 4095910.931 3958923.027 3689635.857 3921496.781 0.924898978 1.044121809 1.044401847 0.985829987 1.040997355 0.884776481 1.044476423 1.009543868 0.940874381 1 21.90297299 KMENCLGESR ddPTM_BT-474_Pertuzumab_2h_R1 4 KMENCLGESR 10 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 145.09 4.98E-05 1763950000 2829220 3005950 2261930 2618180 2599530 2410390 2948710 2904180 2880460 3024390 FALSE TRUE 2718650.955 2920223.249 2670711.067 2753304.584 2683146.243 2459129.737 2984797.195 2844207.668 2553482.257 2819545.371 0.964216069 1.035707132 0.947213368 0.976506571 0.951623716 0.87217243 1.058609386 1.008746905 0.905636165 1 21.42703113 KNGFVVLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KNGFVVLK 8 1 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 129.47 0.003537 0 1507200 1471100 1318900 1392300 1304600 1102900 1631000 1625500 1671000 1752100 FALSE TRUE 1448296.958 1429145.668 1557254.569 1464156.77 1346563.644 1125201.394 1650960.666 1591932.857 1481315.085 1633428.706 0.886660649 0.874936055 0.953365496 0.896370172 0.824378584 0.688858589 1.010733226 0.974595861 0.906874649 1 20.63947206 KNS(ph)FGYR ddPTM_BT-474_Pertuzumab_2h_R1 2 KNSFGYR 7 1 Q92615;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 KNS(1)FGYR;KNS(1)FGYR 116.77 0.0032966 1934650000 3347200 3204200 2435210 2594400 2786000 2450380 2779500 3876500 3274700 2807300 TRUE FALSE 3216387.723 3112819.353 2875306.618 2728297.295 2875614.22 2499928.362 2813516.352 3796448.92 2902969.785 2617159.071 1.228961495 1.189388673 1.098636552 1.042465216 1.098754085 0.955206885 1.075026881 1.450599225 1.109206474 1 21.31957018 KPALGFYDT(ph)SEENYQALDADFR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPALGFYDTSEENYQALDADFR 22 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 1 KPALGFYDT(0.976)S(0.024)EENYQALDADFR 117.54 7.49E-05 80681000 31999 34947 53622 22656 40218 70743 25638 32227 27286 25630 TRUE FALSE 30748.4437 33950.34578 63312.68821 23825.27888 41511.6485 72173.47193 25951.76551 31561.50119 24188.60767 23894.05727 1.28686574 1.420869859 2.649725306 0.997121527 1.737321043 3.020561603 1.086117992 1.320893343 1.01232735 1 14.54436423 KPETEAAR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPETEAAR 8 1 P61964;V9GYQ5;V9GZ59 P61964 WDR5 WD repeat-containing protein 5 0 72.643 0.073154 173320000 171390 153020 161130 140790 169360 95866 169250 162330 154320 204200 FALSE TRUE 164691.8893 148656.0194 190249.7753 148056.1888 174807.6182 97804.4762 171321.3321 158977.8288 136802.2406 190369.3521 0.865117665 0.7808821 0.999371869 0.777731222 0.918255046 0.51376167 0.899941772 0.835102011 0.718614835 1 17.53844171 KPHDCESSTVS(ph)EEDYFSSHRDELQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPHDCESSTVSEEDYFSSHRDELQSR 26 2 A0A087WXK8;Q9H4H8-2;Q9H4H8 A0A087WXK8 FAM83D Protein FAM83D 1 KPHDCESST(0.002)VS(0.998)EEDYFSSHRDELQSR 128.71 4.05E-05 660220000 55789 59227 47378 54933 52207 69651 67595 45809 61940 72209 TRUE FALSE 53608.7042 57537.90395 55940.25852 57768.09871 53886.28557 71059.39094 68422.24783 44863.02814 54908.83087 67318.22011 0.796347618 0.85471517 0.830982436 0.858134672 0.800471039 1.055574417 1.016400132 0.666432179 0.815660764 1 16.03870941 KPS(ph)FSK ddPTM_BT-474_Pertuzumab_2h_R1 2 KPSFSK 6 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 KPS(1)FSK;KPS(0.999)FS(0.001)K 82.287 0.036531 1873580000 4006000 3050000 2157300 2432600 3001800 2457100 2833400 4391100 3495900 2867200 TRUE FALSE 3849441.091 2963016.986 2547172.099 2558146.778 3098355.623 2506784.245 2868075.997 4300422.251 3099060.088 2673001.99 1.440119052 1.10849786 0.952925628 0.957031378 1.159129561 0.937816079 1.072979372 1.608836157 1.159393109 1 21.35002948 KPSPQPSS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 5 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 1 KPSPQPS(0.006)S(0.994)PR;KPSPQPS(0.019)S(0.981)PR;KPSPQPS(0.003)S(0.997)PR;KPSPQPS(0.025)S(0.975)PR;KPSPQPS(0.028)S(0.972)PR 125.03 0.00025714 9689010000 7437290 7719000 5998880 7566640 7081230 7242850 7607390 7865530 7789680 7778550 TRUE FALSE 7146632.484 7498861.678 7083011.06 7957155.197 7309004.194 7389305.389 7700491.514 7703104.057 6905428.183 7251701.88 0.985511071 1.034083006 0.976737761 1.09728107 1.007901913 1.01897534 1.061887491 1.062247757 0.95224932 1 22.78988819 KPYSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 KPYSSR 6 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YIS3;H0YIM2;A0A0U1RQZ1 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 83.377 0.091487 244290000 283700 348180 256360 308480 321610 245380 332890 315580 321160 359950 FALSE TRUE 272612.6904 338250.2473 302689.9547 324400.6898 331954.8777 250341.7517 336964.0074 309063.1627 284703.2632 335570.2659 0.812386311 1.007986349 0.902016613 0.966714643 0.989226137 0.746018873 1.004153352 0.921008785 0.84841624 1 18.35625536 KQDIENILHWNVTQHK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQDIENILHWNVTQHK 16 1 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 97.579 0.0012305 143510000 219680 213180 173120 190300 213840 219760 212940 101000 264560 224900 FALSE TRUE 211094.6627 207100.3151 204406.635 200121.4058 220718.3578 224203.6978 215546.0234 98914.3147 234528.2579 209667.3227 1.006807642 0.987756759 0.974909358 0.954471127 1.052707475 1.069330666 1.028038231 0.47176791 1.118573247 1 17.6777425 KQEAEWK ddPTM_BT-474_Pertuzumab_2h_R1 3 KQEAEWK 7 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496;P09496-5;C9J8P9 P09496-2 CLTA Clathrin light chain A 0 ;; 109.71 0.01117 3868880000 4951600 4984900 4000710 3716520 4194680 3243050 4840700 4744700 5676300 5467100 FALSE TRUE 4758085.998 4842735.533 4723727.292 3908330.043 4329605.692 3308626.693 4899941.935 4646720.287 5031950.221 5096808.447 0.933542244 0.950150586 0.926801025 0.766819095 0.849473889 0.649156571 0.961374551 0.911692157 0.987274737 1 22.2811627 KQELLR ddPTM_BT-474_Pertuzumab_2h_R1 2 KQELLR 6 1 O94804;H0YB71 O94804 STK10 Serine/threonine-protein kinase 10 0 ; 83.843 0.090636 1235540000 1775920 1898830 1490790 1797020 1883270 1731620 1828730 1964390 1999380 2170710 FALSE TRUE 1706515.083 1844677.228 1760208.915 1889764.418 1943847.09 1766634.543 1851110.545 1923824.66 1772418.764 2023685.878 0.843270738 0.911543262 0.869803429 0.933823 0.960547835 0.872978639 0.914722272 0.950653795 0.875836899 1 20.94855394 KQLADETLLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KQLADETLLK 10 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 77.062 0.041874 0 367090 358920 267160 346000 315880 280250 372130 382340 411520 385510 FALSE TRUE 352743.717 348683.953 315441.7549 363857.1015 326040.5671 285916.847 376684.2383 374444.5454 364805.9748 359399.0643 0.981482013 0.970186035 0.877692199 1.012404142 0.907182571 0.795541434 1.048094655 1.041862883 1.015044309 1 18.45522713 KQQNVDR ddPTM_BT-474_Pertuzumab_2h_R1 5 KQQNVDR 7 1 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;; 198.07 0.00065403 3509050000 3367410 4462000 2976360 6534980 2783970 3026470 6089420 4077420 3413450 3920840 FALSE TRUE 3235807.894 4334748.129 3514254.461 6872251.101 2873518.923 3087667.297 6163944.144 3993219.852 3025969.466 3655278.014 0.885242622 1.185887397 0.961419199 1.880089852 0.786128692 0.844714762 1.686313358 1.092453115 0.827835654 1 21.80154971 KRDS(ph)SLR ddPTM_BT-474_Pertuzumab_2h_R1 3 KRDSSLR 7 2 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 KRDS(0.675)S(0.325)LR;KRDS(0.63)S(0.37)LR;KRDS(0.65)S(0.35)LR 84.17 0.017123 494350000 579470 543360 396570 436770 478870 539210 477230 554640 561140 569940 TRUE FALSE 556823.6718 527863.9048 468239.0207 459311.752 494273.2884 550113.1956 483070.4835 543186.4902 497441.7397 531337.4562 1.047966157 0.993462627 0.881246024 0.86444452 0.930243638 1.035336751 0.909159477 1.022300393 0.9362068 1 19.01926889 KREDS(ph)APPSSVAR ddPTM_BT-474_Pertuzumab_2h_R1 2 KREDSAPPSSVAR 13 2 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 1 KREDS(1)APPSSVAR;KREDS(1)APPSSVAR 128.45 0.00013006 150299000 196071 134867 103755 112415 133289 119723 118461 227295 122142 92115 TRUE FALSE 188408.3286 131020.7252 122505.8365 118216.7516 137576.3617 122143.8811 119910.7612 222601.2788 108276.9522 85875.969 2.193958691 1.525697197 1.426543863 1.37659875 1.602035626 1.422329 1.396324985 2.59212538 1.260852756 1 16.38996685 KS(ph)ASPEVSEGHENQHGQESEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSASPEVSEGHENQHGQESEAK 22 1 O60930 O60930 RNASEH1 Ribonuclease H1 1 KS(0.627)AS(0.37)PEVS(0.003)EGHENQHGQESEAK 224.91 2.46E-26 320850000 328870 332610 282890 275400 298060 328730 317550 19081 415290 318960 TRUE FALSE 316017.3968 323124.2885 334014.5159 289613.427 307647.3706 335377.1458 321436.2719 18686.97068 368148.0202 297356.5551 1.062755777 1.086656013 1.123279478 0.973960123 1.034607663 1.127861956 1.08097927 0.062843648 1.238069294 1 18.18183435 KS(ph)PGSTSR ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPGSTSR 8 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KS(0.906)PGS(0.064)T(0.029)S(0.002)R;KS(0.989)PGS(0.003)T(0.003)S(0.004)R 76.927 0.021153 186088000 96779 94671 79475 83464 91704 89275 104040 96169 92305 114578 TRUE FALSE 92996.76969 91971.07577 93837.90041 87771.58704 94653.74244 91080.20167 105313.2726 94183.07654 81826.92337 106817.53 0.870613369 0.86101107 0.878487833 0.821696467 0.886125549 0.852670921 0.985917505 0.881719288 0.766043957 1 16.7047889 KSEQEFSFDTPADR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSEQEFSFDTPADR 14 1 F8VXG7;Q99590-2;Q99590 F8VXG7 SCAF11 Protein SCAF11 0 147.24 1.30E-05 329490000 377190 385500 322050 378710 352900 385740 351150 373480 452680 387420 FALSE TRUE 362448.9978 374505.9174 380251.599 398255.2685 364251.349 393539.9271 355447.4787 365767.5075 401293.6642 361179.6983 1.003514316 1.036896368 1.052804465 1.102651313 1.008504494 1.089595924 0.984129176 1.01270229 1.111063734 1 18.46235728 KSHHANS(ph)PTAGAAK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSHHANSPTAGAAK 14 1 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 KS(0.035)HHANS(0.954)PT(0.011)AGAAK 125.61 4.24E-05 56675000 93487 122640 95453 99534 101710 121090 124550 24704 132770 137760 TRUE FALSE 89833.42468 119142.4273 112703.4804 104670.9617 104981.5945 123538.5228 126074.2802 24193.85377 117698.5062 128429.3925 0.699477144 0.927688164 0.877552079 0.815007839 0.817426545 0.961917832 0.981662201 0.188382529 0.916445246 1 16.97061589 KSLDQDPVVR ddPTM_BT-474_Pertuzumab_2h_R1 1 KSLDQDPVVR 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 92.925 0.014648 546780000 1074000 1131100 837450 937750 939540 1207800 993620 1078200 1167700 1156200 FALSE TRUE 1032026.893 1098842.135 988795.844 986147.3899 969761.1574 1232222.544 1005780.219 1055934.793 1035147.591 1077889.544 0.957451437 1.019438533 0.917344314 0.91488724 0.899685095 1.143180718 0.933101378 0.979631725 0.96034663 1 20.03977792 KSNFAEALAAHK ddPTM_BT-474_Pertuzumab_2h_R1 1 KSNFAEALAAHK 12 1 P07237;H7BZ94;I3L312;I3L3U6;I3L0S0;I3NI03;I3L514;I3L3P5;I3L1Y5 P07237 P4HB Protein disulfide-isomerase 0 89.231 0.0061927 2415400000 3568000 4318100 3317000 2803200 3263100 1753900 4326000 3789800 4430600 4751400 FALSE TRUE 3428558.615 4194952.016 3916455.686 2947873.488 3368060.575 1789365.06 4378942.882 3711539.306 3927656.863 4429583.446 0.774013777 0.947030814 0.884158913 0.665496773 0.760356051 0.403957862 0.988567646 0.837898044 0.886687633 1 22.0787396 KSPSDLWK ddPTM_BT-474_Pertuzumab_2h_R1 2 KSPSDLWK 8 1 Q02880;Q02880-2;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2-alpha 0 ; 105.4 0.0070485 1081330000 2948200 3130100 2050520 2157720 2406300 1136370 3076200 2672600 2861000 3048300 FALSE TRUE 2832981.085 3040832.613 2421094.578 2269080.188 2483700.825 1159348.18 3113847.456 2617409.876 2536231.274 2841835.926 0.996884112 1.070023989 0.851947347 0.798455733 0.873977559 0.407957465 1.095716831 0.921027795 0.892462246 1 21.43839183 KSS(ph)LVTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 KSSLVTSK 8 1 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7 A6NMQ3 ENSA Alpha-endosulfine 1 KS(0.001)S(0.817)LVT(0.091)S(0.091)K;KS(0.164)S(0.82)LVT(0.015)S(0.001)K;KS(0.008)S(0.992)LVTSK;KS(0.001)S(0.999)LVTSK 151.13 0.00029286 8883700000 12960200 12714400 10693700 7449800 11287900 10116800 8672600 13724000 14518100 10542100 TRUE FALSE 12453701.06 12351797.76 12626289.47 7834285.071 11650985.55 10321368.63 8778737.873 13440594.6 12870066.15 9828074.177 1.267155786 1.256787193 1.284716542 0.797133287 1.185480018 1.050192382 0.89323073 1.367571547 1.309520657 1 23.22847732 KSSTPEEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;; 164.65 9.96E-05 23406200000 16040300 13900210 12306740 11298960 12097510 9869600 15384100 15748000 16173200 14973400 FALSE TRUE 15413427.34 13503789.62 14530841.68 11882100.68 12486637.4 10069170.07 15572375.22 15422798.3 14337286.14 13959238.28 1.104173955 0.967372958 1.040948037 0.851199789 0.894507074 0.721326613 1.115560527 1.104845263 1.02708227 1 23.73471688 KT(ph)STSPPPEK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.375)S(0.273)T(0.201)S(0.15)PPPEK 59.185 0.062259 384860000 1353300 1256300 1144100 1083500 1080500 831690 1418600 1543600 1418100 1538900 TRUE FALSE 1300411.54 1220471.554 1350864.32 1139419.565 1115255.264 848507.3416 1435961.251 1511724.121 1257123.233 1434668.932 0.906419252 0.850699089 0.941586097 0.794203833 0.777360713 0.591430763 1.000900778 1.053709387 0.876246223 1 20.45228642 KTES(ph)PIK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTESPIK 7 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KT(0.005)ES(0.995)PIK 56.359 0.074777 1072000000 1894700 1568200 1521100 1298300 1333700 874460 1739800 1746400 1833800 1999200 TRUE FALSE 1820653.029 1523476.471 1795996.607 1365305.419 1376599.672 892142.1803 1761092.193 1710336.23 1625634.712 1863792.403 0.976853981 0.817406739 0.963624813 0.732541573 0.738601396 0.47867036 0.944897184 0.917664557 0.872218767 1 20.82980975 KTPCGEGSK ddPTM_BT-474_Pertuzumab_2h_R1 5 KTPCGEGSK 9 1 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ;;;; 114.86 0.0025163 2852840000 3393490 3123910 2615020 2547800 2783940 2393490 3300700 3160160 3341210 3400100 FALSE TRUE 3260868.659 3034819.145 3087612.285 2679292.263 2873487.958 2441888.008 3341094.954 3094901.592 2961929.848 3169808.199 1.028727436 0.957414126 0.974069121 0.845253749 0.906517927 0.770358285 1.054036946 0.976368726 0.934419265 1 21.59596412 KTPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTPEKLDNTPASPPRSPAEPNDIPIAK 27 3 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 2 KT(0.007)PEKLDNT(0.093)PAS(0.902)PPRS(0.998)PAEPNDIPIAK;KTPEKLDNT(0.101)PAS(0.899)PPRS(1)PAEPNDIPIAK 168.09 1.06E-11 577190000 688580 582400 494600 457610 546550 599000 528910 645060 656750 544300 TRUE FALSE 661669.5323 565790.5222 583985.2223 481227.3069 564130.2771 611112.1904 535382.9588 631739.2856 582198.4933 507434.0762 1.303951712 1.11500301 1.150859293 0.948354337 1.111731166 1.204318391 1.055078845 1.244968194 1.147338188 1 18.95286088 KTSATVGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 KTSATVGPK 9 1 P16104 P16104 H2AFX Histone H2AX 0 ; 115.57 0.0023313 1728090000 3408100 3388100 2216760 2878300 2744500 3097800 3134900 3229400 3435600 3230300 FALSE TRUE 3274907.684 3291474.705 2617377.844 3026849.408 2832779.335 3160439.638 3173265.844 3162711.761 3045605.091 3011508.904 1.087464055 1.092965291 0.869125056 1.005093959 0.940651157 1.049453858 1.053712921 1.050208338 1.011321961 1 21.52205509 KTSEVDLAKPLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 KTSEVDLAKPLVK 13 2 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 96.734 0.0023069 127130000 1041400 630430 391490 480290 597770 463780 509520 1361600 690400 455640 FALSE TRUE 1000700.937 612450.7537 462240.9516 505077.8245 616997.8149 473157.9494 515755.6582 1333482.484 612028.6864 424779.097 2.355814926 1.441810009 1.08819138 1.189036438 1.452514541 1.113891792 1.214173819 3.139237532 1.440816393 1 18.69635325 KVESLWPIFR ddPTM_BT-474_Pertuzumab_2h_R1 2 KVESLWPIFR 10 1 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 ; 150.46 3.45E-05 1900190000 2099700 2207400 1907420 1931660 2047300 1986730 2154100 2139200 2301900 2287800 FALSE TRUE 2017641.403 2144447.113 2252133.224 2031353.204 2113153.264 2026903.042 2180462.52 2095024.772 2040597.962 2132845.268 0.945985831 1.005439609 1.055929025 0.952414708 0.990767261 0.950328217 1.022325695 0.982267586 0.95674918 1 21.02434788 KVTMINAIPVASLDPIKEWLNSCDLK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVTMINAIPVASLDPIKEWLNSCDLK 26 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 164.96 7.42E-12 382260000 901320 851240 689950 558410 784730 866280 737280 795740 975450 834250 FALSE TRUE 866095.4179 826963.4687 814639.3129 587229.607 809971.5531 883796.7751 746303.0532 779307.6909 864721.0054 777745.5044 1.11359746 1.063282866 1.047436865 0.755040825 1.041435211 1.136357292 0.959572314 1.002008609 1.111830284 1 19.56893863 KVTPIDS(ph)PPVWSPEGYMALQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 KVTPIDSPPVWSPEGYMALQSK 22 1 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 KVT(0.491)PIDS(0.509)PPVWSPEGYMALQSK 59.011 0.040561 84820000 95032 93360 61424 69328 82902 94214 70504 90004 88589 88971 TRUE FALSE 91318.04438 90697.46421 72524.68317 72906.02639 85568.61812 96119.07163 71366.84904 88145.38595 78532.74812 82944.91492 1.100948075 1.09346624 0.874371663 0.878969211 1.031631875 1.158830191 0.86041259 1.062697888 0.94680606 1 16.33986592 KYDAFLASESLIK ddPTM_BT-474_Pertuzumab_2h_R1 2 KYDAFLASESLIK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 196.58 2.26E-07 2541700000 8452400 7818600 6125400 6101400 7243300 5900100 7752600 8154200 8480900 8406400 FALSE TRUE 8122070.863 7595621.183 7232396.039 6416293.985 7476287.323 6019404.064 7847478.638 7985812.92 7518183.787 7837027.04 1.036371423 0.969196756 0.922849443 0.818715305 0.953969826 0.768072387 1.001333618 1.01898499 0.95931579 1 22.90187504 KYEDICPSTHNMDVPNIK ddPTM_BT-474_Pertuzumab_2h_R1 10 KYEDICPSTHNMDVPNIK 18 1 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ;;;;;;;;; 205.62 7.07E-16 12970310000 5534760 6116220 5134570 5635090 5616720 5942770 5994640 5927670 6469980 6945120 FALSE TRUE 5318455.46 5941791.394 6062501.017 5925917.67 5797386.9 6062936.881 6068004.198 5805261.543 5735534.995 6474720.836 0.821418497 0.917690746 0.936333963 0.9152391 0.895387932 0.93640128 0.937183911 0.896604146 0.885835102 1 22.62638656 LADAMAESPS(ph)RDVVGSGTDTALDVAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LADAMAESPSRDVVGSGTDTALDVAVK 27 1 Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 LADAMAES(0.426)PS(0.561)RDVVGS(0.002)GT(0.008)DT(0.004)ALDVAVK 72.639 0.011495 118800000 61438 52135 44701 52468 50764 50943 50028 62411 59772 56736 TRUE FALSE 59036.93504 50648.16085 52779.46507 55175.87977 52396.87016 51973.10236 50640.25763 61122.19104 52986.93314 52893.22018 1.116153163 0.957554875 0.997849344 1.043155996 0.990615999 0.982604239 0.957405457 1.155577044 1.001771739 1 15.69079519 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR ddPTM_BT-474_Pertuzumab_2h_R1 14 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR 35 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;;;;;;; 302.41 9.51E-91 32761214000 10685346 11152330 8234751 10769982 10416825 11531566 10862002 1029515.6 11636407 10491829 FALSE TRUE 10267750.87 10834276.47 9722953.687 11325822.06 10751891.64 11764742.17 10994934.43 1008255.743 10315490.86 9781208.077 1.049742607 1.107662406 0.994044254 1.157916484 1.099239639 1.202790297 1.124087571 0.103080901 1.054623394 1 23.22158123 LADILS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 LADILSPR 8 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR 126.71 0.0012667 1719362000 1943762 2418570 2037628 2162260 1940380 2131351 2015160 2295690 2479090 2286290 TRUE FALSE 1867797.632 2349594.752 2405872.706 2273854.498 2002794.085 2174448.378 2039822.131 2248283.199 2197674.096 2131437.542 0.876308874 1.102352148 1.128755903 1.066817325 0.939644745 1.020179262 0.957017079 1.054820118 1.031076001 1 21.02339535 LADVAAPPGGPPPPHSPYS(ph)GPPS(ph)RGSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 LADVAAPPGGPPPPHSPYSGPPSRGSPVR 29 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 LADVAAPPGGPPPPHS(0.037)PY(0.169)S(0.651)GPPS(0.864)RGS(0.278)PVR 78.546 0.0024339 784780000 262440 278520 213210 274480 247800 256210 253060 278030 235130 291730 TRUE FALSE 252183.5547 270576.8823 251741.7898 288645.9457 255770.712 261390.7417 256157.024 272288.5833 208439.0281 271970.8673 0.927244735 0.994874506 0.925620425 1.061312002 0.940434226 0.961098313 0.941854643 1.001168199 0.766402042 1 18.0530926 LAEAPSPAPTPSPTPVEDLGPQTSTSPGRLS(ph)PDFAEELR ddPTM_BT-474_Pertuzumab_2h_R1 2 LAEAPSPAPTPSPTPVEDLGPQTSTSPGRLSPDFAEELR 39 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LAEAPSPAPTPSPTPVEDLGPQT(0.018)S(0.018)T(0.018)S(0.065)PGRLS(0.881)PDFAEELR;LAEAPSPAPTPSPT(0.02)PVEDLGPQT(0.103)S(0.103)T(0.103)S(0.103)PGRLS(0.567)PDFAEELR 135.61 2.38E-09 95126000 67597 74086 54508 94617 61384 68731 93360 96801 71480 55545 TRUE FALSE 64955.23451 71973.13982 64358.80812 99500.19471 63358.47211 70120.78791 94502.56761 94802.02552 63365.89007 51782.88768 1.254376444 1.389902013 1.242858616 1.92148795 1.223540728 1.354130506 1.82497678 1.830759731 1.22368398 1 15.6601878 LAEQAER ddPTM_BT-474_Pertuzumab_2h_R1 10 LAEQAER 7 0 P27348;E9PG15;P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1;P31947-2;P31947;P61981;P62258;B4DJF2;I3L3T1;I3L0W5;Q04917;F8WEB6;A2IDB1 P27348;P31946-2;P63104;P31947-2;P61981;P62258;Q04917 YWHAQ;YWHAB;YWHAZ;SFN;YWHAG;YWHAE;YWHAH "14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein zeta/delta;14-3-3 protein sigma;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein epsilon;14-3-3 protein eta" 0 ;;;;;;;;; 211.87 0.00022076 55656720000 14641710 16199080 13484050 15824300 14475530 13754710 16358860 15987490 15593630 16165090 FALSE TRUE 14069495.79 15737098.1 15920917.79 16640994.02 14941148.57 14032839.66 16559064.62 15657342.74 13823506.5 15070214.06 0.93359628 1.044251796 1.056449346 1.104230767 0.991435723 0.931163924 1.098794255 1.038959545 0.917273401 1 23.84519657 LAGGDWFTSR ddPTM_BT-474_Pertuzumab_2h_R1 4 LAGGDWFTSR 10 0 P30153;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;; 205.12 4.06E-07 2163474000 658949 700571 555169 622486 687465 511639 746209 652991 714832 709779 FALSE TRUE 633196.5446 680591.401 655500.388 654612.5771 709577.9361 521984.6911 755341.329 639506.5077 633687.2682 661705.0361 0.956916617 1.028541969 0.990623242 0.98928154 1.072347794 0.788847995 1.141507602 0.966452532 0.957658222 1 19.33582873 LAGIINFQRPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAGIINFQRPK 11 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 135.55 0.00010736 353860000 279650 269780 224280 238520 231200 147560 301860 263450 294080 293920 FALSE TRUE 268720.9688 262086.1385 264812.3851 250830.0458 238636.758 150543.7643 305554.253 258009.6654 260697.2713 274012.5366 0.980688592 0.956474991 0.966424341 0.91539624 0.870897226 0.549404659 1.115110486 0.941598033 0.951406365 1 18.06388238 LAHGGQVNLDMEDHRDEDFVKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 LAHGGQVNLDMEDHRDEDFVKPK 23 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 281.58 1.76E-52 551630000 521150 463640 436100 375640 447550 520340 477310 289460 711170 569650 FALSE TRUE 500782.8818 450417.4412 514912.971 395026.8254 461945.8522 530861.6313 483151.4626 283482.5498 630440.9631 531067.0981 0.942974783 0.848136597 0.969581759 0.743835999 0.869844609 0.999613106 0.909774799 0.533797991 1.18712111 1 19.01853463 LAHHLVALYYQSEEQAEEELLDMAVLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LAHHLVALYYQSEEQAEEELLDMAVLK 27 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 231.54 1.74E-35 1230780000 264070 243583 234680 249470 253410 267470 320980 85644 324210 302080 FALSE TRUE 253749.8525 236636.2513 277091.8964 262345.1766 261561.1628 272878.4267 324908.2493 83875.42147 287407.04 281619.8525 0.901036806 0.840268359 0.983921744 0.931557822 0.928773879 0.968960193 1.153712163 0.297832062 1.020549643 1 18.10338951 LASLEELKR ddPTM_BT-474_Pertuzumab_2h_R1 2 LASLEELKR 9 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 193.38 5.40E-05 2024770000 2673400 2456500 2098100 2283400 2366000 2139300 2558200 2660700 2784100 2522300 FALSE TRUE 2568920.572 2386443.025 2477273.342 2401246.548 2442104.539 2182558.112 2589508.017 2605755.615 2468060.64 2351462.374 1.092477856 1.014876126 1.053503288 1.02117158 1.038547146 0.928170544 1.101233022 1.108142594 1.049585427 1 21.16512682 LASPS(ph)GSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_BT-474_Pertuzumab_2h_R1 1 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.286)PS(0.329)GS(0.329)T(0.047)S(0.008)S(0.001)GLEVVAPEGTSAPGGGPGTLDDSATICR 150.16 1.43E-13 1536300000 291490 354450 243010 342050 285740 295460 304040 284240 328450 414100 TRUE FALSE 280098.2485 344341.433 286927.3127 359703.2415 294931.0866 301434.4036 307760.9325 278370.3447 291165.733 386052.6382 0.72554419 0.891954617 0.743233654 0.931746622 0.763965992 0.780811666 0.797199402 0.721068365 0.75421252 1 18.55843805 LAVYIDR ddPTM_BT-474_Pertuzumab_2h_R1 8 LAVYIDR 7 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 143.02 0.0056997 5598031000 7663840 8229240 6964480 8423310 7129930 7625810 7573340 7800100 8186000 8223230 FALSE TRUE 7364328.66 7994550.132 8223116.46 8858038.039 7359270.674 7780009.103 7666024.8 7639025.209 7256759.599 7666263.308 0.960615148 1.042822274 1.072636841 1.155457057 0.959955376 1.014837189 0.999968889 0.996447018 0.946583662 1 22.87009212 LDAMFR ddPTM_BT-474_Pertuzumab_2h_R1 4 LDAMFR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EIV0;Q96L46;K7EMQ1 A0A0C4DGQ5 CAPNS1;CAPNS2 Calpain small subunit 1;Calpain small subunit 2 0 ;;; 148.37 0.025066 1681859000 1176696 1236574 1092446 1195521 1248311 843385 1382130 1319882 1289350 1405980 FALSE TRUE 1130709.419 1201308.12 1289875.294 1257221.982 1288464.057 860438.8225 1399044.92 1292625.975 1142988.393 1310751.722 0.862641948 0.916503179 0.984072934 0.959161038 0.982996272 0.656446837 1.067360734 0.986171487 0.872009835 1 20.32196301 LDHINFPVFEPS(ph)TPDPAPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDHINFPVFEPSTPDPAPAK 20 0 Q8ND04;Q8ND04-2;J3KTD7 Q8ND04 SMG8 Protein SMG8 1 LDHINFPVFEPS(0.579)T(0.421)PDPAPAK 122.73 1.93E-05 31929000 33733 35947 37913 37734 43003 36693 38559 35530 47911 49089 TRUE FALSE 32414.67707 34921.82676 44764.72247 39681.45626 44386.23055 37434.9576 39030.89658 34796.29308 42472.34414 45764.15831 0.708298334 0.763082466 0.978161166 0.867085897 0.969890678 0.817997293 0.852870413 0.760339409 0.928070038 1 15.48193053 LDHVNIVHYNGCWDGFDYDPETS(ph)DDSLESSDYDPENSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDHVNIVHYNGCWDGFDYDPETSDDSLESSDYDPENSK 38 0 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 LDHVNIVHYNGCWDGFDYDPET(0.035)S(0.915)DDS(0.05)LESSDYDPENSK 168.52 8.39E-18 53104000 52644 53308 49042 54543 54673 55302 55394 22940 80271 62091 TRUE FALSE 50586.61428 51787.70803 57904.98033 57357.97077 56431.6067 56420.24433 56071.92834 22466.28098 71158.9726 57885.52127 0.873907899 0.894657367 1.000336165 0.990886313 0.974882932 0.974686642 0.968669317 0.388115724 1.229305205 1 15.82091492 LDHVNIVHYNGCWDGFDYDPETSDDSLESSDYDPENSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LDHVNIVHYNGCWDGFDYDPETSDDSLESSDYDPENSK 38 0 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 149.55 1.38E-13 191130000 84795 83527 81592 83758 80257 87601 87916 32496 109910 98956 FALSE TRUE 81481.11765 81144.89174 96337.4894 88080.76042 82838.53929 89372.35224 88991.94231 31824.94624 97433.47758 92253.62198 0.88322947 0.879584888 1.044267828 0.954767504 0.89794349 0.96876795 0.964644427 0.344972323 1.056147992 1 16.49331793 LDPAQSAS(ph)RENLLEEQGSIALR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDPAQSASRENLLEEQGSIALR 22 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 LDPAQSAS(1)RENLLEEQGSIALR;LDPAQS(0.014)AS(0.986)RENLLEEQGSIALR;LDPAQS(0.002)AS(0.998)RENLLEEQGSIALR 292.87 1.18E-55 2837180000 142798 118911 113789 171201 115981 116564 122671 160089 124615 130972 TRUE FALSE 137217.2963 115519.7747 134353.2035 180036.7041 119711.6342 118921.0039 124172.2844 156783.1062 110469.2276 122101.1498 1.123800198 0.946098992 1.100343476 1.474488196 0.980430032 0.973954825 1.01696245 1.284042832 0.904735359 1 16.89771726 LDPNKYPVPENWLHK ddPTM_BT-474_Pertuzumab_2h_R1 2 LDPNKYPVPENWLHK 15 1 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 159.13 1.07E-06 2329400000 2882800 2736400 2482900 2980000 2826100 2901800 3057400 2948300 3225800 3572100 FALSE TRUE 2770136.989 2658360.551 2931615.262 3133798.157 2917004.073 2960476.384 3094817.376 2887416.575 2859620.708 3330158.485 0.83183338 0.79826848 0.880323046 0.941035741 0.875935511 0.888989637 0.929330358 0.867050799 0.858704089 1 21.66715941 LDSQEPGRQT(ph)PDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDSQEPGRQTPDR 13 1 Q8TB03-2;Q8TB03 Q8TB03-2 CXorf38 Uncharacterized protein CXorf38 1 LDS(0.001)QEPGRQT(0.999)PDR;LDS(0.001)QEPGRQT(0.999)PDR;LDSQEPGRQT(1)PDR 119.8 0.00051755 1655190000 1376720 1401570 1066830 1196390 1236840 1440080 1293160 1429410 1405950 1431600 TRUE FALSE 1322916.26 1361598.596 1259629.913 1258135.831 1276624.082 1469199.404 1308986.079 1399892.184 1246352.45 1334636.457 0.991218435 1.02020186 0.943800018 0.942680552 0.956533201 1.100823671 0.980781 1.048894009 0.933851645 1 20.34801539 LDWELEQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LDWELEQR 8 0 Q13769;F8WCP5;C9JXG5;H7C072 Q13769 THOC5 THO complex subunit 5 homolog 0 ;; 143.89 0.0013825 481400000 584410 626140 520990 608550 618820 467840 609510 574490 576220 657950 FALSE TRUE 561570.6111 608283.1003 615144.4824 639957.3384 638724.9073 477300.0453 616969.3657 562626.5807 510809.9213 613386.4605 0.915524954 0.991680025 1.002866092 1.043318331 1.041309107 0.778139193 1.005841187 0.917246495 0.832770128 1 19.2264368 LEAQHQALVTLWHQLHVDMK ddPTM_BT-474_Pertuzumab_2h_R1 2 LEAQHQALVTLWHQLHVDMK 20 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 274.8 5.96E-45 1053920000 1087950 1039280 956590 980340 1076040 1208690 1118480 320140 1423680 1102250 FALSE TRUE 1045431.711 1009640.752 1129467.092 1030935.465 1110651.804 1233130.54 1132168.293 313528.9971 1262069.815 1027593.626 1.017359085 0.982529209 1.099137893 1.003252102 1.080827845 1.200017701 1.101766559 0.305109909 1.228179879 1 19.97083842 LEDLCELQLLYQGMQEEQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LEDLCELQLLYQGMQEEQK 19 0 H0Y876;H7C4R2;Q96JN2-2;Q96JN2;Q96JN2-4 H0Y876 CCDC136 Coiled-coil domain-containing protein 136 0 58.159 0.046894 300850000 46494 78564 46746 108240 48144 84461 89293 78628 61219 59768 FALSE TRUE 44676.96308 76323.43164 55194.04206 113826.2794 49692.59548 86168.85929 90385.79444 77004.30432 54269.67577 55719.86012 0.801813985 1.369770697 0.990563184 2.042831391 0.89182915 1.546465822 1.62214683 1.381990266 0.973973654 1 15.76590402 LEECVR ddPTM_BT-474_Pertuzumab_2h_R1 4 LEECVR 6 0 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 ;;; 152.78 0.023762 2855000000 2010550 2098640 1769370 2017110 2044710 1960300 1972060 2185860 2253900 2341540 FALSE TRUE 1931975.483 2038788.842 2089134.518 2121213.289 2110479.954 1999938.609 1996194.66 2140721.227 1998046.721 2182945.41 0.885031515 0.933962358 0.957025544 0.971720721 0.966803817 0.916165196 0.914450105 0.980657243 0.915298528 1 21.05784462 LETLLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LETLLR 6 0 A0A1W2PR85;O95816-2;O95816;Q9UL42;O15056-3;O15056-2;O15056 A0A1W2PR85 BAG2;PNMA2;SYNJ2 BAG family molecular chaperone regulator 2;Paraneoplastic antigen Ma2;Synaptojanin-2 0 98.513 0.092707 13929000 40458 40737 37051 44794 38716 37183 42185 41028 43955 45947 FALSE TRUE 38876.85663 39575.22065 43746.9399 47105.82371 39961.3353 37934.86574 42701.27265 40180.75746 38965.41267 42834.96876 0.907596241 0.923899837 1.021290342 1.099704869 0.932913842 0.885605075 0.996878809 0.938036343 0.909663618 1 15.38650142 LEVGIQAMEHLIHVLQTDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LEVGIQAMEHLIHVLQTDR 19 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;; 203.71 4.93E-16 544305000 242819 280710 220585 272269 258420 329315.4 282635 46947.2 351322 230037 FALSE TRUE 233329.365 272704.4256 260449.6164 286320.8357 266732.314 335974.383 286093.9717 45977.72391 311441.3994 214456.3891 1.088003794 1.27160784 1.214464244 1.335100516 1.243760165 1.566632659 1.33404266 0.214391952 1.452236516 1 17.71032477 LFDVSEITSAAMVHSLPTAVPES(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFDVSEITSAAMVHSLPTAVPESPR 25 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;D6RJB0 A0A3B3ISF0 LARP1B La-related protein 1B 1 LFDVSEITSAAMVHSLPT(0.013)AVPES(0.987)PR 49.793 0.090979 10354000 10677 10512 8422.3 9795.7 12381 12621 9102.7 10729 9740.8 11031 TRUE FALSE 10259.73104 10212.20805 9944.396963 10301.25725 12779.24611 12876.20527 9214.101566 10507.4424 8635.065221 10283.86054 0.997653653 0.99303253 0.966990647 1.001691651 1.242650662 1.252078946 0.895976907 1.021741043 0.839671559 1 13.32809433 LFEVLEER ddPTM_BT-474_Pertuzumab_2h_R1 4 LFEVLEER 8 0 Q9NQ86-4;Q9NQ86;E9PBG3 Q9NQ86-4 TRIM36 E3 ubiquitin-protein ligase TRIM36 0 ;;; 109.21 0.0085176 92072000 161911 182149 151772 169449 175616 131162 175829 176016 170581 188813 FALSE TRUE 155583.3391 176954.2889 179200.5765 178194.2832 181264.8481 133814.1855 177980.8479 172381.2081 151217.36 176024.5273 0.883873069 1.005282 1.01804322 1.012326441 1.029770401 0.760201931 1.011113909 0.979302207 0.859069826 1 17.42541694 LFKDDIR ddPTM_BT-474_Pertuzumab_2h_R1 1 LFKDDIR 7 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 85.212 0.019131 882030000 2469100 2609400 1861500 2107800 2234700 2580600 2307000 2458600 2760600 2599800 FALSE TRUE 2372604.842 2534982.467 2197914.459 2216583.811 2306581.155 2632781.5 2335233.756 2407829.051 2447228.261 2423713.23 0.978913187 1.045908582 0.90683767 0.914540459 0.951672469 1.086259491 0.963494248 0.993446345 1.009702068 1 21.20878758 LFNIHED ddPTM_BT-474_Pertuzumab_2h_R1 1 LFNIHED 7 0 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 81.32 0.064023 158860000 240160 351280 257320 452150 222740 211720 327050 296590 290810 308680 FALSE TRUE 230774.2817 341261.8383 303823.4481 475485.5157 229904.6344 216001.1235 331052.5357 290465.3129 257798.468 287772.8287 0.801932145 1.185872342 1.055775312 1.652294686 0.798910152 0.750595963 1.150395391 1.009356284 0.895840199 1 18.13457085 LFQLGPPS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 3 LFQLGPPSPVK 11 0 Q9NZH5-2;Q9NZH5;O95997 Q9NZH5-2 PTTG2;PTTG1 Securin-2;Securin 1 LFQLGPPS(1)PVK;LFQLGPPS(1)PVK;LFQLGPPS(1)PVK 151.99 3.48E-05 2312849000 1519840 1463090 1418020 1634330 1489300 1225080 1752400 1845050 1618980 1699370 TRUE FALSE 1460442.973 1421364.106 1674287.758 1718677.967 1537204.687 1249851.957 1773846.395 1806949.073 1435200.178 1584270.156 0.921839603 0.897172809 1.056819603 1.084838946 0.970292018 0.788913401 1.11966156 1.140556152 0.905906213 1 20.59538694 LFQLMVEHTPDEESIDWTK ddPTM_BT-474_Pertuzumab_2h_R1 2 LFQLMVEHTPDEESIDWTK 19 0 Q12907;D6RBV2;D6RDX1 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ; 218.31 3.40E-19 482740000 505490 683100 490550 618240 505450 378730 709660 619410 780660 670650 FALSE TRUE 485734.892 663618.6568 579203.2972 650147.4405 521708.2583 386388.1801 718345.0314 606618.967 692042.7496 625226.2781 0.776894556 1.061405574 0.926389881 1.039859429 0.834431112 0.617997345 1.148936084 0.970239077 1.106867663 1 19.25401889 LFSLELVDESGEIR ddPTM_BT-474_Pertuzumab_2h_R1 4 LFSLELVDESGEIR 14 0 P27694 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 ;;; 257.09 5.74E-24 150589900 217395 231042 203829 244306 262366 240389 229886 251426 235255 240399 FALSE TRUE 208898.9631 224452.9084 240665.4345 256914.6619 270805.2407 245249.8303 232699.4136 246233.9652 208549.8387 224116.5616 0.932099625 1.001500767 1.073840473 1.146343939 1.208323199 1.094295881 1.038296376 1.098687056 0.930541845 1 17.77388974 LFYHIVDSDEVSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 LFYHIVDSDEVSTK 14 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 194.7 1.14E-07 364910000 289840 280410 229260 268020 269980 254860 262170 269740 327950 303740 FALSE TRUE 278512.7324 272412.9814 270692.3819 281852.5443 278664.1519 260013.4438 265378.5149 264169.7747 290722.4909 283167.4193 0.983562068 0.962020921 0.955944658 0.995356546 0.984096803 0.918232205 0.937178845 0.932910204 1.026680582 1 18.11129576 LGEVSVESENYVQAVEEFQSCLNLQEQYLEAHDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGEVSVESENYVQAVEEFQSCLNLQEQYLEAHDR 34 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;E9PI86 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 264.19 4.23E-60 38346000 32947 33785 27107 35407 32085 34566 34155 32675 39270 35956 FALSE TRUE 31659.39482 32821.48488 32005.83789 37234.35951 33117.04316 35264.9482 34572.99911 32000.24983 34812.23423 33520.66809 0.944473861 0.979141728 0.954809069 1.110788109 0.987958923 1.052035959 1.031393498 0.954642364 1.038530441 1 15.03276328 LGGAGMER ddPTM_BT-474_Pertuzumab_2h_R1 2 LGGAGMER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 77.674 0.075846 880960000 1678190 1607340 2081600 919450 1230800 1019070 1239410 5047800 1005200 1433040 FALSE TRUE 1612604.479 1561500.237 2457791.425 966902.9247 1270389.8 1039676.294 1254578.27 4943561.166 891093.9101 1335978.924 1.207058323 1.168806041 1.839693262 0.723741151 0.950905569 0.778213095 0.939070406 3.700328707 0.666996982 1 20.34946582 LGLVEFNILWNR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGLVEFNILWNR 12 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 195.27 1.08E-06 321210000 295600 347670 319160 332100 344480 245540 354500 345240 319000 376220 FALSE TRUE 284047.6252 337754.792 376839.3117 349239.7208 355560.512 250504.987 358838.477 338110.6734 282788.4574 350738.2843 0.809856346 0.962982392 1.074417389 0.995727403 1.013748792 0.714221966 1.023094692 0.963997056 0.806266296 1 18.42003539 LGMENDDTAVQYAIGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LGMENDDTAVQYAIGR 16 0 Q05048;A0A0A0MSZ9;A3KFI9 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 ; 194.85 3.41E-10 161167000 150275 145189 108875 131322 133353 134911 134402 147238 153304 150776 FALSE TRUE 144402.0869 141048.3519 128551.1344 138099.5442 137642.4204 137638.9929 136046.8519 144197.4838 135901.5726 140563.8072 1.027306315 1.003447151 0.914539361 0.982468723 0.97921665 0.979192266 0.967865445 1.025850727 0.966831899 1 17.10086565 LGNPTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGNPTDR 7 0 O95292;E5RK64;O95292-2 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 84.916 0.049308 265690000 243540 311230 233070 373720 235760 205820 291640 334370 292490 258860 FALSE TRUE 234022.1876 302354.0251 275190.9336 393007.734 243343.4345 209981.8214 295209.1776 327465.1427 259287.7614 241327.1816 0.969729916 1.252880107 1.140322991 1.628526598 1.008354852 0.8701126 1.22327363 1.356934351 1.074424189 1 17.8806309 LGPGRPLPTFPTSECTS(ph)DVEPDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPTFPT(0.002)S(0.005)ECT(0.152)S(0.841)DVEPDTR 171.99 3.63E-12 546210000 205670 167310 157450 205100 170930 184230 143600 200710 173110 209470 TRUE FALSE 197632.189 162538.4826 185904.7175 215685.2356 176428.1187 187955.2568 145357.4198 196565.2684 153459.2785 195282.4103 1.012032721 0.832325258 0.951978814 1.104478561 0.903451153 0.962479194 0.744344662 1.006569245 0.785832571 1 17.57520248 LGS(ph)PSGK ddPTM_BT-474_Pertuzumab_2h_R1 8 LGSPSGK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LGS(0.992)PS(0.008)GK;LGS(0.967)PS(0.033)GK;LGS(0.998)PS(0.002)GK;LGS(0.997)PS(0.003)GK;LGS(0.998)PS(0.002)GK;LGS(0.991)PS(0.009)GK;LGS(0.982)PS(0.018)GK;LGS(0.94)PS(0.06)GK 168.74 0.0010887 11360790000 39095400 32765100 29699600 28287000 27601300 30153900 31730500 34820100 34727900 33859800 TRUE FALSE 37567508.55 31830671.43 35066978.38 29746895.46 28489120.88 30763632.52 32118827.35 34101052.77 30785734.38 31566445.59 1.190108923 1.008370465 1.110894107 0.942358093 0.90251279 0.974567518 1.017499017 1.080294348 0.975267687 1 24.91188849 LGS(ph)VSLDLCDGDTGEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 LGSVSLDLCDGDTGEPR 17 0 Q8N6R0-3;Q8N6R0-4;Q8N6R0;Q8N6R0-2 Q8N6R0-3 METTL13 Methyltransferase-like protein 13 1 LGS(0.998)VS(0.002)LDLCDGDTGEPR 126.77 4.46E-05 34826000 50280 40233 36372 38994 47063 43262 42225 69357 44425 47204 TRUE FALSE 48315.00201 39085.59423 42945.22949 41006.48501 48576.82414 44136.78728 42741.76218 67924.75371 39382.06024 44006.83104 1.097897778 0.888171071 0.975876437 0.931820903 1.103847357 1.002953093 0.971252898 1.543504772 0.894907889 1 15.42543987 LHDEKEETAGSYDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHDEKEETAGSYDSR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610;A0A2R8YEF8 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 252.82 7.10E-25 2234400000 1950010 1828920 1704500 1703320 1786740 1978860 1984740 1265800 2474200 2310100 FALSE TRUE 1873801.453 1776760.992 2012541.066 1791228.549 1844212.115 2018873.905 2009029.842 1239660.788 2193339.189 2153634.869 0.870064596 0.825005676 0.934485736 0.831723416 0.856325341 0.937426271 0.932855365 0.57561326 1.018435957 1 21.03834224 LHDNPLTDENKEHEADTANMSDK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHDNPLTDENKEHEADTANMSDK 23 1 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 85.062 0.0046614 578090000 437660 376120 322330 273040 372560 385330 385890 98770 585800 407320 FALSE TRUE 420555.7633 365393.4259 380582.2012 287131.6271 384543.7308 393121.6366 390612.6373 96730.36498 519302.4399 379731.8536 1.107507204 0.962240651 1.002239337 0.756143116 1.012671776 1.035261153 1.028653861 0.254733344 1.367550378 1 18.5346215 LHDTFGFVDEDVFFQLSAVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHDTFGFVDEDVFFQLSAVK 20 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 60.564 0.057483 11221000 10583 13129 10211 12428 10310 14481 12784 7026.1 14778 11560 FALSE TRUE 10169.40466 12754.57377 12056.35484 13069.41057 10641.63051 14773.81574 12940.45442 6881.00858 13100.46339 10777.0309 0.9436184 1.183496075 1.118708386 1.212709761 0.987436207 1.370861406 1.200743928 0.638488341 1.21559115 1 13.39567215 LHEEGIIYR ddPTM_BT-474_Pertuzumab_2h_R1 4 LHEEGIIYR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;; 200.54 2.29E-05 1826480000 999910 1068560 954060 1066970 1033880 1127040 1095650 639670 1188080 1200350 FALSE TRUE 960832.4117 1038085.715 1126479.865 1122036.45 1067135.689 1149829.521 1109058.892 626460.591 1053214.139 1119049.225 0.858614965 0.927649733 1.006640137 1.002669431 0.953609247 1.027505757 0.991072481 0.559815044 0.941168731 1 20.09384207 LHGGFDS(ph)DCSEDGEALNGEPELDLTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHGGFDSDCSEDGEALNGEPELDLTSK 27 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 LHGGFDS(0.783)DCS(0.217)EDGEALNGEPELDLTSK 156.4 1.33E-08 66361000 33337 32215 24283 35788 30267 40182 37352 19125 39057 39175 TRUE FALSE 32034.15318 31296.25974 28671.47827 37635.02297 31240.56554 40994.50757 37809.12495 18730.06207 34623.4131 36521.64236 0.877127947 0.856923668 0.785054461 1.030485502 0.855398704 1.122471634 1.035252593 0.512848296 0.948024537 1 15.15646402 LHGLDEEAEQK ddPTM_BT-474_Pertuzumab_2h_R1 3 LHGLDEEAEQK 11 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ;; 240.1 1.14E-15 2487460000 3485370 3104820 2914090 2777730 3085100 3227890 3254600 1913710 4192030 3682000 FALSE TRUE 3349157.887 3016273.574 3440730.887 2921088.978 3184335.043 3293160.147 3294430.768 1874191.22 3716168.329 3432614.86 0.975687056 0.878710166 1.002364386 0.850980695 0.927670354 0.959373621 0.959743782 0.545995195 1.082605675 1 21.71087657 LHGVNINVEASK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHGVNINVEASK 12 0 Q9BWF3;E9PB51;Q9BQ04;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2;E9PLB0;E9PM61;U3KQD5 Q9BWF3 RBM4;RBM4B RNA-binding protein 4;RNA-binding protein 4B 0 65.043 0.061815 278870000 563310 524480 458150 479050 502090 485790 532360 265040 600720 504830 FALSE TRUE 541295.2224 509522.3439 540947.8965 503773.8279 518240.1808 495613.0066 538875.1809 259566.8314 532528.784 470637.4144 1.150132152 1.082621841 1.149394162 1.070407521 1.101145308 1.053067588 1.144990101 0.55152188 1.131505417 1 18.84425649 LHHCPGNHS(ph)WDSTISGSQR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHHCPGNHSWDSTISGSQR 19 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 LHHCPGNHS(1)WDSTISGSQR;LHHCPGNHS(1)WDSTISGSQR 142.54 2.58E-07 265059000 100341 125277 69790 97903 115401 107766 111885 81392 130345 118048 TRUE FALSE 96419.56279 121704.2226 82402.60547 102955.7856 119112.978 109945.1024 113254.2821 79711.22676 115548.7821 110052.5038 0.8761233 1.105874182 0.748757208 0.935515159 1.082328651 0.999024089 1.029093189 0.724301801 1.049942328 1 16.74783244 LHLPIGDSASNLLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHLPIGDSASNLLFK 15 0 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 ; 196.58 8.86E-09 413820000 1037700 1084290 898440 1043520 1061570 1070200 1133860 715340 1334220 1218090 FALSE TRUE 997145.5368 1053367.111 1060808.094 1097376.192 1095716.363 1091840.177 1147736.518 700567.979 1182764.939 1135587.679 0.878087668 0.92759646 0.934148999 0.966350914 0.964889267 0.961475892 1.010698283 0.616921081 1.041544357 1 20.11500767 LHLQGQTMQDPFGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHLQGQTMQDPFGEK 15 0 Q9H832-2;Q9H832 Q9H832-2 UBE2Z Ubiquitin-conjugating enzyme E2 Z 0 ; 167.71 1.30E-06 1152070000 1981320 1832760 1877700 1917570 1944800 1986980 2184600 1210590 2646700 2492300 FALSE TRUE 1903887.824 1780491.479 2217042.159 2016536.018 2007356.258 2027158.097 2211335.788 1185590.893 2346257.712 2323494.301 0.819407142 0.766299052 0.954184462 0.867889375 0.863938533 0.872460972 0.951728518 0.510262019 1.009797059 1 21.14786468 LHNAIEGGTQLSR ddPTM_BT-474_Pertuzumab_2h_R1 2 LHNAIEGGTQLSR 13 0 O60832;O60832-2;C9IYT0;H7C0M1;H7BZF2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 164.2 3.74E-05 585220000 512630 539870 469540 525660 498830 530050 549570 444820 597560 600920 FALSE TRUE 492595.8529 524473.4362 554396.3229 552789.3756 514875.32 540767.9742 556295.8021 435634.3116 529727.494 560219.1532 0.879291345 0.936193333 0.989606156 0.98673773 0.919060545 0.96527934 0.992996757 0.777614098 0.945571909 1 19.09563178 LHNQVNGTEWSWK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHNQVNGTEWSWK 13 0 O14980 O14980 XPO1 Exportin-1 0 226.59 1.05E-11 1056100000 1627200 1763100 1493400 1664500 1841200 1888400 1840700 1174300 2141500 1977900 FALSE TRUE 1563607.225 1712818.114 1763290.601 1750405.044 1900423.87 1926584.742 1863227.037 1150050.295 1898405.898 1843935.071 0.847973038 0.928892856 0.956265016 0.949276941 1.030634918 1.044822441 1.010462389 0.623693487 1.029540534 1 20.81435643 LHNTIVEINNHK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHNTIVEINNHK 12 0 Q9NTJ3;E9PD53;Q9NTJ3-2 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 149.23 3.88E-05 324770000 193740 229280 203700 261990 224250 239070 237840 136150 251430 274830 FALSE TRUE 186168.4266 222741.1589 240513.1213 275511.3353 231463.2049 243904.1592 240750.7571 133338.4549 222888.7205 256215.5193 0.726608705 0.86935077 0.938714103 1.075310879 0.903392603 0.951949202 0.939641587 0.520415216 0.869926697 1 17.96699834 LHQLAMQQSHFPMTHGNTGFSGIESS(ph)SPEVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHQLAMQQSHFPMTHGNTGFSGIESSSPEVK 31 0 F8VZX2;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 1 LHQLAMQQSHFPMTHGNTGFSGIES(0.015)S(0.674)S(0.311)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.048)S(0.568)S(0.384)PEVK 219.07 1.17E-34 5204900000 2451100 2489320 2184690 2119300 2549500 2761200 2596800 281050 3263400 2736400 TRUE FALSE 2355308.302 2418327.031 2579512.081 2228677.327 2631506.983 2817033.356 2628580.415 275246.2193 2892952.513 2551061.191 0.923266094 0.947969041 1.011152571 0.873627546 1.031534246 1.104259422 1.03038705 0.107894793 1.134019256 1 21.28266607 LHQLAMQQSHFPMTHGNTGFSGIESSS(ph)PEVK ddPTM_BT-474_Pertuzumab_2h_R1 3 LHQLAMQQSHFPMTHGNTGFSGIESSSPEVK 31 0 F8VZX2;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 1 LHQLAMQQSHFPMTHGNTGFSGIESS(0.024)S(0.976)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.101)S(0.13)S(0.769)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.174)S(0.237)S(0.589)PEVK 192.75 1.01E-18 4963450000 1126768 1056743 891286 1024669 1028698 1160219 1145788 98708.3 1481654 1238416 TRUE FALSE 1082732.661 1026605.724 1052361.207 1077552.29 1061787.005 1183679.423 1159810.496 96669.93911 1313462.85 1154536.981 0.937806825 0.889192586 0.911500648 0.933319857 0.919664786 1.02524167 1.004567645 0.083730483 1.137653337 1 20.13888295 LHSELK ddPTM_BT-474_Pertuzumab_2h_R1 2 LHSELK 6 0 D6RBP0;A0A494C0G8;Q96NL6-2;Q96NL6 D6RBP0 SCLT1 Sodium channel and clathrin linker 1 0 ; 127.66 0.016964 500700000 671000 682070 549150 596710 654200 534790 663920 566210 763440 745980 FALSE TRUE 644776.5782 662618.0314 648393.6208 627506.2746 675242.9371 545603.8202 672045.2516 554517.5656 676777.4918 695454.1101 0.927130301 0.952784694 0.93233128 0.902297169 0.970938164 0.78452886 0.966340182 0.797346018 0.973144715 1 19.4075958 LHSLLGDYYQAIK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHSLLGDYYQAIK 13 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 95.508 0.0046642 410450000 238780 227240 243500 217990 259390 190420 280020 176450 311930 303580 FALSE TRUE 229448.2136 220759.3377 287505.8666 229240.49 267733.5149 194270.4229 283446.9685 172806.2458 276521.0141 283018.2562 0.810718774 0.780018012 1.015856258 0.809984815 0.945993797 0.686423644 1.001514787 0.610583388 0.977043028 1 18.11053559 LHVNWVVSELTLGQIWDVDLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHVNWVVSELTLGQIWDVDLQK 22 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 218.72 1.16E-25 78871000 86396 101200 96318 75346 103400 97191 103180 64892 120620 114360 FALSE TRUE 83019.5488 98313.87509 113724.8052 79234.61609 106725.9549 99156.26861 104442.7477 63551.95752 106927.7233 106614.2953 0.778690592 0.922145335 1.066693775 0.743189418 1.001047323 0.930046654 0.97963174 0.596092272 1.00293983 1 16.70204137 LHYGDLTDSTCLVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LHYGDLTDSTCLVK 14 0 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 131.32 5.69E-05 362200000 255030 263920 211280 243010 262870 271120 270780 181990 292240 298490 FALSE TRUE 245063.1456 256393.26 249462.9959 255551.7752 271325.4523 276602.2322 274093.8866 178231.8429 259066.1404 278273.0064 0.880657268 0.921373091 0.89646854 0.918349137 0.975033316 0.993995917 0.984981943 0.640492749 0.930978336 1 18.08614144 LIHLNK ddPTM_BT-474_Pertuzumab_2h_R1 2 LIHLNK 6 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 ; 115.01 0.024796 673770000 1330180 1348110 1144210 1284600 1289670 1194680 1293180 1327450 1472450 1432290 FALSE TRUE 1278195.095 1309663.223 1350994.2 1350898.36 1331153.407 1218837.248 1309006.324 1300037.694 1305303.649 1335279.723 0.957248937 0.98081563 1.011768678 1.011696903 0.996909774 0.912795445 0.980323674 0.973607007 0.977550716 1 20.34871057 LIHTLDDR ddPTM_BT-474_Pertuzumab_2h_R1 7 LIHTLDDR 8 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;;;; 176.4 0.00026053 4691520000 2835920 2941770 2456560 2824730 2913070 2345630 3026540 2756950 2787970 3078480 FALSE TRUE 2725089.111 2857873.6 2900515.038 2970514.654 3006771.542 2393060.246 3063579.702 2700018.019 2471491.334 2869971.808 0.949517728 0.995784555 1.010642345 1.035032695 1.047665881 0.833827092 1.067459859 0.94078207 0.861155265 1 21.45260513 LIILDEIHLLHDDR ddPTM_BT-474_Pertuzumab_2h_R1 5 LIILDEIHLLHDDR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;; 220.21 2.73E-12 691511000 355152 392628 409113 530120 461055 423285 510715 32552.3 497875 448380 FALSE TRUE 341272.2672 381430.6339 483048.8198 557479.5567 475885.2528 431844.1127 516965.2829 31880.08363 441358.3173 418010.8232 0.816419691 0.912489851 1.155589265 1.333648618 1.138451988 1.033093137 1.236727028 0.076266168 1.055853803 1 18.67318077 LIQNLDANHDGR ddPTM_BT-474_Pertuzumab_2h_R1 10 LIQNLDANHDGR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;;; 263.7 1.72E-21 34217260000 9263420 11286960 9390530 12512880 8892630 7112640 11675810 10504790 10205980 11265330 FALSE TRUE 8901395.305 10965066.95 11087607.66 13158671.24 9178669.52 7256462.454 11818702.06 10287862.42 9047439.937 10502319.16 0.84756473 1.044061486 1.055729453 1.252930046 0.873965967 0.690939053 1.125342114 0.979580058 0.861470671 1 23.32420461 LITSDKVENFHEEHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 LITSDKVENFHEEHEK 16 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 0 246.95 1.96E-20 99959000 114660 106650 94762 94189 105170 110450 113590 29197 146670 107180 FALSE TRUE 110178.9604 103608.4464 111887.6014 99050.10558 108552.8886 112683.3747 114980.1484 28594.07175 130020.6365 99920.60313 1.102665086 1.036907736 1.119765072 0.991288107 1.086391446 1.127729128 1.150715116 0.286167926 1.301239508 1 16.60849456 LIVLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LIVLDR 6 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 116.35 0.055015 145280000 109561 125787 105092 121992 123736 86526 125859 124795 115730 131687 FALSE TRUE 105279.235 122199.6779 124084.4622 128288.0217 127716.0808 88275.615 127399.3001 122217.9396 102592.8156 122767.7222 0.857548166 0.995373016 1.010725457 1.044965398 1.040306675 0.7190458 1.037726349 0.995521766 0.835666035 1 16.90557177 LKDALLDHDLALPLCLLMAQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKDALLDHDLALPLCLLMAQQR 22 1 Q8NI27;A0A0C4DG98 Q8NI27 THOC2 THO complex subunit 2 0 153.21 2.14E-08 135860000 240740 224190 147000 172240 204520 218450 208900 195610 241540 230740 FALSE TRUE 231331.6146 217796.3207 173566.17 181129.327 211098.5715 222867.2087 211456.5807 191570.5851 214121.3918 215111.7743 1.075401918 1.012479774 0.806865038 0.842024234 0.98134364 1.036053045 0.983007933 0.890562991 0.995395964 1 17.71472697 LKELIFEETAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LKELIFEETAR 11 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 127.71 0.00025616 378980000 404800 403080 291770 340900 350900 436100 348830 441150 408150 381820 FALSE TRUE 388979.9685 391584.5531 344499.3294 358493.8899 362187.0172 444918.2408 353099.0859 432040.0983 361818.5231 355958.9913 1.09276624 1.100083332 0.96780623 1.007121322 1.01749647 1.249914321 0.991965632 1.213735596 1.016461255 1 18.44135152 LKGVIDLIFEK ddPTM_BT-474_Pertuzumab_2h_R1 2 LKGVIDLIFEK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 112.51 0.00077868 0 831660 880990 746590 668650 704680 576440 883020 863520 930150 979170 FALSE TRUE 799157.8078 855865.0278 881515.4208 703159.1066 727346.6722 588096.0118 893826.6629 845688.0102 824563.2715 912849.9437 0.875453642 0.937574717 0.965673961 0.770289916 0.796786676 0.644241713 0.979160561 0.926426097 0.903284573 1 19.8000182 LKIS(ph)EEDLTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKISEEDLTPR 11 1 E9PGM7;O94988-6;O94988-5;O94988-1;O94988;O94988-3 E9PGM7 FAM13A Protein FAM13A 1 LKIS(1)EEDLTPR;LKIS(1)EEDLTPR 122.31 0.00023832 344380000 787950 758460 621280 627770 724920 665790 692970 923830 847400 707690 TRUE FALSE 757156.0429 736829.4634 733559.1163 660169.2849 748237.7102 679252.73 701450.7742 904752.5877 751206.7046 659757.526 1.147627747 1.11681858 1.111861688 1.000624107 1.134110155 1.029549044 1.063194805 1.371341064 1.138610285 1 19.33157638 LKLPAVVTADLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKLPAVVTADLR 12 1 P38117-2;P38117;M0QY67 P38117-2 ETFB Electron transfer flavoprotein subunit beta 0 ; 122.64 0.00021132 0 1909600 2710800 1729210 3063400 1566930 1514530 3136400 2582600 2233500 1802270 FALSE TRUE 1834970.721 2633490.638 2041716.713 3221502.441 1617331.726 1545154.834 3174784.201 2529268.407 1979962.444 1680200.648 1.092114042 1.567366756 1.215162437 1.917331984 0.962582492 0.919625187 1.889526829 1.505337122 1.178408333 1 20.6802021 LKVPPAINQFTQALDR ddPTM_BT-474_Pertuzumab_2h_R1 2 LKVPPAINQFTQALDR 16 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 264.16 4.94E-27 2525200000 996640 1081190 870390 875120 1038900 948180 1008460 1076460 1082760 1047240 FALSE TRUE 957690.207 1050355.52 1027688.835 920285.0481 1072317.162 967352.8492 1020801.835 1054230.725 959849.6241 976309.502 0.980928901 1.075842771 1.052626071 0.942616093 1.09833732 0.990826011 1.045571955 1.079812009 0.983140717 1 19.89697905 LLACIASRPGQCGR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLACIASRPGQCGR 14 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 237.32 2.49E-17 3452700000 1343250 1761640 1046800 1083220 1282210 1624790 1442540 1390830 1510190 1557200 FALSE TRUE 1290754.305 1711399.752 1235980.046 1139125.114 1323453.449 1657644.367 1460194.236 1362108.874 1338759.562 1451729.457 0.88911491 1.178869619 0.851384561 0.784667631 0.911639178 1.141841105 1.005830824 0.938266333 0.922182543 1 20.46934119 LLALLSLGEVGHHIDLSGQLELK ddPTM_BT-474_Pertuzumab_2h_R1 2 LLALLSLGEVGHHIDLSGQLELK 23 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 193.47 3.49E-18 768750000 508890 597720 490120 587430 564930 572870 595650 181386 734420 665210 FALSE TRUE 489002.0162 580673.6108 578695.5867 617747.3327 583101.4865 584453.8239 602939.7429 177640.3157 651051.7205 620154.7342 0.788516138 0.936336657 0.933147092 0.996118063 0.940251609 0.942432254 0.972240813 0.28644515 1.049821415 1 19.2422687 LLEAQLQAQSLEHEEEVEHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 LLEAQLQAQSLEHEEEVEHLK 21 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q9ULV0 MYO5B Unconventional myosin-Vb 0 209.71 1.41E-22 164910000 110320 117710 97647 112170 125660 120180 122180 51083 154820 130060 FALSE TRUE 106008.5724 114353.0261 115293.985 117959.1071 129701.968 122610.1219 123675.2754 50028.1182 137245.4827 121250.9204 0.874290868 0.943110582 0.95087101 0.972851231 1.069698833 1.011209825 1.019994529 0.412599905 1.131912915 1 16.88763617 LLFEVFDENR ddPTM_BT-474_Pertuzumab_2h_R1 4 LLFEVFDENR 10 0 Q96PU5-7;Q96PU5;Q96PU5-2;Q96PU5-3;H0Y8H4;Q96PU5-5;Q96PU5-6;P46934-4 Q96PU5-7;Q96PU5-5;P46934-4 NEDD4L;NEDD4 E3 ubiquitin-protein ligase NEDD4-like;E3 ubiquitin-protein ligase NEDD4 0 ;;; 182.76 4.05E-06 255076000 454820 464089 394980 416321 402030 355014 475323 464620 510387 501491 FALSE TRUE 437045.1316 450853.6361 466361.6723 437807.3767 414961.6601 362192.6263 481140.1451 455025.4346 452450.0075 467524.5679 0.934806771 0.964342127 0.997512653 0.936437156 0.887571881 0.774702874 1.029122699 0.973265291 0.967756645 1 18.83468265 LLGHWEEAAHDLALACK ddPTM_BT-474_Pertuzumab_2h_R1 3 LLGHWEEAAHDLALACK 17 0 P50502;Q8IZP2;H7C3I1 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;; 198.59 8.13E-12 5622934000 4197641 4041500 3328419 3647431 3654293 3742215 4286778 1779862 4888776 4589283 FALSE TRUE 4033592.549 3926240.377 3929938.354 3835675.351 3771836.653 3817885.151 4339240.871 1743107.228 4333822.644 4278446.775 0.9427703 0.917678911 0.918543238 0.896511176 0.881590178 0.892353079 1.014209385 0.407415896 1.012942984 1 22.02865571 LLHHDDPEVLADTCWAISYLTDGPNER ddPTM_BT-474_Pertuzumab_2h_R1 5 LLHHDDPEVLADTCWAISYLTDGPNER 27 0 P52292 P52292 KPNA2 Importin subunit alpha-1 0 ;;;; 333.36 1.52E-95 1024509000 294338 304800 269967 331021 319724 350295 337058 120757.5 334580 358831 FALSE TRUE 282834.9456 296107.4024 318756.0423 348105.0335 330008.2128 357378.2049 341183.0166 118263.8154 296599.8811 334527.0568 0.845477039 0.885152326 0.952855788 1.040588576 0.986491843 1.068308819 1.019896626 0.353525412 0.88662449 1 18.35176338 LLILDEVHLLHEDR ddPTM_BT-474_Pertuzumab_2h_R1 3 LLILDEVHLLHEDR 14 0 Q8N3C0;Q8N3C0-4 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 0 ;; 229.32 7.67E-13 85034000 48294.9 53266 62343 71936 74445 62928 70812 3521.9 74676 67132 FALSE TRUE 46407.48192 51746.90583 73609.76691 75648.62558 76839.59103 64200.44728 71678.61844 3449.171534 66199.09355 62585.08985 0.741510191 0.826824823 1.176155009 1.208732396 1.227761935 1.025810579 1.145298642 0.055111713 1.057745442 1 15.93353137 LLQETELVEPLT(ph)PSGAMPNQAQMR ddPTM_BT-474_Pertuzumab_2h_R1 10 LLQETELVEPLTPSGAMPNQAQMR 24 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9;P04626-6;J3KTI5;J3QRJ7 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 LLQETELVEPLT(0.926)PS(0.074)GAMPNQAQMR;LLQETELVEPLT(0.99)PS(0.01)GAMPNQAQMR;LLQETELVEPLT(0.996)PS(0.004)GAMPNQAQMR;LLQETELVEPLT(0.994)PS(0.006)GAMPNQAQMR;LLQETELVEPLT(0.948)PS(0.052)GAMPNQAQMR;LLQETELVEPLT(0.967)PS(0.033)GAMPNQAQMR;LLQETELVEPLT(0.999)PS(0.001)GAMPNQAQMR;LLQETELVEPLT(0.993)PS(0.007)GAMPNQAQMR;LLQETELVEPLT(0.992)PS(0.008)GAMPNQAQMR;LLQETELVEPLT(0.999)PS(0.001)GAMPNQAQMR 209.05 2.10E-24 1921564000 769795 2020070 812317 2991330 1120361 1183229 1882965 2048062 1065445 744748 TRUE FALSE 739710.5603 1962459.581 959120.7518 3145712.9 1156398.429 1207154.701 1906009.289 2005768.804 944500.1503 694305.5546 1.065396288 2.826507103 1.381410167 4.530732728 1.665546849 1.738650502 2.74520242 2.888884859 1.360352289 1 19.40521119 LLS(ph)SNEDDANILSSPTDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLSSNEDDANILSSPTDR 18 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 1 LLS(0.96)S(0.04)NEDDANILSSPTDR 145.77 8.77E-07 0 35092 37158 28609 31394 46942 32448 36824 44518 33430 32197 TRUE FALSE 33720.56584 36098.29022 33779.2827 33014.2481 48451.93206 33104.12079 37274.66313 43598.68774 29635.16655 30016.26851 1.123409655 1.202624177 1.125365823 1.099878491 1.614189054 1.102872623 1.241815355 1.452501923 0.987303486 1 14.87345702 LLTVQHPLEESR ddPTM_BT-474_Pertuzumab_2h_R1 1 LLTVQHPLEESR 12 0 Q6P3W7;A0A0U1RQQ9;F8VSC5 Q6P3W7 SCYL2 SCY1-like protein 2 0 94.688 0.0021153 0 330070 335640 282830 300430 319510 229970 321840 290320 336390 369860 FALSE TRUE 317170.4995 326067.8758 333943.6725 315935.2283 329787.3293 234620.151 325778.7742 284324.7905 298204.4175 344809.0528 0.919843887 0.945647666 0.968488704 0.916261408 0.956434661 0.680435009 0.944809226 0.824586212 0.864839293 1 18.39543813 LLYDLADQLHAAVGASR ddPTM_BT-474_Pertuzumab_2h_R1 2 LLYDLADQLHAAVGASR 17 0 H0YL12;P13804-2;P13804;H0YK49;H0YNX6 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 ; 214.19 6.02E-15 1143740000 554410 844600 532520 1228790 550660 683060 1023280 810910 683960 569400 FALSE TRUE 532743.0443 820512.8349 628758.2098 1292207.999 568372.479 696871.9412 1035803.207 794164.4251 606319.7282 530834.0308 1.003596253 1.545705036 1.184472308 2.434297585 1.070715979 1.312786861 1.951275063 1.496069165 1.142202069 1 19.01790134 LMYEHNLQRTACNMTYGSFGGVK ddPTM_BT-474_Pertuzumab_2h_R1 3 LMYEHNLQRTACNMTYGSFGGVK 23 1 F8WCG5;A0A5F9ZGY2;A0A5F9ZHP5;A0A5F9ZH74;A0A5F9ZH37;A0A5F9ZHE7;A0A5F9ZH14;A0A5F9ZGX9;Q3SYG4-5;Q3SYG4-6;Q3SYG4-2;Q3SYG4-4;Q3SYG4-7;Q3SYG4-3;Q3SYG4 F8WCG5 BBS9 Protein PTHB1 0 ;; 56.055 0.055276 86734000000 18340500 20198800 18940400 18935800 18376800 23588100 23293300 6157230 26339600 25239800 FALSE TRUE 17623732.98 19622750 22363351.61 19913078.91 18967906.46 24065067.54 23578370.37 6030081.049 23349639.03 23530285.86 0.748980828 0.833935895 0.950407136 0.846274415 0.806106078 1.022727377 1.002043516 0.256268924 0.992322795 1 24.48801551 LNCQVIGASVDSHFCHLAWVNTPK ddPTM_BT-474_Pertuzumab_2h_R1 3 LNCQVIGASVDSHFCHLAWVNTPK 24 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 221.83 5.17E-33 6347210000 3433670 3472229 3019499 3697191 3367909 3515597 3600710 438664 4104072 3631931 FALSE TRUE 3299478.38 3373204.429 3565189.638 3888003.471 3476240.852 3586684.78 3644776.566 429605.4351 3638194.952 3385937.078 0.974465356 0.996239549 1.05294031 1.148279894 1.026670246 1.059288669 1.076445451 0.126879332 1.074501643 1 21.69112373 LNEHFLNTTDFLDTIK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNEHFLNTTDFLDTIK 16 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 235.95 1.02E-19 1484770000 1108600 1563990 934750 1996740 969330 1160370 1879880 1624840 1510290 1128960 FALSE TRUE 1065274.686 1519386.537 1103680.118 2099791.991 1000509.38 1183833.476 1902886.534 1591286.486 1338848.211 1052494.534 1.012142726 1.443605157 1.048632637 1.995062134 0.950607673 1.124788242 1.807977593 1.511919003 1.272071415 1 20.00538131 LNEQYEHASIHLWDLLEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LNEQYEHASIHLWDLLEGK 19 0 Q14444-2;Q14444;G3V153 Q14444-2 CAPRIN1 Caprin-1 0 155.19 1.64E-08 224640000 77853 125230 109420 138310 109030 143820 132140 22470 126770 146100 FALSE TRUE 74810.41869 121658.563 129194.628 145448.1957 112537.049 146728.1389 133757.1688 22005.98665 112379.6011 136204.5169 0.549250645 0.893205055 0.948534094 1.067866169 0.826235807 1.077263385 0.982031815 0.161565763 0.825079841 1 17.05541502 LNFGDDIPSALR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNFGDDIPSALR 12 0 Q9UNE7;Q9UNE7-2;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 110.84 0.0033655 40836000 77045 85237 71359 80835 80416 82234 86199 87847 88319 98121 FALSE TRUE 74033.99622 82806.12422 84255.15867 85006.90404 83002.65367 83896.82782 87253.92915 86032.92875 78293.39738 91475.17727 0.809334274 0.905230541 0.921071281 0.929289306 0.907378987 0.917154034 0.953853622 0.940505734 0.855897739 1 16.48109269 LNIIIIAEGAIDR ddPTM_BT-474_Pertuzumab_2h_R1 1 LNIIIIAEGAIDR 13 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 96.64 0.0035748 0 66182 54353 39030 36768 58827 60722 50738 54712 64065 52635 FALSE TRUE 63595.53427 52802.90566 46083.58922 38665.60089 60719.22388 61949.84044 51358.94682 53582.17808 56792.60978 49069.98457 1.296017002 1.076073411 0.93914008 0.787968475 1.237400509 1.262479314 1.046646892 1.091954248 1.157379817 1 15.5825532 LNWLSVDFNNWK ddPTM_BT-474_Pertuzumab_2h_R1 2 LNWLSVDFNNWK 12 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 310.21 6.69E-46 1693110000 1513950 1434430 1426760 1433250 1450870 1159720 1700390 1607000 1782330 1842380 FALSE TRUE 1454783.16 1393521.461 1684607.27 1507220.204 1497538.551 1183170.333 1721199.881 1573814.888 1580007.371 1717593.962 0.846988982 0.811321821 0.980794826 0.877518341 0.871881588 0.688853338 1.002099402 0.916290418 0.919895741 1 20.71195759 LPEHEINR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPEHEINR 8 0 O43815-2;O43815 O43815-2 STRN Striatin 0 76.478 0.035699 235800000 169630 189890 154170 172190 176880 140320 190440 159820 181840 192400 FALSE TRUE 163000.6721 184474.5231 182031.9485 181076.7465 182569.5058 143157.3665 192770.6617 156519.6611 161198.2855 179368.5766 0.90874709 1.028466226 1.014848598 1.009523239 1.017845541 0.798118429 1.074718132 0.872614725 0.898698582 1 17.45256764 LPISDS(ph)PPDTQEIHVIEQEKLEAQDSGEEAR ddPTM_BT-474_Pertuzumab_2h_R1 3 LPISDSPPDTQEIHVIEQEKLEAQDSGEEAR 31 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 LPIS(0.024)DS(0.939)PPDT(0.037)QEIHVIEQEKLEAQDSGEEAR;LPIS(0.025)DS(0.956)PPDT(0.019)QEIHVIEQEKLEAQDSGEEAR;LPISDS(0.986)PPDT(0.014)QEIHVIEQEKLEAQDSGEEAR 274.66 7.19E-72 122021000 188463 152696 138540 148560 184000 155822 170658 180428 186793 164329 TRUE FALSE 181097.6576 148341.2596 163577.2598 156227.1994 189918.5271 158972.8276 172746.5637 176702.0987 165589.0417 153198.8505 1.182108463 0.96829225 1.067744695 1.019767439 1.239686372 1.037689429 1.127596997 1.15341661 1.080876529 1 17.22504595 LPNGLGGPNGFPKPTPEEGPPELNRQS(ph)PNSSSAAASVASR ddPTM_BT-474_Pertuzumab_2h_R1 4 LPNGLGGPNGFPKPTPEEGPPELNRQSPNSSSAAASVASR 40 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 LPNGLGGPNGFPKPTPEEGPPELNRQS(1)PNSSSAAASVASR;LPNGLGGPNGFPKPT(0.002)PEEGPPELNRQS(0.953)PNS(0.027)S(0.006)S(0.007)AAAS(0.002)VAS(0.003)R;LPNGLGGPNGFPKPTPEEGPPELNRQS(1)PNSSSAAASVASR;LPNGLGGPNGFPKPTPEEGPPELNRQS(1)PNSSSAAASVASR 259.5 2.01E-63 4002890000 821050 819200 593092 715925 726023 886840 742060 844750 913220 815510 TRUE FALSE 788962.4583 795837.2181 700276.9177 752873.975 749376.1892 904772.5124 751141.5523 827305.6173 809555.0941 760274.7813 1.037733301 1.046775768 0.921083975 0.990265617 0.98566493 1.190059877 0.987986937 1.088166591 1.064819081 1 19.53616141 LPS(ph)SSSEMGSQDGSPLR ddPTM_BT-474_Pertuzumab_2h_R1 1 LPSSSSEMGSQDGSPLR 17 0 A2A2G5;Q9UJ14-5;Q9UJ14 A2A2G5 GGT7 Gamma-glutamyltransferase 7;Gamma-glutamyltransferase 7 heavy chain;Gamma-glutamyltransferase 7 light chain 1 LPS(0.964)S(0.032)S(0.004)SEMGSQDGSPLR 155.2 1.15E-07 58361000 41574 61641 38583 70225 46412 44336 46748 64756 48003 38020 TRUE FALSE 39949.24212 59883.05903 45555.80637 73849.32067 47904.88413 45232.5043 47320.11601 63418.76597 42553.90068 35444.87154 1.127081024 1.689470336 1.285258047 2.083498048 1.35153217 1.276136782 1.335034208 1.789222622 1.200565804 1 15.11328928 LPSETIFVGCEFLHHLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LPSETIFVGCEFLHHLLR 18 0 I3L2C7;P57678 I3L2C7 GEMIN4 Gem-associated protein 4 0 ; 81.317 0.0041323 106844000 71627 83433 69269 76249 82421 83714 85084 35417 85710 91051 FALSE TRUE 68827.73765 81053.57253 81787.44918 80184.22003 85072.14632 85406.75444 86125.28344 34685.62657 75980.56013 84884.03467 0.810844323 0.954874174 0.963519813 0.944632525 1.002216102 1.006158046 1.014622877 0.408623679 0.89511014 1 16.37320561 LQFHDVAGDIFHQQCK ddPTM_BT-474_Pertuzumab_2h_R1 2 LQFHDVAGDIFHQQCK 16 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 260.24 5.13E-27 3857100000 4452900 4697200 4062400 4533500 4258800 3995000 5105200 1688040 5902100 5938000 FALSE TRUE 4278875.745 4563240.455 4796566.048 4767474.478 4395788.17 4075781.637 5167678.965 1653181.384 5232118.352 5535813.971 0.77294428 0.824312464 0.866460844 0.861205688 0.794063564 0.736256973 0.93349939 0.29863384 0.945139844 1 22.40036403 LQINS(ph)PPFDQPMSR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQINSPPFDQPMSR 14 0 Q00537;Q00537-2;F5H6Z0;F8VQZ9 Q00537 CDK17 Cyclin-dependent kinase 17 1 LQINS(1)PPFDQPMSR 62.68 0.096559 66819000 205510 151350 146520 158730 154560 192720 170030 176790 175550 198350 TRUE FALSE 197478.442 147033.6462 172999.4233 166922.0743 159531.5628 196616.9304 172110.878 173139.2247 155622.3 184915.5778 1.067938377 0.795139317 0.935558947 0.902693414 0.862726465 1.063279431 0.930753807 0.936314975 0.841585667 1 17.49650724 LQYAVSGLEPLAWSEDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 LQYAVSGLEPLAWSEDHR 18 0 Q9UKN8;F2Z356 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 0 133.93 1.16E-05 206760000 116900 151810 84842 131500 124250 131450 129660 103370 152560 123840 FALSE TRUE 112331.4188 147480.5274 100174.8367 138286.7308 128246.6141 134108.0091 131246.8179 101235.3734 135242.0284 115452.2065 0.972969007 1.277416274 0.867673644 1.197783351 1.110819949 1.161588965 1.136806492 0.876859581 1.171411379 1 16.81693622 LREIEENQK ddPTM_BT-474_Pertuzumab_2h_R1 1 LREIEENQK 9 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 64.374 0.082041 0 230400 233640 225550 206550 201930 236350 266710 134020 289780 289240 FALSE TRUE 221395.7133 226976.816 266311.9023 217210.0703 208425.2618 241129.1589 269974.0768 131252.4402 256885.3893 269649.5172 0.821049915 0.841747533 0.987622396 0.805527384 0.772948767 0.894231747 1.001203635 0.486751994 0.952664006 1 18.04072593 LRLDSIVIQQGR ddPTM_BT-474_Pertuzumab_2h_R1 1 LRLDSIVIQQGR 12 1 O60264;A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 O60264 SMARCA5;SMARCA1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5;Probable global transcription activator SNF2L1 0 175.48 2.51E-05 245970000 112620 120180 107410 110150 116020 89867 118650 114840 123740 113450 FALSE TRUE 108218.6859 116752.5841 126821.3763 115834.8547 119751.8887 91684.17231 120102.0742 112468.5139 109693.554 105765.9304 1.023190411 1.103877057 1.199075882 1.095200073 1.132235004 0.866859223 1.135545952 1.063371857 1.037135054 1 16.69051545 LRNPSDR ddPTM_BT-474_Pertuzumab_2h_R1 4 LRNPSDR 7 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ;;; 102.41 0.0078502 950600000 661184 1130390 710080 1385090 760194 617455 1094870 1086540 855852 823765 FALSE TRUE 635344.1983 1098152.384 838407.2516 1456574.661 784646.3304 629940.3632 1108269.347 1064102.569 758699.269 767970.6628 0.827302694 1.42994054 1.091717812 1.896654041 1.021713938 0.820266182 1.443114171 1.38560315 0.987927411 1 19.55069167 LRPLWK ddPTM_BT-474_Pertuzumab_2h_R1 2 LRPLWK 6 1 P56559;P40617;P56559-2;P36406-3;P36406-2;P36406 REV__E5RG38 ARL4C;ARL4A;TRIM23 ADP-ribosylation factor-like protein 4C;ADP-ribosylation factor-like protein 4A;E3 ubiquitin-protein ligase TRIM23 0 ; 120.76 0.018192 4085600000 4274800 4657900 3718300 3947800 4280600 2425500 5043400 4528500 4767000 5271700 FALSE TRUE 4107736.09 4525061.253 4390279.523 4151546.431 4418289.387 2474545.272 5105122.638 4434984.892 4225870.145 4914643.063 0.835815752 0.920730396 0.893305875 0.844729999 0.899005142 0.503504576 1.03875756 0.902402237 0.859852911 1 22.22865521 LRS(ph)GS(ph)ASPMDLLS(ph)YFK ddPTM_BT-474_Pertuzumab_2h_R1 1 LRSGSASPMDLLSYFK 16 1 P11678 P11678 EPX Eosinophil peroxidase;Eosinophil peroxidase light chain;Eosinophil peroxidase heavy chain 3 LRS(0.996)GS(0.514)AS(0.41)PMDLLS(0.566)Y(0.513)FK 46.408 0.064712 0 23111 23953 22648 25388 25922 24487 28409 15342 28724 27281 TRUE FALSE 22207.79657 23269.88389 26740.9974 26698.27772 26755.80467 24982.14392 28756.67784 15025.18234 25463.37194 25433.23357 0.873180223 0.914940046 1.051419487 1.049739808 1.052001689 0.982263771 1.130673289 0.590769644 1.001185 1 14.63442728 LRS(ph)GSASPMDLLS(ph)Y(ph)FK ddPTM_BT-474_Pertuzumab_2h_R1 4 LRSGSASPMDLLSYFK 16 1 P11678 P11678 EPX Eosinophil peroxidase;Eosinophil peroxidase light chain;Eosinophil peroxidase heavy chain 3 LRS(0.988)GS(0.041)AS(0.104)PMDLLS(0.934)Y(0.934)FK;LRS(0.983)GS(0.038)AS(0.098)PMDLLS(0.943)Y(0.939)FK;LRS(0.984)GS(0.049)AS(0.196)PMDLLS(0.89)Y(0.882)FK;LRS(0.946)GS(0.09)AS(0.318)PMDLLS(0.827)Y(0.819)FK 49.595 0.043459 0 119360 127137 117418 137143 132481 137095 137093 70969.8 144875 142990 TRUE FALSE 114695.2792 123511.1772 138638.0445 144220.9667 136742.3717 139867.1548 138770.7851 69504.24883 128429.3974 133305.1599 0.860396396 0.926529605 1.040005088 1.081885853 1.025784536 1.049225363 1.041000853 0.521392037 0.963424052 1 17.0243731 LS(ph)GVMVPAPIQDLEALR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSGVMVPAPIQDLEALR 17 0 A0A1W2PQD2;Q9UBB4-2;Q9UBB4 A0A1W2PQD2 ATXN10 Ataxin-10 1 LS(1)GVMVPAPIQDLEALR;LS(1)GVMVPAPIQDLEALR 109.35 0.00064103 19353800 35947 35560 38778 34469 34420 33737 34263 43340 38808 42602 TRUE FALSE 34542.1515 34545.86362 45786.04721 36247.94922 35527.15056 34419.18526 34682.32084 42445.01385 34402.67854 39716.52859 0.869717287 0.869810752 1.152820975 0.912666603 0.894518021 0.86662119 0.873246532 1.068698986 0.866205576 1 15.27745191 LS(ph)PPLHMAPGAGEHHLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSPPLHMAPGAGEHHLAR 18 0 Q6ZN04 Q6ZN04 MEX3B RNA-binding protein MEX3B 1 LS(1)PPLHMAPGAGEHHLAR 158.33 7.65E-11 210400000 114700 134200 127500 148860 119840 125450 148440 54985 163710 144070 TRUE FALSE 110217.3972 130372.7474 150542.0862 156542.6824 123694.7624 127986.685 150256.6531 53849.54054 145126.3271 134312.0106 0.820607157 0.970670805 1.120838602 1.165515145 0.920950866 0.952905733 1.118713453 0.400928706 1.080516378 1 17.0352288 LS(ph)PSTSGPHSHDYLPQER ddPTM_BT-474_Pertuzumab_2h_R1 5 LSPSTSGPHSHDYLPQER 18 0 Q5JR04;Q9HCE1 Q5JR04 MOV10 Putative helicase MOV-10 1 LS(0.994)PS(0.006)TSGPHSHDYLPQER;LS(0.96)PS(0.04)TSGPHSHDYLPQER;LS(0.919)PS(0.081)TSGPHSHDYLPQER;LS(0.749)PS(0.197)T(0.027)S(0.027)GPHSHDYLPQER;LS(0.993)PS(0.007)TSGPHSHDYLPQER 149.67 1.01E-07 1943360000 554275 806900 700580 912634 788000 900700 870130 324232 942359 793224 TRUE FALSE 532613.3202 783888.002 827190.3903 959735.1501 813346.7356 918912.7711 880778.9112 317536.4959 835386.357 739498.2319 0.720236097 1.060026878 1.118583324 1.297819398 1.099862989 1.24261659 1.191049381 0.42939453 1.12966647 1 19.49618717 LS(ph)SLRAS(ph)TSK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.717)S(0.283)LRAS(0.917)T(0.072)S(0.011)K 116.78 0.00059457 1251300000 5583100 2256800 1567400 1511300 1747700 1087400 1330600 7251800 1557000 899910 TRUE FALSE 5364906.28 2192438.274 1850664.047 1589298.374 1803916.358 1109387.973 1346884.281 7102047.796 1380255.887 838958.2941 6.394723453 2.613286368 2.205907087 1.894371133 2.150185975 1.322339836 1.605424596 8.465316864 1.645202029 1 19.67823957 LS(ph)SPISK ddPTM_BT-474_Pertuzumab_2h_R1 1 LSSPISK 7 0 A0A494C142;Q99728-3;Q99728-2;Q99728 A0A494C142 BARD1 BRCA1-associated RING domain protein 1 1 LS(0.5)S(0.5)PISK 94.692 0.0147 100550000 760020 716350 618310 722220 722040 608940 715370 765900 696830 685160 TRUE FALSE 730317.5782 695920.3994 730052.3712 759493.8608 745265.0723 621253.184 724124.9121 750083.8974 617728.7797 638753.5029 1.14334806 1.089497586 1.142932865 1.189024964 1.166749096 0.972602391 1.133653137 1.174293204 0.967084763 1 19.28489977 LSDGFNGADLR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSDGFNGADLR 11 0 A0A087X2I1;P62333;H0YJC0 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 105.52 0.0057095 470990000 466840 546470 473390 524110 507900 472540 599650 531090 554090 643820 FALSE TRUE 448595.3767 530885.2107 558942.1035 551159.3799 524237.0648 482095.0826 606988.6961 520122.8059 491192.0261 600213.4979 0.747393016 0.884493955 0.93123881 0.918272218 0.873417653 0.803206 1.01128798 0.866562994 0.818362179 1 19.19511624 LSEDYGVLK ddPTM_BT-474_Pertuzumab_2h_R1 3 LSEDYGVLK 9 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;; 214.64 1.56E-06 504930000 986140 1008430 889930 885000 882450 649490 1084810 1051450 1159800 1203070 FALSE TRUE 947600.5586 979670.5638 1050760.147 930674.9561 910834.8057 662623.1328 1098086.229 1029737.19 1028144.366 1121584.997 0.844876279 0.873469747 0.936852891 0.82978549 0.812096103 0.590791723 0.979048607 0.91810892 0.916688765 1 20.09710753 LSELLR ddPTM_BT-474_Pertuzumab_2h_R1 8 LSELLR 6 0 P08238;A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2;P07900;P07900-2 P08238;A0A669KBG8;Q92538-3;P07900 HSP90AB1;GBF1;HSP90AA1 Heat shock protein HSP 90-beta;Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1;Heat shock protein HSP 90-alpha 0 ;;;;;;; 176.25 0.0091956 25066950000 5763590 6102560 5234080 6155170 5782200 5429530 6117320 6518410 6334930 6737830 FALSE TRUE 5538342.531 5928520.964 6179994.687 6472839.061 5968189.714 5539318.817 6192185.592 6383802.556 5615815.305 6281470.773 0.881695184 0.943810961 0.983845171 1.030465522 0.950126162 0.881850607 0.985785943 1.016291055 0.894028725 1 22.58267097 LSELSNSQQSVQTLSLWLIHHR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSELSNSQQSVQTLSLWLIHHR 22 0 Q96P16;A0A0C4DGQ6;E9PQF3;K7EQR8;Q9NQG5;E9PIQ9 Q96P16;Q9NQG5 RPRD1A;RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1A;Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ; 199.97 9.85E-23 792280000 592510 620240 584200 646520 736870 685230 674850 357990 764020 663090 FALSE TRUE 569354.0541 602551.3625 689777.9355 679886.9747 760572.0928 699085.8201 683109.0162 350597.3814 677291.6526 618178.3237 0.921019118 0.974720949 1.115823556 1.099823382 1.230344164 1.130880513 1.105035537 0.567146029 1.095625043 1 19.23766354 LSGLTTNVVDIILAHHFGQEELQANLDLIQTYR ddPTM_BT-474_Pertuzumab_2h_R1 1 LSGLTTNVVDIILAHHFGQEELQANLDLIQTYR 33 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 146.58 1.83E-10 79978000 23848 26663 32325 30233 29880 24584 30457 13850 34464 32302 FALSE TRUE 22915.99379 25902.59735 38166.84657 31793.32875 30841.11734 25081.10532 30829.74188 13563.99266 30551.7912 30114.15677 0.760970794 0.860146859 1.267405455 1.055760219 1.02414016 0.832867595 1.023762416 0.450419142 1.014532515 1 14.87815424 LSIPTYGLQCTR ddPTM_BT-474_Pertuzumab_2h_R1 2 LSIPTYGLQCTR 12 0 P49327;A0A0U1RQF0;J3KTF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 128.88 0.00056795 683560000 233830 258560 240880 218557 229240 237693 289460 242060 252320 330780 FALSE TRUE 224691.6651 251186.122 284412.3743 229836.753 236613.7128 242499.3153 293002.4981 237061.3764 223677.6914 308375.976 0.728628955 0.814545041 0.922290958 0.745313419 0.767289709 0.78637551 0.950146966 0.76874139 0.725340846 1 18.23433085 LSLEGDHST(ph)PPSAYGSVK ddPTM_BT-474_Pertuzumab_2h_R1 4 LSLEGDHSTPPSAYGSVK 18 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YNB8;H0YKN4;H0YMD9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 LSLEGDHS(0.003)T(0.997)PPSAYGSVK;LSLEGDHS(0.013)T(0.987)PPSAYGSVK;LSLEGDHS(0.035)T(0.953)PPS(0.012)AYGSVK;LSLEGDHS(0.003)T(0.996)PPSAYGSVK 120.41 0.00016785 2442020000 1257110 1689800 814590 1791700 1081520 1175080 1461230 1549540 1549000 1333550 TRUE FALSE 1207980.751 1641608.558 961804.5335 1884169.852 1116308.073 1198840.923 1479112.97 1517541.458 1373164.014 1243227.471 0.971649018 1.320441027 0.7736352 1.515547151 0.897911363 0.964297324 1.189736396 1.220646658 1.104515502 1 20.24565886 LSLEGDHSTPPSAYGSVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSLEGDHSTPPSAYGSVK 18 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YNB8;H0YKN4;H0YMD9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 190.82 2.57E-14 863860000 463540 783520 317430 906010 435550 478580 658370 754450 599340 497950 FALSE TRUE 445424.3443 761174.7767 374796.6622 952769.2847 449559.8613 488257.2155 666427.329 738870.3439 531305.4358 464223.403 0.959504285 1.639673424 0.807362705 2.052393909 0.968412748 1.051772083 1.435574606 1.591626659 1.144503772 1 18.82445973 LSS(ph)LRAS(ph)TSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.435)S(0.565)LRAS(0.931)T(0.056)S(0.013)K;LS(0.429)S(0.571)LRAS(0.954)T(0.039)S(0.007)K 103.88 0.0015685 1746270000 8616900 3688200 2458950 2377370 2645980 1720710 2031560 11362100 2292830 1425100 TRUE FALSE 8280142.022 3583016.147 2903336.964 2500066.351 2731090.35 1755503.935 2056422.839 11127468.66 2032557.551 1328576.708 6.232340198 2.696883158 2.185298709 1.881762894 2.055651235 1.321341798 1.547838997 8.375480769 1.529875948 1 20.3414501 LSSGLVS(ph)PAPSFYSK ddPTM_BT-474_Pertuzumab_2h_R1 2 LSSGLVSPAPSFYSK 15 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 LSSGLVS(1)PAPSFYSK;LSSGLVS(1)PAPSFYSK 396.03 8.65E-115 1444250000 1475450 1435020 1162880 1254660 1306100 1284720 1291000 1579260 1473320 1408390 TRUE FALSE 1417787.783 1394094.635 1373038.284 1319413.153 1348111.893 1310697.919 1306799.644 1546647.729 1306074.89 1312998.491 1.079809149 1.06176408 1.045727237 1.004885506 1.026742911 0.998247849 0.995278862 1.177950881 0.994726878 1 20.32443383 LSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_BT-474_Pertuzumab_2h_R1 6 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 LS(0.015)VPT(0.986)S(0.999)DEEDEVPAPKPR;LSVPT(1)S(1)DEEDEVPAPKPR;LSVPT(1)S(1)DEEDEVPAPKPR;LS(0.003)VPT(0.998)S(1)DEEDEVPAPKPR;LSVPT(1)S(1)DEEDEVPAPKPR;LS(0.004)VPT(0.997)S(0.999)DEEDEVPAPKPR 213.15 2.62E-16 2688020000 3804200 3796050 3181290 3048550 3417420 3482460 3157160 3984600 3987960 3579370 TRUE FALSE 3655527.658 3687790.371 3756219.87 3205886.031 3527344.418 3552877.727 3195798.268 3902316.618 3535263.5 3336936.082 1.095474282 1.105142646 1.125649332 0.960727431 1.057060828 1.064712551 0.95770437 1.169431036 1.059433988 1 21.67009262 LSYAGGRPPSYAGS(ph)PVHHAAER ddPTM_BT-474_Pertuzumab_2h_R1 7 LSYAGGRPPSYAGSPVHHAAER 22 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LSYAGGRPPS(0.001)YAGS(0.999)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPS(0.001)YAGS(0.999)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER 272.57 1.43E-45 18083130000 3004412 3426259 3190256 3549322 3152096 3820880 4005470 1017019 4290550 4742580 TRUE FALSE 2886996.257 3328545.448 3766806.226 3732502.934 3253486.031 3898140.811 4054490.14 996017.2022 3803504.751 4421360.832 0.652965539 0.752832798 0.851956302 0.844197765 0.735856256 0.881660864 0.917023128 0.225273901 0.860256581 1 22.07605905 LTDCVVMR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTDCVVMR 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 119.17 0.0040598 196810000 163970 161380 139040 159180 162230 121280 172370 188610 182980 175130 FALSE TRUE 157561.8711 156777.6004 164167.6209 167395.2989 167448.2753 123732.3647 174479.5156 184715.1376 162208.8775 163268.2891 0.965048828 0.960245258 1.005508307 1.025277473 1.025601948 0.757846887 1.068667508 1.131359547 0.993511223 1 17.31688508 LTDDHVQFLIYQILR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTDDHVQFLIYQILR 15 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 ; 188.31 3.05E-07 297480000 512240 548830 501190 505390 541120 429550 562290 489830 588730 627840 FALSE TRUE 492221.0945 533177.9058 591766.1819 531473.2385 558525.6162 438235.7953 569171.4732 479714.8393 521899.8386 585315.8376 0.840949557 0.910923422 1.01102028 0.908011033 0.954229461 0.74871679 0.972417687 0.819582879 0.891655078 1 19.15885579 LTEDKADVQSIIGLQR ddPTM_BT-474_Pertuzumab_2h_R1 3 LTEDKADVQSIIGLQR 16 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 244.97 3.95E-20 5512016000 6562460 5849790 4749830 5079480 5909240 6058540 5392340 6307110 7116030 6150420 FALSE TRUE 6305991.808 5682959.717 5608229.94 5341632.572 6099316.071 6181047.83 5458333.07 6176865.974 6308248.107 5733846.575 1.099783841 0.99112518 0.978092083 0.931596704 1.063738974 1.077993237 0.95194962 1.077263909 1.100177346 1 22.45107187 LTHYDHVLIELTQAGLK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTHYDHVLIELTQAGLK 17 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ; 130.06 1.82E-05 604490000 1109020 1070380 986420 1028370 1084560 1073970 1145970 203020 1355180 1138050 FALSE TRUE 1065678.272 1039853.81 1164688.037 1081444.299 1119445.857 1095686.409 1159994.724 198827.5661 1201345.648 1060968.86 1.004438785 0.980098333 1.097758927 1.019298813 1.055116601 1.032722496 1.093335316 0.187401887 1.132309998 1 20.01695088 LTIHGDLYYEGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LTIHGDLYYEGK 12 0 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 112.51 0.0012664 431030000 1439700 1523500 1256900 1444500 1436700 1485700 1465800 1472300 1656800 1693100 FALSE TRUE 1383434.932 1480051.272 1484049.79 1519050.818 1482912.76 1515741.872 1483738.899 1441896.49 1468727.01 1578424.829 0.876465516 0.937676121 0.940209355 0.962384011 0.939488998 0.960287651 0.940012392 0.913503427 0.930501715 1 20.59005412 LTIQNR ddPTM_BT-474_Pertuzumab_2h_R1 1 LTIQNR 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 120.9 0.046264 110920000 130830 153830 101800 156320 119770 122440 130660 119400 129320 153590 FALSE TRUE 125717.019 149442.919 120197.5245 164387.6939 123622.5108 124915.8207 132259.0562 116934.3483 114640.1358 143187.2125 0.877990547 1.043689003 0.839443149 1.148061276 0.863362787 0.872395087 0.923679244 0.81665357 0.800631102 1 17.12754313 LTSNPLASHDYILK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTSNPLASHDYILK 14 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ; 222.75 3.78E-12 2503800000 2311430 3565200 2303750 3265300 2382200 1206900 3592500 3464200 3793300 3406600 FALSE TRUE 2221096.76 3463523.987 2720088.872 3433822.524 2458825.626 1231304.345 3636466.09 3392663.059 3362700.487 3175867.948 0.699366849 1.090575567 0.856486767 1.081223332 0.77422162 0.387706405 1.145030634 1.068263264 1.058828812 1 21.5987195 LTTTGQVT(ph)SPVK ddPTM_BT-474_Pertuzumab_2h_R1 2 LTTTGQVTSPVK 12 0 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.698)S(0.302)PVK;LTTTGQVT(0.5)S(0.5)PVK 260.97 2.72E-20 2079370000 1848620 1612910 1501670 1673500 1550210 1265170 1836110 1913520 1806160 2028220 TRUE FALSE 1776373.887 1566911.386 1773055.173 1759869.536 1600073.913 1290752.604 1858580.863 1874005.143 1601132.289 1890846.853 0.939459419 0.828682335 0.937704273 0.93073087 0.846220787 0.682632019 0.982935694 0.991093034 0.846780524 1 20.85060109 LTVNADVGYYSWR ddPTM_BT-474_Pertuzumab_2h_R1 2 LTVNADVGYYSWR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 299.29 1.82E-40 1794680000 308257 338720 319247 317600 343334 248348 305308 347652 323122 363511 FALSE TRUE 296209.9756 329060.0372 376942.0345 333991.3741 354377.6499 253369.7667 309044.4506 340472.8647 286442.5452 338890.0762 0.874059161 0.970993429 1.112284074 0.985544864 1.045700877 0.747645873 0.91193125 1.004670507 0.845237336 1 18.37045787 LVQAEYWHDPIKEDVYR ddPTM_BT-474_Pertuzumab_2h_R1 3 LVQAEYWHDPIKEDVYR 17 1 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ;; 233.63 2.46E-20 830090000 876690 933570 762250 869670 784020 921270 940010 890970 1027970 1007320 FALSE TRUE 842427.9856 906945.4977 900005.5312 914553.7729 809238.7153 939898.7106 951514.1236 872571.1581 911279.1552 939093.3192 0.897065253 0.96576717 0.958377099 0.973868895 0.861723429 1.000857627 1.013226379 0.929163418 0.970381896 1 19.840909 LYQPEYQEVSTEEQREEISGK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYQPEYQEVSTEEQREEISGK 21 1 A0A494C039;Q9Y4L1;A0A087X054 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 183.24 4.00E-17 353810000 212320 209980 151780 143710 212700 225500 166490 182720 211710 188460 FALSE TRUE 204022.2997 203991.576 179210.0223 151126.8903 219541.6887 230059.7645 168527.5544 178946.7681 187677.5684 175695.4363 1.161227087 1.161052218 1.020003855 0.860164006 1.249558288 1.309423678 0.9592028 1.0185055 1.068198311 1 17.42271719 LYTWVEWVK ddPTM_BT-474_Pertuzumab_2h_R1 1 LYTWVEWVK 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 78.334 0.069943 94290000 206880 147450 116890 129170 138540 127630 136050 233090 150160 172110 FALSE TRUE 198794.9009 143244.8704 138014.6232 135836.4792 142996.2649 130210.766 137715.0206 228276.61 133114.4663 160452.8364 1.238961587 0.892753744 0.860156955 0.846581975 0.891204345 0.8115205 0.858289724 1.422702242 0.829617409 1 17.29178977 MAEELKPMDTDKESIAESK ddPTM_BT-474_Pertuzumab_2h_R1 1 MAEELKPMDTDKESIAESK 19 2 O60502;O60502-3;O60502-2;O60502-4 O60502 MGEA5 Protein O-GlcNAcase 0 55.383 0.058252 68004000 51327 51136 52194 34026 47215 55480 50665 51357 60790 56807 FALSE TRUE 49321.0841 49677.65135 61626.61685 35782.08594 48733.71335 56601.84361 51285.05343 50296.46 53889.37405 52959.41129 0.931299705 0.938032545 1.163657513 0.675651127 0.920208744 1.06877781 0.96838413 0.949717128 1.017559915 1 15.69259946 MDIDVPDVEVQGPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 2 MDIDVPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 339.06 2.89E-75 865370000 1355380 1345750 1201810 1389780 1161360 1353810 1358070 1441940 1541530 1426550 FALSE TRUE 1302410.251 1307370.528 1419003.801 1461506.712 1198716.199 1381184.966 1374690.467 1412163.435 1366541.977 1329928.498 0.979308477 0.983038208 1.066977513 1.098936307 0.901338832 1.03854077 1.033657425 1.061834104 1.027530412 1 20.34291725 MDTLAHVLYYPQKPLVTTR ddPTM_BT-474_Pertuzumab_2h_R1 2 MDTLAHVLYYPQKPLVTTR 19 1 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 ; 99.34 0.00048789 508690000 568360 529890 469410 600020 590890 529930 580110 559150 647980 698410 FALSE TRUE 546147.8628 514778.056 554242.829 630987.1041 609896.5135 540645.5477 587209.5597 547603.3571 574424.027 651106.0686 0.838800142 0.790620885 0.85123278 0.969100327 0.936708384 0.830349422 0.90186467 0.84103556 0.882228034 1 19.31253306 MEIIELANHPYFVGVQFHPEFSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 MEIIELANHPYFVGVQFHPEFSSR 24 0 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 139.28 3.64E-07 256440000 136300 159580 153500 170170 147010 154180 184670 79137 186350 206570 FALSE TRUE 130973.2453 155028.9346 181240.8646 178952.4941 151738.7102 157297.6252 186930.0467 77502.7933 165196.3292 192578.8299 0.680101989 0.805015456 0.941125588 0.929242815 0.787930378 0.816796038 0.970667683 0.402447109 0.85781147 1 17.55508959 MELAGSNTTASS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 3 MELAGSNTTASSPAR 15 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 MELAGSNTTAS(0.028)S(0.972)PAR;MELAGSNTTAS(0.001)S(0.999)PAR;MELAGSNTTAS(0.003)S(0.997)PAR 249.89 1.24E-18 492320000 657720 629020 568720 648660 594310 583610 671340 688850 593480 699580 TRUE FALSE 632015.5753 611080.9655 671500.3551 682137.4203 613426.5209 595410.9941 679556.0597 674625.0068 526110.6385 652196.8235 0.969056506 0.936957899 1.029597709 1.045907302 0.940554291 0.912931454 1.041949355 1.034388673 0.806674641 1 19.31494789 MELGAPEEMGQVPPLDS(ph)RPSSPALYFTHDASLVHK ddPTM_BT-474_Pertuzumab_2h_R1 6 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.373)RPS(0.373)S(0.253)PALYFTHDASLVHK;MELGAPEEMGQVPPLDS(0.168)RPS(0.168)S(0.168)PALY(0.16)FT(0.168)HDAS(0.168)LVHK;MELGAPEEMGQVPPLDS(0.413)RPS(0.293)S(0.293)PALYFTHDASLVHK;MELGAPEEMGQVPPLDS(0.333)RPS(0.333)S(0.333)PALYFT(0.001)HDASLVHK;MELGAPEEMGQVPPLDS(0.168)RPS(0.168)S(0.168)PALY(0.158)FT(0.168)HDAS(0.168)LVHK;MELGAPEEMGQVPPLDS(0.318)RPS(0.318)S(0.318)PALY(0.021)FT(0.026)HDAS(0.001)LVHK 208.35 4.43E-28 3676160000 533882 579250 604388 614670 584815 634885 625110 205369.1 762503 738179 TRUE FALSE 513017.3012 562730.3571 713614.3561 646393.1924 603626.1056 647722.8097 632760.2832 201128.1563 675946.8561 688181.4788 0.745468044 0.817706338 1.036956643 0.939277229 0.877132158 0.941209303 0.919467179 0.292260345 0.982221808 1 19.39242954 MELGAPEEMGQVPPLDSRPS(ph)SPALYFTHDASLVHK ddPTM_BT-474_Pertuzumab_2h_R1 2 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.099)RPS(0.448)S(0.448)PALY(0.004)FT(0.001)HDASLVHK;MELGAPEEMGQVPPLDS(0.132)RPS(0.408)S(0.408)PALY(0.034)FT(0.011)HDAS(0.006)LVHK 180.71 1.88E-20 1688540000 867010 1128810 1098690 1311960 1118040 1202040 1298160 298138 1560360 1441820 TRUE FALSE 833126.2907 1096617.444 1297247.723 1379670.413 1154002.772 1226346.072 1314047.27 291981.3461 1383234.474 1344164.247 0.619809887 0.815835897 0.965096138 1.02641505 0.858528096 0.912348379 0.977594273 0.217221479 1.029066557 1 20.35827801 MEVSQEDDKALQLLHDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 MEVSQEDDKALQLLHDIR 18 1 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 0 ; 170.53 9.34E-12 61435000 98655 101528 74703 84318 89083 116870 102817 93935 102304 100689 FALSE TRUE 94799.45353 98632.52085 88203.49386 88669.66208 91948.4356 119233.1915 104075.3052 91995.20942 90690.87881 93869.24435 1.009909627 1.05074374 0.9396421 0.944608244 0.979537401 1.270205085 1.108726356 0.980035688 0.966140502 1 16.51836493 MGSPAPLLPGDLLGGGS(ph)DSI ddPTM_BT-474_Pertuzumab_2h_R1 1 MGSPAPLLPGDLLGGGSDSI 20 0 Q9UPQ9-1;Q9UPQ9;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 MGSPAPLLPGDLLGGGS(0.5)DS(0.5)I 75.479 0.01304 4728200 8271.8 10577 7043.6 7757.4 8815.4 8408.5 11988 7457.9 9339.8 10099 TRUE FALSE 7948.528911 10275.35432 8316.535204 8157.760344 9098.955347 8578.525631 12134.71273 7303.891759 8279.58506 9414.985735 0.844242268 1.091382887 0.88332956 0.866465502 0.966433259 0.911156519 1.288872131 0.775773003 0.87940495 1 13.20074319 MGSS(ph)PLEVPKPR ddPTM_BT-474_Pertuzumab_2h_R1 1 MGSSPLEVPKPR 12 1 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 MGS(0.235)S(0.765)PLEVPKPR 72.209 0.032955 0 162880 164620 154720 164520 180340 176280 152810 165080 200450 225070 TRUE FALSE 156514.4695 159925.1988 182681.3457 173010.8969 186140.7999 179844.5024 154680.1345 161671.0403 177695.7564 209825.8084 0.745925731 0.762180782 0.870633346 0.824545361 0.887120613 0.857113354 0.737183551 0.770501215 0.846872735 1 17.67883261 MHAPGK ddPTM_BT-474_Pertuzumab_2h_R1 6 MHAPGK 6 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;;;; 78.002 0.065696 3309460000 8906470 8903500 7970090 8313190 8570400 8175090 9524990 5843340 10402400 10351170 FALSE TRUE 8558395.306 8649580.897 9410462.557 8742234.732 8846074.699 8340395.921 9641559.677 5722672.987 9221563.162 9650076.036 0.886873355 0.896322564 0.975169783 0.905923922 0.916684456 0.864282923 0.999117483 0.593018435 0.955594871 1 23.20210888 MHCCDEVQPK ddPTM_BT-474_Pertuzumab_2h_R1 2 MHCCDEVQPK 10 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ; 155.42 1.27E-05 845370000 1222790 1160300 1017280 1085200 1111220 1223080 1176050 632900 1519800 1383800 FALSE TRUE 1175002.015 1127209.38 1201125.125 1141207.302 1146963.4 1247811.516 1190442.852 619830.3938 1347278.676 1290073.993 0.910802032 0.873755603 0.931051344 0.884606083 0.889067919 0.967240268 0.922770987 0.480461118 1.044342171 1 20.29902238 MHSPQTSAMLFTVDNEAGK ddPTM_BT-474_Pertuzumab_2h_R1 1 MHSPQTSAMLFTVDNEAGK 19 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 228.01 1.14E-19 548510000 191510 209960 181140 228460 215530 219850 214960 148340 272980 246360 FALSE TRUE 184025.5775 203972.1464 213876.0274 240250.848 222462.7182 224295.5176 217590.7448 145276.7272 241992.4548 229673.8178 0.801247523 0.888094901 0.931216407 1.046052399 0.968602866 0.976582877 0.94739029 0.632534995 1.053635356 1 17.80922688 MITNSLNHDS(ph)PPST(ph)PPRRPDTSTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 MITNSLNHDSPPSTPPRRPDTSTSK 25 2 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;Q8N9M1-3 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 2 MITNSLNHDS(0.976)PPS(0.172)T(0.851)PPRRPDTSTSK 121.5 0.0003441 413610000 356450 369040 278630 335180 334720 343070 370530 331570 374850 394710 TRUE FALSE 342519.5399 358515.3405 328984.6391 352478.68 345486.5728 350007.1105 375064.657 324722.9636 332298.5995 367975.9401 0.930820476 0.974290168 0.89403845 0.957885127 0.938883593 0.951168466 1.019264077 0.882457053 0.903044366 1 18.48925191 MKETAEAYLGK ddPTM_BT-474_Pertuzumab_2h_R1 3 MKETAEAYLGK 11 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 153.75 2.95E-05 3889080000 5296660 5607570 4391690 4667710 4210160 3774890 5450060 5082700 6368490 6009290 FALSE TRUE 5089660.671 5447647.594 5185366.076 4908611.072 4345583.62 3851220.862 5516759.465 4977740.469 5645565.714 5602275.436 0.908498829 0.9723991 0.925582138 0.876181675 0.775681894 0.687438686 0.984735493 0.888521196 1.007727267 1 22.41758148 MKLDYILGLK ddPTM_BT-474_Pertuzumab_2h_R1 1 MKLDYILGLK 10 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 134.2 0.0041194 0 1741000 1799200 1768100 1217100 1572800 983920 1824400 1833900 1873300 1940800 FALSE TRUE 1672959.795 1747888.578 2087635.001 1279914.677 1623390.54 1003815.537 1846727.553 1796029.324 1660650.838 1809347.887 0.924620305 0.966032342 1.1538052 0.707390041 0.897224106 0.554794102 1.020659192 0.992639026 0.917817325 1 20.78703839 MKLPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MKLPGR 6 1 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;F8VUA6;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 110.54 0.026101 1261030000 2107400 2022000 1856200 1938510 1964750 1994380 2144700 2128600 2317000 2248300 FALSE TRUE 2025040.478 1964334.54 2191656.631 2038556.733 2027947.968 2034707.73 2170947.48 2084643.666 2053983.874 2096020.638 0.966135753 0.937173281 1.04562741 0.972584285 0.967522901 0.970747946 1.035747187 0.994572109 0.979944489 1 20.99922149 MLDEMKDNLLLDMYLAPHVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLDEMKDNLLLDMYLAPHVR 20 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ; 204.29 5.87E-22 359900000 445240 439570 362230 381560 427620 458120 419440 429240 495120 501540 FALSE TRUE 427839.5286 427033.894 427693.0188 401252.3573 441374.7857 467383.5003 424573.2322 420376.044 438916.0533 467570.2491 0.91502727 0.913304246 0.914713927 0.85816486 0.943975342 0.999600597 0.90804159 0.899064996 0.938716811 1 18.83482361 MLPHAPGVQMQAIPEDAVHEDS(ph)GDEDGEDPDKR ddPTM_BT-474_Pertuzumab_2h_R1 38 MLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKR 33 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 1 MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR 405.46 1.72E-186 2.11811E+11 25507608 21912749 18983096 19665981 22945394 21528271 22633085 18846742 28446641 24346258 TRUE FALSE 24510742.48 21287818.85 22413763.72 20680944.64 23683453.44 21963587.39 22910075.46 18457550.19 25217497.57 22697264.26 1.079898537 0.93790241 0.987509484 0.911164641 1.043449694 0.967675537 1.009376073 0.813205943 1.111036876 1 24.43601508 MLSLDFLDDVRR ddPTM_BT-474_Pertuzumab_2h_R1 2 MLSLDFLDDVRR 12 1 H0YKT4;H0YNG3;P67812-4;P67812;P67812-3 H0YKT4 SEC11A Signal peptidase complex catalytic subunit SEC11;Signal peptidase complex catalytic subunit SEC11A 0 ; 107.12 0.0029641 170678000 326330 416910 271630 399330 323820 315370 382290 391310 401680 370610 FALSE TRUE 313576.6628 405020.135 320719.5834 419939.4692 334235.9644 321746.9975 386968.5794 383229.3118 356082.9704 345508.2546 0.907580814 1.172244453 0.928254475 1.215425286 0.967374759 0.931228106 1.119998073 1.10917556 1.030606261 1 18.39836065 MNLRSVFT(ph)VEQQRILQRY(ph)YENGMT(ph)NQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 MNLRSVFTVEQQRILQRYYENGMTNQSK 28 3 Q7Z353 Q7Z353 HDX Highly divergent homeobox 3 MNLRS(0.097)VFT(0.93)VEQQRILQRY(0.488)Y(0.488)ENGMT(0.986)NQS(0.01)K;MNLRS(0.11)VFT(0.91)VEQQRILQRY(0.494)Y(0.494)ENGMT(0.978)NQS(0.015)K 46.351 0.055912 43900000000 1545530 1037550 961600 847010 1171240 1023060 1227530 409670 1637730 1110570 TRUE FALSE 1485128.979 1007960.09 1135382.511 890724.2876 1208913.998 1043746.974 1242552.879 401210.1713 1451821.756 1035350.105 1.434422011 0.973545166 1.096616985 0.860312163 1.167637877 1.008110174 1.200128221 0.387511596 1.402252001 1 19.98168727 MPFLSISS(ph)PK ddPTM_BT-474_Pertuzumab_2h_R1 2 MPFLSISSPK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 MPFLSIS(0.077)S(0.923)PK;MPFLSIS(0.001)S(0.999)PK 150.09 2.33E-05 574830000 1500670 1615980 1671730 1281340 1305530 1298090 1357800 1696980 1825850 1583130 TRUE FALSE 1442022.157 1569893.833 1973848.798 1347470.111 1347523.558 1324338.269 1374417.163 1661936.77 1618587.163 1475903.195 0.977043862 1.063683471 1.337383648 0.912980008 0.913016221 0.897307001 0.931238016 1.126047274 1.096675695 1 20.49316667 MPGGPKPGGGPGLSTPGGHPKPPHR ddPTM_BT-474_Pertuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 97.253 0.0030444 315080000 88055 125290 93207 93286 109430 106440 110440 59476 109390 124300 FALSE TRUE 84613.71325 121716.8519 110051.5783 98100.50164 112949.9153 108592.2897 111791.5978 58247.79982 96972.5058 115881.0503 0.730177307 1.050360275 0.949694346 0.846562069 0.974705658 0.937101359 0.964709911 0.502651639 0.836827985 1 16.82228514 MQMELSHK ddPTM_BT-474_Pertuzumab_2h_R1 5 MQMELSHK 8 0 Q9Y6D9;C9JJ38 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 0 ;;;; 95.358 0.0052374 3547670000 4035900 3401790 6000570 2750070 3742800 3182820 4056040 3856170 3899110 4413450 FALSE TRUE 3878172.566 3304774.28 7085006.481 2892001.442 3863190.561 3247178.801 4105679.031 3776538.742 3456499.379 4114523.1 0.942557004 0.803197406 1.721950833 0.702876463 0.938915754 0.789199312 0.997850524 0.917855764 0.840072906 1 21.97229379 MQQMSEQVHTLR ddPTM_BT-474_Pertuzumab_2h_R1 4 MQQMSEQVHTLR 12 0 Q08379;Q08379-2;B7ZC06 Q08379 GOLGA2 Golgin subfamily A member 2 0 ;;; 235.73 4.69E-16 1394250000 1230087 1321753 1046365 1137038 1181864 1287752 1217315 1279000 1402269 1325996 FALSE TRUE 1182013.84 1284057.899 1235466.432 1195720.667 1219879.729 1313791.228 1232212.865 1252588.203 1243089.302 1236185.11 0.956178675 1.03872623 0.999418632 0.96726668 0.98680992 1.062778719 0.996786691 1.013269124 1.005585079 1 20.23746336 MQSLDKDIVALMVR ddPTM_BT-474_Pertuzumab_2h_R1 2 MQSLDKDIVALMVR 14 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 167.55 3.31E-06 375930000 796830 792500 558180 778290 734340 674810 858850 775020 792990 847820 FALSE TRUE 765689.0027 769898.6759 659055.5426 818457.6402 757960.713 688455.1205 869360.8632 759015.5662 702973.0997 790396.3962 0.968740503 0.974066531 0.833829134 1.035502748 0.958962764 0.871025126 1.099904892 0.960297352 0.889393098 1 19.59221684 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK ddPTM_BT-474_Pertuzumab_2h_R1 1 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK 41 2 A0A2R8Y5Y7;P32969;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 142.04 1.78E-13 167050000 105380 96173 74213 66915 87564 97035 87691 91922 105550 85020 FALSE TRUE 101261.6331 93430.2402 87624.93996 70368.49117 90380.57558 98997.11418 88764.18869 90023.77858 93568.4065 79261.51967 1.277563609 1.178759133 1.105516779 0.887801438 1.140283153 1.24899339 1.119890068 1.135781637 1.180502303 1 16.27433301 MS(ph)SVYLKEIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 MSSVYLKEIAK 11 1 Q09MP3 Q09MP3 RAD51AP2 RAD51-associated protein 2 1 MS(0.355)S(0.355)VY(0.29)LKEIAK;MS(0.36)S(0.36)VY(0.28)LKEIAK 61.344 0.053089 317970000 390190 821270 356620 743030 459330 437250 537090 686760 560050 420820 TRUE FALSE 374940.9434 797848.1837 421069.167 781377.8673 474104.7666 446091.4946 543663.0681 672578.166 496475.4719 392317.4866 0.955707957 2.033679892 1.073286767 1.991697781 1.208472176 1.137067579 1.385773224 1.714372132 1.265494119 1 18.58166212 MSTS(ph)QNSIPFEHHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 MSTSQNSIPFEHHGK 15 0 P48730-2 P48730-2 CSNK1D Casein kinase I isoform delta 1 MS(0.166)T(0.166)S(0.581)QNS(0.088)IPFEHHGK;MS(0.018)T(0.015)S(0.927)QNS(0.04)IPFEHHGK 146.67 6.42E-06 880410000 473790 577360 468860 543950 515690 602030 716470 271679 772920 659560 TRUE FALSE 455273.763 560894.2581 553593.4317 572023.3247 532277.6372 614203.4591 725238.3742 266068.7337 685181.3619 614887.4137 0.740418088 0.912190176 0.90031674 0.930289533 0.865650565 0.998887675 1.17946531 0.432711303 1.114320031 1 19.22996275 MSTSQNS(ph)IPFEHHGK ddPTM_BT-474_Pertuzumab_2h_R1 3 MSTSQNSIPFEHHGK 15 0 P48730-2 P48730-2 CSNK1D Casein kinase I isoform delta 1 MSTSQNS(1)IPFEHHGK;MSTSQNS(1)IPFEHHGK;MSTSQNS(1)IPFEHHGK 178.06 1.22E-06 1490510000 1197720 1101940 945030 1091390 1105740 1038880 1212770 531340 1330530 1271840 TRUE FALSE 1150911.778 1070513.75 1115817.943 1147716.769 1141307.131 1059886.865 1227612.242 520367.6433 1179493.812 1185697.144 0.97066252 0.902855974 0.941064882 0.967967895 0.962562099 0.893893412 1.035350594 0.438870622 0.994768199 1 20.17730413 MSVIEEGDCKR ddPTM_BT-474_Pertuzumab_2h_R1 6 MSVIEEGDCKR 11 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;;; 179.6 1.13E-05 3411380000 2325999 2437180 1932236 2086260 2191860 2316550 2212751 2345202 2542205 2461678 FALSE TRUE 2235096.388 2367674.013 2281434.028 2193932.129 2262363.167 2363392.228 2239831.309 2296772.759 2253624.546 2294946.356 0.973920973 1.031690351 0.994112137 0.955984057 0.9858022 1.029824606 0.975984167 1.000795837 0.981994433 1 21.130029 MSYLELMEHPFFTLHK ddPTM_BT-474_Pertuzumab_2h_R1 1 MSYLELMEHPFFTLHK 16 0 P46734-2;P46734;P46734-3 P46734-2 MAP2K3 Dual specificity mitogen-activated protein kinase kinase 3 0 232.93 7.06E-20 159650000 239150 256100 227910 247370 252630 265290 271910 118370 290180 298180 FALSE TRUE 229803.7536 248796.2787 269098.4068 260136.7953 260756.0734 270654.3456 275237.7159 115925.6181 257239.9829 277984.003 0.826679777 0.895002144 0.968035584 0.935797717 0.938025464 0.973632808 0.990120701 0.417022623 0.925376929 1 18.08464234 MTNGFSGADLTEICQR ddPTM_BT-474_Pertuzumab_2h_R1 4 MTNGFSGADLTEICQR 16 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 301.57 1.35E-45 1091120000 399667 428300 330849 457741 433354 456537 416934 429305 420302 463575 FALSE TRUE 384047.5718 416085.3033 390640.774 481365.0679 447293.225 465768.4909 422036.563 420439.7017 372591.079 432176.6523 0.88863563 0.962766732 0.903891434 1.113815532 1.034977763 1.077727102 0.976537165 0.972842238 0.862126811 1 18.72126161 MVNPTVFFDIAVDGEPLGR ddPTM_BT-474_Pertuzumab_2h_R1 2 MVNPTVFFDIAVDGEPLGR 19 0 P62937;F8WE65;C9J5S7;E5RIZ5 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 197.47 1.83E-15 75324000 38322 40924 26161 36654 37108 40553 33786 37926 36234 45676 FALSE TRUE 36824.33387 39756.88759 30888.87465 38545.71733 38301.61252 41373.00945 34199.48317 37142.81485 32120.86823 42582.32384 0.864779809 0.933647674 0.725391944 0.905204645 0.899472107 0.971600554 0.803138018 0.872258992 0.754323985 1 15.37796706 MWDPHNDPNAQGDAFK ddPTM_BT-474_Pertuzumab_2h_R1 7 MWDPHNDPNAQGDAFK 16 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;;; 170.09 5.40E-09 6688340000 11350400 10840000 8961460 9418570 10439660 10361720 10442390 10006090 12233430 11231260 FALSE TRUE 10906813.82 10530853.81 10580995.17 9904663.526 10775461.14 10571241.08 10570187.09 9799460.745 10844742.31 10470556.76 1.041665126 1.005758725 1.010547521 0.945953855 1.02912017 1.009615947 1.009515285 0.935906368 1.03573693 1 23.31983482 MYPIDFEKDDDSNFHMDFIVAASNLR ddPTM_BT-474_Pertuzumab_2h_R1 5 MYPIDFEKDDDSNFHMDFIVAASNLR 26 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;; 217.7 2.19E-34 1641945000 1425715 1474815 1350488 1228854 1461159 1533188 1455564 1481618 1789260 1611670 FALSE TRUE 1369996.482 1432754.72 1594551.223 1292275.302 1508158.506 1564190.112 1473377.628 1451022.071 1586150.706 1502510.155 0.911805139 0.953574067 1.0612582 0.860077583 1.003759276 1.041051274 0.980610762 0.965731956 1.055667212 1 20.51894331 MYSTDDGVQFHAFGR ddPTM_BT-474_Pertuzumab_2h_R1 1 MYSTDDGVQFHAFGR 15 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 148.52 2.67E-06 179890000 109110 93253 106310 129820 111570 93110 110780 109710 111180 122670 FALSE TRUE 104845.8606 90593.51574 125522.5819 136520.0258 115158.7504 94992.74799 112135.7588 107444.4502 98559.3125 114361.4516 0.916793719 0.792168291 1.097595213 1.193759119 1.006971744 0.830636081 0.980538085 0.93951632 0.861822853 1 16.80324131 NAFACFDEEATGTIQEDYLR ddPTM_BT-474_Pertuzumab_2h_R1 4 NAFACFDEEATGTIQEDYLR 20 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;; 252.43 1.04E-35 210915000 159174 174741 132245 157902 153875 147430 145554 165490 182476 176568 FALSE TRUE 152953.3041 169757.5578 156144.6133 166051.3411 158824.5291 150411.1356 147335.3334 162072.5737 161762.0895 164608.8921 0.929192234 1.031278175 0.948579456 1.008762887 0.964859961 0.913748545 0.895063028 0.98459185 0.982705657 1 17.32868275 NAIEHPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 NAIEHPVR 8 0 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 ; 80.231 0.025984 283240000 328570 528480 445900 537250 358990 214286 496790 486590 586690 586210 FALSE TRUE 315729.1211 513408.2678 526484.049 564977.5369 370537.2394 218619.0097 502869.8646 476541.7465 520091.4108 546505.4746 0.57772362 0.939438472 0.963364639 1.033800324 0.678011944 0.400030777 0.920155219 0.871979822 0.951667339 1 19.05987642 NALFPEVFS(ph)PTPDENSDQNSR ddPTM_BT-474_Pertuzumab_2h_R1 1 NALFPEVFSPTPDENSDQNSR 21 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 NALFPEVFS(0.995)PT(0.005)PDENSDQNSR 78.45 0.0056239 16574000 19924 25438 24411 24852 23097 25939 18718 24114 24831 30784 TRUE FALSE 19145.34805 24712.53315 28822.61072 26134.6147 23839.93598 26463.50435 18947.07648 23616.03747 22012.28898 28698.97226 0.667109187 0.861094708 1.004308115 0.910646363 0.830689537 0.922106343 0.660200523 0.822887916 0.767006176 1 14.80871145 NAPAAVDEGSIS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 6 NAPAAVDEGSISPR 14 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGS(0.006)IS(0.994)PR 299.6 9.14E-44 4122840000 1780120 1670100 1382520 1687390 1660210 1646050 1650150 1745890 1886910 1792280 TRUE FALSE 1710550.942 1622470.383 1632372.118 1774476.4 1713612.162 1679334.259 1670345.029 1709836.761 1672715.887 1670887.279 1.023738084 0.971023242 0.976949276 1.061996475 1.025570177 1.005055386 0.999675472 1.023310658 1.001094393 1 20.67218298 NAS(ph)AS(ph)FQELEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 NASASFQELEDK 12 0 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 2 NAS(1)AS(1)FQELEDK;NAS(1)AS(1)FQELEDK 155.79 0.00010619 401970000 1314480 1004260 912150 853170 920220 795480 803110 1230410 1167520 1102730 TRUE FALSE 1263108.668 975619.4881 1076995.796 897202.2059 949819.712 811565.1506 812938.7004 1205001.604 1034988.024 1028041.115 1.22865579 0.949008239 1.04761938 0.872729887 0.923912184 0.78942869 0.790764775 1.172133669 1.006757424 1 19.97146653 NCHLNENIEK ddPTM_BT-474_Pertuzumab_2h_R1 3 NCHLNENIEK 10 0 Q13907;Q13907-2;Q9BXS1 Q13907 IDI1;IDI2 Isopentenyl-diphosphate Delta-isomerase 1;Isopentenyl-diphosphate delta-isomerase 2 0 ;; 183 1.72E-06 1536180000 3922910 3495130 3079370 3415790 3320010 3315310 3664450 1673060 4427900 3783940 FALSE TRUE 3769598.34 3395452.314 3635880.659 3592079.331 3426801.137 3382347.84 3709296.635 1638510.726 3925263.355 3527650.373 1.068586153 0.962525181 1.030680559 1.018263986 0.971411782 0.958810393 1.051492139 0.464476508 1.112713262 1 21.75027615 NDHDDDEDEEVISK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDHDDDEDEEVISK 14 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 0 132.08 5.25E-05 287280000 415160 390740 339440 353900 374270 404820 404400 131650 509770 448900 FALSE TRUE 398935.0882 379596.4778 400784.3588 372164.8214 386308.7345 413005.7378 409349.1682 128931.3815 451903.0467 418495.6032 0.953259927 0.907050098 0.95767878 0.88929207 0.923089111 0.986881904 0.97814449 0.308083001 1.079827466 1 18.67485294 NDHQEDFWK ddPTM_BT-474_Pertuzumab_2h_R1 6 NDHQEDFWK 9 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 163.66 6.28E-05 6749650000 10847820 9755660 8956470 8860020 9801270 9345390 10605110 3920300 13017100 10927240 FALSE TRUE 10423875.2 9477438.129 10575103.36 9317286.694 10116536.75 9534360.189 10734898.51 3839344.435 11539453.38 10187128.3 1.023239807 0.930334619 1.038084831 0.914613659 0.993070515 0.935922264 1.053770817 0.376881916 1.132748409 1 23.28024408 NDLAVVDVR ddPTM_BT-474_Pertuzumab_2h_R1 4 NDLAVVDVR 9 0 P19338 P19338 NCL Nucleolin 0 ;;; 157.24 0.00016053 4418270000 4742310 4557920 3919680 4275220 4391300 4453470 4346830 4871390 4946310 4951640 FALSE TRUE 4556975.282 4427932.584 4628053.369 4495864.617 4532550.153 4543522.215 4400027.806 4770794.094 4384825.625 4616261.012 0.987157197 0.959203254 1.002554526 0.973919067 0.98186609 0.984242919 0.953158366 1.033475811 0.949865186 1 22.13829337 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_BT-474_Pertuzumab_2h_R1 5 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 41 0 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ;;;; 392.33 1.03E-194 9172150000 1963575 1872079 1663190 1813251 1894438 1897547 2021862 212985 2547713 2034235 FALSE TRUE 1886836.318 1818689.14 1963765.43 1906833.101 1955374.319 1935916.7 2046606.152 208586.7853 2258507.301 1896454.452 0.99492836 0.958994369 1.035493064 1.00547266 1.031068433 1.020808435 1.079174957 0.109987764 1.190910385 1 20.85487329 NDPYHPDHFNCANCGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NDPYHPDHFNCANCGK 16 0 P48059;P48059-4;P48059-2;P48059-5;P48059-3;A0A0J9YXC7 P48059 LIMS1 LIM and senescent cell antigen-like-containing domain protein 1 0 ; 132.84 2.14E-05 471770000 605270 559740 465410 519340 478260 553560 542510 43755 743000 555150 FALSE TRUE 581615.3792 543776.7632 549519.94 546143.1996 493643.6672 564753.3625 549149.3997 42851.44396 658657.7549 517549.196 1.12378762 1.050676472 1.061773343 1.055248861 0.953810133 1.09120711 1.061057391 0.082796852 1.272647625 1 18.98133648 NDYEMTFNNETSVMPCEDDHHLPTVQFDFTGIDDLENK ddPTM_BT-474_Pertuzumab_2h_R1 1 NDYEMTFNNETSVMPCEDDHHLPTVQFDFTGIDDLENK 38 0 P27694;I3L4R8 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 62.27 0.0071616 84296000 12502 12800 10294 11696 10726 13349 12664 8996.5 15790 14622 FALSE TRUE 12013.40802 12434.95653 12154.35479 12299.63196 11071.01153 13618.92593 12818.98582 8810.719131 13997.5854 13631.63892 0.881288603 0.912212875 0.891628282 0.902285634 0.812155574 0.999067391 0.940384784 0.646343348 1.026845377 1 13.73467141 NEHTYVHSSATIPLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAK ddPTM_BT-474_Pertuzumab_2h_R1 1 NEHTYVHSSATIPLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAK 45 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 84.972 2.62E-05 261540000 63099 82927 54716 66888 70372 75117 73446 35318 84774 69640 FALSE TRUE 60633.02132 80562.00315 64604.39835 70340.0977 72635.57929 76635.91721 74344.85412 34588.67096 75150.81092 64923.22077 0.933918875 1.240881185 0.995089239 1.083435123 1.118791989 1.180408432 1.145119623 0.532762709 1.157533622 1 15.98644695 NENESEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 NENESEKR 8 1 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 137.14 0.0012204 740730000 495150 449510 338140 375330 356410 443910 442350 464330 497810 463020 FALSE TRUE 475798.9906 436690.4149 399249.4199 394700.8263 367874.2513 452886.1643 447763.6116 454741.4232 441300.6958 431659.243 1.102256 1.011655425 0.924918037 0.914380574 0.852232999 1.049175181 1.037308059 1.053473152 1.022335796 1 18.71953336 NES(ph)PPQVPVYNNSHK ddPTM_BT-474_Pertuzumab_2h_R1 1 NESPPQVPVYNNSHK 15 0 Q9UKL3;A0A087WTW5 Q9UKL3 CASP8AP2 CASP8-associated protein 2 1 NES(1)PPQVPVYNNSHK 80.98 0.0098951 371940000 366750 362320 297110 346640 343720 326360 394070 309210 448550 373590 TRUE FALSE 352417.0045 351986.9883 350804.3862 364530.1319 354776.066 332959.2228 398892.7465 302824.7054 397632.4845 348286.4165 1.011859745 1.010625082 1.007229595 1.046638958 1.018633082 0.95599256 1.145300901 0.86947033 1.141682436 1 18.40991468 NES(ph)SPIRFDILLDDLDTVPVSTLQR ddPTM_BT-474_Pertuzumab_2h_R1 3 NESSPIRFDILLDDLDTVPVSTLQR 25 1 A0A0A0MTP3;Q99550-2;Q99550;F5H1U6 A0A0A0MTP3 MPHOSPH9 M-phase phosphoprotein 9 1 NES(0.561)S(0.439)PIRFDILLDDLDTVPVSTLQR;NES(0.5)S(0.5)PIRFDILLDDLDTVPVSTLQR;NES(0.5)S(0.5)PIRFDILLDDLDTVPVSTLQR 132.57 4.19E-05 158086000 113408 115768 109788 108055 103774 110547 118995 119634 114218 132921 TRUE FALSE 108975.89 112466.41 129629.1338 113631.7315 107111.985 112782.3361 120451.2964 117163.5161 101252.4515 123918.1423 0.879418364 0.907586314 1.046086807 0.916990276 0.864376943 0.910135788 0.972023097 0.945491225 0.817091425 1 16.9190279 NFHQYSVEGGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NFHQYSVEGGK 11 0 Q9HCY8 Q9HCY8 S100A14 Protein S100-A14 0 ; 133.05 0.00016976 874150000 810560 1517910 685710 1788650 772250 698040 1487420 1471080 1502000 975080 FALSE TRUE 778882.4191 1474620.693 809633.0505 1880962.441 797090.1226 712154.8471 1505623.491 1440701.684 1331499.257 909036.9631 0.856821505 1.622179023 0.890649207 2.069181471 0.876851168 0.78341682 1.656284125 1.584865899 1.464736101 1 19.79397943 NGDECAYHHPIS(ph)PCK ddPTM_BT-474_Pertuzumab_2h_R1 4 NGDECAYHHPISPCK 15 0 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;G3V411;Q6PJT7-8;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6;Q6PJT7-6;H0YJ51 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 NGDECAYHHPIS(1)PCK;NGDECAYHHPIS(1)PCK;NGDECAYHHPIS(1)PCK;NGDECAYHHPIS(1)PCK 207.43 5.68E-09 1698950000 2020860 1687120 1447840 1478920 1531810 1636590 1660490 178881 2397340 1992470 TRUE FALSE 1941882.557 1639004.989 1709496.895 1555247.238 1581082.06 1669682.971 1680811.573 175187.0448 2125204.014 1857518.232 1.045417764 0.882362801 0.92031231 0.837271587 0.851179834 0.898878376 0.904869489 0.094312423 1.14410937 1 20.82494494 NGDLDEVKDYVAKGEDVNR ddPTM_BT-474_Pertuzumab_2h_R1 3 NGDLDEVKDYVAKGEDVNR 19 2 P58546 P58546 MTPN Myotrophin 0 ;; 144.18 7.75E-08 495810000 919710 816760 504540 331752 810610 1029500 837190 849000 662910 365579 FALSE TRUE 883766.7164 793466.8045 595721.6014 348873.7605 836684.0068 1050317.195 847435.7817 831467.8533 587659.2359 340818.0087 2.593075172 2.328124642 1.74791703 1.02363652 2.454928981 3.081753806 2.486475949 2.439624175 1.724261104 1 18.37864204 NGHDGDTHQEDDGEKS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 4 NGHDGDTHQEDDGEKSD 17 1 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D 245.11 8.93E-21 1020670000 1177360 874500 886680 970970 992130 847130 1064520 41428.6 1341820 807930 TRUE FALSE 1131347.47 849560.1162 1046922.8 1021081.878 1024042.762 864259.549 1077547.914 40573.08493 1189502.219 753208.1815 1.502038211 1.12792205 1.389951445 1.355643636 1.359574667 1.147437814 1.430611006 0.053867026 1.579247608 1 19.52268915 NHPFFEGVDWER ddPTM_BT-474_Pertuzumab_2h_R1 1 NHPFFEGVDWER 12 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 0 102.5 0.0023469 206780000 179680 188380 166580 177980 186350 189180 189870 117380 193700 219160 FALSE TRUE 172657.907 183007.5868 196684.7116 187165.5691 192344.117 193005.3492 192193.6859 114956.062 171711.9881 204316.098 0.84505288 0.895708114 0.962649118 0.916058847 0.941404612 0.944640932 0.940668345 0.5626383 0.840423196 1 17.64044335 NIDNPALADIYTEHAHQVVVAK ddPTM_BT-474_Pertuzumab_2h_R1 4 NIDNPALADIYTEHAHQVVVAK 22 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;;; 285.82 2.66E-46 2015730000 1782760 1767150 1583730 1652620 1675810 1679470 1753190 77421 2257430 1648260 FALSE TRUE 1713087.768 1716752.612 1869945.241 1737911.916 1729713.951 1713430.034 1774646.064 75822.22929 2001176.01 1536621.882 1.114840149 1.11722515 1.216919571 1.130995163 1.125660106 1.115062888 1.154900945 0.049343453 1.302321693 1 20.55133077 NIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 8 NIIEATHMYDNAAEACSTTEEVFNSPR 27 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACS(0.001)T(0.004)T(0.001)EEVFNS(0.994)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTT(0.005)EEVFNS(0.995)PR 352.71 1.89E-110 4454843000 1140776 1163347 899742 1208018 1048148 1090656 1039248 1112140 1210539 1245267 TRUE FALSE 1096193.213 1130169.483 1062345.394 1270363.954 1081862.632 1112709.812 1051966.628 1089173.92 1073123.688 1160923.957 0.944242046 0.973508623 0.915086115 1.094269738 0.93189793 0.958469162 0.906146024 0.938195748 0.924370353 1 20.14684204 NLPIMSTAS(ph)VEIDDALYSR ddPTM_BT-474_Pertuzumab_2h_R1 7 NLPIMSTASVEIDDALYSR 19 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 1 NLPIMS(0.004)T(0.208)AS(0.788)VEIDDALYSR;NLPIMS(0.028)T(0.201)AS(0.77)VEIDDALYSR;NLPIMST(0.012)AS(0.987)VEIDDALYSR;NLPIMSTAS(1)VEIDDALYSR;NLPIMSTAS(1)VEIDDALYSR;NLPIMSTAS(1)VEIDDALYSR;NLPIMS(0.045)T(0.032)AS(0.924)VEIDDALYSR 274.75 2.14E-39 758535000 157231.7 168682.4 99245.3 132552.9 174585 144190.7 143039.5 163561.5 172760.5 153404.2 TRUE FALSE 151086.9113 163871.7431 117181.1334 139393.9711 180200.6851 147106.3347 144790.0602 160183.8979 153149.4523 143013.9969 1.056448422 1.14584409 0.819368285 0.974687612 1.26002132 1.028614946 1.012418807 1.120057486 1.070870374 1 17.12579683 NLS(ph)FNELYPSGTLK ddPTM_BT-474_Pertuzumab_2h_R1 3 NLSFNELYPSGTLK 14 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 NLS(1)FNELYPSGTLK;NLS(1)FNELYPSGTLK;NLS(1)FNELYPSGTLK 176.33 2.35E-06 436713000 860160 775480 680490 758480 788640 675460 750000 934700 790010 836530 TRUE FALSE 826543.9962 753364.0697 803469.6804 797625.2437 814007.3218 689118.264 759178.7244 915398.1184 700331.3768 779871.078 1.059846966 0.966011038 1.03025962 1.022765514 1.04377165 0.883631004 0.973466956 1.173781339 0.898009167 1 19.57287612 NLYSDDIPHALR ddPTM_BT-474_Pertuzumab_2h_R1 4 NLYSDDIPHALR 12 0 P60228;H0YBR5;E5RIT4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;;; 204.85 1.09E-07 4154970000 3050330 3217780 2722390 3161530 3044420 2993720 3176900 3223500 3624060 3653340 FALSE TRUE 2931119.731 3126012.065 3214386.432 3324696.942 3142346.534 3054255.07 3215779.853 3156933.599 3212671.902 3405896.028 0.860601647 0.917823691 0.943771156 0.976159259 0.92261963 0.896755228 0.944180276 0.926902516 0.943267756 1 21.69960296 NMDPLNDNIATLLHQSSDKFVSELWK ddPTM_BT-474_Pertuzumab_2h_R1 4 NMDPLNDNIATLLHQSSDKFVSELWK 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 243.35 1.99E-45 1934730000 1301311 1899919 1233996 1375597 1344751 1680543 1316979 1461569 1564392 1684172 FALSE TRUE 1250454.327 1845735.17 1457006.527 1446591.726 1388006.137 1714524.731 1333096.583 1431387.089 1386808.779 1570101.53 0.796416221 1.175551475 0.927969624 0.921336422 0.884023173 1.091983351 0.849051196 0.911652566 0.883260574 1 20.58242642 NMVDLVNTHHLHSSS(ph)DDEDDRLK ddPTM_BT-474_Pertuzumab_2h_R1 2 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHS(0.006)S(0.17)S(0.824)DDEDDRLK;NMVDLVNTHHLHS(0.006)S(0.155)S(0.839)DDEDDRLK 162.92 8.05E-12 2223490000 505480 542640 469510 508530 520960 493990 543850 116744 730900 584990 TRUE FALSE 485725.2828 527164.4385 554360.9012 534775.2942 537717.1515 503978.8163 550505.799 114333.1956 647931.2962 545368.1062 0.890637493 0.96662132 1.016489404 0.980576767 0.985971026 0.924107608 1.009420596 0.209644081 1.188062317 1 19.05687081 NPHLITNWGPAAFTEAELEER ddPTM_BT-474_Pertuzumab_2h_R1 2 NPHLITNWGPAAFTEAELEER 21 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 ; 240.85 5.59E-30 214006000 81819 78737 67087 80089 68731 81232 75172 79476 84808 91284 FALSE TRUE 78621.42302 76491.49785 79211.11324 84222.40289 70941.79503 82874.5667 76091.97742 77834.79283 75180.95138 85101.25337 0.923857404 0.898829275 0.930786682 0.989672884 0.833616336 0.973834855 0.894134627 0.914613942 0.883429426 1 16.37689276 NPPPNSDPNLRR ddPTM_BT-474_Pertuzumab_2h_R1 4 NPPPNSDPNLRR 12 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;; 135.1 0.00021443 513691000 122470 137696 95398 132149 107601 140834 113257 125316 131235 123226 FALSE TRUE 117683.737 133769.0449 112638.5407 138969.2257 111062.0839 143681.76 114643.073 122728.1808 116337.753 114879.7933 1.024407632 1.164426233 0.980490455 1.209692512 0.96676779 1.25071395 0.997939409 1.06831826 1.012691176 1 16.80976553 NQAIYAAVDDDDDDAA ddPTM_BT-474_Pertuzumab_2h_R1 2 NQAIYAAVDDDDDDAA 16 0 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 0 ; 203.51 6.42E-11 557980000 1356440 1343140 1086870 1279740 1215190 1340160 1229150 1343250 1436980 1382720 FALSE TRUE 1303428.825 1304834.962 1283291.586 1345787.535 1254277.69 1367258.953 1244192.705 1315511.418 1273860.055 1289067.143 1.011141144 1.012231961 0.995519584 1.044001115 0.973011916 1.060657671 0.965188441 1.020514273 0.988203029 1 20.29789598 NS(ph)ATSADEQPHIGNYR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSATSADEQPHIGNYR 16 0 E9PC69;Q7KZI7-14;E7ETY4;F5H4J8;F5H6N2;F5H4F6;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 NS(0.333)AT(0.333)S(0.333)ADEQPHIGNYR 56.225 0.089212 0 1120.6 0 819 1229.9 0 1072.9 1064.4 1119.1 1020 1281.1 TRUE FALSE 1076.805713 0 967.0115186 1293.375286 0 1094.594773 1077.426446 1095.990194 904.2138762 1194.329956 0.901598179 0 0.809668646 1.082929621 0 0.916492773 0.902117912 0.917661144 0.757088836 1 10.22198575 NS(ph)QKHSPTSEPTPPGDALPPVSSPHTHR ddPTM_BT-474_Pertuzumab_2h_R1 3 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 NS(0.419)QKHS(0.419)PT(0.079)S(0.079)EPT(0.003)PPGDALPPVSSPHTHR;NS(0.247)QKHS(0.247)PT(0.247)S(0.247)EPT(0.01)PPGDALPPVSSPHTHR;NS(0.481)QKHS(0.481)PT(0.032)S(0.006)EPTPPGDALPPVSSPHTHR 95.652 0.0010848 1122410000 230255 296359 252826 303603 244764 323623 328894 36199 398347 313591 TRUE FALSE 221256.38 287907.1315 298517.2823 319271.9872 252637.0563 330166.8788 332919.1032 35451.478 353128.3186 292351.2023 0.756817069 0.984798863 1.021091345 1.092083716 0.864156037 1.129350166 1.138764269 0.121263322 1.207890769 1 18.157343 NSPGLGS(ph)LVSPHGPHMPPAASIPPPPGLGGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPGLGSLVSPHGPHMPPAASIPPPPGLGGVK 32 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 NS(0.302)PGLGS(0.387)LVS(0.302)PHGPHMPPAAS(0.009)IPPPPGLGGVK 100.41 3.92E-05 423130000 310310 290470 266850 275270 292450 298480 319050 43987 453890 401760 TRUE FALSE 298182.7421 282186.08 315075.731 289476.7177 301856.9198 304515.4701 322954.6293 43078.65308 402366.3101 374548.4373 0.796112632 0.753403437 0.841214913 0.772868577 0.805922251 0.813020266 0.862250639 0.115014905 1.074270428 1 18.51479278 NSPGLGSLVS(ph)PHGPHMPPAASIPPPPGLGGVK ddPTM_BT-474_Pertuzumab_2h_R1 1 NSPGLGSLVSPHGPHMPPAASIPPPPGLGGVK 32 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 NS(0.271)PGLGS(0.324)LVS(0.389)PHGPHMPPAAS(0.017)IPPPPGLGGVK 62.683 0.023204 396390000 308700 345980 247330 245620 257030 319990 301380 29617 403400 376340 TRUE FALSE 296635.6627 336112.9891 292028.0328 258296.4776 265297.6034 326460.417 305068.3786 29005.3986 357607.7232 350850.1566 0.845476786 0.957995836 0.832344029 0.736201688 0.756156434 0.930483886 0.869511878 0.082671756 1.019260549 1 18.42049548 NSQKHS(ph)PTSEPTPPGDALPPVSSPHTHR ddPTM_BT-474_Pertuzumab_2h_R1 2 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 NS(0.389)QKHS(0.575)PT(0.03)S(0.006)EPTPPGDALPPVSSPHTHR;NS(0.134)QKHS(0.809)PT(0.046)S(0.011)EPTPPGDALPPVSSPHTHR 148.94 3.45E-08 2472500000 1094840 1359490 1154560 1401510 1215540 1463080 1421250 58862 1808790 1556370 TRUE FALSE 1052052.442 1320718.676 1363214.675 1473842.099 1254638.948 1492664.48 1438643.683 57646.47913 1603463.742 1450955.674 0.725075522 0.91024054 0.939528822 1.015773346 0.86469833 1.028745748 0.991514564 0.039730007 1.105108703 1 20.46857202 NSVLSDPGLDS(ph)PRT(ph)SPVIMAR ddPTM_BT-474_Pertuzumab_2h_R1 1 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(1)PRT(0.75)S(0.25)PVIMAR 153.12 1.06E-07 112290000 14642 19921 17984 19377 13572 17705 16991 24815 16950 20876 TRUE FALSE 14069.77445 19352.87258 21234.10885 20377.04929 14008.55571 18063.00723 17198.94094 24302.56158 15025.90706 19462.04993 0.722933838 0.994390245 1.091052018 1.047014542 0.719788294 0.92811432 0.883716824 1.248715406 0.772061891 1 14.24837606 NTAEWLLSHTK ddPTM_BT-474_Pertuzumab_2h_R1 1 NTAEWLLSHTK 11 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 103.44 0.0023476 0 355350 519530 364190 566730 366240 352990 453920 448030 388000 438870 FALSE TRUE 341462.5291 504713.5131 430007.2344 595979.0032 378020.4422 360127.6997 459475.2087 438778.0239 343955.8666 409144.944 0.834575947 1.233581205 1.050989975 1.456645162 0.923927933 0.880195894 1.123013288 1.072426851 0.840669967 1 18.6422525 NTDDDRPPRR ddPTM_BT-474_Pertuzumab_2h_R1 4 NTDDDRPPRR 10 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 147.37 1.52E-05 1290141000 1847500 1901320 1567124 1644212 1694987 1972760 1763557 1825590 2077330 2105620 FALSE TRUE 1775297.657 1847096.215 1850338.167 1729069.978 1749507.796 2012650.559 1785139.938 1787890.929 1841520.207 1963004.482 0.904377791 0.940953641 0.942605167 0.88082834 0.891239838 1.025290863 0.909391677 0.910793095 0.938113094 1 20.90463204 NTDLYHCLLEHLQR ddPTM_BT-474_Pertuzumab_2h_R1 2 NTDLYHCLLEHLQR 14 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 0 ; 199.37 1.20E-08 798740000 581610 632290 564370 616900 577400 538730 607260 171268 718820 666290 FALSE TRUE 558880.0382 614257.7083 666364.2133 648738.2829 595972.5954 549623.4897 614691.8295 167731.2559 637222.5671 621161.5848 0.899733744 0.988885538 1.072771127 1.04439537 0.959448572 0.884831746 0.989584425 0.270028379 1.025856368 1 19.24460908 NTENCDFLFS(ph)PPEVTGR ddPTM_BT-474_Pertuzumab_2h_R1 2 NTENCDFLFSPPEVTGR 17 0 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91;C9JWI7;Q8IX09;F8WC55 Q9Y6A5 TACC3;ERIC-1s Transforming acidic coiled-coil-containing protein 3 1 NTENCDFLFS(1)PPEVTGR;NTENCDFLFS(1)PPEVTGR 214.34 6.26E-15 168710000 337540 335870 329570 312780 290270 360800 320080 344930 337190 395010 TRUE FALSE 324348.5636 326291.3165 389130.6302 328922.6133 299606.7982 368095.6232 323997.2348 337807.075 298913.6048 368255.6209 0.880770164 0.886045719 1.056686194 0.893191019 0.813583775 0.999565526 0.879816129 0.91731682 0.811701405 1 18.49034802 NTVDLVTTCHIHSSS(ph)DDEIDFK ddPTM_BT-474_Pertuzumab_2h_R1 3 NTVDLVTTCHIHSSSDDEIDFK 22 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;E9PQP7;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 NTVDLVTTCHIHS(0.003)S(0.017)S(0.98)DDEIDFK;NTVDLVTTCHIHS(0.004)S(0.189)S(0.808)DDEIDFK;NTVDLVTTCHIHS(0.051)S(0.051)S(0.899)DDEIDFK 213.54 5.74E-24 2986270000 2683850 2817390 2693560 2928000 3056560 3112870 3353980 712424 4395390 3208700 TRUE FALSE 2578962.175 2737040.796 3180346.21 3079114.431 3154877.028 3175814.364 3395027.011 697712.1954 3896443.754 2991371.891 0.862133586 0.914978443 1.063173128 1.029331873 1.054658913 1.061658155 1.134939798 0.233241543 1.302560797 1 21.51237585 NVPLPEFPEHPFQEEHLK ddPTM_BT-474_Pertuzumab_2h_R1 1 NVPLPEFPEHPFQEEHLK 18 0 A0A3B3ISG5;P14735 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 123.41 1.97E-05 211820000 124770 126100 101760 116200 120610 120810 123140 54830 164310 157270 FALSE TRUE 119893.8505 122503.7515 120150.2956 122197.0959 124489.5302 123252.861 124647.0242 53697.74134 145658.2176 146617.9628 0.817729616 0.835530307 0.819478687 0.833438779 0.849074205 0.840639568 0.850148384 0.366242582 0.993454109 1 17.16170234 NVSSFPDDATS(ph)PLQENR ddPTM_BT-474_Pertuzumab_2h_R1 4 NVSSFPDDATSPLQENR 17 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 NVSSFPDDAT(0.018)S(0.982)PLQENR;NVSSFPDDAT(0.002)S(0.998)PLQENR;NVSSFPDDAT(0.003)S(0.997)PLQENR;NVSSFPDDAT(0.017)S(0.983)PLQENR 387.29 8.98E-122 3319030000 1550320 1612650 1689240 1624640 1525390 1743750 1588130 1626770 1711040 2012230 TRUE FALSE 1489731.78 1566658.801 1994523.245 1708487.865 1574455.555 1779009.82 1607566.01 1593176.631 1516809.912 1875939.87 0.79412555 0.835132739 1.06321278 0.910737008 0.839288924 0.948329874 0.856938986 0.849268496 0.808559985 1 20.83918215 NYDTTIHGK ddPTM_BT-474_Pertuzumab_2h_R1 2 NYDTTIHGK 9 0 J3QRN6;O94832;K7EIG7;J3KRL0 J3QRN6 MYO1D Unconventional myosin-Id 0 ; 121.83 0.00060287 602770000 826190 867360 692630 829190 744510 731780 802840 923440 875500 861280 FALSE TRUE 793901.5814 842623.742 817803.6485 871984.5953 768457.8403 746577.093 812665.3961 904370.6413 776116.9104 802944.7385 0.98873751 1.049416855 1.01850552 1.085983323 0.957049475 0.929798848 1.01210626 1.126317414 0.966588201 1 19.61494117 PAS(ph)PSLQLLPWR ddPTM_BT-474_Pertuzumab_2h_R1 6 PASPSLQLLPWR 12 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 PAS(0.9)PS(0.1)LQLLPWR;PAS(0.987)PS(0.013)LQLLPWR;PAS(0.993)PS(0.007)LQLLPWR;PAS(0.935)PS(0.065)LQLLPWR;PAS(0.999)PS(0.001)LQLLPWR;PAS(0.998)PS(0.002)LQLLPWR 210.41 4.61E-08 1546050000 1049091 908351 802721 744328 749910 641699 950450 935889 1127706 1033996 TRUE FALSE 1008091.364 882445.7188 947790.5411 782742.8573 774031.5362 654674.5934 962081.8914 916562.5651 999693.5426 963962.5299 1.045778578 0.915435706 0.983223426 0.81200548 0.802968489 0.67914942 0.998049054 0.950828001 1.037066807 1 19.87861754 PHIDNDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 PHIDNDVK 8 0 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YMB3;H0YNH0;H0YMV5;A0A0B4J281;H0YMG3;H0YMR9 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 ; 122.52 0.0014499 231730000 797070 586260 608010 522690 628810 674460 660720 360920 837580 708290 FALSE TRUE 765919.6232 569540.4388 717890.9321 549666.0935 649036.2447 688098.0433 668806.089 353466.8759 742501.4298 660316.8874 1.159927359 0.862525932 1.087191538 0.832427739 0.98291632 1.04207246 1.012856254 0.535298858 1.124462276 1 19.33279902 PHVMS(ph)PGNR ddPTM_BT-474_Pertuzumab_2h_R1 1 PHVMSPGNR 9 0 P54259 P54259 ATN1 Atrophin-1 1 PHVMS(1)PGNR 85.813 0.0077497 0 108910 82024 100880 76127 87923 94871 95421 44692 122300 96385 TRUE FALSE 104653.6768 79684.75583 119111.2601 80055.92359 90751.12314 96789.35662 96588.79074 43769.09458 108417.0167 89856.7581 1.164672296 0.886797582 1.325568189 0.890928243 1.009953231 1.077151665 1.074919603 0.487098528 1.206553842 1 16.45533939 PLENLEEEGLPKNPDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 PLENLEEEGLPKNPDLR 17 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 144.68 4.59E-07 204858000 366220 303420 235323 213045 272280 343120 263070 305580 351900 291010 FALSE TRUE 351907.7175 294766.7587 277851.1008 224040.278 281038.1335 350058.1215 266289.5294 299269.6662 311953.7873 271299.6335 1.297118293 1.08649892 1.024148456 0.825803836 1.035895736 1.290300753 0.981532949 1.103096463 1.149849645 1 18.04952757 PLPPAAIES(ph)PAVAAPAYSR ddPTM_BT-474_Pertuzumab_2h_R1 1 PLPPAAIESPAVAAPAYSR 19 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 PLPPAAIES(1)PAVAAPAYSR 61.375 0.033432 0 8035.5 8931.4 6401.4 13814 9050.1 16783 6092.3 11377 10422 7932.1 TRUE FALSE 7721.463776 8676.685217 7558.275378 14526.9422 9341.204686 17122.36376 6166.85939 11142.06097 9238.938253 7394.851802 1.044167481 1.173341326 1.022099642 1.964466981 1.263203771 2.3154438 0.833939551 1.506732153 1.249374362 1 12.85230552 PQNEYIELHR ddPTM_BT-474_Pertuzumab_2h_R1 1 PQNEYIELHR 10 0 O95478;A0A0A0MQZ6 O95478 NSA2 Ribosome biogenesis protein NSA2 homolog 0 73.781 0.036874 0 140140 140740 105100 128140 126490 130190 103700 137740 142070 146200 FALSE TRUE 134663.1739 136726.233 124093.9079 134753.3208 130558.6657 132822.531 104969.1116 134895.6209 125942.8092 136297.7438 0.988007359 1.003143773 0.910461938 0.988668756 0.957893081 0.974502786 0.770145629 0.989712794 0.924027102 1 17.05640215 PVFAFHHANFPQYVMDVLMDQHFTEPTPIQCQGFPLALSGR ddPTM_BT-474_Pertuzumab_2h_R1 1 PVFAFHHANFPQYVMDVLMDQHFTEPTPIQCQGFPLALSGR 41 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 154.08 2.72E-14 95175000 76680 70642 66807 86067 87869 66850 88028 42152 101580 75882 FALSE TRUE 73683.26083 68627.35933 78880.51101 90508.92818 90695.38619 68201.7528 89105.313 41281.54647 90049.06426 70742.44455 1.041570747 0.97010161 1.115037959 1.279414767 1.282050497 0.964085327 1.259573564 0.583547073 1.272914229 1 16.11028845 PVSS(ph)AASVYAGAGGSGSR ddPTM_BT-474_Pertuzumab_2h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVS(0.001)S(0.559)AAS(0.374)VYAGAGGS(0.065)GS(0.001)R 206.73 8.60E-16 291950000 425960 298170 265340 206310 260250 270820 237490 283120 269450 269780 TRUE FALSE 409313.0123 289666.4835 313292.8405 216957.6838 268621.1776 276296.166 240396.4737 277273.4731 238863.1656 251507.5603 1.627438204 1.15172078 1.245659733 0.862628875 1.068044147 1.098560082 0.955822057 1.102445878 0.949725588 1 17.94024224 QAS(ph)LPVSGSVAGDFVK ddPTM_BT-474_Pertuzumab_2h_R1 1 QASLPVSGSVAGDFVK 16 0 Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;H0Y7R3;H0Y493;H0Y7J9;E9PCD1 Q9Y3S1 WNK2 Serine/threonine-protein kinase WNK2 1 QAS(0.999)LPVS(0.001)GSVAGDFVK 137.44 1.26E-05 92774000 118910 92473 48157 80710 99701 80308 84242 154860 90703 82389 TRUE FALSE 114262.8657 89835.76058 56860.04115 84875.45277 102907.9732 81931.88278 85272.9788 151662.0869 80406.7757 76808.71965 1.48762883 1.169603673 0.74028107 1.105023664 1.339795451 1.06670028 1.110199196 1.974542573 1.04684437 1 16.22898248 QDNCVHDLQAHNK ddPTM_BT-474_Pertuzumab_2h_R1 2 QDNCVHDLQAHNK 13 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ; 199.38 6.84E-08 1211310000 518410 482650 395640 461930 507630 515740 494010 107412 621930 529610 FALSE TRUE 498149.9641 468885.2946 467140.949 485770.2627 523958.38 526168.6162 500055.8422 105193.9047 551331.1137 493739.043 1.008933709 0.949662177 0.946129247 0.98386034 1.061205079 1.065681606 1.012793801 0.213055674 1.116644757 1 18.91338921 QDYINLDESEAAAFDDEWRR ddPTM_BT-474_Pertuzumab_2h_R1 4 QDYINLDESEAAAFDDEWRR 20 1 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 0 ;;; 257.72 5.03E-36 441317000 242034 262766 183221 240544 251211 262317 226100 239319 257805 252479 FALSE TRUE 232575.0437 255272.171 216333.1104 252958.5047 259291.43 267621.2295 228867.0794 234376.979 228540.0572 235378.3724 0.988090118 1.084518379 0.91908661 1.074688817 1.101594115 1.136983091 0.97233691 0.995745601 0.970947563 1 17.84462224 QEFMDGMTELGCDSIEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QEFMDGMTELGCDSIEK 17 0 C9JVE2;Q96GG9;C9J8R4 C9JVE2 DCUN1D1 DCN1-like protein;DCN1-like protein 1 0 151.9 2.66E-08 0 57983 58102 46325 47773 55238 47404 57965 60066 63216 56509 FALSE TRUE 55716.96026 56444.98785 54696.95799 50238.57026 57014.78044 48362.54136 58674.39301 58825.61611 56039.9847 52681.5951 1.057617184 1.071436576 1.038255541 0.953626597 1.082252356 0.918015889 1.113755058 1.116625569 1.063748822 1 15.68501141 QEKRPLFLAPDFDRWLDES(ph)DAEMELR ddPTM_BT-474_Pertuzumab_2h_R1 1 QEKRPLFLAPDFDRWLDESDAEMELR 26 3 H3BS72;Q9P035;H3BPZ1 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 1 QEKRPLFLAPDFDRWLDES(1)DAEMELR 48.697 0.095789 20474000 10444 10274 8307.6 8430.5 16247 12351 15947 7887.3 16376 4151.4 TRUE FALSE 10035.83693 9980.995579 9808.968122 8865.599115 16769.59951 12600.74568 16142.16416 7724.424499 14517.06513 3870.22198 2.59309078 2.5789207 2.53447171 2.290721091 4.332981311 3.255819885 4.170862612 1.995860842 3.750964469 1 11.9182006 QENQEAVGGFFSQIGELYVVHHLWAYK ddPTM_BT-474_Pertuzumab_2h_R1 1 QENQEAVGGFFSQIGELYVVHHLWAYK 27 0 Q9BPW8 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 193.14 1.62E-18 122060000 104490 147190 87670 199320 85498 92020 158510 84312 147340 117650 FALSE TRUE 100406.4153 142992.2853 103513.9192 209606.9291 88248.12082 93880.70745 160449.8928 82570.92774 130614.5809 109681.4607 0.915436525 1.303705151 0.943768605 1.911051583 0.804585572 0.855939617 1.46287159 0.752824837 1.190853769 1 16.74296016 QEVPSWLENMAYEHHYK ddPTM_BT-474_Pertuzumab_2h_R1 6 QEVPSWLENMAYEHHYK 17 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;;;; 188.58 2.33E-10 3048170000 3860110 3980990 3458210 3735020 3943790 4069390 4113820 1796459 4785440 4537210 FALSE TRUE 3709252.634 3867456.063 4083185.474 3927784.83 4070645.587 4151675.854 4164166.16 1759361.494 4242216.913 4229900.725 0.876912456 0.914313672 0.965314729 0.928576126 0.962350148 0.981506689 0.984459549 0.415934465 1.002911697 1 22.01219237 QFCQEGQPHVLEALSPPQTSGLS(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 4 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 QFCQEGQPHVLEALSPPQTSGLS(0.994)PS(0.006)R;QFCQEGQPHVLEALSPPQTSGLS(0.898)PS(0.102)R;QFCQEGQPHVLEALSPPQT(0.004)S(0.123)GLS(0.841)PS(0.032)R;QFCQEGQPHVLEALSPPQTS(0.002)GLS(0.868)PS(0.13)R 251.57 7.69E-48 1611330000 679530 753920 595050 760790 720690 711520 767070 776030 766060 877770 TRUE FALSE 652973.2163 732418.9398 702588.7718 800054.4631 743871.6484 725907.4219 776457.6321 760004.7093 679100.0804 818317.8561 0.797945702 0.895029889 0.858576856 0.977681786 0.909025317 0.88707269 0.948846009 0.928740224 0.829873228 1 19.64230181 QFEEIWER ddPTM_BT-474_Pertuzumab_2h_R1 6 QFEEIWER 8 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;;;; 158.61 0.00084673 1723166000 1307189 1415024 1194020 1385392 1352925 1190397 1360893 1432997 1342071 1406443 FALSE TRUE 1256102.609 1374668.901 1409805.975 1456892.247 1396443.061 1214467.643 1377548.016 1403405.111 1189724.727 1311183.363 0.95799157 1.048418505 1.075216491 1.111127771 1.065025 0.926237838 1.050614319 1.070334746 0.907367162 1 20.32243802 QFGAQVHR ddPTM_BT-474_Pertuzumab_2h_R1 1 QFGAQVHR 8 0 Q8NFW8;Q8NFW8-2 Q8NFW8 CMAS N-acylneuraminate cytidylyltransferase 0 113.71 0.0027969 106110000 242380 199960 177080 215500 177670 163700 213050 256960 194310 221410 FALSE TRUE 232907.5216 194257.3366 209082.2951 226621.9808 183384.9169 167010.1262 215657.3696 251653.6862 172252.7434 206413.7035 1.128353 0.941106784 1.012928365 1.09790182 0.888433829 0.809103869 1.044782231 1.219171411 0.83450246 1 17.65517923 QFQGHTDGASCIDISHDGTK ddPTM_BT-474_Pertuzumab_2h_R1 1 QFQGHTDGASCIDISHDGTK 20 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YNI7 H0YKT5 TLE3 Transducin-like enhancer protein 3 0 192.98 5.21E-18 295940000 131530 124000 96955 111370 104900 128970 118570 72791 138380 129780 FALSE TRUE 126389.6622 120463.6414 114476.9253 117117.819 108274.2038 131577.8618 120021.0951 71287.84041 122671.6825 120989.885 1.044629989 0.995650516 0.946169386 0.96799678 0.89490294 1.087511256 0.991992803 0.58920496 1.013900315 1 16.88452691 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK ddPTM_BT-474_Pertuzumab_2h_R1 2 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK 32 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 188.17 4.88E-20 1115220000 597120 610690 486200 595930 597970 626180 625240 51177 738400 573060 FALSE TRUE 573783.8902 593273.7191 574067.1555 626686.0187 617204.2481 638841.7886 632891.8742 50120.17707 654579.9276 534246.1358 1.074006627 1.110487619 1.074536842 1.173028641 1.155280697 1.195781768 1.184644739 0.093814768 1.22524036 1 19.02714504 QHFPATPLLDYALEVEK ddPTM_BT-474_Pertuzumab_2h_R1 2 QHFPATPLLDYALEVEK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 159.26 3.24E-09 523680000 645180 565440 495250 494900 551860 582990 589220 452290 650590 654770 FALSE TRUE 619965.6523 549314.2048 584752.6918 520441.8483 569611.0781 594778.4572 596431.0506 442950.0534 576737.7507 610421.8447 1.015634774 0.89989277 0.957948502 0.852593748 0.933143339 0.974372825 0.977080122 0.725645809 0.944818335 1 19.21944707 QHIAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 QHIAEK 6 0 Q96TA1 Q96TA1 FAM129B Niban-like protein 1 0 68.422 0.096181 149310000 263740 266890 225790 256980 258980 268100 282710 171530 302470 303100 FALSE TRUE 253432.7492 259278.5585 266595.2757 270242.7686 267310.3269 273521.1657 286169.8895 167987.8456 268134.8737 282570.767 0.896882405 0.917570353 0.943463751 0.956371996 0.945994271 0.967974036 1.012737066 0.594498317 0.94891229 1 18.1082527 QHIPYREDK ddPTM_BT-474_Pertuzumab_2h_R1 2 QHIPYREDK 9 1 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;Q8N752;U3KQ83 P48729-2 CSNK1A1;CSNK1A1L Casein kinase I isoform alpha;Casein kinase I isoform alpha-like 0 ; 64.297 0.042321 1513910000 2798000 2672300 2192420 2199960 2486100 2547000 2538200 1105200 3127000 2702000 FALSE TRUE 2688651.067 2596088.62 2588639.064 2313500.199 2566067.664 2598502.085 2569263.251 1082377.234 2772036.069 2518991.133 1.067352334 1.030606494 1.027649137 0.91842332 1.018688645 1.031564602 1.019957243 0.429686798 1.100454874 1 21.26441461 QHLENDPGSNEDTDIPK ddPTM_BT-474_Pertuzumab_2h_R1 4 QHLENDPGSNEDTDIPK 17 0 O43396;K7ER96;K7EML9 O43396 TXNL1 Thioredoxin-like protein 1 0 ;;; 228.46 1.43E-15 3445120000 2053220 1962000 1719830 1923920 1993210 1968150 2183410 828580 2667990 2346870 FALSE TRUE 1972977.892 1906045.681 2030641.538 2023213.742 2057323.41 2007947.341 2210131.225 811469.5334 2365130.96 2187914.405 0.901761919 0.871170132 0.92811745 0.924722529 0.940312567 0.917744925 1.010154337 0.370887239 1.080997938 1 21.06112487 QHMDITGEENPLNK ddPTM_BT-474_Pertuzumab_2h_R1 4 QHMDITGEENPLNK 14 0 Q9H4A4;A6NKB8;C9JMZ3 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 258.91 2.13E-24 2418420000 1913850 1817650 1610900 1640210 1764700 1950280 1956390 1188520 2357330 2110840 FALSE TRUE 1839054.626 1765812.402 1902025.464 1724861.435 1821463.178 1989715.998 1980332.886 1163976.647 2089735.781 1967870.927 0.934540269 0.897321251 0.966539745 0.876511468 0.925600939 1.011100866 1.006332712 0.591490342 1.06192726 1 20.90820417 QHSITK ddPTM_BT-474_Pertuzumab_2h_R1 1 QHSITK 6 0 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 97.602 0.040885 86768000 305690 297550 271740 303130 277700 291690 312030 203210 341960 313840 FALSE TRUE 293743.2968 289064.1653 320849.4628 318774.5756 286632.4727 297588.1717 315848.7165 199013.6425 303142.1344 292583.3373 1.003964544 0.98797207 1.096608802 1.089517191 0.979660959 1.017105671 1.079517102 0.680194725 1.03608817 1 18.15848808 QHVIDGEK ddPTM_BT-474_Pertuzumab_2h_R1 6 QHVIDGEK 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;;; 103.55 0.0047518 4950709000 8384850 7973250 6767310 7431250 7369830 7764110 7898100 5198220 9435060 8813200 FALSE TRUE 8057160.792 7745860.717 7990313.455 7814777.703 7606887.275 7921105.624 7994759.31 5090874.94 8364031.544 8216274.114 0.98063437 0.942746141 0.972498403 0.951134005 0.92583173 0.964075141 0.973039507 0.619608702 1.017983508 1 22.97005288 QHVPEQHPK ddPTM_BT-474_Pertuzumab_2h_R1 4 QHVPEQHPK 9 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ;;; 95.573 0.0045993 472913000 877380 914360 760290 850540 873760 901780 943390 163327 1061770 888320 FALSE TRUE 843091.0196 888283.3481 897691.3156 894436.4713 901865.2839 920014.6095 954935.489 159954.2404 941242.3209 828153.2952 1.018037391 1.072607394 1.083967571 1.080037327 1.089007662 1.11092308 1.153090249 0.193145691 1.136555667 1 19.65953832 QIFEDHVFCHSL ddPTM_BT-474_Pertuzumab_2h_R1 1 QIFEDHVFCHSL 12 0 Q13137;Q13137-3;Q13137-4;Q13137-5;Q13137-2 Q13137 CALCOCO2 Calcium-binding and coiled-coil domain-containing protein 2 0 114.72 0.0010271 185990000 245110 244040 206890 241500 221770 235720 245330 161860 276930 292530 FALSE TRUE 235530.8302 237080.2181 244279.6252 253963.8439 228903.4335 240486.4199 248332.4219 158517.5344 245494.0674 272716.6825 0.86364658 0.86932789 0.895726741 0.931236922 0.839345182 0.881817781 0.910587572 0.58125353 0.900179868 1 18.05704343 QKIDDR ddPTM_BT-474_Pertuzumab_2h_R1 2 QKIDDR 6 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ; 77.72 0.06537 288950000 1010960 1019490 776480 1162730 1008970 963510 1115310 1026120 1024480 1107670 FALSE TRUE 971450.5655 990415.1434 916807.2087 1222738.635 1041424.436 982992.8324 1128959.497 1004930.263 908185.3254 1032646.524 0.940738716 0.95910374 0.887822878 1.184082458 1.008500403 0.951916081 1.093268094 0.973159973 0.87947357 1 19.97791507 QLHDDYFYHDEL ddPTM_BT-474_Pertuzumab_2h_R1 3 QLHDDYFYHDEL 12 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;; 232.17 1.71E-12 2698330000 1384010 1604810 1403000 1767630 1603540 1756540 1720750 411559 1894340 1648280 FALSE TRUE 1329921.359 1559042.39 1656553.31 1858857.596 1655119.32 1792058.442 1741809.053 403060.1628 1679302.465 1536640.527 0.865473307 1.014578467 1.078035676 1.209689295 1.077102478 1.16621839 1.133517581 0.262299579 1.09284015 1 20.55134828 QLSQHEENELAEEPEALADGLCSMKLS(ph)PPCK ddPTM_BT-474_Pertuzumab_2h_R1 2 QLSQHEENELAEEPEALADGLCSMKLSPPCK 31 1 Q7Z319;A0A499FJN1;A0A499FIS5;Q9BUB5-2;Q9BUB5 Q7Z319 DKFZp686E14208;MKNK1 MAP kinase-interacting serine/threonine-protein kinase 1 1 QLSQHEENELAEEPEALADGLCSMKLS(1)PPCK;QLSQHEENELAEEPEALADGLCS(0.144)MKLS(0.856)PPCK 358.25 4.49E-121 279010000 323490 349210 246020 241190 287570 362540 285440 305370 382690 354440 TRUE FALSE 310847.6532 339250.8727 290481.2867 253637.8448 296819.9502 369870.8072 288933.3001 299064.0028 339248.6356 330433.4631 0.940726917 1.026684372 0.879091615 0.76759128 0.898274489 1.119350334 0.8744069 0.905065728 1.026677602 1 18.33400027 QQADKESEVSPS(ph)R ddPTM_BT-474_Pertuzumab_2h_R1 1 QQADKESEVSPSR 13 1 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 QQADKES(0.008)EVS(0.366)PS(0.625)R 100.23 0.0016491 0 114900 111360 79962 97981 108510 113690 96278 104120 116270 110690 TRUE FALSE 110409.581 108184.1218 94412.91215 103037.8112 112000.3227 115988.8897 97456.27896 101969.8856 103071.517 103192.8677 1.069934225 1.048368208 0.914917031 0.99849741 1.085349455 1.124001031 0.944409058 0.988148579 0.99882404 1 16.65498374 QQHVIETLIGK ddPTM_BT-474_Pertuzumab_2h_R1 1 QQHVIETLIGK 11 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 101.39 0.0077158 204710000 210040 224410 185530 210870 165530 180360 182450 222470 231420 244090 FALSE TRUE 201831.4046 218010.0465 219059.3981 221753.026 170854.4228 184007.0028 184682.8777 217875.9168 205150.1718 227557.5669 0.886946575 0.958043494 0.962654862 0.974491989 0.750818464 0.808617377 0.811587504 0.957454062 0.901530872 1 17.79587203 QQQQQQGEDGS(ph)PQAHRR ddPTM_BT-474_Pertuzumab_2h_R1 1 QQQQQQGEDGSPQAHRR 17 1 A0A087WUX9;E9PEG3;A0A087WZ66;F5GZG9;P10275-3;P10275-4;P10275 A0A087WUX9 AR Androgen receptor 1 QQQQQQGEDGS(1)PQAHRR 56.327 0.033985 0 1802.1 4154.4 2198.8 2282 2294.1 4315.4 2476.4 2428.4 2910.2 2827.9 TRUE FALSE 1731.67194 4035.92058 2596.172072 2399.774293 2367.89181 4402.660345 2506.706924 2378.252691 2579.846297 2636.363814 0.656841036 1.530866323 0.984754857 0.910259153 0.898165798 1.669974501 0.950819804 0.902095788 0.978562322 1 11.36433376 QSHSES(ph)PSLQSK ddPTM_BT-474_Pertuzumab_2h_R1 7 QSHSESPSLQSK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSES(1)PSLQSK;QSHSES(1)PSLQSK;QSHSES(0.999)PS(0.001)LQSK;QSHSES(1)PSLQSK;QSHSES(1)PSLQSK;QSHSES(0.806)PS(0.193)LQSK;QS(0.006)HS(0.002)ES(0.992)PSLQSK 294.26 3.41E-36 30143410000 10987020 10419720 9195460 9936670 9909060 10632110 10475060 9151250 12814440 11448830 TRUE FALSE 10557635.11 10122559.79 10857284.17 10449502.73 10227793.91 10847098.55 10603256.92 8962273.49 11359798.49 10673390.55 0.989154764 0.948392148 1.017229167 0.97902374 0.958251632 1.016274866 0.993429114 0.839683833 1.064310206 1 23.3475152 QSPGHQS(ph)PLASPK ddPTM_BT-474_Pertuzumab_2h_R1 1 QSPGHQSPLASPK 13 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 QS(0.001)PGHQS(0.999)PLASPK 109.87 0.00071054 125690000 195170 207130 175050 207910 193530 189700 207100 206980 228690 232620 TRUE FALSE 187542.5406 201222.8552 206685.429 218640.26 199755.0682 193535.864 209634.5518 202705.7907 202730.0699 216864.4402 0.864791574 0.927873906 0.953062792 1.008188617 0.921105683 0.89242784 0.966661715 0.934711982 0.934823938 1 17.72643398 QSPGS(ph)TSPKPPHTLSR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSPGSTSPKPPHTLSR 16 1 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 QSPGS(0.331)T(0.331)S(0.331)PKPPHT(0.003)LS(0.005)R 64.249 0.037481 214690000 189710 163210 148130 154730 154410 166690 158960 187790 187320 174210 TRUE FALSE 182295.9235 158555.4106 174900.3861 162715.6338 159376.7379 170060.586 160905.4 183912.0709 166056.2189 162410.6015 1.122438571 0.976262689 1.07690252 1.001878155 0.981319793 1.047102741 0.990732123 1.132389568 1.022446918 1 17.30928628 QSTGSAPQGPAYHGVNR ddPTM_BT-474_Pertuzumab_2h_R1 1 QSTGSAPQGPAYHGVNR 17 0 O14497;H0Y488;A0A1B0GTU5;O14497-3 O14497 ARID1A AT-rich interactive domain-containing protein 1A 0 116.29 0.0002732 124390000 55024 63685 45265 55493 52589 61323 57819 53394 68977 66241 FALSE TRUE 52873.60125 61868.76615 53445.39241 58357.00038 54280.57295 62562.99308 58526.60622 52291.39524 61147.02014 61754.43807 0.856191116 1.001851334 0.865450227 0.94498472 0.878974445 1.013093067 0.947731176 0.846763356 0.990163979 1 15.9142552 QVDLESNPQNRSPES(ph)RPSVVYPSTK ddPTM_BT-474_Pertuzumab_2h_R1 1 QVDLESNPQNRSPESRPSVVYPSTK 25 2 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 QVDLES(0.007)NPQNRS(0.432)PES(0.561)RPSVVYPSTK 95.302 0.0052259 488400000 260210 237100 168550 163590 213040 234090 207990 246640 254490 209120 TRUE FALSE 250040.7055 230338.1401 199010.7344 172032.8995 219892.6251 238823.4602 210535.4438 241546.7978 225601.3621 194956.1161 1.28254866 1.18148712 1.020797594 0.882418582 1.127908318 1.225011377 1.079911972 1.238980354 1.157190483 1 17.57278989 QWLQEIDR ddPTM_BT-474_Pertuzumab_2h_R1 4 QWLQEIDR 8 0 Q9H0U4;E9PLD0;Q92928;P62820;E7END7;P62820-2 Q9H0U4;P62820 RAB1B;RAB1C;RAB1A Ras-related protein Rab-1B;Putative Ras-related protein Rab-1C;Ras-related protein Rab-1A 0 ;;; 136.8 0.0018044 5272000000 1163460 1488860 1131680 1476110 1164380 1037560 1523430 1530890 1502900 1578080 FALSE TRUE 1117990.697 1446399.171 1336199.75 1552292.214 1201833.34 1058540.174 1542074.192 1499276.587 1332297.093 1471195.236 0.759920009 0.983145632 0.908240944 1.055123192 0.816909483 0.719510333 1.048177804 1.01908744 0.905588232 1 20.48855728 QYEMGECTR ddPTM_BT-474_Pertuzumab_2h_R1 2 QYEMGECTR 9 0 P0DN76;Q01081;Q8WU68-3;Q8WU68;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1;U2AF1L4 Splicing factor U2AF 35 kDa subunit;Splicing factor U2AF 26 kDa subunit 0 ; 174.48 0.00012712 1237800000 474240 498180 367700 454550 515870 425220 448220 443630 497180 472810 FALSE TRUE 455706.1765 483972.3942 434151.5694 478009.38 532463.4271 433818.2397 453705.4504 434468.8855 440742.2107 440786.1576 1.033848656 1.097975483 0.984948284 1.084447349 1.207985818 0.984192068 1.029309661 0.98566817 0.999900299 1 18.74971939 RAAATQPDAK ddPTM_BT-474_Pertuzumab_2h_R1 2 RAAATQPDAK 10 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 115.57 0.0019319 235980000 411150 398410 295400 331100 318220 381830 373230 400730 429710 434830 FALSE TRUE 395081.8034 387047.7369 348785.3511 348188.1107 328455.8353 389550.8642 377797.7004 392454.7855 380931.1223 405378.5768 0.974599611 0.954780936 0.860394138 0.858920847 0.81024468 0.960955725 0.931962669 0.968119205 0.939692288 1 18.62891032 RAAS(ph)SDQLR ddPTM_BT-474_Pertuzumab_2h_R1 3 RAASSDQLR 9 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RAAS(0.889)S(0.111)DQLR;RAAS(0.904)S(0.096)DQLR;RAAS(0.976)S(0.024)DQLR 126.48 0.00050033 1363466000 1115408 1111794 835557 1124486 1023439 922384 979109 1426528 1014392 1032201 TRUE FALSE 1071816.622 1080086.724 986560.7368 1182520.857 1056358.845 941035.2365 991091.6288 1397069.698 899242.4728 962289.1069 1.11381976 1.122413956 1.025222804 1.228862354 1.097756212 0.977913217 1.029931256 1.451819093 0.934482648 1 19.87611087 RAELPGSSS(ph)PLLAQPR ddPTM_BT-474_Pertuzumab_2h_R1 3 RAELPGSSSPLLAQPR 16 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RAELPGSS(0.003)S(0.997)PLLAQPR;RAELPGSS(0.036)S(0.964)PLLAQPR;RAELPGS(0.001)S(0.207)S(0.792)PLLAQPR 197.88 2.58E-11 2513820000 667740 742900 557950 675670 665060 583170 720390 778770 720890 740420 TRUE FALSE 641643.9826 721713.2194 658783.9765 710541.4097 686452.2589 594962.097 729206.3483 762688.1274 639057.5894 690270.6939 0.929554142 1.045551007 0.954384972 1.029366328 0.994468206 0.861925767 1.056406356 1.104911644 0.925807216 1 19.39680271 RAPAPPPPQPPPPS(ph)PLIPNR ddPTM_BT-474_Pertuzumab_2h_R1 2 RAPAPPPPQPPPPSPLIPNR 20 1 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;A0A0J9YWK3;A0A3B3IU00;O75128-5;O75128-4 H7C1N2;O75128-3 COBL Protein cordon-bleu 1 RAPAPPPPQPPPPS(1)PLIPNR;RAPAPPPPQPPPPS(1)PLIPNR 152.41 3.96E-08 1403110000 235042 306632 294707 338098 264046 277892 239569 318665 298949 335402 TRUE FALSE 225856.2988 297887.1556 347967.1106 355547.2783 272539.2794 283511.1666 242500.9171 312084.4564 265013.5628 312684.9238 0.722312723 0.952675146 1.112836226 1.137078417 0.871609914 0.906699188 0.775544002 0.998079641 0.847541863 1 18.25435014 RAT(ph)SPSSSVSGDFDDGHHSVSTPGPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RATSPSSSVSGDFDDGHHSVSTPGPSR 27 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;Q86U86-6;C9JQF1;C9JPI5;C9JCJ2;C9J053;C9J409 Q86U86-8 PBRM1 Protein polybromo-1 1 RAT(0.489)S(0.489)PS(0.015)S(0.004)S(0.002)VSGDFDDGHHSVSTPGPSR 76.415 0.011837 806780000 119960 159030 135410 165120 164140 158080 147980 102320 207130 178670 TRUE FALSE 115271.8306 154494.6201 159881.5992 173641.863 169419.7122 161276.4859 149791.0235 100207.0562 183617.4708 166568.5218 0.692038504 0.927513905 0.959854824 1.042465054 1.017117222 0.968229076 0.899275697 0.601596599 1.102353967 1 17.34575626 RDDGSWEVIEGYR ddPTM_BT-474_Pertuzumab_2h_R1 4 RDDGSWEVIEGYR 13 1 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;; 238.06 1.47E-16 698840000 236098 359204 240849 519597 298173 305066 465449 402156 317874 329003 FALSE TRUE 226871.0291 348959.8536 284375.772 546413.4634 307764.0053 311234.6435 471145.3041 393851.3381 281790.2762 306719.3338 0.739669803 1.137717174 0.92715307 1.781477081 1.003405953 1.014721308 1.536079576 1.284077313 0.918723553 1 18.22655958 RDPLANK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDPLANK 7 1 F5GWZ1;Q9BTZ2-3;Q9BTZ2-2;Q9BTZ2-5;Q9BTZ2-8;Q9BTZ2-4;Q9BTZ2;Q9BTZ2-7 F5GWZ1 DHRS4 Dehydrogenase/reductase SDR family member 4 0 ; 117.1 0.0085103 425710000 495430 494950 429930 482710 448060 359190 514820 493170 561640 547440 FALSE TRUE 476068.0479 480834.5106 507627.9147 507622.7209 462472.2568 366453.0679 521120.5212 482985.8672 497884.9818 510361.4012 0.932805747 0.942145134 0.994644018 0.994633841 0.90616621 0.718026612 1.021081375 0.946360493 0.975553756 1 18.9611597 RDS(ph)FDNCSLGESSK ddPTM_BT-474_Pertuzumab_2h_R1 2 RDSFDNCSLGESSK 14 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 RDS(1)FDNCSLGESSK;RDS(0.994)FDNCS(0.006)LGESSK 212.41 1.52E-09 1106720000 1012200 666880 345943 467830 677450 446590 503980 1241400 550720 623190 TRUE FALSE 972642.105 647861.2353 408462.5956 491974.7624 699240.7945 455620.3558 510147.858 1215764.656 488204.5744 580980.7862 1.674138161 1.115116456 0.703056978 0.8468004 1.203552357 0.784226203 0.878080429 2.092607337 0.84031105 1 19.14813093 RFDDAVVQSDMK ddPTM_BT-474_Pertuzumab_2h_R1 19 RFDDAVVQSDMK 12 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;;;;;;;;;;; 277.82 1.05E-27 74604875000 47634090 47905820 39019220 39404680 36583490 27162230 48307170 45203980 53272210 53762640 FALSE TRUE 45772497.1 46539592.92 46070861.03 41438360.26 37760231.18 27711468.9 48898367.6 44270502.02 47224972.06 50121248.51 0.913235374 0.928540176 0.919188217 0.826762331 0.753377705 0.55288864 0.975601547 0.883268141 0.942214599 1 25.57891902 RFDSEK ddPTM_BT-474_Pertuzumab_2h_R1 4 RFDSEK 6 1 P17980;E9PM69;E9PKD5;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;; 167.82 0.010487 2269270000 2549790 2577000 2084970 2152640 2237440 1641750 2606590 2510820 2784660 2897210 FALSE TRUE 2450141.388 2503506.483 2461770.459 2263738.008 2309409.29 1674947.31 2638490.228 2458970.69 2468557.071 2700979.386 0.907130725 0.926888408 0.911436226 0.83811747 0.855026625 0.620125914 0.97686426 0.910399651 0.913948875 1 21.3650512 RFDVSGYPTLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RFDVSGYPTLK 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 153.49 5.20E-05 3924000000 4334500 5024500 3594100 4203400 4334700 4557100 4499100 4543900 4997400 4697100 FALSE TRUE 4165102.948 4881206.18 4243633.82 4420337.978 4474129.562 4649247.684 4554161.332 4450066.877 4430116.103 4378961.233 0.951162325 1.114694997 0.969096001 1.009448986 1.021733083 1.061723874 1.040009511 1.016238016 1.011681964 1 22.06215725 RGNDPLTS(ph)SPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.086)S(0.457)S(0.457)PGR;RGNDPLT(0.086)S(0.457)S(0.457)PGR 77.562 0.017205 3479250000 297500 330790 271310 317041 291420 303010 327880 281190 364110 361510 TRUE FALSE 285873.3711 321356.1931 320341.7523 333403.524 300793.789 309137.0698 331892.6935 275383.3282 322777.7593 337024.6057 0.848227003 0.953509588 0.950499598 0.989255735 0.892498007 0.91725371 0.984772886 0.817101552 0.957727578 1 18.3624944 RGPLT(ph)SGSDEENVALPLGDNVLTHNLGIPVLVVCTK ddPTM_BT-474_Pertuzumab_2h_R1 2 RGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVCTK 36 1 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 RGPLT(0.333)S(0.333)GS(0.333)DEENVALPLGDNVLTHNLGIPVLVVCTK;RGPLT(0.405)S(0.298)GS(0.298)DEENVALPLGDNVLTHNLGIPVLVVCTK 226.73 1.82E-39 638580000 347890 391030 283290 291700 352860 397280 340070 360460 402200 379670 TRUE FALSE 334294.0742 379878.2073 334486.8048 306754.672 364210.0624 405313.2738 344231.8784 353016.375 356543.9422 353954.6127 0.944454634 1.073239883 0.94499914 0.866649737 1.028973912 1.145099567 0.972531127 0.997349271 1.007315428 1 18.43320485 RHDS(ph)VENSDSHVEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RHDSVENSDSHVEK 14 1 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 RHDS(1)VENSDSHVEK 178.54 9.27E-07 539280000 547800 528830 527290 585970 558960 583350 598050 291280 695990 649550 TRUE FALSE 526391.3704 513748.2862 622583.0325 616211.9819 576939.456 595145.7367 605369.1148 285264.9662 616984.133 605555.3999 0.869270376 0.848391883 1.028119033 1.01759803 0.952744301 0.982809726 0.999692373 0.471079882 1.018873142 1 19.20789943 RHEHPPNPPVS(ph)PGK ddPTM_BT-474_Pertuzumab_2h_R1 6 RHEHPPNPPVSPGK 14 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 RHEHPPNPPVS(1)PGK;RHEHPPNPPVS(1)PGK;RHEHPPNPPVS(1)PGK;RHEHPPNPPVS(1)PGK;RHEHPPNPPVS(1)PGK;RHEHPPNPPVS(1)PGK 140.95 4.61E-06 3470090000 1983410 1696680 1747720 1735590 1850820 1863180 2011200 122597 2587100 1897400 TRUE FALSE 1905896.144 1648292.348 2063571.882 1825164.008 1910353.306 1900854.776 2035813.667 120065.3291 2293423.254 1768887.408 1.077454753 0.931824343 1.166593121 1.031814687 1.079974507 1.07460473 1.15090065 0.067876185 1.296534332 1 20.75441079 RHPT(ph)GTTPPVK ddPTM_BT-474_Pertuzumab_2h_R1 1 RHPTGTTPPVK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 RHPT(0.461)GT(0.3)T(0.239)PPVK 77.527 0.018971 370970000 770690 831880 711770 804620 747390 774280 876660 862570 842630 899780 TRUE FALSE 740570.5828 808155.5969 840402.6722 846146.5346 771430.4781 789936.4721 887388.8273 844757.6281 746978.175 838837.0992 0.882853874 0.963423766 1.001866361 1.008713772 0.919642776 0.941704263 1.057879806 1.00705802 0.890492535 1 19.67803114 RHS(ph)PPIEK ddPTM_BT-474_Pertuzumab_2h_R1 6 RHSPPIEK 8 1 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK 150.09 0.00030307 7562970000 3977050 4072100 3127160 3771550 3755630 3901800 3940780 2943050 4569730 4115810 TRUE FALSE 3821622.489 3955967.695 3692307.375 3966200.147 3876433.25 3980697.069 3989008.444 2882274.989 4050993.408 3837042.523 0.995981271 1.030993968 0.962279504 1.033660723 1.010265908 1.037438873 1.039604962 0.751170979 1.055759321 1 21.87156332 RIEQHYFEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RIEQHYFEDR 10 1 C9JNK6;O75431-2;O75431 C9JNK6 MTX2 Metaxin-2 0 ; 107.85 0.0014474 877950000 799380 977510 719110 1069440 681390 868420 934740 798850 954890 995940 FALSE TRUE 768139.3458 949632.3719 849069.1735 1124633.927 703307.5282 885980.0474 946179.6277 782353.4683 846494.8904 928484.0967 0.827304796 1.022777208 0.914468192 1.211258147 0.757479348 0.954222103 1.019058518 0.842613752 0.911695627 1 19.82451767 RIS(ph)ACLSDYSLASDSGVFEPLTK ddPTM_BT-474_Pertuzumab_2h_R1 2 RISACLSDYSLASDSGVFEPLTK 23 1 Q9ULE0 Q9ULE0 WWC3 Protein WWC3 1 RIS(0.982)ACLS(0.004)DYS(0.014)LASDSGVFEPLTK;RIS(0.982)ACLS(0.018)DYSLASDSGVFEPLTK 162.1 1.04E-11 245260000 228998 264123 197369 233303 218923 249338 214409 244786 257031 274660 TRUE FALSE 220048.505 256590.4706 233037.9687 245343.7958 225964.8571 254379.7852 217033.0015 239731.0836 227853.9184 256057.0336 0.859373015 1.002083274 0.910101806 0.958160736 0.882478618 0.993449708 0.847596328 0.936240963 0.88985612 1 17.96610566 RKS(ph)ELPQDVYTIK ddPTM_BT-474_Pertuzumab_2h_R1 1 RKSELPQDVYTIK 13 2 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 1 RKS(1)ELPQDVYTIK 94.725 0.002621 329420000 476110 335580 201400 237660 296810 253230 255690 456750 322530 235260 TRUE FALSE 457503.0948 326009.587 237797.4601 249925.6611 306357.1632 258350.4841 258819.2107 447317.9529 285917.7466 219325.6307 2.085953627 1.486418099 1.084221025 1.139518716 1.396814236 1.177931112 1.180068239 2.039515179 1.303622133 1 17.74271489 RLEFENQK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLEFENQK 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 102.62 0.0079046 258620000 104130 119030 96624 109600 107500 66808 123330 114650 124710 127340 FALSE TRUE 100060.4845 115635.3809 114086.1062 115256.4691 110957.8351 68158.90353 124839.3494 112282.4374 110553.4436 118715.1484 0.842861975 0.974057503 0.961007148 0.97086573 0.934656079 0.574138216 1.05158736 0.9458139 0.931249677 1 16.85714451 RLEIS(ph)PDSS(ph)PER ddPTM_BT-474_Pertuzumab_2h_R1 1 RLEISPDSSPER 12 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 RLEIS(0.995)PDS(0.325)S(0.68)PER 130.02 0.0001497 300570000 464430 600940 386420 590030 460190 520520 525340 578740 548930 517840 TRUE FALSE 446279.5621 583801.7796 456254.6899 620481.519 474992.4293 531045.271 531769.2681 566788.8168 486617.7677 482766.2356 0.924421654 1.209284611 0.945084093 1.285262873 0.98389737 1.100004996 1.101504681 1.17404403 1.007978048 1 18.88096525 RLPENLYNDR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLPENLYNDR 10 1 B7Z2R2;P14927;P14927-2;E5RHG9 B7Z2R2 UQCRB Cytochrome b-c1 complex subunit 7 0 ; 122.55 0.0007787 1124530000 335880 575400 363690 851140 328160 277700 703450 534640 419960 321680 FALSE TRUE 322753.4383 558990.1554 429416.8732 895067.4374 338715.5644 283315.2843 712059.0315 523599.4972 372287.9014 299892.3271 1.076231064 1.863969515 1.431903502 2.984629337 1.129457255 0.944723351 2.374382294 1.745958299 1.241405224 1 18.19408508 RLPLNFLSGEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RLPLNFLSGEK 11 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 115.14 0.0018659 567950000 955040 1023500 884210 739080 790360 571450 1088600 984440 1078800 1192900 FALSE TRUE 917715.9809 994310.7821 1044006.416 777224.0074 815782.6472 583005.1105 1101922.612 964110.97 956339.1467 1112103.82 0.825207111 0.894080898 0.938767044 0.698877203 0.733549002 0.524236227 0.990845092 0.866925329 0.859936931 1 20.08486005 RLS(ph)ESSALK ddPTM_BT-474_Pertuzumab_2h_R1 3 RLSESSALK 9 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RLS(0.907)ES(0.062)S(0.031)ALK;RLS(0.927)ES(0.07)S(0.003)ALK;RLS(0.853)ES(0.108)S(0.038)ALK 166.71 6.41E-05 1084320000 1999760 1713810 1533030 1685290 1600520 1357460 1666290 2270470 1652890 1610470 TRUE FALSE 1921607.168 1664933.817 1810082.623 1772268.019 1652002.179 1384908.771 1686682.555 2223584.001 1465260.857 1501391.432 1.279884197 1.108927213 1.205603405 1.180417032 1.100314111 0.92241686 1.123412935 1.481015512 0.975935272 1 20.51786872 RLS(ph)PEKQNCR ddPTM_BT-474_Pertuzumab_2h_R1 2 RLSPEKQNCR 10 2 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 RLS(1)PEKQNCR;RLS(1)PEKQNCR 70.889 0.035271 438300000 313220 333480 234260 240590 300100 279490 325730 282800 353420 327970 TRUE FALSE 300979.0161 323969.4769 276595.9931 253006.8787 309752.989 285141.4793 329716.3812 276960.0812 313301.2433 305756.2998 0.984375518 1.059567627 0.904628926 0.827478874 1.013071486 0.93257761 1.078363329 0.905819705 1.02467633 1 18.2220227 RLS(ph)VELTSSLFR ddPTM_BT-474_Pertuzumab_2h_R1 4 RLSVELTSSLFR 12 1 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0;A0A2R8Y7Z0;A0A2R8YG06 A0A2R8Y804 CTNNB1 Catenin beta-1 1 RLS(0.985)VELT(0.007)S(0.007)S(0.001)LFR;RLS(0.995)VELT(0.004)SSLFR;RLS(1)VELTSSLFR;RLS(1)VELTSSLFR 221.62 2.83E-11 1710010000 800836 1519341 724637 1628360 733907 578984 1472079 1501824 1052506 846450 TRUE FALSE 769538.4437 1476010.882 855595.0254 1712399.855 757513.7852 590691.4532 1490094.743 1470810.81 933029.9313 789119.1876 0.975186583 1.870453672 1.084240554 2.170014216 0.959948506 0.748545293 1.888301244 1.863863955 1.182368831 1 19.58988369 RLVSDGNINSDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RLVSDGNINSDR 12 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 86.405 0.017846 150200000 305780 226700 200600 194700 180110 182600 177890 262670 217890 208850 FALSE TRUE 293829.7795 220234.738 236852.8823 204748.4903 185903.4017 186292.2971 180067.071 257245.7727 193156.0407 194704.4035 1.509107007 1.13112356 1.216474194 1.051586336 0.954798137 0.9567955 0.924822797 1.321211889 0.992047623 1 17.57092599 RMS(ph)FQKPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RMSFQKPK 8 2 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;E5RII8 Q8N573-2 OXR1 Oxidation resistance protein 1 1 RMS(1)FQKPK;RMS(1)FQKPK 136.48 0.00041187 822260000 1057090 541950 328756 438220 441370 368590 375301 1136910 548530 408350 TRUE FALSE 1015777.754 526494.1166 388169.5223 460836.5867 455567.0669 376043.1423 379894.0459 1113432.411 486263.174 380692.0908 2.668239711 1.382992002 1.019641678 1.210523144 1.196681197 0.987788166 0.9979037 2.924758455 1.277313571 1 18.53826507 RNDFQLIGIQDGYLSLLQDSGEVR ddPTM_BT-474_Pertuzumab_2h_R1 4 RNDFQLIGIQDGYLSLLQDSGEVR 24 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;; 279.04 6.04E-52 5592760000 1426199 1524669 1159300 1294603 1343412 1562153 1231967 1331959 1530179 1509118 FALSE TRUE 1370461.566 1481186.933 1368811.298 1361417.616 1386624.067 1593740.804 1247044.181 1304453.581 1356479.495 1406904.094 0.974097362 1.052798794 0.972924384 0.967669098 0.985585352 1.132799891 0.886374691 0.927180173 0.964159178 1 20.42409256 RNEIDAEPPAKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RNEIDAEPPAKR 12 2 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 ; 160.56 3.81E-05 806790000 774460 842890 679110 708210 737000 804740 748100 842060 847410 830660 FALSE TRUE 744193.247 818851.6025 801840.2837 744760.803 760706.2743 821012.3942 757255.4716 824671.1667 751215.5694 774398.6583 0.960995011 1.057403178 1.035436045 0.96172791 0.982318688 1.060193462 0.977862582 1.064918124 0.970063108 1 19.56271693 RPDQQLQGEGK ddPTM_BT-474_Pertuzumab_2h_R1 6 RPDQQLQGEGK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;;; 184.34 7.93E-06 9650780000 6568080 6193150 5590220 6035190 6113800 5667380 6499020 6792540 7204320 6815020 FALSE TRUE 6311392.172 6016527.426 6600497.108 6346666.879 6310455.929 5781978.307 6578556.951 6652271.675 6386515.797 6353432.625 0.993383033 0.946972728 1.038886771 0.998935104 0.993235673 0.910055815 1.035433495 1.047035842 1.005207133 1 22.59910483 RPFDPNDR ddPTM_BT-474_Pertuzumab_2h_R1 6 RPFDPNDR 8 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;;; 115.82 0.0038312 8761140000 1010050 1445570 1109590 2042880 1158630 1262750 1228790 1299220 1303760 1441160 FALSE TRUE 970576.1293 1404343.759 1310117.596 2148313.282 1195898.386 1288283.67 1243828.3 1272390.653 1155762.631 1343548.95 0.722397297 1.045249419 0.97511713 1.598984006 0.890104068 0.958866196 0.925778179 0.947037064 0.86023113 1 20.35761745 RPGFSPT(ph)SHR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 RPGFS(0.269)PT(0.574)S(0.157)HR 113.54 0.00086416 1092500000 217910 261900 186550 335740 250070 256810 278070 275370 276190 309650 TRUE FALSE 209393.8363 254430.8684 220263.7348 353067.5816 258113.7287 262002.8742 281473.1038 269683.5133 244838.0691 288677.1297 0.725356513 0.881368291 0.763010686 1.223053527 0.894126005 0.907598307 0.975044695 0.934204637 0.848138089 1 18.13909729 RPS(ph)DSSRPK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPSDSSRPK 9 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 1 RPS(0.888)DS(0.047)S(0.065)RPK;RPS(0.992)DS(0.004)S(0.004)RPK;RPS(0.686)DS(0.127)S(0.187)RPK;RPS(0.984)DS(0.013)S(0.003)RPK 100.02 0.0038918 739000000 418894 385994 378246 378114 365570 393729 405800 430395 406142 426634 TRUE FALSE 402523.1594 374985.829 446603.4662 397628.5089 377328.8911 401690.4701 410766.3018 421507.1928 360038.4628 397737.6992 1.012031699 0.942796798 1.122859279 0.999725472 0.94868777 1.009938135 1.032756771 1.059761732 0.905215833 1 18.60145779 RPSDSSRPK ddPTM_BT-474_Pertuzumab_2h_R1 4 RPSDSSRPK 9 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 ;;; 122.96 0.0003212 328206000 405114 419074 335348 400158 376320 364814 389679 404631 452805 416310 FALSE TRUE 389281.697 407122.4198 395952.8434 420810.2023 388424.6746 372190.789 394448.0082 396275.2284 401404.4747 388112.9529 1.00301135 1.048979213 1.020200023 1.084246736 1.000803173 0.958975438 1.01632271 1.02103067 1.03424653 1 18.56611706 RPSGVPDR ddPTM_BT-474_Pertuzumab_2h_R1 1 RPSGVPDR 8 1 P01709;P01706 P01709 Ig lambda chain V-II region MGC;Ig lambda chain V-II region BOH 0 79.16 0.046108 87089000 162020 218990 169300 223250 166970 173940 218510 149740 223870 235770 FALSE TRUE 155688.0793 212744.6196 199896.2761 234771.9593 172340.7417 177457.186 221184.1907 146647.8167 198457.2161 219801.0879 0.708313506 0.967896118 0.909441705 1.068110998 0.784075927 0.807353538 1.00629252 0.667184217 0.902894604 1 17.745839 RQEAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RQEAPK 6 1 Q9NWM3;J3QLQ8;Q9NWM3-2;J3KRV3;J3KRK6 Q9NWM3 CUEDC1 CUE domain-containing protein 1 0 90.986 0.077617 24873000 31230 33971 24659 31374 27248 28261 35685 28941 34079 37375 FALSE TRUE 30009.49707 33002.18034 29115.42984 32993.2159 28124.45667 28832.45678 36121.7237 28343.35824 30210.49479 34843.55796 0.861263856 0.947152997 0.835604385 0.94689572 0.807163743 0.827483141 1.036682986 0.813446155 0.867032432 1 15.08860433 RQLHLEGASLELS(ph)DDDTESK ddPTM_BT-474_Pertuzumab_2h_R1 4 RQLHLEGASLELSDDDTESK 20 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 RQLHLEGASLELS(1)DDDTESK;RQLHLEGASLELS(1)DDDTESK;RQLHLEGAS(0.029)LELS(0.971)DDDTESK;RQLHLEGASLELS(1)DDDTESK 370.59 2.43E-112 2370900000 2436800 2220110 1907600 1684940 1918640 2095770 1996960 2035220 2413820 2242500 TRUE FALSE 2341567.162 2156794.637 2252345.754 1771899.955 1980354.798 2138147.905 2021399.394 1993191.996 2139813.273 2090613.478 1.120038298 1.031656334 1.077361157 0.84755024 0.947260132 1.022737071 0.966892931 0.953400529 1.023533664 1 20.99549492 RQS(ph)LELQK ddPTM_BT-474_Pertuzumab_2h_R1 4 RQSLELQK 8 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 RQS(1)LELQK;RQS(1)LELQK;RQS(1)LELQK;RQS(1)LELQK 169.33 0.00018476 2334440000 2130980 1971240 1461630 1964840 1933320 1754570 1893870 2177800 1944150 1935060 TRUE FALSE 2047698.946 1915022.165 1725779.055 2066245.628 1995506.994 1790048.608 1917047.748 2132827.669 1723458.243 1803996.663 1.135090207 1.061544184 0.956642044 1.145371092 1.106158916 0.992268248 1.062667014 1.182279166 0.95535556 1 20.78276524 RQYHES(ph)EEES(ph)EEEEAA ddPTM_BT-474_Pertuzumab_2h_R1 1 RQYHESEEESEEEEAA 16 1 Q8N9N8;E9PNH5 Q8N9N8 EIF1AD Probable RNA-binding protein EIF1AD 2 RQYHES(1)EEES(1)EEEEAA 100.69 0.0013165 157200000 247570 257480 196470 239350 224700 241180 240390 208410 272190 264830 TRUE FALSE 237894.6907 250136.9225 231976.4995 251702.8822 231927.6796 246056.8248 243331.9647 204106.2607 241292.1323 246892.8282 0.96355448 1.013139686 0.939583791 1.019482356 0.939386054 0.996613902 0.985577291 0.826699836 0.977315275 1 17.9135254 RRDSLDS(ph)STEASGSDVVLGGR ddPTM_BT-474_Pertuzumab_2h_R1 1 RRDSLDSSTEASGSDVVLGGR 21 2 Q9Y2I9 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 RRDS(0.329)LDS(0.483)S(0.162)T(0.026)EASGSDVVLGGR 134.45 6.47E-06 1240400000 125820 143830 95907 125500 120470 183450 148430 165470 137360 145430 TRUE FALSE 120902.8153 139728.1092 113239.5283 131977.07 124345.027 187159.4847 150246.5307 162052.9867 121767.4687 135579.8966 0.891745888 1.030596075 0.835223593 0.973426543 0.917134694 1.380436845 1.108177057 1.195258226 0.898123334 1 17.04878375 RREPGGYDSSSTLMSSELETTSFFDS(ph)DEDDSTSR ddPTM_BT-474_Pertuzumab_2h_R1 1 RREPGGYDSSSTLMSSELETTSFFDSDEDDSTSR 34 2 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 RREPGGYDSSSTLMSSELETTSFFDS(0.99)DEDDS(0.009)TSR 110.33 5.75E-06 91783000 24777 24923 29204 30808 29334 21138 25863 26538 30809 34903 TRUE FALSE 23808.68745 24212.22044 34481.81244 32398.00457 30277.55475 21565.42484 26179.51913 25989.98103 27311.69148 32538.98872 0.731697216 0.744098738 1.059707563 0.995667224 0.930500791 0.662756456 0.804558475 0.798733521 0.839352806 1 14.98988179 RRLSES(ph)SALK ddPTM_BT-474_Pertuzumab_2h_R1 2 RRLSESSALK 10 2 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RRLS(0.274)ES(0.477)S(0.249)ALK;RRLS(0.001)ES(0.5)S(0.5)ALK 98.974 0.0039468 977500000 900470 767330 606870 707960 708980 598070 635110 882940 724210 662290 TRUE FALSE 865278.6369 745446.4997 716544.9088 744497.9004 731784.9856 610163.3852 642882.6662 864706.9805 642000.7169 617432.5084 1.401414122 1.207332768 1.160523456 1.205796407 1.185206441 0.988226854 1.041219336 1.400488262 1.039790922 1 19.23592192 RS(ph)KSEDMDNVQSK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSKSEDMDNVQSK 13 2 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 RS(0.5)KS(0.5)EDMDNVQSK 107.34 0.0009979 0 117140 98880 83253 80173 99582 111160 91625 112330 108710 98772 TRUE FALSE 112562.0393 96060.03921 98298.66905 84310.73814 102785.1455 113407.7314 92746.33416 110010.3462 96369.69655 92082.08446 1.222409766 1.043200095 1.067511337 0.915604144 1.116233913 1.231593877 1.007213669 1.194698696 1.046562935 1 16.49063287 RS(ph)PRPDHPGTPPHK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSPRPDHPGTPPHK 14 2 P30291 P30291 WEE1 Wee1-like protein kinase 1 RS(1)PRPDHPGTPPHK;RS(1)PRPDHPGTPPHK 124.45 4.61E-05 251710000 228670 232790 186043 227970 255520 233700 240500 98171 268750 236860 TRUE FALSE 219733.3236 226151.0571 219665.1086 239735.559 263739.0329 238425.5741 243443.3109 96143.73454 238242.6267 220817.2612 0.995091246 1.024154796 0.994782325 1.085673999 1.194376886 1.07974156 1.102465041 0.435399543 1.078913059 1 17.75249343 RS(ph)SAIGIENIQEVQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSAIGIENIQEVQEK 16 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RS(0.524)S(0.476)AIGIENIQEVQEK 303.7 4.04E-46 487070000 498800 473950 425950 400930 459610 426550 417430 643400 526930 469140 TRUE FALSE 479306.3445 460433.41 502928.6402 421622.0453 474393.7731 435175.1333 422538.6332 630113.5652 467115.1155 437364.7299 1.095896198 1.05274472 1.149906716 0.964005592 1.08466399 0.99499366 0.966101298 1.440705027 1.068021913 1 18.73847736 RS(ph)SPAAFINPPIGTVTPALK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSSPAAFINPPIGTVTPALK 20 1 F6VRR5;Q9BY77-2;Q9BY77;Q6R954;F8WEE2;Q8WUT1;F8WCX5 F6VRR5 POLDIP3;PDIP46 Polymerase delta-interacting protein 3 1 RS(0.5)S(0.5)PAAFINPPIGTVTPALK;RS(0.5)S(0.5)PAAFINPPIGTVTPALK 214.05 7.96E-24 1074660000 1012000 1003090 731410 842380 899520 924660 868750 1029870 1020330 979790 TRUE FALSE 972449.9212 974482.8553 863592.0571 885855.3328 928453.8777 943357.2587 879382.0224 1008602.825 904506.416 913427.9506 1.064615902 1.066841511 0.945440805 0.969814129 1.016450041 1.032765921 0.962727298 1.104195272 0.990232908 1 19.80093141 RS(ph)TPAPK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSTPAPK 7 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.5)T(0.5)PAPK;RS(0.5)T(0.5)PAPK 64.04 0.04643 180530000 372750 334956 303358 353040 313294 308523 357290 389110 343940 363920 TRUE FALSE 358182.5179 325403.3828 358181.5388 371260.4367 323371.386 314761.5464 361662.6219 381074.7425 304897.3731 339271.3743 1.055740463 0.959124192 1.055737577 1.094287538 0.953134896 0.927757454 1.065998046 1.123215135 0.898682872 1 18.37208018 RSASAS(ph)HQADIK ddPTM_BT-474_Pertuzumab_2h_R1 2 RSASASHQADIK 12 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 RS(0.074)AS(0.3)AS(0.626)HQADIK;RS(0.182)AS(0.124)AS(0.694)HQADIK 142.54 3.76E-05 704990000 782090 1022910 565870 858240 616770 612960 740170 1235890 889800 596400 TRUE FALSE 751525.0582 993737.6083 668135.2967 902533.8693 636608.9672 625354.4712 749228.4219 1210368.44 788793.6343 556005.2968 1.351650897 1.78728083 1.201670741 1.623246891 1.144969249 1.124727543 1.347520296 2.176900916 1.418680072 1 19.0847391 RSS(ph)NPPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSNPPAR 8 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 RS(0.146)S(0.854)NPPAR 97.734 0.0049135 53374000 17629 17827 15954 22842 18741 25765 16602 17973 18219 18606 TRUE FALSE 16940.03919 17318.59141 18837.24269 24020.87836 19343.82129 26285.98595 16805.18024 17601.85127 16150.8555 17345.79905 0.976607601 0.998431457 1.085982989 1.384823973 1.115187674 1.515409344 0.968832868 1.014761627 0.931110493 1 14.08229868 RSSLDAEIDS(ph)LTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_BT-474_Pertuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.177)S(0.177)LDAEIDS(0.215)LT(0.215)S(0.215)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 74.563 0.0001732 6777800000 61068 83908 54507 89614 62832 72700 56300 73741 87459 72877 TRUE FALSE 58681.39505 81515.02599 64357.6274 94238.98928 64853.04834 74170.04381 56989.01624 72218.22258 77531.02098 67940.97588 0.863711395 1.199791804 0.947257919 1.38707147 0.95454985 1.091683522 0.83880185 1.062955332 1.141152596 1 16.05199432 RT(ph)NSTGGSSGSSVGGGSGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTNSTGGSSGSSVGGGSGK 19 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 RT(0.447)NS(0.334)T(0.072)GGS(0.126)S(0.021)GS(0.001)SVGGGSGK 89.829 0.0030421 0 48840 49586 38954 39838 47146 52077 42919 43593 52763 46570 TRUE FALSE 46931.2788 48171.85583 45993.85433 41894.04395 48662.49391 53130.03262 43444.25556 42692.78932 46773.56544 43415.77242 1.080973024 1.109547364 1.059381229 0.96494987 1.120848282 1.223749565 1.000656055 0.983347455 1.077340396 1 15.40593163 RT(ph)PDYFL ddPTM_BT-474_Pertuzumab_2h_R1 1 RTPDYFL 7 1 P67775;P62714;P67775-2;H0YBN9 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 1 RT(1)PDYFL 87.258 0.037669 92722000 216890 200690 193090 236960 200000 182340 197440 290230 218380 217270 TRUE FALSE 208413.699 194966.5177 227985.6583 249189.534 206433.1816 186027.0397 199856.3298 284236.6491 193590.4179 202554.1094 1.028928515 0.962540421 1.125554347 1.230236872 1.019150795 0.918406644 0.986681191 1.403262812 0.955746682 1 17.62794783 RTMIIS(ph)PERLDPFADGGK ddPTM_BT-474_Pertuzumab_2h_R1 1 RTMIISPERLDPFADGGK 18 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 RT(0.166)MIIS(0.834)PERLDPFADGGK 93.572 0.0011085 30448000 48086 52489 35012 40611 43731 56104 44649 49575 57942 49909 TRUE FALSE 46206.74596 50992.06511 41339.44724 42706.93858 45137.64733 57238.46132 45195.42782 48551.25893 51364.66707 46528.61898 0.993082257 1.095929048 0.888473549 0.917863876 0.97010503 1.230177525 0.971346857 1.043470879 1.103937065 1 15.50583075 RTPDYFL ddPTM_BT-474_Pertuzumab_2h_R1 1 RTPDYFL 7 1 P67775;P62714;P67775-2;H0YBN9 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 0 81.635 0.041092 0 126870 144580 133410 145020 137910 84646 163070 155170 148280 161080 FALSE TRUE 121911.7801 140456.72 157520.1547 152504.4996 142346.0004 86357.60012 165065.6994 151965.6853 131447.876 150169.9081 0.811825629 0.935318678 1.048946201 1.015546333 0.94789963 0.575065945 1.099192918 1.011958302 0.875327672 1 17.19623622 RTPS(ph)PGPVESK ddPTM_BT-474_Pertuzumab_2h_R1 3 RTPSPGPVESK 11 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 RT(0.147)PS(0.853)PGPVESK;RT(0.165)PS(0.835)PGPVESK;RT(0.124)PS(0.876)PGPVESK 98.105 0.0035336 926250000 1517650 1605060 1277420 1488710 1514430 1663230 1410520 1515110 1696340 1611850 TRUE FALSE 1458338.56 1559285.26 1508278.21 1565542.502 1563143.016 1696861.65 1427782.366 1483822.449 1503778.595 1502677.964 0.970493077 1.037670943 1.003726844 1.041835003 1.040238197 1.129225084 0.950158584 0.987452059 1.000732446 1 20.51910443 RVEHNQVGEK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVEHNQVGEK 10 1 P42167-2 P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 ; 106.62 0.0015532 265060000 327860 508780 237830 478100 286570 284440 354270 483020 424500 284680 FALSE TRUE 315046.8687 494270.0925 280811.1715 502774.7983 295787.7843 290191.5717 358605.6622 473045.4682 376312.5396 265398.37 1.187071604 1.86237049 1.058074213 1.894415547 1.114504902 1.093418817 1.351197681 1.78239779 1.417915791 1 18.01779998 RVGMADANS(ph)PPKPLSKPR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVGMADANSPPKPLSKPR 18 3 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 RVGMADANS(1)PPKPLSKPR;RVGMADANS(1)PPKPLSKPR 85.248 0.020272 6900000000 1283410 1139000 971350 908330 1048410 1059110 1238300 1191720 1174930 1254240 TRUE FALSE 1233252.918 1106516.835 1146894.553 955209.0202 1082133.06 1080525.93 1253454.686 1167110.566 1041556.872 1169289.208 1.054703071 0.946315786 0.980847634 0.816914253 0.925462283 0.924087833 1.071980035 0.998136781 0.890760699 1 20.15720037 RVIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_BT-474_Pertuzumab_2h_R1 2 RVIISAPSADAPMFVMGVNHEKYDNSLK 28 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 310.14 7.17E-83 3725500000 1528670 1649460 1195560 1209160 1352070 1717210 1508450 1664690 1763270 1164450 FALSE TRUE 1468927.886 1602419.016 1411624.287 1271564.893 1395560.559 1751933.163 1526910.862 1630313.57 1563110.982 1085580.764 1.353126303 1.476093782 1.300340181 1.17132224 1.285542822 1.613821118 1.406538244 1.501789294 1.439884561 1 20.05003563 RVPSPTPAPK ddPTM_BT-474_Pertuzumab_2h_R1 1 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 86.114 0.024875 0 116050 120030 95078 109330 102540 129590 99793 118410 135880 121680 FALSE TRUE 111514.6377 116606.8619 112260.7096 114972.5344 105838.2922 132210.3986 101014.2966 115964.7921 120455.4721 113438.5052 0.983040437 1.02793017 0.989617321 1.013523002 0.933001471 1.165480789 0.890476266 1.0222701 1.061857011 1 16.7915509 RVS(ph)QDLEVEKPDASPTSLQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 RVSQDLEVEKPDASPTSLQLR 21 2 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 RVS(0.522)QDLEVEKPDAS(0.22)PT(0.129)S(0.129)LQLR;RVS(1)QDLEVEKPDASPTSLQLR 187.26 2.32E-17 983610000 911610 894940 740590 790300 871640 839470 763820 1000980 950320 873530 TRUE FALSE 875983.2734 869417.1874 874431.0873 831087.4777 899677.0922 856444.6586 773167.8576 980309.4132 842443.6577 814365.035 1.07566415 1.067601321 1.073758142 1.020534333 1.104758988 1.051671697 0.949411903 1.203771492 1.03447916 1 19.63531609 RVSHS(ph)PPPK ddPTM_BT-474_Pertuzumab_2h_R1 3 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RVS(0.022)HS(0.978)PPPK;RVS(0.014)HS(0.986)PPPK;RVS(0.187)HS(0.813)PPPK 60.509 0.058346 558650000 509190 540990 444780 476440 455900 515720 521680 421200 552670 575410 TRUE FALSE 489290.2919 525561.4949 525161.6401 501029.1255 470564.4375 526148.2117 528064.4759 412502.0728 489933.2186 536436.9682 0.912111433 0.979726466 0.978981076 0.933994402 0.877203596 0.980820195 0.984392402 0.768966528 0.913309946 1 19.03304914 RWDDSQK ddPTM_BT-474_Pertuzumab_2h_R1 6 RWDDSQK 7 1 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;;;; 219.72 4.80E-05 5609360000 5689470 5688670 4884340 4977680 5157770 4219160 5858960 5780610 6201790 6375660 FALSE TRUE 5467119.222 5526434.701 5767048.89 5234578.661 5323674.356 4304474.306 5930663.705 5661238.383 5497788.799 5943830.869 0.919797239 0.929776574 0.970257905 0.880674228 0.895663836 0.724191923 0.997784734 0.95245617 0.92495714 1 22.50296163 RYS(ph)PS(ph)PPPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 RYSPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.211)S(0.8)PS(0.99)PPPKR;RY(0.057)S(0.947)PS(0.996)PPPKR 65.043 0.037624 1463890000 660120 724470 553290 574390 678880 694270 675300 633140 725180 784430 TRUE FALSE 634321.7806 703808.8249 653281.8109 604034.3367 700716.7917 708308.6151 683564.5234 620065.4377 642860.6066 731299.8574 0.867389449 0.962407989 0.893315928 0.825973546 0.958179856 0.968561128 0.934725361 0.847894925 0.87906568 1 19.48010356 S(ph)ASASHQADIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.554)AS(0.405)AS(0.041)HQADIK 125.97 0.00020426 1058100000 1964700 2581200 1433600 2311500 1497600 1454900 1852300 3132100 2457400 1673600 TRUE FALSE 1887917.352 2507586.703 1692683.41 2430796.792 1545771.664 1484319.075 1874969.001 3067421.04 2178446.254 1560245.581 1.210012946 1.607174366 1.084882682 1.557957812 0.990723308 0.951336823 1.201714028 1.965986046 1.396220108 1 20.5733417 S(ph)DSLILDHQWELEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDSLILDHQWELEK 14 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 S(0.5)DS(0.5)LILDHQWELEK 79.013 0.013058 7820900 16212 17263 17198 15474 13764 17805 18403 17894 18936 20859 TRUE FALSE 15578.41712 16770.67614 20306.06117 16272.61499 14206.73156 18165.0293 18628.22142 17524.48265 16786.46467 19446.20135 0.801103354 0.862413992 1.044217367 0.836801733 0.730565898 0.934117104 0.957936261 0.901177681 0.8632259 1 14.24720074 S(ph)EGFSMDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEGFSMDR 8 0 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 S(1)EGFSMDR;S(1)EGFSMDR 169.93 0.00031272 943250000 429900 438490 364690 469930 380160 360240 358990 509240 350960 416780 TRUE FALSE 413099.0327 425984.6945 430597.5955 494183.1436 392388.1917 367524.2996 363383.427 498724.016 311120.4921 388551.1194 1.063178079 1.096341442 1.108213499 1.27186133 1.009875335 0.945884032 0.935226818 1.28354801 0.800719588 1 18.56774489 S(ph)FSLDEPPLFIPDNIATIR ddPTM_BT-474_Pertuzumab_2h_R1 3 SFSLDEPPLFIPDNIATIR 19 0 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 S(0.86)FS(0.14)LDEPPLFIPDNIATIR;S(0.863)FS(0.137)LDEPPLFIPDNIATIR;S(0.899)FS(0.101)LDEPPLFIPDNIATIR 274.17 2.23E-39 101280000 210125 120709 69963 87782 96429 71245 81259 212949 79539 74693 TRUE FALSE 201913.0827 117266.4975 82606.87042 92312.43954 99530.72636 72685.62271 82253.47195 208551.5287 70510.06617 69633.97658 2.899634526 1.684041373 1.186301206 1.325680998 1.429341411 1.043824097 1.18122612 2.994967959 1.012581352 1 16.08750379 S(ph)GNLHLIHVTSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGNLHLIHVTSK 12 0 E7ES84;P50748 E7ES84 KNTC1 Kinetochore-associated protein 1 1 S(1)GNLHLIHVTSK 59.57 0.044468 101690000 299730 296430 279320 275130 301780 285580 302940 173010 318730 337580 TRUE FALSE 288016.2202 287976.1066 329799.3374 289329.4923 311487.0278 291354.6233 306647.4703 169437.283 282549.1066 314715.4059 0.915164033 0.915036573 1.047928799 0.919336921 0.989741913 0.925771722 0.974364345 0.538382551 0.897792422 1 18.26368828 S(ph)HGLESVPVLPGSGEAGVSFDLPAQADTLHSANK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHGLESVPVLPGSGEAGVSFDLPAQADTLHSANK 34 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 S(0.725)HGLES(0.275)VPVLPGSGEAGVSFDLPAQADTLHSANK;S(0.732)HGLES(0.268)VPVLPGSGEAGVSFDLPAQADTLHSANK 153.77 1.27E-10 131000000 135537 129226 123859 119535 116382 154105 139956 24470 152975 131480 TRUE FALSE 130240.0642 125540.601 146243.0765 125704.2157 120125.5327 157221.1087 141668.8234 23964.68595 135609.9193 122574.7425 1.062535899 1.024196327 1.193093076 1.025531142 0.980018642 1.282655019 1.155775003 0.1955108 1.106344721 1 16.90330221 S(ph)HSGTSPDNTAPPPPPPRPQPSHSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.405)HS(0.349)GT(0.213)S(0.033)PDNTAPPPPPPRPQPSHSR;S(0.272)HS(0.228)GT(0.228)S(0.272)PDNTAPPPPPPRPQPSHSR 94.389 0.006462 284100000 54799 60998 50919 64180 56533 59961 62210 19391.3 69960 58923 TRUE FALSE 52657.3945 59258.39676 60121.19599 67492.33749 58351.43529 61173.4525 62971.34459 18990.86288 62018.4341 54932.09273 0.958590723 1.078757313 1.094463965 1.228650396 1.062246719 1.113619552 1.146348909 0.345715263 1.129001846 1 15.74536163 S(ph)KEYHR ddPTM_BT-474_Pertuzumab_2h_R1 6 SKEYHR 6 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(0.967)KEY(0.033)HR;S(0.966)KEY(0.034)HR;S(0.859)KEY(0.141)HR;S(0.928)KEY(0.072)HR;S(0.995)KEY(0.005)HR;S(0.999)KEY(0.001)HR 81.338 0.037634 2679980000 5356530 4389790 3678330 3672870 3856720 3757190 3892900 4169300 4365030 4264930 TRUE FALSE 5147190.886 4264597.487 4343086.055 3862427.261 3980774.901 3833162.956 3940542.475 4083202.498 3869530.094 3976062.492 1.294544765 1.072568023 1.092308298 0.97142016 1.001185195 0.964060038 0.991066534 1.026946258 0.973206558 1 21.922909 S(ph)KSPIPGQGYLGTERPSSVSSVHSEGDYHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSPIPGQGYLGTERPSSVSSVHSEGDYHR 30 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.604)KS(0.396)PIPGQGYLGTERPSSVSSVHSEGDYHR 194.06 3.16E-19 958840000 160040 199180 206470 271130 210250 231250 256860 22236 299500 272050 TRUE FALSE 153785.4599 193499.5814 243783.7219 285123.0518 217012.8822 235926.0334 260003.5295 21776.81883 265502.0156 253623.8112 0.60635261 0.762939333 0.961202029 1.124196701 0.855648692 0.930220362 1.025154256 0.085862675 1.046833948 1 17.95233067 S(ph)LEDISSDSSNQAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLEDISSDSSNQAK 14 0 A0A0U1RR07;Q9HCH5-7;Q9HCH5-13;Q9HCH5-8;A0A0U1RQP0;Q9HCH5;Q9HCH5-14;A0A0U1RRJ3;Q9HCH5-15;Q9HCH5-11;Q9HCH5-6;A0A0U1RQH1;Q9HCH5-12 A0A0U1RR07;Q9HCH5-12 SYTL2 Synaptotagmin-like protein 2 1 S(1)LEDISSDSSNQAK 323.16 7.45E-43 0 560440 344870 242470 262810 302210 224330 253850 604720 304710 276570 TRUE FALSE 538537.3852 335034.6453 286289.7227 276373.6556 311930.8591 228866.1063 256956.6922 592232.3207 270120.5982 257837.6676 2.088668387 1.299401474 1.110348714 1.071890148 1.209795536 0.887636428 0.996583217 2.296919322 1.047638232 1 17.97610352 S(ph)LEELLLDANQLR ddPTM_BT-474_Pertuzumab_2h_R1 6 SLEELLLDANQLR 13 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JPP5;Q14160-3;Q5T0G3;Q9BTT6-2;Q9BTT6 A0A0G2JNZ2 SCRIB;LRRC1 Protein scribble homolog;Leucine-rich repeat-containing protein 1 1 S(1)LEELLLDANQLR;S(1)LEELLLDANQLR;S(1)LEELLLDANQLR;S(1)LEELLLDANQLR;S(1)LEELLLDANQLR;S(1)LEELLLDANQLR 194.55 9.71E-07 144699600 80025.8 104014.6 65101.3 125662.7 67974 61441.7 98878.4 122037.7 90515.7 70905.4 TRUE FALSE 76898.30326 101048.2054 76866.55308 132148.167 70160.44544 62684.09327 100088.5034 119517.5788 80240.73721 66102.9141 1.16331185 1.528649785 1.162831535 1.999127706 1.061382034 0.948280331 1.514131484 1.808053101 1.213875943 1 16.01242625 S(ph)LEGGGCPAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLEGGGCPAR 10 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 S(1)LEGGGCPAR 76.068 0.038921 296700000 84714 101540 71506 102520 76944 76770 95251 104940 97999 94382 TRUE FALSE 81403.28322 98644.17862 84428.72484 107811.0695 79418.97364 78322.342 96416.71023 102772.9523 86874.56437 87989.42307 0.925148505 1.121091322 0.959532656 1.225273058 0.902596822 0.890133601 1.095776138 1.168014845 0.987329628 1 16.42504249 S(ph)LPAFPTSSLLTQSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLPAFPTSSLLTQSQK 16 0 Q99698 Q99698 LYST Lysosomal-trafficking regulator 1 S(0.993)LPAFPT(0.004)S(0.001)S(0.001)LLTQSQK 88.73 0.0063262 45433000 57263 44270 42556 49612 43271 41764 44349 65040 49353 38767 TRUE FALSE 55025.09865 43007.46294 50246.81585 52172.48127 44662.85101 42608.49669 44891.75633 63696.90127 43750.65434 36141.27656 1.522500141 1.189981845 1.390288906 1.443570516 1.235785098 1.17894277 1.242118724 1.762441932 1.210545352 1 15.14135984 S(ph)LQEEHVAVAQLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLQEEHVAVAQLR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 S(1)LQEEHVAVAQLR;S(1)LQEEHVAVAQLR 180.14 8.47E-06 917170000 743250 673710 289480 552560 721040 456880 537330 749570 595930 543430 TRUE FALSE 714202.9683 654496.4504 341795.4754 581077.6878 744232.9064 466118.4266 543906.0053 734091.1176 528282.5247 506623.0021 1.409732613 1.291880645 0.674654475 1.146962703 1.469007336 0.920049869 1.073591217 1.448988922 1.042752742 1 18.95055306 S(ph)LSSLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SLSSLR 6 0 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7;C9J1G1;Q70YC5-2;Q70YC5;Q70YC5-4;Q70YC5-3;Q8TF61 O94915;Q8TF61 FRYL;ZNF365;FBXO41 Protein furry homolog-like;Protein ZNF365;F-box only protein 41 1 S(1)LSSLR;S(0.994)LS(0.006)SLR;S(1)LSSLR;S(1)LSSLR 165.52 0.007604 1072570000 588480 478317 414214 511950 464307 405737 477795 681460 484746 439004 TRUE FALSE 565481.551 464675.8675 489071.6839 538371.8009 479241.8563 413941.2801 483642.3981 667387.6129 429719.6663 409269.8681 1.381683811 1.135377666 1.194985808 1.31544451 1.170967847 1.011414014 1.181720024 1.630678594 1.049966538 1 18.64269293 S(ph)LVGTPYWMAPELISR ddPTM_BT-474_Pertuzumab_2h_R1 13 SLVGTPYWMAPELISR 16 0 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 S(0.999)LVGT(0.001)PYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(0.987)LVGT(0.013)PYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(0.997)LVGT(0.003)PYWMAPELISR 325.77 5.38E-59 9059741000 2813380 2240264 1577413.7 2185010 2034710 1564066.9 1993453.7 3197980 2007221 1760216.2 TRUE FALSE 2703429.999 2176373.864 1862487.445 2297778.628 2100158.295 1595693.404 2017850.183 3131940.595 1779369.687 1640995.189 1.647433227 1.326252434 1.134974348 1.400234835 1.27980771 0.972393713 1.229650273 1.908561717 1.084323525 1 20.64613958 S(ph)MSDVSAEDVQNLR ddPTM_BT-474_Pertuzumab_2h_R1 4 SMSDVSAEDVQNLR 14 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.752)MS(0.248)DVSAEDVQNLR;S(0.968)MS(0.032)DVSAEDVQNLR;S(0.998)MS(0.002)DVSAEDVQNLR;S(1)MSDVSAEDVQNLR 362.78 5.75E-83 1044800000 1114350 740720 606510 857530 730240 571110 665450 1362430 727480 773850 TRUE FALSE 1070799.97 719595.3908 716119.8487 901787.2261 753728.8328 582658.2355 673593.9762 1334295.344 644899.5202 721436.4502 1.484260976 0.997448064 0.992630534 1.249988444 1.04476123 0.807636259 0.933684424 1.849498101 0.893910365 1 19.46051279 S(ph)MSIDDTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SMSIDDTPR 9 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0C4DGY6;A0A1B0GVW2 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 S(1)MSIDDTPR;S(0.989)MS(0.011)IDDTPR 191.24 3.79E-05 212250000 436220 444900 376420 453030 413590 409190 409620 472150 473530 461250 TRUE FALSE 419172.0401 432211.8876 444447.4674 476410.9326 426893.498 417464.1022 414633.0521 462399.9375 419776.8596 430009.1267 0.974798008 1.005122591 1.033576824 1.107908886 0.992754506 0.970826144 0.964242446 1.075325868 0.976204535 1 18.71400775 S(ph)PAVATSTAAPPPPS(ph)SPLPSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPAVATSTAAPPPPSSPLPSK 21 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 S(1)PAVATSTAAPPPPS(0.707)S(0.293)PLPSK 209.26 8.02E-32 0 178150 168980 208050 188830 178180 175150 196540 219920 195430 218520 TRUE FALSE 171187.701 164160.8558 245649.263 198575.5389 183911.3215 178691.653 198945.3153 215378.5751 173245.6057 203719.4458 0.840311048 0.805818292 1.205821379 0.974750045 0.902767631 0.877145784 0.976565171 1.057231303 0.850412709 1 17.63622417 S(ph)PDQCSSQGSMESLEPSGAYPPCHLSPAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPDQCSSQGSMESLEPSGAYPPCHLSPAK 29 0 A0A2R8Y5P9;Q8TF72;Q8TF72-2 A0A2R8Y5P9;Q8TF72-2 SHROOM3 Protein Shroom3 1 S(0.926)PDQCS(0.03)S(0.03)QGS(0.014)MESLEPSGAYPPCHLSPAK 103.07 0.0002122 164170000 44325 70676 61418 68302 60481 84657 50488 54212 62438 70413 TRUE FALSE 42592.73 68660.38968 72517.59884 71827.07441 62426.42629 86368.82254 51105.88725 53092.50326 55350.3 65643.86479 0.648845557 1.045952884 1.104712513 1.09419326 0.950986455 1.315718123 0.778532577 0.808796122 0.843190756 1 16.00237256 S(ph)PFEHSVEHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPFEHSVEHK 10 0 O14646;O14646-2 O14646 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 S(1)PFEHSVEHK 134.99 0.00010051 322420000 274890 306540 309650 322590 316030 307940 330120 55401 405230 373410 TRUE FALSE 264146.9949 297797.7793 365610.6431 339238.9086 326195.392 314166.7578 334160.1073 54256.94999 359229.9893 348118.6081 0.758784474 0.855449184 1.050247343 0.974492316 0.937023717 0.902470453 0.959903032 0.155857655 1.031918378 1 18.40921941 S(ph)PGMLEPLGSSR ddPTM_BT-474_Pertuzumab_2h_R1 16 SPGMLEPLGSSR 12 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR 225.14 1.93E-11 27069636000 4668299 5228050 5948810 6211273 5170183 5184929 5578283 5964638 5813894 6274708 TRUE FALSE 4485856.714 5078951.133 7023892.298 6531837.544 5336486.632 5289771.817 5646551.696 5841466.141 5153925.127 5849716.438 0.766850284 0.86823886 1.200723552 1.116607551 0.912264156 0.904278331 0.965269301 0.998589624 0.881055549 1 22.47993526 S(ph)PGPGPSQSPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGPGPSQSPR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(1)PGPGPSQSPR 112.44 0.00076063 0 13705 15463 9454.5 14972 10230 15037 13419 14158 15179 15815 TRUE FALSE 13169.39345 15022.01038 11163.13846 15744.70671 10559.05724 15341.05844 13583.22574 13865.63235 13455.94356 14743.83596 0.893213508 1.018867167 0.757139356 1.067884013 0.716167574 1.040506587 0.921281664 0.94043588 0.912648756 1 13.8478243 S(ph)PPHHSGFQQYQQADASK ddPTM_BT-474_Pertuzumab_2h_R1 2 SPPHHSGFQQYQQADASK 18 0 E9PD50;B1ALB4;Q92540-2;Q92540;Q92540-5;Q92540-4 E9PD50 SMG7 Protein SMG7 1 S(0.529)PPHHS(0.461)GFQQY(0.01)QQADASK;S(0.468)PPHHS(0.468)GFQQY(0.064)QQADASK 124.86 5.17E-05 530640000 214924 294728 305184 414696 297316 329307 368726 91660 346390 468990 TRUE FALSE 206524.5325 286322.646 360337.5376 436098.5103 306879.4392 335965.8132 373238.5791 89767.18897 307069.2594 437224.8896 0.472353101 0.654863556 0.824146901 0.997423799 0.701880077 0.76840505 0.85365355 0.205311251 0.702314225 1 18.738016 S(ph)PPLPAVIR ddPTM_BT-474_Pertuzumab_2h_R1 7 SPPLPAVIR 9 0 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR 95.523 0.0083784 22885050000 380934 370104 370099 330049 343418 295523 387860 378617 391040 403945 TRUE FALSE 366046.6781 359548.9963 436984.1221 347082.8684 354464.3519 301498.6775 392606.7467 370798.4266 346650.7786 376585.4454 0.972014938 0.954760734 1.160385053 0.921657681 0.941258767 0.800611604 1.042543602 0.98463292 0.920510293 1 18.52261772 S(ph)PPREGSQGELTPANSQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPREGSQGELTPANSQSR 19 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 S(0.999)PPREGS(0.001)QGELTPANSQSR 116.72 6.83E-05 726890000 12972 8978.3 0 11791 5042.8 0 11567 0 11606 0 TRUE FALSE 12465.0399 8722.247675 0 12399.53492 5205.006242 0 11708.56041 0 10288.53554 0 0 S(ph)PPSVQSLAMR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPPSVQSLAMR 11 0 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7;Q96KQ7-3 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 S(0.999)PPS(0.001)VQSLAMR 64.39 0.071965 518870000 10916 15594 10560 15924 10416 12283 12605 16443 11859 11097 TRUE FALSE 10489.39065 15149.27439 12468.42691 16745.83955 10751.0401 12531.37068 12759.26376 16103.4463 10512.81604 10345.39031 1.013919276 1.464350202 1.205215708 1.61867644 1.03921068 1.211299942 1.233328408 1.556581804 1.016183607 1 13.33670046 S(ph)PRPDHPGTPPHK ddPTM_BT-474_Pertuzumab_2h_R1 5 SPRPDHPGTPPHK 13 1 P30291 P30291 WEE1 Wee1-like protein kinase 1 S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK 146.3 2.55E-05 1451290000 807954 807380 677190 828528 763584 775883 810551 335939 1014720 884960 TRUE FALSE 776378.2644 784354.3129 799573.297 871288.4294 788145.3728 791571.8859 820470.7656 329001.7423 899533.2397 825020.871 0.941040756 0.950708449 0.969155236 1.05608047 0.955303557 0.959456801 0.99448486 0.398779902 1.090315738 1 19.65407109 S(ph)PSLGMLSTATR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSLGMLSTATR 12 0 Q14687;A0A1B0GUL3 Q14687 GSE1 Genetic suppressor element 1 1 S(0.995)PS(0.005)LGMLSTATR 115.35 0.0010065 125390000 16256 17109 19545 20425 24173 15771 19383 19492 21617 19297 TRUE FALSE 15620.69755 16621.06807 23077.21628 21479.1367 24950.5465 16089.90043 19620.21495 19089.48339 19163.12879 17989.997 0.868299063 0.923906106 1.28278044 1.193948876 1.38691221 0.894380384 1.090618022 1.061116541 1.065210227 1 14.13490733 S(ph)PSLGSDLTFATR ddPTM_BT-474_Pertuzumab_2h_R1 3 SPSLGSDLTFATR 13 0 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 S(0.991)PS(0.009)LGSDLTFATR;S(0.942)PS(0.058)LGSDLTFATR;S(0.957)PS(0.042)LGS(0.001)DLTFATR 169.54 2.97E-05 1223800000 631410 567870 529790 599890 593700 537060 667580 487750 786410 616080 TRUE FALSE 606733.7991 551674.9036 625534.8381 630850.3948 612796.8997 547919.7212 675750.0437 477677.7921 697140.0337 574352.3529 1.056379061 0.960516486 1.08911339 1.098368261 1.066935474 0.95397837 1.176542658 0.831680744 1.213784588 1 19.13157655 S(ph)QPLLIPTTGR ddPTM_BT-474_Pertuzumab_2h_R1 3 SQPLLIPTTGR 11 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(1)QPLLIPTTGR;S(1)QPLLIPTTGR;S(1)QPLLIPTTGR 96.135 0.0075925 892570000 303722 282324 198795 236342 260423 220494 242001 369767 260346 253296 TRUE FALSE 291852.2085 274272.3959 234721.6787 248539.6389 268799.7423 224952.5398 244962.6806 362131.1822 230792.6135 236140.0363 1.235928532 1.161481976 0.993993574 1.052509531 1.138306517 0.952623466 1.037361917 1.533544196 0.977354866 1 17.84928314 S(ph)REEENEHHGPSMPALIAPEDSPHCDLFPGASYLVTQIPGTQTESR ddPTM_BT-474_Pertuzumab_2h_R1 1 SREEENEHHGPSMPALIAPEDSPHCDLFPGASYLVTQIPGTQTESR 46 1 A0A2R8YF49;A0A5F9ZH52;A5YM69 A0A2R8YF49;A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 S(0.486)REEENEHHGPS(0.486)MPALIAPEDS(0.027)PHCDLFPGASYLVTQIPGTQTESR 73.238 0.00030629 122990000 17182 17906 12167 21206 20398 17556 20104 7056.1 26676 22646 TRUE FALSE 16510.50844 17395.33841 14365.84755 22300.4442 21054.12019 17910.99435 20350.03877 6910.389069 23647.85231 21112.16625 0.782037629 0.823948533 0.680453506 1.056284037 0.997250587 0.84837312 0.963901029 0.32731786 1.120105442 1 14.365787 S(ph)RS(ph)PTPPSS(ph)AGLGSNSAPPIPDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPTPPSSAGLGSNSAPPIPDSR 24 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 3 S(0.921)RS(0.951)PT(0.145)PPS(0.46)S(0.523)AGLGSNSAPPIPDSR 98.94 0.0085806 358380000 106090 94929 78029 109150 87290 95503 90715 95583 109640 103520 TRUE FALSE 101943.8855 92221.71787 92130.57605 114783.2446 90097.76212 97434.13609 91825.19731 93609.17765 97194.12685 96508.49819 1.056320297 0.955581318 0.954636926 1.189358934 0.933573352 1.009591258 0.951472658 0.969957873 1.007104335 1 16.55836837 S(ph)RS(ph)PVDLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SRSPVDLR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PVDLR;S(1)RS(1)PVDLR 82.85 0.010928 1939170000 1227090 1228150 934190 1035570 1049390 1111740 1095910 1269610 1277140 1133710 TRUE FALSE 1179133.966 1193124.364 1103018.914 1089015.892 1083144.582 1134220.145 1109322.074 1243392.11 1132164.421 1056922.812 1.115629214 1.12886613 1.043613499 1.030364639 1.024809542 1.073134321 1.049577189 1.1764266 1.071189314 1 20.01143859 S(ph)RSGSSQELDVKPSASPQER ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSGSSQELDVKPSASPQER 20 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.312)RS(0.312)GS(0.312)S(0.064)QELDVKPSASPQER 90.836 0.00098104 136800000 95438 122780 59652 95441 82084 84586 90300 118140 105810 83920 TRUE FALSE 91708.17745 119278.4346 70432.44335 100366.7214 84724.30641 86296.38687 91405.11841 115700.3677 93798.89239 78236.02365 1.172198856 1.524597354 0.900255919 1.282870943 1.082932164 1.103026238 1.168325206 1.47886309 1.198922031 1 16.25554543 S(ph)RSPIIHSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPIIHSPK 10 1 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 S(0.5)RS(0.5)PIIHSPK 62.466 0.051275 191960000 361280 400680 315290 390620 381360 344920 413890 266100 474420 389870 TRUE FALSE 347160.7782 389252.9987 372269.9166 410779.945 393626.7907 351894.5187 418955.3096 260604.942 420565.8305 363463.7576 0.955145516 1.070954092 1.024228438 1.130181308 1.082987733 0.968169484 1.152674237 0.717003928 1.157105273 1 18.47145199 S(ph)RTPLLPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SRTPLLPR 8 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.967)RT(0.033)PLLPR;S(0.896)RT(0.104)PLLPR;S(0.793)RT(0.207)PLLPR;S(0.992)RT(0.008)PLLPR 128.03 0.00069692 1520870000 431712 495515 465692 513580 524619 436302 547843 255701 603448 566280 TRUE FALSE 414840.2178 481383.3974 549852.9037 540085.9253 541493.8466 445124.3254 554547.6665 250420.685 534947.1129 527925.3512 0.785793326 0.911839896 1.041535328 1.023034647 1.025701542 0.843157701 1.050428181 0.474348664 1.013300672 1 19.00997442 S(ph)RTSPAPWKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSPAPWKR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.333)RT(0.333)S(0.333)PAPWKR 71.176 0.027013 279320000 168060 233290 164850 191340 222970 232360 219800 165730 233090 219130 TRUE FALSE 161492.0294 226636.7976 194642.0621 201215.0803 230142.0325 237058.4784 222489.9781 162307.6176 206630.6004 204288.1299 0.790511076 1.109397779 0.952782044 0.984957278 1.126556069 1.160412396 1.089098903 0.794503419 1.011466503 1 17.64024585 S(ph)RTSVQT(ph)EDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.938)RT(0.062)S(0.199)VQT(0.8)EDDQLIAGQSAR 203.05 1.31E-14 997720000 623180 739340 587170 857470 541210 669510 625580 810820 714600 713140 TRUE FALSE 598825.4366 718254.7471 693284.6805 901724.1295 558618.5112 683047.9509 633236.0352 794076.2837 633481.6038 664838.3926 0.900708267 1.08034487 1.042786771 1.356305742 0.840232028 1.027389451 0.952466106 1.194389934 0.952835472 1 19.34264417 S(ph)SQSASSLEVAGPGREPLELEVAVEALAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSQSASSLEVAGPGREPLELEVAVEALAR 29 1 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 1 S(0.489)S(0.489)QS(0.023)ASSLEVAGPGREPLELEVAVEALAR 114.03 0.00014273 17037000 937.98 865.06 996.92 0 1352.6 1316.7 0 0 0 0 TRUE FALSE 901.3227046 840.3893358 1177.08562 0 1396.107607 1343.324576 0 0 0 0 0 S(ph)TDKEAQGQQFHHHR ddPTM_BT-474_Pertuzumab_2h_R1 3 STDKEAQGQQFHHHR 15 1 A6ND36 A6ND36 FAM83G Protein FAM83G 1 S(0.5)T(0.5)DKEAQGQQFHHHR;S(0.835)T(0.165)DKEAQGQQFHHHR;S(0.831)T(0.169)DKEAQGQQFHHHR 155.28 1.41E-06 235890000 175307 153510 105226 144107 177261 144386 187183 57832.3 208839 140948 TRUE FALSE 168455.8086 149132.0451 124242.6789 151544.3795 182962.761 147305.5838 189473.8015 56638.0428 185132.4722 131401.4664 1.281993369 1.134934405 0.945519729 1.15329291 1.392395123 1.121034551 1.441945868 0.431030523 1.408907201 1 17.00362185 S(ph)VEDVRPHHTDANNQSACFEAPDQK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVEDVRPHHTDANNQSACFEAPDQK 25 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.999)VEDVRPHHT(0.001)DANNQSACFEAPDQK;S(0.918)VEDVRPHHT(0.082)DANNQSACFEAPDQK;S(0.761)VEDVRPHHT(0.239)DANNQSACFEAPDQK;S(0.943)VEDVRPHHT(0.055)DANNQS(0.002)ACFEAPDQK 201.1 3.83E-25 10066340000 4253990 4061720 3389620 3402530 3547900 3868360 3862570 249029 4743400 3856200 TRUE FALSE 4087739.368 3945883.722 4002199.736 3578134.981 3662021.426 3946580.89 3909841.287 243886.4641 4204949.118 3595016.139 1.137057306 1.097598333 1.113263357 0.995304289 1.018638383 1.097792259 1.087572666 0.067840158 1.169660707 1 21.77756682 S(ph)VSPPPKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.93)VS(0.07)PPPKR;S(0.848)VS(0.152)PPPKR 82.749 0.011923 1308410000 1522980 1607650 1407070 1529190 1548720 1825230 1541850 1404530 1922570 2072130 TRUE FALSE 1463460.258 1561801.396 1661358.849 1608111.679 1598535.985 1862137.401 1560719.622 1375525.965 1704327.914 1931782.789 0.757569777 0.808476711 0.860013278 0.832449532 0.827492612 0.963947609 0.807916723 0.712050015 0.882256495 1 20.88150146 SAATLITHPFHVITLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SAATLITHPFHVITLR 16 0 E9PIE4;Q9Y6C9 E9PIE4 MTCH2 Mitochondrial carrier homolog 2 0 185.12 9.90E-10 163780000 50217 102910 76386 172850 56607 58630 141350 34911 104550 95959 FALSE TRUE 48254.46412 99975.10756 90190.6494 181770.8092 58427.81556 59815.53877 143079.8836 34190.07565 92681.92231 89459.61146 0.539399438 1.117544621 1.008171709 2.031875684 0.653119487 0.668631775 1.599379667 0.382184486 1.036019728 1 16.44894887 SACGVCPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SACGVCPGR 9 0 P49207 P49207 RPL34 60S ribosomal protein L34 0 ; 127.12 0.0010572 154758000 110404 115587 95697 111797 121760 104005 112368 107431 126043 111636 FALSE TRUE 106089.2896 112290.5719 112991.5767 117566.8566 125676.521 106108.0524 113743.1932 105212.5123 111735.1271 104074.7943 1.019356227 1.078941089 1.085676676 1.129638135 1.207559639 1.019536508 1.092898564 1.010931735 1.073604112 1 16.66726118 SAEAFGK ddPTM_BT-474_Pertuzumab_2h_R1 2 SAEAFGK 7 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 107.43 0.0174 523280000 681760 688940 571170 648590 663170 686790 702830 700560 770920 805680 FALSE TRUE 655116.0655 669292.1057 674393.1246 682063.8076 684501.4653 700677.3644 711431.4438 686093.1912 683408.3936 751110.576 0.872196567 0.891070006 0.897861309 0.908073764 0.911319168 0.932855144 0.947172715 0.913438331 0.909863894 1 19.51866579 SALSSS(ph)LR ddPTM_BT-474_Pertuzumab_2h_R1 2 SALSSSLR 8 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SALSS(0.001)S(0.999)LR;SALSS(0.003)S(0.997)LR 125.75 0.0013099 1312320000 2067000 2021700 1895300 2137400 1921640 1747080 1903450 2490600 2093400 2126900 TRUE FALSE 1986219.355 1964043.095 2237822.871 2247711.47 1983451.296 1782407.155 1926744.99 2439168.24 1855766.008 1982843.169 1.0017027 0.990518628 1.128592975 1.133580056 1.000306695 0.898914843 0.971708212 1.230136744 0.935911643 1 20.91913914 SAS(ph)FNTDPYVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SASFNTDPYVR 11 0 Q9UKV8-2;Q9UKV8 Q9UKV8-2 AGO2 Protein argonaute-2 1 S(0.011)AS(0.986)FNT(0.003)DPYVR 77.22 0.034838 144460000 406460 414470 287390 369730 394600 353920 372110 480890 389200 356070 TRUE FALSE 390575.0938 402649.7214 339327.766 388811.8096 407292.6674 361076.5049 376663.9935 470959.4535 345019.6477 331953.0617 1.176597353 1.212971856 1.022216105 1.171285505 1.22695861 1.087733618 1.134690524 1.418753154 1.039362752 1 18.34061973 SDEGSVLLLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDEGSVLLLHR 11 0 O43593-2;O43593 O43593-2 HR Lysine-specific demethylase hairless 0 85.377 0.0088252 65460000 32486 31600 36082 40330 42635 36562 40569 16403 46822 39125 FALSE TRUE 31216.4112 30698.79894 42602.82004 42411.43613 44006.3935 37301.30869 41065.49556 16064.27232 41506.96285 36475.0289 0.85582965 0.841638783 1.167999624 1.16275264 1.206480017 1.0226533 1.12585231 0.440418357 1.137955585 1 15.1546215 SDFFELLSNHHLDSQSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SDFFELLSNHHLDSQSR 17 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 135.27 8.21E-06 304940000 165610 226190 193450 260080 227730 238540 247790 105190 241170 277350 FALSE TRUE 159137.7781 219739.2827 228410.7183 273502.76 235055.1423 243363.4422 250822.5281 103017.7897 213793.3927 258564.8375 0.615465659 0.849842093 0.883378887 1.057772444 0.909076209 0.941208575 0.970056604 0.398421497 0.826846352 1 17.98016657 SDHPGISITDLSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SDHPGISITDLSK 13 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ;;; 162.93 3.96E-05 1798860000 2907070 3434410 2868990 3397260 3067060 3396280 3397850 3101790 3908810 4172620 FALSE TRUE 2793458.49 3336463.989 3387480.313 3572592.996 3165714.77 3464955.109 3439433.905 3037736.953 3465098.276 3890004.731 0.718111849 0.857701782 0.870816502 0.918403252 0.813807435 0.890732878 0.884172165 0.780908293 0.890769682 1 21.89134048 SDQDS(ph)DSDQPSRK ddPTM_BT-474_Pertuzumab_2h_R1 1 SDQDSDSDQPSRK 13 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 S(0.001)DQDS(0.988)DS(0.01)DQPSRK 76.713 0.0063477 0 51038 53931 46797 44402 53540 57816 50712 55353 60555 60835 TRUE FALSE 49043.37853 52392.94068 55254.25889 46693.59254 55262.16272 58985.07913 51332.62863 54209.94121 53681.05027 56714.59126 0.864740051 0.923800022 0.974251205 0.823308279 0.974390567 1.040033575 0.905104445 0.955837642 0.94651216 1 15.79143233 SDRPVYEGPSMFGGER ddPTM_BT-474_Pertuzumab_2h_R1 1 SDRPVYEGPSMFGGER 16 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 124.04 0.00072555 0 55801 68106 57037 64584 62168 60302 54571 87938 58713 66736 FALSE TRUE 53620.23523 66163.68356 67344.85468 67917.18798 64167.69018 61521.34776 55238.85622 86122.04957 52048.14638 62215.91128 0.861841193 1.063452776 1.082437809 1.091636956 1.031371057 0.98883624 0.887857384 1.384244766 0.836572917 1 15.92499597 SDS(ph)DSSTLPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SDSDSSTLPR 10 0 Q9ULE0 Q9ULE0 WWC3 Protein WWC3 1 SDS(1)DSSTLPR;SDS(0.999)DS(0.001)STLPR 209.97 8.99E-08 827660000 894110 931490 669460 817760 868740 830750 822250 1090570 954090 953960 TRUE FALSE 859167.1927 904924.8172 790446.3141 859964.6916 896683.8111 847548.3342 832312.9415 1068049.348 845785.7031 889347.4395 0.966064729 1.017515514 0.888793602 0.966961452 1.008249163 0.953000252 0.935869273 1.200935991 0.951018315 1 19.76238762 SDS(ph)FENPVLQQHFR ddPTM_BT-474_Pertuzumab_2h_R1 6 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 S(0.004)DS(0.996)FENPVLQQHFR;S(0.011)DS(0.989)FENPVLQQHFR;S(0.001)DS(0.999)FENPVLQQHFR;SDS(1)FENPVLQQHFR;SDS(1)FENPVLQQHFR;S(0.011)DS(0.989)FENPVLQQHFR 304.62 2.15E-44 4211910000 3032310 2361840 1656170 2186870 2598870 1835440 2808430 3551520 1943220 1808330 TRUE FALSE 2913803.973 2294482.636 1955476.76 2299734.623 2682465.014 1872553.854 2842800.406 3478179.871 1722633.812 1685850.198 1.728388427 1.361024033 1.159935065 1.364139367 1.591164515 1.110747477 1.686271063 2.063160697 1.021819029 1 20.68504492 SDSFENPVLQQHFR ddPTM_BT-474_Pertuzumab_2h_R1 7 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;;;; 264.29 1.12E-24 16957650000 7104010 7849000 6372270 7330770 7259810 6247930 7696500 6941080 7800880 7828220 FALSE TRUE 6826377.435 7625154.205 7523880.939 7709111.918 7493328.382 6374267.425 7790692.069 6797744.272 6915356.806 7298007.687 0.935375479 1.044826826 1.030949988 1.056331022 1.026763564 0.873425694 1.067509436 0.931452057 0.947567761 1 22.79907124 SDSKSS(ph)PQAGR ddPTM_BT-474_Pertuzumab_2h_R1 3 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.006)KS(0.028)S(0.967)PQAGR;SDS(0.001)KS(0.023)S(0.976)PQAGR;SDS(0.014)KS(0.087)S(0.899)PQAGR 162.94 1.49E-05 1081171000 1162180 1161100 901400 982400 948760 1020510 1210390 1173490 1110600 1194180 TRUE FALSE 1116760.721 1127986.565 1064303.032 1033101.782 979277.727 1041145.411 1225203.115 1149257.021 984529.344 1113297.125 1.003111115 1.013194537 0.955991898 0.927965912 0.87961938 0.935190964 1.100517631 1.032300359 0.884336555 1 20.08640725 SDSQASLTVPLS(ph)PQVVR ddPTM_BT-474_Pertuzumab_2h_R1 4 SDSQASLTVPLSPQVVR 17 0 Q8TEV9;Q8TEV9-2 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR;SDSQASLT(0.007)VPLS(0.993)PQVVR 295.17 4.34E-46 556650000 625490 769810 642830 717520 667960 781970 655250 699290 721560 749260 TRUE FALSE 601045.1593 747855.7725 759003.6807 754551.2932 689445.54 797781.9692 663269.1455 684849.4171 639651.5338 698511.9528 0.860465103 1.070641339 1.086600849 1.080226745 0.98702039 1.142116418 0.949545878 0.980440513 0.915734557 1 19.41392528 SEDFSLPAYMDRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEDFSLPAYMDRR 13 1 H3BN72;H3BNV9;P13073;Q86WV2;H3BNI5 H3BN72 COX4I1 "Cytochrome c oxidase subunit 4 isoform 1, mitochondrial" 0 101.53 0.0030456 245860000 50602 116100 35844 106430 43418 66011 102300 89025 62025 33742 FALSE TRUE 48624.4179 112788.9417 42321.80815 111922.8651 44814.5794 67345.78765 103551.978 87186.60264 54984.18203 31456.62429 1.545760837 3.585538634 1.345402093 3.558006226 1.424646809 2.14090956 3.291897346 2.77164523 1.747936509 1 14.94107624 SEESLEEEPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SEESLEEEPR 10 0 Q495Y7 Q495Y7 SPDYE7P Putative speedy protein E7 0 65.347 0.069241 256020000 268350 293640 234310 267480 268540 339560 228310 246650 260830 289710 FALSE TRUE 257862.5853 285265.6747 276655.0292 281284.6749 277177.833 346426.1359 231104.1261 241556.5913 231221.6719 270087.6837 0.954736558 1.056196532 1.024315605 1.041456874 1.026251287 1.282643219 0.855663327 0.894363593 0.856098541 1 18.04306833 SELDMLDIR ddPTM_BT-474_Pertuzumab_2h_R1 2 SELDMLDIR 9 0 P08133;P08133-2 P08133 ANXA6 Annexin A6 0 ; 118.5 0.0022801 53024000 223482 315610 141288 423600 204563 188286 231270 292280 280300 285610 FALSE TRUE 214748.0764 306609.1118 166821.8845 445462.0468 211142.9547 192093.2719 234100.3514 286244.3159 248481.5191 266265.3803 0.806518955 1.151517 0.626524877 1.673000246 0.792979374 0.721435403 0.879199358 1.075033921 0.933210013 1 18.02250534 SEPLDAVLIEDELEELHR ddPTM_BT-474_Pertuzumab_2h_R1 2 SEPLDAVLIEDELEELHR 18 0 Q8WXH0;Q8WXH0-2;G3V5X4;A0A0A0MRE3;A0A0C4DGK3;Q8WXH0-7;Q8WXH0-10;Q8WXH0-4;Q8WXH0-3;Q8WXH0-13 Q8WXH0;Q8WXH0-13 SYNE2 Nesprin-2 0 ; 200.69 1.49E-15 78657000 63166 97718 57770 105484 67413 72601 77090 96294 89428 76329 FALSE TRUE 60697.40289 94931.17832 68210.32409 110928.0419 69581.40037 74069.04196 78033.45048 94305.49525 79276.50835 71159.16884 0.852980774 1.334068116 0.958559876 1.558872085 0.977827615 1.040892455 1.096604299 1.32527539 1.114072995 1 16.11876204 SESQESLVTS(ph)PSKPK ddPTM_BT-474_Pertuzumab_2h_R1 1 SESQESLVTSPSKPK 15 1 E7EWD6;Q76L83;Q76L83-2;A0A5F9ZHN2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 SESQESLVT(0.071)S(0.909)PS(0.02)KPK 97.081 0.0020903 480410000 525040 473710 370780 382050 482450 462740 437490 546400 528150 446840 TRUE FALSE 504520.8563 460200.2546 437788.194 401767.6463 497968.4424 472096.9198 442844.1335 535116.6491 468196.6262 416575.1288 1.211116126 1.104723309 1.050922544 0.964454233 1.195386877 1.133281579 1.063059465 1.284562164 1.123918818 1 18.66821718 SFS(ph)MQDLR ddPTM_BT-474_Pertuzumab_2h_R1 3 SFSMQDLR 8 0 Q9H6H4;E5RGS2 Q9H6H4 REEP4 Receptor expression-enhancing protein 4;Receptor expression-enhancing protein 1 S(0.007)FS(0.993)MQDLR;S(0.012)FS(0.988)MQDLR;S(0.245)FS(0.755)MQDLR 132.17 0.0010213 674690000 1904030 1450380 734900 1385660 1248920 713000 1067020 2522610 1106700 686840 TRUE FALSE 1829618.403 1409016.582 867712.7778 1457174.079 1289092.646 727417.3485 1080078.51 2470517.222 981072.0557 640319.715 2.857351351 2.200489145 1.355124257 2.275697662 2.013201555 1.136022102 1.686780033 3.858255749 1.532159689 1 19.2884329 SGAHSS(ph)ASPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SGAHSSASPPR 11 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 1 SGAHS(0.007)S(0.668)AS(0.324)PPR 61.212 0.057161 74311000 16607 14166 14675 14009 17138 14496 17542 15045 17937 19694 TRUE FALSE 15957.98008 13761.99955 17327.09894 14732.00617 17689.25933 14789.11905 17756.68424 14734.31549 15900.86696 18360.10784 0.869165923 0.749559843 0.943736229 0.802392137 0.963461625 0.805502842 0.967133984 0.802517917 0.866055205 1 14.16428691 SGGASHSELIHNLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGGASHSELIHNLR 14 0 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8;F8WDT3;F8WAV5;F8WAX2;H7C4X2 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ; 193.28 1.60E-07 1503790000 1587550 1740780 1410260 1755530 1565710 1552640 1692890 656400 1903540 1896600 FALSE TRUE 1525506.791 1691134.659 1665125.353 1846133.114 1616072.484 1584035.445 1713608.094 642845.1106 1687458.119 1768141.593 0.862774111 0.95644753 0.941737562 1.044109319 0.913994949 0.895875902 0.969157731 0.363571059 0.954368206 1 20.75380238 SGLEPAS(ph)SPSKGSEPRPLVPPVSGHATIAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGLEPASSPSKGSEPRPLVPPVSGHATIAR 30 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.001)GLEPAS(0.498)S(0.498)PS(0.003)KGSEPRPLVPPVSGHATIAR;S(0.001)GLEPAS(0.534)S(0.453)PS(0.011)KGS(0.001)EPRPLVPPVSGHATIAR 160.63 2.06E-12 862910000 345860 452050 283910 309850 315390 393960 345880 368630 376920 380870 TRUE FALSE 332343.4088 439157.9766 335218.8525 325841.3956 325534.8058 401926.1411 350112.9829 361017.6617 334133.6218 355073.3357 0.935985261 1.236809224 0.94408343 0.917673514 0.916810059 1.131952475 0.986030061 1.016741122 0.941027073 1 18.4377575 SGPPS(ph)PPSTATSFGGPRPR ddPTM_BT-474_Pertuzumab_2h_R1 4 SGPPSPPSTATSFGGPRPR 19 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 SGPPS(1)PPSTATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR;SGPPS(0.999)PPSTATSFGGPRPR;SGPPS(0.999)PPS(0.001)TATSFGGPRPR 222.06 1.53E-19 6055700000 967190 1000920 837100 865160 943540 985490 907730 985790 1090760 1021110 TRUE FALSE 929391.1455 972374.7416 988382.5912 909811.0113 973889.821 1005417.283 918839.0713 965433.092 966941.4976 951949.3102 0.976303187 1.021456428 1.038272291 0.955734724 1.023047982 1.056166828 0.965218485 1.014164391 1.015748935 1 19.86052523 SGQVYSFGCNDEGALGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SGQVYSFGCNDEGALGR 17 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 ; 100.22 0.0032275 203521000 85608 72645 71957 70730 72955 90243 68952 85092 83897 87240 FALSE TRUE 82262.34472 70573.23573 84961.23057 74380.38378 75301.66383 92067.77529 69795.8552 83334.82046 74373.36428 81331.15709 1.011449334 0.867726936 1.044633245 0.914537386 0.925864902 1.132011133 0.858168723 1.024635865 0.914451078 1 16.31152052 SGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK ddPTM_BT-474_Pertuzumab_2h_R1 1 SGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK 39 0 P28072;A0A087X2I4 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 481.75 5.50E-296 325030000 153090 139520 139240 146690 164520 151600 152540 137810 193900 181750 FALSE TRUE 147107.0736 135541.0262 164403.7654 154260.6885 169811.9352 154665.4559 154406.8301 134964.1753 171889.2849 169439.9106 0.868196123 0.799935657 0.970277692 0.910415308 1.002195614 0.912804163 0.911277807 0.7965312 1.01445571 1 17.37041421 SGSLDDS(ph)FSDFQELPASSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SGSLDDSFSDFQELPASSK 19 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 SGSLDDS(0.999)FS(0.001)DFQELPASSK;SGSLDDS(0.866)FS(0.134)DFQELPASSK;SGSLDDS(0.692)FS(0.308)DFQELPASSK;SGSLDDS(0.94)FS(0.06)DFQELPASSK 410.31 9.58E-116 481970000 848140 724350 700640 674728 801760 713830 721430 899050 790813 847290 TRUE FALSE 814993.7511 703692.2472 827261.2337 709550.7929 827549.3385 728264.1317 730259.0761 880484.3033 701043.2236 789902.2936 1.031765267 0.890859861 1.047295647 0.898276659 1.047660382 0.921967359 0.924492918 1.114674955 0.887506251 1 19.59131469 SGYFDER ddPTM_BT-474_Pertuzumab_2h_R1 2 SGYFDER 7 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J6W7;C9JT96 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 81.635 0.081085 347970000 1618980 1913520 1648830 2180030 1657010 1663690 1879020 1945540 1793040 1689080 FALSE TRUE 1555708.472 1858948.283 1946810.259 2292541.61 1710309.232 1697330.952 1902016.009 1905363.919 1589501.616 1574677.107 0.987953952 1.180526646 1.236323466 1.455880446 1.086133293 1.077891425 1.20787684 1.210002934 1.009414317 1 20.5866246 SHDDGNIDLESDSFLK ddPTM_BT-474_Pertuzumab_2h_R1 3 SHDDGNIDLESDSFLK 16 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 0 ;; 214.22 1.72E-14 718272000 468463 501110 462157 502951 532541 468770 513516 238771 654119 626175 FALSE TRUE 450154.948 486818.8334 545679.0505 528908.3614 549670.6649 478248.8506 519800.5624 233840.2954 579866.1534 583763.6095 0.771125402 0.83393145 0.934760306 0.906031744 0.94159803 0.81925088 0.890429883 0.400573608 0.993323571 1 19.15502475 SHDLKPNGGNILVTEENKEEYIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHDLKPNGGNILVTEENKEEYIR 23 2 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8 A0A590UJQ1 ITCH E3 ubiquitin-protein ligase Itchy homolog 0 152.88 3.42E-08 151900000 328100 274900 284860 283600 305590 336890 341930 138140 443340 409830 FALSE TRUE 315277.4893 267060.1212 336340.5387 298236.63 315419.5799 343702.1466 346114.6416 135287.3607 393013.9018 382071.8491 0.825178537 0.698978796 0.88030704 0.780577346 0.825550432 0.899574641 0.905888886 0.354088795 1.028638731 1 18.54348444 SHISDQS(ph)PLSSK ddPTM_BT-474_Pertuzumab_2h_R1 5 SHISDQSPLSSK 12 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SHISDQS(0.968)PLS(0.016)S(0.016)K;SHISDQS(1)PLSSK;SHISDQS(0.998)PLS(0.001)S(0.001)K;SHISDQS(0.997)PLS(0.003)SK;SHISDQS(1)PLSSK 240.82 3.34E-16 2233150000 2956170 3719160 3422660 3984260 3148910 4018540 3950590 1223648 3575120 4352490 TRUE FALSE 2840639.608 3613093.198 4041210.799 4189888.136 3250197.55 4099797.632 3998938.502 1198379.241 3169287.366 4057691.976 0.700062899 0.890430624 0.995938288 1.032579151 0.800996618 1.01037675 0.98552047 0.295335193 0.781056666 1 21.95222792 SHISDQSPLSSK ddPTM_BT-474_Pertuzumab_2h_R1 2 SHISDQSPLSSK 12 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 ; 117.93 0.00022618 227150000 247080 337580 290870 363590 311560 335490 332350 131713 361630 372580 FALSE TRUE 237423.8404 327952.5489 343436.6794 382354.9235 321581.6104 342273.8377 336417.3987 128993.0805 320579.2785 347344.8247 0.683539306 0.944169959 0.988748514 1.100793495 0.925828132 0.985400712 0.968540121 0.371368943 0.922942435 1 18.40600908 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPS(ph)PPQEEAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTSAPS(0.003)APPAS(0.094)S(0.094)QGPDT(0.156)APRPS(0.654)PPQEEAR 194.23 5.10E-29 1439300000 67318 73962 55714 83213 79741 72949 77641 19594 87757 85062 TRUE FALSE 64687.13814 71852.67618 65782.75915 87507.6329 82305.94168 74424.07876 78591.19378 19189.37705 77795.19327 79300.67497 0.815719893 0.906078999 0.82953593 1.103491653 1.037897114 0.938504985 0.991053277 0.241982519 0.981015525 1 16.27504553 SHQGLDR ddPTM_BT-474_Pertuzumab_2h_R1 2 SHQGLDR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 107.29 0.017471 250730000 206142 205159 185313 247390 214296 222620 223000 73273 240070 236870 FALSE TRUE 198085.7427 199308.0662 218803.1814 260157.8275 221189.0255 227121.5289 225729.1407 71759.88694 212818.2601 220826.5839 0.897019459 0.902554677 0.990837142 1.178109188 1.001641295 1.028506283 1.022200936 0.324960363 0.963734784 1 17.75255433 SHS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.017)HS(0.406)GT(0.256)S(0.322)PDNTAPPPPPPRPQPSHSR;S(0.044)HS(0.742)GT(0.161)S(0.053)PDNTAPPPPPPRPQPSHSR;S(0.051)HS(0.343)GT(0.303)S(0.303)PDNTAPPPPPPRPQPSHSR 153.12 6.61E-08 4357300000 223845 255973 194505 248639 221938 260141 286128 46071.5 317797 250977 TRUE FALSE 215096.8899 248672.9007 229656.3802 261471.2886 229076.8373 265401.2293 289629.7201 45120.10743 281722.0169 233978.1042 0.919303499 1.062804152 0.981529366 1.117503236 0.979052455 1.134299426 1.237849674 0.192839016 1.204052908 1 17.836014 SHSGT(ph)SPDNTAPPPPPPRPQPSHSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.006)HS(0.152)GT(0.467)S(0.375)PDNTAPPPPPPRPQPSHSR 143.27 4.82E-07 1543100000 54689 53333 52618 62217 49051 56480 67944 14331 74801 67080 TRUE FALSE 52551.69342 51811.99506 62127.24308 65428.02683 50628.76996 57622.0643 68775.519 14035.05984 66309.90407 62536.61185 0.840334835 0.82850659 0.993453934 1.046235555 0.809586072 0.921413274 1.099764074 0.224429489 1.060337331 1 15.93241344 SIS(ph)PSALQDLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 SISPSALQDLLR 12 0 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 1 SIS(1)PSALQDLLR;SIS(0.999)PSALQDLLR 178.67 2.28E-05 104305000 97458 101265 79955 96941 94593 78094 103451 103720 101280 103119 TRUE FALSE 93649.23361 98377.02135 94404.64709 101944.1366 97635.66975 79673.11419 104717.0643 101578.1458 89783.119 96134.65828 0.974146424 1.023325231 0.982004292 1.060430634 1.015613635 0.828765771 1.089274838 1.056623569 0.933930807 1 16.55276902 SKEPHELVGS(ph)SPHR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKEPHELVGSSPHR 14 1 Q3T8J9-3;Q3T8J9 Q3T8J9-3 GON4L GON-4-like protein 1 SKEPHELVGS(0.914)S(0.086)PHR;SKEPHELVGS(0.893)S(0.107)PHR;SKEPHELVGS(0.634)S(0.366)PHR 186.97 6.05E-07 917740000 818040 898500 811910 922870 873440 961130 940080 484240 989980 1047890 TRUE FALSE 786070.0924 872875.6597 958640.1978 970499.4313 901534.9908 980564.7071 951584.9802 474240.2748 877601.6207 976915.4769 0.804644937 0.893501721 0.981292876 0.993432343 0.922838272 1.003735462 0.974070943 0.485446577 0.898339356 1 19.89787422 SKEPHELVGSS(ph)PHR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKEPHELVGSSPHR 14 1 Q3T8J9-3;Q3T8J9 Q3T8J9-3 GON4L GON-4-like protein 1 SKEPHELVGS(0.204)S(0.796)PHR 186.05 6.69E-07 162450000 240520 275970 236740 285980 266080 286230 277780 157610 312620 322700 TRUE FALSE 231120.2125 268099.6058 279524.1843 300739.4621 274638.7048 292017.7667 281179.5547 154355.2984 277132.6882 300843.2416 0.768241332 0.891160474 0.929135661 0.999655038 0.912896376 0.970664208 0.934638097 0.513075506 0.921186352 1 18.19865242 SKESSQVTSR ddPTM_BT-474_Pertuzumab_2h_R1 3 SKESSQVTSR 10 1 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;; 127.56 0.00032184 105968000 178746 202668 142016 180092 163454 182326 191755 185373 200816 197504 FALSE TRUE 171760.4087 196888.1071 167681.4503 189386.5697 168711.6464 186012.7566 194101.7551 181544.9828 178020.2096 184126.8782 0.932837239 1.069306714 0.910684263 1.028565583 0.916279296 1.010242277 1.054173932 0.985977629 0.966834453 1 17.49034072 SKGGVVGIK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKGGVVGIK 9 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 130.94 0.0012227 0 2590100 2312800 1844700 2120100 2305500 2084300 2377500 2483700 2832600 2288700 FALSE TRUE 2488876.028 2246841.208 2178078.325 2229518.615 2379658.501 2126445.974 2406596.556 2432410.727 2511055.123 2133684.31 1.16646873 1.053033571 1.020806271 1.044914941 1.115281436 0.996607588 1.127906572 1.140004974 1.176863471 1 21.02491531 SKPAGS(ph)DGERR ddPTM_BT-474_Pertuzumab_2h_R1 7 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.003)KPAGS(0.997)DGERR;SKPAGS(1)DGERR;SKPAGS(1)DGERR;SKPAGS(1)DGERR;S(0.053)KPAGS(0.947)DGERR;S(0.272)KPAGS(0.728)DGERR;S(0.154)KPAGS(0.846)DGERR 114.69 0.00063837 6022910000 6189591 5775515 4493509 5298712 5410665 5506466 5515576 5991363 6352544 5761063 TRUE FALSE 5947694.941 5610802.967 5305586.034 5572179.161 5584703.954 5617810.515 5583077.269 5867639.26 5631429.837 5370861.072 1.107400631 1.044674754 0.987846448 1.037483392 1.039815381 1.045979488 1.039512509 1.092495073 1.048515268 1 22.35672197 SKPAGSDGER ddPTM_BT-474_Pertuzumab_2h_R1 6 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 108.56 0.0019467 2072530000 4011740 3747120 3178110 3742040 3592090 3504640 4021040 3872230 3918090 4318100 FALSE TRUE 3854956.766 3640255.806 3752465.174 3935167.133 3707632.837 3575506.222 4070250.69 3792267.097 3473324.849 4025631.241 0.957603053 0.904269564 0.932143296 0.97752797 0.921006574 0.888185233 1.011083839 0.942030422 0.862802537 1 21.94078359 SKPDPEVGPLLGVQPLPGS(ph)PTADR ddPTM_BT-474_Pertuzumab_2h_R1 2 SKPDPEVGPLLGVQPLPGSPTADR 24 1 A0A6E1W9L1;Q9H5J0 A0A6E1W9L1 ZBTB3 Zinc finger and BTB domain-containing protein 3 1 SKPDPEVGPLLGVQPLPGS(0.976)PT(0.024)ADR;SKPDPEVGPLLGVQPLPGS(0.768)PT(0.232)ADR 107 0.0015669 205618000 349110 348420 304780 341140 327980 329930 327590 372650 375250 359490 TRUE FALSE 335466.3952 338483.4027 359860.5258 358746.2763 338529.7746 336601.4107 331599.1444 364954.6473 332653.1932 335141.4221 1.00096966 1.009971852 1.073757232 1.070432518 1.010110217 1.004356336 0.989430499 1.088957148 0.992575585 1 18.35441048 SKS(ph)IS(ph)SSNPDLAVAPGSVDDEVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SKSISSSNPDLAVAPGSVDDEVSR 24 1 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 2 S(0.456)KS(0.586)IS(0.629)S(0.175)S(0.154)NPDLAVAPGSVDDEVSR 101.14 0.0022294 378240000 575390 468020 313020 394470 468240 378820 409050 642130 429420 357460 TRUE FALSE 552903.1227 454672.5278 369589.6771 414828.644 483301.3648 386479.9999 414056.0763 628869.7911 380674.0419 333248.9158 1.659129547 1.364363112 1.109049901 1.244801181 1.450271379 1.159733705 1.242482891 1.887087283 1.142311419 1 18.34624066 SKVDEAVAVLQAHHAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SKVDEAVAVLQAHHAK 16 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0Y6X6;H0YER0 B1ANR0 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 109.35 0.00063161 980530000 1904900 1771000 1461500 1572700 1663700 1704600 1980000 553800 2396400 1932400 FALSE TRUE 1830454.402 1720492.814 1725625.561 1653867.235 1717214.421 1739068.18 2004231.832 542363.8365 2124370.719 1801516.827 1.016062895 0.95502456 0.957873685 0.918041514 0.953204764 0.965335518 1.112524625 0.301059545 1.179212254 1 20.7807807 SLDGAEFSRPAS(ph)VSENHDAGPDGDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLDGAEFSRPASVSENHDAGPDGDKR 26 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 S(0.016)LDGAEFS(0.051)RPAS(0.917)VS(0.016)ENHDAGPDGDKR;S(0.003)LDGAEFS(0.02)RPAS(0.852)VS(0.125)ENHDAGPDGDKR 91.942 0.0045866 291950000 79580 98352 81374 114132 75404 82291 96460 95734 89462 103366 TRUE FALSE 76469.92562 95547.09726 96080.09195 120022.3662 77829.43814 83954.9804 97640.50633 93757.05945 79306.64882 96364.92875 0.793545189 0.991513183 0.997044186 1.245498417 0.807653149 0.871219244 1.013236948 0.972937568 0.822982488 1 16.55622056 SLDGIPFTVDAGGLIHCIEDFHK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLDGIPFTVDAGGLIHCIEDFHK 23 0 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 209.97 4.31E-25 118890000 77971 66419 48932 65637 79114 73748 70018 38771 90919 72088 FALSE TRUE 74923.80712 64524.79515 57775.10089 69024.53344 81658.77366 75239.23509 70874.90123 37970.3653 80598.25628 67205.41555 1.114847762 0.96011303 0.859679245 1.027068025 1.215062402 1.119541252 1.054601041 0.564989666 1.199282165 1 16.03628987 SLGDDISSETSGDFR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGDDISSETSGDFR 15 0 P12429;D6RA82;D6RFG5 P12429 ANXA3 Annexin A3;Annexin 0 ; 197.07 2.00E-08 77261000 119410 115157 128200 135358 119351 122321 122996 132597 129297 123260 FALSE TRUE 114743.3252 111872.8351 151368.5918 142343.8426 123190.0333 124794.4144 124501.2618 129858.8256 114619.7466 114911.4904 0.998536567 0.973556558 1.317262453 1.238725928 1.072042777 1.086004663 1.083453547 1.130076941 0.997461143 1 16.81016354 SLGS(ph)VQAPSYGAR ddPTM_BT-474_Pertuzumab_2h_R1 2 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR 140.77 3.90E-06 236090000 247651 214127 154257 135325 151309 397300 108071 158086 142042 113501 TRUE FALSE 237972.5251 208020.3076 182134.6713 142309.1395 156175.9914 405333.6782 109393.6052 154821.4689 125917.9876 105813.4762 2.248981261 1.965915072 1.721280483 1.344905627 1.475955588 3.83064325 1.033834339 1.463154548 1.189999537 1 16.69116385 SLLSHEFQDET(ph)DTEEETLYSSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLLSHEFQDETDTEEETLYSSK 22 0 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 1 SLLS(0.001)HEFQDET(0.651)DT(0.348)EEETLYSSK 126.25 7.35E-05 31068000 18471 37421 20073 33327 22564 18873 31841 36166 32293 29927 TRUE FALSE 17749.1329 36353.78972 23700.63762 35047.01046 23289.79155 19254.62499 32230.67968 35419.15946 28627.23402 27900.01763 0.636169236 1.303002392 0.849484683 1.256164456 0.834759026 0.690129492 1.155220764 1.269503121 1.026065087 1 14.76797841 SLNFQEDDDT(ph)SRETFASDTNEALASLDESQEGHAEAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLNFQEDDDTSRETFASDTNEALASLDESQEGHAEAK 37 1 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 SLNFQEDDDT(0.445)S(0.445)RET(0.102)FAS(0.001)DT(0.007)NEALASLDESQEGHAEAK 124.99 2.82E-08 44581000 24123 27601 20780 19890 22025 27603 20977 14430 32090 31959 TRUE FALSE 23180.24649 26813.8465 24535.40825 20916.52528 22733.45413 28161.15157 21233.7228 14132.01546 28447.27773 29794.38846 0.778007124 0.899962976 0.823490916 0.702029018 0.763011268 0.945183071 0.712675235 0.474318024 0.954786428 1 14.86275302 SLNPNLLAVVTESTDAHHER ddPTM_BT-474_Pertuzumab_2h_R1 1 SLNPNLLAVVTESTDAHHER 20 0 Q8N766-4;Q8N766-3;Q8N766-2;Q8N766 Q8N766-4 EMC1 ER membrane protein complex subunit 1 0 99.059 0.00041131 36006000 50391 80121 63888 74700 57787 74745 71892 37729 79536 72603 FALSE TRUE 48421.66401 77836.02753 75433.98278 78555.27595 59645.77134 76256.39511 72771.8358 36949.88297 70507.40672 67685.53414 0.715391621 1.149965477 1.114477174 1.160591801 0.881218891 1.126627662 1.075146067 0.545905169 1.041690926 1 16.04655991 SLS(ph)MDSQVPVYSPSIDLK ddPTM_BT-474_Pertuzumab_2h_R1 8 SLSMDSQVPVYSPSIDLK 18 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 S(0.046)LS(0.914)MDS(0.04)QVPVYSPSIDLK;S(0.026)LS(0.966)MDS(0.008)QVPVYSPSIDLK;S(0.035)LS(0.965)MDSQVPVYSPSIDLK;S(0.35)LS(0.65)MDS(0.001)QVPVYSPSIDLK;S(0.032)LS(0.968)MDSQVPVYSPSIDLK;S(0.17)LS(0.829)MDS(0.001)QVPVYSPSIDLK;S(0.14)LS(0.86)MDSQVPVYSPSIDLK;S(0.089)LS(0.911)MDSQVPVYSPSIDLK 348.19 2.77E-90 1571001000 4021390 3633190 2862350 3086090 3573900 3037770 3356820 4274210 3816520 3454670 TRUE FALSE 3864229.633 3529574.978 3379640.318 3245363.475 3688857.739 3099195.791 3397901.767 4185946.07 3383284.65 3220682.124 1.199817146 1.095909141 1.049355443 1.007663392 1.14536536 0.962279316 1.0550255 1.299707922 1.050486984 1 21.61893485 SLS(ph)TSGESLYHVLGLDKNATSDDIKK ddPTM_BT-474_Pertuzumab_2h_R1 1 SLSTSGESLYHVLGLDKNATSDDIKK 26 2 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.006)LS(0.586)T(0.126)S(0.126)GES(0.155)LYHVLGLDKNATSDDIKK 135.57 1.59E-05 160240000 232660 347990 201200 209770 210390 241970 303700 270720 307550 241900 TRUE FALSE 223567.39 338065.6659 237561.3157 220596.2548 217157.3854 246862.7992 307416.7714 265129.5374 272638.2134 225515.8975 0.991359777 1.49907687 1.053412723 0.978184941 0.96293604 1.094658079 1.363171177 1.17565786 1.20895341 1 17.78286961 SLVLQRPQTWADCVTWACHHWHTQYSNNIR ddPTM_BT-474_Pertuzumab_2h_R1 1 SLVLQRPQTWADCVTWACHHWHTQYSNNIR 30 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 220.67 4.31E-35 1679900000 37199 55809 0 53892 48753 36767 40185 0 44671 0 FALSE TRUE 35745.22195 54217.38196 0 56673.37258 50321.18452 37510.45393 40676.79605 0 39600.13536 0 0 SMLDIVEHDLLKPHLPSVTYLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMLDIVEHDLLKPHLPSVTYLR 22 1 A0A0A0MTH9;O14981;O14981-2 A0A0A0MTH9 BTAF1 TATA-binding protein-associated factor 172 0 128.98 1.02E-05 89787000 94278 96270 83783 95946 92321 83808 94713 22424 102680 97713 FALSE TRUE 90593.51153 93524.47386 98924.45184 100897.7846 95290.58881 85502.65518 95872.12603 21960.93656 91024.19687 91094.81148 0.994496943 1.026671798 1.085950454 1.107612859 1.046059455 0.938611693 1.052443322 0.241077798 0.999224823 1 16.47508126 SMS(ph)FQGIR ddPTM_BT-474_Pertuzumab_2h_R1 7 SMSFQGIR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.021)MS(0.979)FQGIR;S(0.001)MS(0.999)FQGIR;SMS(1)FQGIR;SMS(1)FQGIR;SMS(1)FQGIR;SMS(1)FQGIR;S(0.002)MS(0.998)FQGIR 150.06 0.0005194 3838430000 4122893 3446813 1726790 3324232 4364135 2527754 3235317 5870950 3459827 3048947 TRUE FALSE 3961765.783 3348513.268 2038859.365 3495796.012 4504511.366 2578866.918 3274911.777 5749712.831 3067081.944 2842439.104 1.393790909 1.178042219 0.717292188 1.229857838 1.584734519 0.90727253 1.152148439 2.022809503 1.079031716 1 21.43869801 SMS(ph)GGHGLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SMSGGHGLR 9 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 S(0.01)MS(0.99)GGHGLR 82.008 0.020632 152440000 169840 195540 135850 180220 159370 167490 167020 244860 206320 168850 TRUE FALSE 163202.465 189963.3907 160401.117 189521.1758 164496.2808 170876.7626 169064.0407 239803.5554 182899.4186 157413.6391 1.036774615 1.206778471 1.01897852 1.203969217 1.044993825 1.085527045 1.074011386 1.523397571 1.161903248 1 17.26420102 SMVNTKPEKTEEDSEEVR ddPTM_BT-474_Pertuzumab_2h_R1 2 SMVNTKPEKTEEDSEEVR 18 2 Q16543 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 148.26 3.97E-08 862630000 1022890 863550 562610 558180 727300 854880 759010 820330 993660 757320 FALSE TRUE 982914.3279 838922.3995 664286.1422 586987.7367 750694.265 872166.2593 768298.9914 803389.8988 880863.8826 706026.0418 1.392178574 1.188231524 0.94088051 0.831396722 1.063267104 1.235317407 1.088202058 1.137904059 1.247636532 1 19.42936187 SNAHYNLQNAFNLAEQHLGLTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SNAHYNLQNAFNLAEQHLGLTK 22 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 260.32 1.72E-37 170720000 127780 159020 136090 149470 150850 133350 161150 108840 179940 165260 FALSE TRUE 122786.2163 154484.9053 160684.4903 157184.1646 155702.2272 136046.4284 163122.2019 106592.416 159513.9656 154066.793 0.796967432 1.002713838 1.042953431 1.020233897 1.010615099 0.883035375 1.058775864 0.691858472 1.035355916 1 17.23319642 SNS(ph)FIGVPNGEVEMPLK ddPTM_BT-474_Pertuzumab_2h_R1 2 SNSFIGVPNGEVEMPLK 17 0 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 S(0.267)NS(0.733)FIGVPNGEVEMPLK;S(0.165)NS(0.835)FIGVPNGEVEMPLK 131.67 2.75E-05 147765000 362210 304150 220980 237465 282350 229834 219970 421370 315960 239823 TRUE FALSE 348054.4328 295475.9398 260916.0017 249720.5971 291432.0442 234481.401 222662.0587 412668.5622 280093.5454 223579.5746 1.556736269 1.32156947 1.166993909 1.116920441 1.303482416 1.048760386 0.995896244 1.845734625 1.252768934 1 17.77042887 SNS(ph)FNSTFEHHLPPSPLEHGTPFQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SNSFNSTFEHHLPPSPLEHGTPFQR 25 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.152)NS(0.764)FNS(0.042)T(0.042)FEHHLPPSPLEHGTPFQR 140.94 6.37E-07 98359000 24575 30723 25355 35370 24638 33787 30847 19965 33904 34894 TRUE FALSE 23614.58183 29846.81012 29937.21252 37195.44994 25430.50365 34470.19629 31224.51481 19552.71577 30055.36006 32530.5983 0.725919075 0.917499575 0.920278571 1.143398889 0.781741037 1.059623803 0.959850616 0.601056138 0.923910461 1 14.98950974 SNT(ph)PTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SNTPTPR 7 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9;Q04727-4;Q04727;Q04727-3;Q04727-2;H7C4E4;H7C4W5;H0Y5S0;H7C4P7;Q5JSY7 H0YKT5;Q04727-4 TLE3;TLE4 Transducin-like enhancer protein 3;Transducin-like enhancer protein 4 1 S(0.007)NT(0.99)PT(0.003)PR;S(0.005)NT(0.992)PT(0.003)PR 119.53 0.053225 395720000 366670 340840 263650 300690 307810 321950 325450 348020 343500 345430 TRUE FALSE 352340.131 331119.5769 311297.4199 316208.6469 317710.9882 328460.0496 329432.9545 340833.2654 304507.3201 322033.7184 1.094109439 1.028213997 0.966660949 0.98191161 0.986576778 1.019955461 1.022976588 1.058377573 0.945575891 1 18.29685223 SPAGSQQQFGYSPGQQQTHPQGS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPAGSQQQFGYSPGQQQTHPQGSPR 25 0 Q8TAP9 Q8TAP9 MPLKIP M-phase-specific PLK1-interacting protein 1 SPAGSQQQFGYSPGQQQTHPQGS(1)PR;SPAGSQQQFGYSPGQQQTHPQGS(1)PR;SPAGSQQQFGYSPGQQQTHPQGS(1)PR;SPAGSQQQFGYSPGQQQTHPQGS(1)PR 277.31 2.67E-53 2049730000 429530 459680 382197 492300 409956 424502 449710 466650 445492 485160 TRUE FALSE 412743.4927 446570.3765 451268.4998 517707.662 423142.6071 433085.7213 455213.6855 457013.5144 394921.6158 452299.6811 0.912544293 0.987332946 0.997720137 1.144612043 0.935535939 0.957519405 1.006442641 1.010421925 0.873141486 1 18.78691945 SPGGPGSHVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPGGPGSHVR 10 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 68.355 0.060223 27913000 66924 60679 53968 69356 62904 51782 65419 64785 69834 71299 FALSE TRUE 64308.53609 58948.49433 63721.21811 72935.47147 64927.36429 52829.06752 66219.61729 63447.16711 61906.73709 66469.85522 0.967484221 0.886845535 0.958648366 1.097271406 0.976794128 0.794782347 0.996235317 0.95452543 0.931350563 1 16.02041259 SPILLGSLAHQIYR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPILLGSLAHQIYR 14 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 180.97 1.69E-06 429170000 117720 184720 111260 197240 119390 104180 184610 138160 121680 113790 FALSE TRUE 113119.3723 179451.9665 131367.157 207419.58 123230.2878 106286.591 186869.3124 135306.9477 107867.3965 106082.9019 1.066329919 1.691620074 1.2383443 1.955259295 1.161641372 1.001920093 1.761540352 1.275483091 1.016821698 1 16.69483262 SPLAQMEEERR ddPTM_BT-474_Pertuzumab_2h_R1 4 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 0 ;;; 168.02 2.98E-05 8056000000 2327470 2645390 2107960 2516600 2514960 2081850 2570710 2564730 2642240 2591570 FALSE TRUE 2236509.899 2569946.067 2488915.263 2646482.028 2595855.972 2123946.433 2602171.118 2511767.429 2342303.992 2416040.656 0.925692163 1.063701499 1.030162823 1.095379758 1.074425617 0.879102108 1.077039458 1.039621342 0.969480372 1 21.2042133 SPLIES(ph)TANMDNNQSQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SPLIESTANMDNNQSQK 17 0 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 S(0.011)PLIES(0.858)T(0.131)ANMDNNQSQK 316.58 2.73E-58 426910000 72811 75983 72719 77295 75322 57654 85218 91621 90720 83098 TRUE FALSE 69965.46562 73816.03924 85860.94093 81284.20421 77744.80054 58819.80338 86260.92338 89728.99433 80421.84593 77469.69844 0.903133316 0.95283757 1.108316447 1.049238681 1.003551093 0.759262067 1.11347953 1.158246335 1.038107125 1 16.2413445 SPS(ph)GSAFGSQENLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSGSAFGSQENLR 14 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 S(0.041)PS(0.935)GS(0.024)AFGSQENLR 180.11 1.88E-06 398560000 72659 91886 73498 84120 66500 90751 100080 86024 93242 108200 TRUE FALSE 69819.40595 89265.50125 86780.72355 88461.44328 68639.03289 92586.0474 101304.809 84247.57434 82657.55906 100871.5176 0.692161748 0.884942582 0.860309487 0.876971472 0.68046 0.917861152 1.004295478 0.835196856 0.819434078 1 16.62215934 SPS(ph)MSISEPISVTLPPR ddPTM_BT-474_Pertuzumab_2h_R1 1 SPSMSISEPISVTLPPR 17 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.179)PS(0.821)MSISEPISVTLPPR 154.46 1.44E-07 186420000 23297 19134 17807 18933 27507 22906 18317 53826 18124 25194 TRUE FALSE 22386.52748 18588.31705 21025.12101 19910.1344 28391.78764 23369.17501 18541.16893 52714.47429 16066.6395 23487.58794 0.953121604 0.791410216 0.895158799 0.847687487 1.208799631 0.994958489 0.789402853 2.244354526 0.684048083 1 14.51961094 SPS(ph)PGLFR ddPTM_BT-474_Pertuzumab_2h_R1 6 SPSPGLFR 8 0 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 S(0.198)PS(0.802)PGLFR;S(0.007)PS(0.993)PGLFR;S(0.037)PS(0.963)PGLFR;SPS(1)PGLFR;S(0.02)PS(0.98)PGLFR;S(0.272)PS(0.728)PGLFR 156.18 0.00041655 1368578000 2212181 2510160 1697462 2457095 2066049 1952717 2320160 2326608 2013229 2556066 TRUE FALSE 2125726.521 2438572.695 2004231.143 2583905.967 2132505.342 1992202.276 2348554.812 2278562.732 1784695.684 2382941.373 0.892059933 1.023345653 0.841074466 1.084334678 0.894904661 0.836026559 0.985569699 0.956197562 0.748946535 1 21.18431203 SQKDEESSEGTHHAK ddPTM_BT-474_Pertuzumab_2h_R1 1 SQKDEESSEGTHHAK 15 1 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 0 70.529 0.029946 62550000 78278 87013 67010 70996 72233 75134 81405 15862 99732 88754 FALSE TRUE 75218.80922 84531.47443 79120.19763 74660.11207 74556.44005 76653.26096 82401.25874 15534.44416 88410.84147 82742.61253 0.909069788 1.021619597 0.956220685 0.902317558 0.901064612 0.9264061 0.99587451 0.187744183 1.068504351 1 16.33634289 SQS(ph)LPNSLDYTQTSDPGR ddPTM_BT-474_Pertuzumab_2h_R1 4 SQSLPNSLDYTQTSDPGR 18 0 Q96TC7;H0YLG5;H0YNE5 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 SQS(1)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR;S(0.001)QS(0.999)LPNSLDYTQTSDPGR;S(0.115)QS(0.885)LPNSLDYTQTSDPGR 399.1 2.63E-127 3304820000 1164854 1408120 913112 1661670 910811 1069363 1243320 1398500 1143514 1043079 TRUE FALSE 1119330.218 1367961.796 1078131.65 1747428.988 940108.063 1090986.253 1258536.122 1369620.486 1013707.085 972430.3303 1.151064691 1.4067453 1.108698091 1.796970882 0.966761354 1.121917138 1.294217265 1.408451016 1.042447004 1 19.89123537 SQS(ph)LPTTLLSPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 S(0.004)QS(0.923)LPT(0.036)T(0.036)LLSPVR 74.737 0.034924 153060000 256210 273720 228470 256460 255230 215710 274730 267780 291370 279440 TRUE FALSE 246197.0299 265913.7736 269759.6113 269695.9313 263439.7047 220071.804 278092.2279 262250.2494 258294.8991 260513.2799 0.945045988 1.020730205 1.035492745 1.035248305 1.011233304 0.844762325 1.067478126 1.006667489 0.991484577 1 17.99099739 SQS(ph)TSEQEKR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSTSEQEKR 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 S(0.232)QS(0.715)T(0.046)S(0.007)EQEKR 85.837 0.0085552 449900000 266190 237630 119320 169580 231270 205280 184240 280350 238900 203200 TRUE FALSE 255787.0005 230853.0251 140883.7783 178332.0441 238709.0096 209430.9022 186494.7842 274560.6745 211781.0736 189437.083 1.350247779 1.218626371 0.743696936 0.941378749 1.260096523 1.105543323 0.984468201 1.449350202 1.117949401 1 17.53135925 SQS(ph)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 36 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 S(0.172)QS(0.771)VPAS(0.039)T(0.018)GLGWGSGLVAPLQEGSIDSTLAGTQDTR 120.56 7.16E-08 54846000 16562 12265 4989.5 10078 11955 8542.6 10200 18436 9288.9 9198.4 TRUE FALSE 15914.73873 11915.21421 5891.213641 10598.12679 12339.54343 8715.337225 10324.83065 18055.29016 8234.463014 8575.384175 1.855863062 1.389467103 0.686991221 1.235877784 1.438949344 1.016320324 1.204007942 2.105478867 0.960244211 1 13.06598559 SQTEAVTFLANHDDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SQTEAVTFLANHDDSR 16 0 B4DEM9;Q9Y2S7 B4DEM9 POLDIP2 Polymerase delta-interacting protein 2 0 161.99 8.24E-09 277250000 176290 206570 155760 268890 164500 214210 236070 178260 238260 200630 FALSE TRUE 169400.3919 200678.8259 183909.2969 282767.4451 169791.2919 218541.473 238959.0953 174578.8687 211213.7237 187041.1514 0.905685143 1.072912695 0.9832558 1.511792688 0.907775057 1.168413856 1.27757498 0.933371439 1.129236652 1 17.51299619 SRNDQVVTDLR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRNDQVVTDLR 11 1 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424;F8W943 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 79.23 0.025275 629590000 265410 266690 212930 283500 255610 295800 267190 268260 282880 296140 FALSE TRUE 255037.4838 259084.2623 251411.1876 298131.469 263831.9278 301781.2787 270459.9511 262720.3373 250768.6483 276082.174 0.923773817 0.938431694 0.910638974 1.079864971 0.955628261 1.093084984 0.97963569 0.951601958 0.908311626 1 18.07473821 SRPLATGPSSQSHQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRPLATGPSSQSHQEK 16 1 Q96RL1-2;Q96RL1-3;Q96RL1;D6RC40;D6RCQ3 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 0 144.33 7.97E-07 31775000 39402 45555 31584 42949 39382 41517 39565 44544 47661 48304 FALSE TRUE 37862.12628 44255.816 37291.93138 45165.60304 40648.7578 42356.50219 40049.20831 43624.15083 42250.72309 45032.32706 0.840776588 0.982756586 0.828114686 1.002959562 0.902657279 0.940579911 0.889343521 0.968729659 0.938230952 1 15.45867341 SRPT(ph)SEGSDIESTEPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 1 S(0.007)RPT(0.541)S(0.308)EGS(0.144)DIESTEPQK;S(0.005)RPT(0.395)S(0.395)EGS(0.205)DIESTEPQK 196.62 2.56E-11 3874390000 2308480 2153740 1733800 1829530 2088670 2045070 2034470 2383000 2370130 2204090 TRUE FALSE 2218262.049 2092317.444 2047136.228 1923952.263 2155853.967 2086422.717 2059368.452 2333790.217 2101082.779 2054805.021 1.079548681 1.018255952 0.996267873 0.93631865 1.049176903 1.0153872 1.002220859 1.135772102 1.022521727 1 20.97057007 SRS(ph)ASPS(ph)TQQEK ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSASPSTQQEK 12 1 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 2 S(0.03)RS(0.694)AS(0.281)PS(0.569)T(0.427)QQEK 103.01 0.019759 0 395830 339380 289140 297320 330750 339850 319690 373350 389770 340940 TRUE FALSE 380360.526 329701.2147 341394.0299 312664.7208 341388.8741 346721.9998 323602.4619 365640.192 345524.9436 317847.8301 1.196674918 1.03729264 1.074080102 0.983693111 1.074063881 1.090842746 1.01810499 1.150362398 1.087076616 1 18.27797671 SRS(ph)PIER ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPIER 7 1 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;E7ERW0;G5E9M9;E7EWF5;F8W708;E7EQU6;Q14135-5;F8WBN7;E7EUJ2;C9JX59;C9JBN2 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 S(0.037)RS(0.963)PIER 93.325 0.0090952 858700000 228030 227620 180080 210110 209970 236820 187760 256230 246690 229070 TRUE FALSE 219118.3355 221128.5005 212624.4619 220953.8023 216723.8757 241608.6627 190057.863 250938.761 218686.7854 213554.8849 1.02605162 1.035464492 0.995643167 1.034646444 1.014839234 1.131365657 0.889971977 1.17505512 1.024030827 1 17.70424737 SRS(ph)PLAR ddPTM_BT-474_Pertuzumab_2h_R1 1 SRSPLAR 7 1 Q8N3Y1 Q8N3Y1 FBXW8 F-box/WD repeat-containing protein 8 1 S(0.212)RS(0.788)PLAR 68.893 0.037073 159710000 38531 45685 33408 37889 33280 39737 42659 39615 45458 42478 TRUE FALSE 37025.16592 44382.10853 39445.56876 39844.45583 34350.48142 40540.50937 43181.0736 38796.93641 40297.79842 39600.92722 0.934957046 1.120734075 0.996076898 1.006149568 0.867416089 1.023726266 1.09040562 0.979697677 1.017597345 1 15.27324659 SRS(ph)TTELDDYSTNK ddPTM_BT-474_Pertuzumab_2h_R1 3 SRSTTELDDYSTNK 14 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.002)RS(0.969)T(0.029)T(0.001)ELDDYSTNK;S(0.033)RS(0.881)T(0.083)T(0.003)ELDDYSTNK;S(0.039)RS(0.922)T(0.039)TELDDYSTNK 255.96 7.05E-24 2556760000 2513160 2268000 2000640 2181630 2164370 2137280 2090050 3182060 2506730 2510930 TRUE FALSE 2414942.929 2203318.861 2362200.152 2294224.186 2233988.927 2180497.266 2115628.657 3116349.349 2222176.519 2340862.475 1.031646649 0.941242335 1.009115306 0.980076451 0.954344371 0.93149311 0.903781696 1.331282543 0.949298194 1 21.15860875 SRT(ph)S(ph)VQTEDDQLIAGQSAR ddPTM_BT-474_Pertuzumab_2h_R1 3 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.633)RT(0.637)S(0.73)VQTEDDQLIAGQSAR;S(0.607)RT(0.723)S(0.67)VQTEDDQLIAGQSAR;S(0.114)RT(0.885)S(0.761)VQT(0.24)EDDQLIAGQSAR 186.36 6.08E-14 3240200000 943040 1076660 851807 1133340 781546 1028380 943518 1272450 1046840 1047340 TRUE FALSE 906184.9542 1045954.711 1005747.473 1191831.813 806685.1369 1049174.548 955065.0555 1246173.463 928007.1119 976402.7289 0.928085233 1.071232884 1.030053935 1.22063548 0.826180748 1.074530537 0.978146647 1.276290434 0.950434779 1 19.8971168 SS(ph)LVTSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSLVTSK 7 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7 A6NMQ3 ENSA Alpha-endosulfine 1 S(0.369)S(0.631)LVTSK;S(0.007)S(0.993)LVTSK;S(0.005)S(0.995)LVTSK;S(0.004)S(0.996)LVTSK 168.74 0.0010887 1674800000 4775800 4738040 4101610 3030450 4187970 3935850 3274140 5207560 5455360 3944530 TRUE FALSE 4589156.456 4602915.738 4842862.167 3186851.888 4322679.858 4015435.584 3314209.905 5100022.066 4836090.404 3677363.47 1.247947475 1.251689091 1.316938673 0.866613245 1.175483439 1.091933288 0.901246214 1.386869182 1.3150972 1 21.81024035 SS(ph)PAPHSGPCPSR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSPAPHSGPCPSR 13 0 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 S(0.452)S(0.548)PAPHSGPCPSR 68.481 0.026446 0 50091 53997 45098 55670 53254 58459 50783 58174 53941 68768 TRUE FALSE 48133.38834 52457.05843 53248.2118 58543.13537 54966.96327 59641.08103 51404.49754 56972.68657 47817.84382 64110.28211 0.750790462 0.818231596 0.830572102 0.913162966 0.857381398 0.930288857 0.801813623 0.888666914 0.74586856 1 15.96826814 SS(ph)PGAVAGLSNAPGTPR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;Q9BWG4-2;Q9BWG4;U3KPY3 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 S(0.012)S(0.988)PGAVAGLSNAPGTPR;S(0.174)S(0.826)PGAVAGLSNAPGTPR 213.7 4.55E-13 417730000 431800 426650 359990 402570 366620 410060 364520 480120 405830 400460 TRUE FALSE 414924.7786 414482.3597 425048.2009 423346.6859 378412.6653 418351.6942 368981.1048 470205.3542 359761.8798 373336.4875 1.111396267 1.110211227 1.138512348 1.133954757 1.01359679 1.120575428 0.988333895 1.259467987 0.963639751 1 18.51011699 SS(ph)PQKEVK ddPTM_BT-474_Pertuzumab_2h_R1 4 SSPQKEVK 8 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 1 S(0.179)S(0.821)PQKEVK;S(0.086)S(0.914)PQKEVK;S(0.018)S(0.982)PQKEVK;S(0.228)S(0.772)PQKEVK 113.63 0.0017029 1518170000 4194620 3950830 2267670 2107540 2863020 4162690 2845190 3170280 4248490 2927770 TRUE FALSE 4030689.613 3838156.197 2677488.413 2216310.392 2955111.638 4246862.444 2880010.286 3104812.61 3766219.226 2729469.53 1.476730027 1.40619126 0.980955597 0.811993088 1.08266885 1.555929604 1.055153851 1.137515028 1.3798356 1 21.38018916 SSDVSWSDTRR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSDVSWSDTRR 11 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 79.82 0.041848 508650000 1497220 1184860 1307450 1180390 1383660 1314910 1383080 461980 1915290 1410920 FALSE TRUE 1438706.987 1151068.953 1543735.299 1241310.069 1428166.681 1341498.381 1400006.547 452439.9516 1697874.309 1315357.132 1.093776703 0.875099944 1.173624457 0.943705735 1.085763437 1.01987388 1.064354701 0.343967384 1.290808608 1 20.32702313 SSEPVQHEESIRKPS(ph)PEPR ddPTM_BT-474_Pertuzumab_2h_R1 3 SSEPVQHEESIRKPSPEPR 19 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SSEPVQHEES(0.007)IRKPS(0.993)PEPR;SSEPVQHEES(0.01)IRKPS(0.99)PEPR;SSEPVQHEES(0.021)IRKPS(0.979)PEPR 188.49 8.39E-15 4974730000 3772190 4209160 2593000 2757040 3081450 4049430 3359330 3562610 3949460 3793920 TRUE FALSE 3624768.644 4089118.878 3061612.781 2899331.165 3180567.638 4131312.249 3400442.485 3489040.859 3501133.858 3536954.419 1.024827638 1.15611297 0.865607078 0.81972534 0.89923908 1.168042264 0.961404102 0.986453441 0.989872484 1 21.7540762 SSFFSDRGS(ph)GSR ddPTM_BT-474_Pertuzumab_2h_R1 2 SSFFSDRGSGSR 12 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 1 SSFFSDRGS(0.675)GS(0.325)R;SSFFSDRGS(0.975)GS(0.024)R 111.43 0.00083715 380660000 297520 293210 205332 223220 258780 267280 242700 300930 266950 277720 TRUE FALSE 285892.5895 284847.9379 242440.06 234740.411 267103.8937 272684.5847 245670.2352 294715.6903 236646.9551 258909.777 1.104217047 1.100182238 0.9363882 0.906649465 1.031648541 1.053203119 0.948864265 1.138294945 0.914013205 1 17.98208992 SSQDPSVPQNPPT(ph)PLGHSNPLDHQIPLDPPAPEVVPTPSDWTK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSQDPSVPQNPPTPLGHSNPLDHQIPLDPPAPEVVPTPSDWTK 43 0 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 S(0.12)S(0.12)QDPS(0.137)VPQNPPT(0.312)PLGHS(0.312)NPLDHQIPLDPPAPEVVPTPSDWTK 46.061 0.063123 140230000 56935 64714 59545 59209 54697 61846 61607 29076 64163 69129 TRUE FALSE 54709.91726 62868.42008 70306.10607 62264.78359 56456.37868 63096.56849 62360.96489 28475.57044 56879.48523 64446.83126 0.848915551 0.97550832 1.090916414 0.966141894 0.876014811 0.979048423 0.967634307 0.441845935 0.882580014 1 15.9758218 SSS(ph)DSWEPTSAGSK ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSDSWEPTSAGSK 14 0 A0A3B3IRS8;B1AL16;Q8IX21;Q8IX21-2 A0A3B3IRS8 FAM178A Protein FAM178A 1 SS(0.011)S(0.988)DSWEPTSAGSK 230.5 9.34E-13 126360000 402050 370980 278200 354760 356550 328450 358600 407460 350520 367810 TRUE FALSE 386337.4415 360400.0136 328476.9285 373069.2061 368018.7546 335091.484 362988.6541 399045.8086 310730.4391 342897.9011 1.1266836 1.05104176 0.95794383 1.08798918 1.073260447 0.97723399 1.058591064 1.163745265 0.906189388 1 18.38741955 SSS(ph)LIQLTSQNSS(ph)PNQQR ddPTM_BT-474_Pertuzumab_2h_R1 1 SSSLIQLTSQNSSPNQQR 18 0 O95639;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 2 S(0.284)S(0.33)S(0.386)LIQLT(0.003)S(0.003)QNS(0.19)S(0.805)PNQQR 72.421 0.032005 53515000 123570 95787 77142 94011 109470 95631 84472 130660 90798 95808 TRUE FALSE 118740.7478 93055.24855 91083.27541 98862.91898 112991.202 97564.72434 85505.7936 127961.8253 80490.9917 89318.83882 1.329403174 1.041832269 1.019754361 1.106854055 1.265032142 1.092319668 0.957309731 1.432640941 0.90116478 1 16.44667688 SSS(ph)PAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_BT-474_Pertuzumab_2h_R1 2 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.024)S(0.113)S(0.863)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.292)S(0.292)S(0.342)PAGET(0.075)EGDREPQARPGEGTAPLPPPGQK 241.09 3.35E-46 3592090000 951800 948320 649370 646950 783340 907480 810330 917310 900120 874100 TRUE FALSE 914602.6037 921274.8421 766725.6042 680339.167 808536.8425 925829.8674 820247.0609 898367.2279 797942.1512 814896.4284 1.122354414 1.13054225 0.940887182 0.834878082 0.992195835 1.136131949 1.006566028 1.102431176 0.979194562 1 19.63625718 SSSSSASPSS(ph)PSSR ddPTM_BT-474_Pertuzumab_2h_R1 9 SSSSSASPSSPSSR 14 0 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSSSSASPSS(0.982)PS(0.014)S(0.004)R;SSSSSASPSS(0.987)PS(0.01)S(0.003)R;SSSSSASPS(0.031)S(0.964)PS(0.006)SR;SSSSSASPS(0.003)S(0.9)PS(0.088)S(0.009)R;SSSSSAS(0.005)PS(0.161)S(0.82)PS(0.012)S(0.003)R;SSSSSAS(0.001)PS(0.018)S(0.98)PS(0.001)SR;SSSSSASPS(0.095)S(0.905)PSSR;SSSSSAS(0.01)PS(0.165)S(0.819)PS(0.003)S(0.001)R;SSSSSASPS(0.121)S(0.878)PSSR 297.67 1.13E-43 2934577000 1667814 1771877 1331937 1741152 1599510 1630608 1747570 1768246 1790150 1982631 TRUE FALSE 1602633.985 1721344.803 1572647.645 1831013.063 1650959.692 1663580.011 1768957.284 1731731.102 1586939.677 1848345.636 0.867064013 0.931289456 0.850840673 0.990622656 0.893209397 0.900037297 0.957048968 0.936908697 0.85857301 1 20.81780313 STAS(ph)PASTK ddPTM_BT-474_Pertuzumab_2h_R1 2 STASPASTK 9 0 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 STAS(0.998)PAS(0.002)TK;STAS(0.999)PAS(0.001)TK 124.39 0.00055714 1340370000 2296500 1983670 1621690 1966550 1861640 1950450 2102760 2098400 1964810 2472600 TRUE FALSE 2206750.241 1927097.674 1914765.457 2068043.881 1921521.341 1989889.435 2128494.206 2055067.307 1741773.006 2305128.6 0.957321965 0.83600441 0.830654506 0.897149027 0.833585311 0.863244435 0.923373302 0.891519591 0.755607738 1 21.13641581 STDEPSEKDALQPGR ddPTM_BT-474_Pertuzumab_2h_R1 2 STDEPSEKDALQPGR 15 1 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 197.47 7.67E-09 1675110000 1678750 1567900 1181470 1324720 1396380 1027360 1538410 1511710 1735110 1728120 FALSE TRUE 1613142.594 1523185.027 1394987.911 1393088.958 1441295.831 1048133.923 1557237.522 1480492.66 1538147.587 1611072.893 1.001284672 0.945447617 0.865875105 0.864696417 0.894618634 0.650581316 0.966584149 0.918948278 0.954734943 1 20.61959034 STELLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 STELLIR 7 0 K7EK07;Q71DI3;Q16695;P84243;P68431;Q6NXT2;K7EMV3;A0A590UJJ6;B4DEB1;K7ES00;K7EP01;Q5TEC6 K7EK07;Q5TEC6 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A;H3F3C;HIST2H3PS2 Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3C 0 146.21 0.0051989 165110000 183940 206010 136180 308420 142270 139500 234170 150040 194270 109540 FALSE TRUE 176751.4214 200134.7965 160790.7553 324337.5932 146846.2438 142320.7856 237035.8425 146941.6216 172217.284 102120.7582 1.730807962 1.95978565 1.574515878 3.176020221 1.437966642 1.393651869 2.32113281 1.438900612 1.6864082 1 16.63991663 STQEEIWTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 STQEEIWTLR 10 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 141.88 8.55E-05 85103000 52942 51339 39558 71287 54783 52378 52252 59403 63497 60158 FALSE TRUE 50872.96811 49874.86199 46707.01056 74966.13061 56545.14495 53437.11905 52891.47561 58176.30729 56289.08676 56083.44508 0.907094206 0.889297402 0.832812793 1.336689116 1.008232374 0.952814489 0.943085353 1.037316934 1.003666709 1 15.77528735 STS(ph)QSIVSLLTGTAGEDEK ddPTM_BT-474_Pertuzumab_2h_R1 2 STSQSIVSLLTGTAGEDEK 19 0 V9GZ20;V9GXZ5;Q70EL4-2;Q70EL4-3;Q70EL4-4;Q70EL4 V9GZ20 USP43 Ubiquitin carboxyl-terminal hydrolase 43 1 S(0.022)T(0.022)S(0.956)QSIVSLLTGTAGEDEK;S(0.033)T(0.033)S(0.935)QSIVSLLTGTAGEDEK 342.42 5.81E-76 56841000 294020 212130 135865 158384 145018 133715 137806 328670 170177 128405 TRUE FALSE 282529.3733 206080.2601 160418.8278 166558.2172 149682.6357 136418.8089 139492.5111 321882.8496 150859.2204 119708.015 2.360154192 1.721524328 1.340084269 1.391370638 1.250397776 1.139596283 1.165272944 2.688899734 1.260226564 1 16.86916022 SVPHLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 SVPHLQK 7 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 98.418 0.011277 627930000 1421700 1614800 752370 1943700 1268100 970290 1056700 1630400 1611300 1471500 FALSE TRUE 1366138.392 1568747.485 888339.9954 2044014.59 1308889.588 989909.9286 1069632.211 1596731.67 1428391.979 1371833.994 0.995848184 1.14354032 0.647556482 1.489986834 0.954116601 0.721596004 0.779709655 1.163939425 1.041228009 1 20.38767448 SVQNHNNK ddPTM_BT-474_Pertuzumab_2h_R1 7 SVQNHNNK 8 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;; 107 0.0040871 2852334000 2625149 2862297 2226752 2465481 2431305 2505674 3098928 2608077 2429845 3224431 FALSE TRUE 2522555.275 2780667.092 2629175.62 2592724.77 2509510.133 2556340.445 3136853.608 2554219.299 2154019.182 3006037.416 0.839162966 0.925027439 0.874631702 0.862505821 0.834823319 0.850402071 1.043517819 0.849696442 0.716564328 1 21.51943154 SVS(ph)ANPK ddPTM_BT-474_Pertuzumab_2h_R1 2 SVSANPK 7 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 SVS(1)ANPK;S(0.001)VS(0.999)ANPK 80.755 0.030475 264000000 1494600 661160 323150 376940 479240 336500 367180 1349970 351140 270640 TRUE FALSE 1436189.38 642304.3641 381550.3934 396393.9186 494655.1898 343304.2606 371673.6587 1322092.648 311280.0593 252309.3117 5.69217747 2.545702177 1.512232707 1.571063374 1.960511035 1.360648397 1.473087363 5.239967715 1.233724024 1 17.94483393 SVS(ph)CDNVSK ddPTM_BT-474_Pertuzumab_2h_R1 4 SVSCDNVSK 9 0 Q96CB8;A0A087WXN4 Q96CB8 INTS12 Integrator complex subunit 12 1 SVS(1)CDNVSK;S(0.001)VS(0.999)CDNVSK;SVS(1)CDNVSK;S(0.001)VS(0.999)CDNVSK 171.32 5.98E-05 3605280000 3201910 2567270 1942876 2067700 2829610 2066060 2174370 3584590 2861010 2282420 TRUE FALSE 3076775.817 2494053.973 2293996.912 2174414.245 2920626.975 2107837.149 2200980.59 3510566.964 2536240.139 2127829.66 1.445969043 1.172111668 1.078092366 1.021893005 1.372584953 0.990604271 1.034378189 1.649834585 1.191937581 1 21.02095123 SVS(ph)ENSLVAMDFSGQTGR ddPTM_BT-474_Pertuzumab_2h_R1 6 SVSENSLVAMDFSGQTGR 18 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 S(0.001)VS(0.999)ENSLVAMDFSGQTGR;S(0.117)VS(0.767)ENS(0.117)LVAMDFSGQTGR;S(0.06)VS(0.938)ENS(0.002)LVAMDFSGQTGR;S(0.016)VS(0.982)ENS(0.002)LVAMDFSGQTGR;SVS(1)ENSLVAMDFSGQTGR;S(0.01)VS(0.99)ENSLVAMDFSGQTGR 252.55 1.83E-30 1430873100 1238574 1274269 1103799 1206859 1146972 1268863 1174264 1319622 1346332 1345796 TRUE FALSE 1190169.159 1237928.096 1303280.033 1269145.138 1183865.396 1294520.279 1188634.994 1292371.345 1193502.036 1254644.038 0.948611018 0.986676745 1.038764776 1.011557939 0.943586675 1.031782912 0.94738823 1.030070128 0.951267451 1 20.25884668 SVVCQESDLPDELLYGR ddPTM_BT-474_Pertuzumab_2h_R1 2 SVVCQESDLPDELLYGR 17 0 Q9NS86 Q9NS86 LANCL2 LanC-like protein 2 0 ; 136.51 2.34E-05 49064000 55759 50518 49305 51958 46978 56305 54938 55264 60828 56552 FALSE TRUE 53579.87664 49077.2761 58215.51028 54639.55861 48489.09003 57443.52568 55610.34768 54122.77909 53923.06045 52721.68267 1.016277818 0.930874616 1.10420433 1.036377366 0.91971818 1.08956169 1.054790835 1.026575336 1.022787167 1 15.6861088 SWQGDGS(ph)PMANGAGAVVHHQR ddPTM_BT-474_Pertuzumab_2h_R1 8 SWQGDGSPMANGAGAVVHHQR 21 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;S(0.005)WQGDGS(0.995)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;S(0.001)WQGDGS(0.999)PMANGAGAVVHHQR 315.39 7.22E-67 8288570000 1285381 1437148 1258198 1460814 1297053 1546986 1451041 654105 1649884 1708329 TRUE FALSE 1235146.889 1396161.946 1485582.367 1536206.786 1338773.888 1578267.117 1468799.274 640597.5032 1462596.085 1592622.355 0.775542856 0.876643444 0.932790101 0.964576932 0.840609755 0.990986414 0.922252076 0.402228125 0.918357124 1 20.60297278 SYQSELEALRR ddPTM_BT-474_Pertuzumab_2h_R1 1 SYQSELEALRR 11 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 150.06 5.46E-05 372020000 160360 187590 148550 269650 141530 168750 197500 196250 166210 171970 FALSE TRUE 154092.9539 182240.1169 175396.2895 283566.6688 146082.441 172162.2406 199917.0641 192197.3689 147342.5376 160322.3187 0.961144744 1.136710836 1.094022909 1.76872859 0.911179692 1.07385074 1.24696964 1.198818545 0.919039462 1 17.29061575 T(ph)PPRDLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.991)PPRDLPT(0.009)IPGVT(0.001)SPSSDEPPMEAS(0.415)QS(0.351)HLRNS(0.234)PEDKR;T(0.992)PPRDLPT(0.008)IPGVTSPS(0.001)S(0.001)DEPPMEAS(0.37)QS(0.369)HLRNS(0.259)PEDKR 111.81 1.05E-05 679860000 110923 109742 87243 80134 97521 136612 95192 91499 113604 118278 TRUE FALSE 106588.0065 106612.2656 103009.7508 84269.72534 100657.8515 139374.3882 96356.98817 89609.51368 100708.1502 110266.9257 0.966636241 0.966856244 0.934185388 0.764233924 0.912856243 1.26397274 0.873852132 0.812659944 0.913312397 1 16.7506406 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.995)PPRDLPT(0.005)IPGVTSPSSDEPPMEAS(0.004)QS(0.016)HLRNS(0.98)PEDK;T(0.988)PPRDLPT(0.012)IPGVTSPSSDEPPMEAS(0.079)QS(0.342)HLRNS(0.58)PEDK 191.16 3.56E-22 474970000 560750 581360 482480 422920 476740 613100 521240 534170 644960 618150 TRUE FALSE 538835.2701 564780.182 569674.8687 444746.9519 492074.7751 625497.3021 527619.091 523139.2028 571746.8447 576282.1499 0.935019886 0.980041082 0.988534642 0.771752087 0.853878218 1.085401139 0.915556887 0.907783111 0.992130061 1 19.13641581 T(ph)PPRWAEDQNSLLK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPPRWAEDQNSLLK 14 1 P49792;J3KNE0;A6NKT7;Q7Z3J3 P49792 RANBP2;RGPD3;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4 1 T(1)PPRWAEDQNSLLK;T(1)PPRWAEDQNSLLK 108.71 0.0016795 416090000 623920 622980 440760 470410 585390 656180 591430 584320 653040 593310 TRUE FALSE 599536.5166 605213.2204 520415.1367 494687.9165 604219.601 669448.4092 598668.0973 572253.5878 578909.637 553124.5852 1.083908639 1.094171614 0.940864229 0.894351706 1.092375239 1.210303116 1.082338615 1.034583533 1.046617078 1 19.07724494 T(ph)RTPASINATPANINLADLTR ddPTM_BT-474_Pertuzumab_2h_R1 4 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 T(0.5)RT(0.5)PASINATPANINLADLTR;T(0.622)RT(0.377)PASINATPANINLADLTR;T(0.499)RT(0.499)PAS(0.001)INATPANINLADLTR;T(0.5)RT(0.5)PASINATPANINLADLTR 216.48 9.98E-25 2796270000 646620 663130 540090 652820 614410 578220 599490 791680 688500 672620 TRUE FALSE 621349.3755 644218.1817 637696.2772 686512.1184 634173.0556 589912.0046 606826.7379 775331.5313 610344.3664 627062.8483 0.990888517 1.027358236 1.016957517 1.09480592 1.011338907 0.940754194 0.967728737 1.236449478 0.973338427 1 19.25825052 T(ph)SPDTLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.697)S(0.303)PDTLR;T(0.936)S(0.064)PDTLR 178.99 0.0079101 5528500000 3709620 3417250 3195030 3148420 3332640 3144170 3215290 3414480 4125540 3641940 TRUE FALSE 3564643.949 3319793.376 3772442.994 3310910.334 3439837.392 3207747.272 3254639.681 3343969.795 3657225.995 3395268.16 1.049885836 0.977770597 1.111088378 0.975154296 1.013126867 0.944769933 0.958581039 0.984891218 1.077153798 1 21.69509409 T(ph)SPPLLDR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.703)S(0.297)PPLLDR;T(0.684)S(0.316)PPLLDR;T(0.694)S(0.306)PPLLDR 176.33 0.0029172 42973030000 11733520 11007980 9001300 10667390 10046770 10081690 10872350 11312870 12253250 11598120 TRUE FALSE 11274961.07 10694043.19 10628035.14 11217935.28 10369933.48 10285548.68 11005409.07 11079255.28 10862312.43 10812569 1.042764311 0.989038145 0.982933394 1.037490283 0.959062872 0.951258547 1.017834806 1.02466447 1.004600519 1 23.366206 TAMLLALQRPELVER ddPTM_BT-474_Pertuzumab_2h_R1 2 TAMLLALQRPELVER 15 1 Q8NFV4;Q8NFV4-4 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 ; 153.14 2.47E-06 1028520000 501820 716440 364750 870930 443390 494970 695000 663390 601390 458220 FALSE TRUE 482208.3196 696007.8327 430668.4388 915878.8017 457652.042 504978.6325 703505.6179 649690.7647 533122.7284 427184.3513 1.128806142 1.629291501 1.008155934 2.143989589 1.071322113 1.182109389 1.646843139 1.520867426 1.247992177 1 18.70449927 TAPAAPAEDAVAAAAAAPSEPSEPSRPS(ph)PQPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPK 32 1 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPSEPS(0.003)EPS(0.01)RPS(0.986)PQPK 137.44 1.15E-08 500970000 116360 96125 148080 77803 105630 116520 79480 101670 118390 130930 TRUE FALSE 111812.5226 93383.60912 174841.35 81818.42215 109027.6849 118876.1142 80452.70002 99570.47897 104950.8635 122061.9945 0.916030604 0.765050657 1.432397945 0.670302189 0.893215659 0.973899491 0.659113431 0.815736949 0.859816063 1 16.89725454 TAPTLS(ph)PEHWK ddPTM_BT-474_Pertuzumab_2h_R1 5 TAPTLSPEHWK 11 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPT(0.005)LS(0.995)PEHWK;TAPTLS(1)PEHWK;TAPTLS(1)PEHWK;TAPTLS(1)PEHWK;TAPTLS(1)PEHWK 243.37 5.23E-16 7786310000 3510590 3238770 2883710 3094650 3214540 2703970 3232650 3167830 3284170 3473350 TRUE FALSE 3373392.262 3146403.451 3404860.545 3254365.257 3317938.598 2758646.126 3272212.138 3102413.203 2911364.79 3238096.911 1.041782366 0.971682917 1.051500507 1.005024046 1.024656979 0.851934393 1.010535579 0.9580977 0.899097485 1 21.62671473 TAS(ph)S(ph)VEQLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TASSVEQLR 9 0 Q9H3U1-2 Q9H3U1-2 UNC45A Protein unc-45 homolog A 2 T(0.585)AS(0.742)S(0.674)VEQLR 51.998 0.079772 356300000 10405 6796.6 5918.6 0 7488.2 7344.5 12332 6189 5090.9 5661.4 TRUE FALSE 9998.361097 6602.767623 6988.222679 0 7729.064754 7493.010822 12482.9227 6061.194987 4513.002375 5277.948335 1.894365094 1.25101028 1.324041509 0 1.46440705 1.419682488 2.365108923 1.148399833 0.855067554 1 12.36576151 TASRPDDIPDS(ph)PSSPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TASRPDDIPDSPSSPK 16 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TASRPDDIPDS(0.849)PS(0.12)S(0.031)PK 75.703 0.017416 139610000 141020 132870 121360 126180 126610 119860 137790 139580 159030 147230 TRUE FALSE 135508.7825 129080.6777 143292.4516 132692.1649 130682.5256 122283.6513 139476.3152 136697.6242 140977.5811 137257.981 0.987256126 0.940423841 1.043964443 0.966735515 0.952094186 0.89090376 1.016161787 0.995917492 1.027099336 1 17.06653051 TASTAETPRRLTPVPGSLQEAFIK ddPTM_BT-474_Pertuzumab_2h_R1 1 TASTAETPRRLTPVPGSLQEAFIK 24 2 E9PJY3;Q9C0D2-4;Q9C0D2-3 E9PJY3 CEP295 0 52.853 0.071282 136700000 440650 384450 363530 413000 437790 458260 444400 50772 531230 391690 FALSE TRUE 423428.9108 373485.8624 429227.9577 434314.9795 451871.9129 467526.3312 449838.7001 49723.54046 470926.9975 365160.4874 1.159569355 1.022799222 1.175450172 1.189381093 1.23746114 1.280331107 1.231893142 0.136169006 1.289643907 1 18.47817114 TDDCHPWVLPVVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TDDCHPWVLPVVK 13 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 112.5 0.00089598 404830000 1014100 917900 718160 824020 711770 435560 1034800 1004900 1152500 1215700 FALSE TRUE 974467.8509 891722.3907 847947.4874 866547.771 734664.7285 444367.3216 1047464.192 984148.4638 1021673.032 1133359.556 0.85980468 0.786795669 0.748171648 0.764583284 0.648218586 0.392079741 0.924211726 0.8683462 0.901455347 1 20.1121742 TDDRVER ddPTM_BT-474_Pertuzumab_2h_R1 2 TDDRVER 7 1 P10620;F5H760;F5H7F6;F5H6X2;P10620-2 P10620 MGST1 Microsomal glutathione S-transferase 1 0 ; 122.52 0.0039519 1330290000 2764830 4621710 2329920 4836920 2808950 3149600 3842460 4653290 3794300 2802300 FALSE TRUE 2656777.387 4489903.356 2750988.373 5086554.021 2899302.428 3213287.07 3889485.175 4557197.935 3363586.971 2612497.725 1.016949168 1.718624791 1.05301082 1.947008019 1.1097818 1.229967414 1.48879945 1.744383504 1.287498526 1 21.31699835 TDDYLDQPCLETVNR ddPTM_BT-474_Pertuzumab_2h_R1 2 TDDYLDQPCLETVNR 15 0 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 ; 243.88 1.24E-17 317910000 259100 256470 202221 240090 253790 222900 263280 273730 281880 282160 FALSE TRUE 248974.0855 249155.7267 238766.8331 252481.0737 261953.3858 227407.1907 266502.0994 268077.3798 249882.1641 263049.0519 0.946492997 0.947183519 0.907689389 0.959825066 0.995834746 0.864504886 1.01312701 1.019115553 0.949945124 1 18.00497232 TEDFIIDTLELR ddPTM_BT-474_Pertuzumab_2h_R1 1 TEDFIIDTLELR 12 0 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 86.624 0.025605 10803000 16929 16433 15687 20190 15559 16307 14965 18568 18709 18715 FALSE TRUE 16267.39596 15964.34693 18521.98986 21232.00832 16059.46937 16636.73871 15148.14615 18184.56431 16585.23275 17447.41638 0.93236704 0.914997761 1.061589261 1.216914176 0.920449711 0.953535948 0.868217151 1.04224969 0.95058388 1 14.0907258 TEHAEFLHCK ddPTM_BT-474_Pertuzumab_2h_R1 4 TEHAEFLHCK 10 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ;;; 141.95 2.12E-05 2646570000 2174910 2038520 1774440 1853540 1765630 1643810 2138580 453891 2333490 2241410 FALSE TRUE 2089912.113 1980383.406 2095120.78 1949201.422 1822423.092 1677048.964 2164752.582 444517.9922 2068601.998 2089597.304 1.000150655 0.947734476 1.002643321 0.932811991 0.872140813 0.80257041 1.035966393 0.212729023 0.989952463 1 20.99479351 TFPLCFDDHDPAVIHENASQPEVLVPIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TFPLCFDDHDPAVIHENASQPEVLVPIR 28 0 Q12824-2;Q12824 Q12824-2 SMARCB1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 0 ; 197.08 3.20E-25 235430000 134051 152626 135982 175081 148911 149061 157236 86467 168940 171181 FALSE TRUE 128812.1387 148273.2559 160556.9723 184116.9514 153700.8576 152075.1155 159160.3012 84681.42623 149762.6395 159586.7584 0.807160569 0.929107511 1.006079539 1.153710704 0.963117862 0.952930663 0.997327741 0.530629402 0.938440263 1 17.28398142 TFVVQGFGNVGLHSMR ddPTM_BT-474_Pertuzumab_2h_R1 1 TFVVQGFGNVGLHSMR 16 0 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 122.5 0.00093454 0 184210 202510 165560 236680 157950 136070 214650 168610 194630 175830 FALSE TRUE 177010.8695 196734.6131 195480.3749 248895.0832 163030.6052 138821.4286 217276.9509 165128.1446 172536.4184 163920.8775 1.079855551 1.200180331 1.192528846 1.518385498 0.99456889 0.846880707 1.325498949 1.007364938 1.052559143 1 17.32264009 TGEPS(ph)PPHDILHEPPDVVS(ph)DDEKDHGKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TGEPSPPHDILHEPPDVVSDDEKDHGKK 28 2 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 2 T(0.003)GEPS(0.997)PPHDILHEPPDVVS(1)DDEKDHGKK 125.56 6.62E-05 161680000 161330 130840 149770 108190 141250 140840 154560 32825 253530 172990 TRUE FALSE 155025.0452 127108.5713 176836.7706 113773.6989 145793.4345 143687.8813 156451.5515 32147.15228 224750.3373 161273.2332 0.96125713 0.78815665 1.096504157 0.705471681 0.904015078 0.890959265 0.970102406 0.199333464 1.393599749 1 17.29914749 TGLVEFAR ddPTM_BT-474_Pertuzumab_2h_R1 2 TGLVEFAR 8 0 P31939-2;P31939;F8WEF0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 106.36 0.0097971 144091000 303820 313360 267790 287790 301380 218380 310560 271120 305530 298060 FALSE TRUE 291946.3785 304423.2796 316185.61 302642.8764 311074.1614 222795.7932 314360.7262 265521.2773 270847.5153 277872.1307 1.050650088 1.09555168 1.137881691 1.089144405 1.119486724 0.80179251 1.13131434 0.955552025 0.974719971 1 18.08406162 TGTIVVEGHELHDEDIR ddPTM_BT-474_Pertuzumab_2h_R1 3 TGTIVVEGHELHDEDIR 17 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 162.41 1.65E-09 1490570000 999120 1025880 865520 993220 967990 1051080 1071050 144178 1158830 939790 FALSE TRUE 960073.2858 996622.9068 1021938.717 1044480.203 999126.2775 1072333.558 1084157.83 141200.6739 1027284.477 876137.1862 1.095802462 1.137519241 1.166414043 1.192142303 1.140376522 1.223933391 1.237429306 0.161162745 1.172515552 1 19.74079726 THLEMK ddPTM_BT-474_Pertuzumab_2h_R1 2 THLEMK 6 0 Q9BQI0-3;Q9BQI0;Q9BQI0-2;A6PVM9;Q5JUP3;Q9BQI0-4;Q5JUP1 Q9BQI0-3 AIF1L Allograft inflammatory factor 1-like 0 ; 106.76 0.031846 686340000 1672690 1648340 1408980 1444680 1630490 1427260 1667480 595720 1976530 1678750 FALSE TRUE 1607319.426 1601330.957 1663614.029 1519240.108 1682936.192 1456120.175 1687887.119 583418.1738 1752162.601 1565046.767 1.027010476 1.023184093 1.062980394 0.970731444 1.075326455 0.930400424 1.078489892 0.372780026 1.11955926 1 20.57777434 THLPGFVEQAEALK ddPTM_BT-474_Pertuzumab_2h_R1 4 THLPGFVEQAEALK 14 0 P30044-2;P30044 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;; 171.21 3.05E-06 7769730000 3896050 3793420 3227830 3533130 3407220 3399740 3787190 1037750 4179090 3379680 FALSE TRUE 3743788.059 3685235.376 3811170.684 3715475.263 3516816.326 3468485.072 3833538.764 1016320.1 3704697.223 3150771.263 1.188213217 1.169629614 1.20959929 1.179227228 1.116176336 1.100836837 1.21669853 0.322562324 1.175806466 1 21.58727359 THSLCNGDS(ph)PGPVQK ddPTM_BT-474_Pertuzumab_2h_R1 4 THSLCNGDSPGPVQK 15 0 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7 A0A1B0GWK2 KAZN Kazrin 1 THSLCNGDS(1)PGPVQK;THSLCNGDS(1)PGPVQK;T(0.13)HS(0.118)LCNGDS(0.751)PGPVQK;THSLCNGDS(1)PGPVQK 170.98 7.15E-07 282590000 359316 356766 329350 357345 373820 426794 446491 198348 533998 449638 TRUE FALSE 345273.5335 346591.383 388870.8714 375787.6183 385844.2598 435424.0671 451955.2904 194252.0445 473380.7857 419183.6178 0.823680886 0.826824733 0.927686233 0.896474963 0.920465981 1.038743044 1.078179755 0.46340562 1.12929219 1 18.67722281 THTDS(ph)SEKELEPEAAEEALENGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 T(0.078)HT(0.078)DS(0.422)S(0.422)EKELEPEAAEEALENGPK;T(0.134)HT(0.134)DS(0.366)S(0.366)EKELEPEAAEEALENGPK 200.52 9.19E-25 245170000 512960 423500 349480 329890 403030 385680 418530 108217 560410 372590 TRUE FALSE 492912.9561 411422.1946 412638.8101 346915.6624 415993.826 393478.7139 423652.0953 105982.2811 496794.6062 347354.1474 1.419050153 1.184445897 1.187948419 0.998737643 1.197607194 1.132788299 1.219654633 0.305113044 1.43022506 1 18.4060478 THTMEGK ddPTM_BT-474_Pertuzumab_2h_R1 4 THTMEGK 7 0 P33176;O60282;Q12840 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A 0 ;;; 100.45 0.0097841 759080000 2217160 2142040 1808360 1957820 2048950 1910500 2185400 929730 2324690 2226030 FALSE TRUE 2130510.936 2080951.116 2135170.879 2058863.325 2114856.338 1949131.619 2212145.579 910530.7506 2060800.937 2075259.005 1.026624113 1.002742844 1.028869588 0.992099453 1.01908067 0.939223304 1.0659612 0.438755234 0.993033126 1 20.98485997 TIEAEAAHGTVTR ddPTM_BT-474_Pertuzumab_2h_R1 6 TIEAEAAHGTVTR 13 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;; 299.16 7.92E-41 5562080000 2102951 3606454 2282143 5797870 2322240 2799729 4419750 3551194 2859585 2577876 FALSE TRUE 2020765.35 3503601.463 2694577.006 6097098.766 2396936.959 2856341.439 4473840.223 3477860.603 2534976.899 2403274.162 0.840838462 1.457845101 1.121210825 2.536996761 0.997363096 1.188520845 1.861560488 1.447134354 1.054801378 1 21.19656981 TIFPHTAGS(ph)NK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIFPHTAGSNK 11 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TIFPHT(0.002)AGS(0.998)NK;TIFPHT(0.001)AGS(0.999)NK 81.703 0.013493 637020000 531490 482520 434430 450780 481990 454360 474240 532650 553840 501430 TRUE FALSE 510718.7832 468759.002 512941.1648 474044.8098 497493.6461 463547.4705 480043.891 521650.5914 490970.4051 467467.6995 1.09252208 1.002762335 1.097276166 1.014069657 1.064231062 0.991613904 1.026902803 1.115907242 1.050276641 1 18.83450716 TIHPSGQTTVISSSSSVLQSHGPSDTPQPLLDFDTDDLDLNSLR ddPTM_BT-474_Pertuzumab_2h_R1 1 TIHPSGQTTVISSSSSVLQSHGPSDTPQPLLDFDTDDLDLNSLR 44 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 0 60.959 0.0043478 23940000 5766.6 7162.2 7505.9 6433.6 6836.4 7064.2 6412.8 9863.4 6558.4 7192.9 FALSE TRUE 5541.234897 6957.941069 8862.383098 6765.638867 7056.299015 7207.042964 6491.281765 9659.717343 5813.917927 6705.718476 0.826344696 1.03761306 1.321615742 1.008935715 1.052280832 1.074760742 0.968021814 1.440519368 0.867008949 1 12.7111762 TIPWLEDRVPQK ddPTM_BT-474_Pertuzumab_2h_R1 2 TIPWLEDRVPQK 12 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 169.23 4.05E-05 2440000000 528630 482770 484520 539030 450830 395520 575030 548760 639880 642750 FALSE TRUE 507970.5552 469001.8723 572083.5421 566849.4029 465331.3564 403517.6854 582067.3892 537427.9142 567243.505 599215.97 0.847725329 0.782692545 0.954720119 0.945985139 0.776567014 0.673409431 0.971381636 0.896885165 0.946642836 1 19.19271655 TIS(ph)NPEVVMK ddPTM_BT-474_Pertuzumab_2h_R1 2 TISNPEVVMK 10 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 T(0.006)IS(0.994)NPEVVMK;T(0.004)IS(0.996)NPEVVMK 164.06 6.58E-06 474390000 1284040 1141420 730910 844030 990400 812210 915060 1551930 1166470 923980 TRUE FALSE 1233858.297 1108867.819 863001.696 887590.4894 1022257.115 828633.4427 926258.778 1519882.103 1034057.216 861398.0116 1.432390464 1.287288575 1.001861723 1.03040694 1.186741903 0.961963496 1.075297093 1.764436512 1.200440681 1 19.71632047 TKFAS(ph)DDEHDEHDENGATGPVK ddPTM_BT-474_Pertuzumab_2h_R1 4 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.256)KFAS(0.744)DDEHDEHDENGATGPVK;T(0.464)KFAS(0.536)DDEHDEHDENGATGPVK;T(0.25)KFAS(0.75)DDEHDEHDENGATGPVK;T(0.2)KFAS(0.8)DDEHDEHDENGATGPVK 330.25 5.95E-81 8818790000 4740492 3762134 3444444 2896016 3623125 3675364 3832741 1004398 5065280 3507830 TRUE FALSE 4555228.332 3654841.622 4066931.652 3045479.733 3739666.106 3749682.378 3879647.231 983656.8303 4490290.65 3270241.55 1.392933293 1.117606014 1.243618121 0.931270576 1.143544307 1.146607161 1.186348828 0.300790267 1.373076142 1 21.64096577 TKVFPGER ddPTM_BT-474_Pertuzumab_2h_R1 1 TKVFPGER 8 1 Q7L0J3-2;Q7L0J3 Q7L0J3-2 SV2A Synaptic vesicle glycoprotein 2A 0 58.676 0.094339 943790000 446870 505860 366550 398760 463950 366010 493050 477530 512990 482680 FALSE TRUE 429405.8264 491433.3681 432793.7389 419340.0514 478873.3731 373410.973 499084.0934 467668.8386 454757.5258 449987.6537 0.954261351 1.092104115 0.961790252 0.931892349 1.064192249 0.829824929 1.109106193 1.0392926 1.010600007 1 18.77952589 TKYWELIYEDSMDLIAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TKYWELIYEDSMDLIAK 17 1 O75390;B4DJV2;A0A0C4DGI3;F8VPA1;F8VRI6;F8VR34 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 152.71 1.85E-07 129250000 401900 524550 299520 459720 340890 434350 509680 469860 445000 317010 FALSE TRUE 386193.3037 509590.3476 353649.9268 483446.2043 351855.0364 443132.8546 515917.6163 460157.2268 394485.4656 295538.6303 1.306743904 1.72427661 1.196628429 1.635813916 1.190555143 1.499407553 1.745685888 1.557012111 1.334801698 1 18.17298719 TLDSGTSEIVKS(ph)PR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLDSGTSEIVKSPR 14 1 Q9H501 Q9H501 ESF1 ESF1 homolog 1 TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR 215.51 3.92E-12 3733460000 4066890 4019390 3330360 3120670 3787110 4071680 3650920 3909540 4259850 4262250 TRUE FALSE 3907951.443 3904760.933 3932230.135 3281728.153 3908925.833 4154012.159 3695601.051 3828806.633 3776289.687 3973564.011 0.983487728 0.982684794 0.989597783 0.825890345 0.983732946 1.045412166 0.93004694 0.963569889 0.950353304 1 21.92200215 TLDSWRDEFLIQASPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TLDSWRDEFLIQASPR 16 1 P51149;C9J592 P51149 RAB7A Ras-related protein Rab-7a 0 ; 266.28 3.24E-27 1325680000 569110 924950 477700 869690 634320 578550 815780 844070 822230 616450 FALSE TRUE 546868.552 898571.3316 564031.0164 914574.8051 654723.4789 590248.6774 825763.7597 826639.6595 728893.8975 574697.2924 0.951576698 1.563555881 0.981440184 1.591402669 1.139249284 1.027060133 1.436867322 1.438391429 1.26830926 1 19.13244273 TLDTDLDGVVTFDLFK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLDTDLDGVVTFDLFK 16 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 243.88 1.17E-19 131463000 300495 289132 260781 275182 291486 211588 330605 346741 334558 346190 FALSE TRUE 288751.3232 280886.2384 307909.9277 289384.176 300861.9119 215866.4543 334651.0429 339580.6772 296580.3784 322742.2429 0.894680909 0.870311354 0.954042845 0.89664177 0.932204936 0.668850945 1.036898795 1.05217301 0.918938828 1 18.3000229 TLEPVKPPTVPNDYMTS(ph)PAR ddPTM_BT-474_Pertuzumab_2h_R1 5 TLEPVKPPTVPNDYMTSPAR 20 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 TLEPVKPPTVPNDYMT(0.033)S(0.967)PAR;TLEPVKPPTVPNDYMT(0.09)S(0.91)PAR;TLEPVKPPTVPNDYMT(0.037)S(0.963)PAR;TLEPVKPPTVPNDYMT(0.319)S(0.681)PAR;TLEPVKPPTVPNDYMT(0.178)S(0.822)PAR 190.24 1.15E-17 4772310000 2385600 2335700 2212800 2224360 2110720 2440050 2328520 2594350 2468590 2734690 TRUE FALSE 2292368.115 2269088.123 2612702.183 2339159.486 2178613.226 2489389.483 2357017.124 2540775.766 2188366.012 2549467.01 0.899155826 0.890024508 1.024803291 0.917509219 0.854536739 0.97643526 0.924513679 0.996590956 0.858362161 1 21.28176424 TLEQHDNIVTHYK ddPTM_BT-474_Pertuzumab_2h_R1 5 TLEQHDNIVTHYK 13 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;;; 202.4 5.45E-08 8544280000 10553820 10907240 9197070 10386490 10374640 11429500 11586690 4960160 12768740 11678660 FALSE TRUE 10141365.05 10596176.19 10859185.14 10922537.99 10708349.72 11660612.32 11728491.38 4857730.963 11319286.17 10887653.96 0.93145549 0.973228598 0.99738522 1.003203999 0.983531416 1.070994024 1.077228522 0.446168751 1.039644189 1 23.37618978 TLKDEQTR ddPTM_BT-474_Pertuzumab_2h_R1 1 TLKDEQTR 8 1 Q9H2K8;G3V1Q8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 0 68.893 0.05046 99528000 63496 68578 53320 75826 63327 65264 74550 69045 70394 74632 FALSE TRUE 61014.50612 66622.22258 62956.1101 79739.38895 65363.97047 66583.6828 75462.3652 67619.19662 62403.16824 69577.10816 0.876933631 0.957530779 0.904839419 1.146057821 0.939446496 0.956976864 1.084586112 0.971859832 0.896892238 1 16.0863251 TLMLPLTEGS(ph)LR ddPTM_BT-474_Pertuzumab_2h_R1 4 TLMLPLTEGSLR 12 0 Q7L4E1;Q7L4E1-3 Q7L4E1 FAM73B Protein FAM73B 1 TLMLPLTEGS(1)LR;TLMLPLTEGS(1)LR;TLMLPLTEGS(1)LR;TLMLPLTEGS(1)LR 165.7 5.65E-05 132301000 221149 315542 206908 339524 188594 230198 262609 329657 257084 279095 TRUE FALSE 212506.2526 306543.0511 244300.8782 357046.8743 194660.2973 234852.7613 265822.8875 322849.4677 227900.9021 260191.6471 0.816729726 1.178143321 0.938926676 1.372245721 0.748141993 0.90261453 1.021642664 1.240814113 0.875896304 1 17.98921512 TLTSGGHAEHEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTSGGHAEHEGK 13 0 P50238;K4DIB9;H3BRQ4 P50238 CRIP1 Cysteine-rich protein 1 0 ; 175.88 1.01E-05 431170000 258240 287820 309140 397590 316870 310110 374570 37475 411270 407140 FALSE TRUE 248147.6953 279611.6554 365008.4748 418109.6675 327062.4113 316380.6367 379154.0997 36701.12815 364584.3538 379564.0452 0.653770288 0.736665285 0.961651873 1.101552354 0.861679117 0.833536898 0.998919957 0.096692847 0.960534483 1 18.53398381 TLTSGGHAEHEGKPYCNHPCYAAMFGPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TLTSGGHAEHEGKPYCNHPCYAAMFGPK 28 1 P50238;K4DIB9;H3BRQ4 P50238 CRIP1 Cysteine-rich protein 1 0 ; 133.15 1.09E-05 11087900000 11348660 14006700 10726460 12940300 12197100 13400000 13224400 223180 15077300 11265500 FALSE TRUE 10905141.82 13607242.63 12664969.93 13608150.43 12589430.8 13670957.18 13386244.16 218571.255 13365788.11 10502477.65 1.038339922 1.295622146 1.205903059 1.295708583 1.198710554 1.301688767 1.274579638 0.020811399 1.272631902 1 23.32422638 TLVLSNLSYSATEETLQEVFEK ddPTM_BT-474_Pertuzumab_2h_R1 1 TLVLSNLSYSATEETLQEVFEK 22 0 P19338;H7BY16 P19338 NCL Nucleolin 0 270.47 2.66E-45 90414000 127500 125760 110000 102730 114460 112130 136070 120230 121170 135500 FALSE TRUE 122517.159 122173.4479 129879.4469 108031.9076 118141.7098 114397.3454 137735.2654 117747.2085 107415.2896 126322.4643 0.969876258 0.967155356 1.028157958 0.855207411 0.935239116 0.905597797 1.090346568 0.932116145 0.850326109 1 16.9467517 TMETLHLEYFEEAVNYLLSHPEVK ddPTM_BT-474_Pertuzumab_2h_R1 1 TMETLHLEYFEEAVNYLLSHPEVK 24 0 Q86TX2 Q86TX2 ACOT1 Acyl-coenzyme A thioesterase 1 0 208.39 3.73E-25 128260000 151520 126880 128260 101710 149600 129170 140350 92166 181220 149490 FALSE TRUE 145598.4309 123261.5066 151439.4351 106959.2653 154412.0199 131781.9059 142067.6453 90262.73989 160648.6653 139364.9091 1.044728058 0.884451526 1.086639643 0.767476303 1.10796915 0.945588862 1.019393233 0.647671932 1.152719622 1 17.08850782 TMIIS(ph)PERLDPFADGGKTPDPK ddPTM_BT-474_Pertuzumab_2h_R1 2 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.001)MIIS(0.999)PERLDPFADGGKTPDPK;TMIIS(1)PERLDPFADGGKTPDPK 147.25 4.15E-08 304320000 734830 775250 457640 440530 566310 784920 559690 612850 788090 610750 TRUE FALSE 706112.0312 753140.629 540345.7281 463265.8061 584525.8755 800791.6202 566539.6536 600194.4333 698629.3271 569383.3585 1.240134649 1.322730315 0.949001617 0.813627232 1.02659459 1.406419082 0.995005641 1.054113058 1.22699288 1 19.1190408 TMLELLNQLDGFDSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TMLELLNQLDGFDSR 15 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 172.99 2.32E-06 256440000 192225 208495 155104 226470 186331 188731 208521 232020 191037 210380 FALSE TRUE 184712.6345 202548.9267 183134.7431 238158.1438 192324.5058 192547.2701 211072.9424 227228.7059 169351.2807 196130.7752 0.941783024 1.032723837 0.933737925 1.214282377 0.980593207 0.981729002 1.076184715 1.158557119 0.863461027 1 17.5814564 TMYLEDR ddPTM_BT-474_Pertuzumab_2h_R1 4 TMYLEDR 7 0 P20340-2;P20340;P20340-4;J3KR73;Q9NRW1-2;Q9NRW1;P20340-3;C9JB90;F5GX61 P20340-2;F5GX61 RAB6A;RAB6B Ras-related protein Rab-6A;Ras-related protein Rab-6B 0 ;;; 161.6 0.0030313 2943830000 2469140 3399230 2564500 3321740 2552560 2431610 3228490 3485220 3482550 3215870 FALSE TRUE 2372643.279 3302287.289 3027962.197 3493175.399 2634665.411 2480778.82 3268001.226 3413248.989 3087225.524 2998056.261 0.791393848 1.10147609 1.009975109 1.165146714 0.878791184 0.827462397 1.090039993 1.138487304 1.029742358 1 21.51559603 TNKS(ph)PEAKPLPGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TNKSPEAKPLPGK 13 2 P46087-2;P46087;P46087-4;P46087-3;F5H359;F5GWB7;F5H709;F5H5X6 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 T(0.049)NKS(0.951)PEAKPLPGK;T(0.327)NKS(0.673)PEAKPLPGK 124.46 0.00016661 1414260000 1772460 1096370 1361320 843040 1243820 1023960 1217810 1571860 1472200 1357730 TRUE FALSE 1703190.304 1065102.601 1607340.806 886549.3954 1283828.6 1044665.173 1232713.923 1539400.542 1305082.028 1265769.738 1.345576729 0.841466318 1.269852453 0.700403374 1.014267099 0.825320073 0.973884812 1.216177394 1.031058011 1 20.27158355 TNYNDRYDEIR ddPTM_BT-474_Pertuzumab_2h_R1 6 TNYNDRYDEIR 11 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;; 191.79 1.53E-06 15974670000 9938840 9612320 8628900 8484300 10302220 8970780 9479940 10451370 10611070 10291870 FALSE TRUE 9550419.145 9338186.045 10188334.18 8922175.74 10633600.26 9152175.318 9595958.341 10235545.56 9406545.819 9594792.478 0.995375269 0.973255656 1.061860817 0.929897729 1.108267874 0.953869022 1.00012151 1.066781338 0.98038033 1 23.19382017 TPAQSGAWDPNNPNT(ph)PSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPAQSGAWDPNNPNTPSR 18 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 TPAQSGAWDPNNPNT(0.963)PS(0.037)R 258.81 1.26E-29 226960000 130600 140580 135820 189040 135020 137570 143940 149630 121320 171200 TRUE FALSE 125496.0076 136570.796 160365.6953 198796.3771 139363.0409 140351.7597 145701.5808 146540.0882 107548.2622 159604.4715 0.786293808 0.855682768 1.004769439 1.245556438 0.873177547 0.879372353 0.912891596 0.918145255 0.673842413 1 17.28414155 TPQPSS(ph)PMDQMGK ddPTM_BT-474_Pertuzumab_2h_R1 2 TPQPSSPMDQMGK 13 0 O14497;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 TPQPS(0.327)S(0.673)PMDQMGK;TPQPS(0.215)S(0.785)PMDQMGK 109.6 0.0011797 299830000 2338740 1833620 2355170 1844920 2280520 1664160 2019530 2377560 2019370 2371510 TRUE FALSE 2247339.455 1781326.953 2780801.609 1940136.542 2353874.997 1697810.455 2044245.612 2328462.555 1790139.583 2210885.515 1.016488389 0.80570746 1.257777298 0.877538221 1.064675208 0.767932326 0.92462753 1.053180972 0.809693478 1 21.07619289 TPVAHTTSATSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TPVAHTTSATSSR 13 0 A0A0G2JN42;A0A0G2JNJ8;Q6W4X9 A0A0G2JN42 MUC6 Mucin-6 0 73.219 0.037425 126170000 43247 54973 47474 61473 45128 47501 51724 43625 58292 46775 FALSE TRUE 41556.85943 53405.22386 56053.60785 64645.6289 46579.5831 48461.50277 52357.01378 42724.1285 51674.93654 43606.88759 0.952988432 1.224696988 1.285430145 1.482463722 1.068170321 1.111326798 1.200659269 0.97975643 1.185017767 1 15.4122684 TPVS(ph)PVK ddPTM_BT-474_Pertuzumab_2h_R1 4 TPVSPVK 7 0 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 T(0.01)PVS(0.99)PVK;T(0.009)PVS(0.991)PVK;T(0.078)PVS(0.922)PVK;T(0.017)PVS(0.983)PVK 113.74 0.0063586 14528080000 8132900 7241900 6999900 7720800 7559500 6429500 8554300 9311300 9252900 8519300 TRUE FALSE 7815057.277 7035368.103 8264937.642 8119271.413 7802658.183 6559508.895 8658990.082 9119018.401 8202549.583 7942280.223 0.983981559 0.885812123 1.040625288 1.022284682 0.982420409 0.825897439 1.09023981 1.148161252 1.032770105 1 22.92112183 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK ddPTM_BT-474_Pertuzumab_2h_R1 1 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK 31 0 P49721 P49721 PSMB2 Proteasome subunit beta type-2 0 96.887 0.0001974 597920000 346710 346010 317320 310580 317890 300990 348240 205290 402420 324100 FALSE TRUE 333160.1899 336142.1336 374666.7827 326609.071 328115.2206 307076.224 352501.8653 201050.6898 356738.9687 302148.4183 1.102637544 1.112506679 1.240009082 1.080955753 1.085940553 1.016309222 1.166651367 0.665403747 1.180674619 1 18.20489786 TQEEGEER ddPTM_BT-474_Pertuzumab_2h_R1 2 TQEEGEER 8 0 Q9NR28-2;Q9NR28;Q9NR28-3 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ; 126.82 0.0027977 52557000 164910 188490 163625 214801 151076 163410 170838 171188 161290 161380 FALSE TRUE 158465.1349 183114.4498 193195.6773 225886.9054 155935.4967 166714.2622 172928.7665 167652.908 142981.0354 150449.5889 1.053277288 1.217114989 1.284122335 1.50141258 1.036463429 1.10810713 1.149413354 1.114346069 0.950358432 1 17.19892064 TQHEILR ddPTM_BT-474_Pertuzumab_2h_R1 6 TQHEILR 7 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 ;;;;; 160.54 0.0013426 2042770000 1726380 2360560 1664957 2323940 1713040 1230710 2205290 1741160 2249030 2062060 FALSE TRUE 1658911.161 2293239.14 1965851.767 2443878.822 1768141.487 1255595.799 2232278.999 1705204.438 1993729.543 1922394.84 0.862939874 1.192907457 1.02260562 1.271267885 0.919759797 0.653141474 1.161196937 0.887020919 1.037107207 1 20.87447325 TQPNLDNCPFHDQPHLK ddPTM_BT-474_Pertuzumab_2h_R1 3 TQPNLDNCPFHDQPHLK 17 0 P01034 P01034 CST3 Cystatin-C 0 ;; 220.64 2.28E-15 890820000 629170 622830 557560 680630 567220 656490 715050 124440 781120 711700 FALSE TRUE 604581.3408 605067.4982 658323.4949 715757.3959 585465.1464 669764.6776 723800.9958 121870.2705 692450.5323 663495.9251 0.911205808 0.911938529 0.992204277 1.07876683 0.882394487 1.009448065 1.090889889 0.183679004 1.043639465 1 19.33972808 TRDDEPVCGRPLGIR ddPTM_BT-474_Pertuzumab_2h_R1 4 TRDDEPVCGRPLGIR 15 2 Q9HDC9;H0Y512;Q9HDC9-2 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 ;;; 192.46 7.50E-08 1132550000 203107 297783 151291 284121 190688 173282 270578 268114 286250 200634 FALSE TRUE 195169.3539 289290.5204 178632.6492 298784.5189 196821.6527 176785.8808 273889.4145 262577.3522 253756.1001 187044.8805 1.043435957 1.546636934 0.9550256 1.597394797 1.05226966 0.945152203 1.46429784 1.403820043 1.356658891 1 17.51302495 TRS(ph)PDVISSASTALS(ph)QDIPEIASEALSR ddPTM_BT-474_Pertuzumab_2h_R1 1 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 T(0.442)RS(0.509)PDVIS(0.031)S(0.033)AS(0.032)T(0.032)ALS(0.921)QDIPEIASEALSR 55.919 0.036158 23440000 5805.2 7656.8 7186.8 6538.1 5777.8 6520 4908.8 8422.8 7292.1 8024.9 TRUE FALSE 5578.326366 7438.435561 8485.61463 6875.532125 5963.648184 6651.838867 4968.875363 8248.866237 6464.331379 7481.366375 0.745629352 0.994261635 1.134233268 0.919020909 0.797133556 0.889120855 0.664166826 1.102588194 0.864057587 1 12.86908607 TRS(ph)PDVISSASTALSQDIPEIASEALSR ddPTM_BT-474_Pertuzumab_2h_R1 2 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.204)RS(0.796)PDVISSASTALSQDIPEIASEALSR;T(0.174)RS(0.826)PDVISSASTALSQDIPEIASEALSR 256.15 9.16E-54 743820000 248220 250920 227080 235980 230100 252130 250390 242560 285250 270850 TRUE FALSE 238519.288 243764.0073 268118.4074 248158.9561 237501.3755 257228.2413 253454.3477 237551.0512 252869.6159 252505.0883 0.944611808 0.965382555 1.061833681 0.982787942 0.940580553 1.01870518 1.003759368 0.940777284 1.001443645 1 17.94595293 TSEVNCYR ddPTM_BT-474_Pertuzumab_2h_R1 4 TSEVNCYR 8 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ;;; 174.73 0.00062874 3633190000 1771860 1519980 1431950 1496610 1519640 1365960 1678370 1729510 1856890 1807750 FALSE TRUE 1702613.752 1476631.659 1690735.219 1573850.221 1568520.601 1393580.647 1698910.394 1693795.014 1646103.632 1685309.482 1.010267711 0.876178336 1.00321943 0.933864218 0.930701819 0.826898953 1.008070275 1.005034999 0.976736706 1 20.68458211 TSISDPPES(ph)PPLLPPREPVR ddPTM_BT-474_Pertuzumab_2h_R1 2 TSISDPPESPPLLPPREPVR 20 1 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 TSISDPPES(1)PPLLPPREPVR;TSISDPPES(1)PPLLPPREPVR 112.85 8.93E-05 727480000 789040 834220 586140 699410 655760 779630 804050 837340 817640 723940 TRUE FALSE 758203.4445 810428.8624 692068.5366 735506.6339 676853.1159 795394.6528 813890.2044 820048.6364 724824.935 674906.899 1.123419313 1.200800975 1.025428156 1.08978977 1.002883682 1.178524999 1.205929597 1.215054458 1.073962847 1 19.36432898 TSNKPLMIIHHLDECPHSQALK ddPTM_BT-474_Pertuzumab_2h_R1 2 TSNKPLMIIHHLDECPHSQALK 22 1 O95994;B5MC07;C9J3E2 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 259.93 1.04E-37 8487900000 4321000 4522600 4245600 4591400 4379900 4579000 5158500 524560 6632300 4986900 FALSE TRUE 4152130.543 4393619.876 5012874.363 4828362.704 4520783.461 4671590.517 5221631.266 513727.6527 5879429.109 4649132.821 0.893097853 0.94504073 1.078238578 1.03855125 0.972392839 1.004830513 1.12314091 0.110499672 1.264629198 1 22.14853021 TSNKPLMIIHHLDECPHSQALKK ddPTM_BT-474_Pertuzumab_2h_R1 1 TSNKPLMIIHHLDECPHSQALKK 23 2 O95994;B5MC07;C9J3E2 O95994 AGR2 Anterior gradient protein 2 homolog 0 162.65 5.27E-12 1034500000 704320 753040 553660 495450 505610 753500 694980 85248 896030 752230 FALSE TRUE 676794.3957 731564.0365 653718.6781 521020.2339 521873.4048 768736.2863 703485.3731 83487.59901 794316.4309 701280.7921 0.965083321 1.043182766 0.932178217 0.742955232 0.744171822 1.096188994 1.00314365 0.119050172 1.132665317 1 19.41963269 TSS(ph)LDTITGPYLTGQWPR ddPTM_BT-474_Pertuzumab_2h_R1 3 TSSLDTITGPYLTGQWPR 18 0 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 T(0.135)S(0.135)S(0.729)LDTITGPYLTGQWPR;T(0.026)S(0.026)S(0.948)LDTITGPYLTGQWPR;T(0.001)S(0.063)S(0.936)LDTITGPYLTGQWPR 335.62 4.73E-75 537160000 398763 380331 339595 389920 367915 392328 381333 412738 432183 439708 TRUE FALSE 383178.9011 369484.3323 400967.3707 410043.8179 379749.3201 400261.141 385999.8673 404214.8161 383123.3977 409926.1855 0.934750974 0.901343572 0.978145298 1.00028696 0.926384636 0.976422476 0.941632618 0.986067322 0.934615575 1 18.64500462 TT(ph)PDQELAPASEPVWERPWSVEEIR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPDQELAPASEPVWERPWSVEEIR 25 1 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.212)T(0.788)PDQELAPASEPVWERPWSVEEIR;T(0.174)T(0.826)PDQELAPASEPVWERPWSVEEIR 182.64 3.54E-17 323780000 11253.1 10630.9 9654.7 11167.2 7714.8 12833.5 12416.5 13013.9 11032.3 12395.7 TRUE FALSE 10813.31641 10327.71714 11399.51906 11743.54053 7962.953548 13093.00216 12568.45684 12745.15842 9779.959555 11556.1282 0.935721396 0.893700465 0.986447958 1.016217571 0.689067602 1.132992118 1.087601022 1.102891747 0.846300715 1 13.49637049 TTDGYLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTDGYLLR 8 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ; 123.69 0.00311 392590000 593640 639650 589630 536070 583570 514990 606520 608540 591700 705670 FALSE TRUE 570439.8925 621407.8083 696189.2572 563736.6369 602341.059 525403.4506 613942.7732 595973.4363 524532.6966 657874.3424 0.867095516 0.94456915 1.058240476 0.856906252 0.915586793 0.798638002 0.933221945 0.905907706 0.797314415 1 19.32745252 TTPPPGAQCEVPAS(ph)PQRPSRPGALPEQTR ddPTM_BT-474_Pertuzumab_2h_R1 2 TTPPPGAQCEVPASPQRPSRPGALPEQTR 29 2 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTR 275.2 2.03E-71 1290850000 23822.7 29134.1 25929.1 25173 4269.3 41754 28259 31653 28556.8 28490 TRUE FALSE 22891.68255 28303.22399 30615.06516 26472.18155 4406.625912 42598.29449 28604.8421 30999.35449 25315.15178 26560.34692 0.86187438 1.065619514 1.15266059 0.996680564 0.165909953 1.6038305 1.076975469 1.167129126 0.953118265 1 14.69698637 TVATPLNQVANPNSAIFGGARPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVATPLNQVANPNSAIFGGARPR 23 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 256.92 1.24E-43 1652870000 284990 311780 233850 270080 295830 263390 256850 302520 340370 285490 FALSE TRUE 273852.2757 302888.3397 276111.897 284018.8612 305345.6406 268715.9263 259993.4071 296272.8563 301732.6245 266153.508 1.028926043 1.138021219 1.03741596 1.067124245 1.147253864 1.009627595 0.976855083 1.113165325 1.133678931 1 18.02189906 TVCIYGHLDVQPAALEDGWDSEPFTLVER ddPTM_BT-474_Pertuzumab_2h_R1 1 TVCIYGHLDVQPAALEDGWDSEPFTLVER 29 0 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;J3QRD0;J3QKQ0;J3QLU1;J3QR27;A0A087WVS2;J3KRD5 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 169.57 3.00E-12 343440000 80965 93873 74019 78833 79342 104680 90706 82364 89530 103830 FALSE TRUE 77800.79829 91195.83395 87395.87984 82901.58058 81894.10749 106796.7013 91816.08716 80663.15462 79366.92974 96797.50162 0.803748 0.942130039 0.902873301 0.856443392 0.846035343 1.103300184 0.948537779 0.83331856 0.819927461 1 16.56268219 TVFRPPLDIYDVLIR ddPTM_BT-474_Pertuzumab_2h_R1 1 TVFRPPLDIYDVLIR 15 1 Q9H6R4-4;Q9H6R4;A0A0C4DFX0 Q9H6R4-4 NOL6 Nucleolar protein 6 0 111.22 0.00078391 59741000 75614 77679 47096 73378 65600 76181 62333 72871 89030 72616 FALSE TRUE 72658.92128 75463.67098 55607.29484 77165.04737 67710.08358 77721.43202 63095.8499 71366.18838 78923.68764 67697.65364 1.073285666 1.114716196 0.821406531 1.139848181 1.00018361 1.148066851 0.932024177 1.054189984 1.165826043 1 16.04681821 TVGFGTNNSEHITYLEHNPYEK ddPTM_BT-474_Pertuzumab_2h_R1 2 TVGFGTNNSEHITYLEHNPYEK 22 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 ; 209.75 3.07E-23 262960000 218790 270180 204117 227270 216620 248460 247590 149181 270380 280010 FALSE TRUE 210239.4449 262474.7309 241005.4825 238999.4319 223587.779 253484.0314 250620.0805 146100.3602 239687.5959 261044.6733 0.805377265 1.00547821 0.92323463 0.915549928 0.856511555 0.971036981 0.960065867 0.5596757 0.918186121 1 17.99393719 TVS(ph)ASST(ph)GDLPK ddPTM_BT-474_Pertuzumab_2h_R1 1 TVSASSTGDLPK 12 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 2 T(0.002)VS(0.99)AS(0.221)S(0.316)T(0.471)GDLPK 118.52 0.0032733 598230000 1187500 1043600 922430 935520 927910 965440 983730 1153500 1124800 1025000 TRUE FALSE 1141091.187 1013837.55 1089133.62 983802.2993 957757.0679 984961.8583 995769.182 1129679.822 997117.4195 955575.837 1.19413985 1.060970266 1.139766807 1.029538694 1.002282635 1.03075216 1.04206191 1.182197978 1.043472826 1 19.86601085 TVSS(ph)PPTSPRPGSAATVSASTSNIIPPR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 TVS(0.142)S(0.832)PPT(0.021)S(0.005)PRPGSAATVSASTSNIIPPR;TVS(0.142)S(0.853)PPT(0.004)S(0.001)PRPGSAATVSASTSNIIPPR 175.9 3.09E-13 1625320000 219514 205982 170941 223432 174406 250763 227392 210245 202844 233867 TRUE FALSE 210935.1502 200107.595 201833.8413 234963.3523 180015.9274 255833.5997 230174.8913 205903.3673 179817.9995 218026.9798 0.967472697 0.917811159 0.92572874 1.077680168 0.825658951 1.173403401 1.055717469 0.94439398 0.824751137 1 17.73414715 TVTAMDVVYALKR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVTAMDVVYALKR 13 1 P62805 P62805 HIST1H4A Histone H4 0 ; 200.21 1.79E-07 1698330000 1855740 1891670 1161210 2730900 1234810 1143120 2338400 1335090 2005920 867240 FALSE TRUE 1783215.629 1837721.424 1371066.478 2871842.076 1274528.785 1166234.67 2367018.039 1307519.925 1778216.371 808501.0623 2.205582296 2.272998156 1.695812834 3.55205727 1.576409537 1.442465228 2.927662249 1.617214851 2.19939893 1 19.62489014 TVYGGGCSEMLMAHAVTQLANR ddPTM_BT-474_Pertuzumab_2h_R1 2 TVYGGGCSEMLMAHAVTQLANR 22 0 P78371;P78371-2;F5GWF6 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 246.31 5.98E-31 1166540000 271760 315380 285650 327190 306690 311590 288990 277010 383280 331490 FALSE TRUE 261139.3188 306385.6712 337273.3092 344076.3151 316554.9624 317890.5633 292526.7461 271289.6467 339771.6612 309037.887 0.845007456 0.991417829 1.091365568 1.113379069 1.024324122 1.028645925 0.946572438 0.877852387 1.099449859 1 18.23742419 TWPDHGVPSDPGGVLDFLEEVHHK ddPTM_BT-474_Pertuzumab_2h_R1 2 TWPDHGVPSDPGGVLDFLEEVHHK 24 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 103.95 0.0010911 494867000 172186 182387 149380 172830 165583 169906 178481 33335.8 195487 180958 FALSE TRUE 165456.7808 177185.5013 176376.2889 181749.777 170909.1276 173341.6157 180665.3039 32647.40408 173296.1353 168701.5535 0.980766195 1.050289684 1.045492974 1.077345011 1.013085677 1.027504561 1.070916658 0.193521656 1.02723497 1 17.36411373 TWS(ph)RDEVMGDNLLLSSVFQFSK ddPTM_BT-474_Pertuzumab_2h_R1 1 TWSRDEVMGDNLLLSSVFQFSK 22 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4;E7EWM2;E7EMW0;Q96L14;E5RG47 Q5SW79 CEP170;CEP170P1 Centrosomal protein of 170 kDa;Cep170-like protein 1 T(0.041)WS(0.959)RDEVMGDNLLLSSVFQFSK 224.84 3.98E-26 271990000 156900 167560 127110 141570 184340 171400 150580 165600 189570 169600 TRUE FALSE 150768.1745 162781.3529 150081.6045 148876.4447 190269.4635 174865.8254 152422.8431 162180.3021 168050.8083 158112.8409 0.953547945 1.029526457 0.949205666 0.941583516 1.203377679 1.105955876 0.964013057 1.025725053 1.062853639 1 17.27059501 VAAYDKLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VAAYDKLEK 9 1 P35579 P35579 MYH9 Myosin-9 0 ; 121.83 0.00054982 1961220000 4140100 4209300 3206900 3039500 3223800 2086970 4200200 3978200 4560700 4465700 FALSE TRUE 3978300.315 4089254.885 3786458.167 3196368.959 3327496.455 2129169.963 4251603.304 3896048.78 4042988.456 4163234.161 0.955579283 0.982230335 0.909499207 0.767761033 0.799257579 0.511422101 1.02122608 0.935822639 0.971117237 1 21.98927327 VAEEHAPSIVFIDEIDAIGTKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VAEEHAPSIVFIDEIDAIGTKR 22 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 175.32 1.05E-12 48470000 82310 89087 59734 67170 78259 97863 77307 81367 85150 83649 FALSE TRUE 79093.2342 86546.32599 70529.26258 70636.65175 80776.27181 99841.85691 78253.10619 79686.74302 75484.12898 77983.37872 1.014231949 1.109804774 0.90441404 0.905791117 1.035813953 1.280296629 1.003458782 1.021842658 0.967951507 1 16.25087904 VAEKLDEIYVAGLVAHSDLDER ddPTM_BT-474_Pertuzumab_2h_R1 4 VAEKLDEIYVAGLVAHSDLDER 22 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;; 231.44 7.09E-27 3934920000 4355640 4149170 3168520 3162460 3652160 4185050 3709130 3847440 4534220 4170790 FALSE TRUE 4185416.773 4030839.734 3741142.047 3325674.94 3769635.043 4269674.578 3754523.442 3767989.019 4019514.355 3888298.678 1.076413393 1.036658978 0.96215398 0.855303364 0.969481862 1.098082974 0.965595432 0.969058535 1.033746296 1 21.89070761 VAKPVVEMDGDEMTR ddPTM_BT-474_Pertuzumab_2h_R1 5 VAKPVVEMDGDEMTR 15 1 P48735;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;; 179.9 5.94E-07 8770970000 3020230 3824910 2592570 5234230 2490150 3104390 4735940 4383920 3718040 3022380 FALSE TRUE 2902196.073 3715827.312 3061105.07 5504369.238 2570247.936 3167162.893 4793899.85 4293390.52 3295983.686 2817671.511 1.029998018 1.318758165 1.086395294 1.953517015 0.912188638 1.124035531 1.701369316 1.523737066 1.169754414 1 21.426072 VAMSHFEPNEYIHYDLLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VAMSHFEPNEYIHYDLLEK 19 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 162.33 1.61E-11 404460000 115300 171930 104970 181060 110920 105900 170450 93305 147870 121150 FALSE TRUE 110793.9485 167026.7247 123940.414 190404.5283 114487.8425 108041.3706 172536.0181 91378.21914 131084.4175 112944.4026 0.980960065 1.478840216 1.097357737 1.685825273 1.013665484 0.956588977 1.527619024 0.809054872 1.160610128 1 16.78525325 VASSTLLDDRR ddPTM_BT-474_Pertuzumab_2h_R1 4 VASSTLLDDRR 11 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;; 179.19 1.16E-05 7288700000 3421910 3931100 3080550 3461310 3532880 2579040 3667900 3184390 3788340 3708400 FALSE TRUE 3288177.974 3818988.877 3637273.911 3639948.624 3646518.294 2631189.956 3712788.857 3118631.234 3358303.525 3457226.765 0.951102776 1.104639394 1.052078489 1.052852148 1.054752419 0.761069532 1.073921125 0.902061521 0.971386534 1 21.7211838 VATFHDCEDAAR ddPTM_BT-474_Pertuzumab_2h_R1 2 VATFHDCEDAAR 12 0 Q9P2X0;Q9P2X0-2 Q9P2X0 DPM3 Dolichol-phosphate mannosyltransferase subunit 3 0 ; 158.4 7.36E-05 172960000 252888 335490 243174 365560 267590 226885 308200 326440 317010 291360 FALSE TRUE 243004.8574 325922.1537 287120.9512 384426.5954 276197.2754 231472.7702 311971.8438 319698.8999 281024.3538 271625.9277 0.894630566 1.199893384 1.057045451 1.415279457 1.01682957 0.852174798 1.148534849 1.176982266 1.034600622 1 18.05126167 VATTAGLYGSNLMEHTEIDHWLEFSATK ddPTM_BT-474_Pertuzumab_2h_R1 2 VATTAGLYGSNLMEHTEIDHWLEFSATK 28 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 285.02 2.62E-62 803940000 572160 586770 518160 608930 664220 682070 668680 87060 772810 607790 FALSE TRUE 549799.3546 570035.8941 611803.0384 640356.9503 685585.2395 695861.9227 676863.5059 85262.18058 685083.8487 566623.8419 0.970307484 1.006021724 1.07973402 1.130127084 1.209947744 1.228084438 1.194555287 0.150474043 1.20906287 1 19.11203178 VAVAT(ph)PAKK ddPTM_BT-474_Pertuzumab_2h_R1 3 VAVATPAKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK 74.611 0.023793 5674470000 37638400 11006000 6118900 6320100 5850900 3872600 5230300 29490800 4178200 2514270 TRUE FALSE 36167449.72 10692119.66 7224721.344 6646281.118 6039099.512 3950906.625 5294309.976 28881804.67 3703908.252 2343976.253 15.42995568 4.561530707 3.082250229 2.835472889 2.576433743 1.685557445 2.258687548 12.32171385 1.580181645 1 21.16052652 VAVNDAHLLQYNHR ddPTM_BT-474_Pertuzumab_2h_R1 4 VAVNDAHLLQYNHR 14 0 P17931 P17931 LGALS3 Galectin-3 0 ;;; 278.82 1.97E-33 1644200000 970840 980770 789840 1215490 960830 884190 1067610 482312 1208150 1261890 FALSE TRUE 932898.4995 952799.3999 932581.6579 1278221.585 991735.9696 902068.9276 1080675.731 472352.0887 1071005.877 1176421.066 0.792997105 0.809913582 0.792727778 1.086534083 0.84301106 0.766790865 0.918613039 0.401516177 0.910393317 1 20.16597309 VAVTASEVQQAESEVS(ph)DIESR ddPTM_BT-474_Pertuzumab_2h_R1 4 VAVTASEVQQAESEVSDIESR 21 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 VAVTASEVQQAESEVS(1)DIESR;VAVTASEVQQAESEVS(1)DIESR;VAVTASEVQQAESEVS(0.999)DIES(0.001)R;VAVTASEVQQAESEVS(0.989)DIES(0.011)R 335.98 2.93E-80 408490000 351026 354365 265414 298338 326339 298709 310379 432370 332887 335676 TRUE FALSE 337307.5158 344258.8572 313380.2139 313735.2599 336835.9903 304749.1006 314177.511 423441.4084 295099.0633 312940.3655 1.077865156 1.100078146 1.001405534 1.002540083 1.076358397 0.973824838 1.003953295 1.353105751 0.942988172 1 18.25552824 VCEALEHGHVEWSSR ddPTM_BT-474_Pertuzumab_2h_R1 3 VCEALEHGHVEWSSR 15 0 A0A0A0MTR2;Q8N543;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ;; 160.81 9.76E-07 532830000 206826 241391 202456 242111 224499 232077 234531 61695 266317 283942 FALSE TRUE 198743.0113 234506.765 239044.3028 254606.3777 231720.2142 236769.7559 237401.2605 60420.97669 236085.8107 264710.3554 0.750794244 0.885899475 0.903040995 0.961830063 0.875372684 0.894448408 0.896834051 0.228253166 0.891864658 1 18.01405511 VDAYHLQLQNLLYEVMHLQK ddPTM_BT-474_Pertuzumab_2h_R1 1 VDAYHLQLQNLLYEVMHLQK 20 0 Q13769;F8WCP5;C9JXG5;C9JCL9;H7C441 Q13769 THOC5 THO complex subunit 5 homolog 0 228.63 1.68E-25 33480000 69400 65779 65522 70735 68346 70358 77478 59301 84556 83273 FALSE TRUE 66687.77127 63903.04732 77363.28293 74385.64183 70544.41116 71780.68697 78426.19894 58076.41363 74957.55737 77632.84554 0.859014903 0.823144468 0.996527725 0.958172296 0.908692843 0.924617492 1.010219301 0.74809075 0.965539223 1 16.24437955 VDCDQHSDIAQR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDCDQHSDIAQR 12 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ; 186.16 1.21E-05 2263300000 1848060 2225400 1739480 2162500 1858820 1885060 2133000 1850560 2138400 2184900 FALSE TRUE 1775835.772 2161933.771 2053842.731 2274106.884 1918610.633 1923177.205 2159104.292 1812345.289 1895657.797 2036914.777 0.87182625 1.061376644 1.008310585 1.116446751 0.941919935 0.944161841 1.059987544 0.88975018 0.930651502 1 20.95795419 VDDFLR ddPTM_BT-474_Pertuzumab_2h_R1 4 VDDFLR 6 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ;;; 142.74 0.026724 634219000 759986 795945 720681 791350 791740 668954 836742 845070 847110 877390 FALSE TRUE 730284.9069 773245.4279 850924.0882 832191.6683 817207.0361 682480.7082 846982.2989 827619.0092 750949.6242 817963.5938 0.892808571 0.945329882 1.040295796 1.017394508 0.999075072 0.834365629 1.035476769 1.011804212 0.918072185 1 19.64167711 VDDHDSEEICLDHLCK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDDHDSEEICLDHLCK 16 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;H7C5K1 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 ; 306.69 5.71E-47 532540000 356010 458480 314580 374130 361940 404720 389730 240750 447080 484020 FALSE TRUE 342096.7356 445404.5993 371431.6038 393438.8941 373582.1288 412903.7157 394499.6323 235778.4284 396329.3527 451236.8943 0.758131128 0.987074871 0.823141034 0.871912069 0.827906879 0.915048661 0.874262804 0.522515848 0.878317703 1 18.78352551 VDDSPSTSGGSS(ph)DGDQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VDDSPSTSGGSSDGDQR 17 0 C9J180;Q96LR5;F8WF15;F8W8F0 C9J180 UBE2E2 Ubiquitin-conjugating enzyme E2 E2 1 VDDSPSTS(0.002)GGS(0.126)S(0.872)DGDQR 235.4 3.87E-20 151140000 101400 100180 80274 91017 95075 87731 99389 104230 111280 90410 TRUE FALSE 97437.1759 97322.96449 94781.29749 95714.39828 98133.17372 89504.98093 100605.3523 102077.6141 98647.96092 84286.45017 1.156024197 1.154669158 1.124514051 1.135584641 1.164281726 1.061914231 1.193612403 1.211079763 1.170389318 1 16.3630131 VDIDAPDVEVHDPDWHLK ddPTM_BT-474_Pertuzumab_2h_R1 6 VDIDAPDVEVHDPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;; 274.23 2.86E-39 8700990000 6355320 6106710 5272490 5912160 5187940 5861720 5976510 1804805 7039630 5621940 FALSE TRUE 6106947.068 5932552.61 6225346.229 6217287.286 5354814.802 5980247.995 6049652.317 1767535.146 6240520.715 5241160.996 1.165189749 1.131915737 1.187780004 1.186242378 1.021684853 1.141015893 1.154258059 0.337241147 1.190675257 1 22.321455 VDNDENEHQLSLR ddPTM_BT-474_Pertuzumab_2h_R1 13 VDNDENEHQLSLR 13 0 P06748;P06748-3;P06748-2;E5RGW4 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;;; 283.13 1.46E-32 1.61579E+11 44981061.4 44661582.6 35883615.2 43296583.7 40844154.2 43921743.1 42828600.9 43490841.7 48465974.2 46999634.3 FALSE TRUE 43223151.79 43387877.99 42368582.69 45531125.57 42157943.51 44809870.84 43352750.13 42592740.62 42964319.99 43816307.21 0.986462679 0.990222152 0.96695923 1.039136533 0.962151906 1.022675659 0.989420444 0.972075087 0.980555477 1 25.38496456 VDNLTYR ddPTM_BT-474_Pertuzumab_2h_R1 2 VDNLTYR 7 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 ; 147.16 0.0050496 1328220000 1210310 1239710 970110 1168390 1174520 1035060 1123520 1252350 1245010 1277390 FALSE TRUE 1163009.747 1204354.685 1145430.457 1228690.748 1212299.502 1055989.622 1137269.974 1226488.535 1103681.684 1190871.238 0.976604112 1.011322338 0.961842407 1.03175785 1.017993772 0.886737028 0.954989875 1.029908605 0.926785071 1 20.183586 VDNNAIEFLLLQASDGIHHWTPPK ddPTM_BT-474_Pertuzumab_2h_R1 2 VDNNAIEFLLLQASDGIHHWTPPK 24 0 P50583 P50583 NUDT2 Bis(5-nucleosyl)-tetraphosphatase [asymmetrical] 0 ; 220.23 5.92E-33 337750000 580760 549670 490000 499210 570680 583120 573520 268780 664230 548450 FALSE TRUE 558063.2571 533993.9498 578553.9 524974.2879 589036.4405 594911.0859 580538.9093 263229.5991 588829.3951 511302.993 1.09145314 1.04437869 1.131528483 1.026738148 1.152030105 1.163519663 1.135410739 0.514821158 1.151625168 1 18.96381895 VDTFPQPLAAPQCHTLLAPEMEDNEMSCS(ph)P ddPTM_BT-474_Pertuzumab_2h_R1 1 VDTFPQPLAAPQCHTLLAPEMEDNEMSCSP 30 0 B7Z4K4;Q9UET6-2;Q9UET6 B7Z4K4 FTSJ1 Putative tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase 1 VDTFPQPLAAPQCHTLLAPEMEDNEMS(0.005)CS(0.995)P 129.73 6.33E-06 44651000 48685 56393 35141 44632 50981 56921 42065 45032 46004 48747 TRUE FALSE 46782.33638 54784.72685 41491.76041 46935.46287 52620.85016 58071.98162 42579.80405 44102.07346 40781.81878 45445.32227 1.02942028 1.205508601 0.913003987 1.032789747 1.157893652 1.277842883 0.936945805 0.970442529 0.897382101 1 15.47184418 VEGIYTYSLS(ph)PSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VEGIYTYSLSPSK 13 0 O95197-7;O95197-2;O95197 O95197-7 RTN3 Reticulon-3 1 VEGIYTYSLS(0.999)PS(0.001)K;VEGIYTYSLS(1)PSK 242.07 6.77E-17 135345000 205005 221673 213784 232196 171285 146590 256251 242989 247632 255758 TRUE FALSE 196993.178 215351.1031 252419.5244 244179.6634 176794.5376 149554.1502 259387.0764 237971.1922 219521.8535 238435.2829 0.826191391 0.903184715 1.058650051 1.02409199 0.741478088 0.627231626 1.087872035 0.998053599 0.920676885 1 17.86323821 VFLENVIR ddPTM_BT-474_Pertuzumab_2h_R1 2 VFLENVIR 8 0 P62805 P62805 HIST1H4A Histone H4 0 ; 121.85 0.0032934 387890000 665160 731630 611420 1112730 537670 399920 967770 552610 690210 532920 FALSE TRUE 639164.8118 710764.6287 721917.195 1170158.129 554964.6438 408006.6564 979613.8588 541198.4104 611860.2544 496824.8537 1.28649927 1.430614075 1.453061757 2.355272929 1.117022709 0.821228353 1.9717489 1.089314285 1.231541155 1 18.92237782 VFNTTPDDLDLHVIYDVSHNIAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VFNTTPDDLDLHVIYDVSHNIAK 23 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 272.24 7.12E-52 2515500000 1190300 1074190 934670 1080730 1066410 1153700 1224230 668850 1387980 1284670 FALSE TRUE 1143781.76 1043555.153 1103585.661 1136506.605 1100712.046 1177028.604 1239212.493 655038.0138 1230422.329 1197658.157 0.955015213 0.871329726 0.921452966 0.948940729 0.919053605 0.982775091 1.034696325 0.54693237 1.027356865 1 20.19178475 VGEEQGQENPPDHDPIHDQSWYLDQTLR ddPTM_BT-474_Pertuzumab_2h_R1 1 VGEEQGQENPPDHDPIHDQSWYLDQTLR 28 0 Q7LBC6;Q7LBC6-2;Q7LBC6-3 Q7LBC6 KDM3B Lysine-specific demethylase 3B 0 209.05 9.60E-26 101680000 28552 23678 24452 29801 30445 29838 29507 5548.4 35166 30023 FALSE TRUE 27436.15627 23002.72662 28871.02033 31339.03318 31424.29107 30441.3448 29868.11549 5433.823601 31174.10311 27989.51547 0.980229769 0.821833684 1.031494109 1.119670443 1.122716508 1.087598134 1.06711799 0.194137823 1.113777877 1 14.77259889 VGPATPS(ph)AQVGK ddPTM_BT-474_Pertuzumab_2h_R1 1 VGPATPSAQVGK 12 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 VGPAT(0.241)PS(0.759)AQVGK 130.2 0.00023152 235600000 823750 483290 411370 369410 318410 304560 353250 878910 424570 482640 TRUE FALSE 791556.9393 469507.0424 485713.7099 388475.2944 328651.9468 310718.4119 357573.1792 860760.2014 376374.5935 449950.3629 1.75920947 1.043464082 1.079482872 0.863373666 0.730418228 0.690561532 0.794694723 1.913011462 0.836480253 1 18.77940633 VHAYFAPVT(ph)PPPS(ph)VGGSR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHAYFAPVTPPPSVGGSR 18 0 J3KTA1;Q96IG2-2;Q96IG2 J3KTA1 FBXL20 F-box/LRR-repeat protein 20 2 VHAYFAPVT(0.998)PPPS(0.82)VGGS(0.183)R;VHAYFAPVT(1)PPPS(0.861)VGGS(0.139)R 71.148 0.042593 249560000 172079 323390 141197 416150 155435 157490 285660 271680 248230 148695 TRUE FALSE 165353.9624 314167.2338 166714.4388 437627.5514 160434.7079 160674.5557 289155.9925 266069.7131 220051.9711 138623.7552 1.192825589 2.266330423 1.202639754 3.156944859 1.157339214 1.159069421 2.085905061 1.919365932 1.587404487 1 17.08081498 VHDFDVK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHDFDVK 7 0 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 0 ; 109.01 0.0071238 1278890000 1503030 1394610 1170800 1258360 1340820 1355760 1378140 1133790 1753230 1624590 FALSE TRUE 1444289.926 1354837.088 1382389.604 1323304.11 1383948.693 1383174.396 1395006.09 1110376.84 1554210.681 1514555.072 0.953606741 0.894544618 0.91273644 0.873724657 0.913765843 0.913254606 0.921066599 0.733137316 1.026183008 1 20.53046261 VHEMEK ddPTM_BT-474_Pertuzumab_2h_R1 4 VHEMEK 6 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 141.98 0.011584 1834600000 3440510 3256520 3089060 3127500 3345120 3149300 3742850 2101140 4315600 4017080 FALSE TRUE 3306051.066 3163647.238 3647321.858 3288910.65 3452718.823 3212981.004 3788656.118 2057750.725 3825711.18 3744999.594 0.882790768 0.844765709 0.973917825 0.878213887 0.921954392 0.857938946 1.011657284 0.549466208 1.021551828 1 21.83653413 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(ph)SPR ddPTM_BT-474_Pertuzumab_2h_R1 2 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGSSPR 40 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.58)S(0.42)PR;VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.565)S(0.435)PR 214.45 3.47E-40 2106400000 386180 430800 362260 387680 416220 429470 433800 278737 483450 429310 TRUE FALSE 371087.6587 418514.0058 427728.4404 407688.2113 429608.0943 438154.1777 439108.9742 272980.9835 428570.7828 400232.4513 0.927180336 1.045677342 1.068700049 1.018628574 1.073396455 1.094749254 1.097134859 0.682056097 1.070804682 1 18.61047862 VHHEPQLSDK ddPTM_BT-474_Pertuzumab_2h_R1 4 VHHEPQLSDK 10 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11;O43852-12;O43852-2;O43852-4;O43852-8;O43852-7 O43852;O43852-2 CALU Calumenin 0 ;;; 152.54 1.03E-05 4254790000 2399610 2634750 2109360 2452710 2343990 2337450 2500780 132768 2941660 2349400 FALSE TRUE 2305830.588 2559609.51 2490568.274 2579294.657 2419386.567 2384714.841 2531385.294 130026.2944 2607735.089 2190273.045 1.052759423 1.168625763 1.137104015 1.177613295 1.104605004 1.088775139 1.1557396 0.059365336 1.190598174 1 21.0626793 VHIPNDDAQFDASHCDSDK ddPTM_BT-474_Pertuzumab_2h_R1 1 VHIPNDDAQFDASHCDSDK 19 0 Q16576;E9PC52;Q16576-2;Q5JP01;C9J7L0 Q16576 RBBP7 Histone-binding protein RBBP7 0 189.48 8.05E-15 180570000 196950 176420 181940 211000 209880 204630 213400 45498 261000 250100 FALSE TRUE 189252.9763 171388.6743 214820.6052 221889.7353 216630.9808 208767.7588 216011.653 44558.4504 231372.3742 233160.5042 0.811685396 0.735067352 0.921342171 0.9516609 0.929106675 0.895382172 0.926450446 0.191106339 0.992330905 1 17.8309639 VHIPNDDAQFDASHCDSDKGEFGGFGSVTGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHIPNDDAQFDASHCDSDKGEFGGFGSVTGK 31 1 Q16576;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 ; 98.84 0.0001805 589160000 371668 352169 312802 324552 346366 386514 375085 68663 469188 381170 FALSE TRUE 357142.8037 342125.4849 369332.2796 341302.1676 357507.177 394329.5779 379675.4024 67245.08506 415927.7452 355353.0164 1.005036646 0.962776364 1.039339087 0.960459464 1.00606203 1.10968406 1.0684457 0.189234598 1.170463528 1 18.43889342 VHNDAQSFDYDHDAFLGAEEAK ddPTM_BT-474_Pertuzumab_2h_R1 6 VHNDAQSFDYDHDAFLGAEEAK 22 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11;O43852-12;O43852-2;O43852-4;O43852-8;O43852-7 O43852;O43852-2 CALU Calumenin 0 ;;;;; 222.51 4.90E-26 7443490000 2409630 2479200 2194970 2435890 2265941 2491690 2541520 367486 3103130 2538780 FALSE TRUE 2315458.996 2408495.643 2591649.906 2561606.575 2338827.05 2542073.679 2572623.882 359897.2857 2750875.692 2366826.169 0.978297023 1.017605634 1.094989543 1.082296033 0.988170184 1.074043253 1.08695092 0.152059028 1.16226351 1 21.17452232 VHSPSGALEECYVTEIDQDKYAVR ddPTM_BT-474_Pertuzumab_2h_R1 4 VHSPSGALEECYVTEIDQDKYAVR 24 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 291.78 4.74E-62 3701840000 1038960 1069780 855350 996120 998010 1119930 1033030 680647 1255060 1191930 FALSE TRUE 998356.2946 1039270.922 1009930.772 1047529.873 1030111.898 1142575.752 1045672.53 666591.4016 1112590.85 1111199.519 0.898449178 0.935269413 0.908865379 0.942701877 0.927026947 1.028236363 0.941030402 0.59988453 1.001252098 1 20.08368645 VHTVEDYQAIVDAEWNILYDKLEK ddPTM_BT-474_Pertuzumab_2h_R1 2 VHTVEDYQAIVDAEWNILYDKLEK 24 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 281.28 1.75E-52 2080120000 2739400 2496700 2226600 2095300 2451600 2709200 2493900 1450410 3396000 2859500 FALSE TRUE 2632341.219 2425496.561 2628996.15 2203438.684 2530457.94 2763981.88 2524421.094 1420458.527 3010500.317 2665823.518 0.987440167 0.909848887 0.986185369 0.826550846 0.949221853 1.036821028 0.94695732 0.532840421 1.12929468 1 21.34614984 VIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_BT-474_Pertuzumab_2h_R1 5 VIISAPSADAPMFVMGVNHEKYDNSLK 27 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 314.7 2.39E-82 7347230000 5470720 5528100 3745090 3672640 5065520 5686000 5021670 5502040 5749460 4039510 FALSE TRUE 5256918.214 5370444.001 4421911.072 3862185.391 5228457.051 5800974.816 5083126.7 5388420.951 5096805.405 3765910.39 1.395922279 1.426067921 1.174194448 1.025564868 1.388364701 1.540391092 1.349773673 1.430841521 1.353405917 1 21.84456724 VILHLKEDQTEYLEER ddPTM_BT-474_Pertuzumab_2h_R1 25 VILHLKEDQTEYLEER 16 1 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;;;;;;;;;;;;;;; 336.91 5.28E-72 15301668600 13318345.2 13990822 9520062.3 9815586.7 11631182.3 15259718.2 10867561.4 11417635.5 13048382.3 10824567.6 FALSE TRUE 12797849.55 13591817.46 11240549.33 10322170.31 12005309.84 15568280.16 11000561.87 11181857.34 11567184.64 10091409.99 1.268192408 1.346870007 1.11387302 1.022867004 1.189656336 1.542725959 1.090091659 1.108056985 1.146240679 1 23.26662443 VIPEYCR ddPTM_BT-474_Pertuzumab_2h_R1 2 VIPEYCR 7 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 119.89 0.01089 733950000 436050 477300 324430 429940 381660 234830 514960 427650 472990 467900 FALSE TRUE 419008.6839 463687.8713 383061.7179 452129.2549 393936.4405 239578.4235 521262.2345 418818.8781 419298.1581 436208.7162 0.96056926 1.062995429 0.87816154 1.036497525 0.90309163 0.549228877 1.194983537 0.960134134 0.961232874 1 18.73465907 VITDENWR ddPTM_BT-474_Pertuzumab_2h_R1 1 VITDENWR 8 0 Q9H3N1;G3V448 Q9H3N1 TMX1 Thioredoxin-related transmembrane protein 1 0 99.755 0.018864 0 112820 170260 116480 197780 110830 111370 152360 175600 150660 123990 FALSE TRUE 108410.8697 165404.3515 137530.5271 207987.4495 114394.9476 113621.9777 154224.6273 171973.7986 133557.7084 115592.0469 0.937874816 1.430931937 1.189792298 1.799323181 0.989643758 0.982956707 1.334214866 1.487764974 1.15542299 1 16.81868261 VKEGMNIVEAMER ddPTM_BT-474_Pertuzumab_2h_R1 23 VKEGMNIVEAMER 13 1 P62937;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 ;;;;;;;;;;;;;;;;;;;;;; 223.7 1.40E-11 1.12394E+11 48049170 50314010 40780410 45364030 45782880 41973210 50080190 52471170 54778530 53972470 FALSE TRUE 46171355.32 48879103.7 48150337.24 47705273.02 47255527.91 42821937.06 50693086.35 51387622 48560300.92 50316866.53 0.917611896 0.971425827 0.956942285 0.948097056 0.939158798 0.851045385 1.007477012 1.021280249 0.965089925 1 25.58453875 VLAGDKNFITAEELR ddPTM_BT-474_Pertuzumab_2h_R1 4 VLAGDKNFITAEELR 15 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 216.99 1.94E-12 7093620000 5884860 5990160 5404680 6140340 5716610 5056530 6567870 6781330 7284930 7316000 FALSE TRUE 5654873.165 5819326.502 6381425.902 6457243.683 5900489.952 5158776.501 6648249.558 6641293.166 6457975.287 6820480.804 0.829101837 0.85321353 0.935626987 0.94674318 0.86511349 0.756365519 0.974747932 0.973728005 0.946850445 1 22.70144201 VLEEMESR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLEEMESR 8 0 Q9NUP9;G3V1D4 Q9NUP9 LIN7C Protein lin-7 homolog C 0 81.296 0.052879 0 203270 208220 132520 202080 183020 211140 220940 190580 206150 207820 FALSE TRUE 195325.9837 202281.7695 156469.3119 212509.373 188907.0045 215409.3955 223643.9298 186644.4564 182748.7163 193744.1663 1.008164465 1.044066375 0.807607862 1.096855596 0.975033252 1.111823905 1.154326007 0.963355233 0.943247581 1 17.56379335 VLELYVSDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLELYVSDR 9 0 K7ENF0 K7ENF0 NARS 0 ; 144.12 0.00023336 494870000 206962 206570 195539 232720 198292 197006 230820 217210 234450 254280 FALSE TRUE 198873.6962 200678.8259 230877.247 244730.7071 204670.2423 200989.5963 233644.8442 212724.5376 207836.2189 237057.3891 0.838926375 0.846541112 0.973929764 1.032369031 0.863378455 0.847852063 0.985604562 0.897354596 0.876733772 1 17.85487684 VLGAHILGPGAGEMVNEAALALEYGASCEDIAR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLGAHILGPGAGEMVNEAALALEYGASCEDIAR 33 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 210.11 1.70E-27 88917000 26290 39720 25638 47167 23695 29920 37476 34519 36867 29036 FALSE TRUE 25262.55773 38587.22449 30271.35691 49601.29452 24457.17119 30525.0029 37934.6425 33806.17059 32682.01272 27069.36586 0.933252662 1.425494217 1.118288366 1.832377411 0.903499968 1.127658589 1.401386449 1.248871908 1.207343123 1 14.72437347 VLGQPHHELDSK ddPTM_BT-474_Pertuzumab_2h_R1 1 VLGQPHHELDSK 12 0 B4DHE8;Q96DH6-2;Q96DH6;J3QKT5;J3KTC1 B4DHE8 MSI2 RNA-binding protein Musashi homolog 2 0 78.964 0.014059 262030000 105780 91187 82256 88634 95985 102160 107960 79335 116140 103190 FALSE TRUE 101646.0007 88586.43604 97121.48897 93208.41136 99072.4447 104225.7452 109281.2468 77696.70453 102956.2741 96200.84939 1.056601904 0.920848793 1.009569974 0.96889385 1.02985 1.083418139 1.135969666 0.80765092 1.07022209 1 16.55376201 VLHEEHVELLMEEFAFLK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLHEEHVELLMEEFAFLK 18 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 148.87 3.83E-08 867110000 753170 676460 734630 879710 811650 773390 802960 82013 923620 823680 FALSE TRUE 723735.2837 657168.0231 867393.9828 925111.9385 837757.4594 789028.4757 812786.8647 80319.40289 818774.5297 767891.4199 0.942496901 0.855808525 1.129578949 1.204743164 1.090984269 1.0275261 1.058465876 0.104597344 1.066263418 1 19.5505428 VLS(ph)PTAAK ddPTM_BT-474_Pertuzumab_2h_R1 3 VLSPTAAK 8 0 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 VLS(0.736)PT(0.264)AAK;VLS(0.5)PT(0.5)AAK;VLS(0.74)PT(0.26)AAK 92.428 0.011316 0 939620 828120 781910 988440 911900 700940 817020 1090340 875060 743680 TRUE FALSE 902898.6116 804502.8284 923218.5305 1039453.507 941232.0917 715113.4871 827018.9352 1067824.098 775726.8574 693309.8912 1.302301645 1.160379851 1.331610211 1.49926248 1.357592187 1.031448557 1.192856103 1.540182985 1.118874644 1 19.40314082 VLS(ph)PTAAKPSPFEGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VLSPTAAKPSPFEGK 15 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 VLS(0.987)PT(0.013)AAKPSPFEGK;VLS(0.954)PT(0.046)AAKPSPFEGK 166.91 8.12E-07 4559380000 3488800 2637870 2093550 2181270 2598080 2294840 2139330 4815900 2104590 2194880 TRUE FALSE 3352453.839 2562640.53 2471901.056 2293845.606 2681649.603 2341243.237 2165511.76 4716449.982 1865685.766 2046218.823 1.638365263 1.252378535 1.208033583 1.121016766 1.310539016 1.144180286 1.058299209 2.304958751 0.911772361 1 20.964529 VLST(ph)STDLEAAVADALKKPVR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLSTSTDLEAAVADALKKPVR 21 2 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.062)T(0.438)S(0.438)T(0.062)DLEAAVADALKKPVR 138.35 8.51E-05 558450000 452110 487030 293060 412230 462810 489720 456400 447110 496710 442960 TRUE FALSE 434441.0414 473140.3813 346022.4611 433505.2397 477696.704 499622.4739 461985.5597 437877.0223 440325.5632 412957.9247 1.052022532 1.145735081 0.837912147 1.049756437 1.156768463 1.209862904 1.118723076 1.060342946 1.06627222 1 18.65563527 VLT(ph)PPHDVDSLPHLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VLTPPHDVDSLPHLR 15 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 VLT(1)PPHDVDSLPHLR;VLT(0.999)PPHDVDS(0.001)LPHLR 89.468 0.011923 350210000 130848 128880 122091 126159 135492 139455 142334 70391 170877 158959 TRUE FALSE 125734.3155 125204.4686 144155.5596 132670.0811 139850.2232 142274.8756 144075.9261 68937.40125 151479.7593 148192.5653 0.84845225 0.844876855 0.972758379 0.895254636 0.943706069 0.960067567 0.972221013 0.465187988 1.022181909 1 17.17711355 VLT(ph)PPQAAGDGILATTANQR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLTPPQAAGDGILATTANQR 20 0 Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3;Q96QT6-4;K7EPF7 Q96QT6 PHF12 PHD finger protein 12 1 VLT(1)PPQAAGDGILATTANQR 124.82 0.00029291 119380000 21943 25649 25315 25180 13881 27972 27196 27267 30171 23008 TRUE FALSE 21085.4433 24917.51563 29889.98363 26479.54282 14327.49497 28537.61301 27528.83278 26703.92692 26746.11457 21449.64767 0.983020497 1.161674822 1.39349532 1.234497798 0.667959455 1.330446702 1.283416549 1.244958767 1.24692559 1 14.38866633 VLVRPHEPPPPPPMHGAGDAKPIPTCISSATGLIENRPQS(ph)PATGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VLVRPHEPPPPPPMHGAGDAKPIPTCISSATGLIENRPQSPATGR 45 3 Q92558 Q92558 WASF1 Wiskott-Aldrich syndrome protein family member 1 1 VLVRPHEPPPPPPMHGAGDAKPIPTCISSATGLIENRPQS(0.969)PAT(0.031)GR 238.97 8.12E-56 549600000 125490 135070 127670 103820 106600 142400 129890 95985 168820 161540 TRUE FALSE 120585.7121 131217.9358 150742.809 109178.1626 110028.8858 145279.4256 131479.6327 94002.87621 149656.2614 150598.7519 0.800708575 0.871308256 1.000956562 0.724960607 0.730609546 0.964678815 0.873045965 0.624194258 0.993741711 1 17.20035029 VMEECKR ddPTM_BT-474_Pertuzumab_2h_R1 2 VMEECKR 7 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ; 88.942 0.029242 883000000 274792 514040 261464 415420 328843 278239 346880 441320 362370 291670 FALSE TRUE 264052.8248 499380.0825 308716.361 436859.876 339420.5337 283865.1832 351125.2212 432206.5878 321235.2768 271914.9311 0.971086155 1.836530567 1.135341703 1.606604956 1.248260007 1.043948495 1.291305409 1.589491927 1.181381528 1 18.05279585 VNGDDHHEEDMDMS(ph)D ddPTM_BT-474_Pertuzumab_2h_R1 7 VNGDDHHEEDMDMSD 15 0 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D 380.66 2.45E-98 6695000000 4309904 4604171 3778684 4522809 4578632 4599306 4545692 1775172 5088735 4452417 TRUE FALSE 4141468.187 4472864.551 4461576.255 4756231.715 4725907.856 4692307.119 4601323.538 1738514.078 4511083.137 4150850.831 0.997739585 1.077577763 1.074858249 1.145845011 1.138539555 1.130444651 1.108525391 0.418833186 1.086785173 1 21.98497566 VNVPVIGGHAGK ddPTM_BT-474_Pertuzumab_2h_R1 2 VNVPVIGGHAGK 12 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ; 125.28 0.00030799 3524900000 4979200 5898300 4050200 7407700 4287400 4982600 6868500 6199100 6243100 5300000 FALSE TRUE 4784607.359 5730086.259 4782161.236 7790012.285 4425308.115 5083351.586 6952558.758 6071086.419 5534409.461 4941026.279 0.968342828 1.159695564 0.967847764 1.576598027 0.895625294 1.028804807 1.407108233 1.228709599 1.120093104 1 22.2363793 VPDHHPC ddPTM_BT-474_Pertuzumab_2h_R1 2 VPDHHPC 7 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 103.71 0.0083144 335440000 246617 294398 231576 291878 251793 218717 271173 53280 310792 302365 FALSE TRUE 236978.935 286002.0573 273426.9346 306941.8586 259892.1505 223139.6076 274491.6963 52179.74938 275512.1951 281885.5492 0.840692031 1.014603473 0.969992734 1.088888236 0.921977559 0.791596477 0.973770018 0.1851097 0.977390277 1 18.10474999 VPS(ph)PGPPTLTSYSVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VPSPGPPTLTSYSVLR 16 0 F8W1U0;F8W130;Q12815 F8W1U0 TROAP Tastin 1 VPS(1)PGPPTLTSYSVLR;VPS(1)PGPPTLTSYSVLR 152.17 6.01E-07 454110000 34706 35440 34278 48467 31004 26432 38298 42718 28682.7 23367 TRUE FALSE 33349.65115 34429.2859 40472.79711 50968.38768 32001.27182 26966.47315 38766.70238 41835.85837 25426.76014 21784.33228 1.530900774 1.580460923 1.857885594 2.33968097 1.469004026 1.237883852 1.779568081 1.92045631 1.167204017 1 14.41100327 VPS(ph)PYVR ddPTM_BT-474_Pertuzumab_2h_R1 6 VPSPYVR 7 0 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR 100.98 0.0098527 4298740000 3465670 3686330 2931570 3564050 3268240 3470390 3261970 3577010 3686360 3859940 TRUE FALSE 3330227.785 3581199.478 3461369.911 3747991.048 3373365.908 3540563.664 3301890.965 3503143.493 3267899.867 3598502.826 0.925448151 0.995191515 0.961891675 1.041541783 0.937435948 0.983899092 0.917573537 0.973500276 0.908127637 1 21.77896536 VQEHEDS(ph)GDS(ph)EVENEAK ddPTM_BT-474_Pertuzumab_2h_R1 2 VQEHEDSGDSEVENEAK 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 VQEHEDS(1)GDS(1)EVENEAK;VQEHEDS(1)GDS(1)EVENEAK 213.05 5.38E-13 1065950000 1726320 1460630 1333200 1240390 1302600 1457410 1281140 1492780 1649700 1618480 TRUE FALSE 1658853.506 1418974.263 1574138.897 1304406.677 1344499.312 1486879.829 1296818.975 1461953.571 1462432.972 1508858.908 1.099409293 0.940428727 1.043264475 0.864498774 0.891070268 0.98543331 0.859470006 0.968913371 0.969231095 1 20.52502648 VQEVQVVGVKDDR ddPTM_BT-474_Pertuzumab_2h_R1 1 VQEVQVVGVKDDR 13 1 E9PF16;Q96CM8-3;Q96CM8;Q96CM8-2;Q96CM8-4 E9PF16 ACSF2 "Acyl-CoA synthetase family member 2, mitochondrial" 0 161.82 3.78E-05 505760000 517090 736180 438920 799760 455060 570420 802830 747290 629190 477070 FALSE TRUE 496881.5511 715184.8672 518242.6077 841035.7094 469697.4182 581954.2832 812655.2737 731858.2004 557766.989 444757.624 1.117196253 1.608032845 1.165224787 1.890997847 1.056075023 1.308475115 1.827186831 1.645521428 1.254092024 1 18.76265981 VQIHDTRPVKPELALVYIEYLLTHPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VQIHDTRPVKPELALVYIEYLLTHPK 26 2 H0Y6U5;Q86XI2;Q86XI2-2 H0Y6U5 NCAPG2 Condensin-2 complex subunit G2 0 135.54 9.86E-06 85957000 298210 325090 259940 284440 319300 326450 325860 208370 369920 333790 FALSE TRUE 286555.6235 315818.7515 306916.9403 299119.9825 329570.5745 333051.0427 329847.9722 204067.0867 327928.2324 311182.106 0.920861508 1.014900103 0.986293667 0.961237734 1.059092307 1.070276974 1.059983739 0.655780274 1.053814555 1 18.24739958 VQQLLHICSEHFDSK ddPTM_BT-474_Pertuzumab_2h_R1 2 VQQLLHICSEHFDSK 15 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 215.48 1.35E-12 2500900000 2648100 2998000 2665200 3074300 2906500 3280700 3049900 735280 3522400 3533000 FALSE TRUE 2544609.324 2912499.975 3146860.927 3232964.991 2999990.212 3347038.002 3087225.589 720096.2111 3122551.919 3293706.763 0.772567052 0.884262075 0.955416239 0.981558233 0.910824924 1.01619186 0.937310395 0.218627906 0.948035798 1 21.65128069 VQTT(ph)PSKPGGDR ddPTM_BT-474_Pertuzumab_2h_R1 2 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.102)T(0.847)PS(0.051)KPGGDR;VQT(0.229)T(0.768)PS(0.003)KPGGDR 145.46 0.00010333 5520900000 5817700 4996400 5220200 4778500 4894100 5095000 5234700 6374500 5463400 5664200 TRUE FALSE 5590337.852 4853907.564 6163606.263 5025118.958 5051523.171 5198024.391 5298763.824 6242864.347 4843217.736 5280558.689 1.058664089 0.919203412 1.167226164 0.951626382 0.95662665 0.984370158 1.003447578 1.182235577 0.917179038 1 22.33225915 VREDKQPEQATTSAQVACLYR ddPTM_BT-474_Pertuzumab_2h_R1 3 VREDKQPEQATTSAQVACLYR 21 2 P18858;P18858-3;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ;; 256 1.10E-36 467170000 267004 276286 200939 220036 253425 267333 254519 267627 285080 262478 FALSE TRUE 256569.1885 268406.5938 237253.1472 231392.0843 261576.6453 272738.6564 257633.8797 262100.4089 252718.9136 244700.1313 1.048504499 1.096879648 0.969566898 0.945614876 1.068968144 1.114583204 1.052855502 1.071108575 1.032769832 1 17.90065535 VRELELELDR ddPTM_BT-474_Pertuzumab_2h_R1 3 VRELELELDR 10 1 O94992 O94992 HEXIM1 Protein HEXIM1 0 ;; 201.46 2.20E-07 527520000 325887 342302 259461 301407 301898 279578 331452 341269 335139 330420 FALSE TRUE 313150.9758 332539.8821 306351.3744 316962.6514 311608.8233 285231.2587 335508.4087 334221.6759 297095.4257 308040.3591 1.016590737 1.079533484 0.994517002 1.028964686 1.011584405 0.925954182 1.089170295 1.084993138 0.964469158 1 18.23275986 VRPSSDLNNSTGQS(ph)PHHK ddPTM_BT-474_Pertuzumab_2h_R1 5 VRPSSDLNNSTGQSPHHK 18 1 J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 VRPSSDLNNSTGQS(1)PHHK;VRPSSDLNNSTGQS(1)PHHK;VRPSSDLNNST(0.001)GQS(0.999)PHHK;VRPSSDLNNSTGQS(1)PHHK;VRPSSDLNNSTGQS(1)PHHK 195.03 2.58E-15 1256169000 659828 677912 613924 623204 603380 683476 680077 145275 758217 717837 TRUE FALSE 634041.1923 658578.6135 724873.7235 655367.6331 622788.2657 697296.353 688399.9858 142275.0205 672147.3849 669217.2606 0.947436998 0.98410285 1.083166508 0.979304737 0.93062194 1.041958111 1.028664421 0.21259915 1.004378435 1 19.35211513 VRVDPDGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VRVDPDGR 8 1 Q10570 Q10570 CPSF1 Cleavage and polyadenylation specificity factor subunit 1 0 58.426 0.095783 297490000 120010 133120 123190 136470 131740 116370 126420 208340 144740 154280 FALSE TRUE 115319.8765 129323.5479 145453.1733 143513.2331 135977.5367 118723.0811 127967.1658 204037.7062 128309.722 143830.4782 0.801776355 0.899138691 1.011281998 0.997794312 0.945401409 0.825437575 0.889708269 1.418598539 0.892089935 1 17.13400989 VS(ph)PPAS(ph)PTLEVELGSAELPLQGAVGPELPPGGGHGR ddPTM_BT-474_Pertuzumab_2h_R1 3 VSPPASPTLEVELGSAELPLQGAVGPELPPGGGHGR 36 0 Q7Z6J0 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 2 VS(1)PPAS(0.974)PT(0.026)LEVELGSAELPLQGAVGPELPPGGGHGR;VS(0.991)PPAS(0.862)PT(0.147)LEVELGSAELPLQGAVGPELPPGGGHGR;VS(1)PPAS(0.988)PT(0.011)LEVELGS(0.001)AELPLQGAVGPELPPGGGHGR 117.65 2.63E-06 210648000 35616 31435.2 26082 36068 30741.1 35633 35492 33077 37433 35979.9 TRUE FALSE 34224.08734 30538.69887 30795.59759 37929.4738 31729.9154 36353.52367 35926.36171 32393.94839 33183.76277 33542.94933 1.020306444 0.91043571 0.918094509 1.130773369 0.945948882 1.083790317 1.07105554 0.965745381 0.989291742 1 15.03372193 VSQNPILTSLLQITGNGGSTIGS(ph)SPTPPHHTPPPVSSMAGNTK ddPTM_BT-474_Pertuzumab_2h_R1 1 VSQNPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTK 43 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 VSQNPILTSLLQIT(0.002)GNGGS(0.074)T(0.074)IGS(0.343)S(0.343)PT(0.09)PPHHT(0.072)PPPVS(0.001)SMAGNTK 89.462 0.00025712 116880000 31871 47882 35649 39597 27063 40547 45341 18109 52301 44351 TRUE FALSE 30625.44608 46516.45224 42091.56731 41640.60592 27933.50597 41366.88812 45895.89672 17735.04282 46364.00974 41347.06727 0.7406921 1.125024223 1.018006115 1.007099383 0.67558615 1.000479378 1.11001577 0.428931095 1.121337324 1 15.33549738 VSS(ph)SGLTDSLFILK ddPTM_BT-474_Pertuzumab_2h_R1 2 VSSSGLTDSLFILK 14 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 VS(0.004)S(0.996)SGLTDSLFILK;VS(0.017)S(0.937)S(0.046)GLTDSLFILK 379.4 1.13E-97 866880000 1099310 1137010 945970 1000250 1142110 944500 1147370 1220060 1215230 1198180 TRUE FALSE 1056347.75 1104583.588 1116927.822 1051873.022 1178847.005 963598.4371 1161411.857 1194865.335 1077282.185 1117026.201 0.945678578 0.988860948 0.999911927 0.941672649 1.055344095 0.862646226 1.039735555 1.06968425 0.964419799 1 20.0912316 VTAIHIDPATHR ddPTM_BT-474_Pertuzumab_2h_R1 9 VTAIHIDPATHR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;; 200.82 9.00E-08 53481178400 24711588.7 28782064.6 24320310.9 31063022.2 29012782.3 30722945.1 32404968 12611154.6 31837906 33109043.8 FALSE TRUE 23745832.49 27961228.3 28715532.08 32666188.5 29946004.79 31344184.1 32801549.69 12350729.85 28223800.39 30866538.77 0.769306616 0.905875081 0.930312669 1.058304228 0.970176961 1.015474535 1.062689598 0.400133295 0.914381771 1 24.87954038 VTHAVVTVPAYFNDAQR ddPTM_BT-474_Pertuzumab_2h_R1 4 VTHAVVTVPAYFNDAQR 17 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 173.37 1.49E-09 8949550000 4377147 5218499 3950869 5397680 4136431 3780645 4848119 3936673 4917048 5187520 FALSE TRUE 4206083.256 5069672.518 4664878.915 5676254.912 4269483.06 3857092.232 4907451.731 3855379.327 4358885.325 4836164.65 0.869714652 1.048283689 0.964582319 1.173710021 0.882824173 0.797551885 1.014740416 0.797197698 0.901310365 1 22.20543193 VTLLHHVLEEAEK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTLLHHVLEEAEK 13 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 147.71 2.48E-05 465850000 341270 325870 283700 262350 327840 255650 352590 55921 393460 336560 FALSE TRUE 327932.7911 316576.5067 334970.9009 275889.9149 338385.2713 260819.4182 356905.1019 54766.21181 348796.0703 313764.4914 1.045155842 1.008962184 1.067587028 0.879289794 1.078468981 0.831258556 1.137493603 0.174545601 1.111649278 1 18.25932257 VTPLGYVLPSHVTEEMLWECK ddPTM_BT-474_Pertuzumab_2h_R1 1 VTPLGYVLPSHVTEEMLWECK 21 0 Q2TAL8 Q2TAL8 QRICH1 Glutamine-rich protein 1 0 191.59 1.39E-17 67861000 139550 150500 102180 114200 140920 150860 124720 136820 155610 145610 FALSE TRUE 134096.2317 146207.8874 120646.199 120093.8757 145452.8198 153910.4926 126246.3607 133994.6192 137945.8052 135747.705 0.987834245 1.077056053 0.888753139 0.884684391 1.071493767 1.133798119 0.93000733 0.987085706 1.01619254 1 17.05056828 VTYMEEER ddPTM_BT-474_Pertuzumab_2h_R1 2 VTYMEEER 8 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 134.3 0.0020535 1727160000 1265560 1464060 1196580 1428760 1373520 1034380 1324490 1178170 1496950 1482990 FALSE TRUE 1216100.516 1422306.442 1412828.624 1502498.475 1417700.518 1055295.872 1340699.505 1153840.378 1327022.512 1382545.766 0.879609591 1.028759031 1.021903693 1.086762197 1.02542755 0.763299052 0.969732458 0.834576624 0.959839843 1 20.39889581 VVEAVNSDSDS(ph)EFGIPK ddPTM_BT-474_Pertuzumab_2h_R1 1 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VVEAVNS(0.036)DS(0.348)DS(0.616)EFGIPK 257.2 4.22E-27 135250000 84537 80844 52941 81340 62218 65680 76981 89853 72759 71808 TRUE FALSE 81233.20058 78538.40827 62508.61637 85537.96715 64219.29847 67008.0946 77923.11651 87997.50415 64499.70335 66944.3802 1.213443165 1.173188967 0.933739564 1.277746794 0.959293346 1.000951751 1.163997878 1.314486801 0.963481971 1 16.03067533 VVEVLAGHGHLYSR ddPTM_BT-474_Pertuzumab_2h_R1 4 VVEVLAGHGHLYSR 14 0 P49327 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 198.23 1.29E-08 9253440000 2992019 3780865 3240341 4206726 3952690 3909743 4099842 998639 4256853 4410914 FALSE TRUE 2875087.59 3673038.432 3825942.7 4423835.633 4079831.864 3988800.682 4150017.093 978016.7557 3773632.894 4112158.866 0.699167441 0.893214137 0.93039759 1.075793951 0.992138679 0.970001601 1.009206412 0.237835353 0.917676825 1 21.97146457 VVPGYGHAVLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VVPGYGHAVLR 11 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 203.29 3.71E-08 2004380000 860480 1368900 845430 1662500 787600 836410 1582450 1159990 911040 860350 FALSE TRUE 826851.4903 1329860.312 998218.0075 1748301.824 812933.8693 853322.7833 1601816.496 1136035.801 807622.5586 802077.7282 1.030886984 1.658019249 1.244540239 2.179716208 1.013535024 1.063890385 1.997083874 1.416366221 1.006913084 1 19.61338253 VWDEANLR ddPTM_BT-474_Pertuzumab_2h_R1 2 VWDEANLR 8 0 Q96GA7;F8VYZ3 Q96GA7 SDSL Serine dehydratase-like 0 ; 178.87 0.00057544 419410000 577970 687090 552530 643190 655950 511110 677410 658330 671420 697480 FALSE TRUE 555382.2934 667494.8659 652384.462 676385.113 677049.2275 521444.9944 685700.3462 644735.2554 595203.2164 650239.0583 0.854120167 1.026537636 1.003299407 1.040209911 1.04123125 0.801928133 1.05453577 0.991535724 0.915360603 1 19.31061069 VYFQSPPGAAGEGPGGADDEGPVRR ddPTM_BT-474_Pertuzumab_2h_R1 4 VYFQSPPGAAGEGPGGADDEGPVRR 25 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 ;;; 270 2.41E-46 8539950000 1546670 1909050 1379250 1689870 1750630 1961550 1540750 1679180 1590480 1699830 FALSE TRUE 1486224.426 1854605.763 1628511.156 1777084.393 1806940.604 2001213.885 1559606.159 1644504.346 1409935.378 1584699 0.937859131 1.170320523 1.027646989 1.121401852 1.140242156 1.26283533 0.984165548 1.037739246 0.889718097 1 20.59577741 VYRDDIGR ddPTM_BT-474_Pertuzumab_2h_R1 1 VYRDDIGR 8 1 A0A087WY71;Q96CW1-2;Q96CW1;C9JJ47;C9JJD3;C9JGT8 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 119.86 0.0014704 498620000 514880 529030 495010 551300 534710 525280 565520 402760 648030 608820 FALSE TRUE 494757.9204 513942.5824 584469.3184 579752.6591 551909.4328 535901.5215 572441.0029 394442.8653 574468.3512 567584.0791 0.871690977 0.905491541 1.029749318 1.021439255 0.972383569 0.944179975 1.008557188 0.694950545 1.012129079 1 19.1144746 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_BT-474_Pertuzumab_2h_R1 4 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR 48 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 377.61 1.11E-182 11288876000 825188 1214529 958366 1407522 1185811 1351343 1283233 89603 1325143 1262185 FALSE TRUE 792938.7407 1179891.822 1131564.055 1480164.379 1223953.688 1378668.081 1298937.589 87752.66674 1174718.322 1176696.086 0.673868767 1.002715855 0.961645125 1.257898617 1.040161264 1.171643297 1.103885366 0.074575473 0.998319223 1 20.16631032 WDLPDSDWDNDSSSAR ddPTM_BT-474_Pertuzumab_2h_R1 2 WDLPDSDWDNDSSSAR 16 0 O15020;O15020-2;A4QPE4;E9PJZ2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ; 417.4 3.35E-140 221250000 212651 230260 179616 265990 217673 222457 233626 250320 240235 225462 FALSE TRUE 204340.3638 223693.2102 212076.6067 279717.7758 224674.6497 226955.233 236485.1849 245150.8045 212964.5299 210191.2579 0.972163951 1.064236508 1.008969682 1.3307774 1.068905776 1.079755815 1.125095245 1.166322553 1.013194041 1 17.68134314 WDNIQELLGHPVEKPVVLHR ddPTM_BT-474_Pertuzumab_2h_R1 1 WDNIQELLGHPVEKPVVLHR 20 1 Q9BSU1 Q9BSU1 C16orf70 UPF0183 protein C16orf70 0 97.058 0.00064241 77201000 147700 150750 116970 150680 149420 143090 154410 116010 168290 157300 FALSE TRUE 141927.7207 146450.7576 138109.081 158456.6129 154226.23 145983.3778 156299.7158 113614.353 149186.4247 146645.9309 0.967825836 0.998669085 0.941785975 1.080538764 1.051691166 0.995481954 1.065830568 0.77475285 1.017323998 1 17.16197751 WENFIHSENR ddPTM_BT-474_Pertuzumab_2h_R1 2 WENFIHSENR 10 0 P19784;H3BSA1;H3BV19 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ; 166.14 5.64E-06 373960000 421750 421090 381830 477540 423280 329620 447710 462890 485550 496880 FALSE TRUE 405267.5437 409080.9255 450835.1748 502185.8966 436895.1856 336285.1422 453189.2089 453331.1597 430432.3996 463225.875 0.874881058 0.883113288 0.973251278 1.084105884 0.943157991 0.72596364 0.978333106 0.978639545 0.929206296 1 18.82135632 WEYENELSK ddPTM_BT-474_Pertuzumab_2h_R1 2 WEYENELSK 9 0 P15924;P15924-3 P15924 DSP Desmoplakin 0 ; 147.95 0.00021213 284020000 279060 285590 267360 279480 271940 279320 281360 338370 325770 291440 FALSE TRUE 268154.0267 277445.2528 315677.8994 293903.9963 280687.1971 284968.0418 284803.3678 331382.5413 288789.9553 271700.5092 0.986947089 1.021143662 1.1618598 1.081720447 1.033075712 1.04883146 1.048225374 1.219661097 1.062898101 1 18.05165774 WFDFPFTR ddPTM_BT-474_Pertuzumab_2h_R1 2 WFDFPFTR 8 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ; 145.63 0.0013173 208443000 381460 435660 376120 467000 441550 403450 454220 436700 474610 550670 FALSE TRUE 366552.1215 423235.4034 444093.2507 491101.926 455752.8568 411608.0354 459778.8802 427681.9924 420734.2625 513372.6304 0.714007915 0.82442144 0.8650505 0.956618832 0.88776228 0.801772457 0.895604582 0.833082964 0.819549461 1 18.96964686 WGEEKR ddPTM_BT-474_Pertuzumab_2h_R1 2 WGEEKR 6 1 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 ; 118.06 0.035584 545600000 733850 718510 539900 574200 686850 750390 656790 717410 831010 708840 FALSE TRUE 705170.3307 698018.7983 637471.94 603834.5308 708943.154 765563.3999 664827.9925 702595.2328 736677.2287 660829.6354 1.067098527 1.056276476 0.964653983 0.913752196 1.07280775 1.158488298 1.006050511 1.063201762 1.114776319 1 19.33391886 WLDESDAEMELR ddPTM_BT-474_Pertuzumab_2h_R1 1 WLDESDAEMELR 12 0 H3BS72;Q9P035;H3BPZ1 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 0 122.26 0.00047464 0 20421 32669 15642 30776 19536 21160 21074 26941 27516 20203 FALSE TRUE 19622.92474 31737.31211 18468.85735 32364.35305 20164.39318 21587.8697 21331.90992 26384.65894 24392.49904 18834.63282 1.041853321 1.685050748 0.980579634 1.71834266 1.070601874 1.146179483 1.132589636 1.400858684 1.29508758 1 14.20110029 WLDGIR ddPTM_BT-474_Pertuzumab_2h_R1 2 WLDGIR 6 0 B7Z2R2;P14927;P14927-2 B7Z2R2 UQCRB Cytochrome b-c1 complex subunit 7 0 ; 97.596 0.095131 113698000 235560 471130 257040 586480 195410 104150 599480 401960 306850 245120 FALSE TRUE 226354.0548 457693.8337 303492.8458 616748.3031 201695.5401 106255.9844 606816.6156 393659.3855 272017.6744 228517.8041 0.990531375 2.002880413 1.328092781 2.698907009 0.882625058 0.464979019 2.65544568 1.722663961 1.190356592 1 17.80194705 WSAEASGKPSPSDPGSGTATMMNS(ph)SSR ddPTM_BT-474_Pertuzumab_2h_R1 1 WSAEASGKPSPSDPGSGTATMMNSSSR 27 1 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 WSAEASGKPSPSDPGSGTAT(0.001)MMNS(0.333)S(0.333)S(0.333)R 130.38 2.90E-05 787700000 828760 1170200 794180 1106300 837810 853730 916980 1327800 1078200 855600 TRUE FALSE 796371.143 1136827.042 937705.9924 1163396.276 864758.9195 870993.0055 928202.2755 1300380.466 955807.2562 797649.4499 0.998397408 1.42522137 1.175586584 1.458530782 1.084134039 1.09194961 1.163671931 1.630265609 1.198279841 1 19.60539533 WSAEASGKPSPSDPGSGTATMMNSS(ph)SR ddPTM_BT-474_Pertuzumab_2h_R1 1 WSAEASGKPSPSDPGSGTATMMNSSSR 27 1 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 WSAEASGKPSPSDPGSGTATMMNS(0.1)S(0.529)S(0.371)R 187.09 6.13E-18 587120000 471660 712570 455430 741940 533870 542370 574010 809740 647720 493000 TRUE FALSE 453227.0058 692248.2013 537736.332 780231.6123 551042.4134 553337.093 581034.9061 793018.586 574193.5411 459608.6709 0.986115003 1.506168715 1.169987352 1.697599853 1.198938245 1.203930927 1.264194831 1.72542129 1.249309635 1 18.81004649 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK ddPTM_BT-474_Pertuzumab_2h_R1 2 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK 32 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 340 1.17E-117 4703800000 2677100 2775700 2440800 2852000 2520300 2271200 2884900 381730 3474400 3276300 FALSE TRUE 2572475.972 2696539.754 2881906.855 2999192.062 2601367.738 2317125.22 2920206.269 373847.1421 3080000.678 3054393.283 0.842221592 0.882839734 0.943528416 0.981927271 0.851680677 0.758620454 0.956067539 0.122396531 1.008383791 1 21.5424544 WVDWTVSEPR ddPTM_BT-474_Pertuzumab_2h_R1 3 WVDWTVSEPR 10 0 X6RLT1;H0UI80;Q8IXH7-4;Q8IXH7 X6RLT1 NELFCD;TH1L Negative elongation factor C/D 0 ;; 133.13 0.00047738 171765000 132203 144857 125272 138858 143110 114021 154629 133483 141692 143986 FALSE TRUE 127036.3606 140725.8202 147911.4371 146024.478 147713.2631 116326.5827 156521.396 130726.5294 125607.7182 134233.7 0.946382024 1.04836431 1.101894957 1.087837689 1.100418622 0.866597455 1.166036517 0.973872652 0.935739075 1 17.03438739 WVNDPHR ddPTM_BT-474_Pertuzumab_2h_R1 4 WVNDPHR 7 0 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ;;; 109.86 0.0069328 1404290000 1372730 1459080 1420520 1546750 1476200 859300 1665420 1368070 1505030 1698630 FALSE TRUE 1319082.194 1417468.467 1677239.563 1626577.953 1523683.314 876675.6348 1685801.908 1339818.876 1334185.304 1583580.277 0.832974629 0.895103638 1.059144009 1.027152192 0.962176238 0.553603532 1.064550962 0.846069439 0.842511948 1 20.59475857 WVPFDGDDIQLEFVR ddPTM_BT-474_Pertuzumab_2h_R1 3 WVPFDGDDIQLEFVR 15 0 A0A0C4DGS1;P39656-2;P39656-3;P39656 A0A0C4DGS1 DDOST Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit 0 ;; 196.57 2.06E-08 169750000 152750 195202 120186 199309 141692 130148 175251 182497 177012 123702 FALSE TRUE 146780.3611 189635.0301 141906.2837 209595.3614 146249.6519 132779.6817 177395.7742 178728.3732 156918.3399 115323.5534 1.272770018 1.644373804 1.230505648 1.817454937 1.268168103 1.15136655 1.538244088 1.549799395 1.360679023 1 16.81532767 Y(ph)MEDSTYYK ddPTM_BT-474_Pertuzumab_2h_R1 2 YMEDSTYYK 9 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-4;Q05397-3 E7ESA6 PTK2 Focal adhesion kinase 1 1 Y(1)MEDSTYYK;Y(0.999)MEDS(0.001)TYYK 205.36 0.00015537 458940000 507820 470970 395500 398820 425930 373070 495960 469360 519320 509450 TRUE FALSE 487973.833 457538.3967 466975.6478 419403.148 439630.4253 380613.731 502029.7068 459667.552 460368.9708 474944.4977 1.027433385 0.963351295 0.983221513 0.883057178 0.925645896 0.801385705 1.057028156 0.96783425 0.969311094 1 18.8573994 Y(ph)SPSQNS(ph)PIHHIPSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSPSQNSPIHHIPSR 15 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 Y(0.599)S(0.37)PS(0.031)QNS(1)PIHHIPSR;Y(0.93)S(0.067)PS(0.004)QNS(1)PIHHIPSR 166.29 2.48E-05 16778100000 914900 907860 925210 1206330 1009900 974070 1175500 434710 1218110 1261730 TRUE FALSE 879144.6965 881968.7217 1092416.028 1268588.836 1042384.351 993766.3628 1189886.121 425733.0866 1079835.26 1176271.903 0.747399214 0.749800041 0.928710467 1.078482647 0.886176358 0.844844088 1.011574039 0.361934248 0.918015007 1 20.16579016 YAELLEEHR ddPTM_BT-474_Pertuzumab_2h_R1 4 YAELLEEHR 9 0 P40222 P40222 TXLNA Alpha-taxilin 0 ;;; 149.72 8.70E-05 715490000 827300 909760 741190 876800 881440 676570 905510 828220 863460 1008940 FALSE TRUE 794968.2014 883814.5355 875139.5207 922051.7531 909792.3181 690250.709 916591.9022 811116.9676 765443.6407 940603.5951 0.845168151 0.939624875 0.930402058 0.980276663 0.96724308 0.733838051 0.974472038 0.862336665 0.8137792 1 19.84322732 YCDPDSYHR ddPTM_BT-474_Pertuzumab_2h_R1 4 YCDPDSYHR 9 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;; 188.66 3.91E-05 6181030000 4819150 5318490 4692480 6432920 5203670 4793960 5596000 5221080 5856510 6523860 FALSE TRUE 4630812.29 5166811.873 5540515.52 6764923.772 5371050.771 4890897.156 5664485.522 5113262.873 5191703.537 6081993.151 0.761397156 0.849526092 0.910970365 1.112287305 0.883107007 0.804160254 0.931353486 0.840721577 0.853618774 1 22.53611276 YDLSGRPLNIKEDPDGENAR ddPTM_BT-474_Pertuzumab_2h_R1 3 YDLSGRPLNIKEDPDGENAR 20 2 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 ;; 87.326 0.0013381 1061650000 770818 789176 588420 625822 668067 780154 715248 765211 805830 761052 FALSE TRUE 740693.5804 766669.4732 694760.5833 658120.7484 689555.9818 795929.2484 724001.419 749409.1254 714355.5567 709505.2702 1.043957827 1.080569103 0.979218355 0.92757697 0.971882819 1.12180879 1.020431348 1.056241802 1.006836153 1 19.43645388 YEAVS(ph)PERLELER ddPTM_BT-474_Pertuzumab_2h_R1 1 YEAVSPERLELER 13 1 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 YEAVS(1)PERLELER 138.05 3.25E-05 97624000 128670 133990 117840 108940 136990 158370 113290 132620 141410 140120 TRUE FALSE 123641.4341 130168.7364 139136.3093 114562.4065 141396.4078 161572.3499 114676.4769 129881.3507 125357.7296 130629.5476 0.946504343 0.996472382 1.065121268 0.877002245 1.082422854 1.236874451 0.877875481 0.994272376 0.95964299 1 16.99512174 YEDFSNLGTTHLLR ddPTM_BT-474_Pertuzumab_2h_R1 2 YEDFSNLGTTHLLR 14 0 H3BP04;H3BSJ9;H3BRG4;P22695;A0A087WVZ4;H3BUE4;H3BUI9 H3BP04 UQCRC2 "Cytochrome b-c1 complex subunit 2, mitochondrial" 0 ; 155.56 5.81E-06 264240000 225424 305360 217941 413450 240521 166346 386410 236980 312130 268760 FALSE TRUE 216614.1809 296651.4318 257327.7868 434788.204 248257.5764 169709.6301 391139.0012 232086.2802 276698.311 250556.6458 0.864531771 1.18396952 1.027024392 1.735289051 0.990824153 0.677330388 1.56108013 0.926282675 1.104334351 1 17.93477728 YEDRVPMYEEQWSYYDDKQPYPSRPPFDNQHS(ph)QDLDSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YEDRVPMYEEQWSYYDDKQPYPSRPPFDNQHSQDLDSR 38 3 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 YEDRVPMYEEQWSYYDDKQPYPSRPPFDNQHS(1)QDLDSR 252.56 2.59E-62 598080000 256420 224510 148900 180130 270380 190750 204820 247750 275950 232000 TRUE FALSE 246398.8229 218107.1946 175809.5423 189426.5309 279077.0183 194607.0957 207326.6484 242633.8759 244625.3129 216286.4334 1.139224588 1.008418287 0.812855155 0.875813281 1.290312175 0.899765615 0.958574448 1.121817361 1.131024767 1 17.72258365 YFGGTEDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YFGGTEDR 8 0 Q16658 Q16658 FSCN1 Fascin 0 ; 97.602 0.01888 276970000 870720 990210 708690 824250 829300 986920 828010 878050 1030940 1048720 FALSE TRUE 836691.2998 961970.1803 836766.0477 866789.6413 855975.1877 1006876.199 838143.4341 859917.9607 913912.0133 977689.2603 0.855784485 0.983922213 0.855860938 0.886569666 0.875508428 1.02985298 0.857269756 0.879541175 0.934767365 1 19.89901648 YGDAFIR ddPTM_BT-474_Pertuzumab_2h_R1 4 YGDAFIR 7 0 P62312 P62312 LSM6 U6 snRNA-associated Sm-like protein LSm6 0 ;;; 143.02 0.0056997 1772840000 2148180 2389150 1888470 2315620 2209240 1869970 2296420 2341290 2379680 2479530 FALSE TRUE 2064226.751 2321013.781 2229758.538 2435129.426 2280302.211 1907782.075 2324524.275 2292941.543 2109548.703 2311589.225 0.892990298 1.00407709 0.964599815 1.053443838 0.98646515 0.825311891 1.005595739 0.991932961 0.912596702 1 21.14045362 YGPIADVSIVYDQQSR ddPTM_BT-474_Pertuzumab_2h_R1 2 YGPIADVSIVYDQQSR 16 0 P62995;P62995-3 P62995 TRA2B Transformer-2 protein homolog beta 0 ; 227.57 1.14E-14 76813000 65172 71004 59257 66589 65105 71425 65835 69199 79363 79763 FALSE TRUE 62625.00619 68979.03544 69966.05806 70025.66627 67199.16145 72869.26244 66640.70842 67770.01647 70354.04496 74360.58096 0.842180163 0.927629055 0.940902521 0.941704131 0.903693336 0.97994477 0.896183268 0.911370186 0.946120163 1 16.18225042 YGQFSGLNPGGRPIT(ph)PPR ddPTM_BT-474_Pertuzumab_2h_R1 7 YGQFSGLNPGGRPITPPR 18 1 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 1 YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR 153.65 5.13E-08 12040800000 5604090 4521570 3690260 4821880 4092800 4242170 4407170 6839220 4678880 5163310 TRUE FALSE 5385075.967 4392619.251 4357172.071 5070737.805 4224448.629 4327949.584 4461106.265 6697987.717 4147753.158 4813594.415 1.118722415 0.91254453 0.905180557 1.053420244 0.87760793 0.899109732 0.926772362 1.391473219 0.861674832 1 22.19868316 YGSIIDRDDRDER ddPTM_BT-474_Pertuzumab_2h_R1 2 YGSIIDRDDRDER 13 2 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3;F8WE23 P52756 RBM5 RNA-binding protein 5 0 ; 103.85 0.00088743 857530000 544240 592200 418560 528810 573810 606480 494420 556400 595410 551130 FALSE TRUE 522970.4991 575311.0358 494203.1028 556101.9475 592267.1198 618743.4411 500470.8599 544910.1456 527821.553 513801.4742 1.017845462 1.119714646 0.96185614 1.082328439 1.152715883 1.204246138 0.974054932 1.060546092 1.027286957 1 18.9708515 YHPIDIETSVSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YHPIDIETSVSR 12 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 0 110.31 0.0015041 165310000 81395 95098 71588 76303 83948 82665 92729 80777 102710 96687 FALSE TRUE 78213.99341 92385.89815 84525.54407 80241.00697 86648.26366 84336.54294 93863.84524 79108.92672 91050.7914 90138.30337 0.867710956 1.024934958 0.937731696 0.890198772 0.96128128 0.935634905 1.041331396 0.877639403 1.010123199 1 16.45985267 YHVLVNLGK ddPTM_BT-474_Pertuzumab_2h_R1 2 YHVLVNLGK 9 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 152.63 8.00E-05 1418210000 2395220 2691500 2148480 2418220 2414920 2292980 2816740 1983940 3176600 3050500 FALSE TRUE 2301612.154 2614741.055 2536758.129 2543024.624 2492598.095 2339345.627 2851212.107 1942970.946 2816005.685 2843886.918 0.809319154 0.919425115 0.892003867 0.894207364 0.876475812 0.822587428 1.002575767 0.683209636 0.990196083 1 21.43943267 YIEIFK ddPTM_BT-474_Pertuzumab_2h_R1 1 YIEIFK 6 0 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 100.82 0.086601 912120000 1209300 1310600 1082200 1123200 1090600 1238200 1011500 1285000 1366700 1378600 FALSE TRUE 1162039.219 1273222.971 1277777.613 1181168.487 1125680.139 1263237.252 1023879.04 1258464.301 1211557.946 1285226.194 0.904151522 0.990660615 0.994204459 0.919035491 0.875861498 0.982890995 0.796652795 0.979177289 0.942680714 1 20.29359086 YIHSANVLHR ddPTM_BT-474_Pertuzumab_2h_R1 2 YIHSANVLHR 10 0 P28482;P28482-2;K7EN18;P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49;H0YDH9;K7ELV1;P31152;Q16659 P28482;P27361;K7ELV1;Q16659 MAPK1;MAPK4;MAPK3;MAPK6 Mitogen-activated protein kinase 1;Mitogen-activated protein kinase 3;Mitogen-activated protein kinase;Mitogen-activated protein kinase 4;Mitogen-activated protein kinase 6 0 ; 127.76 0.00020091 807350000 536770 554190 615530 644340 632790 512060 642500 312617 644650 705850 FALSE TRUE 515792.435 538385.0438 726769.9634 677594.4646 653144.265 522414.204 650363.1072 306161.3497 571472.0346 658042.1508 0.783828869 0.818161942 1.104442873 1.029712859 0.992556881 0.793891703 0.988330469 0.465261001 0.868442901 1 19.32782047 YITDWQNVFR ddPTM_BT-474_Pertuzumab_2h_R1 2 YITDWQNVFR 10 0 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 222.42 1.14E-08 9504900000 2954400 3299700 2671300 3561100 3234200 2621800 3362700 3122600 3283900 3499100 FALSE TRUE 2838938.782 3205595.787 3154063.333 3744888.798 3338230.98 2674814.592 3403853.728 3058117.219 2911125.439 3262102.84 0.87027875 0.982677722 0.96688041 1.147998387 1.023337137 0.81996636 1.043453838 0.937468059 0.892407622 1 21.63737083 YLAEKYEWDVAEAR ddPTM_BT-474_Pertuzumab_2h_R1 6 YLAEKYEWDVAEAR 14 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 201.3 1.65E-08 3954060000 4813630 5075420 3146810 3488700 4156250 5366470 4053550 4299840 4725430 4334590 FALSE TRUE 4625508.018 4930673.991 3715508.567 3668752.225 4289939.556 5474983.7 4103158.557 4211046.801 4189018.997 4041004.358 1.144643165 1.220160523 0.919451759 0.907881284 1.061602309 1.354857163 1.015380879 1.042079253 1.036628181 1 21.94628248 YLEMMFT(ph)PT(ph)GVVMGARISEYLLEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YLEMMFTPTGVVMGARISEYLLEK 24 1 F5H2J1;Q8WXR4-6;Q8WXR4-3;Q8WXR4-5;Q8WXR4-2;Q8WXR4-4;Q8WXR4;Q8WXR4-7 F5H2J1 MYO3B Myosin-IIIb 2 Y(0.571)LEMMFT(0.592)PT(0.589)GVVMGARIS(0.127)EY(0.122)LLEK 43.497 0.058607 18853000 16231 15353 11481 11266 15504 14308 14341 2510.2 16110 13462 TRUE FALSE 15596.67458 14915.14747 13555.87209 11847.43961 16002.70024 14597.31756 14516.50945 2458.363493 14281.26034 12550.20675 1.242742441 1.188438388 1.080131377 0.944003541 1.275094551 1.163113712 1.156674925 0.19588231 1.137930285 1 13.61542351 YLMDEGAHLHIYDPK ddPTM_BT-474_Pertuzumab_2h_R1 4 YLMDEGAHLHIYDPK 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;; 155.98 1.28E-06 757157000 1918310 1865780 1644750 1722760 1795510 1779620 1991330 37322.9 2303370 1440860 FALSE TRUE 1843340.324 1812569.781 1941992.912 1811671.85 1853264.21 1815605.136 2015700.492 36552.16907 2041901.094 1343269.269 1.372279086 1.349371882 1.445721239 1.348703415 1.379666946 1.351631559 1.500593023 0.027211349 1.520098123 1 20.3573171 YMEEMADTADAIEMATLDKEMAEER ddPTM_BT-474_Pertuzumab_2h_R1 2 YMEEMADTADAIEMATLDKEMAEER 25 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 153.94 8.33E-08 130023000 61566 69001 46629 54544 65577 75856 56911 60557 64132 61800 FALSE TRUE 59159.93266 67033.15904 55055.89756 57359.02238 67686.34376 77389.86029 57607.49384 59306.47679 56852.00422 57614.23095 1.026828471 1.163482666 0.95559546 0.99557039 1.174819878 1.343242095 0.999883065 1.029372011 0.986770166 1 15.81413759 YNEDLELEDAIHTAILTLK ddPTM_BT-474_Pertuzumab_2h_R1 1 YNEDLELEDAIHTAILTLK 19 0 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 104.06 0.00036061 1911300000 788150 744350 849750 859150 969410 883420 1111100 454250 1164200 1086700 FALSE TRUE 757348.2267 723121.8668 1003318.728 903490.8345 1000591.953 901283.3577 1124697.974 444869.5788 1032044.897 1013096.841 0.747557584 0.713773686 0.990348293 0.891810928 0.987656769 0.889631989 1.110158406 0.439118513 1.018703104 1 19.95034066 YNGLIHR ddPTM_BT-474_Pertuzumab_2h_R1 3 YNGLIHR 7 0 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ;; 135.35 0.0030858 1729740000 2033480 2227400 1924830 2022760 2100210 1665640 2194910 2060500 2193490 2366530 FALSE TRUE 1954009.353 2163876.733 2272689.599 2127154.886 2167765.162 1699320.382 2221771.965 2017949.955 1944494.211 2206242.815 0.885672846 0.980797181 1.03011762 0.964152663 0.982559647 0.77023271 1.007038731 0.914654516 0.88136002 1 21.07316015 YPSSISS(ph)SPQK ddPTM_BT-474_Pertuzumab_2h_R1 1 YPSSISSSPQK 11 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSIS(0.003)S(0.499)S(0.499)PQK 182.55 6.02E-06 1240100000 2405900 1943600 2548800 2207900 2058900 1160600 2980500 2749600 2833300 3343300 TRUE FALSE 2311874.768 1888170.431 3009424.858 2321849.984 2125126.388 1184068.127 3016976.251 2692819.799 2511675.662 3116855.313 0.741733105 0.605793417 0.965532421 0.744933515 0.681817465 0.379891913 0.967955182 0.863954059 0.805836463 1 21.57165975 YPSSISSS(ph)PQK ddPTM_BT-474_Pertuzumab_2h_R1 3 YPSSISSSPQK 11 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSIS(0.008)S(0.042)S(0.949)PQK;YPSSISS(0.077)S(0.922)PQK;YPSSISS(0.068)S(0.932)PQK 237.27 1.48E-15 4270900000 2281890 2160270 2559180 2177760 2102900 1115960 2931350 2658360 2795890 3340870 TRUE FALSE 2192711.216 2098661.215 3021680.755 2290154.455 2170541.688 1138525.476 2967224.738 2603463.937 2478512.289 3114589.899 0.704012819 0.673816227 0.970169702 0.735298877 0.696894859 0.36554587 0.952685533 0.835893014 0.795774843 1 21.57061078 YS(ph)PSQNS(ph)PIHHIPSR ddPTM_BT-474_Pertuzumab_2h_R1 7 YSPSQNSPIHHIPSR 15 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 Y(0.051)S(0.762)PS(0.187)QNS(1)PIHHIPSR;Y(0.257)S(0.739)PS(0.004)QNS(1)PIHHIPSR;Y(0.197)S(0.794)PS(0.31)QNS(0.699)PIHHIPSR;Y(0.37)S(0.521)PS(0.111)QNS(0.997)PIHHIPSR;Y(0.147)S(0.494)PS(0.36)QNS(1)PIHHIPSR;Y(0.095)S(0.561)PS(0.345)QNS(0.999)PIHHIPSR;Y(0.378)S(0.472)PS(0.15)QNS(1)PIHHIPSR 196.36 4.74E-09 32192490000 2645272 2777863 2897709 3496407 3073559 3072856 3504479 1214476 3701024 3918958 TRUE FALSE 2541891.846 2698641.067 3421389.475 3676856.984 3172422.817 3134991.254 3547367.862 1189396.646 3280899.271 3653523.484 0.695737103 0.738640679 0.936462976 1.006386575 0.868318715 0.858073382 0.970944317 0.325547831 0.89800963 1 21.80085705 YSDFHDLHEK ddPTM_BT-474_Pertuzumab_2h_R1 1 YSDFHDLHEK 10 0 Q9Y2I1;C9J715;Q9Y2I1-4;Q9Y2I1-3 Q9Y2I1 NISCH Nischarin 0 125.74 0.00023193 176900000 166070 188630 158940 191740 170190 190870 187420 5410.9 222080 179860 FALSE TRUE 159579.8008 183250.4571 187663.9936 201635.7244 175664.3159 194729.5222 189713.702 5299.163024 196870.4094 167677.922 0.951704308 1.092871708 1.119193221 1.20251803 1.047629371 1.161330722 1.131417301 0.031603225 1.174098576 1 17.35533322 YSDPGPVYDCLVWHDGEVWR ddPTM_BT-474_Pertuzumab_2h_R1 2 YSDPGPVYDCLVWHDGEVWR 20 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 284.88 4.99E-45 1052760000 298060 285900 250640 305530 291200 296070 308850 282240 338230 355370 FALSE TRUE 286411.4857 277746.4119 295936.2235 321298.4399 300566.7125 302056.7383 312629.7987 276411.6454 299835.5484 331300.4734 0.86450672 0.838351992 0.893256265 0.969809782 0.90723297 0.911730476 0.943644286 0.834323122 0.905026019 1 18.33778074 YSEWTSPAEDSS(ph)PGISLSSSR ddPTM_BT-474_Pertuzumab_2h_R1 1 YSEWTSPAEDSSPGISLSSSR 21 0 H0YNU5;A0A3B3IT82;P54132 H0YNU5 BLM Bloom syndrome protein 1 YSEWTSPAEDS(0.153)S(0.846)PGISLSSSR 164.53 2.06E-13 0 46121 43629 36349 52244 41543 39961 40023 52878 42039 42549 TRUE FALSE 44318.54033 42384.74364 42918.07288 54940.3191 42879.26832 40769.0388 40512.81345 51786.05082 37266.90896 39667.11833 1.117261404 1.068510782 1.081955904 1.385034291 1.080977649 1.027779191 1.021319802 1.305515828 0.939491209 1 15.27565597 YSHLQPGDHLTDITLK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSHLQPGDHLTDITLK 16 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ; 166.35 3.88E-09 1386450000 1527030 1732830 1438260 1620450 1527480 1640260 1695310 715450 1942770 1878010 FALSE TRUE 1467351.979 1683411.385 1698185.576 1704081.619 1576612.781 1673427.181 1716057.711 700675.7075 1722234.894 1750810.71 0.838098585 0.961503934 0.969942419 0.973310027 0.900504419 0.955801316 0.980150339 0.40020072 0.983678524 1 20.73959168 YSHVSQHS(ph)PSKK ddPTM_BT-474_Pertuzumab_2h_R1 2 YSHVSQHSPSKK 12 1 A0A3B3IUD7;Q14690 A0A3B3IUD7 PDCD11 Protein RRP5 homolog 1 YSHVS(0.008)QHS(0.937)PS(0.055)KK;YSHVS(0.036)QHS(0.929)PS(0.035)KK 97.797 0.0022192 142467000 139221 195632 158735 201718 166452 222858 194440 60186 211032 227502 TRUE FALSE 133780.0894 190052.7669 187421.9455 212128.6902 171806.0797 227364.3415 196819.6149 58943.13807 187076.5321 212093.0869 0.630761197 0.896081856 0.883677768 1.000167866 0.810050352 1.072002604 0.927986941 0.277911642 0.882049174 1 17.69433807 YSLADQTSGDQS(ph)PLPPCTPTPPCAEMR ddPTM_BT-474_Pertuzumab_2h_R1 1 YSLADQTSGDQSPLPPCTPTPPCAEMR 27 0 Q06124;Q06124-1 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1 YSLADQT(0.004)S(0.017)GDQS(0.978)PLPPCTPTPPCAEMR 121.39 6.16E-05 133340000 69864 58472 54337 57139 63169 52661 73784 64577 66621 61897 TRUE FALSE 67133.63764 56804.43581 64156.90462 60087.95064 65200.88825 53725.8415 74686.99066 63243.46238 59058.46338 57704.66106 1.163400606 0.984399436 1.111814946 1.041301509 1.129906788 0.931048559 1.294297363 1.095985337 1.023460883 1 15.81640024 YSPSQNS(ph)PIHHIPSR ddPTM_BT-474_Pertuzumab_2h_R1 4 YSPSQNSPIHHIPSR 15 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 YS(0.012)PS(0.148)QNS(0.841)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YS(0.002)PS(0.008)QNS(0.989)PIHHIPSR;YSPS(0.003)QNS(0.997)PIHHIPSR 200.39 1.16E-08 6441620000 1226700 1319270 1344420 1557590 1396240 1407430 1458860 530977 1602990 1667020 TRUE FALSE 1178759.208 1281645.711 1587386.6 1637977.407 1441151.328 1435889.199 1476713.965 520012.1394 1421025.295 1554111.251 0.758478009 0.824680801 1.021411176 1.053964062 0.92731542 0.92392948 0.950198362 0.334604192 0.914365233 1 20.56765835 YTEFYHVPTHSDASK ddPTM_BT-474_Pertuzumab_2h_R1 4 YTEFYHVPTHSDASK 15 0 Q96HC4;Q96HC4-4;Q96HC4-7;H0YBI4;Q96HC4-3;Q96HC4-2;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 ;;; 193.16 6.04E-08 1064060000 1490360 1574430 1330050 1339390 1410100 1397210 1490890 707410 1824030 1726030 FALSE TRUE 1432115.084 1529528.798 1570419.622 1408516.078 1455457.147 1425462.544 1509135.958 692801.7363 1616973.761 1609124.451 0.889996472 0.950534806 0.975946653 0.875330729 0.904502536 0.885862211 0.937861554 0.430545777 1.004878001 1 20.61784448 YTIHSQLEHLQSK ddPTM_BT-474_Pertuzumab_2h_R1 2 YTIHSQLEHLQSK 13 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 240.11 4.50E-17 1590970000 1441380 1282500 1136750 1444760 1481240 1358580 1507390 189733 1752430 1606930 FALSE TRUE 1385049.276 1245924.356 1342186.012 1519324.237 1528885.43 1386051.418 1525837.89 185814.9472 1553501.493 1498091.2 0.924542696 0.831674571 0.895930776 1.014173394 1.020555644 0.925211642 1.018521362 0.12403447 1.036987263 1 20.51469402 YVCPHPSCGR ddPTM_BT-474_Pertuzumab_2h_R1 2 YVCPHPSCGR 10 0 A0A0A6YYC7;Q96JP5-2;Q96JP5;H3BTR0 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 0 ; 74.533 0.041706 151606000 177531 234300 183575 225600 195008 181855 222537 194871 212923 245420 FALSE TRUE 170592.8922 227617.9934 216751.0861 237243.243 201280.6094 185532.2327 225260.4744 190846.8458 188752.8737 228797.4848 0.745606502 0.994844824 0.947349077 1.036913685 0.879732614 0.81090154 0.984540868 0.834129999 0.824977923 1 17.80371167 YWGEIISQQYNFDR ddPTM_BT-474_Pertuzumab_2h_R1 2 YWGEIISQQYNFDR 14 0 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 117.79 0.00065807 138829000 71882 82446 71188 87032 86330 71652 88688 92665 92507 106145 FALSE TRUE 69072.77197 80094.7208 84053.25517 91523.73195 89106.88285 73100.85253 89773.39027 90751.43537 82005.99318 98955.70461 0.69801708 0.809399732 0.849402826 0.924895965 0.900472421 0.738722975 0.907207832 0.917091498 0.828714156 1 16.59449526 YWQQVIDMNDYQR ddPTM_BT-474_Pertuzumab_2h_R1 4 YWQQVIDMNDYQR 13 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;; 236.22 2.42E-16 650165000 1029973 1084843 909855 970177 983410 979942 1073357 1049574 1139237 1143652 FALSE TRUE 989720.5165 1053904.34 1074286.038 1020247.951 1015042.276 999757.0987 1086493.064 1027899.93 1009915.592 1066191.431 0.928276562 0.988475717 1.007592076 0.956908789 0.952026293 0.937690052 1.019041264 0.964085717 0.947217884 1 20.02403506 YYDSRPGGYGYGYGR ddPTM_BT-474_Pertuzumab_2h_R1 5 YYDSRPGGYGYGYGR 15 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;;; 183.96 4.41E-07 13490670000 7215690 7672100 5629300 8039620 7043380 6299800 7979460 7861500 7125820 8463990 FALSE TRUE 6933692.857 7453299.22 6646639.733 8454545.752 7269936.714 6427186.272 8077115.018 7699157.278 6316926.787 7890716.418 0.878715251 0.944565591 0.842336663 1.071454771 0.92132784 0.814525061 1.023622519 0.975723479 0.800551744 1 22.91172486 YYGGAEVVDEIELLCQR ddPTM_BT-474_Pertuzumab_2h_R1 1 YYGGAEVVDEIELLCQR 17 0 P34897-3;P34897-2;P34897;G3V540;G3V5L0;G3V4W5;G3V241;G3V3Y8;G3V4T0;G3V4X0;G3V2W0;G3V2E4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial" 0 198.49 3.29E-11 13076000 19754 26158 15474 35280 16236 18889 27319 27046 21400 17086 FALSE TRUE 18981.99184 25411.99945 18270.49602 37100.80503 16758.24569 19270.94852 27653.33809 26487.49065 18970.76172 15928.75 1.191681195 1.595354278 1.147013797 2.32917241 1.052075378 1.20982177 1.736064543 1.662873147 1.190976173 1 13.95934544 YYYVQNVYTPVDEHVYPDHR ddPTM_BT-474_Pertuzumab_2h_R1 1 YYYVQNVYTPVDEHVYPDHR 20 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7 A0A087WXK2 PEG10 Retrotransposon-derived protein PEG10 0 102.99 0.00016876 61690000 28681 25569 30381 27758 28870 30805 34913 11181 37486 35263 FALSE TRUE 27560.11481 24839.79715 35871.52252 29190.59371 29798.62977 31427.89821 35340.27574 10950.10844 33230.74643 32874.6056 0.838340546 0.755592248 1.091162065 0.887937457 0.906433073 0.955993163 1.075002273 0.333087143 1.010833311 1 15.00468597